r364Leu	p.S364L	ENST00000331340	NM_006060.4	364	tCg/tTg	8/8	0.469991508980283	3	FACETS	1	0.997	1	0.809	0.791	0.827	INDETERMINATE	2	TRUE	0	0.950734814351431	3		309	835	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335745	81335745	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	467	317	0	ENST00000222390.5:c.1617-2A>G		p.X539_splice	ENST00000222390	NM_000601.4	539			0.635067718750042	3	FACETS	1	0.994	1	0.415	0.397	0.434	CLONAL	1	TRUE	0	0.950734814351431	3		317	1163	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509849	106509849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426277818	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1444	336	712	0	ENST00000359195.3:c.1843G>A	p.Glu615Lys	p.E615K	ENST00000359195	NM_002649.2	615	Gaa/Aaa	2/11	0.46892123507037	3	FACETS	0.586	0.552	0.621	0.195	0.184	0.207	INDETERMINATE	1	TRUE	0	0.950734814351431	3		712	1780	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339637	116339637	+	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	276	871	358	0	ENST00000397752.3:c.499G>A	p.Glu167Lys	p.E167K	ENST00000397752	NM_000245.2	167	Gaa/Aaa	2/21	0.46892123507037	3	FACETS	1	0.998	1	0.786	0.77	0.801	INDETERMINATE	2	TRUE	0	0.950734814351431	3		358	1147	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395422	116395422	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1348	245	471	0	ENST00000397752.3:c.1715G>T	p.Ser572Ile	p.S572I	ENST00000397752	NM_000245.2	572	aGt/aTt	6/21	0.46892123507037	3	FACETS	0.477	0.444	0.511	0.159	0.148	0.171	INDETERMINATE	1	TRUE	0	0.950734814351431	3		471	1593	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132751	152132751	+	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	365	1231	465	2	ENST00000262189.6:c.121C>T	p.Arg41Cys	p.R41C	ENST00000262189	NM_170606.2	41	Cgc/Tgc	1/59	0.46892123507037	3	FACETS	1	0.998	1	0.798	0.784	0.811	INDETERMINATE	2	TRUE	0	0.950734814351431	3		467	1596	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538897	23538897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1200957711	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	546	437	0	ENST00000380871.4:c.542G>A	p.Arg181Gln	p.R181Q	ENST00000380871	NM_006167.3	181	cGa/cAa	2/2	0.950734814351431	1	FACETS	0.998	0.981	1	0.998	0.981	1	CLONAL	1	TRUE	0	0.950734814351431	1		437	604	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282218	38282218	+	splice_acceptor_variant	Splice_Site	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	32	404	362	0	ENST00000425967.3:c.839-1G>A		p.X280_splice	ENST00000425967	NM_001174067.1	280			0.950734814351431	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.950734814351431	1		362	436	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285945	38285945	+	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	63	508	401	1	ENST00000425967.3:c.466C>T	p.Pro156Ser	p.P156S	ENST00000425967	NM_001174067.1	156	Ccc/Tcc	5/19	0.950734814351431	1	FACETS	0.982	0.964	0.999	0.982	0.964	0.999	CLONAL	1	TRUE	0	0.950734814351431	1		402	571	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981345	68981345	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1249577384	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	563	519	0	ENST00000288368.4:c.1417A>T	p.Asn473Tyr	p.N473Y	ENST00000288368	NM_024870.2	473	Aat/Tat	12/40	1	2	FACETS	0.984	0.948	1	0.984	0.948	1	CLONAL	1	TRUE	1	0.950734814351431	2		519	1204	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68999972	68999972	+	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	719	626	532	0	ENST00000288368.4:c.2041C>T	p.Pro681Ser	p.P681S	ENST00000288368	NM_024870.2	681	Cca/Tca	19/40	1	2	FACETS	0.979	0.945	1	0.979	0.945	1	CLONAL	1	TRUE	1	0.950734814351431	2		532	1345	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69011996	69011996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1005719835	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	959	757	2	ENST00000288368.4:c.2633C>T	p.Pro878Leu	p.P878L	ENST00000288368	NM_024870.2	878	cCt/cTt	23/40	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.950734814351431	2		759	1947	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981887	70981887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs887981235	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	598	592	1	ENST00000276594.2:c.209C>T	p.Pro70Leu	p.P70L	ENST00000276594	NM_024504.3	70	cCc/cTc	2/8	1	2	FACETS	0.962	0.927	0.996	0.962	0.927	0.996	CLONAL	1	TRUE	1	0.950734814351431	2		593	1308	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317926	8317926	+	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	45	507	337	0	ENST00000356435.5:c.5687C>T	p.Ser1896Phe	p.S1896F	ENST00000356435		1896	tCc/tTc	35/35	0.950734814351431	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.950734814351431	1		337	552	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971115	21971116	+	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	52	375	382	1	ENST00000304494.5:c.242_243delinsTT	p.Pro81Leu	p.P81L	ENST00000304494	NM_000077.4	81	cCC/cTT	2/3	0.950734814351431	1	FACETS	0.969	0.947	0.989	0.969	0.947	0.989	CLONAL	1	TRUE	0	0.950734814351431	1		383	427	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624537	93624537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237227040	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	687	532	0	ENST00000375746.1:c.628G>A	p.Glu210Lys	p.E210K	ENST00000375746	NM_001174167.1	210	Gaa/Aaa	4/14	1	2	FACETS	0.963	0.931	0.996	0.963	0.931	0.996	CLONAL	1	TRUE	1	0.950734814351431	2		532	1500	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797283	135797283	+	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	519	437	347	0	ENST00000298552.3:c.586C>T	p.Pro196Ser	p.P196S	ENST00000298552	NM_001162426.1	196	Cct/Tct	7/23	1	2	FACETS	0.962	0.921	1	0.962	0.921	1	CLONAL	1	TRUE	1	0.950734814351431	2		347	956	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411678	63411678	+	stop_gained	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	541	869	717	1	ENST00000330258.3:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000330258	NM_152424.3	497	Cga/Tga	2/2	0.589439945555195	1	FACETS	0.68	0.663	0.697	0.68	0.663	0.697	SUBCLONAL	1	TRUE	0	0.950734814351431	1		718	1410	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776904	76776904	+	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	859	359	582	0	ENST00000373344.5:c.7048C>T	p.Leu2350Phe	p.L2350F	ENST00000373344	NM_000489.3	2350	Ctt/Ttt	33/35	0.476553022551747	1	FACETS	0.325	0.308	0.343	0.325	0.308	0.343	INDETERMINATE	1	TRUE	0	0.950734814351431	1		582	1218	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920223	76920223	+	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	426	775	569	0	ENST00000373344.5:c.3854C>T	p.Ser1285Phe	p.S1285F	ENST00000373344	NM_000489.3	1285	tCc/tTc	11/35	0.476553022551747	1	FACETS	0.712	0.694	0.73	0.712	0.694	0.73	INDETERMINATE	1	TRUE	0	0.950734814351431	1		569	1201	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181333	123181333	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	270	446	0	ENST00000218089.9:c.797T>A	p.Leu266His	p.L266H	ENST00000218089	NM_001042749.1	266	cTc/cAc	9/35	0.476553022551747	1	FACETS	0.36	0.339	0.382	0.36	0.339	0.382	INDETERMINATE	1	TRUE	0	0.950734814351431	1		446	827	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861646	152861646	+	splice_acceptor_variant	Splice_Site	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	386	582	476	1	ENST00000406277.2:c.107-1G>A		p.X36_splice	ENST00000406277	NM_152274.4	36			0.476553022551747		FACETS		0.642	0.684				INDETERMINATE	1	TRUE	0	0.950734814351431	1		477	968	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018646-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	48	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.362	0.307	0.422	0.362	0.307	0.422	SUBCLONAL	1	TRUE	1	0.746903867422664	2		215	355	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0018646-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	32	316	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.295	0.24	0.357	0.295	0.24	0.357	SUBCLONAL	1	TRUE	1	0.746903867422664	2		316	290	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448276	56448276	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018646-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	28	503	0	ENST00000407977.2:c.371G>T	p.Ser124Ile	p.S124I	ENST00000407977		124	aGc/aTc	3/10	0.15673314463469	3	FACETS	0.186	0.148	0.23	0.093	0.074	0.115	INDETERMINATE	1	TRUE	1	0.746903867422664	3		503	553	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7132166	7132167	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	A	novel	NA	P-0018646-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	181	564	0	ENST00000302850.5:c.2842+2dup		p.X948_splice	ENST00000302850	NM_000208.2	948			1	2	FACETS	0.697	0.645	0.751	0.697	0.645	0.751	SUBCLONAL	1	TRUE	1	0.746903867422664	2		564	695	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592103	55592103	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018646-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4394	1503	588	0	ENST00000288135.5:c.1427G>T	p.Ser476Ile	p.S476I	ENST00000288135	NM_000222.2	476	aGt/aTt	9/21	0.746903867422664	24	FACETS	1	0.992	1	0.273	0.266	0.281	CLONAL	6	TRUE	1	0.746903867422664	24		588	5897	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390174	89390174	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	84	369	0	ENST00000336596.2:c.923A>G	p.Asn308Ser	p.N308S	ENST00000336596	NM_005233.5	308	aAt/aGt	4/17	1	2	FACETS	0.834	0.738	0.938	0.834	0.738	0.938	CLONAL	1	TRUE	1	0.325848343696754	2		369	618	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295199	1295200	+	upstream_gene_variant	5'Flank	INS	-	-	GGAAGGGGAGGGGCTGGGAGG	novel	NA	P-0018657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	23	166	0				ENST00000310581	NM_198253.2	-/1132			0.325848343696754	1	FACETS	0.528	0.413	0.659	0.528	0.413	0.659	SUBCLONAL	1	TRUE	0	0.325848343696754	1		166	224	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295164	1295168	+	upstream_gene_variant	5'Flank	INS	AACTC	AACTC	GGGAGG	novel	NA	P-0018657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	35	138	0				ENST00000310581	NM_198253.2	-/1132			0.325848343696754	1	FACETS	0.941	0.78	1	0.941	0.78	1	CLONAL	1	TRUE	0	0.325848343696754	1		138	191	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0018722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	198	351	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.306889918246654	5	FACETS	0.865	0.8	0.932	0.577	0.533	0.622	CLONAL	2	TRUE	2	0.306889918246654	5		351	1089	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0018722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	204	188	2	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	0.301230065678135	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	0	0.306889918246654	2		190	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0018722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	313	412	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.306889918246654	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.306889918246654	2		412	957	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051645	13051645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375135016	NA	P-0018722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	177	466	1	ENST00000316448.5:c.904G>A	p.Asp302Asn	p.D302N	ENST00000316448	NM_004343.3	302	Gat/Aat	7/9	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.306889918246654	2		467	935	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970900	21970900	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0018722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	362	647	0	ENST00000304494.5:c.457+1G>A		p.X153_splice	ENST00000304494	NM_000077.4	153			0.301230065678135	2	FACETS	0.976	0.926	1	0.976	0.926	1	CLONAL	2	TRUE	0	0.306889918246654	2		647	1208	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798814	45798814	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	191	514	1	ENST00000450313.1:c.417G>T	p.Gln139His	p.Q139H	ENST00000450313	NM_012222.2	139	caG/caT	5/16	0.247971161566806	3	FACETS	1	0.985	1	0.639	0.59	0.69	CLONAL	1	TRUE	1	0.306889918246654	3		515	1123	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344574	118344574	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1033324124	NA	P-0018722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	90	346	1	ENST00000534358.1:c.2700G>T	p.Gln900His	p.Q900H	ENST00000534358	NM_005933.3	900	caG/caT	3/36	1	2	FACETS	0.759	0.673	0.851	0.759	0.673	0.851	SUBCLONAL	1	TRUE	1	0.306889918246654	2		347	773	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362583	118362583	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	78	394	0	ENST00000534358.1:c.4944G>T	p.Lys1648Asn	p.K1648N	ENST00000534358	NM_005933.3	1648	aaG/aaT	15/36	1	2	FACETS	0.651	0.571	0.737	0.651	0.571	0.737	SUBCLONAL	1	TRUE	1	0.306889918246654	2		394	781	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416702	121416702	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	215	505	0	ENST00000257555.6:c.131T>C	p.Leu44Pro	p.L44P	ENST00000257555		44	cTg/cCg	1/10	0.247971161566806	3	FACETS	1	0.99	1	0.705	0.654	0.757	CLONAL	1	TRUE	1	0.306889918246654	3		505	1147	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245026	133245026	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs5744800	NA	P-0018722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	310	863	0	ENST00000320574.5:c.2089C>T	p.Pro697Ser	p.P697S	ENST00000320574	NM_006231.2	697	Ccc/Tcc	19/49	0.247971161566806	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	1	0.306889918246654	3		863	1161	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292633	91292633	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	95	285	0	ENST00000355112.3:c.135C>A	p.Asn45Lys	p.N45K	ENST00000355112	NM_000057.2	45	aaC/aaA	3/22	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.306889918246654	2		285	541	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830375	72830375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1178437753	NA	P-0018722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	19	157	1	ENST00000268489.5:c.6206C>T	p.Pro2069Leu	p.P2069L	ENST00000268489	NM_006885.3	2069	cCa/cTa	9/10	1	2	FACETS	0.558	0.424	0.714	0.558	0.424	0.714	SUBCLONAL	1	TRUE	1	0.306889918246654	2		158	222	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55693386	55693386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1201	96	639	1	ENST00000284073.2:c.593G>A	p.Gly198Asp	p.G198D	ENST00000284073	NM_138962.2	198	gGc/gAc	9/14	0.177770004233706	5	FACETS	0.704	0.625	0.789	0.235	0.208	0.263	INDETERMINATE	1	TRUE	2	0.306889918246654	5		640	1297	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117551	4117551	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121434498	NA	P-0018722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	63	282	0	ENST00000262948.5:c.169T>C	p.Phe57Leu	p.F57L	ENST00000262948	NM_030662.3	57	Ttt/Ctt	2/11	NA	2	FACETS	0.741	0.641	0.849			1	INDETERMINATE	1	TRUE	NA	0.306889918246654	2		282	554	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229552	5229552	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	121	209	0	ENST00000357368.4:c.2299G>T	p.Glu767Ter	p.E767*	ENST00000357368	NM_002850.3	767	Gag/Tag	15/38	0.198314533208126	3	FACETS	0.966	0.878	1	0.966	0.878	1	CLONAL	2	TRUE	1	0.306889918246654	3		209	471	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961569	18961569	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	105	337	0	ENST00000262803.5:c.702G>T	p.Gln234His	p.Q234H	ENST00000262803	NM_002911.3	234	caG/caT	5/24	1	2	FACETS	0.987	0.885	1	0.987	0.885	1	CLONAL	1	TRUE	1	0.306889918246654	2		337	693	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877331	40877331	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	137	249	0	ENST00000373198.4:c.2365A>T	p.Arg789Trp	p.R789W	ENST00000373198	NM_133170.3	789	Agg/Tgg	15/32	0.301230065678135	2	FACETS	0.904	0.827	0.983	0.904	0.827	0.983	CLONAL	2	TRUE	0	0.306889918246654	2		249	494	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956531	93956531	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs775894675	NA	P-0018722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	40	268	0	ENST00000369303.4:c.2705C>G	p.Thr902Ser	p.T902S	ENST00000369303	NM_004440.3	902	aCt/aGt	15/17	0.301230065678135	2	FACETS	0.522	0.434	0.621	0.261	0.217	0.311	SUBCLONAL	1	TRUE	0	0.306889918246654	2		268	499	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971046	21971046	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	205	384	1	ENST00000579755.1:c.355G>A	p.Gly119Arg	p.G119R	ENST00000579755		119	Gga/Aga	2/3	0.301230065678135	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.306889918246654	2		385	649	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971199	21971202	+	missense_variant	Missense_Mutation	ONP	CATC	CATC	TATT	novel	NA	P-0018722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	180	303	0	ENST00000304494.5:c.156_159delinsAATA	p.Met52_Met53delinsIleIle	p.M52_M53delinsII	ENST00000304494	NM_000077.4	52	atGATG/atAATA	2/3	0.301230065678135	2	FACETS	0.979	0.908	1	0.979	0.908	1	CLONAL	2	TRUE	0	0.306889918246654	2		303	599	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	382	215	0				ENST00000310581	NM_198253.2	-/1132			0.524751500275866	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.524751500275866	2		215	672	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	82	499	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.32400052033267	3	FACETS	0.669	0.59	0.753	0.334	0.295	0.377	SUBCLONAL	1	TRUE	1	0.524751500275866	3		499	590	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	98	531	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.524751500275866	1	FACETS	0.82	0.739	0.904	0.82	0.739	0.904	CLONAL	1	TRUE	0	0.524751500275866	1		531	336	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	20	512	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.32400052033267	3	FACETS	0.144	0.109	0.185	0.072	0.054	0.093	SUBCLONAL	1	TRUE	1	0.524751500275866	3		512	668	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519999	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	438	537	0	ENST00000269305.4:c.716A>G	p.Asn239Ser	p.N239S	ENST00000269305	NM_001126112.2	239	aAc/aGc	7/11	0.524751500275866	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.524751500275866	2		537	776	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003747	45003747	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs1057519877	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	51	603	0	ENST00000558401.1:c.3G>A	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	atG/atA	1/4	1	2	FACETS	0.305	0.258	0.356	0.305	0.258	0.356	SUBCLONAL	1	TRUE	1	0.524751500275866	2		603	638	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652203	36652203	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	248	908	0	ENST00000244741.5:c.325G>C	p.Asp109His	p.D109H	ENST00000244741	NM_000389.4	109	Gac/Cac	2/3	1	2	FACETS	0.847	0.792	0.904	0.847	0.792	0.904	CLONAL	1	TRUE	1	0.524751500275866	2		908	1116	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183604	185183604	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	121	369	0	ENST00000265026.3:c.1458G>C	p.Leu486Phe	p.L486F	ENST00000265026	NM_004721.4	486	ttG/ttC	9/14	0.32400052033267	3	FACETS	1	0.971	1	0.586	0.532	0.642	CLONAL	1	TRUE	1	0.524751500275866	3		369	497	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077427	30077427	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	29	240	0	ENST00000338641.4:c.1575-1G>C		p.X525_splice	ENST00000338641	NM_000268.3	525			0.524751500275866	1	FACETS	0.293	0.236	0.358	0.293	0.236	0.358	SUBCLONAL	1	TRUE	0	0.524751500275866	1		240	278	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662458	227662458	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	206	701	0	ENST00000305123.5:c.997G>A	p.Glu333Lys	p.E333K	ENST00000305123	NM_005544.2	333	Gaa/Aaa	1/2	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.524751500275866	2		701	772	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070841	30070841	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	45	762	0	ENST00000338641.4:c.1357C>T	p.Gln453Ter	p.Q453*	ENST00000338641	NM_000268.3	453	Cag/Tag	13/16	0.524751500275866	1	FACETS	0.191	0.159	0.225	0.191	0.159	0.225	SUBCLONAL	1	TRUE	0	0.524751500275866	1		762	664	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979275	40979275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867428378	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	147	502	0	ENST00000373198.4:c.1858C>T	p.Pro620Ser	p.P620S	ENST00000373198	NM_133170.3	620	Cct/Tct	11/32	1	2	FACETS	0.934	0.856	1	0.934	0.856	1	CLONAL	1	TRUE	1	0.524751500275866	2		502	600	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305323	65305323	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	63	508	0	ENST00000342505.4:c.2805G>C	p.Glu935Asp	p.E935D	ENST00000342505	NM_002227.2	935	gaG/gaC	20/25	1	2	FACETS	0.454	0.393	0.52	0.454	0.393	0.52	SUBCLONAL	1	TRUE	1	0.524751500275866	2		508	529	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099971	27099971	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	190	927	0	ENST00000324856.7:c.3850C>T	p.Pro1284Ser	p.P1284S	ENST00000324856	NM_006015.4	1284	Cct/Tct	15/20	1	2	FACETS	0.733	0.677	0.791	0.733	0.677	0.791	SUBCLONAL	1	TRUE	1	0.524751500275866	2		927	988	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305355	65305355	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	63	552	0	ENST00000342505.4:c.2773G>T	p.Glu925Ter	p.E925*	ENST00000342505	NM_002227.2	925	Gaa/Taa	20/25	1	2	FACETS	0.436	0.377	0.5	0.436	0.377	0.5	SUBCLONAL	1	TRUE	1	0.524751500275866	2		552	551	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309866	65309866	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	137	626	0	ENST00000342505.4:c.2284G>C	p.Glu762Gln	p.E762Q	ENST00000342505	NM_002227.2	762	Gag/Cag	17/25	1	2	FACETS	0.676	0.616	0.74	0.676	0.616	0.74	SUBCLONAL	1	TRUE	1	0.524751500275866	2		626	772	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339055	65339055	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	31	358	0	ENST00000342505.4:c.481C>T	p.Gln161Ter	p.Q161*	ENST00000342505	NM_002227.2	161	Cag/Tag	5/25	1	2	FACETS	0.281	0.227	0.342	0.281	0.227	0.342	SUBCLONAL	1	TRUE	1	0.524751500275866	2		358	421	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163811	72163811	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	44	356	0	ENST00000357731.5:c.547G>C	p.Glu183Gln	p.E183Q	ENST00000357731	NM_173808.2	183	Gaa/Caa	4/7	1	2	FACETS	0.668	0.565	0.781	0.668	0.565	0.781	SUBCLONAL	1	TRUE	1	0.524751500275866	2		356	251	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139292	108139292	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	45	631	0	ENST00000278616.4:c.2794G>C	p.Asp932His	p.D932H	ENST00000278616	NM_000051.3	932	Gat/Cat	18/63	0.41021655759918	1	FACETS	0.259	0.217	0.305	0.259	0.217	0.305	SUBCLONAL	1	TRUE	0	0.524751500275866	1		631	489	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352639	118352639	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	52	948	0	ENST00000534358.1:c.3844G>C	p.Glu1282Gln	p.E1282Q	ENST00000534358	NM_005933.3	1282	Gaa/Caa	7/36	0.41021655759918	1	FACETS	0.166	0.141	0.194	0.166	0.141	0.194	SUBCLONAL	1	TRUE	0	0.524751500275866	1		948	880	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025878	1025878	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	230	710	0	ENST00000358495.3:c.652C>G	p.Gln218Glu	p.Q218E	ENST00000358495	NM_134424.2	218	Cag/Gag	8/12	0.524751500275866	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.524751500275866	1		710	645	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50482423	50482423	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	T	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	56	510	0	ENST00000394963.4:c.771+3G>T		p.X257_splice	ENST00000394963	NM_003076.4	257			0.524751500275866	1	FACETS	0.427	0.367	0.491	0.427	0.367	0.491	SUBCLONAL	1	TRUE	0	0.524751500275866	1		510	369	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911971	32911971	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	98	373	0	ENST00000380152.3:c.3479G>C	p.Arg1160Thr	p.R1160T	ENST00000380152		1160	aGa/aCa	11/27	0.524751500275866	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.524751500275866	1		373	259	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033917	49033917	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	167	553	0	ENST00000267163.4:c.2054A>C	p.Gln685Pro	p.Q685P	ENST00000267163	NM_000321.2	685	cAg/cCg	20/27	0.524751500275866	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.524751500275866	1		553	436	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49054172	49054172	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	48	285	0	ENST00000267163.4:c.2752G>C	p.Asp918His	p.D918H	ENST00000267163	NM_000321.2	918	Gat/Cat	27/27	0.524751500275866	1	FACETS	0.718	0.616	0.827	0.718	0.616	0.827	SUBCLONAL	1	TRUE	0	0.524751500275866	1		285	188	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49054201	49054201	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	25	257	0	ENST00000267163.4:c.2781G>C	p.Glu927Asp	p.E927D	ENST00000267163	NM_000321.2	927	gaG/gaC	27/27	0.524751500275866	1	FACETS	0.456	0.363	0.561	0.456	0.363	0.561	SUBCLONAL	1	TRUE	0	0.524751500275866	1		257	154	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30047569	30047569	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	69	258	0	ENST00000331968.5:c.2435-3C>T		p.X812_splice	ENST00000331968	NM_002742.2	812			1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.524751500275866	2		258	238	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560255	95560255	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	90	394	0	ENST00000393063.1:c.5334G>C	p.Glu1778Asp	p.E1778D	ENST00000393063	NM_030621.3	1778	gaG/gaC	25/28	1	2	FACETS	0.805	0.718	0.897	0.805	0.718	0.897	CLONAL	1	TRUE	1	0.524751500275866	2		394	426	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630425	90630425	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	241	931	1	ENST00000330062.3:c.886C>T	p.Gln296Ter	p.Q296*	ENST00000330062	NM_002168.2	296	Cag/Tag	7/11	1	2	FACETS	0.755	0.704	0.808	0.755	0.704	0.808	SUBCLONAL	1	TRUE	1	0.524751500275866	2		932	1216	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639000	3639000	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	37	703	0	ENST00000294008.3:c.4636+3G>A		p.X1546_splice	ENST00000294008	NM_032444.2	1546			1	2	FACETS	0.205	0.168	0.246	0.205	0.168	0.246	SUBCLONAL	1	TRUE	1	0.524751500275866	2		703	688	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029192	14029192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	22	182	0	ENST00000311895.7:c.1403G>A	p.Arg468Lys	p.R468K	ENST00000311895	NM_005236.2	468	aGa/aAa	8/11	1	2	FACETS	0.451	0.351	0.565	0.451	0.351	0.565	SUBCLONAL	1	TRUE	1	0.524751500275866	2		182	186	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844119	68844119	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs730881663	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	148	604	0	ENST00000261769.5:c.707C>A	p.Ser236Ter	p.S236*	ENST00000261769	NM_004360.3	236	tCa/tAa	6/16	0.524751500275866	1	FACETS	0.772	0.709	0.837	0.772	0.709	0.837	SUBCLONAL	1	TRUE	0	0.524751500275866	1		604	539	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548865	29548865	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	32	692	0	ENST00000356175.3:c.1642-3C>T		p.X548_splice	ENST00000356175	NM_000267.3	548			1	2	FACETS	0.195	0.158	0.238	0.195	0.158	0.238	SUBCLONAL	1	TRUE	1	0.524751500275866	2		692	625	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684350	29684350	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	25	279	0	ENST00000356175.3:c.7870G>C	p.Glu2624Gln	p.E2624Q	ENST00000356175	NM_000267.3	2624	Gag/Cag	53/57	1	2	FACETS	0.414	0.328	0.513	0.414	0.328	0.513	SUBCLONAL	1	TRUE	1	0.524751500275866	2		279	230	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687508	29687508	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	81	332	0	ENST00000356175.3:c.8101A>G	p.Thr2701Ala	p.T2701A	ENST00000356175	NM_000267.3	2701	Aca/Gca	56/57	1	2	FACETS	0.941	0.837	1	0.941	0.837	1	CLONAL	1	TRUE	1	0.524751500275866	2		332	328	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657560	37657560	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	36	357	0	ENST00000447079.4:c.2477C>G	p.Ser826Cys	p.S826C	ENST00000447079	NM_015083.1	826	tCt/tGt	6/14	1	2	FACETS	0.392	0.323	0.469	0.392	0.323	0.469	SUBCLONAL	1	TRUE	1	0.524751500275866	2		357	350	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40872362	40872362	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	236	1005	0	ENST00000428826.2:c.593C>G	p.Ser198Ter	p.S198*	ENST00000428826		198	tCa/tGa	7/21	1	2	FACETS	0.884	0.825	0.945	0.884	0.825	0.945	CLONAL	1	TRUE	1	0.524751500275866	2		1005	1017	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007614	62007614	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	60	914	0	ENST00000392795.3:c.253G>C	p.Glu85Gln	p.E85Q	ENST00000392795	NM_001039933.1	85	Gag/Cag	3/6	1	2	FACETS	0.232	0.199	0.269	0.232	0.199	0.269	SUBCLONAL	1	TRUE	1	0.524751500275866	2		914	984	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967008	25967008	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	269	950	0	ENST00000435504.4:c.2198G>C	p.Gly733Ala	p.G733A	ENST00000435504		733	gGa/gCa	13/13	1	2	FACETS	0.976	0.916	1	0.976	0.916	1	CLONAL	1	TRUE	1	0.524751500275866	2		950	1050	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525111	9525111	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	93	578	0	ENST00000353224.5:c.1774C>G	p.Gln592Glu	p.Q592E	ENST00000353224	NM_177990.2	592	Caa/Gaa	8/10	1	2	FACETS	0.597	0.531	0.666	0.597	0.531	0.666	SUBCLONAL	1	TRUE	1	0.524751500275866	2		578	594	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067818	30067818	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	37	258	0	ENST00000338641.4:c.1003G>T	p.Glu335Ter	p.E335*	ENST00000338641	NM_000268.3	335	Gag/Tag	11/16	0.524751500275866	1	FACETS	0.539	0.449	0.637	0.539	0.449	0.637	SUBCLONAL	1	TRUE	0	0.524751500275866	1		258	193	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069371	30069371	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	62	888	0	ENST00000338641.4:c.1236C>G	p.Ile412Met	p.I412M	ENST00000338641	NM_000268.3	412	atC/atG	12/16	0.524751500275866	1	FACETS	0.244	0.21	0.281	0.244	0.21	0.281	SUBCLONAL	1	TRUE	0	0.524751500275866	1		888	715	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41562644	41562644	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	24	143	0	ENST00000263253.7:c.3848G>C	p.Arg1283Thr	p.R1283T	ENST00000263253	NM_001429.3	1283	aGg/aCg	23/31	0.524751500275866	1	FACETS	0.661	0.529	0.807	0.661	0.529	0.807	SUBCLONAL	1	TRUE	0	0.524751500275866	1		143	102	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620500	52620500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	145	522	1	ENST00000394830.3:c.3253G>A	p.Glu1085Lys	p.E1085K	ENST00000394830	NM_018313.4	1085	Gag/Aag	21/30	0.513369567436195	1	FACETS	0.822	0.755	0.891	0.822	0.755	0.891	CLONAL	1	TRUE	0	0.524751500275866	1		523	496	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440334	187440334	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	293	553	0	ENST00000232014.4:c.2033G>A	p.Arg678His	p.R678H	ENST00000232014	NM_001130845.1	678	cGc/cAc	10/10	0.32400052033267	3	FACETS	0.825	0.779	0.872	0.825	0.779	0.872	CLONAL	2	TRUE	1	0.524751500275866	3		553	854	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177936	56177936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1275411238	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	33	465	0	ENST00000399503.3:c.2909C>T	p.Ser970Phe	p.S970F	ENST00000399503	NM_005921.1	970	tCt/tTt	14/20	0.326690468457707	2	FACETS	0.265	0.215	0.321	0.132	0.107	0.161	SUBCLONAL	1	TRUE	0	0.524751500275866	2		465	475	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177990	56177990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326307145	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	30	449	1	ENST00000399503.3:c.2963C>T	p.Ser988Phe	p.S988F	ENST00000399503	NM_005921.1	988	tCt/tTt	14/20	0.326690468457707	2	FACETS	0.269	0.216	0.329	0.135	0.108	0.165	SUBCLONAL	1	TRUE	0	0.524751500275866	2		450	425	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923266	131923266	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	19	62	0	ENST00000265335.6:c.769G>C	p.Glu257Gln	p.E257Q	ENST00000265335		257	Gaa/Caa	6/25	0.326690468457707	2	FACETS	1	0.877	1	0.594	0.466	0.732	CLONAL	1	TRUE	0	0.524751500275866	2		62	61	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923690	131923690	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	62	223	0	ENST00000265335.6:c.960G>T	p.Arg320Ser	p.R320S	ENST00000265335		320	agG/agT	7/25	0.326690468457707	2	FACETS	0.957	0.836	1	0.478	0.418	0.542	CLONAL	1	TRUE	0	0.524751500275866	2		223	247	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522626	176522626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766121173	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1368	157	1421	0	ENST00000292408.4:c.1723G>A	p.Asp575Asn	p.D575N	ENST00000292408	NM_213647.1	575	Gac/Aac	13/18	0.326690468457707	2	FACETS	0.392	0.358	0.429	0.196	0.179	0.215	SUBCLONAL	1	TRUE	0	0.524751500275866	2		1421	1525	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056650	26056650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	26	186	0	ENST00000343677.2:c.7G>A	p.Glu3Lys	p.E3K	ENST00000343677	NM_005319.3	3	Gag/Aag	1/1	1	2	FACETS	0.418	0.332	0.515	0.418	0.332	0.515	SUBCLONAL	1	TRUE	1	0.524751500275866	2		186	237	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732930	44732930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1448211324	NA	P-0019005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	260	430	0	ENST00000377967.4:c.133G>A	p.Glu45Lys	p.E45K	ENST00000377967	NM_021140.2	45	Gag/Aag	1/29	1	1	FACETS	0.783	0.744	0.821	1	0.995	1	SUBCLONAL	2	TRUE	0	0.524751500275866	1		430	467	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	99	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.772	0.692	0.856	1	0.983	1	SUBCLONAL	2	TRUE	1	0.262189119427232	2		215	489	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0019028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	90	288	0	ENST00000304494.5:c.151-1G>A		p.X51_splice	ENST00000304494	NM_000077.4	51			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.262189119427232	2		288	519	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0019028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	39	380	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	0.537	0.444	0.641	0.537	0.444	0.641	SUBCLONAL	1	TRUE	1	0.262189119427232	2		380	554	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539564	187539564	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	92	319	1	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	0.262189119427232	2		320	562	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579556	7579560	+	frameshift_variant	Frame_Shift_Del	DEL	ATCAA	ATCAA	-	novel	NA	P-0019028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	234	718	0	ENST00000269305.4:c.127_131del	p.Leu43AlafsTer7	p.L43Afs*7	ENST00000269305	NM_001126112.2	43	TTGATg/g	4/11	0.0684035530227454	3	FACETS	1	0.961	1			1	INDETERMINATE	2	TRUE	NA	0.262189119427232	3		718	970	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149334	119149334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	53	470	0	ENST00000264033.4:c.1342G>A	p.Glu448Lys	p.E448K	ENST00000264033	NM_005188.3	448	Gag/Aag	9/16	1	2	FACETS	0.754	0.643	0.876	0.754	0.643	0.876	SUBCLONAL	1	TRUE	1	0.262189119427232	2		470	536	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630412	90630412	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	81	686	0	ENST00000330062.3:c.899C>G	p.Ser300Cys	p.S300C	ENST00000330062	NM_002168.2	300	tCt/tGt	7/11	1	2	FACETS	0.64	0.563	0.724	0.64	0.563	0.724	SUBCLONAL	1	TRUE	1	0.262189119427232	2		686	965	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943749	9943749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	151	643	1	ENST00000330684.3:c.1192G>A	p.Asp398Asn	p.D398N	ENST00000330684	NM_001134407.1	398	Gac/Aac	5/13	1	2	FACETS	0.761	0.696	0.828	1	0.988	1	SUBCLONAL	2	TRUE	1	0.262189119427232	2		644	757	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2199910	2199910	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	148	632	1	ENST00000398665.3:c.679G>C	p.Glu227Gln	p.E227Q	ENST00000398665	NM_032482.2	227	Gag/Cag	8/28	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.262189119427232	2		633	810	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791524	42791524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747433677	NA	P-0019028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	81	727	2	ENST00000575354.2:c.505C>T	p.Arg169Cys	p.R169C	ENST00000575354	NM_015125.3	169	Cgt/Tgt	4/20	1	2	FACETS	0.572	0.502	0.647	0.572	0.502	0.647	SUBCLONAL	1	TRUE	1	0.262189119427232	2		729	1080	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439938	220439938	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs928419389	NA	P-0019028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	187	785	0	ENST00000243786.2:c.791G>A	p.Arg264Lys	p.R264K	ENST00000243786	NM_002191.3	264	aGa/aAa	2/2	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.262189119427232	2		785	961	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624807	9624807	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	90	420	0	ENST00000353224.5:c.170C>T	p.Ser57Leu	p.S57L	ENST00000353224	NM_177990.2	57	tCa/tTa	3/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.262189119427232	2		420	517	SUCCESS
ATR	545	MSKCC	GRCh37	3	142184047	142184047	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	47	494	0	ENST00000350721.4:c.6933G>C	p.Lys2311Asn	p.K2311N	ENST00000350721	NM_001184.3	2311	aaG/aaC	41/47	1	2	FACETS	0.707	0.597	0.829	0.707	0.597	0.829	SUBCLONAL	1	TRUE	1	0.262189119427232	2		494	507	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542576	187542576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	61	583	0	ENST00000441802.2:c.5164C>T	p.Gln1722Ter	p.Q1722*	ENST00000441802	NM_005245.3	1722	Cag/Tag	10/27	1	2	FACETS	0.654	0.563	0.752	0.654	0.563	0.752	SUBCLONAL	1	TRUE	1	0.262189119427232	2		583	712	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627950	187627950	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1285798739	NA	P-0019028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	85	785	1	ENST00000441802.2:c.3032C>G	p.Ser1011Cys	p.S1011C	ENST00000441802	NM_005245.3	1011	tCt/tGt	2/27	1	2	FACETS	0.699	0.616	0.787	0.699	0.616	0.787	SUBCLONAL	1	TRUE	1	0.262189119427232	2		786	928	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417534	139417534	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	151	774	0	ENST00000277541.6:c.510C>A	p.Phe170Leu	p.F170L	ENST00000277541	NM_017617.3	170	ttC/ttA	4/34	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.262189119427232	2		774	1057	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	54	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.244371038821793	2		215	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0019297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	122	598	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.943	0.851	1	0.943	0.851	1	CLONAL	1	TRUE	1	0.244371038821793	2		598	1059	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0019297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	118	380	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.227593305011021	2	FACETS	0.913	0.827	1	0.913	0.827	1	CLONAL	2	TRUE	0	0.244371038821793	2		380	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0019297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	139	531	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.244371038821793	2		532	938	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	84	215	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	0.95	0.853	1	1	0.985	1	CLONAL	2	TRUE	0	0.31	1		215	241	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	181	458	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.3	2	FACETS	0.863	0.805	0.922	1	0.988	1	CLONAL	3	TRUE	0	0.31	2		458	451	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467675	50467675	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759124417	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	118	668	0	ENST00000331340.3:c.910G>A	p.Glu304Lys	p.E304K	ENST00000331340	NM_006060.4	304	Gaa/Aaa	8/8	1	2	FACETS	0.806	0.732	0.884	1	0.987	1	CLONAL	2	TRUE	1	0.31	2		668	472	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662625	117662625	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	87	644	1	ENST00000368508.3:c.4840C>T	p.Pro1614Ser	p.P1614S	ENST00000368508	NM_002944.2	1614	Cca/Tca	29/43	0.278829906896002	4	FACETS	0.952	0.849	1	0.952	0.849	1	CLONAL	2	TRUE	2	0.31	4		645	386	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645693	12645693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397516827	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	33	318	0	ENST00000251849.4:c.776C>T	p.Ser259Phe	p.S259F	ENST00000251849	NM_002880.3	259	tCc/tTc	7/17	1	2	FACETS	0.959	0.787	1	0.959	0.787	1	CLONAL	1	TRUE	1	0.31	2		318	222	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876467	35876467	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	129	660	0	ENST00000303115.3:c.1259C>T	p.Ser420Phe	p.S420F	ENST00000303115	NM_002185.3	420	tCt/tTt	8/8	0.205140920811218	3	FACETS	1	0.957	1	0.718	0.656	0.783	CLONAL	2	TRUE	0	0.31	3		660	446	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624541	93624541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	103	693	0	ENST00000375746.1:c.632G>A	p.Gly211Glu	p.G211E	ENST00000375746	NM_001174167.1	211	gGg/gAg	4/14	0.3	2	FACETS	0.928	0.839	1	0.928	0.839	1	CLONAL	2	TRUE	0	0.31	2		693	358	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023855	27023855	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	91	380	0	ENST00000324856.7:c.961C>T	p.Gln321Ter	p.Q321*	ENST00000324856	NM_006015.4	321	Cag/Tag	1/20	0.172870811126668	4	FACETS	0.89	0.795	0.991	0.89	0.795	0.991	INDETERMINATE	2	TRUE	2	0.31	4		380	432	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076727	72076727	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	104	675	0	ENST00000357731.5:c.770G>A	p.Trp257Ter	p.W257*	ENST00000357731	NM_173808.2	257	tGg/tAg	5/7	0.172870811126668	4	FACETS	0.792	0.711	0.877	0.792	0.711	0.877	INDETERMINATE	2	TRUE	2	0.31	4		675	555	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406105	70406105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	101	492	0	ENST00000373644.4:c.3619C>T	p.Pro1207Ser	p.P1207S	ENST00000373644	NM_030625.2	1207	Cct/Tct	4/12	1	2	FACETS	0.838	0.755	0.924	1	0.985	1	CLONAL	2	TRUE	1	0.31	2		492	389	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933480	100933480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766277966	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	27	89	0	ENST00000325455.5:c.1910G>A	p.Arg637Gln	p.R637Q	ENST00000325455	NM_001202474.3	637	cGa/cAa	4/8	0.212486527544463	3	FACETS	0.78	0.63	0.945	0.78	0.63	0.945	CLONAL	2	TRUE	1	0.31	3		89	129	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195282	102195282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	48	440	0	ENST00000263464.3:c.42G>A	p.Met14Ile	p.M14I	ENST00000263464	NM_001165.4	14	atG/atA	2/9	0.212486527544463	3	FACETS	0.788	0.667	0.921	0.394	0.333	0.461	CLONAL	1	TRUE	1	0.31	3		440	454	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644490	18644490	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs181773550	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	87	597	0	ENST00000266497.5:c.2668G>A	p.Asp890Asn	p.D890N	ENST00000266497		890	Gat/Aat	18/31	0.3	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.31	1		597	329	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644479	21644479	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	104	494	4	ENST00000421138.2:c.188C>T	p.Ser63Phe	p.S63F	ENST00000421138		63	tCt/tTt	4/16	0.236069114561796	3	FACETS	1	0.965	1	0.76	0.688	0.835	CLONAL	2	TRUE	0	0.31	3		498	340	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859007	57859007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542007910	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	156	693	0	ENST00000228682.2:c.503C>T	p.Pro168Leu	p.P168L	ENST00000228682	NM_005269.2	168	cCt/cTt	5/12	0.3	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.31	2		693	481	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987153	36987153	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	122	792	0	ENST00000354822.5:c.536T>G	p.Val179Gly	p.V179G	ENST00000354822	NM_001079668.2	179	gTg/gGg	3/3	0.152407421804558	4	FACETS	0.929	0.843	1	0.929	0.843	1	INDETERMINATE	2	TRUE	2	0.31	4		792	555	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420258	88420258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550257984	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	132	598	0	ENST00000360948.2:c.2428G>A	p.Glu810Lys	p.E810K	ENST00000360948	NM_001012338.2	810	Gaa/Aaa	19/19	0.212486527544463	3	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	1	0.31	3		598	466	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843480	3843480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756844215	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	50	583	0	ENST00000262367.5:c.1123G>A	p.Gly375Arg	p.G375R	ENST00000262367	NM_004380.2	375	Gga/Aga	4/31	0.3	3	FACETS	0.813	0.691	0.948	0.407	0.345	0.474	CLONAL	1	TRUE	1	0.31	3		583	458	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341532	89341532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	56	603	0	ENST00000301030.4:c.7538G>A	p.Gly2513Glu	p.G2513E	ENST00000301030	NM_001256183.1	2513	gGa/gAa	10/13	0.3	3	FACETS	0.882	0.757	1	0.441	0.378	0.51	CLONAL	1	TRUE	1	0.31	3		603	473	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527613	29527614	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	35	464	1	ENST00000356175.3:c.1062_1062+1delinsAA		p.X354_splice	ENST00000356175	NM_000267.3	354		9/57	0.205140920811218	3	FACETS	1	0.92	1	0.404	0.334	0.482	CLONAL	1	TRUE	0	0.31	3		465	215	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246058	41246058	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555591693	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	159	750	0	ENST00000357654.3:c.1490C>T	p.Pro497Leu	p.P497L	ENST00000357654	NM_007294.3	497	cCc/cTc	10/23	0.205140920811218	3	FACETS	0.916	0.849	0.985	0.916	0.849	0.985	CLONAL	3	TRUE	0	0.31	3		750	431	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222406	2222406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755921261	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	123	604	3	ENST00000398665.3:c.3238G>A	p.Gly1080Arg	p.G1080R	ENST00000398665	NM_032482.2	1080	Ggg/Agg	24/28	0.3	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.31	3		607	381	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290923	15290923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	94	863	0	ENST00000263388.2:c.3287G>A	p.Gly1096Glu	p.G1096E	ENST00000263388	NM_000435.2	1096	gGg/gAg	20/33	0.3	3	FACETS	1	0.966	1	0.607	0.541	0.677	CLONAL	1	TRUE	1	0.31	3		863	577	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272860	18272861	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	AG	AG	TA	novel	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	68	656	0	ENST00000222254.8:c.900_901delinsTA	p.Ala301Thr	p.A301T	ENST00000222254	NM_005027.3	300	ccAGcg/ccTAcg	7/16	0.3	3	FACETS	0.813	0.708	0.928	0.407	0.354	0.464	CLONAL	1	TRUE	1	0.31	3		656	623	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224124	36224124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1276663757	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	195	903	2	ENST00000222270.7:c.6674C>T	p.Ser2225Phe	p.S2225F	ENST00000222270	NM_014727.1	2225	tCc/tTc	28/37	0.3	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.31	3		905	599	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566824	212566824	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs200092686	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	54	361	0	ENST00000342788.4:c.1357A>T	p.Ile453Phe	p.I453F	ENST00000342788	NM_005235.2	453	Atc/Ttc	12/28	0.24303050260255	3	FACETS	0.759	0.654	0.872	0.759	0.654	0.872	SUBCLONAL	2	TRUE	1	0.31	3		361	265	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812260	212812260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751175543	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	59	313	0	ENST00000342788.4:c.316C>T	p.Arg106Cys	p.R106C	ENST00000342788	NM_005235.2	106	Cgt/Tgt	3/28	0.24303050260255	3	FACETS	1	0.963	1	0.674	0.584	0.772	CLONAL	1	TRUE	1	0.31	3		313	326	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561565	9561565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	54	451	0	ENST00000353224.5:c.217G>A	p.Gly73Arg	p.G73R	ENST00000353224	NM_177990.2	73	Gga/Aga	4/10	0.212486527544463	3	FACETS	1	0.937	1	0.587	0.503	0.677	CLONAL	1	TRUE	1	0.31	3		451	343	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022656	31022656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	115	660	1	ENST00000375687.4:c.2141C>T	p.Ser714Phe	p.S714F	ENST00000375687	NM_015338.5	714	tCc/tTc	13/13	0.212486527544463	3	FACETS	0.796	0.72	0.876	0.796	0.72	0.876	SUBCLONAL	2	TRUE	1	0.31	3		661	538	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742679	39742679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	84	465	2	ENST00000361337.2:c.1522C>T	p.Arg508Cys	p.R508C	ENST00000361337	NM_003286.2	508	Cgt/Tgt	15/21	0.212486527544463	3	FACETS	1	0.977	1	0.719	0.638	0.805	CLONAL	1	TRUE	1	0.31	3		467	435	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076954	41076954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	91	554	0	ENST00000373198.4:c.1466C>T	p.Pro489Leu	p.P489L	ENST00000373198	NM_133170.3	489	cCt/cTt	9/32	0.212486527544463	3	FACETS	0.969	0.868	1	0.969	0.868	1	CLONAL	2	TRUE	1	0.31	3		554	350	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252937	36252937	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	121	472	0	ENST00000300305.3:c.425C>T	p.Ala142Val	p.A142V	ENST00000300305		142	gCt/gTt	4/8	0.212486527544463	3	FACETS	0.836	0.759	0.917	0.836	0.759	0.917	CLONAL	2	TRUE	1	0.31	3		472	539	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391162	89391162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	59	511	1	ENST00000336596.2:c.1228G>A	p.Asp410Asn	p.D410N	ENST00000336596	NM_005233.5	410	Gat/Aat	5/17	1	2	FACETS	0.959	0.828	1	0.959	0.828	1	CLONAL	1	TRUE	1	0.31	2		512	397	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391234	89391234	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1317883302	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	26	347	0	ENST00000336596.2:c.1300C>T	p.Gln434Ter	p.Q434*	ENST00000336596	NM_005233.5	434	Cag/Tag	5/17	1	2	FACETS	0.676	0.538	0.834	0.676	0.538	0.834	SUBCLONAL	1	TRUE	1	0.31	2		347	248	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521711	89521711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	34	604	1	ENST00000336596.2:c.2788G>A	p.Glu930Lys	p.E930K	ENST00000336596	NM_005233.5	930	Gaa/Aaa	16/17	1	2	FACETS	0.63	0.516	0.759	0.63	0.516	0.759	SUBCLONAL	1	TRUE	1	0.31	2		605	348	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281853	142281853	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	50	610	0	ENST00000350721.4:c.391T>A	p.Leu131Ile	p.L131I	ENST00000350721	NM_001184.3	131	Tta/Ata	4/47	1	2	FACETS	0.996	0.849	1	0.996	0.849	1	CLONAL	1	TRUE	1	0.31	2		610	324	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582192	189582192	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	70	527	0	ENST00000264731.3:c.751C>T	p.Arg251Cys	p.R251C	ENST00000264731	NM_003722.4	251	Cgt/Tgt	5/14	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.31	2		527	418	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542190	187542213	+	inframe_deletion	In_Frame_Del	DEL	ATGCACTTGGACGGTAAAGTGAAA	ATGCACTTGGACGGTAAAGTGAAA	-	novel	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	40	570	0	ENST00000441802.2:c.5527_5550del	p.Phe1843_His1850del	p.F1843_H1850del	ENST00000441802	NM_005245.3	1843	TTTCACTTTACCGTCCAAGTGCAT/-	10/27	0.212486527544463	3	FACETS	1	0.899	1	0.554	0.463	0.654	CLONAL	1	TRUE	1	0.31	3		570	269	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80160726	80160726	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	117	805	0	ENST00000265081.6:c.3095T>G	p.Phe1032Cys	p.F1032C	ENST00000265081	NM_002439.4	1032	tTc/tGc	22/24	0.205140920811218	3	FACETS	1	0.95	1	0.711	0.646	0.778	CLONAL	2	TRUE	0	0.31	3		805	409	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729720	41729720	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	58	479	1	ENST00000242208.4:c.809A>T	p.Lys270Ile	p.K270I	ENST00000242208	NM_002192.2	270	aAa/aTa	3/3	1	2	FACETS	0.832	0.716	0.957	0.832	0.716	0.957	CLONAL	1	TRUE	1	0.31	2		480	450	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729961	41729961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867739441	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	143	632	1	ENST00000242208.4:c.568G>A	p.Glu190Lys	p.E190K	ENST00000242208	NM_002192.2	190	Gaa/Aaa	3/3	1	2	FACETS	0.874	0.801	0.949	1	0.99	1	CLONAL	2	TRUE	1	0.31	2		633	528	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009359	69009359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755479314	NA	P-0019333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	103	726	1	ENST00000288368.4:c.2476G>A	p.Asp826Asn	p.D826N	ENST00000288368	NM_024870.2	826	Gac/Aac	22/40	1	2	FACETS	0.767	0.691	0.847	1	0.984	1	SUBCLONAL	2	TRUE	1	0.31	2		727	433	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	139	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.541077140448421	2		215	504	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs730881677	NA	P-0019341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	122	465	0	ENST00000304494.5:c.151-1G>T		p.X51_splice	ENST00000304494	NM_000077.4	51			1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.541077140448421	2		465	319	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692884	89692884	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121909222	NA	P-0019341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	137	415	1	ENST00000371953.3:c.368A>G	p.His123Arg	p.H123R	ENST00000371953	NM_000314.4	123	cAc/cGc	5/9	0.541077140448421	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.541077140448421	1		416	334	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549304	21549304	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	219	812	2	ENST00000382592.4:c.2972C>A	p.Pro991His	p.P991H	ENST00000382592	NM_014572.2	991	cCc/cAc	8/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.541077140448421	2		814	767	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916646	178916646	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	152	471	0	ENST00000263967.3:c.33G>A	p.Trp11Ter	p.W11*	ENST00000263967	NM_006218.2	11	tgG/tgA	2/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.541077140448421	2		471	511	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340880	70340880	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	195	814	0	ENST00000374080.3:c.613T>A	p.Tyr205Asn	p.Y205N	ENST00000374080		205	Tac/Aac	5/45	0.541077140448421	3	FACETS	1	0.93	1	0.502	0.465	0.541	CLONAL	1	TRUE	1	0.541077140448421	3		814	912	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020224	123020224	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs111978474	NA	P-0019341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	195	758	0	ENST00000355640.3:c.712C>T	p.Arg238Ter	p.R238*	ENST00000355640		238	Cga/Tga	2/7	0.504748643492705	4	FACETS	0.922	0.852	0.995			1	CLONAL	1	TRUE	NA	0.541077140448421	4		758	1205	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	165	215	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.482988892599837	NA		215	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0019381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	348	616	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.482988892599837	2		617	1113	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50815250	50815250	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	275	692	0	ENST00000398568.2:c.1603A>G	p.Ser535Gly	p.S535G	ENST00000398568	NM_001042412.1	535	Agc/Ggc	9/18	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.482988892599837	2		692	1059	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579555	7579562	+	frameshift_variant	Frame_Shift_Del	DEL	CATCAAAT	CATCAAAT	-	novel	NA	P-0019381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	215	889	0	ENST00000269305.4:c.125_132del	p.Asp42AlafsTer7	p.D42Afs*7	ENST00000269305	NM_001126112.2	42	gATTTGATG/g	4/11	1	2	FACETS	0.76	0.705	0.816	0.76	0.705	0.816	SUBCLONAL	1	TRUE	1	0.482988892599837	2		889	1172	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455254	29455254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200563480	NA	P-0019381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	185	640	0	ENST00000389048.3:c.2548G>A	p.Gly850Arg	p.G850R	ENST00000389048	NM_004304.4	850	Ggg/Agg	15/29	1	2	FACETS	0.919	0.849	0.99	0.919	0.849	0.99	CLONAL	1	TRUE	1	0.482988892599837	2		640	834	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574201	41574201	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	228	619	1	ENST00000263253.7:c.6490del	p.Gln2164ArgfsTer5	p.Q2164Rfs*5	ENST00000263253	NM_001429.3	2162	agC/ag	31/31	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.482988892599837	2		620	903	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732942	30732942	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	109	313	0	ENST00000295754.5:c.1555G>A	p.Glu519Lys	p.E519K	ENST00000295754	NM_003242.5	519	Gag/Aag	7/7	0.482988892599837	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.482988892599837	1		313	308	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271192	153271192	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0019381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	92	276	0	ENST00000281708.4:c.584+2T>C		p.X195_splice	ENST00000281708	NM_033632.3	195			0.482988892599837	1	FACETS	0.914	0.821	1	0.914	0.821	1	CLONAL	1	TRUE	0	0.482988892599837	1		276	316	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628303	187628307	+	frameshift_variant	Frame_Shift_Del	DEL	TAAGG	TAAGG	A	novel	NA	P-0019381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	234	711	0	ENST00000441802.2:c.2675_2679delinsT	p.Ser892LeufsTer21	p.S892Lfs*21	ENST00000441802	NM_005245.3	892	tCCTTA/tT	2/27	0.482988892599837	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.482988892599837	1		711	669	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971068	21971074	+	protein_altering_variant	In_Frame_Del	DEL	AGCACCA	AGCACCA	C	novel	NA	P-0019381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	128	355	0	ENST00000304494.5:c.284_290delinsG	p.Val95_Leu97delinsGly	p.V95_L97delinsG	ENST00000304494	NM_000077.4	95	gTGGTGCTg/gGg	2/3	0.460948011511067	2	FACETS	1	0.985	1	0.683	0.625	0.743	CLONAL	1	TRUE	0	0.482988892599837	2		355	388	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	102	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.902	0.809	1	0.902	0.809	1	CLONAL	1	TRUE	1	0.416583908563163	2		215	543	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980429	1980429	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	267	1390	1	ENST00000382891.5:c.3891C>A	p.His1297Gln	p.H1297Q	ENST00000382891	NM_133335.3	1297	caC/caA	22/22	1	2	FACETS	0.925	0.865	0.986	0.925	0.865	0.986	CLONAL	1	TRUE	1	0.416583908563163	2		1391	1386	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564698	55564698	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs768971014	NA	P-0019409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	123	627	0	ENST00000288135.5:c.586C>A	p.Leu196Met	p.L196M	ENST00000288135	NM_000222.2	196	Ctg/Atg	3/21	1	2	FACETS	0.846	0.766	0.93	0.846	0.766	0.93	CLONAL	1	TRUE	1	0.416583908563163	2		627	698	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295294	1295294	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0019409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	198	988	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.416583908563163	2		988	933	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	34	215	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	0	0.14	1		215	383	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0019468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	33	188	2	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	1	2	FACETS	0.915	0.744	1	0.915	0.744	1	CLONAL	1	TRUE	1	0.14	2		190	515	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0019468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	38	521	0	ENST00000262160.6:c.1391C>G	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tGa	11/11	1	2	FACETS	0.971	0.802	1	0.971	0.802	1	CLONAL	1	TRUE	1	0.14	2		521	559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0019468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	34	717	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	1	2	FACETS	0.731	0.596	0.885	0.731	0.596	0.885	SUBCLONAL	1	TRUE	1	0.14	2		717	664	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526532	66526532	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0019468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	39	621	0	ENST00000358598.2:c.1088C>G	p.Ser363Ter	p.S363*	ENST00000358598	NM_212471.2	363	tCa/tGa	11/11	1	2	FACETS	0.819	0.677	0.978	0.819	0.677	0.978	CLONAL	1	TRUE	1	0.14	2		621	680	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	68	282	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.914	0.794	1	0.914	0.794	1	CLONAL	1	TRUE	1	0.2	2		282	744	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344018	70344018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747113641	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	83	1004	2	ENST00000374080.3:c.1754G>A	p.Arg585Gln	p.R585Q	ENST00000374080		585	cGa/cAa	13/45	1	2	FACETS	0.834	0.734	0.942	0.834	0.734	0.942	CLONAL	1	TRUE	1	0.2	2		1006	995	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508790	106508790	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	53	576	1	ENST00000359195.3:c.784C>T	p.Pro262Ser	p.P262S	ENST00000359195	NM_002649.2	262	Ccc/Tcc	2/11	1	2	FACETS	0.945	0.806	1	0.945	0.806	1	CLONAL	1	TRUE	1	0.2	2		577	561	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735503	40735503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763584414	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	55	759	0	ENST00000373198.4:c.3370G>A	p.Glu1124Lys	p.E1124K	ENST00000373198	NM_133170.3	1124	Gag/Aag	25/32	1	2	FACETS	0.735	0.628	0.853	0.735	0.628	0.853	SUBCLONAL	1	TRUE	1	0.2	2		759	748	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845844	72845844	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760400785	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	57	673	0	ENST00000268489.5:c.3623C>T	p.Ser1208Leu	p.S1208L	ENST00000268489	NM_006885.3	1208	tCg/tTg	6/10	1	2	FACETS	0.818	0.701	0.946	0.818	0.701	0.946	CLONAL	1	TRUE	1	0.2	2		673	697	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547019	9547019	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	19	251	0	ENST00000353224.5:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000353224	NM_177990.2	335	Cga/Tga	5/10	1	2	FACETS	0.785	0.597	1	0.785	0.597	1	CLONAL	1	TRUE	1	0.2	2		251	242	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944422	40944422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	54	765	0	ENST00000373198.4:c.2080C>T	p.Pro694Ser	p.P694S	ENST00000373198	NM_133170.3	694	Cct/Tct	12/32	1	2	FACETS	0.698	0.594	0.811	0.698	0.594	0.811	SUBCLONAL	1	TRUE	1	0.2	2		765	774	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534285	534285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894226	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	455	768	0	ENST00000451590.1:c.38G>A	p.Gly13Asp	p.G13D	ENST00000451590	NM_001130442.1	13	gGt/gAt	2/5	0.3	4	FACETS	0.985	0.943	1			1	CLONAL	5	TRUE	NA	0.2	4		768	1109	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912795	100912795	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	72	600	0	ENST00000325455.5:c.2527G>A	p.Glu843Lys	p.E843K	ENST00000325455	NM_001202474.3	843	Gag/Aag	7/8	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.2	2		600	616	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740416	58740416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777279856	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	86	771	0	ENST00000305921.3:c.1321C>T	p.Arg441Cys	p.R441C	ENST00000305921	NM_003620.3	441	Cgt/Tgt	6/6	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.2	2		771	785	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524603	176524603	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758782236	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	92	955	0	ENST00000292408.4:c.2335G>A	p.Asp779Asn	p.D779N	ENST00000292408	NM_213647.1	779	Gat/Aat	18/18	1	2	FACETS	0.91	0.807	1	0.91	0.807	1	CLONAL	1	TRUE	1	0.2	2		955	1011	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106069	27106069	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	57	602	0	ENST00000324856.7:c.5680C>T	p.Gln1894Ter	p.Q1894*	ENST00000324856	NM_006015.4	1894	Cag/Tag	20/20	1	2	FACETS	0.861	0.738	0.996	0.861	0.738	0.996	CLONAL	1	TRUE	1	0.2	2		602	662	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812502	43812503	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	54	681	1	ENST00000372470.3:c.1205_1206delinsTT	p.Ser402Phe	p.S402F	ENST00000372470	NM_005373.2	402	tCC/tTT	8/12	1	2	FACETS	0.861	0.735	1	0.861	0.735	1	CLONAL	1	TRUE	1	0.2	2		682	627	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330583	65330583	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	70	769	0	ENST00000342505.4:c.1063G>A	p.Glu355Lys	p.E355K	ENST00000342505	NM_002227.2	355	Gag/Aag	8/25	1	2	FACETS	0.8	0.696	0.913	0.8	0.696	0.913	CLONAL	1	TRUE	1	0.2	2		769	875	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166005	118166005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	48	545	0	ENST00000369448.3:c.515C>T	p.Ser172Phe	p.S172F	ENST00000369448	NM_017709.3	172	tCc/tTc	2/2	1	2	FACETS	0.964	0.815	1	0.964	0.815	1	CLONAL	1	TRUE	1	0.2	2		545	498	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562973	21562973	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1227014940	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	60	955	0	ENST00000382592.4:c.946C>T	p.Pro316Ser	p.P316S	ENST00000382592	NM_014572.2	316	Cca/Tca	4/8	1	2	FACETS	0.717	0.616	0.827	0.717	0.616	0.827	SUBCLONAL	1	TRUE	1	0.2	2		955	837	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28611325	28611325	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	78	722	0	ENST00000241453.7:c.1306A>G	p.Arg436Gly	p.R436G	ENST00000241453	NM_004119.2	436	Aga/Gga	10/24	1	2	FACETS	0.955	0.838	1	0.955	0.838	1	CLONAL	1	TRUE	1	0.2	2		722	817	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748779	43748780	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	100	1033	4	ENST00000382044.4:c.2026_2027delinsTT	p.Pro676Phe	p.P676F	ENST00000382044	NM_001141980.1	676	CCt/TTt	12/28	1	2	FACETS	0.878	0.782	0.981	0.878	0.782	0.981	CLONAL	1	TRUE	1	0.2	2		1037	1139	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862944	9862944	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	rs1555483743	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	36	490	0	ENST00000330684.3:c.2359G>T	p.Glu787Ter	p.E787*	ENST00000330684	NM_001134407.1	787	Gag/Tag	12/13	1	2	FACETS	0.717	0.589	0.861	0.717	0.589	0.861	SUBCLONAL	1	TRUE	1	0.2	2		490	502	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974748	15974748	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753195715	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	47	521	1	ENST00000268712.3:c.4127C>T	p.Pro1376Leu	p.P1376L	ENST00000268712	NM_006311.3	1376	cCg/cTg	30/46	1	2	FACETS	0.862	0.727	1	0.862	0.727	1	CLONAL	1	TRUE	1	0.2	2		522	545	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560134	29560146	+	frameshift_variant	Frame_Shift_Del	DEL	GGTTTGAGAGATT	GGTTTGAGAGATT	-	novel	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	43	403	0	ENST00000356175.3:c.3614_3626del	p.Phe1205TrpfsTer6	p.F1205Wfs*6	ENST00000356175	NM_000267.3	1204	cGGTTTGAGAGATTg/cg	27/57	1	2	FACETS	0.909	0.761	1	0.909	0.761	1	CLONAL	1	TRUE	1	0.2	2		403	473	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679299	29679299	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs863224493	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	52	515	0	ENST00000356175.3:c.7419G>A	p.Trp2473Ter	p.W2473*	ENST00000356175	NM_000267.3	2473	tgG/tgA	50/57	1	2	FACETS	0.934	0.795	1	0.934	0.795	1	CLONAL	1	TRUE	1	0.2	2		515	557	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857590	78857590	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	69	761	0	ENST00000306801.3:c.1660C>T	p.Leu554Phe	p.L554F	ENST00000306801	NM_020761.2	554	Ctt/Ttt	16/34	1	2	FACETS	0.953	0.829	1	0.953	0.829	1	CLONAL	1	TRUE	1	0.2	2		761	724	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250268	39250268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264285931	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	115	1221	0	ENST00000402219.2:c.1301G>A	p.Gly434Glu	p.G434E	ENST00000402219	NM_005633.3	434	gGa/gAa	10/23	1	2	FACETS	0.89	0.799	0.987	0.89	0.799	0.987	CLONAL	1	TRUE	1	0.2	2		1221	1292	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920718	96920718	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	54	587	0	ENST00000258439.3:c.262C>T	p.Gln88Ter	p.Q88*	ENST00000258439	NM_001193304.2	88	Cag/Tag	3/4	1	2	FACETS	0.78	0.665	0.907	0.78	0.665	0.907	CLONAL	1	TRUE	1	0.2	2		587	692	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257832	198257832	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	66	637	2	ENST00000335508.6:c.3620C>T	p.Ser1207Leu	p.S1207L	ENST00000335508	NM_012433.2	1207	tCg/tTg	24/25	1	2	FACETS	0.887	0.769	1	0.887	0.769	1	CLONAL	1	TRUE	1	0.2	2		639	744	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657122	215657122	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659356	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	46	606	0	ENST00000260947.4:c.263C>T	p.Thr88Ile	p.T88I	ENST00000260947	NM_000465.2	88	aCc/aTc	3/11	1	2	FACETS	0.662	0.556	0.779	0.662	0.556	0.779	SUBCLONAL	1	TRUE	1	0.2	2		606	695	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37061893	37061893	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	52	567	0	ENST00000231790.2:c.977T>G	p.Val326Gly	p.V326G	ENST00000231790	NM_000249.3	326	gTg/gGg	11/19	1	2	FACETS	0.893	0.76	1	0.893	0.76	1	CLONAL	1	TRUE	1	0.2	2		567	582	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590654	189590654	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	46	476	0	ENST00000264731.3:c.1219G>A	p.Gly407Ser	p.G407S	ENST00000264731	NM_003722.4	407	Ggc/Agc	10/14	1	2	FACETS	0.833	0.701	0.979	0.833	0.701	0.979	CLONAL	1	TRUE	1	0.2	2		476	552	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139838	55139838	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1308521786	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	42	539	1	ENST00000257290.5:c.1499G>A	p.Arg500Gln	p.R500Q	ENST00000257290	NM_006206.4	500	cGa/cAa	10/23	1	2	FACETS	0.775	0.646	0.918	0.775	0.646	0.918	CLONAL	1	TRUE	1	0.2	2		540	542	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630356	187630356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	60	762	0	ENST00000441802.2:c.626G>A	p.Arg209Lys	p.R209K	ENST00000441802	NM_005245.3	209	aGa/aAa	2/27	1	2	FACETS	0.725	0.623	0.836	0.725	0.623	0.836	SUBCLONAL	1	TRUE	1	0.2	2		762	828	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111726	56111726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	26	184	0	ENST00000399503.3:c.326C>T	p.Ala109Val	p.A109V	ENST00000399503	NM_005921.1	109	gCg/gTg	1/20	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.2	2		184	188	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170112	32170112	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	72	953	0	ENST00000375023.3:c.3496C>T	p.Pro1166Ser	p.P1166S	ENST00000375023	NM_004557.3	1166	Cca/Tca	21/30	0.220594967607421	3	FACETS	0.826	0.72	0.941	0.413	0.36	0.471	CLONAL	1	TRUE	1	0.2	3		953	959	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188237	32188238	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	87	985	3	ENST00000375023.3:c.1103_1104delinsTT	p.Ser368Phe	p.S368F	ENST00000375023	NM_004557.3	368	tCC/tTT	6/30	0.220594967607421	3	FACETS	0.867	0.765	0.976	0.433	0.382	0.488	CLONAL	1	TRUE	1	0.2	3		988	1104	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444311	50444311	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778251001	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	46	411	0	ENST00000331340.3:c.241G>A	p.Asp81Asn	p.D81N	ENST00000331340	NM_006060.4	81	Gat/Aat	4/8	1	2	FACETS	0.865	0.728	1	0.865	0.728	1	CLONAL	1	TRUE	1	0.2	2		411	532	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211056	55211056	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	89	801	0	ENST00000275493.2:c.299C>T	p.Pro100Leu	p.P100L	ENST00000275493	NM_005228.3	100	cCt/cTt	3/28	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.2	2		801	856	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436101	116436101	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	50	515	0	ENST00000397752.3:c.4096C>T	p.Pro1366Ser	p.P1366S	ENST00000397752	NM_000245.2	1366	Cct/Tct	21/21	1	2	FACETS	0.894	0.759	1	0.894	0.759	1	CLONAL	1	TRUE	1	0.2	2		515	559	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005924	69005924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	82	939	1	ENST00000288368.4:c.2335G>A	p.Glu779Lys	p.E779K	ENST00000288368	NM_024870.2	779	Gaa/Aaa	21/40	1	2	FACETS	0.941	0.829	1	0.941	0.829	1	CLONAL	1	TRUE	1	0.2	2		940	871	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980586	70980586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	91	871	1	ENST00000276594.2:c.791C>T	p.Pro264Leu	p.P264L	ENST00000276594	NM_024504.3	264	cCa/cTa	4/8	1	2	FACETS	0.975	0.864	1	0.975	0.864	1	CLONAL	1	TRUE	1	0.2	2		872	933	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971117	21971117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334828764	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	68	650	0	ENST00000304494.5:c.241C>T	p.Pro81Ser	p.P81S	ENST00000304494	NM_000077.4	81	Ccc/Tcc	2/3	0.21160503562531	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.2	1		650	552	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802599	139802600	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	81	978	3	ENST00000247668.2:c.444_445delinsAA	p.Glu149Lys	p.E149K	ENST00000247668	NM_021138.3	148	aaGGag/aaAAag	5/11	1	2	FACETS	0.849	0.746	0.96	0.849	0.746	0.96	CLONAL	1	TRUE	1	0.2	2		981	954	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321378	1321378	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	64	708	0	ENST00000400841.2:c.377G>A	p.Arg126Lys	p.R126K	ENST00000400841		126	aGa/aAa	4/6	1	2	FACETS	0.893	0.772	1	0.893	0.772	1	CLONAL	1	TRUE	1	0.2	2		708	717	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	337	215	0				ENST00000310581	NM_198253.2	-/1132			0.731282823744484	4	FACETS	0.913	0.867	0.958	0.913	0.867	0.958	CLONAL	2	TRUE	2	0.799907876709115	4		215	831	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0019504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	453	616	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.799907876709115	2	FACETS	0.97	0.943	0.995	0.97	0.943	0.995	CLONAL	2	TRUE	0	0.799907876709115	2		617	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0019504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	459	691	2	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.799907876709115	2	FACETS	0.983	0.957	1	0.983	0.957	1	CLONAL	2	TRUE	0	0.799907876709115	2		693	584	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871758	12871758	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0019504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	76	303	0	ENST00000228872.4:c.476-1G>C		p.X159_splice	ENST00000228872	NM_004064.3	159			0.769915153499291	3	FACETS	0.796	0.704	0.894	0.398	0.352	0.447	SUBCLONAL	1	TRUE	1	0.799907876709115	3		303	334	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023895	27023895	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	91	266	0	ENST00000324856.7:c.1001C>G	p.Ser334Trp	p.S334W	ENST00000324856	NM_006015.4	334	tCg/tGg	1/20	0.769915153499291	3	FACETS	0.934	0.837	1	0.467	0.418	0.518	CLONAL	1	TRUE	1	0.799907876709115	3		266	341	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404762	404762	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	145	547	0	ENST00000399788.2:c.4432G>A	p.Asp1478Asn	p.D1478N	ENST00000399788	NM_001042603.1	1478	Gac/Aac	26/28	0.769915153499291	3	FACETS	0.989	0.908	1	0.495	0.454	0.537	CLONAL	1	TRUE	1	0.799907876709115	3		547	513	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871797	12871797	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1260635377	NA	P-0019504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	107	428	0	ENST00000228872.4:c.514G>C	p.Glu172Gln	p.E172Q	ENST00000228872	NM_004064.3	172	Gaa/Caa	2/3	0.769915153499291	3	FACETS	0.814	0.734	0.898	0.407	0.367	0.449	CLONAL	1	TRUE	1	0.799907876709115	3		428	460	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871245	12871245	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	57	229	0	ENST00000228872.4:c.472G>A	p.Asp158Asn	p.D158N	ENST00000228872	NM_004064.3	158	Gac/Aac	1/3	0.769915153499291	3	FACETS	0.845	0.734	0.964	0.423	0.367	0.482	CLONAL	1	TRUE	1	0.799907876709115	3		229	236	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023897	27023897	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	193	252	0	ENST00000324856.7:c.1003C>T	p.Gln335Ter	p.Q335*	ENST00000324856	NM_006015.4	335	Cag/Tag	1/20	0.769915153499291	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.799907876709115	3		252	329	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40367113	40367131	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCCTGCGGGAGGGAAGGG	TCCCTGCGGGAGGGAAGGG	-	novel	NA	P-0019504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	143	582	0	ENST00000397332.2:c.82-16_84del		p.X28_splice	ENST00000397332	NM_001033082.2	28		2/3	0.769915153499291	3	FACETS	0.81	0.741	0.882	0.405	0.37	0.441	CLONAL	1	TRUE	1	0.799907876709115	3		582	618	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983000	201983001	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	1191	977	0	ENST00000359651.3:c.850dup	p.Ile284AsnfsTer17	p.I284Nfs*17	ENST00000359651		283	-/A	7/8	0.799907876709115	4	FACETS	0.992	0.979	1	0.992	0.979	1	CLONAL	4	TRUE	0	0.799907876709115	4		977	1351	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374795	118374795	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	139	483	0	ENST00000534358.1:c.8188G>A	p.Asp2730Asn	p.D2730N	ENST00000534358	NM_005933.3	2730	Gat/Aat	27/36	0.769915153499291	3	FACETS	0.971	0.89	1	0.486	0.445	0.528	CLONAL	1	TRUE	1	0.799907876709115	3		483	501	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871234	12871234	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	62	248	0	ENST00000228872.4:c.461G>T	p.Arg154Leu	p.R154L	ENST00000228872	NM_004064.3	154	cGa/cTa	1/3	0.769915153499291	3	FACETS	0.807	0.704	0.916	0.403	0.352	0.458	CLONAL	1	TRUE	1	0.799907876709115	3		248	269	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871991	35871991	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	405	612	0	ENST00000216797.5:c.622G>T	p.Asp208Tyr	p.D208Y	ENST00000216797	NM_020529.2	208	Gat/Tat	4/6	0.769915153499291	3	FACETS	0.98	0.942	1	0.98	0.942	1	CLONAL	2	TRUE	1	0.799907876709115	3		612	723	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304399	91304399	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	464	588	0	ENST00000355112.3:c.1796G>C	p.Arg599Thr	p.R599T	ENST00000355112	NM_000057.2	599	aGa/aCa	7/22	0.799907876709115	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.799907876709115	3		588	768	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350371	89350371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145730800	NA	P-0019504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	256	858	0	ENST00000301030.4:c.2579C>T	p.Ser860Leu	p.S860L	ENST00000301030	NM_001256183.1	860	tCg/tTg	9/13	0.757337987962707	5	FACETS	0.968	0.904	1	0.242	0.226	0.259	CLONAL	1	TRUE	1	0.799907876709115	5		858	1455	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732295	74733310	+	splice_acceptor_variant,splice_donor_variant,start_lost,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	CGCGACCTGGATTTGGATTCCCTCTTGGACACTGGGGGAGGACTCCTGGACCGAGACCGGGACCTGGACCGCGAACGAGATCTGGAGACCGACGAGGACTTGGACTTGGACCTTCGTGCGGATCTGGACTTGGAGGTCGACCGAGATCGAGAACGAGTGCGGGACCGAGACTTCGAGCGGCTGTAGCGAGATCGGCTGCGAGACCTGGAACGACTCCGACTCCGGGATCGGCTGCGGCGACGCCGCCTAGGGCTGCGGGCGGGACGAGCAAGCACAGCGGGGTTAATTCCAGGCAGCGGGGCCGGCCCCGCCCGCGCGCTCCCGCCCAGGCCGCCATTATCTCGCCGCCAGACGCCATTTCCCCAGTCGCGAGGCGGGGTCCTCCGCCCCGCGCCGCCCACACCCCGGCCACTCCCGGGTCGCAGACGGCGGAAGCTCGCGGGGTGGCCGGAGGGTCGCGAGACGCGGCGTGCACCCCCGCCCCGTCCGGGCCCGCACCACGTGCTTCGCCGCGGACCTTTGTGAGGTCGCCCGGGCCTCCCGCGCGCCCCGCCCCGCCTCCCGCGGTCCCCTCAGCCCCGTTTACCTGCGGCTCCGGCGTCCGTAGCCACCGCCCCCGTACCTGCGGGGTGGCGGTCCCCGGCGGCTGTGGTGTGAGTCCGGGGGGCGGCCGTAGCGCGCCATTTGCACCCGCAGCTCGCGGCCGTCCAGCACGGCCCCGTCCATGGCATCCATAGCGTCCTCAGCGTCGCGCTTGTCGTGAAAGCGAACGAAGGCGAAGCCGCGGGACTCCTTGGTGTAGCGGTCCCGCGGGATGTACACGTCGCCGACGCGCCCGTACTTCTCGAAGACGCGCCTCAGCGTGTCGGGCGAGGTGCGGTAGGTCAGGTTGTCCACCTTGAGGGAGGTCATACCCTCCACATCGGGAGGGGGGCGGCCGTAGCTCATAGCTCTGAGTGGCGGCCCGGAGCCCCGCGAACTGGCGCCGGCTTCCTCAGCTCTGGGCGGTGCGACGC	CGCGACCTGGATTTGGATTCCCTCTTGGACACTGGGGGAGGACTCCTGGACCGAGACCGGGACCTGGACCGCGAACGAGATCTGGAGACCGACGAGGACTTGGACTTGGACCTTCGTGCGGATCTGGACTTGGAGGTCGACCGAGATCGAGAACGAGTGCGGGACCGAGACTTCGAGCGGCTGTAGCGAGATCGGCTGCGAGACCTGGAACGACTCCGACTCCGGGATCGGCTGCGGCGACGCCGCCTAGGGCTGCGGGCGGGACGAGCAAGCACAGCGGGGTTAATTCCAGGCAGCGGGGCCGGCCCCGCCCGCGCGCTCCCGCCCAGGCCGCCATTATCTCGCCGCCAGACGCCATTTCCCCAGTCGCGAGGCGGGGTCCTCCGCCCCGCGCCGCCCACACCCCGGCCACTCCCGGGTCGCAGACGGCGGAAGCTCGCGGGGTGGCCGGAGGGTCGCGAGACGCGGCGTGCACCCCCGCCCCGTCCGGGCCCGCACCACGTGCTTCGCCGCGGACCTTTGTGAGGTCGCCCGGGCCTCCCGCGCGCCCCGCCCCGCCTCCCGCGGTCCCCTCAGCCCCGTTTACCTGCGGCTCCGGCGTCCGTAGCCACCGCCCCCGTACCTGCGGGGTGGCGGTCCCCGGCGGCTGTGGTGTGAGTCCGGGGGGCGGCCGTAGCGCGCCATTTGCACCCGCAGCTCGCGGCCGTCCAGCACGGCCCCGTCCATGGCATCCATAGCGTCCTCAGCGTCGCGCTTGTCGTGAAAGCGAACGAAGGCGAAGCCGCGGGACTCCTTGGTGTAGCGGTCCCGCGGGATGTACACGTCGCCGACGCGCCCGTACTTCTCGAAGACGCGCCTCAGCGTGTCGGGCGAGGTGCGGTAGGTCAGGTTGTCCACCTTGAGGGAGGTCATACCCTCCACATCGGGAGGGGGGCGGCCGTAGCTCATAGCTCTGAGTGGCGGCCCGGAGCCCCGCGAACTGGCGCCGGCTTCCTCAGCTCTGGGCGGTGCGACGC	-	novel	NA	P-0019504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	33	310	0	ENST00000359995.5:c.-68_614del		p.X23_splice	ENST00000359995	NM_001195427.1	23		1-2/3	0.799907876709115		FACETS		0.29	0.431				SUBCLONAL	1	TRUE	1	0.799907876709115	4		310	417	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213071	39213071	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	347	1073	0	ENST00000402219.2:c.3896C>G	p.Ser1299Cys	p.S1299C	ENST00000402219	NM_005633.3	1299	tCt/tGt	23/23	1	2	FACETS	0.995	0.946	1	0.995	0.946	1	CLONAL	1	TRUE	1	0.799907876709115	2		1073	872	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637599	52637599	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	211	692	0	ENST00000394830.3:c.2717G>C	p.Arg906Thr	p.R906T	ENST00000394830	NM_018313.4	906	aGa/aCa	18/30	1	2	FACETS	0.964	0.903	1	0.964	0.903	1	CLONAL	1	TRUE	1	0.799907876709115	2		692	547	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665162	138665162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	256	1053	1	ENST00000330315.3:c.403G>A	p.Glu135Lys	p.E135K	ENST00000330315	NM_023067.3	135	Gaa/Aaa	1/1	0.769915153499291	3	FACETS	0.847	0.793	0.902	0.423	0.396	0.451	CLONAL	1	TRUE	1	0.799907876709115	3		1054	1058	SUCCESS
ATR	545	MSKCC	GRCh37	3	142189023	142189023	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	119	445	0	ENST00000350721.4:c.6224C>G	p.Ser2075Cys	p.S2075C	ENST00000350721	NM_001184.3	2075	tCt/tGt	37/47	0.769915153499291	3	FACETS	0.973	0.885	1	0.487	0.442	0.533	CLONAL	1	TRUE	1	0.799907876709115	3		445	428	SUCCESS
APC	324	MSKCC	GRCh37	5	112175994	112175994	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	133	445	0	ENST00000257430.4:c.4703A>G	p.Asp1568Gly	p.D1568G	ENST00000257430	NM_000038.5	1568	gAt/gGt	16/16	0.769915153499291	3	FACETS	0.926	0.846	1	0.463	0.423	0.505	CLONAL	1	TRUE	1	0.799907876709115	3		445	503	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501289	140501506	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACAGCGGAAACCCTGGAAAAGCAGCTTTCGACAAAAGTCACAAAATGCTAAGGTGAAAAACGTTTTTCGTACCTGCAAAGTAAAAAATCACAGAGATTTCAAAAACTCACAAGAAAACTTTCTAGAAACTGACGTATCTACTCTCTTGTTTAAAATAACAAAGTTGTAATATATTTATATCATGAAACTCACATACTAAAGTACTATTATAAAATGAA	ACAGCGGAAACCCTGGAAAAGCAGCTTTCGACAAAAGTCACAAAATGCTAAGGTGAAAAACGTTTTTCGTACCTGCAAAGTAAAAAATCACAGAGATTTCAAAAACTCACAAGAAAACTTTCTAGAAACTGACGTATCTACTCTCTTGTTTAAAATAACAAAGTTGTAATATATTTATATCATGAAACTCACATACTAAAGTACTATTATAAAATGAA	-	novel	NA	P-0019504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	79	587	0	ENST00000288602.6:c.712-146_783del		p.X238_splice	ENST00000288602	NM_004333.4	238		6/18	0.769915153499291	3	FACETS	0.461	0.405	0.52	0.23	0.202	0.26	SUBCLONAL	1	TRUE	1	0.799907876709115	3		587	600	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69143603	69143603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	105	380	0	ENST00000288368.4:c.4811G>A	p.Gly1604Glu	p.G1604E	ENST00000288368	NM_024870.2	1604	gGa/gAa	40/40	0.769915153499291	3	FACETS	0.94	0.849	1	0.47	0.424	0.518	CLONAL	1	TRUE	1	0.799907876709115	3		380	391	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750806	128750806	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	155	595	0	ENST00000377970.2:c.343G>C	p.Glu115Gln	p.E115Q	ENST00000377970	NM_002467.4	115	Gag/Cag	2/3	0.769915153499291	3	FACETS	0.889	0.818	0.964	0.445	0.409	0.482	CLONAL	1	TRUE	1	0.799907876709115	3		595	610	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089788	5089788	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	154	460	0	ENST00000381652.3:c.2686G>C	p.Glu896Gln	p.E896Q	ENST00000381652	NM_004972.3	896	Gaa/Caa	20/25	0.799907876709115	1	FACETS	0.983	0.927	1	0.983	0.927	1	CLONAL	1	TRUE	0	0.799907876709115	1		460	235	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923041	44923041	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	445	398	0	ENST00000377967.4:c.1903del	p.Gln635AsnfsTer56	p.Q635Nfs*56	ENST00000377967	NM_021140.2	634	aaC/aa	16/29	0.799907876709115	2	FACETS	0.999	0.973	1			1	CLONAL	2	TRUE	NA	0.799907876709115	2		398	557	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039686	47039687	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0019504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	587	545	0	ENST00000377604.3:c.1139_1140del	p.Glu380ValfsTer6	p.E380Vfs*6	ENST00000377604	NM_001204468.1	380	GAg/g	11/24	0.799907876709115	2	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.799907876709115	2		545	710	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53253937	53253937	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	198	328	0	ENST00000375401.3:c.135G>T	p.Lys45Asn	p.K45N	ENST00000375401	NM_004187.3	45	aaG/aaT	1/26	0.799907876709115	2	FACETS	1	0.95	1			1	CLONAL	1	TRUE	NA	0.799907876709115	2		328	486	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	304	282	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.979	0.929	1	0.979	0.929	1	CLONAL	1	TRUE	1	0.886971236913493	2		282	700	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	68	499	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.133	0.115	0.153	0.133	0.115	0.153	SUBCLONAL	1	TRUE	1	0.886971236913493	2		499	1152	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725011	47725011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1342443339	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	525	916	1	ENST00000449228.1:c.733C>T	p.Leu245Phe	p.L245F	ENST00000449228	NM_001127240.2	245	Ctc/Ttc	4/4	0.886971236913493	1	FACETS	0.882	0.856	0.907	0.882	0.856	0.907	CLONAL	1	TRUE	0	0.886971236913493	1		917	747	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120984	115120984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	53	689	0	ENST00000257566.3:c.22C>T	p.Pro8Ser	p.P8S	ENST00000257566	NM_016569.3	8	Ccg/Tcg	1/8	1	2	FACETS	0.142	0.12	0.165	0.142	0.12	0.165	SUBCLONAL	1	TRUE	1	0.886971236913493	2		689	844	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874551	35874551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs201084372	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	308	498	0	ENST00000303115.3:c.707G>A	p.Gly236Glu	p.G236E	ENST00000303115	NM_002185.3	236	gGg/gAg	6/8	1	2	FACETS	0.91	0.863	0.958	0.91	0.863	0.958	CLONAL	1	TRUE	1	0.886971236913493	2		498	763	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245939	46245939	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	304	545	0	ENST00000334344.6:c.4033G>A	p.Asp1345Asn	p.D1345N	ENST00000334344	NM_152641.2	1345	Gac/Aac	15/21	1	2	FACETS	0.838	0.793	0.884	0.838	0.793	0.884	CLONAL	1	TRUE	1	0.886971236913493	2		545	818	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	348	611	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	1	2	FACETS	0.956	0.91	1	0.956	0.91	1	CLONAL	1	TRUE	1	0.886971236913493	2		611	821	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412233	139412233	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs753964476	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	320	867	0	ENST00000277541.6:c.1412T>C	p.Ile471Thr	p.I471T	ENST00000277541	NM_017617.3	471	aTt/aCt	8/34	0.275026927969387	2	FACETS	0.655	0.618	0.692	0.327	0.309	0.346	INDETERMINATE	1	TRUE	0	0.886971236913493	2		867	1102	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515397	103515397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	59	528	0	ENST00000355739.4:c.1898C>T	p.Ser633Phe	p.S633F	ENST00000355739	NM_000123.3	633	tCc/tTc	8/15	1	2	FACETS	0.182	0.156	0.211	0.182	0.156	0.211	SUBCLONAL	1	TRUE	1	0.886971236913493	2		528	729	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349226	89349226	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1193737081	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1775	114	1278	1	ENST00000301030.4:c.3724G>A	p.Ala1242Thr	p.A1242T	ENST00000301030	NM_001256183.1	1242	Gct/Act	9/13	1	2	FACETS	0.136	0.122	0.152	0.136	0.122	0.152	SUBCLONAL	1	TRUE	1	0.886971236913493	2		1279	1889	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393165	393165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	82	481	0	ENST00000380956.4:c.13G>A	p.Gly5Ser	p.G5S	ENST00000380956	NM_001195286.1	5	Ggc/Agc	2/9	0.886971236913493	1	FACETS	0.276	0.245	0.309	0.276	0.245	0.309	SUBCLONAL	1	TRUE	0	0.886971236913493	1		481	373	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524933	187524933	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749223648	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	66	881	0	ENST00000441802.2:c.10747G>A	p.Asp3583Asn	p.D3583N	ENST00000441802	NM_005245.3	3583	Gac/Aac	19/27	1	2	FACETS	0.139	0.12	0.16	0.139	0.12	0.16	SUBCLONAL	1	TRUE	1	0.886971236913493	2		881	1070	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075394	8075394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	42	415	0	ENST00000377482.5:c.176C>T	p.Ser59Phe	p.S59F	ENST00000377482	NM_018948.3	59	tCt/tTt	3/4	0.886971236913493	1	FACETS	0.135	0.113	0.16	0.135	0.113	0.16	SUBCLONAL	1	TRUE	0	0.886971236913493	1		415	390	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367278	50367278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	65	476	1	ENST00000331340.3:c.85G>A	p.Glu29Lys	p.E29K	ENST00000331340	NM_006060.4	29	Gag/Aag	3/8	1	2	FACETS	0.218	0.189	0.25	0.218	0.189	0.25	SUBCLONAL	1	TRUE	1	0.886971236913493	2		477	672	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441505	6441505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	149	286	0	ENST00000356142.4:c.352C>T	p.Pro118Ser	p.P118S	ENST00000356142	NM_018890.3	118	Cct/Tct	6/7	1	2	FACETS	0.954	0.885	1	0.954	0.885	1	CLONAL	1	TRUE	1	0.886971236913493	2		286	352	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15365046	15365046	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200802400	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	295	802	0	ENST00000263377.2:c.2075C>T	p.Ser692Phe	p.S692F	ENST00000263377	NM_058243.2	692	tCc/tTc	11/20	1	2	FACETS	0.597	0.562	0.633	0.597	0.562	0.633	SUBCLONAL	1	TRUE	1	0.886971236913493	2		802	1114	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056156	27056156	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	45	617	0	ENST00000324856.7:c.1152G>A	p.Met384Ile	p.M384I	ENST00000324856	NM_006015.4	384	atG/atA	2/20	0.886971236913493	1	FACETS	0.131	0.11	0.154	0.131	0.11	0.154	SUBCLONAL	1	TRUE	0	0.886971236913493	1		617	431	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087360	27087360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	25	622	0	ENST00000324856.7:c.1934C>T	p.Ser645Leu	p.S645L	ENST00000324856	NM_006015.4	645	tCa/tTa	5/20	0.886971236913493	1	FACETS	0.065	0.051	0.082	0.065	0.051	0.082	SUBCLONAL	1	TRUE	0	0.886971236913493	1		622	479	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087531	27087531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	49	827	0	ENST00000324856.7:c.2105C>T	p.Ser702Phe	p.S702F	ENST00000324856	NM_006015.4	702	tCt/tTt	5/20	0.886971236913493	1	FACETS	0.098	0.082	0.115	0.098	0.082	0.115	SUBCLONAL	1	TRUE	0	0.886971236913493	1		827	630	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087895	27087901	+	frameshift_variant	Frame_Shift_Del	DEL	CCACCCA	CCACCCA	-	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	500	884	0	ENST00000324856.7:c.2182_2188del	p.Pro728ValfsTer12	p.P728Vfs*12	ENST00000324856	NM_006015.4	728	CCACCCAgt/gt	6/20	0.886971236913493	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.886971236913493	1		884	583	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099861	27099861	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024139131	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	67	534	0	ENST00000324856.7:c.3740C>T	p.Ser1247Phe	p.S1247F	ENST00000324856	NM_006015.4	1247	tCc/tTc	15/20	0.886971236913493	1	FACETS	0.224	0.195	0.254	0.224	0.195	0.254	SUBCLONAL	1	TRUE	0	0.886971236913493	1		534	376	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100340	27100340	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	60	811	2	ENST00000324856.7:c.4052G>A	p.Gly1351Asp	p.G1351D	ENST00000324856	NM_006015.4	1351	gGc/gAc	17/20	0.886971236913493	1	FACETS	0.111	0.095	0.128	0.111	0.095	0.128	SUBCLONAL	1	TRUE	0	0.886971236913493	1		813	678	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941150	36941150	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	418	699	0	ENST00000361632.4:c.189G>C	p.Trp63Cys	p.W63C	ENST00000361632		63	tgG/tgC	3/16	0.886971236913493	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.886971236913493	1		699	505	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366625	40366625	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	26	756	0	ENST00000397332.2:c.572G>A	p.Ser191Asn	p.S191N	ENST00000397332	NM_001033082.2	191	aGc/aAc	2/3	0.886971236913493	1	FACETS	0.076	0.06	0.095	0.076	0.06	0.095	SUBCLONAL	1	TRUE	0	0.886971236913493	1		756	428	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46512233	46512233	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs895994574	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	66	707	0	ENST00000262741.5:c.1006G>A	p.Asp336Asn	p.D336N	ENST00000262741	NM_003629.3	336	Gat/Aat	8/10	0.886971236913493	1	FACETS	0.138	0.119	0.158	0.138	0.119	0.158	SUBCLONAL	1	TRUE	0	0.886971236913493	1		707	602	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658588	206658588	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1303882419	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	54	639	0	ENST00000367120.3:c.1561A>G	p.Ser521Gly	p.S521G	ENST00000367120	NM_014002.3	521	Agc/Ggc	15/22	1	2	FACETS	0.154	0.131	0.179	0.154	0.131	0.179	SUBCLONAL	1	TRUE	1	0.886971236913493	2		639	792	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552734	226552734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	40	557	0	ENST00000366794.5:c.2627G>A	p.Gly876Asp	p.G876D	ENST00000366794	NM_001618.3	876	gGt/gAt	19/23	1	2	FACETS	0.118	0.097	0.141	0.118	0.097	0.141	SUBCLONAL	1	TRUE	1	0.886971236913493	2		557	765	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578207	226578207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	49	666	0	ENST00000366794.5:c.521C>T	p.Pro174Leu	p.P174L	ENST00000366794	NM_001618.3	174	cCc/cTc	4/23	1	2	FACETS	0.122	0.103	0.144	0.122	0.103	0.144	SUBCLONAL	1	TRUE	1	0.886971236913493	2		666	904	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100495	8100495	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	101	904	2	ENST00000346208.3:c.469C>T	p.Pro157Ser	p.P157S	ENST00000346208		157	Ccg/Tcg	3/6	1	2	FACETS	0.208	0.185	0.233	0.208	0.185	0.233	SUBCLONAL	1	TRUE	1	0.886971236913493	2		906	1093	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104389822	104389822	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	115	643	0	ENST00000369902.3:c.1366-1G>A		p.X456_splice	ENST00000369902	NM_016169.3	456			1	2	FACETS	0.233	0.209	0.258	0.233	0.209	0.258	SUBCLONAL	1	TRUE	1	0.886971236913493	2		643	1113	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243277	123243277	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	345	1004	0	ENST00000358487.5:c.2236C>T	p.Gln746Ter	p.Q746*	ENST00000358487	NM_000141.4	746	Cag/Tag	17/18	1	2	FACETS	0.556	0.525	0.588	0.556	0.525	0.588	SUBCLONAL	1	TRUE	1	0.886971236913493	2		1004	1399	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999207	100999207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	337	736	1	ENST00000325455.5:c.595G>A	p.Ala199Thr	p.A199T	ENST00000325455	NM_001202474.3	199	Gcc/Acc	1/8	0.886971236913493	3	FACETS	0.881	0.833	0.93	0.441	0.416	0.465	CLONAL	1	TRUE	1	0.886971236913493	3		737	1245	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493724	56493724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	400	709	1	ENST00000267101.3:c.3040G>A	p.Asp1014Asn	p.D1014N	ENST00000267101	NM_001982.3	1014	Gac/Aac	25/28	1	2	FACETS	0.864	0.824	0.905	0.864	0.824	0.905	CLONAL	1	TRUE	1	0.886971236913493	2		710	1044	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495459	56495459	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1191071083	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	76	737	0	ENST00000267101.3:c.3649C>T	p.Leu1217Phe	p.L1217F	ENST00000267101	NM_001982.3	1217	Ctt/Ttt	28/28	1	2	FACETS	0.172	0.15	0.196	0.172	0.15	0.196	SUBCLONAL	1	TRUE	1	0.886971236913493	2		737	994	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784021	120784021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	359	1041	1	ENST00000257552.2:c.964G>A	p.Ala322Thr	p.A322T	ENST00000257552	NM_002442.3	322	Gcg/Acg	13/15	1	2	FACETS	0.657	0.623	0.692	0.657	0.623	0.692	SUBCLONAL	1	TRUE	1	0.886971236913493	2		1042	1232	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431986	121431986	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	259	914	0	ENST00000257555.6:c.733G>A	p.Gly245Arg	p.G245R	ENST00000257555		245	Ggg/Agg	4/10	1	2	FACETS	0.617	0.579	0.657	0.617	0.579	0.657	SUBCLONAL	1	TRUE	1	0.886971236913493	2		914	946	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959390	26959390	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	395	602	1	ENST00000381527.3:c.557C>T	p.Pro186Leu	p.P186L	ENST00000381527	NM_001260.1	186	cCt/cTt	6/13	1	2	FACETS	0.903	0.862	0.945	0.903	0.862	0.945	CLONAL	1	TRUE	1	0.886971236913493	2		603	986	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975666	26975666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	48	542	0	ENST00000381527.3:c.1174G>A	p.Asp392Asn	p.D392N	ENST00000381527	NM_001260.1	392	Gac/Aac	12/13	1	2	FACETS	0.126	0.106	0.148	0.126	0.106	0.148	SUBCLONAL	1	TRUE	1	0.886971236913493	2		542	861	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281106	49281106	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1455	98	982	1	ENST00000282018.3:c.153G>A	p.Trp51Ter	p.W51*	ENST00000282018	NM_020377.2	51	tgG/tgA	1/1	1	2	FACETS	0.142	0.126	0.16	0.142	0.126	0.16	SUBCLONAL	1	TRUE	1	0.886971236913493	2		983	1553	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068872	30068872	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	353	782	0	ENST00000331968.5:c.2057T>C	p.Leu686Ser	p.L686S	ENST00000331968	NM_002742.2	686	tTa/tCa	14/18	1	2	FACETS	0.643	0.609	0.678	0.643	0.609	0.678	SUBCLONAL	1	TRUE	1	0.886971236913493	2		782	1237	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871718	35871718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1440576639	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	49	505	0	ENST00000216797.5:c.788C>T	p.Thr263Ile	p.T263I	ENST00000216797	NM_020529.2	263	aCc/aTc	5/6	1	2	FACETS	0.135	0.114	0.159	0.135	0.114	0.159	SUBCLONAL	1	TRUE	1	0.886971236913493	2		505	819	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701245	43701245	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	64	754	0	ENST00000382044.4:c.5450C>T	p.Thr1817Ile	p.T1817I	ENST00000382044	NM_001141980.1	1817	aCc/aTc	26/28	1	2	FACETS	0.134	0.116	0.155	0.134	0.116	0.155	SUBCLONAL	1	TRUE	1	0.886971236913493	2		754	1073	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748629	43748629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1574	93	990	0	ENST00000382044.4:c.2177G>A	p.Ser726Asn	p.S726N	ENST00000382044	NM_001141980.1	726	aGt/aAt	12/28	1	2	FACETS	0.126	0.111	0.142	0.126	0.111	0.142	SUBCLONAL	1	TRUE	1	0.886971236913493	2		990	1667	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348782	11348782	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	36	524	1	ENST00000332029.2:c.554C>T	p.Thr185Ile	p.T185I	ENST00000332029	NM_003745.1	185	aCc/aTc	2/2	1	2	FACETS	0.12	0.098	0.144	0.12	0.098	0.144	SUBCLONAL	1	TRUE	1	0.886971236913493	2		525	678	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81979813	81979813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1425913844	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	48	546	0	ENST00000359376.3:c.3515G>A	p.Ser1172Asn	p.S1172N	ENST00000359376	NM_002661.3	1172	aGc/aAc	31/33	1	2	FACETS	0.14	0.118	0.165	0.14	0.118	0.165	SUBCLONAL	1	TRUE	1	0.886971236913493	2		546	771	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349403	89349403	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	518	977	0	ENST00000301030.4:c.3547G>C	p.Asp1183His	p.D1183H	ENST00000301030	NM_001256183.1	1183	Gac/Cac	9/13	1	2	FACETS	0.851	0.816	0.887	0.851	0.816	0.887	CLONAL	1	TRUE	1	0.886971236913493	2		977	1372	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351512	89351512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	370	817	1	ENST00000301030.4:c.1438G>A	p.Glu480Lys	p.E480K	ENST00000301030	NM_001256183.1	480	Gag/Aag	9/13	1	2	FACETS	0.778	0.74	0.818	0.778	0.74	0.818	SUBCLONAL	1	TRUE	1	0.886971236913493	2		818	1072	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217239	7217239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763892022	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	62	753	0	ENST00000380728.2:c.466C>T	p.Pro156Ser	p.P156S	ENST00000380728		156	Ccc/Tcc	6/11	1	2	FACETS	0.14	0.12	0.161	0.14	0.12	0.161	SUBCLONAL	1	TRUE	1	0.886971236913493	2		753	1002	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556081	29556082	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATGTCCC	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	176	314	0	ENST00000356175.3:c.2453_2459dup	p.Ser821ProfsTer12	p.S821Pfs*12	ENST00000356175	NM_000267.3	816	-/ATGTCCC	21/57	1	2	FACETS	0.792	0.736	0.85	0.792	0.736	0.85	SUBCLONAL	1	TRUE	1	0.886971236913493	2		314	501	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223196	41223196	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145466894	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	57	722	0	ENST00000357654.3:c.4735C>T	p.Pro1579Ser	p.P1579S	ENST00000357654	NM_007294.3	1579	Cct/Tct	15/23	1	2	FACETS	0.121	0.103	0.141	0.121	0.103	0.141	SUBCLONAL	1	TRUE	1	0.886971236913493	2		722	1060	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244253	41244253	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	488	826	0	ENST00000357654.3:c.3295C>T	p.Pro1099Ser	p.P1099S	ENST00000357654	NM_007294.3	1099	Cct/Tct	10/23	1	2	FACETS	0.85	0.814	0.887	0.85	0.814	0.887	CLONAL	1	TRUE	1	0.886971236913493	2		826	1294	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435266	56435266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1366427976	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	336	662	0	ENST00000407977.2:c.1871C>T	p.Pro624Leu	p.P624L	ENST00000407977		624	cCt/cTt	9/10	1	2	FACETS	0.875	0.831	0.92	0.875	0.831	0.92	CLONAL	1	TRUE	1	0.886971236913493	2		662	866	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58701104	58701104	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	130	646	1	ENST00000305921.3:c.695G>A	p.Gly232Asp	p.G232D	ENST00000305921	NM_003620.3	232	gGt/gAt	2/6	1	2	FACETS	0.292	0.264	0.321	0.292	0.264	0.321	SUBCLONAL	1	TRUE	1	0.886971236913493	2		647	1004	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796006	78796006	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	53	674	0	ENST00000306801.3:c.896C>T	p.Pro299Leu	p.P299L	ENST00000306801	NM_020761.2	299	cCt/cTt	8/34	1	2	FACETS	0.114	0.097	0.134	0.114	0.097	0.134	SUBCLONAL	1	TRUE	1	0.886971236913493	2		674	1045	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7174711	7174711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	255	593	0	ENST00000302850.5:c.1006C>T	p.Pro336Ser	p.P336S	ENST00000302850	NM_000208.2	336	Ccc/Tcc	4/22	1	2	FACETS	0.758	0.712	0.804	0.758	0.712	0.804	SUBCLONAL	1	TRUE	1	0.886971236913493	2		593	759	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267902	7267902	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	28	344	0	ENST00000302850.5:c.106C>T	p.Pro36Ser	p.P36S	ENST00000302850	NM_000208.2	36	Ccc/Tcc	2/22	1	2	FACETS	0.12	0.095	0.148	0.12	0.095	0.148	SUBCLONAL	1	TRUE	1	0.886971236913493	2		344	528	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610684	10610684	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	183	555	2	ENST00000171111.5:c.26G>A	p.Gly9Glu	p.G9E	ENST00000171111	NM_203500.1	9	gGg/gAg	2/6	1	2	FACETS	0.528	0.488	0.569	0.528	0.488	0.569	SUBCLONAL	1	TRUE	1	0.886971236913493	2		557	782	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11019818	11019818	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	271	650	0	ENST00000327064.4:c.493G>A	p.Asp165Asn	p.D165N	ENST00000327064	NM_199141.1	165	Gac/Aac	4/16	1	2	FACETS	0.573	0.538	0.61	0.573	0.538	0.61	SUBCLONAL	1	TRUE	1	0.886971236913493	2		650	1066	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11027394	11027394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	86	836	0	ENST00000327064.4:c.961G>A	p.Val321Met	p.V321M	ENST00000327064	NM_199141.1	321	Gtg/Atg	8/16	1	2	FACETS	0.157	0.138	0.178	0.157	0.138	0.178	SUBCLONAL	1	TRUE	1	0.886971236913493	2		836	1233	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097095	11097095	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1199851876	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	68	878	0	ENST00000358026.2:c.586C>T	p.Leu196Phe	p.L196F	ENST00000358026	NM_001128849.1	196	Ctc/Ttc	4/36	1	2	FACETS	0.132	0.114	0.151	0.132	0.114	0.151	SUBCLONAL	1	TRUE	1	0.886971236913493	2		878	1164	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290034	15290034	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1258221482	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	448	915	0	ENST00000263388.2:c.3520C>T	p.Pro1174Ser	p.P1174S	ENST00000263388	NM_000435.2	1174	Ccc/Tcc	22/33	1	2	FACETS	0.869	0.83	0.907	0.869	0.83	0.907	CLONAL	1	TRUE	1	0.886971236913493	2		915	1163	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955222	17955222	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568408509	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	243	838	0	ENST00000458235.1:c.5C>T	p.Ala2Val	p.A2V	ENST00000458235	NM_000215.3	2	gCa/gTa	2/24	1	2	FACETS	0.483	0.45	0.516	0.483	0.45	0.516	SUBCLONAL	1	TRUE	1	0.886971236913493	2		838	1135	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279592	18279592	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1206545279	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	91	797	0	ENST00000222254.8:c.1865G>A	p.Trp622Ter	p.W622*	ENST00000222254	NM_005027.3	622	tGg/tAg	15/16	1	2	FACETS	0.165	0.146	0.186	0.165	0.146	0.186	SUBCLONAL	1	TRUE	1	0.886971236913493	2		797	1241	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211372	36211372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	396	1059	0	ENST00000222270.7:c.1123G>A	p.Asp375Asn	p.D375N	ENST00000222270	NM_014727.1	375	Gac/Aac	3/37	0.886971236913493	1	FACETS	0.633	0.606	0.66	0.633	0.606	0.66	SUBCLONAL	1	TRUE	0	0.886971236913493	1		1059	785	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227690	36227690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	281	883	1	ENST00000222270.7:c.7259G>A	p.Ser2420Asn	p.S2420N	ENST00000222270	NM_014727.1	2420	aGt/aAt	31/37	0.886971236913493	1	FACETS	0.589	0.558	0.619	0.589	0.558	0.619	SUBCLONAL	1	TRUE	0	0.886971236913493	1		884	599	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798415	42798416	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCC	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	521	847	0	ENST00000575354.2:c.4287_4290dup	p.Lys1431CysfsTer11	p.K1431Cfs*11	ENST00000575354	NM_015125.3	1429	agt/agTGCCt	18/20	0.886971236913493	1	FACETS	0.991	0.966	1	0.991	0.966	1	CLONAL	1	TRUE	0	0.886971236913493	1		847	660	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082823	16082823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	41	122	0	ENST00000281043.3:c.637C>T	p.Pro213Ser	p.P213S	ENST00000281043	NM_005378.4	213	Ccg/Tcg	2/3	1	2	FACETS	0.675	0.574	0.782	0.675	0.574	0.782	SUBCLONAL	1	TRUE	1	0.886971236913493	2		122	137	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471058	25471058	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	476	927	0	ENST00000264709.3:c.703G>A	p.Glu235Lys	p.E235K	ENST00000264709	NM_175629.2	235	Gag/Aag	7/23	1	2	FACETS	0.925	0.887	0.964	0.925	0.887	0.964	CLONAL	1	TRUE	1	0.886971236913493	2		927	1160	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213260	39213260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs533661246	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1309	75	1080	1	ENST00000402219.2:c.3707C>T	p.Pro1236Leu	p.P1236L	ENST00000402219	NM_005633.3	1236	cCc/cTc	23/23	1	2	FACETS	0.122	0.106	0.14	0.122	0.106	0.14	SUBCLONAL	1	TRUE	1	0.886971236913493	2		1081	1384	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026450	48026450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	58	606	0	ENST00000234420.5:c.1328G>A	p.Gly443Glu	p.G443E	ENST00000234420	NM_000179.2	443	gGa/gAa	4/10	1	2	FACETS	0.149	0.128	0.173	0.149	0.128	0.173	SUBCLONAL	1	TRUE	1	0.886971236913493	2		606	875	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61722592	61722592	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	169	335	1	ENST00000401558.2:c.1045G>A	p.Glu349Lys	p.E349K	ENST00000401558	NM_003400.3	349	Gag/Aag	11/25	1	2	FACETS	0.584	0.538	0.63	0.584	0.538	0.63	SUBCLONAL	1	TRUE	1	0.886971236913493	2		336	653	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047830	128047830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1192	213	863	0	ENST00000285398.2:c.491G>A	p.Gly164Glu	p.G164E	ENST00000285398	NM_000122.1	164	gGa/gAa	4/15	1	2	FACETS	0.342	0.316	0.368	0.342	0.316	0.368	SUBCLONAL	1	TRUE	1	0.886971236913493	2		863	1405	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495285	212495285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1267104585	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	443	886	0	ENST00000342788.4:c.1981C>T	p.Leu661Phe	p.L661F	ENST00000342788	NM_005235.2	661	Ctc/Ttc	17/28	1	2	FACETS	0.816	0.779	0.853	0.816	0.779	0.853	CLONAL	1	TRUE	1	0.886971236913493	2		886	1224	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812220	212812220	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs761676413	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	304	577	0	ENST00000342788.4:c.356T>C	p.Ile119Thr	p.I119T	ENST00000342788	NM_005235.2	119	aTa/aCa	3/28	1	2	FACETS	0.819	0.775	0.864	0.819	0.775	0.864	CLONAL	1	TRUE	1	0.886971236913493	2		577	837	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242800951	242800951	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	75	1003	0	ENST00000334409.5:c.40G>A	p.Val14Met	p.V14M	ENST00000334409	NM_005018.2	14	Gtg/Atg	1/5	1	2	FACETS	0.156	0.135	0.177	0.156	0.135	0.177	SUBCLONAL	1	TRUE	1	0.886971236913493	2		1003	1087	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714485	40714485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	53	619	0	ENST00000373198.4:c.3912G>A	p.Met1304Ile	p.M1304I	ENST00000373198	NM_133170.3	1304	atG/atA	29/32	1	2	FACETS	0.138	0.117	0.162	0.138	0.117	0.162	SUBCLONAL	1	TRUE	1	0.886971236913493	2		619	864	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62294203	62294203	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs578196292	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	71	790	1	ENST00000360203.5:c.499G>A	p.Val167Met	p.V167M	ENST00000360203	NM_001283009.1	167	Gtg/Atg	6/35	1	2	FACETS	0.135	0.117	0.155	0.135	0.117	0.155	SUBCLONAL	1	TRUE	1	0.886971236913493	2		791	1186	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074308	30074308	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	70	509	0	ENST00000338641.4:c.1570G>A	p.Glu524Lys	p.E524K	ENST00000338641	NM_000268.3	524	Gaa/Aaa	14/16	1	2	FACETS	0.229	0.199	0.261	0.229	0.199	0.261	SUBCLONAL	1	TRUE	1	0.886971236913493	2		509	690	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641731	12641731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	87	661	2	ENST00000251849.4:c.910G>A	p.Gly304Ser	p.G304S	ENST00000251849	NM_002880.3	304	Ggc/Agc	9/17	1	2	FACETS	0.193	0.17	0.217	0.193	0.17	0.217	SUBCLONAL	1	TRUE	1	0.886971236913493	2		663	1019	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732924	30732924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	90	298	0	ENST00000295754.5:c.1537G>A	p.Val513Met	p.V513M	ENST00000295754	NM_003242.5	513	Gtg/Atg	7/7	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.886971236913493	NA		298	404	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163794	47163794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	364	516	0	ENST00000409792.3:c.2332C>T	p.Pro778Ser	p.P778S	ENST00000409792	NM_014159.6	778	Cca/Tca	3/21	1	2	FACETS	0.872	0.83	0.915	0.872	0.83	0.915	CLONAL	1	TRUE	1	0.886971236913493	2		516	941	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932669	49932669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	61	848	1	ENST00000296474.3:c.3202G>A	p.Ala1068Thr	p.A1068T	ENST00000296474	NM_002447.2	1068	Gct/Act	14/20	1	2	FACETS	0.121	0.104	0.14	0.121	0.104	0.14	SUBCLONAL	1	TRUE	1	0.886971236913493	2		849	1136	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72842128	72842128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	425	586	0	ENST00000325599.8:c.1120C>T	p.Pro374Ser	p.P374S	ENST00000325599	NM_018130.2	374	Cca/Tca	10/11	1	2	FACETS	0.799	0.762	0.836	0.799	0.762	0.836	SUBCLONAL	1	TRUE	1	0.886971236913493	2		586	1200	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72873604	72873604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1174	65	632	0	ENST00000325599.8:c.698G>A	p.Ser233Asn	p.S233N	ENST00000325599	NM_018130.2	233	aGt/aAt	6/11	1	2	FACETS	0.118	0.102	0.136	0.118	0.102	0.136	SUBCLONAL	1	TRUE	1	0.886971236913493	2		632	1239	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898819	134898819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	224	483	1	ENST00000398015.3:c.1877G>A	p.Gly626Glu	p.G626E	ENST00000398015	NM_004441.4	626	gGa/gAa	10/16	1	2	FACETS	0.842	0.789	0.895	0.842	0.789	0.895	CLONAL	1	TRUE	1	0.886971236913493	2		484	600	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967236	134967236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	53	722	0	ENST00000398015.3:c.2575G>A	p.Asp859Asn	p.D859N	ENST00000398015	NM_004441.4	859	Gac/Aac	14/16	1	2	FACETS	0.125	0.106	0.146	0.125	0.106	0.146	SUBCLONAL	1	TRUE	1	0.886971236913493	2		722	955	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442746	187442746	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	279	544	1	ENST00000232014.4:c.1960G>A	p.Gly654Arg	p.G654R	ENST00000232014	NM_001130845.1	654	Gga/Aga	9/10	1	2	FACETS	0.873	0.824	0.922	0.873	0.824	0.922	CLONAL	1	TRUE	1	0.886971236913493	2		545	721	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151580	55151580	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555553917	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	292	656	0	ENST00000257290.5:c.2366G>A	p.Gly789Asp	p.G789D	ENST00000257290	NM_006206.4	789	gGc/gAc	17/23	1	2	FACETS	0.562	0.528	0.596	0.562	0.528	0.596	SUBCLONAL	1	TRUE	1	0.886971236913493	2		656	1172	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332774	153332774	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	51	640	0	ENST00000281708.4:c.182G>A	p.Gly61Glu	p.G61E	ENST00000281708	NM_033632.3	61	gGa/gAa	2/12	1	2	FACETS	0.142	0.12	0.166	0.142	0.12	0.166	SUBCLONAL	1	TRUE	1	0.886971236913493	2		640	810	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554974	187554974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	26	393	1	ENST00000441802.2:c.4187G>A	p.Gly1396Asp	p.G1396D	ENST00000441802	NM_005245.3	1396	gGc/gAc	7/27	1	2	FACETS	0.115	0.09	0.143	0.115	0.09	0.143	SUBCLONAL	1	TRUE	1	0.886971236913493	2		394	511	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629360	187629360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1350253216	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1283	96	986	0	ENST00000441802.2:c.1622C>T	p.Ser541Leu	p.S541L	ENST00000441802	NM_005245.3	541	tCa/tTa	2/27	1	2	FACETS	0.157	0.139	0.176	0.157	0.139	0.176	SUBCLONAL	1	TRUE	1	0.886971236913493	2		986	1379	SUCCESS
APC	324	MSKCC	GRCh37	5	112174739	112174739	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	52	468	0	ENST00000257430.4:c.3448G>A	p.Glu1150Lys	p.E1150K	ENST00000257430	NM_000038.5	1150	Gaa/Aaa	16/16	1	2	FACETS	0.148	0.125	0.173	0.148	0.125	0.173	SUBCLONAL	1	TRUE	1	0.886971236913493	2		468	791	SUCCESS
APC	324	MSKCC	GRCh37	5	112178511	112178511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1312870922	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	334	463	0	ENST00000257430.4:c.7220G>A	p.Gly2407Asp	p.G2407D	ENST00000257430	NM_000038.5	2407	gGt/gAt	16/16	1	2	FACETS	0.945	0.898	0.992	0.945	0.898	0.992	CLONAL	1	TRUE	1	0.886971236913493	2		463	797	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940548	131940548	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	60	681	0	ENST00000265335.6:c.2575C>T	p.Gln859Ter	p.Q859*	ENST00000265335		859	Cag/Tag	16/25	1	2	FACETS	0.12	0.103	0.139	0.12	0.103	0.139	SUBCLONAL	1	TRUE	1	0.886971236913493	2		681	1125	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818722	170818722	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	75	573	0	ENST00000296930.5:c.271G>A	p.Gly91Ser	p.G91S	ENST00000296930	NM_002520.6	91	Ggc/Agc	4/11	1	2	FACETS	0.182	0.159	0.207	0.182	0.159	0.207	SUBCLONAL	1	TRUE	1	0.886971236913493	2		573	930	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637889	176637889	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1239	75	887	1	ENST00000439151.2:c.2489G>A	p.Ser830Asn	p.S830N	ENST00000439151	NM_022455.4	830	aGt/aAt	5/23	1	2	FACETS	0.129	0.112	0.147	0.129	0.112	0.147	SUBCLONAL	1	TRUE	1	0.886971236913493	2		888	1314	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694655	176694655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	70	848	0	ENST00000439151.2:c.5239G>A	p.Asp1747Asn	p.D1747N	ENST00000439151	NM_022455.4	1747	Gac/Aac	15/23	1	2	FACETS	0.131	0.114	0.151	0.131	0.114	0.151	SUBCLONAL	1	TRUE	1	0.886971236913493	2		848	1201	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393217	393217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	41	736	1	ENST00000380956.4:c.65G>A	p.Gly22Glu	p.G22E	ENST00000380956	NM_001195286.1	22	gGg/gAg	2/9	0.886971236913493	1	FACETS	0.091	0.075	0.108	0.091	0.075	0.108	SUBCLONAL	1	TRUE	0	0.886971236913493	1		737	567	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322255	31322255	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	46	518	0	ENST00000412585.2:c.*4+1del			ENST00000412585	NM_005514.6	-/362			1	2	FACETS	0.162	0.135	0.19	0.162	0.135	0.19	SUBCLONAL	1	TRUE	1	0.886971236913493	2		518	642	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117650525	117650525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1341	184	882	0	ENST00000368508.3:c.5333G>A	p.Gly1778Glu	p.G1778E	ENST00000368508	NM_002944.2	1778	gGa/gAa	32/43	1	2	FACETS	0.272	0.25	0.295	0.272	0.25	0.295	SUBCLONAL	1	TRUE	1	0.886971236913493	2		882	1525	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525102	157525102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	196	364	0	ENST00000346085.5:c.4997G>A	p.Ser1666Asn	p.S1666N	ENST00000346085	NM_020732.3	1666	aGc/aAc	19/20	1	2	FACETS	0.884	0.826	0.943	0.884	0.826	0.943	CLONAL	1	TRUE	1	0.886971236913493	2		364	500	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435776	116435776	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1238	77	803	0	ENST00000397752.3:c.3866C>T	p.Thr1289Ile	p.T1289I	ENST00000397752	NM_000245.2	1289	aCc/aTc	20/21	1	2	FACETS	0.132	0.115	0.15	0.132	0.115	0.15	SUBCLONAL	1	TRUE	1	0.886971236913493	2		803	1315	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852272	128852272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778689	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	285	879	0	ENST00000249373.3:c.2344G>A	p.Asp782Asn	p.D782N	ENST00000249373	NM_005631.4	782	Gat/Aat	12/12	1	2	FACETS	0.663	0.624	0.703	0.663	0.624	0.703	SUBCLONAL	1	TRUE	1	0.886971236913493	2		879	969	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836283	151836283	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	63	617	0	ENST00000262189.6:c.14522G>A	p.Gly4841Glu	p.G4841E	ENST00000262189	NM_170606.2	4841	gGa/gAa	57/59	1	2	FACETS	0.141	0.121	0.163	0.141	0.121	0.163	SUBCLONAL	1	TRUE	1	0.886971236913493	2		617	1007	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874697	151874697	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	123	491	0	ENST00000262189.6:c.7841G>A	p.Gly2614Asp	p.G2614D	ENST00000262189	NM_170606.2	2614	gGt/gAt	38/59	1	2	FACETS	0.444	0.402	0.487	0.444	0.402	0.487	SUBCLONAL	1	TRUE	1	0.886971236913493	2		491	625	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877872	151877872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	39	446	0	ENST00000262189.6:c.7073C>T	p.Pro2358Leu	p.P2358L	ENST00000262189	NM_170606.2	2358	cCt/cTt	36/59	1	2	FACETS	0.122	0.1	0.146	0.122	0.1	0.146	SUBCLONAL	1	TRUE	1	0.886971236913493	2		446	721	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879294	151879294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	194	674	0	ENST00000262189.6:c.5651C>T	p.Pro1884Leu	p.P1884L	ENST00000262189	NM_170606.2	1884	cCt/cTt	36/59	1	2	FACETS	0.505	0.468	0.544	0.505	0.468	0.544	SUBCLONAL	1	TRUE	1	0.886971236913493	2		674	866	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38139056	38139056	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1493	172	814	0	ENST00000317025.8:c.3547G>A	p.Glu1183Lys	p.E1183K	ENST00000317025	NM_023034.1	1183	Gaa/Aaa	20/24	1	2	FACETS	0.233	0.213	0.254	0.233	0.213	0.254	SUBCLONAL	1	TRUE	1	0.886971236913493	2		814	1665	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172225	38172225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	56	631	0	ENST00000317025.8:c.2182G>A	p.Glu728Lys	p.E728K	ENST00000317025	NM_023034.1	728	Gag/Aag	12/24	1	2	FACETS	0.137	0.117	0.16	0.137	0.117	0.16	SUBCLONAL	1	TRUE	1	0.886971236913493	2		631	919	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752770	128752770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	54	333	0	ENST00000377970.2:c.931G>A	p.Val311Ile	p.V311I	ENST00000377970	NM_002467.4	311	Gtc/Atc	3/3	1	2	FACETS	0.245	0.209	0.284	0.245	0.209	0.284	SUBCLONAL	1	TRUE	1	0.886971236913493	2		333	497	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971135	21971135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1202706337	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	58	580	2	ENST00000304494.5:c.223C>T	p.Pro75Ser	p.P75S	ENST00000304494	NM_000077.4	75	Ccc/Tcc	2/3	0.886971236913493	2	FACETS	0.183	0.156	0.211	0.091	0.078	0.106	SUBCLONAL	1	TRUE	0	0.886971236913493	2		582	716	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27209151	27209151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	266	761	0	ENST00000380036.4:c.2608G>A	p.Ala870Thr	p.A870T	ENST00000380036	NM_000459.3	870	Gca/Aca	16/23	0.886971236913493	2	FACETS	0.532	0.499	0.567	0.266	0.249	0.284	SUBCLONAL	1	TRUE	0	0.886971236913493	2		761	1127	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128230249	128230249	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	129	696	0	ENST00000265960.3:c.1345+2T>C		p.X449_splice	ENST00000265960	NM_001006617.1	449			0.275026927969387	2	FACETS	0.285	0.258	0.314	0.142	0.129	0.157	INDETERMINATE	1	TRUE	0	0.886971236913493	2		696	1021	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128432122	128432122	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	82	725	0	ENST00000265960.3:c.324G>A	p.Trp108Ter	p.W108*	ENST00000265960	NM_001006617.1	108	tgG/tgA	3/12	0.275026927969387	2	FACETS	0.139	0.122	0.158	0.07	0.061	0.079	INDETERMINATE	1	TRUE	0	0.886971236913493	2		725	1327	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750256	133750256	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	73	525	0	ENST00000318560.5:c.1087G>A	p.Asp363Asn	p.D363N	ENST00000318560	NM_005157.4	363	Gat/Aat	7/11	0.275026927969387	2	FACETS	0.239	0.208	0.271	0.119	0.104	0.136	INDETERMINATE	1	TRUE	0	0.886971236913493	2		525	690	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798767	135798767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	153	442	1	ENST00000298552.3:c.476G>A	p.Gly159Asp	p.G159D	ENST00000298552	NM_001162426.1	159	gGc/gAc	6/23	0.275026927969387	2	FACETS	0.539	0.495	0.585	0.27	0.247	0.293	INDETERMINATE	1	TRUE	0	0.886971236913493	2		443	640	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412735	139412735	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564199987	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	626	695	1	ENST00000277541.6:c.1109G>A	p.Cys370Tyr	p.C370Y	ENST00000277541	NM_017617.3	370	tGc/tAc	7/34	0.275026927969387	2	FACETS	1	0.997	1	0.686	0.665	0.706	INDETERMINATE	1	TRUE	0	0.886971236913493	2		696	1029	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139804436	139804436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769250719	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	393	771	0	ENST00000247668.2:c.593C>T	p.Pro198Leu	p.P198L	ENST00000247668	NM_021138.3	198	cCc/cTc	6/11	0.275026927969387	2	FACETS	0.974	0.93	1	0.487	0.465	0.509	INDETERMINATE	1	TRUE	0	0.886971236913493	2		771	910	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815650	139815650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	133	624	0	ENST00000247668.2:c.1121C>T	p.Pro374Leu	p.P374L	ENST00000247668	NM_021138.3	374	cCc/cTc	9/11	0.275026927969387	2	FACETS	0.361	0.328	0.396	0.181	0.164	0.198	INDETERMINATE	1	TRUE	0	0.886971236913493	2		624	830	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923594	39923594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	25	321	0	ENST00000378444.4:c.3497C>T	p.Ser1166Phe	p.S1166F	ENST00000378444	NM_001123385.1	1166	tCt/tTt	7/15	1	1	FACETS	0.07	0.055	0.088	0.07	0.055	0.088	SUBCLONAL	1	TRUE	0	0.886971236913493	1		321	446	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933002	39933002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	133	430	1	ENST00000378444.4:c.1597G>A	p.Asp533Asn	p.D533N	ENST00000378444	NM_001123385.1	533	Gac/Aac	4/15	1	1	FACETS	0.274	0.249	0.299	0.274	0.249	0.299	SUBCLONAL	1	TRUE	0	0.886971236913493	1		431	610	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480560	123480560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	339	359	0	ENST00000371139.4:c.68C>T	p.Thr23Ile	p.T23I	ENST00000371139	NM_001114937.2	23	aCt/aTt	1/4	1	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.886971236913493	1		359	423	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	83	215	0				ENST00000310581	NM_198253.2	-/1132			0.27212665723886	3	FACETS	1	0.948	1	0.564	0.499	0.632	CLONAL	1	TRUE	1	0.360604824072451	3		215	482	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0019915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	278	458	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.360604824072451	2	FACETS	0.913	0.867	0.959	1	0.994	1	CLONAL	3	TRUE	0	0.360604824072451	2		458	563	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	235	390	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.360604824072451	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.360604824072451	3		390	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0019915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	351	633	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.354326916047999	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.360604824072451	2		633	884	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412321	139412321	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	356	630	1	ENST00000277541.6:c.1324C>T	p.Gln442Ter	p.Q442*	ENST00000277541	NM_017617.3	442	Cag/Tag	8/34	0.360604824072451	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.360604824072451	2		631	840	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436128	56436128	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	75	672	0	ENST00000407977.2:c.1009C>T	p.Arg337Ter	p.R337*	ENST00000407977		337	Cga/Tga	9/10	1	2	FACETS	0.568	0.497	0.645	0.568	0.497	0.645	SUBCLONAL	1	TRUE	1	0.360604824072451	2		672	732	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348772	118348772	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	75	429	0	ENST00000534358.1:c.3425A>T	p.Gln1142Leu	p.Q1142L	ENST00000534358	NM_005933.3	1142	cAg/cTg	5/36	1	2	FACETS	0.62	0.543	0.703	0.62	0.543	0.703	SUBCLONAL	1	TRUE	1	0.360604824072451	2		429	671	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106994	11106994	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	40	567	0	ENST00000358026.2:c.1699C>G	p.Leu567Val	p.L567V	ENST00000358026	NM_001128849.1	567	Ctg/Gtg	10/36	1	2	FACETS	0.303	0.25	0.361	0.303	0.25	0.361	SUBCLONAL	1	TRUE	1	0.360604824072451	2		567	733	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131112	55131112	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	153	545	0	ENST00000257290.5:c.655G>A	p.Glu219Lys	p.E219K	ENST00000257290	NM_006206.4	219	Gaa/Aaa	5/23	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.360604824072451	2		545	820	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143326451	143326451	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs776542387	NA	P-0019915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	118	365	0	ENST00000262992.4:c.163C>G	p.Arg55Gly	p.R55G	ENST00000262992	NM_001101669.1	55	Cgt/Ggt	4/24	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.360604824072451	2		365	503	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671823	30671823	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	59	597	1	ENST00000376406.3:c.5137G>T	p.Glu1713Ter	p.E1713*	ENST00000376406	NM_014641.2	1713	Gag/Tag	10/15	1	2	FACETS	0.432	0.371	0.499	0.432	0.371	0.499	SUBCLONAL	1	TRUE	1	0.360604824072451	2		598	757	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672129	30672129	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	78	571	0	ENST00000376406.3:c.4831C>G	p.Pro1611Ala	p.P1611A	ENST00000376406	NM_014641.2	1611	Cca/Gca	10/15	1	2	FACETS	0.636	0.559	0.719	0.636	0.559	0.719	SUBCLONAL	1	TRUE	1	0.360604824072451	2		571	680	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995474	68995474	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0019915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	54	411	1	ENST00000288368.4:c.1879-1G>T		p.X627_splice	ENST00000288368	NM_024870.2	627			0.360604824072451	3	FACETS	0.517	0.441	0.601	0.258	0.22	0.301	SUBCLONAL	1	TRUE	1	0.360604824072451	3		412	684	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352241	70352241	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	21	276	0	ENST00000374080.3:c.4268C>G	p.Ser1423Cys	p.S1423C	ENST00000374080		1423	tCt/tGt	31/45	1	1	FACETS	0.307	0.236	0.39	0.307	0.236	0.39	SUBCLONAL	1	TRUE	0	0.360604824072451	1		276	311	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	93	282	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.771	0.687	0.86	0.771	0.687	0.86	SUBCLONAL	1	TRUE	1	0.418178241985506	2		282	577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	197	598	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.418178241985506	1	FACETS	0.927	0.86	0.996	0.927	0.86	0.996	CLONAL	1	TRUE	0	0.418178241985506	1		598	804	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256873	16256896	+	protein_altering_variant	In_Frame_Del	DEL	TCTGATTCTGACGAAGATGGTGAA	TCTGATTCTGACGAAGATGGTGAA	CTG	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	128	937	5	ENST00000375759.3:c.4138_4161delinsCTG	p.Ser1380_Glu1387delinsLeu	p.S1380_E1387delinsL	ENST00000375759	NM_015001.2	1380	TCTGATTCTGACGAAGATGGTGAA/CTG	11/15	1	2	FACETS	0.668	0.604	0.734	0.668	0.604	0.734	SUBCLONAL	1	TRUE	1	0.418178241985506	2		942	917	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797374	45797374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	123	645	0	ENST00000450313.1:c.1145C>T	p.Ala382Val	p.A382V	ENST00000450313	NM_012222.2	382	gCc/gTc	12/16	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.418178241985506	2		645	581	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838327	156838327	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	121	1037	0	ENST00000524377.1:c.605A>C	p.Asn202Thr	p.N202T	ENST00000524377	NM_002529.3	202	aAt/aCt	6/17	1	2	FACETS	0.667	0.603	0.736	0.667	0.603	0.736	SUBCLONAL	1	TRUE	1	0.418178241985506	2		1037	867	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844404	156844404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199826686	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	178	767	1	ENST00000524377.1:c.1237G>A	p.Glu413Lys	p.E413K	ENST00000524377	NM_002529.3	413	Gaa/Aaa	10/17	1	2	FACETS	0.681	0.626	0.738	0.681	0.626	0.738	SUBCLONAL	1	TRUE	1	0.418178241985506	2		768	1251	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204506621	204506622	+	missense_variant	Missense_Mutation	DNP	TG	TG	AT	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	109	574	2	ENST00000367182.3:c.407_408delinsAT	p.Leu136His	p.L136H	ENST00000367182	NM_001278516.1	136	cTG/cAT	6/11	1	2	FACETS	0.775	0.696	0.857	0.775	0.696	0.857	SUBCLONAL	1	TRUE	1	0.418178241985506	2		576	673	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851600	63851600	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	137	706	0	ENST00000279873.7:c.2378T>A	p.Leu793His	p.L793H	ENST00000279873	NM_032199.2	793	cTt/cAt	10/10	1	2	FACETS	0.839	0.764	0.918	0.839	0.764	0.918	CLONAL	1	TRUE	1	0.418178241985506	2		706	781	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123324058	123324058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs938460066	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	146	796	5	ENST00000358487.5:c.412G>A	p.Asp138Asn	p.D138N	ENST00000358487	NM_000141.4	138	Gat/Aat	4/18	1	2	FACETS	0.844	0.771	0.921	0.844	0.771	0.921	CLONAL	1	TRUE	1	0.418178241985506	2		801	827	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	532685	532685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	170	1073	1	ENST00000451590.1:c.521C>T	p.Pro174Leu	p.P174L	ENST00000451590	NM_001130442.1	174	cCt/cTt	5/5	0.418178241985506	1	FACETS	0.835	0.769	0.903	0.835	0.769	0.903	CLONAL	1	TRUE	0	0.418178241985506	1		1074	770	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946990	71946990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	174	1084	1	ENST00000298229.2:c.2839C>T	p.Pro947Ser	p.P947S	ENST00000298229	NM_001567.3	947	Cca/Tca	25/28	0.325920282349222	2	FACETS	0.877	0.807	0.95	0.438	0.403	0.475	CLONAL	1	TRUE	0	0.418178241985506	2		1085	949	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503154	125503154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1158434447	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	216	532	1	ENST00000428830.2:c.521T>C	p.Val174Ala	p.V174A	ENST00000428830	NM_001114121.2	174	gTt/gCt	6/14	0.407980754926857	2	FACETS	0.955	0.895	1	0.955	0.895	1	CLONAL	2	TRUE	0	0.418178241985506	2		533	541	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394761	394762	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	149	836	3	ENST00000399788.2:c.4933_4934delinsTT	p.Pro1645Leu	p.P1645L	ENST00000399788	NM_001042603.1	1645	CCa/TTa	28/28	1	2	FACETS	0.909	0.831	0.99	0.909	0.831	0.99	CLONAL	1	TRUE	1	0.418178241985506	2		839	784	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444255	49444255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	174	1007	0	ENST00000301067.7:c.3116C>T	p.Pro1039Leu	p.P1039L	ENST00000301067	NM_003482.3	1039	cCt/cTt	11/54	1	2	FACETS	0.721	0.663	0.782	0.721	0.663	0.782	SUBCLONAL	1	TRUE	1	0.418178241985506	2		1007	1154	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444810	49444810	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199946966	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	177	1067	1	ENST00000301067.7:c.2656C>T	p.Pro886Ser	p.P886S	ENST00000301067	NM_003482.3	886	Cct/Tct	10/54	1	2	FACETS	0.866	0.798	0.938	0.866	0.798	0.938	CLONAL	1	TRUE	1	0.418178241985506	2		1068	977	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109677	115109678	+	missense_variant	Missense_Mutation	DNP	TT	TT	CG	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	165	1046	1	ENST00000257566.3:c.2200_2201delinsCG	p.Lys734Arg	p.K734R	ENST00000257566	NM_016569.3	734	AAg/CGg	8/8	1	2	FACETS	0.713	0.653	0.775	0.713	0.653	0.775	SUBCLONAL	1	TRUE	1	0.418178241985506	2		1047	1107	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109994	115109994	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	184	1041	0	ENST00000257566.3:c.1884C>G	p.Phe628Leu	p.F628L	ENST00000257566	NM_016569.3	628	ttC/ttG	8/8	1	2	FACETS	0.972	0.898	1	0.972	0.898	1	CLONAL	1	TRUE	1	0.418178241985506	2		1041	905	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602423	28602423	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	125	534	0	ENST00000241453.7:c.1945A>T	p.Lys649Ter	p.K649*	ENST00000241453	NM_004119.2	649	Aaa/Taa	16/24	1	2	FACETS	0.972	0.882	1	0.972	0.882	1	CLONAL	1	TRUE	1	0.418178241985506	2		534	615	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28886154	28886154	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	117	678	0	ENST00000282397.4:c.3468T>G	p.Asp1156Glu	p.D1156E	ENST00000282397	NM_002019.4	1156	gaT/gaG	26/30	1	2	FACETS	0.749	0.676	0.826	0.749	0.676	0.826	SUBCLONAL	1	TRUE	1	0.418178241985506	2		678	747	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914707	32914707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80358862	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	105	805	0	ENST00000380152.3:c.6215C>T	p.Ser2072Phe	p.S2072F	ENST00000380152		2072	tCc/tTc	11/27	1	2	FACETS	0.72	0.646	0.799	0.72	0.646	0.799	SUBCLONAL	1	TRUE	1	0.418178241985506	2		805	697	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352611	68352611	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	107	672	0	ENST00000487270.1:c.478T>A	p.Phe160Ile	p.F160I	ENST00000487270	NM_133509.3	160	Ttt/Att	6/11	0.418178241985506	1	FACETS	0.805	0.725	0.888	0.805	0.725	0.888	CLONAL	1	TRUE	0	0.418178241985506	1		672	503	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610426	81610426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	121	620	0	ENST00000298171.2:c.2024C>T	p.Pro675Leu	p.P675L	ENST00000298171	NM_000369.2	675	cCa/cTa	10/10	0.418178241985506	1	FACETS	0.919	0.835	1	0.919	0.835	1	CLONAL	1	TRUE	0	0.418178241985506	1		620	498	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727550	66727550	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	89	545	1	ENST00000307102.5:c.266C>A	p.Pro89His	p.P89H	ENST00000307102	NM_002755.3	89	cCt/cAt	2/11	1	2	FACETS	0.825	0.734	0.922	0.825	0.734	0.922	CLONAL	1	TRUE	1	0.418178241985506	2		546	516	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420191	88420191	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	111	715	0	ENST00000360948.2:c.2495C>T	p.Pro832Leu	p.P832L	ENST00000360948	NM_001012338.2	832	cCa/cTa	19/19	1	2	FACETS	0.828	0.746	0.915	0.828	0.746	0.915	CLONAL	1	TRUE	1	0.418178241985506	2		715	641	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646280	3646280	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	121	978	2	ENST00000294008.3:c.1798C>T	p.Pro600Ser	p.P600S	ENST00000294008	NM_032444.2	600	Ccg/Tcg	8/15	1	2	FACETS	0.683	0.617	0.753	0.683	0.617	0.753	SUBCLONAL	1	TRUE	1	0.418178241985506	2		980	847	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274121	10274121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	111	431	0	ENST00000330684.3:c.148G>A	p.Glu50Lys	p.E50K	ENST00000330684	NM_001134407.1	50	Gaa/Aaa	2/13	1	2	FACETS	0.831	0.748	0.918	0.831	0.748	0.918	CLONAL	1	TRUE	1	0.418178241985506	2		431	639	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662319	67662319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	140	657	0	ENST00000264010.4:c.1565C>T	p.Pro522Leu	p.P522L	ENST00000264010	NM_006565.3	522	cCt/cTt	9/12	1	2	FACETS	0.965	0.88	1	0.965	0.88	1	CLONAL	1	TRUE	1	0.418178241985506	2		657	694	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946257	81946258	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	152	916	2	ENST00000359376.3:c.1990_1991delinsTT	p.Pro664Phe	p.P664F	ENST00000359376	NM_002661.3	664	CCc/TTc	19/33	1	2	FACETS	0.846	0.774	0.922	0.846	0.774	0.922	CLONAL	1	TRUE	1	0.418178241985506	2		918	859	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942860	15942860	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	140	672	0	ENST00000268712.3:c.6842A>G	p.Asp2281Gly	p.D2281G	ENST00000268712	NM_006311.3	2281	gAt/gGt	44/46	0.418178241985506	1	FACETS	0.898	0.821	0.978	0.898	0.821	0.978	CLONAL	1	TRUE	0	0.418178241985506	1		672	590	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490396	29490396	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	85	579	0	ENST00000356175.3:c.479+2T>C		p.X160_splice	ENST00000356175	NM_000267.3	160			0.418178241985506	1	FACETS	0.638	0.565	0.715	0.638	0.565	0.715	SUBCLONAL	1	TRUE	0	0.418178241985506	1		579	504	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508416	29508472	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTAAAAATTGTGTTTTTTCCAGAAACAGCATTTAAATTTAAAGCCCTAAAGAAGG	TTTTAAAAATTGTGTTTTTTCCAGAAACAGCATTTAAATTTAAAGCCCTAAAGAAGG	-	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	87	370	0	ENST00000356175.3:c.587-22_621del		p.X196_splice	ENST00000356175	NM_000267.3	196		6/57	0.418178241985506	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.418178241985506	1		370	309	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56338948	56338948	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437258417	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	10	82	0	ENST00000348428.3:c.73C>T	p.Pro25Ser	p.P25S	ENST00000348428	NM_006785.3	25	Ccg/Tcg	1/17	1	2	FACETS	0.703	0.484	0.968	0.703	0.484	0.968	CLONAL	1	TRUE	1	0.418178241985506	2		82	68	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414892	56414892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	160	841	0	ENST00000348428.3:c.2293C>T	p.Pro765Ser	p.P765S	ENST00000348428	NM_006785.3	765	Cct/Tct	17/17	1	2	FACETS	0.949	0.871	1	0.949	0.871	1	CLONAL	1	TRUE	1	0.418178241985506	2		841	806	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125509	7125509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147176789	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	139	839	0	ENST00000302850.5:c.3043G>A	p.Glu1015Lys	p.E1015K	ENST00000302850	NM_000208.2	1015	Gag/Aag	17/22	1	2	FACETS	0.83	0.756	0.908	0.83	0.756	0.908	CLONAL	1	TRUE	1	0.418178241985506	2		839	801	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184610	7184610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1228919172	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	87	459	1	ENST00000302850.5:c.691G>A	p.Glu231Lys	p.E231K	ENST00000302850	NM_000208.2	231	Gaa/Aaa	3/22	1	2	FACETS	0.802	0.712	0.897	0.802	0.712	0.897	CLONAL	1	TRUE	1	0.418178241985506	2		460	519	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251567	10251567	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	145	649	1	ENST00000340748.4:c.3365C>T	p.Ser1122Phe	p.S1122F	ENST00000340748		1122	tCc/tTc	31/40	1	2	FACETS	0.902	0.824	0.983	0.902	0.824	0.983	CLONAL	1	TRUE	1	0.418178241985506	2		650	769	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296350	15296350	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	189	1003	2	ENST00000263388.2:c.2092C>T	p.Pro698Ser	p.P698S	ENST00000263388	NM_000435.2	698	Ccc/Tcc	13/33	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.418178241985506	2		1005	903	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743901	41743901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	172	1092	0	ENST00000301178.4:c.836C>T	p.Pro279Leu	p.P279L	ENST00000301178	NM_021913.4	279	cCa/cTa	7/20	1	2	FACETS	0.824	0.758	0.894	0.824	0.758	0.894	CLONAL	1	TRUE	1	0.418178241985506	2		1092	998	SUCCESS
AXL	558	MSKCC	GRCh37	19	41749525	41749525	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	110	658	2	ENST00000301178.4:c.1450G>C	p.Val484Leu	p.V484L	ENST00000301178	NM_021913.4	484	Gtg/Ctg	12/20	1	2	FACETS	0.786	0.707	0.87	0.786	0.707	0.87	SUBCLONAL	1	TRUE	1	0.418178241985506	2		660	669	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753429	42753429	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	155	879	0	ENST00000222329.4:c.835C>T	p.Pro279Ser	p.P279S	ENST00000222329	NM_006494.2	279	Ccc/Tcc	4/4	1	2	FACETS	0.876	0.803	0.953	0.876	0.803	0.953	CLONAL	1	TRUE	1	0.418178241985506	2		879	846	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753714	42753714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	170	1003	1	ENST00000222329.4:c.550G>A	p.Gly184Ser	p.G184S	ENST00000222329	NM_006494.2	184	Ggc/Agc	4/4	1	2	FACETS	0.864	0.794	0.937	0.864	0.794	0.937	CLONAL	1	TRUE	1	0.418178241985506	2		1004	941	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905596	50905596	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910905700	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	159	1020	0	ENST00000440232.2:c.724G>A	p.Ala242Thr	p.A242T	ENST00000440232	NM_002691.3	242	Gcg/Acg	6/27	1	2	FACETS	0.795	0.728	0.864	0.795	0.728	0.864	SUBCLONAL	1	TRUE	1	0.418178241985506	2		1020	957	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917119	50917119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057522945	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	186	974	1	ENST00000440232.2:c.2371C>T	p.Arg791Trp	p.R791W	ENST00000440232	NM_002691.3	791	Cgg/Tgg	19/27	1	2	FACETS	0.953	0.881	1	0.953	0.881	1	CLONAL	1	TRUE	1	0.418178241985506	2		975	933	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39214714	39214714	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	114	561	0	ENST00000402219.2:c.3410C>A	p.Ser1137Tyr	p.S1137Y	ENST00000402219	NM_005633.3	1137	tCt/tAt	22/23	1	2	FACETS	0.97	0.877	1	0.97	0.877	1	CLONAL	1	TRUE	1	0.418178241985506	2		561	562	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698184	47698184	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	126	668	0	ENST00000233146.2:c.1742T>G	p.Ile581Ser	p.I581S	ENST00000233146	NM_000251.2	581	aTt/aGt	11/16	1	2	FACETS	0.863	0.783	0.948	0.863	0.783	0.948	CLONAL	1	TRUE	1	0.418178241985506	2		668	698	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251691	212251691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	80	534	0	ENST00000342788.4:c.3368G>A	p.Ser1123Asn	p.S1123N	ENST00000342788	NM_005235.2	1123	aGt/aAt	27/28	1	2	FACETS	0.846	0.748	0.951	0.846	0.748	0.951	CLONAL	1	TRUE	1	0.418178241985506	2		534	452	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543858	212543858	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	127	643	0	ENST00000342788.4:c.1541G>A	p.Gly514Glu	p.G514E	ENST00000342788	NM_005235.2	514	gGa/gAa	13/28	1	2	FACETS	0.801	0.726	0.88	0.801	0.726	0.88	CLONAL	1	TRUE	1	0.418178241985506	2		643	758	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570084	212570084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1366336180	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	112	600	0	ENST00000342788.4:c.1157C>T	p.Pro386Leu	p.P386L	ENST00000342788	NM_005235.2	386	cCa/cTa	10/28	1	2	FACETS	0.757	0.681	0.836	0.757	0.681	0.836	SUBCLONAL	1	TRUE	1	0.418178241985506	2		600	708	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661495	227661495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	121	817	0	ENST00000305123.5:c.1960C>T	p.Pro654Ser	p.P654S	ENST00000305123	NM_005544.2	654	Ccc/Tcc	1/2	1	2	FACETS	0.817	0.739	0.9	0.817	0.739	0.9	CLONAL	1	TRUE	1	0.418178241985506	2		817	708	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733337	40733337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746243026	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	119	655	0	ENST00000373198.4:c.3469G>A	p.Asp1157Asn	p.D1157N	ENST00000373198	NM_133170.3	1157	Gat/Aat	26/32	1	2	FACETS	0.878	0.794	0.967	0.878	0.794	0.967	CLONAL	1	TRUE	1	0.418178241985506	2		655	648	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420017	41420017	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	114	641	0	ENST00000373198.4:c.304T>C	p.Cys102Arg	p.C102R	ENST00000373198	NM_133170.3	102	Tgc/Cgc	3/32	1	2	FACETS	0.91	0.822	1	0.91	0.822	1	CLONAL	1	TRUE	1	0.418178241985506	2		641	599	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655401	45655402	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	138	908	1	ENST00000407780.3:c.450_451delinsTT	p.Gln151Ter	p.Q151*	ENST00000407780	NM_001283052.1	150	tcCCag/tcTTag	4/7	1	2	FACETS	0.678	0.616	0.743	0.678	0.616	0.743	SUBCLONAL	1	TRUE	1	0.418178241985506	2		909	974	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24134037	24134037	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	185	764	0	ENST00000263121.7:c.188T>G	p.Ile63Arg	p.I63R	ENST00000263121	NM_003073.3	63	aTa/aGa	2/9	1	2	FACETS	0.937	0.865	1	0.937	0.865	1	CLONAL	1	TRUE	1	0.418178241985506	2		764	944	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637690	52637690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239654517	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	148	535	0	ENST00000394830.3:c.2626C>T	p.Arg876Cys	p.R876C	ENST00000394830	NM_018313.4	876	Cgt/Tgt	18/30	0.418178241985506	1	FACETS	0.846	0.775	0.92	0.846	0.775	0.92	CLONAL	1	TRUE	0	0.418178241985506	1		535	662	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259568	89259568	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	61	489	0	ENST00000336596.2:c.712G>A	p.Asp238Asn	p.D238N	ENST00000336596	NM_005233.5	238	Gat/Aat	3/17	1	2	FACETS	0.691	0.598	0.792	0.691	0.598	0.792	SUBCLONAL	1	TRUE	1	0.418178241985506	2		489	422	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968322	134968322	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	123	768	0	ENST00000398015.3:c.2835G>T	p.Gln945His	p.Q945H	ENST00000398015	NM_004441.4	945	caG/caT	15/16	1	2	FACETS	0.809	0.732	0.89	0.809	0.732	0.89	CLONAL	1	TRUE	1	0.418178241985506	2		768	727	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146625	185146625	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	144	756	0	ENST00000265026.3:c.256C>T	p.Gln86Ter	p.Q86*	ENST00000265026	NM_004721.4	86	Cag/Tag	2/14	1	2	FACETS	0.891	0.813	0.972	0.891	0.813	0.972	CLONAL	1	TRUE	1	0.418178241985506	2		756	773	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502411	186502411	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	96	573	0	ENST00000323963.5:c.134T>G	p.Leu45Arg	p.L45R	ENST00000323963		45	cTt/cGt	3/11	1	2	FACETS	0.674	0.601	0.752	0.674	0.601	0.752	SUBCLONAL	1	TRUE	1	0.418178241985506	2		573	681	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081666	143081666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	76	564	1	ENST00000262992.4:c.1408C>T	p.Leu470Phe	p.L470F	ENST00000262992	NM_001101669.1	470	Ctt/Ttt	15/24	1	2	FACETS	0.808	0.711	0.911	0.808	0.711	0.911	CLONAL	1	TRUE	1	0.418178241985506	2		565	450	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541073	187541073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	111	479	0	ENST00000441802.2:c.6667C>T	p.Pro2223Ser	p.P2223S	ENST00000441802	NM_005245.3	2223	Cct/Tct	10/27	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.418178241985506	2		479	529	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873720	35873720	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	88	520	0	ENST00000303115.3:c.676T>A	p.Phe226Ile	p.F226I	ENST00000303115	NM_002185.3	226	Ttc/Atc	5/8	1	2	FACETS	0.703	0.623	0.787	0.703	0.623	0.787	SUBCLONAL	1	TRUE	1	0.418178241985506	2		520	599	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047912	180047912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	165	1038	0	ENST00000261937.6:c.2263G>A	p.Gly755Ser	p.G755S	ENST00000261937	NM_182925.4	755	Ggc/Agc	15/30	0.418178241985506	1	FACETS	0.756	0.694	0.819	0.756	0.694	0.819	SUBCLONAL	1	TRUE	0	0.418178241985506	1		1038	826	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163617	32163617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1383899056	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	82	670	0	ENST00000375023.3:c.5609C>T	p.Pro1870Leu	p.P1870L	ENST00000375023	NM_004557.3	1870	cCt/cTt	30/30	1	2	FACETS	0.759	0.671	0.852	0.759	0.671	0.852	SUBCLONAL	1	TRUE	1	0.418178241985506	2		670	517	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967969	93967969	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	133	658	0	ENST00000369303.4:c.1958A>C	p.Lys653Thr	p.K653T	ENST00000369303	NM_004440.3	653	aAa/aCa	11/17	0.418178241985506	1	FACETS	0.889	0.811	0.97	0.889	0.811	0.97	CLONAL	1	TRUE	0	0.418178241985506	1		658	566	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979475	2979475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	143	885	0	ENST00000396946.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000396946	NM_032415.4	258	Gaa/Aaa	6/25	1	2	FACETS	0.773	0.704	0.845	0.773	0.704	0.845	SUBCLONAL	1	TRUE	1	0.418178241985506	2		885	885	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374353	81374353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	89	616	0	ENST00000222390.5:c.709C>T	p.His237Tyr	p.H237Y	ENST00000222390	NM_000601.4	237	Cat/Tat	6/18	1	2	FACETS	0.764	0.679	0.855	0.764	0.679	0.855	SUBCLONAL	1	TRUE	1	0.418178241985506	2		616	557	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509774	106509774	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	122	826	1	ENST00000359195.3:c.1768C>T	p.Pro590Ser	p.P590S	ENST00000359195	NM_002649.2	590	Cct/Tct	2/11	1	2	FACETS	0.738	0.667	0.812	0.738	0.667	0.812	SUBCLONAL	1	TRUE	1	0.418178241985506	2		827	791	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453145	140453146	+	missense_variant	Missense_Mutation	DNP	AG	AG	GA	rs121913368	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	127	749	0	ENST00000288602.6:c.1789_1790delinsTC	p.Leu597Ser	p.L597S	ENST00000288602	NM_004333.4	597	CTa/TCa	15/18	1	2	FACETS	0.895	0.812	0.981	0.895	0.812	0.981	CLONAL	1	TRUE	1	0.418178241985506	2		749	679	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750847	128750847	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	149	845	0	ENST00000377970.2:c.384G>C	p.Gln128His	p.Q128H	ENST00000377970	NM_002467.4	128	caG/caC	2/3	1	2	FACETS	0.797	0.728	0.869	0.797	0.728	0.869	SUBCLONAL	1	TRUE	1	0.418178241985506	2		845	894	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5534921	5534921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	117	763	1	ENST00000397747.3:c.232G>A	p.Glu78Lys	p.E78K	ENST00000397747	NM_025239.3	78	Gag/Aag	3/7	0.418178241985506	1	FACETS	0.692	0.625	0.762	0.692	0.625	0.762	SUBCLONAL	1	TRUE	0	0.418178241985506	1		764	640	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971016	21971017	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	93	679	4	ENST00000304494.5:c.341_342delinsTT	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCC/cTT	2/3	0.418178241985506	1	FACETS	0.654	0.583	0.729	0.654	0.583	0.729	SUBCLONAL	1	TRUE	0	0.418178241985506	1		683	538	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27172722	27172722	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	139	761	0	ENST00000380036.4:c.737T>C	p.Phe246Ser	p.F246S	ENST00000380036	NM_000459.3	246	tTt/tCt	5/23	0.418178241985506	1	FACETS	0.869	0.794	0.947	0.869	0.794	0.947	CLONAL	1	TRUE	0	0.418178241985506	1		761	605	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430550	80430550	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	130	810	0	ENST00000286548.4:c.458T>G	p.Leu153Ter	p.L153*	ENST00000286548	NM_002072.3	153	tTa/tGa	3/7	1	2	FACETS	0.9	0.818	0.986	0.9	0.818	0.986	CLONAL	1	TRUE	1	0.418178241985506	2		810	691	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20153923	20153923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	124	328	0	ENST00000379607.5:c.137G>A	p.Arg46Gln	p.R46Q	ENST00000379607	NM_001412.3	46	cGg/cAg	3/7	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.418178241985506	1		328	318	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933448	39933448	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754561886	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	112	404	0	ENST00000378444.4:c.1151C>T	p.Pro384Leu	p.P384L	ENST00000378444	NM_001123385.1	384	cCc/cTc	4/15	1	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.418178241985506	1		404	400	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356191	70356191	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	184	581	0	ENST00000374080.3:c.5086C>T	p.Pro1696Ser	p.P1696S	ENST00000374080		1696	Ccg/Tcg	37/45	1	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.418178241985506	1		581	607	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858171	152858171	+	synonymous_variant	Silent	SNP	A	A	T	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	194	602	0	ENST00000406277.2:c.444T>A	p.Val148=	p.V148=	ENST00000406277	NM_152274.4	148	gtT/gtA	6/7	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.418178241985506	1		602	543	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256872	16256878	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTGAT	TTCTGAT	-	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	129	924	0	ENST00000375759.3:c.4138_4144del	p.Ser1380LeufsTer27	p.S1380Lfs*27	ENST00000375759	NM_015001.2	1379	ccTTCTGAT/cc	11/15	1	2	FACETS	0.671	0.608	0.738	0.671	0.608	0.738	SUBCLONAL	1	TRUE	1	0.418178241985506	2		924	919	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256883	16256896	+	frameshift_variant	Frame_Shift_Del	DEL	ACGAAGATGGTGAA	ACGAAGATGGTGAA	-	novel	NA	P-0019939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	128	923	0	ENST00000375759.3:c.4148_4161del	p.Asp1383AlafsTer13	p.D1383Afs*13	ENST00000375759	NM_015001.2	1383	gACGAAGATGGTGAA/g	11/15	1	2	FACETS	0.701	0.635	0.771	0.701	0.635	0.771	SUBCLONAL	1	TRUE	1	0.418178241985506	2		923	873	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	78	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	FALSE	1	0.205213467163748	2		215	721	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0020065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	166	696	1	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	1	2	FACETS	0.783	0.719	0.851	1	0.989	1	SUBCLONAL	2	FALSE	1	0.205213467163748	2		697	1033	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449764	8449764	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	63	811	0	ENST00000356435.5:c.3949G>C	p.Asp1317His	p.D1317H	ENST00000356435		1317	Gac/Cac	23/35	1	2	FACETS	0.54	0.465	0.622	0.54	0.465	0.622	SUBCLONAL	1	FALSE	1	0.205213467163748	2		811	1137	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069599	69069599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	65	789	3	ENST00000288368.4:c.4274C>T	p.Ser1425Phe	p.S1425F	ENST00000288368	NM_024870.2	1425	tCt/tTt	35/40	1	2	FACETS	0.531	0.458	0.61	0.531	0.458	0.61	SUBCLONAL	1	FALSE	1	0.205213467163748	2		792	1193	SUCCESS
REL	5966	MSKCC	GRCh37	2	61148994	61148994	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0020065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	54	509	0	ENST00000295025.8:c.1184C>G	p.Ser395Ter	p.S395*	ENST00000295025	NM_002908.2	395	tCa/tGa	11/11	0.166879925143725	3	FACETS	0.718	0.612	0.835	0.359	0.306	0.418	SUBCLONAL	1	FALSE	1	0.205213467163748	3		509	808	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344825	65344825	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	46	418	0	ENST00000342505.4:c.212C>T	p.Ser71Phe	p.S71F	ENST00000342505	NM_002227.2	71	tCt/tTt	4/25	1	2	FACETS	0.838	0.705	0.985	0.838	0.705	0.985	CLONAL	1	FALSE	1	0.205213467163748	2		418	535	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165816	118165816	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	49	573	0	ENST00000369448.3:c.326G>C	p.Arg109Thr	p.R109T	ENST00000369448	NM_017709.3	109	aGa/aCa	2/2	1	2	FACETS	0.585	0.494	0.685	0.585	0.494	0.685	SUBCLONAL	1	FALSE	1	0.205213467163748	2		573	817	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176145127	176145127	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	78	643	0	ENST00000367669.3:c.484C>G	p.Gln162Glu	p.Q162E	ENST00000367669	NM_022457.5	162	Cag/Gag	3/20	1	2	FACETS	0.861	0.755	0.975	0.861	0.755	0.975	CLONAL	1	FALSE	1	0.205213467163748	2		643	883	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577361	64577361	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424266863	NA	P-0020065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	54	710	0	ENST00000312049.6:c.221G>A	p.Gly74Asp	p.G74D	ENST00000312049	NM_130799.2	74	gGc/gAc	2/10	NA	2	FACETS	0.6	0.511	0.698			1	INDETERMINATE	1	FALSE	NA	0.205213467163748	2		710	877	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245849	46245849	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	77	505	0	ENST00000334344.6:c.3943G>T	p.Glu1315Ter	p.E1315*	ENST00000334344	NM_152641.2	1315	Gag/Tag	15/21	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	FALSE	1	0.205213467163748	2		505	693	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480377	56480377	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759585997	NA	P-0020065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	76	846	0	ENST00000267101.3:c.484G>A	p.Asp162Asn	p.D162N	ENST00000267101	NM_001982.3	162	Gac/Aac	4/28	1	2	FACETS	0.626	0.547	0.711	0.626	0.547	0.711	SUBCLONAL	1	FALSE	1	0.205213467163748	2		846	1184	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609627	81609627	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149237353	NA	P-0020065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	130	835	0	ENST00000298171.2:c.1225G>A	p.Glu409Lys	p.E409K	ENST00000298171	NM_000369.2	409	Gaa/Aaa	10/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.205213467163748	2		835	1078	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354575	91354575	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	58	706	0	ENST00000355112.3:c.4015A>T	p.Met1339Leu	p.M1339L	ENST00000355112	NM_000057.2	1339	Atg/Ttg	21/22	1	2	FACETS	0.646	0.553	0.748	0.646	0.553	0.748	SUBCLONAL	1	FALSE	1	0.205213467163748	2		706	875	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226056	2226056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	88	951	0	ENST00000326181.6:c.1753G>A	p.Asp585Asn	p.D585N	ENST00000326181	NM_032271.2	585	Gac/Aac	19/21	0.205213467163748	1	FACETS	0.678	0.599	0.763	0.678	0.599	0.763	SUBCLONAL	1	FALSE	0	0.205213467163748	1		951	1135	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976481	25976481	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs774776226	NA	P-0020065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	64	721	0	ENST00000435504.4:c.1064G>C	p.Arg355Thr	p.R355T	ENST00000435504		355	aGa/aCa	11/13	1	2	FACETS	0.634	0.547	0.729	0.634	0.547	0.729	SUBCLONAL	1	FALSE	1	0.205213467163748	2		721	984	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940141	49940141	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	146	821	0	ENST00000296474.3:c.902G>C	p.Arg301Thr	p.R301T	ENST00000296474	NM_002447.2	301	aGa/aCa	1/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.205213467163748	2		821	1087	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456513	89456513	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	42	544	0	ENST00000336596.2:c.1689G>C	p.Leu563Phe	p.L563F	ENST00000336596	NM_005233.5	563	ttG/ttC	8/17	1	2	FACETS	0.543	0.452	0.645	0.543	0.452	0.645	SUBCLONAL	1	FALSE	1	0.205213467163748	2		544	754	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266718	142266718	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	107	772	0	ENST00000350721.4:c.3206G>C	p.Arg1069Thr	p.R1069T	ENST00000350721	NM_001184.3	1069	aGa/aCa	16/47	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	FALSE	1	0.205213467163748	2		772	1010	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158420	26158420	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1335	84	1128	0	ENST00000289316.2:c.23C>A	p.Ala8Asp	p.A8D	ENST00000289316	NM_138720.2	8	gCt/gAt	1/2	1	2	FACETS	0.577	0.507	0.652	0.577	0.507	0.652	SUBCLONAL	1	FALSE	1	0.205213467163748	2		1128	1419	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611769	100611769	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	G	novel	NA	P-0020065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	53	363	0	ENST00000308731.7:c.1349+3G>C		p.X450_splice	ENST00000308731	NM_000061.2	450			0.144397015800819	2	FACETS	1	0.927	1			1	CLONAL	1	FALSE	NA	0.205213467163748	2		363	452	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	31	282	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.508	0.41	0.62	0.508	0.41	0.62	SUBCLONAL	1	TRUE	1	0.231820750372709	2		282	526	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	174	380	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.231820750372709	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.231820750372709	2		380	650	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	189	720	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.231820750372709	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.231820750372709	2		722	768	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857368	9857368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	62	774	3	ENST00000330684.3:c.4033C>T	p.Pro1345Ser	p.P1345S	ENST00000330684	NM_001134407.1	1345	Ccc/Tcc	13/13	1	2	FACETS	0.917	0.793	1	0.917	0.793	1	CLONAL	1	TRUE	1	0.231820750372709	2		777	583	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969189	93969189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868510824	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	49	288	0	ENST00000369303.4:c.1807C>T	p.Pro603Ser	p.P603S	ENST00000369303	NM_004440.3	603	Cca/Tca	10/17	1	2	FACETS	0.815	0.69	0.952	0.815	0.69	0.952	CLONAL	1	TRUE	1	0.231820750372709	2		288	519	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857436	9857436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	74	514	0	ENST00000330684.3:c.3965G>A	p.Gly1322Glu	p.G1322E	ENST00000330684	NM_001134407.1	1322	gGa/gAa	13/13	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.231820750372709	2		514	622	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295705	212295705	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	83	966	1	ENST00000342788.4:c.2608G>A	p.Gly870Arg	p.G870R	ENST00000342788	NM_005235.2	870	Gga/Aga	21/28	1	2	FACETS	0.981	0.865	1	0.981	0.865	1	CLONAL	1	TRUE	1	0.231820750372709	2		967	730	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498375	89498375	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	39	229	0	ENST00000336596.2:c.2347G>A	p.Gly783Arg	p.G783R	ENST00000336596	NM_005233.5	783	Gga/Aga	14/17	1	2	FACETS	0.961	0.799	1	0.961	0.799	1	CLONAL	1	TRUE	1	0.231820750372709	2		229	350	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932112	36932112	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	64	825	1	ENST00000361632.4:c.2357C>T	p.Ser786Phe	p.S786F	ENST00000361632		786	tCc/tTc	16/16	1	2	FACETS	0.931	0.806	1	0.931	0.806	1	CLONAL	1	TRUE	1	0.231820750372709	2		826	593	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306568	41306568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	69	962	4	ENST00000373198.4:c.1091G>A	p.Arg364Gln	p.R364Q	ENST00000373198	NM_133170.3	364	cGa/cAa	7/32	1	2	FACETS	0.819	0.712	0.934	0.819	0.712	0.934	CLONAL	1	TRUE	1	0.231820750372709	2		966	727	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388076	81388076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	70	1015	2	ENST00000222390.5:c.299C>T	p.Pro100Leu	p.P100L	ENST00000222390	NM_000601.4	100	cCc/cTc	3/18	1	2	FACETS	0.938	0.818	1	0.938	0.818	1	CLONAL	1	TRUE	1	0.231820750372709	2		1017	644	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509619	106509619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142822484	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	115	856	0	ENST00000359195.3:c.1613C>T	p.Pro538Leu	p.P538L	ENST00000359195	NM_002649.2	538	cCg/cTg	2/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.231820750372709	2		856	704	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629184	187629184	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	90	958	0	ENST00000441802.2:c.1798C>T	p.Gln600Ter	p.Q600*	ENST00000441802	NM_005245.3	600	Cag/Tag	2/27	1	2	FACETS	0.995	0.883	1	0.995	0.883	1	CLONAL	1	TRUE	1	0.231820750372709	2		958	780	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286791	212286791	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	72	461	0	ENST00000342788.4:c.2905G>A	p.Glu969Lys	p.E969K	ENST00000342788	NM_005235.2	969	Gaa/Aaa	24/28	1	2	FACETS	0.984	0.86	1	0.984	0.86	1	CLONAL	1	TRUE	1	0.231820750372709	2		461	631	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55154995	55154995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	74	990	0	ENST00000257290.5:c.2704G>A	p.Asp902Asn	p.D902N	ENST00000257290	NM_006206.4	902	Gat/Aat	20/23	1	2	FACETS	0.842	0.736	0.956	0.842	0.736	0.956	CLONAL	1	TRUE	1	0.231820750372709	2		990	758	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121013	29121013	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786203973	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	102	1129	1	ENST00000328354.6:c.544C>T	p.Pro182Ser	p.P182S	ENST00000328354	NM_007194.3	182	Cct/Tct	4/15	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.231820750372709	2		1130	805	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807399	36807399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	99	1020	1	ENST00000373129.3:c.1265C>T	p.Ser422Phe	p.S422F	ENST00000373129	NM_032017.1	422	tCc/tTc	12/12	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.231820750372709	2		1021	819	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508169	106508169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381484125	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	30	432	0	ENST00000359195.3:c.163G>A	p.Glu55Lys	p.E55K	ENST00000359195	NM_002649.2	55	Gaa/Aaa	2/11	1	2	FACETS	0.759	0.612	0.925	0.759	0.612	0.925	CLONAL	1	TRUE	1	0.231820750372709	2		432	341	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514308	69514308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142959398	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	120	904	0	ENST00000294312.3:c.373G>A	p.Glu125Lys	p.E125K	ENST00000294312	NM_005117.2	125	Gag/Aag	3/3	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.231820750372709	2		904	724	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405968	157405968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	68	929	2	ENST00000346085.5:c.2210C>T	p.Pro737Leu	p.P737L	ENST00000346085	NM_020732.3	737	cCc/cTc	6/20	1	2	FACETS	0.798	0.694	0.912	0.798	0.694	0.912	CLONAL	1	TRUE	1	0.231820750372709	2		931	735	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086052	16086052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	103	945	0	ENST00000281043.3:c.1228G>A	p.Glu410Lys	p.E410K	ENST00000281043	NM_005378.4	410	Gag/Aag	3/3	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.231820750372709	2		945	777	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641087	117641087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	76	960	0	ENST00000368508.3:c.5884G>A	p.Gly1962Arg	p.G1962R	ENST00000368508	NM_002944.2	1962	Gga/Aga	36/43	1	2	FACETS	0.926	0.812	1	0.926	0.812	1	CLONAL	1	TRUE	1	0.231820750372709	2		960	708	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258745	16258745	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	78	737	0	ENST00000375759.3:c.6010C>T	p.Pro2004Ser	p.P2004S	ENST00000375759	NM_015001.2	2004	Ccg/Tcg	11/15	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.231820750372709	2		737	620	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325240	39325240	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	69	924	2	ENST00000373001.3:c.79G>A	p.Gly27Ser	p.G27S	ENST00000373001	NM_022157.3	27	Ggc/Agc	1/7	1	2	FACETS	0.885	0.77	1	0.885	0.77	1	CLONAL	1	TRUE	1	0.231820750372709	2		926	673	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46512280	46512281	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TA	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	77	793	0	ENST00000262741.5:c.958_959delinsTA	p.Gly320Ter	p.G320*	ENST00000262741	NM_003629.3	320	GGa/TAa	8/10	1	2	FACETS	0.9	0.79	1	0.9	0.79	1	CLONAL	1	TRUE	1	0.231820750372709	2		793	738	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309880	65309880	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	46	826	0	ENST00000342505.4:c.2270C>T	p.Pro757Leu	p.P757L	ENST00000342505	NM_002227.2	757	cCa/cTa	17/25	1	2	FACETS	0.53	0.445	0.624	0.53	0.445	0.624	SUBCLONAL	1	TRUE	1	0.231820750372709	2		826	749	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156836749	156836749	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	67	1074	0	ENST00000524377.1:c.407A>C	p.Gln136Pro	p.Q136P	ENST00000524377	NM_002529.3	136	cAg/cCg	4/17	1	2	FACETS	0.734	0.637	0.84	0.734	0.637	0.84	SUBCLONAL	1	TRUE	1	0.231820750372709	2		1074	787	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119741	108119741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs864622650	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	32	561	0	ENST00000278616.4:c.1147C>T	p.Pro383Ser	p.P383S	ENST00000278616	NM_000051.3	383	Cct/Tct	9/63	1	2	FACETS	0.554	0.449	0.673	0.554	0.449	0.673	SUBCLONAL	1	TRUE	1	0.231820750372709	2		561	498	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224510	108224510	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	28	655	0	ENST00000278616.4:c.8689G>A	p.Gly2897Ser	p.G2897S	ENST00000278616	NM_000051.3	2897	Ggc/Agc	60/63	1	2	FACETS	0.458	0.365	0.565	0.458	0.365	0.565	SUBCLONAL	1	TRUE	1	0.231820750372709	2		655	527	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307502	118307502	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782112520	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	44	929	0	ENST00000534358.1:c.275C>T	p.Ser92Leu	p.S92L	ENST00000534358	NM_005933.3	92	tCg/tTg	1/36	1	2	FACETS	0.566	0.473	0.668	0.566	0.473	0.668	SUBCLONAL	1	TRUE	1	0.231820750372709	2		929	671	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342550	118342551	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	59	525	1	ENST00000534358.1:c.676_677delinsTT	p.Pro226Phe	p.P226F	ENST00000534358	NM_005933.3	226	CCc/TTc	3/36	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.231820750372709	2		526	438	SUCCESS
CBL	867	MSKCC	GRCh37	11	119146745	119146745	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs767877131	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	131	979	1	ENST00000264033.4:c.908G>A	p.Trp303Ter	p.W303*	ENST00000264033	NM_005188.3	303	tGg/tAg	6/16	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.231820750372709	2		980	759	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426709	49426709	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	44	440	1	ENST00000301067.7:c.11779C>T	p.Gln3927Ter	p.Q3927*	ENST00000301067	NM_003482.3	3927	Cag/Tag	39/54	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.231820750372709	2		441	358	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813325	102813326	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	100	882	2	ENST00000307046.8:c.363_364delinsTT	p.Arg122Cys	p.R122C	ENST00000307046	NM_001111285.1	121	gtCCgt/gtTTgt	3/4	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.231820750372709	2		884	678	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120806065	120806065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1339175713	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	117	1056	1	ENST00000257552.2:c.112G>A	p.Glu38Lys	p.E38K	ENST00000257552	NM_002442.3	38	Gaa/Aaa	3/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.231820750372709	2		1057	862	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133242002	133242002	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	99	1031	0	ENST00000320574.5:c.2354T>G	p.Val785Gly	p.V785G	ENST00000320574	NM_006231.2	785	gTg/gGg	21/49	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.231820750372709	2		1031	849	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947585	48947585	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	38	1088	1	ENST00000267163.4:c.1172C>T	p.Ser391Leu	p.S391L	ENST00000267163	NM_000321.2	391	tCa/tTa	12/27	1	2	FACETS	0.5	0.412	0.598	0.5	0.412	0.598	SUBCLONAL	1	TRUE	1	0.231820750372709	2		1089	656	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194766	30194766	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370180862	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	84	1021	2	ENST00000331968.5:c.379G>A	p.Asp127Asn	p.D127N	ENST00000331968	NM_002742.2	127	Gat/Aat	2/18	1	2	FACETS	0.829	0.731	0.935	0.829	0.731	0.935	CLONAL	1	TRUE	1	0.231820750372709	2		1023	874	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479786	67479786	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	95	883	2	ENST00000327367.4:c.1093C>T	p.Gln365Ter	p.Q365*	ENST00000327367	NM_005902.3	365	Cag/Tag	8/9	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.231820750372709	2		885	715	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472453	88472453	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	41	924	1	ENST00000360948.2:c.2102C>T	p.Ser701Phe	p.S701F	ENST00000360948	NM_001012338.2	701	tCc/tTc	16/19	1	2	FACETS	0.479	0.398	0.57	0.479	0.398	0.57	SUBCLONAL	1	TRUE	1	0.231820750372709	2		925	738	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134252	2134253	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	75	994	1	ENST00000219476.3:c.4029_4030delinsAA	p.Glu1344Lys	p.E1344K	ENST00000219476	NM_000548.3	1343	gaGGag/gaAAag	34/42	1	2	FACETS	0.892	0.781	1	0.892	0.781	1	CLONAL	1	TRUE	1	0.231820750372709	2		995	725	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3651052	3651052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	52	968	0	ENST00000294008.3:c.1091C>T	p.Pro364Leu	p.P364L	ENST00000294008	NM_032444.2	364	cCc/cTc	5/15	1	2	FACETS	0.591	0.502	0.689	0.591	0.502	0.689	SUBCLONAL	1	TRUE	1	0.231820750372709	2		968	759	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216608	7216608	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	77	722	0	ENST00000380728.2:c.727T>C	p.Phe243Leu	p.F243L	ENST00000380728		243	Ttc/Ctc	9/11	0.231820750372709	2	FACETS	1	0.926	1	0.538	0.473	0.609	CLONAL	1	TRUE	0	0.231820750372709	2		722	617	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979010	7979010	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	100	1031	1	ENST00000319144.4:c.1557T>A	p.Tyr519Ter	p.Y519*	ENST00000319144	NM_001139.2	519	taT/taA	12/15	0.231820750372709	2	FACETS	1	0.928	1	0.525	0.469	0.586	CLONAL	1	TRUE	0	0.231820750372709	2		1032	821	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453400	40453400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	131	1202	1	ENST00000345506.4:c.1097C>T	p.Pro366Leu	p.P366L	ENST00000345506	NM_003152.3	366	cCc/cTc	10/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.231820750372709	2		1203	1077	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215582	5215583	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	87	1003	2	ENST00000357368.4:c.4120_4121delinsTT	p.Pro1374Phe	p.P1374F	ENST00000357368	NM_002850.3	1374	CCc/TTc	27/38	1	2	FACETS	0.877	0.775	0.986	0.877	0.775	0.986	CLONAL	1	TRUE	1	0.231820750372709	2		1005	856	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184613	7184613	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	27	530	0	ENST00000302850.5:c.688G>C	p.Ala230Pro	p.A230P	ENST00000302850	NM_000208.2	230	Gcc/Ccc	3/22	1	2	FACETS	0.454	0.36	0.562	0.454	0.36	0.562	SUBCLONAL	1	TRUE	1	0.231820750372709	2		530	513	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602537	10602538	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	76	888	3	ENST00000171111.5:c.1040_1041delinsTT	p.Pro347Leu	p.P347L	ENST00000171111	NM_203500.1	347	cCC/cTT	3/6	1	2	FACETS	0.903	0.792	1	0.903	0.792	1	CLONAL	1	TRUE	1	0.231820750372709	2		891	726	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212296	36212296	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1400839972	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	87	996	1	ENST00000222270.7:c.2047C>T	p.Pro683Ser	p.P683S	ENST00000222270	NM_014727.1	683	Cct/Tct	3/37	1	2	FACETS	0.956	0.846	1	0.956	0.846	1	CLONAL	1	TRUE	1	0.231820750372709	2		997	785	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753315	42753315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	62	1254	1	ENST00000222329.4:c.949C>T	p.His317Tyr	p.H317Y	ENST00000222329	NM_006494.2	317	Cac/Tac	4/4	1	2	FACETS	0.526	0.453	0.606	0.526	0.453	0.606	SUBCLONAL	1	TRUE	1	0.231820750372709	2		1255	1017	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791573	42791573	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	70	954	0	ENST00000575354.2:c.554C>T	p.Ser185Phe	p.S185F	ENST00000575354	NM_015125.3	185	tCt/tTt	4/20	1	2	FACETS	0.805	0.701	0.918	0.805	0.701	0.918	CLONAL	1	TRUE	1	0.231820750372709	2		954	750	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793142	42793143	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	58	1071	4	ENST00000575354.2:c.1034_1035delinsAA	p.Gly345Glu	p.G345E	ENST00000575354	NM_015125.3	345	gGG/gAA	7/20	1	2	FACETS	0.544	0.466	0.63	0.544	0.466	0.63	SUBCLONAL	1	TRUE	1	0.231820750372709	2		1075	920	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965920	25965920	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	96	957	2	ENST00000435504.4:c.3286C>T	p.Gln1096Ter	p.Q1096*	ENST00000435504		1096	Cag/Tag	13/13	1	2	FACETS	0.922	0.821	1	0.922	0.821	1	CLONAL	1	TRUE	1	0.231820750372709	2		959	898	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131388	202131389	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	38	900	1	ENST00000358485.4:c.356_357delinsTT	p.Ser119Phe	p.S119F	ENST00000358485	NM_001080125.1	119	tCC/tTT	2/9	1	2	FACETS	0.497	0.41	0.596	0.497	0.41	0.596	SUBCLONAL	1	TRUE	1	0.231820750372709	2		901	659	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437316	220437316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	92	1161	0	ENST00000243786.2:c.220C>T	p.Pro74Ser	p.P74S	ENST00000243786	NM_002191.3	74	Ccc/Tcc	1/2	1	2	FACETS	0.974	0.865	1	0.974	0.865	1	CLONAL	1	TRUE	1	0.231820750372709	2		1161	815	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023536	31023540	+	frameshift_variant	Frame_Shift_Del	DEL	TCACC	TCACC	-	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	71	805	0	ENST00000375687.4:c.3025_3029del	p.Leu1009GlyfsTer5	p.L1009Gfs*5	ENST00000375687	NM_015338.5	1007	ggTCACCtc/ggtc	13/13	1	2	FACETS	0.945	0.825	1	0.945	0.825	1	CLONAL	1	TRUE	1	0.231820750372709	2		805	648	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572329	41572329	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1246489818	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	83	1130	1	ENST00000263253.7:c.4858C>T	p.Pro1620Ser	p.P1620S	ENST00000263253	NM_001429.3	1620	Ccc/Tcc	30/31	1	2	FACETS	0.842	0.742	0.95	0.842	0.742	0.95	CLONAL	1	TRUE	1	0.231820750372709	2		1131	850	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412899	49412899	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	95	1162	1	ENST00000418115.1:c.124T>A	p.Tyr42Asn	p.Y42N	ENST00000418115	NM_001664.2	42	Tat/Aat	2/5	1	2	FACETS	0.878	0.781	0.983	0.878	0.781	0.983	CLONAL	1	TRUE	1	0.231820750372709	2		1163	933	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468387	89468387	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	69	531	0	ENST00000336596.2:c.1921A>C	p.Lys641Gln	p.K641Q	ENST00000336596	NM_005233.5	641	Aaa/Caa	11/17	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.231820750372709	2		531	425	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960120	134960120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	79	954	0	ENST00000398015.3:c.2477G>A	p.Trp826Ter	p.W826*	ENST00000398015	NM_004441.4	826	tGg/tAg	13/16	1	2	FACETS	0.858	0.754	0.971	0.858	0.754	0.971	CLONAL	1	TRUE	1	0.231820750372709	2		954	794	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955939	55955939	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	88	951	0	ENST00000263923.4:c.3223G>A	p.Glu1075Lys	p.E1075K	ENST00000263923	NM_002253.2	1075	Gaa/Aaa	24/30	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.231820750372709	2		951	755	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629061	187629061	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	92	1081	0	ENST00000441802.2:c.1921C>T	p.His641Tyr	p.H641Y	ENST00000441802	NM_005245.3	641	Cac/Tac	2/27	1	2	FACETS	0.988	0.878	1	0.988	0.878	1	CLONAL	1	TRUE	1	0.231820750372709	2		1081	803	SUCCESS
APC	324	MSKCC	GRCh37	5	112175609	112175609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	62	606	0	ENST00000257430.4:c.4318C>T	p.Pro1440Ser	p.P1440S	ENST00000257430	NM_000038.5	1440	Cca/Tca	16/16	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.231820750372709	2		606	483	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150448	157150448	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	88	944	0	ENST00000346085.5:c.1630C>T	p.Pro544Ser	p.P544S	ENST00000346085	NM_020732.3	544	Ccg/Tcg	2/20	1	2	FACETS	0.967	0.856	1	0.967	0.856	1	CLONAL	1	TRUE	1	0.231820750372709	2		944	785	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2969694	2969694	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	203	1032	0	ENST00000396946.4:c.1585G>A	p.Glu529Lys	p.E529K	ENST00000396946	NM_032415.4	529	Gaa/Aaa	12/25	0.231820750372709	3	FACETS	0.918	0.851	0.988	0.918	0.851	0.988	CLONAL	2	TRUE	1	0.231820750372709	3		1032	1064	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946053	13946053	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	118	538	0	ENST00000405192.2:c.1041+2T>C		p.X347_splice	ENST00000405192	NM_001163147.1	347			0.231820750372709	3	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	1	0.231820750372709	3		538	539	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459435	50459435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	139	428	0	ENST00000331340.3:c.724G>A	p.Glu242Lys	p.E242K	ENST00000331340	NM_006060.4	242	Gaa/Aaa	7/8	0.231820750372709	3	FACETS	0.901	0.826	0.979	1	0.985	1	CLONAL	3	TRUE	1	0.231820750372709	3		428	495	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515187	106515187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	80	884	1	ENST00000359195.3:c.2330C>T	p.Ser777Phe	p.S777F	ENST00000359195	NM_002649.2	777	tCt/tTt	5/11	1	2	FACETS	0.942	0.828	1	0.942	0.828	1	CLONAL	1	TRUE	1	0.231820750372709	2		885	733	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524301	148524301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	88	949	0	ENST00000320356.2:c.683C>T	p.Ser228Phe	p.S228F	ENST00000320356	NM_004456.4	228	tCc/tTc	7/20	1	2	FACETS	0.908	0.804	1	0.908	0.804	1	CLONAL	1	TRUE	1	0.231820750372709	2		949	836	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874644	151874644	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	75	727	0	ENST00000262189.6:c.7894C>T	p.Gln2632Ter	p.Q2632*	ENST00000262189	NM_170606.2	2632	Caa/Taa	38/59	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.231820750372709	2		727	597	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68984737	68984737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	51	751	0	ENST00000288368.4:c.1501G>A	p.Asp501Asn	p.D501N	ENST00000288368	NM_024870.2	501	Gat/Aat	14/40	0.231820750372709	3	FACETS	0.891	0.757	1	0.446	0.378	0.519	CLONAL	1	TRUE	1	0.231820750372709	3		751	551	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989633	68989633	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs866647316	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	107	671	0	ENST00000288368.4:c.1571G>A	p.Gly524Glu	p.G524E	ENST00000288368	NM_024870.2	524	gGa/gAa	15/40	0.231820750372709	3	FACETS	1	0.967	1	0.598	0.535	0.664	CLONAL	1	TRUE	1	0.231820750372709	3		671	862	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341725	8341725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	204	1086	0	ENST00000356435.5:c.4915G>A	p.Glu1639Lys	p.E1639K	ENST00000356435		1639	Gag/Aag	29/35	0.231820750372709	2	FACETS	0.994	0.923	1	0.994	0.923	1	CLONAL	2	TRUE	0	0.231820750372709	2		1086	885	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518087	8518087	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	124	872	0	ENST00000356435.5:c.1304T>C	p.Leu435Ser	p.L435S	ENST00000356435		435	tTg/tCg	10/35	0.231820750372709	2	FACETS	0.815	0.739	0.895	0.815	0.739	0.895	CLONAL	2	TRUE	0	0.231820750372709	2		872	656	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293489	137293489	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	222	1217	1	ENST00000481739.1:c.40C>T	p.Gln14Ter	p.Q14*	ENST00000481739	NM_002957.4	14	Cag/Tag	2/10	0.231820750372709	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.231820750372709	2		1218	880	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393442	139393442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	179	954	3	ENST00000277541.6:c.6089C>T	p.Ser2030Phe	p.S2030F	ENST00000277541	NM_017617.3	2030	tCc/tTc	33/34	0.231820750372709	2	FACETS	0.957	0.883	1	0.957	0.883	1	CLONAL	2	TRUE	0	0.231820750372709	2		957	807	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412268	63412268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	105	576	0	ENST00000330258.3:c.899C>T	p.Pro300Leu	p.P300L	ENST00000330258	NM_152424.3	300	cCa/cTa	2/2	1	1	FACETS	0.89	0.802	0.982	1	0.987	1	CLONAL	2	TRUE	0	0.231820750372709	1		576	450	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0020146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	52	282	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.891	0.764	1	0.891	0.764	1	CLONAL	1	TRUE	1	0.418529626529565	2		282	279	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0020146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	147	448	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	0.183959075161	3	FACETS	0.754	0.692	0.819	0.754	0.692	0.819	INDETERMINATE	2	TRUE	1	0.418529626529565	3		448	563	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141586	202141586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760898260	NA	P-0020146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	123	835	0	ENST00000358485.4:c.874C>T	p.Arg292Trp	p.R292W	ENST00000358485	NM_001080125.1	292	Cgg/Tgg	7/9	1	2	FACETS	0.986	0.895	1	0.986	0.895	1	CLONAL	1	TRUE	1	0.418529626529565	2		835	596	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0020146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	215	415	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	0.418529626529565	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.418529626529565	2		415	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577508	7577508	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060501201	NA	P-0020146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	196	855	0	ENST00000269305.4:c.773A>G	p.Glu258Gly	p.E258G	ENST00000269305	NM_001126112.2	258	gAa/gGa	7/11	0.416411369282044	2	FACETS	0.966	0.903	1	0.966	0.903	1	CLONAL	2	TRUE	0	0.418529626529565	2		855	485	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658589	206658589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	56	787	0	ENST00000367120.3:c.1562G>A	p.Ser521Asn	p.S521N	ENST00000367120	NM_014002.3	521	aGc/aAc	15/22	0.313498112659131	1	FACETS	0.507	0.436	0.585	0.507	0.436	0.585	SUBCLONAL	1	TRUE	0	0.418529626529565	1		787	417	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552174	29552174	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780412565	NA	P-0020146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	54	651	0	ENST00000356175.3:c.1907C>T	p.Ser636Phe	p.S636F	ENST00000356175	NM_000267.3	636	tCt/tTt	17/57	1	2	FACETS	0.827	0.711	0.953	0.827	0.711	0.953	CLONAL	1	TRUE	1	0.418529626529565	2		651	312	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681060	37681060	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	89	806	1	ENST00000447079.4:c.3229G>T	p.Glu1077Ter	p.E1077*	ENST00000447079	NM_015083.1	1077	Gag/Tag	12/14	1	2	FACETS	0.897	0.799	1	0.897	0.799	1	CLONAL	1	TRUE	1	0.418529626529565	2		807	474	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604240	189604240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	158	933	1	ENST00000264731.3:c.1407G>A	p.Met469Ile	p.M469I	ENST00000264731	NM_003722.4	469	atG/atA	11/14	0.398930249673908	3	FACETS	1	0.939	1	0.515	0.472	0.56	CLONAL	1	TRUE	1	0.418529626529565	3		934	886	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187560905	187560905	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1302189943	NA	P-0020146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	89	332	0	ENST00000441802.2:c.3613C>T	p.Arg1205Ter	p.R1205*	ENST00000441802	NM_005245.3	1205	Cga/Tga	4/27	0.375505738810392	1	FACETS	0.934	0.835	1	0.934	0.835	1	CLONAL	1	TRUE	0	0.418529626529565	1		332	360	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946060	13946060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	66	520	0	ENST00000405192.2:c.1036G>A	p.Glu346Lys	p.E346K	ENST00000405192	NM_001163147.1	346	Gaa/Aaa	10/12	1	2	FACETS	0.906	0.792	1	0.906	0.792	1	CLONAL	1	TRUE	1	0.418529626529565	2		520	348	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	243	215	0				ENST00000310581	NM_198253.2	-/1132			0.580904791302734	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.580904791302734	3		215	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0020156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	420	720	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.580904791302734	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.580904791302734	2		722	669	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538374	9538374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868564987	NA	P-0020156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	187	517	0	ENST00000353224.5:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000353224	NM_177990.2	542	Gaa/Aaa	7/10	0.391129856271021	3	FACETS	0.843	0.786	0.901	0.843	0.786	0.901	CLONAL	2	TRUE	1	0.580904791302734	3		517	493	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872105	76872105	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	193	835	0	ENST00000373344.5:c.5542C>T	p.Gln1848Ter	p.Q1848*	ENST00000373344	NM_000489.3	1848	Cag/Tag	22/35	0.580904791302734	3	FACETS	1	0.971	1	0.545	0.505	0.586	CLONAL	1	TRUE	1	0.580904791302734	3		835	787	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939031	76939031	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs782746892	NA	P-0020156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	183	835	1	ENST00000373344.5:c.1717G>T	p.Gly573Cys	p.G573C	ENST00000373344	NM_000489.3	573	Ggt/Tgt	9/35	0.580904791302734	3	FACETS	0.989	0.914	1	0.495	0.457	0.534	CLONAL	1	TRUE	1	0.580904791302734	3		836	822	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421078	49421078	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	164	729	2	ENST00000301067.7:c.14671C>T	p.Gln4891Ter	p.Q4891*	ENST00000301067	NM_003482.3	4891	Cag/Tag	48/54	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.580904791302734	2		731	535	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163297306	163297306	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	175	869	0	ENST00000271452.3:c.152G>C	p.Arg51Thr	p.R51T	ENST00000271452	NM_145697.2	51	aGa/aCa	3/14	0.568886037879553	5	FACETS	0.986	0.906	1	0.246	0.226	0.268	CLONAL	1	TRUE	1	0.580904791302734	5		869	1144	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211669	46211669	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	125	470	0	ENST00000334344.6:c.635A>G	p.Asp212Gly	p.D212G	ENST00000334344	NM_152641.2	212	gAc/gGc	5/21	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.580904791302734	2		470	405	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624949	9624949	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	53	417	0	ENST00000353224.5:c.28G>C	p.Glu10Gln	p.E10Q	ENST00000353224	NM_177990.2	10	Gaa/Caa	3/10	0.391129856271021	3	FACETS	0.577	0.493	0.668	0.289	0.246	0.334	SUBCLONAL	1	TRUE	1	0.580904791302734	3		417	408	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170009685	170009685	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	550	680	0	ENST00000295797.4:c.1247C>T	p.Thr416Ile	p.T416I	ENST00000295797	NM_002740.5	416	aCt/aTt	13/18	0.580904791302734	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	1	0.580904791302734	4		680	988	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230855	66230855	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	168	644	0	ENST00000273854.3:c.2116A>T	p.Ile706Phe	p.I706F	ENST00000273854	NM_004439.5	706	Atc/Ttc	12/18	0.391129856271021	3	FACETS	1	0.974	1	0.564	0.52	0.609	CLONAL	1	TRUE	1	0.580904791302734	3		644	662	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628172	187628172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765299769	NA	P-0020156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	102	1077	0	ENST00000441802.2:c.2810G>A	p.Arg937Gln	p.R937Q	ENST00000441802	NM_005245.3	937	cGa/cAa	2/27	0.391129856271021	3	FACETS	0.494	0.441	0.55	0.247	0.22	0.275	SUBCLONAL	1	TRUE	1	0.580904791302734	3		1077	918	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170036	32170036	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	241	1134	0	ENST00000375023.3:c.3572G>C	p.Cys1191Ser	p.C1191S	ENST00000375023	NM_004557.3	1191	tGc/tCc	21/30	0.407001857068256	4	FACETS	1	0.941	1			1	CLONAL	1	TRUE	NA	0.580904791302734	4		1134	1298	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969086	93969086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774868013	NA	P-0020156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	98	491	1	ENST00000369303.4:c.1910G>A	p.Arg637His	p.R637H	ENST00000369303	NM_004440.3	637	cGt/cAt	10/17	1	2	FACETS	0.975	0.879	1	0.975	0.879	1	CLONAL	1	TRUE	1	0.580904791302734	2		492	346	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187174	38187174	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	102	1044	1	ENST00000317025.8:c.1303G>T	p.Ala435Ser	p.A435S	ENST00000317025	NM_023034.1	435	Gca/Tca	6/24	0.580904791302734	2	FACETS	0.46	0.411	0.512	0.23	0.205	0.256	SUBCLONAL	1	TRUE	0	0.580904791302734	2		1045	763	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370918	55370918	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	225	902	2	ENST00000297316.4:c.220G>A	p.Ala74Thr	p.A74T	ENST00000297316	NM_022454.3	74	Gct/Act	1/2	0.502705622305361	4	FACETS	1	0.973	1	0.545	0.507	0.585	CLONAL	1	TRUE	2	0.580904791302734	4		904	1123	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020426	69020426	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	218	953	0	ENST00000288368.4:c.2798T>A	p.Phe933Tyr	p.F933Y	ENST00000288368	NM_024870.2	933	tTc/tAc	24/40	0.502705622305361	4	FACETS	1	0.946	1	0.511	0.474	0.549	CLONAL	1	TRUE	2	0.580904791302734	4		953	1161	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878843	117878843	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	146	605	0	ENST00000297338.2:c.126G>C	p.Glu42Asp	p.E42D	ENST00000297338	NM_006265.2	42	gaG/gaC	2/14	0.502705622305361	4	FACETS	0.855	0.78	0.934	0.428	0.39	0.467	CLONAL	1	TRUE	2	0.580904791302734	4		605	929	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971156	21971157	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCGTGGAGCAGCAGCA	novel	NA	P-0020156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	30	598	0	ENST00000304494.5:c.185_201dup	p.Ala68CysfsTer84	p.A68Cfs*84	ENST00000304494	NM_000077.4	67	-/TGCTGCTGCTCCACGGC	2/3	0.4267306578765	1	FACETS	0.232	0.187	0.283	0.232	0.187	0.283	SUBCLONAL	1	TRUE	0	0.580904791302734	1		598	316	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	305	738	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	0.510685426697983	2		738	1087	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	19	775	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.081	0.061	0.105	0.081	0.061	0.105	SUBCLONAL	1	TRUE	1	0.510685426697983	2		775	916	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	183	495	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.938	0.868	1	0.938	0.868	1	CLONAL	1	TRUE	1	0.510685426697983	2		497	764	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467573	66467573	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	183	321	0	ENST00000273854.3:c.696del	p.Lys232AsnfsTer36	p.K232Nfs*36	ENST00000273854	NM_004439.5	232	aaA/aa	3/18	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.510685426697983	2		321	682	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	252	457	0	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.510685426697983	2		457	892	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37058999	37058999	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs63751194	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	185	673	4	ENST00000231790.2:c.793C>T	p.Arg265Cys	p.R265C	ENST00000231790	NM_000249.3	265	Cgt/Tgt	10/19	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.510685426697983	2		677	716	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	246	484	8	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.992	0.928	1	0.992	0.928	1	CLONAL	1	TRUE	1	0.510685426697983	2		492	971	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213905	2213905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750798710	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	357	976	6	ENST00000398665.3:c.1717G>A	p.Ala573Thr	p.A573T	ENST00000398665	NM_032482.2	573	Gcc/Acc	18/28	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.510685426697983	2		982	1156	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644874	67644874	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	268	341	0	ENST00000264010.4:c.143del	p.Gly48ValfsTer14	p.G48Vfs*14	ENST00000264010	NM_006565.3	47	Ggg/gg	3/12	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.510685426697983	2		341	874	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984025	7984025	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	199	757	0	ENST00000319144.4:c.601C>T	p.Arg201Cys	p.R201C	ENST00000319144	NM_001139.2	201	Cgc/Tgc	5/15	1	2	FACETS	0.972	0.902	1	0.972	0.902	1	CLONAL	1	TRUE	1	0.510685426697983	2		757	802	SUCCESS
AR	367	MSKCC	GRCh37	X	66766255	66766255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1202977049	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	175	355	0	ENST00000374690.3:c.1267G>A	p.Gly423Ser	p.G423S	ENST00000374690	NM_000044.3	423	Ggt/Agt	1/8	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.510685426697983	1		355	341	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524933	187524933	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749223648	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	51	881	0	ENST00000441802.2:c.10747G>A	p.Asp3583Asn	p.D3583N	ENST00000441802	NM_005245.3	3583	Gac/Aac	19/27	1	2	FACETS	0.207	0.175	0.243	0.207	0.175	0.243	SUBCLONAL	1	TRUE	1	0.510685426697983	2		881	964	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258295	16258295	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368453661	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	294	923	2	ENST00000375759.3:c.5560C>T	p.Arg1854Trp	p.R1854W	ENST00000375759	NM_015001.2	1854	Cgg/Tgg	11/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.510685426697983	2		925	1017	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258694	16258694	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	282	889	1	ENST00000375759.3:c.5959C>A	p.Gln1987Lys	p.Q1987K	ENST00000375759	NM_015001.2	1987	Cag/Aag	11/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.510685426697983	2		890	1008	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261625	16261625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761093715	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	264	852	6	ENST00000375759.3:c.8890G>A	p.Val2964Ile	p.V2964I	ENST00000375759	NM_015001.2	2964	Gtc/Atc	11/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.510685426697983	2		858	948	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17380507	17380507	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs11203289	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	260	855	0	ENST00000375499.3:c.8C>G	p.Ala3Gly	p.A3G	ENST00000375499	NM_003000.2	3	gCg/gGg	1/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.510685426697983	2		855	913	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107083	27107083	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	234	669	0	ENST00000324856.7:c.6694C>T	p.Arg2232Trp	p.R2232W	ENST00000324856	NM_006015.4	2232	Cgg/Tgg	20/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.510685426697983	2		669	815	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598940	28598940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886369318	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	302	875	2	ENST00000253063.3:c.500C>T	p.Ala167Val	p.A167V	ENST00000253063	NM_031459.4	167	gCg/gTg	4/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.510685426697983	2		877	1034	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429956	78429956	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	197	760	2	ENST00000370768.2:c.923G>A	p.Arg308His	p.R308H	ENST00000370768	NM_003902.3	308	cGc/cAc	11/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.510685426697983	2		762	741	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176132950	176132950	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs150041404	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	164	694	4	ENST00000367669.3:c.642+1G>A		p.X214_splice	ENST00000367669	NM_022457.5	214			1	2	FACETS	0.954	0.879	1	0.954	0.879	1	CLONAL	1	TRUE	1	0.510685426697983	2		698	673	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094309	193094309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748952219	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	216	775	0	ENST00000367435.3:c.199G>A	p.Val67Met	p.V67M	ENST00000367435	NM_024529.4	67	Gtg/Atg	2/17	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.510685426697983	2		775	764	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206943197	206943197	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	192	620	1	ENST00000423557.1:c.421C>T	p.Gln141Ter	p.Q141*	ENST00000423557	NM_000572.2	141	Cag/Tag	4/5	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.510685426697983	2		621	693	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246091265	246091265	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs777672375	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	240	841	1	ENST00000388985.4:c.670C>T	p.Arg224Ter	p.R224*	ENST00000388985		224	Cga/Tga	7/12	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.510685426697983	2		842	877	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606811	43606811	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775842917	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	283	934	3	ENST00000355710.3:c.1420C>T	p.Arg474Trp	p.R474W	ENST00000355710	NM_020975.4	474	Cgg/Tgg	7/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.510685426697983	2		937	1040	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451194	70451194	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1202179982	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	266	768	2	ENST00000373644.4:c.6034G>A	p.Ala2012Thr	p.A2012T	ENST00000373644	NM_030625.2	2012	Gca/Aca	12/12	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.510685426697983	2		770	894	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104377161	104377162	+	missense_variant	Missense_Mutation	DNP	CG	CG	TA	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	324	1086	2	ENST00000369902.3:c.1272_1273delinsTA	p.Ala425Thr	p.A425T	ENST00000369902	NM_016169.3	424	taCGcg/taTAcg	10/12	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.510685426697983	2		1088	1133	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114799802	114799802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	243	744	2	ENST00000543371.1:c.469C>T	p.Pro157Ser	p.P157S	ENST00000543371	NM_001198531.1	157	Cca/Tca	5/14	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.510685426697983	2		746	866	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310932	123310932	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	170	623	2	ENST00000358487.5:c.496C>A	p.Leu166Ile	p.L166I	ENST00000358487	NM_000141.4	166	Ctc/Atc	5/18	1	2	FACETS	0.946	0.872	1	0.946	0.872	1	CLONAL	1	TRUE	1	0.510685426697983	2		625	704	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741573	17741573	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1285231710	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	236	585	1	ENST00000250003.3:c.244C>T	p.Arg82Cys	p.R82C	ENST00000250003	NM_002478.4	82	Cgc/Tgc	1/3	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.510685426697983	2		586	714	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200479	67200479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370932588	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	327	947	0	ENST00000312629.5:c.673G>A	p.Val225Ile	p.V225I	ENST00000312629	NM_003952.2	225	Gtc/Atc	8/15	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.510685426697983	2		947	1112	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462783	69462783	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1222442441	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	236	722	3	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	0.976	1	CLONAL	1	TRUE	1	0.510685426697983	2		725	849	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514262	69514262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780705411	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	349	955	1	ENST00000294312.3:c.419G>A	p.Arg140His	p.R140H	ENST00000294312	NM_005117.2	140	cGc/cAc	3/3	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.510685426697983	2		956	1134	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518463	69518463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	170	505	1	ENST00000294312.3:c.182G>A	p.Arg61His	p.R61H	ENST00000294312	NM_005117.2	61	cGc/cAc	1/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.510685426697983	2		506	602	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941437	71941437	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	258	981	1	ENST00000298229.2:c.1122G>T	p.Gln374His	p.Q374H	ENST00000298229	NM_001567.3	374	caG/caT	10/28	1	2	FACETS	0.96	0.899	1	0.96	0.899	1	CLONAL	1	TRUE	1	0.510685426697983	2		982	1053	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942193	71942193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749091098	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	267	820	0	ENST00000298229.2:c.1457G>A	p.Arg486His	p.R486H	ENST00000298229	NM_001567.3	486	cGc/cAc	12/28	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.510685426697983	2		820	1038	SUCCESS
EED	8726	MSKCC	GRCh37	11	85961378	85961378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1306469162	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	154	673	2	ENST00000263360.6:c.155G>A	p.Arg52His	p.R52H	ENST00000263360	NM_003797.3	52	cGc/cAc	2/12	1	2	FACETS	0.96	0.882	1	0.96	0.882	1	CLONAL	1	TRUE	1	0.510685426697983	2		675	628	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998357	100998357	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	34	82	0	ENST00000325455.5:c.1445C>T	p.Ala482Val	p.A482V	ENST00000325455	NM_001202474.3	482	gCg/gTg	1/8	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.510685426697983	2		82	92	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998888	100998888	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	286	903	0	ENST00000325455.5:c.914A>G	p.His305Arg	p.H305R	ENST00000325455	NM_001202474.3	305	cAc/cGc	1/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.510685426697983	2		903	1034	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195921	102195921	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	46	640	0	ENST00000263464.3:c.681A>C	p.Arg227Ser	p.R227S	ENST00000263464	NM_001165.4	227	agA/agC	2/9	1	2	FACETS	0.242	0.203	0.285	0.242	0.203	0.285	SUBCLONAL	1	TRUE	1	0.510685426697983	2		640	744	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117840	108117840	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	169	637	1	ENST00000278616.4:c.1051G>T	p.Asp351Tyr	p.D351Y	ENST00000278616	NM_000051.3	351	Gat/Tat	8/63	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.510685426697983	2		638	599	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158444	108158444	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	143	674	0	ENST00000278616.4:c.4109+2T>C		p.X1370_splice	ENST00000278616	NM_000051.3	1370			1	2	FACETS	0.909	0.832	0.99	0.909	0.832	0.99	CLONAL	1	TRUE	1	0.510685426697983	2		674	616	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377027	118377027	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	218	593	0	ENST00000534358.1:c.10420G>C	p.Asp3474His	p.D3474H	ENST00000534358	NM_005933.3	3474	Gat/Cat	27/36	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.510685426697983	2		593	701	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416952	416953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs771545848	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	190	386	4	ENST00000399788.2:c.3597dup	p.Gly1200ArgfsTer7	p.G1200Rfs*7	ENST00000399788	NM_001042603.1	1199	-/A	23/28	1	2	FACETS	0.979	0.907	1	0.979	0.907	1	CLONAL	1	TRUE	1	0.510685426697983	2		390	760	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420184	420184	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	258	638	0	ENST00000399788.2:c.3083C>A	p.Ala1028Glu	p.A1028E	ENST00000399788	NM_001042603.1	1028	gCg/gAg	21/28	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.510685426697983	2		638	862	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475154	475154	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	314	1121	1	ENST00000399788.2:c.483T>A	p.His161Gln	p.H161Q	ENST00000399788	NM_001042603.1	161	caT/caA	4/28	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.510685426697983	2		1122	1007	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793382	18793382	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs77070108	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	181	706	2	ENST00000266497.5:c.4079C>T	p.Ala1360Val	p.A1360V	ENST00000266497		1360	gCg/gTg	30/31	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.510685426697983	2		708	609	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418717	49418717	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201481646	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	231	699	1	ENST00000301067.7:c.15797G>A	p.Arg5266His	p.R5266H	ENST00000301067	NM_003482.3	5266	cGc/cAc	49/54	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.510685426697983	2		700	803	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421039	49421039	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398123721	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	220	634	1	ENST00000301067.7:c.14710C>T	p.Arg4904Ter	p.R4904*	ENST00000301067	NM_003482.3	4904	Cga/Tga	48/54	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.510685426697983	2		635	748	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426244	49426244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	289	974	1	ENST00000301067.7:c.12244C>T	p.Pro4082Ser	p.P4082S	ENST00000301067	NM_003482.3	4082	Ccc/Tcc	39/54	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.510685426697983	2		975	1109	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427950	49427950	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775632051	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	290	892	2	ENST00000301067.7:c.10640G>A	p.Arg3547His	p.R3547H	ENST00000301067	NM_003482.3	3547	cGc/cAc	38/54	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.510685426697983	2		894	1049	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437701	49437701	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555194045	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	329	997	3	ENST00000301067.7:c.5269C>T	p.Arg1757Ter	p.R1757*	ENST00000301067	NM_003482.3	1757	Cga/Tga	22/54	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.510685426697983	2		1000	1128	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438659	49438659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780961989	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	257	862	3	ENST00000301067.7:c.4831C>T	p.Arg1611Trp	p.R1611W	ENST00000301067	NM_003482.3	1611	Cgg/Tgg	19/54	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.510685426697983	2		865	958	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444058	49444058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751231330	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	220	667	0	ENST00000301067.7:c.3313G>A	p.Ala1105Thr	p.A1105T	ENST00000301067	NM_003482.3	1105	Gcc/Acc	11/54	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.510685426697983	2		667	721	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444993	49444993	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	154	607	0	ENST00000301067.7:c.2473T>C	p.Ser825Pro	p.S825P	ENST00000301067	NM_003482.3	825	Tcc/Ccc	10/54	1	2	FACETS	0.877	0.804	0.952	0.877	0.804	0.952	CLONAL	1	TRUE	1	0.510685426697983	2		607	688	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490980	56490980	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs931676601	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	332	839	0	ENST00000267101.3:c.2426A>G	p.Gln809Arg	p.Q809R	ENST00000267101	NM_001982.3	809	cAg/cGg	20/28	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.510685426697983	2		839	1062	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856395	111856395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	142	335	2	ENST00000341259.2:c.446G>A	p.Arg149His	p.R149H	ENST00000341259	NM_005475.2	149	cGc/cAc	2/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.510685426697983	2		337	388	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856623	111856623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	174	449	1	ENST00000341259.2:c.674G>A	p.Arg225His	p.R225H	ENST00000341259	NM_005475.2	225	cGc/cAc	2/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.510685426697983	2		450	516	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112919962	112919962	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1214118543	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	168	482	0	ENST00000351677.2:c.1177G>A	p.Ala393Thr	p.A393T	ENST00000351677	NM_002834.3	393	Gct/Act	10/16	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.510685426697983	2		482	639	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117422	115117422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151047347	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	186	460	0	ENST00000257566.3:c.752G>A	p.Arg251Gln	p.R251Q	ENST00000257566	NM_016569.3	251	cGg/cAg	4/8	1	2	FACETS	0.964	0.892	1	0.964	0.892	1	CLONAL	1	TRUE	1	0.510685426697983	2		460	756	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434071	121434071	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751761766	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	260	729	2	ENST00000257555.6:c.962G>A	p.Arg321His	p.R321H	ENST00000257555		321	cGc/cAc	5/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.510685426697983	2		731	891	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201522	133201522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs190813054	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	336	1024	1	ENST00000320574.5:c.6716C>T	p.Ala2239Val	p.A2239V	ENST00000320574	NM_006231.2	2239	gCg/gTg	48/49	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.510685426697983	2		1025	1099	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219309	133219309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500802	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	208	661	1	ENST00000320574.5:c.4735C>T	p.Arg1579Cys	p.R1579C	ENST00000320574	NM_006231.2	1579	Cgc/Tgc	37/49	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.510685426697983	2		662	775	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219579	133219579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542430685	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	227	431	0	ENST00000320574.5:c.4555C>T	p.Arg1519Cys	p.R1519C	ENST00000320574	NM_006231.2	1519	Cgc/Tgc	36/49	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.510685426697983	2		431	734	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220026	133220026	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528264567	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	279	842	1	ENST00000320574.5:c.4411C>T	p.Arg1471Cys	p.R1471C	ENST00000320574	NM_006231.2	1471	Cgc/Tgc	34/49	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.510685426697983	2		843	978	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248884	133248884	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	260	937	0	ENST00000320574.5:c.1711C>A	p.Leu571Met	p.L571M	ENST00000320574	NM_006231.2	571	Ctg/Atg	16/49	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.510685426697983	2		937	1003	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252326	133252328	+	inframe_deletion	In_Frame_Del	DEL	AAA	AAA	-	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	190	683	0	ENST00000320574.5:c.1099_1101del	p.Phe367del	p.F367del	ENST00000320574	NM_006231.2	367	TTT/-	11/49	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.510685426697983	2		683	704	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562373	21562373	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	217	775	0	ENST00000382592.4:c.1546C>G	p.Pro516Ala	p.P516A	ENST00000382592	NM_014572.2	516	Ccg/Gcg	4/8	1	2	FACETS	0.93	0.865	0.996	0.93	0.865	0.996	CLONAL	1	TRUE	1	0.510685426697983	2		775	914	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563108	21563108	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746991718	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	283	978	4	ENST00000382592.4:c.811C>T	p.Arg271Cys	p.R271C	ENST00000382592	NM_014572.2	271	Cgc/Tgc	4/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.510685426697983	2		982	1025	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563311	21563311	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs77919685	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	322	1005	0	ENST00000382592.4:c.608C>T	p.Ala203Val	p.A203V	ENST00000382592	NM_014572.2	203	gCg/gTg	4/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.510685426697983	2		1005	1167	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008324	29008324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770377283	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	156	440	0	ENST00000282397.4:c.547C>T	p.Arg183Cys	p.R183C	ENST00000282397	NM_002019.4	183	Cgc/Tgc	5/30	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.510685426697983	2		440	563	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134133	41134133	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	189	532	0	ENST00000379561.5:c.1495G>A	p.Gly499Ser	p.G499S	ENST00000379561	NM_002015.3	499	Ggc/Agc	2/3	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.510685426697983	2		532	653	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955464	48955465	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs398123332	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	202	748	0	ENST00000267163.4:c.1585dup	p.Tyr529LeufsTer26	p.Y529Lfs*26	ENST00000267163	NM_000321.2	527	gat/gaTt	17/27	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.510685426697983	2		748	679	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	192	552	8	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.510685426697983	2		560	621	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527951	103527951	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	212	661	1	ENST00000355739.4:c.3263del	p.Leu1088TrpfsTer23	p.L1088Wfs*23	ENST00000355739	NM_000123.3	1087	Ttt/tt	15/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.510685426697983	2		662	730	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528225	103528225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188710607	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	182	678	0	ENST00000355739.4:c.3533G>A	p.Arg1178His	p.R1178H	ENST00000355739	NM_000123.3	1178	cGt/cAt	15/15	1	2	FACETS	0.883	0.816	0.953	0.883	0.816	0.953	CLONAL	1	TRUE	1	0.510685426697983	2		678	807	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437019	110437019	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1203012473	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	42	114	0	ENST00000375856.3:c.1382C>T	p.Pro461Leu	p.P461L	ENST00000375856	NM_003749.2	461	cCg/cTg	1/2	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.510685426697983	2		114	148	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105238745	105238745	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143266084	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	356	969	2	ENST00000349310.3:c.1217G>A	p.Arg406His	p.R406H	ENST00000349310	NM_001014432.1	406	cGc/cAc	13/15	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.510685426697983	2		971	1127	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40993338	40993338	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145617142	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	255	726	1	ENST00000267868.3:c.164C>T	p.Ala55Val	p.A55V	ENST00000267868	NM_002875.4	55	gCg/gTg	3/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.510685426697983	2		727	827	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782062	66782062	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	206	579	1	ENST00000307102.5:c.1034del	p.Asn345ThrfsTer8	p.N345Tfs*8	ENST00000307102	NM_002755.3	343	atA/at	10/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.510685426697983	2		580	753	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994934	73994934	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs373331287	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	79	240	0	ENST00000318443.5:c.418G>A	p.Ala140Thr	p.A140T	ENST00000318443	NM_001024736.1	140	Gct/Act	3/10	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.510685426697983	2		240	308	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478220	99478220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	191	633	1	ENST00000268035.6:c.3124C>T	p.Arg1042Cys	p.R1042C	ENST00000268035	NM_000875.3	1042	Cgt/Tgt	16/21	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.510685426697983	2		634	715	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347909	347909	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	358	1074	0	ENST00000262320.3:c.1597C>T	p.Arg533Ter	p.R533*	ENST00000262320	NM_003502.3	533	Cga/Tga	6/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.510685426697983	2		1074	1248	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396998	396999	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	337	996	0	ENST00000262320.3:c.27dup	p.Asp11GlyfsTer18	p.D11Gfs*18	ENST00000262320	NM_003502.3	9	-/C	2/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.510685426697983	2		996	1145	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640560	3640560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	331	1029	2	ENST00000294008.3:c.3079G>A	p.Ala1027Thr	p.A1027T	ENST00000294008	NM_032444.2	1027	Gca/Aca	12/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.510685426697983	2		1031	1206	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641128	3641128	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	365	1255	0	ENST00000294008.3:c.2511G>T	p.Lys837Asn	p.K837N	ENST00000294008	NM_032444.2	837	aaG/aaT	12/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.510685426697983	2		1255	1325	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647571	3647571	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	291	1007	0	ENST00000294008.3:c.1492T>C	p.Ser498Pro	p.S498P	ENST00000294008	NM_032444.2	498	Tct/Cct	7/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.510685426697983	2		1007	1048	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3651139	3651139	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	356	1031	1	ENST00000294008.3:c.1004A>T	p.Glu335Val	p.E335V	ENST00000294008	NM_032444.2	335	gAg/gTg	5/15	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.510685426697983	2		1032	1224	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56872886	56872886	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs190565265	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	192	725	1	ENST00000308159.5:c.2041G>A	p.Ala681Thr	p.A681T	ENST00000308159	NM_014669.4	681	Gca/Aca	19/22	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.510685426697983	2		726	752	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842734	68842734	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200310662	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	253	818	0	ENST00000261769.5:c.670C>T	p.Arg224Cys	p.R224C	ENST00000261769	NM_004360.3	224	Cgc/Tgc	5/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.510685426697983	2		818	910	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845673	68845674	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	302	969	1	ENST00000261769.5:c.921dup	p.Asp308ArgfsTer3	p.D308Rfs*3	ENST00000261769	NM_004360.3	307	caa/cAaa	7/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.510685426697983	2		970	1121	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827474	72827474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749152788	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	260	884	0	ENST00000268489.5:c.9107G>A	p.Arg3036Gln	p.R3036Q	ENST00000268489	NM_006885.3	3036	cGg/cAg	9/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.510685426697983	2		884	968	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829974	72829974	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	286	862	3	ENST00000268489.5:c.6607C>T	p.Arg2203Cys	p.R2203C	ENST00000268489	NM_006885.3	2203	Cgt/Tgt	9/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.510685426697983	2		865	1016	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830135	72830135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	210	654	1	ENST00000268489.5:c.6446G>A	p.Arg2149His	p.R2149H	ENST00000268489	NM_006885.3	2149	cGc/cAc	9/10	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.510685426697983	2		655	812	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984837	72984837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761672999	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	203	661	0	ENST00000268489.5:c.2747G>A	p.Arg916Gln	p.R916Q	ENST00000268489	NM_006885.3	916	cGg/cAg	3/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.510685426697983	2		661	744	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992222	72992222	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	285	982	0	ENST00000268489.5:c.1823G>T	p.Ser608Ile	p.S608I	ENST00000268489	NM_006885.3	608	aGc/aTc	2/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.510685426697983	2		982	1000	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346492	89346492	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781685166	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	253	877	1	ENST00000301030.4:c.6458C>T	p.Ala2153Val	p.A2153V	ENST00000301030	NM_001256183.1	2153	gCg/gTg	9/13	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.510685426697983	2		878	986	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350710	89350710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138898373	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	345	1064	2	ENST00000301030.4:c.2240C>T	p.Ser747Leu	p.S747L	ENST00000301030	NM_001256183.1	747	tCg/tTg	9/13	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.510685426697983	2		1066	1175	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371710	89371710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764805663	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	271	823	0	ENST00000301030.4:c.130C>T	p.Arg44Cys	p.R44C	ENST00000301030	NM_001256183.1	44	Cgt/Tgt	4/13	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.510685426697983	2		823	987	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89869671	89869671	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768965612	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	316	857	0	ENST00000389301.3:c.788C>T	p.Pro263Leu	p.P263L	ENST00000389301	NM_000135.2	263	cCg/cTg	8/43	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.510685426697983	2		857	1088	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15943797	15943797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	187	634	0	ENST00000268712.3:c.6691C>T	p.Pro2231Ser	p.P2231S	ENST00000268712	NM_006311.3	2231	Cca/Tca	43/46	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.510685426697983	2		634	722	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973700	15973700	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	222	647	0	ENST00000268712.3:c.4292A>G	p.Glu1431Gly	p.E1431G	ENST00000268712	NM_006311.3	1431	gAa/gGa	31/46	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.510685426697983	2		647	799	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16055259	16055259	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	203	756	2	ENST00000268712.3:c.842+1G>A		p.X281_splice	ENST00000268712	NM_006311.3	281			1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.510685426697983	2		758	794	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16097786	16097786	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201037902	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	241	808	2	ENST00000268712.3:c.98G>A	p.Arg33His	p.R33H	ENST00000268712	NM_006311.3	33	cGc/cAc	2/46	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.510685426697983	2		810	826	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556079	29556079	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886041347	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	222	337	1	ENST00000356175.3:c.2446C>T	p.Arg816Ter	p.R816*	ENST00000356175	NM_000267.3	816	Cga/Tga	21/57	1	2	FACETS	1	0.979	1	1	0.995	1	CLONAL	2	TRUE	1	0.510685426697983	2		338	406	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556292	29556292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1251621684	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	249	540	1	ENST00000356175.3:c.2659G>A	p.Ala887Thr	p.A887T	ENST00000356175	NM_000267.3	887	Gca/Aca	21/57	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.510685426697983	2		541	832	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649059	37649059	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1488101050	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	329	871	2	ENST00000447079.4:c.2164C>T	p.Arg722Cys	p.R722C	ENST00000447079	NM_015083.1	722	Cgc/Tgc	4/14	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.510685426697983	2		873	1046	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657656	37657656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	242	895	1	ENST00000447079.4:c.2573G>A	p.Arg858Gln	p.R858Q	ENST00000447079	NM_015083.1	858	cGg/cAg	6/14	1	2	FACETS	0.908	0.848	0.969	0.908	0.848	0.969	CLONAL	1	TRUE	1	0.510685426697983	2		896	1044	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	323	956	3	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.510685426697983	2		959	1128	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512370	38512370	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567767560	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	145	712	2	ENST00000254066.5:c.1286del	p.Gly429ValfsTer214	p.G429Vfs*214	ENST00000254066	NM_000964.3	427	ccG/cc	9/9	1	2	FACETS	0.765	0.699	0.834	0.765	0.699	0.834	SUBCLONAL	1	TRUE	1	0.510685426697983	2		714	742	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	278	426	1	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	0.964	1	CLONAL	1	TRUE	1	0.510685426697983	2		427	1051	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534326	63534326	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1157452251	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	347	940	2	ENST00000307078.5:c.1195C>T	p.Arg399Ter	p.R399*	ENST00000307078	NM_004655.3	399	Cga/Tga	5/11	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.510685426697983	2		942	1134	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732953	74732953	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	127	486	0	ENST00000359995.5:c.290A>G	p.Asp97Gly	p.D97G	ENST00000359995	NM_001195427.1	97	gAc/gGc	1/3	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.510685426697983	2		486	493	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78866606	78866606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	299	954	2	ENST00000306801.3:c.2179C>T	p.Arg727Cys	p.R727C	ENST00000306801	NM_020761.2	727	Cgt/Tgt	19/34	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.510685426697983	2		956	1036	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56401588	56401588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367866327	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	183	786	1	ENST00000348428.3:c.1450G>A	p.Ala484Thr	p.A484T	ENST00000348428	NM_006785.3	484	Gcc/Acc	12/17	1	2	FACETS	0.979	0.906	1	0.979	0.906	1	CLONAL	1	TRUE	1	0.510685426697983	2		787	732	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985895	60985895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1273284492	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	213	561	0	ENST00000333681.4:c.5C>T	p.Ala2Val	p.A2V	ENST00000333681		2	gCg/gTg	2/3	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.510685426697983	2		561	677	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220394	1220394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	288	869	1	ENST00000326873.7:c.487G>A	p.Gly163Ser	p.G163S	ENST00000326873	NM_000455.4	163	Ggc/Agc	4/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.510685426697983	2		870	1041	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210645	2210645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369996787	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	272	917	4	ENST00000398665.3:c.1142C>T	p.Ala381Val	p.A381V	ENST00000398665	NM_032482.2	381	gCg/gTg	14/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.510685426697983	2		921	956	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210815	2210815	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200004531	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	278	774	0	ENST00000398665.3:c.1312G>A	p.Ala438Thr	p.A438T	ENST00000398665	NM_032482.2	438	Gct/Act	14/28	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.510685426697983	2		774	931	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210830	2210830	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	215	669	1	ENST00000398665.3:c.1327C>A	p.Gln443Lys	p.Q443K	ENST00000398665	NM_032482.2	443	Cag/Aag	14/28	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.510685426697983	2		670	821	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218538	5218538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767763908	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	325	957	2	ENST00000357368.4:c.3941G>A	p.Arg1314His	p.R1314H	ENST00000357368	NM_002850.3	1314	cGc/cAc	25/38	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.510685426697983	2		959	1041	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219369	5219369	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	325	1037	1	ENST00000357368.4:c.3875C>T	p.Ala1292Val	p.A1292V	ENST00000357368	NM_002850.3	1292	gCc/gTc	23/38	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.510685426697983	2		1038	1126	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220015	5220015	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866165812	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	329	1055	3	ENST00000357368.4:c.3700C>T	p.Arg1234Trp	p.R1234W	ENST00000357368	NM_002850.3	1234	Cgg/Tgg	22/38	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.510685426697983	2		1058	1131	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238941	5238941	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs913402227	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	197	532	0	ENST00000357368.4:c.1838C>T	p.Thr613Met	p.T613M	ENST00000357368	NM_002850.3	613	aCg/aTg	13/38	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.510685426697983	2		532	657	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238944	5238944	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs946180785	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	199	551	0	ENST00000357368.4:c.1835G>A	p.Arg612His	p.R612H	ENST00000357368	NM_002850.3	612	cGc/cAc	13/38	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.510685426697983	2		551	664	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170598	7170598	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750676016	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	219	761	1	ENST00000302850.5:c.1433G>A	p.Arg478His	p.R478H	ENST00000302850	NM_000208.2	478	cGc/cAc	6/22	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.510685426697983	2		762	807	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184553	7184553	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	248	674	0	ENST00000302850.5:c.748A>G	p.Thr250Ala	p.T250A	ENST00000302850	NM_000208.2	250	Acc/Gcc	3/22	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.510685426697983	2		674	873	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262513	10262513	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1568232544	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	289	848	0	ENST00000340748.4:c.1982A>G	p.Gln661Arg	p.Q661R	ENST00000340748		661	cAg/cGg	22/40	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.510685426697983	2		848	915	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291083	10291084	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755889652	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	214	557	2	ENST00000340748.4:c.387dup	p.Lys130GlnfsTer19	p.K130Qfs*19	ENST00000340748		129	-/C	4/40	1	2	FACETS	0.879	0.817	0.942	0.879	0.817	0.942	CLONAL	1	TRUE	1	0.510685426697983	2		559	954	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096931	11096931	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060502073	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	307	1020	0	ENST00000358026.2:c.422C>T	p.Ser141Leu	p.S141L	ENST00000358026	NM_001128849.1	141	tCg/tTg	4/36	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.510685426697983	2		1020	1120	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097160	11097160	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	329	924	1	ENST00000358026.2:c.651G>T	p.Met217Ile	p.M217I	ENST00000358026	NM_001128849.1	217	atG/atT	4/36	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.510685426697983	2		925	1124	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132617	11132617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1445478818	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	348	317	1	ENST00000358026.2:c.2833G>A	p.Ala945Thr	p.A945T	ENST00000358026	NM_001128849.1	945	Gca/Aca	19/36	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.510685426697983	2		318	1162	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134234	11134234	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1085307769	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	286	911	0	ENST00000358026.2:c.2900G>A	p.Arg967His	p.R967H	ENST00000358026	NM_001128849.1	967	cGt/cAt	20/36	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.510685426697983	2		911	940	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152025	11152025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057518049	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	340	822	2	ENST00000358026.2:c.4309C>T	p.Arg1437Trp	p.R1437W	ENST00000358026	NM_001128849.1	1437	Cgg/Tgg	31/36	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.510685426697983	2		824	1062	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152139	11152139	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	336	868	2	ENST00000358026.2:c.4423C>T	p.Arg1475Cys	p.R1475C	ENST00000358026	NM_001128849.1	1475	Cgc/Tgc	31/36	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.510685426697983	2		870	1189	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288715	15288715	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	65	80	0	ENST00000263388.2:c.4024G>A	p.Ala1342Thr	p.A1342T	ENST00000263388	NM_000435.2	1342	Gcc/Acc	24/33	1	2	FACETS	0.821	0.73	0.914	1	0.98	1	CLONAL	2	TRUE	1	0.510685426697983	2		80	155	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291812	15291812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779592020	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	304	920	1	ENST00000263388.2:c.2954G>A	p.Arg985His	p.R985H	ENST00000263388	NM_000435.2	985	cGc/cAc	18/33	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.510685426697983	2		921	1033	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296410	15296410	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	372	1052	0	ENST00000263388.2:c.2032G>T	p.Gly678Cys	p.G678C	ENST00000263388	NM_000435.2	678	Ggc/Tgc	13/33	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.510685426697983	2		1052	1225	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349736	15349736	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755237120	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	79	753	0	ENST00000263377.2:c.3838C>T	p.Arg1280Cys	p.R1280C	ENST00000263377	NM_058243.2	1280	Cgt/Tgt	19/20	1	2	FACETS	0.367	0.322	0.416	0.367	0.322	0.416	SUBCLONAL	1	TRUE	1	0.510685426697983	2		753	843	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366162	15366162	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1005077274	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	286	875	4	ENST00000263377.2:c.1993C>T	p.Arg665Cys	p.R665C	ENST00000263377	NM_058243.2	665	Cgt/Tgt	10/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.510685426697983	2		879	973	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366335	15366335	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	224	701	0	ENST00000263377.2:c.1820G>A	p.Cys607Tyr	p.C607Y	ENST00000263377	NM_058243.2	607	tGc/tAc	10/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.510685426697983	2		701	757	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280036	18280036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	224	540	0	ENST00000222254.8:c.2119G>A	p.Ala707Thr	p.A707T	ENST00000222254	NM_005027.3	707	Gcg/Acg	16/16	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.510685426697983	2		540	636	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18963028	18963028	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	340	1078	4	ENST00000262803.5:c.895G>A	p.Ala299Thr	p.A299T	ENST00000262803	NM_002911.3	299	Gcc/Acc	6/24	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.510685426697983	2		1082	1185	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974365	18974365	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	312	820	1	ENST00000262803.5:c.2719C>T	p.Arg907Cys	p.R907C	ENST00000262803	NM_002911.3	907	Cgt/Tgt	19/24	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.510685426697983	2		821	1059	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258640	19258640	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	237	648	0	ENST00000162023.5:c.260C>G	p.Thr87Arg	p.T87R	ENST00000162023		87	aCg/aGg	8/13	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.510685426697983	2		648	761	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313000	30313000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs189673443	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	255	842	0	ENST00000262643.3:c.803C>T	p.Pro268Leu	p.P268L	ENST00000262643	NM_001238.2	268	cCg/cTg	9/12	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.510685426697983	2		842	979	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792889	33792889	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555742184	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	110	271	0	ENST00000498907.2:c.432G>T	p.Glu144Asp	p.E144D	ENST00000498907	NM_004364.3	144	gaG/gaT	1/1	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.510685426697983	2		271	298	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219725	36219725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568377293	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	305	993	2	ENST00000222270.7:c.4622C>T	p.Ala1541Val	p.A1541V	ENST00000222270	NM_014727.1	1541	gCg/gTg	20/37	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.510685426697983	2		995	1091	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223293	36223293	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	356	1060	0	ENST00000222270.7:c.5843T>C	p.Val1948Ala	p.V1948A	ENST00000222270	NM_014727.1	1948	gTc/gCc	28/37	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.510685426697983	2		1060	1280	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227825	36227826	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	340	1030	0	ENST00000222270.7:c.7312_7313del	p.Leu2438AspfsTer19	p.L2438Dfs*19	ENST00000222270	NM_014727.1	2437	aCT/a	32/37	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.510685426697983	2		1030	1191	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40740985	40740985	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	323	959	1	ENST00000392038.2:c.1333G>A	p.Ala445Thr	p.A445T	ENST00000392038	NM_001626.4	445	Gcc/Acc	13/14	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.510685426697983	2		960	1160	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762504	41762504	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	173	529	1	ENST00000301178.4:c.2184C>A	p.Ser728Arg	p.S728R	ENST00000301178	NM_021913.4	728	agC/agA	18/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.510685426697983	2		530	615	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752804	42752804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1286494808	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	322	930	0	ENST00000222329.4:c.1460G>A	p.Arg487His	p.R487H	ENST00000222329	NM_006494.2	487	cGc/cAc	4/4	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.510685426697983	2		930	1116	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793421	42793422	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	221	673	0	ENST00000575354.2:c.1224dup	p.Ala409CysfsTer24	p.A409Cfs*24	ENST00000575354	NM_015125.3	408	ggt/ggTt	8/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.510685426697983	2		673	752	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860791	45860791	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768677952	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	264	882	1	ENST00000391945.4:c.1318G>A	p.Ala440Thr	p.A440T	ENST00000391945	NM_000400.3	440	Gcc/Acc	14/23	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.510685426697983	2		883	902	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867355	45867355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781402308	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	301	872	4	ENST00000391945.4:c.838C>T	p.Arg280Cys	p.R280C	ENST00000391945	NM_000400.3	280	Cgc/Tgc	10/23	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.510685426697983	2		876	1006	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139073	50139073	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	252	816	0	ENST00000246792.3:c.490C>A	p.His164Asn	p.H164N	ENST00000246792	NM_006270.3	164	Cac/Aac	5/6	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.510685426697983	2		816	885	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467169	25467169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772310511	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	251	813	2	ENST00000264709.3:c.1706C>T	p.Pro569Leu	p.P569L	ENST00000264709	NM_175629.2	569	cCg/cTg	15/23	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.510685426697983	2		815	899	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015025	27015025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754932895	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	216	709	1	ENST00000335756.4:c.127C>T	p.Arg43Trp	p.R43W	ENST00000335756	NM_001809.3	43	Cgg/Tgg	2/5	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.510685426697983	2		710	816	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702366	47702366	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs751939698	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	184	715	0	ENST00000233146.2:c.1962C>G	p.Asp654Glu	p.D654E	ENST00000233146	NM_000251.2	654	gaC/gaG	12/16	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.510685426697983	2		715	716	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030670	48030670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750253	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	188	659	0	ENST00000234420.5:c.3284G>A	p.Arg1095His	p.R1095H	ENST00000234420	NM_000179.2	1095	cGc/cAc	5/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.510685426697983	2		659	686	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147533	61147533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561660110	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	13	32	0	ENST00000295025.8:c.938G>A	p.Arg313His	p.R313H	ENST00000295025	NM_002908.2	313	cGc/cAc	9/11	1	2	FACETS	0.893	0.655	1	0.893	0.655	1	CLONAL	1	TRUE	1	0.510685426697983	2		32	57	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149329	61149329	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	164	517	0	ENST00000295025.8:c.1519G>A	p.Gly507Arg	p.G507R	ENST00000295025	NM_002908.2	507	Gga/Aga	11/11	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.510685426697983	2		517	634	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726051	61726053	+	splice_region_variant,intron_variant	Splice_Region	DEL	AAA	AAA	-	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	189	656	0	ENST00000401558.2:c.591-5_591-3del		p.X197_splice	ENST00000401558	NM_003400.3	197			1	2	FACETS	0.961	0.89	1	0.961	0.89	1	CLONAL	1	TRUE	1	0.510685426697983	2		656	770	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172271	99172271	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	186	651	2	ENST00000074304.5:c.1837C>T	p.His613Tyr	p.H613Y	ENST00000074304	NM_001134224.1	613	Cat/Tat	17/26	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.510685426697983	2		653	719	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907683	111907683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146318804	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	237	662	3	ENST00000393256.3:c.457C>T	p.Arg153Trp	p.R153W	ENST00000393256	NM_006538.4	153	Cgg/Tgg	3/4	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.510685426697983	2		665	795	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921773	111921773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765527733	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	244	721	0	ENST00000393256.3:c.562C>T	p.Arg188Cys	p.R188C	ENST00000393256	NM_006538.4	188	Cgt/Tgt	4/4	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.510685426697983	2		721	837	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281489	198281489	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	226	678	0	ENST00000335508.6:c.642del	p.Lys214AsnfsTer17	p.K214Nfs*17	ENST00000335508	NM_012433.2	214	aaA/aa	6/25	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.510685426697983	2		678	885	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632303	215632303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782003	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	231	826	1	ENST00000260947.4:c.1471G>A	p.Gly491Arg	p.G491R	ENST00000260947	NM_000465.2	491	Ggg/Agg	6/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.510685426697983	2		827	866	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339003	225339003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	174	876	0	ENST00000264414.4:c.2266C>T	p.Arg756Ter	p.R756*	ENST00000264414	NM_003590.4	756	Cga/Tga	16/16	1	2	FACETS	0.888	0.82	0.96	0.888	0.82	0.96	CLONAL	1	TRUE	1	0.510685426697983	2		876	767	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663169	227663169	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	256	759	3	ENST00000305123.5:c.286G>A	p.Ala96Thr	p.A96T	ENST00000305123	NM_005544.2	96	Gcg/Acg	1/2	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.510685426697983	2		762	913	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021277	31021277	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	247	400	2	ENST00000375687.4:c.1281del	p.Lys427AsnfsTer35	p.K427Nfs*35	ENST00000375687	NM_015338.5	426	Aaa/aa	12/13	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.510685426697983	2		402	937	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022346	31022346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372418554	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	170	540	2	ENST00000375687.4:c.1831G>A	p.Ala611Thr	p.A611T	ENST00000375687	NM_015338.5	611	Gcc/Acc	13/13	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.510685426697983	2		542	623	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31369177	31369177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17123590	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	260	745	0	ENST00000328111.2:c.161G>A	p.Arg54Gln	p.R54Q	ENST00000328111	NM_006892.3	54	cGa/cAa	3/23	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.510685426697983	2		745	878	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384997	31384997	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768977355	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	198	674	0	ENST00000328111.2:c.1382G>A	p.Arg461His	p.R461H	ENST00000328111	NM_006892.3	461	cGc/cAc	14/23	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.510685426697983	2		674	732	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419974	41419974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	231	746	1	ENST00000373198.4:c.347G>A	p.Ser116Asn	p.S116N	ENST00000373198	NM_133170.3	116	aGc/aAc	3/32	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.510685426697983	2		747	814	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419987	41419987	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376239850	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	207	763	0	ENST00000373198.4:c.334C>T	p.Arg112Cys	p.R112C	ENST00000373198	NM_133170.3	112	Cgt/Tgt	3/32	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.510685426697983	2		763	804	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252917	36252917	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752926959	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	221	620	2	ENST00000300305.3:c.445G>A	p.Ala149Thr	p.A149T	ENST00000300305		149	Gca/Aca	4/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.510685426697983	2		622	804	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755579	39755579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779273424	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	204	562	3	ENST00000288319.7:c.1186G>A	p.Ala396Thr	p.A396T	ENST00000288319	NM_182918.3	396	Gcc/Acc	10/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.510685426697983	2		565	713	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288221	21288221	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	281	940	3	ENST00000354336.3:c.466C>T	p.Pro156Ser	p.P156S	ENST00000354336	NM_005207.3	156	Cct/Tct	2/3	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.510685426697983	2		943	1011	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30061040	30061040	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755200117	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	231	739	0	ENST00000338641.4:c.872G>A	p.Arg291His	p.R291H	ENST00000338641	NM_000268.3	291	cGt/cAt	9/16	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.510685426697983	2		739	900	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650388	12650388	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	254	777	0	ENST00000251849.4:c.458A>G	p.Asp153Gly	p.D153G	ENST00000251849	NM_002880.3	153	gAc/gGc	5/17	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.510685426697983	2		777	884	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12653479	12653479	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	187	672	0	ENST00000251849.4:c.290C>T	p.Ala97Val	p.A97V	ENST00000251849	NM_002880.3	97	gCa/gTa	3/17	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.510685426697983	2		672	681	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37061871	37061871	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63750796	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	205	690	3	ENST00000231790.2:c.955G>T	p.Glu319Ter	p.E319*	ENST00000231790	NM_000249.3	319	Gag/Tag	11/19	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.510685426697983	2		693	767	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412922	49412922	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	326	998	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	0.510685426697983	2		998	1185	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940426	49940426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	297	894	0	ENST00000296474.3:c.617C>T	p.Ala206Val	p.A206V	ENST00000296474	NM_002447.2	206	gCc/gTc	1/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.510685426697983	2		894	1093	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436835	52436835	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755915077	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	286	914	1	ENST00000460680.1:c.1943C>T	p.Ala648Val	p.A648V	ENST00000460680	NM_004656.3	648	gCg/gTg	15/17	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.510685426697983	2		915	1052	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440855	52440855	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553645702	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	329	792	0	ENST00000460680.1:c.649G>A	p.Ala217Thr	p.A217T	ENST00000460680	NM_004656.3	217	Gcc/Acc	8/17	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.510685426697983	2		792	1026	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651532	52651532	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	197	708	2	ENST00000394830.3:c.1564C>T	p.Arg522Ter	p.R522*	ENST00000394830	NM_018313.4	522	Cga/Tga	15/30	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.510685426697983	2		710	709	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987159	69987159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	217	667	0	ENST00000394351.3:c.220C>T	p.Pro74Ser	p.P74S	ENST00000394351	NM_000248.3	74	Ccc/Tcc	2/9	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.510685426697983	2		667	802	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021818	71021818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs869025203	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	139	305	0	ENST00000318789.4:c.1540C>T	p.Arg514Cys	p.R514C	ENST00000318789	NM_032682.5	514	Cgt/Tgt	18/21	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.510685426697983	2		305	434	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468417	89468417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1559689115	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	140	493	0	ENST00000336596.2:c.1951G>A	p.Ala651Thr	p.A651T	ENST00000336596	NM_005233.5	651	Gcc/Acc	11/17	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.510685426697983	2		493	538	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898759	134898759	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	170	595	0	ENST00000398015.3:c.1817C>A	p.Ala606Asp	p.A606D	ENST00000398015	NM_004441.4	606	gCt/gAt	10/16	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.510685426697983	2		595	662	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911444	134911444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149160192	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	245	579	1	ENST00000398015.3:c.1909C>T	p.Arg637Cys	p.R637C	ENST00000398015	NM_004441.4	637	Cgt/Tgt	11/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.510685426697983	2		580	899	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269009	142269009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369913351	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	214	814	1	ENST00000350721.4:c.2941G>A	p.Val981Ile	p.V981I	ENST00000350721	NM_001184.3	981	Gtt/Att	14/47	1	2	FACETS	0.989	0.921	1	0.989	0.921	1	CLONAL	1	TRUE	1	0.510685426697983	2		815	847	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183566	185183566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776368621	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	185	568	7	ENST00000265026.3:c.1420C>T	p.Arg474Trp	p.R474W	ENST00000265026	NM_004721.4	474	Cgg/Tgg	9/14	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.510685426697983	2		575	675	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184615	185184615	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs151275315	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	186	511	3	ENST00000265026.3:c.1507C>T	p.Arg503Cys	p.R503C	ENST00000265026	NM_004721.4	503	Cgt/Tgt	10/14	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.510685426697983	2		514	636	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447565	187447565	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151194132	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	189	758	1	ENST00000232014.4:c.628G>A	p.Asp210Asn	p.D210N	ENST00000232014	NM_001130845.1	210	Gat/Aat	5/10	1	2	FACETS	0.916	0.848	0.986	0.916	0.848	0.986	CLONAL	1	TRUE	1	0.510685426697983	2		759	808	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1918645	1918645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372805518	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	282	860	2	ENST00000382891.5:c.808G>A	p.Ala270Thr	p.A270T	ENST00000382891	NM_133335.3	270	Gcc/Acc	4/22	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.510685426697983	2		862	989	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920217	1920217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200784805	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	337	1007	1	ENST00000382891.5:c.1277C>T	p.Thr426Met	p.T426M	ENST00000382891	NM_133335.3	426	aCg/aTg	5/22	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.510685426697983	2		1008	1067	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747999	41747999	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	32	79	2	ENST00000226382.2:c.770C>T	p.Ala257Val	p.A257V	ENST00000226382	NM_003924.3	257	gCg/gTg	3/3	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.510685426697983	2		81	88	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749496	41749496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	270	741	2	ENST00000226382.2:c.299G>A	p.Arg100His	p.R100H	ENST00000226382	NM_003924.3	100	cGc/cAc	2/3	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.510685426697983	2		743	858	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391525	84391525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748680448	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	140	762	0	ENST00000321945.7:c.307C>T	p.Arg103Cys	p.R103C	ENST00000321945	NM_139076.2	103	Cgt/Tgt	5/9	1	2	FACETS	0.805	0.735	0.879	0.805	0.735	0.879	CLONAL	1	TRUE	1	0.510685426697983	2		762	681	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808246	99808246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776434815	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	211	777	0	ENST00000280892.6:c.443G>A	p.Arg148His	p.R148H	ENST00000280892	NM_001130678.1	148	cGc/cAc	5/7	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.510685426697983	2		777	788	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106162524	106162524	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	179	731	0	ENST00000380013.4:c.3442del	p.Tyr1148IlefsTer4	p.Y1148Ifs*4	ENST00000380013	NM_001127208.2	1146	ccT/cc	4/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.510685426697983	2		731	644	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527277	187527277	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	295	755	0	ENST00000441802.2:c.10297G>T	p.Val3433Phe	p.V3433F	ENST00000441802	NM_005245.3	3433	Gtc/Ttc	17/27	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.510685426697983	2		755	901	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541678	187541678	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377498159	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	145	513	1	ENST00000441802.2:c.6062G>A	p.Arg2021His	p.R2021H	ENST00000441802	NM_005245.3	2021	cGc/cAc	10/27	1	2	FACETS	0.974	0.893	1	0.974	0.893	1	CLONAL	1	TRUE	1	0.510685426697983	2		514	583	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541756	187541756	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	189	682	0	ENST00000441802.2:c.5984C>T	p.Ala1995Val	p.A1995V	ENST00000441802	NM_005245.3	1995	gCc/gTc	10/27	1	2	FACETS	0.996	0.923	1	0.996	0.923	1	CLONAL	1	TRUE	1	0.510685426697983	2		682	743	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628149	187628149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377150532	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	292	956	2	ENST00000441802.2:c.2833G>A	p.Val945Ile	p.V945I	ENST00000441802	NM_005245.3	945	Gtc/Atc	2/27	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.510685426697983	2		958	1074	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1258719	1258719	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	235	863	1	ENST00000310581.5:c.3026C>T	p.Ala1009Val	p.A1009V	ENST00000310581	NM_198253.2	1009	gCg/gTg	13/16	1	2	FACETS	0.946	0.883	1	0.946	0.883	1	CLONAL	1	TRUE	1	0.510685426697983	2		864	973	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155654	56155654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746479827	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	229	685	1	ENST00000399503.3:c.746G>A	p.Arg249His	p.R249H	ENST00000399503	NM_005921.1	249	cGc/cAc	3/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.510685426697983	2		686	791	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575480	67575480	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765008592	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	226	622	0	ENST00000274335.5:c.553G>A	p.Ala185Thr	p.A185T	ENST00000274335		185	Gct/Act	4/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.510685426697983	2		622	756	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80021333	80021333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	297	1044	2	ENST00000265081.6:c.1402G>A	p.Ala468Thr	p.A468T	ENST00000265081	NM_002439.4	468	Gct/Act	9/24	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.510685426697983	2		1046	995	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672330	86672330	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	198	727	0	ENST00000274376.6:c.2132G>A	p.Arg711Gln	p.R711Q	ENST00000274376	NM_002890.2	711	cGa/cAa	16/25	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.510685426697983	2		727	743	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675571	86675571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1561325048	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	143	588	2	ENST00000274376.6:c.2513del	p.Asn838MetfsTer4	p.N838Mfs*4	ENST00000274376	NM_002890.2	836	gAa/ga	19/25	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.510685426697983	2		590	524	SUCCESS
APC	324	MSKCC	GRCh37	5	112175486	112175486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424719678	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	144	546	1	ENST00000257430.4:c.4195C>T	p.Arg1399Cys	p.R1399C	ENST00000257430	NM_000038.5	1399	Cgt/Tgt	16/16	1	2	FACETS	0.977	0.895	1	0.977	0.895	1	CLONAL	1	TRUE	1	0.510685426697983	2		547	577	SUCCESS
APC	324	MSKCC	GRCh37	5	112177368	112177368	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	163	580	0	ENST00000257430.4:c.6077C>T	p.Ser2026Phe	p.S2026F	ENST00000257430	NM_000038.5	2026	tCt/tTt	16/16	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.510685426697983	2		580	631	SUCCESS
APC	324	MSKCC	GRCh37	5	112178864	112178864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774952444	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	153	525	0	ENST00000257430.4:c.7573C>T	p.Arg2525Cys	p.R2525C	ENST00000257430	NM_000038.5	2525	Cgc/Tgc	16/16	1	2	FACETS	0.97	0.891	1	0.97	0.891	1	CLONAL	1	TRUE	1	0.510685426697983	2		525	618	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924403	131924403	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1184353235	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	189	639	0	ENST00000265335.6:c.1076G>A	p.Arg359His	p.R359H	ENST00000265335		359	cGc/cAc	8/25	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.510685426697983	2		639	643	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931468	131931468	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369560280	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	233	624	2	ENST00000265335.6:c.2173C>T	p.Arg725Trp	p.R725W	ENST00000265335		725	Cgg/Tgg	13/25	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.510685426697983	2		626	822	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459776	149459776	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	278	839	0	ENST00000286301.3:c.431G>C	p.Arg144Pro	p.R144P	ENST00000286301	NM_005211.3	144	cGt/cCt	4/22	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.510685426697983	2		839	956	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562975	176562975	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	261	935	0	ENST00000439151.2:c.871A>C	p.Asn291His	p.N291H	ENST00000439151	NM_022455.4	291	Aac/Cac	2/23	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.510685426697983	2		935	957	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048667	180048667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749960761	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	278	748	0	ENST00000261937.6:c.1895G>A	p.Arg632His	p.R632H	ENST00000261937	NM_182925.4	632	cGc/cAc	13/30	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.510685426697983	2		748	909	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165126	32165126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1213449936	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	560	840	1	ENST00000375023.3:c.5002C>T	p.Arg1668Cys	p.R1668C	ENST00000375023	NM_004557.3	1668	Cgc/Tgc	27/30	1	2	FACETS	1	0.994	1	1	0.998	1	CLONAL	2	TRUE	1	0.510685426697983	2		841	974	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64290032	64290032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757501922	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	247	868	4	ENST00000370651.3:c.475C>T	p.Arg159Cys	p.R159C	ENST00000370651	NM_003463.4	159	Cgt/Tgt	6/6	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.510685426697983	2		872	902	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469779	157469779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749077422	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	277	954	2	ENST00000346085.5:c.2573C>T	p.Ala858Val	p.A858V	ENST00000346085	NM_020732.3	858	gCg/gTg	9/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.510685426697983	2		956	987	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976706	2976706	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1044557293	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	297	748	0	ENST00000396946.4:c.1306C>T	p.Arg436Trp	p.R436W	ENST00000396946	NM_032415.4	436	Cgg/Tgg	9/25	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.510685426697983	2		748	908	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976745	2976745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748839211	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	331	1016	2	ENST00000396946.4:c.1267C>T	p.Arg423Trp	p.R423W	ENST00000396946	NM_032415.4	423	Cgg/Tgg	9/25	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.510685426697983	2		1018	1151	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372694	81372694	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	153	560	0	ENST00000222390.5:c.840G>A	p.Trp280Ter	p.W280*	ENST00000222390	NM_000601.4	280	tgG/tgA	7/18	1	2	FACETS	0.995	0.915	1	0.995	0.915	1	CLONAL	1	TRUE	1	0.510685426697983	2		560	602	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372746	81372746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	165	716	0	ENST00000222390.5:c.788C>T	p.Pro263Leu	p.P263L	ENST00000222390	NM_000601.4	263	cCc/cTc	7/18	1	2	FACETS	0.9	0.828	0.974	0.9	0.828	0.974	CLONAL	1	TRUE	1	0.510685426697983	2		716	718	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508152	106508152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1446853033	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	153	358	0	ENST00000359195.3:c.146G>A	p.Arg49His	p.R49H	ENST00000359195	NM_002649.2	49	cGc/cAc	2/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.510685426697983	2		358	439	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508557	106508557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	36	423	1	ENST00000359195.3:c.551G>A	p.Arg184His	p.R184H	ENST00000359195	NM_002649.2	184	cGc/cAc	2/11	1	2	FACETS	0.237	0.194	0.285	0.237	0.194	0.285	SUBCLONAL	1	TRUE	1	0.510685426697983	2		424	596	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515213	106515213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267601224	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	195	734	0	ENST00000359195.3:c.2356C>T	p.Pro786Ser	p.P786S	ENST00000359195	NM_002649.2	786	Cca/Tca	5/11	1	2	FACETS	0.946	0.878	1	0.946	0.878	1	CLONAL	1	TRUE	1	0.510685426697983	2		734	807	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526657	106526657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1304506191	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	261	816	3	ENST00000359195.3:c.2950C>T	p.Pro984Ser	p.P984S	ENST00000359195	NM_002649.2	984	Cca/Tca	10/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.510685426697983	2		819	871	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436065	116436065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761522694	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	297	800	1	ENST00000397752.3:c.4060G>A	p.Ala1354Thr	p.A1354T	ENST00000397752	NM_000245.2	1354	Gct/Act	21/21	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.510685426697983	2		801	923	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845545	128845545	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	291	760	1	ENST00000249373.3:c.842G>T	p.Trp281Leu	p.W281L	ENST00000249373	NM_005631.4	281	tGg/tTg	4/12	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.510685426697983	2		761	955	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434533	140434533	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	196	463	0	ENST00000288602.6:c.2165C>A	p.Pro722Gln	p.P722Q	ENST00000288602	NM_004333.4	722	cCa/cAa	18/18	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.510685426697983	2		463	617	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482927	140482927	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	285	854	6	ENST00000288602.6:c.1208del	p.Pro403LeufsTer8	p.P403Lfs*8	ENST00000288602	NM_004333.4	403	cCt/ct	10/18	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.510685426697983	2		860	943	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523623	148523623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	180	597	0	ENST00000320356.2:c.830G>A	p.Ser277Asn	p.S277N	ENST00000320356	NM_004456.4	277	aGc/aAc	8/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.510685426697983	2		597	653	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845243	151845243	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1323051494	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	180	584	0	ENST00000262189.6:c.13769G>A	p.Arg4590His	p.R4590H	ENST00000262189	NM_170606.2	4590	cGc/cAc	52/59	1	2	FACETS	0.978	0.904	1	0.978	0.904	1	CLONAL	1	TRUE	1	0.510685426697983	2		584	721	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884475	151884475	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	163	587	0	ENST00000262189.6:c.4880A>G	p.Asp1627Gly	p.D1627G	ENST00000262189	NM_170606.2	1627	gAc/gGc	33/59	1	2	FACETS	0.956	0.88	1	0.956	0.88	1	CLONAL	1	TRUE	1	0.510685426697983	2		587	668	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194727	29194727	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	306	983	0	ENST00000240100.2:c.1001T>C	p.Val334Ala	p.V334A	ENST00000240100	NM_001394.6	334	gTg/gCg	4/4	0.510685426697983	5	FACETS	0.769	0.724	0.816	0.513	0.482	0.544	SUBCLONAL	2	TRUE	2	0.510685426697983	5		983	1376	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981315	68981315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866864487	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	292	705	3	ENST00000288368.4:c.1387C>T	p.Arg463Cys	p.R463C	ENST00000288368	NM_024870.2	463	Cgc/Tgc	12/40	0.510685426697983	5	FACETS	0.936	0.886	0.987	0.936	0.886	0.987	CLONAL	3	TRUE	2	0.510685426697983	5		708	719	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737817	145737817	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368982201	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	296	962	0	ENST00000428558.2:c.3013C>T	p.Arg1005Trp	p.R1005W	ENST00000428558	NM_004260.3	1005	Cgg/Tgg	18/22	0.510685426697983	5	FACETS	0.77	0.724	0.818	0.513	0.482	0.545	SUBCLONAL	2	TRUE	2	0.510685426697983	5		962	1329	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741410	145741410	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1220847881	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1244	343	1131	3	ENST00000428558.2:c.1093C>T	p.Arg365Trp	p.R365W	ENST00000428558	NM_004260.3	365	Cgg/Tgg	5/22	0.510685426697983	5	FACETS	1	0.994	1	0.498	0.47	0.527	CLONAL	1	TRUE	2	0.510685426697983	5		1134	1587	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054649	5054649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373174105	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	164	596	0	ENST00000381652.3:c.701G>A	p.Arg234His	p.R234H	ENST00000381652	NM_004972.3	234	cGc/cAc	7/25	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.510685426697983	2		596	585	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5065007	5065007	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	168	766	0	ENST00000381652.3:c.1184del	p.Asn395IlefsTer19	p.N395Ifs*19	ENST00000381652	NM_004972.3	394	gAa/ga	9/25	1	2	FACETS	0.955	0.88	1	0.955	0.88	1	CLONAL	1	TRUE	1	0.510685426697983	2		766	689	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126342	5126342	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746602942	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	121	471	1	ENST00000381652.3:c.3187C>T	p.Arg1063Cys	p.R1063C	ENST00000381652	NM_004972.3	1063	Cgt/Tgt	24/25	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.510685426697983	2		472	397	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524949	8524949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771217760	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	177	574	0	ENST00000356435.5:c.655G>A	p.Ala219Thr	p.A219T	ENST00000356435		219	Gct/Act	7/35	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.510685426697983	2		574	646	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971105	21971105	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878853646	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	233	653	1	ENST00000304494.5:c.253G>A	p.Ala85Thr	p.A85T	ENST00000304494	NM_000077.4	85	Gct/Act	2/3	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.510685426697983	2		654	684	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27205001	27205001	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	230	768	0	ENST00000380036.4:c.2302A>G	p.Ile768Val	p.I768V	ENST00000380036	NM_000459.3	768	Atc/Gtc	14/23	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.510685426697983	2		768	866	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs767894241	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	226	868	0	ENST00000358127.4:c.76dup	p.Val26GlyfsTer49	p.V26Gfs*49	ENST00000358127	NM_001280556.1	26	gtt/gGtt	2/10	1	2	FACETS	0.949	0.884	1	0.949	0.884	1	CLONAL	1	TRUE	1	0.510685426697983	2		868	933	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430668	80430668	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	214	804	0	ENST00000286548.4:c.340C>T	p.Arg114Ter	p.R114*	ENST00000286548	NM_002072.3	114	Cga/Tga	3/7	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.510685426697983	2		804	698	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240431	98240431	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	205	740	1	ENST00000331920.6:c.1253del	p.Lys418ArgfsTer14	p.K418Rfs*14	ENST00000331920	NM_000264.3	418	aAg/ag	9/24	1	2	FACETS	0.997	0.927	1	0.997	0.927	1	CLONAL	1	TRUE	1	0.510685426697983	2		741	805	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128420019	128420019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	281	1124	1	ENST00000265960.3:c.409G>A	p.Gly137Arg	p.G137R	ENST00000265960	NM_001006617.1	137	Ggg/Agg	4/12	1	2	FACETS	0.948	0.89	1	0.948	0.89	1	CLONAL	1	TRUE	1	0.510685426697983	2		1125	1161	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771923	135771923	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753388676	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	222	690	0	ENST00000298552.3:c.3194C>T	p.Thr1065Met	p.T1065M	ENST00000298552	NM_001162426.1	1065	aCg/aTg	23/23	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.510685426697983	2		690	825	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772874	135772874	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514873	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	295	873	1	ENST00000298552.3:c.2749G>A	p.Ala917Thr	p.A917T	ENST00000298552	NM_001162426.1	917	Gcc/Acc	21/23	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.510685426697983	2		874	1015	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309069	137309069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756234164	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	342	1131	4	ENST00000481739.1:c.676G>A	p.Ala226Thr	p.A226T	ENST00000481739	NM_002957.4	226	Gcc/Acc	5/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.510685426697983	2		1135	1194	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393421	139393421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	300	852	1	ENST00000277541.6:c.6110C>T	p.Ala2037Val	p.A2037V	ENST00000277541	NM_017617.3	2037	gCc/gTc	33/34	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.510685426697983	2		853	1071	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223725	53223725	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	347	549	0	ENST00000375401.3:c.3634C>T	p.Arg1212Trp	p.R1212W	ENST00000375401	NM_004187.3	1212	Cgg/Tgg	23/26	1	1	FACETS	0.816	0.781	0.851	1	0.996	1	CLONAL	2	TRUE	0	0.510685426697983	1		549	620	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	262	426	1	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	1	1	FACETS	0.78	0.74	0.819	1	0.995	1	SUBCLONAL	2	TRUE	0	0.510685426697983	1		427	490	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229234	123229234	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	194	278	0	ENST00000218089.9:c.3718A>T	p.Asn1240Tyr	p.N1240Y	ENST00000218089	NM_001042749.1	1240	Aac/Tac	34/35	1	1	FACETS	0.873	0.825	0.92	1	0.994	1	CLONAL	2	TRUE	0	0.510685426697983	1		278	324	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104377162	104377162	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748099523	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	324	1079	1	ENST00000369902.3:c.1273G>A	p.Ala425Thr	p.A425T	ENST00000369902	NM_016169.3	425	Gcg/Acg	10/12	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.510685426697983	2		1080	1126	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793423	42793423	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	223	676	1	ENST00000575354.2:c.1225G>T	p.Ala409Ser	p.A409S	ENST00000575354	NM_015125.3	409	Gcc/Tcc	8/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.510685426697983	2		677	758	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	100	215	0				ENST00000310581	NM_198253.2	-/1132			0.373716518401155	3	FACETS	1	0.909	1	0.505	0.454	0.558	INDETERMINATE	1	TRUE	1	0.682727286456601	3		215	389	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894228	NA	P-0020542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	217	933	0	ENST00000451590.1:c.37G>C	p.Gly13Arg	p.G13R	ENST00000451590	NM_001130442.1	13	Ggt/Cgt	2/5	0.349399768562392	1	FACETS	0.726	0.68	0.772	0.726	0.68	0.772	INDETERMINATE	1	TRUE	0	0.682727286456601	1		933	577	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984448	201984449	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	437	776	0	ENST00000359651.3:c.1114dup	p.Ter372LeufsTer99	p.*372Lfs*99	ENST00000359651		371	-/T	8/8	0.682727286456601	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.682727286456601	3		776	840	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428616	49428616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	73	1152	0	ENST00000301067.7:c.10334G>A	p.Gly3445Glu	p.G3445E	ENST00000301067	NM_003482.3	3445	gGg/gAg	35/54	1	2	FACETS	0.221	0.192	0.252	0.221	0.192	0.252	SUBCLONAL	1	TRUE	1	0.682727286456601	2		1152	969	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38504625	38504625	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	172	1120	1	ENST00000254066.5:c.236C>T	p.Pro79Leu	p.P79L	ENST00000254066	NM_000964.3	79	cCc/cTc	3/9	1	2	FACETS	0.503	0.462	0.545	0.503	0.462	0.545	SUBCLONAL	1	TRUE	1	0.682727286456601	2		1121	1002	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295295	1295295	+	upstream_gene_variant	5'Flank	SNP	G	G	C	novel	NA	P-0020542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	168	859	0				ENST00000310581	NM_198253.2	-/1132			0.373716518401155	3	FACETS	0.917	0.845	0.992	0.458	0.422	0.496	INDETERMINATE	1	TRUE	1	0.682727286456601	3		859	720	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652087	36652088	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	297	1065	0	ENST00000244741.5:c.211dup	p.Leu71ProfsTer18	p.L71Pfs*18	ENST00000244741	NM_000389.4	70	ggc/ggCc	2/3	1	2	FACETS	0.979	0.924	1	0.979	0.924	1	CLONAL	1	TRUE	1	0.682727286456601	2		1065	889	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176132087	176132087	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	131	818	0	ENST00000367669.3:c.680G>T	p.Gly227Val	p.G227V	ENST00000367669	NM_022457.5	227	gGa/gTa	5/20	0.354682142858273	3	FACETS	1	0.934	1	0.515	0.469	0.562	INDETERMINATE	1	TRUE	1	0.616392872753382	3		818	540	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426082	49426082	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398123711	NA	P-0020694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	252	841	0	ENST00000301067.7:c.12406C>T	p.Gln4136Ter	p.Q4136*	ENST00000301067	NM_003482.3	4136	Cag/Tag	39/54	0.354682142858273	3	FACETS	1	0.989	1	0.628	0.589	0.668	INDETERMINATE	1	TRUE	1	0.616392872753382	3		841	852	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589316	28589316	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	229	658	0	ENST00000241453.7:c.2731C>A	p.Pro911Thr	p.P911T	ENST00000241453	NM_004119.2	911	Cca/Aca	22/24	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.616392872753382	2		658	738	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961930	41961930	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	72	489	0	ENST00000219905.7:c.838G>C	p.Glu280Gln	p.E280Q	ENST00000219905	NM_001164273.1	280	Gaa/Caa	2/24	0.616392872753382	1	FACETS	0.474	0.417	0.535	0.474	0.417	0.535	SUBCLONAL	1	TRUE	0	0.616392872753382	1		489	341	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50816240	50816241	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGA	novel	NA	P-0020694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	69	362	0	ENST00000398568.2:c.1683_1685dup	p.Gly562dup	p.G562dup	ENST00000398568	NM_001042412.1	562	-/GGA	10/18	0.616392872753382	1	FACETS	0.89	0.793	0.99	0.89	0.793	0.99	CLONAL	1	TRUE	0	0.616392872753382	1		362	174	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574026	7574026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	540	792	0	ENST00000269305.4:c.1001G>T	p.Gly334Val	p.G334V	ENST00000269305	NM_001126112.2	334	gGg/gTg	10/11	0.0946301190229835	6	FACETS	1	0.991	1			1	INDETERMINATE	4	TRUE	NA	0.616392872753382	6		792	912	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726726	41726726	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	129	865	2	ENST00000301178.4:c.271G>A	p.Asp91Asn	p.D91N	ENST00000301178	NM_021913.4	91	Gat/Aat	2/20	0.175984581760929	3	FACETS	0.502	0.454	0.553	0.251	0.227	0.277	INDETERMINATE	1	TRUE	1	0.616392872753382	3		867	1091	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61760992	61760992	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1411091081	NA	P-0020694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	30	623	0	ENST00000401558.2:c.41G>A	p.Arg14His	p.R14H	ENST00000401558	NM_003400.3	14	cGt/cAt	2/25	0.0946301190229835	6	FACETS	0.399	0.32	0.488			1	INDETERMINATE	1	TRUE	NA	0.616392872753382	6		623	545	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021380	31021381	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0020694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	203	593	1	ENST00000375687.4:c.1379_1380delinsCT	p.Gly460Ala	p.G460A	ENST00000375687	NM_015338.5	460	gGG/gCT	12/13	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.616392872753382	2		594	589	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566510	41566510	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	314	617	0	ENST00000263253.7:c.4387C>G	p.Leu1463Val	p.L1463V	ENST00000263253	NM_001429.3	1463	Ctg/Gtg	27/31	0.467893557908537	2	FACETS	0.859	0.819	0.899	0.859	0.819	0.899	CLONAL	2	TRUE	0	0.616392872753382	2		617	593	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602743	55602743	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	84	606	0	ENST00000288135.5:c.2564A>T	p.Tyr855Phe	p.Y855F	ENST00000288135	NM_000222.2	855	tAt/tTt	18/21	0.442738687834465	1	FACETS	0.449	0.398	0.502	0.449	0.398	0.502	SUBCLONAL	1	TRUE	0	0.616392872753382	1		606	420	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157188	106157188	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	186	524	0	ENST00000380013.4:c.2089C>A	p.Pro697Thr	p.P697T	ENST00000380013	NM_001127208.2	697	Cca/Aca	3/11	1	2	FACETS	0.998	0.926	1	0.998	0.926	1	CLONAL	1	TRUE	1	0.616392872753382	2		524	605	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295204	1295204	+	upstream_gene_variant	5'Flank	SNP	G	G	C	novel	NA	P-0020694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	71	405	0				ENST00000310581	NM_198253.2	-/1132			0.616392872753382	3	FACETS	0.491	0.428	0.558	0.245	0.214	0.279	SUBCLONAL	1	TRUE	1	0.616392872753382	3		405	614	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323175	31323175	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	276	746	0	ENST00000412585.2:c.814del	p.Val272TrpfsTer25	p.V272Wfs*25	ENST00000412585	NM_005514.6	272	Gtg/tg	4/8	0.616392872753382	1	FACETS	0.915	0.865	0.966	0.915	0.865	0.966	CLONAL	1	TRUE	0	0.616392872753382	1		746	677	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140500278	140500278	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	119	418	0	ENST00000288602.6:c.864G>T	p.Leu288Phe	p.L288F	ENST00000288602	NM_004333.4	288	ttG/ttT	7/18	0.175984581760929	3	FACETS	1	0.98	1	0.638	0.581	0.697	INDETERMINATE	1	TRUE	1	0.616392872753382	3		418	396	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021697	69021697	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	176	653	0	ENST00000288368.4:c.2985G>C	p.Met995Ile	p.M995I	ENST00000288368	NM_024870.2	995	atG/atC	25/40	0.328587179834588	1	FACETS	0.805	0.748	0.863	0.805	0.748	0.863	INDETERMINATE	1	TRUE	0	0.616392872753382	1		653	491	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022105	5022105	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	43	768	0	ENST00000381652.3:c.118C>A	p.Gln40Lys	p.Q40K	ENST00000381652	NM_004972.3	40	Cag/Aag	3/25	0.616392872753382	1	FACETS	0.204	0.17	0.241	0.204	0.17	0.241	SUBCLONAL	1	TRUE	0	0.616392872753382	1		768	473	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971026	21971026	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	191	557	0	ENST00000304494.5:c.332del	p.Gly111AlafsTer35	p.G111Afs*35	ENST00000304494	NM_000077.4	111	gGc/gc	2/3	0.616392872753382	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.616392872753382	1		557	424	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249881	110249881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	457	683	1	ENST00000374672.4:c.794C>T	p.Pro265Leu	p.P265L	ENST00000374672	NM_004235.4	265	cCc/cTc	3/5	0.616392872753382	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.616392872753382	2		684	683	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405258	139405258	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0020694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	255	704	0	ENST00000277541.6:c.2588-1G>A		p.X863_splice	ENST00000277541	NM_017617.3	863			0.616392872753382	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.616392872753382	1		704	484	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	471	215	0				ENST00000310581	NM_198253.2	-/1132			0.407458056255654	6	FACETS	0.977	0.945	1	1	0.995	1	CLONAL	6	FALSE	1	0.407458056255654	6		215	716	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs730881677	NA	P-0020720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	307	465	0	ENST00000304494.5:c.151-1G>T		p.X51_splice	ENST00000304494	NM_000077.4	51			1	2	FACETS	1	0.967	1	1	0.996	1	CLONAL	2	FALSE	1	0.407458056255654	2		465	735	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0020720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	296	199	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.995	0.942	1	1	0.996	1	CLONAL	2	FALSE	1	0.407458056255654	2		199	730	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740809	145740809	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1237	510	850	2	ENST00000428558.2:c.1291G>T	p.Glu431Ter	p.E431*	ENST00000428558	NM_004260.3	431	Gag/Tag	7/22	0.371310830066307	4	FACETS	1	0.963	1	0.672	0.643	0.703	CLONAL	2	FALSE	1	0.407458056255654	4		852	1747	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15821914	15821914	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	336	305	1	ENST00000307771.7:c.307C>T	p.Gln103Ter	p.Q103*	ENST00000307771	NM_005089.3	103	Caa/Taa	4/11	1	1	FACETS	1	0.991	1	1	0.997	1	CLONAL	3	FALSE	0	0.407458056255654	1		306	415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0020803-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	209	573	0	ENST00000269305.4:c.97-1G>T		p.X33_splice	ENST00000269305	NM_001126112.2	33			NA	2	FACETS	0.99	0.926	1			1	INDETERMINATE	2	TRUE	NA	0.371058623030669	2		573	569	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242481	+	protein_altering_variant	In_Frame_Del	DEL	GAATTAAGAGAAGCAA	GAATTAAGAGAAGCAA	ATTC	novel	NA	P-0020803-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	99	518	1	ENST00000275493.2:c.2236_2251delinsATTC	p.Glu746_Thr751delinsIlePro	p.E746_T751delinsIP	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCAAca/ATTCca	19/28	0.29123091936104	4	FACETS	1	0.981	1	0.727	0.652	0.807	CLONAL	1	TRUE	2	0.371058623030669	4		519	503	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352389	70352389	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0020803-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	172	522	1	ENST00000374080.3:c.4415+1G>C		p.X1472_splice	ENST00000374080		1472			0.319273334353809	3	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	1	0.371058623030669	3		523	545	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	367	446	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.397913935895928	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	FALSE	1	0.397913935895928	3		446	1016	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0020841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	297	1071	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.335164053730023	2	FACETS	0.933	0.882	0.984	0.933	0.882	0.984	CLONAL	2	FALSE	0	0.397913935895928	2		1071	800	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953883	32953884	+	splice_region_variant,intron_variant	Splice_Region	DEL	AC	AC	-	novel	NA	P-0020841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	132	587	0	ENST00000380152.3:c.8954-3_8954-2del		p.X2985_splice	ENST00000380152		2985			0.397913935895928	3	FACETS	1	0.984	1			1	CLONAL	1	FALSE	NA	0.397913935895928	3		587	580	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74005292	74005292	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	93	921	1	ENST00000318443.5:c.1600G>A	p.Ala534Thr	p.A534T	ENST00000318443	NM_001024736.1	534	Gcc/Acc	10/10	0.397913935895928	2	FACETS	0.796	0.709	0.889	0.398	0.354	0.445	SUBCLONAL	1	FALSE	0	0.397913935895928	2		922	587	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971176	21971200	+	frameshift_variant	Frame_Shift_Del	DEL	TCCGCCACTCGGGCGCTGCCCATCA	TCCGCCACTCGGGCGCTGCCCATCA	-	novel	NA	P-0020841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	271	795	0	ENST00000304494.5:c.158_182del	p.Met53SerfsTer85	p.M53Sfs*85	ENST00000304494	NM_000077.4	53	aTGATGGGCAGCGCCCGAGTGGCGGAg/ag	2/3	0.396404540781573	2	FACETS	0.923	0.87	0.976	0.923	0.87	0.976	CLONAL	2	FALSE	0	0.397913935895928	2		795	738	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0020846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	31	282	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.558	0.45	0.681	0.558	0.45	0.681	SUBCLONAL	1	TRUE	1	0.18	2		282	617	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0020846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	117	458	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	0.86	0.776	0.949	1	0.987	1	CLONAL	2	TRUE	1	0.18	2		458	756	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0020846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	93	452	0	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.18	2		452	889	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104386947	104386947	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	36	576	0	ENST00000369902.3:c.1312G>C	p.Glu438Gln	p.E438Q	ENST00000369902	NM_016169.3	438	Gag/Cag	11/12	1	2	FACETS	0.602	0.493	0.724	0.602	0.493	0.724	SUBCLONAL	1	TRUE	1	0.18	2		576	665	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	200	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.567379203043946	2		215	628	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806089	1806089	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913479	NA	P-0020904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	324	1199	4	ENST00000260795.2:c.1108G>T	p.Gly370Cys	p.G370C	ENST00000260795		370	Ggc/Tgc	8/17	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.567379203043946	2		1203	1066	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045016	47045016	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0020904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	352	659	0	ENST00000377604.3:c.2342C>G	p.Ser781Ter	p.S781*	ENST00000377604	NM_001204468.1	781	tCa/tGa	20/24	1	1	FACETS	0.764	0.733	0.794	1	0.996	1	SUBCLONAL	2	TRUE	0	0.567379203043946	1		659	582	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884842	134884842	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	71	763	0	ENST00000398015.3:c.1621del	p.Leu541Ter	p.L541*	ENST00000398015	NM_004441.4	540	Ccc/cc	8/16	1	2	FACETS	0.346	0.301	0.394	0.346	0.301	0.394	SUBCLONAL	1	TRUE	1	0.567379203043946	2		763	724	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971188	21971189	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0020904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	151	847	0	ENST00000304494.5:c.169_170del	p.Ala57ProfsTer62	p.A57Pfs*62	ENST00000304494	NM_000077.4	57	GCc/c	2/3	0.567379203043946	1	FACETS	0.761	0.701	0.823	0.761	0.701	0.823	SUBCLONAL	1	TRUE	0	0.567379203043946	1		847	501	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786956	135786956	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0020904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	23	462	2	ENST00000298552.3:c.914-1G>A		p.X305_splice	ENST00000298552	NM_001162426.1	305			0.567379203043946	1	FACETS	0.218	0.17	0.274	0.218	0.17	0.274	SUBCLONAL	1	TRUE	0	0.567379203043946	1		464	266	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969330	44969330	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	103	340	1	ENST00000377967.4:c.4012G>T	p.Val1338Phe	p.V1338F	ENST00000377967	NM_021140.2	1338	Gtt/Ttt	28/29	1	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.567379203043946	1		341	201	SUCCESS
AR	367	MSKCC	GRCh37	X	66766348	66766348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	73	124	0	ENST00000374690.3:c.1360G>A	p.Gly454Arg	p.G454R	ENST00000374690	NM_000044.3	454	Ggg/Agg	1/8	1	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.567379203043946	1		124	145	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185186	123185187	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	39	519	0	ENST00000218089.9:c.1140dup	p.Asp381Ter	p.D381*	ENST00000218089	NM_001042749.1	380	ctt/cTtt	13/35	1	1	FACETS	0.271	0.224	0.322	0.271	0.224	0.322	SUBCLONAL	1	TRUE	0	0.567379203043946	1		519	364	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205047	123205048	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	111	475	0	ENST00000218089.9:c.2408dup	p.Met803IlefsTer6	p.M803Ifs*6	ENST00000218089	NM_001042749.1	803	atg/aTtg	25/35	1	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.567379203043946	1		475	243	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	267	215	0				ENST00000310581	NM_198253.2	-/1132			0.291365376424027	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.752133983398344	0		215	563	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	392	288	0	ENST00000304494.5:c.151-1G>A		p.X51_splice	ENST00000304494	NM_000077.4	51			0.752133983398344	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.752133983398344	1		288	561	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560824	9560824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376118527	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	185	667	0	ENST00000353224.5:c.958C>T	p.Arg320Cys	p.R320C	ENST00000353224	NM_177990.2	320	Cgc/Tgc	4/10	0.199573986404822	3	FACETS	0.895	0.829	0.964	0.298	0.276	0.322	INDETERMINATE	1	TRUE	0	0.752133983398344	3		667	756	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893589	28893589	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	261	691	0	ENST00000282397.4:c.3257G>A	p.Gly1086Glu	p.G1086E	ENST00000282397	NM_002019.4	1086	gGa/gAa	24/30	0.43854487224366	1	FACETS	0.811	0.768	0.854	0.811	0.768	0.854	INDETERMINATE	1	TRUE	0	0.752133983398344	1		691	534	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041073	29041073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	191	542	0	ENST00000282397.4:c.355G>A	p.Glu119Lys	p.E119K	ENST00000282397	NM_002019.4	119	Gaa/Aaa	3/30	0.43854487224366	1	FACETS	0.683	0.638	0.728	0.683	0.638	0.728	INDETERMINATE	1	TRUE	0	0.752133983398344	1		542	464	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729613	41729613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs564878978	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	266	501	1	ENST00000242208.4:c.916C>T	p.Arg306Cys	p.R306C	ENST00000242208	NM_002192.2	306	Cgc/Tgc	3/3	0.337897196466084	3	FACETS	1	0.99	1	0.415	0.391	0.44	INDETERMINATE	1	TRUE	0	0.752133983398344	3		502	781	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631935	90631935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267606870	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	454	1050	1	ENST00000330062.3:c.418C>T	p.Arg140Trp	p.R140W	ENST00000330062	NM_002168.2	140	Cgg/Tgg	4/11	0.400117511548334	1	FACETS	0.8	0.768	0.833	0.8	0.768	0.833	INDETERMINATE	1	TRUE	0	0.752133983398344	1		1051	941	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546769	9546769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	235	394	1	ENST00000353224.5:c.1253C>T	p.Ser418Phe	p.S418F	ENST00000353224	NM_177990.2	418	tCc/tTc	5/10	0.199573986404822	3	FACETS	0.977	0.925	1	0.651	0.617	0.686	INDETERMINATE	2	TRUE	0	0.752133983398344	3		395	440	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149002	119149002	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs755557498	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	371	551	0	ENST00000264033.4:c.1222T>C	p.Trp408Arg	p.W408R	ENST00000264033	NM_005188.3	408	Tgg/Cgg	8/16	0.752133983398344	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.752133983398344	1		551	542	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409089	4409089	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777848359	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	150	533	1	ENST00000261254.3:c.784C>T	p.Arg262Cys	p.R262C	ENST00000261254	NM_001759.3	262	Cgt/Tgt	5/5	0.283512413580735	2	FACETS	0.694	0.637	0.753	0.347	0.318	0.377	INDETERMINATE	1	TRUE	0	0.752133983398344	2		534	575	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381514	81381514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	165	526	0	ENST00000222390.5:c.547G>A	p.Glu183Lys	p.E183K	ENST00000222390	NM_000601.4	183	Gaa/Aaa	5/18	0.484216204518972	5	FACETS	1	0.924	1	0.335	0.308	0.364	CLONAL	1	TRUE	2	0.752133983398344	5		526	928	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459890	149459890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs535129002	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	345	932	2	ENST00000286301.3:c.317G>A	p.Arg106Gln	p.R106Q	ENST00000286301	NM_005211.3	106	cGg/cAg	4/22	0.392434767179156	1	FACETS	0.74	0.704	0.775	0.74	0.704	0.775	INDETERMINATE	1	TRUE	0	0.752133983398344	1		934	774	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992729	68992729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779079528	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	314	1050	2	ENST00000288368.4:c.1694C>T	p.Ser565Leu	p.S565L	ENST00000288368	NM_024870.2	565	tCg/tTg	16/40	0.389069779680292	3	FACETS	1	0.99	1	0.744	0.712	0.775	INDETERMINATE	2	TRUE	0	0.752133983398344	3		1052	515	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013719	170013719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388201066	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	135	374	0	ENST00000295797.4:c.1438C>T	p.Arg480Cys	p.R480C	ENST00000295797	NM_002740.5	480	Cgc/Tgc	15/18	0.372298821109131	1	FACETS	0.377	0.344	0.412	0.377	0.344	0.412	INDETERMINATE	1	TRUE	0	0.752133983398344	1		374	594	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937983	36937983	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	455	1115	1	ENST00000361632.4:c.853C>T	p.Leu285Phe	p.L285F	ENST00000361632		285	Ctc/Ttc	7/16	0.752133983398344	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.752133983398344	1		1116	737	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980421	201980421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	387	846	1	ENST00000359651.3:c.157G>A	p.Gly53Ser	p.G53S	ENST00000359651		53	Ggt/Agt	1/8	0.149623518119485	3	FACETS	1	0.995	1	0.705	0.671	0.738	INDETERMINATE	1	TRUE	1	0.752133983398344	3		847	1005	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691123	18691123	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	64	781	1	ENST00000266497.5:c.3234G>A	p.Met1078Ile	p.M1078I	ENST00000266497		1078	atG/atA	23/31	0.668481430029615	1	FACETS	0.328	0.285	0.373	0.328	0.285	0.373	SUBCLONAL	1	TRUE	0	0.752133983398344	1		782	324	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432034	121432034	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	392	1224	0	ENST00000257555.6:c.781G>A	p.Glu261Lys	p.E261K	ENST00000257555		261	Gag/Aag	4/10	0.48290348927925	1	FACETS	0.699	0.667	0.731	0.699	0.667	0.731	SUBCLONAL	1	TRUE	0	0.752133983398344	1		1224	931	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281117	49281117	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	192	1299	1	ENST00000282018.3:c.164G>A	p.Gly55Glu	p.G55E	ENST00000282018	NM_020377.2	55	gGa/gAa	1/1	0.392434767179156	1	FACETS	0.381	0.353	0.41	0.381	0.353	0.41	INDETERMINATE	1	TRUE	0	0.752133983398344	1		1300	836	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779008	3779008	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	237	753	0	ENST00000262367.5:c.6040C>T	p.Pro2014Ser	p.P2014S	ENST00000262367	NM_004380.2	2014	Ccc/Tcc	31/31	1	2	FACETS	0.784	0.734	0.835	0.784	0.734	0.835	SUBCLONAL	1	TRUE	1	0.752133983398344	2		753	804	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858073	9858073	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	380	867	0	ENST00000330684.3:c.3328T>C	p.Ser1110Pro	p.S1110P	ENST00000330684	NM_001134407.1	1110	Tca/Cca	13/13	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.752133983398344	2		867	830	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842719	68842719	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	363	854	0	ENST00000261769.5:c.655C>G	p.Pro219Ala	p.P219A	ENST00000261769	NM_004360.3	219	Cct/Gct	5/16	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.752133983398344	2		854	825	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828116	72828116	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	357	981	0	ENST00000268489.5:c.8465A>G	p.Asn2822Ser	p.N2822S	ENST00000268489	NM_006885.3	2822	aAt/aGt	9/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.752133983398344	2		981	917	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993263	72993263	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408016900	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	502	1234	1	ENST00000268489.5:c.782C>T	p.Pro261Leu	p.P261L	ENST00000268489	NM_006885.3	261	cCc/cTc	2/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.752133983398344	2		1235	1254	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554546	29554546	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555613983	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	110	312	0	ENST00000356175.3:c.2331G>A	p.Trp777Ter	p.W777*	ENST00000356175	NM_000267.3	777	tgG/tgA	20/57	0.372298821109131	1	FACETS	0.808	0.742	0.873	0.808	0.742	0.873	INDETERMINATE	1	TRUE	0	0.752133983398344	1		312	226	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685994	29685994	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	95	651	0	ENST00000356175.3:c.8061del	p.Phe2687LeufsTer31	p.F2687Lfs*31	ENST00000356175	NM_000267.3	2686	ggT/gg	55/57	0.372298821109131	1	FACETS	0.413	0.37	0.457	0.413	0.37	0.457	INDETERMINATE	1	TRUE	0	0.752133983398344	1		651	382	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273456	5273457	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	291	954	3	ENST00000357368.4:c.375_376delinsTT	p.Arg126Ter	p.R126*	ENST00000357368	NM_002850.3	125	ctCCga/ctTTga	4/38	1	2	FACETS	0.822	0.775	0.87	0.822	0.775	0.87	CLONAL	1	TRUE	1	0.752133983398344	2		957	941	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19261516	19261516	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767519545	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	358	1002	2	ENST00000162023.5:c.29G>A	p.Arg10His	p.R10H	ENST00000162023		10	cGc/cAc	6/13	1	2	FACETS	0.943	0.896	0.991	0.943	0.896	0.991	CLONAL	1	TRUE	1	0.752133983398344	2		1004	1009	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743963	41743963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	378	1306	0	ENST00000301178.4:c.898C>T	p.His300Tyr	p.H300Y	ENST00000301178	NM_021913.4	300	Cat/Tat	7/20	1	2	FACETS	0.84	0.798	0.883	0.84	0.798	0.883	CLONAL	1	TRUE	1	0.752133983398344	2		1306	1197	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270187	198270187	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	92	438	1	ENST00000335508.6:c.1249C>T	p.Pro417Ser	p.P417S	ENST00000335508	NM_012433.2	417	Cct/Tct	10/25	0.372298821109131	1	FACETS	0.367	0.328	0.408	0.367	0.328	0.408	INDETERMINATE	1	TRUE	0	0.752133983398344	1		439	416	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437158	220437158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs75409408	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	240	1194	1	ENST00000243786.2:c.62G>A	p.Gly21Glu	p.G21E	ENST00000243786	NM_002191.3	21	gGg/gAg	1/2	0.668481430029615	1	FACETS	0.482	0.451	0.514	0.482	0.451	0.514	SUBCLONAL	1	TRUE	0	0.752133983398344	1		1195	826	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573354	41573354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	449	1047	2	ENST00000263253.7:c.5639C>T	p.Pro1880Leu	p.P1880L	ENST00000263253	NM_001429.3	1880	cCc/cTc	31/31	0.149623518119485	3	FACETS	1	0.995	1	0.666	0.636	0.696	INDETERMINATE	1	TRUE	1	0.752133983398344	3		1049	1234	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37061814	37061814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752430684	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	307	709	0	ENST00000231790.2:c.898C>T	p.Pro300Ser	p.P300S	ENST00000231790	NM_000249.3	300	Ccc/Tcc	11/19	0.372298821109131	1	FACETS	0.751	0.714	0.789	0.751	0.714	0.789	INDETERMINATE	1	TRUE	0	0.752133983398344	1		709	678	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164177	47164177	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	83	604	0	ENST00000409792.3:c.1949del	p.Lys650ArgfsTer3	p.K650Rfs*3	ENST00000409792	NM_014159.6	650	aAg/ag	3/21	0.372298821109131	1	FACETS	0.343	0.304	0.384	0.343	0.304	0.384	INDETERMINATE	1	TRUE	0	0.752133983398344	1		604	402	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405914	49405914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	426	953	0	ENST00000418115.1:c.224C>T	p.Pro75Leu	p.P75L	ENST00000418115	NM_001664.2	75	cCa/cTa	3/5	0.372298821109131	1	FACETS	0.742	0.711	0.774	0.742	0.711	0.774	INDETERMINATE	1	TRUE	0	0.752133983398344	1		953	952	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480384	89480384	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763688148	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	101	425	0	ENST00000336596.2:c.2221G>A	p.Gly741Ser	p.G741S	ENST00000336596	NM_005233.5	741	Ggc/Agc	13/17	0.372298821109131	1	FACETS	0.377	0.338	0.417	0.377	0.338	0.417	INDETERMINATE	1	TRUE	0	0.752133983398344	1		425	445	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825359	134825359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761687482	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	321	629	0	ENST00000398015.3:c.875G>A	p.Arg292His	p.R292H	ENST00000398015	NM_004441.4	292	cGc/cAc	4/16	0.372298821109131	1	FACETS	0.833	0.794	0.873	0.833	0.794	0.873	INDETERMINATE	1	TRUE	0	0.752133983398344	1		629	639	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161272	185161272	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	403	1046	2	ENST00000265026.3:c.699G>A	p.Met233Ile	p.M233I	ENST00000265026	NM_004721.4	233	atG/atA	4/14	0.372298821109131	1	FACETS	0.821	0.787	0.856	0.821	0.787	0.856	INDETERMINATE	1	TRUE	0	0.752133983398344	1		1048	814	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607251	189607251	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	226	1042	0	ENST00000264731.3:c.1630C>T	p.Pro544Ser	p.P544S	ENST00000264731	NM_003722.4	544	Ccc/Tcc	12/14	0.372298821109131	1	FACETS	0.388	0.361	0.415	0.388	0.361	0.415	INDETERMINATE	1	TRUE	0	0.752133983398344	1		1042	967	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749407	41749407	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	236	634	0	ENST00000226382.2:c.388G>A	p.Glu130Lys	p.E130K	ENST00000226382	NM_003924.3	130	Gag/Aag	2/3	0.48290348927925	1	FACETS	0.726	0.684	0.769	0.726	0.684	0.769	SUBCLONAL	1	TRUE	0	0.752133983398344	1		634	539	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156487	106156487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	115	597	0	ENST00000380013.4:c.1388C>T	p.Pro463Leu	p.P463L	ENST00000380013	NM_001127208.2	463	cCt/cTt	3/11	0.48290348927925	1	FACETS	0.446	0.404	0.489	0.446	0.404	0.489	SUBCLONAL	1	TRUE	0	0.752133983398344	1		597	428	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196349	106196349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	159	259	1	ENST00000380013.4:c.4682C>T	p.Ser1561Phe	p.S1561F	ENST00000380013	NM_001127208.2	1561	tCt/tTt	11/11	0.48290348927925	1	FACETS	0.604	0.559	0.65	0.604	0.559	0.65	SUBCLONAL	1	TRUE	0	0.752133983398344	1		260	437	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293690	1293691	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	176	1069	2	ENST00000310581.5:c.1310_1311delinsTT	p.Ala437Val	p.A437V	ENST00000310581	NM_198253.2	437	gCC/gTT	2/16	0.291365376424027	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.752133983398344	0		1071	817	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056376	180056376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	196	932	1	ENST00000261937.6:c.868G>A	p.Glu290Lys	p.E290K	ENST00000261937	NM_182925.4	290	Gaa/Aaa	7/30	0.668481430029615	1	FACETS	0.441	0.409	0.474	0.441	0.409	0.474	SUBCLONAL	1	TRUE	0	0.752133983398344	1		933	737	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271584	26271584	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	201	528	1	ENST00000305910.3:c.29A>T	p.Lys10Met	p.K10M	ENST00000305910	NM_003534.2	10	aAg/aTg	1/1	0.729658491750776	4	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.752133983398344	4		529	808	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672612	30672613	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	346	956	1	ENST00000376406.3:c.4347_4348delinsTT	p.Pro1450Ser	p.P1450S	ENST00000376406	NM_014641.2	1449	gtCCcc/gtTTcc	10/15	0.481447913979808	4	FACETS	1	0.982	1	0.362	0.342	0.383	CLONAL	1	TRUE	1	0.752133983398344	4		957	1484	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120270	94120270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	190	429	0	ENST00000369303.4:c.781G>A	p.Gly261Arg	p.G261R	ENST00000369303	NM_004440.3	261	Gga/Aga	3/17	0.752133983398344	1	FACETS	0.958	0.904	1	0.958	0.904	1	CLONAL	1	TRUE	0	0.752133983398344	1		429	329	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641144	117641144	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	369	1013	1	ENST00000368508.3:c.5827G>T	p.Glu1943Ter	p.E1943*	ENST00000368508	NM_002944.2	1943	Gaa/Taa	36/43	0.752133983398344	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.752133983398344	1		1014	563	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367248	50367248	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	182	528	1	ENST00000331340.3:c.55C>T	p.Pro19Ser	p.P19S	ENST00000331340	NM_006060.4	19	Cct/Tct	3/8	0.337897196466084	3	FACETS	1	0.947	1	0.342	0.317	0.368	INDETERMINATE	1	TRUE	0	0.752133983398344	3		529	649	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939502	68939502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	86	772	1	ENST00000288368.4:c.487G>A	p.Glu163Lys	p.E163K	ENST00000288368	NM_024870.2	163	Gaa/Aaa	5/40	0.389069779680292	3	FACETS	0.668	0.593	0.748	0.223	0.197	0.25	INDETERMINATE	1	TRUE	0	0.752133983398344	3		773	471	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	116	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.683	0.618	0.752	0.683	0.618	0.752	SUBCLONAL	1	TRUE	1	0.587575695671917	2		215	578	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652035	36652035	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	184	906	0	ENST00000244741.5:c.159del	p.Phe53LeufsTer95	p.F53Lfs*95	ENST00000244741	NM_000389.4	53	Ttt/tt	2/3	0.487855704553275	1	FACETS	0.631	0.584	0.679	0.631	0.584	0.679	SUBCLONAL	1	TRUE	0	0.587575695671917	1		906	701	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0021013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	144	563	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.727	0.665	0.792	0.727	0.665	0.792	SUBCLONAL	1	TRUE	1	0.587575695671917	2		563	674	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0021013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	257	413	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	TRUE	1	0.587575695671917	2		413	664	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696435	47696435	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	170	653	0	ENST00000347630.2:c.388G>C	p.Asp130His	p.D130H	ENST00000347630	NM_001007230.1	130	Gac/Cac	6/11	1	2	FACETS	0.777	0.716	0.84	0.777	0.716	0.84	SUBCLONAL	1	TRUE	1	0.587575695671917	2		653	745	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733218	74733218	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	150	625	0	ENST00000359995.5:c.25G>A	p.Asp9Asn	p.D9N	ENST00000359995	NM_001195427.1	9	Gat/Aat	1/3	1	2	FACETS	0.696	0.637	0.757	0.696	0.637	0.757	SUBCLONAL	1	TRUE	1	0.587575695671917	2		625	734	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870984	12870984	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1337857330	NA	P-0021013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	88	360	0	ENST00000228872.4:c.211G>C	p.Glu71Gln	p.E71Q	ENST00000228872	NM_004064.3	71	Gag/Cag	1/3	1	2	FACETS	0.655	0.583	0.732	0.655	0.583	0.732	SUBCLONAL	1	TRUE	1	0.587575695671917	2		360	457	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871042	12871042	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	84	344	0	ENST00000228872.4:c.269G>C	p.Arg90Thr	p.R90T	ENST00000228872	NM_004064.3	90	aGa/aCa	1/3	1	2	FACETS	0.728	0.647	0.813	0.728	0.647	0.813	SUBCLONAL	1	TRUE	1	0.587575695671917	2		344	393	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871104	12871104	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	71	277	0	ENST00000228872.4:c.331G>C	p.Gly111Arg	p.G111R	ENST00000228872	NM_004064.3	111	Ggg/Cgg	1/3	1	2	FACETS	0.709	0.623	0.8	0.709	0.623	0.8	SUBCLONAL	1	TRUE	1	0.587575695671917	2		277	341	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861958	57861958	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs762501146	NA	P-0021013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	171	579	0	ENST00000228682.2:c.1259G>C	p.Gly420Ala	p.G420A	ENST00000228682	NM_005269.2	420	gGa/gCa	10/12	1	2	FACETS	0.874	0.807	0.943	0.874	0.807	0.943	CLONAL	1	TRUE	1	0.587575695671917	2		579	666	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459238	99459238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	243	813	0	ENST00000268035.6:c.1874C>T	p.Ser625Phe	p.S625F	ENST00000268035	NM_000875.3	625	tCt/tTt	9/21	1	2	FACETS	0.77	0.719	0.823	0.77	0.719	0.823	SUBCLONAL	1	TRUE	1	0.587575695671917	2		813	1074	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46275928	46275928	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs756248799	NA	P-0021013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	183	776	0	ENST00000371998.3:c.3364A>G	p.Met1122Val	p.M1122V	ENST00000371998		1122	Atg/Gtg	18/23	1	2	FACETS	0.751	0.694	0.811	0.751	0.694	0.811	SUBCLONAL	1	TRUE	1	0.587575695671917	2		776	829	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295176	1295176	+	upstream_gene_variant	5'Flank	SNP	G	G	C	novel	NA	P-0021013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	82	287	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.598	0.529	0.671	0.598	0.529	0.671	SUBCLONAL	1	TRUE	1	0.587575695671917	2		287	467	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295311	1295311	+	upstream_gene_variant	5'Flank	SNP	G	G	C	novel	NA	P-0021013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	170	760	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.751	0.692	0.813	0.751	0.692	0.813	SUBCLONAL	1	TRUE	1	0.587575695671917	2		760	770	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937759	76937759	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	141	698	0	ENST00000373344.5:c.2989G>C	p.Asp997His	p.D997H	ENST00000373344	NM_000489.3	997	Gac/Cac	9/35	1	2	FACETS	0.653	0.596	0.713	0.653	0.596	0.713	SUBCLONAL	1	TRUE	1	0.587575695671917	2		698	735	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938911	76938911	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	183	755	0	ENST00000373344.5:c.1837G>C	p.Asp613His	p.D613H	ENST00000373344	NM_000489.3	613	Gat/Cat	9/35	1	2	FACETS	0.705	0.651	0.761	0.705	0.651	0.761	SUBCLONAL	1	TRUE	1	0.587575695671917	2		755	884	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	111	351	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.878	0.793	0.967	0.878	0.793	0.967	CLONAL	1	TRUE	1	0.495954247426447	2		351	510	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	16	390	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.142	0.104	0.188	0.142	0.104	0.188	SUBCLONAL	1	TRUE	1	0.495954247426447	2		390	454	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965666	90965666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	90	746	0	ENST00000265433.3:c.1651del	p.Arg551GlyfsTer8	p.R551Gfs*8	ENST00000265433	NM_002485.4	551	Agg/gg	11/16	0.495954247426447	3	FACETS	0.839	0.746	0.937	0.419	0.373	0.469	CLONAL	1	TRUE	1	0.495954247426447	3		746	540	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	205	519	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.912	0.847	0.98	0.912	0.847	0.98	CLONAL	1	TRUE	1	0.495954247426447	2		524	906	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	154	817	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.495954247426447	1	FACETS	0.963	0.888	1	0.963	0.888	1	CLONAL	1	TRUE	0	0.495954247426447	1		817	485	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	360	736	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.977	1	1	0.997	1	CLONAL	2	TRUE	1	0.495954247426447	2		741	702	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344018	70344018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747113641	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	175	1004	2	ENST00000374080.3:c.1754G>A	p.Arg585Gln	p.R585Q	ENST00000374080		585	cGa/cAa	13/45	0.426440146581942	3	FACETS	0.807	0.742	0.874	0.403	0.371	0.437	CLONAL	1	TRUE	1	0.495954247426447	3		1006	1092	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	151	391	1	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.495954247426447	2		392	569	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726051	61726052	+	splice_region_variant,intron_variant	Splice_Region	DEL	AA	AA	-	rs372688892	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	101	485	1	ENST00000401558.2:c.591-4_591-3del		p.X197_splice	ENST00000401558	NM_003400.3	197			1	2	FACETS	0.868	0.78	0.961	0.868	0.78	0.961	CLONAL	1	TRUE	1	0.495954247426447	2		486	469	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	141	402	7	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.893	0.816	0.973	0.893	0.816	0.973	CLONAL	1	TRUE	1	0.495954247426447	2		409	637	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100728	8100728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs771019738	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	174	315	3	ENST00000346208.3:c.708del	p.Ser237AlafsTer28	p.S237Afs*28	ENST00000346208		234	ttC/tt	3/6	1	2	FACETS	0.856	0.789	0.925	0.856	0.789	0.925	CLONAL	1	TRUE	1	0.495954247426447	2		318	820	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849887	156849887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759190964	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	228	1038	2	ENST00000524377.1:c.2143G>A	p.Val715Met	p.V715M	ENST00000524377	NM_002529.3	715	Gtg/Atg	16/17	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.495954247426447	2		1040	896	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	163	1155	9	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	0.663	0.608	0.721	0.663	0.608	0.721	SUBCLONAL	1	TRUE	1	0.495954247426447	2		1164	991	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39772564	39772564	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	111	521	0	ENST00000288319.7:c.677del	p.Gly226ValfsTer65	p.G226Vfs*65	ENST00000288319	NM_182918.3	226	gGt/gt	6/10	1	2	FACETS	0.886	0.8	0.976	0.886	0.8	0.976	CLONAL	1	TRUE	1	0.495954247426447	2		521	505	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348566	89348568	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs753054998	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	239	1189	2	ENST00000301030.4:c.4382_4384del	p.Lys1461del	p.K1461del	ENST00000301030	NM_001256183.1	1461	aAGAga/aga	9/13	1	2	FACETS	0.868	0.809	0.927	0.868	0.809	0.927	CLONAL	1	TRUE	1	0.495954247426447	2		1191	1111	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777134	9777134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1445282622	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	193	1052	1	ENST00000377346.4:c.898C>T	p.Arg300Cys	p.R300C	ENST00000377346	NM_005026.3	300	Cgt/Tgt	7/24	1	2	FACETS	0.901	0.834	0.97	0.901	0.834	0.97	CLONAL	1	TRUE	1	0.495954247426447	2		1053	864	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100462	8100462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752779081	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	183	998	2	ENST00000346208.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000346208		146	Gcc/Acc	3/6	1	2	FACETS	0.946	0.875	1	0.946	0.875	1	CLONAL	1	TRUE	1	0.495954247426447	2		1000	780	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54963247	54963247	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	102	546	3	ENST00000312783.6:c.7C>T	p.Arg3Ter	p.R3*	ENST00000312783	NM_198436.1	3	Cga/Tga	3/10	1	2	FACETS	0.794	0.713	0.88	0.794	0.713	0.88	SUBCLONAL	1	TRUE	1	0.495954247426447	2		549	518	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163554	32163554	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	150	803	2	ENST00000375023.3:c.5672del	p.Gly1891AlafsTer13	p.G1891Afs*13	ENST00000375023	NM_004557.3	1891	gGc/gc	30/30	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.495954247426447	2		805	596	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5466787	5466787	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	81	291	0	ENST00000381577.3:c.813del	p.Lys271AsnfsTer44	p.K271Nfs*44	ENST00000381577	NM_014143.3	270	Aaa/aa	6/7	0.495954247426447	3	FACETS	1	0.954	1	0.574	0.509	0.642	CLONAL	1	TRUE	1	0.495954247426447	3		291	355	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991709	72991711	+	inframe_deletion	In_Frame_Del	DEL	GCA	GCA	-	rs752963945	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	64	210	10	ENST00000268489.5:c.2334_2336del	p.Ala784del	p.A784del	ENST00000268489	NM_006885.3	778	gcTGCg/gcg	2/10	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.495954247426447	2		220	230	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354393	354393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1488869543	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	245	1017	1	ENST00000262320.3:c.1165G>A	p.Ala389Thr	p.A389T	ENST00000262320	NM_003502.3	389	Gcg/Acg	5/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.495954247426447	2		1018	882	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962610	100962610	+	splice_region_variant,intron_variant	Splice_Region	DEL	A	A	-	rs761514775	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	108	584	0	ENST00000325455.5:c.1790-3del		p.X597_splice	ENST00000325455	NM_001202474.3	597			1	2	FACETS	0.869	0.784	0.959	0.869	0.784	0.959	CLONAL	1	TRUE	1	0.495954247426447	2		584	501	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829075	128829075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1247591045	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	11	50	0	ENST00000249373.3:c.88del	p.Ala30ArgfsTer25	p.A30Rfs*25	ENST00000249373	NM_005631.4	28	cGg/cg	1/12	1	2	FACETS	0.905	0.644	1	0.905	0.644	1	CLONAL	1	TRUE	1	0.495954247426447	2		50	49	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615143	43615143	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	62	1051	1	ENST00000355710.3:c.2557T>A	p.Ser853Thr	p.S853T	ENST00000355710	NM_020975.4	853	Tca/Aca	14/20	1	2	FACETS	0.299	0.257	0.344	0.299	0.257	0.344	SUBCLONAL	1	TRUE	1	0.495954247426447	2		1052	837	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209593	98209593	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	118	630	1	ENST00000331920.6:c.3945del	p.Tyr1316ThrfsTer56	p.Y1316Tfs*56	ENST00000331920	NM_000264.3	1315	ccC/cc	23/24	0.495954247426447	3	FACETS	0.871	0.787	0.959	0.435	0.393	0.48	CLONAL	1	TRUE	1	0.495954247426447	3		631	682	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228384	228384	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774160524	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	116	582	0	ENST00000264932.6:c.706G>A	p.Ala236Thr	p.A236T	ENST00000264932	NM_004168.2	236	Gca/Aca	6/15	1	2	FACETS	0.777	0.702	0.856	0.777	0.702	0.856	SUBCLONAL	1	TRUE	1	0.495954247426447	2		582	602	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78923344	78923344	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	119	644	0	ENST00000306801.3:c.3367C>T	p.Arg1123Ter	p.R1123*	ENST00000306801	NM_020761.2	1123	Cga/Tga	28/34	1	2	FACETS	0.983	0.893	1	0.983	0.893	1	CLONAL	1	TRUE	1	0.495954247426447	2		644	488	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38631981	38631981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1255149646	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	167	515	2	ENST00000299084.4:c.471del	p.Gln158SerfsTer16	p.Q158Sfs*16	ENST00000299084	NM_152594.2	156	cTt/ct	5/7	0.495954247426447	1	FACETS	0.885	0.818	0.955	0.885	0.818	0.955	CLONAL	1	TRUE	0	0.495954247426447	1		517	572	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391778	139391778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756571156	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	162	933	2	ENST00000277541.6:c.6413C>T	p.Pro2138Leu	p.P2138L	ENST00000277541	NM_017617.3	2138	cCg/cTg	34/34	0.495954247426447	3	FACETS	0.922	0.846	1	0.461	0.423	0.501	CLONAL	1	TRUE	1	0.495954247426447	3		935	884	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552705	226552705	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs776746526	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	88	498	0	ENST00000366794.5:c.2656G>A	p.Val886Met	p.V886M	ENST00000366794	NM_001618.3	886	Gtg/Atg	19/23	1	2	FACETS	0.861	0.768	0.96	0.861	0.768	0.96	CLONAL	1	TRUE	1	0.495954247426447	2		498	412	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104264048	104264048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	206	877	0	ENST00000369902.3:c.139G>A	p.Asp47Asn	p.D47N	ENST00000369902	NM_016169.3	47	Gac/Aac	1/12	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.495954247426447	2		877	824	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999225	100999225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	216	941	0	ENST00000325455.5:c.577C>T	p.Arg193Trp	p.R193W	ENST00000325455	NM_001202474.3	193	Cgg/Tgg	1/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.495954247426447	2		941	748	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143330	108143330	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555085890	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	119	680	0	ENST00000278616.4:c.3149T>C	p.Leu1050Pro	p.L1050P	ENST00000278616	NM_000051.3	1050	cTt/cCt	21/63	1	2	FACETS	0.848	0.768	0.932	0.848	0.768	0.932	CLONAL	1	TRUE	1	0.495954247426447	2		680	566	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864355	57864355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765569651	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	173	935	1	ENST00000228682.2:c.1832G>A	p.Arg611Gln	p.R611Q	ENST00000228682	NM_005269.2	611	cGg/cAg	12/12	1	2	FACETS	0.994	0.917	1	0.994	0.917	1	CLONAL	1	TRUE	1	0.495954247426447	2		936	702	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347947	73347947	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	64	362	0	ENST00000377767.4:c.1114C>G	p.Leu372Val	p.L372V	ENST00000377767	NM_014953.3	372	Ctc/Gtc	8/21	1	2	FACETS	0.755	0.657	0.859	0.755	0.657	0.859	SUBCLONAL	1	TRUE	1	0.495954247426447	2		362	342	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019540	42019540	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	160	996	1	ENST00000219905.7:c.3593T>C	p.Val1198Ala	p.V1198A	ENST00000219905	NM_001164273.1	1198	gTg/gCg	10/24	0.495954247426447	1	FACETS	0.841	0.775	0.909	0.841	0.775	0.909	CLONAL	1	TRUE	0	0.495954247426447	1		997	577	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881303	37881303	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	184	929	0	ENST00000269571.5:c.2495G>T	p.Gly832Val	p.G832V	ENST00000269571		832	gGg/gTg	21/27	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.495954247426447	2		929	684	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349246	15349246	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	140	712	0	ENST00000263377.2:c.4031C>G	p.Thr1344Ser	p.T1344S	ENST00000263377	NM_058243.2	1344	aCc/aGc	20/20	1	2	FACETS	0.927	0.847	1	0.927	0.847	1	CLONAL	1	TRUE	1	0.495954247426447	2		712	609	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260156	19260156	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1347318789	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	192	1005	0	ENST00000162023.5:c.137T>C	p.Ile46Thr	p.I46T	ENST00000162023		46	aTc/aCc	7/13	1	2	FACETS	0.881	0.815	0.949	0.881	0.815	0.949	CLONAL	1	TRUE	1	0.495954247426447	2		1005	879	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222938	36222938	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	245	1135	1	ENST00000222270.7:c.5572del	p.Arg1858ValfsTer37	p.R1858Vfs*37	ENST00000222270	NM_014727.1	1856	gCc/gc	27/37	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.495954247426447	2		1136	981	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142939	30142939	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1235761698	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	223	1155	1	ENST00000389048.3:c.587C>T	p.Ser196Leu	p.S196L	ENST00000389048	NM_004304.4	196	tCg/tTg	1/29	1	2	FACETS	0.979	0.912	1	0.979	0.912	1	CLONAL	1	TRUE	1	0.495954247426447	2		1156	919	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143212	30143212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772569032	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	156	647	1	ENST00000389048.3:c.314C>T	p.Ala105Val	p.A105V	ENST00000389048	NM_004304.4	105	gCg/gTg	1/29	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.495954247426447	2		648	560	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524960	187524960	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767643023	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	176	910	1	ENST00000441802.2:c.10720G>A	p.Val3574Met	p.V3574M	ENST00000441802	NM_005245.3	3574	Gtg/Atg	19/27	1	2	FACETS	0.909	0.839	0.982	0.909	0.839	0.982	CLONAL	1	TRUE	1	0.495954247426447	2		911	781	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294565	1294565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	185	721	0	ENST00000310581.5:c.436G>A	p.Asp146Asn	p.D146N	ENST00000310581	NM_198253.2	146	Gac/Aac	2/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.495954247426447	2		721	690	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751213	57751213	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	129	587	0	ENST00000274289.3:c.1654C>T	p.Gln552Ter	p.Q552*	ENST00000274289	NM_006622.3	552	Caa/Taa	12/14	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.495954247426447	2		587	508	SUCCESS
APC	324	MSKCC	GRCh37	5	112173849	112173849	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1554084263	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	94	568	0	ENST00000257430.4:c.2558A>G	p.Glu853Gly	p.E853G	ENST00000257430	NM_000038.5	853	gAg/gGg	16/16	1	2	FACETS	0.871	0.78	0.968	0.871	0.78	0.968	CLONAL	1	TRUE	1	0.495954247426447	2		568	435	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839708	27839708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773656938	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	140	745	4	ENST00000328488.2:c.386G>A	p.Arg129His	p.R129H	ENST00000328488	NM_003533.2	129	cGc/cAc	1/1	1	2	FACETS	0.972	0.889	1	0.972	0.889	1	CLONAL	1	TRUE	1	0.495954247426447	2		749	581	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969165	93969165	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	137	680	2	ENST00000369303.4:c.1831C>A	p.Pro611Thr	p.P611T	ENST00000369303	NM_004440.3	611	Cct/Act	10/17	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.495954247426447	2		682	462	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459537	50459537	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	136	568	0	ENST00000331340.3:c.826A>G	p.Ser276Gly	p.S276G	ENST00000331340	NM_006060.4	276	Agc/Ggc	7/8	1	2	FACETS	0.992	0.906	1	0.992	0.906	1	CLONAL	1	TRUE	1	0.495954247426447	2		568	553	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829122	128829122	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	24	44	0	ENST00000249373.3:c.130G>A	p.Ala44Thr	p.A44T	ENST00000249373	NM_005631.4	44	Gcg/Acg	1/12	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.495954247426447	2		44	73	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371725	55371725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	206	750	4	ENST00000297316.4:c.415C>T	p.Pro139Ser	p.P139S	ENST00000297316	NM_022454.3	139	Ccg/Tcg	2/2	0.495954247426447	3	FACETS	1	0.985	1	0.609	0.566	0.654	CLONAL	1	TRUE	1	0.495954247426447	3		754	851	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759607	133759607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763315791	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	200	1057	0	ENST00000318560.5:c.1930G>A	p.Gly644Arg	p.G644R	ENST00000318560	NM_005157.4	644	Ggg/Agg	11/11	0.495954247426447	3	FACETS	0.935	0.866	1	0.468	0.433	0.504	CLONAL	1	TRUE	1	0.495954247426447	3		1057	1076	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411521	63411521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs937173075	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	212	1047	0	ENST00000330258.3:c.1646G>A	p.Arg549Gln	p.R549Q	ENST00000330258	NM_152424.3	549	cGg/cAg	2/2	0.426440146581942	3	FACETS	0.915	0.849	0.984	0.458	0.424	0.492	CLONAL	1	TRUE	1	0.495954247426447	3		1047	1166	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608924	100608924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs128621204	NA	P-0021049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	64	833	1	ENST00000308731.7:c.1684C>T	p.Arg562Trp	p.R562W	ENST00000308731	NM_000061.2	562	Cgg/Tgg	17/19	0.426440146581942	3	FACETS	0.355	0.306	0.408	0.178	0.153	0.204	SUBCLONAL	1	TRUE	1	0.495954247426447	3		834	907	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0021177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	50	446	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.928	0.787	1	0.928	0.787	1	CLONAL	1	TRUE	1	0.20485676906619	2		446	526	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278180	15278180	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775425174	NA	P-0021177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	100	1175	4	ENST00000263388.2:c.5242C>T	p.Arg1748Cys	p.R1748C	ENST00000263388	NM_000435.2	1748	Cgt/Tgt	29/33	0.177961688044465	1	FACETS	0.977	0.872	1	0.977	0.872	1	CLONAL	1	TRUE	0	0.20485676906619	1		1179	897	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578266	7578266	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs942158624	NA	P-0021177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	170	976	1	ENST00000269305.4:c.583A>T	p.Ile195Phe	p.I195F	ENST00000269305	NM_001126112.2	195	Atc/Ttc	6/11	0.20485676906619	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.20485676906619	2		977	776	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199310	16199310	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0021177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	35	493	0	ENST00000375759.3:c.84-1G>T		p.X28_splice	ENST00000375759	NM_015001.2	28			1	2	FACETS	0.696	0.57	0.838	0.696	0.57	0.838	SUBCLONAL	1	TRUE	1	0.20485676906619	2		493	491	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057835	27057835	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	106	1421	0	ENST00000324856.7:c.1543C>G	p.Gln515Glu	p.Q515E	ENST00000324856	NM_006015.4	515	Cag/Gag	3/20	1	2	FACETS	0.895	0.8	0.996	0.895	0.8	0.996	CLONAL	1	TRUE	1	0.20485676906619	2		1421	1156	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65312358	65312358	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs758681867	NA	P-0021177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	71	850	0	ENST00000342505.4:c.1961A>G	p.Tyr654Cys	p.Y654C	ENST00000342505	NM_002227.2	654	tAt/tGt	14/25	1	2	FACETS	0.917	0.799	1	0.917	0.799	1	CLONAL	1	TRUE	1	0.20485676906619	2		850	756	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623572	43623572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760625882	NA	P-0021177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	55	574	1	ENST00000355710.3:c.3200C>T	p.Pro1067Leu	p.P1067L	ENST00000355710	NM_020975.4	1067	cCg/cTg	20/20	0.177961688044465	1	FACETS	0.879	0.752	1	0.879	0.752	1	CLONAL	1	TRUE	0	0.20485676906619	1		575	548	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420233	420233	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	novel	NA	P-0021177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	75	533	0	ENST00000399788.2:c.3037-3C>T		p.X1013_splice	ENST00000399788	NM_001042603.1	1013			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.20485676906619	2		533	611	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233496	69233496	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	59	660	1	ENST00000462284.1:c.1361G>A	p.Gly454Asp	p.G454D	ENST00000462284	NM_002392.5	454	gGt/gAt	11/11	1	2	FACETS	0.864	0.742	0.996	0.864	0.742	0.996	CLONAL	1	TRUE	1	0.20485676906619	2		661	667	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068451	16068451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	14	196	0	ENST00000268712.3:c.460G>A	p.Glu154Lys	p.E154K	ENST00000268712	NM_006311.3	154	Gaa/Aaa	5/46	0.20485676906619	2	FACETS	0.768	0.557	1	0.384	0.278	0.511	CLONAL	1	TRUE	0	0.20485676906619	2		196	178	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748601	40748601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200545231	NA	P-0021177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	39	446	0	ENST00000373198.4:c.2915G>A	p.Arg972Gln	p.R972Q	ENST00000373198	NM_133170.3	972	cGa/cAa	21/32	0.20485676906619	1	FACETS	0.695	0.575	0.828	0.695	0.575	0.828	SUBCLONAL	1	TRUE	0	0.20485676906619	1		446	492	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186501409	186501409	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	100	511	0	ENST00000323963.5:c.10G>T	p.Gly4Cys	p.G4C	ENST00000323963		4	Ggc/Tgc	1/11	0.20485676906619	6	FACETS	0.971	0.867	1	0.647	0.578	0.72	CLONAL	2	TRUE	3	0.20485676906619	6		511	709	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323216	31323216	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	73	1014	1	ENST00000412585.2:c.773G>C	p.Arg258Thr	p.R258T	ENST00000412585	NM_005514.6	258	aGa/aCa	4/8	1	2	FACETS	0.822	0.717	0.935	0.822	0.717	0.935	CLONAL	1	TRUE	1	0.20485676906619	2		1015	867	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992752	68992752	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	97	1179	1	ENST00000288368.4:c.1717A>G	p.Asn573Asp	p.N573D	ENST00000288368	NM_024870.2	573	Aat/Gat	16/40	1	2	FACETS	0.92	0.819	1	0.92	0.819	1	CLONAL	1	TRUE	1	0.20485676906619	2		1180	1029	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971152	21971164	+	frameshift_variant	Frame_Shift_Del	DEL	TCCGCGCCGTGGA	TCCGCGCCGTGGA	CG	novel	NA	P-0021177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	65	670	2	ENST00000304494.5:c.194_206delinsCG	p.Leu65ProfsTer51	p.L65Pfs*51	ENST00000304494	NM_000077.4	65	cTCCACGGCGCGGAg/cCGg	2/3	0.177961688044465	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.20485676906619	1		672	530	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0021217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	461	354	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.234252169846829	3	FACETS	0.923	0.89	0.955	1	0.998	1	CLONAL	6	TRUE	1	0.246778412913091	3		354	758	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	107	215	0				ENST00000310581	NM_198253.2	-/1132			0.235366998875888	3	FACETS	0.939	0.845	1	0.939	0.845	1	CLONAL	2	TRUE	1	0.246778412913091	3		215	519	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0021217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	168	908	0	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	0.221217010841523	2	FACETS	0.942	0.868	1	0.942	0.868	1	CLONAL	2	TRUE	0	0.246778412913091	2		908	723	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971039	21971040	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0021217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	142	707	0	ENST00000304494.5:c.318dup	p.Arg107AlafsTer13	p.R107Afs*13	ENST00000304494	NM_000077.4	106	-/G	2/3	0.229429395810553	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.246778412913091	2		707	553	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820588	44820589	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	61	501	0	ENST00000377967.4:c.289dup	p.Cys97LeufsTer29	p.C97Lfs*29	ENST00000377967	NM_021140.2	95	-/T	3/29	0.195110619209947	2	FACETS	1	0.945	1			1	CLONAL	2	TRUE	NA	0.246778412913091	2		501	215	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0021390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	196	660	2	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	0.582980771553544	1	FACETS	0.953	0.893	1	0.953	0.893	1	CLONAL	1	TRUE	0	0.632957861665229	1		662	444	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954915	2954915	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	577	626	2	ENST00000396946.4:c.2795G>T	p.Arg932Leu	p.R932L	ENST00000396946	NM_032415.4	932	cGg/cTg	21/25	0.632957861665229	3	FACETS	0.965	0.938	0.991	0.965	0.938	0.991	CLONAL	3	TRUE	0	0.632957861665229	3		628	829	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39638005	39638005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	303	480	0	ENST00000262039.4:c.2422C>T	p.His808Tyr	p.H808Y	ENST00000262039	NM_002647.2	808	Cac/Tac	22/25	0.571903126140342	4	FACETS	0.929	0.879	0.981	0.929	0.879	0.981	CLONAL	2	TRUE	2	0.632957861665229	4		480	841	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923102	48923102	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	257	333	0	ENST00000267163.4:c.550G>T	p.Glu184Ter	p.E184*	ENST00000267163	NM_000321.2	184	Gaa/Taa	6/27	0.590543422260807	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.632957861665229	2		333	398	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202634	108202634	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs864622368	NA	P-0021390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	227	384	0	ENST00000278616.4:c.7658C>A	p.Pro2553His	p.P2553H	ENST00000278616	NM_000051.3	2553	cCc/cAc	52/63	0.632957861665229	3	FACETS	0.854	0.802	0.906	0.854	0.802	0.906	CLONAL	2	TRUE	1	0.632957861665229	3		384	553	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503222	125503222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	88	276	1	ENST00000428830.2:c.589G>A	p.Val197Ile	p.V197I	ENST00000428830	NM_001114121.2	197	Gta/Ata	6/14	0.632957861665229	3	FACETS	0.931	0.831	1	0.466	0.415	0.519	CLONAL	1	TRUE	1	0.632957861665229	3		277	393	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644940	67644940	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	388	488	0	ENST00000264010.4:c.205A>T	p.Thr69Ser	p.T69S	ENST00000264010	NM_006565.3	69	Acc/Tcc	3/12	0.556402951569767	3	FACETS	0.894	0.861	0.926	0.894	0.861	0.926	CLONAL	3	TRUE	0	0.632957861665229	3		488	602	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224517	36224517	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	264	890	1	ENST00000222270.7:c.6979A>G	p.Lys2327Glu	p.K2327E	ENST00000222270	NM_014727.1	2327	Aaa/Gaa	29/37	1	2	FACETS	0.99	0.93	1	0.99	0.93	1	CLONAL	1	TRUE	1	0.632957861665229	2		891	843	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128028917	128028917	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	158	513	0	ENST00000285398.2:c.1940A>T	p.Lys647Ile	p.K647I	ENST00000285398	NM_000122.1	647	aAa/aTa	12/15	0.632957861665229	3	FACETS	0.955	0.878	1	0.478	0.439	0.518	CLONAL	1	TRUE	1	0.632957861665229	3		513	688	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098936	178098936	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	264	364	0	ENST00000397062.3:c.109T>G	p.Phe37Val	p.F37V	ENST00000397062	NM_006164.4	37	Ttt/Gtt	2/5	0.632957861665229	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.632957861665229	3		364	536	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379374	225379375	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1553523940	NA	P-0021390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	353	573	0	ENST00000264414.4:c.493_494del	p.Leu165IlefsTer37	p.L165Ifs*37	ENST00000264414	NM_003590.4	165	CTa/a	4/16	0.632957861665229	3	FACETS	0.892	0.85	0.935	0.892	0.85	0.935	CLONAL	2	TRUE	1	0.632957861665229	3		573	823	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57474003	57474003	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	243	340	0	ENST00000371085.3:c.220G>A	p.Glu74Lys	p.E74K	ENST00000371085	NM_000516.4	74	Gaa/Aaa	3/13	0.632957861665229	3	FACETS	0.993	0.938	1	0.993	0.938	1	CLONAL	2	TRUE	1	0.632957861665229	3		340	509	SUCCESS
ATR	545	MSKCC	GRCh37	3	142212009	142212009	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	316	492	0	ENST00000350721.4:c.6043A>T	p.Asn2015Tyr	p.N2015Y	ENST00000350721	NM_001184.3	2015	Aac/Tac	35/47	0.571903126140342	4	FACETS	0.988	0.937	1	0.988	0.937	1	CLONAL	2	TRUE	2	0.632957861665229	4		492	825	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535413	187535413	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	425	466	0	ENST00000441802.2:c.9161C>G	p.Ser3054Cys	p.S3054C	ENST00000441802	NM_005245.3	3054	tCt/tGt	12/27	0.616073115371424	3	FACETS	0.968	0.936	0.998	0.968	0.936	0.998	CLONAL	3	TRUE	0	0.632957861665229	3		466	609	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045769	26045769	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	245	337	0	ENST00000540144.1:c.131C>A	p.Pro44Gln	p.P44Q	ENST00000540144	NM_003531.2	44	cCg/cAg	1/1	0.529129508323152	3	FACETS	0.864	0.824	0.904	0.864	0.824	0.904	CLONAL	3	TRUE	0	0.632957861665229	3		337	393	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509848	106509848	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1043937061	NA	P-0021390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	565	615	0	ENST00000359195.3:c.1842G>T	p.Arg614Ser	p.R614S	ENST00000359195	NM_002649.2	614	agG/agT	2/11	0.632957861665229	4	FACETS	0.867	0.836	0.898	0.867	0.836	0.898	CLONAL	3	TRUE	1	0.632957861665229	4		615	1121	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127920550	127920550	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	178	542	0	ENST00000373547.4:c.349A>G	p.Arg117Gly	p.R117G	ENST00000373547	NM_002721.4	117	Aga/Gga	4/7	0.632957861665229	4	FACETS	0.985	0.908	1	0.328	0.302	0.356	CLONAL	1	TRUE	1	0.632957861665229	4		542	932	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760307	133760307	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	168	552	0	ENST00000318560.5:c.2630G>T	p.Arg877Met	p.R877M	ENST00000318560	NM_005157.4	877	aGg/aTg	11/11	0.632957861665229	4	FACETS	1	0.945	1	0.345	0.317	0.374	CLONAL	1	TRUE	1	0.632957861665229	4		552	838	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27086255	27087277	+	intron_variant	Intron	DEL	CCAAGTTCTCACTGAAAAACATAAAAGCTGGGAAAAAAACAGAATTTGTTCAATTGGCAAACATTTGTTGATTACTGTTATAGACCAGGTGTTAGGAGTGTAGTCCCAGACCTTCTTGGCAGTTAAGAAATTGTCTTTCTCATCCAATGTCTCTCTTTCTTACCTCCTACCCCTTATGTTGCAAAGTATGGTGACTTGGAGTGAGTCCTTGGCAAATGGAGGCTGTGATAATCTATAGTAATAATCATCATTGTAATATATAATAGAAGGAGAGGGGATCTATAAATGTTTCCCAAACTTGTTAACATTCTCTTGTAGCTCCTGGTGCCATCCTGGCAGCATTTTGTAAAGTTTTGCTATTAGAAAAGAACTAAAGCCTCACTGAAATAGTTGCTTTCTTATGACTGTAGAAGTTATGACTGGGAAAGAAGACAAAAGTGCTAGATCTGCTTCTGAGGGGATAGAATAGGAGTCAGCAAAACTCAGTCACACCATTGTTTGTATATTGTCTGACTACTGTTGCACTATAGTGTCAGAGTTGAGTAGTTTTGAAGGAGGCTTTATGGCCCACAAAGGTCTAATATATATTCCACCTGGTCCTTAACAGAGTTTGCCATATGTAAGTTATAGTATGATGACTAGGGCCGGGCGCGGTGGCTCACGCCTATAATCCCAGCACTTTGGGAGGCCAAGGAGGGTGGATCACCTGAGGTCGGGAGTTCAAGACCAGCCTGACCAACATGGAGAAAACCCGTCTCTACTAAAAATACAAAAATTTAGCCGGGCGTGGTGGTGCTTGCCTGTAATCCCAGCCACTCGGGAGGCTGAGGCAGGAGAATTGCTTGAACCCAGGAGTCAGAGGTTGCGATGAGCCGAGACGTGCCATTGCACTCCAGCCTGGGCAACGAGTGAAACACTGTCTCAAAAAAAAAAATTTTTTTTTTTAATAAAAATAGTATCATGACTAAAGAACGTGTGTGATGTATTTGCTCTTGGTTGTTTAAGGAAAATGCTAAGCAAGTA	CCAAGTTCTCACTGAAAAACATAAAAGCTGGGAAAAAAACAGAATTTGTTCAATTGGCAAACATTTGTTGATTACTGTTATAGACCAGGTGTTAGGAGTGTAGTCCCAGACCTTCTTGGCAGTTAAGAAATTGTCTTTCTCATCCAATGTCTCTCTTTCTTACCTCCTACCCCTTATGTTGCAAAGTATGGTGACTTGGAGTGAGTCCTTGGCAAATGGAGGCTGTGATAATCTATAGTAATAATCATCATTGTAATATATAATAGAAGGAGAGGGGATCTATAAATGTTTCCCAAACTTGTTAACATTCTCTTGTAGCTCCTGGTGCCATCCTGGCAGCATTTTGTAAAGTTTTGCTATTAGAAAAGAACTAAAGCCTCACTGAAATAGTTGCTTTCTTATGACTGTAGAAGTTATGACTGGGAAAGAAGACAAAAGTGCTAGATCTGCTTCTGAGGGGATAGAATAGGAGTCAGCAAAACTCAGTCACACCATTGTTTGTATATTGTCTGACTACTGTTGCACTATAGTGTCAGAGTTGAGTAGTTTTGAAGGAGGCTTTATGGCCCACAAAGGTCTAATATATATTCCACCTGGTCCTTAACAGAGTTTGCCATATGTAAGTTATAGTATGATGACTAGGGCCGGGCGCGGTGGCTCACGCCTATAATCCCAGCACTTTGGGAGGCCAAGGAGGGTGGATCACCTGAGGTCGGGAGTTCAAGACCAGCCTGACCAACATGGAGAAAACCCGTCTCTACTAAAAATACAAAAATTTAGCCGGGCGTGGTGGTGCTTGCCTGTAATCCCAGCCACTCGGGAGGCTGAGGCAGGAGAATTGCTTGAACCCAGGAGTCAGAGGTTGCGATGAGCCGAGACGTGCCATTGCACTCCAGCCTGGGCAACGAGTGAAACACTGTCTCAAAAAAAAAAATTTTTTTTTTTAATAAAAATAGTATCATGACTAAAGAACGTGTGTGATGTATTTGCTCTTGGTTGTTTAAGGAAAATGCTAAGCAAGTA	-	novel	NA	P-0021390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	0	261	0	0	ENST00000324856.7:c.1921-1092_1921-70del		p.*641*	ENST00000324856	NM_006015.4	-/2285			NA	2	FACETS	1	0.997	1			1	INDETERMINATE	3	TRUE	NA	0.632957861665229	2		0	261	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737367	145737367	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	86	734	0	ENST00000428558.2:c.3320A>C	p.Tyr1107Ser	p.Y1107S	ENST00000428558	NM_004260.3	1107	tAc/tCc	20/22	0.274415914951329	5	FACETS	0.526	0.464	0.593			1	INDETERMINATE	1	TRUE	NA	0.632957861665229	5		734	1007	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737370	145737370	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	75	715	0	ENST00000428558.2:c.3317G>T	p.Arg1106Leu	p.R1106L	ENST00000428558	NM_004260.3	1106	cGc/cTc	20/22	0.274415914951329	5	FACETS	0.47	0.411	0.534			1	INDETERMINATE	1	TRUE	NA	0.632957861665229	5		715	983	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0021433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	553	772	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.74041786501825	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.754960159975414	2		772	729	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	117	225	1	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	0.691723391709861	3	FACETS	0.795	0.72	0.874	0.398	0.36	0.437	SUBCLONAL	1	TRUE	1	0.754960159975414	3		226	537	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560500	65560500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs387906651	NA	P-0021433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	384	621	1	ENST00000358664.4:c.97C>T	p.Arg33Ter	p.R33*	ENST00000358664	NM_002382.4	33	Cga/Tga	3/5	0.74041786501825	2	FACETS	0.958	0.927	0.988	0.958	0.927	0.988	CLONAL	2	TRUE	0	0.754960159975414	2		622	531	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0021433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	44	196	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.736934233233201	2	FACETS	1	0.905	1	0.53	0.458	0.604	CLONAL	1	TRUE	0	0.754960159975414	2		196	110	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729601	41729601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	445	617	1	ENST00000242208.4:c.928C>T	p.Arg310Trp	p.R310W	ENST00000242208	NM_002192.2	310	Cgg/Tgg	3/3	0.691723391709861	3	FACETS	0.981	0.943	1	0.981	0.943	1	CLONAL	2	TRUE	1	0.754960159975414	3		618	828	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395000	395001	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	315	457	3	ENST00000380956.4:c.402dup	p.Gly135ArgfsTer77	p.G135Rfs*77	ENST00000380956	NM_001195286.1	132	-/A	3/9	NA	2	FACETS	0.846	0.812	0.88			1	INDETERMINATE	2	TRUE	NA	0.754960159975414	2		460	493	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641560	47641560	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	T	rs193922376	NA	P-0021433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	94	223	0	ENST00000233146.2:c.942+3A>T		p.X314_splice	ENST00000233146	NM_000251.2	314			0.736934233233201	2	FACETS	1	0.983	1	0.692	0.633	0.75	CLONAL	1	TRUE	0	0.754960159975414	2		223	180	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699275	18699275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	213	446	0	ENST00000266497.5:c.3376C>T	p.Pro1126Ser	p.P1126S	ENST00000266497		1126	Cct/Tct	24/31	0.736934233233201	2	FACETS	0.976	0.934	1	0.976	0.934	1	CLONAL	2	TRUE	0	0.754960159975414	2		446	289	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624458	21624458	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	322	791	0	ENST00000421138.2:c.1571C>T	p.Ala524Val	p.A524V	ENST00000421138		524	gCa/gTa	14/16	0.736934233233201	2	FACETS	0.906	0.871	0.939	0.906	0.871	0.939	CLONAL	2	TRUE	0	0.754960159975414	2		791	471	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885560	111885560	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	604	870	2	ENST00000341259.2:c.1337T>A	p.Ile446Asn	p.I446N	ENST00000341259	NM_005475.2	446	aTc/aAc	7/8	0.736934233233201	2	FACETS	0.977	0.952	1	0.977	0.952	1	CLONAL	2	TRUE	0	0.754960159975414	2		872	819	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557553	21557553	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	591	723	0	ENST00000382592.4:c.2292del	p.Glu765SerfsTer11	p.E765Sfs*11	ENST00000382592	NM_014572.2	764	ccT/cc	5/8	0.736934233233201	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.754960159975414	2		723	777	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100122	30100122	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1042770328	NA	P-0021433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	419	761	0	ENST00000331968.5:c.1498G>A	p.Val500Met	p.V500M	ENST00000331968	NM_002742.2	500	Gtg/Atg	10/18	0.74041786501825	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.754960159975414	2		761	528	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422129	81422129	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	448	656	0	ENST00000298171.2:c.105G>C	p.Glu35Asp	p.E35D	ENST00000298171	NM_000369.2	35	gaG/gaC	1/10	0.74041786501825	2	FACETS	0.898	0.869	0.926	0.898	0.869	0.926	CLONAL	2	TRUE	0	0.754960159975414	2		656	661	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041641	14041641	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	182	527	0	ENST00000311895.7:c.2188A>G	p.Ser730Gly	p.S730G	ENST00000311895	NM_005236.2	730	Agt/Ggt	11/11	0.736934233233201	2	FACETS	0.929	0.864	0.995	0.464	0.432	0.498	CLONAL	1	TRUE	0	0.754960159975414	2		527	519	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661869	29661880	+	inframe_deletion	In_Frame_Del	DEL	ACACCTTTGTTT	ACACCTTTGTTT	-	novel	NA	P-0021433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	243	638	0	ENST00000356175.3:c.5763_5774del	p.His1922_Leu1925del	p.H1922_L1925del	ENST00000356175	NM_000267.3	1921	aaACACCTTTGTTTg/aag	39/57	NA	2	FACETS	1	0.967	1			1	INDETERMINATE	2	TRUE	NA	0.754960159975414	2		638	320	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097101	11097101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1195533596	NA	P-0021433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	252	762	1	ENST00000358026.2:c.592G>A	p.Asp198Asn	p.D198N	ENST00000358026	NM_001128849.1	198	Gac/Aac	4/36	0.736934233233201	2	FACETS	0.962	0.905	1	0.481	0.452	0.51	CLONAL	1	TRUE	0	0.754960159975414	2		763	694	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292486	15292486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	294	830	1	ENST00000263388.2:c.2693C>T	p.Pro898Leu	p.P898L	ENST00000263388	NM_000435.2	898	cCg/cTg	17/33	0.736934233233201	2	FACETS	0.999	0.944	1	0.499	0.472	0.527	CLONAL	1	TRUE	0	0.754960159975414	2		831	780	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967090	18967091	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0021433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	239	772	0	ENST00000262803.5:c.1814_1815dup	p.Leu606SerfsTer3	p.L606Sfs*3	ENST00000262803	NM_002911.3	602	gca/gcAGa	13/24	0.736934233233201	2	FACETS	0.808	0.756	0.86	0.404	0.378	0.43	CLONAL	1	TRUE	0	0.754960159975414	2		772	784	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968249	18968249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	242	710	2	ENST00000262803.5:c.2089C>T	p.Arg697Cys	p.R697C	ENST00000262803	NM_002911.3	697	Cgc/Tgc	15/24	0.736934233233201	2	FACETS	0.985	0.926	1	0.492	0.463	0.523	CLONAL	1	TRUE	0	0.754960159975414	2		712	651	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741169	40741169	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0021433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	239	757	2	ENST00000392038.2:c.1263+1G>A		p.X421_splice	ENST00000392038	NM_001626.4	421			0.736934233233201	2	FACETS	1	0.96	1	0.513	0.482	0.544	CLONAL	1	TRUE	0	0.754960159975414	2		759	617	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867085	45867085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764502577	NA	P-0021433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	557	678	0	ENST00000391945.4:c.1034G>A	p.Arg345His	p.R345H	ENST00000391945	NM_000400.3	345	cGt/cAt	11/23	0.736934233233201	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.754960159975414	2		678	738	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989533	212989533	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	169	445	0	ENST00000342788.4:c.178A>G	p.Met60Val	p.M60V	ENST00000342788	NM_005235.2	60	Atg/Gtg	2/28	0.736934233233201	2	FACETS	1	0.97	1	0.538	0.5	0.576	CLONAL	1	TRUE	0	0.754960159975414	2		445	416	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39708793	39708793	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	74	471	0	ENST00000361337.2:c.404C>A	p.Pro135Gln	p.P135Q	ENST00000361337	NM_003286.2	135	cCa/cAa	6/21	0.74041786501825	2	FACETS	0.827	0.735	0.923	0.414	0.367	0.462	CLONAL	1	TRUE	0	0.754960159975414	2		471	237	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275688	41275688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	210	630	1	ENST00000349496.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000349496	NM_001904.3	528	cGt/cAt	10/15	0.74041786501825	2	FACETS	0.893	0.834	0.953	0.446	0.417	0.477	CLONAL	1	TRUE	0	0.754960159975414	2		631	623	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197361	26197361	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	214	508	0	ENST00000356476.2:c.118del	p.His40ThrfsTer23	p.H40Tfs*23	ENST00000356476		40	Cac/ac	1/1	0.639314913602131	3	FACETS	1	0.986	1	0.399	0.372	0.426	CLONAL	1	TRUE	0	0.754960159975414	3		508	653	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005614	150005615	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0021433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	260	397	0	ENST00000253339.5:c.610_611del	p.Pro205GlnfsTer24	p.P205Qfs*24	ENST00000253339		204	AGt/t	3/7	0.747631021585194	2	FACETS	0.957	0.919	0.993	0.957	0.919	0.993	CLONAL	2	TRUE	0	0.754960159975414	2		397	360	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851502	151851502	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	137	450	0	ENST00000262189.6:c.11989A>G	p.Thr3997Ala	p.T3997A	ENST00000262189	NM_170606.2	3997	Act/Gct	47/59	0.691723391709861	3	FACETS	0.971	0.888	1	0.485	0.444	0.528	CLONAL	1	TRUE	1	0.754960159975414	3		450	515	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868457	117868459	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	rs1280816264	NA	P-0021433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	323	718	0	ENST00000297338.2:c.883_885del	p.Thr295del	p.T295del	ENST00000297338	NM_006265.2	295	ACA/-	8/14	0.74041786501825	2	FACETS	0.955	0.921	0.988	0.955	0.921	0.988	CLONAL	2	TRUE	0	0.754960159975414	2		718	448	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970901	21970901	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs45476696	NA	P-0021433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	630	765	0	ENST00000304494.5:c.457G>T	p.Asp153Tyr	p.D153Y	ENST00000304494	NM_000077.4	153	Gac/Tac	2/3	0.736934233233201	2	FACETS	0.961	0.937	0.985	0.961	0.937	0.985	CLONAL	2	TRUE	0	0.754960159975414	2		765	868	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639991	93639991	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	152	462	0	ENST00000375746.1:c.1320G>T	p.Glu440Asp	p.E440D	ENST00000375746	NM_001174167.1	440	gaG/gaT	10/14	0.736934233233201	2	FACETS	0.973	0.899	1	0.486	0.449	0.524	CLONAL	1	TRUE	0	0.754960159975414	2		462	414	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0021605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	96	282	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.281770116935371	2		282	652	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295230	+	upstream_gene_variant	5'Flank	TNP	GGG	GGG	AGA	novel	NA	P-0021605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	52	646	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.643	0.547	0.748	0.643	0.547	0.748	SUBCLONAL	1	TRUE	1	0.281770116935371	2		646	574	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0021605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	118	433	3	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	0.162807593239136	2	FACETS	1	0.981	1	0.683	0.618	0.752	INDETERMINATE	1	TRUE	0	0.281770116935371	2		436	613	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879904	44879904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs912069418	NA	P-0021605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	171	740	3	ENST00000377967.4:c.493C>T	p.Arg165Ter	p.R165*	ENST00000377967	NM_021140.2	165	Cga/Tga	6/29	0.281770116935371	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.281770116935371	1		743	794	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434325	49434325	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	85	922	0	ENST00000301067.7:c.7228C>T	p.Arg2410Ter	p.R2410*	ENST00000301067	NM_003482.3	2410	Cga/Tga	31/54	1	2	FACETS	0.652	0.575	0.734	0.652	0.575	0.734	SUBCLONAL	1	TRUE	1	0.281770116935371	2		922	926	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436952	110436954	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	novel	NA	P-0021605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	23	470	0	ENST00000375856.3:c.1447_1449del	p.Ser483del	p.S483del	ENST00000375856	NM_003749.2	483	AGC/-	1/2	0.145768724220454	2	FACETS	0.364	0.283	0.459	0.182	0.141	0.23	INDETERMINATE	1	TRUE	0	0.281770116935371	2		470	448	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808916	1808916	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0021605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	54	931	0	ENST00000260795.2:c.2348C>G	p.Ser783Ter	p.S783*	ENST00000260795		783	tCa/tGa	17/17	0.162807593239136	2	FACETS	0.444	0.378	0.517	0.222	0.189	0.259	INDETERMINATE	1	TRUE	0	0.281770116935371	2		931	863	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820527	44820527	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0021605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	61	615	0	ENST00000377967.4:c.226-2A>G		p.X76_splice	ENST00000377967	NM_021140.2	76			0.281770116935371	1	FACETS	0.569	0.49	0.654	0.569	0.49	0.654	SUBCLONAL	1	TRUE	0	0.281770116935371	1		615	654	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44896900	44896905	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TTCAAT	TTCAAT	-	novel	NA	P-0021605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	79	809	0	ENST00000377967.4:c.624_629del	p.Gln208_Phe209del	p.Q208_F209del	ENST00000377967	NM_021140.2	207	aTTCAATtt/att	8/29	0.281770116935371	1	FACETS	0.528	0.463	0.598	0.528	0.463	0.598	SUBCLONAL	1	TRUE	0	0.281770116935371	1		809	913	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524576	103524576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	31	284	0	ENST00000355739.4:c.2707C>T	p.Pro903Ser	p.P903S	ENST00000355739	NM_000123.3	903	Cca/Tca	13/15	1	2	FACETS	0.677	0.549	0.821	0.677	0.549	0.821	SUBCLONAL	1	TRUE	1	0.30847442743585	2		284	297	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892299	9892299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs796052549	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	64	475	0	ENST00000330684.3:c.2191G>A	p.Asp731Asn	p.D731N	ENST00000330684	NM_001134407.1	731	Gat/Aat	11/13	1	2	FACETS	0.943	0.819	1	0.943	0.819	1	CLONAL	1	TRUE	1	0.30847442743585	2		475	440	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	129	779	1	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	1	2	FACETS	0.977	0.886	1	0.977	0.886	1	CLONAL	1	TRUE	1	0.30847442743585	2		780	856	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518175	8518175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1354824749	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	155	453	1	ENST00000356435.5:c.1216G>A	p.Glu406Lys	p.E406K	ENST00000356435		406	Gaa/Aaa	10/35	0.267325039675376	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.30847442743585	2		454	473	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	120	586	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.941	0.849	1	0.941	0.849	1	CLONAL	1	TRUE	1	0.30847442743585	2		586	827	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509849	106509849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426277818	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	94	712	0	ENST00000359195.3:c.1843G>A	p.Glu615Lys	p.E615K	ENST00000359195	NM_002649.2	615	Gaa/Aaa	2/11	1	2	FACETS	0.831	0.74	0.929	0.831	0.74	0.929	CLONAL	1	TRUE	1	0.30847442743585	2		712	733	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317926	8317926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	140	337	0	ENST00000356435.5:c.5687C>T	p.Ser1896Phe	p.S1896F	ENST00000356435		1896	tCc/tTc	35/35	0.267325039675376	2	FACETS	0.921	0.844	1	0.921	0.844	1	CLONAL	2	TRUE	0	0.30847442743585	2		337	493	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041073	29041073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	59	542	0	ENST00000282397.4:c.355G>A	p.Glu119Lys	p.E119K	ENST00000282397	NM_002019.4	119	Gaa/Aaa	3/30	1	2	FACETS	0.789	0.68	0.907	0.789	0.68	0.907	CLONAL	1	TRUE	1	0.30847442743585	2		542	485	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971029	21971029	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519852	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	215	564	0	ENST00000304494.5:c.329G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tGg/tAg	2/3	0.267325039675376	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.30847442743585	2		564	581	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612073	189612073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142762485	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	91	538	0	ENST00000264731.3:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000264731	NM_003722.4	609	Gaa/Aaa	14/14	1	2	FACETS	0.802	0.712	0.898	0.802	0.712	0.898	CLONAL	1	TRUE	1	0.30847442743585	2		538	736	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730850	40730850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	131	840	0	ENST00000373198.4:c.3685G>A	p.Asp1229Asn	p.D1229N	ENST00000373198	NM_133170.3	1229	Gac/Aac	27/32	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.30847442743585	2		840	791	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032045	26032045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	63	493	0	ENST00000244661.2:c.244G>A	p.Asp82Asn	p.D82N	ENST00000244661	NM_003537.3	82	Gat/Aat	1/1	0.30847442743585	3	FACETS	0.868	0.752	0.995	0.434	0.376	0.498	CLONAL	1	TRUE	1	0.30847442743585	3		493	543	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572483	95572483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	70	521	0	ENST00000393063.1:c.2882C>T	p.Pro961Leu	p.P961L	ENST00000393063	NM_030621.3	961	cCt/cTt	19/28	1	2	FACETS	0.953	0.834	1	0.953	0.834	1	CLONAL	1	TRUE	1	0.30847442743585	2		521	476	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858390	9858390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	60	485	0	ENST00000330684.3:c.3011C>T	p.Ser1004Phe	p.S1004F	ENST00000330684	NM_001134407.1	1004	tCc/tTc	13/13	1	2	FACETS	0.799	0.689	0.918	0.799	0.689	0.918	CLONAL	1	TRUE	1	0.30847442743585	2		485	487	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994833	73994833	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	24	249	0	ENST00000318443.5:c.317C>T	p.Ser106Phe	p.S106F	ENST00000318443	NM_001024736.1	106	tCc/tTc	3/10	1	2	FACETS	0.64	0.504	0.797	0.64	0.504	0.797	SUBCLONAL	1	TRUE	1	0.30847442743585	2		249	243	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353866	15353866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	137	737	0	ENST00000263377.2:c.3014C>T	p.Ser1005Phe	p.S1005F	ENST00000263377	NM_058243.2	1005	tCc/tTc	14/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.30847442743585	2		737	714	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520257	9520257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	93	504	1	ENST00000353224.5:c.2012C>T	p.Ser671Leu	p.S671L	ENST00000353224	NM_177990.2	671	tCa/tTa	10/10	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.30847442743585	2		505	520	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164451	36164451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	54	283	0	ENST00000300305.3:c.1424C>T	p.Ala475Val	p.A475V	ENST00000300305		475	gCc/gTc	8/8	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.30847442743585	2		283	321	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956149	55956149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	98	652	0	ENST00000263923.4:c.3166G>A	p.Asp1056Asn	p.D1056N	ENST00000263923	NM_002253.2	1056	Gat/Aat	23/30	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.30847442743585	2		652	612	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630059	187630059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866303516	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	119	695	0	ENST00000441802.2:c.923C>T	p.Ser308Phe	p.S308F	ENST00000441802	NM_005245.3	308	tCc/tTc	2/27	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.30847442743585	2		695	633	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684323	29684323	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs567988442	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	91	633	0	ENST00000356175.3:c.7843C>T	p.Gln2615Ter	p.Q2615*	ENST00000356175	NM_000267.3	2615	Caa/Taa	53/57	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.30847442743585	2		633	538	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260485	16260486	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	44	465	0	ENST00000375759.3:c.7756dup	p.Thr2586AsnfsTer10	p.T2586Nfs*10	ENST00000375759	NM_015001.2	2584	gaa/gAaa	11/15	1	2	FACETS	0.668	0.561	0.786	0.668	0.561	0.786	SUBCLONAL	1	TRUE	1	0.30847442743585	2		465	427	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713479	40713479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	98	691	0	ENST00000373198.4:c.4036G>A	p.Asp1346Asn	p.D1346N	ENST00000373198	NM_133170.3	1346	Gat/Aat	30/32	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.30847442743585	2		691	621	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339799	116339799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	57	573	0	ENST00000397752.3:c.661G>A	p.Glu221Lys	p.E221K	ENST00000397752	NM_000245.2	221	Gaa/Aaa	2/21	1	2	FACETS	0.715	0.614	0.825	0.715	0.614	0.825	SUBCLONAL	1	TRUE	1	0.30847442743585	2		573	517	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422104	81422104	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532920088	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	73	636	0	ENST00000298171.2:c.80C>T	p.Pro27Leu	p.P27L	ENST00000298171	NM_000369.2	27	cCa/cTa	1/10	1	2	FACETS	0.851	0.745	0.965	0.851	0.745	0.965	CLONAL	1	TRUE	1	0.30847442743585	2		636	556	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673718	176673718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754590923	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	70	494	0	ENST00000439151.2:c.4418G>A	p.Arg1473Gln	p.R1473Q	ENST00000439151	NM_022455.4	1473	cGa/cAa	10/23	1	2	FACETS	0.856	0.748	0.973	0.856	0.748	0.973	CLONAL	1	TRUE	1	0.30847442743585	2		494	530	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043464	180043464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	93	844	0	ENST00000261937.6:c.3122G>A	p.Arg1041Gln	p.R1041Q	ENST00000261937	NM_182925.4	1041	cGg/cAg	23/30	1	2	FACETS	0.849	0.755	0.949	0.849	0.755	0.949	CLONAL	1	TRUE	1	0.30847442743585	2		844	710	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375890	118375890	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	84	540	1	ENST00000534358.1:c.9283C>T	p.Gln3095Ter	p.Q3095*	ENST00000534358	NM_005933.3	3095	Caa/Taa	27/36	0.30847442743585	1	FACETS	0.964	0.854	1	0.964	0.854	1	CLONAL	1	TRUE	0	0.30847442743585	1		541	478	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173622	108173622	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881373	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	35	571	0	ENST00000278616.4:c.5362G>A	p.Gly1788Ser	p.G1788S	ENST00000278616	NM_000051.3	1788	Ggc/Agc	36/63	0.30847442743585	1	FACETS	0.55	0.451	0.66	0.55	0.451	0.66	SUBCLONAL	1	TRUE	0	0.30847442743585	1		571	349	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371984	55371984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	104	636	0	ENST00000297316.4:c.674C>T	p.Ser225Phe	p.S225F	ENST00000297316	NM_022454.3	225	tCc/tTc	2/2	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.30847442743585	2		636	544	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295253	+	upstream_gene_variant	5'Flank	ONP	GAGG	GAGG	AAGA	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	50	480	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.752	0.639	0.876	0.752	0.639	0.876	SUBCLONAL	1	TRUE	1	0.30847442743585	2		481	431	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695875	117695875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768482698	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	141	768	0	ENST00000369458.3:c.562G>A	p.Gly188Arg	p.G188R	ENST00000369458	NM_024626.3	188	Gga/Aga	4/6	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.30847442743585	2		768	772	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596101	43596101	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	84	725	1	ENST00000355710.3:c.268G>A	p.Glu90Lys	p.E90K	ENST00000355710	NM_020975.4	90	Gag/Aag	2/20	1	2	FACETS	0.888	0.785	0.998	0.888	0.785	0.998	CLONAL	1	TRUE	1	0.30847442743585	2		726	613	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-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	27	289	0	ENST00000371953.3:c.1027-3_1045del		p.X343_splice	ENST00000371953	NM_000314.4	343		9/9	0.300178520956313	2	FACETS	0.854	0.684	1	0.427	0.342	0.523	CLONAL	1	TRUE	0	0.30847442743585	2		289	205	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588130	69588130	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	125	713	0	ENST00000168712.1:c.568G>C	p.Gly190Arg	p.G190R	ENST00000168712	NM_002007.2	190	Ggg/Cgg	3/3	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.30847442743585	2		713	705	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94224082	94224082	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	73	595	4	ENST00000323929.3:c.70G>T	p.Gly24Ter	p.G24*	ENST00000323929	NM_005591.3	24	Gga/Tga	3/20	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.30847442743585	2		599	472	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524124	18524124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1161481962	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	36	419	0	ENST00000266497.5:c.1636C>T	p.Pro546Ser	p.P546S	ENST00000266497		546	Ccc/Tcc	11/31	1	2	FACETS	0.741	0.611	0.886	0.741	0.611	0.886	SUBCLONAL	1	TRUE	1	0.30847442743585	2		419	315	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432471	49432471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	87	730	2	ENST00000301067.7:c.8668C>T	p.Pro2890Ser	p.P2890S	ENST00000301067	NM_003482.3	2890	Cct/Tct	34/54	1	2	FACETS	0.837	0.741	0.939	0.837	0.741	0.939	CLONAL	1	TRUE	1	0.30847442743585	2		732	674	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434291	49434291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	160	1066	0	ENST00000301067.7:c.7262C>T	p.Ser2421Phe	p.S2421F	ENST00000301067	NM_003482.3	2421	tCc/tTc	31/54	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.30847442743585	2		1066	981	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445719	49445719	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	188	1316	1	ENST00000301067.7:c.1747C>T	p.Pro583Ser	p.P583S	ENST00000301067	NM_003482.3	583	Cct/Tct	10/54	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.30847442743585	2		1317	1164	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225957	133225958	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	106	857	1	ENST00000320574.5:c.3939_3940delinsAA	p.Gly1314Arg	p.G1314R	ENST00000320574	NM_006231.2	1313	acGGgg/acAAgg	31/49	1	2	FACETS	0.913	0.818	1	0.913	0.818	1	CLONAL	1	TRUE	1	0.30847442743585	2		858	753	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589298	28589298	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	64	476	0	ENST00000241453.7:c.2749G>A	p.Glu917Lys	p.E917K	ENST00000241453	NM_004119.2	917	Gaa/Aaa	22/24	1	2	FACETS	0.914	0.794	1	0.914	0.794	1	CLONAL	1	TRUE	1	0.30847442743585	2		476	454	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012476	29012476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140749618	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	43	500	0	ENST00000282397.4:c.395G>A	p.Gly132Asp	p.G132D	ENST00000282397	NM_002019.4	132	gGt/gAt	4/30	1	2	FACETS	0.642	0.538	0.758	0.642	0.538	0.758	SUBCLONAL	1	TRUE	1	0.30847442743585	2		500	434	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779500	3779500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	128	1141	0	ENST00000262367.5:c.5548C>T	p.Leu1850Phe	p.L1850F	ENST00000262367	NM_004380.2	1850	Ctc/Ttc	31/31	1	2	FACETS	0.935	0.847	1	0.935	0.847	1	CLONAL	1	TRUE	1	0.30847442743585	2		1141	888	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129737	30129737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	104	797	0	ENST00000263025.4:c.476C>T	p.Ser159Phe	p.S159F	ENST00000263025	NM_002746.2	159	tCc/tTc	3/9	1	2	FACETS	0.93	0.833	1	0.93	0.833	1	CLONAL	1	TRUE	1	0.30847442743585	2		797	725	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821080	72821081	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	97	695	1	ENST00000268489.5:c.11094_11095delinsAA	p.Asp3699Asn	p.D3699N	ENST00000268489	NM_006885.3	3698	acGGac/acAAac	10/10	1	2	FACETS	0.828	0.738	0.923	0.828	0.738	0.923	CLONAL	1	TRUE	1	0.30847442743585	2		696	760	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81902851	81902852	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	89	687	1	ENST00000359376.3:c.512_513delinsTT	p.Pro171Leu	p.P171L	ENST00000359376	NM_002661.3	171	cCC/cTT	6/33	1	2	FACETS	0.874	0.776	0.98	0.874	0.776	0.98	CLONAL	1	TRUE	1	0.30847442743585	2		688	660	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652904	29652904	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	65	401	0	ENST00000356175.3:c.4839T>A	p.Tyr1613Ter	p.Y1613*	ENST00000356175	NM_000267.3	1613	taT/taA	36/57	1	2	FACETS	0.967	0.841	1	0.967	0.841	1	CLONAL	1	TRUE	1	0.30847442743585	2		401	436	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40864381	40864381	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	135	694	0	ENST00000428826.2:c.1327C>T	p.Arg443Ter	p.R443*	ENST00000428826		443	Cga/Tga	12/21	1	2	FACETS	0.952	0.865	1	0.952	0.865	1	CLONAL	1	TRUE	1	0.30847442743585	2		694	919	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2185873	2185873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	126	896	1	ENST00000398665.3:c.145C>T	p.Pro49Ser	p.P49S	ENST00000398665	NM_032482.2	49	Ccg/Tcg	3/28	1	2	FACETS	0.995	0.901	1	0.995	0.901	1	CLONAL	1	TRUE	1	0.30847442743585	2		897	821	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39214723	39214723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749989638	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	54	454	0	ENST00000402219.2:c.3401C>T	p.Ser1134Phe	p.S1134F	ENST00000402219	NM_005633.3	1134	tCt/tTt	22/23	1	2	FACETS	0.75	0.641	0.868	0.75	0.641	0.868	SUBCLONAL	1	TRUE	1	0.30847442743585	2		454	467	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262578	39262578	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867539471	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	57	674	0	ENST00000402219.2:c.928C>T	p.Arg310Cys	p.R310C	ENST00000402219	NM_005633.3	310	Cgt/Tgt	7/23	1	2	FACETS	0.716	0.615	0.827	0.716	0.615	0.827	SUBCLONAL	1	TRUE	1	0.30847442743585	2		674	516	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285854	39285854	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1553362937	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	53	723	0	ENST00000402219.2:c.305C>G	p.Pro102Arg	p.P102R	ENST00000402219	NM_005633.3	102	cCt/cGt	3/23	1	2	FACETS	0.696	0.594	0.807	0.696	0.594	0.807	SUBCLONAL	1	TRUE	1	0.30847442743585	2		723	494	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99162485	99162485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	81	477	0	ENST00000074304.5:c.1003C>T	p.Pro335Ser	p.P335S	ENST00000074304	NM_001134224.1	335	Ccc/Tcc	12/26	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.30847442743585	2		477	507	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212289013	212289013	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	52	601	0	ENST00000342788.4:c.2733G>A	p.Trp911Ter	p.W911*	ENST00000342788	NM_005235.2	911	tgG/tgA	23/28	1	2	FACETS	0.746	0.636	0.866	0.746	0.636	0.866	SUBCLONAL	1	TRUE	1	0.30847442743585	2		601	452	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36014544	36014544	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	97	753	0	ENST00000358208.4:c.317A>C	p.Lys106Thr	p.K106T	ENST00000358208		106	aAg/aCg	3/12	1	2	FACETS	0.873	0.779	0.974	0.873	0.779	0.974	CLONAL	1	TRUE	1	0.30847442743585	2		753	720	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727143	40727143	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	113	673	0	ENST00000373198.4:c.3821A>G	p.Asn1274Ser	p.N1274S	ENST00000373198	NM_133170.3	1274	aAc/aGc	28/32	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.30847442743585	2		673	718	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306605	41306605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	96	857	0	ENST00000373198.4:c.1054C>T	p.Pro352Ser	p.P352S	ENST00000373198	NM_133170.3	352	Ccc/Tcc	7/32	1	2	FACETS	0.837	0.745	0.934	0.837	0.745	0.934	CLONAL	1	TRUE	1	0.30847442743585	2		857	744	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866385	42866386	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	85	755	3	ENST00000398585.3:c.246_247delinsTT	p.Pro83Ser	p.P83S	ENST00000398585	NM_001135099.1	82	taCCcg/taTTcg	3/14	1	2	FACETS	0.742	0.655	0.834	0.742	0.655	0.834	SUBCLONAL	1	TRUE	1	0.30847442743585	2		758	743	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421272	12421272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372494308	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	123	828	1	ENST00000287820.6:c.152C>T	p.Ser51Phe	p.S51F	ENST00000287820	NM_015869.4	51	tCc/tTc	2/7	1	2	FACETS	0.893	0.807	0.984	0.893	0.807	0.984	CLONAL	1	TRUE	1	0.30847442743585	2		829	893	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799950	72799950	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	59	453	0	ENST00000325599.8:c.1219G>A	p.Glu407Lys	p.E407K	ENST00000325599	NM_018130.2	407	Gaa/Aaa	11/11	1	2	FACETS	0.837	0.722	0.962	0.837	0.722	0.962	CLONAL	1	TRUE	1	0.30847442743585	2		453	457	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204578	128204578	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768892880	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	125	702	0	ENST00000341105.2:c.863C>T	p.Ser288Phe	p.S288F	ENST00000341105	NM_032638.4	288	tCc/tTc	3/6	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.30847442743585	2		702	700	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670600	134670600	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	142	879	1	ENST00000398015.3:c.511A>T	p.Asn171Tyr	p.N171Y	ENST00000398015	NM_004441.4	171	Aat/Tat	3/16	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.30847442743585	2		880	877	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272191	142272191	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	80	529	0	ENST00000350721.4:c.2683T>C	p.Cys895Arg	p.C895R	ENST00000350721	NM_001184.3	895	Tgt/Cgt	13/47	1	2	FACETS	0.94	0.829	1	0.94	0.829	1	CLONAL	1	TRUE	1	0.30847442743585	2		529	552	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281508	142281508	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	54	789	0	ENST00000350721.4:c.736del	p.Ser246ProfsTer2	p.S246Pfs*2	ENST00000350721	NM_001184.3	246	Tcc/cc	4/47	1	2	FACETS	0.588	0.502	0.683	0.588	0.502	0.683	SUBCLONAL	1	TRUE	1	0.30847442743585	2		789	595	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502443	186502444	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	45	541	1	ENST00000323963.5:c.166_167delinsTT	p.Pro56Phe	p.P56F	ENST00000323963		56	CCt/TTt	3/11	1	2	FACETS	0.633	0.532	0.744	0.633	0.532	0.744	SUBCLONAL	1	TRUE	1	0.30847442743585	2		542	461	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446271	187446271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	121	662	1	ENST00000232014.4:c.1417C>T	p.Pro473Ser	p.P473S	ENST00000232014	NM_001130845.1	473	Ccg/Tcg	6/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.30847442743585	2		663	667	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961761	55961761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	87	457	0	ENST00000263923.4:c.2800G>A	p.Glu934Lys	p.E934K	ENST00000263923	NM_002253.2	934	Gaa/Aaa	20/30	1	2	FACETS	0.891	0.79	0.999	0.891	0.79	0.999	CLONAL	1	TRUE	1	0.30847442743585	2		457	633	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99823118	99823118	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	44	429	0	ENST00000280892.6:c.94C>T	p.Pro32Ser	p.P32S	ENST00000280892	NM_001130678.1	32	Cct/Tct	2/7	1	2	FACETS	0.645	0.542	0.76	0.645	0.542	0.76	SUBCLONAL	1	TRUE	1	0.30847442743585	2		429	442	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155721	106155721	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	57	449	0	ENST00000380013.4:c.622C>T	p.Pro208Ser	p.P208S	ENST00000380013	NM_001127208.2	208	Cct/Tct	3/11	1	2	FACETS	0.791	0.68	0.912	0.791	0.68	0.912	CLONAL	1	TRUE	1	0.30847442743585	2		449	467	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294364	1294364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	97	730	0	ENST00000310581.5:c.637C>T	p.Pro213Ser	p.P213S	ENST00000310581	NM_198253.2	213	Ccc/Tcc	2/16	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.30847442743585	2		730	615	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80021355	80021355	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	81	705	0	ENST00000265081.6:c.1424T>C	p.Phe475Ser	p.F475S	ENST00000265081	NM_002439.4	475	tTt/tCt	9/24	1	2	FACETS	0.822	0.724	0.926	0.822	0.724	0.926	CLONAL	1	TRUE	1	0.30847442743585	2		705	639	SUCCESS
APC	324	MSKCC	GRCh37	5	112178340	112178341	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	43	590	1	ENST00000257430.4:c.7049_7050delinsTT	p.Ser2350Phe	p.S2350F	ENST00000257430	NM_000038.5	2350	tCC/tTT	16/16	1	2	FACETS	0.606	0.507	0.715	0.606	0.507	0.715	SUBCLONAL	1	TRUE	1	0.30847442743585	2		591	460	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674156	117674156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867084033	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	87	639	0	ENST00000368508.3:c.4318C>T	p.Pro1440Ser	p.P1440S	ENST00000368508	NM_002944.2	1440	Cca/Tca	26/43	1	2	FACETS	0.887	0.786	0.995	0.887	0.786	0.995	CLONAL	1	TRUE	1	0.30847442743585	2		639	636	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704499	117704499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	63	494	0	ENST00000368508.3:c.2477C>T	p.Pro826Leu	p.P826L	ENST00000368508	NM_002944.2	826	cCt/cTt	16/43	1	2	FACETS	0.999	0.867	1	0.999	0.867	1	CLONAL	1	TRUE	1	0.30847442743585	2		494	409	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201844	152201844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	72	495	0	ENST00000206249.3:c.698G>A	p.Arg233Lys	p.R233K	ENST00000206249	NM_000125.3	233	aGg/aAg	3/8	1	2	FACETS	0.849	0.743	0.963	0.849	0.743	0.963	CLONAL	1	TRUE	1	0.30847442743585	2		495	550	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382134	152382134	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	56	410	0	ENST00000206249.3:c.1244G>A	p.Gly415Glu	p.G415E	ENST00000206249	NM_000125.3	415	gGa/gAa	6/8	1	2	FACETS	0.922	0.792	1	0.922	0.792	1	CLONAL	1	TRUE	1	0.30847442743585	2		410	394	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968206	68968206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	98	798	0	ENST00000288368.4:c.1235G>A	p.Gly412Glu	p.G412E	ENST00000288368	NM_024870.2	412	gGa/gAa	10/40	1	2	FACETS	0.831	0.741	0.926	0.831	0.741	0.926	CLONAL	1	TRUE	1	0.30847442743585	2		798	765	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5534822	5534822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	174	583	0	ENST00000397747.3:c.133G>A	p.Asp45Asn	p.D45N	ENST00000397747	NM_025239.3	45	Gac/Aac	3/7	0.267325039675376	2	FACETS	0.932	0.863	1	0.932	0.863	1	CLONAL	2	TRUE	0	0.30847442743585	2		583	605	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518411	8518411	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	88	253	0	ENST00000356435.5:c.980G>A	p.Gly327Glu	p.G327E	ENST00000356435		327	gGa/gAa	10/35	0.267325039675376	2	FACETS	0.948	0.849	1	0.948	0.849	1	CLONAL	2	TRUE	0	0.30847442743585	2		253	301	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966641	36966641	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	80	675	0	ENST00000358127.4:c.685T>C	p.Phe229Leu	p.F229L	ENST00000358127	NM_001280556.1	229	Ttc/Ctc	6/10	1	2	FACETS	0.888	0.783	1	0.888	0.783	1	CLONAL	1	TRUE	1	0.30847442743585	2		675	584	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342592	87342592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1456574135	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	87	575	0	ENST00000277120.3:c.877G>A	p.Glu293Lys	p.E293K	ENST00000277120		293	Gaa/Aaa	9/19	1	2	FACETS	0.988	0.876	1	0.988	0.876	1	CLONAL	1	TRUE	1	0.30847442743585	2		575	571	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93636995	93636995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	74	420	0	ENST00000375746.1:c.1045G>A	p.Glu349Lys	p.E349K	ENST00000375746	NM_001174167.1	349	Gag/Aag	9/14	1	2	FACETS	0.946	0.83	1	0.946	0.83	1	CLONAL	1	TRUE	1	0.30847442743585	2		420	507	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409009	139409009	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	124	983	0	ENST00000277541.6:c.2160C>A	p.Cys720Ter	p.C720*	ENST00000277541	NM_017617.3	720	tgC/tgA	13/34	1	2	FACETS	0.926	0.838	1	0.926	0.838	1	CLONAL	1	TRUE	1	0.30847442743585	2		983	868	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317541	1317541	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	99	714	0	ENST00000400841.2:c.524T>G	p.Leu175Trp	p.L175W	ENST00000400841		175	tTg/tGg	5/6	1	1	FACETS	0.776	0.693	0.864	0.776	0.693	0.864	SUBCLONAL	1	TRUE	0	0.30847442743585	1		714	700	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77051713	77051713	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	83	629	0	ENST00000356341.3:c.1094A>G	p.Gln365Arg	p.Q365R	ENST00000356341	NM_002576.4	365	cAa/cGa	11/15	1	2	FACETS	0.775	0.684	0.873	0.775	0.684	0.873	SUBCLONAL	1	TRUE	1	0.30847442743585	2		629	694	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856271	111856271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	12	66	0	ENST00000341259.2:c.322C>T	p.Pro108Ser	p.P108S	ENST00000341259	NM_005475.2	108	Ccc/Tcc	2/8	1	2	FACETS	0.973	0.694	1	0.973	0.694	1	CLONAL	1	TRUE	1	0.30847442743585	2		66	80	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42843804	42843804	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1185182900	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	86	676	0	ENST00000398585.3:c.1115C>T	p.Pro372Leu	p.P372L	ENST00000398585	NM_001135099.1	372	cCa/cTa	10/14	1	2	FACETS	0.844	0.747	0.947	0.844	0.747	0.947	CLONAL	1	TRUE	1	0.30847442743585	2		676	661	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939980	49939980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	119	851	1	ENST00000296474.3:c.1063G>A	p.Asp355Asn	p.D355N	ENST00000296474	NM_002447.2	355	Gat/Aat	1/20	1	2	FACETS	0.92	0.83	1	0.92	0.83	1	CLONAL	1	TRUE	1	0.30847442743585	2		852	839	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172069	32172069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781344689	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	147	827	0	ENST00000375023.3:c.2963G>A	p.Gly988Glu	p.G988E	ENST00000375023	NM_004557.3	988	gGa/gAa	19/30	0.30847442743585	3	FACETS	1	0.966	1	0.558	0.509	0.61	CLONAL	1	TRUE	1	0.30847442743585	3		827	986	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066707	94066711	+	stop_gained	Nonsense_Mutation	ONP	CATTC	CATTC	TATTT	novel	NA	P-0021708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	82	624	1	ENST00000369303.4:c.1048_1052delinsAAATA	p.Glu350_Trp351delinsLysTer	p.E350_W351delinsK*	ENST00000369303	NM_004440.3	350	GAATGg/AAATAg	5/17	1	2	FACETS	0.891	0.786	1	0.891	0.786	1	CLONAL	1	TRUE	1	0.30847442743585	2		625	597	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295168	1295168	+	upstream_gene_variant	5'Flank	SNP	C	C	G	novel	NA	P-0021736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	100	290	0				ENST00000310581	NM_198253.2	-/1132			0.266014697903901	3	FACETS	0.773	0.693	0.858	0.773	0.693	0.858	SUBCLONAL	2	TRUE	1	0.270850422729581	3		290	542	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0021736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	226	515	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.266014697903901	3	FACETS	0.872	0.811	0.934	0.872	0.811	0.934	CLONAL	2	TRUE	1	0.270850422729581	3		515	1087	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039815	47039815	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	G	novel	NA	P-0021736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	155	415	0	ENST00000377604.3:c.1161-3C>G		p.X387_splice	ENST00000377604	NM_001204468.1	387			0.230210434218254	2	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.270850422729581	2		415	800	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318820	163318821	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0021736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	76	641	4	ENST00000271452.3:c.1210_1211delinsTT	p.Gly404Leu	p.G404L	ENST00000271452	NM_145697.2	404	GGa/TTa	13/14	1	2	FACETS	0.87	0.763	0.985	0.87	0.763	0.985	CLONAL	1	TRUE	1	0.270850422729581	2		645	645	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945435	71945435	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	114	740	4	ENST00000298229.2:c.2323G>T	p.Glu775Ter	p.E775*	ENST00000298229	NM_001567.3	775	Gag/Tag	20/28	0.266014697903901	3	FACETS	0.857	0.77	0.95	0.429	0.385	0.475	CLONAL	1	TRUE	1	0.270850422729581	3		744	1115	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295166	1295166	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0021736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	101	296	0				ENST00000310581	NM_198253.2	-/1132			0.266014697903901	3	FACETS	0.757	0.679	0.84	0.757	0.679	0.84	SUBCLONAL	2	TRUE	1	0.270850422729581	3		296	559	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971207	21971207	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	202	458	0	ENST00000304494.5:c.151G>T	p.Val51Phe	p.V51F	ENST00000304494	NM_000077.4	51	Gtc/Ttc	2/3	0.270850422729581	2	FACETS	0.951	0.884	1	0.951	0.884	1	CLONAL	2	TRUE	0	0.270850422729581	2		458	784	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040669	47040670	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0021736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	272	468	0	ENST00000377604.3:c.1305_1306del	p.Tyr435Ter	p.Y435*	ENST00000377604	NM_001204468.1	435	tAC/t	13/24	0.230210434218254	2	FACETS	0.915	0.863	0.967			1	CLONAL	3	TRUE	NA	0.270850422729581	2		468	732	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	179	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.529924793094939	2		215	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	175	720	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	NA	2	FACETS	0.731	0.674	0.792			1	INDETERMINATE	1	TRUE	NA	0.529924793094939	2		722	903	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857436	9857436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	152	514	0	ENST00000330684.3:c.3965G>A	p.Gly1322Glu	p.G1322E	ENST00000330684	NM_001134407.1	1322	gGa/gAa	13/13	0.468302841473784	0	FACETS	0.672	0.622	0.724			1	SUBCLONAL	1	TRUE	0	0.529924793094939	0		514	401	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971187	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	440	418	0	ENST00000304494.5:c.171_172delinsTT	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	57	gcCCga/gcTTga	2/3	0.525379987449428	2	FACETS	0.88	0.844	0.917	0.88	0.844	0.917	CLONAL	2	TRUE	0	0.529924793094939	2		418	943	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259352	16259352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	91	396	0	ENST00000375759.3:c.6617C>T	p.Pro2206Leu	p.P2206L	ENST00000375759	NM_015001.2	2206	cCt/cTt	11/15	0.210939659082469	3	FACETS	0.959	0.856	1	0.48	0.428	0.534	INDETERMINATE	1	TRUE	1	0.529924793094939	3		396	453	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259955	16259955	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1482002539	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	239	813	1	ENST00000375759.3:c.7220C>T	p.Ser2407Phe	p.S2407F	ENST00000375759	NM_015001.2	2407	tCc/tTc	11/15	0.210939659082469	3	FACETS	1	0.966	1	0.527	0.491	0.563	INDETERMINATE	1	TRUE	1	0.529924793094939	3		814	1083	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939164	36939164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757964586	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	319	1020	0	ENST00000361632.4:c.545G>A	p.Gly182Glu	p.G182E	ENST00000361632		182	gGg/gAg	5/16	0.210939659082469	3	FACETS	1	0.985	1	0.565	0.532	0.598	INDETERMINATE	1	TRUE	1	0.529924793094939	3		1020	1348	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511759	46511759	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	146	596	0	ENST00000262741.5:c.1018A>G	p.Asn340Asp	p.N340D	ENST00000262741	NM_003629.3	340	Aac/Gac	9/10	0.210939659082469	3	FACETS	1	0.964	1	0.548	0.502	0.596	INDETERMINATE	1	TRUE	1	0.529924793094939	3		596	636	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256477	115256477	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	241	744	1	ENST00000369535.4:c.234C>A	p.Phe78Leu	p.F78L	ENST00000369535	NM_002524.4	78	ttC/ttA	3/7	0.210939659082469	3	FACETS	1	0.972	1	0.536	0.5	0.573	INDETERMINATE	1	TRUE	1	0.529924793094939	3		745	1073	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165957	118165957	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	176	490	1	ENST00000369448.3:c.467C>T	p.Ser156Phe	p.S156F	ENST00000369448	NM_017709.3	156	tCc/tTc	2/2	0.210939659082469	3	FACETS	1	0.978	1	0.579	0.535	0.625	INDETERMINATE	1	TRUE	1	0.529924793094939	3		491	725	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458131	120458131	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1399142103	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	229	763	2	ENST00000256646.2:c.7214G>A	p.Ser2405Asn	p.S2405N	ENST00000256646	NM_024408.3	2405	aGt/aAt	34/34	0.210939659082469	3	FACETS	1	0.984	1	0.587	0.548	0.628	INDETERMINATE	1	TRUE	1	0.529924793094939	3		765	931	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466432	120466432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194257253	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	271	740	0	ENST00000256646.2:c.4687C>T	p.Arg1563Cys	p.R1563C	ENST00000256646	NM_024408.3	1563	Cgc/Tgc	26/34	0.210939659082469	3	FACETS	1	0.987	1	0.591	0.554	0.628	INDETERMINATE	1	TRUE	1	0.529924793094939	3		740	1095	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468036	120468036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs919872084	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	301	881	0	ENST00000256646.2:c.4403C>T	p.Ser1468Phe	p.S1468F	ENST00000256646	NM_024408.3	1468	tCc/tTc	25/34	0.210939659082469	3	FACETS	1	0.99	1	0.617	0.581	0.654	INDETERMINATE	1	TRUE	1	0.529924793094939	3		881	1164	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446333	70446333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	246	677	0	ENST00000373644.4:c.5273G>A	p.Arg1758Lys	p.R1758K	ENST00000373644	NM_030625.2	1758	aGg/aAg	11/12	1	2	FACETS	0.925	0.865	0.986	0.925	0.865	0.986	CLONAL	1	TRUE	1	0.529924793094939	2		677	1004	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066824	77066824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779095416	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	177	593	0	ENST00000356341.3:c.661C>T	p.Pro221Ser	p.P221S	ENST00000356341	NM_002576.4	221	Ccc/Tcc	7/15	1	2	FACETS	0.879	0.812	0.949	0.879	0.812	0.949	CLONAL	1	TRUE	1	0.529924793094939	2		593	760	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404956	404956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773583219	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	227	666	0	ENST00000399788.2:c.4238C>T	p.Ser1413Phe	p.S1413F	ENST00000399788	NM_001042603.1	1413	tCt/tTt	26/28	0.489356239128795	1	FACETS	0.853	0.798	0.91	0.853	0.798	0.91	CLONAL	1	TRUE	0	0.529924793094939	1		666	738	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416224	416224	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	166	558	0	ENST00000399788.2:c.3962T>C	p.Phe1321Ser	p.F1321S	ENST00000399788	NM_001042603.1	1321	tTt/tCt	24/28	0.489356239128795	1	FACETS	0.892	0.826	0.961	0.892	0.826	0.961	CLONAL	1	TRUE	0	0.529924793094939	1		558	516	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244112	46244112	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	193	617	0	ENST00000334344.6:c.2206G>A	p.Gly736Arg	p.G736R	ENST00000334344	NM_152641.2	736	Gga/Aga	15/21	0.210939659082469	3	FACETS	1	0.972	1	0.549	0.508	0.591	INDETERMINATE	1	TRUE	1	0.529924793094939	3		617	839	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420493	49420494	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	265	737	7	ENST00000301067.7:c.15255_15256delinsTT	p.Arg5086Ter	p.R5086*	ENST00000301067	NM_003482.3	5085	caCCga/caTTga	48/54	0.210939659082469	3	FACETS	1	0.978	1	0.547	0.512	0.582	INDETERMINATE	1	TRUE	1	0.529924793094939	3		744	1157	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421706	49421706	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	261	902	1	ENST00000301067.7:c.14523G>T	p.Lys4841Asn	p.K4841N	ENST00000301067	NM_003482.3	4841	aaG/aaT	47/54	0.210939659082469	3	FACETS	1	0.985	1	0.581	0.544	0.619	INDETERMINATE	1	TRUE	1	0.529924793094939	3		903	1072	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434445	49434445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1028524252	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	291	1070	3	ENST00000301067.7:c.7108C>T	p.Arg2370Cys	p.R2370C	ENST00000301067	NM_003482.3	2370	Cgc/Tgc	31/54	0.210939659082469	3	FACETS	1	0.985	1	0.573	0.538	0.608	INDETERMINATE	1	TRUE	1	0.529924793094939	3		1073	1213	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437451	49437452	+	missense_variant	Missense_Mutation	DNP	AG	AG	TA	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	212	832	0	ENST00000301067.7:c.5433_5434delinsTA	p.Ser1812Thr	p.S1812T	ENST00000301067	NM_003482.3	1811	ggCTca/ggTAca	23/54	0.210939659082469	3	FACETS	0.942	0.874	1	0.471	0.437	0.506	INDETERMINATE	1	TRUE	1	0.529924793094939	3		832	1075	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861988	57861988	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	170	542	0	ENST00000228682.2:c.1289C>T	p.Thr430Ile	p.T430I	ENST00000228682	NM_005269.2	430	aCt/aTt	10/12	0.210939659082469	3	FACETS	1	0.969	1	0.549	0.506	0.594	INDETERMINATE	1	TRUE	1	0.529924793094939	3		542	739	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874009	123874009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	26	52	0	ENST00000330479.4:c.40G>A	p.Glu14Lys	p.E14K	ENST00000330479	NM_020382.3	14	Gag/Aag	2/9	1	2	FACETS	0.798	0.642	0.97	0.798	0.642	0.97	CLONAL	1	TRUE	1	0.529924793094939	2		52	123	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100221	30100221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	137	511	0	ENST00000331968.5:c.1399C>T	p.Pro467Ser	p.P467S	ENST00000331968	NM_002742.2	467	Cct/Tct	10/18	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.529924793094939	2		511	516	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132959	30132960	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	274	767	0	ENST00000331968.5:c.641_642delinsTT	p.Thr214Ile	p.T214I	ENST00000331968	NM_002742.2	214	aCC/aTT	4/18	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.529924793094939	2		767	1030	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353847	68353847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	150	671	1	ENST00000487270.1:c.682C>T	p.Leu228Phe	p.L228F	ENST00000487270	NM_133509.3	228	Ctc/Ttc	7/11	0.190444445843301	3	FACETS	1	0.926	1	0.337	0.308	0.367	INDETERMINATE	1	TRUE	0	0.529924793094939	3		672	708	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675049	40675049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764271025	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	352	832	0	ENST00000249776.8:c.13G>A	p.Glu5Lys	p.E5K	ENST00000249776	NM_033286.3	5	Gaa/Aaa	1/9	0.519630256685123	1	FACETS	0.865	0.82	0.911	0.865	0.82	0.911	CLONAL	1	TRUE	0	0.529924793094939	1		832	1129	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003747	45003747	+	start_lost	Translation_Start_Site	SNP	G	G	T	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	227	601	1	ENST00000558401.1:c.3G>T	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	atG/atT	1/4	0.519630256685123	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.529924793094939	1		602	589	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831501	72831501	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	176	733	0	ENST00000268489.5:c.5080G>A	p.Gly1694Arg	p.G1694R	ENST00000268489	NM_006885.3	1694	Ggg/Agg	9/10	1	2	FACETS	0.837	0.772	0.904	0.837	0.772	0.904	CLONAL	1	TRUE	1	0.529924793094939	2		733	794	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574004	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	226	852	1	ENST00000269305.4:c.1023_1024delinsTT	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	341	ttCCga/ttTTga	10/11	NA	2	FACETS	0.706	0.657	0.757			1	INDETERMINATE	1	TRUE	NA	0.529924793094939	2		853	1208	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958298	11958298	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	119	532	0	ENST00000353533.5:c.208A>T	p.Asn70Tyr	p.N70Y	ENST00000353533	NM_003010.3	70	Aac/Tac	2/11	NA	2	FACETS	0.803	0.728	0.883			1	INDETERMINATE	1	TRUE	NA	0.529924793094939	2		532	559	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496952	29496952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	193	585	0	ENST00000356175.3:c.523C>T	p.His175Tyr	p.H175Y	ENST00000356175	NM_000267.3	175	Cat/Tat	5/57	1	2	FACETS	0.858	0.795	0.923	0.858	0.795	0.923	CLONAL	1	TRUE	1	0.529924793094939	2		585	849	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883636	37883636	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	268	948	1	ENST00000269571.5:c.3248C>T	p.Ser1083Phe	p.S1083F	ENST00000269571		1083	tCc/tTc	26/27	1	2	FACETS	0.876	0.821	0.932	0.876	0.821	0.932	CLONAL	1	TRUE	1	0.529924793094939	2		949	1155	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752420	55752421	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	295	1214	2	ENST00000284073.2:c.878_879delinsTT	p.Ser293Phe	p.S293F	ENST00000284073	NM_138962.2	293	tCC/tTT	12/14	1	2	FACETS	0.761	0.715	0.809	0.761	0.715	0.809	SUBCLONAL	1	TRUE	1	0.529924793094939	2		1216	1463	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66518954	66518954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	197	425	0	ENST00000358598.2:c.235G>A	p.Glu79Lys	p.E79K	ENST00000358598	NM_212471.2	79	Gag/Aag	3/11	1	2	FACETS	0.894	0.829	0.961	0.894	0.829	0.961	CLONAL	1	TRUE	1	0.529924793094939	2		425	832	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39576673	39576673	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	137	555	0	ENST00000262039.4:c.963T>G	p.Tyr321Ter	p.Y321*	ENST00000262039	NM_002647.2	321	taT/taG	9/25	1	2	FACETS	0.773	0.705	0.844	0.773	0.705	0.844	SUBCLONAL	1	TRUE	1	0.529924793094939	2		555	669	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271657	15271657	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269967598	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	313	1309	2	ENST00000263388.2:c.6782C>T	p.Pro2261Leu	p.P2261L	ENST00000263388	NM_000435.2	2261	cCc/cTc	33/33	1	2	FACETS	0.89	0.839	0.943	0.89	0.839	0.943	CLONAL	1	TRUE	1	0.529924793094939	2		1311	1327	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212141	36212141	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	173	629	1	ENST00000222270.7:c.1892C>T	p.Pro631Leu	p.P631L	ENST00000222270	NM_014727.1	631	cCc/cTc	3/37	0.489356239128795	1	FACETS	0.742	0.685	0.8	0.742	0.685	0.8	SUBCLONAL	1	TRUE	0	0.529924793094939	1		630	647	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762420	41762421	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	181	769	2	ENST00000301178.4:c.2100_2101delinsAA	p.Asp701Asn	p.D701N	ENST00000301178	NM_021913.4	700	ggGGac/ggAAac	18/20	NA	2	FACETS	0.761	0.702	0.822			1	INDETERMINATE	1	TRUE	NA	0.529924793094939	2		771	898	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797166	42797167	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	254	1104	2	ENST00000575354.2:c.3528_3529delinsTT	p.Pro1177Ser	p.P1177S	ENST00000575354	NM_015125.3	1176	gcCCcc/gcTTcc	15/20	NA	2	FACETS	0.754	0.705	0.805			1	INDETERMINATE	1	TRUE	NA	0.529924793094939	2		1106	1271	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446340	29446340	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	245	922	0	ENST00000389048.3:c.3227C>T	p.Pro1076Leu	p.P1076L	ENST00000389048	NM_004304.4	1076	cCt/cTt	20/29	1	2	FACETS	0.812	0.758	0.867	0.812	0.758	0.867	CLONAL	1	TRUE	1	0.529924793094939	2		922	1139	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095926	178095926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	180	549	0	ENST00000397062.3:c.1405C>T	p.Pro469Ser	p.P469S	ENST00000397062	NM_006164.4	469	Cct/Tct	5/5	1	2	FACETS	0.862	0.796	0.93	0.862	0.796	0.93	CLONAL	1	TRUE	1	0.529924793094939	2		549	788	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719778	190719778	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	125	387	0	ENST00000441310.2:c.1780C>T	p.Pro594Ser	p.P594S	ENST00000441310	NM_000534.4	594	Cct/Tct	9/13	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.529924793094939	2		387	472	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281575	198281575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	255	697	0	ENST00000335508.6:c.556G>A	p.Gly186Arg	p.G186R	ENST00000335508	NM_012433.2	186	Gga/Aga	6/25	1	2	FACETS	0.8	0.748	0.854	0.8	0.748	0.854	SUBCLONAL	1	TRUE	1	0.529924793094939	2		697	1203	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537919	212537919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	249	318	0	ENST00000342788.4:c.1686G>A	p.Met562Ile	p.M562I	ENST00000342788	NM_005235.2	562	atG/atA	14/28	1	2	FACETS	0.988	0.925	1	0.988	0.925	1	CLONAL	1	TRUE	1	0.529924793094939	2		318	951	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661897	227661897	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs544750977	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	289	986	1	ENST00000305123.5:c.1558C>T	p.Arg520Trp	p.R520W	ENST00000305123	NM_005544.2	520	Cgg/Tgg	1/2	1	2	FACETS	0.872	0.819	0.926	0.872	0.819	0.926	CLONAL	1	TRUE	1	0.529924793094939	2		987	1251	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793364	242793364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	398	717	0	ENST00000334409.5:c.713C>T	p.Pro238Leu	p.P238L	ENST00000334409	NM_005018.2	238	cCc/cTc	5/5	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.529924793094939	2		717	1420	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944436	40944436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	220	812	1	ENST00000373198.4:c.2066G>A	p.Gly689Asp	p.G689D	ENST00000373198	NM_133170.3	689	gGc/gAc	12/32	0.530267391726731	1	FACETS	0.734	0.685	0.786	0.734	0.685	0.786	SUBCLONAL	1	TRUE	0	0.529924793094939	1		813	831	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164808	36164808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	334	1105	0	ENST00000300305.3:c.1067C>T	p.Ser356Phe	p.S356F	ENST00000300305		356	tCc/tTc	8/8	1	2	FACETS	0.928	0.876	0.981	0.928	0.876	0.981	CLONAL	1	TRUE	1	0.529924793094939	2		1105	1359	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764327	39764327	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	346	839	0	ENST00000288319.7:c.785G>A	p.Gly262Asp	p.G262D	ENST00000288319	NM_182918.3	262	gGt/gAt	7/10	1	2	FACETS	0.993	0.939	1	0.993	0.939	1	CLONAL	1	TRUE	1	0.529924793094939	2		839	1315	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574184	41574185	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	167	649	1	ENST00000263253.7:c.6469_6470delinsTT	p.Pro2157Phe	p.P2157F	ENST00000263253	NM_001429.3	2157	CCc/TTc	31/31	1	2	FACETS	0.795	0.731	0.861	0.795	0.731	0.861	SUBCLONAL	1	TRUE	1	0.529924793094939	2		650	793	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266970	41266970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	214	557	0	ENST00000349496.5:c.641C>T	p.Thr214Ile	p.T214I	ENST00000349496	NM_001904.3	214	aCc/aTc	5/15	0.210939659082469	3	FACETS	1	0.944	1	0.509	0.473	0.547	INDETERMINATE	1	TRUE	1	0.529924793094939	3		557	1003	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098669	47098669	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	285	665	0	ENST00000409792.3:c.6605C>T	p.Pro2202Leu	p.P2202L	ENST00000409792	NM_014159.6	2202	cCt/cTt	15/21	0.210939659082469	3	FACETS	1	0.988	1	0.596	0.56	0.633	INDETERMINATE	1	TRUE	1	0.529924793094939	3		665	1141	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098720	47098721	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	236	641	1	ENST00000409792.3:c.6553_6554delinsAA	p.Gly2185Lys	p.G2185K	ENST00000409792	NM_014159.6	2185	GGa/AAa	15/21	0.210939659082469	3	FACETS	1	0.96	1	0.52	0.485	0.556	INDETERMINATE	1	TRUE	1	0.529924793094939	3		642	1083	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935504	49935505	+	missense_variant	Missense_Mutation	DNP	GG	GG	TA	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	255	882	2	ENST00000296474.3:c.1859_1860delinsTA	p.Pro620Leu	p.P620L	ENST00000296474	NM_002447.2	620	cCC/cTA	5/20	NA	2	FACETS	0.843	0.789	0.9			1	INDETERMINATE	1	TRUE	NA	0.529924793094939	2		884	1141	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259388	89259388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	170	642	0	ENST00000336596.2:c.532G>A	p.Gly178Arg	p.G178R	ENST00000336596	NM_005233.5	178	Gga/Aga	3/17	1	2	FACETS	0.909	0.838	0.982	0.909	0.838	0.982	CLONAL	1	TRUE	1	0.529924793094939	2		642	706	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119562156	119562156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772550262	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	197	555	0	ENST00000316626.5:c.1180C>T	p.His394Tyr	p.H394Y	ENST00000316626		394	Cat/Tat	11/12	1	2	FACETS	0.897	0.832	0.964	0.897	0.832	0.964	CLONAL	1	TRUE	1	0.529924793094939	2		555	829	SUCCESS
ATR	545	MSKCC	GRCh37	3	142212098	142212098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	234	758	0	ENST00000350721.4:c.5954C>T	p.Pro1985Leu	p.P1985L	ENST00000350721	NM_001184.3	1985	cCt/cTt	35/47	0.530267391726731	3	FACETS	0.944	0.88	1	0.472	0.44	0.506	CLONAL	1	TRUE	1	0.529924793094939	3		758	1183	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215867	142215867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	149	436	1	ENST00000350721.4:c.5726G>A	p.Ser1909Asn	p.S1909N	ENST00000350721	NM_001184.3	1909	aGc/aAc	33/47	0.530267391726731	3	FACETS	0.961	0.88	1	0.481	0.44	0.523	CLONAL	1	TRUE	1	0.529924793094939	3		437	740	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502378	186502378	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	159	571	0	ENST00000323963.5:c.101A>G	p.Asn34Ser	p.N34S	ENST00000323963		34	aAc/aGc	3/11	0.530267391726731	4	FACETS	0.835	0.764	0.909	0.278	0.254	0.303	CLONAL	1	TRUE	1	0.529924793094939	4		571	1100	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973911	55973911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs941528100	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	204	506	1	ENST00000263923.4:c.1405G>A	p.Glu469Lys	p.E469K	ENST00000263923	NM_002253.2	469	Gag/Aag	10/30	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.529924793094939	2		507	747	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247247	153247247	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	212	532	0	ENST00000281708.4:c.1555T>C	p.Tyr519His	p.Y519H	ENST00000281708	NM_033632.3	519	Tat/Cat	10/12	1	2	FACETS	0.8	0.743	0.859	0.8	0.743	0.859	SUBCLONAL	1	TRUE	1	0.529924793094939	2		532	1000	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557870	187557870	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	251	657	2	ENST00000441802.2:c.3841G>T	p.Glu1281Ter	p.E1281*	ENST00000441802	NM_005245.3	1281	Gag/Tag	5/27	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.529924793094939	2		659	882	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628266	187628266	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	231	761	0	ENST00000441802.2:c.2716C>T	p.Gln906Ter	p.Q906*	ENST00000441802	NM_005245.3	906	Cag/Tag	2/27	1	2	FACETS	0.974	0.91	1	0.974	0.91	1	CLONAL	1	TRUE	1	0.529924793094939	2		761	895	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226087	226088	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	153	544	2	ENST00000264932.6:c.546_547delinsAA	p.Gly183Ser	p.G183S	ENST00000264932	NM_004168.2	182	aaGGgc/aaAAgc	5/15	1	2	FACETS	0.745	0.682	0.81	0.745	0.682	0.81	SUBCLONAL	1	TRUE	1	0.529924793094939	2		546	775	SUCCESS
APC	324	MSKCC	GRCh37	5	112174754	112174754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774847322	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	98	394	0	ENST00000257430.4:c.3463G>A	p.Glu1155Lys	p.E1155K	ENST00000257430	NM_000038.5	1155	Gaa/Aaa	16/16	1	2	FACETS	0.785	0.704	0.871	0.785	0.704	0.871	SUBCLONAL	1	TRUE	1	0.529924793094939	2		394	471	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184753	32184754	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	310	852	1	ENST00000375023.3:c.1829_1830delinsTT	p.Ala610Val	p.A610V	ENST00000375023	NM_004557.3	610	gCC/gTT	11/30	0.388897610132869	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.529924793094939	1		853	742	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956522	93956522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	130	450	1	ENST00000369303.4:c.2714G>A	p.Gly905Glu	p.G905E	ENST00000369303	NM_004440.3	905	gGa/gAa	15/17	1	2	FACETS	0.894	0.814	0.976	0.894	0.814	0.976	CLONAL	1	TRUE	1	0.529924793094939	2		451	549	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708087	117708087	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1350752092	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	182	705	0	ENST00000368508.3:c.2090G>C	p.Gly697Ala	p.G697A	ENST00000368508	NM_002944.2	697	gGa/gCa	14/43	0.530267391726731	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.529924793094939	1		705	476	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150410	157150410	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs141260832	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	341	808	0	ENST00000346085.5:c.1592T>C	p.Met531Thr	p.M531T	ENST00000346085	NM_020732.3	531	aTg/aCg	2/20	0.210939659082469	3	FACETS	1	0.992	1	0.642	0.607	0.678	INDETERMINATE	1	TRUE	1	0.529924793094939	3		808	1267	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528667	157528667	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	305	803	1	ENST00000346085.5:c.6392C>T	p.Ser2131Phe	p.S2131F	ENST00000346085	NM_020732.3	2131	tCc/tTc	20/20	0.210939659082469	3	FACETS	1	0.99	1	0.618	0.582	0.655	INDETERMINATE	1	TRUE	1	0.529924793094939	3		804	1178	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026402	6026402	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	131	620	0	ENST00000265849.7:c.1994G>A	p.Arg665Lys	p.R665K	ENST00000265849	NM_000535.5	665	aGa/aAa	11/15	1	2	FACETS	0.877	0.799	0.958	0.877	0.799	0.958	CLONAL	1	TRUE	1	0.529924793094939	2		620	564	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266482	55266482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	270	713	0	ENST00000275493.2:c.2774C>T	p.Ser925Phe	p.S925F	ENST00000275493	NM_005228.3	925	tCc/tTc	23/28	NA	2	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.529924793094939	2		713	973	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386505	81386505	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1305340910	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	134	485	0	ENST00000222390.5:c.482G>T	p.Ser161Ile	p.S161I	ENST00000222390	NM_000601.4	161	aGc/aTc	4/18	1	2	FACETS	0.944	0.862	1	0.944	0.862	1	CLONAL	1	TRUE	1	0.529924793094939	2		485	536	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508811	106508811	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	149	603	2	ENST00000359195.3:c.805G>A	p.Asp269Asn	p.D269N	ENST00000359195	NM_002649.2	269	Gat/Aat	2/11	1	2	FACETS	0.605	0.552	0.66	0.605	0.552	0.66	SUBCLONAL	1	TRUE	1	0.529924793094939	2		605	930	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117874180	117874180	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	131	562	0	ENST00000297338.2:c.275-1G>A		p.X92_splice	ENST00000297338	NM_006265.2	92			1	2	FACETS	0.852	0.776	0.932	0.852	0.776	0.932	CLONAL	1	TRUE	1	0.529924793094939	2		562	580	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27172623	27172624	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	337	711	1	ENST00000380036.4:c.638_639delinsTT	p.Ala213Val	p.A213V	ENST00000380036	NM_000459.3	213	gCC/gTT	5/23	0.525379987449428	2	FACETS	0.962	0.918	1	0.962	0.918	1	CLONAL	2	TRUE	0	0.529924793094939	2		712	661	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779196	135779196	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746909024	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	148	530	1	ENST00000298552.3:c.2050C>T	p.Pro684Ser	p.P684S	ENST00000298552	NM_001162426.1	684	Cct/Tct	17/23	0.190444445843301	3	FACETS	0.823	0.751	0.897	0.274	0.25	0.299	INDETERMINATE	1	TRUE	0	0.529924793094939	3		531	859	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391585	139391586	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	373	1165	4	ENST00000277541.6:c.6605_6606delinsTT	p.Ser2202Phe	p.S2202F	ENST00000277541	NM_017617.3	2202	tCC/tTT	34/34	0.440390322646382	2	FACETS	1	0.995	1	0.732	0.697	0.768	CLONAL	1	TRUE	0	0.529924793094939	2		1169	961	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401760	139401760	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	398	939	0	ENST00000277541.6:c.3640C>T	p.Gln1214Ter	p.Q1214*	ENST00000277541	NM_017617.3	1214	Cag/Tag	22/34	0.440390322646382	2	FACETS	0.774	0.739	0.81	0.774	0.739	0.81	SUBCLONAL	2	TRUE	0	0.529924793094939	2		939	970	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933165	39933166	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	253	478	2	ENST00000378444.4:c.1433_1434delinsTT	p.Ser478Phe	p.S478F	ENST00000378444	NM_001123385.1	478	tCC/tTT	4/15	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.529924793094939	1		480	593	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933166	39933166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1296402443	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	251	480	0	ENST00000378444.4:c.1433C>T	p.Ser478Phe	p.S478F	ENST00000378444	NM_001123385.1	478	tCc/tTc	4/15	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.529924793094939	1		480	588	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44733181	44733182	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	187	335	2	ENST00000377967.4:c.173_174delinsAA	p.Gly58Glu	p.G58E	ENST00000377967	NM_021140.2	58	gGG/gAA	2/29	1	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.529924793094939	1		337	492	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356210	70356210	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	290	525	0	ENST00000374080.3:c.5105G>T	p.Trp1702Leu	p.W1702L	ENST00000374080		1702	tGg/tTg	37/45	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.529924793094939	1		525	708	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	441	215	0				ENST00000310581	NM_198253.2	-/1132			0.54877998091093	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.555035004080696	2		215	766	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	654	316	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.236390164382367	6	FACETS	0.898	0.867	0.928			1	INDETERMINATE	4	TRUE	NA	0.555035004080696	6		316	1385	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155953	119155953	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764340189	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	381	923	0	ENST00000264033.4:c.1618C>T	p.Arg540Ter	p.R540*	ENST00000264033	NM_005188.3	540	Cga/Tga	11/16	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.555035004080696	2		923	1239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	332	596	1	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.555035004080696	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.555035004080696	1		597	845	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	163	779	1	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	0.376719847779552	1	FACETS	0.356	0.325	0.387	0.356	0.325	0.387	SUBCLONAL	1	TRUE	0	0.555035004080696	1		780	1193	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	410	173	1				ENST00000310581	NM_198253.2	-/1132			0.54877998091093	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.555035004080696	2		174	684	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912815	100912815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1000609240	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	172	579	0	ENST00000325455.5:c.2507G>A	p.Arg836Gln	p.R836Q	ENST00000325455	NM_001202474.3	836	cGa/cAa	7/8	1	2	FACETS	0.952	0.879	1	0.952	0.879	1	CLONAL	1	TRUE	1	0.555035004080696	2		579	651	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	119	449	0	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	1	2	FACETS	0.836	0.758	0.917	0.836	0.758	0.917	CLONAL	1	TRUE	1	0.555035004080696	2		449	513	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971187	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	411	418	0	ENST00000304494.5:c.171_172delinsTT	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	57	gcCCga/gcTTga	2/3	0.513066642430504	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.555035004080696	2		418	736	SUCCESS
BLM	641	MSKCC	GRCh37	15	91290720	91290720	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs139282091	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	63	291	0	ENST00000355112.3:c.98C>T	p.Ser33Leu	p.S33L	ENST00000355112	NM_000057.2	33	tCa/tTa	2/22	0.376719847779552	1	FACETS	0.304	0.263	0.349	0.304	0.263	0.349	SUBCLONAL	1	TRUE	0	0.555035004080696	1		291	539	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610608	52610608	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	260	809	1	ENST00000394830.3:c.3565G>A	p.Glu1189Lys	p.E1189K	ENST00000394830	NM_018313.4	1189	Gaa/Aaa	23/30	0.413148278862495	3	FACETS	1	0.978	1	0.548	0.513	0.584	CLONAL	1	TRUE	1	0.555035004080696	3		810	1092	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989633	68989633	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs866647316	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	314	671	0	ENST00000288368.4:c.1571G>A	p.Gly524Glu	p.G524E	ENST00000288368	NM_024870.2	524	gGa/gAa	15/40	0.208895863219656	4	FACETS	0.907	0.857	0.957	0.907	0.857	0.957	INDETERMINATE	2	TRUE	2	0.555035004080696	4		671	970	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781830	9781830	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	173	1024	0	ENST00000377346.4:c.1967A>G	p.His656Arg	p.H656R	ENST00000377346	NM_005026.3	656	cAc/cGc	16/24	0.209080177491699	3	FACETS	0.595	0.546	0.647	0.198	0.182	0.216	INDETERMINATE	1	TRUE	0	0.555035004080696	3		1024	1338	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256667	16256667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1387045955	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	354	659	0	ENST00000375759.3:c.3932C>T	p.Pro1311Leu	p.P1311L	ENST00000375759	NM_015001.2	1311	cCt/cTt	11/15	0.209080177491699	3	FACETS	1	0.987	1	0.728	0.695	0.762	INDETERMINATE	2	TRUE	0	0.555035004080696	3		659	746	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259715	16259715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765733962	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	461	533	1	ENST00000375759.3:c.6980G>A	p.Arg2327Gln	p.R2327Q	ENST00000375759	NM_015001.2	2327	cGg/cAg	11/15	0.209080177491699	3	FACETS	1	0.994	1	0.785	0.755	0.816	INDETERMINATE	2	TRUE	0	0.555035004080696	3		534	901	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262237	16262237	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs576149674	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	169	262	0	ENST00000375759.3:c.9502C>G	p.Arg3168Gly	p.R3168G	ENST00000375759	NM_015001.2	3168	Cga/Gga	11/15	0.209080177491699	3	FACETS	1	0.955	1	0.688	0.641	0.735	INDETERMINATE	2	TRUE	0	0.555035004080696	3		262	377	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087515	27087515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866476464	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1181	245	1055	1	ENST00000324856.7:c.2089C>T	p.Pro697Ser	p.P697S	ENST00000324856	NM_006015.4	697	Ccg/Tcg	5/20	0.555035004080696	3	FACETS	0.791	0.737	0.847	0.395	0.368	0.424	SUBCLONAL	1	TRUE	1	0.555035004080696	3		1056	1426	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121434595	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	423	632	0	ENST00000369535.4:c.37G>T	p.Gly13Cys	p.G13C	ENST00000369535	NM_002524.4	13	Ggt/Tgt	2/7	0.555035004080696	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	1	0.555035004080696	3		632	971	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458089	120458089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	196	831	2	ENST00000256646.2:c.7256C>T	p.Pro2419Leu	p.P2419L	ENST00000256646	NM_024408.3	2419	cCa/cTa	34/34	0.555035004080696	3	FACETS	0.776	0.718	0.838	0.388	0.359	0.419	SUBCLONAL	1	TRUE	1	0.555035004080696	3		833	1162	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834189	156834189	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	853	1103	0	ENST00000524377.1:c.256G>A	p.Asp86Asn	p.D86N	ENST00000524377	NM_002529.3	86	Gat/Aat	2/17	0.555035004080696	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.555035004080696	2		1103	1428	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246498703	246498703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	149	930	0	ENST00000388985.4:c.302C>T	p.Ser101Phe	p.S101F	ENST00000388985		101	tCc/tTc	3/12	0.296333946541196	3	FACETS	0.645	0.588	0.705	0.215	0.196	0.235	INDETERMINATE	1	TRUE	0	0.555035004080696	3		930	1063	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619252	43619254	+	missense_variant,splice_region_variant	Missense_Mutation	TNP	GAG	GAG	TAT	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	202	505	0	ENST00000355710.3:c.2935_2937delinsTAT	p.Glu979Tyr	p.E979Y	ENST00000355710	NM_020975.4	979	GAG/TAT	17/20	0.429101490930598	1	FACETS	0.968	0.905	1	0.968	0.905	1	CLONAL	1	TRUE	0	0.555035004080696	1		505	543	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852439	63852439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748374587	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	69	776	0	ENST00000279873.7:c.3217C>T	p.Leu1073Phe	p.L1073F	ENST00000279873	NM_032199.2	1073	Ctc/Ttc	10/10	0.429101490930598	1	FACETS	0.218	0.189	0.25	0.218	0.189	0.25	SUBCLONAL	1	TRUE	0	0.555035004080696	1		776	823	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446201	70446201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	276	604	2	ENST00000373644.4:c.5141C>T	p.Ser1714Leu	p.S1714L	ENST00000373644	NM_030625.2	1714	tCa/tTa	11/12	0.429101490930598	1	FACETS	0.992	0.937	1	0.992	0.937	1	CLONAL	1	TRUE	0	0.555035004080696	1		606	724	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	219	720	1	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	0.98	0.914	1	0.98	0.914	1	CLONAL	1	TRUE	1	0.555035004080696	2		721	805	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150217	108150217	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	167	674	0	ENST00000278616.4:c.3285-1G>C		p.X1095_splice	ENST00000278616	NM_000051.3	1095			1	2	FACETS	0.894	0.824	0.967	0.894	0.824	0.967	CLONAL	1	TRUE	1	0.555035004080696	2		674	673	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118353205	118353205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	103	426	0	ENST00000534358.1:c.4081G>A	p.Glu1361Lys	p.E1361K	ENST00000534358	NM_005933.3	1361	Gaa/Aaa	8/36	1	2	FACETS	0.805	0.724	0.89	0.805	0.724	0.89	CLONAL	1	TRUE	1	0.555035004080696	2		426	461	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376289	118376289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778675942	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	274	668	1	ENST00000534358.1:c.9682C>T	p.Arg3228Cys	p.R3228C	ENST00000534358	NM_005933.3	3228	Cgt/Tgt	27/36	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.555035004080696	2		669	915	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699293	18699293	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	76	583	0	ENST00000266497.5:c.3394C>G	p.Gln1132Glu	p.Q1132E	ENST00000266497		1132	Caa/Gaa	24/31	0.14377163622093	4	FACETS	0.505	0.442	0.573			1	INDETERMINATE	1	TRUE	NA	0.555035004080696	4		583	843	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715735	18715735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	229	521	0	ENST00000266497.5:c.3566C>T	p.Ser1189Leu	p.S1189L	ENST00000266497		1189	tCa/tTa	25/31	0.14377163622093	4	FACETS	0.815	0.762	0.87			1	INDETERMINATE	2	TRUE	NA	0.555035004080696	4		521	787	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944914	31944914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	161	428	2	ENST00000340398.3:c.187C>T	p.Arg63Trp	p.R63W	ENST00000340398	NM_001013699.2	63	Cgg/Tgg	1/1	0.14377163622093	4	FACETS	0.758	0.699	0.82			1	INDETERMINATE	2	TRUE	NA	0.555035004080696	4		430	595	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120807	115120807	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	105	650	0	ENST00000257566.3:c.199C>T	p.Gln67Ter	p.Q67*	ENST00000257566	NM_016569.3	67	Caa/Taa	1/8	0.304282175007398	2	FACETS	0.467	0.418	0.519	0.234	0.209	0.26	INDETERMINATE	1	TRUE	0	0.555035004080696	2		650	810	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431385	121431385	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	97	684	1	ENST00000257555.6:c.589A>T	p.Lys197Ter	p.K197*	ENST00000257555		197	Aag/Tag	3/10	0.304282175007398	2	FACETS	0.398	0.354	0.444	0.199	0.177	0.222	INDETERMINATE	1	TRUE	0	0.555035004080696	2		685	879	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218393	133218393	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	517	942	0	ENST00000320574.5:c.5218C>T	p.Leu1740Phe	p.L1740F	ENST00000320574	NM_006231.2	1740	Ctc/Ttc	39/49	0.304282175007398	2	FACETS	0.761	0.731	0.792	0.761	0.731	0.792	INDETERMINATE	2	TRUE	0	0.555035004080696	2		942	1224	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32903613	32903613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555281352	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	175	688	0	ENST00000380152.3:c.665C>T	p.Pro222Leu	p.P222L	ENST00000380152		222	cCt/cTt	8/27	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.555035004080696	2		688	615	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240225	41240225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	75	264	0	ENST00000379561.5:c.125C>T	p.Pro42Leu	p.P42L	ENST00000379561	NM_002015.3	42	cCg/cTg	1/3	1	2	FACETS	0.711	0.627	0.801	0.711	0.627	0.801	SUBCLONAL	1	TRUE	1	0.555035004080696	2		264	380	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041074	42041074	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	130	646	1	ENST00000219905.7:c.5452C>T	p.Arg1818Ter	p.R1818*	ENST00000219905	NM_001164273.1	1818	Cga/Tga	16/24	0.376719847779552	1	FACETS	0.349	0.316	0.384	0.349	0.316	0.384	SUBCLONAL	1	TRUE	0	0.555035004080696	1		647	970	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762085	43762085	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	301	738	0	ENST00000382044.4:c.1360C>T	p.Pro454Ser	p.P454S	ENST00000382044	NM_001141980.1	454	Cct/Tct	11/28	0.376719847779552	1	FACETS	0.9	0.85	0.95	0.9	0.85	0.95	CLONAL	1	TRUE	0	0.555035004080696	1		738	871	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396238	396238	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	372	985	2	ENST00000262320.3:c.788C>T	p.Pro263Leu	p.P263L	ENST00000262320	NM_003502.3	263	cCc/cTc	2/11	0.2125262709173	1	FACETS	0.891	0.847	0.936	0.891	0.847	0.936	INDETERMINATE	1	TRUE	0	0.555035004080696	1		987	1087	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121599	2121599	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	99	962	0	ENST00000219476.3:c.1928A>T	p.Tyr643Phe	p.Y643F	ENST00000219476	NM_000548.3	643	tAc/tTc	18/42	0.2125262709173	1	FACETS	0.229	0.204	0.257	0.229	0.204	0.257	INDETERMINATE	1	TRUE	0	0.555035004080696	1		962	1124	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639572	3639572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764254888	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	225	1127	0	ENST00000294008.3:c.4067C>T	p.Pro1356Leu	p.P1356L	ENST00000294008	NM_032444.2	1356	cCg/cTg	12/15	0.2125262709173	1	FACETS	0.5	0.465	0.536	0.5	0.465	0.536	INDETERMINATE	1	TRUE	0	0.555035004080696	1		1127	1172	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777965	3777966	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	441	1461	1	ENST00000262367.5:c.7082_7083delinsTT	p.Ser2361Phe	p.S2361F	ENST00000262367	NM_004380.2	2361	tCC/tTT	31/31	0.2125262709173	1	FACETS	0.817	0.779	0.856	0.817	0.779	0.856	INDETERMINATE	1	TRUE	0	0.555035004080696	1		1462	1405	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858201	9858201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	291	451	0	ENST00000330684.3:c.3200G>A	p.Arg1067Gln	p.R1067Q	ENST00000330684	NM_001134407.1	1067	cGg/cAg	13/13	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.555035004080696	2		451	837	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273929	10273929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	273	1109	1	ENST00000330684.3:c.340G>A	p.Asp114Asn	p.D114N	ENST00000330684	NM_001134407.1	114	Gat/Aat	2/13	1	2	FACETS	0.786	0.736	0.836	0.786	0.736	0.836	SUBCLONAL	1	TRUE	1	0.555035004080696	2		1110	1252	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646654	23646654	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	198	594	0	ENST00000261584.4:c.1213C>T	p.Pro405Ser	p.P405S	ENST00000261584	NM_024675.3	405	Cct/Tct	4/13	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.555035004080696	2		594	680	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644985	67644985	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	303	676	0	ENST00000264010.4:c.250C>T	p.Pro84Ser	p.P84S	ENST00000264010	NM_006565.3	84	Cca/Tca	3/12	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.555035004080696	2		676	892	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827265	72827265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	209	734	0	ENST00000268489.5:c.9316C>T	p.Leu3106Phe	p.L3106F	ENST00000268489	NM_006885.3	3106	Ctt/Ttt	9/10	1	2	FACETS	0.812	0.755	0.872	0.812	0.755	0.872	CLONAL	1	TRUE	1	0.555035004080696	2		734	927	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992910	72992910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147445846	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	292	949	0	ENST00000268489.5:c.1135C>T	p.Leu379Phe	p.L379F	ENST00000268489	NM_006885.3	379	Ctc/Ttc	2/10	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.555035004080696	2		949	1046	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836354	89836354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762439008	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	271	818	1	ENST00000389301.3:c.2395C>T	p.Pro799Ser	p.P799S	ENST00000389301	NM_000135.2	799	Cca/Tca	26/43	1	2	FACETS	0.938	0.881	0.997	0.938	0.881	0.997	CLONAL	1	TRUE	1	0.555035004080696	2		819	1041	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676264	29676264	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	131	515	2	ENST00000356175.3:c.7253T>A	p.Leu2418Ter	p.L2418*	ENST00000356175	NM_000267.3	2418	tTa/tAa	48/57	1	2	FACETS	0.881	0.803	0.961	0.881	0.803	0.961	CLONAL	1	TRUE	1	0.555035004080696	2		517	536	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247772	10247772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769347864	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	486	1083	0	ENST00000340748.4:c.4430C>T	p.Ser1477Phe	p.S1477F	ENST00000340748		1477	tCc/tTc	36/40	0.266948475559893	4	FACETS	0.914	0.874	0.955	0.914	0.874	0.955	INDETERMINATE	2	TRUE	2	0.555035004080696	4		1083	1490	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271888	15271888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269752929	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	482	1093	1	ENST00000263388.2:c.6551C>T	p.Ser2184Leu	p.S2184L	ENST00000263388	NM_000435.2	2184	tCg/tTg	33/33	0.208895863219656	4	FACETS	0.9	0.86	0.941	0.9	0.86	0.941	INDETERMINATE	2	TRUE	2	0.555035004080696	4		1094	1500	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296349	15296349	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	517	1090	1	ENST00000263388.2:c.2093C>T	p.Pro698Leu	p.P698L	ENST00000263388	NM_000435.2	698	cCc/cTc	13/33	0.208895863219656	4	FACETS	0.96	0.919	1	0.96	0.919	1	INDETERMINATE	2	TRUE	2	0.555035004080696	4		1091	1509	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218426	36218426	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746495710	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	488	840	2	ENST00000222270.7:c.4205G>A	p.Arg1402Gln	p.R1402Q	ENST00000222270	NM_014727.1	1402	cGa/cAa	16/37	0.208895863219656	4	FACETS	1	0.985	1	1	0.985	1	INDETERMINATE	2	TRUE	2	0.555035004080696	4		842	1292	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224527	36224527	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	608	1212	0	ENST00000222270.7:c.6989C>T	p.Thr2330Ile	p.T2330I	ENST00000222270	NM_014727.1	2330	aCa/aTa	29/37	0.208895863219656	4	FACETS	0.981	0.943	1	0.981	0.943	1	INDETERMINATE	2	TRUE	2	0.555035004080696	4		1212	1736	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868374	45868374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	529	1128	0	ENST00000391945.4:c.403C>T	p.His135Tyr	p.H135Y	ENST00000391945	NM_000400.3	135	Cac/Tac	6/23	0.208895863219656	4	FACETS	0.877	0.84	0.916	0.877	0.84	0.916	INDETERMINATE	2	TRUE	2	0.555035004080696	4		1128	1689	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919914	50919914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs550922227	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	515	990	0	ENST00000440232.2:c.3001G>A	p.Gly1001Ser	p.G1001S	ENST00000440232	NM_002691.3	1001	Ggc/Agc	24/27	0.208895863219656	4	FACETS	0.958	0.918	0.999	0.958	0.918	0.999	INDETERMINATE	2	TRUE	2	0.555035004080696	4		990	1506	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085863	16085863	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	226	625	0	ENST00000281043.3:c.1039C>A	p.Gln347Lys	p.Q347K	ENST00000281043	NM_005378.4	347	Cag/Aag	3/3	0.309912393662049	1	FACETS	0.937	0.878	0.997	0.937	0.878	0.997	INDETERMINATE	1	TRUE	0	0.555035004080696	1		625	628	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467462	25467463	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	320	1027	2	ENST00000264709.3:c.1613_1614delinsTT	p.Thr538Ile	p.T538I	ENST00000264709	NM_175629.2	538	aCC/aTT	14/23	0.309912393662049	1	FACETS	0.816	0.771	0.861	0.816	0.771	0.861	INDETERMINATE	1	TRUE	0	0.555035004080696	1		1029	1021	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497836	25497836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	168	822	0	ENST00000264709.3:c.613G>A	p.Glu205Lys	p.E205K	ENST00000264709	NM_175629.2	205	Gag/Aag	6/23	0.309912393662049	1	FACETS	0.467	0.429	0.507	0.467	0.429	0.507	INDETERMINATE	1	TRUE	0	0.555035004080696	1		822	936	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917787	29917787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	227	970	0	ENST00000389048.3:c.881C>T	p.Pro294Leu	p.P294L	ENST00000389048	NM_004304.4	294	cCc/cTc	3/29	0.309912393662049	1	FACETS	0.546	0.508	0.585	0.546	0.508	0.585	INDETERMINATE	1	TRUE	0	0.555035004080696	1		970	1083	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718720	190718720	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	106	681	0	ENST00000441310.2:c.878C>T	p.Pro293Leu	p.P293L	ENST00000441310	NM_000534.4	293	cCt/cTt	8/13	0.309912393662049	1	FACETS	0.399	0.358	0.443	0.399	0.358	0.443	INDETERMINATE	1	TRUE	0	0.555035004080696	1		681	691	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248440	212248440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	159	417	0	ENST00000342788.4:c.3827C>T	p.Pro1276Leu	p.P1276L	ENST00000342788	NM_005235.2	1276	cCt/cTt	28/28	0.309912393662049	1	FACETS	0.943	0.873	1	0.943	0.873	1	INDETERMINATE	1	TRUE	0	0.555035004080696	1		417	439	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248504	212248504	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	217	695	0	ENST00000342788.4:c.3763C>A	p.His1255Asn	p.H1255N	ENST00000342788	NM_005235.2	1255	Cac/Aac	28/28	0.309912393662049	1	FACETS	0.937	0.877	0.998	0.937	0.877	0.998	INDETERMINATE	1	TRUE	0	0.555035004080696	1		695	603	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293205	212293205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747975697	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	162	554	0	ENST00000342788.4:c.2647C>T	p.Pro883Ser	p.P883S	ENST00000342788	NM_005235.2	883	Cca/Tca	22/28	0.309912393662049	1	FACETS	0.837	0.773	0.902	0.837	0.773	0.902	INDETERMINATE	1	TRUE	0	0.555035004080696	1		554	504	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794820	242794820	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	184	746	1	ENST00000334409.5:c.389C>T	p.Pro130Leu	p.P130L	ENST00000334409	NM_005018.2	130	cCc/cTc	2/5	0.2125262709173	1	FACETS	0.583	0.539	0.629	0.583	0.539	0.629	INDETERMINATE	1	TRUE	0	0.555035004080696	1		747	821	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546743	9546743	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	179	366	0	ENST00000353224.5:c.1279G>A	p.Val427Met	p.V427M	ENST00000353224	NM_177990.2	427	Gtg/Atg	5/10	0.208895863219656	4	FACETS	0.888	0.823	0.953	0.888	0.823	0.953	INDETERMINATE	2	TRUE	2	0.555035004080696	4		366	565	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546847	9546847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	267	613	0	ENST00000353224.5:c.1175C>T	p.Ser392Leu	p.S392L	ENST00000353224	NM_177990.2	392	tCg/tTg	5/10	0.208895863219656	4	FACETS	0.907	0.853	0.961	0.907	0.853	0.961	INDETERMINATE	2	TRUE	2	0.555035004080696	4		613	825	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561201	9561201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	270	604	1	ENST00000353224.5:c.581G>A	p.Arg194Lys	p.R194K	ENST00000353224	NM_177990.2	194	aGa/aAa	4/10	0.208895863219656	4	FACETS	0.821	0.772	0.872	0.821	0.772	0.872	INDETERMINATE	2	TRUE	2	0.555035004080696	4		605	921	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561263	9561263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769939031	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	322	346	1	ENST00000353224.5:c.519G>A	p.Met173Ile	p.M173I	ENST00000353224	NM_177990.2	173	atG/atA	4/10	0.208895863219656	4	FACETS	0.929	0.879	0.98	0.929	0.879	0.98	INDETERMINATE	2	TRUE	2	0.555035004080696	4		347	971	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790158	40790158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781621750	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	349	638	0	ENST00000373198.4:c.2573C>T	p.Ser858Phe	p.S858F	ENST00000373198	NM_133170.3	858	tCc/tTc	18/32	0.208895863219656	4	FACETS	1	0.973	1	1	0.973	1	INDETERMINATE	2	TRUE	2	0.555035004080696	4		638	943	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62325742	62325742	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	383	858	0	ENST00000360203.5:c.3010C>T	p.Pro1004Ser	p.P1004S	ENST00000360203	NM_001283009.1	1004	Ccc/Tcc	31/35	0.208895863219656	4	FACETS	0.897	0.853	0.943	0.897	0.853	0.943	INDETERMINATE	2	TRUE	2	0.555035004080696	4		858	1196	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42851187	42851187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	337	798	0	ENST00000398585.3:c.706G>A	p.Gly236Arg	p.G236R	ENST00000398585	NM_001135099.1	236	Gga/Aga	7/14	0.304282175007398	2	FACETS	1	0.995	1	0.741	0.705	0.778	INDETERMINATE	1	TRUE	0	0.555035004080696	2		798	819	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545057	41545057	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	464	699	0	ENST00000263253.7:c.2257C>T	p.Pro753Ser	p.P753S	ENST00000263253	NM_001429.3	753	Cct/Tct	13/31	0.555035004080696	3	FACETS	0.985	0.944	1	0.985	0.944	1	CLONAL	2	TRUE	1	0.555035004080696	3		699	1084	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637740	52637740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	271	589	0	ENST00000394830.3:c.2576C>T	p.Ser859Leu	p.S859L	ENST00000394830	NM_018313.4	859	tCa/tTa	18/30	0.413148278862495	3	FACETS	0.781	0.735	0.827	0.781	0.735	0.827	SUBCLONAL	2	TRUE	1	0.555035004080696	3		589	799	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390149	89390149	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	200	531	0	ENST00000336596.2:c.898G>A	p.Gly300Ser	p.G300S	ENST00000336596	NM_005233.5	300	Ggt/Agt	4/17	0.291642928436873	3	FACETS	1	0.989	1	0.662	0.616	0.71	INDETERMINATE	1	TRUE	1	0.555035004080696	3		531	695	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462410	89462410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	244	787	0	ENST00000336596.2:c.1882G>A	p.Gly628Arg	p.G628R	ENST00000336596	NM_005233.5	628	Gga/Aga	10/17	0.291642928436873	3	FACETS	1	0.989	1	0.625	0.585	0.667	INDETERMINATE	1	TRUE	1	0.555035004080696	3		787	898	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480466	89480466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446890859	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	149	439	0	ENST00000336596.2:c.2303C>T	p.Ser768Leu	p.S768L	ENST00000336596	NM_005233.5	768	tCg/tTg	13/17	0.291642928436873	3	FACETS	1	0.955	1	0.532	0.487	0.578	INDETERMINATE	1	TRUE	1	0.555035004080696	3		439	645	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884833	134884833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371609605	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	306	649	0	ENST00000398015.3:c.1609G>A	p.Glu537Lys	p.E537K	ENST00000398015	NM_004441.4	537	Gag/Aag	8/16	0.291642928436873	3	FACETS	0.845	0.799	0.891	0.845	0.799	0.891	INDETERMINATE	2	TRUE	1	0.555035004080696	3		649	834	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920326	134920326	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	254	584	0	ENST00000398015.3:c.2141G>A	p.Gly714Glu	p.G714E	ENST00000398015	NM_004441.4	714	gGg/gAg	12/16	0.291642928436873	3	FACETS	0.782	0.735	0.829	0.782	0.735	0.829	INDETERMINATE	2	TRUE	1	0.555035004080696	3		584	748	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176504	142176504	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1196005889	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	208	634	1	ENST00000350721.4:c.7597C>T	p.Arg2533Ter	p.R2533*	ENST00000350721	NM_001184.3	2533	Cga/Tga	45/47	0.291642928436873	3	FACETS	1	0.976	1	0.555	0.515	0.595	INDETERMINATE	1	TRUE	1	0.555035004080696	3		635	863	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582157	189582157	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	315	707	2	ENST00000264731.3:c.716A>T	p.Glu239Val	p.E239V	ENST00000264731	NM_003722.4	239	gAg/gTg	5/14	0.291642928436873	3	FACETS	0.786	0.743	0.829	0.786	0.743	0.829	INDETERMINATE	2	TRUE	1	0.555035004080696	3		709	923	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526934	31526934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	660	1032	3	ENST00000344624.3:c.106C>T	p.Pro36Ser	p.P36S	ENST00000344624		36	Ccc/Tcc	2/33	0.54877998091093	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.555035004080696	2		1035	1170	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867469	35867469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs191585195	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	280	566	0	ENST00000303115.3:c.283G>A	p.Glu95Lys	p.E95K	ENST00000303115	NM_002185.3	95	Gag/Aag	3/8	0.54877998091093	2	FACETS	0.902	0.857	0.948	0.902	0.857	0.948	CLONAL	2	TRUE	0	0.555035004080696	2		566	559	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80057385	80057385	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	349	607	0	ENST00000265081.6:c.1784A>G	p.Asp595Gly	p.D595G	ENST00000265081	NM_002439.4	595	gAt/gGt	13/24	0.54877998091093	2	FACETS	0.975	0.933	1	0.975	0.933	1	CLONAL	2	TRUE	0	0.555035004080696	2		607	645	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672362	30672364	+	frameshift_variant	Frame_Shift_Del	DEL	GCG	GCG	CA	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1262	315	876	3	ENST00000376406.3:c.4596_4598delinsTG	p.Ala1533GlufsTer42	p.A1533Efs*42	ENST00000376406	NM_014641.2	1532	ccCGCa/ccTGa	10/15	0.555035004080696	3	FACETS	0.92	0.865	0.975	0.46	0.432	0.488	CLONAL	1	TRUE	1	0.555035004080696	3		879	1577	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188196	32188196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	268	723	0	ENST00000375023.3:c.1145C>T	p.Pro382Leu	p.P382L	ENST00000375023	NM_004557.3	382	cCa/cTa	6/30	0.555035004080696	3	FACETS	1	0.955	1	0.512	0.479	0.545	CLONAL	1	TRUE	1	0.555035004080696	3		723	1205	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188847	32188847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	369	739	0	ENST00000375023.3:c.707G>A	p.Gly236Glu	p.G236E	ENST00000375023	NM_004557.3	236	gGa/gAa	4/30	0.555035004080696	3	FACETS	1	0.991	1	0.595	0.563	0.627	CLONAL	1	TRUE	1	0.555035004080696	3		739	1428	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979332	93979332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	316	701	1	ENST00000369303.4:c.1496C>T	p.Ser499Leu	p.S499L	ENST00000369303	NM_004440.3	499	tCa/tTa	7/17	0.54877998091093	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.555035004080696	2		702	544	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242451	55242451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	533	410	0	ENST00000275493.2:c.2221C>T	p.Pro741Ser	p.P741S	ENST00000275493	NM_005228.3	741	Ccc/Tcc	19/28	0.555035004080696	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.555035004080696	3		410	1192	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509537	106509537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774366285	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	316	735	0	ENST00000359195.3:c.1531G>A	p.Glu511Lys	p.E511K	ENST00000359195	NM_002649.2	511	Gag/Aag	2/11	0.555035004080696	3	FACETS	1	0.974	1	0.528	0.497	0.56	CLONAL	1	TRUE	1	0.555035004080696	3		735	1377	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939506	68939506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1309816810	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	292	719	0	ENST00000288368.4:c.491G>A	p.Gly164Glu	p.G164E	ENST00000288368	NM_024870.2	164	gGa/gAa	5/40	0.208895863219656	4	FACETS	0.852	0.803	0.902	0.852	0.803	0.902	INDETERMINATE	2	TRUE	2	0.555035004080696	4		719	960	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020471	69020471	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	418	963	1	ENST00000288368.4:c.2843C>T	p.Pro948Leu	p.P948L	ENST00000288368	NM_024870.2	948	cCc/cTc	24/40	0.208895863219656	4	FACETS	0.933	0.889	0.978	0.933	0.889	0.978	INDETERMINATE	2	TRUE	2	0.555035004080696	4		964	1255	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058471	69058471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	227	705	0	ENST00000288368.4:c.4115G>A	p.Gly1372Glu	p.G1372E	ENST00000288368	NM_024870.2	1372	gGa/gAa	34/40	0.208895863219656	4	FACETS	0.837	0.782	0.893	0.837	0.782	0.893	INDETERMINATE	2	TRUE	2	0.555035004080696	4		705	760	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058549	69058549	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	336	1026	0	ENST00000288368.4:c.4193G>A	p.Gly1398Glu	p.G1398E	ENST00000288368	NM_024870.2	1398	gGa/gAa	34/40	0.208895863219656	4	FACETS	0.864	0.817	0.911	0.864	0.817	0.911	INDETERMINATE	2	TRUE	2	0.555035004080696	4		1026	1090	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69143608	69143608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	208	485	2	ENST00000288368.4:c.4816G>A	p.Glu1606Lys	p.E1606K	ENST00000288368	NM_024870.2	1606	Gaa/Aaa	40/40	0.208895863219656	4	FACETS	0.852	0.794	0.911	0.852	0.794	0.911	INDETERMINATE	2	TRUE	2	0.555035004080696	4		487	684	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978524	70978524	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1280479464	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	279	743	0	ENST00000276594.2:c.1129C>T	p.Pro377Ser	p.P377S	ENST00000276594	NM_024504.3	377	Cct/Tct	5/8	0.208895863219656	4	FACETS	0.851	0.801	0.903	0.851	0.801	0.903	INDETERMINATE	2	TRUE	2	0.555035004080696	4		743	918	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145743087	145743088	+	stop_gained,splice_region_variant	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	50	69	1	ENST00000428558.2:c.81_82delinsTT	p.Gln28Ter	p.Q28*	ENST00000428558	NM_004260.3	27	agCCag/agTTag	1/22	0.339933588531544	4	FACETS	1	0.893	1	1	0.893	1	CLONAL	2	TRUE	2	0.555035004080696	4		70	136	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340396	8340397	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	338	682	2	ENST00000356435.5:c.5199_5200delinsAA	p.Trp1733_Glu1734delinsTer	p.W1733_E1734delins*	ENST00000356435		1733	tgGGaa/tgAAaa	31/35	0.513066642430504	2	FACETS	0.889	0.848	0.93	0.889	0.848	0.93	CLONAL	2	TRUE	0	0.555035004080696	2		684	685	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404555	8404555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	215	442	0	ENST00000356435.5:c.4192C>T	p.Leu1398Phe	p.L1398F	ENST00000356435		1398	Ctc/Ttc	25/35	0.513066642430504	2	FACETS	0.966	0.913	1	0.966	0.913	1	CLONAL	2	TRUE	0	0.555035004080696	2		442	401	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482167	87482167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	399	850	0	ENST00000277120.3:c.1454C>T	p.Ser485Phe	p.S485F	ENST00000277120		485	tCc/tTc	14/19	0.555035004080696	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.555035004080696	1		850	838	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391574	139391574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	466	1171	2	ENST00000277541.6:c.6617C>T	p.Pro2206Leu	p.P2206L	ENST00000277541	NM_017617.3	2206	cCc/cTc	34/34	0.555035004080696	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.555035004080696	1		1173	1061	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0021849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	97	282	0				ENST00000310581	NM_198253.2	-/1132			0.205770785886475	4	FACETS	0.872	0.78	0.969	0.872	0.78	0.969	CLONAL	2	TRUE	2	0.26575491209323	4		282	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764146326	NA	P-0021849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	94	660	1	ENST00000269305.4:c.841G>A	p.Asp281Asn	p.D281N	ENST00000269305	NM_001126112.2	281	Gac/Aac	8/11	1	2	FACETS	0.795	0.706	0.89	0.795	0.706	0.89	SUBCLONAL	1	TRUE	1	0.26575491209323	2		661	890	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412046	116412046	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	G	novel	NA	P-0021849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	191	832	0	ENST00000397752.3:c.3028+3A>G		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.26575491209323	2	FACETS	0.956	0.886	1	0.956	0.886	1	CLONAL	2	TRUE	0	0.26575491209323	2		832	752	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971012	21971012	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1477500164	NA	P-0021864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	465	544	0	ENST00000304494.5:c.346G>T	p.Asp116Tyr	p.D116Y	ENST00000304494	NM_000077.4	116	Gac/Tac	2/3	0.457407711615655	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.457407711615655	2		544	836	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278092	18278092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	528	851	4	ENST00000222254.8:c.1712G>A	p.Arg571His	p.R571H	ENST00000222254	NM_005027.3	571	cGc/cAc	13/16	0.457407711615655	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.457407711615655	2		855	1138	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600428	10600428	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	602	895	0	ENST00000171111.5:c.1427G>T	p.Gly476Val	p.G476V	ENST00000171111	NM_203500.1	476	gGg/gTg	4/6	0.457407711615655	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.457407711615655	2		895	1234	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111404	56111404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	272	480	1	ENST00000399503.3:c.4G>A	p.Ala2Thr	p.A2T	ENST00000399503	NM_005921.1	2	Gcg/Acg	1/20	0.457407711615655	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.457407711615655	2		481	563	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373183	118373183	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	212	656	0	ENST00000534358.1:c.6576C>A	p.Ser2192Arg	p.S2192R	ENST00000534358	NM_005933.3	2192	agC/agA	27/36	0.207235261091416	3	FACETS	1	0.986	1	0.415	0.386	0.445	INDETERMINATE	1	TRUE	0	0.457407711615655	3		656	915	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133238241	133238241	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	402	599	0	ENST00000320574.5:c.2736G>T	p.Glu912Asp	p.E912D	ENST00000320574	NM_006231.2	912	gaG/gaT	24/49	0.387040973543433	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	2	0.457407711615655	4		599	1227	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250252	133250252	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1292	223	855	0	ENST00000320574.5:c.1268A>G	p.Asn423Ser	p.N423S	ENST00000320574	NM_006231.2	423	aAt/aGt	13/49	0.387040973543433	4	FACETS	0.938	0.871	1	0.469	0.435	0.504	CLONAL	1	TRUE	2	0.457407711615655	4		855	1515	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829667	72829667	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	375	820	0	ENST00000268489.5:c.6914G>C	p.Gly2305Ala	p.G2305A	ENST00000268489	NM_006885.3	2305	gGa/gCa	9/10	0.207235261091416	3	FACETS	0.947	0.9	0.994	0.631	0.6	0.663	INDETERMINATE	2	TRUE	0	0.457407711615655	3		820	1064	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579350	7579360	+	frameshift_variant	Frame_Shift_Del	DEL	AGCCCAGACGG	AGCCCAGACGG	-	novel	NA	P-0021864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	408	762	0	ENST00000269305.4:c.327_337del	p.Arg110LeufsTer35	p.R110Lfs*35	ENST00000269305	NM_001126112.2	109	ttCCGTCTGGGCTtc/tttc	4/11	0.457407711615655	2	FACETS	0.917	0.876	0.958	0.917	0.876	0.958	CLONAL	2	TRUE	0	0.457407711615655	2		762	973	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976132	7976132	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	475	829	0	ENST00000319144.4:c.2063A>G	p.Tyr688Cys	p.Y688C	ENST00000319144	NM_001139.2	688	tAc/tGc	15/15	0.457407711615655	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.457407711615655	2		829	973	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39623724	39623724	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	92	609	0	ENST00000262039.4:c.2131G>C	p.Glu711Gln	p.E711Q	ENST00000262039	NM_002647.2	711	Gag/Cag	20/25	1	2	FACETS	0.969	0.867	1	0.969	0.867	1	CLONAL	1	TRUE	1	0.457407711615655	2		609	415	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765745	41765745	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	378	617	0	ENST00000301178.4:c.2621C>T	p.Pro874Leu	p.P874L	ENST00000301178	NM_021913.4	874	cCt/cTt	20/20	0.457407711615655	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.457407711615655	2		617	789	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101116	41101116	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1321294629	NA	P-0021864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	579	762	0	ENST00000373198.4:c.1240G>T	p.Val414Leu	p.V414L	ENST00000373198	NM_133170.3	414	Gtg/Ttg	8/32	0.457407711615655	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	2	0.457407711615655	4		762	1588	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146454	185146454	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	141	497	0	ENST00000265026.3:c.85G>T	p.Asp29Tyr	p.D29Y	ENST00000265026	NM_004721.4	29	Gat/Tat	2/14	0.280173119255056	5	FACETS	1	0.967	1	0.376	0.342	0.412	CLONAL	1	TRUE	2	0.457407711615655	5		497	921	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502237	186502237	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	222	406	0	ENST00000323963.5:c.46G>C	p.Glu16Gln	p.E16Q	ENST00000323963		16	Gag/Cag	2/11	0.280173119255056	5	FACETS	1	0.968	1	0.707	0.66	0.755	CLONAL	2	TRUE	2	0.457407711615655	5		406	772	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722054	176722054	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	323	504	2	ENST00000439151.2:c.7685G>T	p.Gly2562Val	p.G2562V	ENST00000439151	NM_022455.4	2562	gGg/gTg	23/23	0.457407711615655	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.457407711615655	2		506	647	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798403	32798403	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	198	765	0	ENST00000374899.4:c.1453G>C	p.Val485Leu	p.V485L	ENST00000374899	NM_018833.2	485	Gtg/Ctg	8/12	1	2	FACETS	0.918	0.851	0.988	0.918	0.851	0.988	CLONAL	1	TRUE	1	0.457407711615655	2		765	943	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172275	38172276	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0021864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	256	541	0	ENST00000317025.8:c.2131_2132delinsTT	p.Gly711Phe	p.G711F	ENST00000317025	NM_023034.1	711	GGt/TTt	12/24	0.418274573552331	4	FACETS	0.784	0.734	0.835			1	SUBCLONAL	2	TRUE	NA	0.457407711615655	4		541	1041	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030812	69030812	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	301	549	0	ENST00000288368.4:c.3354C>G	p.Ile1118Met	p.I1118M	ENST00000288368	NM_024870.2	1118	atC/atG	27/40	0.226572797081433	3	FACETS	1	0.975	1	0.699	0.662	0.737	INDETERMINATE	2	TRUE	0	0.457407711615655	3		549	771	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521416	8521416	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	448	833	1	ENST00000356435.5:c.822A>C	p.Glu274Asp	p.E274D	ENST00000356435		274	gaA/gaC	9/35	0.457407711615655	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.457407711615655	2		834	916	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971060	21971060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200863613	NA	P-0021864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	384	456	0	ENST00000304494.5:c.298G>A	p.Ala100Thr	p.A100T	ENST00000304494	NM_000077.4	100	Gcc/Acc	2/3	0.457407711615655	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.457407711615655	2		456	706	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0022350-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	27	228	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.781	0.631	0.946	0.781	0.631	0.946	CLONAL	1	TRUE	1	0.54454962950067	2		228	127	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346437	89346437	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555525603	NA	P-0022350-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	13	536	2	ENST00000301030.4:c.6513del	p.Val2173SerfsTer2	p.V2173Sfs*2	ENST00000301030	NM_001256183.1	2171	ccC/cc	9/13	0.54454962950067	1	FACETS	0.217	0.155	0.292	0.217	0.155	0.292	SUBCLONAL	1	TRUE	0	0.54454962950067	1		538	160	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772209	68772231	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCTCTGCCAGGAGCCGGAGCC	TGGCTCTGCCAGGAGCCGGAGCC	-	novel	NA	P-0022350-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	98	523	1	ENST00000261769.5:c.58_80del	p.Trp20LeufsTer6	p.W20Lfs*6	ENST00000261769	NM_004360.3	20	TGGCTCTGCCAGGAGCCGGAGCCc/c	2/16	0.54454962950067	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.54454962950067	1		524	213	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79974857	79974857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022350-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	36	335	0	ENST00000265081.6:c.1285C>T	p.Pro429Ser	p.P429S	ENST00000265081	NM_002439.4	429	Cct/Tct	8/24	0.150042919479414	4	FACETS	0.888	0.735	1	0.444	0.367	0.528	INDETERMINATE	1	TRUE	2	0.54454962950067	4		335	230	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668729	52668729	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022350-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	25	319	0	ENST00000394830.3:c.1190G>T	p.Arg397Leu	p.R397L	ENST00000394830	NM_018313.4	397	cGg/cTg	12/30	1	2	FACETS	0.496	0.394	0.612	0.496	0.394	0.612	SUBCLONAL	1	TRUE	1	0.54454962950067	2		319	185	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971023	21971023	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	115	624	0	ENST00000304494.5:c.335del	p.Arg112LeufsTer34	p.R112Lfs*34	ENST00000304494	NM_000077.4	112	cGt/ct	2/3	0.247720835035614	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	0	0.247720835035614	2		624	450	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0022393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	95	512	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.247720835035614	5	FACETS	0.817	0.728	0.911	0.408	0.364	0.456	CLONAL	2	TRUE	1	0.247720835035614	5		512	644	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971024	21971024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	114	611	1	ENST00000304494.5:c.334C>T	p.Arg112Cys	p.R112C	ENST00000304494	NM_000077.4	112	Cgt/Tgt	2/3	0.247720835035614	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	0	0.247720835035614	2		612	450	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0022393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	162	563	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	0.21736669148065	3	FACETS	0.947	0.87	1	0.947	0.87	1	CLONAL	2	TRUE	1	0.247720835035614	3		563	776	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42788861	42788861	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	110	723	0	ENST00000575354.2:c.5A>G	p.Tyr2Cys	p.Y2C	ENST00000575354	NM_015125.3	2	tAt/tGt	1/20	0.247720835035614	5	FACETS	0.908	0.817	1	0.605	0.544	0.669	CLONAL	2	TRUE	2	0.247720835035614	5		723	671	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280007	66280007	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	18	332	0	ENST00000273854.3:c.1682C>A	p.Pro561Gln	p.P561Q	ENST00000273854	NM_004439.5	561	cCa/cAa	7/18	0.21736669148065	3	FACETS	0.571	0.43	0.738	0.286	0.215	0.369	SUBCLONAL	1	TRUE	1	0.247720835035614	3		332	286	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339147	65339147	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	41	723	0	ENST00000342505.4:c.389C>G	p.Ser130Cys	p.S130C	ENST00000342505	NM_002227.2	130	tCt/tGt	5/25	0.247720835035614	3	FACETS	0.611	0.508	0.726	0.305	0.254	0.363	SUBCLONAL	1	TRUE	1	0.247720835035614	3		723	609	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233243	46233243	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	24	666	1	ENST00000334344.6:c.1462C>T	p.Gln488Ter	p.Q488*	ENST00000334344	NM_152641.2	488	Caa/Taa	11/21	0.159292043390182	4	FACETS	0.58	0.454	0.725	0.29	0.227	0.363	SUBCLONAL	1	TRUE	2	0.247720835035614	4		667	417	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434606	49434610	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	AGGTG	AGGTG	TCA	novel	NA	P-0022393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	116	1212	2	ENST00000301067.7:c.6943_6947delinsTGA	p.His2315Ter	p.H2315*	ENST00000301067	NM_003482.3	2315	CACCTg/TGAg	31/54	0.159292043390182	4	FACETS	1	0.97	1	0.603	0.542	0.667	CLONAL	1	TRUE	2	0.247720835035614	4		1214	969	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265428	152265428	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	142	739	1	ENST00000206249.3:c.881G>T	p.Ser294Ile	p.S294I	ENST00000206249	NM_000125.3	294	aGc/aTc	4/8	0.247720835035614	4	FACETS	0.923	0.842	1	0.923	0.842	1	CLONAL	2	TRUE	2	0.247720835035614	4		740	775	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820231	139820231	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	69	1008	1	ENST00000247668.2:c.1384G>T	p.Asp462Tyr	p.D462Y	ENST00000247668	NM_021138.3	462	Gac/Tac	11/11	0.247720835035614	2	FACETS	0.685	0.596	0.782	0.343	0.298	0.391	SUBCLONAL	1	TRUE	0	0.247720835035614	2		1009	813	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937390	76937390	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1557137601	NA	P-0022393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	93	454	2	ENST00000373344.5:c.3358G>T	p.Asp1120Tyr	p.D1120Y	ENST00000373344	NM_000489.3	1120	Gat/Tat	9/35	0.247720835035614	2	FACETS	1	0.916	1			1	CLONAL	3	TRUE	NA	0.247720835035614	2		456	247	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	89	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.327	0.29	0.366	0.327	0.29	0.366	SUBCLONAL	1	FALSE	1	0.874824132261367	2		215	623	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0022528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	52	720	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.174	0.147	0.203	0.174	0.147	0.203	SUBCLONAL	1	FALSE	1	0.874824132261367	2		722	684	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913381	NA	P-0022528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	71	219	1	ENST00000304494.5:c.322G>T	p.Asp108Tyr	p.D108Y	ENST00000304494	NM_000077.4	108	Gat/Tat	2/3	1	2	FACETS	0.272	0.237	0.309	0.272	0.237	0.309	SUBCLONAL	1	FALSE	1	0.874824132261367	2		220	597	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36208923	36208925	+	start_lost,inframe_deletion	Translation_Start_Site	DEL	GGC	GGC	-	rs898578503	NA	P-0022528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	10	53	0	ENST00000222270.7:c.14_16del	p.Ala5?	p.A5?	ENST00000222270	NM_014727.1	1	atGGCg/atg	1/37	1	2	FACETS	0.191	0.129	0.266	0.191	0.129	0.266	SUBCLONAL	1	FALSE	1	0.874824132261367	2		53	120	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	203	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.936	0.877	0.995	0.936	0.877	0.995	CLONAL	1	TRUE	1	0.91501814814052	2		215	474	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0022605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	253	499	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.91501814814052	2		499	539	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0022605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	219	413	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.981	0.923	1	0.981	0.923	1	CLONAL	1	TRUE	1	0.91501814814052	2		413	488	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913381	NA	P-0022605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	296	219	1	ENST00000304494.5:c.322G>T	p.Asp108Tyr	p.D108Y	ENST00000304494	NM_000077.4	108	Gat/Tat	2/3	0.91501814814052	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.91501814814052	1		220	334	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652225	36652226	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	276	720	0	ENST00000244741.5:c.349dup	p.Cys117LeufsTer12	p.C117Lfs*12	ENST00000244741	NM_000389.4	116	tct/tcTt	2/3	1	2	FACETS	0.93	0.879	0.98	0.93	0.879	0.98	CLONAL	1	TRUE	1	0.91501814814052	2		720	649	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313274	65313274	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	289	661	0	ENST00000342505.4:c.1840G>C	p.Glu614Gln	p.E614Q	ENST00000342505	NM_002227.2	614	Gag/Cag	13/25	1	2	FACETS	0.975	0.924	1	0.975	0.924	1	CLONAL	1	TRUE	1	0.91501814814052	2		661	648	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426235	49426235	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	363	771	2	ENST00000301067.7:c.12253C>T	p.Gln4085Ter	p.Q4085*	ENST00000301067	NM_003482.3	4085	Cag/Tag	39/54	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.91501814814052	2		773	780	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40681810	40681810	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs768877625	NA	P-0022605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	102	239	0	ENST00000249776.8:c.589C>G	p.Gln197Glu	p.Q197E	ENST00000249776	NM_033286.3	197	Cag/Gag	5/9	1	2	FACETS	0.851	0.774	0.93	0.851	0.774	0.93	CLONAL	1	TRUE	1	0.91501814814052	2		239	262	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832898	3832898	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	197	427	1	ENST00000262367.5:c.1360C>T	p.Gln454Ter	p.Q454*	ENST00000262367	NM_004380.2	454	Caa/Taa	6/31	1	2	FACETS	0.914	0.856	0.974	0.914	0.856	0.974	CLONAL	1	TRUE	1	0.91501814814052	2		428	471	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368369	225368370	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	209	436	0	ENST00000264414.4:c.1376dup	p.Thr460AspfsTer2	p.T460Dfs*2	ENST00000264414	NM_003590.4	459	aag/aaAg	9/16	1	2	FACETS	0.89	0.835	0.947	0.89	0.835	0.947	CLONAL	1	TRUE	1	0.91501814814052	2		436	513	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922932	44922947	+	frameshift_variant	Frame_Shift_Del	DEL	TAACAGGAAGTGGAAG	TAACAGGAAGTGGAAG	-	novel	NA	P-0022605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	241	259	0	ENST00000377967.4:c.1796_1811del	p.Thr599MetfsTer21	p.T599Mfs*21	ENST00000377967	NM_021140.2	598	aTAACAGGAAGTGGAAGt/at	16/29	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.91501814814052	1		259	276	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0022763-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	288	505	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.271453502634642	6	FACETS	1	0.96	1	0.769	0.724	0.816	CLONAL	3	FALSE	2	0.271453502634642	6		505	1064	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782369	9782369	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022763-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	62	715	0	ENST00000377346.4:c.2302G>A	p.Ala768Thr	p.A768T	ENST00000377346	NM_005026.3	768	Gca/Aca	18/24	0.262942947574006	3	FACETS	0.534	0.459	0.615	0.267	0.229	0.308	SUBCLONAL	1	FALSE	1	0.271453502634642	3		715	972	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348743	89348743	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542863039	NA	P-0022763-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	130	872	0	ENST00000301030.4:c.4207G>A	p.Gly1403Arg	p.G1403R	ENST00000301030	NM_001256183.1	1403	Gga/Aga	9/13	0.257798987311023	3	FACETS	0.945	0.855	1	0.315	0.285	0.347	CLONAL	1	FALSE	0	0.271453502634642	3		872	1151	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971003	21971003	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	43	484	0	ENST00000304494.5:c.355G>T	p.Glu119Ter	p.E119*	ENST00000304494	NM_000077.4	119	Gag/Tag	2/3	0.154532751127728	1	FACETS	0.663	0.553	0.785	0.663	0.553	0.785	SUBCLONAL	1	TRUE	0	0.18	1		484	656	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578496	7578496	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	100	1095	0	ENST00000269305.4:c.434T>G	p.Leu145Arg	p.L145R	ENST00000269305	NM_001126112.2	145	cTg/cGg	5/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.18	2		1095	908	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46727002	46727002	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	64	839	1	ENST00000371975.4:c.836G>T	p.Arg279Leu	p.R279L	ENST00000371975	NM_003579.3	279	cGc/cTc	8/18	1	2	FACETS	0.925	0.799	1	0.925	0.799	1	CLONAL	1	TRUE	1	0.18	2		840	769	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862887	9862887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868222927	NA	P-0022794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	42	906	2	ENST00000330684.3:c.2416G>A	p.Glu806Lys	p.E806K	ENST00000330684	NM_001134407.1	806	Gag/Aag	12/13	1	2	FACETS	0.647	0.539	0.768	0.647	0.539	0.768	SUBCLONAL	1	TRUE	1	0.18	2		908	721	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635130	87635130	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	47	574	0	ENST00000277120.3:c.2182C>A	p.His728Asn	p.H728N	ENST00000277120		728	Cac/Aac	18/19	1	2	FACETS	0.989	0.834	1	0.989	0.834	1	CLONAL	1	TRUE	1	0.18	2		574	528	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100949	27100949	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	44	557	0	ENST00000324856.7:c.4231C>T	p.Gln1411Ter	p.Q1411*	ENST00000324856	NM_006015.4	1411	Cag/Tag	18/20	1	2	FACETS	0.745	0.624	0.88	0.745	0.624	0.88	SUBCLONAL	1	TRUE	1	0.18	2		557	656	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273016	115273016	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	58	952	0	ENST00000438362.2:c.1357G>T	p.Ala453Ser	p.A453S	ENST00000438362	NM_001242891.1	453	Gct/Tct	12/20	1	2	FACETS	0.852	0.731	0.985	0.852	0.731	0.985	CLONAL	1	TRUE	1	0.18	2		952	756	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465976	69465976	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	108	934	2	ENST00000227507.2:c.814G>T	p.Glu272Ter	p.E272*	ENST00000227507	NM_053056.2	272	Gag/Tag	5/5	0.281609792026025	3	FACETS	0.919	0.825	1	0.919	0.825	1	CLONAL	2	TRUE	1	0.18	3		936	712	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912760	100912760	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	98	903	1	ENST00000325455.5:c.2562G>T	p.Lys854Asn	p.K854N	ENST00000325455	NM_001202474.3	854	aaG/aaT	7/8	0.3	3	FACETS	1	0.979	1	0.716	0.638	0.799	CLONAL	1	TRUE	1	0.18	3		904	829	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442712	442712	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs754959640	NA	P-0022794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	47	851	0	ENST00000399788.2:c.1594C>A	p.Leu532Ile	p.L532I	ENST00000399788	NM_001042603.1	532	Ctt/Att	12/28	1	2	FACETS	0.717	0.604	0.843	0.717	0.604	0.843	SUBCLONAL	1	TRUE	1	0.18	2		851	728	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691155	18691155	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1405941337	NA	P-0022794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	46	777	0	ENST00000266497.5:c.3266C>G	p.Pro1089Arg	p.P1089R	ENST00000266497		1089	cCa/cGa	23/31	1	2	FACETS	0.863	0.726	1	0.863	0.726	1	CLONAL	1	TRUE	1	0.18	2		777	592	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112251	115112251	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	14	369	0	ENST00000257566.3:c.1489C>A	p.Pro497Thr	p.P497T	ENST00000257566	NM_016569.3	497	Ccc/Acc	7/8	1	2	FACETS	0.625	0.451	0.835	0.625	0.451	0.835	SUBCLONAL	1	TRUE	1	0.18	2		369	249	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49054175	49054175	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555295597	NA	P-0022794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	47	654	2	ENST00000267163.4:c.2755A>G	p.Ser919Gly	p.S919G	ENST00000267163	NM_000321.2	919	Agc/Ggc	27/27	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.18	2		656	508	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554344	81554344	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	55	860	0	ENST00000298171.2:c.364C>T	p.Leu122Phe	p.L122F	ENST00000298171	NM_000369.2	122	Ctc/Ttc	4/10	0.281609792026025	3	FACETS	0.964	0.823	1	0.482	0.411	0.559	CLONAL	1	TRUE	1	0.18	3		860	691	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007554	62007554	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	55	1189	1	ENST00000392795.3:c.313C>A	p.Leu105Ile	p.L105I	ENST00000392795	NM_001039933.1	105	Ctc/Atc	3/6	0.182755873193919	3	FACETS	0.728	0.621	0.846	0.364	0.31	0.423	SUBCLONAL	1	TRUE	1	0.18	3		1190	915	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584427	39584427	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	29	631	1	ENST00000262039.4:c.1092G>T	p.Leu364Phe	p.L364F	ENST00000262039	NM_002647.2	364	ttG/ttT	10/25	1	2	FACETS	0.643	0.515	0.789	0.643	0.515	0.789	SUBCLONAL	1	TRUE	1	0.18	2		632	501	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211199	2211199	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	50	998	1	ENST00000398665.3:c.1453C>T	p.Gln485Ter	p.Q485*	ENST00000398665	NM_032482.2	485	Cag/Tag	15/28	1	2	FACETS	0.678	0.573	0.793	0.678	0.573	0.793	SUBCLONAL	1	TRUE	1	0.18	2		999	820	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375445	15375445	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	40	904	0	ENST00000263377.2:c.982G>T	p.Val328Leu	p.V328L	ENST00000263377	NM_058243.2	328	Gtg/Ttg	6/20	1	2	FACETS	0.558	0.462	0.665	0.558	0.462	0.665	SUBCLONAL	1	TRUE	1	0.18	2		904	797	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143106	30143106	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	84	1014	0	ENST00000389048.3:c.420G>T	p.Gln140His	p.Q140H	ENST00000389048	NM_004304.4	140	caG/caT	1/29	0.231128970406774	3	FACETS	1	0.939	1	0.551	0.486	0.622	CLONAL	1	TRUE	1	0.18	3		1014	923	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050344	128050344	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	83	780	1	ENST00000285398.2:c.313G>T	p.Glu105Ter	p.E105*	ENST00000285398	NM_000122.1	105	Gag/Tag	3/15	0.182755873193919	3	FACETS	1	0.972	1	0.683	0.602	0.769	CLONAL	1	TRUE	1	0.18	3		781	736	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274496	198274496	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	30	741	0	ENST00000335508.6:c.902G>C	p.Arg301Thr	p.R301T	ENST00000335508	NM_012433.2	301	aGa/aCa	7/25	0.182755873193919	3	FACETS	0.615	0.494	0.753	0.307	0.247	0.377	SUBCLONAL	1	TRUE	1	0.18	3		741	591	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248674	212248674	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	49	699	0	ENST00000342788.4:c.3593C>G	p.Ala1198Gly	p.A1198G	ENST00000342788	NM_005235.2	1198	gCc/gGc	28/28	0.182755873193919	3	FACETS	0.943	0.798	1	0.472	0.399	0.552	CLONAL	1	TRUE	1	0.18	3		699	629	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162153	47162153	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	34	735	0	ENST00000409792.3:c.3973G>T	p.Gly1325Ter	p.G1325*	ENST00000409792	NM_014159.6	1325	Gga/Tga	3/21	1	2	FACETS	0.628	0.511	0.759	0.628	0.511	0.759	SUBCLONAL	1	TRUE	1	0.18	2		735	602	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964347	55964347	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0022794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	61	859	1	ENST00000263923.4:c.2466T>A	p.Tyr822Ter	p.Y822*	ENST00000263923	NM_002253.2	822	taT/taA	17/30	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.18	2		860	644	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143029255	143029255	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	35	629	0	ENST00000262992.4:c.2365C>A	p.Pro789Thr	p.P789T	ENST00000262992	NM_001101669.1	789	Cct/Act	21/24	1	2	FACETS	0.851	0.697	1	0.851	0.697	1	CLONAL	1	TRUE	1	0.18	2		629	457	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295338	1295338	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0022794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	35	705	0				ENST00000310581	NM_198253.2	-/1132			0.3	3	FACETS	0.769	0.629	0.927	0.385	0.314	0.464	CLONAL	1	TRUE	1	0.18	3		705	551	SUCCESS
APC	324	MSKCC	GRCh37	5	112177665	112177665	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs759624605	NA	P-0022794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	29	583	0	ENST00000257430.4:c.6374C>G	p.Ser2125Cys	p.S2125C	ENST00000257430	NM_000038.5	2125	tCt/tGt	16/16	1	2	FACETS	0.684	0.548	0.839	0.684	0.548	0.839	SUBCLONAL	1	TRUE	1	0.18	2		583	471	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188318	32188318	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs779016849	NA	P-0022794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	101	1055	1	ENST00000375023.3:c.1023C>A	p.Cys341Ter	p.C341*	ENST00000375023	NM_004557.3	341	tgC/tgA	6/30	0.182755873193919	3	FACETS	1	0.97	1	0.627	0.559	0.699	CLONAL	1	TRUE	1	0.18	3		1056	976	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527739	157527739	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	40	719	0	ENST00000346085.5:c.5464G>T	p.Gly1822Cys	p.G1822C	ENST00000346085	NM_020732.3	1822	Ggc/Tgc	20/20	1	2	FACETS	0.732	0.607	0.872	0.732	0.607	0.872	SUBCLONAL	1	TRUE	1	0.18	2		719	607	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962767	2962767	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	42	777	0	ENST00000396946.4:c.2141T>A	p.Leu714Gln	p.L714Q	ENST00000396946	NM_032415.4	714	cTg/cAg	16/25	0.182755873193919	3	FACETS	0.773	0.644	0.917	0.387	0.322	0.459	CLONAL	1	TRUE	1	0.18	3		777	658	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524971	8524971	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	29	687	0	ENST00000356435.5:c.633C>A	p.Asn211Lys	p.N211K	ENST00000356435		211	aaC/aaA	7/35	0.154532751127728	1	FACETS	0.538	0.431	0.661	0.538	0.431	0.661	SUBCLONAL	1	TRUE	0	0.18	1		687	545	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209467	98209467	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	39	902	0	ENST00000331920.6:c.4071G>T	p.Met1357Ile	p.M1357I	ENST00000331920	NM_000264.3	1357	atG/atT	23/24	1	2	FACETS	0.64	0.529	0.764	0.64	0.529	0.764	SUBCLONAL	1	TRUE	1	0.18	2		902	677	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409902	63409902	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	47	351	0	ENST00000330258.3:c.3265A>T	p.Arg1089Trp	p.R1089W	ENST00000330258	NM_152424.3	1089	Agg/Tgg	2/2	1	1	FACETS	0.855	0.726	0.994	1	0.969	1	CLONAL	2	TRUE	0	0.18	1		351	278	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412027	63412027	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	33	548	0	ENST00000330258.3:c.1140G>T	p.Glu380Asp	p.E380D	ENST00000330258	NM_152424.3	380	gaG/gaT	2/2	1	1	FACETS	0.867	0.706	1	0.867	0.706	1	CLONAL	1	TRUE	0	0.18	1		548	385	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	56	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.92	1	1	0.979	1	CLONAL	2	TRUE	1	0.14	2		215	363	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039374	49039374	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853293	NA	P-0022795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	71	1062	0	ENST00000267163.4:c.2359C>T	p.Arg787Ter	p.R787*	ENST00000267163	NM_000321.2	787	Cga/Tga	23/27	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.14	2		1062	1014	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0022795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	24	423	1	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	0.556	0.434	0.697	0.556	0.434	0.697	SUBCLONAL	1	TRUE	1	0.14	2		424	617	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817412	39817412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200306085	NA	P-0022795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	49	754	0	ENST00000288319.7:c.151G>A	p.Val51Ile	p.V51I	ENST00000288319	NM_182918.3	51	Gtc/Atc	2/10	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.14	2		754	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782177	NA	P-0022795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	23	993	1	ENST00000269305.4:c.644G>A	p.Ser215Asn	p.S215N	ENST00000269305	NM_001126112.2	215	aGt/aAt	6/11	1	2	FACETS	0.35	0.271	0.442	0.35	0.271	0.442	SUBCLONAL	1	TRUE	1	0.14	2		994	940	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381502	81381502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	28	636	1	ENST00000222390.5:c.559C>T	p.Pro187Ser	p.P187S	ENST00000222390	NM_000601.4	187	Ccc/Tcc	5/18	1	2	FACETS	0.717	0.571	0.884	0.717	0.571	0.884	SUBCLONAL	1	TRUE	1	0.14	2		637	558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780068	NA	P-0022795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	26	1032	0	ENST00000269305.4:c.472C>T	p.Arg158Cys	p.R158C	ENST00000269305	NM_001126112.2	158	Cgc/Tgc	5/11	1	2	FACETS	0.454	0.357	0.565	0.454	0.357	0.565	SUBCLONAL	1	TRUE	1	0.14	2		1032	819	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577537	7577538	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0022795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	19	702	0	ENST00000269305.4:c.743_744delinsAA	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGG/cAA	7/11	1	2	FACETS	0.362	0.273	0.467	0.362	0.273	0.467	SUBCLONAL	1	TRUE	1	0.14	2		702	750	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940120	31940120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	42	856	0	ENST00000375333.2:c.262G>A	p.Glu88Lys	p.E88K	ENST00000375333	NM_032454.1	88	Gaa/Aaa	2/8	1	2	FACETS	0.719	0.598	0.853	0.719	0.598	0.853	SUBCLONAL	1	TRUE	1	0.14	2		856	835	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087516	27087516	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370916036	NA	P-0022795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	56	970	2	ENST00000324856.7:c.2090C>T	p.Pro697Leu	p.P697L	ENST00000324856	NM_006015.4	697	cCg/cTg	5/20	1	2	FACETS	0.977	0.835	1	0.977	0.835	1	CLONAL	1	TRUE	1	0.14	2		972	819	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363517	40363517	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	56	815	3	ENST00000397332.2:c.712C>T	p.His238Tyr	p.H238Y	ENST00000397332	NM_001033082.2	238	Cat/Tat	3/3	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.14	2		818	675	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577540	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	rs1555525498	NA	P-0022795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	29	684	1	ENST00000269305.4:c.741_742delinsTT	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	247	aaCCgg/aaTTgg	7/11	1	2	FACETS	0.553	0.442	0.68	0.553	0.442	0.68	SUBCLONAL	1	TRUE	1	0.14	2		685	749	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412817	116412817	+	intron_variant	Intron	SNP	C	C	T	novel	NA	P-0022795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1194	51	1343	1	ENST00000397752.3:c.3028+774C>T		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.585	0.495	0.685	0.585	0.495	0.685	SUBCLONAL	1	TRUE	1	0.14	2		1344	1245	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332634	65332634	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	44	728	1	ENST00000342505.4:c.905T>G	p.Phe302Cys	p.F302C	ENST00000342505	NM_002227.2	302	tTt/tGt	7/25	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.14	2		729	584	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444042	49444042	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	40	797	1	ENST00000301067.7:c.3329del	p.Pro1110GlnfsTer9	p.P1110Qfs*9	ENST00000301067	NM_003482.3	1110	cCa/ca	11/54	1	2	FACETS	0.978	0.812	1	0.978	0.812	1	CLONAL	1	TRUE	1	0.14	2		798	584	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936756	32936757	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0022795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	54	849	0	ENST00000380152.3:c.7902_7903delinsAA	p.Met2634_Glu2635delinsIleLys	p.M2634_E2635delinsIK	ENST00000380152		2634	atGGaa/atAAaa	17/27	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.14	2		849	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578476	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0022795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	42	1056	5	ENST00000269305.4:c.454_455delinsTT	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	CCg/TTg	5/11	1	2	FACETS	0.666	0.554	0.791	0.666	0.554	0.791	SUBCLONAL	1	TRUE	1	0.14	2		1061	901	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752792	42752792	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1005681632	NA	P-0022795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	53	1011	0	ENST00000222329.4:c.1472A>G	p.Asp491Gly	p.D491G	ENST00000222329	NM_006494.2	491	gAc/gGc	4/4	1	2	FACETS	0.991	0.843	1	0.991	0.843	1	CLONAL	1	TRUE	1	0.14	2		1011	764	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42788891	42788891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	32	772	1	ENST00000575354.2:c.35C>T	p.Ser12Phe	p.S12F	ENST00000575354	NM_015125.3	12	tCc/tTc	1/20	1	2	FACETS	0.762	0.617	0.927	0.762	0.617	0.927	CLONAL	1	TRUE	1	0.14	2		773	600	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29099550	29099550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876658150	NA	P-0022795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	35	637	0	ENST00000328354.6:c.851G>A	p.Cys284Tyr	p.C284Y	ENST00000328354	NM_007194.3	284	tGc/tAc	8/15	1	2	FACETS	0.839	0.686	1	0.839	0.686	1	CLONAL	1	TRUE	1	0.14	2		637	596	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934291	49934291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	30	786	1	ENST00000296474.3:c.2216C>T	p.Pro739Leu	p.P739L	ENST00000296474	NM_002447.2	739	cCc/cTc	8/20	1	2	FACETS	0.715	0.575	0.876	0.715	0.575	0.876	SUBCLONAL	1	TRUE	1	0.14	2		787	599	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228330	228330	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	20	411	0	ENST00000264932.6:c.652G>A	p.Glu218Lys	p.E218K	ENST00000264932	NM_004168.2	218	Gag/Aag	6/15	1	2	FACETS	0.871	0.666	1	0.871	0.666	1	CLONAL	1	TRUE	1	0.14	2		411	328	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293678	1293678	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1213914911	NA	P-0022795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	105	1002	0	ENST00000310581.5:c.1323G>T	p.Glu441Asp	p.E441D	ENST00000310581	NM_198253.2	441	gaG/gaT	2/16	1	2	FACETS	0.916	0.82	1	1	0.986	1	CLONAL	2	TRUE	1	0.14	2		1002	819	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0022891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	101	282	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.258469622287596	2		282	687	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	73	635	0	ENST00000304494.5:c.172del	p.Arg58GlufsTer88	p.R58Efs*88	ENST00000304494	NM_000077.4	58	Cga/ga	2/3	0.258469622287596	1	FACETS	0.909	0.796	1	0.909	0.796	1	CLONAL	1	TRUE	0	0.258469622287596	1		635	541	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477837	140477851	+	inframe_deletion	In_Frame_Del	DEL	TAGGTGCTGTCACAT	TAGGTGCTGTCACAT	-	novel	NA	P-0022891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	125	845	0	ENST00000288602.6:c.1457_1471del	p.Asn486_Pro490del	p.N486_P490del	ENST00000288602	NM_004333.4	486	aATGTGACAGCACCTAca/aca	12/18	0.180116375894906	3	FACETS	1	0.967	1	0.579	0.523	0.637	CLONAL	1	TRUE	1	0.258469622287596	3		845	944	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0022891-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	149	282	0				ENST00000310581	NM_198253.2	-/1132			0.135502805305704	0	FACETS	0.667	0.61	0.725			1	INDETERMINATE	1	TRUE	0	0.389730440456764	0		282	700	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022891-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	113	390	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.954	0.86	1	0.954	0.86	1	CLONAL	1	TRUE	1	0.389730440456764	2		390	608	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0022891-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	109	503	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.389730440456764	2		503	528	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022891-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	111	635	0	ENST00000304494.5:c.172del	p.Arg58GlufsTer88	p.R58Efs*88	ENST00000304494	NM_000077.4	58	Cga/ga	2/3	0.389730440456764	1	FACETS	0.856	0.772	0.943	0.856	0.772	0.943	CLONAL	1	TRUE	0	0.389730440456764	1		635	536	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477837	140477851	+	inframe_deletion	In_Frame_Del	DEL	TAGGTGCTGTCACAT	TAGGTGCTGTCACAT	-	novel	NA	P-0022891-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	318	845	0	ENST00000288602.6:c.1457_1471del	p.Asn486_Pro490del	p.N486_P490del	ENST00000288602	NM_004333.4	486	aATGTGACAGCACCTAca/aca	12/18	0.389730440456764	3	FACETS	0.876	0.827	0.926	0.876	0.827	0.926	CLONAL	2	TRUE	1	0.389730440456764	3		845	1113	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577543	7577543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1019340046	NA	P-0022891-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	34	955	0	ENST00000269305.4:c.738G>A	p.Met246Ile	p.M246I	ENST00000269305	NM_001126112.2	246	atG/atA	7/11	0.389730440456764	1	FACETS	0.186	0.151	0.226	0.186	0.151	0.226	SUBCLONAL	1	TRUE	0	0.389730440456764	1		955	754	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196791	108196791	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022891-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	90	437	1	ENST00000278616.4:c.6814G>T	p.Glu2272Ter	p.E2272*	ENST00000278616	NM_000051.3	2272	Gaa/Taa	47/63	1	2	FACETS	0.802	0.713	0.897	0.802	0.713	0.897	CLONAL	1	TRUE	1	0.389730440456764	2		438	576	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438102	438102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022891-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	151	627	0	ENST00000399788.2:c.1867G>A	p.Asp623Asn	p.D623N	ENST00000399788	NM_001042603.1	623	Gat/Aat	14/28	NA	2	FACETS	1	0.92	1			1	INDETERMINATE	1	TRUE	NA	0.389730440456764	2		627	771	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56839461	56839461	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022891-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	172	736	1	ENST00000308159.5:c.406G>A	p.Glu136Lys	p.E136K	ENST00000308159	NM_014669.4	136	Gag/Aag	5/22	1	2	FACETS	0.995	0.916	1	0.995	0.916	1	CLONAL	1	TRUE	1	0.389730440456764	2		737	887	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397530	116397530	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022891-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	169	750	0	ENST00000397752.3:c.1902C>A	p.Phe634Leu	p.F634L	ENST00000397752	NM_000245.2	634	ttC/ttA	7/21	0.389730440456764	3	FACETS	1	0.944	1	0.518	0.475	0.562	CLONAL	1	TRUE	1	0.389730440456764	3		750	1001	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398518	116398518	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022891-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	157	629	0	ENST00000397752.3:c.2108C>T	p.Ser703Leu	p.S703L	ENST00000397752	NM_000245.2	703	tCa/tTa	9/21	0.389730440456764	3	FACETS	1	0.964	1	0.548	0.502	0.596	CLONAL	1	TRUE	1	0.389730440456764	3		629	879	SUCCESS
AR	367	MSKCC	GRCh37	X	66765910	66765910	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022891-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	180	1024	0	ENST00000374690.3:c.922G>C	p.Glu308Gln	p.E308Q	ENST00000374690	NM_000044.3	308	Gag/Cag	1/8	1	2	FACETS	0.913	0.841	0.987	0.913	0.841	0.987	CLONAL	1	TRUE	1	0.389730440456764	2		1024	1012	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	99	215	0				ENST00000310581	NM_198253.2	-/1132			0.40189168806098	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.447303658676093	4		215	265	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0022950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	238	458	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.447303658676093	3	FACETS	0.892	0.851	0.932	1	0.991	1	CLONAL	4	TRUE	0	0.447303658676093	3		458	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0022950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	479	691	2	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.399318475089715	4	FACETS	0.999	0.965	1	0.999	0.965	1	CLONAL	4	TRUE	0	0.447303658676093	4		693	776	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023272	1023272	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	39	503	0	ENST00000358495.3:c.983A>T	p.Asn328Ile	p.N328I	ENST00000358495	NM_134424.2	328	aAc/aTc	11/12	0.207139636875451	5	FACETS	0.601	0.498	0.716	0.2	0.166	0.239	INDETERMINATE	1	TRUE	2	0.447303658676093	5		503	485	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422612	49422612	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	239	653	1	ENST00000301067.7:c.14381A>G	p.Lys4794Arg	p.K4794R	ENST00000301067	NM_003482.3	4794	aAg/aGg	45/54	0.447303658676093	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.447303658676093	3		654	581	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	251	215	0				ENST00000310581	NM_198253.2	-/1132			0.112338668329969	6	FACETS	0.931	0.874	0.988			1	INDETERMINATE	3	TRUE	NA	0.473967611969976	6		215	739	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0023002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	377	512	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.432297953976382	4	FACETS	0.91	0.868	0.952	0.91	0.868	0.952	CLONAL	3	TRUE	1	0.473967611969976	4		512	859	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	133	506	0	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	0.366698035508207	3	FACETS	1	0.963	1	0.554	0.504	0.605	CLONAL	1	TRUE	1	0.473967611969976	3		506	627	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049694	16049694	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	284	752	0	ENST00000268712.3:c.1078C>T	p.Gln360Ter	p.Q360*	ENST00000268712	NM_006311.3	360	Cag/Tag	10/46	0.473967611969976	2	FACETS	0.979	0.929	1	0.979	0.929	1	CLONAL	2	TRUE	0	0.473967611969976	2		752	612	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295195	1295195	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0023002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	234	403	0				ENST00000310581	NM_198253.2	-/1132			0.112338668329969	6	FACETS	0.988	0.927	1			1	INDETERMINATE	3	TRUE	NA	0.473967611969976	6		403	649	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675145	40675145	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	203	789	0	ENST00000249776.8:c.109G>C	p.Glu37Gln	p.E37Q	ENST00000249776	NM_033286.3	37	Gaa/Caa	1/9	1	2	FACETS	0.965	0.895	1	0.965	0.895	1	CLONAL	1	TRUE	1	0.473967611969976	2		789	888	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784380	9784380	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	204	871	0	ENST00000377346.4:c.2765A>T	p.Lys922Met	p.K922M	ENST00000377346	NM_005026.3	922	aAg/aTg	22/24	NA	2	FACETS	0.747	0.692	0.805			1	INDETERMINATE	1	TRUE	NA	0.473967611969976	2		871	1152	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240125	41240125	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1218986039	NA	P-0023002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	20	180	0	ENST00000379561.5:c.225C>G	p.Ser75Arg	p.S75R	ENST00000379561	NM_002015.3	75	agC/agG	1/3	0.366698035508207	3	FACETS	0.454	0.348	0.577	0.227	0.174	0.289	SUBCLONAL	1	TRUE	1	0.473967611969976	3		180	230	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675213	40675213	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1424504422	NA	P-0023002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	174	721	0	ENST00000249776.8:c.177G>C	p.Glu59Asp	p.E59D	ENST00000249776	NM_033286.3	59	gaG/gaC	1/9	1	2	FACETS	0.984	0.908	1	0.984	0.908	1	CLONAL	1	TRUE	1	0.473967611969976	2		721	746	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675461	40675461	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	188	813	0	ENST00000249776.8:c.242G>C	p.Ser81Thr	p.S81T	ENST00000249776	NM_033286.3	81	aGt/aCt	2/9	1	2	FACETS	0.985	0.912	1	0.985	0.912	1	CLONAL	1	TRUE	1	0.473967611969976	2		813	805	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675508	40675508	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1390264577	NA	P-0023002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	142	631	0	ENST00000249776.8:c.289G>A	p.Gly97Ser	p.G97S	ENST00000249776	NM_033286.3	97	Ggc/Agc	2/9	1	2	FACETS	0.959	0.877	1	0.959	0.877	1	CLONAL	1	TRUE	1	0.473967611969976	2		631	625	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639867	3639867	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755975486	NA	P-0023002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	200	742	1	ENST00000294008.3:c.3772C>T	p.Pro1258Ser	p.P1258S	ENST00000294008	NM_032444.2	1258	Ccc/Tcc	12/15	0.140795367029496	3	FACETS	1	0.983	1	0.398	0.369	0.428	INDETERMINATE	1	TRUE	0	0.473967611969976	3		743	874	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579415	7579416	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0023002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	340	820	1	ENST00000269305.4:c.270_271dup	p.Trp91SerfsTer33	p.W91Sfs*33	ENST00000269305	NM_001126112.2	91	tgg/tCTgg	4/11	0.473967611969976	2	FACETS	0.894	0.851	0.938	0.894	0.851	0.938	CLONAL	2	TRUE	0	0.473967611969976	2		821	802	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40469236	40469236	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	107	434	0	ENST00000264657.5:c.2108C>A	p.Ala703Asp	p.A703D	ENST00000264657	NM_139276.2	703	gCc/gAc	22/24	0.366698035508207	3	FACETS	1	0.901	1	0.5	0.45	0.553	CLONAL	1	TRUE	1	0.473967611969976	3		434	558	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615713	1615713	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	232	959	0	ENST00000344749.5:c.1558G>T	p.Glu520Ter	p.E520*	ENST00000344749	NM_001136139.2	520	Gag/Tag	17/19	NA	2	FACETS	0.868	0.809	0.929			1	INDETERMINATE	1	TRUE	NA	0.473967611969976	2		959	1128	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7150535	7150535	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	328	754	0	ENST00000302850.5:c.2240C>G	p.Ser747Cys	p.S747C	ENST00000302850	NM_000208.2	747	tCt/tGt	11/22	0.140795367029496	3	FACETS	1	0.977	1	0.699	0.663	0.734	INDETERMINATE	2	TRUE	0	0.473967611969976	3		754	817	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610289	10610302	+	frameshift_variant	Frame_Shift_Del	DEL	AGGCGAATTCAATG	AGGCGAATTCAATG	-	novel	NA	P-0023002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	199	944	0	ENST00000171111.5:c.408_421del	p.Ile137HisfsTer32	p.I137Hfs*32	ENST00000171111	NM_203500.1	136	ctCATTGAATTCGCCTac/ctac	2/6	0.140795367029496	3	FACETS	0.889	0.823	0.959	0.296	0.274	0.32	INDETERMINATE	1	TRUE	0	0.473967611969976	3		944	1168	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727811	41727811	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779440422	NA	P-0023002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	1292	899	1	ENST00000301178.4:c.436G>A	p.Glu146Lys	p.E146K	ENST00000301178	NM_021913.4	146	Gaa/Aaa	4/20	0.473967611969976	7	FACETS	1	0.996	1			1	CLONAL	5	TRUE	NA	0.473967611969976	7		900	2212	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543665	29543665	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	319	836	0	ENST00000389048.3:c.1498C>T	p.Gln500Ter	p.Q500*	ENST00000389048	NM_004304.4	500	Caa/Taa	7/29	0.188785439644715	5	FACETS	1	0.984	1	0.738	0.698	0.78	INDETERMINATE	2	TRUE	2	0.473967611969976	5		836	1040	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670250	134670250	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	55	547	0	ENST00000398015.3:c.161C>A	p.Thr54Asn	p.T54N	ENST00000398015	NM_004441.4	54	aCc/aAc	3/16	0.140795367029496	3	FACETS	0.386	0.33	0.449	0.129	0.11	0.15	INDETERMINATE	1	TRUE	0	0.473967611969976	3		547	743	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127432	55127432	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	197	735	0	ENST00000257290.5:c.220G>C	p.Glu74Gln	p.E74Q	ENST00000257290	NM_006206.4	74	Gaa/Caa	3/23	0.473967611969976	2	FACETS	1	0.966	1	0.534	0.495	0.573	CLONAL	1	TRUE	0	0.473967611969976	2		735	779	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271219	26271219	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	382	568	0	ENST00000305910.3:c.394C>G	p.Arg132Gly	p.R132G	ENST00000305910	NM_003534.2	132	Cgt/Ggt	1/1	0.473967611969976	4	FACETS	0.986	0.943	1	0.986	0.943	1	CLONAL	3	TRUE	1	0.473967611969976	4		568	803	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381528	81381528	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	93	468	0	ENST00000222390.5:c.533G>C	p.Arg178Pro	p.R178P	ENST00000222390	NM_000601.4	178	cGa/cCa	5/18	1	2	FACETS	0.876	0.783	0.974	0.876	0.783	0.974	CLONAL	1	TRUE	1	0.473967611969976	2		468	448	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922884	44922884	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0023002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	280	693	0	ENST00000377967.4:c.1745C>G	p.Ser582Ter	p.S582*	ENST00000377967	NM_021140.2	582	tCa/tGa	16/29	0.175717472622744	6	FACETS	0.869	0.818	0.92	0.869	0.818	0.92	INDETERMINATE	3	TRUE	3	0.473967611969976	6		693	883	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949083	44949083	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	143	677	0	ENST00000377967.4:c.3644G>C	p.Gly1215Ala	p.G1215A	ENST00000377967	NM_021140.2	1215	gGa/gCa	25/29	0.175717472622744	6	FACETS	1	0.97	1	0.384	0.349	0.42	INDETERMINATE	1	TRUE	3	0.473967611969976	6		677	1021	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939255	76939255	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	405	981	0	ENST00000373344.5:c.1493G>C	p.Arg498Thr	p.R498T	ENST00000373344	NM_000489.3	498	aGa/aCa	9/35	0.175717472622744	6	FACETS	0.868	0.826	0.91	0.868	0.826	0.91	INDETERMINATE	3	TRUE	3	0.473967611969976	6		981	1279	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940499	76940499	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0023002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	212	560	0	ENST00000373344.5:c.595-1G>A		p.X199_splice	ENST00000373344	NM_000489.3	199			0.175717472622744	6	FACETS	0.844	0.788	0.902	0.844	0.788	0.902	INDETERMINATE	3	TRUE	3	0.473967611969976	6		560	688	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019670	123019670	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	129	717	0	ENST00000355640.3:c.158T>G	p.Leu53Arg	p.L53R	ENST00000355640		53	cTt/cGt	2/7	0.175717472622744	6	FACETS	0.969	0.877	1	0.323	0.292	0.356	INDETERMINATE	1	TRUE	3	0.473967611969976	6		717	1094	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	9	563	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	NA	2	FACETS	0.069	0.045	0.1			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		563	379	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247070	53247070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	120	776	0	ENST00000375401.3:c.430C>T	p.Pro144Ser	p.P144S	ENST00000375401	NM_004187.3	144	Cca/Tca	4/26	0.476022737996448	5	FACETS	0.866	0.782	0.955	0.289	0.26	0.319	CLONAL	1	TRUE	2	0.687150504376923	5		776	819	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	40	960	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.687150504376923	NA		960	999	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665752	29665755	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1555535032	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	304	573	0	ENST00000356175.3:c.6789_6792del	p.Tyr2264ThrfsTer5	p.Y2264Tfs*5	ENST00000356175	NM_000267.3	2263	ACTTac/ac	45/57	0.25365618841227	3	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.687150504376923	3		573	479	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604533	43604533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs546866208	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	45	799	1	ENST00000355710.3:c.1118C>T	p.Ala373Val	p.A373V	ENST00000355710	NM_020975.4	373	gCg/gTg	6/20	0.641153435786728	2	FACETS	0.302	0.254	0.355	0.151	0.127	0.178	SUBCLONAL	1	TRUE	0	0.687150504376923	2		800	434	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301898	65301898	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	40	488	0	ENST00000342505.4:c.3141G>A	p.Trp1047Ter	p.W1047*	ENST00000342505	NM_002227.2	1047	tgG/tgA	23/25	0.476022737996448	5	FACETS	0.473	0.392	0.562	0.158	0.13	0.188	SUBCLONAL	1	TRUE	2	0.687150504376923	5		488	500	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673625	30673625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28987085	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	40	856	0	ENST00000376406.3:c.3335C>T	p.Ser1112Phe	p.S1112F	ENST00000376406	NM_014641.2	1112	tCc/tTc	10/15	0.591956589237621	3	FACETS	0.243	0.201	0.29	0.081	0.067	0.097	SUBCLONAL	1	TRUE	0	0.687150504376923	3		856	643	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294315	11294315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	55	712	3	ENST00000361445.4:c.2216C>T	p.Thr739Ile	p.T739I	ENST00000361445	NM_004958.3	739	aCa/aTa	14/58	0.377332965442675	3	FACETS	0.355	0.303	0.412	0.177	0.151	0.206	INDETERMINATE	1	TRUE	1	0.687150504376923	3		715	606	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287235	46287235	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	41	577	1	ENST00000334344.6:c.5180C>T	p.Pro1727Leu	p.P1727L	ENST00000334344	NM_152641.2	1727	cCt/cTt	19/21	0.591145040389059	3	FACETS	0.324	0.269	0.384	0.108	0.089	0.128	SUBCLONAL	1	TRUE	0	0.687150504376923	3		578	495	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500868	149500868	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1320275282	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	52	768	0	ENST00000261799.4:c.2362C>T	p.Arg788Ter	p.R788*	ENST00000261799	NM_002609.3	788	Cga/Tga	17/23	0.591145040389059	3	FACETS	0.374	0.318	0.435	0.125	0.106	0.145	SUBCLONAL	1	TRUE	0	0.687150504376923	3		768	544	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725463	117725463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	38	682	0	ENST00000368508.3:c.418G>A	p.Gly140Arg	p.G140R	ENST00000368508	NM_002944.2	140	Gga/Aga	5/43	0.591956589237621	3	FACETS	0.231	0.191	0.277	0.077	0.063	0.093	SUBCLONAL	1	TRUE	0	0.687150504376923	3		682	642	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586472	189586472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	40	470	0	ENST00000264731.3:c.1096G>A	p.Asp366Asn	p.D366N	ENST00000264731	NM_003722.4	366	Gac/Aac	8/14	0.265262754418753	4	FACETS	0.333	0.276	0.397	0.167	0.138	0.199	INDETERMINATE	1	TRUE	2	0.687150504376923	4		470	589	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050356	37050356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	38	610	3	ENST00000231790.2:c.505C>T	p.Pro169Ser	p.P169S	ENST00000231790	NM_000249.3	169	Cca/Tca	6/19	0.355492757372604	2	FACETS	0.207	0.171	0.248	0.104	0.085	0.124	INDETERMINATE	1	TRUE	0	0.687150504376923	2		613	534	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022862	31022862	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	41	640	0	ENST00000375687.4:c.2347C>T	p.Pro783Ser	p.P783S	ENST00000375687	NM_015338.5	783	Ccg/Tcg	13/13	0.687150504376923	3	FACETS	0.274	0.227	0.325	0.137	0.113	0.163	SUBCLONAL	1	TRUE	1	0.687150504376923	3		640	586	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213953	2213953	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759408599	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	28	441	1	ENST00000326181.6:c.32G>A	p.Arg11His	p.R11H	ENST00000326181	NM_032271.2	11	cGc/cAc	2/21	0.651021105723252	2	FACETS	0.21	0.167	0.259	0.105	0.083	0.13	SUBCLONAL	1	TRUE	0	0.687150504376923	2		442	388	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876347	35876347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	113	674	0	ENST00000303115.3:c.1139C>T	p.Pro380Leu	p.P380L	ENST00000303115	NM_002185.3	380	cCt/cTt	8/8	0.48445197354186	3	FACETS	0.942	0.853	1			1	CLONAL	1	TRUE	NA	0.687150504376923	3		674	469	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821209	72821209	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779473080	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	29	733	0	ENST00000268489.5:c.10966C>T	p.Pro3656Ser	p.P3656S	ENST00000268489	NM_006885.3	3656	Cca/Tca	10/10	0.641153435786728	2	FACETS	0.149	0.119	0.183	0.074	0.059	0.092	SUBCLONAL	1	TRUE	0	0.687150504376923	2		733	567	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73992046	73992046	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	41	888	1	ENST00000318443.5:c.66G>A	p.Trp22Ter	p.W22*	ENST00000318443	NM_001024736.1	22	tgG/tgA	2/10	0.674143188393259	2	FACETS	0.269	0.224	0.32	0.135	0.112	0.16	SUBCLONAL	1	TRUE	0	0.687150504376923	2		889	443	SUCCESS
ALK	238	MSKCC	GRCh37	2	29430064	29430064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1013688370	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	67	768	0	ENST00000389048.3:c.3911G>A	p.Gly1304Glu	p.G1304E	ENST00000389048	NM_004304.4	1304	gGa/gAa	26/29	0.641153435786728	2	FACETS	0.367	0.319	0.419	0.184	0.159	0.21	SUBCLONAL	1	TRUE	0	0.687150504376923	2		768	531	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683747	162683747	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	108	669	0	ENST00000366898.1:c.222G>A	p.Trp74Ter	p.W74*	ENST00000366898	NM_004562.2	74	tgG/tgA	3/12	0.591956589237621	3	FACETS	0.678	0.61	0.75	0.226	0.203	0.25	SUBCLONAL	1	TRUE	0	0.687150504376923	3		669	623	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411071	63411071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750971248	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	54	722	1	ENST00000330258.3:c.2096G>A	p.Arg699His	p.R699H	ENST00000330258	NM_152424.3	699	cGt/cAt	2/2	0.476022737996448	5	FACETS	0.511	0.436	0.593	0.17	0.145	0.198	SUBCLONAL	1	TRUE	2	0.687150504376923	5		723	625	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436101	51436101	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	116	548	0	ENST00000262662.1:c.61C>T	p.Leu21Phe	p.L21F	ENST00000262662		21	Ctt/Ttt	3/4	0.476022737996448	5	FACETS	0.881	0.794	0.973	0.294	0.264	0.325	CLONAL	1	TRUE	2	0.687150504376923	5		548	778	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535405	66535405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	88	449	0	ENST00000273854.3:c.56G>A	p.Gly19Asp	p.G19D	ENST00000273854	NM_004439.5	19	gGc/gAc	1/18	0.602194039340019	3	FACETS	1	0.949	1	0.366	0.328	0.407	CLONAL	1	TRUE	0	0.687150504376923	3		449	313	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553539	29553539	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1131691099	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	44	398	0	ENST00000356175.3:c.2088G>A	p.Trp696Ter	p.W696*	ENST00000356175	NM_000267.3	696	tgG/tgA	18/57	0.25365618841227	3	FACETS	0.468	0.393	0.55			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	3		398	368	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945263	54945263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	29	513	1	ENST00000312783.6:c.1163C>T	p.Ser388Leu	p.S388L	ENST00000312783	NM_198436.1	388	tCa/tTa	10/10	0.687150504376923	3	FACETS	0.225	0.18	0.276	0.112	0.09	0.138	SUBCLONAL	1	TRUE	1	0.687150504376923	3		514	505	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574035	41574035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	77	586	0	ENST00000263253.7:c.6320C>T	p.Pro2107Leu	p.P2107L	ENST00000263253	NM_001429.3	2107	cCc/cTc	31/31	0.641153435786728	2	FACETS	0.75	0.665	0.839	0.375	0.332	0.42	SUBCLONAL	1	TRUE	0	0.687150504376923	2		586	299	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94224031	94224031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs116679717	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	177	796	0	ENST00000323929.3:c.121G>A	p.Asp41Asn	p.D41N	ENST00000323929	NM_005591.3	41	Gat/Aat	3/20	0.591145040389059	3	FACETS	0.891	0.822	0.962	0.297	0.274	0.321	CLONAL	1	TRUE	0	0.687150504376923	3		796	777	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227920	123227920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	44	638	0	ENST00000218089.9:c.3631G>A	p.Val1211Ile	p.V1211I	ENST00000218089	NM_001042749.1	1211	Gtt/Att	33/35	0.667377551654336	4	FACETS	0.253	0.211	0.299	0.126	0.105	0.15	SUBCLONAL	1	TRUE	2	0.687150504376923	4		638	855	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033352	48033352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750949	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	52	338	0	ENST00000234420.5:c.3656C>T	p.Thr1219Ile	p.T1219I	ENST00000234420	NM_000179.2	1219	aCt/aTt	8/10	0.591145040389059	3	FACETS	0.361	0.307	0.42	0.12	0.102	0.14	SUBCLONAL	1	TRUE	0	0.687150504376923	3		338	563	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711875	89711875	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587782603	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	349	567	0	ENST00000371953.3:c.493G>A	p.Gly165Arg	p.G165R	ENST00000371953	NM_000314.4	165	Gga/Aga	6/9	0.674143188393259	2	FACETS	0.949	0.913	0.985	0.949	0.913	0.985	CLONAL	2	TRUE	0	0.687150504376923	2		567	535	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578509	7578509	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519978	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	395	969	1	ENST00000269305.4:c.421T>C	p.Cys141Arg	p.C141R	ENST00000269305	NM_001126112.2	141	Tgc/Cgc	5/11	0.355492757372604	2	FACETS	1	0.984	1	1	0.984	1	INDETERMINATE	2	TRUE	0	0.687150504376923	2		970	558	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631706	90631706	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749096156	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	49	702	3	ENST00000330062.3:c.563G>A	p.Arg188Gln	p.R188Q	ENST00000330062	NM_002168.2	188	cGg/cAg	5/11	0.591145040389059	3	FACETS	0.365	0.309	0.427	0.122	0.103	0.143	SUBCLONAL	1	TRUE	0	0.687150504376923	3		705	525	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710962	117710962	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	100	452	1	ENST00000368508.3:c.1310C>T	p.Pro437Leu	p.P437L	ENST00000368508	NM_002944.2	437	cCt/cTt	12/43	0.591956589237621	3	FACETS	0.983	0.884	1	0.328	0.294	0.362	CLONAL	1	TRUE	0	0.687150504376923	3		453	398	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372427	55372427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	34	928	0	ENST00000297316.4:c.1117C>T	p.Pro373Ser	p.P373S	ENST00000297316	NM_022454.3	373	Cct/Tct	2/2	0.632865446864237	3	FACETS	0.202	0.165	0.245	0.101	0.082	0.123	SUBCLONAL	1	TRUE	1	0.687150504376923	3		928	657	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947386	38947386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776016149	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	73	340	0	ENST00000357387.3:c.4294G>A	p.Asp1432Asn	p.D1432N	ENST00000357387	NM_152756.3	1432	Gat/Aat	32/38	0.48445197354186	3	FACETS	0.74	0.65	0.835			1	SUBCLONAL	1	TRUE	NA	0.687150504376923	3		340	386	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288504	15288504	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	17	244	0	ENST00000263388.2:c.4235G>A	p.Trp1412Ter	p.W1412*	ENST00000263388	NM_000435.2	1412	tGg/tAg	24/33	NA	2	FACETS	0.334	0.251	0.432			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		244	148	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819780	170819780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	47	435	0	ENST00000296930.5:c.419G>A	p.Gly140Glu	p.G140E	ENST00000296930	NM_002520.6	140	gGa/gAa	5/11	0.591145040389059	3	FACETS	0.557	0.472	0.65	0.186	0.157	0.217	SUBCLONAL	1	TRUE	0	0.687150504376923	3		435	330	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115006	3115006	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1391552100	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	122	1062	5	ENST00000078429.4:c.541C>T	p.Arg181Trp	p.R181W	ENST00000078429	NM_002067.2	181	Cgg/Tgg	4/7	1	2	FACETS	0.649	0.589	0.712	0.649	0.589	0.712	SUBCLONAL	1	TRUE	1	0.687150504376923	2		1067	547	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343567	343567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1369221706	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	23	877	1	ENST00000262320.3:c.2107C>T	p.Pro703Ser	p.P703S	ENST00000262320	NM_003502.3	703	Ccc/Tcc	8/11	0.651021105723252	2	FACETS	0.188	0.146	0.236	0.094	0.073	0.118	SUBCLONAL	1	TRUE	0	0.687150504376923	2		878	356	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805588	46805588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201428095	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	39	892	0	ENST00000290295.7:c.368G>A	p.Arg123His	p.R123H	ENST00000290295	NM_006361.5	123	cGc/cAc	1/2	0.669366583482874	2	FACETS	0.269	0.223	0.32	0.134	0.111	0.16	SUBCLONAL	1	TRUE	0	0.687150504376923	2		892	422	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041073	180041073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	38	1188	0	ENST00000261937.6:c.3326C>T	p.Ser1109Phe	p.S1109F	ENST00000261937	NM_182925.4	1109	tCt/tTt	24/30	0.643885768200923	2	FACETS	0.22	0.182	0.264	0.11	0.091	0.132	SUBCLONAL	1	TRUE	0	0.687150504376923	2		1188	502	SUCCESS
APC	324	MSKCC	GRCh37	5	112162862	112162862	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	44	712	1	ENST00000257430.4:c.1466C>T	p.Thr489Ile	p.T489I	ENST00000257430	NM_000038.5	489	aCt/aTt	12/16	0.591145040389059	3	FACETS	0.278	0.232	0.328	0.093	0.077	0.11	SUBCLONAL	1	TRUE	0	0.687150504376923	3		713	620	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859924	117859924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139935751	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	86	362	0	ENST00000297338.2:c.1711C>T	p.Leu571Phe	p.L571F	ENST00000297338	NM_006265.2	571	Ctt/Ttt	14/14	0.57626145183418	4	FACETS	0.918	0.816	1	0.306	0.272	0.343	CLONAL	1	TRUE	1	0.687150504376923	4		362	460	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514274	69514274	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	28	790	0	ENST00000294312.3:c.407C>T	p.Ser136Phe	p.S136F	ENST00000294312	NM_005117.2	136	tCc/tTc	3/3	0.485602631663668	1	FACETS	0.143	0.114	0.177	0.143	0.114	0.177	SUBCLONAL	1	TRUE	0	0.687150504376923	1		790	373	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877386	89877386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139160837	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	43	664	0	ENST00000389301.3:c.377C>T	p.Thr126Met	p.T126M	ENST00000389301	NM_000135.2	126	aCg/aTg	4/43	0.25365618841227	3	FACETS	0.326	0.272	0.385			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	3		664	516	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428410	49428411	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1284500089	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	329	835	0	ENST00000301067.7:c.10394dup	p.Pro3466ThrfsTer2	p.P3466Tfs*2	ENST00000301067	NM_003482.3	3465	gga/ggGa	36/54	0.591145040389059	3	FACETS	1	0.99	1	0.741	0.708	0.773	CLONAL	2	TRUE	0	0.687150504376923	3		835	579	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206910	102206910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776938400	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	53	388	0	ENST00000263464.3:c.1538C>T	p.Ser513Phe	p.S513F	ENST00000263464	NM_001165.4	513	tCt/tTt	7/9	0.591145040389059	3	FACETS	0.334	0.285	0.389	0.111	0.094	0.13	SUBCLONAL	1	TRUE	0	0.687150504376923	3		388	620	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815632	139815632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	82	714	0	ENST00000247668.2:c.1103C>T	p.Ala368Val	p.A368V	ENST00000247668	NM_021138.3	368	gCt/gTt	9/11	0.651021105723252	2	FACETS	0.597	0.529	0.668	0.298	0.264	0.334	SUBCLONAL	1	TRUE	0	0.687150504376923	2		714	400	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671853	30671853	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	76	886	1	ENST00000376406.3:c.5107C>T	p.Pro1703Ser	p.P1703S	ENST00000376406	NM_014641.2	1703	Cct/Tct	10/15	0.591956589237621	3	FACETS	0.448	0.392	0.507	0.149	0.13	0.169	SUBCLONAL	1	TRUE	0	0.687150504376923	3		887	664	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210484	5210484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	73	654	1	ENST00000357368.4:c.5483C>T	p.Ala1828Val	p.A1828V	ENST00000357368	NM_002850.3	1828	gCc/gTc	35/38	1	2	FACETS	0.537	0.471	0.606	0.537	0.471	0.606	SUBCLONAL	1	TRUE	1	0.687150504376923	2		655	396	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117746795	117746795	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	61	517	0	ENST00000368508.3:c.25C>T	p.Pro9Ser	p.P9S	ENST00000368508	NM_002944.2	9	Ccg/Tcg	1/43	0.591956589237621	3	FACETS	0.385	0.332	0.443	0.128	0.11	0.148	SUBCLONAL	1	TRUE	0	0.687150504376923	3		517	620	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073944	8073944	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762311909	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	55	660	0	ENST00000377482.5:c.715C>T	p.Pro239Ser	p.P239S	ENST00000377482	NM_018948.3	239	Cca/Tca	4/4	0.377332965442675	3	FACETS	0.333	0.284	0.386	0.166	0.142	0.193	INDETERMINATE	1	TRUE	1	0.687150504376923	3		660	646	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073971	8073971	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	47	594	0	ENST00000377482.5:c.688G>A	p.Gly230Arg	p.G230R	ENST00000377482	NM_018948.3	230	Gga/Aga	4/4	0.377332965442675	3	FACETS	0.298	0.251	0.35	0.149	0.125	0.175	INDETERMINATE	1	TRUE	1	0.687150504376923	3		594	617	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074073	8074073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	68	523	0	ENST00000377482.5:c.586C>T	p.Pro196Ser	p.P196S	ENST00000377482	NM_018948.3	196	Cct/Tct	4/4	0.377332965442675	3	FACETS	0.467	0.406	0.532	0.233	0.203	0.266	INDETERMINATE	1	TRUE	1	0.687150504376923	3		523	570	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781209	9781209	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	40	707	2	ENST00000377346.4:c.1714C>T	p.Pro572Ser	p.P572S	ENST00000377346	NM_005026.3	572	Ccg/Tcg	14/24	0.377332965442675	3	FACETS	0.315	0.261	0.374	0.157	0.13	0.187	INDETERMINATE	1	TRUE	1	0.687150504376923	3		709	497	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217258	11217258	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	91	829	1	ENST00000361445.4:c.4420C>T	p.Pro1474Ser	p.P1474S	ENST00000361445	NM_004958.3	1474	Cca/Tca	30/58	0.377332965442675	3	FACETS	0.576	0.512	0.644	0.288	0.256	0.322	INDETERMINATE	1	TRUE	1	0.687150504376923	3		830	618	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256618	16256618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	43	658	0	ENST00000375759.3:c.3883C>T	p.Leu1295Phe	p.L1295F	ENST00000375759	NM_015001.2	1295	Ctc/Ttc	11/15	0.687150504376923	3	FACETS	0.299	0.25	0.354	0.15	0.125	0.177	SUBCLONAL	1	TRUE	1	0.687150504376923	3		658	562	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259877	16259877	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	37	677	1	ENST00000375759.3:c.7142C>A	p.Pro2381Gln	p.P2381Q	ENST00000375759	NM_015001.2	2381	cCa/cAa	11/15	0.687150504376923	3	FACETS	0.235	0.193	0.282	0.117	0.096	0.141	SUBCLONAL	1	TRUE	1	0.687150504376923	3		678	616	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261490	16261490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1246778455	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	40	660	0	ENST00000375759.3:c.8755G>A	p.Val2919Met	p.V2919M	ENST00000375759	NM_015001.2	2919	Gtg/Atg	11/15	0.687150504376923	3	FACETS	0.289	0.24	0.344	0.145	0.12	0.172	SUBCLONAL	1	TRUE	1	0.687150504376923	3		660	541	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023655	27023655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1486055371	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	27	446	1	ENST00000324856.7:c.761C>T	p.Ser254Phe	p.S254F	ENST00000324856	NM_006015.4	254	tCc/tTc	1/20	0.687150504376923	3	FACETS	0.238	0.189	0.294	0.119	0.094	0.147	SUBCLONAL	1	TRUE	1	0.687150504376923	3		447	444	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087507	27087507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	115	889	2	ENST00000324856.7:c.2081G>A	p.Gly694Asp	p.G694D	ENST00000324856	NM_006015.4	694	gGc/gAc	5/20	0.687150504376923	3	FACETS	0.593	0.534	0.655	0.297	0.267	0.328	SUBCLONAL	1	TRUE	1	0.687150504376923	3		891	758	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087875	27087875	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	34	742	0	ENST00000324856.7:c.2162G>A	p.Gly721Asp	p.G721D	ENST00000324856	NM_006015.4	721	gGc/gAc	6/20	0.687150504376923	3	FACETS	0.238	0.194	0.288	0.119	0.097	0.144	SUBCLONAL	1	TRUE	1	0.687150504376923	3		742	559	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099388	27099388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146611677	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	77	716	2	ENST00000324856.7:c.3625C>T	p.Pro1209Ser	p.P1209S	ENST00000324856	NM_006015.4	1209	Cct/Tct	14/20	0.687150504376923	3	FACETS	0.431	0.378	0.488	0.215	0.189	0.244	SUBCLONAL	1	TRUE	1	0.687150504376923	3		718	699	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101557	27101557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	121	804	1	ENST00000324856.7:c.4839G>A	p.Met1613Ile	p.M1613I	ENST00000324856	NM_006015.4	1613	atG/atA	18/20	0.687150504376923	3	FACETS	0.633	0.573	0.698	0.317	0.286	0.349	SUBCLONAL	1	TRUE	1	0.687150504376923	3		805	747	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937178	36937178	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	41	867	0	ENST00000361632.4:c.1141G>A	p.Ala381Thr	p.A381T	ENST00000361632		381	Gct/Act	9/16	0.48445197354186	3	FACETS	0.277	0.23	0.329			1	SUBCLONAL	1	TRUE	NA	0.687150504376923	3		867	579	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938193	36938193	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	32	844	1	ENST00000361632.4:c.768G>A	p.Trp256Ter	p.W256*	ENST00000361632		256	tgG/tgA	6/16	0.48445197354186	3	FACETS	0.233	0.188	0.284			1	SUBCLONAL	1	TRUE	NA	0.687150504376923	3		845	537	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366611	40366611	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	62	724	0	ENST00000397332.2:c.586G>A	p.Glu196Lys	p.E196K	ENST00000397332	NM_001033082.2	196	Gag/Aag	2/3	0.48445197354186	3	FACETS	0.437	0.377	0.501			1	SUBCLONAL	1	TRUE	NA	0.687150504376923	3		724	555	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46512294	46512294	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	39	695	1	ENST00000262741.5:c.945G>A	p.Trp315Ter	p.W315*	ENST00000262741	NM_003629.3	315	tgG/tgA	8/10	0.476022737996448	5	FACETS	0.356	0.294	0.425	0.119	0.098	0.142	SUBCLONAL	1	TRUE	2	0.687150504376923	5		696	648	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46736457	46736457	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	34	584	0	ENST00000371975.4:c.1169G>A	p.Arg390Lys	p.R390K	ENST00000371975	NM_003579.3	390	aGa/aAa	10/18	0.476022737996448	5	FACETS	0.338	0.275	0.409	0.113	0.091	0.137	SUBCLONAL	1	TRUE	2	0.687150504376923	5		584	595	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439613	51439613	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	47	557	1	ENST00000262662.1:c.178G>A	p.Gly60Ser	p.G60S	ENST00000262662		60	Ggt/Agt	4/4	0.476022737996448	5	FACETS	0.335	0.282	0.394	0.112	0.094	0.132	SUBCLONAL	1	TRUE	2	0.687150504376923	5		558	829	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439815	51439815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	40	476	0	ENST00000262662.1:c.380C>T	p.Ala127Val	p.A127V	ENST00000262662		127	gCc/gTc	4/4	0.476022737996448	5	FACETS	0.386	0.32	0.46	0.129	0.106	0.154	SUBCLONAL	1	TRUE	2	0.687150504376923	5		476	612	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248064	59248064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	31	440	0	ENST00000371222.2:c.679G>A	p.Glu227Lys	p.E227K	ENST00000371222	NM_002228.3	227	Gag/Aag	1/1	0.476022737996448	5	FACETS	0.398	0.322	0.485	0.133	0.107	0.162	SUBCLONAL	1	TRUE	2	0.687150504376923	5		440	460	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65316530	65316530	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	40	576	0	ENST00000342505.4:c.1712G>A	p.Ser571Asn	p.S571N	ENST00000342505	NM_002227.2	571	aGc/aAc	12/25	0.476022737996448	5	FACETS	0.441	0.366	0.525	0.147	0.122	0.175	SUBCLONAL	1	TRUE	2	0.687150504376923	5		576	536	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78422377	78422377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	38	424	0	ENST00000370768.2:c.1585G>A	p.Gly529Arg	p.G529R	ENST00000370768	NM_003902.3	529	Gga/Aga	17/20	0.476022737996448	5	FACETS	0.403	0.333	0.482	0.134	0.111	0.161	SUBCLONAL	1	TRUE	2	0.687150504376923	5		424	557	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78425919	78425919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	34	591	0	ENST00000370768.2:c.1526G>A	p.Gly509Glu	p.G509E	ENST00000370768	NM_003902.3	509	gGa/gAa	16/20	0.476022737996448	5	FACETS	0.299	0.243	0.362	0.1	0.081	0.121	SUBCLONAL	1	TRUE	2	0.687150504376923	5		591	672	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85742010	85742010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	114	765	1	ENST00000370580.1:c.26C>T	p.Thr9Ile	p.T9I	ENST00000370580	NM_003921.4	9	aCc/aTc	1/3	0.476022737996448	5	FACETS	0.865	0.779	0.956	0.288	0.259	0.319	CLONAL	1	TRUE	2	0.687150504376923	5		766	779	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458037	120458037	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	116	728	0	ENST00000256646.2:c.7308G>A	p.Trp2436Ter	p.W2436*	ENST00000256646	NM_024408.3	2436	tgG/tgA	34/34	0.476022737996448	5	FACETS	1	0.928	1	0.345	0.311	0.38	CLONAL	1	TRUE	2	0.687150504376923	5		728	663	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870211	155870211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757684037	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	51	854	1	ENST00000368323.3:c.628C>T	p.Pro210Ser	p.P210S	ENST00000368323	NM_006912.5	210	Cca/Tca	6/6	0.476022737996448	5	FACETS	0.35	0.296	0.409	0.117	0.098	0.137	SUBCLONAL	1	TRUE	2	0.687150504376923	5		855	861	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851403	156851403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761207548	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	32	851	1	ENST00000524377.1:c.2360C>T	p.Ala787Val	p.A787V	ENST00000524377	NM_002529.3	787	gCa/gTa	17/17	0.687150504376923	3	FACETS	0.209	0.169	0.254	0.104	0.084	0.127	SUBCLONAL	1	TRUE	1	0.687150504376923	3		852	599	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518586	204518586	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	51	416	0	ENST00000367182.3:c.1249C>T	p.Leu417Phe	p.L417F	ENST00000367182	NM_001278516.1	417	Ctt/Ttt	11/11	0.687150504376923	3	FACETS	0.475	0.404	0.552	0.237	0.202	0.276	SUBCLONAL	1	TRUE	1	0.687150504376923	3		416	420	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651181	206651181	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	80	824	0	ENST00000367120.3:c.791C>T	p.Pro264Leu	p.P264L	ENST00000367120	NM_014002.3	264	cCc/cTc	8/22	0.687150504376923	3	FACETS	0.473	0.416	0.533	0.236	0.208	0.267	SUBCLONAL	1	TRUE	1	0.687150504376923	3		824	662	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555251	226555251	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	50	709	1	ENST00000366794.5:c.2336G>A	p.Arg779Lys	p.R779K	ENST00000366794	NM_001618.3	779	aGg/aAg	17/23	0.687150504376923	3	FACETS	0.297	0.251	0.348	0.149	0.125	0.174	SUBCLONAL	1	TRUE	1	0.687150504376923	3		710	658	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615551	43615551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	22	692	1	ENST00000355710.3:c.2630C>T	p.Ala877Val	p.A877V	ENST00000355710	NM_020975.4	877	gCc/gTc	15/20	0.641153435786728	2	FACETS	0.148	0.114	0.187	0.074	0.057	0.094	SUBCLONAL	1	TRUE	0	0.687150504376923	2		693	434	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63810721	63810721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	74	588	0	ENST00000279873.7:c.808G>A	p.Asp270Asn	p.D270N	ENST00000279873	NM_032199.2	270	Gat/Aat	5/10	0.408108183140173	4	FACETS	0.513	0.448	0.582			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	4		588	709	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406426	70406426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	33	759	1	ENST00000373644.4:c.3940G>A	p.Ala1314Thr	p.A1314T	ENST00000373644	NM_030625.2	1314	Gca/Aca	4/12	0.674143188393259	2	FACETS	0.146	0.118	0.178	0.073	0.059	0.089	SUBCLONAL	1	TRUE	0	0.687150504376923	2		760	657	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692895	89692895	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs587781255	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	31	565	0	ENST00000371953.3:c.379G>T	p.Gly127Ter	p.G127*	ENST00000371953	NM_000314.4	127	Gga/Tga	5/9	0.674143188393259	2	FACETS	0.193	0.155	0.235	0.096	0.077	0.118	SUBCLONAL	1	TRUE	0	0.687150504376923	2		565	468	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104377150	104377150	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	76	910	1	ENST00000369902.3:c.1261G>A	p.Glu421Lys	p.E421K	ENST00000369902	NM_016169.3	421	Gag/Aag	10/12	0.674143188393259	2	FACETS	0.414	0.364	0.468	0.207	0.182	0.234	SUBCLONAL	1	TRUE	0	0.687150504376923	2		911	534	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32449505	32449505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	23	684	0	ENST00000332351.3:c.869G>A	p.Ser290Asn	p.S290N	ENST00000332351	NM_024426.4	290	aGc/aAc	3/10	0.674143188393259	2	FACETS	0.173	0.134	0.217	0.086	0.067	0.109	SUBCLONAL	1	TRUE	0	0.687150504376923	2		684	388	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205155	61205155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1277577700	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	32	822	0	ENST00000301761.2:c.95G>A	p.Arg32Lys	p.R32K	ENST00000301761	NM_017841.2	32	aGa/aAa	2/4	0.674143188393259	2	FACETS	0.161	0.13	0.196	0.081	0.065	0.098	SUBCLONAL	1	TRUE	0	0.687150504376923	2		822	578	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129171	64129171	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	24	793	0	ENST00000334205.4:c.709C>T	p.Pro237Ser	p.P237S	ENST00000334205	NM_003942.2	237	Ccc/Tcc	7/17	0.674143188393259	2	FACETS	0.18	0.141	0.225	0.09	0.07	0.113	SUBCLONAL	1	TRUE	0	0.687150504376923	2		793	388	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137790	64137790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	36	996	0	ENST00000334205.4:c.1891G>A	p.Gly631Arg	p.G631R	ENST00000334205	NM_003942.2	631	Ggg/Agg	15/17	0.674143188393259	2	FACETS	0.225	0.185	0.271	0.113	0.092	0.136	SUBCLONAL	1	TRUE	0	0.687150504376923	2		996	465	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575394	64575394	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	26	891	3	ENST00000312049.6:c.623G>A	p.Gly208Asp	p.G208D	ENST00000312049	NM_130799.2	208	gGc/gAc	3/10	0.674143188393259	2	FACETS	0.158	0.124	0.196	0.079	0.062	0.098	SUBCLONAL	1	TRUE	0	0.687150504376923	2		894	480	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462891	69462891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	57	757	0	ENST00000227507.2:c.704G>A	p.Arg235Lys	p.R235K	ENST00000227507	NM_053056.2	235	aGa/aAa	4/5	0.485602631663668	1	FACETS	0.341	0.294	0.392	0.341	0.294	0.392	SUBCLONAL	1	TRUE	0	0.687150504376923	1		757	319	SUCCESS
EED	8726	MSKCC	GRCh37	11	85967508	85967508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	135	590	1	ENST00000263360.6:c.506G>A	p.Arg169Lys	p.R169K	ENST00000263360	NM_003797.3	169	aGa/aAa	5/12	0.591145040389059	3	FACETS	0.898	0.819	0.98	0.299	0.273	0.327	CLONAL	1	TRUE	0	0.687150504376923	3		591	588	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998568	100998568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759171409	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	46	687	0	ENST00000325455.5:c.1234G>A	p.Ala412Thr	p.A412T	ENST00000325455	NM_001202474.3	412	Gca/Aca	1/8	0.591145040389059	3	FACETS	0.405	0.341	0.475	0.135	0.113	0.159	SUBCLONAL	1	TRUE	0	0.687150504376923	3		687	444	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999102	100999102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	36	733	1	ENST00000325455.5:c.700G>A	p.Gly234Ser	p.G234S	ENST00000325455	NM_001202474.3	234	Ggt/Agt	1/8	0.591145040389059	3	FACETS	0.275	0.225	0.331	0.092	0.075	0.111	SUBCLONAL	1	TRUE	0	0.687150504376923	3		734	512	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201952	102201952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	39	313	0	ENST00000263464.3:c.1304C>T	p.Ala435Val	p.A435V	ENST00000263464	NM_001165.4	435	gCa/gTa	6/9	0.591145040389059	3	FACETS	0.531	0.442	0.63	0.177	0.147	0.21	SUBCLONAL	1	TRUE	0	0.687150504376923	3		313	287	SUCCESS
ATM	472	MSKCC	GRCh37	11	108127062	108127062	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660163	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	48	456	0	ENST00000278616.4:c.2245G>A	p.Ala749Thr	p.A749T	ENST00000278616	NM_000051.3	749	Gcc/Acc	14/63	0.591145040389059	3	FACETS	0.438	0.37	0.511	0.146	0.123	0.171	SUBCLONAL	1	TRUE	0	0.687150504376923	3		456	429	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307439	118307439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	18	189	0	ENST00000534358.1:c.212G>A	p.Gly71Glu	p.G71E	ENST00000534358	NM_005933.3	71	gGg/gAg	1/36	0.591145040389059	3	FACETS	0.634	0.484	0.806	0.211	0.161	0.269	SUBCLONAL	1	TRUE	0	0.687150504376923	3		189	111	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118370615	118370615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	75	468	0	ENST00000534358.1:c.6145C>T	p.Pro2049Ser	p.P2049S	ENST00000534358	NM_005933.3	2049	Cct/Tct	24/36	0.669366583482874	2	FACETS	0.629	0.555	0.707	0.315	0.277	0.354	SUBCLONAL	1	TRUE	0	0.687150504376923	2		468	347	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394692	394692	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	42	823	0	ENST00000399788.2:c.5003G>A	p.Gly1668Asp	p.G1668D	ENST00000399788	NM_001042603.1	1668	gGt/gAt	28/28	NA	2	FACETS	0.211	0.176	0.251			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		823	578	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416910	416910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	24	562	1	ENST00000399788.2:c.3640C>T	p.Leu1214Phe	p.L1214F	ENST00000399788	NM_001042603.1	1214	Ctt/Ttt	23/28	NA	2	FACETS	0.158	0.124	0.199			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		563	441	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	430255	430255	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	26	473	0	ENST00000399788.2:c.2447G>A	p.Arg816Lys	p.R816K	ENST00000399788	NM_001042603.1	816	aGg/aAg	18/28	NA	2	FACETS	0.213	0.169	0.264			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		473	355	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498227	498227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	27	292	0	ENST00000399788.2:c.31G>A	p.Ala11Thr	p.A11T	ENST00000399788	NM_001042603.1	11	Gcg/Acg	1/28	0.591145040389059	3	FACETS	0.435	0.347	0.534	0.145	0.115	0.178	SUBCLONAL	1	TRUE	0	0.687150504376923	3		292	243	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870843	12870843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	15	192	0	ENST00000228872.4:c.70C>T	p.Pro24Ser	p.P24S	ENST00000228872	NM_004064.3	24	Ccc/Tcc	1/3	0.591145040389059	3	FACETS	0.256	0.187	0.339	0.085	0.062	0.113	SUBCLONAL	1	TRUE	0	0.687150504376923	3		192	229	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871054	12871054	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757917082	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	20	407	1	ENST00000228872.4:c.281C>T	p.Pro94Leu	p.P94L	ENST00000228872	NM_004064.3	94	cCc/cTc	1/3	0.591145040389059	3	FACETS	0.225	0.172	0.288	0.075	0.057	0.096	SUBCLONAL	1	TRUE	0	0.687150504376923	3		408	347	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18439842	18439842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	42	366	0	ENST00000266497.5:c.740C>T	p.Ser247Phe	p.S247F	ENST00000266497		247	tCt/tTt	2/31	0.591145040389059	3	FACETS	0.264	0.22	0.313	0.088	0.073	0.105	SUBCLONAL	1	TRUE	0	0.687150504376923	3		366	622	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243404	46243404	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	33	478	1	ENST00000334344.6:c.1757C>T	p.Ser586Phe	p.S586F	ENST00000334344	NM_152641.2	586	tCc/tTc	14/21	0.591145040389059	3	FACETS	0.326	0.265	0.394	0.109	0.088	0.132	SUBCLONAL	1	TRUE	0	0.687150504376923	3		479	396	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287413	46287413	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs200266987	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	63	542	0	ENST00000334344.6:c.5272G>A	p.Asp1758Asn	p.D1758N	ENST00000334344	NM_152641.2	1758	Gat/Aat	20/21	0.591145040389059	3	FACETS	0.498	0.431	0.57	0.166	0.143	0.19	SUBCLONAL	1	TRUE	0	0.687150504376923	3		542	495	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418601	49418601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	51	624	0	ENST00000301067.7:c.15913G>A	p.Ala5305Thr	p.A5305T	ENST00000301067	NM_003482.3	5305	Gct/Act	49/54	0.591145040389059	3	FACETS	0.426	0.362	0.496	0.142	0.12	0.166	SUBCLONAL	1	TRUE	0	0.687150504376923	3		624	468	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422918	49422918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748432945	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	94	739	1	ENST00000301067.7:c.14177G>A	p.Gly4726Asp	p.G4726D	ENST00000301067	NM_003482.3	4726	gGc/gAc	44/54	0.591145040389059	3	FACETS	0.796	0.711	0.885	0.265	0.237	0.295	SUBCLONAL	1	TRUE	0	0.687150504376923	3		740	462	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426957	49426957	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	57	672	0	ENST00000301067.7:c.11531G>A	p.Gly3844Asp	p.G3844D	ENST00000301067	NM_003482.3	3844	gGt/gAt	39/54	0.591145040389059	3	FACETS	0.524	0.451	0.604	0.175	0.15	0.202	SUBCLONAL	1	TRUE	0	0.687150504376923	3		672	425	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431967	49431967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	74	975	0	ENST00000301067.7:c.9172G>A	p.Asp3058Asn	p.D3058N	ENST00000301067	NM_003482.3	3058	Gac/Aac	34/54	0.591145040389059	3	FACETS	0.481	0.421	0.545	0.16	0.14	0.182	SUBCLONAL	1	TRUE	0	0.687150504376923	3		975	602	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435078	49435078	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	45	628	0	ENST00000301067.7:c.6475C>T	p.Leu2159Phe	p.L2159F	ENST00000301067	NM_003482.3	2159	Ctc/Ttc	31/54	0.591145040389059	3	FACETS	0.416	0.35	0.489	0.139	0.116	0.163	SUBCLONAL	1	TRUE	0	0.687150504376923	3		628	423	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482592	56482592	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	42	871	1	ENST00000267101.3:c.1049G>A	p.Gly350Glu	p.G350E	ENST00000267101	NM_001982.3	350	gGa/gAa	9/28	0.591145040389059	3	FACETS	0.299	0.249	0.355	0.1	0.083	0.119	SUBCLONAL	1	TRUE	0	0.687150504376923	3		872	549	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864898	57864898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	109	893	0	ENST00000228682.2:c.2375G>A	p.Gly792Asp	p.G792D	ENST00000228682	NM_005269.2	792	gGc/gAc	12/12	0.591145040389059	3	FACETS	0.785	0.707	0.867	0.262	0.235	0.289	SUBCLONAL	1	TRUE	0	0.687150504376923	3		893	543	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869463	102869463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	34	612	0	ENST00000307046.8:c.178G>A	p.Asp60Asn	p.D60N	ENST00000307046	NM_001111285.1	60	Gat/Aat	2/4	0.591145040389059	3	FACETS	0.314	0.256	0.378	0.105	0.085	0.126	SUBCLONAL	1	TRUE	0	0.687150504376923	3		612	424	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856526	111856526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	40	414	0	ENST00000341259.2:c.577C>T	p.Pro193Ser	p.P193S	ENST00000341259	NM_005475.2	193	Ccc/Tcc	2/8	0.591145040389059	3	FACETS	0.708	0.593	0.833	0.236	0.197	0.278	SUBCLONAL	1	TRUE	0	0.687150504376923	3		414	221	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915695	112915695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	50	635	2	ENST00000351677.2:c.968C>T	p.Pro323Leu	p.P323L	ENST00000351677	NM_002834.3	323	cCc/cTc	9/16	0.651021105723252	2	FACETS	0.338	0.287	0.393	0.169	0.143	0.197	SUBCLONAL	1	TRUE	0	0.687150504376923	2		637	431	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112151	115112151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	39	771	2	ENST00000257566.3:c.1589C>T	p.Ala530Val	p.A530V	ENST00000257566	NM_016569.3	530	gCc/gTc	7/8	0.651021105723252	2	FACETS	0.343	0.285	0.407	0.171	0.142	0.204	SUBCLONAL	1	TRUE	0	0.687150504376923	2		773	331	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536914	120536914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	98	820	1	ENST00000229340.5:c.272C>T	p.Thr91Ile	p.T91I	ENST00000229340	NM_006861.6	91	aCc/aTc	4/6	0.651021105723252	2	FACETS	0.559	0.501	0.621	0.28	0.25	0.311	SUBCLONAL	1	TRUE	0	0.687150504376923	2		821	510	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120805843	120805843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	28	917	2	ENST00000257552.2:c.235G>A	p.Ala79Thr	p.A79T	ENST00000257552	NM_002442.3	79	Gcg/Acg	4/15	0.651021105723252	2	FACETS	0.167	0.133	0.206	0.083	0.066	0.103	SUBCLONAL	1	TRUE	0	0.687150504376923	2		919	489	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201341	133201341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373791036	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	23	768	4	ENST00000320574.5:c.6803C>T	p.Ser2268Leu	p.S2268L	ENST00000320574	NM_006231.2	2268	tCg/tTg	49/49	0.651021105723252	2	FACETS	0.156	0.121	0.197	0.078	0.06	0.099	SUBCLONAL	1	TRUE	0	0.687150504376923	2		772	428	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237719	133237719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	74	574	0	ENST00000320574.5:c.2896G>A	p.Ala966Thr	p.A966T	ENST00000320574	NM_006231.2	966	Gct/Act	25/49	0.651021105723252	2	FACETS	0.628	0.554	0.707	0.314	0.277	0.354	SUBCLONAL	1	TRUE	0	0.687150504376923	2		574	343	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828866	26828866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	30	568	0	ENST00000381527.3:c.88G>A	p.Gly30Ser	p.G30S	ENST00000381527	NM_001260.1	30	Ggc/Agc	1/13	0.641153435786728	2	FACETS	0.2	0.161	0.245	0.1	0.08	0.123	SUBCLONAL	1	TRUE	0	0.687150504376923	2		568	436	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610112	28610112	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	40	738	0	ENST00000241453.7:c.1378C>T	p.Pro460Ser	p.P460S	ENST00000241453	NM_004119.2	460	Cca/Tca	11/24	0.641153435786728	2	FACETS	0.219	0.182	0.261	0.11	0.091	0.131	SUBCLONAL	1	TRUE	0	0.687150504376923	2		738	531	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911893	32911893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	51	762	0	ENST00000380152.3:c.3401G>A	p.Ser1134Asn	p.S1134N	ENST00000380152		1134	aGc/aAc	11/27	0.605647464795697	3	FACETS	0.277	0.234	0.323	0.092	0.078	0.108	SUBCLONAL	1	TRUE	0	0.687150504376923	3		762	721	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912318	32912318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878853575	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	146	632	2	ENST00000380152.3:c.3826G>A	p.Glu1276Lys	p.E1276K	ENST00000380152		1276	Gaa/Aaa	11/27	0.605647464795697	3	FACETS	0.837	0.766	0.911	0.279	0.255	0.304	CLONAL	1	TRUE	0	0.687150504376923	3		634	682	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914118	32914118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507793	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	70	651	0	ENST00000380152.3:c.5626G>A	p.Glu1876Lys	p.E1876K	ENST00000380152		1876	Gaa/Aaa	11/27	0.605647464795697	3	FACETS	0.451	0.393	0.513	0.15	0.131	0.171	SUBCLONAL	1	TRUE	0	0.687150504376923	3		651	607	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134315	41134315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	49	632	1	ENST00000379561.5:c.1313C>T	p.Pro438Leu	p.P438L	ENST00000379561	NM_002015.3	438	cCt/cTt	2/3	0.605647464795697	3	FACETS	0.412	0.349	0.481	0.137	0.116	0.161	SUBCLONAL	1	TRUE	0	0.687150504376923	3		633	465	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955454	48955457	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	437	659	0	ENST00000267163.4:c.1570_1573del	p.Lys524ProfsTer7	p.K524Pfs*7	ENST00000267163	NM_000321.2	524	AAAGcc/cc	17/27	0.605647464795697	3	FACETS	0.887	0.858	0.916	0.887	0.858	0.916	CLONAL	3	TRUE	0	0.687150504376923	3		659	642	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355849	73355849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764982259	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	29	552	1	ENST00000377767.4:c.122G>A	p.Gly41Glu	p.G41E	ENST00000377767	NM_014953.3	41	gGg/gAg	1/21	0.605647464795697	3	FACETS	0.264	0.211	0.324	0.088	0.07	0.108	SUBCLONAL	1	TRUE	0	0.687150504376923	3		553	430	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100024	30100024	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	33	757	1	ENST00000331968.5:c.1596G>A	p.Trp532Ter	p.W532*	ENST00000331968	NM_002742.2	532	tgG/tgA	10/18	0.591145040389059	3	FACETS	0.205	0.166	0.248	0.068	0.055	0.083	SUBCLONAL	1	TRUE	0	0.687150504376923	3		758	631	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194867	30194867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	54	575	0	ENST00000331968.5:c.278G>A	p.Gly93Asp	p.G93D	ENST00000331968	NM_002742.2	93	gGt/gAt	2/18	0.591145040389059	3	FACETS	0.364	0.311	0.423	0.121	0.103	0.141	SUBCLONAL	1	TRUE	0	0.687150504376923	3		575	580	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562980	95562980	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060503648	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	90	571	1	ENST00000393063.1:c.4277G>A	p.Ser1426Asn	p.S1426N	ENST00000393063	NM_030621.3	1426	aGc/aAc	24/28	0.591145040389059	3	FACETS	0.804	0.717	0.895	0.268	0.239	0.299	CLONAL	1	TRUE	0	0.687150504376923	3		572	438	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591712	38591712	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	78	662	0	ENST00000299084.4:c.171del	p.Phe59LeufsTer62	p.F59Lfs*62	ENST00000299084	NM_152594.2	57	gaC/ga	2/7	0.674143188393259	2	FACETS	0.329	0.288	0.372	0.164	0.144	0.186	SUBCLONAL	1	TRUE	0	0.687150504376923	2		662	691	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38616987	38616987	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755991015	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	78	527	0	ENST00000299084.4:c.400G>A	p.Ala134Thr	p.A134T	ENST00000299084	NM_152594.2	134	Gct/Act	4/7	0.674143188393259	2	FACETS	0.371	0.326	0.419	0.185	0.163	0.21	SUBCLONAL	1	TRUE	0	0.687150504376923	2		527	612	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035176	42035176	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1411091108	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	142	939	0	ENST00000219905.7:c.5018T>C	p.Val1673Ala	p.V1673A	ENST00000219905	NM_001164273.1	1673	gTt/gCt	15/24	0.674143188393259	2	FACETS	0.605	0.553	0.66	0.303	0.276	0.33	SUBCLONAL	1	TRUE	0	0.687150504376923	2		939	683	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748285	43748285	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	41	985	0	ENST00000382044.4:c.2521C>T	p.Pro841Ser	p.P841S	ENST00000382044	NM_001141980.1	841	Cct/Tct	12/28	0.674143188393259	2	FACETS	0.164	0.136	0.196	0.082	0.068	0.098	SUBCLONAL	1	TRUE	0	0.687150504376923	2		985	727	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762099	43762099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	46	844	0	ENST00000382044.4:c.1346C>T	p.Pro449Leu	p.P449L	ENST00000382044	NM_001141980.1	449	cCt/cTt	11/28	0.674143188393259	2	FACETS	0.206	0.173	0.243	0.103	0.086	0.122	SUBCLONAL	1	TRUE	0	0.687150504376923	2		844	649	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784294	43784294	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	49	742	0	ENST00000382044.4:c.193-1G>A		p.X65_splice	ENST00000382044	NM_001141980.1	65			0.674143188393259	2	FACETS	0.212	0.179	0.249	0.106	0.089	0.125	SUBCLONAL	1	TRUE	0	0.687150504376923	2		742	672	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774102	66774102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	68	966	2	ENST00000307102.5:c.578C>T	p.Pro193Leu	p.P193L	ENST00000307102	NM_002755.3	193	cCc/cTc	6/11	0.674143188393259	2	FACETS	0.319	0.277	0.364	0.16	0.138	0.182	SUBCLONAL	1	TRUE	0	0.687150504376923	2		968	620	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358331	91358331	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	72	531	0	ENST00000355112.3:c.4077-1G>A		p.X1359_splice	ENST00000355112	NM_000057.2	1359			0.591145040389059	3	FACETS	0.699	0.613	0.79	0.233	0.204	0.264	SUBCLONAL	1	TRUE	0	0.687150504376923	3		531	403	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348227	348227	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	95	847	0	ENST00000262320.3:c.1279C>T	p.Pro427Ser	p.P427S	ENST00000262320	NM_003502.3	427	Cca/Tca	6/11	0.651021105723252	2	FACETS	0.658	0.59	0.731	0.329	0.295	0.366	SUBCLONAL	1	TRUE	0	0.687150504376923	2		847	420	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396661	396661	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	41	732	0	ENST00000262320.3:c.365C>T	p.Thr122Ile	p.T122I	ENST00000262320	NM_003502.3	122	aCt/aTt	2/11	0.651021105723252	2	FACETS	0.293	0.244	0.347	0.147	0.122	0.174	SUBCLONAL	1	TRUE	0	0.687150504376923	2		732	407	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106246	2106246	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs45488893	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	64	757	0	ENST00000219476.3:c.648+1G>A		p.X216_splice	ENST00000219476	NM_000548.3	216			0.651021105723252	2	FACETS	0.461	0.401	0.526	0.231	0.2	0.263	SUBCLONAL	1	TRUE	0	0.687150504376923	2		757	404	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126117	2126117	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397514913	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	87	889	1	ENST00000219476.3:c.2688G>A	p.Trp896Ter	p.W896*	ENST00000219476	NM_000548.3	896	tgG/tgA	24/42	0.651021105723252	2	FACETS	0.575	0.512	0.643	0.288	0.256	0.322	SUBCLONAL	1	TRUE	0	0.687150504376923	2		890	440	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127663	2127663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	55	852	2	ENST00000219476.3:c.2902G>A	p.Glu968Lys	p.E968K	ENST00000219476	NM_000548.3	968	Gag/Aag	26/42	0.651021105723252	2	FACETS	0.373	0.32	0.431	0.187	0.16	0.216	SUBCLONAL	1	TRUE	0	0.687150504376923	2		854	429	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134649	2134649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376946970	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	38	804	0	ENST00000219476.3:c.4426G>A	p.Glu1476Lys	p.E1476K	ENST00000219476	NM_000548.3	1476	Gag/Aag	34/42	0.651021105723252	2	FACETS	0.251	0.207	0.3	0.125	0.103	0.15	SUBCLONAL	1	TRUE	0	0.687150504376923	2		804	441	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213886	2213886	+	splice_region_variant,5_prime_UTR_variant	Splice_Region	SNP	G	G	A	rs370938292	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	18	573	1	ENST00000326181.6:c.-36G>A		p.X12_splice	ENST00000326181	NM_032271.2	12		2/21	0.651021105723252	2	FACETS	0.215	0.162	0.277	0.107	0.081	0.139	SUBCLONAL	1	TRUE	0	0.687150504376923	2		574	244	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640613	3640613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	45	882	1	ENST00000294008.3:c.3026G>A	p.Gly1009Asp	p.G1009D	ENST00000294008	NM_032444.2	1009	gGc/gAc	12/15	0.651021105723252	2	FACETS	0.249	0.208	0.293	0.124	0.104	0.147	SUBCLONAL	1	TRUE	0	0.687150504376923	2		883	527	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641160	3641160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	86	1198	0	ENST00000294008.3:c.2479G>A	p.Glu827Lys	p.E827K	ENST00000294008	NM_032444.2	827	Gag/Aag	12/15	0.651021105723252	2	FACETS	0.404	0.358	0.454	0.202	0.179	0.227	SUBCLONAL	1	TRUE	0	0.687150504376923	2		1198	619	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777729	3777729	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	142	998	0	ENST00000262367.5:c.7319A>G	p.Glu2440Gly	p.E2440G	ENST00000262367	NM_004380.2	2440	gAg/gGg	31/31	0.651021105723252	2	FACETS	0.695	0.635	0.756	0.347	0.317	0.378	SUBCLONAL	1	TRUE	0	0.687150504376923	2		998	595	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789700	3789700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	22	624	0	ENST00000262367.5:c.4159G>A	p.Glu1387Lys	p.E1387K	ENST00000262367	NM_004380.2	1387	Gaa/Aaa	25/31	0.651021105723252	2	FACETS	0.15	0.116	0.19	0.075	0.058	0.095	SUBCLONAL	1	TRUE	0	0.687150504376923	2		624	426	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790432	3790433	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	41	606	0	ENST00000262367.5:c.4100dup	p.Thr1368AspfsTer20	p.T1368Dfs*20	ENST00000262367	NM_004380.2	1367	aag/aaAg	24/31	0.651021105723252	2	FACETS	0.318	0.265	0.377	0.159	0.132	0.189	SUBCLONAL	1	TRUE	0	0.687150504376923	2		606	375	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3929832	3929832	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	20	515	0	ENST00000262367.5:c.85+1G>A		p.X29_splice	ENST00000262367	NM_004380.2	29			0.651021105723252	2	FACETS	0.17	0.129	0.217	0.085	0.064	0.109	SUBCLONAL	1	TRUE	0	0.687150504376923	2		515	343	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857305	9857305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766598240	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	82	371	0	ENST00000330684.3:c.4096C>T	p.Pro1366Ser	p.P1366S	ENST00000330684	NM_001134407.1	1366	Cct/Tct	13/13	0.651021105723252	2	FACETS	0.631	0.56	0.707	0.316	0.28	0.354	SUBCLONAL	1	TRUE	0	0.687150504376923	2		371	378	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349230	11349230	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	18	152	0	ENST00000332029.2:c.106C>T	p.Pro36Ser	p.P36S	ENST00000332029	NM_003745.1	36	Ccc/Tcc	2/2	0.25365618841227	3	FACETS	0.964	0.745	1			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	3		152	73	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014065	14014065	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	43	567	0	ENST00000311895.7:c.43C>A	p.Leu15Met	p.L15M	ENST00000311895	NM_005236.2	15	Ctg/Atg	1/11	0.25365618841227	3	FACETS	0.382	0.32	0.451			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	3		567	440	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813819	50813819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1249728850	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	50	852	1	ENST00000398568.2:c.1373C>T	p.Ala458Val	p.A458V	ENST00000398568	NM_001042412.1	458	gCc/gTc	8/18	NA	2	FACETS	0.228	0.193	0.267			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		853	637	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663362	67663362	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1405972345	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	59	627	1	ENST00000264010.4:c.1763G>A	p.Gly588Glu	p.G588E	ENST00000264010	NM_006565.3	588	gGa/gAa	10/12	0.641153435786728	2	FACETS	0.39	0.336	0.449	0.195	0.168	0.225	SUBCLONAL	1	TRUE	0	0.687150504376923	2		628	440	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821956	72821956	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	14	357	0	ENST00000268489.5:c.10219G>A	p.Ala3407Thr	p.A3407T	ENST00000268489	NM_006885.3	3407	Gct/Act	10/10	0.641153435786728	2	FACETS	0.146	0.105	0.195	0.073	0.052	0.098	SUBCLONAL	1	TRUE	0	0.687150504376923	2		357	280	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822342	72822342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	108	919	0	ENST00000268489.5:c.9833C>T	p.Thr3278Ile	p.T3278I	ENST00000268489	NM_006885.3	3278	aCc/aTc	10/10	0.641153435786728	2	FACETS	0.562	0.506	0.622	0.281	0.253	0.311	SUBCLONAL	1	TRUE	0	0.687150504376923	2		919	559	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822747	72822747	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	41	601	1	ENST00000268489.5:c.9428C>T	p.Ala3143Val	p.A3143V	ENST00000268489	NM_006885.3	3143	gCt/gTt	10/10	0.641153435786728	2	FACETS	0.298	0.249	0.353	0.149	0.124	0.177	SUBCLONAL	1	TRUE	0	0.687150504376923	2		602	400	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827369	72827369	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	39	902	0	ENST00000268489.5:c.9212C>T	p.Thr3071Ile	p.T3071I	ENST00000268489	NM_006885.3	3071	aCc/aTc	9/10	0.641153435786728	2	FACETS	0.198	0.164	0.237	0.099	0.082	0.119	SUBCLONAL	1	TRUE	0	0.687150504376923	2		902	572	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831566	72831566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	48	747	2	ENST00000268489.5:c.5015G>A	p.Gly1672Asp	p.G1672D	ENST00000268489	NM_006885.3	1672	gGc/gAc	9/10	0.641153435786728	2	FACETS	0.265	0.223	0.31	0.132	0.111	0.155	SUBCLONAL	1	TRUE	0	0.687150504376923	2		749	528	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923846	72923846	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	23	596	0	ENST00000268489.5:c.3232G>A	p.Glu1078Lys	p.E1078K	ENST00000268489	NM_006885.3	1078	Gag/Aag	4/10	0.641153435786728	2	FACETS	0.163	0.127	0.206	0.082	0.063	0.103	SUBCLONAL	1	TRUE	0	0.687150504376923	2		596	410	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984568	72984568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	46	847	2	ENST00000268489.5:c.3016G>A	p.Asp1006Asn	p.D1006N	ENST00000268489	NM_006885.3	1006	Gac/Aac	3/10	0.641153435786728	2	FACETS	0.249	0.21	0.293	0.125	0.105	0.147	SUBCLONAL	1	TRUE	0	0.687150504376923	2		849	537	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993116	72993116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	36	850	0	ENST00000268489.5:c.929G>A	p.Ser310Asn	p.S310N	ENST00000268489	NM_006885.3	310	aGc/aAc	2/10	0.641153435786728	2	FACETS	0.176	0.144	0.212	0.088	0.072	0.106	SUBCLONAL	1	TRUE	0	0.687150504376923	2		850	596	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81927313	81927313	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	35	704	0	ENST00000359376.3:c.987-1G>A		p.X329_splice	ENST00000359376	NM_002661.3	329			0.641153435786728	2	FACETS	0.258	0.211	0.31	0.129	0.105	0.155	SUBCLONAL	1	TRUE	0	0.687150504376923	2		704	395	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81939074	81939074	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	69	760	1	ENST00000359376.3:c.1429C>T	p.Gln477Ter	p.Q477*	ENST00000359376	NM_002661.3	477	Caa/Taa	15/33	0.641153435786728	2	FACETS	0.514	0.449	0.582	0.257	0.224	0.291	SUBCLONAL	1	TRUE	0	0.687150504376923	2		761	391	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969879	81969879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	47	673	1	ENST00000359376.3:c.2948C>T	p.Thr983Ile	p.T983I	ENST00000359376	NM_002661.3	983	aCc/aTc	27/33	0.641153435786728	2	FACETS	0.267	0.225	0.314	0.134	0.112	0.157	SUBCLONAL	1	TRUE	0	0.687150504376923	2		674	512	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341244	89341244	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	21	539	0	ENST00000301030.4:c.7691A>G	p.Tyr2564Cys	p.Y2564C	ENST00000301030	NM_001256183.1	2564	tAc/tGc	11/13	0.641153435786728	2	FACETS	0.224	0.172	0.284	0.112	0.086	0.142	SUBCLONAL	1	TRUE	0	0.687150504376923	2		539	273	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813244	89813244	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	62	729	0	ENST00000389301.3:c.3403T>C	p.Phe1135Leu	p.F1135L	ENST00000389301	NM_000135.2	1135	Ttc/Ctc	34/43	0.25365618841227	3	FACETS	0.464	0.401	0.533			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	3		729	522	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838183	89838183	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1183781456	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	105	803	0	ENST00000389301.3:c.2054G>A	p.Arg685Lys	p.R685K	ENST00000389301	NM_000135.2	685	aGg/aAg	23/43	0.25365618841227	3	FACETS	0.751	0.675	0.831			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	3		803	547	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216589	7216589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	100	660	1	ENST00000380728.2:c.746C>T	p.Ala249Val	p.A249V	ENST00000380728		249	gCc/gTc	9/11	0.355492757372604	2	FACETS	0.617	0.553	0.683	0.308	0.276	0.342	INDETERMINATE	1	TRUE	0	0.687150504376923	2		661	472	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983980	7983980	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	11	316	0	ENST00000319144.4:c.646C>T	p.Pro216Ser	p.P216S	ENST00000319144	NM_001139.2	216	Ccc/Tcc	5/15	0.355492757372604	2	FACETS	0.169	0.117	0.235	0.085	0.058	0.118	INDETERMINATE	1	TRUE	0	0.687150504376923	2		316	189	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965023	15965023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	56	674	0	ENST00000268712.3:c.5573C>T	p.Ala1858Val	p.A1858V	ENST00000268712	NM_006311.3	1858	gCa/gTa	37/46	0.355492757372604	2	FACETS	0.281	0.24	0.325	0.141	0.12	0.163	INDETERMINATE	1	TRUE	0	0.687150504376923	2		674	580	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983990	15983990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	36	548	0	ENST00000268712.3:c.3229G>A	p.Glu1077Lys	p.E1077K	ENST00000268712	NM_006311.3	1077	Gaa/Aaa	24/46	0.355492757372604	2	FACETS	0.199	0.163	0.239	0.099	0.081	0.12	INDETERMINATE	1	TRUE	0	0.687150504376923	2		548	527	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687339	37687339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	62	697	1	ENST00000447079.4:c.4243G>A	p.Val1415Met	p.V1415M	ENST00000447079	NM_015083.1	1415	Gtg/Atg	14/14	0.669366583482874	2	FACETS	0.391	0.339	0.449	0.196	0.169	0.225	SUBCLONAL	1	TRUE	0	0.687150504376923	2		698	461	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868676	37868676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752664566	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	93	786	1	ENST00000269571.5:c.1123G>A	p.Ala375Thr	p.A375T	ENST00000269571		375	Gca/Aca	9/27	0.669366583482874	2	FACETS	0.632	0.565	0.703	0.316	0.282	0.352	SUBCLONAL	1	TRUE	0	0.687150504376923	2		787	428	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370206	40370206	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	37	901	0	ENST00000293328.3:c.1132C>T	p.Gln378Ter	p.Q378*	ENST00000293328	NM_012448.3	378	Cag/Tag	9/19	0.669366583482874	2	FACETS	0.193	0.158	0.231	0.096	0.079	0.116	SUBCLONAL	1	TRUE	0	0.687150504376923	2		901	559	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870636	40870636	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	40	600	0	ENST00000428826.2:c.768-1G>A		p.X256_splice	ENST00000428826		256			0.669366583482874	2	FACETS	0.31	0.257	0.367	0.155	0.128	0.184	SUBCLONAL	1	TRUE	0	0.687150504376923	2		600	376	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805633	46805633	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774095240	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	20	847	0	ENST00000290295.7:c.323C>T	p.Ala108Val	p.A108V	ENST00000290295	NM_006361.5	108	gCg/gTg	1/2	0.669366583482874	2	FACETS	0.164	0.125	0.209	0.082	0.062	0.105	SUBCLONAL	1	TRUE	0	0.687150504376923	2		847	356	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677780	47677780	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1052158260	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	24	390	0	ENST00000347630.2:c.1085C>T	p.Pro362Leu	p.P362L	ENST00000347630	NM_001007230.1	362	cCt/cTt	11/11	0.669366583482874	2	FACETS	0.169	0.132	0.212	0.085	0.066	0.106	SUBCLONAL	1	TRUE	0	0.687150504376923	2		390	413	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47679281	47679281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	107	707	1	ENST00000347630.2:c.926C>T	p.Ala309Val	p.A309V	ENST00000347630	NM_001007230.1	309	gCc/gTc	10/11	0.669366583482874	2	FACETS	0.674	0.608	0.743	0.337	0.304	0.372	SUBCLONAL	1	TRUE	0	0.687150504376923	2		708	462	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59871091	59871091	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	40	401	0	ENST00000259008.2:c.1341-1G>A		p.X447_splice	ENST00000259008	NM_032043.2	447			0.669366583482874	2	FACETS	0.306	0.254	0.363	0.153	0.127	0.182	SUBCLONAL	1	TRUE	0	0.687150504376923	2		401	381	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78811733	78811733	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	22	775	0	ENST00000306801.3:c.1148A>G	p.Asp383Gly	p.D383G	ENST00000306801	NM_020761.2	383	gAc/gGc	10/34	0.669366583482874	2	FACETS	0.146	0.112	0.185	0.073	0.056	0.093	SUBCLONAL	1	TRUE	0	0.687150504376923	2		775	439	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736904	736904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	82	826	1	ENST00000314574.4:c.1195G>A	p.Ala399Thr	p.A399T	ENST00000314574	NM_005433.3	399	Gct/Act	10/12	0.208326357674362	5	FACETS	0.548	0.482	0.619	0.11	0.096	0.124	INDETERMINATE	1	TRUE	0	0.687150504376923	5		827	884	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374897	45374897	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	84	861	0	ENST00000262160.6:c.946C>T	p.Leu316Phe	p.L316F	ENST00000262160	NM_005901.5	316	Ctc/Ttc	8/11	0.208326357674362	5	FACETS	0.592	0.522	0.668	0.118	0.104	0.134	INDETERMINATE	1	TRUE	0	0.687150504376923	5		861	838	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625619	1625619	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	41	927	1	ENST00000344749.5:c.455C>T	p.Ser152Phe	p.S152F	ENST00000344749	NM_001136139.2	152	tCc/tTc	7/19	1	2	FACETS	0.285	0.237	0.338	0.285	0.237	0.338	SUBCLONAL	1	TRUE	1	0.687150504376923	2		928	419	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125365	7125365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759020723	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	44	880	1	ENST00000302850.5:c.3187G>A	p.Ala1063Thr	p.A1063T	ENST00000302850	NM_000208.2	1063	Gcc/Acc	17/22	1	2	FACETS	0.228	0.191	0.27	0.228	0.191	0.27	SUBCLONAL	1	TRUE	1	0.687150504376923	2		881	561	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246459	10246459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	28	789	0	ENST00000340748.4:c.4678C>T	p.Pro1560Ser	p.P1560S	ENST00000340748		1560	Cct/Tct	38/40	NA	2	FACETS	0.17	0.136	0.21			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		789	478	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248648	10248648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	86	667	1	ENST00000340748.4:c.4105G>A	p.Asp1369Asn	p.D1369N	ENST00000340748		1369	Gac/Aac	35/40	NA	2	FACETS	0.595	0.529	0.664			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		668	421	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251005	10251005	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	38	675	0	ENST00000340748.4:c.3476-1G>A		p.X1159_splice	ENST00000340748		1159			NA	2	FACETS	0.287	0.237	0.342			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		675	386	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260628	10260628	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	51	687	0	ENST00000340748.4:c.2234G>A	p.Ser745Asn	p.S745N	ENST00000340748		745	aGt/aAt	24/40	NA	2	FACETS	0.309	0.263	0.36			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		687	480	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602850	10602850	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	28	946	1	ENST00000171111.5:c.728C>T	p.Ser243Phe	p.S243F	ENST00000171111	NM_203500.1	243	tCc/tTc	3/6	NA	2	FACETS	0.146	0.116	0.181			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		947	557	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138594	11138594	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755069412	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	99	833	3	ENST00000358026.2:c.3350C>T	p.Ala1117Val	p.A1117V	ENST00000358026	NM_001128849.1	1117	gCg/gTg	24/36	NA	2	FACETS	0.612	0.549	0.678			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		836	471	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050033	13050033	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	45	594	0	ENST00000316448.5:c.177C>G	p.Asp59Glu	p.D59E	ENST00000316448	NM_004343.3	59	gaC/gaG	2/9	0.408108183140173	4	FACETS	0.417	0.35	0.491			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	4		594	530	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302234	15302234	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	53	701	0	ENST00000263388.2:c.1036+1G>A		p.X346_splice	ENST00000263388	NM_000435.2	346			NA	2	FACETS	0.321	0.273	0.372			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		701	481	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350265	15350265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	36	899	0	ENST00000263377.2:c.3514C>T	p.Pro1172Ser	p.P1172S	ENST00000263377	NM_058243.2	1172	Cca/Tca	17/20	NA	2	FACETS	0.227	0.186	0.272			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		899	462	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376326	15376326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1221320388	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	53	964	0	ENST00000263377.2:c.688C>T	p.Pro230Ser	p.P230S	ENST00000263377	NM_058243.2	230	Ccg/Tcg	5/20	NA	2	FACETS	0.262	0.223	0.305			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		964	589	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273893	18273893	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	46	837	0	ENST00000222254.8:c.1226C>T	p.Ser409Phe	p.S409F	ENST00000222254	NM_005027.3	409	tCt/tTt	10/16	0.25365618841227	3	FACETS	0.343	0.288	0.403			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	3		837	525	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30311721	30311721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	46	687	1	ENST00000262643.3:c.575G>A	p.Gly192Glu	p.G192E	ENST00000262643	NM_001238.2	192	gGg/gAg	7/12	NA	2	FACETS	0.245	0.206	0.288			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		688	546	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793188	33793188	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	10	207	1	ENST00000498907.2:c.133C>T	p.Pro45Ser	p.P45S	ENST00000498907	NM_004364.3	45	Cca/Tca	1/1	NA	2	FACETS	0.275	0.187	0.383			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		208	106	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210845	36210845	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	83	832	1	ENST00000222270.7:c.596G>T	p.Arg199Leu	p.R199L	ENST00000222270	NM_014727.1	199	cGg/cTg	3/37	NA	2	FACETS	0.554	0.491	0.621			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		833	436	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218671	36218671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	28	871	2	ENST00000222270.7:c.4375G>A	p.Gly1459Ser	p.G1459S	ENST00000222270	NM_014727.1	1459	Ggc/Agc	17/37	NA	2	FACETS	0.175	0.139	0.216			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		873	466	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223620	36223620	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374062006	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	50	912	4	ENST00000222270.7:c.6170G>A	p.Arg2057His	p.R2057H	ENST00000222270	NM_014727.1	2057	cGc/cAc	28/37	NA	2	FACETS	0.266	0.225	0.311			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		916	547	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224181	36224181	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	68	758	1	ENST00000222270.7:c.6731C>T	p.Pro2244Leu	p.P2244L	ENST00000222270	NM_014727.1	2244	cCc/cTc	28/37	NA	2	FACETS	0.507	0.443	0.576			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		759	390	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793151	42793151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	93	881	1	ENST00000575354.2:c.1043G>A	p.Gly348Asp	p.G348D	ENST00000575354	NM_015125.3	348	gGc/gAc	7/20	NA	2	FACETS	0.549	0.49	0.612			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		882	493	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794929	42794929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	55	744	1	ENST00000575354.2:c.2009C>T	p.Thr670Ile	p.T670I	ENST00000575354	NM_015125.3	670	aCc/aTc	10/20	NA	2	FACETS	0.37	0.317	0.427			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		745	433	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795298	42795298	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	58	652	1	ENST00000575354.2:c.2378G>A	p.Gly793Asp	p.G793D	ENST00000575354	NM_015125.3	793	gGc/gAc	10/20	NA	2	FACETS	0.515	0.445	0.59			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		653	328	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797892	42797892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	29	769	1	ENST00000575354.2:c.3944C>T	p.Ala1315Val	p.A1315V	ENST00000575354	NM_015125.3	1315	gCc/gTc	16/20	NA	2	FACETS	0.283	0.228	0.346			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		770	298	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855603	45855603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	76	672	0	ENST00000391945.4:c.2054C>T	p.Ala685Val	p.A685V	ENST00000391945	NM_000400.3	685	gCc/gTc	22/23	NA	2	FACETS	0.668	0.591	0.75			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		672	331	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729917	47729917	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	102	600	1	ENST00000449228.1:c.472C>T	p.Pro158Ser	p.P158S	ENST00000449228	NM_001127240.2	158	Ccc/Tcc	3/4	0.25365618841227	3	FACETS	0.672	0.602	0.745			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	3		601	594	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139947	50139947	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1379523599	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	60	900	0	ENST00000246792.3:c.382C>T	p.Arg128Trp	p.R128W	ENST00000246792	NM_006270.3	128	Cgg/Tgg	4/6	0.25365618841227	3	FACETS	0.28	0.24	0.323			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	3		900	838	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910627	50910627	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1181610918	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	71	895	2	ENST00000440232.2:c.1730G>A	p.Gly577Asp	p.G577D	ENST00000440232	NM_002691.3	577	gGc/gAc	14/27	0.25365618841227	3	FACETS	0.503	0.439	0.572			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	3		897	552	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920355	50920355	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	66	544	1	ENST00000440232.2:c.3120+1G>A		p.X1040_splice	ENST00000440232	NM_002691.3	1040			0.25365618841227	3	FACETS	0.553	0.481	0.63			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	3		545	467	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25990546	25990547	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	125	805	0	ENST00000435504.4:c.680dup	p.Asn227LysfsTer11	p.N227Kfs*11	ENST00000435504		227	aac/aaAc	8/13	0.605647464795697	3	FACETS	0.715	0.648	0.785	0.238	0.216	0.262	SUBCLONAL	1	TRUE	0	0.687150504376923	3		805	684	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009108	27009108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	14	249	0	ENST00000335756.4:c.44G>A	p.Arg15Lys	p.R15K	ENST00000335756	NM_001809.3	15	aGg/aAg	1/5	0.605647464795697	3	FACETS	0.232	0.167	0.31	0.077	0.055	0.104	SUBCLONAL	1	TRUE	0	0.687150504376923	3		249	236	SUCCESS
ALK	238	MSKCC	GRCh37	2	29436851	29436851	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs145028315	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	74	583	1	ENST00000389048.3:c.3742C>T	p.Arg1248Ter	p.R1248*	ENST00000389048	NM_004304.4	1248	Cga/Tga	24/29	0.641153435786728	2	FACETS	0.577	0.508	0.651	0.289	0.254	0.326	SUBCLONAL	1	TRUE	0	0.687150504376923	2		584	373	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278290	39278290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	70	804	4	ENST00000402219.2:c.859G>A	p.Ala287Thr	p.A287T	ENST00000402219	NM_005633.3	287	Gca/Aca	6/23	0.591145040389059	3	FACETS	0.403	0.351	0.459	0.134	0.117	0.153	SUBCLONAL	1	TRUE	0	0.687150504376923	3		808	680	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027316	48027316	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63751127	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	87	497	0	ENST00000234420.5:c.2194C>T	p.Arg732Ter	p.R732*	ENST00000234420	NM_000179.2	732	Cga/Tga	4/10	0.591145040389059	3	FACETS	0.797	0.709	0.889	0.266	0.236	0.297	SUBCLONAL	1	TRUE	0	0.687150504376923	3		497	427	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030798	48030798	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	54	364	0	ENST00000234420.5:c.3412G>A	p.Gly1138Arg	p.G1138R	ENST00000234420	NM_000179.2	1138	Ggg/Agg	5/10	0.591145040389059	3	FACETS	0.588	0.504	0.679	0.196	0.168	0.227	SUBCLONAL	1	TRUE	0	0.687150504376923	3		364	359	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61760906	61760906	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	62	639	2	ENST00000401558.2:c.126+1G>A		p.X42_splice	ENST00000401558	NM_003400.3	42			0.675069161063107	3	FACETS	0.344	0.297	0.396	0.115	0.099	0.132	SUBCLONAL	1	TRUE	0	0.687150504376923	3		641	704	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128016910	128016910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1454673438	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	102	772	0	ENST00000285398.2:c.2179G>A	p.Glu727Lys	p.E727K	ENST00000285398	NM_000122.1	727	Gag/Aag	14/15	0.591956589237621	3	FACETS	0.689	0.618	0.764	0.23	0.206	0.255	SUBCLONAL	1	TRUE	0	0.687150504376923	3		772	579	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047309	128047309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	65	616	1	ENST00000285398.2:c.613G>A	p.Glu205Lys	p.E205K	ENST00000285398	NM_000122.1	205	Gag/Aag	5/15	0.591956589237621	3	FACETS	0.456	0.395	0.521	0.152	0.131	0.174	SUBCLONAL	1	TRUE	0	0.687150504376923	3		617	558	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873205	136873205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	36	425	0	ENST00000241393.3:c.293C>T	p.Ala98Val	p.A98V	ENST00000241393	NM_003467.2	98	gCc/gTc	2/2	0.687150504376923	3	FACETS	0.323	0.265	0.388	0.108	0.088	0.13	SUBCLONAL	1	TRUE	0	0.687150504376923	3		425	436	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096070	178096070	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	102	587	1	ENST00000397062.3:c.1261C>T	p.Gln421Ter	p.Q421*	ENST00000397062	NM_006164.4	421	Caa/Taa	5/5	0.687150504376923	3	FACETS	0.648	0.58	0.719	0.216	0.193	0.24	SUBCLONAL	1	TRUE	0	0.687150504376923	3		588	616	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097173	178097173	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	52	610	0	ENST00000397062.3:c.541C>T	p.Gln181Ter	p.Q181*	ENST00000397062	NM_006164.4	181	Caa/Taa	4/5	0.687150504376923	3	FACETS	0.28	0.237	0.326	0.093	0.079	0.109	SUBCLONAL	1	TRUE	0	0.687150504376923	3		610	727	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257115	198257115	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	53	767	0	ENST00000335508.6:c.3827C>T	p.Ser1276Phe	p.S1276F	ENST00000335508	NM_012433.2	1276	tCc/tTc	25/25	0.591956589237621	3	FACETS	0.296	0.251	0.344	0.099	0.083	0.115	SUBCLONAL	1	TRUE	0	0.687150504376923	3		767	701	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266249	198266249	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	115	500	0	ENST00000335508.6:c.2371G>A	p.Val791Met	p.V791M	ENST00000335508	NM_012433.2	791	Gtg/Atg	17/25	0.591956589237621	3	FACETS	0.8	0.723	0.881	0.267	0.241	0.294	SUBCLONAL	1	TRUE	0	0.687150504376923	3		500	562	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274659	198274659	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	83	674	0	ENST00000335508.6:c.739G>A	p.Ala247Thr	p.A247T	ENST00000335508	NM_012433.2	247	Gca/Aca	7/25	0.591956589237621	3	FACETS	0.47	0.414	0.529	0.157	0.138	0.177	SUBCLONAL	1	TRUE	0	0.687150504376923	3		674	691	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295755	212295755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	82	749	1	ENST00000342788.4:c.2558C>T	p.Ser853Phe	p.S853F	ENST00000342788	NM_005235.2	853	tCt/tTt	21/28	0.591956589237621	3	FACETS	0.452	0.398	0.51	0.151	0.132	0.17	SUBCLONAL	1	TRUE	0	0.687150504376923	3		750	709	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439631	220439631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	57	769	0	ENST00000243786.2:c.484C>T	p.Pro162Ser	p.P162S	ENST00000243786	NM_002191.3	162	Ccc/Tcc	2/2	0.591956589237621	3	FACETS	0.499	0.429	0.575	0.166	0.143	0.192	SUBCLONAL	1	TRUE	0	0.687150504376923	3		769	447	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225362514	225362514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	39	675	0	ENST00000264414.4:c.1663G>A	p.Gly555Ser	p.G555S	ENST00000264414	NM_003590.4	555	Ggt/Agt	12/16	0.591956589237621	3	FACETS	0.212	0.174	0.253	0.071	0.058	0.085	SUBCLONAL	1	TRUE	0	0.687150504376923	3		675	721	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660370	227660370	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	37	552	0	ENST00000305123.5:c.3085G>A	p.Ala1029Thr	p.A1029T	ENST00000305123	NM_005544.2	1029	Gcc/Acc	1/2	0.591956589237621	3	FACETS	0.378	0.312	0.452	0.126	0.104	0.151	SUBCLONAL	1	TRUE	0	0.687150504376923	3		552	383	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793217	242793217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	80	875	0	ENST00000334409.5:c.860C>T	p.Pro287Leu	p.P287L	ENST00000334409	NM_005018.2	287	cCc/cTc	5/5	NA	2	FACETS	0.585	0.518	0.656			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		875	398	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31020733	31020733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	32	485	0	ENST00000375687.4:c.1030G>A	p.Glu344Lys	p.E344K	ENST00000375687	NM_015338.5	344	Gaa/Aaa	11/13	0.687150504376923	3	FACETS	0.294	0.239	0.357	0.147	0.119	0.179	SUBCLONAL	1	TRUE	1	0.687150504376923	3		485	425	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024492	31024492	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757562094	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	56	729	0	ENST00000375687.4:c.3977C>T	p.Pro1326Leu	p.P1326L	ENST00000375687	NM_015338.5	1326	cCt/cTt	13/13	0.687150504376923	3	FACETS	0.338	0.289	0.392	0.169	0.144	0.196	SUBCLONAL	1	TRUE	1	0.687150504376923	3		729	647	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733333	40733333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	29	598	1	ENST00000373198.4:c.3473C>T	p.Ala1158Val	p.A1158V	ENST00000373198	NM_133170.3	1158	gCc/gTc	26/32	0.25365618841227	3	FACETS	0.262	0.21	0.321			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	3		599	433	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827977	40827977	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1403411484	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	29	644	0	ENST00000373198.4:c.2451G>A	p.Met817Ile	p.M817I	ENST00000373198	NM_133170.3	817	atG/atA	17/32	0.25365618841227	3	FACETS	0.213	0.17	0.262			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	3		644	533	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306523	41306523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	27	543	0	ENST00000373198.4:c.1136C>T	p.Thr379Ile	p.T379I	ENST00000373198	NM_133170.3	379	aCc/aTc	7/32	0.25365618841227	3	FACETS	0.247	0.196	0.305			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	3		543	428	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46271048	46271048	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	46	646	1	ENST00000371998.3:c.3172C>T	p.His1058Tyr	p.H1058Y	ENST00000371998		1058	Cac/Tac	17/23	0.687150504376923	3	FACETS	0.299	0.251	0.352	0.149	0.125	0.176	SUBCLONAL	1	TRUE	1	0.687150504376923	3		647	602	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46276012	46276012	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766130780	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	83	792	0	ENST00000371998.3:c.3448C>T	p.Leu1150Phe	p.L1150F	ENST00000371998		1150	Ctc/Ttc	18/23	0.687150504376923	3	FACETS	0.507	0.448	0.571	0.254	0.224	0.286	SUBCLONAL	1	TRUE	1	0.687150504376923	3		792	640	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281804	46281804	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	37	837	1	ENST00000371998.3:c.4251G>A	p.Met1417Ile	p.M1417I	ENST00000371998		1417	atG/atA	22/23	0.687150504376923	3	FACETS	0.204	0.167	0.245	0.102	0.083	0.123	SUBCLONAL	1	TRUE	1	0.687150504376923	3		838	710	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326150	62326150	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	69	733	1	ENST00000360203.5:c.3166G>A	p.Gly1056Ser	p.G1056S	ENST00000360203	NM_001283009.1	1056	Ggc/Agc	32/35	0.687150504376923	3	FACETS	0.45	0.392	0.512	0.225	0.196	0.256	SUBCLONAL	1	TRUE	1	0.687150504376923	3		734	600	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817484	39817484	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	62	663	0	ENST00000288319.7:c.79C>A	p.His27Asn	p.H27N	ENST00000288319	NM_182918.3	27	Cac/Aac	2/10	0.560194169550725	3	FACETS	0.397	0.343	0.457	0.199	0.171	0.229	SUBCLONAL	1	TRUE	1	0.687150504376923	3		663	610	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42879883	42879883	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	13	258	0	ENST00000398585.3:c.49G>C	p.Ala17Pro	p.A17P	ENST00000398585	NM_001135099.1	17	Gcg/Ccg	1/14	0.560194169550725	3	FACETS	0.213	0.151	0.288	0.106	0.075	0.144	SUBCLONAL	1	TRUE	1	0.687150504376923	3		258	239	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24133991	24133991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	26	548	0	ENST00000263121.7:c.142C>T	p.Pro48Ser	p.P48S	ENST00000263121	NM_003073.3	48	Ccc/Tcc	2/9	0.641153435786728	2	FACETS	0.175	0.138	0.218	0.088	0.069	0.109	SUBCLONAL	1	TRUE	0	0.687150504376923	2		548	432	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057227	30057227	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	53	651	0	ENST00000338641.4:c.709G>A	p.Asp237Asn	p.D237N	ENST00000338641	NM_000268.3	237	Gat/Aat	8/16	0.641153435786728	2	FACETS	0.292	0.248	0.339	0.146	0.124	0.17	SUBCLONAL	1	TRUE	0	0.687150504376923	2		651	529	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627316	37627316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	46	1187	1	ENST00000249071.6:c.403G>A	p.Ala135Thr	p.A135T	ENST00000249071	NM_002872.4	135	Gct/Act	5/7	0.641153435786728	2	FACETS	0.23	0.193	0.271	0.115	0.096	0.136	SUBCLONAL	1	TRUE	0	0.687150504376923	2		1188	582	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41562617	41562617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	50	667	0	ENST00000263253.7:c.3821G>A	p.Gly1274Asp	p.G1274D	ENST00000263253	NM_001429.3	1274	gGc/gAc	23/31	0.641153435786728	2	FACETS	0.25	0.211	0.292	0.125	0.105	0.146	SUBCLONAL	1	TRUE	0	0.687150504376923	2		667	583	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035100	37035100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750706	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	121	581	1	ENST00000231790.2:c.62C>T	p.Ala21Val	p.A21V	ENST00000231790	NM_000249.3	21	gCg/gTg	1/19	0.355492757372604	2	FACETS	0.621	0.563	0.682	0.311	0.281	0.341	INDETERMINATE	1	TRUE	0	0.687150504376923	2		582	567	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37083815	37083815	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	150	715	0	ENST00000231790.2:c.1724G>A	p.Arg575Lys	p.R575K	ENST00000231790	NM_000249.3	575	aGg/aAg	15/19	0.355492757372604	2	FACETS	0.734	0.673	0.796	0.367	0.336	0.398	INDETERMINATE	1	TRUE	0	0.687150504376923	2		715	595	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163052	47163052	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	126	567	0	ENST00000409792.3:c.3074G>A	p.Gly1025Asp	p.G1025D	ENST00000409792	NM_014159.6	1025	gGt/gAt	3/21	0.355492757372604	2	FACETS	0.777	0.708	0.849	0.388	0.354	0.425	INDETERMINATE	1	TRUE	0	0.687150504376923	2		567	472	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164702	47164702	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	22	531	0	ENST00000409792.3:c.1424C>T	p.Ser475Phe	p.S475F	ENST00000409792	NM_014159.6	475	tCt/tTt	3/21	0.355492757372604	2	FACETS	0.175	0.135	0.222	0.088	0.067	0.111	INDETERMINATE	1	TRUE	0	0.687150504376923	2		531	365	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588791	52588791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1429210453	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	42	648	1	ENST00000394830.3:c.4237C>T	p.Pro1413Ser	p.P1413S	ENST00000394830	NM_018313.4	1413	Ccc/Tcc	27/30	0.355492757372604	2	FACETS	0.273	0.228	0.323	0.136	0.114	0.162	INDETERMINATE	1	TRUE	0	0.687150504376923	2		649	448	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643959	52643959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1188313069	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	42	612	2	ENST00000394830.3:c.1937G>A	p.Gly646Asp	p.G646D	ENST00000394830	NM_018313.4	646	gGc/gAc	17/30	0.355492757372604	2	FACETS	0.277	0.231	0.327	0.138	0.115	0.164	INDETERMINATE	1	TRUE	0	0.687150504376923	2		614	442	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70005611	70005611	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs104893746	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	59	602	3	ENST00000394351.3:c.640C>T	p.Arg214Ter	p.R214*	ENST00000394351	NM_000248.3	214	Cga/Tga	7/9	0.355492757372604	2	FACETS	0.332	0.285	0.382	0.166	0.142	0.191	INDETERMINATE	1	TRUE	0	0.687150504376923	2		605	518	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670550	134670550	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	73	843	0	ENST00000398015.3:c.461G>A	p.Arg154Lys	p.R154K	ENST00000398015	NM_004441.4	154	aGg/aAg	3/16	0.265262754418753	4	FACETS	0.556	0.486	0.631	0.278	0.243	0.316	INDETERMINATE	1	TRUE	2	0.687150504376923	4		843	645	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911456	134911456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774889053	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	134	726	4	ENST00000398015.3:c.1921C>T	p.Pro641Ser	p.P641S	ENST00000398015	NM_004441.4	641	Cca/Tca	11/16	0.265262754418753	4	FACETS	1	0.975	1	0.594	0.542	0.648	INDETERMINATE	1	TRUE	2	0.687150504376923	4		730	554	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911498	134911498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	34	741	1	ENST00000398015.3:c.1963G>A	p.Ala655Thr	p.A655T	ENST00000398015	NM_004441.4	655	Gca/Aca	11/16	0.265262754418753	4	FACETS	0.292	0.238	0.353	0.146	0.119	0.177	INDETERMINATE	1	TRUE	2	0.687150504376923	4		742	572	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665167	138665167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	68	680	0	ENST00000330315.3:c.398C>T	p.Ala133Val	p.A133V	ENST00000330315	NM_023067.3	133	gCc/gTc	1/1	0.265262754418753	4	FACETS	0.729	0.636	0.829	0.365	0.318	0.415	INDETERMINATE	1	TRUE	2	0.687150504376923	4		680	458	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176479	142176479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	47	533	0	ENST00000350721.4:c.7622G>A	p.Arg2541Lys	p.R2541K	ENST00000350721	NM_001184.3	2541	aGg/aAg	45/47	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.687150504376923	NA		533	644	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226841	142226841	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200547342	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	46	666	0	ENST00000350721.4:c.4963G>A	p.Val1655Ile	p.V1655I	ENST00000350721	NM_001184.3	1655	Gta/Ata	28/47	0.425129269221886	4	FACETS	0.3	0.251	0.353	0.15	0.125	0.177	SUBCLONAL	1	TRUE	2	0.687150504376923	4		666	754	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281910	142281910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	60	648	2	ENST00000350721.4:c.334G>A	p.Ala112Thr	p.A112T	ENST00000350721	NM_001184.3	112	Gca/Aca	4/47	0.425129269221886	4	FACETS	0.37	0.318	0.427	0.185	0.159	0.214	SUBCLONAL	1	TRUE	2	0.687150504376923	4		650	796	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374777	149374777	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	39	434	0	ENST00000360632.3:c.317C>T	p.Pro106Leu	p.P106L	ENST00000360632	NM_015472.4	106	cCc/cTc	2/7	0.425129269221886	4	FACETS	0.426	0.353	0.507	0.213	0.176	0.254	SUBCLONAL	1	TRUE	2	0.687150504376923	4		434	450	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916618	178916618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	51	513	0	ENST00000263967.3:c.5C>T	p.Pro2Leu	p.P2L	ENST00000263967	NM_006218.2	2	cCt/cTt	2/21	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.687150504376923	NA		513	600	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927468	178927468	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	137	627	1	ENST00000263967.3:c.1231G>A	p.Gly411Ser	p.G411S	ENST00000263967	NM_006218.2	411	Ggc/Agc	7/21	0.265262754418753	4	FACETS	1	0.917	1	0.503	0.458	0.549	INDETERMINATE	1	TRUE	2	0.687150504376923	4		628	669	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190890	185190890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs979026761	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	44	862	2	ENST00000265026.3:c.1771C>T	p.Arg591Cys	p.R591C	ENST00000265026	NM_004721.4	591	Cgc/Tgc	11/14	0.265262754418753	4	FACETS	0.309	0.258	0.366	0.155	0.129	0.183	INDETERMINATE	1	TRUE	2	0.687150504376923	4		864	699	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808018	1808018	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	101	937	0	ENST00000260795.2:c.1994C>T	p.Ala665Val	p.A665V	ENST00000260795		665	gCc/gTc	14/17	NA	2	FACETS	0.627	0.563	0.694			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		937	469	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980549	1980549	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	30	849	0	ENST00000382891.5:c.4011G>C	p.Lys1337Asn	p.K1337N	ENST00000382891	NM_133335.3	1337	aaG/aaC	22/22	NA	2	FACETS	0.23	0.185	0.281			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		849	379	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970968	55970968	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	57	784	2	ENST00000263923.4:c.1829G>A	p.Trp610Ter	p.W610*	ENST00000263923	NM_002253.2	610	tGg/tAg	13/30	NA	2	FACETS	0.297	0.255	0.344			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		786	558	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383722	84383722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1298747950	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	67	881	0	ENST00000321945.7:c.1130G>A	p.Ser377Asn	p.S377N	ENST00000321945	NM_139076.2	377	aGt/aAt	9/9	0.602194039340019	3	FACETS	0.315	0.273	0.361	0.105	0.091	0.121	SUBCLONAL	1	TRUE	0	0.687150504376923	3		881	832	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84403363	84403363	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780156756	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	176	779	0	ENST00000321945.7:c.122C>T	p.Ala41Val	p.A41V	ENST00000321945	NM_139076.2	41	gCc/gTc	2/9	0.602194039340019	3	FACETS	0.959	0.885	1	0.32	0.295	0.345	CLONAL	1	TRUE	0	0.687150504376923	3		779	718	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155293	106155293	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	91	466	0	ENST00000380013.4:c.194G>A	p.Cys65Tyr	p.C65Y	ENST00000380013	NM_001127208.2	65	tGt/tAt	3/11	0.602194039340019	3	FACETS	0.864	0.772	0.961	0.288	0.257	0.321	CLONAL	1	TRUE	0	0.687150504376923	3		466	412	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196841	106196841	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	42	528	0	ENST00000380013.4:c.5174C>T	p.Pro1725Leu	p.P1725L	ENST00000380013	NM_001127208.2	1725	cCc/cTc	11/11	0.602194039340019	3	FACETS	0.404	0.337	0.477	0.135	0.112	0.159	SUBCLONAL	1	TRUE	0	0.687150504376923	3		528	407	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524450	187524450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	34	731	0	ENST00000441802.2:c.11230C>T	p.Pro3744Ser	p.P3744S	ENST00000441802	NM_005245.3	3744	Ccc/Tcc	19/27	0.641153435786728	2	FACETS	0.207	0.169	0.25	0.104	0.084	0.125	SUBCLONAL	1	TRUE	0	0.687150504376923	2		731	478	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539548	187539548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	37	517	0	ENST00000441802.2:c.8192G>A	p.Gly2731Glu	p.G2731E	ENST00000441802	NM_005245.3	2731	gGg/gAg	10/27	0.641153435786728	2	FACETS	0.292	0.241	0.349	0.146	0.12	0.175	SUBCLONAL	1	TRUE	0	0.687150504376923	2		517	369	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539737	187539737	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1329265997	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	23	636	0	ENST00000441802.2:c.8003T>C	p.Phe2668Ser	p.F2668S	ENST00000441802	NM_005245.3	2668	tTc/tCc	10/27	0.641153435786728	2	FACETS	0.159	0.123	0.2	0.079	0.061	0.1	SUBCLONAL	1	TRUE	0	0.687150504376923	2		636	422	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557867	187557867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1336360117	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	141	713	0	ENST00000441802.2:c.3844G>A	p.Gly1282Ser	p.G1282S	ENST00000441802	NM_005245.3	1282	Ggc/Agc	5/27	0.641153435786728	2	FACETS	0.818	0.749	0.888	0.409	0.374	0.444	CLONAL	1	TRUE	0	0.687150504376923	2		713	502	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526345	31526345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	59	1084	0	ENST00000344624.3:c.695G>A	p.Arg232Lys	p.R232K	ENST00000344624		232	aGg/aAg	2/33	NA	2	FACETS	0.244	0.21	0.282			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		1084	703	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589130	67589130	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	19	366	0	ENST00000274335.5:c.1119-1G>A		p.X373_splice	ENST00000274335		373			0.674143188393259	2	FACETS	0.171	0.129	0.22	0.086	0.064	0.11	SUBCLONAL	1	TRUE	0	0.687150504376923	2		366	323	SUCCESS
APC	324	MSKCC	GRCh37	5	112137015	112137015	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1296097556	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	52	596	0	ENST00000257430.4:c.769G>A	p.Ala257Thr	p.A257T	ENST00000257430	NM_000038.5	257	Gct/Act	8/16	0.591145040389059	3	FACETS	0.375	0.319	0.437	0.125	0.106	0.146	SUBCLONAL	1	TRUE	0	0.687150504376923	3		596	542	SUCCESS
APC	324	MSKCC	GRCh37	5	112179582	112179582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520223	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	32	550	0	ENST00000257430.4:c.8291C>T	p.Ser2764Phe	p.S2764F	ENST00000257430	NM_000038.5	2764	tCt/tTt	16/16	0.591145040389059	3	FACETS	0.264	0.214	0.321	0.088	0.071	0.107	SUBCLONAL	1	TRUE	0	0.687150504376923	3		550	474	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927570	131927570	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	22	323	0	ENST00000265335.6:c.1637C>T	p.Ala546Val	p.A546V	ENST00000265335		546	gCt/gTt	11/25	0.591145040389059	3	FACETS	0.261	0.202	0.329	0.087	0.067	0.11	SUBCLONAL	1	TRUE	0	0.687150504376923	3		323	330	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131972870	131972870	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	45	568	1	ENST00000265335.6:c.3453G>A	p.Trp1151Ter	p.W1151*	ENST00000265335		1151	tgG/tgA	22/25	0.591145040389059	3	FACETS	0.366	0.307	0.431	0.122	0.102	0.144	SUBCLONAL	1	TRUE	0	0.687150504376923	3		569	481	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510195	149510195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	50	806	0	ENST00000261799.4:c.1274G>A	p.Ser425Asn	p.S425N	ENST00000261799	NM_002609.3	425	aGc/aAc	9/23	0.591145040389059	3	FACETS	0.327	0.277	0.382	0.109	0.092	0.128	SUBCLONAL	1	TRUE	0	0.687150504376923	3		806	598	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176516677	176516677	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	32	707	0	ENST00000292408.4:c.74C>T	p.Ser25Phe	p.S25F	ENST00000292408	NM_213647.1	25	tCt/tTt	2/18	0.591145040389059	3	FACETS	0.336	0.273	0.408	0.112	0.091	0.136	SUBCLONAL	1	TRUE	0	0.687150504376923	3		707	372	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637082	176637082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	52	795	0	ENST00000439151.2:c.1682C>T	p.Ser561Phe	p.S561F	ENST00000439151	NM_022455.4	561	tCc/tTc	5/23	0.591145040389059	3	FACETS	0.326	0.277	0.38	0.109	0.092	0.127	SUBCLONAL	1	TRUE	0	0.687150504376923	3		795	623	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696641	176696641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	31	395	1	ENST00000439151.2:c.5342C>T	p.Pro1781Leu	p.P1781L	ENST00000439151	NM_022455.4	1781	cCt/cTt	16/23	0.591145040389059	3	FACETS	0.336	0.272	0.408	0.112	0.09	0.136	SUBCLONAL	1	TRUE	0	0.687150504376923	3		396	361	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721460	176721460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	103	646	0	ENST00000439151.2:c.7091C>T	p.Ser2364Phe	p.S2364F	ENST00000439151	NM_022455.4	2364	tCc/tTc	23/23	0.591145040389059	3	FACETS	0.837	0.753	0.926	0.279	0.251	0.309	CLONAL	1	TRUE	0	0.687150504376923	3		646	481	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721727	176721727	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	31	560	0	ENST00000439151.2:c.7358C>T	p.Ala2453Val	p.A2453V	ENST00000439151	NM_022455.4	2453	gCt/gTt	23/23	0.591145040389059	3	FACETS	0.274	0.221	0.333	0.091	0.073	0.111	SUBCLONAL	1	TRUE	0	0.687150504376923	3		560	443	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057764	180057764	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1174986122	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	23	634	0	ENST00000261937.6:c.191C>T	p.Ala64Val	p.A64V	ENST00000261937	NM_182925.4	64	gCt/gTt	3/30	0.643885768200923	2	FACETS	0.211	0.164	0.265	0.106	0.082	0.133	SUBCLONAL	1	TRUE	0	0.687150504376923	2		634	317	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393321	393321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	78	606	1	ENST00000380956.4:c.169G>A	p.Ala57Thr	p.A57T	ENST00000380956	NM_001195286.1	57	Gcg/Acg	2/9	0.25365618841227	3	FACETS	0.761	0.672	0.855			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	3		607	401	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407557	407557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	55	734	2	ENST00000380956.4:c.1315G>A	p.Asp439Asn	p.D439N	ENST00000380956	NM_001195286.1	439	Gat/Aat	9/9	0.25365618841227	3	FACETS	0.377	0.322	0.437			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	3		736	570	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402540	20402540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	32	509	0	ENST00000346618.3:c.77C>T	p.Ala26Val	p.A26V	ENST00000346618	NM_001949.4	26	gCc/gTc	1/7	0.25365618841227	3	FACETS	0.298	0.241	0.362			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	3		509	420	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680326	30680326	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	61	864	1	ENST00000376406.3:c.1393G>A	p.Glu465Lys	p.E465K	ENST00000376406	NM_014641.2	465	Gaa/Aaa	5/15	0.591956589237621	3	FACETS	0.369	0.318	0.425	0.123	0.106	0.142	SUBCLONAL	1	TRUE	0	0.687150504376923	3		865	646	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190836	32190836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	57	886	1	ENST00000375023.3:c.101C>T	p.Pro34Leu	p.P34L	ENST00000375023	NM_004557.3	34	cCc/cTc	2/30	NA	2	FACETS	0.292	0.25	0.337			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		887	569	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965670	93965670	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	159	692	2	ENST00000369303.4:c.2258G>A	p.Gly753Glu	p.G753E	ENST00000369303	NM_004440.3	753	gGa/gAa	13/17	0.591956589237621	3	FACETS	1	0.955	1	0.351	0.323	0.38	CLONAL	1	TRUE	0	0.687150504376923	3		694	590	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969198	93969198	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	36	425	0	ENST00000369303.4:c.1799-1G>A		p.X600_splice	ENST00000369303	NM_004440.3	600			0.591956589237621	3	FACETS	0.305	0.25	0.366	0.102	0.083	0.122	SUBCLONAL	1	TRUE	0	0.687150504376923	3		425	462	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982060	93982060	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	52	611	1	ENST00000369303.4:c.1405C>T	p.Pro469Ser	p.P469S	ENST00000369303	NM_004440.3	469	Ccc/Tcc	6/17	0.591956589237621	3	FACETS	0.283	0.24	0.33	0.094	0.08	0.11	SUBCLONAL	1	TRUE	0	0.687150504376923	3		612	718	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068046	94068046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41273627	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	53	560	0	ENST00000369303.4:c.916G>A	p.Gly306Ser	p.G306S	ENST00000369303	NM_004440.3	306	Ggc/Agc	4/17	0.591956589237621	3	FACETS	0.332	0.283	0.386	0.111	0.094	0.129	SUBCLONAL	1	TRUE	0	0.687150504376923	3		560	624	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109415059	109415059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	70	860	1	ENST00000436639.2:c.218C>T	p.Ser73Phe	p.S73F	ENST00000436639	NM_014454.2	73	tCt/tTt	1/10	0.591956589237621	3	FACETS	0.315	0.274	0.36	0.105	0.091	0.12	SUBCLONAL	1	TRUE	0	0.687150504376923	3		861	869	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109415230	109415230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	208	1023	0	ENST00000436639.2:c.47G>A	p.Arg16Lys	p.R16K	ENST00000436639	NM_014454.2	16	aGa/aAa	1/10	0.591956589237621	3	FACETS	0.818	0.759	0.879	0.273	0.253	0.293	CLONAL	1	TRUE	0	0.687150504376923	3		1023	994	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117630053	117630053	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	51	567	1	ENST00000368508.3:c.6473G>A	p.Gly2158Asp	p.G2158D	ENST00000368508	NM_002944.2	2158	gGt/gAt	41/43	0.591956589237621	3	FACETS	0.353	0.3	0.412	0.118	0.1	0.138	SUBCLONAL	1	TRUE	0	0.687150504376923	3		568	565	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708064	117708064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	39	629	1	ENST00000368508.3:c.2113G>A	p.Gly705Arg	p.G705R	ENST00000368508	NM_002944.2	705	Gga/Aga	14/43	0.591956589237621	3	FACETS	0.248	0.204	0.296	0.083	0.068	0.099	SUBCLONAL	1	TRUE	0	0.687150504376923	3		630	616	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117730777	117730777	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	45	738	0	ENST00000368508.3:c.257G>A	p.Ser86Asn	p.S86N	ENST00000368508	NM_002944.2	86	aGc/aAc	4/43	0.591956589237621	3	FACETS	0.245	0.205	0.29	0.082	0.068	0.097	SUBCLONAL	1	TRUE	0	0.687150504376923	3		738	717	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004462	150004462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1368213585	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	46	701	0	ENST00000253339.5:c.1763C>T	p.Pro588Leu	p.P588L	ENST00000253339		588	cCc/cTc	3/7	0.591956589237621	3	FACETS	0.286	0.241	0.337	0.095	0.08	0.113	SUBCLONAL	1	TRUE	0	0.687150504376923	3		701	628	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265433	152265433	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769618543	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	25	684	1	ENST00000206249.3:c.886C>T	p.Leu296Phe	p.L296F	ENST00000206249	NM_000125.3	296	Ctc/Ttc	4/8	0.591956589237621	3	FACETS	0.229	0.18	0.286	0.076	0.06	0.096	SUBCLONAL	1	TRUE	0	0.687150504376923	3		685	426	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222519	157222519	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554265250	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	58	696	1	ENST00000346085.5:c.1786C>T	p.Gln596Ter	p.Q596*	ENST00000346085	NM_020732.3	596	Cag/Tag	4/20	0.591956589237621	3	FACETS	0.409	0.351	0.472	0.136	0.117	0.158	SUBCLONAL	1	TRUE	0	0.687150504376923	3		697	555	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976691	2976691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	54	604	1	ENST00000396946.4:c.1321G>A	p.Asp441Asn	p.D441N	ENST00000396946	NM_032415.4	441	Gac/Aac	9/25	NA	2	FACETS	0.385	0.33	0.446			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		605	408	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979556	2979556	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	65	475	0	ENST00000396946.4:c.691C>T	p.Gln231Ter	p.Q231*	ENST00000396946	NM_032415.4	231	Cag/Tag	6/25	NA	2	FACETS	0.397	0.344	0.453			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		475	477	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935706	13935706	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	41	557	0	ENST00000405192.2:c.1150G>T	p.Gly384Ter	p.G384*	ENST00000405192	NM_001163147.1	384	Gga/Tga	12/12	0.667377551654336	4	FACETS	0.259	0.215	0.309	0.13	0.107	0.155	SUBCLONAL	1	TRUE	2	0.687150504376923	4		557	777	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55225431	55225431	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs606231253	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	38	530	1	ENST00000275493.2:c.1283G>A	p.Gly428Asp	p.G428D	ENST00000275493	NM_005228.3	428	gGc/gAc	11/28	0.667377551654336	4	FACETS	0.275	0.227	0.33	0.138	0.113	0.165	SUBCLONAL	1	TRUE	2	0.687150504376923	4		531	678	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240744	55240744	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	110	913	0	ENST00000275493.2:c.1988G>A	p.Gly663Glu	p.G663E	ENST00000275493	NM_005228.3	663	gGg/gAg	17/28	0.667377551654336	4	FACETS	0.674	0.605	0.746	0.337	0.302	0.373	SUBCLONAL	1	TRUE	2	0.687150504376923	4		913	802	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240750	55240750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	51	887	3	ENST00000275493.2:c.1994G>A	p.Gly665Asp	p.G665D	ENST00000275493	NM_005228.3	665	gGc/gAc	17/28	0.667377551654336	4	FACETS	0.322	0.273	0.376	0.161	0.136	0.188	SUBCLONAL	1	TRUE	2	0.687150504376923	4		890	778	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412488	116412488	+	intron_variant	Intron	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	218	1102	1	ENST00000397752.3:c.3028+445G>A		p.*1010*	ENST00000397752	NM_000245.2	-/1390			0.632865446864237	3	FACETS	0.677	0.628	0.728	0.339	0.314	0.364	SUBCLONAL	1	TRUE	1	0.687150504376923	3		1103	1259	SUCCESS
MET	4233	MSKCC	GRCh37	7	116413618	116413618	+	intron_variant	Intron	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	20	931	1	ENST00000397752.3:c.3029-1317G>A		p.*1010*	ENST00000397752	NM_000245.2	-/1390			0.632865446864237	3	FACETS	0.086	0.065	0.111	0.043	0.032	0.056	SUBCLONAL	1	TRUE	1	0.687150504376923	3		932	910	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140500181	140500181	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760952736	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	78	791	1	ENST00000288602.6:c.961C>T	p.Pro321Ser	p.P321S	ENST00000288602	NM_004333.4	321	Ccc/Tcc	7/18	0.632865446864237	3	FACETS	0.334	0.293	0.379	0.167	0.146	0.19	SUBCLONAL	1	TRUE	1	0.687150504376923	3		792	913	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515119	148515119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	93	640	0	ENST00000320356.2:c.1090C>T	p.Pro364Ser	p.P364S	ENST00000320356	NM_004456.4	364	Ccc/Tcc	10/20	0.632865446864237	3	FACETS	0.634	0.564	0.707	0.317	0.282	0.354	SUBCLONAL	1	TRUE	1	0.687150504376923	3		640	574	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848538	151848538	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	31	470	0	ENST00000262189.6:c.12655C>T	p.Leu4219Phe	p.L4219F	ENST00000262189	NM_170606.2	4219	Ctt/Ttt	50/59	0.632865446864237	3	FACETS	0.252	0.203	0.307	0.126	0.101	0.154	SUBCLONAL	1	TRUE	1	0.687150504376923	3		470	482	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859201	151859201	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	34	561	0	ENST00000262189.6:c.11460+1G>A		p.X3820_splice	ENST00000262189	NM_170606.2	3820			0.632865446864237	3	FACETS	0.237	0.193	0.287	0.119	0.096	0.144	SUBCLONAL	1	TRUE	1	0.687150504376923	3		561	561	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859528	151859528	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	96	688	0	ENST00000262189.6:c.11134C>T	p.Pro3712Ser	p.P3712S	ENST00000262189	NM_170606.2	3712	Cct/Tct	43/59	0.632865446864237	3	FACETS	0.679	0.606	0.756	0.339	0.303	0.378	SUBCLONAL	1	TRUE	1	0.687150504376923	3		688	553	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859951	151859951	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	43	469	1	ENST00000262189.6:c.10711G>T	p.Gly3571Cys	p.G3571C	ENST00000262189	NM_170606.2	3571	Ggc/Tgc	43/59	0.632865446864237	3	FACETS	0.346	0.289	0.409	0.173	0.144	0.205	SUBCLONAL	1	TRUE	1	0.687150504376923	3		470	486	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860308	151860308	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	37	646	0	ENST00000262189.6:c.10354C>T	p.Pro3452Ser	p.P3452S	ENST00000262189	NM_170606.2	3452	Ccc/Tcc	43/59	0.632865446864237	3	FACETS	0.278	0.228	0.333	0.139	0.114	0.167	SUBCLONAL	1	TRUE	1	0.687150504376923	3		646	521	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860772	151860772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1469113009	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	30	588	0	ENST00000262189.6:c.9890C>T	p.Pro3297Leu	p.P3297L	ENST00000262189	NM_170606.2	3297	cCc/cTc	43/59	0.632865446864237	3	FACETS	0.263	0.211	0.322	0.132	0.105	0.161	SUBCLONAL	1	TRUE	1	0.687150504376923	3		588	446	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873426	151873426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	40	522	1	ENST00000262189.6:c.9112G>A	p.Ala3038Thr	p.A3038T	ENST00000262189	NM_170606.2	3038	Gca/Aca	38/59	0.632865446864237	3	FACETS	0.312	0.259	0.372	0.156	0.129	0.186	SUBCLONAL	1	TRUE	1	0.687150504376923	3		523	501	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873942	151873942	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	112	689	0	ENST00000262189.6:c.8596G>A	p.Glu2866Lys	p.E2866K	ENST00000262189	NM_170606.2	2866	Gaa/Aaa	38/59	0.632865446864237	3	FACETS	0.686	0.619	0.758	0.343	0.309	0.379	SUBCLONAL	1	TRUE	1	0.687150504376923	3		689	638	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877951	151877951	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754298459	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	57	453	1	ENST00000262189.6:c.6994G>A	p.Gly2332Arg	p.G2332R	ENST00000262189	NM_170606.2	2332	Ggg/Agg	36/59	0.632865446864237	3	FACETS	0.494	0.425	0.57	0.247	0.212	0.285	SUBCLONAL	1	TRUE	1	0.687150504376923	3		454	451	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884438	151884438	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	38	562	0	ENST00000262189.6:c.4917G>A	p.Trp1639Ter	p.W1639*	ENST00000262189	NM_170606.2	1639	tgG/tgA	33/59	0.632865446864237	3	FACETS	0.28	0.231	0.335	0.14	0.115	0.168	SUBCLONAL	1	TRUE	1	0.687150504376923	3		562	531	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194683	29194683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	42	793	1	ENST00000240100.2:c.1045C>T	p.Pro349Ser	p.P349S	ENST00000240100	NM_001394.6	349	Ccc/Tcc	4/4	0.632865446864237	3	FACETS	0.299	0.249	0.355	0.15	0.124	0.178	SUBCLONAL	1	TRUE	1	0.687150504376923	3		794	549	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29197629	29197629	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	46	692	0	ENST00000240100.2:c.565C>T	p.Pro189Ser	p.P189S	ENST00000240100	NM_001394.6	189	Cca/Tca	2/4	0.632865446864237	3	FACETS	0.299	0.251	0.352	0.15	0.125	0.176	SUBCLONAL	1	TRUE	1	0.687150504376923	3		692	601	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207771	29207771	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	38	717	0	ENST00000240100.2:c.25G>A	p.Glu9Lys	p.E9K	ENST00000240100	NM_001394.6	9	Gag/Aag	1/4	0.632865446864237	3	FACETS	0.24	0.198	0.288	0.12	0.099	0.144	SUBCLONAL	1	TRUE	1	0.687150504376923	3		717	619	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172210	38172210	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772089664	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	128	601	1	ENST00000317025.8:c.2197G>A	p.Ala733Thr	p.A733T	ENST00000317025	NM_023034.1	733	Gca/Aca	12/24	0.632865446864237	3	FACETS	0.662	0.6	0.727	0.331	0.3	0.364	SUBCLONAL	1	TRUE	1	0.687150504376923	3		602	756	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205139	38205139	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	43	878	0	ENST00000317025.8:c.551A>C	p.Glu184Ala	p.E184A	ENST00000317025	NM_023034.1	184	gAg/gCg	2/24	0.632865446864237	3	FACETS	0.205	0.17	0.243	0.102	0.085	0.122	SUBCLONAL	1	TRUE	1	0.687150504376923	3		878	822	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275840	38275840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752038121	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	122	761	1	ENST00000425967.3:c.1429C>T	p.Pro477Ser	p.P477S	ENST00000425967	NM_001174067.1	477	Cca/Tca	11/19	0.632865446864237	3	FACETS	0.789	0.715	0.866	0.394	0.357	0.433	SUBCLONAL	1	TRUE	1	0.687150504376923	3		762	605	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371950	55371950	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	47	507	1	ENST00000297316.4:c.640C>T	p.Leu214Phe	p.L214F	ENST00000297316	NM_022454.3	214	Ctc/Ttc	2/2	0.632865446864237	3	FACETS	0.42	0.354	0.491	0.21	0.177	0.246	SUBCLONAL	1	TRUE	1	0.687150504376923	3		508	438	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70967611	70967611	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	58	695	0	ENST00000276594.2:c.1412C>T	p.Ser471Phe	p.S471F	ENST00000276594	NM_024504.3	471	tCt/tTt	7/8	0.632865446864237	3	FACETS	0.363	0.312	0.42	0.182	0.156	0.21	SUBCLONAL	1	TRUE	1	0.687150504376923	3		695	624	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74858912	74858912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	168	922	0	ENST00000284811.8:c.292G>A	p.Glu98Lys	p.E98K	ENST00000284811		98	Gaa/Aaa	4/4	0.632865446864237	3	FACETS	0.718	0.66	0.779	0.359	0.33	0.39	SUBCLONAL	1	TRUE	1	0.687150504376923	3		922	915	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737567	145737567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	61	795	1	ENST00000428558.2:c.3196G>A	p.Ala1066Thr	p.A1066T	ENST00000428558	NM_004260.3	1066	Gcc/Acc	19/22	0.687150504376923	3	FACETS	0.401	0.346	0.461	0.2	0.173	0.231	SUBCLONAL	1	TRUE	1	0.687150504376923	3		796	595	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5081857	5081857	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	22	359	0	ENST00000381652.3:c.2567G>A	p.Gly856Asp	p.G856D	ENST00000381652	NM_004972.3	856	gGc/gAc	19/25	0.591145040389059	3	FACETS	0.238	0.184	0.301	0.079	0.061	0.101	SUBCLONAL	1	TRUE	0	0.687150504376923	3		359	361	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549403	5549403	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	60	745	0	ENST00000397747.3:c.430C>A	p.Gln144Lys	p.Q144K	ENST00000397747	NM_025239.3	144	Cag/Aag	4/7	0.591145040389059	3	FACETS	0.362	0.311	0.417	0.121	0.103	0.139	SUBCLONAL	1	TRUE	0	0.687150504376923	3		745	649	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375978	8375978	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556078617	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	54	493	0	ENST00000356435.5:c.4619C>T	p.Thr1540Ile	p.T1540I	ENST00000356435		1540	aCc/aTc	28/35	0.591145040389059	3	FACETS	0.393	0.336	0.456	0.131	0.112	0.152	SUBCLONAL	1	TRUE	0	0.687150504376923	3		493	537	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22008892	22008892	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	35	677	0	ENST00000276925.6:c.61G>C	p.Ala21Pro	p.A21P	ENST00000276925	NM_004936.3	21	Gcc/Ccc	1/2	0.591145040389059	3	FACETS	0.235	0.192	0.284	0.078	0.064	0.095	SUBCLONAL	1	TRUE	0	0.687150504376923	3		677	582	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212752	27212752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	31	879	1	ENST00000380036.4:c.2734G>A	p.Asp912Asn	p.D912N	ENST00000380036	NM_000459.3	912	Gac/Aac	17/23	0.669366583482874	2	FACETS	0.149	0.12	0.182	0.074	0.06	0.091	SUBCLONAL	1	TRUE	0	0.687150504376923	2		880	606	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882051	36882051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	50	851	1	ENST00000358127.4:c.962C>T	p.Pro321Leu	p.P321L	ENST00000358127	NM_001280556.1	321	cCc/cTc	8/10	0.669366583482874	2	FACETS	0.308	0.261	0.359	0.154	0.13	0.18	SUBCLONAL	1	TRUE	0	0.687150504376923	2		852	473	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900359	101900359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	49	472	1	ENST00000374994.4:c.793G>A	p.Ala265Thr	p.A265T	ENST00000374994	NM_004612.2	265	Gca/Aca	4/9	NA	2	FACETS	0.353	0.299	0.412			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		473	404	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904847	101904847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	110	573	0	ENST00000374994.4:c.835G>A	p.Val279Met	p.V279M	ENST00000374994	NM_004612.2	279	Gtg/Atg	5/9	NA	2	FACETS	0.642	0.579	0.707			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		573	499	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133729463	133729463	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368476764	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	30	534	0	ENST00000318560.5:c.92G>A	p.Arg31Gln	p.R31Q	ENST00000318560	NM_005157.4	31	cGg/cAg	2/11	NA	2	FACETS	0.203	0.163	0.248			1	INDETERMINATE	1	TRUE	NA	0.687150504376923	2		534	431	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759791	133759791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	39	571	0	ENST00000318560.5:c.2114G>A	p.Gly705Asp	p.G705D	ENST00000318560	NM_005157.4	705	gGc/gAc	11/11	0.651021105723252	2	FACETS	0.383	0.319	0.455	0.192	0.159	0.228	SUBCLONAL	1	TRUE	0	0.687150504376923	2		571	296	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759872	133759872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	50	743	1	ENST00000318560.5:c.2195G>A	p.Arg732Lys	p.R732K	ENST00000318560	NM_005157.4	732	aGg/aAg	11/11	0.651021105723252	2	FACETS	0.359	0.305	0.418	0.18	0.152	0.209	SUBCLONAL	1	TRUE	0	0.687150504376923	2		744	405	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309156	137309156	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	23	756	2	ENST00000481739.1:c.763G>A	p.Gly255Arg	p.G255R	ENST00000481739	NM_002957.4	255	Ggg/Agg	5/10	0.651021105723252	2	FACETS	0.171	0.133	0.215	0.085	0.066	0.108	SUBCLONAL	1	TRUE	0	0.687150504376923	2		758	392	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396826	139396826	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750318685	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	82	788	0	ENST00000277541.6:c.5282G>A	p.Arg1761Gln	p.R1761Q	ENST00000277541	NM_017617.3	1761	cGg/cAg	28/34	0.651021105723252	2	FACETS	0.582	0.516	0.652	0.291	0.258	0.326	SUBCLONAL	1	TRUE	0	0.687150504376923	2		788	410	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399242	139399242	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	26	845	0	ENST00000277541.6:c.4901C>G	p.Ala1634Gly	p.A1634G	ENST00000277541	NM_017617.3	1634	gCc/gGc	26/34	0.651021105723252	2	FACETS	0.185	0.146	0.229	0.092	0.073	0.115	SUBCLONAL	1	TRUE	0	0.687150504376923	2		845	410	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566409	139566409	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	36	716	0	ENST00000308874.7:c.668G>A	p.Ser223Asn	p.S223N	ENST00000308874		223	aGc/aAc	9/10	0.651021105723252	2	FACETS	0.302	0.248	0.362	0.151	0.124	0.181	SUBCLONAL	1	TRUE	0	0.687150504376923	2		716	347	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815580	139815580	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747252505	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	30	812	0	ENST00000247668.2:c.1051G>A	p.Asp351Asn	p.D351N	ENST00000247668	NM_021138.3	351	Gat/Aat	9/11	0.651021105723252	2	FACETS	0.213	0.171	0.26	0.106	0.085	0.13	SUBCLONAL	1	TRUE	0	0.687150504376923	2		812	410	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930255	39930255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	103	838	0	ENST00000378444.4:c.3209C>T	p.Ala1070Val	p.A1070V	ENST00000378444	NM_001123385.1	1070	gCc/gTc	6/15	0.660999684346161	4	FACETS	0.626	0.56	0.696			1	SUBCLONAL	1	TRUE	NA	0.687150504376923	4		838	808	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932590	39932590	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	93	877	1	ENST00000378444.4:c.2009C>T	p.Pro670Leu	p.P670L	ENST00000378444	NM_001123385.1	670	cCc/cTc	4/15	0.660999684346161	4	FACETS	0.602	0.535	0.673			1	SUBCLONAL	1	TRUE	NA	0.687150504376923	4		878	759	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933559	39933559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1477574479	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	38	725	2	ENST00000378444.4:c.1040C>T	p.Thr347Ile	p.T347I	ENST00000378444	NM_001123385.1	347	aCc/aTc	4/15	0.660999684346161	4	FACETS	0.282	0.232	0.338			1	SUBCLONAL	1	TRUE	NA	0.687150504376923	4		727	661	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933599	39933599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	35	584	0	ENST00000378444.4:c.1000C>T	p.Pro334Ser	p.P334S	ENST00000378444	NM_001123385.1	334	Ccc/Tcc	4/15	0.660999684346161	4	FACETS	0.291	0.238	0.351			1	SUBCLONAL	1	TRUE	NA	0.687150504376923	4		584	590	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732936	44732936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	39	621	0	ENST00000377967.4:c.139G>A	p.Glu47Lys	p.E47K	ENST00000377967	NM_021140.2	47	Gag/Aag	1/29	0.660999684346161	4	FACETS	0.278	0.23	0.333			1	SUBCLONAL	1	TRUE	NA	0.687150504376923	4		621	688	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929439	44929439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	128	848	1	ENST00000377967.4:c.2539C>T	p.Pro847Ser	p.P847S	ENST00000377967	NM_021140.2	847	Cct/Tct	17/29	0.660999684346161	4	FACETS	0.599	0.541	0.659			1	SUBCLONAL	1	TRUE	NA	0.687150504376923	4		849	1050	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045489	47045489	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	82	743	1	ENST00000377604.3:c.2456C>T	p.Ala819Val	p.A819V	ENST00000377604	NM_001204468.1	819	gCt/gTt	22/24	0.476022737996448	5	FACETS	0.674	0.594	0.76	0.225	0.198	0.254	SUBCLONAL	1	TRUE	2	0.687150504376923	5		744	719	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243924	53243924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	126	1009	1	ENST00000375401.3:c.1069C>T	p.Pro357Ser	p.P357S	ENST00000375401	NM_004187.3	357	Cct/Tct	8/26	0.476022737996448	5	FACETS	0.796	0.72	0.876	0.265	0.24	0.292	SUBCLONAL	1	TRUE	2	0.687150504376923	5		1010	936	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245054	53245054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	108	889	0	ENST00000375401.3:c.886G>A	p.Glu296Lys	p.E296K	ENST00000375401	NM_004187.3	296	Gag/Aag	7/26	0.476022737996448	5	FACETS	0.829	0.744	0.919	0.276	0.248	0.307	CLONAL	1	TRUE	2	0.687150504376923	5		889	770	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411524	63411524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	124	879	0	ENST00000330258.3:c.1643C>T	p.Ser548Phe	p.S548F	ENST00000330258	NM_152424.3	548	tCc/tTc	2/2	0.476022737996448	5	FACETS	0.859	0.777	0.946	0.286	0.259	0.316	CLONAL	1	TRUE	2	0.687150504376923	5		879	853	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413114	63413114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	87	860	0	ENST00000330258.3:c.53G>A	p.Gly18Glu	p.G18E	ENST00000330258	NM_152424.3	18	gGg/gAg	2/2	0.476022737996448	5	FACETS	0.713	0.631	0.801	0.238	0.21	0.267	SUBCLONAL	1	TRUE	2	0.687150504376923	5		860	721	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341418	70341418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	56	823	0	ENST00000374080.3:c.853G>A	p.Gly285Arg	p.G285R	ENST00000374080		285	Ggg/Agg	7/45	0.476022737996448	5	FACETS	0.456	0.39	0.529	0.152	0.13	0.177	SUBCLONAL	1	TRUE	2	0.687150504376923	5		823	726	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357586	70357586	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	39	824	0	ENST00000374080.3:c.5837C>T	p.Pro1946Leu	p.P1946L	ENST00000374080		1946	cCt/cTt	41/45	0.476022737996448	5	FACETS	0.302	0.249	0.361	0.101	0.083	0.121	SUBCLONAL	1	TRUE	2	0.687150504376923	5		824	764	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891487	76891487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	70	874	1	ENST00000373344.5:c.4618G>A	p.Asp1540Asn	p.D1540N	ENST00000373344	NM_000489.3	1540	Gat/Aat	16/35	0.476022737996448	5	FACETS	0.366	0.318	0.418	0.122	0.106	0.14	SUBCLONAL	1	TRUE	2	0.687150504376923	5		875	1131	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76931778	76931778	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	52	759	1	ENST00000373344.5:c.3752C>T	p.Ser1251Phe	p.S1251F	ENST00000373344	NM_000489.3	1251	tCt/tTt	10/35	0.476022737996448	5	FACETS	0.305	0.258	0.356	0.102	0.086	0.119	SUBCLONAL	1	TRUE	2	0.687150504376923	5		760	1008	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171428	123171428	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	83	946	1	ENST00000218089.9:c.340C>T	p.Leu114Phe	p.L114F	ENST00000218089	NM_001042749.1	114	Ctt/Ttt	6/35	0.667377551654336	4	FACETS	0.322	0.283	0.364	0.161	0.141	0.182	SUBCLONAL	1	TRUE	2	0.687150504376923	4		947	1266	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123505215	123505215	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	115	630	1	ENST00000371139.4:c.361C>T	p.Pro121Ser	p.P121S	ENST00000371139	NM_001114937.2	121	Cct/Tct	4/4	0.667377551654336	4	FACETS	0.616	0.554	0.681	0.308	0.277	0.341	SUBCLONAL	1	TRUE	2	0.687150504376923	4		631	917	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11301713	11301713	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	41	760	0	ENST00000361445.4:c.1438G>C	p.Ala480Pro	p.A480P	ENST00000361445	NM_004958.3	480	Gcc/Ccc	10/58	0.377332965442675	3	FACETS	0.306	0.254	0.363	0.153	0.127	0.182	INDETERMINATE	1	TRUE	1	0.687150504376923	3		760	524	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	363	215	0				ENST00000310581	NM_198253.2	-/1132			0.557560893590308	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	1	0.78651733321359	4		215	536	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295204	1295204	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs2735943	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	341	586	2				ENST00000310581	NM_198253.2	-/1132			0.557560893590308	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	1	0.78651733321359	4		588	494	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933480	100933480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766277966	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	53	89	0	ENST00000325455.5:c.1910G>A	p.Arg637Gln	p.R637Q	ENST00000325455	NM_001202474.3	637	cGa/cAa	4/8	0.273023014198869	1	FACETS	0.496	0.431	0.564	0.496	0.431	0.564	INDETERMINATE	1	TRUE	0	0.78651733321359	1		89	165	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041074	42041074	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	150	646	1	ENST00000219905.7:c.5452C>T	p.Arg1818Ter	p.R1818*	ENST00000219905	NM_001164273.1	1818	Cga/Tga	16/24	0.78651733321359	3	FACETS	0.788	0.723	0.857	0.394	0.361	0.429	SUBCLONAL	1	TRUE	1	0.78651733321359	3		647	674	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940120	31940120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	343	856	0	ENST00000375333.2:c.262G>A	p.Glu88Lys	p.E88K	ENST00000375333	NM_032454.1	88	Gaa/Aaa	2/8	0.2797461983069	4	FACETS	0.912	0.867	0.958	0.912	0.867	0.958	INDETERMINATE	2	TRUE	2	0.78651733321359	4		856	854	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956220	55956220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190050670	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	136	545	1	ENST00000263923.4:c.3095G>A	p.Arg1032Gln	p.R1032Q	ENST00000263923	NM_002253.2	1032	cGa/cAa	23/30	0.170788097381601	2	FACETS	0.716	0.655	0.779	0.358	0.327	0.39	INDETERMINATE	1	TRUE	0	0.78651733321359	2		546	483	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498004	29498004	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1208550472	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	244	746	2	ENST00000389048.3:c.2002G>A	p.Glu668Lys	p.E668K	ENST00000389048	NM_004304.4	668	Gaa/Aaa	11/29	0.2797461983069	4	FACETS	0.938	0.883	0.993	0.938	0.883	0.993	INDETERMINATE	2	TRUE	2	0.78651733321359	4		748	591	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560175	29560175	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	145	463	1	ENST00000356175.3:c.3652C>T	p.Gln1218Ter	p.Q1218*	ENST00000356175	NM_000267.3	1218	Caa/Taa	27/57	0.261107164982854	2	FACETS	1	0.979	1	0.574	0.532	0.617	INDETERMINATE	1	TRUE	0	0.78651733321359	2		464	321	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514563	41514563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	165	636	0	ENST00000373198.4:c.98C>T	p.Ser33Phe	p.S33F	ENST00000373198	NM_133170.3	33	tCc/tTc	2/32	0.338793537072976	4	FACETS	0.801	0.742	0.861	0.801	0.742	0.861	INDETERMINATE	2	TRUE	2	0.78651733321359	4		636	468	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481412	140481412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913353	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	109	658	3	ENST00000288602.6:c.1396G>A	p.Gly466Arg	p.G466R	ENST00000288602	NM_004333.4	466	Gga/Aga	11/18	0.2797461983069	4	FACETS	1	0.915	1	0.507	0.458	0.559	INDETERMINATE	1	TRUE	2	0.78651733321359	4		661	488	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264965	46264965	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	225	598	0	ENST00000371998.3:c.1835C>T	p.Pro612Leu	p.P612L	ENST00000371998		612	cCt/cTt	12/23	0.338793537072976	4	FACETS	0.934	0.878	0.991	0.934	0.878	0.991	INDETERMINATE	2	TRUE	2	0.78651733321359	4		598	547	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312725	91312725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	291	633	0	ENST00000355112.3:c.2464C>T	p.Pro822Ser	p.P822S	ENST00000355112	NM_000057.2	822	Cct/Tct	12/22	0.78651733321359	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.78651733321359	3		633	489	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913250	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	212	610	3	ENST00000369535.4:c.34G>T	p.Gly12Cys	p.G12C	ENST00000369535	NM_002524.4	12	Ggt/Tgt	2/7	0.526056103441396	4	FACETS	0.752	0.703	0.803	0.752	0.703	0.803	SUBCLONAL	2	TRUE	2	0.78651733321359	4		613	640	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31025023	31025023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	227	578	1	ENST00000375687.4:c.4508C>T	p.Ser1503Leu	p.S1503L	ENST00000375687	NM_015338.5	1503	tCg/tTg	13/13	0.338793537072976	4	FACETS	0.995	0.937	1	0.995	0.937	1	INDETERMINATE	2	TRUE	2	0.78651733321359	4		579	518	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134123	41134123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751383976	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	208	531	3	ENST00000379561.5:c.1505C>T	p.Ser502Leu	p.S502L	ENST00000379561	NM_002015.3	502	tCg/tTg	2/3	0.2797461983069	4	FACETS	0.914	0.856	0.972	0.914	0.856	0.972	INDETERMINATE	2	TRUE	2	0.78651733321359	4		534	517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863224683	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	355	758	0	ENST00000269305.4:c.388C>T	p.Leu130Phe	p.L130F	ENST00000269305	NM_001126112.2	130	Ctc/Ttc	5/11	0.261107164982854	2	FACETS	1	0.995	1	0.693	0.664	0.723	INDETERMINATE	1	TRUE	0	0.78651733321359	2		758	651	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435469	18435469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	130	332	1	ENST00000266497.5:c.454G>A	p.Asp152Asn	p.D152N	ENST00000266497		152	Gat/Aat	1/31	0.244129748329512	4	FACETS	0.981	0.905	1	0.981	0.905	1	INDETERMINATE	2	TRUE	2	0.78651733321359	4		333	301	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971370	13971370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748346103	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	161	411	0	ENST00000405192.2:c.559C>T	p.Arg187Cys	p.R187C	ENST00000405192	NM_001163147.1	187	Cgc/Tgc	8/12	0.2797461983069	4	FACETS	0.894	0.83	0.96	0.894	0.83	0.96	INDETERMINATE	2	TRUE	2	0.78651733321359	4		411	409	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587251	212587251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868149408	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	183	510	1	ENST00000342788.4:c.750G>A	p.Met250Ile	p.M250I	ENST00000342788	NM_005235.2	250	atG/atA	7/28	0.2797461983069	4	FACETS	0.943	0.88	1	0.943	0.88	1	INDETERMINATE	2	TRUE	2	0.78651733321359	4		511	441	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764328	39764328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747584221	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	44	822	0	ENST00000288319.7:c.784G>A	p.Gly262Ser	p.G262S	ENST00000288319	NM_182918.3	262	Ggt/Agt	7/10	0.498993829161787	1	FACETS	0.128	0.107	0.152	0.128	0.107	0.152	SUBCLONAL	1	TRUE	0	0.78651733321359	1		822	529	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226103	226103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs553257776	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	135	521	0	ENST00000264932.6:c.562C>T	p.Arg188Trp	p.R188W	ENST00000264932	NM_004168.2	188	Cgg/Tgg	5/15	0.557560893590308	4	FACETS	1	0.957	1	0.359	0.328	0.392	CLONAL	1	TRUE	1	0.78651733321359	4		521	569	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115392	115115392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	228	963	0	ENST00000257566.3:c.934G>A	p.Glu312Lys	p.E312K	ENST00000257566	NM_016569.3	312	Gaa/Aaa	5/8	0.244129748329512	4	FACETS	0.905	0.851	0.961	0.905	0.851	0.961	INDETERMINATE	2	TRUE	2	0.78651733321359	4		963	572	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979524	2979524	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	258	818	0	ENST00000396946.4:c.723G>T	p.Glu241Asp	p.E241D	ENST00000396946	NM_032415.4	241	gaG/gaT	6/25	0.2797461983069	4	FACETS	0.965	0.912	1	0.965	0.912	1	INDETERMINATE	2	TRUE	2	0.78651733321359	4		818	607	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295215	1295215	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	364	360	1				ENST00000310581	NM_198253.2	-/1132			0.557560893590308	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	1	0.78651733321359	4		361	521	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212484001	212484001	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	113	521	0	ENST00000342788.4:c.2203-1G>A		p.X735_splice	ENST00000342788	NM_005235.2	735			0.2797461983069	4	FACETS	0.856	0.781	0.932	0.856	0.781	0.932	INDETERMINATE	2	TRUE	2	0.78651733321359	4		521	300	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251578	212251578	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	100	583	0	ENST00000342788.4:c.3481G>A	p.Glu1161Lys	p.E1161K	ENST00000342788	NM_005235.2	1161	Gaa/Aaa	27/28	0.2797461983069	4	FACETS	0.893	0.8	0.99	0.446	0.4	0.495	INDETERMINATE	1	TRUE	2	0.78651733321359	4		583	509	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131411	202131411	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs777784105	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	117	663	0	ENST00000358485.4:c.379C>T	p.Arg127Ter	p.R127*	ENST00000358485	NM_001080125.1	127	Cga/Tga	2/9	0.2797461983069	4	FACETS	0.956	0.865	1	0.478	0.432	0.526	INDETERMINATE	1	TRUE	2	0.78651733321359	4		663	556	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351388	89351388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	155	886	1	ENST00000301030.4:c.1562C>T	p.Ser521Phe	p.S521F	ENST00000301030	NM_001256183.1	521	tCc/tTc	9/13	0.244129748329512	4	FACETS	0.981	0.9	1	0.49	0.45	0.533	INDETERMINATE	1	TRUE	2	0.78651733321359	4		887	718	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637685	176637685	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	202	737	0	ENST00000439151.2:c.2285C>T	p.Ser762Phe	p.S762F	ENST00000439151	NM_022455.4	762	tCc/tTc	5/23	1	2	FACETS	0.978	0.915	1	0.978	0.915	1	CLONAL	1	TRUE	1	0.78651733321359	2		737	525	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606553	93606553	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267602311	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	410	645	0	ENST00000375746.1:c.373G>A	p.Glu125Lys	p.E125K	ENST00000375746	NM_001174167.1	125	Gaa/Aaa	2/14	0.78651733321359	2	FACETS	0.985	0.957	1	0.985	0.957	1	CLONAL	2	TRUE	0	0.78651733321359	2		645	529	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156149	119156149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	164	802	1	ENST00000264033.4:c.1814C>T	p.Ser605Phe	p.S605F	ENST00000264033	NM_005188.3	605	tCc/tTc	11/16	0.273023014198869	1	FACETS	0.53	0.491	0.571	0.53	0.491	0.571	INDETERMINATE	1	TRUE	0	0.78651733321359	1		803	477	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644451	18644451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	123	754	0	ENST00000266497.5:c.2629C>T	p.Pro877Ser	p.P877S	ENST00000266497		877	Cct/Tct	18/31	0.244129748329512	4	FACETS	0.98	0.89	1	0.49	0.445	0.538	INDETERMINATE	1	TRUE	2	0.78651733321359	4		754	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579421	7579421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881994	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	157	912	3	ENST00000269305.4:c.266C>T	p.Pro89Leu	p.P89L	ENST00000269305	NM_001126112.2	89	cCc/cTc	4/11	0.261107164982854	2	FACETS	0.646	0.594	0.7	0.323	0.297	0.35	INDETERMINATE	1	TRUE	0	0.78651733321359	2		915	618	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780216	9780217	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	129	946	3	ENST00000377346.4:c.1386_1387delinsAT	p.Asn462_Pro463delinsLysSer	p.N462_P463delinsKS	ENST00000377346	NM_005026.3	462	aaCCcc/aaATcc	11/24	0.526056103441396	4	FACETS	0.648	0.587	0.712	0.324	0.293	0.356	SUBCLONAL	1	TRUE	2	0.78651733321359	4		949	905	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11193191	11193192	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	261	865	1	ENST00000361445.4:c.5309_5310delinsTT	p.Pro1770Leu	p.P1770L	ENST00000361445	NM_004958.3	1770	cCC/cTT	38/58	0.526056103441396	4	FACETS	1	0.993	1	0.738	0.694	0.783	CLONAL	1	TRUE	2	0.78651733321359	4		866	803	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106081	27106081	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	122	626	1	ENST00000324856.7:c.5692C>T	p.Pro1898Ser	p.P1898S	ENST00000324856	NM_006015.4	1898	Cca/Tca	20/20	0.526056103441396	4	FACETS	0.822	0.744	0.904	0.411	0.372	0.452	CLONAL	1	TRUE	2	0.78651733321359	4		627	674	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28600014	28600014	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1242575706	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	235	862	0	ENST00000253063.3:c.896C>T	p.Pro299Leu	p.P299L	ENST00000253063	NM_031459.4	299	cCc/cTc	6/10	0.526056103441396	4	FACETS	1	0.993	1	0.743	0.697	0.791	CLONAL	1	TRUE	2	0.78651733321359	4		862	718	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458317	120458317	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	239	741	1	ENST00000256646.2:c.7028C>T	p.Pro2343Leu	p.P2343L	ENST00000256646	NM_024408.3	2343	cCa/cTa	34/34	0.526056103441396	4	FACETS	1	0.993	1	0.748	0.701	0.795	CLONAL	1	TRUE	2	0.78651733321359	4		742	726	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176176057	176176058	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	256	833	0	ENST00000367669.3:c.57_58delinsAA	p.Ala20Thr	p.A20T	ENST00000367669	NM_022457.5	19	tcGGcg/tcAAcg	1/20	0.402017199786669	3	FACETS	1	0.993	1	0.719	0.678	0.76	INDETERMINATE	1	TRUE	1	0.78651733321359	3		833	631	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094324	193094324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	156	677	0	ENST00000367435.3:c.214C>T	p.Pro72Ser	p.P72S	ENST00000367435	NM_024529.4	72	Cct/Tct	2/17	0.402017199786669	3	FACETS	1	0.986	1	0.643	0.594	0.692	INDETERMINATE	1	TRUE	1	0.78651733321359	3		677	430	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245912926	245912926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	248	639	0	ENST00000388985.4:c.1226G>A	p.Ser409Asn	p.S409N	ENST00000388985		409	aGc/aAc	12/12	0.402017199786669	3	FACETS	0.84	0.794	0.886	0.84	0.794	0.886	INDETERMINATE	2	TRUE	1	0.78651733321359	3		639	523	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625228	69625228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868995912	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	215	971	2	ENST00000334134.2:c.565G>A	p.Glu189Lys	p.E189K	ENST00000334134	NM_005247.2	189	Gag/Aag	3/3	0.273023014198869	1	FACETS	0.721	0.678	0.764	0.721	0.678	0.764	INDETERMINATE	1	TRUE	0	0.78651733321359	1		973	460	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999588	100999588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868064003	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	161	1241	3	ENST00000325455.5:c.214G>A	p.Glu72Lys	p.E72K	ENST00000325455	NM_001202474.3	72	Gaa/Aaa	1/8	0.273023014198869	1	FACETS	0.444	0.41	0.48	0.444	0.41	0.48	INDETERMINATE	1	TRUE	0	0.78651733321359	1		1244	559	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373727	118373727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1192437631	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	83	546	0	ENST00000534358.1:c.7120C>T	p.His2374Tyr	p.H2374Y	ENST00000534358	NM_005933.3	2374	Cat/Tat	27/36	0.273023014198869	1	FACETS	0.405	0.361	0.452	0.405	0.361	0.452	INDETERMINATE	1	TRUE	0	0.78651733321359	1		546	316	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415607	49415607	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	238	620	0	ENST00000301067.7:c.16570C>T	p.Pro5524Ser	p.P5524S	ENST00000301067	NM_003482.3	5524	Ccc/Tcc	54/54	0.244129748329512	4	FACETS	1	0.984	1	1	0.984	1	INDETERMINATE	2	TRUE	2	0.78651733321359	4		620	486	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443886	49443887	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	271	995	1	ENST00000301067.7:c.3484_3485delinsTT	p.Pro1162Phe	p.P1162F	ENST00000301067	NM_003482.3	1162	CCt/TTt	11/54	0.244129748329512	4	FACETS	0.888	0.839	0.939	0.888	0.839	0.939	INDETERMINATE	2	TRUE	2	0.78651733321359	4		996	693	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222564	69222564	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	89	571	0	ENST00000462284.1:c.537T>A	p.Asp179Glu	p.D179E	ENST00000462284	NM_002392.5	179	gaT/gaA	8/11	0.244129748329512	4	FACETS	0.94	0.838	1	0.47	0.419	0.524	INDETERMINATE	1	TRUE	2	0.78651733321359	4		571	430	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896406	28896406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	194	508	0	ENST00000282397.4:c.3044C>T	p.Ser1015Phe	p.S1015F	ENST00000282397	NM_002019.4	1015	tCc/tTc	22/30	0.2797461983069	4	FACETS	0.968	0.906	1	0.968	0.906	1	INDETERMINATE	2	TRUE	2	0.78651733321359	4		508	455	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434716	99434717	+	missense_variant	Missense_Mutation	DNP	CC	CC	GT	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	244	911	3	ENST00000268035.6:c.803_804delinsGT	p.Thr268Ser	p.T268S	ENST00000268035	NM_000875.3	268	aCC/aGT	3/21	0.78651733321359	3	FACETS	1	0.991	1	0.66	0.62	0.7	CLONAL	1	TRUE	1	0.78651733321359	3		914	655	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133699	2133699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1027773484	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	237	865	1	ENST00000219476.3:c.3887C>T	p.Ser1296Phe	p.S1296F	ENST00000219476	NM_000548.3	1296	tCc/tTc	33/42	0.244129748329512	4	FACETS	0.896	0.842	0.95	0.896	0.842	0.95	INDETERMINATE	2	TRUE	2	0.78651733321359	4		866	601	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640868	3640868	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	296	1005	1	ENST00000294008.3:c.2771G>T	p.Gly924Val	p.G924V	ENST00000294008	NM_032444.2	924	gGa/gTa	12/15	0.244129748329512	4	FACETS	0.94	0.891	0.99	0.94	0.891	0.99	INDETERMINATE	2	TRUE	2	0.78651733321359	4		1006	715	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9928024	9928024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	180	560	0	ENST00000330684.3:c.1715C>T	p.Ala572Val	p.A572V	ENST00000330684	NM_001134407.1	572	gCt/gTt	8/13	0.244129748329512	4	FACETS	0.946	0.883	1	0.946	0.883	1	INDETERMINATE	2	TRUE	2	0.78651733321359	4		560	432	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041824	14041824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	204	429	0	ENST00000311895.7:c.2371C>T	p.Leu791Phe	p.L791F	ENST00000311895	NM_005236.2	791	Ctt/Ttt	11/11	0.244129748329512	4	FACETS	0.893	0.835	0.951	0.893	0.835	0.951	INDETERMINATE	2	TRUE	2	0.78651733321359	4		429	519	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371652	89371652	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	125	941	0	ENST00000301030.4:c.188C>T	p.Thr63Ile	p.T63I	ENST00000301030	NM_001256183.1	63	aCc/aTc	4/13	0.244129748329512	4	FACETS	0.866	0.785	0.95	0.433	0.392	0.475	INDETERMINATE	1	TRUE	2	0.78651733321359	4		941	656	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557384	29557384	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691104	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	60	331	0	ENST00000356175.3:c.3097C>T	p.Gln1033Ter	p.Q1033*	ENST00000356175	NM_000267.3	1033	Caa/Taa	23/57	0.261107164982854	2	FACETS	0.771	0.675	0.871	0.385	0.337	0.436	INDETERMINATE	1	TRUE	0	0.78651733321359	2		331	198	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686956	37686956	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750674097	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	239	694	0	ENST00000447079.4:c.3860C>T	p.Ser1287Phe	p.S1287F	ENST00000447079	NM_015083.1	1287	tCc/tTc	14/14	0.261107164982854	2	FACETS	1	0.991	1	0.636	0.601	0.67	INDETERMINATE	1	TRUE	0	0.78651733321359	2		694	478	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55339536	55339536	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	143	802	1	ENST00000284073.2:c.295C>T	p.Arg99Cys	p.R99C	ENST00000284073	NM_138962.2	99	Cgt/Tgt	5/14	0.261107164982854	2	FACETS	0.724	0.665	0.786	0.362	0.332	0.393	INDETERMINATE	1	TRUE	0	0.78651733321359	2		803	502	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727850	78727850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	146	1019	0	ENST00000306801.3:c.695C>T	p.Pro232Leu	p.P232L	ENST00000306801	NM_020761.2	232	cCt/cTt	6/34	0.261107164982854	2	FACETS	0.65	0.596	0.706	0.325	0.298	0.353	INDETERMINATE	1	TRUE	0	0.78651733321359	2		1019	571	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226483	1226483	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1247102370	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	169	1045	0	ENST00000326873.7:c.1139A>G	p.Asn380Ser	p.N380S	ENST00000326873	NM_000455.4	380	aAt/aGt	9/10	0.267100742102848	2	FACETS	0.652	0.602	0.704	0.326	0.301	0.352	INDETERMINATE	1	TRUE	0	0.78651733321359	2		1045	659	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152167	11152167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	138	749	0	ENST00000358026.2:c.4451C>T	p.Ser1484Phe	p.S1484F	ENST00000358026	NM_001128849.1	1484	tCc/tTc	31/36	0.267100742102848	2	FACETS	0.663	0.607	0.722	0.332	0.303	0.361	INDETERMINATE	1	TRUE	0	0.78651733321359	2		749	529	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976875	18976875	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	137	762	0	ENST00000262803.5:c.3260T>C	p.Phe1087Ser	p.F1087S	ENST00000262803	NM_002911.3	1087	tTt/tCt	23/24	0.267100742102848	2	FACETS	0.67	0.613	0.729	0.335	0.306	0.365	INDETERMINATE	1	TRUE	0	0.78651733321359	2		762	520	SUCCESS
REL	5966	MSKCC	GRCh37	2	61128210	61128210	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1317942425	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	107	352	0	ENST00000295025.8:c.386C>T	p.Pro129Leu	p.P129L	ENST00000295025	NM_002908.2	129	cCa/cTa	4/11	0.2797461983069	4	FACETS	0.76	0.69	0.832	0.76	0.69	0.832	INDETERMINATE	2	TRUE	2	0.78651733321359	4		352	320	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021697	31021697	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780823171	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	226	673	1	ENST00000375687.4:c.1696G>A	p.Glu566Lys	p.E566K	ENST00000375687	NM_015338.5	566	Gag/Aag	12/13	0.338793537072976	4	FACETS	0.867	0.814	0.921	0.867	0.814	0.921	INDETERMINATE	2	TRUE	2	0.78651733321359	4		674	592	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012801	36012801	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	82	301	0	ENST00000358208.4:c.245T>A	p.Leu82Gln	p.L82Q	ENST00000358208		82	cTg/cAg	2/12	0.338793537072976	4	FACETS	1	0.976	1	0.682	0.609	0.758	INDETERMINATE	1	TRUE	2	0.78651733321359	4		301	273	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031729	36031729	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	272	953	2	ENST00000358208.4:c.1558G>A	p.Glu520Lys	p.E520K	ENST00000358208		520	Gag/Aag	12/12	0.338793537072976	4	FACETS	0.915	0.865	0.967	0.915	0.865	0.967	INDETERMINATE	2	TRUE	2	0.78651733321359	4		955	675	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739060	40739060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs724159846	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	140	793	1	ENST00000373198.4:c.3224C>T	p.Pro1075Leu	p.P1075L	ENST00000373198	NM_133170.3	1075	cCc/cTc	24/32	0.338793537072976	4	FACETS	1	0.947	1	0.525	0.479	0.572	INDETERMINATE	1	TRUE	2	0.78651733321359	4		794	606	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979344	40979344	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	231	736	0	ENST00000373198.4:c.1789G>A	p.Asp597Asn	p.D597N	ENST00000373198	NM_133170.3	597	Gac/Aac	11/32	0.338793537072976	4	FACETS	0.874	0.821	0.929	0.874	0.821	0.929	INDETERMINATE	2	TRUE	2	0.78651733321359	4		736	600	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485401	57485402	+	missense_variant	Missense_Mutation	DNP	CC	CC	GT	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	62	459	0	ENST00000371085.3:c.983_984delinsGT	p.Pro328Arg	p.P328R	ENST00000371085	NM_000516.4	328	cCC/cGT	12/13	0.338793537072976	4	FACETS	0.661	0.573	0.757	0.331	0.286	0.379	INDETERMINATE	1	TRUE	2	0.78651733321359	4		459	426	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288384	21288384	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	275	882	0	ENST00000354336.3:c.629C>T	p.Pro210Leu	p.P210L	ENST00000354336	NM_005207.3	210	cCt/cTt	2/3	0.261107164982854	2	FACETS	1	0.993	1	0.644	0.611	0.676	INDETERMINATE	1	TRUE	0	0.78651733321359	2		882	543	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545877	41545877	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	313	1106	0	ENST00000263253.7:c.2492C>T	p.Ser831Leu	p.S831L	ENST00000263253	NM_001429.3	831	tCa/tTa	14/31	0.261107164982854	2	FACETS	1	0.994	1	0.665	0.634	0.696	INDETERMINATE	1	TRUE	0	0.78651733321359	2		1106	598	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89478276	89478276	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	156	781	0	ENST00000336596.2:c.2095A>C	p.Thr699Pro	p.T699P	ENST00000336596	NM_005233.5	699	Aca/Cca	12/17	0.2797461983069	4	FACETS	0.856	0.792	0.921	0.856	0.792	0.921	INDETERMINATE	2	TRUE	2	0.78651733321359	4		781	414	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119634978	119634978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	137	406	0	ENST00000316626.5:c.521C>T	p.Ser174Phe	p.S174F	ENST00000316626		174	tCc/tTc	5/12	0.2797461983069	4	FACETS	0.905	0.834	0.976	0.905	0.834	0.976	INDETERMINATE	2	TRUE	2	0.78651733321359	4		406	344	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413746	138413746	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs748721844	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	64	368	1	ENST00000289153.2:c.1774C>T	p.Gln592Ter	p.Q592*	ENST00000289153	NM_006219.2	592	Cag/Tag	12/22	0.2797461983069	4	FACETS	0.779	0.678	0.888	0.39	0.339	0.444	INDETERMINATE	1	TRUE	2	0.78651733321359	4		369	373	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431025	181431025	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	313	962	1	ENST00000325404.1:c.877C>T	p.His293Tyr	p.H293Y	ENST00000325404	NM_003106.3	293	Cac/Tac	1/1	0.2797461983069	4	FACETS	0.911	0.864	0.959	0.911	0.864	0.959	INDETERMINATE	2	TRUE	2	0.78651733321359	4		963	780	SUCCESS
APC	324	MSKCC	GRCh37	5	112103005	112103005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	95	629	1	ENST00000257430.4:c.340C>T	p.Pro114Ser	p.P114S	ENST00000257430	NM_000038.5	114	Cct/Tct	4/16	1	2	FACETS	0.604	0.541	0.67	0.604	0.541	0.67	SUBCLONAL	1	TRUE	1	0.78651733321359	2		630	400	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519493	176519493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	163	1146	0	ENST00000292408.4:c.899C>T	p.Pro300Leu	p.P300L	ENST00000292408	NM_213647.1	300	cCc/cTc	7/18	1	2	FACETS	0.629	0.579	0.681	0.629	0.579	0.681	SUBCLONAL	1	TRUE	1	0.78651733321359	2		1146	659	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271506	26271506	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	174	550	0	ENST00000305910.3:c.107T>G	p.Val36Gly	p.V36G	ENST00000305910	NM_003534.2	36	gTg/gGg	1/1	0.521137810117873	6	FACETS	0.955	0.884	1	0.478	0.442	0.514	CLONAL	2	TRUE	2	0.78651733321359	6		550	596	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554975	106554975	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	190	616	0	ENST00000369096.4:c.2092C>T	p.His698Tyr	p.H698Y	ENST00000369096	NM_001198.3	698	Cat/Tat	7/7	0.261107164982854	2	FACETS	1	0.987	1	0.601	0.563	0.639	INDETERMINATE	1	TRUE	0	0.78651733321359	2		616	402	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117650555	117650555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	120	843	1	ENST00000368508.3:c.5303C>T	p.Ser1768Leu	p.S1768L	ENST00000368508	NM_002944.2	1768	tCa/tTa	32/43	NA	2	FACETS	0.671	0.61	0.734			1	INDETERMINATE	1	TRUE	NA	0.78651733321359	2		844	455	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527793	157527794	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	82	554	0	ENST00000346085.5:c.5520dup	p.Pro1841SerfsTer15	p.P1841Sfs*15	ENST00000346085	NM_020732.3	1840	att/aTtt	20/20	0.261107164982854	2	FACETS	0.565	0.502	0.632	0.283	0.251	0.316	INDETERMINATE	1	TRUE	0	0.78651733321359	2		554	369	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528181	157528181	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	241	684	2	ENST00000346085.5:c.5906C>T	p.Pro1969Leu	p.P1969L	ENST00000346085	NM_020732.3	1969	cCa/cTa	20/20	0.261107164982854	2	FACETS	1	0.994	1	0.714	0.678	0.75	INDETERMINATE	1	TRUE	0	0.78651733321359	2		686	429	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508032	106508032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1199243117	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	72	199	0	ENST00000359195.3:c.26C>T	p.Pro9Leu	p.P9L	ENST00000359195	NM_002649.2	9	cCc/cTc	2/11	0.2797461983069	4	FACETS	0.852	0.759	0.947	0.852	0.759	0.947	INDETERMINATE	2	TRUE	2	0.78651733321359	4		199	192	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859705	151859705	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771311951	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	64	405	0	ENST00000262189.6:c.10957C>T	p.Pro3653Ser	p.P3653S	ENST00000262189	NM_170606.2	3653	Cct/Tct	43/59	0.525668860305975	3	FACETS	0.575	0.5	0.656			1	SUBCLONAL	1	TRUE	NA	0.78651733321359	3		405	394	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876958	151876958	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	98	421	0	ENST00000262189.6:c.7403C>A	p.Pro2468His	p.P2468H	ENST00000262189	NM_170606.2	2468	cCt/cAt	37/59	0.525668860305975	3	FACETS	0.849	0.763	0.939			1	CLONAL	1	TRUE	NA	0.78651733321359	3		421	409	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965463	68965463	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1206854674	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	231	914	0	ENST00000288368.4:c.1075G>A	p.Glu359Lys	p.E359K	ENST00000288368	NM_024870.2	359	Gaa/Aaa	9/40	0.402017199786669	3	FACETS	0.791	0.746	0.838	0.791	0.746	0.838	INDETERMINATE	2	TRUE	1	0.78651733321359	3		914	517	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862948	117862948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	216	822	1	ENST00000297338.2:c.1529C>T	p.Pro510Leu	p.P510L	ENST00000297338	NM_006265.2	510	cCa/cTa	12/14	0.402017199786669	3	FACETS	1	0.993	1	0.743	0.697	0.789	INDETERMINATE	1	TRUE	1	0.78651733321359	3		823	515	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5029854	5029854	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	206	779	0	ENST00000381652.3:c.298C>T	p.His100Tyr	p.H100Y	ENST00000381652	NM_004972.3	100	Cat/Tat	4/25	0.78651733321359	2	FACETS	1	0.99	1	0.642	0.604	0.679	CLONAL	1	TRUE	0	0.78651733321359	2		779	408	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410714	63410715	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0023163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	132	446	2	ENST00000330258.3:c.2452_2453delinsAA	p.Gly818Lys	p.G818K	ENST00000330258	NM_152424.3	818	GGg/AAg	2/2	1	1	FACETS	0.597	0.549	0.646	0.597	0.549	0.646	SUBCLONAL	1	TRUE	0	0.78651733321359	1		448	341	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0023249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	304	772	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.817541172237621	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.817541172237621	1		772	435	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16055257	16055258	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	A	novel	NA	P-0023249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	243	428	0	ENST00000268712.3:c.842+2dup		p.X281_splice	ENST00000268712	NM_006311.3	281			0.778708554826522	1	FACETS	0.958	0.915	1	0.958	0.915	1	CLONAL	1	TRUE	0	0.817541172237621	1		428	367	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913412	NA	P-0023249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	169	271	0	ENST00000349496.5:c.121A>C	p.Thr41Pro	p.T41P	ENST00000349496	NM_001904.3	41	Acc/Ccc	3/15	1	2	FACETS	0.917	0.851	0.983	0.917	0.851	0.983	CLONAL	1	TRUE	1	0.817541172237621	2		271	451	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	193	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.969	0.905	1	0.969	0.905	1	CLONAL	1	TRUE	1	0.812658840847374	2		215	490	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	632	458	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.812658840847374	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.812658840847374	2		458	753	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729162	66729162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519732	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	337	668	0	ENST00000307102.5:c.370C>T	p.Pro124Ser	p.P124S	ENST00000307102	NM_002755.3	124	Ccg/Tcg	3/11	1	2	FACETS	0.924	0.877	0.971	0.924	0.877	0.971	CLONAL	1	TRUE	1	0.812658840847374	2		668	898	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295230	1295230	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs796516131	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	193	262	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.973	0.909	1	0.973	0.909	1	CLONAL	1	TRUE	1	0.812658840847374	2		263	488	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934225	49934225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868140197	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	378	835	1	ENST00000296474.3:c.2282C>T	p.Ser761Phe	p.S761F	ENST00000296474	NM_002447.2	761	tCc/tTc	8/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.812658840847374	2		836	899	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	150	500	2	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	1	2	FACETS	0.912	0.842	0.982	0.912	0.842	0.982	CLONAL	1	TRUE	1	0.812658840847374	2		502	405	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546769	9546769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	146	394	1	ENST00000353224.5:c.1253C>T	p.Ser418Phe	p.S418F	ENST00000353224	NM_177990.2	418	tCc/tTc	5/10	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.812658840847374	NA		395	337	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973911	55973911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs941528100	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	241	506	1	ENST00000263923.4:c.1405G>A	p.Glu469Lys	p.E469K	ENST00000263923	NM_002253.2	469	Gag/Aag	10/30	1	2	FACETS	0.92	0.864	0.976	0.92	0.864	0.976	CLONAL	1	TRUE	1	0.812658840847374	2		507	645	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653840	206653840	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	401	871	1	ENST00000367120.3:c.1391C>T	p.Ser464Phe	p.S464F	ENST00000367120	NM_014002.3	464	tCc/tTc	13/22	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.812658840847374	2		872	965	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667461	241667461	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	188	468	1	ENST00000366560.3:c.989C>T	p.Thr330Ile	p.T330I	ENST00000366560	NM_000143.3	330	aCt/aTt	7/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.812658840847374	2		469	432	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100754	8100754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749708566	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	372	844	0	ENST00000346208.3:c.728C>T	p.Ser243Phe	p.S243F	ENST00000346208		243	tCc/tTc	3/6	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.812658840847374	2		844	866	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962583	100962583	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	240	603	0	ENST00000325455.5:c.1814G>A	p.Gly605Glu	p.G605E	ENST00000325455	NM_001202474.3	605	gGa/gAa	3/8	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.812658840847374	2		603	578	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170471	119170471	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	219	468	2	ENST00000264033.4:c.2701C>T	p.Pro901Ser	p.P901S	ENST00000264033	NM_005188.3	901	Cct/Tct	16/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.812658840847374	2		470	509	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109764	115109764	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	468	966	2	ENST00000257566.3:c.2114C>T	p.Ser705Phe	p.S705F	ENST00000257566	NM_016569.3	705	tCc/tTc	8/8	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.812658840847374	2		968	1029	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004300	29004300	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	172	386	0	ENST00000282397.4:c.993A>C	p.Lys331Asn	p.K331N	ENST00000282397	NM_002019.4	331	aaA/aaC	8/30	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.812658840847374	2		386	421	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936695	32936695	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	143	521	0	ENST00000380152.3:c.7841T>C	p.Leu2614Pro	p.L2614P	ENST00000380152		2614	cTt/cCt	17/27	1	2	FACETS	0.886	0.817	0.958	0.886	0.817	0.958	CLONAL	1	TRUE	1	0.812658840847374	2		521	397	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435409	110435409	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1472585307	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	355	764	1	ENST00000375856.3:c.2992C>T	p.Pro998Ser	p.P998S	ENST00000375856	NM_003749.2	998	Ccc/Tcc	1/2	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.812658840847374	2		765	871	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989091	41989091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	261	686	0	ENST00000219905.7:c.1883C>T	p.Pro628Leu	p.P628L	ENST00000219905	NM_001164273.1	628	cCa/cTa	3/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.812658840847374	2		686	616	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99452012	99452012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	245	561	0	ENST00000268035.6:c.1346C>T	p.Ala449Val	p.A449V	ENST00000268035	NM_000875.3	449	gCt/gTt	6/21	1	2	FACETS	0.995	0.937	1	0.995	0.937	1	CLONAL	1	TRUE	1	0.812658840847374	2		561	606	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857784	9857784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145861983	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	236	676	0	ENST00000330684.3:c.3617G>A	p.Arg1206Gln	p.R1206Q	ENST00000330684	NM_001134407.1	1206	cGa/cAa	13/13	1	2	FACETS	0.875	0.821	0.93	0.875	0.821	0.93	CLONAL	1	TRUE	1	0.812658840847374	2		676	664	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031851	10031851	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	349	782	1	ENST00000330684.3:c.972G>A	p.Met324Ile	p.M324I	ENST00000330684	NM_001134407.1	324	atG/atA	3/13	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.812658840847374	2		783	839	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830958	72830958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393698686	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	236	577	1	ENST00000268489.5:c.5623G>A	p.Glu1875Lys	p.E1875K	ENST00000268489	NM_006885.3	1875	Gaa/Aaa	9/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.812658840847374	2		578	572	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857845	89857845	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1002730067	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	352	830	0	ENST00000389301.3:c.1325C>T	p.Pro442Leu	p.P442L	ENST00000389301	NM_000135.2	442	cCc/cTc	14/43	1	2	FACETS	0.979	0.931	1	0.979	0.931	1	CLONAL	1	TRUE	1	0.812658840847374	2		830	885	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89862411	89862411	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	295	729	0	ENST00000389301.3:c.909T>G	p.Ser303Arg	p.S303R	ENST00000389301	NM_000135.2	303	agT/agG	11/43	1	2	FACETS	0.99	0.938	1	0.99	0.938	1	CLONAL	1	TRUE	1	0.812658840847374	2		729	733	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2225431	2225431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	317	637	0	ENST00000398665.3:c.3641C>T	p.Pro1214Leu	p.P1214L	ENST00000398665	NM_032482.2	1214	cCc/cTc	26/28	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.812658840847374	2		637	715	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143975	11143975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1085307556	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	256	620	0	ENST00000358026.2:c.3556G>A	p.Ala1186Thr	p.A1186T	ENST00000358026	NM_001128849.1	1186	Gcg/Acg	26/36	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.812658840847374	2		620	617	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946809	17946809	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257320432	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	403	914	1	ENST00000458235.1:c.1838G>A	p.Arg613Gln	p.R613Q	ENST00000458235	NM_000215.3	613	cGa/cAa	14/24	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.812658840847374	2		915	957	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39251178	39251178	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	230	896	1	ENST00000402219.2:c.1175C>T	p.Ser392Phe	p.S392F	ENST00000402219	NM_005633.3	392	tCt/tTt	9/23	0.571052348305233	1	FACETS	0.653	0.614	0.691	0.653	0.614	0.691	SUBCLONAL	1	TRUE	0	0.812658840847374	1		897	515	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660221	227660221	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	207	939	0	ENST00000305123.5:c.3234T>G	p.Ser1078Arg	p.S1078R	ENST00000305123	NM_005544.2	1078	agT/agG	1/2	0.571052348305233	1	FACETS	0.373	0.347	0.401	0.373	0.347	0.401	SUBCLONAL	1	TRUE	0	0.812658840847374	1		939	810	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024225	31024225	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749636650	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	244	668	0	ENST00000375687.4:c.3710C>T	p.Ser1237Phe	p.S1237F	ENST00000375687	NM_015338.5	1237	tCc/tTc	13/13	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.812658840847374	2		668	593	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730904	40730904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770182876	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	314	698	1	ENST00000373198.4:c.3631G>A	p.Glu1211Lys	p.E1211K	ENST00000373198	NM_133170.3	1211	Gag/Aag	27/32	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.812658840847374	2		699	739	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264830	46264830	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1251975090	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	224	586	0	ENST00000371998.3:c.1700C>T	p.Ser567Phe	p.S567F	ENST00000371998		567	tCc/tTc	12/23	1	2	FACETS	0.99	0.929	1	0.99	0.929	1	CLONAL	1	TRUE	1	0.812658840847374	2		586	557	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42861469	42861469	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1305373683	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	319	744	0	ENST00000398585.3:c.401G>A	p.Gly134Glu	p.G134E	ENST00000398585	NM_001135099.1	134	gGa/gAa	4/14	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.812658840847374	2		744	764	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42870057	42870057	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	300	843	1	ENST00000398585.3:c.115G>A	p.Ala39Thr	p.A39T	ENST00000398585	NM_001135099.1	39	Gct/Act	2/14	1	2	FACETS	0.945	0.895	0.997	0.945	0.895	0.997	CLONAL	1	TRUE	1	0.812658840847374	2		844	781	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873092	134873092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	257	791	0	ENST00000398015.3:c.1396G>A	p.Asp466Asn	p.D466N	ENST00000398015	NM_004441.4	466	Gac/Aac	6/16	1	2	FACETS	0.855	0.804	0.906	0.855	0.804	0.906	CLONAL	1	TRUE	1	0.812658840847374	2		791	740	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922300	178922300	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	168	505	0	ENST00000263967.3:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000263967	NM_006218.2	357	Cga/Tga	6/21	1	2	FACETS	0.971	0.902	1	0.971	0.902	1	CLONAL	1	TRUE	1	0.812658840847374	2		505	426	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586422	189586422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866267914	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	276	516	0	ENST00000264731.3:c.1046G>A	p.Gly349Glu	p.G349E	ENST00000264731	NM_003722.4	349	gGa/gAa	8/14	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.812658840847374	2		516	600	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612285	189612286	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	133	343	1	ENST00000264731.3:c.2037_2038delinsAA	p.Glu680Lys	p.E680K	ENST00000264731	NM_003722.4	679	ggGGag/ggAAag	14/14	1	2	FACETS	0.917	0.843	0.992	0.917	0.843	0.992	CLONAL	1	TRUE	1	0.812658840847374	2		344	357	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294050	1294050	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	488	1231	1	ENST00000310581.5:c.951G>A	p.Trp317Ter	p.W317*	ENST00000310581	NM_198253.2	317	tgG/tgA	2/16	1	2	FACETS	0.938	0.898	0.978	0.938	0.898	0.978	CLONAL	1	TRUE	1	0.812658840847374	2		1232	1281	SUCCESS
APC	324	MSKCC	GRCh37	5	112154853	112154853	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	295	667	0	ENST00000257430.4:c.1124G>C	p.Gly375Ala	p.G375A	ENST00000257430	NM_000038.5	375	gGc/gCc	10/16	1	2	FACETS	0.949	0.898	1	0.949	0.898	1	CLONAL	1	TRUE	1	0.812658840847374	2		667	765	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449565	149449565	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1178794165	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	416	811	2	ENST00000286301.3:c.1381G>A	p.Glu461Lys	p.E461K	ENST00000286301	NM_005211.3	461	Gag/Aag	10/22	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.812658840847374	2		813	980	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721588	176721588	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057524329	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	326	720	0	ENST00000439151.2:c.7219A>G	p.Thr2407Ala	p.T2407A	ENST00000439151	NM_022455.4	2407	Act/Gct	23/23	1	2	FACETS	0.962	0.913	1	0.962	0.913	1	CLONAL	1	TRUE	1	0.812658840847374	2		720	834	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163591	32163592	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	350	632	2	ENST00000375023.3:c.5634_5635delinsAA	p.Ala1879Thr	p.A1879T	ENST00000375023	NM_004557.3	1878	caGGct/caAAct	30/30	0.812658840847374	3	FACETS	0.958	0.917	0.999	0.958	0.917	0.999	CLONAL	2	TRUE	1	0.812658840847374	3		634	632	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982080	93982080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	336	648	2	ENST00000369303.4:c.1385C>T	p.Ser462Phe	p.S462F	ENST00000369303	NM_004440.3	462	tCc/tTc	6/17	0.812658840847374	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.812658840847374	1		650	472	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609759	117609759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	294	664	2	ENST00000368508.3:c.6940G>A	p.Asp2314Asn	p.D2314N	ENST00000368508	NM_002944.2	2314	Gat/Aat	43/43	0.812658840847374	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.812658840847374	1		666	420	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708088	117708088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	218	681	2	ENST00000368508.3:c.2089G>A	p.Gly697Arg	p.G697R	ENST00000368508	NM_002944.2	697	Gga/Aga	14/43	0.812658840847374	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.812658840847374	1		683	305	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026639	6026639	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	519	1222	1	ENST00000265849.7:c.1757C>T	p.Ser586Phe	p.S586F	ENST00000265849	NM_000535.5	586	tCc/tTc	11/15	1	2	FACETS	0.972	0.933	1	0.972	0.933	1	CLONAL	1	TRUE	1	0.812658840847374	2		1223	1314	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739958	41739958	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	244	646	0	ENST00000242208.4:c.15G>A	p.Trp5Ter	p.W5*	ENST00000242208	NM_002192.2	5	tgG/tgA	2/3	1	2	FACETS	0.959	0.903	1	0.959	0.903	1	CLONAL	1	TRUE	1	0.812658840847374	2		646	626	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467669	50467669	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	236	697	0	ENST00000331340.3:c.904G>A	p.Glu302Lys	p.E302K	ENST00000331340	NM_006060.4	302	Gag/Aag	8/8	1	2	FACETS	0.965	0.907	1	0.965	0.907	1	CLONAL	1	TRUE	1	0.812658840847374	2		697	602	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515012	148515012	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	290	763	0	ENST00000320356.2:c.1197T>A	p.Asp399Glu	p.D399E	ENST00000320356	NM_004456.4	399	gaT/gaA	10/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.812658840847374	2		763	692	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873924	151873924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	209	687	0	ENST00000262189.6:c.8614C>T	p.Pro2872Ser	p.P2872S	ENST00000262189	NM_170606.2	2872	Cct/Tct	38/59	1	2	FACETS	0.972	0.911	1	0.972	0.911	1	CLONAL	1	TRUE	1	0.812658840847374	2		687	529	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992993	68992993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	254	534	0	ENST00000288368.4:c.1798G>A	p.Glu600Lys	p.E600K	ENST00000288368	NM_024870.2	600	Gaa/Aaa	17/40	0.812658840847374	3	FACETS	0.876	0.83	0.922	0.876	0.83	0.922	CLONAL	2	TRUE	1	0.812658840847374	3		534	502	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127911974	127911974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144776498	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	232	558	0	ENST00000373547.4:c.896C>T	p.Thr299Met	p.T299M	ENST00000373547	NM_002721.4	299	aCg/aTg	7/7	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.812658840847374	2		558	566	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040723	47040723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	392	993	2	ENST00000377604.3:c.1358C>T	p.Ser453Phe	p.S453F	ENST00000377604	NM_001204468.1	453	tCc/tTc	13/24	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.812658840847374	2		995	965	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410327	63410327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	359	1048	0	ENST00000330258.3:c.2840C>T	p.Ser947Phe	p.S947F	ENST00000330258	NM_152424.3	947	tCc/tTc	2/2	1	2	FACETS	0.906	0.861	0.952	0.906	0.861	0.952	CLONAL	1	TRUE	1	0.812658840847374	2		1048	975	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937864	76937864	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	256	870	0	ENST00000373344.5:c.2884T>C	p.Ser962Pro	p.S962P	ENST00000373344	NM_000489.3	962	Tct/Cct	9/35	1	2	FACETS	0.984	0.928	1	0.984	0.928	1	CLONAL	1	TRUE	1	0.812658840847374	2		870	640	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200029	123200029	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	104	402	0	ENST00000218089.9:c.2101C>T	p.His701Tyr	p.H701Y	ENST00000218089	NM_001042749.1	701	Cat/Tat	22/35	1	2	FACETS	0.927	0.843	1	0.927	0.843	1	CLONAL	1	TRUE	1	0.812658840847374	2		402	276	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0023461-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	136	446	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.438246636490227	3	FACETS	0.988	0.908	1	0.988	0.908	1	CLONAL	2	TRUE	1	0.438246636490227	3		446	383	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0023461-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	95	512	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.438246636490227	3	FACETS	1	0.981	1	0.732	0.657	0.81	CLONAL	1	TRUE	1	0.438246636490227	3		512	361	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0023461-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	144	572	1	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	0.438246636490227	3	FACETS	1	0.923	1	1	0.923	1	CLONAL	2	TRUE	1	0.438246636490227	3		573	400	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790813	89790813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1192495729	NA	P-0023461-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	51	684	0	ENST00000336032.3:c.200G>A	p.Cys67Tyr	p.C67Y	ENST00000336032	NM_006813.2	67	tGt/tAt	1/2	0.424350858277444	4	FACETS	0.362	0.307	0.424	0.181	0.153	0.212	SUBCLONAL	1	TRUE	2	0.438246636490227	4		684	924	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806228	1806228	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868356240	NA	P-0023461-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	263	740	3	ENST00000260795.2:c.1247G>A	p.Arg416His	p.R416H	ENST00000260795		416	cGc/cAc	8/17	0.438246636490227	3	FACETS	0.993	0.935	1	0.993	0.935	1	CLONAL	2	TRUE	1	0.438246636490227	3		743	737	SUCCESS
APC	324	MSKCC	GRCh37	5	112175148	112175148	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023461-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	88	259	0	ENST00000257430.4:c.3859del	p.Ile1287Ter	p.I1287*	ENST00000257430	NM_000038.5	1286	gAa/ga	16/16	0.438246636490227	3	FACETS	0.846	0.767	0.925	0.846	0.767	0.925	CLONAL	3	TRUE	0	0.438246636490227	3		259	193	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052633	42052633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023461-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	238	528	1	ENST00000219905.7:c.7304G>A	p.Arg2435Gln	p.R2435Q	ENST00000219905	NM_001164273.1	2435	cGg/cAg	20/24	0.438246636490227	3	FACETS	0.984	0.923	1	0.984	0.923	1	CLONAL	2	TRUE	1	0.438246636490227	3		529	673	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087892	27087907	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCCACCCAGTGGCC	CGGCCACCCAGTGGCC	-	novel	NA	P-0023461-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	115	647	1	ENST00000324856.7:c.2179_2194del	p.Arg727SerfsTer10	p.R727Sfs*10	ENST00000324856	NM_006015.4	727	CGGCCACCCAGTGGCCag/ag	6/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.438246636490227	2		648	487	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120229	70120230	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGCA	novel	NA	P-0023461-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	147	753	0	ENST00000245479.2:c.1232_1235dup	p.His413AlafsTer166	p.H413Afs*166	ENST00000245479	NM_000346.3	411	cag/cAGCAag	3/3	0.438246636490227	3	FACETS	1	0.936	1	0.514	0.47	0.561	CLONAL	1	TRUE	1	0.438246636490227	3		753	795	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220579	1220579	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0023461-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	197	722	0	ENST00000326873.7:c.598del		p.X200_splice	ENST00000326873	NM_000455.4	200			0.257813375520465	5	FACETS	1	0.963	1	0.705	0.655	0.756	INDETERMINATE	2	TRUE	2	0.438246636490227	5		722	705	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215674254	215674268	+	inframe_deletion	In_Frame_Del	DEL	TCCTCGGCTGCCGGT	TCCTCGGCTGCCGGT	-	rs587781979	NA	P-0023461-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	58	570	0	ENST00000260947.4:c.26_40del	p.Asn9_Arg13del	p.N9_R13del	ENST00000260947	NM_000465.2	9	aACCGGCAGCCGAGGAtc/atc	1/11	0.420191227911238	4	FACETS	0.656	0.564	0.757	0.219	0.188	0.253	SUBCLONAL	1	TRUE	1	0.438246636490227	4		570	580	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259664	89259664	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023461-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	33	279	0	ENST00000336596.2:c.808T>C	p.Cys270Arg	p.C270R	ENST00000336596	NM_005233.5	270	Tgc/Cgc	3/17	0.438246636490227	3	FACETS	1	0.843	1	0.513	0.422	0.613	CLONAL	1	TRUE	1	0.438246636490227	3		279	179	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98011444	98011444	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023461-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	178	584	0	ENST00000289081.3:c.130T>A	p.Phe44Ile	p.F44I	ENST00000289081	NM_000136.2	44	Ttc/Atc	2/15	0.424350858277444	4	FACETS	0.966	0.895	1	0.966	0.895	1	CLONAL	2	TRUE	2	0.438246636490227	4		584	605	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440643	56440643	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023461-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	37	589	0	ENST00000407977.2:c.575C>G	p.Pro192Arg	p.P192R	ENST00000407977		192	cCg/cGg	5/10	0.438246636490227	3	FACETS	0.313	0.257	0.376	0.156	0.128	0.188	SUBCLONAL	1	TRUE	1	0.438246636490227	3		589	658	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	239	215	0				ENST00000310581	NM_198253.2	-/1132			0.763907731858288	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.793658944516732	3		215	411	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761021	59761021	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	560	757	0	ENST00000259008.2:c.3386C>T	p.Ser1129Phe	p.S1129F	ENST00000259008	NM_032043.2	1129	tCt/tTt	20/20	0.793658944516732	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	1	0.793658944516732	4		757	815	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367278	50367278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	252	476	1	ENST00000331340.3:c.85G>A	p.Glu29Lys	p.E29K	ENST00000331340	NM_006060.4	29	Gag/Aag	3/8	0.595356123536656	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	2	0.793658944516732	4		477	553	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612073	189612073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142762485	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	287	538	0	ENST00000264731.3:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000264731	NM_003722.4	609	Gaa/Aaa	14/14	0.793658944516732	4	FACETS	0.884	0.836	0.932	0.884	0.836	0.932	CLONAL	2	TRUE	2	0.793658944516732	4		538	734	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956220	55956220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190050670	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	316	545	1	ENST00000263923.4:c.3095G>A	p.Arg1032Gln	p.R1032Q	ENST00000263923	NM_002253.2	1032	cGa/cAa	23/30	0.595356123536656	4	FACETS	0.941	0.893	0.989	0.941	0.893	0.989	CLONAL	2	TRUE	2	0.793658944516732	4		546	759	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7978952	7978952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139689690	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	181	674	1	ENST00000319144.4:c.1615G>A	p.Glu539Lys	p.E539K	ENST00000319144	NM_001139.2	539	Gaa/Aaa	12/15	0.763907731858288	3	FACETS	1	0.958	1	0.524	0.486	0.563	CLONAL	1	TRUE	1	0.793658944516732	3		675	608	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	261	418	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.793658944516732	4	FACETS	0.915	0.863	0.967	0.915	0.863	0.967	CLONAL	2	TRUE	2	0.793658944516732	4		418	645	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652452	206652452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	277	693	1	ENST00000367120.3:c.1159C>T	p.Pro387Ser	p.P387S	ENST00000367120	NM_014002.3	387	Cct/Tct	10/22	0.745006750264285	4	FACETS	0.923	0.873	0.974	0.923	0.873	0.974	CLONAL	2	TRUE	2	0.793658944516732	4		694	678	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956205	55956205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148668147	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	354	882	1	ENST00000263923.4:c.3110C>T	p.Ser1037Leu	p.S1037L	ENST00000263923	NM_002253.2	1037	tCg/tTg	23/30	0.595356123536656	4	FACETS	0.969	0.922	1	0.969	0.922	1	CLONAL	2	TRUE	2	0.793658944516732	4		883	826	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858549	9858549	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	333	721	0	ENST00000330684.3:c.2852G>A	p.Gly951Glu	p.G951E	ENST00000330684	NM_001134407.1	951	gGg/gAg	13/13	0.296797458839691	3	FACETS	1	0.985	1			1	INDETERMINATE	2	TRUE	NA	0.793658944516732	3		721	553	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115729	8115729	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	268	572	0	ENST00000346208.3:c.1075G>A	p.Glu359Lys	p.E359K	ENST00000346208		359	Gaa/Aaa	6/6	0.793658944516732	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.793658944516732	3		572	463	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166010	118166010	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767827215	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	307	634	0	ENST00000369448.3:c.520C>T	p.Arg174Trp	p.R174W	ENST00000369448	NM_017709.3	174	Cgg/Tgg	2/2	0.792339628868557	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.793658944516732	2		634	371	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40462641	40462641	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147384091	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	211	796	1	ENST00000345506.4:c.2339C>T	p.Ser780Leu	p.S780L	ENST00000345506	NM_003152.3	780	tCg/tTg	20/20	0.763907731858288	3	FACETS	1	0.944	1	0.507	0.473	0.543	CLONAL	1	TRUE	1	0.793658944516732	3		797	732	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113095	209113095	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	168	315	0	ENST00000345146.2:c.412C>T	p.Gln138Ter	p.Q138*	ENST00000345146	NM_005896.2	138	Caa/Taa	4/10	0.793658944516732	3	FACETS	0.989	0.929	1	0.989	0.929	1	CLONAL	2	TRUE	1	0.793658944516732	3		315	299	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349058	89349058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555528234	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	532	1159	4	ENST00000301030.4:c.3892G>A	p.Asp1298Asn	p.D1298N	ENST00000301030	NM_001256183.1	1298	Gat/Aat	9/13	0.731617878825997	3	FACETS	1	0.983	1			1	CLONAL	2	TRUE	NA	0.793658944516732	3		1163	912	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560043	29560043	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs868450405	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	117	403	0	ENST00000356175.3:c.3520C>T	p.Gln1174Ter	p.Q1174*	ENST00000356175	NM_000267.3	1174	Cag/Tag	27/57	0.763907731858288	3	FACETS	1	0.963	1	0.555	0.505	0.606	CLONAL	1	TRUE	1	0.793658944516732	3		403	371	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771562	112771562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1247102305	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	137	680	0	ENST00000369452.4:c.1735C>T	p.Arg579Cys	p.R579C	ENST00000369452	NM_007373.3	579	Cgt/Tgt	9/9	0.763907731858288	3	FACETS	0.905	0.827	0.985	0.452	0.413	0.493	CLONAL	1	TRUE	1	0.793658944516732	3		680	533	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971088	21971088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746459174	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	338	643	0	ENST00000579755.1:c.313C>T	p.Pro105Ser	p.P105S	ENST00000579755		105	Cct/Tct	2/3	0.763907731858288	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.793658944516732	3		643	539	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355186	15355186	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	487	1151	2	ENST00000263377.2:c.2437C>T	p.Pro813Ser	p.P813S	ENST00000263377	NM_058243.2	813	Cca/Tca	13/20	0.793658944516732	3	FACETS	0.993	0.958	1	0.993	0.958	1	CLONAL	2	TRUE	1	0.793658944516732	3		1153	863	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670153	29670153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1135402900	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	263	593	1	ENST00000356175.3:c.7126G>A	p.Gly2376Arg	p.G2376R	ENST00000356175	NM_000267.3	2376	Ggg/Agg	47/57	0.763907731858288	3	FACETS	0.964	0.917	1	0.964	0.917	1	CLONAL	2	TRUE	1	0.793658944516732	3		594	480	SUCCESS
ALK	238	MSKCC	GRCh37	2	29419721	29419721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1215186876	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	512	652	0	ENST00000389048.3:c.4079G>A	p.Arg1360Gln	p.R1360Q	ENST00000389048	NM_004304.4	1360	cGg/cAg	28/29	0.793658944516732	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.793658944516732	3		652	575	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156836738	156836738	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs747976486	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	396	1032	0	ENST00000524377.1:c.396G>A	p.Trp132Ter	p.W132*	ENST00000524377	NM_002529.3	132	tgG/tgA	4/17	0.745006750264285	4	FACETS	0.87	0.829	0.911	0.87	0.829	0.911	CLONAL	2	TRUE	2	0.793658944516732	4		1032	1029	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943308	71943308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	207	916	0	ENST00000298229.2:c.1640C>T	p.Ser547Phe	p.S547F	ENST00000298229	NM_001567.3	547	tCc/tTc	14/28	1	2	FACETS	0.975	0.913	1	0.975	0.913	1	CLONAL	1	TRUE	1	0.793658944516732	2		916	535	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385232	4385232	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	158	730	0	ENST00000261254.3:c.257G>C	p.Arg86Pro	p.R86P	ENST00000261254	NM_001759.3	86	cGt/cCt	2/5	0.793658944516732	3	FACETS	0.89	0.819	0.964	0.445	0.409	0.482	CLONAL	1	TRUE	1	0.793658944516732	3		730	625	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871887	12871887	+	splice_region_variant,3_prime_UTR_variant	Splice_Region	SNP	C	C	T	rs200321335	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	68	278	0	ENST00000228872.4:c.*7C>T			ENST00000228872	NM_004064.3	-/198		2/3	0.793658944516732	3	FACETS	1	0.937	1	0.546	0.483	0.613	CLONAL	1	TRUE	1	0.793658944516732	3		278	219	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244517	46244517	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	179	725	0	ENST00000334344.6:c.2611C>T	p.Gln871Ter	p.Q871*	ENST00000334344	NM_152641.2	871	Cag/Tag	15/21	0.793658944516732	3	FACETS	1	0.967	1	0.537	0.497	0.577	CLONAL	1	TRUE	1	0.793658944516732	3		725	587	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427546	49427546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777215324	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	173	676	0	ENST00000301067.7:c.10942C>T	p.Pro3648Ser	p.P3648S	ENST00000301067	NM_003482.3	3648	Ccg/Tcg	39/54	0.793658944516732	3	FACETS	1	0.963	1	0.532	0.493	0.573	CLONAL	1	TRUE	1	0.793658944516732	3		676	572	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434604	49434604	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1234512305	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	214	901	0	ENST00000301067.7:c.6949G>A	p.Gly2317Ser	p.G2317S	ENST00000301067	NM_003482.3	2317	Ggt/Agt	31/54	0.793658944516732	3	FACETS	1	0.935	1	0.502	0.467	0.537	CLONAL	1	TRUE	1	0.793658944516732	3		901	751	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562483	21562484	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGCGA	novel	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	86	169	0	ENST00000382592.4:c.1435_1436insTCGCCC	p.Ala478_Pro479insLeuAla	p.A478_P479insLA	ENST00000382592	NM_014572.2	479	ccg/cTCGCCCcg	4/8	0.745006750264285	4	FACETS	0.93	0.84	1	0.93	0.84	1	CLONAL	2	TRUE	2	0.793658944516732	4		169	209	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915120	32915120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	274	749	1	ENST00000380152.3:c.6628G>A	p.Glu2210Lys	p.E2210K	ENST00000380152		2210	Gaa/Aaa	11/27	0.745006750264285	4	FACETS	0.887	0.838	0.937	0.887	0.838	0.937	CLONAL	2	TRUE	2	0.793658944516732	4		750	698	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347934	73347934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	207	230	0	ENST00000377767.4:c.1127C>T	p.Ala376Val	p.A376V	ENST00000377767	NM_014953.3	376	gCt/gTt	8/21	0.745006750264285	4	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	2	0.793658944516732	4		230	461	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396964	396964	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	481	865	0	ENST00000262320.3:c.62C>A	p.Pro21His	p.P21H	ENST00000262320	NM_003502.3	21	cCc/cAc	2/11	0.731617878825997	3	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.793658944516732	3		865	798	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646498	23646498	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	412	882	1	ENST00000261584.4:c.1369G>A	p.Glu457Lys	p.E457K	ENST00000261584	NM_024675.3	457	Gaa/Aaa	4/13	0.793658944516732	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.793658944516732	3		883	716	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974877	15974877	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1298450215	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	335	729	0	ENST00000268712.3:c.3998C>T	p.Thr1333Ile	p.T1333I	ENST00000268712	NM_006311.3	1333	aCc/aTc	30/46	0.763907731858288	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.793658944516732	3		729	587	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246274	41246274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1260879887	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	217	902	0	ENST00000357654.3:c.1274C>T	p.Ser425Phe	p.S425F	ENST00000357654	NM_007294.3	425	tCt/tTt	10/23	0.763907731858288	3	FACETS	1	0.976	1	0.547	0.511	0.584	CLONAL	1	TRUE	1	0.793658944516732	3		902	698	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7120629	7120629	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	170	759	0	ENST00000302850.5:c.3659+2T>A		p.X1220_splice	ENST00000302850	NM_000208.2	1220			0.793658944516732	3	FACETS	0.896	0.827	0.967	0.448	0.413	0.484	CLONAL	1	TRUE	1	0.793658944516732	3		759	668	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952292	17952292	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	457	868	3	ENST00000458235.1:c.1048C>T	p.Arg350Trp	p.R350W	ENST00000458235	NM_000215.3	350	Cgg/Tgg	8/24	0.793658944516732	3	FACETS	0.988	0.951	1	0.988	0.951	1	CLONAL	2	TRUE	1	0.793658944516732	3		871	814	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42759150	42759150	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	101	433	0	ENST00000222329.4:c.2T>C	p.Met1?	p.M1?	ENST00000222329	NM_006494.2	1	aTg/aCg	1/4	0.793658944516732	3	FACETS	0.801	0.72	0.886	0.4	0.36	0.443	CLONAL	1	TRUE	1	0.793658944516732	3		433	444	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371592	225371592	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	283	803	0	ENST00000264414.4:c.1012C>T	p.Pro338Ser	p.P338S	ENST00000264414	NM_003590.4	338	Cct/Tct	7/16	0.793658944516732	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.793658944516732	3		803	497	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710549	40710549	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	390	891	1	ENST00000373198.4:c.4302C>A	p.Asn1434Lys	p.N1434K	ENST00000373198	NM_133170.3	1434	aaC/aaA	31/32	0.499660916642438	4	FACETS	1	0.962	1			1	CLONAL	2	TRUE	NA	0.793658944516732	4		892	875	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827942	40827942	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	389	803	0	ENST00000373198.4:c.2486A>G	p.Lys829Arg	p.K829R	ENST00000373198	NM_133170.3	829	aAg/aGg	17/32	0.499660916642438	4	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.793658944516732	4		803	805	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306530	41306530	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	224	569	0	ENST00000373198.4:c.1129C>T	p.Leu377Phe	p.L377F	ENST00000373198	NM_133170.3	377	Ctc/Ttc	7/32	0.499660916642438	4	FACETS	0.894	0.84	0.95			1	CLONAL	2	TRUE	NA	0.793658944516732	4		569	566	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845396	42845396	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	361	814	0	ENST00000398585.3:c.866G>C	p.Arg289Pro	p.R289P	ENST00000398585	NM_001135099.1	289	cGc/cCc	9/14	0.686156233589023	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	2	0.793658944516732	4		814	796	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950694	38950694	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	247	581	0	ENST00000357387.3:c.3256C>T	p.Pro1086Ser	p.P1086S	ENST00000357387	NM_152756.3	1086	Cct/Tct	31/38	0.763907731858288	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	1	0.793658944516732	3		581	434	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940672	131940672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	352	615	0	ENST00000265335.6:c.2699C>T	p.Ser900Phe	p.S900F	ENST00000265335		900	tCt/tTt	16/25	0.793658944516732	3	FACETS	0.99	0.948	1	0.99	0.948	1	CLONAL	2	TRUE	1	0.793658944516732	3		615	626	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32182010	32182011	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	381	997	3	ENST00000375023.3:c.2043_2044delinsAA	p.Gly682Ser	p.G682S	ENST00000375023	NM_004557.3	681	gtGGgt/gtAAgt	13/30	0.793658944516732	5	FACETS	0.967	0.919	1	0.644	0.613	0.676	CLONAL	2	TRUE	2	0.793658944516732	5		1000	1088	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708980	117708981	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	111	684	2	ENST00000368508.3:c.1976_1977delinsTT	p.Pro659Leu	p.P659L	ENST00000368508	NM_002944.2	659	cCC/cTT	13/43	0.414954635260643	4	FACETS	1	0.912	1	0.336	0.304	0.371	INDETERMINATE	1	TRUE	1	0.793658944516732	4		686	497	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29195889	29195889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753038586	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	407	1068	1	ENST00000240100.2:c.709G>A	p.Glu237Lys	p.E237K	ENST00000240100	NM_001394.6	237	Gaa/Aaa	3/4	0.758172559621781	6	FACETS	0.981	0.933	1	0.49	0.466	0.515	CLONAL	2	TRUE	2	0.793658944516732	6		1069	1353	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864641	56864641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	697	910	0	ENST00000519728.1:c.604C>T	p.Pro202Ser	p.P202S	ENST00000519728	NM_002350.3	202	Ccc/Tcc	7/13	0.631582960288791	6	FACETS	1	0.986	1			1	CLONAL	3	TRUE	NA	0.793658944516732	6		910	1464	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27213554	27213554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	171	851	1	ENST00000380036.4:c.2950G>A	p.Gly984Arg	p.G984R	ENST00000380036	NM_000459.3	984	Gga/Aga	18/23	0.763907731858288	3	FACETS	0.949	0.877	1	0.475	0.438	0.512	CLONAL	1	TRUE	1	0.793658944516732	3		852	634	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624597	93624597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200498885	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	294	614	2	ENST00000375746.1:c.688G>A	p.Glu230Lys	p.E230K	ENST00000375746	NM_001174167.1	230	Gag/Aag	4/14	0.763907731858288	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.793658944516732	3		616	503	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250208	110250208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	339	728	0	ENST00000374672.4:c.467C>T	p.Ala156Val	p.A156V	ENST00000374672	NM_004235.4	156	gCc/gTc	3/5	0.793658944516732	3	FACETS	0.962	0.92	1	0.962	0.92	1	CLONAL	2	TRUE	1	0.793658944516732	3		728	620	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401390	139401390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777652834	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	404	849	1	ENST00000277541.6:c.3679C>T	p.Pro1227Ser	p.P1227S	ENST00000277541	NM_017617.3	1227	Ccc/Tcc	23/34	0.793658944516732	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.793658944516732	3		850	687	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911636	39911636	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	77	400	0	ENST00000378444.4:c.4994T>A	p.Leu1665Gln	p.L1665Q	ENST00000378444	NM_001123385.1	1665	cTg/cAg	15/15	0.776534191771545	2	FACETS	0.399	0.351	0.451			1	SUBCLONAL	1	TRUE	NA	0.793658944516732	2		400	486	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872090	76872090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs895159127	NA	P-0023510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	250	376	0	ENST00000373344.5:c.5557C>T	p.His1853Tyr	p.H1853Y	ENST00000373344	NM_000489.3	1853	Cac/Tac	22/35	0.776534191771545	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.793658944516732	2		376	272	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	34	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.592	0.484	0.713	0.592	0.484	0.713	SUBCLONAL	1	FALSE	1	0.320040599804742	2		215	359	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0023573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	49	512	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.608	0.515	0.71	0.608	0.515	0.71	SUBCLONAL	1	FALSE	1	0.320040599804742	2		512	504	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247247	153247247	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	37	532	0	ENST00000281708.4:c.1555T>C	p.Tyr519His	p.Y519H	ENST00000281708	NM_033632.3	519	Tat/Cat	10/12	1	2	FACETS	0.575	0.474	0.688	0.575	0.474	0.688	SUBCLONAL	1	FALSE	1	0.320040599804742	2		532	402	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199469669	NA	P-0023573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	65	337	0	ENST00000374080.3:c.130G>T	p.Gly44Cys	p.G44C	ENST00000374080		44	Ggt/Tgt	2/45	1	1	FACETS	0.983	0.858	1	0.983	0.858	1	CLONAL	1	FALSE	0	0.320040599804742	1		337	347	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420607	49420607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123724	NA	P-0023573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	48	658	2	ENST00000301067.7:c.15142C>T	p.Arg5048Cys	p.R5048C	ENST00000301067	NM_003482.3	5048	Cgt/Tgt	48/54	1	2	FACETS	0.509	0.43	0.597	0.509	0.43	0.597	SUBCLONAL	1	FALSE	1	0.320040599804742	2		660	589	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270111	66270111	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs539707153	NA	P-0023573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	52	434	0	ENST00000273854.3:c.1771G>A	p.Gly591Ser	p.G591S	ENST00000273854	NM_004439.5	591	Ggc/Agc	8/18	1	2	FACETS	0.747	0.637	0.867	0.747	0.637	0.867	SUBCLONAL	1	FALSE	1	0.320040599804742	2		434	435	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023724	27023734	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGCCCCTCC	GCGGCCCCTCC	-	novel	NA	P-0023573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	51	612	0	ENST00000324856.7:c.836_846del	p.Pro279ArgfsTer117	p.P279Rfs*117	ENST00000324856	NM_006015.4	277	gGCGGCCCCTCC/g	1/20	1	2	FACETS	0.809	0.689	0.939	0.809	0.689	0.939	CLONAL	1	FALSE	1	0.320040599804742	2		612	394	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385319	4385319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	53	442	0	ENST00000261254.3:c.344C>T	p.Thr115Ile	p.T115I	ENST00000261254	NM_001759.3	115	aCc/aTc	2/5	1	2	FACETS	0.714	0.609	0.828	0.714	0.609	0.828	SUBCLONAL	1	FALSE	1	0.320040599804742	2		442	464	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900636	3900636	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	64	634	1	ENST00000262367.5:c.460C>T	p.Gln154Ter	p.Q154*	ENST00000262367	NM_004380.2	154	Caa/Taa	2/31	1	2	FACETS	0.71	0.615	0.813	0.71	0.615	0.813	SUBCLONAL	1	FALSE	1	0.320040599804742	2		635	563	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831728	72831728	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	59	627	0	ENST00000268489.5:c.4853T>C	p.Val1618Ala	p.V1618A	ENST00000268489	NM_006885.3	1618	gTg/gCg	9/10	1	2	FACETS	0.674	0.58	0.776	0.674	0.58	0.776	SUBCLONAL	1	FALSE	1	0.320040599804742	2		627	547	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094865	11094865	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	64	762	0	ENST00000358026.2:c.38G>T	p.Arg13Leu	p.R13L	ENST00000358026	NM_001128849.1	13	cGg/cTg	2/36	1	2	FACETS	0.624	0.54	0.715	0.624	0.54	0.715	SUBCLONAL	1	FALSE	1	0.320040599804742	2		762	641	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967002	18967002	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	49	510	0	ENST00000262803.5:c.1717G>A	p.Glu573Lys	p.E573K	ENST00000262803	NM_002911.3	573	Gag/Aag	13/24	1	2	FACETS	0.687	0.582	0.801	0.687	0.582	0.801	SUBCLONAL	1	FALSE	1	0.320040599804742	2		510	446	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098956	178098956	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	38	402	0	ENST00000397062.3:c.89T>C	p.Leu30Pro	p.L30P	ENST00000397062	NM_006164.4	30	cTt/cCt	2/5	1	2	FACETS	0.604	0.5	0.72	0.604	0.5	0.72	SUBCLONAL	1	FALSE	1	0.320040599804742	2		402	393	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513283	41513283	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	51	569	0	ENST00000263253.7:c.187C>T	p.Gln63Ter	p.Q63*	ENST00000263253	NM_001429.3	63	Cag/Tag	2/31	1	2	FACETS	0.62	0.527	0.722	0.62	0.527	0.722	SUBCLONAL	1	FALSE	1	0.320040599804742	2		569	514	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295375	1295375	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0023573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	36	303	4				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.839	1	1	0.839	1	CLONAL	1	FALSE	1	0.320040599804742	2		307	222	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197336	26197336	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	51	598	0	ENST00000356476.2:c.143C>T	p.Ala48Val	p.A48V	ENST00000356476		48	gCt/gTt	1/1	1	2	FACETS	0.649	0.552	0.756	0.649	0.552	0.756	SUBCLONAL	1	FALSE	1	0.320040599804742	2		598	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0023713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	52	693	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.159033270960889	2	FACETS	1	0.927	1	0.574	0.489	0.666	CLONAL	1	TRUE	0	0.207329637734164	2		693	437	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0023713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	71	288	0	ENST00000304494.5:c.151-1G>A		p.X51_splice	ENST00000304494	NM_000077.4	51			0.12692378260686	4	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	2	0.207329637734164	4		288	376	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123199792	123199792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	61	548	0	ENST00000218089.9:c.2092C>T	p.His698Tyr	p.H698Y	ENST00000218089	NM_001042749.1	698	Cat/Tat	21/35	0.176495507051319	1	FACETS	0.99	0.854	1	0.99	0.854	1	CLONAL	1	TRUE	0	0.207329637734164	1		548	533	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324205	31324205	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs281864615	NA	P-0023713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	137	529	1	ENST00000412585.2:c.358C>T	p.Gln120Ter	p.Q120*	ENST00000412585	NM_005514.6	120	Cag/Tag	3/8	0.207329637734164	3	FACETS	0.889	0.817	0.964	1	0.978	1	CLONAL	4	TRUE	0	0.207329637734164	3		530	410	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076799	72076799	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs778071072	NA	P-0023713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	97	587	2	ENST00000357731.5:c.698G>T	p.Gly233Val	p.G233V	ENST00000357731	NM_173808.2	233	gGc/gTc	5/7	0.195915897813875	4	FACETS	1	0.98	1	0.733	0.653	0.818	CLONAL	1	TRUE	2	0.207329637734164	4		589	771	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120508073	120508074	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	A	novel	NA	P-0023713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	49	416	0	ENST00000256646.2:c.1681+2dup		p.X561_splice	ENST00000256646	NM_024408.3	561			NA	2	FACETS	1	0.962	1			1	INDETERMINATE	1	TRUE	NA	0.207329637734164	2		416	321	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32438069	32438069	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	60	712	0	ENST00000332351.3:c.968C>A	p.Ser323Tyr	p.S323Y	ENST00000332351	NM_024426.4	323	tCc/tAc	5/10	0.12395974641983	3	FACETS	1	0.953	1	0.625	0.539	0.718	INDETERMINATE	1	TRUE	1	0.207329637734164	3		712	511	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944157	71944157	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	42	782	0	ENST00000298229.2:c.1990G>C	p.Glu664Gln	p.E664Q	ENST00000298229	NM_001567.3	664	Gag/Cag	17/28	0.137435812754911	4	FACETS	0.852	0.711	1			1	CLONAL	1	TRUE	NA	0.207329637734164	4		782	574	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118368773	118368773	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	55	483	0	ENST00000534358.1:c.5787C>G	p.Ile1929Met	p.I1929M	ENST00000534358	NM_005933.3	1929	atC/atG	21/36	0.207329637734164	5	FACETS	1	0.925	1	0.378	0.323	0.438	CLONAL	1	TRUE	2	0.207329637734164	5		483	614	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427144	49427144	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	63	795	0	ENST00000301067.7:c.11344del	p.His3782ThrfsTer48	p.H3782Tfs*48	ENST00000301067	NM_003482.3	3782	Cac/ac	39/54	0.0717018841219832	3	FACETS	1	0.962	1			1	INDETERMINATE	1	TRUE	NA	0.207329637734164	3		795	506	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879617	123879617	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	37	429	0	ENST00000330479.4:c.313G>T	p.Val105Leu	p.V105L	ENST00000330479	NM_020382.3	105	Gta/Tta	4/9	1	2	FACETS	0.973	0.803	1	0.973	0.803	1	CLONAL	1	TRUE	1	0.207329637734164	2		429	367	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052679	42052679	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	44	737	0	ENST00000219905.7:c.7350G>C	p.Leu2450Phe	p.L2450F	ENST00000219905	NM_001164273.1	2450	ttG/ttC	20/24	1	2	FACETS	0.628	0.525	0.742	0.628	0.525	0.742	SUBCLONAL	1	TRUE	1	0.207329637734164	2		737	676	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780619	56780619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137947462	NA	P-0023713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	52	792	2	ENST00000337432.4:c.634C>T	p.Arg212Cys	p.R212C	ENST00000337432	NM_058216.2	212	Cgc/Tgc	4/9	1	2	FACETS	0.658	0.559	0.768	0.658	0.559	0.768	SUBCLONAL	1	TRUE	1	0.207329637734164	2		794	762	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554684	63554684	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	55	516	0	ENST00000307078.5:c.55G>A	p.Glu19Lys	p.E19K	ENST00000307078	NM_004655.3	19	Gag/Aag	2/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.207329637734164	2		516	403	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285108	15285108	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	57	869	1	ENST00000263388.2:c.4507G>T	p.Glu1503Ter	p.E1503*	ENST00000263388	NM_000435.2	1503	Gag/Tag	25/33	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.207329637734164	2		870	525	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705565	47705565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	30	488	0	ENST00000233146.2:c.2365G>A	p.Ala789Thr	p.A789T	ENST00000233146	NM_000251.2	789	Gcc/Acc	14/16	0.12395974641983	3	FACETS	0.697	0.561	0.852	0.349	0.28	0.426	INDETERMINATE	1	TRUE	1	0.207329637734164	3		488	458	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628403	187628403	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0023713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	121	913	0	ENST00000441802.2:c.2579C>G	p.Ser860Ter	p.S860*	ENST00000441802	NM_005245.3	860	tCa/tGa	2/27	NA	2	FACETS	0.781	0.706	0.86			1	INDETERMINATE	2	TRUE	NA	0.207329637734164	2		913	747	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1255446	1255446	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	104	912	0	ENST00000310581.5:c.3113A>G	p.Asp1038Gly	p.D1038G	ENST00000310581	NM_198253.2	1038	gAc/gGc	14/16	NA	2	FACETS	0.874	0.785	0.968			1	INDETERMINATE	2	TRUE	NA	0.207329637734164	2		912	574	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958573	38958573	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	42	355	0	ENST00000357387.3:c.2392G>A	p.Gly798Arg	p.G798R	ENST00000357387	NM_152756.3	798	Gga/Aga	24/38	0.12692378260686	4	FACETS	1	0.922	1	0.592	0.495	0.7	CLONAL	1	TRUE	2	0.207329637734164	4		355	413	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683683	162683683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377591051	NA	P-0023713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	48	619	0	ENST00000366898.1:c.286G>A	p.Glu96Lys	p.E96K	ENST00000366898	NM_004562.2	96	Gag/Aag	3/12	0.207329637734164	5	FACETS	0.94	0.793	1	0.313	0.264	0.368	CLONAL	1	TRUE	2	0.207329637734164	5		619	646	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389387	8389387	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	70	542	0	ENST00000356435.5:c.4231G>T	p.Val1411Leu	p.V1411L	ENST00000356435		1411	Gtg/Ttg	26/35	0.12692378260686	4	FACETS	0.822	0.718	0.933	0.822	0.718	0.933	CLONAL	2	TRUE	2	0.207329637734164	4		542	496	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417598	139417598	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	71	1046	0	ENST00000277541.6:c.446G>C	p.Cys149Ser	p.C149S	ENST00000277541	NM_017617.3	149	tGc/tCc	4/34	0.207329637734164	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	0	0.207329637734164	1		1046	585	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650499	48650499	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	74	1067	0	ENST00000376670.3:c.469C>A	p.Pro157Thr	p.P157T	ENST00000376670	NM_002049.3	157	Cct/Act	3/6	0.176495507051319	1	FACETS	0.942	0.825	1	0.942	0.825	1	CLONAL	1	TRUE	0	0.207329637734164	1		1067	679	SUCCESS
AR	367	MSKCC	GRCh37	X	66766483	66766483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	77	639	0	ENST00000374690.3:c.1495G>A	p.Ala499Thr	p.A499T	ENST00000374690	NM_000044.3	499	Gca/Aca	1/8	0.176495507051319	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.207329637734164	1		639	521	SUCCESS
AR	367	MSKCC	GRCh37	X	66941733	66941733	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	44	813	0	ENST00000374690.3:c.2377C>G	p.Gln793Glu	p.Q793E	ENST00000374690	NM_000044.3	793	Caa/Gaa	6/8	0.176495507051319	1	FACETS	0.746	0.625	0.88	0.746	0.625	0.88	SUBCLONAL	1	TRUE	0	0.207329637734164	1		813	510	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	20	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.17595721812196	2		215	171	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0023759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	27	380	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.17595721812196	2		380	259	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0023759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	94	799	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.888	0.796	0.985	1	0.989	1	CLONAL	3	TRUE	1	0.17595721812196	2		799	401	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385182	41385182	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367872006	NA	P-0023759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	31	420	0	ENST00000373198.4:c.779G>A	p.Arg260Gln	p.R260Q	ENST00000373198	NM_133170.3	260	cGg/cAg	6/32	1	2	FACETS	0.987	0.799	1	0.987	0.799	1	CLONAL	1	TRUE	1	0.17595721812196	2		420	357	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224701	36224701	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	51	533	1	ENST00000222270.7:c.7087G>T	p.Glu2363Ter	p.E2363*	ENST00000222270	NM_014727.1	2363	Gaa/Taa	30/37	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.17595721812196	2		534	452	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	14	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.52	0.38	0.686	0.52	0.38	0.686	SUBCLONAL	1	TRUE	1	0.48959079447632	2		215	110	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0023763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	48	458	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	0.757	0.645	0.878	0.757	0.645	0.878	SUBCLONAL	1	TRUE	1	0.48959079447632	2		458	259	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547343	106547343	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	32	353	0	ENST00000369096.4:c.580C>A	p.Gln194Lys	p.Q194K	ENST00000369096	NM_001198.3	194	Cag/Aag	4/7	1	2	FACETS	0.467	0.38	0.564	0.467	0.38	0.564	SUBCLONAL	1	TRUE	1	0.48959079447632	2		353	280	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874865	151874866	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	110	260	0	ENST00000262189.6:c.7672dup	p.Tyr2558LeufsTer3	p.Y2558Lfs*3	ENST00000262189	NM_170606.2	2558	tat/tTat	38/59	0.254520936380231	5	FACETS	1	0.946	1			1	INDETERMINATE	3	TRUE	NA	0.48959079447632	5		260	249	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0024020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	229	633	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.284253281967476	2	FACETS	0.995	0.929	1	0.995	0.929	1	CLONAL	2	TRUE	0	0.284253281967476	2		633	810	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377113	118377113	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	167	426	0	ENST00000534358.1:c.10506G>C	p.Lys3502Asn	p.K3502N	ENST00000534358	NM_005933.3	3502	aaG/aaC	27/36	0.281777968457603	3	FACETS	1	0.95	1	1	0.95	1	CLONAL	3	TRUE	0	0.284253281967476	3		426	435	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556697	41556863	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTGGGGGATGACCCTTCCCAGCCTCAAACGTAAGTAACTGCATTATTTTGAAAAGTGCTAATTAGTTTGTTGTCCAGTGATTATGCACAGCTTATTTCTAAATGAACTTAAGCTATGCTGTTGAATATGGTAGCCATTAGCCACATGTTGCTATTTAAATGCATAT	TTTGGGGGATGACCCTTCCCAGCCTCAAACGTAAGTAACTGCATTATTTTGAAAAGTGCTAATTAGTTTGTTGTCCAGTGATTATGCACAGCTTATTTCTAAATGAACTTAAGCTATGCTGTTGAATATGGTAGCCATTAGCCACATGTTGCTATTTAAATGCATAT	-	novel	NA	P-0024020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	87	642	0	ENST00000263253.7:c.3643_3671+138del		p.X1215_splice	ENST00000263253	NM_001429.3	1215		20/31	0.284253281967476	3	FACETS	1	0.961	1	0.598	0.53	0.67	CLONAL	1	TRUE	1	0.284253281967476	3		642	585	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	133	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.454035682003139	2		215	577	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971003	21971003	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	166	484	0	ENST00000304494.5:c.355G>T	p.Glu119Ter	p.E119*	ENST00000304494	NM_000077.4	119	Gag/Tag	2/3	1	2	FACETS	0.958	0.882	1	0.958	0.882	1	CLONAL	1	TRUE	1	0.454035682003139	2		484	763	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	142	288	0	ENST00000304494.5:c.151-1G>A		p.X51_splice	ENST00000304494	NM_000077.4	51			1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.454035682003139	2		288	616	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230691	46230691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424958105	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	160	320	0	ENST00000334344.6:c.940C>T	p.Arg314Cys	p.R314C	ENST00000334344	NM_152641.2	314	Cgt/Tgt	8/21	1	2	FACETS	0.846	0.776	0.919	0.846	0.776	0.919	CLONAL	1	TRUE	1	0.454035682003139	2		320	833	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578551	7578551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	456	792	2	ENST00000269305.4:c.379T>C	p.Ser127Pro	p.S127P	ENST00000269305	NM_001126112.2	127	Tcc/Ccc	5/11	0.384076704121291	2	FACETS	0.836	0.8	0.873	0.836	0.8	0.873	CLONAL	2	TRUE	0	0.454035682003139	2		794	1201	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662582	117662582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	142	555	0	ENST00000368508.3:c.4883G>A	p.Gly1628Glu	p.G1628E	ENST00000368508	NM_002944.2	1628	gGa/gAa	29/43	1	2	FACETS	0.842	0.768	0.919	0.842	0.768	0.919	CLONAL	1	TRUE	1	0.454035682003139	2		555	743	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686868	117686868	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	160	462	0	ENST00000368508.3:c.2849C>T	p.Ser950Phe	p.S950F	ENST00000368508	NM_002944.2	950	tCt/tTt	19/43	1	2	FACETS	0.952	0.875	1	0.952	0.875	1	CLONAL	1	TRUE	1	0.454035682003139	2		462	740	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591116	67591116	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	114	400	1	ENST00000274335.5:c.1709T>C	p.Leu570Pro	p.L570P	ENST00000274335		570	cTt/cCt	12/15	1	2	FACETS	0.886	0.8	0.976	0.886	0.8	0.976	CLONAL	1	TRUE	1	0.454035682003139	2		401	567	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256666	16256666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	175	485	0	ENST00000375759.3:c.3931C>T	p.Pro1311Ser	p.P1311S	ENST00000375759	NM_015001.2	1311	Cct/Tct	11/15	1	2	FACETS	0.872	0.803	0.943	0.872	0.803	0.943	CLONAL	1	TRUE	1	0.454035682003139	2		485	884	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924638	94924638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754657751	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	203	760	0	ENST00000536441.1:c.272G>A	p.Arg91Gln	p.R91Q	ENST00000536441	NM_144665.3	91	cGg/cAg	3/10	1	2	FACETS	0.905	0.839	0.973	0.905	0.839	0.973	CLONAL	1	TRUE	1	0.454035682003139	2		760	988	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228130	36228130	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	192	758	2	ENST00000222270.7:c.7516C>T	p.Pro2506Ser	p.P2506S	ENST00000222270	NM_014727.1	2506	Ccc/Tcc	33/37	1	2	FACETS	0.833	0.77	0.899	0.833	0.77	0.899	CLONAL	1	TRUE	1	0.454035682003139	2		760	1015	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023819	27023819	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	138	489	1	ENST00000324856.7:c.925C>T	p.Gln309Ter	p.Q309*	ENST00000324856	NM_006015.4	309	Cag/Tag	1/20	1	2	FACETS	0.898	0.819	0.98	0.898	0.819	0.98	CLONAL	1	TRUE	1	0.454035682003139	2		490	677	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782159	9782159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	160	627	1	ENST00000377346.4:c.2182C>T	p.Leu728Phe	p.L728F	ENST00000377346	NM_005026.3	728	Ctc/Ttc	17/24	1	2	FACETS	0.869	0.798	0.944	0.869	0.798	0.944	CLONAL	1	TRUE	1	0.454035682003139	2		628	811	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259465	16259465	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	128	484	1	ENST00000375759.3:c.6730C>A	p.Gln2244Lys	p.Q2244K	ENST00000375759	NM_015001.2	2244	Cag/Aag	11/15	1	2	FACETS	0.817	0.742	0.896	0.817	0.742	0.896	CLONAL	1	TRUE	1	0.454035682003139	2		485	690	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36814337	36814337	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	221	676	1	ENST00000373129.3:c.703G>A	p.Gly235Arg	p.G235R	ENST00000373129	NM_032017.1	235	Ggg/Agg	8/12	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.454035682003139	2		677	967	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330651	65330651	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	136	372	0	ENST00000342505.4:c.995T>C	p.Val332Ala	p.V332A	ENST00000342505	NM_002227.2	332	gTt/gCt	8/25	1	2	FACETS	0.839	0.764	0.917	0.839	0.764	0.917	CLONAL	1	TRUE	1	0.454035682003139	2		372	714	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276355	115276355	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	209	692	0	ENST00000438362.2:c.973C>T	p.Gln325Ter	p.Q325*	ENST00000438362	NM_001242891.1	325	Cag/Tag	9/20	1	2	FACETS	0.86	0.798	0.925	0.86	0.798	0.925	CLONAL	1	TRUE	1	0.454035682003139	2		692	1070	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551502	150551503	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	216	841	0	ENST00000369026.2:c.504_505delinsAA	p.Glu169Lys	p.E169K	ENST00000369026	NM_021960.4	168	gaGGag/gaAAag	1/3	1	2	FACETS	0.83	0.771	0.892	0.83	0.771	0.892	CLONAL	1	TRUE	1	0.454035682003139	2		841	1146	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246498707	246498707	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	259	712	0	ENST00000388985.4:c.298G>A	p.Asp100Asn	p.D100N	ENST00000388985		100	Gac/Aac	3/12	1	2	FACETS	0.956	0.895	1	0.956	0.895	1	CLONAL	1	TRUE	1	0.454035682003139	2		712	1193	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944166	71944166	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	174	593	0	ENST00000298229.2:c.1999T>A	p.Ser667Thr	p.S667T	ENST00000298229	NM_001567.3	667	Tcc/Acc	17/28	1	2	FACETS	0.786	0.723	0.852	0.786	0.723	0.852	SUBCLONAL	1	TRUE	1	0.454035682003139	2		593	975	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948382	71948383	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	207	929	2	ENST00000298229.2:c.3094_3095delinsTT	p.Pro1032Phe	p.P1032F	ENST00000298229	NM_001567.3	1032	CCt/TTt	26/28	1	2	FACETS	0.772	0.715	0.831	0.772	0.715	0.831	SUBCLONAL	1	TRUE	1	0.454035682003139	2		931	1181	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186809	108186809	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1565499875	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	159	704	0	ENST00000278616.4:c.6167C>T	p.Pro2056Leu	p.P2056L	ENST00000278616	NM_000051.3	2056	cCc/cTc	42/63	1	2	FACETS	0.715	0.655	0.778	0.715	0.655	0.778	SUBCLONAL	1	TRUE	1	0.454035682003139	2		704	979	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022790	12022790	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1365939019	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	124	530	0	ENST00000396373.4:c.896G>A	p.Arg299Lys	p.R299K	ENST00000396373	NM_001987.4	299	aGg/aAg	5/8	1	2	FACETS	0.802	0.727	0.881	0.802	0.727	0.881	CLONAL	1	TRUE	1	0.454035682003139	2		530	681	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244367	46244367	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	212	581	0	ENST00000334344.6:c.2462del	p.Leu821Ter	p.L821*	ENST00000334344	NM_152641.2	821	Tta/ta	15/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.454035682003139	2		581	870	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432566	49432566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1439459361	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	186	715	0	ENST00000301067.7:c.8573C>T	p.Ser2858Phe	p.S2858F	ENST00000301067	NM_003482.3	2858	tCc/tTc	34/54	1	2	FACETS	0.919	0.849	0.991	0.919	0.849	0.991	CLONAL	1	TRUE	1	0.454035682003139	2		715	892	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117443	115117443	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	146	521	1	ENST00000257566.3:c.731C>T	p.Ser244Phe	p.S244F	ENST00000257566	NM_016569.3	244	tCc/tTc	4/8	1	2	FACETS	0.808	0.738	0.881	0.808	0.738	0.881	CLONAL	1	TRUE	1	0.454035682003139	2		522	796	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907389	32907389	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	145	510	0	ENST00000380152.3:c.1774T>C	p.Tyr592His	p.Y592H	ENST00000380152		592	Tat/Cat	10/27	1	2	FACETS	0.893	0.817	0.973	0.893	0.817	0.973	CLONAL	1	TRUE	1	0.454035682003139	2		510	715	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911487	32911487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	180	513	0	ENST00000380152.3:c.2995C>T	p.Pro999Ser	p.P999S	ENST00000380152		999	Cca/Tca	11/27	1	2	FACETS	0.995	0.919	1	0.995	0.919	1	CLONAL	1	TRUE	1	0.454035682003139	2		513	797	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609667	81609667	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1369204545	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	199	626	0	ENST00000298171.2:c.1265G>A	p.Trp422Ter	p.W422*	ENST00000298171	NM_000369.2	422	tGg/tAg	10/10	1	2	FACETS	0.906	0.84	0.976	0.906	0.84	0.976	CLONAL	1	TRUE	1	0.454035682003139	2		626	967	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292713	91292714	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	207	645	2	ENST00000355112.3:c.215_216delinsTA	p.Ser72Leu	p.S72L	ENST00000355112	NM_000057.2	72	tCC/tTA	3/22	1	2	FACETS	0.941	0.873	1	0.941	0.873	1	CLONAL	1	TRUE	1	0.454035682003139	2		647	969	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828396	72828396	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	182	540	0	ENST00000268489.5:c.8185C>T	p.His2729Tyr	p.H2729Y	ENST00000268489	NM_006885.3	2729	Cat/Tat	9/10	1	2	FACETS	0.997	0.922	1	0.997	0.922	1	CLONAL	1	TRUE	1	0.454035682003139	2		540	804	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578548	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	441	823	2	ENST00000269305.4:c.382_383delinsTT	p.Pro128Phe	p.P128F	ENST00000269305	NM_001126112.2	128	CCt/TTt	5/11	0.384076704121291	2	FACETS	0.808	0.772	0.845	0.808	0.772	0.845	CLONAL	2	TRUE	0	0.454035682003139	2		825	1202	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979663	7979663	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1437299933	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	233	434	0	ENST00000319144.4:c.1363-1G>A		p.X455_splice	ENST00000319144	NM_001139.2	455			0.384076704121291	2	FACETS	0.925	0.87	0.98	0.925	0.87	0.98	CLONAL	2	TRUE	0	0.454035682003139	2		434	555	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576057	29576057	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1555617328	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	200	661	0	ENST00000356175.3:c.4030G>T	p.Glu1344Ter	p.E1344*	ENST00000356175	NM_000267.3	1344	Gaa/Taa	30/57	0.422894493100807	3	FACETS	0.825	0.763	0.89	0.413	0.381	0.445	CLONAL	1	TRUE	1	0.454035682003139	3		661	1310	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664880	29664880	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	321	497	0	ENST00000356175.3:c.6623G>A	p.Trp2208Ter	p.W2208*	ENST00000356175	NM_000267.3	2208	tGg/tAg	43/57	0.422894493100807	3	FACETS	0.988	0.936	1	0.988	0.936	1	CLONAL	2	TRUE	1	0.454035682003139	3		497	878	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435689	56435690	+	missense_variant	Missense_Mutation	DNP	GT	GT	AA	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	145	509	4	ENST00000407977.2:c.1447_1448delinsTT	p.Thr483Leu	p.T483L	ENST00000407977		483	ACg/TTg	9/10	0.405905396767058	3	FACETS	0.828	0.755	0.905	0.276	0.251	0.302	CLONAL	1	TRUE	0	0.454035682003139	3		513	946	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119911	70119911	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	161	503	0	ENST00000245479.2:c.913G>A	p.Gly305Arg	p.G305R	ENST00000245479	NM_000346.3	305	Ggg/Agg	3/3	0.405905396767058	3	FACETS	0.952	0.873	1	0.317	0.291	0.345	CLONAL	1	TRUE	0	0.454035682003139	3		503	914	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096033	11096033	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	185	737	0	ENST00000358026.2:c.307C>T	p.His103Tyr	p.H103Y	ENST00000358026	NM_001128849.1	103	Cat/Tat	3/36	1	2	FACETS	0.825	0.761	0.891	0.825	0.761	0.891	CLONAL	1	TRUE	1	0.454035682003139	2		737	988	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971135	18971135	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1195464113	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	255	735	0	ENST00000262803.5:c.2188C>T	p.Arg730Cys	p.R730C	ENST00000262803	NM_002911.3	730	Cgt/Tgt	16/24	1	2	FACETS	0.971	0.908	1	0.971	0.908	1	CLONAL	1	TRUE	1	0.454035682003139	2		735	1157	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47710042	47710042	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	122	406	0	ENST00000233146.2:c.2759A>T	p.Asn920Ile	p.N920I	ENST00000233146	NM_000251.2	920	aAt/aTt	16/16	1	2	FACETS	0.824	0.747	0.906	0.824	0.747	0.906	CLONAL	1	TRUE	1	0.454035682003139	2		406	652	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030657	48030657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060502914	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	182	609	0	ENST00000234420.5:c.3271C>T	p.Leu1091Phe	p.L1091F	ENST00000234420	NM_000179.2	1091	Ctt/Ttt	5/10	1	2	FACETS	0.845	0.779	0.913	0.845	0.779	0.913	CLONAL	1	TRUE	1	0.454035682003139	2		609	949	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775497	39775497	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	180	673	2	ENST00000288319.7:c.523G>A	p.Asp175Asn	p.D175N	ENST00000288319	NM_182918.3	175	Gac/Aac	4/10	1	2	FACETS	0.835	0.77	0.903	0.835	0.77	0.903	CLONAL	1	TRUE	1	0.454035682003139	2		675	949	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655202	45655202	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	139	517	1	ENST00000407780.3:c.650T>C	p.Ile217Thr	p.I217T	ENST00000407780	NM_001283052.1	217	aTa/aCa	4/7	1	2	FACETS	0.875	0.798	0.955	0.875	0.798	0.955	CLONAL	1	TRUE	1	0.454035682003139	2		518	700	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143259	24143259	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	433	807	0	ENST00000263121.7:c.491T>A	p.Phe164Tyr	p.F164Y	ENST00000263121	NM_003073.3	164	tTc/tAc	4/9	0.384076704121291	2	FACETS	0.896	0.857	0.936	0.896	0.857	0.936	CLONAL	2	TRUE	0	0.454035682003139	2		807	1064	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902632	1902632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	221	701	0	ENST00000382891.5:c.251C>T	p.Ser84Phe	p.S84F	ENST00000382891	NM_133335.3	84	tCc/tTc	2/22	1	2	FACETS	0.857	0.797	0.919	0.857	0.797	0.919	CLONAL	1	TRUE	1	0.454035682003139	2		701	1136	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979471	55979471	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	129	502	0	ENST00000263923.4:c.976G>A	p.Glu326Lys	p.E326K	ENST00000263923	NM_002253.2	326	Gaa/Aaa	7/30	1	2	FACETS	0.781	0.708	0.856	0.781	0.708	0.856	SUBCLONAL	1	TRUE	1	0.454035682003139	2		502	728	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753095	57753101	+	frameshift_variant	Frame_Shift_Del	DEL	GGCAGGA	GGCAGGA	-	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	180	496	0	ENST00000274289.3:c.915_921del	p.Pro306SerfsTer3	p.P306Sfs*3	ENST00000274289	NM_006622.3	305	gcTCCTGCC/gc	7/14	1	2	FACETS	0.995	0.919	1	0.995	0.919	1	CLONAL	1	TRUE	1	0.454035682003139	2		496	797	SUCCESS
APC	324	MSKCC	GRCh37	5	112174853	112174853	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	145	412	0	ENST00000257430.4:c.3562C>T	p.Pro1188Ser	p.P1188S	ENST00000257430	NM_000038.5	1188	Cct/Tct	16/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.454035682003139	2		412	608	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057767	180057767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	177	471	0	ENST00000261937.6:c.188G>A	p.Gly63Glu	p.G63E	ENST00000261937	NM_182925.4	63	gGa/gAa	3/30	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.454035682003139	2		471	777	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983136	149983136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	214	751	1	ENST00000253339.5:c.3122C>T	p.Pro1041Leu	p.P1041L	ENST00000253339		1041	cCt/cTt	7/7	1	2	FACETS	0.836	0.776	0.899	0.836	0.776	0.899	CLONAL	1	TRUE	1	0.454035682003139	2		752	1127	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001480	150001480	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	253	788	0	ENST00000253339.5:c.2124A>G	p.Ile708Met	p.I708M	ENST00000253339		708	atA/atG	4/7	1	2	FACETS	0.93	0.87	0.993	0.93	0.87	0.993	CLONAL	1	TRUE	1	0.454035682003139	2		788	1198	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522250	157522250	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	211	665	1	ENST00000346085.5:c.4522C>T	p.His1508Tyr	p.H1508Y	ENST00000346085	NM_020732.3	1508	Cat/Tat	18/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.454035682003139	2		666	866	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843715	151843715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	150	477	0	ENST00000262189.6:c.14000C>T	p.Thr4667Ile	p.T4667I	ENST00000262189	NM_170606.2	4667	aCc/aTc	53/59	1	2	FACETS	0.854	0.781	0.929	0.854	0.781	0.929	CLONAL	1	TRUE	1	0.454035682003139	2		477	774	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189029	38189029	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	271	919	0	ENST00000317025.8:c.985G>A	p.Glu329Lys	p.E329K	ENST00000317025	NM_023034.1	329	Gag/Aag	5/24	1	2	FACETS	0.93	0.871	0.99	0.93	0.871	0.99	CLONAL	1	TRUE	1	0.454035682003139	2		919	1284	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890138	76890138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	215	346	0	ENST00000373344.5:c.4756C>T	p.Pro1586Ser	p.P1586S	ENST00000373344	NM_000489.3	1586	Cca/Tca	17/35	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.454035682003139	1		346	531	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858164	152858165	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0024070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	209	444	3	ENST00000406277.2:c.450_451delinsTT	p.Gln151Ter	p.Q151*	ENST00000406277	NM_152274.4	150	ctCCag/ctTTag	6/7	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.454035682003139	1		447	546	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612028	189612028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs900140738	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	123	475	0	ENST00000264731.3:c.1780C>T	p.Arg594Ter	p.R594*	ENST00000264731	NM_003722.4	594	Cga/Tga	14/14	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.537184908779177	2		475	441	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	369	705	0	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	0.529325812162651	4	FACETS	0.95	0.903	0.999	0.634	0.602	0.666	CLONAL	2	TRUE	1	0.537184908779177	4		705	1111	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573894	18573894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759658584	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	164	416	0	ENST00000266497.5:c.2212C>T	p.Arg738Cys	p.R738C	ENST00000266497		738	Cgt/Tgt	15/31	1	2	FACETS	0.988	0.911	1	0.988	0.911	1	CLONAL	1	TRUE	1	0.537184908779177	2		416	618	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518175	8518175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1354824749	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	197	453	1	ENST00000356435.5:c.1216G>A	p.Glu406Lys	p.E406K	ENST00000356435		406	Gaa/Aaa	10/35	0.537184908779177	2	FACETS	0.96	0.903	1	0.96	0.903	1	CLONAL	2	TRUE	0	0.537184908779177	2		454	382	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956771	68956771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774302685	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	161	644	2	ENST00000288368.4:c.889C>T	p.Arg297Cys	p.R297C	ENST00000288368	NM_024870.2	297	Cgt/Tgt	8/40	1	2	FACETS	0.862	0.793	0.934	0.862	0.793	0.934	CLONAL	1	TRUE	1	0.537184908779177	2		646	695	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913384	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	245	322	0	ENST00000304494.5:c.262G>T	p.Glu88Ter	p.E88*	ENST00000304494	NM_000077.4	88	Gag/Tag	2/3	0.537184908779177	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.537184908779177	2		322	396	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295253	+	upstream_gene_variant	5'Flank	ONP	GAGG	GAGG	AAGA	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	250	480	1				ENST00000310581	NM_198253.2	-/1132			0.139078920061504	5	FACETS	1	0.989	1			1	INDETERMINATE	3	TRUE	NA	0.537184908779177	5		481	482	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652904	29652904	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	140	401	0	ENST00000356175.3:c.4839T>A	p.Tyr1613Ter	p.Y1613*	ENST00000356175	NM_000267.3	1613	taT/taA	36/57	1	2	FACETS	0.987	0.904	1	0.987	0.904	1	CLONAL	1	TRUE	1	0.537184908779177	2		401	528	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967135	25967135	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	90	571	0	ENST00000435504.4:c.2071C>T	p.Pro691Ser	p.P691S	ENST00000435504		691	Cca/Tca	13/13	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.537184908779177	2		571	331	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645286	67645286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	129	517	1	ENST00000264010.4:c.551C>T	p.Pro184Leu	p.P184L	ENST00000264010	NM_006565.3	184	cCa/cTa	3/12	1	2	FACETS	0.838	0.763	0.917	0.838	0.763	0.917	CLONAL	1	TRUE	1	0.537184908779177	2		518	573	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974826	15974826	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	150	526	0	ENST00000268712.3:c.4049C>T	p.Ser1350Phe	p.S1350F	ENST00000268712	NM_006311.3	1350	tCc/tTc	30/46	1	2	FACETS	0.999	0.918	1	0.999	0.918	1	CLONAL	1	TRUE	1	0.537184908779177	2		526	559	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967209	93967209	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	150	567	0	ENST00000369303.4:c.2143G>A	p.Glu715Lys	p.E715K	ENST00000369303	NM_004440.3	715	Gaa/Aaa	12/17	1	2	FACETS	0.942	0.864	1	0.942	0.864	1	CLONAL	1	TRUE	1	0.537184908779177	2		567	593	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117645576	117645576	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	153	552	0	ENST00000368508.3:c.5560G>A	p.Asp1854Asn	p.D1854N	ENST00000368508	NM_002944.2	1854	Gat/Aat	34/43	1	2	FACETS	0.94	0.864	1	0.94	0.864	1	CLONAL	1	TRUE	1	0.537184908779177	2		552	606	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259967	16259967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	167	653	1	ENST00000375759.3:c.7232C>T	p.Ser2411Leu	p.S2411L	ENST00000375759	NM_015001.2	2411	tCg/tTg	11/15	1	2	FACETS	0.941	0.867	1	0.941	0.867	1	CLONAL	1	TRUE	1	0.537184908779177	2		654	661	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476265	88476265	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	147	725	0	ENST00000360948.2:c.1867G>A	p.Gly623Arg	p.G623R	ENST00000360948	NM_001012338.2	623	Gga/Aga	15/19	0.537184908779177	3	FACETS	0.886	0.809	0.965	0.443	0.404	0.483	CLONAL	1	TRUE	1	0.537184908779177	3		725	784	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584548	189584548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	150	511	2	ENST00000264731.3:c.844G>A	p.Gly282Arg	p.G282R	ENST00000264731	NM_003722.4	282	Gga/Aga	6/14	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.537184908779177	2		513	510	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182052	38182052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1190702008	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	120	416	1	ENST00000396334.3:c.676G>A	p.Glu226Lys	p.E226K	ENST00000396334	NM_002468.4	226	Gaa/Aaa	3/5	1	2	FACETS	0.951	0.864	1	0.951	0.864	1	CLONAL	1	TRUE	1	0.537184908779177	2		417	470	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44970634	44970634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	194	315	0	ENST00000377967.4:c.4184C>T	p.Pro1395Leu	p.P1395L	ENST00000377967	NM_021140.2	1395	cCa/cTa	29/29	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.537184908779177	1		315	358	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170061	32170061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	157	669	0	ENST00000375023.3:c.3547G>A	p.Gly1183Arg	p.G1183R	ENST00000375023	NM_004557.3	1183	Gga/Aga	21/30	0.529325812162651	4	FACETS	1	0.924	1	0.337	0.308	0.366	CLONAL	1	TRUE	1	0.537184908779177	4		669	890	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520183	9520183	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781425219	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	136	457	3	ENST00000353224.5:c.2086G>A	p.Gly696Arg	p.G696R	ENST00000353224	NM_177990.2	696	Gga/Aga	10/10	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.537184908779177	2		460	504	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864769	68864769	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	124	436	0	ENST00000288368.4:c.140C>T	p.Ser47Leu	p.S47L	ENST00000288368	NM_024870.2	47	tCg/tTg	1/40	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.537184908779177	2		436	397	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923328	9923328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	149	492	0	ENST00000330684.3:c.1959G>A	p.Met653Ile	p.M653I	ENST00000330684	NM_001134407.1	653	atG/atA	9/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.537184908779177	2		492	509	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	231076	231076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	211	391	1	ENST00000264932.6:c.856C>T	p.Pro286Ser	p.P286S	ENST00000264932	NM_004168.2	286	Cct/Tct	7/15	0.139078920061504	5	FACETS	0.946	0.887	1			1	INDETERMINATE	3	TRUE	NA	0.537184908779177	5		392	500	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313316	65313316	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	123	600	0	ENST00000342505.4:c.1798G>T	p.Gly600Trp	p.G600W	ENST00000342505	NM_002227.2	600	Ggg/Tgg	13/25	1	2	FACETS	0.886	0.805	0.97	0.886	0.805	0.97	CLONAL	1	TRUE	1	0.537184908779177	2		600	517	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176085803	176085803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	176	511	0	ENST00000367669.3:c.983C>T	p.Ser328Phe	p.S328F	ENST00000367669	NM_022457.5	328	tCc/tTc	9/20	0.15852130338628	3	FACETS	1	0.98	1	0.588	0.543	0.634	INDETERMINATE	1	TRUE	1	0.537184908779177	3		511	707	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421535	32421536	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	143	571	3	ENST00000332351.3:c.1056_1057delinsTT	p.Gln353Ter	p.Q353*	ENST00000332351	NM_024426.4	352	gcCCaa/gcTTaa	6/10	1	2	FACETS	0.966	0.885	1	0.966	0.885	1	CLONAL	1	TRUE	1	0.537184908779177	2		574	551	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518491	69518491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	90	317	0	ENST00000294312.3:c.154C>T	p.Pro52Ser	p.P52S	ENST00000294312	NM_005117.2	52	Ccc/Tcc	1/3	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.537184908779177	2		317	310	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218876	133218876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	170	692	0	ENST00000320574.5:c.5060C>T	p.Ser1687Phe	p.S1687F	ENST00000320574	NM_006231.2	1687	tCc/tTc	38/49	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.537184908779177	2		692	613	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41021737	41021737	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	150	447	0	ENST00000267868.3:c.679C>T	p.Leu227Phe	p.L227F	ENST00000267868	NM_002875.4	227	Ctt/Ttt	8/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.537184908779177	2		447	525	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042050	42042050	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	188	629	2	ENST00000219905.7:c.6245C>T	p.Ala2082Val	p.A2082V	ENST00000219905	NM_001164273.1	2082	gCt/gTt	17/24	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.537184908779177	2		631	682	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857224	9857224	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	143	479	0	ENST00000330684.3:c.4177T>A	p.Ser1393Thr	p.S1393T	ENST00000330684	NM_001134407.1	1393	Tcc/Acc	13/13	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.537184908779177	2		479	512	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041782	14041782	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	148	520	1	ENST00000311895.7:c.2329C>T	p.Gln777Ter	p.Q777*	ENST00000311895	NM_005236.2	777	Cag/Tag	11/11	1	2	FACETS	0.993	0.912	1	0.993	0.912	1	CLONAL	1	TRUE	1	0.537184908779177	2		521	555	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347680	89347680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1406602469	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	117	589	1	ENST00000301030.4:c.5270C>T	p.Ser1757Phe	p.S1757F	ENST00000301030	NM_001256183.1	1757	tCc/tTc	9/13	0.537184908779177	1	FACETS	0.908	0.828	0.99	0.908	0.828	0.99	CLONAL	1	TRUE	0	0.537184908779177	1		590	351	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509550	29509550	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	139	479	0	ENST00000356175.3:c.755T>A	p.Leu252Ter	p.L252*	ENST00000356175	NM_000267.3	252	tTg/tAg	8/57	1	2	FACETS	0.905	0.827	0.985	0.905	0.827	0.985	CLONAL	1	TRUE	1	0.537184908779177	2		479	572	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528485	29528486	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	177	588	0	ENST00000356175.3:c.1242_1243delinsTT	p.His415Tyr	p.H415Y	ENST00000356175	NM_000267.3	414	ctCCat/ctTTat	11/57	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.537184908779177	2		588	623	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740603	58740603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	189	589	1	ENST00000305921.3:c.1508C>T	p.Ser503Leu	p.S503L	ENST00000305921	NM_003620.3	503	tCa/tTa	6/6	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.537184908779177	2		590	666	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59937253	59937253	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1256465650	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	176	529	0	ENST00000259008.2:c.109A>G	p.Asn37Asp	p.N37D	ENST00000259008	NM_032043.2	37	Aac/Gac	3/20	1	2	FACETS	0.971	0.897	1	0.971	0.897	1	CLONAL	1	TRUE	1	0.537184908779177	2		529	675	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212480	36212480	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	157	635	0	ENST00000222270.7:c.2231T>G	p.Leu744Trp	p.L744W	ENST00000222270	NM_014727.1	744	tTg/tGg	3/37	1	2	FACETS	0.923	0.849	1	0.923	0.849	1	CLONAL	1	TRUE	1	0.537184908779177	2		635	633	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31393199	31393199	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	112	428	0	ENST00000328111.2:c.2287A>T	p.Asn763Tyr	p.N763Y	ENST00000328111	NM_006892.3	763	Aat/Tat	21/23	1	2	FACETS	0.948	0.858	1	0.948	0.858	1	CLONAL	1	TRUE	1	0.537184908779177	2		428	440	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702561	52702561	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	175	691	0	ENST00000394830.3:c.337A>G	p.Thr113Ala	p.T113A	ENST00000394830	NM_018313.4	113	Act/Gct	4/30	1	2	FACETS	0.882	0.814	0.952	0.882	0.814	0.952	CLONAL	1	TRUE	1	0.537184908779177	2		691	739	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014032	70014032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	150	413	0	ENST00000394351.3:c.893C>T	p.Ser298Phe	p.S298F	ENST00000394351	NM_000248.3	298	tCc/tTc	9/9	0.537184908779177	3	FACETS	1	0.962	1			1	CLONAL	1	TRUE	NA	0.537184908779177	3		413	653	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403593	138403593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768628634	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	167	601	3	ENST00000289153.2:c.2189C>T	p.Ala730Val	p.A730V	ENST00000289153	NM_006219.2	730	gCc/gTc	15/22	1	2	FACETS	0.827	0.761	0.895	0.827	0.761	0.895	CLONAL	1	TRUE	1	0.537184908779177	2		604	752	SUCCESS
ATR	545	MSKCC	GRCh37	3	142257420	142257420	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	132	482	0	ENST00000350721.4:c.3629C>T	p.Ser1210Phe	p.S1210F	ENST00000350721	NM_001184.3	1210	tCc/tTc	19/47	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.537184908779177	2		482	491	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446217	187446217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	147	697	1	ENST00000232014.4:c.1471C>T	p.His491Tyr	p.H491Y	ENST00000232014	NM_001130845.1	491	Cac/Tac	6/10	1	2	FACETS	0.939	0.861	1	0.939	0.861	1	CLONAL	1	TRUE	1	0.537184908779177	2		698	583	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197281	106197281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	90	342	0	ENST00000380013.4:c.5614C>T	p.Leu1872Phe	p.L1872F	ENST00000380013	NM_001127208.2	1872	Ctc/Ttc	11/11	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.537184908779177	2		342	326	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674224	86674224	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	202	351	0	ENST00000274376.6:c.2356A>T	p.Thr786Ser	p.T786S	ENST00000274376	NM_002890.2	786	Acc/Tcc	18/25	0.537184908779177	3	FACETS	0.887	0.829	0.946	0.887	0.829	0.946	CLONAL	2	TRUE	1	0.537184908779177	3		351	538	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149453015	149453015	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	126	438	0	ENST00000286301.3:c.931C>T	p.Gln311Ter	p.Q311*	ENST00000286301	NM_005211.3	311	Cag/Tag	7/22	0.537184908779177	3	FACETS	1	0.928	1	0.512	0.465	0.561	CLONAL	1	TRUE	1	0.537184908779177	3		438	581	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324128	31324128	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	68	441	0	ENST00000412585.2:c.435G>C	p.Lys145Asn	p.K145N	ENST00000412585	NM_005514.6	145	aaG/aaC	3/8	0.529325812162651	4	FACETS	0.766	0.668	0.872	0.255	0.222	0.291	SUBCLONAL	1	TRUE	1	0.537184908779177	4		441	508	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166850	32166850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	172	707	1	ENST00000375023.3:c.4388G>A	p.Gly1463Glu	p.G1463E	ENST00000375023	NM_004557.3	1463	gGg/gAg	24/30	0.529325812162651	4	FACETS	1	0.944	1	0.344	0.316	0.373	CLONAL	1	TRUE	1	0.537184908779177	4		708	953	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922655	56922655	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	136	558	1	ENST00000519728.1:c.1525C>T	p.Gln509Ter	p.Q509*	ENST00000519728	NM_002350.3	509	Cag/Tag	13/13	1	2	FACETS	0.922	0.843	1	0.922	0.843	1	CLONAL	1	TRUE	1	0.537184908779177	2		559	549	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069604	69069604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777049204	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	167	613	0	ENST00000288368.4:c.4279G>A	p.Glu1427Lys	p.E1427K	ENST00000288368	NM_024870.2	1427	Gaa/Aaa	35/40	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.537184908779177	2		613	612	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242859	98242859	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	134	393	0	ENST00000331920.6:c.758C>T	p.Pro253Leu	p.P253L	ENST00000331920	NM_000264.3	253	cCt/cTt	6/24	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.537184908779177	2		393	430	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760688	133760688	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1440408888	NA	P-0024072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	206	796	0	ENST00000318560.5:c.3011C>T	p.Pro1004Leu	p.P1004L	ENST00000318560	NM_005157.4	1004	cCt/cTt	11/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.537184908779177	2		796	694	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	117	215	0				ENST00000310581	NM_198253.2	-/1132			0.263007283646769	1	FACETS	0.897	0.811	0.987	0.897	0.811	0.987	CLONAL	1	TRUE	0	0.361567585000095	1		215	591	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0024144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	210	380	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.361567585000095	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.361567585000095	1		380	833	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863224683	NA	P-0024144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1447	296	758	0	ENST00000269305.4:c.388C>T	p.Leu130Phe	p.L130F	ENST00000269305	NM_001126112.2	130	Ctc/Ttc	5/11	1	2	FACETS	0.939	0.881	0.999	0.939	0.881	0.999	CLONAL	1	TRUE	1	0.361567585000095	2		758	1743	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578516	7578516	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs137852794	NA	P-0024144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1529	303	754	0	ENST00000269305.4:c.414del	p.Lys139ArgfsTer31	p.K139Rfs*31	ENST00000269305	NM_001126112.2	138	gcC/gc	5/11	1	2	FACETS	0.915	0.859	0.973	0.915	0.859	0.973	CLONAL	1	TRUE	1	0.361567585000095	2		754	1832	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909663	76909663	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	105	343	0	ENST00000373344.5:c.4242A>C	p.Glu1414Asp	p.E1414D	ENST00000373344	NM_000489.3	1414	gaA/gaC	14/35	1	2	FACETS	0.781	0.7	0.867	0.781	0.7	0.867	SUBCLONAL	1	TRUE	1	0.361567585000095	2		343	744	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577595	7577598	+	frameshift_variant	Frame_Shift_Del	DEL	CAGT	CAGT	-	novel	NA	P-0024450-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	494	575	0	ENST00000269305.4:c.683_686del	p.Asp228ValfsTer18	p.D228Vfs*18	ENST00000269305	NM_001126112.2	228	gACTGt/gt	7/11	0.670054604777301	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.670054604777301	2		575	720	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204499917	204499917	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200898280	NA	P-0024450-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	212	531	0	ENST00000367182.3:c.259C>T	p.Arg87Cys	p.R87C	ENST00000367182	NM_001278516.1	87	Cgt/Tgt	4/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.670054604777301	2		531	622	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565592	41565607	+	frameshift_variant	Frame_Shift_Del	DEL	GGATATTTAGAATATG	GGATATTTAGAATATG	-	novel	NA	P-0024450-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	154	523	0	ENST00000263253.7:c.4258_4273del	p.Gly1420SerfsTer4	p.G1420Sfs*4	ENST00000263253	NM_001429.3	1420	GGATATTTAGAATATGtc/tc	26/31	0.670054604777301	2	FACETS	0.784	0.721	0.85	0.392	0.36	0.425	SUBCLONAL	1	TRUE	0	0.670054604777301	2		523	586	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7141770	7141770	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024450-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	311	629	0	ENST00000302850.5:c.2600T>C	p.Val867Ala	p.V867A	ENST00000302850	NM_000208.2	867	gTc/gCc	13/22	0.670054604777301	3	FACETS	0.991	0.934	1	0.495	0.467	0.525	CLONAL	1	TRUE	1	0.670054604777301	3		629	1251	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878478	151878478	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024450-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	248	716	0	ENST00000262189.6:c.6467C>G	p.Thr2156Arg	p.T2156R	ENST00000262189	NM_170606.2	2156	aCa/aGa	36/59	0.670054604777301	3	FACETS	0.842	0.787	0.9	0.281	0.262	0.3	CLONAL	1	TRUE	0	0.670054604777301	3		716	1173	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	117	282	0				ENST00000310581	NM_198253.2	-/1132			0.346396425906507	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.513101505603654	1		282	293	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	73	173	1				ENST00000310581	NM_198253.2	-/1132			0.346396425906507	1	FACETS	0.944	0.839	1	0.944	0.839	1	CLONAL	1	TRUE	0	0.513101505603654	1		174	224	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549725	187549725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199516712	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	126	457	0	ENST00000441802.2:c.4516C>T	p.Arg1506Cys	p.R1506C	ENST00000441802	NM_005245.3	1506	Cgt/Tgt	8/27	0.427817846028305	3	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.513101505603654	3		457	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691039	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	97	616	1	ENST00000269305.4:c.919+1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.398712450099056	3	FACETS	0.801	0.716	0.892	0.401	0.358	0.446	CLONAL	1	TRUE	1	0.513101505603654	3		617	593	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374403	81374403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372600489	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	149	456	0	ENST00000222390.5:c.659G>A	p.Arg220Gln	p.R220Q	ENST00000222390	NM_000601.4	220	cGa/cAa	6/18	0.298131487315182	5	FACETS	0.762	0.698	0.829	0.508	0.465	0.553	INDETERMINATE	2	TRUE	2	0.513101505603654	5		456	674	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78811795	78811795	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	127	341	0	ENST00000306801.3:c.1210C>T	p.Arg404Trp	p.R404W	ENST00000306801	NM_020761.2	404	Cgg/Tgg	10/34	0.398712450099056	3	FACETS	1	0.986	1	0.734	0.67	0.799	CLONAL	1	TRUE	1	0.513101505603654	3		341	424	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003314	143003314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1451831325	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	166	523	0	ENST00000262992.4:c.2512C>T	p.Arg838Cys	p.R838C	ENST00000262992	NM_001101669.1	838	Cgt/Tgt	23/24	0.227285486106902	5	FACETS	0.791	0.728	0.856	0.527	0.485	0.571	INDETERMINATE	2	TRUE	2	0.513101505603654	5		523	724	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873104	134873104	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202048188	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	107	514	0	ENST00000398015.3:c.1408C>T	p.Arg470Trp	p.R470W	ENST00000398015	NM_004441.4	470	Cgg/Tgg	6/16	0.440636026789723	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.513101505603654	1		514	306	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489787	2489787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139725610	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	110	520	0	ENST00000355716.4:c.184C>T	p.Arg62Cys	p.R62C	ENST00000355716	NM_003820.2	62	Cgt/Tgt	3/8	0.21117107009509	4	FACETS	1	0.983	1	0.724	0.655	0.797	INDETERMINATE	1	TRUE	2	0.513101505603654	4		520	448	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950309	17950309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	69	685	0	ENST00000458235.1:c.1418C>T	p.Ser473Phe	p.S473F	ENST00000458235	NM_000215.3	473	tCc/tTc	10/24	0.336947893095607	3	FACETS	0.632	0.551	0.719	0.316	0.275	0.36	SUBCLONAL	1	TRUE	1	0.513101505603654	3		685	535	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169092	32169092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs189264181	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	190	614	1	ENST00000375023.3:c.3941C>T	p.Ala1314Val	p.A1314V	ENST00000375023	NM_004557.3	1314	gCc/gTc	22/30	0.298131487315182	5	FACETS	0.991	0.92	1	0.661	0.613	0.71	INDETERMINATE	2	TRUE	2	0.513101505603654	5		615	661	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557744	187557744	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	114	269	0	ENST00000441802.2:c.3967C>T	p.Leu1323Phe	p.L1323F	ENST00000441802	NM_005245.3	1323	Ctt/Ttt	5/27	0.427817846028305	3	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.513101505603654	3		269	398	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28595723	28595724	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	208	661	1	ENST00000253063.3:c.120_121delinsTT	p.Pro41Ser	p.P41S	ENST00000253063	NM_031459.4	40	ggCCct/ggTTct	2/10	0.513101505603654	4	FACETS	1	0.991	1	0.749	0.696	0.803	CLONAL	1	TRUE	2	0.513101505603654	4		662	819	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939140	36939140	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754176065	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	193	717	0	ENST00000361632.4:c.569G>A	p.Arg190His	p.R190H	ENST00000361632		190	cGc/cAc	5/16	0.513101505603654	4	FACETS	1	0.99	1	0.73	0.676	0.785	CLONAL	1	TRUE	2	0.513101505603654	4		717	780	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740290	162740290	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	70	238	1	ENST00000367921.3:c.1492G>A	p.Glu498Lys	p.E498K	ENST00000367921	NM_006182.2	498	Gag/Aag	12/18	0.254954614896787	4	FACETS	1	0.975	1			1	INDETERMINATE	1	TRUE	NA	0.513101505603654	4		239	280	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622151	43622151	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	163	562	0	ENST00000355710.3:c.3168G>A	p.Trp1056Ter	p.W1056*	ENST00000355710	NM_020975.4	1056	tgG/tgA	19/20	0.21117107009509	4	FACETS	1	0.987	1	0.69	0.635	0.747	INDETERMINATE	1	TRUE	2	0.513101505603654	4		562	697	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394673	394674	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	160	593	0	ENST00000399788.2:c.5021_5022delinsTT	p.Ser1674Phe	p.S1674F	ENST00000399788	NM_001042603.1	1674	tCC/tTT	28/28	0.227285486106902	5	FACETS	0.799	0.734	0.865	0.532	0.489	0.577	INDETERMINATE	2	TRUE	2	0.513101505603654	5		593	691	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444812	49444813	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	210	717	1	ENST00000301067.7:c.2653_2654delinsTT	p.Pro885Phe	p.P885F	ENST00000301067	NM_003482.3	885	CCc/TTc	10/54	0.320195692922428	3	FACETS	0.794	0.741	0.848	0.529	0.494	0.565	SUBCLONAL	2	TRUE	0	0.513101505603654	3		718	648	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112920002	112920002	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs760221298	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	174	760	0	ENST00000351677.2:c.1217T>C	p.Val406Ala	p.V406A	ENST00000351677	NM_002834.3	406	gTt/gCt	10/16	0.253132984928931	4	FACETS	1	0.976	1	0.573	0.527	0.62	INDETERMINATE	1	TRUE	2	0.513101505603654	4		760	896	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562790	21562790	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1327443204	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	133	557	0	ENST00000382592.4:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000382592	NM_014572.2	377	Cgc/Tgc	4/8	0.21117107009509	4	FACETS	1	0.983	1	0.67	0.611	0.732	INDETERMINATE	1	TRUE	2	0.513101505603654	4		557	585	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597513	28597513	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	151	541	0	ENST00000241453.7:c.2392G>A	p.Gly798Arg	p.G798R	ENST00000241453	NM_004119.2	798	Gga/Aga	19/24	0.21117107009509	4	FACETS	1	0.986	1	0.681	0.624	0.74	INDETERMINATE	1	TRUE	2	0.513101505603654	4		541	654	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601290	28601290	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	166	466	0	ENST00000241453.7:c.2142G>A	p.Trp714Ter	p.W714*	ENST00000241453	NM_004119.2	714	tgG/tgA	17/24	0.21117107009509	4	FACETS	0.854	0.789	0.922	0.854	0.789	0.922	INDETERMINATE	2	TRUE	2	0.513101505603654	4		466	573	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068238	30068238	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	125	322	1	ENST00000331968.5:c.2161C>T	p.Pro721Ser	p.P721S	ENST00000331968	NM_002742.2	721	Cct/Tct	15/18	0.128405166505304	3	FACETS	1	0.983	1	0.449	0.409	0.49	INDETERMINATE	1	TRUE	0	0.513101505603654	3		323	455	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30103717	30103717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	140	509	0	ENST00000331968.5:c.1221G>A	p.Met407Ile	p.M407I	ENST00000331968	NM_002742.2	407	atG/atA	8/18	0.128405166505304	3	FACETS	1	0.985	1	0.451	0.413	0.49	INDETERMINATE	1	TRUE	0	0.513101505603654	3		509	507	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060743	38060743	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	98	773	1	ENST00000250448.2:c.1246G>A	p.Asp416Asn	p.D416N	ENST00000250448	NM_004496.3	416	Gac/Aac	2/2	0.128405166505304	3	FACETS	0.695	0.62	0.774	0.232	0.206	0.258	INDETERMINATE	1	TRUE	0	0.513101505603654	3		774	691	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358581	67358581	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	99	526	0	ENST00000327367.4:c.89G>A	p.Trp30Ter	p.W30*	ENST00000327367	NM_005902.3	30	tGg/tAg	1/9	1	2	FACETS	0.754	0.675	0.836	0.754	0.675	0.836	SUBCLONAL	1	TRUE	1	0.513101505603654	2		526	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578549	7578550	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	227	676	2	ENST00000269305.4:c.380_381delinsTT	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCC/tTT	5/11	0.398712450099056	3	FACETS	1	0.99	1	0.66	0.616	0.705	CLONAL	1	TRUE	1	0.513101505603654	3		678	842	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868179	37868179	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	177	539	0	ENST00000269571.5:c.902-2A>T		p.X301_splice	ENST00000269571		301			0.398712450099056	3	FACETS	0.909	0.845	0.974	0.909	0.845	0.974	CLONAL	2	TRUE	1	0.513101505603654	3		539	477	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4095386	4095386	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	247	732	0	ENST00000262948.5:c.1046G>A	p.Cys349Tyr	p.C349Y	ENST00000262948	NM_030662.3	349	tGc/tAc	9/11	0.513101505603654	2	FACETS	0.86	0.811	0.908	0.86	0.811	0.908	CLONAL	2	TRUE	0	0.513101505603654	2		732	560	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11022908	11022908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768673985	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	88	755	1	ENST00000327064.4:c.607G>A	p.Ala203Thr	p.A203T	ENST00000327064	NM_199141.1	203	Gcc/Acc	5/16	0.336947893095607	3	FACETS	0.62	0.549	0.696	0.31	0.274	0.348	SUBCLONAL	1	TRUE	1	0.513101505603654	3		756	695	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266989	18266990	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	30	296	1	ENST00000222254.8:c.300_301delinsTT	p.Arg101Cys	p.R101C	ENST00000222254	NM_005027.3	100	ccCCgt/ccTTgt	2/16	0.336947893095607	3	FACETS	0.653	0.529	0.792	0.327	0.264	0.396	SUBCLONAL	1	TRUE	1	0.513101505603654	3		297	225	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308119	30308119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	114	577	0	ENST00000262643.3:c.256G>A	p.Val86Ile	p.V86I	ENST00000262643	NM_001238.2	86	Gtt/Att	5/12	0.336947893095607	3	FACETS	1	0.967	1	0.576	0.521	0.633	CLONAL	1	TRUE	1	0.513101505603654	3		577	485	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213480	36213480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	111	803	1	ENST00000222270.7:c.2582C>T	p.Ser861Phe	p.S861F	ENST00000222270	NM_014727.1	861	tCc/tTc	5/37	0.336947893095607	3	FACETS	0.813	0.731	0.898	0.406	0.365	0.449	CLONAL	1	TRUE	1	0.513101505603654	3		804	669	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46611762	46611762	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	160	554	0	ENST00000263734.3:c.2576G>A	p.Gly859Glu	p.G859E	ENST00000263734	NM_001430.4	859	gGa/gAa	16/16	0.227285486106902	5	FACETS	0.908	0.836	0.982	0.605	0.557	0.655	INDETERMINATE	2	TRUE	2	0.513101505603654	5		554	608	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380510	31380510	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	161	531	0	ENST00000328111.2:c.1000G>A	p.Glu334Lys	p.E334K	ENST00000328111	NM_006892.3	334	Gag/Aag	9/23	0.298131487315182	5	FACETS	0.951	0.876	1	0.634	0.584	0.685	INDETERMINATE	2	TRUE	2	0.513101505603654	5		531	584	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038230	30038231	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	71	463	0	ENST00000338641.4:c.403_404delinsTT	p.Pro135Phe	p.P135F	ENST00000338641	NM_000268.3	135	CCt/TTt	4/16	1	2	FACETS	0.577	0.504	0.654	0.577	0.504	0.654	SUBCLONAL	1	TRUE	1	0.513101505603654	2		463	480	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569786	41569786	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	45	212	0	ENST00000263253.7:c.4777G>A	p.Glu1593Lys	p.E1593K	ENST00000263253	NM_001429.3	1593	Gag/Aag	29/31	1	2	FACETS	0.769	0.653	0.895	0.769	0.653	0.895	SUBCLONAL	1	TRUE	1	0.513101505603654	2		212	228	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967345	134967345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	129	416	0	ENST00000398015.3:c.2684C>T	p.Thr895Ile	p.T895I	ENST00000398015	NM_004441.4	895	aCc/aTc	14/16	0.440636026789723	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.513101505603654	1		416	288	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80063932	80063932	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	91	415	0	ENST00000265081.6:c.2077G>C	p.Ala693Pro	p.A693P	ENST00000265081	NM_002439.4	693	Gct/Cct	14/24	0.227285486106902	5	FACETS	1	0.932	1	0.355	0.316	0.397	INDETERMINATE	1	TRUE	2	0.513101505603654	5		415	589	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524651	176524651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	93	598	0	ENST00000292408.4:c.2383C>T	p.Pro795Ser	p.P795S	ENST00000292408	NM_213647.1	795	Ccc/Tcc	18/18	0.398712450099056	3	FACETS	0.853	0.761	0.951	0.426	0.38	0.476	CLONAL	1	TRUE	1	0.513101505603654	3		598	534	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721003	176721003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	141	515	1	ENST00000439151.2:c.6634C>T	p.Pro2212Ser	p.P2212S	ENST00000439151	NM_022455.4	2212	Cct/Tct	23/23	0.398712450099056	3	FACETS	1	0.988	1	0.739	0.679	0.802	CLONAL	1	TRUE	1	0.513101505603654	3		516	467	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663707	117663707	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1489503636	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	105	273	0	ENST00000368508.3:c.4525G>A	p.Glu1509Lys	p.E1509K	ENST00000368508	NM_002944.2	1509	Gaa/Aaa	28/43	0.298131487315182	5	FACETS	0.812	0.732	0.896	0.541	0.488	0.597	INDETERMINATE	2	TRUE	2	0.513101505603654	5		273	446	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674218	117674218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	226	616	0	ENST00000368508.3:c.4256C>T	p.Ser1419Phe	p.S1419F	ENST00000368508	NM_002944.2	1419	tCc/tTc	26/43	0.298131487315182	5	FACETS	0.907	0.847	0.97	0.605	0.564	0.647	INDETERMINATE	2	TRUE	2	0.513101505603654	5		616	859	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517395	157517395	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	154	526	0	ENST00000346085.5:c.3959A>G	p.Asn1320Ser	p.N1320S	ENST00000346085	NM_020732.3	1320	aAc/aGc	16/20	0.192891732291721	5	FACETS	0.858	0.788	0.93	0.572	0.525	0.62	INDETERMINATE	2	TRUE	2	0.513101505603654	5		526	619	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846411	128846412	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	115	479	2	ENST00000249373.3:c.1247_1248delinsAA	p.Gly416Glu	p.G416E	ENST00000249373	NM_005631.4	416	gGC/gAA	6/12	0.298131487315182	5	FACETS	0.842	0.763	0.925	0.561	0.508	0.617	INDETERMINATE	2	TRUE	2	0.513101505603654	5		481	471	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27172698	27172698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	72	579	0	ENST00000380036.4:c.713G>A	p.Gly238Glu	p.G238E	ENST00000380036	NM_000459.3	238	gGa/gAa	5/23	1	2	FACETS	0.636	0.558	0.72	0.636	0.558	0.72	SUBCLONAL	1	TRUE	1	0.513101505603654	2		579	441	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759654	133759655	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	57	572	1	ENST00000318560.5:c.1977_1978delinsTT	p.Pro660Ser	p.P660S	ENST00000318560	NM_005157.4	659	tcCCca/tcTTca	11/11	1	2	FACETS	0.694	0.599	0.797	0.694	0.599	0.797	SUBCLONAL	1	TRUE	1	0.513101505603654	2		573	320	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412291	139412291	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	97	750	0	ENST00000277541.6:c.1354G>T	p.Asp452Tyr	p.D452Y	ENST00000277541	NM_017617.3	452	Gac/Tac	8/34	1	2	FACETS	0.736	0.658	0.817	0.736	0.658	0.817	SUBCLONAL	1	TRUE	1	0.513101505603654	2		750	514	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349220	70349220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	206	270	0	ENST00000374080.3:c.3632C>T	p.Ser1211Phe	p.S1211F	ENST00000374080		1211	tCc/tTc	26/45	0.462096198400237	2	FACETS	0.989	0.931	1			1	CLONAL	2	TRUE	NA	0.513101505603654	2		270	406	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	54	215	0				ENST00000310581	NM_198253.2	-/1132			0.34635824105645	1	FACETS	0.945	0.823	1	0.945	0.823	1	CLONAL	1	TRUE	0	0.516871034240336	1		215	164	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913381	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	152	441	0	ENST00000304494.5:c.322G>A	p.Asp108Asn	p.D108N	ENST00000304494	NM_000077.4	108	Gat/Aat	2/3	0.51641478928805	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.516871034240336	1		441	303	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	12	413	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.193	0.135	0.264	0.193	0.135	0.264	SUBCLONAL	1	TRUE	1	0.516871034240336	2		413	241	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781386	135781386	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203549	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	133	834	1	ENST00000298552.3:c.1579C>T	p.Gln527Ter	p.Q527*	ENST00000298552	NM_001162426.1	527	Cag/Tag	15/23	0.51641478928805	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.516871034240336	1		835	316	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56867273	56867273	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	21	531	0	ENST00000308159.5:c.1492G>C	p.Glu498Gln	p.E498Q	ENST00000308159	NM_014669.4	498	Gag/Cag	13/22	0.516871034240336	1	FACETS	0.22	0.169	0.279	0.22	0.169	0.279	SUBCLONAL	1	TRUE	0	0.516871034240336	1		531	274	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551935	150551946	+	inframe_deletion	In_Frame_Del	DEL	GCCGGCCCCCAA	GCCGGCCCCCAA	-	rs779327179	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	135	687	7	ENST00000369026.2:c.61_72del	p.Leu21_Gly24del	p.L21_G24del	ENST00000369026	NM_021960.4	21	TTGGGGGCCGGC/-	1/3	0.516871034240336	8	FACETS	0.792	0.72	0.868			1	SUBCLONAL	2	TRUE	NA	0.516871034240336	8		694	841	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651106	206651106	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148172544	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	245	849	0	ENST00000367120.3:c.716C>T	p.Thr239Met	p.T239M	ENST00000367120	NM_014002.3	239	aCg/aTg	8/22	0.379492704814739	4	FACETS	0.838	0.79	0.886	1	0.991	1	CLONAL	3	TRUE	2	0.516871034240336	4		849	572	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032069	26032069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	148	566	0	ENST00000244661.2:c.220G>A	p.Glu74Lys	p.E74K	ENST00000244661	NM_003537.3	74	Gaa/Aaa	1/1	0.516871034240336	7	FACETS	0.848	0.775	0.924	0.424	0.387	0.462	CLONAL	2	TRUE	3	0.516871034240336	7		566	774	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868168	45868168	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	176	1014	0	ENST00000391945.4:c.522C>G	p.Ile174Met	p.I174M	ENST00000391945	NM_000400.3	174	atC/atG	7/23	0.37236845175139	4	FACETS	1	0.95	1			1	CLONAL	2	TRUE	NA	0.516871034240336	4		1014	502	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772254	68772254	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	216	920	2	ENST00000261769.5:c.103G>T	p.Glu35Ter	p.E35*	ENST00000261769	NM_004360.3	35	Gag/Tag	2/16	0.516871034240336	1	FACETS	0.789	0.746	0.831	1	0.994	1	SUBCLONAL	2	TRUE	0	0.516871034240336	1		922	393	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056200	27056201	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	223	739	0	ENST00000324856.7:c.1196_1197del	p.Asn399ThrfsTer223	p.N399Tfs*223	ENST00000324856	NM_006015.4	399	aAC/a	2/20	0.516871034240336	4	FACETS	0.931	0.871	0.993	0.931	0.871	0.993	CLONAL	2	TRUE	2	0.516871034240336	4		739	703	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400984	72400984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	81	522	0	ENST00000357731.5:c.187G>A	p.Glu63Lys	p.E63K	ENST00000357731	NM_173808.2	63	Gaa/Aaa	2/7	0.194843623885559	3	FACETS	1	0.968	1	0.626	0.557	0.699	INDETERMINATE	1	TRUE	1	0.516871034240336	3		522	315	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107221	193107221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	81	452	0	ENST00000367435.3:c.430G>A	p.Glu144Lys	p.E144K	ENST00000367435	NM_024529.4	144	Gag/Aag	6/17	0.379492704814739	4	FACETS	1	0.971	1	0.653	0.579	0.731	CLONAL	1	TRUE	2	0.516871034240336	4		452	364	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945654	206945654	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	128	740	0	ENST00000423557.1:c.127G>C	p.Asp43His	p.D43H	ENST00000423557	NM_000572.2	43	Gat/Cat	1/5	0.379492704814739	4	FACETS	0.953	0.864	1	0.477	0.432	0.524	CLONAL	1	TRUE	2	0.516871034240336	4		740	788	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948464	71948464	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769801718	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	303	1032	1	ENST00000298229.2:c.3176C>T	p.Pro1059Leu	p.P1059L	ENST00000298229	NM_001567.3	1059	cCg/cTg	26/28	0.454892951400498	4	FACETS	0.885	0.84	0.93	1	0.993	1	CLONAL	3	TRUE	2	0.516871034240336	4		1033	670	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917686	94917686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	134	870	0	ENST00000536441.1:c.835G>A	p.Glu279Lys	p.E279K	ENST00000536441	NM_144665.3	279	Gaa/Aaa	6/10	0.454892951400498	4	FACETS	1	0.929	1	0.513	0.466	0.562	CLONAL	1	TRUE	2	0.516871034240336	4		870	767	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418709	49418709	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	100	671	0	ENST00000301067.7:c.15805G>C	p.Glu5269Gln	p.E5269Q	ENST00000301067	NM_003482.3	5269	Gag/Cag	49/54	0.37236845175139	4	FACETS	1	0.946	1			1	CLONAL	1	TRUE	NA	0.516871034240336	4		671	540	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054046	42054046	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	71	433	0	ENST00000219905.7:c.7508C>T	p.Ser2503Leu	p.S2503L	ENST00000219905	NM_001164273.1	2503	tCa/tTa	21/24	0.241035844749288	4	FACETS	1	0.963	1	0.63	0.553	0.71	INDETERMINATE	1	TRUE	2	0.516871034240336	4		433	331	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641001	23641001	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs146218439	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	36	741	0	ENST00000261584.4:c.2474G>C	p.Arg825Thr	p.R825T	ENST00000261584	NM_024675.3	825	aGa/aCa	5/13	0.194843623885559	3	FACETS	0.417	0.343	0.501	0.209	0.171	0.251	INDETERMINATE	1	TRUE	1	0.516871034240336	3		741	420	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763332	59763332	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	43	1004	1	ENST00000259008.2:c.2770G>T	p.Glu924Ter	p.E924*	ENST00000259008	NM_032043.2	924	Gaa/Taa	19/20	0.194843623885559	3	FACETS	0.365	0.305	0.432	0.182	0.152	0.216	INDETERMINATE	1	TRUE	1	0.516871034240336	3		1005	574	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626850	14626850	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749934387	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	175	942	1	ENST00000254322.2:c.925G>A	p.Glu309Lys	p.E309K	ENST00000254322	NM_006145.1	309	Gag/Aag	3/3	1	2	FACETS	0.873	0.805	0.943	0.873	0.805	0.943	CLONAL	1	TRUE	1	0.516871034240336	2		943	776	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61753598	61753598	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	97	826	0	ENST00000401558.2:c.185G>C	p.Arg62Thr	p.R62T	ENST00000401558	NM_003400.3	62	aGa/aCa	3/25	1	2	FACETS	0.711	0.636	0.79	0.711	0.636	0.79	SUBCLONAL	1	TRUE	1	0.516871034240336	2		826	528	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380431	31380431	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	88	527	0	ENST00000328111.2:c.922-1G>A		p.X308_splice	ENST00000328111	NM_006892.3	308			1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.516871034240336	2		527	310	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267844	46267844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	130	800	0	ENST00000371998.3:c.2605C>T	p.Pro869Ser	p.P869S	ENST00000371998		869	Cca/Tca	14/23	NA	2	FACETS	0.971	0.886	1			1	INDETERMINATE	1	TRUE	NA	0.516871034240336	2		800	518	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24134024	24134024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	49	662	0	ENST00000263121.7:c.175G>A	p.Glu59Lys	p.E59K	ENST00000263121	NM_003073.3	59	Gag/Aag	2/9	1	2	FACETS	0.476	0.404	0.555	0.476	0.404	0.555	SUBCLONAL	1	TRUE	1	0.516871034240336	2		662	398	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176327	24176327	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1320049303	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	138	858	0	ENST00000263121.7:c.1119-1G>A		p.X373_splice	ENST00000263121	NM_003073.3	373			1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.516871034240336	2		858	403	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091193	29091193	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	55	339	0	ENST00000328354.6:c.1297C>G	p.Gln433Glu	p.Q433E	ENST00000328354	NM_007194.3	433	Caa/Gaa	12/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.516871034240336	2		339	148	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091764	29091764	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555913751	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	36	576	0	ENST00000328354.6:c.1193C>T	p.Ser398Phe	p.S398F	ENST00000328354	NM_007194.3	398	tCt/tTt	11/15	1	2	FACETS	0.496	0.409	0.592	0.496	0.409	0.592	SUBCLONAL	1	TRUE	1	0.516871034240336	2		576	281	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091821	29091821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267606211	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	34	552	1	ENST00000328354.6:c.1136C>T	p.Ser379Phe	p.S379F	ENST00000328354	NM_007194.3	379	tCt/tTt	11/15	1	2	FACETS	0.439	0.359	0.527	0.439	0.359	0.527	SUBCLONAL	1	TRUE	1	0.516871034240336	2		553	300	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447396	12447396	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553647989	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	156	667	0	ENST00000287820.6:c.635G>A	p.Arg212Gln	p.R212Q	ENST00000287820	NM_015869.4	212	cGg/cAg	5/7	0.287520868389602	4	FACETS	0.788	0.725	0.853	0.788	0.725	0.853	INDETERMINATE	2	TRUE	2	0.516871034240336	4		667	581	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447412	12447412	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	177	735	0	ENST00000287820.6:c.651G>C	p.Glu217Asp	p.E217D	ENST00000287820	NM_015869.4	217	gaG/gaC	5/7	0.287520868389602	4	FACETS	0.813	0.752	0.875	0.813	0.752	0.875	INDETERMINATE	2	TRUE	2	0.516871034240336	4		735	639	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458395	12458395	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	168	865	0	ENST00000287820.6:c.1012G>C	p.Asp338His	p.D338H	ENST00000287820	NM_015869.4	338	Gac/Cac	6/7	0.287520868389602	4	FACETS	1	0.989	1	0.74	0.683	0.8	INDETERMINATE	1	TRUE	2	0.516871034240336	4		865	666	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458599	12458599	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1400424764	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	175	804	0	ENST00000287820.6:c.1216G>C	p.Glu406Gln	p.E406Q	ENST00000287820	NM_015869.4	406	Gaa/Caa	6/7	0.287520868389602	4	FACETS	0.826	0.764	0.889	0.826	0.764	0.889	INDETERMINATE	2	TRUE	2	0.516871034240336	4		804	622	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542708	187542708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	73	659	0	ENST00000441802.2:c.5032G>A	p.Glu1678Lys	p.E1678K	ENST00000441802	NM_005245.3	1678	Gaa/Aaa	10/27	0.516871034240336	1	FACETS	0.997	0.888	1	0.997	0.888	1	CLONAL	1	TRUE	0	0.516871034240336	1		659	210	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542729	187542729	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	88	659	0	ENST00000441802.2:c.5011G>C	p.Glu1671Gln	p.E1671Q	ENST00000441802	NM_005245.3	1671	Gaa/Caa	10/27	0.516871034240336	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.516871034240336	1		659	231	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099209	157099209	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375486386	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	143	708	1	ENST00000346085.5:c.146C>T	p.Ser49Phe	p.S49F	ENST00000346085	NM_020732.3	49	tCt/tTt	1/20	0.362396719491048	2	FACETS	1	0.973	1	0.57	0.524	0.619	CLONAL	1	TRUE	0	0.516871034240336	2		709	485	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224457	55224457	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	93	741	0	ENST00000275493.2:c.1139C>G	p.Ser380Cys	p.S380C	ENST00000275493	NM_005228.3	380	tCc/tGc	10/28	0.161559081327953	1	FACETS	0.837	0.752	0.925	0.837	0.752	0.925	INDETERMINATE	1	TRUE	0	0.516871034240336	1		741	319	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845271	151845271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	86	579	1	ENST00000262189.6:c.13741G>A	p.Glu4581Lys	p.E4581K	ENST00000262189	NM_170606.2	4581	Gaa/Aaa	52/59	0.241035844749288	4	FACETS	1	0.979	1	0.723	0.645	0.805	INDETERMINATE	1	TRUE	2	0.516871034240336	4		580	349	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971003	21971003	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1563888963	NA	P-0024544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	219	761	1	ENST00000304494.5:c.355G>A	p.Glu119Lys	p.E119K	ENST00000304494	NM_000077.4	119	Gag/Aag	2/3	0.51641478928805	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.516871034240336	1		762	440	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	28	215	0				ENST00000310581	NM_198253.2	-/1132			0.187314236978952	0	FACETS	1	0.852	1			1	CLONAL	1	TRUE	0	0.28620285234466	0		215	132	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0024676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	145	923	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.28620285234466	1	FACETS	0.832	0.763	0.902	1	0.99	1	CLONAL	2	TRUE	0	0.28620285234466	1		923	522	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974769	21974772	+	frameshift_variant	Frame_Shift_Del	DEL	CGGC	CGGC	-	novel	NA	P-0024676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	25	161	0	ENST00000304494.5:c.55_58del	p.Ala19ArgfsTer6	p.A19Rfs*6	ENST00000304494	NM_000077.4	19	GCCGcg/cg	1/3	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.28620285234466	2		161	128	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213842	66213842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	111	612	1	ENST00000273854.3:c.2588G>A	p.Ser863Asn	p.S863N	ENST00000273854	NM_004439.5	863	aGt/aAt	15/18	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.28620285234466	2		613	670	SUCCESS
APC	324	MSKCC	GRCh37	5	112173600	112173600	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1060503310	NA	P-0024676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	45	372	0	ENST00000257430.4:c.2309C>G	p.Ser770Ter	p.S770*	ENST00000257430	NM_000038.5	770	tCa/tGa	16/16	0.28620285234466	5	FACETS	0.863	0.725	1	0.216	0.181	0.254	CLONAL	1	TRUE	1	0.28620285234466	5		372	521	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784000	120784000	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1196203379	NA	P-0024676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	31	757	0	ENST00000257552.2:c.985G>C	p.Val329Leu	p.V329L	ENST00000257552	NM_002442.3	329	Gtc/Ctc	13/15	1	2	FACETS	0.449	0.363	0.548	0.449	0.363	0.548	SUBCLONAL	1	TRUE	1	0.28620285234466	2		757	482	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687589	29687589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	111	750	1	ENST00000356175.3:c.8182G>A	p.Glu2728Lys	p.E2728K	ENST00000356175	NM_000267.3	2728	Gaa/Aaa	56/57	0.28620285234466	3	FACETS	1	0.923	1	0.516	0.463	0.572	CLONAL	1	TRUE	1	0.28620285234466	3		751	859	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225362543	225362543	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	53	605	0	ENST00000264414.4:c.1634G>T	p.Gly545Val	p.G545V	ENST00000264414	NM_003590.4	545	gGt/gTt	12/16	1	2	FACETS	0.681	0.58	0.791	0.681	0.58	0.791	SUBCLONAL	1	TRUE	1	0.28620285234466	2		605	544	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458286	12458286	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	40	628	0	ENST00000287820.6:c.903G>C	p.Gln301His	p.Q301H	ENST00000287820	NM_015869.4	301	caG/caC	6/7	1	2	FACETS	0.487	0.404	0.58	0.487	0.404	0.58	SUBCLONAL	1	TRUE	1	0.28620285234466	2		628	574	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193769	106193769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	81	308	0	ENST00000380013.4:c.4231G>A	p.Glu1411Lys	p.E1411K	ENST00000380013	NM_001127208.2	1411	Gag/Aag	10/11	0.22294321368902	4	FACETS	0.884	0.783	0.991	0.884	0.783	0.991	CLONAL	2	TRUE	2	0.28620285234466	4		308	412	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973833	131973833	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	26	498	0	ENST00000265335.6:c.3536G>C	p.Arg1179Thr	p.R1179T	ENST00000265335		1179	aGg/aCg	23/25	NA	2	FACETS	0.417	0.329	0.517			1	INDETERMINATE	1	TRUE	NA	0.28620285234466	2		498	436	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971066	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGCACGTCCAGCCGCGCCCCGGCCCGGTG	CGCGCACGTCCAGCCGCGCCCCGGCCCGGTG	-	novel	NA	P-0024676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	92	216	0	ENST00000304494.5:c.292_322del	p.His98MetfsTer38	p.H98Mfs*38	ENST00000304494	NM_000077.4	98	CACCGGGCCGGGGCGCGGCTGGACGTGCGCGat/at	2/3	1	2	FACETS	1	0.957	1	1	0.988	1	CLONAL	2	TRUE	1	0.28620285234466	2		216	287	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15808631	15808631	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	53	564	0	ENST00000307771.7:c.13G>C	p.Glu5Gln	p.E5Q	ENST00000307771	NM_005089.3	5	Gag/Cag	1/11	1	2	FACETS	0.897	0.767	1	0.897	0.767	1	CLONAL	1	TRUE	1	0.28620285234466	2		564	413	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	83	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.92	0.824	1	0.92	0.824	1	CLONAL	1	TRUE	1	0.704782798284537	2		215	256	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	53	596	1	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	1	2	FACETS	0.284	0.242	0.33	0.284	0.242	0.33	SUBCLONAL	1	TRUE	1	0.704782798284537	2		597	529	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959151	28959151	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1418663249	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	22	263	0	ENST00000282397.4:c.1987C>T	p.Leu663Phe	p.L663F	ENST00000282397	NM_002019.4	663	Ctc/Ttc	14/30	1	2	FACETS	0.178	0.137	0.225	0.178	0.137	0.225	SUBCLONAL	1	TRUE	1	0.704782798284537	2		263	351	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587167	189587167	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1209841422	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	40	325	0	ENST00000264731.3:c.1184C>T	p.Ser395Phe	p.S395F	ENST00000264731	NM_003722.4	395	tCc/tTc	9/14	1	2	FACETS	0.223	0.184	0.265	0.223	0.184	0.265	SUBCLONAL	1	TRUE	1	0.704782798284537	2		325	510	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99452056	99452056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	29	364	0	ENST00000268035.6:c.1390G>A	p.Glu464Lys	p.E464K	ENST00000268035	NM_000875.3	464	Gaa/Aaa	6/21	1	2	FACETS	0.199	0.159	0.244	0.199	0.159	0.244	SUBCLONAL	1	TRUE	1	0.704782798284537	2		364	414	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920355	50920355	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	30	544	1	ENST00000440232.2:c.3120+1G>A		p.X1040_splice	ENST00000440232	NM_002691.3	1040			NA	2	FACETS	0.174	0.139	0.213			1	INDETERMINATE	1	TRUE	NA	0.704782798284537	2		545	490	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494650	2494650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762829374	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	32	561	0	ENST00000355716.4:c.790G>A	p.Val264Ile	p.V264I	ENST00000355716	NM_003820.2	264	Gtc/Atc	8/8	NA	2	FACETS	0.224	0.182	0.272			1	INDETERMINATE	1	TRUE	NA	0.704782798284537	2		561	405	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777894	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	8	700	0	ENST00000361445.4:c.6644C>T	p.Ser2215Phe	p.S2215F	ENST00000361445	NM_004958.3	2215	tCt/tTt	47/58	0.704782798284537	1	FACETS	0.05	0.032	0.074	0.05	0.032	0.074	SUBCLONAL	1	TRUE	0	0.704782798284537	1		700	293	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11276215	11276215	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	31	364	0	ENST00000361445.4:c.3107C>T	p.Thr1036Ile	p.T1036I	ENST00000361445	NM_004958.3	1036	aCc/aTc	20/58	0.704782798284537	1	FACETS	0.209	0.17	0.254	0.209	0.17	0.254	SUBCLONAL	1	TRUE	0	0.704782798284537	1		364	272	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294267	11294267	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1187856229	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	44	394	0	ENST00000361445.4:c.2264G>A	p.Arg755His	p.R755H	ENST00000361445	NM_004958.3	755	cGc/cAc	14/58	0.704782798284537	1	FACETS	0.28	0.236	0.328	0.28	0.236	0.328	SUBCLONAL	1	TRUE	0	0.704782798284537	1		394	289	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11301736	11301736	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	20	392	0	ENST00000361445.4:c.1415G>A	p.Arg472Lys	p.R472K	ENST00000361445	NM_004958.3	472	aGg/aAg	10/58	0.704782798284537	1	FACETS	0.166	0.127	0.212	0.166	0.127	0.212	SUBCLONAL	1	TRUE	0	0.704782798284537	1		392	221	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255739	16255739	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778866039	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	19	372	0	ENST00000375759.3:c.3004G>A	p.Val1002Ile	p.V1002I	ENST00000375759	NM_015001.2	1002	Gtc/Atc	11/15	NA	2	FACETS	0.148	0.112	0.19			1	INDETERMINATE	1	TRUE	NA	0.704782798284537	2		372	365	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256999	16256999	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388540196	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	38	461	0	ENST00000375759.3:c.4264C>T	p.Leu1422Phe	p.L1422F	ENST00000375759	NM_015001.2	1422	Ctc/Ttc	11/15	NA	2	FACETS	0.181	0.149	0.217			1	INDETERMINATE	1	TRUE	NA	0.704782798284537	2		461	595	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023358	27023358	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	15	172	0	ENST00000324856.7:c.464G>A	p.Gly155Asp	p.G155D	ENST00000324856	NM_006015.4	155	gGc/gAc	1/20	1	2	FACETS	0.235	0.172	0.31	0.235	0.172	0.31	SUBCLONAL	1	TRUE	1	0.704782798284537	2		172	181	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099302	27099302	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	22	383	0	ENST00000324856.7:c.3540-1G>A		p.X1180_splice	ENST00000324856	NM_006015.4	1180			1	2	FACETS	0.159	0.123	0.202	0.159	0.123	0.202	SUBCLONAL	1	TRUE	1	0.704782798284537	2		383	392	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101280	27101280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	22	460	0	ENST00000324856.7:c.4562C>T	p.Pro1521Leu	p.P1521L	ENST00000324856	NM_006015.4	1521	cCc/cTc	18/20	1	2	FACETS	0.163	0.126	0.206	0.163	0.126	0.206	SUBCLONAL	1	TRUE	1	0.704782798284537	2		460	383	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598357	28598357	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748874332	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	30	459	0	ENST00000253063.3:c.329C>T	p.Ser110Phe	p.S110F	ENST00000253063	NM_031459.4	110	tCc/tTc	3/10	1	2	FACETS	0.168	0.135	0.206	0.168	0.135	0.206	SUBCLONAL	1	TRUE	1	0.704782798284537	2		459	507	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932910	36932910	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	22	441	0	ENST00000361632.4:c.1961G>A	p.Arg654Lys	p.R654K	ENST00000361632		654	aGg/aAg	15/16	1	2	FACETS	0.15	0.116	0.191	0.15	0.116	0.191	SUBCLONAL	1	TRUE	1	0.704782798284537	2		441	415	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812237	43812237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	37	427	0	ENST00000372470.3:c.1102G>A	p.Val368Met	p.V368M	ENST00000372470	NM_005373.2	368	Gtg/Atg	7/12	1	2	FACETS	0.213	0.175	0.255	0.213	0.175	0.255	SUBCLONAL	1	TRUE	1	0.704782798284537	2		427	493	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814636	43814636	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1169744090	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	28	351	1	ENST00000372470.3:c.1431G>A	p.Trp477Ter	p.W477*	ENST00000372470	NM_005373.2	477	tgG/tgA	9/12	1	2	FACETS	0.224	0.179	0.275	0.224	0.179	0.275	SUBCLONAL	1	TRUE	1	0.704782798284537	2		352	355	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799243	45799243	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	24	299	0	ENST00000450313.1:c.190G>A	p.Ala64Thr	p.A64T	ENST00000450313	NM_012222.2	64	Gcc/Acc	3/16	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.704782798284537	NA		299	306	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248510	59248510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	42	423	0	ENST00000371222.2:c.233G>A	p.Arg78His	p.R78H	ENST00000371222	NM_002228.3	78	cGc/cAc	1/1	1	2	FACETS	0.254	0.212	0.301	0.254	0.212	0.301	SUBCLONAL	1	TRUE	1	0.704782798284537	2		423	469	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241978	72241978	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	34	218	0	ENST00000357731.5:c.412C>T	p.Pro138Ser	p.P138S	ENST00000357731	NM_173808.2	138	Cct/Tct	3/7	1	2	FACETS	0.251	0.205	0.302	0.251	0.205	0.302	SUBCLONAL	1	TRUE	1	0.704782798284537	2		218	385	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268925	115268925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	53	502	0	ENST00000438362.2:c.1685C>T	p.Ser562Phe	p.S562F	ENST00000438362	NM_001242891.1	562	tCc/tTc	14/20	1	2	FACETS	0.186	0.158	0.217	0.186	0.158	0.217	SUBCLONAL	1	TRUE	1	0.704782798284537	2		502	809	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458347	120458347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768047492	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	30	382	0	ENST00000256646.2:c.6998C>T	p.Ala2333Val	p.A2333V	ENST00000256646	NM_024408.3	2333	gCg/gTg	34/34	1	2	FACETS	0.209	0.168	0.255	0.209	0.168	0.255	SUBCLONAL	1	TRUE	1	0.704782798284537	2		382	408	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120496253	120496253	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	43	374	0	ENST00000256646.2:c.2278G>A	p.Glu760Lys	p.E760K	ENST00000256646	NM_024408.3	760	Gaa/Aaa	14/34	1	2	FACETS	0.187	0.156	0.222	0.187	0.156	0.222	SUBCLONAL	1	TRUE	1	0.704782798284537	2		374	653	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120529622	120529622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	55	369	0	ENST00000256646.2:c.835G>A	p.Val279Ile	p.V279I	ENST00000256646	NM_024408.3	279	Gtc/Atc	5/34	1	2	FACETS	0.224	0.191	0.261	0.224	0.191	0.261	SUBCLONAL	1	TRUE	1	0.704782798284537	2		369	696	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841524	156841524	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	41	549	0	ENST00000524377.1:c.827T>C	p.Val276Ala	p.V276A	ENST00000524377	NM_002529.3	276	gTc/gCc	7/17	1	2	FACETS	0.186	0.155	0.222	0.186	0.155	0.222	SUBCLONAL	1	TRUE	1	0.704782798284537	2		549	624	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746119	162746119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	20	230	0	ENST00000367921.3:c.2242G>A	p.Val748Met	p.V748M	ENST00000367921	NM_006182.2	748	Gtg/Atg	16/18	1	2	FACETS	0.142	0.108	0.182	0.142	0.108	0.182	SUBCLONAL	1	TRUE	1	0.704782798284537	2		230	400	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175996717	175996717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	29	335	0	ENST00000367669.3:c.1720G>A	p.Gly574Ser	p.G574S	ENST00000367669	NM_022457.5	574	Ggc/Agc	15/20	1	2	FACETS	0.149	0.119	0.183	0.149	0.119	0.183	SUBCLONAL	1	TRUE	1	0.704782798284537	2		335	554	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193181209	193181209	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	32	253	0	ENST00000367435.3:c.1045C>T	p.Pro349Ser	p.P349S	ENST00000367435	NM_024529.4	349	Cct/Tct	12/17	1	2	FACETS	0.16	0.129	0.195	0.16	0.129	0.195	SUBCLONAL	1	TRUE	1	0.704782798284537	2		253	568	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193202136	193202136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	29	247	0	ENST00000367435.3:c.1168G>A	p.Asp390Asn	p.D390N	ENST00000367435	NM_024529.4	390	Gat/Aat	14/17	1	2	FACETS	0.193	0.155	0.237	0.193	0.155	0.237	SUBCLONAL	1	TRUE	1	0.704782798284537	2		247	426	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226568808	226568808	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	77	514	0	ENST00000366794.5:c.1261G>A	p.Gly421Arg	p.G421R	ENST00000366794	NM_001618.3	421	Ggg/Agg	9/23	1	2	FACETS	0.319	0.28	0.362	0.319	0.28	0.362	SUBCLONAL	1	TRUE	1	0.704782798284537	2		514	684	SUCCESS
FH	2271	MSKCC	GRCh37	1	241665865	241665865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	28	296	0	ENST00000366560.3:c.1114G>A	p.Val372Met	p.V372M	ENST00000366560	NM_000143.3	372	Gtg/Atg	8/10	1	2	FACETS	0.164	0.13	0.202	0.164	0.13	0.202	SUBCLONAL	1	TRUE	1	0.704782798284537	2		296	485	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845643	63845643	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	26	203	0	ENST00000279873.7:c.1382C>T	p.Pro461Leu	p.P461L	ENST00000279873	NM_032199.2	461	cCc/cTc	9/10	NA	2	FACETS	0.338	0.269	0.417			1	INDETERMINATE	1	TRUE	NA	0.704782798284537	2		203	218	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332477	70332477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142008363	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	26	487	0	ENST00000373644.4:c.382G>A	p.Val128Ile	p.V128I	ENST00000373644	NM_030625.2	128	Gtt/Att	2/12	0.704782798284537	1	FACETS	0.139	0.11	0.173	0.139	0.11	0.173	SUBCLONAL	1	TRUE	0	0.704782798284537	1		487	343	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711891	89711891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	157	305	0	ENST00000371953.3:c.509G>A	p.Ser170Asn	p.S170N	ENST00000371953	NM_000314.4	170	aGt/aAt	6/9	0.704782798284537	1	FACETS	0.978	0.915	1	0.978	0.915	1	CLONAL	1	TRUE	0	0.704782798284537	1		305	295	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156713	2156713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	36	488	1	ENST00000434045.2:c.209C>T	p.Thr70Ile	p.T70I	ENST00000434045	NM_001127598.1	70	aCc/aTc	3/5	1	2	FACETS	0.263	0.216	0.315	0.263	0.216	0.315	SUBCLONAL	1	TRUE	1	0.704782798284537	2		489	389	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741895	17741895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1273747887	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	19	92	0	ENST00000250003.3:c.566G>A	p.Gly189Asp	p.G189D	ENST00000250003	NM_002478.4	189	gGc/gAc	1/3	1	2	FACETS	0.634	0.492	0.794	0.634	0.492	0.794	SUBCLONAL	1	TRUE	1	0.704782798284537	2		92	85	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742801	17742801	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	31	494	0	ENST00000250003.3:c.710-1G>A		p.X237_splice	ENST00000250003	NM_002478.4	237			1	2	FACETS	0.206	0.166	0.251	0.206	0.166	0.251	SUBCLONAL	1	TRUE	1	0.704782798284537	2		494	427	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129442	64129442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	28	591	0	ENST00000334205.4:c.874G>A	p.Ala292Thr	p.A292T	ENST00000334205	NM_003942.2	292	Gca/Aca	8/17	1	2	FACETS	0.179	0.142	0.22	0.179	0.142	0.22	SUBCLONAL	1	TRUE	1	0.704782798284537	2		591	445	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577385	64577385	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	40	503	0	ENST00000312049.6:c.197G>A	p.Ser66Asn	p.S66N	ENST00000312049	NM_130799.2	66	aGc/aAc	2/10	1	2	FACETS	0.255	0.212	0.303	0.255	0.212	0.303	SUBCLONAL	1	TRUE	1	0.704782798284537	2		503	445	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200309	67200309	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1170806235	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	19	427	0	ENST00000312629.5:c.616+1G>A		p.X206_splice	ENST00000312629	NM_003952.2	206			1	2	FACETS	0.152	0.115	0.196	0.152	0.115	0.196	SUBCLONAL	1	TRUE	1	0.704782798284537	2		427	355	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69458645	69458645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	37	331	0	ENST00000227507.2:c.460G>A	p.Ala154Thr	p.A154T	ENST00000227507	NM_053056.2	154	Gca/Aca	3/5	1	2	FACETS	0.273	0.225	0.327	0.273	0.225	0.327	SUBCLONAL	1	TRUE	1	0.704782798284537	2		331	384	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462789	69462789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	30	422	1	ENST00000227507.2:c.602C>T	p.Ser201Phe	p.S201F	ENST00000227507	NM_053056.2	201	tCc/tTc	4/5	1	2	FACETS	0.254	0.205	0.31	0.254	0.205	0.31	SUBCLONAL	1	TRUE	1	0.704782798284537	2		423	335	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94910947	94910947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1372388226	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	68	227	0	ENST00000536441.1:c.1183G>A	p.Asp395Asn	p.D395N	ENST00000536441	NM_144665.3	395	Gat/Aat	8/10	1	2	FACETS	0.441	0.384	0.501	0.441	0.384	0.501	SUBCLONAL	1	TRUE	1	0.704782798284537	2		227	438	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996890	100996890	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	31	339	0	ENST00000325455.5:c.1638-1G>A		p.X546_splice	ENST00000325455	NM_001202474.3	546			1	2	FACETS	0.156	0.125	0.19	0.156	0.125	0.19	SUBCLONAL	1	TRUE	1	0.704782798284537	2		339	565	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998909	100998909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	38	468	0	ENST00000325455.5:c.893C>T	p.Thr298Ile	p.T298I	ENST00000325455	NM_001202474.3	298	aCc/aTc	1/8	1	2	FACETS	0.256	0.211	0.305	0.256	0.211	0.305	SUBCLONAL	1	TRUE	1	0.704782798284537	2		468	422	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122645	108122645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786202469	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	43	422	0	ENST00000278616.4:c.1689G>A	p.Met563Ile	p.M563I	ENST00000278616	NM_000051.3	563	atG/atA	11/63	1	2	FACETS	0.164	0.137	0.195	0.164	0.137	0.195	SUBCLONAL	1	TRUE	1	0.704782798284537	2		422	743	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151870	108151870	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	40	341	1	ENST00000278616.4:c.3551G>A	p.Gly1184Glu	p.G1184E	ENST00000278616	NM_000051.3	1184	gGa/gAa	24/63	1	2	FACETS	0.163	0.135	0.194	0.163	0.135	0.194	SUBCLONAL	1	TRUE	1	0.704782798284537	2		342	697	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155193	108155193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	38	348	1	ENST00000278616.4:c.3986G>A	p.Gly1329Glu	p.G1329E	ENST00000278616	NM_000051.3	1329	gGa/gAa	26/63	1	2	FACETS	0.207	0.171	0.248	0.207	0.171	0.248	SUBCLONAL	1	TRUE	1	0.704782798284537	2		349	521	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204630	108204630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	31	222	1	ENST00000278616.4:c.7945G>A	p.Ala2649Thr	p.A2649T	ENST00000278616	NM_000051.3	2649	Gca/Aca	54/63	1	2	FACETS	0.183	0.148	0.224	0.183	0.148	0.224	SUBCLONAL	1	TRUE	1	0.704782798284537	2		223	480	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344147	118344147	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	45	426	0	ENST00000534358.1:c.2273G>A	p.Arg758Lys	p.R758K	ENST00000534358	NM_005933.3	758	aGa/aAa	3/36	1	2	FACETS	0.251	0.211	0.296	0.251	0.211	0.296	SUBCLONAL	1	TRUE	1	0.704782798284537	2		426	508	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373518	118373518	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	16	307	0	ENST00000534358.1:c.6911C>T	p.Ser2304Phe	p.S2304F	ENST00000534358	NM_005933.3	2304	tCc/tTc	27/36	1	2	FACETS	0.143	0.105	0.189	0.143	0.105	0.189	SUBCLONAL	1	TRUE	1	0.704782798284537	2		307	317	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376881	118376881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140200473	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	20	266	0	ENST00000534358.1:c.10274C>T	p.Ala3425Val	p.A3425V	ENST00000534358	NM_005933.3	3425	gCg/gTg	27/36	1	2	FACETS	0.209	0.16	0.267	0.209	0.16	0.267	SUBCLONAL	1	TRUE	1	0.704782798284537	2		266	271	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390332	118390332	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	23	351	0	ENST00000534358.1:c.11147-1G>A		p.X3716_splice	ENST00000534358	NM_005933.3	3716			1	2	FACETS	0.151	0.117	0.191	0.151	0.117	0.191	SUBCLONAL	1	TRUE	1	0.704782798284537	2		351	431	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169163	119169163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	47	366	0	ENST00000264033.4:c.2347G>A	p.Ala783Thr	p.A783T	ENST00000264033	NM_005188.3	783	Gcc/Acc	15/16	1	2	FACETS	0.266	0.224	0.312	0.266	0.224	0.312	SUBCLONAL	1	TRUE	1	0.704782798284537	2		366	502	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404879	404879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	43	410	0	ENST00000399788.2:c.4315C>T	p.Pro1439Ser	p.P1439S	ENST00000399788	NM_001042603.1	1439	Cct/Tct	26/28	NA	2	FACETS	0.199	0.166	0.235			1	INDETERMINATE	1	TRUE	NA	0.704782798284537	2		410	614	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023204	1023204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1369707039	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	28	386	0	ENST00000358495.3:c.1051C>T	p.Pro351Ser	p.P351S	ENST00000358495	NM_134424.2	351	Cca/Tca	11/12	NA	2	FACETS	0.158	0.125	0.195			1	INDETERMINATE	1	TRUE	NA	0.704782798284537	2		386	504	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466981	18466981	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376507510	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	33	348	1	ENST00000266497.5:c.1120G>A	p.Gly374Arg	p.G374R	ENST00000266497		374	Gga/Aga	5/31	NA	2	FACETS	0.144	0.116	0.175			1	INDETERMINATE	1	TRUE	NA	0.704782798284537	2		349	652	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636397	21636397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1298732040	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	45	474	0	ENST00000421138.2:c.613G>A	p.Glu205Lys	p.E205K	ENST00000421138		205	Gag/Aag	7/16	NA	2	FACETS	0.156	0.13	0.184			1	INDETERMINATE	1	TRUE	NA	0.704782798284537	2		474	821	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230775	46230775	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	16	240	0	ENST00000334344.6:c.1023+1G>A		p.X341_splice	ENST00000334344	NM_152641.2	341			NA	2	FACETS	0.155	0.114	0.205			1	INDETERMINATE	1	TRUE	NA	0.704782798284537	2		240	292	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245165	46245165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561939993	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	37	368	0	ENST00000334344.6:c.3259C>T	p.Pro1087Ser	p.P1087S	ENST00000334344	NM_152641.2	1087	Cct/Tct	15/21	NA	2	FACETS	0.213	0.175	0.255			1	INDETERMINATE	1	TRUE	NA	0.704782798284537	2		368	494	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246344	46246344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	33	285	0	ENST00000334344.6:c.4438G>A	p.Gly1480Arg	p.G1480R	ENST00000334344	NM_152641.2	1480	Gga/Aga	15/21	NA	2	FACETS	0.217	0.177	0.263			1	INDETERMINATE	1	TRUE	NA	0.704782798284537	2		285	431	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415656	49415656	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1057520667	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	19	257	0	ENST00000301067.7:c.16522-1G>A		p.X5508_splice	ENST00000301067	NM_003482.3	5508			NA	2	FACETS	0.189	0.143	0.243			1	INDETERMINATE	1	TRUE	NA	0.704782798284537	2		257	285	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420624	49420624	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	38	431	2	ENST00000301067.7:c.15125C>T	p.Ala5042Val	p.A5042V	ENST00000301067	NM_003482.3	5042	gCc/gTc	48/54	NA	2	FACETS	0.255	0.211	0.304			1	INDETERMINATE	1	TRUE	NA	0.704782798284537	2		433	423	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433991	49433991	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	26	546	0	ENST00000301067.7:c.7562C>T	p.Ser2521Phe	p.S2521F	ENST00000301067	NM_003482.3	2521	tCc/tTc	31/54	1	2	FACETS	0.156	0.123	0.194	0.156	0.123	0.194	SUBCLONAL	1	TRUE	1	0.704782798284537	2		546	472	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446482	49446482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781037238	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	27	318	1	ENST00000301067.7:c.1123C>T	p.Pro375Ser	p.P375S	ENST00000301067	NM_003482.3	375	Cca/Tca	9/54	1	2	FACETS	0.253	0.201	0.312	0.253	0.201	0.312	SUBCLONAL	1	TRUE	1	0.704782798284537	2		319	303	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479316	50479316	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	19	299	0	ENST00000394963.4:c.164G>A	p.Gly55Glu	p.G55E	ENST00000394963	NM_003076.4	55	gGa/gAa	1/13	1	2	FACETS	0.212	0.161	0.272	0.212	0.161	0.272	SUBCLONAL	1	TRUE	1	0.704782798284537	2		299	254	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143084	58143084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1474793589	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	30	464	0	ENST00000257904.6:c.700C>T	p.Pro234Ser	p.P234S	ENST00000257904	NM_000075.3	234	Cca/Tca	7/8	1	2	FACETS	0.159	0.128	0.195	0.159	0.128	0.195	SUBCLONAL	1	TRUE	1	0.704782798284537	2		464	535	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143250	58143250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555201123	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	15	256	0	ENST00000257904.6:c.670G>A	p.Gly224Ser	p.G224S	ENST00000257904	NM_000075.3	224	Ggc/Agc	6/8	1	2	FACETS	0.148	0.108	0.196	0.148	0.108	0.196	SUBCLONAL	1	TRUE	1	0.704782798284537	2		256	288	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924302	112924302	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	50	501	0	ENST00000351677.2:c.1248G>A	p.Trp416Ter	p.W416*	ENST00000351677	NM_002834.3	416	tgG/tgA	11/16	1	2	FACETS	0.3	0.254	0.35	0.3	0.254	0.35	SUBCLONAL	1	TRUE	1	0.704782798284537	2		501	473	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118938	115118938	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267603321	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	25	213	0	ENST00000257566.3:c.403C>T	p.Pro135Ser	p.P135S	ENST00000257566	NM_016569.3	135	Cca/Tca	2/8	1	2	FACETS	0.315	0.249	0.39	0.315	0.249	0.39	SUBCLONAL	1	TRUE	1	0.704782798284537	2		213	225	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431499	121431499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	35	448	0	ENST00000257555.6:c.703G>A	p.Glu235Lys	p.E235K	ENST00000257555		235	Gag/Aag	3/10	1	2	FACETS	0.223	0.183	0.269	0.223	0.183	0.269	SUBCLONAL	1	TRUE	1	0.704782798284537	2		448	445	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133236092	133236092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	23	288	0	ENST00000320574.5:c.3064G>A	p.Ala1022Thr	p.A1022T	ENST00000320574	NM_006231.2	1022	Gcc/Acc	26/49	1	2	FACETS	0.19	0.148	0.239	0.19	0.148	0.239	SUBCLONAL	1	TRUE	1	0.704782798284537	2		288	343	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28901642	28901642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	25	339	0	ENST00000282397.4:c.2753C>T	p.Ser918Phe	p.S918F	ENST00000282397	NM_002019.4	918	tCc/tTc	20/30	1	2	FACETS	0.16	0.126	0.2	0.16	0.126	0.2	SUBCLONAL	1	TRUE	1	0.704782798284537	2		339	443	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28903838	28903838	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1319953709	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	38	437	0	ENST00000282397.4:c.2621C>T	p.Ala874Val	p.A874V	ENST00000282397	NM_002019.4	874	gCt/gTt	19/30	1	2	FACETS	0.286	0.237	0.341	0.286	0.237	0.341	SUBCLONAL	1	TRUE	1	0.704782798284537	2		437	377	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910689	32910689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658303	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	36	395	0	ENST00000380152.3:c.2197G>A	p.Val733Ile	p.V733I	ENST00000380152		733	Gtc/Atc	11/27	1	2	FACETS	0.17	0.139	0.204	0.17	0.139	0.204	SUBCLONAL	1	TRUE	1	0.704782798284537	2		395	602	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913110	32913110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1176598028	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	71	432	1	ENST00000380152.3:c.4618G>A	p.Asp1540Asn	p.D1540N	ENST00000380152		1540	Gac/Aac	11/27	1	2	FACETS	0.282	0.246	0.322	0.282	0.246	0.322	SUBCLONAL	1	TRUE	1	0.704782798284537	2		433	714	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434724	110434724	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	53	466	0	ENST00000375856.3:c.3677G>A	p.Gly1226Glu	p.G1226E	ENST00000375856	NM_003749.2	1226	gGg/gAg	1/2	1	2	FACETS	0.342	0.292	0.396	0.342	0.292	0.396	SUBCLONAL	1	TRUE	1	0.704782798284537	2		466	440	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435559	110435559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	19	279	0	ENST00000375856.3:c.2842C>T	p.Leu948Phe	p.L948F	ENST00000375856	NM_003749.2	948	Ctc/Ttc	1/2	1	2	FACETS	0.203	0.154	0.261	0.203	0.154	0.261	SUBCLONAL	1	TRUE	1	0.704782798284537	2		279	265	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30103679	30103679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	38	394	0	ENST00000331968.5:c.1259G>A	p.Ser420Asn	p.S420N	ENST00000331968	NM_002742.2	420	aGc/aAc	8/18	1	2	FACETS	0.156	0.128	0.187	0.156	0.128	0.187	SUBCLONAL	1	TRUE	1	0.704782798284537	2		394	691	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986851	36986851	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	21	136	0	ENST00000354822.5:c.838G>A	p.Ala280Thr	p.A280T	ENST00000354822	NM_001079668.2	280	Gct/Act	3/3	1	2	FACETS	0.327	0.253	0.413	0.327	0.253	0.413	SUBCLONAL	1	TRUE	1	0.704782798284537	2		136	182	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988471	36988471	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	33	382	0	ENST00000354822.5:c.182G>A	p.Gly61Asp	p.G61D	ENST00000354822	NM_001079668.2	61	gGc/gAc	2/3	1	2	FACETS	0.241	0.196	0.292	0.241	0.196	0.292	SUBCLONAL	1	TRUE	1	0.704782798284537	2		382	388	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061385	38061385	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	30	343	0	ENST00000250448.2:c.604G>A	p.Asp202Asn	p.D202N	ENST00000250448	NM_004496.3	202	Gac/Aac	2/2	1	2	FACETS	0.171	0.137	0.209	0.171	0.137	0.209	SUBCLONAL	1	TRUE	1	0.704782798284537	2		343	498	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061705	38061705	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	26	253	0	ENST00000250448.2:c.284G>A	p.Ser95Asn	p.S95N	ENST00000250448	NM_004496.3	95	aGc/aAc	2/2	1	2	FACETS	0.342	0.272	0.421	0.342	0.272	0.421	SUBCLONAL	1	TRUE	1	0.704782798284537	2		253	216	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609343	81609343	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	18	296	0	ENST00000298171.2:c.941C>T	p.Ser314Phe	p.S314F	ENST00000298171	NM_000369.2	314	tCt/tTt	10/10	1	2	FACETS	0.16	0.12	0.207	0.16	0.12	0.207	SUBCLONAL	1	TRUE	1	0.704782798284537	2		296	320	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562435	95562435	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	28	303	0	ENST00000393063.1:c.4822G>A	p.Glu1608Lys	p.E1608K	ENST00000393063	NM_030621.3	1608	Gag/Aag	24/28	1	2	FACETS	0.162	0.129	0.2	0.162	0.129	0.2	SUBCLONAL	1	TRUE	1	0.704782798284537	2		303	489	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95593029	95593029	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	46	436	0	ENST00000393063.1:c.791G>A	p.Ser264Asn	p.S264N	ENST00000393063	NM_030621.3	264	aGt/aAt	8/28	1	2	FACETS	0.203	0.17	0.239	0.203	0.17	0.239	SUBCLONAL	1	TRUE	1	0.704782798284537	2		436	643	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246534	105246534	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	33	396	0	ENST00000349310.3:c.66G>A	p.Trp22Ter	p.W22*	ENST00000349310	NM_001014432.1	22	tgG/tgA	4/15	1	2	FACETS	0.231	0.188	0.28	0.231	0.188	0.28	SUBCLONAL	1	TRUE	1	0.704782798284537	2		396	405	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105258952	105258952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	24	542	0	ENST00000349310.3:c.29G>A	p.Gly10Asp	p.G10D	ENST00000349310	NM_001014432.1	10	gGt/gAt	3/15	1	2	FACETS	0.156	0.122	0.195	0.156	0.122	0.195	SUBCLONAL	1	TRUE	1	0.704782798284537	2		542	437	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991330	41991330	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	44	409	0	ENST00000219905.7:c.2161C>T	p.Gln721Ter	p.Q721*	ENST00000219905	NM_001164273.1	721	Cag/Tag	5/24	1	2	FACETS	0.202	0.169	0.239	0.202	0.169	0.239	SUBCLONAL	1	TRUE	1	0.704782798284537	2		409	617	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019434	42019434	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754995618	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	40	442	0	ENST00000219905.7:c.3487G>A	p.Val1163Ile	p.V1163I	ENST00000219905	NM_001164273.1	1163	Gta/Ata	10/24	1	2	FACETS	0.182	0.15	0.217	0.182	0.15	0.217	SUBCLONAL	1	TRUE	1	0.704782798284537	2		442	624	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041039	42041039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	64	478	0	ENST00000219905.7:c.5417G>A	p.Gly1806Glu	p.G1806E	ENST00000219905	NM_001164273.1	1806	gGg/gAg	16/24	1	2	FACETS	0.272	0.235	0.312	0.272	0.235	0.312	SUBCLONAL	1	TRUE	1	0.704782798284537	2		478	668	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058640	42058640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	20	288	0	ENST00000219905.7:c.8360G>A	p.Ser2787Asn	p.S2787N	ENST00000219905	NM_001164273.1	2787	aGc/aAc	24/24	1	2	FACETS	0.171	0.131	0.219	0.171	0.131	0.219	SUBCLONAL	1	TRUE	1	0.704782798284537	2		288	331	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059120	42059120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	23	333	1	ENST00000219905.7:c.8840G>A	p.Gly2947Glu	p.G2947E	ENST00000219905	NM_001164273.1	2947	gGa/gAa	24/24	1	2	FACETS	0.191	0.149	0.241	0.191	0.149	0.241	SUBCLONAL	1	TRUE	1	0.704782798284537	2		334	341	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714324	43714324	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	35	328	0	ENST00000382044.4:c.3829G>A	p.Glu1277Lys	p.E1277K	ENST00000382044	NM_001141980.1	1277	Gag/Aag	19/28	1	2	FACETS	0.257	0.21	0.309	0.257	0.21	0.309	SUBCLONAL	1	TRUE	1	0.704782798284537	2		328	387	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66777515	66777515	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	28	382	0	ENST00000307102.5:c.881G>A	p.Gly294Glu	p.G294E	ENST00000307102	NM_002755.3	294	gGg/gAg	7/11	1	2	FACETS	0.191	0.152	0.235	0.191	0.152	0.235	SUBCLONAL	1	TRUE	1	0.704782798284537	2		382	416	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250892	99250892	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs200131538	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	31	409	0	ENST00000268035.6:c.196A>G	p.Lys66Glu	p.K66E	ENST00000268035	NM_000875.3	66	Aag/Gag	2/21	1	2	FACETS	0.196	0.158	0.239	0.196	0.158	0.239	SUBCLONAL	1	TRUE	1	0.704782798284537	2		409	449	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096218	2096218	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	32	612	0	ENST00000219066.1:c.289G>A	p.Val97Ile	p.V97I	ENST00000219066	NM_002528.5	97	Gtc/Atc	2/6	0.173192818931189	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.704782798284537	0		612	504	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121538	2121538	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	31	521	1	ENST00000219476.3:c.1867G>A	p.Ala623Thr	p.A623T	ENST00000219476	NM_000548.3	623	Gcc/Acc	18/42	0.173192818931189	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.704782798284537	0		522	414	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658667	3658667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	52	692	1	ENST00000294008.3:c.299C>T	p.Thr100Ile	p.T100I	ENST00000294008	NM_032444.2	100	aCc/aTc	2/15	0.173192818931189	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.704782798284537	0		693	837	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778101	3778101	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	33	642	0	ENST00000262367.5:c.6947C>T	p.Pro2316Leu	p.P2316L	ENST00000262367	NM_004380.2	2316	cCc/cTc	31/31	0.173192818931189	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.704782798284537	0		642	494	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779415	3779415	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	36	534	1	ENST00000262367.5:c.5633C>T	p.Pro1878Leu	p.P1878L	ENST00000262367	NM_004380.2	1878	cCt/cTt	31/31	0.173192818931189	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.704782798284537	0		535	422	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029291	14029291	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	39	322	1	ENST00000311895.7:c.1502C>T	p.Pro501Leu	p.P501L	ENST00000311895	NM_005236.2	501	cCt/cTt	8/11	1	2	FACETS	0.224	0.186	0.268	0.224	0.186	0.268	SUBCLONAL	1	TRUE	1	0.704782798284537	2		323	493	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632797	23632797	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	41	349	0	ENST00000261584.4:c.2999G>A	p.Gly1000Asp	p.G1000D	ENST00000261584	NM_024675.3	1000	gGc/gAc	10/13	1	2	FACETS	0.26	0.217	0.309	0.26	0.217	0.309	SUBCLONAL	1	TRUE	1	0.704782798284537	2		349	447	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641043	23641043	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	45	446	0	ENST00000261584.4:c.2432C>T	p.Pro811Leu	p.P811L	ENST00000261584	NM_024675.3	811	cCa/cTa	5/13	1	2	FACETS	0.216	0.181	0.254	0.216	0.181	0.254	SUBCLONAL	1	TRUE	1	0.704782798284537	2		446	592	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100696	67100696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	39	375	0	ENST00000412916.2:c.394G>A	p.Ala132Thr	p.A132T	ENST00000412916		132	Gcc/Acc	4/6	1	2	FACETS	0.2	0.165	0.239	0.2	0.165	0.239	SUBCLONAL	1	TRUE	1	0.704782798284537	2		375	553	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645517	67645517	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	15	203	0	ENST00000264010.4:c.781+1G>A		p.X261_splice	ENST00000264010	NM_006565.3	261			1	2	FACETS	0.197	0.144	0.261	0.197	0.144	0.261	SUBCLONAL	1	TRUE	1	0.704782798284537	2		203	216	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821823	72821823	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	32	411	0	ENST00000268489.5:c.10352C>T	p.Ser3451Phe	p.S3451F	ENST00000268489	NM_006885.3	3451	tCc/tTc	10/10	1	2	FACETS	0.188	0.152	0.228	0.188	0.152	0.228	SUBCLONAL	1	TRUE	1	0.704782798284537	2		411	484	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821832	72821832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	39	403	0	ENST00000268489.5:c.10343G>A	p.Ser3448Asn	p.S3448N	ENST00000268489	NM_006885.3	3448	aGt/aAt	10/10	1	2	FACETS	0.233	0.192	0.277	0.233	0.192	0.277	SUBCLONAL	1	TRUE	1	0.704782798284537	2		403	476	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827199	72827199	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	46	374	0	ENST00000268489.5:c.9382G>A	p.Gly3128Ser	p.G3128S	ENST00000268489	NM_006885.3	3128	Ggc/Agc	9/10	1	2	FACETS	0.353	0.298	0.413	0.353	0.298	0.413	SUBCLONAL	1	TRUE	1	0.704782798284537	2		374	370	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984718	72984718	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	40	481	0	ENST00000268489.5:c.2866G>A	p.Asp956Asn	p.D956N	ENST00000268489	NM_006885.3	956	Gac/Aac	3/10	1	2	FACETS	0.202	0.167	0.241	0.202	0.167	0.241	SUBCLONAL	1	TRUE	1	0.704782798284537	2		481	562	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341284	89341284	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1402333853	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	10	153	1	ENST00000301030.4:c.7651C>T	p.Pro2551Ser	p.P2551S	ENST00000301030	NM_001256183.1	2551	Cca/Tca	11/13	0.14304506606078	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.704782798284537	0		154	133	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351707	89351707	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	63	579	0	ENST00000301030.4:c.1243G>A	p.Asp415Asn	p.D415N	ENST00000301030	NM_001256183.1	415	Gac/Aac	9/13	0.14304506606078	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.704782798284537	0		579	548	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805083	89805083	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769243354	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	20	423	0	ENST00000389301.3:c.4294G>A	p.Val1432Met	p.V1432M	ENST00000389301	NM_000135.2	1432	Gtg/Atg	43/43	0.14304506606078	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.704782798284537	0		423	361	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805950	89805950	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1178460453	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	24	421	1	ENST00000389301.3:c.3946G>A	p.Gly1316Arg	p.G1316R	ENST00000389301	NM_000135.2	1316	Ggg/Agg	40/43	0.14304506606078	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.704782798284537	0		422	389	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89809320	89809320	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771111655	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	130	329	0	ENST00000389301.3:c.3653C>T	p.Pro1218Leu	p.P1218L	ENST00000389301	NM_000135.2	1218	cCa/cTa	37/43	0.14304506606078	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.704782798284537	0		329	385	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89871778	89871778	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	27	436	1	ENST00000389301.3:c.619G>A	p.Gly207Arg	p.G207R	ENST00000389301	NM_000135.2	207	Gga/Aga	7/43	0.14304506606078	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.704782798284537	0		437	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578491	7578491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555526226	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	13	625	0	ENST00000269305.4:c.439G>A	p.Val147Ile	p.V147I	ENST00000269305	NM_001126112.2	147	Gtt/Att	5/11	1	2	FACETS	0.06	0.042	0.082	0.06	0.042	0.082	SUBCLONAL	1	TRUE	1	0.704782798284537	2		625	615	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004835	16004835	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	41	418	0	ENST00000268712.3:c.2419G>A	p.Glu807Lys	p.E807K	ENST00000268712	NM_006311.3	807	Gag/Aag	20/46	1	2	FACETS	0.2	0.166	0.238	0.2	0.166	0.238	SUBCLONAL	1	TRUE	1	0.704782798284537	2		418	581	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118532	17118532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	33	541	0	ENST00000285071.4:c.1399G>A	p.Val467Met	p.V467M	ENST00000285071	NM_144997.5	467	Gtg/Atg	12/14	1	2	FACETS	0.201	0.163	0.243	0.201	0.163	0.243	SUBCLONAL	1	TRUE	1	0.704782798284537	2		541	467	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29497016	29497016	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1555607126	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	48	204	0	ENST00000356175.3:c.586+1G>A		p.X196_splice	ENST00000356175	NM_000267.3	196			1	2	FACETS	0.322	0.272	0.376	0.322	0.272	0.376	SUBCLONAL	1	TRUE	1	0.704782798284537	2		204	423	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325969	30325969	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	55	335	0	ENST00000322652.5:c.2167G>A	p.Glu723Lys	p.E723K	ENST00000322652	NM_015355.2	723	Gaa/Aaa	16/16	1	2	FACETS	0.243	0.207	0.282	0.243	0.207	0.282	SUBCLONAL	1	TRUE	1	0.704782798284537	2		335	642	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627376	37627376	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265808600	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	37	622	1	ENST00000447079.4:c.1291G>A	p.Glu431Lys	p.E431K	ENST00000447079	NM_015083.1	431	Gag/Aag	2/14	1	2	FACETS	0.148	0.121	0.178	0.148	0.121	0.178	SUBCLONAL	1	TRUE	1	0.704782798284537	2		623	709	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868249	37868249	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	38	473	0	ENST00000269571.5:c.970G>A	p.Ala324Thr	p.A324T	ENST00000269571		324	Gca/Aca	8/27	1	2	FACETS	0.239	0.197	0.285	0.239	0.197	0.285	SUBCLONAL	1	TRUE	1	0.704782798284537	2		473	452	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872120	37872120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	58	525	0	ENST00000269571.5:c.1441C>T	p.Pro481Ser	p.P481S	ENST00000269571		481	Ccc/Tcc	12/27	1	2	FACETS	0.337	0.289	0.388	0.337	0.289	0.388	SUBCLONAL	1	TRUE	1	0.704782798284537	2		525	489	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872856	37872856	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	22	416	0	ENST00000269571.5:c.1735C>T	p.Pro579Ser	p.P579S	ENST00000269571		579	Ccg/Tcg	14/27	1	2	FACETS	0.187	0.144	0.236	0.187	0.144	0.236	SUBCLONAL	1	TRUE	1	0.704782798284537	2		416	334	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881608	37881608	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	36	463	0	ENST00000269571.5:c.2678C>T	p.Ser893Phe	p.S893F	ENST00000269571		893	tCc/tTc	22/27	1	2	FACETS	0.226	0.185	0.272	0.226	0.185	0.272	SUBCLONAL	1	TRUE	1	0.704782798284537	2		463	452	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38504705	38504705	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	22	442	0	ENST00000254066.5:c.316G>A	p.Glu106Lys	p.E106K	ENST00000254066	NM_000964.3	106	Gag/Aag	3/9	1	2	FACETS	0.143	0.11	0.181	0.143	0.11	0.181	SUBCLONAL	1	TRUE	1	0.704782798284537	2		442	436	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369471	40369471	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	42	506	0	ENST00000293328.3:c.1181G>A	p.Gly394Asp	p.G394D	ENST00000293328	NM_012448.3	394	gGc/gAc	10/19	1	2	FACETS	0.272	0.227	0.322	0.272	0.227	0.322	SUBCLONAL	1	TRUE	1	0.704782798284537	2		506	438	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40880851	40880851	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	34	439	0	ENST00000428826.2:c.109G>A	p.Gly37Ser	p.G37S	ENST00000428826		37	Ggt/Agt	3/21	1	2	FACETS	0.191	0.155	0.231	0.191	0.155	0.231	SUBCLONAL	1	TRUE	1	0.704782798284537	2		439	506	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244433	41244433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	48	510	0	ENST00000357654.3:c.3115G>A	p.Ala1039Thr	p.A1039T	ENST00000357654	NM_007294.3	1039	Gcc/Acc	10/23	1	2	FACETS	0.2	0.168	0.235	0.2	0.168	0.235	SUBCLONAL	1	TRUE	1	0.704782798284537	2		510	681	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56811575	56811575	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555605640	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	35	270	1	ENST00000337432.4:c.1123G>A	p.Glu375Lys	p.E375K	ENST00000337432	NM_058216.2	375	Gaa/Aaa	9/9	1	2	FACETS	0.186	0.152	0.224	0.186	0.152	0.224	SUBCLONAL	1	TRUE	1	0.704782798284537	2		271	535	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763463	59763463	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1217852974	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	36	450	0	ENST00000259008.2:c.2639C>T	p.Ser880Phe	p.S880F	ENST00000259008	NM_032043.2	880	tCc/tTc	19/20	1	2	FACETS	0.148	0.121	0.179	0.148	0.121	0.179	SUBCLONAL	1	TRUE	1	0.704782798284537	2		450	689	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007704	62007704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	14	313	0	ENST00000392795.3:c.163G>A	p.Ala55Thr	p.A55T	ENST00000392795	NM_001039933.1	55	Gcc/Acc	3/6	1	2	FACETS	0.152	0.11	0.204	0.152	0.11	0.204	SUBCLONAL	1	TRUE	1	0.704782798284537	2		313	261	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775206	73775206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	29	347	0	ENST00000254810.4:c.50C>T	p.Pro17Leu	p.P17L	ENST00000254810	NM_005324.3	17	cCc/cTc	2/4	1	2	FACETS	0.163	0.13	0.2	0.163	0.13	0.2	SUBCLONAL	1	TRUE	1	0.704782798284537	2		347	505	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857285	78857285	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	36	302	0	ENST00000306801.3:c.1650+1G>A		p.X550_splice	ENST00000306801	NM_020761.2	550			1	2	FACETS	0.371	0.307	0.443	0.371	0.307	0.443	SUBCLONAL	1	TRUE	1	0.704782798284537	2		302	275	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867513	78867513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202047167	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	17	359	0	ENST00000306801.3:c.2249G>A	p.Gly750Asp	p.G750D	ENST00000306801	NM_020761.2	750	gGc/gAc	20/34	1	2	FACETS	0.158	0.118	0.206	0.158	0.118	0.206	SUBCLONAL	1	TRUE	1	0.704782798284537	2		359	305	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899233	78899233	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	44	365	0	ENST00000306801.3:c.2872G>A	p.Gly958Arg	p.G958R	ENST00000306801	NM_020761.2	958	Ggg/Agg	24/34	1	2	FACETS	0.315	0.264	0.37	0.315	0.264	0.37	SUBCLONAL	1	TRUE	1	0.704782798284537	2		365	397	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724498	724498	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	42	284	0	ENST00000314574.4:c.1558G>A	p.Glu520Lys	p.E520K	ENST00000314574	NM_005433.3	520	Gaa/Aaa	12/12	1	2	FACETS	0.257	0.214	0.304	0.257	0.214	0.304	SUBCLONAL	1	TRUE	1	0.704782798284537	2		284	464	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39535294	39535294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	20	139	0	ENST00000262039.4:c.38G>A	p.Cys13Tyr	p.C13Y	ENST00000262039	NM_002647.2	13	tGt/tAt	1/25	1	2	FACETS	0.2	0.153	0.255	0.2	0.153	0.255	SUBCLONAL	1	TRUE	1	0.704782798284537	2		139	284	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622344	1622344	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	40	575	1	ENST00000344749.5:c.620G>A	p.Ser207Asn	p.S207N	ENST00000344749	NM_001136139.2	207	aGc/aAc	9/19	0.514569973434755	3	FACETS	0.273	0.226	0.325	0.136	0.113	0.163	SUBCLONAL	1	TRUE	1	0.704782798284537	3		576	563	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625656	1625656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	40	551	1	ENST00000344749.5:c.418C>T	p.Pro140Ser	p.P140S	ENST00000344749	NM_001136139.2	140	Cct/Tct	7/19	0.514569973434755	3	FACETS	0.248	0.205	0.295	0.124	0.102	0.148	SUBCLONAL	1	TRUE	1	0.704782798284537	3		552	620	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222144	5222144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1195525448	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	28	395	0	ENST00000357368.4:c.3191C>T	p.Thr1064Ile	p.T1064I	ENST00000357368	NM_002850.3	1064	aCa/aTa	19/38	0.514569973434755	3	FACETS	0.235	0.187	0.29	0.118	0.093	0.145	SUBCLONAL	1	TRUE	1	0.704782798284537	3		395	457	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245868	5245868	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	52	599	1	ENST00000357368.4:c.907G>A	p.Val303Ile	p.V303I	ENST00000357368	NM_002850.3	303	Gtc/Atc	10/38	0.514569973434755	3	FACETS	0.298	0.253	0.348	0.149	0.126	0.174	SUBCLONAL	1	TRUE	1	0.704782798284537	3		600	669	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245997	5245997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	30	468	0	ENST00000357368.4:c.778G>A	p.Gly260Ser	p.G260S	ENST00000357368	NM_002850.3	260	Ggc/Agc	10/38	0.514569973434755	3	FACETS	0.248	0.199	0.304	0.124	0.099	0.152	SUBCLONAL	1	TRUE	1	0.704782798284537	3		468	464	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117201	7117201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374120246	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	36	582	0	ENST00000302850.5:c.4015G>A	p.Glu1339Lys	p.E1339K	ENST00000302850	NM_000208.2	1339	Gag/Aag	22/22	0.514569973434755	3	FACETS	0.251	0.205	0.302	0.125	0.102	0.151	SUBCLONAL	1	TRUE	1	0.704782798284537	3		582	551	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7132192	7132192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	34	514	0	ENST00000302850.5:c.2819C>T	p.Thr940Ile	p.T940I	ENST00000302850	NM_000208.2	940	aCc/aTc	14/22	0.514569973434755	3	FACETS	0.211	0.172	0.256	0.106	0.086	0.128	SUBCLONAL	1	TRUE	1	0.704782798284537	3		514	618	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094991	11094991	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747185602	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	34	635	0	ENST00000358026.2:c.164C>T	p.Pro55Leu	p.P55L	ENST00000358026	NM_001128849.1	55	cCc/cTc	2/36	0.514569973434755	3	FACETS	0.238	0.194	0.288	0.119	0.097	0.144	SUBCLONAL	1	TRUE	1	0.704782798284537	3		635	548	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145589	11145589	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	31	394	0	ENST00000358026.2:c.3952-1G>A		p.X1318_splice	ENST00000358026	NM_001128849.1	1318			0.632032851179726	3	FACETS	0.258	0.208	0.314	0.129	0.104	0.157	SUBCLONAL	1	TRUE	1	0.704782798284537	3		394	462	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11172470	11172470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555797457	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	48	470	0	ENST00000358026.2:c.5018G>A	p.Gly1673Glu	p.G1673E	ENST00000358026	NM_001128849.1	1673	gGa/gAa	36/36	0.632032851179726	3	FACETS	0.287	0.242	0.337	0.144	0.121	0.169	SUBCLONAL	1	TRUE	1	0.704782798284537	3		470	641	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15273275	15273275	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	42	428	2	ENST00000263388.2:c.5913+1G>A		p.X1971_splice	ENST00000263388	NM_000435.2	1971			0.632032851179726	3	FACETS	0.278	0.231	0.33	0.139	0.115	0.165	SUBCLONAL	1	TRUE	1	0.704782798284537	3		430	580	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367927	15367927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	41	557	0	ENST00000263377.2:c.1399G>A	p.Ala467Thr	p.A467T	ENST00000263377	NM_058243.2	467	Gcc/Acc	8/20	0.632032851179726	3	FACETS	0.246	0.204	0.293	0.123	0.102	0.147	SUBCLONAL	1	TRUE	1	0.704782798284537	3		557	639	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945783	17945783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	34	438	0	ENST00000458235.1:c.2077C>T	p.Pro693Ser	p.P693S	ENST00000458235	NM_000215.3	693	Ccc/Tcc	16/24	0.632032851179726	3	FACETS	0.241	0.196	0.291	0.12	0.098	0.146	SUBCLONAL	1	TRUE	1	0.704782798284537	3		438	542	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279284	18279284	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	30	363	0	ENST00000222254.8:c.1737-1G>A		p.X579_splice	ENST00000222254	NM_005027.3	579			0.632032851179726	3	FACETS	0.262	0.21	0.32	0.131	0.105	0.16	SUBCLONAL	1	TRUE	1	0.704782798284537	3		363	440	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211526	36211526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779063102	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	24	425	0	ENST00000222270.7:c.1277C>T	p.Pro426Leu	p.P426L	ENST00000222270	NM_014727.1	426	cCc/cTc	3/37	0.632032851179726	3	FACETS	0.214	0.167	0.268	0.107	0.083	0.134	SUBCLONAL	1	TRUE	1	0.704782798284537	3		425	430	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213348	36213348	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1275595789	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	38	581	0	ENST00000222270.7:c.2545G>A	p.Val849Met	p.V849M	ENST00000222270	NM_014727.1	849	Gtg/Atg	4/37	0.632032851179726	3	FACETS	0.211	0.173	0.253	0.105	0.086	0.127	SUBCLONAL	1	TRUE	1	0.704782798284537	3		581	692	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753347	42753347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	56	597	0	ENST00000222329.4:c.917G>A	p.Ser306Asn	p.S306N	ENST00000222329	NM_006494.2	306	aGc/aAc	4/4	0.632032851179726	3	FACETS	0.272	0.232	0.315	0.136	0.116	0.158	SUBCLONAL	1	TRUE	1	0.704782798284537	3		597	791	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791790	42791790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	35	511	0	ENST00000575354.2:c.676G>A	p.Asp226Asn	p.D226N	ENST00000575354	NM_015125.3	226	Gac/Aac	5/20	0.632032851179726	3	FACETS	0.228	0.186	0.275	0.114	0.093	0.138	SUBCLONAL	1	TRUE	1	0.704782798284537	3		511	589	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794791	42794791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	25	486	0	ENST00000575354.2:c.1871G>A	p.Gly624Glu	p.G624E	ENST00000575354	NM_015125.3	624	gGa/gAa	10/20	0.632032851179726	3	FACETS	0.205	0.161	0.256	0.103	0.08	0.128	SUBCLONAL	1	TRUE	1	0.704782798284537	3		486	467	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905325	50905325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	35	673	0	ENST00000440232.2:c.533G>A	p.Gly178Glu	p.G178E	ENST00000440232	NM_002691.3	178	gGg/gAg	5/27	NA	2	FACETS	0.175	0.142	0.211			1	INDETERMINATE	1	TRUE	NA	0.704782798284537	2		673	569	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910376	50910376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	47	528	0	ENST00000440232.2:c.1631G>A	p.Ser544Asn	p.S544N	ENST00000440232	NM_002691.3	544	aGc/aAc	13/27	NA	2	FACETS	0.259	0.219	0.305			1	INDETERMINATE	1	TRUE	NA	0.704782798284537	2		528	514	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451770	29451770	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	42	532	0	ENST00000389048.3:c.2795G>A	p.Gly932Glu	p.G932E	ENST00000389048	NM_004304.4	932	gGa/gAa	16/29	1	2	FACETS	0.266	0.222	0.315	0.266	0.222	0.315	SUBCLONAL	1	TRUE	1	0.704782798284537	2		532	448	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250125	39250125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	58	508	1	ENST00000402219.2:c.1444G>A	p.Gly482Ser	p.G482S	ENST00000402219	NM_005633.3	482	Ggt/Agt	10/23	1	2	FACETS	0.183	0.157	0.212	0.183	0.157	0.212	SUBCLONAL	1	TRUE	1	0.704782798284537	2		509	898	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630337	47630337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1257347271	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	21	409	1	ENST00000233146.2:c.7G>A	p.Val3Met	p.V3M	ENST00000233146	NM_000251.2	3	Gtg/Atg	1/16	0.704782798284537	1	FACETS	0.169	0.13	0.214	0.169	0.13	0.214	SUBCLONAL	1	TRUE	0	0.704782798284537	1		410	228	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657081	47657081	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs267607950	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	12	198	0	ENST00000233146.2:c.1276+1G>C		p.X426_splice	ENST00000233146	NM_000251.2	426			0.704782798284537	1	FACETS	0.119	0.083	0.162	0.119	0.083	0.162	SUBCLONAL	1	TRUE	0	0.704782798284537	1		198	186	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47672785	47672785	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	21	349	0	ENST00000233146.2:c.1375G>A	p.Asp459Asn	p.D459N	ENST00000233146	NM_000251.2	459	Gat/Aat	8/16	0.704782798284537	1	FACETS	0.108	0.083	0.138	0.108	0.083	0.138	SUBCLONAL	1	TRUE	0	0.704782798284537	1		349	356	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010586	48010586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201910	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	20	341	0	ENST00000234420.5:c.214C>T	p.Leu72Phe	p.L72F	ENST00000234420	NM_000179.2	72	Ctc/Ttc	1/10	0.704782798284537	1	FACETS	0.171	0.131	0.218	0.171	0.131	0.218	SUBCLONAL	1	TRUE	0	0.704782798284537	1		341	215	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026501	48026501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	26	399	0	ENST00000234420.5:c.1379G>A	p.Gly460Asp	p.G460D	ENST00000234420	NM_000179.2	460	gGc/gAc	4/10	0.704782798284537	1	FACETS	0.164	0.129	0.203	0.164	0.129	0.203	SUBCLONAL	1	TRUE	0	0.704782798284537	1		399	292	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026675	48026675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	45	381	0	ENST00000234420.5:c.1553C>T	p.Thr518Ile	p.T518I	ENST00000234420	NM_000179.2	518	aCc/aTc	4/10	0.704782798284537	1	FACETS	0.284	0.24	0.333	0.284	0.24	0.333	SUBCLONAL	1	TRUE	0	0.704782798284537	1		381	291	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027634	48027634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	22	256	0	ENST00000234420.5:c.2512C>T	p.Pro838Ser	p.P838S	ENST00000234420	NM_000179.2	838	Cca/Tca	4/10	0.704782798284537	1	FACETS	0.201	0.156	0.253	0.201	0.156	0.253	SUBCLONAL	1	TRUE	0	0.704782798284537	1		256	201	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027886	48027886	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779246	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	17	246	1	ENST00000234420.5:c.2764C>T	p.Arg922Ter	p.R922*	ENST00000234420	NM_000179.2	922	Cga/Tga	4/10	0.704782798284537	1	FACETS	0.121	0.09	0.157	0.121	0.09	0.157	SUBCLONAL	1	TRUE	0	0.704782798284537	1		247	259	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919814	96919814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	25	329	0	ENST00000258439.3:c.449C>T	p.Ala150Val	p.A150V	ENST00000258439	NM_001193304.2	150	gCt/gTt	4/4	1	2	FACETS	0.182	0.143	0.227	0.182	0.143	0.227	SUBCLONAL	1	TRUE	1	0.704782798284537	2		329	389	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044528	128044528	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	25	410	0	ENST00000285398.2:c.1093G>A	p.Gly365Ser	p.G365S	ENST00000285398	NM_000122.1	365	Ggc/Agc	8/15	1	2	FACETS	0.165	0.129	0.206	0.165	0.129	0.206	SUBCLONAL	1	TRUE	1	0.704782798284537	2		410	430	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158655984	158655984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	40	379	0	ENST00000263640.3:c.22C>T	p.Leu8Phe	p.L8F	ENST00000263640	NM_001105.4	8	Ctt/Ttt	3/11	1	2	FACETS	0.183	0.151	0.218	0.183	0.151	0.218	SUBCLONAL	1	TRUE	1	0.704782798284537	2		379	621	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273252	198273252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	43	407	0	ENST00000335508.6:c.958G>A	p.Gly320Arg	p.G320R	ENST00000335508	NM_012433.2	320	Gga/Aga	8/25	1	2	FACETS	0.209	0.174	0.247	0.209	0.174	0.247	SUBCLONAL	1	TRUE	1	0.704782798284537	2		407	585	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274682	198274682	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	24	312	0	ENST00000335508.6:c.716C>T	p.Ala239Val	p.A239V	ENST00000335508	NM_012433.2	239	gCa/gTa	7/25	1	2	FACETS	0.151	0.118	0.189	0.151	0.118	0.189	SUBCLONAL	1	TRUE	1	0.704782798284537	2		312	451	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137436	202137436	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	37	358	0	ENST00000358485.4:c.664G>A	p.Val222Ile	p.V222I	ENST00000358485	NM_001080125.1	222	Gtc/Atc	4/9	1	2	FACETS	0.2	0.165	0.24	0.2	0.165	0.24	SUBCLONAL	1	TRUE	1	0.704782798284537	2		358	524	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587258	212587258	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs537320227	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	34	276	0	ENST00000342788.4:c.743C>T	p.Ala248Val	p.A248V	ENST00000342788	NM_005235.2	248	gCc/gTc	7/28	1	2	FACETS	0.204	0.166	0.247	0.204	0.166	0.247	SUBCLONAL	1	TRUE	1	0.704782798284537	2		276	473	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023430	31023430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	35	364	0	ENST00000375687.4:c.2915G>A	p.Gly972Asp	p.G972D	ENST00000375687	NM_015338.5	972	gGc/gAc	13/13	1	2	FACETS	0.247	0.202	0.297	0.247	0.202	0.297	SUBCLONAL	1	TRUE	1	0.704782798284537	2		364	402	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380469	31380469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	28	390	0	ENST00000328111.2:c.959G>A	p.Ser320Asn	p.S320N	ENST00000328111	NM_006892.3	320	aGc/aAc	9/23	1	2	FACETS	0.201	0.16	0.248	0.201	0.16	0.248	SUBCLONAL	1	TRUE	1	0.704782798284537	2		390	395	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389143	31389143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	39	374	0	ENST00000328111.2:c.2056G>A	p.Glu686Lys	p.E686K	ENST00000328111	NM_006892.3	686	Gag/Aag	19/23	1	2	FACETS	0.254	0.21	0.302	0.254	0.21	0.302	SUBCLONAL	1	TRUE	1	0.704782798284537	2		374	436	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264083	46264083	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	22	221	0	ENST00000371998.3:c.1130G>A	p.Arg377Lys	p.R377K	ENST00000371998		377	aGa/aAa	11/23	1	2	FACETS	0.181	0.14	0.229	0.181	0.14	0.229	SUBCLONAL	1	TRUE	1	0.704782798284537	2		221	345	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264143	46264143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746732554	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	27	231	0	ENST00000371998.3:c.1190C>T	p.Ser397Leu	p.S397L	ENST00000371998		397	tCg/tTg	11/23	1	2	FACETS	0.234	0.186	0.288	0.234	0.186	0.288	SUBCLONAL	1	TRUE	1	0.704782798284537	2		231	328	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265103	46265103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	27	309	0	ENST00000371998.3:c.1973G>A	p.Gly658Glu	p.G658E	ENST00000371998		658	gGa/gAa	12/23	1	2	FACETS	0.201	0.16	0.248	0.201	0.16	0.248	SUBCLONAL	1	TRUE	1	0.704782798284537	2		309	381	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46266416	46266416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	34	359	0	ENST00000371998.3:c.2401G>A	p.Asp801Asn	p.D801N	ENST00000371998		801	Gat/Aat	13/23	1	2	FACETS	0.191	0.155	0.231	0.191	0.155	0.231	SUBCLONAL	1	TRUE	1	0.704782798284537	2		359	506	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267836	46267836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1485661563	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	57	429	0	ENST00000371998.3:c.2597C>T	p.Ser866Leu	p.S866L	ENST00000371998		866	tCa/tTa	14/23	1	2	FACETS	0.252	0.215	0.291	0.252	0.215	0.291	SUBCLONAL	1	TRUE	1	0.704782798284537	2		429	643	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958128	54958128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	53	315	0	ENST00000312783.6:c.479C>T	p.Ala160Val	p.A160V	ENST00000312783	NM_198436.1	160	gCt/gTt	6/10	1	2	FACETS	0.263	0.224	0.306	0.263	0.224	0.306	SUBCLONAL	1	TRUE	1	0.704782798284537	2		315	571	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514606	44514606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	24	373	0	ENST00000291552.4:c.550G>A	p.Glu184Lys	p.E184K	ENST00000291552	NM_006758.2	184	Gag/Aag	7/8	1	2	FACETS	0.152	0.119	0.191	0.152	0.119	0.191	SUBCLONAL	1	TRUE	1	0.704782798284537	2		373	447	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546027	41546027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1486901560	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	24	567	1	ENST00000263253.7:c.2642C>T	p.Pro881Leu	p.P881L	ENST00000263253	NM_001429.3	881	cCt/cTt	14/31	0.704782798284537	1	FACETS	0.113	0.088	0.141	0.113	0.088	0.141	SUBCLONAL	1	TRUE	0	0.704782798284537	1		568	392	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574889	41574889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs975210038	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	32	493	0	ENST00000263253.7:c.7174G>A	p.Asp2392Asn	p.D2392N	ENST00000263253	NM_001429.3	2392	Gac/Aac	31/31	0.704782798284537	1	FACETS	0.154	0.125	0.187	0.154	0.125	0.187	SUBCLONAL	1	TRUE	0	0.704782798284537	1		493	381	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421382	12421382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	39	475	0	ENST00000287820.6:c.262C>T	p.Pro88Ser	p.P88S	ENST00000287820	NM_015869.4	88	Cca/Tca	2/7	1	2	FACETS	0.152	0.125	0.182	0.152	0.125	0.182	SUBCLONAL	1	TRUE	1	0.704782798284537	2		475	727	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713325	30713325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	24	352	1	ENST00000295754.5:c.650C>T	p.Ala217Val	p.A217V	ENST00000295754	NM_003242.5	217	gCc/gTc	4/7	1	2	FACETS	0.161	0.126	0.202	0.161	0.126	0.202	SUBCLONAL	1	TRUE	1	0.704782798284537	2		353	423	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042513	37042513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768132746	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	44	395	0	ENST00000231790.2:c.275C>T	p.Ala92Val	p.A92V	ENST00000231790	NM_000249.3	92	gCc/gTc	3/19	1	2	FACETS	0.207	0.173	0.244	0.207	0.173	0.244	SUBCLONAL	1	TRUE	1	0.704782798284537	2		395	604	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47079220	47079220	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	46	448	0	ENST00000409792.3:c.7286C>T	p.Ala2429Val	p.A2429V	ENST00000409792	NM_014159.6	2429	gCc/gTc	18/21	1	2	FACETS	0.25	0.21	0.294	0.25	0.21	0.294	SUBCLONAL	1	TRUE	1	0.704782798284537	2		448	522	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129691	47129691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	39	331	0	ENST00000409792.3:c.5189C>T	p.Ser1730Phe	p.S1730F	ENST00000409792	NM_014159.6	1730	tCt/tTt	10/21	1	2	FACETS	0.214	0.177	0.256	0.214	0.177	0.256	SUBCLONAL	1	TRUE	1	0.704782798284537	2		331	516	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164097	47164097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764219907	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	43	290	0	ENST00000409792.3:c.2029C>T	p.Pro677Ser	p.P677S	ENST00000409792	NM_014159.6	677	Cct/Tct	3/21	1	2	FACETS	0.257	0.215	0.304	0.257	0.215	0.304	SUBCLONAL	1	TRUE	1	0.704782798284537	2		290	475	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164892	47164892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	27	253	0	ENST00000409792.3:c.1234G>A	p.Gly412Ser	p.G412S	ENST00000409792	NM_014159.6	412	Ggc/Agc	3/21	1	2	FACETS	0.245	0.195	0.302	0.245	0.195	0.302	SUBCLONAL	1	TRUE	1	0.704782798284537	2		253	313	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928971	49928971	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264677042	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	31	553	0	ENST00000296474.3:c.3395G>A	p.Gly1132Glu	p.G1132E	ENST00000296474	NM_002447.2	1132	gGg/gAg	16/20	1	2	FACETS	0.21	0.17	0.256	0.21	0.17	0.256	SUBCLONAL	1	TRUE	1	0.704782798284537	2		553	418	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934021	49934021	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1272472014	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	30	515	0	ENST00000296474.3:c.2391G>A	p.Trp797Ter	p.W797*	ENST00000296474	NM_002447.2	797	tgG/tgA	9/20	1	2	FACETS	0.165	0.133	0.203	0.165	0.133	0.203	SUBCLONAL	1	TRUE	1	0.704782798284537	2		515	515	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936112	49936112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200821496	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	20	438	0	ENST00000296474.3:c.1558G>A	p.Val520Ile	p.V520I	ENST00000296474	NM_002447.2	520	Gta/Ata	4/20	1	2	FACETS	0.154	0.117	0.197	0.154	0.117	0.197	SUBCLONAL	1	TRUE	1	0.704782798284537	2		438	368	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939985	49939985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777931738	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	38	572	0	ENST00000296474.3:c.1058G>A	p.Gly353Asp	p.G353D	ENST00000296474	NM_002447.2	353	gGc/gAc	1/20	1	2	FACETS	0.227	0.187	0.271	0.227	0.187	0.271	SUBCLONAL	1	TRUE	1	0.704782798284537	2		572	475	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940703	49940703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	23	376	0	ENST00000296474.3:c.340C>T	p.Pro114Ser	p.P114S	ENST00000296474	NM_002447.2	114	Cct/Tct	1/20	1	2	FACETS	0.211	0.164	0.264	0.211	0.164	0.264	SUBCLONAL	1	TRUE	1	0.704782798284537	2		376	310	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713645	52713645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	33	339	0	ENST00000394830.3:c.83C>T	p.Thr28Ile	p.T28I	ENST00000394830	NM_018313.4	28	aCa/aTa	2/30	1	2	FACETS	0.164	0.133	0.199	0.164	0.133	0.199	SUBCLONAL	1	TRUE	1	0.704782798284537	2		339	572	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69788764	69788764	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1207755717	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	27	296	0	ENST00000352241.4:c.16G>A	p.Gly6Arg	p.G6R	ENST00000352241	NM_198159.2	6	Ggg/Agg	1/10	1	2	FACETS	0.193	0.154	0.239	0.193	0.154	0.239	SUBCLONAL	1	TRUE	1	0.704782798284537	2		296	396	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015143	71015143	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	25	228	0	ENST00000318789.4:c.1787G>A	p.Gly596Asp	p.G596D	ENST00000318789	NM_032682.5	596	gGc/gAc	20/21	1	2	FACETS	0.209	0.165	0.261	0.209	0.165	0.261	SUBCLONAL	1	TRUE	1	0.704782798284537	2		228	339	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102822	71102822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	20	239	0	ENST00000318789.4:c.385C>T	p.Leu129Phe	p.L129F	ENST00000318789	NM_032682.5	129	Ctc/Ttc	8/21	1	2	FACETS	0.184	0.14	0.235	0.184	0.14	0.235	SUBCLONAL	1	TRUE	1	0.704782798284537	2		239	309	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102839	71102839	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	20	242	0	ENST00000318789.4:c.368C>T	p.Pro123Leu	p.P123L	ENST00000318789	NM_032682.5	123	cCt/cTt	8/21	1	2	FACETS	0.17	0.13	0.218	0.17	0.13	0.218	SUBCLONAL	1	TRUE	1	0.704782798284537	2		242	333	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499409	89499409	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	39	320	0	ENST00000336596.2:c.2579G>A	p.Cys860Tyr	p.C860Y	ENST00000336596	NM_005233.5	860	tGc/tAc	15/17	1	2	FACETS	0.188	0.155	0.225	0.188	0.155	0.225	SUBCLONAL	1	TRUE	1	0.704782798284537	2		320	588	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521657	89521657	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs531837299	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	36	341	0	ENST00000336596.2:c.2734A>G	p.Thr912Ala	p.T912A	ENST00000336596	NM_005233.5	912	Acc/Gcc	16/17	1	2	FACETS	0.159	0.13	0.192	0.159	0.13	0.192	SUBCLONAL	1	TRUE	1	0.704782798284537	2		341	641	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205047	128205047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	22	477	0	ENST00000341105.2:c.394G>A	p.Gly132Arg	p.G132R	ENST00000341105	NM_032638.4	132	Gga/Aga	3/6	1	2	FACETS	0.175	0.135	0.221	0.175	0.135	0.221	SUBCLONAL	1	TRUE	1	0.704782798284537	2		477	357	SUCCESS
ATR	545	MSKCC	GRCh37	3	142189026	142189026	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	38	254	0	ENST00000350721.4:c.6222-1G>A		p.X2074_splice	ENST00000350721	NM_001184.3	2074			1	2	FACETS	0.285	0.235	0.339	0.285	0.235	0.339	SUBCLONAL	1	TRUE	1	0.704782798284537	2		254	379	SUCCESS
ATR	545	MSKCC	GRCh37	3	142243017	142243017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	32	322	0	ENST00000350721.4:c.3970G>A	p.Asp1324Asn	p.D1324N	ENST00000350721	NM_001184.3	1324	Gac/Aac	22/47	1	2	FACETS	0.158	0.128	0.193	0.158	0.128	0.193	SUBCLONAL	1	TRUE	1	0.704782798284537	2		322	574	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272494	142272494	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	40	470	0	ENST00000350721.4:c.2621G>A	p.Gly874Glu	p.G874E	ENST00000350721	NM_001184.3	874	gGg/gAg	12/47	1	2	FACETS	0.178	0.148	0.213	0.178	0.148	0.213	SUBCLONAL	1	TRUE	1	0.704782798284537	2		470	636	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279171	142279171	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	70	425	1	ENST00000350721.4:c.1475G>A	p.Gly492Glu	p.G492E	ENST00000350721	NM_001184.3	492	gGa/gAa	6/47	1	2	FACETS	0.287	0.25	0.328	0.287	0.25	0.328	SUBCLONAL	1	TRUE	1	0.704782798284537	2		426	691	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281085	142281085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	35	298	0	ENST00000350721.4:c.1159G>A	p.Val387Ile	p.V387I	ENST00000350721	NM_001184.3	387	Gta/Ata	4/47	1	2	FACETS	0.188	0.153	0.227	0.188	0.153	0.227	SUBCLONAL	1	TRUE	1	0.704782798284537	2		298	529	SUCCESS
ATR	545	MSKCC	GRCh37	3	142297492	142297492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	34	393	0	ENST00000350721.4:c.55G>A	p.Gly19Ser	p.G19S	ENST00000350721	NM_001184.3	19	Ggc/Agc	1/47	1	2	FACETS	0.227	0.185	0.274	0.227	0.185	0.274	SUBCLONAL	1	TRUE	1	0.704782798284537	2		393	425	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928113	178928113	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	49	339	0	ENST00000263967.3:c.1391C>T	p.Ser464Leu	p.S464L	ENST00000263967	NM_006218.2	464	tCa/tTa	8/21	1	2	FACETS	0.244	0.206	0.286	0.244	0.206	0.286	SUBCLONAL	1	TRUE	1	0.704782798284537	2		339	570	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455623	189455623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	72	328	0	ENST00000264731.3:c.157G>A	p.Glu53Lys	p.E53K	ENST00000264731	NM_003722.4	53	Gag/Aag	2/14	1	2	FACETS	0.272	0.237	0.31	0.272	0.237	0.31	SUBCLONAL	1	TRUE	1	0.704782798284537	2		328	750	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587194	189587194	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	38	287	0	ENST00000264731.3:c.1211C>T	p.Pro404Leu	p.P404L	ENST00000264731	NM_003722.4	404	cCa/cTa	9/14	1	2	FACETS	0.224	0.185	0.268	0.224	0.185	0.268	SUBCLONAL	1	TRUE	1	0.704782798284537	2		287	481	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608669	189608669	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs865905084	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	28	319	0	ENST00000264731.3:c.1744G>A	p.Asp582Asn	p.D582N	ENST00000264731	NM_003722.4	582	Gat/Aat	13/14	1	2	FACETS	0.169	0.135	0.209	0.169	0.135	0.209	SUBCLONAL	1	TRUE	1	0.704782798284537	2		319	469	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612286	189612286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	26	242	0	ENST00000264731.3:c.2038G>A	p.Glu680Lys	p.E680K	ENST00000264731	NM_003722.4	680	Gag/Aag	14/14	1	2	FACETS	0.229	0.181	0.284	0.229	0.181	0.284	SUBCLONAL	1	TRUE	1	0.704782798284537	2		242	322	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1976676	1976676	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	25	531	0	ENST00000382891.5:c.3459G>A	p.Trp1153Ter	p.W1153*	ENST00000382891	NM_133335.3	1153	tgG/tgA	19/22	1	2	FACETS	0.149	0.117	0.186	0.149	0.117	0.186	SUBCLONAL	1	TRUE	1	0.704782798284537	2		531	477	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55524198	55524198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	22	348	0	ENST00000288135.5:c.17G>A	p.Gly6Asp	p.G6D	ENST00000288135	NM_000222.2	6	gGc/gAc	1/21	1	2	FACETS	0.212	0.164	0.267	0.212	0.164	0.267	SUBCLONAL	1	TRUE	1	0.704782798284537	2		348	295	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561915	55561915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	22	217	0	ENST00000288135.5:c.305G>A	p.Gly102Asp	p.G102D	ENST00000288135	NM_000222.2	102	gGc/gAc	2/21	1	2	FACETS	0.192	0.149	0.243	0.192	0.149	0.243	SUBCLONAL	1	TRUE	1	0.704782798284537	2		217	325	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598054	55598054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	27	272	0	ENST00000288135.5:c.2251G>A	p.Asp751Asn	p.D751N	ENST00000288135	NM_000222.2	751	Gat/Aat	16/21	1	2	FACETS	0.164	0.13	0.203	0.164	0.13	0.203	SUBCLONAL	1	TRUE	1	0.704782798284537	2		272	467	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973970	55973970	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	57	393	0	ENST00000263923.4:c.1346C>T	p.Ala449Val	p.A449V	ENST00000263923	NM_002253.2	449	gCc/gTc	10/30	1	2	FACETS	0.257	0.22	0.298	0.257	0.22	0.298	SUBCLONAL	1	TRUE	1	0.704782798284537	2		393	629	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356425	66356425	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762220456	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	25	255	0	ENST00000273854.3:c.1072C>T	p.Pro358Ser	p.P358S	ENST00000273854	NM_004439.5	358	Ccc/Tcc	5/18	1	2	FACETS	0.175	0.137	0.218	0.175	0.137	0.218	SUBCLONAL	1	TRUE	1	0.704782798284537	2		255	406	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143181693	143181693	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	48	343	0	ENST00000262992.4:c.640G>A	p.Ala214Thr	p.A214T	ENST00000262992	NM_001101669.1	214	Gcc/Acc	9/24	1	2	FACETS	0.229	0.193	0.268	0.229	0.193	0.268	SUBCLONAL	1	TRUE	1	0.704782798284537	2		343	596	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247255	153247255	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	49	350	0	ENST00000281708.4:c.1547G>A	p.Ser516Asn	p.S516N	ENST00000281708	NM_033632.3	516	aGt/aAt	10/12	1	2	FACETS	0.219	0.185	0.256	0.219	0.185	0.256	SUBCLONAL	1	TRUE	1	0.704782798284537	2		350	636	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510349	187510349	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	18	156	0	ENST00000441802.2:c.13164G>A	p.Trp4388Ter	p.W4388*	ENST00000441802	NM_005245.3	4388	tgG/tgA	27/27	1	2	FACETS	0.188	0.141	0.243	0.188	0.141	0.243	SUBCLONAL	1	TRUE	1	0.704782798284537	2		156	272	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518843	187518843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	32	343	0	ENST00000441802.2:c.12361G>A	p.Gly4121Arg	p.G4121R	ENST00000441802	NM_005245.3	4121	Gga/Aga	24/27	1	2	FACETS	0.167	0.135	0.204	0.167	0.135	0.204	SUBCLONAL	1	TRUE	1	0.704782798284537	2		343	543	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549713	187549713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	39	360	0	ENST00000441802.2:c.4528G>A	p.Ala1510Thr	p.A1510T	ENST00000441802	NM_005245.3	1510	Gca/Aca	8/27	1	2	FACETS	0.248	0.205	0.295	0.248	0.205	0.295	SUBCLONAL	1	TRUE	1	0.704782798284537	2		360	447	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629331	187629331	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	47	529	1	ENST00000441802.2:c.1651G>A	p.Val551Ile	p.V551I	ENST00000441802	NM_005245.3	551	Gtc/Atc	2/27	1	2	FACETS	0.181	0.152	0.213	0.181	0.152	0.213	SUBCLONAL	1	TRUE	1	0.704782798284537	2		530	737	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235260	235260	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	32	278	0	ENST00000264932.6:c.1066G>A	p.Gly356Ser	p.G356S	ENST00000264932	NM_004168.2	356	Ggc/Agc	9/15	1	2	FACETS	0.261	0.212	0.316	0.261	0.212	0.316	SUBCLONAL	1	TRUE	1	0.704782798284537	2		278	348	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236598	236598	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374086655	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	16	190	0	ENST00000264932.6:c.1316G>A	p.Gly439Glu	p.G439E	ENST00000264932	NM_004168.2	439	gGg/gAg	10/15	1	2	FACETS	0.252	0.187	0.33	0.252	0.187	0.33	SUBCLONAL	1	TRUE	1	0.704782798284537	2		190	180	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271315	1271315	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369810792	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	21	492	0	ENST00000310581.5:c.2387C>T	p.Ser796Phe	p.S796F	ENST00000310581	NM_198253.2	796	tCc/tTc	8/16	1	2	FACETS	0.171	0.131	0.217	0.171	0.131	0.217	SUBCLONAL	1	TRUE	1	0.704782798284537	2		492	349	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295278	1295278	+	upstream_gene_variant	5'Flank	SNP	C	C	T	rs914835735	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	21	282	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.216	0.166	0.274	0.216	0.166	0.274	SUBCLONAL	1	TRUE	1	0.704782798284537	2		282	276	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31464365	31464365	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	53	541	0	ENST00000344624.3:c.2552G>A	p.Gly851Asp	p.G851D	ENST00000344624		851	gGc/gAc	17/33	0.140670844744254	4	FACETS	0.257	0.218	0.3	0.129	0.109	0.15	INDETERMINATE	1	TRUE	2	0.704782798284537	4		541	996	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515136	31515136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	43	516	0	ENST00000344624.3:c.1249C>T	p.His417Tyr	p.H417Y	ENST00000344624		417	Cat/Tat	5/33	0.140670844744254	4	FACETS	0.277	0.231	0.328	0.138	0.115	0.164	INDETERMINATE	1	TRUE	2	0.704782798284537	4		516	751	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526706	31526706	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	52	605	0	ENST00000344624.3:c.334C>T	p.Pro112Ser	p.P112S	ENST00000344624		112	Cca/Tca	2/33	0.140670844744254	4	FACETS	0.337	0.286	0.393	0.168	0.143	0.197	INDETERMINATE	1	TRUE	2	0.704782798284537	4		605	747	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160560	56160560	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs983191003	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	18	193	0	ENST00000399503.3:c.835-1G>A		p.X279_splice	ENST00000399503	NM_005921.1	279			0.140670844744254	4	FACETS	0.253	0.19	0.328	0.127	0.095	0.164	INDETERMINATE	1	TRUE	2	0.704782798284537	4		193	344	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170998	56170998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766159820	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	21	202	0	ENST00000399503.3:c.1826G>A	p.Ser609Asn	p.S609N	ENST00000399503	NM_005921.1	609	aGc/aAc	10/20	0.140670844744254	4	FACETS	0.314	0.241	0.398	0.157	0.12	0.199	INDETERMINATE	1	TRUE	2	0.704782798284537	4		202	324	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176984	56176984	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	52	330	0	ENST00000399503.3:c.2254C>T	p.Gln752Ter	p.Q752*	ENST00000399503	NM_005921.1	752	Caa/Taa	13/20	0.140670844744254	4	FACETS	0.449	0.382	0.523	0.225	0.191	0.262	INDETERMINATE	1	TRUE	2	0.704782798284537	4		330	560	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751969	57751969	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	35	317	0	ENST00000274289.3:c.1268C>T	p.Pro423Leu	p.P423L	ENST00000274289	NM_006622.3	423	cCt/cTt	10/14	0.140670844744254	4	FACETS	0.359	0.294	0.433	0.18	0.147	0.217	INDETERMINATE	1	TRUE	2	0.704782798284537	4		317	471	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754638	57754638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	19	258	0	ENST00000274289.3:c.409C>T	p.Leu137Phe	p.L137F	ENST00000274289	NM_006622.3	137	Ctt/Ttt	3/14	0.140670844744254	4	FACETS	0.246	0.186	0.317	0.123	0.093	0.159	INDETERMINATE	1	TRUE	2	0.704782798284537	4		258	373	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593346	67593346	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	152	285	1	ENST00000274335.5:c.2092T>A	p.Tyr698Asn	p.Y698N	ENST00000274335		698	Tac/Aac	15/15	0.140670844744254	4	FACETS	0.931	0.861	1	0.931	0.861	1	INDETERMINATE	2	TRUE	2	0.704782798284537	4		286	395	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064787	80064787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs931950562	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	42	388	0	ENST00000265081.6:c.2218C>T	p.Pro740Ser	p.P740S	ENST00000265081	NM_002439.4	740	Cct/Tct	15/24	0.140670844744254	4	FACETS	0.336	0.28	0.399	0.168	0.14	0.2	INDETERMINATE	1	TRUE	2	0.704782798284537	4		388	604	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564360	86564360	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1484820367	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	18	310	0	ENST00000274376.6:c.92C>T	p.Pro31Leu	p.P31L	ENST00000274376	NM_002890.2	31	cCc/cTc	1/25	0.140670844744254	4	FACETS	0.255	0.192	0.331	0.128	0.096	0.166	INDETERMINATE	1	TRUE	2	0.704782798284537	4		310	341	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564686	86564686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751440049	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	36	471	0	ENST00000274376.6:c.418C>T	p.Pro140Ser	p.P140S	ENST00000274376	NM_002890.2	140	Ccc/Tcc	1/25	0.140670844744254	4	FACETS	0.335	0.275	0.403	0.167	0.137	0.202	INDETERMINATE	1	TRUE	2	0.704782798284537	4		471	520	SUCCESS
APC	324	MSKCC	GRCh37	5	112173906	112173906	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	31	324	0	ENST00000257430.4:c.2615C>T	p.Thr872Ile	p.T872I	ENST00000257430	NM_000038.5	872	aCt/aTt	16/16	0.140670844744254	4	FACETS	0.297	0.239	0.362	0.148	0.119	0.181	INDETERMINATE	1	TRUE	2	0.704782798284537	4		324	505	SUCCESS
APC	324	MSKCC	GRCh37	5	112174008	112174008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554084407	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	48	296	0	ENST00000257430.4:c.2717C>T	p.Ser906Phe	p.S906F	ENST00000257430	NM_000038.5	906	tCt/tTt	16/16	0.140670844744254	4	FACETS	0.544	0.46	0.635	0.272	0.23	0.318	INDETERMINATE	1	TRUE	2	0.704782798284537	4		296	427	SUCCESS
APC	324	MSKCC	GRCh37	5	112175595	112175595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	43	324	0	ENST00000257430.4:c.4304G>A	p.Arg1435Lys	p.R1435K	ENST00000257430	NM_000038.5	1435	aGa/aAa	16/16	0.140670844744254	4	FACETS	0.422	0.353	0.499	0.211	0.176	0.25	INDETERMINATE	1	TRUE	2	0.704782798284537	4		324	493	SUCCESS
APC	324	MSKCC	GRCh37	5	112176971	112176971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	55	445	0	ENST00000257430.4:c.5680G>A	p.Val1894Ile	p.V1894I	ENST00000257430	NM_000038.5	1894	Gtt/Att	16/16	0.140670844744254	4	FACETS	0.439	0.375	0.509	0.22	0.187	0.255	INDETERMINATE	1	TRUE	2	0.704782798284537	4		445	606	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131976422	131976422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	40	374	0	ENST00000265335.6:c.3677G>A	p.Gly1226Asp	p.G1226D	ENST00000265335		1226	gGc/gAc	24/25	0.140670844744254	4	FACETS	0.323	0.268	0.385	0.162	0.134	0.193	INDETERMINATE	1	TRUE	2	0.704782798284537	4		374	599	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457752	149457752	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	36	449	0	ENST00000286301.3:c.652G>A	p.Glu218Lys	p.E218K	ENST00000286301	NM_005211.3	218	Gag/Aag	5/22	1	2	FACETS	0.2	0.163	0.24	0.2	0.163	0.24	SUBCLONAL	1	TRUE	1	0.704782798284537	2		449	512	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505094	149505094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	38	460	0	ENST00000261799.4:c.1721C>T	p.Ser574Phe	p.S574F	ENST00000261799	NM_002609.3	574	tCt/tTt	12/23	1	2	FACETS	0.193	0.159	0.231	0.193	0.159	0.231	SUBCLONAL	1	TRUE	1	0.704782798284537	2		460	558	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819800	170819800	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	33	390	0	ENST00000296930.5:c.439G>A	p.Gly147Ser	p.G147S	ENST00000296930	NM_002520.6	147	Ggt/Agt	5/11	1	2	FACETS	0.143	0.116	0.174	0.143	0.116	0.174	SUBCLONAL	1	TRUE	1	0.704782798284537	2		390	654	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051009	180051009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772365375	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	37	564	1	ENST00000261937.6:c.1474G>A	p.Val492Met	p.V492M	ENST00000261937	NM_182925.4	492	Gtg/Atg	11/30	NA	2	FACETS	0.26	0.214	0.311			1	INDETERMINATE	1	TRUE	NA	0.704782798284537	2		565	404	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056568	26056568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41266789	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	10	173	0	ENST00000343677.2:c.89G>A	p.Gly30Asp	p.G30D	ENST00000343677	NM_005319.3	30	gGt/gAt	1/1	1	2	FACETS	0.151	0.102	0.212	0.151	0.102	0.212	SUBCLONAL	1	TRUE	1	0.704782798284537	2		173	188	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858303	27858303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	42	444	0	ENST00000359303.2:c.268G>A	p.Val90Met	p.V90M	ENST00000359303	NM_003535.2	90	Gtg/Atg	1/1	1	2	FACETS	0.238	0.198	0.282	0.238	0.198	0.282	SUBCLONAL	1	TRUE	1	0.704782798284537	2		444	501	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322997	31322997	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1206176477	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	39	698	1	ENST00000412585.2:c.899C>T	p.Pro300Leu	p.P300L	ENST00000412585	NM_005514.6	300	cCg/cTg	5/8	1	2	FACETS	0.172	0.142	0.206	0.172	0.142	0.206	SUBCLONAL	1	TRUE	1	0.704782798284537	2		699	642	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324600	31324600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs72558108	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	44	672	0	ENST00000412585.2:c.208G>A	p.Glu70Lys	p.E70K	ENST00000412585	NM_005514.6	70	Gag/Aag	2/8	1	2	FACETS	0.223	0.187	0.264	0.223	0.187	0.264	SUBCLONAL	1	TRUE	1	0.704782798284537	2		672	559	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793491	89793491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	33	219	0	ENST00000336032.3:c.560G>A	p.Gly187Glu	p.G187E	ENST00000336032	NM_006813.2	187	gGa/gAa	2/2	1	2	FACETS	0.259	0.211	0.313	0.259	0.211	0.313	SUBCLONAL	1	TRUE	1	0.704782798284537	2		219	362	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109312027	109312027	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	49	408	0	ENST00000436639.2:c.1245G>A	p.Trp415Ter	p.W415*	ENST00000436639	NM_014454.2	415	tgG/tgA	8/10	1	2	FACETS	0.219	0.185	0.256	0.219	0.185	0.256	SUBCLONAL	1	TRUE	1	0.704782798284537	2		408	636	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662760	117662760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199762082	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	40	247	0	ENST00000368508.3:c.4705C>T	p.Arg1569Trp	p.R1569W	ENST00000368508	NM_002944.2	1569	Cgg/Tgg	29/43	1	2	FACETS	0.293	0.243	0.347	0.293	0.243	0.347	SUBCLONAL	1	TRUE	1	0.704782798284537	2		247	388	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708154	117708154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	53	338	1	ENST00000368508.3:c.2023C>T	p.Pro675Ser	p.P675S	ENST00000368508	NM_002944.2	675	Cca/Tca	14/43	1	2	FACETS	0.26	0.221	0.303	0.26	0.221	0.303	SUBCLONAL	1	TRUE	1	0.704782798284537	2		339	578	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137528212	137528212	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1203393893	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	20	177	0	ENST00000367739.4:c.88C>T	p.Pro30Ser	p.P30S	ENST00000367739	NM_000416.2	30	Cct/Tct	2/7	1	2	FACETS	0.182	0.139	0.233	0.182	0.139	0.233	SUBCLONAL	1	TRUE	1	0.704782798284537	2		177	311	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005446	150005446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1301685686	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	37	378	0	ENST00000253339.5:c.779G>A	p.Gly260Asp	p.G260D	ENST00000253339		260	gGt/gAt	3/7	1	2	FACETS	0.205	0.168	0.246	0.205	0.168	0.246	SUBCLONAL	1	TRUE	1	0.704782798284537	2		378	513	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099103	157099103	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	14	144	0	ENST00000346085.5:c.40C>T	p.His14Tyr	p.H14Y	ENST00000346085	NM_020732.3	14	Cac/Tac	1/20	1	2	FACETS	0.218	0.158	0.291	0.218	0.158	0.291	SUBCLONAL	1	TRUE	1	0.704782798284537	2		144	182	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099869	157099869	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774432900	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	38	326	0	ENST00000346085.5:c.806C>T	p.Ala269Val	p.A269V	ENST00000346085	NM_020732.3	269	gCc/gTc	1/20	1	2	FACETS	0.252	0.208	0.301	0.252	0.208	0.301	SUBCLONAL	1	TRUE	1	0.704782798284537	2		326	428	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522581	157522581	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	49	548	0	ENST00000346085.5:c.4853C>T	p.Pro1618Leu	p.P1618L	ENST00000346085	NM_020732.3	1618	cCa/cTa	18/20	1	2	FACETS	0.173	0.146	0.203	0.173	0.146	0.203	SUBCLONAL	1	TRUE	1	0.704782798284537	2		548	804	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528150	157528150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	29	379	1	ENST00000346085.5:c.5875C>T	p.Pro1959Ser	p.P1959S	ENST00000346085	NM_020732.3	1959	Cct/Tct	20/20	1	2	FACETS	0.178	0.142	0.219	0.178	0.142	0.219	SUBCLONAL	1	TRUE	1	0.704782798284537	2		380	462	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6045531	6045531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	18	151	0	ENST00000265849.7:c.155C>T	p.Thr52Ile	p.T52I	ENST00000265849	NM_000535.5	52	aCt/aTt	2/15	0.704782798284537	3	FACETS	0.231	0.174	0.299	0.116	0.087	0.15	SUBCLONAL	1	TRUE	1	0.704782798284537	3		151	299	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730081	41730081	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	41	369	0	ENST00000242208.4:c.448G>A	p.Val150Met	p.V150M	ENST00000242208	NM_002192.2	150	Gtg/Atg	3/3	0.704782798284537	3	FACETS	0.299	0.248	0.355	0.149	0.124	0.178	SUBCLONAL	1	TRUE	1	0.704782798284537	3		369	527	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249130	55249130	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913230	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	47	578	1	ENST00000275493.2:c.2428G>A	p.Gly810Ser	p.G810S	ENST00000275493	NM_005228.3	810	Ggc/Agc	20/28	0.704782798284537	3	FACETS	0.221	0.186	0.261	0.111	0.093	0.131	SUBCLONAL	1	TRUE	1	0.704782798284537	3		579	815	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374324	81374324	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	35	208	0	ENST00000222390.5:c.738G>C	p.Leu246Phe	p.L246F	ENST00000222390	NM_000601.4	246	ttG/ttC	6/18	0.704782798284537	3	FACETS	0.227	0.185	0.274	0.113	0.092	0.137	SUBCLONAL	1	TRUE	1	0.704782798284537	3		208	592	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1297	73	725	0	ENST00000397752.3:c.3028+1G>A		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.704782798284537	3	FACETS	0.204	0.178	0.234	0.102	0.089	0.117	SUBCLONAL	1	TRUE	1	0.704782798284537	3		725	1370	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435713	116435713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	42	225	0	ENST00000397752.3:c.3803C>T	p.Ser1268Phe	p.S1268F	ENST00000397752	NM_000245.2	1268	tCc/tTc	20/21	0.704782798284537	3	FACETS	0.32	0.267	0.38	0.16	0.133	0.19	SUBCLONAL	1	TRUE	1	0.704782798284537	3		225	503	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845231	128845231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	27	343	0	ENST00000249373.3:c.725G>A	p.Gly242Asp	p.G242D	ENST00000249373	NM_005631.4	242	gGc/gAc	3/12	0.704782798284537	3	FACETS	0.252	0.2	0.312	0.126	0.1	0.156	SUBCLONAL	1	TRUE	1	0.704782798284537	3		343	411	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842292	151842292	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	35	302	0	ENST00000262189.6:c.14120G>A	p.Gly4707Asp	p.G4707D	ENST00000262189	NM_170606.2	4707	gGt/gAt	54/59	0.704782798284537	3	FACETS	0.2	0.163	0.242	0.1	0.081	0.121	SUBCLONAL	1	TRUE	1	0.704782798284537	3		302	671	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851499	151851499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766640263	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	39	335	0	ENST00000262189.6:c.11992C>T	p.Pro3998Ser	p.P3998S	ENST00000262189	NM_170606.2	3998	Cct/Tct	47/59	0.704782798284537	3	FACETS	0.28	0.232	0.335	0.14	0.116	0.168	SUBCLONAL	1	TRUE	1	0.704782798284537	3		335	534	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859965	151859965	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	25	227	0	ENST00000262189.6:c.10697G>A	p.Ser3566Asn	p.S3566N	ENST00000262189	NM_170606.2	3566	aGc/aAc	43/59	0.704782798284537	3	FACETS	0.217	0.17	0.271	0.109	0.085	0.136	SUBCLONAL	1	TRUE	1	0.704782798284537	3		227	442	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873390	151873390	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	26	259	0	ENST00000262189.6:c.9148G>A	p.Glu3050Lys	p.E3050K	ENST00000262189	NM_170606.2	3050	Gaa/Aaa	38/59	0.704782798284537	3	FACETS	0.207	0.163	0.257	0.104	0.081	0.129	SUBCLONAL	1	TRUE	1	0.704782798284537	3		259	482	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877160	151877160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	42	293	0	ENST00000262189.6:c.7201G>A	p.Ala2401Thr	p.A2401T	ENST00000262189	NM_170606.2	2401	Gca/Aca	37/59	0.704782798284537	3	FACETS	0.287	0.239	0.341	0.144	0.119	0.171	SUBCLONAL	1	TRUE	1	0.704782798284537	3		293	561	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878848	151878848	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756581028	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	42	448	0	ENST00000262189.6:c.6097C>T	p.Pro2033Ser	p.P2033S	ENST00000262189	NM_170606.2	2033	Cct/Tct	36/59	0.704782798284537	3	FACETS	0.206	0.171	0.245	0.103	0.085	0.123	SUBCLONAL	1	TRUE	1	0.704782798284537	3		448	782	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879036	151879036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	40	430	0	ENST00000262189.6:c.5909C>T	p.Pro1970Leu	p.P1970L	ENST00000262189	NM_170606.2	1970	cCt/cTt	36/59	0.704782798284537	3	FACETS	0.199	0.164	0.237	0.099	0.082	0.119	SUBCLONAL	1	TRUE	1	0.704782798284537	3		430	773	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879531	151879531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	34	270	0	ENST00000262189.6:c.5414G>A	p.Gly1805Glu	p.G1805E	ENST00000262189	NM_170606.2	1805	gGg/gAg	36/59	0.704782798284537	3	FACETS	0.251	0.204	0.303	0.125	0.102	0.152	SUBCLONAL	1	TRUE	1	0.704782798284537	3		270	520	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540194	23540194	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	19	211	0	ENST00000380871.4:c.209G>A	p.Gly70Glu	p.G70E	ENST00000380871	NM_006167.3	70	gGg/gAg	1/2	1	2	FACETS	0.245	0.186	0.314	0.245	0.186	0.314	SUBCLONAL	1	TRUE	1	0.704782798284537	2		211	220	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194850	29194850	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	50	632	1	ENST00000240100.2:c.878C>T	p.Ala293Val	p.A293V	ENST00000240100	NM_001394.6	293	gCc/gTc	4/4	1	2	FACETS	0.249	0.211	0.291	0.249	0.211	0.291	SUBCLONAL	1	TRUE	1	0.704782798284537	2		633	570	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172969	38172969	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	53	450	0	ENST00000317025.8:c.2080G>A	p.Gly694Ser	p.G694S	ENST00000317025	NM_023034.1	694	Ggc/Agc	11/24	1	2	FACETS	0.207	0.176	0.241	0.207	0.176	0.241	SUBCLONAL	1	TRUE	1	0.704782798284537	2		450	726	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205401	38205401	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	57	567	0	ENST00000317025.8:c.289G>A	p.Ala97Thr	p.A97T	ENST00000317025	NM_023034.1	97	Gcc/Acc	2/24	1	2	FACETS	0.188	0.16	0.218	0.188	0.16	0.218	SUBCLONAL	1	TRUE	1	0.704782798284537	2		567	861	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939505	68939505	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777220819	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	45	348	0	ENST00000288368.4:c.490G>A	p.Gly164Arg	p.G164R	ENST00000288368	NM_024870.2	164	Gga/Aga	5/40	1	2	FACETS	0.211	0.177	0.249	0.211	0.177	0.249	SUBCLONAL	1	TRUE	1	0.704782798284537	2		348	604	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942852	68942852	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	65	479	0	ENST00000288368.4:c.664G>A	p.Glu222Lys	p.E222K	ENST00000288368	NM_024870.2	222	Gaa/Aaa	6/40	1	2	FACETS	0.197	0.17	0.226	0.197	0.17	0.226	SUBCLONAL	1	TRUE	1	0.704782798284537	2		479	937	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950458	68950458	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	35	366	0	ENST00000288368.4:c.770C>T	p.Ser257Phe	p.S257F	ENST00000288368	NM_024870.2	257	tCt/tTt	7/40	1	2	FACETS	0.149	0.121	0.18	0.149	0.121	0.18	SUBCLONAL	1	TRUE	1	0.704782798284537	2		366	667	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002864	69002864	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	35	227	0	ENST00000288368.4:c.2164G>A	p.Val722Met	p.V722M	ENST00000288368	NM_024870.2	722	Gtg/Atg	20/40	1	2	FACETS	0.209	0.171	0.251	0.209	0.171	0.251	SUBCLONAL	1	TRUE	1	0.704782798284537	2		227	476	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141567247	141567247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	30	486	0	ENST00000220592.5:c.967C>T	p.Pro323Ser	p.P323S	ENST00000220592	NM_012154.3	323	Ccc/Tcc	8/19	1	2	FACETS	0.173	0.139	0.212	0.173	0.139	0.212	SUBCLONAL	1	TRUE	1	0.704782798284537	2		486	493	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141569493	141569493	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	25	286	0	ENST00000220592.5:c.790+1G>A		p.X264_splice	ENST00000220592	NM_012154.3	264			1	2	FACETS	0.214	0.169	0.267	0.214	0.169	0.267	SUBCLONAL	1	TRUE	1	0.704782798284537	2		286	331	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080635	5080635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	58	369	0	ENST00000381652.3:c.2386C>T	p.Pro796Ser	p.P796S	ENST00000381652	NM_004972.3	796	Cct/Tct	18/25	0.699133593655009	1	FACETS	0.242	0.208	0.279	0.242	0.208	0.279	SUBCLONAL	1	TRUE	0	0.704782798284537	1		369	440	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465471	8465471	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	24	377	2	ENST00000356435.5:c.3709G>A	p.Glu1237Lys	p.E1237K	ENST00000356435		1237	Gag/Aag	21/35	0.699133593655009	1	FACETS	0.139	0.108	0.174	0.139	0.108	0.174	SUBCLONAL	1	TRUE	0	0.704782798284537	1		379	318	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485774	8485774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767662106	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	28	193	0	ENST00000356435.5:c.3043C>T	p.Pro1015Ser	p.P1015S	ENST00000356435		1015	Cct/Tct	17/35	0.699133593655009	1	FACETS	0.247	0.199	0.302	0.247	0.199	0.302	SUBCLONAL	1	TRUE	0	0.704782798284537	1		193	208	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8527354	8527354	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	40	244	0	ENST00000356435.5:c.542-1G>A		p.X181_splice	ENST00000356435		181			0.699133593655009	1	FACETS	0.271	0.226	0.321	0.271	0.226	0.321	SUBCLONAL	1	TRUE	0	0.704782798284537	1		244	271	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840582	36840582	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1287572963	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	19	575	3	ENST00000358127.4:c.1151C>T	p.Ala384Val	p.A384V	ENST00000358127	NM_001280556.1	384	gCc/gTc	10/10	0.704782798284537	1	FACETS	0.106	0.08	0.137	0.106	0.08	0.137	SUBCLONAL	1	TRUE	0	0.704782798284537	1		578	328	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87322828	87322828	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	37	278	0	ENST00000277120.3:c.428+1G>A		p.X143_splice	ENST00000277120		143			1	2	FACETS	0.176	0.145	0.212	0.176	0.145	0.212	SUBCLONAL	1	TRUE	1	0.704782798284537	2		278	596	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97869545	97869545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564641759	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	21	311	0	ENST00000289081.3:c.1336G>A	p.Val446Met	p.V446M	ENST00000289081	NM_000136.2	446	Gtg/Atg	14/15	1	2	FACETS	0.234	0.18	0.296	0.234	0.18	0.296	SUBCLONAL	1	TRUE	1	0.704782798284537	2		311	255	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215827	98215827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	44	464	0	ENST00000331920.6:c.3382G>A	p.Asp1128Asn	p.D1128N	ENST00000331920	NM_000264.3	1128	Gat/Aat	20/24	1	2	FACETS	0.233	0.195	0.276	0.233	0.195	0.276	SUBCLONAL	1	TRUE	1	0.704782798284537	2		464	535	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220455	98220455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769866360	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	47	467	1	ENST00000331920.6:c.3008G>A	p.Ser1003Asn	p.S1003N	ENST00000331920	NM_000264.3	1003	aGc/aAc	18/24	1	2	FACETS	0.238	0.2	0.279	0.238	0.2	0.279	SUBCLONAL	1	TRUE	1	0.704782798284537	2		468	561	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242284	98242284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1288810300	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	35	370	1	ENST00000331920.6:c.1034G>A	p.Gly345Asp	p.G345D	ENST00000331920	NM_000264.3	345	gGc/gAc	7/24	1	2	FACETS	0.187	0.152	0.225	0.187	0.152	0.225	SUBCLONAL	1	TRUE	1	0.704782798284537	2		371	532	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250365	110250365	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	54	598	0	ENST00000374672.4:c.310G>A	p.Asp104Asn	p.D104N	ENST00000374672	NM_004235.4	104	Gac/Aac	3/5	1	2	FACETS	0.282	0.241	0.328	0.282	0.241	0.328	SUBCLONAL	1	TRUE	1	0.704782798284537	2		598	543	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771785	135771785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554812642	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	31	522	1	ENST00000298552.3:c.3332G>A	p.Ser1111Asn	p.S1111N	ENST00000298552	NM_001162426.1	1111	aGt/aAt	23/23	1	2	FACETS	0.15	0.121	0.183	0.15	0.121	0.183	SUBCLONAL	1	TRUE	1	0.704782798284537	2		523	587	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309103	137309103	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	166	695	0	ENST00000481739.1:c.710A>G	p.Glu237Gly	p.E237G	ENST00000481739	NM_002957.4	237	gAg/gGg	5/10	0.14304506606078	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.704782798284537	0		695	535	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137325977	137325977	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	29	477	0	ENST00000481739.1:c.1165G>T	p.Val389Leu	p.V389L	ENST00000481739	NM_002957.4	389	Gtg/Ttg	9/10	0.14304506606078	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.704782798284537	0		477	452	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391046	139391046	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1564567924	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	38	608	0	ENST00000277541.6:c.7145C>T	p.Thr2382Ile	p.T2382I	ENST00000277541	NM_017617.3	2382	aCc/aTc	34/34	0.14304506606078	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.704782798284537	0		608	466	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396740	139396740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	23	467	0	ENST00000277541.6:c.5368G>A	p.Asp1790Asn	p.D1790N	ENST00000277541	NM_017617.3	1790	Gac/Aac	28/34	0.14304506606078	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.704782798284537	0		467	435	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913523	39913523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	15	249	0	ENST00000378444.4:c.4805G>A	p.Gly1602Asp	p.G1602D	ENST00000378444	NM_001123385.1	1602	gGc/gAc	13/15	1	1	FACETS	0.092	0.067	0.123	0.092	0.067	0.123	SUBCLONAL	1	TRUE	0	0.704782798284537	1		249	299	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937122	39937122	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	23	269	0	ENST00000378444.4:c.61C>T	p.Arg21Cys	p.R21C	ENST00000378444	NM_001123385.1	21	Cgc/Tgc	2/15	1	1	FACETS	0.163	0.127	0.204	0.163	0.127	0.204	SUBCLONAL	1	TRUE	0	0.704782798284537	1		269	260	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225145	53225145	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	18	255	0	ENST00000375401.3:c.3073G>A	p.Ala1025Thr	p.A1025T	ENST00000375401	NM_004187.3	1025	Gct/Act	20/26	1	1	FACETS	0.121	0.091	0.157	0.121	0.091	0.157	SUBCLONAL	1	TRUE	0	0.704782798284537	1		255	273	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225900	53225900	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	24	256	0	ENST00000375401.3:c.2949G>A	p.Trp983Ter	p.W983*	ENST00000375401	NM_004187.3	983	tgG/tgA	19/26	1	1	FACETS	0.179	0.14	0.223	0.179	0.14	0.223	SUBCLONAL	1	TRUE	0	0.704782798284537	1		256	247	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356392	70356392	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	29	245	0	ENST00000374080.3:c.5287G>A	p.Ala1763Thr	p.A1763T	ENST00000374080		1763	Gct/Act	37/45	1	1	FACETS	0.247	0.199	0.3	0.247	0.199	0.3	SUBCLONAL	1	TRUE	0	0.704782798284537	1		245	216	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872183	76872183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	30	175	0	ENST00000373344.5:c.5464G>A	p.Ala1822Thr	p.A1822T	ENST00000373344	NM_000489.3	1822	Gca/Aca	22/35	1	1	FACETS	0.173	0.14	0.212	0.173	0.14	0.212	SUBCLONAL	1	TRUE	0	0.704782798284537	1		175	318	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937599	76937599	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868968269	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	27	153	0	ENST00000373344.5:c.3149G>A	p.Arg1050Lys	p.R1050K	ENST00000373344	NM_000489.3	1050	aGa/aAa	9/35	1	1	FACETS	0.195	0.155	0.239	0.195	0.155	0.239	SUBCLONAL	1	TRUE	0	0.704782798284537	1		153	255	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210314	123210314	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	30	165	0	ENST00000218089.9:c.2666A>G	p.Tyr889Cys	p.Y889C	ENST00000218089	NM_001042749.1	889	tAt/tGt	26/35	1	1	FACETS	0.235	0.19	0.285	0.235	0.19	0.285	SUBCLONAL	1	TRUE	0	0.704782798284537	1		165	235	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435667	18435667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	54	313	2	ENST00000266497.5:c.652G>A	p.Glu218Lys	p.E218K	ENST00000266497		218	Gaa/Aaa	1/31	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.692084648788604	2		315	145	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	58	630	1	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.873	0.763	0.989	0.873	0.763	0.989	CLONAL	1	TRUE	1	0.692084648788604	2		631	192	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972936	68972936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	79	507	0	ENST00000288368.4:c.1261G>A	p.Glu421Lys	p.E421K	ENST00000288368	NM_024870.2	421	Gaa/Aaa	11/40	1	2	FACETS	0.984	0.88	1	0.984	0.88	1	CLONAL	1	TRUE	1	0.692084648788604	2		507	232	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374293	138374293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	181	606	0	ENST00000289153.2:c.3151G>A	p.Glu1051Lys	p.E1051K	ENST00000289153	NM_006219.2	1051	Gaa/Aaa	22/22	0.644722919763156	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.692084648788604	3		606	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	118	679	1	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.692084648788604	2		680	288	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	63	430	2	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.813	0.713	0.918	0.813	0.713	0.918	CLONAL	1	TRUE	1	0.692084648788604	2		432	224	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	70	391	1	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.692084648788604	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.692084648788604	1		392	121	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	61	531	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.943	0.828	1	0.943	0.828	1	CLONAL	1	TRUE	1	0.692084648788604	2		532	187	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347756	347756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769767245	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	26	692	0	ENST00000262320.3:c.1750G>A	p.Ala584Thr	p.A584T	ENST00000262320	NM_003502.3	584	Gct/Act	6/11	NA	2	FACETS	0.501	0.401	0.612			1	INDETERMINATE	1	TRUE	NA	0.692084648788604	2		692	150	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737622	145737624	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs747349932	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	19	647	0	ENST00000428558.2:c.3139_3141del	p.Glu1047del	p.E1047del	ENST00000428558	NM_004260.3	1047	GAG/-	19/22	1	2	FACETS	0.384	0.294	0.488	0.384	0.294	0.488	SUBCLONAL	1	TRUE	1	0.692084648788604	2		647	143	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447240	187447240	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763822826	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	92	497	1	ENST00000232014.4:c.953C>T	p.Pro318Leu	p.P318L	ENST00000232014	NM_001130845.1	318	cCc/cTc	5/10	0.692084648788604	3	FACETS	1	0.958	1	0.564	0.507	0.624	CLONAL	1	TRUE	1	0.692084648788604	3		498	317	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149974	202149974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301592633	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	86	538	1	ENST00000358485.4:c.1415G>A	p.Arg472Gln	p.R472Q	ENST00000358485	NM_001080125.1	472	cGa/cAa	8/9	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.692084648788604	2		539	228	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971138	21971138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760640852	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	87	338	0	ENST00000304494.5:c.220G>A	p.Asp74Asn	p.D74N	ENST00000304494	NM_000077.4	74	Gac/Aac	2/3	1	2	FACETS	0.898	0.827	0.967	1	0.988	1	CLONAL	2	TRUE	1	0.692084648788604	2		338	140	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953748	48953748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759079385	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	89	293	1	ENST00000267163.4:c.1351C>T	p.Arg451Cys	p.R451C	ENST00000267163	NM_000321.2	451	Cgc/Tgc	14/27	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.692084648788604	2		294	199	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857152	9857152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369508378	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	61	397	2	ENST00000330684.3:c.4249C>T	p.Arg1417Trp	p.R1417W	ENST00000330684	NM_001134407.1	1417	Cgg/Tgg	13/13	NA	2	FACETS	1	0.929	1			1	INDETERMINATE	1	TRUE	NA	0.692084648788604	2		399	164	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916463	39916463	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	88	389	1	ENST00000378444.4:c.4540C>T	p.Arg1514Ter	p.R1514*	ENST00000378444	NM_001123385.1	1514	Cga/Tga	11/15	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.692084648788604	1		390	125	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971133	21971133	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	46	267	0	ENST00000304494.5:c.225del	p.Ala76ProfsTer70	p.A76Pfs*70	ENST00000304494	NM_000077.4	75	ccC/cc	2/3	1	2	FACETS	0.791	0.678	0.912	0.791	0.678	0.912	CLONAL	1	TRUE	1	0.692084648788604	2		267	168	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271747	15271747	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs773656789	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	13	628	2	ENST00000263388.2:c.6692del	p.Pro2231GlnfsTer15	p.P2231Qfs*15	ENST00000263388	NM_000435.2	2231	cCa/ca	33/33	0.129421883070166	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.692084648788604	0		630	145	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808929	3808929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	86	665	1	ENST00000262367.5:c.3295G>A	p.Glu1099Lys	p.E1099K	ENST00000262367	NM_004380.2	1099	Gaa/Aaa	17/31	NA	2	FACETS	0.854	0.764	0.947			1	INDETERMINATE	1	TRUE	NA	0.692084648788604	2		666	291	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	29	509	1	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	1	2	FACETS	0.448	0.363	0.544	0.448	0.363	0.544	SUBCLONAL	1	TRUE	1	0.692084648788604	2		510	187	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509208	106509208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	78	585	0	ENST00000359195.3:c.1202C>T	p.Pro401Leu	p.P401L	ENST00000359195	NM_002649.2	401	cCc/cTc	2/11	1	2	FACETS	0.928	0.827	1	0.928	0.827	1	CLONAL	1	TRUE	1	0.692084648788604	2		585	243	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720727	89720727	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	14	171	0	ENST00000371953.3:c.878G>T	p.Gly293Val	p.G293V	ENST00000371953	NM_000314.4	293	gGa/gTa	8/9	0.692084648788604	1	FACETS	0.63	0.476	0.798	0.63	0.476	0.798	SUBCLONAL	1	TRUE	0	0.692084648788604	1		171	42	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995569	68995569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775560862	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	103	430	1	ENST00000288368.4:c.1973C>T	p.Ser658Leu	p.S658L	ENST00000288368	NM_024870.2	658	tCg/tTg	18/40	1	2	FACETS	0.986	0.894	1	0.986	0.894	1	CLONAL	1	TRUE	1	0.692084648788604	2		431	302	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444960	49444960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	60	438	1	ENST00000301067.7:c.2506del	p.Gln836SerfsTer94	p.Q836Sfs*94	ENST00000301067	NM_003482.3	836	Cag/ag	10/54	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.692084648788604	2		439	160	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637211	176637211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61744451	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	90	575	2	ENST00000439151.2:c.1811G>A	p.Arg604Gln	p.R604Q	ENST00000439151	NM_022455.4	604	cGa/cAa	5/23	1	2	FACETS	0.919	0.826	1	0.919	0.826	1	CLONAL	1	TRUE	1	0.692084648788604	2		577	283	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435227	18435227	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1368182752	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	61	329	0	ENST00000266497.5:c.212G>A	p.Trp71Ter	p.W71*	ENST00000266497		71	tGg/tAg	1/31	1	2	FACETS	0.985	0.866	1	0.985	0.866	1	CLONAL	1	TRUE	1	0.692084648788604	2		329	179	SUCCESS
MET	4233	MSKCC	GRCh37	7	116413630	116413630	+	intron_variant	Intron	SNP	C	C	T	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	93	836	0	ENST00000397752.3:c.3029-1305C>T		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.867	0.78	0.958	0.867	0.78	0.958	CLONAL	1	TRUE	1	0.692084648788604	2		836	310	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969978	81969978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755551138	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	53	335	0	ENST00000359376.3:c.3047C>T	p.Thr1016Met	p.T1016M	ENST00000359376	NM_002661.3	1016	aCg/aTg	27/33	1	2	FACETS	0.945	0.823	1	0.945	0.823	1	CLONAL	1	TRUE	1	0.692084648788604	2		335	162	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261326	16261326	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	59	550	0	ENST00000375759.3:c.8591C>G	p.Ser2864Trp	p.S2864W	ENST00000375759	NM_015001.2	2864	tCg/tGg	11/15	1	2	FACETS	0.974	0.855	1	0.974	0.855	1	CLONAL	1	TRUE	1	0.692084648788604	2		550	175	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105769	27105769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	83	385	0	ENST00000324856.7:c.5380G>A	p.Asp1794Asn	p.D1794N	ENST00000324856	NM_006015.4	1794	Gac/Aac	20/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.692084648788604	2		385	197	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106094	27106094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	75	487	0	ENST00000324856.7:c.5705C>T	p.Pro1902Leu	p.P1902L	ENST00000324856	NM_006015.4	1902	cCt/cTt	20/20	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.692084648788604	2		487	204	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36826917	36826917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772438289	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	65	605	2	ENST00000373129.3:c.17C>T	p.Ser6Leu	p.S6L	ENST00000373129	NM_032017.1	6	tCa/tTa	3/12	1	2	FACETS	0.831	0.731	0.936	0.831	0.731	0.936	CLONAL	1	TRUE	1	0.692084648788604	2		607	226	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795098	45795099	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	70	388	0	ENST00000450313.1:c.1529_1530delinsAA	p.Arg510Lys	p.R510K	ENST00000450313	NM_012222.2	510	aGG/aAA	16/16	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.692084648788604	2		388	179	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115260810	115260810	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1321899897	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	94	550	1	ENST00000438362.2:c.2515C>T	p.Gln839Ter	p.Q839*	ENST00000438362	NM_001242891.1	839	Caa/Taa	20/20	1	2	FACETS	0.967	0.872	1	0.967	0.872	1	CLONAL	1	TRUE	1	0.692084648788604	2		551	281	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206665025	206665025	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	15	539	0	ENST00000367120.3:c.1778A>C	p.Gln593Pro	p.Q593P	ENST00000367120	NM_014002.3	593	cAg/cCg	18/22	1	2	FACETS	0.174	0.127	0.231	0.174	0.127	0.231	SUBCLONAL	1	TRUE	1	0.692084648788604	2		539	249	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298115	123298115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	79	482	0	ENST00000358487.5:c.739G>A	p.Asp247Asn	p.D247N	ENST00000358487	NM_000141.4	247	Gat/Aat	6/18	0.692084648788604	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.692084648788604	1		482	139	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945396	71945396	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	71	822	0	ENST00000298229.2:c.2284C>A	p.Arg762Ser	p.R762S	ENST00000298229	NM_001567.3	762	Cgc/Agc	20/28	1	2	FACETS	0.904	0.801	1	0.904	0.801	1	CLONAL	1	TRUE	1	0.692084648788604	2		822	227	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94923032	94923032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764529249	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	128	695	0	ENST00000536441.1:c.436G>A	p.Glu146Lys	p.E146K	ENST00000536441	NM_144665.3	146	Gaa/Aaa	4/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.692084648788604	2		695	334	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170564	108170564	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	88	545	0	ENST00000278616.4:c.5129G>A	p.Trp1710Ter	p.W1710*	ENST00000278616	NM_000051.3	1710	tGg/tAg	34/63	1	2	FACETS	0.902	0.809	0.998	0.902	0.809	0.998	CLONAL	1	TRUE	1	0.692084648788604	2		545	282	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103364	119103365	+	missense_variant	Missense_Mutation	DNP	GG	GG	AC	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	50	517	2	ENST00000264033.4:c.402_403delinsAC	p.Glu135Gln	p.E135Q	ENST00000264033	NM_005188.3	134	aaGGag/aaACag	2/16	NA	2	FACETS	0.803	0.692	0.92			1	INDETERMINATE	1	TRUE	NA	0.692084648788604	2		519	180	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497554	125497554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	19	345	0	ENST00000428830.2:c.118G>A	p.Val40Ile	p.V40I	ENST00000428830	NM_001114121.2	40	Gta/Ata	3/14	NA	2	FACETS	0.257	0.195	0.328			1	INDETERMINATE	1	TRUE	NA	0.692084648788604	2		345	214	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439868	49439868	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226418607	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	90	575	1	ENST00000301067.7:c.4673C>T	p.Pro1558Leu	p.P1558L	ENST00000301067	NM_003482.3	1558	cCc/cTc	17/54	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.692084648788604	2		576	220	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096209	2096209	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148104494	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	87	747	0	ENST00000219066.1:c.298C>T	p.Arg100Cys	p.R100C	ENST00000219066	NM_002528.5	100	Cgt/Tgt	2/6	NA	2	FACETS	1	0.963	1			1	INDETERMINATE	1	TRUE	NA	0.692084648788604	2		747	220	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858243	9858243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	59	406	0	ENST00000330684.3:c.3158C>T	p.Pro1053Leu	p.P1053L	ENST00000330684	NM_001134407.1	1053	cCa/cTa	13/13	NA	2	FACETS	1	0.952	1			1	INDETERMINATE	1	TRUE	NA	0.692084648788604	2		406	147	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835741	68835741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567501376	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	124	589	1	ENST00000261769.5:c.332C>T	p.Ser111Phe	p.S111F	ENST00000261769	NM_004360.3	111	tCc/tTc	3/16	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.692084648788604	2		590	357	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346178	89346178	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	25	160	0	ENST00000301030.4:c.6772del	p.Ala2258LeufsTer79	p.A2258Lfs*79	ENST00000301030	NM_001256183.1	2258	Gct/ct	9/13	1	2	FACETS	0.99	0.807	1	0.99	0.807	1	CLONAL	1	TRUE	1	0.692084648788604	2		160	73	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37672036	37672036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	174	565	0	ENST00000447079.4:c.2821G>A	p.Glu941Lys	p.E941K	ENST00000447079	NM_015083.1	941	Gaa/Aaa	9/14	0.692084648788604	2	FACETS	0.994	0.943	1	0.994	0.943	1	CLONAL	2	TRUE	0	0.692084648788604	2		565	253	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435948	56435948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs531889929	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	62	364	2	ENST00000407977.2:c.1189C>T	p.Arg397Trp	p.R397W	ENST00000407977		397	Cgg/Tgg	9/10	0.692084648788604	2	FACETS	0.914	0.829	0.995	0.914	0.829	0.995	CLONAL	2	TRUE	0	0.692084648788604	2		366	98	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280022	18280022	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	26	301	0	ENST00000222254.8:c.2105T>C	p.Val702Ala	p.V702A	ENST00000222254	NM_005027.3	702	gTg/gCg	16/16	0.129421883070166	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.692084648788604	0		301	77	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743850	41743850	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	83	559	1	ENST00000301178.4:c.785C>A	p.Ala262Asp	p.A262D	ENST00000301178	NM_021913.4	262	gCt/gAt	7/20	0.129421883070166	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.692084648788604	0		560	190	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982462	25982463	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	99	405	2	ENST00000435504.4:c.827_828delinsTT	p.Ser276Phe	p.S276F	ENST00000435504		276	tCC/tTT	9/13	NA	2	FACETS	0.96	0.868	1			1	INDETERMINATE	1	TRUE	NA	0.692084648788604	2		407	298	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991688	25991689	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	70	507	0	ENST00000435504.4:c.553dup	p.Ser185LysfsTer20	p.S185Kfs*20	ENST00000435504		185	agc/aAgc	7/13	NA	2	FACETS	0.872	0.771	0.977			1	INDETERMINATE	1	TRUE	NA	0.692084648788604	2		507	232	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917736	29917736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150966028	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	68	680	2	ENST00000389048.3:c.932G>A	p.Arg311His	p.R311H	ENST00000389048	NM_004304.4	311	cGt/cAt	3/29	0.5366388246548	1	FACETS	0.652	0.578	0.729	0.652	0.578	0.729	SUBCLONAL	1	TRUE	0	0.692084648788604	1		682	197	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026320	48026320	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	61	414	0	ENST00000234420.5:c.1198G>A	p.Glu400Lys	p.E400K	ENST00000234420	NM_000179.2	400	Gag/Aag	4/10	1	2	FACETS	0.99	0.871	1	0.99	0.871	1	CLONAL	1	TRUE	1	0.692084648788604	2		414	178	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866477	42866477	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs774327563	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	96	781	0	ENST00000398585.3:c.155A>G	p.Tyr52Cys	p.Y52C	ENST00000398585	NM_001135099.1	52	tAt/tGt	3/14	0.692084648788604	3	FACETS	1	0.933	1	0.524	0.471	0.58	CLONAL	1	TRUE	1	0.692084648788604	3		781	356	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37061817	37061817	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750489	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	70	529	0	ENST00000231790.2:c.901C>T	p.Gln301Ter	p.Q301*	ENST00000231790	NM_000249.3	301	Cag/Tag	11/19	0.668296730249036	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.692084648788604	1		529	128	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461521	138461521	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	101	556	0	ENST00000289153.2:c.500C>T	p.Ser167Phe	p.S167F	ENST00000289153	NM_006219.2	167	tCt/tTt	3/22	0.644722919763156	3	FACETS	1	0.96	1	0.561	0.506	0.618	CLONAL	1	TRUE	1	0.692084648788604	3		556	350	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013720	170013720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	75	636	2	ENST00000295797.4:c.1439G>A	p.Arg480His	p.R480H	ENST00000295797	NM_002740.5	480	cGc/cAc	15/18	0.692084648788604	3	FACETS	0.685	0.603	0.773	0.342	0.301	0.387	SUBCLONAL	1	TRUE	1	0.692084648788604	3		638	426	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165730	185165730	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	61	350	0	ENST00000265026.3:c.1005T>A	p.Asp335Glu	p.D335E	ENST00000265026	NM_004721.4	335	gaT/gaA	5/14	0.692084648788604	3	FACETS	0.815	0.709	0.929	0.408	0.354	0.465	CLONAL	1	TRUE	1	0.692084648788604	3		350	291	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324690	31324691	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	29	161	0	ENST00000412585.2:c.117dup	p.Gly40ArgfsTer59	p.G40Rfs*59	ENST00000412585	NM_005514.6	39	-/C	2/8	1	2	FACETS	0.931	0.806	1	1	0.967	1	CLONAL	2	TRUE	1	0.692084648788604	2		161	45	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172078	32172079	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	81	685	4	ENST00000375023.3:c.2953_2954delinsTT	p.Pro985Phe	p.P985F	ENST00000375023	NM_004557.3	985	CCc/TTc	19/30	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.692084648788604	2		689	207	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821490	32821490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777221320	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	57	479	0	ENST00000354258.4:c.104G>A	p.Gly35Asp	p.G35D	ENST00000354258	NM_000593.5	35	gGt/gAt	1/11	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.692084648788604	2		479	151	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289651	33289651	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	53	486	0	ENST00000374542.5:c.52G>T	p.Ala18Ser	p.A18S	ENST00000374542	NM_001141970.1	18	Gca/Tca	2/8	1	2	FACETS	0.798	0.691	0.911	0.798	0.691	0.911	CLONAL	1	TRUE	1	0.692084648788604	2		486	192	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138201268	138201268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1490946222	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	108	505	0	ENST00000237289.4:c.1967C>T	p.Pro656Leu	p.P656L	ENST00000237289	NM_001270507.1	656	cCg/cTg	8/9	0.379946092969595	4	FACETS	0.833	0.757	0.911			1	INDETERMINATE	2	TRUE	NA	0.692084648788604	4		505	317	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622219	162622219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	114	488	0	ENST00000366898.1:c.478G>A	p.Gly160Arg	p.G160R	ENST00000366898	NM_004562.2	160	Gga/Aga	4/12	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.692084648788604	2		488	271	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339554	81339554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs571102402	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	89	464	0	ENST00000222390.5:c.1450G>A	p.Val484Ile	p.V484I	ENST00000222390	NM_000601.4	484	Gta/Ata	13/18	1	2	FACETS	0.932	0.837	1	0.932	0.837	1	CLONAL	1	TRUE	1	0.692084648788604	2		464	276	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106519994	106519994	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	51	329	0	ENST00000359195.3:c.2427del	p.Lys809AsnfsTer68	p.K809Nfs*68	ENST00000359195	NM_002649.2	808	Aaa/aa	6/11	1	2	FACETS	0.833	0.72	0.952	0.833	0.72	0.952	CLONAL	1	TRUE	1	0.692084648788604	2		329	177	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128849225	128849225	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756828715	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	82	532	0	ENST00000249373.3:c.1453C>T	p.Arg485Trp	p.R485W	ENST00000249373	NM_005631.4	485	Cgg/Tgg	8/12	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.692084648788604	2		532	181	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950413	68950413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	88	553	0	ENST00000288368.4:c.725C>T	p.Thr242Ile	p.T242I	ENST00000288368	NM_024870.2	242	aCc/aTc	7/40	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.692084648788604	2		553	229	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486071	8486071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	73	454	0	ENST00000356435.5:c.2746G>A	p.Glu916Lys	p.E916K	ENST00000356435		916	Gaa/Aaa	17/35	1	2	FACETS	0.968	0.861	1	0.968	0.861	1	CLONAL	1	TRUE	1	0.692084648788604	2		454	218	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528675	8528675	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	91	392	0	ENST00000356435.5:c.457C>T	p.Pro153Ser	p.P153S	ENST00000356435		153	Ccg/Tcg	4/35	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.692084648788604	2		392	241	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401756	139401757	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0024731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	40	649	1	ENST00000277541.6:c.3643_3643+1delinsAA		p.X1215_splice	ENST00000277541	NM_017617.3	1215		22/34	NA	2	FACETS	0.869	0.738	1			1	INDETERMINATE	1	TRUE	NA	0.692084648788604	2		650	133	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0024949-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	34	446	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.421	0.343	0.508	0.421	0.343	0.508	SUBCLONAL	1	TRUE	1	0.316800019537567	2		446	510	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289934	15289934	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs141418355	NA	P-0024949-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	36	785	0	ENST00000263388.2:c.3620A>G	p.Asn1207Ser	p.N1207S	ENST00000263388	NM_000435.2	1207	aAt/aGt	22/33	1	2	FACETS	0.373	0.305	0.448	0.373	0.305	0.448	SUBCLONAL	1	TRUE	1	0.316800019537567	2		785	610	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934801	49934801	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024949-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	33	621	1	ENST00000296474.3:c.2095G>A	p.Gly699Ser	p.G699S	ENST00000296474	NM_002447.2	699	Ggc/Agc	7/20	1	2	FACETS	0.385	0.313	0.467	0.385	0.313	0.467	SUBCLONAL	1	TRUE	1	0.316800019537567	2		622	541	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	62	215	0				ENST00000310581	NM_198253.2	-/1132			0.367280036890647	1	FACETS	0.312	0.27	0.357	0.312	0.27	0.357	INDETERMINATE	1	TRUE	0	0.667446201248727	1		215	397	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520008	NA	P-0024981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	107	116	0	ENST00000269305.4:c.613T>C	p.Tyr205His	p.Y205H	ENST00000269305	NM_001126112.2	205	Tat/Cat	6/11	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.667446201248727	2		116	250	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971114	21971115	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0024981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	303	227	0	ENST00000304494.5:c.243dup	p.Val82ArgfsTer38	p.V82Rfs*38	ENST00000304494	NM_000077.4	81	-/C	2/3	NA	2	FACETS	0.934	0.894	0.973			1	INDETERMINATE	2	TRUE	NA	0.667446201248727	2		227	486	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870799	12870799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	19	61	0	ENST00000228872.4:c.26G>A	p.Gly9Glu	p.G9E	ENST00000228872	NM_004064.3	9	gGg/gAg	1/3	0.667446201248727	6	FACETS	0.373	0.283	0.48	0.093	0.07	0.12	SUBCLONAL	1	TRUE	2	0.667446201248727	6		61	356	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992151	72992152	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0024981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	60	199	0	ENST00000268489.5:c.1893dup	p.Gly632TrpfsTer35	p.G632Wfs*35	ENST00000268489	NM_006885.3	631	-/T	2/10	1	2	FACETS	0.421	0.364	0.483	0.421	0.364	0.483	SUBCLONAL	1	TRUE	1	0.667446201248727	2		199	427	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323151	31323151	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0024981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	169	130	1	ENST00000412585.2:c.838A>T	p.Arg280Ter	p.R280*	ENST00000412585	NM_005514.6	280	Aga/Tga	4/8	0.40324278836417	3	FACETS	0.836	0.778	0.894	0.836	0.778	0.894	CLONAL	2	TRUE	1	0.667446201248727	3		131	404	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249692	110249692	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	176	215	0	ENST00000374672.4:c.983G>A	p.Arg328Lys	p.R328K	ENST00000374672	NM_004235.4	328	aGg/aAg	3/5	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.667446201248727	2		215	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0025018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1277	64	738	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.157	0.135	0.181	0.157	0.135	0.181	SUBCLONAL	1	TRUE	1	0.607199565463383	2		738	1341	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0025018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	40	179	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.174	0.144	0.208	0.174	0.144	0.208	SUBCLONAL	1	TRUE	1	0.607199565463383	2		179	756	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0025018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	59	415	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	1	2	FACETS	0.201	0.172	0.232	0.201	0.172	0.232	SUBCLONAL	1	TRUE	1	0.607199565463383	2		415	968	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412905	49412905	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519951	NA	P-0025018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1266	48	789	0	ENST00000418115.1:c.118G>C	p.Glu40Gln	p.E40Q	ENST00000418115	NM_001664.2	40	Gag/Cag	2/5	1	2	FACETS	0.12	0.101	0.142	0.12	0.101	0.142	SUBCLONAL	1	TRUE	1	0.607199565463383	2		789	1314	SUCCESS
RET	5979	MSKCC	GRCh37	10	43614979	43614979	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1453303247	NA	P-0025018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	54	565	1	ENST00000355710.3:c.2393G>A	p.Gly798Asp	p.G798D	ENST00000355710	NM_020975.4	798	gGc/gAc	14/20	1	2	FACETS	0.202	0.171	0.235	0.202	0.171	0.235	SUBCLONAL	1	TRUE	1	0.607199565463383	2		566	882	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	216	430	0				ENST00000310581	NM_198253.2	-/1132			0.395149441899274	5	FACETS	1	0.979	1	0.746	0.695	0.798	CLONAL	2	TRUE	2	0.395149441899274	5		430	778	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857127	9857127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs976259560	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	198	391	1	ENST00000330684.3:c.4274C>T	p.Ser1425Leu	p.S1425L	ENST00000330684	NM_001134407.1	1425	tCg/tTg	13/13	0.356386664640249	2	FACETS	0.956	0.893	1	0.956	0.893	1	CLONAL	2	TRUE	0	0.395149441899274	2		392	524	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841532	156841532	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs368040165	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	462	723	2	ENST00000524377.1:c.835C>T	p.Gln279Ter	p.Q279*	ENST00000524377	NM_002529.3	279	Cag/Tag	7/17	0.395149441899274	5	FACETS	0.939	0.897	0.981			1	CLONAL	3	TRUE	NA	0.395149441899274	5		725	1322	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221981	1221981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	168	634	0	ENST00000326873.7:c.896C>T	p.Ser299Phe	p.S299F	ENST00000326873	NM_000455.4	299	tCc/tTc	7/10	0.288033964770371	2	FACETS	1	0.974	1	0.566	0.521	0.613	CLONAL	1	TRUE	0	0.395149441899274	2		634	751	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646419	23646419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057520736	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	301	533	1	ENST00000261584.4:c.1448C>T	p.Ser483Leu	p.S483L	ENST00000261584	NM_024675.3	483	tCa/tTa	4/13	0.395149441899274	3	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.395149441899274	3		534	759	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421012	49421012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	129	417	0	ENST00000301067.7:c.14737G>A	p.Glu4913Lys	p.E4913K	ENST00000301067	NM_003482.3	4913	Gaa/Aaa	48/54	0.213005908153922	4	FACETS	1	0.984	1	0.701	0.637	0.768	INDETERMINATE	1	TRUE	2	0.395149441899274	4		417	650	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325430	1325430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	144	512	0	ENST00000400841.2:c.245C>T	p.Ser82Leu	p.S82L	ENST00000400841		82	tCg/tTg	3/6	0.395149441899274	2	FACETS	0.584	0.531	0.64			1	SUBCLONAL	1	TRUE	NA	0.395149441899274	2		512	1248	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522401	157522401	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	189	667	0	ENST00000346085.5:c.4673C>T	p.Ser1558Phe	p.S1558F	ENST00000346085	NM_020732.3	1558	tCc/tTc	18/20	0.395149441899274	5	FACETS	1	0.989	1	0.484	0.446	0.522	CLONAL	1	TRUE	2	0.395149441899274	5		667	1050	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561767	55561767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780349712	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	50	449	0	ENST00000288135.5:c.157G>A	p.Glu53Lys	p.E53K	ENST00000288135	NM_000222.2	53	Gag/Aag	2/21	1	2	FACETS	0.52	0.441	0.606	0.52	0.441	0.606	SUBCLONAL	1	TRUE	1	0.395149441899274	2		449	487	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499732	8499732	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	144	586	0	ENST00000356435.5:c.2237G>A	p.Gly746Glu	p.G746E	ENST00000356435		746	gGa/gAa	14/35	0.291212320972008	3	FACETS	1	0.942	1	0.348	0.317	0.38	CLONAL	1	TRUE	0	0.395149441899274	3		586	837	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739066	40739066	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	132	506	0	ENST00000373198.4:c.3218G>A	p.Gly1073Asp	p.G1073D	ENST00000373198	NM_133170.3	1073	gGc/gAc	24/32	0.395149441899274	5	FACETS	1	0.963	1	0.559	0.507	0.615	CLONAL	1	TRUE	3	0.395149441899274	5		506	951	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346082	89346082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374668457	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	32	78	0	ENST00000301030.4:c.6868C>T	p.Pro2290Ser	p.P2290S	ENST00000301030	NM_001256183.1	2290	Ccc/Tcc	9/13	0.140103083785021	4	FACETS	0.837	0.691	0.996	0.837	0.691	0.996	INDETERMINATE	2	TRUE	2	0.395149441899274	4		78	135	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451888	29451888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764014697	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	173	665	0	ENST00000389048.3:c.2677G>A	p.Gly893Arg	p.G893R	ENST00000389048	NM_004304.4	893	Gga/Aga	16/29	0.395149441899274	3	FACETS	1	0.979	1	0.589	0.542	0.638	CLONAL	1	TRUE	1	0.395149441899274	3		665	890	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543748	29543748	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	51	375	0	ENST00000389048.3:c.1415G>A	p.Arg472Gln	p.R472Q	ENST00000389048	NM_004304.4	472	cGg/cAg	7/29	0.395149441899274	3	FACETS	0.583	0.496	0.679	0.292	0.248	0.34	SUBCLONAL	1	TRUE	1	0.395149441899274	3		375	530	SUCCESS
ATR	545	MSKCC	GRCh37	3	142222283	142222283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	128	444	0	ENST00000350721.4:c.5209C>T	p.His1737Tyr	p.H1737Y	ENST00000350721	NM_001184.3	1737	Cat/Tat	30/47	0.20068623071569	3	FACETS	1	0.982	1	0.663	0.603	0.726	INDETERMINATE	1	TRUE	1	0.395149441899274	3		444	585	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568590	41568590	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	227	627	0	ENST00000263253.7:c.4540G>A	p.Glu1514Lys	p.E1514K	ENST00000263253	NM_001429.3	1514	Gaa/Aaa	28/31	0.327474852304198	5	FACETS	0.879	0.819	0.941	0.586	0.546	0.628	CLONAL	2	TRUE	2	0.395149441899274	5		627	1041	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254614	1254614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201330213	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	128	380	0	ENST00000310581.5:c.3164C>T	p.Ser1055Leu	p.S1055L	ENST00000310581	NM_198253.2	1055	tCg/tTg	15/16	0.395149441899274	5	FACETS	0.793	0.72	0.869	0.528	0.48	0.579	SUBCLONAL	2	TRUE	2	0.395149441899274	5		380	651	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600324	10600324	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	142	541	2	ENST00000171111.5:c.1531G>A	p.Gly511Ser	p.G511S	ENST00000171111	NM_203500.1	511	Ggc/Agc	4/6	0.213005908153922	4	FACETS	1	0.984	1	0.671	0.612	0.733	INDETERMINATE	1	TRUE	2	0.395149441899274	4		543	747	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133269	30133269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778826879	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	122	613	0	ENST00000263025.4:c.229G>A	p.Glu77Lys	p.E77K	ENST00000263025	NM_002746.2	77	Gaa/Aaa	2/9	0.395149441899274	3	FACETS	0.696	0.627	0.768			1	SUBCLONAL	1	TRUE	NA	0.395149441899274	3		613	1063	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653814	89653815	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	241	480	1	ENST00000371953.3:c.112_113delinsTT	p.Pro38Phe	p.P38F	ENST00000371953	NM_000314.4	38	CCt/TTt	2/9	0.395149441899274	3	FACETS	1	0.99	1	0.823	0.774	0.871	CLONAL	2	TRUE	0	0.395149441899274	3		481	592	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264595	1264595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	88	516	0	ENST00000310581.5:c.2767C>T	p.Pro923Ser	p.P923S	ENST00000310581	NM_198253.2	923	Ccg/Tcg	11/16	0.395149441899274	5	FACETS	0.683	0.604	0.769	0.228	0.201	0.257	SUBCLONAL	1	TRUE	2	0.395149441899274	5		516	1038	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267787	46267787	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	184	656	1	ENST00000371998.3:c.2548C>T	p.Pro850Ser	p.P850S	ENST00000371998		850	Cct/Tct	14/23	0.395149441899274	5	FACETS	1	0.982	1	0.606	0.558	0.656	CLONAL	1	TRUE	3	0.395149441899274	5		657	1224	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794481	42794481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	244	848	0	ENST00000575354.2:c.1561C>T	p.Pro521Ser	p.P521S	ENST00000575354	NM_015125.3	521	Cct/Tct	10/20	0.213005908153922	4	FACETS	0.75	0.701	0.802	0.75	0.701	0.802	INDETERMINATE	2	TRUE	2	0.395149441899274	4		848	1148	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415558	152415558	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770516501	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	145	633	0	ENST00000206249.3:c.1408G>A	p.Glu470Lys	p.E470K	ENST00000206249	NM_000125.3	470	Gaa/Aaa	7/8	0.395149441899274	5	FACETS	1	0.97	1	0.383	0.348	0.419	CLONAL	1	TRUE	2	0.395149441899274	5		633	1018	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356248	66356248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202046693	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	80	631	0	ENST00000273854.3:c.1249C>T	p.Arg417Trp	p.R417W	ENST00000273854	NM_004439.5	417	Cgg/Tgg	5/18	1	2	FACETS	0.46	0.404	0.52	0.46	0.404	0.52	SUBCLONAL	1	TRUE	1	0.395149441899274	2		631	881	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137830	64137830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	454	393	0	ENST00000334205.4:c.1931C>T	p.Ser644Phe	p.S644F	ENST00000334205	NM_003942.2	644	tCc/tTc	15/17	0.395149441899274	5	FACETS	0.921	0.879	0.963	0.921	0.879	0.963	CLONAL	3	TRUE	2	0.395149441899274	5		393	1325	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687321	37687321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	159	516	0	ENST00000447079.4:c.4225C>T	p.Pro1409Ser	p.P1409S	ENST00000447079	NM_015083.1	1409	Ccc/Tcc	14/14	0.236232060093931	5	FACETS	0.751	0.689	0.816	0.501	0.459	0.544	INDETERMINATE	2	TRUE	2	0.395149441899274	5		516	853	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868112	56868112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374706761	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	170	595	0	ENST00000308159.5:c.1610G>A	p.Arg537Gln	p.R537Q	ENST00000308159	NM_014669.4	537	cGg/cAg	14/22	0.140103083785021	4	FACETS	1	0.989	1	0.745	0.686	0.806	INDETERMINATE	1	TRUE	2	0.395149441899274	4		595	806	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158594124	158594125	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	114	501	0	ENST00000263640.3:c.1448_1449delinsTT	p.Ser483Phe	p.S483F	ENST00000263640	NM_001105.4	483	tCC/tTT	11/11	1	2	FACETS	0.934	0.843	1	0.934	0.843	1	CLONAL	1	TRUE	1	0.395149441899274	2		501	618	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982038	70982039	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	75	610	0	ENST00000276594.2:c.57_58delinsAA	p.Glu20Lys	p.E20K	ENST00000276594	NM_024504.3	19	ccGGag/ccAAag	2/8	0.236232060093931	5	FACETS	0.608	0.531	0.691	0.203	0.177	0.231	INDETERMINATE	1	TRUE	2	0.395149441899274	5		610	994	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937094	48937094	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	31	215	1	ENST00000267163.4:c.861+1G>A		p.X287_splice	ENST00000267163	NM_000321.2	287			0.395149441899274	6	FACETS	0.711	0.575	0.865			1	SUBCLONAL	1	TRUE	NA	0.395149441899274	6		216	395	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068039	94068039	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	112	462	0	ENST00000369303.4:c.923C>G	p.Ser308Cys	p.S308C	ENST00000369303	NM_004440.3	308	tCc/tGc	4/17	0.395149441899274	4	FACETS	1	0.924	1			1	CLONAL	1	TRUE	NA	0.395149441899274	4		462	766	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306556	41306556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	132	576	1	ENST00000373198.4:c.1103G>A	p.Gly368Glu	p.G368E	ENST00000373198	NM_133170.3	368	gGg/gAg	7/32	0.395149441899274	5	FACETS	1	0.952	1	0.54	0.489	0.593	CLONAL	1	TRUE	3	0.395149441899274	5		577	986	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141549464	141549464	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	246	427	0	ENST00000220592.5:c.2124G>C	p.Gln708His	p.Q708H	ENST00000220592	NM_012154.3	708	caG/caC	16/19	0.322683603734263	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.395149441899274	4		427	742	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474026	29474026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147858673	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	86	680	1	ENST00000389048.3:c.2149G>A	p.Glu717Lys	p.E717K	ENST00000389048	NM_004304.4	717	Gag/Aag	12/29	0.395149441899274	3	FACETS	0.594	0.524	0.668	0.297	0.262	0.334	SUBCLONAL	1	TRUE	1	0.395149441899274	3		681	878	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612807	228612807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	128	574	0	ENST00000366696.1:c.220G>A	p.Glu74Lys	p.E74K	ENST00000366696	NM_003493.2	74	Gag/Aag	1/1	0.395149441899274	3	FACETS	1	0.91	1	0.502	0.455	0.551	CLONAL	1	TRUE	1	0.395149441899274	3		574	773	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965694	93965694	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	125	527	0	ENST00000369303.4:c.2234G>A	p.Gly745Glu	p.G745E	ENST00000369303	NM_004440.3	745	gGa/gAa	13/17	0.395149441899274	4	FACETS	1	0.955	1			1	CLONAL	1	TRUE	NA	0.395149441899274	4		527	807	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120881	115120881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	88	415	0	ENST00000257566.3:c.125C>T	p.Pro42Leu	p.P42L	ENST00000257566	NM_016569.3	42	cCc/cTc	1/8	0.232701475719622	3	FACETS	1	0.928	1			1	INDETERMINATE	1	TRUE	NA	0.395149441899274	3		415	504	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467767	66467767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	68	447	0	ENST00000273854.3:c.502G>A	p.Glu168Lys	p.E168K	ENST00000273854	NM_004439.5	168	Gaa/Aaa	3/18	1	2	FACETS	0.552	0.48	0.629	0.552	0.48	0.629	SUBCLONAL	1	TRUE	1	0.395149441899274	2		447	624	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599871	10599871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1433112931	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	202	598	0	ENST00000171111.5:c.1705C>T	p.Leu569Phe	p.L569F	ENST00000171111	NM_203500.1	569	Ctt/Ttt	5/6	0.213005908153922	4	FACETS	1	0.99	1	0.721	0.668	0.776	INDETERMINATE	1	TRUE	2	0.395149441899274	4		598	989	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426978	49426978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	119	443	0	ENST00000301067.7:c.11510C>T	p.Ser3837Phe	p.S3837F	ENST00000301067	NM_003482.3	3837	tCc/tTc	39/54	0.213005908153922	4	FACETS	1	0.971	1	0.596	0.538	0.657	INDETERMINATE	1	TRUE	2	0.395149441899274	4		443	705	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546694	9546694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs942131023	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	176	371	0	ENST00000353224.5:c.1328G>A	p.Gly443Glu	p.G443E	ENST00000353224	NM_177990.2	443	gGa/gAa	5/10	0.395149441899274	5	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	3	0.395149441899274	5		371	667	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967912	93967912	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	167	557	0	ENST00000369303.4:c.2015C>G	p.Thr672Arg	p.T672R	ENST00000369303	NM_004440.3	672	aCa/aGa	11/17	0.395149441899274	4	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.395149441899274	4		557	991	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562918	95562918	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	64	480	0	ENST00000393063.1:c.4339C>G	p.Gln1447Glu	p.Q1447E	ENST00000393063	NM_030621.3	1447	Cag/Gag	24/28	0.384207937365636	4	FACETS	0.696	0.603	0.798	0.348	0.301	0.399	SUBCLONAL	1	TRUE	2	0.395149441899274	4		480	649	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782158	9782159	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	263	500	1	ENST00000377346.4:c.2181_2182delinsTT	p.Leu728Phe	p.L728F	ENST00000377346	NM_005026.3	727	gcCCtc/gcTTtc	17/24	0.327474852304198	5	FACETS	1	0.987	1	0.79	0.742	0.839	CLONAL	2	TRUE	2	0.395149441899274	5		501	895	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259448	16259448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755281306	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	253	499	0	ENST00000375759.3:c.6713C>T	p.Pro2238Leu	p.P2238L	ENST00000375759	NM_015001.2	2238	cCt/cTt	11/15	0.327474852304198	5	FACETS	1	0.979	1	0.734	0.688	0.782	CLONAL	2	TRUE	2	0.395149441899274	5		499	926	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937985	36937985	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237845502	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	85	609	2	ENST00000361632.4:c.851C>T	p.Pro284Leu	p.P284L	ENST00000361632		284	cCc/cTc	7/16	0.327474852304198	5	FACETS	0.561	0.494	0.633	0.187	0.164	0.211	SUBCLONAL	1	TRUE	2	0.395149441899274	5		611	1221	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363194	40363195	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	241	599	0	ENST00000397332.2:c.1034_1035delinsTT	p.Ser345Phe	p.S345F	ENST00000397332	NM_001033082.2	345	tCC/tTT	3/3	0.327474852304198	5	FACETS	1	0.974	1	0.718	0.671	0.766	CLONAL	2	TRUE	2	0.395149441899274	5		599	902	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330511	65330511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	293	552	0	ENST00000342505.4:c.1135G>A	p.Glu379Lys	p.E379K	ENST00000342505	NM_002227.2	379	Gag/Aag	8/25	0.327474852304198	5	FACETS	1	0.985	1	0.752	0.708	0.797	CLONAL	2	TRUE	2	0.395149441899274	5		552	1047	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165600	118165600	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	99	413	0	ENST00000369448.3:c.110G>A	p.Gly37Glu	p.G37E	ENST00000369448	NM_017709.3	37	gGa/gAa	2/2	0.322683603734263	4	FACETS	1	0.91	1	0.51	0.456	0.568	CLONAL	1	TRUE	2	0.395149441899274	4		413	685	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166112	118166112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	118	413	0	ENST00000369448.3:c.622C>T	p.Pro208Ser	p.P208S	ENST00000369448	NM_017709.3	208	Ccc/Tcc	2/2	0.322683603734263	4	FACETS	1	0.969	1	0.587	0.53	0.647	CLONAL	1	TRUE	2	0.395149441899274	4		413	710	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458221	120458222	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	66	604	3	ENST00000256646.2:c.7123_7124delinsTT	p.Pro2375Phe	p.P2375F	ENST00000256646	NM_024408.3	2375	CCt/TTt	34/34	0.322683603734263	4	FACETS	0.499	0.432	0.572	0.249	0.216	0.286	SUBCLONAL	1	TRUE	2	0.395149441899274	4		607	934	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466369	120466369	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	232	554	1	ENST00000256646.2:c.4750C>T	p.Gln1584Ter	p.Q1584*	ENST00000256646	NM_024408.3	1584	Cag/Tag	26/34	0.322683603734263	4	FACETS	0.982	0.918	1	0.982	0.918	1	CLONAL	2	TRUE	2	0.395149441899274	4		555	834	SUCCESS
H3C13	653604	MSKCC	GRCh37	1	149784861	149784861	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	77	224	0	ENST00000331491.1:c.376C>T	p.Gln126Ter	p.Q126*	ENST00000331491	NM_001123375.2	126	Cag/Tag	1/1	0.395149441899274	6	FACETS	1	0.973	1	0.352	0.309	0.397	CLONAL	1	TRUE	2	0.395149441899274	6		224	496	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551667	150551668	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	246	399	1	ENST00000369026.2:c.339_340delinsTT	p.Pro114Ser	p.P114S	ENST00000369026	NM_021960.4	113	gcCCcg/gcTTcg	1/3	0.395149441899274	6	FACETS	1	0.984	1	0.575	0.537	0.613	CLONAL	2	TRUE	2	0.395149441899274	6		400	970	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843718	156843719	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	437	746	0	ENST00000524377.1:c.1144_1145delinsTT	p.Pro382Phe	p.P382F	ENST00000524377	NM_002529.3	382	CCt/TTt	8/17	0.395149441899274	5	FACETS	0.926	0.884	0.969			1	CLONAL	3	TRUE	NA	0.395149441899274	5		746	1268	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746130	162746131	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	87	357	1	ENST00000367921.3:c.2253_2254delinsTT	p.Arg752Cys	p.R752C	ENST00000367921	NM_006182.2	751	atCCgc/atTTgc	16/18	0.395149441899274	5	FACETS	1	0.943	1			1	CLONAL	1	TRUE	NA	0.395149441899274	5		358	634	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175951	176175951	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	23	147	0	ENST00000367669.3:c.164C>G	p.Ala55Gly	p.A55G	ENST00000367669	NM_022457.5	55	gCc/gGc	1/20	0.395149441899274	3	FACETS	0.511	0.399	0.64	0.255	0.199	0.32	SUBCLONAL	1	TRUE	1	0.395149441899274	3		147	273	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984418	201984418	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	75	606	0	ENST00000359651.3:c.1083G>A	p.Trp361Ter	p.W361*	ENST00000359651		361	tgG/tgA	8/8	0.395149441899274	3	FACETS	0.55	0.481	0.625	0.275	0.24	0.313	SUBCLONAL	1	TRUE	1	0.395149441899274	3		606	826	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226551747	226551747	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	149	458	0	ENST00000366794.5:c.2683A>C	p.Ile895Leu	p.I895L	ENST00000366794	NM_001618.3	895	Atc/Ctc	20/23	0.395149441899274	3	FACETS	0.76	0.697	0.825	0.76	0.697	0.825	SUBCLONAL	2	TRUE	1	0.395149441899274	3		458	594	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246027169	246027169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776156757	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	78	614	0	ENST00000388985.4:c.833G>A	p.Gly278Asp	p.G278D	ENST00000388985		278	gGt/gAt	9/12	0.395149441899274	3	FACETS	0.615	0.54	0.696	0.307	0.27	0.348	SUBCLONAL	1	TRUE	1	0.395149441899274	3		614	769	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446252	70446252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	157	521	0	ENST00000373644.4:c.5192C>T	p.Ser1731Phe	p.S1731F	ENST00000373644	NM_030625.2	1731	tCt/tTt	11/12	0.395149441899274	3	FACETS	1	0.983	1	0.424	0.389	0.461	CLONAL	1	TRUE	0	0.395149441899274	3		521	748	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903687	114903687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	137	526	1	ENST00000543371.1:c.691C>T	p.Pro231Ser	p.P231S	ENST00000543371	NM_001198531.1	231	Cca/Tca	7/14	0.356386664640249	2	FACETS	0.92	0.837	1	0.46	0.418	0.503	CLONAL	1	TRUE	0	0.395149441899274	2		527	754	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263415	123263415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757125418	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	193	459	0	ENST00000358487.5:c.1328C>T	p.Pro443Leu	p.P443L	ENST00000358487	NM_000141.4	443	cCg/cTg	10/18	0.356386664640249	2	FACETS	0.895	0.834	0.957	0.895	0.834	0.957	CLONAL	2	TRUE	0	0.395149441899274	2		459	546	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201753	102201753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	158	467	0	ENST00000263464.3:c.1105G>A	p.Asp369Asn	p.D369N	ENST00000263464	NM_001165.4	369	Gac/Aac	6/9	0.356386664640249	2	FACETS	0.793	0.732	0.856	0.793	0.732	0.856	SUBCLONAL	2	TRUE	0	0.395149441899274	2		467	504	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344593	118344593	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064797056	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	162	538	0	ENST00000534358.1:c.2719C>T	p.Pro907Ser	p.P907S	ENST00000534358	NM_005933.3	907	Cct/Tct	3/36	0.395149441899274	3	FACETS	1	0.952	1			1	CLONAL	1	TRUE	NA	0.395149441899274	3		538	932	SUCCESS
CBL	867	MSKCC	GRCh37	11	119167698	119167699	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	223	601	1	ENST00000264033.4:c.2107_2108delinsTT	p.Pro703Phe	p.P703F	ENST00000264033	NM_005188.3	703	CCc/TTc	13/16	0.395149441899274	3	FACETS	0.753	0.701	0.805			1	SUBCLONAL	2	TRUE	NA	0.395149441899274	3		602	898	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420145	420146	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	74	482	1	ENST00000399788.2:c.3121_3122delinsTT	p.Pro1041Leu	p.P1041L	ENST00000399788	NM_001042603.1	1041	CCg/TTg	21/28	0.395149441899274	3	FACETS	0.662	0.579	0.751	0.331	0.289	0.376	SUBCLONAL	1	TRUE	1	0.395149441899274	3		483	678	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037493	12037493	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	142	357	0	ENST00000396373.4:c.1124G>T	p.Gly375Val	p.G375V	ENST00000396373	NM_001987.4	375	gGa/gTa	6/8	0.395149441899274	3	FACETS	0.914	0.839	0.991	0.914	0.839	0.991	CLONAL	2	TRUE	1	0.395149441899274	3		357	471	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244268	46244268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	69	462	0	ENST00000334344.6:c.2362C>T	p.Pro788Ser	p.P788S	ENST00000334344	NM_152641.2	788	Cct/Tct	15/21	0.213005908153922	4	FACETS	0.738	0.643	0.842	0.369	0.321	0.421	INDETERMINATE	1	TRUE	2	0.395149441899274	4		462	660	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424191	49424191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886043233	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	79	292	1	ENST00000301067.7:c.13871C>T	p.Ser4624Leu	p.S4624L	ENST00000301067	NM_003482.3	4624	tCg/tTg	42/54	0.213005908153922	4	FACETS	1	0.97	1	0.661	0.584	0.743	INDETERMINATE	1	TRUE	2	0.395149441899274	4		293	422	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436360	49436360	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	141	587	0	ENST00000301067.7:c.5851C>T	p.Pro1951Ser	p.P1951S	ENST00000301067	NM_003482.3	1951	Ccg/Tcg	27/54	0.213005908153922	4	FACETS	1	0.981	1	0.644	0.587	0.704	INDETERMINATE	1	TRUE	2	0.395149441899274	4		587	773	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444331	49444331	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1240886578	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	139	621	1	ENST00000301067.7:c.3040C>T	p.Pro1014Ser	p.P1014S	ENST00000301067	NM_003482.3	1014	Ccc/Tcc	11/54	0.213005908153922	4	FACETS	1	0.94	1	0.522	0.474	0.571	INDETERMINATE	1	TRUE	2	0.395149441899274	4		622	941	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445836	49445836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	128	977	1	ENST00000301067.7:c.1630C>T	p.Pro544Ser	p.P544S	ENST00000301067	NM_003482.3	544	Ccc/Tcc	10/54	0.213005908153922	4	FACETS	0.697	0.63	0.769	0.349	0.315	0.385	INDETERMINATE	1	TRUE	2	0.395149441899274	4		978	1296	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478850	56478851	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	77	695	2	ENST00000267101.3:c.306_307delinsTT	p.Arg103Cys	p.R103C	ENST00000267101	NM_001982.3	102	ctCCgc/ctTTgc	3/28	0.213005908153922	4	FACETS	0.533	0.466	0.604	0.266	0.233	0.302	INDETERMINATE	1	TRUE	2	0.395149441899274	4		697	1021	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811666	102811666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	223	347	1	ENST00000307046.8:c.518G>A	p.Gly173Glu	p.G173E	ENST00000307046	NM_001111285.1	173	gGa/gAa	4/4	0.213005908153922	4	FACETS	1	0.99	1	0.695	0.646	0.745	INDETERMINATE	1	TRUE	2	0.395149441899274	4		348	1133	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856193	111856193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1424493907	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	58	340	1	ENST00000341259.2:c.244G>A	p.Gly82Arg	p.G82R	ENST00000341259	NM_005475.2	82	Gga/Aga	2/8	0.213005908153922	4	FACETS	0.773	0.664	0.891	0.386	0.332	0.446	INDETERMINATE	1	TRUE	2	0.395149441899274	4		341	530	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112257	115112257	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1060505020	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	75	249	1	ENST00000257566.3:c.1483C>T	p.Gln495Ter	p.Q495*	ENST00000257566	NM_016569.3	495	Cag/Tag	7/8	0.213005908153922	4	FACETS	0.83	0.734	0.932	0.83	0.734	0.932	INDETERMINATE	2	TRUE	2	0.395149441899274	4		250	319	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112281	115112281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	65	202	0	ENST00000257566.3:c.1459G>A	p.Asp487Asn	p.D487N	ENST00000257566	NM_016569.3	487	Gac/Aac	7/8	0.213005908153922	4	FACETS	0.883	0.774	0.998	0.883	0.774	0.998	INDETERMINATE	2	TRUE	2	0.395149441899274	4		202	260	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26974671	26974671	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	73	565	0	ENST00000381527.3:c.1015C>T	p.Pro339Ser	p.P339S	ENST00000381527	NM_001260.1	339	Cca/Tca	10/13	0.356611306492659	4	FACETS	0.607	0.53	0.691	0.202	0.176	0.231	SUBCLONAL	1	TRUE	1	0.395149441899274	4		565	849	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601378	28601378	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	46	446	1	ENST00000241453.7:c.2054G>A	p.Gly685Glu	p.G685E	ENST00000241453	NM_004119.2	685	gGa/gAa	17/24	0.356611306492659	4	FACETS	0.512	0.431	0.603	0.171	0.143	0.201	SUBCLONAL	1	TRUE	1	0.395149441899274	4		447	634	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950926	32950926	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs1555288179	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	51	545	0	ENST00000380152.3:c.8752G>C	p.Glu2918Gln	p.E2918Q	ENST00000380152		2918	Gag/Cag	21/27	0.356611306492659	4	FACETS	0.456	0.386	0.533	0.152	0.128	0.178	SUBCLONAL	1	TRUE	1	0.395149441899274	4		545	790	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954222	32954222	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs80359180	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	239	647	1	ENST00000380152.3:c.9196C>T	p.Gln3066Ter	p.Q3066*	ENST00000380152		3066	Cag/Tag	24/27	0.356611306492659	4	FACETS	0.938	0.877	1	0.625	0.584	0.667	CLONAL	2	TRUE	1	0.395149441899274	4		648	900	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033944	49033944	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	327	448	0	ENST00000267163.4:c.2081T>C	p.Leu694Pro	p.L694P	ENST00000267163	NM_000321.2	694	cTc/cCc	20/27	0.395149441899274	6	FACETS	1	0.985	1			1	CLONAL	3	TRUE	NA	0.395149441899274	6		448	898	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519191	103519191	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	173	437	0	ENST00000355739.4:c.2529A>T	p.Gln843His	p.Q843H	ENST00000355739	NM_000123.3	843	caA/caT	11/15	0.327474852304198	5	FACETS	0.868	0.8	0.939	0.579	0.533	0.626	CLONAL	2	TRUE	2	0.395149441899274	5		437	803	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434796	110434796	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	219	631	0	ENST00000375856.3:c.3605C>A	p.Thr1202Asn	p.T1202N	ENST00000375856	NM_003749.2	1202	aCc/aAc	1/2	0.327474852304198	5	FACETS	0.842	0.783	0.903	0.562	0.522	0.602	CLONAL	2	TRUE	2	0.395149441899274	5		631	1048	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436052	110436052	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	364	737	0	ENST00000375856.3:c.2349C>G	p.Phe783Leu	p.F783L	ENST00000375856	NM_003749.2	783	ttC/ttG	1/2	0.327474852304198	5	FACETS	1	0.991	1	0.793	0.751	0.835	CLONAL	2	TRUE	2	0.395149441899274	5		737	1234	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436929	110436929	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	63	423	0	ENST00000375856.3:c.1472C>T	p.Ser491Phe	p.S491F	ENST00000375856	NM_003749.2	491	tCc/tTc	1/2	0.327474852304198	5	FACETS	0.629	0.543	0.723	0.21	0.181	0.241	SUBCLONAL	1	TRUE	2	0.395149441899274	5		423	807	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438388	110438388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	57	89	1	ENST00000375856.3:c.13C>T	p.Pro5Ser	p.P5S	ENST00000375856	NM_003749.2	5	Ccg/Tcg	1/2	0.327474852304198	5	FACETS	1	0.949	1	0.79	0.688	0.896	CLONAL	2	TRUE	2	0.395149441899274	5		90	194	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560431	65560431	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	204	362	0	ENST00000358664.4:c.166G>T	p.Glu56Ter	p.E56*	ENST00000358664	NM_002382.4	56	Gag/Tag	3/5	0.384207937365636	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.395149441899274	4		362	637	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95556844	95556845	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	102	388	1	ENST00000393063.1:c.5759_5760delinsTT	p.Pro1920Leu	p.P1920L	ENST00000393063	NM_030621.3	1920	cCC/cTT	28/28	0.384207937365636	4	FACETS	1	0.975	1	0.649	0.582	0.72	CLONAL	1	TRUE	2	0.395149441899274	4		389	555	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40678574	40678574	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1291020860	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	58	596	0	ENST00000249776.8:c.316C>T	p.Arg106Trp	p.R106W	ENST00000249776	NM_033286.3	106	Cgg/Tgg	3/9	0.291212320972008	3	FACETS	0.423	0.362	0.489	0.141	0.12	0.163	SUBCLONAL	1	TRUE	0	0.395149441899274	3		596	832	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961946	41961946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	63	426	0	ENST00000219905.7:c.854C>T	p.Ser285Phe	p.S285F	ENST00000219905	NM_001164273.1	285	tCc/tTc	2/24	0.310973608823765	1	FACETS	0.494	0.428	0.566	0.494	0.428	0.566	SUBCLONAL	1	TRUE	0	0.395149441899274	1		426	518	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988796	41988796	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777837339	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	84	594	0	ENST00000219905.7:c.1588C>T	p.Leu530Phe	p.L530F	ENST00000219905	NM_001164273.1	530	Ctt/Ttt	3/24	0.310973608823765	1	FACETS	0.553	0.489	0.622	0.553	0.489	0.622	SUBCLONAL	1	TRUE	0	0.395149441899274	1		594	617	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292995	91292995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs896357448	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	73	635	2	ENST00000355112.3:c.497C>T	p.Ser166Leu	p.S166L	ENST00000355112	NM_000057.2	166	tCa/tTa	3/22	0.395149441899274	3	FACETS	0.431	0.376	0.491	0.216	0.188	0.246	SUBCLONAL	1	TRUE	1	0.395149441899274	3		637	1026	SUCCESS
BLM	641	MSKCC	GRCh37	15	91334006	91334006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	71	550	1	ENST00000355112.3:c.2951G>A	p.Gly984Glu	p.G984E	ENST00000355112	NM_000057.2	984	gGg/gAg	15/22	0.395149441899274	3	FACETS	0.478	0.416	0.545	0.239	0.208	0.273	SUBCLONAL	1	TRUE	1	0.395149441899274	3		551	901	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226066	2226066	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	95	611	0	ENST00000326181.6:c.1763C>T	p.Ser588Phe	p.S588F	ENST00000326181	NM_032271.2	588	tCc/tTc	19/21	0.356386664640249	2	FACETS	0.583	0.518	0.652	0.291	0.259	0.326	SUBCLONAL	1	TRUE	0	0.395149441899274	2		611	825	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778678	3778678	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	229	563	0	ENST00000262367.5:c.6370C>T	p.Gln2124Ter	p.Q2124*	ENST00000262367	NM_004380.2	2124	Cag/Tag	31/31	0.356386664640249	2	FACETS	0.766	0.716	0.816	0.766	0.716	0.816	SUBCLONAL	2	TRUE	0	0.395149441899274	2		563	757	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786710	3786711	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	229	717	1	ENST00000262367.5:c.4500_4501delinsAA	p.Glu1501Lys	p.E1501K	ENST00000262367	NM_004380.2	1500	caGGag/caAAag	27/31	0.356386664640249	2	FACETS	1	0.991	1	0.689	0.644	0.736	CLONAL	1	TRUE	0	0.395149441899274	2		718	841	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274177	10274178	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	98	442	3	ENST00000330684.3:c.91_92delinsTT	p.Pro31Phe	p.P31F	ENST00000330684	NM_001134407.1	31	CCc/TTc	2/13	0.395149441899274	3	FACETS	1	0.942	1			1	CLONAL	1	TRUE	NA	0.395149441899274	3		445	551	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041990	14041990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762753294	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	199	441	1	ENST00000311895.7:c.2537C>T	p.Pro846Leu	p.P846L	ENST00000311895	NM_005236.2	846	cCt/cTt	11/11	0.395149441899274	3	FACETS	1	0.974	1			1	CLONAL	2	TRUE	NA	0.395149441899274	3		442	555	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070600	67070600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1466296973	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	90	340	0	ENST00000412916.2:c.224G>A	p.Gly75Glu	p.G75E	ENST00000412916		75	gGa/gAa	3/6	0.140103083785021	4	FACETS	1	0.968	1	0.619	0.551	0.692	INDETERMINATE	1	TRUE	2	0.395149441899274	4		340	513	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828617	72828617	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	137	688	0	ENST00000268489.5:c.7964T>A	p.Ile2655Asn	p.I2655N	ENST00000268489	NM_006885.3	2655	aTt/aAt	9/10	0.140103083785021	4	FACETS	1	0.964	1	0.559	0.508	0.613	INDETERMINATE	1	TRUE	2	0.395149441899274	4		688	865	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845860	72845860	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	148	594	0	ENST00000268489.5:c.3607G>A	p.Glu1203Lys	p.E1203K	ENST00000268489	NM_006885.3	1203	Gag/Aag	6/10	0.140103083785021	4	FACETS	1	0.982	1	0.644	0.588	0.702	INDETERMINATE	1	TRUE	2	0.395149441899274	4		594	812	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836288	89836289	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	155	681	1	ENST00000389301.3:c.2460_2461delinsTT	p.Leu821Phe	p.L821F	ENST00000389301	NM_000135.2	820	agCCtc/agTTtc	26/43	0.140103083785021	4	FACETS	1	0.976	1	0.589	0.539	0.642	INDETERMINATE	1	TRUE	2	0.395149441899274	4		682	929	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849269	89849269	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	160	599	0	ENST00000389301.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000389301	NM_000135.2	542	Gag/Aag	17/43	0.140103083785021	4	FACETS	1	0.987	1	0.696	0.638	0.755	INDETERMINATE	1	TRUE	2	0.395149441899274	4		599	812	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577537	7577538	+	missense_variant	Missense_Mutation	DNP	CC	CC	GT	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	324	628	2	ENST00000269305.4:c.743_744delinsAC	p.Arg248His	p.R248H	ENST00000269305	NM_001126112.2	248	cGG/cAC	7/11	0.291212320972008	3	FACETS	1	0.988	1	0.754	0.715	0.794	CLONAL	2	TRUE	0	0.395149441899274	3		630	868	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619091	37619091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	251	582	0	ENST00000447079.4:c.767C>T	p.Ser256Leu	p.S256L	ENST00000447079	NM_015083.1	256	tCg/tTg	1/14	0.236232060093931	5	FACETS	1	0.971	1	0.709	0.664	0.756	INDETERMINATE	2	TRUE	2	0.395149441899274	5		582	951	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657580	37657580	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	247	665	0	ENST00000447079.4:c.2497G>A	p.Glu833Lys	p.E833K	ENST00000447079	NM_015083.1	833	Gag/Aag	6/14	0.236232060093931	5	FACETS	1	0.964	1	0.696	0.651	0.742	INDETERMINATE	2	TRUE	2	0.395149441899274	5		665	954	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687232	37687232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	161	584	1	ENST00000447079.4:c.4136C>T	p.Ser1379Phe	p.S1379F	ENST00000447079	NM_015083.1	1379	tCt/tTt	14/14	0.236232060093931	5	FACETS	0.811	0.745	0.88	0.541	0.496	0.587	INDETERMINATE	2	TRUE	2	0.395149441899274	5		585	800	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475346	40475347	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	224	603	1	ENST00000264657.5:c.1679_1680delinsTT	p.Ser560Phe	p.S560F	ENST00000264657	NM_139276.2	560	tCC/tTT	19/24	0.236232060093931	5	FACETS	1	0.956	1	0.688	0.641	0.736	INDETERMINATE	2	TRUE	2	0.395149441899274	5		604	875	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215924	41215924	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	183	581	0	ENST00000357654.3:c.5119A>T	p.Ile1707Phe	p.I1707F	ENST00000357654	NM_007294.3	1707	Att/Ttt	17/23	0.236232060093931	5	FACETS	0.769	0.71	0.831	0.513	0.473	0.554	INDETERMINATE	2	TRUE	2	0.395149441899274	5		581	959	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223097	41223097	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786202064	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	85	645	0	ENST00000357654.3:c.4834C>T	p.Gln1612Ter	p.Q1612*	ENST00000357654	NM_007294.3	1612	Cag/Tag	15/23	0.236232060093931	5	FACETS	0.714	0.629	0.804	0.238	0.209	0.268	INDETERMINATE	1	TRUE	2	0.395149441899274	5		645	960	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47679314	47679314	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	151	516	1	ENST00000347630.2:c.893C>T	p.Ser298Phe	p.S298F	ENST00000347630	NM_001007230.1	298	tCc/tTc	10/11	0.236232060093931	5	FACETS	1	0.986	1	0.466	0.426	0.508	INDETERMINATE	1	TRUE	2	0.395149441899274	5		517	870	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414997	56414997	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	172	541	0	ENST00000348428.3:c.2398A>G	p.Arg800Gly	p.R800G	ENST00000348428	NM_006785.3	800	Aga/Gga	17/17	0.213005908153922	4	FACETS	1	0.989	1	0.745	0.686	0.806	INDETERMINATE	1	TRUE	2	0.395149441899274	4		541	815	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208276	5208277	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	35	622	1	ENST00000357368.4:c.5613_5614delinsTT	p.Gln1872Ter	p.Q1872*	ENST00000357368	NM_002850.3	1871	ggCCag/ggTTag	36/38	0.288033964770371	2	FACETS	0.257	0.21	0.311	0.129	0.105	0.156	SUBCLONAL	1	TRUE	0	0.395149441899274	2		623	689	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291077	10291077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	171	621	1	ENST00000340748.4:c.394C>T	p.Leu132Phe	p.L132F	ENST00000340748		132	Ctt/Ttt	4/40	0.213005908153922	4	FACETS	1	0.987	1	0.687	0.632	0.744	INDETERMINATE	1	TRUE	2	0.395149441899274	4		622	879	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169485	11169485	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	162	670	0	ENST00000358026.2:c.4651T>C	p.Tyr1551His	p.Y1551H	ENST00000358026	NM_001128849.1	1551	Tac/Cac	33/36	0.213005908153922	4	FACETS	1	0.982	1	0.629	0.576	0.683	INDETERMINATE	1	TRUE	2	0.395149441899274	4		670	910	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629065	14629066	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	95	365	1	ENST00000254322.2:c.96_97delinsTT	p.Pro33Ser	p.P33S	ENST00000254322	NM_006145.1	32	caCCcg/caTTcg	1/3	0.213005908153922	4	FACETS	1	0.899	1	0.504	0.449	0.563	INDETERMINATE	1	TRUE	2	0.395149441899274	4		366	665	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271711	15271711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	209	722	0	ENST00000263388.2:c.6728C>T	p.Pro2243Leu	p.P2243L	ENST00000263388	NM_000435.2	2243	cCt/cTt	33/33	0.213005908153922	4	FACETS	1	0.989	1	0.675	0.626	0.725	INDETERMINATE	1	TRUE	2	0.395149441899274	4		722	1094	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272312	15272312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1486848902	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	178	616	1	ENST00000263388.2:c.6127C>T	p.Leu2043Phe	p.L2043F	ENST00000263388	NM_000435.2	2043	Ctc/Ttc	33/33	0.213005908153922	4	FACETS	1	0.989	1	0.718	0.662	0.776	INDETERMINATE	1	TRUE	2	0.395149441899274	4		617	875	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299052	15299052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1300888829	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	156	507	0	ENST00000263388.2:c.1486C>T	p.Pro496Ser	p.P496S	ENST00000263388	NM_000435.2	496	Ccc/Tcc	9/33	0.213005908153922	4	FACETS	1	0.986	1	0.697	0.639	0.758	INDETERMINATE	1	TRUE	2	0.395149441899274	4		507	790	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303085	15303086	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	186	765	0	ENST00000263388.2:c.364_365delinsTT	p.Pro122Phe	p.P122F	ENST00000263388	NM_000435.2	122	CCc/TTc	4/33	0.213005908153922	4	FACETS	1	0.982	1	0.608	0.56	0.657	INDETERMINATE	1	TRUE	2	0.395149441899274	4		765	1081	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308431	30308431	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	131	590	0	ENST00000262643.3:c.445C>G	p.Leu149Val	p.L149V	ENST00000262643	NM_001238.2	149	Ctg/Gtg	6/12	0.213005908153922	4	FACETS	1	0.963	1	0.559	0.507	0.614	INDETERMINATE	1	TRUE	2	0.395149441899274	4		590	827	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211084	36211085	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	173	737	1	ENST00000222270.7:c.835_836delinsTT	p.Pro279Phe	p.P279F	ENST00000222270	NM_014727.1	279	CCc/TTc	3/37	0.213005908153922	4	FACETS	1	0.981	1	0.608	0.559	0.659	INDETERMINATE	1	TRUE	2	0.395149441899274	4		738	1005	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215967	36215968	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	164	717	3	ENST00000222270.7:c.3507_3508delinsTT	p.Arg1170Cys	p.R1170C	ENST00000222270	NM_014727.1	1169	caCCgc/caTTgc	10/37	0.213005908153922	4	FACETS	1	0.97	1	0.562	0.515	0.611	INDETERMINATE	1	TRUE	2	0.395149441899274	4		720	1031	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222850	36222850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	204	674	1	ENST00000222270.7:c.5479C>T	p.Leu1827Phe	p.L1827F	ENST00000222270	NM_014727.1	1827	Ctt/Ttt	27/37	0.213005908153922	4	FACETS	1	0.989	1	0.685	0.634	0.737	INDETERMINATE	1	TRUE	2	0.395149441899274	4		675	1052	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905086	50905086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	159	621	1	ENST00000440232.2:c.368C>T	p.Pro123Leu	p.P123L	ENST00000440232	NM_002691.3	123	cCt/cTt	4/27	0.213005908153922	4	FACETS	1	0.982	1	0.624	0.572	0.679	INDETERMINATE	1	TRUE	2	0.395149441899274	4		622	899	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912865	50912866	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	158	628	3	ENST00000440232.2:c.2096_2097delinsAT	p.Ser699Tyr	p.S699Y	ENST00000440232	NM_002691.3	699	tCC/tAT	17/27	0.213005908153922	4	FACETS	1	0.981	1	0.618	0.566	0.672	INDETERMINATE	1	TRUE	2	0.395149441899274	4		631	903	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786205228	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	30	547	0	ENST00000322088.6:c.536C>T	p.Pro179Leu	p.P179L	ENST00000322088	NM_014225.5	179	cCc/cTc	5/15	0.213005908153922	4	FACETS	0.259	0.207	0.318	0.129	0.103	0.159	INDETERMINATE	1	TRUE	2	0.395149441899274	4		547	818	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25458628	25458628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	200	572	0	ENST00000264709.3:c.2545C>T	p.Pro849Ser	p.P849S	ENST00000264709	NM_175629.2	849	Cct/Tct	22/23	0.395149441899274	3	FACETS	1	0.991	1	0.738	0.685	0.793	CLONAL	1	TRUE	1	0.395149441899274	3		572	821	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872482	136872482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	71	365	2	ENST00000241393.3:c.1016C>T	p.Ser339Phe	p.S339F	ENST00000241393	NM_003467.2	339	tCt/tTt	2/2	1	2	FACETS	0.85	0.744	0.962	0.85	0.744	0.962	CLONAL	1	TRUE	1	0.395149441899274	2		367	423	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793350	242793350	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	191	666	2	ENST00000334409.5:c.727C>T	p.Pro243Ser	p.P243S	ENST00000334409	NM_005018.2	243	Cct/Tct	5/5	0.155485085679776	4	FACETS	1	0.989	1	0.714	0.66	0.769	INDETERMINATE	1	TRUE	2	0.395149441899274	4		668	945	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022763	31022763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1218506765	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	153	551	1	ENST00000375687.4:c.2248C>T	p.Pro750Ser	p.P750S	ENST00000375687	NM_015338.5	750	Ccc/Tcc	13/13	0.395149441899274	5	FACETS	1	0.976	1	0.592	0.541	0.646	CLONAL	1	TRUE	3	0.395149441899274	5		552	1041	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024690	31024691	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	120	542	1	ENST00000375687.4:c.4175_4176delinsTT	p.Pro1392Leu	p.P1392L	ENST00000375687	NM_015338.5	1392	cCC/cTT	13/13	0.395149441899274	5	FACETS	0.949	0.856	1	0.475	0.428	0.524	CLONAL	1	TRUE	3	0.395149441899274	5		543	1019	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911165	40911165	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	227	523	0	ENST00000373198.4:c.2140G>A	p.Glu714Lys	p.E714K	ENST00000373198	NM_133170.3	714	Gag/Aag	13/32	0.395149441899274	5	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	3	0.395149441899274	5		523	859	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306741	41306741	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	112	483	0	ENST00000373198.4:c.918G>A	p.Trp306Ter	p.W306*	ENST00000373198	NM_133170.3	306	tgG/tgA	7/32	0.395149441899274	5	FACETS	1	0.915	1	0.51	0.458	0.565	CLONAL	1	TRUE	3	0.395149441899274	5		483	885	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319102	62319102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764219586	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1152	166	599	0	ENST00000360203.5:c.1460C>T	p.Ser487Phe	p.S487F	ENST00000360203	NM_001283009.1	487	tCc/tTc	17/35	0.395149441899274	5	FACETS	1	0.929	1	0.508	0.465	0.553	CLONAL	1	TRUE	3	0.395149441899274	5		599	1318	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259360	36259360	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	360	523	0	ENST00000300305.3:c.131C>T	p.Ser44Phe	p.S44F	ENST00000300305		44	tCc/tTc	3/8	0.395149441899274	5	FACETS	1	0.99	1	0.79	0.749	0.832	CLONAL	2	TRUE	2	0.395149441899274	5		523	1224	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44515850	44515850	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	153	605	0	ENST00000291552.4:c.203C>T	p.Ala68Val	p.A68V	ENST00000291552	NM_006758.2	68	gCc/gTc	4/8	0.395149441899274	5	FACETS	1	0.942	1	0.347	0.317	0.379	CLONAL	1	TRUE	2	0.395149441899274	5		605	1184	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160189	22160189	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	118	411	0	ENST00000215832.6:c.442C>T	p.Arg148Cys	p.R148C	ENST00000215832	NM_002745.4	148	Cgt/Tgt	3/9	0.395149441899274	3	FACETS	1	0.943	1	0.531	0.479	0.585	CLONAL	1	TRUE	1	0.395149441899274	3		411	674	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41521904	41521904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	227	781	1	ENST00000263253.7:c.766C>T	p.Pro256Ser	p.P256S	ENST00000263253	NM_001429.3	256	Cca/Tca	3/31	0.327474852304198	5	FACETS	0.793	0.738	0.85	0.529	0.492	0.567	SUBCLONAL	2	TRUE	2	0.395149441899274	5		782	1154	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588862	52588862	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	151	531	0	ENST00000394830.3:c.4166C>T	p.Pro1389Leu	p.P1389L	ENST00000394830	NM_018313.4	1389	cCt/cTt	27/30	0.20068623071569	3	FACETS	1	0.984	1	0.658	0.602	0.715	INDETERMINATE	1	TRUE	1	0.395149441899274	3		531	696	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199894	128199895	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	72	387	0	ENST00000341105.2:c.1410_1411delinsTT	p.His471Tyr	p.H471Y	ENST00000341105	NM_032638.4	470	ccCCac/ccTTac	6/6	0.20068623071569	3	FACETS	0.919	0.805	1	0.459	0.402	0.521	INDETERMINATE	1	TRUE	1	0.395149441899274	3		387	475	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670237	134670237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	175	499	0	ENST00000398015.3:c.148G>A	p.Glu50Lys	p.E50K	ENST00000398015	NM_004441.4	50	Gaa/Aaa	3/16	0.20068623071569	3	FACETS	0.8	0.739	0.863	0.8	0.739	0.863	INDETERMINATE	2	TRUE	1	0.395149441899274	3		499	663	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161369	185161369	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	181	611	0	ENST00000265026.3:c.796G>A	p.Gly266Arg	p.G266R	ENST00000265026	NM_004721.4	266	Gga/Aga	4/14	0.20068623071569	3	FACETS	1	0.988	1	0.688	0.636	0.743	INDETERMINATE	1	TRUE	1	0.395149441899274	3		611	797	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1800999	1801000	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	177	711	2	ENST00000260795.2:c.128_129delinsTT	p.Pro43Leu	p.P43L	ENST00000260795		43	cCC/cTT	2/17	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.395149441899274	2		713	889	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957846	1957846	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	173	563	0	ENST00000382891.5:c.2812C>T	p.Pro938Ser	p.P938S	ENST00000382891	NM_133335.3	938	Ccg/Tcg	15/22	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.395149441899274	2		563	830	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964923	55964923	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1062832	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	53	497	0	ENST00000263923.4:c.2314G>A	p.Ala772Thr	p.A772T	ENST00000263923	NM_002253.2	772	Gcg/Acg	16/30	1	2	FACETS	0.459	0.391	0.534	0.459	0.391	0.534	SUBCLONAL	1	TRUE	1	0.395149441899274	2		497	584	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361143	66361143	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	108	468	0	ENST00000273854.3:c.1029C>G	p.Phe343Leu	p.F343L	ENST00000273854	NM_004439.5	343	ttC/ttG	4/18	1	2	FACETS	0.899	0.809	0.994	0.899	0.809	0.994	CLONAL	1	TRUE	1	0.395149441899274	2		468	608	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519202	187519202	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	76	646	0	ENST00000441802.2:c.12181T>A	p.Cys4061Ser	p.C4061S	ENST00000441802	NM_005245.3	4061	Tgc/Agc	23/27	0.356611306492659	4	FACETS	0.606	0.531	0.688	0.202	0.177	0.23	SUBCLONAL	1	TRUE	1	0.395149441899274	4		646	885	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525595	187525595	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	80	628	0	ENST00000441802.2:c.10484G>C	p.Gly3495Ala	p.G3495A	ENST00000441802	NM_005245.3	3495	gGa/gCa	18/27	0.356611306492659	4	FACETS	0.633	0.556	0.716	0.211	0.185	0.239	SUBCLONAL	1	TRUE	1	0.395149441899274	4		628	892	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224608	224608	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	224	312	0	ENST00000264932.6:c.284C>T	p.Pro95Leu	p.P95L	ENST00000264932	NM_004168.2	95	cCt/cTt	3/15	0.395149441899274	5	FACETS	1	0.962	1	1	0.962	1	CLONAL	3	TRUE	2	0.395149441899274	5		312	582	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280392	1280392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554041095	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	299	623	0	ENST00000310581.5:c.1831G>A	p.Glu611Lys	p.E611K	ENST00000310581	NM_198253.2	611	Gaa/Aaa	4/16	0.395149441899274	5	FACETS	1	0.987	1	0.764	0.72	0.809	CLONAL	2	TRUE	2	0.395149441899274	5		623	1051	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293719	1293719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1400139919	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	319	625	1	ENST00000310581.5:c.1282C>T	p.Arg428Trp	p.R428W	ENST00000310581	NM_198253.2	428	Cgg/Tgg	2/16	0.395149441899274	5	FACETS	1	0.983	1	0.732	0.691	0.774	CLONAL	2	TRUE	2	0.395149441899274	5		626	1171	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31521233	31521233	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756137496	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	272	551	0	ENST00000344624.3:c.944G>A	p.Gly315Glu	p.G315E	ENST00000344624		315	gGa/gAa	3/33	0.395149441899274	5	FACETS	1	0.973	1	0.708	0.664	0.752	CLONAL	2	TRUE	2	0.395149441899274	5		551	1033	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953568	38953569	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	194	464	0	ENST00000357387.3:c.2784_2785delinsAA	p.Trp928_Ala929delinsTer	p.W928_A929delins*	ENST00000357387	NM_152756.3	928	tgGGcc/tgAAcc	28/38	0.395149441899274	5	FACETS	1	0.939	1	0.676	0.627	0.727	CLONAL	2	TRUE	2	0.395149441899274	5		464	771	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671293	30671293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746504351	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	141	514	0	ENST00000376406.3:c.5584G>A	p.Gly1862Ser	p.G1862S	ENST00000376406	NM_014641.2	1862	Ggc/Agc	11/15	0.395149441899274	3	FACETS	1	0.966	1	0.373	0.34	0.408	CLONAL	1	TRUE	0	0.395149441899274	3		514	764	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681112	30681112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1234996738	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	206	368	0	ENST00000376406.3:c.607C>T	p.Pro203Ser	p.P203S	ENST00000376406	NM_014641.2	203	Ccg/Tcg	5/15	0.395149441899274	3	FACETS	1	0.979	1	0.739	0.691	0.788	CLONAL	2	TRUE	0	0.395149441899274	3		368	563	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323312	31323312	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	43	155	0	ENST00000412585.2:c.677G>C	p.Arg226Thr	p.R226T	ENST00000412585	NM_005514.6	226	aGg/aCg	4/8	0.395149441899274	3	FACETS	1	0.953	1	0.455	0.385	0.53	CLONAL	1	TRUE	0	0.395149441899274	3		155	191	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163506	32163506	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774201468	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	337	491	0	ENST00000375023.3:c.5720G>A	p.Gly1907Glu	p.G1907E	ENST00000375023	NM_004557.3	1907	gGa/gAa	30/30	0.395149441899274	3	FACETS	1	0.99	1	0.774	0.735	0.813	CLONAL	2	TRUE	0	0.395149441899274	3		491	880	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803463	32803464	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	172	659	1	ENST00000374899.4:c.695_696delinsTT	p.Ser232Phe	p.S232F	ENST00000374899	NM_018833.2	232	tCC/tTT	4/12	0.395149441899274	3	FACETS	1	0.957	1	0.354	0.325	0.383	CLONAL	1	TRUE	0	0.395149441899274	3		660	983	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43746208	43746208	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1218	83	554	0	ENST00000523873.1:c.327C>G	p.Ile109Met	p.I109M	ENST00000523873		109	atC/atG	4/8	0.395149441899274	6	FACETS	0.578	0.508	0.654			1	SUBCLONAL	1	TRUE	NA	0.395149441899274	6		554	1301	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066706	94066706	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	94	575	0	ENST00000369303.4:c.1053G>A	p.Trp351Ter	p.W351*	ENST00000369303	NM_004440.3	351	tgG/tgA	5/17	0.395149441899274	4	FACETS	0.765	0.679	0.856			1	SUBCLONAL	1	TRUE	NA	0.395149441899274	4		575	868	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554996	106554996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190911457	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	258	458	0	ENST00000369096.4:c.2113C>T	p.His705Tyr	p.H705Y	ENST00000369096	NM_001198.3	705	Cac/Tac	7/7	0.395149441899274	4	FACETS	1	0.986	1			1	CLONAL	2	TRUE	NA	0.395149441899274	4		458	785	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015627	112015627	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	258	403	0	ENST00000368678.4:c.1215C>G	p.Asp405Glu	p.D405E	ENST00000368678		405	gaC/gaG	11/13	0.395149441899274	6	FACETS	0.916	0.86	0.973			1	CLONAL	3	TRUE	NA	0.395149441899274	6		403	851	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663617	117663617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751502071	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	328	635	0	ENST00000368508.3:c.4615C>T	p.Pro1539Ser	p.P1539S	ENST00000368508	NM_002944.2	1539	Cct/Tct	28/43	0.290127078450496	4	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.395149441899274	4		635	957	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117730772	117730773	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	280	653	3	ENST00000368508.3:c.261_262delinsAA	p.Glu88Lys	p.E88K	ENST00000368508	NM_002944.2	87	gcGGaa/gcAAaa	4/43	0.290127078450496	4	FACETS	1	0.975	1			1	CLONAL	2	TRUE	NA	0.395149441899274	4		656	930	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137540440	137540440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777571593	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	75	438	0	ENST00000367739.4:c.25C>T	p.Leu9Phe	p.L9F	ENST00000367739	NM_000416.2	9	Ctt/Ttt	1/7	0.395149441899274	5	FACETS	0.681	0.595	0.773	0.227	0.198	0.258	SUBCLONAL	1	TRUE	2	0.395149441899274	5		438	888	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202344	138202345	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	128	515	0	ENST00000237289.4:c.2261_2262delinsTT	p.Pro754Leu	p.P754L	ENST00000237289	NM_001270507.1	754	cCC/cTT	9/9	0.395149441899274	5	FACETS	1	0.961	1	0.371	0.336	0.409	CLONAL	1	TRUE	2	0.395149441899274	5		515	926	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983308	149983308	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	129	673	0	ENST00000253339.5:c.2950C>T	p.Leu984Phe	p.L984F	ENST00000253339		984	Ctt/Ttt	7/7	0.395149441899274	5	FACETS	0.925	0.837	1	0.308	0.279	0.34	CLONAL	1	TRUE	2	0.395149441899274	5		673	1124	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522512	157522512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1252761521	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	215	757	0	ENST00000346085.5:c.4784C>T	p.Pro1595Leu	p.P1595L	ENST00000346085	NM_020732.3	1595	cCa/cTa	18/20	0.395149441899274	5	FACETS	1	0.991	1	0.486	0.451	0.522	CLONAL	1	TRUE	2	0.395149441899274	5		757	1189	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527443	157527443	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	188	468	0	ENST00000346085.5:c.5168C>T	p.Ser1723Phe	p.S1723F	ENST00000346085	NM_020732.3	1723	tCc/tTc	20/20	0.395149441899274	5	FACETS	1	0.941	1	0.678	0.628	0.73	CLONAL	2	TRUE	2	0.395149441899274	5		468	745	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2998136	2998136	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	393	681	1	ENST00000396946.4:c.5C>T	p.Pro2Leu	p.P2L	ENST00000396946	NM_032415.4	2	cCa/cTa	2/25	0.291212320972008	3	FACETS	1	0.992	1	0.781	0.744	0.818	CLONAL	2	TRUE	0	0.395149441899274	3		682	1017	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227984	55227984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	123	487	2	ENST00000275493.2:c.1451C>T	p.Ser484Phe	p.S484F	ENST00000275493	NM_005228.3	484	tCc/tTc	12/28	0.291212320972008	3	FACETS	1	0.979	1	0.425	0.385	0.466	CLONAL	1	TRUE	0	0.395149441899274	3		489	585	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508411	106508412	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	59	248	0	ENST00000359195.3:c.405_406delinsTT	p.His136Tyr	p.H136Y	ENST00000359195	NM_002649.2	135	atCCac/atTTac	2/11	0.395149441899274	7	FACETS	1	0.943	1	0.297	0.256	0.342	CLONAL	1	TRUE	3	0.395149441899274	7		248	499	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523577	106523577	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	89	414	0	ENST00000359195.3:c.2729G>A	p.Trp910Ter	p.W910*	ENST00000359195	NM_002649.2	910	tGg/tAg	8/11	0.395149441899274	7	FACETS	1	0.9	1	0.254	0.225	0.286	CLONAL	1	TRUE	3	0.395149441899274	7		414	880	SUCCESS
MET	4233	MSKCC	GRCh37	7	116413218	116413218	+	intron_variant	Intron	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	475	801	0	ENST00000397752.3:c.3028+1175C>T		p.*1010*	ENST00000397752	NM_000245.2	-/1390			0.33693887255862	3	FACETS	0.92	0.883	0.957	0.92	0.883	0.957	CLONAL	3	TRUE	0	0.395149441899274	3		801	1043	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515115	148515115	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	120	464	0	ENST00000320356.2:c.1094A>T	p.Asn365Ile	p.N365I	ENST00000320356	NM_004456.4	365	aAt/aTt	10/20	0.33693887255862	3	FACETS	1	0.947	1	0.357	0.322	0.393	CLONAL	1	TRUE	0	0.395149441899274	3		464	680	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846132	151846132	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	252	409	1	ENST00000262189.6:c.12880C>T	p.Gln4294Ter	p.Q4294*	ENST00000262189	NM_170606.2	4294	Cag/Tag	52/59	0.33693887255862	3	FACETS	1	0.986	1	0.766	0.721	0.811	CLONAL	2	TRUE	0	0.395149441899274	3		410	665	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874835	151874836	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	233	317	1	ENST00000262189.6:c.7702_7703delinsAA	p.Gly2568Lys	p.G2568K	ENST00000262189	NM_170606.2	2568	GGa/AAa	38/59	0.33693887255862	3	FACETS	0.898	0.846	0.951	0.898	0.846	0.951	CLONAL	3	TRUE	0	0.395149441899274	3		318	524	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29197692	29197692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747088146	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	95	717	1	ENST00000240100.2:c.502C>T	p.Pro168Ser	p.P168S	ENST00000240100	NM_001394.6	168	Cca/Tca	2/4	1	2	FACETS	0.6	0.534	0.671	0.6	0.534	0.671	SUBCLONAL	1	TRUE	1	0.395149441899274	2		718	801	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968107	68968107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1222948221	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	74	595	0	ENST00000288368.4:c.1136C>T	p.Ser379Phe	p.S379F	ENST00000288368	NM_024870.2	379	tCt/tTt	10/40	0.236232060093931	5	FACETS	0.688	0.601	0.782	0.229	0.2	0.261	INDETERMINATE	1	TRUE	2	0.395149441899274	5		595	867	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69032477	69032478	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	66	635	1	ENST00000288368.4:c.3551_3552delinsTT	p.Ala1184Val	p.A1184V	ENST00000288368	NM_024870.2	1184	gCC/gTT	29/40	0.236232060093931	5	FACETS	0.531	0.459	0.609	0.177	0.153	0.203	INDETERMINATE	1	TRUE	2	0.395149441899274	5		636	1002	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970957	70970957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	87	747	0	ENST00000276594.2:c.1304C>T	p.Ser435Phe	p.S435F	ENST00000276594	NM_024504.3	435	tCt/tTt	6/8	0.236232060093931	5	FACETS	0.677	0.598	0.762	0.226	0.199	0.254	INDETERMINATE	1	TRUE	2	0.395149441899274	5		747	1036	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866521	117866521	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	145	532	0	ENST00000297338.2:c.1124del	p.Leu375TyrfsTer12	p.L375Yfs*12	ENST00000297338	NM_006265.2	375	tTa/ta	9/14	0.395149441899274	5	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.395149441899274	5		532	920	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561432	141561432	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	66	445	0	ENST00000220592.5:c.1373C>T	p.Pro458Leu	p.P458L	ENST00000220592	NM_012154.3	458	cCc/cTc	11/19	0.322683603734263	4	FACETS	0.626	0.543	0.717	0.313	0.271	0.359	SUBCLONAL	1	TRUE	2	0.395149441899274	4		445	744	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740447	145740447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376587038	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	268	584	0	ENST00000428558.2:c.1493C>T	p.Thr498Met	p.T498M	ENST00000428558	NM_004260.3	498	aCg/aTg	9/22	0.322683603734263	4	FACETS	0.954	0.896	1	0.954	0.896	1	CLONAL	2	TRUE	2	0.395149441899274	4		584	992	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202823	27202823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	253	524	0	ENST00000380036.4:c.1915C>T	p.Pro639Ser	p.P639S	ENST00000380036	NM_000459.3	639	Cct/Tct	13/23	0.291212320972008	3	FACETS	1	0.988	1	0.788	0.742	0.834	CLONAL	2	TRUE	0	0.395149441899274	3		524	649	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020745	37020745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	322	672	0	ENST00000358127.4:c.100C>T	p.Pro34Ser	p.P34S	ENST00000358127	NM_001280556.1	34	Ccg/Tcg	2/10	0.291212320972008	3	FACETS	1	0.992	1	0.829	0.787	0.871	CLONAL	2	TRUE	0	0.395149441899274	3		672	785	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342676	87342677	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	143	678	2	ENST00000277120.3:c.961_962delinsAA	p.Gly321Lys	p.G321K	ENST00000277120		321	GGg/AAg	9/19	0.322683603734263	4	FACETS	1	0.94	1	0.521	0.474	0.57	CLONAL	1	TRUE	2	0.395149441899274	4		680	970	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93607810	93607810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	281	482	1	ENST00000375746.1:c.512G>A	p.Gly171Glu	p.G171E	ENST00000375746	NM_001174167.1	171	gGa/gAa	3/14	0.322683603734263	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.395149441899274	4		483	844	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250124	110250124	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	171	560	0	ENST00000374672.4:c.551C>T	p.Pro184Leu	p.P184L	ENST00000374672	NM_004235.4	184	cCc/cTc	3/5	0.322683603734263	4	FACETS	1	0.981	1	0.606	0.557	0.657	CLONAL	1	TRUE	2	0.395149441899274	4		560	997	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250217	110250218	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	141	548	3	ENST00000374672.4:c.457_458delinsTT	p.Pro153Leu	p.P153L	ENST00000374672	NM_004235.4	153	CCg/TTg	3/5	0.322683603734263	4	FACETS	1	0.942	1	0.523	0.476	0.572	CLONAL	1	TRUE	2	0.395149441899274	4		551	952	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797328	135797329	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	100	357	0	ENST00000298552.3:c.540_541delinsTT	p.His181Tyr	p.H181Y	ENST00000298552	NM_001162426.1	180	ctCCat/ctTTat	7/23	0.322683603734263	4	FACETS	1	0.96	1	0.574	0.514	0.638	CLONAL	1	TRUE	2	0.395149441899274	4		357	615	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405231	139405231	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762050048	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	171	598	1	ENST00000277541.6:c.2614G>A	p.Glu872Lys	p.E872K	ENST00000277541	NM_017617.3	872	Gag/Aag	17/34	0.232701475719622	3	FACETS	1	0.975	1			1	INDETERMINATE	1	TRUE	NA	0.395149441899274	3		599	906	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321321	1321321	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	502	571	0	ENST00000400841.2:c.434A>T	p.Asp145Val	p.D145V	ENST00000400841		145	gAt/gTt	4/6	0.395149441899274	2	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.395149441899274	2		571	1156	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933854	39933854	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	196	360	0	ENST00000378444.4:c.745C>T	p.Pro249Ser	p.P249S	ENST00000378444	NM_001123385.1	249	Cca/Tca	4/15	0.395149441899274	2	FACETS	0.844	0.786	0.903			1	CLONAL	2	TRUE	NA	0.395149441899274	2		360	588	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732912	44732912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	226	241	0	ENST00000377967.4:c.115C>T	p.Pro39Ser	p.P39S	ENST00000377967	NM_021140.2	39	Ccc/Tcc	1/29	0.395149441899274	2	FACETS	1	0.986	1			1	CLONAL	2	TRUE	NA	0.395149441899274	2		241	498	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938493	44938493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	205	274	0	ENST00000377967.4:c.3041C>T	p.Pro1014Leu	p.P1014L	ENST00000377967	NM_021140.2	1014	cCc/cTc	20/29	0.395149441899274	2	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.395149441899274	2		274	432	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412685	63412685	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	33	282	0	ENST00000330258.3:c.482C>G	p.Ser161Cys	p.S161C	ENST00000330258	NM_152424.3	161	tCt/tGt	2/2	0.395149441899274	2	FACETS	0.382	0.311	0.463			1	SUBCLONAL	1	TRUE	NA	0.395149441899274	2		282	437	SUCCESS
AR	367	MSKCC	GRCh37	X	66765571	66765571	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	280	370	0	ENST00000374690.3:c.583C>T	p.Gln195Ter	p.Q195*	ENST00000374690	NM_000044.3	195	Cag/Tag	1/8	0.395149441899274	2	FACETS	0.853	0.81	0.895			1	CLONAL	3	TRUE	NA	0.395149441899274	2		370	554	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341560	70341560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	161	320	0	ENST00000374080.3:c.995C>T	p.Pro332Leu	p.P332L	ENST00000374080		332	cCt/cTt	7/45	0.395149441899274	2	FACETS	1	0.989	1			1	CLONAL	1	TRUE	NA	0.395149441899274	2		320	549	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345283	70345284	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	72	285	1	ENST00000374080.3:c.2309_2310delinsTT	p.Ala770Val	p.A770V	ENST00000374080		770	gCC/gTT	16/45	0.395149441899274	2	FACETS	0.681	0.596	0.773			1	SUBCLONAL	1	TRUE	NA	0.395149441899274	2		286	535	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0025345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	58	282	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.21359289679561	2		282	509	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0025345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	178	458	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.21359289679561	2	FACETS	0.838	0.775	0.903	1	0.985	1	CLONAL	3	TRUE	0	0.21359289679561	2		458	663	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0025345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	128	760	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.189563791994356	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.21359289679561	1		760	851	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584693	187584693	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	88	588	1	ENST00000441802.2:c.3340C>T	p.Gln1114Ter	p.Q1114*	ENST00000441802	NM_005245.3	1114	Cag/Tag	3/27	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.21359289679561	2		589	792	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541642	187541642	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0025345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	54	359	0	ENST00000441802.2:c.6098C>G	p.Ser2033Ter	p.S2033*	ENST00000441802	NM_005245.3	2033	tCa/tGa	10/27	1	2	FACETS	0.909	0.777	1	0.909	0.777	1	CLONAL	1	TRUE	1	0.21359289679561	2		359	556	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528399	157528399	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	108	556	0	ENST00000346085.5:c.6124G>C	p.Glu2042Gln	p.E2042Q	ENST00000346085	NM_020732.3	2042	Gaa/Caa	20/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.21359289679561	2		556	880	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	116	351	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.934	0.846	1	0.934	0.846	1	CLONAL	1	TRUE	1	0.487833773872691	2		351	509	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	141	380	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.487833773872691	2		380	472	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390736	139390736	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	51	798	0	ENST00000277541.6:c.7455del	p.Ser2486ArgfsTer103	p.S2486Rfs*103	ENST00000277541	NM_017617.3	2485	ccC/cc	34/34	1	2	FACETS	0.244	0.206	0.285	0.244	0.206	0.285	SUBCLONAL	1	TRUE	1	0.487833773872691	2		798	858	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	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	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.487833773872691	2		524	840	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	298	736	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.967	0.918	1	1	0.996	1	CLONAL	2	TRUE	1	0.487833773872691	2		741	632	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	120	495	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.726	0.656	0.799	0.726	0.656	0.799	SUBCLONAL	1	TRUE	1	0.487833773872691	2		497	678	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	138	417	2	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.487833773872691	2		419	535	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	157	930	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.972	0.894	1	0.972	0.894	1	CLONAL	1	TRUE	1	0.487833773872691	2		933	662	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	174	504	7	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.903	0.833	0.976	0.903	0.833	0.976	CLONAL	1	TRUE	1	0.487833773872691	2		511	790	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	125	402	7	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.942	0.856	1	0.942	0.856	1	CLONAL	1	TRUE	1	0.487833773872691	2		409	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	179	531	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.487833773872691	2		532	731	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291083	10291084	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755889652	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	181	557	2	ENST00000340748.4:c.387dup	p.Lys130GlnfsTer19	p.K130Qfs*19	ENST00000340748		129	-/C	4/40	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.487833773872691	2		559	732	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021277	31021277	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	264	400	2	ENST00000375687.4:c.1281del	p.Lys427AsnfsTer35	p.K427Nfs*35	ENST00000375687	NM_015338.5	426	Aaa/aa	12/13	0.487833773872691	3	FACETS	0.98	0.924	1	0.98	0.924	1	CLONAL	2	TRUE	1	0.487833773872691	3		402	687	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	139	406	1	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	1	2	FACETS	0.889	0.812	0.97	0.889	0.812	0.97	CLONAL	1	TRUE	1	0.487833773872691	2		407	641	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	133	705	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.982	0.896	1	0.982	0.896	1	CLONAL	1	TRUE	1	0.487833773872691	2		705	555	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	214	534	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.487833773872691	3	FACETS	0.824	0.77	0.88			1	CLONAL	2	TRUE	NA	0.487833773872691	3		534	662	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221313	1221314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs121913321	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	41	636	2	ENST00000326873.7:c.842dup	p.Leu282AlafsTer3	p.L282Afs*3	ENST00000326873	NM_000455.4	279	ggc/ggCc	6/10	1	2	FACETS	0.23	0.19	0.273	0.23	0.19	0.273	SUBCLONAL	1	TRUE	1	0.487833773872691	2		638	732	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968322	2968323	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs762770988	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	164	604	2	ENST00000396946.4:c.1663dup	p.Arg555ProfsTer38	p.R555Pfs*38	ENST00000396946	NM_032415.4	555	cgg/cCgg	13/25	1	2	FACETS	0.914	0.84	0.989	0.914	0.84	0.989	CLONAL	1	TRUE	1	0.487833773872691	2		606	736	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832688	3832688	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	83	350	0	ENST00000262367.5:c.1570del	p.Leu524TrpfsTer6	p.L524Wfs*6	ENST00000262367	NM_004380.2	524	Ctg/tg	6/31	1	2	FACETS	0.905	0.804	1	0.905	0.804	1	CLONAL	1	TRUE	1	0.487833773872691	2		350	376	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925435	114925435	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs375657594	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	190	569	1	ENST00000543371.1:c.1513C>T	p.Arg505Ter	p.R505*	ENST00000543371	NM_001198531.1	505	Cga/Tga	14/14	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.487833773872691	2		570	671	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	125	372	0	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	0.118897352372575	4	FACETS	1	0.983	1	0.686	0.623	0.751	INDETERMINATE	1	TRUE	2	0.487833773872691	4		372	556	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	127	410	2	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	0.487833773872691	2		412	456	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165687	185165687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	155	390	2	ENST00000265026.3:c.962C>T	p.Ala321Val	p.A321V	ENST00000265026	NM_004721.4	321	gCg/gTg	5/14	0.118897352372575	4	FACETS	0.799	0.734	0.865	0.799	0.734	0.865	INDETERMINATE	2	TRUE	2	0.487833773872691	4		392	592	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227982	53227982	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1556840029	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	176	785	1	ENST00000375401.3:c.2332C>T	p.Arg778Ter	p.R778*	ENST00000375401	NM_004187.3	778	Cga/Tga	16/26	1	2	FACETS	0.953	0.88	1	0.953	0.88	1	CLONAL	1	TRUE	1	0.487833773872691	2		786	757	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109731	115109731	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369538205	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	203	761	3	ENST00000257566.3:c.2147C>T	p.Ala716Val	p.A716V	ENST00000257566	NM_016569.3	716	gCg/gTg	8/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.487833773872691	2		764	756	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41962049	41962049	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	129	450	1	ENST00000219905.7:c.957G>T	p.Lys319Asn	p.K319N	ENST00000219905	NM_001164273.1	319	aaG/aaT	2/24	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.487833773872691	2		451	506	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499363	89499363	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1317589623	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	113	357	0	ENST00000336596.2:c.2538del	p.Met847TrpfsTer10	p.M847Wfs*10	ENST00000336596	NM_005233.5	845	Ccc/cc	15/17	1	2	FACETS	0.963	0.871	1	0.963	0.871	1	CLONAL	1	TRUE	1	0.487833773872691	2		357	481	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383944	84383944	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	164	308	0	ENST00000321945.7:c.908del	p.Asn303IlefsTer17	p.N303Ifs*17	ENST00000321945	NM_139076.2	303	aAt/at	9/9	1	2	FACETS	0.984	0.906	1	0.984	0.906	1	CLONAL	1	TRUE	1	0.487833773872691	2		308	683	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972585	25972585	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	84	282	0	ENST00000435504.4:c.1840C>T	p.Arg614Ter	p.R614*	ENST00000435504		614	Cga/Tga	12/13	1	2	FACETS	0.797	0.707	0.892	0.797	0.707	0.892	SUBCLONAL	1	TRUE	1	0.487833773872691	2		282	432	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492581	50492581	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	136	569	0	ENST00000394963.4:c.1477C>T	p.Arg493Ter	p.R493*	ENST00000394963	NM_003076.4	493	Cga/Tga	12/13	1	2	FACETS	0.738	0.672	0.808	0.738	0.672	0.808	SUBCLONAL	1	TRUE	1	0.487833773872691	2		569	755	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564074	139564074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773216266	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	137	625	0	ENST00000308874.7:c.214G>A	p.Ala72Thr	p.A72T	ENST00000308874		72	Gcc/Acc	5/10	1	2	FACETS	0.728	0.662	0.796	0.728	0.662	0.796	SUBCLONAL	1	TRUE	1	0.487833773872691	2		625	772	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123041018	123041018	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs61752968	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	24	166	0	ENST00000355640.3:c.1481T>A	p.Ile494Asn	p.I494N	ENST00000355640		494	aTt/aAt	7/7	1	2	FACETS	0.619	0.49	0.764	0.619	0.49	0.764	SUBCLONAL	1	TRUE	1	0.487833773872691	2		166	159	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15378304	15378305	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	160	447	0	ENST00000263377.2:c.481dup	p.Ile161AsnfsTer3	p.I161Nfs*3	ENST00000263377	NM_058243.2	161	ata/aAta	4/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.487833773872691	2		447	617	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	165	579	5	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.9	0.828	0.974	0.9	0.828	0.974	CLONAL	1	TRUE	1	0.487833773872691	2		584	752	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967091	18967092	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1384543747	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	157	553	0	ENST00000262803.5:c.1814_1815del	p.Glu605AlafsTer17	p.E605Afs*17	ENST00000262803	NM_002911.3	602	gcAGag/gcag	13/24	1	2	FACETS	0.78	0.715	0.848	0.78	0.715	0.848	SUBCLONAL	1	TRUE	1	0.487833773872691	2		553	825	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046312	69046312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769708831	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	84	341	0	ENST00000288368.4:c.3785G>A	p.Arg1262His	p.R1262H	ENST00000288368	NM_024870.2	1262	cGt/cAt	32/40	0.36490564940946	3	FACETS	0.855	0.758	0.959	0.428	0.378	0.48	CLONAL	1	TRUE	1	0.487833773872691	3		341	501	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590421	67590421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	61	179	0	ENST00000274335.5:c.1483G>A	p.Glu495Lys	p.E495K	ENST00000274335		495	Gaa/Aaa	11/15	1	2	FACETS	0.815	0.708	0.929	0.815	0.708	0.929	CLONAL	1	TRUE	1	0.487833773872691	2		179	307	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412563	116412563	+	intron_variant	Intron	DEL	A	A	-	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	133	811	1	ENST00000397752.3:c.3028+526del		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.546	0.495	0.6	0.546	0.495	0.6	SUBCLONAL	1	TRUE	1	0.487833773872691	2		812	998	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420204	49420204	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	202	672	1	ENST00000301067.7:c.15545del	p.Gly5182AlafsTer61	p.G5182Afs*61	ENST00000301067	NM_003482.3	5182	gGc/gc	48/54	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.487833773872691	2		673	743	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245932	16245932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760738868	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	115	313	0	ENST00000375759.3:c.1555G>A	p.Val519Met	p.V519M	ENST00000375759	NM_015001.2	519	Gtg/Atg	8/15	1	2	FACETS	0.958	0.868	1	0.958	0.868	1	CLONAL	1	TRUE	1	0.487833773872691	2		313	492	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815761	32815761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755212442	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	185	692	0	ENST00000354258.4:c.1855G>A	p.Gly619Arg	p.G619R	ENST00000354258	NM_000593.5	619	Ggg/Agg	8/11	1	2	FACETS	0.974	0.901	1	0.974	0.901	1	CLONAL	1	TRUE	1	0.487833773872691	2		692	779	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195544	102195544	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs922637067	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	158	487	1	ENST00000263464.3:c.304G>A	p.Val102Ile	p.V102I	ENST00000263464	NM_001165.4	102	Gtt/Att	2/9	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.487833773872691	2		488	610	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259384	16259384	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	60	304	0	ENST00000375759.3:c.6649G>A	p.Ala2217Thr	p.A2217T	ENST00000375759	NM_015001.2	2217	Gcg/Acg	11/15	1	2	FACETS	0.764	0.662	0.873	0.764	0.662	0.873	SUBCLONAL	1	TRUE	1	0.487833773872691	2		304	322	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363329	40363329	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	185	622	3	ENST00000397332.2:c.900del	p.Lys301AsnfsTer10	p.K301Nfs*10	ENST00000397332	NM_001033082.2	300	ccC/cc	3/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.487833773872691	2		625	690	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46740297	46740297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	150	435	2	ENST00000371975.4:c.1777C>T	p.Pro593Ser	p.P593S	ENST00000371975	NM_003579.3	593	Cct/Tct	16/18	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.487833773872691	2		437	578	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458824	120458824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	161	547	0	ENST00000256646.2:c.6521G>A	p.Gly2174Glu	p.G2174E	ENST00000256646	NM_024408.3	2174	gGg/gAg	34/34	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.487833773872691	2		547	638	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32449514	32449514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	175	645	2	ENST00000332351.3:c.860C>T	p.Thr287Met	p.T287M	ENST00000332351	NM_024426.4	287	aCg/aTg	3/10	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.487833773872691	2		647	694	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456784	32456785	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	100	556	0	ENST00000332351.3:c.107dup	p.Gly38ArgfsTer14	p.G38Rfs*14	ENST00000332351	NM_024426.4	36	ccg/ccCg	1/10	1	2	FACETS	0.649	0.58	0.721	0.649	0.58	0.721	SUBCLONAL	1	TRUE	1	0.487833773872691	2		556	632	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572206	64572206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	104	409	0	ENST00000312049.6:c.1433G>A	p.Gly478Asp	p.G478D	ENST00000312049	NM_130799.2	478	gGc/gAc	10/10	1	2	FACETS	0.83	0.746	0.918	0.83	0.746	0.918	CLONAL	1	TRUE	1	0.487833773872691	2		409	514	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936058	71936058	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	15	31	0	ENST00000298229.2:c.35del	p.Gly12AlafsTer15	p.G12Afs*15	ENST00000298229	NM_001567.3	10	ccG/cc	1/28	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.487833773872691	2		31	41	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022360	12022360	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	229	765	0	ENST00000396373.4:c.466A>G	p.Asn156Asp	p.N156D	ENST00000396373	NM_001987.4	156	Aac/Gac	5/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.487833773872691	2		765	857	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416483	49416483	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	116	481	0	ENST00000301067.7:c.16228G>T	p.Gly5410Trp	p.G5410W	ENST00000301067	NM_003482.3	5410	Ggg/Tgg	51/54	1	2	FACETS	0.762	0.688	0.84	0.762	0.688	0.84	SUBCLONAL	1	TRUE	1	0.487833773872691	2		481	624	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914812	32914812	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	125	388	0	ENST00000380152.3:c.6320C>A	p.Pro2107His	p.P2107H	ENST00000380152		2107	cCt/cAt	11/27	1	2	FACETS	0.913	0.83	1	0.913	0.83	1	CLONAL	1	TRUE	1	0.487833773872691	2		388	561	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591575	38591575	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	86	288	0	ENST00000299084.4:c.34A>G	p.Asn12Asp	p.N12D	ENST00000299084	NM_152594.2	12	Aat/Gat	2/7	1	2	FACETS	0.834	0.741	0.931	0.834	0.741	0.931	CLONAL	1	TRUE	1	0.487833773872691	2		288	423	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99482515	99482515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	104	596	0	ENST00000268035.6:c.3383C>T	p.Ala1128Val	p.A1128V	ENST00000268035	NM_000875.3	1128	gCc/gTc	18/21	1	2	FACETS	0.605	0.542	0.672	0.605	0.542	0.672	SUBCLONAL	1	TRUE	1	0.487833773872691	2		596	705	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216587	7216587	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	118	404	0	ENST00000380728.2:c.748C>A	p.Leu250Met	p.L250M	ENST00000380728		250	Ctg/Atg	9/11	1	2	FACETS	0.977	0.886	1	0.977	0.886	1	CLONAL	1	TRUE	1	0.487833773872691	2		404	495	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33430274	33430274	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	99	600	0	ENST00000345365.6:c.737T>C	p.Val246Ala	p.V246A	ENST00000345365	NM_002878.3	246	gTg/gCg	8/10	1	2	FACETS	0.619	0.553	0.689	0.619	0.553	0.689	SUBCLONAL	1	TRUE	1	0.487833773872691	2		600	656	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508194	38508194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	108	380	0	ENST00000254066.5:c.502G>A	p.Glu168Lys	p.E168K	ENST00000254066	NM_000964.3	168	Gag/Aag	5/9	1	2	FACETS	0.9	0.812	0.993	0.9	0.812	0.993	CLONAL	1	TRUE	1	0.487833773872691	2		380	492	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007242	62007242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	176	565	0	ENST00000392795.3:c.440G>A	p.Ser147Asn	p.S147N	ENST00000392795	NM_001039933.1	147	aGc/aAc	4/6	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.487833773872691	2		565	663	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223104	1223109	+	inframe_deletion	In_Frame_Del	DEL	GGACGA	GGACGA	-	rs762810203	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	170	552	0	ENST00000326873.7:c.1051_1056del	p.Glu351_Asp352del	p.E351_D352del	ENST00000326873	NM_000455.4	347	gcGGACGAg/gcg	8/10	1	2	FACETS	0.855	0.787	0.926	0.855	0.787	0.926	CLONAL	1	TRUE	1	0.487833773872691	2		552	815	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5225821	5225821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772609224	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	182	671	3	ENST00000357368.4:c.2411C>T	p.Ala804Val	p.A804V	ENST00000357368	NM_002850.3	804	gCg/gTg	17/38	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.487833773872691	2		674	726	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300121	15300122	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	167	656	0	ENST00000263388.2:c.1154dup	p.Gly386TrpfsTer4	p.G386Wfs*4	ENST00000263388	NM_000435.2	385	ggt/ggGt	7/33	1	2	FACETS	0.903	0.832	0.978	0.903	0.832	0.978	CLONAL	1	TRUE	1	0.487833773872691	2		656	758	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082406	16082406	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	195	728	0	ENST00000281043.3:c.220C>A	p.Pro74Thr	p.P74T	ENST00000281043	NM_005378.4	74	Ccc/Acc	2/3	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.487833773872691	2		728	721	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605146	46605146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	66	470	0	ENST00000263734.3:c.1363C>T	p.Pro455Ser	p.P455S	ENST00000263734	NM_001430.4	455	Cct/Tct	10/16	1	2	FACETS	0.493	0.428	0.563	0.493	0.428	0.563	SUBCLONAL	1	TRUE	1	0.487833773872691	2		470	549	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485422	57485422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	80	261	0	ENST00000371085.3:c.1004C>T	p.Thr335Ile	p.T335I	ENST00000371085	NM_000516.4	335	aCc/aTc	12/13	0.487833773872691	3	FACETS	0.74	0.653	0.834			1	SUBCLONAL	1	TRUE	NA	0.487833773872691	3		261	551	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319391	62319391	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760398738	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	398	735	0	ENST00000360203.5:c.1583C>T	p.Ala528Val	p.A528V	ENST00000360203	NM_001283009.1	528	gCg/gTg	18/35	0.487833773872691	3	FACETS	1	0.976	1			1	CLONAL	2	TRUE	NA	0.487833773872691	3		735	981	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29083898	29083899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	21	214	0	ENST00000328354.6:c.1617_1618dup	p.Ala540ValfsTer27	p.A540Vfs*27	ENST00000328354	NM_007194.3	540	gct/gTGct	15/15	1	2	FACETS	0.356	0.274	0.45	0.356	0.274	0.45	SUBCLONAL	1	TRUE	1	0.487833773872691	2		214	242	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665375	138665375	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	291	744	0	ENST00000330315.3:c.190G>A	p.Ala64Thr	p.A64T	ENST00000330315	NM_023067.3	64	Gcc/Acc	1/1	0.118897352372575	4	FACETS	0.93	0.877	0.985	0.93	0.877	0.985	INDETERMINATE	2	TRUE	2	0.487833773872691	4		744	954	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169977822	169977822	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	206	466	0	ENST00000295797.4:c.289A>G	p.Lys97Glu	p.K97E	ENST00000295797	NM_002740.5	97	Aag/Gag	3/18	0.118897352372575	4	FACETS	0.78	0.726	0.837	0.78	0.726	0.837	INDETERMINATE	2	TRUE	2	0.487833773872691	4		466	805	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506921	186506922	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	65	207	0	ENST00000323963.5:c.1089_1090del	p.Gly365SerfsTer14	p.G365Sfs*14	ENST00000323963		363	AGa/a	11/11	0.118897352372575	4	FACETS	1	0.96	1	0.631	0.551	0.717	INDETERMINATE	1	TRUE	2	0.487833773872691	4		207	314	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007353	143007353	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	101	328	0	ENST00000262992.4:c.2431C>T	p.Gln811Ter	p.Q811*	ENST00000262992	NM_001101669.1	811	Caa/Taa	22/24	1	2	FACETS	0.904	0.812	1	0.904	0.812	1	CLONAL	1	TRUE	1	0.487833773872691	2		328	458	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947466	38947466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	87	327	0	ENST00000357387.3:c.4214G>A	p.Arg1405Gln	p.R1405Q	ENST00000357387	NM_152756.3	1405	cGa/cAa	32/38	1	2	FACETS	0.791	0.703	0.884	0.791	0.703	0.884	SUBCLONAL	1	TRUE	1	0.487833773872691	2		327	451	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056323	26056323	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770255220	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	130	340	0	ENST00000343677.2:c.334G>A	p.Ala112Thr	p.A112T	ENST00000343677	NM_005319.3	112	Gcc/Acc	1/1	0.487833773872691	2	FACETS	1	0.965	1	0.556	0.508	0.607	CLONAL	1	TRUE	0	0.487833773872691	2		340	479	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911170	29911170	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199474532	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	64	259	0	ENST00000376809.5:c.469T>C	p.Trp157Arg	p.W157R	ENST00000376809	NM_002116.7	157	Tgg/Cgg	3/8	0.487833773872691	2	FACETS	1	0.967	1	0.656	0.578	0.738	CLONAL	1	TRUE	0	0.487833773872691	2		259	200	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324596	31324596	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs778050851	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	172	375	0	ENST00000412585.2:c.212C>A	p.Pro71Gln	p.P71Q	ENST00000412585	NM_005514.6	71	cCg/cAg	2/8	1	2	FACETS	0.866	0.807	0.926	1	0.992	1	CLONAL	2	TRUE	1	0.487833773872691	2		375	407	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724371	117724371	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	147	594	0	ENST00000368508.3:c.508T>C	p.Trp170Arg	p.W170R	ENST00000368508	NM_002944.2	170	Tgg/Cgg	6/43	NA	2	FACETS	0.893	0.817	0.972			1	INDETERMINATE	1	TRUE	NA	0.487833773872691	2		594	675	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196024	138196024	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	21	204	0	ENST00000237289.4:c.338G>T	p.Trp113Leu	p.W113L	ENST00000237289	NM_001270507.1	113	tGg/tTg	3/9	1	2	FACETS	0.294	0.226	0.373	0.294	0.226	0.373	SUBCLONAL	1	TRUE	1	0.487833773872691	2		204	293	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138197235	138197235	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	32	378	0	ENST00000237289.4:c.737A>G	p.Tyr246Cys	p.Y246C	ENST00000237289	NM_001270507.1	246	tAc/tGc	5/9	1	2	FACETS	0.255	0.206	0.31	0.255	0.206	0.31	SUBCLONAL	1	TRUE	1	0.487833773872691	2		378	514	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002701	37002701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	112	554	0	ENST00000358127.4:c.548G>A	p.Gly183Asp	p.G183D	ENST00000358127	NM_001280556.1	183	gGc/gAc	5/10	1	2	FACETS	0.745	0.672	0.823	0.745	0.672	0.823	SUBCLONAL	1	TRUE	1	0.487833773872691	2		554	616	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760462	133760462	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	166	526	0	ENST00000318560.5:c.2785G>T	p.Gly929Cys	p.G929C	ENST00000318560	NM_005157.4	929	Ggc/Tgc	11/11	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.487833773872691	2		526	671	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418355	139418356	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	218	786	0	ENST00000277541.6:c.216dup	p.Thr73AspfsTer70	p.T73Dfs*70	ENST00000277541	NM_017617.3	72	-/G	3/34	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.487833773872691	2		786	872	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916505	39916505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1228402564	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	234	718	0	ENST00000378444.4:c.4498G>A	p.Ala1500Thr	p.A1500T	ENST00000378444	NM_001123385.1	1500	Gcc/Acc	11/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.487833773872691	2		718	834	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929125	44929125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1298658636	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	143	402	0	ENST00000377967.4:c.2225C>T	p.Ala742Val	p.A742V	ENST00000377967	NM_021140.2	742	gCc/gTc	17/29	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.487833773872691	2		402	530	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422383	47422384	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1453474773	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	98	379	0	ENST00000377045.4:c.23dup	p.Ala9CysfsTer84	p.A9Cfs*84	ENST00000377045	NM_001654.4	6	ggc/ggCc	2/16	1	2	FACETS	0.99	0.889	1	0.99	0.889	1	CLONAL	1	TRUE	1	0.487833773872691	2		379	406	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424466	47424466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	122	557	0	ENST00000377045.4:c.386G>A	p.Gly129Asp	p.G129D	ENST00000377045	NM_001654.4	129	gGc/gAc	5/16	1	2	FACETS	0.75	0.679	0.824	0.75	0.679	0.824	SUBCLONAL	1	TRUE	1	0.487833773872691	2		557	667	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223584	53223584	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	102	416	0	ENST00000375401.3:c.3775C>A	p.Leu1259Met	p.L1259M	ENST00000375401	NM_004187.3	1259	Ctg/Atg	23/26	1	2	FACETS	0.989	0.89	1	0.989	0.89	1	CLONAL	1	TRUE	1	0.487833773872691	2		416	423	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615574	100615574	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	176	442	0	ENST00000308731.7:c.758G>T	p.Arg253Ile	p.R253I	ENST00000308731	NM_000061.2	253	aGa/aTa	8/19	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.487833773872691	2		442	609	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	66	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.709	0.617	0.807	0.709	0.617	0.807	SUBCLONAL	1	FALSE	1	0.437266010231208	2		215	426	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0025544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	125	458	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.437266010231208	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	0	0.437266010231208	1		458	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0025544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	284	923	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.369268502025911	2	FACETS	0.783	0.738	0.828	0.783	0.738	0.828	SUBCLONAL	2	FALSE	0	0.437266010231208	2		923	830	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	97	452	2	ENST00000295754.5:c.1583G>T	p.Arg528Leu	p.R528L	ENST00000295754	NM_003242.5	528	cGt/cTt	7/7	0.358048284332894	1	FACETS	0.917	0.824	1	0.917	0.824	1	CLONAL	1	FALSE	0	0.437266010231208	1		454	378	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193202241	193202241	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	93	562	0	ENST00000367435.3:c.1273T>G	p.Tyr425Asp	p.Y425D	ENST00000367435	NM_024529.4	425	Tat/Gat	14/17	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.437266010231208	2		562	374	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2105406	2105406	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	124	555	0	ENST00000219476.3:c.485A>G	p.Asp162Gly	p.D162G	ENST00000219476	NM_000548.3	162	gAc/gGc	6/42	1	2	FACETS	0.839	0.76	0.922	0.839	0.76	0.922	CLONAL	1	FALSE	1	0.437266010231208	2		555	676	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118378	17118378	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	115	732	0	ENST00000285071.4:c.1459G>A	p.Glu487Lys	p.E487K	ENST00000285071	NM_144997.5	487	Gaa/Aaa	13/14	0.369268502025911	2	FACETS	0.695	0.626	0.768	0.347	0.313	0.384	SUBCLONAL	1	FALSE	0	0.437266010231208	2		732	757	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158586	26158586	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	115	613	0	ENST00000289316.2:c.189G>C	p.Met63Ile	p.M63I	ENST00000289316	NM_138720.2	63	atG/atC	1/2	0.437266010231208	6	FACETS	1	0.949	1	0.272	0.244	0.301	CLONAL	1	FALSE	2	0.437266010231208	6		613	907	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0025678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	52	611	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	1	2	FACETS	0.474	0.402	0.553	0.474	0.402	0.553	SUBCLONAL	1	TRUE	1	0.25	2		611	878	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610695	52610695	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	39	369	1	ENST00000394830.3:c.3478C>T	p.Arg1160Ter	p.R1160*	ENST00000394830	NM_018313.4	1160	Cga/Tga	23/30	1	2	FACETS	0.937	0.779	1	0.937	0.779	1	CLONAL	1	TRUE	1	0.25	2		370	333	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039206	49039206	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	78	509	0	ENST00000267163.4:c.2284del	p.Gln762ArgfsTer3	p.Q762Rfs*3	ENST00000267163	NM_000321.2	762	Cag/ag	22/27	1	2	FACETS	0.994	0.874	1	0.994	0.874	1	CLONAL	1	TRUE	1	0.25	2		509	628	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801058	1801058	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	128	939	1	ENST00000260795.2:c.187C>T	p.Pro63Ser	p.P63S	ENST00000260795		63	Ccg/Tcg	2/17	1	2	FACETS	0.769	0.695	0.848	0.769	0.695	0.848	SUBCLONAL	1	TRUE	1	0.25	2		940	1331	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023171	27023172	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0025678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	40	110	0	ENST00000324856.7:c.278_279del	p.Gly93AlafsTer17	p.G93Afs*17	ENST00000324856	NM_006015.4	93	GGg/g	1/20	1	2	FACETS	0.842	0.708	0.987	1	0.964	1	CLONAL	2	TRUE	1	0.25	2		110	190	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023178	27023186	+	inframe_deletion	In_Frame_Del	DEL	GCGCGGAGC	GCGCGGAGC	-	novel	NA	P-0025678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	39	126	0	ENST00000324856.7:c.284_292del	p.Gly95_Pro98delinsAla	p.G95_P98delinsA	ENST00000324856	NM_006015.4	95	gGCGCGGAGCcg/gcg	1/20	1	2	FACETS	0.754	0.631	0.888	1	0.956	1	SUBCLONAL	2	TRUE	1	0.25	2		126	207	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0025813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	207	282	0				ENST00000310581	NM_198253.2	-/1132			0.588322745215476	2	FACETS	0.973	0.922	1	0.973	0.922	1	CLONAL	2	TRUE	0	0.614699868789489	2		282	346	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11552822	NA	P-0025813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	386	563	0	ENST00000304494.5:c.250G>T	p.Asp84Tyr	p.D84Y	ENST00000304494	NM_000077.4	84	Gac/Tac	2/3	0.614699868789489	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.614699868789489	2		563	549	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0025813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	87	173	1				ENST00000310581	NM_198253.2	-/1132			0.588322745215476	2	FACETS	0.86	0.769	0.956	0.43	0.384	0.478	CLONAL	1	TRUE	0	0.614699868789489	2		174	329	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560970	9560970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781706438	NA	P-0025813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	351	452	1	ENST00000353224.5:c.812C>T	p.Ser271Leu	p.S271L	ENST00000353224	NM_177990.2	271	tCg/tTg	4/10	0.614699868789489	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	1	0.614699868789489	4		453	595	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0025813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	376	995	0	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	0.50124624448819	4	FACETS	0.967	0.921	1	0.967	0.921	1	CLONAL	2	TRUE	2	0.614699868789489	4		995	1021	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0025813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	357	372	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	0.614699868789489	7	FACETS	1	0.986	1			1	CLONAL	4	TRUE	NA	0.614699868789489	7		372	686	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2969697	2969697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367917190	NA	P-0025813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	171	697	1	ENST00000396946.4:c.1582G>A	p.Glu528Lys	p.E528K	ENST00000396946	NM_032415.4	528	Gag/Aag	12/25	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.614699868789489	2		698	520	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633229	12633229	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs368807126	NA	P-0025813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	904	473	0	ENST00000251849.4:c.1171A>T	p.Arg391Trp	p.R391W	ENST00000251849	NM_002880.3	391	Agg/Tgg	11/17	0.614699868789489	6	FACETS	0.968	0.95	0.985			1	CLONAL	6	TRUE	NA	0.614699868789489	6		473	1129	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524185	187524185	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	77	440	0	ENST00000441802.2:c.11354G>A	p.Gly3785Glu	p.G3785E	ENST00000441802	NM_005245.3	3785	gGa/gAa	20/27	1	2	FACETS	0.746	0.66	0.836	0.746	0.66	0.836	SUBCLONAL	1	TRUE	1	0.614699868789489	2		440	336	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245399	46245399	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	222	523	0	ENST00000334344.6:c.3493C>T	p.Gln1165Ter	p.Q1165*	ENST00000334344	NM_152641.2	1165	Caa/Taa	15/21	0.614699868789489	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	2	0.614699868789489	4		523	569	SUCCESS
APC	324	MSKCC	GRCh37	5	112174098	112174098	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs878853433	NA	P-0025813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	243	408	0	ENST00000257430.4:c.2807A>G	p.Asn936Ser	p.N936S	ENST00000257430	NM_000038.5	936	aAt/aGt	16/16	0.578074388361551	4	FACETS	0.933	0.894	0.971	0.933	0.894	0.971	CLONAL	4	TRUE	0	0.614699868789489	4		408	342	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406184	70406184	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	208	641	0	ENST00000373644.4:c.3698A>C	p.Lys1233Thr	p.K1233T	ENST00000373644	NM_030625.2	1233	aAa/aCa	4/12	0.580003727360914	2	FACETS	0.95	0.9	1	0.95	0.9	1	CLONAL	2	TRUE	0	0.614699868789489	2		641	356	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102196235	102196235	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	69	399	0	ENST00000263464.3:c.892G>A	p.Gly298Arg	p.G298R	ENST00000263464	NM_001165.4	298	Gga/Aga	3/9	0.249294955433735	3	FACETS	1	0.95	1	0.575	0.507	0.647	INDETERMINATE	1	TRUE	1	0.614699868789489	3		399	255	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50784036	50784036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567421073	NA	P-0025813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	81	673	3	ENST00000398568.2:c.427C>T	p.Pro143Ser	p.P143S	ENST00000398568	NM_001042412.1	143	Cct/Tct	3/18	0.575024683003266	3	FACETS	0.754	0.667	0.847	0.377	0.333	0.424	SUBCLONAL	1	TRUE	1	0.614699868789489	3		676	457	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27016085	27016085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	307	554	0	ENST00000335756.4:c.361C>T	p.Leu121Phe	p.L121F	ENST00000335756	NM_001809.3	121	Ctc/Ttc	4/5	0.575024683003266	3	FACETS	0.994	0.945	1	0.994	0.945	1	CLONAL	2	TRUE	1	0.614699868789489	3		554	657	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100905	41100906	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0025813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	109	488	1	ENST00000373198.4:c.1450_1450+1delinsAA		p.X484_splice	ENST00000373198	NM_133170.3	484		8/32	0.614699868789489	4	FACETS	0.899	0.809	0.994	0.3	0.269	0.332	CLONAL	1	TRUE	1	0.614699868789489	4		489	637	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322440	31322440	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1282028277	NA	P-0025813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	135	577	0	ENST00000412585.2:c.1015G>A	p.Gly339Arg	p.G339R	ENST00000412585	NM_005514.6	339	Gga/Aga	6/8	0.614699868789489	3	FACETS	0.949	0.866	1	0.475	0.433	0.518	CLONAL	1	TRUE	1	0.614699868789489	3		577	605	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005204	150005204	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	62	460	0	ENST00000253339.5:c.1021C>T	p.Pro341Ser	p.P341S	ENST00000253339		341	Cca/Tca	3/7	1	2	FACETS	0.791	0.691	0.897	0.791	0.691	0.897	SUBCLONAL	1	TRUE	1	0.614699868789489	2		460	255	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962283	2962283	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	161	651	0	ENST00000396946.4:c.2254A>C	p.Lys752Gln	p.K752Q	ENST00000396946	NM_032415.4	752	Aag/Cag	17/25	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.614699868789489	2		651	509	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874557	151874557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	220	419	1	ENST00000262189.6:c.7981C>T	p.Pro2661Ser	p.P2661S	ENST00000262189	NM_170606.2	2661	Cct/Tct	38/59	0.583647626367896	4	FACETS	0.966	0.914	1	0.966	0.914	1	CLONAL	3	TRUE	1	0.614699868789489	4		420	399	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129850	69129850	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0025813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	160	264	0	ENST00000288368.4:c.4605-1G>A		p.X1535_splice	ENST00000288368	NM_024870.2	1535			0.577798306399132	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.614699868789489	3		264	318	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0025871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	96	354	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	0.366834287897353	2		354	460	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1485978447	NA	P-0025871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	241	409	0	ENST00000324856.7:c.5164C>T	p.Arg1722Ter	p.R1722*	ENST00000324856	NM_006015.4	1722	Cga/Tga	20/20	NA	2	FACETS	0.991	0.931	1			1	INDETERMINATE	2	TRUE	NA	0.366834287897353	2		409	663	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057520006	NA	P-0025871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	196	550	0	ENST00000269305.4:c.821T>A	p.Val274Asp	p.V274D	ENST00000269305	NM_001126112.2	274	gTt/gAt	8/11	0.366834287897353	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.366834287897353	1		550	777	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264673	1264673	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559028617	NA	P-0025871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	171	655	0	ENST00000310581.5:c.2689G>A	p.Val897Met	p.V897M	ENST00000310581	NM_198253.2	897	Gtg/Atg	11/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.366834287897353	2		655	880	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971101	21971110	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGCGTCGT	GCAGCGTCGT	-	novel	NA	P-0025871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	49	218	0	ENST00000304494.5:c.248_257del	p.His83ProfsTer60	p.H83Pfs*60	ENST00000304494	NM_000077.4	83	cACGACGCTGCc/cc	2/3	0.366834287897353	1	FACETS	0.752	0.641	0.873	0.752	0.641	0.873	SUBCLONAL	1	TRUE	0	0.366834287897353	1		218	290	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971163	21971184	+	frameshift_variant	Frame_Shift_Del	DEL	GAGCAGCAGCAGCTCCGCCACT	GAGCAGCAGCAGCTCCGCCACT	-	novel	NA	P-0025871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	23	275	0	ENST00000304494.5:c.174_195del	p.Val59ThrfsTer80	p.V59Tfs*80	ENST00000304494	NM_000077.4	58	cgAGTGGCGGAGCTGCTGCTGCTC/cg	2/3	0.366834287897353	1	FACETS	0.27	0.21	0.34	0.27	0.21	0.34	SUBCLONAL	1	TRUE	0	0.366834287897353	1		275	379	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53254023	53254023	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	128	506	0	ENST00000375401.3:c.49T>G	p.Phe17Val	p.F17V	ENST00000375401	NM_004187.3	17	Ttc/Gtc	1/26	0.222914406123057	1	FACETS	0.896	0.814	0.982	0.896	0.814	0.982	CLONAL	1	TRUE	0	0.366834287897353	1		506	636	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578419	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587781845	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	157	547	0	ENST00000269305.4:c.511G>T	p.Glu171Ter	p.E171*	ENST00000269305	NM_001126112.2	171	Gag/Tag	5/11	0.246341925686229	2	FACETS	0.821	0.755	0.888	0.821	0.755	0.888	CLONAL	2	TRUE	0	0.327629744002206	2		547	584	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015133	37015133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223489007	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	65	565	1	ENST00000358127.4:c.271G>A	p.Ala91Thr	p.A91T	ENST00000358127	NM_001280556.1	91	Gcc/Acc	3/10	0.327629744002206	3	FACETS	0.604	0.522	0.692			1	SUBCLONAL	1	TRUE	NA	0.327629744002206	3		566	765	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778096	135778096	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203671	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	43	447	1	ENST00000298552.3:c.2287C>T	p.Gln763Ter	p.Q763*	ENST00000298552	NM_001162426.1	763	Cag/Tag	18/23	0.251272807990151	1	FACETS	0.387	0.323	0.458	0.387	0.323	0.458	SUBCLONAL	1	TRUE	0	0.327629744002206	1		448	567	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651292	52651292	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	31	427	0	ENST00000394830.3:c.1804G>A	p.Glu602Lys	p.E602K	ENST00000394830	NM_018313.4	602	Gag/Aag	15/30	0.246341925686229	2	FACETS	0.378	0.305	0.461	0.189	0.152	0.231	SUBCLONAL	1	TRUE	0	0.327629744002206	2		427	500	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439656	140439656	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	39	328	0	ENST00000288602.6:c.2083G>C	p.Glu695Gln	p.E695Q	ENST00000288602	NM_004333.4	695	Gag/Cag	17/18	0.315831957858332	3	FACETS	0.671	0.556	0.798	0.335	0.278	0.399	SUBCLONAL	1	TRUE	1	0.327629744002206	3		328	413	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905343	50905343	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	80	550	0	ENST00000440232.2:c.551G>T	p.Gly184Val	p.G184V	ENST00000440232	NM_002691.3	184	gGg/gTg	5/27	NA	2	FACETS	0.829	0.731	0.935			1	INDETERMINATE	1	TRUE	NA	0.327629744002206	2		550	589	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655372	67655372	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	52	533	1	ENST00000264010.4:c.1235G>T	p.Cys412Phe	p.C412F	ENST00000264010	NM_006565.3	412	tGt/tTt	7/12	1	2	FACETS	0.412	0.35	0.481	0.412	0.35	0.481	SUBCLONAL	1	TRUE	1	0.327629744002206	2		534	770	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372783	81372783	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	108	348	0	ENST00000222390.5:c.751C>A	p.Pro251Thr	p.P251T	ENST00000222390	NM_000601.4	251	Ccc/Acc	7/18	0.315831957858332	3	FACETS	1	0.982	1	0.72	0.648	0.795	CLONAL	1	TRUE	1	0.327629744002206	3		348	533	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748159	72748159	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	72	288	0	ENST00000357731.5:c.19G>T	p.Val7Leu	p.V7L	ENST00000357731	NM_173808.2	7	Gtg/Ttg	1/7	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.327629744002206	2		288	314	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120509013	120509013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	129	572	0	ENST00000256646.2:c.1553G>A	p.Cys518Tyr	p.C518Y	ENST00000256646	NM_024408.3	518	tGc/tAc	9/34	0.327629744002206	3	FACETS	1	0.976	1			1	CLONAL	1	TRUE	NA	0.327629744002206	3		572	749	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746083	162746083	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	118	364	0	ENST00000367921.3:c.2206T>C	p.Tyr736His	p.Y736H	ENST00000367921	NM_006182.2	736	Tac/Cac	16/18	0.315831957858332	3	FACETS	0.782	0.708	0.859	0.782	0.708	0.859	SUBCLONAL	2	TRUE	1	0.327629744002206	3		364	536	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163325201	163325201	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs777331725	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	140	589	0	ENST00000271452.3:c.1337C>G	p.Ala446Gly	p.A446G	ENST00000271452	NM_145697.2	446	gCt/gGt	14/14	0.315831957858332	3	FACETS	1	0.982	1	0.648	0.59	0.708	CLONAL	1	TRUE	1	0.327629744002206	3		589	768	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850714	63850714	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	33	464	0	ENST00000279873.7:c.1492G>C	p.Glu498Gln	p.E498Q	ENST00000279873	NM_032199.2	498	Gaa/Caa	10/10	1	2	FACETS	0.321	0.26	0.389	0.321	0.26	0.389	SUBCLONAL	1	TRUE	1	0.327629744002206	2		464	628	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333992	70333992	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	86	439	0	ENST00000373644.4:c.1897G>T	p.Val633Phe	p.V633F	ENST00000373644	NM_030625.2	633	Gtt/Ttt	2/12	1	2	FACETS	0.972	0.862	1	0.972	0.862	1	CLONAL	1	TRUE	1	0.327629744002206	2		439	540	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450798	70450798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	82	401	0	ENST00000373644.4:c.5638C>T	p.His1880Tyr	p.H1880Y	ENST00000373644	NM_030625.2	1880	Cac/Tac	12/12	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.327629744002206	2		401	417	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098401	108098401	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1242444722	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	149	519	0	ENST00000278616.4:c.50A>G	p.His17Arg	p.H17R	ENST00000278616	NM_000051.3	17	cAt/cGt	2/63	0.246341925686229	2	FACETS	1	0.987	1	0.73	0.669	0.793	CLONAL	1	TRUE	0	0.327629744002206	2		519	623	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435113	18435113	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	171	505	0	ENST00000266497.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000266497		33	tCt/tGt	1/31	0.273496926900907	2	FACETS	0.888	0.821	0.956	0.888	0.821	0.956	CLONAL	2	TRUE	0	0.327629744002206	2		505	588	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423519	88423519	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	182	616	0	ENST00000360948.2:c.2316C>A	p.Phe772Leu	p.F772L	ENST00000360948	NM_001012338.2	772	ttC/ttA	18/19	0.327629744002206	2	FACETS	0.804	0.744	0.866	0.804	0.744	0.866	CLONAL	2	TRUE	0	0.327629744002206	2		616	691	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346930	91346930	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	81	495	0	ENST00000355112.3:c.3538G>T	p.Val1180Leu	p.V1180L	ENST00000355112	NM_000057.2	1180	Gta/Tta	18/22	0.327629744002206	2	FACETS	0.722	0.636	0.814	0.361	0.318	0.407	SUBCLONAL	1	TRUE	0	0.327629744002206	2		495	685	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858797	9858797	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	42	152	0	ENST00000330684.3:c.2604C>A	p.Tyr868Ter	p.Y868*	ENST00000330684	NM_001134407.1	868	taC/taA	13/13	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.327629744002206	2		152	172	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274189	10274189	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	101	280	0	ENST00000330684.3:c.80C>A	p.Ala27Glu	p.A27E	ENST00000330684	NM_001134407.1	27	gCg/gAg	2/13	1	2	FACETS	0.84	0.758	0.926	1	0.986	1	CLONAL	2	TRUE	1	0.327629744002206	2		280	367	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805690	46805690	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	163	509	0	ENST00000290295.7:c.266C>G	p.Ser89Cys	p.S89C	ENST00000290295	NM_006361.5	89	tCc/tGc	1/2	0.327629744002206	2	FACETS	0.91	0.84	0.981	0.91	0.84	0.981	CLONAL	2	TRUE	0	0.327629744002206	2		509	547	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440751	56440752	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	126	395	0	ENST00000407977.2:c.466_467delinsTT	p.Gly156Leu	p.G156L	ENST00000407977		156	GGg/TTg	5/10	0.327629744002206	2	FACETS	0.924	0.844	1	0.924	0.844	1	CLONAL	2	TRUE	0	0.327629744002206	2		395	416	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575066	48575066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500735	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	132	356	0	ENST00000342988.3:c.260G>A	p.Arg87Gln	p.R87Q	ENST00000342988	NM_005359.5	87	cGg/cAg	3/12	NA	2	FACETS	0.887	0.812	0.966			1	INDETERMINATE	2	TRUE	NA	0.327629744002206	2		356	454	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217909	2217909	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	165	535	0	ENST00000398665.3:c.2683G>T	p.Glu895Ter	p.E895*	ENST00000398665	NM_032482.2	895	Gag/Tag	22/28	0.246341925686229	2	FACETS	0.957	0.885	1	0.957	0.885	1	CLONAL	2	TRUE	0	0.327629744002206	2		535	526	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210583	5210583	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	143	450	0	ENST00000357368.4:c.5384C>G	p.Pro1795Arg	p.P1795R	ENST00000357368	NM_002850.3	1795	cCg/cGg	35/38	0.246341925686229	2	FACETS	0.861	0.79	0.934	0.861	0.79	0.934	CLONAL	2	TRUE	0	0.327629744002206	2		450	507	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905893	50905893	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	84	549	0	ENST00000440232.2:c.865G>T	p.Asp289Tyr	p.D289Y	ENST00000440232	NM_002691.3	289	Gac/Tac	8/27	NA	2	FACETS	0.853	0.754	0.959			1	INDETERMINATE	1	TRUE	NA	0.327629744002206	2		549	601	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624867	9624868	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	139	507	0	ENST00000353224.5:c.109dup	p.Gln37ProfsTer36	p.Q37Pfs*36	ENST00000353224	NM_177990.2	37	cag/cCag	3/10	0.315831957858332	3	FACETS	0.753	0.687	0.821	0.753	0.687	0.821	SUBCLONAL	2	TRUE	1	0.327629744002206	3		507	656	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309483	30309483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746751843	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	155	521	0	ENST00000307677.4:c.539C>T	p.Pro180Leu	p.P180L	ENST00000307677	NM_138578.1	180	cCt/cTt	2/3	0.315831957858332	3	FACETS	1	0.988	1	0.736	0.675	0.8	CLONAL	1	TRUE	1	0.327629744002206	3		521	748	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268694	46268694	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	88	390	0	ENST00000371998.3:c.2983del	p.Ala995LeufsTer94	p.A995Lfs*94	ENST00000371998		993	atG/at	16/23	0.297131867719184	1	FACETS	0.989	0.881	1	0.989	0.881	1	CLONAL	1	TRUE	0	0.327629744002206	1		390	454	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161736	47161736	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	86	351	0	ENST00000409792.3:c.4390G>C	p.Ala1464Pro	p.A1464P	ENST00000409792	NM_014159.6	1464	Gcc/Ccc	3/21	0.246341925686229	2	FACETS	1	0.976	1	0.694	0.619	0.774	CLONAL	1	TRUE	0	0.327629744002206	2		351	378	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52692281	52692281	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	161	538	0	ENST00000394830.3:c.579A>G	p.Ile193Met	p.I193M	ENST00000394830	NM_018313.4	193	atA/atG	6/30	0.246341925686229	2	FACETS	0.804	0.741	0.87	0.804	0.741	0.87	CLONAL	2	TRUE	0	0.327629744002206	2		538	611	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960047	134960047	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	78	530	0	ENST00000398015.3:c.2404A>G	p.Thr802Ala	p.T802A	ENST00000398015	NM_004441.4	802	Act/Gct	13/16	1	2	FACETS	0.769	0.676	0.869	0.769	0.676	0.869	SUBCLONAL	1	TRUE	1	0.327629744002206	2		530	619	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446334	187446334	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	96	317	0	ENST00000232014.4:c.1356-2A>C		p.X452_splice	ENST00000232014	NM_001130845.1	452			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.327629744002206	2		317	431	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146563	55146563	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	113	465	0	ENST00000257290.5:c.2237T>A	p.Leu746Gln	p.L746Q	ENST00000257290	NM_006206.4	746	cTa/cAa	16/23	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.327629744002206	2		465	550	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161352	55161352	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138036141	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	140	527	0	ENST00000257290.5:c.3183G>C	p.Lys1061Asn	p.K1061N	ENST00000257290	NM_006206.4	1061	aaG/aaC	23/23	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.327629744002206	2		527	614	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286253	66286253	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	126	413	0	ENST00000273854.3:c.1433G>T	p.Gly478Val	p.G478V	ENST00000273854	NM_004439.5	478	gGg/gTg	6/18	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.327629744002206	2		413	604	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541678	187541678	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	95	321	0	ENST00000441802.2:c.6062G>T	p.Arg2021Leu	p.R2021L	ENST00000441802	NM_005245.3	2021	cGc/cTc	10/27	0.246341925686229	2	FACETS	1	0.98	1	0.718	0.643	0.796	CLONAL	1	TRUE	0	0.327629744002206	2		321	404	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295388	1295388	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs796440492	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	20	122	1				ENST00000310581	NM_198253.2	-/1132			0.293812000432451	3	FACETS	0.856	0.659	1	0.428	0.329	0.542	CLONAL	1	TRUE	1	0.327629744002206	3		123	166	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31468154	31468154	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	142	568	0	ENST00000344624.3:c.2258G>T	p.Arg753Leu	p.R753L	ENST00000344624		753	cGt/cTt	15/33	0.293812000432451	3	FACETS	1	0.977	1	0.604	0.551	0.66	CLONAL	1	TRUE	1	0.327629744002206	3		568	835	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225765	26225765	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	44	453	0	ENST00000360408.1:c.383C>G	p.Ala128Gly	p.A128G	ENST00000360408	NM_003532.2	128	gCc/gGc	1/1	0.293812000432451	3	FACETS	0.556	0.466	0.656	0.278	0.233	0.328	SUBCLONAL	1	TRUE	1	0.327629744002206	3		453	562	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172160	32172160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	60	482	2	ENST00000375023.3:c.2872C>T	p.Pro958Ser	p.P958S	ENST00000375023	NM_004557.3	958	Cca/Tca	19/30	1	2	FACETS	0.673	0.58	0.774	0.673	0.58	0.774	SUBCLONAL	1	TRUE	1	0.327629744002206	2		484	544	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37141752	37141752	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	53	529	0	ENST00000373509.5:c.827C>G	p.Ser276Ter	p.S276*	ENST00000373509	NM_002648.3	276	tCa/tGa	6/6	0.217415710951326	3	FACETS	0.586	0.499	0.681			1	SUBCLONAL	1	TRUE	NA	0.327629744002206	3		529	643	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975463	13975463	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	93	347	0	ENST00000405192.2:c.424A>T	p.Ser142Cys	p.S142C	ENST00000405192	NM_001163147.1	142	Agc/Tgc	7/12	0.315831957858332	3	FACETS	0.863	0.773	0.957	0.863	0.773	0.957	CLONAL	2	TRUE	1	0.327629744002206	3		347	383	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266409	55266409	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	107	371	0	ENST00000275493.2:c.2702-1G>C		p.X901_splice	ENST00000275493	NM_005228.3	901			0.315831957858332	3	FACETS	1	0.98	1	0.695	0.625	0.768	CLONAL	1	TRUE	1	0.327629744002206	3		371	547	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381508	81381508	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	99	340	0	ENST00000222390.5:c.553G>T	p.Gly185Trp	p.G185W	ENST00000222390	NM_000601.4	185	Ggg/Tgg	5/18	0.315831957858332	3	FACETS	1	0.973	1	0.638	0.571	0.709	CLONAL	1	TRUE	1	0.327629744002206	3		340	551	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392072	81392072	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	131	470	2	ENST00000222390.5:c.205C>A	p.Gln69Lys	p.Q69K	ENST00000222390	NM_000601.4	69	Caa/Aaa	2/18	0.315831957858332	3	FACETS	1	0.977	1	0.616	0.56	0.676	CLONAL	1	TRUE	1	0.327629744002206	3		472	755	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864632	68864632	+	start_lost	Translation_Start_Site	SNP	G	G	T	rs1563466771	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	41	111	0	ENST00000288368.4:c.3G>T	p.Met1?	p.M1?	ENST00000288368	NM_024870.2	1	atG/atT	1/40	0.327629744002206	3	FACETS	0.991	0.841	1			1	CLONAL	2	TRUE	NA	0.327629744002206	3		111	147	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971156	21971156	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	64	307	0	ENST00000304494.5:c.202G>C	p.Ala68Pro	p.A68P	ENST00000304494	NM_000077.4	68	Gcg/Ccg	2/3	0.327629744002206	1	FACETS	0.941	0.82	1	0.941	0.82	1	CLONAL	1	TRUE	0	0.327629744002206	1		307	347	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97933361	97933361	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	55	462	1	ENST00000289081.3:c.521G>T	p.Arg174Leu	p.R174L	ENST00000289081	NM_000136.2	174	cGa/cTa	6/15	0.251272807990151	1	FACETS	0.464	0.396	0.538	0.464	0.396	0.538	SUBCLONAL	1	TRUE	0	0.327629744002206	1		463	605	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417552	139417552	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	81	617	0	ENST00000277541.6:c.492C>G	p.Cys164Trp	p.C164W	ENST00000277541	NM_017617.3	164	tgC/tgG	4/34	0.251272807990151	1	FACETS	0.76	0.671	0.855	0.76	0.671	0.855	SUBCLONAL	1	TRUE	0	0.327629744002206	1		617	544	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820300	139820300	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	37	569	0	ENST00000247668.2:c.1453G>T	p.Val485Leu	p.V485L	ENST00000247668	NM_021138.3	485	Gtg/Ttg	11/11	0.251272807990151	1	FACETS	0.37	0.304	0.443	0.37	0.304	0.443	SUBCLONAL	1	TRUE	0	0.327629744002206	1		569	511	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410409	63410409	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	114	318	0	ENST00000330258.3:c.2758G>T	p.Glu920Ter	p.E920*	ENST00000330258	NM_152424.3	920	Gag/Tag	2/2	0.217415710951326	2	FACETS	1	0.956	1			1	CLONAL	2	TRUE	NA	0.327629744002206	2		318	323	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	120	282	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.742325525142501	2		282	309	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	146	458	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.742325525142501	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.742325525142501	1		458	234	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755685	39755685	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	128	475	0	ENST00000288319.7:c.1080G>A	p.Met360Ile	p.M360I	ENST00000288319	NM_182918.3	360	atG/atA	10/10	1	2	FACETS	0.893	0.818	0.971	0.893	0.818	0.971	CLONAL	1	TRUE	1	0.742325525142501	2		475	386	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271823	15271823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778006941	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	156	667	0	ENST00000263388.2:c.6616G>A	p.Glu2206Lys	p.E2206K	ENST00000263388	NM_000435.2	2206	Gag/Aag	33/33	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.742325525142501	2		667	391	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042498	37042498	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	165	466	0	ENST00000231790.2:c.260C>T	p.Ser87Phe	p.S87F	ENST00000231790	NM_000249.3	87	tCc/tTc	3/19	1	2	FACETS	0.934	0.865	1	0.934	0.865	1	CLONAL	1	TRUE	1	0.742325525142501	2		466	476	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969189	93969189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868510824	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	83	288	0	ENST00000369303.4:c.1807C>T	p.Pro603Ser	p.P603S	ENST00000369303	NM_004440.3	603	Cca/Tca	10/17	1	2	FACETS	0.828	0.741	0.919	0.828	0.741	0.919	CLONAL	1	TRUE	1	0.742325525142501	2		288	270	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	162	435	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.742325525142501	2		435	410	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288996	212288996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	144	463	0	ENST00000342788.4:c.2750G>A	p.Gly917Glu	p.G917E	ENST00000342788	NM_005235.2	917	gGa/gAa	23/28	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.742325525142501	2		463	388	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435253	18435253	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	99	258	0	ENST00000266497.5:c.238G>A	p.Glu80Lys	p.E80K	ENST00000266497		80	Gaa/Aaa	1/31	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.742325525142501	2		258	238	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495372	149495372	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146614144	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	155	556	0	ENST00000261799.4:c.3275C>T	p.Ser1092Leu	p.S1092L	ENST00000261799	NM_002609.3	1092	tCg/tTg	23/23	0.627754567634647	1	FACETS	0.958	0.898	1	0.958	0.898	1	CLONAL	1	TRUE	0	0.742325525142501	1		556	274	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274121	10274121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	168	431	0	ENST00000330684.3:c.148G>A	p.Glu50Lys	p.E50K	ENST00000330684	NM_001134407.1	50	Gaa/Aaa	2/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.742325525142501	2		431	379	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748601	40748601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200545231	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	108	446	0	ENST00000373198.4:c.2915G>A	p.Arg972Gln	p.R972Q	ENST00000373198	NM_133170.3	972	cGa/cAa	21/32	1	2	FACETS	0.861	0.781	0.943	0.861	0.781	0.943	CLONAL	1	TRUE	1	0.742325525142501	2		446	338	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857305	9857305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766598240	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	83	371	0	ENST00000330684.3:c.4096C>T	p.Pro1366Ser	p.P1366S	ENST00000330684	NM_001134407.1	1366	Cct/Tct	13/13	1	2	FACETS	0.799	0.713	0.887	0.799	0.713	0.887	SUBCLONAL	1	TRUE	1	0.742325525142501	2		371	280	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923328	9923328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	132	492	0	ENST00000330684.3:c.1959G>A	p.Met653Ile	p.M653I	ENST00000330684	NM_001134407.1	653	atG/atA	9/13	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.742325525142501	2		492	353	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310821	123310821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	147	481	0	ENST00000358487.5:c.607C>T	p.Arg203Cys	p.R203C	ENST00000358487	NM_000141.4	203	Cgc/Tgc	5/18	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.742325525142501	2		481	387	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953136	17953136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	149	546	0	ENST00000458235.1:c.850G>A	p.Gly284Arg	p.G284R	ENST00000458235	NM_000215.3	284	Gga/Aga	6/24	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.742325525142501	2		546	392	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171607	36171607	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1569008655	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	66	241	0	ENST00000300305.3:c.958C>T	p.Arg320Ter	p.R320*	ENST00000300305		320	Cga/Tga	7/8	1	2	FACETS	0.936	0.828	1	0.936	0.828	1	CLONAL	1	TRUE	1	0.742325525142501	2		241	190	SUCCESS
APC	324	MSKCC	GRCh37	5	112177701	112177701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554087411	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	110	275	0	ENST00000257430.4:c.6410C>T	p.Ser2137Phe	p.S2137F	ENST00000257430	NM_000038.5	2137	tCc/tTc	16/16	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.742325525142501	2		275	292	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271975	15271975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs567953412	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	137	561	1	ENST00000263388.2:c.6464G>A	p.Gly2155Glu	p.G2155E	ENST00000263388	NM_000435.2	2155	gGa/gAa	33/33	1	2	FACETS	0.951	0.875	1	0.951	0.875	1	CLONAL	1	TRUE	1	0.742325525142501	2		562	388	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346583	81346583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	127	358	0	ENST00000222390.5:c.1370C>T	p.Pro457Leu	p.P457L	ENST00000222390	NM_000601.4	457	cCa/cTa	11/18	1	2	FACETS	0.995	0.913	1	0.995	0.913	1	CLONAL	1	TRUE	1	0.742325525142501	2		358	344	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273811	18273811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	169	551	0	ENST00000222254.8:c.1144C>T	p.His382Tyr	p.H382Y	ENST00000222254	NM_005027.3	382	Cac/Tac	10/16	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.742325525142501	2		551	441	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244400	5244400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs79388082	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	184	638	1	ENST00000357368.4:c.1082C>T	p.Ser361Phe	p.S361F	ENST00000357368	NM_002850.3	361	tCc/tTc	11/38	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.742325525142501	2		639	488	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243484	46243484	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	133	368	0	ENST00000334344.6:c.1837C>T	p.Gln613Ter	p.Q613*	ENST00000334344	NM_152641.2	613	Cag/Tag	14/21	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.742325525142501	2		368	344	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271543	15271543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	199	807	1	ENST00000263388.2:c.6896C>T	p.Ser2299Phe	p.S2299F	ENST00000263388	NM_000435.2	2299	tCc/tTc	33/33	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.742325525142501	2		808	508	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873672	35873672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	122	313	0	ENST00000303115.3:c.628G>A	p.Asp210Asn	p.D210N	ENST00000303115	NM_002185.3	210	Gat/Aat	5/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.742325525142501	2		313	286	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609925	81609925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772490052	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	75	356	1	ENST00000298171.2:c.1523C>T	p.Ser508Leu	p.S508L	ENST00000298171	NM_000369.2	508	tCg/tTg	10/10	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.742325525142501	2		357	192	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704520	117704520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	103	334	0	ENST00000368508.3:c.2456C>T	p.Ser819Phe	p.S819F	ENST00000368508	NM_002944.2	819	tCc/tTc	16/43	1	2	FACETS	0.881	0.798	0.967	0.881	0.798	0.967	CLONAL	1	TRUE	1	0.742325525142501	2		334	315	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967228	93967228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1247358846	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	113	330	0	ENST00000369303.4:c.2124G>A	p.Met708Ile	p.M708I	ENST00000369303	NM_004440.3	708	atG/atA	12/17	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.742325525142501	2		330	298	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629514	187629514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769874804	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	182	473	0	ENST00000441802.2:c.1468C>T	p.Pro490Ser	p.P490S	ENST00000441802	NM_005245.3	490	Cct/Tct	2/27	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.742325525142501	2		473	457	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	360056	360056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	138	433	1	ENST00000262320.3:c.1033C>T	p.Pro345Ser	p.P345S	ENST00000262320	NM_003502.3	345	Cca/Tca	4/11	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.742325525142501	2		434	370	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057657	180057657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775457696	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	185	612	2	ENST00000261937.6:c.298G>A	p.Glu100Lys	p.E100K	ENST00000261937	NM_182925.4	100	Gag/Aag	3/30	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.742325525142501	2		614	481	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120509023	120509023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782444829	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	167	489	0	ENST00000256646.2:c.1543C>T	p.Arg515Cys	p.R515C	ENST00000256646	NM_024408.3	515	Cgt/Tgt	9/34	1	2	FACETS	0.955	0.886	1	0.955	0.886	1	CLONAL	1	TRUE	1	0.742325525142501	2		489	471	SUCCESS
ATR	545	MSKCC	GRCh37	3	142241667	142241667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	138	348	0	ENST00000350721.4:c.4169C>T	p.Ser1390Leu	p.S1390L	ENST00000350721	NM_001184.3	1390	tCa/tTa	23/47	1	2	FACETS	0.958	0.882	1	0.958	0.882	1	CLONAL	1	TRUE	1	0.742325525142501	2		348	388	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858754	9858754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	55	245	0	ENST00000330684.3:c.2647C>T	p.Pro883Ser	p.P883S	ENST00000330684	NM_001134407.1	883	Cca/Tca	13/13	1	2	FACETS	0.788	0.685	0.897	0.788	0.685	0.897	SUBCLONAL	1	TRUE	1	0.742325525142501	2		245	188	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066482	94066482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542602078	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	74	258	0	ENST00000369303.4:c.1277G>A	p.Arg426Gln	p.R426Q	ENST00000369303	NM_004440.3	426	cGa/cAa	5/17	1	2	FACETS	0.827	0.735	0.924	0.827	0.735	0.924	CLONAL	1	TRUE	1	0.742325525142501	2		258	241	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355048	15355048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	189	646	0	ENST00000263377.2:c.2575C>T	p.Pro859Ser	p.P859S	ENST00000263377	NM_058243.2	859	Cct/Tct	13/20	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.742325525142501	2		646	509	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281227	15281227	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	142	590	3	ENST00000263388.2:c.5029C>T	p.Pro1677Ser	p.P1677S	ENST00000263388	NM_000435.2	1677	Cct/Tct	27/33	1	2	FACETS	0.823	0.756	0.892	0.823	0.756	0.892	CLONAL	1	TRUE	1	0.742325525142501	2		593	465	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384651	31384651	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	144	751	2	ENST00000328111.2:c.1359del	p.Leu454SerfsTer136	p.L454Sfs*136	ENST00000328111	NM_006892.3	451	gaG/ga	13/23	1	2	FACETS	0.995	0.918	1	0.995	0.918	1	CLONAL	1	TRUE	1	0.742325525142501	2		753	390	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561090	9561090	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	74	272	0	ENST00000353224.5:c.692C>T	p.Ser231Leu	p.S231L	ENST00000353224	NM_177990.2	231	tCa/tTa	4/10	1	2	FACETS	0.845	0.751	0.943	0.845	0.751	0.943	CLONAL	1	TRUE	1	0.742325525142501	2		272	236	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412267	139412267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1266989706	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	168	898	1	ENST00000277541.6:c.1378C>T	p.Pro460Ser	p.P460S	ENST00000277541	NM_017617.3	460	Ccg/Tcg	8/34	1	2	FACETS	0.928	0.86	0.997	0.928	0.86	0.997	CLONAL	1	TRUE	1	0.742325525142501	2		899	488	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858202	9858202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	114	397	0	ENST00000330684.3:c.3199C>T	p.Arg1067Trp	p.R1067W	ENST00000330684	NM_001134407.1	1067	Cgg/Tgg	13/13	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.742325525142501	2		397	307	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513378	106513378	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1290751197	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	73	291	0	ENST00000359195.3:c.2282C>T	p.Ser761Phe	p.S761F	ENST00000359195	NM_002649.2	761	tCc/tTc	4/11	1	2	FACETS	0.739	0.654	0.829	0.739	0.654	0.829	SUBCLONAL	1	TRUE	1	0.742325525142501	2		291	266	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858359	9858359	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1306036000	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	105	302	0	ENST00000330684.3:c.3042G>A	p.Trp1014Ter	p.W1014*	ENST00000330684	NM_001134407.1	1014	tgG/tgA	13/13	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.742325525142501	2		302	272	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28980009	28980009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866351272	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	105	395	0	ENST00000282397.4:c.1459G>A	p.Glu487Lys	p.E487K	ENST00000282397	NM_002019.4	487	Gaa/Aaa	11/30	0.742325525142501	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.742325525142501	1		395	175	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971178	13971178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs904139873	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	96	254	0	ENST00000405192.2:c.751C>T	p.Pro251Ser	p.P251S	ENST00000405192	NM_001163147.1	251	Ccc/Tcc	8/12	1	2	FACETS	0.995	0.901	1	0.995	0.901	1	CLONAL	1	TRUE	1	0.742325525142501	2		254	260	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024170	31024170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774688930	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	150	539	0	ENST00000375687.4:c.3655C>T	p.Pro1219Ser	p.P1219S	ENST00000375687	NM_015338.5	1219	Ccc/Tcc	13/13	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.742325525142501	2		539	401	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899067	40899067	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	133	442	0	ENST00000373198.4:c.2203C>A	p.Pro735Thr	p.P735T	ENST00000373198	NM_133170.3	735	Ccg/Acg	14/32	1	2	FACETS	0.961	0.883	1	0.961	0.883	1	CLONAL	1	TRUE	1	0.742325525142501	2		442	373	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191141	2191141	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	172	599	1	ENST00000398665.3:c.395C>T	p.Ser132Phe	p.S132F	ENST00000398665	NM_032482.2	132	tCc/tTc	5/28	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.742325525142501	2		600	448	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220154	36220154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	205	596	0	ENST00000222270.7:c.4874C>T	p.Ser1625Phe	p.S1625F	ENST00000222270	NM_014727.1	1625	tCc/tTc	22/37	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.742325525142501	2		596	470	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945794	17945794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	151	535	0	ENST00000458235.1:c.2066C>T	p.Pro689Leu	p.P689L	ENST00000458235	NM_000215.3	689	cCc/cTc	16/24	1	2	FACETS	0.992	0.917	1	0.992	0.917	1	CLONAL	1	TRUE	1	0.742325525142501	2		535	410	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989511	7989511	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	124	435	0	ENST00000319144.4:c.175C>T	p.Gln59Ter	p.Q59*	ENST00000319144	NM_001139.2	59	Cag/Tag	2/15	0.742325525142501	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.742325525142501	1		435	201	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981348	68981348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	109	357	1	ENST00000288368.4:c.1420G>A	p.Glu474Lys	p.E474K	ENST00000288368	NM_024870.2	474	Gag/Aag	12/40	1	2	FACETS	0.904	0.821	0.988	0.904	0.821	0.988	CLONAL	1	TRUE	1	0.742325525142501	2		358	325	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435040	18435040	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	111	337	0	ENST00000266497.5:c.25C>T	p.Pro9Ser	p.P9S	ENST00000266497		9	Cca/Tca	1/31	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.742325525142501	2		337	263	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289869	15289869	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	206	615	1	ENST00000263388.2:c.3685G>A	p.Gly1229Ser	p.G1229S	ENST00000263388	NM_000435.2	1229	Ggt/Agt	22/33	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.742325525142501	2		616	520	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624493	93624493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1276980680	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	94	297	0	ENST00000375746.1:c.584G>A	p.Arg195Gln	p.R195Q	ENST00000375746	NM_001174167.1	195	cGa/cAa	4/14	1	2	FACETS	0.952	0.86	1	0.952	0.86	1	CLONAL	1	TRUE	1	0.742325525142501	2		297	266	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222961	36222961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	171	712	3	ENST00000222270.7:c.5590C>T	p.Arg1864Ter	p.R1864*	ENST00000222270	NM_014727.1	1864	Cga/Tga	27/37	1	2	FACETS	0.942	0.874	1	0.942	0.874	1	CLONAL	1	TRUE	1	0.742325525142501	2		715	489	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187102	11187102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	157	557	0	ENST00000361445.4:c.6316C>T	p.His2106Tyr	p.H2106Y	ENST00000361445	NM_004958.3	2106	Cat/Tat	45/58	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.742325525142501	2		557	417	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885658	23885658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	134	453	0	ENST00000374561.5:c.260C>T	p.Pro87Leu	p.P87L	ENST00000374561	NM_002167.4	87	cCa/cTa	1/3	1	2	FACETS	0.978	0.899	1	0.978	0.899	1	CLONAL	1	TRUE	1	0.742325525142501	2		453	369	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521597	46521597	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	141	440	0	ENST00000262741.5:c.811C>T	p.His271Tyr	p.H271Y	ENST00000262741	NM_003629.3	271	Cat/Tat	7/10	1	2	FACETS	0.974	0.897	1	0.974	0.897	1	CLONAL	1	TRUE	1	0.742325525142501	2		440	390	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166533	118166533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	106	369	0	ENST00000369448.3:c.1043C>T	p.Pro348Leu	p.P348L	ENST00000369448	NM_017709.3	348	cCc/cTc	2/2	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.742325525142501	2		369	277	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731107	162731107	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	161	438	1	ENST00000367921.3:c.962C>T	p.Pro321Leu	p.P321L	ENST00000367921	NM_006182.2	321	cCc/cTc	9/18	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.742325525142501	2		439	405	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663812	241663812	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	71	252	0	ENST00000366560.3:c.1315C>T	p.Gln439Ter	p.Q439*	ENST00000366560	NM_000143.3	439	Cag/Tag	9/10	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.742325525142501	2		252	175	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100474	8100474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	146	604	0	ENST00000346208.3:c.448C>T	p.Leu150Phe	p.L150F	ENST00000346208		150	Ctc/Ttc	3/6	1	2	FACETS	0.926	0.853	1	0.926	0.853	1	CLONAL	1	TRUE	1	0.742325525142501	2		604	425	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606655	43606655	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	114	405	0	ENST00000355710.3:c.1264A>T	p.Ile422Phe	p.I422F	ENST00000355710	NM_020975.4	422	Atc/Ttc	7/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.742325525142501	2		405	273	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683183	88683183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	92	256	0	ENST00000372037.3:c.1393C>T	p.Pro465Ser	p.P465S	ENST00000372037	NM_004329.2	465	Ccg/Tcg	12/13	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.742325525142501	2		256	232	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309747	104309747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	195	578	1	ENST00000369902.3:c.338C>T	p.Pro113Leu	p.P113L	ENST00000369902	NM_016169.3	113	cCt/cTt	3/12	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.742325525142501	2		579	497	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625285	69625285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782512706	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	144	549	0	ENST00000334134.2:c.508C>T	p.Arg170Cys	p.R170C	ENST00000334134	NM_005247.2	170	Cgc/Tgc	3/3	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.742325525142501	2		549	378	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94224048	94224048	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	132	464	0	ENST00000323929.3:c.104A>G	p.Asp35Gly	p.D35G	ENST00000323929	NM_005591.3	35	gAt/gGt	3/20	1	2	FACETS	0.831	0.761	0.903	0.831	0.761	0.903	CLONAL	1	TRUE	1	0.742325525142501	2		464	428	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363797	118363797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	132	375	0	ENST00000534358.1:c.5030C>T	p.Pro1677Leu	p.P1677L	ENST00000534358	NM_005933.3	1677	cCc/cTc	16/36	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.742325525142501	2		375	328	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118382704	118382704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555050211	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	157	406	1	ENST00000534358.1:c.11110C>T	p.Arg3704Ter	p.R3704*	ENST00000534358	NM_005933.3	3704	Cga/Tga	31/36	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.742325525142501	2		407	390	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170447	119170447	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368138875	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	115	430	1	ENST00000264033.4:c.2677C>T	p.Arg893Trp	p.R893W	ENST00000264033	NM_005188.3	893	Cgg/Tgg	16/16	1	2	FACETS	0.996	0.91	1	0.996	0.91	1	CLONAL	1	TRUE	1	0.742325525142501	2		431	311	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398059	4398059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	135	473	2	ENST00000261254.3:c.623G>A	p.Gly208Glu	p.G208E	ENST00000261254	NM_001759.3	208	gGa/gAa	4/5	1	2	FACETS	0.999	0.919	1	0.999	0.919	1	CLONAL	1	TRUE	1	0.742325525142501	2		475	364	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573966	18573966	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1363775683	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	84	286	0	ENST00000266497.5:c.2284C>T	p.Gln762Ter	p.Q762*	ENST00000266497		762	Cag/Tag	15/31	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.742325525142501	2		286	218	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793421	18793421	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	183	440	0	ENST00000266497.5:c.4118C>T	p.Pro1373Leu	p.P1373L	ENST00000266497		1373	cCc/cTc	30/31	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.742325525142501	2		440	450	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245184	46245184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	131	395	0	ENST00000334344.6:c.3278C>T	p.Pro1093Leu	p.P1093L	ENST00000334344	NM_152641.2	1093	cCt/cTt	15/21	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.742325525142501	2		395	335	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433554	49433554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	216	662	0	ENST00000301067.7:c.7999C>T	p.Pro2667Ser	p.P2667S	ENST00000301067	NM_003482.3	2667	Cca/Tca	31/54	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.742325525142501	2		662	522	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445746	49445746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	222	873	3	ENST00000301067.7:c.1720C>T	p.Pro574Ser	p.P574S	ENST00000301067	NM_003482.3	574	Cca/Tca	10/54	1	2	FACETS	0.974	0.913	1	0.974	0.913	1	CLONAL	1	TRUE	1	0.742325525142501	2		876	614	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857574	57857574	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1383562588	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	90	292	0	ENST00000228682.2:c.100G>A	p.Gly34Arg	p.G34R	ENST00000228682	NM_005269.2	34	Gga/Aga	2/12	1	2	FACETS	0.905	0.814	0.998	0.905	0.814	0.998	CLONAL	1	TRUE	1	0.742325525142501	2		292	268	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256148	133256149	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	87	472	1	ENST00000320574.5:c.512_513delinsTT	p.Ser171Phe	p.S171F	ENST00000320574	NM_006231.2	171	tCC/tTT	6/49	1	2	FACETS	0.814	0.729	0.902	0.814	0.729	0.902	CLONAL	1	TRUE	1	0.742325525142501	2		473	288	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896963	28896963	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868166954	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	168	410	0	ENST00000282397.4:c.2917G>A	p.Glu973Lys	p.E973K	ENST00000282397	NM_002019.4	973	Gaa/Aaa	21/30	0.742325525142501	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.742325525142501	1		410	239	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504557	103504557	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	123	312	0	ENST00000355739.4:c.178C>T	p.His60Tyr	p.H60Y	ENST00000355739	NM_000123.3	60	Cat/Tat	2/15	0.742325525142501	1	FACETS	0.978	0.91	1	0.978	0.91	1	CLONAL	1	TRUE	0	0.742325525142501	1		312	213	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88428947	88428947	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1460807501	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	100	333	1	ENST00000360948.2:c.2153A>T	p.Asn718Ile	p.N718I	ENST00000360948	NM_001012338.2	718	aAt/aTt	17/19	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.742325525142501	2		334	269	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679837	88679837	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	101	341	0	ENST00000360948.2:c.626T>C	p.Leu209Pro	p.L209P	ENST00000360948	NM_001012338.2	209	cTt/cCt	7/19	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.742325525142501	2		341	258	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222315	2222315	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	137	499	1	ENST00000326181.6:c.599C>T	p.Pro200Leu	p.P200L	ENST00000326181	NM_032271.2	200	cCc/cTc	8/21	1	2	FACETS	0.949	0.873	1	0.949	0.873	1	CLONAL	1	TRUE	1	0.742325525142501	2		500	389	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789595	3789595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	130	371	1	ENST00000262367.5:c.4264C>T	p.Pro1422Ser	p.P1422S	ENST00000262367	NM_004380.2	1422	Ccc/Tcc	25/31	1	2	FACETS	0.968	0.888	1	0.968	0.888	1	CLONAL	1	TRUE	1	0.742325525142501	2		372	362	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858709	9858709	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	81	341	1	ENST00000330684.3:c.2692C>T	p.Leu898Phe	p.L898F	ENST00000330684	NM_001134407.1	898	Ctc/Ttc	13/13	1	2	FACETS	0.805	0.719	0.896	0.805	0.719	0.896	CLONAL	1	TRUE	1	0.742325525142501	2		342	271	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984954	9984954	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	147	438	0	ENST00000330684.3:c.1011T>A	p.Phe337Leu	p.F337L	ENST00000330684	NM_001134407.1	337	ttT/ttA	4/13	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.742325525142501	2		438	395	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032006	10032006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	171	523	0	ENST00000330684.3:c.817C>T	p.Pro273Ser	p.P273S	ENST00000330684	NM_001134407.1	273	Cca/Tca	3/13	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.742325525142501	2		523	454	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032293	10032293	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	125	414	1	ENST00000330684.3:c.530T>G	p.Phe177Cys	p.F177C	ENST00000330684	NM_001134407.1	177	tTc/tGc	3/13	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.742325525142501	2		415	332	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641511	23641511	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	142	540	0	ENST00000261584.4:c.1964T>G	p.Phe655Cys	p.F655C	ENST00000261584	NM_024675.3	655	tTt/tGt	5/13	1	2	FACETS	0.896	0.824	0.97	0.896	0.824	0.97	CLONAL	1	TRUE	1	0.742325525142501	2		540	427	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56871593	56871593	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1299064324	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	144	417	0	ENST00000308159.5:c.1973C>T	p.Ser658Phe	p.S658F	ENST00000308159	NM_014669.4	658	tCc/tTc	18/22	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.742325525142501	2		417	386	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044560	12044560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	145	443	0	ENST00000353533.5:c.1183C>T	p.Pro395Ser	p.P395S	ENST00000353533	NM_003010.3	395	Ccc/Tcc	11/11	0.742325525142501	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.742325525142501	1		443	232	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528079	29528079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	53	161	1	ENST00000356175.3:c.1087C>T	p.Pro363Ser	p.P363S	ENST00000356175	NM_000267.3	363	Cca/Tca	10/57	0.742325525142501	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.742325525142501	1		162	85	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528166	29528166	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	158	494	0	ENST00000356175.3:c.1174C>T	p.Gln392Ter	p.Q392*	ENST00000356175	NM_000267.3	392	Caa/Taa	10/57	0.742325525142501	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.742325525142501	1		494	252	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362264	40362264	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	131	443	2	ENST00000293328.3:c.1831C>T	p.Pro611Ser	p.P611S	ENST00000293328	NM_012448.3	611	Cca/Tca	15/19	0.742325525142501	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.742325525142501	1		445	220	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459505	40459505	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	126	468	0	ENST00000345506.4:c.1766G>A	p.Trp589Ter	p.W589*	ENST00000345506	NM_003152.3	589	tGg/tAg	15/20	0.742325525142501	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.742325525142501	1		468	200	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244595	41244595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555588649	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	180	519	1	ENST00000357654.3:c.2953C>T	p.Pro985Ser	p.P985S	ENST00000357654	NM_007294.3	985	Ccc/Tcc	10/23	0.742325525142501	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.742325525142501	1		520	290	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56801401	56801401	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	166	423	0	ENST00000337432.4:c.905G>A	p.Gly302Glu	p.G302E	ENST00000337432	NM_058216.2	302	gGg/gAg	7/9	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.742325525142501	2		423	438	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120493	70120493	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	207	698	1	ENST00000245479.2:c.1495G>A	p.Glu499Lys	p.E499K	ENST00000245479	NM_000346.3	499	Gaa/Aaa	3/3	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.742325525142501	2		699	532	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172397	7172397	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	113	460	0	ENST00000302850.5:c.1172T>A	p.Ile391Asn	p.I391N	ENST00000302850	NM_000208.2	391	aTt/aAt	5/22	1	2	FACETS	0.843	0.767	0.922	0.843	0.767	0.922	CLONAL	1	TRUE	1	0.742325525142501	2		460	361	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105610	11105610	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	178	642	2	ENST00000358026.2:c.1526C>T	p.Ala509Val	p.A509V	ENST00000358026	NM_001128849.1	509	gCc/gTc	9/36	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.742325525142501	2		644	450	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132633	11132633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217938288	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	159	573	0	ENST00000358026.2:c.2849C>T	p.Thr950Ile	p.T950I	ENST00000358026	NM_001128849.1	950	aCc/aTc	19/36	1	2	FACETS	0.98	0.908	1	0.98	0.908	1	CLONAL	1	TRUE	1	0.742325525142501	2		573	437	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299836	15299836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	142	648	0	ENST00000263388.2:c.1342G>A	p.Asp448Asn	p.D448N	ENST00000263388	NM_000435.2	448	Gac/Aac	8/33	1	2	FACETS	0.862	0.792	0.933	0.862	0.792	0.933	CLONAL	1	TRUE	1	0.742325525142501	2		648	444	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353735	15353736	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	147	670	1	ENST00000263377.2:c.3144_3145delinsTT	p.His1049Tyr	p.H1049Y	ENST00000263377	NM_058243.2	1048	caCCac/caTTac	14/20	1	2	FACETS	0.857	0.789	0.927	0.857	0.789	0.927	CLONAL	1	TRUE	1	0.742325525142501	2		671	462	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354229	15354229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	197	667	0	ENST00000263377.2:c.2651C>T	p.Pro884Leu	p.P884L	ENST00000263377	NM_058243.2	884	cCc/cTc	14/20	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.742325525142501	2		667	523	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210703	36210703	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200918556	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	136	544	0	ENST00000222270.7:c.454C>T	p.Arg152Trp	p.R152W	ENST00000222270	NM_014727.1	152	Cgg/Tgg	3/37	1	2	FACETS	0.93	0.855	1	0.93	0.855	1	CLONAL	1	TRUE	1	0.742325525142501	2		544	394	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794482	42794482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs958141258	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	169	644	0	ENST00000575354.2:c.1562C>T	p.Pro521Leu	p.P521L	ENST00000575354	NM_015125.3	521	cCt/cTt	10/20	1	2	FACETS	0.879	0.814	0.946	0.879	0.814	0.946	CLONAL	1	TRUE	1	0.742325525142501	2		644	518	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796328	42796329	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	181	696	0	ENST00000575354.2:c.2977_2978delinsTT	p.Pro993Phe	p.P993F	ENST00000575354	NM_015125.3	993	CCt/TTt	12/20	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.742325525142501	2		696	486	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262373	39262373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	182	591	0	ENST00000402219.2:c.1054C>T	p.His352Tyr	p.H352Y	ENST00000402219	NM_005633.3	352	Cat/Tat	8/23	1	2	FACETS	0.892	0.828	0.956	0.892	0.828	0.956	CLONAL	1	TRUE	1	0.742325525142501	2		591	550	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606921	47606921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	119	266	0	ENST00000263735.4:c.671C>T	p.Ser224Phe	p.S224F	ENST00000263735	NM_002354.2	224	tCc/tTc	7/9	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.742325525142501	2		266	304	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872836	136872836	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	106	306	0	ENST00000241393.3:c.662T>A	p.Ile221Asn	p.I221N	ENST00000241393	NM_003467.2	221	aTt/aAt	2/2	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.742325525142501	2		306	267	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728659	190728659	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	155	480	4	ENST00000441310.2:c.2047C>T	p.Gln683Ter	p.Q683*	ENST00000441310	NM_000534.4	683	Cag/Tag	10/13	1	2	FACETS	0.924	0.853	0.996	0.924	0.853	0.996	CLONAL	1	TRUE	1	0.742325525142501	2		484	452	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735497	204735497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	127	377	0	ENST00000302823.3:c.298G>A	p.Asp100Asn	p.D100N	ENST00000302823	NM_005214.4	100	Gat/Aat	2/4	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.742325525142501	2		377	337	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248614	212248614	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	128	399	1	ENST00000342788.4:c.3653A>T	p.Lys1218Ile	p.K1218I	ENST00000342788	NM_005235.2	1218	aAa/aTa	28/28	1	2	FACETS	0.961	0.881	1	0.961	0.881	1	CLONAL	1	TRUE	1	0.742325525142501	2		400	359	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568867	212568868	+	missense_variant	Missense_Mutation	DNP	AA	AA	TG	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	150	526	1	ENST00000342788.4:c.1250_1251delinsCA	p.Phe417Ser	p.F417S	ENST00000342788	NM_005235.2	417	tTT/tCA	11/28	1	2	FACETS	0.983	0.908	1	0.983	0.908	1	CLONAL	1	TRUE	1	0.742325525142501	2		527	411	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561349	9561349	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	115	323	0	ENST00000353224.5:c.433A>T	p.Lys145Ter	p.K145*	ENST00000353224	NM_177990.2	145	Aag/Tag	4/10	1	2	FACETS	0.953	0.87	1	0.953	0.87	1	CLONAL	1	TRUE	1	0.742325525142501	2		323	325	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026144	36026144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	165	562	0	ENST00000358208.4:c.746C>T	p.Pro249Leu	p.P249L	ENST00000358208		249	cCc/cTc	7/12	1	2	FACETS	0.944	0.874	1	0.944	0.874	1	CLONAL	1	TRUE	1	0.742325525142501	2		562	471	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757459	40757460	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	154	596	2	ENST00000373198.4:c.2838_2839delinsTT	p.Arg947Trp	p.R947W	ENST00000373198	NM_133170.3	946	tcCCgg/tcTTgg	20/32	1	2	FACETS	0.997	0.923	1	0.997	0.923	1	CLONAL	1	TRUE	1	0.742325525142501	2		598	416	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827984	40827984	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1174893851	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	82	369	0	ENST00000373198.4:c.2444G>A	p.Arg815Lys	p.R815K	ENST00000373198	NM_133170.3	815	aGg/aAg	17/32	1	2	FACETS	0.877	0.784	0.972	0.877	0.784	0.972	CLONAL	1	TRUE	1	0.742325525142501	2		369	252	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795373	39795373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	134	515	0	ENST00000288319.7:c.347C>T	p.Pro116Leu	p.P116L	ENST00000288319	NM_182918.3	116	cCa/cTa	3/10	1	2	FACETS	0.968	0.89	1	0.968	0.89	1	CLONAL	1	TRUE	1	0.742325525142501	2		515	373	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866495	42866495	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767591322	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	230	686	1	ENST00000398585.3:c.137C>T	p.Pro46Leu	p.P46L	ENST00000398585	NM_001135099.1	46	cCa/cTa	3/14	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.742325525142501	2		687	574	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657086	45657086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	75	240	0	ENST00000407780.3:c.70G>A	p.Glu24Lys	p.E24K	ENST00000407780	NM_001283052.1	24	Gaa/Aaa	3/7	1	2	FACETS	0.986	0.88	1	0.986	0.88	1	CLONAL	1	TRUE	1	0.742325525142501	2		240	205	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180202	38180202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	120	324	0	ENST00000396334.3:c.50G>A	p.Gly17Glu	p.G17E	ENST00000396334	NM_002468.4	17	gGa/gAa	1/5	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.742325525142501	2		324	298	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939898	49939898	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	142	688	0	ENST00000296474.3:c.1145T>G	p.Val382Gly	p.V382G	ENST00000296474	NM_002447.2	382	gTg/gGg	1/20	1	2	FACETS	0.817	0.751	0.886	0.817	0.751	0.886	CLONAL	1	TRUE	1	0.742325525142501	2		688	468	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259137	89259137	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	96	305	1	ENST00000336596.2:c.281A>T	p.Lys94Met	p.K94M	ENST00000336596	NM_005233.5	94	aAg/aTg	3/17	1	2	FACETS	0.92	0.832	1	0.92	0.832	1	CLONAL	1	TRUE	1	0.742325525142501	2		306	281	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448615	89448615	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	168	455	0	ENST00000336596.2:c.1579G>A	p.Glu527Lys	p.E527K	ENST00000336596	NM_005233.5	527	Gaa/Aaa	7/17	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.742325525142501	2		455	425	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586382	189586382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867300924	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	100	267	0	ENST00000264731.3:c.1006G>A	p.Gly336Ser	p.G336S	ENST00000264731	NM_003722.4	336	Ggc/Agc	8/14	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.742325525142501	2		267	251	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587144	189587144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140374868	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	128	393	0	ENST00000264731.3:c.1161G>A	p.Met387Ile	p.M387I	ENST00000264731	NM_003722.4	387	atG/atA	9/14	1	2	FACETS	0.903	0.827	0.981	0.903	0.827	0.981	CLONAL	1	TRUE	1	0.742325525142501	2		393	382	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607131	189607131	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	163	454	0	ENST00000264731.3:c.1510C>T	p.Pro504Ser	p.P504S	ENST00000264731	NM_003722.4	504	Ccc/Tcc	12/14	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.742325525142501	2		454	439	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612106	189612106	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	133	478	0	ENST00000264731.3:c.1858C>G	p.Pro620Ala	p.P620A	ENST00000264731	NM_003722.4	620	Cca/Gca	14/14	1	2	FACETS	0.953	0.875	1	0.953	0.875	1	CLONAL	1	TRUE	1	0.742325525142501	2		478	376	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806648	1806648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	157	590	0	ENST00000260795.2:c.1364C>T	p.Ser455Phe	p.S455F	ENST00000260795		455	tCc/tTc	9/17	1	2	FACETS	0.968	0.896	1	0.968	0.896	1	CLONAL	1	TRUE	1	0.742325525142501	2		590	437	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750452	41750452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	155	424	0	ENST00000226382.2:c.176C>T	p.Ser59Phe	p.S59F	ENST00000226382	NM_003924.3	59	tCc/tTc	1/3	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.742325525142501	2		424	383	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356421	66356421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	130	296	1	ENST00000273854.3:c.1076C>T	p.Ser359Phe	p.S359F	ENST00000273854	NM_004439.5	359	tCt/tTt	5/18	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.742325525142501	2		297	277	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157506	106157506	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs368508787	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	121	294	0	ENST00000380013.4:c.2407C>T	p.Gln803Ter	p.Q803*	ENST00000380013	NM_001127208.2	803	Caa/Taa	3/11	1	2	FACETS	0.97	0.888	1	0.97	0.888	1	CLONAL	1	TRUE	1	0.742325525142501	2		294	336	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190815	106190815	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	128	417	0	ENST00000380013.4:c.4093G>C	p.Gly1365Arg	p.G1365R	ENST00000380013	NM_001127208.2	1365	Ggc/Cgc	9/11	1	2	FACETS	0.988	0.907	1	0.988	0.907	1	CLONAL	1	TRUE	1	0.742325525142501	2		417	349	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282739	1282739	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	114	378	0	ENST00000310581.5:c.1574G>A	p.Gly525Glu	p.G525E	ENST00000310581	NM_198253.2	525	gGg/gAg	3/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.742325525142501	2		378	283	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950465	38950465	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	115	340	0	ENST00000357387.3:c.3485C>T	p.Ser1162Leu	p.S1162L	ENST00000357387	NM_152756.3	1162	tCa/tTa	31/38	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.742325525142501	2		340	301	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449857	149449857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	169	558	0	ENST00000286301.3:c.1207G>A	p.Glu403Lys	p.E403K	ENST00000286301	NM_005211.3	403	Gag/Aag	9/22	0.627754567634647	1	FACETS	0.936	0.878	0.993	0.936	0.878	0.993	CLONAL	1	TRUE	0	0.742325525142501	1		558	306	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459896	149459896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	34	543	0	ENST00000286301.3:c.311C>T	p.Pro104Leu	p.P104L	ENST00000286301	NM_005211.3	104	cCt/cTt	4/22	0.627754567634647	1	FACETS	0.201	0.165	0.242	0.201	0.165	0.242	SUBCLONAL	1	TRUE	0	0.742325525142501	1		543	286	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460492	149460492	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745585475	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	43	551	0	ENST00000286301.3:c.145G>A	p.Glu49Lys	p.E49K	ENST00000286301	NM_005211.3	49	Gaa/Aaa	3/22	0.627754567634647	1	FACETS	0.236	0.198	0.277	0.236	0.198	0.277	SUBCLONAL	1	TRUE	0	0.742325525142501	1		551	309	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818753	170818753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	136	280	1	ENST00000296930.5:c.302G>A	p.Arg101Lys	p.R101K	ENST00000296930	NM_002520.6	101	aGg/aAg	4/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.742325525142501	2		281	344	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520534	176520534	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	140	600	0	ENST00000292408.4:c.1379G>A	p.Trp460Ter	p.W460*	ENST00000292408	NM_213647.1	460	tGg/tAg	10/18	1	2	FACETS	0.916	0.842	0.991	0.916	0.842	0.991	CLONAL	1	TRUE	1	0.742325525142501	2		600	412	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030382	180030382	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1382151235	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	177	591	0	ENST00000261937.6:c.3902G>A	p.Gly1301Glu	p.G1301E	ENST00000261937	NM_182925.4	1301	gGa/gAa	30/30	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.742325525142501	2		591	470	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180049814	180049814	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs757097428	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	182	589	0	ENST00000261937.6:c.1574A>G	p.Asn525Ser	p.N525S	ENST00000261937	NM_182925.4	525	aAt/aGt	12/30	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.742325525142501	2		589	466	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056334	180056334	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751948166	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	192	602	1	ENST00000261937.6:c.910G>A	p.Asp304Asn	p.D304N	ENST00000261937	NM_182925.4	304	Gac/Aac	7/30	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.742325525142501	2		603	481	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187453	32187453	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	170	524	0	ENST00000375023.3:c.1426C>T	p.His476Tyr	p.H476Y	ENST00000375023	NM_004557.3	476	Cac/Tac	8/30	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.742325525142501	2		524	449	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187527	32187527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	153	566	1	ENST00000375023.3:c.1352C>T	p.Ser451Phe	p.S451F	ENST00000375023	NM_004557.3	451	tCc/tTc	8/30	1	2	FACETS	0.924	0.853	0.997	0.924	0.853	0.997	CLONAL	1	TRUE	1	0.742325525142501	2		567	446	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289095	33289095	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	153	564	0	ENST00000374542.5:c.457A>T	p.Asn153Tyr	p.N153Y	ENST00000374542	NM_001141970.1	153	Aat/Tat	3/8	1	2	FACETS	0.948	0.875	1	0.948	0.875	1	CLONAL	1	TRUE	1	0.742325525142501	2		564	435	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120489	94120489	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	109	319	0	ENST00000369303.4:c.562G>A	p.Asp188Asn	p.D188N	ENST00000369303	NM_004440.3	188	Gat/Aat	3/17	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.742325525142501	2		319	269	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106543511	106543511	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	106	321	0	ENST00000369096.4:c.313G>A	p.Glu105Lys	p.E105K	ENST00000369096	NM_001198.3	105	Gaa/Aaa	3/7	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.742325525142501	2		321	277	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109322511	109322511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769935193	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	167	511	0	ENST00000436639.2:c.526C>T	p.Arg176Cys	p.R176C	ENST00000436639	NM_014454.2	176	Cgt/Tgt	3/10	1	2	FACETS	0.949	0.88	1	0.949	0.88	1	CLONAL	1	TRUE	1	0.742325525142501	2		511	474	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687313	117687313	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	108	299	0	ENST00000368508.3:c.2738C>T	p.Thr913Ile	p.T913I	ENST00000368508	NM_002944.2	913	aCc/aTc	18/43	1	2	FACETS	0.927	0.842	1	0.927	0.842	1	CLONAL	1	TRUE	1	0.742325525142501	2		299	314	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985552	2985552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	147	468	0	ENST00000396946.4:c.259G>A	p.Gly87Ser	p.G87S	ENST00000396946	NM_032415.4	87	Ggc/Agc	4/25	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.742325525142501	2		468	374	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729363	41729363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	140	428	1	ENST00000242208.4:c.1166C>T	p.Ser389Leu	p.S389L	ENST00000242208	NM_002192.2	389	tCg/tTg	3/3	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.742325525142501	2		429	363	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435824	116435824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	172	524	0	ENST00000397752.3:c.3914C>T	p.Pro1305Leu	p.P1305L	ENST00000397752	NM_000245.2	1305	cCc/cTc	20/21	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.742325525142501	2		524	463	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879333	151879333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	105	353	0	ENST00000262189.6:c.5612C>T	p.Ala1871Val	p.A1871V	ENST00000262189	NM_170606.2	1871	gCt/gTt	36/59	1	2	FACETS	0.918	0.834	1	0.918	0.834	1	CLONAL	1	TRUE	1	0.742325525142501	2		353	308	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945102	151945102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	45	342	1	ENST00000262189.6:c.2417C>T	p.Ser806Phe	p.S806F	ENST00000262189	NM_170606.2	806	tCc/tTc	14/59	1	2	FACETS	0.501	0.424	0.584	0.501	0.424	0.584	SUBCLONAL	1	TRUE	1	0.742325525142501	2		343	242	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864738	68864738	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	148	513	0	ENST00000288368.4:c.109G>A	p.Asp37Asn	p.D37N	ENST00000288368	NM_024870.2	37	Gac/Aac	1/40	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.742325525142501	2		513	348	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931898	68931898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	170	475	0	ENST00000288368.4:c.328C>T	p.Leu110Phe	p.L110F	ENST00000288368	NM_024870.2	110	Ctt/Ttt	3/40	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.742325525142501	2		475	432	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968143	68968143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	185	582	0	ENST00000288368.4:c.1172G>A	p.Arg391Lys	p.R391K	ENST00000288368	NM_024870.2	391	aGa/aAa	10/40	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.742325525142501	2		582	456	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995520	68995520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	170	512	1	ENST00000288368.4:c.1924G>A	p.Asp642Asn	p.D642N	ENST00000288368	NM_024870.2	642	Gac/Aac	18/40	1	2	FACETS	0.954	0.885	1	0.954	0.885	1	CLONAL	1	TRUE	1	0.742325525142501	2		513	480	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69000009	69000009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	170	511	0	ENST00000288368.4:c.2078G>A	p.Gly693Glu	p.G693E	ENST00000288368	NM_024870.2	693	gGa/gAa	19/40	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.742325525142501	2		511	447	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030850	69030850	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150128151	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	81	327	0	ENST00000288368.4:c.3392C>T	p.Ser1131Leu	p.S1131L	ENST00000288368	NM_024870.2	1131	tCg/tTg	27/40	1	2	FACETS	0.866	0.774	0.961	0.866	0.774	0.961	CLONAL	1	TRUE	1	0.742325525142501	2		327	252	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340386	8340386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	119	459	0	ENST00000356435.5:c.5210C>T	p.Ser1737Phe	p.S1737F	ENST00000356435		1737	tCc/tTc	31/35	1	2	FACETS	0.828	0.755	0.905	0.828	0.755	0.905	CLONAL	1	TRUE	1	0.742325525142501	2		459	387	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449773	8449773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	137	478	0	ENST00000356435.5:c.3940C>T	p.His1314Tyr	p.H1314Y	ENST00000356435		1314	Cac/Tac	23/35	1	2	FACETS	0.911	0.837	0.987	0.911	0.837	0.987	CLONAL	1	TRUE	1	0.742325525142501	2		478	405	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27183606	27183606	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	110	390	0	ENST00000380036.4:c.1180C>T	p.His394Tyr	p.H394Y	ENST00000380036	NM_000459.3	394	Cat/Tat	8/23	0.742325525142501	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.742325525142501	1		390	174	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206694	27206694	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	145	503	0	ENST00000380036.4:c.2479C>T	p.Gln827Ter	p.Q827*	ENST00000380036	NM_000459.3	827	Caa/Taa	15/23	0.742325525142501	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.742325525142501	1		503	242	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624598	93624599	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	111	443	0	ENST00000375746.1:c.692dup	p.Lys233GlufsTer15	p.K233Efs*15	ENST00000375746	NM_001174167.1	230	gag/gaGg	4/14	1	2	FACETS	0.835	0.759	0.915	0.835	0.759	0.915	CLONAL	1	TRUE	1	0.742325525142501	2		443	358	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317433	1317433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	139	523	0	ENST00000400841.2:c.632G>A	p.Arg211Lys	p.R211K	ENST00000400841		211	aGa/aAa	5/6	1	1	FACETS	0.633	0.583	0.684	0.633	0.583	0.684	SUBCLONAL	1	TRUE	0	0.742325525142501	1		523	372	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	159	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.855	0.793	0.919	1	0.991	1	CLONAL	2	TRUE	1	0.456791619324904	2		215	407	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0025959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	240	458	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.456791619324904	0	FACETS	0.852	0.816	0.886			1	CLONAL	2	TRUE	0	0.456791619324904	0		458	335	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0025959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	304	738	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	0.889	0.842	0.936	1	0.995	1	CLONAL	2	TRUE	1	0.456791619324904	2		738	749	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709505	176709505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	156	363	1	ENST00000439151.2:c.5932G>A	p.Glu1978Lys	p.E1978K	ENST00000439151	NM_022455.4	1978	Gaa/Aaa	19/23	1	2	FACETS	0.885	0.82	0.95	1	0.992	1	CLONAL	2	TRUE	1	0.456791619324904	2		364	386	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056190	27056193	+	frameshift_variant	Frame_Shift_Del	DEL	GGCG	GGCG	-	novel	NA	P-0025959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	213	531	0	ENST00000324856.7:c.1188_1191del	p.Gly397LeufsTer35	p.G397Lfs*35	ENST00000324856	NM_006015.4	396	GGCGgg/gg	2/20	1	2	FACETS	0.822	0.77	0.876	1	0.993	1	CLONAL	2	TRUE	1	0.456791619324904	2		531	567	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981851	201981852	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0025959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	284	672	0	ENST00000359651.3:c.567dup	p.Ser190LeufsTer6	p.S190Lfs*6	ENST00000359651		188	gcc/gCcc	4/8	1	2	FACETS	0.792	0.748	0.837	1	0.994	1	SUBCLONAL	2	TRUE	1	0.456791619324904	2		672	785	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264139	46264139	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	143	330	0	ENST00000371998.3:c.1186A>G	p.Ser396Gly	p.S396G	ENST00000371998		396	Agt/Ggt	11/23	1	2	FACETS	0.897	0.829	0.966	1	0.991	1	CLONAL	2	TRUE	1	0.456791619324904	2		330	349	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356290	66356290	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs539105044	NA	P-0025959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	251	455	0	ENST00000273854.3:c.1207G>T	p.Gly403Cys	p.G403C	ENST00000273854	NM_004439.5	403	Ggt/Tgt	5/18	1	2	FACETS	0.872	0.822	0.923	1	0.995	1	CLONAL	2	TRUE	1	0.456791619324904	2		455	630	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942835	44942835	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	255	589	0	ENST00000377967.4:c.3416del	p.Pro1139GlnfsTer19	p.P1139Qfs*19	ENST00000377967	NM_021140.2	1139	Cca/ca	23/29	0.456791619324904	1	FACETS	0.879	0.834	0.924	1	0.995	1	CLONAL	2	TRUE	0	0.456791619324904	1		589	490	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039294	47039294	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	322	739	0	ENST00000377604.3:c.917A>T	p.Asn306Ile	p.N306I	ENST00000377604	NM_001204468.1	306	aAc/aTc	10/24	0.456791619324904	1	FACETS	1	0.971	1	1	0.997	1	CLONAL	2	TRUE	0	0.456791619324904	1		739	535	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	220	282	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.543881188426209	2		282	743	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	219	458	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.543881188426209	1	FACETS	0.952	0.891	1	0.952	0.891	1	CLONAL	1	TRUE	0	0.543881188426209	1		458	616	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	214	316	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	1	2	FACETS	0.936	0.871	1	0.936	0.871	1	CLONAL	1	TRUE	1	0.543881188426209	2		316	841	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561325	9561325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	164	446	1	ENST00000353224.5:c.457G>A	p.Gly153Arg	p.G153R	ENST00000353224	NM_177990.2	153	Gga/Aga	4/10	1	2	FACETS	0.912	0.84	0.987	0.912	0.84	0.987	CLONAL	1	TRUE	1	0.543881188426209	2		447	661	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587118	189587118	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761885185	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	183	271	0	ENST00000264731.3:c.1135C>T	p.Arg379Cys	p.R379C	ENST00000264731	NM_003722.4	379	Cgt/Tgt	9/14	1	2	FACETS	0.95	0.88	1	0.95	0.88	1	CLONAL	1	TRUE	1	0.543881188426209	2		271	708	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	156	173	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.944	0.868	1	0.944	0.868	1	CLONAL	1	TRUE	1	0.543881188426209	2		174	608	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	304	705	0	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	0.543881188426209	3	FACETS	0.966	0.908	1	0.483	0.454	0.513	CLONAL	1	TRUE	1	0.543881188426209	3		705	1472	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46276009	46276009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369514609	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	299	667	0	ENST00000371998.3:c.3445C>T	p.Pro1149Ser	p.P1149S	ENST00000371998		1149	Cct/Tct	18/23	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.543881188426209	2		667	1025	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308081	30308081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762615251	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	234	623	1	ENST00000262643.3:c.218C>T	p.Ser73Phe	p.S73F	ENST00000262643	NM_001238.2	73	tCc/tTc	5/12	1	2	FACETS	0.86	0.802	0.919	0.86	0.802	0.919	CLONAL	1	TRUE	1	0.543881188426209	2		624	1001	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857436	9857436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	233	514	0	ENST00000330684.3:c.3965G>A	p.Gly1322Glu	p.G1322E	ENST00000330684	NM_001134407.1	1322	gGa/gAa	13/13	0.543881188426209	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.543881188426209	1		514	572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	238	696	1	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.53972772795819	1	FACETS	0.929	0.872	0.987	0.929	0.872	0.987	CLONAL	1	TRUE	0	0.543881188426209	1		697	686	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498375	89498375	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	108	229	0	ENST00000336596.2:c.2347G>A	p.Gly783Arg	p.G783R	ENST00000336596	NM_005233.5	783	Gga/Aga	14/17	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.543881188426209	2		229	360	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911514	131911514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143802516	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	212	507	0	ENST00000265335.6:c.259C>T	p.Arg87Cys	p.R87C	ENST00000265335		87	Cgt/Tgt	3/25	1	2	FACETS	0.981	0.913	1	0.981	0.913	1	CLONAL	1	TRUE	1	0.543881188426209	2		507	795	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547022	9547022	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs58486349	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	98	224	0	ENST00000353224.5:c.1000G>A	p.Asp334Asn	p.D334N	ENST00000353224	NM_177990.2	334	Gat/Aat	5/10	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.543881188426209	2		224	348	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604319	189604319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	199	389	0	ENST00000264731.3:c.1486C>T	p.Pro496Ser	p.P496S	ENST00000264731	NM_003722.4	496	Cct/Tct	11/14	1	2	FACETS	0.972	0.903	1	0.972	0.903	1	CLONAL	1	TRUE	1	0.543881188426209	2		389	753	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873660	35873660	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs201559094	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	148	257	0	ENST00000303115.3:c.616C>T	p.Arg206Ter	p.R206*	ENST00000303115	NM_002185.3	206	Cga/Tga	5/8	1	2	FACETS	0.948	0.87	1	0.948	0.87	1	CLONAL	1	TRUE	1	0.543881188426209	2		257	574	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491360	18491360	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	127	363	0	ENST00000266497.5:c.1273G>A	p.Glu425Lys	p.E425K	ENST00000266497		425	Gaa/Aaa	8/31	1	2	FACETS	0.921	0.839	1	0.921	0.839	1	CLONAL	1	TRUE	1	0.543881188426209	2		363	507	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455150	50455150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	136	341	0	ENST00000331340.3:c.697C>T	p.Pro233Ser	p.P233S	ENST00000331340	NM_006060.4	233	Ccg/Tcg	6/8	1	2	FACETS	0.89	0.813	0.97	0.89	0.813	0.97	CLONAL	1	TRUE	1	0.543881188426209	2		341	562	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602354	28602354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1367367961	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	232	576	0	ENST00000241453.7:c.2014G>A	p.Glu672Lys	p.E672K	ENST00000241453	NM_004119.2	672	Gag/Aag	16/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.543881188426209	2		576	808	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525059	9525059	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	264	646	0	ENST00000353224.5:c.1826G>A	p.Trp609Ter	p.W609*	ENST00000353224	NM_177990.2	609	tGg/tAg	8/10	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.543881188426209	2		646	967	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695728	117695728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057433609	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	235	495	0	ENST00000369458.3:c.709G>A	p.Asp237Asn	p.D237N	ENST00000369458	NM_024626.3	237	Gat/Aat	4/6	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.543881188426209	2		495	804	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872696	136872696	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	196	442	0	ENST00000241393.3:c.802G>A	p.Glu268Lys	p.E268K	ENST00000241393	NM_003467.2	268	Gaa/Aaa	2/2	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.543881188426209	2		442	718	SUCCESS
APC	324	MSKCC	GRCh37	5	112179155	112179155	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	163	384	0	ENST00000257430.4:c.7864C>T	p.Pro2622Ser	p.P2622S	ENST00000257430	NM_000038.5	2622	Ccc/Tcc	16/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.543881188426209	2		384	555	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047002	128047002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752490818	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	95	696	1	ENST00000285398.2:c.733C>T	p.Pro245Ser	p.P245S	ENST00000285398	NM_000122.1	245	Ccc/Tcc	6/15	1	2	FACETS	0.37	0.328	0.414	0.37	0.328	0.414	SUBCLONAL	1	TRUE	1	0.543881188426209	2		697	945	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008078	29008078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	157	347	0	ENST00000282397.4:c.691G>A	p.Asp231Asn	p.D231N	ENST00000282397	NM_002019.4	231	Gat/Aat	6/30	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.543881188426209	2		347	557	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444401	50444401	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	197	363	0	ENST00000331340.3:c.331C>T	p.Arg111Ter	p.R111*	ENST00000331340	NM_006060.4	111	Cga/Tga	4/8	1	2	FACETS	0.994	0.923	1	0.994	0.923	1	CLONAL	1	TRUE	1	0.543881188426209	2		363	729	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164832	47164832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1017636782	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	168	382	0	ENST00000409792.3:c.1294C>T	p.Arg432Cys	p.R432C	ENST00000409792	NM_014159.6	432	Cgt/Tgt	3/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.543881188426209	2		382	553	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101134	41101134	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	241	607	0	ENST00000373198.4:c.1222G>A	p.Glu408Lys	p.E408K	ENST00000373198	NM_133170.3	408	Gag/Aag	8/32	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.543881188426209	2		607	874	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453185	140453185	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	114	388	0	ENST00000288602.6:c.1750C>T	p.Leu584Phe	p.L584F	ENST00000288602	NM_004333.4	584	Ctt/Ttt	15/18	1	2	FACETS	0.787	0.711	0.866	0.787	0.711	0.866	SUBCLONAL	1	TRUE	1	0.543881188426209	2		388	533	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266967	18266967	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064796518	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	38	323	0	ENST00000222254.8:c.278C>T	p.Pro93Leu	p.P93L	ENST00000222254	NM_005027.3	93	cCc/cTc	2/16	1	2	FACETS	0.259	0.214	0.31	0.259	0.214	0.31	SUBCLONAL	1	TRUE	1	0.543881188426209	2		323	539	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405122	70405122	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771580099	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	300	666	0	ENST00000373644.4:c.2636C>T	p.Ser879Leu	p.S879L	ENST00000373644	NM_030625.2	879	tCg/tTg	4/12	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.543881188426209	2		666	1016	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641487	18641487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	206	554	0	ENST00000266497.5:c.2486C>T	p.Ser829Phe	p.S829F	ENST00000266497		829	tCc/tTc	17/31	1	2	FACETS	0.943	0.877	1	0.943	0.877	1	CLONAL	1	TRUE	1	0.543881188426209	2		554	803	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114159	115114159	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	100	727	0	ENST00000257566.3:c.1058C>T	p.Ser353Phe	p.S353F	ENST00000257566	NM_016569.3	353	tCt/tTt	6/8	1	2	FACETS	0.37	0.33	0.413	0.37	0.33	0.413	SUBCLONAL	1	TRUE	1	0.543881188426209	2		727	994	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102196012	102196012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	174	318	1	ENST00000263464.3:c.772C>T	p.Arg258Cys	p.R258C	ENST00000263464	NM_001165.4	258	Cgc/Tgc	2/9	0.543881188426209	3	FACETS	1	0.961	1	0.533	0.491	0.576	CLONAL	1	TRUE	1	0.543881188426209	3		319	764	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560894	9560894	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	66	484	0	ENST00000353224.5:c.888G>A	p.Met296Ile	p.M296I	ENST00000353224	NM_177990.2	296	atG/atA	4/10	1	2	FACETS	0.312	0.27	0.358	0.312	0.27	0.358	SUBCLONAL	1	TRUE	1	0.543881188426209	2		484	778	SUCCESS
APC	324	MSKCC	GRCh37	5	112175372	112175372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	103	257	0	ENST00000257430.4:c.4081C>T	p.Pro1361Ser	p.P1361S	ENST00000257430	NM_000038.5	1361	Ccc/Tcc	16/16	1	2	FACETS	0.836	0.752	0.924	0.836	0.752	0.924	CLONAL	1	TRUE	1	0.543881188426209	2		257	453	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523329	9523329	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867092977	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	48	489	0	ENST00000353224.5:c.1908G>A	p.Met636Ile	p.M636I	ENST00000353224	NM_177990.2	636	atG/atA	9/10	1	2	FACETS	0.22	0.185	0.259	0.22	0.185	0.259	SUBCLONAL	1	TRUE	1	0.543881188426209	2		489	802	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792618	33792618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	51	71	0	ENST00000498907.2:c.703C>T	p.Pro235Ser	p.P235S	ENST00000498907	NM_004364.3	235	Ccg/Tcg	1/1	1	2	FACETS	0.815	0.716	0.917	1	0.975	1	CLONAL	2	TRUE	1	0.543881188426209	2		71	115	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097020	11097021	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	302	820	2	ENST00000358026.2:c.511_512delinsTT	p.Pro171Leu	p.P171L	ENST00000358026	NM_001128849.1	171	CCa/TTa	4/36	1	2	FACETS	0.989	0.932	1	0.989	0.932	1	CLONAL	1	TRUE	1	0.543881188426209	2		822	1123	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085641	16085641	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	270	654	1	ENST00000281043.3:c.817G>A	p.Glu273Lys	p.E273K	ENST00000281043	NM_005378.4	273	Gaa/Aaa	3/3	1	2	FACETS	0.979	0.919	1	0.979	0.919	1	CLONAL	1	TRUE	1	0.543881188426209	2		655	1014	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832265	72832265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267604632	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	199	396	0	ENST00000268489.5:c.4316G>A	p.Arg1439Gln	p.R1439Q	ENST00000268489	NM_006885.3	1439	cGa/cAa	9/10	0.543881188426209	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.543881188426209	1		396	522	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381567	81381567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370760302	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	116	279	0	ENST00000222390.5:c.494C>T	p.Ser165Leu	p.S165L	ENST00000222390	NM_000601.4	165	tCg/tTg	5/18	1	2	FACETS	0.913	0.828	1	0.913	0.828	1	CLONAL	1	TRUE	1	0.543881188426209	2		279	467	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265314	152265314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781741770	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	100	260	0	ENST00000206249.3:c.767G>A	p.Arg256Gln	p.R256Q	ENST00000206249	NM_000125.3	256	cGa/cAa	4/8	1	2	FACETS	0.773	0.693	0.856	0.773	0.693	0.856	SUBCLONAL	1	TRUE	1	0.543881188426209	2		260	476	SUCCESS
AR	367	MSKCC	GRCh37	X	66766408	66766408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	50	48	0	ENST00000374690.3:c.1420G>A	p.Glu474Lys	p.E474K	ENST00000374690	NM_000044.3	474	Gag/Aag	1/8	1	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.543881188426209	1		48	92	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045832	143045832	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	242	601	1	ENST00000262992.4:c.1802C>T	p.Ser601Phe	p.S601F	ENST00000262992	NM_001101669.1	601	tCc/tTc	17/24	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.543881188426209	2		602	869	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559101	29559101	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202023	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	96	100	0	ENST00000356175.3:c.3208C>T	p.Gln1070Ter	p.Q1070*	ENST00000356175	NM_000267.3	1070	Cag/Tag	25/57	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.543881188426209	2		100	291	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760616	133760616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	371	457	0	ENST00000318560.5:c.2939C>T	p.Pro980Leu	p.P980L	ENST00000318560	NM_005157.4	980	cCc/cTc	11/11	0.543881188426209	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.543881188426209	1		457	924	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392143	81392143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	139	395	1	ENST00000222390.5:c.134C>T	p.Ser45Leu	p.S45L	ENST00000222390	NM_000601.4	45	tCa/tTa	2/18	1	2	FACETS	0.849	0.776	0.925	0.849	0.776	0.925	CLONAL	1	TRUE	1	0.543881188426209	2		396	602	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532729	46532729	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756800675	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	196	447	0	ENST00000262741.5:c.349C>T	p.His117Tyr	p.H117Y	ENST00000262741	NM_003629.3	117	Cac/Tac	4/10	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.543881188426209	2		447	716	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644487	18644487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	200	533	0	ENST00000266497.5:c.2665C>T	p.His889Tyr	p.H889Y	ENST00000266497		889	Cac/Tac	18/31	1	2	FACETS	0.901	0.837	0.968	0.901	0.837	0.968	CLONAL	1	TRUE	1	0.543881188426209	2		533	816	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243926	53243926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	322	427	0	ENST00000375401.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000375401	NM_004187.3	356	cCt/cTt	8/26	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.543881188426209	1		427	628	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40476791	40476791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	334	758	0	ENST00000264657.5:c.1538C>T	p.Ser513Phe	p.S513F	ENST00000264657	NM_139276.2	513	tCc/tTc	17/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.543881188426209	2		758	1105	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852443	42852443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139092674	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	219	618	0	ENST00000398585.3:c.643G>A	p.Glu215Lys	p.E215K	ENST00000398585	NM_001135099.1	215	Gag/Aag	6/14	1	2	FACETS	0.889	0.828	0.952	0.889	0.828	0.952	CLONAL	1	TRUE	1	0.543881188426209	2		618	906	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561016	9561016	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	166	374	0	ENST00000353224.5:c.766G>A	p.Glu256Lys	p.E256K	ENST00000353224	NM_177990.2	256	Gaa/Aaa	4/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.543881188426209	2		374	571	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47700144	47700144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767367200	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	218	497	2	ENST00000347630.2:c.29C>T	p.Pro10Leu	p.P10L	ENST00000347630	NM_001007230.1	10	cCg/cTg	3/11	1	2	FACETS	0.973	0.907	1	0.973	0.907	1	CLONAL	1	TRUE	1	0.543881188426209	2		499	824	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157568	106157568	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	176	452	1	ENST00000380013.4:c.2469G>A	p.Met823Ile	p.M823I	ENST00000380013	NM_001127208.2	823	atG/atA	3/11	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.543881188426209	2		453	640	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211624	36211624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs574808075	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	210	429	0	ENST00000222270.7:c.1375C>T	p.Pro459Ser	p.P459S	ENST00000222270	NM_014727.1	459	Cct/Tct	3/37	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.543881188426209	2		429	692	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607598	43607598	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752830820	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	316	823	2	ENST00000355710.3:c.1574G>A	p.Arg525Gln	p.R525Q	ENST00000355710	NM_020975.4	525	cGg/cAg	8/20	NA	2	FACETS	0.963	0.908	1			1	INDETERMINATE	1	TRUE	NA	0.543881188426209	2		825	1207	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584539	189584539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	234	586	1	ENST00000264731.3:c.835C>T	p.Pro279Ser	p.P279S	ENST00000264731	NM_003722.4	279	Ccc/Tcc	6/14	1	2	FACETS	0.973	0.91	1	0.973	0.91	1	CLONAL	1	TRUE	1	0.543881188426209	2		587	884	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426731	47426731	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1452639448	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	291	503	2	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	0.543881188426209	1		505	539	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981516	70981516	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	336	1008	0	ENST00000276594.2:c.580C>T	p.Arg194Trp	p.R194W	ENST00000276594	NM_024504.3	194	Cgg/Tgg	2/8	1	2	FACETS	0.931	0.88	0.984	0.931	0.88	0.984	CLONAL	1	TRUE	1	0.543881188426209	2		1008	1327	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12393114	12393114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	259	643	0	ENST00000287820.6:c.23C>T	p.Ser8Phe	p.S8F	ENST00000287820	NM_015869.4	8	tCt/tTt	1/7	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.543881188426209	2		643	924	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074235	8074235	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	232	478	0	ENST00000377482.5:c.424T>A	p.Cys142Ser	p.C142S	ENST00000377482	NM_018948.3	142	Tgt/Agt	4/4	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.543881188426209	2		478	836	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366800	40366800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762331288	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	248	569	0	ENST00000397332.2:c.397G>A	p.Glu133Lys	p.E133K	ENST00000397332	NM_001033082.2	133	Gaa/Aaa	2/3	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.543881188426209	2		569	883	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484356	120484356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	182	442	0	ENST00000256646.2:c.2774C>T	p.Ser925Phe	p.S925F	ENST00000256646	NM_024408.3	925	tCc/tTc	18/34	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.543881188426209	2		442	656	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838434	156838434	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	319	697	0	ENST00000524377.1:c.712G>A	p.Val238Met	p.V238M	ENST00000524377	NM_002529.3	238	Gtg/Atg	6/17	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.543881188426209	2		697	1066	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156848960	156848960	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	302	682	0	ENST00000524377.1:c.1852G>A	p.Ala618Thr	p.A618T	ENST00000524377	NM_002529.3	618	Gct/Act	15/17	1	2	FACETS	0.985	0.928	1	0.985	0.928	1	CLONAL	1	TRUE	1	0.543881188426209	2		682	1127	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849107	156849107	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	358	896	0	ENST00000524377.1:c.1999G>A	p.Gly667Ser	p.G667S	ENST00000524377	NM_002529.3	667	Ggt/Agt	15/17	1	2	FACETS	0.981	0.929	1	0.981	0.929	1	CLONAL	1	TRUE	1	0.543881188426209	2		896	1342	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163309203	163309203	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	241	559	0	ENST00000271452.3:c.542A>G	p.Lys181Arg	p.K181R	ENST00000271452	NM_145697.2	181	aAg/aGg	8/14	1	2	FACETS	0.946	0.884	1	0.946	0.884	1	CLONAL	1	TRUE	1	0.543881188426209	2		559	937	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333887	70333887	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	371	413	0	ENST00000373644.4:c.1792C>T	p.Gln598Ter	p.Q598*	ENST00000373644	NM_030625.2	598	Cag/Tag	2/12	NA	2	FACETS	1	0.961	1			1	INDETERMINATE	2	TRUE	NA	0.543881188426209	2		413	680	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258081	123258081	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	235	647	0	ENST00000358487.5:c.1600G>A	p.Glu534Lys	p.E534K	ENST00000358487	NM_000141.4	534	Gag/Aag	12/18	0.543881188426209	1	FACETS	0.962	0.903	1	0.962	0.903	1	CLONAL	1	TRUE	0	0.543881188426209	1		647	654	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123260438	123260438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	215	549	0	ENST00000358487.5:c.1463G>A	p.Gly488Glu	p.G488E	ENST00000358487	NM_000141.4	488	gGa/gAa	11/18	0.543881188426209	1	FACETS	0.933	0.873	0.994	0.933	0.873	0.994	CLONAL	1	TRUE	0	0.543881188426209	1		549	617	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138127	64138127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1412221175	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	249	670	1	ENST00000334205.4:c.2050C>T	p.Pro684Ser	p.P684S	ENST00000334205	NM_003942.2	684	Ccg/Tcg	16/17	0.543881188426209	3	FACETS	0.952	0.889	1	0.476	0.444	0.508	CLONAL	1	TRUE	1	0.543881188426209	3		671	1224	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138867	64138867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	270	644	2	ENST00000334205.4:c.2234C>T	p.Ser745Phe	p.S745F	ENST00000334205	NM_003942.2	745	tCc/tTc	17/17	0.543881188426209	3	FACETS	1	0.972	1	0.532	0.498	0.566	CLONAL	1	TRUE	1	0.543881188426209	3		646	1188	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572238	64572239	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	194	472	0	ENST00000312049.6:c.1400_1401delinsTT	p.Ala467Val	p.A467V	ENST00000312049	NM_130799.2	467	gCC/gTT	10/10	0.543881188426209	3	FACETS	0.984	0.911	1	0.492	0.455	0.53	CLONAL	1	TRUE	1	0.543881188426209	3		472	922	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948499	71948499	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1342079410	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1293	337	823	1	ENST00000298229.2:c.3211C>T	p.Pro1071Ser	p.P1071S	ENST00000298229	NM_001567.3	1071	Cct/Tct	26/28	0.543881188426209	3	FACETS	0.967	0.912	1	0.484	0.456	0.512	CLONAL	1	TRUE	1	0.543881188426209	3		824	1630	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998331	100998331	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	25	50	0	ENST00000325455.5:c.1471C>T	p.Pro491Ser	p.P491S	ENST00000325455	NM_001202474.3	491	Ccg/Tcg	1/8	0.543881188426209	3	FACETS	1	0.871	1	0.557	0.448	0.677	CLONAL	1	TRUE	1	0.543881188426209	3		50	105	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111959725	111959725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	288	674	1	ENST00000375549.3:c.304C>T	p.His102Tyr	p.H102Y	ENST00000375549	NM_003002.3	102	Cat/Tat	3/4	0.543881188426209	3	FACETS	0.965	0.906	1	0.482	0.453	0.513	CLONAL	1	TRUE	1	0.543881188426209	3		675	1396	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342785	118342785	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	159	377	0	ENST00000534358.1:c.911G>A	p.Gly304Glu	p.G304E	ENST00000534358	NM_005933.3	304	gGa/gAa	3/36	0.543881188426209	3	FACETS	0.962	0.883	1	0.481	0.441	0.522	CLONAL	1	TRUE	1	0.543881188426209	3		377	773	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343175	118343175	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	183	421	0	ENST00000534358.1:c.1301A>G	p.Tyr434Cys	p.Y434C	ENST00000534358	NM_005933.3	434	tAt/tGt	3/36	0.543881188426209	3	FACETS	1	0.956	1	0.524	0.484	0.565	CLONAL	1	TRUE	1	0.543881188426209	3		421	817	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360579	118360579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	257	621	1	ENST00000534358.1:c.4552C>T	p.Pro1518Ser	p.P1518S	ENST00000534358	NM_005933.3	1518	Ccc/Tcc	12/36	0.543881188426209	3	FACETS	0.906	0.847	0.967	0.453	0.423	0.484	CLONAL	1	TRUE	1	0.543881188426209	3		622	1327	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699287	18699287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1370164516	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	170	463	1	ENST00000266497.5:c.3388G>A	p.Gly1130Arg	p.G1130R	ENST00000266497		1130	Gga/Aga	24/31	1	2	FACETS	0.902	0.832	0.975	0.902	0.832	0.975	CLONAL	1	TRUE	1	0.543881188426209	2		464	693	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425044	49425044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	272	781	1	ENST00000301067.7:c.13444G>A	p.Gly4482Arg	p.G4482R	ENST00000301067	NM_003482.3	4482	Ggg/Agg	39/54	1	2	FACETS	0.905	0.849	0.963	0.905	0.849	0.963	CLONAL	1	TRUE	1	0.543881188426209	2		782	1105	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427477	49427477	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	286	736	0	ENST00000301067.7:c.11011C>T	p.Pro3671Ser	p.P3671S	ENST00000301067	NM_003482.3	3671	Ccc/Tcc	39/54	1	2	FACETS	0.99	0.932	1	0.99	0.932	1	CLONAL	1	TRUE	1	0.543881188426209	2		736	1062	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859685	57859685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	159	421	1	ENST00000228682.2:c.739G>A	p.Asp247Asn	p.D247N	ENST00000228682	NM_005269.2	247	Gac/Aac	7/12	1	2	FACETS	0.855	0.786	0.927	0.855	0.786	0.927	CLONAL	1	TRUE	1	0.543881188426209	2		422	684	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222614	69222614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	243	681	1	ENST00000462284.1:c.587C>T	p.Ser196Phe	p.S196F	ENST00000462284	NM_002392.5	196	tCc/tTc	8/11	1	2	FACETS	0.915	0.855	0.976	0.915	0.855	0.976	CLONAL	1	TRUE	1	0.543881188426209	2		682	977	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109947	115109947	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	273	763	0	ENST00000257566.3:c.1931C>T	p.Ser644Phe	p.S644F	ENST00000257566	NM_016569.3	644	tCc/tTc	8/8	1	2	FACETS	0.9	0.844	0.957	0.9	0.844	0.957	CLONAL	1	TRUE	1	0.543881188426209	2		763	1116	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879807	123879807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755330697	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	226	412	0	ENST00000330479.4:c.503G>A	p.Arg168Gln	p.R168Q	ENST00000330479	NM_020382.3	168	cGa/cAa	4/9	1	2	FACETS	0.903	0.842	0.966	0.903	0.842	0.966	CLONAL	1	TRUE	1	0.543881188426209	2		412	920	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578239	28578239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	220	602	0	ENST00000241453.7:c.2932G>A	p.Glu978Lys	p.E978K	ENST00000241453	NM_004119.2	978	Gag/Aag	24/24	1	2	FACETS	0.935	0.872	1	0.935	0.872	1	CLONAL	1	TRUE	1	0.543881188426209	2		602	865	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28883032	28883032	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	87	645	0	ENST00000282397.4:c.3668A>G	p.Glu1223Gly	p.E1223G	ENST00000282397	NM_002019.4	1223	gAa/gGa	28/30	1	2	FACETS	0.346	0.305	0.389	0.346	0.305	0.389	SUBCLONAL	1	TRUE	1	0.543881188426209	2		645	925	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919670	28919670	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	182	562	0	ENST00000282397.4:c.2267A>G	p.Asn756Ser	p.N756S	ENST00000282397	NM_002019.4	756	aAt/aGt	16/30	1	2	FACETS	0.848	0.784	0.915	0.848	0.784	0.915	CLONAL	1	TRUE	1	0.543881188426209	2		562	789	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28931711	28931711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	183	462	0	ENST00000282397.4:c.2228C>T	p.Ser743Leu	p.S743L	ENST00000282397	NM_002019.4	743	tCa/tTa	15/30	1	2	FACETS	0.96	0.889	1	0.96	0.889	1	CLONAL	1	TRUE	1	0.543881188426209	2		462	701	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435133	110435133	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	296	725	0	ENST00000375856.3:c.3268C>A	p.Pro1090Thr	p.P1090T	ENST00000375856	NM_003749.2	1090	Ccc/Acc	1/2	0.543881188426209	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.543881188426209	1		725	783	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422074	81422074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334550660	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	203	486	0	ENST00000298171.2:c.50G>A	p.Arg17Lys	p.R17K	ENST00000298171	NM_000369.2	17	aGg/aAg	1/10	0.533306085104735	2	FACETS	1	0.954	1	0.516	0.48	0.553	CLONAL	1	TRUE	0	0.543881188426209	2		486	723	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678469	88678469	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	250	506	0	ENST00000360948.2:c.1067G>A	p.Gly356Glu	p.G356E	ENST00000360948	NM_001012338.2	356	gGa/gAa	9/19	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.543881188426209	2		506	916	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777915	3777915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161965489	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	420	914	2	ENST00000262367.5:c.7133C>T	p.Pro2378Leu	p.P2378L	ENST00000262367	NM_004380.2	2378	cCc/cTc	31/31	0.543881188426209	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.543881188426209	1		916	1047	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820920	3820920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	287	658	0	ENST00000262367.5:c.2531C>T	p.Pro844Leu	p.P844L	ENST00000262367	NM_004380.2	844	cCt/cTt	14/31	0.543881188426209	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.543881188426209	1		658	727	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984946	9984946	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	233	625	0	ENST00000330684.3:c.1019A>T	p.Asn340Ile	p.N340I	ENST00000330684	NM_001134407.1	340	aAt/aTt	4/13	0.543881188426209	1	FACETS	0.979	0.919	1	0.979	0.919	1	CLONAL	1	TRUE	0	0.543881188426209	1		625	637	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819634	81819634	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	222	592	0	ENST00000359376.3:c.40G>A	p.Glu14Lys	p.E14K	ENST00000359376	NM_002661.3	14	Gag/Aag	2/33	0.543881188426209	1	FACETS	0.906	0.848	0.965	0.906	0.848	0.965	CLONAL	1	TRUE	0	0.543881188426209	1		592	656	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965255	81965255	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	183	484	0	ENST00000359376.3:c.2735C>T	p.Thr912Ile	p.T912I	ENST00000359376	NM_002661.3	912	aCc/aTc	25/33	0.543881188426209	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.543881188426209	1		484	455	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982820	7982820	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	349	782	0	ENST00000319144.4:c.965A>T	p.Glu322Val	p.E322V	ENST00000319144	NM_001139.2	322	gAg/gTg	8/15	0.53972772795819	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.543881188426209	1		782	878	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961373	15961373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	190	497	2	ENST00000268712.3:c.6016C>T	p.Pro2006Ser	p.P2006S	ENST00000268712	NM_006311.3	2006	Cct/Tct	39/46	1	2	FACETS	0.877	0.812	0.944	0.877	0.812	0.944	CLONAL	1	TRUE	1	0.543881188426209	2		499	797	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528427	29528427	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	139	415	0	ENST00000356175.3:c.1186-2A>G		p.X396_splice	ENST00000356175	NM_000267.3	396			1	2	FACETS	0.948	0.868	1	0.948	0.868	1	CLONAL	1	TRUE	1	0.543881188426209	2		415	539	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78882689	78882689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393327607	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	337	724	1	ENST00000306801.3:c.2480C>T	p.Ser827Leu	p.S827L	ENST00000306801	NM_020761.2	827	tCg/tTg	21/34	0.155527347648607	3	FACETS	1	0.994	1	0.705	0.667	0.744	INDETERMINATE	1	TRUE	1	0.543881188426209	3		725	1118	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374892	45374893	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	270	686	2	ENST00000262160.6:c.950_951delinsTT	p.Ser317Phe	p.S317F	ENST00000262160	NM_005901.5	317	tCC/tTT	8/11	1	2	FACETS	0.944	0.886	1	0.944	0.886	1	CLONAL	1	TRUE	1	0.543881188426209	2		688	1052	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581268	48581268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752575871	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	259	646	0	ENST00000342988.3:c.572C>T	p.Ser191Leu	p.S191L	ENST00000342988	NM_005359.5	191	tCg/tTg	5/12	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.543881188426209	2		646	886	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135098	11135098	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1198	64	822	0	ENST00000358026.2:c.3065C>T	p.Ser1022Phe	p.S1022F	ENST00000358026	NM_001128849.1	1022	tCc/tTc	21/36	1	2	FACETS	0.186	0.16	0.215	0.186	0.16	0.215	SUBCLONAL	1	TRUE	1	0.543881188426209	2		822	1262	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281362	15281362	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	243	595	0	ENST00000263388.2:c.4894G>A	p.Glu1632Lys	p.E1632K	ENST00000263388	NM_000435.2	1632	Gag/Aag	27/33	1	2	FACETS	0.996	0.932	1	0.996	0.932	1	CLONAL	1	TRUE	1	0.543881188426209	2		595	897	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289992	15289992	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	341	860	0	ENST00000263388.2:c.3562G>A	p.Gly1188Ser	p.G1188S	ENST00000263388	NM_000435.2	1188	Ggt/Agt	22/33	1	2	FACETS	0.965	0.912	1	0.965	0.912	1	CLONAL	1	TRUE	1	0.543881188426209	2		860	1300	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943480	17943480	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	208	598	0	ENST00000458235.1:c.2528C>A	p.Pro843Gln	p.P843Q	ENST00000458235	NM_000215.3	843	cCg/cAg	19/24	1	2	FACETS	0.9	0.837	0.965	0.9	0.837	0.965	CLONAL	1	TRUE	1	0.543881188426209	2		598	850	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943675	17943675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	320	723	0	ENST00000458235.1:c.2414G>A	p.Gly805Asp	p.G805D	ENST00000458235	NM_000215.3	805	gGt/gAt	18/24	1	2	FACETS	0.961	0.906	1	0.961	0.906	1	CLONAL	1	TRUE	1	0.543881188426209	2		723	1225	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968294	18968294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	292	730	1	ENST00000262803.5:c.2134C>T	p.Pro712Ser	p.P712S	ENST00000262803	NM_002911.3	712	Cca/Tca	15/24	1	2	FACETS	0.938	0.882	0.995	0.938	0.882	0.995	CLONAL	1	TRUE	1	0.543881188426209	2		731	1145	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216193	36216194	+	frameshift_variant	Frame_Shift_Ins	INS	CC	CC	TTA	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	253	590	1	ENST00000222270.7:c.3601_3602delinsTTA	p.Pro1201LeufsTer23	p.P1201Lfs*23	ENST00000222270	NM_014727.1	1201	CCg/TTAg	11/37	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.543881188426209	2		591	919	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216476	36216476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	344	818	1	ENST00000222270.7:c.3739C>T	p.Arg1247Cys	p.R1247C	ENST00000222270	NM_014727.1	1247	Cgt/Tgt	12/37	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.543881188426209	2		819	1246	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223533	36223533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1347423104	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	322	740	1	ENST00000222270.7:c.6083C>T	p.Ser2028Phe	p.S2028F	ENST00000222270	NM_014727.1	2028	tCc/tTc	28/37	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.543881188426209	2		741	1090	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224016	36224016	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	370	970	0	ENST00000222270.7:c.6566C>T	p.Ser2189Phe	p.S2189F	ENST00000222270	NM_014727.1	2189	tCc/tTc	28/37	1	2	FACETS	0.984	0.932	1	0.984	0.932	1	CLONAL	1	TRUE	1	0.543881188426209	2		970	1383	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42790979	42790979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	279	618	0	ENST00000575354.2:c.124C>T	p.Pro42Ser	p.P42S	ENST00000575354	NM_015125.3	42	Ccc/Tcc	2/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.543881188426209	2		618	941	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082286	16082286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	335	830	2	ENST00000281043.3:c.100G>A	p.Asp34Asn	p.D34N	ENST00000281043	NM_005378.4	34	Gac/Aac	2/3	1	2	FACETS	0.966	0.913	1	0.966	0.913	1	CLONAL	1	TRUE	1	0.543881188426209	2		832	1275	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456462	29456462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	328	833	0	ENST00000389048.3:c.2456G>A	p.Gly819Glu	p.G819E	ENST00000389048	NM_004304.4	819	gGa/gAa	14/29	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.543881188426209	2		833	1190	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498006	29498006	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	232	567	0	ENST00000389048.3:c.2000G>A	p.Gly667Glu	p.G667E	ENST00000389048	NM_004304.4	667	gGg/gAg	11/29	1	2	FACETS	0.85	0.793	0.909	0.85	0.793	0.909	CLONAL	1	TRUE	1	0.543881188426209	2		567	1004	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519863	29519864	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	226	653	1	ENST00000389048.3:c.1707_1708delinsAA	p.Glu570Lys	p.E570K	ENST00000389048	NM_004304.4	569	gtGGag/gtAAag	9/29	1	2	FACETS	0.892	0.831	0.954	0.892	0.831	0.954	CLONAL	1	TRUE	1	0.543881188426209	2		654	932	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917833	29917833	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	346	811	0	ENST00000389048.3:c.835C>T	p.Pro279Ser	p.P279S	ENST00000389048	NM_004304.4	279	Cca/Tca	3/29	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.543881188426209	2		811	1219	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693856	47693856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755818010	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	228	434	0	ENST00000233146.2:c.1570C>T	p.Arg524Cys	p.R524C	ENST00000233146	NM_000251.2	524	Cgt/Tgt	10/16	1	2	FACETS	0.996	0.93	1	0.996	0.93	1	CLONAL	1	TRUE	1	0.543881188426209	2		434	842	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027424	48027424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35946687	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	174	458	0	ENST00000234420.5:c.2302C>T	p.Pro768Ser	p.P768S	ENST00000234420	NM_000179.2	768	Cct/Tct	4/10	1	2	FACETS	0.929	0.858	1	0.929	0.858	1	CLONAL	1	TRUE	1	0.543881188426209	2		458	689	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189383	99189383	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	276	654	0	ENST00000074304.5:c.2639C>T	p.Ala880Val	p.A880V	ENST00000074304	NM_001134224.1	880	gCt/gTt	24/26	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.543881188426209	2		654	1001	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682844	190682844	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1372328007	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	264	687	1	ENST00000441310.2:c.520G>A	p.Asp174Asn	p.D174N	ENST00000441310	NM_000534.4	174	Gat/Aat	5/13	1	2	FACETS	0.963	0.903	1	0.963	0.903	1	CLONAL	1	TRUE	1	0.543881188426209	2		688	1008	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561313	9561313	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	183	404	0	ENST00000353224.5:c.469G>A	p.Asp157Asn	p.D157N	ENST00000353224	NM_177990.2	157	Gat/Aat	4/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.543881188426209	2		404	638	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36022375	36022375	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	318	811	1	ENST00000358208.4:c.428C>T	p.Ser143Phe	p.S143F	ENST00000358208		143	tCc/tTc	4/12	1	2	FACETS	0.98	0.925	1	0.98	0.925	1	CLONAL	1	TRUE	1	0.543881188426209	2		812	1193	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306616	41306616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	295	687	0	ENST00000373198.4:c.1043G>A	p.Trp348Ter	p.W348*	ENST00000373198	NM_133170.3	348	tGg/tAg	7/32	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.543881188426209	2		687	1045	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755759	39755759	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs947562455	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	183	441	0	ENST00000288319.7:c.1006A>G	p.Asn336Asp	p.N336D	ENST00000288319	NM_182918.3	336	Aac/Gac	10/10	1	2	FACETS	0.959	0.888	1	0.959	0.888	1	CLONAL	1	TRUE	1	0.543881188426209	2		441	702	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259290	89259290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	190	502	1	ENST00000336596.2:c.434C>T	p.Thr145Ile	p.T145I	ENST00000336596	NM_005233.5	145	aCc/aTc	3/17	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.543881188426209	2		503	663	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961005	55961005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	220	571	1	ENST00000263923.4:c.2935G>A	p.Glu979Lys	p.E979K	ENST00000263923	NM_002253.2	979	Gag/Aag	21/30	1	2	FACETS	0.978	0.912	1	0.978	0.912	1	CLONAL	1	TRUE	1	0.543881188426209	2		572	827	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961775	55961775	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1355087765	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	225	561	0	ENST00000263923.4:c.2786G>A	p.Arg929Lys	p.R929K	ENST00000263923	NM_002253.2	929	aGg/aAg	20/30	1	2	FACETS	0.918	0.856	0.982	0.918	0.856	0.982	CLONAL	1	TRUE	1	0.543881188426209	2		561	901	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55962506	55962506	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780022671	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	219	496	0	ENST00000263923.4:c.2618G>A	p.Gly873Glu	p.G873E	ENST00000263923	NM_002253.2	873	gGa/gAa	19/30	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.543881188426209	2		496	763	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981537	55981537	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770805149	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	174	459	0	ENST00000263923.4:c.400G>A	p.Gly134Arg	p.G134R	ENST00000263923	NM_002253.2	134	Gga/Aga	4/30	1	2	FACETS	0.847	0.782	0.916	0.847	0.782	0.916	CLONAL	1	TRUE	1	0.543881188426209	2		459	755	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157635	106157635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	175	438	0	ENST00000380013.4:c.2536G>A	p.Glu846Lys	p.E846K	ENST00000380013	NM_001127208.2	846	Gaa/Aaa	3/11	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.543881188426209	2		438	633	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158002	106158002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	148	387	0	ENST00000380013.4:c.2903C>T	p.Pro968Leu	p.P968L	ENST00000380013	NM_001127208.2	968	cCc/cTc	3/11	1	2	FACETS	0.882	0.809	0.958	0.882	0.809	0.958	CLONAL	1	TRUE	1	0.543881188426209	2		387	617	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510155	187510155	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	202	535	0	ENST00000441802.2:c.13358C>T	p.Pro4453Leu	p.P4453L	ENST00000441802	NM_005245.3	4453	cCc/cTc	27/27	1	2	FACETS	0.918	0.853	0.986	0.918	0.853	0.986	CLONAL	1	TRUE	1	0.543881188426209	2		535	809	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538257	187538257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	269	790	2	ENST00000441802.2:c.8977C>T	p.Leu2993Phe	p.L2993F	ENST00000441802	NM_005245.3	2993	Ctt/Ttt	11/27	1	2	FACETS	0.936	0.878	0.995	0.936	0.878	0.995	CLONAL	1	TRUE	1	0.543881188426209	2		792	1057	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	231043	231043	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553998629	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	50	573	0	ENST00000264932.6:c.823G>A	p.Asp275Asn	p.D275N	ENST00000264932	NM_004168.2	275	Gac/Aac	7/15	1	2	FACETS	0.218	0.184	0.255	0.218	0.184	0.255	SUBCLONAL	1	TRUE	1	0.543881188426209	2		573	844	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31451654	31451654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600599	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	198	505	0	ENST00000344624.3:c.2668C>T	p.Arg890Cys	p.R890C	ENST00000344624		890	Cgt/Tgt	18/33	1	2	FACETS	0.949	0.881	1	0.949	0.881	1	CLONAL	1	TRUE	1	0.543881188426209	2		505	767	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174882	56174882	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	166	484	1	ENST00000399503.3:c.2041C>T	p.Gln681Ter	p.Q681*	ENST00000399503	NM_005921.1	681	Cag/Tag	11/20	1	2	FACETS	0.807	0.743	0.874	0.807	0.743	0.874	CLONAL	1	TRUE	1	0.543881188426209	2		485	756	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685304	86685304	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	84	214	0	ENST00000274376.6:c.3020A>G	p.Asp1007Gly	p.D1007G	ENST00000274376	NM_002890.2	1007	gAt/gGt	24/25	1	2	FACETS	0.87	0.775	0.971	0.87	0.775	0.971	CLONAL	1	TRUE	1	0.543881188426209	2		214	355	SUCCESS
APC	324	MSKCC	GRCh37	5	112176606	112176606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	164	464	0	ENST00000257430.4:c.5315C>T	p.Pro1772Leu	p.P1772L	ENST00000257430	NM_000038.5	1772	cCa/cTa	16/16	1	2	FACETS	0.878	0.808	0.95	0.878	0.808	0.95	CLONAL	1	TRUE	1	0.543881188426209	2		464	687	SUCCESS
APC	324	MSKCC	GRCh37	5	112177991	112177991	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749507584	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	210	486	0	ENST00000257430.4:c.6700C>T	p.Pro2234Ser	p.P2234S	ENST00000257430	NM_000038.5	2234	Cca/Tca	16/16	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.543881188426209	2		486	764	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953803	131953803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	186	499	0	ENST00000265335.6:c.3206G>A	p.Arg1069Lys	p.R1069K	ENST00000265335		1069	aGa/aAa	21/25	1	2	FACETS	0.878	0.813	0.946	0.878	0.813	0.946	CLONAL	1	TRUE	1	0.543881188426209	2		499	779	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459720	149459720	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs776871942	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	280	736	0	ENST00000286301.3:c.487A>G	p.Thr163Ala	p.T163A	ENST00000286301	NM_005211.3	163	Acc/Gcc	4/22	1	2	FACETS	0.974	0.916	1	0.974	0.916	1	CLONAL	1	TRUE	1	0.543881188426209	2		736	1057	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497362	149497362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	229	623	1	ENST00000261799.4:c.2956C>T	p.Leu986Phe	p.L986F	ENST00000261799	NM_002609.3	986	Ctt/Ttt	22/23	1	2	FACETS	0.913	0.852	0.976	0.913	0.852	0.976	CLONAL	1	TRUE	1	0.543881188426209	2		624	922	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499070	149499070	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	264	735	1	ENST00000261799.4:c.2758G>A	p.Gly920Ser	p.G920S	ENST00000261799	NM_002609.3	920	Ggt/Agt	20/23	1	2	FACETS	0.967	0.907	1	0.967	0.907	1	CLONAL	1	TRUE	1	0.543881188426209	2		736	1004	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046704	180046704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	283	755	1	ENST00000261937.6:c.2608G>A	p.Gly870Ser	p.G870S	ENST00000261937	NM_182925.4	870	Ggc/Agc	18/30	1	2	FACETS	0.899	0.844	0.955	0.899	0.844	0.955	CLONAL	1	TRUE	1	0.543881188426209	2		756	1158	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032249	26032249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	103	222	0	ENST00000244661.2:c.40G>A	p.Gly14Ser	p.G14S	ENST00000244661	NM_003537.3	14	Ggt/Agt	1/1	0.543881188426209	3	FACETS	0.965	0.868	1	0.483	0.434	0.534	CLONAL	1	TRUE	1	0.543881188426209	3		222	499	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672345	30672345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1271	124	652	3	ENST00000376406.3:c.4615C>T	p.Pro1539Ser	p.P1539S	ENST00000376406	NM_014641.2	1539	Cct/Tct	10/15	0.543881188426209	3	FACETS	0.416	0.375	0.459	0.208	0.187	0.23	SUBCLONAL	1	TRUE	1	0.543881188426209	3		655	1395	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188656	32188656	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	226	612	1	ENST00000375023.3:c.800-1G>A		p.X267_splice	ENST00000375023	NM_004557.3	267			0.543881188426209	3	FACETS	0.916	0.852	0.982	0.458	0.426	0.491	CLONAL	1	TRUE	1	0.543881188426209	3		613	1154	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805935	32805935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762904431	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1284	301	890	0	ENST00000374899.4:c.76C>T	p.Pro26Ser	p.P26S	ENST00000374899	NM_018833.2	26	Cct/Tct	2/12	0.543881188426209	3	FACETS	0.888	0.834	0.944	0.444	0.417	0.472	CLONAL	1	TRUE	1	0.543881188426209	3		890	1585	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332070	81332071	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	104	291	0	ENST00000222390.5:c.2013_2014delinsAA	p.Asp672Asn	p.D672N	ENST00000222390	NM_000601.4	671	ggGGat/ggAAat	18/18	1	2	FACETS	0.852	0.767	0.94	0.852	0.767	0.94	CLONAL	1	TRUE	1	0.543881188426209	2		291	449	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508363	106508364	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	121	285	1	ENST00000359195.3:c.357_358delinsAA	p.Asp120Asn	p.D120N	ENST00000359195	NM_002649.2	119	ctGGac/ctAAac	2/11	1	2	FACETS	0.967	0.88	1	0.967	0.88	1	CLONAL	1	TRUE	1	0.543881188426209	2		286	460	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403314	116403314	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	259	627	0	ENST00000397752.3:c.2575G>A	p.Glu859Lys	p.E859K	ENST00000397752	NM_000245.2	859	Gaa/Aaa	11/21	1	2	FACETS	0.967	0.907	1	0.967	0.907	1	CLONAL	1	TRUE	1	0.543881188426209	2		627	985	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205281	38205281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	357	1026	0	ENST00000317025.8:c.409C>T	p.Pro137Ser	p.P137S	ENST00000317025	NM_023034.1	137	Cct/Tct	2/24	1	2	FACETS	0.871	0.823	0.919	0.871	0.823	0.919	CLONAL	1	TRUE	1	0.543881188426209	2		1026	1508	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992757	68992757	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	305	822	1	ENST00000288368.4:c.1722G>A	p.Met574Ile	p.M574I	ENST00000288368	NM_024870.2	574	atG/atA	16/40	1	2	FACETS	0.973	0.917	1	0.973	0.917	1	CLONAL	1	TRUE	1	0.543881188426209	2		823	1153	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980527	70980527	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	261	759	2	ENST00000276594.2:c.850C>T	p.Gln284Ter	p.Q284*	ENST00000276594	NM_024504.3	284	Caa/Taa	4/8	1	2	FACETS	0.838	0.785	0.893	0.838	0.785	0.893	CLONAL	1	TRUE	1	0.543881188426209	2		761	1145	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521486	8521486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752937985	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	258	649	0	ENST00000356435.5:c.752G>A	p.Gly251Glu	p.G251E	ENST00000356435		251	gGa/gAa	9/35	0.543881188426209	1	FACETS	0.93	0.875	0.986	0.93	0.875	0.986	CLONAL	1	TRUE	0	0.543881188426209	1		649	743	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27183498	27183498	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779939521	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	217	611	0	ENST00000380036.4:c.1072C>T	p.His358Tyr	p.H358Y	ENST00000380036	NM_000459.3	358	Cat/Tat	8/23	0.543881188426209	1	FACETS	0.912	0.853	0.972	0.912	0.853	0.972	CLONAL	1	TRUE	0	0.543881188426209	1		611	637	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760330	133760330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	233	586	0	ENST00000318560.5:c.2653C>T	p.Pro885Ser	p.P885S	ENST00000318560	NM_005157.4	885	Cca/Tca	11/11	0.543881188426209	1	FACETS	0.967	0.908	1	0.967	0.908	1	CLONAL	1	TRUE	0	0.543881188426209	1		586	645	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796750	135796750	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs118203436	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	137	371	0	ENST00000298552.3:c.737G>A	p.Arg246Lys	p.R246K	ENST00000298552	NM_001162426.1	246	aGg/aAg	8/23	0.543881188426209	1	FACETS	0.981	0.903	1	0.981	0.903	1	CLONAL	1	TRUE	0	0.543881188426209	1		371	374	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391767	139391767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764176079	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	272	584	0	ENST00000277541.6:c.6424C>T	p.Pro2142Ser	p.P2142S	ENST00000277541	NM_017617.3	2142	Ccc/Tcc	34/34	0.543881188426209	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.543881188426209	1		584	678	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913179	39913179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	223	257	0	ENST00000378444.4:c.4936C>T	p.Leu1646Phe	p.L1646F	ENST00000378444	NM_001123385.1	1646	Ctc/Ttc	14/15	1	1	FACETS	0.752	0.712	0.791	1	0.994	1	SUBCLONAL	2	TRUE	0	0.543881188426209	1		257	397	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820548	44820548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	205	310	0	ENST00000377967.4:c.245C>T	p.Ser82Phe	p.S82F	ENST00000377967	NM_021140.2	82	tCt/tTt	3/29	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.543881188426209	1		310	398	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305441	65305441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	181	473	0	ENST00000342505.4:c.2687C>T	p.Pro896Leu	p.P896L	ENST00000342505	NM_002227.2	896	cCc/cTc	20/25	1	2	FACETS	0.901	0.833	0.971	0.901	0.833	0.971	CLONAL	1	TRUE	1	0.543881188426209	2		473	739	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238359	98238359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	225	556	2	ENST00000331920.6:c.1685C>T	p.Ala562Val	p.A562V	ENST00000331920	NM_000264.3	562	gCc/gTc	12/24	0.543881188426209	1	FACETS	0.973	0.912	1	0.973	0.912	1	CLONAL	1	TRUE	0	0.543881188426209	1		558	619	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928690	49928690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1234497922	NA	P-0025973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	355	828	0	ENST00000296474.3:c.3584G>A	p.Ser1195Asn	p.S1195N	ENST00000296474	NM_002447.2	1195	aGc/aAc	17/20	1	2	FACETS	0.989	0.936	1	0.989	0.936	1	CLONAL	1	TRUE	1	0.543881188426209	2		828	1320	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	125	282	0				ENST00000310581	NM_198253.2	-/1132			0.420317287814443	1	FACETS	0.542	0.495	0.591	0.542	0.495	0.591	INDETERMINATE	1	TRUE	0	0.726816161462676	1		282	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	661	593	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.600235742743101	3	FACETS	0.838	0.816	0.861	0.838	0.816	0.861	CLONAL	3	TRUE	0	0.726816161462676	3		593	986	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	112	173	1				ENST00000310581	NM_198253.2	-/1132			0.420317287814443	1	FACETS	0.554	0.504	0.606	0.554	0.504	0.606	INDETERMINATE	1	TRUE	0	0.726816161462676	1		174	354	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058566	69058566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866534903	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	122	819	0	ENST00000288368.4:c.4210C>T	p.His1404Tyr	p.H1404Y	ENST00000288368	NM_024870.2	1404	Cat/Tat	34/40	0.261653520663214	2	FACETS	0.583	0.528	0.64	0.291	0.264	0.32	INDETERMINATE	1	TRUE	0	0.726816161462676	2		819	576	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940120	31940120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	311	856	0	ENST00000375333.2:c.262G>A	p.Glu88Lys	p.E88K	ENST00000375333	NM_032454.1	88	Gaa/Aaa	2/8	0.679490023417883	1	FACETS	0.855	0.814	0.897	0.855	0.814	0.897	CLONAL	1	TRUE	0	0.726816161462676	1		856	637	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169400	11169400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs911296767	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	131	514	1	ENST00000361445.4:c.7475C>T	p.Ala2492Val	p.A2492V	ENST00000361445	NM_004958.3	2492	gCc/gTc	56/58	1	2	FACETS	0.754	0.689	0.822	0.754	0.689	0.822	SUBCLONAL	1	TRUE	1	0.726816161462676	2		515	478	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184682	11184682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	98	368	0	ENST00000361445.4:c.6535G>A	p.Gly2179Arg	p.G2179R	ENST00000361445	NM_004958.3	2179	Gga/Aga	47/58	1	2	FACETS	0.739	0.665	0.816	0.739	0.665	0.816	SUBCLONAL	1	TRUE	1	0.726816161462676	2		368	365	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187740	11187740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	191	762	0	ENST00000361445.4:c.6157C>T	p.Pro2053Ser	p.P2053S	ENST00000361445	NM_004958.3	2053	Ccc/Tcc	44/58	1	2	FACETS	0.704	0.652	0.757	0.704	0.652	0.757	SUBCLONAL	1	TRUE	1	0.726816161462676	2		762	747	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101479	27101480	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	235	900	3	ENST00000324856.7:c.4761_4762delinsTT	p.Pro1588Ser	p.P1588S	ENST00000324856	NM_006015.4	1587	agCCct/agTTct	18/20	1	2	FACETS	0.813	0.761	0.867	0.813	0.761	0.867	CLONAL	1	TRUE	1	0.726816161462676	2		903	795	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804372	43804373	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	132	502	1	ENST00000372470.3:c.372_373delinsTT	p.Leu125Phe	p.L125F	ENST00000372470	NM_005373.2	124	gtCCtc/gtTTtc	3/12	1	2	FACETS	0.849	0.777	0.923	0.849	0.777	0.923	CLONAL	1	TRUE	1	0.726816161462676	2		503	428	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156836758	156836758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	554	756	0	ENST00000524377.1:c.416C>T	p.Ser139Phe	p.S139F	ENST00000524377	NM_002529.3	139	tCc/tTc	4/17	0.550622682360391	4	FACETS	0.897	0.867	0.927	0.897	0.867	0.927	CLONAL	3	TRUE	1	0.726816161462676	4		756	978	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944012	71944012	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs777831045	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	215	699	1	ENST00000298229.2:c.1945C>T	p.Arg649Ter	p.R649*	ENST00000298229	NM_001567.3	649	Cga/Tga	16/28	1	2	FACETS	0.822	0.767	0.878	0.822	0.767	0.878	CLONAL	1	TRUE	1	0.726816161462676	2		700	720	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103385	77103385	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	96	344	0	ENST00000356341.3:c.181G>A	p.Gly61Arg	p.G61R	ENST00000356341	NM_002576.4	61	Gga/Aga	2/15	1	2	FACETS	0.789	0.71	0.871	0.789	0.71	0.871	SUBCLONAL	1	TRUE	1	0.726816161462676	2		344	335	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207793	102207793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	105	467	1	ENST00000263464.3:c.1775G>A	p.Arg592Lys	p.R592K	ENST00000263464	NM_001165.4	592	aGg/aAg	9/9	1	2	FACETS	0.777	0.702	0.854	0.777	0.702	0.854	SUBCLONAL	1	TRUE	1	0.726816161462676	2		468	372	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115594	108115594	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730881336	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	94	500	2	ENST00000278616.4:c.742C>T	p.Arg248Ter	p.R248*	ENST00000278616	NM_000051.3	248	Cga/Tga	7/63	1	2	FACETS	0.723	0.648	0.8	0.723	0.648	0.8	SUBCLONAL	1	TRUE	1	0.726816161462676	2		502	358	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170464	108170464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	99	428	0	ENST00000278616.4:c.5029G>A	p.Glu1677Lys	p.E1677K	ENST00000278616	NM_000051.3	1677	Gaa/Aaa	34/63	1	2	FACETS	0.778	0.701	0.858	0.778	0.701	0.858	SUBCLONAL	1	TRUE	1	0.726816161462676	2		428	350	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856571	111856571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	161	274	0	ENST00000341259.2:c.622G>A	p.Glu208Lys	p.E208K	ENST00000341259	NM_005475.2	208	Gag/Aag	2/8	0.611134198985382	3	FACETS	0.888	0.828	0.949	0.888	0.828	0.949	CLONAL	2	TRUE	1	0.726816161462676	3		274	340	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098699	2098699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	466	696	0	ENST00000219476.3:c.83C>T	p.Pro28Leu	p.P28L	ENST00000219476	NM_000548.3	28	cCc/cTc	2/42	0.604999680493568	3	FACETS	0.874	0.839	0.91	0.874	0.839	0.91	CLONAL	2	TRUE	1	0.726816161462676	3		696	1000	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23640966	23640966	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778587	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	218	409	0	ENST00000261584.4:c.2509G>A	p.Glu837Lys	p.E837K	ENST00000261584	NM_024675.3	837	Gaa/Aaa	5/13	0.604999680493568	3	FACETS	0.845	0.795	0.896	0.845	0.795	0.896	CLONAL	2	TRUE	1	0.726816161462676	3		409	484	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50830322	50830322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	119	504	0	ENST00000398568.2:c.2765C>T	p.Ser922Phe	p.S922F	ENST00000398568	NM_001042412.1	922	tCc/tTc	18/18	0.604999680493568	3	FACETS	0.879	0.797	0.964	0.439	0.398	0.482	CLONAL	1	TRUE	1	0.726816161462676	3		504	508	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40872429	40872429	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	171	667	0	ENST00000428826.2:c.526T>C	p.Phe176Leu	p.F176L	ENST00000428826		176	Ttt/Ctt	7/21	0.611134198985382	3	FACETS	0.751	0.691	0.813	0.376	0.345	0.407	SUBCLONAL	1	TRUE	1	0.726816161462676	3		667	854	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246196	41246196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	226	607	0	ENST00000357654.3:c.1352C>T	p.Ser451Leu	p.S451L	ENST00000357654	NM_007294.3	451	tCa/tTa	10/23	0.611134198985382	3	FACETS	0.778	0.731	0.825	0.778	0.731	0.825	SUBCLONAL	2	TRUE	1	0.726816161462676	3		607	545	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858322	59858322	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	344	502	0	ENST00000259008.2:c.1673G>A	p.Trp558Ter	p.W558*	ENST00000259008	NM_032043.2	558	tGg/tAg	12/20	0.550622682360391	4	FACETS	0.846	0.809	0.883	0.846	0.809	0.883	CLONAL	3	TRUE	1	0.726816161462676	4		502	644	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372168	45372168	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	133	451	0	ENST00000262160.6:c.1001G>A	p.Arg334Lys	p.R334K	ENST00000262160	NM_005901.5	334	aGa/aAa	9/11	0.213889129862943	3	FACETS	1	0.937	1	0.515	0.471	0.562	INDETERMINATE	1	TRUE	1	0.726816161462676	3		451	484	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350615	15350616	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	252	891	3	ENST00000263377.2:c.3299_3300delinsTT	p.Ser1100Phe	p.S1100F	ENST00000263377	NM_058243.2	1100	tCC/tTT	16/20	1	2	FACETS	0.823	0.772	0.875	0.823	0.772	0.875	CLONAL	1	TRUE	1	0.726816161462676	2		894	843	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387372	17387372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	311	1064	2	ENST00000359435.4:c.638C>T	p.Thr213Ile	p.T213I	ENST00000359435	NM_001033549.1	213	aCc/aTc	7/9	1	2	FACETS	0.909	0.86	0.96	0.909	0.86	0.96	CLONAL	1	TRUE	1	0.726816161462676	2		1066	941	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279576	18279576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	241	745	2	ENST00000222254.8:c.1849C>T	p.His617Tyr	p.H617Y	ENST00000222254	NM_005027.3	617	Cac/Tac	15/16	1	2	FACETS	0.885	0.83	0.942	0.885	0.83	0.942	CLONAL	1	TRUE	1	0.726816161462676	2		747	749	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798198	42798199	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	216	768	4	ENST00000575354.2:c.4152_4153delinsAA	p.Ala1385Thr	p.A1385T	ENST00000575354	NM_015125.3	1384	cgGGcc/cgAAcc	17/20	0.611134198985382	3	FACETS	0.819	0.762	0.879	0.41	0.381	0.44	CLONAL	1	TRUE	1	0.726816161462676	3		772	989	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155363	99155363	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	137	445	0	ENST00000074304.5:c.589C>T	p.Pro197Ser	p.P197S	ENST00000074304	NM_001134224.1	197	Cct/Tct	9/26	0.726816161462676	3	FACETS	0.851	0.777	0.928	0.425	0.388	0.464	CLONAL	1	TRUE	1	0.726816161462676	3		445	604	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547018	9547018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11700112	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	53	224	0	ENST00000353224.5:c.1004G>A	p.Arg335Gln	p.R335Q	ENST00000353224	NM_177990.2	335	cGa/cAa	5/10	0.726816161462676	3	FACETS	0.815	0.702	0.936	0.407	0.351	0.468	CLONAL	1	TRUE	1	0.726816161462676	3		224	244	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024885	31024885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	316	638	0	ENST00000375687.4:c.4370C>T	p.Ser1457Phe	p.S1457F	ENST00000375687	NM_015338.5	1457	tCc/tTc	13/13	0.170086862788288	3	FACETS	0.844	0.803	0.886	0.563	0.535	0.591	INDETERMINATE	2	TRUE	0	0.726816161462676	3		638	702	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164718	36164718	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	278	777	0	ENST00000300305.3:c.1157C>T	p.Pro386Leu	p.P386L	ENST00000300305		386	cCc/cTc	8/8	0.514727740885829	1	FACETS	0.618	0.583	0.654	0.618	0.583	0.654	SUBCLONAL	1	TRUE	0	0.726816161462676	1		777	788	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164890	36164890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1415582429	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	209	702	1	ENST00000300305.3:c.985G>A	p.Ala329Thr	p.A329T	ENST00000300305		329	Gcg/Acg	8/8	0.514727740885829	1	FACETS	0.538	0.502	0.576	0.538	0.502	0.576	SUBCLONAL	1	TRUE	0	0.726816161462676	1		703	680	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37061932	37061932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	119	408	0	ENST00000231790.2:c.1016C>T	p.Ser339Phe	p.S339F	ENST00000231790	NM_000249.3	339	tCc/tTc	11/19	0.213889129862943	3	FACETS	1	0.97	1	0.574	0.523	0.627	INDETERMINATE	1	TRUE	1	0.726816161462676	3		408	389	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400015	49400015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	189	712	0	ENST00000418115.1:c.322C>T	p.Pro108Ser	p.P108S	ENST00000418115	NM_001664.2	108	Ccc/Tcc	4/5	0.213889129862943	3	FACETS	0.979	0.908	1	0.49	0.454	0.527	INDETERMINATE	1	TRUE	1	0.726816161462676	3		712	724	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637604	52637604	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	148	514	0	ENST00000394830.3:c.2712A>T	p.Lys904Asn	p.K904N	ENST00000394830	NM_018313.4	904	aaA/aaT	18/30	0.213889129862943	3	FACETS	1	0.977	1	0.581	0.534	0.629	INDETERMINATE	1	TRUE	1	0.726816161462676	3		514	478	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161300	185161300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1363166292	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	195	684	2	ENST00000265026.3:c.727G>A	p.Glu243Lys	p.E243K	ENST00000265026	NM_004721.4	243	Gag/Aag	4/14	1	2	FACETS	0.86	0.8	0.921	0.86	0.8	0.921	CLONAL	1	TRUE	1	0.726816161462676	2		686	624	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455588	189455589	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	151	690	2	ENST00000264731.3:c.122_123delinsTT	p.Ser41Phe	p.S41F	ENST00000264731	NM_003722.4	41	tCC/tTT	2/14	1	2	FACETS	0.784	0.721	0.849	0.784	0.721	0.849	SUBCLONAL	1	TRUE	1	0.726816161462676	2		692	530	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159060	143159060	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	72	496	0	ENST00000262992.4:c.793C>T	p.Pro265Ser	p.P265S	ENST00000262992	NM_001101669.1	265	Cct/Tct	10/24	1	2	FACETS	0.809	0.716	0.905	0.809	0.716	0.905	CLONAL	1	TRUE	1	0.726816161462676	2		496	245	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287373	33287373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	255	487	0	ENST00000374542.5:c.1724C>T	p.Pro575Leu	p.P575L	ENST00000374542	NM_001141970.1	575	cCc/cTc	6/8	0.576871972458024	3	FACETS	0.788	0.744	0.833	0.788	0.744	0.833	SUBCLONAL	2	TRUE	1	0.726816161462676	3		487	607	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287475	33287475	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	163	594	0	ENST00000374542.5:c.1622C>T	p.Ser541Phe	p.S541F	ENST00000374542	NM_001141970.1	541	tCc/tTc	6/8	0.576871972458024	3	FACETS	0.864	0.795	0.935	0.432	0.397	0.468	CLONAL	1	TRUE	1	0.726816161462676	3		594	708	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710812	117710812	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	121	381	0	ENST00000368508.3:c.1460C>T	p.Ser487Phe	p.S487F	ENST00000368508	NM_002944.2	487	tCc/tTc	12/43	0.170086862788288	3	FACETS	0.938	0.852	1	0.313	0.284	0.343	INDETERMINATE	1	TRUE	0	0.726816161462676	3		381	484	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725482	117725482	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs867025812	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	130	482	0	ENST00000368508.3:c.399G>A	p.Trp133Ter	p.W133*	ENST00000368508	NM_002944.2	133	tgG/tgA	5/43	0.170086862788288	3	FACETS	0.931	0.849	1	0.31	0.283	0.339	INDETERMINATE	1	TRUE	0	0.726816161462676	3		482	524	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522271	157522271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	222	636	0	ENST00000346085.5:c.4543C>T	p.His1515Tyr	p.H1515Y	ENST00000346085	NM_020732.3	1515	Cac/Tac	18/20	0.170086862788288	3	FACETS	0.964	0.899	1	0.321	0.299	0.344	INDETERMINATE	1	TRUE	0	0.726816161462676	3		636	864	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007140	152007140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	163	543	0	ENST00000262189.6:c.760C>T	p.Arg254Cys	p.R254C	ENST00000262189	NM_170606.2	254	Cgt/Tgt	6/59	1	2	FACETS	0.805	0.743	0.869	0.805	0.743	0.869	CLONAL	1	TRUE	1	0.726816161462676	2		543	557	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982782	90982782	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	139	278	0	ENST00000265433.3:c.706A>T	p.Lys236Ter	p.K236*	ENST00000265433	NM_002485.4	236	Aag/Tag	7/16	0.576871972458024	3	FACETS	0.793	0.732	0.854	0.793	0.732	0.854	SUBCLONAL	2	TRUE	1	0.726816161462676	3		278	329	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5534805	5534806	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	230	574	0	ENST00000397747.3:c.116_117delinsTT	p.Thr39Ile	p.T39I	ENST00000397747	NM_025239.3	39	aCC/aTT	3/7	0.1642510117396	5	FACETS	0.957	0.897	1	0.638	0.598	0.68	INDETERMINATE	2	TRUE	2	0.726816161462676	5		574	691	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229651	98229652	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	A	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	202	314	1	ENST00000331920.6:c.2306_2307delinsT	p.Thr769IlefsTer3	p.T769Ifs*3	ENST00000331920	NM_000264.3	769	aCC/aT	15/24	NA	2	FACETS	0.792	0.748	0.835			1	INDETERMINATE	2	TRUE	NA	0.726816161462676	2		315	351	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417370	139417370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs553542677	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	506	929	1	ENST00000277541.6:c.674C>T	p.Ser225Leu	p.S225L	ENST00000277541	NM_017617.3	225	tCg/tTg	4/34	0.642322305849841	2	FACETS	0.897	0.869	0.925	0.897	0.869	0.925	CLONAL	2	TRUE	0	0.726816161462676	2		930	776	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411137	63411137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	275	317	0	ENST00000330258.3:c.2030C>T	p.Ser677Phe	p.S677F	ENST00000330258	NM_152424.3	677	tCc/tTc	2/2	0.726816161462676	2	FACETS	0.968	0.929	1			1	CLONAL	2	TRUE	NA	0.726816161462676	2		317	391	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645465	215645465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	116	693	0	ENST00000260947.4:c.1133G>A	p.Arg378Lys	p.R378K	ENST00000260947	NM_000465.2	378	aGg/aAg	4/11	0.726816161462676	3	FACETS	0.584	0.527	0.645	0.292	0.263	0.323	SUBCLONAL	1	TRUE	1	0.726816161462676	3		693	745	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	51	354	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.235005908248492	2		354	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs28934577	NA	P-0026172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	86	576	1	ENST00000269305.4:c.770T>A	p.Leu257Gln	p.L257Q	ENST00000269305	NM_001126112.2	257	cTg/cAg	7/11	0.214661795811859	1	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	0	0.235005908248492	1		577	639	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971088	21971088	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	33	581	0	ENST00000304494.5:c.270C>G	p.Phe90Leu	p.F90L	ENST00000304494	NM_000077.4	90	ttC/ttG	2/3	1	2	FACETS	0.612	0.498	0.741	0.612	0.498	0.741	SUBCLONAL	1	TRUE	1	0.235005908248492	2		581	459	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971144	21971144	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	33	314	0	ENST00000304494.5:c.214T>G	p.Cys72Gly	p.C72G	ENST00000304494	NM_000077.4	72	Tgc/Ggc	2/3	1	2	FACETS	0.64	0.521	0.774	0.64	0.521	0.774	SUBCLONAL	1	TRUE	1	0.235005908248492	2		314	439	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970969	21970971	+	stop_gained	Nonsense_Mutation	TNP	AGG	AGG	TGT	novel	NA	P-0026172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	84	518	0	ENST00000304494.5:c.387_389delinsACA	p.Tyr129_Leu130delinsTer	p.Y129_L130delins*	ENST00000304494	NM_000077.4	129	taCCTg/taACAg	2/3	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.235005908248492	2		518	669	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	40	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.852	1	1	0.97	1	CLONAL	2	TRUE	1	0.259370257295218	2		215	153	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0026274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	81	458	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	0.961	0.854	1	1	0.984	1	CLONAL	2	TRUE	1	0.259370257295218	2		458	325	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127920559	127920559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	69	643	0	ENST00000373547.4:c.340C>T	p.His114Tyr	p.H114Y	ENST00000373547	NM_002721.4	114	Cat/Tat	4/7	1	2	FACETS	0.993	0.866	1	0.993	0.866	1	CLONAL	1	TRUE	1	0.259370257295218	2		643	536	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149002	119149002	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs755557498	NA	P-0026274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	105	551	0	ENST00000264033.4:c.1222T>C	p.Trp408Arg	p.W408R	ENST00000264033	NM_005188.3	408	Tgg/Cgg	8/16	0.259370257295218	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.259370257295218	1		551	549	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913514	NA	P-0026274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	93	526	1	ENST00000288135.5:c.2466T>A	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaA	17/21	1	2	FACETS	0.758	0.677	0.844	1	0.981	1	SUBCLONAL	2	TRUE	1	0.259370257295218	2		527	473	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742054	145742054	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748466411	NA	P-0026274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	56	726	0	ENST00000428558.2:c.449C>T	p.Ser150Phe	p.S150F	ENST00000428558	NM_004260.3	150	tCc/tTc	5/22	0.142956281902783	3	FACETS	0.765	0.654	0.885	0.255	0.218	0.295	INDETERMINATE	1	TRUE	0	0.259370257295218	3		726	638	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024503	31024503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1470476757	NA	P-0026274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	160	531	0	ENST00000375687.4:c.3988C>T	p.Pro1330Ser	p.P1330S	ENST00000375687	NM_015338.5	1330	Cct/Tct	13/13	1	2	FACETS	0.885	0.814	0.959	1	0.991	1	CLONAL	2	TRUE	1	0.259370257295218	2		531	697	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857172	9857172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555481986	NA	P-0026274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	33	517	0	ENST00000330684.3:c.4229C>T	p.Ser1410Leu	p.S1410L	ENST00000330684	NM_001134407.1	1410	tCg/tTg	13/13	1	2	FACETS	0.476	0.387	0.576	0.476	0.387	0.576	SUBCLONAL	1	TRUE	1	0.259370257295218	2		517	535	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518854	187518854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1263240063	NA	P-0026274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	40	523	0	ENST00000441802.2:c.12350C>T	p.Ser4117Leu	p.S4117L	ENST00000441802	NM_005245.3	4117	tCg/tTg	24/27	1	2	FACETS	0.505	0.419	0.601	0.505	0.419	0.601	SUBCLONAL	1	TRUE	1	0.259370257295218	2		523	611	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610078	43610078	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536038262	NA	P-0026274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	63	588	2	ENST00000355710.3:c.2030G>A	p.Arg677Gln	p.R677Q	ENST00000355710	NM_020975.4	677	cGg/cAg	11/20	1	2	FACETS	0.807	0.698	0.925	0.807	0.698	0.925	CLONAL	1	TRUE	1	0.259370257295218	2		590	602	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437443	110437443	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753666571	NA	P-0026274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	30	396	0	ENST00000375856.3:c.958C>T	p.Pro320Ser	p.P320S	ENST00000375856	NM_003749.2	320	Ccc/Tcc	1/2	1	2	FACETS	0.756	0.611	0.92	0.756	0.611	0.92	CLONAL	1	TRUE	1	0.259370257295218	2		396	306	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032077	10032077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	103	612	0	ENST00000330684.3:c.746C>T	p.Thr249Ile	p.T249I	ENST00000330684	NM_001134407.1	249	aCc/aTc	3/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.259370257295218	2		612	560	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129397	30129397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764219989	NA	P-0026274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	50	622	3	ENST00000263025.4:c.631C>T	p.Arg211Trp	p.R211W	ENST00000263025	NM_002746.2	211	Cgg/Tgg	4/9	1	2	FACETS	0.647	0.548	0.755	0.647	0.548	0.755	SUBCLONAL	1	TRUE	1	0.259370257295218	2		625	596	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262616	39262616	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779162761	NA	P-0026274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	29	644	0	ENST00000402219.2:c.890C>T	p.Ser297Leu	p.S297L	ENST00000402219	NM_005633.3	297	tCg/tTg	7/23	0.148415390513697	2	FACETS	0.38	0.304	0.467	0.19	0.152	0.234	INDETERMINATE	1	TRUE	0	0.259370257295218	2		644	588	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99160399	99160399	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	51	598	3	ENST00000074304.5:c.878A>T	p.Gln293Leu	p.Q293L	ENST00000074304	NM_001134224.1	293	cAa/cTa	11/26	0.148415390513697	2	FACETS	0.618	0.525	0.721	0.309	0.262	0.361	INDETERMINATE	1	TRUE	0	0.259370257295218	2		601	636	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198283274	198283274	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	27	605	0	ENST00000335508.6:c.454T>C	p.Tyr152His	p.Y152H	ENST00000335508	NM_012433.2	152	Tac/Cac	5/25	0.148415390513697	2	FACETS	0.363	0.288	0.45	0.182	0.144	0.225	INDETERMINATE	1	TRUE	0	0.259370257295218	2		605	573	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566759	212566759	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	98	423	0	ENST00000342788.4:c.1422G>A	p.Trp474Ter	p.W474*	ENST00000342788	NM_005235.2	474	tgG/tgA	12/28	0.148415390513697	2	FACETS	1	0.98	1	0.725	0.649	0.806	INDETERMINATE	1	TRUE	0	0.259370257295218	2		423	521	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400176	41400176	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	108	582	0	ENST00000373198.4:c.583T>G	p.Phe195Val	p.F195V	ENST00000373198	NM_133170.3	195	Ttt/Gtt	5/32	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.259370257295218	2		582	693	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397727	49397727	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	156	629	1	ENST00000418115.1:c.497G>A	p.Gly166Glu	p.G166E	ENST00000418115	NM_001664.2	166	gGa/gAa	5/5	1	2	FACETS	0.78	0.715	0.848	1	0.989	1	SUBCLONAL	2	TRUE	1	0.259370257295218	2		630	771	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281184	142281184	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	85	529	0	ENST00000350721.4:c.1060C>T	p.Leu354Phe	p.L354F	ENST00000350721	NM_001184.3	354	Ctt/Ttt	4/47	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.259370257295218	2		529	573	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456518	189456518	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	101	570	0	ENST00000264731.3:c.279G>A	p.Met93Ile	p.M93I	ENST00000264731	NM_003722.4	93	atG/atA	3/14	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.259370257295218	2		570	701	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683951	117683951	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	27	634	0	ENST00000368508.3:c.3196G>A	p.Glu1066Lys	p.E1066K	ENST00000368508	NM_002944.2	1066	Gaa/Aaa	21/43	0.239232528953059	1	FACETS	0.357	0.283	0.441	0.357	0.283	0.441	SUBCLONAL	1	TRUE	0	0.259370257295218	1		634	508	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415600	152415600	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	56	688	1	ENST00000206249.3:c.1450G>A	p.Asp484Asn	p.D484N	ENST00000206249	NM_000125.3	484	Gac/Aac	7/8	0.239232528953059	1	FACETS	0.654	0.56	0.756	0.654	0.56	0.756	SUBCLONAL	1	TRUE	0	0.259370257295218	1		689	575	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397829	116397832	+	splice_donor_variant,intron_variant	Splice_Site	DEL	GTGT	GTGT	TA	novel	NA	P-0026274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	35	519	2	ENST00000397752.3:c.2102+1_2102+4delinsTA		p.X701_splice	ENST00000397752	NM_000245.2	701			0.171745492573507	3	FACETS	0.569	0.465	0.685	0.284	0.232	0.343	SUBCLONAL	1	TRUE	1	0.259370257295218	3		521	536	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026274-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	177	215	0				ENST00000310581	NM_198253.2	-/1132			0.840804088516307	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	2	0.840804088516307	4		215	313	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0026274-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	255	458	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.840804088516307	3	FACETS	0.977	0.929	1	0.977	0.929	1	CLONAL	2	TRUE	1	0.840804088516307	3		458	441	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127920559	127920559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026274-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	460	643	0	ENST00000373547.4:c.340C>T	p.His114Tyr	p.H114Y	ENST00000373547	NM_002721.4	114	Cat/Tat	4/7	0.840804088516307	3	FACETS	0.977	0.942	1	0.977	0.942	1	CLONAL	2	TRUE	1	0.840804088516307	3		643	795	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149002	119149002	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs755557498	NA	P-0026274-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	472	551	0	ENST00000264033.4:c.1222T>C	p.Trp408Arg	p.W408R	ENST00000264033	NM_005188.3	408	Tgg/Cgg	8/16	0.840804088516307	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.840804088516307	2		551	540	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913514	NA	P-0026274-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	327	526	1	ENST00000288135.5:c.2466T>A	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaA	17/21	0.840804088516307	3	FACETS	0.981	0.939	1	0.981	0.939	1	CLONAL	2	TRUE	1	0.840804088516307	3		527	563	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742054	145742054	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748466411	NA	P-0026274-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	496	726	0	ENST00000428558.2:c.449C>T	p.Ser150Phe	p.S150F	ENST00000428558	NM_004260.3	150	tCc/tTc	5/22	0.840804088516307	6	FACETS	0.99	0.946	1	0.495	0.473	0.517	CLONAL	2	TRUE	2	0.840804088516307	6		726	1598	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024503	31024503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1470476757	NA	P-0026274-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	439	531	0	ENST00000375687.4:c.3988C>T	p.Pro1330Ser	p.P1330S	ENST00000375687	NM_015338.5	1330	Cct/Tct	13/13	0.840804088516307	4	FACETS	0.956	0.916	0.997	0.956	0.916	0.997	CLONAL	2	TRUE	2	0.840804088516307	4		531	1005	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857172	9857172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555481986	NA	P-0026274-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	185	517	0	ENST00000330684.3:c.4229C>T	p.Ser1410Leu	p.S1410L	ENST00000330684	NM_001134407.1	1410	tCg/tTg	13/13	0.840804088516307	3	FACETS	0.939	0.87	1	0.469	0.435	0.505	CLONAL	1	TRUE	1	0.840804088516307	3		517	666	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518854	187518854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1263240063	NA	P-0026274-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	172	523	0	ENST00000441802.2:c.12350C>T	p.Ser4117Leu	p.S4117L	ENST00000441802	NM_005245.3	4117	tCg/tTg	24/27	0.840804088516307	3	FACETS	0.83	0.766	0.897	0.415	0.383	0.449	CLONAL	1	TRUE	1	0.840804088516307	3		523	700	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610078	43610078	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536038262	NA	P-0026274-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	262	588	2	ENST00000355710.3:c.2030G>A	p.Arg677Gln	p.R677Q	ENST00000355710	NM_020975.4	677	cGg/cAg	11/20	0.840804088516307	3	FACETS	1	0.959	1	0.513	0.482	0.545	CLONAL	1	TRUE	1	0.840804088516307	3		590	863	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437443	110437443	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753666571	NA	P-0026274-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	155	396	0	ENST00000375856.3:c.958C>T	p.Pro320Ser	p.P320S	ENST00000375856	NM_003749.2	320	Ccc/Tcc	1/2	0.840804088516307	3	FACETS	1	0.966	1	0.542	0.5	0.585	CLONAL	1	TRUE	1	0.840804088516307	3		396	483	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032077	10032077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026274-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	460	612	0	ENST00000330684.3:c.746C>T	p.Thr249Ile	p.T249I	ENST00000330684	NM_001134407.1	249	aCc/aTc	3/13	0.840804088516307	3	FACETS	0.974	0.938	1	0.974	0.938	1	CLONAL	2	TRUE	1	0.840804088516307	3		612	798	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129397	30129397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764219989	NA	P-0026274-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	233	622	3	ENST00000263025.4:c.631C>T	p.Arg211Trp	p.R211W	ENST00000263025	NM_002746.2	211	Cgg/Tgg	4/9	0.840804088516307	3	FACETS	0.946	0.885	1	0.473	0.442	0.505	CLONAL	1	TRUE	1	0.840804088516307	3		625	832	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262616	39262616	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779162761	NA	P-0026274-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	193	644	0	ENST00000402219.2:c.890C>T	p.Ser297Leu	p.S297L	ENST00000402219	NM_005633.3	297	tCg/tTg	7/23	0.55013409427851	4	FACETS	1	0.985	1	0.408	0.378	0.438	CLONAL	1	TRUE	1	0.840804088516307	4		644	691	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99160399	99160399	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026274-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	271	598	3	ENST00000074304.5:c.878A>T	p.Gln293Leu	p.Q293L	ENST00000074304	NM_001134224.1	293	cAa/cTa	11/26	0.55013409427851	4	FACETS	1	0.992	1	0.457	0.43	0.485	CLONAL	1	TRUE	1	0.840804088516307	4		601	865	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198283274	198283274	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026274-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	244	605	0	ENST00000335508.6:c.454T>C	p.Tyr152His	p.Y152H	ENST00000335508	NM_012433.2	152	Tac/Cac	5/25	0.55013409427851	4	FACETS	1	0.991	1	0.444	0.416	0.473	CLONAL	1	TRUE	1	0.840804088516307	4		605	802	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566759	212566759	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026274-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	365	423	0	ENST00000342788.4:c.1422G>A	p.Trp474Ter	p.W474*	ENST00000342788	NM_005235.2	474	tgG/tgA	12/28	0.55013409427851	4	FACETS	0.847	0.812	0.881	0.847	0.812	0.881	CLONAL	3	TRUE	1	0.840804088516307	4		423	629	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400176	41400176	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026274-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	411	582	0	ENST00000373198.4:c.583T>G	p.Phe195Val	p.F195V	ENST00000373198	NM_133170.3	195	Ttt/Gtt	5/32	0.840804088516307	4	FACETS	0.935	0.894	0.977	0.935	0.894	0.977	CLONAL	2	TRUE	2	0.840804088516307	4		582	962	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397727	49397727	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026274-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	263	629	1	ENST00000418115.1:c.497G>A	p.Gly166Glu	p.G166E	ENST00000418115	NM_001664.2	166	gGa/gAa	5/5	0.840804088516307	3	FACETS	1	0.967	1	0.521	0.489	0.553	CLONAL	1	TRUE	1	0.840804088516307	3		630	853	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281184	142281184	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026274-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	385	529	0	ENST00000350721.4:c.1060C>T	p.Leu354Phe	p.L354F	ENST00000350721	NM_001184.3	354	Ctt/Ttt	4/47	0.840804088516307	3	FACETS	0.964	0.925	1	0.964	0.925	1	CLONAL	2	TRUE	1	0.840804088516307	3		529	675	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456518	189456518	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026274-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	237	570	0	ENST00000264731.3:c.279G>A	p.Met93Ile	p.M93I	ENST00000264731	NM_003722.4	93	atG/atA	3/14	1	2	FACETS	0.993	0.934	1	0.993	0.934	1	CLONAL	1	TRUE	1	0.840804088516307	2		570	568	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683951	117683951	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026274-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	208	634	0	ENST00000368508.3:c.3196G>A	p.Glu1066Lys	p.E1066K	ENST00000368508	NM_002944.2	1066	Gaa/Aaa	21/43	1	2	FACETS	0.964	0.904	1	0.964	0.904	1	CLONAL	1	TRUE	1	0.840804088516307	2		634	513	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415600	152415600	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026274-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	264	688	1	ENST00000206249.3:c.1450G>A	p.Asp484Asn	p.D484N	ENST00000206249	NM_000125.3	484	Gac/Aac	7/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.840804088516307	2		689	604	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397829	116397832	+	splice_donor_variant,intron_variant	Splice_Site	DEL	GTGT	GTGT	TA	novel	NA	P-0026274-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	244	519	2	ENST00000397752.3:c.2102+1_2102+4delinsTA		p.X701_splice	ENST00000397752	NM_000245.2	701			0.840804088516307	5	FACETS	0.861	0.808	0.916	0.574	0.538	0.611	CLONAL	2	TRUE	2	0.840804088516307	5		521	762	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0026281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	47	282	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.755	0.641	0.88	1	0.962	1	SUBCLONAL	2	TRUE	1	0.207468614483073	2		282	300	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0026281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	111	351	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.207468614483073	2		351	886	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0026281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	15	499	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.22	0.16	0.293	0.22	0.16	0.293	SUBCLONAL	1	TRUE	1	0.207468614483073	2		499	657	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0026281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	55	415	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	0.207468614483073	2		415	429	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43766952	43766952	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	57	441	0	ENST00000382044.4:c.1099C>G	p.Leu367Val	p.L367V	ENST00000382044	NM_001141980.1	367	Ctt/Gtt	10/28	1	2	FACETS	0.928	0.796	1	0.928	0.796	1	CLONAL	1	TRUE	1	0.207468614483073	2		441	592	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971187	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0026488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	534	418	0	ENST00000304494.5:c.171_172delinsTT	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	57	gcCCga/gcTTga	2/3	0.808330233813586	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.808330233813586	2		418	646	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295253	+	upstream_gene_variant	5'Flank	ONP	GAGG	GAGG	AAGA	novel	NA	P-0026488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	609	480	1				ENST00000310581	NM_198253.2	-/1132			0.808330233813586	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.808330233813586	3		481	1016	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727453	66727453	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397516790	NA	P-0026488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	476	421	0	ENST00000307102.5:c.169A>G	p.Lys57Glu	p.K57E	ENST00000307102	NM_002755.3	57	Aag/Gag	2/11	0.75977854391744	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.808330233813586	4		421	1009	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021422	42021422	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	482	498	0	ENST00000219905.7:c.3718C>T	p.Arg1240Ter	p.R1240*	ENST00000219905	NM_001164273.1	1240	Cga/Tga	11/24	0.75977854391744	4	FACETS	0.953	0.913	0.992	0.953	0.913	0.992	CLONAL	2	TRUE	2	0.808330233813586	4		498	1132	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112362	115112362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1440126149	NA	P-0026488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	478	425	0	ENST00000257566.3:c.1378G>A	p.Glu460Lys	p.E460K	ENST00000257566	NM_016569.3	460	Gag/Aag	7/8	0.808330233813586	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.808330233813586	3		425	826	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161294	55161294	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs764265933	NA	P-0026488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	182	305	0	ENST00000257290.5:c.3125C>T	p.Ser1042Leu	p.S1042L	ENST00000257290	NM_006206.4	1042	tCg/tTg	23/23	0.808330233813586	3	FACETS	1	0.967	1	0.536	0.497	0.576	CLONAL	1	TRUE	1	0.808330233813586	3		305	590	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163315582	163315582	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	301	373	1	ENST00000271452.3:c.922G>A	p.Glu308Lys	p.E308K	ENST00000271452	NM_145697.2	308	Gaa/Aaa	11/14	0.808330233813586	5	FACETS	0.96	0.915	1	0.96	0.915	1	CLONAL	3	TRUE	2	0.808330233813586	5		374	572	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104353474	104353474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	323	616	0	ENST00000369902.3:c.679C>T	p.Pro227Ser	p.P227S	ENST00000369902	NM_016169.3	227	Cct/Tct	5/12	1	2	FACETS	0.978	0.928	1	0.978	0.928	1	CLONAL	1	TRUE	1	0.808330233813586	2		616	817	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169197	119169197	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201620100	NA	P-0026488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	241	462	0	ENST00000264033.4:c.2381C>T	p.Ser794Phe	p.S794F	ENST00000264033	NM_005188.3	794	tCt/tTt	15/16	1	2	FACETS	0.984	0.926	1	0.984	0.926	1	CLONAL	1	TRUE	1	0.808330233813586	2		462	606	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415920	49415920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	350	344	0	ENST00000301067.7:c.16427C>T	p.Ser5476Phe	p.S5476F	ENST00000301067	NM_003482.3	5476	tCc/tTc	53/54	0.808330233813586	3	FACETS	0.916	0.875	0.956	0.916	0.875	0.956	CLONAL	2	TRUE	1	0.808330233813586	3		344	664	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434310	49434310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	948	787	2	ENST00000301067.7:c.7243C>T	p.Pro2415Ser	p.P2415S	ENST00000301067	NM_003482.3	2415	Cct/Tct	31/54	0.808330233813586	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.808330233813586	3		789	1604	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913395	28913395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	260	552	0	ENST00000282397.4:c.2398G>A	p.Asp800Asn	p.D800N	ENST00000282397	NM_002019.4	800	Gac/Aac	17/30	0.808330233813586	3	FACETS	0.952	0.893	1	0.476	0.446	0.506	CLONAL	1	TRUE	1	0.808330233813586	3		552	949	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059056	42059056	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	313	337	0	ENST00000219905.7:c.8776C>T	p.Leu2926Phe	p.L2926F	ENST00000219905	NM_001164273.1	2926	Ctt/Ttt	24/24	0.75977854391744	4	FACETS	0.94	0.892	0.988	0.94	0.892	0.988	CLONAL	2	TRUE	2	0.808330233813586	4		337	745	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779313	3779313	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	569	623	1	ENST00000262367.5:c.5735C>T	p.Ser1912Leu	p.S1912L	ENST00000262367	NM_004380.2	1912	tCa/tTa	31/31	0.808330233813586	3	FACETS	0.942	0.91	0.974	0.942	0.91	0.974	CLONAL	2	TRUE	1	0.808330233813586	3		624	1049	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992648	72992648	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	405	389	0	ENST00000268489.5:c.1397A>T	p.Glu466Val	p.E466V	ENST00000268489	NM_006885.3	466	gAa/gTa	2/10	0.808330233813586	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.808330233813586	3		389	679	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605057	46605057	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201157854	NA	P-0026488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	874	766	1	ENST00000263734.3:c.1274C>T	p.Ser425Leu	p.S425L	ENST00000263734	NM_001430.4	425	tCa/tTa	10/16	0.808330233813586	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.808330233813586	3		767	1513	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251649	212251649	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	180	376	0	ENST00000342788.4:c.3410C>A	p.Pro1137Gln	p.P1137Q	ENST00000342788	NM_005235.2	1137	cCa/cAa	27/28	0.765249022793037	2	FACETS	0.882	0.82	0.945	0.441	0.41	0.473	CLONAL	1	TRUE	0	0.808330233813586	2		376	505	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727139	40727140	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0026488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	462	614	2	ENST00000373198.4:c.3824_3825delinsTT	p.Thr1275Ile	p.T1275I	ENST00000373198	NM_133170.3	1275	aCC/aTT	28/32	0.75977854391744	4	FACETS	0.822	0.786	0.858	0.822	0.786	0.858	CLONAL	2	TRUE	2	0.808330233813586	4		616	1258	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944429	40944429	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	506	554	0	ENST00000373198.4:c.2073G>A	p.Trp691Ter	p.W691*	ENST00000373198	NM_133170.3	691	tgG/tgA	12/32	0.75977854391744	4	FACETS	0.9	0.863	0.937	0.9	0.863	0.937	CLONAL	2	TRUE	2	0.808330233813586	4		554	1258	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130520	29130520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141568342	NA	P-0026488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	504	436	0	ENST00000328354.6:c.190G>A	p.Glu64Lys	p.E64K	ENST00000328354	NM_007194.3	64	Gag/Aag	2/15	0.808330233813586	3	FACETS	0.973	0.938	1	0.973	0.938	1	CLONAL	2	TRUE	1	0.808330233813586	3		436	900	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431005	181431005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	400	649	0	ENST00000325404.1:c.857C>T	p.Pro286Leu	p.P286L	ENST00000325404	NM_003106.3	286	cCc/cTc	1/1	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.808330233813586	2		649	906	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441390	149441390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	324	606	0	ENST00000286301.3:c.1649G>A	p.Trp550Ter	p.W550*	ENST00000286301	NM_005211.3	550	tGg/tAg	12/22	0.808330233813586	3	FACETS	1	0.957	1	0.507	0.479	0.536	CLONAL	1	TRUE	1	0.808330233813586	3		606	1110	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275812	38275813	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0026488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	823	675	1	ENST00000425967.3:c.1456_1457delinsTT	p.Pro486Phe	p.P486F	ENST00000425967	NM_001174067.1	486	CCc/TTc	11/19	0.781237295765006	4	FACETS	0.96	0.936	0.984	0.96	0.936	0.984	CLONAL	3	TRUE	1	0.808330233813586	4		676	1278	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372150	55372151	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0026488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	296	582	3	ENST00000297316.4:c.840_841delinsAT	p.Pro281Ser	p.P281S	ENST00000297316	NM_022454.3	280	ggTCcc/ggATcc	2/2	0.781237295765006	4	FACETS	1	0.97	1	0.35	0.328	0.371	CLONAL	1	TRUE	1	0.808330233813586	4		585	1263	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934313	68934313	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	238	619	0	ENST00000288368.4:c.379G>A	p.Glu127Lys	p.E127K	ENST00000288368	NM_024870.2	127	Gag/Aag	4/40	0.781237295765006	4	FACETS	0.877	0.818	0.939	0.292	0.272	0.313	CLONAL	1	TRUE	1	0.808330233813586	4		619	1214	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971187	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0026488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	380	418	0	ENST00000304494.5:c.171_172delinsTT	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	57	gcCCga/gcTTga	2/3	0.698912916836568	2	FACETS	0.912	0.878	0.946	0.912	0.878	0.946	CLONAL	2	TRUE	0	0.698912916836568	2		418	596	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295253	+	upstream_gene_variant	5'Flank	ONP	GAGG	GAGG	AAGA	novel	NA	P-0026488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	473	480	1				ENST00000310581	NM_198253.2	-/1132			0.698912916836568	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.698912916836568	3		481	836	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727453	66727453	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397516790	NA	P-0026488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	351	421	0	ENST00000307102.5:c.169A>G	p.Lys57Glu	p.K57E	ENST00000307102	NM_002755.3	57	Aag/Gag	2/11	0.65877489541444	4	FACETS	0.961	0.914	1	0.961	0.914	1	CLONAL	2	TRUE	2	0.698912916836568	4		421	888	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021422	42021422	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	365	498	0	ENST00000219905.7:c.3718C>T	p.Arg1240Ter	p.R1240*	ENST00000219905	NM_001164273.1	1240	Cga/Tga	11/24	0.65877489541444	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.698912916836568	4		498	828	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112362	115112362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1440126149	NA	P-0026488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	376	425	0	ENST00000257566.3:c.1378G>A	p.Glu460Lys	p.E460K	ENST00000257566	NM_016569.3	460	Gag/Aag	7/8	0.529489105642859	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.698912916836568	3		425	716	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161294	55161294	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs764265933	NA	P-0026488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	158	305	0	ENST00000257290.5:c.3125C>T	p.Ser1042Leu	p.S1042L	ENST00000257290	NM_006206.4	1042	tCg/tTg	23/23	0.234532882744059	4	FACETS	1	0.989	1	0.744	0.687	0.804	INDETERMINATE	1	TRUE	2	0.698912916836568	4		305	516	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163315582	163315582	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	219	373	1	ENST00000271452.3:c.922G>A	p.Glu308Lys	p.E308K	ENST00000271452	NM_145697.2	308	Gaa/Aaa	11/14	0.57984695835817	5	FACETS	1	0.989	1	0.824	0.774	0.875	CLONAL	2	TRUE	2	0.698912916836568	5		374	519	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104353474	104353474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	264	616	0	ENST00000369902.3:c.679C>T	p.Pro227Ser	p.P227S	ENST00000369902	NM_016169.3	227	Cct/Tct	5/12	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.698912916836568	2		616	753	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169197	119169197	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201620100	NA	P-0026488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	180	462	0	ENST00000264033.4:c.2381C>T	p.Ser794Phe	p.S794F	ENST00000264033	NM_005188.3	794	tCt/tTt	15/16	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.698912916836568	2		462	508	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415920	49415920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	215	344	0	ENST00000301067.7:c.16427C>T	p.Ser5476Phe	p.S5476F	ENST00000301067	NM_003482.3	5476	tCc/tTc	53/54	0.529489105642859	3	FACETS	0.876	0.824	0.928	0.876	0.824	0.928	CLONAL	2	TRUE	1	0.698912916836568	3		344	474	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434310	49434310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	630	787	2	ENST00000301067.7:c.7243C>T	p.Pro2415Ser	p.P2415S	ENST00000301067	NM_003482.3	2415	Cct/Tct	31/54	0.529489105642859	3	FACETS	0.904	0.873	0.936	0.904	0.873	0.936	CLONAL	2	TRUE	1	0.698912916836568	3		789	1345	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913395	28913395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	184	552	0	ENST00000282397.4:c.2398G>A	p.Asp800Asn	p.D800N	ENST00000282397	NM_002019.4	800	Gac/Aac	17/30	0.698912916836568	3	FACETS	0.839	0.775	0.905	0.419	0.387	0.453	CLONAL	1	TRUE	1	0.698912916836568	3		552	847	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059056	42059056	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	235	337	0	ENST00000219905.7:c.8776C>T	p.Leu2926Phe	p.L2926F	ENST00000219905	NM_001164273.1	2926	Ctt/Ttt	24/24	0.65877489541444	4	FACETS	0.973	0.915	1	0.973	0.915	1	CLONAL	2	TRUE	2	0.698912916836568	4		337	587	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779313	3779313	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	500	623	1	ENST00000262367.5:c.5735C>T	p.Ser1912Leu	p.S1912L	ENST00000262367	NM_004380.2	1912	tCa/tTa	31/31	0.698912916836568	3	FACETS	0.983	0.946	1	0.983	0.946	1	CLONAL	2	TRUE	1	0.698912916836568	3		624	982	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992648	72992648	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	328	389	0	ENST00000268489.5:c.1397A>T	p.Glu466Val	p.E466V	ENST00000268489	NM_006885.3	466	gAa/gTa	2/10	0.698912916836568	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.698912916836568	3		389	588	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605057	46605057	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201157854	NA	P-0026488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	623	766	1	ENST00000263734.3:c.1274C>T	p.Ser425Leu	p.S425L	ENST00000263734	NM_001430.4	425	tCa/tTa	10/16	0.684044425740779	3	FACETS	0.988	0.955	1	0.988	0.955	1	CLONAL	2	TRUE	1	0.698912916836568	3		767	1217	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251649	212251649	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	199	376	0	ENST00000342788.4:c.3410C>A	p.Pro1137Gln	p.P1137Q	ENST00000342788	NM_005235.2	1137	cCa/cAa	27/28	0.374676624562198	3	FACETS	1	0.99	1	0.457	0.426	0.488	INDETERMINATE	1	TRUE	0	0.698912916836568	3		376	561	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727139	40727140	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0026488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	417	614	2	ENST00000373198.4:c.3824_3825delinsTT	p.Thr1275Ile	p.T1275I	ENST00000373198	NM_133170.3	1275	aCC/aTT	28/32	0.69559526908702	4	FACETS	0.834	0.794	0.873	0.834	0.794	0.873	CLONAL	2	TRUE	2	0.698912916836568	4		616	1216	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944429	40944429	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	475	554	0	ENST00000373198.4:c.2073G>A	p.Trp691Ter	p.W691*	ENST00000373198	NM_133170.3	691	tgG/tgA	12/32	0.69559526908702	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	2	0.698912916836568	4		554	1153	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130520	29130520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141568342	NA	P-0026488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	438	436	0	ENST00000328354.6:c.190G>A	p.Glu64Lys	p.E64K	ENST00000328354	NM_007194.3	64	Gag/Aag	2/15	0.684044425740779	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.698912916836568	3		436	839	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431005	181431005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	276	649	0	ENST00000325404.1:c.857C>T	p.Pro286Leu	p.P286L	ENST00000325404	NM_003106.3	286	cCc/cTc	1/1	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.698912916836568	2		649	780	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441390	149441390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	248	606	0	ENST00000286301.3:c.1649G>A	p.Trp550Ter	p.W550*	ENST00000286301	NM_005211.3	550	tGg/tAg	12/22	0.698912916836568	3	FACETS	0.942	0.881	1	0.471	0.44	0.502	CLONAL	1	TRUE	1	0.698912916836568	3		606	1017	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275812	38275813	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0026488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	578	675	1	ENST00000425967.3:c.1456_1457delinsTT	p.Pro486Phe	p.P486F	ENST00000425967	NM_001174067.1	486	CCc/TTc	11/19	0.50082682578821	4	FACETS	0.915	0.885	0.945	0.915	0.885	0.945	CLONAL	3	TRUE	1	0.698912916836568	4		676	1024	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372150	55372151	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0026488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	201	582	3	ENST00000297316.4:c.840_841delinsAT	p.Pro281Ser	p.P281S	ENST00000297316	NM_022454.3	280	ggTCcc/ggATcc	2/2	0.50082682578821	4	FACETS	1	0.944	1	0.34	0.315	0.366	CLONAL	1	TRUE	1	0.698912916836568	4		585	957	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934313	68934313	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	146	619	0	ENST00000288368.4:c.379G>A	p.Glu127Lys	p.E127K	ENST00000288368	NM_024870.2	127	Gag/Aag	4/40	0.50082682578821	4	FACETS	0.91	0.831	0.992	0.303	0.277	0.331	CLONAL	1	TRUE	1	0.698912916836568	4		619	780	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285222	212285222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	33	496	1	ENST00000342788.4:c.3079G>A	p.Ala1027Thr	p.A1027T	ENST00000342788	NM_005235.2	1027	Gct/Act	25/28	0.374676624562198	3	FACETS	0.313	0.255	0.379	0.104	0.085	0.127	INDETERMINATE	1	TRUE	0	0.698912916836568	3		497	407	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372151	55372151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	198	585	0	ENST00000297316.4:c.841C>T	p.Pro281Ser	p.P281S	ENST00000297316	NM_022454.3	281	Ccc/Tcc	2/2	0.50082682578821	4	FACETS	1	0.942	1	0.34	0.315	0.366	CLONAL	1	TRUE	1	0.698912916836568	4		585	944	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729162	66729162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519732	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	68	668	0	ENST00000307102.5:c.370C>T	p.Pro124Ser	p.P124S	ENST00000307102	NM_002755.3	124	Ccg/Tcg	3/11	1	2	FACETS	0.502	0.435	0.575	0.502	0.435	0.575	SUBCLONAL	1	TRUE	1	0.263000998481622	2		668	1030	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	71	720	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.567	0.493	0.646	0.567	0.493	0.646	SUBCLONAL	1	TRUE	1	0.263000998481622	2		722	953	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554840	187554840	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	27	309	0	ENST00000441802.2:c.4321C>T	p.Gln1441Ter	p.Q1441*	ENST00000441802	NM_005245.3	1441	Cag/Tag	7/27	1	2	FACETS	0.441	0.35	0.545	0.441	0.35	0.545	SUBCLONAL	1	TRUE	1	0.263000998481622	2		309	466	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	58	173	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.663	0.569	0.766	0.663	0.569	0.766	SUBCLONAL	1	TRUE	1	0.263000998481622	2		174	665	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434325	49434325	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	106	922	0	ENST00000301067.7:c.7228C>T	p.Arg2410Ter	p.R2410*	ENST00000301067	NM_003482.3	2410	Cga/Tga	31/54	1	2	FACETS	0.634	0.567	0.706	0.634	0.567	0.706	SUBCLONAL	1	TRUE	1	0.263000998481622	2		922	1271	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041824	14041824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	63	429	0	ENST00000311895.7:c.2371C>T	p.Leu791Phe	p.L791F	ENST00000311895	NM_005236.2	791	Ctt/Ttt	11/11	1	2	FACETS	0.769	0.665	0.882	0.769	0.665	0.882	SUBCLONAL	1	TRUE	1	0.263000998481622	2		429	623	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319348	11319348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	59	661	0	ENST00000361445.4:c.119C>T	p.Ala40Val	p.A40V	ENST00000361445	NM_004958.3	40	gCc/gTc	2/58	1	2	FACETS	0.469	0.402	0.543	0.469	0.402	0.543	SUBCLONAL	1	TRUE	1	0.263000998481622	2		661	956	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262742	16262742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769028117	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	37	355	2	ENST00000375759.3:c.10007G>A	p.Arg3336Gln	p.R3336Q	ENST00000375759	NM_015001.2	3336	cGg/cAg	11/15	1	2	FACETS	0.529	0.435	0.634	0.529	0.435	0.634	SUBCLONAL	1	TRUE	1	0.263000998481622	2		357	532	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36823971	36823971	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	78	736	0	ENST00000373129.3:c.211G>A	p.Glu71Lys	p.E71K	ENST00000373129	NM_032017.1	71	Gag/Aag	5/12	1	2	FACETS	0.539	0.472	0.611	0.539	0.472	0.611	SUBCLONAL	1	TRUE	1	0.263000998481622	2		736	1101	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812494	43812495	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	68	591	1	ENST00000372470.3:c.1197_1198delinsAA	p.Glu400Lys	p.E400K	ENST00000372470	NM_005373.2	399	agGGag/agAAag	8/12	1	2	FACETS	0.669	0.581	0.764	0.669	0.581	0.764	SUBCLONAL	1	TRUE	1	0.263000998481622	2		592	773	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799242	45799242	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	36	535	1	ENST00000450313.1:c.191C>T	p.Ala64Val	p.A64V	ENST00000450313	NM_012222.2	64	gCc/gTc	3/16	1	2	FACETS	0.407	0.334	0.49	0.407	0.334	0.49	SUBCLONAL	1	TRUE	1	0.263000998481622	2		536	672	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459287	120459287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	64	534	0	ENST00000256646.2:c.6058G>A	p.Glu2020Lys	p.E2020K	ENST00000256646	NM_024408.3	2020	Gag/Aag	34/34	1	2	FACETS	0.7	0.606	0.803	0.7	0.606	0.803	SUBCLONAL	1	TRUE	1	0.263000998481622	2		534	695	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845330	156845330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	100	777	1	ENST00000524377.1:c.1373C>T	p.Pro458Leu	p.P458L	ENST00000524377	NM_002529.3	458	cCa/cTa	12/17	1	2	FACETS	0.746	0.665	0.833	0.746	0.665	0.833	SUBCLONAL	1	TRUE	1	0.263000998481622	2		778	1019	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162722958	162722958	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	72	724	0	ENST00000367921.3:c.156G>A	p.Trp52Ter	p.W52*	ENST00000367921	NM_006182.2	52	tgG/tgA	4/18	1	2	FACETS	0.54	0.47	0.616	0.54	0.47	0.616	SUBCLONAL	1	TRUE	1	0.263000998481622	2		724	1014	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012892	176012892	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	49	528	0	ENST00000367669.3:c.1484T>G	p.Val495Gly	p.V495G	ENST00000367669	NM_022457.5	495	gTt/gGt	13/20	1	2	FACETS	0.479	0.404	0.561	0.479	0.404	0.561	SUBCLONAL	1	TRUE	1	0.263000998481622	2		528	778	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204513663	204513663	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	30	205	0	ENST00000367182.3:c.673G>A	p.Asp225Asn	p.D225N	ENST00000367182	NM_001278516.1	225	Gat/Aat	9/11	1	2	FACETS	0.588	0.474	0.718	0.588	0.474	0.718	SUBCLONAL	1	TRUE	1	0.263000998481622	2		205	388	SUCCESS
FH	2271	MSKCC	GRCh37	1	241677004	241677004	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	39	460	0	ENST00000366560.3:c.277A>C	p.Ile93Leu	p.I93L	ENST00000366560	NM_000143.3	93	Att/Ctt	3/10	1	2	FACETS	0.422	0.348	0.504	0.422	0.348	0.504	SUBCLONAL	1	TRUE	1	0.263000998481622	2		460	703	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759946	63759946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	39	411	0	ENST00000279873.7:c.599C>T	p.Ser200Phe	p.S200F	ENST00000279873	NM_032199.2	200	tCc/tTc	4/10	1	2	FACETS	0.551	0.456	0.657	0.551	0.456	0.657	SUBCLONAL	1	TRUE	1	0.263000998481622	2		411	538	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717612	89717612	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	55	456	0	ENST00000371953.3:c.637C>T	p.Pro213Ser	p.P213S	ENST00000371953	NM_000314.4	213	Cct/Tct	7/9	1	2	FACETS	0.656	0.56	0.76	0.656	0.56	0.76	SUBCLONAL	1	TRUE	1	0.263000998481622	2		456	638	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903681	114903681	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	64	639	1	ENST00000543371.1:c.686-1G>A		p.X229_splice	ENST00000543371	NM_001198531.1	229			1	2	FACETS	0.563	0.486	0.646	0.563	0.486	0.646	SUBCLONAL	1	TRUE	1	0.263000998481622	2		640	865	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925412	114925412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs573425555	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	97	793	0	ENST00000543371.1:c.1490C>T	p.Pro497Leu	p.P497L	ENST00000543371	NM_001198531.1	497	cCg/cTg	14/14	1	2	FACETS	0.702	0.624	0.785	0.702	0.624	0.785	SUBCLONAL	1	TRUE	1	0.263000998481622	2		793	1051	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925496	114925496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1356807409	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	70	762	0	ENST00000543371.1:c.1574C>T	p.Pro525Leu	p.P525L	ENST00000543371	NM_001198531.1	525	cCc/cTc	14/14	1	2	FACETS	0.553	0.481	0.632	0.553	0.481	0.632	SUBCLONAL	1	TRUE	1	0.263000998481622	2		762	962	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129346	64129346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780738455	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	66	774	0	ENST00000334205.4:c.778C>T	p.Pro260Ser	p.P260S	ENST00000334205	NM_003942.2	260	Ccc/Tcc	8/17	1	2	FACETS	0.495	0.428	0.568	0.495	0.428	0.568	SUBCLONAL	1	TRUE	1	0.263000998481622	2		774	1014	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572026	64572026	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	91	803	1	ENST00000312049.6:c.1613C>A	p.Pro538Gln	p.P538Q	ENST00000312049	NM_130799.2	538	cCa/cAa	10/10	1	2	FACETS	0.604	0.534	0.678	0.604	0.534	0.678	SUBCLONAL	1	TRUE	1	0.263000998481622	2		804	1146	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939797	71939797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376049368	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	92	844	0	ENST00000298229.2:c.424C>T	p.Pro142Ser	p.P142S	ENST00000298229	NM_001567.3	142	Ccc/Tcc	4/28	1	2	FACETS	0.621	0.55	0.697	0.621	0.55	0.697	SUBCLONAL	1	TRUE	1	0.263000998481622	2		844	1127	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125525118	125525118	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	35	376	0	ENST00000428830.2:c.1336-2A>G		p.X446_splice	ENST00000428830	NM_001114121.2	446			1	2	FACETS	0.533	0.437	0.642	0.533	0.437	0.642	SUBCLONAL	1	TRUE	1	0.263000998481622	2		376	499	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398219	25398219	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	45	546	0	ENST00000311936.3:c.100C>T	p.Pro34Ser	p.P34S	ENST00000311936	NM_004985.3	34	Cca/Tca	2/5	1	2	FACETS	0.496	0.416	0.585	0.496	0.416	0.585	SUBCLONAL	1	TRUE	1	0.263000998481622	2		546	690	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243466	46243466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	43	498	0	ENST00000334344.6:c.1819C>T	p.Pro607Ser	p.P607S	ENST00000334344	NM_152641.2	607	Ccc/Tcc	14/21	1	2	FACETS	0.503	0.42	0.596	0.503	0.42	0.596	SUBCLONAL	1	TRUE	1	0.263000998481622	2		498	650	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416618	49416618	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	70	547	1	ENST00000301067.7:c.16093C>T	p.Gln5365Ter	p.Q5365*	ENST00000301067	NM_003482.3	5365	Cag/Tag	51/54	1	2	FACETS	0.623	0.542	0.71	0.623	0.542	0.71	SUBCLONAL	1	TRUE	1	0.263000998481622	2		548	855	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424179	49424179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	60	488	1	ENST00000301067.7:c.13883C>T	p.Pro4628Leu	p.P4628L	ENST00000301067	NM_003482.3	4628	cCc/cTc	42/54	1	2	FACETS	0.759	0.654	0.874	0.759	0.654	0.874	SUBCLONAL	1	TRUE	1	0.263000998481622	2		489	601	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490964	56490964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	68	724	1	ENST00000267101.3:c.2410G>A	p.Gly804Arg	p.G804R	ENST00000267101	NM_001982.3	804	Ggg/Agg	20/28	1	2	FACETS	0.546	0.474	0.625	0.546	0.474	0.625	SUBCLONAL	1	TRUE	1	0.263000998481622	2		725	947	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859583	57859583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	70	636	0	ENST00000228682.2:c.637G>A	p.Gly213Arg	p.G213R	ENST00000228682	NM_005269.2	213	Ggg/Agg	7/12	1	2	FACETS	0.679	0.591	0.774	0.679	0.591	0.774	SUBCLONAL	1	TRUE	1	0.263000998481622	2		636	784	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813421	102813421	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	68	681	1	ENST00000307046.8:c.268G>A	p.Gly90Ser	p.G90S	ENST00000307046	NM_001111285.1	90	Ggc/Agc	3/4	1	2	FACETS	0.571	0.496	0.654	0.571	0.496	0.654	SUBCLONAL	1	TRUE	1	0.263000998481622	2		682	905	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416876	121416876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1179	87	1009	2	ENST00000257555.6:c.305C>T	p.Ala102Val	p.A102V	ENST00000257555		102	gCc/gTc	1/10	1	2	FACETS	0.523	0.461	0.589	0.523	0.461	0.589	SUBCLONAL	1	TRUE	1	0.263000998481622	2		1011	1266	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562160	21562160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1560	140	1287	2	ENST00000382592.4:c.1759G>A	p.Glu587Lys	p.E587K	ENST00000382592	NM_014572.2	587	Gaa/Aaa	4/8	1	2	FACETS	0.626	0.568	0.688	0.626	0.568	0.688	SUBCLONAL	1	TRUE	1	0.263000998481622	2		1289	1700	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913678	32913678	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs772860507	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	43	387	0	ENST00000380152.3:c.5186A>G	p.Lys1729Arg	p.K1729R	ENST00000380152		1729	aAa/aGa	11/27	1	2	FACETS	0.533	0.445	0.63	0.533	0.445	0.63	SUBCLONAL	1	TRUE	1	0.263000998481622	2		387	614	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955467	48955467	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	40	449	1	ENST00000267163.4:c.1583T>C	p.Phe528Ser	p.F528S	ENST00000267163	NM_000321.2	528	tTt/tCt	17/27	1	2	FACETS	0.457	0.379	0.545	0.457	0.379	0.545	SUBCLONAL	1	TRUE	1	0.263000998481622	2		450	665	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281462	49281462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	46	584	0	ENST00000282018.3:c.509C>T	p.Ser170Leu	p.S170L	ENST00000282018	NM_020377.2	170	tCa/tTa	1/1	1	2	FACETS	0.515	0.433	0.607	0.515	0.433	0.607	SUBCLONAL	1	TRUE	1	0.263000998481622	2		584	679	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135334	30135334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	54	573	0	ENST00000331968.5:c.484C>T	p.His162Tyr	p.H162Y	ENST00000331968	NM_002742.2	162	Cac/Tac	3/18	1	2	FACETS	0.494	0.42	0.574	0.494	0.42	0.574	SUBCLONAL	1	TRUE	1	0.263000998481622	2		573	832	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023066	33023066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1230965844	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	48	463	0	ENST00000300177.4:c.175G>A	p.Gly59Arg	p.G59R	ENST00000300177	NM_001191322.1	59	Ggg/Agg	2/2	1	2	FACETS	0.677	0.572	0.793	0.677	0.572	0.793	SUBCLONAL	1	TRUE	1	0.263000998481622	2		463	539	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675046	40675047	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	63	679	0	ENST00000249776.8:c.10_11delinsTT	p.Pro4Phe	p.P4F	ENST00000249776	NM_033286.3	4	CCc/TTc	1/9	1	2	FACETS	0.499	0.43	0.574	0.499	0.43	0.574	SUBCLONAL	1	TRUE	1	0.263000998481622	2		679	960	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41021757	41021758	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	54	514	1	ENST00000267868.3:c.699_700delinsAA	p.Gly234Ser	p.G234S	ENST00000267868	NM_002875.4	233	tcGGgt/tcAAgt	8/10	1	2	FACETS	0.492	0.419	0.572	0.492	0.419	0.572	SUBCLONAL	1	TRUE	1	0.263000998481622	2		515	835	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714279	43714279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	75	785	0	ENST00000382044.4:c.3874G>A	p.Val1292Ile	p.V1292I	ENST00000382044	NM_001141980.1	1292	Gtt/Att	19/28	1	2	FACETS	0.512	0.447	0.582	0.512	0.447	0.582	SUBCLONAL	1	TRUE	1	0.263000998481622	2		785	1115	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43766936	43766936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778059786	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	40	396	0	ENST00000382044.4:c.1115C>T	p.Pro372Leu	p.P372L	ENST00000382044	NM_001141980.1	372	cCt/cTt	10/28	1	2	FACETS	0.455	0.377	0.542	0.455	0.377	0.542	SUBCLONAL	1	TRUE	1	0.263000998481622	2		396	669	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358694	67358694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1307168753	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	52	456	0	ENST00000327367.4:c.202C>T	p.Pro68Ser	p.P68S	ENST00000327367	NM_005902.3	68	Ccc/Tcc	1/9	1	2	FACETS	0.61	0.519	0.711	0.61	0.519	0.711	SUBCLONAL	1	TRUE	1	0.263000998481622	2		456	648	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457650	67457650	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	101	856	0	ENST00000327367.4:c.460G>A	p.Asp154Asn	p.D154N	ENST00000327367	NM_005902.3	154	Gac/Aac	3/9	1	2	FACETS	0.608	0.541	0.679	0.608	0.541	0.679	SUBCLONAL	1	TRUE	1	0.263000998481622	2		856	1264	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423535	88423535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	61	674	0	ENST00000360948.2:c.2300G>A	p.Gly767Glu	p.G767E	ENST00000360948	NM_001012338.2	767	gGa/gAa	18/19	1	2	FACETS	0.521	0.448	0.6	0.521	0.448	0.6	SUBCLONAL	1	TRUE	1	0.263000998481622	2		674	891	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442728	99442728	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	73	666	0	ENST00000268035.6:c.1125G>C	p.Glu375Asp	p.E375D	ENST00000268035	NM_000875.3	375	gaG/gaC	5/21	1	2	FACETS	0.585	0.51	0.666	0.585	0.51	0.666	SUBCLONAL	1	TRUE	1	0.263000998481622	2		666	949	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640478	3640478	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373091194	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	88	899	2	ENST00000294008.3:c.3161C>T	p.Ser1054Leu	p.S1054L	ENST00000294008	NM_032444.2	1054	tCg/tTg	12/15	1	2	FACETS	0.609	0.538	0.686	0.609	0.538	0.686	SUBCLONAL	1	TRUE	1	0.263000998481622	2		901	1098	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646198	3646199	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	90	772	3	ENST00000294008.3:c.1879_1880delinsTT	p.Pro627Leu	p.P627L	ENST00000294008	NM_032444.2	627	CCg/TTg	8/15	1	2	FACETS	0.679	0.601	0.763	0.679	0.601	0.763	SUBCLONAL	1	TRUE	1	0.263000998481622	2		775	1008	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3841988	3841988	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	48	384	0	ENST00000262367.5:c.1324C>G	p.Gln442Glu	p.Q442E	ENST00000262367	NM_004380.2	442	Caa/Gaa	5/31	1	2	FACETS	0.589	0.497	0.69	0.589	0.497	0.69	SUBCLONAL	1	TRUE	1	0.263000998481622	2		384	620	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646819	23646819	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1060502788	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	63	604	0	ENST00000261584.4:c.1048C>T	p.Gln350Ter	p.Q350*	ENST00000261584	NM_024675.3	350	Caa/Taa	4/13	1	2	FACETS	0.495	0.427	0.57	0.495	0.427	0.57	SUBCLONAL	1	TRUE	1	0.263000998481622	2		604	968	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134413	30134413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555123973	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	87	889	0	ENST00000263025.4:c.118C>T	p.Pro40Ser	p.P40S	ENST00000263025	NM_002746.2	40	Ccg/Tcg	1/9	1	2	FACETS	0.534	0.471	0.601	0.534	0.471	0.601	SUBCLONAL	1	TRUE	1	0.263000998481622	2		889	1240	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134452	30134452	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1302416785	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	66	764	0	ENST00000263025.4:c.79G>A	p.Glu27Lys	p.E27K	ENST00000263025	NM_002746.2	27	Gag/Aag	1/9	1	2	FACETS	0.477	0.412	0.547	0.477	0.412	0.547	SUBCLONAL	1	TRUE	1	0.263000998481622	2		764	1053	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825577	50825577	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	55	454	0	ENST00000398568.2:c.2208C>G	p.Ile736Met	p.I736M	ENST00000398568	NM_001042412.1	736	atC/atG	14/18	1	2	FACETS	0.571	0.487	0.662	0.571	0.487	0.662	SUBCLONAL	1	TRUE	1	0.263000998481622	2		454	733	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828213	50828213	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	50	576	0	ENST00000398568.2:c.2551A>T	p.Ile851Phe	p.I851F	ENST00000398568	NM_001042412.1	851	Atc/Ttc	17/18	1	2	FACETS	0.464	0.393	0.543	0.464	0.393	0.543	SUBCLONAL	1	TRUE	1	0.263000998481622	2		576	819	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991739	72991739	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	27	351	0	ENST00000268489.5:c.2306C>G	p.Thr769Ser	p.T769S	ENST00000268489	NM_006885.3	769	aCt/aGt	2/10	1	2	FACETS	0.44	0.349	0.544	0.44	0.349	0.544	SUBCLONAL	1	TRUE	1	0.263000998481622	2		351	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578400	7578400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751477326	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	19	732	0	ENST00000269305.4:c.530C>T	p.Pro177Leu	p.P177L	ENST00000269305	NM_001126112.2	177	cCc/cTc	5/11	1	2	FACETS	0.154	0.116	0.2	0.154	0.116	0.2	SUBCLONAL	1	TRUE	1	0.263000998481622	2		732	937	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579875	7579876	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	81	776	0	ENST00000269305.4:c.37_38delinsTT	p.Pro13Phe	p.P13F	ENST00000269305	NM_001126112.2	13	CCt/TTt	2/11	1	2	FACETS	0.614	0.539	0.694	0.614	0.539	0.694	SUBCLONAL	1	TRUE	1	0.263000998481622	2		776	1004	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508736	29508736	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555608737	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	42	478	0	ENST00000356175.3:c.663G>A	p.Trp221Ter	p.W221*	ENST00000356175	NM_000267.3	221	tgG/tgA	7/57	1	2	FACETS	0.446	0.371	0.53	0.446	0.371	0.53	SUBCLONAL	1	TRUE	1	0.263000998481622	2		478	716	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508746	29508746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	46	508	0	ENST00000356175.3:c.673G>A	p.Glu225Lys	p.E225K	ENST00000356175	NM_000267.3	225	Gaa/Aaa	7/57	1	2	FACETS	0.474	0.398	0.558	0.474	0.398	0.558	SUBCLONAL	1	TRUE	1	0.263000998481622	2		508	738	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592354	29592354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659197	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	41	493	1	ENST00000356175.3:c.4769G>A	p.Arg1590Gln	p.R1590Q	ENST00000356175	NM_000267.3	1590	cGg/cAg	35/57	1	2	FACETS	0.459	0.381	0.545	0.459	0.381	0.545	SUBCLONAL	1	TRUE	1	0.263000998481622	2		494	680	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653057	29653057	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555533354	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	41	411	0	ENST00000356175.3:c.4992G>A	p.Trp1664Ter	p.W1664*	ENST00000356175	NM_000267.3	1664	tgG/tgA	36/57	1	2	FACETS	0.543	0.452	0.645	0.543	0.452	0.645	SUBCLONAL	1	TRUE	1	0.263000998481622	2		411	574	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508692	38508692	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	78	833	1	ENST00000254066.5:c.740C>T	p.Pro247Leu	p.P247L	ENST00000254066	NM_000964.3	247	cCc/cTc	6/9	1	2	FACETS	0.479	0.419	0.544	0.479	0.419	0.544	SUBCLONAL	1	TRUE	1	0.263000998481622	2		834	1239	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804295	46804295	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	77	677	0	ENST00000290295.7:c.712A>G	p.Asn238Asp	p.N238D	ENST00000290295	NM_006361.5	238	Aac/Gac	2/2	1	2	FACETS	0.562	0.492	0.638	0.562	0.492	0.638	SUBCLONAL	1	TRUE	1	0.263000998481622	2		677	1041	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533740	63533740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	53	485	0	ENST00000307078.5:c.1414C>T	p.His472Tyr	p.H472Y	ENST00000307078	NM_004655.3	472	Cac/Tac	6/11	1	2	FACETS	0.542	0.461	0.632	0.542	0.461	0.632	SUBCLONAL	1	TRUE	1	0.263000998481622	2		485	743	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534430	63534430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	87	770	0	ENST00000307078.5:c.1091C>T	p.Pro364Leu	p.P364L	ENST00000307078	NM_004655.3	364	cCc/cTc	5/11	1	2	FACETS	0.614	0.542	0.691	0.614	0.542	0.691	SUBCLONAL	1	TRUE	1	0.263000998481622	2		770	1078	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240319	5240319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773233463	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	86	892	1	ENST00000357368.4:c.1595G>A	p.Arg532Gln	p.R532Q	ENST00000357368	NM_002850.3	532	cGg/cAg	12/38	1	2	FACETS	0.541	0.477	0.61	0.541	0.477	0.61	SUBCLONAL	1	TRUE	1	0.263000998481622	2		893	1209	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243951	5243951	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	50	694	0	ENST00000357368.4:c.1531C>T	p.Pro511Ser	p.P511S	ENST00000357368	NM_002850.3	511	Ccc/Tcc	11/38	1	2	FACETS	0.392	0.331	0.46	0.392	0.331	0.46	SUBCLONAL	1	TRUE	1	0.263000998481622	2		694	969	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273477	5273477	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	99	772	0	ENST00000357368.4:c.355C>T	p.His119Tyr	p.H119Y	ENST00000357368	NM_002850.3	119	Cat/Tat	4/38	1	2	FACETS	0.616	0.548	0.688	0.616	0.548	0.688	SUBCLONAL	1	TRUE	1	0.263000998481622	2		772	1223	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122624	7122624	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	71	562	0	ENST00000302850.5:c.3529+1G>A		p.X1177_splice	ENST00000302850	NM_000208.2	1177			1	2	FACETS	0.622	0.542	0.709	0.622	0.542	0.709	SUBCLONAL	1	TRUE	1	0.263000998481622	2		562	868	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184556	7184556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	57	592	1	ENST00000302850.5:c.745C>T	p.Pro249Ser	p.P249S	ENST00000302850	NM_000208.2	249	Ccc/Tcc	3/22	1	2	FACETS	0.457	0.391	0.53	0.457	0.391	0.53	SUBCLONAL	1	TRUE	1	0.263000998481622	2		593	948	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248656	10248656	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	51	569	0	ENST00000340748.4:c.4097C>G	p.Thr1366Arg	p.T1366R	ENST00000340748		1366	aCg/aGg	35/40	1	2	FACETS	0.488	0.413	0.57	0.488	0.413	0.57	SUBCLONAL	1	TRUE	1	0.263000998481622	2		569	795	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051178	13051178	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	69	587	1	ENST00000316448.5:c.614C>T	p.Pro205Leu	p.P205L	ENST00000316448	NM_004343.3	205	cCc/cTc	5/9	1	2	FACETS	0.529	0.46	0.605	0.529	0.46	0.605	SUBCLONAL	1	TRUE	1	0.263000998481622	2		588	991	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308372	15308372	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748968901	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	101	811	0	ENST00000263388.2:c.136G>A	p.Gly46Arg	p.G46R	ENST00000263388	NM_000435.2	46	Gga/Aga	2/33	1	2	FACETS	0.702	0.626	0.784	0.702	0.626	0.784	SUBCLONAL	1	TRUE	1	0.263000998481622	2		811	1094	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366957	15366957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761750069	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	61	597	0	ENST00000263377.2:c.1669G>A	p.Val557Met	p.V557M	ENST00000263377	NM_058243.2	557	Gtg/Atg	9/20	1	2	FACETS	0.485	0.417	0.559	0.485	0.417	0.559	SUBCLONAL	1	TRUE	1	0.263000998481622	2		597	957	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376368	15376368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758207588	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1619	155	1179	0	ENST00000263377.2:c.646C>T	p.Pro216Ser	p.P216S	ENST00000263377	NM_058243.2	216	Cct/Tct	5/20	1	2	FACETS	0.664	0.606	0.727	0.664	0.606	0.727	SUBCLONAL	1	TRUE	1	0.263000998481622	2		1179	1774	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966754	18966754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568279022	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1257	76	914	0	ENST00000262803.5:c.1565C>T	p.Pro522Leu	p.P522L	ENST00000262803	NM_002911.3	522	cCg/cTg	12/24	1	2	FACETS	0.434	0.379	0.493	0.434	0.379	0.493	SUBCLONAL	1	TRUE	1	0.263000998481622	2		914	1333	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256769	19256770	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	55	662	2	ENST00000162023.5:c.943_944delinsTT	p.Pro315Leu	p.P315L	ENST00000162023		315	CCa/TTa	13/13	1		FACETS		0.37	0.506				SUBCLONAL	1	TRUE	1	0.263000998481622	2		664	962	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210728	36210728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	93	820	0	ENST00000222270.7:c.479C>T	p.Pro160Leu	p.P160L	ENST00000222270	NM_014727.1	160	cCc/cTc	3/37	1	2	FACETS	0.58	0.514	0.651	0.58	0.514	0.651	SUBCLONAL	1	TRUE	1	0.263000998481622	2		820	1220	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223703	36223703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	96	901	1	ENST00000222270.7:c.6253C>T	p.Pro2085Ser	p.P2085S	ENST00000222270	NM_014727.1	2085	Cct/Tct	28/37	1	2	FACETS	0.602	0.534	0.674	0.602	0.534	0.674	SUBCLONAL	1	TRUE	1	0.263000998481622	2		902	1213	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753633	42753633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	101	855	0	ENST00000222329.4:c.631C>T	p.Pro211Ser	p.P211S	ENST00000222329	NM_006494.2	211	Cct/Tct	4/4	1	2	FACETS	0.656	0.584	0.732	0.656	0.584	0.732	SUBCLONAL	1	TRUE	1	0.263000998481622	2		855	1171	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45854973	45854973	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	81	740	0	ENST00000391945.4:c.2197C>T	p.Gln733Ter	p.Q733*	ENST00000391945	NM_000400.3	733	Cag/Tag	23/23	1	2	FACETS	0.634	0.557	0.717	0.634	0.557	0.717	SUBCLONAL	1	TRUE	1	0.263000998481622	2		740	972	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082767	16082767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	39	250	2	ENST00000281043.3:c.581C>T	p.Pro194Leu	p.P194L	ENST00000281043	NM_005378.4	194	cCc/cTc	2/3	NA	2	FACETS	0.584	0.483	0.696			1	INDETERMINATE	1	TRUE	NA	0.263000998481622	2		252	508	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735323	204735323	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	21	238	0	ENST00000302823.3:c.124C>T	p.Gln42Ter	p.Q42*	ENST00000302823	NM_005214.4	42	Cag/Tag	2/4	1	2	FACETS	0.496	0.382	0.629	0.496	0.382	0.629	SUBCLONAL	1	TRUE	1	0.263000998481622	2		238	322	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735636	204735636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	38	380	1	ENST00000302823.3:c.437G>A	p.Gly146Glu	p.G146E	ENST00000302823	NM_005214.4	146	gGa/gAa	2/4	1	2	FACETS	0.467	0.385	0.559	0.467	0.385	0.559	SUBCLONAL	1	TRUE	1	0.263000998481622	2		381	619	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523294	9523294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	58	585	0	ENST00000353224.5:c.1943C>T	p.Pro648Leu	p.P648L	ENST00000353224	NM_177990.2	648	cCc/cTc	9/10	0.263000998481622	1	FACETS	0.525	0.45	0.607	0.525	0.45	0.607	SUBCLONAL	1	TRUE	0	0.263000998481622	1		585	730	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561450	9561450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	64	564	0	ENST00000353224.5:c.332G>A	p.Gly111Glu	p.G111E	ENST00000353224	NM_177990.2	111	gGa/gAa	4/10	0.263000998481622	1	FACETS	0.658	0.57	0.755	0.658	0.57	0.755	SUBCLONAL	1	TRUE	0	0.263000998481622	1		564	642	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024344	31024344	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	68	625	1	ENST00000375687.4:c.3829C>T	p.Pro1277Ser	p.P1277S	ENST00000375687	NM_015338.5	1277	Cca/Tca	13/13	0.183574610661476	2	FACETS	0.616	0.534	0.704	0.308	0.267	0.352	SUBCLONAL	1	TRUE	0	0.263000998481622	2		626	840	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46252827	46252827	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	23	266	0	ENST00000371998.3:c.256G>A	p.Gly86Arg	p.G86R	ENST00000371998		86	Gga/Aga	4/23	0.183574610661476	2	FACETS	0.491	0.383	0.617	0.246	0.191	0.309	SUBCLONAL	1	TRUE	0	0.263000998481622	2		266	356	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326526	62326526	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	96	895	2	ENST00000360203.5:c.3451G>T	p.Glu1151Ter	p.E1151*	ENST00000360203	NM_001283009.1	1151	Gag/Tag	33/35	0.183574610661476	2	FACETS	0.621	0.552	0.696	0.311	0.276	0.348	SUBCLONAL	1	TRUE	0	0.263000998481622	2		897	1175	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655200	45655200	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	68	618	0	ENST00000407780.3:c.652G>C	p.Glu218Gln	p.E218Q	ENST00000407780	NM_001283052.1	218	Gag/Cag	4/7	1	2	FACETS	0.581	0.504	0.665	0.581	0.504	0.665	SUBCLONAL	1	TRUE	1	0.263000998481622	2		618	890	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121112	29121112	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs587782560	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	78	515	0	ENST00000328354.6:c.445G>A	p.Glu149Lys	p.E149K	ENST00000328354	NM_007194.3	149	Gaa/Aaa	4/15	1	2	FACETS	0.787	0.691	0.89	0.787	0.691	0.89	SUBCLONAL	1	TRUE	1	0.263000998481622	2		515	754	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556658	41556658	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	178	536	0	ENST00000263253.7:c.3603T>G	p.Cys1201Trp	p.C1201W	ENST00000263253	NM_001429.3	1201	tgT/tgG	20/31	1	2	FACETS	0.822	0.759	0.888	1	0.991	1	CLONAL	2	TRUE	1	0.263000998481622	2		536	823	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713495	30713495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	51	572	1	ENST00000295754.5:c.820G>A	p.Val274Met	p.V274M	ENST00000295754	NM_003242.5	274	Gtg/Atg	4/7	1	2	FACETS	0.541	0.459	0.632	0.541	0.459	0.632	SUBCLONAL	1	TRUE	1	0.263000998481622	2		573	717	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799688	72799688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	57	674	0	ENST00000325599.8:c.1481C>T	p.Pro494Leu	p.P494L	ENST00000325599	NM_018130.2	494	cCc/cTc	11/11	1	2	FACETS	0.517	0.442	0.599	0.517	0.442	0.599	SUBCLONAL	1	TRUE	1	0.263000998481622	2		674	838	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391074	89391075	+	missense_variant	Missense_Mutation	DNP	CC	CC	GT	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	56	746	2	ENST00000336596.2:c.1140_1141delinsGT	p.Arg381Cys	p.R381C	ENST00000336596	NM_005233.5	380	gtCCgc/gtGTgc	5/17	1	2	FACETS	0.436	0.372	0.507	0.436	0.372	0.507	SUBCLONAL	1	TRUE	1	0.263000998481622	2		748	976	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499478	89499479	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	52	540	3	ENST00000336596.2:c.2648_2649delinsAA	p.Arg883Gln	p.R883Q	ENST00000336596	NM_005233.5	883	cGG/cAA	15/17	1	2	FACETS	0.545	0.463	0.635	0.545	0.463	0.635	SUBCLONAL	1	TRUE	1	0.263000998481622	2		543	726	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920463	134920463	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	69	771	1	ENST00000398015.3:c.2278G>A	p.Val760Met	p.V760M	ENST00000398015	NM_004441.4	760	Gtg/Atg	12/16	1	2	FACETS	0.55	0.478	0.629	0.55	0.478	0.629	SUBCLONAL	1	TRUE	1	0.263000998481622	2		772	954	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170011212	170011212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	67	644	0	ENST00000295797.4:c.1333G>A	p.Glu445Lys	p.E445K	ENST00000295797	NM_002740.5	445	Gag/Aag	14/18	1	2	FACETS	0.544	0.472	0.624	0.544	0.472	0.624	SUBCLONAL	1	TRUE	1	0.263000998481622	2		644	936	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808880	1808880	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755526507	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	100	854	0	ENST00000260795.2:c.2312C>T	p.Ser771Phe	p.S771F	ENST00000260795		771	tCc/tTc	17/17	1	2	FACETS	0.648	0.577	0.724	0.648	0.577	0.724	SUBCLONAL	1	TRUE	1	0.263000998481622	2		854	1173	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561684	55561684	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	30	243	0	ENST00000288135.5:c.74C>T	p.Ser25Phe	p.S25F	ENST00000288135	NM_000222.2	25	tCt/tTt	2/21	1	2	FACETS	0.576	0.464	0.703	0.576	0.464	0.703	SUBCLONAL	1	TRUE	1	0.263000998481622	2		243	396	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970899	55970899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	49	610	0	ENST00000263923.4:c.1898C>T	p.Ser633Phe	p.S633F	ENST00000263923	NM_002253.2	633	tCc/tTc	13/30	1	2	FACETS	0.509	0.43	0.596	0.509	0.43	0.596	SUBCLONAL	1	TRUE	1	0.263000998481622	2		610	732	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143324108	143324108	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	20	295	0	ENST00000262992.4:c.355G>A	p.Asp119Asn	p.D119N	ENST00000262992	NM_001101669.1	119	Gat/Aat	5/24	1	2	FACETS	0.418	0.319	0.534	0.418	0.319	0.534	SUBCLONAL	1	TRUE	1	0.263000998481622	2		295	364	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554842	187554842	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1316533546	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	28	310	0	ENST00000441802.2:c.4319C>T	p.Thr1440Ile	p.T1440I	ENST00000441802	NM_005245.3	1440	aCt/aTt	7/27	1	2	FACETS	0.445	0.354	0.548	0.445	0.354	0.548	SUBCLONAL	1	TRUE	1	0.263000998481622	2		310	479	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294891	1294891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs943289163	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	11	126	0	ENST00000310581.5:c.214C>T	p.Arg72Cys	p.R72C	ENST00000310581	NM_198253.2	72	Cgc/Tgc	1/16	1	2	FACETS	0.393	0.271	0.544	0.393	0.271	0.544	SUBCLONAL	1	TRUE	1	0.263000998481622	2		126	213	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295253	+	upstream_gene_variant	5'Flank	ONP	GAGG	GAGG	AAAA	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	70	631	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.714	0.621	0.813	0.714	0.621	0.813	SUBCLONAL	1	TRUE	1	0.263000998481622	2		631	746	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526835	31526835	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780968053	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	96	888	0	ENST00000344624.3:c.205C>T	p.Pro69Ser	p.P69S	ENST00000344624		69	Ccc/Tcc	2/33	1	2	FACETS	0.595	0.528	0.667	0.595	0.528	0.667	SUBCLONAL	1	TRUE	1	0.263000998481622	2		888	1227	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750742	57750742	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	57	399	0	ENST00000274289.3:c.1862T>A	p.Phe621Tyr	p.F621Y	ENST00000274289	NM_006622.3	621	tTt/tAt	13/14	1	2	FACETS	0.677	0.58	0.783	0.677	0.58	0.783	SUBCLONAL	1	TRUE	1	0.263000998481622	2		399	640	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589255	67589255	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	33	366	0	ENST00000274335.5:c.1243C>T	p.Gln415Ter	p.Q415*	ENST00000274335		415	Cag/Tag	9/15	1	2	FACETS	0.467	0.38	0.566	0.467	0.38	0.566	SUBCLONAL	1	TRUE	1	0.263000998481622	2		366	537	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590363	67590364	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	18	164	0	ENST00000274335.5:c.1426-1_1426delinsAA		p.X476_splice	ENST00000274335		476		11/15	1	2	FACETS	0.561	0.423	0.724	0.561	0.423	0.724	SUBCLONAL	1	TRUE	1	0.263000998481622	2		164	244	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80021292	80021292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144798521	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	46	386	0	ENST00000265081.6:c.1361G>A	p.Arg454Gln	p.R454Q	ENST00000265081	NM_002439.4	454	cGa/cAa	9/24	1	2	FACETS	0.471	0.396	0.555	0.471	0.396	0.555	SUBCLONAL	1	TRUE	1	0.263000998481622	2		386	742	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131976400	131976400	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs587781569	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	54	634	4	ENST00000265335.6:c.3655G>T	p.Glu1219Ter	p.E1219*	ENST00000265335		1219	Gaa/Taa	24/25	1	2	FACETS	0.485	0.413	0.564	0.485	0.413	0.564	SUBCLONAL	1	TRUE	1	0.263000998481622	2		638	847	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497209	149497210	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	50	574	1	ENST00000261799.4:c.3108_3109delinsTT	p.Pro1037Ser	p.P1037S	ENST00000261799	NM_002609.3	1036	ggCCca/ggTTca	22/23	1	2	FACETS	0.434	0.367	0.508	0.434	0.367	0.508	SUBCLONAL	1	TRUE	1	0.263000998481622	2		575	876	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036982	180036983	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	54	757	2	ENST00000261937.6:c.3729_3730delinsAA	p.Ala1244Thr	p.A1244T	ENST00000261937	NM_182925.4	1243	ggGGct/ggAAct	28/30	1	2	FACETS	0.419	0.357	0.488	0.419	0.357	0.488	SUBCLONAL	1	TRUE	1	0.263000998481622	2		759	979	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672192	30672192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1159759969	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	63	732	2	ENST00000376406.3:c.4768C>T	p.Pro1590Ser	p.P1590S	ENST00000376406	NM_014641.2	1590	Cct/Tct	10/15	1	2	FACETS	0.482	0.415	0.555	0.482	0.415	0.555	SUBCLONAL	1	TRUE	1	0.263000998481622	2		734	994	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673752	30673752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	59	579	0	ENST00000376406.3:c.3208C>T	p.Leu1070Phe	p.L1070F	ENST00000376406	NM_014641.2	1070	Ctt/Ttt	10/15	1	2	FACETS	0.493	0.423	0.57	0.493	0.423	0.57	SUBCLONAL	1	TRUE	1	0.263000998481622	2		579	910	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322925	31322925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1230	73	900	1	ENST00000412585.2:c.971G>A	p.Gly324Glu	p.G324E	ENST00000412585	NM_005514.6	324	gGa/gAa	5/8	1	2	FACETS	0.426	0.371	0.486	0.426	0.371	0.486	SUBCLONAL	1	TRUE	1	0.263000998481622	2		901	1303	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109314067	109314067	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs557313505	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	60	573	0	ENST00000436639.2:c.1156C>T	p.Arg386Cys	p.R386C	ENST00000436639	NM_014454.2	386	Cgt/Tgt	7/10	1	2	FACETS	0.575	0.494	0.663	0.575	0.494	0.663	SUBCLONAL	1	TRUE	1	0.263000998481622	2		573	794	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117707020	117707020	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	54	378	0	ENST00000368508.3:c.2130G>A	p.Met710Ile	p.M710I	ENST00000368508	NM_002944.2	710	atG/atA	15/43	1	2	FACETS	0.527	0.449	0.613	0.527	0.449	0.613	SUBCLONAL	1	TRUE	1	0.263000998481622	2		378	779	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527821	157527821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202194222	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	44	492	0	ENST00000346085.5:c.5546C>T	p.Pro1849Leu	p.P1849L	ENST00000346085	NM_020732.3	1849	cCc/cTc	20/20	1	2	FACETS	0.485	0.406	0.573	0.485	0.406	0.573	SUBCLONAL	1	TRUE	1	0.263000998481622	2		492	690	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729966	41729966	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	50	723	0	ENST00000242208.4:c.563C>A	p.Thr188Lys	p.T188K	ENST00000242208	NM_002192.2	188	aCa/aAa	3/3	1	2	FACETS	0.438	0.37	0.513	0.438	0.37	0.513	SUBCLONAL	1	TRUE	1	0.263000998481622	2		723	868	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334975	81334975	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	36	487	0	ENST00000222390.5:c.1852G>A	p.Gly618Ser	p.G618S	ENST00000222390	NM_000601.4	618	Ggc/Agc	16/18	1	2	FACETS	0.397	0.325	0.478	0.397	0.325	0.478	SUBCLONAL	1	TRUE	1	0.263000998481622	2		487	690	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358961	81358961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	54	572	0	ENST00000222390.5:c.1000C>T	p.Pro334Ser	p.P334S	ENST00000222390	NM_000601.4	334	Cct/Tct	8/18	1	2	FACETS	0.524	0.447	0.61	0.524	0.447	0.61	SUBCLONAL	1	TRUE	1	0.263000998481622	2		572	783	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388023	81388023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	40	481	0	ENST00000222390.5:c.352C>T	p.Leu118Phe	p.L118F	ENST00000222390	NM_000601.4	118	Ctc/Ttc	3/18	1	2	FACETS	0.424	0.351	0.506	0.424	0.351	0.506	SUBCLONAL	1	TRUE	1	0.263000998481622	2		481	717	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395519	116395520	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	57	497	1	ENST00000397752.3:c.1812_1813delinsTT	p.Leu605Phe	p.L605F	ENST00000397752	NM_000245.2	604	ctCCtt/ctTTtt	6/21	1	2	FACETS	0.579	0.495	0.67	0.579	0.495	0.67	SUBCLONAL	1	TRUE	1	0.263000998481622	2		498	749	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418986	116418986	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199763277	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	43	294	0	ENST00000397752.3:c.3497G>A	p.Arg1166Gln	p.R1166Q	ENST00000397752	NM_000245.2	1166	cGa/cAa	17/21	1	2	FACETS	0.72	0.603	0.85	0.72	0.603	0.85	SUBCLONAL	1	TRUE	1	0.263000998481622	2		294	454	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873923	151873923	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	50	416	1	ENST00000262189.6:c.8615C>T	p.Pro2872Leu	p.P2872L	ENST00000262189	NM_170606.2	2872	cCt/cTt	38/59	1	2	FACETS	0.632	0.535	0.738	0.632	0.535	0.738	SUBCLONAL	1	TRUE	1	0.263000998481622	2		417	602	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876986	151876986	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	35	402	1	ENST00000262189.6:c.7375C>T	p.Pro2459Ser	p.P2459S	ENST00000262189	NM_170606.2	2459	Cca/Tca	37/59	1	2	FACETS	0.46	0.376	0.554	0.46	0.376	0.554	SUBCLONAL	1	TRUE	1	0.263000998481622	2		403	579	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194553	29194553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	85	873	0	ENST00000240100.2:c.1175C>T	p.Pro392Leu	p.P392L	ENST00000240100	NM_001394.6	392	cCc/cTc	4/4	0.263000998481622	1	FACETS	0.524	0.461	0.591	0.524	0.461	0.591	SUBCLONAL	1	TRUE	0	0.263000998481622	1		873	1072	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968118	68968118	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	59	622	0	ENST00000288368.4:c.1147G>A	p.Glu383Lys	p.E383K	ENST00000288368	NM_024870.2	383	Gag/Aag	10/40	1	2	FACETS	0.516	0.442	0.596	0.516	0.442	0.596	SUBCLONAL	1	TRUE	1	0.263000998481622	2		622	870	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484138	8484138	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1388350160	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	44	531	0	ENST00000356435.5:c.3394C>A	p.Pro1132Thr	p.P1132T	ENST00000356435		1132	Cct/Act	19/35	0.263000998481622	1	FACETS	0.476	0.398	0.562	0.476	0.398	0.562	SUBCLONAL	1	TRUE	0	0.263000998481622	1		531	611	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974799	21974799	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	23	189	0	ENST00000304494.5:c.28G>T	p.Glu10Ter	p.E10*	ENST00000304494	NM_000077.4	10	Gag/Tag	1/3	0.263000998481622	1	FACETS	0.795	0.624	0.991	0.795	0.624	0.991	CLONAL	1	TRUE	0	0.263000998481622	1		189	191	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635227	87635227	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	67	694	0	ENST00000277120.3:c.2279G>A	p.Trp760Ter	p.W760*	ENST00000277120		760	tGg/tAg	18/19	0.183574610661476	2	FACETS	0.545	0.472	0.624	0.272	0.236	0.312	SUBCLONAL	1	TRUE	0	0.263000998481622	2		694	935	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250511	110250511	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	49	626	2	ENST00000374672.4:c.164C>T	p.Pro55Leu	p.P55L	ENST00000374672	NM_004235.4	55	cCc/cTc	3/5	0.183574610661476	2	FACETS	0.489	0.413	0.573	0.245	0.206	0.287	SUBCLONAL	1	TRUE	0	0.263000998481622	2		628	762	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412730	139412730	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	195	738	0	ENST00000277541.6:c.1114C>T	p.Leu372Phe	p.L372F	ENST00000277541	NM_017617.3	372	Ctc/Ttc	7/34	0.183574610661476	2	FACETS	1	0.987	1	0.662	0.612	0.714	CLONAL	1	TRUE	0	0.263000998481622	2		738	1120	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413049	139413049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064795070	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	109	593	0	ENST00000277541.6:c.1093C>T	p.Arg365Cys	p.R365C	ENST00000277541	NM_017617.3	365	Cgc/Tgc	6/34	0.183574610661476	2	FACETS	1	0.96	1	0.567	0.509	0.628	CLONAL	1	TRUE	0	0.263000998481622	2		593	731	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223668	53223669	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	101	525	3	ENST00000375401.3:c.3690_3691delinsTT	p.Pro1231Ser	p.P1231S	ENST00000375401	NM_004187.3	1230	tcCCca/tcTTca	23/26	1	1	FACETS	0.977	0.874	1	0.977	0.874	1	CLONAL	1	TRUE	0	0.263000998481622	1		528	683	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410945	63410945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	61	356	1	ENST00000330258.3:c.2222C>T	p.Pro741Leu	p.P741L	ENST00000330258	NM_152424.3	741	cCc/cTc	2/2	1	1	FACETS	0.882	0.762	1	0.882	0.762	1	CLONAL	1	TRUE	0	0.263000998481622	1		357	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs587781525	NA	P-0026506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	106	780	0	ENST00000269305.4:c.842A>C	p.Asp281Ala	p.D281A	ENST00000269305	NM_001126112.2	281	gAc/gCc	8/11	0.236356196650514	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.236356196650514	1		780	543	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	66	288	0	ENST00000304494.5:c.151-1G>A		p.X51_splice	ENST00000304494	NM_000077.4	51			0.253639933287336	2	FACETS	0.797	0.7	0.899	0.797	0.7	0.899	SUBCLONAL	2	TRUE	0	0.33	2		288	251	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	31	179	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.752	0.611	0.909	0.752	0.611	0.909	CLONAL	1	TRUE	1	0.33	2		179	250	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940145	31940145	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779960597	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	100	382	1	ENST00000375333.2:c.287C>T	p.Ser96Phe	p.S96F	ENST00000375333	NM_032454.1	96	tCc/tTc	2/8	0.3	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.33	1		383	425	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	52	779	1	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	1	2	FACETS	0.958	0.82	1	0.958	0.82	1	CLONAL	1	TRUE	1	0.33	2		780	329	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522148	157522148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	50	438	0	ENST00000346085.5:c.4420C>T	p.Pro1474Ser	p.P1474S	ENST00000346085	NM_020732.3	1474	Ccc/Tcc	18/20	1	2	FACETS	0.894	0.762	1	0.894	0.762	1	CLONAL	1	TRUE	1	0.33	2		438	339	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748581	43748581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139206878	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	54	219	0	ENST00000523873.1:c.535C>T	p.Pro179Ser	p.P179S	ENST00000523873		179	Cct/Tct	6/8	0.3	1	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	0	0.33	1		219	263	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344985	70344985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1365839691	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	67	145	0	ENST00000374080.3:c.2215C>T	p.Pro739Ser	p.P739S	ENST00000374080		739	Ccc/Tcc	15/45	0.186647668080246	2	FACETS	1	0.955	1			1	INDETERMINATE	2	TRUE	NA	0.33	2		145	176	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933480	100933480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766277966	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	18	89	0	ENST00000325455.5:c.1910G>A	p.Arg637Gln	p.R637Q	ENST00000325455	NM_001202474.3	637	cGa/cAa	4/8	1	2	FACETS	0.873	0.664	1	0.873	0.664	1	CLONAL	1	TRUE	1	0.33	2		89	125	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137830	64137830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	50	393	0	ENST00000334205.4:c.1931C>T	p.Ser644Phe	p.S644F	ENST00000334205	NM_003942.2	644	tCc/tTc	15/17	1	2	FACETS	0.706	0.6	0.822	0.706	0.6	0.822	SUBCLONAL	1	TRUE	1	0.33	2		393	429	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811666	102811666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	139	347	1	ENST00000307046.8:c.518G>A	p.Gly173Glu	p.G173E	ENST00000307046	NM_001111285.1	173	gGa/gAa	4/4	1	2	FACETS	0.834	0.764	0.907	1	0.989	1	CLONAL	2	TRUE	1	0.33	2		348	505	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760616	133760616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	36	457	0	ENST00000318560.5:c.2939C>T	p.Pro980Leu	p.P980L	ENST00000318560	NM_005157.4	980	cCc/cTc	11/11	0.253299341596759	3	FACETS	0.458	0.376	0.551	0.153	0.125	0.184	SUBCLONAL	1	TRUE	0	0.33	3		457	555	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491283	2491283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776730987	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	60	345	0	ENST00000355716.4:c.326G>A	p.Arg109Gln	p.R109Q	ENST00000355716	NM_003820.2	109	cGg/cAg	4/8	1	2	FACETS	0.918	0.794	1	0.918	0.794	1	CLONAL	1	TRUE	1	0.33	2		345	396	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2493248	2493249	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	34	268	1	ENST00000355716.4:c.688_689delinsTT	p.Pro230Leu	p.P230L	ENST00000355716	NM_003820.2	230	CCa/TTa	6/8	1	2	FACETS	0.814	0.669	0.976	0.814	0.669	0.976	CLONAL	1	TRUE	1	0.33	2		269	253	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780075	9780075	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	35	314	1	ENST00000377346.4:c.1339G>A	p.Asp447Asn	p.D447N	ENST00000377346	NM_005026.3	447	Gat/Aat	10/24	1	2	FACETS	0.726	0.598	0.87	0.726	0.598	0.87	SUBCLONAL	1	TRUE	1	0.33	2		315	292	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182050	11182050	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	47	580	0	ENST00000361445.4:c.6796C>T	p.Arg2266Cys	p.R2266C	ENST00000361445	NM_004958.3	2266	Cgc/Tgc	48/58	1	2	FACETS	0.989	0.84	1	0.989	0.84	1	CLONAL	1	TRUE	1	0.33	2		580	288	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11301673	11301673	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs770410760	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	54	321	0	ENST00000361445.4:c.1478T>C	p.Met493Thr	p.M493T	ENST00000361445	NM_004958.3	493	aTg/aCg	10/58	1	2	FACETS	0.924	0.793	1	0.924	0.793	1	CLONAL	1	TRUE	1	0.33	2		321	354	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256549	16256549	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	51	310	2	ENST00000375759.3:c.3814G>A	p.Asp1272Asn	p.D1272N	ENST00000375759	NM_015001.2	1272	Gat/Aat	11/15	1	2	FACETS	0.773	0.658	0.897	0.773	0.658	0.897	SUBCLONAL	1	TRUE	1	0.33	2		312	400	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260195	16260195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748710481	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	42	263	0	ENST00000375759.3:c.7460G>A	p.Gly2487Glu	p.G2487E	ENST00000375759	NM_015001.2	2487	gGg/gAg	11/15	1	2	FACETS	0.953	0.801	1	0.953	0.801	1	CLONAL	1	TRUE	1	0.33	2		263	267	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260516	16260516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	29	286	0	ENST00000375759.3:c.7781C>T	p.Ser2594Phe	p.S2594F	ENST00000375759	NM_015001.2	2594	tCt/tTt	11/15	1	2	FACETS	0.604	0.486	0.737	0.604	0.486	0.737	SUBCLONAL	1	TRUE	1	0.33	2		286	291	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260788	16260788	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	32	314	0	ENST00000375759.3:c.8053A>C	p.Thr2685Pro	p.T2685P	ENST00000375759	NM_015001.2	2685	Acc/Ccc	11/15	1	2	FACETS	0.64	0.521	0.774	0.64	0.521	0.774	SUBCLONAL	1	TRUE	1	0.33	2		314	303	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260792	16260792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	33	319	0	ENST00000375759.3:c.8057C>T	p.Pro2686Leu	p.P2686L	ENST00000375759	NM_015001.2	2686	cCt/cTt	11/15	1	2	FACETS	0.658	0.537	0.793	0.658	0.537	0.793	SUBCLONAL	1	TRUE	1	0.33	2		319	304	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023622	27023622	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1356791422	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	33	259	0	ENST00000324856.7:c.728C>T	p.Ala243Val	p.A243V	ENST00000324856	NM_006015.4	243	gCg/gTg	1/20	1	2	FACETS	0.922	0.756	1	0.922	0.756	1	CLONAL	1	TRUE	1	0.33	2		259	217	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101169	27101169	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	51	332	0	ENST00000324856.7:c.4451C>T	p.Pro1484Leu	p.P1484L	ENST00000324856	NM_006015.4	1484	cCc/cTc	18/20	1	2	FACETS	0.829	0.707	0.961	0.829	0.707	0.961	CLONAL	1	TRUE	1	0.33	2		332	373	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106808	27106808	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	52	307	0	ENST00000324856.7:c.6419C>T	p.Pro2140Leu	p.P2140L	ENST00000324856	NM_006015.4	2140	cCc/cTc	20/20	1	2	FACETS	0.911	0.779	1	0.911	0.779	1	CLONAL	1	TRUE	1	0.33	2		307	346	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107108	27107108	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	54	244	0	ENST00000324856.7:c.6719C>T	p.Ala2240Val	p.A2240V	ENST00000324856	NM_006015.4	2240	gCc/gTc	20/20	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.33	2		244	285	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599140	28599140	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	56	389	1	ENST00000253063.3:c.586C>T	p.Gln196Ter	p.Q196*	ENST00000253063	NM_031459.4	196	Cag/Tag	5/10	1	2	FACETS	0.882	0.758	1	0.882	0.758	1	CLONAL	1	TRUE	1	0.33	2		390	385	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414968	78414968	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	49	234	0	ENST00000370768.2:c.1798C>T	p.Pro600Ser	p.P600S	ENST00000370768	NM_003902.3	600	Ccg/Tcg	19/20	1	2	FACETS	0.886	0.754	1	0.886	0.754	1	CLONAL	1	TRUE	1	0.33	2		234	335	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510816	120510816	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	31	482	0	ENST00000256646.2:c.1148C>T	p.Pro383Leu	p.P383L	ENST00000256646	NM_024408.3	383	cCt/cTt	7/34	1	2	FACETS	0.706	0.574	0.855	0.706	0.574	0.855	SUBCLONAL	1	TRUE	1	0.33	2		482	266	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510856	120510856	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	22	197	0	ENST00000256646.2:c.1109-1G>A		p.X370_splice	ENST00000256646	NM_024408.3	370			1	2	FACETS	0.749	0.584	0.937	0.749	0.584	0.937	CLONAL	1	TRUE	1	0.33	2		197	178	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729635	162729635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	26	251	0	ENST00000367921.3:c.721G>A	p.Asp241Asn	p.D241N	ENST00000367921	NM_006182.2	241	Gat/Aat	8/18	1	2	FACETS	0.536	0.425	0.662	0.536	0.425	0.662	SUBCLONAL	1	TRUE	1	0.33	2		251	294	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737090	162737090	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	37	301	0	ENST00000367921.3:c.1234C>T	p.Leu412Phe	p.L412F	ENST00000367921	NM_006182.2	412	Ctc/Ttc	11/18	1	2	FACETS	0.68	0.562	0.81	0.68	0.562	0.81	SUBCLONAL	1	TRUE	1	0.33	2		301	330	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204515968	204515968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	62	233	0	ENST00000367182.3:c.866C>T	p.Ser289Phe	p.S289F	ENST00000367182	NM_001278516.1	289	tCc/tTc	10/11	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.33	2		233	358	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226562028	226562028	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	53	267	0	ENST00000366794.5:c.1969G>A	p.Val657Ile	p.V657I	ENST00000366794	NM_001618.3	657	Gta/Ata	14/23	1	2	FACETS	0.905	0.775	1	0.905	0.775	1	CLONAL	1	TRUE	1	0.33	2		267	355	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226574047	226574047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	34	213	0	ENST00000366794.5:c.814G>A	p.Val272Met	p.V272M	ENST00000366794	NM_001618.3	272	Gtg/Atg	6/23	1	2	FACETS	0.772	0.634	0.926	0.772	0.634	0.926	CLONAL	1	TRUE	1	0.33	2		213	267	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097760	8097760	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	51	316	0	ENST00000346208.3:c.142G>A	p.Asp48Asn	p.D48N	ENST00000346208		48	Gat/Aat	2/6	1	2	FACETS	0.849	0.724	0.985	0.849	0.724	0.985	CLONAL	1	TRUE	1	0.33	2		316	364	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615613	43615613	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	44	279	0	ENST00000355710.3:c.2692G>C	p.Asp898His	p.D898H	ENST00000355710	NM_020975.4	898	Gat/Cat	15/20	1	2	FACETS	0.869	0.732	1	0.869	0.732	1	CLONAL	1	TRUE	1	0.33	2		279	307	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426982	70426982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	37	250	0	ENST00000373644.4:c.4642C>T	p.Pro1548Ser	p.P1548S	ENST00000373644	NM_030625.2	1548	Cct/Tct	7/12	1	2	FACETS	0.658	0.543	0.785	0.658	0.543	0.785	SUBCLONAL	1	TRUE	1	0.33	2		250	341	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450771	70450772	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	43	214	1	ENST00000373644.4:c.5611_5612delinsAA	p.Gly1871Lys	p.G1871K	ENST00000373644	NM_030625.2	1871	GGg/AAg	12/12	1	2	FACETS	0.958	0.807	1	0.958	0.807	1	CLONAL	1	TRUE	1	0.33	2		215	272	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104356989	104356990	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	40	236	2	ENST00000369902.3:c.849_850delinsAA	p.Asp284Asn	p.D284N	ENST00000369902	NM_016169.3	283	gaGGat/gaAAat	7/12	1	2	FACETS	0.811	0.677	0.959	0.811	0.677	0.959	CLONAL	1	TRUE	1	0.33	2		238	299	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112764446	112764446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	77	292	0	ENST00000369452.4:c.1055C>T	p.Ser352Phe	p.S352F	ENST00000369452	NM_007373.3	352	tCt/tTt	5/9	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.33	2		292	465	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112769577	112769577	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	53	303	0	ENST00000369452.4:c.1529C>T	p.Pro510Leu	p.P510L	ENST00000369452	NM_007373.3	510	cCt/cTt	8/9	1	2	FACETS	0.828	0.708	0.958	0.828	0.708	0.958	CLONAL	1	TRUE	1	0.33	2		303	388	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263314	123263314	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	28	232	0	ENST00000358487.5:c.1429C>T	p.Pro477Ser	p.P477S	ENST00000358487	NM_000141.4	477	Cca/Tca	10/18	1	2	FACETS	0.653	0.523	0.799	0.653	0.523	0.799	SUBCLONAL	1	TRUE	1	0.33	2		232	260	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150268	108150268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064795850	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	51	269	0	ENST00000278616.4:c.3335C>T	p.Pro1112Leu	p.P1112L	ENST00000278616	NM_000051.3	1112	cCt/cTt	23/63	1	2	FACETS	0.948	0.81	1	0.948	0.81	1	CLONAL	1	TRUE	1	0.33	2		269	326	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352555	118352555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	42	297	1	ENST00000534358.1:c.3760C>T	p.Pro1254Ser	p.P1254S	ENST00000534358	NM_005933.3	1254	Cca/Tca	7/36	1	2	FACETS	0.644	0.539	0.761	0.644	0.539	0.761	SUBCLONAL	1	TRUE	1	0.33	2		298	395	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362609	118362611	+	frameshift_variant	Frame_Shift_Del	DEL	CTC	CTC	TT	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	33	213	1	ENST00000534358.1:c.4970_4972delinsTT	p.Ser1657PhefsTer19	p.S1657Ffs*19	ENST00000534358	NM_005933.3	1657	tCTCgg/tTTgg	15/36	1	2	FACETS	0.709	0.58	0.854	0.709	0.58	0.854	SUBCLONAL	1	TRUE	1	0.33	2		214	282	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362638	118362638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555042614	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	31	178	0	ENST00000534358.1:c.4999C>T	p.Arg1667Trp	p.R1667W	ENST00000534358	NM_005933.3	1667	Cgg/Tgg	15/36	1	2	FACETS	0.78	0.634	0.942	0.78	0.634	0.942	CLONAL	1	TRUE	1	0.33	2		178	241	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022552	12022552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	78	304	1	ENST00000396373.4:c.658G>A	p.Gly220Arg	p.G220R	ENST00000396373	NM_001987.4	220	Gga/Aga	5/8	0.285841170457306	2	FACETS	0.826	0.734	0.923	0.826	0.734	0.923	CLONAL	2	TRUE	0	0.33	2		305	286	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244994	46244994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	25	310	0	ENST00000334344.6:c.3088G>A	p.Val1030Ile	p.V1030I	ENST00000334344	NM_152641.2	1030	Gtt/Att	15/21	1	2	FACETS	0.37	0.291	0.462	0.37	0.291	0.462	SUBCLONAL	1	TRUE	1	0.33	2		310	409	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285842	46285842	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	22	312	0	ENST00000334344.6:c.5110G>T	p.Glu1704Ter	p.E1704*	ENST00000334344	NM_152641.2	1704	Gaa/Taa	18/21	1	2	FACETS	0.369	0.286	0.467	0.369	0.286	0.467	SUBCLONAL	1	TRUE	1	0.33	2		312	361	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421799	49421799	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	96	335	0	ENST00000301067.7:c.14508G>C	p.Glu4836Asp	p.E4836D	ENST00000301067	NM_003482.3	4836	gaG/gaC	46/54	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.33	2		335	433	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426048	49426048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	29	352	0	ENST00000301067.7:c.12440C>T	p.Ser4147Phe	p.S4147F	ENST00000301067	NM_003482.3	4147	tCc/tTc	39/54	1	2	FACETS	0.433	0.347	0.531	0.433	0.347	0.531	SUBCLONAL	1	TRUE	1	0.33	2		352	406	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433541	49433542	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	37	403	0	ENST00000301067.7:c.8011_8012del	p.Gly2671ProfsTer2	p.G2671Pfs*2	ENST00000301067	NM_003482.3	2671	GGc/c	31/54	1	2	FACETS	0.469	0.386	0.562	0.469	0.386	0.562	SUBCLONAL	1	TRUE	1	0.33	2		403	478	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440500	49440500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	131	370	0	ENST00000301067.7:c.4310C>T	p.Ser1437Phe	p.S1437F	ENST00000301067	NM_003482.3	1437	tCc/tTc	15/54	1	2	FACETS	0.825	0.754	0.9	1	0.988	1	CLONAL	2	TRUE	1	0.33	2		370	481	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487972	56487972	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs748595358	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	84	259	0	ENST00000267101.3:c.1703C>T	p.Ser568Leu	p.S568L	ENST00000267101	NM_001982.3	568	tCg/tTg	14/28	1	2	FACETS	0.818	0.73	0.911	1	0.982	1	CLONAL	2	TRUE	1	0.33	2		259	311	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495039	56495040	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	31	333	0	ENST00000267101.3:c.3396_3397delinsTT	p.His1133Tyr	p.H1133Y	ENST00000267101	NM_001982.3	1132	taCCat/taTTat	27/28	1	2	FACETS	0.602	0.488	0.731	0.602	0.488	0.731	SUBCLONAL	1	TRUE	1	0.33	2		333	312	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865686	57865686	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	111	383	1	ENST00000228682.2:c.3163G>A	p.Glu1055Lys	p.E1055K	ENST00000228682	NM_005269.2	1055	Gag/Aag	12/12	1	2	FACETS	0.768	0.695	0.844	1	0.985	1	SUBCLONAL	2	TRUE	1	0.33	2		384	438	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924309	112924309	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1306943402	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	111	387	1	ENST00000351677.2:c.1255C>T	p.His419Tyr	p.H419Y	ENST00000351677	NM_002834.3	419	Cac/Tac	11/16	1	2	FACETS	0.824	0.747	0.905	1	0.986	1	CLONAL	2	TRUE	1	0.33	2		388	408	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112401	115112401	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs888338239	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	70	283	0	ENST00000257566.3:c.1339C>T	p.Arg447Cys	p.R447C	ENST00000257566	NM_016569.3	447	Cgc/Tgc	7/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.33	2		283	293	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220050	133220057	+	frameshift_variant	Frame_Shift_Del	DEL	AGGTCTCT	AGGTCTCT	-	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	35	311	0	ENST00000320574.5:c.4380_4387del	p.Glu1461CysfsTer3	p.E1461Cfs*3	ENST00000320574	NM_006231.2	1460	gcAGAGACCTtt/gctt	34/49	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.33	NA		311	432	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563276	21563277	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	56	384	1	ENST00000382592.4:c.642_643delinsTT	p.Leu215Phe	p.L215F	ENST00000382592	NM_014572.2	214	taCCtt/taTTtt	4/8	0.175865660287792	3	FACETS	0.957	0.823	1	0.479	0.411	0.552	INDETERMINATE	1	TRUE	1	0.33	3		385	413	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623896	28623896	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	50	242	1	ENST00000241453.7:c.758C>G	p.Pro253Arg	p.P253R	ENST00000241453	NM_004119.2	253	cCt/cGt	7/24	0.175865660287792	3	FACETS	0.994	0.847	1	0.497	0.423	0.578	INDETERMINATE	1	TRUE	1	0.33	3		243	355	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012419	29012419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867762505	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	81	309	0	ENST00000282397.4:c.452G>A	p.Gly151Glu	p.G151E	ENST00000282397	NM_002019.4	151	gGa/gAa	4/30	0.175865660287792	3	FACETS	1	0.973	1	0.678	0.6	0.76	INDETERMINATE	1	TRUE	1	0.33	3		309	422	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912277	32912277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80358620	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	84	262	0	ENST00000380152.3:c.3785C>T	p.Ser1262Leu	p.S1262L	ENST00000380152		1262	tCa/tTa	11/27	0.175865660287792	3	FACETS	1	0.976	1	0.706	0.627	0.79	INDETERMINATE	1	TRUE	1	0.33	3		262	420	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913169	32913171	+	missense_variant	Missense_Mutation	TNP	TAG	TAG	AAA	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	73	313	0	ENST00000380152.3:c.4677_4679delinsAAA	p.Phe1559_Ser1560delinsLeuAsn	p.F1559_S1560delinsLN	ENST00000380152		1559	ttTAGc/ttAAAc	11/27	0.175865660287792	3	FACETS	1	0.963	1	0.627	0.551	0.708	INDETERMINATE	1	TRUE	1	0.33	3		313	411	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972351	32972351	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	69	268	0	ENST00000380152.3:c.9701T>C	p.Met3234Thr	p.M3234T	ENST00000380152		3234	aTg/aCg	27/27	0.175865660287792	3	FACETS	1	0.948	1	0.581	0.508	0.66	INDETERMINATE	1	TRUE	1	0.33	3		268	419	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435531	110435531	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	77	300	0	ENST00000375856.3:c.2870C>G	p.Ser957Trp	p.S957W	ENST00000375856	NM_003749.2	957	tCg/tGg	1/2	0.175865660287792	3	FACETS	0.772	0.683	0.867	0.772	0.683	0.867	INDETERMINATE	2	TRUE	1	0.33	3		300	352	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100227	30100227	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	47	193	0	ENST00000331968.5:c.1393G>A	p.Glu465Lys	p.E465K	ENST00000331968	NM_002742.2	465	Gaa/Aaa	10/18	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.33	2		193	249	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81534606	81534606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	64	271	0	ENST00000298171.2:c.251C>T	p.Ser84Phe	p.S84F	ENST00000298171	NM_000369.2	84	tCt/tTt	3/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.33	2		271	337	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021492	42021492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	52	370	0	ENST00000219905.7:c.3788C>T	p.Ser1263Leu	p.S1263L	ENST00000219905	NM_001164273.1	1263	tCa/tTa	11/24	1	2	FACETS	0.684	0.583	0.794	0.684	0.583	0.794	SUBCLONAL	1	TRUE	1	0.33	2		370	461	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396436	396436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773096813	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	64	345	0	ENST00000262320.3:c.590C>T	p.Thr197Ile	p.T197I	ENST00000262320	NM_003502.3	197	aCc/aTc	2/11	1	2	FACETS	0.962	0.837	1	0.962	0.837	1	CLONAL	1	TRUE	1	0.33	2		345	403	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639407	3639407	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	60	356	0	ENST00000294008.3:c.4232G>A	p.Arg1411Lys	p.R1411K	ENST00000294008	NM_032444.2	1411	aGa/aAa	12/15	1	2	FACETS	0.985	0.853	1	0.985	0.853	1	CLONAL	1	TRUE	1	0.33	2		356	369	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639422	3639422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	55	696	0	ENST00000294008.3:c.4217C>T	p.Ser1406Phe	p.S1406F	ENST00000294008	NM_032444.2	1406	tCc/tTc	12/15	1	2	FACETS	0.903	0.776	1	0.903	0.776	1	CLONAL	1	TRUE	1	0.33	2		696	369	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639900	3639900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs978074181	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	49	356	0	ENST00000294008.3:c.3739G>A	p.Glu1247Lys	p.E1247K	ENST00000294008	NM_032444.2	1247	Gag/Aag	12/15	1	2	FACETS	0.844	0.717	0.981	0.844	0.717	0.981	CLONAL	1	TRUE	1	0.33	2		356	352	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857061	9857061	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	38	300	1	ENST00000330684.3:c.4340C>T	p.Ser1447Phe	p.S1447F	ENST00000330684	NM_001134407.1	1447	tCc/tTc	13/13	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.33	2		301	219	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857464	9857464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	52	252	0	ENST00000330684.3:c.3937C>T	p.Leu1313Phe	p.L1313F	ENST00000330684	NM_001134407.1	1313	Ctc/Ttc	13/13	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.33	2		252	283	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273977	10273977	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	52	380	1	ENST00000330684.3:c.292C>T	p.Leu98Phe	p.L98F	ENST00000330684	NM_001134407.1	98	Ctc/Ttc	2/13	1	2	FACETS	0.8	0.683	0.927	0.8	0.683	0.927	CLONAL	1	TRUE	1	0.33	2		381	394	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662381	67662381	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	51	358	0	ENST00000264010.4:c.1627A>T	p.Lys543Ter	p.K543*	ENST00000264010	NM_006565.3	543	Aag/Tag	9/12	1	2	FACETS	0.767	0.654	0.891	0.767	0.654	0.891	SUBCLONAL	1	TRUE	1	0.33	2		358	403	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350234	89350234	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	66	366	1	ENST00000301030.4:c.2716C>T	p.Arg906Ter	p.R906*	ENST00000301030	NM_001256183.1	906	Cga/Tga	9/13	1	2	FACETS	0.905	0.788	1	0.905	0.788	1	CLONAL	1	TRUE	1	0.33	2		367	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579357	7579359	+	frameshift_variant	Frame_Shift_Del	DEL	ACG	ACG	CA	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	56	381	0	ENST00000269305.4:c.328_330delinsTG	p.Arg110CysfsTer13	p.R110Cfs*13	ENST00000269305	NM_001126112.2	110	CGT/TG	4/11	1	2	FACETS	0.763	0.655	0.88	0.763	0.655	0.88	SUBCLONAL	1	TRUE	1	0.33	2		381	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579536	7579536	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567556930	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	61	407	1	ENST00000269305.4:c.151G>T	p.Glu51Ter	p.E51*	ENST00000269305	NM_001126112.2	51	Gaa/Taa	4/11	1	2	FACETS	0.842	0.728	0.965	0.842	0.728	0.965	CLONAL	1	TRUE	1	0.33	2		408	439	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044470	12044470	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	26	161	0	ENST00000353533.5:c.1093C>T	p.Pro365Ser	p.P365S	ENST00000353533	NM_003010.3	365	Ccc/Tcc	11/11	1	2	FACETS	0.875	0.699	1	0.875	0.699	1	CLONAL	1	TRUE	1	0.33	2		161	180	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965120	15965121	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	23	220	0	ENST00000268712.3:c.5475_5476delinsAA	p.Asp1826Asn	p.D1826N	ENST00000268712	NM_006311.3	1825	gtGGat/gtAAat	37/46	1	2	FACETS	0.625	0.489	0.781	0.625	0.489	0.781	SUBCLONAL	1	TRUE	1	0.33	2		220	223	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17124889	17124889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748031634	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	54	364	1	ENST00000285071.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000285071	NM_144997.5	278	cCg/cTg	8/14	1	2	FACETS	0.949	0.814	1	0.949	0.814	1	CLONAL	1	TRUE	1	0.33	2		365	345	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587393	29587394	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	42	210	1	ENST00000356175.3:c.4374_4375delinsTT	p.Leu1459Phe	p.L1459F	ENST00000356175	NM_000267.3	1458	ttCCtt/ttTTtt	33/57	1	2	FACETS	0.929	0.78	1	0.929	0.78	1	CLONAL	1	TRUE	1	0.33	2		211	274	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441883	40441884	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	55	381	2	ENST00000345506.4:c.129-1_129delinsAA		p.X43_splice	ENST00000345506	NM_003152.3	43		4/20	1	2	FACETS	0.891	0.765	1	0.891	0.765	1	CLONAL	1	TRUE	1	0.33	2		383	374	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59770793	59770793	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1064793893	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	45	208	0	ENST00000259008.2:c.2573C>T	p.Ser858Phe	p.S858F	ENST00000259008	NM_032043.2	858	tCt/tTt	18/20	1	2	FACETS	0.764	0.644	0.896	0.764	0.644	0.896	SUBCLONAL	1	TRUE	1	0.33	2		208	357	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533089	63533090	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	29	255	1	ENST00000307078.5:c.1804_1805delinsAA	p.Gly602Lys	p.G602K	ENST00000307078	NM_004655.3	602	GGa/AAa	7/11	1	2	FACETS	0.706	0.569	0.86	0.706	0.569	0.86	SUBCLONAL	1	TRUE	1	0.33	2		256	249	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211120	2211121	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	57	359	1	ENST00000398665.3:c.1374_1375delinsTT	p.Pro459Ser	p.P459S	ENST00000398665	NM_032482.2	458	agCCcg/agTTcg	15/28	1	2	FACETS	0.785	0.675	0.905	0.785	0.675	0.905	CLONAL	1	TRUE	1	0.33	2		360	440	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226410	2226410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	40	404	0	ENST00000398665.3:c.3890C>T	p.Pro1297Leu	p.P1297L	ENST00000398665	NM_032482.2	1297	cCc/cTc	27/28	1	2	FACETS	0.681	0.567	0.807	0.681	0.567	0.807	SUBCLONAL	1	TRUE	1	0.33	2		404	356	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274223	5274223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	42	321	0	ENST00000357368.4:c.224C>T	p.Ser75Phe	p.S75F	ENST00000357368	NM_002850.3	75	tCt/tTt	3/38	1	2	FACETS	0.764	0.64	0.901	0.764	0.64	0.901	CLONAL	1	TRUE	1	0.33	2		321	333	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602775	10602775	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	53	331	0	ENST00000171111.5:c.803T>G	p.Leu268Arg	p.L268R	ENST00000171111	NM_203500.1	268	cTg/cGg	3/6	1	2	FACETS	0.776	0.663	0.899	0.776	0.663	0.899	SUBCLONAL	1	TRUE	1	0.33	2		331	414	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094996	11094996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	46	362	0	ENST00000358026.2:c.169C>T	p.Pro57Ser	p.P57S	ENST00000358026	NM_001128849.1	57	Ccc/Tcc	2/36	1	2	FACETS	0.827	0.699	0.967	0.827	0.699	0.967	CLONAL	1	TRUE	1	0.33	2		362	337	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376238	15376238	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	47	308	0	ENST00000263377.2:c.776C>T	p.Pro259Leu	p.P259L	ENST00000263377	NM_058243.2	259	cCc/cTc	5/20	1	2	FACETS	0.899	0.762	1	0.899	0.762	1	CLONAL	1	TRUE	1	0.33	2		308	317	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387377	17387377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	63	411	0	ENST00000359435.4:c.643C>T	p.Leu215Phe	p.L215F	ENST00000359435	NM_001033549.1	215	Ctt/Ttt	7/9	1	2	FACETS	0.797	0.691	0.912	0.797	0.691	0.912	CLONAL	1	TRUE	1	0.33	2		411	479	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256784	19256784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1297266623	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	44	271	2	ENST00000162023.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000162023		310	tCc/tTc	13/13	1	2	FACETS	0.946	0.798	1	0.946	0.798	1	CLONAL	1	TRUE	1	0.33	2		273	282	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224313	36224313	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	108	404	0	ENST00000222270.7:c.6863C>T	p.Ser2288Phe	p.S2288F	ENST00000222270	NM_014727.1	2288	tCc/tTc	28/37	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.33	2		404	458	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40739813	40739813	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	96	379	0	ENST00000392038.2:c.1412C>T	p.Pro471Leu	p.P471L	ENST00000392038	NM_001626.4	471	cCc/cTc	14/14	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.33	2		379	530	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753764	42753764	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	60	405	0	ENST00000222329.4:c.500C>T	p.Ser167Leu	p.S167L	ENST00000222329	NM_006494.2	167	tCa/tTa	4/4	1	2	FACETS	0.727	0.627	0.836	0.727	0.627	0.836	SUBCLONAL	1	TRUE	1	0.33	2		405	500	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463244	25463244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	41	311	1	ENST00000264709.3:c.2249C>T	p.Pro750Leu	p.P750L	ENST00000264709	NM_175629.2	750	cCc/cTc	19/23	1	2	FACETS	0.755	0.631	0.892	0.755	0.631	0.892	SUBCLONAL	1	TRUE	1	0.33	2		312	329	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471028	25471028	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775861139	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	55	337	0	ENST00000264709.3:c.733C>T	p.Pro245Ser	p.P245S	ENST00000264709	NM_175629.2	245	Cct/Tct	7/23	1	2	FACETS	0.929	0.798	1	0.929	0.798	1	CLONAL	1	TRUE	1	0.33	2		337	359	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966405	25966405	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	98	399	1	ENST00000435504.4:c.2801A>T	p.Asn934Ile	p.N934I	ENST00000435504		934	aAc/aTc	13/13	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.33	2		400	493	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543651	29543652	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	79	296	1	ENST00000389048.3:c.1511_1512delinsAA	p.Arg504Lys	p.R504K	ENST00000389048	NM_004304.4	504	aGG/aAA	7/29	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.33	2		297	424	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656991	47656991	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	94	243	0	ENST00000233146.2:c.1187G>T	p.Arg396Ile	p.R396I	ENST00000233146	NM_000251.2	396	aGa/aTa	7/16	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.33	2		243	424	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137453	202137453	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	73	315	0	ENST00000358485.4:c.681C>A	p.Asn227Lys	p.N227K	ENST00000358485	NM_001080125.1	227	aaC/aaA	4/9	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.33	2		315	365	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732733	204732733	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1365829864	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	57	282	0	ENST00000302823.3:c.68C>T	p.Thr23Ile	p.T23I	ENST00000302823	NM_005214.4	23	aCt/aTt	1/4	1	2	FACETS	0.934	0.805	1	0.934	0.805	1	CLONAL	1	TRUE	1	0.33	2		282	370	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248452	212248452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	39	195	0	ENST00000342788.4:c.3815G>A	p.Gly1272Glu	p.G1272E	ENST00000342788	NM_005235.2	1272	gGg/gAg	28/28	1	2	FACETS	0.965	0.805	1	0.965	0.805	1	CLONAL	1	TRUE	1	0.33	2		195	245	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488712	212488712	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	42	310	0	ENST00000342788.4:c.2137T>G	p.Leu713Val	p.L713V	ENST00000342788	NM_005235.2	713	Ttg/Gtg	18/28	1	2	FACETS	0.713	0.597	0.841	0.713	0.597	0.841	SUBCLONAL	1	TRUE	1	0.33	2		310	357	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403203	213403203	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	39	286	0	ENST00000342788.4:c.52G>A	p.Gly18Arg	p.G18R	ENST00000342788	NM_005235.2	18	Ggg/Agg	1/28	1	2	FACETS	0.755	0.628	0.896	0.755	0.628	0.896	SUBCLONAL	1	TRUE	1	0.33	2		286	313	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561352	9561352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773981325	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	64	241	1	ENST00000353224.5:c.430G>A	p.Glu144Lys	p.E144K	ENST00000353224	NM_177990.2	144	Gaa/Aaa	4/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.33	2		242	288	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624795	9624795	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	51	226	1	ENST00000353224.5:c.182C>T	p.Pro61Leu	p.P61L	ENST00000353224	NM_177990.2	61	cCc/cTc	3/10	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.33	2		227	261	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031164	36031165	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	57	275	1	ENST00000358208.4:c.1283_1284delinsTT	p.Pro428Leu	p.P428L	ENST00000358208		428	cCC/cTT	11/12	1	2	FACETS	0.979	0.844	1	0.979	0.844	1	CLONAL	1	TRUE	1	0.33	2		276	353	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741513	39741513	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	64	258	0	ENST00000361337.2:c.1400C>T	p.Ser467Phe	p.S467F	ENST00000361337	NM_003286.2	467	tCc/tTc	14/21	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.33	2		258	344	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40864890	40864890	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	55	266	0	ENST00000373198.4:c.2378C>G	p.Ala793Gly	p.A793G	ENST00000373198	NM_133170.3	793	gCt/gGt	16/32	1	2	FACETS	0.882	0.757	1	0.882	0.757	1	CLONAL	1	TRUE	1	0.33	2		266	378	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319699	62319699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	47	366	0	ENST00000360203.5:c.1682C>T	p.Pro561Leu	p.P561L	ENST00000360203	NM_001283009.1	561	cCt/cTt	20/35	1	2	FACETS	0.729	0.616	0.852	0.729	0.616	0.852	SUBCLONAL	1	TRUE	1	0.33	2		366	391	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62325771	62325772	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	52	378	3	ENST00000360203.5:c.3039_3040delinsTT	p.Gln1014Ter	p.Q1014*	ENST00000360203	NM_001283009.1	1013	gcCCag/gcTTag	31/35	1	2	FACETS	0.916	0.784	1	0.916	0.784	1	CLONAL	1	TRUE	1	0.33	2		381	344	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206731	36206731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	69	367	1	ENST00000300305.3:c.781C>T	p.Pro261Ser	p.P261S	ENST00000300305		261	Cct/Tct	6/8	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.33	2		368	388	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656905	45656905	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	95	324	0	ENST00000407780.3:c.251C>T	p.Ala84Val	p.A84V	ENST00000407780	NM_001283052.1	84	gCc/gTc	3/7	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.33	2		324	450	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45658336	45658336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760455624	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	49	319	1	ENST00000407780.3:c.50G>A	p.Arg17Gln	p.R17Q	ENST00000407780	NM_001283052.1	17	cGa/cAa	2/7	1	2	FACETS	0.752	0.638	0.876	0.752	0.638	0.876	SUBCLONAL	1	TRUE	1	0.33	2		320	395	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130436	29130436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555932172	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	60	338	0	ENST00000328354.6:c.274C>T	p.Pro92Ser	p.P92S	ENST00000328354	NM_007194.3	92	Ccc/Tcc	2/15	1	2	FACETS	0.988	0.855	1	0.988	0.855	1	CLONAL	1	TRUE	1	0.33	2		338	368	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057282	30057282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	54	285	0	ENST00000338641.4:c.764C>T	p.Ser255Phe	p.S255F	ENST00000338641	NM_000268.3	255	tCc/tTc	8/16	1	2	FACETS	0.875	0.75	1	0.875	0.75	1	CLONAL	1	TRUE	1	0.33	2		285	374	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584776	52584777	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	47	304	0	ENST00000394830.3:c.4345_4346delinsTT	p.Pro1449Leu	p.P1449L	ENST00000394830	NM_018313.4	1449	CCa/TTa	28/30	1	2	FACETS	0.789	0.668	0.922	0.789	0.668	0.922	CLONAL	1	TRUE	1	0.33	2		304	361	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259510	89259510	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770106113	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	36	253	0	ENST00000336596.2:c.654G>A	p.Met218Ile	p.M218I	ENST00000336596	NM_005233.5	218	atG/atA	3/17	1	2	FACETS	0.894	0.74	1	0.894	0.74	1	CLONAL	1	TRUE	1	0.33	2		253	244	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445085	89445085	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	52	260	0	ENST00000336596.2:c.1405G>A	p.Asp469Asn	p.D469N	ENST00000336596	NM_005233.5	469	Gac/Aac	6/17	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.33	2		260	307	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480459	89480459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	52	238	1	ENST00000336596.2:c.2296G>A	p.Gly766Arg	p.G766R	ENST00000336596	NM_005233.5	766	Gga/Aga	13/17	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.33	2		239	270	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498474	89498474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	37	217	0	ENST00000336596.2:c.2446G>A	p.Glu816Lys	p.E816K	ENST00000336596	NM_005233.5	816	Gag/Aag	14/17	1	2	FACETS	0.818	0.678	0.974	0.818	0.678	0.974	CLONAL	1	TRUE	1	0.33	2		217	274	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499371	89499371	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	44	228	0	ENST00000336596.2:c.2541G>A	p.Met847Ile	p.M847I	ENST00000336596	NM_005233.5	847	atG/atA	15/17	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.33	2		228	248	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215363	142215363	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	45	231	0	ENST00000350721.4:c.5739-1G>A		p.X1913_splice	ENST00000350721	NM_001184.3	1913			1	2	FACETS	0.915	0.773	1	0.915	0.773	1	CLONAL	1	TRUE	1	0.33	2		231	298	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927472	178927472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	38	182	0	ENST00000263967.3:c.1235G>A	p.Arg412Gln	p.R412Q	ENST00000263967	NM_006218.2	412	cGa/cAa	7/21	1	2	FACETS	0.85	0.706	1	0.85	0.706	1	CLONAL	1	TRUE	1	0.33	2		182	271	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167818	185167818	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	55	241	0	ENST00000265026.3:c.1141G>A	p.Gly381Arg	p.G381R	ENST00000265026	NM_004721.4	381	Gga/Aga	6/14	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.33	2		241	295	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129869	55129869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	64	315	1	ENST00000257290.5:c.403G>A	p.Asp135Asn	p.D135N	ENST00000257290	NM_006206.4	135	Gat/Aat	4/23	1	2	FACETS	0.96	0.835	1	0.96	0.835	1	CLONAL	1	TRUE	1	0.33	2		316	404	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565847	55565847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	96	308	0	ENST00000288135.5:c.671G>A	p.Arg224Lys	p.R224K	ENST00000288135	NM_000222.2	224	aGg/aAg	4/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.33	2		308	485	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467539	66467539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	42	199	0	ENST00000273854.3:c.730C>T	p.Pro244Ser	p.P244S	ENST00000273854	NM_004439.5	244	Cct/Tct	3/18	1	2	FACETS	0.972	0.817	1	0.972	0.817	1	CLONAL	1	TRUE	1	0.33	2		199	262	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467835	66467835	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	25	213	0	ENST00000273854.3:c.434G>A	p.Gly145Glu	p.G145E	ENST00000273854	NM_004439.5	145	gGg/gAg	3/18	1	2	FACETS	0.624	0.493	0.772	0.624	0.493	0.772	SUBCLONAL	1	TRUE	1	0.33	2		213	243	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467998	66467998	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	19	151	0	ENST00000273854.3:c.271G>A	p.Glu91Lys	p.E91K	ENST00000273854	NM_004439.5	91	Gaa/Aaa	3/18	1	2	FACETS	0.476	0.362	0.609	0.476	0.362	0.609	SUBCLONAL	1	TRUE	1	0.33	2		151	242	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196300	106196300	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	40	149	0	ENST00000380013.4:c.4633C>A	p.Gln1545Lys	p.Q1545K	ENST00000380013	NM_001127208.2	1545	Cag/Aag	11/11	0.3	1	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	0	0.33	1		149	183	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278800	1278800	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	43	280	0	ENST00000310581.5:c.2242C>T	p.Gln748Ter	p.Q748*	ENST00000310581	NM_198253.2	748	Cag/Tag	6/16	1	2	FACETS	0.677	0.568	0.798	0.677	0.568	0.798	SUBCLONAL	1	TRUE	1	0.33	2		280	385	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31511271	31511271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	68	321	0	ENST00000344624.3:c.1303G>A	p.Val435Met	p.V435M	ENST00000344624		435	Gtg/Atg	6/33	1	2	FACETS	0.882	0.77	1	0.882	0.77	1	CLONAL	1	TRUE	1	0.33	2		321	467	SUCCESS
APC	324	MSKCC	GRCh37	5	112176282	112176282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	39	251	0	ENST00000257430.4:c.4991C>T	p.Ser1664Phe	p.S1664F	ENST00000257430	NM_000038.5	1664	tCc/tTc	16/16	1	2	FACETS	0.916	0.764	1	0.916	0.764	1	CLONAL	1	TRUE	1	0.33	2		251	258	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456989	149456989	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1411349452	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	35	230	0	ENST00000286301.3:c.739C>T	p.Pro247Ser	p.P247S	ENST00000286301	NM_005211.3	247	Cct/Tct	6/22	1	2	FACETS	0.813	0.67	0.971	0.813	0.67	0.971	CLONAL	1	TRUE	1	0.33	2		230	261	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459889	149459890	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	47	750	1	ENST00000286301.3:c.317_318delinsAA	p.Arg106Gln	p.R106Q	ENST00000286301	NM_005211.3	106	cGG/cAA	4/22	1	2	FACETS	0.748	0.632	0.874	0.748	0.632	0.874	SUBCLONAL	1	TRUE	1	0.33	2		751	381	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500876	149500876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	52	329	0	ENST00000261799.4:c.2354G>A	p.Arg785Lys	p.R785K	ENST00000261799	NM_002609.3	785	aGg/aAg	17/23	1	2	FACETS	0.97	0.83	1	0.97	0.83	1	CLONAL	1	TRUE	1	0.33	2		329	325	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518076	176518076	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	50	342	0	ENST00000292408.4:c.574C>A	p.His192Asn	p.H192N	ENST00000292408	NM_213647.1	192	Cat/Aat	5/18	1	2	FACETS	0.746	0.635	0.868	0.746	0.635	0.868	SUBCLONAL	1	TRUE	1	0.33	2		342	406	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522624	176522624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	46	404	1	ENST00000292408.4:c.1721C>T	p.Pro574Leu	p.P574L	ENST00000292408	NM_213647.1	574	cCc/cTc	13/18	1	2	FACETS	0.781	0.66	0.914	0.781	0.66	0.914	CLONAL	1	TRUE	1	0.33	2		405	357	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524595	176524595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757780576	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	58	466	0	ENST00000292408.4:c.2327C>T	p.Ser776Phe	p.S776F	ENST00000292408	NM_213647.1	776	tCc/tTc	18/18	1	2	FACETS	0.781	0.673	0.899	0.781	0.673	0.899	SUBCLONAL	1	TRUE	1	0.33	2		466	450	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176684094	176684095	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	46	280	0	ENST00000439151.2:c.4908_4909delinsTT	p.Leu1637Phe	p.L1637F	ENST00000439151	NM_022455.4	1636	tcCCtc/tcTTtc	13/23	1	2	FACETS	0.72	0.608	0.844	0.72	0.608	0.844	SUBCLONAL	1	TRUE	1	0.33	2		280	387	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722200	176722200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	37	233	1	ENST00000439151.2:c.7831C>T	p.Pro2611Ser	p.P2611S	ENST00000439151	NM_022455.4	2611	Ccc/Tcc	23/23	1	2	FACETS	0.934	0.776	1	0.934	0.776	1	CLONAL	1	TRUE	1	0.33	2		234	240	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031939	26031939	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	47	204	0	ENST00000244661.2:c.350G>A	p.Arg117Gln	p.R117Q	ENST00000244661	NM_003537.3	117	cGa/cAa	1/1	0.3	1	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	0	0.33	1		204	215	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032257	26032257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	22	277	0	ENST00000244661.2:c.32C>T	p.Ser11Phe	p.S11F	ENST00000244661	NM_003537.3	11	tCc/tTc	1/1	0.3	1	FACETS	0.819	0.642	1	0.819	0.642	1	CLONAL	1	TRUE	0	0.33	1		277	136	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671212	30671212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1270731396	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	77	383	0	ENST00000376406.3:c.5665G>A	p.Glu1889Lys	p.E1889K	ENST00000376406	NM_014641.2	1889	Gaa/Aaa	11/15	0.3	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.33	1		383	361	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673218	30673218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	33	270	0	ENST00000376406.3:c.3742C>T	p.Pro1248Ser	p.P1248S	ENST00000376406	NM_014641.2	1248	Cct/Tct	10/15	0.3	1	FACETS	0.913	0.751	1	0.913	0.751	1	CLONAL	1	TRUE	0	0.33	1		270	183	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188003	32188003	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	92	384	0	ENST00000375023.3:c.1218A>T	p.Gln406His	p.Q406H	ENST00000375023	NM_004557.3	406	caA/caT	7/30	0.3	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.33	1		384	397	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815727	32815728	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	79	363	0	ENST00000354258.4:c.1888_1889delinsTT	p.Pro630Phe	p.P630F	ENST00000354258	NM_000593.5	630	CCc/TTc	8/11	0.3	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.33	1		363	358	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964481	93964481	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775779069	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	61	236	0	ENST00000369303.4:c.2416G>A	p.Glu806Lys	p.E806K	ENST00000369303	NM_004440.3	806	Gaa/Aaa	14/17	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.33	2		236	314	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965586	93965586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372024057	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	60	276	1	ENST00000369303.4:c.2342G>A	p.Arg781Gln	p.R781Q	ENST00000369303	NM_004440.3	781	cGa/cAa	13/17	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.33	2		277	343	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967841	93967841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	66	274	0	ENST00000369303.4:c.2086C>T	p.His696Tyr	p.H696Y	ENST00000369303	NM_004440.3	696	Cat/Tat	11/17	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.33	2		274	324	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066549	94066549	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	45	224	1	ENST00000369303.4:c.1210G>A	p.Asp404Asn	p.D404N	ENST00000369303	NM_004440.3	404	Gac/Aac	5/17	1	2	FACETS	0.981	0.83	1	0.981	0.83	1	CLONAL	1	TRUE	1	0.33	2		225	278	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066611	94066611	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	47	254	0	ENST00000369303.4:c.1148G>A	p.Gly383Glu	p.G383E	ENST00000369303	NM_004440.3	383	gGg/gAg	5/17	1	2	FACETS	0.907	0.769	1	0.907	0.769	1	CLONAL	1	TRUE	1	0.33	2		254	314	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709081	117709081	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	40	305	0	ENST00000368508.3:c.1876T>G	p.Phe626Val	p.F626V	ENST00000368508	NM_002944.2	626	Ttc/Gtc	13/43	1	2	FACETS	0.741	0.618	0.878	0.741	0.618	0.878	SUBCLONAL	1	TRUE	1	0.33	2		305	327	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138197163	138197164	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	55	198	0	ENST00000237289.4:c.665_666delinsTT	p.Ser222Phe	p.S222F	ENST00000237289	NM_001270507.1	222	tCC/tTT	5/9	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.33	2		198	307	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005666	150005666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	40	212	0	ENST00000253339.5:c.559C>T	p.Pro187Ser	p.P187S	ENST00000253339		187	Cct/Tct	3/7	1	2	FACETS	0.825	0.688	0.975	0.825	0.688	0.975	CLONAL	1	TRUE	1	0.33	2		212	294	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100526	157100526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769085274	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	36	119	0	ENST00000346085.5:c.1463C>T	p.Pro488Leu	p.P488L	ENST00000346085	NM_020732.3	488	cCg/cTg	1/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.33	2		119	170	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157431689	157431689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	66	301	0	ENST00000346085.5:c.2365G>A	p.Glu789Lys	p.E789K	ENST00000346085	NM_020732.3	789	Gaa/Aaa	7/20	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.33	2		301	363	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527796	157527796	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	41	280	0	ENST00000346085.5:c.5521C>T	p.Pro1841Ser	p.P1841S	ENST00000346085	NM_020732.3	1841	Cct/Tct	20/20	1	2	FACETS	0.837	0.7	0.987	0.837	0.7	0.987	CLONAL	1	TRUE	1	0.33	2		280	297	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528682	157528682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	70	311	0	ENST00000346085.5:c.6407C>T	p.Ser2136Leu	p.S2136L	ENST00000346085	NM_020732.3	2136	tCg/tTg	20/20	1	2	FACETS	0.966	0.846	1	0.966	0.846	1	CLONAL	1	TRUE	1	0.33	2		311	439	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983863	2983863	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	23	289	0	ENST00000396946.4:c.667C>G	p.Arg223Gly	p.R223G	ENST00000396946	NM_032415.4	223	Cga/Gga	5/25	0.3	3	FACETS	0.415	0.323	0.522	0.138	0.107	0.174	SUBCLONAL	1	TRUE	0	0.33	3		289	391	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729381	41729381	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1157959739	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	34	298	0	ENST00000242208.4:c.1148C>T	p.Pro383Leu	p.P383L	ENST00000242208	NM_002192.2	383	cCc/cTc	3/3	0.3	3	FACETS	0.562	0.459	0.678	0.187	0.153	0.226	SUBCLONAL	1	TRUE	0	0.33	3		298	427	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367282	50367282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	102	263	0	ENST00000331340.3:c.89C>T	p.Pro30Leu	p.P30L	ENST00000331340	NM_006060.4	30	cCc/cTc	3/8	0.3	3	FACETS	0.834	0.756	0.913	0.834	0.756	0.913	CLONAL	3	TRUE	0	0.33	3		263	288	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274841	38274841	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1563450187	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	38	249	0	ENST00000425967.3:c.1739G>A	p.Gly580Glu	p.G580E	ENST00000425967	NM_001174067.1	580	gGg/gAg	13/19	1	2	FACETS	0.808	0.671	0.959	0.808	0.671	0.959	CLONAL	1	TRUE	1	0.33	2		249	285	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981941	70981941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	52	396	0	ENST00000276594.2:c.155C>T	p.Pro52Leu	p.P52L	ENST00000276594	NM_024504.3	52	cCt/cTt	2/8	1	2	FACETS	0.696	0.593	0.808	0.696	0.593	0.808	SUBCLONAL	1	TRUE	1	0.33	2		396	453	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145736900	145736900	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs765804620	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	91	411	0	ENST00000428558.2:c.3541C>T	p.Arg1181Ter	p.R1181*	ENST00000428558	NM_004260.3	1181	Cga/Tga	22/22	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.33	2		411	431	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339164	87339164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	125	260	0	ENST00000277120.3:c.746C>T	p.Ser249Phe	p.S249F	ENST00000277120		249	tCc/tTc	8/19	0.253299341596759	3	FACETS	1	0.98	1	0.829	0.759	0.9	CLONAL	2	TRUE	0	0.33	3		260	355	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220479	98220479	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	62	336	0	ENST00000331920.6:c.2984G>T	p.Arg995Met	p.R995M	ENST00000331920	NM_000264.3	995	aGg/aTg	18/24	0.253299341596759	3	FACETS	0.877	0.759	1	0.292	0.253	0.335	CLONAL	1	TRUE	0	0.33	3		336	499	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395288	139395288	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs755032609	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	155	298	0	ENST00000277541.6:c.5650C>A	p.Pro1884Thr	p.P1884T	ENST00000277541	NM_017617.3	1884	Ccg/Acg	31/34	0.253299341596759	3	FACETS	0.948	0.878	1	0.948	0.878	1	CLONAL	3	TRUE	0	0.33	3		298	385	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396538	139396538	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs557319054	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	20	286	0	ENST00000277541.6:c.5387C>T	p.Pro1796Leu	p.P1796L	ENST00000277541	NM_017617.3	1796	cCc/cTc	29/34	0.253299341596759	3	FACETS	0.374	0.285	0.478	0.125	0.095	0.16	SUBCLONAL	1	TRUE	0	0.33	3		286	378	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396774	139396775	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	54	325	1	ENST00000277541.6:c.5333_5334delinsTT	p.Ala1778Val	p.A1778V	ENST00000277541	NM_017617.3	1778	gCC/gTT	28/34	0.253299341596759	3	FACETS	0.838	0.717	0.97	0.279	0.239	0.324	CLONAL	1	TRUE	0	0.33	3		326	455	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410118	139410118	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	97	356	1	ENST00000277541.6:c.1720C>T	p.Pro574Ser	p.P574S	ENST00000277541	NM_017617.3	574	Ccc/Tcc	11/34	0.253299341596759	3	FACETS	0.777	0.696	0.861	0.518	0.464	0.574	SUBCLONAL	2	TRUE	0	0.33	3		357	441	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418372	139418372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	61	725	0	ENST00000277541.6:c.200C>T	p.Pro67Leu	p.P67L	ENST00000277541	NM_017617.3	67	cCc/cTc	3/34	0.253299341596759	3	FACETS	0.922	0.797	1	0.307	0.265	0.353	CLONAL	1	TRUE	0	0.33	3		725	467	SUCCESS
AR	367	MSKCC	GRCh37	X	66931393	66931393	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343361020	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	72	173	0	ENST00000374690.3:c.2035G>A	p.Glu679Lys	p.E679K	ENST00000374690	NM_000044.3	679	Gaa/Aaa	4/8	0.186647668080246	2	FACETS	1	0.954	1			1	INDETERMINATE	2	TRUE	NA	0.33	2		173	192	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2493248	2493248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1275298759	NA	P-0026663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	34	269	0	ENST00000355716.4:c.688C>T	p.Pro230Ser	p.P230S	ENST00000355716	NM_003820.2	230	Cca/Tca	6/8	1	2	FACETS	0.814	0.669	0.976	0.814	0.669	0.976	CLONAL	1	TRUE	1	0.33	2		269	253	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	145	463	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.601235212743434	2		463	469	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	143	244	2	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.601235212743434	2		246	404	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438211	49438211	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	51	435	0	ENST00000301067.7:c.5058del	p.Lys1686AsnfsTer36	p.K1686Nfs*36	ENST00000301067	NM_003482.3	1686	aaA/aa	20/54	0.539046585139534	3	FACETS	0.219	0.185	0.257	0.11	0.092	0.129	SUBCLONAL	1	TRUE	1	0.601235212743434	3		435	1007	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	376	519	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.881	0.844	0.918	1	0.997	1	CLONAL	2	TRUE	1	0.601235212743434	2		524	710	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	165	469	3	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	1	2	FACETS	0.717	0.66	0.777	0.717	0.66	0.777	SUBCLONAL	1	TRUE	1	0.601235212743434	2		472	765	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	291	417	2	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	0.218868711518164	5	FACETS	0.862	0.816	0.908			1	INDETERMINATE	3	TRUE	NA	0.601235212743434	5		419	712	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	155	391	1	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.982	0.905	1	0.982	0.905	1	CLONAL	1	TRUE	1	0.601235212743434	2		392	525	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	166	487	1	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.997	0.921	1	0.997	0.921	1	CLONAL	1	TRUE	1	0.601235212743434	2		488	554	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	287	504	7	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	0.539046585139534	3	FACETS	0.858	0.811	0.905	0.858	0.811	0.905	CLONAL	2	TRUE	1	0.601235212743434	3		511	724	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989481	85989481	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	126	296	0	ENST00000263360.6:c.1240C>T	p.Arg414Ter	p.R414*	ENST00000263360	NM_003797.3	414	Cga/Tga	12/12	1	2	FACETS	0.859	0.782	0.938	0.859	0.782	0.938	CLONAL	1	TRUE	1	0.601235212743434	2		296	488	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175868	24175868	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886039520	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	132	366	0	ENST00000263121.7:c.1096C>T	p.Arg366Cys	p.R366C	ENST00000263121	NM_003073.3	366	Cgc/Tgc	8/9	1	2	FACETS	0.758	0.691	0.829	0.758	0.691	0.829	SUBCLONAL	1	TRUE	1	0.601235212743434	2		366	579	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	216	426	1	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	0.601235212743434	2	FACETS	0.972	0.907	1	0.486	0.453	0.52	CLONAL	1	TRUE	0	0.601235212743434	2		427	739	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537919	212537919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	183	318	0	ENST00000342788.4:c.1686G>A	p.Met562Ile	p.M562I	ENST00000342788	NM_005235.2	562	atG/atA	14/28	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.601235212743434	2		318	599	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598909	28598909	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765112783	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	203	400	2	ENST00000253063.3:c.469C>T	p.Arg157Cys	p.R157C	ENST00000253063	NM_031459.4	157	Cgc/Tgc	4/10	1	2	FACETS	0.956	0.89	1	0.956	0.89	1	CLONAL	1	TRUE	1	0.601235212743434	2		402	706	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807516	36807516	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	196	442	0	ENST00000373129.3:c.1148T>A	p.Leu383Gln	p.L383Q	ENST00000373129	NM_032017.1	383	cTg/cAg	12/12	1	2	FACETS	0.98	0.912	1	0.98	0.912	1	CLONAL	1	TRUE	1	0.601235212743434	2		442	665	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248285	59248285	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	25	48	0	ENST00000371222.2:c.458del	p.Gly153AlafsTer29	p.G153Afs*29	ENST00000371222	NM_002228.3	153	gGc/gc	1/1	1	2	FACETS	0.785	0.631	0.954	0.785	0.631	0.954	CLONAL	1	TRUE	1	0.601235212743434	2		48	106	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117093	193117093	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	108	223	0	ENST00000367435.3:c.826G>A	p.Val276Met	p.V276M	ENST00000367435	NM_024529.4	276	Gtg/Atg	8/17	1	2	FACETS	0.874	0.79	0.961	0.874	0.79	0.961	CLONAL	1	TRUE	1	0.601235212743434	2		223	411	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981881	201981881	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs879165146	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	205	456	0	ENST00000359651.3:c.592A>G	p.Thr198Ala	p.T198A	ENST00000359651		198	Acc/Gcc	4/8	1	2	FACETS	0.841	0.782	0.902	0.841	0.782	0.902	CLONAL	1	TRUE	1	0.601235212743434	2		456	811	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649643	206649643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1344445148	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	208	403	1	ENST00000367120.3:c.478G>A	p.Ala160Thr	p.A160T	ENST00000367120	NM_014002.3	160	Gct/Act	6/22	1	2	FACETS	0.853	0.794	0.915	0.853	0.794	0.915	CLONAL	1	TRUE	1	0.601235212743434	2		404	811	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771485	112771485	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	175	385	0	ENST00000369452.4:c.1658T>C	p.Leu553Pro	p.L553P	ENST00000369452	NM_007373.3	553	cTc/cCc	9/9	1	2	FACETS	0.961	0.889	1	0.961	0.889	1	CLONAL	1	TRUE	1	0.601235212743434	2		385	606	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900984	114900984	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778855667	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	211	579	0	ENST00000543371.1:c.598del	p.Leu200SerfsTer25	p.L200Sfs*25	ENST00000543371	NM_001198531.1	198	caC/ca	6/14	1	2	FACETS	0.945	0.88	1	0.945	0.88	1	CLONAL	1	TRUE	1	0.601235212743434	2		579	743	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137271	64137271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	218	620	0	ENST00000334205.4:c.1703C>T	p.Thr568Met	p.T568M	ENST00000334205	NM_003942.2	568	aCg/aTg	14/17	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.601235212743434	2		620	694	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196695	67196696	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	129	406	0	ENST00000312629.5:c.230dup	p.Tyr78LeufsTer42	p.Y78Lfs*42	ENST00000312629	NM_003952.2	75	aag/aaGg	3/15	1	2	FACETS	0.879	0.802	0.959	0.879	0.802	0.959	CLONAL	1	TRUE	1	0.601235212743434	2		406	488	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948808	71948808	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150912074	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	219	527	0	ENST00000298229.2:c.3520C>T	p.Arg1174Trp	p.R1174W	ENST00000298229	NM_001567.3	1174	Cgg/Tgg	26/28	1	2	FACETS	0.959	0.895	1	0.959	0.895	1	CLONAL	1	TRUE	1	0.601235212743434	2		527	760	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918571	94918571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	138	349	0	ENST00000536441.1:c.611C>T	p.Ala204Val	p.A204V	ENST00000536441	NM_144665.3	204	gCa/gTa	5/10	1	2	FACETS	0.853	0.78	0.929	0.853	0.78	0.929	CLONAL	1	TRUE	1	0.601235212743434	2		349	538	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402268	402268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs539682097	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	53	474	0	ENST00000399788.2:c.4523G>A	p.Arg1508Gln	p.R1508Q	ENST00000399788	NM_001042603.1	1508	cGg/cAg	27/28	0.218868711518164	5	FACETS	0.348	0.295	0.406			1	INDETERMINATE	1	TRUE	NA	0.601235212743434	5		474	964	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	166	267	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.539046585139534	3	FACETS	0.829	0.77	0.89	0.829	0.77	0.89	CLONAL	2	TRUE	1	0.601235212743434	3		267	433	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378676	25378676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	73	255	0	ENST00000311936.3:c.322G>A	p.Asp108Asn	p.D108N	ENST00000311936	NM_004985.3	108	Gat/Aat	4/5	0.539046585139534	3	FACETS	0.854	0.751	0.963	0.427	0.375	0.482	CLONAL	1	TRUE	1	0.601235212743434	3		255	370	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416504	49416504	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	181	360	2	ENST00000301067.7:c.16207C>T	p.Arg5403Cys	p.R5403C	ENST00000301067	NM_003482.3	5403	Cgc/Tgc	51/54	0.539046585139534	3	FACETS	0.931	0.86	1	0.466	0.43	0.503	CLONAL	1	TRUE	1	0.601235212743434	3		362	841	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420075	49420075	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	194	352	0	ENST00000301067.7:c.15674G>A	p.Arg5225His	p.R5225H	ENST00000301067	NM_003482.3	5225	cGc/cAc	48/54	0.539046585139534	3	FACETS	1	0.97	1	0.542	0.503	0.583	CLONAL	1	TRUE	1	0.601235212743434	3		352	774	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433394	49433394	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783727	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	411	472	2	ENST00000301067.7:c.8053C>T	p.Arg2685Ter	p.R2685*	ENST00000301067	NM_003482.3	2685	Cga/Tga	32/54	0.539046585139534	3	FACETS	0.906	0.866	0.947	0.906	0.866	0.947	CLONAL	2	TRUE	1	0.601235212743434	3		474	981	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	290	467	0	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	0.539046585139534	3	FACETS	1	0.991	1	0.634	0.597	0.671	CLONAL	1	TRUE	1	0.601235212743434	3		467	990	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447799	49447799	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	172	382	0	ENST00000301067.7:c.635T>G	p.Leu212Arg	p.L212R	ENST00000301067	NM_003482.3	212	cTg/cGg	5/54	0.539046585139534	3	FACETS	0.877	0.807	0.949	0.438	0.403	0.475	CLONAL	1	TRUE	1	0.601235212743434	3		382	849	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487334	56487334	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	95	186	0	ENST00000267101.3:c.1480G>A	p.Val494Met	p.V494M	ENST00000267101	NM_001982.3	494	Gtg/Atg	12/28	0.539046585139534	3	FACETS	0.771	0.689	0.858	0.386	0.344	0.429	SUBCLONAL	1	TRUE	1	0.601235212743434	3		186	533	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878069	48878069	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	74	173	0	ENST00000267163.4:c.25del	p.Thr9ArgfsTer56	p.T9Rfs*56	ENST00000267163	NM_000321.2	7	cgA/cg	1/27	1	2	FACETS	0.932	0.826	1	0.932	0.826	1	CLONAL	1	TRUE	1	0.601235212743434	2		173	264	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	338208	338208	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	272	459	0	ENST00000262320.3:c.2503del	p.Val835TrpfsTer103	p.V835Wfs*103	ENST00000262320	NM_003502.3	835	Gtg/tg	11/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.601235212743434	2		459	852	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133797	2133797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747695245	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	120	379	0	ENST00000219476.3:c.3985C>T	p.Arg1329Cys	p.R1329C	ENST00000219476	NM_000548.3	1329	Cgc/Tgc	33/42	1	2	FACETS	0.678	0.614	0.745	0.678	0.614	0.745	SUBCLONAL	1	TRUE	1	0.601235212743434	2		379	589	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781261	3781261	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	271	535	0	ENST00000262367.5:c.5104C>T	p.Arg1702Cys	p.R1702C	ENST00000262367	NM_004380.2	1702	Cgc/Tgc	30/31	1	2	FACETS	0.974	0.915	1	0.974	0.915	1	CLONAL	1	TRUE	1	0.601235212743434	2		535	926	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781354	3781354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	221	509	0	ENST00000262367.5:c.5011G>A	p.Ala1671Thr	p.A1671T	ENST00000262367	NM_004380.2	1671	Gcc/Acc	30/31	1	2	FACETS	0.91	0.849	0.973	0.91	0.849	0.973	CLONAL	1	TRUE	1	0.601235212743434	2		509	808	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645493	67645493	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	133	185	0	ENST00000264010.4:c.758A>C	p.Lys253Thr	p.K253T	ENST00000264010	NM_006565.3	253	aAg/aCg	3/12	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.601235212743434	2		185	351	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855967	68855967	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	31	452	1	ENST00000261769.5:c.1779del	p.Ile594TyrfsTer19	p.I594Yfs*19	ENST00000261769	NM_004360.3	592	gCc/gc	12/16	0.494793996524474	1	FACETS	0.147	0.118	0.179	0.147	0.118	0.179	SUBCLONAL	1	TRUE	0	0.601235212743434	1		453	491	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855984	68855984	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121964877	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	207	447	0	ENST00000261769.5:c.1792C>T	p.Arg598Ter	p.R598*	ENST00000261769	NM_004360.3	598	Cga/Tga	12/16	0.494793996524474	1	FACETS	0.965	0.905	1	0.965	0.905	1	CLONAL	1	TRUE	0	0.601235212743434	1		447	499	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346439	89346439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567556635	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	212	461	0	ENST00000301030.4:c.6511C>T	p.Pro2171Ser	p.P2171S	ENST00000301030	NM_001256183.1	2171	Ccc/Tcc	9/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.601235212743434	2		461	683	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349640	89349641	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs772267579	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	191	487	5	ENST00000301030.4:c.3309dup	p.Asp1104ArgfsTer2	p.D1104Rfs*2	ENST00000301030	NM_001256183.1	1103	-/A	9/13	1	2	FACETS	0.801	0.742	0.862	0.801	0.742	0.862	CLONAL	1	TRUE	1	0.601235212743434	2		492	793	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805351	89805351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149851163	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	152	330	0	ENST00000389301.3:c.4199G>A	p.Arg1400His	p.R1400H	ENST00000389301	NM_000135.2	1400	cGt/cAt	42/43	1	2	FACETS	0.805	0.739	0.874	0.805	0.739	0.874	CLONAL	1	TRUE	1	0.601235212743434	2		330	628	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979619	7979619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140306846	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	131	344	0	ENST00000319144.4:c.1406G>A	p.Arg469Gln	p.R469Q	ENST00000319144	NM_001139.2	469	cGg/cAg	11/15	1	2	FACETS	0.704	0.641	0.77	0.704	0.641	0.77	SUBCLONAL	1	TRUE	1	0.601235212743434	2		344	619	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024503	16024503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	173	284	0	ENST00000268712.3:c.1715G>A	p.Arg572Gln	p.R572Q	ENST00000268712	NM_006311.3	572	cGa/cAa	16/46	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.601235212743434	2		284	572	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30326004	30326005	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs769517721	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	108	262	0	ENST00000322652.5:c.2208dup	p.Gln737ThrfsTer20	p.Q737Tfs*20	ENST00000322652	NM_015355.2	734	-/A	16/16	1	2	FACETS	0.894	0.808	0.982	0.894	0.808	0.982	CLONAL	1	TRUE	1	0.601235212743434	2		262	402	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881106	37881106	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	37	369	2	ENST00000269571.5:c.2438del	p.Asn813ThrfsTer11	p.N813Tfs*11	ENST00000269571		812	gAa/ga	20/27	1	2	FACETS	0.163	0.134	0.196	0.163	0.134	0.196	SUBCLONAL	1	TRUE	1	0.601235212743434	2		371	754	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40462589	40462589	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	209	404	0	ENST00000345506.4:c.2287C>T	p.His763Tyr	p.H763Y	ENST00000345506	NM_003152.3	763	Cac/Tac	20/20	1	2	FACETS	0.96	0.895	1	0.96	0.895	1	CLONAL	1	TRUE	1	0.601235212743434	2		404	724	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870544	40870544	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	264	455	1	ENST00000428826.2:c.859C>T	p.Arg287Trp	p.R287W	ENST00000428826		287	Cgg/Tgg	9/21	0.601235212743434	2	FACETS	1	0.971	1	0.526	0.495	0.559	CLONAL	1	TRUE	0	0.601235212743434	2		456	834	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805624	46805624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781117900	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	44	437	0	ENST00000290295.7:c.332C>T	p.Ala111Val	p.A111V	ENST00000290295	NM_006361.5	111	gCg/gTg	1/2	0.601235212743434	2	FACETS	0.191	0.159	0.226	0.095	0.079	0.113	SUBCLONAL	1	TRUE	0	0.601235212743434	2		437	767	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	415	443	0	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	0.601235212743434	2	FACETS	0.888	0.853	0.924	0.888	0.853	0.924	CLONAL	2	TRUE	0	0.601235212743434	2		443	777	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533905	63533905	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	329	335	1	ENST00000307078.5:c.1249del	p.Ala417ArgfsTer41	p.A417Rfs*41	ENST00000307078	NM_004655.3	417	Gcg/cg	6/11	0.601235212743434	2	FACETS	0.935	0.895	0.976	0.935	0.895	0.976	CLONAL	2	TRUE	0	0.601235212743434	2		336	585	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617690	39617690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141329274	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	114	261	1	ENST00000262039.4:c.1874C>T	p.Thr625Met	p.T625M	ENST00000262039	NM_002647.2	625	aCg/aTg	17/25	1	2	FACETS	0.96	0.872	1	0.96	0.872	1	CLONAL	1	TRUE	1	0.601235212743434	2		262	395	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39629506	39629506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1431988901	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	115	263	0	ENST00000262039.4:c.2200G>A	p.Val734Met	p.V734M	ENST00000262039	NM_002647.2	734	Gtg/Atg	21/25	1	2	FACETS	0.894	0.811	0.98	0.894	0.811	0.98	CLONAL	1	TRUE	1	0.601235212743434	2		263	428	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1650237	1650237	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757916399	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	187	387	1	ENST00000344749.5:c.11C>T	p.Pro4Leu	p.P4L	ENST00000344749	NM_001136139.2	4	cCg/cTg	2/19	1	2	FACETS	0.882	0.818	0.949	0.882	0.818	0.949	CLONAL	1	TRUE	1	0.601235212743434	2		388	705	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226943	2226943	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150855728	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	198	331	1	ENST00000398665.3:c.4423G>A	p.Ala1475Thr	p.A1475T	ENST00000398665	NM_032482.2	1475	Gcg/Acg	27/28	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.601235212743434	2		332	617	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	184	368	3	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	0.922	0.854	0.991	0.922	0.854	0.991	CLONAL	1	TRUE	1	0.601235212743434	2		371	664	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184534	7184534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775222338	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	221	310	3	ENST00000302850.5:c.767G>A	p.Arg256His	p.R256H	ENST00000302850	NM_000208.2	256	cGc/cAc	3/22	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.601235212743434	2		313	649	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610285	10610285	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	243	478	0	ENST00000171111.5:c.425C>T	p.Thr142Met	p.T142M	ENST00000171111	NM_203500.1	142	aCg/aTg	2/6	1	2	FACETS	0.987	0.925	1	0.987	0.925	1	CLONAL	1	TRUE	1	0.601235212743434	2		478	819	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11022965	11022965	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	191	329	1	ENST00000327064.4:c.664G>A	p.Ala222Thr	p.A222T	ENST00000327064	NM_199141.1	222	Gct/Act	5/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.601235212743434	2		330	594	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098540	11098540	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	156	361	0	ENST00000358026.2:c.1062del	p.Ile355SerfsTer56	p.I355Sfs*56	ENST00000358026	NM_001128849.1	353	aCc/ac	6/36	1	2	FACETS	0.768	0.705	0.833	0.768	0.705	0.833	SUBCLONAL	1	TRUE	1	0.601235212743434	2		361	676	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145752	11145752	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	210	454	0	ENST00000358026.2:c.4114C>T	p.Arg1372Cys	p.R1372C	ENST00000358026	NM_001128849.1	1372	Cgc/Tgc	29/36	1	2	FACETS	0.922	0.858	0.987	0.922	0.858	0.987	CLONAL	1	TRUE	1	0.601235212743434	2		454	758	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627670	14627670	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	43	345	0	ENST00000254322.2:c.400T>G	p.Phe134Val	p.F134V	ENST00000254322	NM_006145.1	134	Ttc/Gtc	2/3	1	2	FACETS	0.218	0.182	0.258	0.218	0.182	0.258	SUBCLONAL	1	TRUE	1	0.601235212743434	2		345	656	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272116	15272116	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	219	429	2	ENST00000263388.2:c.6323C>T	p.Pro2108Leu	p.P2108L	ENST00000263388	NM_000435.2	2108	cCg/cTg	33/33	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.601235212743434	2		431	727	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272337	15272337	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs771517374	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	199	747	5	ENST00000263388.2:c.6102del	p.Gly2035ValfsTer50	p.G2035Vfs*50	ENST00000263388	NM_000435.2	2034	ccC/cc	33/33	1	2	FACETS	0.878	0.816	0.942	0.878	0.816	0.942	CLONAL	1	TRUE	1	0.601235212743434	2		752	754	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278068	15278068	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747646930	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	180	351	0	ENST00000263388.2:c.5354G>A	p.Arg1785His	p.R1785H	ENST00000263388	NM_000435.2	1785	cGt/cAt	29/33	1	2	FACETS	0.903	0.836	0.972	0.903	0.836	0.972	CLONAL	1	TRUE	1	0.601235212743434	2		351	663	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366237	15366237	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141552564	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	187	451	1	ENST00000263377.2:c.1918C>T	p.Arg640Trp	p.R640W	ENST00000263377	NM_058243.2	640	Cgg/Tgg	10/20	0.505544729769647	1	FACETS	0.757	0.703	0.811	0.757	0.703	0.811	SUBCLONAL	1	TRUE	0	0.601235212743434	1		452	575	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961589	18961589	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	36	332	0	ENST00000262803.5:c.722G>T	p.Trp241Leu	p.W241L	ENST00000262803	NM_002911.3	241	tGg/tTg	5/24	1	2	FACETS	0.188	0.154	0.226	0.188	0.154	0.226	SUBCLONAL	1	TRUE	1	0.601235212743434	2		332	637	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19261529	19261529	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	108	389	0	ENST00000162023.5:c.16del	p.Ile6SerfsTer14	p.I6Sfs*14	ENST00000162023		6	Atc/tc	6/13	1	2	FACETS	0.512	0.46	0.568	0.512	0.46	0.568	SUBCLONAL	1	TRUE	1	0.601235212743434	2		389	701	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744449	41744449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143593613	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	40	448	0	ENST00000301178.4:c.1069C>T	p.Arg357Trp	p.R357W	ENST00000301178	NM_021913.4	357	Cgg/Tgg	8/20	1	2	FACETS	0.17	0.141	0.204	0.17	0.141	0.204	SUBCLONAL	1	TRUE	1	0.601235212743434	2		448	781	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763500	41763500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	173	518	1	ENST00000301178.4:c.2299C>T	p.Arg767Cys	p.R767C	ENST00000301178	NM_021913.4	767	Cgc/Tgc	19/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.601235212743434	2		519	569	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	228	730	0	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.842	0.785	0.9	0.842	0.785	0.9	CLONAL	1	TRUE	1	0.601235212743434	2		730	901	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867298	45867298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760337216	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	199	411	0	ENST00000391945.4:c.895C>T	p.Arg299Trp	p.R299W	ENST00000391945	NM_000400.3	299	Cgg/Tgg	10/23	1	2	FACETS	0.904	0.84	0.97	0.904	0.84	0.97	CLONAL	1	TRUE	1	0.601235212743434	2		411	732	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972584	25972584	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1307171996	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	103	238	0	ENST00000435504.4:c.1841G>A	p.Arg614Gln	p.R614Q	ENST00000435504		614	cGa/cAa	12/13	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.601235212743434	2		238	305	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606696	29606696	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769910087	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	132	352	0	ENST00000389048.3:c.1184G>A	p.Arg395His	p.R395H	ENST00000389048	NM_004304.4	395	cGt/cAt	5/29	1	2	FACETS	0.824	0.752	0.899	0.824	0.752	0.899	CLONAL	1	TRUE	1	0.601235212743434	2		352	533	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095568	178095568	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	28	243	0	ENST00000397062.3:c.1763A>G	p.Asp588Gly	p.D588G	ENST00000397062	NM_006164.4	588	gAt/gGt	5/5	1	2	FACETS	0.232	0.185	0.285	0.232	0.185	0.285	SUBCLONAL	1	TRUE	1	0.601235212743434	2		243	402	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736166	204736166	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	122	364	4	ENST00000302823.3:c.529del	p.Tyr177IlefsTer10	p.Y177Ifs*10	ENST00000302823	NM_005214.4	175	Ttt/tt	3/4	1	2	FACETS	0.81	0.736	0.887	0.81	0.736	0.887	CLONAL	1	TRUE	1	0.601235212743434	2		368	501	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660205	227660205	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	202	456	0	ENST00000305123.5:c.3250A>C	p.Ser1084Arg	p.S1084R	ENST00000305123	NM_005544.2	1084	Agt/Cgt	1/2	1	2	FACETS	0.885	0.823	0.95	0.885	0.823	0.95	CLONAL	1	TRUE	1	0.601235212743434	2		456	759	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386391	31386391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1051749732	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	163	328	0	ENST00000328111.2:c.1616G>A	p.Arg539Gln	p.R539Q	ENST00000328111	NM_006892.3	539	cGg/cAg	15/23	1	2	FACETS	0.914	0.843	0.988	0.914	0.843	0.988	CLONAL	1	TRUE	1	0.601235212743434	2		328	593	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845259	42845259	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747772174	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	28	271	0	ENST00000398585.3:c.1003G>A	p.Val335Met	p.V335M	ENST00000398585	NM_001135099.1	335	Gtg/Atg	9/14	1	2	FACETS	0.167	0.132	0.206	0.167	0.132	0.206	SUBCLONAL	1	TRUE	1	0.601235212743434	2		271	559	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45649958	45649958	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	177	314	0	ENST00000407780.3:c.877A>G	p.Ser293Gly	p.S293G	ENST00000407780	NM_001283052.1	293	Agt/Ggt	6/7	1	2	FACETS	0.993	0.92	1	0.993	0.92	1	CLONAL	1	TRUE	1	0.601235212743434	2		314	593	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221706	22221706	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	40	73	0	ENST00000215832.6:c.25G>C	p.Ala9Pro	p.A9P	ENST00000215832	NM_002745.4	9	Gcg/Ccg	1/9	1	2	FACETS	0.858	0.725	1	0.858	0.725	1	CLONAL	1	TRUE	1	0.601235212743434	2		73	155	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191636	10191636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138780791	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	187	342	0	ENST00000256474.2:c.629G>A	p.Arg210Gln	p.R210Q	ENST00000256474	NM_000551.3	210	cGg/cAg	3/3	1	2	FACETS	0.973	0.904	1	0.973	0.904	1	CLONAL	1	TRUE	1	0.601235212743434	2		342	639	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713715	30713715	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	151	316	0	ENST00000295754.5:c.1040T>C	p.Leu347Pro	p.L347P	ENST00000295754	NM_003242.5	347	cTg/cCg	4/7	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.601235212743434	2		316	489	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275192	41275192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	99	235	1	ENST00000349496.5:c.1358G>A	p.Arg453Gln	p.R453Q	ENST00000349496	NM_001904.3	453	cGg/cAg	9/15	1	2	FACETS	0.855	0.77	0.945	0.855	0.77	0.945	CLONAL	1	TRUE	1	0.601235212743434	2		236	385	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165918	47165918	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs775039657	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	116	313	1	ENST00000409792.3:c.208C>T	p.Arg70Ter	p.R70*	ENST00000409792	NM_014159.6	70	Cga/Tga	3/21	1	2	FACETS	0.797	0.722	0.875	0.797	0.722	0.875	SUBCLONAL	1	TRUE	1	0.601235212743434	2		314	484	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940589	49940590	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	186	363	0	ENST00000296474.3:c.453dup	p.Gly152ArgfsTer18	p.G152Rfs*18	ENST00000296474	NM_002447.2	151	-/A	1/20	1	2	FACETS	0.955	0.886	1	0.955	0.886	1	CLONAL	1	TRUE	1	0.601235212743434	2		363	648	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651496	52651496	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	37	490	1	ENST00000394830.3:c.1600C>T	p.Arg534Ter	p.R534*	ENST00000394830	NM_018313.4	534	Cga/Tga	15/30	1	2	FACETS	0.183	0.15	0.22	0.183	0.15	0.22	SUBCLONAL	1	TRUE	1	0.601235212743434	2		491	671	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391020	89391020	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1230921861	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	213	377	0	ENST00000336596.2:c.1086A>G	p.Ile362Met	p.I362M	ENST00000336596	NM_005233.5	362	atA/atG	5/17	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.601235212743434	2		377	633	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806153	1806153	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28931615	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	235	455	0	ENST00000260795.2:c.1172C>T	p.Ala391Val	p.A391V	ENST00000260795		391	gCg/gTg	8/17	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.601235212743434	2		455	764	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931452	131931453	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	123	318	0	ENST00000265335.6:c.2164_2165del	p.Lys722GlyfsTer5	p.K722Gfs*5	ENST00000265335		719	ctAAaa/ctaa	13/25	1	2	FACETS	0.858	0.78	0.938	0.858	0.78	0.938	CLONAL	1	TRUE	1	0.601235212743434	2		318	477	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514337	149514337	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	132	328	0	ENST00000261799.4:c.607G>A	p.Ala203Thr	p.A203T	ENST00000261799	NM_002609.3	203	Gcc/Acc	4/23	1	2	FACETS	0.969	0.887	1	0.969	0.887	1	CLONAL	1	TRUE	1	0.601235212743434	2		328	453	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031990	26031990	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	71	256	0	ENST00000244661.2:c.299A>G	p.Tyr100Cys	p.Y100C	ENST00000244661	NM_003537.3	100	tAc/tGc	1/1	1	2	FACETS	0.532	0.466	0.603	0.532	0.466	0.603	SUBCLONAL	1	TRUE	1	0.601235212743434	2		256	444	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045802	26045802	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	68	350	0	ENST00000540144.1:c.164A>G	p.Tyr55Cys	p.Y55C	ENST00000540144	NM_003531.2	55	tAc/tGc	1/1	1	2	FACETS	0.461	0.401	0.524	0.461	0.401	0.524	SUBCLONAL	1	TRUE	1	0.601235212743434	2		350	491	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805363	32805363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	186	411	0	ENST00000374899.4:c.559del	p.His187MetfsTer63	p.H187Mfs*63	ENST00000374899	NM_018833.2	187	Cat/at	3/12	1	2	FACETS	0.968	0.898	1	0.968	0.898	1	CLONAL	1	TRUE	1	0.601235212743434	2		411	639	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805787	32805788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1174402903	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	199	443	0	ENST00000374899.4:c.223dup	p.Leu75ProfsTer92	p.L75Pfs*92	ENST00000374899	NM_018833.2	75	ctg/cCtg	2/12	1	2	FACETS	0.79	0.733	0.849	0.79	0.733	0.849	SUBCLONAL	1	TRUE	1	0.601235212743434	2		443	838	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41904337	41904337	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	83	323	0	ENST00000372991.4:c.671A>C	p.Glu224Ala	p.E224A	ENST00000372991	NM_001760.3	224	gAg/gCg	4/5	1	2	FACETS	0.523	0.462	0.587	0.523	0.462	0.587	SUBCLONAL	1	TRUE	1	0.601235212743434	2		323	528	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983058	149983058	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	151	365	0	ENST00000253339.5:c.3200del	p.Asn1067MetfsTer61	p.N1067Mfs*61	ENST00000253339		1067	aAt/at	7/7	1	2	FACETS	0.948	0.872	1	0.948	0.872	1	CLONAL	1	TRUE	1	0.601235212743434	2		365	530	SUCCESS
MET	4233	MSKCC	GRCh37	7	116414571	116414571	+	intron_variant	Intron	SNP	C	C	T	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	33	428	1	ENST00000397752.3:c.3029-364C>T		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.16	0.13	0.195	0.16	0.13	0.195	SUBCLONAL	1	TRUE	1	0.601235212743434	2		429	684	SUCCESS
MET	4233	MSKCC	GRCh37	7	116414767	116414768	+	intron_variant	Intron	INS	-	-	A	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	153	386	0	ENST00000397752.3:c.3029-164dup		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.924	0.85	1	0.924	0.85	1	CLONAL	1	TRUE	1	0.601235212743434	2		386	551	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272337	38272337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1484920710	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	188	357	1	ENST00000425967.3:c.2030G>A	p.Arg677Gln	p.R677Q	ENST00000425967	NM_001174067.1	677	cGg/cAg	15/19	0.539046585139534	3	FACETS	0.966	0.894	1	0.483	0.447	0.521	CLONAL	1	TRUE	1	0.601235212743434	3		358	842	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279429	38279429	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	185	379	0	ENST00000425967.3:c.1060A>G	p.Met354Val	p.M354V	ENST00000425967	NM_001174067.1	354	Atg/Gtg	9/19	0.539046585139534	3	FACETS	1	0.937	1	0.507	0.469	0.547	CLONAL	1	TRUE	1	0.601235212743434	3		379	789	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554345	141554345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748399150	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	238	335	0	ENST00000220592.5:c.1806del	p.Ala603ProfsTer92	p.A603Pfs*92	ENST00000220592	NM_012154.3	602	ccC/cc	14/19	0.539046585139534	3	FACETS	0.888	0.828	0.95	0.444	0.414	0.475	CLONAL	1	TRUE	1	0.601235212743434	3		335	1160	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738660	145738660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs897118164	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	350	367	2	ENST00000428558.2:c.2404G>A	p.Val802Met	p.V802M	ENST00000428558	NM_004260.3	802	Gtg/Atg	15/22	0.539046585139534	3	FACETS	0.875	0.833	0.919	0.875	0.833	0.919	CLONAL	2	TRUE	1	0.601235212743434	3		369	865	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742150	145742150	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	129	261	0	ENST00000428558.2:c.355-2A>C		p.X119_splice	ENST00000428558	NM_004260.3	119			0.539046585139534	3	FACETS	0.817	0.742	0.896	0.409	0.371	0.448	CLONAL	1	TRUE	1	0.601235212743434	3		261	683	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504293	8504293	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	94	324	0	ENST00000356435.5:c.1790C>T	p.Thr597Ile	p.T597I	ENST00000356435		597	aCt/aTt	12/35	1	2	FACETS	0.571	0.509	0.636	0.571	0.509	0.636	SUBCLONAL	1	TRUE	1	0.601235212743434	2		324	548	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760378	133760378	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	169	407	1	ENST00000318560.5:c.2705del	p.Pro902HisfsTer40	p.P902Hfs*40	ENST00000318560	NM_005157.4	901	Ccc/cc	11/11	1	2	FACETS	0.931	0.86	1	0.931	0.86	1	CLONAL	1	TRUE	1	0.601235212743434	2		408	604	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399976	139399976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200495793	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	223	468	1	ENST00000277541.6:c.4372G>A	p.Ala1458Thr	p.A1458T	ENST00000277541	NM_017617.3	1458	Gcg/Acg	25/34	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.601235212743434	2		469	742	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1315005	1315005	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	170	342	0	ENST00000400841.2:c.656C>A	p.Ala219Glu	p.A219E	ENST00000400841		219	gCa/gAa	6/6	1	1	FACETS	0.586	0.54	0.633	0.586	0.54	0.633	SUBCLONAL	1	TRUE	0	0.601235212743434	1		342	675	SUCCESS
AR	367	MSKCC	GRCh37	X	66765149	66765151	+	inframe_deletion	In_Frame_Del	DEL	TGC	TGC	-	rs752055010	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	16	123	2	ENST00000374690.3:c.170_172del	p.Leu57del	p.L57del	ENST00000374690	NM_000044.3	54	tTGCtg/ttg	1/8	1	1	FACETS	0.338	0.253	0.438	0.338	0.253	0.438	SUBCLONAL	1	TRUE	0	0.601235212743434	1		125	110	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220539	123220539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	159	209	0	ENST00000218089.9:c.3196C>T	p.Arg1066Trp	p.R1066W	ENST00000218089	NM_001042749.1	1066	Cgg/Tgg	30/35	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.601235212743434	1		209	317	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0026715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	82	282	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.228736420704859	2		282	530	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0026715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	68	458	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.228736420704859	1	FACETS	0.875	0.761	0.997	0.875	0.761	0.997	CLONAL	1	TRUE	0	0.228736420704859	1		458	602	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0026715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	83	351	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.95	0.838	1	0.95	0.838	1	CLONAL	1	TRUE	1	0.228736420704859	2		351	764	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748610	40748610	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	55	480	0	ENST00000373198.4:c.2906G>A	p.Gly969Glu	p.G969E	ENST00000373198	NM_133170.3	969	gGa/gAa	21/32	1	2	FACETS	0.689	0.588	0.799	0.689	0.588	0.799	SUBCLONAL	1	TRUE	1	0.228736420704859	2		480	698	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526735	106526735	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	54	394	0	ENST00000359195.3:c.3028C>T	p.Gln1010Ter	p.Q1010*	ENST00000359195	NM_002649.2	1010	Cag/Tag	10/11	1	2	FACETS	0.739	0.63	0.858	0.739	0.63	0.858	SUBCLONAL	1	TRUE	1	0.228736420704859	2		394	639	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681009	37681009	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	103	618	0	ENST00000447079.4:c.3178C>T	p.Pro1060Ser	p.P1060S	ENST00000447079	NM_015083.1	1060	Cca/Tca	12/14	1	2	FACETS	0.943	0.843	1	0.943	0.843	1	CLONAL	1	TRUE	1	0.228736420704859	2		618	955	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	96	282	0				ENST00000310581	NM_198253.2	-/1132			0.464498691853033	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	0	0.464498691853033	1		282	279	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	190	779	1	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	1	2	FACETS	0.958	0.887	1	0.958	0.887	1	CLONAL	1	FALSE	1	0.464498691853033	2		780	854	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	214	593	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.464498691853033	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	0	0.464498691853033	1		593	630	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	190	392	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.430294407495082	2	FACETS	0.838	0.782	0.895	0.838	0.782	0.895	CLONAL	2	FALSE	0	0.464498691853033	2		392	488	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913255	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	275	476	0	ENST00000369535.4:c.183A>C	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caC	3/7	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	FALSE	1	0.464498691853033	2		476	799	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857061	9857061	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	89	300	1	ENST00000330684.3:c.4340C>T	p.Ser1447Phe	p.S1447F	ENST00000330684	NM_001134407.1	1447	tCc/tTc	13/13	0.108881041174156	0	FACETS	0.457	0.407	0.51			1	INDETERMINATE	1	FALSE	0	0.464498691853033	0		301	449	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561564	9561564	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867333778	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	106	432	0	ENST00000353224.5:c.218G>A	p.Gly73Glu	p.G73E	ENST00000353224	NM_177990.2	73	gGa/gAa	4/10	1	2	FACETS	0.815	0.733	0.902	0.815	0.733	0.902	CLONAL	1	FALSE	1	0.464498691853033	2		432	560	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444333	50444333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775004468	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	150	367	1	ENST00000331340.3:c.263C>T	p.Ser88Leu	p.S88L	ENST00000331340	NM_006060.4	88	tCg/tTg	4/8	0.219459223170625	4	FACETS	0.803	0.737	0.871	0.803	0.737	0.871	INDETERMINATE	2	FALSE	2	0.464498691853033	4		368	589	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552823	106552823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1042709746	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	173	666	0	ENST00000369096.4:c.788G>A	p.Gly263Glu	p.G263E	ENST00000369096	NM_001198.3	263	gGa/gAa	5/7	0.386097999789057	1	FACETS	0.804	0.742	0.869	0.804	0.742	0.869	CLONAL	1	FALSE	0	0.464498691853033	1		666	711	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538263	9538263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748547848	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	163	538	0	ENST00000353224.5:c.1735G>A	p.Asp579Asn	p.D579N	ENST00000353224	NM_177990.2	579	Gat/Aat	7/10	1	2	FACETS	0.839	0.77	0.91	0.839	0.77	0.91	CLONAL	1	FALSE	1	0.464498691853033	2		538	837	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156354	106156354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	75	362	0	ENST00000380013.4:c.1255C>T	p.Pro419Ser	p.P419S	ENST00000380013	NM_001127208.2	419	Cct/Tct	3/11	0.272437325696529	1	FACETS	0.53	0.466	0.598	0.53	0.466	0.598	INDETERMINATE	1	FALSE	0	0.464498691853033	1		362	468	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803598	43803598	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	159	522	0	ENST00000372470.3:c.79G>A	p.Asp27Asn	p.D27N	ENST00000372470	NM_005373.2	27	Gat/Aat	1/12	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.464498691853033	2		522	459	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275812	38275812	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	114	592	0	ENST00000425967.3:c.1457C>T	p.Pro486Leu	p.P486L	ENST00000425967	NM_001174067.1	486	cCc/cTc	11/19	0.108881041174156	0	FACETS	0.429	0.387	0.474			1	INDETERMINATE	1	FALSE	0	0.464498691853033	0		592	612	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699486	117699486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	209	394	0	ENST00000369458.3:c.155G>A	p.Gly52Glu	p.G52E	ENST00000369458	NM_024626.3	52	gGa/gAa	3/6	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	1	0.464498691853033	2		394	645	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650090	206650090	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	45	638	0	ENST00000367120.3:c.610C>T	p.Leu204Phe	p.L204F	ENST00000367120	NM_014002.3	204	Ctc/Ttc	7/22	0.439908239300276	1	FACETS	0.231	0.193	0.272	0.231	0.193	0.272	SUBCLONAL	1	FALSE	0	0.464498691853033	1		638	645	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263992	104263992	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758001170	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	30	336	2	ENST00000369902.3:c.83C>T	p.Ser28Leu	p.S28L	ENST00000369902	NM_016169.3	28	tCg/tTg	1/12	0.386097999789057	1	FACETS	0.34	0.274	0.413	0.34	0.274	0.413	SUBCLONAL	1	FALSE	0	0.464498691853033	1		338	292	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155956	119155956	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	136	640	0	ENST00000264033.4:c.1621G>A	p.Asp541Asn	p.D541N	ENST00000264033	NM_005188.3	541	Gat/Aat	11/16	1	2	FACETS	0.841	0.766	0.92	0.841	0.766	0.92	CLONAL	1	FALSE	1	0.464498691853033	2		640	696	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1039250	1039250	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	97	568	2	ENST00000358495.3:c.247G>A	p.Gly83Ser	p.G83S	ENST00000358495	NM_134424.2	83	Ggc/Agc	4/12	0.151872621226784	1	FACETS	0.522	0.466	0.582	0.522	0.466	0.582	INDETERMINATE	1	FALSE	0	0.464498691853033	1		570	614	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446049	49446049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	144	811	2	ENST00000301067.7:c.1417G>A	p.Glu473Lys	p.E473K	ENST00000301067	NM_003482.3	473	Gaa/Aaa	10/54	0.151872621226784	1	FACETS	0.674	0.616	0.735	0.674	0.616	0.735	INDETERMINATE	1	FALSE	0	0.464498691853033	1		813	706	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861939	57861939	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	150	527	2	ENST00000228682.2:c.1240C>T	p.Pro414Ser	p.P414S	ENST00000228682	NM_005269.2	414	Ccc/Tcc	10/12	0.151872621226784	1	FACETS	0.895	0.822	0.97	0.895	0.822	0.97	INDETERMINATE	1	FALSE	0	0.464498691853033	1		529	554	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257841	133257842	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACTG	novel	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	128	402	0	ENST00000320574.5:c.83_86dup	p.Ala31PhefsTer14	p.A31Ffs*14	ENST00000320574	NM_006231.2	29	gtt/gtCAGTt	2/49	0.151872621226784	1	FACETS	0.758	0.69	0.83	0.758	0.69	0.83	INDETERMINATE	1	FALSE	0	0.464498691853033	1		402	558	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28624325	28624325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	159	484	0	ENST00000241453.7:c.649G>A	p.Glu217Lys	p.E217K	ENST00000241453	NM_004119.2	217	Gag/Aag	6/24	0.464498691853033	1	FACETS	0.916	0.844	0.99	0.916	0.844	0.99	CLONAL	1	FALSE	0	0.464498691853033	1		484	574	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054042	42054042	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	154	439	1	ENST00000219905.7:c.7504C>T	p.Leu2502Phe	p.L2502F	ENST00000219905	NM_001164273.1	2502	Ctt/Ttt	21/24	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.464498691853033	2		440	599	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303915	91303915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752884341	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	229	548	0	ENST00000355112.3:c.1312C>T	p.Pro438Ser	p.P438S	ENST00000355112	NM_000057.2	438	Cct/Tct	7/22	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.464498691853033	2		548	745	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198263254	198263254	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	175	534	0	ENST00000335508.6:c.3065C>T	p.Pro1022Leu	p.P1022L	ENST00000335508	NM_012433.2	1022	cCc/cTc	21/25	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.464498691853033	2		534	726	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525099	9525099	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	176	528	0	ENST00000353224.5:c.1786G>C	p.Glu596Gln	p.E596Q	ENST00000353224	NM_177990.2	596	Gag/Cag	8/10	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	FALSE	1	0.464498691853033	2		528	756	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42840355	42840355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1416299734	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	158	533	1	ENST00000398585.3:c.1393G>A	p.Gly465Ser	p.G465S	ENST00000398585	NM_001135099.1	465	Ggc/Agc	12/14	1	2	FACETS	0.972	0.893	1	0.972	0.893	1	CLONAL	1	FALSE	1	0.464498691853033	2		534	700	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114085	73114085	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	85	247	0	ENST00000356692.5:c.721G>A	p.Glu241Lys	p.E241K	ENST00000356692		241	Gag/Aag	8/9	1	2	FACETS	0.976	0.869	1	0.976	0.869	1	CLONAL	1	FALSE	1	0.464498691853033	2		247	375	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540803	187540803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	100	337	0	ENST00000441802.2:c.6937G>A	p.Glu2313Lys	p.E2313K	ENST00000441802	NM_005245.3	2313	Gaa/Aaa	10/27	0.272437325696529	1	FACETS	0.81	0.729	0.895	0.81	0.729	0.895	INDETERMINATE	1	FALSE	0	0.464498691853033	1		337	408	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295259	1295259	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	97	466	0				ENST00000310581	NM_198253.2	-/1132			0.464498691853033	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	0	0.464498691853033	1		466	288	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490632	20490632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	179	510	0	ENST00000346618.3:c.1369C>T	p.Pro457Ser	p.P457S	ENST00000346618	NM_001949.4	457	Cca/Tca	7/7	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.464498691853033	2		510	694	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797859	32797859	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	93	348	0	ENST00000374899.4:c.1643C>T	p.Ser548Leu	p.S548L	ENST00000374899	NM_018833.2	548	tCa/tTa	10/12	1	2	FACETS	0.929	0.831	1	0.929	0.831	1	CLONAL	1	FALSE	1	0.464498691853033	2		348	431	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287810	33287811	+	missense_variant	Missense_Mutation	DNP	GT	GT	AG	novel	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	179	726	0	ENST00000374542.5:c.1442_1443delinsCT	p.Asp481Ala	p.D481A	ENST00000374542	NM_001141970.1	481	gAC/gCT	5/8	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	FALSE	1	0.464498691853033	2		726	761	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117730789	117730789	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	56	536	0	ENST00000368508.3:c.245T>C	p.Val82Ala	p.V82A	ENST00000368508	NM_002944.2	82	gTt/gCt	4/43	0.386097999789057	1	FACETS	0.317	0.271	0.367	0.317	0.271	0.367	SUBCLONAL	1	FALSE	0	0.464498691853033	1		536	584	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477855	140477856	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	novel	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	226	610	1	ENST00000288602.6:c.1452_1453delinsAA	p.Met484_Leu485delinsIleMet	p.M484_L485delinsIM	ENST00000288602	NM_004333.4	484	atGTtg/atAAtg	12/18	0.219459223170625	4	FACETS	0.775	0.723	0.829	0.775	0.723	0.829	INDETERMINATE	2	FALSE	2	0.464498691853033	4		611	919	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879260	151879260	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	185	511	1	ENST00000262189.6:c.5685G>A	p.Met1895Ile	p.M1895I	ENST00000262189	NM_170606.2	1895	atG/atA	36/59	0.219459223170625	4	FACETS	0.836	0.774	0.899	0.836	0.774	0.899	INDETERMINATE	2	FALSE	2	0.464498691853033	4		512	698	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27203019	27203019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1168331105	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	248	592	1	ENST00000380036.4:c.2111C>T	p.Pro704Leu	p.P704L	ENST00000380036	NM_000459.3	704	cCt/cTt	13/23	0.430294407495082	2	FACETS	0.87	0.819	0.921	0.87	0.819	0.921	CLONAL	2	FALSE	0	0.464498691853033	2		593	614	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27204924	27204924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	154	412	0	ENST00000380036.4:c.2225G>A	p.Gly742Glu	p.G742E	ENST00000380036	NM_000459.3	742	gGa/gAa	14/23	0.430294407495082	2	FACETS	0.835	0.773	0.898	0.835	0.773	0.898	CLONAL	2	FALSE	0	0.464498691853033	2		412	397	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	38	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.614	0.507	0.734	0.614	0.507	0.734	SUBCLONAL	1	TRUE	1	0.253503344337655	2		215	488	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0026868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	88	458	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.253503344337655	2		458	683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0026868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	102	772	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	0.253503344337655	2		772	731	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533881	533881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs727503093	NA	P-0026868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	84	640	0	ENST00000451590.1:c.175G>A	p.Ala59Thr	p.A59T	ENST00000451590	NM_001130442.1	59	Gcc/Acc	3/5	1	2	FACETS	0.719	0.633	0.811	0.719	0.633	0.811	SUBCLONAL	1	TRUE	1	0.253503344337655	2		640	922	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0026868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	87	576	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.253503344337655	2		576	641	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271784	15271784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559474673	NA	P-0026868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	77	666	0	ENST00000263388.2:c.6655G>A	p.Glu2219Lys	p.E2219K	ENST00000263388	NM_000435.2	2219	Gag/Aag	33/33	1	2	FACETS	0.716	0.628	0.812	0.716	0.628	0.812	SUBCLONAL	1	TRUE	1	0.253503344337655	2		666	848	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212706	36212712	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTGAGT	GGTGAGT	-	novel	NA	P-0026868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	55	532	0	ENST00000222270.7:c.2457+1_2457+7del		p.X819_splice	ENST00000222270	NM_014727.1	819		3/37	1	2	FACETS	0.558	0.476	0.648	0.558	0.476	0.648	SUBCLONAL	1	TRUE	1	0.253503344337655	2		532	778	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306554	41306554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	62	545	1	ENST00000373198.4:c.1105G>A	p.Gly369Ser	p.G369S	ENST00000373198	NM_133170.3	369	Ggt/Agt	7/32	1	2	FACETS	0.689	0.594	0.792	0.689	0.594	0.792	SUBCLONAL	1	TRUE	1	0.253503344337655	2		546	710	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	136	354	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	0.334604324583065	2		354	689	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0026910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	86	429	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.32897621335391	1	FACETS	0.843	0.748	0.944	0.843	0.748	0.944	CLONAL	1	TRUE	0	0.334604324583065	1		429	508	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0026910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	49	415	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	0.32897621335391	1	FACETS	0.521	0.442	0.608	0.521	0.442	0.608	SUBCLONAL	1	TRUE	0	0.334604324583065	1		415	468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0026910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	139	585	1	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	0.334604324583065	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.334604324583065	1		586	649	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	324	215	0				ENST00000310581	NM_198253.2	-/1132			0.739576807497685	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.786027581002073	3		215	493	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883246	37883246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199905364	NA	P-0027060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	381	634	0	ENST00000269571.5:c.3149C>T	p.Ser1050Leu	p.S1050L	ENST00000269571		1050	tCa/tTa	25/27	0.450856172579531	3	FACETS	1	0.989	1	0.377	0.358	0.396	INDETERMINATE	1	TRUE	0	0.786027581002073	3		634	1194	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115260807	115260819	+	frameshift_variant	Frame_Shift_Del	DEL	CTTGACGGATCTT	CTTGACGGATCTT	-	novel	NA	P-0027060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	102	531	0	ENST00000438362.2:c.2506_2518del	p.Lys836LeufsTer14	p.K836Lfs*14	ENST00000438362	NM_001242891.1	836	AAGATCCGTCAAGct/ct	20/20	0.415066270504419	1	FACETS	0.205	0.183	0.229	0.205	0.183	0.229	INDETERMINATE	1	TRUE	0	0.786027581002073	1		531	767	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434618	49434618	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	1060	793	0	ENST00000301067.7:c.6935C>A	p.Ser2312Ter	p.S2312*	ENST00000301067	NM_003482.3	2312	tCa/tAa	31/54	0.768827866294251	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.786027581002073	3		793	1233	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0027060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	444	656	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	0.786027581002073	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.786027581002073	1		656	628	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965514	18965514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	419	671	0	ENST00000262803.5:c.1261G>A	p.Asp421Asn	p.D421N	ENST00000262803	NM_002911.3	421	Gac/Aac	9/24	1	2	FACETS	0.98	0.935	1	0.98	0.935	1	CLONAL	1	TRUE	1	0.786027581002073	2		671	1088	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141567292	141567292	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	139	561	0	ENST00000220592.5:c.922G>A	p.Val308Met	p.V308M	ENST00000220592	NM_012154.3	308	Gtg/Atg	8/19	1	2	FACETS	0.354	0.322	0.389	0.354	0.322	0.389	SUBCLONAL	1	TRUE	1	0.786027581002073	2		561	998	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971092	21971092	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	168	304	0	ENST00000304494.5:c.266del	p.Gly89AlafsTer57	p.G89Afs*57	ENST00000304494	NM_000077.4	89	gGc/gc	2/3	0.786027581002073	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.786027581002073	1		304	234	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393645	139393645	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	429	758	0	ENST00000277541.6:c.6001del	p.Leu2001TrpfsTer24	p.L2001Wfs*24	ENST00000277541	NM_017617.3	2001	Ctg/tg	32/34	0.786027581002073	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.786027581002073	1		758	637	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	134	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.730496808557624	2		215	355	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0027084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	323	351	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.698993083250256	3	FACETS	0.977	0.932	1	0.977	0.932	1	CLONAL	2	TRUE	1	0.730496808557624	3		351	618	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0027084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	125	173	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.730496808557624	2		174	316	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0027084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	473	696	1	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.730496808557624	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.730496808557624	2		697	609	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724308	117724308	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	164	402	0	ENST00000368508.3:c.571C>T	p.His191Tyr	p.H191Y	ENST00000368508	NM_002944.2	191	Cat/Tat	6/43	0.698993083250256	3	FACETS	0.916	0.844	0.991	0.458	0.422	0.496	CLONAL	1	TRUE	1	0.730496808557624	3		402	669	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033970	49033970	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0027084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	383	323	0	ENST00000267163.4:c.2106+1G>A		p.X702_splice	ENST00000267163	NM_000321.2	702			0.730496808557624	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.730496808557624	2		323	514	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066699	94066699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	143	401	0	ENST00000369303.4:c.1060C>T	p.Pro354Ser	p.P354S	ENST00000369303	NM_004440.3	354	Cct/Tct	5/17	0.698993083250256	3	FACETS	0.848	0.776	0.924	0.424	0.388	0.462	CLONAL	1	TRUE	1	0.730496808557624	3		401	630	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292391	15292391	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	164	528	0	ENST00000263388.2:c.2788C>T	p.Pro930Ser	p.P930S	ENST00000263388	NM_000435.2	930	Ccc/Tcc	17/33	1	2	FACETS	0.865	0.8	0.932	0.865	0.8	0.932	CLONAL	1	TRUE	1	0.730496808557624	2		528	519	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660731	227660731	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0027084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	397	532	0	ENST00000305123.5:c.2724C>G	p.Tyr908Ter	p.Y908*	ENST00000305123	NM_005544.2	908	taC/taG	1/2	0.698993083250256	3	FACETS	0.974	0.933	1	0.974	0.933	1	CLONAL	2	TRUE	1	0.730496808557624	3		532	762	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803776	43803776	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	144	455	3	ENST00000372470.3:c.86C>T	p.Ser29Phe	p.S29F	ENST00000372470	NM_005373.2	29	tCc/tTc	2/12	0.726798024740829	2	FACETS	0.844	0.776	0.915	0.422	0.388	0.458	CLONAL	1	TRUE	0	0.730496808557624	2		458	467	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459206	120459207	+	missense_variant	Missense_Mutation	DNP	GG	GG	AC	novel	NA	P-0027084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	313	392	0	ENST00000256646.2:c.6138_6139delinsGT	p.Arg2047Trp	p.R2047W	ENST00000256646	NM_024408.3	2046	ccCCgg/ccGTgg	34/34	0.726798024740829	2	FACETS	0.974	0.938	1	0.974	0.938	1	CLONAL	2	TRUE	0	0.730496808557624	2		392	440	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843731	156843731	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	499	766	0	ENST00000524377.1:c.1157A>G	p.Asn386Ser	p.N386S	ENST00000524377	NM_002529.3	386	aAc/aGc	8/17	0.318772197713561	6	FACETS	0.856	0.82	0.892	0.856	0.82	0.892	INDETERMINATE	3	TRUE	3	0.730496808557624	6		766	1309	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161326621	161326622	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0027084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	424	576	0	ENST00000367975.2:c.396_397delinsTT	p.Arg133Ter	p.R133*	ENST00000367975	NM_003001.3	132	atCCga/atTTga	5/6	0.318772197713561	6	FACETS	1	0.993	1	0.798	0.761	0.835	INDETERMINATE	2	TRUE	3	0.730496808557624	6		576	1194	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567274	226567274	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	312	405	0	ENST00000366794.5:c.1612G>A	p.Gly538Arg	p.G538R	ENST00000366794	NM_001618.3	538	Gga/Aga	11/23	0.318772197713561	6	FACETS	1	0.992	1	0.829	0.785	0.874	INDETERMINATE	2	TRUE	3	0.730496808557624	6		405	845	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18473954	18473954	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	109	269	0	ENST00000266497.5:c.1196G>A	p.Trp399Ter	p.W399*	ENST00000266497		399	tGg/tAg	6/31	0.730496808557624	2	FACETS	0.834	0.756	0.914	0.417	0.378	0.457	CLONAL	1	TRUE	0	0.730496808557624	2		269	358	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491477	18491477	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	150	258	0	ENST00000266497.5:c.1390G>A	p.Gly464Arg	p.G464R	ENST00000266497		464	Gga/Aga	8/31	0.730496808557624	2	FACETS	0.923	0.851	0.996	0.461	0.425	0.498	CLONAL	1	TRUE	0	0.730496808557624	2		258	445	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895664	28895664	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	36	549	0	ENST00000282397.4:c.3110A>T	p.Lys1037Met	p.K1037M	ENST00000282397	NM_002019.4	1037	aAg/aTg	23/30	0.730496808557624	2	FACETS	0.168	0.137	0.202	0.084	0.068	0.101	SUBCLONAL	1	TRUE	0	0.730496808557624	2		549	588	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246507	105246507	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	245	545	0	ENST00000349310.3:c.93T>G	p.Asn31Lys	p.N31K	ENST00000349310	NM_001014432.1	31	aaT/aaG	4/15	0.730496808557624	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.730496808557624	1		545	387	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89862376	89862376	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764121307	NA	P-0027084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	263	520	0	ENST00000389301.3:c.944C>T	p.Pro315Leu	p.P315L	ENST00000389301	NM_000135.2	315	cCt/cTt	11/43	0.474575320948568	1	FACETS	0.84	0.796	0.885	0.84	0.796	0.885	CLONAL	1	TRUE	0	0.730496808557624	1		520	544	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110558	4110558	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	226	529	1	ENST00000262948.5:c.399C>A	p.Phe133Leu	p.F133L	ENST00000262948	NM_030662.3	133	ttC/ttA	3/11	1	2	FACETS	0.913	0.854	0.972	0.913	0.854	0.972	CLONAL	1	TRUE	1	0.730496808557624	2		530	678	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210905	36210907	+	frameshift_variant	Frame_Shift_Del	DEL	CTC	CTC	TT	novel	NA	P-0027084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	224	660	2	ENST00000222270.7:c.656_658delinsTT	p.Ser219PhefsTer20	p.S219Ffs*20	ENST00000222270	NM_014727.1	219	tCTCgg/tTTgg	3/37	1	2	FACETS	0.935	0.875	0.996	0.935	0.875	0.996	CLONAL	1	TRUE	1	0.730496808557624	2		662	656	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560838	9560838	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	150	337	0	ENST00000353224.5:c.944C>T	p.Ser315Phe	p.S315F	ENST00000353224	NM_177990.2	315	tCc/tTc	4/10	NA	2	FACETS	0.962	0.888	1			1	INDETERMINATE	1	TRUE	NA	0.730496808557624	2		337	427	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022245	31022245	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0027084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	94	212	0	ENST00000375687.4:c.1730C>G	p.Ser577Ter	p.S577*	ENST00000375687	NM_015338.5	577	tCa/tGa	13/13	0.698993083250256	3	FACETS	0.915	0.82	1	0.457	0.41	0.507	CLONAL	1	TRUE	1	0.730496808557624	3		212	384	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155303	185155303	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	172	370	0	ENST00000265026.3:c.544G>A	p.Val182Ile	p.V182I	ENST00000265026	NM_004721.4	182	Gtc/Atc	3/14	1	2	FACETS	0.864	0.8	0.93	0.864	0.8	0.93	CLONAL	1	TRUE	1	0.730496808557624	2		370	545	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140785	55140785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	158	328	0	ENST00000257290.5:c.1646G>A	p.Trp549Ter	p.W549*	ENST00000257290	NM_006206.4	549	tGg/tAg	11/23	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.730496808557624	2		328	424	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231661	66231661	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs942599588	NA	P-0027084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	105	311	0	ENST00000273854.3:c.2039T>C	p.Val680Ala	p.V680A	ENST00000273854	NM_004439.5	680	gTt/gCt	11/18	1	2	FACETS	0.876	0.794	0.961	0.876	0.794	0.961	CLONAL	1	TRUE	1	0.730496808557624	2		311	328	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940668	131940668	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	195	358	0	ENST00000265335.6:c.2695C>T	p.Gln899Ter	p.Q899*	ENST00000265335		899	Cag/Tag	16/25	1	2	FACETS	0.976	0.91	1	0.976	0.91	1	CLONAL	1	TRUE	1	0.730496808557624	2		358	547	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139045	37139045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	345	466	0	ENST00000373509.5:c.385C>T	p.Leu129Phe	p.L129F	ENST00000373509	NM_002648.3	129	Ctc/Ttc	4/6	0.698993083250256	3	FACETS	0.904	0.863	0.946	0.904	0.863	0.946	CLONAL	2	TRUE	1	0.730496808557624	3		466	713	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976777	2976777	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	232	549	0	ENST00000396946.4:c.1235A>C	p.Glu412Ala	p.E412A	ENST00000396946	NM_032415.4	412	gAg/gCg	9/25	0.698993083250256	3	FACETS	0.936	0.874	1	0.468	0.437	0.501	CLONAL	1	TRUE	1	0.730496808557624	3		549	926	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55272960	55272960	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	178	354	0	ENST00000275493.2:c.3283C>T	p.Gln1095Ter	p.Q1095*	ENST00000275493	NM_005228.3	1095	Cag/Tag	28/28	0.698993083250256	3	FACETS	0.998	0.923	1	0.499	0.461	0.538	CLONAL	1	TRUE	1	0.730496808557624	3		354	667	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737780	145737780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554896820	NA	P-0027084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	402	547	0	ENST00000428558.2:c.3050G>A	p.Arg1017Lys	p.R1017K	ENST00000428558	NM_004260.3	1017	aGg/aAg	18/22	0.726798024740829	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.730496808557624	2		547	538	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	118	215	0				ENST00000310581	NM_198253.2	-/1132			0.337229140744822	1	FACETS	0.675	0.614	0.738	0.675	0.614	0.738	INDETERMINATE	1	TRUE	0	0.603014128842505	1		215	405	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631443	117631443	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	158	328	0	ENST00000368508.3:c.6235G>A	p.Asp2079Asn	p.D2079N	ENST00000368508	NM_002944.2	2079	Gat/Aat	40/43	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.603014128842505	2		328	513	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566709	212566709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	198	345	1	ENST00000342788.4:c.1472G>A	p.Arg491Lys	p.R491K	ENST00000342788	NM_005235.2	491	aGa/aAa	12/28	1	2	FACETS	0.992	0.923	1	0.992	0.923	1	CLONAL	1	TRUE	1	0.603014128842505	2		346	662	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612176	189612176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	243	560	1	ENST00000264731.3:c.1928G>A	p.Arg643Gln	p.R643Q	ENST00000264731	NM_003722.4	643	cGa/cAa	14/14	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.603014128842505	2		561	769	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	118	173	1				ENST00000310581	NM_198253.2	-/1132			0.337229140744822	1	FACETS	0.749	0.683	0.817	0.749	0.683	0.817	INDETERMINATE	1	TRUE	0	0.603014128842505	1		174	365	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	685	586	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.597318600695604	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.603014128842505	2		586	1068	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754793	29754793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	169	455	1	ENST00000389048.3:c.1142C>T	p.Pro381Leu	p.P381L	ENST00000389048	NM_004304.4	381	cCa/cTa	4/29	1	2	FACETS	0.955	0.883	1	0.955	0.883	1	CLONAL	1	TRUE	1	0.603014128842505	2		456	587	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661663	227661664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761880048	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	192	572	6	ENST00000305123.5:c.1791dup	p.His598AlafsTer13	p.H598Afs*13	ENST00000305123	NM_005544.2	597	-/G	1/2	1	2	FACETS	0.915	0.849	0.983	0.915	0.849	0.983	CLONAL	1	TRUE	1	0.603014128842505	2		578	696	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021422	42021422	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	281	498	0	ENST00000219905.7:c.3718C>T	p.Arg1240Ter	p.R1240*	ENST00000219905	NM_001164273.1	1240	Cga/Tga	11/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.603014128842505	2		498	835	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546761	9546761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768724288	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	95	314	0	ENST00000353224.5:c.1261G>A	p.Asp421Asn	p.D421N	ENST00000353224	NM_177990.2	421	Gac/Aac	5/10	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.603014128842505	2		314	308	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105955	27105955	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	297	482	0	ENST00000324856.7:c.5566C>T	p.Gln1856Ter	p.Q1856*	ENST00000324856	NM_006015.4	1856	Cag/Tag	20/20	0.564824982179649	2	FACETS	0.921	0.878	0.963	0.921	0.878	0.963	CLONAL	2	TRUE	0	0.603014128842505	2		482	535	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495442	149495442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576668629	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	253	891	1	ENST00000261799.4:c.3205G>A	p.Glu1069Lys	p.E1069K	ENST00000261799	NM_002609.3	1069	Gaa/Aaa	23/23	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.603014128842505	2		892	829	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888120	81888120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199638859	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	229	627	0	ENST00000359376.3:c.265C>T	p.Arg89Cys	p.R89C	ENST00000359376	NM_002661.3	89	Cgc/Tgc	3/33	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.603014128842505	2		627	756	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546799	9546799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	119	428	0	ENST00000353224.5:c.1223C>T	p.Ser408Phe	p.S408F	ENST00000353224	NM_177990.2	408	tCc/tTc	5/10	1	2	FACETS	0.949	0.863	1	0.949	0.863	1	CLONAL	1	TRUE	1	0.603014128842505	2		428	416	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710984	117710984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	142	323	0	ENST00000368508.3:c.1288G>A	p.Gly430Ser	p.G430S	ENST00000368508	NM_002944.2	430	Ggc/Agc	12/43	1	2	FACETS	0.961	0.882	1	0.961	0.882	1	CLONAL	1	TRUE	1	0.603014128842505	2		323	490	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521456	8521456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	326	682	0	ENST00000356435.5:c.782G>A	p.Gly261Glu	p.G261E	ENST00000356435		261	gGg/gAg	9/35	0.603014128842505	1	FACETS	0.992	0.943	1	0.992	0.943	1	CLONAL	1	TRUE	0	0.603014128842505	1		682	761	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932690	49932690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	228	753	0	ENST00000296474.3:c.3181G>A	p.Asp1061Asn	p.D1061N	ENST00000296474	NM_002447.2	1061	Gac/Aac	14/20	1	2	FACETS	0.937	0.876	1	0.937	0.876	1	CLONAL	1	TRUE	1	0.603014128842505	2		753	807	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188626	32188626	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	172	731	0	ENST00000375023.3:c.829C>T	p.Pro277Ser	p.P277S	ENST00000375023	NM_004557.3	277	Cca/Tca	5/30	1	2	FACETS	0.844	0.779	0.911	0.844	0.779	0.911	CLONAL	1	TRUE	1	0.603014128842505	2		731	676	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8338947	8338947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	190	565	0	ENST00000356435.5:c.5354G>A	p.Arg1785Lys	p.R1785K	ENST00000356435		1785	aGg/aAg	32/35	0.603014128842505	1	FACETS	0.896	0.837	0.957	0.896	0.837	0.957	CLONAL	1	TRUE	0	0.603014128842505	1		565	491	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46733270	46733270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	438	529	0	ENST00000371975.4:c.1031C>T	p.Ser344Phe	p.S344F	ENST00000371975	NM_003579.3	344	tCc/tTc	9/18	0.597318600695604	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.603014128842505	2		529	677	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248105	59248105	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	162	219	0	ENST00000371222.2:c.638A>G	p.Gln213Arg	p.Q213R	ENST00000371222	NM_002228.3	213	cAg/cGg	1/1	0.597318600695604	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.603014128842505	2		219	245	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115272907	115272907	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs925356784	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	544	687	1	ENST00000438362.2:c.1466C>T	p.Thr489Ile	p.T489I	ENST00000438362	NM_001242891.1	489	aCc/aTc	12/20	0.597318600695604	2	FACETS	0.963	0.931	0.995	0.963	0.931	0.995	CLONAL	2	TRUE	0	0.603014128842505	2		688	937	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651136	206651136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553385811	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	211	656	1	ENST00000367120.3:c.746C>T	p.Ala249Val	p.A249V	ENST00000367120	NM_014002.3	249	gCc/gTc	8/22	1	2	FACETS	0.878	0.817	0.94	0.878	0.817	0.94	CLONAL	1	TRUE	1	0.603014128842505	2		657	797	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333429	70333429	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	258	689	0	ENST00000373644.4:c.1334C>A	p.Ala445Asp	p.A445D	ENST00000373644	NM_030625.2	445	gCt/gAt	2/12	1	2	FACETS	0.958	0.899	1	0.958	0.899	1	CLONAL	1	TRUE	1	0.603014128842505	2		689	893	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164119	108164119	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	211	411	0	ENST00000278616.4:c.4691C>T	p.Pro1564Leu	p.P1564L	ENST00000278616	NM_000051.3	1564	cCt/cTt	31/63	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.603014128842505	2		411	676	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435418	18435418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	162	384	0	ENST00000266497.5:c.403G>A	p.Gly135Ser	p.G135S	ENST00000266497		135	Ggt/Agt	1/31	1	2	FACETS	0.915	0.844	0.989	0.915	0.844	0.989	CLONAL	1	TRUE	1	0.603014128842505	2		384	587	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945097	31945097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	169	570	0	ENST00000340398.3:c.4G>A	p.Ala2Thr	p.A2T	ENST00000340398	NM_001013699.2	2	Gcc/Acc	1/1	1	2	FACETS	0.864	0.797	0.933	0.864	0.797	0.933	CLONAL	1	TRUE	1	0.603014128842505	2		570	649	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248851	133248851	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	226	713	2	ENST00000320574.5:c.1744C>A	p.Leu582Ile	p.L582I	ENST00000320574	NM_006231.2	582	Ctt/Att	16/49	1	2	FACETS	0.885	0.826	0.946	0.885	0.826	0.946	CLONAL	1	TRUE	1	0.603014128842505	2		715	847	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913308	32913308	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	248	542	0	ENST00000380152.3:c.4816T>A	p.Ser1606Thr	p.S1606T	ENST00000380152		1606	Tct/Act	11/27	0.57955524683439	3	FACETS	0.912	0.852	0.974	0.456	0.426	0.487	CLONAL	1	TRUE	1	0.603014128842505	3		542	1174	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936989	48936989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	263	662	1	ENST00000267163.4:c.757C>T	p.Pro253Ser	p.P253S	ENST00000267163	NM_000321.2	253	Ccc/Tcc	8/27	0.57955524683439	3	FACETS	0.931	0.872	0.993	0.466	0.436	0.497	CLONAL	1	TRUE	1	0.603014128842505	3		663	1219	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348713	11348714	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	251	668	1	ENST00000332029.2:c.622_623delinsTT	p.Pro208Phe	p.P208F	ENST00000332029	NM_003745.1	208	CCc/TTc	2/2	1	2	FACETS	0.99	0.929	1	0.99	0.929	1	CLONAL	1	TRUE	1	0.603014128842505	2		669	841	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829881	72829881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	250	706	0	ENST00000268489.5:c.6700C>T	p.Pro2234Ser	p.P2234S	ENST00000268489	NM_006885.3	2234	Cca/Tca	9/10	NA	2	FACETS	0.971	0.91	1			1	INDETERMINATE	1	TRUE	NA	0.603014128842505	2		706	854	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686929	37686929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	203	575	0	ENST00000447079.4:c.3833C>T	p.Pro1278Leu	p.P1278L	ENST00000447079	NM_015083.1	1278	cCa/cTa	14/14	1	2	FACETS	0.924	0.859	0.99	0.924	0.859	0.99	CLONAL	1	TRUE	1	0.603014128842505	2		575	729	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436035	56436035	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	125	399	0	ENST00000407977.2:c.1102C>G	p.Arg368Gly	p.R368G	ENST00000407977		368	Cgg/Ggg	9/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.603014128842505	2		399	398	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050953	13050953	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776958612	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	199	505	0	ENST00000316448.5:c.484C>T	p.Arg162Cys	p.R162C	ENST00000316448	NM_004343.3	162	Cgt/Tgt	4/9	1	2	FACETS	0.913	0.849	0.979	0.913	0.849	0.979	CLONAL	1	TRUE	1	0.603014128842505	2		505	723	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214707	36214707	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	110	555	1	ENST00000222270.7:c.3133C>T	p.Pro1045Ser	p.P1045S	ENST00000222270	NM_014727.1	1045	Cca/Tca	8/37	1	2	FACETS	0.776	0.701	0.855	0.776	0.701	0.855	SUBCLONAL	1	TRUE	1	0.603014128842505	2		556	470	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856035	45856035	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	153	700	0	ENST00000391945.4:c.1871C>G	p.Pro624Arg	p.P624R	ENST00000391945	NM_000400.3	624	cCc/cGc	20/23	1	2	FACETS	0.724	0.664	0.787	0.724	0.664	0.787	SUBCLONAL	1	TRUE	1	0.603014128842505	2		700	701	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150027	202150027	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	259	611	0	ENST00000358485.4:c.1468G>A	p.Glu490Lys	p.E490K	ENST00000358485	NM_001080125.1	490	Gag/Aag	8/9	1	2	FACETS	0.972	0.912	1	0.972	0.912	1	CLONAL	1	TRUE	1	0.603014128842505	2		611	884	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39721132	39721132	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	262	580	0	ENST00000361337.2:c.635C>A	p.Pro212His	p.P212H	ENST00000361337	NM_003286.2	212	cCt/cAt	9/21	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.603014128842505	2		580	847	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656794	45656794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	118	683	0	ENST00000407780.3:c.362G>A	p.Gly121Glu	p.G121E	ENST00000407780	NM_001283052.1	121	gGa/gAa	3/7	1	2	FACETS	0.729	0.66	0.801	0.729	0.66	0.801	SUBCLONAL	1	TRUE	1	0.603014128842505	2		683	537	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164498	47164498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	144	395	0	ENST00000409792.3:c.1628C>T	p.Ser543Leu	p.S543L	ENST00000409792	NM_014159.6	543	tCa/tTa	3/21	1	2	FACETS	0.864	0.792	0.938	0.864	0.792	0.938	CLONAL	1	TRUE	1	0.603014128842505	2		395	553	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391196	89391196	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	203	495	0	ENST00000336596.2:c.1262C>G	p.Pro421Arg	p.P421R	ENST00000336596	NM_005233.5	421	cCa/cGa	5/17	1	2	FACETS	0.911	0.847	0.977	0.911	0.847	0.977	CLONAL	1	TRUE	1	0.603014128842505	2		495	739	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920106	1920106	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	266	690	0	ENST00000382891.5:c.1166C>T	p.Ser389Phe	p.S389F	ENST00000382891	NM_133335.3	389	tCt/tTt	5/22	0.543262511556751	1	FACETS	0.709	0.666	0.753	0.709	0.666	0.753	SUBCLONAL	1	TRUE	0	0.603014128842505	1		690	869	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748159	41748159	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1292727082	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	135	367	0	ENST00000226382.2:c.610C>T	p.Pro204Ser	p.P204S	ENST00000226382	NM_003924.3	204	Ccc/Tcc	3/3	1	2	FACETS	0.986	0.903	1	0.986	0.903	1	CLONAL	1	TRUE	1	0.603014128842505	2		367	454	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55597574	55597574	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	239	494	0	ENST00000288135.5:c.2222C>T	p.Ser741Phe	p.S741F	ENST00000288135	NM_000222.2	741	tCt/tTt	15/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.603014128842505	2		494	753	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176662858	176662858	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	227	549	0	ENST00000439151.2:c.3833G>C	p.Ser1278Thr	p.S1278T	ENST00000439151	NM_022455.4	1278	aGc/aCc	6/23	1	2	FACETS	0.973	0.909	1	0.973	0.909	1	CLONAL	1	TRUE	1	0.603014128842505	2		549	774	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039533	180039534	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	175	740	2	ENST00000261937.6:c.3509_3510delinsAA	p.Gly1170Glu	p.G1170E	ENST00000261937	NM_182925.4	1170	gGG/gAA	26/30	1	2	FACETS	0.914	0.845	0.985	0.914	0.845	0.985	CLONAL	1	TRUE	1	0.603014128842505	2		742	635	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166443	32166443	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	269	731	1	ENST00000375023.3:c.4600G>A	p.Gly1534Arg	p.G1534R	ENST00000375023	NM_004557.3	1534	Gga/Aga	25/30	1	2	FACETS	0.994	0.934	1	0.994	0.934	1	CLONAL	1	TRUE	1	0.603014128842505	2		732	898	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372774	81372774	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	210	474	0	ENST00000222390.5:c.760G>A	p.Gly254Ser	p.G254S	ENST00000222390	NM_000601.4	254	Ggc/Agc	7/18	1	2	FACETS	0.949	0.884	1	0.949	0.884	1	CLONAL	1	TRUE	1	0.603014128842505	2		474	734	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395452	116395452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	295	526	0	ENST00000397752.3:c.1745C>T	p.Thr582Ile	p.T582I	ENST00000397752	NM_000245.2	582	aCc/aTc	6/21	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.603014128842505	2		526	957	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371962	55371962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	192	498	0	ENST00000297316.4:c.652C>T	p.Pro218Ser	p.P218S	ENST00000297316	NM_022454.3	218	Ccg/Tcg	2/2	0.57955524683439	3	FACETS	0.995	0.922	1	0.497	0.461	0.536	CLONAL	1	TRUE	1	0.603014128842505	3		498	833	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139804438	139804438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774024927	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	223	625	0	ENST00000247668.2:c.595C>T	p.Arg199Trp	p.R199W	ENST00000247668	NM_021138.3	199	Cgg/Tgg	6/11	0.603014128842505	1	FACETS	0.931	0.874	0.988	0.931	0.874	0.988	CLONAL	1	TRUE	0	0.603014128842505	1		625	555	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928908	44928908	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	211	253	1	ENST00000377967.4:c.2008C>T	p.Gln670Ter	p.Q670*	ENST00000377967	NM_021140.2	670	Cag/Tag	17/29	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.603014128842505	1		254	335	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343496	70343497	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0027258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	282	338	1	ENST00000374080.3:c.1670_1671delinsTT	p.Ser557Phe	p.S557F	ENST00000374080		557	tCC/tTT	12/45	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.603014128842505	1		339	451	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	496	215	0				ENST00000310581	NM_198253.2	-/1132			0.859334170231009	3	FACETS	0.994	0.96	1	0.994	0.96	1	CLONAL	2	TRUE	1	0.859334170231009	3		215	830	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0027265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	243	351	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.874	0.822	0.927	0.874	0.822	0.927	CLONAL	1	TRUE	1	0.859334170231009	2		351	647	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913381	NA	P-0027265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	277	441	0	ENST00000304494.5:c.322G>A	p.Asp108Asn	p.D108N	ENST00000304494	NM_000077.4	108	Gat/Aat	2/3	0.859334170231009	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.859334170231009	1		441	367	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88677041	88677041	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	216	267	0	ENST00000372037.3:c.826G>A	p.Glu276Lys	p.E276K	ENST00000372037	NM_004329.2	276	Gaa/Aaa	9/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.859334170231009	2		267	451	SUCCESS
APC	324	MSKCC	GRCh37	5	112177831	112177831	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1465288890	NA	P-0027265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	184	290	0	ENST00000257430.4:c.6540G>C	p.Lys2180Asn	p.K2180N	ENST00000257430	NM_000038.5	2180	aaG/aaC	16/16	0.830700299091408	4	FACETS	0.879	0.812	0.949	0.293	0.27	0.317	CLONAL	1	TRUE	1	0.859334170231009	4		290	906	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793250	139793251	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0027265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	384	592	0	ENST00000247668.2:c.60dup	p.Lys21GlnfsTer59	p.K21Qfs*59	ENST00000247668	NM_021138.3	20	tcc/tCcc	2/11	0.859334170231009	1	FACETS	0.946	0.914	0.976	0.946	0.914	0.976	CLONAL	1	TRUE	0	0.859334170231009	1		592	539	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	86	430	0				ENST00000310581	NM_198253.2	-/1132			0.502926867988882	1	FACETS	0.571	0.508	0.639	0.571	0.508	0.639	SUBCLONAL	1	TRUE	0	0.502926867988882	1		430	448	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974715	21974732	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCCCCCGCCTCCA	GCAGCGCCCCCGCCTCCA	-	novel	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	69	347	0	ENST00000304494.5:c.95_112del	p.Leu32_Leu37del	p.L32_L37del	ENST00000304494	NM_000077.4	32	cTGGAGGCGGGGGCGCTGCcc/ccc	1/3	0.502926867988882	1	FACETS	0.764	0.672	0.86	0.764	0.672	0.86	SUBCLONAL	1	TRUE	0	0.502926867988882	1		347	269	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764146326	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	234	660	1	ENST00000269305.4:c.841G>A	p.Asp281Asn	p.D281N	ENST00000269305	NM_001126112.2	281	Gac/Aac	8/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.502926867988882	2		661	844	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579359	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587780066	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	211	623	1	ENST00000269305.4:c.328del	p.Arg110ValfsTer13	p.R110Vfs*13	ENST00000269305	NM_001126112.2	110	Cgt/gt	4/11	1	2	FACETS	0.984	0.915	1	0.984	0.915	1	CLONAL	1	TRUE	1	0.502926867988882	2		624	853	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057302	30057302	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315496	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	128	470	0	ENST00000338641.4:c.784C>T	p.Arg262Ter	p.R262*	ENST00000338641	NM_000268.3	262	Cga/Tga	8/16	0.502926867988882	1	FACETS	0.957	0.876	1	0.957	0.876	1	CLONAL	1	TRUE	0	0.502926867988882	1		470	398	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979610	7979610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781269323	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	156	518	0	ENST00000319144.4:c.1415C>T	p.Ser472Leu	p.S472L	ENST00000319144	NM_001139.2	472	tCg/tTg	11/15	1	2	FACETS	0.869	0.797	0.943	0.869	0.797	0.943	CLONAL	1	TRUE	1	0.502926867988882	2		518	714	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71161721	71161721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	81	332	0	ENST00000318789.4:c.248C>T	p.Ser83Phe	p.S83F	ENST00000318789	NM_032682.5	83	tCt/tTt	7/21	1	2	FACETS	0.791	0.701	0.887	0.791	0.701	0.887	SUBCLONAL	1	TRUE	1	0.502926867988882	2		332	407	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507393	8507393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	212	271	0	ENST00000356435.5:c.1585G>A	p.Glu529Lys	p.E529K	ENST00000356435		529	Gaa/Aaa	11/35	0.430162373636415	6	FACETS	1	0.952	1	0.809	0.763	0.855	CLONAL	4	TRUE	1	0.502926867988882	6		271	418	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609590	81609590	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377272347	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	98	410	0	ENST00000298171.2:c.1188G>A	p.Met396Ile	p.M396I	ENST00000298171	NM_000369.2	396	atG/atA	10/10	1	2	FACETS	0.849	0.761	0.941	0.849	0.761	0.941	CLONAL	1	TRUE	1	0.502926867988882	2		410	459	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188182	32188182	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	100	442	0	ENST00000375023.3:c.1159G>A	p.Gly387Arg	p.G387R	ENST00000375023	NM_004557.3	387	Gga/Aga	6/30	1	2	FACETS	0.904	0.812	1	0.904	0.812	1	CLONAL	1	TRUE	1	0.502926867988882	2		442	440	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378643	25378643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730880471	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	117	453	0	ENST00000311936.3:c.355G>A	p.Asp119Asn	p.D119N	ENST00000311936	NM_004985.3	119	Gat/Aat	4/5	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.502926867988882	2		453	389	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380017	116380017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752842662	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	93	555	0	ENST00000397752.3:c.1406G>A	p.Arg469Gln	p.R469Q	ENST00000397752	NM_000245.2	469	cGa/cAa	4/21	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.502926867988882	2		555	345	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286760	212286760	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763644012	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	51	405	1	ENST00000342788.4:c.2936G>A	p.Arg979Gln	p.R979Q	ENST00000342788	NM_005235.2	979	cGa/cAa	24/28	1	2	FACETS	0.768	0.658	0.887	0.768	0.658	0.887	SUBCLONAL	1	TRUE	1	0.502926867988882	2		406	264	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527614	29527614	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	48	373	0	ENST00000356175.3:c.1062+1G>A		p.X354_splice	ENST00000356175	NM_000267.3	354			1	2	FACETS	0.799	0.682	0.925	0.799	0.682	0.925	CLONAL	1	TRUE	1	0.502926867988882	2		373	239	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678602	88678602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243717189	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	42	258	0	ENST00000360948.2:c.934G>A	p.Glu312Lys	p.E312K	ENST00000360948	NM_001012338.2	312	Gag/Aag	9/19	1	2	FACETS	0.607	0.51	0.714	0.607	0.51	0.714	SUBCLONAL	1	TRUE	1	0.502926867988882	2		258	275	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535354	187535354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	49	380	0	ENST00000441802.2:c.9220C>T	p.Pro3074Ser	p.P3074S	ENST00000441802	NM_005245.3	3074	Cca/Tca	12/27	1	2	FACETS	0.689	0.587	0.799	0.689	0.587	0.799	SUBCLONAL	1	TRUE	1	0.502926867988882	2		380	283	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11308063	11308063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	182	695	0	ENST00000361445.4:c.929C>T	p.Pro310Leu	p.P310L	ENST00000361445	NM_004958.3	310	cCt/cTt	7/58	1	2	FACETS	0.952	0.881	1	0.952	0.881	1	CLONAL	1	TRUE	1	0.502926867988882	2		695	760	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263661	16263661	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1050094513	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	62	323	0	ENST00000375759.3:c.10030C>T	p.Pro3344Ser	p.P3344S	ENST00000375759	NM_015001.2	3344	Cct/Tct	12/15	1	2	FACETS	0.661	0.574	0.755	0.661	0.574	0.755	SUBCLONAL	1	TRUE	1	0.502926867988882	2		323	373	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699450	117699450	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	111	483	0	ENST00000369458.3:c.191T>A	p.Leu64His	p.L64H	ENST00000369458	NM_024626.3	64	cTt/cAt	3/6	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.502926867988882	2		483	440	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658395	18658395	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1355916927	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	47	265	1	ENST00000266497.5:c.3200G>A	p.Arg1067Lys	p.R1067K	ENST00000266497		1067	aGg/aAg	22/31	1	2	FACETS	0.968	0.828	1	0.968	0.828	1	CLONAL	1	TRUE	1	0.502926867988882	2		266	193	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434960	49434960	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	115	462	0	ENST00000301067.7:c.6593C>T	p.Pro2198Leu	p.P2198L	ENST00000301067	NM_003482.3	2198	cCc/cTc	31/54	1	2	FACETS	0.951	0.861	1	0.951	0.861	1	CLONAL	1	TRUE	1	0.502926867988882	2		462	481	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487629	56487629	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779911233	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	154	505	3	ENST00000267101.3:c.1562G>A	p.Arg521Gln	p.R521Q	ENST00000267101	NM_001982.3	521	cGa/cAa	13/28	1	2	FACETS	0.922	0.847	1	0.922	0.847	1	CLONAL	1	TRUE	1	0.502926867988882	2		508	664	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034840	42034840	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769653790	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	114	487	0	ENST00000219905.7:c.4682C>T	p.Thr1561Ile	p.T1561I	ENST00000219905	NM_001164273.1	1561	aCc/aTc	15/24	1	2	FACETS	0.859	0.776	0.945	0.859	0.776	0.945	CLONAL	1	TRUE	1	0.502926867988882	2		487	528	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724636	43724636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1299648700	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	141	608	0	ENST00000382044.4:c.3431C>T	p.Pro1144Leu	p.P1144L	ENST00000382044	NM_001141980.1	1144	cCt/cTt	17/28	1	2	FACETS	0.965	0.883	1	0.965	0.883	1	CLONAL	1	TRUE	1	0.502926867988882	2		608	581	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56862896	56862896	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	47	231	0	ENST00000308159.5:c.802A>C	p.Asn268His	p.N268H	ENST00000308159	NM_014669.4	268	Aat/Cat	9/22	1	2	FACETS	0.869	0.742	1	0.869	0.742	1	CLONAL	1	TRUE	1	0.502926867988882	2		231	215	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346900	89346900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1474785996	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	40	228	0	ENST00000301030.4:c.6050C>T	p.Ala2017Val	p.A2017V	ENST00000301030	NM_001256183.1	2017	gCc/gTc	9/13	1	2	FACETS	0.812	0.682	0.952	0.812	0.682	0.952	CLONAL	1	TRUE	1	0.502926867988882	2		228	196	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16001803	16001803	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771889820	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	105	426	0	ENST00000268712.3:c.2698C>T	p.Pro900Ser	p.P900S	ENST00000268712	NM_006311.3	900	Cct/Tct	21/46	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.502926867988882	2		426	376	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17116983	17116983	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	144	446	0	ENST00000285071.4:c.1726G>A	p.Glu576Lys	p.E576K	ENST00000285071	NM_144997.5	576	Gag/Aag	14/14	1	2	FACETS	0.939	0.859	1	0.939	0.859	1	CLONAL	1	TRUE	1	0.502926867988882	2		446	610	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550537	29550537	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567845906	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	69	399	0	ENST00000356175.3:c.1797G>A	p.Trp599Ter	p.W599*	ENST00000356175	NM_000267.3	599	tgG/tgA	16/57	1	2	FACETS	0.695	0.608	0.788	0.695	0.608	0.788	SUBCLONAL	1	TRUE	1	0.502926867988882	2		399	395	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554283	29554283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	123	560	0	ENST00000356175.3:c.2299G>A	p.Glu767Lys	p.E767K	ENST00000356175	NM_000267.3	767	Gag/Aag	19/57	1	2	FACETS	0.815	0.739	0.895	0.815	0.739	0.895	CLONAL	1	TRUE	1	0.502926867988882	2		560	600	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560065	29560065	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	66	252	0	ENST00000356175.3:c.3542A>G	p.Glu1181Gly	p.E1181G	ENST00000356175	NM_000267.3	1181	gAa/gGa	27/57	1	2	FACETS	0.813	0.71	0.921	0.813	0.71	0.921	CLONAL	1	TRUE	1	0.502926867988882	2		252	323	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37863369	37863369	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752339377	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	214	596	0	ENST00000269571.5:c.200C>T	p.Thr67Ile	p.T67I	ENST00000269571		67	aCc/aTc	2/27	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.502926867988882	2		596	819	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119040	3119040	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	164	529	0	ENST00000078429.4:c.724T>C	p.Ser242Pro	p.S242P	ENST00000078429	NM_002067.2	242	Tcg/Ccg	5/7	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.502926867988882	2		529	548	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117074	7117074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	186	454	0	ENST00000302850.5:c.4142C>T	p.Pro1381Leu	p.P1381L	ENST00000302850	NM_000208.2	1381	cCt/cTt	22/22	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.502926867988882	2		454	618	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262087	10262087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	223	469	1	ENST00000340748.4:c.2204G>A	p.Gly735Glu	p.G735E	ENST00000340748		735	gGa/gAa	23/40	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.502926867988882	2		470	671	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974277	18974278	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	126	546	1	ENST00000262803.5:c.2631_2632delinsAA	p.Ala878Thr	p.A878T	ENST00000262803	NM_002911.3	877	aaGGca/aaAAca	19/24	1	2	FACETS	0.666	0.604	0.732	0.666	0.604	0.732	SUBCLONAL	1	TRUE	1	0.502926867988882	2		547	752	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223957	36223965	+	inframe_deletion	In_Frame_Del	DEL	CCCAGGGGT	CCCAGGGGT	-	novel	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	261	826	0	ENST00000222270.7:c.6509_6517del	p.Pro2170_Val2172del	p.P2170_V2172del	ENST00000222270	NM_014727.1	2169	gcCCCAGGGGTc/gcc	28/37	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.502926867988882	2		826	1033	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964984	25964984	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	108	375	0	ENST00000435504.4:c.4222A>T	p.Ile1408Phe	p.I1408F	ENST00000435504		1408	Atc/Ttc	13/13	1	2	FACETS	0.934	0.843	1	0.934	0.843	1	CLONAL	1	TRUE	1	0.502926867988882	2		375	460	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719406	190719406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	24	256	0	ENST00000441310.2:c.1408G>A	p.Gly470Ser	p.G470S	ENST00000441310	NM_000534.4	470	Ggc/Agc	9/13	1	2	FACETS	0.593	0.469	0.733	0.593	0.469	0.733	SUBCLONAL	1	TRUE	1	0.502926867988882	2		256	161	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719434	190719435	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	45	267	0	ENST00000441310.2:c.1436_1437delinsAA	p.Gly479Glu	p.G479E	ENST00000441310	NM_000534.4	479	gGG/gAA	9/13	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.502926867988882	2		267	169	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265488	198265488	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	132	442	0	ENST00000335508.6:c.2669A>T	p.Glu890Val	p.E890V	ENST00000335508	NM_012433.2	890	gAa/gTa	18/25	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.502926867988882	2		442	496	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646147	215646147	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	78	388	0	ENST00000260947.4:c.451A>T	p.Ser151Cys	p.S151C	ENST00000260947	NM_000465.2	151	Agt/Tgt	4/11	1	2	FACETS	0.896	0.794	1	0.896	0.794	1	CLONAL	1	TRUE	1	0.502926867988882	2		388	346	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742782	39742782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	89	399	0	ENST00000361337.2:c.1625C>T	p.Pro542Leu	p.P542L	ENST00000361337	NM_003286.2	542	cCt/cTt	15/21	1	2	FACETS	0.711	0.632	0.794	0.711	0.632	0.794	SUBCLONAL	1	TRUE	1	0.502926867988882	2		399	498	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164102	47164103	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	47	274	2	ENST00000409792.3:c.2023_2024delinsAA	p.Gly675Lys	p.G675K	ENST00000409792	NM_014159.6	675	GGa/AAa	3/21	0.16867771675904	3	FACETS	0.873	0.742	1	0.436	0.371	0.508	INDETERMINATE	1	TRUE	1	0.502926867988882	3		276	268	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958861	55958861	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	82	386	0	ENST00000263923.4:c.2992G>A	p.Asp998Asn	p.D998N	ENST00000263923	NM_002253.2	998	Gac/Aac	22/30	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.502926867988882	2		386	323	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295207	1295207	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	95	472	0				ENST00000310581	NM_198253.2	-/1132			0.502926867988882	1	FACETS	0.705	0.632	0.782	0.705	0.632	0.782	SUBCLONAL	1	TRUE	0	0.502926867988882	1		472	401	SUCCESS
APC	324	MSKCC	GRCh37	5	112177323	112177323	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554087155	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	49	324	0	ENST00000257430.4:c.6032C>T	p.Ser2011Leu	p.S2011L	ENST00000257430	NM_000038.5	2011	tCa/tTa	16/16	1	2	FACETS	0.847	0.725	0.979	0.847	0.725	0.979	CLONAL	1	TRUE	1	0.502926867988882	2		324	230	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460368	149460368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	65	406	1	ENST00000286301.3:c.269C>T	p.Pro90Leu	p.P90L	ENST00000286301	NM_005211.3	90	cCc/cTc	3/22	1	2	FACETS	0.536	0.466	0.612	0.536	0.466	0.612	SUBCLONAL	1	TRUE	1	0.502926867988882	2		407	482	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515276	149515276	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	132	498	0	ENST00000261799.4:c.206C>T	p.Pro69Leu	p.P69L	ENST00000261799	NM_002609.3	69	cCc/cTc	3/23	1	2	FACETS	0.99	0.904	1	0.99	0.904	1	CLONAL	1	TRUE	1	0.502926867988882	2		498	530	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271219	26271219	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	93	337	0	ENST00000305910.3:c.394C>T	p.Arg132Cys	p.R132C	ENST00000305910	NM_003534.2	132	Cgt/Tgt	1/1	1	2	FACETS	0.835	0.746	0.928	0.835	0.746	0.928	CLONAL	1	TRUE	1	0.502926867988882	2		337	443	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517376	157517376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437511816	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	159	536	1	ENST00000346085.5:c.3940C>T	p.Pro1314Ser	p.P1314S	ENST00000346085	NM_020732.3	1314	Ccc/Tcc	16/20	0.502926867988882	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.502926867988882	1		537	466	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979530	2979530	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868565027	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	97	414	0	ENST00000396946.4:c.717G>A	p.Met239Ile	p.M239I	ENST00000396946	NM_032415.4	239	atG/atA	6/25	1	2	FACETS	0.75	0.671	0.834	0.75	0.671	0.834	SUBCLONAL	1	TRUE	1	0.502926867988882	2		414	514	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729808	41729808	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150182559	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	55	213	0	ENST00000242208.4:c.721C>T	p.Arg241Trp	p.R241W	ENST00000242208	NM_002192.2	241	Cgg/Tgg	3/3	1	2	FACETS	0.968	0.838	1	0.968	0.838	1	CLONAL	1	TRUE	1	0.502926867988882	2		213	226	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340168	116340168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761768345	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	68	225	1	ENST00000397752.3:c.1030G>A	p.Gly344Arg	p.G344R	ENST00000397752	NM_000245.2	344	Ggg/Agg	2/21	1	2	FACETS	0.983	0.865	1	0.983	0.865	1	CLONAL	1	TRUE	1	0.502926867988882	2		226	275	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205490	38205491	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	122	612	1	ENST00000317025.8:c.199_200delinsTT	p.Pro67Phe	p.P67F	ENST00000317025	NM_023034.1	67	CCt/TTt	2/24	1	2	FACETS	0.831	0.753	0.912	0.831	0.753	0.912	CLONAL	1	TRUE	1	0.502926867988882	2		613	584	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5077464	5077464	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	55	257	0	ENST00000381652.3:c.1876C>T	p.Gln626Ter	p.Q626*	ENST00000381652	NM_004972.3	626	Cag/Tag	15/25	0.430162373636415	6	FACETS	0.75	0.641	0.869	0.15	0.128	0.174	SUBCLONAL	1	TRUE	1	0.502926867988882	6		257	585	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169585	27169585	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	421	642	0	ENST00000380036.4:c.586G>A	p.Gly196Arg	p.G196R	ENST00000380036	NM_000459.3	196	Gga/Aga	4/23	0.193611564099727	3	FACETS	0.846	0.811	0.88	0.846	0.811	0.88	INDETERMINATE	3	TRUE	0	0.502926867988882	3		642	826	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250274	110250274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777396288	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	63	615	0	ENST00000374672.4:c.401C>T	p.Ser134Leu	p.S134L	ENST00000374672	NM_004235.4	134	tCg/tTg	3/5	1	2	FACETS	0.296	0.255	0.34	0.296	0.255	0.34	SUBCLONAL	1	TRUE	1	0.502926867988882	2		615	847	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860031	152860032	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0027338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	108	238	0	ENST00000406277.2:c.396_397delinsTT	p.Gln133Ter	p.Q133*	ENST00000406277	NM_152274.4	132	ttCCag/ttTTag	5/7	1		FACETS		0.986	1				CLONAL	1	TRUE	0	0.502926867988882	1		238	222	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0027651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	36	282	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.723	0.593	0.87	0.723	0.593	0.87	SUBCLONAL	1	TRUE	1	0.15	2		282	664	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0027651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	59	458	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.15	2		458	699	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971122	21971123	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	45	538	0	ENST00000304494.5:c.235dup	p.Thr79AsnfsTer41	p.T79Nfs*41	ENST00000304494	NM_000077.4	79	acc/aAcc	2/3	1	2	FACETS	0.849	0.712	1	0.849	0.712	1	CLONAL	1	TRUE	1	0.15	2		538	707	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0027651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	67	823	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	1	2	FACETS	0.92	0.797	1	0.92	0.797	1	CLONAL	1	TRUE	1	0.15	2		823	971	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038526	47038526	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	56	303	1	ENST00000377604.3:c.688C>T	p.Arg230Ter	p.R230*	ENST00000377604	NM_001204468.1	230	Cga/Tga	8/24	1	1	FACETS	0.816	0.701	0.941	1	0.971	1	CLONAL	2	TRUE	0	0.15	1		304	423	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056560	26056560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766992808	NA	P-0027651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	28	224	1	ENST00000343677.2:c.97C>T	p.Arg33Cys	p.R33C	ENST00000343677	NM_005319.3	33	Cgt/Tgt	1/1	1	2	FACETS	1	0.832	1	1	0.832	1	CLONAL	1	TRUE	1	0.15	2		225	357	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322994	31322994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	58	658	1	ENST00000412585.2:c.902C>T	p.Ser301Phe	p.S301F	ENST00000412585	NM_005514.6	301	tCt/tTt	5/8	1	2	FACETS	0.715	0.612	0.829	0.715	0.612	0.829	SUBCLONAL	1	TRUE	1	0.15	2		659	1081	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	244	458	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.981	1	1	0.996	1	CLONAL	3	TRUE	1	0.21	2		458	700	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	79	390	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.92	0.813	1	1	0.983	1	CLONAL	2	TRUE	1	0.21	2		390	409	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	131	513	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	1	0.973	1	1	0.991	1	CLONAL	2	TRUE	1	0.21	2		513	534	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448480	49448480	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	105	665	0	ENST00000301067.7:c.231del	p.His77GlnfsTer53	p.H77Qfs*53	ENST00000301067	NM_003482.3	77	caC/ca	3/54	1	2	FACETS	0.767	0.688	0.85	1	0.983	1	SUBCLONAL	2	TRUE	1	0.21	2		665	652	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	91	402	7	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.813	0.724	0.908	1	0.982	1	CLONAL	2	TRUE	1	0.21	2		409	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	158	923	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.3	1	FACETS	1	0.926	1	1	0.992	1	CLONAL	2	TRUE	0	0.21	1		923	668	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	32	449	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	1	2	FACETS	0.546	0.442	0.664	0.546	0.442	0.664	SUBCLONAL	1	TRUE	1	0.21	2		449	558	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952006	178952006	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	92	511	0	ENST00000263967.3:c.3061T>C	p.Tyr1021His	p.Y1021H	ENST00000263967	NM_006218.2	1021	Tac/Cac	21/21	1	2	FACETS	1	0.952	1	1	0.987	1	CLONAL	2	TRUE	1	0.21	2		511	394	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161222	56161222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	134	513	1	ENST00000399503.3:c.1091G>A	p.Arg364Gln	p.R364Q	ENST00000399503	NM_005921.1	364	cGg/cAg	5/20	1	2	FACETS	1	0.963	1	1	0.991	1	CLONAL	2	TRUE	1	0.21	2		514	578	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	64	374	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.21	2		374	468	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750394	133750394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	99	671	1	ENST00000318560.5:c.1225G>A	p.Glu409Lys	p.E409K	ENST00000318560	NM_005157.4	409	Gag/Aag	7/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.21	2		672	649	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962848	2962848	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41493047	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	99	793	0	ENST00000396946.4:c.2060C>T	p.Ala687Val	p.A687V	ENST00000396946	NM_032415.4	687	gCg/gTg	16/25	1	2	FACETS	0.799	0.715	0.888	1	0.983	1	SUBCLONAL	2	TRUE	1	0.21	2		793	590	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088788	27088788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	102	604	0	ENST00000324856.7:c.2402del	p.Gly801ValfsTer32	p.G801Vfs*32	ENST00000324856	NM_006015.4	799	caG/ca	7/20	1	2	FACETS	0.819	0.734	0.909	1	0.984	1	CLONAL	2	TRUE	1	0.21	2		604	593	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204842	128204842	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs768767517	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	117	904	4	ENST00000341105.2:c.599del	p.Gly200ValfsTer18	p.G200Vfs*18	ENST00000341105	NM_032638.4	200	gGt/gt	3/6	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.21	2		908	791	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148544345	148544345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	132	706	3	ENST00000320356.2:c.46C>T	p.Arg16Trp	p.R16W	ENST00000320356	NM_004456.4	16	Cgg/Tgg	2/20	1	2	FACETS	0.978	0.89	1	1	0.99	1	CLONAL	2	TRUE	1	0.21	2		709	643	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225663	225663	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375576259	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	121	901	2	ENST00000264932.6:c.442G>A	p.Ala148Thr	p.A148T	ENST00000264932	NM_004168.2	148	Gcc/Acc	4/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.21	2		903	836	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781122	161781122	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	97	647	7	ENST00000366898.1:c.1283del	p.Asn428MetfsTer7	p.N428Mfs*7	ENST00000366898	NM_004562.2	428	aAt/at	11/12	1	2	FACETS	0.795	0.71	0.885	1	0.983	1	SUBCLONAL	2	TRUE	1	0.21	2		654	581	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243237	123243237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55774317	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	132	867	0	ENST00000358487.5:c.2276G>A	p.Arg759Gln	p.R759Q	ENST00000358487	NM_000141.4	759	cGa/cAa	17/18	1	2	FACETS	0.985	0.897	1	1	0.99	1	CLONAL	2	TRUE	1	0.21	2		867	638	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2949715	2949715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	108	830	1	ENST00000396946.4:c.3229C>T	p.Arg1077Trp	p.R1077W	ENST00000396946	NM_032415.4	1077	Cgg/Tgg	24/25	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.21	2		831	688	SUCCESS
EED	8726	MSKCC	GRCh37	11	85961399	85961399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1343373792	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	55	457	0	ENST00000263360.6:c.176C>T	p.Thr59Met	p.T59M	ENST00000263360	NM_003797.3	59	aCg/aTg	2/12	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.21	2		457	437	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262680	16262680	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	75	354	2	ENST00000375759.3:c.9950del	p.Pro3317ArgfsTer83	p.P3317Rfs*83	ENST00000375759	NM_015001.2	3315	caC/ca	11/15	1	2	FACETS	0.854	0.752	0.963	1	0.98	1	CLONAL	2	TRUE	1	0.21	2		356	418	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716329	52716329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863225094	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	103	628	0	ENST00000322088.6:c.773G>A	p.Arg258His	p.R258H	ENST00000322088	NM_014225.5	258	cGc/cAc	6/15	1	2	FACETS	0.841	0.755	0.933	1	0.985	1	CLONAL	2	TRUE	1	0.21	2		628	583	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098365	11098365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs970190031	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	109	783	0	ENST00000358026.2:c.883C>T	p.Pro295Ser	p.P295S	ENST00000358026	NM_001128849.1	295	Ccc/Tcc	6/36	0.149405919869779	0	FACETS	1	0.973	1			1	CLONAL	1	TRUE	0	0.21	0		783	658	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151254	202151254	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	101	562	0	ENST00000358485.4:c.1557del	p.Lys520AsnfsTer10	p.K520Nfs*10	ENST00000358485	NM_001080125.1	518	atG/at	9/9	1	2	FACETS	0.923	0.828	1	1	0.986	1	CLONAL	2	TRUE	1	0.21	2		562	521	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829404	72829404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200268844	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	104	597	1	ENST00000268489.5:c.7177G>A	p.Ala2393Thr	p.A2393T	ENST00000268489	NM_006885.3	2393	Gcc/Acc	9/10	1	2	FACETS	0.831	0.746	0.921	1	0.985	1	CLONAL	2	TRUE	1	0.21	2		598	596	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023831	27023831	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1415214478	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	103	542	0	ENST00000324856.7:c.941del	p.Gly314AlafsTer49	p.G314Afs*49	ENST00000324856	NM_006015.4	313	Ggg/gg	1/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.21	2		542	666	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696461	47696461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	84	422	0	ENST00000347630.2:c.362G>A	p.Arg121Gln	p.R121Q	ENST00000347630	NM_001007230.1	121	cGg/cAg	6/11	1	2	FACETS	0.966	0.858	1	1	0.984	1	CLONAL	2	TRUE	1	0.21	2		422	414	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137430	202137431	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	103	556	0	ENST00000358485.4:c.660_661del	p.Arg221SerfsTer17	p.R221Sfs*17	ENST00000358485	NM_001080125.1	220	AAa/a	4/9	1	2	FACETS	0.947	0.851	1	1	0.987	1	CLONAL	2	TRUE	1	0.21	2		556	518	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267002	41267002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	79	459	1	ENST00000349496.5:c.673C>T	p.Arg225Cys	p.R225C	ENST00000349496	NM_001904.3	225	Cgt/Tgt	5/15	1	2	FACETS	0.79	0.697	0.889	1	0.979	1	SUBCLONAL	2	TRUE	1	0.21	2		460	476	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100975	41100975	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	77	525	1	ENST00000373198.4:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000373198	NM_133170.3	461	Cga/Tga	8/32	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.21	2		526	594	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082321	16082321	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	89	997	1	ENST00000281043.3:c.139del	p.Glu47ArgfsTer84	p.E47Rfs*84	ENST00000281043	NM_005378.4	45	ccG/cc	2/3	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.21	2		998	727	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976962	18976962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	78	563	0	ENST00000262803.5:c.3347C>T	p.Ser1116Phe	p.S1116F	ENST00000262803	NM_002911.3	1116	tCc/tTc	23/24	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.21	2		563	560	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874710	151874710	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	103	431	2	ENST00000262189.6:c.7828C>T	p.Arg2610Ter	p.R2610*	ENST00000262189	NM_170606.2	2610	Cga/Tga	38/59	1	2	FACETS	0.917	0.823	1	1	0.986	1	CLONAL	2	TRUE	1	0.21	2		433	535	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366353	15366353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200484332	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	67	464	1	ENST00000263377.2:c.1802C>T	p.Ser601Leu	p.S601L	ENST00000263377	NM_058243.2	601	tCg/tTg	10/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.21	2		465	441	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480428	89480428	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	28	405	0	ENST00000336596.2:c.2265C>A	p.Asn755Lys	p.N755K	ENST00000336596	NM_005233.5	755	aaC/aaA	13/17	1	2	FACETS	0.595	0.475	0.733	0.595	0.475	0.733	SUBCLONAL	1	TRUE	1	0.21	2		405	448	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551934	150551934	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	113	536	0	ENST00000369026.2:c.73A>G	p.Ser25Gly	p.S25G	ENST00000369026	NM_021960.4	25	Agc/Ggc	1/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.21	2		536	871	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267849	46267849	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	65	649	1	ENST00000371998.3:c.2615del	p.Asn872IlefsTer20	p.N872Ifs*20	ENST00000371998		870	gtA/gt	14/23	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.21	2		650	597	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307639	118307639	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	146	762	5	ENST00000534358.1:c.416del	p.Gly139GlufsTer11	p.G139Efs*11	ENST00000534358	NM_005933.3	138	Ggg/gg	1/36	1	2	FACETS	0.807	0.737	0.881	1	0.988	1	CLONAL	2	TRUE	1	0.21	2		767	861	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655328	45655328	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776339033	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	106	957	0	ENST00000407780.3:c.524C>T	p.Thr175Met	p.T175M	ENST00000407780	NM_001283052.1	175	aCg/aTg	4/7	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.21	2		957	800	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191157	185191157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs903937665	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	41	480	0	ENST00000265026.3:c.2038C>T	p.Arg680Trp	p.R680W	ENST00000265026	NM_004721.4	680	Cgg/Tgg	11/14	1	2	FACETS	0.744	0.619	0.883	0.744	0.619	0.883	SUBCLONAL	1	TRUE	1	0.21	2		480	525	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107098	27107098	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746165075	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	80	466	0	ENST00000324856.7:c.6709G>A	p.Ala2237Thr	p.A2237T	ENST00000324856	NM_006015.4	2237	Gcg/Acg	20/20	1	2	FACETS	0.751	0.663	0.846	1	0.977	1	SUBCLONAL	2	TRUE	1	0.21	2		466	507	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608363	43608363	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750958377	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	97	970	1	ENST00000355710.3:c.1711G>A	p.Asp571Asn	p.D571N	ENST00000355710	NM_020975.4	571	Gat/Aat	9/20	0.128645976253699	0	FACETS	0.969	0.864	1			1	CLONAL	1	TRUE	0	0.21	0		971	753	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610086	43610086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs184498773	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	84	678	0	ENST00000355710.3:c.2038G>A	p.Ala680Thr	p.A680T	ENST00000355710	NM_020975.4	680	Gcc/Acc	11/20	0.128645976253699	0	FACETS	1	0.964	1			1	CLONAL	1	TRUE	0	0.21	0		678	516	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161396	2161396	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	100	707	0	ENST00000434045.2:c.131T>C	p.Leu44Pro	p.L44P	ENST00000434045	NM_001127598.1	44	cTt/cCt	2/5	1	2	FACETS	0.879	0.787	0.975	1	0.985	1	CLONAL	2	TRUE	1	0.21	2		707	542	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153474	108153474	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769106895	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	95	543	0	ENST00000278616.4:c.3614G>A	p.Arg1205His	p.R1205H	ENST00000278616	NM_000051.3	1205	cGt/cAt	25/63	1	2	FACETS	0.975	0.872	1	1	0.986	1	CLONAL	2	TRUE	1	0.21	2		543	464	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1039243	1039243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	49	614	1	ENST00000358495.3:c.254C>T	p.Ala85Val	p.A85V	ENST00000358495	NM_134424.2	85	gCa/gTa	4/12	1	2	FACETS	0.842	0.713	0.985	0.842	0.713	0.985	CLONAL	1	TRUE	1	0.21	2		615	554	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25368445	25368445	+	intron_variant	Intron	SNP	C	C	A	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	34	528	1	ENST00000311936.3:c.451-5600G>T		p.*151*	ENST00000311936	NM_004985.3	167/189			1	2	FACETS	0.83	0.679	1	0.83	0.679	1	CLONAL	1	TRUE	1	0.21	2		529	390	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438650	49438650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375118713	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	111	745	1	ENST00000301067.7:c.4840C>T	p.Arg1614Trp	p.R1614W	ENST00000301067	NM_003482.3	1614	Cgg/Tgg	19/54	1	2	FACETS	0.797	0.718	0.881	1	0.985	1	SUBCLONAL	2	TRUE	1	0.21	2		746	663	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869523	102869523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	40	566	0	ENST00000307046.8:c.118C>T	p.Leu40Phe	p.L40F	ENST00000307046	NM_001111285.1	40	Ctc/Ttc	2/4	1	2	FACETS	0.679	0.563	0.808	0.679	0.563	0.808	SUBCLONAL	1	TRUE	1	0.21	2		566	561	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784077	120784077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1210006090	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	119	790	1	ENST00000257552.2:c.908G>A	p.Arg303His	p.R303H	ENST00000257552	NM_002442.3	303	cGc/cAc	13/15	1	2	FACETS	0.833	0.753	0.918	1	0.987	1	CLONAL	2	TRUE	1	0.21	2		791	680	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120805882	120805882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	126	884	1	ENST00000257552.2:c.196G>A	p.Val66Ile	p.V66I	ENST00000257552	NM_002442.3	66	Gtc/Atc	4/15	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.21	2		885	821	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514607	103514607	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	33	429	0	ENST00000355739.4:c.1108C>A	p.Arg370Ser	p.R370S	ENST00000355739	NM_000123.3	370	Cgt/Agt	8/15	1	2	FACETS	0.729	0.594	0.882	0.729	0.594	0.882	SUBCLONAL	1	TRUE	1	0.21	2		429	431	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873837	35873837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	73	260	2	ENST00000216797.5:c.14C>T	p.Ala5Val	p.A5V	ENST00000216797	NM_020529.2	5	gCc/gTc	1/6	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.21	2		262	553	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838097	89838097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200284845	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	79	528	0	ENST00000389301.3:c.2140C>T	p.Arg714Trp	p.R714W	ENST00000389301	NM_000135.2	714	Cgg/Tgg	23/43	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.21	2		528	521	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627757	37627757	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	112	746	1	ENST00000447079.4:c.1672C>T	p.Pro558Ser	p.P558S	ENST00000447079	NM_015083.1	558	Cca/Tca	2/14	1	2	FACETS	0.772	0.695	0.853	1	0.984	1	SUBCLONAL	2	TRUE	1	0.21	2		747	691	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244925	41244925	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	102	604	1	ENST00000357654.3:c.2623C>A	p.Pro875Thr	p.P875T	ENST00000357654	NM_007294.3	875	Cca/Aca	10/23	1	2	FACETS	1	0.955	1	1	0.989	1	CLONAL	2	TRUE	1	0.21	2		605	438	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213594	36213594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201585209	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	141	955	0	ENST00000222270.7:c.2696G>A	p.Arg899Gln	p.R899Q	ENST00000222270	NM_014727.1	899	cGg/cAg	5/37	1	2	FACETS	0.848	0.773	0.926	1	0.989	1	CLONAL	2	TRUE	1	0.21	2		955	792	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228146	36228146	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1232711537	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	130	749	0	ENST00000222270.7:c.7532G>A	p.Arg2511Gln	p.R2511Q	ENST00000222270	NM_014727.1	2511	cGg/cAg	33/37	1	2	FACETS	0.834	0.758	0.915	1	0.988	1	CLONAL	2	TRUE	1	0.21	2		749	742	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716081	52716081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	119	803	0	ENST00000322088.6:c.646G>A	p.Glu216Lys	p.E216K	ENST00000322088	NM_014225.5	216	Gag/Aag	5/15	1	2	FACETS	0.842	0.761	0.927	1	0.987	1	CLONAL	2	TRUE	1	0.21	2		803	673	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52728977	52728977	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	79	587	1	ENST00000322088.6:c.1669C>T	p.Gln557Ter	p.Q557*	ENST00000322088	NM_014225.5	557	Cag/Tag	14/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.21	2		588	511	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639551	47639551	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs587779169	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	62	366	0	ENST00000233146.2:c.646-2A>G		p.X216_splice	ENST00000233146	NM_000251.2	216			1	2	FACETS	1	0.915	1	1	0.981	1	CLONAL	2	TRUE	1	0.21	2		366	277	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395615	31395615	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	108	710	0	ENST00000328111.2:c.2468G>A	p.Arg823His	p.R823H	ENST00000328111	NM_006892.3	823	cGt/cAt	23/23	1	2	FACETS	0.824	0.741	0.912	1	0.985	1	CLONAL	2	TRUE	1	0.21	2		710	624	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262827	46262827	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	148	540	1	ENST00000371998.3:c.1000C>T	p.Arg334Ter	p.R334*	ENST00000371998		334	Cga/Tga	10/23	1	2	FACETS	0.883	0.811	0.957	1	0.993	1	CLONAL	3	TRUE	1	0.21	2		541	532	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57470732	57470732	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	94	354	0	ENST00000371085.3:c.205A>G	p.Asn69Asp	p.N69D	ENST00000371085	NM_000516.4	69	Aat/Gat	2/13	1	2	FACETS	1	0.926	1	1	0.987	1	CLONAL	2	TRUE	1	0.21	2		354	429	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163339	47163339	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	66	414	0	ENST00000409792.3:c.2787A>G	p.Ile929Met	p.I929M	ENST00000409792	NM_014159.6	929	atA/atG	3/21	1	2	FACETS	0.985	0.862	1	1	0.981	1	CLONAL	2	TRUE	1	0.21	2		414	319	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280015	66280015	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	41	274	0	ENST00000273854.3:c.1674A>T	p.Glu558Asp	p.E558D	ENST00000273854	NM_004439.5	558	gaA/gaT	7/18	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.21	2		274	275	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39074468	39074468	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1031851536	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	146	476	0	ENST00000357387.3:c.12C>G	p.Ile4Met	p.I4M	ENST00000357387	NM_152756.3	4	atC/atG	1/38	1	2	FACETS	0.823	0.751	0.898	1	0.989	1	CLONAL	2	TRUE	1	0.21	2		476	845	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591217	67591261	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AATGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGGTTGACTCAAA	AATGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGGTTGACTCAAA	-	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	47	425	0	ENST00000274335.5:c.1746-29_1761del		p.X582_splice	ENST00000274335		582		13/15	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.21	2		425	350	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912307	29912307	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	78	772	0	ENST00000376809.5:c.926T>C	p.Val309Ala	p.V309A	ENST00000376809	NM_002116.7	309	gTg/gCg	5/8	0.136296337582961	4	FACETS	1	0.961	1	0.618	0.543	0.699	CLONAL	1	TRUE	2	0.21	4		772	727	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683673	162683673	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1443653639	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	31	574	0	ENST00000366898.1:c.296C>A	p.Pro99His	p.P99H	ENST00000366898	NM_004562.2	99	cCc/cAc	3/12	1	2	FACETS	0.479	0.386	0.585	0.479	0.386	0.585	SUBCLONAL	1	TRUE	1	0.21	2		574	616	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542570	141542570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	96	649	1	ENST00000220592.5:c.2416G>A	p.Ala806Thr	p.A806T	ENST00000220592	NM_012154.3	806	Gct/Act	18/19	1	2	FACETS	0.787	0.702	0.876	1	0.982	1	SUBCLONAL	2	TRUE	1	0.21	2		650	581	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375937	8375937	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1235110923	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	22	341	0	ENST00000356435.5:c.4660A>G	p.Ser1554Gly	p.S1554G	ENST00000356435		1554	Agt/Ggt	28/35	1	2	FACETS	0.547	0.423	0.691	0.547	0.423	0.691	SUBCLONAL	1	TRUE	1	0.21	2		341	383	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399937	139399937	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1414066424	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	115	878	1	ENST00000277541.6:c.4411G>A	p.Ala1471Thr	p.A1471T	ENST00000277541	NM_017617.3	1471	Gcg/Acg	25/34	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.21	2		879	780	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401047	139401047	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	124	788	0	ENST00000277541.6:c.3946T>C	p.Cys1316Arg	p.C1316R	ENST00000277541	NM_017617.3	1316	Tgc/Cgc	24/34	1	2	FACETS	0.848	0.769	0.932	1	0.987	1	CLONAL	2	TRUE	1	0.21	2		788	696	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314945	1314945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1256843059	NA	P-0027698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	59	673	1	ENST00000400841.2:c.716C>T	p.Ala239Val	p.A239V	ENST00000400841		239	gCc/gTc	6/6	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.21	2		674	532	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	684	215	0				ENST00000310581	NM_198253.2	-/1132			0.571371963153876	7	FACETS	0.963	0.934	0.992	0.963	0.934	0.992	CLONAL	5	TRUE	2	0.571371963153876	7		215	1207	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983048	111983048	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	244	692	1	ENST00000368678.4:c.1499G>A	p.Trp500Ter	p.W500*	ENST00000368678		500	tGg/tAg	13/13	0.571371963153876	3	FACETS	1	0.978	1	0.55	0.514	0.587	CLONAL	1	TRUE	1	0.571371963153876	3		693	998	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152167	11152167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	295	749	0	ENST00000358026.2:c.4451C>T	p.Ser1484Phe	p.S1484F	ENST00000358026	NM_001128849.1	1484	tCc/tTc	31/36	0.571371963153876	3	FACETS	1	0.987	1	0.581	0.547	0.617	CLONAL	1	TRUE	1	0.571371963153876	3		749	1142	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	336	466	0	ENST00000304494.5:c.322G>C	p.Asp108His	p.D108H	ENST00000304494	NM_000077.4	108	Gat/Cat	2/3	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.571371963153876	2		466	541	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952333	38952333	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs910266255	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	79	332	0	ENST00000357387.3:c.3092C>G	p.Ser1031Cys	p.S1031C	ENST00000357387	NM_152756.3	1031	tCt/tGt	30/38	0.571371963153876	7	FACETS	0.799	0.702	0.905	0.16	0.14	0.181	CLONAL	1	TRUE	2	0.571371963153876	7		332	840	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197054	106197054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	178	322	0	ENST00000380013.4:c.5387G>A	p.Gly1796Glu	p.G1796E	ENST00000380013	NM_001127208.2	1796	gGg/gAg	11/11	0.484495815164338	4	FACETS	0.9	0.835	0.966	0.9	0.835	0.966	CLONAL	2	TRUE	2	0.571371963153876	4		322	544	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483067	29483067	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	120	692	0	ENST00000356175.3:c.127C>G	p.Leu43Val	p.L43V	ENST00000356175	NM_000267.3	43	Cta/Gta	2/57	0.571371963153876	6	FACETS	0.789	0.711	0.872	0.197	0.177	0.218	SUBCLONAL	1	TRUE	2	0.571371963153876	6		692	1141	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237644	133237644	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	544	701	3	ENST00000320574.5:c.2971G>A	p.Glu991Lys	p.E991K	ENST00000320574	NM_006231.2	991	Gag/Aag	25/49	0.571371963153876	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.571371963153876	3		704	1126	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217330	11217330	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	373	719	0	ENST00000361445.4:c.4348T>G	p.Tyr1450Asp	p.Y1450D	ENST00000361445	NM_004958.3	1450	Tat/Gat	30/58	0.484495815164338	4	FACETS	0.928	0.882	0.975	0.928	0.882	0.975	CLONAL	2	TRUE	2	0.571371963153876	4		719	1105	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783766	50783766	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1196482079	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	202	756	0	ENST00000398568.2:c.157C>T	p.Arg53Cys	p.R53C	ENST00000398568	NM_001042412.1	53	Cgt/Tgt	3/18	0.484495815164338	4	FACETS	0.99	0.917	1	0.495	0.458	0.533	CLONAL	1	TRUE	2	0.571371963153876	4		756	1122	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331667	8331667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147793450	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	183	519	1	ENST00000356435.5:c.5449G>A	p.Gly1817Arg	p.G1817R	ENST00000356435		1817	Gga/Aga	33/35	0.103468886680764	6	FACETS	0.863	0.798	0.931			1	INDETERMINATE	2	TRUE	NA	0.571371963153876	6		520	795	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979543	2979543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148083162	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	191	494	0	ENST00000396946.4:c.704G>A	p.Arg235Gln	p.R235Q	ENST00000396946	NM_032415.4	235	cGg/cAg	6/25	0.484495815164338	4	FACETS	1	0.979	1	0.58	0.536	0.625	CLONAL	1	TRUE	2	0.571371963153876	4		494	906	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242737	98242737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	342	453	3	ENST00000331920.6:c.880C>T	p.Arg294Cys	p.R294C	ENST00000331920	NM_000264.3	294	Cgc/Tgc	6/24	0.571371963153876	5	FACETS	1	0.967	1	0.514	0.486	0.541	CLONAL	2	TRUE	1	0.571371963153876	5		456	1082	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579312	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	350	537	2	ENST00000269305.4:c.375_375+1delinsAA		p.X125_splice	ENST00000269305	NM_001126112.2	125		4/11	0.571371963153876	2	FACETS	0.965	0.923	1	0.965	0.923	1	CLONAL	2	TRUE	0	0.571371963153876	2		539	635	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174943	11174943	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	167	616	0	ENST00000361445.4:c.7091T>C	p.Val2364Ala	p.V2364A	ENST00000361445	NM_004958.3	2364	gTt/gCt	52/58	0.484495815164338	4	FACETS	0.893	0.819	0.969	0.446	0.409	0.485	CLONAL	1	TRUE	2	0.571371963153876	4		616	1029	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597957	43597957	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374514956	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	316	746	0	ENST00000355710.3:c.505G>A	p.Glu169Lys	p.E169K	ENST00000355710	NM_020975.4	169	Gag/Aag	3/20	0.571371963153876	3	FACETS	1	0.988	1	0.584	0.551	0.618	CLONAL	1	TRUE	1	0.571371963153876	3		746	1217	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416120	49416125	+	inframe_deletion	In_Frame_Del	DEL	ATGTAG	ATGTAG	-	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	184	450	0	ENST00000301067.7:c.16350_16355del	p.Ile5450_Tyr5451del	p.I5450_Y5451del	ENST00000301067	NM_003482.3	5450	atCTACATg/atg	52/54	0.571371963153876	4	FACETS	1	0.976	1	0.569	0.525	0.614	CLONAL	1	TRUE	2	0.571371963153876	4		450	890	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860090	57860090	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	564	827	1	ENST00000228682.2:c.832del	p.Glu278SerfsTer2	p.E278Sfs*2	ENST00000228682	NM_005269.2	277	aGg/ag	8/12	0.571371963153876	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.571371963153876	4		828	1502	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860092	57860092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768066916	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	564	818	1	ENST00000228682.2:c.832G>A	p.Glu278Lys	p.E278K	ENST00000228682	NM_005269.2	278	Gag/Aag	8/12	0.571371963153876	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.571371963153876	4		819	1468	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610095	28610095	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	427	562	0	ENST00000241453.7:c.1395G>T	p.Lys465Asn	p.K465N	ENST00000241453	NM_004119.2	465	aaG/aaT	11/24	0.484495815164338	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	2	0.571371963153876	4		562	1167	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911074	32911074	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	245	592	0	ENST00000380152.3:c.2582A>G	p.Gln861Arg	p.Q861R	ENST00000380152		861	cAa/cGa	11/27	0.484495815164338	4	FACETS	0.936	0.879	0.994	0.936	0.879	0.994	CLONAL	2	TRUE	2	0.571371963153876	4		592	720	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913105	32913105	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	315	655	0	ENST00000380152.3:c.4613C>G	p.Ser1538Cys	p.S1538C	ENST00000380152		1538	tCt/tGt	11/27	0.484495815164338	4	FACETS	0.917	0.867	0.967	0.917	0.867	0.967	CLONAL	2	TRUE	2	0.571371963153876	4		655	945	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32932014	32932014	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80359002	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	255	413	2	ENST00000380152.3:c.7753G>A	p.Gly2585Arg	p.G2585R	ENST00000380152		2585	Gga/Aga	16/27	0.484495815164338	4	FACETS	0.945	0.889	1	0.945	0.889	1	CLONAL	2	TRUE	2	0.571371963153876	4		415	742	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557654	95557654	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	182	626	0	ENST00000393063.1:c.5413C>T	p.Pro1805Ser	p.P1805S	ENST00000393063	NM_030621.3	1805	Cca/Tca	26/28	0.571371963153876	4	FACETS	0.898	0.827	0.972	0.449	0.413	0.486	CLONAL	1	TRUE	2	0.571371963153876	4		626	1115	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643281	38643281	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1172820756	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	238	455	0	ENST00000299084.4:c.751C>T	p.Arg251Ter	p.R251*	ENST00000299084	NM_152594.2	251	Cga/Tga	7/7	0.484495815164338	4	FACETS	0.867	0.812	0.923	0.867	0.812	0.923	CLONAL	2	TRUE	2	0.571371963153876	4		455	755	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639296	3639296	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751536069	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	247	688	1	ENST00000294008.3:c.4343C>T	p.Pro1448Leu	p.P1448L	ENST00000294008	NM_032444.2	1448	cCc/cTc	12/15	0.484495815164338	4	FACETS	1	0.964	1	0.525	0.489	0.561	CLONAL	1	TRUE	2	0.571371963153876	4		689	1295	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821671	72821671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	94	193	0	ENST00000268489.5:c.10504C>T	p.Leu3502Phe	p.L3502F	ENST00000268489	NM_006885.3	3502	Ctt/Ttt	10/10	0.484495815164338	4	FACETS	1	0.954	1	0.562	0.502	0.625	CLONAL	1	TRUE	2	0.571371963153876	4		193	460	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89828373	89828373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	433	565	1	ENST00000389301.3:c.2836C>T	p.Leu946Phe	p.L946F	ENST00000389301	NM_000135.2	946	Ctt/Ttt	29/43	0.484495815164338	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.571371963153876	4		566	1152	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15978900	15978901	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	369	665	0	ENST00000268712.3:c.3617_3618delinsTT	p.Ser1206Phe	p.S1206F	ENST00000268712	NM_006311.3	1206	tCC/tTT	27/46	0.571371963153876	2	FACETS	0.94	0.9	0.98	0.94	0.9	0.98	CLONAL	2	TRUE	0	0.571371963153876	2		665	687	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15978901	15978901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	368	662	0	ENST00000268712.3:c.3617C>T	p.Ser1206Phe	p.S1206F	ENST00000268712	NM_006311.3	1206	tCc/tTc	27/46	0.571371963153876	2	FACETS	0.938	0.898	0.977	0.938	0.898	0.977	CLONAL	2	TRUE	0	0.571371963153876	2		662	687	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657459	29657459	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	552	577	0	ENST00000356175.3:c.5692G>C	p.Glu1898Gln	p.E1898Q	ENST00000356175	NM_000267.3	1898	Gag/Cag	38/57	0.571371963153876	6	FACETS	0.918	0.884	0.951	0.918	0.884	0.951	CLONAL	4	TRUE	2	0.571371963153876	6		577	1128	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245024	41245024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876658552	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1266	477	713	1	ENST00000357654.3:c.2524G>A	p.Glu842Lys	p.E842K	ENST00000357654	NM_007294.3	842	Gaa/Aaa	10/23	0.571371963153876	6	FACETS	1	0.972	1	0.513	0.489	0.537	CLONAL	2	TRUE	2	0.571371963153876	6		714	1743	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66518960	66518960	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	370	518	0	ENST00000358598.2:c.241G>T	p.Glu81Ter	p.E81*	ENST00000358598	NM_212471.2	81	Gag/Tag	3/11	0.571371963153876	6	FACETS	0.982	0.93	1	0.491	0.465	0.518	CLONAL	2	TRUE	2	0.571371963153876	6		518	1413	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120290	70120290	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770400142	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1982	334	911	0	ENST00000245479.2:c.1292C>T	p.Ser431Phe	p.S431F	ENST00000245479	NM_000346.3	431	tCc/tTc	3/3	0.571371963153876	6	FACETS	1	0.979	1	0.27	0.254	0.287	CLONAL	1	TRUE	2	0.571371963153876	6		911	2316	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372079	45372079	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	189	621	0	ENST00000262160.6:c.1090C>T	p.Gln364Ter	p.Q364*	ENST00000262160	NM_005901.5	364	Cag/Tag	9/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.571371963153876	2		621	590	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619821	1619822	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	496	797	2	ENST00000344749.5:c.1124_1125delinsTT	p.Pro375Leu	p.P375L	ENST00000344749	NM_001136139.2	375	cCC/cTT	14/19	0.571371963153876	3	FACETS	0.958	0.919	0.997	0.958	0.919	0.997	CLONAL	2	TRUE	1	0.571371963153876	3		799	1165	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279988	18279988	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	189	559	0	ENST00000222254.8:c.2071G>T	p.Glu691Ter	p.E691*	ENST00000222254	NM_005027.3	691	Gag/Tag	16/16	0.571371963153876	3	FACETS	0.921	0.851	0.993	0.46	0.425	0.497	CLONAL	1	TRUE	1	0.571371963153876	3		559	924	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229054	36229054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	273	753	2	ENST00000222270.7:c.7834G>A	p.Val2612Met	p.V2612M	ENST00000222270	NM_014727.1	2612	Gtg/Atg	36/37	0.571371963153876	3	FACETS	0.981	0.919	1	0.49	0.459	0.522	CLONAL	1	TRUE	1	0.571371963153876	3		755	1253	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762465	41762465	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	197	577	0	ENST00000301178.4:c.2145G>A	p.Trp715Ter	p.W715*	ENST00000301178	NM_021913.4	715	tgG/tgA	18/20	0.571371963153876	3	FACETS	1	0.952	1	0.517	0.479	0.556	CLONAL	1	TRUE	1	0.571371963153876	3		577	857	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455202	29455202	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	403	615	0	ENST00000389048.3:c.2600T>A	p.Val867Asp	p.V867D	ENST00000389048	NM_004304.4	867	gTt/gAt	15/29	0.484495815164338	4	FACETS	0.983	0.936	1	0.983	0.936	1	CLONAL	2	TRUE	2	0.571371963153876	4		615	1128	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421202	12421202	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	156	481	0	ENST00000287820.6:c.83-1G>T		p.X28_splice	ENST00000287820	NM_015869.4	28			0.571371963153876	3	FACETS	1	0.968	1	0.551	0.506	0.598	CLONAL	1	TRUE	1	0.571371963153876	3		481	637	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598102	52598102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	220	611	0	ENST00000394830.3:c.3764C>T	p.Ser1255Phe	p.S1255F	ENST00000394830	NM_018313.4	1255	tCt/tTt	24/30	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.571371963153876	2		611	753	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269104	142269105	+	missense_variant	Missense_Mutation	DNP	AG	AG	TA	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	138	429	0	ENST00000350721.4:c.2845_2846delinsTA	p.Leu949Tyr	p.L949Y	ENST00000350721	NM_001184.3	949	CTt/TAt	14/47	0.571371963153876	6	FACETS	0.946	0.859	1	0.189	0.171	0.208	CLONAL	1	TRUE	1	0.571371963153876	6		429	1094	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167819	185167819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1365836504	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	858	495	1	ENST00000265026.3:c.1142G>A	p.Gly381Glu	p.G381E	ENST00000265026	NM_004721.4	381	gGa/gAa	6/14	0.571371963153876	7	FACETS	0.98	0.958	1			1	CLONAL	6	TRUE	NA	0.571371963153876	7		496	1240	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1977026	1977026	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	455	643	0	ENST00000382891.5:c.3520G>A	p.Glu1174Lys	p.E1174K	ENST00000382891	NM_133335.3	1174	Gag/Aag	20/22	0.484495815164338	4	FACETS	0.955	0.912	0.999	0.955	0.912	0.999	CLONAL	2	TRUE	2	0.571371963153876	4		643	1310	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218790	66218790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776482836	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	208	454	0	ENST00000273854.3:c.2268G>A	p.Met756Ile	p.M756I	ENST00000273854	NM_004439.5	756	atG/atA	13/18	0.484495815164338	4	FACETS	0.888	0.829	0.949	0.888	0.829	0.949	CLONAL	2	TRUE	2	0.571371963153876	4		454	644	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149498376	149498376	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs761730723	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	221	704	0	ENST00000261799.4:c.2838G>C	p.Glu946Asp	p.E946D	ENST00000261799	NM_002609.3	946	gaG/gaC	21/23	0.571371963153876	3	FACETS	0.923	0.858	0.989	0.461	0.429	0.495	CLONAL	1	TRUE	1	0.571371963153876	3		704	1078	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169960	32169961	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	238	741	1	ENST00000375023.3:c.3647_3648delinsTT	p.Ser1216Phe	p.S1216F	ENST00000375023	NM_004557.3	1216	tCC/tTT	21/30	0.571371963153876	3	FACETS	1	0.949	1	0.51	0.476	0.545	CLONAL	1	TRUE	1	0.571371963153876	3		742	1050	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519539	137519539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	138	366	0	ENST00000367739.4:c.1099C>T	p.Pro367Ser	p.P367S	ENST00000367739	NM_000416.2	367	Ccg/Tcg	7/7	0.571371963153876	3	FACETS	1	0.949	1	0.527	0.481	0.575	CLONAL	1	TRUE	1	0.571371963153876	3		366	589	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200033	138200034	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	141	463	0	ENST00000237289.4:c.1451_1452delinsTT	p.Pro484Leu	p.P484L	ENST00000237289	NM_001270507.1	484	cCC/cTT	7/9	0.571371963153876	3	FACETS	0.96	0.877	1	0.48	0.438	0.524	CLONAL	1	TRUE	1	0.571371963153876	3		463	661	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140507863	140507863	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	99	436	0	ENST00000288602.6:c.609-1G>A		p.X203_splice	ENST00000288602	NM_004333.4	203			0.535340645835838	5	FACETS	1	0.933	1	0.353	0.315	0.393	CLONAL	1	TRUE	2	0.571371963153876	5		436	608	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273417	38273418	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	494	1008	2	ENST00000425967.3:c.1917_1918delinsTT	p.Arg640Ter	p.R640*	ENST00000425967	NM_001174067.1	639	gcCCga/gcTTga	14/19	0.484495815164338	4	FACETS	0.909	0.869	0.949	0.909	0.869	0.949	CLONAL	2	TRUE	2	0.571371963153876	4		1010	1495	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407472	139407473	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	657	484	0	ENST00000277541.6:c.2467_2467+1delinsAA		p.X823_splice	ENST00000277541	NM_017617.3	823		15/34	0.571371963153876	5	FACETS	0.957	0.928	0.985	0.957	0.928	0.985	CLONAL	4	TRUE	1	0.571371963153876	5		484	1116	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347799	70347799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	459	318	0	ENST00000374080.3:c.3038C>T	p.Ser1013Leu	p.S1013L	ENST00000374080		1013	tCa/tTa	22/45	0.500172109116876	2	FACETS	0.912	0.888	0.936			1	CLONAL	3	TRUE	NA	0.571371963153876	2		318	587	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152857981	152857981	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	53	91	0	ENST00000406277.2:c.634G>C	p.Glu212Gln	p.E212Q	ENST00000406277	NM_152274.4	212	Gag/Cag	6/7	0.500172109116876	2	FACETS	0.987	0.855	1			1	CLONAL	1	TRUE	NA	0.571371963153876	2		91	188	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269104	142269104	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	138	429	0	ENST00000350721.4:c.2846T>A	p.Leu949His	p.L949H	ENST00000350721	NM_001184.3	949	cTt/cAt	14/47	0.571371963153876	6	FACETS	0.946	0.859	1	0.189	0.171	0.208	CLONAL	1	TRUE	1	0.571371963153876	6		429	1094	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269105	142269105	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	136	425	0	ENST00000350721.4:c.2845C>T	p.Leu949Phe	p.L949F	ENST00000350721	NM_001184.3	949	Ctt/Ttt	14/47	0.571371963153876	6	FACETS	0.946	0.859	1	0.189	0.171	0.208	CLONAL	1	TRUE	1	0.571371963153876	6		425	1078	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0027768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	32	282	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.938	0.763	1	0.938	0.763	1	CLONAL	1	TRUE	1	0.19	2		282	359	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0027768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	12	281	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.421	0.295	0.577	0.421	0.295	0.577	SUBCLONAL	1	TRUE	1	0.19	2		281	300	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0027768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	68	779	1	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.19	2		780	640	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0027768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	29	173	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.936	0.753	1	0.936	0.753	1	CLONAL	1	TRUE	1	0.19	2		174	326	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0027768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	66	500	2	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	1	2	FACETS	0.875	0.763	0.995	1	0.978	1	CLONAL	2	TRUE	1	0.19	2		502	397	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185169106	185169106	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775670152	NA	P-0027768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	25	531	0	ENST00000265026.3:c.1201C>T	p.Arg401Trp	p.R401W	ENST00000265026	NM_004721.4	401	Cgg/Tgg	7/14	1	2	FACETS	0.666	0.525	0.829	0.666	0.525	0.829	SUBCLONAL	1	TRUE	1	0.19	2		531	395	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56912075	56912075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	55	643	3	ENST00000519728.1:c.1303G>A	p.Glu435Lys	p.E435K	ENST00000519728	NM_002350.3	435	Gaa/Aaa	12/13	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.19	2		646	536	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057021	180057021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752512978	NA	P-0027768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	43	703	0	ENST00000261937.6:c.598G>A	p.Asp200Asn	p.D200N	ENST00000261937	NM_182925.4	200	Gat/Aat	5/30	1	2	FACETS	0.849	0.71	1	0.849	0.71	1	CLONAL	1	TRUE	1	0.19	2		703	533	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212847	94212847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	28	488	0	ENST00000323929.3:c.395C>T	p.Pro132Leu	p.P132L	ENST00000323929	NM_005591.3	132	cCc/cTc	5/20	1	2	FACETS	0.864	0.691	1	0.864	0.691	1	CLONAL	1	TRUE	1	0.19	2		488	341	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910810	32910810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1177705048	NA	P-0027768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	28	416	1	ENST00000380152.3:c.2318C>T	p.Pro773Leu	p.P773L	ENST00000380152		773	cCt/cTt	11/27	1	2	FACETS	0.877	0.702	1	0.877	0.702	1	CLONAL	1	TRUE	1	0.19	2		417	336	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41962081	41962081	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs914770778	NA	P-0027768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	28	427	0	ENST00000219905.7:c.989G>A	p.Arg330Gln	p.R330Q	ENST00000219905	NM_001164273.1	330	cGa/cAa	2/24	1	2	FACETS	0.719	0.574	0.884	0.719	0.574	0.884	SUBCLONAL	1	TRUE	1	0.19	2		427	410	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996805	73996805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	19	325	0	ENST00000318443.5:c.1361C>T	p.Thr454Ile	p.T454I	ENST00000318443	NM_001024736.1	454	aCc/aTc	6/10	1	2	FACETS	0.685	0.52	0.879	0.685	0.52	0.879	SUBCLONAL	1	TRUE	1	0.19	2		325	292	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346868	91346868	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	44	574	0	ENST00000355112.3:c.3476T>C	p.Leu1159Ser	p.L1159S	ENST00000355112	NM_000057.2	1159	tTa/tCa	18/22	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.19	2		574	387	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302267	15302267	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	60	667	0	ENST00000263388.2:c.1004C>A	p.Ser335Tyr	p.S335Y	ENST00000263388	NM_000435.2	335	tCt/tAt	6/33	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.19	2		667	533	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266748	18266748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs929809973	NA	P-0027768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	38	630	1	ENST00000222254.8:c.59C>T	p.Pro20Leu	p.P20L	ENST00000222254	NM_005027.3	20	cCg/cTg	2/16	1	2	FACETS	0.871	0.72	1	0.871	0.72	1	CLONAL	1	TRUE	1	0.19	2		631	459	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224112	36224112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	44	669	0	ENST00000222270.7:c.6662C>T	p.Pro2221Leu	p.P2221L	ENST00000222270	NM_014727.1	2221	cCc/cTc	28/37	1	2	FACETS	0.803	0.672	0.947	0.803	0.672	0.947	CLONAL	1	TRUE	1	0.19	2		669	577	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578302	212578302	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759603522	NA	P-0027768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	32	556	0	ENST00000342788.4:c.955G>A	p.Gly319Arg	p.G319R	ENST00000342788	NM_005235.2	319	Ggg/Agg	8/28	1	2	FACETS	1	0.82	1	1	0.82	1	CLONAL	1	TRUE	1	0.19	2		556	334	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408930	41408930	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	22	435	0	ENST00000373198.4:c.496G>A	p.Glu166Lys	p.E166K	ENST00000373198	NM_133170.3	166	Gaa/Aaa	4/32	1	2	FACETS	0.687	0.532	0.867	0.687	0.532	0.867	SUBCLONAL	1	TRUE	1	0.19	2		435	337	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446315	187446315	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1044213121	NA	P-0027768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	41	443	0	ENST00000232014.4:c.1373C>T	p.Pro458Leu	p.P458L	ENST00000232014	NM_001130845.1	458	cCc/cTc	6/10	1	2	FACETS	0.981	0.818	1	0.981	0.818	1	CLONAL	1	TRUE	1	0.19	2		443	440	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970978	55970978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	49	525	0	ENST00000263923.4:c.1819G>A	p.Asp607Asn	p.D607N	ENST00000263923	NM_002253.2	607	Gat/Aat	13/30	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.19	2		525	427	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864473	162864473	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1159057404	NA	P-0027768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	33	450	1	ENST00000366898.1:c.40C>T	p.Pro14Ser	p.P14S	ENST00000366898	NM_004562.2	14	Cca/Tca	2/12	0.166056107693977	3	FACETS	0.93	0.758	1			1	CLONAL	1	TRUE	NA	0.19	3		451	409	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026825	6026825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63751257	NA	P-0027768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	32	450	0	ENST00000265849.7:c.1571C>T	p.Pro524Leu	p.P524L	ENST00000265849	NM_000535.5	524	cCa/cTa	11/15	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.19	2		450	282	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859443	151859443	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	89	421	0	ENST00000262189.6:c.11219A>T	p.Asn3740Ile	p.N3740I	ENST00000262189	NM_170606.2	3740	aAt/aTt	43/59	0.3	3	FACETS	1	0.968	1			1	CLONAL	2	TRUE	NA	0.19	3		421	416	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156918	89156920	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	rs768142526	NA	P-0028268-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	82	502	0	ENST00000336596.2:c.27_29del	p.Leu11del	p.L11del	ENST00000336596	NM_005233.5	7	aTCCtc/atc	1/17	0.235271611014897	1	FACETS	0.706	0.626	0.791	0.706	0.626	0.791	INDETERMINATE	1	TRUE	0	0.44499238643683	1		502	406	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919271	48919272	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATGC	novel	NA	P-0028268-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	114	275	0	ENST00000267163.4:c.437_440dup	p.Met148CysfsTer10	p.M148Cfs*10	ENST00000267163	NM_000321.2	146	aat/aATGCat	4/27	0.44499238643683	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.44499238643683	1		275	330	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24129371	24129398	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGAGCAAGACCTTCGGGCAGAAGCCC	GCTGAGCAAGACCTTCGGGCAGAAGCCC	CAA	novel	NA	P-0028268-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	147	413	4	ENST00000263121.7:c.15_42delinsCAA	p.Leu6LysfsTer2	p.L6Kfs*2	ENST00000263121	NM_003073.3	5	gcGCTGAGCAAGACCTTCGGGCAGAAGCCC/gcCAA	1/9	0.207709840235665	3	FACETS	1	0.949	1			1	INDETERMINATE	2	TRUE	NA	0.44499238643683	3		417	390	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431814	49431827	+	frameshift_variant	Frame_Shift_Del	DEL	GTTCAGAGGCATCA	GTTCAGAGGCATCA	-	novel	NA	P-0028268-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	104	570	0	ENST00000301067.7:c.9312_9325del	p.Asp3105ProfsTer8	p.D3105Pfs*8	ENST00000301067	NM_003482.3	3104	gcTGATGCCTCTGAACcc/gccc	34/54	0.235271611014897	1	FACETS	0.773	0.696	0.854	0.773	0.696	0.854	INDETERMINATE	1	TRUE	0	0.44499238643683	1		570	470	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754286	57754286	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028268-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	95	468	0	ENST00000274289.3:c.565A>G	p.Ile189Val	p.I189V	ENST00000274289	NM_006622.3	189	Att/Gtt	4/14	0.196421159238979	3	FACETS	0.985	0.88	1	0.492	0.44	0.548	INDETERMINATE	1	TRUE	1	0.44499238643683	3		468	530	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801012	135801013	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	rs397514795	NA	P-0028268-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	117	511	1	ENST00000298552.3:c.324_325del	p.Gln109SerfsTer16	p.Q109Sfs*16	ENST00000298552	NM_001162426.1	108	tcTCaa/tcaa	5/23	0.44499238643683	1	FACETS	0.936	0.85	1	0.936	0.85	1	CLONAL	1	TRUE	0	0.44499238643683	1		512	437	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	72	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.645	0.568	0.727	0.645	0.568	0.727	SUBCLONAL	1	TRUE	1	0.690848333713365	2		215	323	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0028407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	156	586	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.817	0.752	0.883	0.817	0.752	0.883	CLONAL	1	TRUE	1	0.690848333713365	2		586	553	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0028407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	284	302	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	0.451367323719852	4	FACETS	1	0.987	1	0.805	0.771	0.837	CLONAL	3	TRUE	0	0.690848333713365	4		302	432	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508614	38508614	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	185	573	0	ENST00000254066.5:c.662A>G	p.Asp221Gly	p.D221G	ENST00000254066	NM_000964.3	221	gAc/gGc	6/9	1	2	FACETS	0.823	0.763	0.884	0.823	0.763	0.884	CLONAL	1	TRUE	1	0.690848333713365	2		573	651	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510630	38510630	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	182	623	0	ENST00000254066.5:c.884C>G	p.Thr295Ser	p.T295S	ENST00000254066	NM_000964.3	295	aCc/aGc	7/9	1	2	FACETS	0.715	0.661	0.77	0.715	0.661	0.77	SUBCLONAL	1	TRUE	1	0.690848333713365	2		623	737	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295214	+	upstream_gene_variant	5'Flank	DEL	GGGAGGGGCT	GGGAGGGGCT	-	novel	NA	P-0028407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	58	365	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.528	0.456	0.605	0.528	0.456	0.605	SUBCLONAL	1	TRUE	1	0.690848333713365	2		365	318	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0028530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	337	282	0				ENST00000310581	NM_198253.2	-/1132			0.670244968659425	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	1	0.670244968659425	4		282	518	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0028530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	551	351	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.670244968659425	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	1	0.670244968659425	4		351	880	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295230	1295230	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs796516131	NA	P-0028530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	339	262	1				ENST00000310581	NM_198253.2	-/1132			0.670244968659425	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	1	0.670244968659425	4		263	509	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0028530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	321	173	1				ENST00000310581	NM_198253.2	-/1132			0.670244968659425	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	1	0.670244968659425	4		174	493	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956220	55956220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190050670	NA	P-0028530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	310	545	1	ENST00000263923.4:c.3095G>A	p.Arg1032Gln	p.R1032Q	ENST00000263923	NM_002253.2	1032	cGa/cAa	23/30	0.670244968659425	3	FACETS	0.883	0.839	0.928	0.883	0.839	0.928	CLONAL	2	TRUE	1	0.670244968659425	3		546	699	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137271	64137271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	147	620	0	ENST00000334205.4:c.1703C>T	p.Thr568Met	p.T568M	ENST00000334205	NM_003942.2	568	aCg/aTg	14/17	0.445589266755974	4	FACETS	0.874	0.798	0.954	0.437	0.399	0.477	CLONAL	1	TRUE	2	0.670244968659425	4		620	838	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223550	55223550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	213	664	1	ENST00000275493.2:c.917C>T	p.Ser306Leu	p.S306L	ENST00000275493	NM_005228.3	306	tCg/tTg	8/28	1	2	FACETS	0.964	0.901	1	0.964	0.901	1	CLONAL	1	TRUE	1	0.670244968659425	2		665	659	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459558	50459558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	149	438	2	ENST00000331340.3:c.847C>T	p.Leu283Phe	p.L283F	ENST00000331340	NM_006060.4	283	Ctt/Ttt	7/8	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.670244968659425	2		440	443	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005419	29005419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55687105	NA	P-0028530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	192	453	1	ENST00000282397.4:c.842G>A	p.Arg281Gln	p.R281Q	ENST00000282397	NM_002019.4	281	cGa/cAa	7/30	0.293503414279254	5	FACETS	1	0.977	1	0.739	0.689	0.79	INDETERMINATE	2	TRUE	2	0.670244968659425	5		454	518	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755919	133755919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759795929	NA	P-0028530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	398	604	5	ENST00000318560.5:c.1546C>T	p.Arg516Cys	p.R516C	ENST00000318560	NM_005157.4	516	Cgt/Tgt	10/11	0.623870597039094	2	FACETS	0.907	0.872	0.94	0.907	0.872	0.94	CLONAL	2	TRUE	0	0.670244968659425	2		609	655	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404750	70404750	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	486	708	2	ENST00000373644.4:c.2264C>T	p.Thr755Ile	p.T755I	ENST00000373644	NM_030625.2	755	aCc/aTc	4/12	0.638056543798745	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.670244968659425	2		710	687	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950519	38950519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	169	516	0	ENST00000357387.3:c.3431G>A	p.Ser1144Asn	p.S1144N	ENST00000357387	NM_152756.3	1144	aGt/aAt	31/38	0.670244968659425	4	FACETS	1	0.935	1	0.339	0.312	0.368	CLONAL	1	TRUE	1	0.670244968659425	4		516	828	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433632	49433632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	429	936	2	ENST00000301067.7:c.7921C>T	p.Pro2641Ser	p.P2641S	ENST00000301067	NM_003482.3	2641	Cct/Tct	31/54	0.627049165174139	3	FACETS	0.952	0.912	0.991	0.952	0.912	0.991	CLONAL	2	TRUE	1	0.670244968659425	3		938	898	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480624	50480624	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	294	503	1	ENST00000394963.4:c.494G>A	p.Arg165Gln	p.R165Q	ENST00000394963	NM_003076.4	165	cGg/cAg	4/13	0.627049165174139	3	FACETS	0.942	0.894	0.989	0.942	0.894	0.989	CLONAL	2	TRUE	1	0.670244968659425	3		504	622	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571531	95571531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	523	582	0	ENST00000393063.1:c.3146G>A	p.Arg1049Lys	p.R1049K	ENST00000393063	NM_030621.3	1049	aGa/aAa	21/28	0.670244968659425	3	FACETS	0.931	0.904	0.957	0.931	0.904	0.957	CLONAL	3	TRUE	0	0.670244968659425	3		582	746	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554290	29554290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	360	596	0	ENST00000356175.3:c.2306C>T	p.Pro769Leu	p.P769L	ENST00000356175	NM_000267.3	769	cCc/cTc	19/57	0.61603493791143	3	FACETS	0.884	0.843	0.926	0.884	0.843	0.926	CLONAL	2	TRUE	1	0.670244968659425	3		596	811	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805639	46805639	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	351	794	1	ENST00000290295.7:c.317T>A	p.Leu106Gln	p.L106Q	ENST00000290295	NM_006361.5	106	cTg/cAg	1/2	0.61603493791143	3	FACETS	0.9	0.858	0.942	0.9	0.858	0.942	CLONAL	2	TRUE	1	0.670244968659425	3		795	777	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223455	36223455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768738947	NA	P-0028530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	173	828	0	ENST00000222270.7:c.6005C>T	p.Pro2002Leu	p.P2002L	ENST00000222270	NM_014727.1	2002	cCc/cTc	28/37	0.61603493791143	3	FACETS	0.91	0.84	0.984	0.455	0.42	0.492	CLONAL	1	TRUE	1	0.670244968659425	3		828	757	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752787	42752787	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	55	785	0	ENST00000222329.4:c.1477C>G	p.Arg493Gly	p.R493G	ENST00000222329	NM_006494.2	493	Cgc/Ggc	4/4	0.61603493791143	3	FACETS	0.272	0.232	0.316	0.136	0.116	0.158	SUBCLONAL	1	TRUE	1	0.670244968659425	3		785	806	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190717469	190717469	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1437241846	NA	P-0028530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	168	481	0	ENST00000441310.2:c.788A>G	p.Asn263Ser	p.N263S	ENST00000441310	NM_000534.4	263	aAc/aGc	7/13	0.440723530235097	3	FACETS	1	0.99	1	0.744	0.69	0.798	CLONAL	1	TRUE	1	0.670244968659425	3		481	450	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52692292	52692292	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	349	616	1	ENST00000394830.3:c.568C>T	p.Leu190Phe	p.L190F	ENST00000394830	NM_018313.4	190	Ctt/Ttt	6/30	0.61603493791143	3	FACETS	0.954	0.91	0.998	0.954	0.91	0.998	CLONAL	2	TRUE	1	0.670244968659425	3		617	729	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980432	55980432	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	182	368	0	ENST00000263923.4:c.659G>A	p.Gly220Glu	p.G220E	ENST00000263923	NM_002253.2	220	gGg/gAg	6/30	0.670244968659425	3	FACETS	0.859	0.802	0.916	0.859	0.802	0.916	CLONAL	2	TRUE	1	0.670244968659425	3		368	422	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93973605	93973605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	235	512	0	ENST00000369303.4:c.1771G>A	p.Glu591Lys	p.E591K	ENST00000369303	NM_004440.3	591	Gaa/Aaa	9/17	0.445589266755974	4	FACETS	0.894	0.839	0.95	0.894	0.839	0.95	CLONAL	2	TRUE	2	0.670244968659425	4		512	655	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434720	128434720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	456	693	0	ENST00000265960.3:c.134C>T	p.Ser45Leu	p.S45L	ENST00000265960	NM_001006617.1	45	tCa/tTa	2/12	0.623870597039094	2	FACETS	0.965	0.933	0.997	0.965	0.933	0.997	CLONAL	2	TRUE	0	0.670244968659425	2		693	705	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0028581-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	251	590	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.236910178004873	2	FACETS	1	0.991	1	0.676	0.632	0.722	CLONAL	1	TRUE	0	0.31	2		590	1197	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0028581-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	60	384	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	0.796	0.687	0.915	0.796	0.687	0.915	CLONAL	1	TRUE	1	0.31	2		384	486	SUCCESS
APC	324	MSKCC	GRCh37	5	112175487	112175487	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028581-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	42	376	0	ENST00000257430.4:c.4196del	p.Arg1399LeufsTer16	p.R1399Lfs*16	ENST00000257430	NM_000038.5	1399	cGt/ct	16/16	1	2	FACETS	0.58	0.484	0.687	0.58	0.484	0.687	SUBCLONAL	1	TRUE	1	0.31	2		376	467	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711330	114711330	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0028581-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	37	375	0	ENST00000543371.1:c.345C>G	p.Tyr115Ter	p.Y115*	ENST00000543371	NM_001198531.1	115	taC/taG	3/14	1	2	FACETS	0.338	0.278	0.406	0.338	0.278	0.406	SUBCLONAL	1	TRUE	1	0.31	2		375	706	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17941344	17941344	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028581-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1184	124	740	1	ENST00000458235.1:c.3064A>G	p.Thr1022Ala	p.T1022A	ENST00000458235	NM_000215.3	1022	Acc/Gcc	22/24	0.266457471366384	3	FACETS	0.706	0.637	0.78	0.353	0.318	0.39	SUBCLONAL	1	TRUE	1	0.31	3		741	1308	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42381382	42381382	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028581-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	89	611	0	ENST00000221972.3:c.8G>A	p.Gly3Glu	p.G3E	ENST00000221972	NM_021601.3	3	gGg/gAg	1/5	0.266457471366384	3	FACETS	0.632	0.558	0.71	0.316	0.279	0.355	SUBCLONAL	1	TRUE	1	0.31	3		611	1050	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463509	25463509	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028581-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	109	601	1	ENST00000264709.3:c.2173G>A	p.Glu725Lys	p.E725K	ENST00000264709	NM_175629.2	725	Gag/Aag	18/23	1	2	FACETS	0.835	0.749	0.926	0.835	0.749	0.926	CLONAL	1	TRUE	1	0.31	2		602	842	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587222	212587222	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028581-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	33	558	0	ENST00000342788.4:c.779C>G	p.Thr260Ser	p.T260S	ENST00000342788	NM_005235.2	260	aCt/aGt	7/28	0.174066563198796	2	FACETS	0.354	0.288	0.43	0.177	0.144	0.215	INDETERMINATE	1	TRUE	0	0.31	2		558	601	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0028639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	168	282	0				ENST00000310581	NM_198253.2	-/1132			0.465804314099899	1	FACETS	0.446	0.414	0.479	0.446	0.414	0.479	INDETERMINATE	1	TRUE	0	0.922481712864637	1		282	440	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0028639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	1492	446	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.922481712864637	4	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	1	0.922481712864637	4		446	2020	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317572	1317572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	505	317	0	ENST00000400841.2:c.493G>A	p.Glu165Lys	p.E165K	ENST00000400841		165	Gaa/Aaa	5/6	0.846108271389565	2	FACETS	0.867	0.831	0.903			1	CLONAL	1	TRUE	NA	0.922481712864637	2		317	1263	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662482	227662482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	342	461	0	ENST00000305123.5:c.973C>T	p.Arg325Cys	p.R325C	ENST00000305123	NM_005544.2	325	Cgt/Tgt	1/2	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.922481712864637	2		461	720	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829734	72829734	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	808	694	0	ENST00000268489.5:c.6847A>G	p.Thr2283Ala	p.T2283A	ENST00000268489	NM_006885.3	2283	Acc/Gcc	9/10	0.152079725807696	5	FACETS	0.942	0.915	0.968			1	INDETERMINATE	3	TRUE	NA	0.922481712864637	5		694	1478	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265162	5265162	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	628	682	0	ENST00000357368.4:c.425A>T	p.Gln142Leu	p.Q142L	ENST00000357368	NM_002850.3	142	cAg/cTg	5/38	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.922481712864637	2		682	1264	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483963	212483963	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	344	504	0	ENST00000342788.4:c.2240C>A	p.Pro747His	p.P747H	ENST00000342788	NM_005235.2	747	cCt/cAt	19/28	1	2	FACETS	0.924	0.879	0.969	0.924	0.879	0.969	CLONAL	1	TRUE	1	0.922481712864637	2		504	807	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205133	38205133	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	522	583	0	ENST00000317025.8:c.557C>G	p.Thr186Arg	p.T186R	ENST00000317025	NM_023034.1	186	aCg/aGg	2/24	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.922481712864637	2		583	1090	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0028804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	113	282	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.310012126460139	2		282	606	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0028804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	94	173	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.310012126460139	2		174	515	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0028804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	142	705	0	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	1	2	FACETS	0.958	0.873	1	0.958	0.873	1	CLONAL	1	TRUE	1	0.310012126460139	2		705	956	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184737	32184737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	115	626	1	ENST00000375023.3:c.1846C>T	p.Pro616Ser	p.P616S	ENST00000375023	NM_004557.3	616	Ccc/Tcc	11/30	1	2	FACETS	0.937	0.844	1	0.937	0.844	1	CLONAL	1	TRUE	1	0.310012126460139	2		627	792	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265323	152265323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866869178	NA	P-0028804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	90	335	0	ENST00000206249.3:c.776G>A	p.Arg259Gln	p.R259Q	ENST00000206249	NM_000125.3	259	cGa/cAa	4/8	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.310012126460139	2		335	540	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973911	55973911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs941528100	NA	P-0028804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	57	506	1	ENST00000263923.4:c.1405G>A	p.Glu469Lys	p.E469K	ENST00000263923	NM_002253.2	469	Gag/Aag	10/30	1	2	FACETS	0.575	0.492	0.664	0.575	0.492	0.664	SUBCLONAL	1	TRUE	1	0.310012126460139	2		507	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0028804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	88	525	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.310012126460139	1	FACETS	0.559	0.494	0.628	0.559	0.494	0.628	SUBCLONAL	1	TRUE	0	0.310012126460139	1		525	858	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509081	106509081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs187257485	NA	P-0028804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	73	641	0	ENST00000359195.3:c.1075C>T	p.Arg359Cys	p.R359C	ENST00000359195	NM_002649.2	359	Cgc/Tgc	2/11	1	2	FACETS	0.613	0.535	0.697	0.613	0.535	0.697	SUBCLONAL	1	TRUE	1	0.310012126460139	2		641	768	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979378	93979378	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	55	268	0	ENST00000369303.4:c.1450G>A	p.Asp484Asn	p.D484N	ENST00000369303	NM_004440.3	484	Gat/Aat	7/17	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.310012126460139	2		268	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578260	7578260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204041	NA	P-0028804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	57	694	0	ENST00000269305.4:c.589G>A	p.Val197Met	p.V197M	ENST00000269305	NM_001126112.2	197	Gtg/Atg	6/11	0.310012126460139	1	FACETS	0.436	0.373	0.504	0.436	0.373	0.504	SUBCLONAL	1	TRUE	0	0.310012126460139	1		694	713	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162722903	162722903	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	128	687	0	ENST00000367921.3:c.101T>G	p.Leu34Arg	p.L34R	ENST00000367921	NM_006182.2	34	cTg/cGg	4/18	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.310012126460139	2		687	762	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448535	49448535	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0028804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	85	540	2	ENST00000301067.7:c.177-1G>A		p.X59_splice	ENST00000301067	NM_003482.3	59			1	2	FACETS	0.919	0.813	1	0.919	0.813	1	CLONAL	1	TRUE	1	0.310012126460139	2		542	597	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480572	50480572	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	104	579	0	ENST00000394963.4:c.442A>T	p.Met148Leu	p.M148L	ENST00000394963	NM_003076.4	148	Atg/Ttg	4/13	1	2	FACETS	0.936	0.838	1	0.936	0.838	1	CLONAL	1	TRUE	1	0.310012126460139	2		579	717	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777989	3777990	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0028804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	206	973	2	ENST00000262367.5:c.7058_7059delinsTA	p.Arg2353Leu	p.R2353L	ENST00000262367	NM_004380.2	2353	cGG/cTA	31/31	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.310012126460139	2		975	1127	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682479	37682479	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	76	554	1	ENST00000447079.4:c.3670G>T	p.Ala1224Ser	p.A1224S	ENST00000447079	NM_015083.1	1224	Gca/Tca	13/14	1	2	FACETS	0.69	0.604	0.781	0.69	0.604	0.781	SUBCLONAL	1	TRUE	1	0.310012126460139	2		555	711	SUCCESS
AXL	558	MSKCC	GRCh37	19	41736914	41736915	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0028804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	67	700	2	ENST00000301178.4:c.629_630delinsTT	p.Ala210Val	p.A210V	ENST00000301178	NM_021913.4	210	gCC/gTT	5/20	0.288059974516738	1	FACETS	0.413	0.358	0.473	0.413	0.358	0.473	SUBCLONAL	1	TRUE	0	0.310012126460139	1		702	884	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752686	42752687	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0028804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	74	680	2	ENST00000222329.4:c.1577_1578delinsTT	p.Thr526Ile	p.T526I	ENST00000222329	NM_006494.2	526	aCC/aTT	4/4	0.288059974516738	1	FACETS	0.557	0.487	0.633	0.557	0.487	0.633	SUBCLONAL	1	TRUE	0	0.310012126460139	1		682	724	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794472	42794473	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0028804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	76	868	3	ENST00000575354.2:c.1552_1553delinsTT	p.Pro518Leu	p.P518L	ENST00000575354	NM_015125.3	518	CCg/TTg	10/20	0.288059974516738	1	FACETS	0.445	0.389	0.505	0.445	0.389	0.505	SUBCLONAL	1	TRUE	0	0.310012126460139	1		871	932	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531170	187531170	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0028804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	67	367	0	ENST00000441802.2:c.9854-1G>A		p.X3285_splice	ENST00000441802	NM_005245.3	3285			1	2	FACETS	0.965	0.841	1	0.965	0.841	1	CLONAL	1	TRUE	1	0.310012126460139	2		367	448	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80040367	80040367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	124	713	0	ENST00000265081.6:c.1696C>T	p.His566Tyr	p.H566Y	ENST00000265081	NM_002439.4	566	Cac/Tac	12/24	0.310012126460139	1	FACETS	0.907	0.822	0.998	0.907	0.822	0.998	CLONAL	1	TRUE	0	0.310012126460139	1		713	745	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673473	30673473	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	128	571	0	ENST00000376406.3:c.3487C>T	p.Pro1163Ser	p.P1163S	ENST00000376406	NM_014641.2	1163	Ccc/Tcc	10/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.310012126460139	2		571	629	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800507	32800507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	94	835	2	ENST00000374899.4:c.1040C>T	p.Ala347Val	p.A347V	ENST00000374899	NM_018833.2	347	gCc/gTc	6/12	1	2	FACETS	0.555	0.492	0.622	0.555	0.492	0.622	SUBCLONAL	1	TRUE	1	0.310012126460139	2		837	1093	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964484	93964484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	64	548	0	ENST00000369303.4:c.2413C>T	p.Pro805Ser	p.P805S	ENST00000369303	NM_004440.3	805	Ccc/Tcc	14/17	1	2	FACETS	0.566	0.49	0.65	0.566	0.49	0.65	SUBCLONAL	1	TRUE	1	0.310012126460139	2		548	729	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725549	117725550	+	frameshift_variant	Frame_Shift_Ins	INS	CC	CC	AAA	novel	NA	P-0028804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	136	596	1	ENST00000368508.3:c.331_332delinsTTT	p.Gly111PhefsTer36	p.G111Ffs*36	ENST00000368508	NM_002944.2	111	GGa/TTTa	5/43	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.310012126460139	2		597	758	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141557686	141557687	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0028804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	203	689	1	ENST00000220592.5:c.1628_1629delinsTT	p.Ala543Val	p.A543V	ENST00000220592	NM_012154.3	543	gCC/gTT	13/19	0.234086920358188	3	FACETS	0.838	0.777	0.9	0.838	0.777	0.9	CLONAL	2	TRUE	1	0.310012126460139	3		690	903	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97876930	97876930	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	46	579	0	ENST00000289081.3:c.1135G>C	p.Val379Leu	p.V379L	ENST00000289081	NM_000136.2	379	Gtt/Ctt	12/15	0.234086920358188	3	FACETS	0.385	0.323	0.454	0.193	0.161	0.227	SUBCLONAL	1	TRUE	1	0.310012126460139	3		579	890	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	71	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.837	0.732	0.95	0.837	0.732	0.95	CLONAL	1	TRUE	1	0.329291633496714	2		215	515	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573894	18573894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759658584	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	39	416	0	ENST00000266497.5:c.2212C>T	p.Arg738Cys	p.R738C	ENST00000266497		738	Cgt/Tgt	15/31	1	2	FACETS	0.5	0.414	0.595	0.5	0.414	0.595	SUBCLONAL	1	TRUE	1	0.329291633496714	2		416	474	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170021	32170021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	171	679	0	ENST00000375023.3:c.3587G>A	p.Gly1196Glu	p.G1196E	ENST00000375023	NM_004557.3	1196	gGa/gAa	21/30	0.314696082408733	3	FACETS	1	0.962	1	0.54	0.496	0.587	CLONAL	1	TRUE	1	0.329291633496714	3		679	1119	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40789994	40789994	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs746391800	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	89	329	0	ENST00000373198.4:c.2737G>A	p.Glu913Lys	p.E913K	ENST00000373198	NM_133170.3	913	Gag/Aag	18/32	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.329291633496714	2		329	512	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78811795	78811795	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	90	341	0	ENST00000306801.3:c.1210C>T	p.Arg404Trp	p.R404W	ENST00000306801	NM_020761.2	404	Cgg/Tgg	10/34	0.284208419214418	1	FACETS	0.858	0.764	0.959	0.858	0.764	0.959	CLONAL	1	TRUE	0	0.329291633496714	1		341	532	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317572	1317572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	127	317	0	ENST00000400841.2:c.493G>A	p.Glu165Lys	p.E165K	ENST00000400841		165	Gaa/Aaa	5/6	1	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.329291633496714	1		317	561	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	125	641	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.903	0.817	0.993	0.903	0.817	0.993	CLONAL	1	TRUE	1	0.329291633496714	2		641	841	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519998	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	136	537	0	ENST00000269305.4:c.581T>A	p.Leu194His	p.L194H	ENST00000269305	NM_001126112.2	194	cTt/cAt	6/11	0.329291633496714	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.329291633496714	1		537	667	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467780	50467780	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760454379	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	93	474	0	ENST00000331340.3:c.1015G>A	p.Glu339Lys	p.E339K	ENST00000331340	NM_006060.4	339	Gag/Aag	8/8	1	2	FACETS	0.964	0.859	1	0.964	0.859	1	CLONAL	1	TRUE	1	0.329291633496714	2		474	586	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756577	756577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	107	417	0	ENST00000314574.4:c.251C>T	p.Ser84Leu	p.S84L	ENST00000314574	NM_005433.3	84	tCa/tTa	2/12	1	2	FACETS	0.94	0.844	1	0.94	0.844	1	CLONAL	1	TRUE	1	0.329291633496714	2		417	691	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048115	180048115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	122	588	0	ENST00000261937.6:c.2158G>A	p.Glu720Lys	p.E720K	ENST00000261937	NM_182925.4	720	Gaa/Aaa	14/30	1	2	FACETS	0.89	0.804	0.98	0.89	0.804	0.98	CLONAL	1	TRUE	1	0.329291633496714	2		588	833	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127776	47127776	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	167	400	0	ENST00000409792.3:c.5306C>T	p.Ser1769Phe	p.S1769F	ENST00000409792	NM_014159.6	1769	tCc/tTc	11/21	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.329291633496714	2		400	681	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211166	55211166	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs754854319	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	102	417	0	ENST00000275493.2:c.409A>G	p.Met137Val	p.M137V	ENST00000275493	NM_005228.3	137	Atg/Gtg	3/28	1	2	FACETS	0.946	0.847	1	0.946	0.847	1	CLONAL	1	TRUE	1	0.329291633496714	2		417	655	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120290	94120290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	60	232	0	ENST00000369303.4:c.761G>A	p.Gly254Glu	p.G254E	ENST00000369303	NM_004440.3	254	gGa/gAa	3/17	0.314696082408733	3	FACETS	1	0.894	1	0.52	0.449	0.596	CLONAL	1	TRUE	1	0.329291633496714	3		232	408	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938278	76938278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	124	240	0	ENST00000373344.5:c.2470G>A	p.Glu824Lys	p.E824K	ENST00000373344	NM_000489.3	824	Gag/Aag	9/35	1	1	FACETS	0.832	0.761	0.906	1	0.988	1	CLONAL	2	TRUE	0	0.329291633496714	1		240	378	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625326	69625326	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	77	533	0	ENST00000334134.2:c.467C>G	p.Ser156Cys	p.S156C	ENST00000334134	NM_005247.2	156	tCt/tGt	3/3	1	2	FACETS	0.61	0.535	0.691	0.61	0.535	0.691	SUBCLONAL	1	TRUE	1	0.329291633496714	2		533	767	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102199674	102199674	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs868604617	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	139	391	0	ENST00000263464.3:c.1079C>T	p.Ser360Leu	p.S360L	ENST00000263464	NM_001165.4	360	tCa/tTa	5/9	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.329291633496714	2		391	580	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376235	118376235	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	43	360	0	ENST00000534358.1:c.9628C>A	p.Leu3210Ile	p.L3210I	ENST00000534358	NM_005933.3	3210	Ctc/Atc	27/36	1	2	FACETS	0.413	0.344	0.488	0.413	0.344	0.488	SUBCLONAL	1	TRUE	1	0.329291633496714	2		360	633	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800924	18800924	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	21	433	0	ENST00000266497.5:c.4300A>C	p.Lys1434Gln	p.K1434Q	ENST00000266497		1434	Aaa/Caa	31/31	1	2	FACETS	0.334	0.256	0.424	0.334	0.256	0.424	SUBCLONAL	1	TRUE	1	0.329291633496714	2		433	382	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563339	21563339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	195	732	0	ENST00000382592.4:c.580C>T	p.Pro194Ser	p.P194S	ENST00000382592	NM_014572.2	194	Cca/Tca	4/8	0.250719450296215	4	FACETS	1	0.975	1	0.376	0.347	0.407	CLONAL	1	TRUE	1	0.329291633496714	4		732	1395	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678467	88678467	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	51	536	0	ENST00000360948.2:c.1069G>A	p.Glu357Lys	p.E357K	ENST00000360948	NM_001012338.2	357	Gag/Aag	9/19	0.284208419214418	1	FACETS	0.418	0.355	0.488	0.418	0.355	0.488	SUBCLONAL	1	TRUE	0	0.329291633496714	1		536	619	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858117	9858117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1410758105	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	128	523	0	ENST00000330684.3:c.3284C>T	p.Pro1095Leu	p.P1095L	ENST00000330684	NM_001134407.1	1095	cCc/cTc	13/13	0.329291633496714	1	FACETS	0.943	0.856	1	0.943	0.856	1	CLONAL	1	TRUE	0	0.329291633496714	1		523	689	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883161	37883161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	64	613	0	ENST00000269571.5:c.3064G>A	p.Glu1022Lys	p.E1022K	ENST00000269571		1022	Gag/Aag	25/27	0.284208419214418	1	FACETS	0.386	0.333	0.443	0.386	0.333	0.443	SUBCLONAL	1	TRUE	0	0.329291633496714	1		613	842	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805726	46805726	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	70	568	0	ENST00000290295.7:c.230C>T	p.Pro77Leu	p.P77L	ENST00000290295	NM_006361.5	77	cCc/cTc	1/2	0.284208419214418	1	FACETS	0.477	0.415	0.544	0.477	0.415	0.544	SUBCLONAL	1	TRUE	0	0.329291633496714	1		568	744	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285186	15285186	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs975580649	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	181	664	1	ENST00000263388.2:c.4429G>A	p.Asp1477Asn	p.D1477N	ENST00000263388	NM_000435.2	1477	Gac/Aac	25/33	1	2	FACETS	0.995	0.916	1	0.995	0.916	1	CLONAL	1	TRUE	1	0.329291633496714	2		665	1105	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89444995	89444995	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	31	393	0	ENST00000336596.2:c.1315C>G	p.Pro439Ala	p.P439A	ENST00000336596	NM_005233.5	439	Cct/Gct	6/17	0.284208419214418	1	FACETS	0.313	0.252	0.381	0.313	0.252	0.381	SUBCLONAL	1	TRUE	0	0.329291633496714	1		393	503	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664798	138664798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	35	185	1	ENST00000330315.3:c.767G>A	p.Gly256Glu	p.G256E	ENST00000330315	NM_023067.3	256	gGg/gAg	1/1	0.284208419214418	1	FACETS	0.592	0.487	0.709	0.592	0.487	0.709	SUBCLONAL	1	TRUE	0	0.329291633496714	1		186	300	SUCCESS
ATR	545	MSKCC	GRCh37	3	142234298	142234298	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	99	414	0	ENST00000350721.4:c.4442G>A	p.Ser1481Asn	p.S1481N	ENST00000350721	NM_001184.3	1481	aGt/aAt	25/47	0.284208419214418	1	FACETS	0.859	0.768	0.954	0.859	0.768	0.954	CLONAL	1	TRUE	0	0.329291633496714	1		414	585	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976849	55976849	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	96	526	0	ENST00000263923.4:c.1063C>A	p.Leu355Ile	p.L355I	ENST00000263923	NM_002253.2	355	Ctt/Att	8/30	0.329291633496714	1	FACETS	0.711	0.634	0.793	0.711	0.634	0.793	SUBCLONAL	1	TRUE	0	0.329291633496714	1		526	685	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557848	187557848	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	104	396	0	ENST00000441802.2:c.3863C>T	p.Ser1288Phe	p.S1288F	ENST00000441802	NM_005245.3	1288	tCc/tTc	5/27	0.329291633496714	1	FACETS	0.999	0.898	1	0.999	0.898	1	CLONAL	1	TRUE	0	0.329291633496714	1		396	528	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068102	94068102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	80	292	0	ENST00000369303.4:c.860C>T	p.Ser287Phe	p.S287F	ENST00000369303	NM_004440.3	287	tCc/tTc	4/17	0.314696082408733	3	FACETS	1	0.96	1	0.602	0.532	0.677	CLONAL	1	TRUE	1	0.329291633496714	3		292	470	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555155	106555155	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	130	552	0	ENST00000369096.4:c.2272G>A	p.Glu758Lys	p.E758K	ENST00000369096	NM_001198.3	758	Gaa/Aaa	7/7	0.329291633496714	1	FACETS	0.986	0.896	1	0.986	0.896	1	CLONAL	1	TRUE	0	0.329291633496714	1		552	669	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109315667	109315667	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	75	360	0	ENST00000436639.2:c.1118C>T	p.Ser373Leu	p.S373L	ENST00000436639	NM_014454.2	373	tCa/tTa	6/10	0.329291633496714	1	FACETS	0.842	0.74	0.95	0.842	0.74	0.95	CLONAL	1	TRUE	0	0.329291633496714	1		360	452	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968135	68968135	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	241	664	0	ENST00000288368.4:c.1164G>A	p.Met388Ile	p.M388I	ENST00000288368	NM_024870.2	388	atG/atA	10/40	0.301583421673451	2	FACETS	0.913	0.855	0.972	0.913	0.855	0.972	CLONAL	2	TRUE	0	0.329291633496714	2		664	802	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020344	69020344	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	138	331	0	ENST00000288368.4:c.2716T>A	p.Phe906Ile	p.F906I	ENST00000288368	NM_024870.2	906	Ttt/Att	24/40	0.301583421673451	2	FACETS	0.895	0.821	0.973	0.895	0.821	0.973	CLONAL	2	TRUE	0	0.329291633496714	2		331	468	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412909	63412910	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0028910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	133	315	0	ENST00000330258.3:c.257_258delinsTT	p.Ser86Phe	p.S86F	ENST00000330258	NM_152424.3	86	tCC/tTT	2/2	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.329291633496714	1		315	490	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	31	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.961	0.776	1	0.961	0.776	1	CLONAL	1	TRUE	1	0.14	2		215	461	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733239	74733239	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	50	416	0	ENST00000359995.5:c.4A>T	p.Ser2Cys	p.S2C	ENST00000359995	NM_001195427.1	2	Agc/Tgc	1/3	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.14	2		416	509	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591855	48591855	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	41	497	0	ENST00000342988.3:c.1018A>G	p.Lys340Glu	p.K340E	ENST00000342988	NM_005359.5	340	Aag/Gag	9/12	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.14	2		497	540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578476	7578476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767328513	NA	P-0028977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	78	828	0	ENST00000269305.4:c.454C>T	p.Pro152Ser	p.P152S	ENST00000269305	NM_001126112.2	152	Ccg/Tcg	5/11	1	2	FACETS	0.928	0.812	1	0.928	0.812	1	CLONAL	1	TRUE	1	0.14	2		828	1201	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720876	89720876	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0028977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	38	380	0	ENST00000371953.3:c.1026+1G>T		p.X342_splice	ENST00000371953	NM_000314.4	342			1	2	FACETS	0.983	0.812	1	0.983	0.812	1	CLONAL	1	TRUE	1	0.14	2		380	552	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717664	89717665	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	48	566	0	ENST00000371953.3:c.689_690insT	p.Pro231ThrfsTer12	p.P231Tfs*12	ENST00000371953	NM_000314.4	230	gga/ggTa	7/9	1	2	FACETS	0.969	0.817	1	0.969	0.817	1	CLONAL	1	TRUE	1	0.14	2		566	708	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971165	21971178	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGCAGCAGCTCC	GCAGCAGCAGCTCC	-	novel	NA	P-0028977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	58	398	0	ENST00000304494.5:c.180_193del	p.Glu61ProfsTer54	p.E61Pfs*54	ENST00000304494	NM_000077.4	60	gcGGAGCTGCTGCTGCtc/gctc	2/3	0.234175307963915	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.14	1		398	564	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0028988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	323	282	0				ENST00000310581	NM_198253.2	-/1132			0.559609233914179	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.559609233914179	3		282	730	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745609	162745609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	360	474	0	ENST00000367921.3:c.2024C>T	p.Ser675Phe	p.S675F	ENST00000367921	NM_006182.2	675	tCc/tTc	15/18	0.558733023354219	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.559609233914179	4		474	930	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0028988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	374	415	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	0.559609233914179	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.559609233914179	2		415	590	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0028988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	371	641	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.559609233914179	3	FACETS	0.931	0.887	0.976	0.931	0.887	0.976	CLONAL	2	TRUE	1	0.559609233914179	3		641	911	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293683	1293683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	432	659	1	ENST00000310581.5:c.1318G>A	p.Glu440Lys	p.E440K	ENST00000310581	NM_198253.2	440	Gag/Aag	2/16	0.559609233914179	3	FACETS	0.979	0.937	1	0.979	0.937	1	CLONAL	2	TRUE	1	0.559609233914179	3		660	1009	SUCCESS
APC	324	MSKCC	GRCh37	5	112177901	112177901	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs752654519	NA	P-0028988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	461	424	1	ENST00000257430.4:c.6610C>T	p.Arg2204Ter	p.R2204*	ENST00000257430	NM_000038.5	2204	Cga/Tga	16/16	0.559609233914179	4	FACETS	1	0.971	1			1	CLONAL	3	TRUE	NA	0.559609233914179	4		425	848	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578401	7578401	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147002414	NA	P-0028988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	423	561	0	ENST00000269305.4:c.529C>T	p.Pro177Ser	p.P177S	ENST00000269305	NM_001126112.2	177	Ccc/Tcc	5/11	0.543287389397129	2	FACETS	0.953	0.915	0.991	0.953	0.915	0.991	CLONAL	2	TRUE	0	0.559609233914179	2		561	793	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218390	133218390	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs781481160	NA	P-0028988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	190	677	0	ENST00000320574.5:c.5221C>T	p.Gln1741Ter	p.Q1741*	ENST00000320574	NM_006231.2	1741	Cag/Tag	39/49	0.401262218247502	3	FACETS	0.845	0.78	0.911			1	CLONAL	1	TRUE	NA	0.559609233914179	3		677	1029	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812605	43812605	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	181	589	0	ENST00000372470.3:c.1308G>T	p.Lys436Asn	p.K436N	ENST00000372470	NM_005373.2	436	aaG/aaT	8/12	0.559609233914179	3	FACETS	0.886	0.818	0.958	0.443	0.409	0.479	CLONAL	1	TRUE	1	0.559609233914179	3		589	934	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94224081	94224081	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	114	492	0	ENST00000323929.3:c.71G>A	p.Gly24Glu	p.G24E	ENST00000323929	NM_005591.3	24	gGa/gAa	3/20	0.559609233914179	3	FACETS	0.825	0.744	0.91	0.413	0.372	0.455	CLONAL	1	TRUE	1	0.559609233914179	3		492	632	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658283	18658283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	270	538	0	ENST00000266497.5:c.3088G>A	p.Gly1030Arg	p.G1030R	ENST00000266497		1030	Gga/Aga	22/31	0.559609233914179	3	FACETS	0.859	0.81	0.908	0.859	0.81	0.908	CLONAL	2	TRUE	1	0.559609233914179	3		538	719	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224698	36224698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	526	776	0	ENST00000222270.7:c.7084C>T	p.Pro2362Ser	p.P2362S	ENST00000222270	NM_014727.1	2362	Ccg/Tcg	30/37	0.512139492044005	4	FACETS	0.968	0.928	1	0.968	0.928	1	CLONAL	2	TRUE	2	0.559609233914179	4		776	1514	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944365	40944365	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	240	453	0	ENST00000373198.4:c.2137G>A	p.Gly713Arg	p.G713R	ENST00000373198	NM_133170.3	713	Gga/Aga	12/32	0.559609233914179	3	FACETS	0.929	0.874	0.984	0.929	0.874	0.984	CLONAL	2	TRUE	1	0.559609233914179	3		453	591	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980726	40980726	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	127	399	0	ENST00000373198.4:c.1760C>T	p.Ser587Leu	p.S587L	ENST00000373198	NM_133170.3	587	tCa/tTa	10/32	0.559609233914179	3	FACETS	1	0.953	1	0.537	0.488	0.587	CLONAL	1	TRUE	1	0.559609233914179	3		399	541	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775595	39775595	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	131	440	0	ENST00000288319.7:c.425G>A	p.Trp142Ter	p.W142*	ENST00000288319	NM_182918.3	142	tGg/tAg	4/10	0.559609233914179	3	FACETS	0.909	0.827	0.995	0.455	0.413	0.498	CLONAL	1	TRUE	1	0.559609233914179	3		440	659	SUCCESS
ATR	545	MSKCC	GRCh37	3	142180887	142180887	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs868378229	NA	P-0028988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	271	438	0	ENST00000350721.4:c.7087C>T	p.Arg2363Ter	p.R2363*	ENST00000350721	NM_001184.3	2363	Cga/Tga	42/47	0.559609233914179	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.559609233914179	3		438	586	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249505	153249505	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	385	584	0	ENST00000281708.4:c.1273T>C	p.Trp425Arg	p.W425R	ENST00000281708	NM_033632.3	425	Tgg/Cgg	9/12	0.559609233914179	2	FACETS	0.958	0.918	0.998	0.958	0.918	0.998	CLONAL	2	TRUE	0	0.559609233914179	2		584	718	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681443	30681443	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	309	459	0	ENST00000376406.3:c.569C>T	p.Ser190Phe	p.S190F	ENST00000376406	NM_014641.2	190	tCt/tTt	4/15	0.559609233914179	4	FACETS	0.86	0.812	0.909	0.86	0.812	0.909	CLONAL	2	TRUE	2	0.559609233914179	4		459	1001	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967835	93967835	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138518092	NA	P-0028988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	281	472	0	ENST00000369303.4:c.2092G>A	p.Glu698Lys	p.E698K	ENST00000369303	NM_004440.3	698	Gaa/Aaa	11/17	0.559609233914179	2	FACETS	0.932	0.886	0.977	0.932	0.886	0.977	CLONAL	2	TRUE	0	0.559609233914179	2		472	539	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339799	116339799	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	272	429	0	ENST00000397752.3:c.661G>C	p.Glu221Gln	p.E221Q	ENST00000397752	NM_000245.2	221	Gaa/Caa	2/21	0.559609233914179	4	FACETS	0.886	0.833	0.939	0.886	0.833	0.939	CLONAL	2	TRUE	2	0.559609233914179	4		429	856	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902217	151902217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	295	509	0	ENST00000262189.6:c.3935C>T	p.Ser1312Phe	p.S1312F	ENST00000262189	NM_170606.2	1312	tCc/tTc	25/59	0.559609233914179	4	FACETS	0.937	0.885	0.991	0.937	0.885	0.991	CLONAL	2	TRUE	2	0.559609233914179	4		509	877	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	89	215	0				ENST00000310581	NM_198253.2	-/1132			0.682833337730238	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.697752875505064	2		215	106	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0029305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	88	173	1				ENST00000310581	NM_198253.2	-/1132			0.682833337730238	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.697752875505064	2		174	102	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559101	29559101	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202023	NA	P-0029305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	24	100	0	ENST00000356175.3:c.3208C>T	p.Gln1070Ter	p.Q1070*	ENST00000356175	NM_000267.3	1070	Cag/Tag	25/57	0.579642039950661	1	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	0	0.697752875505064	1		100	43	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812235	212812235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767277487	NA	P-0029305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	87	282	2	ENST00000342788.4:c.341G>A	p.Arg114Gln	p.R114Q	ENST00000342788	NM_005235.2	114	cGa/cAa	3/28	0.697752875505064	3	FACETS	0.793	0.717	0.871	0.793	0.717	0.871	SUBCLONAL	2	TRUE	1	0.697752875505064	3		284	212	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337290	89337290	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	71	417	0	ENST00000301030.4:c.7741C>T	p.Arg2581Cys	p.R2581C	ENST00000301030	NM_001256183.1	2581	Cgt/Tgt	12/13	0.678622670216946	3	FACETS	1	0.975	1	0.704	0.626	0.784	CLONAL	1	TRUE	1	0.697752875505064	3		417	195	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451281	70451281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	144	559	1	ENST00000373644.4:c.6121C>T	p.Pro2041Ser	p.P2041S	ENST00000373644	NM_030625.2	2041	Cca/Tca	12/12	0.697752875505064	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	1	0.697752875505064	3		560	273	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460463	149460463	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	144	615	0	ENST00000286301.3:c.174G>A	p.Trp58Ter	p.W58*	ENST00000286301	NM_005211.3	58	tgG/tgA	3/22	0.682833337730238	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.697752875505064	2		615	203	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1042209	1042209	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	320	455	0	ENST00000358495.3:c.16G>A	p.Glu6Lys	p.E6K	ENST00000358495	NM_134424.2	6	Gaa/Aaa	2/12	0.697752875505064	7	FACETS	1	0.967	1			1	CLONAL	5	TRUE	NA	0.697752875505064	7		455	499	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95556870	95556870	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	79	301	0	ENST00000393063.1:c.5734C>T	p.Leu1912Phe	p.L1912F	ENST00000393063	NM_030621.3	1912	Ctc/Ttc	28/28	0.697752875505064	4	FACETS	1	0.905	1	1	0.905	1	CLONAL	2	TRUE	2	0.697752875505064	4		301	191	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972502	81972502	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	87	377	0	ENST00000359376.3:c.3295T>C	p.Phe1099Leu	p.F1099L	ENST00000359376	NM_002661.3	1099	Ttc/Ctc	29/33	0.678622670216946	3	FACETS	0.899	0.816	0.983	0.899	0.816	0.983	CLONAL	2	TRUE	1	0.697752875505064	3		377	187	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794545	42794545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs917011887	NA	P-0029305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	233	719	0	ENST00000575354.2:c.1625C>T	p.Ser542Phe	p.S542F	ENST00000575354	NM_015125.3	542	tCc/tTc	10/20	0.687332786801802	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	0	0.697752875505064	3		719	296	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152631	99152631	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	89	352	0	ENST00000074304.5:c.427C>G	p.Leu143Val	p.L143V	ENST00000074304	NM_001134224.1	143	Ctg/Gtg	7/26	0.697752875505064	6	FACETS	1	0.901	1			1	CLONAL	2	TRUE	NA	0.697752875505064	6		352	304	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248501	212248501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	89	376	0	ENST00000342788.4:c.3766C>T	p.Pro1256Ser	p.P1256S	ENST00000342788	NM_005235.2	1256	Cca/Tca	28/28	0.697752875505064	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.697752875505064	3		376	153	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256333	46256334	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0029305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	147	371	0	ENST00000371998.3:c.561_562delinsTT	p.Gln188Ter	p.Q188*	ENST00000371998		187	acCCaa/acTTaa	7/23	0.697752875505064	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	TRUE	1	0.697752875505064	4		371	228	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981567	55981567	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	47	268	0	ENST00000263923.4:c.370C>T	p.Pro124Ser	p.P124S	ENST00000263923	NM_002253.2	124	Cca/Tca	4/30	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.697752875505064	2		268	114	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188851	32188851	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	112	532	0	ENST00000375023.3:c.703G>C	p.Ala235Pro	p.A235P	ENST00000375023	NM_004557.3	235	Gca/Cca	4/30	0.482846751113357	4	FACETS	0.95	0.867	1			1	CLONAL	2	TRUE	NA	0.697752875505064	4		532	287	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816814	32816815	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0029305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	138	571	3	ENST00000354258.4:c.1509_1510delinsTT	p.Leu504Phe	p.L504F	ENST00000354258	NM_000593.5	503	aaCCtt/aaTTtt	6/11	0.482846751113357	4	FACETS	0.87	0.8	0.941			1	CLONAL	2	TRUE	NA	0.697752875505064	4		574	386	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687345	117687345	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	45	319	0	ENST00000368508.3:c.2706G>T	p.Arg902Ser	p.R902S	ENST00000368508	NM_002944.2	902	agG/agT	18/43	0.678393028420981	3	FACETS	1	0.924	1			1	CLONAL	1	TRUE	NA	0.697752875505064	3		319	154	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525576	137525576	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	51	451	0	ENST00000367739.4:c.439C>T	p.His147Tyr	p.H147Y	ENST00000367739	NM_000416.2	147	Cac/Tac	4/7	1	2	FACETS	0.881	0.763	1	0.881	0.763	1	CLONAL	1	TRUE	1	0.697752875505064	2		451	166	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224457	55224457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	147	389	0	ENST00000275493.2:c.1139C>T	p.Ser380Phe	p.S380F	ENST00000275493	NM_005228.3	380	tCc/tTc	10/28	0.697752875505064	6	FACETS	1	0.983	1			1	CLONAL	2	TRUE	NA	0.697752875505064	6		389	409	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874034	151874034	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	263	428	0	ENST00000262189.6:c.8504C>T	p.Ser2835Phe	p.S2835F	ENST00000262189	NM_170606.2	2835	tCc/tTc	38/59	0.65799190316465	6	FACETS	0.971	0.942	0.998	0.971	0.942	0.998	CLONAL	6	TRUE	0	0.697752875505064	6		428	310	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209360	98209360	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	51	498	0	ENST00000331920.6:c.4178C>T	p.Pro1393Leu	p.P1393L	ENST00000331920	NM_000264.3	1393	cCc/cTc	23/24	0.697752875505064	3	FACETS	1	0.884	1	0.513	0.443	0.589	CLONAL	1	TRUE	1	0.697752875505064	3		498	192	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	209	430	0				ENST00000310581	NM_198253.2	-/1132			0.530609809087734	5	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	TRUE	2	0.62025293401221	5		430	407	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	121	705	0	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	0.517272277201329	4	FACETS	0.852	0.77	0.938	0.426	0.385	0.469	CLONAL	1	TRUE	2	0.62025293401221	4		705	742	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419837	41419837	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs267605939	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	83	449	0	ENST00000373198.4:c.484C>T	p.Gln162Ter	p.Q162*	ENST00000373198	NM_133170.3	162	Cag/Tag	3/32	0.443005910487167	4	FACETS	1	0.955	1	0.575	0.511	0.643	CLONAL	1	TRUE	2	0.62025293401221	4		449	377	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432368	432368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1362895739	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	59	134	0	ENST00000399788.2:c.2155C>T	p.Arg719Cys	p.R719C	ENST00000399788	NM_001042603.1	719	Cgc/Tgc	16/28	0.62025293401221	3	FACETS	1	0.968	1	0.685	0.6	0.773	CLONAL	1	TRUE	1	0.62025293401221	3		134	182	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	175	995	0	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	0.62025293401221	3	FACETS	1	0.928	1	0.503	0.464	0.543	CLONAL	1	TRUE	1	0.62025293401221	3		995	735	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	222	354	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.62025293401221	7	FACETS	1	0.951	1			1	CLONAL	2	TRUE	NA	0.62025293401221	7		354	891	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587161	189587161	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173679499	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	121	522	0	ENST00000264731.3:c.1178G>A	p.Arg393Gln	p.R393Q	ENST00000264731	NM_003722.4	393	cGa/cAa	9/14	0.62025293401221	3	FACETS	1	0.969	1	0.573	0.521	0.627	CLONAL	1	TRUE	1	0.62025293401221	3		522	446	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244913	123244913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1224606327	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	106	831	2	ENST00000358487.5:c.2191G>A	p.Glu731Lys	p.E731K	ENST00000358487	NM_000141.4	731	Gaa/Aaa	16/18	0.613862499052016	3	FACETS	0.798	0.718	0.883	0.266	0.239	0.295	SUBCLONAL	1	TRUE	0	0.62025293401221	3		833	561	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	229	531	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.62025293401221	3	FACETS	0.993	0.937	1	0.993	0.937	1	CLONAL	2	TRUE	1	0.62025293401221	3		532	487	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246058	41246058	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555591693	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	124	750	0	ENST00000357654.3:c.1490C>T	p.Pro497Leu	p.P497L	ENST00000357654	NM_007294.3	497	cCc/cTc	10/23	0.443005910487167	4	FACETS	0.964	0.874	1	0.482	0.437	0.53	CLONAL	1	TRUE	2	0.62025293401221	4		750	672	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637690	52637690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239654517	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	104	535	0	ENST00000394830.3:c.2626C>T	p.Arg876Cys	p.R876C	ENST00000394830	NM_018313.4	876	Cgt/Tgt	18/30	0.62025293401221	3	FACETS	0.941	0.847	1	0.47	0.423	0.52	CLONAL	1	TRUE	1	0.62025293401221	3		535	467	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164451	36164451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	38	283	0	ENST00000300305.3:c.1424C>T	p.Ala475Val	p.A475V	ENST00000300305		475	gCc/gTc	8/8	0.62025293401221	3	FACETS	1	0.891	1	0.539	0.453	0.631	CLONAL	1	TRUE	1	0.62025293401221	3		283	149	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041782	14041782	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	94	520	1	ENST00000311895.7:c.2329C>T	p.Gln777Ter	p.Q777*	ENST00000311895	NM_005236.2	777	Cag/Tag	11/11	0.62025293401221	3	FACETS	0.93	0.832	1	0.465	0.416	0.517	CLONAL	1	TRUE	1	0.62025293401221	3		521	427	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129850	69129850	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	36	264	0	ENST00000288368.4:c.4605-1G>A		p.X1535_splice	ENST00000288368	NM_024870.2	1535			0.443005910487167	4	FACETS	0.777	0.643	0.925	0.389	0.321	0.463	CLONAL	1	TRUE	2	0.62025293401221	4		264	242	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412267	139412267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1266989706	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	131	898	1	ENST00000277541.6:c.1378C>T	p.Pro460Ser	p.P460S	ENST00000277541	NM_017617.3	460	Ccg/Tcg	8/34	0.62025293401221	3	FACETS	0.907	0.826	0.992	0.454	0.413	0.496	CLONAL	1	TRUE	1	0.62025293401221	3		899	610	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873660	35873660	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs201559094	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	166	257	0	ENST00000303115.3:c.616C>T	p.Arg206Ter	p.R206*	ENST00000303115	NM_002185.3	206	Cga/Tga	5/8	0.530609809087734	5	FACETS	1	0.98	1	0.769	0.713	0.826	CLONAL	2	TRUE	2	0.62025293401221	5		257	448	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678469	88678469	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	194	506	0	ENST00000360948.2:c.1067G>A	p.Gly356Glu	p.G356E	ENST00000360948	NM_001012338.2	356	gGa/gAa	9/19	0.62025293401221	3	FACETS	0.913	0.854	0.972	0.913	0.854	0.972	CLONAL	2	TRUE	1	0.62025293401221	3		506	449	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459889	149459890	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	107	750	1	ENST00000286301.3:c.317_318delinsAA	p.Arg106Gln	p.R106Q	ENST00000286301	NM_005211.3	106	cGG/cAA	4/22	0.256712411979749	2	FACETS	0.725	0.653	0.8	0.362	0.326	0.4	INDETERMINATE	1	TRUE	0	0.62025293401221	2		751	476	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968135	68968135	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	113	664	0	ENST00000288368.4:c.1164G>A	p.Met388Ile	p.M388I	ENST00000288368	NM_024870.2	388	atG/atA	10/40	0.443005910487167	4	FACETS	0.849	0.765	0.938	0.425	0.382	0.469	CLONAL	1	TRUE	2	0.62025293401221	4		664	695	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877197	89877197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138744489	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	127	624	1	ENST00000389301.3:c.440C>T	p.Ser147Phe	p.S147F	ENST00000389301	NM_000135.2	147	tCc/tTc	5/43	0.62025293401221	3	FACETS	1	0.919	1	0.505	0.46	0.553	CLONAL	1	TRUE	1	0.62025293401221	3		625	531	SUCCESS
APC	324	MSKCC	GRCh37	5	112176824	112176824	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060503338	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	104	483	0	ENST00000257430.4:c.5533C>T	p.His1845Tyr	p.H1845Y	ENST00000257430	NM_000038.5	1845	Cat/Tat	16/16	0.62025293401221	3	FACETS	1	0.91	1	0.505	0.455	0.557	CLONAL	1	TRUE	1	0.62025293401221	3		483	435	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245197	41245197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55914168	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	151	836	1	ENST00000357654.3:c.2351C>T	p.Ser784Leu	p.S784L	ENST00000357654	NM_007294.3	784	tCg/tTg	10/23	0.443005910487167	4	FACETS	1	0.948	1	0.525	0.48	0.571	CLONAL	1	TRUE	2	0.62025293401221	4		837	752	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058631	72058631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	91	435	1	ENST00000357731.5:c.809G>A	p.Gly270Glu	p.G270E	ENST00000357731	NM_173808.2	270	gGa/gAa	6/7	0.62025293401221	3	FACETS	1	0.925	1	0.521	0.466	0.579	CLONAL	1	TRUE	1	0.62025293401221	3		436	369	SUCCESS
ATR	545	MSKCC	GRCh37	3	142204079	142204079	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	112	652	0	ENST00000350721.4:c.6124C>T	p.Leu2042Phe	p.L2042F	ENST00000350721	NM_001184.3	2042	Ctt/Ttt	36/47	0.62025293401221	3	FACETS	1	0.912	1	0.504	0.456	0.555	CLONAL	1	TRUE	1	0.62025293401221	3		652	469	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001422	29001422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752383804	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	62	336	0	ENST00000282397.4:c.1310C>T	p.Ser437Leu	p.S437L	ENST00000282397	NM_002019.4	437	tCg/tTg	10/30	0.517272277201329	4	FACETS	0.844	0.732	0.964	0.422	0.366	0.482	CLONAL	1	TRUE	2	0.62025293401221	4		336	384	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78921067	78921067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	149	768	0	ENST00000306801.3:c.3181C>T	p.His1061Tyr	p.H1061Y	ENST00000306801	NM_020761.2	1061	Cac/Tac	27/34	0.443005910487167	4	FACETS	1	0.968	1	0.557	0.51	0.606	CLONAL	1	TRUE	2	0.62025293401221	4		768	699	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608325	100608325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	124	325	0	ENST00000308731.7:c.1765G>A	p.Glu589Lys	p.E589K	ENST00000308731	NM_000061.2	589	Gaa/Aaa	18/19	0.598726729837581	2	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.62025293401221	2		325	319	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130427	29130427	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587781269	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	115	716	1	ENST00000328354.6:c.283C>T	p.Arg95Ter	p.R95*	ENST00000328354	NM_007194.3	95	Cga/Tga	2/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.62025293401221	2		717	343	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965761	25965761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377352572	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	137	863	0	ENST00000435504.4:c.3445C>T	p.Arg1149Cys	p.R1149C	ENST00000435504		1149	Cgt/Tgt	13/13	0.62025293401221	3	FACETS	0.936	0.855	1	0.468	0.427	0.511	CLONAL	1	TRUE	1	0.62025293401221	3		863	618	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508316	106508316	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	46	334	0	ENST00000359195.3:c.310G>A	p.Gly104Arg	p.G104R	ENST00000359195	NM_002649.2	104	Ggg/Agg	2/11	0.62025293401221	4	FACETS	0.84	0.712	0.98	0.28	0.237	0.327	CLONAL	1	TRUE	1	0.62025293401221	4		334	286	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919595	28919595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs553261958	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	145	652	2	ENST00000282397.4:c.2342G>A	p.Arg781Gln	p.R781Q	ENST00000282397	NM_002019.4	781	cGa/cAa	16/30	0.517272277201329	4	FACETS	1	0.978	1	0.605	0.554	0.658	CLONAL	1	TRUE	2	0.62025293401221	4		654	626	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572484	95572484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	104	453	0	ENST00000393063.1:c.2881C>T	p.Pro961Ser	p.P961S	ENST00000393063	NM_030621.3	961	Cct/Tct	19/28	0.517272277201329	4	FACETS	0.953	0.856	1	0.477	0.428	0.528	CLONAL	1	TRUE	2	0.62025293401221	4		453	570	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467511	66467511	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	50	386	0	ENST00000273854.3:c.758C>T	p.Ser253Phe	p.S253F	ENST00000273854	NM_004439.5	253	tCc/tTc	3/18	1	2	FACETS	0.881	0.759	1	0.881	0.759	1	CLONAL	1	TRUE	1	0.62025293401221	2		386	183	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612764	228612764	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1482262254	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	108	712	1	ENST00000366696.1:c.263C>T	p.Ser88Leu	p.S88L	ENST00000366696	NM_003493.2	88	tCg/tTg	1/1	0.517272277201329	4	FACETS	1	0.939	1	0.529	0.477	0.585	CLONAL	1	TRUE	2	0.62025293401221	4		713	533	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225525	133225525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762090058	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	105	592	0	ENST00000320574.5:c.4139C>T	p.Ser1380Leu	p.S1380L	ENST00000320574	NM_006231.2	1380	tCg/tTg	32/49	0.443005910487167	4	FACETS	1	0.96	1	0.566	0.509	0.625	CLONAL	1	TRUE	2	0.62025293401221	4		592	485	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195371	102195371	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	84	527	0	ENST00000263464.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000263464	NM_001165.4	44	cCt/cTt	2/9	0.62025293401221	3	FACETS	0.915	0.813	1	0.457	0.406	0.511	CLONAL	1	TRUE	1	0.62025293401221	3		527	388	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405194	70405194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1169743622	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	102	639	0	ENST00000373644.4:c.2708C>T	p.Ala903Val	p.A903V	ENST00000373644	NM_030625.2	903	gCc/gTc	4/12	0.613862499052016	3	FACETS	1	0.917	1	0.34	0.306	0.376	CLONAL	1	TRUE	0	0.62025293401221	3		639	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	86	417	1	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.62025293401221	3	FACETS	0.987	0.88	1	0.494	0.44	0.55	CLONAL	1	TRUE	1	0.62025293401221	3		418	368	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911606	134911606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767340477	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	80	549	0	ENST00000398015.3:c.2071C>T	p.Arg691Trp	p.R691W	ENST00000398015	NM_004441.4	691	Cgg/Tgg	11/16	0.62025293401221	3	FACETS	0.871	0.771	0.977	0.436	0.385	0.489	CLONAL	1	TRUE	1	0.62025293401221	3		549	388	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347177	89347177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199914958	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	61	590	0	ENST00000301030.4:c.5773C>T	p.Pro1925Ser	p.P1925S	ENST00000301030	NM_001256183.1	1925	Ccc/Tcc	9/13	0.62025293401221	3	FACETS	0.839	0.73	0.957	0.42	0.365	0.479	CLONAL	1	TRUE	1	0.62025293401221	3		590	307	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431691	49431691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1477770161	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	198	740	0	ENST00000301067.7:c.9448C>T	p.Leu3150Phe	p.L3150F	ENST00000301067	NM_003482.3	3150	Ctt/Ttt	34/54	0.598726729837581	4	FACETS	0.963	0.899	1			1	CLONAL	2	TRUE	NA	0.62025293401221	4		740	537	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30099969	30099969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375956203	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	156	475	1	ENST00000331968.5:c.1651G>A	p.Gly551Ser	p.G551S	ENST00000331968	NM_002742.2	551	Ggt/Agt	10/18	0.517272277201329	4	FACETS	0.957	0.885	1	0.957	0.885	1	CLONAL	2	TRUE	2	0.62025293401221	4		476	426	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068057	94068057	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	74	361	0	ENST00000369303.4:c.905C>T	p.Ser302Phe	p.S302F	ENST00000369303	NM_004440.3	302	tCt/tTt	4/17	0.62025293401221	2	FACETS	0.911	0.807	1	0.455	0.403	0.51	CLONAL	1	TRUE	0	0.62025293401221	2		361	262	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557417	95557417	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	94	506	0	ENST00000393063.1:c.5557C>T	p.Pro1853Ser	p.P1853S	ENST00000393063	NM_030621.3	1853	Cct/Tct	27/28	0.517272277201329	4	FACETS	0.879	0.784	0.979	0.439	0.392	0.49	CLONAL	1	TRUE	2	0.62025293401221	4		506	559	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028124	69028124	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	123	808	0	ENST00000288368.4:c.3283G>A	p.Glu1095Lys	p.E1095K	ENST00000288368	NM_024870.2	1095	Gaa/Aaa	26/40	0.443005910487167	4	FACETS	0.855	0.773	0.94	0.427	0.386	0.47	CLONAL	1	TRUE	2	0.62025293401221	4		808	752	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876497	35876497	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	187	631	0	ENST00000303115.3:c.1289C>T	p.Pro430Leu	p.P430L	ENST00000303115	NM_002185.3	430	cCa/cTa	8/8	0.530609809087734	5	FACETS	0.986	0.917	1	0.658	0.611	0.705	CLONAL	2	TRUE	2	0.62025293401221	5		631	590	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976766	2976766	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1562490836	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	98	830	1	ENST00000396946.4:c.1246G>A	p.Glu416Lys	p.E416K	ENST00000396946	NM_032415.4	416	Gag/Aag	9/25	0.62025293401221	3	FACETS	0.885	0.793	0.981	0.442	0.396	0.491	CLONAL	1	TRUE	1	0.62025293401221	3		831	468	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285171	15285171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202085803	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	158	898	0	ENST00000263388.2:c.4444G>A	p.Gly1482Ser	p.G1482S	ENST00000263388	NM_000435.2	1482	Ggc/Agc	25/33	0.443005910487167	4	FACETS	1	0.97	1	0.559	0.513	0.606	CLONAL	1	TRUE	2	0.62025293401221	4		898	739	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41818301	41818301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388377310	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	14	29	0	ENST00000373198.4:c.73G>A	p.Ala25Thr	p.A25T	ENST00000373198	NM_133170.3	25	Gct/Act	1/32	0.443005910487167	4	FACETS	0.871	0.658	1	0.871	0.658	1	CLONAL	2	TRUE	2	0.62025293401221	4		29	42	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727078	40727078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs896375033	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	66	541	0	ENST00000373198.4:c.3886G>A	p.Glu1296Lys	p.E1296K	ENST00000373198	NM_133170.3	1296	Gag/Aag	28/32	0.443005910487167	4	FACETS	0.782	0.681	0.891	0.391	0.34	0.446	SUBCLONAL	1	TRUE	2	0.62025293401221	4		541	441	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416658	29416658	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1374838786	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	126	456	0	ENST00000389048.3:c.4295G>A	p.Arg1432Gln	p.R1432Q	ENST00000389048	NM_004304.4	1432	cGg/cAg	29/29	0.62025293401221	3	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	1	0.62025293401221	3		456	266	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295220	1295221	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	110	430	1				ENST00000310581	NM_198253.2	-/1132			0.530609809087734	5	FACETS	0.938	0.851	1	0.625	0.567	0.685	CLONAL	2	TRUE	2	0.62025293401221	5		431	365	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209694	98209694	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	108	679	0	ENST00000331920.6:c.3844C>T	p.Pro1282Ser	p.P1282S	ENST00000331920	NM_000264.3	1282	Ccg/Tcg	23/24	0.62025293401221	3	FACETS	0.914	0.824	1	0.457	0.412	0.505	CLONAL	1	TRUE	1	0.62025293401221	3		679	499	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972955	68972955	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141759315	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	98	564	0	ENST00000288368.4:c.1280G>A	p.Arg427Lys	p.R427K	ENST00000288368	NM_024870.2	427	aGg/aAg	11/40	0.443005910487167	4	FACETS	1	0.92	1	0.516	0.462	0.573	CLONAL	1	TRUE	2	0.62025293401221	4		564	496	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432350	49432350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777025180	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	157	812	0	ENST00000301067.7:c.8789C>T	p.Pro2930Leu	p.P2930L	ENST00000301067	NM_003482.3	2930	cCc/cTc	34/54	0.598726729837581	4	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.62025293401221	4		812	637	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62293892	62293892	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	139	859	1	ENST00000360203.5:c.396-7C>T		p.X132_splice	ENST00000360203	NM_001283009.1	132			0.443005910487167	4	FACETS	0.983	0.896	1	0.491	0.448	0.537	CLONAL	1	TRUE	2	0.62025293401221	4		860	739	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293686	1293686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	306	821	0	ENST00000310581.5:c.1315G>A	p.Glu439Lys	p.E439K	ENST00000310581	NM_198253.2	439	Gag/Aag	2/16	0.530609809087734	5	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	2	0.62025293401221	5		821	613	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38148059	38148059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	159	837	1	ENST00000317025.8:c.3052C>T	p.Pro1018Ser	p.P1018S	ENST00000317025	NM_023034.1	1018	Cct/Tct	17/24	0.62025293401221	3	FACETS	1	0.966	1	0.545	0.502	0.59	CLONAL	1	TRUE	1	0.62025293401221	3		838	616	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560226	29560226	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555615109	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	47	292	0	ENST00000356175.3:c.3703C>T	p.Gln1235Ter	p.Q1235*	ENST00000356175	NM_000267.3	1235	Cag/Tag	27/57	1	2	FACETS	0.947	0.814	1	0.947	0.814	1	CLONAL	1	TRUE	1	0.62025293401221	2		292	160	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804995	43804995	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267598615	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	72	529	0	ENST00000372470.3:c.445G>A	p.Glu149Lys	p.E149K	ENST00000372470	NM_005373.2	149	Gaa/Aaa	4/12	0.62025293401221	3	FACETS	1	0.919	1	0.526	0.464	0.592	CLONAL	1	TRUE	1	0.62025293401221	3		529	289	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450321	50450321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	104	626	1	ENST00000331340.3:c.505G>A	p.Gly169Arg	p.G169R	ENST00000331340	NM_006060.4	169	Ggg/Agg	5/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.62025293401221	2		627	286	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641222	12641222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	222	567	0	ENST00000251849.4:c.1076C>T	p.Ser359Phe	p.S359F	ENST00000251849	NM_002880.3	359	tCt/tTt	10/17	0.62025293401221	3	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	1	0.62025293401221	3		567	468	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316114	11316114	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746557535	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	111	586	0	ENST00000361445.4:c.640C>T	p.Arg214Cys	p.R214C	ENST00000361445	NM_004958.3	214	Cgt/Tgt	5/58	0.62025293401221	3	FACETS	1	0.91	1	0.503	0.455	0.554	CLONAL	1	TRUE	1	0.62025293401221	3		586	466	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317158	11317159	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	194	683	2	ENST00000361445.4:c.335_336delinsAA	p.Arg112Gln	p.R112Q	ENST00000361445	NM_004958.3	112	cGG/cAA	4/58	0.62025293401221	3	FACETS	0.921	0.862	0.98	0.921	0.862	0.98	CLONAL	2	TRUE	1	0.62025293401221	3		685	445	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260090	16260090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559906789	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	110	635	0	ENST00000375759.3:c.7355C>T	p.Ser2452Phe	p.S2452F	ENST00000375759	NM_015001.2	2452	tCc/tTc	11/15	0.62025293401221	3	FACETS	1	0.914	1	0.506	0.457	0.557	CLONAL	1	TRUE	1	0.62025293401221	3		635	459	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260137	16260138	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	83	581	0	ENST00000375759.3:c.7402_7403delinsAT	p.Pro2468Ile	p.P2468I	ENST00000375759	NM_015001.2	2468	CCc/ATc	11/15	0.62025293401221	3	FACETS	0.862	0.765	0.964	0.431	0.382	0.482	CLONAL	1	TRUE	1	0.62025293401221	3		581	407	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28607287	28607287	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778863205	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	85	531	0	ENST00000253063.3:c.1417C>T	p.Arg473Cys	p.R473C	ENST00000253063	NM_031459.4	473	Cgt/Tgt	10/10	0.62025293401221	3	FACETS	0.978	0.871	1	0.489	0.435	0.546	CLONAL	1	TRUE	1	0.62025293401221	3		531	367	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163295953	163295953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	249	793	0	ENST00000271452.3:c.112C>T	p.Pro38Ser	p.P38S	ENST00000271452	NM_145697.2	38	Cca/Tca	2/14	0.517272277201329	4	FACETS	0.903	0.849	0.959	0.903	0.849	0.959	CLONAL	2	TRUE	2	0.62025293401221	4		793	720	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927428	245927428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	117	635	0	ENST00000388985.4:c.1100C>T	p.Pro367Leu	p.P367L	ENST00000388985		367	cCc/cTc	11/12	0.128553819169528	3	FACETS	0.76	0.687	0.838			1	INDETERMINATE	1	TRUE	NA	0.62025293401221	3		635	650	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115958	8115958	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	56	399	0	ENST00000346208.3:c.1304C>T	p.Pro435Leu	p.P435L	ENST00000346208		435	cCc/cTc	6/6	0.609317860881474	2	FACETS	0.981	0.855	1	0.491	0.427	0.557	CLONAL	1	TRUE	0	0.62025293401221	2		399	184	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112769042	112769042	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1362516887	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	125	631	1	ENST00000369452.4:c.1321C>T	p.Pro441Ser	p.P441S	ENST00000369452	NM_007373.3	441	Ccc/Tcc	7/9	0.613862499052016	3	FACETS	0.972	0.884	1	0.324	0.294	0.355	CLONAL	1	TRUE	0	0.62025293401221	3		632	543	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925402	114925402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766781345	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	129	746	0	ENST00000543371.1:c.1480C>T	p.Pro494Ser	p.P494S	ENST00000543371	NM_001198531.1	494	Ccc/Tcc	14/14	0.613862499052016	3	FACETS	1	0.955	1	0.358	0.326	0.391	CLONAL	1	TRUE	0	0.62025293401221	3		746	507	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123353275	123353276	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	304	686	1	ENST00000358487.5:c.56_57delinsTT	p.Ser19Phe	p.S19F	ENST00000358487	NM_000141.4	19	tCC/tTT	2/18	0.613862499052016	3	FACETS	0.945	0.907	0.982	0.945	0.907	0.982	CLONAL	3	TRUE	0	0.62025293401221	3		687	453	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575553	64575553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	81	622	0	ENST00000312049.6:c.464C>T	p.Ser155Phe	p.S155F	ENST00000312049	NM_130799.2	155	tCc/tTc	3/10	0.62025293401221	3	FACETS	0.886	0.786	0.993	0.443	0.393	0.497	CLONAL	1	TRUE	1	0.62025293401221	3		622	386	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195580	102195580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	107	545	0	ENST00000263464.3:c.340C>T	p.Pro114Ser	p.P114S	ENST00000263464	NM_001165.4	114	Cct/Tct	2/9	0.62025293401221	3	FACETS	0.972	0.877	1	0.486	0.438	0.536	CLONAL	1	TRUE	1	0.62025293401221	3		545	465	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195928	102195928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770838087	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	70	394	0	ENST00000263464.3:c.688C>T	p.Pro230Ser	p.P230S	ENST00000263464	NM_001165.4	230	Ccc/Tcc	2/9	0.62025293401221	3	FACETS	0.986	0.867	1	0.493	0.433	0.556	CLONAL	1	TRUE	1	0.62025293401221	3		394	300	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123552	108123552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1565387411	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	204	429	0	ENST00000278616.4:c.1811C>T	p.Pro604Leu	p.P604L	ENST00000278616	NM_000051.3	604	cCt/cTt	12/63	0.62025293401221	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.62025293401221	3		429	405	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363817	118363817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	211	506	0	ENST00000534358.1:c.5050C>T	p.Pro1684Ser	p.P1684S	ENST00000534358	NM_005933.3	1684	Cct/Tct	16/36	0.62025293401221	3	FACETS	0.919	0.863	0.976	0.919	0.863	0.976	CLONAL	2	TRUE	1	0.62025293401221	3		506	485	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376905	118376905	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	116	425	0	ENST00000534358.1:c.10298C>T	p.Pro3433Leu	p.P3433L	ENST00000534358	NM_005933.3	3433	cCc/cTc	27/36	0.62025293401221	3	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	TRUE	1	0.62025293401221	3		425	243	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245315	46245315	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	196	568	0	ENST00000334344.6:c.3409T>G	p.Ser1137Ala	p.S1137A	ENST00000334344	NM_152641.2	1137	Tca/Gca	15/21	0.598726729837581	4	FACETS	1	0.952	1			1	CLONAL	2	TRUE	NA	0.62025293401221	4		568	501	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246051	46246051	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	77	494	0	ENST00000334344.6:c.4145C>T	p.Ser1382Phe	p.S1382F	ENST00000334344	NM_152641.2	1382	tCc/tTc	15/21	0.598726729837581	4	FACETS	0.944	0.833	1			1	CLONAL	1	TRUE	NA	0.62025293401221	4		494	426	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425497	49425497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	285	887	0	ENST00000301067.7:c.12991C>T	p.Pro4331Ser	p.P4331S	ENST00000301067	NM_003482.3	4331	Ccc/Tcc	39/54	0.598726729837581	4	FACETS	1	0.979	1			1	CLONAL	2	TRUE	NA	0.62025293401221	4		887	698	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440417	49440417	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	251	761	0	ENST00000301067.7:c.4393C>T	p.Pro1465Ser	p.P1465S	ENST00000301067	NM_003482.3	1465	Ccc/Tcc	15/54	0.598726729837581	4	FACETS	0.98	0.922	1			1	CLONAL	2	TRUE	NA	0.62025293401221	4		761	669	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480058	50480058	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	224	684	1	ENST00000394963.4:c.292C>T	p.Gln98Ter	p.Q98*	ENST00000394963	NM_003076.4	98	Cag/Tag	2/13	0.598726729837581	4	FACETS	0.956	0.896	1			1	CLONAL	2	TRUE	NA	0.62025293401221	4		685	612	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888307	112888308	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	141	492	1	ENST00000351677.2:c.323_324delinsTT	p.Thr108Ile	p.T108I	ENST00000351677	NM_002834.3	108	aCC/aTT	3/16	0.62025293401221	3	FACETS	0.853	0.788	0.92	0.853	0.788	0.92	CLONAL	2	TRUE	1	0.62025293401221	3		493	349	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563270	21563271	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	93	890	4	ENST00000382592.4:c.648_649delinsTT	p.Pro217Ser	p.P217S	ENST00000382592	NM_014572.2	216	ttCCcc/ttTTcc	4/8	0.517272277201329	4	FACETS	0.896	0.799	0.999	0.448	0.399	0.5	CLONAL	1	TRUE	2	0.62025293401221	4		894	542	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623580	28623580	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	218	536	0	ENST00000241453.7:c.977G>T	p.Gly326Val	p.G326V	ENST00000241453	NM_004119.2	326	gGa/gTa	8/24	0.517272277201329	4	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	2	0.62025293401221	4		536	566	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896945	28896945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	112	484	0	ENST00000282397.4:c.2935G>A	p.Asp979Asn	p.D979N	ENST00000282397	NM_002019.4	979	Gat/Aat	21/30	0.517272277201329	4	FACETS	1	0.967	1	0.582	0.525	0.641	CLONAL	1	TRUE	2	0.62025293401221	4		484	503	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041063	29041063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	75	543	0	ENST00000282397.4:c.365C>T	p.Ser122Phe	p.S122F	ENST00000282397	NM_002019.4	122	tCt/tTt	3/30	0.517272277201329	4	FACETS	0.832	0.731	0.94	0.416	0.365	0.47	CLONAL	1	TRUE	2	0.62025293401221	4		543	471	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041220	29041220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1351200892	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	100	607	1	ENST00000282397.4:c.208G>A	p.Glu70Lys	p.E70K	ENST00000282397	NM_002019.4	70	Gaa/Aaa	3/30	0.517272277201329	4	FACETS	0.898	0.804	0.997	0.449	0.402	0.499	CLONAL	1	TRUE	2	0.62025293401221	4		608	582	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915094	32915094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	136	645	0	ENST00000380152.3:c.6602C>T	p.Ser2201Phe	p.S2201F	ENST00000380152		2201	tCt/tTt	11/27	0.517272277201329	4	FACETS	1	0.912	1	0.5	0.456	0.547	CLONAL	1	TRUE	2	0.62025293401221	4		645	710	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504536	103504536	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	91	401	0	ENST00000355739.4:c.157C>T	p.Pro53Ser	p.P53S	ENST00000355739	NM_000123.3	53	Cct/Tct	2/15	0.62025293401221	5	FACETS	1	0.908	1	0.341	0.303	0.381	CLONAL	1	TRUE	2	0.62025293401221	5		401	554	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434566	110434566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	302	681	0	ENST00000375856.3:c.3835G>A	p.Gly1279Arg	p.G1279R	ENST00000375856	NM_003749.2	1279	Gga/Aga	1/2	0.62025293401221	5	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	2	0.62025293401221	5		681	573	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609791	81609791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	74	437	0	ENST00000298171.2:c.1389G>A	p.Met463Ile	p.M463I	ENST00000298171	NM_000369.2	463	atG/atA	10/10	0.517272277201329	4	FACETS	1	0.948	1	0.569	0.501	0.64	CLONAL	1	TRUE	2	0.62025293401221	4		437	340	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239692	105239693	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	127	743	0	ENST00000349310.3:c.852_853delinsAA	p.Asp285Asn	p.D285N	ENST00000349310	NM_001014432.1	284	aaGGac/aaAAac	11/15	0.517272277201329	4	FACETS	1	0.929	1	0.514	0.466	0.563	CLONAL	1	TRUE	2	0.62025293401221	4		743	646	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43730541	43730541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	87	496	0	ENST00000382044.4:c.3172C>T	p.Pro1058Ser	p.P1058S	ENST00000382044	NM_001141980.1	1058	Ccc/Tcc	16/28	0.62025293401221	3	FACETS	0.877	0.781	0.979	0.439	0.39	0.49	CLONAL	1	TRUE	1	0.62025293401221	3		496	419	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472571	88472571	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	79	575	0	ENST00000360948.2:c.1984C>T	p.Gln662Ter	p.Q662*	ENST00000360948	NM_001012338.2	662	Cag/Tag	16/19	0.62025293401221	3	FACETS	0.973	0.863	1	0.486	0.431	0.545	CLONAL	1	TRUE	1	0.62025293401221	3		575	343	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99486209	99486210	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	231	679	0	ENST00000268035.6:c.3515_3516delinsAA	p.Gly1172Glu	p.G1172E	ENST00000268035	NM_000875.3	1172	gGG/gAA	19/21	0.62025293401221	3	FACETS	0.976	0.92	1	0.976	0.92	1	CLONAL	2	TRUE	1	0.62025293401221	3		679	500	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658656	3658656	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	172	934	0	ENST00000294008.3:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000294008	NM_032444.2	104	Caa/Taa	2/15	0.62025293401221	3	FACETS	0.945	0.871	1	0.472	0.435	0.511	CLONAL	1	TRUE	1	0.62025293401221	3		934	769	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857769	9857769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	97	506	0	ENST00000330684.3:c.3632C>T	p.Ser1211Phe	p.S1211F	ENST00000330684	NM_001134407.1	1211	tCc/tTc	13/13	0.62025293401221	3	FACETS	1	0.962	1	0.574	0.516	0.634	CLONAL	1	TRUE	1	0.62025293401221	3		506	357	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934575	9934575	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779507103	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	110	631	1	ENST00000330684.3:c.1580C>T	p.Pro527Leu	p.P527L	ENST00000330684	NM_001134407.1	527	cCc/cTc	7/13	0.62025293401221	3	FACETS	1	0.952	1	0.542	0.49	0.596	CLONAL	1	TRUE	1	0.62025293401221	3		632	429	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984854	9984854	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149344082	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	91	556	0	ENST00000330684.3:c.1111G>A	p.Glu371Lys	p.E371K	ENST00000330684	NM_001134407.1	371	Gaa/Aaa	4/13	0.62025293401221	3	FACETS	0.961	0.859	1	0.481	0.429	0.534	CLONAL	1	TRUE	1	0.62025293401221	3		556	400	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865762	56865762	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	56	358	0	ENST00000308159.5:c.1094C>T	p.Pro365Leu	p.P365L	ENST00000308159	NM_014669.4	365	cCa/cTa	11/22	0.62025293401221	3	FACETS	0.896	0.775	1	0.448	0.387	0.513	CLONAL	1	TRUE	1	0.62025293401221	3		358	264	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72863732	72863732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	102	536	1	ENST00000268489.5:c.3475C>T	p.Pro1159Ser	p.P1159S	ENST00000268489	NM_006885.3	1159	Ccc/Tcc	5/10	0.62025293401221	3	FACETS	0.988	0.889	1	0.494	0.444	0.546	CLONAL	1	TRUE	1	0.62025293401221	3		537	436	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990322	81990322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	203	479	0	ENST00000359376.3:c.3593C>T	p.Ser1198Phe	p.S1198F	ENST00000359376	NM_002661.3	1198	tCc/tTc	32/33	0.62025293401221	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.62025293401221	3		479	411	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351211	89351211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs558841201	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	123	736	0	ENST00000301030.4:c.1739C>T	p.Ser580Phe	p.S580F	ENST00000301030	NM_001256183.1	580	tCc/tTc	9/13	0.62025293401221	3	FACETS	1	0.953	1	0.538	0.489	0.589	CLONAL	1	TRUE	1	0.62025293401221	3		736	483	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831350	89831350	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	98	501	0	ENST00000389301.3:c.2726C>T	p.Ser909Phe	p.S909F	ENST00000389301	NM_000135.2	909	tCt/tTt	28/43	0.62025293401221	3	FACETS	0.943	0.846	1	0.472	0.423	0.523	CLONAL	1	TRUE	1	0.62025293401221	3		501	439	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976480	7976480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	92	549	0	ENST00000319144.4:c.1912G>A	p.Glu638Lys	p.E638K	ENST00000319144	NM_001139.2	638	Gag/Aag	14/15	0.62025293401221	3	FACETS	0.953	0.852	1	0.476	0.426	0.53	CLONAL	1	TRUE	1	0.62025293401221	3		549	408	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980418	7980418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777344454	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	132	767	0	ENST00000319144.4:c.1165G>A	p.Glu389Lys	p.E389K	ENST00000319144	NM_001139.2	389	Gag/Aag	9/15	0.62025293401221	3	FACETS	1	0.959	1	0.544	0.496	0.593	CLONAL	1	TRUE	1	0.62025293401221	3		767	513	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980483	7980483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	192	401	0	ENST00000319144.4:c.1100C>T	p.Pro367Leu	p.P367L	ENST00000319144	NM_001139.2	367	cCc/cTc	9/15	0.62025293401221	3	FACETS	0.968	0.907	1	0.968	0.907	1	CLONAL	2	TRUE	1	0.62025293401221	3		401	419	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546050	29546050	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	124	610	1	ENST00000356175.3:c.1555C>T	p.Gln519Ter	p.Q519*	ENST00000356175	NM_000267.3	519	Caa/Taa	14/57	1	2	FACETS	0.992	0.906	1	0.992	0.906	1	CLONAL	1	TRUE	1	0.62025293401221	2		611	403	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40857185	40857185	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	84	360	1	ENST00000428826.2:c.1856C>T	p.Pro619Leu	p.P619L	ENST00000428826		619	cCc/cTc	17/21	0.443005910487167	4	FACETS	0.784	0.701	0.87	0.784	0.701	0.87	SUBCLONAL	2	TRUE	2	0.62025293401221	4		361	280	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63537665	63537665	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	98	552	0	ENST00000307078.5:c.967C>T	p.Pro323Ser	p.P323S	ENST00000307078	NM_004655.3	323	Cct/Tct	4/11	0.443005910487167	4	FACETS	1	0.936	1	0.531	0.476	0.589	CLONAL	1	TRUE	2	0.62025293401221	4		552	482	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099207	4099207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	78	570	0	ENST00000262948.5:c.911C>T	p.Pro304Leu	p.P304L	ENST00000262948	NM_030662.3	304	cCc/cTc	7/11	0.443005910487167	4	FACETS	1	0.927	1	0.533	0.471	0.599	CLONAL	1	TRUE	2	0.62025293401221	4		570	382	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170620	7170620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	268	697	0	ENST00000302850.5:c.1411G>A	p.Glu471Lys	p.E471K	ENST00000302850	NM_000208.2	471	Gaa/Aaa	6/22	0.443005910487167	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.62025293401221	4		697	673	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281493	15281493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1407627346	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	71	771	1	ENST00000263388.2:c.4880G>A	p.Arg1627Gln	p.R1627Q	ENST00000263388	NM_000435.2	1627	cGg/cAg	26/33	0.443005910487167	4	FACETS	0.865	0.758	0.979	0.432	0.379	0.49	CLONAL	1	TRUE	2	0.62025293401221	4		772	429	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376236	15376237	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	83	663	1	ENST00000263377.2:c.777_778delinsTT	p.Pro260Ser	p.P260S	ENST00000263377	NM_058243.2	259	ccCCca/ccTTca	5/20	0.443005910487167	4	FACETS	0.933	0.826	1	0.466	0.413	0.523	CLONAL	1	TRUE	2	0.62025293401221	4		664	465	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945512	17945512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	193	652	0	ENST00000458235.1:c.2218G>A	p.Asp740Asn	p.D740N	ENST00000458235	NM_000215.3	740	Gac/Aac	17/24	0.443005910487167	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.62025293401221	4		652	469	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18963074	18963074	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1485824312	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	122	832	3	ENST00000262803.5:c.941C>T	p.Ala314Val	p.A314V	ENST00000262803	NM_002911.3	314	gCc/gTc	6/24	0.443005910487167	4	FACETS	0.89	0.806	0.979	0.445	0.403	0.49	CLONAL	1	TRUE	2	0.62025293401221	4		835	716	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211793	36211793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	135	966	0	ENST00000222270.7:c.1544C>T	p.Pro515Leu	p.P515L	ENST00000222270	NM_014727.1	515	cCc/cTc	3/37	0.443005910487167	4	FACETS	0.918	0.835	1	0.459	0.417	0.503	CLONAL	1	TRUE	2	0.62025293401221	4		966	768	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744411	41744411	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1255166048	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	117	815	0	ENST00000301178.4:c.1031G>A	p.Arg344Gln	p.R344Q	ENST00000301178	NM_021913.4	344	cGg/cAg	8/20	0.443005910487167	4	FACETS	0.963	0.87	1	0.481	0.435	0.53	CLONAL	1	TRUE	2	0.62025293401221	4		815	635	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383212	42383212	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	125	753	0	ENST00000221972.3:c.232C>T	p.Pro78Ser	p.P78S	ENST00000221972	NM_021601.3	78	Cct/Tct	2/5	0.443005910487167	4	FACETS	1	0.975	1	0.606	0.551	0.663	CLONAL	1	TRUE	2	0.62025293401221	4		753	539	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50138856	50138856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	134	1016	0	ENST00000246792.3:c.634G>A	p.Gly212Ser	p.G212S	ENST00000246792	NM_006270.3	212	Ggc/Agc	6/6	0.443005910487167	4	FACETS	0.979	0.891	1	0.49	0.445	0.536	CLONAL	1	TRUE	2	0.62025293401221	4		1016	715	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906319	50906319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514633	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	73	624	0	ENST00000440232.2:c.980C>T	p.Pro327Leu	p.P327L	ENST00000440232	NM_002691.3	327	cCt/cTt	9/27	0.443005910487167	4	FACETS	0.953	0.838	1	0.477	0.419	0.539	CLONAL	1	TRUE	2	0.62025293401221	4		624	400	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909526	50909526	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	240	740	0	ENST00000440232.2:c.1330C>G	p.Arg444Gly	p.R444G	ENST00000440232	NM_002691.3	444	Cgg/Ggg	11/27	0.443005910487167	4	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	2	0.62025293401221	4		740	622	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967069	25967069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	72	562	0	ENST00000435504.4:c.2137G>A	p.Gly713Ser	p.G713S	ENST00000435504		713	Ggc/Agc	13/13	0.62025293401221	3	FACETS	0.836	0.735	0.943	0.418	0.367	0.472	CLONAL	1	TRUE	1	0.62025293401221	3		562	364	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47600601	47600601	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	92	386	0	ENST00000263735.4:c.77-1G>A		p.X26_splice	ENST00000263735	NM_002354.2	26			0.62025293401221	3	FACETS	0.989	0.885	1	0.494	0.442	0.549	CLONAL	1	TRUE	1	0.62025293401221	3		386	393	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096559	178096559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	80	370	0	ENST00000397062.3:c.772C>T	p.Leu258Phe	p.L258F	ENST00000397062	NM_006164.4	258	Ctc/Ttc	5/5	0.62025293401221	3	FACETS	1	0.933	1	0.535	0.475	0.598	CLONAL	1	TRUE	1	0.62025293401221	3		370	316	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285221	212285221	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1169528920	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	92	537	1	ENST00000342788.4:c.3080C>T	p.Ala1027Val	p.A1027V	ENST00000342788	NM_005235.2	1027	gCt/gTt	25/28	0.62025293401221	3	FACETS	1	0.946	1	0.544	0.488	0.604	CLONAL	1	TRUE	1	0.62025293401221	3		538	357	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530138	212530138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	80	418	0	ENST00000342788.4:c.1781C>T	p.Pro594Leu	p.P594L	ENST00000342788	NM_005235.2	594	cCa/cTa	15/28	0.62025293401221	3	FACETS	1	0.898	1	0.506	0.449	0.566	CLONAL	1	TRUE	1	0.62025293401221	3		418	334	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578317	212578318	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	89	527	1	ENST00000342788.4:c.939_940delinsAA	p.Met313_Glu314delinsIleLys	p.M313_E314delinsIK	ENST00000342788	NM_005235.2	313	atGGaa/atAAaa	8/28	0.62025293401221	3	FACETS	0.94	0.839	1	0.47	0.419	0.524	CLONAL	1	TRUE	1	0.62025293401221	3		528	400	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812299	212812299	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	77	418	0	ENST00000342788.4:c.277C>T	p.Gln93Ter	p.Q93*	ENST00000342788	NM_005235.2	93	Cag/Tag	3/28	0.62025293401221	3	FACETS	0.904	0.799	1	0.452	0.399	0.508	CLONAL	1	TRUE	1	0.62025293401221	3		418	360	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403230	213403230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	65	545	1	ENST00000342788.4:c.25G>A	p.Val9Ile	p.V9I	ENST00000342788	NM_005235.2	9	Gtc/Atc	1/28	0.62025293401221	3	FACETS	0.877	0.766	0.995	0.439	0.383	0.498	CLONAL	1	TRUE	1	0.62025293401221	3		546	313	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593663	215593664	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	53	484	1	ENST00000260947.4:c.2070_2071delinsTT	p.Leu691Phe	p.L691F	ENST00000260947	NM_000465.2	690	aaCCtt/aaTTtt	11/11	0.62025293401221	3	FACETS	0.788	0.677	0.908	0.394	0.338	0.454	CLONAL	1	TRUE	1	0.62025293401221	3		485	284	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022319	31022319	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs907795578	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	191	446	1	ENST00000375687.4:c.1804G>T	p.Glu602Ter	p.E602*	ENST00000375687	NM_015338.5	602	Gag/Tag	13/13	0.443005910487167	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.62025293401221	4		447	463	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770600	40770600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159844	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	73	518	1	ENST00000373198.4:c.2782G>A	p.Glu928Lys	p.E928K	ENST00000373198	NM_133170.3	928	Gag/Aag	19/32	0.443005910487167	4	FACETS	0.885	0.777	1	0.442	0.388	0.5	CLONAL	1	TRUE	2	0.62025293401221	4		519	431	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980762	40980762	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	60	508	0	ENST00000373198.4:c.1724G>A	p.Gly575Glu	p.G575E	ENST00000373198	NM_133170.3	575	gGg/gAg	10/32	0.443005910487167	4	FACETS	0.778	0.673	0.892	0.389	0.336	0.446	SUBCLONAL	1	TRUE	2	0.62025293401221	4		508	403	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980798	40980798	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	114	582	0	ENST00000373198.4:c.1688C>T	p.Ser563Phe	p.S563F	ENST00000373198	NM_133170.3	563	tCc/tTc	10/32	0.443005910487167	4	FACETS	1	0.971	1	0.594	0.538	0.654	CLONAL	1	TRUE	2	0.62025293401221	4		582	501	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385263	41385263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	80	587	0	ENST00000373198.4:c.698G>A	p.Arg233Lys	p.R233K	ENST00000373198	NM_133170.3	233	aGg/aAg	6/32	0.443005910487167	4	FACETS	1	0.901	1	0.51	0.451	0.572	CLONAL	1	TRUE	2	0.62025293401221	4		587	410	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514555	41514555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	110	572	0	ENST00000373198.4:c.106G>A	p.Glu36Lys	p.E36K	ENST00000373198	NM_133170.3	36	Gag/Aag	2/32	0.443005910487167	4	FACETS	1	0.952	1	0.545	0.492	0.602	CLONAL	1	TRUE	2	0.62025293401221	4		572	527	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62320915	62320916	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	117	927	2	ENST00000360203.5:c.1939_1940delinsTT	p.Pro647Leu	p.P647L	ENST00000360203	NM_001283009.1	647	CCg/TTg	23/35	0.443005910487167	4	FACETS	0.894	0.807	0.985	0.447	0.403	0.493	CLONAL	1	TRUE	2	0.62025293401221	4		929	684	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860396	42860396	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	108	707	1	ENST00000398585.3:c.481G>A	p.Gly161Ser	p.G161S	ENST00000398585	NM_001135099.1	161	Ggt/Agt	5/14	0.62025293401221	3	FACETS	0.836	0.753	0.923	0.418	0.376	0.462	CLONAL	1	TRUE	1	0.62025293401221	3		708	546	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458479	12458479	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	121	767	1	ENST00000287820.6:c.1096G>A	p.Gly366Arg	p.G366R	ENST00000287820	NM_015869.4	366	Ggg/Agg	6/7	0.62025293401221	3	FACETS	0.961	0.872	1	0.48	0.436	0.527	CLONAL	1	TRUE	1	0.62025293401221	3		768	532	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927489	49927489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777797719	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	123	676	1	ENST00000296474.3:c.3815C>T	p.Ser1272Leu	p.S1272L	ENST00000296474	NM_002447.2	1272	tCa/tTa	19/20	0.62025293401221	3	FACETS	1	0.97	1	0.575	0.523	0.628	CLONAL	1	TRUE	1	0.62025293401221	3		677	452	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643906	52643906	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	83	586	0	ENST00000394830.3:c.1990G>A	p.Glu664Lys	p.E664K	ENST00000394830	NM_018313.4	664	Gag/Aag	17/30	0.62025293401221	3	FACETS	0.883	0.784	0.988	0.442	0.392	0.494	CLONAL	1	TRUE	1	0.62025293401221	3		586	397	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247495	71247495	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	91	549	1	ENST00000318789.4:c.38G>A	p.Gly13Asp	p.G13D	ENST00000318789	NM_032682.5	13	gGt/gAt	6/21	0.62025293401221	3	FACETS	0.963	0.861	1	0.482	0.43	0.536	CLONAL	1	TRUE	1	0.62025293401221	3		550	399	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1918742	1918742	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	108	515	0	ENST00000382891.5:c.905C>T	p.Pro302Leu	p.P302L	ENST00000382891	NM_133335.3	302	cCc/cTc	4/22	0.62025293401221	3	FACETS	0.939	0.847	1	0.469	0.423	0.518	CLONAL	1	TRUE	1	0.62025293401221	3		515	486	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957419	1957419	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	56	487	0	ENST00000382891.5:c.2519-1G>A		p.X840_splice	ENST00000382891	NM_133335.3	840			0.62025293401221	3	FACETS	1	0.889	1	0.514	0.446	0.587	CLONAL	1	TRUE	1	0.62025293401221	3		487	230	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139787	55139788	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	96	635	0	ENST00000257290.5:c.1448_1449delinsTT	p.Thr483Ile	p.T483I	ENST00000257290	NM_006206.4	483	aCC/aTT	10/23	0.62025293401221	3	FACETS	0.911	0.816	1	0.456	0.408	0.506	CLONAL	1	TRUE	1	0.62025293401221	3		635	445	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31401661	31401661	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	91	415	0	ENST00000344624.3:c.4003C>T	p.Pro1335Ser	p.P1335S	ENST00000344624		1335	Ccc/Tcc	33/33	0.530609809087734	5	FACETS	1	0.941	1	0.362	0.322	0.404	CLONAL	1	TRUE	2	0.62025293401221	5		415	522	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873668	35873669	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	67	435	1	ENST00000303115.3:c.624_625delinsTT	p.Pro209Ser	p.P209S	ENST00000303115	NM_002185.3	208	atCCct/atTTct	5/8	0.530609809087734	5	FACETS	0.836	0.728	0.952	0.279	0.242	0.318	CLONAL	1	TRUE	2	0.62025293401221	5		436	499	SUCCESS
APC	324	MSKCC	GRCh37	5	112179783	112179783	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773513581	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	67	352	0	ENST00000257430.4:c.8492C>T	p.Pro2831Leu	p.P2831L	ENST00000257430	NM_000038.5	2831	cCt/cTt	16/16	0.62025293401221	3	FACETS	0.811	0.709	0.92	0.406	0.354	0.46	CLONAL	1	TRUE	1	0.62025293401221	3		352	349	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501548	149501548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756210461	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	110	642	2	ENST00000261799.4:c.2239G>A	p.Glu747Lys	p.E747K	ENST00000261799	NM_002609.3	747	Gag/Aag	16/23	0.256712411979749	2	FACETS	0.806	0.729	0.887	0.403	0.364	0.444	INDETERMINATE	1	TRUE	0	0.62025293401221	2		644	440	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055892	180055892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369919880	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	72	569	1	ENST00000261937.6:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000261937	NM_182925.4	365	Gag/Aag	8/30	0.62025293401221	3	FACETS	0.988	0.871	1	0.494	0.435	0.556	CLONAL	1	TRUE	1	0.62025293401221	3		570	308	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271243	26271243	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	81	538	0	ENST00000305910.3:c.370G>A	p.Asp124Asn	p.D124N	ENST00000305910	NM_003534.2	124	Gac/Aac	1/1	0.517272277201329	4	FACETS	0.926	0.819	1	0.463	0.409	0.52	CLONAL	1	TRUE	2	0.62025293401221	4		538	457	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680247	30680247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	108	840	0	ENST00000376406.3:c.1472C>T	p.Pro491Leu	p.P491L	ENST00000376406	NM_014641.2	491	cCt/cTt	5/15	0.517272277201329	4	FACETS	0.827	0.743	0.916	0.414	0.371	0.458	CLONAL	1	TRUE	2	0.62025293401221	4		840	682	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168773	32168773	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	128	789	0	ENST00000375023.3:c.4150G>A	p.Val1384Ile	p.V1384I	ENST00000375023	NM_004557.3	1384	Gtc/Atc	23/30	0.517272277201329	4	FACETS	1	0.974	1	0.597	0.543	0.653	CLONAL	1	TRUE	2	0.62025293401221	4		789	560	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178606	32178606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs980873402	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	98	757	0	ENST00000375023.3:c.2788C>T	p.His930Tyr	p.H930Y	ENST00000375023	NM_004557.3	930	Cac/Tac	18/30	0.517272277201329	4	FACETS	0.875	0.783	0.973	0.438	0.391	0.487	CLONAL	1	TRUE	2	0.62025293401221	4		757	585	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793635	89793635	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	92	485	0	ENST00000336032.3:c.704T>C	p.Phe235Ser	p.F235S	ENST00000336032	NM_006813.2	235	tTt/tCt	2/2	0.517272277201329	4	FACETS	0.957	0.854	1	0.479	0.427	0.534	CLONAL	1	TRUE	2	0.62025293401221	4		485	502	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120714	94120714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	82	319	0	ENST00000369303.4:c.337C>T	p.Pro113Ser	p.P113S	ENST00000369303	NM_004440.3	113	Cct/Tct	3/17	0.62025293401221	2	FACETS	0.965	0.862	1	0.482	0.431	0.537	CLONAL	1	TRUE	0	0.62025293401221	2		319	274	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525627	137525627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	151	504	0	ENST00000367739.4:c.388C>T	p.Pro130Ser	p.P130S	ENST00000367739	NM_000416.2	130	Cct/Tct	4/7	0.62025293401221	2	FACETS	0.863	0.806	0.92	0.863	0.806	0.92	CLONAL	2	TRUE	0	0.62025293401221	2		504	282	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6045527	6045527	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	48	189	0	ENST00000265849.7:c.159T>A	p.Asn53Lys	p.N53K	ENST00000265849	NM_000535.5	53	aaT/aaA	2/15	0.62025293401221	3	FACETS	1	0.915	1	0.548	0.47	0.631	CLONAL	1	TRUE	1	0.62025293401221	3		189	185	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729498	41729498	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	95	656	0	ENST00000242208.4:c.1031G>A	p.Gly344Asp	p.G344D	ENST00000242208	NM_002192.2	344	gGc/gAc	3/3	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.62025293401221	2		656	303	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92252399	92252399	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	62	313	0	ENST00000265734.4:c.649C>T	p.Pro217Ser	p.P217S	ENST00000265734	NM_001259.6	217	Cct/Tct	6/8	0.62025293401221	4	FACETS	0.72	0.623	0.824	0.24	0.207	0.275	SUBCLONAL	1	TRUE	1	0.62025293401221	4		313	450	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508121	106508122	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	26	227	0	ENST00000359195.3:c.115_116delinsTT	p.Pro39Phe	p.P39F	ENST00000359195	NM_002649.2	39	CCc/TTc	2/11	0.62025293401221	4	FACETS	0.854	0.684	1	0.285	0.228	0.349	CLONAL	1	TRUE	1	0.62025293401221	4		227	159	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515171	106515171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765226775	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	99	508	0	ENST00000359195.3:c.2314G>A	p.Glu772Lys	p.E772K	ENST00000359195	NM_002649.2	772	Gaa/Aaa	5/11	0.62025293401221	4	FACETS	0.77	0.688	0.857	0.257	0.229	0.286	SUBCLONAL	1	TRUE	1	0.62025293401221	4		508	672	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340318	116340318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	81	347	0	ENST00000397752.3:c.1180C>T	p.His394Tyr	p.H394Y	ENST00000397752	NM_000245.2	394	Cat/Tat	2/21	0.62025293401221	4	FACETS	1	0.947	1	0.372	0.33	0.417	CLONAL	1	TRUE	1	0.62025293401221	4		347	379	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151181890	151181890	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	71	315	0	ENST00000262187.5:c.125C>T	p.Thr42Ile	p.T42I	ENST00000262187	NM_005614.3	42	aCt/aTt	3/8	0.62025293401221	7	FACETS	0.94	0.821	1	0.157	0.136	0.179	CLONAL	1	TRUE	1	0.62025293401221	7		315	621	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849837	151849837	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1340576708	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	60	395	0	ENST00000262189.6:c.12479C>T	p.Ser4160Phe	p.S4160F	ENST00000262189	NM_170606.2	4160	tCt/tTt	49/59	0.62025293401221	7	FACETS	0.933	0.804	1	0.155	0.134	0.179	CLONAL	1	TRUE	1	0.62025293401221	7		395	529	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878140	151878140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	101	531	0	ENST00000262189.6:c.6805C>T	p.Pro2269Ser	p.P2269S	ENST00000262189	NM_170606.2	2269	Cct/Tct	36/59	0.62025293401221	7	FACETS	1	0.964	1	0.196	0.175	0.219	CLONAL	1	TRUE	1	0.62025293401221	7		531	706	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972987	68972987	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	71	495	0	ENST00000288368.4:c.1312T>A	p.Leu438Ile	p.L438I	ENST00000288368	NM_024870.2	438	Tta/Ata	11/40	0.443005910487167	4	FACETS	0.815	0.714	0.924	0.408	0.357	0.462	CLONAL	1	TRUE	2	0.62025293401221	4		495	455	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020480	69020480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	131	723	0	ENST00000288368.4:c.2852C>T	p.Ser951Leu	p.S951L	ENST00000288368	NM_024870.2	951	tCa/tTa	24/40	0.443005910487167	4	FACETS	1	0.943	1	0.525	0.477	0.575	CLONAL	1	TRUE	2	0.62025293401221	4		723	652	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964515	70964515	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148573764	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	127	630	1	ENST00000276594.2:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000276594	NM_024504.3	505	Cgc/Tgc	8/8	0.443005910487167	4	FACETS	1	0.938	1	0.521	0.473	0.571	CLONAL	1	TRUE	2	0.62025293401221	4		631	637	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978697	70978697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760525174	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	129	762	0	ENST00000276594.2:c.956G>A	p.Gly319Glu	p.G319E	ENST00000276594	NM_024504.3	319	gGa/gAa	5/8	0.443005910487167	4	FACETS	0.956	0.868	1	0.478	0.434	0.524	CLONAL	1	TRUE	2	0.62025293401221	4		762	705	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022020	5022020	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs945180127	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	109	500	0	ENST00000381652.3:c.33G>A	p.Met11Ile	p.M11I	ENST00000381652	NM_004972.3	11	atG/atA	3/25	0.62025293401221	2	FACETS	1	0.963	1	0.556	0.506	0.608	CLONAL	1	TRUE	0	0.62025293401221	2		500	316	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054672	5054672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	82	451	1	ENST00000381652.3:c.724C>T	p.Gln242Ter	p.Q242*	ENST00000381652	NM_004972.3	242	Caa/Taa	7/25	0.62025293401221	2	FACETS	0.99	0.885	1	0.495	0.442	0.55	CLONAL	1	TRUE	0	0.62025293401221	2		452	267	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485286	8485286	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	103	608	0	ENST00000356435.5:c.3094A>G	p.Thr1032Ala	p.T1032A	ENST00000356435		1032	Act/Gct	18/35	0.62025293401221	2	FACETS	1	0.905	1	0.5	0.452	0.55	CLONAL	1	TRUE	0	0.62025293401221	2		608	332	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966652	36966652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749999635	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	72	537	0	ENST00000358127.4:c.674G>A	p.Arg225Gln	p.R225Q	ENST00000358127	NM_001280556.1	225	cGg/cAg	6/10	0.62025293401221	3	FACETS	0.742	0.651	0.839	0.371	0.325	0.42	SUBCLONAL	1	TRUE	1	0.62025293401221	3		537	410	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931969	39931969	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	154	402	1	ENST00000378444.4:c.2630C>T	p.Thr877Ile	p.T877I	ENST00000378444	NM_001123385.1	877	aCc/aTc	4/15	0.598726729837581	2	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.62025293401221	2		403	371	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410921	63410921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	124	339	1	ENST00000330258.3:c.2246C>T	p.Ser749Leu	p.S749L	ENST00000330258	NM_152424.3	749	tCa/tTa	2/2	0.598726729837581	2	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.62025293401221	2		340	281	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420292	49420292	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	222	662	1	ENST00000301067.7:c.15457del	p.Arg5153GlyfsTer10	p.R5153Gfs*10	ENST00000301067	NM_003482.3	5153	Cgg/gg	48/54	0.598726729837581	4	FACETS	0.925	0.866	0.985			1	CLONAL	2	TRUE	NA	0.62025293401221	4		663	627	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0029539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	117	282	0				ENST00000310581	NM_198253.2	-/1132			0.269000032798017	4	FACETS	0.877	0.795	0.961	0.877	0.795	0.961	CLONAL	2	TRUE	2	0.403726487060186	4		282	464	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913381	NA	P-0029539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	48	441	0	ENST00000304494.5:c.322G>A	p.Asp108Asn	p.D108N	ENST00000304494	NM_000077.4	108	Gat/Aat	2/3	0.209561968802893	2	FACETS	0.515	0.435	0.602	0.257	0.217	0.301	INDETERMINATE	1	TRUE	0	0.403726487060186	2		441	462	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045000	47045000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556782020	NA	P-0029539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	139	304	1	ENST00000377604.3:c.2326C>T	p.Arg776Trp	p.R776W	ENST00000377604	NM_001204468.1	776	Cgg/Tgg	20/24	1	1	FACETS	0.806	0.744	0.869	1	0.99	1	CLONAL	2	TRUE	0	0.403726487060186	1		305	341	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089755	27089755	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	50	394	0	ENST00000324856.7:c.2711C>T	p.Ala904Val	p.A904V	ENST00000324856	NM_006015.4	904	gCt/gTt	8/20	0.403726487060186	3	FACETS	0.574	0.487	0.669	0.287	0.243	0.335	SUBCLONAL	1	TRUE	1	0.403726487060186	3		394	519	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246498729	246498729	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	42	411	0	ENST00000388985.4:c.276C>A	p.Ser92Arg	p.S92R	ENST00000388985		92	agC/agA	3/12	0.24825169049444	3	FACETS	0.395	0.329	0.469	0.198	0.164	0.235	SUBCLONAL	1	TRUE	1	0.403726487060186	3		411	633	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906987	32906987	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	64	322	0	ENST00000380152.3:c.1372C>G	p.Pro458Ala	p.P458A	ENST00000380152		458	Cca/Gca	10/27	0.403726487060186	3	FACETS	0.799	0.693	0.913	0.399	0.346	0.457	CLONAL	1	TRUE	1	0.403726487060186	3		322	477	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082273	16082279	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGGAC	CCCGGAC	-	novel	NA	P-0029539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	56	564	0	ENST00000281043.3:c.87_93del	p.Tyr29Ter	p.Y29*	ENST00000281043	NM_005378.4	29	taCCCGGAC/ta	2/3	0.403726487060186	3	FACETS	0.371	0.317	0.431	0.185	0.158	0.216	SUBCLONAL	1	TRUE	1	0.403726487060186	3		564	899	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190742054	190742054	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	43	421	0	ENST00000441310.2:c.2691C>G	p.Ile897Met	p.I897M	ENST00000441310	NM_000534.4	897	atC/atG	13/13	0.403726487060186	3	FACETS	0.418	0.349	0.495	0.139	0.116	0.165	SUBCLONAL	1	TRUE	0	0.403726487060186	3		421	612	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274699	198274699	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	37	277	0	ENST00000335508.6:c.699T>A	p.Asp233Glu	p.D233E	ENST00000335508	NM_012433.2	233	gaT/gaA	7/25	0.331700360136966	2	FACETS	0.524	0.433	0.625	0.262	0.216	0.313	SUBCLONAL	1	TRUE	0	0.403726487060186	2		277	350	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945551	54945551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	78	681	0	ENST00000312783.6:c.1019G>A	p.Arg340Lys	p.R340K	ENST00000312783	NM_198436.1	340	aGa/aAa	9/10	0.3751073690006	3	FACETS	0.549	0.481	0.622	0.274	0.24	0.311	SUBCLONAL	1	TRUE	1	0.403726487060186	3		681	846	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840010	27840010	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	31	352	1	ENST00000328488.2:c.84G>C	p.Lys28Asn	p.K28N	ENST00000328488	NM_003533.2	28	aaG/aaC	1/1	0.403726487060186	3	FACETS	0.405	0.327	0.493	0.202	0.163	0.247	SUBCLONAL	1	TRUE	1	0.403726487060186	3		353	456	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983144	149983144	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	54	435	0	ENST00000253339.5:c.3114T>A	p.Asn1038Lys	p.N1038K	ENST00000253339		1038	aaT/aaA	7/7	0.175732445776709	3	FACETS	0.552	0.471	0.641	0.184	0.157	0.214	INDETERMINATE	1	TRUE	0	0.403726487060186	3		435	582	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923022	39923022	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	51	212	0	ENST00000378444.4:c.3686C>A	p.Pro1229His	p.P1229H	ENST00000378444	NM_001123385.1	1229	cCt/cAt	8/15	1	1	FACETS	0.761	0.652	0.878	0.761	0.652	0.878	SUBCLONAL	1	TRUE	0	0.403726487060186	1		212	265	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971199	21971199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894095	NA	P-0029549-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	70	315	0	ENST00000304494.5:c.159G>A	p.Met53Ile	p.M53I	ENST00000304494	NM_000077.4	53	atG/atA	2/3	0.316450140116508	1	FACETS	0.962	0.843	1	0.962	0.843	1	CLONAL	1	TRUE	0	0.316450140116508	1		315	387	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913381	NA	P-0029549-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	106	441	0	ENST00000304494.5:c.322G>A	p.Asp108Asn	p.D108N	ENST00000304494	NM_000077.4	108	Gat/Aat	2/3	0.316450140116508	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.316450140116508	1		441	525	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0029549-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	107	659	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.316450140116508	3	FACETS	0.917	0.822	1	0.459	0.411	0.509	CLONAL	1	TRUE	1	0.316450140116508	3		659	854	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0029549-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	193	699	0	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.306455039506446	2	FACETS	1	0.99	1	0.72	0.667	0.775	CLONAL	1	TRUE	0	0.316450140116508	2		699	847	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785572	50785572	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029549-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	92	577	0	ENST00000398568.2:c.562C>T	p.Gln188Ter	p.Q188*	ENST00000398568	NM_001042412.1	188	Cag/Tag	4/18	1	2	FACETS	0.594	0.526	0.666	0.594	0.526	0.666	SUBCLONAL	1	TRUE	1	0.316450140116508	2		577	979	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22008861	22008861	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029549-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	120	565	0	ENST00000276925.6:c.92G>C	p.Arg31Pro	p.R31P	ENST00000276925	NM_004936.3	31	cGa/cCa	1/2	0.316450140116508	1	FACETS	0.975	0.882	1	0.975	0.882	1	CLONAL	1	TRUE	0	0.316450140116508	1		565	655	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	115	354	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.785	0.71	0.864	1	0.985	1	SUBCLONAL	2	TRUE	1	0.28	2		354	523	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570334	87570334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	178	517	0	ENST00000277120.3:c.2074G>A	p.Asp692Asn	p.D692N	ENST00000277120		692	Gat/Aat	17/19	1	2	FACETS	0.825	0.761	0.89	1	0.991	1	CLONAL	2	TRUE	1	0.28	2		517	771	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136231	2136231	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs45517364	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	46	511	0	ENST00000219476.3:c.4700G>T	p.Gly1567Val	p.G1567V	ENST00000219476	NM_000548.3	1567	gGc/gTc	37/42	1	2	FACETS	0.51	0.429	0.6	0.51	0.429	0.6	SUBCLONAL	1	TRUE	1	0.28	2		511	644	SUCCESS
APC	324	MSKCC	GRCh37	5	112175921	112175921	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	106	227	0	ENST00000257430.4:c.4630G>T	p.Glu1544Ter	p.E1544*	ENST00000257430	NM_000038.5	1544	Gaa/Taa	16/16	1	2	FACETS	0.988	0.894	1	1	0.988	1	CLONAL	2	TRUE	1	0.28	2		227	383	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346365	73346365	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	125	400	0	ENST00000377767.4:c.1435G>T	p.Asp479Tyr	p.D479Y	ENST00000377767	NM_014953.3	479	Gac/Tac	10/21	1	2	FACETS	0.917	0.835	1	1	0.989	1	CLONAL	2	TRUE	1	0.28	2		400	487	SUCCESS
APC	324	MSKCC	GRCh37	5	112175060	112175060	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	62	209	0	ENST00000257430.4:c.3769G>T	p.Glu1257Ter	p.E1257*	ENST00000257430	NM_000038.5	1257	Gaa/Taa	16/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.28	2		209	309	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952086	178952086	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519932	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	145	349	0	ENST00000263967.3:c.3141T>G	p.His1047Gln	p.H1047Q	ENST00000263967	NM_006218.2	1047	caT/caG	21/21	1	2	FACETS	0.843	0.772	0.917	1	0.99	1	CLONAL	2	TRUE	1	0.28	2		349	614	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138500	11138500	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	61	541	0	ENST00000358026.2:c.3256G>T	p.Asp1086Tyr	p.D1086Y	ENST00000358026	NM_001128849.1	1086	Gat/Tat	24/36	1	2	FACETS	0.608	0.523	0.7	0.608	0.523	0.7	SUBCLONAL	1	TRUE	1	0.28	2		541	717	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188288	142188288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1470834016	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	65	447	1	ENST00000350721.4:c.6443G>A	p.Arg2148Gln	p.R2148Q	ENST00000350721	NM_001184.3	2148	cGa/cAa	38/47	1	2	FACETS	0.852	0.739	0.974	0.852	0.739	0.974	CLONAL	1	TRUE	1	0.28	2		448	545	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068393	26068393	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	123	416	0	ENST00000435504.4:c.97G>T	p.Glu33Ter	p.E33*	ENST00000435504		33	Gaa/Taa	2/13	1	2	FACETS	1	0.92	1	1	0.99	1	CLONAL	2	TRUE	1	0.28	2		416	435	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683734	162683734	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs770994041	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	34	452	0	ENST00000366898.1:c.235G>T	p.Glu79Ter	p.E79*	ENST00000366898	NM_004562.2	79	Gaa/Taa	3/12	1	2	FACETS	0.381	0.31	0.461	0.381	0.31	0.461	SUBCLONAL	1	TRUE	1	0.28	2		452	637	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003283	42003283	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	177	554	0	ENST00000219905.7:c.2820G>T	p.Lys940Asn	p.K940N	ENST00000219905	NM_001164273.1	940	aaG/aaT	8/24	1	2	FACETS	0.939	0.869	1	1	0.992	1	CLONAL	2	TRUE	1	0.28	2		554	673	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635252	87635252	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	148	462	1	ENST00000277120.3:c.2304G>T	p.Gln768His	p.Q768H	ENST00000277120		768	caG/caT	18/19	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.28	2		463	731	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839785	42839785	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773001010	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	163	452	1	ENST00000398585.3:c.1454C>T	p.Ser485Leu	p.S485L	ENST00000398585	NM_001135099.1	485	tCg/tTg	13/14	1	2	FACETS	0.969	0.893	1	1	0.992	1	CLONAL	2	TRUE	1	0.28	2		453	601	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638912	176638912	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs111638717	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	105	535	1	ENST00000439151.2:c.3512G>A	p.Arg1171His	p.R1171H	ENST00000439151	NM_022455.4	1171	cGt/cAt	5/23	1	2	FACETS	0.894	0.8	0.993	0.894	0.8	0.993	CLONAL	1	TRUE	1	0.28	2		536	839	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059183	27059183	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	158	384	0	ENST00000324856.7:c.1820C>A	p.Ser607Ter	p.S607*	ENST00000324856	NM_006015.4	607	tCa/tAa	4/20	1	2	FACETS	0.89	0.819	0.964	1	0.991	1	CLONAL	2	TRUE	1	0.28	2		384	634	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376182	225376182	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	74	535	1	ENST00000264414.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000264414	NM_003590.4	258	Gaa/Taa	6/16	1	2	FACETS	0.966	0.847	1	0.966	0.847	1	CLONAL	1	TRUE	1	0.28	2		536	547	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888096	81888096	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	176	429	2	ENST00000359376.3:c.241G>T	p.Asp81Tyr	p.D81Y	ENST00000359376	NM_002661.3	81	Gat/Tat	3/33	1	2	FACETS	1	0.955	1	1	0.993	1	CLONAL	2	TRUE	1	0.28	2		431	602	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877455	89877455	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	207	540	0	ENST00000389301.3:c.308C>G	p.Ser103Ter	p.S103*	ENST00000389301	NM_000135.2	103	tCa/tGa	4/43	1	2	FACETS	1	0.962	1	1	0.994	1	CLONAL	2	TRUE	1	0.28	2		540	706	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330628	65330628	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	107	337	1	ENST00000342505.4:c.1018A>T	p.Lys340Ter	p.K340*	ENST00000342505	NM_002227.2	340	Aaa/Taa	8/25	0.214068910060946	3	FACETS	0.941	0.849	1	0.941	0.849	1	CLONAL	2	TRUE	1	0.28	3		338	463	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108787	2108788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs137854024	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	172	725	0	ENST00000219476.3:c.894dup	p.Val299CysfsTer39	p.V299Cfs*39	ENST00000219476	NM_000548.3	296	-/T	10/42	1	2	FACETS	0.875	0.808	0.945	1	0.991	1	CLONAL	2	TRUE	1	0.28	2		725	702	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675064	40675064	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	49	537	0	ENST00000249776.8:c.28G>A	p.Asp10Asn	p.D10N	ENST00000249776	NM_033286.3	10	Gac/Aac	1/9	1	2	FACETS	0.418	0.352	0.49	0.418	0.352	0.49	SUBCLONAL	1	TRUE	1	0.28	2		537	838	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720857	89720857	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	85	224	0	ENST00000371953.3:c.1008C>A	p.Tyr336Ter	p.Y336*	ENST00000371953	NM_000314.4	336	taC/taA	8/9	1	2	FACETS	0.946	0.844	1	1	0.985	1	CLONAL	2	TRUE	1	0.28	2		224	321	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745581	162745581	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	91	411	0	ENST00000367921.3:c.1996C>A	p.Leu666Ile	p.L666I	ENST00000367921	NM_006182.2	666	Ctt/Att	15/18	1	2	FACETS	0.907	0.805	1	0.907	0.805	1	CLONAL	1	TRUE	1	0.28	2		411	717	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829847	72829847	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750842718	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	204	577	1	ENST00000268489.5:c.6734C>T	p.Ser2245Leu	p.S2245L	ENST00000268489	NM_006885.3	2245	tCa/tTa	9/10	1	2	FACETS	0.863	0.802	0.927	1	0.993	1	CLONAL	2	TRUE	1	0.28	2		578	844	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724337	112724337	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	257	546	0	ENST00000369452.4:c.221G>T	p.Arg74Leu	p.R74L	ENST00000369452	NM_007373.3	74	cGg/cTg	2/9	1	2	FACETS	0.849	0.795	0.905	1	0.994	1	CLONAL	2	TRUE	1	0.28	2		546	1081	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967567	26967567	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	35	433	0	ENST00000381527.3:c.710G>T	p.Arg237Leu	p.R237L	ENST00000381527	NM_001260.1	237	cGa/cTa	7/13	0.205694040898709	1	FACETS	0.471	0.386	0.567	0.471	0.386	0.567	SUBCLONAL	1	TRUE	0	0.28	1		433	456	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11177125	11177125	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	85	458	0	ENST00000361445.4:c.6952A>C	p.Thr2318Pro	p.T2318P	ENST00000361445	NM_004958.3	2318	Acc/Ccc	50/58	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.28	2		458	601	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259459	11259459	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs879111850	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	55	379	0	ENST00000361445.4:c.4109G>C	p.Gly1370Ala	p.G1370A	ENST00000361445	NM_004958.3	1370	gGc/gCc	28/58	1	2	FACETS	0.613	0.524	0.711	0.613	0.524	0.711	SUBCLONAL	1	TRUE	1	0.28	2		379	641	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16248794	16248794	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	117	468	0	ENST00000375759.3:c.1800G>T	p.Glu600Asp	p.E600D	ENST00000375759	NM_015001.2	600	gaG/gaT	10/15	1	2	FACETS	0.899	0.815	0.985	1	0.988	1	CLONAL	2	TRUE	1	0.28	2		468	465	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255350	16255350	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	216	463	1	ENST00000375759.3:c.2615T>C	p.Leu872Pro	p.L872P	ENST00000375759	NM_015001.2	872	cTg/cCg	11/15	1	2	FACETS	0.904	0.842	0.968	1	0.993	1	CLONAL	2	TRUE	1	0.28	2		464	853	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259459	16259459	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	173	395	0	ENST00000375759.3:c.6724G>T	p.Glu2242Ter	p.E2242*	ENST00000375759	NM_015001.2	2242	Gaa/Taa	11/15	1	2	FACETS	1	0.966	1	1	0.993	1	CLONAL	2	TRUE	1	0.28	2		395	574	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885713	23885713	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	211	585	0	ENST00000374561.5:c.205A>G	p.Ile69Val	p.I69V	ENST00000374561	NM_002167.4	69	Atc/Gtc	1/3	1	2	FACETS	0.916	0.852	0.981	1	0.993	1	CLONAL	2	TRUE	1	0.28	2		585	823	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726620	46726620	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1485410090	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	189	490	0	ENST00000371975.4:c.699G>T	p.Trp233Cys	p.W233C	ENST00000371975	NM_003579.3	233	tgG/tgT	7/18	1	2	FACETS	0.96	0.89	1	1	0.993	1	CLONAL	2	TRUE	1	0.28	2		490	703	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344811	65344811	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	47	293	0	ENST00000342505.4:c.226A>G	p.Asn76Asp	p.N76D	ENST00000342505	NM_002227.2	76	Aac/Gac	4/25	0.214068910060946	3	FACETS	0.755	0.637	0.885	0.377	0.318	0.443	SUBCLONAL	1	TRUE	1	0.28	3		293	507	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736501	85736501	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	28	273	0	ENST00000370580.1:c.146G>T	p.Arg49Ile	p.R49I	ENST00000370580	NM_003921.4	49	aGa/aTa	2/3	0.214068910060946	3	FACETS	0.582	0.465	0.715	0.291	0.232	0.358	SUBCLONAL	1	TRUE	1	0.28	3		273	392	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273187	115273187	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	216	510	0	ENST00000438362.2:c.1271A>G	p.Glu424Gly	p.E424G	ENST00000438362	NM_001242891.1	424	gAa/gGa	11/20	0.214068910060946	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	1	0.28	3		510	854	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161298273	161298273	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	95	313	0	ENST00000367975.2:c.165C>A	p.His55Gln	p.H55Q	ENST00000367975	NM_003001.3	55	caC/caA	3/6	1	2	FACETS	0.798	0.715	0.886	1	0.983	1	SUBCLONAL	2	TRUE	1	0.28	2		313	425	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015326	176015326	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	17	325	0	ENST00000367669.3:c.1412C>A	p.Ser471Ter	p.S471*	ENST00000367669	NM_022457.5	471	tCg/tAg	12/20	1	2	FACETS	0.74	0.556	0.957	0.74	0.556	0.957	CLONAL	1	TRUE	1	0.28	2		325	164	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176145050	176145050	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	95	337	0	ENST00000367669.3:c.561C>A	p.Phe187Leu	p.F187L	ENST00000367669	NM_022457.5	187	ttC/ttA	3/20	1	2	FACETS	0.812	0.727	0.9	1	0.983	1	CLONAL	2	TRUE	1	0.28	2		337	418	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099303	193099303	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	58	261	0	ENST00000367435.3:c.238-1G>T		p.X80_splice	ENST00000367435	NM_024529.4	80			1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.28	2		261	284	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193181546	193181546	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	32	454	0	ENST00000367435.3:c.1093C>T	p.Pro365Ser	p.P365S	ENST00000367435	NM_024529.4	365	Cct/Tct	13/17	1	2	FACETS	0.6	0.487	0.727	0.6	0.487	0.727	SUBCLONAL	1	TRUE	1	0.28	2		454	381	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981769	201981769	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	78	501	0	ENST00000359651.3:c.480C>A	p.Asp160Glu	p.D160E	ENST00000359651		160	gaC/gaA	4/8	1	2	FACETS	0.827	0.726	0.934	0.827	0.726	0.934	CLONAL	1	TRUE	1	0.28	2		501	674	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651584	206651584	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	89	617	0	ENST00000367120.3:c.894C>A	p.Phe298Leu	p.F298L	ENST00000367120	NM_014002.3	298	ttC/ttA	9/22	1	2	FACETS	0.8	0.708	0.897	0.8	0.708	0.897	SUBCLONAL	1	TRUE	1	0.28	2		617	795	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675399	241675399	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	26	316	0	ENST00000366560.3:c.423G>T	p.Trp141Cys	p.W141C	ENST00000366560	NM_000143.3	141	tgG/tgT	4/10	1	2	FACETS	0.38	0.3	0.472	0.38	0.3	0.472	SUBCLONAL	1	TRUE	1	0.28	2		316	489	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63661957	63661957	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	150	329	0	ENST00000279873.7:c.61T>G	p.Phe21Val	p.F21V	ENST00000279873	NM_032199.2	21	Ttc/Gtc	2/10	1	2	FACETS	0.9	0.826	0.977	1	0.991	1	CLONAL	2	TRUE	1	0.28	2		329	595	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845558	63845558	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	93	365	1	ENST00000279873.7:c.1297G>T	p.Glu433Ter	p.E433*	ENST00000279873	NM_032199.2	433	Gag/Tag	9/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.28	2		366	476	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851217	63851218	+	missense_variant	Missense_Mutation	DNP	CA	CA	AT	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	204	508	0	ENST00000279873.7:c.1995_1996delinsAT	p.Met666Leu	p.M666L	ENST00000279873	NM_032199.2	665	ccCAtg/ccATtg	10/10	1	2	FACETS	0.859	0.798	0.922	1	0.993	1	CLONAL	2	TRUE	1	0.28	2		508	848	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404898	70404898	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	58	447	0	ENST00000373644.4:c.2412G>T	p.Met804Ile	p.M804I	ENST00000373644	NM_030625.2	804	atG/atT	4/12	1	2	FACETS	0.712	0.611	0.821	0.712	0.611	0.821	SUBCLONAL	1	TRUE	1	0.28	2		447	582	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405447	70405447	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs774651932	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	216	541	0	ENST00000373644.4:c.2961C>A	p.Asn987Lys	p.N987K	ENST00000373644	NM_030625.2	987	aaC/aaA	4/12	1	2	FACETS	1	0.945	1	1	0.994	1	CLONAL	2	TRUE	1	0.28	2		541	760	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711914	89711914	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	130	464	0	ENST00000371953.3:c.532T>G	p.Tyr178Asp	p.Y178D	ENST00000371953	NM_000314.4	178	Tat/Gat	6/9	1	2	FACETS	0.831	0.757	0.908	1	0.988	1	CLONAL	2	TRUE	1	0.28	2		464	559	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717744	89717744	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	116	334	0	ENST00000371953.3:c.769T>A	p.Phe257Ile	p.F257I	ENST00000371953	NM_000314.4	257	Ttc/Atc	7/9	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.28	2		334	558	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573776	64573776	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	201	597	0	ENST00000312049.6:c.977G>T	p.Gly326Val	p.G326V	ENST00000312049	NM_130799.2	326	gGc/gTc	7/10	1	2	FACETS	0.865	0.803	0.929	1	0.993	1	CLONAL	2	TRUE	1	0.28	2		597	830	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77064612	77064612	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	196	464	0	ENST00000356341.3:c.805A>C	p.Lys269Gln	p.K269Q	ENST00000356341	NM_002576.4	269	Aaa/Caa	8/15	1	2	FACETS	0.822	0.762	0.884	1	0.992	1	CLONAL	2	TRUE	1	0.28	2		464	852	SUCCESS
EED	8726	MSKCC	GRCh37	11	85979605	85979605	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	123	338	0	ENST00000263360.6:c.966+2T>G		p.X322_splice	ENST00000263360	NM_003797.3	322			1	2	FACETS	0.86	0.781	0.941	1	0.988	1	CLONAL	2	TRUE	1	0.28	2		338	511	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121564	108121564	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660619	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	132	464	0	ENST00000278616.4:c.1372T>C	p.Cys458Arg	p.C458R	ENST00000278616	NM_000051.3	458	Tgc/Cgc	10/63	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.28	2		464	790	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150232	108150232	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs189445371	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	105	414	0	ENST00000278616.4:c.3299C>G	p.Thr1100Arg	p.T1100R	ENST00000278616	NM_000051.3	1100	aCg/aGg	23/63	1	2	FACETS	0.897	0.809	0.989	1	0.987	1	CLONAL	2	TRUE	1	0.28	2		414	418	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202199	108202199	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	90	374	0	ENST00000278616.4:c.7544A>C	p.Lys2515Thr	p.K2515T	ENST00000278616	NM_000051.3	2515	aAa/aCa	51/63	1	2	FACETS	0.913	0.817	1	1	0.985	1	CLONAL	2	TRUE	1	0.28	2		374	352	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374642	118374642	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	158	349	0	ENST00000534358.1:c.8035G>T	p.Glu2679Ter	p.E2679*	ENST00000534358	NM_005933.3	2679	Gaa/Taa	27/36	1	2	FACETS	0.973	0.896	1	1	0.992	1	CLONAL	2	TRUE	1	0.28	2		349	580	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374844	118374844	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	102	352	0	ENST00000534358.1:c.8237G>T	p.Arg2746Ile	p.R2746I	ENST00000534358	NM_005933.3	2746	aGa/aTa	27/36	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.28	2		352	487	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244924	46244924	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	193	538	0	ENST00000334344.6:c.3018G>C	p.Met1006Ile	p.M1006I	ENST00000334344	NM_152641.2	1006	atG/atC	15/21	1	2	FACETS	0.802	0.743	0.864	1	0.991	1	CLONAL	2	TRUE	1	0.28	2		538	859	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246017	46246017	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	144	355	0	ENST00000334344.6:c.4111C>A	p.His1371Asn	p.H1371N	ENST00000334344	NM_152641.2	1371	Cat/Aat	15/21	1	2	FACETS	1	0.937	1	1	0.991	1	CLONAL	2	TRUE	1	0.28	2		355	502	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246565	46246565	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	30	205	0	ENST00000334344.6:c.4659G>T	p.Met1553Ile	p.M1553I	ENST00000334344	NM_152641.2	1553	atG/atT	15/21	1	2	FACETS	0.502	0.404	0.613	0.502	0.404	0.613	SUBCLONAL	1	TRUE	1	0.28	2		205	427	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416430	49416430	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	168	439	0	ENST00000301067.7:c.16281T>G	p.Ile5427Met	p.I5427M	ENST00000301067	NM_003482.3	5427	atT/atG	51/54	1	2	FACETS	0.893	0.823	0.965	1	0.992	1	CLONAL	2	TRUE	1	0.28	2		439	672	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435720	49435720	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	161	495	0	ENST00000301067.7:c.6163G>T	p.Ala2055Ser	p.A2055S	ENST00000301067	NM_003482.3	2055	Gct/Tct	29/54	1	2	FACETS	0.896	0.825	0.969	1	0.991	1	CLONAL	2	TRUE	1	0.28	2		495	642	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437443	49437443	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	147	502	0	ENST00000301067.7:c.5442G>T	p.Arg1814Ser	p.R1814S	ENST00000301067	NM_003482.3	1814	agG/agT	23/54	1	2	FACETS	0.841	0.771	0.915	1	0.99	1	CLONAL	2	TRUE	1	0.28	2		502	624	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495012	56495012	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1357321306	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	67	520	0	ENST00000267101.3:c.3369C>A	p.Ser1123Arg	p.S1123R	ENST00000267101	NM_001982.3	1123	agC/agA	27/28	1	2	FACETS	0.636	0.551	0.727	0.636	0.551	0.727	SUBCLONAL	1	TRUE	1	0.28	2		520	753	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222641	69222641	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	194	519	0	ENST00000462284.1:c.614T>A	p.Leu205Gln	p.L205Q	ENST00000462284	NM_002392.5	205	cTg/cAg	8/11	1	2	FACETS	1	0.953	1	1	0.994	1	CLONAL	2	TRUE	1	0.28	2		519	671	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219175	133219175	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	185	595	0	ENST00000320574.5:c.4869C>A	p.Asp1623Glu	p.D1623E	ENST00000320574	NM_006231.2	1623	gaC/gaA	37/49	1	2	FACETS	0.856	0.792	0.922	1	0.992	1	CLONAL	2	TRUE	1	0.28	2		595	772	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249812	133249812	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs749021187	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	140	452	0	ENST00000320574.5:c.1411A>G	p.Met471Val	p.M471V	ENST00000320574	NM_006231.2	471	Atg/Gtg	14/49	1	2	FACETS	0.856	0.783	0.932	1	0.989	1	CLONAL	2	TRUE	1	0.28	2		452	584	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557761	21557761	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	182	548	0	ENST00000382592.4:c.2084C>A	p.Ala695Asp	p.A695D	ENST00000382592	NM_014572.2	695	gCc/gAc	5/8	NA	2	FACETS	0.894	0.827	0.963			1	INDETERMINATE	2	TRUE	NA	0.28	2		548	727	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562679	21562679	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs959120275	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	186	497	1	ENST00000382592.4:c.1240C>A	p.Pro414Thr	p.P414T	ENST00000382592	NM_014572.2	414	Ccg/Acg	4/8	NA	2	FACETS	0.918	0.85	0.987			1	INDETERMINATE	2	TRUE	NA	0.28	2		498	724	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28631537	28631537	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	50	434	0	ENST00000241453.7:c.431T>G	p.Phe144Cys	p.F144C	ENST00000241453	NM_004119.2	144	tTt/tGt	4/24	0.205694040898709	1	FACETS	0.627	0.532	0.731	0.627	0.532	0.731	SUBCLONAL	1	TRUE	0	0.28	1		434	490	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900709	32900709	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	29	452	0	ENST00000380152.3:c.590C>A	p.Ser197Tyr	p.S197Y	ENST00000380152		197	tCt/tAt	7/27	0.205694040898709	1	FACETS	0.35	0.28	0.43	0.35	0.28	0.43	SUBCLONAL	1	TRUE	0	0.28	1		452	509	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911098	32911098	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	104	397	0	ENST00000380152.3:c.2606C>A	p.Ser869Ter	p.S869*	ENST00000380152		869	tCa/tAa	11/27	0.205694040898709	1	FACETS	0.863	0.78	0.95	1	0.986	1	CLONAL	2	TRUE	0	0.28	1		397	370	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336244	73336244	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	58	248	0	ENST00000377767.4:c.2159C>A	p.Ser720Tyr	p.S720Y	ENST00000377767	NM_014953.3	720	tCt/tAt	17/21	1	2	FACETS	0.982	0.846	1	0.982	0.846	1	CLONAL	1	TRUE	1	0.28	2		248	422	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518658	103518658	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	54	311	0	ENST00000355739.4:c.2246C>A	p.Ser749Ter	p.S749*	ENST00000355739	NM_000123.3	749	tCa/tAa	10/15	1	2	FACETS	0.759	0.649	0.88	0.759	0.649	0.88	SUBCLONAL	1	TRUE	1	0.28	2		311	508	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519048	103519048	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	34	390	0	ENST00000355739.4:c.2386A>T	p.Ile796Phe	p.I796F	ENST00000355739	NM_000123.3	796	Atc/Ttc	11/15	1	2	FACETS	0.364	0.296	0.441	0.364	0.296	0.441	SUBCLONAL	1	TRUE	1	0.28	2		390	667	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527765	103527765	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	45	418	0	ENST00000355739.4:c.3073A>G	p.Lys1025Glu	p.K1025E	ENST00000355739	NM_000123.3	1025	Aaa/Gaa	15/15	1	2	FACETS	0.554	0.465	0.653	0.554	0.465	0.653	SUBCLONAL	1	TRUE	1	0.28	2		418	580	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093417	30093417	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	42	480	0	ENST00000331968.5:c.1846A>C	p.Lys616Gln	p.K616Q	ENST00000331968	NM_002742.2	616	Aaa/Caa	13/18	1	2	FACETS	0.909	0.762	1	0.909	0.762	1	CLONAL	1	TRUE	1	0.28	2		480	330	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989171	41989171	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs758377676	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	79	489	0	ENST00000219905.7:c.1963C>G	p.Pro655Ala	p.P655A	ENST00000219905	NM_001164273.1	655	Cct/Gct	3/24	1	2	FACETS	0.762	0.669	0.861	0.762	0.669	0.861	SUBCLONAL	1	TRUE	1	0.28	2		489	741	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035305	42035305	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	176	396	0	ENST00000219905.7:c.5147C>A	p.Ser1716Tyr	p.S1716Y	ENST00000219905	NM_001164273.1	1716	tCt/tAt	15/24	1	2	FACETS	1	0.937	1	1	0.993	1	CLONAL	2	TRUE	1	0.28	2		396	620	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041716	42041716	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	129	358	0	ENST00000219905.7:c.5911G>T	p.Glu1971Ter	p.E1971*	ENST00000219905	NM_001164273.1	1971	Gaa/Taa	17/24	1	2	FACETS	0.898	0.819	0.981	1	0.989	1	CLONAL	2	TRUE	1	0.28	2		358	513	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042019	42042019	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	169	563	0	ENST00000219905.7:c.6214A>G	p.Arg2072Gly	p.R2072G	ENST00000219905	NM_001164273.1	2072	Agg/Ggg	17/24	1	2	FACETS	0.92	0.849	0.994	1	0.992	1	CLONAL	2	TRUE	1	0.28	2		563	656	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714080	43714080	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	44	569	0	ENST00000382044.4:c.4073G>T	p.Ser1358Ile	p.S1358I	ENST00000382044	NM_001141980.1	1358	aGc/aTc	19/28	1	2	FACETS	0.383	0.32	0.454	0.383	0.32	0.454	SUBCLONAL	1	TRUE	1	0.28	2		569	820	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714231	43714231	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	185	643	0	ENST00000382044.4:c.3922A>T	p.Ser1308Cys	p.S1308C	ENST00000382044	NM_001141980.1	1308	Agc/Tgc	19/28	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.28	2		643	962	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748672	43748672	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	189	614	0	ENST00000382044.4:c.2134A>C	p.Met712Leu	p.M712L	ENST00000382044	NM_001141980.1	712	Atg/Ctg	12/28	1	2	FACETS	0.915	0.848	0.984	1	0.993	1	CLONAL	2	TRUE	1	0.28	2		614	738	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748747	43748747	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	99	600	0	ENST00000382044.4:c.2059G>T	p.Glu687Ter	p.E687*	ENST00000382044	NM_001141980.1	687	Gaa/Taa	12/28	1	2	FACETS	0.914	0.815	1	0.914	0.815	1	CLONAL	1	TRUE	1	0.28	2		600	774	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749379	43749379	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	124	410	0	ENST00000382044.4:c.1427C>A	p.Ser476Ter	p.S476*	ENST00000382044	NM_001141980.1	476	tCa/tAa	12/28	1	2	FACETS	1	0.927	1	1	0.99	1	CLONAL	2	TRUE	1	0.28	2		410	435	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483986	88483986	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	115	350	0	ENST00000360948.2:c.1586-2A>C		p.X529_splice	ENST00000360948	NM_001012338.2	529			1	2	FACETS	0.85	0.77	0.934	1	0.987	1	CLONAL	2	TRUE	1	0.28	2		350	483	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679723	88679723	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	51	431	0	ENST00000360948.2:c.740G>T	p.Gly247Val	p.G247V	ENST00000360948	NM_001012338.2	247	gGg/gTg	7/19	1	2	FACETS	0.512	0.434	0.598	0.512	0.434	0.598	SUBCLONAL	1	TRUE	1	0.28	2		431	711	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303464	91303464	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	32	412	0	ENST00000355112.3:c.1175A>G	p.Lys392Arg	p.K392R	ENST00000355112	NM_000057.2	392	aAa/aGa	6/22	1	2	FACETS	0.38	0.307	0.462	0.38	0.307	0.462	SUBCLONAL	1	TRUE	1	0.28	2		412	602	SUCCESS
BLM	641	MSKCC	GRCh37	15	91334044	91334044	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	26	355	0	ENST00000355112.3:c.2989G>T	p.Asp997Tyr	p.D997Y	ENST00000355112	NM_000057.2	997	Gat/Tat	15/22	1	2	FACETS	0.363	0.286	0.451	0.363	0.286	0.451	SUBCLONAL	1	TRUE	1	0.28	2		355	512	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467911	99467911	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	51	227	0	ENST00000268035.6:c.2780A>C	p.Lys927Thr	p.K927T	ENST00000268035	NM_000875.3	927	aAa/aCa	13/21	1	2	FACETS	0.908	0.774	1	0.908	0.774	1	CLONAL	1	TRUE	1	0.28	2		227	401	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396156	396156	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	139	340	0	ENST00000262320.3:c.870A>C	p.Arg290Ser	p.R290S	ENST00000262320	NM_003502.3	290	agA/agC	2/11	1	2	FACETS	0.971	0.89	1	1	0.991	1	CLONAL	2	TRUE	1	0.28	2		340	511	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2105486	2105486	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	227	535	0	ENST00000219476.3:c.565T>G	p.Cys189Gly	p.C189G	ENST00000219476	NM_000548.3	189	Tgt/Ggt	6/42	1	2	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	1	0.28	2		535	669	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778801	3778801	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	208	638	0	ENST00000262367.5:c.6247C>A	p.Gln2083Lys	p.Q2083K	ENST00000262367	NM_004380.2	2083	Caa/Aaa	31/31	1	2	FACETS	0.915	0.851	0.981	1	0.993	1	CLONAL	2	TRUE	1	0.28	2		638	812	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14028048	14028048	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	21	295	0	ENST00000311895.7:c.1103-1G>T		p.X368_splice	ENST00000311895	NM_005236.2	368			1	2	FACETS	0.515	0.397	0.653	0.515	0.397	0.653	SUBCLONAL	1	TRUE	1	0.28	2		295	291	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23635372	23635372	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs773831304	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	43	619	0	ENST00000261584.4:c.2792T>C	p.Leu931Pro	p.L931P	ENST00000261584	NM_024675.3	931	cTc/cCc	8/13	1	2	FACETS	0.611	0.511	0.721	0.611	0.511	0.721	SUBCLONAL	1	TRUE	1	0.28	2		619	503	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641772	23641772	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	45	289	1	ENST00000261584.4:c.1703A>T	p.Gln568Leu	p.Q568L	ENST00000261584	NM_024675.3	568	cAa/cTa	5/13	1	2	FACETS	0.974	0.822	1	0.974	0.822	1	CLONAL	1	TRUE	1	0.28	2		290	330	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647500	23647500	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	194	495	0	ENST00000261584.4:c.367G>T	p.Asp123Tyr	p.D123Y	ENST00000261584	NM_024675.3	123	Gac/Tac	4/13	1	2	FACETS	0.995	0.925	1	1	0.993	1	CLONAL	2	TRUE	1	0.28	2		495	696	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649233	23649233	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	49	398	0	ENST00000261584.4:c.149A>T	p.Lys50Ile	p.K50I	ENST00000261584	NM_024675.3	50	aAa/aTa	3/13	1	2	FACETS	0.746	0.633	0.871	0.746	0.633	0.871	SUBCLONAL	1	TRUE	1	0.28	2		398	469	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828412	72828413	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	154	393	1	ENST00000268489.5:c.8168dup	p.Thr2724AspfsTer4	p.T2724Dfs*4	ENST00000268489	NM_006885.3	2723	aag/aaAg	9/10	1	2	FACETS	0.857	0.787	0.929	1	0.99	1	CLONAL	2	TRUE	1	0.28	2		394	642	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993096	72993096	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	222	600	0	ENST00000268489.5:c.949C>A	p.Leu317Ile	p.L317I	ENST00000268489	NM_006885.3	317	Ctt/Att	2/10	1	2	FACETS	0.978	0.912	1	1	0.994	1	CLONAL	2	TRUE	1	0.28	2		600	811	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348650	89348650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	74	673	0	ENST00000301030.4:c.4300G>A	p.Glu1434Lys	p.E1434K	ENST00000301030	NM_001256183.1	1434	Gag/Aag	9/13	1	2	FACETS	0.737	0.645	0.837	0.737	0.645	0.837	SUBCLONAL	1	TRUE	1	0.28	2		673	717	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016566	12016566	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	36	284	0	ENST00000353533.5:c.702T>A	p.Asn234Lys	p.N234K	ENST00000353533	NM_003010.3	234	aaT/aaA	7/11	1	2	FACETS	0.559	0.459	0.671	0.559	0.459	0.671	SUBCLONAL	1	TRUE	1	0.28	2		284	460	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965140	15965140	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	72	309	0	ENST00000268712.3:c.5456A>G	p.Asp1819Gly	p.D1819G	ENST00000268712	NM_006311.3	1819	gAt/gGt	37/46	1	2	FACETS	0.89	0.778	1	0.89	0.778	1	CLONAL	1	TRUE	1	0.28	2		309	578	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663675	29663675	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	123	353	0	ENST00000356175.3:c.6107T>G	p.Ile2036Arg	p.I2036R	ENST00000356175	NM_000267.3	2036	aTa/aGa	41/57	1	2	FACETS	0.796	0.723	0.872	1	0.987	1	SUBCLONAL	2	TRUE	1	0.28	2		353	552	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37865697	37865697	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	47	465	0	ENST00000269571.5:c.566C>A	p.Ser189Tyr	p.S189Y	ENST00000269571		189	tCt/tAt	4/27	1	2	FACETS	0.614	0.517	0.72	0.614	0.517	0.72	SUBCLONAL	1	TRUE	1	0.28	2		465	547	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883981	37883981	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	65	525	0	ENST00000269571.5:c.3452C>A	p.Ser1151Ter	p.S1151*	ENST00000269571		1151	tCg/tAg	27/27	1	2	FACETS	0.645	0.558	0.739	0.645	0.558	0.739	SUBCLONAL	1	TRUE	1	0.28	2		525	720	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38504609	38504609	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	115	532	0	ENST00000254066.5:c.220A>G	p.Ser74Gly	p.S74G	ENST00000254066	NM_000964.3	74	Agc/Ggc	3/9	1	2	FACETS	0.988	0.89	1	0.988	0.89	1	CLONAL	1	TRUE	1	0.28	2		532	831	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40447738	40447738	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	51	578	0	ENST00000345506.4:c.477G>T	p.Glu159Asp	p.E159D	ENST00000345506	NM_003152.3	159	gaG/gaT	6/20	0.199689494643179	1	FACETS	0.375	0.318	0.439	0.375	0.318	0.439	SUBCLONAL	1	TRUE	0	0.28	1		578	835	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40860102	40860102	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	53	356	0	ENST00000428826.2:c.1535-1G>T		p.X512_splice	ENST00000428826		512			0.199689494643179	1	FACETS	0.719	0.614	0.833	0.719	0.614	0.833	SUBCLONAL	1	TRUE	0	0.28	1		356	453	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40860936	40860936	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	78	401	0	ENST00000428826.2:c.1494-2A>C		p.X498_splice	ENST00000428826		498			0.199689494643179	1	FACETS	0.808	0.711	0.912	0.808	0.711	0.912	CLONAL	1	TRUE	0	0.28	1		401	593	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245028	41245028	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	47	610	2	ENST00000357654.3:c.2520T>A	p.Ser840Arg	p.S840R	ENST00000357654	NM_007294.3	840	agT/agA	10/23	0.199689494643179	1	FACETS	0.375	0.316	0.442	0.375	0.316	0.442	SUBCLONAL	1	TRUE	0	0.28	1		612	769	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41258477	41258477	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	77	421	0	ENST00000357654.3:c.208A>T	p.Lys70Ter	p.K70*	ENST00000357654	NM_007294.3	70	Aaa/Taa	4/23	0.199689494643179	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.28	1		421	360	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436038	56436038	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	128	324	0	ENST00000407977.2:c.1099G>T	p.Ala367Ser	p.A367S	ENST00000407977		367	Gct/Tct	9/10	1	2	FACETS	0.929	0.847	1	1	0.99	1	CLONAL	2	TRUE	1	0.28	2		324	492	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492893	56492893	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	120	222	0	ENST00000407977.2:c.46C>A	p.Leu16Met	p.L16M	ENST00000407977		16	Ctg/Atg	2/10	1	2	FACETS	0.897	0.814	0.982	1	0.988	1	CLONAL	2	TRUE	1	0.28	2		222	478	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857697	59857697	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	116	397	0	ENST00000259008.2:c.1860G>T	p.Met620Ile	p.M620I	ENST00000259008	NM_032043.2	620	atG/atT	13/20	1	2	FACETS	0.776	0.702	0.853	1	0.985	1	SUBCLONAL	2	TRUE	1	0.28	2		397	534	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876642	59876642	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	137	254	0	ENST00000259008.2:c.1159G>T	p.Glu387Ter	p.E387*	ENST00000259008	NM_032043.2	387	Gaa/Taa	9/20	1	2	FACETS	0.893	0.816	0.973	1	0.99	1	CLONAL	2	TRUE	1	0.28	2		254	548	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117664	70117664	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	77	525	1	ENST00000245479.2:c.132G>T	p.Glu44Asp	p.E44D	ENST00000245479	NM_000346.3	44	gaG/gaT	1/3	1	2	FACETS	0.766	0.672	0.867	0.766	0.672	0.867	SUBCLONAL	1	TRUE	1	0.28	2		526	718	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39537617	39537617	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	83	325	1	ENST00000262039.4:c.151C>A	p.Gln51Lys	p.Q51K	ENST00000262039	NM_002647.2	51	Caa/Aaa	2/25	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.28	2		326	495	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615821	1615822	+	splice_acceptor_variant	Splice_Site	INS	-	-	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	29	369	0	ENST00000344749.5:c.1451-2_1451-1insT		p.X484_splice	ENST00000344749	NM_001136139.2	484			1	2	FACETS	0.487	0.391	0.597	0.487	0.391	0.597	SUBCLONAL	1	TRUE	1	0.28	2		369	425	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7167999	7167999	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	135	481	0	ENST00000302850.5:c.1590C>A	p.Phe530Leu	p.F530L	ENST00000302850	NM_000208.2	530	ttC/ttA	7/22	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.28	2		481	676	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602682	10602682	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	178	610	0	ENST00000171111.5:c.896A>T	p.Asp299Val	p.D299V	ENST00000171111	NM_203500.1	299	gAc/gTc	3/6	1	2	FACETS	0.909	0.841	0.98	1	0.992	1	CLONAL	2	TRUE	1	0.28	2		610	699	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350323	15350323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	126	418	1	ENST00000263377.2:c.3456G>T	p.Met1152Ile	p.M1152I	ENST00000263377	NM_058243.2	1152	atG/atT	17/20	1	2	FACETS	0.877	0.798	0.959	1	0.989	1	CLONAL	2	TRUE	1	0.28	2		419	513	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375259	15375259	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	72	491	0	ENST00000263377.2:c.1168T>G	p.Tyr390Asp	p.Y390D	ENST00000263377	NM_058243.2	390	Tac/Gac	6/20	1	2	FACETS	0.738	0.644	0.839	0.738	0.644	0.839	SUBCLONAL	1	TRUE	1	0.28	2		491	697	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223404	36223404	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	102	706	0	ENST00000222270.7:c.5954G>T	p.Gly1985Val	p.G1985V	ENST00000222270	NM_014727.1	1985	gGa/gTa	28/37	0.3	2	FACETS	0.797	0.712	0.888	0.399	0.356	0.444	SUBCLONAL	1	TRUE	0	0.28	2		706	914	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754506	42754506	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	47	578	0	ENST00000222329.4:c.234C>A	p.Tyr78Ter	p.Y78*	ENST00000222329	NM_006494.2	78	taC/taA	2/4	0.3	2	FACETS	0.42	0.353	0.494	0.21	0.176	0.247	SUBCLONAL	1	TRUE	0	0.28	2		578	800	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791255	42791255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	56	548	1	ENST00000575354.2:c.315C>A	p.Ser105Arg	p.S105R	ENST00000575354	NM_015125.3	105	agC/agA	3/20	0.3	2	FACETS	0.517	0.442	0.599	0.258	0.221	0.3	SUBCLONAL	1	TRUE	0	0.28	2		549	774	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222417	39222417	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	278	494	1	ENST00000402219.2:c.3193T>A	p.Tyr1065Asn	p.Y1065N	ENST00000402219	NM_005633.3	1065	Tat/Aat	20/23	1	2	FACETS	0.946	0.889	1	1	0.995	1	CLONAL	2	TRUE	1	0.28	2		495	1049	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705635	47705635	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	23	332	0	ENST00000233146.2:c.2435C>A	p.Thr812Asn	p.T812N	ENST00000233146	NM_000251.2	812	aCt/aAt	14/16	1	2	FACETS	0.387	0.301	0.486	0.387	0.301	0.486	SUBCLONAL	1	TRUE	1	0.28	2		332	425	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47709944	47709944	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	110	449	0	ENST00000233146.2:c.2661C>A	p.Phe887Leu	p.F887L	ENST00000233146	NM_000251.2	887	ttC/ttA	16/16	1	2	FACETS	0.873	0.789	0.961	1	0.987	1	CLONAL	2	TRUE	1	0.28	2		449	450	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028104	48028104	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	115	329	0	ENST00000234420.5:c.2982C>A	p.Tyr994Ter	p.Y994*	ENST00000234420	NM_000179.2	994	taC/taA	4/10	1	2	FACETS	0.801	0.725	0.88	1	0.986	1	CLONAL	2	TRUE	1	0.28	2		329	513	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032077	48032077	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876659549	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	95	326	0	ENST00000234420.5:c.3467T>C	p.Met1156Thr	p.M1156T	ENST00000234420	NM_000179.2	1156	aTg/aCg	6/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.28	2		326	482	SUCCESS
REL	5966	MSKCC	GRCh37	2	61144077	61144077	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	60	510	0	ENST00000295025.8:c.460G>C	p.Val154Leu	p.V154L	ENST00000295025	NM_002908.2	154	Gtt/Ctt	5/11	1	2	FACETS	0.797	0.687	0.916	0.797	0.687	0.916	CLONAL	1	TRUE	1	0.28	2		510	538	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715379	61715379	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	26	432	0	ENST00000401558.2:c.2234T>G	p.Ile745Ser	p.I745S	ENST00000401558	NM_003400.3	745	aTt/aGt	19/25	1	2	FACETS	0.51	0.404	0.632	0.51	0.404	0.632	SUBCLONAL	1	TRUE	1	0.28	2		432	364	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172062	99172062	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	55	460	0	ENST00000074304.5:c.1628A>T	p.Gln543Leu	p.Q543L	ENST00000074304	NM_001134224.1	543	cAg/cTg	17/26	1	2	FACETS	0.52	0.444	0.604	0.52	0.444	0.604	SUBCLONAL	1	TRUE	1	0.28	2		460	755	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095778	178095778	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	35	373	0	ENST00000397062.3:c.1553A>C	p.Lys518Thr	p.K518T	ENST00000397062	NM_006164.4	518	aAa/aCa	5/5	1	2	FACETS	0.424	0.347	0.512	0.424	0.347	0.512	SUBCLONAL	1	TRUE	1	0.28	2		373	589	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738249	190738249	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	43	278	0	ENST00000441310.2:c.2501A>T	p.Glu834Val	p.E834V	ENST00000441310	NM_000534.4	834	gAa/gTa	12/13	1	2	FACETS	0.737	0.617	0.869	0.737	0.617	0.869	SUBCLONAL	1	TRUE	1	0.28	2		278	417	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137479	202137479	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	89	511	0	ENST00000358485.4:c.707A>C	p.Asp236Ala	p.D236A	ENST00000358485	NM_001080125.1	236	gAc/gCc	4/9	1	2	FACETS	0.971	0.861	1	0.971	0.861	1	CLONAL	1	TRUE	1	0.28	2		511	655	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209103819	209103819	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	179	464	1	ENST00000345146.2:c.1130C>A	p.Ala377Asp	p.A377D	ENST00000345146	NM_005896.2	377	gCt/gAt	9/10	1	2	FACETS	0.943	0.872	1	1	0.992	1	CLONAL	2	TRUE	1	0.28	2		465	678	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215633994	215633994	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	150	493	0	ENST00000260947.4:c.1357G>T	p.Asp453Tyr	p.D453Y	ENST00000260947	NM_000465.2	453	Gat/Tat	5/11	1	2	FACETS	0.906	0.832	0.984	1	0.991	1	CLONAL	2	TRUE	1	0.28	2		493	591	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225367759	225367759	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	34	320	0	ENST00000264414.4:c.1408C>A	p.Leu470Met	p.L470M	ENST00000264414	NM_003590.4	470	Ctg/Atg	10/16	1	2	FACETS	0.506	0.413	0.611	0.506	0.413	0.611	SUBCLONAL	1	TRUE	1	0.28	2		320	480	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023417	31023417	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	51	436	1	ENST00000375687.4:c.2902A>T	p.Ser968Cys	p.S968C	ENST00000375687	NM_015338.5	968	Agt/Tgt	13/13	1	2	FACETS	0.584	0.495	0.681	0.584	0.495	0.681	SUBCLONAL	1	TRUE	1	0.28	2		437	624	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024383	31024383	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	87	519	0	ENST00000375687.4:c.3868G>T	p.Ala1290Ser	p.A1290S	ENST00000375687	NM_015338.5	1290	Gcc/Tcc	13/13	1	2	FACETS	0.779	0.689	0.875	0.779	0.689	0.875	SUBCLONAL	1	TRUE	1	0.28	2		519	798	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024849	31024849	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	86	526	0	ENST00000375687.4:c.4334C>A	p.Ser1445Tyr	p.S1445Y	ENST00000375687	NM_015338.5	1445	tCt/tAt	13/13	1	2	FACETS	0.839	0.742	0.943	0.839	0.742	0.943	CLONAL	1	TRUE	1	0.28	2		526	732	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733217	40733217	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	125	490	0	ENST00000373198.4:c.3589G>T	p.Glu1197Ter	p.E1197*	ENST00000373198	NM_133170.3	1197	Gaa/Taa	26/32	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.28	2		490	609	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264254	46264254	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	77	297	0	ENST00000371998.3:c.1301G>A	p.Gly434Glu	p.G434E	ENST00000371998		434	gGg/gAg	11/23	1	2	FACETS	0.952	0.836	1	0.952	0.836	1	CLONAL	1	TRUE	1	0.28	2		297	578	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54948528	54948528	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	28	427	0	ENST00000312783.6:c.790C>A	p.Leu264Ile	p.L264I	ENST00000312783	NM_198436.1	264	Ctt/Att	8/10	1	2	FACETS	0.365	0.291	0.45	0.365	0.291	0.45	SUBCLONAL	1	TRUE	1	0.28	2		427	548	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288217	21288217	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	175	559	1	ENST00000354336.3:c.462G>T	p.Glu154Asp	p.E154D	ENST00000354336	NM_005207.3	154	gaG/gaT	2/3	1	2	FACETS	0.954	0.882	1	1	0.992	1	CLONAL	2	TRUE	1	0.28	2		560	655	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143251	24143251	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	178	564	0	ENST00000263121.7:c.483G>C	p.Lys161Asn	p.K161N	ENST00000263121	NM_003073.3	161	aaG/aaC	4/9	1	2	FACETS	0.848	0.783	0.915	1	0.991	1	CLONAL	2	TRUE	1	0.28	2		564	750	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37637643	37637643	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	246	688	1	ENST00000249071.6:c.91G>T	p.Glu31Ter	p.E31*	ENST00000249071	NM_002872.4	31	Gag/Tag	2/7	1	2	FACETS	0.96	0.899	1	1	0.994	1	CLONAL	2	TRUE	1	0.28	2		689	915	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513231	41513232	+	stop_gained	Nonsense_Mutation	DNP	TG	TG	AT	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	40	494	0	ENST00000263253.7:c.135_136delinsAT	p.Asp45_Glu46delinsGluTer	p.D45_E46delinsE*	ENST00000263253	NM_001429.3	45	gaTGaa/gaATaa	2/31	1	2	FACETS	0.468	0.388	0.558	0.468	0.388	0.558	SUBCLONAL	1	TRUE	1	0.28	2		494	610	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573342	41573342	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	217	572	0	ENST00000263253.7:c.5627A>G	p.Gln1876Arg	p.Q1876R	ENST00000263253	NM_001429.3	1876	cAg/cGg	31/31	1	2	FACETS	0.915	0.852	0.979	1	0.993	1	CLONAL	2	TRUE	1	0.28	2		572	847	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12647784	12647784	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1463627261	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	151	387	0	ENST00000251849.4:c.596C>A	p.Ser199Tyr	p.S199Y	ENST00000251849	NM_002880.3	199	tCc/tAc	6/17	1	2	FACETS	0.995	0.915	1	1	0.992	1	CLONAL	2	TRUE	1	0.28	2		387	542	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37038202	37038202	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	106	223	1	ENST00000231790.2:c.207+2T>A		p.X69_splice	ENST00000231790	NM_000249.3	69			1	2	FACETS	1	0.938	1	1	0.989	1	CLONAL	2	TRUE	1	0.28	2		224	361	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37055950	37055950	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	35	334	0	ENST00000231790.2:c.705T>A	p.Asp235Glu	p.D235E	ENST00000231790	NM_000249.3	235	gaT/gaA	9/19	1	2	FACETS	0.527	0.432	0.635	0.527	0.432	0.635	SUBCLONAL	1	TRUE	1	0.28	2		334	474	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098653	47098653	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	223	483	0	ENST00000409792.3:c.6621G>T	p.Gln2207His	p.Q2207H	ENST00000409792	NM_014159.6	2207	caG/caT	15/21	1	2	FACETS	0.934	0.871	0.998	1	0.994	1	CLONAL	2	TRUE	1	0.28	2		483	853	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161911	47161911	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	102	316	0	ENST00000409792.3:c.4215A>C	p.Lys1405Asn	p.K1405N	ENST00000409792	NM_014159.6	1405	aaA/aaC	3/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.28	2		316	577	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162357	47162357	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	97	318	0	ENST00000409792.3:c.3769A>C	p.Asn1257His	p.N1257H	ENST00000409792	NM_014159.6	1257	Aac/Cac	3/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.28	2		318	516	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428570	72428570	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	37	241	0	ENST00000477973.2:c.434G>T	p.Arg145Leu	p.R145L	ENST00000477973	NM_012234.5	145	cGg/cTg	2/4	1	2	FACETS	0.646	0.533	0.773	0.646	0.533	0.773	SUBCLONAL	1	TRUE	1	0.28	2		241	409	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89478269	89478269	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	21	413	0	ENST00000336596.2:c.2088G>T	p.Met696Ile	p.M696I	ENST00000336596	NM_005233.5	696	atG/atT	12/17	1	2	FACETS	0.414	0.319	0.526	0.414	0.319	0.526	SUBCLONAL	1	TRUE	1	0.28	2		413	362	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199964	128199964	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1338194519	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	105	488	0	ENST00000341105.2:c.1341C>A	p.Ser447Arg	p.S447R	ENST00000341105	NM_032638.4	447	agC/agA	6/6	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.28	2		488	716	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851722	134851722	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	68	430	0	ENST00000398015.3:c.1128T>G	p.Asn376Lys	p.N376K	ENST00000398015	NM_004441.4	376	aaT/aaG	5/16	1	2	FACETS	0.803	0.699	0.916	0.803	0.699	0.916	CLONAL	1	TRUE	1	0.28	2		430	605	SUCCESS
ATR	545	MSKCC	GRCh37	3	142177934	142177934	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	157	393	0	ENST00000350721.4:c.7369T>G	p.Tyr2457Asp	p.Y2457D	ENST00000350721	NM_001184.3	2457	Tac/Gac	44/47	1	2	FACETS	0.918	0.844	0.994	1	0.991	1	CLONAL	2	TRUE	1	0.28	2		393	611	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170002254	170002254	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	32	136	0	ENST00000295797.4:c.1073A>T	p.Tyr358Phe	p.Y358F	ENST00000295797	NM_002740.5	358	tAc/tTc	12/18	1	2	FACETS	0.805	0.664	0.959	1	0.953	1	CLONAL	2	TRUE	1	0.28	2		136	142	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170016826	170016826	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	141	523	0	ENST00000295797.4:c.1631C>A	p.Ser544Tyr	p.S544Y	ENST00000295797	NM_002740.5	544	tCt/tAt	17/18	1	2	FACETS	0.862	0.789	0.939	1	0.99	1	CLONAL	2	TRUE	1	0.28	2		523	584	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170020904	170020904	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	26	79	0	ENST00000295797.4:c.1780G>T	p.Glu594Ter	p.E594*	ENST00000295797	NM_002740.5	594	Gaa/Taa	18/18	1	2	FACETS	0.957	0.776	1	1	0.954	1	CLONAL	2	TRUE	1	0.28	2		79	97	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928244	178928244	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	69	326	0	ENST00000263967.3:c.1430T>C	p.Phe477Ser	p.F477S	ENST00000263967	NM_006218.2	477	tTt/tCt	9/21	1	2	FACETS	0.826	0.719	0.94	0.826	0.719	0.94	CLONAL	1	TRUE	1	0.28	2		326	597	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957054	1957054	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	183	400	0	ENST00000382891.5:c.2505C>A	p.Phe835Leu	p.F835L	ENST00000382891	NM_133335.3	835	ttC/ttA	13/22	1	2	FACETS	1	0.96	1	1	0.993	1	CLONAL	2	TRUE	1	0.28	2		400	622	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1962782	1962782	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	138	347	0	ENST00000382891.5:c.3276C>A	p.Tyr1092Ter	p.Y1092*	ENST00000382891	NM_133335.3	1092	taC/taA	18/22	1	2	FACETS	0.819	0.748	0.893	1	0.989	1	CLONAL	2	TRUE	1	0.28	2		347	602	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980388	1980388	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	216	688	0	ENST00000382891.5:c.3850C>A	p.His1284Asn	p.H1284N	ENST00000382891	NM_133335.3	1284	Cat/Aat	22/22	1	2	FACETS	0.875	0.814	0.937	1	0.993	1	CLONAL	2	TRUE	1	0.28	2		688	882	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55569894	55569894	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	42	166	0	ENST00000288135.5:c.761A>C	p.Lys254Thr	p.K254T	ENST00000288135	NM_000222.2	254	aAa/aCa	5/21	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.28	2		166	245	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55569997	55569997	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	67	358	0	ENST00000288135.5:c.864C>A	p.Phe288Leu	p.F288L	ENST00000288135	NM_000222.2	288	ttC/ttA	5/21	1	2	FACETS	0.853	0.742	0.973	0.853	0.742	0.973	CLONAL	1	TRUE	1	0.28	2		358	561	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201795	66201795	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	208	438	0	ENST00000273854.3:c.2707T>G	p.Cys903Gly	p.C903G	ENST00000273854	NM_004439.5	903	Tgt/Ggt	16/18	1	2	FACETS	0.85	0.79	0.912	1	0.993	1	CLONAL	2	TRUE	1	0.28	2		438	874	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218770	66218770	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	17	341	0	ENST00000273854.3:c.2288C>A	p.Thr763Lys	p.T763K	ENST00000273854	NM_004439.5	763	aCa/aAa	13/18	1	2	FACETS	0.422	0.314	0.549	0.422	0.314	0.549	SUBCLONAL	1	TRUE	1	0.28	2		341	288	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467884	66467884	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	134	461	0	ENST00000273854.3:c.385G>T	p.Glu129Ter	p.E129*	ENST00000273854	NM_004439.5	129	Gaa/Taa	3/18	1	2	FACETS	0.924	0.844	1	1	0.99	1	CLONAL	2	TRUE	1	0.28	2		461	518	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196515	106196515	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	149	342	0	ENST00000380013.4:c.4848C>A	p.Asn1616Lys	p.N1616K	ENST00000380013	NM_001127208.2	1616	aaC/aaA	11/11	0.29317737234638	3	FACETS	0.998	0.915	1	0.998	0.915	1	CLONAL	2	TRUE	1	0.28	3		342	608	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143043391	143043391	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs749719033	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	64	340	0	ENST00000262992.4:c.2025A>C	p.Glu675Asp	p.E675D	ENST00000262992	NM_001101669.1	675	gaA/gaC	19/24	0.29317737234638	3	FACETS	0.969	0.84	1	0.484	0.42	0.554	CLONAL	1	TRUE	1	0.28	3		340	538	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143044445	143044445	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	133	288	0	ENST00000262992.4:c.2017A>C	p.Ser673Arg	p.S673R	ENST00000262992	NM_001101669.1	673	Agc/Cgc	18/24	0.29317737234638	3	FACETS	0.938	0.861	1	1	0.986	1	CLONAL	3	TRUE	1	0.28	3		288	385	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249367	153249367	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	155	376	0	ENST00000281708.4:c.1411G>T	p.Glu471Ter	p.E471*	ENST00000281708	NM_033632.3	471	Gaa/Taa	9/12	0.29317737234638	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.28	3		376	598	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249460	153249460	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	58	465	0	ENST00000281708.4:c.1318G>T	p.Asp440Tyr	p.D440Y	ENST00000281708	NM_033632.3	440	Gat/Tat	9/12	0.29317737234638	3	FACETS	0.6	0.514	0.694	0.3	0.257	0.347	SUBCLONAL	1	TRUE	1	0.28	3		465	787	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253775	153253775	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	149	341	1	ENST00000281708.4:c.958C>A	p.Leu320Ile	p.L320I	ENST00000281708	NM_033632.3	320	Ctc/Atc	6/12	0.29317737234638	3	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	1	0.28	3		342	598	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516884	187516884	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	49	399	0	ENST00000441802.2:c.13097A>G	p.Gln4366Arg	p.Q4366R	ENST00000441802	NM_005245.3	4366	cAg/cGg	26/27	1	2	FACETS	0.494	0.417	0.578	0.494	0.417	0.578	SUBCLONAL	1	TRUE	1	0.28	2		399	709	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517799	187517799	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	25	241	0	ENST00000441802.2:c.12895G>C	p.Val4299Leu	p.V4299L	ENST00000441802	NM_005245.3	4299	Gtg/Ctg	25/27	1	2	FACETS	0.419	0.33	0.522	0.419	0.33	0.522	SUBCLONAL	1	TRUE	1	0.28	2		241	426	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627919	187627919	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	74	565	0	ENST00000441802.2:c.3063G>T	p.Glu1021Asp	p.E1021D	ENST00000441802	NM_005245.3	1021	gaG/gaT	2/27	1	2	FACETS	0.657	0.574	0.746	0.657	0.574	0.746	SUBCLONAL	1	TRUE	1	0.28	2		565	805	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39021146	39021146	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1443609803	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	106	302	0	ENST00000357387.3:c.190A>T	p.Thr64Ser	p.T64S	ENST00000357387	NM_152756.3	64	Act/Tct	3/38	0.29317737234638	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.28	3		302	369	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111794	56111794	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs557606535	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	10	42	0	ENST00000399503.3:c.394G>A	p.Asp132Asn	p.D132N	ENST00000399503	NM_005921.1	132	Gac/Aac	1/20	0.29317737234638	3	FACETS	1	0.753	1	0.558	0.383	0.769	CLONAL	1	TRUE	1	0.28	3		42	73	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177947	56177947	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	173	391	1	ENST00000399503.3:c.2920C>A	p.His974Asn	p.H974N	ENST00000399503	NM_005921.1	974	Cat/Aat	14/20	0.29317737234638	3	FACETS	0.995	0.918	1	0.995	0.918	1	CLONAL	2	TRUE	1	0.28	3		392	708	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752372	57752372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	107	307	0	ENST00000274289.3:c.1201G>A	p.Asp401Asn	p.D401N	ENST00000274289	NM_006622.3	401	Gat/Aat	9/14	0.29317737234638	3	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	1	0.28	3		307	409	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755531	57755531	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	170	444	0	ENST00000274289.3:c.256A>T	p.Lys86Ter	p.K86*	ENST00000274289	NM_006622.3	86	Aaa/Taa	1/14	0.29317737234638	3	FACETS	0.976	0.9	1	0.976	0.9	1	CLONAL	2	TRUE	1	0.28	3		444	709	SUCCESS
APC	324	MSKCC	GRCh37	5	112175364	112175364	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	33	223	0	ENST00000257430.4:c.4073C>A	p.Ala1358Glu	p.A1358E	ENST00000257430	NM_000038.5	1358	gCg/gAg	16/16	1	2	FACETS	0.557	0.454	0.674	0.557	0.454	0.674	SUBCLONAL	1	TRUE	1	0.28	2		223	423	SUCCESS
APC	324	MSKCC	GRCh37	5	112177286	112177286	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	137	320	0	ENST00000257430.4:c.5995C>A	p.Pro1999Thr	p.P1999T	ENST00000257430	NM_000038.5	1999	Cca/Aca	16/16	1	2	FACETS	0.92	0.841	1	1	0.99	1	CLONAL	2	TRUE	1	0.28	2		320	532	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944976	131944976	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	86	242	0	ENST00000265335.6:c.2924A>C	p.Gln975Pro	p.Q975P	ENST00000265335		975	cAa/cCa	19/25	1	2	FACETS	0.86	0.767	0.958	1	0.983	1	CLONAL	2	TRUE	1	0.28	2		242	357	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501556	149501556	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	44	451	0	ENST00000261799.4:c.2231G>T	p.Ser744Ile	p.S744I	ENST00000261799	NM_002609.3	744	aGc/aTc	16/23	1	2	FACETS	0.478	0.4	0.564	0.478	0.4	0.564	SUBCLONAL	1	TRUE	1	0.28	2		451	658	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510194	149510194	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	109	520	0	ENST00000261799.4:c.1275C>A	p.Ser425Arg	p.S425R	ENST00000261799	NM_002609.3	425	agC/agA	9/23	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.28	2		520	759	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176666868	176666868	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	43	293	0	ENST00000439151.2:c.4302+2T>A		p.X1434_splice	ENST00000439151	NM_022455.4	1434			1	2	FACETS	0.981	0.825	1	0.981	0.825	1	CLONAL	1	TRUE	1	0.28	2		293	313	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250530	26250530	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1445488826	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	63	510	0	ENST00000446824.2:c.304G>T	p.Val102Leu	p.V102L	ENST00000446824	NM_021018.2	102	Gtg/Ttg	1/1	1	2	FACETS	0.582	0.502	0.669	0.582	0.502	0.669	SUBCLONAL	1	TRUE	1	0.28	2		510	773	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681850	30681850	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	191	501	0	ENST00000376406.3:c.247T>A	p.Trp83Arg	p.W83R	ENST00000376406	NM_014641.2	83	Tgg/Agg	3/15	1	2	FACETS	0.898	0.832	0.965	1	0.993	1	CLONAL	2	TRUE	1	0.28	2		501	760	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168948	32168948	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	217	625	0	ENST00000375023.3:c.4085G>T	p.Arg1362Ile	p.R1362I	ENST00000375023	NM_004557.3	1362	aGa/aTa	22/30	1	2	FACETS	0.904	0.842	0.968	1	0.993	1	CLONAL	2	TRUE	1	0.28	2		625	857	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188288	32188288	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	56	631	0	ENST00000375023.3:c.1053C>A	p.Ser351Arg	p.S351R	ENST00000375023	NM_004557.3	351	agC/agA	6/30	1	2	FACETS	0.48	0.41	0.557	0.48	0.41	0.557	SUBCLONAL	1	TRUE	1	0.28	2		631	833	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289126	33289126	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	96	525	1	ENST00000374542.5:c.426G>T	p.Lys142Asn	p.K142N	ENST00000374542	NM_001141970.1	142	aaG/aaT	3/8	1	2	FACETS	0.906	0.807	1	0.906	0.807	1	CLONAL	1	TRUE	1	0.28	2		526	757	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33290664	33290664	+	5_prime_UTR_variant	5'UTR	SNP	C	C	G	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	226	525	0	ENST00000374542.5:c.-78G>C		p.*26*	ENST00000374542	NM_001141970.1	-/740		1/8	1	2	FACETS	0.955	0.892	1	1	0.994	1	CLONAL	2	TRUE	1	0.28	2		525	845	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979344	93979344	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	28	369	0	ENST00000369303.4:c.1484C>A	p.Thr495Asn	p.T495N	ENST00000369303	NM_004440.3	495	aCc/aAc	7/17	1	2	FACETS	0.363	0.289	0.448	0.363	0.289	0.448	SUBCLONAL	1	TRUE	1	0.28	2		369	551	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066545	94066545	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	101	344	0	ENST00000369303.4:c.1214T>A	p.Leu405Gln	p.L405Q	ENST00000369303	NM_004440.3	405	cTg/cAg	5/17	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.28	2		344	611	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120421	94120421	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	143	316	0	ENST00000369303.4:c.630G>T	p.Glu210Asp	p.E210D	ENST00000369303	NM_004440.3	210	gaG/gaT	3/17	1	2	FACETS	0.904	0.828	0.983	1	0.99	1	CLONAL	2	TRUE	1	0.28	2		316	565	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553295	106553295	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	155	381	0	ENST00000369096.4:c.1260G>T	p.Met420Ile	p.M420I	ENST00000369096	NM_001198.3	420	atG/atT	5/7	1	2	FACETS	0.921	0.847	0.998	1	0.991	1	CLONAL	2	TRUE	1	0.28	2		381	601	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109309868	109309868	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	63	390	0	ENST00000436639.2:c.1447G>T	p.Glu483Ter	p.E483*	ENST00000436639	NM_014454.2	483	Gaa/Taa	9/10	1	2	FACETS	0.794	0.687	0.91	0.794	0.687	0.91	CLONAL	1	TRUE	1	0.28	2		390	567	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109415183	109415183	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	260	735	0	ENST00000436639.2:c.94A>T	p.Ile32Phe	p.I32F	ENST00000436639	NM_014454.2	32	Att/Ttt	1/10	1	2	FACETS	0.776	0.726	0.827	1	0.993	1	SUBCLONAL	2	TRUE	1	0.28	2		735	1197	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638425	117638425	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	134	345	0	ENST00000368508.3:c.6016C>A	p.His2006Asn	p.H2006N	ENST00000368508	NM_002944.2	2006	Cat/Aat	38/43	1	2	FACETS	0.922	0.842	1	1	0.99	1	CLONAL	2	TRUE	1	0.28	2		345	519	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678991	117678991	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	79	340	0	ENST00000368508.3:c.3830C>A	p.Ser1277Tyr	p.S1277Y	ENST00000368508	NM_002944.2	1277	tCt/tAt	24/43	1	2	FACETS	0.769	0.681	0.862	1	0.979	1	SUBCLONAL	2	TRUE	1	0.28	2		340	367	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525576	137525576	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	120	494	0	ENST00000367739.4:c.439C>A	p.His147Asn	p.H147N	ENST00000367739	NM_000416.2	147	Cac/Aac	4/7	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.28	2		494	746	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200335	138200335	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	170	346	0	ENST00000237289.4:c.1753G>T	p.Asp585Tyr	p.D585Y	ENST00000237289	NM_001270507.1	585	Gac/Tac	7/9	1	2	FACETS	0.99	0.915	1	1	0.992	1	CLONAL	2	TRUE	1	0.28	2		346	613	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983088	149983088	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	56	466	0	ENST00000253339.5:c.3170T>A	p.Val1057Glu	p.V1057E	ENST00000253339		1057	gTa/gAa	7/7	1	2	FACETS	0.593	0.508	0.687	0.593	0.508	0.687	SUBCLONAL	1	TRUE	1	0.28	2		466	674	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100090	157100090	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	27	38	0	ENST00000346085.5:c.1027G>T	p.Ala343Ser	p.A343S	ENST00000346085	NM_020732.3	343	Gcc/Tcc	1/20	1	2	FACETS	1	0.828	1	1	0.958	1	CLONAL	2	TRUE	1	0.28	2		38	95	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426860	6426860	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	119	440	0	ENST00000356142.4:c.53G>T	p.Cys18Phe	p.C18F	ENST00000356142	NM_018890.3	18	tGc/tTc	2/7	0.139948027442252	0	FACETS	0.64	0.581	0.702			1	INDETERMINATE	2	TRUE	0	0.28	0		440	478	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509393	106509393	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	189	457	0	ENST00000359195.3:c.1387T>G	p.Tyr463Asp	p.Y463D	ENST00000359195	NM_002649.2	463	Tat/Gat	2/11	1	2	FACETS	0.884	0.818	0.951	1	0.992	1	CLONAL	2	TRUE	1	0.28	2		457	764	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509790	106509790	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	187	546	0	ENST00000359195.3:c.1784C>A	p.Ser595Ter	p.S595*	ENST00000359195	NM_002649.2	595	tCa/tAa	2/11	1	2	FACETS	0.91	0.843	0.979	1	0.992	1	CLONAL	2	TRUE	1	0.28	2		546	734	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339815	116339815	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	38	363	0	ENST00000397752.3:c.677T>G	p.Phe226Cys	p.F226C	ENST00000397752	NM_000245.2	226	tTt/tGt	2/21	1	2	FACETS	0.408	0.336	0.489	0.408	0.336	0.489	SUBCLONAL	1	TRUE	1	0.28	2		363	665	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380994	116380994	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	120	467	0	ENST00000397752.3:c.1616G>T	p.Gly539Val	p.G539V	ENST00000397752	NM_000245.2	539	gGc/gTc	5/21	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.28	2		467	857	SUCCESS
MET	4233	MSKCC	GRCh37	7	116413487	116413488	+	intron_variant	Intron	INS	-	-	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1227	97	719	0	ENST00000397752.3:c.3028+1444_3028+1445insT		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.523	0.465	0.586	0.523	0.465	0.586	SUBCLONAL	1	TRUE	1	0.28	2		719	1324	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843334	128843334	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	58	625	1	ENST00000249373.3:c.441C>A	p.Cys147Ter	p.C147*	ENST00000249373	NM_005631.4	147	tgC/tgA	2/12	1	2	FACETS	0.55	0.472	0.636	0.55	0.472	0.636	SUBCLONAL	1	TRUE	1	0.28	2		626	753	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477797	140477797	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	45	439	0	ENST00000288602.6:c.1511T>A	p.Val504Glu	p.V504E	ENST00000288602	NM_004333.4	504	gTa/gAa	12/18	1	2	FACETS	0.587	0.492	0.691	0.587	0.492	0.691	SUBCLONAL	1	TRUE	1	0.28	2		439	548	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860875	151860875	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	140	322	0	ENST00000262189.6:c.9787G>T	p.Glu3263Ter	p.E3263*	ENST00000262189	NM_170606.2	3263	Gaa/Taa	43/59	1	2	FACETS	0.931	0.852	1	1	0.99	1	CLONAL	2	TRUE	1	0.28	2		322	537	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007058	152007058	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	35	316	0	ENST00000262189.6:c.842G>T	p.Ser281Ile	p.S281I	ENST00000262189	NM_170606.2	281	aGc/aTc	6/59	1	2	FACETS	0.524	0.429	0.631	0.524	0.429	0.631	SUBCLONAL	1	TRUE	1	0.28	2		316	477	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346080	152346080	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	144	399	0	ENST00000359321.1:c.490G>T	p.Glu164Ter	p.E164*	ENST00000359321	NM_005431.1	164	Gaa/Taa	3/3	1	2	FACETS	0.922	0.845	1	1	0.991	1	CLONAL	2	TRUE	1	0.28	2		399	558	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540165	23540165	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	173	329	1	ENST00000380871.4:c.238C>A	p.Pro80Thr	p.P80T	ENST00000380871	NM_006167.3	80	Ccc/Acc	1/2	1	2	FACETS	1	0.961	1	1	0.993	1	CLONAL	2	TRUE	1	0.28	2		330	584	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38139074	38139074	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	145	539	0	ENST00000317025.8:c.3529G>T	p.Glu1177Ter	p.E1177*	ENST00000317025	NM_023034.1	1177	Gaa/Taa	20/24	1	2	FACETS	0.921	0.845	1	1	0.991	1	CLONAL	2	TRUE	1	0.28	2		539	562	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272129	38272129	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1563433902	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	74	578	0	ENST00000425967.3:c.2089T>C	p.Trp697Arg	p.W697R	ENST00000425967	NM_001174067.1	697	Tgg/Cgg	16/19	1	2	FACETS	0.642	0.561	0.73	0.642	0.561	0.73	SUBCLONAL	1	TRUE	1	0.28	2		578	823	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372044	55372044	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	60	516	0	ENST00000297316.4:c.734G>T	p.Cys245Phe	p.C245F	ENST00000297316	NM_022454.3	245	tGc/tTc	2/2	1	2	FACETS	0.59	0.508	0.681	0.59	0.508	0.681	SUBCLONAL	1	TRUE	1	0.28	2		516	726	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965872	90965872	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs775451862	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	81	262	0	ENST00000265433.3:c.1445G>T	p.Arg482Ile	p.R482I	ENST00000265433	NM_002485.4	482	aGa/aTa	11/16	1	2	FACETS	0.851	0.756	0.951	1	0.982	1	CLONAL	2	TRUE	1	0.28	2		262	340	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866698	117866698	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	42	298	1	ENST00000297338.2:c.947C>A	p.Thr316Lys	p.T316K	ENST00000297338	NM_006265.2	316	aCa/aAa	9/14	1	2	FACETS	0.548	0.457	0.65	0.548	0.457	0.65	SUBCLONAL	1	TRUE	1	0.28	2		299	547	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868987	117868987	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	41	417	0	ENST00000297338.2:c.712G>T	p.Asp238Tyr	p.D238Y	ENST00000297338	NM_006265.2	238	Gat/Tat	7/14	1	2	FACETS	0.389	0.323	0.463	0.389	0.323	0.463	SUBCLONAL	1	TRUE	1	0.28	2		417	752	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869578	117869578	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	102	377	0	ENST00000297338.2:c.616A>C	p.Ile206Leu	p.I206L	ENST00000297338	NM_006265.2	206	Att/Ctt	6/14	1	2	FACETS	1	0.913	1	1	0.988	1	CLONAL	2	TRUE	1	0.28	2		377	360	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542156	141542157	+	missense_variant	Missense_Mutation	DNP	AT	AT	CA	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	185	543	1	ENST00000220592.5:c.2566_2567delinsTG	p.Met856Trp	p.M856W	ENST00000220592	NM_012154.3	856	ATg/TGg	19/19	1	2	FACETS	0.956	0.886	1	1	0.993	1	CLONAL	2	TRUE	1	0.28	2		544	691	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141569503	141569503	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	42	355	0	ENST00000220592.5:c.781G>T	p.Glu261Ter	p.E261*	ENST00000220592	NM_012154.3	261	Gaa/Taa	6/19	1	2	FACETS	0.575	0.479	0.681	0.575	0.479	0.681	SUBCLONAL	1	TRUE	1	0.28	2		355	522	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080314	5080314	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	46	315	0	ENST00000381652.3:c.2217T>A	p.Phe739Leu	p.F739L	ENST00000381652	NM_004972.3	739	ttT/ttA	17/25	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.28	2		315	316	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5557746	5557746	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	25	304	0	ENST00000397747.3:c.760T>G	p.Ser254Ala	p.S254A	ENST00000397747	NM_025239.3	254	Tca/Gca	5/7	1	2	FACETS	0.392	0.309	0.489	0.392	0.309	0.489	SUBCLONAL	1	TRUE	1	0.28	2		304	455	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340365	8340365	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	58	445	0	ENST00000356435.5:c.5231C>A	p.Thr1744Asn	p.T1744N	ENST00000356435		1744	aCc/aAc	31/35	1	2	FACETS	0.537	0.46	0.621	0.537	0.46	0.621	SUBCLONAL	1	TRUE	1	0.28	2		445	772	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180250	27180250	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	65	434	0	ENST00000380036.4:c.914G>T	p.Gly305Val	p.G305V	ENST00000380036	NM_000459.3	305	gGt/gTt	7/23	1	2	FACETS	0.605	0.523	0.693	0.605	0.523	0.693	SUBCLONAL	1	TRUE	1	0.28	2		434	768	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27203047	27203047	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	211	472	0	ENST00000380036.4:c.2139T>A	p.Phe713Leu	p.F713L	ENST00000380036	NM_000459.3	713	ttT/ttA	13/23	1	2	FACETS	0.868	0.807	0.931	1	0.993	1	CLONAL	2	TRUE	1	0.28	2		472	868	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563469	87563469	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	45	552	0	ENST00000277120.3:c.1857C>A	p.Phe619Leu	p.F619L	ENST00000277120		619	ttC/ttA	16/19	1	2	FACETS	0.406	0.34	0.479	0.406	0.34	0.479	SUBCLONAL	1	TRUE	1	0.28	2		552	792	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268780	98268780	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	40	500	0	ENST00000331920.6:c.303C>A	p.Phe101Leu	p.F101L	ENST00000331920	NM_000264.3	101	ttC/ttA	2/24	1	2	FACETS	0.396	0.328	0.472	0.396	0.328	0.472	SUBCLONAL	1	TRUE	1	0.28	2		500	722	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904859	101904859	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	124	346	0	ENST00000374994.4:c.847C>A	p.His283Asn	p.H283N	ENST00000374994	NM_004612.2	283	Cat/Aat	5/9	1	2	FACETS	0.858	0.78	0.939	1	0.988	1	CLONAL	2	TRUE	1	0.28	2		346	516	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750269	133750269	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	142	399	1	ENST00000318560.5:c.1100G>T	p.Arg367Leu	p.R367L	ENST00000318560	NM_005157.4	367	cGa/cTa	7/11	1	2	FACETS	0.936	0.857	1	1	0.991	1	CLONAL	2	TRUE	1	0.28	2		400	542	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771828	135771828	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	192	546	0	ENST00000298552.3:c.3289C>A	p.Arg1097Ser	p.R1097S	ENST00000298552	NM_001162426.1	1097	Cgt/Agt	23/23	1	2	FACETS	0.88	0.816	0.947	1	0.992	1	CLONAL	2	TRUE	1	0.28	2		546	779	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776186	135776186	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	168	494	0	ENST00000298552.3:c.2541C>A	p.Phe847Leu	p.F847L	ENST00000298552	NM_001162426.1	847	ttC/ttA	20/23	1	2	FACETS	0.886	0.817	0.958	1	0.991	1	CLONAL	2	TRUE	1	0.28	2		494	677	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781494	135781494	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	119	386	0	ENST00000298552.3:c.1471A>G	p.Thr491Ala	p.T491A	ENST00000298552	NM_001162426.1	491	Aca/Gca	15/23	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.28	2		386	579	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934085	39934085	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs776199630	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	40	484	0	ENST00000378444.4:c.514G>T	p.Ala172Ser	p.A172S	ENST00000378444	NM_001123385.1	172	Gcc/Tcc	4/15	1	2	FACETS	0.398	0.33	0.475	0.398	0.33	0.475	SUBCLONAL	1	TRUE	1	0.28	2		484	717	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949993	44949993	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	32	411	0	ENST00000377967.4:c.3762A>C	p.Glu1254Asp	p.E1254D	ENST00000377967	NM_021140.2	1254	gaA/gaC	26/29	1	2	FACETS	0.405	0.327	0.492	0.405	0.327	0.492	SUBCLONAL	1	TRUE	1	0.28	2		411	565	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045488	47045488	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	52	561	0	ENST00000377604.3:c.2455G>T	p.Ala819Ser	p.A819S	ENST00000377604	NM_001204468.1	819	Gct/Tct	22/24	1	2	FACETS	0.507	0.431	0.592	0.507	0.431	0.592	SUBCLONAL	1	TRUE	1	0.28	2		561	732	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410124	63410124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	187	564	0	ENST00000330258.3:c.3043G>A	p.Glu1015Lys	p.E1015K	ENST00000330258	NM_152424.3	1015	Gaa/Aaa	2/2	1	2	FACETS	0.871	0.806	0.938	1	0.992	1	CLONAL	2	TRUE	1	0.28	2		564	767	SUCCESS
AR	367	MSKCC	GRCh37	X	66931354	66931354	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	135	476	0	ENST00000374690.3:c.1996G>T	p.Glu666Ter	p.E666*	ENST00000374690	NM_000044.3	666	Gaa/Taa	4/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.28	2		476	749	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875930	76875930	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	111	533	1	ENST00000373344.5:c.5205G>T	p.Met1735Ile	p.M1735I	ENST00000373344	NM_000489.3	1735	atG/atT	20/35	1	2	FACETS	0.877	0.793	0.964	1	0.987	1	CLONAL	2	TRUE	1	0.28	2		534	452	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626663	100626663	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	61	459	0	ENST00000308731.7:c.267G>T	p.Met89Ile	p.M89I	ENST00000308731	NM_000061.2	89	atG/atT	4/19	1	2	FACETS	0.669	0.577	0.77	0.669	0.577	0.77	SUBCLONAL	1	TRUE	1	0.28	2		459	651	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191825	123191825	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	17	369	0	ENST00000218089.9:c.1414G>T	p.Glu472Ter	p.E472*	ENST00000218089	NM_001042749.1	472	Gag/Tag	15/35	1	2	FACETS	0.362	0.27	0.473	0.362	0.27	0.473	SUBCLONAL	1	TRUE	1	0.28	2		369	335	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224604	123224604	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	40	395	1	ENST00000218089.9:c.3457C>A	p.Leu1153Ile	p.L1153I	ENST00000218089	NM_001042749.1	1153	Ctt/Att	31/35	1	2	FACETS	0.52	0.432	0.619	0.52	0.432	0.619	SUBCLONAL	1	TRUE	1	0.28	2		396	549	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224726	123224726	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	99	415	0	ENST00000218089.9:c.3490G>T	p.Ala1164Ser	p.A1164S	ENST00000218089	NM_001042749.1	1164	Gct/Tct	32/35	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.28	2		415	628	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224754	123224754	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	223	473	0	ENST00000218089.9:c.3518A>G	p.Gln1173Arg	p.Q1173R	ENST00000218089	NM_001042749.1	1173	cAa/cGa	32/35	1	2	FACETS	1	0.98	1	1	0.995	1	CLONAL	2	TRUE	1	0.28	2		473	713	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0029790-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	33	380	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	0.474	0.385	0.575	0.474	0.385	0.575	SUBCLONAL	1	TRUE	1	0.22	2		380	633	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0029790-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	139	230	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.871	0.795	0.952	1	0.989	1	CLONAL	2	TRUE	1	0.22	2		230	725	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0029790-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	89	760	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	0.928	0.821	1	0.928	0.821	1	CLONAL	1	TRUE	1	0.22	2		760	872	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0029790-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	111	525	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	1	2	FACETS	0.891	0.799	0.99	0.891	0.799	0.99	CLONAL	1	TRUE	1	0.22	2		525	1132	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117861203	117861203	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029790-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	43	378	0	ENST00000297338.2:c.1686G>C	p.Gln562His	p.Q562H	ENST00000297338	NM_006265.2	562	caG/caC	13/14	1	2	FACETS	0.59	0.493	0.699	0.59	0.493	0.699	SUBCLONAL	1	TRUE	1	0.22	2		378	662	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15809122	15809122	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029790-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	50	229	0	ENST00000307771.7:c.107G>A	p.Arg36Gln	p.R36Q	ENST00000307771	NM_005089.3	36	cGa/cAa	2/11	1	1	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	0	0.22	1		229	368	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971053	21971054	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0029790-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	95	400	0	ENST00000304494.5:c.304dup	p.Ala102GlyfsTer18	p.A102Gfs*18	ENST00000304494	NM_000077.4	102	gcg/gGcg	2/3	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.22	2		400	727	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542087	187542088	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029790-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	67	252	0	ENST00000441802.2:c.5652dup	p.Glu1885Ter	p.E1885*	ENST00000441802	NM_005245.3	1884	-/T	10/27	1	2	FACETS	0.759	0.663	0.863	1	0.974	1	SUBCLONAL	2	TRUE	1	0.22	2		252	401	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0029845-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	318	563	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	NA	2	FACETS	0.996	0.954	1			1	INDETERMINATE	2	TRUE	NA	0.599887198612779	2		563	532	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862204	68862205	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0029845-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	159	380	0	ENST00000261769.5:c.2293_2294dup	p.Gln765HisfsTer6	p.Q765Hfs*6	ENST00000261769	NM_004360.3	764	-/CA	14/16	0.599887198612779	1	FACETS	0.823	0.761	0.886	0.823	0.761	0.886	CLONAL	1	TRUE	0	0.599887198612779	1		380	451	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244613	41244613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80356970	NA	P-0029845-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	211	501	0	ENST00000357654.3:c.2935C>T	p.Arg979Cys	p.R979C	ENST00000357654	NM_007294.3	979	Cgt/Tgt	10/23	1	2	FACETS	0.807	0.75	0.865	0.807	0.75	0.865	CLONAL	1	TRUE	1	0.599887198612779	2		501	872	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178217	56178217	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0029845-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	177	266	0	ENST00000399503.3:c.3190A>T	p.Arg1064Ter	p.R1064*	ENST00000399503	NM_005921.1	1064	Aga/Tga	14/20	0.483793226049095	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.599887198612779	1		266	397	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962846	2962846	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	110	761	2	ENST00000396946.4:c.2062C>T	p.Arg688Ter	p.R688*	ENST00000396946	NM_032415.4	688	Cga/Tga	16/25	0.293186235539789	3	FACETS	0.962	0.864	1	0.481	0.432	0.534	CLONAL	1	TRUE	1	0.293186235539789	3		763	894	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409382	31409382	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1233387563	NA	P-0029846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	68	395	0	ENST00000344624.3:c.3725A>G	p.Asn1242Ser	p.N1242S	ENST00000344624		1242	aAt/aGt	29/33	1	2	FACETS	0.811	0.706	0.924	0.811	0.706	0.924	CLONAL	1	TRUE	1	0.293186235539789	2		395	572	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041244	47041245	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0029846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	139	322	0	ENST00000377604.3:c.1672_1673del	p.Gln558GlyfsTer18	p.Q558Gfs*18	ENST00000377604	NM_001204468.1	558	CAg/g	15/24	1	1	FACETS	0.827	0.758	0.899	1	0.989	1	CLONAL	2	TRUE	0	0.293186235539789	1		322	489	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971209	21971209	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0029846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	71	235	0	ENST00000304494.5:c.151-2A>T		p.X51_splice	ENST00000304494	NM_000077.4	51			0.293186235539789	1	FACETS	0.97	0.85	1	0.97	0.85	1	CLONAL	1	TRUE	0	0.293186235539789	1		235	426	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411866	116411893	+	intron_variant	Intron	DEL	CGTCTTTAACAAGCTCTTTCTTTCTCTC	CGTCTTTAACAAGCTCTTTCTTTCTCTC	G	novel	NA	P-0029846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	159	786	0	ENST00000397752.3:c.2888-37_2888-10delinsG		p.*963*	ENST00000397752	NM_000245.2	-/1390			0.293186235539789	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.293186235539789	1		786	890	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0029919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	924	499	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.906694705217258	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	1	0.906694705217258	4		499	1296	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0029919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	434	440	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.4024103383604	4	FACETS	1	0.988	1	1	0.988	1	INDETERMINATE	2	TRUE	2	0.906694705217258	4		440	854	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562133	21562133	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	268	852	0	ENST00000382592.4:c.1786A>T	p.Ser596Cys	p.S596C	ENST00000382592	NM_014572.2	596	Agc/Tgc	4/8	0.906694705217258	2	FACETS	0.985	0.932	1	0.493	0.466	0.52	CLONAL	1	TRUE	0	0.906694705217258	2		852	600	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169977787	169977787	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1309	193	529	0	ENST00000295797.4:c.254A>T	p.Glu85Val	p.E85V	ENST00000295797	NM_002740.5	85	gAg/gTg	3/18	0.906694705217258	4	FACETS	0.54	0.498	0.585	0.18	0.166	0.195	SUBCLONAL	1	TRUE	1	0.906694705217258	4		529	1502	SUCCESS
APC	324	MSKCC	GRCh37	5	112164593	112164596	+	frameshift_variant	Frame_Shift_Del	DEL	ATGT	ATGT	-	novel	NA	P-0029919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	214	268	0	ENST00000257430.4:c.1668_1671del	p.Asp556GlufsTer13	p.D556Efs*13	ENST00000257430	NM_000038.5	556	gATGTa/ga	14/16	0.615397136802722	4	FACETS	0.955	0.898	1			1	CLONAL	2	TRUE	NA	0.906694705217258	4		268	471	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0029932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	338	515	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.218340383550537	5	FACETS	1	0.964	1			1	INDETERMINATE	3	TRUE	NA	0.440994786538694	5		515	835	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0029932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	96	534	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.783	0.699	0.872	0.783	0.699	0.872	SUBCLONAL	1	TRUE	1	0.440994786538694	2		534	556	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249345	110249348	+	missense_variant	Missense_Mutation	ONP	TCTT	TCTT	ACTC	novel	NA	P-0029932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	225	877	0	ENST00000374672.4:c.1225_1228delinsGAGT	p.Lys409_Ser410delinsGluCys	p.K409_S410delinsEC	ENST00000374672	NM_004235.4	409	AAGAgt/GAGTgt	4/5	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.440994786538694	2		877	997	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0029959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	120	188	2	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	0.456735402293989	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.456735402293989	1		190	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519999	NA	P-0029959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	151	537	0	ENST00000269305.4:c.716A>G	p.Asn239Ser	p.N239S	ENST00000269305	NM_001126112.2	239	aAc/aGc	7/11	0.456735402293989	1	FACETS	0.865	0.794	0.938	0.865	0.794	0.938	CLONAL	1	TRUE	0	0.456735402293989	1		537	590	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899272	78899272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368064754	NA	P-0029959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	126	452	0	ENST00000306801.3:c.2911G>A	p.Val971Ile	p.V971I	ENST00000306801	NM_020761.2	971	Gtc/Atc	24/34	1	2	FACETS	0.9	0.817	0.987	0.9	0.817	0.987	CLONAL	1	TRUE	1	0.456735402293989	2		452	613	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349280	11349280	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	105	353	0	ENST00000332029.2:c.56C>T	p.Pro19Leu	p.P19L	ENST00000332029	NM_003745.1	19	cCc/cTc	2/2	0.456735402293989	1	FACETS	0.939	0.848	1	0.939	0.848	1	CLONAL	1	TRUE	0	0.456735402293989	1		353	378	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729696	162729696	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	132	484	0	ENST00000367921.3:c.782A>G	p.Asn261Ser	p.N261S	ENST00000367921	NM_006182.2	261	aAc/aGc	8/18	1	2	FACETS	0.96	0.875	1	0.96	0.875	1	CLONAL	1	TRUE	1	0.456735402293989	2		484	602	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741450	17741450	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs771216938	NA	P-0029959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	363	614	0	ENST00000250003.3:c.121C>A	p.Arg41Ser	p.R41S	ENST00000250003	NM_002478.4	41	Cgc/Agc	1/3	0.145913550993533	2	FACETS	0.832	0.791	0.873	0.832	0.791	0.873	INDETERMINATE	2	TRUE	0	0.456735402293989	2		614	955	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427998	49427998	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	153	544	0	ENST00000301067.7:c.10592A>C	p.Gln3531Pro	p.Q3531P	ENST00000301067	NM_003482.3	3531	cAg/cCg	38/54	1	2	FACETS	0.938	0.86	1	0.938	0.86	1	CLONAL	1	TRUE	1	0.456735402293989	2		544	714	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95563052	95563052	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0029959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	40	191	0	ENST00000393063.1:c.4207-2A>T		p.X1403_splice	ENST00000393063	NM_030621.3	1403			1	2	FACETS	0.778	0.652	0.916	0.778	0.652	0.916	CLONAL	1	TRUE	1	0.456735402293989	2		191	225	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138559	11138559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	43	587	0	ENST00000358026.2:c.3315G>A	p.Met1105Ile	p.M1105I	ENST00000358026	NM_001128849.1	1105	atG/atA	24/36	1	2	FACETS	0.232	0.193	0.275	0.232	0.193	0.275	SUBCLONAL	1	TRUE	1	0.456735402293989	2		587	813	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271980	15271981	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0029959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	142	689	1	ENST00000263388.2:c.6458dup	p.Gly2154TrpfsTer88	p.G2154Wfs*88	ENST00000263388	NM_000435.2	2153	cct/ccCt	33/33	1	2	FACETS	0.887	0.81	0.967	0.887	0.81	0.967	CLONAL	1	TRUE	1	0.456735402293989	2		690	701	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794462	242794462	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	187	699	1	ENST00000334409.5:c.480del	p.Arg161GlyfsTer24	p.R161Gfs*24	ENST00000334409	NM_005018.2	160	ccC/cc	3/5	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.456735402293989	2		700	797	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46276030	46276030	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1242786925	NA	P-0029959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	137	577	0	ENST00000371998.3:c.3466C>T	p.Arg1156Ter	p.R1156*	ENST00000371998		1156	Cga/Tga	18/23	1	2	FACETS	0.809	0.736	0.884	0.809	0.736	0.884	CLONAL	1	TRUE	1	0.456735402293989	2		577	742	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670403	134670403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	96	418	0	ENST00000398015.3:c.314C>T	p.Ser105Phe	p.S105F	ENST00000398015	NM_004441.4	105	tCc/tTc	3/16	0.427860470791751	3	FACETS	0.903	0.806	1	0.451	0.403	0.503	CLONAL	1	TRUE	1	0.456735402293989	3		418	572	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873595	35873596	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0029959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	101	225	0	ENST00000303115.3:c.551_552delinsAA	p.Ser184Ter	p.S184*	ENST00000303115	NM_002185.3	184	tCC/tAA	5/8	0.370660312902258	3	FACETS	0.811	0.733	0.892	0.811	0.733	0.892	CLONAL	2	TRUE	1	0.456735402293989	3		225	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0030005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	520	997	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.792701884688799	2	FACETS	0.932	0.909	0.953	0.932	0.909	0.953	CLONAL	2	FALSE	0	0.858413630653312	2		997	650	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243777042	243777042	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0030005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	81	350	0	ENST00000263826.5:c.628-1G>A		p.X210_splice	ENST00000263826	NM_005465.4	210			0.858413630653312	4	FACETS	0.999	0.887	1	0.25	0.221	0.28	CLONAL	1	FALSE	0	0.858413630653312	4		350	351	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436686	8436686	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	61	373	0	ENST00000356435.5:c.3992T>A	p.Met1331Lys	p.M1331K	ENST00000356435		1331	aTg/aAg	24/35	0.510898251827303	4	FACETS	1	0.94	1	0.378	0.33	0.429	INDETERMINATE	1	FALSE	1	0.858413630653312	4		373	233	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424239	47424239	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	16	617	0	ENST00000377045.4:c.244G>A	p.Asp82Asn	p.D82N	ENST00000377045	NM_001654.4	82	Gat/Aat	4/16	0.822722021082187	1	FACETS	0.074	0.054	0.098	0.074	0.054	0.098	SUBCLONAL	1	FALSE	0	0.858413630653312	1		617	287	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573991	7573991	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567542019	NA	P-0030010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	337	731	0	ENST00000269305.4:c.1036G>T	p.Glu346Ter	p.E346*	ENST00000269305	NM_001126112.2	346	Gag/Tag	10/11	0.311267981715487	2	FACETS	0.934	0.889	0.98	1	0.995	1	CLONAL	3	FALSE	0	0.312645128988664	2		731	769	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161293406	161293406	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs776123707	NA	P-0030010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	84	402	0	ENST00000367975.2:c.23A>G	p.His8Arg	p.H8R	ENST00000367975	NM_003001.3	8	cAc/cGc	2/6	1	2	FACETS	0.858	0.759	0.965	0.858	0.759	0.965	CLONAL	1	FALSE	1	0.312645128988664	2		402	626	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724421	112724421	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	69	660	0	ENST00000369452.4:c.305C>T	p.Ser102Leu	p.S102L	ENST00000369452	NM_007373.3	102	tCa/tTa	2/9	0.255297963316521	5	FACETS	0.866	0.753	0.988	0.289	0.251	0.33	CLONAL	1	FALSE	2	0.312645128988664	5		660	749	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618489	37618498	+	frameshift_variant	Frame_Shift_Del	DEL	GGTGACCCCC	GGTGACCCCC	-	novel	NA	P-0030010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	283	549	0	ENST00000447079.4:c.166_175del	p.Val56LysfsTer33	p.V56Kfs*33	ENST00000447079	NM_015083.1	55	ttGGTGACCCCC/tt	1/14	0.312645128988664	6	FACETS	1	0.983	1			1	CLONAL	5	FALSE	NA	0.312645128988664	6		549	548	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223139	36223139	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	107	949	0	ENST00000222270.7:c.5689C>T	p.His1897Tyr	p.H1897Y	ENST00000222270	NM_014727.1	1897	Cac/Tac	28/37	0.312645299318211	4	FACETS	1	0.974	1			1	CLONAL	1	FALSE	NA	0.312645128988664	4		949	709	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0030012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	42	390	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.27	2		390	298	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0030012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	136	740	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.222706566742247	3	FACETS	1	0.976	1			1	CLONAL	2	TRUE	NA	0.27	3		740	484	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023477	27023478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACGCGGGGCCCCAGCAGAA	novel	NA	P-0030012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	27	511	0	ENST00000324856.7:c.584_602dup	p.Asn201LysfsTer205	p.N201Kfs*205	ENST00000324856	NM_006015.4	195	tac/tACGCGGGGCCCCAGCAGAAac	1/20	1	2	FACETS	0.575	0.457	0.709	0.575	0.457	0.709	SUBCLONAL	1	TRUE	1	0.27	2		511	348	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660744	227660744	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs144228243	NA	P-0030012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	59	646	0	ENST00000305123.5:c.2711A>G	p.Asp904Gly	p.D904G	ENST00000305123	NM_005544.2	904	gAt/gGt	1/2	1	2	FACETS	0.869	0.748	1	0.869	0.748	1	CLONAL	1	TRUE	1	0.27	2		646	503	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971186	13971186	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	41	299	0	ENST00000405192.2:c.743A>G	p.Gln248Arg	p.Q248R	ENST00000405192	NM_001163147.1	248	cAa/cGa	8/12	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.27	2		299	286	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518106	103518106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759972289	NA	P-0030084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	72	230	2	ENST00000355739.4:c.2044G>A	p.Glu682Lys	p.E682K	ENST00000355739	NM_000123.3	682	Gaa/Aaa	9/15	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.323850495403602	2		232	364	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85741981	85741981	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	75	430	0	ENST00000370580.1:c.55G>C	p.Asp19His	p.D19H	ENST00000370580	NM_003921.4	19	Gac/Cac	1/3	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.323850495403602	2		430	442	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202708	133202708	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	65	356	0	ENST00000320574.5:c.6526T>A	p.Ser2176Thr	p.S2176T	ENST00000320574	NM_006231.2	2176	Tca/Aca	46/49	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.323850495403602	2		356	339	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440891	52440891	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0030084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	95	520	0	ENST00000460680.1:c.613A>T	p.Lys205Ter	p.K205*	ENST00000460680	NM_004656.3	205	Aag/Tag	8/17	0.323850495403602	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.323850495403602	1		520	409	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054030	42054030	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	50	206	0	ENST00000219905.7:c.7494del	p.Val2499TyrfsTer13	p.V2499Yfs*13	ENST00000219905	NM_001164273.1	2498	Aaa/aa	21/24	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.323850495403602	2		206	279	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054025	42054026	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGAAA	novel	NA	P-0030084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	55	225	0	ENST00000219905.7:c.7487_7488insCGAAA	p.Arg2497GlufsTer17	p.R2497Efs*17	ENST00000219905	NM_001164273.1	2496	ata/atCGAAAa	21/24	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.323850495403602	2		225	294	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0030090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	352	446	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.714821246933964	2		446	665	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040650	47040650	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	275	607	1	ENST00000377604.3:c.1285G>T	p.Glu429Ter	p.E429*	ENST00000377604	NM_001204468.1	429	Gag/Tag	13/24	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.714821246933964	2		608	700	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008548	70008548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771113831	NA	P-0030090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	169	339	1	ENST00000394351.3:c.835C>T	p.Arg279Trp	p.R279W	ENST00000394351	NM_000248.3	279	Cgg/Tgg	8/9	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.714821246933964	2		340	452	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937125	39937125	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	48	604	0	ENST00000378444.4:c.58G>T	p.Val20Phe	p.V20F	ENST00000378444	NM_001123385.1	20	Gtc/Ttc	2/15	NA	2	FACETS	0.193	0.163	0.227			1	INDETERMINATE	1	TRUE	NA	0.714821246933964	2		604	695	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384726	17384726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368554117	NA	P-0030090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	264	646	0	ENST00000359435.4:c.358G>A	p.Ala120Thr	p.A120T	ENST00000359435	NM_001033549.1	120	Gcc/Acc	4/9	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.714821246933964	2		646	710	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288961	11288961	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs780002014	NA	P-0030090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	188	397	0	ENST00000361445.4:c.2794A>G	p.Ser932Gly	p.S932G	ENST00000361445	NM_004958.3	932	Agt/Ggt	19/58	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.714821246933964	2		397	451	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563201	21563201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1389815235	NA	P-0030090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	267	679	0	ENST00000382592.4:c.718G>A	p.Glu240Lys	p.E240K	ENST00000382592	NM_014572.2	240	Gag/Aag	4/8	0.714821246933964	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.714821246933964	1		679	444	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451888	29451889	+	missense_variant	Missense_Mutation	DNP	CG	CG	TC	novel	NA	P-0030090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	256	643	1	ENST00000389048.3:c.2676_2677delinsGA	p.Gly893Arg	p.G893R	ENST00000389048	NM_004304.4	892	gcCGga/gcGAga	16/29	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.714821246933964	2		644	679	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719487	190719487	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	103	197	0	ENST00000441310.2:c.1489G>T	p.Glu497Ter	p.E497*	ENST00000441310	NM_000534.4	497	Gag/Tag	9/13	1	2	FACETS	0.977	0.886	1	0.977	0.886	1	CLONAL	1	TRUE	1	0.714821246933964	2		197	295	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346604	81346604	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	119	287	0	ENST00000222390.5:c.1349C>A	p.Pro450His	p.P450H	ENST00000222390	NM_000601.4	450	cCc/cAc	11/18	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.714821246933964	2		287	328	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920200	76920200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	133	273	0	ENST00000373344.5:c.3877G>T	p.Asp1293Tyr	p.D1293Y	ENST00000373344	NM_000489.3	1293	Gat/Tat	11/35	1	2	FACETS	0.869	0.796	0.945	0.869	0.796	0.945	CLONAL	1	TRUE	1	0.714821246933964	2		273	428	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	83	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.954	0.844	1	0.954	0.844	1	CLONAL	1	TRUE	1	0.326454297640894	2		215	533	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	178	188	2	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	0.326454297640894	1	FACETS	0.788	0.73	0.847	1	0.991	1	SUBCLONAL	2	TRUE	0	0.326454297640894	1		190	579	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913255	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	33	476	0	ENST00000369535.4:c.183A>C	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caC	3/7	1	2	FACETS	0.269	0.218	0.327	0.269	0.218	0.327	SUBCLONAL	1	TRUE	1	0.326454297640894	2		476	751	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	103	799	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.765	0.684	0.851	0.765	0.684	0.851	SUBCLONAL	1	TRUE	1	0.326454297640894	2		799	825	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007620	45007620	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs111947448	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	18	196	0	ENST00000558401.1:c.68-1G>T		p.X23_splice	ENST00000558401	NM_004048.2	23			0.326454297640894	1	FACETS	0.408	0.308	0.526	0.408	0.308	0.526	SUBCLONAL	1	TRUE	0	0.326454297640894	1		196	226	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032209	26032209	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	103	243	0	ENST00000244661.2:c.80G>A	p.Arg27His	p.R27H	ENST00000244661	NM_003537.3	27	cGc/cAc	1/1	0.284914502055522	2	FACETS	0.953	0.863	1	0.953	0.863	1	CLONAL	2	TRUE	0	0.326454297640894	2		243	331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	218	1018	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.326454297640894	2		1018	1056	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156747	106156747	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs572712965	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	70	419	0	ENST00000380013.4:c.1648C>T	p.Arg550Ter	p.R550*	ENST00000380013	NM_001127208.2	550	Cga/Tga	3/11	0.146678064161932	0	FACETS	0.542	0.473	0.616			1	INDETERMINATE	1	TRUE	0	0.326454297640894	0		419	533	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166773	32166773	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1231739465	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	101	655	0	ENST00000375023.3:c.4465C>T	p.Arg1489Ter	p.R1489*	ENST00000375023	NM_004557.3	1489	Cga/Tga	24/30	0.284914502055522	2	FACETS	0.703	0.628	0.784	0.352	0.314	0.392	SUBCLONAL	1	TRUE	0	0.326454297640894	2		655	880	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058747	180058748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755445139	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	92	252	4	ENST00000261937.6:c.89dup	p.Thr31AspfsTer15	p.T31Dfs*15	ENST00000261937	NM_182925.4	30	ccg/ccCg	2/30	1	2	FACETS	0.621	0.551	0.697	0.621	0.551	0.697	SUBCLONAL	1	TRUE	1	0.326454297640894	2		256	907	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46738149	46738149	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748839524	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	37	386	1	ENST00000371975.4:c.1181G>A	p.Arg394Gln	p.R394Q	ENST00000371975	NM_003579.3	394	cGg/cAg	11/18	0.326454297640894	3	FACETS	0.36	0.295	0.432	0.18	0.147	0.216	SUBCLONAL	1	TRUE	1	0.326454297640894	3		387	733	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441974	6441974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	342	477	0	ENST00000356142.4:c.533C>T	p.Ala178Val	p.A178V	ENST00000356142	NM_018890.3	178	gCg/gTg	7/7	0.307974713418071	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.326454297640894	2		477	932	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436686	110436686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	49	688	1	ENST00000375856.3:c.1715G>A	p.Arg572His	p.R572H	ENST00000375856	NM_003749.2	572	cGc/cAc	1/2	0.326454297640894	1	FACETS	0.298	0.252	0.35	0.298	0.252	0.35	SUBCLONAL	1	TRUE	0	0.326454297640894	1		689	842	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023894	31023894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201009558	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	63	525	0	ENST00000375687.4:c.3379G>A	p.Asp1127Asn	p.D1127N	ENST00000375687	NM_015338.5	1127	Gat/Aat	13/13	1	2	FACETS	0.468	0.404	0.538	0.468	0.404	0.538	SUBCLONAL	1	TRUE	1	0.326454297640894	2		525	825	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994829	73994829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751833994	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	57	236	0	ENST00000318443.5:c.313G>A	p.Ala105Thr	p.A105T	ENST00000318443	NM_001024736.1	105	Gca/Aca	3/10	0.326454297640894	3	FACETS	1	0.883	1	0.514	0.443	0.592	CLONAL	1	TRUE	1	0.326454297640894	3		236	395	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003775	45003775	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs104894481	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	20	338	0	ENST00000558401.1:c.31G>C	p.Ala11Pro	p.A11P	ENST00000558401	NM_004048.2	11	Gcg/Ccg	1/4	0.326454297640894	1	FACETS	0.26	0.198	0.332	0.26	0.198	0.332	SUBCLONAL	1	TRUE	0	0.326454297640894	1		338	395	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27228299	27228299	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759970580	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	88	365	0	ENST00000380036.4:c.3296G>A	p.Arg1099Gln	p.R1099Q	ENST00000380036	NM_000459.3	1099	cGa/cAa	22/23	0.326454297640894	1	FACETS	0.737	0.654	0.826	0.737	0.654	0.826	SUBCLONAL	1	TRUE	0	0.326454297640894	1		365	612	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256566	115256566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746572499	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	54	429	0	ENST00000369535.4:c.145G>A	p.Glu49Lys	p.E49K	ENST00000369535	NM_002524.4	49	Gaa/Aaa	3/7	1	2	FACETS	0.507	0.432	0.588	0.507	0.432	0.588	SUBCLONAL	1	TRUE	1	0.326454297640894	2		429	653	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404749	70404749	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	49	540	0	ENST00000373644.4:c.2263A>C	p.Thr755Pro	p.T755P	ENST00000373644	NM_030625.2	755	Acc/Ccc	4/12	1	2	FACETS	0.397	0.335	0.465	0.397	0.335	0.465	SUBCLONAL	1	TRUE	1	0.326454297640894	2		540	757	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406526	70406526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139453548	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	46	662	0	ENST00000373644.4:c.4040C>T	p.Pro1347Leu	p.P1347L	ENST00000373644	NM_030625.2	1347	cCg/cTg	4/12	1	2	FACETS	0.316	0.265	0.372	0.316	0.265	0.372	SUBCLONAL	1	TRUE	1	0.326454297640894	2		662	893	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189446	94189446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753148077	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	90	369	0	ENST00000323929.3:c.1559G>A	p.Arg520His	p.R520H	ENST00000323929	NM_005591.3	520	cGt/cAt	14/20	0.326454297640894	1	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	0	0.326454297640894	1		369	450	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375320	118375320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	75	295	0	ENST00000534358.1:c.8713C>T	p.Pro2905Ser	p.P2905S	ENST00000534358	NM_005933.3	2905	Cct/Tct	27/36	0.326454297640894	1	FACETS	0.909	0.8	1	0.909	0.8	1	CLONAL	1	TRUE	0	0.326454297640894	1		295	423	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244682	46244682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766416912	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	43	495	0	ENST00000334344.6:c.2776G>A	p.Val926Ile	p.V926I	ENST00000334344	NM_152641.2	926	Gta/Ata	15/21	1	2	FACETS	0.325	0.271	0.385	0.325	0.271	0.385	SUBCLONAL	1	TRUE	1	0.326454297640894	2		495	811	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440041	49440041	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	66	549	0	ENST00000301067.7:c.4583+2T>C		p.X1528_splice	ENST00000301067	NM_003482.3	1528			1	2	FACETS	0.429	0.371	0.492	0.429	0.371	0.492	SUBCLONAL	1	TRUE	1	0.326454297640894	2		549	942	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134987	41134987	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	22	222	0	ENST00000379561.5:c.641G>A	p.Arg214His	p.R214H	ENST00000379561	NM_002015.3	214	cGt/cAt	2/3	0.326454297640894	1	FACETS	0.47	0.365	0.591	0.47	0.365	0.591	SUBCLONAL	1	TRUE	0	0.326454297640894	1		222	240	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106669	2106669	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142919353	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	121	530	0	ENST00000219476.3:c.673G>A	p.Val225Met	p.V225M	ENST00000219476	NM_000548.3	225	Gtg/Atg	8/42	0.194118216124793	0	FACETS	0.641	0.579	0.706			1	INDETERMINATE	1	TRUE	0	0.326454297640894	0		530	779	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658551	3658551	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	51	605	2	ENST00000294008.3:c.415G>T	p.Gly139Trp	p.G139W	ENST00000294008	NM_032444.2	139	Ggg/Tgg	2/15	0.194118216124793	0	FACETS	0.238	0.201	0.279			1	INDETERMINATE	1	TRUE	0	0.326454297640894	0		607	884	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024560	11024560	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	90	429	0	ENST00000327064.4:c.677T>C	p.Val226Ala	p.V226A	ENST00000327064	NM_199141.1	226	gTg/gCg	6/16	1	2	FACETS	0.817	0.725	0.915	0.817	0.725	0.915	CLONAL	1	TRUE	1	0.326454297640894	2		429	675	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350235	15350235	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	192	682	0	ENST00000263377.2:c.3544C>T	p.Gln1182Ter	p.Q1182*	ENST00000263377	NM_058243.2	1182	Cag/Tag	17/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.326454297640894	2		682	928	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46587863	46587863	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747275399	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	55	433	0	ENST00000263734.3:c.541C>T	p.Arg181Cys	p.R181C	ENST00000263734	NM_001430.4	181	Cgt/Tgt	5/16	1	2	FACETS	0.463	0.395	0.537	0.463	0.395	0.537	SUBCLONAL	1	TRUE	1	0.326454297640894	2		433	728	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288689	198288689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	150	367	0	ENST00000335508.6:c.38C>T	p.Ala13Val	p.A13V	ENST00000335508	NM_012433.2	13	gCa/gTa	2/25	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.326454297640894	2		367	615	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480309	89480309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	17	195	0	ENST00000336596.2:c.2146G>A	p.Ala716Thr	p.A716T	ENST00000336596	NM_005233.5	716	Gcc/Acc	13/17	0.102250817798547	3	FACETS	0.412	0.307	0.537	0.137	0.102	0.179	INDETERMINATE	1	TRUE	0	0.326454297640894	3		195	294	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665110	182665110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1361986556	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	66	306	1	ENST00000292782.4:c.616C>T	p.Arg206Ter	p.R206*	ENST00000292782	NM_020640.2	206	Cga/Tga	6/7	0.102250817798547	3	FACETS	1	0.899	1	0.346	0.301	0.395	INDETERMINATE	1	TRUE	0	0.326454297640894	3		307	453	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539488	187539488	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	38	312	0	ENST00000441802.2:c.8252T>C	p.Phe2751Ser	p.F2751S	ENST00000441802	NM_005245.3	2751	tTt/tCt	10/27	0.146678064161932	0	FACETS	0.357	0.295	0.426			1	INDETERMINATE	1	TRUE	0	0.326454297640894	0		312	439	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750519	57750519	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	40	449	0	ENST00000274289.3:c.1949G>T	p.Arg650Met	p.R650M	ENST00000274289	NM_006622.3	650	aGg/aTg	14/14	1	2	FACETS	0.364	0.301	0.433	0.364	0.301	0.433	SUBCLONAL	1	TRUE	1	0.326454297640894	2		449	674	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172244	38172244	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	32	420	1	ENST00000317025.8:c.2163C>A	p.Cys721Ter	p.C721*	ENST00000317025	NM_023034.1	721	tgC/tgA	12/24	1	2	FACETS	0.309	0.25	0.376	0.309	0.25	0.376	SUBCLONAL	1	TRUE	1	0.326454297640894	2		421	635	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15833909	15833909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1392977402	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	17	17	1	ENST00000307771.7:c.667G>A	p.Ala223Thr	p.A223T	ENST00000307771	NM_005089.3	223	Gca/Aca	8/11	0.326454297640894	1	FACETS	1	0.844	1	1	0.953	1	CLONAL	3	TRUE	0	0.326454297640894	1		18	28	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339247	70339273	+	inframe_deletion	In_Frame_Del	DEL	AAACAAGGTTTCAATAACCAGCCTGCT	AAACAAGGTTTCAATAACCAGCCTGCT	-	novel	NA	P-0030108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	164	550	0	ENST00000374080.3:c.124_150del	p.Lys42_Ala50del	p.K42_A50del	ENST00000374080		42	AAACAAGGTTTCAATAACCAGCCTGCT/-	2/45	0.326454297640894	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.326454297640894	1		550	782	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270508	98270508	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	101	370	0	ENST00000331920.6:c.136G>T	p.Asp46Tyr	p.D46Y	ENST00000331920	NM_000264.3	46	Gac/Tac	1/24	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.397515258636056	2		370	482	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	45	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.858	0.721	1	0.858	0.721	1	CLONAL	1	TRUE	1	0.214456004139801	2		215	489	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0030136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	44	380	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.203728606335697	3	FACETS	1	0.904	1	0.555	0.466	0.654	CLONAL	1	TRUE	1	0.214456004139801	3		380	409	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981761	101981761	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	84	425	0	ENST00000282441.5:c.182C>G	p.Ser61Trp	p.S61W	ENST00000282441	NM_001130145.2	61	tCg/tGg	1/9	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.214456004139801	2		425	679	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0030136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	40	290	0	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	1	2	FACETS	0.872	0.725	1	0.872	0.725	1	CLONAL	1	TRUE	1	0.214456004139801	2		290	428	SUCCESS
ATM	472	MSKCC	GRCh37	11	108183205	108183205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	30	288	0	ENST00000278616.4:c.5986G>A	p.Glu1996Lys	p.E1996K	ENST00000278616	NM_000051.3	1996	Gaa/Aaa	40/63	1	2	FACETS	0.835	0.674	1	0.835	0.674	1	CLONAL	1	TRUE	1	0.214456004139801	2		288	335	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984923	101984923	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	45	305	0	ENST00000282441.5:c.370C>G	p.Arg124Gly	p.R124G	ENST00000282441	NM_001130145.2	124	Cga/Gga	2/9	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.214456004139801	2		305	372	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913277	NA	P-0030136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	38	354	0	ENST00000263967.3:c.3145G>A	p.Gly1049Ser	p.G1049S	ENST00000263967	NM_006218.2	1049	Ggt/Agt	21/21	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.214456004139801	2		354	339	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188187	32188187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754712190	NA	P-0030136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	66	473	0	ENST00000375023.3:c.1154G>A	p.Arg385His	p.R385H	ENST00000375023	NM_004557.3	385	cGc/cAc	6/30	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.214456004139801	2		473	564	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102098231	102098231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	54	394	0	ENST00000282441.5:c.1195G>A	p.Asp399Asn	p.D399N	ENST00000282441	NM_001130145.2	399	Gac/Aac	8/9	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.214456004139801	2		394	502	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857517	57857517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs890327478	NA	P-0030136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	79	663	1	ENST00000228682.2:c.43G>A	p.Glu15Lys	p.E15K	ENST00000228682	NM_005269.2	15	Gag/Aag	2/12	1	2	FACETS	0.82	0.72	0.929	0.82	0.72	0.929	CLONAL	1	TRUE	1	0.214456004139801	2		664	898	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260162	10260162	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	81	519	0	ENST00000340748.4:c.2505C>G	p.Ile835Met	p.I835M	ENST00000340748		835	atC/atG	25/40	1	2	FACETS	0.947	0.833	1	0.947	0.833	1	CLONAL	1	TRUE	1	0.214456004139801	2		519	798	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143318	30143345	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGGGCGTAGACACGGAAGAGCGAGGG	CCCGGGCGTAGACACGGAAGAGCGAGGG	-	novel	NA	P-0030136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	57	637	0	ENST00000389048.3:c.181_208del	p.Pro61ThrfsTer11	p.P61Tfs*11	ENST00000389048	NM_004304.4	61	CCCTCGCTCTTCCGTGTCTACGCCCGGGac/ac	1/29	1	2	FACETS	0.798	0.684	0.923	0.798	0.684	0.923	CLONAL	1	TRUE	1	0.214456004139801	2		637	666	SUCCESS
REL	5966	MSKCC	GRCh37	2	61148952	61148952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	32	286	0	ENST00000295025.8:c.1142C>T	p.Ser381Leu	p.S381L	ENST00000295025	NM_002908.2	381	tCa/tTa	11/11	1	2	FACETS	0.875	0.712	1	0.875	0.712	1	CLONAL	1	TRUE	1	0.214456004139801	2		286	341	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151181	202151181	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs1354563506	NA	P-0030136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	39	231	0	ENST00000358485.4:c.1482-1G>C		p.X494_splice	ENST00000358485	NM_001080125.1	494			0.214456004139801	2	FACETS	1	0.953	1	0.73	0.609	0.863	CLONAL	1	TRUE	0	0.214456004139801	2		231	249	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538328	9538328	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	56	415	0	ENST00000353224.5:c.1670C>G	p.Ser557Cys	p.S557C	ENST00000353224	NM_177990.2	557	tCc/tGc	7/10	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.214456004139801	2		415	516	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713768	30713768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	77	398	0	ENST00000295754.5:c.1093C>T	p.His365Tyr	p.H365Y	ENST00000295754	NM_003242.5	365	Cac/Tac	4/7	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.214456004139801	2		398	532	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260707	1260707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755707625	NA	P-0030136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	57	462	0	ENST00000310581.5:c.2852G>A	p.Arg951Gln	p.R951Q	ENST00000310581	NM_198253.2	951	cGg/cAg	12/16	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.214456004139801	2		462	518	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672638	30672638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	79	582	0	ENST00000376406.3:c.4322C>T	p.Ser1441Phe	p.S1441F	ENST00000376406	NM_014641.2	1441	tCt/tTt	10/15	1	2	FACETS	0.883	0.776	0.999	0.883	0.776	0.999	CLONAL	1	TRUE	1	0.214456004139801	2		582	834	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700262	117700262	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	33	461	0	ENST00000368508.3:c.2557C>T	p.Gln853Ter	p.Q853*	ENST00000368508	NM_002944.2	853	Caa/Taa	17/43	1	2	FACETS	0.703	0.572	0.85	0.703	0.572	0.85	SUBCLONAL	1	TRUE	1	0.214456004139801	2		461	438	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412690	139412690	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	314	679	0	ENST00000277541.6:c.1154C>G	p.Ser385Cys	p.S385C	ENST00000277541	NM_017617.3	385	tCc/tGc	7/34	0.214456004139801	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	0	0.214456004139801	3		679	1008	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259527	16259527	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	116	486	0	ENST00000375759.3:c.6792G>C	p.Glu2264Asp	p.E2264D	ENST00000375759	NM_015001.2	2264	gaG/gaC	11/15	1	2	FACETS	0.81	0.735	0.887	0.81	0.735	0.887	CLONAL	1	TRUE	1	0.675711368235781	2		486	424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577512	7577518	+	frameshift_variant	Frame_Shift_Del	DEL	GTGTGAT	GTGTGAT	-	novel	NA	P-0030139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	166	564	0	ENST00000269305.4:c.763_769del	p.Ile255TrpfsTer88	p.I255Wfs*88	ENST00000269305	NM_001126112.2	255	ATCACACtg/tg	7/11	0.675711368235781	1	FACETS	0.911	0.85	0.973	0.911	0.85	0.973	CLONAL	1	TRUE	0	0.675711368235781	1		564	357	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015193	37015193	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0030139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	103	361	0	ENST00000358127.4:c.213-2A>T		p.X71_splice	ENST00000358127	NM_001280556.1	71			1	2	FACETS	0.871	0.787	0.958	0.871	0.787	0.958	CLONAL	1	TRUE	1	0.675711368235781	2		361	350	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0030156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	347	354	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.203145242572419	6	FACETS	0.917	0.872	0.963	0.917	0.872	0.963	CLONAL	6	TRUE	0	0.203145242572419	6		354	873	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625303	69625303	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1335560620	NA	P-0030156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	175	599	0	ENST00000334134.2:c.490C>T	p.Arg164Cys	p.R164C	ENST00000334134	NM_005247.2	164	Cgc/Tgc	3/3	0.203145242572419	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.203145242572419	3		599	890	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	362	519	0	ENST00000269305.4:c.542G>C	p.Arg181Pro	p.R181P	ENST00000269305	NM_001126112.2	181	cGc/cCc	5/11	0.203145242572419	5	FACETS	0.968	0.92	1	0.968	0.92	1	CLONAL	5	TRUE	0	0.203145242572419	5		519	961	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231036	53231036	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	139	461	0	ENST00000375401.3:c.1866G>T	p.Trp622Cys	p.W622C	ENST00000375401	NM_004187.3	622	tgG/tgT	13/26	1	2	FACETS	0.953	0.869	1	1	0.99	1	CLONAL	2	TRUE	1	0.203145242572419	2		461	718	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729697	41729697	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	192	447	1	ENST00000242208.4:c.832G>T	p.Gly278Trp	p.G278W	ENST00000242208	NM_002192.2	278	Ggg/Tgg	3/3	0.203145242572419	9	FACETS	0.994	0.918	1	0.497	0.459	0.536	CLONAL	3	TRUE	3	0.203145242572419	9		448	1085	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332760	70332760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749194238	NA	P-0030156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	64	492	1	ENST00000373644.4:c.665G>A	p.Arg222His	p.R222H	ENST00000373644	NM_030625.2	222	cGc/cAc	2/12	0.203145242572419	3	FACETS	0.857	0.741	0.984	0.428	0.37	0.492	CLONAL	1	TRUE	1	0.203145242572419	3		493	810	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205113	61205113	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	74	444	0	ENST00000301761.2:c.53G>C	p.Arg18Thr	p.R18T	ENST00000301761	NM_017841.2	18	aGg/aCg	2/4	0.203145242572419	3	FACETS	1	0.914	1	0.529	0.462	0.601	CLONAL	1	TRUE	1	0.203145242572419	3		444	759	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211512	46211512	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0030156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	99	245	0	ENST00000334344.6:c.478A>T	p.Lys160Ter	p.K160*	ENST00000334344	NM_152641.2	160	Aaa/Taa	5/21	0.203145242572419	3	FACETS	0.89	0.8	0.984	0.89	0.8	0.984	CLONAL	3	TRUE	0	0.203145242572419	3		245	402	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608288	28608288	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs759729774	NA	P-0030156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	64	499	0	ENST00000241453.7:c.1768T>C	p.Phe590Leu	p.F590L	ENST00000241453	NM_004119.2	590	Ttc/Ctc	14/24	0.203145242572419	3	FACETS	0.851	0.735	0.976	0.425	0.367	0.488	CLONAL	1	TRUE	1	0.203145242572419	3		499	816	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609432	81609432	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	77	437	0	ENST00000298171.2:c.1030C>A	p.Gln344Lys	p.Q344K	ENST00000298171	NM_000369.2	344	Cag/Aag	10/10	0.203145242572419	4	FACETS	1	0.931	1	0.546	0.479	0.619	CLONAL	1	TRUE	2	0.203145242572419	4		437	835	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609504	81609504	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	104	446	0	ENST00000298171.2:c.1102C>A	p.Gln368Lys	p.Q368K	ENST00000298171	NM_000369.2	368	Cag/Aag	10/10	0.203145242572419	4	FACETS	0.786	0.703	0.873	0.786	0.703	0.873	SUBCLONAL	2	TRUE	2	0.203145242572419	4		446	784	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032333	10032333	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	61	412	0	ENST00000330684.3:c.490G>T	p.Asp164Tyr	p.D164Y	ENST00000330684	NM_001134407.1	164	Gat/Tat	3/13	NA	2	FACETS	1	0.884	1			1	INDETERMINATE	1	TRUE	NA	0.203145242572419	2		412	585	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961830	15961830	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	65	401	0	ENST00000268712.3:c.5965C>G	p.Leu1989Val	p.L1989V	ENST00000268712	NM_006311.3	1989	Ctg/Gtg	38/46	0.203145242572419	5	FACETS	0.91	0.787	1	0.182	0.157	0.209	CLONAL	1	TRUE	0	0.203145242572419	5		401	918	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302332	15302332	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	433	730	0	ENST00000263388.2:c.939G>T	p.Gln313His	p.Q313H	ENST00000263388	NM_000435.2	313	caG/caT	6/33	0.203145242572419	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	4	TRUE	0	0.203145242572419	4		730	1243	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210982	36210982	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1186795675	NA	P-0030156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1902	106	811	0	ENST00000222270.7:c.733G>A	p.Val245Met	p.V245M	ENST00000222270	NM_014727.1	245	Gtg/Atg	3/37	0.203145242572419	9	FACETS	0.889	0.793	0.992	0.099	0.088	0.111	CLONAL	1	TRUE	0	0.203145242572419	9		811	2008	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085975	16085975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	228	452	1	ENST00000281043.3:c.1151G>A	p.Arg384Lys	p.R384K	ENST00000281043	NM_005378.4	384	aGa/aAa	3/3	0.203145242572419	3	FACETS	0.971	0.907	1			1	CLONAL	3	TRUE	NA	0.203145242572419	3		453	849	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416321	29416321	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs763403897	NA	P-0030156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	99	622	2	ENST00000389048.3:c.4632C>A	p.Asn1544Lys	p.N1544K	ENST00000389048	NM_004304.4	1544	aaC/aaA	29/29	0.185558639023351	4	FACETS	1	0.933	1	0.355	0.316	0.397	CLONAL	1	TRUE	1	0.203145242572419	4		624	1101	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645618	215645618	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	238	505	0	ENST00000260947.4:c.980G>T	p.Arg327Ile	p.R327I	ENST00000260947	NM_000465.2	327	aGa/aTa	4/11	0.185558639023351	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	3	TRUE	1	0.203145242572419	4		505	905	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733358	40733358	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	44	389	0	ENST00000373198.4:c.3448G>C	p.Glu1150Gln	p.E1150Q	ENST00000373198	NM_133170.3	1150	Gag/Cag	26/32	0.203145242572419	4	FACETS	0.753	0.63	0.89	0.377	0.315	0.445	SUBCLONAL	1	TRUE	2	0.203145242572419	4		389	692	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504926	186504926	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	79	262	0	ENST00000323963.5:c.782T>C	p.Leu261Ser	p.L261S	ENST00000323963		261	tTg/tCg	8/11	0.172647618103181	4	FACETS	0.983	0.867	1	0.983	0.867	1	CLONAL	2	TRUE	2	0.203145242572419	4		262	476	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557945	187557945	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	89	317	0	ENST00000441802.2:c.3766G>T	p.Glu1256Ter	p.E1256*	ENST00000441802	NM_005245.3	1256	Gag/Tag	5/27	0.203145242572419	3	FACETS	0.874	0.777	0.978	0.874	0.777	0.978	CLONAL	2	TRUE	1	0.203145242572419	3		317	552	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748535	43748535	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	49	423	2	ENST00000523873.1:c.489G>T	p.Trp163Cys	p.W163C	ENST00000523873		163	tgG/tgT	6/8	0.203145242572419	3	FACETS	0.775	0.655	0.907	0.387	0.327	0.454	CLONAL	1	TRUE	1	0.203145242572419	3		425	686	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638401	117638401	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	84	363	0	ENST00000368508.3:c.6040G>C	p.Gly2014Arg	p.G2014R	ENST00000368508	NM_002944.2	2014	Gga/Cga	38/43	0.199756040097394	2	FACETS	0.851	0.754	0.954	0.851	0.754	0.954	CLONAL	2	TRUE	0	0.203145242572419	2		363	486	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846187	128846187	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	389	532	0	ENST00000249373.3:c.1117G>T	p.Val373Leu	p.V373L	ENST00000249373	NM_005631.4	373	Gtg/Ttg	5/12	0.203145242572419	6	FACETS	0.98	0.933	1	0.98	0.933	1	CLONAL	5	TRUE	1	0.203145242572419	6		532	1099	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501281	140501281	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	317	383	0	ENST00000288602.6:c.791G>T	p.Cys264Phe	p.C264F	ENST00000288602	NM_004333.4	264	tGt/tTt	6/18	0.203145242572419	6	FACETS	0.982	0.93	1	0.982	0.93	1	CLONAL	5	TRUE	1	0.203145242572419	6		383	894	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914688	39914688	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	150	527	2	ENST00000378444.4:c.4674G>T	p.Leu1558Phe	p.L1558F	ENST00000378444	NM_001123385.1	1558	ttG/ttT	12/15	1	2	FACETS	0.848	0.775	0.924	1	0.989	1	CLONAL	2	TRUE	1	0.203145242572419	2		529	871	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230836	53230836	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	97	617	0	ENST00000375401.3:c.1957G>T	p.Ala653Ser	p.A653S	ENST00000375401	NM_004187.3	653	Gcc/Tcc	14/26	1	2	FACETS	0.95	0.845	1	0.95	0.845	1	CLONAL	1	TRUE	1	0.203145242572419	2		617	1005	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76954061	76954061	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0030156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	147	520	0	ENST00000373344.5:c.189+1G>C		p.X63_splice	ENST00000373344	NM_000489.3	63			1	2	FACETS	0.945	0.864	1	1	0.991	1	CLONAL	2	TRUE	1	0.203145242572419	2		520	766	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696644	47696644	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519964	NA	P-0030180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	209	494	0	ENST00000347630.2:c.304T>G	p.Phe102Val	p.F102V	ENST00000347630	NM_001007230.1	102	Ttc/Gtc	5/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.787925539907239	2		494	516	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830915	72830918	+	frameshift_variant	Frame_Shift_Del	DEL	CTTT	CTTT	-	novel	NA	P-0030180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	27	400	0	ENST00000268489.5:c.5663_5666del	p.Glu1888AlafsTer25	p.E1888Afs*25	ENST00000268489	NM_006885.3	1888	gAAAGc/gc	9/10	0.787925539907239	1	FACETS	0.141	0.112	0.174	0.141	0.112	0.174	SUBCLONAL	1	TRUE	0	0.787925539907239	1		400	295	SUCCESS
APC	324	MSKCC	GRCh37	5	112174269	112174285	+	frameshift_variant	Frame_Shift_Del	DEL	AGTTTTGCAGTTATGGT	AGTTTTGCAGTTATGGT	-	novel	NA	P-0030180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	84	372	0	ENST00000257430.4:c.2978_2994del	p.Lys993ThrfsTer9	p.K993Tfs*9	ENST00000257430	NM_000038.5	993	aAGTTTTGCAGTTATGGT/a	16/16	0.787925539907239	1	FACETS	0.93	0.853	1	0.93	0.853	1	CLONAL	1	TRUE	0	0.787925539907239	1		372	139	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0030195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	166	282	0				ENST00000310581	NM_198253.2	-/1132			0.150503130966845	4	FACETS	0.773	0.716	0.831	0.386	0.358	0.416	INDETERMINATE	2	TRUE	0	0.786135290443747	4		282	488	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0030195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	346	351	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.786135290443747	3	FACETS	0.992	0.95	1	0.992	0.95	1	CLONAL	2	TRUE	1	0.786135290443747	3		351	618	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93636995	93636995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	361	420	0	ENST00000375746.1:c.1045G>A	p.Glu349Lys	p.E349K	ENST00000375746	NM_001174167.1	349	Gag/Aag	9/14	0.461054344637729	4	FACETS	1	0.99	1	1	0.99	1	INDETERMINATE	2	TRUE	2	0.786135290443747	4		420	730	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256666	16256666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	179	485	0	ENST00000375759.3:c.3931C>T	p.Pro1311Ser	p.P1311S	ENST00000375759	NM_015001.2	1311	Cct/Tct	11/15	0.261308227617599	1	FACETS	0.562	0.522	0.602	0.562	0.522	0.602	INDETERMINATE	1	TRUE	0	0.786135290443747	1		485	492	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687321	37687321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	211	516	0	ENST00000447079.4:c.4225C>T	p.Pro1409Ser	p.P1409S	ENST00000447079	NM_015083.1	1409	Ccc/Tcc	14/14	0.786135290443747	3	FACETS	1	0.941	1	0.337	0.314	0.361	CLONAL	1	TRUE	0	0.786135290443747	3		516	740	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004922	150004922	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	185	426	0	ENST00000253339.5:c.1303C>T	p.Gln435Ter	p.Q435*	ENST00000253339		435	Cag/Tag	3/7	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.786135290443747	2		426	415	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729163	66729163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516792	NA	P-0030195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	237	540	0	ENST00000307102.5:c.371C>T	p.Pro124Leu	p.P124L	ENST00000307102	NM_002755.3	124	cCg/cTg	3/11	0.786135290443747	2	FACETS	0.947	0.889	1	0.473	0.444	0.503	CLONAL	1	TRUE	0	0.786135290443747	2		540	637	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123245021	123245021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	314	480	0	ENST00000358487.5:c.2083G>A	p.Glu695Lys	p.E695K	ENST00000358487	NM_000141.4	695	Gag/Aag	16/18	0.786135290443747	2	FACETS	0.962	0.93	0.994	0.962	0.93	0.994	CLONAL	2	TRUE	0	0.786135290443747	2		480	415	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878115	48878117	+	inframe_deletion	In_Frame_Del	DEL	CCG	CCG	-	rs587778823	NA	P-0030195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	13	100	0	ENST00000267163.4:c.78_80del	p.Pro29del	p.P29del	ENST00000267163	NM_000321.2	23	CCG/-	1/27	0.702815809638281	4	FACETS	0.238	0.169	0.322	0.119	0.084	0.161	SUBCLONAL	1	TRUE	2	0.786135290443747	4		100	248	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306721	41306721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	267	502	0	ENST00000373198.4:c.938C>T	p.Ser313Phe	p.S313F	ENST00000373198	NM_133170.3	313	tCc/tTc	7/32	0.786135290443747	3	FACETS	0.886	0.84	0.932	0.886	0.84	0.932	CLONAL	2	TRUE	1	0.786135290443747	3		502	534	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306677	41306677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs724159835	NA	P-0030195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	312	731	0	ENST00000373198.4:c.982C>T	p.Arg328Cys	p.R328C	ENST00000373198	NM_133170.3	328	Cgc/Tgc	7/32	0.786135290443747	3	FACETS	0.886	0.844	0.928	0.886	0.844	0.928	CLONAL	2	TRUE	1	0.786135290443747	3		731	624	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968610	55968610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374980446	NA	P-0030195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	502	569	0	ENST00000263923.4:c.2053G>A	p.Glu685Lys	p.E685K	ENST00000263923	NM_002253.2	685	Gaa/Aaa	14/30	0.786135290443747	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.786135290443747	3		569	873	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721964	176721964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	385	482	1	ENST00000439151.2:c.7595C>T	p.Ser2532Leu	p.S2532L	ENST00000439151	NM_022455.4	2532	tCa/tTa	23/23	0.786135290443747	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.786135290443747	3		483	660	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622239	162622239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55654276	NA	P-0030195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	149	387	0	ENST00000366898.1:c.458C>T	p.Pro153Leu	p.P153L	ENST00000366898	NM_004562.2	153	cCc/cTc	4/12	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.786135290443747	2		387	369	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518406	8518406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	180	203	0	ENST00000356435.5:c.985C>T	p.Pro329Ser	p.P329S	ENST00000356435		329	Cct/Tct	10/35	0.770938987257409	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.786135290443747	2		203	219	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597849	43597849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564490056	NA	P-0030195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	222	673	0	ENST00000355710.3:c.397C>T	p.Arg133Cys	p.R133C	ENST00000355710	NM_020975.4	133	Cgt/Tgt	3/20	0.786135290443747	2	FACETS	1	0.953	1	0.509	0.477	0.541	CLONAL	1	TRUE	0	0.786135290443747	2		673	555	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55272964	55272964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	188	469	1	ENST00000275493.2:c.3287C>T	p.Ser1096Phe	p.S1096F	ENST00000275493	NM_005228.3	1096	tCc/tTc	28/28	0.786135290443747	3	FACETS	0.949	0.88	1	0.475	0.44	0.51	CLONAL	1	TRUE	1	0.786135290443747	3		470	702	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215582	5215582	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	362	566	0	ENST00000357368.4:c.4121C>T	p.Pro1374Leu	p.P1374L	ENST00000357368	NM_002850.3	1374	cCc/cTc	27/38	0.461054344637729	4	FACETS	1	0.978	1	1	0.978	1	INDETERMINATE	2	TRUE	2	0.786135290443747	4		566	789	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295217	1295217	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs796849347	NA	P-0030195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	140	321	0				ENST00000310581	NM_198253.2	-/1132			0.150503130966845	4	FACETS	0.783	0.721	0.848	0.392	0.36	0.424	INDETERMINATE	2	TRUE	0	0.786135290443747	4		321	406	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105556	27105557	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0030195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	172	453	0	ENST00000324856.7:c.5168dup	p.Cys1723TrpfsTer4	p.C1723Wfs*4	ENST00000324856	NM_006015.4	1723	tgc/tGgc	20/20	0.261308227617599	1	FACETS	0.566	0.526	0.608	0.566	0.526	0.608	INDETERMINATE	1	TRUE	0	0.786135290443747	1		453	469	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222620	69222620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	502	472	0	ENST00000462284.1:c.593C>T	p.Ser198Phe	p.S198F	ENST00000462284	NM_002392.5	198	tCc/tTc	8/11	0.786135290443747	2	FACETS	0.995	0.969	1	0.995	0.969	1	CLONAL	2	TRUE	0	0.786135290443747	2		472	642	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740372	58740372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	516	415	0	ENST00000305921.3:c.1277C>T	p.Pro426Leu	p.P426L	ENST00000305921	NM_003620.3	426	cCa/cTa	6/6	0.786135290443747	3	FACETS	0.998	0.976	1	0.998	0.976	1	CLONAL	3	TRUE	0	0.786135290443747	3		415	611	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554497	63554497	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146238336	NA	P-0030195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	611	513	1	ENST00000307078.5:c.242C>T	p.Ser81Phe	p.S81F	ENST00000307078	NM_004655.3	81	tCc/tTc	2/11	0.786135290443747	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.786135290443747	3		514	710	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222947	36222947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	582	776	0	ENST00000222270.7:c.5576C>T	p.Ser1859Phe	p.S1859F	ENST00000222270	NM_014727.1	1859	tCt/tTt	27/37	0.461054344637729	4	FACETS	1	0.986	1	1	0.986	1	INDETERMINATE	2	TRUE	2	0.786135290443747	4		776	1264	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376777	31376778	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCGGTGGGTCCAGTGGTTTGGCGATGGCAAGTTCTCC	novel	NA	P-0030195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	114	404	0	ENST00000328111.2:c.773_810dup	p.Glu271CysfsTer72	p.E271Cfs*72	ENST00000328111	NM_006892.3	258	atg/aTGCGGTGGGTCCAGTGGTTTGGCGATGGCAAGTTCTCCtg	7/23	0.786135290443747	3	FACETS	0.623	0.561	0.687	0.311	0.28	0.344	SUBCLONAL	1	TRUE	1	0.786135290443747	3		404	649	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400109	41400110	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0030195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	121	411	0	ENST00000373198.4:c.649_650delinsAA	p.Gly217Lys	p.G217K	ENST00000373198	NM_133170.3	217	GGg/AAg	5/32	0.786135290443747	3	FACETS	0.764	0.693	0.839	0.382	0.346	0.42	SUBCLONAL	1	TRUE	1	0.786135290443747	3		411	561	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62294244	62294244	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0030195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	234	539	0	ENST00000360203.5:c.538+2T>A		p.X180_splice	ENST00000360203	NM_001283009.1	180			0.786135290443747	3	FACETS	1	0.938	1	0.501	0.469	0.535	CLONAL	1	TRUE	1	0.786135290443747	3		539	827	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39774533	39774533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	177	347	0	ENST00000288319.7:c.619G>A	p.Asp207Asn	p.D207N	ENST00000288319	NM_182918.3	207	Gat/Aat	5/10	0.261308227617599	1	FACETS	0.618	0.576	0.661	0.618	0.576	0.661	INDETERMINATE	1	TRUE	0	0.786135290443747	1		347	442	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808322	1808322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	251	771	2	ENST00000260795.2:c.2080C>T	p.Pro694Ser	p.P694S	ENST00000260795		694	Ccg/Tcg	15/17	0.786135290443747	3	FACETS	0.965	0.904	1	0.482	0.452	0.514	CLONAL	1	TRUE	1	0.786135290443747	3		773	922	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508803	31508803	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	286	518	0	ENST00000344624.3:c.1512del	p.Ile505LeufsTer26	p.I505Lfs*26	ENST00000344624		504	gtT/gt	7/33	0.786135290443747	3	FACETS	1	0.962	1	0.514	0.484	0.545	CLONAL	1	TRUE	1	0.786135290443747	3		518	986	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38966823	38966823	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1561470102	NA	P-0030195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	209	206	0	ENST00000357387.3:c.1219G>A	p.Gly407Ser	p.G407S	ENST00000357387	NM_152756.3	407	Ggt/Agt	15/38	0.786135290443747	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.786135290443747	3		206	366	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30676042	30676042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	209	400	0	ENST00000376406.3:c.2314C>T	p.Leu772Phe	p.L772F	ENST00000376406	NM_014641.2	772	Ctt/Ttt	8/15	0.541777869148937	4	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.786135290443747	4		400	802	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954955	2954955	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	405	597	1	ENST00000396946.4:c.2755G>A	p.Val919Ile	p.V919I	ENST00000396946	NM_032415.4	919	Gtc/Atc	21/25	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	1	TRUE	NA	0.786135290443747	2		598	747	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	95	282	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.396828495485923	2		282	424	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	300	380	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.396828495485923	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.396828495485923	3		380	528	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644465	3644465	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	138	595	0	ENST00000294008.3:c.2149C>T	p.Leu717Phe	p.L717F	ENST00000294008	NM_032444.2	717	Ctc/Ttc	10/15	1	2	FACETS	0.935	0.852	1	0.935	0.852	1	CLONAL	1	TRUE	1	0.396828495485923	2		595	744	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230641	46230641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	98	464	0	ENST00000334344.6:c.890C>T	p.Ser297Phe	p.S297F	ENST00000334344	NM_152641.2	297	tCc/tTc	8/21	1	2	FACETS	0.982	0.88	1	0.982	0.88	1	CLONAL	1	TRUE	1	0.396828495485923	2		464	503	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056437	26056437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781281855	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	22	249	0	ENST00000343677.2:c.220G>A	p.Glu74Lys	p.E74K	ENST00000343677	NM_005319.3	74	Gag/Aag	1/1	0.219183460153834	2	FACETS	0.478	0.371	0.601	0.239	0.185	0.301	INDETERMINATE	1	TRUE	0	0.396828495485923	2		249	232	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539564	187539564	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	74	319	1	ENST00000441802.2:c.8176C>T	p.Arg2726Ter	p.R2726*	ENST00000441802	NM_005245.3	2726	Cga/Tga	10/27	0.396828495485923	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.396828495485923	1		320	274	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578419	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587781845	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	154	547	0	ENST00000269305.4:c.511G>T	p.Glu171Ter	p.E171*	ENST00000269305	NM_001126112.2	171	Gag/Tag	5/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.396828495485923	2		547	668	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11313952	11313952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	88	602	1	ENST00000361445.4:c.784C>T	p.His262Tyr	p.H262Y	ENST00000361445	NM_004958.3	262	Cat/Tat	6/58	0.305038182656985	1	FACETS	0.509	0.45	0.571	0.509	0.45	0.571	SUBCLONAL	1	TRUE	0	0.396828495485923	1		603	699	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199567	16199568	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	41	392	1	ENST00000375759.3:c.340_341delinsTT	p.Pro114Phe	p.P114F	ENST00000375759	NM_015001.2	114	CCt/TTt	2/15	0.305038182656985	1	FACETS	0.301	0.25	0.357	0.301	0.25	0.357	SUBCLONAL	1	TRUE	0	0.396828495485923	1		393	551	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598338	28598338	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	79	610	0	ENST00000253063.3:c.310G>T	p.Asp104Tyr	p.D104Y	ENST00000253063	NM_031459.4	104	Gat/Tat	3/10	0.305038182656985	1	FACETS	0.425	0.373	0.481	0.425	0.373	0.481	SUBCLONAL	1	TRUE	0	0.396828495485923	1		610	751	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935253	36935253	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	63	627	1	ENST00000361632.4:c.1474G>A	p.Glu492Lys	p.E492K	ENST00000361632		492	Gag/Aag	10/16	0.305038182656985	1	FACETS	0.4	0.345	0.459	0.4	0.345	0.459	SUBCLONAL	1	TRUE	0	0.396828495485923	1		628	637	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937160	36937160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	55	645	0	ENST00000361632.4:c.1159C>T	p.Leu387Phe	p.L387F	ENST00000361632		387	Ctc/Ttc	9/16	0.305038182656985	1	FACETS	0.354	0.303	0.411	0.354	0.303	0.411	SUBCLONAL	1	TRUE	0	0.396828495485923	1		645	627	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511611	46511612	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	51	483	1	ENST00000262741.5:c.1165_1166delinsAA	p.Gly389Lys	p.G389K	ENST00000262741	NM_003629.3	389	GGa/AAa	9/10	0.305038182656985	1	FACETS	0.326	0.276	0.381	0.326	0.276	0.381	SUBCLONAL	1	TRUE	0	0.396828495485923	1		484	632	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335136	65335136	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	127	445	0	ENST00000342505.4:c.505T>C	p.Cys169Arg	p.C169R	ENST00000342505	NM_002227.2	169	Tgc/Cgc	6/25	0.305038182656985	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.396828495485923	1		445	477	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163804	72163804	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	96	416	1	ENST00000357731.5:c.554G>A	p.Gly185Glu	p.G185E	ENST00000357731	NM_173808.2	185	gGa/gAa	4/7	0.305038182656985	1	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	0	0.396828495485923	1		417	386	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332487	70332487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	140	536	0	ENST00000373644.4:c.392C>T	p.Ser131Phe	p.S131F	ENST00000373644	NM_030625.2	131	tCt/tTt	2/12	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.396828495485923	2		536	682	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533552	533552	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	236	658	1	ENST00000451590.1:c.351G>T	p.Lys117Asn	p.K117N	ENST00000451590	NM_001130442.1	117	aaG/aaT	4/5	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.396828495485923	2		659	802	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118365427	118365427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	79	365	0	ENST00000534358.1:c.5308C>T	p.Pro1770Ser	p.P1770S	ENST00000534358	NM_005933.3	1770	Cca/Tca	18/36	1	2	FACETS	0.665	0.585	0.75	0.665	0.585	0.75	SUBCLONAL	1	TRUE	1	0.396828495485923	2		365	599	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514084	125514085	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	146	505	1	ENST00000428830.2:c.1022_1023delinsAA	p.Gly341Glu	p.G341E	ENST00000428830	NM_001114121.2	341	gGG/gAA	10/14	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.396828495485923	2		506	572	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691241	18691241	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	73	261	1	ENST00000266497.5:c.3352G>A	p.Glu1118Lys	p.E1118K	ENST00000266497		1118	Gaa/Aaa	23/31	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.396828495485923	2		262	299	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857536	57857536	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	156	654	0	ENST00000228682.2:c.62C>T	p.Pro21Leu	p.P21L	ENST00000228682	NM_005269.2	21	cCc/cTc	2/12	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.396828495485923	2		654	625	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233835	133233835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	118	522	1	ENST00000320574.5:c.3469C>T	p.Pro1157Ser	p.P1157S	ENST00000320574	NM_006231.2	1157	Cca/Tca	29/49	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.396828495485923	2		523	545	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135283	30135283	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	70	365	0	ENST00000331968.5:c.535G>A	p.Gly179Arg	p.G179R	ENST00000331968	NM_002742.2	179	Ggg/Agg	3/18	1	2	FACETS	0.713	0.623	0.809	0.713	0.623	0.809	SUBCLONAL	1	TRUE	1	0.396828495485923	2		365	495	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104396	2104396	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs997604465	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	179	659	0	ENST00000219476.3:c.436C>T	p.Leu146Phe	p.L146F	ENST00000219476	NM_000548.3	146	Ctc/Ttc	5/42	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.396828495485923	2		659	765	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972440	81972440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs891516801	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	93	393	0	ENST00000359376.3:c.3233G>A	p.Arg1078Gln	p.R1078Q	ENST00000359376	NM_002661.3	1078	cGa/cAa	29/33	1	2	FACETS	0.9	0.803	1	0.9	0.803	1	CLONAL	1	TRUE	1	0.396828495485923	2		393	521	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89839723	89839723	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	63	662	0	ENST00000389301.3:c.1970T>G	p.Leu657Arg	p.L657R	ENST00000389301	NM_000135.2	657	cTg/cGg	22/43	1	2	FACETS	0.48	0.415	0.551	0.48	0.415	0.551	SUBCLONAL	1	TRUE	1	0.396828495485923	2		662	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579503	7579503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	113	629	2	ENST00000269305.4:c.184G>A	p.Glu62Lys	p.E62K	ENST00000269305	NM_001126112.2	62	Gaa/Aaa	4/11	1	2	FACETS	0.829	0.747	0.916	0.829	0.747	0.916	CLONAL	1	TRUE	1	0.396828495485923	2		631	687	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691003	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	149	543	0	ENST00000269305.4:c.96+1G>T		p.X32_splice	ENST00000269305	NM_001126112.2	32			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.396828495485923	2		543	642	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17125858	17125859	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGTCAGCGA	rs1209487287	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	98	600	0	ENST00000285071.4:c.727_735dup	p.Leu244_Ser246dup	p.L244_S246dup	ENST00000285071	NM_144997.5	244	-/TCGCTGACA	7/14	1	2	FACETS	0.696	0.621	0.775	0.696	0.621	0.775	SUBCLONAL	1	TRUE	1	0.396828495485923	2		600	710	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276799	15276800	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	117	580	1	ENST00000263388.2:c.5465_5466delinsTT	p.Ser1822Phe	p.S1822F	ENST00000263388	NM_000435.2	1822	tCC/tTT	30/33	1	2	FACETS	0.911	0.823	1	0.911	0.823	1	CLONAL	1	TRUE	1	0.396828495485923	2		581	647	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082896	16082896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767711936	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	38	192	0	ENST00000281043.3:c.710C>T	p.Pro237Leu	p.P237L	ENST00000281043	NM_005378.4	237	cCg/cTg	2/3	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.396828495485923	2		192	163	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464460	25464460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779176507	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	105	430	0	ENST00000264709.3:c.2053G>A	p.Gly685Arg	p.G685R	ENST00000264709	NM_175629.2	685	Ggg/Agg	17/23	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.396828495485923	2		430	460	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268351	46268351	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	160	383	0	ENST00000371998.3:c.2738A>G	p.Gln913Arg	p.Q913R	ENST00000371998		913	cAg/cGg	15/23	1	2	FACETS	0.792	0.731	0.855	1	0.99	1	SUBCLONAL	2	TRUE	1	0.396828495485923	2		383	509	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839814	42839814	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	105	332	0	ENST00000398585.3:c.1426-1G>A		p.X476_splice	ENST00000398585	NM_001135099.1	476			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.396828495485923	2		332	401	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513297	44513297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1355087638	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	171	601	0	ENST00000291552.4:c.638G>A	p.Gly213Asp	p.G213D	ENST00000291552	NM_006758.2	213	gGt/gAt	8/8	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.396828495485923	2		601	784	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631622	119631622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	158	392	0	ENST00000316626.5:c.644C>T	p.Ser215Leu	p.S215L	ENST00000316626		215	tCg/tTg	6/12	0.134141308378596	5	FACETS	1	0.973	1	0.748	0.689	0.809	INDETERMINATE	2	TRUE	2	0.396828495485923	5		392	566	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911561	134911561	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	135	482	0	ENST00000398015.3:c.2026G>C	p.Asp676His	p.D676H	ENST00000398015	NM_004441.4	676	Gac/Cac	11/16	0.134141308378596	5	FACETS	0.863	0.787	0.942	0.575	0.524	0.628	INDETERMINATE	2	TRUE	2	0.396828495485923	5		482	629	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502245	186502245	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	75	294	0	ENST00000323963.5:c.54G>A	p.Met18Ile	p.M18I	ENST00000323963		18	atG/atA	2/11	0.134141308378596	5	FACETS	1	0.973	1	0.469	0.412	0.529	INDETERMINATE	1	TRUE	2	0.396828495485923	5		294	429	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979282	93979282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	46	426	0	ENST00000369303.4:c.1546C>T	p.Arg516Trp	p.R516W	ENST00000369303	NM_004440.3	516	Cgg/Tgg	7/17	0.219183460153834	2	FACETS	0.555	0.468	0.65	0.277	0.234	0.325	INDETERMINATE	1	TRUE	0	0.396828495485923	2		426	418	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508631	106508631	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	108	426	0	ENST00000359195.3:c.625G>A	p.Glu209Lys	p.E209K	ENST00000359195	NM_002649.2	209	Gag/Aag	2/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.396828495485923	2		426	471	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542228	141542228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	144	390	1	ENST00000220592.5:c.2495G>A	p.Gly832Glu	p.G832E	ENST00000220592	NM_012154.3	832	gGg/gAg	19/19	0.134141308378596	5	FACETS	1	0.942	1	0.69	0.633	0.75	INDETERMINATE	2	TRUE	2	0.396828495485923	5		391	559	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738222	133738223	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	182	462	2	ENST00000318560.5:c.622_623delinsAT	p.Gly208Met	p.G208M	ENST00000318560	NM_005157.4	208	GGg/ATg	4/11	0.179966738674072	2	FACETS	0.799	0.742	0.858	0.799	0.742	0.858	INDETERMINATE	2	TRUE	0	0.396828495485923	2		464	574	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650787	48650787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	139	354	1	ENST00000376670.3:c.656G>A	p.Arg219Lys	p.R219K	ENST00000376670	NM_002049.3	219	aGg/aAg	4/6	1	1	FACETS	0.791	0.729	0.854	1	0.989	1	SUBCLONAL	2	TRUE	0	0.396828495485923	1		355	355	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0030199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	363	563	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	0.344494198324024	5	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.598244753070404	5		563	996	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0030199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	439	529	1	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.598244753070404	2	FACETS	0.981	0.945	1	0.981	0.945	1	CLONAL	2	TRUE	0	0.598244753070404	2		530	748	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693008	89693008	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	rs1564830522	NA	P-0030199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	144	348	0	ENST00000371953.3:c.492+1del		p.K164fs	ENST00000371953	NM_000314.4	164	aaG/aa	5/9	0.598244753070404	2	FACETS	0.944	0.882	1	0.944	0.882	1	CLONAL	2	TRUE	0	0.598244753070404	2		348	255	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864537	56864537	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	169	454	0	ENST00000308159.5:c.1025A>G	p.Gln342Arg	p.Q342R	ENST00000308159	NM_014669.4	342	cAg/cGg	10/22	0.557978452731912	4	FACETS	1	0.956	1	0.529	0.487	0.574	CLONAL	1	TRUE	2	0.598244753070404	4		454	853	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635154	87635156	+	frameshift_variant	Frame_Shift_Del	DEL	ATG	ATG	TT	novel	NA	P-0030199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	267	377	1	ENST00000277120.3:c.2206_2208delinsTT	p.Met736PhefsTer43	p.M736Ffs*43	ENST00000277120		736	ATG/TT	18/19	0.597680697972105	2	FACETS	0.948	0.902	0.993	0.948	0.902	0.993	CLONAL	2	TRUE	0	0.598244753070404	2		378	471	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411011	63411011	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	126	547	0	ENST00000330258.3:c.2156T>C	p.Met719Thr	p.M719T	ENST00000330258	NM_152424.3	719	aTg/aCg	2/2	0.598244753070404	6	FACETS	0.793	0.716	0.874	0.159	0.143	0.175	SUBCLONAL	1	TRUE	1	0.598244753070404	6		547	1167	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0030219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	271	354	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.371693925413009	3	FACETS	0.946	0.893	1	0.946	0.893	1	CLONAL	2	TRUE	1	0.50880737762012	3		354	706	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0030219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	155	772	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.50880737762012	1	FACETS	0.925	0.853	0.999	0.925	0.853	0.999	CLONAL	1	TRUE	0	0.50880737762012	1		772	491	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604701	48604701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555687572	NA	P-0030219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	142	331	0	ENST00000342988.3:c.1523G>A	p.Gly508Asp	p.G508D	ENST00000342988	NM_005359.5	508	gGc/gAc	12/12	0.50880737762012	1	FACETS	0.986	0.907	1	0.986	0.907	1	CLONAL	1	TRUE	0	0.50880737762012	1		331	422	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448321	56448321	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	223	521	0	ENST00000407977.2:c.326T>C	p.Leu109Pro	p.L109P	ENST00000407977		109	cTg/cCg	3/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.50880737762012	2		521	840	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	203	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.961	0.901	1	0.961	0.901	1	CLONAL	1	TRUE	1	0.910520875932822	2		215	464	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057520005	NA	P-0030222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	20	592	0	ENST00000269305.4:c.820G>T	p.Val274Phe	p.V274F	ENST00000269305	NM_001126112.2	274	Gtt/Ttt	8/11	1	2	FACETS	0.045	0.034	0.058	0.045	0.034	0.058	SUBCLONAL	1	TRUE	1	0.910520875932822	2		592	983	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653857	89653857	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	141	418	0	ENST00000371953.3:c.155A>G	p.Asp52Gly	p.D52G	ENST00000371953	NM_000314.4	52	gAt/gGt	2/9	0.910520875932822	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.910520875932822	1		418	167	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	455	215	0				ENST00000310581	NM_198253.2	-/1132			0.344566611729675	7	FACETS	1	0.978	1	1	0.978	1	CLONAL	5	TRUE	2	0.344566611729675	7		215	956	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0030253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	65	654	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.229727787848959	3	FACETS	0.482	0.417	0.554	0.161	0.139	0.185	SUBCLONAL	1	TRUE	0	0.344566611729675	3		654	917	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0030253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	49	701	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.229727787848959	3	FACETS	0.377	0.318	0.443	0.126	0.106	0.148	SUBCLONAL	1	TRUE	0	0.344566611729675	3		701	884	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39618752	39618752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1331467644	NA	P-0030253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	44	331	0	ENST00000262039.4:c.1976G>A	p.Arg659Gln	p.R659Q	ENST00000262039	NM_002647.2	659	cGg/cAg	18/25	0.170462572629724	5	FACETS	0.72	0.603	0.849	0.24	0.201	0.283	INDETERMINATE	1	TRUE	2	0.344566611729675	5		331	538	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045718	47045718	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	258	456	0	ENST00000377604.3:c.2599C>T	p.Gln867Ter	p.Q867*	ENST00000377604	NM_001204468.1	867	Cag/Tag	23/24	0.344566611729675	2	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.344566611729675	2		456	634	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852788	63852788	+	frameshift_variant,stop_lost	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	108	339	0	ENST00000279873.7:c.3566del	p.Ter1189TrpfsTer26	p.*1189Wfs*26	ENST00000279873	NM_032199.2	1189	tAg/tg	10/10	0.288033236661117	2	FACETS	1	0.983	1	0.739	0.668	0.814	CLONAL	1	TRUE	0	0.344566611729675	2		339	424	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3824665	3824665	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	121	556	0	ENST00000262367.5:c.2188G>A	p.Gly730Arg	p.G730R	ENST00000262367	NM_004380.2	730	Ggg/Agg	12/31	0.344566611729675	3	FACETS	0.98	0.885	1	0.327	0.295	0.36	CLONAL	1	TRUE	0	0.344566611729675	3		556	840	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619285	23619288	+	frameshift_variant	Frame_Shift_Del	DEL	ACTC	ACTC	-	novel	NA	P-0030253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	123	691	0	ENST00000261584.4:c.3247_3250del	p.Glu1083ArgfsTer11	p.E1083Rfs*11	ENST00000261584	NM_024675.3	1083	GAGTcg/cg	12/13	0.344566611729675	3	FACETS	0.841	0.759	0.928	0.28	0.253	0.31	CLONAL	1	TRUE	0	0.344566611729675	3		691	995	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541583	29541583	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	58	422	1	ENST00000356175.3:c.1507G>T	p.Asp503Tyr	p.D503Y	ENST00000356175	NM_000267.3	503	Gat/Tat	13/57	0.229727787848959	3	FACETS	0.702	0.603	0.81	0.234	0.201	0.27	SUBCLONAL	1	TRUE	0	0.344566611729675	3		423	562	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71008511	71008511	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	49	319	0	ENST00000318789.4:c.1921G>C	p.Asp641His	p.D641H	ENST00000318789	NM_032682.5	641	Gat/Cat	21/21	0.237238053940182	3	FACETS	0.703	0.596	0.821	0.352	0.298	0.411	SUBCLONAL	1	TRUE	1	0.344566611729675	3		319	474	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1941455	1941455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866345564	NA	P-0030253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	69	603	0	ENST00000382891.5:c.1831C>G	p.Leu611Val	p.L611V	ENST00000382891	NM_133335.3	611	Ctt/Gtt	9/22	1	2	FACETS	0.537	0.467	0.613	0.537	0.467	0.613	SUBCLONAL	1	TRUE	1	0.344566611729675	2		603	746	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940381	13940381	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1562584261	NA	P-0030253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	130	368	0	ENST00000405192.2:c.1125G>C	p.Glu375Asp	p.E375D	ENST00000405192	NM_001163147.1	375	gaG/gaC	11/12	0.344566611729675	4	FACETS	0.794	0.722	0.869	0.794	0.722	0.869	SUBCLONAL	2	TRUE	2	0.344566611729675	4		368	639	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	84	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.91	1	1	0.988	1	CLONAL	3	TRUE	1	0.125759583319084	2		215	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	348	598	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.125759583319084	2	FACETS	1	0.983	1	1	0.997	1	CLONAL	6	TRUE	0	0.125759583319084	2		598	859	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850705	63850705	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs201178069	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	61	409	1	ENST00000279873.7:c.1489del	p.Ile497Ter	p.I497*	ENST00000279873	NM_032199.2	495	Aaa/aa	10/10	1	2	FACETS	0.76	0.655	0.874	1	0.97	1	SUBCLONAL	2	TRUE	1	0.125759583319084	2		410	638	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140869	37140869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	137	543	1	ENST00000373509.5:c.705G>A	p.Met235Ile	p.M235I	ENST00000373509	NM_002648.3	235	atG/atA	5/6	1	2	FACETS	0.967	0.881	1	1	0.992	1	CLONAL	3	TRUE	1	0.125759583319084	2		544	751	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678469	88678469	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	127	506	0	ENST00000360948.2:c.1067G>A	p.Gly356Glu	p.G356E	ENST00000360948	NM_001012338.2	356	gGa/gAa	9/19	1	2	FACETS	0.997	0.905	1	1	0.992	1	CLONAL	3	TRUE	1	0.125759583319084	2		506	675	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651496	52651496	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	158	490	1	ENST00000394830.3:c.1600C>T	p.Arg534Ter	p.R534*	ENST00000394830	NM_018313.4	534	Cga/Tga	15/30	1	2	FACETS	0.971	0.89	1	1	0.993	1	CLONAL	3	TRUE	1	0.125759583319084	2		491	863	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412375	139412375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1341448592	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	416	426	0	ENST00000277541.6:c.1270G>A	p.Glu424Lys	p.E424K	ENST00000277541	NM_017617.3	424	Gag/Aag	8/34	0.125759583319084	6	FACETS	1	0.976	1	1	0.997	1	CLONAL	10	TRUE	0	0.125759583319084	6		426	808	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681353	88681353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140592056	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	14	124	1	ENST00000372037.3:c.1243G>A	p.Glu415Lys	p.E415K	ENST00000372037	NM_004329.2	415	Gaa/Aaa	11/13	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.125759583319084	2		125	160	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231707	66231707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1211795184	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	104	350	1	ENST00000273854.3:c.1993G>A	p.Glu665Lys	p.E665K	ENST00000273854	NM_004439.5	665	Gaa/Aaa	11/18	1	2	FACETS	1	0.917	1	1	0.99	1	CLONAL	3	TRUE	1	0.125759583319084	2		351	539	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829243	128829243	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	104	403	0	ENST00000249373.3:c.251C>T	p.Pro84Leu	p.P84L	ENST00000249373	NM_005631.4	84	cCc/cTc	1/12	1	2	FACETS	0.92	0.826	1	1	0.99	1	CLONAL	3	TRUE	1	0.125759583319084	2		403	599	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460401	149460401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	126	450	0	ENST00000286301.3:c.236C>T	p.Thr79Met	p.T79M	ENST00000286301	NM_005211.3	79	aCg/aTg	3/22	1	2	FACETS	0.946	0.858	1	1	0.992	1	CLONAL	3	TRUE	1	0.125759583319084	2		450	706	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438316	110438317	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	rs532810290	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	22	148	0	ENST00000375856.3:c.82_84dup	p.Asn28dup	p.N28dup	ENST00000375856	NM_003749.2	28	-/AAC	1/2	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.125759583319084	2		148	277	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	149	322	2	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	1	2	FACETS	0.912	0.833	0.994	1	0.993	1	CLONAL	3	TRUE	1	0.125759583319084	2		324	866	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024480	16024480	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1432273966	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	135	368	0	ENST00000268712.3:c.1738C>T	p.Arg580Cys	p.R580C	ENST00000268712	NM_006311.3	580	Cgc/Tgc	16/46	1	2	FACETS	0.88	0.802	0.961	1	0.993	1	CLONAL	4	TRUE	1	0.125759583319084	2		368	610	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248726	212248726	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	93	356	0	ENST00000342788.4:c.3541C>T	p.Gln1181Ter	p.Q1181*	ENST00000342788	NM_005235.2	1181	Caa/Taa	28/28	1	2	FACETS	1	0.894	1	1	0.989	1	CLONAL	3	TRUE	1	0.125759583319084	2		356	492	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933640	39933640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780396086	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	122	213	0	ENST00000378444.4:c.959C>T	p.Ala320Val	p.A320V	ENST00000378444	NM_001123385.1	320	gCg/gTg	4/15	1	1	FACETS	0.978	0.897	1	1	0.993	1	CLONAL	6	TRUE	0	0.125759583319084	1		213	310	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873458	136873458	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1558837039	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	106	381	0	ENST00000241393.3:c.40G>A	p.Glu14Lys	p.E14K	ENST00000241393	NM_003467.2	14	Gag/Aag	2/2	1	2	FACETS	0.993	0.893	1	1	0.99	1	CLONAL	3	TRUE	1	0.125759583319084	2		381	566	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514302	69514302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1255340343	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	146	482	1	ENST00000294312.3:c.379C>T	p.Arg127Cys	p.R127C	ENST00000294312	NM_005117.2	127	Cgc/Tgc	3/3	1	2	FACETS	1	0.938	1	1	0.993	1	CLONAL	3	TRUE	1	0.125759583319084	2		483	750	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845529	63845529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771981107	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	106	458	0	ENST00000279873.7:c.1268G>A	p.Arg423Gln	p.R423Q	ENST00000279873	NM_032199.2	423	cGg/cAg	9/10	1	2	FACETS	0.923	0.829	1	1	0.99	1	CLONAL	3	TRUE	1	0.125759583319084	2		458	609	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387086	31387086	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775949142	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	171	481	1	ENST00000328111.2:c.1711C>T	p.Arg571Ter	p.R571*	ENST00000328111	NM_006892.3	571	Cga/Tga	16/23	1	2	FACETS	1	0.971	1	1	0.994	1	CLONAL	3	TRUE	1	0.125759583319084	2		482	815	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117650567	117650567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	145	580	0	ENST00000368508.3:c.5291G>A	p.Gly1764Glu	p.G1764E	ENST00000368508	NM_002944.2	1764	gGg/gAg	32/43	1	2	FACETS	1	0.918	1	1	0.993	1	CLONAL	3	TRUE	1	0.125759583319084	2		580	765	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350674	89350674	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	189	712	0	ENST00000301030.4:c.2276G>A	p.Arg759Lys	p.R759K	ENST00000301030	NM_001256183.1	759	aGa/aAa	9/13	1	2	FACETS	1	0.983	1	1	0.994	1	CLONAL	2	TRUE	1	0.125759583319084	2		712	1226	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731464	47731464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	67	81	0	ENST00000449228.1:c.328C>T	p.Pro110Ser	p.P110S	ENST00000449228	NM_001127240.2	110	Ccg/Tcg	2/4	1	2	FACETS	1	0.896	1	1	0.988	1	CLONAL	5	TRUE	1	0.125759583319084	2		81	210	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270726	10270726	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	141	449	0	ENST00000340748.4:c.1009del	p.Met337TrpfsTer8	p.M337Wfs*8	ENST00000340748		337	Atg/tg	14/40	1	2	FACETS	1	0.946	1	1	0.993	1	CLONAL	3	TRUE	1	0.125759583319084	2		449	712	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156046	119156046	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs483352825	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	146	491	0	ENST00000264033.4:c.1711G>A	p.Asp571Asn	p.D571N	ENST00000264033	NM_005188.3	571	Gac/Aac	11/16	1	2	FACETS	0.851	0.776	0.929	1	0.992	1	CLONAL	3	TRUE	1	0.125759583319084	2		491	910	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628323	86628323	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	79	254	0	ENST00000274376.6:c.693-1G>A		p.X231_splice	ENST00000274376	NM_002890.2	231			1	2	FACETS	0.963	0.851	1	1	0.987	1	CLONAL	3	TRUE	1	0.125759583319084	2		254	435	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113208	209113208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	117	424	0	ENST00000345146.2:c.299G>A	p.Arg100Gln	p.R100Q	ENST00000345146	NM_005896.2	100	cGa/cAa	4/10	1	2	FACETS	0.899	0.812	0.991	1	0.991	1	CLONAL	3	TRUE	1	0.125759583319084	2		424	690	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961148	41961148	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	89	403	0	ENST00000219905.7:c.56G>A	p.Gly19Glu	p.G19E	ENST00000219905	NM_001164273.1	19	gGa/gAa	2/24	1	2	FACETS	1	0.967	1	1	0.987	1	CLONAL	2	TRUE	1	0.125759583319084	2		403	571	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971209	21971209	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1554654224	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	96	307	0	ENST00000304494.5:c.151-2A>G		p.X51_splice	ENST00000304494	NM_000077.4	51			0.125759583319084	1	FACETS	0.919	0.825	1	1	0.99	1	CLONAL	4	TRUE	0	0.125759583319084	1		307	389	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117650583	117650583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	130	550	0	ENST00000368508.3:c.5275C>T	p.Pro1759Ser	p.P1759S	ENST00000368508	NM_002944.2	1759	Ccc/Tcc	32/43	1	2	FACETS	0.96	0.872	1	1	0.992	1	CLONAL	3	TRUE	1	0.125759583319084	2		550	718	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	rs267608078	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	91	404	0	ENST00000234420.5:c.3260_3261dup	p.Phe1088ProfsTer3	p.F1088Pfs*3	ENST00000234420	NM_000179.2	1085	acc/aCCcc	5/10	1	2	FACETS	0.971	0.862	1	1	0.985	1	CLONAL	2	TRUE	1	0.125759583319084	2		404	745	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858935	45858935	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	198	537	2	ENST00000391945.4:c.1531C>T	p.Arg511Trp	p.R511W	ENST00000391945	NM_000400.3	511	Cgg/Tgg	16/23	1	2	FACETS	0.888	0.823	0.955	1	0.995	1	CLONAL	4	TRUE	1	0.125759583319084	2		539	887	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786784	3786784	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	98	359	0	ENST00000262367.5:c.4427C>T	p.Pro1476Leu	p.P1476L	ENST00000262367	NM_004380.2	1476	cCa/cTa	27/31	1	2	FACETS	0.913	0.817	1	1	0.989	1	CLONAL	3	TRUE	1	0.125759583319084	2		359	569	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447848	49447848	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	185	531	0	ENST00000301067.7:c.586C>T	p.Pro196Ser	p.P196S	ENST00000301067	NM_003482.3	196	Ccc/Tcc	5/54	1	2	FACETS	0.914	0.845	0.985	1	0.995	1	CLONAL	4	TRUE	1	0.125759583319084	2		531	805	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916206	9916206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	90	491	0	ENST00000330684.3:c.2083C>T	p.Arg695Trp	p.R695W	ENST00000330684	NM_001134407.1	695	Cgg/Tgg	10/13	1	2	FACETS	1	0.929	1	1	0.986	1	CLONAL	2	TRUE	1	0.125759583319084	2		491	673	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662972	52662972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779427834	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	103	445	1	ENST00000394830.3:c.1381C>T	p.Arg461Cys	p.R461C	ENST00000394830	NM_018313.4	461	Cgc/Tgc	13/30	1	2	FACETS	0.854	0.766	0.948	1	0.989	1	CLONAL	3	TRUE	1	0.125759583319084	2		446	639	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3645613	3645613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200807331	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	187	498	1	ENST00000294008.3:c.2006G>A	p.Arg669His	p.R669H	ENST00000294008	NM_032444.2	669	cGc/cAc	9/15	1	2	FACETS	0.991	0.918	1	1	0.995	1	CLONAL	4	TRUE	1	0.125759583319084	2		499	750	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81979857	81979857	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764693069	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	107	346	0	ENST00000359376.3:c.3559C>T	p.Arg1187Trp	p.R1187W	ENST00000359376	NM_002661.3	1187	Cgg/Tgg	31/33	1	2	FACETS	0.985	0.886	1	1	0.99	1	CLONAL	3	TRUE	1	0.125759583319084	2		346	576	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546635	9546635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	133	426	0	ENST00000353224.5:c.1387G>A	p.Val463Ile	p.V463I	ENST00000353224	NM_177990.2	463	Gta/Ata	5/10	1	2	FACETS	0.898	0.818	0.981	1	0.993	1	CLONAL	4	TRUE	1	0.125759583319084	2		426	589	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702367	47702367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs549467183	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	107	386	0	ENST00000233146.2:c.1963G>A	p.Val655Ile	p.V655I	ENST00000233146	NM_000251.2	655	Gta/Ata	12/16	1	2	FACETS	1	0.971	1	1	0.989	1	CLONAL	2	TRUE	1	0.125759583319084	2		386	692	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096907	11096907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	166	586	0	ENST00000358026.2:c.398C>T	p.Pro133Leu	p.P133L	ENST00000358026	NM_001128849.1	133	cCa/cTa	4/36	1	2	FACETS	0.995	0.915	1	1	0.994	1	CLONAL	3	TRUE	1	0.125759583319084	2		586	884	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609955	43609955	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035958105	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	178	641	1	ENST00000355710.3:c.1907C>T	p.Thr636Met	p.T636M	ENST00000355710	NM_020975.4	636	aCg/aTg	11/20	1	2	FACETS	0.907	0.838	0.979	1	0.994	1	CLONAL	4	TRUE	1	0.125759583319084	2		642	780	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348560	56348561	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1450997592	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	82	289	1	ENST00000348428.3:c.374dup	p.Gly126ArgfsTer40	p.G126Rfs*40	ENST00000348428	NM_006785.3	123	agc/agCc	2/17	0.125759583319084	1	FACETS	0.88	0.783	0.984	1	0.989	1	CLONAL	4	TRUE	0	0.125759583319084	1		290	347	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601854	43601854	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	78	425	0	ENST00000355710.3:c.898G>A	p.Asp300Asn	p.D300N	ENST00000355710	NM_020975.4	300	Gat/Aat	5/20	1	2	FACETS	0.934	0.821	1	1	0.982	1	CLONAL	2	TRUE	1	0.125759583319084	2		425	664	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36823877	36823877	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373166224	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	90	420	0	ENST00000373129.3:c.305C>T	p.Thr102Met	p.T102M	ENST00000373129	NM_032017.1	102	aCg/aTg	5/12	1	2	FACETS	0.858	0.763	0.959	1	0.988	1	CLONAL	3	TRUE	1	0.125759583319084	2		420	556	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46738343	46738343	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs759647251	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	119	437	0	ENST00000371975.4:c.1245-1G>A		p.X415_splice	ENST00000371975	NM_003579.3	415			1	2	FACETS	0.971	0.878	1	1	0.991	1	CLONAL	3	TRUE	1	0.125759583319084	2		437	650	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484362	120484363	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	69	382	1	ENST00000256646.2:c.2767_2768delinsAA	p.Gly923Lys	p.G923K	ENST00000256646	NM_024408.3	923	GGa/AAa	18/34	1	2	FACETS	1	0.903	1	1	0.982	1	CLONAL	2	TRUE	1	0.125759583319084	2		383	527	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716193	243716193	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	261	533	0	ENST00000263826.5:c.1001T>C	p.Val334Ala	p.V334A	ENST00000263826	NM_005465.4	334	gTt/gCt	10/13	0.125759583319084	3	FACETS	0.989	0.929	1			1	CLONAL	5	TRUE	NA	0.125759583319084	3		533	892	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939774	71939774	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	128	550	0	ENST00000298229.2:c.401G>A	p.Gly134Glu	p.G134E	ENST00000298229	NM_001567.3	134	gGg/gAg	4/28	1	2	FACETS	0.914	0.83	1	1	0.992	1	CLONAL	3	TRUE	1	0.125759583319084	2		550	742	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948488	71948488	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	196	632	0	ENST00000298229.2:c.3200C>A	p.Pro1067His	p.P1067H	ENST00000298229	NM_001567.3	1067	cCc/cAc	26/28	1	2	FACETS	0.947	0.878	1	1	0.995	1	CLONAL	4	TRUE	1	0.125759583319084	2		632	823	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205695	108205695	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	82	308	0	ENST00000278616.4:c.8011-1G>A		p.X2671_splice	ENST00000278616	NM_000051.3	2671			1	2	FACETS	1	0.916	1	1	0.988	1	CLONAL	3	TRUE	1	0.125759583319084	2		308	418	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	459927	459927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	121	448	0	ENST00000399788.2:c.1168G>A	p.Val390Ile	p.V390I	ENST00000399788	NM_001042603.1	390	Gta/Ata	10/28	1	2	FACETS	0.835	0.755	0.92	1	0.991	1	CLONAL	3	TRUE	1	0.125759583319084	2		448	768	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1022611	1022611	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	133	488	0	ENST00000358495.3:c.1203G>T	p.Trp401Cys	p.W401C	ENST00000358495	NM_134424.2	401	tgG/tgT	12/12	1	2	FACETS	0.95	0.864	1	1	0.992	1	CLONAL	3	TRUE	1	0.125759583319084	2		488	742	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420777	49420777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761108868	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	137	479	1	ENST00000301067.7:c.14972G>A	p.Arg4991Gln	p.R4991Q	ENST00000301067	NM_003482.3	4991	cGg/cAg	48/54	1	2	FACETS	1	0.926	1	1	0.992	1	CLONAL	3	TRUE	1	0.125759583319084	2		480	713	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865504	57865504	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	142	563	1	ENST00000228682.2:c.2981C>G	p.Pro994Arg	p.P994R	ENST00000228682	NM_005269.2	994	cCa/cGa	12/12	1	2	FACETS	1	0.944	1	1	0.993	1	CLONAL	3	TRUE	1	0.125759583319084	2		564	721	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69210681	69210683	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	81	400	0	ENST00000462284.1:c.266_268del	p.Gly89del	p.G89del	ENST00000462284	NM_002392.5	88	ctAGGa/cta	4/11	1	2	FACETS	0.995	0.877	1	1	0.984	1	CLONAL	2	TRUE	1	0.125759583319084	2		400	647	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811741	102811741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769928521	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	163	490	0	ENST00000307046.8:c.443G>A	p.Arg148Lys	p.R148K	ENST00000307046	NM_001111285.1	148	aGa/aAa	4/4	1	2	FACETS	1	0.93	1	1	0.994	1	CLONAL	3	TRUE	1	0.125759583319084	2		490	852	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930573	32930573	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1566241850	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	84	337	0	ENST00000380152.3:c.7444A>G	p.Thr2482Ala	p.T2482A	ENST00000380152		2482	Aca/Gca	15/27	1	2	FACETS	1	0.966	1	1	0.987	1	CLONAL	2	TRUE	1	0.125759583319084	2		337	536	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504512	103504512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs569799893	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	99	348	0	ENST00000355739.4:c.133C>T	p.Arg45Cys	p.R45C	ENST00000355739	NM_000123.3	45	Cgc/Tgc	2/15	1	2	FACETS	0.942	0.843	1	1	0.989	1	CLONAL	3	TRUE	1	0.125759583319084	2		348	557	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986674	36986674	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	32	42	1	ENST00000354822.5:c.1015G>A	p.Gly339Ser	p.G339S	ENST00000354822	NM_001079668.2	339	Ggt/Agt	3/3	1	2	FACETS	0.975	0.817	1	1	0.975	1	CLONAL	6	TRUE	1	0.125759583319084	2		43	87	SUCCESS
BLM	641	MSKCC	GRCh37	15	91328163	91328163	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	86	367	0	ENST00000355112.3:c.2675T>C	p.Ile892Thr	p.I892T	ENST00000355112	NM_000057.2	892	aTa/aCa	14/22	1	2	FACETS	1	0.954	1	1	0.986	1	CLONAL	2	TRUE	1	0.125759583319084	2		367	593	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	360054	360055	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	99	433	0	ENST00000262320.3:c.1034dup	p.Tyr346IlefsTer5	p.Y346Ifs*5	ENST00000262320	NM_003502.3	345	cca/ccCa	4/11	1	2	FACETS	0.863	0.772	0.96	1	0.989	1	CLONAL	3	TRUE	1	0.125759583319084	2		433	608	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663359	67663359	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	138	461	0	ENST00000264010.4:c.1760A>T	p.Asn587Ile	p.N587I	ENST00000264010	NM_006565.3	587	aAt/aTt	10/12	1	2	FACETS	0.948	0.863	1	1	0.992	1	CLONAL	3	TRUE	1	0.125759583319084	2		461	772	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829961	72829961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	148	626	0	ENST00000268489.5:c.6620C>T	p.Ser2207Phe	p.S2207F	ENST00000268489	NM_006885.3	2207	tCc/tTc	9/10	1	2	FACETS	0.943	0.862	1	1	0.993	1	CLONAL	3	TRUE	1	0.125759583319084	2		626	832	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81954849	81954849	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	190	528	0	ENST00000359376.3:c.2282A>C	p.Asp761Ala	p.D761A	ENST00000359376	NM_002661.3	761	gAt/gCt	21/33	1	2	FACETS	1	0.978	1	1	0.995	1	CLONAL	3	TRUE	1	0.125759583319084	2		528	877	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974748	15974748	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	119	420	0	ENST00000268712.3:c.4127C>G	p.Pro1376Arg	p.P1376R	ENST00000268712	NM_006311.3	1376	cCg/cGg	30/46	1	2	FACETS	0.887	0.802	0.977	1	0.991	1	CLONAL	3	TRUE	1	0.125759583319084	2		420	711	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375529	40375529	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	168	574	0	ENST00000293328.3:c.421C>T	p.His141Tyr	p.H141Y	ENST00000293328	NM_012448.3	141	Cac/Tac	5/19	1	2	FACETS	1	0.926	1	1	0.994	1	CLONAL	3	TRUE	1	0.125759583319084	2		574	884	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40462635	40462635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762056710	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	154	480	0	ENST00000345506.4:c.2333G>A	p.Arg778His	p.R778H	ENST00000345506	NM_003152.3	778	cGc/cAc	20/20	1	2	FACETS	1	0.943	1	1	0.993	1	CLONAL	3	TRUE	1	0.125759583319084	2		480	787	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573583	48573583	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	110	409	0	ENST00000342988.3:c.167C>T	p.Ser56Phe	p.S56F	ENST00000342988	NM_005359.5	56	tCt/tTt	2/12	0.125759583319084	1	FACETS	0.897	0.811	0.987	1	0.991	1	CLONAL	4	TRUE	0	0.125759583319084	1		409	457	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210762	2210762	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748856790	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	154	499	2	ENST00000398665.3:c.1259C>T	p.Ala420Val	p.A420V	ENST00000398665	NM_032482.2	420	gCg/gTg	14/28	1	2	FACETS	0.991	0.907	1	1	0.993	1	CLONAL	3	TRUE	1	0.125759583319084	2		501	824	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954282	17954282	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	133	563	0	ENST00000458235.1:c.327G>A	p.Trp109Ter	p.W109*	ENST00000458235	NM_000215.3	109	tgG/tgA	4/24	1	2	FACETS	0.906	0.824	0.993	1	0.992	1	CLONAL	3	TRUE	1	0.125759583319084	2		563	778	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18956905	18956906	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	93	459	1	ENST00000262803.5:c.348_349delinsAA	p.Asp117Asn	p.D117N	ENST00000262803	NM_002911.3	116	aaGGac/aaAAac	2/24	1	2	FACETS	1	0.961	1	1	0.987	1	CLONAL	2	TRUE	1	0.125759583319084	2		460	630	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222808	36222808	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	147	510	0	ENST00000222270.7:c.5438-1G>A		p.X1813_splice	ENST00000222270	NM_014727.1	1813			1	2	FACETS	1	0.926	1	1	0.993	1	CLONAL	3	TRUE	1	0.125759583319084	2		510	768	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796254	42796254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	144	479	1	ENST00000575354.2:c.2903C>T	p.Pro968Leu	p.P968L	ENST00000575354	NM_015125.3	968	cCg/cTg	12/20	1	2	FACETS	1	0.951	1	1	0.993	1	CLONAL	3	TRUE	1	0.125759583319084	2		480	721	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446229	29446229	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199987354	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	130	445	0	ENST00000389048.3:c.3338G>A	p.Arg1113Gln	p.R1113Q	ENST00000389048	NM_004304.4	1113	cGg/cAg	20/29	1	2	FACETS	0.902	0.821	0.986	1	0.993	1	CLONAL	4	TRUE	1	0.125759583319084	2		445	573	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639559	47639559	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779170	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	86	298	0	ENST00000233146.2:c.652C>T	p.Gln218Ter	p.Q218*	ENST00000233146	NM_000251.2	218	Caa/Taa	4/16	1	2	FACETS	0.88	0.781	0.986	1	0.987	1	CLONAL	3	TRUE	1	0.125759583319084	2		298	518	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47643538	47643538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779067	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	145	546	0	ENST00000233146.2:c.1046C>T	p.Pro349Leu	p.P349L	ENST00000233146	NM_000251.2	349	cCt/cTt	6/16	1	2	FACETS	0.967	0.883	1	1	0.993	1	CLONAL	3	TRUE	1	0.125759583319084	2		546	795	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149831	202149831	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	131	487	0	ENST00000358485.4:c.1272C>A	p.Tyr424Ter	p.Y424*	ENST00000358485	NM_001080125.1	424	taC/taA	8/9	1	2	FACETS	1	0.929	1	1	0.992	1	CLONAL	3	TRUE	1	0.125759583319084	2		487	677	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439553	220439553	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1184216895	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	149	463	1	ENST00000243786.2:c.406G>A	p.Gly136Arg	p.G136R	ENST00000243786	NM_002191.3	136	Ggg/Agg	2/2	1	2	FACETS	1	0.973	1	1	0.993	1	CLONAL	3	TRUE	1	0.125759583319084	2		464	686	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067399	37067400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	133	418	0	ENST00000231790.2:c.1311dup	p.Ala438CysfsTer2	p.A438Cfs*2	ENST00000231790	NM_000249.3	437	cct/ccTt	12/19	1	2	FACETS	1	0.956	1	1	0.992	1	CLONAL	3	TRUE	1	0.125759583319084	2		418	651	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275708	41275708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886039332	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	143	448	1	ENST00000349496.5:c.1603C>T	p.Arg535Ter	p.R535*	ENST00000349496	NM_001904.3	535	Cga/Tga	10/15	1	2	FACETS	1	0.924	1	1	0.993	1	CLONAL	3	TRUE	1	0.125759583319084	2		449	748	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278202	41278202	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1553632414	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	109	380	0	ENST00000349496.5:c.2076+2T>C		p.X692_splice	ENST00000349496	NM_001904.3	692			1	2	FACETS	0.958	0.863	1	1	0.99	1	CLONAL	3	TRUE	1	0.125759583319084	2		380	603	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990449	69990450	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	104	407	0	ENST00000394351.3:c.410dup	p.Leu137PhefsTer20	p.L137Ffs*20	ENST00000394351	NM_000248.3	136	-/T	4/9	1	2	FACETS	0.925	0.83	1	1	0.99	1	CLONAL	3	TRUE	1	0.125759583319084	2		407	596	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260193	149260194	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTG	rs748784098	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	99	455	0	ENST00000360632.3:c.697_699dup	p.Gln233dup	p.Q233dup	ENST00000360632	NM_015472.4	233	-/CAG	4/7	1	2	FACETS	1	0.955	1	1	0.988	1	CLONAL	2	TRUE	1	0.125759583319084	2		455	696	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127399	55127400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	156	525	0	ENST00000257290.5:c.189dup	p.Glu64ArgfsTer11	p.E64Rfs*11	ENST00000257290	NM_006206.4	63	gaa/gAaa	3/23	1	2	FACETS	0.973	0.891	1	1	0.993	1	CLONAL	3	TRUE	1	0.125759583319084	2		525	850	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948725	55948725	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	135	505	0	ENST00000263923.4:c.3740C>T	p.Pro1247Leu	p.P1247L	ENST00000263923	NM_002253.2	1247	cCa/cTa	28/30	1	2	FACETS	0.857	0.779	0.939	1	0.992	1	CLONAL	3	TRUE	1	0.125759583319084	2		505	835	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524341	187524341	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	122	350	0	ENST00000441802.2:c.11339G>A	p.Cys3780Tyr	p.C3780Y	ENST00000441802	NM_005245.3	3780	tGt/tAt	19/27	1	2	FACETS	1	0.967	1	1	0.992	1	CLONAL	3	TRUE	1	0.125759583319084	2		350	565	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539548	187539548	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	110	350	0	ENST00000441802.2:c.8192G>C	p.Gly2731Ala	p.G2731A	ENST00000441802	NM_005245.3	2731	gGg/gCg	10/27	1	2	FACETS	1	0.926	1	1	0.991	1	CLONAL	3	TRUE	1	0.125759583319084	2		350	565	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628905	187628908	+	frameshift_variant	Frame_Shift_Del	DEL	ATTT	ATTT	-	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	120	547	0	ENST00000441802.2:c.2074_2077del	p.Lys692TyrfsTer34	p.K692Yfs*34	ENST00000441802	NM_005245.3	692	AAATta/ta	2/27	1	2	FACETS	1	0.975	1	1	0.991	1	CLONAL	2	TRUE	1	0.125759583319084	2		547	765	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575558	67575558	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1295057906	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	85	287	0	ENST00000274335.5:c.631C>T	p.Pro211Ser	p.P211S	ENST00000274335		211	Cca/Tca	4/15	1	2	FACETS	1	0.965	1	1	0.987	1	CLONAL	2	TRUE	1	0.125759583319084	2		287	548	SUCCESS
APC	324	MSKCC	GRCh37	5	112176287	112176288	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	127	421	1	ENST00000257430.4:c.4996_4997delinsTT	p.Pro1666Leu	p.P1666L	ENST00000257430	NM_000038.5	1666	CCa/TTa	16/16	1	2	FACETS	1	0.96	1	1	0.992	1	CLONAL	3	TRUE	1	0.125759583319084	2		422	610	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20486964	20486964	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	110	400	0	ENST00000346618.3:c.929T>G	p.Leu310Arg	p.L310R	ENST00000346618	NM_001949.4	310	cTt/cGt	5/7	0.125759583319084	2	FACETS	0.885	0.796	0.978	1	0.978	1	CLONAL	3	TRUE	0	0.125759583319084	2		400	659	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169167	32169167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	291	561	0	ENST00000375023.3:c.3866G>A	p.Gly1289Glu	p.G1289E	ENST00000375023	NM_004557.3	1289	gGg/gAg	22/30	0.125759583319084	2	FACETS	1	0.981	1	1	0.996	1	CLONAL	6	TRUE	0	0.125759583319084	2		561	718	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641151	117641152	+	missense_variant	Missense_Mutation	DNP	GA	GA	AG	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	151	588	1	ENST00000368508.3:c.5819_5820delinsCT	p.Phe1940Ser	p.F1940S	ENST00000368508	NM_002944.2	1940	tTC/tCT	36/43	1	2	FACETS	0.834	0.762	0.909	1	0.992	1	CLONAL	3	TRUE	1	0.125759583319084	2		589	960	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686288	117686288	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	122	394	0	ENST00000368508.3:c.3053T>C	p.Val1018Ala	p.V1018A	ENST00000368508	NM_002944.2	1018	gTc/gCc	20/43	1	2	FACETS	1	0.961	1	1	0.992	1	CLONAL	3	TRUE	1	0.125759583319084	2		394	582	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233129	55233129	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs753315940	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	170	486	0	ENST00000275493.2:c.1879G>A	p.Gly627Arg	p.G627R	ENST00000275493	NM_005228.3	627	Gga/Aga	15/28	1	2	FACETS	1	0.973	1	1	0.994	1	CLONAL	3	TRUE	1	0.125759583319084	2		486	802	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418854	116418855	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	96	281	0	ENST00000397752.3:c.3365_3366delinsTT	p.Ser1122Phe	p.S1122F	ENST00000397752	NM_000245.2	1122	tCC/tTT	17/21	1	2	FACETS	1	0.934	1	1	0.99	1	CLONAL	3	TRUE	1	0.125759583319084	2		281	480	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372104	55372104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	171	369	0	ENST00000297316.4:c.794C>T	p.Pro265Leu	p.P265L	ENST00000297316	NM_022454.3	265	cCt/cTt	2/2	1	2	FACETS	1	0.969	1	1	0.995	1	CLONAL	4	TRUE	1	0.125759583319084	2		369	622	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69011941	69011941	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239248046	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	137	523	0	ENST00000288368.4:c.2578G>A	p.Asp860Asn	p.D860N	ENST00000288368	NM_024870.2	860	Gat/Aat	23/40	1	2	FACETS	1	0.965	1	1	0.991	1	CLONAL	2	TRUE	1	0.125759583319084	2		523	967	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021759	69021763	+	missense_variant	Missense_Mutation	ONP	AAGAA	AAGAA	CTAAG	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	109	549	2	ENST00000288368.4:c.3047_3051delinsCTAAG	p.Lys1016_Glu1017delinsThrLys	p.K1016_E1017delinsTK	ENST00000288368	NM_024870.2	1016	aAAGAA/aCTAAG	25/40	1	2	FACETS	1	0.958	1	1	0.989	1	CLONAL	2	TRUE	1	0.125759583319084	2		551	769	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341138	8341139	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	72	494	0	ENST00000356435.5:c.5077_5078delinsAA	p.Gly1693Lys	p.G1693K	ENST00000356435		1693	GGa/AAa	30/35	0.125759583319084	1	FACETS	1	0.944	1	1	0.984	1	CLONAL	2	TRUE	0	0.125759583319084	1		494	471	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8501056	8501056	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs905180868	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	74	260	0	ENST00000356435.5:c.1826C>T	p.Pro609Leu	p.P609L	ENST00000356435		609	cCg/cTg	13/35	0.125759583319084	1	FACETS	1	0.935	1	1	0.987	1	CLONAL	3	TRUE	0	0.125759583319084	1		260	337	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27172728	27172728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	110	496	1	ENST00000380036.4:c.743G>A	p.Gly248Glu	p.G248E	ENST00000380036	NM_000459.3	248	gGa/gAa	5/23	0.125759583319084	1	FACETS	0.952	0.858	1	1	0.991	1	CLONAL	3	TRUE	0	0.125759583319084	1		497	574	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400180	139400180	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	314	571	0	ENST00000277541.6:c.4168C>T	p.Pro1390Ser	p.P1390S	ENST00000277541	NM_017617.3	1390	Ccc/Tcc	25/34	0.125759583319084	6	FACETS	0.984	0.931	1	1	0.988	1	CLONAL	7	TRUE	0	0.125759583319084	6		571	907	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410466	139410466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764185451	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	346	570	1	ENST00000277541.6:c.1636G>A	p.Gly546Arg	p.G546R	ENST00000277541	NM_017617.3	546	Gga/Aga	10/34	0.125759583319084	6	FACETS	1	0.983	1	1	0.983	1	CLONAL	6	TRUE	0	0.125759583319084	6		571	1061	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021761	69021761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	106	550	1	ENST00000288368.4:c.3049G>A	p.Glu1017Lys	p.E1017K	ENST00000288368	NM_024870.2	1017	Gaa/Aaa	25/40	1	2	FACETS	1	0.954	1	1	0.988	1	CLONAL	2	TRUE	1	0.125759583319084	2		551	757	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18956906	18956906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	92	446	0	ENST00000262803.5:c.349G>A	p.Asp117Asn	p.D117N	ENST00000262803	NM_002911.3	117	Gac/Aac	2/24	1	2	FACETS	1	0.958	1	1	0.987	1	CLONAL	2	TRUE	1	0.125759583319084	2		446	630	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	329	341	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	0.84264689448455	1	FACETS	0.761	0.727	0.794	0.761	0.727	0.794	SUBCLONAL	1	TRUE	0	0.84264689448455	1		341	594	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430395	78430395	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	48	515	0	ENST00000370768.2:c.773A>G	p.Gln258Arg	p.Q258R	ENST00000370768	NM_003902.3	258	cAa/cGa	10/20	0.84264689448455	1	FACETS	0.11	0.092	0.129	0.11	0.092	0.129	SUBCLONAL	1	TRUE	0	0.84264689448455	1		515	601	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115780	8115780	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	400	630	0	ENST00000346208.3:c.1131del	p.Val378CysfsTer26	p.V378Cfs*26	ENST00000346208		376	Aaa/aa	6/6	0.84264689448455	1	FACETS	0.618	0.591	0.646	0.618	0.591	0.646	SUBCLONAL	1	TRUE	0	0.84264689448455	1		630	889	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653796	89653798	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs1554893765	NA	P-0030296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	312	442	1	ENST00000371953.3:c.97_99del	p.Ile33del	p.I33del	ENST00000371953	NM_000314.4	32	ATT/-	2/9	0.84264689448455	1	FACETS	0.983	0.947	1	0.983	0.947	1	CLONAL	1	TRUE	0	0.84264689448455	1		443	436	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858503	57858503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753380800	NA	P-0030296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	565	560	2	ENST00000228682.2:c.241C>T	p.Arg81Trp	p.R81W	ENST00000228682	NM_005269.2	81	Cgg/Tgg	4/12	1	2	FACETS	0.847	0.813	0.881	0.847	0.813	0.881	CLONAL	1	TRUE	1	0.84264689448455	2		562	1584	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856208	111856208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1342201193	NA	P-0030296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	273	180	0	ENST00000341259.2:c.259C>T	p.Arg87Cys	p.R87C	ENST00000341259	NM_005475.2	87	Cgc/Tgc	2/8	1	2	FACETS	0.961	0.908	1	0.961	0.908	1	CLONAL	1	TRUE	1	0.84264689448455	2		180	674	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986752	36986752	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	147	71	0	ENST00000354822.5:c.937C>A	p.Gln313Lys	p.Q313K	ENST00000354822	NM_001079668.2	313	Caa/Aaa	3/3	0.84264689448455	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.84264689448455	1		71	189	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749160	43749161	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0030296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	456	669	1	ENST00000382044.4:c.1645_1646del	p.Gln549AspfsTer2	p.Q549Dfs*2	ENST00000382044	NM_001141980.1	549	CAg/g	12/28	0.84264689448455	1	FACETS	0.767	0.738	0.795	0.767	0.738	0.795	SUBCLONAL	1	TRUE	0	0.84264689448455	1		670	817	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472489	88472489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144852342	NA	P-0030296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	534	556	5	ENST00000360948.2:c.2066C>T	p.Ala689Val	p.A689V	ENST00000360948	NM_001012338.2	689	gCg/gTg	16/19	0.84264689448455	1	FACETS	0.841	0.814	0.868	0.841	0.814	0.868	CLONAL	1	TRUE	0	0.84264689448455	1		561	872	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434566	99434566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773552392	NA	P-0030296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	428	447	0	ENST00000268035.6:c.653C>T	p.Thr218Met	p.T218M	ENST00000268035	NM_000875.3	218	aCg/aTg	3/21	0.84264689448455	1	FACETS	0.841	0.81	0.871	0.841	0.81	0.871	CLONAL	1	TRUE	0	0.84264689448455	1		447	699	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0030296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	399	392	1	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	0.84264689448455	1	FACETS	0.823	0.791	0.854	0.823	0.791	0.854	CLONAL	1	TRUE	0	0.84264689448455	1		393	666	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0030296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	813	594	0	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	0.84264689448455	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.84264689448455	1		594	1050	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670036	29670046	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGTATTTAT	GAAGTATTTAT	-	novel	NA	P-0030296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	374	396	0	ENST00000356175.3:c.7010_7020del	p.Glu2337GlyfsTer24	p.E2337Gfs*24	ENST00000356175	NM_000267.3	2337	GAAGTATTTATg/g	47/57	0.84264689448455	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.84264689448455	1		396	497	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120021	70120104	+	inframe_deletion	In_Frame_Del	DEL	GCCGCCGCCACCCCCGCAGCAGCCCCCACAGGCCCCGCCGGCCCCGCAGGCGCCCCCGCAGCCGCAGGCGGCGCCCCCACAGCA	GCCGCCGCCACCCCCGCAGCAGCCCCCACAGGCCCCGCCGGCCCCGCAGGCGCCCCCGCAGCCGCAGGCGGCGCCCCCACAGCA	-	novel	NA	P-0030296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	23	106	0	ENST00000245479.2:c.1027_1110del	p.Pro343_Pro370del	p.P343_P370del	ENST00000245479	NM_000346.3	341	gcGCCGCCGCCACCCCCGCAGCAGCCCCCACAGGCCCCGCCGGCCCCGCAGGCGCCCCCGCAGCCGCAGGCGGCGCCCCCACAGCAg/gcg	3/3	0.84264689448455	1	FACETS	0.165	0.129	0.206	0.165	0.129	0.206	SUBCLONAL	1	TRUE	0	0.84264689448455	1		106	191	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118632	11118632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555771625	NA	P-0030296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	533	551	0	ENST00000358026.2:c.2056G>A	p.Glu686Lys	p.E686K	ENST00000358026	NM_001128849.1	686	Gag/Aag	14/36	0.84264689448455	1	FACETS	0.817	0.79	0.844	0.817	0.79	0.844	CLONAL	1	TRUE	0	0.84264689448455	1		551	896	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799164	42799164	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	457	480	1	ENST00000575354.2:c.4648A>G	p.Thr1550Ala	p.T1550A	ENST00000575354	NM_015125.3	1550	Act/Gct	20/20	0.84264689448455	1	FACETS	0.873	0.843	0.902	0.873	0.843	0.902	CLONAL	1	TRUE	0	0.84264689448455	1		481	719	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37081734	37081734	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs267607843	NA	P-0030296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	552	452	0	ENST00000231790.2:c.1616C>A	p.Ala539Asp	p.A539D	ENST00000231790	NM_000249.3	539	gCc/gAc	14/19	0.84264689448455	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.84264689448455	1		452	719	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098550	47098550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750393537	NA	P-0030296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	40	512	1	ENST00000409792.3:c.6724G>A	p.Ala2242Thr	p.A2242T	ENST00000409792	NM_014159.6	2242	Gcc/Acc	15/21	0.84264689448455	1	FACETS	0.077	0.064	0.093	0.077	0.064	0.093	SUBCLONAL	1	TRUE	0	0.84264689448455	1		513	711	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49413015	49413015	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	563	598	0	ENST00000418115.1:c.8C>A	p.Ala3Asp	p.A3D	ENST00000418115	NM_001664.2	3	gCc/gAc	2/5	0.84264689448455	1	FACETS	0.824	0.798	0.851	0.824	0.798	0.851	CLONAL	1	TRUE	0	0.84264689448455	1		598	938	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858188	27858188	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	401	508	1	ENST00000359303.2:c.383C>T	p.Ala128Val	p.A128V	ENST00000359303	NM_003535.2	128	gCg/gTg	1/1	0.84264689448455	1	FACETS	0.774	0.743	0.804	0.774	0.743	0.804	SUBCLONAL	1	TRUE	0	0.84264689448455	1		509	712	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776168	135776169	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	153	490	0	ENST00000298552.3:c.2558dup	p.Leu853PhefsTer51	p.L853Ffs*51	ENST00000298552	NM_001162426.1	853	ttg/ttTg	20/23	0.84264689448455	1	FACETS	0.245	0.224	0.267	0.245	0.224	0.267	SUBCLONAL	1	TRUE	0	0.84264689448455	1		490	858	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422384	47422384	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	349	186	0	ENST00000377045.4:c.23del	p.Pro8LeufsTer26	p.P8Lfs*26	ENST00000377045	NM_001654.4	6	ggC/gg	2/16	1	1	FACETS	0.828	0.794	0.861	0.828	0.794	0.861	CLONAL	1	TRUE	0	0.84264689448455	1		186	579	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778785	76778787	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs1557042392	NA	P-0030296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	301	291	2	ENST00000373344.5:c.6792_6794del	p.Glu2265del	p.E2265del	ENST00000373344	NM_000489.3	2264	gaAGAg/gag	31/35	1	1	FACETS	0.994	0.957	1	0.994	0.957	1	CLONAL	1	TRUE	0	0.84264689448455	1		293	416	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0030298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	8	499	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.915	0.596	1	0.915	0.596	1	CLONAL	1	TRUE	1	0.224144983024395	2		499	78	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486194	8486194	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	30	478	1	ENST00000356435.5:c.2623G>A	p.Glu875Lys	p.E875K	ENST00000356435		875	Gaa/Aaa	17/35	0.199705574987249	2	FACETS	1	0.929	1	0.673	0.546	0.813	CLONAL	1	TRUE	0	0.224144983024395	2		479	199	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971121	21971125	+	frameshift_variant	Frame_Shift_Del	DEL	GGTGA	GGTGA	ACC	novel	NA	P-0030298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	19	415	1	ENST00000304494.5:c.233_237delinsGGT	p.Leu78ArgfsTer41	p.L78Rfs*41	ENST00000304494	NM_000077.4	78	cTCACC/cGGT	2/3	0.199705574987249	2	FACETS	0.98	0.748	1	0.49	0.374	0.625	CLONAL	1	TRUE	0	0.224144983024395	2		416	173	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402595	20402595	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	42	309	0	ENST00000346618.3:c.132C>A	p.Phe44Leu	p.F44L	ENST00000346618	NM_001949.4	44	ttC/ttA	1/7	0.231457492444643	3	FACETS	0.772	0.645	0.913	0.386	0.322	0.457	CLONAL	1	FALSE	1	0.284385951763277	3		309	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0030299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	149	631	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.284385951763277	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	0	0.284385951763277	1		631	812	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145513	24145513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	64	540	0	ENST00000263121.7:c.532G>A	p.Glu178Lys	p.E178K	ENST00000263121	NM_003073.3	178	Gag/Aag	5/9	0.121670087986534	0	FACETS	0.423	0.365	0.485			1	INDETERMINATE	1	FALSE	0	0.284385951763277	0		540	762	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523718	176523718	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	190	578	0	ENST00000292408.4:c.2129G>T	p.Arg710Leu	p.R710L	ENST00000292408	NM_213647.1	710	cGa/cTa	16/18	0.231457492444643	3	FACETS	0.834	0.771	0.899	0.834	0.771	0.899	CLONAL	2	FALSE	1	0.284385951763277	3		578	915	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459236	120459236	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	58	526	0	ENST00000256646.2:c.6109G>C	p.Asp2037His	p.D2037H	ENST00000256646	NM_024408.3	2037	Gac/Cac	34/34	1	2	FACETS	0.5	0.429	0.579	0.5	0.429	0.579	SUBCLONAL	1	FALSE	1	0.284385951763277	2		526	815	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102196262	102196262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	27	326	0	ENST00000263464.3:c.919G>A	p.Asp307Asn	p.D307N	ENST00000263464	NM_001165.4	307	Gat/Aat	3/9	0.255935526868893	2	FACETS	0.403	0.32	0.498	0.202	0.16	0.249	SUBCLONAL	1	FALSE	0	0.284385951763277	2		326	471	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17129558	17129558	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	139	692	0	ENST00000285071.4:c.328C>A	p.Gln110Lys	p.Q110K	ENST00000285071	NM_144997.5	110	Cag/Aag	5/14	0.284385951763277	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	FALSE	0	0.284385951763277	1		692	813	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632081	1632081	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs374558465	NA	P-0030299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	143	613	1	ENST00000344749.5:c.254A>G	p.His85Arg	p.H85R	ENST00000344749	NM_001136139.2	85	cAc/cGc	5/19	0.284385951763277	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	0	0.284385951763277	1		614	786	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096957	11096957	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	138	693	0	ENST00000358026.2:c.448G>T	p.Gly150Ter	p.G150*	ENST00000358026	NM_001128849.1	150	Gga/Tga	4/36	0.284385951763277	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	FALSE	0	0.284385951763277	1		693	802	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134236	11134236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	100	557	0	ENST00000358026.2:c.2902C>T	p.Leu968Phe	p.L968F	ENST00000358026	NM_001128849.1	968	Ctc/Ttc	20/36	0.284385951763277	1	FACETS	0.934	0.835	1	0.934	0.835	1	CLONAL	1	FALSE	0	0.284385951763277	1		557	646	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009150	27009150	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	40	174	0	ENST00000335756.4:c.86G>T	p.Arg29Leu	p.R29L	ENST00000335756	NM_001809.3	29	cGg/cTg	1/5	0.190100599831771	1	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	FALSE	0	0.284385951763277	1		174	219	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462642	29462642	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	63	640	0	ENST00000389048.3:c.2259del	p.Ser754ProfsTer36	p.S754Pfs*36	ENST00000389048	NM_004304.4	753	cgG/cg	13/29	0.190100599831771	1	FACETS	0.429	0.37	0.493	0.429	0.37	0.493	SUBCLONAL	1	FALSE	0	0.284385951763277	1		640	886	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259286	89259286	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	98	494	0	ENST00000336596.2:c.430G>T	p.Asp144Tyr	p.D144Y	ENST00000336596	NM_005233.5	144	Gac/Tac	3/17	1	2	FACETS	0.99	0.884	1	0.99	0.884	1	CLONAL	1	FALSE	1	0.284385951763277	2		494	696	SUCCESS
ATR	545	MSKCC	GRCh37	3	142218547	142218547	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs369378664	NA	P-0030299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	39	403	0	ENST00000350721.4:c.5302G>C	p.Asp1768His	p.D1768H	ENST00000350721	NM_001184.3	1768	Gat/Cat	31/47	1	2	FACETS	0.485	0.401	0.578	0.485	0.401	0.578	SUBCLONAL	1	FALSE	1	0.284385951763277	2		403	566	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972039	55972039	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	107	473	0	ENST00000263923.4:c.1605A>T	p.Lys535Asn	p.K535N	ENST00000263923	NM_002253.2	535	aaA/aaT	12/30	0.190100599831771	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	FALSE	0	0.284385951763277	1		473	631	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532783	187532783	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	73	572	0	ENST00000441802.2:c.9610C>A	p.Gln3204Lys	p.Q3204K	ENST00000441802	NM_005245.3	3204	Caa/Aaa	14/27	0.190100599831771	1	FACETS	0.605	0.528	0.688	0.605	0.528	0.688	SUBCLONAL	1	FALSE	0	0.284385951763277	1		572	728	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005504	150005504	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs769758085	NA	P-0030299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	41	422	0	ENST00000253339.5:c.721C>G	p.Gln241Glu	p.Q241E	ENST00000253339		241	Caa/Gaa	3/7	0.255935526868893	2	FACETS	0.498	0.414	0.592	0.249	0.207	0.296	SUBCLONAL	1	FALSE	0	0.284385951763277	2		422	579	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370781	55370781	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199550282	NA	P-0030299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	48	399	0	ENST00000297316.4:c.83G>T	p.Gly28Val	p.G28V	ENST00000297316	NM_022454.3	28	gGc/gTc	1/2	0.190100599831771	1	FACETS	0.492	0.415	0.576	0.492	0.415	0.576	SUBCLONAL	1	FALSE	0	0.284385951763277	1		399	589	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992741	68992741	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	73	671	0	ENST00000288368.4:c.1706T>C	p.Met569Thr	p.M569T	ENST00000288368	NM_024870.2	569	aTg/aCg	16/40	0.190100599831771	1	FACETS	0.49	0.428	0.558	0.49	0.428	0.558	SUBCLONAL	1	FALSE	0	0.284385951763277	1		671	898	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964445	70964445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	115	544	1	ENST00000276594.2:c.1583C>T	p.Ser528Phe	p.S528F	ENST00000276594	NM_024504.3	528	tCc/tTc	8/8	0.190100599831771	1	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	FALSE	0	0.284385951763277	1		545	694	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404576	8404576	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	53	348	0	ENST00000356435.5:c.4171G>C	p.Ala1391Pro	p.A1391P	ENST00000356435		1391	Gca/Cca	25/35	0.284385951763277	1	FACETS	0.874	0.748	1	0.874	0.748	1	CLONAL	1	FALSE	0	0.284385951763277	1		348	366	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347814	70347814	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	101	537	1	ENST00000374080.3:c.3053C>A	p.Ala1018Glu	p.A1018E	ENST00000374080		1018	gCa/gAa	22/45	1	2	FACETS	0.841	0.751	0.936	0.841	0.751	0.936	CLONAL	1	FALSE	1	0.284385951763277	2		538	845	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354961	70354961	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	112	551	0	ENST00000374080.3:c.4883A>T	p.Gln1628Leu	p.Q1628L	ENST00000374080		1628	cAg/cTg	36/45	1	2	FACETS	0.929	0.835	1	0.929	0.835	1	CLONAL	1	FALSE	1	0.284385951763277	2		551	848	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207077	1207077	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	TT	novel	NA	P-0030299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	143	639	0	ENST00000326873.7:c.165delinsTT	p.Gly56TrpfsTer107	p.G56Wfs*107	ENST00000326873	NM_000455.4	55	ctG/ctTT	1/10	0.284385951763277	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	0	0.284385951763277	1		639	842	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0030309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	269	725	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		725	1400	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	67	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.377409722286527	2		215	326	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0030314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	194	452	0	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	1	2	FACETS	1	0.968	1	1	0.994	1	CLONAL	2	TRUE	1	0.377409722286527	2		452	485	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150030	202150030	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs931648756	NA	P-0030314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	116	495	0	ENST00000358485.4:c.1471C>T	p.Arg491Ter	p.R491*	ENST00000358485	NM_001080125.1	491	Cga/Tga	8/9	0.376611577446111	3	FACETS	0.985	0.888	1	0.492	0.444	0.544	CLONAL	1	TRUE	1	0.377409722286527	3		495	742	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40486032	40486032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	83	561	0	ENST00000264657.5:c.833G>A	p.Arg278His	p.R278H	ENST00000264657	NM_139276.2	278	cGt/cAt	9/24	1	2	FACETS	0.905	0.801	1	0.905	0.801	1	CLONAL	1	TRUE	1	0.377409722286527	2		561	486	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217293	7217293	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752902884	NA	P-0030314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	115	568	0	ENST00000380728.2:c.412C>T	p.His138Tyr	p.H138Y	ENST00000380728		138	Cac/Tac	6/11	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.377409722286527	2		568	585	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0030317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	78	354	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.754	0.664	0.851	0.754	0.664	0.851	SUBCLONAL	1	TRUE	1	0.37	2		354	559	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457653	67457653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs973219546	NA	P-0030317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	104	607	0	ENST00000327367.4:c.463G>A	p.Asp155Asn	p.D155N	ENST00000327367	NM_005902.3	155	Gac/Aac	3/9	1	2	FACETS	0.645	0.577	0.717	0.645	0.577	0.717	SUBCLONAL	1	TRUE	1	0.37	2		607	872	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571407	95571407	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0030317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	51	230	0	ENST00000393063.1:c.3269+1G>A		p.X1090_splice	ENST00000393063	NM_030621.3	1090			1	2	FACETS	0.951	0.814	1	0.951	0.814	1	CLONAL	1	TRUE	1	0.37	2		230	290	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967287	25967287	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	133	495	0	ENST00000435504.4:c.1919C>G	p.Ala640Gly	p.A640G	ENST00000435504		640	gCt/gGt	13/13	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.37	2		495	656	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644703	134644703	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536029159	NA	P-0030317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	115	509	1	ENST00000398015.3:c.104C>T	p.Thr35Met	p.T35M	ENST00000398015	NM_004441.4	35	aCg/aTg	2/16	1	2	FACETS	0.883	0.796	0.975	0.883	0.796	0.975	CLONAL	1	TRUE	1	0.37	2		510	704	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229536	98229536	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	105	478	0	ENST00000331920.6:c.2422C>T	p.Gln808Ter	p.Q808*	ENST00000331920	NM_000264.3	808	Cag/Tag	15/24	1	2	FACETS	0.872	0.782	0.967	0.872	0.782	0.967	CLONAL	1	TRUE	1	0.37	2		478	651	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426132	47426132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1345707414	NA	P-0030317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	134	681	0	ENST00000377045.4:c.652G>A	p.Val218Ile	p.V218I	ENST00000377045	NM_001654.4	218	Gtc/Atc	7/16	1	2	FACETS	0.901	0.819	0.987	0.901	0.819	0.987	CLONAL	1	TRUE	1	0.37	2		681	804	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	78	215	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		215	478	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0030326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	107	555	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.254031912345426	2		555	747	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279674	123279674	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs77543610	NA	P-0030326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	62	331	0	ENST00000358487.5:c.758C>G	p.Pro253Arg	p.P253R	ENST00000358487	NM_000141.4	253	cCt/cGt	7/18	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	1	0.254031912345426	2		331	373	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942090	71942090	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	136	706	0	ENST00000298229.2:c.1354G>A	p.Gly452Arg	p.G452R	ENST00000298229	NM_001567.3	452	Ggg/Agg	12/28	0.127594145404787	3	FACETS	1	0.982	1	0.669	0.608	0.733	INDETERMINATE	1	FALSE	1	0.254031912345426	3		706	902	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579722	7579722	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0030326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	93	574	1	ENST00000269305.4:c.75-1G>T		p.X25_splice	ENST00000269305	NM_001126112.2	25			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.254031912345426	2		575	645	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019126	31019126	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	80	442	0	ENST00000375687.4:c.721C>A	p.Gln241Lys	p.Q241K	ENST00000375687	NM_015338.5	241	Caa/Aaa	9/13	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	FALSE	1	0.254031912345426	2		442	556	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47061249	47061249	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0030326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	83	409	0	ENST00000409792.3:c.7431+1G>T		p.X2477_splice	ENST00000409792	NM_014159.6	2477			0.254031912345426	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	0	0.254031912345426	1		409	438	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974762	21974762	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	41	243	0	ENST00000304494.5:c.65G>C	p.Arg22Pro	p.R22P	ENST00000304494	NM_000077.4	22	cGg/cCg	1/3	0.254031912345426	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	FALSE	0	0.254031912345426	1		243	244	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787783	135787783	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	89	520	0	ENST00000298552.3:c.799del	p.Thr267GlnfsTer51	p.T267Qfs*51	ENST00000298552	NM_001162426.1	267	Aca/ca	9/23	0.254031912345426	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	0	0.254031912345426	1		520	541	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356437	70356437	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	93	654	0	ENST00000374080.3:c.5332A>T	p.Ser1778Cys	p.S1778C	ENST00000374080		1778	Agt/Tgt	37/45	1	2	FACETS	0.979	0.87	1	0.979	0.87	1	CLONAL	1	FALSE	1	0.254031912345426	2		654	748	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034349	123034349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	68	380	0	ENST00000355640.3:c.1106C>A	p.Thr369Asn	p.T369N	ENST00000355640		369	aCc/aAc	6/7	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	FALSE	1	0.254031912345426	2		380	525	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313368	30313368	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	148	638	0	ENST00000262643.3:c.968A>G	p.Asp323Gly	p.D323G	ENST00000262643	NM_001238.2	323	gAc/gGc	11/12	0.739559907473035	5	FACETS	0.905	0.826	0.988	0.226	0.206	0.247	CLONAL	1	TRUE	1	0.739559907473035	5		638	933	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0030344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	230	498	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	0.166416361149746	2	FACETS	0.928	0.872	0.983	1	0.992	1	INDETERMINATE	3	FALSE	0	0.3	2		498	551	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937896	76937896	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	62	518	0	ENST00000373344.5:c.2852C>G	p.Thr951Ser	p.T951S	ENST00000373344	NM_000489.3	951	aCc/aGc	9/35	1	2	FACETS	0.726	0.628	0.834	0.726	0.628	0.834	SUBCLONAL	1	FALSE	1	0.3	2		518	569	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	213	446	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.363565977721194	4	FACETS	0.907	0.849	0.967	0.907	0.849	0.967	CLONAL	3	TRUE	1	0.366970735977115	4		446	583	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905485	50905485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs914238978	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	101	633	0	ENST00000440232.2:c.613G>A	p.Gly205Ser	p.G205S	ENST00000440232	NM_002691.3	205	Ggc/Agc	6/27	0.366970735977115	3	FACETS	0.792	0.707	0.882	0.396	0.353	0.441	SUBCLONAL	1	TRUE	1	0.366970735977115	3		633	823	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	222	472	4	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	0.363565977721194	4	FACETS	0.999	0.932	1	0.666	0.621	0.712	CLONAL	2	TRUE	1	0.366970735977115	4		476	828	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	72	405	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.366970735977115	3	FACETS	0.89	0.779	1	0.297	0.259	0.337	CLONAL	1	TRUE	0	0.366970735977115	3		405	522	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	87	537	1	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	0.366970735977115	3	FACETS	0.858	0.76	0.963	0.429	0.38	0.482	CLONAL	1	TRUE	1	0.366970735977115	3		538	654	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555057	106555057	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs940196192	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	92	371	0	ENST00000369096.4:c.2174G>A	p.Arg725Gln	p.R725Q	ENST00000369096	NM_001198.3	725	cGa/cAa	7/7	0.366970735977115	3	FACETS	1	0.915	1	0.344	0.306	0.384	CLONAL	1	TRUE	0	0.366970735977115	3		371	575	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882049	36882050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs780753361	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	200	639	0	ENST00000358127.4:c.963dup	p.Ala322ArgfsTer19	p.A322Rfs*19	ENST00000358127	NM_001280556.1	321	-/C	8/10	0.363565977721194	4	FACETS	0.837	0.776	0.9	0.558	0.517	0.6	CLONAL	2	TRUE	1	0.366970735977115	4		639	890	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	89	432	10	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	0.363565977721194	4	FACETS	0.864	0.766	0.97	0.288	0.255	0.324	CLONAL	1	TRUE	1	0.366970735977115	4		442	767	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	99	348	1	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.366970735977115	2		349	514	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098411	11098411	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766422429	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	116	424	1	ENST00000358026.2:c.929G>A	p.Arg310His	p.R310H	ENST00000358026	NM_001128849.1	310	cGc/cAc	6/36	0.366970735977115	3	FACETS	1	0.972	1	0.6	0.542	0.662	CLONAL	1	TRUE	1	0.366970735977115	3		425	623	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066648	94066648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371089003	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	230	366	0	ENST00000369303.4:c.1111C>T	p.Arg371Trp	p.R371W	ENST00000369303	NM_004440.3	371	Cgg/Tgg	5/17	0.366970735977115	3	FACETS	0.894	0.841	0.948	0.894	0.841	0.948	CLONAL	3	TRUE	0	0.366970735977115	3		366	553	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303029	15303029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1174625611	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	118	691	0	ENST00000263388.2:c.421C>T	p.Arg141Cys	p.R141C	ENST00000263388	NM_000435.2	141	Cgc/Tgc	4/33	0.366970735977115	3	FACETS	0.9	0.811	0.993	0.45	0.405	0.497	CLONAL	1	TRUE	1	0.366970735977115	3		691	846	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628340	187628340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536104649	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	98	460	0	ENST00000441802.2:c.2642G>A	p.Arg881His	p.R881H	ENST00000441802	NM_005245.3	881	cGc/cAc	2/27	0.366970735977115	3	FACETS	0.985	0.88	1	0.492	0.44	0.548	CLONAL	1	TRUE	1	0.366970735977115	3		460	642	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348011	348011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769972546	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	134	547	0	ENST00000262320.3:c.1495G>A	p.Val499Met	p.V499M	ENST00000262320	NM_003502.3	499	Gtg/Atg	6/11	0.366970735977115	5	FACETS	1	0.97	1	0.388	0.352	0.426	CLONAL	1	TRUE	2	0.366970735977115	5		547	973	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38184289	38184289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149768452	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	68	494	0	ENST00000317025.8:c.1667C>T	p.Thr556Met	p.T556M	ENST00000317025	NM_023034.1	556	aCg/aTg	7/24	0.366970735977115	3	FACETS	0.694	0.604	0.792	0.347	0.302	0.396	SUBCLONAL	1	TRUE	1	0.366970735977115	3		494	632	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61709534	61709534	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	40	294	0	ENST00000401558.2:c.2953G>A	p.Ala985Thr	p.A985T	ENST00000401558	NM_003400.3	985	Gcc/Acc	23/25	0.314381179861388	4	FACETS	0.645	0.536	0.766	0.323	0.268	0.383	SUBCLONAL	1	TRUE	2	0.366970735977115	4		294	462	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139794895	139794895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758348510	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	68	309	0	ENST00000247668.2:c.289C>T	p.Arg97Cys	p.R97C	ENST00000247668	NM_021138.3	97	Cgc/Tgc	4/11	0.363565977721194	4	FACETS	0.98	0.854	1	0.327	0.284	0.372	CLONAL	1	TRUE	1	0.366970735977115	4		309	517	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433960	49433960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	92	604	0	ENST00000301067.7:c.7593del	p.Ser2532LeufsTer11	p.S2532Lfs*11	ENST00000301067	NM_003482.3	2531	ccC/cc	31/54	0.363565977721194	4	FACETS	0.772	0.685	0.865	0.257	0.228	0.289	SUBCLONAL	1	TRUE	1	0.366970735977115	4		604	888	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182095	11182095	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1365408542	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	83	465	0	ENST00000361445.4:c.6751C>T	p.Arg2251Trp	p.R2251W	ENST00000361445	NM_004958.3	2251	Cgg/Tgg	48/58	0.366970735977115	3	FACETS	0.833	0.735	0.937			1	CLONAL	1	TRUE	NA	0.366970735977115	3		465	643	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17349218	17349218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747518441	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	62	314	0	ENST00000375499.3:c.650G>A	p.Arg217His	p.R217H	ENST00000375499	NM_003000.2	217	cGc/cAc	7/8	0.366970735977115	3	FACETS	0.959	0.831	1			1	CLONAL	1	TRUE	NA	0.366970735977115	3		314	417	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023810	27023811	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	85	338	0	ENST00000324856.7:c.920dup	p.Tyr308LeufsTer92	p.Y308Lfs*92	ENST00000324856	NM_006015.4	306	cgg/cGgg	1/20	0.366970735977115	3	FACETS	1	0.964	1	0.405	0.359	0.454	CLONAL	1	TRUE	0	0.366970735977115	3		338	451	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226564886	226564886	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	76	366	1	ENST00000366794.5:c.1864del	p.Thr622ProfsTer31	p.T622Pfs*31	ENST00000366794	NM_001618.3	622	Acc/cc	13/23	0.366970735977115	7	FACETS	0.871	0.762	0.988	0.174	0.152	0.198	CLONAL	1	TRUE	2	0.366970735977115	7		367	912	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123324999	123324999	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	66	379	0	ENST00000358487.5:c.329G>A	p.Ser110Asn	p.S110N	ENST00000358487	NM_000141.4	110	aGt/aAt	3/18	0.366970735977115	5	FACETS	0.768	0.666	0.879	0.256	0.222	0.293	SUBCLONAL	1	TRUE	2	0.366970735977115	5		379	726	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103409	77103409	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	94	278	0	ENST00000356341.3:c.157C>T	p.Arg53Ter	p.R53*	ENST00000356341	NM_002576.4	53	Cga/Tga	2/15	0.366970735977115	4	FACETS	0.805	0.72	0.894	0.805	0.72	0.894	CLONAL	2	TRUE	2	0.366970735977115	4		278	435	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404932	404932	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866992140	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	79	337	0	ENST00000399788.2:c.4262G>A	p.Arg1421Gln	p.R1421Q	ENST00000399788	NM_001042603.1	1421	cGg/cAg	26/28	0.363565977721194	4	FACETS	1	0.923	1	0.355	0.312	0.4	CLONAL	1	TRUE	1	0.366970735977115	4		337	553	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219879	133219879	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	205	460	0	ENST00000320574.5:c.4482G>T	p.Gln1494His	p.Q1494H	ENST00000320574	NM_006231.2	1494	caG/caT	35/49	0.363565977721194	4	FACETS	0.99	0.921	1	0.66	0.614	0.708	CLONAL	2	TRUE	1	0.366970735977115	4		460	771	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562187	21562187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774885199	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	157	751	0	ENST00000382592.4:c.1732G>A	p.Val578Ile	p.V578I	ENST00000382592	NM_014572.2	578	Gtt/Att	4/8	1	2	FACETS	0.947	0.867	1	0.947	0.867	1	CLONAL	1	TRUE	1	0.366970735977115	2		751	904	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914152	32914152	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507795	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	84	410	0	ENST00000380152.3:c.5660C>T	p.Thr1887Met	p.T1887M	ENST00000380152		1887	aCg/aTg	11/27	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.366970735977115	2		410	458	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134150	41134150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	63	268	0	ENST00000379561.5:c.1478G>A	p.Gly493Asp	p.G493D	ENST00000379561	NM_002015.3	493	gGc/gAc	2/3	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.366970735977115	2		268	324	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046586	30046586	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	81	438	0	ENST00000331968.5:c.2597A>G	p.Asp866Gly	p.D866G	ENST00000331968	NM_002742.2	866	gAc/gGc	18/18	0.366970735977115	3	FACETS	0.92	0.812	1	0.46	0.406	0.518	CLONAL	1	TRUE	1	0.366970735977115	3		438	568	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121868	2121868	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	86	565	1	ENST00000219476.3:c.2030C>A	p.Pro677His	p.P677H	ENST00000219476	NM_000548.3	677	cCc/cAc	19/42	0.366970735977115	5	FACETS	0.805	0.711	0.906	0.268	0.237	0.302	CLONAL	1	TRUE	2	0.366970735977115	5		566	903	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777766	3777766	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761138453	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	130	767	0	ENST00000262367.5:c.7282G>A	p.Gly2428Arg	p.G2428R	ENST00000262367	NM_004380.2	2428	Ggg/Agg	31/31	0.366970735977115	5	FACETS	0.849	0.768	0.935	0.283	0.256	0.312	CLONAL	1	TRUE	2	0.366970735977115	5		767	1294	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274172	10274172	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	71	353	0	ENST00000330684.3:c.97G>C	p.Ala33Pro	p.A33P	ENST00000330684	NM_001134407.1	33	Gcg/Ccg	2/13	0.366970735977115	5	FACETS	1	0.897	1	0.344	0.3	0.391	CLONAL	1	TRUE	2	0.366970735977115	5		353	582	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652996	29652996	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1135402867	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	69	367	0	ENST00000356175.3:c.4935del	p.Pro1646LeufsTer31	p.P1646Lfs*31	ENST00000356175	NM_000267.3	1644	gTt/gt	36/57	0.363565977721194	4	FACETS	0.93	0.811	1	0.31	0.27	0.353	CLONAL	1	TRUE	1	0.366970735977115	4		367	553	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325891	30325891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	63	345	0	ENST00000322652.5:c.2089G>A	p.Ala697Thr	p.A697T	ENST00000322652	NM_015355.2	697	Gca/Aca	16/16	0.363565977721194	4	FACETS	0.863	0.747	0.988	0.288	0.249	0.33	CLONAL	1	TRUE	1	0.366970735977115	4		345	544	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441539	40441539	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	112	618	0	ENST00000345506.4:c.110G>A	p.Trp37Ter	p.W37*	ENST00000345506	NM_003152.3	37	tGg/tAg	3/20	0.363565977721194	4	FACETS	0.888	0.797	0.984	0.296	0.265	0.328	CLONAL	1	TRUE	1	0.366970735977115	4		618	940	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761145	59761145	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	84	496	0	ENST00000259008.2:c.3262C>G	p.His1088Asp	p.H1088D	ENST00000259008	NM_032043.2	1088	Cat/Gat	20/20	0.363565977721194	4	FACETS	0.845	0.745	0.951	0.282	0.248	0.317	CLONAL	1	TRUE	1	0.366970735977115	4		496	741	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532613	63532613	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121908568	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	127	582	0	ENST00000307078.5:c.1966C>T	p.Arg656Ter	p.R656*	ENST00000307078	NM_004655.3	656	Cga/Tga	8/11	0.363565977721194	4	FACETS	1	0.908	1	0.334	0.302	0.368	CLONAL	1	TRUE	1	0.366970735977115	4		582	943	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637932	39637932	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	82	379	0	ENST00000262039.4:c.2349G>T	p.Met783Ile	p.M783I	ENST00000262039	NM_002647.2	783	atG/atT	22/25	0.366970735977115	3	FACETS	1	0.905	1	0.513	0.454	0.577	CLONAL	1	TRUE	1	0.366970735977115	3		379	515	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599915	10599915	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	216	503	2	ENST00000171111.5:c.1661G>A	p.Arg554Gln	p.R554Q	ENST00000171111	NM_203500.1	554	cGa/cAa	5/6	0.366970735977115	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.366970735977115	3		505	674	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793508	42793508	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	134	570	0	ENST00000575354.2:c.1310A>G	p.Asp437Gly	p.D437G	ENST00000575354	NM_015125.3	437	gAt/gGt	8/20	0.366970735977115	3	FACETS	1	0.957	1	0.544	0.495	0.596	CLONAL	1	TRUE	1	0.366970735977115	3		570	794	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46597007	46597007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	114	353	0	ENST00000263734.3:c.821G>A	p.Gly274Asp	p.G274D	ENST00000263734	NM_001430.4	274	gGc/gAc	7/16	0.314381179861388	4	FACETS	0.771	0.696	0.849	0.771	0.696	0.849	SUBCLONAL	2	TRUE	2	0.366970735977115	4		353	551	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149549	61149549	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	62	357	1	ENST00000295025.8:c.1739C>A	p.Pro580Gln	p.P580Q	ENST00000295025	NM_002908.2	580	cCa/cAa	11/11	0.314381179861388	4	FACETS	0.928	0.802	1	0.464	0.401	0.532	CLONAL	1	TRUE	2	0.366970735977115	4		358	498	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719198	190719198	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	87	253	0	ENST00000441310.2:c.1205del	p.Asn402ThrfsTer6	p.N402Tfs*6	ENST00000441310	NM_000534.4	400	ggA/gg	9/13	0.314381179861388	4	FACETS	0.789	0.702	0.88	0.789	0.702	0.88	SUBCLONAL	2	TRUE	2	0.366970735977115	4		253	411	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560813	9560813	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	84	301	0	ENST00000353224.5:c.969G>T	p.Glu323Asp	p.E323D	ENST00000353224	NM_177990.2	323	gaG/gaT	4/10	0.366970735977115	5	FACETS	0.777	0.689	0.87	0.518	0.459	0.58	SUBCLONAL	2	TRUE	2	0.366970735977115	5		301	457	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31020715	31020715	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	56	273	2	ENST00000375687.4:c.1012C>T	p.Arg338Ter	p.R338*	ENST00000375687	NM_015338.5	338	Cga/Tga	11/13	0.366970735977115	5	FACETS	0.87	0.745	1	0.29	0.248	0.336	CLONAL	1	TRUE	2	0.366970735977115	5		275	544	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513336	44513336	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	100	515	0	ENST00000291552.4:c.599G>A	p.Arg200Gln	p.R200Q	ENST00000291552	NM_006758.2	200	cGg/cAg	8/8	0.366970735977115	3	FACETS	0.902	0.806	1	0.451	0.403	0.502	CLONAL	1	TRUE	1	0.366970735977115	3		515	715	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37091975	37091975	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs267607889	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	161	285	0	ENST00000231790.2:c.2104-2A>T		p.X702_splice	ENST00000231790	NM_000249.3	702			0.366970735977115	3	FACETS	0.897	0.833	0.961	0.897	0.833	0.961	CLONAL	3	TRUE	0	0.366970735977115	3		285	386	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178070	142178072	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	ATG	ATG	-	novel	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	44	248	0	ENST00000350721.4:c.7346_7348del	p.Ser2449del	p.S2449del	ENST00000350721	NM_001184.3	2449	tCATgg/tgg	43/47	0.366970735977115	3	FACETS	0.809	0.68	0.95	0.27	0.226	0.317	CLONAL	1	TRUE	0	0.366970735977115	3		248	351	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361193	66361193	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	102	222	1	ENST00000273854.3:c.979T>C	p.Tyr327His	p.Y327H	ENST00000273854	NM_004439.5	327	Tat/Cat	4/18	0.366970735977115	3	FACETS	0.894	0.807	0.985	0.894	0.807	0.985	CLONAL	2	TRUE	1	0.366970735977115	3		223	368	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522573	176522573	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs765645716	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	224	589	0	ENST00000292408.4:c.1670A>G	p.Asn557Ser	p.N557S	ENST00000292408	NM_213647.1	557	aAc/aGc	13/18	0.366970735977115	6	FACETS	0.987	0.919	1	0.658	0.612	0.706	CLONAL	2	TRUE	3	0.366970735977115	6		589	1072	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958387	90958387	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	54	305	0	ENST00000265433.3:c.2051A>T	p.Asn684Ile	p.N684I	ENST00000265433	NM_002485.4	684	aAt/aTt	13/16	0.366970735977115	3	FACETS	0.926	0.794	1	0.463	0.397	0.535	CLONAL	1	TRUE	1	0.366970735977115	3		305	376	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798846	135798846	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs118203381	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	75	236	0	ENST00000298552.3:c.397G>A	p.Val133Ile	p.V133I	ENST00000298552	NM_001162426.1	133	Gtc/Atc	6/23	0.363565977721194	4	FACETS	0.81	0.715	0.91	0.54	0.476	0.607	CLONAL	2	TRUE	1	0.366970735977115	4		236	345	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391398	139391398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777902922	NA	P-0030368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	114	571	0	ENST00000277541.6:c.6793G>A	p.Ala2265Thr	p.A2265T	ENST00000277541	NM_017617.3	2265	Gcc/Acc	34/34	0.363565977721194	4	FACETS	0.958	0.861	1	0.319	0.287	0.353	CLONAL	1	TRUE	1	0.366970735977115	4		571	887	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254623	16254623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749814808	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	29	564	0	ENST00000375759.3:c.1888C>T	p.Arg630Cys	p.R630C	ENST00000375759	NM_015001.2	630	Cgt/Tgt	11/15	0.212625506962056	6	FACETS	1	0.93	1	0.464	0.374	0.567	CLONAL	1	FALSE	3	0.212625506962056	6		564	279	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175723	176175723	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	30	763	1	ENST00000367669.3:c.392G>T	p.Ser131Ile	p.S131I	ENST00000367669	NM_022457.5	131	aGc/aTc	1/20	0.212625506962056	1	FACETS	0.689	0.555	0.84	0.689	0.555	0.84	SUBCLONAL	1	FALSE	0	0.212625506962056	1		764	366	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193181526	193181526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	73	454	0	ENST00000367435.3:c.1073G>A	p.Arg358Gln	p.R358Q	ENST00000367435	NM_024529.4	358	cGa/cAa	13/17	0.212625506962056	1	FACETS	0.867	0.769	0.968	1	0.986	1	CLONAL	3	FALSE	0	0.212625506962056	1		454	236	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639116	3639116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs112694849	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	137	688	1	ENST00000294008.3:c.4523C>T	p.Ser1508Leu	p.S1508L	ENST00000294008	NM_032444.2	1508	tCg/tTg	12/15	0.160482769171991	3	FACETS	0.993	0.915	1	1	0.991	1	CLONAL	4	FALSE	1	0.212625506962056	3		689	359	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041557	14041557	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180030515	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	32	473	0	ENST00000311895.7:c.2104C>T	p.Arg702Trp	p.R702W	ENST00000311895	NM_005236.2	702	Cgg/Tgg	11/11	0.160482769171991	3	FACETS	0.89	0.73	1	0.89	0.73	1	CLONAL	2	FALSE	1	0.212625506962056	3		473	187	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81954827	81954827	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	35	616	0	ENST00000359376.3:c.2260G>A	p.Asp754Asn	p.D754N	ENST00000359376	NM_002661.3	754	Gac/Aac	21/33	0.212625506962056	0	FACETS	0.771	0.641	0.914			1	CLONAL	2	FALSE	0	0.212625506962056	0		616	168	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621011	1621011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs963433488	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	128	822	1	ENST00000344749.5:c.1049C>T	p.Ser350Leu	p.S350L	ENST00000344749	NM_001136139.2	350	tCg/tTg	13/19	0.148300535650375	4	FACETS	0.968	0.887	1	1	0.99	1	CLONAL	4	FALSE	2	0.212625506962056	4		823	377	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159001	24159001	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768379745	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	26	640	1	ENST00000263121.7:c.673G>A	p.Asp225Asn	p.D225N	ENST00000263121	NM_003073.3	225	Gat/Aat	6/9	0.148300535650375	4	FACETS	0.989	0.784	1	0.494	0.392	0.611	CLONAL	1	FALSE	2	0.212625506962056	4		641	300	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456592	138456592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	41	548	0	ENST00000289153.2:c.758G>T	p.Arg253Ile	p.R253I	ENST00000289153	NM_006219.2	253	aGa/aTa	4/22	1	2	FACETS	0.75	0.629	0.883	1	0.957	1	SUBCLONAL	2	FALSE	1	0.212625506962056	2		548	257	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	89	487	1	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	0.160482769171991	3	FACETS	1	0.944	1	1	0.988	1	CLONAL	4	FALSE	1	0.212625506962056	3		488	218	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725528	117725528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867759865	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	14	482	1	ENST00000368508.3:c.353G>A	p.Arg118Gln	p.R118Q	ENST00000368508	NM_002944.2	118	cGa/cAa	5/43	0.160482769171991	3	FACETS	0.857	0.622	1	0.428	0.311	0.57	CLONAL	1	FALSE	1	0.212625506962056	3		483	170	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117422	115117422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151047347	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	26	460	0	ENST00000257566.3:c.752G>A	p.Arg251Gln	p.R251Q	ENST00000257566	NM_016569.3	251	cGg/cAg	4/8	0.148300535650375	4	FACETS	0.753	0.6	0.925	0.753	0.6	0.925	CLONAL	2	FALSE	2	0.212625506962056	4		460	197	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041074	42041074	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	94	646	1	ENST00000219905.7:c.5452C>T	p.Arg1818Ter	p.R1818*	ENST00000219905	NM_001164273.1	1818	Cga/Tga	16/24	1	2	FACETS	1	0.909	1	1	0.99	1	CLONAL	3	FALSE	1	0.212625506962056	2		647	292	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786205228	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	62	547	0	ENST00000322088.6:c.536C>T	p.Pro179Leu	p.P179L	ENST00000322088	NM_014225.5	179	cCc/cTc	5/15	0.148300535650375	4	FACETS	0.893	0.784	1	1	0.979	1	CLONAL	4	FALSE	2	0.212625506962056	4		547	198	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693856	47693856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755818010	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	83	434	0	ENST00000233146.2:c.1570C>T	p.Arg524Cys	p.R524C	ENST00000233146	NM_000251.2	524	Cgt/Tgt	10/16	1	2	FACETS	0.933	0.833	1	1	0.988	1	CLONAL	3	FALSE	1	0.212625506962056	2		434	279	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968610	55968610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374980446	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	36	569	0	ENST00000263923.4:c.2053G>A	p.Glu685Lys	p.E685K	ENST00000263923	NM_002253.2	685	Gaa/Aaa	14/30	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.212625506962056	2		569	228	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631622	119631622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	19	392	0	ENST00000316626.5:c.644C>T	p.Ser215Leu	p.S215L	ENST00000316626		215	tCg/tTg	6/12	1	2	FACETS	1	0.842	1	1	0.842	1	CLONAL	1	FALSE	1	0.212625506962056	2		392	157	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662972	52662972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779427834	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	76	445	1	ENST00000394830.3:c.1381C>T	p.Arg461Cys	p.R461C	ENST00000394830	NM_018313.4	461	Cgc/Tgc	13/30	1	2	FACETS	0.91	0.808	1	1	0.987	1	CLONAL	3	FALSE	1	0.212625506962056	2		446	262	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637295	176637295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201702515	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	40	652	0	ENST00000439151.2:c.1895G>A	p.Arg632Gln	p.R632Q	ENST00000439151	NM_022455.4	632	cGa/cAa	5/23	1	2	FACETS	0.784	0.656	0.923	1	0.959	1	CLONAL	2	FALSE	1	0.212625506962056	2		652	240	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370767	225370767	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	81	504	0	ENST00000264414.4:c.1112C>T	p.Ala371Val	p.A371V	ENST00000264414	NM_003590.4	371	gCg/gTg	8/16	1	2	FACETS	1	0.907	1	1	0.988	1	CLONAL	3	FALSE	1	0.212625506962056	2		504	250	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295795	212295795	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369248674	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	34	564	0	ENST00000342788.4:c.2518G>A	p.Val840Ile	p.V840I	ENST00000342788	NM_005235.2	840	Gtt/Att	21/28	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	FALSE	1	0.212625506962056	2		564	214	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432068	121432068	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137853238	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	148	684	2	ENST00000257555.6:c.815G>A	p.Arg272His	p.R272H	ENST00000257555		272	cGc/cAc	4/10	0.148300535650375	4	FACETS	0.962	0.891	1	1	0.993	1	CLONAL	5	FALSE	2	0.212625506962056	4		686	351	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380223	25380223	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	33	575	1	ENST00000311936.3:c.235C>A	p.Leu79Ile	p.L79I	ENST00000311936	NM_004985.3	79	Ctt/Att	3/5	0.148300535650375	4	FACETS	0.804	0.659	0.966	0.804	0.659	0.966	CLONAL	2	FALSE	2	0.212625506962056	4		576	234	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250908	99250908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780055504	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	98	520	0	ENST00000268035.6:c.212G>A	p.Arg71His	p.R71H	ENST00000268035	NM_000875.3	71	cGc/cAc	2/21	1	2	FACETS	0.998	0.908	1	1	0.991	1	CLONAL	4	FALSE	1	0.212625506962056	2		520	231	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	43	656	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.212625506962056	5	FACETS	0.834	0.7	0.98	0.556	0.467	0.653	CLONAL	2	FALSE	2	0.212625506962056	5		656	320	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103510736	103510736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56255799	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	40	542	0	ENST00000355739.4:c.640C>T	p.Arg214Cys	p.R214C	ENST00000355739	NM_000123.3	214	Cgc/Tgc	6/15	1	2	FACETS	0.784	0.656	0.923	1	0.959	1	CLONAL	2	FALSE	1	0.212625506962056	2		542	240	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610217	10610217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752325770	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	116	707	0	ENST00000171111.5:c.493G>A	p.Asp165Asn	p.D165N	ENST00000171111	NM_203500.1	165	Gac/Aac	2/6	0.148300535650375	4	FACETS	0.932	0.849	1	1	0.989	1	CLONAL	4	FALSE	2	0.212625506962056	4		707	355	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589848	212589848	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	76	473	0	ENST00000342788.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000342788	NM_005235.2	232	Cga/Tga	6/28	1	2	FACETS	1	0.964	1	1	0.986	1	CLONAL	2	FALSE	1	0.212625506962056	2		473	292	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033886	49033886	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs137853295	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	31	503	0	ENST00000267163.4:c.2023G>T	p.Glu675Ter	p.E675*	ENST00000267163	NM_000321.2	675	Gaa/Taa	20/27	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	FALSE	1	0.212625506962056	2		503	206	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951919	178951919	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	54	482	0	ENST00000263967.3:c.2974C>T	p.Arg992Ter	p.R992*	ENST00000263967	NM_006218.2	992	Cga/Tga	21/21	1	2	FACETS	1	0.928	1	1	0.979	1	CLONAL	2	FALSE	1	0.212625506962056	2		482	227	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944624	38944624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1377027840	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	66	410	1	ENST00000357387.3:c.4837C>T	p.Arg1613Cys	p.R1613C	ENST00000357387	NM_152756.3	1613	Cgc/Tgc	36/38	1	2	FACETS	0.958	0.845	1	1	0.985	1	CLONAL	3	FALSE	1	0.212625506962056	2		411	216	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	101	531	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	0.148300535650375	4	FACETS	1	0.931	1	1	0.989	1	CLONAL	4	FALSE	2	0.212625506962056	4		531	279	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142000	108142000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779830	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	53	423	0	ENST00000278616.4:c.2944C>T	p.Arg982Cys	p.R982C	ENST00000278616	NM_000051.3	982	Cgt/Tgt	20/63	1	2	FACETS	1	0.947	1	1	0.98	1	CLONAL	2	FALSE	1	0.212625506962056	2		423	207	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541874	187541874	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs549753426	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	37	480	0	ENST00000441802.2:c.5866G>A	p.Asp1956Asn	p.D1956N	ENST00000441802	NM_005245.3	1956	Gat/Aat	10/27	1	2	FACETS	0.837	0.696	0.99	1	0.96	1	CLONAL	2	FALSE	1	0.212625506962056	2		480	208	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257249	133257249	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500889	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	108	533	0	ENST00000320574.5:c.229C>T	p.Arg77Cys	p.R77C	ENST00000320574	NM_006231.2	77	Cgc/Tgc	3/49	0.148300535650375	4	FACETS	0.984	0.895	1	1	0.989	1	CLONAL	4	FALSE	2	0.212625506962056	4		533	313	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850870	63850870	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	40	487	0	ENST00000279873.7:c.1648G>T	p.Glu550Ter	p.E550*	ENST00000279873	NM_032199.2	550	Gaa/Taa	10/10	1	2	FACETS	0.829	0.695	0.975	1	0.962	1	CLONAL	2	FALSE	1	0.212625506962056	2		487	227	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439832	51439832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	20	321	0	ENST00000262662.1:c.397C>T	p.Arg133Trp	p.R133W	ENST00000262662		133	Cgg/Tgg	4/4	1	2	FACETS	0.851	0.653	1	0.851	0.653	1	CLONAL	1	FALSE	1	0.212625506962056	2		321	221	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418997	116418997	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200754673	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	38	246	0	ENST00000397752.3:c.3508C>T	p.Arg1170Ter	p.R1170*	ENST00000397752	NM_000245.2	1170	Cga/Tga	17/21	0.160482769171991	3	FACETS	0.883	0.749	1	1	0.967	1	CLONAL	4	FALSE	1	0.212625506962056	3		246	112	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679547	86679547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	32	325	0	ENST00000274376.6:c.2708G>A	p.Arg903Gln	p.R903Q	ENST00000274376	NM_002890.2	903	cGa/cAa	21/25	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	1	0.212625506962056	2		325	226	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518437	204518437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201947927	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	77	477	0	ENST00000367182.3:c.1100C>T	p.Ser367Leu	p.S367L	ENST00000367182	NM_001278516.1	367	tCg/tTg	11/11	0.212625506962056	1	FACETS	0.84	0.747	0.936	1	0.986	1	CLONAL	3	FALSE	0	0.212625506962056	1		477	257	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654643	67654643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs968244943	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	101	649	0	ENST00000264010.4:c.1130G>A	p.Arg377His	p.R377H	ENST00000264010	NM_006565.3	377	cGt/cAt	6/12	0.160482769171991	3	FACETS	0.897	0.813	0.984	1	0.987	1	CLONAL	4	FALSE	1	0.212625506962056	3		649	293	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226021	53226021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781785252	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	14	735	0	ENST00000375401.3:c.2828G>A	p.Arg943Gln	p.R943Q	ENST00000375401	NM_004187.3	943	cGa/cAa	19/26	0.212625684210489	1	FACETS	0.542	0.392	0.724	0.542	0.392	0.724	SUBCLONAL	1	FALSE	0	0.212625506962056	1		735	217	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021428	42021428	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	38	536	2	ENST00000219905.7:c.3724C>T	p.Arg1242Ter	p.R1242*	ENST00000219905	NM_001164273.1	1242	Cga/Tga	11/24	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	FALSE	1	0.212625506962056	2		538	324	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106355	27106355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773909963	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	45	595	0	ENST00000324856.7:c.5966G>A	p.Arg1989Gln	p.R1989Q	ENST00000324856	NM_006015.4	1989	cGa/cAa	20/20	0.212625506962056	6	FACETS	0.979	0.827	1	0.653	0.551	0.764	CLONAL	2	FALSE	3	0.212625506962056	6		595	308	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922301	178922301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	46	415	0	ENST00000263967.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000263967	NM_006218.2	357	cGa/cAa	6/21	1	2	FACETS	1	0.936	1	1	0.977	1	CLONAL	2	FALSE	1	0.212625506962056	2		415	183	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159104	143159104	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1405228238	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	71	522	1	ENST00000262992.4:c.749G>A	p.Arg250Gln	p.R250Q	ENST00000262992	NM_001101669.1	250	cGa/cAa	10/24	1	2	FACETS	0.935	0.828	1	1	0.986	1	CLONAL	3	FALSE	1	0.212625506962056	2		523	238	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267600319	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	23	349	1	ENST00000257430.4:c.4199C>T	p.Ser1400Leu	p.S1400L	ENST00000257430	NM_000038.5	1400	tCg/tTg	16/16	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	FALSE	1	0.212625506962056	2		350	178	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219113	133219113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771896231	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	79	601	0	ENST00000320574.5:c.4931C>T	p.Ser1644Leu	p.S1644L	ENST00000320574	NM_006231.2	1644	tCg/tTg	37/49	0.148300535650375	4	FACETS	1	0.936	1	1	0.986	1	CLONAL	4	FALSE	2	0.212625506962056	4		601	212	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693002	89693003	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	10	471	0	ENST00000371953.3:c.491dup	p.Val166SerfsTer14	p.V166Sfs*14	ENST00000371953	NM_000314.4	162	-/A	5/9	1	2	FACETS	0.55	0.373	0.772	0.55	0.373	0.772	SUBCLONAL	1	FALSE	1	0.212625506962056	2		471	171	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	35	519	0	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	1	2	FACETS	0.799	0.661	0.951	1	0.955	1	CLONAL	2	FALSE	1	0.212625506962056	2		519	206	SUCCESS
APC	324	MSKCC	GRCh37	5	112176873	112176873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	65	434	0	ENST00000257430.4:c.5582C>A	p.Ser1861Tyr	p.S1861Y	ENST00000257430	NM_000038.5	1861	tCt/tAt	16/16	1	2	FACETS	1	0.918	1	1	0.986	1	CLONAL	3	FALSE	1	0.212625506962056	2		434	194	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023160	150023160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	72	577	0	ENST00000253339.5:c.103C>T	p.Arg35Trp	p.R35W	ENST00000253339		35	Cgg/Tgg	1/7	0.160482769171991	3	FACETS	1	0.913	1	1	0.978	1	CLONAL	3	FALSE	1	0.212625506962056	3		577	241	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003060	42003060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756706031	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	111	652	3	ENST00000219905.7:c.2597G>A	p.Arg866Gln	p.R866Q	ENST00000219905	NM_001164273.1	866	cGa/cAa	8/24	1	2	FACETS	0.997	0.906	1	1	0.991	1	CLONAL	3	FALSE	1	0.212625506962056	2		655	349	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499354	89499354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	15	377	0	ENST00000336596.2:c.2524C>T	p.Arg842Ter	p.R842*	ENST00000336596	NM_005233.5	842	Cga/Tga	15/17	1	2	FACETS	0.887	0.652	1	0.887	0.652	1	CLONAL	1	FALSE	1	0.212625506962056	2		377	159	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169179	119169179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150811339	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	87	446	1	ENST00000264033.4:c.2363G>A	p.Arg788Gln	p.R788Q	ENST00000264033	NM_005188.3	788	cGa/cAa	15/16	1	2	FACETS	0.957	0.858	1	1	0.989	1	CLONAL	3	FALSE	1	0.212625506962056	2		447	285	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131412	202131412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339962485	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	52	525	0	ENST00000358485.4:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000358485	NM_001080125.1	127	cGa/cAa	2/9	1	2	FACETS	1	0.945	1	1	0.979	1	CLONAL	2	FALSE	1	0.212625506962056	2		525	204	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122881	2122881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749593050	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	78	690	0	ENST00000219476.3:c.2252G>A	p.Arg751Gln	p.R751Q	ENST00000219476	NM_000548.3	751	cGa/cAa	21/42	0.160482769171991	3	FACETS	1	0.914	1	1	0.914	1	CLONAL	2	FALSE	1	0.212625506962056	3		690	390	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827732	72827732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241554729	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	68	462	0	ENST00000268489.5:c.8849G>A	p.Arg2950His	p.R2950H	ENST00000268489	NM_006885.3	2950	cGc/cAc	9/10	0.160482769171991	3	FACETS	1	0.933	1	1	0.979	1	CLONAL	3	FALSE	1	0.212625506962056	3		462	218	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228613019	228613019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773567566	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	23	313	0	ENST00000366696.1:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000366696	NM_003493.2	3	cGa/cAa	1/1	0.212625506962056	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	FALSE	0	0.212625506962056	1		313	148	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698180	47698180	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63751411	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	73	213	0	ENST00000233146.2:c.1738G>T	p.Glu580Ter	p.E580*	ENST00000233146	NM_000251.2	580	Gaa/Taa	11/16	1	2	FACETS	0.88	0.785	0.978	1	0.988	1	CLONAL	4	FALSE	1	0.212625506962056	2		213	195	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584501	189584501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908849	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	25	336	0	ENST00000264731.3:c.797G>A	p.Arg266Gln	p.R266Q	ENST00000264731	NM_003722.4	266	cGa/cAa	6/14	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	FALSE	1	0.212625506962056	2		336	166	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	67	314	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	1	0.928	1	1	0.986	1	CLONAL	3	FALSE	1	0.212625506962056	2		314	197	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662397	117662397	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	36	586	0	ENST00000368508.3:c.4980G>T	p.Glu1660Asp	p.E1660D	ENST00000368508	NM_002944.2	1660	gaG/gaT	30/43	0.160482769171991	3	FACETS	0.909	0.754	1	0.909	0.754	1	CLONAL	2	FALSE	1	0.212625506962056	3		586	206	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176470	123176470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	81	406	1	ENST00000218089.9:c.437G>A	p.Arg146Gln	p.R146Q	ENST00000218089	NM_001042749.1	146	cGa/cAa	7/35	0.212625684210489	1	FACETS	0.94	0.849	1	1	0.989	1	CLONAL	4	FALSE	0	0.212625506962056	1		407	181	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100998	41100998	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772057709	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	39	454	1	ENST00000373198.4:c.1358G>A	p.Arg453His	p.R453H	ENST00000373198	NM_133170.3	453	cGc/cAc	8/32	0.135652639616145	0	FACETS	0.881	0.741	1			1	CLONAL	2	FALSE	0	0.212625506962056	0		455	164	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641430	47641430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs34136999	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	36	449	0	ENST00000233146.2:c.815C>T	p.Ala272Val	p.A272V	ENST00000233146	NM_000251.2	272	gCg/gTg	5/16	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	FALSE	1	0.212625506962056	2		449	236	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743859	40743859	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369430281	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	65	507	1	ENST00000373198.4:c.3136C>T	p.Arg1046Cys	p.R1046C	ENST00000373198	NM_133170.3	1046	Cgc/Tgc	23/32	0.135652639616145	0	FACETS	1	0.902	1			1	CLONAL	3	FALSE	0	0.212625506962056	0		508	158	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317921	8317921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150063446	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	26	425	1	ENST00000356435.5:c.5692C>T	p.Arg1898Cys	p.R1898C	ENST00000356435		1898	Cgt/Tgt	35/35	0.167533035722701	1	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	FALSE	0	0.212625506962056	1		426	182	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717609	89717609	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs876661024	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	19	426	0	ENST00000371953.3:c.635-1G>A		p.X212_splice	ENST00000371953	NM_000314.4	212			1	2	FACETS	1	0.813	1	1	0.813	1	CLONAL	1	FALSE	1	0.212625506962056	2		426	166	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266828	198266828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs16865307	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	90	546	1	ENST00000335508.6:c.2104C>T	p.Arg702Trp	p.R702W	ENST00000335508	NM_012433.2	702	Cgg/Tgg	15/25	1	2	FACETS	0.858	0.769	0.951	1	0.988	1	CLONAL	3	FALSE	1	0.212625506962056	2		547	329	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015094	37015094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	34	692	1	ENST00000358127.4:c.310C>T	p.Arg104Cys	p.R104C	ENST00000358127	NM_001280556.1	104	Cgc/Tgc	3/10	0.167533035722701	1	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	FALSE	0	0.212625506962056	1		693	249	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203791	94203791	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs190142346	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	13	202	0	ENST00000323929.3:c.863G>A	p.Arg288His	p.R288H	ENST00000323929	NM_005591.3	288	cGt/cAt	9/20	1	2	FACETS	1	0.785	1	1	0.785	1	CLONAL	1	FALSE	1	0.212625506962056	2		202	110	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029408	14029408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368830992	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	60	410	0	ENST00000311895.7:c.1619C>T	p.Ser540Leu	p.S540L	ENST00000311895	NM_005236.2	540	tCg/tTg	8/11	0.160482769171991	3	FACETS	1	0.879	1	1	0.973	1	CLONAL	3	FALSE	1	0.212625506962056	3		410	207	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625652	1625652	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs533848977	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	37	699	1	ENST00000344749.5:c.422C>T	p.Ser141Leu	p.S141L	ENST00000344749	NM_001136139.2	141	tCg/tTg	7/19	0.148300535650375	4	FACETS	1	0.935	1	0.649	0.537	0.774	CLONAL	1	FALSE	2	0.212625506962056	4		700	325	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405905	157405905	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774701560	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	49	421	0	ENST00000346085.5:c.2147C>T	p.Ala716Val	p.A716V	ENST00000346085	NM_020732.3	716	gCg/gTg	6/20	0.160482769171991	3	FACETS	0.969	0.828	1	0.969	0.828	1	CLONAL	2	FALSE	1	0.212625506962056	3		421	263	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553011	106553011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs955184509	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	31	608	1	ENST00000369096.4:c.976C>T	p.Arg326Cys	p.R326C	ENST00000369096	NM_001198.3	326	Cgc/Tgc	5/7	0.160482769171991	3	FACETS	1	0.942	1	0.737	0.6	0.889	CLONAL	1	FALSE	1	0.212625506962056	3		609	219	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829200	72829200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779491169	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	63	628	0	ENST00000268489.5:c.7381G>A	p.Glu2461Lys	p.E2461K	ENST00000268489	NM_006885.3	2461	Gag/Aag	9/10	0.160482769171991	3	FACETS	1	0.933	1	1	0.977	1	CLONAL	3	FALSE	1	0.212625506962056	3		628	200	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258610	16258610	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200615625	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	36	548	0	ENST00000375759.3:c.5875C>T	p.Arg1959Ter	p.R1959*	ENST00000375759	NM_015001.2	1959	Cga/Tga	11/15	0.212625506962056	6	FACETS	0.871	0.72	1	0.581	0.48	0.693	CLONAL	2	FALSE	3	0.212625506962056	6		548	277	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523486	106523486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750632554	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	43	284	0	ENST00000359195.3:c.2638G>A	p.Glu880Lys	p.E880K	ENST00000359195	NM_002649.2	880	Gag/Aag	8/11	0.160482769171991	3	FACETS	1	0.898	1	1	0.966	1	CLONAL	3	FALSE	1	0.212625506962056	3		284	140	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65304233	65304233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1163790865	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	37	458	2	ENST00000342505.4:c.2882C>T	p.Ser961Leu	p.S961L	ENST00000342505	NM_002227.2	961	tCg/tTg	21/25	1	2	FACETS	1	0.925	1	1	0.971	1	CLONAL	2	FALSE	1	0.212625506962056	2		460	146	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158224	47158224	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	55	397	0	ENST00000409792.3:c.4475G>A	p.Arg1492Gln	p.R1492Q	ENST00000409792	NM_014159.6	1492	cGa/cAa	4/21	1	2	FACETS	0.924	0.797	1	1	0.976	1	CLONAL	2	FALSE	1	0.212625506962056	2		397	280	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956553	93956553	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1035177735	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	43	331	0	ENST00000369303.4:c.2683C>T	p.Arg895Ter	p.R895*	ENST00000369303	NM_004440.3	895	Cga/Tga	15/17	0.160482769171991	3	FACETS	0.877	0.746	1	1	0.95	1	CLONAL	3	FALSE	1	0.212625506962056	3		331	170	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869692	117869692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1337189031	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	14	370	0	ENST00000297338.2:c.502C>T	p.Arg168Cys	p.R168C	ENST00000297338	NM_006265.2	168	Cgt/Tgt	6/14	1	2	FACETS	0.855	0.621	1	0.855	0.621	1	CLONAL	1	FALSE	1	0.212625506962056	2		370	154	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944562	40944562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868189942	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	28	465	0	ENST00000373198.4:c.1940C>T	p.Ser647Leu	p.S647L	ENST00000373198	NM_133170.3	647	tCg/tTg	12/32	0.135652639616145	0	FACETS	0.673	0.545	0.816			1	SUBCLONAL	2	FALSE	0	0.212625506962056	0		465	154	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72893510	72893510	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	21	576	0	ENST00000325599.8:c.208G>T	p.Gly70Ter	p.G70*	ENST00000325599	NM_018130.2	70	Gga/Tga	2/11	1	2	FACETS	0.729	0.562	0.923	0.729	0.562	0.923	CLONAL	1	FALSE	1	0.212625506962056	2		576	271	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358367	91358367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779891	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	18	536	0	ENST00000355112.3:c.4112C>T	p.Thr1371Met	p.T1371M	ENST00000355112	NM_000057.2	1371	aCg/aTg	22/22	1	2	FACETS	0.842	0.637	1	0.842	0.637	1	CLONAL	1	FALSE	1	0.212625506962056	2		536	201	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39570433	39570433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747825815	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	37	167	0	ENST00000262039.4:c.629G>A	p.Arg210Gln	p.R210Q	ENST00000262039	NM_002647.2	210	cGa/cAa	6/25	0.167533035722701	1	FACETS	0.972	0.835	1	1	0.978	1	CLONAL	4	FALSE	0	0.212625506962056	1		167	80	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030384	49030384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554834063	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	46	440	0	ENST00000267163.4:c.1859C>T	p.Thr620Met	p.T620M	ENST00000267163	NM_000321.2	620	aCg/aTg	19/27	1	2	FACETS	1	0.853	1	1	0.973	1	CLONAL	2	FALSE	1	0.212625506962056	2		440	216	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749389	41749389	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	27	350	0	ENST00000226382.2:c.406G>A	p.Asp136Asn	p.D136N	ENST00000226382	NM_003924.3	136	Gac/Aac	2/3	1	2	FACETS	0.955	0.771	1	1	0.953	1	CLONAL	2	FALSE	1	0.212625506962056	2		350	133	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149516607	149516607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148272095	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	39	630	3	ENST00000261799.4:c.4C>T	p.Arg2Trp	p.R2W	ENST00000261799	NM_002609.3	2	Cgg/Tgg	2/23	0.212625684210489	0	FACETS	1	0.932	1			1	CLONAL	1	FALSE	0	0.212625506962056	0		633	233	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397187	397187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	22	408	0	ENST00000380956.4:c.572C>T	p.Pro191Leu	p.P191L	ENST00000380956	NM_001195286.1	191	cCg/cTg	5/9	NA	2	FACETS	1	0.844	1			1	INDETERMINATE	1	FALSE	NA	0.212625506962056	2		408	187	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846307	156846307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762542314	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	37	662	0	ENST00000524377.1:c.1748G>A	p.Arg583His	p.R583H	ENST00000524377	NM_002529.3	583	cGc/cAc	14/17	0.212625506962056	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	0	0.212625506962056	1		662	234	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707951	47707951	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63749830	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	43	520	0	ENST00000233146.2:c.2575G>T	p.Glu859Ter	p.E859*	ENST00000233146	NM_000251.2	859	Gaa/Taa	15/16	1	2	FACETS	1	0.888	1	1	0.973	1	CLONAL	2	FALSE	1	0.212625506962056	2		520	191	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511714	66511714	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	21	300	0	ENST00000358598.2:c.174G>T	p.Glu58Asp	p.E58D	ENST00000358598	NM_212471.2	58	gaG/gaT	2/11	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	FALSE	1	0.212625506962056	2		300	133	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617210	100617210	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	14	516	0	ENST00000308731.7:c.539C>A	p.Ser180Tyr	p.S180Y	ENST00000308731	NM_000061.2	180	tCt/tAt	7/19	0.212625684210489	1	FACETS	0.566	0.409	0.754	0.566	0.409	0.754	SUBCLONAL	1	FALSE	0	0.212625506962056	1		516	208	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796793	135796793	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs118203429	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	25	356	0	ENST00000298552.3:c.694G>T	p.Glu232Ter	p.E232*	ENST00000298552	NM_001162426.1	232	Gaa/Taa	8/23	0.167533035722701	1	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	FALSE	0	0.212625506962056	1		356	172	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188035	151188035	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	44	348	0	ENST00000262187.5:c.118G>T	p.Glu40Ter	p.E40*	ENST00000262187	NM_005614.3	40	Gaa/Taa	2/8	0.160482769171991	3	FACETS	0.867	0.738	1	1	0.95	1	CLONAL	3	FALSE	1	0.212625506962056	3		348	176	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861149	57861149	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774058977	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	31	560	0	ENST00000228682.2:c.946G>A	p.Glu316Lys	p.E316K	ENST00000228682	NM_005269.2	316	Gaa/Aaa	9/12	0.148300535650375	4	FACETS	1	0.939	1	0.719	0.584	0.869	CLONAL	1	FALSE	2	0.212625506962056	4		560	246	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2105507	2105507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45517113	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	53	570	2	ENST00000219476.3:c.586G>A	p.Ala196Thr	p.A196T	ENST00000219476	NM_000548.3	196	Gca/Aca	6/42	0.160482769171991	3	FACETS	1	0.964	1	0.73	0.624	0.844	CLONAL	1	FALSE	1	0.212625506962056	3		572	378	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293545	1293545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199422293	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	30	792	1	ENST00000310581.5:c.1456C>T	p.Arg486Cys	p.R486C	ENST00000310581	NM_198253.2	486	Cgc/Tgc	2/16	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	FALSE	1	0.212625506962056	2		793	219	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152295	99152295	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	21	514	0	ENST00000074304.5:c.374G>T	p.Arg125Ile	p.R125I	ENST00000074304	NM_001134224.1	125	aGa/aTa	6/26	1	2	FACETS	0.823	0.635	1	0.823	0.635	1	CLONAL	1	FALSE	1	0.212625506962056	2		514	240	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430786	181430786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	81	659	0	ENST00000325404.1:c.638C>T	p.Ser213Leu	p.S213L	ENST00000325404	NM_003106.3	213	tCg/tTg	1/1	1	2	FACETS	0.907	0.815	1	1	0.989	1	CLONAL	4	FALSE	1	0.212625506962056	2		659	210	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131893077	131893077	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	101	403	0	ENST00000265335.6:c.61G>T	p.Asp21Tyr	p.D21Y	ENST00000265335		21	Gat/Tat	1/25	1	2	FACETS	1	0.968	1	1	0.991	1	CLONAL	3	FALSE	1	0.212625506962056	2		403	275	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513352	41513352	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	110	604	1	ENST00000263253.7:c.256C>T	p.Arg86Ter	p.R86*	ENST00000263253	NM_001429.3	86	Cga/Tga	2/31	0.148300535650375	4	FACETS	0.928	0.843	1	1	0.988	1	CLONAL	4	FALSE	2	0.212625506962056	4		605	338	SUCCESS
APC	324	MSKCC	GRCh37	5	112111411	112111411	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	35	383	0	ENST00000257430.4:c.508G>T	p.Asp170Tyr	p.D170Y	ENST00000257430	NM_000038.5	170	Gat/Tat	5/16	1	2	FACETS	0.827	0.684	0.984	1	0.957	1	CLONAL	2	FALSE	1	0.212625506962056	2		383	199	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39647367	39647367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373107502	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	25	368	0	ENST00000262039.4:c.2539C>T	p.Arg847Cys	p.R847C	ENST00000262039	NM_002647.2	847	Cgc/Tgc	24/25	0.167533035722701	1	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	FALSE	0	0.212625506962056	1		368	177	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864776	37864776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs185670819	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	39	385	2	ENST00000269571.5:c.428G>A	p.Arg143Gln	p.R143Q	ENST00000269571		143	cGa/cAa	3/27	0.212625506962056	5	FACETS	0.911	0.765	1	0.911	0.765	1	CLONAL	3	FALSE	2	0.212625506962056	5		387	177	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143015	7143015	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145643501	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	105	630	0	ENST00000302850.5:c.2354C>T	p.Ser785Leu	p.S785L	ENST00000302850	NM_000208.2	785	tCg/tTg	12/22	0.148300535650375	4	FACETS	0.913	0.827	1	1	0.988	1	CLONAL	4	FALSE	2	0.212625506962056	4		630	328	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667422	241667422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756990249	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	32	477	0	ENST00000366560.3:c.1028G>A	p.Arg343Gln	p.R343Q	ENST00000366560	NM_000143.3	343	cGa/cAa	7/10	0.212625506962056	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	FALSE	0	0.212625506962056	1		477	198	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176614	56176614	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	81	439	0	ENST00000399503.3:c.2164G>T	p.Glu722Ter	p.E722*	ENST00000399503	NM_005921.1	722	Gaa/Taa	12/20	1	2	FACETS	1	0.927	1	1	0.988	1	CLONAL	3	FALSE	1	0.212625506962056	2		439	243	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346224	152346224	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	60	642	0	ENST00000359321.1:c.346T>G	p.Phe116Val	p.F116V	ENST00000359321	NM_005431.1	116	Ttt/Gtt	3/3	0.160482769171991	3	FACETS	1	0.912	1	1	0.975	1	CLONAL	3	FALSE	1	0.212625506962056	3		642	198	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10292722	10292722	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	100	512	0	ENST00000340748.4:c.112G>T	p.Glu38Ter	p.E38*	ENST00000340748		38	Gaa/Taa	2/40	0.148300535650375	4	FACETS	0.888	0.799	0.983	1	0.978	1	CLONAL	3	FALSE	2	0.212625506962056	4		512	428	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321280	1321280	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763471203	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	52	486	0	ENST00000400841.2:c.475G>A	p.Glu159Lys	p.E159K	ENST00000400841		159	Gag/Aag	4/6	0.212625684210489	1	FACETS	0.905	0.786	1	1	0.981	1	CLONAL	3	FALSE	0	0.212625506962056	1		486	161	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349604	89349604	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs924589358	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	137	805	1	ENST00000301030.4:c.3346G>A	p.Ala1116Thr	p.A1116T	ENST00000301030	NM_001256183.1	1116	Gca/Aca	9/13	0.186344826990072	4	FACETS	0.914	0.843	0.986	1	0.992	1	CLONAL	5	FALSE	2	0.212625506962056	4		806	342	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56787223	56787223	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770637624	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	32	478	1	ENST00000337432.4:c.709C>T	p.Arg237Ter	p.R237*	ENST00000337432	NM_058216.2	237	Cga/Tga	5/9	1	2	FACETS	0.822	0.674	0.986	1	0.953	1	CLONAL	2	FALSE	1	0.212625506962056	2		479	183	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98244310	98244310	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1266754583	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	42	602	0	ENST00000331920.6:c.667C>A	p.Leu223Ile	p.L223I	ENST00000331920	NM_000264.3	223	Ctt/Att	5/24	0.167533035722701	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	0	0.212625506962056	1		602	257	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485052	57485052	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	49	365	0	ENST00000371085.3:c.886C>A	p.Leu296Met	p.L296M	ENST00000371085	NM_000516.4	296	Ctg/Atg	11/13	0.135652639616145	0	FACETS	0.812	0.702	0.927			1	CLONAL	3	FALSE	0	0.212625506962056	0		365	149	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983307	149983307	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	47	584	0	ENST00000253339.5:c.2951T>G	p.Leu984Arg	p.L984R	ENST00000253339		984	cTt/cGt	7/7	0.160482769171991	3	FACETS	0.967	0.822	1	0.967	0.822	1	CLONAL	2	FALSE	1	0.212625506962056	3		584	253	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142910	30142910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141093002	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	35	671	0	ENST00000389048.3:c.616G>A	p.Ala206Thr	p.A206T	ENST00000389048	NM_004304.4	206	Gcg/Acg	1/29	1	2	FACETS	0.866	0.718	1	1	0.959	1	CLONAL	2	FALSE	1	0.212625506962056	2		671	190	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411777	63411777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767567473	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	25	815	0	ENST00000330258.3:c.1390G>A	p.Ala464Thr	p.A464T	ENST00000330258	NM_152424.3	464	Gcc/Acc	2/2	0.212625684210489	1	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	FALSE	0	0.212625506962056	1		815	167	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236697	236697	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs200305419	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	10	246	0	ENST00000264932.6:c.1415A>C	p.Glu472Ala	p.E472A	ENST00000264932	NM_004168.2	472	gAa/gCa	10/15	1	2	FACETS	0.687	0.467	0.96	0.687	0.467	0.96	SUBCLONAL	1	FALSE	1	0.212625506962056	2		246	137	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741000	40741000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	46	775	0	ENST00000392038.2:c.1318G>A	p.Asp440Asn	p.D440N	ENST00000392038	NM_001626.4	440	Gat/Aat	13/14	0.148300535650375	4	FACETS	0.983	0.833	1	0.983	0.833	1	CLONAL	2	FALSE	2	0.212625506962056	4		775	267	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212851	27212851	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760084463	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	100	629	3	ENST00000380036.4:c.2833G>A	p.Ala945Thr	p.A945T	ENST00000380036	NM_000459.3	945	Gct/Act	17/23	0.167533035722701	1	FACETS	0.94	0.851	1	1	0.99	1	CLONAL	3	FALSE	0	0.212625506962056	1		632	298	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093455	30093455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776034417	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	47	375	0	ENST00000331968.5:c.1808G>A	p.Arg603His	p.R603H	ENST00000331968	NM_002742.2	603	cGt/cAt	13/18	0.212625506962056	1	FACETS	0.861	0.741	0.987	1	0.979	1	CLONAL	3	FALSE	0	0.212625506962056	1		375	153	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936153	71936153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	35	258	0	ENST00000298229.2:c.125G>A	p.Gly42Asp	p.G42D	ENST00000298229	NM_001567.3	42	gGc/gAc	1/28	1	2	FACETS	1	0.849	1	1	0.966	1	CLONAL	2	FALSE	1	0.212625506962056	2		258	161	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416417	49416417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565753611	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	24	553	0	ENST00000301067.7:c.16294C>T	p.Arg5432Trp	p.R5432W	ENST00000301067	NM_003482.3	5432	Cgg/Tgg	51/54	0.148300535650375	4	FACETS	0.883	0.693	1	0.442	0.346	0.551	CLONAL	1	FALSE	2	0.212625506962056	4		553	310	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257270	133257270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	66	476	0	ENST00000320574.5:c.208G>A	p.Glu70Lys	p.E70K	ENST00000320574	NM_006231.2	70	Gag/Aag	3/49	0.148300535650375	4	FACETS	0.976	0.857	1	1	0.973	1	CLONAL	3	FALSE	2	0.212625506962056	4		476	257	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273417	38273417	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121909639	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	44	903	0	ENST00000425967.3:c.1918C>T	p.Arg640Ter	p.R640*	ENST00000425967	NM_001174067.1	640	Cga/Tga	14/19	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.212625506962056	2		903	283	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851550	63851550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	76	577	1	ENST00000279873.7:c.2328G>T	p.Glu776Asp	p.E776D	ENST00000279873	NM_032199.2	776	gaG/gaT	10/10	1	2	FACETS	1	0.957	1	1	0.985	1	CLONAL	2	FALSE	1	0.212625506962056	2		578	304	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123324988	123324988	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	50	518	0	ENST00000358487.5:c.340G>T	p.Asp114Tyr	p.D114Y	ENST00000358487	NM_000141.4	114	Gac/Tac	3/18	1	2	FACETS	1	0.888	1	1	0.976	1	CLONAL	2	FALSE	1	0.212625506962056	2		518	226	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951086	17951086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1257606008	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	167	639	0	ENST00000458235.1:c.1207C>T	p.Arg403Cys	p.R403C	ENST00000458235	NM_000215.3	403	Cgc/Tgc	9/24	0.148300535650375	4	FACETS	0.909	0.845	0.974	1	0.993	1	CLONAL	5	FALSE	2	0.212625506962056	4		639	419	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411780	116411780	+	intron_variant	Intron	SNP	C	C	T	rs553445059	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	49	1057	1	ENST00000397752.3:c.2887+72C>T		p.*963*	ENST00000397752	NM_000245.2	-/1390			0.160482769171991	3	FACETS	1	0.933	1	0.594	0.504	0.693	CLONAL	1	FALSE	1	0.212625506962056	3		1058	429	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039665	47039665	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	72	693	0	ENST00000377604.3:c.1117G>A	p.Asp373Asn	p.D373N	ENST00000377604	NM_001204468.1	373	Gac/Aac	11/24	0.212625684210489	1	FACETS	0.859	0.761	0.96	1	0.986	1	CLONAL	3	FALSE	0	0.212625506962056	1		693	235	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22405002	22405002	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	15	87	0	ENST00000344548.3:c.31G>A	p.Asp11Asn	p.D11N	ENST00000344548	NM_001039802.1	11	Gat/Aat	3/7	0.212625506962056	6	FACETS	0.958	0.754	1	1	0.938	1	CLONAL	7	FALSE	3	0.212625506962056	6		87	30	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31468149	31468149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	38	620	0	ENST00000344624.3:c.2263G>A	p.Asp755Asn	p.D755N	ENST00000344624		755	Gat/Aat	15/33	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	FALSE	1	0.212625506962056	2		620	253	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271269	153271269	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	27	285	0	ENST00000281708.4:c.509G>T	p.Arg170Ile	p.R170I	ENST00000281708	NM_033632.3	170	aGa/aTa	3/12	1	2	FACETS	0.907	0.732	1	1	0.951	1	CLONAL	2	FALSE	1	0.212625506962056	2		285	140	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325247	39325247	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	39	409	0	ENST00000373001.3:c.72G>T	p.Lys24Asn	p.K24N	ENST00000373001	NM_022157.3	24	aaG/aaT	1/7	1	2	FACETS	0.777	0.649	0.918	1	0.957	1	CLONAL	2	FALSE	1	0.212625506962056	2		409	236	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176469	123176469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	33	404	0	ENST00000218089.9:c.436C>T	p.Arg146Ter	p.R146*	ENST00000218089	NM_001042749.1	146	Cga/Tga	7/35	0.212625684210489	1	FACETS	0.784	0.645	0.936	1	0.951	1	CLONAL	2	FALSE	0	0.212625506962056	1		404	177	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813902	50813902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1162538506	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	33	644	1	ENST00000398568.2:c.1456C>T	p.Arg486Cys	p.R486C	ENST00000398568	NM_001042412.1	486	Cgt/Tgt	8/18	0.160482769171991	3	FACETS	0.822	0.675	0.984	0.822	0.675	0.984	CLONAL	2	FALSE	1	0.212625506962056	3		645	209	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31493373	31493373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	23	440	0	ENST00000344624.3:c.1783G>A	p.Asp595Asn	p.D595N	ENST00000344624		595	Gat/Aat	10/33	1	2	FACETS	1	0.795	1	1	0.795	1	CLONAL	1	FALSE	1	0.212625506962056	2		440	213	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915524	112915524	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121918455	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	67	533	0	ENST00000351677.2:c.923A>C	p.Asn308Thr	p.N308T	ENST00000351677	NM_002834.3	308	aAt/aCt	8/16	0.148300535650375	4	FACETS	0.955	0.845	1	1	0.982	1	CLONAL	4	FALSE	2	0.212625506962056	4		533	200	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198261	185198261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376662287	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	77	439	1	ENST00000265026.3:c.2743C>T	p.Arg915Cys	p.R915C	ENST00000265026	NM_004721.4	915	Cgt/Tgt	13/14	1	2	FACETS	0.977	0.87	1	1	0.987	1	CLONAL	3	FALSE	1	0.212625506962056	2		440	247	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807815	3807815	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	124	445	0	ENST00000262367.5:c.3604C>T	p.Arg1202Cys	p.R1202C	ENST00000262367	NM_004380.2	1202	Cgc/Tgc	18/31	0.160482769171991	3	FACETS	1	0.966	1	1	0.991	1	CLONAL	4	FALSE	1	0.212625506962056	3		445	295	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740468	58740468	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371199697	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	81	603	0	ENST00000305921.3:c.1373G>A	p.Arg458Gln	p.R458Q	ENST00000305921	NM_003620.3	458	cGa/cAa	6/6	1	2	FACETS	1	0.931	1	1	0.988	1	CLONAL	3	FALSE	1	0.212625506962056	2		603	241	SUCCESS
MET	4233	MSKCC	GRCh37	7	116414341	116414341	+	intron_variant	Intron	SNP	G	G	A	rs929061044	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	44	905	0	ENST00000397752.3:c.3029-594G>A		p.*1010*	ENST00000397752	NM_000245.2	-/1390			0.160482769171991	3	FACETS	1	0.952	1	0.687	0.579	0.807	CLONAL	1	FALSE	1	0.212625506962056	3		905	333	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288290	21288290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1260646700	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	38	673	0	ENST00000354336.3:c.535G>A	p.Glu179Lys	p.E179K	ENST00000354336	NM_005207.3	179	Gaa/Aaa	2/3	0.148300535650375	4	FACETS	1	0.947	1	0.704	0.584	0.836	CLONAL	1	FALSE	2	0.212625506962056	4		673	308	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938141	36938141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759587248	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	38	634	1	ENST00000361632.4:c.820C>T	p.Arg274Cys	p.R274C	ENST00000361632		274	Cgt/Tgt	6/16	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	FALSE	1	0.212625506962056	2		635	255	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020558	69020558	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61753700	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	60	494	0	ENST00000288368.4:c.2930C>T	p.Ser977Leu	p.S977L	ENST00000288368	NM_024870.2	977	tCg/tTg	24/40	1	2	FACETS	0.893	0.787	1	1	0.985	1	CLONAL	4	FALSE	1	0.212625506962056	2		494	158	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724358	117724358	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772261492	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	44	642	1	ENST00000368508.3:c.521C>T	p.Ala174Val	p.A174V	ENST00000368508	NM_002944.2	174	gCg/gTg	6/43	0.160482769171991	3	FACETS	0.908	0.768	1	0.908	0.768	1	CLONAL	2	FALSE	1	0.212625506962056	3		643	252	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770576	40770576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	23	471	0	ENST00000373198.4:c.2806C>T	p.Arg936Ter	p.R936*	ENST00000373198	NM_133170.3	936	Cga/Tga	19/32	0.135652639616145	0	FACETS	0.665	0.526	0.822			1	SUBCLONAL	2	FALSE	0	0.212625506962056	0		471	128	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215621	36215621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1268488101	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	99	616	0	ENST00000222270.7:c.3418C>T	p.Arg1140Cys	p.R1140C	ENST00000222270	NM_014727.1	1140	Cgc/Tgc	9/37	0.148300535650375	4	FACETS	0.984	0.89	1	1	0.988	1	CLONAL	4	FALSE	2	0.212625506962056	4		616	287	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211940	36211940	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374728315	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	39	829	0	ENST00000222270.7:c.1691G>A	p.Arg564Gln	p.R564Q	ENST00000222270	NM_014727.1	564	cGa/cAa	3/37	0.148300535650375	4	FACETS	0.77	0.641	0.912	0.77	0.641	0.912	CLONAL	2	FALSE	2	0.212625506962056	4		829	289	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246498697	246498697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143920876	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	37	567	0	ENST00000388985.4:c.308G>A	p.Arg103Gln	p.R103Q	ENST00000388985		103	cGa/cAa	3/12	0.212625506962056	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	FALSE	0	0.212625506962056	1		567	265	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152120	55152120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745464928	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	90	608	1	ENST00000257290.5:c.2552C>T	p.Ser851Leu	p.S851L	ENST00000257290	NM_006206.4	851	tCg/tTg	18/23	1	2	FACETS	1	0.93	1	1	0.989	1	CLONAL	3	FALSE	1	0.212625506962056	2		609	271	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988800	41988800	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	83	559	0	ENST00000219905.7:c.1592G>T	p.Arg531Ile	p.R531I	ENST00000219905	NM_001164273.1	531	aGa/aTa	3/24	1	2	FACETS	1	0.936	1	1	0.989	1	CLONAL	3	FALSE	1	0.212625506962056	2		559	245	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701263	43701263	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1157211964	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	91	525	0	ENST00000382044.4:c.5432C>T	p.Ala1811Val	p.A1811V	ENST00000382044	NM_001141980.1	1811	gCg/gTg	26/28	1	2	FACETS	1	0.955	1	1	0.99	1	CLONAL	3	FALSE	1	0.212625506962056	2		525	258	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466770	25466770	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	18	510	0	ENST00000264709.3:c.1933A>G	p.Thr645Ala	p.T645A	ENST00000264709	NM_175629.2	645	Aca/Gca	16/23	1	2	FACETS	0.834	0.63	1	0.834	0.63	1	CLONAL	1	FALSE	1	0.212625506962056	2		510	203	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665230	117665230	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1258207555	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	15	318	0	ENST00000368508.3:c.4517G>T	p.Arg1506Ile	p.R1506I	ENST00000368508	NM_002944.2	1506	aGa/aTa	27/43	0.160482769171991	3	FACETS	1	0.842	1	0.61	0.45	0.799	CLONAL	1	FALSE	1	0.212625506962056	3		318	128	SUCCESS
AR	367	MSKCC	GRCh37	X	66765677	66765677	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1315081227	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	27	896	0	ENST00000374690.3:c.689C>T	p.Ser230Leu	p.S230L	ENST00000374690	NM_000044.3	230	tCg/tTg	1/8	0.212625684210489	1	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	FALSE	0	0.212625506962056	1		896	200	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950389	38950389	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	24	499	0	ENST00000357387.3:c.3561G>T	p.Lys1187Asn	p.K1187N	ENST00000357387	NM_152756.3	1187	aaG/aaT	31/38	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	FALSE	1	0.212625506962056	2		499	171	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244255	153244255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	41	349	0	ENST00000281708.4:c.1902G>T	p.Lys634Asn	p.K634N	ENST00000281708	NM_033632.3	634	aaG/aaT	12/12	1	2	FACETS	1	0.931	1	1	0.974	1	CLONAL	2	FALSE	1	0.212625506962056	2		349	162	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685284	86685284	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	31	247	0	ENST00000274376.6:c.3000G>T	p.Glu1000Asp	p.E1000D	ENST00000274376	NM_002890.2	1000	gaG/gaT	24/25	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.212625506962056	2		247	197	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951105	48951105	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	37	398	0	ENST00000267163.4:c.1267G>T	p.Gly423Ter	p.G423*	ENST00000267163	NM_000321.2	423	Gga/Tga	13/27	1	2	FACETS	0.757	0.628	0.898	1	0.953	1	SUBCLONAL	2	FALSE	1	0.212625506962056	2		398	230	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027887	48027887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752839086	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	54	408	1	ENST00000234420.5:c.2765G>A	p.Arg922Gln	p.R922Q	ENST00000234420	NM_000179.2	922	cGa/cAa	4/10	1	2	FACETS	0.927	0.813	1	1	0.984	1	CLONAL	4	FALSE	1	0.212625506962056	2		409	137	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665353	138665353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	62	687	0	ENST00000330315.3:c.212C>T	p.Ala71Val	p.A71V	ENST00000330315	NM_023067.3	71	gCg/gTg	1/1	1	2	FACETS	0.838	0.733	0.948	1	0.983	1	CLONAL	3	FALSE	1	0.212625506962056	2		687	232	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937034	48937034	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	48	464	0	ENST00000267163.4:c.802G>T	p.Glu268Ter	p.E268*	ENST00000267163	NM_000321.2	268	Gaa/Taa	8/27	1	2	FACETS	0.842	0.717	0.978	1	0.969	1	CLONAL	2	FALSE	1	0.212625506962056	2		464	268	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526816	31526816	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs546365755	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	34	772	0	ENST00000344624.3:c.224G>A	p.Arg75Gln	p.R75Q	ENST00000344624		75	cGa/cAa	2/33	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	1	0.212625506962056	2		772	219	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344108	118344108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	26	469	0	ENST00000534358.1:c.2234G>A	p.Arg745Gln	p.R745Q	ENST00000534358	NM_005933.3	745	cGa/cAa	3/36	1	2	FACETS	0.769	0.616	0.941	1	0.937	1	CLONAL	2	FALSE	1	0.212625506962056	2		469	159	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627677	14627677	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	90	629	1	ENST00000254322.2:c.393C>A	p.Phe131Leu	p.F131L	ENST00000254322	NM_006145.1	131	ttC/ttA	2/3	0.148300535650375	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	FALSE	2	0.212625506962056	4		630	447	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710875	117710875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140178288	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	44	428	0	ENST00000368508.3:c.1397G>A	p.Arg466Gln	p.R466Q	ENST00000368508	NM_002944.2	466	cGa/cAa	12/43	0.160482769171991	3	FACETS	0.936	0.799	1	1	0.958	1	CLONAL	3	FALSE	1	0.212625506962056	3		428	163	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248362	212248362	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	34	258	0	ENST00000342788.4:c.3905G>T	p.Arg1302Ile	p.R1302I	ENST00000342788	NM_005235.2	1302	aGa/aTa	28/28	1	2	FACETS	0.978	0.819	1	1	0.972	1	CLONAL	3	FALSE	1	0.212625506962056	2		258	109	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199541	16199541	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	112	437	0	ENST00000375759.3:c.314C>A	p.Ser105Tyr	p.S105Y	ENST00000375759	NM_015001.2	105	tCt/tAt	2/15	0.212625506962056	6	FACETS	0.934	0.855	1	1	0.989	1	CLONAL	6	FALSE	3	0.212625506962056	6		437	268	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257868	16257868	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	25	525	0	ENST00000375759.3:c.5133A>C	p.Glu1711Asp	p.E1711D	ENST00000375759	NM_015001.2	1711	gaA/gaC	11/15	0.212625506962056	6	FACETS	1	0.897	1	0.415	0.328	0.515	CLONAL	1	FALSE	3	0.212625506962056	6		525	269	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36808981	36808981	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs534849916	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	60	601	0	ENST00000373129.3:c.1073C>T	p.Ala358Val	p.A358V	ENST00000373129	NM_032017.1	358	gCg/gTg	11/12	1	2	FACETS	1	0.923	1	1	0.985	1	CLONAL	3	FALSE	1	0.212625506962056	2		601	176	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939431	36939431	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	30	679	0	ENST00000361632.4:c.419T>G	p.Leu140Arg	p.L140R	ENST00000361632		140	cTc/cGc	4/16	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	FALSE	1	0.212625506962056	2		679	254	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798286	45798286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147754007	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	34	609	0	ENST00000450313.1:c.650G>A	p.Arg217His	p.R217H	ENST00000450313	NM_012222.2	217	cGc/cAc	8/16	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	FALSE	1	0.212625506962056	2		609	241	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509368	46509368	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs767870414	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	86	563	0	ENST00000262741.5:c.1363C>T	p.Gln455Ter	p.Q455*	ENST00000262741	NM_003629.3	455	Cag/Tag	10/10	1	2	FACETS	1	0.934	1	1	0.989	1	CLONAL	3	FALSE	1	0.212625506962056	2		563	256	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46527605	46527605	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	77	483	0	ENST00000262741.5:c.760G>T	p.Glu254Ter	p.E254*	ENST00000262741	NM_003629.3	254	Gaa/Taa	6/10	1	2	FACETS	0.904	0.804	1	1	0.987	1	CLONAL	3	FALSE	1	0.212625506962056	2		483	267	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531767	46531767	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	94	414	2	ENST00000262741.5:c.580G>T	p.Glu194Ter	p.E194*	ENST00000262741	NM_003629.3	194	Gag/Tag	5/10	1	2	FACETS	0.901	0.81	0.996	1	0.989	1	CLONAL	3	FALSE	1	0.212625506962056	2		416	327	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46543230	46543230	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	31	606	0	ENST00000262741.5:c.271G>T	p.Asp91Tyr	p.D91Y	ENST00000262741	NM_003629.3	91	Gat/Tat	3/10	1	2	FACETS	0.956	0.775	1	0.956	0.775	1	CLONAL	1	FALSE	1	0.212625506962056	2		606	305	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46733273	46733273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	34	473	1	ENST00000371975.4:c.1034G>A	p.Gly345Asp	p.G345D	ENST00000371975	NM_003579.3	345	gGc/gAc	9/18	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	FALSE	1	0.212625506962056	2		474	250	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310463	65310463	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	19	476	0	ENST00000342505.4:c.2225T>G	p.Ile742Ser	p.I742S	ENST00000342505	NM_002227.2	742	aTc/aGc	16/25	1	2	FACETS	0.831	0.633	1	0.831	0.633	1	CLONAL	1	FALSE	1	0.212625506962056	2		476	215	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313272	65313272	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	23	580	2	ENST00000342505.4:c.1842G>T	p.Glu614Asp	p.E614D	ENST00000342505	NM_002227.2	614	gaG/gaT	13/25	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	FALSE	1	0.212625506962056	2		582	182	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058508	72058508	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	14	400	0	ENST00000357731.5:c.932C>A	p.Pro311His	p.P311H	ENST00000357731	NM_173808.2	311	cCt/cAt	6/7	1	2	FACETS	0.72	0.521	0.958	0.72	0.521	0.958	CLONAL	1	FALSE	1	0.212625506962056	2		400	183	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78422258	78422258	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	35	338	0	ENST00000370768.2:c.1704A>C	p.Gln568His	p.Q568H	ENST00000370768	NM_003902.3	568	caA/caC	17/20	1	2	FACETS	1	0.892	1	1	0.968	1	CLONAL	2	FALSE	1	0.212625506962056	2		338	150	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461173	120461173	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	18	385	0	ENST00000256646.2:c.5785C>A	p.Leu1929Met	p.L1929M	ENST00000256646	NM_024408.3	1929	Ctg/Atg	32/34	1	2	FACETS	0.896	0.677	1	0.896	0.677	1	CLONAL	1	FALSE	1	0.212625506962056	2		385	189	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510215	120510215	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	43	425	0	ENST00000256646.2:c.1294A>C	p.Lys432Gln	p.K432Q	ENST00000256646	NM_024408.3	432	Aaa/Caa	8/34	1	2	FACETS	0.907	0.766	1	1	0.968	1	CLONAL	2	FALSE	1	0.212625506962056	2		425	223	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512289	120512289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782615247	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	49	449	1	ENST00000256646.2:c.953G>A	p.Arg318His	p.R318H	ENST00000256646	NM_024408.3	318	cGc/cAc	6/34	1	2	FACETS	1	0.929	1	1	0.977	1	CLONAL	2	FALSE	1	0.212625506962056	2		450	202	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740231	162740231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773598662	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	70	516	2	ENST00000367921.3:c.1433G>A	p.Arg478His	p.R478H	ENST00000367921	NM_006182.2	478	cGc/cAc	12/18	0.212625506962056	1	FACETS	0.868	0.768	0.972	1	0.985	1	CLONAL	3	FALSE	0	0.212625506962056	1		518	226	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162742010	162742010	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	56	448	0	ENST00000367921.3:c.1701G>T	p.Glu567Asp	p.E567D	ENST00000367921	NM_006182.2	567	gaG/gaT	13/18	0.212625506962056	1	FACETS	0.912	0.797	1	1	0.983	1	CLONAL	3	FALSE	0	0.212625506962056	1		448	172	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176145105	176145105	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	52	557	0	ENST00000367669.3:c.506G>T	p.Arg169Ile	p.R169I	ENST00000367669	NM_022457.5	169	aGa/aTa	3/20	0.212625506962056	1	FACETS	0.98	0.844	1	1	0.976	1	CLONAL	2	FALSE	0	0.212625506962056	1		557	223	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226574091	226574091	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	56	480	0	ENST00000366794.5:c.770C>T	p.Ser257Leu	p.S257L	ENST00000366794	NM_001618.3	257	tCa/tTa	6/23	0.212625506962056	1	FACETS	1	0.941	1	1	0.981	1	CLONAL	2	FALSE	0	0.212625506962056	1		480	204	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828116	243828116	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	59	477	0	ENST00000263826.5:c.242C>A	p.Thr81Asn	p.T81N	ENST00000263826	NM_005465.4	81	aCt/aAt	3/13	0.212625506962056	1	FACETS	0.866	0.758	0.979	1	0.983	1	CLONAL	3	FALSE	0	0.212625506962056	1		477	191	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619124	43619124	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	14	475	0	ENST00000355710.3:c.2807C>A	p.Ser936Tyr	p.S936Y	ENST00000355710	NM_020975.4	936	tCt/tAt	17/20	1	2	FACETS	0.808	0.586	1	0.808	0.586	1	CLONAL	1	FALSE	1	0.212625506962056	2		475	163	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404999	70404999	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	19	578	1	ENST00000373644.4:c.2513C>A	p.Ser838Tyr	p.S838Y	ENST00000373644	NM_030625.2	838	tCt/tAt	4/12	1	2	FACETS	0.745	0.566	0.953	0.745	0.566	0.953	CLONAL	1	FALSE	1	0.212625506962056	2		579	240	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450609	70450609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759851979	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	79	548	1	ENST00000373644.4:c.5449G>A	p.Glu1817Lys	p.E1817K	ENST00000373644	NM_030625.2	1817	Gaa/Aaa	12/12	1	2	FACETS	0.971	0.866	1	1	0.988	1	CLONAL	3	FALSE	1	0.212625506962056	2		549	255	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88678938	88678938	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	16	371	2	ENST00000372037.3:c.878C>T	p.Ala293Val	p.A293V	ENST00000372037	NM_004329.2	293	gCg/gTg	10/13	1	2	FACETS	0.971	0.722	1	0.971	0.722	1	CLONAL	1	FALSE	1	0.212625506962056	2		373	155	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685274	89685274	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	29	259	0	ENST00000371953.3:c.169T>G	p.Leu57Val	p.L57V	ENST00000371953	NM_000314.4	57	Ttg/Gtg	3/9	1	2	FACETS	1	0.835	1	1	0.959	1	CLONAL	2	FALSE	1	0.212625506962056	2		259	133	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724715	112724715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	58	519	0	ENST00000369452.4:c.599G>A	p.Arg200His	p.R200H	ENST00000369452	NM_007373.3	200	cGc/cAc	2/9	1	2	FACETS	0.905	0.789	1	1	0.983	1	CLONAL	3	FALSE	1	0.212625506962056	2		519	201	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710585	114710585	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	138	474	0	ENST00000543371.1:c.70G>A	p.Glu24Lys	p.E24K	ENST00000543371	NM_001198531.1	24	Gag/Aag	1/14	1	2	FACETS	1	0.945	1	1	0.994	1	CLONAL	4	FALSE	1	0.212625506962056	2		474	316	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711256	114711256	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	87	355	0	ENST00000543371.1:c.271G>T	p.Asp91Tyr	p.D91Y	ENST00000543371	NM_001198531.1	91	Gat/Tat	3/14	1	2	FACETS	1	0.932	1	1	0.989	1	CLONAL	3	FALSE	1	0.212625506962056	2		355	260	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911615	114911615	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1181251391	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	45	591	1	ENST00000543371.1:c.1133C>T	p.Ala378Val	p.A378V	ENST00000543371	NM_001198531.1	378	gCg/gTg	10/14	1	2	FACETS	0.767	0.649	0.896	1	0.962	1	SUBCLONAL	2	FALSE	1	0.212625506962056	2		592	276	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161441	2161441	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	98	568	0	ENST00000434045.2:c.86T>C	p.Val29Ala	p.V29A	ENST00000434045	NM_001127598.1	29	gTa/gCa	2/5	1	2	FACETS	0.88	0.797	0.964	1	0.991	1	CLONAL	4	FALSE	1	0.212625506962056	2		568	262	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137186	64137186	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752564591	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	125	592	0	ENST00000334205.4:c.1618G>A	p.Asp540Asn	p.D540N	ENST00000334205	NM_003942.2	540	Gac/Aac	14/17	1	2	FACETS	1	0.974	1	1	0.993	1	CLONAL	3	FALSE	1	0.212625506962056	2		592	338	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946392	71946392	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	36	816	0	ENST00000298229.2:c.2556C>A	p.Phe852Leu	p.F852L	ENST00000298229	NM_001567.3	852	ttC/ttA	23/28	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	FALSE	1	0.212625506962056	2		816	311	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204785	94204785	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	35	493	0	ENST00000323929.3:c.800G>T	p.Gly267Val	p.G267V	ENST00000323929	NM_005591.3	267	gGa/gTa	8/20	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	FALSE	1	0.212625506962056	2		493	245	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207504	102207504	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1164535753	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	70	452	0	ENST00000263464.3:c.1596del	p.Lys532AsnfsTer36	p.K532Nfs*36	ENST00000263464	NM_001165.4	531	atA/at	8/9	1	2	FACETS	1	0.903	1	1	0.986	1	CLONAL	3	FALSE	1	0.212625506962056	2		452	215	SUCCESS
ATM	472	MSKCC	GRCh37	11	108128211	108128211	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	13	358	0	ENST00000278616.4:c.2254C>A	p.Leu752Ile	p.L752I	ENST00000278616	NM_000051.3	752	Cta/Ata	15/63	1	2	FACETS	0.832	0.596	1	0.832	0.596	1	CLONAL	1	FALSE	1	0.212625506962056	2		358	147	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201035	108201035	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	55	401	0	ENST00000278616.4:c.7402G>T	p.Glu2468Ter	p.E2468*	ENST00000278616	NM_000051.3	2468	Gaa/Taa	50/63	1	2	FACETS	1	0.935	1	1	0.984	1	CLONAL	3	FALSE	1	0.212625506962056	2		401	155	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206668	108206668	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	78	457	0	ENST00000278616.4:c.8248T>G	p.Leu2750Val	p.L2750V	ENST00000278616	NM_000051.3	2750	Tta/Gta	56/63	1	2	FACETS	1	0.959	1	1	0.988	1	CLONAL	3	FALSE	1	0.212625506962056	2		457	213	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343094	118343094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	15	392	0	ENST00000534358.1:c.1220G>A	p.Arg407Gln	p.R407Q	ENST00000534358	NM_005933.3	407	cGa/cAa	3/36	1	2	FACETS	0.916	0.674	1	0.916	0.674	1	CLONAL	1	FALSE	1	0.212625506962056	2		392	154	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344333	118344333	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	12	365	0	ENST00000534358.1:c.2459C>A	p.Thr820Asn	p.T820N	ENST00000534358	NM_005933.3	820	aCt/aAt	3/36	1	2	FACETS	0.973	0.689	1	0.973	0.689	1	CLONAL	1	FALSE	1	0.212625506962056	2		365	116	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359409	118359410	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AT	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	73	415	0	ENST00000534358.1:c.4413_4414delinsAT	p.Glu1472Ter	p.E1472*	ENST00000534358	NM_005933.3	1471	ctGGaa/ctATaa	11/36	1	2	FACETS	1	0.909	1	1	0.987	1	CLONAL	3	FALSE	1	0.212625506962056	2		415	223	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359410	118359410	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	73	409	0	ENST00000534358.1:c.4414G>T	p.Glu1472Ter	p.E1472*	ENST00000534358	NM_005933.3	1472	Gaa/Taa	11/36	1	2	FACETS	1	0.909	1	1	0.987	1	CLONAL	3	FALSE	1	0.212625506962056	2		409	223	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118368666	118368666	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	50	440	0	ENST00000534358.1:c.5680C>A	p.Leu1894Ile	p.L1894I	ENST00000534358	NM_005933.3	1894	Cta/Ata	21/36	1	2	FACETS	1	0.945	1	1	0.979	1	CLONAL	2	FALSE	1	0.212625506962056	2		440	194	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373248	118373248	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	21	469	0	ENST00000534358.1:c.6641C>A	p.Ser2214Tyr	p.S2214Y	ENST00000534358	NM_005933.3	2214	tCt/tAt	27/36	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	FALSE	1	0.212625506962056	2		469	168	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416872	416872	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	22	457	0	ENST00000399788.2:c.3678T>G	p.Ile1226Met	p.I1226M	ENST00000399788	NM_001042603.1	1226	atT/atG	23/28	0.148300535650375	4	FACETS	1	0.881	1	0.609	0.474	0.764	CLONAL	1	FALSE	2	0.212625506962056	4		457	206	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	463378	463378	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	80	388	0	ENST00000399788.2:c.893T>G	p.Phe298Cys	p.F298C	ENST00000399788	NM_001042603.1	298	tTt/tGt	8/28	0.148300535650375	4	FACETS	0.946	0.851	1	1	0.987	1	CLONAL	5	FALSE	2	0.212625506962056	4		388	193	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398101	4398101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762849458	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	31	526	0	ENST00000261254.3:c.665C>T	p.Ser222Leu	p.S222L	ENST00000261254	NM_001759.3	222	tCg/tTg	4/5	0.148300535650375	4	FACETS	0.769	0.625	0.929	0.769	0.625	0.929	CLONAL	2	FALSE	2	0.212625506962056	4		526	230	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870891	12870891	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	41	271	1	ENST00000228872.4:c.118G>T	p.Glu40Ter	p.E40*	ENST00000228872	NM_004064.3	40	Gag/Tag	1/3	0.148300535650375	4	FACETS	0.804	0.673	0.947	0.804	0.673	0.947	CLONAL	2	FALSE	2	0.212625506962056	4		272	291	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443796	18443796	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1185264920	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	13	317	0	ENST00000266497.5:c.769G>T	p.Glu257Ter	p.E257*	ENST00000266497		257	Gaa/Taa	3/31	0.148300535650375	4	FACETS	0.904	0.647	1	0.452	0.323	0.608	CLONAL	1	FALSE	2	0.212625506962056	4		317	164	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18473942	18473942	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	88	426	0	ENST00000266497.5:c.1184T>G	p.Phe395Cys	p.F395C	ENST00000266497		395	tTt/tGt	6/31	0.148300535650375	4	FACETS	0.98	0.882	1	1	0.986	1	CLONAL	4	FALSE	2	0.212625506962056	4		426	256	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244821	46244821	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	23	655	0	ENST00000334344.6:c.2915C>A	p.Ser972Tyr	p.S972Y	ENST00000334344	NM_152641.2	972	tCt/tAt	15/21	0.148300535650375	4	FACETS	0.986	0.771	1	0.493	0.385	0.618	CLONAL	1	FALSE	2	0.212625506962056	4		655	266	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246081	46246081	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	39	378	0	ENST00000334344.6:c.4175C>A	p.Pro1392Gln	p.P1392Q	ENST00000334344	NM_152641.2	1392	cCa/cAa	15/21	0.148300535650375	4	FACETS	1	0.912	1	1	0.912	1	CLONAL	2	FALSE	2	0.212625506962056	4		378	195	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287318	46287318	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	61	475	1	ENST00000334344.6:c.5263G>T	p.Asp1755Tyr	p.D1755Y	ENST00000334344	NM_152641.2	1755	Gat/Tat	19/21	0.148300535650375	4	FACETS	0.913	0.796	1	1	0.967	1	CLONAL	3	FALSE	2	0.212625506962056	4		476	254	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427507	49427507	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752735386	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	50	600	0	ENST00000301067.7:c.10981G>A	p.Gly3661Ser	p.G3661S	ENST00000301067	NM_003482.3	3661	Ggt/Agt	39/54	0.148300535650375	4	FACETS	0.905	0.778	1	1	0.959	1	CLONAL	3	FALSE	2	0.212625506962056	4		600	210	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435917	49435917	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	31	787	0	ENST00000301067.7:c.6064C>T	p.Leu2022Phe	p.L2022F	ENST00000301067	NM_003482.3	2022	Ctc/Ttc	28/54	0.148300535650375	4	FACETS	1	0.893	1	0.578	0.468	0.701	CLONAL	1	FALSE	2	0.212625506962056	4		787	306	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438282	49438282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs192216625	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	38	535	0	ENST00000301067.7:c.4987G>A	p.Glu1663Lys	p.E1663K	ENST00000301067	NM_003482.3	1663	Gaa/Aaa	20/54	0.148300535650375	4	FACETS	0.959	0.799	1	0.959	0.799	1	CLONAL	2	FALSE	2	0.212625506962056	4		535	226	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443745	49443745	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	102	710	0	ENST00000301067.7:c.3626C>A	p.Ser1209Tyr	p.S1209Y	ENST00000301067	NM_003482.3	1209	tCt/tAt	11/54	0.148300535650375	4	FACETS	0.938	0.85	1	1	0.988	1	CLONAL	4	FALSE	2	0.212625506962056	4		710	310	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49449081	49449081	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	47	530	0	ENST00000301067.7:c.27G>T	p.Glu9Asp	p.E9D	ENST00000301067	NM_003482.3	9	gaG/gaT	1/54	0.148300535650375	4	FACETS	0.971	0.825	1	0.971	0.825	1	CLONAL	2	FALSE	2	0.212625506962056	4		530	276	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50481208	50481208	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	44	448	0	ENST00000394963.4:c.594G>T	p.Glu198Asp	p.E198D	ENST00000394963	NM_003076.4	198	gaG/gaT	5/13	0.148300535650375	4	FACETS	0.82	0.691	0.961	0.82	0.691	0.961	CLONAL	2	FALSE	2	0.212625506962056	4		448	306	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50483697	50483697	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	110	438	0	ENST00000394963.4:c.802G>A	p.Asp268Asn	p.D268N	ENST00000394963	NM_003076.4	268	Gat/Aat	7/13	0.148300535650375	4	FACETS	0.986	0.898	1	1	0.989	1	CLONAL	4	FALSE	2	0.212625506962056	4		438	318	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811667	102811667	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	38	700	0	ENST00000307046.8:c.517G>T	p.Gly173Ter	p.G173*	ENST00000307046	NM_001111285.1	173	Gga/Tga	4/4	0.148300535650375	4	FACETS	1	0.943	1	0.684	0.567	0.813	CLONAL	1	FALSE	2	0.212625506962056	4		700	317	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102874155	102874155	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	26	417	0	ENST00000307046.8:c.5G>T	p.Gly2Val	p.G2V	ENST00000307046	NM_001111285.1	2	gGa/gTa	1/4	0.148300535650375	4	FACETS	0.734	0.581	0.91	0.367	0.29	0.455	CLONAL	1	FALSE	2	0.212625506962056	4		417	404	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856489	111856489	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs370747546	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	71	273	0	ENST00000341259.2:c.540G>T	p.Lys180Asn	p.K180N	ENST00000341259	NM_005475.2	180	aaG/aaT	2/8	0.148300535650375	4	FACETS	0.912	0.809	1	1	0.982	1	CLONAL	4	FALSE	2	0.212625506962056	4		273	222	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110004	115110004	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1201751425	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	34	607	0	ENST00000257566.3:c.1874G>A	p.Arg625His	p.R625H	ENST00000257566	NM_016569.3	625	cGc/cAc	8/8	0.148300535650375	4	FACETS	0.769	0.632	0.922	0.769	0.632	0.922	CLONAL	2	FALSE	2	0.212625506962056	4		607	252	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431462	121431462	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	30	667	0	ENST00000257555.6:c.666G>T	p.Lys222Asn	p.K222N	ENST00000257555		222	aaG/aaT	3/10	0.148300535650375	4	FACETS	1	0.889	1	0.576	0.465	0.701	CLONAL	1	FALSE	2	0.212625506962056	4		667	297	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257806	133257806	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148269473	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	101	492	1	ENST00000320574.5:c.122C>T	p.Thr41Met	p.T41M	ENST00000320574	NM_006231.2	41	aCg/aTg	2/49	0.148300535650375	4	FACETS	1	0.916	1	1	0.988	1	CLONAL	4	FALSE	2	0.212625506962056	4		493	285	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549342	21549342	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	39	612	0	ENST00000382592.4:c.2934C>A	p.Phe978Leu	p.F978L	ENST00000382592	NM_014572.2	978	ttC/ttA	8/8	1	2	FACETS	0.941	0.788	1	1	0.967	1	CLONAL	2	FALSE	1	0.212625506962056	2		612	195	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619951	21619951	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	38	571	0	ENST00000382592.4:c.215C>T	p.Pro72Leu	p.P72L	ENST00000382592	NM_014572.2	72	cCt/cTt	2/8	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	FALSE	1	0.212625506962056	2		571	256	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610108	28610108	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	41	509	0	ENST00000241453.7:c.1382C>A	p.Ser461Tyr	p.S461Y	ENST00000241453	NM_004119.2	461	tCt/tAt	11/24	1	2	FACETS	0.759	0.637	0.893	1	0.958	1	SUBCLONAL	2	FALSE	1	0.212625506962056	2		509	254	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28971138	28971138	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	17	400	0	ENST00000282397.4:c.1619A>C	p.Lys540Thr	p.K540T	ENST00000282397	NM_002019.4	540	aAa/aCa	12/30	1	2	FACETS	0.888	0.666	1	0.888	0.666	1	CLONAL	1	FALSE	1	0.212625506962056	2		400	180	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906573	32906573	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	49	470	0	ENST00000380152.3:c.958C>A	p.Leu320Ile	p.L320I	ENST00000380152		320	Cta/Ata	10/27	1	2	FACETS	0.878	0.756	1	1	0.979	1	CLONAL	3	FALSE	1	0.212625506962056	2		470	175	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907018	32907018	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	31	499	0	ENST00000380152.3:c.1403G>T	p.Arg468Ile	p.R468I	ENST00000380152		468	aGa/aTa	10/27	1	2	FACETS	0.771	0.63	0.929	1	0.947	1	CLONAL	2	FALSE	1	0.212625506962056	2		499	189	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910615	32910615	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	22	526	0	ENST00000380152.3:c.2123C>A	p.Ser708Tyr	p.S708Y	ENST00000380152		708	tCt/tAt	11/27	1	2	FACETS	0.945	0.735	1	0.945	0.735	1	CLONAL	1	FALSE	1	0.212625506962056	2		526	219	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911286	32911286	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	36	617	0	ENST00000380152.3:c.2794G>T	p.Asp932Tyr	p.D932Y	ENST00000380152		932	Gac/Tac	11/27	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	FALSE	1	0.212625506962056	2		617	295	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913187	32913187	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587782522	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	68	609	0	ENST00000380152.3:c.4695G>T	p.Lys1565Asn	p.K1565N	ENST00000380152		1565	aaG/aaT	11/27	1	2	FACETS	0.974	0.86	1	1	0.986	1	CLONAL	3	FALSE	1	0.212625506962056	2		609	219	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914572	32914572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs431825337	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	82	707	0	ENST00000380152.3:c.6080G>A	p.Arg2027Lys	p.R2027K	ENST00000380152		2027	aGa/aAa	11/27	1	2	FACETS	1	0.968	1	1	0.987	1	CLONAL	2	FALSE	1	0.212625506962056	2		707	310	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929306	32929306	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	26	602	0	ENST00000380152.3:c.7316G>T	p.Gly2439Val	p.G2439V	ENST00000380152		2439	gGa/gTa	14/27	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	FALSE	1	0.212625506962056	2		602	183	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881515	48881515	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	75	356	0	ENST00000267163.4:c.237G>T	p.Glu79Asp	p.E79D	ENST00000267163	NM_000321.2	79	gaG/gaT	2/27	1	2	FACETS	1	0.945	1	1	0.988	1	CLONAL	3	FALSE	1	0.212625506962056	2		356	214	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939075	48939075	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	33	371	0	ENST00000267163.4:c.907C>A	p.Leu303Ile	p.L303I	ENST00000267163	NM_000321.2	303	Ctt/Att	9/27	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	FALSE	1	0.212625506962056	2		371	207	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337698	73337698	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1566240526	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	31	318	1	ENST00000377767.4:c.2018C>A	p.Ser673Tyr	p.S673Y	ENST00000377767	NM_014953.3	673	tCt/tAt	16/21	1	2	FACETS	1	0.892	1	1	0.964	1	CLONAL	2	FALSE	1	0.212625506962056	2		319	130	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514997	103514997	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137877463	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	30	360	0	ENST00000355739.4:c.1498C>T	p.Arg500Trp	p.R500W	ENST00000355739	NM_000123.3	500	Cgg/Tgg	8/15	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	FALSE	1	0.212625506962056	2		360	197	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518653	103518653	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	25	309	0	ENST00000355739.4:c.2241G>T	p.Gln747His	p.Q747H	ENST00000355739	NM_000123.3	747	caG/caT	10/15	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	FALSE	1	0.212625506962056	2		309	188	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066951	30066951	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	35	398	0	ENST00000331968.5:c.2180A>C	p.Asp727Ala	p.D727A	ENST00000331968	NM_002742.2	727	gAt/gCt	16/18	0.212625506962056	1	FACETS	0.774	0.641	0.92	1	0.953	1	CLONAL	2	FALSE	0	0.212625506962056	1		398	190	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352661	68352661	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	68	445	0	ENST00000487270.1:c.528A>C	p.Lys176Asn	p.K176N	ENST00000487270	NM_133509.3	176	aaA/aaC	6/11	0.212625506962056	1	FACETS	0.869	0.761	0.983	1	0.979	1	CLONAL	2	FALSE	0	0.212625506962056	1		445	329	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610165	81610165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs185776618	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	30	407	0	ENST00000298171.2:c.1763C>T	p.Thr588Met	p.T588M	ENST00000298171	NM_000369.2	588	aCg/aTg	10/10	0.212625506962056	1	FACETS	0.846	0.691	1	1	0.952	1	CLONAL	2	FALSE	0	0.212625506962056	1		407	149	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610328	81610328	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	28	458	1	ENST00000298171.2:c.1926C>A	p.Phe642Leu	p.F642L	ENST00000298171	NM_000369.2	642	ttC/ttA	10/10	0.212625506962056	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	FALSE	0	0.212625506962056	1		459	163	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582887	95582887	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	28	387	0	ENST00000393063.1:c.1655G>T	p.Arg552Ile	p.R552I	ENST00000393063	NM_030621.3	552	aGa/aTa	11/28	0.212625506962056	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	FALSE	0	0.212625506962056	1		387	157	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582975	95582975	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	21	368	0	ENST00000393063.1:c.1567G>T	p.Glu523Ter	p.E523*	ENST00000393063	NM_030621.3	523	Gaa/Taa	11/28	0.212625506962056	1	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	FALSE	0	0.212625506962056	1		368	145	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590927	95590927	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	18	337	0	ENST00000393063.1:c.982G>T	p.Glu328Ter	p.E328*	ENST00000393063	NM_030621.3	328	Gaa/Taa	9/28	0.212625506962056	1	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	FALSE	0	0.212625506962056	1		337	128	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95592940	95592940	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	32	460	0	ENST00000393063.1:c.880G>T	p.Asp294Tyr	p.D294Y	ENST00000393063	NM_030621.3	294	Gat/Tat	8/28	0.212625506962056	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	FALSE	0	0.212625506962056	1		460	214	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961189	41961189	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	17	416	1	ENST00000219905.7:c.97A>C	p.Asn33His	p.N33H	ENST00000219905	NM_001164273.1	33	Aat/Cat	2/24	1	2	FACETS	0.941	0.706	1	0.941	0.706	1	CLONAL	1	FALSE	1	0.212625506962056	2		417	170	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988814	41988814	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	29	583	0	ENST00000219905.7:c.1606G>T	p.Asp536Tyr	p.D536Y	ENST00000219905	NM_001164273.1	536	Gat/Tat	3/24	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	FALSE	1	0.212625506962056	2		583	248	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989002	41989002	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	58	648	0	ENST00000219905.7:c.1794G>T	p.Lys598Asn	p.K598N	ENST00000219905	NM_001164273.1	598	aaG/aaT	3/24	1	2	FACETS	1	0.879	1	1	0.979	1	CLONAL	2	FALSE	1	0.212625506962056	2		648	269	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041116	42041116	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780889520	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	71	565	0	ENST00000219905.7:c.5494C>T	p.Arg1832Trp	p.R1832W	ENST00000219905	NM_001164273.1	1832	Cgg/Tgg	16/24	1	2	FACETS	1	0.961	1	1	0.985	1	CLONAL	2	FALSE	1	0.212625506962056	2		565	273	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041312	42041312	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	67	455	0	ENST00000219905.7:c.5507C>A	p.Ser1836Tyr	p.S1836Y	ENST00000219905	NM_001164273.1	1836	tCt/tAt	17/24	1	2	FACETS	1	0.91	1	1	0.986	1	CLONAL	3	FALSE	1	0.212625506962056	2		455	203	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041980	42041980	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	31	590	0	ENST00000219905.7:c.6175G>T	p.Asp2059Tyr	p.D2059Y	ENST00000219905	NM_001164273.1	2059	Gat/Tat	17/24	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	FALSE	1	0.212625506962056	2		590	262	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712526	43712526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767934572	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	113	687	0	ENST00000382044.4:c.4658C>T	p.Ser1553Leu	p.S1553L	ENST00000382044	NM_001141980.1	1553	tCg/tTg	21/28	1	2	FACETS	1	0.965	1	1	0.992	1	CLONAL	3	FALSE	1	0.212625506962056	2		687	317	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43783870	43783870	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1312529923	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	100	591	0	ENST00000382044.4:c.368G>A	p.Ser123Asn	p.S123N	ENST00000382044	NM_001141980.1	123	aGc/aAc	4/28	1	2	FACETS	0.944	0.853	1	1	0.99	1	CLONAL	3	FALSE	1	0.212625506962056	2		591	332	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007838	45007838	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	87	466	1	ENST00000558401.1:c.285A>T	p.Lys95Asn	p.K95N	ENST00000558401	NM_004048.2	95	aaA/aaT	2/4	1	2	FACETS	0.869	0.777	0.964	1	0.988	1	CLONAL	3	FALSE	1	0.212625506962056	2		467	314	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90627542	90627542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1222149957	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	30	564	3	ENST00000330062.3:c.1315G>A	p.Asp439Asn	p.D439N	ENST00000330062	NM_002168.2	439	Gac/Aac	11/11	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	FALSE	1	0.212625506962056	2		567	237	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90627572	90627572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	77	544	1	ENST00000330062.3:c.1285G>A	p.Glu429Lys	p.E429K	ENST00000330062	NM_002168.2	429	Gag/Aag	11/11	1	2	FACETS	0.901	0.807	0.997	1	0.988	1	CLONAL	4	FALSE	1	0.212625506962056	2		545	201	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250808	99250808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	24	423	0	ENST00000268035.6:c.112G>A	p.Asp38Asn	p.D38N	ENST00000268035	NM_000875.3	38	Gac/Aac	2/21	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	FALSE	1	0.212625506962056	2		423	179	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106690	2106690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751846529	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	137	654	0	ENST00000219476.3:c.694C>T	p.Pro232Ser	p.P232S	ENST00000219476	NM_000548.3	232	Ccg/Tcg	8/42	0.160482769171991	3	FACETS	1	0.976	1	1	0.99	1	CLONAL	3	FALSE	1	0.212625506962056	3		654	408	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110736	2110736	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	75	809	1	ENST00000219476.3:c.1041G>T	p.Lys347Asn	p.K347N	ENST00000219476	NM_000548.3	347	aaG/aaT	11/42	0.160482769171991	3	FACETS	0.998	0.879	1	0.998	0.879	1	CLONAL	2	FALSE	1	0.212625506962056	3		810	391	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639181	3639181	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1387319346	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	43	702	0	ENST00000294008.3:c.4458G>T	p.Arg1486Ser	p.R1486S	ENST00000294008	NM_032444.2	1486	agG/agT	12/15	0.160482769171991	3	FACETS	1	0.945	1	0.656	0.551	0.772	CLONAL	1	FALSE	1	0.212625506962056	3		702	341	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652273	3652273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543071212	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	37	593	0	ENST00000294008.3:c.796G>A	p.Ala266Thr	p.A266T	ENST00000294008	NM_032444.2	266	Gct/Act	4/15	0.160482769171991	3	FACETS	1	0.915	1	0.592	0.49	0.706	CLONAL	1	FALSE	1	0.212625506962056	3		593	325	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3824685	3824685	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	118	532	0	ENST00000262367.5:c.2168C>A	p.Ser723Ter	p.S723*	ENST00000262367	NM_004380.2	723	tCa/tAa	12/31	0.160482769171991	3	FACETS	1	0.97	1	1	0.991	1	CLONAL	4	FALSE	1	0.212625506962056	3		532	273	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934583	9934583	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	29	549	0	ENST00000330684.3:c.1572C>A	p.Phe524Leu	p.F524L	ENST00000330684	NM_001134407.1	524	ttC/ttA	7/13	0.160482769171991	3	FACETS	1	0.934	1	0.708	0.572	0.861	CLONAL	1	FALSE	1	0.212625506962056	3		549	213	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349145	11349145	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	24	244	0	ENST00000332029.2:c.191A>G	p.Tyr64Cys	p.Y64C	ENST00000332029	NM_003745.1	64	tAc/tGc	2/2	0.160482769171991	3	FACETS	1	0.922	1	0.71	0.561	0.878	CLONAL	1	FALSE	1	0.212625506962056	3		244	176	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641409	23641409	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749602688	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	74	868	0	ENST00000261584.4:c.2066C>T	p.Ser689Leu	p.S689L	ENST00000261584	NM_024675.3	689	tCg/tTg	5/13	0.160482769171991	3	FACETS	1	0.905	1	1	0.978	1	CLONAL	3	FALSE	1	0.212625506962056	3		868	251	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50816324	50816324	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	64	519	0	ENST00000398568.2:c.1764G>T	p.Lys588Asn	p.K588N	ENST00000398568	NM_001042412.1	588	aaG/aaT	10/18	0.160482769171991	3	FACETS	0.888	0.778	1	1	0.966	1	CLONAL	3	FALSE	1	0.212625506962056	3		519	250	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863690	68863690	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1236811420	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	69	359	0	ENST00000261769.5:c.2429T>G	p.Phe810Cys	p.F810C	ENST00000261769	NM_004360.3	810	tTt/tGt	15/16	0.160482769171991	3	FACETS	0.93	0.826	1	1	0.982	1	CLONAL	4	FALSE	1	0.212625506962056	3		359	193	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832418	72832418	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	36	424	1	ENST00000268489.5:c.4163G>T	p.Arg1388Met	p.R1388M	ENST00000268489	NM_006885.3	1388	aGg/aTg	9/10	0.160482769171991	3	FACETS	0.991	0.824	1	0.991	0.824	1	CLONAL	2	FALSE	1	0.212625506962056	3		425	189	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352007	89352007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1364167746	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	148	785	1	ENST00000301030.4:c.943G>A	p.Asp315Asn	p.D315N	ENST00000301030	NM_001256183.1	315	Gac/Aac	9/13	0.186344826990072	4	FACETS	1	0.958	1	1	0.992	1	CLONAL	4	FALSE	2	0.212625506962056	4		786	400	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352049	89352049	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	37	636	0	ENST00000301030.4:c.901G>T	p.Glu301Ter	p.E301*	ENST00000301030	NM_001256183.1	301	Gaa/Taa	9/13	0.186344826990072	4	FACETS	1	0.937	1	0.657	0.544	0.784	CLONAL	1	FALSE	2	0.212625506962056	4		636	321	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357087	89357087	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	40	541	0	ENST00000301030.4:c.547C>T	p.Arg183Cys	p.R183C	ENST00000301030	NM_001256183.1	183	Cgc/Tgc	6/13	0.186344826990072	4	FACETS	1	0.95	1	0.706	0.589	0.836	CLONAL	1	FALSE	2	0.212625506962056	4		541	323	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89842162	89842162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	102	567	0	ENST00000389301.3:c.1888G>A	p.Glu630Lys	p.E630K	ENST00000389301	NM_000135.2	630	Gag/Aag	21/43	0.186344826990072	4	FACETS	1	0.922	1	1	0.984	1	CLONAL	3	FALSE	2	0.212625506962056	4		567	378	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89880963	89880963	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs747368109	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	47	629	2	ENST00000389301.3:c.248C>A	p.Ser83Tyr	p.S83Y	ENST00000389301	NM_000135.2	83	tCt/tAt	3/43	0.186344826990072	4	FACETS	1	0.924	1	0.58	0.49	0.68	CLONAL	1	FALSE	2	0.212625506962056	4		631	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577148	7577148	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	113	595	0	ENST00000269305.4:c.790C>A	p.Leu264Ile	p.L264I	ENST00000269305	NM_001126112.2	264	Cta/Ata	8/11	0.212625506962056	5	FACETS	1	0.966	1	1	0.986	1	CLONAL	4	FALSE	2	0.212625506962056	5		595	312	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15976847	15976847	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	58	467	0	ENST00000268712.3:c.3707G>T	p.Arg1236Ile	p.R1236I	ENST00000268712	NM_006311.3	1236	aGa/aTa	28/46	0.212625506962056	5	FACETS	0.944	0.82	1	0.944	0.82	1	CLONAL	3	FALSE	2	0.212625506962056	5		467	254	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16040659	16040659	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	44	460	0	ENST00000268712.3:c.1475G>T	p.Arg492Ile	p.R492I	ENST00000268712	NM_006311.3	492	aGa/aTa	14/46	0.212625506962056	5	FACETS	1	0.93	1	0.788	0.667	0.919	CLONAL	2	FALSE	2	0.212625506962056	5		460	231	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527439	29527439	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs587781517	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	38	381	0	ENST00000356175.3:c.889-1G>T		p.X297_splice	ENST00000356175	NM_000267.3	297			0.212625506962056	5	FACETS	1	0.93	1	0.818	0.684	0.965	CLONAL	2	FALSE	2	0.212625506962056	5		381	192	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321730	30321730	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	34	510	1	ENST00000322652.5:c.1585C>A	p.Leu529Ile	p.L529I	ENST00000322652	NM_015355.2	529	Ctt/Att	13/16	0.212625506962056	5	FACETS	0.937	0.771	1	0.625	0.514	0.747	CLONAL	2	FALSE	2	0.212625506962056	5		511	225	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619268	37619268	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	28	448	0	ENST00000447079.4:c.944G>T	p.Arg315Ile	p.R315I	ENST00000447079	NM_015083.1	315	aGa/aTa	1/14	0.212625506962056	5	FACETS	1	0.935	1	0.489	0.392	0.597	CLONAL	1	FALSE	2	0.212625506962056	5		448	237	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804230	46804230	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	42	627	0	ENST00000290295.7:c.777G>T	p.Gln259His	p.Q259H	ENST00000290295	NM_006361.5	259	caG/caT	2/2	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	1	0.212625506962056	2		627	308	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804300	46804300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754487444	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	29	560	0	ENST00000290295.7:c.707C>T	p.Ala236Val	p.A236V	ENST00000290295	NM_006361.5	236	gCg/gTg	2/2	1	2	FACETS	0.974	0.784	1	0.974	0.784	1	CLONAL	1	FALSE	1	0.212625506962056	2		560	280	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59861668	59861668	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs4988350	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	72	538	0	ENST00000259008.2:c.1591T>G	p.Phe531Val	p.F531V	ENST00000259008	NM_032043.2	531	Ttt/Gtt	11/20	1	2	FACETS	0.858	0.759	0.963	1	0.986	1	CLONAL	3	FALSE	1	0.212625506962056	2		538	263	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59938814	59938814	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs769585673	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	75	442	0	ENST00000259008.2:c.87G>T	p.Met29Ile	p.M29I	ENST00000259008	NM_032043.2	29	atG/atT	2/20	1	2	FACETS	0.887	0.787	0.992	1	0.986	1	CLONAL	3	FALSE	1	0.212625506962056	2		442	265	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78829317	78829317	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	87	511	0	ENST00000306801.3:c.1368T>G	p.Phe456Leu	p.F456L	ENST00000306801	NM_020761.2	456	ttT/ttG	12/34	1	2	FACETS	0.912	0.817	1	1	0.988	1	CLONAL	3	FALSE	1	0.212625506962056	2		511	299	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39576601	39576601	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs1256255399	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	51	333	0	ENST00000262039.4:c.892-1G>T		p.X298_splice	ENST00000262039	NM_002647.2	298			0.167533035722701	1	FACETS	0.922	0.8	1	1	0.981	1	CLONAL	3	FALSE	0	0.212625506962056	1		333	155	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584577	48584577	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	54	489	0	ENST00000342988.3:c.750G>T	p.Gln250His	p.Q250H	ENST00000342988	NM_005359.5	250	caG/caT	6/12	0.167533035722701	1	FACETS	1	0.949	1	1	0.98	1	CLONAL	2	FALSE	0	0.212625506962056	1		489	189	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56376746	56376746	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	12	540	0	ENST00000348428.3:c.786A>C	p.Lys262Asn	p.K262N	ENST00000348428	NM_006785.3	262	aaA/aaC	5/17	0.167533035722701	1	FACETS	0.454	0.319	0.621	0.454	0.319	0.621	SUBCLONAL	1	FALSE	0	0.212625506962056	1		540	222	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414754	56414754	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	25	714	0	ENST00000348428.3:c.2155C>T	p.Arg719Ter	p.R719*	ENST00000348428	NM_006785.3	719	Cga/Tga	17/17	0.167533035722701	1	FACETS	0.918	0.727	1	0.918	0.727	1	CLONAL	1	FALSE	0	0.212625506962056	1		714	229	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220604	1220604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555738372	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	132	694	2	ENST00000326873.7:c.622G>A	p.Asp208Asn	p.D208N	ENST00000326873	NM_000455.4	208	Gac/Aac	5/10	0.148300535650375	4	FACETS	1	0.94	1	1	0.991	1	CLONAL	4	FALSE	2	0.212625506962056	4		696	366	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2194526	2194526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770148694	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	90	584	0	ENST00000398665.3:c.601G>A	p.Glu201Lys	p.E201K	ENST00000398665	NM_032482.2	201	Gag/Aag	7/28	0.148300535650375	4	FACETS	1	0.945	1	1	0.983	1	CLONAL	3	FALSE	2	0.212625506962056	4		584	316	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2206746	2206746	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	43	608	0	ENST00000398665.3:c.806C>T	p.Ser269Leu	p.S269L	ENST00000398665	NM_032482.2	269	tCg/tTg	10/28	0.148300535650375	4	FACETS	1	0.919	1	0.581	0.487	0.685	CLONAL	1	FALSE	2	0.212625506962056	4		608	422	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217039	2217039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs986823780	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	106	644	0	ENST00000398665.3:c.2494C>T	p.Pro832Ser	p.P832S	ENST00000398665	NM_032482.2	832	Ccc/Tcc	21/28	0.148300535650375	4	FACETS	0.922	0.836	1	1	0.988	1	CLONAL	4	FALSE	2	0.212625506962056	4		644	328	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3113442	3113442	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778757346	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	31	596	1	ENST00000078429.4:c.436G>A	p.Asp146Asn	p.D146N	ENST00000078429	NM_002067.2	146	Gac/Aac	3/7	0.148300535650375	4	FACETS	1	0.895	1	0.582	0.471	0.705	CLONAL	1	FALSE	2	0.212625506962056	4		597	304	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117148	7117148	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	40	610	0	ENST00000302850.5:c.4068G>T	p.Glu1356Asp	p.E1356D	ENST00000302850	NM_000208.2	1356	gaG/gaT	22/22	0.148300535650375	4	FACETS	1	0.948	1	0.698	0.582	0.826	CLONAL	1	FALSE	2	0.212625506962056	4		610	327	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122652	7122652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs926877336	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	121	611	0	ENST00000302850.5:c.3502G>A	p.Ala1168Thr	p.A1168T	ENST00000302850	NM_000208.2	1168	Gcc/Acc	19/22	0.148300535650375	4	FACETS	0.945	0.863	1	1	0.99	1	CLONAL	4	FALSE	2	0.212625506962056	4		611	365	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125392	7125392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1135401741	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	36	724	0	ENST00000302850.5:c.3160G>A	p.Val1054Met	p.V1054M	ENST00000302850	NM_000208.2	1054	Gtg/Atg	17/22	0.148300535650375	4	FACETS	1	0.881	1	0.546	0.449	0.654	CLONAL	1	FALSE	2	0.212625506962056	4		724	376	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10279032	10279032	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	46	465	1	ENST00000340748.4:c.729G>T	p.Lys243Asn	p.K243N	ENST00000340748		243	aaG/aaT	9/40	0.148300535650375	4	FACETS	1	0.956	1	0.711	0.6	0.832	CLONAL	1	FALSE	2	0.212625506962056	4		466	369	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354025	15354025	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	44	337	0	ENST00000263377.2:c.2855C>T	p.Ser952Phe	p.S952F	ENST00000263377	NM_058243.2	952	tCc/tTc	14/20	0.148300535650375	4	FACETS	1	0.877	1	1	0.975	1	CLONAL	4	FALSE	2	0.212625506962056	4		337	123	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366220	15366220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	104	632	0	ENST00000263377.2:c.1935G>T	p.Lys645Asn	p.K645N	ENST00000263377	NM_058243.2	645	aaG/aaT	10/20	0.148300535650375	4	FACETS	0.899	0.814	0.986	1	0.987	1	CLONAL	4	FALSE	2	0.212625506962056	4		632	330	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971188	18971188	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs749150105	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	125	711	0	ENST00000262803.5:c.2241C>A	p.Phe747Leu	p.F747L	ENST00000262803	NM_002911.3	747	ttC/ttA	16/24	0.148300535650375	4	FACETS	0.919	0.84	1	1	0.99	1	CLONAL	4	FALSE	2	0.212625506962056	4		711	388	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314579	30314579	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	96	666	0	ENST00000262643.3:c.1128G>T	p.Lys376Asn	p.K376N	ENST00000262643	NM_001238.2	376	aaG/aaT	12/12	0.148300535650375	4	FACETS	1	0.957	1	1	0.989	1	CLONAL	4	FALSE	2	0.212625506962056	4		666	249	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229336	36229336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777603343	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	22	510	0	ENST00000222270.7:c.8026G>A	p.Ala2676Thr	p.A2676T	ENST00000222270	NM_014727.1	2676	Gcc/Acc	37/37	0.148300535650375	4	FACETS	0.919	0.714	1	0.46	0.357	0.579	CLONAL	1	FALSE	2	0.212625506962056	4		510	273	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383687	42383687	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	105	538	1	ENST00000221972.3:c.462C>A	p.Phe154Leu	p.F154L	ENST00000221972	NM_021601.3	154	ttC/ttA	3/5	0.148300535650375	4	FACETS	1	0.926	1	1	0.989	1	CLONAL	4	FALSE	2	0.212625506962056	4		539	293	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798818	42798818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	16	635	2	ENST00000575354.2:c.4390C>T	p.Arg1464Trp	p.R1464W	ENST00000575354	NM_015125.3	1464	Cgg/Tgg	19/20	0.148300535650375	4	FACETS	0.6	0.443	0.788	0.3	0.221	0.394	SUBCLONAL	1	FALSE	2	0.212625506962056	4		637	304	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45854910	45854910	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	116	793	1	ENST00000391945.4:c.2260G>T	p.Glu754Ter	p.E754*	ENST00000391945	NM_000400.3	754	Gag/Tag	23/23	0.148300535650375	4	FACETS	1	0.934	1	1	0.99	1	CLONAL	4	FALSE	2	0.212625506962056	4		794	322	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868103	45868103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753293260	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	24	732	0	ENST00000391945.4:c.587G>A	p.Arg196Gln	p.R196Q	ENST00000391945	NM_000400.3	196	cGa/cAa	7/23	0.148300535650375	4	FACETS	0.985	0.774	1	0.492	0.387	0.614	CLONAL	1	FALSE	2	0.212625506962056	4		732	278	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714741	52714741	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	46	475	0	ENST00000322088.6:c.499C>T	p.Arg167Ter	p.R167*	ENST00000322088	NM_014225.5	167	Cga/Tga	4/15	0.148300535650375	4	FACETS	1	0.869	1	1	0.965	1	CLONAL	3	FALSE	2	0.212625506962056	4		475	172	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966510	25966510	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	40	641	0	ENST00000435504.4:c.2696T>G	p.Leu899Arg	p.L899R	ENST00000435504		899	cTt/cGt	13/13	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.212625506962056	2		641	256	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068355	26068355	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	61	499	0	ENST00000435504.4:c.135A>C	p.Glu45Asp	p.E45D	ENST00000435504		45	gaA/gaC	2/13	1	2	FACETS	1	0.938	1	1	0.982	1	CLONAL	2	FALSE	1	0.212625506962056	2		499	254	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754852	29754852	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	26	379	0	ENST00000389048.3:c.1083C>A	p.Tyr361Ter	p.Y361*	ENST00000389048	NM_004304.4	361	taC/taA	4/29	1	2	FACETS	0.764	0.612	0.935	1	0.936	1	CLONAL	2	FALSE	1	0.212625506962056	2		379	160	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278412	39278412	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	46	633	0	ENST00000402219.2:c.737T>G	p.Phe246Cys	p.F246C	ENST00000402219	NM_005633.3	246	tTt/tGt	6/23	1	2	FACETS	0.81	0.687	0.944	1	0.966	1	CLONAL	2	FALSE	1	0.212625506962056	2		633	267	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281915	39281915	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs730881038	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	32	458	1	ENST00000402219.2:c.560C>A	p.Ser187Tyr	p.S187Y	ENST00000402219	NM_005633.3	187	tCt/tAt	5/23	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	FALSE	1	0.212625506962056	2		459	260	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285837	39285837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397517164	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	120	605	1	ENST00000402219.2:c.322G>A	p.Glu108Lys	p.E108K	ENST00000402219	NM_005633.3	108	Gaa/Aaa	3/23	1	2	FACETS	0.966	0.887	1	1	0.993	1	CLONAL	4	FALSE	1	0.212625506962056	2		606	292	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656960	47656960	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	21	416	0	ENST00000233146.2:c.1156G>T	p.Asp386Tyr	p.D386Y	ENST00000233146	NM_000251.2	386	Gat/Tat	7/16	1	2	FACETS	1	0.835	1	1	0.835	1	CLONAL	1	FALSE	1	0.212625506962056	2		416	180	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018167	48018167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769279475	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	37	607	0	ENST00000234420.5:c.362G>A	p.Arg121His	p.R121H	ENST00000234420	NM_000179.2	121	cGc/cAc	2/10	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	1	0.212625506962056	2		607	261	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027217	48027217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	30	429	0	ENST00000234420.5:c.2095G>A	p.Glu699Lys	p.E699K	ENST00000234420	NM_000179.2	699	Gag/Aag	4/10	1	2	FACETS	0.835	0.68	1	1	0.951	1	CLONAL	2	FALSE	1	0.212625506962056	2		429	169	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118866	61118866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	76	368	0	ENST00000295025.8:c.59G>A	p.Gly20Glu	p.G20E	ENST00000295025	NM_002908.2	20	gGa/gAa	2/11	1	2	FACETS	0.899	0.799	1	1	0.987	1	CLONAL	3	FALSE	1	0.212625506962056	2		368	265	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99136593	99136593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770686205	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	29	493	0	ENST00000074304.5:c.82G>A	p.Asp28Asn	p.D28N	ENST00000074304	NM_001134224.1	28	Gac/Aac	3/26	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	1	0.212625506962056	2		493	207	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193603	99193603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	11	370	2	ENST00000074304.5:c.2798G>A	p.Arg933His	p.R933H	ENST00000074304	NM_001134224.1	933	cGc/cAc	25/26	1	2	FACETS	0.985	0.687	1	0.985	0.687	1	CLONAL	1	FALSE	1	0.212625506962056	2		372	105	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719263	190719263	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	17	422	0	ENST00000441310.2:c.1265G>T	p.Ser422Ile	p.S422I	ENST00000441310	NM_000534.4	422	aGt/aTt	9/13	1	2	FACETS	0.812	0.608	1	0.812	0.608	1	CLONAL	1	FALSE	1	0.212625506962056	2		422	197	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274644	198274644	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs763348948	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	76	507	0	ENST00000335508.6:c.754A>C	p.Lys252Gln	p.K252Q	ENST00000335508	NM_012433.2	252	Aaa/Caa	7/25	1	2	FACETS	1	0.931	1	1	0.988	1	CLONAL	3	FALSE	1	0.212625506962056	2		507	225	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248449	212248449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1256468343	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	22	363	0	ENST00000342788.4:c.3818G>A	p.Arg1273Gln	p.R1273Q	ENST00000342788	NM_005235.2	1273	cGg/cAg	28/28	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	FALSE	1	0.212625506962056	2		363	141	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285186	212285186	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1398681951	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	47	447	0	ENST00000342788.4:c.3115G>T	p.Ala1039Ser	p.A1039S	ENST00000342788	NM_005235.2	1039	Gca/Tca	25/28	1	2	FACETS	0.91	0.782	1	1	0.979	1	CLONAL	3	FALSE	1	0.212625506962056	2		447	162	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295675	212295675	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	31	415	0	ENST00000342788.4:c.2638G>T	p.Gly880Ter	p.G880*	ENST00000342788	NM_005235.2	880	Gga/Tga	21/28	1	2	FACETS	0.923	0.756	1	1	0.958	1	CLONAL	2	FALSE	1	0.212625506962056	2		415	158	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295755	212295755	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	38	527	0	ENST00000342788.4:c.2558C>A	p.Ser853Tyr	p.S853Y	ENST00000342788	NM_005235.2	853	tCt/tAt	21/28	1	2	FACETS	0.824	0.687	0.973	1	0.96	1	CLONAL	2	FALSE	1	0.212625506962056	2		527	217	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593657	215593657	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	32	376	0	ENST00000260947.4:c.2077A>C	p.Lys693Gln	p.K693Q	ENST00000260947	NM_000465.2	693	Aag/Cag	11/11	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	FALSE	1	0.212625506962056	2		376	218	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645796	215645796	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	23	537	0	ENST00000260947.4:c.802G>T	p.Glu268Ter	p.E268*	ENST00000260947	NM_000465.2	268	Gaa/Taa	4/11	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	FALSE	1	0.212625506962056	2		537	186	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645925	215645926	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	78	584	0	ENST00000260947.4:c.672dup	p.Glu225ArgfsTer4	p.E225Rfs*4	ENST00000260947	NM_000465.2	224	-/A	4/11	1	2	FACETS	1	0.914	1	1	0.988	1	CLONAL	3	FALSE	1	0.212625506962056	2		584	238	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645978	215645978	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	37	513	0	ENST00000260947.4:c.620A>C	p.Lys207Thr	p.K207T	ENST00000260947	NM_000465.2	207	aAa/aCa	4/11	1	2	FACETS	1	0.925	1	1	0.971	1	CLONAL	2	FALSE	1	0.212625506962056	2		513	146	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225367696	225367696	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	63	391	0	ENST00000264414.4:c.1471C>A	p.Leu491Ile	p.L491I	ENST00000264414	NM_003590.4	491	Cta/Ata	10/16	1	2	FACETS	1	0.891	1	1	0.985	1	CLONAL	3	FALSE	1	0.212625506962056	2		391	195	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663258	227663259	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	66	422	0	ENST00000305123.5:c.196_197insA	p.Leu66HisfsTer2	p.L66Hfs*2	ENST00000305123	NM_005544.2	66	ctt/cAtt	1/2	1	2	FACETS	0.941	0.829	1	1	0.985	1	CLONAL	3	FALSE	1	0.212625506962056	2		422	220	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021424	31021424	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754658635	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	27	480	2	ENST00000375687.4:c.1423G>A	p.Asp475Asn	p.D475N	ENST00000375687	NM_015338.5	475	Gac/Aac	12/13	0.135652639616145	0	FACETS	0.881	0.705	1			1	CLONAL	1	FALSE	0	0.212625506962056	0		482	227	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023931	31023932	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs35239404	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	49	604	0	ENST00000375687.4:c.3420dup	p.Asp1141ArgfsTer23	p.D1141Rfs*23	ENST00000375687	NM_015338.5	1139	aca/acAa	13/13	0.135652639616145	0	FACETS	0.799	0.684	0.923			1	CLONAL	2	FALSE	0	0.212625506962056	0		604	227	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030841	36030841	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs994208712	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	31	345	1	ENST00000358208.4:c.1120G>A	p.Ala374Thr	p.A374T	ENST00000358208		374	Gcc/Acc	10/12	0.135652639616145	0	FACETS	1	0.865	1			1	CLONAL	2	FALSE	0	0.212625506962056	0		346	109	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256391	46256391	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	46	545	0	ENST00000371998.3:c.619A>G	p.Ile207Val	p.I207V	ENST00000371998		207	Att/Gtt	7/23	0.135652639616145	0	FACETS	1	0.949	1			1	CLONAL	1	FALSE	0	0.212625506962056	0		545	262	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265470	46265470	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	14	295	0	ENST00000371998.3:c.2340G>T	p.Glu780Asp	p.E780D	ENST00000371998		780	gaG/gaT	12/23	0.135652639616145	0	FACETS	0.66	0.479	0.877			1	SUBCLONAL	1	FALSE	0	0.212625506962056	0		295	157	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62294199	62294199	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	34	564	1	ENST00000360203.5:c.495G>T	p.Lys165Asn	p.K165N	ENST00000360203	NM_001283009.1	165	aaG/aaT	6/35	0.135652639616145	0	FACETS	0.899	0.738	1			1	CLONAL	1	FALSE	0	0.212625506962056	0		565	280	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62303960	62303960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123019	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	117	651	0	ENST00000360203.5:c.751G>A	p.Glu251Lys	p.E251K	ENST00000360203	NM_001283009.1	251	Gaa/Aaa	9/35	0.135652639616145	0	FACETS	0.935	0.855	1			1	CLONAL	3	FALSE	0	0.212625506962056	0		651	309	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860366	42860366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	42	657	0	ENST00000398585.3:c.511G>A	p.Asp171Asn	p.D171N	ENST00000398585	NM_001135099.1	171	Gat/Aat	5/14	0.212625506962056	1	FACETS	0.989	0.828	1	0.989	0.828	1	CLONAL	1	FALSE	0	0.212625506962056	1		657	357	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288176	21288176	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	52	646	0	ENST00000354336.3:c.421G>T	p.Asp141Tyr	p.D141Y	ENST00000354336	NM_005207.3	141	Gac/Tac	2/3	0.148300535650375	4	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	FALSE	2	0.212625506962056	4		646	255	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41489012	41489012	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	59	378	0	ENST00000263253.7:c.4G>A	p.Ala2Thr	p.A2T	ENST00000263253	NM_001429.3	2	Gcc/Acc	1/31	0.148300535650375	4	FACETS	1	0.923	1	1	0.923	1	CLONAL	2	FALSE	2	0.212625506962056	4		378	307	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513265	41513265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1186074560	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	68	584	0	ENST00000263253.7:c.169A>G	p.Asn57Asp	p.N57D	ENST00000263253	NM_001429.3	57	Aat/Gat	2/31	0.148300535650375	4	FACETS	1	0.92	1	1	0.92	1	CLONAL	2	FALSE	2	0.212625506962056	4		584	363	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729932	30729932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	67	397	0	ENST00000295754.5:c.1453G>A	p.Glu485Lys	p.E485K	ENST00000295754	NM_003242.5	485	Gaa/Aaa	6/7	1	2	FACETS	0.847	0.745	0.954	1	0.984	1	CLONAL	3	FALSE	1	0.212625506962056	2		397	248	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158180	47158180	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	70	502	0	ENST00000409792.3:c.4519G>T	p.Asp1507Tyr	p.D1507Y	ENST00000409792	NM_014159.6	1507	Gat/Tat	4/21	1	2	FACETS	1	0.908	1	1	0.983	1	CLONAL	2	FALSE	1	0.212625506962056	2		502	317	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163137	47163137	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	60	384	0	ENST00000409792.3:c.2989G>T	p.Glu997Ter	p.E997*	ENST00000409792	NM_014159.6	997	Gaa/Taa	3/21	1	2	FACETS	1	0.891	1	1	0.984	1	CLONAL	3	FALSE	1	0.212625506962056	2		384	185	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49399973	49399973	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	108	615	1	ENST00000418115.1:c.364C>T	p.Arg122Trp	p.R122W	ENST00000418115	NM_001664.2	122	Cgg/Tgg	4/5	1	2	FACETS	0.923	0.836	1	1	0.991	1	CLONAL	3	FALSE	1	0.212625506962056	2		616	367	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440320	52440320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	29	549	0	ENST00000460680.1:c.732G>T	p.Arg244Ser	p.R244S	ENST00000460680	NM_004656.3	244	agG/agT	9/17	1	2	FACETS	0.915	0.736	1	0.915	0.736	1	CLONAL	1	FALSE	1	0.212625506962056	2		549	298	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595813	52595813	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	36	470	0	ENST00000394830.3:c.4102C>A	p.Leu1368Ile	p.L1368I	ENST00000394830	NM_018313.4	1368	Ctt/Att	26/30	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	FALSE	1	0.212625506962056	2		470	259	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643381	52643381	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	25	577	0	ENST00000394830.3:c.2515T>G	p.Leu839Val	p.L839V	ENST00000394830	NM_018313.4	839	Tta/Gta	17/30	1	2	FACETS	0.825	0.652	1	0.825	0.652	1	CLONAL	1	FALSE	1	0.212625506962056	2		577	285	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247496	71247496	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	42	461	0	ENST00000318789.4:c.37G>T	p.Gly13Cys	p.G13C	ENST00000318789	NM_032682.5	13	Ggt/Tgt	6/21	1	2	FACETS	0.826	0.696	0.969	1	0.964	1	CLONAL	2	FALSE	1	0.212625506962056	2		461	239	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448516	89448516	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	61	513	0	ENST00000336596.2:c.1480G>T	p.Val494Phe	p.V494F	ENST00000336596	NM_005233.5	494	Gtt/Ttt	7/17	1	2	FACETS	1	0.904	1	1	0.985	1	CLONAL	3	FALSE	1	0.212625506962056	2		513	185	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582404	119582404	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	30	297	0	ENST00000316626.5:c.997C>A	p.Leu333Met	p.L333M	ENST00000316626		333	Ctg/Atg	10/12	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	FALSE	1	0.212625506962056	2		297	197	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188262	142188262	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	77	507	0	ENST00000350721.4:c.6469T>G	p.Phe2157Val	p.F2157V	ENST00000350721	NM_001184.3	2157	Ttt/Gtt	38/47	1	2	FACETS	1	0.954	1	1	0.988	1	CLONAL	3	FALSE	1	0.212625506962056	2		507	214	SUCCESS
ATR	545	MSKCC	GRCh37	3	142238616	142238616	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	12	253	0	ENST00000350721.4:c.4277C>A	p.Ser1426Tyr	p.S1426Y	ENST00000350721	NM_001184.3	1426	tCt/tAt	24/47	1	2	FACETS	0.99	0.702	1	0.99	0.702	1	CLONAL	1	FALSE	1	0.212625506962056	2		253	114	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281714	142281714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532495501	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	79	645	0	ENST00000350721.4:c.530G>A	p.Arg177Gln	p.R177Q	ENST00000350721	NM_001184.3	177	cGa/cAa	4/47	1	2	FACETS	1	0.928	1	1	0.988	1	CLONAL	3	FALSE	1	0.212625506962056	2		645	236	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951971	178951971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	37	552	0	ENST00000263967.3:c.3026G>A	p.Gly1009Glu	p.G1009E	ENST00000263967	NM_006218.2	1009	gGa/gAa	21/21	1	2	FACETS	0.78	0.649	0.925	1	0.956	1	CLONAL	2	FALSE	1	0.212625506962056	2		552	223	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155238	185155238	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	41	309	0	ENST00000265026.3:c.479C>A	p.Thr160Asn	p.T160N	ENST00000265026	NM_004721.4	160	aCt/aAt	3/14	1	2	FACETS	0.857	0.727	0.996	1	0.975	1	CLONAL	3	FALSE	1	0.212625506962056	2		309	150	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198085	185198085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	26	436	0	ENST00000265026.3:c.2567C>T	p.Ser856Phe	p.S856F	ENST00000265026	NM_004721.4	856	tCt/tTt	13/14	1	2	FACETS	0.75	0.6	0.918	1	0.934	1	CLONAL	2	FALSE	1	0.212625506962056	2		436	163	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447065	187447065	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	37	643	0	ENST00000232014.4:c.1128G>T	p.Lys376Asn	p.K376N	ENST00000232014	NM_001130845.1	376	aaG/aaT	5/10	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.212625506962056	2		643	240	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1952912	1952912	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	48	606	0	ENST00000382891.5:c.1995A>C	p.Lys665Asn	p.K665N	ENST00000382891	NM_133335.3	665	aaA/aaC	10/22	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	FALSE	1	0.212625506962056	2		606	352	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749425	41749425	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	15	393	0	ENST00000226382.2:c.370G>A	p.Asp124Asn	p.D124N	ENST00000226382	NM_003924.3	124	Gac/Aac	2/3	1	2	FACETS	1	0.842	1	1	0.842	1	CLONAL	1	FALSE	1	0.212625506962056	2		393	116	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139789	55139789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149031291	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	51	610	2	ENST00000257290.5:c.1450G>A	p.Val484Met	p.V484M	ENST00000257290	NM_006206.4	484	Gtg/Atg	10/23	1	2	FACETS	0.923	0.791	1	1	0.974	1	CLONAL	2	FALSE	1	0.212625506962056	2		612	260	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564710	55564710	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	26	463	0	ENST00000288135.5:c.598T>A	p.Phe200Ile	p.F200I	ENST00000288135	NM_000222.2	200	Ttc/Atc	3/21	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	FALSE	1	0.212625506962056	2		463	218	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593581	55593581	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	13	424	0	ENST00000288135.5:c.1648-1G>T		p.X550_splice	ENST00000288135	NM_000222.2	550			1	2	FACETS	1	0.732	1	1	0.732	1	CLONAL	1	FALSE	1	0.212625506962056	2		424	120	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233111	66233111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	24	395	0	ENST00000273854.3:c.1888C>T	p.Pro630Ser	p.P630S	ENST00000273854	NM_004439.5	630	Cca/Tca	10/18	1	2	FACETS	1	0.794	1	1	0.794	1	CLONAL	1	FALSE	1	0.212625506962056	2		395	224	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467895	66467895	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	26	354	0	ENST00000273854.3:c.374G>T	p.Arg125Ile	p.R125I	ENST00000273854	NM_004439.5	125	aGa/aTa	3/18	1	2	FACETS	1	0.902	1	1	0.96	1	CLONAL	2	FALSE	1	0.212625506962056	2		354	102	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383738	84383738	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	36	695	0	ENST00000321945.7:c.1114G>A	p.Ala372Thr	p.A372T	ENST00000321945	NM_139076.2	372	Gca/Aca	9/9	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	1	0.212625506962056	2		695	266	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155429	106155429	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	36	481	0	ENST00000380013.4:c.330G>T	p.Lys110Asn	p.K110N	ENST00000380013	NM_001127208.2	110	aaG/aaT	3/11	1	2	FACETS	0.873	0.725	1	1	0.961	1	CLONAL	2	FALSE	1	0.212625506962056	2		481	194	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156840	106156840	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560827535	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	46	508	1	ENST00000380013.4:c.1741C>T	p.Arg581Cys	p.R581C	ENST00000380013	NM_001127208.2	581	Cgt/Tgt	3/11	1	2	FACETS	1	0.945	1	1	0.977	1	CLONAL	2	FALSE	1	0.212625506962056	2		509	175	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094812	143094812	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	10	343	1	ENST00000262992.4:c.1332G>T	p.Lys444Asn	p.K444N	ENST00000262992	NM_001101669.1	444	aaG/aaT	14/24	1	2	FACETS	0.667	0.453	0.934	0.667	0.453	0.934	SUBCLONAL	1	FALSE	1	0.212625506962056	2		344	141	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094828	143094828	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	39	412	0	ENST00000262992.4:c.1316C>A	p.Ser439Tyr	p.S439Y	ENST00000262992	NM_001101669.1	439	tCt/tAt	14/24	1	2	FACETS	1	0.897	1	1	0.971	1	CLONAL	2	FALSE	1	0.212625506962056	2		412	168	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130127	143130127	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs748052310	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	73	528	1	ENST00000262992.4:c.889C>T	p.Arg297Ter	p.R297*	ENST00000262992	NM_001101669.1	297	Cga/Tga	11/24	1	2	FACETS	0.916	0.811	1	1	0.986	1	CLONAL	3	FALSE	1	0.212625506962056	2		529	250	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130130	143130130	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	72	541	1	ENST00000262992.4:c.886C>A	p.Leu296Met	p.L296M	ENST00000262992	NM_001101669.1	296	Ctg/Atg	11/24	1	2	FACETS	0.889	0.786	0.996	1	0.986	1	CLONAL	3	FALSE	1	0.212625506962056	2		542	254	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143235911	143235911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1048276811	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	48	310	0	ENST00000262992.4:c.377G>A	p.Arg126Gln	p.R126Q	ENST00000262992	NM_001101669.1	126	cGa/cAa	6/24	1	2	FACETS	0.947	0.816	1	1	0.98	1	CLONAL	3	FALSE	1	0.212625506962056	2		310	159	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250882	153250882	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1390822119	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	42	444	1	ENST00000281708.4:c.1178G>A	p.Arg393Gln	p.R393Q	ENST00000281708	NM_033632.3	393	cGa/cAa	8/12	1	2	FACETS	0.923	0.779	1	1	0.968	1	CLONAL	2	FALSE	1	0.212625506962056	2		445	214	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519235	187519235	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	14	627	0	ENST00000441802.2:c.12148G>T	p.Glu4050Ter	p.E4050*	ENST00000441802	NM_005245.3	4050	Gag/Tag	23/27	1	2	FACETS	0.518	0.374	0.693	0.518	0.374	0.693	SUBCLONAL	1	FALSE	1	0.212625506962056	2		627	254	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524804	187524804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753458608	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	35	657	0	ENST00000441802.2:c.10876G>A	p.Asp3626Asn	p.D3626N	ENST00000441802	NM_005245.3	3626	Gac/Aac	19/27	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	1	0.212625506962056	2		657	255	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539563	187539563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748950954	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	23	407	2	ENST00000441802.2:c.8177G>A	p.Arg2726Gln	p.R2726Q	ENST00000441802	NM_005245.3	2726	cGa/cAa	10/27	1	2	FACETS	0.917	0.726	1	1	0.944	1	CLONAL	2	FALSE	1	0.212625506962056	2		409	118	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539577	187539577	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	13	394	0	ENST00000441802.2:c.8163G>T	p.Glu2721Asp	p.E2721D	ENST00000441802	NM_005245.3	2721	gaG/gaT	10/27	1	2	FACETS	1	0.76	1	1	0.76	1	CLONAL	1	FALSE	1	0.212625506962056	2		394	115	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628419	187628419	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	50	749	0	ENST00000441802.2:c.2563G>T	p.Gly855Ter	p.G855*	ENST00000441802	NM_005245.3	855	Gga/Tga	2/27	1	2	FACETS	0.771	0.658	0.894	1	0.966	1	SUBCLONAL	2	FALSE	1	0.212625506962056	2		749	305	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295240	1295240	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	15	362	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	FALSE	1	0.212625506962056	2		362	101	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31431718	31431718	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	37	537	0	ENST00000344624.3:c.3110G>A	p.Arg1037Gln	p.R1037Q	ENST00000344624		1037	cGa/cAa	23/33	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.212625506962056	2		537	238	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31521239	31521239	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	69	483	0	ENST00000344624.3:c.938G>T	p.Arg313Ile	p.R313I	ENST00000344624		313	aGa/aTa	3/33	1	2	FACETS	0.882	0.784	0.982	1	0.987	1	CLONAL	4	FALSE	1	0.212625506962056	2		483	184	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38964899	38964899	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	16	196	0	ENST00000357387.3:c.1395G>T	p.Lys465Asn	p.K465N	ENST00000357387	NM_152756.3	465	aaG/aaT	16/38	1	2	FACETS	0.827	0.621	1	1	0.911	1	CLONAL	2	FALSE	1	0.212625506962056	2		196	91	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56171126	56171126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376758896	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	57	251	0	ENST00000399503.3:c.1954G>A	p.Val652Ile	p.V652I	ENST00000399503	NM_005921.1	652	Gtt/Att	10/20	1	2	FACETS	1	0.918	1	1	0.985	1	CLONAL	4	FALSE	1	0.212625506962056	2		251	128	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178041	56178041	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	25	348	0	ENST00000399503.3:c.3014G>T	p.Arg1005Ile	p.R1005I	ENST00000399503	NM_005921.1	1005	aGa/aTa	14/20	1	2	FACETS	0.822	0.656	1	1	0.941	1	CLONAL	2	FALSE	1	0.212625506962056	2		348	143	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754659	57754659	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	42	314	1	ENST00000274289.3:c.388G>T	p.Glu130Ter	p.E130*	ENST00000274289	NM_006622.3	130	Gaa/Taa	3/14	1	2	FACETS	0.921	0.784	1	1	0.977	1	CLONAL	3	FALSE	1	0.212625506962056	2		315	143	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80160661	80160661	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	32	709	0	ENST00000265081.6:c.3030T>G	p.His1010Gln	p.H1010Q	ENST00000265081	NM_002439.4	1010	caT/caG	22/24	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	FALSE	1	0.212625506962056	2		709	251	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86642504	86642504	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	23	399	0	ENST00000274376.6:c.1065G>T	p.Lys355Asn	p.K355N	ENST00000274376	NM_002890.2	355	aaG/aaT	7/25	1	2	FACETS	1	0.815	1	1	0.815	1	CLONAL	1	FALSE	1	0.212625506962056	2		399	207	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86681117	86681117	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	17	265	0	ENST00000274376.6:c.2759-1G>T		p.X920_splice	ENST00000274376	NM_002890.2	920			1	2	FACETS	1	0.814	1	1	0.814	1	CLONAL	1	FALSE	1	0.212625506962056	2		265	145	SUCCESS
APC	324	MSKCC	GRCh37	5	112090712	112090712	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	45	325	0	ENST00000257430.4:c.125C>T	p.Ser42Phe	p.S42F	ENST00000257430	NM_000038.5	42	tCt/tTt	2/16	1	2	FACETS	1	0.943	1	1	0.977	1	CLONAL	2	FALSE	1	0.212625506962056	2		325	172	SUCCESS
APC	324	MSKCC	GRCh37	5	112136975	112136975	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	23	356	0	ENST00000257430.4:c.730-1G>T		p.X244_splice	ENST00000257430	NM_000038.5	244			1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	FALSE	1	0.212625506962056	2		356	150	SUCCESS
APC	324	MSKCC	GRCh37	5	112175931	112175931	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786201876	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	42	319	0	ENST00000257430.4:c.4640A>G	p.Glu1547Gly	p.E1547G	ENST00000257430	NM_000038.5	1547	gAa/gGa	16/16	1	2	FACETS	1	0.893	1	1	0.978	1	CLONAL	3	FALSE	1	0.212625506962056	2		319	125	SUCCESS
APC	324	MSKCC	GRCh37	5	112176480	112176480	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	21	380	0	ENST00000257430.4:c.5189C>A	p.Ser1730Tyr	p.S1730Y	ENST00000257430	NM_000038.5	1730	tCt/tAt	16/16	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	FALSE	1	0.212625506962056	2		380	140	SUCCESS
APC	324	MSKCC	GRCh37	5	112177104	112177104	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	26	531	0	ENST00000257430.4:c.5813A>C	p.Lys1938Thr	p.K1938T	ENST00000257430	NM_000038.5	1938	aAa/aCa	16/16	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	FALSE	1	0.212625506962056	2		531	172	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940623	131940623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755939251	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	62	396	1	ENST00000265335.6:c.2650C>T	p.Arg884Cys	p.R884C	ENST00000265335		884	Cgt/Tgt	16/25	1	2	FACETS	0.935	0.82	1	1	0.984	1	CLONAL	3	FALSE	1	0.212625506962056	2		397	208	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637987	176637987	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755866685	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	20	640	1	ENST00000439151.2:c.2587G>A	p.Glu863Lys	p.E863K	ENST00000439151	NM_022455.4	863	Gag/Aag	5/23	1	2	FACETS	0.674	0.516	0.859	0.674	0.516	0.859	SUBCLONAL	1	FALSE	1	0.212625506962056	2		641	279	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046084	180046084	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	20	272	0	ENST00000261937.6:c.2787C>A	p.Phe929Leu	p.F929L	ENST00000261937	NM_182925.4	929	ttC/ttA	20/30	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	FALSE	1	0.212625506962056	2		272	136	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048002	180048002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775336901	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	28	583	0	ENST00000261937.6:c.2173G>A	p.Asp725Asn	p.D725N	ENST00000261937	NM_182925.4	725	Gac/Aac	15/30	1	2	FACETS	0.808	0.653	0.98	1	0.945	1	CLONAL	2	FALSE	1	0.212625506962056	2		583	163	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048561	180048561	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	65	590	0	ENST00000261937.6:c.2001G>T	p.Lys667Asn	p.K667N	ENST00000261937	NM_182925.4	667	aaG/aaT	13/30	1	2	FACETS	0.926	0.822	1	1	0.987	1	CLONAL	4	FALSE	1	0.212625506962056	2		590	165	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393290	393290	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	62	492	0	ENST00000380956.4:c.138G>T	p.Glu46Asp	p.E46D	ENST00000380956	NM_001195286.1	46	gaG/gaT	2/9	NA	2	FACETS	1	0.916	1			1	INDETERMINATE	3	FALSE	NA	0.212625506962056	2		492	185	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480168	20480168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765868574	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	30	386	0	ENST00000346618.3:c.485G>A	p.Arg162Gln	p.R162Q	ENST00000346618	NM_001949.4	162	cGa/cAa	2/7	NA	2	FACETS	1	0.929	1			1	INDETERMINATE	1	FALSE	NA	0.212625506962056	2		386	209	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056407	26056407	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	64	268	0	ENST00000343677.2:c.250C>A	p.Leu84Ile	p.L84I	ENST00000343677	NM_005319.3	84	Ctc/Atc	1/1	0.212625506962056	14	FACETS	1	0.926	1	0.623	0.544	0.708	CLONAL	4	FALSE	7	0.212625506962056	14		268	314	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225560	26225560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375842011	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	120	497	0	ENST00000360408.1:c.178G>A	p.Glu60Lys	p.E60K	ENST00000360408	NM_003532.2	60	Gag/Aag	1/1	0.212625506962056	14	FACETS	1	0.944	1	0.754	0.684	0.826	CLONAL	5	FALSE	7	0.212625506962056	14		497	487	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672884	30672884	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	100	725	0	ENST00000376406.3:c.4076C>A	p.Ser1359Tyr	p.S1359Y	ENST00000376406	NM_014641.2	1359	tCt/tAt	10/15	0.160482769171991	3	FACETS	1	0.938	1	1	0.984	1	CLONAL	3	FALSE	1	0.212625506962056	3		725	330	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672917	30672917	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	35	788	0	ENST00000376406.3:c.4043C>A	p.Ser1348Tyr	p.S1348Y	ENST00000376406	NM_014641.2	1348	tCt/tAt	10/15	0.160482769171991	3	FACETS	1	0.911	1	0.593	0.488	0.711	CLONAL	1	FALSE	1	0.212625506962056	3		788	307	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679750	30679750	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	20	526	0	ENST00000376406.3:c.1969G>T	p.Glu657Ter	p.E657*	ENST00000376406	NM_014641.2	657	Gaa/Taa	5/15	0.160482769171991	3	FACETS	0.933	0.716	1	0.467	0.358	0.593	CLONAL	1	FALSE	1	0.212625506962056	3		526	223	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168970	32168970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763391002	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	94	745	0	ENST00000375023.3:c.4063C>T	p.Arg1355Trp	p.R1355W	ENST00000375023	NM_004557.3	1355	Cgg/Tgg	22/30	0.160482769171991	3	FACETS	0.877	0.791	0.965	1	0.986	1	CLONAL	4	FALSE	1	0.212625506962056	3		745	279	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803444	32803444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779665536	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	127	685	2	ENST00000374899.4:c.715G>A	p.Gly239Ser	p.G239S	ENST00000374899	NM_018833.2	239	Ggt/Agt	4/12	0.160482769171991	3	FACETS	1	0.968	1	1	0.989	1	CLONAL	3	FALSE	1	0.212625506962056	3		687	393	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805543	32805543	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	48	899	1	ENST00000374899.4:c.468C>A	p.Phe156Leu	p.F156L	ENST00000374899	NM_018833.2	156	ttC/ttA	2/12	0.160482769171991	3	FACETS	1	0.896	1	0.538	0.455	0.629	CLONAL	1	FALSE	1	0.212625506962056	3		900	464	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815404	32815404	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	131	653	0	ENST00000354258.4:c.1969G>T	p.Glu657Ter	p.E657*	ENST00000354258	NM_000593.5	657	Gaa/Taa	9/11	0.160482769171991	3	FACETS	1	0.974	1	1	0.99	1	CLONAL	3	FALSE	1	0.212625506962056	3		653	393	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816569	32816569	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	130	802	1	ENST00000354258.4:c.1606G>T	p.Glu536Ter	p.E536*	ENST00000354258	NM_000593.5	536	Gag/Tag	7/11	0.160482769171991	3	FACETS	0.939	0.858	1	1	0.985	1	CLONAL	3	FALSE	1	0.212625506962056	3		803	480	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820183	32820183	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	28	590	1	ENST00000354258.4:c.875C>A	p.Ser292Tyr	p.S292Y	ENST00000354258	NM_000593.5	292	tCc/tAc	2/11	0.160482769171991	3	FACETS	0.702	0.561	0.864	0.351	0.28	0.432	SUBCLONAL	1	FALSE	1	0.212625506962056	3		591	415	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287813	33287813	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	198	822	0	ENST00000374542.5:c.1440G>T	p.Glu480Asp	p.E480D	ENST00000374542	NM_001141970.1	480	gaG/gaT	5/8	0.160482769171991	3	FACETS	1	0.981	1	1	0.993	1	CLONAL	3	FALSE	1	0.212625506962056	3		822	600	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289167	33289167	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	65	503	0	ENST00000374542.5:c.385G>T	p.Glu129Ter	p.E129*	ENST00000374542	NM_001141970.1	129	Gag/Tag	3/8	0.160482769171991	3	FACETS	0.972	0.848	1	0.972	0.848	1	CLONAL	2	FALSE	1	0.212625506962056	3		503	348	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43749739	43749739	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	38	526	0	ENST00000523873.1:c.592G>A	p.Asp198Asn	p.D198N	ENST00000523873		198	Gat/Aat	7/8	0.160482769171991	3	FACETS	0.788	0.655	0.933	0.788	0.655	0.933	CLONAL	2	FALSE	1	0.212625506962056	3		526	251	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955069	93955069	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	10	381	0	ENST00000369303.4:c.2829T>A	p.Asn943Lys	p.N943K	ENST00000369303	NM_004440.3	943	aaT/aaA	16/17	0.160482769171991	3	FACETS	0.777	0.528	1	0.388	0.264	0.543	CLONAL	1	FALSE	1	0.212625506962056	3		381	134	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024222	112024222	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	18	327	0	ENST00000368678.4:c.563C>A	p.Ser188Tyr	p.S188Y	ENST00000368678		188	tCt/tAt	7/13	0.160482769171991	3	FACETS	1	0.872	1	0.629	0.477	0.805	CLONAL	1	FALSE	1	0.212625506962056	3		327	149	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631331	117631331	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	17	456	0	ENST00000368508.3:c.6347G>T	p.Arg2116Ile	p.R2116I	ENST00000368508	NM_002944.2	2116	aGa/aTa	40/43	0.160482769171991	3	FACETS	0.988	0.741	1	0.494	0.37	0.64	CLONAL	1	FALSE	1	0.212625506962056	3		456	179	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662727	117662727	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	32	390	0	ENST00000368508.3:c.4738G>T	p.Glu1580Ter	p.E1580*	ENST00000368508	NM_002944.2	1580	Gaa/Taa	29/43	0.160482769171991	3	FACETS	0.895	0.741	1	1	0.938	1	CLONAL	3	FALSE	1	0.212625506962056	3		390	124	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700224	117700224	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	30	424	0	ENST00000368508.3:c.2595G>T	p.Gln865His	p.Q865H	ENST00000368508	NM_002944.2	865	caG/caT	17/43	0.160482769171991	3	FACETS	0.918	0.748	1	0.918	0.748	1	CLONAL	2	FALSE	1	0.212625506962056	3		424	170	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710987	117710987	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	15	261	0	ENST00000368508.3:c.1285G>T	p.Asp429Tyr	p.D429Y	ENST00000368508	NM_002944.2	429	Gat/Tat	12/43	0.160482769171991	3	FACETS	1	0.886	1	0.723	0.535	0.943	CLONAL	1	FALSE	1	0.212625506962056	3		261	108	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519596	137519596	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	55	383	0	ENST00000367739.4:c.1042G>T	p.Glu348Ter	p.E348*	ENST00000367739	NM_000416.2	348	Gaa/Taa	7/7	0.160482769171991	3	FACETS	1	0.946	1	1	0.976	1	CLONAL	3	FALSE	1	0.212625506962056	3		383	164	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983145	149983145	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	28	577	0	ENST00000253339.5:c.3113A>C	p.Asn1038Thr	p.N1038T	ENST00000253339		1038	aAt/aCt	7/7	0.160482769171991	3	FACETS	1	0.879	1	0.569	0.456	0.696	CLONAL	1	FALSE	1	0.212625506962056	3		577	256	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001523	150001523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264217871	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	49	525	0	ENST00000253339.5:c.2081G>A	p.Arg694His	p.R694H	ENST00000253339		694	cGt/cAt	4/7	0.160482769171991	3	FACETS	0.962	0.821	1	0.962	0.821	1	CLONAL	2	FALSE	1	0.212625506962056	3		525	265	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023255	150023255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	31	394	0	ENST00000253339.5:c.8G>T	p.Arg3Met	p.R3M	ENST00000253339		3	aGg/aTg	1/7	0.160482769171991	3	FACETS	1	0.89	1	1	0.89	1	CLONAL	2	FALSE	1	0.212625506962056	3		394	144	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528829	157528829	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775203171	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	24	466	1	ENST00000346085.5:c.6554C>T	p.Pro2185Leu	p.P2185L	ENST00000346085	NM_020732.3	2185	cCg/cTg	20/20	0.160482769171991	3	FACETS	1	0.891	1	0.612	0.483	0.76	CLONAL	1	FALSE	1	0.212625506962056	3		467	204	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976705	2976705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765239761	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	19	470	0	ENST00000396946.4:c.1307G>A	p.Arg436Gln	p.R436Q	ENST00000396946	NM_032415.4	436	cGg/cAg	9/25	1	2	FACETS	1	0.81	1	1	0.81	1	CLONAL	1	FALSE	1	0.212625506962056	2		470	167	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730114	41730114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	34	381	0	ENST00000242208.4:c.415G>A	p.Glu139Lys	p.E139K	ENST00000242208	NM_002192.2	139	Gag/Aag	3/3	1	2	FACETS	1	0.865	1	1	0.973	1	CLONAL	3	FALSE	1	0.212625506962056	2		381	103	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55087027	55087027	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	47	281	0	ENST00000275493.2:c.57C>G	p.Cys19Trp	p.C19W	ENST00000275493	NM_005228.3	19	tgC/tgG	1/28	1	2	FACETS	0.899	0.779	1	1	0.981	1	CLONAL	4	FALSE	1	0.212625506962056	2		281	123	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355323	81355323	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	47	323	0	ENST00000222390.5:c.1051G>T	p.Glu351Ter	p.E351*	ENST00000222390	NM_000601.4	351	Gaa/Taa	9/18	0.160482769171991	3	FACETS	1	0.92	1	1	0.97	1	CLONAL	3	FALSE	1	0.212625506962056	3		323	148	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392159	81392159	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	33	315	0	ENST00000222390.5:c.118C>T	p.His40Tyr	p.H40Y	ENST00000222390	NM_000601.4	40	Cat/Tat	2/18	0.160482769171991	3	FACETS	1	0.832	1	1	0.832	1	CLONAL	2	FALSE	1	0.212625506962056	3		315	170	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403130	116403130	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	67	486	2	ENST00000397752.3:c.2391G>T	p.Glu797Asp	p.E797D	ENST00000397752	NM_000245.2	797	gaG/gaT	11/21	0.160482769171991	3	FACETS	1	0.947	1	1	0.98	1	CLONAL	3	FALSE	1	0.212625506962056	3		488	206	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411651	116411651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	50	706	0	ENST00000397752.3:c.2830G>A	p.Ala944Thr	p.A944T	ENST00000397752	NM_000245.2	944	Gca/Aca	13/21	0.160482769171991	3	FACETS	0.816	0.696	0.946	0.816	0.696	0.946	CLONAL	2	FALSE	1	0.212625506962056	3		706	319	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411954	116411954	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	31	788	0	ENST00000397752.3:c.2939T>G	p.Leu980Trp	p.L980W	ENST00000397752	NM_000245.2	980	tTg/tGg	14/21	0.160482769171991	3	FACETS	1	0.845	1	0.524	0.424	0.635	CLONAL	1	FALSE	1	0.212625506962056	3		788	308	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412373	116412373	+	intron_variant	Intron	SNP	A	A	G	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	67	850	0	ENST00000397752.3:c.3028+330A>G		p.*1010*	ENST00000397752	NM_000245.2	-/1390			0.160482769171991	3	FACETS	0.996	0.871	1	0.996	0.871	1	CLONAL	2	FALSE	1	0.212625506962056	3		850	350	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412705	116412705	+	intron_variant	Intron	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	53	1004	0	ENST00000397752.3:c.3028+662G>T		p.*1010*	ENST00000397752	NM_000245.2	-/1390			0.160482769171991	3	FACETS	1	0.965	1	0.745	0.638	0.862	CLONAL	1	FALSE	1	0.212625506962056	3		1004	370	SUCCESS
MET	4233	MSKCC	GRCh37	7	116413479	116413479	+	intron_variant	Intron	SNP	C	C	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	108	985	2	ENST00000397752.3:c.3028+1436C>T		p.*1010*	ENST00000397752	NM_000245.2	-/1390			0.160482769171991	3	FACETS	0.988	0.895	1	1	0.984	1	CLONAL	3	FALSE	1	0.212625506962056	3		987	379	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418916	116418916	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	26	394	0	ENST00000397752.3:c.3427C>A	p.Leu1143Met	p.L1143M	ENST00000397752	NM_000245.2	1143	Ctg/Atg	17/21	0.160482769171991	3	FACETS	1	0.905	1	0.629	0.501	0.774	CLONAL	1	FALSE	1	0.212625506962056	3		394	215	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852263	128852263	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	48	722	1	ENST00000249373.3:c.2335G>T	p.Glu779Ter	p.E779*	ENST00000249373	NM_005631.4	779	Gaa/Taa	12/12	0.160482769171991	3	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	FALSE	1	0.212625506962056	3		723	210	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140549948	140549948	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	79	471	0	ENST00000288602.6:c.203T>G	p.Phe68Cys	p.F68C	ENST00000288602	NM_004333.4	68	tTt/tGt	2/18	0.160482769171991	3	FACETS	0.943	0.844	1	1	0.985	1	CLONAL	4	FALSE	1	0.212625506962056	3		471	218	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842344	151842344	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs749571160	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	22	310	0	ENST00000262189.6:c.14068C>T	p.Arg4690Ter	p.R4690*	ENST00000262189	NM_170606.2	4690	Cga/Tga	54/59	0.160482769171991	3	FACETS	1	0.84	1	0.55	0.428	0.69	CLONAL	1	FALSE	1	0.212625506962056	3		310	208	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151850033	151850033	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	51	331	0	ENST00000262189.6:c.12283A>C	p.Ser4095Arg	p.S4095R	ENST00000262189	NM_170606.2	4095	Agc/Cgc	49/59	0.160482769171991	3	FACETS	0.903	0.785	1	1	0.975	1	CLONAL	4	FALSE	1	0.212625506962056	3		331	147	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873923	151873923	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	28	487	0	ENST00000262189.6:c.8615C>A	p.Pro2872His	p.P2872H	ENST00000262189	NM_170606.2	2872	cCt/cAt	38/59	0.160482769171991	3	FACETS	1	0.916	1	0.645	0.518	0.787	CLONAL	1	FALSE	1	0.212625506962056	3		487	226	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874140	151874140	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	77	504	0	ENST00000262189.6:c.8398G>T	p.Glu2800Ter	p.E2800*	ENST00000262189	NM_170606.2	2800	Gaa/Taa	38/59	0.160482769171991	3	FACETS	1	0.913	1	1	0.979	1	CLONAL	3	FALSE	1	0.212625506962056	3		504	259	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874636	151874636	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	43	381	0	ENST00000262189.6:c.7902G>T	p.Glu2634Asp	p.E2634D	ENST00000262189	NM_170606.2	2634	gaG/gaT	38/59	0.160482769171991	3	FACETS	1	0.918	1	1	0.918	1	CLONAL	2	FALSE	1	0.212625506962056	3		381	197	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880126	151880126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146495785	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	31	484	2	ENST00000262189.6:c.5198C>T	p.Ser1733Leu	p.S1733L	ENST00000262189	NM_170606.2	1733	tCg/tTg	35/59	0.160482769171991	3	FACETS	1	0.934	1	0.689	0.561	0.833	CLONAL	1	FALSE	1	0.212625506962056	3		486	234	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151893066	151893066	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	18	396	0	ENST00000262189.6:c.4304C>A	p.Ser1435Tyr	p.S1435Y	ENST00000262189	NM_170606.2	1435	tCt/tAt	28/59	0.160482769171991	3	FACETS	0.851	0.643	1	0.426	0.321	0.549	CLONAL	1	FALSE	1	0.212625506962056	3		396	220	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38173555	38173555	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	60	360	0	ENST00000317025.8:c.1861A>G	p.Ser621Gly	p.S621G	ENST00000317025	NM_023034.1	621	Agc/Ggc	10/24	1	2	FACETS	0.97	0.85	1	1	0.984	1	CLONAL	3	FALSE	1	0.212625506962056	2		360	194	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38196093	38196093	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	115	706	1	ENST00000317025.8:c.708A>T	p.Glu236Asp	p.E236D	ENST00000317025	NM_023034.1	236	gaA/gaT	3/24	1	2	FACETS	1	0.972	1	1	0.992	1	CLONAL	3	FALSE	1	0.212625506962056	2		707	312	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020534	69020534	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	59	581	0	ENST00000288368.4:c.2906C>A	p.Ser969Tyr	p.S969Y	ENST00000288368	NM_024870.2	969	tCt/tAt	24/40	1	2	FACETS	0.954	0.834	1	1	0.984	1	CLONAL	3	FALSE	1	0.212625506962056	2		581	194	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566114	141566114	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	20	549	1	ENST00000220592.5:c.1150C>T	p.Arg384Ter	p.R384*	ENST00000220592	NM_012154.3	384	Cga/Tga	10/19	1	2	FACETS	1	0.831	1	1	0.831	1	CLONAL	1	FALSE	1	0.212625506962056	2		550	171	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738074	145738074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763161407	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	48	675	2	ENST00000428558.2:c.2836C>T	p.Arg946Cys	p.R946C	ENST00000428558	NM_004260.3	946	Cgt/Tgt	17/22	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.212625506962056	2		677	303	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090807	5090807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	24	467	0	ENST00000381652.3:c.2955G>T	p.Glu985Asp	p.E985D	ENST00000381652	NM_004972.3	985	gaG/gaT	22/25	0.167533035722701	1	FACETS	0.862	0.679	1	0.862	0.679	1	CLONAL	1	FALSE	0	0.212625506962056	1		467	234	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457390	5457390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1224180886	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	21	186	0	ENST00000381577.3:c.364G>A	p.Asp122Asn	p.D122N	ENST00000381577	NM_014143.3	122	Gac/Aac	3/7	0.167533035722701	1	FACETS	0.833	0.652	1	1	0.932	1	CLONAL	2	FALSE	0	0.212625506962056	1		186	106	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015012	37015012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	51	457	0	ENST00000358127.4:c.392G>A	p.Ser131Asn	p.S131N	ENST00000358127	NM_001280556.1	131	aGc/aAc	3/10	0.167533035722701	1	FACETS	0.836	0.723	0.954	1	0.98	1	CLONAL	3	FALSE	0	0.212625506962056	1		457	171	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606259	93606259	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	26	599	0	ENST00000375746.1:c.79G>T	p.Asp27Tyr	p.D27Y	ENST00000375746	NM_001174167.1	27	Gat/Tat	2/14	0.167533035722701	1	FACETS	0.98	0.78	1	0.98	0.78	1	CLONAL	1	FALSE	0	0.212625506962056	1		599	223	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639906	93639906	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	19	272	0	ENST00000375746.1:c.1235C>T	p.Ala412Val	p.A412V	ENST00000375746	NM_001174167.1	412	gCt/gTt	10/14	0.167533035722701	1	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	FALSE	0	0.212625506962056	1		272	134	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98241322	98241322	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	76	546	1	ENST00000331920.6:c.1175C>T	p.Ala392Val	p.A392V	ENST00000331920	NM_000264.3	392	gCg/gTg	8/24	0.167533035722701	1	FACETS	1	0.956	1	1	0.986	1	CLONAL	2	FALSE	0	0.212625506962056	1		547	275	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268785	98268785	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	52	503	0	ENST00000331920.6:c.298A>C	p.Lys100Gln	p.K100Q	ENST00000331920	NM_000264.3	100	Aag/Cag	2/24	0.167533035722701	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	0	0.212625506962056	1		503	342	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250350	110250350	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs768719572	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	79	698	1	ENST00000374672.4:c.325C>A	p.Leu109Ile	p.L109I	ENST00000374672	NM_004235.4	109	Ctc/Atc	3/5	0.167533035722701	1	FACETS	0.885	0.79	0.985	1	0.987	1	CLONAL	3	FALSE	0	0.212625506962056	1		699	250	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797291	135797291	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	24	341	0	ENST00000298552.3:c.578G>T	p.Gly193Val	p.G193V	ENST00000298552	NM_001162426.1	193	gGa/gTa	7/23	0.167533035722701	1	FACETS	0.893	0.703	1	0.893	0.703	1	CLONAL	1	FALSE	0	0.212625506962056	1		341	226	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820237	139820237	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	113	701	0	ENST00000247668.2:c.1391del	p.Asn464ThrfsTer35	p.N464Tfs*35	ENST00000247668	NM_021138.3	464	Aac/ac	11/11	0.167533035722701	1	FACETS	1	0.922	1	1	0.991	1	CLONAL	3	FALSE	0	0.212625506962056	1		701	313	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934141	39934141	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	45	657	0	ENST00000378444.4:c.458C>A	p.Pro153His	p.P153H	ENST00000378444	NM_001123385.1	153	cCt/cAt	4/15	0.212625684210489	1	FACETS	1	0.895	1	1	0.974	1	CLONAL	2	FALSE	0	0.212625506962056	1		657	178	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040914	47040914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	24	759	0	ENST00000377604.3:c.1444G>A	p.Ala482Thr	p.A482T	ENST00000377604	NM_001204468.1	482	Gcc/Acc	14/24	0.212625684210489	1	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	FALSE	0	0.212625506962056	1		759	171	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041687	47041687	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	55	717	1	ENST00000377604.3:c.1912G>T	p.Glu638Ter	p.E638*	ENST00000377604	NM_001204468.1	638	Gag/Tag	17/24	0.212625684210489	1	FACETS	1	0.927	1	1	0.98	1	CLONAL	2	FALSE	0	0.212625506962056	1		718	209	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044600	47044600	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	21	790	1	ENST00000377604.3:c.2097G>T	p.Lys699Asn	p.K699N	ENST00000377604	NM_001204468.1	699	aaG/aaT	18/24	0.212625684210489	1	FACETS	0.929	0.719	1	0.929	0.719	1	CLONAL	1	FALSE	0	0.212625506962056	1		791	190	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429003	47429003	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	18	622	0	ENST00000377045.4:c.1366C>T	p.Arg456Ter	p.R456*	ENST00000377045	NM_001654.4	456	Cga/Tga	13/16	0.212625684210489	1	FACETS	0.78	0.59	1	0.78	0.59	1	CLONAL	1	FALSE	0	0.212625506962056	1		622	194	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429410	47429410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	19	448	1	ENST00000377045.4:c.1538G>A	p.Gly513Asp	p.G513D	ENST00000377045	NM_001654.4	513	gGc/gAc	14/16	0.212625684210489	1	FACETS	1	0.828	1	1	0.828	1	CLONAL	1	FALSE	0	0.212625506962056	1		449	145	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649718	48649718	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	46	692	0	ENST00000376670.3:c.202G>A	p.Ala68Thr	p.A68T	ENST00000376670	NM_002049.3	68	Gcc/Acc	2/6	0.212625684210489	1	FACETS	0.903	0.769	1	1	0.971	1	CLONAL	2	FALSE	0	0.212625506962056	1		692	214	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230767	53230767	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	25	711	0	ENST00000375401.3:c.2026G>T	p.Glu676Ter	p.E676*	ENST00000375401	NM_004187.3	676	Gaa/Taa	14/26	0.212625684210489	1	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	FALSE	0	0.212625506962056	1		711	187	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411034	63411034	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	17	645	0	ENST00000330258.3:c.2133G>T	p.Lys711Asn	p.K711N	ENST00000330258	NM_152424.3	711	aaG/aaT	2/2	0.212625684210489	1	FACETS	1	0.837	1	1	0.837	1	CLONAL	1	FALSE	0	0.212625506962056	1		645	124	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412763	63412763	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	15	582	0	ENST00000330258.3:c.404G>T	p.Gly135Val	p.G135V	ENST00000330258	NM_152424.3	135	gGg/gTg	2/2	0.212625684210489	1	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	FALSE	0	0.212625506962056	1		582	104	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413060	63413060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769613326	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	51	775	1	ENST00000330258.3:c.107C>T	p.Ala36Val	p.A36V	ENST00000330258	NM_152424.3	36	gCg/gTg	2/2	0.212625684210489	1	FACETS	1	0.903	1	1	0.977	1	CLONAL	2	FALSE	0	0.212625506962056	1		776	202	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342108	70342108	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	34	547	0	ENST00000374080.3:c.1160G>T	p.Arg387Ile	p.R387I	ENST00000374080		387	aGa/aTa	8/45	0.212625684210489	1	FACETS	0.836	0.691	0.994	1	0.957	1	CLONAL	2	FALSE	0	0.212625506962056	1		547	171	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342994	70342994	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	27	524	0	ENST00000374080.3:c.1535T>C	p.Val512Ala	p.V512A	ENST00000374080		512	gTc/gCc	11/45	0.212625684210489	1	FACETS	1	0.836	1	1	0.836	1	CLONAL	1	FALSE	0	0.212625506962056	1		524	216	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343525	70343525	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	44	607	0	ENST00000374080.3:c.1699C>T	p.Gln567Ter	p.Q567*	ENST00000374080		567	Cag/Tag	12/45	0.212625684210489	1	FACETS	0.989	0.841	1	1	0.972	1	CLONAL	2	FALSE	0	0.212625506962056	1		607	187	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829757	76829757	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	88	668	0	ENST00000373344.5:c.6284G>T	p.Arg2095Met	p.R2095M	ENST00000373344	NM_000489.3	2095	aGg/aTg	28/35	0.212625684210489	1	FACETS	0.878	0.788	0.971	1	0.988	1	CLONAL	3	FALSE	0	0.212625506962056	1		668	281	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855003	76855003	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	30	650	0	ENST00000373344.5:c.5833G>T	p.Gly1945Ter	p.G1945*	ENST00000373344	NM_000489.3	1945	Gga/Tga	25/35	0.212625684210489	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	FALSE	0	0.212625506962056	1		650	176	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937351	76937351	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	10	504	1	ENST00000373344.5:c.3397G>T	p.Glu1133Ter	p.E1133*	ENST00000373344	NM_000489.3	1133	Gaa/Taa	9/35	0.212625684210489	1	FACETS	0.568	0.386	0.795	0.568	0.386	0.795	SUBCLONAL	1	FALSE	0	0.212625506962056	1		505	148	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938581	76938581	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	33	555	0	ENST00000373344.5:c.2167G>T	p.Glu723Ter	p.E723*	ENST00000373344	NM_000489.3	723	Gag/Tag	9/35	0.212625684210489	1	FACETS	0.771	0.634	0.92	1	0.95	1	CLONAL	2	FALSE	0	0.212625506962056	1		555	180	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939340	76939340	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	50	655	0	ENST00000373344.5:c.1408G>T	p.Asp470Tyr	p.D470Y	ENST00000373344	NM_000489.3	470	Gat/Tat	9/35	0.212625684210489	1	FACETS	1	0.899	1	1	0.977	1	CLONAL	2	FALSE	0	0.212625506962056	1		655	199	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939402	76939402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	45	699	0	ENST00000373344.5:c.1346C>T	p.Pro449Leu	p.P449L	ENST00000373344	NM_000489.3	449	cCt/cTt	9/35	0.212625684210489	1	FACETS	0.833	0.707	0.97	1	0.967	1	CLONAL	2	FALSE	0	0.212625506962056	1		699	227	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611208	100611208	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	31	537	0	ENST00000308731.7:c.1398G>T	p.Lys466Asn	p.K466N	ENST00000308731	NM_000061.2	466	aaG/aaT	15/19	0.212625684210489	1	FACETS	0.819	0.671	0.983	1	0.952	1	CLONAL	2	FALSE	0	0.212625506962056	1		537	159	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611926	100611926	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	44	600	0	ENST00000308731.7:c.1195C>A	p.Pro399Thr	p.P399T	ENST00000308731	NM_000061.2	399	Cca/Aca	14/19	0.212625684210489	1	FACETS	0.841	0.712	0.98	1	0.967	1	CLONAL	2	FALSE	0	0.212625506962056	1		600	220	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171398	123171398	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	66	572	0	ENST00000218089.9:c.310G>A	p.Glu104Lys	p.E104K	ENST00000218089	NM_001042749.1	104	Gaa/Aaa	6/35	0.212625684210489	1	FACETS	1	0.945	1	1	0.986	1	CLONAL	3	FALSE	0	0.212625506962056	1		572	167	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196761	123196761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	23	413	0	ENST00000218089.9:c.1648G>A	p.Ala550Thr	p.A550T	ENST00000218089	NM_001042749.1	550	Gca/Aca	18/35	0.212625684210489	1	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	FALSE	0	0.212625506962056	1		413	177	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210272	123210272	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	48	520	0	ENST00000218089.9:c.2624C>A	p.Thr875Asn	p.T875N	ENST00000218089	NM_001042749.1	875	aCt/aAt	26/35	0.212625684210489	1	FACETS	1	0.872	1	1	0.975	1	CLONAL	2	FALSE	0	0.212625506962056	1		520	198	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123499626	123499626	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	25	579	0	ENST00000371139.4:c.153T>G	p.Ile51Met	p.I51M	ENST00000371139	NM_001114937.2	51	atT/atG	2/4	0.212625684210489	1	FACETS	0.942	0.746	1	0.942	0.746	1	CLONAL	1	FALSE	0	0.212625506962056	1		579	223	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819769	81819769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	42	455	0	ENST00000359376.3:c.175G>A	p.Asp59Asn	p.D59N	ENST00000359376	NM_002661.3	59	Gac/Aac	2/33	0.212625506962056	0	FACETS	0.823	0.696	0.96			1	CLONAL	2	FALSE	0	0.212625506962056	0		455	189	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577499	7577500	+	inframe_insertion,splice_region_variant	In_Frame_Ins	INS	-	-	TGGAGTCTT	novel	NA	P-0030376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	629	473	0	ENST00000269305.4:c.773_781dup	p.Ser260_Ser261insLysAspSer	p.S260_S261insKDS	ENST00000269305	NM_001126112.2	261	agt/aAAGACTCCAgt	7/11	0.78677833999839	3	FACETS	0.913	0.892	0.934			1	CLONAL	3	FALSE	NA	0.784266621290723	3		473	815	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015667	27015667	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	181	461	0	ENST00000335756.4:c.254A>C	p.Asn85Thr	p.N85T	ENST00000335756	NM_001809.3	85	aAt/aCt	3/5	0.654788457141461	3	FACETS	0.842	0.778	0.908	0.281	0.259	0.303	CLONAL	1	FALSE	0	0.784266621290723	3		461	763	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6038825	6038825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368847322	NA	P-0030376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	420	522	2	ENST00000265849.7:c.619G>A	p.Gly207Arg	p.G207R	ENST00000265849	NM_000535.5	207	Gga/Aga	6/15	0.653096171088257	3	FACETS	0.883	0.847	0.92	0.883	0.847	0.92	CLONAL	2	FALSE	1	0.784266621290723	3		524	844	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8501018	8501018	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	258	269	0	ENST00000356435.5:c.1864A>G	p.Ser622Gly	p.S622G	ENST00000356435		622	Agt/Ggt	13/35	0.78677833999839	2	FACETS	0.997	0.961	1	0.997	0.961	1	CLONAL	2	FALSE	0	0.784266621290723	2		269	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763098116	NA	P-0030384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	58	734	0	ENST00000269305.4:c.830G>A	p.Cys277Tyr	p.C277Y	ENST00000269305	NM_001126112.2	277	tGt/tAt	8/11	0.178411583725031	1	FACETS	0.963	0.84	1	1	0.983	1	CLONAL	3	TRUE	0	0.178411583725031	1		734	205	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	44	529	3	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.533	0.446	0.629	0.533	0.446	0.629	SUBCLONAL	1	TRUE	1	0.289326526539984	2		532	571	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	37	341	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.633	0.522	0.757	0.633	0.522	0.757	SUBCLONAL	1	TRUE	1	0.289326526539984	2		341	404	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	73	495	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	0.180735896539409	3	FACETS	1	0.92	1	0.534	0.467	0.605	CLONAL	1	TRUE	1	0.289326526539984	3		497	541	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	223	548	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.180735896539409	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.289326526539984	3		548	744	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	110	484	8	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.289326526539984	2		492	562	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366939	15366939	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	52	548	3	ENST00000263377.2:c.1687del	p.Ser563AlafsTer21	p.S563Afs*21	ENST00000263377	NM_058243.2	563	Agc/gc	9/20	1	2	FACETS	0.493	0.419	0.575	0.493	0.419	0.575	SUBCLONAL	1	TRUE	1	0.289326526539984	2		551	729	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	64	683	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	NA	2	FACETS	1	0.904	1			1	INDETERMINATE	1	TRUE	NA	0.289326526539984	2		683	422	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023904	27023904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1232964733	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	10	89	0	ENST00000324856.7:c.1015del	p.Ala339LeufsTer24	p.A339Lfs*24	ENST00000324856	NM_006015.4	337	tGg/tg	1/20	1	2	FACETS	0.536	0.365	0.749	0.536	0.365	0.749	SUBCLONAL	1	TRUE	1	0.289326526539984	2		89	129	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789591	3789591	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	42	373	1	ENST00000262367.5:c.4268del	p.Pro1423LeufsTer36	p.P1423Lfs*36	ENST00000262367	NM_004380.2	1423	cCt/ct	25/31	1	2	FACETS	0.713	0.596	0.843	0.713	0.596	0.843	SUBCLONAL	1	TRUE	1	0.289326526539984	2		374	407	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	23	447	1	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	0.289326526539984	1	FACETS	0.38	0.296	0.477	0.38	0.296	0.477	SUBCLONAL	1	TRUE	0	0.289326526539984	1		448	358	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	284	597	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.289326526539984	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.289326526539984	3		597	1097	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673750	176673750	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	38	324	0	ENST00000439151.2:c.4455del	p.Val1486Ter	p.V1486*	ENST00000439151	NM_022455.4	1484	Aaa/aa	10/23	1	2	FACETS	0.519	0.429	0.62	0.519	0.429	0.62	SUBCLONAL	1	TRUE	1	0.289326526539984	2		324	506	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	464400	464400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	94	352	0	ENST00000399788.2:c.794G>A	p.Arg265Lys	p.R265K	ENST00000399788	NM_001042603.1	265	aGa/aAa	7/28	0.180735896539409	3	FACETS	1	0.967	1	0.613	0.546	0.684	CLONAL	1	TRUE	1	0.289326526539984	3		352	607	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007332	143007332	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	41	335	0	ENST00000262992.4:c.2452del	p.Arg818GlufsTer4	p.R818Efs*4	ENST00000262992	NM_001101669.1	818	Aga/ga	22/24	1	2	FACETS	0.574	0.478	0.681	0.574	0.478	0.681	SUBCLONAL	1	TRUE	1	0.289326526539984	2		335	494	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687472	37687472	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	29	202	0	ENST00000447079.4:c.4382del	p.Gly1461AlafsTer38	p.G1461Afs*38	ENST00000447079	NM_015083.1	1459	tGg/tg	14/14	1	2	FACETS	0.649	0.522	0.793	0.649	0.522	0.793	SUBCLONAL	1	TRUE	1	0.289326526539984	2		202	309	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870205	155870205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs563231684	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	64	430	0	ENST00000368323.3:c.634C>T	p.Arg212Trp	p.R212W	ENST00000368323	NM_006912.5	212	Cgg/Tgg	6/6	0.180735896539409	3	FACETS	0.758	0.656	0.869	0.379	0.328	0.435	SUBCLONAL	1	TRUE	1	0.289326526539984	3		430	668	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041242	112041242	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	46	234	0	ENST00000368678.4:c.13C>T	p.Gln5Ter	p.Q5*	ENST00000368678		5	Caa/Taa	3/13	0.197845690000536	3	FACETS	0.963	0.813	1	0.481	0.406	0.564	CLONAL	1	TRUE	1	0.289326526539984	3		234	378	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244133	133244133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759398253	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	56	383	0	ENST00000320574.5:c.2275C>T	p.Arg759Cys	p.R759C	ENST00000320574	NM_006231.2	759	Cgt/Tgt	20/49	NA	2	FACETS	0.795	0.682	0.918			1	INDETERMINATE	1	TRUE	NA	0.289326526539984	2		383	487	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799050	42799050	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	73	613	1	ENST00000575354.2:c.4534C>T	p.Arg1512Cys	p.R1512C	ENST00000575354	NM_015125.3	1512	Cgt/Tgt	20/20	0.289326526539984	3	FACETS	0.635	0.554	0.723	0.318	0.277	0.362	SUBCLONAL	1	TRUE	1	0.289326526539984	3		614	909	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974378	93974378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753621830	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	79	390	0	ENST00000369303.4:c.1676C>T	p.Ala559Val	p.A559V	ENST00000369303	NM_004440.3	559	gCt/gTt	8/17	0.197845690000536	3	FACETS	0.885	0.778	1	0.443	0.389	0.5	CLONAL	1	TRUE	1	0.289326526539984	3		390	706	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359681	40359681	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148568485	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	69	487	0	ENST00000293328.3:c.1972G>A	p.Asp658Asn	p.D658N	ENST00000293328	NM_012448.3	658	Gac/Aac	16/19	1	2	FACETS	0.698	0.608	0.796	0.698	0.608	0.796	SUBCLONAL	1	TRUE	1	0.289326526539984	2		487	683	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183632	185183632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746343770	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	58	356	0	ENST00000265026.3:c.1486C>T	p.Arg496Trp	p.R496W	ENST00000265026	NM_004721.4	496	Cgg/Tgg	9/14	0.289326526539984	3	FACETS	0.825	0.709	0.952	0.413	0.354	0.476	CLONAL	1	TRUE	1	0.289326526539984	3		356	556	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087462	27087463	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	73	489	0	ENST00000324856.7:c.2037dup	p.Pro680SerfsTer137	p.P680Sfs*137	ENST00000324856	NM_006015.4	679	tct/tcTt	5/20	1	2	FACETS	0.71	0.62	0.806	0.71	0.62	0.806	SUBCLONAL	1	TRUE	1	0.289326526539984	2		489	711	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426640	49426640	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555188430	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	53	366	0	ENST00000301067.7:c.11848C>T	p.Gln3950Ter	p.Q3950*	ENST00000301067	NM_003482.3	3950	Cag/Tag	39/54	0.197845690000536	3	FACETS	0.858	0.732	0.995	0.429	0.366	0.498	CLONAL	1	TRUE	1	0.289326526539984	3		366	489	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465526	99465526	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	60	430	0	ENST00000268035.6:c.2351A>G	p.Asn784Ser	p.N784S	ENST00000268035	NM_000875.3	784	aAc/aGc	11/21	1	2	FACETS	0.813	0.701	0.935	0.813	0.701	0.935	CLONAL	1	TRUE	1	0.289326526539984	2		430	510	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222334	2222334	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	54	527	0	ENST00000326181.6:c.622del	p.Arg208GlufsTer38	p.R208Efs*38	ENST00000326181	NM_032271.2	206	gaC/ga	8/21	1	2	FACETS	0.698	0.596	0.809	0.698	0.596	0.809	SUBCLONAL	1	TRUE	1	0.289326526539984	2		527	535	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640593	3640593	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	56	647	2	ENST00000294008.3:c.3046C>A	p.Leu1016Met	p.L1016M	ENST00000294008	NM_032444.2	1016	Ctg/Atg	12/15	1	2	FACETS	0.572	0.489	0.662	0.572	0.489	0.662	SUBCLONAL	1	TRUE	1	0.289326526539984	2		649	677	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3929831	3929831	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs77109850	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	30	321	0	ENST00000262367.5:c.85+2T>C		p.X29_splice	ENST00000262367	NM_004380.2	29			1	2	FACETS	0.543	0.437	0.662	0.543	0.437	0.662	SUBCLONAL	1	TRUE	1	0.289326526539984	2		321	382	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637688	23637688	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	45	445	0	ENST00000261584.4:c.2617A>G	p.Ser873Gly	p.S873G	ENST00000261584	NM_024675.3	873	Agt/Ggt	7/13	1	2	FACETS	0.468	0.392	0.552	0.468	0.392	0.552	SUBCLONAL	1	TRUE	1	0.289326526539984	2		445	665	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991376	72991376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	68	449	0	ENST00000268489.5:c.2669del	p.Gly890AspfsTer13	p.G890Dfs*13	ENST00000268489	NM_006885.3	890	gGa/ga	2/10	1	2	FACETS	0.88	0.767	1	0.88	0.767	1	CLONAL	1	TRUE	1	0.289326526539984	2		449	534	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346985	89346985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755371317	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	44	327	0	ENST00000301030.4:c.5965G>A	p.Glu1989Lys	p.E1989K	ENST00000301030	NM_001256183.1	1989	Gag/Aag	9/13	1	2	FACETS	0.911	0.767	1	0.911	0.767	1	CLONAL	1	TRUE	1	0.289326526539984	2		327	334	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211614	5211614	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	30	326	0	ENST00000357368.4:c.5221A>G	p.Ile1741Val	p.I1741V	ENST00000357368	NM_002850.3	1741	Att/Gtt	33/38	1	2	FACETS	0.571	0.46	0.697	0.571	0.46	0.697	SUBCLONAL	1	TRUE	1	0.289326526539984	2		326	363	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52693359	52693359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	68	461	1	ENST00000322088.6:c.10G>A	p.Ala4Thr	p.A4T	ENST00000322088	NM_014225.5	4	Gcc/Acc	1/15	0.289326526539984	3	FACETS	0.813	0.707	0.928	0.406	0.353	0.464	CLONAL	1	TRUE	1	0.289326526539984	3		462	662	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022444	+	inframe_deletion	In_Frame_Del	DEL	GGG	GGG	-	novel	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	14	214	0	ENST00000375687.4:c.1932_1934del	p.Gly646del	p.G646del	ENST00000375687	NM_015338.5	643	GGG/-	13/13	1	2	FACETS	0.509	0.369	0.678	0.509	0.369	0.678	SUBCLONAL	1	TRUE	1	0.289326526539984	2		214	190	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008572	70008572	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	49	276	0	ENST00000394351.3:c.858+1G>A		p.X286_splice	ENST00000394351	NM_000248.3	286			1	2	FACETS	0.822	0.698	0.958	0.822	0.698	0.958	CLONAL	1	TRUE	1	0.289326526539984	2		276	412	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968672	55968672	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540277686	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	42	379	0	ENST00000263923.4:c.1991G>A	p.Arg664His	p.R664H	ENST00000263923	NM_002253.2	664	cGt/cAt	14/30	1	2	FACETS	0.735	0.615	0.868	0.735	0.615	0.868	SUBCLONAL	1	TRUE	1	0.289326526539984	2		379	395	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235304	235304	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	53	322	0	ENST00000264932.6:c.1111del	p.Leu371TyrfsTer18	p.L371Yfs*18	ENST00000264932	NM_004168.2	370	caC/ca	9/15	1	2	FACETS	0.947	0.81	1	0.947	0.81	1	CLONAL	1	TRUE	1	0.289326526539984	2		322	387	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251128	251128	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs979815942	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	13	165	0	ENST00000264932.6:c.1573G>A	p.Val525Met	p.V525M	ENST00000264932	NM_004168.2	525	Gtg/Atg	12/15	1	2	FACETS	0.396	0.282	0.534	0.396	0.282	0.534	SUBCLONAL	1	TRUE	1	0.289326526539984	2		165	227	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410996	31410996	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	45	374	0	ENST00000344624.3:c.3526-2A>G		p.X1176_splice	ENST00000344624		1176			1	2	FACETS	0.564	0.473	0.664	0.564	0.473	0.664	SUBCLONAL	1	TRUE	1	0.289326526539984	2		374	552	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181766	56181766	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	51	293	0	ENST00000399503.3:c.3991del	p.Val1331TrpfsTer5	p.V1331Wfs*5	ENST00000399503	NM_005921.1	1330	tcG/tc	17/20	0.180735896539409	3	FACETS	0.965	0.822	1	0.483	0.411	0.561	CLONAL	1	TRUE	1	0.289326526539984	3		293	418	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969131	93969131	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs200277966	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	41	275	0	ENST00000369303.4:c.1865A>G	p.His622Arg	p.H622R	ENST00000369303	NM_004440.3	622	cAt/cGt	10/17	0.197845690000536	3	FACETS	0.619	0.515	0.735	0.31	0.257	0.368	SUBCLONAL	1	TRUE	1	0.289326526539984	3		275	524	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945707	151945707	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0030391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	50	358	0	ENST00000262189.6:c.1814-2A>G		p.X605_splice	ENST00000262189	NM_170606.2	605			1	2	FACETS	0.534	0.452	0.624	0.534	0.452	0.624	SUBCLONAL	1	TRUE	1	0.289326526539984	2		358	647	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0030444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	113	696	1	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.3	1	FACETS	0.811	0.729	0.897	0.811	0.729	0.897	CLONAL	1	TRUE	0	0.3	1		697	790	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612095	43612095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	50	467	0	ENST00000355710.3:c.2200G>A	p.Glu734Lys	p.E734K	ENST00000355710	NM_020975.4	734	Gaa/Aaa	12/20	0.192977949333069	2	FACETS	0.43	0.363	0.503	0.215	0.181	0.252	SUBCLONAL	1	TRUE	0	0.3	2		467	776	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995477	68995477	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	99	489	0	ENST00000288368.4:c.1881G>T	p.Met627Ile	p.M627I	ENST00000288368	NM_024870.2	627	atG/atT	18/40	0.192977949333069	2	FACETS	0.685	0.61	0.764	0.342	0.305	0.382	SUBCLONAL	1	TRUE	0	0.3	2		489	964	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808903	3808904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0030468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	94	647	1	ENST00000262367.5:c.3320_3321del	p.Glu1107ValfsTer20	p.E1107Vfs*20	ENST00000262367	NM_004380.2	1107	gAG/g	17/31	1	2	FACETS	0.907	0.806	1	0.907	0.806	1	CLONAL	1	TRUE	1	0.253450787383375	2		648	818	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796603	42796603	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	736	573	1	ENST00000575354.2:c.3160C>T	p.Gln1054Ter	p.Q1054*	ENST00000575354	NM_015125.3	1054	Cag/Tag	13/20	0.692355609439283	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.692355609439283	3		574	881	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551457	150551457	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	351	775	0	ENST00000369026.2:c.550C>G	p.Arg184Gly	p.R184G	ENST00000369026	NM_021960.4	184	Cgg/Ggg	1/3	0.692355609439283	3	FACETS	1	0.949	1	0.501	0.474	0.529	CLONAL	1	TRUE	1	0.692355609439283	3		775	1361	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593702	55593702	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	149	494	0	ENST00000288135.5:c.1768A>C	p.Ser590Arg	p.S590R	ENST00000288135	NM_000222.2	590	Agt/Cgt	11/21	0.692355609439283	3	FACETS	1	0.972	1	0.564	0.518	0.611	CLONAL	1	TRUE	1	0.692355609439283	3		494	514	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0030479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	447	446	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.537730693000437	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.537730693000437	3		446	901	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0030479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	795	694	3	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.537730693000437	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.537730693000437	2		697	1452	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880962	134880962	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1290751781	NA	P-0030479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	457	527	1	ENST00000398015.3:c.1525C>T	p.Arg509Cys	p.R509C	ENST00000398015	NM_004441.4	509	Cgc/Tgc	7/16	0.537730693000437	3	FACETS	0.988	0.946	1	0.988	0.946	1	CLONAL	2	TRUE	1	0.537730693000437	3		528	1092	SUCCESS
APC	324	MSKCC	GRCh37	5	112154992	112154992	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554080106	NA	P-0030479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	565	585	3	ENST00000257430.4:c.1263G>A	p.Trp421Ter	p.W421*	ENST00000257430	NM_000038.5	421	tgG/tgA	10/16	0.537730693000437	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.537730693000437	2		588	990	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205093	128205093	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1594	435	716	2	ENST00000341105.2:c.348G>A	p.Trp116Ter	p.W116*	ENST00000341105	NM_032638.4	116	tgG/tgA	3/6	0.537730693000437	3	FACETS	1	0.96	1	0.506	0.48	0.532	CLONAL	1	TRUE	1	0.537730693000437	3		718	2029	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473708	67473708	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	616	551	5	ENST00000327367.4:c.788C>A	p.Pro263His	p.P263H	ENST00000327367	NM_005902.3	263	cCc/cAc	6/9	0.537730693000437	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.537730693000437	2		556	1095	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374930	45374930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	224	582	0	ENST00000262160.6:c.913C>T	p.Pro305Ser	p.P305S	ENST00000262160	NM_005901.5	305	Cca/Tca	8/11	1	2	FACETS	0.783	0.736	0.831	1	0.993	1	SUBCLONAL	2	TRUE	1	0.537730693000437	2		582	532	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411255	63411256	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1555933313	NA	P-0030479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	586	351	1	ENST00000330258.3:c.1911_1912del	p.Glu637AspfsTer69	p.E637Dfs*69	ENST00000330258	NM_152424.3	637	gaGAct/gact	2/2	0.518266980645231	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.537730693000437	2		352	951	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0030506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	89	446	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.174786423551531	3	FACETS	0.801	0.711	0.898	0.401	0.355	0.449	INDETERMINATE	1	TRUE	1	0.398995876507058	3		446	668	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0030506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	114	555	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.159427221151929	2	FACETS	0.788	0.71	0.871	0.394	0.355	0.436	INDETERMINATE	1	TRUE	0	0.398995876507058	2		555	725	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864068	97864068	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1293282237	NA	P-0030506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	151	371	0	ENST00000289081.3:c.1598G>A	p.Trp533Ter	p.W533*	ENST00000289081	NM_000136.2	533	tGg/tAg	15/15	0.398995876507058	1	FACETS	0.838	0.768	0.911	0.838	0.768	0.911	CLONAL	1	TRUE	0	0.398995876507058	1		371	723	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	76	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.975	0.872	1	0.975	0.872	1	CLONAL	1	TRUE	1	0.771869382151068	2		215	202	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56477621	56477621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	632	473	0	ENST00000267101.3:c.169G>A	p.Glu57Lys	p.E57K	ENST00000267101	NM_001982.3	57	Gag/Aag	2/28	0.771869382151068	2	FACETS	0.999	0.975	1	0.999	0.975	1	CLONAL	2	TRUE	0	0.771869382151068	2		473	820	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0030508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	227	563	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.964	0.905	1	0.964	0.905	1	CLONAL	1	TRUE	1	0.771869382151068	2		563	610	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0030508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	180	433	3	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.771869382151068	2		436	426	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781467	135781467	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203537	NA	P-0030508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	249	367	0	ENST00000298552.3:c.1498C>T	p.Arg500Ter	p.R500*	ENST00000298552	NM_001162426.1	500	Cga/Tga	15/23	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.771869382151068	2		367	634	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931471	131931471	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753002904	NA	P-0030508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	247	352	2	ENST00000265335.6:c.2176C>T	p.Arg726Cys	p.R726C	ENST00000265335		726	Cgt/Tgt	13/25	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.771869382151068	2		354	617	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447106	187447106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	257	518	0	ENST00000232014.4:c.1087C>T	p.Pro363Ser	p.P363S	ENST00000232014	NM_001130845.1	363	Cca/Tca	5/10	1	2	FACETS	0.965	0.909	1	0.965	0.909	1	CLONAL	1	TRUE	1	0.771869382151068	2		518	690	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872210	45872210	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	317	507	0	ENST00000391945.4:c.224G>A	p.Arg75Lys	p.R75K	ENST00000391945	NM_000400.3	75	aGa/aAa	4/23	1	2	FACETS	0.941	0.891	0.991	0.941	0.891	0.991	CLONAL	1	TRUE	1	0.771869382151068	2		507	873	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349149	89349149	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	546	785	2	ENST00000301030.4:c.3801G>C	p.Glu1267Asp	p.E1267D	ENST00000301030	NM_001256183.1	1267	gaG/gaC	9/13	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.771869382151068	2		787	1307	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864663	68864663	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773560075	NA	P-0030508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	98	152	0	ENST00000288368.4:c.34G>A	p.Glu12Lys	p.E12K	ENST00000288368	NM_024870.2	12	Gag/Aag	1/40	1	2	FACETS	0.992	0.9	1	0.992	0.9	1	CLONAL	1	TRUE	1	0.771869382151068	2		152	256	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443864	52443864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	299	548	0	ENST00000460680.1:c.31G>A	p.Asp11Asn	p.D11N	ENST00000460680	NM_004656.3	11	Gac/Aac	1/17	1	2	FACETS	0.909	0.859	0.96	0.909	0.859	0.96	CLONAL	1	TRUE	1	0.771869382151068	2		548	852	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056171	27056172	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	256	447	0	ENST00000324856.7:c.1168dup	p.Met390AsnfsTer10	p.M390Nfs*10	ENST00000324856	NM_006015.4	389	-/A	2/20	1	2	FACETS	0.907	0.854	0.962	0.907	0.854	0.962	CLONAL	1	TRUE	1	0.771869382151068	2		447	731	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737043	162737043	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	241	377	1	ENST00000367921.3:c.1187G>A	p.Ser396Asn	p.S396N	ENST00000367921	NM_006182.2	396	aGc/aAc	11/18	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.771869382151068	2		378	610	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115983	8115984	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0030508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	122	238	0	ENST00000346208.3:c.1330_1331dup	p.Ter444TyrfsTer32	p.*444Yfs*32	ENST00000346208		443	-/TA	6/6	1	2	FACETS	0.843	0.77	0.918	0.843	0.77	0.918	CLONAL	1	TRUE	1	0.771869382151068	2		238	375	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186598	108186598	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	162	264	0	ENST00000278616.4:c.6055T>C	p.Tyr2019His	p.Y2019H	ENST00000278616	NM_000051.3	2019	Tat/Cat	41/63	1	2	FACETS	0.963	0.892	1	0.963	0.892	1	CLONAL	1	TRUE	1	0.771869382151068	2		264	436	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061270	38061289	+	frameshift_variant	Frame_Shift_Del	DEL	TTGCCCGGCTTGTCCGGGGA	TTGCCCGGCTTGTCCGGGGA	-	novel	NA	P-0030508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	333	581	0	ENST00000250448.2:c.700_719del	p.Ser234GlyfsTer52	p.S234Gfs*52	ENST00000250448	NM_004496.3	234	TCCCCGGACAAGCCGGGCAAg/g	2/2	1	2	FACETS	0.958	0.908	1	0.958	0.908	1	CLONAL	1	TRUE	1	0.771869382151068	2		581	901	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003760	45003760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763258605	NA	P-0030508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	209	319	0	ENST00000558401.1:c.16G>A	p.Ala6Thr	p.A6T	ENST00000558401	NM_004048.2	6	Gcc/Acc	1/4	1	2	FACETS	0.979	0.916	1	0.979	0.916	1	CLONAL	1	TRUE	1	0.771869382151068	2		319	553	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134241	11134241	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	335	529	0	ENST00000358026.2:c.2907C>G	p.His969Gln	p.H969Q	ENST00000358026	NM_001128849.1	969	caC/caG	20/36	1	2	FACETS	0.975	0.926	1	0.975	0.926	1	CLONAL	1	TRUE	1	0.771869382151068	2		529	890	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665199	138665210	+	inframe_deletion	In_Frame_Del	DEL	CTCGCCGCCGCC	CTCGCCGCCGCC	-	novel	NA	P-0030508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	329	645	0	ENST00000330315.3:c.355_366del	p.Gly119_Glu122del	p.G119_E122del	ENST00000330315	NM_023067.3	119	GGCGGCGGCGAG/-	1/1	1	2	FACETS	0.925	0.876	0.974	0.925	0.876	0.974	CLONAL	1	TRUE	1	0.771869382151068	2		645	922	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652081	36652106	+	frameshift_variant	Frame_Shift_Del	DEL	TGCGGGGCCTTGGCCTGCCCAAGCTC	TGCGGGGCCTTGGCCTGCCCAAGCTC	-	novel	NA	P-0030508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	265	596	0	ENST00000244741.5:c.204_229del	p.Arg69ProfsTer11	p.R69Pfs*11	ENST00000244741	NM_000389.4	68	gTGCGGGGCCTTGGCCTGCCCAAGCTC/g	2/3	1	2	FACETS	0.779	0.731	0.827	0.779	0.731	0.827	SUBCLONAL	1	TRUE	1	0.771869382151068	2		596	882	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002759	37002759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	216	315	0	ENST00000358127.4:c.490G>A	p.Val164Met	p.V164M	ENST00000358127	NM_001280556.1	164	Gtg/Atg	5/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.771869382151068	2		315	513	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945217	44945217	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	274	208	0	ENST00000377967.4:c.3541T>C	p.Cys1181Arg	p.C1181R	ENST00000377967	NM_021140.2	1181	Tgt/Cgt	24/29	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.771869382151068	1		208	354	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0030523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	52	446	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.3	1	FACETS	0.648	0.551	0.755	0.648	0.551	0.755	SUBCLONAL	1	TRUE	0	0.21	1		446	684	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970991	21970991	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	54	495	0	ENST00000304494.5:c.367del	p.His123IlefsTer23	p.H123Ifs*23	ENST00000304494	NM_000077.4	123	Cat/at	2/3	0.3	1	FACETS	0.755	0.644	0.876	0.755	0.644	0.876	SUBCLONAL	1	TRUE	0	0.21	1		495	610	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249348	110249348	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	133	973	0	ENST00000374672.4:c.1225A>C	p.Lys409Gln	p.K409Q	ENST00000374672	NM_004235.4	409	Aag/Cag	4/5	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.21	2		973	1246	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975681	26975681	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	56	494	0	ENST00000381527.3:c.1189C>T	p.Gln397Ter	p.Q397*	ENST00000381527	NM_001260.1	397	Cag/Tag	12/13	1	2	FACETS	0.788	0.674	0.912	0.788	0.674	0.912	CLONAL	1	TRUE	1	0.21	2		494	677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577586	7577593	+	frameshift_variant	Frame_Shift_Del	DEL	ATGGTGGT	ATGGTGGT	-	novel	NA	P-0030523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	56	614	0	ENST00000269305.4:c.688_695del	p.Thr230ProfsTer7	p.T230Pfs*7	ENST00000269305	NM_001126112.2	230	ACCACCATc/c	7/11	0.3	1	FACETS	0.703	0.601	0.814	0.703	0.601	0.814	SUBCLONAL	1	TRUE	0	0.21	1		614	679	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898710	134898710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1559863812	NA	P-0030523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	37	324	0	ENST00000398015.3:c.1768G>A	p.Gly590Arg	p.G590R	ENST00000398015	NM_004441.4	590	Ggg/Agg	10/16	1	2	FACETS	0.845	0.697	1	0.845	0.697	1	CLONAL	1	TRUE	1	0.21	2		324	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0030539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	571	633	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.663903696096349	2	FACETS	0.999	0.971	1	0.999	0.971	1	CLONAL	2	TRUE	0	0.704896776456319	2		633	811	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36931999	36931999	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	61	500	1	ENST00000361632.4:c.2470G>A	p.Gly824Arg	p.G824R	ENST00000361632		824	Ggg/Agg	16/16	0.331504538333353	1	FACETS	0.158	0.136	0.182	0.158	0.136	0.182	INDETERMINATE	1	TRUE	0	0.704896776456319	1		501	709	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444432	49444432	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	169	596	1	ENST00000301067.7:c.2939C>T	p.Thr980Ile	p.T980I	ENST00000301067	NM_003482.3	980	aCa/aTa	11/54	0.445031725117393	2	FACETS	0.541	0.497	0.586	0.27	0.248	0.293	SUBCLONAL	1	TRUE	0	0.704896776456319	2		597	887	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863687	68863687	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1427872591	NA	P-0030539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	129	296	1	ENST00000261769.5:c.2426A>G	p.Asn809Ser	p.N809S	ENST00000261769	NM_004360.3	809	aAt/aGt	15/16	0.704896776456319	1	FACETS	0.531	0.485	0.579	0.531	0.485	0.579	SUBCLONAL	1	TRUE	0	0.704896776456319	1		297	446	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981996	70981996	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	121	694	0	ENST00000276594.2:c.100C>A	p.Pro34Thr	p.P34T	ENST00000276594	NM_024504.3	34	Ccg/Acg	2/8	0.620507544033354	4	FACETS	0.451	0.406	0.499	0.15	0.135	0.167	SUBCLONAL	1	TRUE	1	0.704896776456319	4		694	1298	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	88	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.637917286051547	2		215	250	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268448	142268448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564283952	NA	P-0030547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	109	355	0	ENST00000350721.4:c.3044G>A	p.Arg1015Gln	p.R1015Q	ENST00000350721	NM_001184.3	1015	cGa/cAa	15/47	1	2	FACETS	0.814	0.736	0.895	0.814	0.736	0.895	CLONAL	1	TRUE	1	0.637917286051547	2		355	420	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103828	47103828	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs976581260	NA	P-0030547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	109	304	0	ENST00000409792.3:c.6118C>T	p.Arg2040Ter	p.R2040*	ENST00000409792	NM_014159.6	2040	Cga/Tga	14/21	1	2	FACETS	0.863	0.781	0.948	0.863	0.781	0.948	CLONAL	1	TRUE	1	0.637917286051547	2		304	396	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244878	46244878	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	205	495	0	ENST00000334344.6:c.2973del	p.Ser992LeufsTer18	p.S992Lfs*18	ENST00000334344	NM_152641.2	991	tCc/tc	15/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.637917286051547	2		495	613	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916881	178916881	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	223	528	0	ENST00000263967.3:c.268T>C	p.Cys90Arg	p.C90R	ENST00000263967	NM_006218.2	90	Tgt/Cgt	2/21	1	2	FACETS	0.975	0.912	1	0.975	0.912	1	CLONAL	1	TRUE	1	0.637917286051547	2		528	717	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0030558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	122	583	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.92	0.835	1	0.92	0.835	1	CLONAL	1	TRUE	1	0.476312195579993	2		583	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0030558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	179	509	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.476312195579993	1	FACETS	0.958	0.888	1	0.958	0.888	1	CLONAL	1	TRUE	0	0.476312195579993	1		509	598	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44733226	44733226	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	77	145	0	ENST00000377967.4:c.218T>C	p.Leu73Pro	p.L73P	ENST00000377967	NM_021140.2	73	cTg/cCg	2/29	1	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.476312195579993	1		145	177	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0030586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	195	279	0	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	0.489315657066153	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.489315657066153	2		279	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577552	+	frameshift_variant	Frame_Shift_Del	DEL	TGCCGCCC	TGCCGCCC	-	novel	NA	P-0030586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	347	525	0	ENST00000269305.4:c.729_736del	p.Met243IlefsTer18	p.M243Ifs*18	ENST00000269305	NM_001126112.2	243	atGGGCGGCAtg/attg	7/11	0.489315657066153	2	FACETS	0.923	0.88	0.967	0.923	0.88	0.967	CLONAL	2	TRUE	0	0.489315657066153	2		525	768	SUCCESS
ALK	238	MSKCC	GRCh37	2	29448393	29448393	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	353	733	0	ENST00000389048.3:c.3106A>G	p.Ile1036Val	p.I1036V	ENST00000389048	NM_004304.4	1036	Atc/Gtc	19/29	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.489315657066153	2		733	1296	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0030587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	248	633	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.348858778008306	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.370977578226961	2		633	632	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493443	56493443	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	61	389	0	ENST00000267101.3:c.2851G>C	p.Asp951His	p.D951H	ENST00000267101	NM_001982.3	951	Gat/Cat	24/28	0.263607331668747	3	FACETS	0.71	0.613	0.816	0.355	0.306	0.408	SUBCLONAL	1	TRUE	1	0.370977578226961	3		389	549	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176153826	176153826	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	25	259	0	ENST00000367669.3:c.410C>T	p.Pro137Leu	p.P137L	ENST00000367669	NM_022457.5	137	cCc/cTc	2/20	0.235176389745849	4	FACETS	0.398	0.313	0.497	0.199	0.156	0.249	SUBCLONAL	1	TRUE	2	0.370977578226961	4		259	464	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104352409	104352409	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	42	566	0	ENST00000369902.3:c.525G>T	p.Gln175His	p.Q175H	ENST00000369902	NM_016169.3	175	caG/caT	4/12	0.231731534652597	3	FACETS	0.43	0.358	0.51	0.215	0.179	0.255	SUBCLONAL	1	TRUE	1	0.370977578226961	3		566	624	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3824635	3824635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	67	424	0	ENST00000262367.5:c.2218G>A	p.Gly740Arg	p.G740R	ENST00000262367	NM_004380.2	740	Gga/Aga	12/31	0.370977578226961	3	FACETS	0.671	0.583	0.767	0.336	0.291	0.384	SUBCLONAL	1	TRUE	1	0.370977578226961	3		424	638	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216124	7216124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754267121	NA	P-0030587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	29	344	0	ENST00000380728.2:c.935G>A	p.Arg312Gln	p.R312Q	ENST00000380728		312	cGg/cAg	11/11	0.348858778008306	2	FACETS	0.415	0.333	0.508	0.207	0.166	0.254	SUBCLONAL	1	TRUE	0	0.370977578226961	2		344	377	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540295	187540295	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	40	440	0	ENST00000441802.2:c.7445T>C	p.Val2482Ala	p.V2482A	ENST00000441802	NM_005245.3	2482	gTa/gCa	10/27	0.291363047099752	2	FACETS	0.446	0.37	0.53	0.223	0.185	0.265	SUBCLONAL	1	TRUE	0	0.370977578226961	2		440	484	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342796	87342796	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	170	444	0	ENST00000277120.3:c.1081C>G	p.Leu361Val	p.L361V	ENST00000277120		361	Cta/Gta	9/19	0.348858778008306	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.370977578226961	2		444	449	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0030621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	185	512	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.318006088589804	5	FACETS	0.917	0.85	0.985	0.917	0.85	0.985	CLONAL	3	TRUE	2	0.318006088589804	5		512	625	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169853	32169853	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs751390609	NA	P-0030621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	203	547	0	ENST00000375023.3:c.3755C>T	p.Thr1252Ile	p.T1252I	ENST00000375023	NM_004557.3	1252	aCt/aTt	21/30	0.318006088589804	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.318006088589804	4		547	805	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579442	7579442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	228	721	0	ENST00000269305.4:c.245del	p.Pro82ArgfsTer41	p.P82Rfs*41	ENST00000269305	NM_001126112.2	82	cCg/cg	4/11	0.318006088589804	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.318006088589804	2		721	698	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054416	42054416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	78	395	0	ENST00000219905.7:c.7600G>A	p.Gly2534Arg	p.G2534R	ENST00000219905	NM_001164273.1	2534	Gga/Aga	22/24	0.318006088589804	2	FACETS	1	0.945	1	0.561	0.495	0.632	CLONAL	1	TRUE	0	0.318006088589804	2		395	437	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0030638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	212	683	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	0.454305716121303	2		683	752	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519922	NA	P-0030638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	250	568	0	ENST00000397062.3:c.235G>A	p.Glu79Lys	p.E79K	ENST00000397062	NM_006164.4	79	Gag/Aag	2/5	0.454305716121303	1	FACETS	0.764	0.721	0.806	1	0.994	1	SUBCLONAL	2	TRUE	0	0.454305716121303	1		568	557	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225060	NA	P-0030638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	128	444	0	ENST00000263967.3:c.311C>T	p.Pro104Leu	p.P104L	ENST00000263967	NM_006218.2	104	cCa/cTa	2/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.454305716121303	2		444	458	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692964	89692964	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs786204934	NA	P-0030638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	179	484	0	ENST00000371953.3:c.448G>T	p.Glu150Ter	p.E150*	ENST00000371953	NM_000314.4	150	Gag/Tag	5/9	0.454305716121303	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.454305716121303	3		484	458	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105512	27105512	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0030638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	57	306	0	ENST00000324856.7:c.5125-2A>C		p.X1709_splice	ENST00000324856	NM_006015.4	1709			1	2	FACETS	0.736	0.635	0.845	0.736	0.635	0.845	SUBCLONAL	1	TRUE	1	0.454305716121303	2		306	341	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797429	45797429	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151316420	NA	P-0030638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	230	529	0	ENST00000450313.1:c.1090C>T	p.Arg364Cys	p.R364C	ENST00000450313	NM_012222.2	364	Cgc/Tgc	12/16	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.454305716121303	2		529	990	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941230	36941230	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	210	622	0	ENST00000361632.4:c.109C>T	p.His37Tyr	p.H37Y	ENST00000361632		37	Cac/Tac	3/16	1	2	FACETS	0.936	0.869	1	0.936	0.869	1	CLONAL	1	TRUE	1	0.454305716121303	2		622	988	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692967	89692968	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0030638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	69	483	2	ENST00000371953.3:c.451_452delinsTT	p.Ala151Phe	p.A151F	ENST00000371953	NM_000314.4	151	GCc/TTc	5/9	0.454305716121303	3	FACETS	0.823	0.719	0.935	0.411	0.359	0.468	CLONAL	1	TRUE	1	0.454305716121303	3		485	453	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948658	71948658	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	391	558	0	ENST00000298229.2:c.3370del	p.Leu1124CysfsTer7	p.L1124Cfs*7	ENST00000298229	NM_001567.3	1124	Ctg/tg	26/28	0.454305716121303	2	FACETS	0.997	0.953	1	0.997	0.953	1	CLONAL	2	TRUE	0	0.454305716121303	2		558	863	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650629	67650648	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TACTCCATCCTTTCTCTAGG	TACTCCATCCTTTCTCTAGG	-	novel	NA	P-0030638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	26	221	0	ENST00000264010.4:c.953-14_958del		p.X318_splice	ENST00000264010	NM_006565.3	318		5/12	1	2	FACETS	0.302	0.239	0.374	0.302	0.239	0.374	SUBCLONAL	1	TRUE	1	0.454305716121303	2		221	379	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589604	67589605	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCAAGA	novel	NA	P-0030638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	61	307	0	ENST00000274335.5:c.1368_1373dup	p.Gln457_Glu458insAspGln	p.Q457_E458insDQ	ENST00000274335		456	ttt/ttTCAAGAt	10/15	1	2	FACETS	0.872	0.758	0.994	0.872	0.758	0.994	CLONAL	1	TRUE	1	0.454305716121303	2		307	308	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs786202525	NA	P-0030645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	111	508	1	ENST00000269305.4:c.532del	p.His178ThrfsTer69	p.H178Tfs*69	ENST00000269305	NM_001126112.2	178	Cac/ac	5/11	0.31235160656553	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.31235160656553	1		509	536	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943658	9943658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	70	560	1	ENST00000330684.3:c.1283C>T	p.Thr428Met	p.T428M	ENST00000330684	NM_001134407.1	428	aCg/aTg	5/13	0.31235160656553	1	FACETS	0.622	0.542	0.708	0.622	0.542	0.708	SUBCLONAL	1	TRUE	0	0.31235160656553	1		561	608	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060806	38060807	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	GTAGTGGGGGTCCCCTTTCAGGTGCAGCTGGGACTCGTGGG	novel	NA	P-0030645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	99	870	0	ENST00000250448.2:c.1142_1182dup	p.Ser395ProfsTer8	p.S395Pfs*8	ENST00000250448	NM_004496.3	394	-/CCCACGAGTCCCAGCTGCACCTGAAAGGGGACCCCCACTAC	2/2	0.171566439544717	3	FACETS	0.61	0.542	0.682	0.305	0.271	0.341	INDETERMINATE	1	TRUE	1	0.31235160656553	3		870	1202	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0030663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	63	515	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.393221513987343	3	FACETS	1	0.959	1	0.633	0.551	0.719	CLONAL	1	TRUE	1	0.393221513987343	3		515	303	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220707	1220707	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	140	475	0	ENST00000326873.7:c.725G>T	p.Gly242Val	p.G242V	ENST00000326873	NM_000455.4	242	gGg/gTg	5/10	0.393221513987343	2	FACETS	0.879	0.818	0.94	1	0.987	1	CLONAL	3	TRUE	0	0.393221513987343	2		475	270	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574027	7574027	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882028	NA	P-0030663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	145	591	1	ENST00000269305.4:c.1000G>T	p.Gly334Trp	p.G334W	ENST00000269305	NM_001126112.2	334	Ggg/Tgg	10/11	0.393221513987343	2	FACETS	0.842	0.783	0.901	1	0.986	1	CLONAL	3	TRUE	0	0.393221513987343	2		592	292	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132501	11132501	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	137	647	1	ENST00000358026.2:c.2717G>T	p.Arg906Leu	p.R906L	ENST00000358026	NM_001128849.1	906	cGc/cTc	19/36	0.393221513987343	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.393221513987343	2		648	321	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088723	27088724	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0030663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	147	630	1	ENST00000324856.7:c.2332_2333delinsTT	p.Gly778Leu	p.G778L	ENST00000324856	NM_006015.4	778	GGa/TTa	7/20	0.385596990566151	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.393221513987343	3		631	400	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366751	40366751	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs976643781	NA	P-0030663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	76	226	0	ENST00000397332.2:c.446G>T	p.Arg149Leu	p.R149L	ENST00000397332	NM_001033082.2	149	cGg/cTg	2/3	0.385596990566151	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.393221513987343	3		226	202	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321197	65321197	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	97	379	0	ENST00000342505.4:c.1643C>T	p.Pro548Leu	p.P548L	ENST00000342505	NM_002227.2	548	cCc/cTc	11/25	0.385596990566151	3	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	1	0.393221513987343	3		379	284	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245912941	245912941	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	80	433	1	ENST00000388985.4:c.1211A>G	p.His404Arg	p.H404R	ENST00000388985		404	cAt/cGt	12/12	0.349869342052562	4	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	2	0.393221513987343	4		434	268	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225620	133225620	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	171	640	1	ENST00000320574.5:c.4044G>T	p.Trp1348Cys	p.W1348C	ENST00000320574	NM_006231.2	1348	tgG/tgT	32/49	0.393221513987343	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.393221513987343	3		641	485	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082785	16082785	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	30	67	0	ENST00000281043.3:c.599G>T	p.Arg200Leu	p.R200L	ENST00000281043	NM_005378.4	200	cGc/cTc	2/3	0.349869342052562	4	FACETS	1	0.88	1	1	0.88	1	CLONAL	2	TRUE	2	0.393221513987343	4		67	98	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89478264	89478264	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	28	506	1	ENST00000336596.2:c.2083G>T	p.Val695Phe	p.V695F	ENST00000336596	NM_005233.5	695	Gtt/Ttt	12/17	0.349869342052562	4	FACETS	1	0.933	1	0.699	0.566	0.845	CLONAL	1	TRUE	2	0.393221513987343	4		507	142	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411893	116411893	+	intron_variant	Intron	SNP	C	C	T	novel	NA	P-0030663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	119	811	0	ENST00000397752.3:c.2888-10C>T		p.*963*	ENST00000397752	NM_000245.2	-/1390			0.349869342052562	4	FACETS	0.985	0.896	1	0.985	0.896	1	CLONAL	2	TRUE	2	0.393221513987343	4		811	428	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850354	128850354	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	132	580	0	ENST00000249373.3:c.1617G>T	p.Lys539Asn	p.K539N	ENST00000249373	NM_005631.4	539	aaG/aaT	9/12	0.349869342052562	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	2	0.393221513987343	4		580	401	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971005	21971005	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501270	NA	P-0030663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	59	636	0	ENST00000304494.5:c.353C>T	p.Ala118Val	p.A118V	ENST00000304494	NM_000077.4	118	gCt/gTt	2/3	0.393221513987343	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.393221513987343	1		636	210	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44921902	44921902	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	68	249	1	ENST00000377967.4:c.1436A>T	p.Gln479Leu	p.Q479L	ENST00000377967	NM_021140.2	479	cAg/cTg	15/29	0.297656229344865	2	FACETS	0.908	0.819	0.996			1	CLONAL	3	TRUE	NA	0.393221513987343	2		250	127	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0030676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	105	772	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.366954403287489	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.408799259653026	1		772	404	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	159	390	0	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	0.559096231497853	1	FACETS	0.923	0.854	0.993	0.923	0.854	0.993	CLONAL	1	TRUE	0	0.559096231497853	1		390	444	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016218	31016218	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	129	292	0	ENST00000375687.4:c.464C>T	p.Ser155Phe	p.S155F	ENST00000375687	NM_015338.5	155	tCc/tTc	6/13	0.538767330964766	3	FACETS	1	0.952	1	0.534	0.486	0.584	CLONAL	1	TRUE	1	0.559096231497853	3		292	553	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31493322	31493322	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	129	385	0	ENST00000344624.3:c.1834del	p.Leu612Ter	p.L612*	ENST00000344624		612	Ctg/tg	10/33	1	2	FACETS	0.863	0.786	0.942	0.863	0.786	0.942	CLONAL	1	TRUE	1	0.559096231497853	2		385	535	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228795	36228795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1193546654	NA	P-0030687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	181	592	0	ENST00000222270.7:c.7694G>A	p.Arg2565His	p.R2565H	ENST00000222270	NM_014727.1	2565	cGt/cAt	35/37	0.343741213086273	1	FACETS	0.669	0.619	0.721	0.669	0.619	0.721	SUBCLONAL	1	TRUE	0	0.559096231497853	1		592	697	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438548	49438548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779260688	NA	P-0030687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	174	562	0	ENST00000301067.7:c.4942G>A	p.Asp1648Asn	p.D1648N	ENST00000301067	NM_003482.3	1648	Gat/Aat	19/54	1	2	FACETS	0.99	0.915	1	0.99	0.915	1	CLONAL	1	TRUE	1	0.559096231497853	2		562	629	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7977045	7977045	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	138	485	0	ENST00000319144.4:c.1685A>C	p.Glu562Ala	p.E562A	ENST00000319144	NM_001139.2	562	gAg/gCg	13/15	1	2	FACETS	0.803	0.733	0.875	0.803	0.733	0.875	CLONAL	1	TRUE	1	0.559096231497853	2		485	615	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600032	10600032	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	181	612	0	ENST00000171111.5:c.1544T>A	p.Leu515Gln	p.L515Q	ENST00000171111	NM_203500.1	515	cTg/cAg	5/6	0.343741213086273	1	FACETS	0.732	0.678	0.788	0.732	0.678	0.788	SUBCLONAL	1	TRUE	0	0.559096231497853	1		612	637	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683507	182683507	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	210	460	1	ENST00000292782.4:c.38G>A	p.Arg13His	p.R13H	ENST00000292782	NM_020640.2	13	cGt/cAt	2/7	0.559096231497853	1	FACETS	0.922	0.862	0.983	0.922	0.862	0.983	CLONAL	1	TRUE	0	0.559096231497853	1		461	587	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819785	170819785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	148	316	2	ENST00000296930.5:c.424C>T	p.Arg142Trp	p.R142W	ENST00000296930	NM_002520.6	142	Cgg/Tgg	5/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.559096231497853	2		318	497	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099760	157099760	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	57	208	0	ENST00000346085.5:c.697T>A	p.Tyr233Asn	p.Y233N	ENST00000346085	NM_020732.3	233	Tac/Aac	1/20	0.559096231497853	1	FACETS	0.769	0.671	0.872	0.769	0.671	0.872	SUBCLONAL	1	TRUE	0	0.559096231497853	1		208	191	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0030688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	100	418	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	1	2	FACETS	0.992	0.889	1	0.992	0.889	1	CLONAL	1	TRUE	1	0.39	2		418	517	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729181	66729181	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121908595	NA	P-0030688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	114	656	0	ENST00000307102.5:c.389A>G	p.Tyr130Cys	p.Y130C	ENST00000307102	NM_002755.3	130	tAt/tGt	3/11	1	2	FACETS	0.993	0.896	1	0.993	0.896	1	CLONAL	1	TRUE	1	0.39	2		656	589	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552249	29552250	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAAAGGGAACTCCTCT	novel	NA	P-0030688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	26	464	0	ENST00000356175.3:c.1984_1999dup	p.Met667LysfsTer8	p.M667Kfs*8	ENST00000356175	NM_000267.3	661	gga/ggAAAAGGGAACTCCTCTa	17/57	1	2	FACETS	0.267	0.211	0.332	0.267	0.211	0.332	SUBCLONAL	1	TRUE	1	0.39	2		464	499	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28929495	NA	P-0030694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	179	570	0	ENST00000275493.2:c.2155G>T	p.Gly719Cys	p.G719C	ENST00000275493	NM_005228.3	719	Ggc/Tgc	18/28	0.142546360880717	5	FACETS	0.93	0.859	1	0.62	0.573	0.669	INDETERMINATE	2	TRUE	2	0.431497467576031	5		570	735	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0030694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	161	416	2	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.142546360880717	5	FACETS	1	0.954	1	0.699	0.644	0.756	INDETERMINATE	2	TRUE	2	0.431497467576031	5		418	586	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560493	65560493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	157	419	0	ENST00000358664.4:c.104G>T	p.Arg35Leu	p.R35L	ENST00000358664	NM_002382.4	35	cGt/cTt	3/5	0.354687486124398	5	FACETS	0.861	0.791	0.934	0.574	0.527	0.623	CLONAL	2	TRUE	2	0.431497467576031	5		419	696	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111140	193111140	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	181	435	1	ENST00000367435.3:c.673G>T	p.Val225Phe	p.V225F	ENST00000367435	NM_024529.4	225	Gtc/Ttc	7/17	0.123183292380288	6	FACETS	1	0.957	1	1	0.957	1	INDETERMINATE	3	TRUE	3	0.431497467576031	6		436	501	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41228538	41228538	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	98	535	0	ENST00000357654.3:c.4451C>A	p.Ser1484Tyr	p.S1484Y	ENST00000357654	NM_007294.3	1484	tCt/tAt	13/23	0.167653095844801	2	FACETS	0.797	0.713	0.886	0.398	0.356	0.443	INDETERMINATE	1	TRUE	0	0.431497467576031	2		535	570	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41228619	41228619	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	66	394	0	ENST00000357654.3:c.4370C>T	p.Ser1457Leu	p.S1457L	ENST00000357654	NM_007294.3	1457	tCa/tTa	13/23	0.167653095844801	2	FACETS	0.728	0.634	0.829	0.364	0.317	0.415	INDETERMINATE	1	TRUE	0	0.431497467576031	2		394	420	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41228631	41228631	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1171055085	NA	P-0030694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	54	358	0	ENST00000357654.3:c.4358C>T	p.Ala1453Val	p.A1453V	ENST00000357654	NM_007294.3	1453	gCa/gTa	13/23	0.167653095844801	2	FACETS	0.693	0.595	0.8	0.347	0.297	0.4	INDETERMINATE	1	TRUE	0	0.431497467576031	2		358	361	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293195	212293195	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	39	335	0	ENST00000342788.4:c.2657G>T	p.Trp886Leu	p.W886L	ENST00000342788	NM_005235.2	886	tGg/tTg	22/28	0.315601415043237	3	FACETS	0.6	0.499	0.714	0.3	0.249	0.357	SUBCLONAL	1	TRUE	1	0.431497467576031	3		335	366	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346413	152346413	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	80	395	0	ENST00000359321.1:c.157G>T	p.Gly53Ter	p.G53*	ENST00000359321	NM_005431.1	53	Gga/Tga	3/3	0.431497467576031	4	FACETS	0.804	0.708	0.907	0.268	0.236	0.303	CLONAL	1	TRUE	1	0.431497467576031	4		395	660	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760603	133760603	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	95	637	0	ENST00000318560.5:c.2926A>G	p.Ile976Val	p.I976V	ENST00000318560	NM_005157.4	976	Atc/Gtc	11/11	1	2	FACETS	0.687	0.612	0.766	0.687	0.612	0.766	SUBCLONAL	1	TRUE	1	0.431497467576031	2		637	641	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	137	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	0.41	2		351	578	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	271	519	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.943	0.89	0.997	1	0.995	1	CLONAL	2	TRUE	1	0.41	2		524	701	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120535147	120535147	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771876856	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	215	278	0	ENST00000229340.5:c.508C>T	p.Arg170Ter	p.R170*	ENST00000229340	NM_006861.6	170	Cga/Tga	6/6	0.410112488721364	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.41	3		278	563	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264985	46264985	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	105	294	0	ENST00000371998.3:c.1860del	p.Lys620AsnfsTer18	p.K620Nfs*18	ENST00000371998		619	Aaa/aa	12/23	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.41	2		294	488	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430901	181430901	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	118	383	0	ENST00000325404.1:c.758del	p.Pro253LeufsTer21	p.P253Lfs*21	ENST00000325404	NM_003106.3	251	agC/ag	1/1	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.41	2		383	555	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221756	36221756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377420237	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	108	358	0	ENST00000222270.7:c.5425G>A	p.Ala1809Thr	p.A1809T	ENST00000222270	NM_014727.1	1809	Gcc/Acc	26/37	1	2	FACETS	0.915	0.823	1	0.915	0.823	1	CLONAL	1	TRUE	1	0.41	2		358	576	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	70	216	0	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	0.959	0.842	1	0.959	0.842	1	CLONAL	1	TRUE	1	0.41	2		216	356	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	85	430	2	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	0.410112488721364	3	FACETS	0.709	0.626	0.797	0.354	0.313	0.399	SUBCLONAL	1	TRUE	1	0.41	3		432	705	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	166	391	1	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.410112488721364	3	FACETS	0.935	0.865	1			1	CLONAL	2	TRUE	NA	0.41	3		392	522	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132617	11132617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1445478818	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	127	317	1	ENST00000358026.2:c.2833G>A	p.Ala945Thr	p.A945T	ENST00000358026	NM_001128849.1	945	Gca/Aca	19/36	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.41	2		318	527	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100728	8100728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs771019738	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	83	315	3	ENST00000346208.3:c.708del	p.Ser237AlafsTer28	p.S237Afs*28	ENST00000346208		234	ttC/tt	3/6	1	2	FACETS	0.854	0.757	0.958	0.854	0.757	0.958	CLONAL	1	TRUE	1	0.41	2		318	474	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383944	84383944	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	122	308	0	ENST00000321945.7:c.908del	p.Asn303IlefsTer17	p.N303Ifs*17	ENST00000321945	NM_139076.2	303	aAt/at	9/9	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.41	2		308	551	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554345	141554345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748399150	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	111	335	0	ENST00000220592.5:c.1806del	p.Ala603ProfsTer92	p.A603Pfs*92	ENST00000220592	NM_012154.3	602	ccC/cc	14/19	0.116619168862843	3	FACETS	1	0.929	1	0.519	0.468	0.574	INDETERMINATE	1	TRUE	1	0.41	3		335	628	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058747	180058748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755445139	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	127	252	4	ENST00000261937.6:c.89dup	p.Thr31AspfsTer15	p.T31Dfs*15	ENST00000261937	NM_182925.4	30	ccg/ccCg	2/30	1	2	FACETS	0.79	0.723	0.86	1	0.988	1	SUBCLONAL	2	TRUE	1	0.41	2		256	392	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	104	322	2	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	1	2	FACETS	0.86	0.772	0.953	0.86	0.772	0.953	CLONAL	1	TRUE	1	0.41	2		324	590	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	101	392	1	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.41	2		393	460	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391024	89391024	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	118	365	0	ENST00000336596.2:c.1095del	p.Lys365AsnfsTer6	p.K365Nfs*6	ENST00000336596	NM_005233.5	364	Aaa/aa	5/17	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.41	2		365	572	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256768	19256769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1202792889	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	48	218	0	ENST00000162023.5:c.944dup	p.Val316SerfsTer6	p.V316Sfs*6	ENST00000162023		315	cca/ccCa	13/13	1	2	FACETS	0.697	0.592	0.812	0.697	0.592	0.812	SUBCLONAL	1	TRUE	1	0.41	2		218	336	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289863	15289863	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201680145	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	59	355	0	ENST00000263388.2:c.3691C>T	p.Arg1231Cys	p.R1231C	ENST00000263388	NM_000435.2	1231	Cgt/Tgt	22/33	1	2	FACETS	0.56	0.482	0.645	0.56	0.482	0.645	SUBCLONAL	1	TRUE	1	0.41	2		355	514	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	19	80	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	0.747	0.574	0.946	0.747	0.574	0.946	CLONAL	1	TRUE	1	0.41	2		80	124	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664989	138664989	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	34	82	0	ENST00000330315.3:c.576del	p.Lys193SerfsTer78	p.K193Sfs*78	ENST00000330315	NM_023067.3	192	ccC/cc	1/1	1	2	FACETS	0.797	0.657	0.952	0.797	0.657	0.952	CLONAL	1	TRUE	1	0.41	2		82	208	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	104	297	0	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	0.963	0.865	1	0.963	0.865	1	CLONAL	1	TRUE	1	0.41	2		297	527	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245587	41245587	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357522	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	106	342	1	ENST00000357654.3:c.1961del	p.Lys654SerfsTer47	p.K654Sfs*47	ENST00000357654	NM_007294.3	654	aAg/ag	10/23	1	2	FACETS	0.781	0.701	0.866	0.781	0.701	0.866	SUBCLONAL	1	TRUE	1	0.41	2		343	662	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675170	30675172	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs1472156046	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	116	393	0	ENST00000376406.3:c.3073_3075del	p.Lys1025del	p.K1025del	ENST00000376406	NM_014641.2	1025	AAG/-	9/15	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.41	2		393	565	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831357	72831358	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTG	rs34918837	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	57	160	2	ENST00000268489.5:c.5221_5223dup	p.Gln1741dup	p.Q1741dup	ENST00000268489	NM_006885.3	1741	-/CAA	9/10	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.41	2		162	268	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533939	63533940	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs771001164	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	59	232	0	ENST00000307078.5:c.1214_1215del	p.Glu405GlyfsTer56	p.E405Gfs*56	ENST00000307078	NM_004655.3	405	gAG/g	6/11	1	2	FACETS	0.827	0.715	0.947	0.827	0.715	0.947	CLONAL	1	TRUE	1	0.41	2		232	348	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749374	41749374	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	43	162	0	ENST00000226382.2:c.421C>T	p.Arg141Ter	p.R141*	ENST00000226382	NM_003924.3	141	Cga/Tga	2/3	1	2	FACETS	0.804	0.677	0.942	0.804	0.677	0.942	CLONAL	1	TRUE	1	0.41	2		162	261	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760024	133760024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	104	334	1	ENST00000318560.5:c.2352del	p.Arg785GlyfsTer3	p.R785Gfs*3	ENST00000318560	NM_005157.4	783	Ccc/cc	11/11	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.41	2		335	489	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085825	16085825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	82	263	0	ENST00000281043.3:c.1005del	p.Ser336LeufsTer15	p.S336Lfs*15	ENST00000281043	NM_005378.4	334	gCc/gc	3/3	0.410112488721364	2	FACETS	0.946	0.838	1			1	CLONAL	1	TRUE	NA	0.41	2		263	423	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792546	33792546	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	17	38	0	ENST00000498907.2:c.775G>A	p.Ala259Thr	p.A259T	ENST00000498907	NM_004364.3	259	Gcg/Acg	1/1	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.41	2		38	66	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383707	42383707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782414774	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	104	315	1	ENST00000221972.3:c.482C>T	p.Thr161Met	p.T161M	ENST00000221972	NM_021601.3	161	aCg/aTg	3/5	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.41	2		316	451	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508257	106508257	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766854286	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	54	337	1	ENST00000359195.3:c.251C>T	p.Ala84Val	p.A84V	ENST00000359195	NM_002649.2	84	gCg/gTg	2/11	1	2	FACETS	0.748	0.642	0.864	0.748	0.642	0.864	SUBCLONAL	1	TRUE	1	0.41	2		338	352	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974830	15974830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	81	247	0	ENST00000268712.3:c.4045C>T	p.Arg1349Cys	p.R1349C	ENST00000268712	NM_006311.3	1349	Cgt/Tgt	30/46	1	2	FACETS	0.837	0.74	0.94	0.837	0.74	0.94	CLONAL	1	TRUE	1	0.41	2		247	472	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564569	41564569	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	36	359	0	ENST00000263253.7:c.3994del	p.Thr1332ProfsTer4	p.T1332Pfs*4	ENST00000263253	NM_001429.3	1331	Aaa/aa	24/31	0.410112488721364	2	FACETS	0.277	0.227	0.333			1	SUBCLONAL	1	TRUE	NA	0.41	2		359	634	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	60	217	2	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	0.92	0.798	1	0.92	0.798	1	CLONAL	1	TRUE	1	0.41	2		219	318	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176118142	176118143	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	65	211	0	ENST00000367669.3:c.830_831del	p.Glu277AlafsTer17	p.E277Afs*17	ENST00000367669	NM_022457.5	277	gAG/g	6/20	1	2	FACETS	0.906	0.79	1	0.906	0.79	1	CLONAL	1	TRUE	1	0.41	2		211	350	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948208	71948209	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs749079348	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	107	399	0	ENST00000298229.2:c.2927dup	p.Pro977ThrfsTer7	p.P977Tfs*7	ENST00000298229	NM_001567.3	974	gcc/gCcc	26/28	1	2	FACETS	0.888	0.798	0.982	0.888	0.798	0.982	CLONAL	1	TRUE	1	0.41	2		399	588	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570180	95570180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150514959	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	79	178	1	ENST00000393063.1:c.3553G>A	p.Ala1185Thr	p.A1185T	ENST00000393063	NM_030621.3	1185	Gcc/Acc	22/28	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.41	2		179	384	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	364555	364555	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs534120185	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	121	321	0	ENST00000262320.3:c.1007C>T	p.Thr336Met	p.T336M	ENST00000262320	NM_003502.3	336	aCg/aTg	3/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.41	2		321	492	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143140	30143140	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760041708	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	82	189	0	ENST00000389048.3:c.386G>A	p.Gly129Asp	p.G129D	ENST00000389048	NM_004304.4	129	gGc/gAc	1/29	0.410112488721364	3	FACETS	1	0.961	1	0.597	0.529	0.668	CLONAL	1	TRUE	1	0.41	3		189	404	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914175	32914175	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146351301	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	131	292	1	ENST00000380152.3:c.5683G>A	p.Glu1895Lys	p.E1895K	ENST00000380152		1895	Gag/Aag	11/27	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.41	2		293	536	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278070	18278070	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs886041602	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	127	425	0	ENST00000222254.8:c.1690A>G	p.Lys564Glu	p.K564E	ENST00000222254	NM_005027.3	564	Aag/Gag	13/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.41	2		425	551	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264407	46264407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529456958	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	96	282	0	ENST00000371998.3:c.1454G>A	p.Arg485His	p.R485H	ENST00000371998		485	cGt/cAt	11/23	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.41	2		282	467	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371900	55371900	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	36	99	0	ENST00000297316.4:c.590C>T	p.Pro197Leu	p.P197L	ENST00000297316	NM_022454.3	197	cCg/cTg	2/2	0.116619168862843	3	FACETS	1	0.924	1	0.605	0.503	0.715	INDETERMINATE	1	TRUE	1	0.41	3		99	175	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351844	89351844	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1041612791	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	170	506	1	ENST00000301030.4:c.1106A>G	p.Lys369Arg	p.K369R	ENST00000301030	NM_001256183.1	369	aAg/aGg	9/13	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.41	2		507	722	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223138	5223138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148744813	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	71	234	0	ENST00000357368.4:c.2665C>T	p.Arg889Cys	p.R889C	ENST00000357368	NM_002850.3	889	Cgc/Tgc	18/38	1	2	FACETS	0.978	0.86	1	0.978	0.86	1	CLONAL	1	TRUE	1	0.41	2		234	354	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464968	120464968	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	105	334	0	ENST00000256646.2:c.5104C>T	p.Arg1702Ter	p.R1702*	ENST00000256646	NM_024408.3	1702	Cga/Tga	28/34	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.41	2		334	494	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471815	120471815	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	77	236	0	ENST00000256646.2:c.3676A>G	p.Ile1226Val	p.I1226V	ENST00000256646	NM_024408.3	1226	Att/Gtt	23/34	1	2	FACETS	0.988	0.873	1	0.988	0.873	1	CLONAL	1	TRUE	1	0.41	2		236	380	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450870	70450870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	95	237	0	ENST00000373644.4:c.5710C>T	p.Leu1904Phe	p.L1904F	ENST00000373644	NM_030625.2	1904	Ctt/Ttt	12/12	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.41	2		237	422	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154299	2154299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146962483	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	69	292	1	ENST00000434045.2:c.629G>A	p.Arg210His	p.R210H	ENST00000434045	NM_001127598.1	210	cGt/cAt	5/5	1	2	FACETS	0.823	0.72	0.933	0.823	0.72	0.933	CLONAL	1	TRUE	1	0.41	2		293	409	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456491	32456491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	28	59	1	ENST00000332351.3:c.401C>T	p.Pro134Leu	p.P134L	ENST00000332351	NM_024426.4	134	cCg/cTg	1/10	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.41	2		60	105	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998597	100998597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	91	255	0	ENST00000325455.5:c.1205G>A	p.Arg402His	p.R402H	ENST00000325455	NM_001202474.3	402	cGt/cAt	1/8	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.41	2		255	399	SUCCESS
CBL	867	MSKCC	GRCh37	11	119077259	119077259	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	95	246	0	ENST00000264033.4:c.136del	p.His46ThrfsTer32	p.H46Tfs*32	ENST00000264033	NM_005188.3	44	agC/ag	1/16	1	2	FACETS	0.988	0.884	1	0.988	0.884	1	CLONAL	1	TRUE	1	0.41	2		246	469	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123622	46123622	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	23	148	0	ENST00000334344.6:c.3G>A	p.Met1?	p.M1?	ENST00000334344	NM_152641.2	1	atG/atA	1/21	0.410112488721364	3	FACETS	0.319	0.248	0.401	0.159	0.124	0.201	SUBCLONAL	1	TRUE	1	0.41	3		148	424	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432375	49432375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751964761	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	91	362	1	ENST00000301067.7:c.8764C>T	p.Arg2922Trp	p.R2922W	ENST00000301067	NM_003482.3	2922	Cgg/Tgg	34/54	0.410112488721364	3	FACETS	0.808	0.718	0.904	0.404	0.359	0.452	CLONAL	1	TRUE	1	0.41	3		363	662	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856008	111856008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1222585515	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	38	212	1	ENST00000341259.2:c.59C>T	p.Ala20Val	p.A20V	ENST00000341259	NM_005475.2	20	gCg/gTg	2/8	0.410112488721364	3	FACETS	0.714	0.592	0.848	0.357	0.296	0.424	SUBCLONAL	1	TRUE	1	0.41	3		213	313	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118814	115118814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	35	280	0	ENST00000257566.3:c.527C>T	p.Ala176Val	p.A176V	ENST00000257566	NM_016569.3	176	gCc/gTc	2/8	0.410112488721364	3	FACETS	0.313	0.256	0.378	0.157	0.128	0.189	SUBCLONAL	1	TRUE	1	0.41	3		280	657	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426787	121426787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	114	329	0	ENST00000257555.6:c.478G>A	p.Ala160Thr	p.A160T	ENST00000257555		160	Gcc/Acc	2/10	0.410112488721364	3	FACETS	1	0.973	1	0.606	0.547	0.667	CLONAL	1	TRUE	1	0.41	3		329	553	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245404	133245404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754616313	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	81	321	0	ENST00000320574.5:c.1916G>A	p.Arg639His	p.R639H	ENST00000320574	NM_006231.2	639	cGc/cAc	17/49	0.410112488721364	3	FACETS	0.72	0.635	0.812	0.36	0.317	0.406	SUBCLONAL	1	TRUE	1	0.41	3		321	661	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434458	110434458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770967453	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	58	190	0	ENST00000375856.3:c.3943C>T	p.Pro1315Ser	p.P1315S	ENST00000375856	NM_003749.2	1315	Ccc/Tcc	1/2	1	2	FACETS	0.83	0.717	0.951	0.83	0.717	0.951	CLONAL	1	TRUE	1	0.41	2		190	341	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574683	95574683	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	96	204	0	ENST00000393063.1:c.2414T>C	p.Leu805Pro	p.L805P	ENST00000393063	NM_030621.3	805	cTg/cCg	16/28	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.41	2		204	429	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41011085	41011085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	99	326	0	ENST00000267868.3:c.518C>T	p.Ala173Val	p.A173V	ENST00000267868	NM_002875.4	173	gCa/gTa	6/10	1	2	FACETS	0.889	0.796	0.988	0.889	0.796	0.988	CLONAL	1	TRUE	1	0.41	2		326	543	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250803	99250803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	50	201	2	ENST00000268035.6:c.107G>A	p.Gly36Asp	p.G36D	ENST00000268035	NM_000875.3	36	gGc/gAc	2/21	1	2	FACETS	0.624	0.531	0.726	0.624	0.531	0.726	SUBCLONAL	1	TRUE	1	0.41	2		203	391	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459973	99459973	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	87	298	0	ENST00000268035.6:c.2069A>G	p.Glu690Gly	p.E690G	ENST00000268035	NM_000875.3	690	gAg/gGg	10/21	1	2	FACETS	0.852	0.757	0.953	0.852	0.757	0.953	CLONAL	1	TRUE	1	0.41	2		298	498	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500433	99500433	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	47	287	0	ENST00000268035.6:c.3866A>C	p.Glu1289Ala	p.E1289A	ENST00000268035	NM_000875.3	1289	gAg/gCg	21/21	1	2	FACETS	0.491	0.414	0.575	0.491	0.414	0.575	SUBCLONAL	1	TRUE	1	0.41	2		287	467	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929486	81929488	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	106	347	0	ENST00000359376.3:c.1151_1153del	p.Asp384del	p.D384del	ENST00000359376	NM_002661.3	383	GAC/-	13/33	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.41	2		347	513	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349946	89349946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779328307	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	144	358	0	ENST00000301030.4:c.3004C>T	p.Arg1002Trp	p.R1002W	ENST00000301030	NM_001256183.1	1002	Cgg/Tgg	9/13	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.41	2		358	609	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217622	7217622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	98	290	0	ENST00000380728.2:c.305G>A	p.Arg102Gln	p.R102Q	ENST00000380728		102	cGa/cAa	4/11	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.41	2		290	464	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485766	40485766	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1281630344	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	97	336	0	ENST00000264657.5:c.974G>A	p.Arg325Gln	p.R325Q	ENST00000264657	NM_139276.2	325	cGg/cAg	10/24	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.41	2		336	458	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743328	743328	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	135	337	0	ENST00000314574.4:c.812A>G	p.Glu271Gly	p.E271G	ENST00000314574	NM_005433.3	271	gAa/gGa	7/12	1	2	FACETS	0.868	0.789	0.95	0.868	0.789	0.95	CLONAL	1	TRUE	1	0.41	2		337	759	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39535259	39535259	+	frameshift_variant,start_lost	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	69	130	1	ENST00000262039.4:c.7del	p.Glu3?	p.E3?	ENST00000262039	NM_002647.2	1	atG/at	1/25	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.41	2		131	275	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56376693	56376694	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	145	378	0	ENST00000348428.3:c.737dup	p.Leu246PhefsTer19	p.L246Ffs*19	ENST00000348428	NM_006785.3	245	gtt/gTtt	5/17	1	2	FACETS	0.995	0.909	1	0.995	0.909	1	CLONAL	1	TRUE	1	0.41	2		378	711	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222382	2222382	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769094667	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	89	210	0	ENST00000398665.3:c.3214C>T	p.Arg1072Cys	p.R1072C	ENST00000398665	NM_032482.2	1072	Cgt/Tgt	24/28	1	2	FACETS	0.784	0.704	0.866	1	0.983	1	SUBCLONAL	2	TRUE	1	0.41	2		210	277	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297763	15297763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753234965	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	127	309	0	ENST00000263388.2:c.1877G>A	p.Ser626Asn	p.S626N	ENST00000263388	NM_000435.2	626	aGc/aAc	12/33	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.41	2		309	583	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298074	15298074	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	121	294	0	ENST00000263388.2:c.1682A>G	p.Asp561Gly	p.D561G	ENST00000263388	NM_000435.2	561	gAt/gGt	11/33	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.41	2		294	536	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367046	15367046	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	16	192	0	ENST00000263377.2:c.1580C>T	p.Ala527Val	p.A527V	ENST00000263377	NM_058243.2	527	gCc/gTc	9/20	1	2	FACETS	0.274	0.202	0.36	0.274	0.202	0.36	SUBCLONAL	1	TRUE	1	0.41	2		192	285	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379841	17379841	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	154	371	0	ENST00000359435.4:c.230del	p.Pro77ArgfsTer19	p.P77Rfs*19	ENST00000359435	NM_001033549.1	76	Ccc/cc	2/9	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.41	2		371	562	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218522	36218522	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	85	210	0	ENST00000222270.7:c.4301A>G	p.Gln1434Arg	p.Q1434R	ENST00000222270	NM_014727.1	1434	cAg/cGg	16/37	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.41	2		210	367	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797894	42797894	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	78	305	0	ENST00000575354.2:c.3949del	p.Asp1317ThrfsTer15	p.D1317Tfs*15	ENST00000575354	NM_015125.3	1316	Ggg/gg	16/20	1	2	FACETS	0.683	0.601	0.771	0.683	0.601	0.771	SUBCLONAL	1	TRUE	1	0.41	2		305	557	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281502	198281502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	40	409	0	ENST00000335508.6:c.629C>T	p.Ala210Val	p.A210V	ENST00000335508	NM_012433.2	210	gCc/gTc	6/25	1	2	FACETS	0.289	0.24	0.345	0.289	0.24	0.345	SUBCLONAL	1	TRUE	1	0.41	2		409	674	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839714	42839714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1569008278	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	113	305	0	ENST00000398585.3:c.1525G>A	p.Gly509Arg	p.G509R	ENST00000398585	NM_001135099.1	509	Gga/Aga	13/14	0.228325561874827	3	FACETS	1	0.948	1	0.539	0.486	0.595	INDETERMINATE	1	TRUE	1	0.41	3		305	616	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144844	47144844	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	64	381	0	ENST00000409792.3:c.4909A>G	p.Thr1637Ala	p.T1637A	ENST00000409792	NM_014159.6	1637	Acc/Gcc	7/21	1	2	FACETS	0.523	0.453	0.599	0.523	0.453	0.599	SUBCLONAL	1	TRUE	1	0.41	2		381	597	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998192	169998192	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	152	385	0	ENST00000295797.4:c.882+1G>A		p.X294_splice	ENST00000295797	NM_002740.5	294			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.41	2		385	698	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197694	66197694	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	84	270	0	ENST00000273854.3:c.3005T>C	p.Leu1002Ser	p.L1002S	ENST00000273854	NM_004439.5	1002	tTg/tCg	17/18	1	2	FACETS	0.868	0.77	0.973	0.868	0.77	0.973	CLONAL	1	TRUE	1	0.41	2		270	472	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31493321	31493322	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1330233722	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	61	249	0	ENST00000344624.3:c.1834dup	p.Leu612ProfsTer8	p.L612Pfs*8	ENST00000344624		612	ctg/cCtg	10/33	1	2	FACETS	0.699	0.604	0.8	0.699	0.604	0.8	SUBCLONAL	1	TRUE	1	0.41	2		249	426	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576437	67576437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141981005	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	114	279	0	ENST00000274335.5:c.716C>T	p.Thr239Met	p.T239M	ENST00000274335		239	aCg/aTg	5/15	1	2	FACETS	0.989	0.894	1	0.989	0.894	1	CLONAL	1	TRUE	1	0.41	2		279	562	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950656	79950658	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-	rs1049679865	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	25	204	0	ENST00000265081.6:c.118_120del	p.Ser40del	p.S40del	ENST00000265081	NM_002439.4	37	aCCTcc/acc	1/24	1	2	FACETS	0.425	0.335	0.527	0.425	0.335	0.527	SUBCLONAL	1	TRUE	1	0.41	2		204	287	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046022	180046022	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	28	40	0	ENST00000261937.6:c.2849C>T	p.Ala950Val	p.A950V	ENST00000261937	NM_182925.4	950	gCg/gTg	20/30	1	2	FACETS	0.823	0.678	0.976	1	0.952	1	CLONAL	2	TRUE	1	0.41	2		40	83	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048231	180048231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201884197	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	109	353	1	ENST00000261937.6:c.2042C>T	p.Thr681Met	p.T681M	ENST00000261937	NM_182925.4	681	aCg/aTg	14/30	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.41	2		354	487	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850897	128850897	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	68	318	1	ENST00000249373.3:c.1744A>T	p.Asn582Tyr	p.N582Y	ENST00000249373	NM_005631.4	582	Aac/Tac	10/12	1	2	FACETS	0.654	0.57	0.745	0.654	0.57	0.745	SUBCLONAL	1	TRUE	1	0.41	2		319	507	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859494	151859494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	71	246	0	ENST00000262189.6:c.11168C>T	p.Ala3723Val	p.A3723V	ENST00000262189	NM_170606.2	3723	gCt/gTt	43/59	1	2	FACETS	0.675	0.59	0.766	0.675	0.59	0.766	SUBCLONAL	1	TRUE	1	0.41	2		246	513	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866524	117866525	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	126	297	0	ENST00000297338.2:c.1120dup	p.Ser374PhefsTer10	p.S374Ffs*10	ENST00000297338	NM_006265.2	374	tct/tTct	9/14	0.116619168862843	3	FACETS	1	0.98	1	0.65	0.59	0.712	INDETERMINATE	1	TRUE	1	0.41	3		297	570	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971031	21971031	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	67	143	0	ENST00000579755.1:c.370C>A	p.Leu124Met	p.L124M	ENST00000579755		124	Ctg/Atg	2/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.41	2		143	228	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393614	139393614	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	89	337	0	ENST00000277541.6:c.6032T>C	p.Leu2011Pro	p.L2011P	ENST00000277541	NM_017617.3	2011	cTg/cCg	32/34	1	2	FACETS	0.875	0.779	0.978	0.875	0.779	0.978	CLONAL	1	TRUE	1	0.41	2		337	496	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402418	139402418	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	80	316	1	ENST00000277541.6:c.3499T>C	p.Tyr1167His	p.Y1167H	ENST00000277541	NM_017617.3	1167	Tac/Cac	21/34	1	2	FACETS	0.943	0.834	1	0.943	0.834	1	CLONAL	1	TRUE	1	0.41	2		317	414	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918250	44918250	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	63	280	0	ENST00000377967.4:c.876-1G>T		p.X292_splice	ENST00000377967	NM_021140.2	292			1	2	FACETS	0.782	0.679	0.893	0.782	0.679	0.893	SUBCLONAL	1	TRUE	1	0.41	2		280	393	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222804	53222804	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	146	327	0	ENST00000375401.3:c.4132T>G	p.Ser1378Ala	p.S1378A	ENST00000375401	NM_004187.3	1378	Tcc/Gcc	25/26	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.41	2		327	586	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239600	53239600	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	89	270	0	ENST00000375401.3:c.1742T>C	p.Val581Ala	p.V581A	ENST00000375401	NM_004187.3	581	gTg/gCg	12/26	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.41	2		270	434	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938920	76938920	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	118	371	0	ENST00000373344.5:c.1828C>T	p.Gln610Ter	p.Q610*	ENST00000373344	NM_000489.3	610	Caa/Taa	9/35	1	2	FACETS	0.934	0.845	1	0.934	0.845	1	CLONAL	1	TRUE	1	0.41	2		371	616	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271526	26271527	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	T	novel	NA	P-0030708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	72	184	0	ENST00000305910.3:c.86_87delinsA	p.Ser29LysfsTer8	p.S29Kfs*8	ENST00000305910	NM_003534.2	29	aGC/aA	1/1	1	2	FACETS	0.922	0.81	1	0.922	0.81	1	CLONAL	1	TRUE	1	0.41	2		184	381	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0030710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	119	659	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.996	0.9	1	0.996	0.9	1	CLONAL	1	TRUE	1	0.327414275204178	2		659	730	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0030710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	127	612	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.327414275204178	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.327414275204178	1		612	634	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226590002	226590002	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	59	592	1	ENST00000366794.5:c.199C>T	p.Pro67Ser	p.P67S	ENST00000366794	NM_001618.3	67	Cct/Tct	2/23	0.22201810729719	2	FACETS	0.442	0.379	0.511	0.221	0.189	0.256	SUBCLONAL	1	TRUE	0	0.327414275204178	2		593	815	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628093	90628093	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	58	725	0	ENST00000330062.3:c.1226G>C	p.Gly409Ala	p.G409A	ENST00000330062	NM_002168.2	409	gGa/gCa	10/11	0.283995049213102	1	FACETS	0.405	0.347	0.468	0.405	0.347	0.468	SUBCLONAL	1	TRUE	0	0.327414275204178	1		725	732	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	128	215	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		215	369	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295196	1295196	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0030722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	120	259	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		259	332	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060845	38060845	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	46	647	0	ENST00000250448.2:c.1144del	p.His382ThrfsTer7	p.H382Tfs*7	ENST00000250448	NM_004496.3	382	Cac/ac	2/2	0.103840562185507	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		647	541	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65568280	65568280	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	25	321	0	ENST00000358664.4:c.47C>T	p.Pro16Leu	p.P16L	ENST00000358664	NM_002382.4	16	cCg/cTg	2/5	0.103840562185507	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		321	178	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281884	142281902	+	frameshift_variant	Frame_Shift_Del	DEL	GTGTAACAAATGACAGGAG	GTGTAACAAATGACAGGAG	-	novel	NA	P-0030725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	21	453	0	ENST00000350721.4:c.342_360del	p.Ser115ArgfsTer44	p.S115Rfs*44	ENST00000350721	NM_001184.3	114	ccCTCCTGTCATTTGTTACAC/cc	4/47	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		453	201	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522405	157522405	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	27	529	0	ENST00000346085.5:c.4677C>G	p.Phe1559Leu	p.F1559L	ENST00000346085	NM_020732.3	1559	ttC/ttG	18/20	0.176747452727947	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		529	469	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0030729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	1850	740	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.676390923277246	6	FACETS	0.987	0.972	1			1	CLONAL	5	TRUE	NA	0.676390923277246	6		740	2607	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061208	38061208	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1292426539	NA	P-0030729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	209	484	0	ENST00000250448.2:c.781C>G	p.Arg261Gly	p.R261G	ENST00000250448	NM_004496.3	261	Cgc/Ggc	2/2	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.676390923277246	2		484	575	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139873	55139873	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs866988382	NA	P-0030729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	251	466	0	ENST00000257290.5:c.1534C>T	p.Arg512Ter	p.R512*	ENST00000257290	NM_006206.4	512	Cga/Tga	10/23	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.676390923277246	2		466	710	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176105675	176105675	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	251	512	0	ENST00000367669.3:c.840A>C	p.Glu280Asp	p.E280D	ENST00000367669	NM_022457.5	280	gaA/gaC	7/20	0.676390923277246	4	FACETS	0.925	0.864	0.989	0.308	0.288	0.33	CLONAL	1	TRUE	1	0.676390923277246	4		512	1345	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853186	68853186	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0030729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	324	531	0	ENST00000261769.5:c.1569T>G	p.Tyr523Ter	p.Y523*	ENST00000261769	NM_004360.3	523	taT/taG	11/16	0.676390923277246	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.676390923277246	1		531	560	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120227	70120236	+	frameshift_variant	Frame_Shift_Del	DEL	AGCAGCAGCA	AGCAGCAGCA	-	novel	NA	P-0030729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	309	685	0	ENST00000245479.2:c.1229_1238del	p.Gln410ProfsTer57	p.Q410Pfs*57	ENST00000245479	NM_000346.3	410	cAGCAGCAGCAc/cc	3/3	0.676269694679115	3	FACETS	0.988	0.931	1	0.494	0.465	0.524	CLONAL	1	TRUE	1	0.676390923277246	3		685	1237	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578419	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	966	866	0	ENST00000269305.4:c.511del	p.Glu171ArgfsTer3	p.E171Rfs*3	ENST00000269305	NM_001126112.2	171	Gag/ag	5/11	0.924623221044105	3	FACETS	0.937	0.924	0.949			1	CLONAL	3	TRUE	NA	0.924623221044105	3		866	1087	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435219	110435219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746894027	NA	P-0030731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	124	411	2	ENST00000375856.3:c.3182C>T	p.Ser1061Leu	p.S1061L	ENST00000375856	NM_003749.2	1061	tCg/tTg	1/2	0.885849442900991	2	FACETS	0.599	0.545	0.654	0.299	0.272	0.327	SUBCLONAL	1	TRUE	0	0.924623221044105	2		413	448	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563296	21563296	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1253	320	807	0	ENST00000382592.4:c.623C>T	p.Pro208Leu	p.P208L	ENST00000382592	NM_014572.2	208	cCg/cTg	4/8	0.924623221044105	4	FACETS	0.847	0.797	0.898	0.212	0.199	0.225	CLONAL	1	TRUE	0	0.924623221044105	4		807	1573	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954379	48954379	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0030731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	744	512	0	ENST00000267163.4:c.1498+2T>G		p.X500_splice	ENST00000267163	NM_000321.2	500			0.924623221044105	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	4	TRUE	0	0.924623221044105	4		512	771	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001334	29001334	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	169	526	0	ENST00000282397.4:c.1398G>C	p.Trp466Cys	p.W466C	ENST00000282397	NM_002019.4	466	tgG/tgC	10/30	0.924623221044105	4	FACETS	0.695	0.638	0.754	0.174	0.159	0.189	SUBCLONAL	1	TRUE	0	0.924623221044105	4		526	1013	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988554	36988554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1461014578	NA	P-0030731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	355	818	2	ENST00000354822.5:c.99G>A	p.Met33Ile	p.M33I	ENST00000354822	NM_001079668.2	33	atG/atA	2/3	0.862160636168553	3	FACETS	1	0.969	1	0.515	0.488	0.542	CLONAL	1	TRUE	1	0.924623221044105	3		820	1090	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628428	86628428	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	293	423	0	ENST00000274376.6:c.801del	p.Lys267AsnfsTer12	p.K267Nfs*12	ENST00000274376	NM_002890.2	266	gAa/ga	3/25	0.884554475730621	3	FACETS	0.922	0.898	0.944	0.922	0.898	0.944	CLONAL	3	TRUE	0	0.924623221044105	3		423	335	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517301	157517301	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	389	547	1	ENST00000346085.5:c.3865C>T	p.Pro1289Ser	p.P1289S	ENST00000346085	NM_020732.3	1289	Cct/Tct	16/20	0.862160636168553	3	FACETS	0.935	0.899	0.971	0.935	0.899	0.971	CLONAL	2	TRUE	1	0.924623221044105	3		548	658	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355313	81355313	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	136	440	0	ENST00000222390.5:c.1061G>A	p.Cys354Tyr	p.C354Y	ENST00000222390	NM_000601.4	354	tGc/tAc	9/18	0.862160636168553	3	FACETS	0.786	0.718	0.857	0.393	0.359	0.429	SUBCLONAL	1	TRUE	1	0.924623221044105	3		440	547	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	85	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.871	0.775	0.971	1	0.988	1	CLONAL	3	TRUE	1	0.175895366602772	2		215	370	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0030738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	116	458	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.175895366602772	3	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	1	0.175895366602772	3		458	674	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0030738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	243	923	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.175895366602772	3	FACETS	1	0.94	1	1	0.992	1	CLONAL	3	TRUE	1	0.175895366602772	3		923	996	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8497264	8497264	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	32	460	0	ENST00000356435.5:c.2327A>G	p.Glu776Gly	p.E776G	ENST00000356435		776	gAa/gGa	15/35	0.175895366602772	3	FACETS	0.992	0.806	1	0.496	0.403	0.602	CLONAL	1	TRUE	1	0.175895366602772	3		460	399	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0030739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	76	491	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.84	0.737	0.952	0.84	0.737	0.952	CLONAL	1	TRUE	1	0.27	2		492	670	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939260	71939260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	80	747	0	ENST00000298229.2:c.209G>A	p.Arg70His	p.R70H	ENST00000298229	NM_001567.3	70	cGc/cAc	2/28	0.263517891767442	1	FACETS	0.773	0.681	0.872	0.773	0.681	0.872	SUBCLONAL	1	TRUE	0	0.27	1		747	663	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0030739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	91	448	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.27	2		448	651	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176338	24176338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	76	613	3	ENST00000263121.7:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000263121	NM_003073.3	377	Cgt/Tgt	9/9	1	2	FACETS	0.938	0.824	1	0.938	0.824	1	CLONAL	1	TRUE	1	0.27	2		616	600	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937219	36937219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140159756	NA	P-0030739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	94	740	1	ENST00000361632.4:c.1100G>A	p.Arg367Gln	p.R367Q	ENST00000361632		367	cGg/cAg	9/16	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.27	2		741	684	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188125	108188125	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	75	445	0	ENST00000278616.4:c.6224A>T	p.His2075Leu	p.H2075L	ENST00000278616	NM_000051.3	2075	cAt/cTt	43/63	0.263517891767442	1	FACETS	0.813	0.713	0.921	0.813	0.713	0.921	CLONAL	1	TRUE	0	0.27	1		445	591	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226352	2226352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758688224	NA	P-0030739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	83	695	1	ENST00000398665.3:c.3832G>A	p.Ala1278Thr	p.A1278T	ENST00000398665	NM_032482.2	1278	Gcc/Acc	27/28	1	2	FACETS	0.962	0.85	1	0.962	0.85	1	CLONAL	1	TRUE	1	0.27	2		696	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0030789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	316	590	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.270510771752993	3	FACETS	1	0.99	1			1	CLONAL	2	TRUE	NA	0.266097233584468	3		590	1125	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610208	10610208	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	226	622	0	ENST00000171111.5:c.502G>T	p.Val168Phe	p.V168F	ENST00000171111	NM_203500.1	168	Gtc/Ttc	2/6	0.161551743714608	3	FACETS	0.915	0.852	0.98	0.61	0.568	0.653	CLONAL	2	TRUE	0	0.266097233584468	3		622	1052	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028585	42028585	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	151	612	0	ENST00000219905.7:c.4123G>C	p.Glu1375Gln	p.E1375Q	ENST00000219905	NM_001164273.1	1375	Gag/Cag	13/24	0.147091605020544	3	FACETS	1	0.975	1	0.591	0.539	0.645	INDETERMINATE	1	TRUE	1	0.266097233584468	3		612	1088	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198246	138198246	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200840068	NA	P-0030789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	56	290	0	ENST00000237289.4:c.839G>A	p.Arg280Gln	p.R280Q	ENST00000237289	NM_001270507.1	280	cGg/cAg	6/9	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.266097233584468	2		290	402	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233316	69233316	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0030789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	146	262	0	ENST00000462284.1:c.1181C>G	p.Ser394Ter	p.S394*	ENST00000462284	NM_002392.5	394	tCa/tGa	11/11	0.266097233584468	3	FACETS	1	0.975	1	0.77	0.707	0.836	CLONAL	2	TRUE	0	0.266097233584468	3		262	538	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892214	9892215	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	234	570	0	ENST00000330684.3:c.2275dup	p.Thr759AsnfsTer27	p.T759Nfs*27	ENST00000330684	NM_001134407.1	759	acc/aAcc	11/13	0.264585499098566	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	2	0.266097233584468	4		570	1046	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101931	11101931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	80	673	1	ENST00000358026.2:c.1351C>T	p.Arg451Cys	p.R451C	ENST00000358026	NM_001128849.1	451	Cgc/Tgc	8/36	0.161551743714608	3	FACETS	0.589	0.516	0.667	0.196	0.172	0.223	SUBCLONAL	1	TRUE	0	0.266097233584468	3		674	1157	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416536	29416536	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1463792690	NA	P-0030789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	81	545	2	ENST00000389048.3:c.4417G>A	p.Gly1473Arg	p.G1473R	ENST00000389048	NM_004304.4	1473	Ggg/Agg	29/29	0.270510771752993	3	FACETS	0.788	0.693	0.891	0.394	0.346	0.446	SUBCLONAL	1	TRUE	1	0.266097233584468	3		547	875	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39726936	39726936	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	75	326	0	ENST00000361337.2:c.934C>G	p.Gln312Glu	p.Q312E	ENST00000361337	NM_003286.2	312	Cag/Gag	11/21	0.270510771752993	4	FACETS	1	0.924	1	0.359	0.314	0.407	CLONAL	1	TRUE	1	0.266097233584468	4		326	663	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267295	41267295	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	42	369	0	ENST00000349496.5:c.879C>G	p.Phe293Leu	p.F293L	ENST00000349496	NM_001904.3	293	ttC/ttG	6/15	0.134474670472773	4	FACETS	0.638	0.532	0.757	0.319	0.266	0.379	INDETERMINATE	1	TRUE	2	0.266097233584468	4		369	626	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268517	142268517	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0030789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	72	307	0	ENST00000350721.4:c.2977-2A>C		p.X993_splice	ENST00000350721	NM_001184.3	993			0.134474670472773	4	FACETS	1	0.966	1	0.658	0.575	0.746	INDETERMINATE	1	TRUE	2	0.266097233584468	4		307	521	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099127	157099127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1212813613	NA	P-0030789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	41	263	1	ENST00000346085.5:c.64G>A	p.Glu22Lys	p.E22K	ENST00000346085	NM_020732.3	22	Gag/Aag	1/20	0.161551743714608	3	FACETS	0.823	0.687	0.975	0.274	0.229	0.325	CLONAL	1	TRUE	0	0.266097233584468	3		264	424	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099149	157099149	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	45	316	0	ENST00000346085.5:c.86G>A	p.Gly29Glu	p.G29E	ENST00000346085	NM_020732.3	29	gGa/gAa	1/20	0.161551743714608	3	FACETS	0.787	0.661	0.926	0.262	0.22	0.309	CLONAL	1	TRUE	0	0.266097233584468	3		316	487	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874065	151874065	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	59	479	0	ENST00000262189.6:c.8473G>A	p.Glu2825Lys	p.E2825K	ENST00000262189	NM_170606.2	2825	Gaa/Aaa	38/59	0.266097233584468	6	FACETS	0.657	0.563	0.76	0.164	0.14	0.19	SUBCLONAL	1	TRUE	2	0.266097233584468	6		479	1034	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0030790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	96	446	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	1	0.963	1			1	INDETERMINATE	1	TRUE	NA	0.361795580255766	2		446	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0030790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	160	616	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.361795580255766	1	FACETS	0.819	0.751	0.89	0.819	0.751	0.89	CLONAL	1	TRUE	0	0.361795580255766	1		617	885	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0030790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	123	512	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	0.361795580255766	2		512	663	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193121548	193121548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	66	320	0	ENST00000367435.3:c.946C>T	p.His316Tyr	p.H316Y	ENST00000367435	NM_024529.4	316	Cat/Tat	10/17	1	2	FACETS	0.704	0.612	0.804	0.704	0.612	0.804	SUBCLONAL	1	TRUE	1	0.361795580255766	2		320	518	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518630	69518630	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0030790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	119	697	0	ENST00000294312.3:c.15T>A	p.Cys5Ter	p.C5*	ENST00000294312	NM_005117.2	5	tgT/tgA	1/3	1	2	FACETS	0.905	0.817	0.997	0.905	0.817	0.997	CLONAL	1	TRUE	1	0.361795580255766	2		697	727	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218357	133218357	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1335665224	NA	P-0030790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	100	600	1	ENST00000320574.5:c.5254G>A	p.Asp1752Asn	p.D1752N	ENST00000320574	NM_006231.2	1752	Gac/Aac	39/49	NA	2	FACETS	0.813	0.727	0.904			1	INDETERMINATE	1	TRUE	NA	0.361795580255766	2		601	680	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919673	28919673	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	51	396	0	ENST00000282397.4:c.2264C>A	p.Ser755Tyr	p.S755Y	ENST00000282397	NM_002019.4	755	tCt/tAt	16/30	0.31556111697491	1	FACETS	0.583	0.497	0.677	0.583	0.497	0.677	SUBCLONAL	1	TRUE	0	0.361795580255766	1		396	396	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041881	42041881	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	98	466	1	ENST00000219905.7:c.6076G>T	p.Glu2026Ter	p.E2026*	ENST00000219905	NM_001164273.1	2026	Gaa/Taa	17/24	0.361795580255766	1	FACETS	0.904	0.81	1	0.904	0.81	1	CLONAL	1	TRUE	0	0.361795580255766	1		467	491	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679798	88679798	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	101	504	0	ENST00000360948.2:c.665G>C	p.Arg222Pro	p.R222P	ENST00000360948	NM_001012338.2	222	cGa/cCa	7/19	0.361795580255766	1	FACETS	0.788	0.706	0.875	0.788	0.706	0.875	SUBCLONAL	1	TRUE	0	0.361795580255766	1		504	580	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640135	3640135	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	148	769	0	ENST00000294008.3:c.3504G>C	p.Met1168Ile	p.M1168I	ENST00000294008	NM_032444.2	1168	atG/atC	12/15	1	2	FACETS	0.895	0.817	0.977	0.895	0.817	0.977	CLONAL	1	TRUE	1	0.361795580255766	2		769	914	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303891	30303891	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	105	654	0	ENST00000262643.3:c.127G>C	p.Asp43His	p.D43H	ENST00000262643	NM_001238.2	43	Gat/Cat	4/12	1	2	FACETS	0.651	0.583	0.724	0.651	0.583	0.724	SUBCLONAL	1	TRUE	1	0.361795580255766	2		654	891	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267382	198267382	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	73	465	1	ENST00000335508.6:c.1975C>A	p.Gln659Lys	p.Q659K	ENST00000335508	NM_012433.2	659	Caa/Aaa	14/25	1	2	FACETS	0.651	0.569	0.739	0.651	0.569	0.739	SUBCLONAL	1	TRUE	1	0.361795580255766	2		466	620	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520153	9520153	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	63	430	0	ENST00000353224.5:c.2116C>A	p.Pro706Thr	p.P706T	ENST00000353224	NM_177990.2	706	Ccg/Acg	10/10	1	2	FACETS	0.736	0.638	0.842	0.736	0.638	0.842	SUBCLONAL	1	TRUE	1	0.361795580255766	2		430	473	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730876	40730876	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	130	559	1	ENST00000373198.4:c.3659G>T	p.Arg1220Leu	p.R1220L	ENST00000373198	NM_133170.3	1220	cGg/cTg	27/32	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.361795580255766	2		560	709	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720978	119720978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	69	480	0	ENST00000316626.5:c.197C>T	p.Ser66Leu	p.S66L	ENST00000316626		66	tCa/tTa	2/12	0.361795580255766	1	FACETS	0.502	0.437	0.573	0.502	0.437	0.573	SUBCLONAL	1	TRUE	0	0.361795580255766	1		480	622	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721988	176721988	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1230044949	NA	P-0030790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	64	412	0	ENST00000439151.2:c.7619C>G	p.Ser2540Cys	p.S2540C	ENST00000439151	NM_022455.4	2540	tCt/tGt	23/23	0.257511304953518	2	FACETS	0.642	0.556	0.735	0.321	0.278	0.368	SUBCLONAL	1	TRUE	0	0.361795580255766	2		412	551	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068097	94068097	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	34	325	0	ENST00000369303.4:c.865C>G	p.Gln289Glu	p.Q289E	ENST00000369303	NM_004440.3	289	Caa/Gaa	4/17	0.361795580255766	1	FACETS	0.536	0.44	0.644	0.536	0.44	0.644	SUBCLONAL	1	TRUE	0	0.361795580255766	1		325	287	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522637	106522637	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs772770447	NA	P-0030790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	55	393	0	ENST00000359195.3:c.2614A>G	p.Thr872Ala	p.T872A	ENST00000359195	NM_002649.2	872	Act/Gct	7/11	1	2	FACETS	0.614	0.526	0.711	0.614	0.526	0.711	SUBCLONAL	1	TRUE	1	0.361795580255766	2		393	495	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371803	116371803	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	103	404	0	ENST00000397752.3:c.1282G>C	p.Asp428His	p.D428H	ENST00000397752	NM_000245.2	428	Gac/Cac	3/21	1	2	FACETS	0.967	0.867	1	0.967	0.867	1	CLONAL	1	TRUE	1	0.361795580255766	2		404	589	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151893037	151893037	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs763476421	NA	P-0030790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	59	388	0	ENST00000262189.6:c.4333C>G	p.Leu1445Val	p.L1445V	ENST00000262189	NM_170606.2	1445	Ctt/Gtt	28/59	1	2	FACETS	0.62	0.534	0.714	0.62	0.534	0.714	SUBCLONAL	1	TRUE	1	0.361795580255766	2		388	526	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538982	23538982	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs774732037	NA	P-0030790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	126	452	0	ENST00000380871.4:c.457G>C	p.Glu153Gln	p.E153Q	ENST00000380871	NM_006167.3	153	Gaa/Caa	2/2	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.361795580255766	2		452	636	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157993	27157993	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	82	585	0	ENST00000380036.4:c.217G>T	p.Glu73Ter	p.E73*	ENST00000380036	NM_000459.3	73	Gaa/Taa	2/23	0.242099313861805	0	FACETS	0.417	0.367	0.47			1	SUBCLONAL	1	TRUE	0	0.361795580255766	0		585	694	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030585	47030585	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs377667483	NA	P-0030807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	44	754	1	ENST00000377604.3:c.360T>G	p.Asp120Glu	p.D120E	ENST00000377604	NM_001204468.1	120	gaT/gaG	4/24	0.226025320285461	2	FACETS	0.525	0.44	0.619	0.262	0.22	0.31	SUBCLONAL	1	FALSE	0	0.334082846584837	2		755	502	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0030807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	131	659	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.334082846584837	9	FACETS	1	0.952	1	0.901	0.838	0.963	CLONAL	7	FALSE	1	0.334082846584837	9		659	236	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426788	49426789	+	missense_variant	Missense_Mutation	DNP	AA	AA	TT	novel	NA	P-0030807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	10	317	0	ENST00000301067.7:c.11699_11700inv	p.Leu3900Gln	p.L3900Q	ENST00000301067	NM_003482.3	3900	cTT/cAA	39/54	0.226025320285461	2	FACETS	0.32	0.217	0.45	0.16	0.108	0.225	SUBCLONAL	1	FALSE	0	0.334082846584837	2		317	187	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054402	42054402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752413385	NA	P-0030807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	19	418	0	ENST00000219905.7:c.7586G>A	p.Arg2529Lys	p.R2529K	ENST00000219905	NM_001164273.1	2529	aGa/aAa	22/24	0.226025320285461	2	FACETS	0.625	0.477	0.797	0.312	0.238	0.399	SUBCLONAL	1	FALSE	0	0.334082846584837	2		418	182	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14026103	14026103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	10	401	0	ENST00000311895.7:c.1063G>A	p.Glu355Lys	p.E355K	ENST00000311895	NM_005236.2	355	Gaa/Aaa	6/11	0.334082846584837	3	FACETS	0.554	0.377	0.775	0.277	0.188	0.388	SUBCLONAL	1	FALSE	1	0.334082846584837	3		401	126	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992630	72992630	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1189486286	NA	P-0030807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	16	371	2	ENST00000268489.5:c.1415C>A	p.Ala472Glu	p.A472E	ENST00000268489	NM_006885.3	472	gCg/gAg	2/10	0.334082846584837	3	FACETS	0.356	0.263	0.468	0.178	0.131	0.234	SUBCLONAL	1	FALSE	1	0.334082846584837	3		373	314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578242	7578242	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882003	NA	P-0030807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	23	726	3	ENST00000269305.4:c.607G>T	p.Val203Leu	p.V203L	ENST00000269305	NM_001126112.2	203	Gtg/Ttg	6/11	0.25093231143075	3	FACETS	0.812	0.646	0.995	0.812	0.646	0.995	CLONAL	2	FALSE	1	0.334082846584837	3		729	99	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138376634	138376634	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	12	530	0	ENST00000289153.2:c.2840C>G	p.Ser947Cys	p.S947C	ENST00000289153	NM_006219.2	947	tCt/tGt	20/22	0.291016633479588	1	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	FALSE	0	0.334082846584837	1		530	46	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278791	1278791	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs772070672	NA	P-0030807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	11	614	1	ENST00000310581.5:c.2251G>T	p.Ala751Ser	p.A751S	ENST00000310581	NM_198253.2	751	Gcc/Tcc	6/16	0.268632505608831	4	FACETS	0.483	0.334	0.667	0.161	0.111	0.223	SUBCLONAL	1	FALSE	1	0.334082846584837	4		615	182	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170817081	170817081	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	11	533	0	ENST00000296930.5:c.85T>G	p.Tyr29Asp	p.Y29D	ENST00000296930	NM_002520.6	29	Tat/Gat	2/11	0.268632505608831	4	FACETS	0.451	0.311	0.623	0.15	0.103	0.208	SUBCLONAL	1	FALSE	1	0.334082846584837	4		533	195	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170827907	170827909	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	rs761817600	NA	P-0030807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	30	703	0	ENST00000296930.5:c.652_654del	p.Ser218del	p.S218del	ENST00000296930	NM_002520.6	216	cCATca/cca	8/11	0.268632505608831	4	FACETS	0.527	0.424	0.644	0.176	0.141	0.215	SUBCLONAL	1	FALSE	1	0.334082846584837	4		703	455	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467863	50467863	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	42	426	0	ENST00000331340.3:c.1098G>C	p.Gln366His	p.Q366H	ENST00000331340	NM_006060.4	366	caG/caC	8/8	0.334082846584837	9	FACETS	1	0.94	1	0.161	0.134	0.191	CLONAL	1	FALSE	1	0.334082846584837	9		426	423	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249028	55249028	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1275022697	NA	P-0030807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	181	558	0	ENST00000275493.2:c.2326C>T	p.Arg776Cys	p.R776C	ENST00000275493	NM_005228.3	776	Cgc/Tgc	20/28	0.334082846584837	9	FACETS	1	0.969	1	1	0.989	1	CLONAL	9	FALSE	1	0.334082846584837	9		558	255	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	265	499	0	ENST00000304494.5:c.247C>A	p.His83Asn	p.H83N	ENST00000304494	NM_000077.4	83	Cac/Aac	2/3	0.291016633479588	1	FACETS	1	0.983	1	1	0.996	1	CLONAL	2	FALSE	0	0.334082846584837	1		499	605	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044568	47044568	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	32	862	0	ENST00000377604.3:c.2065A>C	p.Thr689Pro	p.T689P	ENST00000377604	NM_001204468.1	689	Act/Cct	18/24	0.226025320285461	2	FACETS	1	0.948	1	0.743	0.614	0.882	CLONAL	1	FALSE	0	0.334082846584837	2		862	129	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652359	48652359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141479621	NA	P-0030807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	20	930	2	ENST00000376670.3:c.1030G>A	p.Gly344Arg	p.G344R	ENST00000376670	NM_002049.3	344	Ggg/Agg	6/6	0.226025320285461	2	FACETS	0.466	0.357	0.593	0.233	0.178	0.297	SUBCLONAL	1	FALSE	0	0.334082846584837	2		932	257	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419049	419049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	28	588	0	ENST00000399788.2:c.3298G>A	p.Glu1100Lys	p.E1100K	ENST00000399788	NM_001042603.1	1100	Gaa/Aaa	22/28	0.20974131091726	3	FACETS	0.389	0.31	0.479			1	SUBCLONAL	1	FALSE	NA	0.334082846584837	3		588	503	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644703	134644703	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536029159	NA	P-0030818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	122	509	1	ENST00000398015.3:c.104C>T	p.Thr35Met	p.T35M	ENST00000398015	NM_004441.4	35	aCg/aTg	2/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.333631866755596	2		510	647	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0030818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	202	370	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.333631866755596	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.333631866755596	3		370	656	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141568623	141568623	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	169	657	0	ENST00000220592.5:c.839G>C	p.Arg280Pro	p.R280P	ENST00000220592	NM_012154.3	280	cGc/cCc	7/19	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.333631866755596	2		657	922	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099982	157099993	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGCGGC	GGCGGCGGCGGC	-	rs587779747	NA	P-0030818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	61	275	0	ENST00000346085.5:c.933_944del	p.Gly316_Gly319del	p.G316_G319del	ENST00000346085	NM_020732.3	307	GGCGGCGGCGGC/-	1/20	1	2	FACETS	0.869	0.752	0.995	0.869	0.752	0.995	CLONAL	1	TRUE	1	0.333631866755596	2		275	421	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249013	55249013	+	protein_altering_variant	In_Frame_Ins	INS	A	A	GGGG	novel	NA	P-0030818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	452	578	0	ENST00000275493.2:c.2311delinsGGGG	p.Asn771delinsGlyAsp	p.N771delinsGD	ENST00000275493	NM_005228.3	771	Aac/GGGGac	20/28	0.333631866755596	5	FACETS	0.994	0.952	1			1	CLONAL	4	TRUE	NA	0.333631866755596	5		578	1023	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347934	73347934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	66	230	0	ENST00000377767.4:c.1127C>T	p.Ala376Val	p.A376V	ENST00000377767	NM_014953.3	376	gCt/gTt	8/21	0.440554401619563	5	FACETS	1	0.879	1	0.336	0.293	0.383	CLONAL	1	TRUE	2	0.545533597430261	5		230	436	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0030844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	72	302	1	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.509800414832944	1	FACETS	0.762	0.674	0.854	0.762	0.674	0.854	SUBCLONAL	1	TRUE	0	0.545533597430261	1		303	252	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0030844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	620	892	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.529122962740135	3	FACETS	0.99	0.961	1	0.99	0.961	1	CLONAL	3	TRUE	0	0.545533597430261	3		892	974	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610608	52610609	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	96	574	0	ENST00000394830.3:c.3564dup	p.Glu1189ArgfsTer6	p.E1189Rfs*6	ENST00000394830	NM_018313.4	1188	-/A	23/30	0.525384648658313	3	FACETS	0.789	0.704	0.878			1	SUBCLONAL	1	TRUE	NA	0.545533597430261	3		574	568	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223300	5223300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141070507	NA	P-0030844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	65	686	1	ENST00000357368.4:c.2503C>T	p.Arg835Cys	p.R835C	ENST00000357368	NM_002850.3	835	Cgc/Tgc	18/38	0.329271506199534	4	FACETS	0.631	0.547	0.721	0.158	0.136	0.181	SUBCLONAL	1	TRUE	0	0.545533597430261	4		687	584	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028025	69028025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200550325	NA	P-0030844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	94	516	1	ENST00000288368.4:c.3184C>T	p.Arg1062Cys	p.R1062C	ENST00000288368	NM_024870.2	1062	Cgt/Tgt	26/40	0.545533597430261	3	FACETS	0.783	0.699	0.873	0.392	0.349	0.437	SUBCLONAL	1	TRUE	1	0.545533597430261	3		517	560	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273269	115273269	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	224	463	0	ENST00000438362.2:c.1189G>A	p.Gly397Ser	p.G397S	ENST00000438362	NM_001242891.1	397	Ggt/Agt	11/20	0.231165742046379	5	FACETS	0.933	0.871	0.997	0.622	0.581	0.665	INDETERMINATE	2	TRUE	2	0.545533597430261	5		463	800	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681694	30681694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1281141743	NA	P-0030844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	102	505	1	ENST00000376406.3:c.403G>A	p.Val135Ile	p.V135I	ENST00000376406	NM_014641.2	135	Gtc/Atc	3/15	0.545533597430261	4	FACETS	0.752	0.672	0.836	0.188	0.168	0.209	SUBCLONAL	1	TRUE	0	0.545533597430261	4		506	769	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911444	134911444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149160192	NA	P-0030846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	131	579	1	ENST00000398015.3:c.1909C>T	p.Arg637Cys	p.R637C	ENST00000398015	NM_004441.4	637	Cgt/Tgt	11/16	0.163336645823311	3	FACETS	1	0.956	1	0.54	0.492	0.591	INDETERMINATE	1	FALSE	1	0.495941470434564	3		580	610	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663812	241663812	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	56	252	0	ENST00000366560.3:c.1315C>T	p.Gln439Ter	p.Q439*	ENST00000366560	NM_000143.3	439	Cag/Tag	9/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.495941470434564	2		252	152	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713544	30713546	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0030846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	188	450	0	ENST00000295754.5:c.871_873del	p.Lys291del	p.K291del	ENST00000295754	NM_003242.5	290	gAGAag/gag	4/7	0.304075169073055	1	FACETS	0.752	0.697	0.81	0.752	0.697	0.81	SUBCLONAL	1	FALSE	0	0.495941470434564	1		450	758	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TC	novel	NA	P-0030846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	102	577	0	ENST00000311936.3:c.180_181inv	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggGAaa	3/5	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.495941470434564	2		577	332	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715739	30715739	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0030846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	34	372	0	ENST00000295754.5:c.1396+1G>T		p.X466_splice	ENST00000295754	NM_003242.5	466			0.304075169073055	1	FACETS	0.444	0.365	0.532	0.444	0.365	0.532	SUBCLONAL	1	FALSE	0	0.495941470434564	1		372	232	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0030848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	87	515	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.943	0.834	1	0.943	0.834	1	CLONAL	1	TRUE	1	0.23	2		515	802	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045518	47045518	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	145	644	0	ENST00000377604.3:c.2485G>T	p.Glu829Ter	p.E829*	ENST00000377604	NM_001204468.1	829	Gag/Tag	22/24	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.23	2		644	1103	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192026	108192026	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs539978799	NA	P-0030848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	68	325	0	ENST00000278616.4:c.6453-2A>G		p.X2151_splice	ENST00000278616	NM_000051.3	2151			1	2	FACETS	0.954	0.83	1	0.954	0.83	1	CLONAL	1	TRUE	1	0.23	2		325	620	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120795651	120795651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	53	476	1	ENST00000257552.2:c.502G>A	p.Glu168Lys	p.E168K	ENST00000257552	NM_002442.3	168	Gaa/Aaa	8/15	1	2	FACETS	0.459	0.39	0.536	0.459	0.39	0.536	SUBCLONAL	1	TRUE	1	0.23	2		477	1003	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913464	32913464	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	62	544	0	ENST00000380152.3:c.4972C>G	p.Gln1658Glu	p.Q1658E	ENST00000380152		1658	Cag/Gag	11/27	0.211975850169792	1	FACETS	0.533	0.459	0.613	0.533	0.459	0.613	SUBCLONAL	1	TRUE	0	0.23	1		544	896	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5256120	5256120	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	103	457	1	ENST00000357368.4:c.717A>T	p.Glu239Asp	p.E239D	ENST00000357368	NM_002850.3	239	gaA/gaT	9/38	1	2	FACETS	0.984	0.88	1	0.984	0.88	1	CLONAL	1	TRUE	1	0.23	2		458	910	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137524823	137524823	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0030848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	76	333	1	ENST00000367739.4:c.547-1G>T		p.X183_splice	ENST00000367739	NM_000416.2	183			1	2	FACETS	0.985	0.864	1	0.985	0.864	1	CLONAL	1	TRUE	1	0.23	2		334	671	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630227	100630227	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	77	437	0	ENST00000308731.7:c.46C>A	p.Gln16Lys	p.Q16K	ENST00000308731	NM_000061.2	16	Cag/Aag	2/19	1	2	FACETS	0.872	0.765	0.987	0.872	0.765	0.987	CLONAL	1	TRUE	1	0.23	2		437	768	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	71	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.929	0.828	1	0.929	0.828	1	CLONAL	1	FALSE	1	0.821946164610221	2		215	186	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578393	7578393	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876660821	NA	P-0030866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	465	525	0	ENST00000269305.4:c.537T>G	p.His179Gln	p.H179Q	ENST00000269305	NM_001126112.2	179	caT/caG	5/11	0.814310801603434	2	FACETS	0.991	0.966	1	0.991	0.966	1	CLONAL	2	FALSE	0	0.821946164610221	2		525	571	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719535	190719535	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	122	371	0	ENST00000441310.2:c.1537G>C	p.Glu513Gln	p.E513Q	ENST00000441310	NM_000534.4	513	Gaa/Caa	9/13	1	2	FACETS	0.896	0.813	0.983	0.896	0.813	0.983	CLONAL	1	TRUE	1	0.476125860812656	2		371	572	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629815	187629816	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	123	618	0	ENST00000441802.2:c.1166dup	p.Ala391GlyfsTer13	p.A391Gfs*13	ENST00000441802	NM_005245.3	389	gta/gtTa	2/27	0.476125860812656	1	FACETS	0.487	0.44	0.536	0.487	0.44	0.536	SUBCLONAL	1	TRUE	0	0.476125860812656	1		618	809	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1258720	1258720	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	191	463	0	ENST00000310581.5:c.3025G>C	p.Ala1009Pro	p.A1009P	ENST00000310581	NM_198253.2	1009	Gcg/Ccg	13/16	0.430678242700171	3	FACETS	0.965	0.892	1	0.483	0.446	0.521	CLONAL	1	TRUE	1	0.476125860812656	3		463	1029	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123065	5123065	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	167	454	0	ENST00000381652.3:c.3121G>A	p.Gly1041Arg	p.G1041R	ENST00000381652	NM_004972.3	1041	Gga/Aga	23/25	0.476125860812656	1	FACETS	0.914	0.844	0.986	0.914	0.844	0.986	CLONAL	1	TRUE	0	0.476125860812656	1		454	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0030877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	385	610	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.531634808918144	2	FACETS	0.978	0.937	1	0.978	0.937	1	CLONAL	2	TRUE	0	0.547494900877689	2		610	719	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519505	137519508	+	frameshift_variant	Frame_Shift_Del	DEL	CTCT	CTCT	-	novel	NA	P-0030877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	361	419	0	ENST00000367739.4:c.1130_1133del	p.Glu377ValfsTer5	p.E377Vfs*5	ENST00000367739	NM_000416.2	377	gAGAGt/gt	7/7	0.547494900877689	3	FACETS	0.863	0.827	0.899			1	CLONAL	3	TRUE	NA	0.547494900877689	3		419	649	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189855	66189855	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	261	475	0	ENST00000273854.3:c.3091G>T	p.Val1031Leu	p.V1031L	ENST00000273854	NM_004439.5	1031	Gta/Tta	18/18	0.540564472002754	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.547494900877689	2		475	476	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446343	49446354	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCACCTAGTGGT	TCACCTAGTGGT	-	novel	NA	P-0030877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	294	577	0	ENST00000301067.7:c.1251_1258+4del		p.X417_splice	ENST00000301067	NM_003482.3	417		9/54	0.547494900877689	4	FACETS	0.885	0.835	0.936	0.885	0.835	0.936	CLONAL	2	TRUE	2	0.547494900877689	4		577	939	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988524	41988549	+	frameshift_variant	Frame_Shift_Del	DEL	ACCATCTATCTTCTAAATGGCTTCCA	ACCATCTATCTTCTAAATGGCTTCCA	-	novel	NA	P-0030877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	332	601	0	ENST00000219905.7:c.1317_1342del	p.Asp439GlufsTer8	p.D439Efs*8	ENST00000219905	NM_001164273.1	439	gACCATCTATCTTCTAAATGGCTTCCA/g	3/24	0.522546901090621	3	FACETS	0.857	0.813	0.902	0.857	0.813	0.902	CLONAL	2	TRUE	1	0.547494900877689	3		601	901	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472547	88472547	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	291	599	0	ENST00000360948.2:c.2008C>G	p.Leu670Val	p.L670V	ENST00000360948	NM_001012338.2	670	Ctg/Gtg	16/19	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.547494900877689	2		599	736	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870050	40870050	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	325	512	0	ENST00000428826.2:c.967A>T	p.Asn323Tyr	p.N323Y	ENST00000428826		323	Aat/Tat	10/21	0.547494900877689	4	FACETS	0.937	0.887	0.988	0.937	0.887	0.988	CLONAL	2	TRUE	2	0.547494900877689	4		512	980	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5207939	5207939	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	160	562	0	ENST00000357368.4:c.5772G>C	p.Gln1924His	p.Q1924H	ENST00000357368	NM_002850.3	1924	caG/caC	37/38	0.522546901090621	3	FACETS	0.962	0.883	1	0.481	0.441	0.522	CLONAL	1	TRUE	1	0.547494900877689	3		562	774	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247195	153247195	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	273	415	0	ENST00000281708.4:c.1607C>A	p.Thr536Lys	p.T536K	ENST00000281708	NM_033632.3	536	aCg/aAg	10/12	0.540564472002754	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.547494900877689	2		415	476	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046317	180046317	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	225	453	0	ENST00000261937.6:c.2697C>G	p.Ile899Met	p.I899M	ENST00000261937	NM_182925.4	899	atC/atG	19/30	NA	2	FACETS	0.938	0.886	0.99			1	INDETERMINATE	2	TRUE	NA	0.547494900877689	2		453	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0030888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	48	799	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	NA	2	FACETS	0.104	0.087	0.123			1	INDETERMINATE	1	TRUE	NA	0.911896997819306	2		799	1010	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441252	52441252	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	369	513	0	ENST00000460680.1:c.518A>G	p.Tyr173Cys	p.Y173C	ENST00000460680	NM_004656.3	173	tAt/tGt	7/17	0.911896997819306	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.911896997819306	1		513	437	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	71	215	0				ENST00000310581	NM_198253.2	-/1132			0.669900720685425	3	FACETS	1	0.969	1	0.646	0.573	0.722	CLONAL	1	TRUE	1	0.669900720685425	3		215	219	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916614	178916614	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0030898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	168	432	0	ENST00000263967.3:c.1A>G	p.Met1?	p.M1?	ENST00000263967	NM_006218.2	1	Atg/Gtg	2/21	1	2	FACETS	0.98	0.907	1	0.98	0.907	1	CLONAL	1	TRUE	1	0.669900720685425	2		432	512	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133724	55133724	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2107	1755	467	0	ENST00000257290.5:c.937G>C	p.Gly313Arg	p.G313R	ENST00000257290	NM_006206.4	313	Ggt/Cgt	7/23	0.669900720685425	16	FACETS	0.965	0.944	0.985			1	CLONAL	8	TRUE	NA	0.669900720685425	16		467	3862	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888198	112888198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121918453	NA	P-0030898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	45	518	1	ENST00000351677.2:c.214G>A	p.Ala72Thr	p.A72T	ENST00000351677	NM_002834.3	72	Gcc/Acc	3/16	1	2	FACETS	0.181	0.152	0.214	0.181	0.152	0.214	SUBCLONAL	1	TRUE	1	0.669900720685425	2		519	741	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720826	89720826	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	122	279	0	ENST00000371953.3:c.977A>G	p.Asp326Gly	p.D326G	ENST00000371953	NM_000314.4	326	gAc/gGc	8/9	0.669900720685425	1	FACETS	0.985	0.91	1	0.985	0.91	1	CLONAL	1	TRUE	0	0.669900720685425	1		279	246	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52705207	52705207	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	170	426	0	ENST00000322088.6:c.89A>G	p.Asn30Ser	p.N30S	ENST00000322088	NM_014225.5	30	aAc/aGc	2/15	0.137379539991696	4	FACETS	1	0.969	1	0.367	0.338	0.397	INDETERMINATE	1	TRUE	1	0.669900720685425	4		426	770	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026223	48026223	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	102	451	0	ENST00000234420.5:c.1101T>G	p.His367Gln	p.H367Q	ENST00000234420	NM_000179.2	367	caT/caG	4/10	1	2	FACETS	0.561	0.503	0.622	0.561	0.503	0.622	SUBCLONAL	1	TRUE	1	0.669900720685425	2		451	543	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211863	123211866	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	novel	NA	P-0030898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	53	313	0	ENST00000218089.9:c.2731_2734del	p.Asp911LysfsTer19	p.D911Kfs*19	ENST00000218089	NM_001042749.1	910	atAGAC/at	27/35	1	1	FACETS	0.368	0.316	0.424	0.368	0.316	0.424	SUBCLONAL	1	TRUE	0	0.669900720685425	1		313	286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0030901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	109	772	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.177374465884198	3	FACETS	0.977	0.88	1	0.651	0.586	0.72	CLONAL	2	TRUE	0	0.210059202985647	3		772	587	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230691	46230691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424958105	NA	P-0030901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	63	320	0	ENST00000334344.6:c.940C>T	p.Arg314Cys	p.R314C	ENST00000334344	NM_152641.2	314	Cgt/Tgt	8/21	1	2	FACETS	0.952	0.823	1	0.952	0.823	1	CLONAL	1	TRUE	1	0.210059202985647	2		320	630	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101155	41101155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1328848371	NA	P-0030901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	71	495	0	ENST00000373198.4:c.1201C>T	p.Arg401Trp	p.R401W	ENST00000373198	NM_133170.3	401	Cgg/Tgg	8/32	0.139066882952287	3	FACETS	1	0.972	1	0.718	0.628	0.815	CLONAL	1	TRUE	1	0.210059202985647	3		495	520	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604707	48604707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	30	395	0	ENST00000342988.3:c.1529G>A	p.Gly510Glu	p.G510E	ENST00000342988	NM_005359.5	510	gGa/gAa	12/12	1	2	FACETS	0.613	0.493	0.749	0.613	0.493	0.749	SUBCLONAL	1	TRUE	1	0.210059202985647	2		395	466	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738305	190738305	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	48	365	0	ENST00000441310.2:c.2557A>G	p.Ile853Val	p.I853V	ENST00000441310	NM_000534.4	853	Att/Gtt	12/13	1	2	FACETS	0.775	0.654	0.908	0.775	0.654	0.908	CLONAL	1	TRUE	1	0.210059202985647	2		365	590	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280643	115280643	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	183	683	0	ENST00000438362.2:c.388G>A	p.Ala130Thr	p.A130T	ENST00000438362	NM_001242891.1	130	Gct/Act	4/20	0.528362841624608	1	FACETS	0.913	0.849	0.98	0.913	0.849	0.98	CLONAL	1	TRUE	0	0.528362841624608	1		683	558	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653834	89653835	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTAT	novel	NA	P-0030910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	129	518	0	ENST00000371953.3:c.133_136dup	p.Tyr46CysfsTer7	p.Y46Cfs*7	ENST00000371953	NM_000314.4	44	-/GTAT	2/9	0.528362841624608	1	FACETS	0.843	0.771	0.918	0.843	0.771	0.918	CLONAL	1	TRUE	0	0.528362841624608	1		518	426	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0030921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	84	354	0	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	0.911	1	CLONAL	1	TRUE	1	0.68	2		354	243	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0030921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	51	539	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	0.882	0.764	1	0.882	0.764	1	CLONAL	1	TRUE	1	0.68	2		539	170	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0030921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	163	683	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.299496187599276	1	FACETS	0.655	0.606	0.705	0.655	0.606	0.705	INDETERMINATE	1	TRUE	0	0.68	1		683	483	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0030921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	243	1004	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.68	2		1004	617	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0030921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	156	515	0	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.68	2		515	426	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282115	38282115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554562012	NA	P-0030921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	238	821	0	ENST00000425967.3:c.941C>T	p.Pro314Leu	p.P314L	ENST00000425967	NM_001174067.1	314	cCg/cTg	8/19	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.68	2		821	618	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012684	36012684	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	53	83	0	ENST00000358208.4:c.128C>T	p.Ser43Leu	p.S43L	ENST00000358208		43	tCg/tTg	2/12	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.68	2		83	154	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106792	27106793	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	183	595	0	ENST00000324856.7:c.6405dup	p.Leu2136SerfsTer14	p.L2136Sfs*14	ENST00000324856	NM_006015.4	2135	att/aTtt	20/20	1	2	FACETS	0.938	0.871	1	0.938	0.871	1	CLONAL	1	TRUE	1	0.68	2		595	574	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692970	89692975	+	inframe_deletion	In_Frame_Del	DEL	CTAGAT	CTAGAT	-	novel	NA	P-0030921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	72	550	0	ENST00000371953.3:c.454_459del	p.Leu152_Asp153del	p.L152_D153del	ENST00000371953	NM_000314.4	152	CTAGAT/-	5/9	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.68	2		550	171	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720798	89720798	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876658837	NA	P-0030921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	21	258	0	ENST00000371953.3:c.949del	p.Val317TyrfsTer4	p.V317Yfs*4	ENST00000371953	NM_000314.4	317	Gta/ta	8/9	1	2	FACETS	0.802	0.635	0.986	0.802	0.635	0.986	CLONAL	1	TRUE	1	0.68	2		258	77	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991646	72991647	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	136	535	2	ENST00000268489.5:c.2398dup	p.Thr800AsnfsTer11	p.T800Nfs*11	ENST00000268489	NM_006885.3	800	acc/aAcc	2/10	1	2	FACETS	0.948	0.87	1	0.948	0.87	1	CLONAL	1	TRUE	1	0.68	2		537	422	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045654	26045654	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1447457563	NA	P-0030921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	82	307	1	ENST00000540144.1:c.16C>T	p.Gln6Ter	p.Q6*	ENST00000540144	NM_003531.2	6	Caa/Taa	1/1	0.215938478370223	5	FACETS	0.906	0.809	1	0.604	0.539	0.671	INDETERMINATE	2	TRUE	2	0.68	5		308	269	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522121	157522122	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0030921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	168	637	0	ENST00000346085.5:c.4396dup	p.Ala1466GlyfsTer5	p.A1466Gfs*5	ENST00000346085	NM_020732.3	1465	tgg/tGgg	18/20	0.116841993836059	3	FACETS	1	0.985	1	0.626	0.579	0.674	INDETERMINATE	1	TRUE	1	0.68	3		637	529	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696425	47696425	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519967	NA	P-0030943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	206	638	0	ENST00000347630.2:c.398T>G	p.Phe133Cys	p.F133C	ENST00000347630	NM_001007230.1	133	tTc/tGc	6/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.434931213838416	2		638	914	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1131691023	NA	P-0030943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	213	725	0	ENST00000269305.4:c.470T>C	p.Val157Ala	p.V157A	ENST00000269305	NM_001126112.2	157	gTc/gCc	5/11	0.364283821897221	1	FACETS	0.97	0.904	1	0.97	0.904	1	CLONAL	1	TRUE	0	0.434931213838416	1		725	790	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250825	10250825	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	194	656	0	ENST00000340748.4:c.3655A>T	p.Met1219Leu	p.M1219L	ENST00000340748		1219	Atg/Ttg	32/40	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.434931213838416	2		656	837	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135012	11135012	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	171	608	0	ENST00000358026.2:c.2979G>C	p.Glu993Asp	p.E993D	ENST00000358026	NM_001128849.1	993	gaG/gaC	21/36	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.434931213838416	2		608	778	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973236	25973236	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	104	439	0	ENST00000435504.4:c.1189A>C	p.Ser397Arg	p.S397R	ENST00000435504		397	Agt/Cgt	12/13	1	2	FACETS	0.848	0.761	0.939	0.848	0.761	0.939	CLONAL	1	TRUE	1	0.434931213838416	2		439	564	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0030952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	297	390	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.371142829166557	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.520563736890564	3		390	666	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0030952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	164	463	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.520563736890564	3	FACETS	1	0.97	1	0.555	0.51	0.601	CLONAL	1	TRUE	1	0.520563736890564	3		463	716	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0030952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	454	676	2	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.520563736890564	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.520563736890564	1		678	967	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12632306	12632306	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	136	465	0	ENST00000251849.4:c.1361A>C	p.Gln454Pro	p.Q454P	ENST00000251849	NM_002880.3	454	cAg/cCg	12/17	0.505867885817151	2	FACETS	0.867	0.791	0.946	0.433	0.395	0.473	CLONAL	1	TRUE	0	0.520563736890564	2		465	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0030975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	56	799	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.633	0.541	0.733	0.633	0.541	0.733	SUBCLONAL	1	FALSE	1	0.257711342914145	2		799	687	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0030975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	44	358	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.200706807315186	0	FACETS	0.421	0.352	0.497			1	SUBCLONAL	1	FALSE	0	0.257711342914145	0		358	602	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434440	110434440	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754818980	NA	P-0030975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	42	348	0	ENST00000375856.3:c.3961G>A	p.Ala1321Thr	p.A1321T	ENST00000375856	NM_003749.2	1321	Gcc/Acc	1/2	1	2	FACETS	0.54	0.45	0.64	0.54	0.45	0.64	SUBCLONAL	1	FALSE	1	0.257711342914145	2		348	604	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586464	189586464	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	36	374	0	ENST00000264731.3:c.1088A>T	p.Gln363Leu	p.Q363L	ENST00000264731	NM_003722.4	363	cAa/cTa	8/14	1	2	FACETS	0.481	0.394	0.578	0.481	0.394	0.578	SUBCLONAL	1	FALSE	1	0.257711342914145	2		374	581	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012309	152012309	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	28	319	0	ENST00000262189.6:c.504del	p.Asn169ThrfsTer37	p.N169Tfs*37	ENST00000262189	NM_170606.2	168	tcT/tc	4/59	1	2	FACETS	0.432	0.344	0.532	0.432	0.344	0.532	SUBCLONAL	1	FALSE	1	0.257711342914145	2		319	503	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0030978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	44	282	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.831	0.699	0.977	0.831	0.699	0.977	CLONAL	1	TRUE	1	0.29	2		282	365	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259407	89259409	+	missense_variant	Missense_Mutation	TNP	AAG	AAG	CAT	novel	NA	P-0030978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	48	316	0	ENST00000336596.2:c.551_553delinsCAT	p.Gln184_Asp185delinsProTyr	p.Q184_D185delinsPY	ENST00000336596	NM_005233.5	184	cAAGat/cCATat	3/17	0.238378422084365	3	FACETS	1	0.882	1	0.524	0.444	0.611	CLONAL	1	TRUE	1	0.29	3		316	362	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863680	68863691	+	inframe_deletion	In_Frame_Del	DEL	ATTGGAAATTTT	ATTGGAAATTTT	-	novel	NA	P-0031008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	107	511	0	ENST00000261769.5:c.2423_2434del	p.Gly808_Ile811del	p.G808_I811del	ENST00000261769	NM_004360.3	807	ATTGGAAATTTT/-	15/16	0.690833920128982	1	FACETS	0.719	0.655	0.785	0.719	0.655	0.785	SUBCLONAL	1	TRUE	0	0.690833920128982	1		511	282	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248998	55248999	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCCAGCG	rs727504263	NA	P-0031010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	479	486	0	ENST00000275493.2:c.2300_2308dup	p.Ala767_Val769dup	p.A767_V769dup	ENST00000275493	NM_005228.3	767	atg/aTGGCCAGCGtg	20/28	0.405479379940937	6	FACETS	0.918	0.88	0.957	0.735	0.704	0.765	CLONAL	4	TRUE	1	0.405479379940937	6		486	1165	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	232	215	0				ENST00000310581	NM_198253.2	-/1132			0.206760096639482	3	FACETS	0.921	0.864	0.98	1	0.988	1	CLONAL	4	TRUE	0	0.206760096639482	3		215	672	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0031029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	115	376	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	0.206760096639482	3	FACETS	0.924	0.834	1	0.924	0.834	1	CLONAL	2	TRUE	1	0.206760096639482	3		376	664	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0031029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	487	616	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.206760096639482	5	FACETS	0.921	0.882	0.961			1	CLONAL	5	TRUE	NA	0.206760096639482	5		617	1340	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339981	70339981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	99	302	0	ENST00000374080.3:c.514G>A	p.Glu172Lys	p.E172K	ENST00000374080		172	Gag/Aag	4/45	1	1	FACETS	1	0.915	1	1	0.987	1	CLONAL	2	TRUE	0	0.206760096639482	1		302	421	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571841	64571841	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	125	888	1	ENST00000312049.6:c.1798C>G	p.Leu600Val	p.L600V	ENST00000312049	NM_130799.2	600	Ctg/Gtg	10/10	0.206760096639482	3	FACETS	1	0.904	1	0.501	0.452	0.553	CLONAL	1	TRUE	1	0.206760096639482	3		889	1332	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044449	5044449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371826393	NA	P-0031029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	76	618	0	ENST00000381652.3:c.397C>T	p.Arg133Trp	p.R133W	ENST00000381652	NM_004972.3	133	Cgg/Tgg	5/25	0.206760096639482	10	FACETS	1	0.925	1	0.135	0.118	0.154	CLONAL	1	TRUE	2	0.206760096639482	10		618	1240	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786770	3786770	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	79	574	0	ENST00000262367.5:c.4441G>A	p.Asp1481Asn	p.D1481N	ENST00000262367	NM_004380.2	1481	Gat/Aat	27/31	0.206760096639482	3	FACETS	0.966	0.848	1	0.483	0.424	0.547	CLONAL	1	TRUE	1	0.206760096639482	3		574	873	SUCCESS
APC	324	MSKCC	GRCh37	5	112176877	112176877	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	57	480	0	ENST00000257430.4:c.5586G>C	p.Leu1862Phe	p.L1862F	ENST00000257430	NM_000038.5	1862	ttG/ttC	16/16	0.206760096639482	3	FACETS	0.951	0.815	1	0.317	0.271	0.367	CLONAL	1	TRUE	0	0.206760096639482	3		480	640	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003189	143003189	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764114435	NA	P-0031029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	153	407	0	ENST00000262992.4:c.2637G>A	p.Met879Ile	p.M879I	ENST00000262992	NM_001101669.1	879	atG/atA	23/24	0.206760096639482	5	FACETS	0.978	0.897	1	0.978	0.897	1	CLONAL	3	TRUE	2	0.206760096639482	5		407	661	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710657	114710657	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	95	544	0	ENST00000543371.1:c.142C>G	p.Leu48Val	p.L48V	ENST00000543371	NM_001198531.1	48	Cta/Gta	1/14	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.206760096639482	2		544	761	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373698	118373698	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	75	475	0	ENST00000534358.1:c.7091C>A	p.Ser2364Tyr	p.S2364Y	ENST00000534358	NM_005933.3	2364	tCt/tAt	27/36	0.206760096639482	3	FACETS	0.988	0.865	1	0.329	0.288	0.374	CLONAL	1	TRUE	0	0.206760096639482	3		475	810	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041458	42041458	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	71	530	0	ENST00000219905.7:c.5653T>A	p.Ser1885Thr	p.S1885T	ENST00000219905	NM_001164273.1	1885	Tca/Aca	17/24	0.206760096639482	2	FACETS	0.997	0.87	1	0.498	0.435	0.567	CLONAL	1	TRUE	0	0.206760096639482	2		530	689	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129653	11129655	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	ACG	ACG	-	novel	NA	P-0031029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	99	744	1	ENST00000358026.2:c.2460_2462del	p.Tyr820_Glu821delinsTer	p.Y820_E821delins*	ENST00000358026	NM_001128849.1	820	tACGag/tag	17/36	0.206760096639482	5	FACETS	1	0.919	1	0.26	0.231	0.291	CLONAL	1	TRUE	1	0.206760096639482	5		745	1208	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265477	198265477	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	407	613	0	ENST00000335508.6:c.2680G>C	p.Asp894His	p.D894H	ENST00000335508	NM_012433.2	894	Gat/Cat	18/25	0.206760096639482	5	FACETS	0.986	0.941	1	0.986	0.941	1	CLONAL	5	TRUE	0	0.206760096639482	5		613	1046	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103729	47103729	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	75	542	0	ENST00000409792.3:c.6217G>C	p.Glu2073Gln	p.E2073Q	ENST00000409792	NM_014159.6	2073	Gag/Cag	14/21	0.206760096639482	4	FACETS	1	0.877	1			1	CLONAL	1	TRUE	NA	0.206760096639482	4		542	873	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	C	novel	NA	P-0031029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	266	566	0				ENST00000310581	NM_198253.2	-/1132			0.206760096639482	3	FACETS	0.915	0.861	0.969	1	0.989	1	CLONAL	4	TRUE	0	0.206760096639482	3		566	776	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671781	30671781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373515222	NA	P-0031029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	67	634	0	ENST00000376406.3:c.5179G>A	p.Ala1727Thr	p.A1727T	ENST00000376406	NM_014641.2	1727	Gct/Act	10/15	0.206760096639482	5	FACETS	0.795	0.689	0.911	0.265	0.229	0.304	CLONAL	1	TRUE	2	0.206760096639482	5		634	1068	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671918	30671918	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	79	776	0	ENST00000376406.3:c.5042G>A	p.Ser1681Asn	p.S1681N	ENST00000376406	NM_014641.2	1681	aGc/aAc	10/15	0.206760096639482	5	FACETS	0.809	0.709	0.918	0.27	0.236	0.306	CLONAL	1	TRUE	2	0.206760096639482	5		776	1237	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004440	150004440	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	63	500	0	ENST00000253339.5:c.1785G>C	p.Lys595Asn	p.K595N	ENST00000253339		595	aaG/aaC	3/7	0.206760096639482	2	FACETS	0.795	0.686	0.913	0.397	0.343	0.457	CLONAL	1	TRUE	0	0.206760096639482	2		500	767	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859445	151859445	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	61	472	0	ENST00000262189.6:c.11217G>T	p.Gln3739His	p.Q3739H	ENST00000262189	NM_170606.2	3739	caG/caT	43/59	0.206760096639482	4	FACETS	0.937	0.807	1	0.468	0.403	0.54	CLONAL	1	TRUE	2	0.206760096639482	4		472	760	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654856	29654856	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1049849034	NA	P-0031031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	57	201	0	ENST00000356175.3:c.5545C>T	p.Arg1849Trp	p.R1849W	ENST00000356175	NM_000267.3	1849	Cgg/Tgg	37/57	1	2	FACETS	0.962	0.828	1	0.962	0.828	1	CLONAL	1	FALSE	1	0.3	2		201	395	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242470	+	missense_variant	Missense_Mutation	DNP	TT	TT	CC	rs397517096	NA	P-0031031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	101	449	1	ENST00000275493.2:c.2239_2240delinsCC	p.Leu747Pro	p.L747P	ENST00000275493	NM_005228.3	747	TTa/CCa	19/28	0.273497864004983	3	FACETS	0.789	0.704	0.88	0.395	0.352	0.44	SUBCLONAL	1	FALSE	1	0.3	3		450	981	SUCCESS
AR	367	MSKCC	GRCh37	X	66766406	66766406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1238856883	NA	P-0031031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	78	196	0	ENST00000374690.3:c.1418G>A	p.Gly473Asp	p.G473D	ENST00000374690	NM_000044.3	473	gGc/gAc	1/8	1	2	FACETS	0.818	0.725	0.915	1	0.98	1	CLONAL	2	FALSE	1	0.3	2		196	318	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0031049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	232	531	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.459900093883293	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.687452222644184	1		532	342	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631392	117631392	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371087942	NA	P-0031049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	94	351	2	ENST00000368508.3:c.6286C>T	p.Arg2096Trp	p.R2096W	ENST00000368508	NM_002944.2	2096	Cgg/Tgg	40/43	0.584242649966657	1	FACETS	0.598	0.539	0.66	0.598	0.539	0.66	SUBCLONAL	1	TRUE	0	0.687452222644184	1		353	300	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	39	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.824	0.691	0.968	0.824	0.691	0.968	CLONAL	1	TRUE	1	0.493219855141761	2		215	192	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181379	185181379	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	113	367	0	ENST00000265026.3:c.1320C>G	p.Ile440Met	p.I440M	ENST00000265026	NM_004721.4	440	atC/atG	8/14	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.493219855141761	2		367	453	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223590	55223590	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4045	446	410	0	ENST00000275493.2:c.957G>T	p.Glu319Asp	p.E319D	ENST00000275493	NM_005228.3	319	gaG/gaT	8/28	0.493219855141761	39	FACETS	1	0.962	1			1	CLONAL	4	TRUE	NA	0.493219855141761	39		410	4491	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	73	446	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.399866895298869	2		446	350	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	117	736	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.999	0.903	1	0.999	0.903	1	CLONAL	1	TRUE	1	0.399866895298869	2		741	586	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	188	730	0	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.399866895298869	2		730	863	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	121	385	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	1	2	FACETS	0.967	0.876	1	0.967	0.876	1	CLONAL	1	TRUE	1	0.399866895298869	2		385	626	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591132	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	rs1057519842	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	50	256	0	ENST00000274335.5:c.1727_1729del	p.Thr576del	p.T576del	ENST00000274335		575	aaGACg/aag	12/15	1	2	FACETS	0.842	0.719	0.975	0.842	0.719	0.975	CLONAL	1	TRUE	1	0.399866895298869	2		256	297	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692790	89692790	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554898067	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	127	263	0	ENST00000371953.3:c.274G>T	p.Asp92Tyr	p.D92Y	ENST00000371953	NM_000314.4	92	Gac/Tac	5/9	0.399866895298869	2	FACETS	0.96	0.881	1	0.96	0.881	1	CLONAL	2	TRUE	0	0.399866895298869	2		263	331	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	89	275	3	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.399866895298869	2		278	311	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465952	69465952	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	124	536	0	ENST00000227507.2:c.790C>T	p.Gln264Ter	p.Q264*	ENST00000227507	NM_053056.2	264	Cag/Tag	5/5	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.399866895298869	2		536	604	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161939	47161939	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	18	227	0	ENST00000409792.3:c.4187del	p.Asn1396MetfsTer16	p.N1396Mfs*16	ENST00000409792	NM_014159.6	1396	aAt/at	3/21	1	2	FACETS	0.288	0.216	0.372	0.288	0.216	0.372	SUBCLONAL	1	TRUE	1	0.399866895298869	2		227	313	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435815	56435815	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755967475	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	68	282	2	ENST00000407977.2:c.1322del	p.Pro441LeufsTer61	p.P441Lfs*61	ENST00000407977		441	cCt/ct	9/10	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.399866895298869	2		284	328	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214398	36214398	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs868041281	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	150	522	0	ENST00000222270.7:c.3057del	p.Gly1020AlafsTer4	p.G1020Afs*4	ENST00000222270	NM_014727.1	1018	Aaa/aa	7/37	1	2	FACETS	0.945	0.864	1	0.945	0.864	1	CLONAL	1	TRUE	1	0.399866895298869	2		522	794	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915853	127915853	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	68	354	2	ENST00000373547.4:c.628C>T	p.Arg210Ter	p.R210*	ENST00000373547	NM_002721.4	210	Cga/Tga	6/7	1	2	FACETS	0.691	0.603	0.787	0.691	0.603	0.787	SUBCLONAL	1	TRUE	1	0.399866895298869	2		356	492	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538991	187538991	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	100	398	0	ENST00000441802.2:c.8749C>T	p.Arg2917Ter	p.R2917*	ENST00000441802	NM_005245.3	2917	Cga/Tga	10/27	1	2	FACETS	0.918	0.822	1	0.918	0.822	1	CLONAL	1	TRUE	1	0.399866895298869	2		398	545	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831345	89831346	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs878853663	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	140	404	0	ENST00000389301.3:c.2730_2731del	p.Trp911AspfsTer31	p.W911Dfs*31	ENST00000389301	NM_000135.2	910	ctCTgg/ctgg	28/43	NA	2	FACETS	1	0.928	1			1	INDETERMINATE	1	TRUE	NA	0.399866895298869	2		404	687	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348341	89348341	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1347006212	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	194	678	0	ENST00000301030.4:c.4609G>A	p.Gly1537Ser	p.G1537S	ENST00000301030	NM_001256183.1	1537	Ggt/Agt	9/13	0.399866895298869	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.399866895298869	1		678	667	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540533	187540533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770573765	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	82	298	0	ENST00000441802.2:c.7207G>A	p.Ala2403Thr	p.A2403T	ENST00000441802	NM_005245.3	2403	Gcc/Acc	10/27	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.399866895298869	2		298	349	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779331	3779331	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	152	437	0	ENST00000262367.5:c.5717del	p.Pro1906LeufsTer9	p.P1906Lfs*9	ENST00000262367	NM_004380.2	1906	cCt/ct	31/31	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.399866895298869	2		437	684	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089471	27089471	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	105	482	0	ENST00000324856.7:c.2430del	p.Arg811GlyfsTer22	p.R811Gfs*22	ENST00000324856	NM_006015.4	809	taC/ta	8/20	1	2	FACETS	0.912	0.819	1	0.912	0.819	1	CLONAL	1	TRUE	1	0.399866895298869	2		482	576	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261357	115261357	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	81	270	0	ENST00000438362.2:c.2364del	p.Lys789ArgfsTer15	p.K789Rfs*15	ENST00000438362	NM_001242891.1	788	ccC/cc	19/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.399866895298869	2		270	309	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681393	88681393	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	38	192	0	ENST00000372037.3:c.1283C>A	p.Ala428Asp	p.A428D	ENST00000372037	NM_004329.2	428	gCt/gAt	11/13	0.399866895298869	2	FACETS	0.819	0.682	0.969	0.41	0.341	0.485	CLONAL	1	TRUE	0	0.399866895298869	2		192	232	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102098304	102098304	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	107	387	0	ENST00000282441.5:c.1268T>C	p.Met423Thr	p.M423T	ENST00000282441	NM_001130145.2	423	aTg/aCg	8/9	1	2	FACETS	0.995	0.896	1	0.995	0.896	1	CLONAL	1	TRUE	1	0.399866895298869	2		387	538	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374784	118374784	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	62	291	0	ENST00000534358.1:c.8177G>A	p.Gly2726Glu	p.G2726E	ENST00000534358	NM_005933.3	2726	gGg/gAg	27/36	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.399866895298869	2		291	305	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495380	56495380	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	123	482	1	ENST00000267101.3:c.3570A>T	p.Glu1190Asp	p.E1190D	ENST00000267101	NM_001982.3	1190	gaA/gaT	28/28	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.399866895298869	2		483	551	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134151	41134151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	16	253	0	ENST00000379561.5:c.1477G>A	p.Gly493Ser	p.G493S	ENST00000379561	NM_002015.3	493	Ggc/Agc	2/3	1	2	FACETS	0.275	0.203	0.361	0.275	0.203	0.361	SUBCLONAL	1	TRUE	1	0.399866895298869	2		253	291	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788575	3788575	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	22	330	0	ENST00000262367.5:c.4379A>G	p.Tyr1460Cys	p.Y1460C	ENST00000262367	NM_004380.2	1460	tAt/tGt	26/31	1	2	FACETS	0.271	0.209	0.343	0.271	0.209	0.343	SUBCLONAL	1	TRUE	1	0.399866895298869	2		330	406	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262204	10262204	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	127	458	0	ENST00000340748.4:c.2087T>C	p.Met696Thr	p.M696T	ENST00000340748		696	aTg/aCg	23/40	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.399866895298869	2		458	605	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855483	45855483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1427305754	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	156	503	0	ENST00000391945.4:c.2174C>T	p.Ala725Val	p.A725V	ENST00000391945	NM_000400.3	725	gCa/gTa	22/23	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.399866895298869	2		503	721	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572906	41572906	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	135	449	0	ENST00000263253.7:c.5191C>T	p.Arg1731Cys	p.R1731C	ENST00000263253	NM_001429.3	1731	Cgc/Tgc	31/31	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.399866895298869	2		449	574	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950607	79950607	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	168	451	1	ENST00000265081.6:c.61C>T	p.Gln21Ter	p.Q21*	ENST00000265081	NM_002439.4	21	Caa/Taa	1/24	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.399866895298869	2		452	697	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457767	149457767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746530522	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	121	412	0	ENST00000286301.3:c.637G>A	p.Val213Met	p.V213M	ENST00000286301	NM_005211.3	213	Gtg/Atg	5/22	1	2	FACETS	0.924	0.836	1	0.924	0.836	1	CLONAL	1	TRUE	1	0.399866895298869	2		412	655	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324485	31324485	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs78545099	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	151	564	0	ENST00000412585.2:c.323A>G	p.Tyr108Cys	p.Y108C	ENST00000412585	NM_005514.6	108	tAc/tGc	2/8	1	2	FACETS	0.963	0.882	1	0.963	0.882	1	CLONAL	1	TRUE	1	0.399866895298869	2		564	784	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642527	117642528	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	126	502	0	ENST00000368508.3:c.5671dup	p.Ser1891LysfsTer18	p.S1891Kfs*18	ENST00000368508	NM_002944.2	1891	agt/aAgt	35/43	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.399866895298869	2		502	628	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554320	141554320	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	174	607	0	ENST00000220592.5:c.1831A>G	p.Ile611Val	p.I611V	ENST00000220592	NM_012154.3	611	Att/Gtt	14/19	1	2	FACETS	0.982	0.905	1	0.982	0.905	1	CLONAL	1	TRUE	1	0.399866895298869	2		607	886	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGG	novel	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	120	619	0	ENST00000220592.5:c.1804_1806dup	p.Pro602dup	p.P602dup	ENST00000220592	NM_012154.3	602	-/CCC	14/19	1	2	FACETS	0.639	0.576	0.705	0.639	0.576	0.705	SUBCLONAL	1	TRUE	1	0.399866895298869	2		619	940	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404560	8404561	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	52	188	0	ENST00000356435.5:c.4186dup	p.Arg1396ProfsTer14	p.R1396Pfs*14	ENST00000356435		1396	cgg/cCgg	25/35	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.399866895298869	2		188	209	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250136	110250136	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	137	511	0	ENST00000374672.4:c.539del	p.Pro180LeufsTer14	p.P180Lfs*14	ENST00000374672	NM_004235.4	180	cCt/ct	3/5	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.399866895298869	2		511	580	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772061	135772061	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	85	335	0	ENST00000298552.3:c.3056A>G	p.Lys1019Arg	p.K1019R	ENST00000298552	NM_001162426.1	1019	aAg/aGg	23/23	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.399866895298869	2		335	409	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139562748	139562748	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	198	579	0	ENST00000308874.7:c.14A>G	p.Gln5Arg	p.Q5R	ENST00000308874		5	cAg/cGg	3/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.399866895298869	2		579	756	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949981	44949981	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	66	308	0	ENST00000377967.4:c.3750A>T	p.Lys1250Asn	p.K1250N	ENST00000377967	NM_021140.2	1250	aaA/aaT	26/29	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.399866895298869	2		308	321	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650769	48650769	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	160	504	0	ENST00000376670.3:c.638C>A	p.Pro213Gln	p.P213Q	ENST00000376670	NM_002049.3	213	cCa/cAa	4/6	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.399866895298869	2		504	734	SUCCESS
AR	367	MSKCC	GRCh37	X	66863118	66863118	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1416092874	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	42	458	0	ENST00000374690.3:c.1637A>G	p.His546Arg	p.H546R	ENST00000374690	NM_000044.3	546	cAt/cGt	2/8	1	2	FACETS	0.368	0.307	0.436	0.368	0.307	0.436	SUBCLONAL	1	TRUE	1	0.399866895298869	2		458	571	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352308	70352308	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	155	566	0	ENST00000374080.3:c.4335G>T	p.Lys1445Asn	p.K1445N	ENST00000374080		1445	aaG/aaT	31/45	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.399866895298869	2		566	689	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089720	27089721	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	T	novel	NA	P-0031059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	89	460	0	ENST00000324856.7:c.2676_2677delinsT	p.Thr894ProfsTer25	p.T894Pfs*25	ENST00000324856	NM_006015.4	892	cgGAaa/cgTaa	8/20	1	2	FACETS	0.78	0.693	0.872	0.78	0.693	0.872	SUBCLONAL	1	TRUE	1	0.399866895298869	2		460	571	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	97	590	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.29	2		590	668	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868166	56868166	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	47	495	0	ENST00000308159.5:c.1664G>T	p.Arg555Met	p.R555M	ENST00000308159	NM_014669.4	555	aGg/aTg	14/22	1	2	FACETS	0.596	0.502	0.699	0.596	0.502	0.699	SUBCLONAL	1	TRUE	1	0.29	2		495	544	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793364	242793364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	105	717	0	ENST00000334409.5:c.713C>T	p.Pro238Leu	p.P238L	ENST00000334409	NM_005018.2	238	cCc/cTc	5/5	0.3	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.29	1		717	597	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407472	139407473	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	78	484	0	ENST00000277541.6:c.2467_2467+1delinsAA		p.X823_splice	ENST00000277541	NM_017617.3	823		15/34	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.29	2		484	491	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962804	2962804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772900135	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	71	598	2	ENST00000396946.4:c.2104G>A	p.Glu702Lys	p.E702K	ENST00000396946	NM_032415.4	702	Gag/Aag	16/25	1	2	FACETS	0.812	0.709	0.923	0.812	0.709	0.923	CLONAL	1	TRUE	1	0.29	2		600	603	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242662	46242662	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	60	378	1	ENST00000334344.6:c.1624C>T	p.Arg542Ter	p.R542*	ENST00000334344	NM_152641.2	542	Cga/Tga	13/21	1	2	FACETS	0.947	0.818	1	0.947	0.818	1	CLONAL	1	TRUE	1	0.29	2		379	437	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971017	55971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	31	563	0	ENST00000263923.4:c.1780C>T	p.His594Tyr	p.H594Y	ENST00000263923	NM_002253.2	594	Cat/Tat	13/30	0.3	1	FACETS	0.378	0.305	0.461	0.378	0.305	0.461	SUBCLONAL	1	TRUE	0	0.29	1		563	483	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186613	108186613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565499041	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	68	402	0	ENST00000278616.4:c.6070G>A	p.Gly2024Arg	p.G2024R	ENST00000278616	NM_000051.3	2024	Ggg/Agg	41/63	1	2	FACETS	0.947	0.826	1	0.947	0.826	1	CLONAL	1	TRUE	1	0.29	2		402	495	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971029	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	114	332	0	ENST00000304494.5:c.329_330delinsAA	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tGG/tAA	2/3	0.228132686337643	3	FACETS	1	0.964	1	0.748	0.679	0.82	CLONAL	2	TRUE	0	0.29	3		332	401	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041725	29041725	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	43	449	0	ENST00000282397.4:c.94C>T	p.Pro32Ser	p.P32S	ENST00000282397	NM_002019.4	32	Cct/Tct	2/30	1	2	FACETS	0.59	0.493	0.697	0.59	0.493	0.697	SUBCLONAL	1	TRUE	1	0.29	2		449	503	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866465	42866465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	58	667	0	ENST00000398585.3:c.167G>A	p.Gly56Glu	p.G56E	ENST00000398585	NM_001135099.1	56	gGa/gAa	3/14	1	2	FACETS	0.506	0.433	0.585	0.506	0.433	0.585	SUBCLONAL	1	TRUE	1	0.29	2		667	791	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965111	81965111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	79	413	0	ENST00000359376.3:c.2591C>T	p.Pro864Leu	p.P864L	ENST00000359376	NM_002661.3	864	cCt/cTt	25/33	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.29	2		413	446	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194858	30194858	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771807174	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	32	429	0	ENST00000331968.5:c.287G>A	p.Gly96Glu	p.G96E	ENST00000331968	NM_002742.2	96	gGa/gAa	2/18	1	2	FACETS	0.447	0.362	0.543	0.447	0.362	0.543	SUBCLONAL	1	TRUE	1	0.29	2		429	494	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058575	69058575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	59	628	0	ENST00000288368.4:c.4219C>T	p.Leu1407Phe	p.L1407F	ENST00000288368	NM_024870.2	1407	Ctt/Ttt	34/40	1	2	FACETS	0.596	0.512	0.687	0.596	0.512	0.687	SUBCLONAL	1	TRUE	1	0.29	2		628	683	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363246	40363246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1337002326	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	40	575	1	ENST00000397332.2:c.983G>A	p.Arg328His	p.R328H	ENST00000397332	NM_001033082.2	328	cGt/cAt	3/3	1	2	FACETS	0.466	0.386	0.555	0.466	0.386	0.555	SUBCLONAL	1	TRUE	1	0.29	2		576	592	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2215901	2215901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201132936	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	91	566	1	ENST00000326181.6:c.103G>A	p.Gly35Arg	p.G35R	ENST00000326181	NM_032271.2	35	Gga/Aga	3/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.29	2		567	555	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391980	139391980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	65	575	0	ENST00000277541.6:c.6211G>A	p.Glu2071Lys	p.E2071K	ENST00000277541	NM_017617.3	2071	Gag/Aag	34/34	1	2	FACETS	0.777	0.674	0.889	0.777	0.674	0.889	SUBCLONAL	1	TRUE	1	0.29	2		575	577	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189841	11189841	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1376396626	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	36	480	0	ENST00000361445.4:c.5668C>T	p.Arg1890Cys	p.R1890C	ENST00000361445	NM_004958.3	1890	Cgt/Tgt	40/58	0.3	1	FACETS	0.395	0.324	0.474	0.395	0.324	0.474	SUBCLONAL	1	TRUE	0	0.29	1		480	538	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39613899	39613899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775480477	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	18	322	0	ENST00000262039.4:c.1817C>T	p.Pro606Leu	p.P606L	ENST00000262039	NM_002647.2	606	cCg/cTg	16/25	0.3	1	FACETS	0.371	0.279	0.48	0.371	0.279	0.48	SUBCLONAL	1	TRUE	0	0.29	1		322	286	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	81	462	1				ENST00000310581	NM_198253.2	-/1132			0.197448317636838	3	FACETS	0.922	0.818	1	0.922	0.818	1	CLONAL	2	TRUE	1	0.29	3		463	347	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784385	9784385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	68	681	0	ENST00000377346.4:c.2770G>A	p.Gly924Arg	p.G924R	ENST00000377346	NM_005026.3	924	Gga/Aga	22/24	0.3	1	FACETS	0.648	0.563	0.739	0.648	0.563	0.739	SUBCLONAL	1	TRUE	0	0.29	1		681	619	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259952	16259952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1167650185	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	33	527	0	ENST00000375759.3:c.7217C>T	p.Pro2406Leu	p.P2406L	ENST00000375759	NM_015001.2	2406	cCc/cTc	11/15	0.3	1	FACETS	0.38	0.309	0.461	0.38	0.309	0.461	SUBCLONAL	1	TRUE	0	0.29	1		527	512	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023748	27023748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	27	299	0	ENST00000324856.7:c.854G>A	p.Gly285Glu	p.G285E	ENST00000324856	NM_006015.4	285	gGa/gAa	1/20	1	2	FACETS	0.532	0.423	0.656	0.532	0.423	0.656	SUBCLONAL	1	TRUE	1	0.29	2		299	350	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459318	120459318	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	26	321	0	ENST00000256646.2:c.6028-1G>A		p.X2010_splice	ENST00000256646	NM_024408.3	2010			1	2	FACETS	0.6	0.476	0.741	0.6	0.476	0.741	SUBCLONAL	1	TRUE	1	0.29	2		321	299	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263380	123263380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1251168391	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	77	439	0	ENST00000358487.5:c.1363G>A	p.Ala455Thr	p.A455T	ENST00000358487	NM_000141.4	455	Gca/Aca	10/18	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.29	2		439	511	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416735	416735	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	72	355	0	ENST00000399788.2:c.3815C>T	p.Ala1272Val	p.A1272V	ENST00000399788	NM_001042603.1	1272	gCc/gTc	23/28	0.075336775421162	3	FACETS	1	0.958	1			1	INDETERMINATE	1	TRUE	NA	0.29	3		355	464	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	459852	459867	+	frameshift_variant	Frame_Shift_Del	DEL	AGGAGATATCTGCTCC	AGGAGATATCTGCTCC	-	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	129	623	0	ENST00000399788.2:c.1228_1243del	p.Gly410GlnfsTer10	p.G410Qfs*10	ENST00000399788	NM_001042603.1	410	GGAGCAGATATCTCCTca/ca	10/28	0.075336775421162	3	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.29	3		623	922	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46240694	46240694	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	71	450	0	ENST00000334344.6:c.1554A>G	p.Ile518Met	p.I518M	ENST00000334344	NM_152641.2	518	atA/atG	12/21	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.29	2		450	466	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427621	49427622	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	61	564	1	ENST00000301067.7:c.10866_10867delinsTT	p.Gln3623Ter	p.Q3623*	ENST00000301067	NM_003482.3	3622	tcCCag/tcTTag	39/54	1	2	FACETS	0.913	0.789	1	0.913	0.789	1	CLONAL	1	TRUE	1	0.29	2		565	461	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858468	57858468	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763536538	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	35	535	0	ENST00000228682.2:c.206C>T	p.Ser69Phe	p.S69F	ENST00000228682	NM_005269.2	69	tCt/tTt	4/12	1	2	FACETS	0.418	0.341	0.504	0.418	0.341	0.504	SUBCLONAL	1	TRUE	1	0.29	2		535	578	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112893802	112893802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	23	350	0	ENST00000351677.2:c.691C>T	p.Arg231Ter	p.R231*	ENST00000351677	NM_002834.3	231	Cga/Tga	6/16	1	2	FACETS	0.373	0.29	0.47	0.373	0.29	0.47	SUBCLONAL	1	TRUE	1	0.29	2		350	425	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28908200	28908200	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	59	544	0	ENST00000282397.4:c.2555C>T	p.Ser852Leu	p.S852L	ENST00000282397	NM_002019.4	852	tCa/tTa	18/30	1	2	FACETS	0.725	0.624	0.835	0.725	0.624	0.835	SUBCLONAL	1	TRUE	1	0.29	2		544	561	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937639	32937639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507401	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	42	479	0	ENST00000380152.3:c.8300C>T	p.Pro2767Leu	p.P2767L	ENST00000380152		2767	cCt/cTt	18/27	1	2	FACETS	0.588	0.49	0.695	0.588	0.49	0.695	SUBCLONAL	1	TRUE	1	0.29	2		479	493	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557423	95557424	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	29	396	0	ENST00000393063.1:c.5550_5551delinsTT	p.Arg1851Cys	p.R1851C	ENST00000393063	NM_030621.3	1850	ccCCgt/ccTTgt	27/28	1	2	FACETS	0.356	0.285	0.437	0.356	0.285	0.437	SUBCLONAL	1	TRUE	1	0.29	2		396	562	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632477	3632477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371875095	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	104	699	0	ENST00000294008.3:c.5371C>T	p.Arg1791Cys	p.R1791C	ENST00000294008	NM_032444.2	1791	Cgt/Tgt	15/15	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.29	2		699	698	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633275	3633276	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	135	804	2	ENST00000294008.3:c.4975_4976delinsTT	p.Pro1659Phe	p.P1659F	ENST00000294008	NM_032444.2	1659	CCt/TTt	14/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.29	2		806	786	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923344	9923344	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs796052545	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	44	554	0	ENST00000330684.3:c.1943A>G	p.Asn648Ser	p.N648S	ENST00000330684	NM_001134407.1	648	aAt/aGt	9/13	1	2	FACETS	0.544	0.455	0.642	0.544	0.455	0.642	SUBCLONAL	1	TRUE	1	0.29	2		554	558	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645289	67645289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	57	474	0	ENST00000264010.4:c.554C>T	p.Pro185Leu	p.P185L	ENST00000264010	NM_006565.3	185	cCc/cTc	3/12	1	2	FACETS	0.855	0.735	0.985	0.855	0.735	0.985	CLONAL	1	TRUE	1	0.29	2		474	460	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245173	41245173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	117	713	0	ENST00000357654.3:c.2375G>A	p.Gly792Glu	p.G792E	ENST00000357654	NM_007294.3	792	gGg/gAg	10/23	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.29	2		713	774	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59937265	59937265	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772319724	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	37	349	0	ENST00000259008.2:c.97C>T	p.Leu33Phe	p.L33F	ENST00000259008	NM_032043.2	33	Ctc/Ttc	3/20	1	2	FACETS	0.534	0.44	0.639	0.534	0.44	0.639	SUBCLONAL	1	TRUE	1	0.29	2		349	478	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10267151	10267151	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1181209213	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	47	422	1	ENST00000340748.4:c.1267G>A	p.Asp423Asn	p.D423N	ENST00000340748		423	Gac/Aac	17/40	0.3	1	FACETS	0.532	0.449	0.624	0.532	0.449	0.624	SUBCLONAL	1	TRUE	0	0.29	1		423	521	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953400	17953400	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs565101202	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	64	610	0	ENST00000458235.1:c.586C>G	p.Pro196Ala	p.P196A	ENST00000458235	NM_000215.3	196	Cca/Gca	6/24	0.3	1	FACETS	0.679	0.588	0.777	0.679	0.588	0.777	SUBCLONAL	1	TRUE	0	0.29	1		610	556	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279931	18279931	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1006826088	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	51	557	0	ENST00000222254.8:c.2014C>T	p.Arg672Cys	p.R672C	ENST00000222254	NM_005027.3	672	Cgc/Tgc	16/16	0.3	1	FACETS	0.517	0.439	0.602	0.517	0.439	0.602	SUBCLONAL	1	TRUE	0	0.29	1		557	582	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753800	42753800	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	55	731	1	ENST00000222329.4:c.464C>T	p.Pro155Leu	p.P155L	ENST00000222329	NM_006494.2	155	cCc/cTc	4/4	0.3	1	FACETS	0.465	0.397	0.539	0.465	0.397	0.539	SUBCLONAL	1	TRUE	0	0.29	1		732	698	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964906	25964907	+	missense_variant	Missense_Mutation	DNP	CG	CG	AA	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	31	386	1	ENST00000435504.4:c.4299_4300delinsTT	p.Val1434Phe	p.V1434F	ENST00000435504		1433	gtCGtt/gtTTtt	13/13	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.29	NA		387	445	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101089	26101089	+	start_lost	Translation_Start_Site	SNP	C	C	A	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	68	383	0	ENST00000435504.4:c.3G>T	p.Met1?	p.M1?	ENST00000435504		1	atG/atT	1/13	1	2	FACETS	0.883	0.769	1	0.883	0.769	1	CLONAL	1	TRUE	1	0.29	2		383	531	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158636990	158636990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	83	484	0	ENST00000263640.3:c.190C>T	p.His64Tyr	p.H64Y	ENST00000263640	NM_001105.4	64	Cac/Tac	4/11	1	2	FACETS	0.987	0.872	1	0.987	0.872	1	CLONAL	1	TRUE	1	0.29	2		484	580	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738302	190738302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	31	316	0	ENST00000441310.2:c.2554G>A	p.Glu852Lys	p.E852K	ENST00000441310	NM_000534.4	852	Gaa/Aaa	12/13	1	2	FACETS	0.57	0.461	0.693	0.57	0.461	0.693	SUBCLONAL	1	TRUE	1	0.29	2		316	375	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525105	9525105	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	37	384	0	ENST00000353224.5:c.1780T>C	p.Ser594Pro	p.S594P	ENST00000353224	NM_177990.2	594	Tcc/Ccc	8/10	0.27424633395991	3	FACETS	0.614	0.506	0.735	0.307	0.253	0.368	SUBCLONAL	1	TRUE	1	0.29	3		384	476	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309626	30309627	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	198	621	0	ENST00000307677.4:c.395_396delinsAA	p.Arg132Gln	p.R132Q	ENST00000307677	NM_138578.1	132	cGG/cAA	2/3	0.27424633395991	3	FACETS	0.912	0.846	0.981	0.912	0.846	0.981	CLONAL	2	TRUE	1	0.29	3		621	857	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267060	41267060	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	30	394	0	ENST00000349496.5:c.731T>C	p.Leu244Pro	p.L244P	ENST00000349496	NM_001904.3	244	cTt/cCt	5/15	1	2	FACETS	0.52	0.419	0.635	0.52	0.419	0.635	SUBCLONAL	1	TRUE	1	0.29	2		394	398	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158147	47158147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	44	515	0	ENST00000409792.3:c.4552G>A	p.Glu1518Lys	p.E1518K	ENST00000409792	NM_014159.6	1518	Gaa/Aaa	4/21	1	2	FACETS	0.496	0.415	0.586	0.496	0.415	0.586	SUBCLONAL	1	TRUE	1	0.29	2		515	612	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935520	49935520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	39	654	0	ENST00000296474.3:c.1844C>T	p.Pro615Leu	p.P615L	ENST00000296474	NM_002447.2	615	cCc/cTc	5/20	1	2	FACETS	0.416	0.344	0.497	0.416	0.344	0.497	SUBCLONAL	1	TRUE	1	0.29	2		654	647	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456482	89456482	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	77	476	0	ENST00000336596.2:c.1658T>A	p.Ile553Asn	p.I553N	ENST00000336596	NM_005233.5	553	aTt/aAt	8/17	1	2	FACETS	0.948	0.834	1	0.948	0.834	1	CLONAL	1	TRUE	1	0.29	2		476	560	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920046	1920046	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	64	547	1	ENST00000382891.5:c.1106C>T	p.Ser369Phe	p.S369F	ENST00000382891	NM_133335.3	369	tCt/tTt	5/22	0.3	1	FACETS	0.653	0.565	0.748	0.653	0.565	0.748	SUBCLONAL	1	TRUE	0	0.29	1		548	578	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31464450	31464450	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	125	544	0	ENST00000344624.3:c.2467G>A	p.Glu823Lys	p.E823K	ENST00000344624		823	Gaa/Aaa	17/33	0.197448317636838	3	FACETS	1	0.954	1	0.546	0.494	0.601	CLONAL	1	TRUE	1	0.29	3		544	904	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721844	176721844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	64	510	0	ENST00000439151.2:c.7475C>T	p.Pro2492Leu	p.P2492L	ENST00000439151	NM_022455.4	2492	cCt/cTt	23/23	1	2	FACETS	0.808	0.701	0.925	0.808	0.701	0.925	CLONAL	1	TRUE	1	0.29	2		510	546	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020838	26020838	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	45	298	0	ENST00000357647.3:c.121C>T	p.Arg41Cys	p.R41C	ENST00000357647	NM_003529.2	41	Cgc/Tgc	1/1	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.29	2		298	294	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165149	32165149	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	77	670	2	ENST00000375023.3:c.4979C>T	p.Pro1660Leu	p.P1660L	ENST00000375023	NM_004557.3	1660	cCc/cTc	27/30	1	2	FACETS	0.828	0.727	0.937	0.828	0.727	0.937	CLONAL	1	TRUE	1	0.29	2		672	641	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150544	157150544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457449058	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	58	397	0	ENST00000346085.5:c.1726C>T	p.Pro576Ser	p.P576S	ENST00000346085	NM_020732.3	576	Cct/Tct	2/20	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.29	2		397	393	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92300793	92300794	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	51	330	0	ENST00000265734.4:c.593_594delinsTT	p.Thr198Ile	p.T198I	ENST00000265734	NM_001259.6	198	aCC/aTT	5/8	1	2	FACETS	0.9	0.767	1	0.9	0.767	1	CLONAL	1	TRUE	1	0.29	2		330	391	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526652	106526652	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1460186533	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	50	442	1	ENST00000359195.3:c.2945G>A	p.Arg982Lys	p.R982K	ENST00000359195	NM_002649.2	982	aGa/aAa	10/11	1	2	FACETS	0.587	0.498	0.686	0.587	0.498	0.686	SUBCLONAL	1	TRUE	1	0.29	2		443	587	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860568	151860569	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	91	571	1	ENST00000262189.6:c.10093_10094delinsTT	p.Pro3365Leu	p.P3365L	ENST00000262189	NM_170606.2	3365	CCa/TTa	43/59	1	2	FACETS	0.958	0.851	1	0.958	0.851	1	CLONAL	1	TRUE	1	0.29	2		572	655	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931854	68931854	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	65	556	0	ENST00000288368.4:c.284T>C	p.Leu95Ser	p.L95S	ENST00000288368	NM_024870.2	95	tTa/tCa	3/40	1	2	FACETS	0.698	0.605	0.799	0.698	0.605	0.799	SUBCLONAL	1	TRUE	1	0.29	2		556	642	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864860	117864860	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1236205322	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	94	504	0	ENST00000297338.2:c.1249C>T	p.Leu417Phe	p.L417F	ENST00000297338	NM_006265.2	417	Ctc/Ttc	10/14	1	2	FACETS	0.912	0.811	1	0.912	0.811	1	CLONAL	1	TRUE	1	0.29	2		504	711	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542715	141542715	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	61	478	1	ENST00000220592.5:c.2272-1G>A		p.X758_splice	ENST00000220592	NM_012154.3	758			1	2	FACETS	0.778	0.671	0.893	0.778	0.671	0.893	SUBCLONAL	1	TRUE	1	0.29	2		479	541	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471000	8471000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	84	383	0	ENST00000356435.5:c.3499G>A	p.Asp1167Asn	p.D1167N	ENST00000356435		1167	Gat/Aat	20/35	0.228132686337643	3	FACETS	1	0.973	1	0.449	0.398	0.504	CLONAL	1	TRUE	0	0.29	3		383	492	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759720	133759721	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	51	521	0	ENST00000318560.5:c.2043_2044delinsTT	p.Arg682Trp	p.R682W	ENST00000318560	NM_005157.4	681	ttCCgg/ttTTgg	11/11	1	2	FACETS	0.848	0.722	0.985	0.848	0.722	0.985	CLONAL	1	TRUE	1	0.29	2		521	415	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483180	120483182	+	stop_gained	Nonsense_Mutation	TNP	GAC	GAC	AAA	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	68	298	0	ENST00000256646.2:c.3179_3181delinsTTT	p.Cys1060_Gln1061delinsPheTer	p.C1060_Q1061delinsF*	ENST00000256646	NM_024408.3	1060	tGTCag/tTTTag	19/34	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.29	2		298	354	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4095409	4095411	+	missense_variant	Missense_Mutation	TNP	GTC	GTC	TTT	novel	NA	P-0031069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	74	680	0	ENST00000262948.5:c.1021_1023delinsAAA	p.Asp341Lys	p.D341K	ENST00000262948	NM_030662.3	341	GAC/AAA	9/11	0.3	1	FACETS	0.631	0.552	0.717	0.631	0.552	0.717	SUBCLONAL	1	TRUE	0	0.29	1		680	691	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	73	215	0				ENST00000310581	NM_198253.2	-/1132			0.4796173312286	4	FACETS	1	0.972	1	0.445	0.395	0.498	INDETERMINATE	1	TRUE	1	0.810860054163225	4		215	244	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0031077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	251	576	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.810860054163225	2		576	563	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294382	1294382	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs943176303	NA	P-0031077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	174	335	0	ENST00000310581.5:c.619G>A	p.Val207Ile	p.V207I	ENST00000310581	NM_198253.2	207	Gtc/Atc	2/16	0.4796173312286	4	FACETS	1	0.988	1	0.457	0.423	0.492	INDETERMINATE	1	TRUE	1	0.810860054163225	4		335	567	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461053	120461053	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	210	413	0	ENST00000256646.2:c.5905G>A	p.Asp1969Asn	p.D1969N	ENST00000256646	NM_024408.3	1969	Gat/Aat	32/34	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.810860054163225	2		413	494	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938898	178938898	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	151	320	0	ENST00000263967.3:c.2140A>G	p.Asn714Asp	p.N714D	ENST00000263967	NM_006218.2	714	Aac/Gac	14/21	0.592400771652586	3	FACETS	0.77	0.715	0.825	0.77	0.715	0.825	SUBCLONAL	2	TRUE	1	0.810860054163225	3		320	340	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	130	341	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.953	1	1	0.991	1	CLONAL	2	TRUE	1	0.267487183507935	2		341	456	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510806	157510806	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	40	392	1	ENST00000346085.5:c.3586del	p.Gln1196SerfsTer15	p.Q1196Sfs*15	ENST00000346085	NM_020732.3	1194	aCc/ac	14/20	1	2	FACETS	0.443	0.367	0.528	0.443	0.367	0.528	SUBCLONAL	1	TRUE	1	0.267487183507935	2		393	675	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	20	225	1	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	1	2	FACETS	0.39	0.298	0.499	0.39	0.298	0.499	SUBCLONAL	1	TRUE	1	0.267487183507935	2		226	383	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644874	67644874	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	37	341	0	ENST00000264010.4:c.143del	p.Gly48ValfsTer14	p.G48Vfs*14	ENST00000264010	NM_006565.3	47	Ggg/gg	3/12	1	2	FACETS	0.392	0.322	0.471	0.392	0.322	0.471	SUBCLONAL	1	TRUE	1	0.267487183507935	2		341	706	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466022	69466022	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	123	444	2	ENST00000227507.2:c.860C>A	p.Pro287His	p.P287H	ENST00000227507	NM_053056.2	287	cCc/cAc	5/5	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.267487183507935	2		446	756	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	73	374	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.924	0.808	1	0.924	0.808	1	CLONAL	1	TRUE	1	0.267487183507935	2		374	591	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	86	432	10	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	0.961	0.851	1	0.961	0.851	1	CLONAL	1	TRUE	1	0.267487183507935	2		442	669	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	67	348	1	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.267487183507935	2		349	474	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101267	27101268	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	113	465	1	ENST00000324856.7:c.4555dup	p.Gln1519ProfsTer13	p.Q1519Pfs*13	ENST00000324856	NM_006015.4	1517	gcc/gCcc	18/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.267487183507935	2		466	676	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199610	16199610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1405372960	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	74	288	0	ENST00000375759.3:c.383G>A	p.Arg128His	p.R128H	ENST00000375759	NM_015001.2	128	cGt/cAt	2/15	1	2	FACETS	0.901	0.789	1	0.901	0.789	1	CLONAL	1	TRUE	1	0.267487183507935	2		288	614	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	114	415	1	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.267487183507935	2		416	665	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351056	89351057	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	91	471	0	ENST00000301030.4:c.1893dup	p.His632ThrfsTer2	p.H632Tfs*2	ENST00000301030	NM_001256183.1	631	-/A	9/13	1	2	FACETS	0.777	0.689	0.871	0.777	0.689	0.871	SUBCLONAL	1	TRUE	1	0.267487183507935	2		471	876	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	55	232	0	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.267487183507935	2		232	379	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349641	89349641	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs772267579	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	119	488	4	ENST00000301030.4:c.3309del	p.Asp1104MetfsTer214	p.D1104Mfs*214	ENST00000301030	NM_001256183.1	1103	aaA/aa	9/13	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.267487183507935	2		492	868	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919935	50919935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1044937882	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	38	484	1	ENST00000440232.2:c.3022C>T	p.Arg1008Cys	p.R1008C	ENST00000440232	NM_002691.3	1008	Cgc/Tgc	24/27	1	2	FACETS	0.393	0.324	0.471	0.393	0.324	0.471	SUBCLONAL	1	TRUE	1	0.267487183507935	2		485	723	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119758	70119758	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	129	481	0	ENST00000245479.2:c.760C>T	p.Arg254Ter	p.R254*	ENST00000245479	NM_000346.3	254	Cga/Tga	3/3	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.267487183507935	2		481	728	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569765	95569765	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs35252236	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	57	177	1	ENST00000393063.1:c.3968del	p.Leu1323Ter	p.L1323*	ENST00000393063	NM_030621.3	1323	tTa/ta	22/28	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.267487183507935	2		178	366	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845624	63845627	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	57	211	1	ENST00000279873.7:c.1366_1369del	p.Glu456MetfsTer22	p.E456Mfs*22	ENST00000279873	NM_032199.2	455	AAAGaa/aa	9/10	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.267487183507935	2		212	331	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862767	9862767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1285952756	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	105	383	0	ENST00000330684.3:c.2536C>T	p.Arg846Cys	p.R846C	ENST00000330684	NM_001134407.1	846	Cgc/Tgc	12/13	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.267487183507935	2		383	687	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845366	151845366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	109	372	1	ENST00000262189.6:c.13646G>A	p.Arg4549His	p.R4549H	ENST00000262189	NM_170606.2	4549	cGc/cAc	52/59	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.267487183507935	2		373	762	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968233	134968233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753895808	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	93	378	0	ENST00000398015.3:c.2746G>A	p.Val916Met	p.V916M	ENST00000398015	NM_004441.4	916	Gtg/Atg	15/16	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.267487183507935	2		378	623	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1955176	1955176	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	116	377	1	ENST00000382891.5:c.2263C>T	p.Arg755Ter	p.R755*	ENST00000382891	NM_133335.3	755	Cga/Tga	12/22	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.267487183507935	2		378	792	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559231	141559231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	138	389	0	ENST00000220592.5:c.1570G>A	p.Gly524Ser	p.G524S	ENST00000220592	NM_012154.3	524	Ggc/Agc	12/19	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.267487183507935	2		389	795	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595382	141595382	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	148	399	1	ENST00000220592.5:c.51del	p.Ile18SerfsTer121	p.I18Sfs*121	ENST00000220592	NM_012154.3	17	ccC/cc	2/19	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.267487183507935	2		400	760	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942071	71942071	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	129	558	0	ENST00000298229.2:c.1335G>A	p.Trp445Ter	p.W445*	ENST00000298229	NM_001567.3	445	tgG/tgA	12/28	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.267487183507935	2		558	943	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561430	141561430	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	85	276	0	ENST00000220592.5:c.1375del	p.Gln459SerfsTer9	p.Q459Sfs*9	ENST00000220592	NM_012154.3	459	Cag/ag	11/19	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.267487183507935	2		276	573	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074189	8074189	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	107	264	1	ENST00000377482.5:c.470C>A	p.Pro157Gln	p.P157Q	ENST00000377482	NM_018948.3	157	cCa/cAa	4/4	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.267487183507935	2		265	608	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057881	27057881	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	125	406	1	ENST00000324856.7:c.1592del	p.Pro531ArgfsTer88	p.P531Rfs*88	ENST00000324856	NM_006015.4	530	tCc/tc	3/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.267487183507935	2		407	850	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870391	155870391	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	87	284	0	ENST00000368323.3:c.448T>A	p.Leu150Met	p.L150M	ENST00000368323	NM_006912.5	150	Ttg/Atg	6/6	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.267487183507935	2		284	573	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405778	70405778	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	52	372	1	ENST00000373644.4:c.3297del	p.Val1100LeufsTer40	p.V1100Lfs*40	ENST00000373644	NM_030625.2	1098	Aaa/aa	4/12	0.267487183507935	2	FACETS	0.627	0.533	0.73	0.314	0.266	0.365	SUBCLONAL	1	TRUE	0	0.267487183507935	2		373	620	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685305	89685305	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	53	188	0	ENST00000371953.3:c.200T>A	p.Ile67Lys	p.I67K	ENST00000371953	NM_000314.4	67	aTa/aAa	3/9	0.267487183507935	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	2	TRUE	0	0.267487183507935	2		188	191	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942110	71942111	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	157	597	0	ENST00000298229.2:c.1376_1377del	p.Thr459SerfsTer6	p.T459Sfs*6	ENST00000298229	NM_001567.3	458	gtCAca/gtca	12/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.267487183507935	2		597	940	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076749	102076749	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	135	372	0	ENST00000282441.5:c.928C>T	p.Gln310Ter	p.Q310*	ENST00000282441	NM_001130145.2	310	Caa/Taa	5/9	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.267487183507935	2		372	788	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440121	49440121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	116	412	0	ENST00000301067.7:c.4505C>T	p.Ala1502Val	p.A1502V	ENST00000301067	NM_003482.3	1502	gCc/gTc	16/54	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.267487183507935	2		412	826	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335853	73335853	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	30	267	0	ENST00000377767.4:c.2442T>G	p.Cys814Trp	p.C814W	ENST00000377767	NM_014953.3	814	tgT/tgG	18/21	1	2	FACETS	0.493	0.397	0.603	0.493	0.397	0.603	SUBCLONAL	1	TRUE	1	0.267487183507935	2		267	455	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30133003	30133003	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	102	346	0	ENST00000331968.5:c.598A>T	p.Arg200Trp	p.R200W	ENST00000331968	NM_002742.2	200	Agg/Tgg	4/18	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.267487183507935	2		346	686	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708507	43708507	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	114	388	0	ENST00000382044.4:c.4789C>T	p.Gln1597Ter	p.Q1597*	ENST00000382044	NM_001141980.1	1597	Caa/Taa	22/28	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.267487183507935	2		388	788	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096296	2096296	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	146	540	0	ENST00000219066.1:c.211T>C	p.Ser71Pro	p.S71P	ENST00000219066	NM_002528.5	71	Tcg/Ccg	2/6	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.267487183507935	2		540	842	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265006	46265006	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs773912198	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	104	289	1	ENST00000371998.3:c.1876A>T	p.Thr626Ser	p.T626S	ENST00000371998		626	Acc/Tcc	12/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.267487183507935	2		290	553	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528623	89528623	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1237297238	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	32	180	0	ENST00000336596.2:c.2923C>T	p.Gln975Ter	p.Q975*	ENST00000336596	NM_005233.5	975	Caa/Taa	17/17	1	2	FACETS	0.762	0.62	0.921	0.762	0.62	0.921	CLONAL	1	TRUE	1	0.267487183507935	2		180	314	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157790	106157790	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	52	220	0	ENST00000380013.4:c.2691G>T	p.Gln897His	p.Q897H	ENST00000380013	NM_001127208.2	897	caG/caT	3/11	1	2	FACETS	0.984	0.841	1	0.984	0.841	1	CLONAL	1	TRUE	1	0.267487183507935	2		220	395	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228307	228307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762108779	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	33	168	0	ENST00000264932.6:c.629G>A	p.Arg210Gln	p.R210Q	ENST00000264932	NM_004168.2	210	cGa/cAa	6/15	1	2	FACETS	0.942	0.771	1	0.942	0.771	1	CLONAL	1	TRUE	1	0.267487183507935	2		168	262	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161277	56161277	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	26	183	0	ENST00000399503.3:c.1149del	p.Phe383LeufsTer53	p.F383Lfs*53	ENST00000399503	NM_005921.1	382	aaT/aa	5/20	1	2	FACETS	0.657	0.521	0.812	0.657	0.521	0.812	SUBCLONAL	1	TRUE	1	0.267487183507935	2		183	296	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459425	50459425	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	25	175	0	ENST00000331340.3:c.716-2A>G		p.X239_splice	ENST00000331340	NM_006060.4	239			1	2	FACETS	0.625	0.493	0.776	0.625	0.493	0.776	SUBCLONAL	1	TRUE	1	0.267487183507935	2		175	299	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151216593	151216593	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	24	67	0	ENST00000262187.5:c.5C>A	p.Pro2Gln	p.P2Q	ENST00000262187	NM_005614.3	2	cCg/cAg	1/8	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.267487183507935	2		67	146	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965571	90965571	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	55	255	0	ENST00000265433.3:c.1746del	p.Lys582AsnfsTer16	p.K582Nfs*16	ENST00000265433	NM_002485.4	582	aaA/aa	11/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.267487183507935	2		255	311	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141568602	141568602	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	114	358	0	ENST00000220592.5:c.860G>T	p.Arg287Leu	p.R287L	ENST00000220592	NM_012154.3	287	cGg/cTg	7/19	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.267487183507935	2		358	729	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929418	44929419	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	137	477	0	ENST00000377967.4:c.2518_2519del	p.Ser840CysfsTer5	p.S840Cfs*5	ENST00000377967	NM_021140.2	840	AGt/t	17/29	0.267487183507935	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.267487183507935	1		477	822	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652222	48652222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	72	362	0	ENST00000376670.3:c.893G>A	p.Arg298Gln	p.R298Q	ENST00000376670	NM_002049.3	298	cGg/cAg	6/6	0.267487183507935	1	FACETS	0.74	0.647	0.841	0.74	0.647	0.841	SUBCLONAL	1	TRUE	0	0.267487183507935	1		362	630	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285053	15285053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	123	407	2	ENST00000263388.2:c.4562C>T	p.Pro1521Leu	p.P1521L	ENST00000263388	NM_000435.2	1521	cCa/cTa	25/33	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.267487183507935	2		409	701	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522619	106522619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	24	416	0	ENST00000359195.3:c.2596C>T	p.Pro866Ser	p.P866S	ENST00000359195	NM_002649.2	866	Cca/Tca	7/11	1	2	FACETS	0.81	0.637	1	0.81	0.637	1	CLONAL	1	TRUE	1	0.250132669401232	2		416	237	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0031134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	50	456	0	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.250132669401232	2		456	344	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692919	89692919	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782360	NA	P-0031134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	55	521	0	ENST00000371953.3:c.403A>G	p.Ile135Val	p.I135V	ENST00000371953	NM_000314.4	135	Ata/Gta	5/9	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.250132669401232	2		521	299	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244999	123244999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150015885	NA	P-0031134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	87	504	0	ENST00000358487.5:c.2105C>T	p.Ser702Leu	p.S702L	ENST00000358487	NM_000141.4	702	tCg/tTg	16/18	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.250132669401232	2		504	560	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685281	89685281	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	18	266	0	ENST00000371953.3:c.176C>A	p.Ser59Ter	p.S59*	ENST00000371953	NM_000314.4	59	tCa/tAa	3/9	1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	1	0.250132669401232	2		266	130	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156719	20156719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	39	386	0	ENST00000379607.5:c.38G>A	p.Arg13His	p.R13H	ENST00000379607	NM_001412.3	13	cGc/cAc	2/7	0.173486396052124	1	FACETS	0.944	0.786	1	0.944	0.786	1	CLONAL	1	TRUE	0	0.250132669401232	1		386	289	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288098	21288098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	28	344	0	ENST00000354336.3:c.343G>A	p.Ala115Thr	p.A115T	ENST00000354336	NM_005207.3	115	Gca/Aca	2/3	1	2	FACETS	0.925	0.743	1	0.925	0.743	1	CLONAL	1	TRUE	1	0.250132669401232	2		344	242	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525889	148525891	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	rs587778303	NA	P-0031134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	27	476	1	ENST00000320356.2:c.566_568del	p.Asp189del	p.D189del	ENST00000320356	NM_004456.4	189	gATGga/gga	6/20	1	2	FACETS	0.688	0.548	0.847	0.688	0.548	0.847	SUBCLONAL	1	TRUE	1	0.250132669401232	2		477	314	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206647765	206647765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782640857	NA	P-0031134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	73	516	0	ENST00000367120.3:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000367120	NM_014002.3	60	cGg/cAg	4/22	0.250132669401232	4	FACETS	0.739	0.644	0.841	0.369	0.322	0.421	SUBCLONAL	1	TRUE	2	0.250132669401232	4		516	988	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916211	9916211	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	47	464	0	ENST00000330684.3:c.2078A>G	p.Asn693Ser	p.N693S	ENST00000330684	NM_001134407.1	693	aAc/aGc	10/13	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.250132669401232	2		464	323	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597355	10597355	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	46	583	0	ENST00000171111.5:c.1848G>T	p.Gln616His	p.Q616H	ENST00000171111	NM_203500.1	616	caG/caT	6/6	1	2	FACETS	0.463	0.389	0.546	0.463	0.389	0.546	SUBCLONAL	1	TRUE	1	0.250132669401232	2		583	794	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11032341	11032341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	84	620	2	ENST00000327064.4:c.1735G>A	p.Ala579Thr	p.A579T	ENST00000327064	NM_199141.1	579	Gca/Aca	16/16	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.250132669401232	2		622	639	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354151	15354152	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0031134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	61	496	1	ENST00000263377.2:c.2728dup	p.Gln910ProfsTer7	p.Q910Pfs*7	ENST00000263377	NM_058243.2	910	caa/cCaa	14/20	1	2	FACETS	0.805	0.694	0.925	0.805	0.694	0.925	CLONAL	1	TRUE	1	0.250132669401232	2		497	606	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55143564	55143565	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0031134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	17	262	0	ENST00000257290.5:c.1800dup	p.Ser601ValfsTer9	p.S601Vfs*9	ENST00000257290	NM_006206.4	599	ttg/ttGg	13/23	1	2	FACETS	0.401	0.299	0.523	0.401	0.299	0.523	SUBCLONAL	1	TRUE	1	0.250132669401232	2		262	339	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589603	67589611	+	inframe_deletion	In_Frame_Del	DEL	TTTCAAGAA	TTTCAAGAA	-	novel	NA	P-0031134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	33	326	0	ENST00000274335.5:c.1366_1374del	p.Phe456_Glu458del	p.F456_E458del	ENST00000274335		456	TTTCAAGAA/-	10/15	0.250132669401232	2	FACETS	1	0.903	1	0.581	0.476	0.697	CLONAL	1	TRUE	0	0.250132669401232	2		326	227	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339622	70339622	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	74	538	1	ENST00000374080.3:c.291C>A	p.Asn97Lys	p.N97K	ENST00000374080		97	aaC/aaA	3/45	0.173486396052124	1	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	0	0.250132669401232	1		539	502	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858113	152858113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1178567203	NA	P-0031134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	141	613	1	ENST00000406277.2:c.502G>A	p.Ala168Thr	p.A168T	ENST00000406277	NM_152274.4	168	Gcc/Acc	6/7	0.173486396052124	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.250132669401232	1		614	901	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281800	46281800	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	219	530	0	ENST00000371998.3:c.4247C>G	p.Pro1416Arg	p.P1416R	ENST00000371998		1416	cCt/cGt	22/23	1	2	FACETS	0.615	0.574	0.658	0.615	0.574	0.658	SUBCLONAL	1	TRUE	1	0.92	2		530	774	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74868197	74868197	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	88	108	0	ENST00000284811.8:c.97A>G	p.Arg33Gly	p.R33G	ENST00000284811		33	Aga/Gga	3/4	1	2	FACETS	0.911	0.824	0.999	0.911	0.824	0.999	CLONAL	1	TRUE	1	0.92	2		108	210	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0031230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	211	583	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.278557544196762	4	FACETS	1	0.933	1	1	0.933	1	CLONAL	2	FALSE	2	0.3	4		583	911	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0031230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	371	799	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.3	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	FALSE	0	0.3	2		799	1090	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604790	48604790	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1568211615	NA	P-0031230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	219	489	1	ENST00000342988.3:c.1612G>T	p.Glu538Ter	p.E538*	ENST00000342988	NM_005359.5	538	Gaa/Taa	12/12	0.3	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	FALSE	0	0.3	2		490	638	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042095	14042095	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	157	444	2	ENST00000311895.7:c.2642A>G	p.Gln881Arg	p.Q881R	ENST00000311895	NM_005236.2	881	cAa/cGa	11/11	0.278557544196762	4	FACETS	0.911	0.836	0.989	0.911	0.836	0.989	CLONAL	2	FALSE	2	0.3	4		446	747	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	263	354	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.99	0.929	1	1	0.995	1	CLONAL	2	TRUE	1	0.281774156792769	2		354	943	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863296	57863296	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	147	821	2	ENST00000228682.2:c.1391G>T	p.Gly464Val	p.G464V	ENST00000228682	NM_005269.2	464	gGt/gTt	11/12	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.281774156792769	2		823	987	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207059	1207059	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	148	926	0	ENST00000326873.7:c.148del	p.Leu50Ter	p.L50*	ENST00000326873	NM_000455.4	49	taC/ta	1/10	0.281774156792769	1	FACETS	0.83	0.757	0.907	0.83	0.757	0.907	CLONAL	1	TRUE	0	0.281774156792769	1		926	1087	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799273	45799273	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	70	462	0	ENST00000450313.1:c.160T>G	p.Cys54Gly	p.C54G	ENST00000450313	NM_012222.2	54	Tgt/Ggt	3/16	0.26650210559755	1	FACETS	0.884	0.772	1	0.884	0.772	1	CLONAL	1	TRUE	0	0.281774156792769	1		462	483	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347410	89347410	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	112	961	0	ENST00000301030.4:c.5540C>G	p.Ser1847Trp	p.S1847W	ENST00000301030	NM_001256183.1	1847	tCg/tGg	9/13	1	2	FACETS	0.721	0.647	0.8	0.721	0.647	0.8	SUBCLONAL	1	TRUE	1	0.281774156792769	2		961	1103	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805562	46805562	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	164	1006	0	ENST00000290295.7:c.394G>T	p.Gly132Ter	p.G132*	ENST00000290295	NM_006361.5	132	Gga/Tga	1/2	1	2	FACETS	0.981	0.898	1	0.981	0.898	1	CLONAL	1	TRUE	1	0.281774156792769	2		1006	1187	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602891	10602891	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	195	1059	1	ENST00000171111.5:c.687del	p.Thr230ProfsTer8	p.T230Pfs*8	ENST00000171111	NM_203500.1	229	gtG/gt	3/6	0.281774156792769	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.281774156792769	1		1060	1157	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910253	50910253	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	131	805	1	ENST00000440232.2:c.1508A>T	p.Gln503Leu	p.Q503L	ENST00000440232	NM_002691.3	503	cAg/cTg	13/27	1	2	FACETS	0.979	0.887	1	0.979	0.887	1	CLONAL	1	TRUE	1	0.281774156792769	2		806	950	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595803	52595804	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTGTCTCAAGATTTCTCCATT	novel	NA	P-0031232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	37	653	0	ENST00000394830.3:c.4091_4111dup	p.Glu1364_Thr1370dup	p.E1364_T1370dup	ENST00000394830	NM_018313.4	1364	gcc/gAATGGAGAAATCTTGAGACAGcc	26/30	0.26650210559755	1	FACETS	0.309	0.254	0.372	0.309	0.254	0.372	SUBCLONAL	1	TRUE	0	0.281774156792769	1		653	729	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851784	134851784	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	135	795	0	ENST00000398015.3:c.1190G>T	p.Trp397Leu	p.W397L	ENST00000398015	NM_004441.4	397	tGg/tTg	5/16	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.281774156792769	2		795	891	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940480	76940480	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	106	781	1	ENST00000373344.5:c.613A>G	p.Met205Val	p.M205V	ENST00000373344	NM_000489.3	205	Atg/Gtg	8/35	1	2	FACETS	0.908	0.813	1	0.908	0.813	1	CLONAL	1	TRUE	1	0.281774156792769	2		782	829	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0031234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	189	390	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.3	4	FACETS	0.986	0.918	1			1	CLONAL	4	TRUE	NA	0.21	4		390	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs747342068	NA	P-0031234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	143	818	0	ENST00000269305.4:c.394A>C	p.Lys132Gln	p.K132Q	ENST00000269305	NM_001126112.2	132	Aag/Cag	5/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.21	2		818	998	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	321	215	0				ENST00000310581	NM_198253.2	-/1132			0.376244640629259	3	FACETS	0.883	0.844	0.922	1	0.996	1	CLONAL	4	TRUE	1	0.376244640629259	3		215	574	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0031254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	398	512	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.376244640629259	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.376244640629259	3		512	1055	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0031254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	489	691	2	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.298229974299584	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.376244640629259	2		693	1068	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954198	48954198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123331	NA	P-0031254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	99	211	0	ENST00000267163.4:c.1399C>T	p.Arg467Ter	p.R467*	ENST00000267163	NM_000321.2	467	Cga/Tga	15/27	0.376244640629259	1	FACETS	0.755	0.683	0.828	1	0.984	1	SUBCLONAL	2	TRUE	0	0.376244640629259	1		211	283	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789661	3789661	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	277	565	0	ENST00000262367.5:c.4198G>C	p.Glu1400Gln	p.E1400Q	ENST00000262367	NM_004380.2	1400	Gag/Cag	25/31	0.276716921973777	1	FACETS	0.791	0.746	0.836	1	0.994	1	SUBCLONAL	2	TRUE	0	0.376244640629259	1		565	756	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578227	7578227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	152	746	1	ENST00000269305.4:c.622G>A	p.Asp208Asn	p.D208N	ENST00000269305	NM_001126112.2	208	Gac/Aac	6/11	0.298229974299584	2	FACETS	0.743	0.679	0.811	0.372	0.339	0.406	SUBCLONAL	1	TRUE	0	0.376244640629259	2		747	1087	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217909	2217909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1230117726	NA	P-0031254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	266	709	0	ENST00000398665.3:c.2683G>A	p.Glu895Lys	p.E895K	ENST00000398665	NM_032482.2	895	Gag/Aag	22/28	1	2	FACETS	0.797	0.749	0.846	1	0.994	1	SUBCLONAL	2	TRUE	1	0.376244640629259	2		709	887	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087395	27087396	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0031254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	400	677	0	ENST00000324856.7:c.1970dup	p.Ser658GlufsTer18	p.S658Efs*18	ENST00000324856	NM_006015.4	657	ctg/cTtg	5/20	0.376244640629259	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.376244640629259	4		677	1312	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405200	70405200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	222	587	0	ENST00000373644.4:c.2714C>T	p.Ser905Leu	p.S905L	ENST00000373644	NM_030625.2	905	tCa/tTa	4/12	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.376244640629259	2		587	831	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099479	27099479	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0031254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	272	398	0	ENST00000324856.7:c.3715+1G>C		p.X1239_splice	ENST00000324856	NM_006015.4	1239			0.376244640629259	4	FACETS	0.869	0.819	0.92	1	0.992	1	CLONAL	3	TRUE	2	0.376244640629259	4		398	763	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991077	41991077	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	285	480	0	ENST00000219905.7:c.2030A>T	p.His677Leu	p.H677L	ENST00000219905	NM_001164273.1	677	cAt/cTt	4/24	0.276716921973777	1	FACETS	0.884	0.836	0.932	1	0.995	1	CLONAL	2	TRUE	0	0.376244640629259	1		480	696	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786066	3786066	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	145	700	0	ENST00000262367.5:c.4699G>C	p.Glu1567Gln	p.E1567Q	ENST00000262367	NM_004380.2	1567	Gag/Cag	28/31	0.276716921973777	1	FACETS	0.72	0.657	0.786	0.72	0.657	0.786	SUBCLONAL	1	TRUE	0	0.376244640629259	1		700	869	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882311	89882311	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555580427	NA	P-0031254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	255	575	0	ENST00000389301.3:c.163C>T	p.Gln55Ter	p.Q55*	ENST00000389301	NM_000135.2	55	Cag/Tag	2/43	1	2	FACETS	0.889	0.836	0.944	1	0.994	1	CLONAL	2	TRUE	1	0.376244640629259	2		575	762	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534462	63534462	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0031254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	128	678	0	ENST00000307078.5:c.1060-1G>C		p.X354_splice	ENST00000307078	NM_004655.3	354			0.298229974299584	2	FACETS	0.729	0.66	0.802	0.365	0.33	0.401	SUBCLONAL	1	TRUE	0	0.376244640629259	2		678	933	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054393	13054393	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs530463916	NA	P-0031254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	247	618	0	ENST00000316448.5:c.1003G>C	p.Asp335His	p.D335H	ENST00000316448	NM_004343.3	335	Gat/Cat	8/9	1	2	FACETS	0.766	0.718	0.816	1	0.993	1	SUBCLONAL	2	TRUE	1	0.376244640629259	2		618	857	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755631	39755631	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	221	625	0	ENST00000288319.7:c.1134G>C	p.Met378Ile	p.M378I	ENST00000288319	NM_182918.3	378	atG/atC	10/10	0.289564421367916	4	FACETS	0.76	0.707	0.815	0.507	0.471	0.544	SUBCLONAL	2	TRUE	1	0.376244640629259	4		625	1063	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295173	1295173	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0031254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	201	203	0				ENST00000310581	NM_198253.2	-/1132			0.376244640629259	3	FACETS	1	0.987	1	1	0.994	1	CLONAL	3	TRUE	1	0.376244640629259	3		203	366	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590466	67590466	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	85	319	0	ENST00000274335.5:c.1528G>C	p.Glu510Gln	p.E510Q	ENST00000274335		510	Gaa/Caa	11/15	1	2	FACETS	0.974	0.864	1	0.974	0.864	1	CLONAL	1	TRUE	1	0.376244640629259	2		319	464	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041089	180041089	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	467	952	0	ENST00000261937.6:c.3310C>G	p.Leu1104Val	p.L1104V	ENST00000261937	NM_182925.4	1104	Ctc/Gtc	24/30	0.243325758470624	3	FACETS	1	0.993	1	0.795	0.76	0.83	CLONAL	2	TRUE	0	0.376244640629259	3		952	1237	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020724	26020724	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	421	254	0	ENST00000357647.3:c.7C>A	p.Arg3Ser	p.R3S	ENST00000357647	NM_003529.2	3	Cgc/Agc	1/1	0.376244640629259	8	FACETS	1	0.99	1	1	0.99	1	CLONAL	6	TRUE	2	0.376244640629259	8		254	736	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054861	5054861	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	338	486	0	ENST00000381652.3:c.913G>A	p.Glu305Lys	p.E305K	ENST00000381652	NM_004972.3	305	Gaa/Aaa	7/25	0.298229974299584	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.376244640629259	2		486	773	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0031267-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	13	515	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.459	0.326	0.622	0.459	0.326	0.622	SUBCLONAL	1	TRUE	1	0.15	2		515	378	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278791	1278791	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs772070672	NA	P-0031267-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	27	614	1	ENST00000310581.5:c.2251G>T	p.Ala751Ser	p.A751S	ENST00000310581	NM_198253.2	751	Gcc/Tcc	6/16	1	2	FACETS	0.703	0.558	0.87	0.703	0.558	0.87	SUBCLONAL	1	TRUE	1	0.15	2		615	512	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0031267-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	11	370	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.522	0.36	0.725	0.522	0.36	0.725	SUBCLONAL	1	TRUE	1	0.15	2		370	281	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161326593	161326593	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031267-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	25	488	0	ENST00000367975.2:c.368C>G	p.Pro123Arg	p.P123R	ENST00000367975	NM_003001.3	123	cCt/cGt	5/6	1	2	FACETS	1	0.803	1	1	0.803	1	CLONAL	1	TRUE	1	0.15	2		488	327	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0031283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	44	446	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.0062577382599267	3	FACETS	1	0.854	1	0.51	0.427	0.602	INDETERMINATE	1	TRUE	1	0.180563047887561	3		446	521	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544661	65544661	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0031283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	81	595	0	ENST00000358664.4:c.265A>T	p.Lys89Ter	p.K89*	ENST00000358664	NM_002382.4	89	Aag/Tag	4/5	1	2	FACETS	0.798	0.704	0.899	1	0.979	1	SUBCLONAL	2	TRUE	1	0.180563047887561	2		595	562	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391103	89391103	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	35	639	1	ENST00000336596.2:c.1169C>A	p.Thr390Asn	p.T390N	ENST00000336596	NM_005233.5	390	aCc/aAc	5/17	1	2	FACETS	0.642	0.525	0.774	0.642	0.525	0.774	SUBCLONAL	1	TRUE	1	0.180563047887561	2		640	604	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70350037	70350037	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	51	484	0	ENST00000374080.3:c.4020G>C	p.Gln1340His	p.Q1340H	ENST00000374080		1340	caG/caC	28/45	0.180563047887561	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	0	0.180563047887561	1		484	469	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	56	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.211338679146379	2		215	421	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156493	106156493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	10	374	0	ENST00000380013.4:c.1394C>T	p.Pro465Leu	p.P465L	ENST00000380013	NM_001127208.2	465	cCa/cTa	3/11	1	2	FACETS	0.588	0.399	0.824	0.588	0.399	0.824	SUBCLONAL	1	FALSE	1	0.211338679146379	2		374	161	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875648	35875648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	16	266	0	ENST00000303115.3:c.835C>T	p.His279Tyr	p.H279Y	ENST00000303115	NM_002185.3	279	Cat/Tat	7/8	1	2	FACETS	0.704	0.522	0.922	0.704	0.522	0.922	CLONAL	1	FALSE	1	0.211338679146379	2		266	215	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858201	9858201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	13	451	0	ENST00000330684.3:c.3200G>A	p.Arg1067Gln	p.R1067Q	ENST00000330684	NM_001134407.1	1067	cGg/cAg	13/13	1	2	FACETS	0.488	0.348	0.66	0.488	0.348	0.66	SUBCLONAL	1	FALSE	1	0.211338679146379	2		451	252	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633229	12633229	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs368807126	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	61	473	0	ENST00000251849.4:c.1171A>T	p.Arg391Trp	p.R391W	ENST00000251849	NM_002880.3	391	Agg/Tgg	11/17	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	FALSE	1	0.211338679146379	2		473	504	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057857	27057857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	36	670	0	ENST00000324856.7:c.1565C>T	p.Pro522Leu	p.P522L	ENST00000324856	NM_006015.4	522	cCa/cTa	3/20	1	2	FACETS	0.519	0.425	0.624	0.519	0.425	0.624	SUBCLONAL	1	FALSE	1	0.211338679146379	2		670	657	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458221	120458221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	29	613	0	ENST00000256646.2:c.7124C>T	p.Pro2375Leu	p.P2375L	ENST00000256646	NM_024408.3	2375	cCt/cTt	34/34	1	2	FACETS	0.613	0.491	0.751	0.613	0.491	0.751	SUBCLONAL	1	FALSE	1	0.211338679146379	2		613	448	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451005	70451005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	31	491	0	ENST00000373644.4:c.5845C>T	p.Pro1949Ser	p.P1949S	ENST00000373644	NM_030625.2	1949	Cct/Tct	12/12	1	2	FACETS	0.76	0.615	0.924	0.76	0.615	0.924	CLONAL	1	FALSE	1	0.211338679146379	2		491	386	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200942	108200942	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	14	273	0	ENST00000278616.4:c.7309T>G	p.Tyr2437Asp	p.Y2437D	ENST00000278616	NM_000051.3	2437	Tac/Gac	50/63	0.165241653928147	1	FACETS	0.933	0.68	1	0.933	0.68	1	CLONAL	1	FALSE	0	0.211338679146379	1		273	127	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494872	56494872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112651994	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	40	403	0	ENST00000267101.3:c.3229C>T	p.Arg1077Trp	p.R1077W	ENST00000267101	NM_001982.3	1077	Cgg/Tgg	27/28	0.181329227697662	3	FACETS	0.808	0.671	0.961	0.404	0.335	0.481	CLONAL	1	FALSE	1	0.211338679146379	3		403	518	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134480	41134480	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	19	515	0	ENST00000379561.5:c.1148C>T	p.Ser383Leu	p.S383L	ENST00000379561	NM_002015.3	383	tCa/tTa	2/3	0.165241653928147	1	FACETS	0.506	0.383	0.65	0.506	0.383	0.65	SUBCLONAL	1	FALSE	0	0.211338679146379	1		515	318	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643248	38643248	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	10	358	0	ENST00000299084.4:c.718C>T	p.Gln240Ter	p.Q240*	ENST00000299084	NM_152594.2	240	Caa/Taa	7/7	1	2	FACETS	0.717	0.488	1	0.717	0.488	1	CLONAL	1	FALSE	1	0.211338679146379	2		358	132	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849631	68849631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659244	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	32	578	0	ENST00000261769.5:c.1534G>A	p.Glu512Lys	p.E512K	ENST00000261769	NM_004360.3	512	Gag/Aag	10/16	1	2	FACETS	0.771	0.626	0.934	0.771	0.626	0.934	CLONAL	1	FALSE	1	0.211338679146379	2		578	393	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828150	72828150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377589097	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	12	592	1	ENST00000268489.5:c.8431G>A	p.Glu2811Lys	p.E2811K	ENST00000268489	NM_006885.3	2811	Gaa/Aaa	9/10	1	2	FACETS	0.485	0.341	0.663	0.485	0.341	0.663	SUBCLONAL	1	FALSE	1	0.211338679146379	2		593	234	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347110	89347110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	42	564	0	ENST00000301030.4:c.5840C>T	p.Pro1947Leu	p.P1947L	ENST00000301030	NM_001256183.1	1947	cCc/cTc	9/13	1	2	FACETS	0.737	0.615	0.873	0.737	0.615	0.873	SUBCLONAL	1	FALSE	1	0.211338679146379	2		564	539	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29422344	29422344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs864622210	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	95	403	1	ENST00000356175.3:c.17C>T	p.Pro6Leu	p.P6L	ENST00000356175	NM_000267.3	6	cCg/cTg	1/57	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.211338679146379	2		404	697	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41251898	41251898	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	10	330	0	ENST00000357654.3:c.442-1G>A		p.X148_splice	ENST00000357654	NM_007294.3	148			1	2	FACETS	0.701	0.477	0.98	0.701	0.477	0.98	CLONAL	1	FALSE	1	0.211338679146379	2		330	135	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435533	56435533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369428576	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	39	632	0	ENST00000407977.2:c.1604C>T	p.Ser535Leu	p.S535L	ENST00000407977		535	tCg/tTg	9/10	1	2	FACETS	0.624	0.517	0.745	0.624	0.517	0.745	SUBCLONAL	1	FALSE	1	0.211338679146379	2		632	591	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821921	59821921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768393936	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	13	400	0	ENST00000259008.2:c.2129C>T	p.Ser710Phe	p.S710F	ENST00000259008	NM_032043.2	710	tCt/tTt	15/20	1	2	FACETS	0.658	0.47	0.886	0.658	0.47	0.886	SUBCLONAL	1	FALSE	1	0.211338679146379	2		400	187	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220920	36220920	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	25	301	1	ENST00000222270.7:c.4970C>T	p.Ser1657Phe	p.S1657F	ENST00000222270	NM_014727.1	1657	tCc/tTc	23/37	1	2	FACETS	0.917	0.725	1	0.917	0.725	1	CLONAL	1	FALSE	1	0.211338679146379	2		302	258	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449836	29449836	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	71	844	0	ENST00000389048.3:c.3019T>A	p.Phe1007Ile	p.F1007I	ENST00000389048	NM_004304.4	1007	Ttc/Atc	18/29	1	2	FACETS	0.995	0.868	1	0.995	0.868	1	CLONAL	1	FALSE	1	0.211338679146379	2		844	675	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736159	204736160	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	15	379	1	ENST00000302823.3:c.516_517delinsAA	p.Gly173Arg	p.G173R	ENST00000302823	NM_005214.4	172	tcGGgg/tcAAgg	3/4	1	2	FACETS	0.495	0.361	0.655	0.495	0.361	0.655	SUBCLONAL	1	FALSE	1	0.211338679146379	2		380	287	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40709548	40709548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754318111	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	21	493	0	ENST00000373198.4:c.4354G>A	p.Val1452Met	p.V1452M	ENST00000373198	NM_133170.3	1452	Gtg/Atg	32/32	0.126160293778438	0	FACETS	0.493	0.379	0.625			1	INDETERMINATE	1	FALSE	0	0.211338679146379	0		493	318	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604638	55604638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	60	535	0	ENST00000288135.5:c.2846C>T	p.Pro949Leu	p.P949L	ENST00000288135	NM_000222.2	949	cCc/cTc	21/21	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	FALSE	1	0.211338679146379	2		535	519	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522582	176522582	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	58	643	0	ENST00000292408.4:c.1679A>T	p.Glu560Val	p.E560V	ENST00000292408	NM_213647.1	560	gAg/gTg	13/18	1	2	FACETS	0.71	0.609	0.821	0.71	0.609	0.821	SUBCLONAL	1	FALSE	1	0.211338679146379	2		643	773	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169869	32169869	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	75	588	0	ENST00000375023.3:c.3739A>G	p.Thr1247Ala	p.T1247A	ENST00000375023	NM_004557.3	1247	Acc/Gcc	21/30	0.208844510103971	2	FACETS	0.945	0.827	1	0.473	0.413	0.536	CLONAL	1	FALSE	0	0.211338679146379	2		588	751	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547241	106547241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	35	317	0	ENST00000369096.4:c.478C>T	p.Arg160Cys	p.R160C	ENST00000369096	NM_001198.3	160	Cgc/Tgc	4/7	0.208844510103971	2	FACETS	1	0.879	1	0.545	0.448	0.653	CLONAL	1	FALSE	0	0.211338679146379	2		317	304	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641180	117641180	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	20	675	0	ENST00000368508.3:c.5791C>T	p.Gln1931Ter	p.Q1931*	ENST00000368508	NM_002944.2	1931	Caa/Taa	36/43	0.208844510103971	2	FACETS	0.631	0.482	0.805	0.315	0.241	0.403	SUBCLONAL	1	FALSE	0	0.211338679146379	2		675	300	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979457	2979457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769402864	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	77	489	0	ENST00000396946.4:c.790G>A	p.Glu264Lys	p.E264K	ENST00000396946	NM_032415.4	264	Gag/Aag	6/25	0.211338679146379	3	FACETS	0.864	0.762	0.974	0.576	0.508	0.65	CLONAL	2	FALSE	0	0.211338679146379	3		489	466	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987422	2987422	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	54	365	0	ENST00000396946.4:c.8-1G>A		p.X3_splice	ENST00000396946	NM_032415.4	3			0.211338679146379	3	FACETS	0.833	0.715	0.961	0.556	0.477	0.641	CLONAL	2	FALSE	0	0.211338679146379	3		365	339	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514433	148514433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	32	428	0	ENST00000320356.2:c.1291C>T	p.Pro431Ser	p.P431S	ENST00000320356	NM_004456.4	431	Cct/Tct	11/20	0.211338679146379	3	FACETS	0.925	0.759	1	0.617	0.506	0.739	CLONAL	2	FALSE	0	0.211338679146379	3		428	181	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995553	68995553	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771763123	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	26	600	0	ENST00000288368.4:c.1957G>A	p.Asp653Asn	p.D653N	ENST00000288368	NM_024870.2	653	Gat/Aat	18/40	1	2	FACETS	1	0.805	1	1	0.805	1	CLONAL	1	FALSE	1	0.211338679146379	2		600	243	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136794	69136794	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs372981486	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	30	405	0	ENST00000288368.4:c.4708G>A	p.Gly1570Arg	p.G1570R	ENST00000288368	NM_024870.2	1570	Gga/Aga	39/40	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	FALSE	1	0.211338679146379	2		405	246	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964333	70964333	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	18	351	0	ENST00000276594.2:c.1695G>A	p.Met565Ile	p.M565I	ENST00000276594	NM_024504.3	565	atG/atA	8/8	1	2	FACETS	0.852	0.644	1	0.852	0.644	1	CLONAL	1	FALSE	1	0.211338679146379	2		351	200	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27183567	27183567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1296261695	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	20	438	0	ENST00000380036.4:c.1141G>A	p.Glu381Lys	p.E381K	ENST00000380036	NM_000459.3	381	Gaa/Aaa	8/23	0.17302938787221	0	FACETS	0.675	0.518	0.858			1	SUBCLONAL	1	FALSE	0	0.211338679146379	0		438	221	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778168	135778168	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554815054	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	26	378	2	ENST00000298552.3:c.2215C>T	p.Gln739Ter	p.Q739*	ENST00000298552	NM_001162426.1	739	Cag/Tag	18/23	0.17302938787221	0	FACETS	0.878	0.699	1			1	CLONAL	1	FALSE	0	0.211338679146379	0		380	221	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860118	152860118	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	57	315	0	ENST00000406277.2:c.310G>T	p.Glu104Ter	p.E104*	ENST00000406277	NM_152274.4	104	Gag/Tag	5/7	0.176929359646692		FACETS		0.651	0.868				SUBCLONAL	2	FALSE	NA	0.211338679146379	2		315	357	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0031288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	319	598	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.468995708492658	4	FACETS	0.967	0.915	1	0.967	0.915	1	CLONAL	2	TRUE	2	0.490673956211095	4		598	1002	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913351	NA	P-0031288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	237	400	1	ENST00000288602.6:c.1397G>T	p.Gly466Val	p.G466V	ENST00000288602	NM_004333.4	466	gGa/gTa	11/18	0.468995708492658	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	2	0.490673956211095	4		401	703	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576857	7576857	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	307	562	0	ENST00000269305.4:c.989T>A	p.Leu330His	p.L330H	ENST00000269305	NM_001126112.2	330	cTt/cAt	9/11	0.490673956211095	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.490673956211095	2		562	581	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468324	120468324	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	287	532	0	ENST00000256646.2:c.4115G>T	p.Arg1372Leu	p.R1372L	ENST00000256646	NM_024408.3	1372	cGg/cTg	25/34	0.468995708492658	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	2	0.490673956211095	4		532	835	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865436	57865436	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	604	805	0	ENST00000228682.2:c.2913T>A	p.His971Gln	p.H971Q	ENST00000228682	NM_005269.2	971	caT/caA	12/12	0.490673956211095	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	0	0.490673956211095	3		805	1001	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73348118	73348118	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	235	502	0	ENST00000377767.4:c.1067A>G	p.Tyr356Cys	p.Y356C	ENST00000377767	NM_014953.3	356	tAt/tGt	7/21	0.490673956211095	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.490673956211095	2		502	473	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476287	88476287	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	302	663	1	ENST00000360948.2:c.1845G>T	p.Met615Ile	p.M615I	ENST00000360948	NM_001012338.2	615	atG/atT	15/19	0.490673956211095	2	FACETS	0.977	0.929	1	0.977	0.929	1	CLONAL	2	TRUE	0	0.490673956211095	2		664	630	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609582	46609582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	346	719	1	ENST00000263734.3:c.2306C>T	p.Pro769Leu	p.P769L	ENST00000263734	NM_001430.4	769	cCc/cTc	15/16	0.490673956211095	3	FACETS	0.904	0.858	0.951	0.904	0.858	0.951	CLONAL	2	TRUE	1	0.490673956211095	3		720	971	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980778	40980778	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	232	560	0	ENST00000373198.4:c.1708A>T	p.Thr570Ser	p.T570S	ENST00000373198	NM_133170.3	570	Aca/Tca	10/32	0.468995708492658	4	FACETS	0.902	0.844	0.962	0.902	0.844	0.962	CLONAL	2	TRUE	2	0.490673956211095	4		560	781	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46266419	46266419	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs770024913	NA	P-0031288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	218	441	0	ENST00000371998.3:c.2404G>T	p.Ala802Ser	p.A802S	ENST00000371998		802	Gct/Tct	13/23	0.468995708492658	4	FACETS	0.98	0.916	1	0.98	0.916	1	CLONAL	2	TRUE	2	0.490673956211095	4		441	676	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183108	32183108	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	821	900	0	ENST00000375023.3:c.1916T>C	p.Ile639Thr	p.I639T	ENST00000375023	NM_004557.3	639	aTa/aCa	12/30	0.490673956211095	6	FACETS	0.956	0.927	0.985	0.956	0.927	0.985	CLONAL	4	TRUE	2	0.490673956211095	6		900	1734	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066662	94066662	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	222	467	0	ENST00000369303.4:c.1097G>T	p.Arg366Ile	p.R366I	ENST00000369303	NM_004440.3	366	aGa/aTa	5/17	0.490673956211095	2	FACETS	0.973	0.917	1	0.973	0.917	1	CLONAL	2	TRUE	0	0.490673956211095	2		467	465	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341138	8341138	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	223	511	0	ENST00000356435.5:c.5078G>T	p.Gly1693Val	p.G1693V	ENST00000356435		1693	gGa/gTa	30/35	0.490673956211095	2	FACETS	0.945	0.89	1	0.945	0.89	1	CLONAL	2	TRUE	0	0.490673956211095	2		511	481	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123499669	123499669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	233	266	0	ENST00000371139.4:c.196G>T	p.Ala66Ser	p.A66S	ENST00000371139	NM_001114937.2	66	Gct/Tct	2/4	0.462307188217624	2	FACETS	0.835	0.794	0.875			1	CLONAL	3	TRUE	NA	0.490673956211095	2		266	379	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81562997	81562997	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	187	375	0	ENST00000298171.2:c.560A>G	p.Asn187Ser	p.N187S	ENST00000298171	NM_000369.2	187	aAt/aGt	7/10	0.468995708492658	4	FACETS	0.881	0.817	0.946	0.881	0.817	0.946	CLONAL	2	TRUE	2	0.490673956211095	4		375	645	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0031306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	525	760	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.670400545942611	3	FACETS	0.876	0.852	0.899	0.876	0.852	0.899	CLONAL	3	TRUE	0	0.785071008973252	3		760	709	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177011	56177014	+	frameshift_variant	Frame_Shift_Del	DEL	ATAG	ATAG	-	novel	NA	P-0031306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	150	496	0	ENST00000399503.3:c.2286_2289del	p.Arg763CysfsTer35	p.R763Cfs*35	ENST00000399503	NM_005921.1	761	ATAGat/at	13/20	1	2	FACETS	0.84	0.774	0.907	0.84	0.774	0.907	CLONAL	1	TRUE	1	0.785071008973252	2		496	455	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324690	31324690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1399078190	NA	P-0031306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	50	138	12	ENST00000412585.2:c.118G>A	p.Gly40Ser	p.G40S	ENST00000412585	NM_005514.6	40	Ggc/Agc	2/8	0.785071008973252	6	FACETS	0.983	0.863	1	0.59	0.517	0.663	CLONAL	3	TRUE	1	0.785071008973252	6		150	111	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324674	31324674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11546719	NA	P-0031306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	29	196	6	ENST00000412585.2:c.134G>A	p.Arg45His	p.R45H	ENST00000412585	NM_005514.6	45	cGc/cAc	2/8	0.785071008973252	6	FACETS	1	0.941	1	0.294	0.24	0.354	CLONAL	1	TRUE	1	0.785071008973252	6		202	129	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416761	29416761	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	102	441	0	ENST00000389048.3:c.4192C>G	p.Pro1398Ala	p.P1398A	ENST00000389048	NM_004304.4	1398	Ccg/Gcg	29/29	0.785071008973252	4	FACETS	0.704	0.63	0.782	0.235	0.21	0.261	SUBCLONAL	1	TRUE	1	0.785071008973252	4		441	659	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671216	30671216	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1226	104	775	0	ENST00000376406.3:c.5661C>G	p.Asn1887Lys	p.N1887K	ENST00000376406	NM_014641.2	1887	aaC/aaG	11/15	0.785071008973252	6	FACETS	0.512	0.457	0.571	0.102	0.091	0.115	SUBCLONAL	1	TRUE	1	0.785071008973252	6		775	1330	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753029	128753029	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141095253	NA	P-0031306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1844	149	658	0	ENST00000377970.2:c.1190C>T	p.Pro397Leu	p.P397L	ENST00000377970	NM_002467.4	397	cCg/cTg	3/3	0.785071008973252	8	FACETS	0.639	0.581	0.701	0.107	0.096	0.117	SUBCLONAL	1	TRUE	2	0.785071008973252	8		658	1993	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	49	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.517660954949637	2		215	136	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0031320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	62	433	3	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	0.809	0.705	0.921	0.809	0.705	0.921	CLONAL	1	TRUE	1	0.517660954949637	2		436	296	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717609	89717609	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs876661024	NA	P-0031320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	59	426	0	ENST00000371953.3:c.635-1G>A		p.X212_splice	ENST00000371953	NM_000314.4	212			0.342077822969437	1	FACETS	0.816	0.713	0.925	0.816	0.713	0.925	CLONAL	1	TRUE	0	0.517660954949637	1		426	207	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092809	27092809	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	102	656	0	ENST00000324856.7:c.2830C>T	p.Gln944Ter	p.Q944*	ENST00000324856	NM_006015.4	944	Cag/Tag	9/20	0.4382685160389	1	FACETS	0.83	0.749	0.913	0.83	0.749	0.913	CLONAL	1	TRUE	0	0.517660954949637	1		656	352	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65323437	65323437	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1240783724	NA	P-0031320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	65	481	0	ENST00000342505.4:c.1360C>T	p.Arg454Trp	p.R454W	ENST00000342505	NM_002227.2	454	Cgg/Tgg	10/25	1	2	FACETS	0.747	0.652	0.849	0.747	0.652	0.849	SUBCLONAL	1	TRUE	1	0.517660954949637	2		481	336	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602878	10602878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	135	775	1	ENST00000171111.5:c.700C>T	p.Arg234Trp	p.R234W	ENST00000171111	NM_203500.1	234	Cgg/Tgg	3/6	1	2	FACETS	0.988	0.903	1	0.988	0.903	1	CLONAL	1	TRUE	1	0.517660954949637	2		776	528	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602863	10602863	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	127	792	0	ENST00000171111.5:c.715G>T	p.Val239Leu	p.V239L	ENST00000171111	NM_203500.1	239	Gtg/Ttg	3/6	1	2	FACETS	0.929	0.846	1	0.929	0.846	1	CLONAL	1	TRUE	1	0.517660954949637	2		792	528	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979556	7979556	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	108	688	0	ENST00000319144.4:c.1469T>C	p.Val490Ala	p.V490A	ENST00000319144	NM_001139.2	490	gTc/gCc	11/15	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.517660954949637	2		688	405	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125737	47125737	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	91	390	0	ENST00000409792.3:c.5533A>T	p.Ser1845Cys	p.S1845C	ENST00000409792	NM_014159.6	1845	Agt/Tgt	12/21	1	2	FACETS	0.988	0.884	1	0.988	0.884	1	CLONAL	1	TRUE	1	0.517660954949637	2		390	356	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405915	157405915	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	89	509	0	ENST00000346085.5:c.2159del	p.Phe720SerfsTer25	p.F720Sfs*25	ENST00000346085	NM_020732.3	719	ccT/cc	6/20	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.517660954949637	2		509	335	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929293	44929324	+	frameshift_variant	Frame_Shift_Del	DEL	ACAAAGTCAATAACATCCACCCAGCTGTTCAT	ACAAAGTCAATAACATCCACCCAGCTGTTCAT	-	novel	NA	P-0031320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	81	758	0	ENST00000377967.4:c.2399_2430del	p.Val800AspfsTer2	p.V800Dfs*2	ENST00000377967	NM_021140.2	798	gACAAAGTCAATAACATCCACCCAGCTGTTCAT/g	17/29	0.517660954949637	1	FACETS	0.711	0.632	0.795	0.711	0.632	0.795	SUBCLONAL	1	TRUE	0	0.517660954949637	1		758	326	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	108	215	0				ENST00000310581	NM_198253.2	-/1132			0.3	3	FACETS	0.964	0.871	1	1	0.983	1	CLONAL	3	TRUE	1	0.2	3		215	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0031460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	78	593	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.2	2		593	752	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412282	139412282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	218	810	0	ENST00000277541.6:c.1363G>A	p.Glu455Lys	p.E455K	ENST00000277541	NM_017617.3	455	Gag/Aag	8/34	0.209347049299938	2	FACETS	0.918	0.856	0.981	1	0.99	1	CLONAL	3	TRUE	0	0.2	2		810	792	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630411	187630411	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	91	686	3	ENST00000441802.2:c.571C>T	p.Arg191Ter	p.R191*	ENST00000441802	NM_005245.3	191	Cga/Tga	2/27	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.2	2		689	783	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971093	21971094	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0031460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	38	534	0	ENST00000304494.5:c.264_265delinsAA	p.Gly89Ser	p.G89S	ENST00000304494	NM_000077.4	88	gaGGgc/gaAAgc	2/3	0.199883174820746	3	FACETS	0.88	0.727	1	0.44	0.363	0.526	CLONAL	1	TRUE	1	0.2	3		534	475	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740225	162740225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	49	503	0	ENST00000367921.3:c.1427C>T	p.Pro476Leu	p.P476L	ENST00000367921	NM_006182.2	476	cCc/cTc	12/18	1	2	FACETS	0.966	0.819	1	0.966	0.819	1	CLONAL	1	TRUE	1	0.2	2		503	507	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546763	9546763	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	31	345	0	ENST00000353224.5:c.1259C>T	p.Ser420Phe	p.S420F	ENST00000353224	NM_177990.2	420	tCc/tTc	5/10	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.2	2		345	289	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28601354	28601354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	51	607	0	ENST00000253063.3:c.1039C>T	p.His347Tyr	p.H347Y	ENST00000253063	NM_031459.4	347	Cat/Tat	8/10	1	2	FACETS	0.875	0.743	1	0.875	0.743	1	CLONAL	1	TRUE	1	0.2	2		607	583	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39317384	39317384	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	75	645	0	ENST00000373001.3:c.802A>G	p.Ile268Val	p.I268V	ENST00000373001	NM_022157.3	268	Atc/Gtc	5/7	1	2	FACETS	0.96	0.84	1	0.96	0.84	1	CLONAL	1	TRUE	1	0.2	2		645	781	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484264	120484264	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	63	524	1	ENST00000256646.2:c.2866G>T	p.Glu956Ter	p.E956*	ENST00000256646	NM_024408.3	956	Gaa/Taa	18/34	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.2	2		525	593	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243778402	243778402	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0031460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	50	386	0	ENST00000263826.5:c.623T>G	p.Leu208Ter	p.L208*	ENST00000263826	NM_005465.4	208	tTa/tGa	6/13	1	2	FACETS	0.99	0.84	1	0.99	0.84	1	CLONAL	1	TRUE	1	0.2	2		386	505	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422843	49422843	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0031460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	57	609	0	ENST00000301067.7:c.14251+1G>A		p.X4751_splice	ENST00000301067	NM_003482.3	4751			1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.2	2		609	470	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112856923	112856923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	26	329	0	ENST00000351677.2:c.8C>T	p.Ser3Leu	p.S3L	ENST00000351677	NM_002834.3	3	tCg/tTg	1/16	1	2	FACETS	0.681	0.539	0.843	0.681	0.539	0.843	SUBCLONAL	1	TRUE	1	0.2	2		329	382	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873760	35873760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	62	546	0	ENST00000216797.5:c.91G>A	p.Asp31Asn	p.D31N	ENST00000216797	NM_020529.2	31	Gac/Aac	1/6	1	2	FACETS	0.987	0.853	1	0.987	0.853	1	CLONAL	1	TRUE	1	0.2	2		546	628	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457674	67457674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749178459	NA	P-0031460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	53	678	2	ENST00000327367.4:c.484G>A	p.Glu162Lys	p.E162K	ENST00000327367	NM_005902.3	162	Gaa/Aaa	3/9	1	2	FACETS	0.827	0.704	0.961	0.827	0.704	0.961	CLONAL	1	TRUE	1	0.2	2		680	641	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892233	9892233	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	43	584	0	ENST00000330684.3:c.2257G>A	p.Gly753Arg	p.G753R	ENST00000330684	NM_001134407.1	753	Ggg/Agg	11/13	1	2	FACETS	0.776	0.649	0.918	0.776	0.649	0.918	CLONAL	1	TRUE	1	0.2	2		584	554	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351104	89351105	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0031460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	50	635	1	ENST00000301030.4:c.1845_1846delinsAA	p.Glu616Lys	p.E616K	ENST00000301030	NM_001256183.1	615	gcGGag/gcAAag	9/13	1	2	FACETS	0.845	0.716	0.986	0.845	0.716	0.986	CLONAL	1	TRUE	1	0.2	2		636	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573967	7573967	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs755394212	NA	P-0031460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	70	725	0	ENST00000269305.4:c.1060C>T	p.Gln354Ter	p.Q354*	ENST00000269305	NM_001126112.2	354	Cag/Tag	10/11	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.2	2		725	650	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78921145	78921145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	44	446	0	ENST00000306801.3:c.3259G>A	p.Ala1087Thr	p.A1087T	ENST00000306801	NM_020761.2	1087	Gcc/Acc	27/34	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.2	2		446	402	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312680	30312680	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	54	599	0	ENST00000262643.3:c.661T>A	p.Cys221Ser	p.C221S	ENST00000262643	NM_001238.2	221	Tgt/Agt	8/12	1	2	FACETS	0.836	0.713	0.971	0.836	0.713	0.971	CLONAL	1	TRUE	1	0.2	2		599	646	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205723	128205723	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	60	684	0	ENST00000341105.2:c.152A>C	p.His51Pro	p.H51P	ENST00000341105	NM_032638.4	51	cAc/cCc	2/6	1	2	FACETS	0.957	0.824	1	0.957	0.824	1	CLONAL	1	TRUE	1	0.2	2		684	627	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467670	66467670	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	41	417	0	ENST00000273854.3:c.599G>C	p.Arg200Thr	p.R200T	ENST00000273854	NM_004439.5	200	aGa/aCa	3/18	1	2	FACETS	0.919	0.766	1	0.919	0.766	1	CLONAL	1	TRUE	1	0.2	2		417	446	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629961	187629961	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0031460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	60	671	0	ENST00000441802.2:c.1021A>T	p.Lys341Ter	p.K341*	ENST00000441802	NM_005245.3	341	Aaa/Taa	2/27	1	2	FACETS	0.83	0.714	0.956	0.83	0.714	0.956	CLONAL	1	TRUE	1	0.2	2		671	723	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179481	56179481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	29	347	0	ENST00000399503.3:c.3794C>T	p.Thr1265Ile	p.T1265I	ENST00000399503	NM_005921.1	1265	aCt/aTt	15/20	1	2	FACETS	0.692	0.555	0.848	0.692	0.555	0.848	SUBCLONAL	1	TRUE	1	0.2	2		347	419	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469821	157469821	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	142	693	0	ENST00000346085.5:c.2615C>T	p.Pro872Leu	p.P872L	ENST00000346085	NM_020732.3	872	cCc/cTc	9/20	0.209347049299938	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.2	2		693	624	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457167	5457167	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	76	428	0	ENST00000381577.3:c.141A>T	p.Gln47His	p.Q47H	ENST00000381577	NM_014143.3	47	caA/caT	3/7	0.199883174820746	3	FACETS	0.831	0.731	0.938	0.831	0.731	0.938	CLONAL	2	TRUE	1	0.2	3		428	503	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389300	8389300	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	121	651	0	ENST00000356435.5:c.4318T>C	p.Trp1440Arg	p.W1440R	ENST00000356435		1440	Tgg/Cgg	26/35	0.199883174820746	3	FACETS	0.883	0.798	0.972	0.883	0.798	0.972	CLONAL	2	TRUE	1	0.2	3		651	754	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882045	36882045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	149	762	2	ENST00000358127.4:c.968G>A	p.Gly323Glu	p.G323E	ENST00000358127	NM_001280556.1	323	gGa/gAa	8/10	0.199883174820746	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.2	3		764	764	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0031684-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	351	662	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.681624136823246	1	FACETS	0.967	0.924	1	0.967	0.924	1	CLONAL	1	TRUE	0	0.681624136823246	1		662	702	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031684-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	413	548	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	0.681624136823246	2		548	1162	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0031684-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	402	563	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.681624136823246	2		563	978	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111502	8111503	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0031684-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	516	626	0	ENST00000346208.3:c.990dup	p.Asn331GlufsTer21	p.N331Efs*21	ENST00000346208		330	agg/aGgg	5/6	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.681624136823246	2		626	1359	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585453	29585463	+	frameshift_variant	Frame_Shift_Del	DEL	ATGAAGCAGGG	ATGAAGCAGGG	-	novel	NA	P-0031684-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	233	511	0	ENST00000356175.3:c.4204_4214del	p.Glu1402PhefsTer3	p.E1402Ffs*3	ENST00000356175	NM_000267.3	1401	tATGAAGCAGGG/t	31/57	0.681624136823246	1	FACETS	0.827	0.778	0.876	0.827	0.778	0.876	CLONAL	1	TRUE	0	0.681624136823246	1		511	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0031824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	369	696	1	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.567921513813196	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.567397117855956	2		697	628	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400009	49400009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2107830267	NA	P-0031824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	185	678	1	ENST00000418115.1:c.328G>A	p.Val110Met	p.V110M	ENST00000418115	NM_001664.2	110	Gtg/Atg	4/5	1	2	FACETS	0.969	0.898	1	0.969	0.898	1	CLONAL	1	TRUE	1	0.567397117855956	2		679	673	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427491	49427491	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	492	684	1	ENST00000301067.7:c.10997G>C	p.Gly3666Ala	p.G3666A	ENST00000301067	NM_003482.3	3666	gGa/gCa	39/54	0.567397117855956	6	FACETS	0.981	0.94	1			1	CLONAL	3	TRUE	NA	0.567397117855956	6		685	1258	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974745	21974789	+	inframe_deletion	In_Frame_Del	DEL	CCTCCTCTACCCGACCCCGGGCCGCGGCCGTGGCCAGCCAGTCAG	CCTCCTCTACCCGACCCCGGGCCGCGGCCGTGGCCAGCCAGTCAG	-	novel	NA	P-0031824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	119	298	0	ENST00000304494.5:c.38_82del	p.Ala13_Glu27del	p.A13_E27del	ENST00000304494	NM_000077.4	13	gCTGACTGGCTGGCCACGGCCGCGGCCCGGGGTCGGGTAGAGGAGGtg/gtg	1/3	0.567921513813196	2	FACETS	0.874	0.807	0.941	0.874	0.807	0.941	CLONAL	2	TRUE	0	0.567397117855956	2		298	240	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0031946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	497	696	1	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.237342937194736	5	FACETS	0.943	0.907	0.979			1	CLONAL	6	TRUE	NA	0.237342937194736	5		697	1004	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032205	26032205	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	26	287	0	ENST00000244661.2:c.84G>C	p.Lys28Asn	p.K28N	ENST00000244661	NM_003537.3	28	aaG/aaC	1/1	0.216027495242888	4	FACETS	0.741	0.587	0.917	0.247	0.195	0.306	CLONAL	1	TRUE	1	0.237342937194736	4		287	366	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433686	49433686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1236327026	NA	P-0031946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1644	128	896	2	ENST00000301067.7:c.7867G>A	p.Gly2623Arg	p.G2623R	ENST00000301067	NM_003482.3	2623	Gga/Aga	31/54	0.237342937194736	9	FACETS	1	0.958	1	0.159	0.143	0.176	CLONAL	1	TRUE	2	0.237342937194736	9		898	1772	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475123	40475124	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCCGCT	novel	NA	P-0031946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	54	603	0	ENST00000264657.5:c.1781_1786dup	p.Glu594_Arg595dup	p.E594_R595dup	ENST00000264657	NM_139276.2	594	gcc/gAGCGGGcc	20/24	0.237342937194736	2	FACETS	0.664	0.566	0.772	0.332	0.283	0.386	SUBCLONAL	1	TRUE	0	0.237342937194736	2		603	685	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295314	1295314	+	upstream_gene_variant	5'Flank	SNP	G	G	C	novel	NA	P-0031946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	52	476	0				ENST00000310581	NM_198253.2	-/1132			0.237342937194736	6	FACETS	0.899	0.764	1	0.18	0.152	0.21	CLONAL	1	TRUE	1	0.237342937194736	6		476	719	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047690	180047690	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	87	675	0	ENST00000261937.6:c.2325G>C	p.Glu775Asp	p.E775D	ENST00000261937	NM_182925.4	775	gaG/gaC	16/30	0.237342937194736	5	FACETS	0.927	0.819	1			1	CLONAL	1	TRUE	NA	0.237342937194736	5		675	1072	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030540	47030547	+	frameshift_variant	Frame_Shift_Del	DEL	GGACTATC	GGACTATC	-	novel	NA	P-0031946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	54	495	0	ENST00000377604.3:c.319_326del	p.Tyr107ArgfsTer12	p.Y107Rfs*12	ENST00000377604	NM_001204468.1	105	caGGACTATCgg/cagg	4/24	0.216027495242888	4	FACETS	0.835	0.712	0.97	0.278	0.237	0.324	CLONAL	1	TRUE	1	0.237342937194736	4		495	674	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70362044	70362044	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1272	119	671	1	ENST00000374080.3:c.6510T>A	p.Ser2170Arg	p.S2170R	ENST00000374080		2170	agT/agA	45/45	0.237342937194736	7	FACETS	1	0.963	1			1	CLONAL	1	TRUE	NA	0.237342937194736	7		672	1391	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	58	215	0				ENST00000310581	NM_198253.2	-/1132			0.162936756785123	3	FACETS	0.846	0.737	0.962	0.846	0.737	0.962	INDETERMINATE	2	TRUE	1	0.365056813708454	3		215	222	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0032255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	146	458	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.336381597480742	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.365056813708454	2		458	345	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121912651	NA	P-0032255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	92	601	0	ENST00000269305.4:c.742C>G	p.Arg248Gly	p.R248G	ENST00000269305	NM_001126112.2	248	Cgg/Ggg	7/11	1	2	FACETS	0.725	0.644	0.811	0.725	0.644	0.811	SUBCLONAL	1	TRUE	1	0.365056813708454	2		601	695	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0032255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	123	512	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.162936756785123	3	FACETS	1	0.932	1	0.518	0.469	0.57	INDETERMINATE	1	TRUE	1	0.365056813708454	3		512	769	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0032255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	158	676	2	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.365056813708454	2		678	850	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573451	48573455	+	frameshift_variant	Frame_Shift_Del	DEL	GTAAT	GTAAT	-	novel	NA	P-0032255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	19	154	0	ENST00000342988.3:c.36_40del	p.Ser12ArgfsTer9	p.S12Rfs*9	ENST00000342988	NM_005359.5	12	aGTAAT/a	2/12	0.365056813708454	1	FACETS	0.468	0.357	0.596	0.468	0.357	0.596	SUBCLONAL	1	TRUE	0	0.365056813708454	1		154	182	SUCCESS
APC	324	MSKCC	GRCh37	5	112178331	112178331	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	42	333	0	ENST00000257430.4:c.7040G>T	p.Arg2347Met	p.R2347M	ENST00000257430	NM_000038.5	2347	aGg/aTg	16/16	0.154684883381048	2	FACETS	0.595	0.497	0.702	0.297	0.248	0.351	INDETERMINATE	1	TRUE	0	0.365056813708454	2		333	387	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225784	26225784	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	40	280	0	ENST00000360408.1:c.402G>C	p.Glu134Asp	p.E134D	ENST00000360408	NM_003532.2	134	gaG/gaC	1/1	0.365056813708454	2	FACETS	0.489	0.406	0.581	0.245	0.203	0.291	SUBCLONAL	1	TRUE	0	0.365056813708454	2		280	448	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409740	139409760	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ACCTGTGTAGCCCGGCTCACA	ACCTGTGTAGCCCGGCTCACA	CG	novel	NA	P-0032255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	86	571	2	ENST00000277541.6:c.1996_2014+2delinsCG		p.X666_splice	ENST00000277541	NM_017617.3	666		12/34	0.116457761872087	3	FACETS	0.897	0.794	1	0.449	0.397	0.504	INDETERMINATE	1	TRUE	1	0.365056813708454	3		573	621	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417633	139417634	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GATTT	novel	NA	P-0032255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	111	637	0	ENST00000277541.6:c.406_410dup	p.Cys138AsnfsTer141	p.C138Nfs*141	ENST00000277541	NM_017617.3	137	tcg/tcAAATCg	4/34	0.116457761872087	3	FACETS	1	0.957	1	0.557	0.501	0.615	INDETERMINATE	1	TRUE	1	0.365056813708454	3		637	646	SUCCESS
AR	367	MSKCC	GRCh37	X	66765853	66765853	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750324117	NA	P-0032255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	110	834	1	ENST00000374690.3:c.865G>A	p.Glu289Lys	p.E289K	ENST00000374690	NM_000044.3	289	Gaa/Aaa	1/8	0.365056813708454	1	FACETS	0.659	0.592	0.729	0.659	0.592	0.729	SUBCLONAL	1	TRUE	0	0.365056813708454	1		835	748	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	154	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.937742396080016	2		215	311	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0032398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	125	173	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.937742396080016	2		174	248	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0032398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	818	586	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.937742396080016	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	1	0.937742396080016	3		586	1195	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992838	72992838	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758176150	NA	P-0032398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	277	587	0	ENST00000268489.5:c.1207C>T	p.Leu403Phe	p.L403F	ENST00000268489	NM_006885.3	403	Ctt/Ttt	2/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.937742396080016	2		587	588	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716344	18716344	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778895247	NA	P-0032398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	212	300	0	ENST00000266497.5:c.3691G>A	p.Glu1231Lys	p.E1231K	ENST00000266497		1231	Gaa/Aaa	26/31	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.937742396080016	2		300	440	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913384	NA	P-0032398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	194	322	0	ENST00000304494.5:c.262G>T	p.Glu88Ter	p.E88*	ENST00000304494	NM_000077.4	88	Gag/Tag	2/3	0.937742396080016	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.937742396080016	1		322	215	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726561	41726561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	236	537	0	ENST00000301178.4:c.106C>T	p.Pro36Ser	p.P36S	ENST00000301178	NM_021913.4	36	Ccc/Tcc	2/20	1	2	FACETS	0.917	0.864	0.971	0.917	0.864	0.971	CLONAL	1	TRUE	1	0.937742396080016	2		537	549	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352349	70352349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	312	453	0	ENST00000374080.3:c.4376C>T	p.Ser1459Phe	p.S1459F	ENST00000374080		1459	tCc/tTc	31/45	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.937742396080016	2		453	644	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005269	150005269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1449883955	NA	P-0032398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	235	494	0	ENST00000253339.5:c.956G>A	p.Gly319Asp	p.G319D	ENST00000253339		319	gGc/gAc	3/7	0.937742396080016	1	FACETS	0.99	0.961	1	0.99	0.961	1	CLONAL	1	TRUE	0	0.937742396080016	1		494	269	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455063	50455063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	155	280	0	ENST00000331340.3:c.610G>A	p.Gly204Arg	p.G204R	ENST00000331340	NM_006060.4	204	Gga/Aga	6/8	1	2	FACETS	0.964	0.896	1	0.964	0.896	1	CLONAL	1	TRUE	1	0.937742396080016	2		280	343	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923394	36923394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759191217	NA	P-0032398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	397	657	0	ENST00000358127.4:c.868G>A	p.Gly290Arg	p.G290R	ENST00000358127	NM_001280556.1	290	Ggg/Agg	7/10	0.937742396080016	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.937742396080016	1		657	441	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285228	212285228	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	221	396	0	ENST00000342788.4:c.3073C>T	p.Pro1025Ser	p.P1025S	ENST00000342788	NM_005235.2	1025	Cct/Tct	25/28	1	2	FACETS	0.997	0.939	1	0.997	0.939	1	CLONAL	1	TRUE	1	0.937742396080016	2		396	473	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757438	40757438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	355	598	0	ENST00000373198.4:c.2860G>A	p.Asp954Asn	p.D954N	ENST00000373198	NM_133170.3	954	Gat/Aat	20/32	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.937742396080016	2		598	727	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001305	150001305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568586257	NA	P-0032398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	231	426	0	ENST00000253339.5:c.2299C>T	p.Arg767Cys	p.R767C	ENST00000253339		767	Cgt/Tgt	4/7	0.937742396080016	1	FACETS	0.98	0.95	1	0.98	0.95	1	CLONAL	1	TRUE	0	0.937742396080016	1		426	267	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733605	85733605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	214	425	0	ENST00000370580.1:c.407C>T	p.Ser136Leu	p.S136L	ENST00000370580	NM_003921.4	136	tCa/tTa	3/3	1	2	FACETS	0.856	0.803	0.91	0.856	0.803	0.91	CLONAL	1	TRUE	1	0.937742396080016	2		425	533	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437328	121437328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	401	802	0	ENST00000257555.6:c.1666C>T	p.His556Tyr	p.H556Y	ENST00000257555		556	Cac/Tac	9/10	1	2	FACETS	0.981	0.938	1	0.981	0.938	1	CLONAL	1	TRUE	1	0.937742396080016	2		802	872	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589754	28589754	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	204	401	0	ENST00000241453.7:c.2626A>T	p.Ile876Leu	p.I876L	ENST00000241453	NM_004119.2	876	Ata/Tta	21/24	1	2	FACETS	0.996	0.935	1	0.996	0.935	1	CLONAL	1	TRUE	1	0.937742396080016	2		401	437	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623652	28623652	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	245	410	0	ENST00000241453.7:c.905C>T	p.Thr302Ile	p.T302I	ENST00000241453	NM_004119.2	302	aCc/aTc	8/24	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.937742396080016	2		410	514	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213939	2213939	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	333	621	0	ENST00000326181.6:c.18T>G	p.Ser6Arg	p.S6R	ENST00000326181	NM_032271.2	6	agT/agG	2/21	1	2	FACETS	0.977	0.93	1	0.977	0.93	1	CLONAL	1	TRUE	1	0.937742396080016	2		621	727	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108214	8108214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	328	504	0	ENST00000585124.1:c.1010C>T	p.Pro337Leu	p.P337L	ENST00000585124	NM_004217.3	337	cCc/cTc	9/9	1	2	FACETS	0.947	0.9	0.993	0.947	0.9	0.993	CLONAL	1	TRUE	1	0.937742396080016	2		504	739	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899037	40899037	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1162796558	NA	P-0032398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	251	493	1	ENST00000373198.4:c.2233G>A	p.Gly745Ser	p.G745S	ENST00000373198	NM_133170.3	745	Ggt/Agt	14/32	1	2	FACETS	0.934	0.882	0.987	0.934	0.882	0.987	CLONAL	1	TRUE	1	0.937742396080016	2		494	573	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526215	189526215	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	370	596	0	ENST00000264731.3:c.479C>T	p.Ser160Phe	p.S160F	ENST00000264731	NM_003722.4	160	tCt/tTt	4/14	0.937742396080016	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.937742396080016	1		596	405	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968587	55968588	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0032398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	317	532	1	ENST00000263923.4:c.2075_2076delinsAA	p.Gly692Glu	p.G692E	ENST00000263923	NM_002253.2	692	gGG/gAA	14/30	1	2	FACETS	0.925	0.879	0.972	0.925	0.879	0.972	CLONAL	1	TRUE	1	0.937742396080016	2		533	731	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156904	106156904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568199594	NA	P-0032398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	173	354	0	ENST00000380013.4:c.1805C>T	p.Ser602Phe	p.S602F	ENST00000380013	NM_001127208.2	602	tCc/tTc	3/11	1	2	FACETS	0.927	0.865	0.99	0.927	0.865	0.99	CLONAL	1	TRUE	1	0.937742396080016	2		354	398	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250900	153250901	+	missense_variant	Missense_Mutation	DNP	AA	AA	GG	novel	NA	P-0032398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	137	183	0	ENST00000281708.4:c.1159_1160delinsCC	p.Leu387Pro	p.L387P	ENST00000281708	NM_033632.3	387	TTa/CCa	8/12	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.937742396080016	2		183	285	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282664	1282664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	373	606	0	ENST00000310581.5:c.1649G>A	p.Ser550Asn	p.S550N	ENST00000310581	NM_198253.2	550	aGt/aAt	3/16	1	2	FACETS	0.969	0.925	1	0.969	0.925	1	CLONAL	1	TRUE	1	0.937742396080016	2		606	821	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673407	30673407	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	436	718	0	ENST00000376406.3:c.3553C>T	p.Gln1185Ter	p.Q1185*	ENST00000376406	NM_014641.2	1185	Cag/Tag	10/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.937742396080016	2		718	916	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287155	33287155	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0032398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	268	527	0	ENST00000374542.5:c.1940+2T>G		p.X647_splice	ENST00000374542	NM_001141970.1	647			1	2	FACETS	0.929	0.879	0.98	0.929	0.879	0.98	CLONAL	1	TRUE	1	0.937742396080016	2		527	615	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553407	106553407	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	190	339	0	ENST00000369096.4:c.1372C>T	p.His458Tyr	p.H458Y	ENST00000369096	NM_001198.3	458	Cac/Tac	5/7	0.937742396080016	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.937742396080016	1		339	215	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968588	55968588	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	316	532	1	ENST00000263923.4:c.2075G>A	p.Gly692Glu	p.G692E	ENST00000263923	NM_002253.2	692	gGg/gAg	14/30	1	2	FACETS	0.927	0.881	0.974	0.927	0.881	0.974	CLONAL	1	TRUE	1	0.937742396080016	2		533	727	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250900	153250900	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	137	182	0	ENST00000281708.4:c.1160T>C	p.Leu387Ser	p.L387S	ENST00000281708	NM_033632.3	387	tTa/tCa	8/12	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.937742396080016	2		182	285	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265323	152265323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866869178	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	79	335	0	ENST00000206249.3:c.776G>A	p.Arg259Gln	p.R259Q	ENST00000206249	NM_000125.3	259	cGa/cAa	4/8	1	2	FACETS	0.88	0.779	0.986	1	0.982	1	CLONAL	2	FALSE	1	0.24404690936315	2		335	368	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	76	548	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.998	0.884	1	1	0.984	1	CLONAL	2	FALSE	1	0.24404690936315	2		548	312	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144724	119144724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253824253	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	63	427	0	ENST00000264033.4:c.737G>A	p.Arg246Gln	p.R246Q	ENST00000264033	NM_005188.3	246	cGa/cAa	4/16	NA	2	FACETS	0.757	0.659	0.862			1	INDETERMINATE	2	FALSE	NA	0.24404690936315	2		427	341	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319887	62319887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371161995	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	131	588	0	ENST00000360203.5:c.1729G>A	p.Asp577Asn	p.D577N	ENST00000360203	NM_001283009.1	577	Gac/Aac	21/35	1	2	FACETS	0.791	0.719	0.866	1	0.987	1	SUBCLONAL	2	FALSE	1	0.24404690936315	2		588	679	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033753	48033753	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1553333707	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	30	233	0	ENST00000234420.5:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000234420	NM_000179.2	1322	Gaa/Taa	9/10	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	1	0.24404690936315	2		233	183	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332774	153332774	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	153	640	0	ENST00000281708.4:c.182G>A	p.Gly61Glu	p.G61E	ENST00000281708	NM_033632.3	61	gGa/gAa	2/12	1	2	FACETS	1	0.935	1	1	0.992	1	CLONAL	2	FALSE	1	0.24404690936315	2		640	614	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844404	156844404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199826686	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	201	767	1	ENST00000524377.1:c.1237G>A	p.Glu413Lys	p.E413K	ENST00000524377	NM_002529.3	413	Gaa/Aaa	10/17	1	2	FACETS	0.818	0.758	0.88	1	0.992	1	CLONAL	2	FALSE	1	0.24404690936315	2		768	1007	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748601	40748601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200545231	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	101	446	0	ENST00000373198.4:c.2915G>A	p.Arg972Gln	p.R972Q	ENST00000373198	NM_133170.3	972	cGa/cAa	21/32	1	2	FACETS	0.755	0.677	0.838	1	0.982	1	SUBCLONAL	2	FALSE	1	0.24404690936315	2		446	548	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170447	119170447	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368138875	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	122	430	1	ENST00000264033.4:c.2677C>T	p.Arg893Trp	p.R893W	ENST00000264033	NM_005188.3	893	Cgg/Tgg	16/16	NA	2	FACETS	0.885	0.803	0.971			1	INDETERMINATE	2	FALSE	NA	0.24404690936315	2		431	565	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467884	66467884	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	62	461	0	ENST00000273854.3:c.385G>T	p.Glu129Ter	p.E129*	ENST00000273854	NM_004439.5	129	Gaa/Taa	3/18	1	2	FACETS	0.765	0.665	0.872	1	0.972	1	SUBCLONAL	2	FALSE	1	0.24404690936315	2		461	332	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	164	531	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	NA	4	FACETS	1	0.973	1	1	0.973	1	INDETERMINATE	2	FALSE	2	0.24404690936315	4		531	739	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922301	178922301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	47	415	0	ENST00000263967.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000263967	NM_006218.2	357	cGa/cAa	6/21	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	1	0.24404690936315	2		415	313	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131412	202131412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339962485	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	91	525	0	ENST00000358485.4:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000358485	NM_001080125.1	127	cGa/cAa	2/9	1	2	FACETS	0.782	0.697	0.871	1	0.981	1	SUBCLONAL	2	FALSE	1	0.24404690936315	2		525	477	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667422	241667422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756990249	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	97	477	0	ENST00000366560.3:c.1028G>A	p.Arg343Gln	p.R343Q	ENST00000366560	NM_000143.3	343	cGa/cAa	7/10	1	2	FACETS	0.79	0.707	0.878	1	0.983	1	SUBCLONAL	2	FALSE	1	0.24404690936315	2		477	503	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	81	597	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.24404690936315	2		597	464	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993645	90993645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs12721593	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	54	372	0	ENST00000265433.3:c.278C>T	p.Ser93Leu	p.S93L	ENST00000265433	NM_002485.4	93	tCg/tTg	3/16	1	2	FACETS	0.76	0.654	0.875	1	0.968	1	SUBCLONAL	2	FALSE	1	0.24404690936315	2		372	291	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584569	189584569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757045273	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	79	371	1	ENST00000264731.3:c.865C>T	p.Pro289Ser	p.P289S	ENST00000264731	NM_003722.4	289	Cct/Tct	6/14	1	2	FACETS	1	0.907	1	1	0.985	1	CLONAL	2	FALSE	1	0.24404690936315	2		372	316	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	51	457	1	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.765	0.656	0.884	1	0.967	1	SUBCLONAL	2	FALSE	1	0.24404690936315	2		458	273	SUCCESS
AR	367	MSKCC	GRCh37	X	66942700	66942700	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs200801099	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	86	509	0	ENST00000374690.3:c.2481C>A	p.Phe827Leu	p.F827L	ENST00000374690	NM_000044.3	827	ttC/ttA	7/8	1	2	FACETS	0.751	0.667	0.841	1	0.979	1	SUBCLONAL	2	FALSE	1	0.24404690936315	2		509	469	SUCCESS
APC	324	MSKCC	GRCh37	5	112179480	112179480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs976132108	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	86	452	0	ENST00000257430.4:c.8189C>T	p.Ala2730Val	p.A2730V	ENST00000257430	NM_000038.5	2730	gCc/gTc	16/16	1	2	FACETS	0.95	0.846	1	1	0.985	1	CLONAL	2	FALSE	1	0.24404690936315	2		452	371	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342433	70342433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs5981075	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	192	652	1	ENST00000374080.3:c.1324G>A	p.Asp442Asn	p.D442N	ENST00000374080		442	Gat/Aat	9/45	1	2	FACETS	0.965	0.894	1	1	0.993	1	CLONAL	2	FALSE	1	0.24404690936315	2		653	815	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259071	153259071	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	51	292	0	ENST00000281708.4:c.744G>T	p.Glu248Asp	p.E248D	ENST00000281708	NM_033632.3	248	gaG/gaT	5/12	1	2	FACETS	1	0.888	1	1	0.977	1	CLONAL	2	FALSE	1	0.24404690936315	2		292	202	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740215	162740215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771675675	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	155	488	1	ENST00000367921.3:c.1417C>T	p.Arg473Cys	p.R473C	ENST00000367921	NM_006182.2	473	Cgc/Tgc	12/18	1	2	FACETS	0.91	0.835	0.988	1	0.991	1	CLONAL	2	FALSE	1	0.24404690936315	2		489	698	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485442	57485442	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	119	391	0	ENST00000371085.3:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000371085	NM_000516.4	342	Cga/Tga	12/13	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.24404690936315	2		391	690	SUCCESS
AR	367	MSKCC	GRCh37	X	66905909	66905909	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	69	564	0	ENST00000374690.3:c.1826G>T	p.Arg609Met	p.R609M	ENST00000374690	NM_000044.3	609	aGg/aTg	3/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.24404690936315	2		564	396	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944326	81944326	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	116	398	0	ENST00000359376.3:c.1934+1G>A		p.X645_splice	ENST00000359376	NM_002661.3	645			1	2	FACETS	0.874	0.791	0.961	1	0.987	1	CLONAL	2	FALSE	1	0.24404690936315	2		398	544	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677876	47677876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	109	395	0	ENST00000347630.2:c.989C>T	p.Ser330Leu	p.S330L	ENST00000347630	NM_001007230.1	330	tCg/tTg	11/11	1	2	FACETS	0.827	0.745	0.913	1	0.986	1	CLONAL	2	FALSE	1	0.24404690936315	2		395	540	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131418	17131418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751171641	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	162	591	1	ENST00000285071.4:c.34G>A	p.Glu12Lys	p.E12K	ENST00000285071	NM_144997.5	12	Gag/Aag	4/14	1	2	FACETS	0.871	0.801	0.945	1	0.991	1	CLONAL	2	FALSE	1	0.24404690936315	2		592	762	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029218	14029218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41557814	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	54	288	0	ENST00000311895.7:c.1429C>T	p.Arg477Trp	p.R477W	ENST00000311895	NM_005236.2	477	Cgg/Tgg	8/11	1	2	FACETS	0.988	0.854	1	1	0.977	1	CLONAL	2	FALSE	1	0.24404690936315	2		288	224	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953890	55953890	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	78	462	0	ENST00000263923.4:c.3546G>T	p.Glu1182Asp	p.E1182D	ENST00000263923	NM_002253.2	1182	gaG/gaT	27/30	1	2	FACETS	0.9	0.797	1	1	0.982	1	CLONAL	2	FALSE	1	0.24404690936315	2		462	355	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645121	86645121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	51	375	1	ENST00000274376.6:c.1193G>A	p.Arg398Gln	p.R398Q	ENST00000274376	NM_002890.2	398	cGa/cAa	8/25	1	2	FACETS	0.774	0.663	0.894	1	0.967	1	SUBCLONAL	2	FALSE	1	0.24404690936315	2		376	270	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098533	108098533	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs55861249	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	51	379	0	ENST00000278616.4:c.103C>T	p.Arg35Ter	p.R35*	ENST00000278616	NM_000051.3	35	Cga/Tga	3/63	0.24404690936315	1	FACETS	0.777	0.668	0.895	1	0.968	1	SUBCLONAL	2	FALSE	0	0.24404690936315	1		379	236	SUCCESS
AR	367	MSKCC	GRCh37	X	66766441	66766441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	67	267	1	ENST00000374690.3:c.1453C>T	p.Arg485Trp	p.R485W	ENST00000374690	NM_000044.3	485	Cgg/Tgg	1/8	1	2	FACETS	0.998	0.877	1	1	0.982	1	CLONAL	2	FALSE	1	0.24404690936315	2		268	275	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702537	52702538	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	30	484	0	ENST00000394830.3:c.360dup	p.Asn121Ter	p.N121*	ENST00000394830	NM_018313.4	120	-/T	4/30	1	2	FACETS	0.848	0.685	1	0.848	0.685	1	CLONAL	1	FALSE	1	0.24404690936315	2		484	290	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467875	99467875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1469290616	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	135	411	0	ENST00000268035.6:c.2744C>T	p.Ser915Leu	p.S915L	ENST00000268035	NM_000875.3	915	tCg/tTg	13/21	1	2	FACETS	0.911	0.831	0.995	1	0.99	1	CLONAL	2	FALSE	1	0.24404690936315	2		411	607	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978320	2978320	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749237424	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	168	566	0	ENST00000396946.4:c.1010G>A	p.Arg337Gln	p.R337Q	ENST00000396946	NM_032415.4	337	cGa/cAa	7/25	1	2	FACETS	0.982	0.905	1	1	0.992	1	CLONAL	2	FALSE	1	0.24404690936315	2		566	701	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6027082	6027082	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	63	232	0	ENST00000265849.7:c.1314G>T	p.Lys438Asn	p.K438N	ENST00000265849	NM_000535.5	438	aaG/aaT	11/15	1	2	FACETS	0.855	0.745	0.972	1	0.977	1	CLONAL	2	FALSE	1	0.24404690936315	2		232	302	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412494	80412494	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	139	456	0	ENST00000286548.4:c.547C>T	p.Arg183Ter	p.R183*	ENST00000286548	NM_002072.3	183	Cga/Tga	4/7	1	2	FACETS	1	0.943	1	1	0.991	1	CLONAL	2	FALSE	1	0.24404690936315	2		456	548	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231757	66231757	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	62	487	0	ENST00000273854.3:c.1943G>T	p.Arg648Ile	p.R648I	ENST00000273854	NM_004439.5	648	aGa/aTa	11/18	1	2	FACETS	1	0.887	1	1	0.981	1	CLONAL	2	FALSE	1	0.24404690936315	2		487	250	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119666150	119666150	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	16	431	0	ENST00000316626.5:c.331C>T	p.Arg111Ter	p.R111*	ENST00000316626		111	Cga/Tga	3/12	1	2	FACETS	0.422	0.311	0.554	0.422	0.311	0.554	SUBCLONAL	1	FALSE	1	0.24404690936315	2		431	311	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021206	31021206	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755749479	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	146	577	0	ENST00000375687.4:c.1205G>A	p.Arg402Gln	p.R402Q	ENST00000375687	NM_015338.5	402	cGa/cAa	12/13	1	2	FACETS	0.85	0.777	0.926	1	0.989	1	CLONAL	2	FALSE	1	0.24404690936315	2		577	704	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099271	4099271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs185999703	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	164	552	3	ENST00000262948.5:c.847G>A	p.Val283Met	p.V283M	ENST00000262948	NM_030662.3	283	Gtg/Atg	7/11	NA	4	FACETS	1	0.941	1	1	0.941	1	INDETERMINATE	2	FALSE	2	0.24404690936315	4		555	812	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624245	89624245	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554890335	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	42	175	0	ENST00000371953.3:c.19G>T	p.Glu7Ter	p.E7*	ENST00000371953	NM_000314.4	7	Gag/Tag	1/9	1	2	FACETS	0.874	0.738	1	1	0.967	1	CLONAL	2	FALSE	1	0.24404690936315	2		175	197	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251860	212251860	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764544368	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	87	314	0	ENST00000342788.4:c.3199C>T	p.Arg1067Ter	p.R1067*	ENST00000342788	NM_005235.2	1067	Cga/Tga	27/28	1	2	FACETS	0.985	0.879	1	1	0.985	1	CLONAL	2	FALSE	1	0.24404690936315	2		314	362	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943753	9943753	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	73	541	0	ENST00000330684.3:c.1188C>A	p.Phe396Leu	p.F396L	ENST00000330684	NM_001134407.1	396	ttC/ttA	5/13	1	2	FACETS	0.798	0.697	0.907	0.798	0.697	0.907	CLONAL	1	FALSE	1	0.24404690936315	2		541	750	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070325	37070325	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778917	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	95	434	0	ENST00000231790.2:c.1460G>A	p.Arg487Gln	p.R487Q	ENST00000231790	NM_000249.3	487	cGa/cAa	13/19	1	2	FACETS	0.885	0.792	0.982	1	0.985	1	CLONAL	2	FALSE	1	0.24404690936315	2		434	440	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193889	106193889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1395976555	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	104	357	0	ENST00000380013.4:c.4351C>T	p.Arg1451Trp	p.R1451W	ENST00000380013	NM_001127208.2	1451	Cgg/Tgg	10/11	1	2	FACETS	0.861	0.774	0.952	1	0.986	1	CLONAL	2	FALSE	1	0.24404690936315	2		357	495	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285871	87285871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408094711	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	130	433	0	ENST00000277120.3:c.208G>A	p.Glu70Lys	p.E70K	ENST00000277120		70	Gaa/Aaa	2/19	1	2	FACETS	0.999	0.911	1	1	0.99	1	CLONAL	2	FALSE	1	0.24404690936315	2		433	533	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137487	202137487	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	117	490	0	ENST00000358485.4:c.715G>T	p.Glu239Ter	p.E239*	ENST00000358485	NM_001080125.1	239	Gaa/Taa	4/9	1	2	FACETS	1	0.976	1	1	0.991	1	CLONAL	2	FALSE	1	0.24404690936315	2		490	395	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494188	140494188	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	136	751	1	ENST00000288602.6:c.1060C>T	p.Arg354Ter	p.R354*	ENST00000288602	NM_004333.4	354	Cga/Tga	8/18	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.24404690936315	2		752	767	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023197	27023197	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	25	79	0	ENST00000324856.7:c.303G>T	p.Lys101Asn	p.K101N	ENST00000324856	NM_006015.4	101	aaG/aaT	1/20	1	2	FACETS	0.923	0.741	1	1	0.949	1	CLONAL	2	FALSE	1	0.24404690936315	2		79	111	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763488	41763488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746364612	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	46	495	1	ENST00000301178.4:c.2287C>T	p.Arg763Cys	p.R763C	ENST00000301178	NM_021913.4	763	Cgc/Tgc	19/20	NA	4	FACETS	0.666	0.56	0.784	0.333	0.28	0.392	INDETERMINATE	1	FALSE	2	0.24404690936315	4		496	704	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149872	99149872	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs777176771	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	143	447	0	ENST00000074304.5:c.184C>T	p.Arg62Ter	p.R62*	ENST00000074304	NM_001134224.1	62	Cga/Tga	5/26	1	2	FACETS	0.853	0.779	0.93	1	0.989	1	CLONAL	2	FALSE	1	0.24404690936315	2		447	687	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961036	15961036	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	88	428	0	ENST00000268712.3:c.6184G>T	p.Asp2062Tyr	p.D2062Y	ENST00000268712	NM_006311.3	2062	Gat/Tat	40/46	1	2	FACETS	0.897	0.8	1	1	0.984	1	CLONAL	2	FALSE	1	0.24404690936315	2		428	402	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543620	148543620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	110	569	0	ENST00000320356.2:c.188G>A	p.Arg63Gln	p.R63Q	ENST00000320356	NM_004456.4	63	cGa/cAa	3/20	1	2	FACETS	0.815	0.735	0.899	1	0.985	1	CLONAL	2	FALSE	1	0.24404690936315	2		569	553	SUCCESS
AR	367	MSKCC	GRCh37	X	66905935	66905935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1218564193	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	66	565	1	ENST00000374690.3:c.1852C>T	p.Arg618Trp	p.R618W	ENST00000374690	NM_000044.3	618	Cgg/Tgg	3/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.24404690936315	2		566	382	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247523	71247523	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	90	393	0	ENST00000318789.4:c.10G>T	p.Glu4Ter	p.E4*	ENST00000318789	NM_032682.5	4	Gaa/Taa	6/21	1	2	FACETS	0.778	0.693	0.868	1	0.981	1	SUBCLONAL	2	FALSE	1	0.24404690936315	2		393	474	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161374	55161374	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	146	480	0	ENST00000257290.5:c.3205G>T	p.Asp1069Tyr	p.D1069Y	ENST00000257290	NM_006206.4	1069	Gac/Tac	23/23	1	2	FACETS	0.929	0.85	1	1	0.991	1	CLONAL	2	FALSE	1	0.24404690936315	2		480	644	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715319	61715319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	77	644	1	ENST00000401558.2:c.2294G>A	p.Arg765Gln	p.R765Q	ENST00000401558	NM_003400.3	765	cGa/cAa	19/25	1	2	FACETS	0.773	0.682	0.87	1	0.978	1	SUBCLONAL	2	FALSE	1	0.24404690936315	2		645	408	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411948	63411948	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	155	813	0	ENST00000330258.3:c.1219G>T	p.Glu407Ter	p.E407*	ENST00000330258	NM_152424.3	407	Gaa/Taa	2/2	1	2	FACETS	0.794	0.727	0.863	1	0.989	1	SUBCLONAL	2	FALSE	1	0.24404690936315	2		813	800	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395570	116395570	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1013431413	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	64	491	0	ENST00000397752.3:c.1862+1G>A		p.X621_splice	ENST00000397752	NM_000245.2	621			1	2	FACETS	0.792	0.691	0.901	1	0.975	1	CLONAL	2	FALSE	1	0.24404690936315	2		491	331	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108091	30108091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80271647	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	80	647	0	ENST00000331968.5:c.716C>T	p.Ser239Leu	p.S239L	ENST00000331968	NM_002742.2	239	tCg/tTg	5/18	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.24404690936315	2		647	461	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358979	81358979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754502188	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	68	607	1	ENST00000222390.5:c.982C>T	p.Arg328Cys	p.R328C	ENST00000222390	NM_000601.4	328	Cgt/Tgt	8/18	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.24404690936315	2		608	396	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63829504	63829504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529464997	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	80	482	0	ENST00000279873.7:c.1147G>A	p.Gly383Ser	p.G383S	ENST00000279873	NM_032199.2	383	Ggt/Agt	8/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.24404690936315	2		482	484	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048737	180048737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144803521	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	177	654	0	ENST00000261937.6:c.1825G>A	p.Asp609Asn	p.D609N	ENST00000261937	NM_182925.4	609	Gac/Aac	13/30	1	2	FACETS	0.882	0.814	0.953	1	0.992	1	CLONAL	2	FALSE	1	0.24404690936315	2		654	822	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196207	106196208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	77	283	0	ENST00000380013.4:c.4544dup	p.Leu1515PhefsTer63	p.L1515Ffs*63	ENST00000380013	NM_001127208.2	1514	ctt/cTtt	11/11	1	2	FACETS	0.837	0.739	0.94	1	0.98	1	CLONAL	2	FALSE	1	0.24404690936315	2		283	377	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073692	8073692	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	171	458	0	ENST00000377482.5:c.967G>T	p.Glu323Ter	p.E323*	ENST00000377482	NM_018948.3	323	Gaa/Taa	4/4	1	2	FACETS	1	0.96	1	1	0.993	1	CLONAL	2	FALSE	1	0.24404690936315	2		458	661	SUCCESS
FH	2271	MSKCC	GRCh37	1	241669404	241669404	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	33	533	0	ENST00000366560.3:c.803G>T	p.Arg268Ile	p.R268I	ENST00000366560	NM_000143.3	268	aGa/aTa	6/10	1	2	FACETS	0.565	0.459	0.684	0.565	0.459	0.684	SUBCLONAL	1	FALSE	1	0.24404690936315	2		533	479	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931826	68931826	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs759461290	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	93	618	0	ENST00000288368.4:c.256G>T	p.Glu86Ter	p.E86*	ENST00000288368	NM_024870.2	86	Gaa/Taa	3/40	1	2	FACETS	0.903	0.808	1	1	0.985	1	CLONAL	2	FALSE	1	0.24404690936315	2		618	422	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266570	115266570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	119	602	0	ENST00000438362.2:c.1945C>T	p.Arg649Cys	p.R649C	ENST00000438362	NM_001242891.1	649	Cgc/Tgc	16/20	1	2	FACETS	0.896	0.812	0.984	1	0.988	1	CLONAL	2	FALSE	1	0.24404690936315	2		602	544	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412470	80412470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28764015	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	32	422	0	ENST00000286548.4:c.571G>A	p.Glu191Lys	p.E191K	ENST00000286548	NM_002072.3	191	Gaa/Aaa	4/7	1	2	FACETS	0.522	0.423	0.635	0.522	0.423	0.635	SUBCLONAL	1	FALSE	1	0.24404690936315	2		422	502	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623783	28623783	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	59	636	0	ENST00000241453.7:c.871G>T	p.Ala291Ser	p.A291S	ENST00000241453	NM_004119.2	291	Gca/Tca	7/24	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.24404690936315	2		636	341	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859879	117859879	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	72	337	1	ENST00000297338.2:c.1756C>T	p.Arg586Ter	p.R586*	ENST00000297338	NM_006265.2	586	Cga/Tga	14/14	1	2	FACETS	1	0.941	1	1	0.984	1	CLONAL	2	FALSE	1	0.24404690936315	2		338	267	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1795713	1795713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs908992323	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	16	145	0	ENST00000260795.2:c.52G>A	p.Ala18Thr	p.A18T	ENST00000260795		18	Gcc/Acc	1/17	1	2	FACETS	0.637	0.472	0.832	0.637	0.472	0.832	SUBCLONAL	1	FALSE	1	0.24404690936315	2		145	206	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31405819	31405819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	47	268	0	ENST00000344624.3:c.3959C>T	p.Ala1320Val	p.A1320V	ENST00000344624		1320	gCg/gTg	32/33	1	2	FACETS	0.837	0.714	0.971	1	0.969	1	CLONAL	2	FALSE	1	0.24404690936315	2		268	230	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268949	115268949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781496859	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	107	479	1	ENST00000438362.2:c.1661G>A	p.Arg554Gln	p.R554Q	ENST00000438362	NM_001242891.1	554	cGa/cAa	14/20	1	2	FACETS	1	0.917	1	1	0.988	1	CLONAL	2	FALSE	1	0.24404690936315	2		480	431	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395770	45395770	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	59	373	2	ENST00000262160.6:c.364G>T	p.Gly122Ter	p.G122*	ENST00000262160	NM_005901.5	122	Gga/Tga	4/11	1	2	FACETS	0.751	0.65	0.859	1	0.97	1	SUBCLONAL	2	FALSE	1	0.24404690936315	2		375	322	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166227	7166227	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745372291	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	143	628	1	ENST00000302850.5:c.1799C>T	p.Ser600Leu	p.S600L	ENST00000302850	NM_000208.2	600	tCg/tTg	8/22	NA	4	FACETS	0.936	0.854	1	0.936	0.854	1	INDETERMINATE	2	FALSE	2	0.24404690936315	4		629	779	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108080	30108080	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1239799730	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	110	681	0	ENST00000331968.5:c.727C>T	p.Arg243Ter	p.R243*	ENST00000331968	NM_002742.2	243	Cga/Tga	5/18	1	2	FACETS	0.933	0.843	1	1	0.988	1	CLONAL	2	FALSE	1	0.24404690936315	2		681	483	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422393	225422393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1417750087	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	74	571	0	ENST00000264414.4:c.247G>A	p.Glu83Lys	p.E83K	ENST00000264414	NM_003590.4	83	Gaa/Aaa	2/16	1	2	FACETS	0.826	0.728	0.931	1	0.979	1	CLONAL	2	FALSE	1	0.24404690936315	2		571	367	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750417	133750417	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	181	579	0	ENST00000318560.5:c.1248C>A	p.Phe416Leu	p.F416L	ENST00000318560	NM_005157.4	416	ttC/ttA	7/11	1	2	FACETS	0.851	0.785	0.919	1	0.991	1	CLONAL	2	FALSE	1	0.24404690936315	2		579	872	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312915	30312915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1411284279	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	46	617	0	ENST00000262643.3:c.718C>T	p.Arg240Cys	p.R240C	ENST00000262643	NM_001238.2	240	Cgt/Tgt	9/12	NA	4	FACETS	0.907	0.764	1	0.454	0.382	0.533	INDETERMINATE	1	FALSE	2	0.24404690936315	4		617	517	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180350	38180350	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	181	649	0	ENST00000396334.3:c.198G>T	p.Glu66Asp	p.E66D	ENST00000396334	NM_002468.4	66	gaG/gaT	1/5	1	2	FACETS	1	0.941	1	1	0.993	1	CLONAL	2	FALSE	1	0.24404690936315	2		649	727	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39237759	39237759	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	85	517	0	ENST00000402219.2:c.2476C>T	p.Arg826Ter	p.R826*	ENST00000402219	NM_005633.3	826	Cga/Tga	15/23	1	2	FACETS	0.781	0.693	0.874	1	0.98	1	SUBCLONAL	2	FALSE	1	0.24404690936315	2		517	446	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261337	115261337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772339521	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	104	430	0	ENST00000438362.2:c.2384G>A	p.Arg795Gln	p.R795Q	ENST00000438362	NM_001242891.1	795	cGa/cAa	19/20	1	2	FACETS	0.792	0.712	0.877	1	0.984	1	SUBCLONAL	2	FALSE	1	0.24404690936315	2		430	538	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816896	32816896	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1159721335	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	109	434	0	ENST00000354258.4:c.1429-1G>T		p.X477_splice	ENST00000354258	NM_000593.5	477			1	2	FACETS	0.94	0.849	1	1	0.988	1	CLONAL	2	FALSE	1	0.24404690936315	2		434	475	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902622	1902622	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs771287635	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	214	593	0	ENST00000382891.5:c.241G>T	p.Asp81Tyr	p.D81Y	ENST00000382891	NM_133335.3	81	Gat/Tat	2/22	1	2	FACETS	0.944	0.878	1	1	0.993	1	CLONAL	2	FALSE	1	0.24404690936315	2		593	929	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008522	70008522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542163629	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	120	412	0	ENST00000394351.3:c.809G>A	p.Arg270Gln	p.R270Q	ENST00000394351	NM_000248.3	270	cGa/cAa	8/9	1	2	FACETS	0.818	0.741	0.899	1	0.987	1	CLONAL	2	FALSE	1	0.24404690936315	2		412	601	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520524	176520524	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763461529	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	180	692	1	ENST00000292408.4:c.1369G>A	p.Asp457Asn	p.D457N	ENST00000292408	NM_213647.1	457	Gac/Aac	10/18	1	2	FACETS	0.885	0.817	0.956	1	0.992	1	CLONAL	2	FALSE	1	0.24404690936315	2		693	833	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356750	70356750	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372271659	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	161	542	0	ENST00000374080.3:c.5422C>T	p.Arg1808Trp	p.R1808W	ENST00000374080		1808	Cgg/Tgg	38/45	1	2	FACETS	0.848	0.779	0.92	1	0.99	1	CLONAL	2	FALSE	1	0.24404690936315	2		542	778	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380071	116380071	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	124	610	0	ENST00000397752.3:c.1460C>A	p.Ser487Tyr	p.S487Y	ENST00000397752	NM_000245.2	487	tCt/tAt	4/21	1	2	FACETS	1	0.942	1	1	0.99	1	CLONAL	2	FALSE	1	0.24404690936315	2		610	486	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99162524	99162524	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1024484850	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	30	351	0	ENST00000074304.5:c.1042G>A	p.Asp348Asn	p.D348N	ENST00000074304	NM_001134224.1	348	Gat/Aat	12/26	1	2	FACETS	0.7	0.565	0.854	0.7	0.565	0.854	SUBCLONAL	1	FALSE	1	0.24404690936315	2		351	351	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539619	187539619	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	67	497	0	ENST00000441802.2:c.8121C>A	p.Phe2707Leu	p.F2707L	ENST00000441802	NM_005245.3	2707	ttC/ttA	10/27	1	2	FACETS	0.791	0.692	0.897	1	0.976	1	SUBCLONAL	2	FALSE	1	0.24404690936315	2		497	347	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181978	38181978	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs566004944	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	149	483	0	ENST00000396334.3:c.602G>A	p.Arg201Gln	p.R201Q	ENST00000396334	NM_002468.4	201	cGa/cAa	3/5	1	2	FACETS	0.885	0.81	0.962	1	0.99	1	CLONAL	2	FALSE	1	0.24404690936315	2		483	690	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419991	152419991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745984515	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	190	662	0	ENST00000206249.3:c.1678G>A	p.Val560Met	p.V560M	ENST00000206249	NM_000125.3	560	Gtg/Atg	8/8	1	2	FACETS	0.967	0.896	1	1	0.993	1	CLONAL	2	FALSE	1	0.24404690936315	2		662	805	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292520	15292520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	149	635	0	ENST00000263388.2:c.2659G>A	p.Asp887Asn	p.D887N	ENST00000263388	NM_000435.2	887	Gat/Aat	17/33	NA	4	FACETS	0.915	0.836	0.997	0.915	0.836	0.997	INDETERMINATE	2	FALSE	2	0.24404690936315	4		635	830	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463300	25463300	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	103	398	0	ENST00000264709.3:c.2193C>A	p.Phe731Leu	p.F731L	ENST00000264709	NM_175629.2	731	ttC/ttA	19/23	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.24404690936315	2		398	606	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2493176	2493176	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	155	669	0	ENST00000355716.4:c.616C>A	p.Leu206Ile	p.L206I	ENST00000355716	NM_003820.2	206	Ctc/Atc	6/8	1	2	FACETS	0.926	0.85	1	1	0.991	1	CLONAL	2	FALSE	1	0.24404690936315	2		669	686	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11193160	11193160	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	195	545	0	ENST00000361445.4:c.5341G>T	p.Glu1781Ter	p.E1781*	ENST00000361445	NM_004958.3	1781	Gag/Tag	38/58	1	2	FACETS	0.865	0.801	0.931	1	0.992	1	CLONAL	2	FALSE	1	0.24404690936315	2		545	924	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100151	27100151	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749727660	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	142	522	0	ENST00000324856.7:c.3947C>T	p.Ser1316Leu	p.S1316L	ENST00000324856	NM_006015.4	1316	tCg/tTg	16/20	1	2	FACETS	0.836	0.763	0.912	1	0.989	1	CLONAL	2	FALSE	1	0.24404690936315	2		522	696	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532736	46532736	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	27	436	0	ENST00000262741.5:c.342G>T	p.Lys114Asn	p.K114N	ENST00000262741	NM_003629.3	114	aaG/aaT	4/10	1	2	FACETS	0.74	0.59	0.911	0.74	0.59	0.911	CLONAL	1	FALSE	1	0.24404690936315	2		436	299	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739399	46739399	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	116	500	1	ENST00000371975.4:c.1590G>T	p.Glu530Asp	p.E530D	ENST00000371975	NM_003579.3	530	gaG/gaT	14/18	1	2	FACETS	0.849	0.768	0.934	1	0.987	1	CLONAL	2	FALSE	1	0.24404690936315	2		501	560	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439599	51439599	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	66	421	0	ENST00000262662.1:c.164G>T	p.Arg55Ile	p.R55I	ENST00000262662		55	aGa/aTa	4/4	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	1	0.24404690936315	2		421	465	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414881	78414881	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	121	431	0	ENST00000370768.2:c.1885A>C	p.Thr629Pro	p.T629P	ENST00000370768	NM_003902.3	629	Aca/Cca	19/20	1	2	FACETS	0.939	0.852	1	1	0.989	1	CLONAL	2	FALSE	1	0.24404690936315	2		431	528	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273024	115273024	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	82	598	0	ENST00000438362.2:c.1349G>T	p.Arg450Ile	p.R450I	ENST00000438362	NM_001242891.1	450	aGa/aTa	12/20	1	2	FACETS	0.851	0.755	0.952	1	0.982	1	CLONAL	2	FALSE	1	0.24404690936315	2		598	395	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176153803	176153803	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	80	461	0	ENST00000367669.3:c.433G>T	p.Glu145Ter	p.E145*	ENST00000367669	NM_022457.5	145	Gaa/Taa	2/20	1	2	FACETS	1	0.903	1	1	0.985	1	CLONAL	2	FALSE	1	0.24404690936315	2		461	322	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851720	63851720	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1322695665	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	77	584	0	ENST00000279873.7:c.2498C>T	p.Ser833Leu	p.S833L	ENST00000279873	NM_032199.2	833	tCg/tTg	10/10	1	2	FACETS	0.854	0.749	0.967	0.854	0.749	0.967	CLONAL	1	FALSE	1	0.24404690936315	2		584	739	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309791	104309791	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	187	535	0	ENST00000369902.3:c.382A>G	p.Thr128Ala	p.T128A	ENST00000369902	NM_016169.3	128	Act/Gct	3/12	1	2	FACETS	1	0.947	1	1	0.993	1	CLONAL	2	FALSE	1	0.24404690936315	2		535	746	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710674	114710674	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	106	422	0	ENST00000543371.1:c.159A>C	p.Glu53Asp	p.E53D	ENST00000543371	NM_001198531.1	53	gaA/gaC	1/14	1	2	FACETS	1	0.953	1	1	0.989	1	CLONAL	2	FALSE	1	0.24404690936315	2		422	398	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14317386	14317386	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	81	513	0	ENST00000256196.4:c.124G>A	p.Asp42Asn	p.D42N	ENST00000256196		42	Gat/Aat	2/6	NA	4	FACETS	1	0.942	1	1	0.942	1	INDETERMINATE	2	FALSE	2	0.24404690936315	4		513	376	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741354	17741354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755476517	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	123	534	0	ENST00000250003.3:c.25C>T	p.Arg9Cys	p.R9C	ENST00000250003	NM_002478.4	9	Cgc/Tgc	1/3	NA	4	FACETS	0.91	0.824	1	0.91	0.824	1	INDETERMINATE	2	FALSE	2	0.24404690936315	4		534	689	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136198	64136198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	150	503	0	ENST00000334205.4:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000334205	NM_003942.2	453	Gaa/Aaa	12/17	NA	4	FACETS	1	0.97	1	1	0.97	1	INDETERMINATE	2	FALSE	2	0.24404690936315	4		503	679	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573220	64573220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	137	661	0	ENST00000312049.6:c.1072G>A	p.Glu358Lys	p.E358K	ENST00000312049	NM_130799.2	358	Gag/Aag	8/10	NA	4	FACETS	0.864	0.787	0.946	0.864	0.787	0.946	INDETERMINATE	2	FALSE	2	0.24404690936315	4		661	808	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943686	71943686	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	203	628	0	ENST00000298229.2:c.1729T>G	p.Leu577Val	p.L577V	ENST00000298229	NM_001567.3	577	Ttg/Gtg	15/28	NA	4	FACETS	1	0.981	1	1	0.981	1	INDETERMINATE	2	FALSE	2	0.24404690936315	4		628	888	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047169	77047169	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	141	630	0	ENST00000356341.3:c.1375G>T	p.Glu459Ter	p.E459*	ENST00000356341	NM_002576.4	459	Gaa/Taa	13/15	NA	4	FACETS	1	0.96	1	1	0.96	1	INDETERMINATE	2	FALSE	2	0.24404690936315	4		630	661	SUCCESS
EED	8726	MSKCC	GRCh37	11	85961420	85961420	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	25	288	0	ENST00000263360.6:c.197A>C	p.Lys66Thr	p.K66T	ENST00000263360	NM_003797.3	66	aAa/aCa	2/12	NA	4	FACETS	1	0.845	1	0.542	0.429	0.671	INDETERMINATE	1	FALSE	2	0.24404690936315	4		288	235	SUCCESS
EED	8726	MSKCC	GRCh37	11	85975288	85975288	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	73	367	0	ENST00000263360.6:c.709G>A	p.Asp237Asn	p.D237N	ENST00000263360	NM_003797.3	237	Gat/Aat	7/12	0.24404690936315	1	FACETS	0.816	0.719	0.918	1	0.979	1	CLONAL	2	FALSE	0	0.24404690936315	1		367	322	SUCCESS
ATM	472	MSKCC	GRCh37	11	108137967	108137967	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	66	477	0	ENST00000278616.4:c.2536C>A	p.Leu846Ile	p.L846I	ENST00000278616	NM_000051.3	846	Cta/Ata	17/63	0.24404690936315	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	0	0.24404690936315	1		477	354	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497542	125497542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753180922	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	41	365	0	ENST00000428830.2:c.106G>A	p.Ala36Thr	p.A36T	ENST00000428830	NM_001114121.2	36	Gca/Aca	3/14	NA	2	FACETS	0.8	0.673	0.938			1	INDETERMINATE	2	FALSE	NA	0.24404690936315	2		365	210	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	422251	422251	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	124	681	0	ENST00000399788.2:c.3007G>T	p.Glu1003Ter	p.E1003*	ENST00000399788	NM_001042603.1	1003	Gaa/Taa	20/28	NA	4	FACETS	1	0.976	1	1	0.976	1	INDETERMINATE	2	FALSE	2	0.24404690936315	4		681	517	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18762513	18762513	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1038531296	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	27	483	0	ENST00000266497.5:c.4009T>C	p.Ser1337Pro	p.S1337P	ENST00000266497		1337	Tcc/Ccc	29/31	0.24404690936315	1	FACETS	0.627	0.499	0.772	0.627	0.499	0.772	SUBCLONAL	1	FALSE	0	0.24404690936315	1		483	310	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636366	21636366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561515655	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	104	653	0	ENST00000421138.2:c.644G>A	p.Arg215Gln	p.R215Q	ENST00000421138		215	cGa/cAa	7/16	0.24404690936315	1	FACETS	0.757	0.681	0.837	1	0.983	1	SUBCLONAL	2	FALSE	0	0.24404690936315	1		653	494	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644535	21644535	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	85	648	0	ENST00000421138.2:c.132G>T	p.Lys44Asn	p.K44N	ENST00000421138		44	aaG/aaT	4/16	0.24404690936315	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	0	0.24404690936315	1		648	457	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246599	46246599	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138175128	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	50	240	1	ENST00000334344.6:c.4693G>A	p.Val1565Ile	p.V1565I	ENST00000334344	NM_152641.2	1565	Gta/Ata	15/21	NA	4	FACETS	0.888	0.759	1	0.888	0.759	1	INDETERMINATE	2	FALSE	2	0.24404690936315	4		241	287	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434090	49434090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779629382	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	151	547	0	ENST00000301067.7:c.7463C>T	p.Ser2488Leu	p.S2488L	ENST00000301067	NM_003482.3	2488	tCg/tTg	31/54	NA	4	FACETS	1	0.966	1	1	0.966	1	INDETERMINATE	2	FALSE	2	0.24404690936315	4		547	698	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440080	49440080	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	199	663	0	ENST00000301067.7:c.4546G>T	p.Glu1516Ter	p.E1516*	ENST00000301067	NM_003482.3	1516	Gaa/Taa	16/54	NA	4	FACETS	1	0.978	1	1	0.978	1	INDETERMINATE	2	FALSE	2	0.24404690936315	4		663	895	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858918	57858918	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1019239130	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	77	685	0	ENST00000228682.2:c.414G>T	p.Gln138His	p.Q138H	ENST00000228682	NM_005269.2	138	caG/caT	5/12	NA	4	FACETS	0.992	0.87	1	0.496	0.435	0.562	INDETERMINATE	1	FALSE	2	0.24404690936315	4		685	791	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864690	57864690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	185	752	1	ENST00000228682.2:c.2167G>A	p.Asp723Asn	p.D723N	ENST00000228682	NM_005269.2	723	Gac/Aac	12/12	NA	4	FACETS	1	0.984	1	1	0.984	1	INDETERMINATE	2	FALSE	2	0.24404690936315	4		753	768	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865440	57865440	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	51	770	0	ENST00000228682.2:c.2917A>G	p.Asn973Asp	p.N973D	ENST00000228682	NM_005269.2	973	Aat/Gat	12/12	NA	4	FACETS	0.628	0.532	0.734	0.314	0.266	0.367	INDETERMINATE	1	FALSE	2	0.24404690936315	4		770	828	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118806	115118806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754023417	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	162	572	0	ENST00000257566.3:c.535G>A	p.Glu179Lys	p.E179K	ENST00000257566	NM_016569.3	179	Gaa/Aaa	2/8	NA	4	FACETS	1	0.976	1	1	0.976	1	INDETERMINATE	2	FALSE	2	0.24404690936315	4		572	717	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120672	115120672	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	197	694	0	ENST00000257566.3:c.334C>A	p.Leu112Ile	p.L112I	ENST00000257566	NM_016569.3	112	Ctt/Att	1/8	NA	4	FACETS	1	0.955	1	1	0.955	1	INDETERMINATE	2	FALSE	2	0.24404690936315	4		694	964	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536722	120536722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762605816	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	148	608	0	ENST00000229340.5:c.370G>A	p.Asp124Asn	p.D124N	ENST00000229340	NM_006861.6	124	Gac/Aac	5/6	NA	4	FACETS	0.976	0.892	1	0.976	0.892	1	INDETERMINATE	2	FALSE	2	0.24404690936315	4		608	773	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120789156	120789156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1433178108	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	131	481	1	ENST00000257552.2:c.781G>A	p.Glu261Lys	p.E261K	ENST00000257552	NM_002442.3	261	Gag/Aag	11/15	NA	4	FACETS	1	0.915	1	1	0.915	1	INDETERMINATE	2	FALSE	2	0.24404690936315	4		482	664	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212579	133212579	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	112	516	0	ENST00000320574.5:c.5710A>G	p.Thr1904Ala	p.T1904A	ENST00000320574	NM_006231.2	1904	Aca/Gca	42/49	NA	4	FACETS	1	0.964	1	1	0.964	1	INDETERMINATE	2	FALSE	2	0.24404690936315	4		516	501	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226007	133226007	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746585658	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	164	659	0	ENST00000320574.5:c.3890C>T	p.Ser1297Leu	p.S1297L	ENST00000320574	NM_006231.2	1297	tCg/tTg	31/49	NA	4	FACETS	1	0.964	1	1	0.964	1	INDETERMINATE	2	FALSE	2	0.24404690936315	4		659	771	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609641	28609641	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1289193122	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	88	533	0	ENST00000241453.7:c.1588A>C	p.Asn530His	p.N530H	ENST00000241453	NM_004119.2	530	Aac/Cac	12/24	1	2	FACETS	0.841	0.749	0.938	1	0.983	1	CLONAL	2	FALSE	1	0.24404690936315	2		533	429	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911082	32911082	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	12	384	0	ENST00000380152.3:c.2590C>A	p.Gln864Lys	p.Q864K	ENST00000380152		864	Caa/Aaa	11/27	1	2	FACETS	0.437	0.307	0.597	0.437	0.307	0.597	SUBCLONAL	1	FALSE	1	0.24404690936315	2		384	225	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953953	32953953	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	46	399	0	ENST00000380152.3:c.9020G>T	p.Arg3007Ile	p.R3007I	ENST00000380152		3007	aGa/aTa	23/27	1	2	FACETS	0.763	0.648	0.888	1	0.963	1	SUBCLONAL	2	FALSE	1	0.24404690936315	2		399	247	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32968912	32968912	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	26	481	0	ENST00000380152.3:c.9343A>C	p.Lys3115Gln	p.K3115Q	ENST00000380152		3115	Aag/Cag	25/27	1	2	FACETS	0.775	0.615	0.957	0.775	0.615	0.957	CLONAL	1	FALSE	1	0.24404690936315	2		481	275	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039195	49039195	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754814477	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	82	457	0	ENST00000267163.4:c.2273C>T	p.Ser758Leu	p.S758L	ENST00000267163	NM_000321.2	758	tCg/tTg	22/27	1	2	FACETS	0.923	0.82	1	1	0.984	1	CLONAL	2	FALSE	1	0.24404690936315	2		457	364	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506127	103506127	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	32	277	0	ENST00000355739.4:c.285G>T	p.Lys95Asn	p.K95N	ENST00000355739	NM_000123.3	95	aaG/aaT	3/15	1	2	FACETS	0.771	0.633	0.923	1	0.949	1	CLONAL	2	FALSE	1	0.24404690936315	2		277	170	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524572	103524572	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	29	220	0	ENST00000355739.4:c.2703A>C	p.Lys901Asn	p.K901N	ENST00000355739	NM_000123.3	901	aaA/aaC	13/15	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	FALSE	1	0.24404690936315	2		220	213	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066949	30066949	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	69	346	0	ENST00000331968.5:c.2182T>G	p.Phe728Val	p.F728V	ENST00000331968	NM_002742.2	728	Ttt/Gtt	16/18	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.24404690936315	2		346	406	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610544	81610544	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	88	410	0	ENST00000298171.2:c.2142G>T	p.Lys714Asn	p.K714N	ENST00000298171	NM_000369.2	714	aaG/aaT	10/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.24404690936315	2		410	498	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557374	95557374	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	70	545	0	ENST00000393063.1:c.5600T>G	p.Phe1867Cys	p.F1867C	ENST00000393063	NM_030621.3	1867	tTt/tGt	27/28	1	2	FACETS	0.773	0.678	0.875	1	0.976	1	SUBCLONAL	2	FALSE	1	0.24404690936315	2		545	371	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562324	95562324	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	106	491	0	ENST00000393063.1:c.4933C>A	p.Pro1645Thr	p.P1645T	ENST00000393063	NM_030621.3	1645	Cca/Aca	24/28	1	2	FACETS	1	0.933	1	1	0.989	1	CLONAL	2	FALSE	1	0.24404690936315	2		491	417	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569693	95569693	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	46	196	0	ENST00000393063.1:c.4040G>T	p.Arg1347Ile	p.R1347I	ENST00000393063	NM_030621.3	1347	aGa/aTa	22/28	1	2	FACETS	0.865	0.736	1	1	0.969	1	CLONAL	2	FALSE	1	0.24404690936315	2		196	218	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989216	41989216	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	107	562	1	ENST00000219905.7:c.2008T>G	p.Ser670Ala	p.S670A	ENST00000219905	NM_001164273.1	670	Tca/Gca	3/24	1	2	FACETS	0.981	0.885	1	1	0.988	1	CLONAL	2	FALSE	1	0.24404690936315	2		563	447	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034972	42034972	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	196	672	0	ENST00000219905.7:c.4814T>G	p.Phe1605Cys	p.F1605C	ENST00000219905	NM_001164273.1	1605	tTt/tGt	15/24	1	2	FACETS	1	0.964	1	1	0.994	1	CLONAL	2	FALSE	1	0.24404690936315	2		672	757	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054533	42054533	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	57	353	0	ENST00000219905.7:c.7717C>A	p.Leu2573Ile	p.L2573I	ENST00000219905	NM_001164273.1	2573	Ctt/Att	22/24	1	2	FACETS	0.773	0.668	0.886	1	0.97	1	SUBCLONAL	2	FALSE	1	0.24404690936315	2		353	302	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748112	43748112	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	188	531	0	ENST00000382044.4:c.2694A>C	p.Gln898His	p.Q898H	ENST00000382044	NM_001141980.1	898	caA/caC	12/28	1	2	FACETS	0.974	0.902	1	1	0.993	1	CLONAL	2	FALSE	1	0.24404690936315	2		531	791	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727493	88727493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765088970	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	161	521	1	ENST00000360948.2:c.286G>A	p.Ala96Thr	p.A96T	ENST00000360948	NM_001012338.2	96	Gcc/Acc	3/19	1	2	FACETS	0.784	0.719	0.851	1	0.989	1	SUBCLONAL	2	FALSE	1	0.24404690936315	2		522	842	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631975	90631975	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	153	520	0	ENST00000330062.3:c.378C>A	p.Phe126Leu	p.F126L	ENST00000330062	NM_002168.2	126	ttC/ttA	4/11	1	2	FACETS	1	0.932	1	1	0.992	1	CLONAL	2	FALSE	1	0.24404690936315	2		520	617	SUCCESS
BLM	641	MSKCC	GRCh37	15	91341451	91341451	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	52	421	0	ENST00000355112.3:c.3242T>C	p.Val1081Ala	p.V1081A	ENST00000355112	NM_000057.2	1081	gTg/gCg	17/22	1	2	FACETS	0.922	0.794	1	1	0.975	1	CLONAL	2	FALSE	1	0.24404690936315	2		421	231	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456503	99456503	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	22	352	1	ENST00000268035.6:c.1820A>C	p.Asn607Thr	p.N607T	ENST00000268035	NM_000875.3	607	aAt/aCt	8/21	1	2	FACETS	0.411	0.317	0.519	0.411	0.317	0.519	SUBCLONAL	1	FALSE	1	0.24404690936315	2		353	439	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348003	348003	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	204	703	0	ENST00000262320.3:c.1503G>T	p.Lys501Asn	p.K501N	ENST00000262320	NM_003502.3	501	aaG/aaT	6/11	1	2	FACETS	0.989	0.919	1	1	0.994	1	CLONAL	2	FALSE	1	0.24404690936315	2		703	845	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639062	3639062	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	210	698	0	ENST00000294008.3:c.4577C>A	p.Pro1526His	p.P1526H	ENST00000294008	NM_032444.2	1526	cCt/cAt	12/15	1	2	FACETS	0.975	0.906	1	1	0.994	1	CLONAL	2	FALSE	1	0.24404690936315	2		698	883	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639963	3639963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142008398	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	58	694	0	ENST00000294008.3:c.3676C>T	p.Arg1226Trp	p.R1226W	ENST00000294008	NM_032444.2	1226	Cgg/Tgg	12/15	1	2	FACETS	0.569	0.487	0.658	0.569	0.487	0.658	SUBCLONAL	1	FALSE	1	0.24404690936315	2		694	836	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858294	9858296	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	115	521	0	ENST00000330684.3:c.3105_3107del	p.Asp1035del	p.D1035del	ENST00000330684	NM_001134407.1	1035	gaTGAg/gag	13/13	1	2	FACETS	0.834	0.754	0.918	1	0.986	1	CLONAL	2	FALSE	1	0.24404690936315	2		521	565	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646423	23646423	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	169	626	0	ENST00000261584.4:c.1444C>A	p.Leu482Ile	p.L482I	ENST00000261584	NM_024675.3	482	Ctc/Atc	4/13	1	2	FACETS	1	0.942	1	1	0.993	1	CLONAL	2	FALSE	1	0.24404690936315	2		626	675	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133234	30133234	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	184	635	0	ENST00000263025.4:c.264G>T	p.Glu88Asp	p.E88D	ENST00000263025	NM_002746.2	88	gaG/gaT	2/9	1	2	FACETS	0.87	0.803	0.938	1	0.992	1	CLONAL	2	FALSE	1	0.24404690936315	2		635	867	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650701	67650701	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	214	596	0	ENST00000264010.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000264010	NM_006565.3	336	Gaa/Taa	5/12	1	2	FACETS	0.959	0.892	1	1	0.994	1	CLONAL	2	FALSE	1	0.24404690936315	2		596	914	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830023	72830023	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	157	727	1	ENST00000268489.5:c.6558G>T	p.Gln2186His	p.Q2186H	ENST00000268489	NM_006885.3	2186	caG/caT	9/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.24404690936315	2		728	860	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984568	72984568	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	206	698	0	ENST00000268489.5:c.3016G>T	p.Asp1006Tyr	p.D1006Y	ENST00000268489	NM_006885.3	1006	Gac/Tac	3/10	1	2	FACETS	0.851	0.789	0.915	1	0.992	1	CLONAL	2	FALSE	1	0.24404690936315	2		698	992	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349727	89349727	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs750471983	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	183	795	0	ENST00000301030.4:c.3223G>T	p.Glu1075Ter	p.E1075*	ENST00000301030	NM_001256183.1	1075	Gaa/Taa	9/13	1	2	FACETS	0.881	0.814	0.951	1	0.992	1	CLONAL	2	FALSE	1	0.24404690936315	2		795	851	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351257	89351257	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	211	728	0	ENST00000301030.4:c.1693T>G	p.Leu565Val	p.L565V	ENST00000301030	NM_001256183.1	565	Tta/Gta	9/13	1	2	FACETS	0.909	0.845	0.976	1	0.993	1	CLONAL	2	FALSE	1	0.24404690936315	2		728	951	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805305	89805305	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	165	557	1	ENST00000389301.3:c.4245C>A	p.Phe1415Leu	p.F1415L	ENST00000389301	NM_000135.2	1415	ttC/ttA	42/43	1	2	FACETS	0.938	0.863	1	1	0.992	1	CLONAL	2	FALSE	1	0.24404690936315	2		558	721	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950343	15950343	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	129	675	0	ENST00000268712.3:c.6601A>G	p.Thr2201Ala	p.T2201A	ENST00000268712	NM_006311.3	2201	Aca/Gca	42/46	1	2	FACETS	0.915	0.832	1	1	0.989	1	CLONAL	2	FALSE	1	0.24404690936315	2		675	578	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042336	16042336	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	41	472	0	ENST00000268712.3:c.1338G>T	p.Glu446Asp	p.E446D	ENST00000268712	NM_006311.3	446	gaG/gaT	12/46	1	2	FACETS	0.808	0.68	0.947	1	0.962	1	CLONAL	2	FALSE	1	0.24404690936315	2		472	208	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496955	29496955	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	64	458	0	ENST00000356175.3:c.526G>T	p.Asp176Tyr	p.D176Y	ENST00000356175	NM_000267.3	176	Gat/Tat	5/57	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.24404690936315	2		458	362	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687088	37687088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs543570439	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	139	446	1	ENST00000447079.4:c.3992G>A	p.Arg1331Gln	p.R1331Q	ENST00000447079	NM_015083.1	1331	cGa/cAa	14/14	1	2	FACETS	0.962	0.879	1	1	0.99	1	CLONAL	2	FALSE	1	0.24404690936315	2		447	592	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884100	37884100	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167419546	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	167	642	1	ENST00000269571.5:c.3571G>A	p.Val1191Met	p.V1191M	ENST00000269571		1191	Gtg/Atg	27/27	1	2	FACETS	0.808	0.743	0.876	1	0.99	1	CLONAL	2	FALSE	1	0.24404690936315	2		643	847	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459482	40459482	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	151	517	1	ENST00000345506.4:c.1743G>T	p.Leu581Phe	p.L581F	ENST00000345506	NM_003152.3	581	ttG/ttT	15/20	1	2	FACETS	0.958	0.879	1	1	0.991	1	CLONAL	2	FALSE	1	0.24404690936315	2		518	646	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40462559	40462559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780160492	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	154	616	0	ENST00000345506.4:c.2257G>A	p.Asp753Asn	p.D753N	ENST00000345506	NM_003152.3	753	Gac/Aac	20/20	1	2	FACETS	0.893	0.819	0.969	1	0.991	1	CLONAL	2	FALSE	1	0.24404690936315	2		616	707	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40864380	40864380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	107	676	0	ENST00000428826.2:c.1328G>A	p.Arg443Gln	p.R443Q	ENST00000428826		443	cGa/cAa	12/21	1	2	FACETS	0.853	0.764	0.948	0.853	0.764	0.948	CLONAL	1	FALSE	1	0.24404690936315	2		676	1028	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40880887	40880887	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	165	679	2	ENST00000428826.2:c.73C>T	p.Arg25Ter	p.R25*	ENST00000428826		25	Cga/Tga	3/21	1	2	FACETS	1	0.932	1	1	0.992	1	CLONAL	2	FALSE	1	0.24404690936315	2		681	668	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245728	41245728	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	90	752	0	ENST00000357654.3:c.1820A>C	p.Lys607Thr	p.K607T	ENST00000357654	NM_007294.3	607	aAa/aCa	10/23	1	2	FACETS	0.868	0.774	0.966	1	0.984	1	CLONAL	2	FALSE	1	0.24404690936315	2		752	425	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760661	59760661	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	71	519	0	ENST00000259008.2:c.3746A>C	p.Lys1249Thr	p.K1249T	ENST00000259008	NM_032043.2	1249	aAg/aCg	20/20	1	2	FACETS	0.912	0.803	1	1	0.981	1	CLONAL	2	FALSE	1	0.24404690936315	2		519	319	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760937	59760937	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	98	682	0	ENST00000259008.2:c.3470G>T	p.Arg1157Ile	p.R1157I	ENST00000259008	NM_032043.2	1157	aGa/aTa	20/20	1	2	FACETS	0.838	0.751	0.93	1	0.984	1	CLONAL	2	FALSE	1	0.24404690936315	2		682	479	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761390	59761390	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	100	513	0	ENST00000259008.2:c.3017A>C	p.Asn1006Thr	p.N1006T	ENST00000259008	NM_032043.2	1006	aAt/aCt	20/20	1	2	FACETS	1	0.958	1	1	0.989	1	CLONAL	2	FALSE	1	0.24404690936315	2		513	367	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59820423	59820423	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747568830	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	93	544	0	ENST00000259008.2:c.2330G>A	p.Arg777His	p.R777H	ENST00000259008	NM_032043.2	777	cGt/cAt	16/20	1	2	FACETS	0.972	0.871	1	1	0.986	1	CLONAL	2	FALSE	1	0.24404690936315	2		544	392	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371710	45371710	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	61	477	0	ENST00000262160.6:c.1280+1G>A		p.X427_splice	ENST00000262160	NM_005901.5	427			1	2	FACETS	0.82	0.712	0.934	1	0.975	1	CLONAL	2	FALSE	1	0.24404690936315	2		477	305	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573507	48573507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	40	357	0	ENST00000342988.3:c.91G>A	p.Glu31Lys	p.E31K	ENST00000342988	NM_005359.5	31	Gag/Aag	2/12	1	2	FACETS	0.796	0.668	0.935	1	0.961	1	CLONAL	2	FALSE	1	0.24404690936315	2		357	206	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985593	60985593	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1259350145	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	64	238	0	ENST00000333681.4:c.307G>T	p.Asp103Tyr	p.D103Y	ENST00000333681		103	Gac/Tac	2/3	1	2	FACETS	1	0.92	1	1	0.982	1	CLONAL	2	FALSE	1	0.24404690936315	2		238	246	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117083	7117083	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	200	508	2	ENST00000302850.5:c.4133G>T	p.Arg1378Leu	p.R1378L	ENST00000302850	NM_000208.2	1378	cGg/cTg	22/22	NA	4	FACETS	1	0.979	1	1	0.979	1	INDETERMINATE	2	FALSE	2	0.24404690936315	4		510	888	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142908	7142908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471585411	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	181	597	0	ENST00000302850.5:c.2461G>A	p.Glu821Lys	p.E821K	ENST00000302850	NM_000208.2	821	Gag/Aag	12/22	NA	4	FACETS	1	0.967	1	1	0.967	1	INDETERMINATE	2	FALSE	2	0.24404690936315	4		597	849	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254578	10254578	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	155	553	0	ENST00000340748.4:c.2932G>A	p.Asp978Asn	p.D978N	ENST00000340748		978	Gac/Aac	28/40	NA	4	FACETS	1	0.968	1	1	0.968	1	INDETERMINATE	2	FALSE	2	0.24404690936315	4		553	712	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270389	10270389	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	203	662	0	ENST00000340748.4:c.1177G>A	p.Glu393Lys	p.E393K	ENST00000340748		393	Gag/Aag	16/40	NA	4	FACETS	1	0.984	1	1	0.984	1	INDETERMINATE	2	FALSE	2	0.24404690936315	4		662	863	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101967	11101967	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779161503	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	89	589	0	ENST00000358026.2:c.1387G>A	p.Glu463Lys	p.E463K	ENST00000358026	NM_001128849.1	463	Gag/Aag	8/36	NA	4	FACETS	1	0.94	1	0.549	0.486	0.616	INDETERMINATE	1	FALSE	2	0.24404690936315	4		589	827	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627443	14627443	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	131	605	1	ENST00000254322.2:c.627G>T	p.Lys209Asn	p.K209N	ENST00000254322	NM_006145.1	209	aaG/aaT	2/3	NA	4	FACETS	1	0.958	1	1	0.958	1	INDETERMINATE	2	FALSE	2	0.24404690936315	4		606	614	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271691	15271691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	161	765	1	ENST00000263388.2:c.6748G>A	p.Glu2250Lys	p.E2250K	ENST00000263388	NM_000435.2	2250	Gaa/Aaa	33/33	NA	4	FACETS	1	0.923	1	1	0.923	1	INDETERMINATE	2	FALSE	2	0.24404690936315	4		766	816	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285027	15285027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777398556	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	200	603	0	ENST00000263388.2:c.4588G>A	p.Asp1530Asn	p.D1530N	ENST00000263388	NM_000435.2	1530	Gac/Aac	25/33	NA	4	FACETS	1	0.982	1	1	0.982	1	INDETERMINATE	2	FALSE	2	0.24404690936315	4		603	866	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271295	18271295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754343201	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	200	623	0	ENST00000222254.8:c.337G>A	p.Asp113Asn	p.D113N	ENST00000222254	NM_005027.3	113	Gac/Aac	3/16	NA	4	FACETS	1	0.978	1	1	0.978	1	INDETERMINATE	2	FALSE	2	0.24404690936315	4		623	898	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18963087	18963087	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	183	622	0	ENST00000262803.5:c.954G>T	p.Lys318Asn	p.K318N	ENST00000262803	NM_002911.3	318	aaG/aaT	6/24	NA	4	FACETS	1	0.981	1	1	0.981	1	INDETERMINATE	2	FALSE	2	0.24404690936315	4		622	784	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218098	36218098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	107	415	0	ENST00000222270.7:c.4045G>A	p.Asp1349Asn	p.D1349N	ENST00000222270	NM_014727.1	1349	Gac/Aac	15/37	NA	4	FACETS	1	0.916	1	1	0.916	1	INDETERMINATE	2	FALSE	2	0.24404690936315	4		415	535	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228581	36228581	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	210	661	0	ENST00000222270.7:c.7595G>T	p.Arg2532Leu	p.R2532L	ENST00000222270	NM_014727.1	2532	cGg/cTg	34/37	NA	4	FACETS	1	0.979	1	1	0.979	1	INDETERMINATE	2	FALSE	2	0.24404690936315	4		661	942	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229393	36229393	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	150	562	0	ENST00000222270.7:c.8083G>A	p.Glu2695Lys	p.E2695K	ENST00000222270	NM_014727.1	2695	Gag/Aag	37/37	NA	4	FACETS	1	0.966	1	1	0.966	1	INDETERMINATE	2	FALSE	2	0.24404690936315	4		562	693	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42384736	42384736	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	104	342	0	ENST00000221972.3:c.499-1G>T		p.X167_splice	ENST00000221972	NM_021601.3	167			NA	4	FACETS	1	0.949	1	1	0.949	1	INDETERMINATE	2	FALSE	2	0.24404690936315	4		342	487	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868392	45868392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	70	668	1	ENST00000391945.4:c.385G>A	p.Asp129Asn	p.D129N	ENST00000391945	NM_000400.3	129	Gac/Aac	6/23	NA	4	FACETS	0.83	0.722	0.947	0.415	0.361	0.474	INDETERMINATE	1	FALSE	2	0.24404690936315	4		669	860	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082955	16082955	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	88	329	0	ENST00000281043.3:c.769G>T	p.Glu257Ter	p.E257*	ENST00000281043	NM_005378.4	257	Gag/Tag	2/3	1	2	FACETS	0.831	0.74	0.927	1	0.982	1	CLONAL	2	FALSE	1	0.24404690936315	2		329	434	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222500	39222500	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	53	638	0	ENST00000402219.2:c.3110C>A	p.Ser1037Tyr	p.S1037Y	ENST00000402219	NM_005633.3	1037	tCt/tAt	20/23	1	2	FACETS	0.714	0.609	0.83	0.714	0.609	0.83	SUBCLONAL	1	FALSE	1	0.24404690936315	2		638	608	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281838	39281838	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	58	572	0	ENST00000402219.2:c.637C>T	p.Arg213Ter	p.R213*	ENST00000402219	NM_005633.3	213	Cga/Tga	5/23	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.24404690936315	2		572	364	SUCCESS
REL	5966	MSKCC	GRCh37	2	61121626	61121626	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	22	410	0	ENST00000295025.8:c.248A>G	p.Asp83Gly	p.D83G	ENST00000295025	NM_002908.2	83	gAc/gGc	3/11	1	2	FACETS	0.567	0.439	0.715	0.567	0.439	0.715	SUBCLONAL	1	FALSE	1	0.24404690936315	2		410	318	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61722723	61722723	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1198868283	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	83	478	0	ENST00000401558.2:c.914G>A	p.Arg305Gln	p.R305Q	ENST00000401558	NM_003400.3	305	cGa/cAa	11/25	1	2	FACETS	0.8	0.71	0.896	1	0.98	1	SUBCLONAL	2	FALSE	1	0.24404690936315	2		478	425	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095749	178095749	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	76	550	0	ENST00000397062.3:c.1582G>T	p.Asp528Tyr	p.D528Y	ENST00000397062	NM_006164.4	528	Gat/Tat	5/5	1	2	FACETS	0.89	0.786	1	1	0.982	1	CLONAL	2	FALSE	1	0.24404690936315	2		550	350	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190656569	190656569	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs374261058	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	51	271	0	ENST00000441310.2:c.34C>A	p.Leu12Ile	p.L12I	ENST00000441310	NM_000534.4	12	Ctt/Att	2/13	1	2	FACETS	0.849	0.729	0.979	1	0.971	1	CLONAL	2	FALSE	1	0.24404690936315	2		271	246	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190656579	190656579	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	24	280	0	ENST00000441310.2:c.44C>A	p.Ser15Tyr	p.S15Y	ENST00000441310	NM_000534.4	15	tCt/tAt	2/13	1	2	FACETS	0.78	0.614	0.972	0.78	0.614	0.972	CLONAL	1	FALSE	1	0.24404690936315	2		280	252	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682764	190682764	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	41	350	0	ENST00000441310.2:c.440G>T	p.Arg147Ile	p.R147I	ENST00000441310	NM_000534.4	147	aGa/aTa	5/13	1	2	FACETS	0.824	0.693	0.965	1	0.963	1	CLONAL	2	FALSE	1	0.24404690936315	2		350	204	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728717	190728717	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	31	354	0	ENST00000441310.2:c.2105C>A	p.Ser702Tyr	p.S702Y	ENST00000441310	NM_000534.4	702	tCt/tAt	10/13	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	1	0.24404690936315	2		354	177	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204737531	204737531	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1444367175	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	38	278	0	ENST00000302823.3:c.668A>G	p.Asn223Ser	p.N223S	ENST00000302823	NM_005214.4	223	aAt/aGt	4/4	1	2	FACETS	0.979	0.822	1	1	0.968	1	CLONAL	2	FALSE	1	0.24404690936315	2		278	159	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657105	215657105	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	69	558	0	ENST00000260947.4:c.280G>T	p.Asp94Tyr	p.D94Y	ENST00000260947	NM_000465.2	94	Gac/Tac	3/11	1	2	FACETS	0.775	0.679	0.877	1	0.975	1	SUBCLONAL	2	FALSE	1	0.24404690936315	2		558	365	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439527	220439527	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	68	616	1	ENST00000243786.2:c.380C>A	p.Thr127Asn	p.T127N	ENST00000243786	NM_002191.3	127	aCt/aAt	2/2	1	2	FACETS	0.73	0.634	0.834	0.73	0.634	0.834	SUBCLONAL	1	FALSE	1	0.24404690936315	2		617	763	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660093	227660093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143913301	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	138	517	1	ENST00000305123.5:c.3362C>T	p.Ala1121Val	p.A1121V	ENST00000305123	NM_005544.2	1121	gCg/gTg	1/2	1	2	FACETS	0.911	0.831	0.993	1	0.99	1	CLONAL	2	FALSE	1	0.24404690936315	2		518	621	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739013	40739013	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	135	437	0	ENST00000373198.4:c.3271C>A	p.Leu1091Ile	p.L1091I	ENST00000373198	NM_133170.3	1091	Ctc/Atc	24/32	1	2	FACETS	0.836	0.761	0.913	1	0.988	1	CLONAL	2	FALSE	1	0.24404690936315	2		437	662	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265474	46265474	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	34	237	0	ENST00000371998.3:c.2344G>T	p.Asp782Tyr	p.D782Y	ENST00000371998		782	Gac/Tac	12/23	1	2	FACETS	0.778	0.643	0.927	1	0.952	1	CLONAL	2	FALSE	1	0.24404690936315	2		237	179	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54956596	54956596	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	17	483	0	ENST00000312783.6:c.598T>G	p.Phe200Val	p.F200V	ENST00000312783	NM_198436.1	200	Ttc/Gtc	7/10	1	2	FACETS	0.461	0.344	0.601	0.461	0.344	0.601	SUBCLONAL	1	FALSE	1	0.24404690936315	2		483	302	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321707	62321707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746677388	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	135	549	0	ENST00000360203.5:c.2326G>A	p.Glu776Lys	p.E776K	ENST00000360203	NM_001283009.1	776	Gag/Aag	26/35	1	2	FACETS	0.778	0.708	0.851	1	0.987	1	SUBCLONAL	2	FALSE	1	0.24404690936315	2		549	711	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513345	44513345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	137	566	0	ENST00000291552.4:c.590C>T	p.Ser197Phe	p.S197F	ENST00000291552	NM_006758.2	197	tCc/tTc	8/8	NA	4	FACETS	0.86	0.783	0.941	0.86	0.783	0.941	INDETERMINATE	2	FALSE	2	0.24404690936315	4		566	812	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514895	44514895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	99	359	0	ENST00000291552.4:c.352C>T	p.Arg118Cys	p.R118C	ENST00000291552	NM_006758.2	118	Cgc/Tgc	6/8	NA	4	FACETS	1	0.951	1	1	0.951	1	INDETERMINATE	2	FALSE	2	0.24404690936315	4		359	458	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22143007	22143007	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	58	466	0	ENST00000215832.6:c.700C>A	p.Leu234Ile	p.L234I	ENST00000215832	NM_002745.4	234	Ctt/Att	5/9	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	FALSE	1	0.24404690936315	2		466	414	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143243	24143243	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	65	683	0	ENST00000263121.7:c.475G>T	p.Asp159Tyr	p.D159Y	ENST00000263121	NM_003073.3	159	Gac/Tac	4/9	1	2	FACETS	0.524	0.453	0.602	0.524	0.453	0.602	SUBCLONAL	1	FALSE	1	0.24404690936315	2		683	1016	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29099528	29099528	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	70	342	0	ENST00000328354.6:c.873T>G	p.Phe291Leu	p.F291L	ENST00000328354	NM_007194.3	291	ttT/ttG	8/15	1	2	FACETS	0.851	0.747	0.961	1	0.979	1	CLONAL	2	FALSE	1	0.24404690936315	2		342	337	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434126	12434126	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	51	409	0	ENST00000287820.6:c.494G>T	p.Arg165Ile	p.R165I	ENST00000287820	NM_015869.4	165	aGa/aTa	4/7	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.24404690936315	2		409	311	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52685784	52685784	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	29	593	0	ENST00000394830.3:c.688C>A	p.Leu230Ile	p.L230I	ENST00000394830	NM_018313.4	230	Ctc/Atc	7/30	1	2	FACETS	0.681	0.547	0.833	0.681	0.547	0.833	SUBCLONAL	1	FALSE	1	0.24404690936315	2		593	349	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987063	69987063	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	182	500	0	ENST00000394351.3:c.124A>G	p.Asn42Asp	p.N42D	ENST00000394351	NM_000248.3	42	Aat/Gat	2/9	1	2	FACETS	1	0.952	1	1	0.993	1	CLONAL	2	FALSE	1	0.24404690936315	2		500	718	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73112849	73112849	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	76	362	1	ENST00000356692.5:c.445C>T	p.Arg149Ter	p.R149*	ENST00000356692		149	Cga/Tga	6/9	1	2	FACETS	1	0.92	1	1	0.984	1	CLONAL	2	FALSE	1	0.24404690936315	2		363	297	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977855	134977855	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	65	408	0	ENST00000398015.3:c.2848G>T	p.Asp950Tyr	p.D950Y	ENST00000398015	NM_004441.4	950	Gac/Tac	16/16	1	2	FACETS	0.774	0.675	0.88	1	0.974	1	SUBCLONAL	2	FALSE	1	0.24404690936315	2		408	344	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279297	142279297	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	21	413	0	ENST00000350721.4:c.1350-1G>T		p.X450_splice	ENST00000350721	NM_001184.3	450			1	2	FACETS	0.816	0.631	1	0.816	0.631	1	CLONAL	1	FALSE	1	0.24404690936315	2		413	211	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281633	142281633	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	56	559	0	ENST00000350721.4:c.611T>G	p.Phe204Cys	p.F204C	ENST00000350721	NM_001184.3	204	tTt/tGt	4/47	1	2	FACETS	0.797	0.688	0.914	1	0.971	1	CLONAL	2	FALSE	1	0.24404690936315	2		559	288	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431050	181431050	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	162	553	0	ENST00000325404.1:c.902G>C	p.Gly301Ala	p.G301A	ENST00000325404	NM_003106.3	301	gGc/gCc	1/1	1	2	FACETS	0.855	0.786	0.928	1	0.991	1	CLONAL	2	FALSE	1	0.24404690936315	2		553	776	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451361	187451361	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	103	361	0	ENST00000232014.4:c.121G>T	p.Glu41Ter	p.E41*	ENST00000232014	NM_001130845.1	41	Gag/Tag	3/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.24404690936315	2		361	585	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957783	1957783	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	195	673	0	ENST00000382891.5:c.2749G>T	p.Glu917Ter	p.E917*	ENST00000382891	NM_133335.3	917	Gaa/Taa	15/22	1	2	FACETS	1	0.939	1	1	0.993	1	CLONAL	2	FALSE	1	0.24404690936315	2		673	788	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133484	55133484	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	96	470	0	ENST00000257290.5:c.788A>C	p.Glu263Ala	p.E263A	ENST00000257290	NM_006206.4	263	gAa/gCa	6/23	1	2	FACETS	0.818	0.732	0.909	1	0.984	1	CLONAL	2	FALSE	1	0.24404690936315	2		470	481	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956198	55956198	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	113	577	1	ENST00000263923.4:c.3117G>T	p.Lys1039Asn	p.K1039N	ENST00000263923	NM_002253.2	1039	aaG/aaT	23/30	1	2	FACETS	0.781	0.705	0.861	1	0.985	1	SUBCLONAL	2	FALSE	1	0.24404690936315	2		578	593	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55987310	55987310	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	25	612	0	ENST00000263923.4:c.115G>T	p.Asp39Tyr	p.D39Y	ENST00000263923	NM_002253.2	39	Gac/Tac	2/30	1	2	FACETS	0.482	0.379	0.601	0.482	0.379	0.601	SUBCLONAL	1	FALSE	1	0.24404690936315	2		612	425	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218764	66218764	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	51	280	0	ENST00000273854.3:c.2294del	p.Leu765Ter	p.L765*	ENST00000273854	NM_004439.5	765	tTg/tg	13/18	1	2	FACETS	1	0.921	1	1	0.978	1	CLONAL	2	FALSE	1	0.24404690936315	2		280	190	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286238	66286238	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1229443873	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	95	488	0	ENST00000273854.3:c.1448A>G	p.Asn483Ser	p.N483S	ENST00000273854	NM_004439.5	483	aAc/aGc	6/18	1	2	FACETS	1	0.952	1	1	0.988	1	CLONAL	2	FALSE	1	0.24404690936315	2		488	353	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66468010	66468010	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	19	377	0	ENST00000273854.3:c.259G>T	p.Gly87Cys	p.G87C	ENST00000273854	NM_004439.5	87	Ggt/Tgt	3/18	1	2	FACETS	0.745	0.567	0.952	0.745	0.567	0.952	CLONAL	1	FALSE	1	0.24404690936315	2		377	209	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157251	106157251	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	98	464	0	ENST00000380013.4:c.2152C>A	p.Leu718Ile	p.L718I	ENST00000380013	NM_001127208.2	718	Ctt/Att	3/11	1	2	FACETS	0.927	0.832	1	1	0.986	1	CLONAL	2	FALSE	1	0.24404690936315	2		464	433	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142950066	142950066	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	55	454	0	ENST00000262992.4:c.2644G>T	p.Glu882Ter	p.E882*	ENST00000262992	NM_001101669.1	882	Gaa/Taa	24/24	1	2	FACETS	0.88	0.76	1	1	0.975	1	CLONAL	2	FALSE	1	0.24404690936315	2		454	256	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516946	187516946	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	40	518	0	ENST00000441802.2:c.13035G>T	p.Lys4345Asn	p.K4345N	ENST00000441802	NM_005245.3	4345	aaG/aaT	26/27	1	2	FACETS	0.498	0.413	0.594	0.498	0.413	0.594	SUBCLONAL	1	FALSE	1	0.24404690936315	2		518	658	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521211	187521211	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	128	688	0	ENST00000441802.2:c.11944T>G	p.Leu3982Val	p.L3982V	ENST00000441802	NM_005245.3	3982	Ttg/Gtg	22/27	1	2	FACETS	0.806	0.732	0.883	1	0.987	1	CLONAL	2	FALSE	1	0.24404690936315	2		688	651	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629031	187629031	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	117	672	0	ENST00000441802.2:c.1951G>T	p.Glu651Ter	p.E651*	ENST00000441802	NM_005245.3	651	Gaa/Taa	2/27	1	2	FACETS	0.908	0.822	0.998	1	0.988	1	CLONAL	2	FALSE	1	0.24404690936315	2		672	528	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260639	1260639	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	178	587	0	ENST00000310581.5:c.2920C>T	p.Leu974Phe	p.L974F	ENST00000310581	NM_198253.2	974	Ctc/Ttc	12/16	1	2	FACETS	0.831	0.766	0.898	1	0.991	1	CLONAL	2	FALSE	1	0.24404690936315	2		587	878	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515145	31515145	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1202201920	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	198	790	1	ENST00000344624.3:c.1240C>T	p.Arg414Ter	p.R414*	ENST00000344624		414	Cga/Tga	5/33	1	2	FACETS	0.991	0.919	1	1	0.993	1	CLONAL	2	FALSE	1	0.24404690936315	2		791	819	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38968131	38968131	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs143280630	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	37	306	0	ENST00000357387.3:c.974G>A	p.Arg325Gln	p.R325Q	ENST00000357387	NM_152756.3	325	cGa/cAa	12/38	1	2	FACETS	0.806	0.672	0.953	1	0.958	1	CLONAL	2	FALSE	1	0.24404690936315	2		306	188	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38991143	38991143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	83	545	0	ENST00000357387.3:c.491C>T	p.Ser164Phe	p.S164F	ENST00000357387	NM_152756.3	164	tCt/tTt	7/38	1	2	FACETS	0.95	0.845	1	1	0.984	1	CLONAL	2	FALSE	1	0.24404690936315	2		545	358	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178670	56178670	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	52	286	0	ENST00000399503.3:c.3643G>T	p.Asp1215Tyr	p.D1215Y	ENST00000399503	NM_005921.1	1215	Gat/Tat	14/20	1	2	FACETS	0.823	0.707	0.948	1	0.971	1	CLONAL	2	FALSE	1	0.24404690936315	2		286	259	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752417	57752417	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	39	334	0	ENST00000274289.3:c.1157-1G>T		p.X386_splice	ENST00000274289	NM_006622.3	386			1	2	FACETS	0.811	0.68	0.954	1	0.961	1	CLONAL	2	FALSE	1	0.24404690936315	2		334	197	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522657	67522657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	68	358	0	ENST00000274335.5:c.154G>T	p.Glu52Ter	p.E52*	ENST00000274335		52	Gaa/Taa	1/15	1	2	FACETS	0.839	0.735	0.95	1	0.978	1	CLONAL	2	FALSE	1	0.24404690936315	2		358	332	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79966120	79966120	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	16	497	0	ENST00000265081.6:c.784G>T	p.Asp262Tyr	p.D262Y	ENST00000265081	NM_002439.4	262	Gat/Tat	4/24	1	2	FACETS	0.427	0.315	0.561	0.427	0.315	0.561	SUBCLONAL	1	FALSE	1	0.24404690936315	2		497	307	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064770	80064770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1261908217	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	62	472	1	ENST00000265081.6:c.2201G>A	p.Arg734Gln	p.R734Q	ENST00000265081	NM_002439.4	734	cGa/cAa	15/24	1	2	FACETS	0.981	0.856	1	1	0.98	1	CLONAL	2	FALSE	1	0.24404690936315	2		473	259	SUCCESS
APC	324	MSKCC	GRCh37	5	112173284	112173284	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	14	243	0	ENST00000257430.4:c.1993T>G	p.Leu665Val	p.L665V	ENST00000257430	NM_000038.5	665	Tta/Gta	16/16	1	2	FACETS	0.708	0.514	0.941	0.708	0.514	0.941	CLONAL	1	FALSE	1	0.24404690936315	2		243	162	SUCCESS
APC	324	MSKCC	GRCh37	5	112174926	112174926	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	19	322	1	ENST00000257430.4:c.3635C>A	p.Ser1212Tyr	p.S1212Y	ENST00000257430	NM_000038.5	1212	tCt/tAt	16/16	1	2	FACETS	0.692	0.527	0.885	0.692	0.527	0.885	SUBCLONAL	1	FALSE	1	0.24404690936315	2		323	225	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911583	131911583	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	28	418	0	ENST00000265335.6:c.328G>T	p.Glu110Ter	p.E110*	ENST00000265335		110	Gaa/Taa	3/25	1	2	FACETS	0.773	0.619	0.947	0.773	0.619	0.947	CLONAL	1	FALSE	1	0.24404690936315	2		418	297	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460452	149460452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	194	705	0	ENST00000286301.3:c.185C>T	p.Ser62Phe	p.S62F	ENST00000286301	NM_005211.3	62	tCt/tTt	3/22	1	2	FACETS	1	0.945	1	1	0.993	1	CLONAL	2	FALSE	1	0.24404690936315	2		705	778	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170832364	170832364	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	42	242	0	ENST00000296930.5:c.728C>A	p.Ser243Tyr	p.S243Y	ENST00000296930	NM_002520.6	243	tCt/tAt	9/11	1	2	FACETS	1	0.871	1	1	0.972	1	CLONAL	2	FALSE	1	0.24404690936315	2		242	167	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180040063	180040063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	164	604	1	ENST00000261937.6:c.3379C>T	p.Arg1127Trp	p.R1127W	ENST00000261937	NM_182925.4	1127	Cgg/Tgg	25/30	1	2	FACETS	0.888	0.816	0.962	1	0.991	1	CLONAL	2	FALSE	1	0.24404690936315	2		605	757	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043477	180043477	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	172	609	0	ENST00000261937.6:c.3109G>T	p.Asp1037Tyr	p.D1037Y	ENST00000261937	NM_182925.4	1037	Gac/Tac	23/30	1	2	FACETS	0.975	0.899	1	1	0.992	1	CLONAL	2	FALSE	1	0.24404690936315	2		609	723	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057000	180057000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762995809	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	181	741	0	ENST00000261937.6:c.619G>A	p.Glu207Lys	p.E207K	ENST00000261937	NM_182925.4	207	Gag/Aag	5/30	1	2	FACETS	0.873	0.806	0.942	1	0.992	1	CLONAL	2	FALSE	1	0.24404690936315	2		741	850	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911137	29911137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	59	419	0	ENST00000376809.5:c.436G>A	p.Asp146Asn	p.D146N	ENST00000376809	NM_002116.7	146	Gat/Aat	3/8	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	FALSE	1	0.24404690936315	2		419	447	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675739	30675739	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	179	898	0	ENST00000376406.3:c.2617G>T	p.Glu873Ter	p.E873*	ENST00000376406	NM_014641.2	873	Gaa/Taa	8/15	1	2	FACETS	0.766	0.706	0.829	1	0.99	1	SUBCLONAL	2	FALSE	1	0.24404690936315	2		898	957	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288561	33288561	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1373347535	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	121	469	1	ENST00000374542.5:c.991G>A	p.Asp331Asn	p.D331N	ENST00000374542	NM_001141970.1	331	Gat/Aat	3/8	1	2	FACETS	0.772	0.699	0.849	1	0.986	1	SUBCLONAL	2	FALSE	1	0.24404690936315	2		470	642	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120673	94120673	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	97	477	0	ENST00000369303.4:c.378C>A	p.Tyr126Ter	p.Y126*	ENST00000369303	NM_004440.3	126	taC/taA	3/17	1	2	FACETS	1	0.946	1	1	0.988	1	CLONAL	2	FALSE	1	0.24404690936315	2		477	368	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041049	112041049	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	150	464	0	ENST00000368678.4:c.206C>A	p.Ser69Tyr	p.S69Y	ENST00000368678		69	tCt/tAt	3/13	1	2	FACETS	0.84	0.769	0.914	1	0.99	1	CLONAL	2	FALSE	1	0.24404690936315	2		464	732	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710660	117710660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	78	394	0	ENST00000368508.3:c.1612G>A	p.Glu538Lys	p.E538K	ENST00000368508	NM_002944.2	538	Gaa/Aaa	12/43	1	2	FACETS	0.809	0.715	0.909	1	0.98	1	CLONAL	2	FALSE	1	0.24404690936315	2		394	395	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199684	138199684	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs754444866	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	129	497	0	ENST00000237289.4:c.1102C>G	p.His368Asp	p.H368D	ENST00000237289	NM_001270507.1	368	Cac/Gac	7/9	1	2	FACETS	0.784	0.712	0.86	1	0.987	1	SUBCLONAL	2	FALSE	1	0.24404690936315	2		497	674	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444392	50444392	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	124	424	0	ENST00000331340.3:c.322G>A	p.Gly108Arg	p.G108R	ENST00000331340	NM_006060.4	108	Gga/Aga	4/8	1	2	FACETS	0.863	0.783	0.946	1	0.988	1	CLONAL	2	FALSE	1	0.24404690936315	2		424	589	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224493	55224493	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	87	529	0	ENST00000275493.2:c.1175T>G	p.Leu392Arg	p.L392R	ENST00000275493	NM_005228.3	392	cTg/cGg	10/28	1	2	FACETS	0.816	0.726	0.911	1	0.982	1	CLONAL	2	FALSE	1	0.24404690936315	2		529	437	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55269044	55269044	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs765496858	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	214	653	0	ENST00000275493.2:c.3110C>A	p.Ser1037Tyr	p.S1037Y	ENST00000275493	NM_005228.3	1037	tCt/tAt	25/28	1	2	FACETS	1	0.955	1	1	0.994	1	CLONAL	2	FALSE	1	0.24404690936315	2		653	848	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513046	106513046	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	43	382	0	ENST00000359195.3:c.2060G>T	p.Arg687Ile	p.R687I	ENST00000359195	NM_002649.2	687	aGa/aTa	3/11	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	1	0.24404690936315	2		382	277	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340036	116340036	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	14	394	0	ENST00000397752.3:c.898C>A	p.Leu300Ile	p.L300I	ENST00000397752	NM_000245.2	300	Ctc/Atc	2/21	1	2	FACETS	0.519	0.375	0.693	0.519	0.375	0.693	SUBCLONAL	1	FALSE	1	0.24404690936315	2		394	221	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340213	116340213	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs753762177	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	68	346	0	ENST00000397752.3:c.1075C>T	p.Arg359Ter	p.R359*	ENST00000397752	NM_000245.2	359	Cga/Tga	2/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.24404690936315	2		346	374	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879198	151879198	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	131	579	0	ENST00000262189.6:c.5747G>T	p.Arg1916Ile	p.R1916I	ENST00000262189	NM_170606.2	1916	aGa/aTa	36/59	1	2	FACETS	0.911	0.83	0.996	1	0.989	1	CLONAL	2	FALSE	1	0.24404690936315	2		579	589	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884431	151884431	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	72	427	0	ENST00000262189.6:c.4924G>T	p.Glu1642Ter	p.E1642*	ENST00000262189	NM_170606.2	1642	Gag/Tag	33/59	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.24404690936315	2		427	465	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884454	151884454	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	36	439	0	ENST00000262189.6:c.4901G>T	p.Arg1634Ile	p.R1634I	ENST00000262189	NM_170606.2	1634	aGa/aTa	33/59	1	2	FACETS	0.621	0.51	0.746	0.621	0.51	0.746	SUBCLONAL	1	FALSE	1	0.24404690936315	2		439	475	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132814	152132815	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	32	388	0	ENST00000262189.6:c.57dup	p.Glu20ArgfsTer39	p.E20Rfs*39	ENST00000262189	NM_170606.2	19	-/C	1/59	1	2	FACETS	0.423	0.342	0.515	0.423	0.342	0.515	SUBCLONAL	1	FALSE	1	0.24404690936315	2		388	620	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205277	38205277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775297532	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	197	815	0	ENST00000317025.8:c.413C>T	p.Ser138Leu	p.S138L	ENST00000317025	NM_023034.1	138	tCg/tTg	2/24	1	2	FACETS	1	0.97	1	1	0.994	1	CLONAL	2	FALSE	1	0.24404690936315	2		815	747	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866459	56866459	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	173	635	0	ENST00000519728.1:c.706G>T	p.Asp236Tyr	p.D236Y	ENST00000519728	NM_002350.3	236	Gat/Tat	8/13	1	2	FACETS	0.825	0.76	0.893	1	0.991	1	CLONAL	2	FALSE	1	0.24404690936315	2		635	859	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922484	56922484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	106	451	0	ENST00000519728.1:c.1354G>A	p.Val452Met	p.V452M	ENST00000519728	NM_002350.3	452	Gtg/Atg	13/13	1	2	FACETS	0.797	0.717	0.881	1	0.984	1	SUBCLONAL	2	FALSE	1	0.24404690936315	2		451	545	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69012059	69012059	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	61	495	0	ENST00000288368.4:c.2696G>T	p.Arg899Ile	p.R899I	ENST00000288368	NM_024870.2	899	aGa/aTa	23/40	1	2	FACETS	0.767	0.666	0.875	1	0.972	1	SUBCLONAL	2	FALSE	1	0.24404690936315	2		495	326	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70971078	70971078	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	115	590	0	ENST00000276594.2:c.1184-1G>A		p.X395_splice	ENST00000276594	NM_024504.3	395			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.24404690936315	2		590	637	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993708	90993708	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	65	402	0	ENST00000265433.3:c.215C>A	p.Ser72Tyr	p.S72Y	ENST00000265433	NM_002485.4	72	tCt/tAt	3/16	1	2	FACETS	0.832	0.727	0.945	1	0.977	1	CLONAL	2	FALSE	1	0.24404690936315	2		402	320	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559274	141559274	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	181	631	1	ENST00000220592.5:c.1527G>T	p.Lys509Asn	p.K509N	ENST00000220592	NM_012154.3	509	aaG/aaT	12/19	1	2	FACETS	0.907	0.837	0.978	1	0.992	1	CLONAL	2	FALSE	1	0.24404690936315	2		632	818	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518048	8518048	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	131	584	2	ENST00000356435.5:c.1343T>G	p.Ile448Ser	p.I448S	ENST00000356435		448	aTc/aGc	10/35	1	2	FACETS	0.98	0.893	1	1	0.99	1	CLONAL	2	FALSE	1	0.24404690936315	2		586	548	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635202	87635202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1170229422	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	156	545	0	ENST00000277120.3:c.2254G>A	p.Val752Ile	p.V752I	ENST00000277120		752	Gtc/Atc	18/19	1	2	FACETS	0.83	0.761	0.902	1	0.99	1	CLONAL	2	FALSE	1	0.24404690936315	2		545	770	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786013	135786013	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs118203504	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	189	617	0	ENST00000298552.3:c.1208C>T	p.Ser403Leu	p.S403L	ENST00000298552	NM_001162426.1	403	tCg/tTg	12/23	1	2	FACETS	0.911	0.843	0.982	1	0.992	1	CLONAL	2	FALSE	1	0.24404690936315	2		617	850	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137325974	137325974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540374192	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	164	593	0	ENST00000481739.1:c.1162G>A	p.Glu388Lys	p.E388K	ENST00000481739	NM_002957.4	388	Gag/Aag	9/10	1	2	FACETS	0.874	0.804	0.947	1	0.991	1	CLONAL	2	FALSE	1	0.24404690936315	2		593	769	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402759	139402759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766361207	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	200	669	2	ENST00000277541.6:c.3250G>A	p.Glu1084Lys	p.E1084K	ENST00000277541	NM_017617.3	1084	Gag/Aag	20/34	1	2	FACETS	0.897	0.831	0.964	1	0.993	1	CLONAL	2	FALSE	1	0.24404690936315	2		671	914	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409778	139409778	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368996332	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	177	604	1	ENST00000277541.6:c.1978G>A	p.Asp660Asn	p.D660N	ENST00000277541	NM_017617.3	660	Gat/Aat	12/34	1	2	FACETS	0.82	0.756	0.887	1	0.991	1	CLONAL	2	FALSE	1	0.24404690936315	2		605	884	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814941	139814941	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	155	474	2	ENST00000247668.2:c.934G>T	p.Asp312Tyr	p.D312Y	ENST00000247668	NM_021138.3	312	Gac/Tac	8/11	1	2	FACETS	0.877	0.805	0.953	1	0.99	1	CLONAL	2	FALSE	1	0.24404690936315	2		476	724	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317485	1317485	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	53	726	0	ENST00000400841.2:c.580T>C	p.Tyr194His	p.Y194H	ENST00000400841		194	Tat/Cat	5/6	1	2	FACETS	0.512	0.435	0.596	0.512	0.435	0.596	SUBCLONAL	1	FALSE	1	0.24404690936315	2		726	849	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321378	1321378	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	121	477	0	ENST00000400841.2:c.377G>T	p.Arg126Ile	p.R126I	ENST00000400841		126	aGa/aTa	4/6	1	2	FACETS	0.822	0.745	0.903	1	0.987	1	CLONAL	2	FALSE	1	0.24404690936315	2		477	603	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325375	1325375	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762769201	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	141	552	0	ENST00000400841.2:c.300G>T	p.Arg100Ser	p.R100S	ENST00000400841		100	agG/agT	3/6	1	2	FACETS	0.877	0.801	0.956	1	0.99	1	CLONAL	2	FALSE	1	0.24404690936315	2		552	659	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932250	39932250	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	255	847	0	ENST00000378444.4:c.2349G>T	p.Lys783Asn	p.K783N	ENST00000378444	NM_001123385.1	783	aaG/aaT	4/15	1	2	FACETS	0.964	0.902	1	1	0.995	1	CLONAL	2	FALSE	1	0.24404690936315	2		847	1084	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932376	39932376	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	191	830	0	ENST00000378444.4:c.2223G>T	p.Glu741Asp	p.E741D	ENST00000378444	NM_001123385.1	741	gaG/gaT	4/15	1	2	FACETS	0.828	0.766	0.893	1	0.992	1	CLONAL	2	FALSE	1	0.24404690936315	2		830	945	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945216	44945216	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	65	508	0	ENST00000377967.4:c.3540C>A	p.Phe1180Leu	p.F1180L	ENST00000377967	NM_021140.2	1180	ttC/ttA	24/29	1	2	FACETS	0.772	0.673	0.877	1	0.974	1	SUBCLONAL	2	FALSE	1	0.24404690936315	2		508	345	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030456	47030456	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	77	669	0	ENST00000377604.3:c.231G>T	p.Glu77Asp	p.E77D	ENST00000377604	NM_001204468.1	77	gaG/gaT	4/24	1	2	FACETS	0.812	0.712	0.92	0.812	0.712	0.92	CLONAL	1	FALSE	1	0.24404690936315	2		669	777	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413051	63413051	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs199995488	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	194	822	0	ENST00000330258.3:c.116G>T	p.Gly39Val	p.G39V	ENST00000330258	NM_152424.3	39	gGa/gTa	2/2	1	2	FACETS	0.782	0.724	0.844	1	0.991	1	SUBCLONAL	2	FALSE	1	0.24404690936315	2		822	1016	SUCCESS
AR	367	MSKCC	GRCh37	X	66942696	66942696	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1314501209	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	82	501	0	ENST00000374690.3:c.2477A>T	p.Lys826Ile	p.K826I	ENST00000374690	NM_000044.3	826	aAa/aTa	7/8	1	2	FACETS	0.75	0.664	0.841	1	0.978	1	SUBCLONAL	2	FALSE	1	0.24404690936315	2		501	448	SUCCESS
AR	367	MSKCC	GRCh37	X	66942737	66942737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1419690127	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	109	533	0	ENST00000374690.3:c.2518G>A	p.Asp840Asn	p.D840N	ENST00000374690	NM_000044.3	840	Gat/Aat	7/8	1	2	FACETS	0.769	0.692	0.849	1	0.984	1	SUBCLONAL	2	FALSE	1	0.24404690936315	2		533	581	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339602	70339602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	34	614	0	ENST00000374080.3:c.271C>T	p.Arg91Cys	p.R91C	ENST00000374080		91	Cgc/Tgc	3/45	1	2	FACETS	0.423	0.344	0.512	0.423	0.344	0.512	SUBCLONAL	1	FALSE	1	0.24404690936315	2		614	659	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778875	76778875	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	50	573	0	ENST00000373344.5:c.6704C>A	p.Thr2235Asn	p.T2235N	ENST00000373344	NM_000489.3	2235	aCc/aAc	31/35	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.24404690936315	2		573	286	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845325	76845325	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	28	510	0	ENST00000373344.5:c.6196G>T	p.Asp2066Tyr	p.D2066Y	ENST00000373344	NM_000489.3	2066	Gat/Tat	27/35	1	2	FACETS	0.755	0.604	0.925	0.755	0.604	0.925	CLONAL	1	FALSE	1	0.24404690936315	2		510	304	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937764	76937764	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	74	652	0	ENST00000373344.5:c.2984C>A	p.Pro995His	p.P995H	ENST00000373344	NM_000489.3	995	cCt/cAt	9/35	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.24404690936315	2		652	417	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034360	123034360	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	59	391	0	ENST00000355640.3:c.1117A>T	p.Asn373Tyr	p.N373Y	ENST00000355640		373	Aat/Tat	6/7	1	2	FACETS	0.879	0.763	1	1	0.976	1	CLONAL	2	FALSE	1	0.24404690936315	2		391	275	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181301	123181301	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	42	310	0	ENST00000218089.9:c.765G>T	p.Met255Ile	p.M255I	ENST00000218089	NM_001042749.1	255	atG/atT	9/35	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.24404690936315	2		310	247	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190023	123190023	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	118	686	0	ENST00000218089.9:c.1242T>G	p.Tyr414Ter	p.Y414*	ENST00000218089	NM_001042749.1	414	taT/taG	14/35	1	2	FACETS	0.965	0.875	1	1	0.989	1	CLONAL	2	FALSE	1	0.24404690936315	2		686	501	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210233	123210233	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	102	619	1	ENST00000218089.9:c.2585G>T	p.Arg862Ile	p.R862I	ENST00000218089	NM_001042749.1	862	aGa/aTa	26/35	1	2	FACETS	0.965	0.869	1	1	0.987	1	CLONAL	2	FALSE	1	0.24404690936315	2		620	433	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220576	123220576	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	89	515	0	ENST00000218089.9:c.3233C>A	p.Ser1078Tyr	p.S1078Y	ENST00000218089	NM_001042749.1	1078	tCt/tAt	30/35	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.24404690936315	2		515	548	SUCCESS
APC	324	MSKCC	GRCh37	5	112128185	112128185	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779805	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	47	326	1	ENST00000257430.4:c.688C>T	p.Arg230Cys	p.R230C	ENST00000257430	NM_000038.5	230	Cgt/Tgt	7/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.51	2		327	123	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	33	305	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	0.0770245185744091	0	FACETS	0.593	0.495	0.697			1	INDETERMINATE	1	TRUE	0	0.51	0		305	107	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	90	513	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.51	2		513	291	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628590	90628590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61733005	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	97	758	0	ENST00000330062.3:c.997G>A	p.Val333Ile	p.V333I	ENST00000330062	NM_002168.2	333	Gtc/Atc	8/11	0.194530953000023	1	FACETS	0.683	0.613	0.757	0.683	0.613	0.757	INDETERMINATE	1	TRUE	0	0.51	1		758	415	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524603	176524603	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758782236	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	198	955	0	ENST00000292408.4:c.2335G>A	p.Asp779Asn	p.D779N	ENST00000292408	NM_213647.1	779	Gat/Aat	18/18	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.51	2		955	610	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830135	72830135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	123	654	1	ENST00000268489.5:c.6446G>A	p.Arg2149His	p.R2149H	ENST00000268489	NM_006885.3	2149	cGc/cAc	9/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.51	2		655	405	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993116	72993116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	139	850	0	ENST00000268489.5:c.929G>A	p.Ser310Asn	p.S310N	ENST00000268489	NM_006885.3	310	aGc/aAc	2/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.51	2		850	416	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226103	226103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs553257776	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	46	521	0	ENST00000264932.6:c.562C>T	p.Arg188Trp	p.R188W	ENST00000264932	NM_004168.2	188	Cgg/Tgg	5/15	1	2	FACETS	0.35	0.294	0.411	0.35	0.294	0.411	SUBCLONAL	1	TRUE	1	0.51	2		521	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	100	760	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	0.739	0.662	0.819	0.739	0.662	0.819	SUBCLONAL	1	TRUE	1	0.51	2		760	531	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227982	53227982	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1556840029	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	89	785	1	ENST00000375401.3:c.2332C>T	p.Arg778Ter	p.R778*	ENST00000375401	NM_004187.3	778	Cga/Tga	16/26	0.0770245185744091	0	FACETS	0.318	0.282	0.356			1	INDETERMINATE	1	TRUE	0	0.51	0		786	538	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962846	2962846	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	186	761	2	ENST00000396946.4:c.2062C>T	p.Arg688Ter	p.R688*	ENST00000396946	NM_032415.4	688	Cga/Tga	16/25	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.51	2		763	609	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	8	597	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.0770245185744091	0	FACETS	0.056	0.036	0.083			1	INDETERMINATE	1	TRUE	0	0.51	0		597	273	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176338	24176338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	121	613	3	ENST00000263121.7:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000263121	NM_003073.3	377	Cgt/Tgt	9/9	0.151853302930067	0	FACETS	0.433	0.393	0.475			1	INDETERMINATE	1	TRUE	0	0.51	0		616	537	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218098	36218098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	65	415	0	ENST00000222270.7:c.4045G>A	p.Asp1349Asn	p.D1349N	ENST00000222270	NM_014727.1	1349	Gac/Aac	15/37	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.51	2		415	214	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739820	46739820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555234707	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	28	430	0	ENST00000371975.4:c.1621G>A	p.Val541Ile	p.V541I	ENST00000371975	NM_003579.3	541	Gtc/Atc	15/18	1	2	FACETS	0.569	0.458	0.693	0.569	0.458	0.693	SUBCLONAL	1	TRUE	1	0.51	2		430	193	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	43	481	0	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.51	2		481	142	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391338	139391338	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61751489	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	46	950	0	ENST00000277541.6:c.6853G>A	p.Val2285Ile	p.V2285I	ENST00000277541	NM_017617.3	2285	Gtc/Atc	34/34	1	2	FACETS	0.319	0.268	0.375	0.319	0.268	0.375	SUBCLONAL	1	TRUE	1	0.51	2		950	566	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435049	110435049	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1310757868	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	47	843	1	ENST00000375856.3:c.3352G>A	p.Glu1118Lys	p.E1118K	ENST00000375856	NM_003749.2	1118	Gag/Aag	1/2	1	2	FACETS	0.344	0.29	0.404	0.344	0.29	0.404	SUBCLONAL	1	TRUE	1	0.51	2		844	536	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395204	139395204	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375978224	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	155	961	0	ENST00000277541.6:c.5734G>A	p.Asp1912Asn	p.D1912N	ENST00000277541	NM_017617.3	1912	Gac/Aac	31/34	1	2	FACETS	0.751	0.688	0.817	0.751	0.688	0.817	SUBCLONAL	1	TRUE	1	0.51	2		961	809	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090381	77090381	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369339512	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	21	587	0	ENST00000356341.3:c.344C>T	p.Ser115Leu	p.S115L	ENST00000356341	NM_002576.4	115	tCg/tTg	4/15	1	2	FACETS	0.366	0.283	0.463	0.366	0.283	0.463	SUBCLONAL	1	TRUE	1	0.51	2		587	225	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176671198	176671198	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	31	392	0	ENST00000439151.2:c.4305C>A	p.Cys1435Ter	p.C1435*	ENST00000439151	NM_022455.4	1435	tgC/tgA	9/23	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.51	2		392	105	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610056	81610056	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	18	408	0	ENST00000298171.2:c.1654C>A	p.Leu552Ile	p.L552I	ENST00000298171	NM_000369.2	552	Ctc/Atc	10/10	0.151853302930067	0	FACETS	0.149	0.112	0.193			1	INDETERMINATE	1	TRUE	0	0.51	0		408	232	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	24	443	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	0.0770245185744091	0	FACETS	0.457	0.365	0.557			1	INDETERMINATE	1	TRUE	0	0.51	0		443	101	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198272771	198272771	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	35	606	1	ENST00000335508.6:c.1190G>A	p.Arg397His	p.R397H	ENST00000335508	NM_012433.2	397	cGc/cAc	9/25	1	2	FACETS	0.853	0.709	1	0.853	0.709	1	CLONAL	1	TRUE	1	0.51	2		607	161	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293748	1293748	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1561213598	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	67	1005	2	ENST00000310581.5:c.1253C>T	p.Ala418Val	p.A418V	ENST00000310581	NM_198253.2	418	gCg/gTg	2/16	1	2	FACETS	0.416	0.361	0.475	0.416	0.361	0.475	SUBCLONAL	1	TRUE	1	0.51	2		1007	632	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3827631	3827631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141098117	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	39	410	0	ENST00000262367.5:c.2141G>A	p.Arg714His	p.R714H	ENST00000262367	NM_004380.2	714	cGc/cAc	11/31	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.51	2		410	148	SUCCESS
APC	324	MSKCC	GRCh37	5	112178327	112178327	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200756935	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	20	408	0	ENST00000257430.4:c.7036C>T	p.Pro2346Ser	p.P2346S	ENST00000257430	NM_000038.5	2346	Cca/Tca	16/16	1	2	FACETS	1	0.818	1	1	0.818	1	CLONAL	1	TRUE	1	0.51	2		408	75	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453486	138453486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451809865	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	21	343	0	ENST00000289153.2:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000289153	NM_006219.2	321	cGa/cAa	5/22	0.0770245185744091	0	FACETS	0.429	0.337	0.532			1	INDETERMINATE	1	TRUE	0	0.51	0		343	94	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517609	176517609	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs755455944	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	150	889	2	ENST00000292408.4:c.310C>T	p.Arg104Ter	p.R104*	ENST00000292408	NM_213647.1	104	Cga/Tga	3/18	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.51	2		891	563	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295825	212295825	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	36	380	0	ENST00000342788.4:c.2488G>A	p.Gly830Arg	p.G830R	ENST00000342788	NM_005235.2	830	Gga/Aga	21/28	1	2	FACETS	0.767	0.652	0.887	1	0.96	1	SUBCLONAL	2	TRUE	1	0.51	2		380	92	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80343580	80343580	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	22	307	0	ENST00000286548.4:c.739C>T	p.Arg247Ter	p.R247*	ENST00000286548	NM_002072.3	247	Cga/Tga	6/7	1	2	FACETS	0.98	0.778	1	0.98	0.778	1	CLONAL	1	TRUE	1	0.51	2		307	88	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098534	11098534	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1018881303	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	46	582	1	ENST00000358026.2:c.1052G>A	p.Arg351His	p.R351H	ENST00000358026	NM_001128849.1	351	cGc/cAc	6/36	1	2	FACETS	0.309	0.26	0.364	0.309	0.26	0.364	SUBCLONAL	1	TRUE	1	0.51	2		583	583	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101932	11101932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	194	741	2	ENST00000358026.2:c.1352G>A	p.Arg451His	p.R451H	ENST00000358026	NM_001128849.1	451	cGc/cAc	8/36	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.51	2		743	674	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533378	29533378	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs878853865	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	16	237	0	ENST00000356175.3:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000356175	NM_000267.3	461	Cga/Tga	12/57	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.51	2		237	50	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435256	18435256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	12	324	0	ENST00000266497.5:c.241G>A	p.Ala81Thr	p.A81T	ENST00000266497		81	Gca/Aca	1/31	0.151853302930067	3	FACETS	1	0.816	1	0.591	0.428	0.777	INDETERMINATE	1	TRUE	1	0.51	3		324	50	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024619	31024619	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	40	518	0	ENST00000375687.4:c.4104G>T	p.Lys1368Asn	p.K1368N	ENST00000375687	NM_015338.5	1368	aaG/aaT	13/13	0.194530953000023	1	FACETS	0.73	0.617	0.853	0.73	0.617	0.853	INDETERMINATE	1	TRUE	0	0.51	1		518	160	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417596	139417596	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372660483	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	166	1013	0	ENST00000277541.6:c.448G>A	p.Ala150Thr	p.A150T	ENST00000277541	NM_017617.3	150	Gcc/Acc	4/34	1	2	FACETS	0.917	0.844	0.992	0.917	0.844	0.992	CLONAL	1	TRUE	1	0.51	2		1013	710	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289196	33289196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771284147	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	107	525	0	ENST00000374542.5:c.356G>A	p.Arg119Gln	p.R119Q	ENST00000374542	NM_001141970.1	119	cGg/cAg	3/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.51	2		525	343	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849143	156849143	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs775191394	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	73	810	0	ENST00000524377.1:c.2035G>T	p.Asp679Tyr	p.D679Y	ENST00000524377	NM_002529.3	679	Gac/Tac	15/17	1	2	FACETS	0.797	0.702	0.899	0.797	0.702	0.899	SUBCLONAL	1	TRUE	1	0.51	2		810	359	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38955742	38955742	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200337712	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	31	387	0	ENST00000357387.3:c.2564G>A	p.Arg855Gln	p.R855Q	ENST00000357387	NM_152756.3	855	cGg/cAg	26/38	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.51	2		387	103	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877381	40877381	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	124	567	0	ENST00000373198.4:c.2315G>A	p.Gly772Asp	p.G772D	ENST00000373198	NM_133170.3	772	gGc/gAc	15/32	0.194530953000023	1	FACETS	0.846	0.772	0.924	0.846	0.772	0.924	INDETERMINATE	1	TRUE	0	0.51	1		567	428	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856093	68856093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121964878	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	13	536	1	ENST00000261769.5:c.1901C>T	p.Ala634Val	p.A634V	ENST00000261769	NM_004360.3	634	gCg/gTg	12/16	1	2	FACETS	0.206	0.147	0.279	0.206	0.147	0.279	SUBCLONAL	1	TRUE	1	0.51	2		537	247	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116167	67116167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	15	426	0	ENST00000412916.2:c.451C>T	p.Arg151Cys	p.R151C	ENST00000412916		151	Cgc/Tgc	5/6	1	2	FACETS	0.249	0.182	0.33	0.249	0.182	0.33	SUBCLONAL	1	TRUE	1	0.51	2		426	236	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237686	133237686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142563997	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	110	644	1	ENST00000320574.5:c.2929G>A	p.Gly977Arg	p.G977R	ENST00000320574	NM_006231.2	977	Ggg/Agg	25/49	0.151853302930067	3	FACETS	1	0.978	1	0.64	0.579	0.703	INDETERMINATE	1	TRUE	1	0.51	3		645	423	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350792	15350792	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	43	744	0	ENST00000263377.2:c.3211C>T	p.Pro1071Ser	p.P1071S	ENST00000263377	NM_058243.2	1071	Ccc/Tcc	15/20	1	2	FACETS	0.438	0.367	0.516	0.438	0.367	0.516	SUBCLONAL	1	TRUE	1	0.51	2		744	385	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158626970	158626970	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1198616498	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	53	441	0	ENST00000263640.3:c.700G>A	p.Val234Met	p.V234M	ENST00000263640	NM_001105.4	234	Gtg/Atg	7/11	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.51	2		441	203	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651264	45651264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772294235	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	120	735	0	ENST00000407780.3:c.761C>T	p.Ala254Val	p.A254V	ENST00000407780	NM_001283052.1	254	gCg/gTg	5/7	1	2	FACETS	0.73	0.66	0.803	0.73	0.66	0.803	SUBCLONAL	1	TRUE	1	0.51	2		735	645	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225129	53225129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs967652938	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	38	621	0	ENST00000375401.3:c.3089G>A	p.Arg1030Gln	p.R1030Q	ENST00000375401	NM_004187.3	1030	cGg/cAg	20/26	0.0770245185744091	0	FACETS	0.173	0.142	0.206			1	INDETERMINATE	1	TRUE	0	0.51	0		621	423	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841322	15841322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	72	463	0	ENST00000307771.7:c.1406C>T	p.Ser469Leu	p.S469L	ENST00000307771	NM_005089.3	469	tCg/tTg	11/11	0.0770245185744091	0	FACETS	0.421	0.37	0.474			1	INDETERMINATE	1	TRUE	0	0.51	0		463	329	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737052	162737052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765973930	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	14	612	0	ENST00000367921.3:c.1196G>A	p.Arg399Gln	p.R399Q	ENST00000367921	NM_006182.2	399	cGg/cAg	11/18	1	2	FACETS	0.246	0.178	0.329	0.246	0.178	0.329	SUBCLONAL	1	TRUE	1	0.51	2		612	223	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141587	202141587	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771150445	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	11	355	1	ENST00000358485.4:c.875G>A	p.Arg292Gln	p.R292Q	ENST00000358485	NM_001080125.1	292	cGg/cAg	7/9	1	2	FACETS	0.389	0.27	0.533	0.389	0.27	0.533	SUBCLONAL	1	TRUE	1	0.51	2		356	111	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872498	136872498	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs104893624	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	12	276	0	ENST00000241393.3:c.1000C>T	p.Arg334Ter	p.R334*	ENST00000241393	NM_003467.2	334	Cga/Tga	2/2	1	2	FACETS	0.349	0.246	0.473	0.349	0.246	0.473	SUBCLONAL	1	TRUE	1	0.51	2		276	135	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245759	41245759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55650082	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	57	796	0	ENST00000357654.3:c.1789G>A	p.Glu597Lys	p.E597K	ENST00000357654	NM_007294.3	597	Gaa/Aaa	10/23	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.51	2		796	164	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161380	55161380	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376544204	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	9	405	1	ENST00000257290.5:c.3211G>A	p.Asp1071Asn	p.D1071N	ENST00000257290	NM_006206.4	1071	Gac/Aac	23/23	1	2	FACETS	0.154	0.101	0.221	0.154	0.101	0.221	SUBCLONAL	1	TRUE	1	0.51	2		406	229	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244137	153244137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140856583	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	46	550	2	ENST00000281708.4:c.2020C>T	p.Arg674Trp	p.R674W	ENST00000281708	NM_033632.3	674	Cgg/Tgg	12/12	1	2	FACETS	0.584	0.494	0.682	0.584	0.494	0.682	SUBCLONAL	1	TRUE	1	0.51	2		552	309	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196060	138196060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs5029941	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	10	287	0	ENST00000237289.4:c.374C>T	p.Ala125Val	p.A125V	ENST00000237289	NM_001270507.1	125	gCg/gTg	3/9	1	2	FACETS	0.236	0.16	0.332	0.236	0.16	0.332	SUBCLONAL	1	TRUE	1	0.51	2		287	166	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121458	108121458	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	20	251	0	ENST00000278616.4:c.1266G>T	p.Lys422Asn	p.K422N	ENST00000278616	NM_000051.3	422	aaG/aaT	10/63	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.51	2		251	63	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104359255	104359255	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	98	408	0	ENST00000369902.3:c.976C>T	p.Pro326Ser	p.P326S	ENST00000369902	NM_016169.3	326	Cca/Tca	8/12	1	2	FACETS	0.975	0.877	1	0.975	0.877	1	CLONAL	1	TRUE	1	0.51	2		408	394	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675596	30675596	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	26	944	0	ENST00000376406.3:c.2760G>T	p.Glu920Asp	p.E920D	ENST00000376406	NM_014641.2	920	gaG/gaT	8/15	1	2	FACETS	0.311	0.246	0.385	0.311	0.246	0.385	SUBCLONAL	1	TRUE	1	0.51	2		944	328	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039629	47039629	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	79	706	0	ENST00000377604.3:c.1081C>T	p.Gln361Ter	p.Q361*	ENST00000377604	NM_001204468.1	361	Cag/Tag	11/24	0.0770245185744091	0	FACETS	0.37	0.327	0.416			1	INDETERMINATE	1	TRUE	0	0.51	0		706	410	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508280	106508280	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	52	296	1	ENST00000359195.3:c.274G>A	p.Gly92Arg	p.G92R	ENST00000359195	NM_002649.2	92	Gga/Aga	2/11	1	2	FACETS	0.98	0.846	1	0.98	0.846	1	CLONAL	1	TRUE	1	0.51	2		297	208	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033396	48033396	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	31	407	0	ENST00000234420.5:c.3700G>T	p.Glu1234Ter	p.E1234*	ENST00000234420	NM_000179.2	1234	Gaa/Taa	8/10	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.51	2		407	99	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751901	57751901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148954251	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	51	590	0	ENST00000274289.3:c.1336C>T	p.Arg446Trp	p.R446W	ENST00000274289	NM_006622.3	446	Cgg/Tgg	10/14	1	2	FACETS	0.766	0.657	0.884	0.766	0.657	0.884	SUBCLONAL	1	TRUE	1	0.51	2		590	261	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39690066	39690066	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	25	188	0	ENST00000361337.2:c.91C>T	p.Arg31Ter	p.R31*	ENST00000361337	NM_003286.2	31	Cga/Tga	3/21	0.194530953000023	1	FACETS	0.925	0.751	1	0.925	0.751	1	INDETERMINATE	1	TRUE	0	0.51	1		188	79	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946171	13946171	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	22	507	2	ENST00000405192.2:c.925C>T	p.Arg309Ter	p.R309*	ENST00000405192	NM_001163147.1	309	Cga/Tga	10/12	1	2	FACETS	0.369	0.286	0.464	0.369	0.286	0.464	SUBCLONAL	1	TRUE	1	0.51	2		509	234	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851087	63851087	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	86	469	0	ENST00000279873.7:c.1865A>G	p.Tyr622Cys	p.Y622C	ENST00000279873	NM_032199.2	622	tAc/tGc	10/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.51	2		469	281	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729671	162729671	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376303676	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	17	548	0	ENST00000367921.3:c.757G>A	p.Gly253Ser	p.G253S	ENST00000367921	NM_006182.2	253	Ggc/Agc	8/18	1	2	FACETS	0.203	0.151	0.265	0.203	0.151	0.265	SUBCLONAL	1	TRUE	1	0.51	2		548	328	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184141	56184141	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	32	408	0	ENST00000399503.3:c.4346G>A	p.Trp1449Ter	p.W1449*	ENST00000399503	NM_005921.1	1449	tGg/tAg	19/20	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.51	2		408	113	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301111	65301111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370434553	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	30	290	0	ENST00000342505.4:c.3337C>T	p.Arg1113Cys	p.R1113C	ENST00000342505	NM_002227.2	1113	Cgc/Tgc	24/25	1	2	FACETS	0.749	0.611	0.902	0.749	0.611	0.902	CLONAL	1	TRUE	1	0.51	2		290	157	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350069	89350069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758856347	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	215	932	0	ENST00000301030.4:c.2881C>T	p.Arg961Cys	p.R961C	ENST00000301030	NM_001256183.1	961	Cgc/Tgc	9/13	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.51	2		932	675	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760147	133760147	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376162814	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	58	622	0	ENST00000318560.5:c.2470G>A	p.Val824Met	p.V824M	ENST00000318560	NM_005157.4	824	Gtg/Atg	11/11	1	2	FACETS	0.693	0.599	0.795	0.693	0.599	0.795	SUBCLONAL	1	TRUE	1	0.51	2		622	328	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426645	47426645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	73	604	0	ENST00000377045.4:c.890G>A	p.Arg297Gln	p.R297Q	ENST00000377045	NM_001654.4	297	cGg/cAg	10/16	0.0770245185744091	0	FACETS	0.489	0.432	0.549			1	INDETERMINATE	1	TRUE	0	0.51	0		604	287	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245465	41245465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28897681	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	93	814	0	ENST00000357654.3:c.2083G>A	p.Asp695Asn	p.D695N	ENST00000357654	NM_007294.3	695	Gat/Aat	10/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.51	2		814	259	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467829	50467829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	23	454	0	ENST00000331340.3:c.1064C>T	p.Ala355Val	p.A355V	ENST00000331340	NM_006060.4	355	gCg/gTg	8/8	1	2	FACETS	0.322	0.251	0.404	0.322	0.251	0.404	SUBCLONAL	1	TRUE	1	0.51	2		454	280	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434595	110434595	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs555841746	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	45	684	0	ENST00000375856.3:c.3806A>C	p.Gln1269Pro	p.Q1269P	ENST00000375856	NM_003749.2	1269	cAg/cCg	1/2	1	2	FACETS	0.3	0.252	0.354	0.3	0.252	0.354	SUBCLONAL	1	TRUE	1	0.51	2		684	588	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661965	227661965	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756790900	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	38	632	0	ENST00000305123.5:c.1490G>A	p.Gly497Glu	p.G497E	ENST00000305123	NM_005544.2	497	gGa/gAa	1/2	1	2	FACETS	0.498	0.414	0.592	0.498	0.414	0.592	SUBCLONAL	1	TRUE	1	0.51	2		632	299	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443618	29443618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200585833	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	146	631	0	ENST00000389048.3:c.3599C>T	p.Ala1200Val	p.A1200V	ENST00000389048	NM_004304.4	1200	gCg/gTg	23/29	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.51	2		631	461	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028820	47028820	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370571712	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	142	755	0	ENST00000377604.3:c.124C>T	p.Arg42Cys	p.R42C	ENST00000377604	NM_001204468.1	42	Cgt/Tgt	3/24	0.0770245185744091	0	FACETS	0.584	0.536	0.634			1	INDETERMINATE	1	TRUE	0	0.51	0		755	467	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729775	41729775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	46	408	1	ENST00000242208.4:c.754G>A	p.Ala252Thr	p.A252T	ENST00000242208	NM_002192.2	252	Gcc/Acc	3/3	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.51	2		409	175	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795364	42795364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	16	559	0	ENST00000575354.2:c.2444C>T	p.Ala815Val	p.A815V	ENST00000575354	NM_015125.3	815	gCc/gTc	10/20	1	2	FACETS	0.306	0.226	0.401	0.306	0.226	0.401	SUBCLONAL	1	TRUE	1	0.51	2		559	205	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394046	31394046	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	10	331	0	ENST00000328111.2:c.2333C>T	p.Ser778Leu	p.S778L	ENST00000328111	NM_006892.3	778	tCg/tTg	22/23	0.194530953000023	1	FACETS	0.268	0.183	0.374	0.268	0.183	0.374	INDETERMINATE	1	TRUE	0	0.51	1		331	109	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523068	176523068	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1387211815	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	126	661	0	ENST00000292408.4:c.1832G>A	p.Arg611Gln	p.R611Q	ENST00000292408	NM_213647.1	611	cGg/cAg	14/18	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.51	2		661	412	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11308103	11308103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141936187	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	24	808	0	ENST00000361445.4:c.889G>A	p.Asp297Asn	p.D297N	ENST00000361445	NM_004958.3	297	Gac/Aac	7/58	1	2	FACETS	0.34	0.267	0.424	0.34	0.267	0.424	SUBCLONAL	1	TRUE	1	0.51	2		808	277	SUCCESS
BLM	641	MSKCC	GRCh37	15	91352484	91352484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1031421025	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	20	282	0	ENST00000355112.3:c.3869C>T	p.Ser1290Leu	p.S1290L	ENST00000355112	NM_000057.2	1290	tCg/tTg	20/22	0.194530953000023	1	FACETS	0.74	0.58	0.916	0.74	0.58	0.916	INDETERMINATE	1	TRUE	0	0.51	1		282	79	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856469	111856469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	117	265	3	ENST00000341259.2:c.520G>A	p.Ala174Thr	p.A174T	ENST00000341259	NM_005475.2	174	Gcc/Acc	2/8	0.151853302930067	3	FACETS	1	0.979	1	0.644	0.585	0.706	INDETERMINATE	1	TRUE	1	0.51	3		268	447	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894898	101894898	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776680716	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	26	342	0	ENST00000374994.4:c.451C>T	p.Arg151Cys	p.R151C	ENST00000374994	NM_004612.2	151	Cgc/Tgc	3/9	1	2	FACETS	0.708	0.568	0.864	0.708	0.568	0.864	SUBCLONAL	1	TRUE	1	0.51	2		342	144	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007205	62007205	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	71	789	0	ENST00000392795.3:c.477G>T	p.Lys159Asn	p.K159N	ENST00000392795	NM_001039933.1	159	aaG/aaT	4/6	1	2	FACETS	0.643	0.563	0.728	0.643	0.563	0.728	SUBCLONAL	1	TRUE	1	0.51	2		789	433	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622495	158622495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316254232	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	33	518	1	ENST00000263640.3:c.1004G>A	p.Arg335Gln	p.R335Q	ENST00000263640	NM_001105.4	335	cGa/cAa	8/11	1	2	FACETS	0.899	0.744	1	0.899	0.744	1	CLONAL	1	TRUE	1	0.51	2		519	144	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918695	44918695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746746824	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	16	485	0	ENST00000377967.4:c.1178G>A	p.Arg393Gln	p.R393Q	ENST00000377967	NM_021140.2	393	cGa/cAa	12/29	0.0770245185744091	0	FACETS	0.275	0.205	0.355			1	INDETERMINATE	1	TRUE	0	0.51	0		485	112	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779181	135779181	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202241429	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	42	423	1	ENST00000298552.3:c.2065C>T	p.Arg689Cys	p.R689C	ENST00000298552	NM_001162426.1	689	Cgc/Tgc	17/23	1	2	FACETS	0.742	0.625	0.869	0.742	0.625	0.869	SUBCLONAL	1	TRUE	1	0.51	2		424	222	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45396897	45396897	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs984513669	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	29	363	0	ENST00000262160.6:c.275C>T	p.Thr92Met	p.T92M	ENST00000262160	NM_005901.5	92	aCg/aTg	3/11	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.51	2		363	107	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257596	16257596	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	40	443	0	ENST00000375759.3:c.4861G>A	p.Glu1621Lys	p.E1621K	ENST00000375759	NM_015001.2	1621	Gaa/Aaa	11/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.51	2		443	112	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144152	11144152	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	151	599	1	ENST00000358026.2:c.3733G>A	p.Ala1245Thr	p.A1245T	ENST00000358026	NM_001128849.1	1245	Gcc/Acc	26/36	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.51	2		600	524	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610002	81610002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150602845	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	29	365	0	ENST00000298171.2:c.1600C>T	p.Arg534Cys	p.R534C	ENST00000298171	NM_000369.2	534	Cgc/Tgc	10/10	0.151853302930067	0	FACETS	0.283	0.228	0.344			1	INDETERMINATE	1	TRUE	0	0.51	0		365	197	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159099	143159099	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1332432216	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	24	468	0	ENST00000262992.4:c.754C>T	p.Arg252Ter	p.R252*	ENST00000262992	NM_001101669.1	252	Cga/Tga	10/24	1	2	FACETS	0.798	0.635	0.978	0.798	0.635	0.978	CLONAL	1	TRUE	1	0.51	2		468	118	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740750	58740750	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760201595	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	27	480	0	ENST00000305921.3:c.1655G>A	p.Arg552Gln	p.R552Q	ENST00000305921	NM_003620.3	552	cGa/cAa	6/6	1	2	FACETS	0.469	0.375	0.575	0.469	0.375	0.575	SUBCLONAL	1	TRUE	1	0.51	2		480	226	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497824	25497824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	148	610	0	ENST00000264709.3:c.625C>T	p.Arg209Cys	p.R209C	ENST00000264709	NM_175629.2	209	Cgc/Tgc	6/23	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.51	2		610	536	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953156	81953156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381167403	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	48	383	0	ENST00000359376.3:c.2122G>A	p.Ala708Thr	p.A708T	ENST00000359376	NM_002661.3	708	Gcc/Acc	20/33	1	2	FACETS	0.613	0.521	0.713	0.613	0.521	0.713	SUBCLONAL	1	TRUE	1	0.51	2		383	307	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781090	135781090	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	25	661	1	ENST00000298552.3:c.1875G>T	p.Glu625Asp	p.E625D	ENST00000298552	NM_001162426.1	625	gaG/gaT	15/23	1	2	FACETS	0.342	0.269	0.424	0.342	0.269	0.424	SUBCLONAL	1	TRUE	1	0.51	2		662	287	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593543	215593543	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs76744638	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	11	373	0	ENST00000260947.4:c.2191C>T	p.Arg731Cys	p.R731C	ENST00000260947	NM_000465.2	731	Cgc/Tgc	11/11	1	2	FACETS	0.329	0.228	0.453	0.329	0.228	0.453	SUBCLONAL	1	TRUE	1	0.51	2		373	131	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271150	38271150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758677681	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	78	492	2	ENST00000425967.3:c.2558G>A	p.Arg853His	p.R853H	ENST00000425967	NM_001174067.1	853	cGc/cAc	19/19	1	2	FACETS	0.827	0.731	0.928	0.827	0.731	0.928	CLONAL	1	TRUE	1	0.51	2		494	370	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456744	32456744	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	46	566	0	ENST00000332351.3:c.148G>A	p.Ala50Thr	p.A50T	ENST00000332351	NM_024426.4	50	Gct/Act	1/10	1	2	FACETS	0.396	0.334	0.465	0.396	0.334	0.465	SUBCLONAL	1	TRUE	1	0.51	2		566	455	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211003	36211003	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1337392865	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	150	926	1	ENST00000222270.7:c.754C>T	p.Pro252Ser	p.P252S	ENST00000222270	NM_014727.1	252	Ccc/Tcc	3/37	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.51	2		927	498	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513455	41513455	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303897359	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	40	512	0	ENST00000263253.7:c.359G>A	p.Ser120Asn	p.S120N	ENST00000263253	NM_001429.3	120	aGc/aAc	2/31	0.151853302930067	0	FACETS	0.37	0.31	0.434			1	INDETERMINATE	1	TRUE	0	0.51	0		512	208	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137321073	137321073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768721235	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	58	502	0	ENST00000481739.1:c.1030G>A	p.Ala344Thr	p.A344T	ENST00000481739	NM_002957.4	344	Gcc/Acc	7/10	1	2	FACETS	0.727	0.628	0.832	0.727	0.628	0.832	SUBCLONAL	1	TRUE	1	0.51	2		502	313	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128266	30128266	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	100	775	0	ENST00000263025.4:c.966G>T	p.Glu322Asp	p.E322D	ENST00000263025	NM_002746.2	322	gaG/gaT	7/9	1	2	FACETS	0.94	0.846	1	0.94	0.846	1	CLONAL	1	TRUE	1	0.51	2		775	417	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814797	139814797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144427288	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	168	722	0	ENST00000247668.2:c.790G>A	p.Ala264Thr	p.A264T	ENST00000247668	NM_021138.3	264	Gcg/Acg	8/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.51	2		722	556	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725324	49725324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748664213	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	79	548	0	ENST00000449682.2:c.101G>A	p.Arg34His	p.R34H	ENST00000449682	NM_020998.3	34	cGc/cAc	2/18	0.0770245185744091	0	FACETS	0.424	0.375	0.475			1	INDETERMINATE	1	TRUE	0	0.51	0		548	358	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40682085	40682085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761530012	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	67	540	1	ENST00000249776.8:c.640C>T	p.Arg214Trp	p.R214W	ENST00000249776	NM_033286.3	214	Cgg/Tgg	6/9	0.194530953000023	1	FACETS	0.631	0.553	0.715	0.631	0.553	0.715	INDETERMINATE	1	TRUE	0	0.51	1		541	310	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720871	89720871	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	24	300	0	ENST00000371953.3:c.1022T>G	p.Phe341Cys	p.F341C	ENST00000371953	NM_000314.4	341	tTt/tGt	8/9	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.51	2		300	78	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867203	68867203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782024	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	70	473	0	ENST00000261769.5:c.2450C>T	p.Ala817Val	p.A817V	ENST00000261769	NM_004360.3	817	gCg/gTg	16/16	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.51	2		473	266	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397139	397139	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	43	271	0	ENST00000380956.4:c.524A>G	p.Asp175Gly	p.D175G	ENST00000380956	NM_001195286.1	175	gAc/gGc	5/9	1	2	FACETS	0.724	0.611	0.846	0.724	0.611	0.846	SUBCLONAL	1	TRUE	1	0.51	2		271	233	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870376	155870376	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	43	441	1	ENST00000368323.3:c.463G>T	p.Glu155Ter	p.E155*	ENST00000368323	NM_006912.5	155	Gaa/Taa	6/6	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.51	2		442	164	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851591	134851591	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748976557	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	77	551	1	ENST00000398015.3:c.997G>A	p.Val333Ile	p.V333I	ENST00000398015	NM_004441.4	333	Gtc/Atc	5/16	0.0770245185744091	0	FACETS	0.652	0.582	0.725			1	INDETERMINATE	1	TRUE	0	0.51	0		552	227	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021735	69021735	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	42	468	0	ENST00000288368.4:c.3023G>A	p.Gly1008Asp	p.G1008D	ENST00000288368	NM_024870.2	1008	gGc/gAc	25/40	1	2	FACETS	0.931	0.788	1	0.931	0.788	1	CLONAL	1	TRUE	1	0.51	2		468	177	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211880	36211880	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759918812	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	38	991	1	ENST00000222270.7:c.1631G>A	p.Arg544Gln	p.R544Q	ENST00000222270	NM_014727.1	544	cGg/cAg	3/37	1	2	FACETS	0.269	0.222	0.322	0.269	0.222	0.322	SUBCLONAL	1	TRUE	1	0.51	2		992	553	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412607	139412607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373770404	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	32	721	1	ENST00000277541.6:c.1237G>A	p.Val413Met	p.V413M	ENST00000277541	NM_017617.3	413	Gtg/Atg	7/34	1	2	FACETS	0.287	0.232	0.348	0.287	0.232	0.348	SUBCLONAL	1	TRUE	1	0.51	2		722	438	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843242	128843242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs912880810	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	117	756	0	ENST00000249373.3:c.349C>T	p.Arg117Cys	p.R117C	ENST00000249373	NM_005631.4	117	Cgc/Tgc	2/12	1	2	FACETS	0.871	0.788	0.957	0.871	0.788	0.957	CLONAL	1	TRUE	1	0.51	2		756	527	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670340	134670340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415689583	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	35	373	0	ENST00000398015.3:c.251G>A	p.Arg84His	p.R84H	ENST00000398015	NM_004441.4	84	cGc/cAc	3/16	0.0770245185744091	0	FACETS	0.322	0.266	0.383			1	INDETERMINATE	1	TRUE	0	0.51	0		373	209	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929077	44929077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2230018	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	21	456	0	ENST00000377967.4:c.2177C>T	p.Thr726Met	p.T726M	ENST00000377967	NM_021140.2	726	aCg/aTg	17/29	0.0770245185744091	0	FACETS	0.278	0.216	0.349			1	INDETERMINATE	1	TRUE	0	0.51	0		456	145	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73352354	73352354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	23	535	0	ENST00000377767.4:c.551C>T	p.Ala184Val	p.A184V	ENST00000377767	NM_014953.3	184	gCc/gTc	3/21	1	2	FACETS	0.618	0.487	0.766	0.618	0.487	0.766	SUBCLONAL	1	TRUE	1	0.51	2		535	146	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228997	36228997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	129	810	2	ENST00000222270.7:c.7777C>T	p.Arg2593Cys	p.R2593C	ENST00000222270	NM_014727.1	2593	Cgc/Tgc	36/37	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.51	2		812	497	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248598	10248598	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	60	639	0	ENST00000340748.4:c.4155G>T	p.Glu1385Asp	p.E1385D	ENST00000340748		1385	gaG/gaT	35/40	1	2	FACETS	0.513	0.442	0.589	0.513	0.442	0.589	SUBCLONAL	1	TRUE	1	0.51	2		639	459	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62309678	62309678	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	39	549	0	ENST00000360203.5:c.1016G>T	p.Ser339Ile	p.S339I	ENST00000360203	NM_001283009.1	339	aGc/aTc	12/35	0.194530953000023	1	FACETS	0.247	0.204	0.294	0.247	0.204	0.294	INDETERMINATE	1	TRUE	0	0.51	1		549	462	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803059	32803059	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs61736923	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	35	582	0	ENST00000374899.4:c.817C>T	p.Arg273Ter	p.R273*	ENST00000374899	NM_018833.2	273	Cga/Tga	5/12	1	2	FACETS	0.352	0.288	0.423	0.352	0.288	0.423	SUBCLONAL	1	TRUE	1	0.51	2		582	390	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112017	115112017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1156821376	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	49	698	1	ENST00000257566.3:c.1723G>A	p.Ala575Thr	p.A575T	ENST00000257566	NM_016569.3	575	Gcg/Acg	7/8	0.151853302930067	3	FACETS	0.382	0.322	0.447	0.191	0.161	0.224	INDETERMINATE	1	TRUE	1	0.51	3		699	632	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650711	67650711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567610917	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	30	521	0	ENST00000264010.4:c.1016G>A	p.Arg339Gln	p.R339Q	ENST00000264010	NM_006565.3	339	cGg/cAg	5/12	1	2	FACETS	0.281	0.226	0.343	0.281	0.226	0.343	SUBCLONAL	1	TRUE	1	0.51	2		521	419	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288799	15288799	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764992581	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	64	101	0	ENST00000263388.2:c.3940G>A	p.Ala1314Thr	p.A1314T	ENST00000263388	NM_000435.2	1314	Gcc/Acc	24/33	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.51	2		101	208	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420793	49420793	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765693458	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	44	547	0	ENST00000301067.7:c.14956C>T	p.Arg4986Cys	p.R4986C	ENST00000301067	NM_003482.3	4986	Cgc/Tgc	48/54	0.151853302930067	3	FACETS	0.417	0.35	0.492	0.209	0.175	0.246	INDETERMINATE	1	TRUE	1	0.51	3		547	519	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138166	64138166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1017388898	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	138	783	4	ENST00000334205.4:c.2089G>A	p.Ala697Thr	p.A697T	ENST00000334205	NM_003942.2	697	Gca/Aca	16/17	1	2	FACETS	0.77	0.702	0.841	0.77	0.702	0.841	SUBCLONAL	1	TRUE	1	0.51	2		787	703	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420730	49420730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201855029	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	35	618	0	ENST00000301067.7:c.15019C>T	p.Arg5007Trp	p.R5007W	ENST00000301067	NM_003482.3	5007	Cgg/Tgg	48/54	0.151853302930067	3	FACETS	0.308	0.251	0.371	0.154	0.125	0.186	INDETERMINATE	1	TRUE	1	0.51	3		618	560	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2215907	2215907	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746647663	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	58	620	0	ENST00000326181.6:c.109G>A	p.Ala37Thr	p.A37T	ENST00000326181	NM_032271.2	37	Gcc/Acc	3/21	1	2	FACETS	0.623	0.538	0.715	0.623	0.538	0.715	SUBCLONAL	1	TRUE	1	0.51	2		620	365	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256178	133256178	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	81	630	0	ENST00000320574.5:c.483G>T	p.Glu161Asp	p.E161D	ENST00000320574	NM_006231.2	161	gaG/gaT	6/49	0.151853302930067	3	FACETS	1	0.974	1	0.676	0.602	0.753	INDETERMINATE	1	TRUE	1	0.51	3		630	295	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435634	110435634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	60	462	0	ENST00000375856.3:c.2767G>A	p.Asp923Asn	p.D923N	ENST00000375856	NM_003749.2	923	Gac/Aac	1/2	1	2	FACETS	0.372	0.32	0.428	0.372	0.32	0.428	SUBCLONAL	1	TRUE	1	0.51	2		462	633	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584478	52584478	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142726131	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	54	606	1	ENST00000394830.3:c.4535C>T	p.Ala1512Val	p.A1512V	ENST00000394830	NM_018313.4	1512	gCg/gTg	29/30	0.0770245185744091	0	FACETS	0.59	0.513	0.671			1	INDETERMINATE	1	TRUE	0	0.51	0		607	176	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028136	48028136	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782324	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	13	318	0	ENST00000234420.5:c.3014G>A	p.Arg1005Gln	p.R1005Q	ENST00000234420	NM_000179.2	1005	cGa/cAa	4/10	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.51	2		318	40	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850879	128850879	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767688088	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	40	607	0	ENST00000249373.3:c.1726C>T	p.Arg576Trp	p.R576W	ENST00000249373	NM_005631.4	576	Cgg/Tgg	10/12	1	2	FACETS	0.315	0.261	0.375	0.315	0.261	0.375	SUBCLONAL	1	TRUE	1	0.51	2		607	498	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098967	178098967	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	25	308	0	ENST00000397062.3:c.78A>C	p.Gln26His	p.Q26H	ENST00000397062	NM_006164.4	26	caA/caC	2/5	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.51	2		308	77	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845485	128845485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779548739	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	100	758	2	ENST00000249373.3:c.782G>A	p.Arg261His	p.R261H	ENST00000249373	NM_005631.4	261	cGc/cAc	4/12	1	2	FACETS	0.699	0.626	0.776	0.699	0.626	0.776	SUBCLONAL	1	TRUE	1	0.51	2		760	561	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851930	128851930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779777438	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	43	725	1	ENST00000249373.3:c.2002C>T	p.Arg668Cys	p.R668C	ENST00000249373	NM_005631.4	668	Cgc/Tgc	12/12	1	2	FACETS	0.402	0.337	0.475	0.402	0.337	0.475	SUBCLONAL	1	TRUE	1	0.51	2		726	419	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752649	42752649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	35	617	0	ENST00000222329.4:c.1615G>A	p.Ala539Thr	p.A539T	ENST00000222329	NM_006494.2	539	Gcc/Acc	4/4	1	2	FACETS	0.314	0.257	0.378	0.314	0.257	0.378	SUBCLONAL	1	TRUE	1	0.51	2		617	437	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779091	3779091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759638164	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	86	643	1	ENST00000262367.5:c.5957C>T	p.Thr1986Met	p.T1986M	ENST00000262367	NM_004380.2	1986	aCg/aTg	31/31	1	2	FACETS	0.854	0.76	0.953	0.854	0.76	0.953	CLONAL	1	TRUE	1	0.51	2		644	395	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166285	7166285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555743340	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	36	660	0	ENST00000302850.5:c.1741C>T	p.Arg581Trp	p.R581W	ENST00000302850	NM_000208.2	581	Cgg/Tgg	8/22	1	2	FACETS	0.353	0.29	0.423	0.353	0.29	0.423	SUBCLONAL	1	TRUE	1	0.51	2		660	400	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046722	180046722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768562688	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	121	878	0	ENST00000261937.6:c.2590G>A	p.Ala864Thr	p.A864T	ENST00000261937	NM_182925.4	864	Gct/Act	18/30	1	2	FACETS	0.741	0.671	0.815	0.741	0.671	0.815	SUBCLONAL	1	TRUE	1	0.51	2		878	640	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939086	36939086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372288734	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	43	801	1	ENST00000361632.4:c.623C>T	p.Ala208Val	p.A208V	ENST00000361632		208	gCg/gTg	5/16	1	2	FACETS	0.389	0.325	0.459	0.389	0.325	0.459	SUBCLONAL	1	TRUE	1	0.51	2		802	434	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726691	41726691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776776986	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	62	700	1	ENST00000301178.4:c.236C>T	p.Ala79Val	p.A79V	ENST00000301178	NM_021913.4	79	gCg/gTg	2/20	1	2	FACETS	0.659	0.572	0.752	0.659	0.572	0.752	SUBCLONAL	1	TRUE	1	0.51	2		701	369	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857926	9857926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	30	611	0	ENST00000330684.3:c.3475C>T	p.Arg1159Cys	p.R1159C	ENST00000330684	NM_001134407.1	1159	Cgc/Tgc	13/13	1	2	FACETS	0.335	0.27	0.409	0.335	0.27	0.409	SUBCLONAL	1	TRUE	1	0.51	2		611	351	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896990	28896990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753953796	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	79	520	1	ENST00000282397.4:c.2890G>A	p.Glu964Lys	p.E964K	ENST00000282397	NM_002019.4	964	Gaa/Aaa	21/30	1	2	FACETS	0.965	0.857	1	0.965	0.857	1	CLONAL	1	TRUE	1	0.51	2		521	321	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612251	189612251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758317410	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	12	409	0	ENST00000264731.3:c.2003G>A	p.Arg668His	p.R668H	ENST00000264731	NM_003722.4	668	cGc/cAc	14/14	0.0770245185744091	0	FACETS	0.101	0.07	0.138			1	INDETERMINATE	1	TRUE	0	0.51	0		409	229	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772976	135772976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs118203721	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	15	294	0	ENST00000298552.3:c.2647G>A	p.Ala883Thr	p.A883T	ENST00000298552	NM_001162426.1	883	Gcc/Acc	21/23	1	2	FACETS	0.512	0.378	0.668	0.512	0.378	0.668	SUBCLONAL	1	TRUE	1	0.51	2		294	115	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022358	31022358	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1230703370	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	13	266	0	ENST00000375687.4:c.1843G>A	p.Ala615Thr	p.A615T	ENST00000375687	NM_015338.5	615	Gca/Aca	13/13	0.194530953000023	1	FACETS	0.24	0.172	0.323	0.24	0.172	0.323	INDETERMINATE	1	TRUE	0	0.51	1		266	158	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217662	7217662	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	29	574	1	ENST00000380728.2:c.265C>T	p.Gln89Ter	p.Q89*	ENST00000380728		89	Cag/Tag	4/11	1	2	FACETS	0.842	0.687	1	0.842	0.687	1	CLONAL	1	TRUE	1	0.51	2		575	135	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980488	70980488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267601982	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	93	706	2	ENST00000276594.2:c.889G>A	p.Gly297Arg	p.G297R	ENST00000276594	NM_024504.3	297	Gga/Aga	4/8	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.51	2		708	330	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060728	38060728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	188	1090	2	ENST00000250448.2:c.1261G>A	p.Glu421Lys	p.E421K	ENST00000250448	NM_004496.3	421	Gaa/Aaa	2/2	0.151853302930067	0	FACETS	0.635	0.59	0.681			1	INDETERMINATE	1	TRUE	0	0.51	0		1092	569	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270571	10270571	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	96	714	0	ENST00000340748.4:c.1069G>A	p.Gly357Arg	p.G357R	ENST00000340748		357	Ggg/Agg	15/40	1	2	FACETS	0.776	0.694	0.862	0.776	0.694	0.862	SUBCLONAL	1	TRUE	1	0.51	2		714	485	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012175	16012175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184177098	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	19	498	0	ENST00000268712.3:c.2107G>A	p.Ala703Thr	p.A703T	ENST00000268712	NM_006311.3	703	Gct/Act	19/46	1	2	FACETS	0.426	0.325	0.543	0.426	0.325	0.543	SUBCLONAL	1	TRUE	1	0.51	2		498	175	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340270	116340270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749738523	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	37	297	2	ENST00000397752.3:c.1132G>A	p.Val378Ile	p.V378I	ENST00000397752	NM_000245.2	378	Gtc/Atc	2/21	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.51	2		299	110	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31466354	31466354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376262500	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	90	855	1	ENST00000344624.3:c.2401C>T	p.Arg801Cys	p.R801C	ENST00000344624		801	Cgc/Tgc	16/33	1	2	FACETS	0.754	0.681	0.829	1	0.983	1	SUBCLONAL	2	TRUE	1	0.51	2		856	234	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416736	416736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748802448	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	40	302	0	ENST00000399788.2:c.3814G>A	p.Ala1272Thr	p.A1272T	ENST00000399788	NM_001042603.1	1272	Gcc/Acc	23/28	0.151853302930067	3	FACETS	1	0.907	1	0.556	0.468	0.651	INDETERMINATE	1	TRUE	1	0.51	3		302	177	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552212	29552212	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	28	458	0	ENST00000356175.3:c.1945G>T	p.Glu649Ter	p.E649*	ENST00000356175	NM_000267.3	649	Gaa/Taa	17/57	1	2	FACETS	1	0.822	1	1	0.822	1	CLONAL	1	TRUE	1	0.51	2		458	109	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105561	11105561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372078902	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	52	655	0	ENST00000358026.2:c.1477G>A	p.Val493Ile	p.V493I	ENST00000358026	NM_001128849.1	493	Gtc/Atc	9/36	1	2	FACETS	0.639	0.547	0.739	0.639	0.547	0.739	SUBCLONAL	1	TRUE	1	0.51	2		655	319	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210634	2210634	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	86	513	0	ENST00000398665.3:c.1131G>T	p.Glu377Asp	p.E377D	ENST00000398665	NM_032482.2	377	gaG/gaT	14/28	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.51	2		513	280	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020147	123020147	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	25	820	1	ENST00000355640.3:c.635C>A	p.Pro212His	p.P212H	ENST00000355640		212	cCt/cAt	2/7	0.0770245185744091	0	FACETS	0.175	0.138	0.218			1	INDETERMINATE	1	TRUE	0	0.51	0		821	274	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557831	187557831	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	43	498	0	ENST00000441802.2:c.3880G>A	p.Gly1294Arg	p.G1294R	ENST00000441802	NM_005245.3	1294	Ggg/Agg	5/27	1	2	FACETS	0.62	0.522	0.727	0.62	0.522	0.727	SUBCLONAL	1	TRUE	1	0.51	2		498	272	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932521	39932521	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	62	810	0	ENST00000378444.4:c.2078C>A	p.Pro693His	p.P693H	ENST00000378444	NM_001123385.1	693	cCt/cAt	4/15	0.0770245185744091	0	FACETS	0.329	0.285	0.376			1	INDETERMINATE	1	TRUE	0	0.51	0		810	362	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061351	38061351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	33	675	0	ENST00000250448.2:c.638G>A	p.Arg213His	p.R213H	ENST00000250448	NM_004496.3	213	cGc/cAc	2/2	0.151853302930067	0	FACETS	0.116	0.093	0.14			1	INDETERMINATE	1	TRUE	0	0.51	0		675	549	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023135	1023135	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776952629	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	46	687	1	ENST00000358495.3:c.1120G>A	p.Val374Ile	p.V374I	ENST00000358495	NM_134424.2	374	Gtt/Att	11/12	0.151853302930067	3	FACETS	0.631	0.533	0.738	0.315	0.266	0.369	INDETERMINATE	1	TRUE	1	0.51	3		688	359	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024650	11024650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	95	516	0	ENST00000327064.4:c.767C>T	p.Ser256Leu	p.S256L	ENST00000327064	NM_199141.1	256	tCg/tTg	6/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.51	2		516	276	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222513	157222513	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	29	543	0	ENST00000346085.5:c.1780C>T	p.Pro594Ser	p.P594S	ENST00000346085	NM_020732.3	594	Cca/Tca	4/20	1	2	FACETS	0.412	0.332	0.503	0.412	0.332	0.503	SUBCLONAL	1	TRUE	1	0.51	2		543	276	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451328	187451328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	46	296	0	ENST00000232014.4:c.154G>A	p.Ala52Thr	p.A52T	ENST00000232014	NM_001130845.1	52	Gcc/Acc	3/10	0.0770245185744091	0	FACETS	0.574	0.493	0.66			1	INDETERMINATE	1	TRUE	0	0.51	0		296	154	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18276985	18276985	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	14	385	0	ENST00000222254.8:c.1432C>T	p.Arg478Cys	p.R478C	ENST00000222254	NM_005027.3	478	Cgt/Tgt	12/16	1	2	FACETS	0.253	0.183	0.338	0.253	0.183	0.338	SUBCLONAL	1	TRUE	1	0.51	2		385	217	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707863	43707863	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	103	862	0	ENST00000382044.4:c.5018G>T	p.Arg1673Ile	p.R1673I	ENST00000382044	NM_001141980.1	1673	aGa/aTa	23/28	0.194530953000023	1	FACETS	0.725	0.653	0.8	0.725	0.653	0.8	INDETERMINATE	1	TRUE	0	0.51	1		862	415	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006636	62006636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369201285	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	41	724	0	ENST00000392795.3:c.643C>T	p.Arg215Trp	p.R215W	ENST00000392795	NM_001039933.1	215	Cgg/Tgg	6/6	1	2	FACETS	0.445	0.372	0.527	0.445	0.372	0.527	SUBCLONAL	1	TRUE	1	0.51	2		724	361	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845938	72845938	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	55	367	0	ENST00000268489.5:c.3530-1G>A		p.X1177_splice	ENST00000268489	NM_006885.3	1177			1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.51	2		367	173	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466773	25466773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1431156021	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	108	555	0	ENST00000264709.3:c.1930G>A	p.Ala644Thr	p.A644T	ENST00000264709	NM_175629.2	644	Gct/Act	16/23	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.51	2		555	373	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1956968	1956968	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143360610	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	34	622	2	ENST00000382891.5:c.2419G>A	p.Ala807Thr	p.A807T	ENST00000382891	NM_133335.3	807	Gcc/Acc	13/22	1	2	FACETS	0.269	0.219	0.325	0.269	0.219	0.325	SUBCLONAL	1	TRUE	1	0.51	2		624	496	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274136	10274136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866582475	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	39	575	0	ENST00000330684.3:c.133G>A	p.Asp45Asn	p.D45N	ENST00000330684	NM_001134407.1	45	Gac/Aac	2/13	1	2	FACETS	0.373	0.309	0.444	0.373	0.309	0.444	SUBCLONAL	1	TRUE	1	0.51	2		575	410	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933047	39933047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	81	882	1	ENST00000378444.4:c.1552G>A	p.Glu518Lys	p.E518K	ENST00000378444	NM_001123385.1	518	Gaa/Aaa	4/15	0.0770245185744091	0	FACETS	0.458	0.406	0.512			1	INDETERMINATE	1	TRUE	0	0.51	0		883	340	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784981	9784981	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	89	508	0	ENST00000377346.4:c.2984T>G	p.Ile995Ser	p.I995S	ENST00000377346	NM_005026.3	995	aTc/aGc	23/24	1	2	FACETS	0.893	0.797	0.993	0.893	0.797	0.993	CLONAL	1	TRUE	1	0.51	2		508	391	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259324	11259324	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	11	537	0	ENST00000361445.4:c.4244C>A	p.Ser1415Tyr	p.S1415Y	ENST00000361445	NM_004958.3	1415	tCt/tAt	28/58	1	2	FACETS	0.229	0.158	0.318	0.229	0.158	0.318	SUBCLONAL	1	TRUE	1	0.51	2		537	188	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259743	11259743	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	28	360	0	ENST00000361445.4:c.3962C>T	p.Ala1321Val	p.A1321V	ENST00000361445	NM_004958.3	1321	gCa/gTa	27/58	1	2	FACETS	1	0.829	1	1	0.829	1	CLONAL	1	TRUE	1	0.51	2		360	108	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11264638	11264638	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	42	565	0	ENST00000361445.4:c.3924G>T	p.Gln1308His	p.Q1308H	ENST00000361445	NM_004958.3	1308	caG/caT	26/58	1	2	FACETS	0.377	0.315	0.446	0.377	0.315	0.446	SUBCLONAL	1	TRUE	1	0.51	2		565	437	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294225	11294225	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753826002	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	73	554	1	ENST00000361445.4:c.2306G>A	p.Arg769His	p.R769H	ENST00000361445	NM_004958.3	769	cGc/cAc	14/58	1	2	FACETS	0.929	0.82	1	0.929	0.82	1	CLONAL	1	TRUE	1	0.51	2		555	308	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199484	16199484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	27	369	0	ENST00000375759.3:c.257G>A	p.Ser86Asn	p.S86N	ENST00000375759	NM_015001.2	86	aGt/aAt	2/15	1	2	FACETS	0.638	0.513	0.778	0.638	0.513	0.778	SUBCLONAL	1	TRUE	1	0.51	2		369	166	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255769	16255769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	11	337	0	ENST00000375759.3:c.3034G>A	p.Ala1012Thr	p.A1012T	ENST00000375759	NM_015001.2	1012	Gct/Act	11/15	1	2	FACETS	0.241	0.166	0.333	0.241	0.166	0.333	SUBCLONAL	1	TRUE	1	0.51	2		337	179	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256456	16256456	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770680602	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	32	578	1	ENST00000375759.3:c.3721C>T	p.Arg1241Ter	p.R1241*	ENST00000375759	NM_015001.2	1241	Cga/Tga	11/15	1	2	FACETS	0.756	0.621	0.904	0.756	0.621	0.904	CLONAL	1	TRUE	1	0.51	2		579	166	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258647	16258647	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	50	398	0	ENST00000375759.3:c.5912C>A	p.Pro1971His	p.P1971H	ENST00000375759	NM_015001.2	1971	cCt/cAt	11/15	1	2	FACETS	0.654	0.558	0.757	0.654	0.558	0.757	SUBCLONAL	1	TRUE	1	0.51	2		398	300	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259930	16259930	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	21	538	1	ENST00000375759.3:c.7195A>G	p.Thr2399Ala	p.T2399A	ENST00000375759	NM_015001.2	2399	Act/Gct	11/15	1	2	FACETS	0.518	0.402	0.651	0.518	0.402	0.651	SUBCLONAL	1	TRUE	1	0.51	2		539	159	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260417	16260417	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	58	480	1	ENST00000375759.3:c.7682C>A	p.Pro2561His	p.P2561H	ENST00000375759	NM_015001.2	2561	cCt/cAt	11/15	1	2	FACETS	0.677	0.585	0.776	0.677	0.585	0.776	SUBCLONAL	1	TRUE	1	0.51	2		481	336	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261086	16261086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752729354	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	95	393	0	ENST00000375759.3:c.8351G>A	p.Arg2784Gln	p.R2784Q	ENST00000375759	NM_015001.2	2784	cGg/cAg	11/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.51	2		393	305	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262084	16262084	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	12	304	0	ENST00000375759.3:c.9349C>A	p.Leu3117Ile	p.L3117I	ENST00000375759	NM_015001.2	3117	Ctt/Att	11/15	1	2	FACETS	0.218	0.153	0.298	0.218	0.153	0.298	SUBCLONAL	1	TRUE	1	0.51	2		304	216	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264481	16264481	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	88	517	0	ENST00000375759.3:c.10684G>T	p.Gly3562Trp	p.G3562W	ENST00000375759	NM_015001.2	3562	Ggg/Tgg	13/15	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.51	2		517	337	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023806	27023806	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	22	415	0	ENST00000324856.7:c.913del	p.Ala305ProfsTer58	p.A305Pfs*58	ENST00000324856	NM_006015.4	304	tcG/tc	1/20	1	2	FACETS	0.208	0.161	0.264	0.208	0.161	0.264	SUBCLONAL	1	TRUE	1	0.51	2		415	414	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099988	27099988	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	66	626	0	ENST00000324856.7:c.3866+1G>A		p.X1289_splice	ENST00000324856	NM_006015.4	1289			1	2	FACETS	0.952	0.835	1	0.952	0.835	1	CLONAL	1	TRUE	1	0.51	2		626	272	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106114	27106114	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	24	483	1	ENST00000324856.7:c.5725G>T	p.Ala1909Ser	p.A1909S	ENST00000324856	NM_006015.4	1909	Gcc/Tcc	20/20	1	2	FACETS	0.55	0.435	0.681	0.55	0.435	0.681	SUBCLONAL	1	TRUE	1	0.51	2		484	171	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106316	27106316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	103	610	0	ENST00000324856.7:c.5927C>T	p.Ser1976Phe	p.S1976F	ENST00000324856	NM_006015.4	1976	tCt/tTt	20/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.51	2		610	313	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106973	27106973	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	71	464	0	ENST00000324856.7:c.6584T>G	p.Leu2195Arg	p.L2195R	ENST00000324856	NM_006015.4	2195	cTc/cGc	20/20	1	2	FACETS	0.862	0.758	0.972	0.862	0.758	0.972	CLONAL	1	TRUE	1	0.51	2		464	323	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28586390	28586390	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	103	515	0	ENST00000253063.3:c.32A>G	p.Glu11Gly	p.E11G	ENST00000253063	NM_031459.4	11	gAg/gGg	1/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.51	2		515	343	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935417	36935417	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	35	748	0	ENST00000361632.4:c.1310C>A	p.Ala437Asp	p.A437D	ENST00000361632		437	gCc/gAc	10/16	1	2	FACETS	0.28	0.229	0.338	0.28	0.229	0.338	SUBCLONAL	1	TRUE	1	0.51	2		748	490	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937078	36937078	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	95	545	0	ENST00000361632.4:c.1241C>A	p.Ala414Asp	p.A414D	ENST00000361632		414	gCc/gAc	9/16	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.51	2		545	334	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43806077	43806077	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	77	731	0	ENST00000372470.3:c.873C>A	p.Cys291Ter	p.C291*	ENST00000372470	NM_005373.2	291	tgC/tgA	6/12	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.51	2		731	259	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46715742	46715742	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	27	567	2	ENST00000371975.4:c.161C>A	p.Pro54His	p.P54H	ENST00000371975	NM_003579.3	54	cCt/cAt	3/18	1	2	FACETS	0.499	0.4	0.612	0.499	0.4	0.612	SUBCLONAL	1	TRUE	1	0.51	2		569	212	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743633	46743633	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	26	668	1	ENST00000371975.4:c.2014C>A	p.Leu672Ile	p.L672I	ENST00000371975	NM_003579.3	672	Ctc/Atc	17/18	1	2	FACETS	0.335	0.266	0.415	0.335	0.266	0.415	SUBCLONAL	1	TRUE	1	0.51	2		669	304	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873233	71873233	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	14	308	0	ENST00000357731.5:c.961G>A	p.Gly321Arg	p.G321R	ENST00000357731	NM_173808.2	321	Gga/Aga	7/7	1	2	FACETS	0.678	0.498	0.886	0.678	0.498	0.886	SUBCLONAL	1	TRUE	1	0.51	2		308	81	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429394	78429394	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	10	335	2	ENST00000370768.2:c.1048A>G	p.Asn350Asp	p.N350D	ENST00000370768	NM_003902.3	350	Aat/Gat	13/20	1	2	FACETS	0.269	0.182	0.376	0.269	0.182	0.376	SUBCLONAL	1	TRUE	1	0.51	2		337	146	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266612	115266612	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs142765084	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	10	608	0	ENST00000438362.2:c.1903A>G	p.Thr635Ala	p.T635A	ENST00000438362	NM_001242891.1	635	Act/Gct	16/20	1	2	FACETS	0.26	0.176	0.364	0.26	0.176	0.364	SUBCLONAL	1	TRUE	1	0.51	2		608	151	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268832	115268832	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	37	529	0	ENST00000438362.2:c.1778G>T	p.Ser593Ile	p.S593I	ENST00000438362	NM_001242891.1	593	aGt/aTt	14/20	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.51	2		529	135	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458368	120458368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	59	511	0	ENST00000256646.2:c.6977C>T	p.Ser2326Phe	p.S2326F	ENST00000256646	NM_024408.3	2326	tCc/tTc	34/34	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.51	2		511	230	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459307	120459307	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	21	325	0	ENST00000256646.2:c.6038C>A	p.Pro2013His	p.P2013H	ENST00000256646	NM_024408.3	2013	cCt/cAt	34/34	1	2	FACETS	0.597	0.464	0.747	0.597	0.464	0.747	SUBCLONAL	1	TRUE	1	0.51	2		325	138	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120460297	120460297	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	19	470	0	ENST00000256646.2:c.6018G>T	p.Gln2006His	p.Q2006H	ENST00000256646	NM_024408.3	2006	caG/caT	33/34	1	2	FACETS	0.291	0.221	0.373	0.291	0.221	0.373	SUBCLONAL	1	TRUE	1	0.51	2		470	256	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462975	120462975	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1435723160	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	21	505	1	ENST00000256646.2:c.5356C>T	p.Arg1786Ter	p.R1786*	ENST00000256646	NM_024408.3	1786	Cga/Tga	30/34	1	2	FACETS	0.261	0.201	0.332	0.261	0.201	0.332	SUBCLONAL	1	TRUE	1	0.51	2		506	315	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471799	120471799	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1366907623	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	25	328	0	ENST00000256646.2:c.3692G>A	p.Arg1231Gln	p.R1231Q	ENST00000256646	NM_024408.3	1231	cGg/cAg	23/34	1	2	FACETS	0.748	0.598	0.916	0.748	0.598	0.916	CLONAL	1	TRUE	1	0.51	2		328	131	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120478115	120478115	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	20	400	0	ENST00000256646.2:c.3635C>A	p.Ser1212Tyr	p.S1212Y	ENST00000256646	NM_024408.3	1212	tCt/tAt	22/34	1	2	FACETS	0.513	0.395	0.648	0.513	0.395	0.648	SUBCLONAL	1	TRUE	1	0.51	2		400	153	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874544	155874544	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	18	492	0	ENST00000368323.3:c.215A>T	p.Asp72Val	p.D72V	ENST00000368323	NM_006912.5	72	gAc/gTc	4/6	1	2	FACETS	0.344	0.26	0.443	0.344	0.26	0.443	SUBCLONAL	1	TRUE	1	0.51	2		492	205	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834196	156834196	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	142	834	0	ENST00000524377.1:c.263G>T	p.Arg88Met	p.R88M	ENST00000524377	NM_002529.3	88	aGg/aTg	2/17	1	2	FACETS	0.848	0.775	0.924	0.848	0.775	0.924	CLONAL	1	TRUE	1	0.51	2		834	657	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161310401	161310401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760572684	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	16	467	0	ENST00000367975.2:c.197C>T	p.Ala66Val	p.A66V	ENST00000367975	NM_003001.3	66	gCg/gTg	4/6	1	2	FACETS	0.376	0.279	0.49	0.376	0.279	0.49	SUBCLONAL	1	TRUE	1	0.51	2		467	167	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725046	162725046	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	63	462	0	ENST00000367921.3:c.518C>T	p.Ser173Phe	p.S173F	ENST00000367921	NM_006182.2	173	tCc/tTc	6/18	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.51	2		462	214	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652384	206652384	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	127	675	0	ENST00000367120.3:c.1091G>T	p.Ser364Ile	p.S364I	ENST00000367120	NM_014002.3	364	aGc/aTc	10/22	1	2	FACETS	0.786	0.713	0.861	0.786	0.713	0.861	SUBCLONAL	1	TRUE	1	0.51	2		675	634	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944296	206944296	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	78	532	0	ENST00000423557.1:c.334C>A	p.Leu112Met	p.L112M	ENST00000423557	NM_000572.2	112	Ctg/Atg	3/5	1	2	FACETS	0.803	0.71	0.902	0.803	0.71	0.902	CLONAL	1	TRUE	1	0.51	2		532	381	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612662	228612662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	71	734	0	ENST00000366696.1:c.365C>A	p.Pro122His	p.P122H	ENST00000366696	NM_003493.2	122	cCt/cAt	1/1	1	2	FACETS	0.585	0.512	0.663	0.585	0.512	0.663	SUBCLONAL	1	TRUE	1	0.51	2		734	476	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680525	241680525	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	54	514	0	ENST00000366560.3:c.224C>A	p.Ser75Tyr	p.S75Y	ENST00000366560	NM_000143.3	75	tCt/tAt	2/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.51	2		514	158	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100481	8100481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	145	834	0	ENST00000346208.3:c.455C>T	p.Thr152Ile	p.T152I	ENST00000346208		152	aCc/aTc	3/6	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.51	2		834	545	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333783	70333783	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	15	562	0	ENST00000373644.4:c.1688C>A	p.Thr563Asn	p.T563N	ENST00000373644	NM_030625.2	563	aCt/aAt	2/12	1	2	FACETS	0.308	0.226	0.406	0.308	0.226	0.406	SUBCLONAL	1	TRUE	1	0.51	2		562	191	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406432	70406432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779743688	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	18	631	0	ENST00000373644.4:c.3946G>A	p.Asp1316Asn	p.D1316N	ENST00000373644	NM_030625.2	1316	Gat/Aat	4/12	1	2	FACETS	0.234	0.176	0.302	0.234	0.176	0.302	SUBCLONAL	1	TRUE	1	0.51	2		631	302	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70432705	70432705	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	15	532	0	ENST00000373644.4:c.4727C>A	p.Ser1576Tyr	p.S1576Y	ENST00000373644	NM_030625.2	1576	tCt/tAt	8/12	1	2	FACETS	0.354	0.26	0.466	0.354	0.26	0.466	SUBCLONAL	1	TRUE	1	0.51	2		532	166	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450831	70450831	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775369384	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	106	510	0	ENST00000373644.4:c.5671G>A	p.Ala1891Thr	p.A1891T	ENST00000373644	NM_030625.2	1891	Gcc/Acc	12/12	1	2	FACETS	0.764	0.696	0.834	1	0.986	1	SUBCLONAL	2	TRUE	1	0.51	2		510	272	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681315	88681315	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	19	495	0	ENST00000372037.3:c.1205T>C	p.Val402Ala	p.V402A	ENST00000372037	NM_004329.2	402	gTg/gCg	11/13	1	2	FACETS	0.51	0.391	0.648	0.51	0.391	0.648	SUBCLONAL	1	TRUE	1	0.51	2		495	146	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274827	123274827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	13	418	0	ENST00000358487.5:c.1091G>A	p.Gly364Glu	p.G364E	ENST00000358487	NM_000141.4	364	gGa/gAa	9/18	1	2	FACETS	0.378	0.271	0.506	0.378	0.271	0.506	SUBCLONAL	1	TRUE	1	0.51	2		418	135	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279609	123279609	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	23	544	1	ENST00000358487.5:c.823G>T	p.Glu275Ter	p.E275*	ENST00000358487	NM_000141.4	275	Gag/Tag	7/18	1	2	FACETS	0.26	0.202	0.327	0.26	0.202	0.327	SUBCLONAL	1	TRUE	1	0.51	2		545	347	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325077	123325077	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs144714823	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	63	645	2	ENST00000358487.5:c.251G>T	p.Arg84Met	p.R84M	ENST00000358487	NM_000141.4	84	aGg/aTg	3/18	1	2	FACETS	0.77	0.67	0.876	0.77	0.67	0.876	SUBCLONAL	1	TRUE	1	0.51	2		647	321	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154812	2154812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	28	858	0	ENST00000434045.2:c.409G>A	p.Glu137Lys	p.E137K	ENST00000434045	NM_001127598.1	137	Gag/Aag	4/5	1	2	FACETS	0.235	0.187	0.29	0.235	0.187	0.29	SUBCLONAL	1	TRUE	1	0.51	2		858	467	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450159	32450159	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	28	531	0	ENST00000332351.3:c.653G>T	p.Ser218Ile	p.S218I	ENST00000332351	NM_024426.4	218	aGc/aTc	2/10	1	2	FACETS	0.268	0.214	0.33	0.268	0.214	0.33	SUBCLONAL	1	TRUE	1	0.51	2		531	409	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128999	64128999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs565625025	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	37	661	0	ENST00000334205.4:c.629G>A	p.Arg210His	p.R210H	ENST00000334205	NM_003942.2	210	cGt/cAt	6/17	1	2	FACETS	0.416	0.343	0.496	0.416	0.343	0.496	SUBCLONAL	1	TRUE	1	0.51	2		661	349	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138851	64138851	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780033520	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	45	471	0	ENST00000334205.4:c.2218G>A	p.Ala740Thr	p.A740T	ENST00000334205	NM_003942.2	740	Gcc/Acc	17/17	1	2	FACETS	0.341	0.286	0.402	0.341	0.286	0.402	SUBCLONAL	1	TRUE	1	0.51	2		471	517	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936176	71936176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	133	370	0	ENST00000298229.2:c.148G>A	p.Glu50Lys	p.E50K	ENST00000298229	NM_001567.3	50	Gag/Aag	1/28	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.51	2		370	428	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939479	71939479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775305188	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	202	950	1	ENST00000298229.2:c.334G>A	p.Ala112Thr	p.A112T	ENST00000298229	NM_001567.3	112	Gcc/Acc	3/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.51	2		951	719	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942562	71942562	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	29	464	0	ENST00000298229.2:c.1518G>T	p.Trp506Cys	p.W506C	ENST00000298229	NM_001567.3	506	tgG/tgT	13/28	1	2	FACETS	0.58	0.469	0.704	0.58	0.469	0.704	SUBCLONAL	1	TRUE	1	0.51	2		464	196	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946381	71946381	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	29	839	0	ENST00000298229.2:c.2545G>A	p.Ala849Thr	p.A849T	ENST00000298229	NM_001567.3	849	Gcc/Acc	23/28	1	2	FACETS	0.228	0.183	0.281	0.228	0.183	0.281	SUBCLONAL	1	TRUE	1	0.51	2		839	498	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090365	77090365	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	50	632	1	ENST00000356341.3:c.360C>A	p.Asn120Lys	p.N120K	ENST00000356341	NM_002576.4	120	aaC/aaA	4/15	1	2	FACETS	0.751	0.643	0.868	0.751	0.643	0.868	SUBCLONAL	1	TRUE	1	0.51	2		633	261	SUCCESS
EED	8726	MSKCC	GRCh37	11	85966331	85966331	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	19	291	0	ENST00000263360.6:c.426+2T>C		p.X142_splice	ENST00000263360	NM_003797.3	142			1	2	FACETS	0.847	0.656	1	0.847	0.656	1	CLONAL	1	TRUE	1	0.51	2		291	88	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94910925	94910925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749067368	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	27	549	3	ENST00000536441.1:c.1205G>A	p.Arg402His	p.R402H	ENST00000536441	NM_144665.3	402	cGc/cAc	8/10	1	2	FACETS	0.847	0.685	1	0.847	0.685	1	CLONAL	1	TRUE	1	0.51	2		552	125	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924731	94924731	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	13	653	0	ENST00000536441.1:c.179A>G	p.Asn60Ser	p.N60S	ENST00000536441	NM_144665.3	60	aAc/aGc	3/10	1	2	FACETS	0.257	0.184	0.347	0.257	0.184	0.347	SUBCLONAL	1	TRUE	1	0.51	2		653	198	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102056847	102056847	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	27	367	0	ENST00000282441.5:c.787C>A	p.Leu263Ile	p.L263I	ENST00000282441	NM_001130145.2	263	Ctt/Att	4/9	1	2	FACETS	0.834	0.674	1	0.834	0.674	1	CLONAL	1	TRUE	1	0.51	2		367	127	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076639	102076639	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	51	313	0	ENST00000282441.5:c.818T>G	p.Ile273Ser	p.I273S	ENST00000282441	NM_001130145.2	273	aTc/aGc	5/9	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.51	2		313	171	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100439	102100439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs979593484	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	42	400	0	ENST00000282441.5:c.1283C>T	p.Thr428Ile	p.T428I	ENST00000282441	NM_001130145.2	428	aCt/aTt	9/9	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.51	2		400	134	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195539	102195539	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	14	540	0	ENST00000263464.3:c.299A>C	p.Asn100Thr	p.N100T	ENST00000263464	NM_001165.4	100	aAt/aCt	2/9	1	2	FACETS	0.398	0.289	0.527	0.398	0.289	0.527	SUBCLONAL	1	TRUE	1	0.51	2		540	138	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123557	108123557	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	24	437	0	ENST00000278616.4:c.1816C>A	p.Leu606Ile	p.L606I	ENST00000278616	NM_000051.3	606	Ctt/Att	12/63	1	2	FACETS	0.896	0.716	1	0.896	0.716	1	CLONAL	1	TRUE	1	0.51	2		437	105	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196910	108196910	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	23	370	0	ENST00000278616.4:c.6933T>G	p.Ile2311Met	p.I2311M	ENST00000278616	NM_000051.3	2311	atT/atG	47/63	1	2	FACETS	0.673	0.531	0.833	0.673	0.531	0.833	SUBCLONAL	1	TRUE	1	0.51	2		370	134	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307578	118307578	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	28	647	0	ENST00000534358.1:c.351G>T	p.Gln117His	p.Q117H	ENST00000534358	NM_005933.3	117	caG/caT	1/36	1	2	FACETS	0.245	0.195	0.301	0.245	0.195	0.301	SUBCLONAL	1	TRUE	1	0.51	2		647	449	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342681	118342681	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	12	203	0	ENST00000534358.1:c.807G>T	p.Lys269Asn	p.K269N	ENST00000534358	NM_005933.3	269	aaG/aaT	3/36	1	2	FACETS	1	0.728	1	1	0.728	1	CLONAL	1	TRUE	1	0.51	2		203	47	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343169	118343169	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	10	329	0	ENST00000534358.1:c.1295A>G	p.Glu432Gly	p.E432G	ENST00000534358	NM_005933.3	432	gAg/gGg	3/36	1	2	FACETS	0.327	0.222	0.456	0.327	0.222	0.456	SUBCLONAL	1	TRUE	1	0.51	2		329	120	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374322	118374322	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	28	350	0	ENST00000534358.1:c.7715C>A	p.Pro2572Gln	p.P2572Q	ENST00000534358	NM_005933.3	2572	cCa/cAa	27/36	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.51	2		350	88	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156247	119156247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772002109	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	40	399	0	ENST00000264033.4:c.1912G>A	p.Gly638Arg	p.G638R	ENST00000264033	NM_005188.3	638	Gga/Aga	11/16	1	2	FACETS	0.8	0.673	0.939	0.8	0.673	0.939	CLONAL	1	TRUE	1	0.51	2		399	196	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	401941	401941	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	20	374	0	ENST00000399788.2:c.4850G>T	p.Arg1617Met	p.R1617M	ENST00000399788	NM_001042603.1	1617	aGg/aTg	27/28	0.151853302930067	3	FACETS	0.458	0.351	0.582	0.229	0.175	0.291	INDETERMINATE	1	TRUE	1	0.51	3		374	215	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	463357	463357	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	19	304	0	ENST00000399788.2:c.914A>C	p.Glu305Ala	p.E305A	ENST00000399788	NM_001042603.1	305	gAa/gCa	8/28	0.151853302930067	3	FACETS	1	0.854	1	0.57	0.443	0.713	INDETERMINATE	1	TRUE	1	0.51	3		304	82	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245424	46245424	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	32	401	0	ENST00000334344.6:c.3518C>A	p.Thr1173Asn	p.T1173N	ENST00000334344	NM_152641.2	1173	aCc/aAc	15/21	0.151853302930067	3	FACETS	1	0.943	1	0.691	0.573	0.817	INDETERMINATE	1	TRUE	1	0.51	3		401	114	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285661	46285661	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	52	480	0	ENST00000334344.6:c.5021C>A	p.Pro1674His	p.P1674H	ENST00000334344	NM_152641.2	1674	cCt/cAt	17/21	0.151853302930067	3	FACETS	1	0.965	1	0.703	0.608	0.803	INDETERMINATE	1	TRUE	1	0.51	3		480	182	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298853	46298853	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	11	233	0	ENST00000334344.6:c.5500C>A	p.Leu1834Met	p.L1834M	ENST00000334344	NM_152641.2	1834	Ctg/Atg	21/21	0.151853302930067	3	FACETS	0.785	0.552	1	0.392	0.276	0.531	INDETERMINATE	1	TRUE	1	0.51	3		233	69	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420184	49420184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555185701	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	81	676	0	ENST00000301067.7:c.15565G>A	p.Gly5189Arg	p.G5189R	ENST00000301067	NM_003482.3	5189	Gga/Aga	48/54	0.151853302930067	3	FACETS	0.961	0.851	1	0.48	0.425	0.539	INDETERMINATE	1	TRUE	1	0.51	3		676	415	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426345	49426345	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs527255553	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	38	977	1	ENST00000301067.7:c.12143C>T	p.Pro4048Leu	p.P4048L	ENST00000301067	NM_003482.3	4048	cCg/cTg	39/54	0.151853302930067	3	FACETS	0.476	0.394	0.567	0.238	0.197	0.284	INDETERMINATE	1	TRUE	1	0.51	3		978	393	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433065	49433065	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	102	696	0	ENST00000301067.7:c.8306A>G	p.Asp2769Gly	p.D2769G	ENST00000301067	NM_003482.3	2769	gAt/gGt	33/54	0.151853302930067	3	FACETS	1	0.945	1	0.539	0.484	0.596	INDETERMINATE	1	TRUE	1	0.51	3		696	466	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433312	49433312	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	39	649	0	ENST00000301067.7:c.8135G>T	p.Gly2712Val	p.G2712V	ENST00000301067	NM_003482.3	2712	gGa/gTa	32/54	0.151853302930067	3	FACETS	0.486	0.403	0.578	0.243	0.201	0.289	INDETERMINATE	1	TRUE	1	0.51	3		649	395	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434397	49434397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs967482995	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	36	707	1	ENST00000301067.7:c.7156C>T	p.Arg2386Trp	p.R2386W	ENST00000301067	NM_003482.3	2386	Cgg/Tgg	31/54	0.151853302930067	3	FACETS	0.411	0.338	0.493	0.206	0.169	0.247	INDETERMINATE	1	TRUE	1	0.51	3		708	431	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439909	49439909	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs767596564	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	74	634	0	ENST00000301067.7:c.4632G>T	p.Glu1544Asp	p.E1544D	ENST00000301067	NM_003482.3	1544	gaG/gaT	17/54	0.151853302930067	3	FACETS	0.886	0.779	1	0.443	0.389	0.5	INDETERMINATE	1	TRUE	1	0.51	3		634	411	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487594	56487594	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	87	542	0	ENST00000267101.3:c.1527C>A	p.Cys509Ter	p.C509*	ENST00000267101	NM_001982.3	509	tgC/tgA	13/28	0.151853302930067	3	FACETS	1	0.933	1	0.533	0.474	0.594	INDETERMINATE	1	TRUE	1	0.51	3		542	402	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494905	56494905	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	29	561	1	ENST00000267101.3:c.3262C>T	p.Pro1088Ser	p.P1088S	ENST00000267101	NM_001982.3	1088	Cca/Tca	27/28	0.151853302930067	3	FACETS	0.383	0.307	0.469	0.191	0.153	0.235	INDETERMINATE	1	TRUE	1	0.51	3		562	373	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861259	57861259	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	30	458	0	ENST00000228682.2:c.1056G>T	p.Gln352His	p.Q352H	ENST00000228682	NM_005269.2	352	caG/caT	9/12	0.151853302930067	3	FACETS	0.531	0.429	0.646	0.266	0.214	0.323	INDETERMINATE	1	TRUE	1	0.51	3		458	278	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233540	69233540	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	22	325	0	ENST00000462284.1:c.1405A>G	p.Thr469Ala	p.T469A	ENST00000462284	NM_002392.5	469	Aca/Gca	11/11	0.151853302930067	3	FACETS	0.846	0.68	1	0.846	0.68	1	INDETERMINATE	2	TRUE	1	0.51	3		325	64	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856200	111856200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1365917986	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	181	249	0	ENST00000341259.2:c.251C>T	p.Ala84Val	p.A84V	ENST00000341259	NM_005475.2	84	gCg/gTg	2/8	0.151853302930067	3	FACETS	0.909	0.846	0.973	0.909	0.846	0.973	INDETERMINATE	2	TRUE	1	0.51	3		249	490	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924290	112924290	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	46	552	1	ENST00000351677.2:c.1236G>T	p.Glu412Asp	p.E412D	ENST00000351677	NM_002834.3	412	gaG/gaT	11/16	0.151853302930067	3	FACETS	0.597	0.504	0.7	0.299	0.252	0.35	INDETERMINATE	1	TRUE	1	0.51	3		553	379	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926873	112926873	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	31	725	1	ENST00000351677.2:c.1493G>A	p.Arg498Gln	p.R498Q	ENST00000351677	NM_002834.3	498	cGg/cAg	13/16	0.151853302930067	3	FACETS	0.7	0.57	0.845	0.35	0.285	0.423	INDETERMINATE	1	TRUE	1	0.51	3		726	218	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112376	115112376	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	41	455	0	ENST00000257566.3:c.1364G>T	p.Arg455Met	p.R455M	ENST00000257566	NM_016569.3	455	aGg/aTg	7/8	0.151853302930067	3	FACETS	0.397	0.33	0.471	0.199	0.165	0.236	INDETERMINATE	1	TRUE	1	0.51	3		455	508	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120783981	120783981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	152	802	0	ENST00000257552.2:c.1004C>T	p.Ala335Val	p.A335V	ENST00000257552	NM_002442.3	335	gCc/gTc	13/15	0.151853302930067	3	FACETS	1	0.97	1	0.56	0.513	0.608	INDETERMINATE	1	TRUE	1	0.51	3		802	668	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123880968	123880968	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	32	256	0	ENST00000330479.4:c.586G>T	p.Ala196Ser	p.A196S	ENST00000330479	NM_020382.3	196	Gcc/Tcc	5/9	0.151853302930067	3	FACETS	0.895	0.734	1	0.447	0.367	0.536	INDETERMINATE	1	TRUE	1	0.51	3		256	176	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212575	133212575	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	19	478	0	ENST00000320574.5:c.5714T>G	p.Ile1905Ser	p.I1905S	ENST00000320574	NM_006231.2	1905	aTt/aGt	42/49	0.151853302930067	3	FACETS	0.547	0.417	0.697	0.273	0.208	0.349	INDETERMINATE	1	TRUE	1	0.51	3		478	171	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218901	133218901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768244569	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	108	799	0	ENST00000320574.5:c.5035C>T	p.Arg1679Cys	p.R1679C	ENST00000320574	NM_006231.2	1679	Cgc/Tgc	38/49	0.151853302930067	3	FACETS	0.961	0.866	1	0.481	0.433	0.531	INDETERMINATE	1	TRUE	1	0.51	3		799	553	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219420	133219420	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	95	902	0	ENST00000320574.5:c.4714C>A	p.Leu1572Met	p.L1572M	ENST00000320574	NM_006231.2	1572	Ctg/Atg	36/49	0.151853302930067	3	FACETS	0.794	0.708	0.885	0.397	0.354	0.443	INDETERMINATE	1	TRUE	1	0.51	3		902	589	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225918	133225918	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	116	834	0	ENST00000320574.5:c.3979C>A	p.Leu1327Met	p.L1327M	ENST00000320574	NM_006231.2	1327	Ctg/Atg	31/49	0.151853302930067	3	FACETS	1	0.972	1	0.596	0.54	0.654	INDETERMINATE	1	TRUE	1	0.51	3		834	479	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252327	133252327	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	58	408	0	ENST00000320574.5:c.1100T>C	p.Phe367Ser	p.F367S	ENST00000320574	NM_006231.2	367	tTt/tCt	11/49	0.151853302930067	3	FACETS	0.759	0.664	0.859	0.759	0.664	0.859	INDETERMINATE	2	TRUE	1	0.51	3		408	188	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557761	21557761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	53	700	0	ENST00000382592.4:c.2084C>T	p.Ala695Val	p.A695V	ENST00000382592	NM_014572.2	695	gCc/gTc	5/8	1	2	FACETS	0.62	0.532	0.717	0.62	0.532	0.717	SUBCLONAL	1	TRUE	1	0.51	2		700	335	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923319	26923319	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	17	314	0	ENST00000381527.3:c.315G>T	p.Trp105Cys	p.W105C	ENST00000381527	NM_001260.1	105	tgG/tgT	3/13	1	2	FACETS	0.766	0.583	0.975	0.766	0.583	0.975	CLONAL	1	TRUE	1	0.51	2		314	87	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636179	28636179	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	53	409	0	ENST00000241453.7:c.193T>C	p.Cys65Arg	p.C65R	ENST00000241453	NM_004119.2	65	Tgt/Cgt	3/24	1	2	FACETS	0.596	0.51	0.688	0.596	0.51	0.688	SUBCLONAL	1	TRUE	1	0.51	2		409	349	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959139	28959139	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	19	405	0	ENST00000282397.4:c.1999C>A	p.Leu667Ile	p.L667I	ENST00000282397	NM_002019.4	667	Ctc/Atc	14/30	1	2	FACETS	0.475	0.363	0.604	0.475	0.363	0.604	SUBCLONAL	1	TRUE	1	0.51	2		405	157	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964121	28964121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139586546	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	24	479	0	ENST00000282397.4:c.1781C>T	p.Thr594Ile	p.T594I	ENST00000282397	NM_002019.4	594	aCa/aTa	13/30	1	2	FACETS	0.702	0.558	0.864	0.702	0.558	0.864	SUBCLONAL	1	TRUE	1	0.51	2		479	134	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004265	29004265	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	17	385	0	ENST00000282397.4:c.1028T>C	p.Val343Ala	p.V343A	ENST00000282397	NM_002019.4	343	gTg/gCg	8/30	1	2	FACETS	0.338	0.253	0.439	0.338	0.253	0.439	SUBCLONAL	1	TRUE	1	0.51	2		385	197	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914274	32914274	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs56253082	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	14	491	0	ENST00000380152.3:c.5782G>T	p.Glu1928Ter	p.E1928*	ENST00000380152		1928	Gaa/Taa	11/27	1	2	FACETS	0.858	0.636	1	0.858	0.636	1	CLONAL	1	TRUE	1	0.51	2		491	64	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133946	41133946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	39	481	0	ENST00000379561.5:c.1682C>A	p.Pro561His	p.P561H	ENST00000379561	NM_002015.3	561	cCt/cAt	2/3	1	2	FACETS	0.627	0.523	0.741	0.627	0.523	0.741	SUBCLONAL	1	TRUE	1	0.51	2		481	244	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240088	41240088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	27	69	0	ENST00000379561.5:c.262G>A	p.Gly88Ser	p.G88S	ENST00000379561	NM_002015.3	88	Ggc/Agc	1/3	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.51	2		69	79	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281756	49281756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	32	817	0	ENST00000282018.3:c.803C>T	p.Thr268Ile	p.T268I	ENST00000282018	NM_020377.2	268	aCc/aTc	1/1	1	2	FACETS	0.506	0.413	0.61	0.506	0.413	0.61	SUBCLONAL	1	TRUE	1	0.51	2		817	248	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436042	110436042	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1255254387	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	162	915	0	ENST00000375856.3:c.2359G>T	p.Ala787Ser	p.A787S	ENST00000375856	NM_003749.2	787	Gcc/Tcc	1/2	1	2	FACETS	0.868	0.798	0.941	0.868	0.798	0.941	CLONAL	1	TRUE	1	0.51	2		915	732	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061610	38061610	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	39	160	0	ENST00000250448.2:c.379C>A	p.Leu127Met	p.L127M	ENST00000250448	NM_004496.3	127	Ctg/Atg	2/2	0.151853302930067	0	FACETS	0.399	0.334	0.469			1	INDETERMINATE	1	TRUE	0	0.51	0		160	188	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610315	81610315	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	21	442	0	ENST00000298171.2:c.1916del	p.Pro639GlnfsTer11	p.P639Qfs*11	ENST00000298171	NM_000369.2	638	gCc/gc	10/10	0.151853302930067	0	FACETS	0.37	0.289	0.461			1	INDETERMINATE	1	TRUE	0	0.51	0		442	109	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242085	105242085	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	52	793	0	ENST00000349310.3:c.339G>T	p.Gln113His	p.Q113H	ENST00000349310	NM_001014432.1	113	caG/caT	6/15	0.151853302930067	0	FACETS	0.2	0.17	0.233			1	INDETERMINATE	1	TRUE	0	0.51	0		793	499	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023012	33023012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	40	385	0	ENST00000300177.4:c.121C>T	p.His41Tyr	p.H41Y	ENST00000300177	NM_001191322.1	41	Cac/Tac	2/2	0.194530953000023	1	FACETS	0.581	0.488	0.683	0.581	0.488	0.683	INDETERMINATE	1	TRUE	0	0.51	1		385	201	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023350	33023350	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	13	734	2	ENST00000300177.4:c.459G>T	p.Met153Ile	p.M153I	ENST00000300177	NM_001191322.1	153	atG/atT	2/2	0.194530953000023	1	FACETS	0.156	0.111	0.211	0.156	0.111	0.211	INDETERMINATE	1	TRUE	0	0.51	1		736	243	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614583	38614583	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121434312	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	43	546	0	ENST00000299084.4:c.349C>T	p.Arg117Ter	p.R117*	ENST00000299084	NM_152594.2	117	Cga/Tga	3/7	0.194530953000023	1	FACETS	0.924	0.79	1	0.924	0.79	1	INDETERMINATE	1	TRUE	0	0.51	1		546	136	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961986	41961986	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	39	453	0	ENST00000219905.7:c.894G>T	p.Gln298His	p.Q298H	ENST00000219905	NM_001164273.1	298	caG/caT	2/24	0.194530953000023	1	FACETS	0.919	0.779	1	0.919	0.779	1	INDETERMINATE	1	TRUE	0	0.51	1		453	124	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707812	43707812	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	86	721	0	ENST00000382044.4:c.5069A>G	p.Lys1690Arg	p.K1690R	ENST00000382044	NM_001141980.1	1690	aAg/aGg	23/28	0.194530953000023	1	FACETS	0.59	0.524	0.659	0.59	0.524	0.659	INDETERMINATE	1	TRUE	0	0.51	1		721	426	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724595	43724595	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	17	1043	0	ENST00000382044.4:c.3472G>T	p.Gly1158Ter	p.G1158*	ENST00000382044	NM_001141980.1	1158	Gga/Tga	17/28	0.194530953000023	1	FACETS	0.216	0.161	0.281	0.216	0.161	0.281	INDETERMINATE	1	TRUE	0	0.51	1		1043	230	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43769852	43769852	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	50	698	0	ENST00000382044.4:c.894G>T	p.Lys298Asn	p.K298N	ENST00000382044	NM_001141980.1	298	aaG/aaT	8/28	0.194530953000023	1	FACETS	0.686	0.589	0.789	0.686	0.589	0.789	INDETERMINATE	1	TRUE	0	0.51	1		698	213	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996182	73996182	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776412054	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	124	819	0	ENST00000318443.5:c.916G>A	p.Ala306Thr	p.A306T	ENST00000318443	NM_001024736.1	306	Gcc/Acc	5/10	0.194530953000023	1	FACETS	0.587	0.532	0.644	0.587	0.532	0.644	INDETERMINATE	1	TRUE	0	0.51	1		819	617	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472449	88472449	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	59	614	0	ENST00000360948.2:c.2106A>C	p.Arg702Ser	p.R702S	ENST00000360948	NM_001012338.2	702	agA/agC	16/19	0.194530953000023	1	FACETS	0.622	0.54	0.71	0.622	0.54	0.71	INDETERMINATE	1	TRUE	0	0.51	1		614	277	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678458	88678458	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	26	793	2	ENST00000360948.2:c.1078G>T	p.Glu360Ter	p.E360*	ENST00000360948	NM_001012338.2	360	Gag/Tag	9/19	0.194530953000023	1	FACETS	0.253	0.201	0.313	0.253	0.201	0.313	INDETERMINATE	1	TRUE	0	0.51	1		795	300	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679816	88679816	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	30	472	0	ENST00000360948.2:c.647A>G	p.His216Arg	p.H216R	ENST00000360948	NM_001012338.2	216	cAc/cGc	7/19	0.194530953000023	1	FACETS	0.31	0.25	0.377	0.31	0.25	0.377	INDETERMINATE	1	TRUE	0	0.51	1		472	283	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799377	88799377	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	25	300	0	ENST00000360948.2:c.8T>C	p.Val3Ala	p.V3A	ENST00000360948	NM_001012338.2	3	gTc/gCc	2/19	0.194530953000023	1	FACETS	0.451	0.359	0.555	0.451	0.359	0.555	INDETERMINATE	1	TRUE	0	0.51	1		300	162	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628141	90628141	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	89	736	0	ENST00000330062.3:c.1179-1G>T		p.X393_splice	ENST00000330062	NM_002168.2	393			0.194530953000023	1	FACETS	0.808	0.723	0.896	0.808	0.723	0.896	INDETERMINATE	1	TRUE	0	0.51	1		736	322	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99472859	99472859	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	91	639	0	ENST00000268035.6:c.2855T>C	p.Val952Ala	p.V952A	ENST00000268035	NM_000875.3	952	gTg/gCg	14/21	0.194530953000023	1	FACETS	0.88	0.791	0.973	0.88	0.791	0.973	INDETERMINATE	1	TRUE	0	0.51	1		639	302	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	360044	360044	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369325988	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	136	618	0	ENST00000262320.3:c.1045C>T	p.Arg349Cys	p.R349C	ENST00000262320	NM_003502.3	349	Cgt/Tgt	4/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.51	2		618	469	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104315	2104315	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	53	561	0	ENST00000219476.3:c.355C>A	p.Leu119Ile	p.L119I	ENST00000219476	NM_000548.3	119	Ctc/Atc	5/42	1	2	FACETS	0.734	0.631	0.846	0.734	0.631	0.846	SUBCLONAL	1	TRUE	1	0.51	2		561	283	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138301	2138301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766093661	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	107	824	1	ENST00000219476.3:c.5234G>A	p.Arg1745His	p.R1745H	ENST00000219476	NM_000548.3	1745	cGc/cAc	41/42	1	2	FACETS	0.967	0.873	1	0.967	0.873	1	CLONAL	1	TRUE	1	0.51	2		825	434	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220636	2220636	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768139800	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	167	503	0	ENST00000326181.6:c.253C>T	p.Arg85Cys	p.R85C	ENST00000326181	NM_032271.2	85	Cgc/Tgc	5/21	1	2	FACETS	0.836	0.77	0.906	0.836	0.77	0.906	CLONAL	1	TRUE	1	0.51	2		503	783	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2221581	2221581	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	154	858	0	ENST00000326181.6:c.450C>A	p.Phe150Leu	p.F150L	ENST00000326181	NM_032271.2	150	ttC/ttA	7/21	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.51	2		858	581	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639906	3639906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	127	740	0	ENST00000294008.3:c.3733C>T	p.Pro1245Ser	p.P1245S	ENST00000294008	NM_032444.2	1245	Ccc/Tcc	12/15	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.51	2		740	497	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789610	3789610	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	46	406	0	ENST00000262367.5:c.4249T>C	p.Tyr1417His	p.Y1417H	ENST00000262367	NM_004380.2	1417	Tac/Cac	25/31	1	2	FACETS	0.781	0.664	0.907	0.781	0.664	0.907	CLONAL	1	TRUE	1	0.51	2		406	231	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820779	3820779	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	149	1103	0	ENST00000262367.5:c.2672C>A	p.Pro891His	p.P891H	ENST00000262367	NM_004380.2	891	cCt/cAt	14/31	1	2	FACETS	0.806	0.738	0.877	0.806	0.738	0.877	CLONAL	1	TRUE	1	0.51	2		1103	725	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832691	3832691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	74	472	0	ENST00000262367.5:c.1567C>T	p.Pro523Ser	p.P523S	ENST00000262367	NM_004380.2	523	Ccc/Tcc	6/31	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.51	2		472	257	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900303	3900303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753319377	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	119	595	1	ENST00000262367.5:c.793G>A	p.Ala265Thr	p.A265T	ENST00000262367	NM_004380.2	265	Gcc/Acc	2/31	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.51	2		596	430	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900446	3900446	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	99	884	0	ENST00000262367.5:c.650G>T	p.Gly217Val	p.G217V	ENST00000262367	NM_004380.2	217	gGc/gTc	2/31	1	2	FACETS	0.742	0.665	0.824	0.742	0.665	0.824	SUBCLONAL	1	TRUE	1	0.51	2		884	523	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031893	10031893	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	19	672	0	ENST00000330684.3:c.930C>A	p.Phe310Leu	p.F310L	ENST00000330684	NM_001134407.1	310	ttC/ttA	3/13	1	2	FACETS	0.209	0.158	0.269	0.209	0.158	0.269	SUBCLONAL	1	TRUE	1	0.51	2		672	356	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024645	14024645	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	36	493	1	ENST00000311895.7:c.871T>G	p.Leu291Val	p.L291V	ENST00000311895	NM_005236.2	291	Tta/Gta	5/11	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.51	2		494	138	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042055	14042055	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs548842693	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	10	308	0	ENST00000311895.7:c.2602C>T	p.His868Tyr	p.H868Y	ENST00000311895	NM_005236.2	868	Cac/Tac	11/11	1	2	FACETS	0.245	0.166	0.344	0.245	0.166	0.344	SUBCLONAL	1	TRUE	1	0.51	2		308	160	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641355	23641355	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	26	785	1	ENST00000261584.4:c.2120C>A	p.Pro707His	p.P707H	ENST00000261584	NM_024675.3	707	cCt/cAt	5/13	1	2	FACETS	0.573	0.457	0.703	0.573	0.457	0.703	SUBCLONAL	1	TRUE	1	0.51	2		786	178	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647114	23647114	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	44	866	0	ENST00000261584.4:c.753G>T	p.Gln251His	p.Q251H	ENST00000261584	NM_024675.3	251	caG/caT	4/13	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.51	2		866	162	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783785	50783785	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	28	531	0	ENST00000398568.2:c.176G>T	p.Arg59Met	p.R59M	ENST00000398568	NM_001042412.1	59	aGg/aTg	3/18	1	2	FACETS	0.796	0.645	0.962	0.796	0.645	0.962	CLONAL	1	TRUE	1	0.51	2		531	138	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785564	50785564	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs777360812	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	31	702	0	ENST00000398568.2:c.554A>G	p.Gln185Arg	p.Q185R	ENST00000398568	NM_001042412.1	185	cAg/cGg	4/18	1	2	FACETS	0.363	0.294	0.441	0.363	0.294	0.441	SUBCLONAL	1	TRUE	1	0.51	2		702	335	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782307	56782307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765922828	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	104	500	0	ENST00000308159.5:c.148C>T	p.Arg50Cys	p.R50C	ENST00000308159	NM_014669.4	50	Cgc/Tgc	2/22	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.51	2		500	362	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645956	67645956	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	68	476	0	ENST00000264010.4:c.884A>C	p.Lys295Thr	p.K295T	ENST00000264010	NM_006565.3	295	aAg/aCg	4/12	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.51	2		476	256	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660576	67660576	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	16	602	1	ENST00000264010.4:c.1476G>T	p.Glu492Asp	p.E492D	ENST00000264010	NM_006565.3	492	gaG/gaT	8/12	1	2	FACETS	0.233	0.172	0.306	0.233	0.172	0.306	SUBCLONAL	1	TRUE	1	0.51	2		603	269	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772309	68772309	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	159	765	1	ENST00000261769.5:c.158G>T	p.Gly53Val	p.G53V	ENST00000261769	NM_004360.3	53	gGc/gTc	2/16	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.51	2		766	476	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867327	68867327	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1060501245	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	30	462	0	ENST00000261769.5:c.2574C>A	p.Asp858Glu	p.D858E	ENST00000261769	NM_004360.3	858	gaC/gaA	16/16	1	2	FACETS	0.467	0.378	0.567	0.467	0.378	0.567	SUBCLONAL	1	TRUE	1	0.51	2		462	252	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821398	72821398	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	26	541	0	ENST00000268489.5:c.10777T>G	p.Ser3593Ala	p.S3593A	ENST00000268489	NM_006885.3	3593	Tca/Gca	10/10	1	2	FACETS	0.246	0.194	0.305	0.246	0.194	0.305	SUBCLONAL	1	TRUE	1	0.51	2		541	415	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821680	72821680	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	63	279	0	ENST00000268489.5:c.10495G>T	p.Glu3499Ter	p.E3499*	ENST00000268489	NM_006885.3	3499	Gag/Tag	10/10	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.51	2		279	234	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821815	72821815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770453754	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	98	591	1	ENST00000268489.5:c.10360G>A	p.Asp3454Asn	p.D3454N	ENST00000268489	NM_006885.3	3454	Gac/Aac	10/10	1	2	FACETS	0.904	0.812	1	0.904	0.812	1	CLONAL	1	TRUE	1	0.51	2		592	425	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827675	72827675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1362292065	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	70	617	0	ENST00000268489.5:c.8906G>A	p.Arg2969Lys	p.R2969K	ENST00000268489	NM_006885.3	2969	aGg/aAg	9/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.51	2		617	214	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828228	72828228	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	17	663	0	ENST00000268489.5:c.8353C>A	p.Leu2785Ile	p.L2785I	ENST00000268489	NM_006885.3	2785	Ctc/Atc	9/10	1	2	FACETS	0.56	0.423	0.719	0.56	0.423	0.719	SUBCLONAL	1	TRUE	1	0.51	2		663	119	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832527	72832527	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	24	510	0	ENST00000268489.5:c.4054G>T	p.Gly1352Cys	p.G1352C	ENST00000268489	NM_006885.3	1352	Ggc/Tgc	9/10	1	2	FACETS	0.397	0.312	0.494	0.397	0.312	0.494	SUBCLONAL	1	TRUE	1	0.51	2		510	237	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942036	81942036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	39	375	0	ENST00000359376.3:c.1573G>A	p.Glu525Lys	p.E525K	ENST00000359376	NM_002661.3	525	Gaa/Aaa	17/33	1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	1	0.51	2		375	152	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347699	89347699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201278036	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	115	549	0	ENST00000301030.4:c.5251G>A	p.Ala1751Thr	p.A1751T	ENST00000301030	NM_001256183.1	1751	Gct/Act	9/13	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.51	2		549	441	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350530	89350530	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	24	751	0	ENST00000301030.4:c.2420T>G	p.Val807Gly	p.V807G	ENST00000301030	NM_001256183.1	807	gTt/gGt	9/13	1	2	FACETS	0.517	0.408	0.641	0.517	0.408	0.641	SUBCLONAL	1	TRUE	1	0.51	2		751	182	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351463	89351463	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	111	665	0	ENST00000301030.4:c.1487T>G	p.Leu496Arg	p.L496R	ENST00000301030	NM_001256183.1	496	cTg/cGg	9/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.51	2		665	362	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371709	89371709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1010844836	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	56	643	0	ENST00000301030.4:c.131G>A	p.Arg44His	p.R44H	ENST00000301030	NM_001256183.1	44	cGt/cAt	4/13	1	2	FACETS	0.357	0.305	0.414	0.357	0.305	0.414	SUBCLONAL	1	TRUE	1	0.51	2		643	615	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805321	89805321	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765683250	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	23	620	0	ENST00000389301.3:c.4229G>A	p.Cys1410Tyr	p.C1410Y	ENST00000389301	NM_000135.2	1410	tGc/tAc	42/43	1	2	FACETS	0.283	0.22	0.355	0.283	0.22	0.355	SUBCLONAL	1	TRUE	1	0.51	2		620	319	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979545	7979545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	87	595	0	ENST00000319144.4:c.1480C>T	p.Pro494Ser	p.P494S	ENST00000319144	NM_001139.2	494	Cct/Tct	11/15	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.51	2		595	340	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990670	7990670	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	30	804	0	ENST00000319144.4:c.91G>T	p.Gly31Ter	p.G31*	ENST00000319144	NM_001139.2	31	Gga/Tga	1/15	1	2	FACETS	0.257	0.206	0.314	0.257	0.206	0.314	SUBCLONAL	1	TRUE	1	0.51	2		804	458	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108225	8108225	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	26	651	0	ENST00000585124.1:c.999G>T	p.Arg333Ser	p.R333S	ENST00000585124	NM_004217.3	333	agG/agT	9/9	1	2	FACETS	0.206	0.163	0.257	0.206	0.163	0.257	SUBCLONAL	1	TRUE	1	0.51	2		651	494	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028641	12028641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	22	391	0	ENST00000353533.5:c.844C>T	p.Gln282Ter	p.Q282*	ENST00000353533	NM_003010.3	282	Caa/Taa	8/11	1	2	FACETS	0.854	0.675	1	0.854	0.675	1	CLONAL	1	TRUE	1	0.51	2		391	101	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989758	15989758	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	12	216	0	ENST00000268712.3:c.3017-2A>C		p.X1006_splice	ENST00000268712	NM_006311.3	1006			1	2	FACETS	0.406	0.287	0.549	0.406	0.287	0.549	SUBCLONAL	1	TRUE	1	0.51	2		216	116	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16001791	16001791	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	39	481	0	ENST00000268712.3:c.2710A>G	p.Lys904Glu	p.K904E	ENST00000268712	NM_006311.3	904	Aag/Gag	21/46	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.51	2		481	136	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042472	16042472	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	31	494	0	ENST00000268712.3:c.1202C>A	p.Ser401Tyr	p.S401Y	ENST00000268712	NM_006311.3	401	tCt/tAt	12/46	1	2	FACETS	0.928	0.764	1	0.928	0.764	1	CLONAL	1	TRUE	1	0.51	2		494	131	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089930	16089930	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	68	385	0	ENST00000268712.3:c.180G>T	p.Gln60His	p.Q60H	ENST00000268712	NM_006311.3	60	caG/caT	3/46	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.51	2		385	242	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483112	29483112	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	35	517	0	ENST00000356175.3:c.172C>A	p.Leu58Ile	p.L58I	ENST00000356175	NM_000267.3	58	Ctc/Atc	2/57	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.51	2		517	121	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653134	29653134	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	10	348	0	ENST00000356175.3:c.5069G>A	p.Cys1690Tyr	p.C1690Y	ENST00000356175	NM_000267.3	1690	tGt/tAt	36/57	1	2	FACETS	0.332	0.226	0.464	0.332	0.226	0.464	SUBCLONAL	1	TRUE	1	0.51	2		348	118	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665804	29665804	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	18	224	0	ENST00000356175.3:c.6839T>C	p.Leu2280Ser	p.L2280S	ENST00000356175	NM_000267.3	2280	tTa/tCa	45/57	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.51	2		224	50	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428052	33428052	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786203444	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	17	524	0	ENST00000345365.6:c.907A>G	p.Thr303Ala	p.T303A	ENST00000345365	NM_002878.3	303	Aca/Gca	10/10	1	2	FACETS	0.447	0.336	0.577	0.447	0.336	0.577	SUBCLONAL	1	TRUE	1	0.51	2		524	149	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459723	40459723	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	155	619	0	ENST00000345506.4:c.1888G>A	p.Ala630Thr	p.A630T	ENST00000345506	NM_003152.3	630	Gcc/Acc	16/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.51	2		619	491	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485694	40485694	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	75	495	0	ENST00000264657.5:c.1046T>C	p.Val349Ala	p.V349A	ENST00000264657	NM_139276.2	349	gTc/gCc	10/24	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.51	2		495	287	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489864	40489864	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs749529243	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	51	537	0	ENST00000264657.5:c.562C>A	p.Leu188Met	p.L188M	ENST00000264657	NM_139276.2	188	Ctg/Atg	7/24	1	2	FACETS	0.823	0.706	0.948	0.823	0.706	0.948	CLONAL	1	TRUE	1	0.51	2		537	243	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41199659	41199659	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs80358145	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	66	574	0	ENST00000357654.3:c.5467+1G>A		p.X1823_splice	ENST00000357654	NM_007294.3	1823			1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.51	2		574	254	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244591	41244591	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	17	710	0	ENST00000357654.3:c.2957T>C	p.Ile986Thr	p.I986T	ENST00000357654	NM_007294.3	986	aTc/aCc	10/23	1	2	FACETS	0.687	0.521	0.878	0.687	0.521	0.878	SUBCLONAL	1	TRUE	1	0.51	2		710	97	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804244	46804244	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	46	829	0	ENST00000290295.7:c.763C>A	p.Leu255Ile	p.L255I	ENST00000290295	NM_006361.5	255	Ctc/Atc	2/2	1	2	FACETS	0.332	0.279	0.391	0.332	0.279	0.391	SUBCLONAL	1	TRUE	1	0.51	2		829	543	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804283	46804283	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	26	810	1	ENST00000290295.7:c.724A>G	p.Thr242Ala	p.T242A	ENST00000290295	NM_006361.5	242	Acc/Gcc	2/2	1	2	FACETS	0.212	0.167	0.263	0.212	0.167	0.263	SUBCLONAL	1	TRUE	1	0.51	2		811	481	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688726	47688726	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	50	397	0	ENST00000347630.2:c.574G>T	p.Gly192Ter	p.G192*	ENST00000347630	NM_001007230.1	192	Gga/Tga	7/11	1	2	FACETS	0.778	0.666	0.899	0.778	0.666	0.899	SUBCLONAL	1	TRUE	1	0.51	2		397	252	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688800	47688800	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	18	349	0	ENST00000347630.2:c.500C>A	p.Ser167Tyr	p.S167Y	ENST00000347630	NM_001007230.1	167	tCt/tAt	7/11	1	2	FACETS	0.685	0.524	0.87	0.685	0.524	0.87	SUBCLONAL	1	TRUE	1	0.51	2		349	103	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55335633	55335633	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	44	586	0	ENST00000284073.2:c.188G>T	p.Gly63Val	p.G63V	ENST00000284073	NM_138962.2	63	gGc/gTc	4/14	1	2	FACETS	0.788	0.667	0.918	0.788	0.667	0.918	CLONAL	1	TRUE	1	0.51	2		586	219	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435986	56435986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs919729695	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	18	417	0	ENST00000407977.2:c.1151G>A	p.Gly384Asp	p.G384D	ENST00000407977		384	gGc/gAc	9/10	1	2	FACETS	0.377	0.285	0.485	0.377	0.285	0.485	SUBCLONAL	1	TRUE	1	0.51	2		417	187	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772437	56772437	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	10	594	0	ENST00000337432.4:c.291G>T	p.Gln97His	p.Q97H	ENST00000337432	NM_058216.2	97	caG/caT	2/9	1	2	FACETS	0.231	0.156	0.324	0.231	0.156	0.324	SUBCLONAL	1	TRUE	1	0.51	2		594	170	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56811498	56811498	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	40	412	0	ENST00000337432.4:c.1046C>A	p.Thr349Asn	p.T349N	ENST00000337432	NM_058216.2	349	aCt/aAt	9/9	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.51	2		412	129	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858225	59858225	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	23	513	0	ENST00000259008.2:c.1770C>A	p.Asn590Lys	p.N590K	ENST00000259008	NM_032043.2	590	aaC/aaA	12/20	1	2	FACETS	0.609	0.48	0.756	0.609	0.48	0.756	SUBCLONAL	1	TRUE	1	0.51	2		513	148	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62009580	62009580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	101	660	0	ENST00000392795.3:c.42G>A	p.Met14Ile	p.M14I	ENST00000392795	NM_001039933.1	14	atG/atA	1/6	1	2	FACETS	0.797	0.715	0.883	0.797	0.715	0.883	SUBCLONAL	1	TRUE	1	0.51	2		660	497	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727859	78727859	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	113	721	0	ENST00000306801.3:c.704C>A	p.Pro235Gln	p.P235Q	ENST00000306801	NM_020761.2	235	cCg/cAg	6/34	1	2	FACETS	0.825	0.745	0.909	0.825	0.745	0.909	CLONAL	1	TRUE	1	0.51	2		721	537	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796990	78796990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1301463689	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	147	590	0	ENST00000306801.3:c.1103C>T	p.Pro368Leu	p.P368L	ENST00000306801	NM_020761.2	368	cCg/cTg	9/34	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.51	2		590	504	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736906	736906	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	38	573	0	ENST00000314574.4:c.1193G>A	p.Arg398Gln	p.R398Q	ENST00000314574	NM_005433.3	398	cGg/cAg	10/12	1	2	FACETS	0.987	0.83	1	0.987	0.83	1	CLONAL	1	TRUE	1	0.51	2		573	151	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39613875	39613875	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs989194578	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	13	369	0	ENST00000262039.4:c.1793A>G	p.Gln598Arg	p.Q598R	ENST00000262039	NM_002647.2	598	cAa/cGa	16/25	1	2	FACETS	0.554	0.4	0.736	0.554	0.4	0.736	SUBCLONAL	1	TRUE	1	0.51	2		369	92	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637886	39637886	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1209901264	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	14	433	0	ENST00000262039.4:c.2303G>A	p.Arg768Gln	p.R768Q	ENST00000262039	NM_002647.2	768	cGg/cAg	22/25	1	2	FACETS	0.578	0.423	0.759	0.578	0.423	0.759	SUBCLONAL	1	TRUE	1	0.51	2		433	95	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372160	45372160	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1040132520	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	24	407	1	ENST00000262160.6:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000262160	NM_005901.5	337	Cgc/Tgc	9/11	1	2	FACETS	1	0.812	1	1	0.812	1	CLONAL	1	TRUE	1	0.51	2		408	93	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45423111	45423111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	37	226	0	ENST00000262160.6:c.17C>T	p.Pro6Leu	p.P6L	ENST00000262160	NM_005901.5	6	cCa/cTa	2/11	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.51	2		226	132	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348516	56348516	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	28	353	0	ENST00000348428.3:c.324T>G	p.Asp108Glu	p.D108E	ENST00000348428	NM_006785.3	108	gaT/gaG	2/17	1	2	FACETS	0.784	0.636	0.948	0.784	0.636	0.948	CLONAL	1	TRUE	1	0.51	2		353	140	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612308	1612308	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753925052	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	151	916	1	ENST00000344749.5:c.1711C>T	p.Arg571Cys	p.R571C	ENST00000344749	NM_001136139.2	571	Cgc/Tgc	18/19	1	2	FACETS	0.815	0.746	0.886	0.815	0.746	0.886	CLONAL	1	TRUE	1	0.51	2		917	727	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216622	2216622	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569621521	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	207	894	0	ENST00000398665.3:c.2266G>A	p.Gly756Ser	p.G756S	ENST00000398665	NM_032482.2	756	Ggc/Agc	20/28	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.51	2		894	674	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115043	3115043	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	46	809	0	ENST00000078429.4:c.578C>A	p.Pro193His	p.P193H	ENST00000078429	NM_002067.2	193	cCt/cAt	4/7	1	2	FACETS	0.276	0.232	0.325	0.276	0.232	0.325	SUBCLONAL	1	TRUE	1	0.51	2		809	653	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4090640	4090640	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	28	688	0	ENST00000262948.5:c.1159C>A	p.Leu387Met	p.L387M	ENST00000262948	NM_030662.3	387	Ctg/Atg	11/11	1	2	FACETS	0.223	0.178	0.275	0.223	0.178	0.275	SUBCLONAL	1	TRUE	1	0.51	2		688	492	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4102375	4102375	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs775661458	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	190	679	2	ENST00000262948.5:c.527C>T	p.Ala176Val	p.A176V	ENST00000262948	NM_030662.3	176	gCg/gTg	4/11	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.51	2		681	521	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244472	5244472	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1030053885	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	36	827	2	ENST00000357368.4:c.1010C>A	p.Thr337Asn	p.T337N	ENST00000357368	NM_002850.3	337	aCt/aAt	11/38	1	2	FACETS	0.212	0.173	0.255	0.212	0.173	0.255	SUBCLONAL	1	TRUE	1	0.51	2		829	666	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265040	5265040	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770043743	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	133	792	1	ENST00000357368.4:c.547C>T	p.Arg183Cys	p.R183C	ENST00000357368	NM_002850.3	183	Cgc/Tgc	5/38	1	2	FACETS	0.98	0.895	1	0.98	0.895	1	CLONAL	1	TRUE	1	0.51	2		793	532	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248627	10248627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	57	587	0	ENST00000340748.4:c.4126G>A	p.Glu1376Lys	p.E1376K	ENST00000340748		1376	Gag/Aag	35/40	1	2	FACETS	0.599	0.516	0.689	0.599	0.516	0.689	SUBCLONAL	1	TRUE	1	0.51	2		587	373	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250831	10250831	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	145	673	3	ENST00000340748.4:c.3649G>A	p.Val1217Met	p.V1217M	ENST00000340748		1217	Gtg/Atg	32/40	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.51	2		676	509	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265026	10265026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	74	567	0	ENST00000340748.4:c.1914G>T	p.Lys638Asn	p.K638N	ENST00000340748		638	aaG/aaT	21/40	1	2	FACETS	0.971	0.858	1	0.971	0.858	1	CLONAL	1	TRUE	1	0.51	2		567	299	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610103	10610103	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	124	712	0	ENST00000171111.5:c.607G>A	p.Ala203Thr	p.A203T	ENST00000171111	NM_203500.1	203	Gcc/Acc	2/6	1	2	FACETS	0.994	0.905	1	0.994	0.905	1	CLONAL	1	TRUE	1	0.51	2		712	489	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170541	11170541	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	103	666	0	ENST00000358026.2:c.4844A>G	p.Glu1615Gly	p.E1615G	ENST00000358026	NM_001128849.1	1615	gAg/gGg	34/36	1	2	FACETS	0.985	0.888	1	0.985	0.888	1	CLONAL	1	TRUE	1	0.51	2		666	410	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054599	13054599	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760388477	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	42	462	0	ENST00000316448.5:c.1126C>T	p.Arg376Cys	p.R376C	ENST00000316448	NM_004343.3	376	Cgc/Tgc	9/9	1	2	FACETS	0.876	0.741	1	0.876	0.741	1	CLONAL	1	TRUE	1	0.51	2		462	188	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271928	15271928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1453074278	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	91	717	0	ENST00000263388.2:c.6511G>A	p.Asp2171Asn	p.D2171N	ENST00000263388	NM_000435.2	2171	Gat/Aat	33/33	1	2	FACETS	0.702	0.626	0.784	0.702	0.626	0.784	SUBCLONAL	1	TRUE	1	0.51	2		717	508	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281222	15281222	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	52	805	1	ENST00000263388.2:c.5034G>T	p.Glu1678Asp	p.E1678D	ENST00000263388	NM_000435.2	1678	gaG/gaT	27/33	1	2	FACETS	0.281	0.239	0.328	0.281	0.239	0.328	SUBCLONAL	1	TRUE	1	0.51	2		806	725	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295201	15295201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	136	932	0	ENST00000263388.2:c.2471G>A	p.Gly824Asp	p.G824D	ENST00000263388	NM_000435.2	824	gGt/gAt	16/33	1	2	FACETS	0.928	0.847	1	0.928	0.847	1	CLONAL	1	TRUE	1	0.51	2		932	575	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383716	15383716	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	133	718	0	ENST00000263377.2:c.195C>A	p.Tyr65Ter	p.Y65*	ENST00000263377	NM_058243.2	65	taC/taA	2/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.51	2		718	469	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379649	17379649	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	35	415	1	ENST00000359435.4:c.34G>T	p.Glu12Ter	p.E12*	ENST00000359435	NM_001033549.1	12	Gag/Tag	2/9	1	2	FACETS	0.666	0.551	0.793	0.666	0.551	0.793	SUBCLONAL	1	TRUE	1	0.51	2		416	206	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945683	17945683	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	138	684	0	ENST00000458235.1:c.2177T>G	p.Ile726Ser	p.I726S	ENST00000458235	NM_000215.3	726	aTc/aGc	16/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.51	2		684	418	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18972897	18972897	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	86	703	0	ENST00000262803.5:c.2536G>A	p.Glu846Lys	p.E846K	ENST00000262803	NM_002911.3	846	Gag/Aag	18/24	1	2	FACETS	0.721	0.64	0.806	0.721	0.64	0.806	SUBCLONAL	1	TRUE	1	0.51	2		703	468	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974319	18974319	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	65	600	0	ENST00000262803.5:c.2673C>A	p.Tyr891Ter	p.Y891*	ENST00000262803	NM_002911.3	891	taC/taA	19/24	1	2	FACETS	0.666	0.58	0.758	0.666	0.58	0.758	SUBCLONAL	1	TRUE	1	0.51	2		600	383	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258533	19258533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569051000	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	67	841	1	ENST00000162023.5:c.367C>T	p.Pro123Ser	p.P123S	ENST00000162023		123	Ccg/Tcg	8/13	1	2	FACETS	0.367	0.318	0.42	0.367	0.318	0.42	SUBCLONAL	1	TRUE	1	0.51	2		842	716	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212380	36212380	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1323876213	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	177	876	0	ENST00000222270.7:c.2131G>A	p.Val711Ile	p.V711I	ENST00000222270	NM_014727.1	711	Gtc/Atc	3/37	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.51	2		876	532	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218081	36218081	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774047474	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	20	368	0	ENST00000222270.7:c.4028G>A	p.Arg1343His	p.R1343H	ENST00000222270	NM_014727.1	1343	cGc/cAc	15/37	1	2	FACETS	0.413	0.317	0.524	0.413	0.317	0.524	SUBCLONAL	1	TRUE	1	0.51	2		368	190	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222995	36222995	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	127	974	0	ENST00000222270.7:c.5624G>T	p.Arg1875Met	p.R1875M	ENST00000222270	NM_014727.1	1875	aGg/aTg	27/37	1	2	FACETS	0.978	0.891	1	0.978	0.891	1	CLONAL	1	TRUE	1	0.51	2		974	509	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223115	36223115	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	26	970	0	ENST00000222270.7:c.5666-1G>T		p.X1889_splice	ENST00000222270	NM_014727.1	1889			1	2	FACETS	0.207	0.163	0.258	0.207	0.163	0.258	SUBCLONAL	1	TRUE	1	0.51	2		970	492	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224180	36224180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	112	778	0	ENST00000222270.7:c.6730C>T	p.Pro2244Ser	p.P2244S	ENST00000222270	NM_014727.1	2244	Ccc/Tcc	28/37	1	2	FACETS	0.929	0.84	1	0.929	0.84	1	CLONAL	1	TRUE	1	0.51	2		778	473	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228564	36228564	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	45	735	0	ENST00000222270.7:c.7578C>A	p.Phe2526Leu	p.F2526L	ENST00000222270	NM_014727.1	2526	ttC/ttA	34/37	1	2	FACETS	0.376	0.316	0.443	0.376	0.316	0.443	SUBCLONAL	1	TRUE	1	0.51	2		735	469	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40742283	40742283	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	32	682	1	ENST00000392038.2:c.841C>A	p.Leu281Ile	p.L281I	ENST00000392038	NM_001626.4	281	Ctc/Atc	10/14	1	2	FACETS	0.39	0.317	0.472	0.39	0.317	0.472	SUBCLONAL	1	TRUE	1	0.51	2		683	322	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40743974	40743974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760399082	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	103	466	3	ENST00000392038.2:c.733C>T	p.Arg245Cys	p.R245C	ENST00000392038	NM_001626.4	245	Cgt/Tgt	9/14	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.51	2		469	381	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40744879	40744879	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs758767505	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	64	581	0	ENST00000392038.2:c.641C>T	p.Ala214Val	p.A214V	ENST00000392038	NM_001626.4	214	gCg/gTg	8/14	1	2	FACETS	0.763	0.665	0.867	0.763	0.665	0.867	SUBCLONAL	1	TRUE	1	0.51	2		581	329	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40771166	40771166	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	36	605	0	ENST00000392038.2:c.9G>T	p.Glu3Asp	p.E3D	ENST00000392038	NM_001626.4	3	gaG/gaT	2/14	1	2	FACETS	0.355	0.292	0.425	0.355	0.292	0.425	SUBCLONAL	1	TRUE	1	0.51	2		605	398	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748812	41748812	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	60	796	0	ENST00000301178.4:c.1337T>G	p.Phe446Cys	p.F446C	ENST00000301178	NM_021913.4	446	tTc/tGc	11/20	1	2	FACETS	0.468	0.403	0.538	0.468	0.403	0.538	SUBCLONAL	1	TRUE	1	0.51	2		796	503	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765556	41765556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1568420141	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	28	705	0	ENST00000301178.4:c.2432C>A	p.Pro811His	p.P811H	ENST00000301178	NM_021913.4	811	cCt/cAt	20/20	1	2	FACETS	0.289	0.231	0.355	0.289	0.231	0.355	SUBCLONAL	1	TRUE	1	0.51	2		705	380	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383701	42383701	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	148	596	0	ENST00000221972.3:c.476C>A	p.Pro159His	p.P159H	ENST00000221972	NM_021601.3	159	cCt/cAt	3/5	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.51	2		596	448	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794979	42794979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749021269	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	69	706	1	ENST00000575354.2:c.2059G>A	p.Ala687Thr	p.A687T	ENST00000575354	NM_015125.3	687	Gcc/Acc	10/20	1	2	FACETS	0.64	0.559	0.726	0.64	0.559	0.726	SUBCLONAL	1	TRUE	1	0.51	2		707	423	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856059	45856059	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376556895	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	45	692	0	ENST00000391945.4:c.1847G>A	p.Arg616Gln	p.R616Q	ENST00000391945	NM_000400.3	616	cGg/cAg	20/23	1	2	FACETS	0.309	0.259	0.364	0.309	0.259	0.364	SUBCLONAL	1	TRUE	1	0.51	2		692	572	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872363	45872363	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	77	807	0	ENST00000391945.4:c.148G>T	p.Val50Leu	p.V50L	ENST00000391945	NM_000400.3	50	Gta/Tta	3/23	1	2	FACETS	0.719	0.634	0.809	0.719	0.634	0.809	SUBCLONAL	1	TRUE	1	0.51	2		807	420	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457180	25457180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749167103	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	34	533	0	ENST00000264709.3:c.2707G>A	p.Ala903Thr	p.A903T	ENST00000264709	NM_175629.2	903	Gct/Act	23/23	1	2	FACETS	0.29	0.236	0.35	0.29	0.236	0.35	SUBCLONAL	1	TRUE	1	0.51	2		533	460	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505382	25505382	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	125	634	0	ENST00000264709.3:c.376C>T	p.Pro126Ser	p.P126S	ENST00000264709	NM_175629.2	126	Cct/Tct	4/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.51	2		634	383	SUCCESS
ALK	238	MSKCC	GRCh37	2	29420489	29420489	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs370364694	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	47	486	0	ENST00000389048.3:c.3992C>A	p.Pro1331His	p.P1331H	ENST00000389048	NM_004304.4	1331	cCc/cAc	27/29	1	2	FACETS	0.791	0.674	0.917	0.791	0.674	0.917	CLONAL	1	TRUE	1	0.51	2		486	233	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451905	29451905	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	93	713	1	ENST00000389048.3:c.2660C>T	p.Thr887Ile	p.T887I	ENST00000389048	NM_004304.4	887	aCt/aTt	16/29	1	2	FACETS	0.916	0.82	1	0.916	0.82	1	CLONAL	1	TRUE	1	0.51	2		714	398	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222323	39222323	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	50	662	0	ENST00000402219.2:c.3287C>A	p.Ser1096Tyr	p.S1096Y	ENST00000402219	NM_005633.3	1096	tCc/tAc	20/23	1	2	FACETS	0.769	0.658	0.888	0.769	0.658	0.888	SUBCLONAL	1	TRUE	1	0.51	2		662	255	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702296	47702296	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1361816581	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	22	446	0	ENST00000233146.2:c.1892G>T	p.Arg631Ile	p.R631I	ENST00000233146	NM_000251.2	631	aGa/aTa	12/16	1	2	FACETS	0.763	0.601	0.945	0.763	0.601	0.945	CLONAL	1	TRUE	1	0.51	2		446	113	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919724	96919724	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	36	508	1	ENST00000258439.3:c.539T>C	p.Val180Ala	p.V180A	ENST00000258439	NM_001193304.2	180	gTg/gCg	4/4	1	2	FACETS	0.441	0.364	0.528	0.441	0.364	0.528	SUBCLONAL	1	TRUE	1	0.51	2		509	320	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99154325	99154325	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	17	331	0	ENST00000074304.5:c.468-1G>T		p.X156_splice	ENST00000074304	NM_001134224.1	156			1	2	FACETS	0.425	0.319	0.549	0.425	0.319	0.549	SUBCLONAL	1	TRUE	1	0.51	2		331	157	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128036891	128036891	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1302552127	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	12	610	2	ENST00000285398.2:c.1588C>T	p.Arg530Ter	p.R530*	ENST00000285398	NM_000122.1	530	Cga/Tga	10/15	1	2	FACETS	0.257	0.181	0.351	0.257	0.181	0.351	SUBCLONAL	1	TRUE	1	0.51	2		612	183	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096607	178096607	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	11	296	0	ENST00000397062.3:c.724T>C	p.Cys242Arg	p.C242R	ENST00000397062	NM_006164.4	242	Tgt/Cgt	5/5	1	2	FACETS	1	0.735	1	1	0.735	1	CLONAL	1	TRUE	1	0.51	2		296	42	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265543	198265543	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	19	617	0	ENST00000335508.6:c.2614A>C	p.Ile872Leu	p.I872L	ENST00000335508	NM_012433.2	872	Att/Ctt	18/25	1	2	FACETS	0.484	0.37	0.615	0.484	0.37	0.615	SUBCLONAL	1	TRUE	1	0.51	2		617	154	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141686	202141686	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	11	266	0	ENST00000358485.4:c.974A>G	p.Asp325Gly	p.D325G	ENST00000358485	NM_001080125.1	325	gAt/gGt	7/9	1	2	FACETS	0.814	0.577	1	0.814	0.577	1	CLONAL	1	TRUE	1	0.51	2		266	53	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149931	202149931	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	35	689	0	ENST00000358485.4:c.1372T>A	p.Phe458Ile	p.F458I	ENST00000358485	NM_001080125.1	458	Ttt/Att	8/9	1	2	FACETS	0.73	0.605	0.868	0.73	0.605	0.868	SUBCLONAL	1	TRUE	1	0.51	2		689	188	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151184	202151184	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1235505270	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	10	230	0	ENST00000358485.4:c.1484G>A	p.Gly495Asp	p.G495D	ENST00000358485	NM_001080125.1	495	gGc/gAc	9/9	1	2	FACETS	0.871	0.609	1	0.871	0.609	1	CLONAL	1	TRUE	1	0.51	2		230	45	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204737455	204737455	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	11	327	0	ENST00000302823.3:c.592A>C	p.Thr198Pro	p.T198P	ENST00000302823	NM_005214.4	198	Aca/Cca	4/4	1	2	FACETS	0.449	0.313	0.614	0.449	0.313	0.614	SUBCLONAL	1	TRUE	1	0.51	2		327	96	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209106729	209106729	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	26	579	0	ENST00000345146.2:c.839C>A	p.Ser280Tyr	p.S280Y	ENST00000345146	NM_005896.2	280	tCt/tAt	7/10	1	2	FACETS	0.31	0.245	0.384	0.31	0.245	0.384	SUBCLONAL	1	TRUE	1	0.51	2		579	329	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209108313	209108313	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	25	416	0	ENST00000345146.2:c.536C>T	p.Ala179Val	p.A179V	ENST00000345146	NM_005896.2	179	gCc/gTc	6/10	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.51	2		416	90	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439649	220439649	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	84	816	0	ENST00000243786.2:c.502T>C	p.Ser168Pro	p.S168P	ENST00000243786	NM_002191.3	168	Tct/Cct	2/2	1	2	FACETS	0.681	0.603	0.763	0.681	0.603	0.763	SUBCLONAL	1	TRUE	1	0.51	2		816	484	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439986	220439986	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	68	998	0	ENST00000243786.2:c.839T>C	p.Ile280Thr	p.I280T	ENST00000243786	NM_002191.3	280	aTc/aCc	2/2	1	2	FACETS	0.569	0.496	0.647	0.569	0.496	0.647	SUBCLONAL	1	TRUE	1	0.51	2		998	469	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660376	227660376	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756650445	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	20	522	0	ENST00000305123.5:c.3079C>T	p.Pro1027Ser	p.P1027S	ENST00000305123	NM_005544.2	1027	Ccc/Tcc	1/2	1	2	FACETS	0.375	0.288	0.477	0.375	0.288	0.477	SUBCLONAL	1	TRUE	1	0.51	2		522	209	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662661	227662661	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776343218	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	33	692	1	ENST00000305123.5:c.794G>A	p.Arg265His	p.R265H	ENST00000305123	NM_005544.2	265	cGc/cAc	1/2	1	2	FACETS	0.291	0.237	0.353	0.291	0.237	0.353	SUBCLONAL	1	TRUE	1	0.51	2		693	444	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794790	242794790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	56	471	0	ENST00000334409.5:c.419C>T	p.Ala140Val	p.A140V	ENST00000334409	NM_005018.2	140	gCa/gTa	2/5	1	2	FACETS	0.998	0.866	1	0.998	0.866	1	CLONAL	1	TRUE	1	0.51	2		471	220	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546596	9546596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	56	531	0	ENST00000353224.5:c.1426G>A	p.Ala476Thr	p.A476T	ENST00000353224	NM_177990.2	476	Gca/Aca	5/10	0.194530953000023	1	FACETS	0.558	0.482	0.641	0.558	0.482	0.641	INDETERMINATE	1	TRUE	0	0.51	1		531	293	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023034	31023034	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	35	531	0	ENST00000375687.4:c.2519C>A	p.Pro840His	p.P840H	ENST00000375687	NM_015338.5	840	cCt/cAt	13/13	0.194530953000023	1	FACETS	0.571	0.474	0.678	0.571	0.474	0.678	INDETERMINATE	1	TRUE	0	0.51	1		531	179	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023688	31023688	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	106	695	0	ENST00000375687.4:c.3173G>T	p.Gly1058Val	p.G1058V	ENST00000375687	NM_015338.5	1058	gGg/gTg	13/13	0.194530953000023	1	FACETS	0.906	0.821	0.993	0.906	0.821	0.993	INDETERMINATE	1	TRUE	0	0.51	1		695	342	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376781	31376781	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772383693	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	34	558	1	ENST00000328111.2:c.776G>A	p.Arg259Gln	p.R259Q	ENST00000328111	NM_006892.3	259	cGg/cAg	7/23	0.194530953000023	1	FACETS	0.272	0.222	0.328	0.272	0.222	0.328	INDETERMINATE	1	TRUE	0	0.51	1		559	365	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36014514	36014514	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	99	564	0	ENST00000358208.4:c.287A>C	p.Glu96Ala	p.E96A	ENST00000358208		96	gAg/gCg	3/12	0.194530953000023	1	FACETS	0.939	0.849	1	0.939	0.849	1	INDETERMINATE	1	TRUE	0	0.51	1		564	308	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265154	46265154	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1213644996	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	22	328	0	ENST00000371998.3:c.2024G>A	p.Gly675Glu	p.G675E	ENST00000371998		675	gGg/gAg	12/23	0.194530953000023	1	FACETS	0.656	0.518	0.808	0.656	0.518	0.808	INDETERMINATE	1	TRUE	0	0.51	1		328	98	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292847	62292847	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	21	200	0	ENST00000360203.5:c.299T>C	p.Ile100Thr	p.I100T	ENST00000360203	NM_001283009.1	100	aTa/aCa	3/35	0.194530953000023	1	FACETS	0.797	0.63	0.979	0.797	0.63	0.979	INDETERMINATE	1	TRUE	0	0.51	1		200	77	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164820	36164820	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	150	915	1	ENST00000300305.3:c.1055C>A	p.Ala352Asp	p.A352D	ENST00000300305		352	gCc/gAc	8/8	1	2	FACETS	0.79	0.723	0.859	0.79	0.723	0.859	SUBCLONAL	1	TRUE	1	0.51	2		916	745	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288366	21288366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	15	580	0	ENST00000354336.3:c.611C>T	p.Ala204Val	p.A204V	ENST00000354336	NM_005207.3	204	gCt/gTt	2/3	0.151853302930067	0	FACETS	0.118	0.086	0.156			1	INDETERMINATE	1	TRUE	0	0.51	0		580	245	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160312	22160312	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	15	341	0	ENST00000215832.6:c.319C>A	p.Leu107Ile	p.L107I	ENST00000215832	NM_002745.4	107	Ctc/Atc	3/9	0.151853302930067	0	FACETS	0.331	0.246	0.43			1	INDETERMINATE	1	TRUE	0	0.51	0		341	87	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130452	29130452	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1201436179	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	20	662	0	ENST00000328354.6:c.258G>T	p.Glu86Asp	p.E86D	ENST00000328354	NM_007194.3	86	gaG/gaT	2/15	0.151853302930067	0	FACETS	0.114	0.087	0.146			1	INDETERMINATE	1	TRUE	0	0.51	0		662	336	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032832	30032832	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	14	346	0	ENST00000338641.4:c.207G>T	p.Lys69Asn	p.K69N	ENST00000338641	NM_000268.3	69	aaG/aaT	2/16	0.151853302930067	0	FACETS	0.13	0.094	0.174			1	INDETERMINATE	1	TRUE	0	0.51	0		346	207	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077478	30077478	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	28	309	0	ENST00000338641.4:c.1625T>A	p.Leu542His	p.L542H	ENST00000338641	NM_000268.3	542	cTc/cAc	15/16	0.151853302930067	0	FACETS	0.393	0.318	0.475			1	INDETERMINATE	1	TRUE	0	0.51	0		309	137	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574521	41574521	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	80	709	0	ENST00000263253.7:c.6806T>C	p.Met2269Thr	p.M2269T	ENST00000263253	NM_001429.3	2269	aTg/aCg	31/31	0.151853302930067	0	FACETS	0.439	0.389	0.492			1	INDETERMINATE	1	TRUE	0	0.51	0		709	350	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458524	12458524	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	49	772	0	ENST00000287820.6:c.1141C>A	p.Leu381Ile	p.L381I	ENST00000287820	NM_015869.4	381	Cta/Ata	6/7	0.0770245185744091	0	FACETS	0.453	0.388	0.522			1	INDETERMINATE	1	TRUE	0	0.51	0		772	208	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12632335	12632335	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	25	610	0	ENST00000251849.4:c.1332G>T	p.Gln444His	p.Q444H	ENST00000251849	NM_002880.3	444	caG/caT	12/17	0.0770245185744091	0	FACETS	0.143	0.112	0.178			1	INDETERMINATE	1	TRUE	0	0.51	0		610	336	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12632425	12632425	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	35	696	0	ENST00000251849.4:c.1242G>T	p.Lys414Asn	p.K414N	ENST00000251849	NM_002880.3	414	aaG/aaT	12/17	0.0770245185744091	0	FACETS	0.211	0.173	0.253			1	INDETERMINATE	1	TRUE	0	0.51	0		696	319	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12653552	12653552	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	13	442	0	ENST00000251849.4:c.217C>T	p.Arg73Ter	p.R73*	ENST00000251849	NM_002880.3	73	Cga/Tga	3/17	0.0770245185744091	0	FACETS	0.121	0.086	0.163			1	INDETERMINATE	1	TRUE	0	0.51	0		442	207	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686387	30686387	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs765447350	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	14	312	0	ENST00000295754.5:c.243G>T	p.Gln81His	p.Q81H	ENST00000295754	NM_003242.5	81	caG/caT	2/7	0.0770245185744091	0	FACETS	0.186	0.134	0.246			1	INDETERMINATE	1	TRUE	0	0.51	0		312	145	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182285	38182285	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	50	490	0	ENST00000396334.3:c.721C>A	p.Leu241Met	p.L241M	ENST00000396334	NM_002468.4	241	Ctg/Atg	4/5	0.0770245185744091	0	FACETS	0.347	0.296	0.402			1	INDETERMINATE	1	TRUE	0	0.51	0		490	277	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165210	47165210	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	20	379	0	ENST00000409792.3:c.916G>T	p.Gly306Cys	p.G306C	ENST00000409792	NM_014159.6	306	Ggt/Tgt	3/21	0.0770245185744091	0	FACETS	0.506	0.397	0.626			1	INDETERMINATE	1	TRUE	0	0.51	0		379	76	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165664	47165664	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	32	513	0	ENST00000409792.3:c.462G>T	p.Arg154Ser	p.R154S	ENST00000409792	NM_014159.6	154	agG/agT	3/21	0.0770245185744091	0	FACETS	0.358	0.293	0.428			1	INDETERMINATE	1	TRUE	0	0.51	0		513	172	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437191	52437191	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	54	681	0	ENST00000460680.1:c.1853C>A	p.Pro618His	p.P618H	ENST00000460680	NM_004656.3	618	cCt/cAt	14/17	0.0770245185744091	0	FACETS	0.183	0.156	0.212			1	INDETERMINATE	1	TRUE	0	0.51	0		681	568	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69988319	69988319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182533927	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	22	354	0	ENST00000394351.3:c.332C>T	p.Ala111Val	p.A111V	ENST00000394351	NM_000248.3	111	gCg/gTg	3/9	0.0770245185744091	0	FACETS	0.194	0.151	0.244			1	INDETERMINATE	1	TRUE	0	0.51	0		354	218	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499490	89499490	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs745567462	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	58	371	0	ENST00000336596.2:c.2660G>T	p.Ser887Ile	p.S887I	ENST00000336596	NM_005233.5	887	aGc/aTc	15/17	0.0770245185744091	0	FACETS	0.577	0.504	0.654			1	INDETERMINATE	1	TRUE	0	0.51	0		371	193	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967261	134967261	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	32	583	1	ENST00000398015.3:c.2600G>T	p.Ser867Ile	p.S867I	ENST00000398015	NM_004441.4	867	aGc/aTc	14/16	0.0770245185744091	0	FACETS	0.143	0.116	0.174			1	INDETERMINATE	1	TRUE	0	0.51	0		584	430	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138431083	138431083	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	33	372	0	ENST00000289153.2:c.1366G>T	p.Asp456Tyr	p.D456Y	ENST00000289153	NM_006219.2	456	Gac/Tac	8/22	0.0770245185744091	0	FACETS	0.622	0.52	0.73			1	INDETERMINATE	1	TRUE	0	0.51	0		372	102	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665023	138665023	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	21	115	0	ENST00000330315.3:c.542C>A	p.Ala181Asp	p.A181D	ENST00000330315	NM_023067.3	181	gCc/gAc	1/1	0.0770245185744091	0	FACETS	0.232	0.179	0.292			1	INDETERMINATE	1	TRUE	0	0.51	0		115	174	SUCCESS
ATR	545	MSKCC	GRCh37	3	142168378	142168378	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	46	403	0	ENST00000350721.4:c.7828A>G	p.Thr2610Ala	p.T2610A	ENST00000350721	NM_001184.3	2610	Aca/Gca	47/47	0.0770245185744091	0	FACETS	0.702	0.606	0.801			1	INDETERMINATE	1	TRUE	0	0.51	0		403	126	SUCCESS
ATR	545	MSKCC	GRCh37	3	142234278	142234278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	24	502	0	ENST00000350721.4:c.4462G>A	p.Ala1488Thr	p.A1488T	ENST00000350721	NM_001184.3	1488	Gca/Aca	25/47	0.0770245185744091	0	FACETS	0.448	0.358	0.547			1	INDETERMINATE	1	TRUE	0	0.51	0		502	103	SUCCESS
ATR	545	MSKCC	GRCh37	3	142241617	142241617	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	29	532	0	ENST00000350721.4:c.4219T>C	p.Tyr1407His	p.Y1407H	ENST00000350721	NM_001184.3	1407	Tat/Cat	23/47	0.0770245185744091	0	FACETS	0.387	0.315	0.467			1	INDETERMINATE	1	TRUE	0	0.51	0		532	144	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275300	142275300	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878996572	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	28	518	0	ENST00000350721.4:c.2003G>A	p.Arg668Gln	p.R668Q	ENST00000350721	NM_001184.3	668	cGg/cAg	9/47	0.0770245185744091	0	FACETS	0.304	0.245	0.37			1	INDETERMINATE	1	TRUE	0	0.51	0		518	177	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936089	178936089	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	67	612	0	ENST00000263967.3:c.1631C>A	p.Thr544Asn	p.T544N	ENST00000263967	NM_006218.2	544	aCt/aAt	10/21	0.0770245185744091	0	FACETS	0.771	0.686	0.858			1	INDETERMINATE	1	TRUE	0	0.51	0		612	167	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430861	181430861	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	197	964	1	ENST00000325404.1:c.713G>A	p.Gly238Asp	p.G238D	ENST00000325404	NM_003106.3	238	gGc/gAc	1/1	0.0770245185744091	0	FACETS	0.599	0.557	0.642			1	INDETERMINATE	1	TRUE	0	0.51	0		965	632	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430930	181430930	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	61	799	0	ENST00000325404.1:c.782C>A	p.Ser261Tyr	p.S261Y	ENST00000325404	NM_003106.3	261	tCc/tAc	1/1	0.0770245185744091	0	FACETS	0.327	0.283	0.373			1	INDETERMINATE	1	TRUE	0	0.51	0		799	359	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665360	182665360	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	13	220	0	ENST00000292782.4:c.581A>G	p.Asp194Gly	p.D194G	ENST00000292782	NM_020640.2	194	gAc/gGc	5/7	0.0770245185744091	0	FACETS	0.438	0.321	0.572			1	INDETERMINATE	1	TRUE	0	0.51	0		220	57	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446859	187446859	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761002552	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	142	800	1	ENST00000232014.4:c.1334G>A	p.Arg445Gln	p.R445Q	ENST00000232014	NM_001130845.1	445	cGg/cAg	5/10	0.0770245185744091	0	FACETS	0.512	0.469	0.557			1	INDETERMINATE	1	TRUE	0	0.51	0		801	533	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447462	187447462	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772973428	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	51	595	0	ENST00000232014.4:c.731G>A	p.Arg244Gln	p.R244Q	ENST00000232014	NM_001130845.1	244	cGg/cAg	5/10	0.0770245185744091	0	FACETS	0.292	0.249	0.338			1	INDETERMINATE	1	TRUE	0	0.51	0		595	336	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586497	189586497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199807776	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	41	307	0	ENST00000264731.3:c.1121C>T	p.Thr374Met	p.T374M	ENST00000264731	NM_003722.4	374	aCg/aTg	8/14	0.0770245185744091	0	FACETS	0.426	0.359	0.498			1	INDETERMINATE	1	TRUE	0	0.51	0		307	185	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902555	1902555	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	78	697	0	ENST00000382891.5:c.174G>T	p.Gln58His	p.Q58H	ENST00000382891	NM_133335.3	58	caG/caT	2/22	1	2	FACETS	0.678	0.598	0.764	0.678	0.598	0.764	SUBCLONAL	1	TRUE	1	0.51	2		697	451	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902635	1902635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759803629	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	33	613	0	ENST00000382891.5:c.254G>A	p.Arg85Gln	p.R85Q	ENST00000382891	NM_133335.3	85	cGg/cAg	2/22	1	2	FACETS	0.315	0.256	0.381	0.315	0.256	0.381	SUBCLONAL	1	TRUE	1	0.51	2		613	411	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920179	1920179	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	17	641	0	ENST00000382891.5:c.1239G>T	p.Glu413Asp	p.E413D	ENST00000382891	NM_133335.3	413	gaG/gaT	5/22	1	2	FACETS	0.203	0.151	0.265	0.203	0.151	0.265	SUBCLONAL	1	TRUE	1	0.51	2		641	328	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957034	1957034	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146318719	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	50	524	0	ENST00000382891.5:c.2485G>A	p.Val829Ile	p.V829I	ENST00000382891	NM_133335.3	829	Gtc/Atc	13/22	1	2	FACETS	0.431	0.366	0.502	0.431	0.366	0.502	SUBCLONAL	1	TRUE	1	0.51	2		524	455	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957731	1957731	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	44	635	1	ENST00000382891.5:c.2697C>A	p.Cys899Ter	p.C899*	ENST00000382891	NM_133335.3	899	tgC/tgA	15/22	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.51	2		636	148	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1978297	1978297	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	44	770	0	ENST00000382891.5:c.3717G>T	p.Glu1239Asp	p.E1239D	ENST00000382891	NM_133335.3	1239	gaG/gaT	21/22	1	2	FACETS	0.255	0.213	0.301	0.255	0.213	0.301	SUBCLONAL	1	TRUE	1	0.51	2		770	677	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750429	41750429	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	30	455	1	ENST00000226382.2:c.199C>A	p.Leu67Met	p.L67M	ENST00000226382	NM_003924.3	67	Ctg/Atg	1/3	1	2	FACETS	0.3	0.242	0.367	0.3	0.242	0.367	SUBCLONAL	1	TRUE	1	0.51	2		456	392	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155041	55155041	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	22	402	0	ENST00000257290.5:c.2750A>C	p.Lys917Thr	p.K917T	ENST00000257290	NM_006206.4	917	aAg/aCg	20/23	1	2	FACETS	0.523	0.408	0.653	0.523	0.408	0.653	SUBCLONAL	1	TRUE	1	0.51	2		402	165	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604698	55604698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1560426544	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	75	425	0	ENST00000288135.5:c.2906C>T	p.Pro969Leu	p.P969L	ENST00000288135	NM_000222.2	969	cCt/cTt	21/21	1	2	FACETS	0.801	0.707	0.902	0.801	0.707	0.902	CLONAL	1	TRUE	1	0.51	2		425	367	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953916	55953916	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	19	370	1	ENST00000263923.4:c.3520G>T	p.Asp1174Tyr	p.D1174Y	ENST00000263923	NM_002253.2	1174	Gac/Tac	27/30	1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	1	0.51	2		371	67	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968652	55968652	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	35	512	1	ENST00000263923.4:c.2011G>T	p.Gly671Ter	p.G671*	ENST00000263923	NM_002253.2	671	Gga/Tga	14/30	1	2	FACETS	0.7	0.58	0.833	0.7	0.58	0.833	SUBCLONAL	1	TRUE	1	0.51	2		513	196	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356122	66356122	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	49	493	0	ENST00000273854.3:c.1375T>C	p.Ser459Pro	p.S459P	ENST00000273854	NM_004439.5	459	Tct/Cct	5/18	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.51	2		493	191	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535288	66535288	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	38	690	0	ENST00000273854.3:c.173G>T	p.Ser58Ile	p.S58I	ENST00000273854	NM_004439.5	58	aGc/aTc	1/18	1	2	FACETS	0.304	0.25	0.363	0.304	0.25	0.363	SUBCLONAL	1	TRUE	1	0.51	2		690	491	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535325	66535325	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	56	745	2	ENST00000273854.3:c.136C>A	p.Leu46Met	p.L46M	ENST00000273854	NM_004439.5	46	Ctg/Atg	1/18	1	2	FACETS	0.347	0.297	0.403	0.347	0.297	0.403	SUBCLONAL	1	TRUE	1	0.51	2		747	632	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155982	106155982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	18	332	0	ENST00000380013.4:c.883G>A	p.Ala295Thr	p.A295T	ENST00000380013	NM_001127208.2	295	Gcc/Acc	3/11	1	2	FACETS	0.699	0.534	0.886	0.699	0.534	0.886	SUBCLONAL	1	TRUE	1	0.51	2		332	101	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158144	106158144	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	26	319	0	ENST00000380013.4:c.3045C>A	p.Ser1015Arg	p.S1015R	ENST00000380013	NM_001127208.2	1015	agC/agA	3/11	1	2	FACETS	0.902	0.728	1	0.902	0.728	1	CLONAL	1	TRUE	1	0.51	2		319	113	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193926	106193926	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	11	255	0	ENST00000380013.4:c.4388C>A	p.Thr1463Asn	p.T1463N	ENST00000380013	NM_001127208.2	1463	aCt/aAt	10/11	1	2	FACETS	0.392	0.273	0.538	0.392	0.273	0.538	SUBCLONAL	1	TRUE	1	0.51	2		255	110	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196725	106196725	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	15	440	0	ENST00000380013.4:c.5058C>A	p.Ser1686Arg	p.S1686R	ENST00000380013	NM_001127208.2	1686	agC/agA	11/11	1	2	FACETS	0.84	0.629	1	0.84	0.629	1	CLONAL	1	TRUE	1	0.51	2		440	70	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143029264	143029264	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	20	315	0	ENST00000262992.4:c.2356G>T	p.Glu786Ter	p.E786*	ENST00000262992	NM_001101669.1	786	Gaa/Taa	21/24	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.51	2		315	68	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143191893	143191893	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	21	400	0	ENST00000262992.4:c.538G>T	p.Glu180Ter	p.E180*	ENST00000262992	NM_001101669.1	180	Gaa/Taa	8/24	1	2	FACETS	0.535	0.415	0.671	0.535	0.415	0.671	SUBCLONAL	1	TRUE	1	0.51	2		400	154	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541553	187541553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	50	386	1	ENST00000441802.2:c.6187G>A	p.Ala2063Thr	p.A2063T	ENST00000441802	NM_005245.3	2063	Gcc/Acc	10/27	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.51	2		387	193	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541559	187541559	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	21	394	1	ENST00000441802.2:c.6181G>A	p.Ala2061Thr	p.A2061T	ENST00000441802	NM_005245.3	2061	Gca/Aca	10/27	1	2	FACETS	0.414	0.32	0.522	0.414	0.32	0.522	SUBCLONAL	1	TRUE	1	0.51	2		395	199	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584534	187584534	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	20	525	0	ENST00000441802.2:c.3499G>T	p.Asp1167Tyr	p.D1167Y	ENST00000441802	NM_005245.3	1167	Gat/Tat	3/27	1	2	FACETS	0.676	0.524	0.848	0.676	0.524	0.848	SUBCLONAL	1	TRUE	1	0.51	2		525	116	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31472177	31472177	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	10	702	0	ENST00000344624.3:c.2234C>A	p.Pro745His	p.P745H	ENST00000344624		745	cCt/cAt	14/33	1	2	FACETS	0.196	0.132	0.276	0.196	0.132	0.276	SUBCLONAL	1	TRUE	1	0.51	2		702	200	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950691	38950691	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	29	357	0	ENST00000357387.3:c.3259T>G	p.Phe1087Val	p.F1087V	ENST00000357387	NM_152756.3	1087	Ttc/Gtc	31/38	1	2	FACETS	0.79	0.659	0.926	1	0.954	1	CLONAL	2	TRUE	1	0.51	2		357	72	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38955748	38955748	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	28	399	0	ENST00000357387.3:c.2558C>A	p.Thr853Asn	p.T853N	ENST00000357387	NM_152756.3	853	aCt/aAt	26/38	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.51	2		399	96	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967325	38967325	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	19	262	0	ENST00000357387.3:c.1156G>T	p.Asp386Tyr	p.D386Y	ENST00000357387	NM_152756.3	386	Gac/Tac	14/38	1	2	FACETS	1	0.805	1	1	0.805	1	CLONAL	1	TRUE	1	0.51	2		262	72	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751185	57751185	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	12	349	0	ENST00000274289.3:c.1682C>T	p.Ala561Val	p.A561V	ENST00000274289	NM_006622.3	561	gCt/gTt	12/14	1	2	FACETS	0.475	0.337	0.641	0.475	0.337	0.641	SUBCLONAL	1	TRUE	1	0.51	2		349	99	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751920	57751920	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	54	618	0	ENST00000274289.3:c.1317G>T	p.Gln439His	p.Q439H	ENST00000274289	NM_006622.3	439	caG/caT	10/14	1	2	FACETS	0.664	0.57	0.765	0.664	0.57	0.765	SUBCLONAL	1	TRUE	1	0.51	2		618	319	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755783	57755783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	131	564	0	ENST00000274289.3:c.4G>A	p.Glu2Lys	p.E2K	ENST00000274289	NM_006622.3	2	Gag/Aag	1/14	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.51	2		564	368	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576493	67576493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	16	411	0	ENST00000274335.5:c.772C>A	p.Leu258Met	p.L258M	ENST00000274335		258	Ctg/Atg	5/15	1	2	FACETS	0.56	0.419	0.725	0.56	0.419	0.725	SUBCLONAL	1	TRUE	1	0.51	2		411	112	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589223	67589223	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	16	295	0	ENST00000274335.5:c.1211T>C	p.Leu404Ser	p.L404S	ENST00000274335		404	tTa/tCa	9/15	1	2	FACETS	0.705	0.53	0.906	0.705	0.53	0.906	CLONAL	1	TRUE	1	0.51	2		295	89	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961074	79961074	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	35	602	0	ENST00000265081.6:c.471G>T	p.Gln157His	p.Q157H	ENST00000265081	NM_002439.4	157	caG/caT	3/24	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.51	2		602	119	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564478	86564478	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	32	532	0	ENST00000274376.6:c.210G>T	p.Glu70Asp	p.E70D	ENST00000274376	NM_002890.2	70	gaG/gaT	1/25	1	2	FACETS	0.434	0.353	0.525	0.434	0.353	0.525	SUBCLONAL	1	TRUE	1	0.51	2		532	289	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672286	86672286	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	17	447	0	ENST00000274376.6:c.2088A>G	p.Ile696Met	p.I696M	ENST00000274376	NM_002890.2	696	atA/atG	16/25	1	2	FACETS	0.525	0.396	0.675	0.525	0.396	0.675	SUBCLONAL	1	TRUE	1	0.51	2		447	127	SUCCESS
APC	324	MSKCC	GRCh37	5	112173899	112173899	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	30	300	0	ENST00000257430.4:c.2608C>A	p.Pro870Thr	p.P870T	ENST00000257430	NM_000038.5	870	Cca/Aca	16/16	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.51	2		300	112	SUCCESS
APC	324	MSKCC	GRCh37	5	112175270	112175270	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	30	207	0	ENST00000257430.4:c.3979T>G	p.Ser1327Ala	p.S1327A	ENST00000257430	NM_000038.5	1327	Tca/Gca	16/16	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.51	2		207	96	SUCCESS
APC	324	MSKCC	GRCh37	5	112175924	112175924	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	12	212	0	ENST00000257430.4:c.4633T>G	p.Ser1545Ala	p.S1545A	ENST00000257430	NM_000038.5	1545	Tca/Gca	16/16	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.51	2		212	34	SUCCESS
APC	324	MSKCC	GRCh37	5	112178876	112178876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	18	331	0	ENST00000257430.4:c.7585G>A	p.Ala2529Thr	p.A2529T	ENST00000257430	NM_000038.5	2529	Gca/Aca	16/16	1	2	FACETS	1	0.78	1	1	0.78	1	CLONAL	1	TRUE	1	0.51	2		331	70	SUCCESS
APC	324	MSKCC	GRCh37	5	112179699	112179699	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	10	208	0	ENST00000257430.4:c.8408C>A	p.Ser2803Tyr	p.S2803Y	ENST00000257430	NM_000038.5	2803	tCt/tAt	16/16	1	2	FACETS	0.33	0.224	0.46	0.33	0.224	0.46	SUBCLONAL	1	TRUE	1	0.51	2		208	119	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131972871	131972871	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs745797941	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	24	264	0	ENST00000265335.6:c.3454C>T	p.Arg1152Ter	p.R1152*	ENST00000265335		1152	Cga/Tga	22/25	1	2	FACETS	1	0.812	1	1	0.812	1	CLONAL	1	TRUE	1	0.51	2		264	93	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500861	149500861	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	29	660	0	ENST00000261799.4:c.2369C>T	p.Thr790Ile	p.T790I	ENST00000261799	NM_002609.3	790	aCt/aTt	17/23	1	2	FACETS	0.298	0.239	0.366	0.298	0.239	0.366	SUBCLONAL	1	TRUE	1	0.51	2		660	381	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523064	176523064	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	69	623	0	ENST00000292408.4:c.1828C>A	p.His610Asn	p.H610N	ENST00000292408	NM_213647.1	610	Cac/Aac	14/18	1	2	FACETS	0.687	0.601	0.779	0.687	0.601	0.779	SUBCLONAL	1	TRUE	1	0.51	2		623	394	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631207	176631207	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759976291	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	17	397	1	ENST00000439151.2:c.1150G>A	p.Val384Ile	p.V384I	ENST00000439151	NM_022455.4	384	Gtc/Atc	4/23	1	2	FACETS	0.34	0.254	0.441	0.34	0.254	0.441	SUBCLONAL	1	TRUE	1	0.51	2		398	196	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707682	176707682	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	45	432	0	ENST00000439151.2:c.5739C>A	p.Asn1913Lys	p.N1913K	ENST00000439151	NM_022455.4	1913	aaC/aaA	18/23	1	2	FACETS	0.799	0.678	0.929	0.799	0.678	0.929	CLONAL	1	TRUE	1	0.51	2		432	221	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176715859	176715859	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	57	493	1	ENST00000439151.2:c.6191G>T	p.Gly2064Val	p.G2064V	ENST00000439151	NM_022455.4	2064	gGg/gTg	21/23	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.51	2		494	165	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393318	393318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	24	505	0	ENST00000380956.4:c.166C>T	p.His56Tyr	p.H56Y	ENST00000380956	NM_001195286.1	56	Cac/Tac	2/9	1	2	FACETS	0.268	0.21	0.335	0.268	0.21	0.335	SUBCLONAL	1	TRUE	1	0.51	2		505	351	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398831	398831	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	55	437	0	ENST00000380956.4:c.641G>A	p.Cys214Tyr	p.C214Y	ENST00000380956	NM_001195286.1	214	tGc/tAc	6/9	1	2	FACETS	0.999	0.865	1	0.999	0.865	1	CLONAL	1	TRUE	1	0.51	2		437	216	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401616	401616	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	20	444	0	ENST00000380956.4:c.938G>T	p.Arg313Met	p.R313M	ENST00000380956	NM_001195286.1	313	aGg/aTg	7/9	1	2	FACETS	0.381	0.292	0.484	0.381	0.292	0.484	SUBCLONAL	1	TRUE	1	0.51	2		444	206	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020999	26020999	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	56	440	0	ENST00000357647.3:c.282G>T	p.Gln94His	p.Q94H	ENST00000357647	NM_003529.2	94	caG/caT	1/1	1	2	FACETS	0.985	0.854	1	0.985	0.854	1	CLONAL	1	TRUE	1	0.51	2		440	223	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858176	27858176	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	10	433	0	ENST00000359303.2:c.395G>A	p.Arg132His	p.R132H	ENST00000359303	NM_003535.2	132	cGt/cAt	1/1	1	2	FACETS	0.205	0.139	0.289	0.205	0.139	0.289	SUBCLONAL	1	TRUE	1	0.51	2		433	191	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672309	30672309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269292330	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	99	856	1	ENST00000376406.3:c.4651C>T	p.Pro1551Ser	p.P1551S	ENST00000376406	NM_014641.2	1551	Ccc/Tcc	10/15	1	2	FACETS	0.861	0.773	0.954	0.861	0.773	0.954	CLONAL	1	TRUE	1	0.51	2		857	451	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681673	30681673	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1379883443	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	60	521	0	ENST00000376406.3:c.424C>T	p.Arg142Trp	p.R142W	ENST00000376406	NM_014641.2	142	Cgg/Tgg	3/15	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.51	2		521	226	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681928	30681928	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	10	398	0	ENST00000376406.3:c.169G>T	p.Gly57Cys	p.G57C	ENST00000376406	NM_014641.2	57	Ggc/Tgc	3/15	1	2	FACETS	0.214	0.145	0.301	0.214	0.145	0.301	SUBCLONAL	1	TRUE	1	0.51	2		398	183	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948312	31948312	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	97	649	1	ENST00000375333.2:c.900G>T	p.Lys300Asn	p.K300N	ENST00000375333	NM_032454.1	300	aaG/aaT	6/8	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.51	2		650	349	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164165	32164165	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	139	506	0	ENST00000375023.3:c.5234A>G	p.Asn1745Ser	p.N1745S	ENST00000375023	NM_004557.3	1745	aAc/aGc	29/30	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.51	2		506	435	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187523	32187523	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	76	714	0	ENST00000375023.3:c.1356C>A	p.Cys452Ter	p.C452*	ENST00000375023	NM_004557.3	452	tgC/tgA	8/30	1	2	FACETS	0.648	0.57	0.731	0.648	0.57	0.731	SUBCLONAL	1	TRUE	1	0.51	2		714	460	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188913	32188913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	34	791	0	ENST00000375023.3:c.641C>T	p.Thr214Ile	p.T214I	ENST00000375023	NM_004557.3	214	aCc/aTc	4/30	1	2	FACETS	0.318	0.26	0.384	0.318	0.26	0.384	SUBCLONAL	1	TRUE	1	0.51	2		791	419	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800446	32800446	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs781370484	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	43	966	0	ENST00000374899.4:c.1101G>A	p.Trp367Ter	p.W367*	ENST00000374899	NM_018833.2	367	tgG/tgA	6/12	1	2	FACETS	0.258	0.215	0.306	0.258	0.215	0.306	SUBCLONAL	1	TRUE	1	0.51	2		966	653	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803527	32803527	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	29	631	1	ENST00000374899.4:c.632G>T	p.Gly211Val	p.G211V	ENST00000374899	NM_018833.2	211	gGa/gTa	4/12	1	2	FACETS	0.206	0.164	0.253	0.206	0.164	0.253	SUBCLONAL	1	TRUE	1	0.51	2		632	553	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32814845	32814845	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	20	706	0	ENST00000354258.4:c.2220G>T	p.Gln740His	p.Q740H	ENST00000354258	NM_000593.5	740	caG/caT	10/11	1	2	FACETS	0.223	0.17	0.286	0.223	0.17	0.286	SUBCLONAL	1	TRUE	1	0.51	2		706	351	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287828	33287828	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	88	925	0	ENST00000374542.5:c.1425G>T	p.Glu475Asp	p.E475D	ENST00000374542	NM_001141970.1	475	gaG/gaT	5/8	1	2	FACETS	0.84	0.748	0.936	0.84	0.748	0.936	CLONAL	1	TRUE	1	0.51	2		925	411	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36653548	36653548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374154006	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	114	547	0	ENST00000244741.5:c.466C>T	p.Arg156Trp	p.R156W	ENST00000244741	NM_000389.4	156	Cgg/Tgg	3/3	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.51	2		547	428	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138365	37138365	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	49	497	0	ENST00000373509.5:c.14A>G	p.Lys5Arg	p.K5R	ENST00000373509	NM_002648.3	5	aAa/aGa	1/6	1	2	FACETS	0.371	0.314	0.434	0.371	0.314	0.434	SUBCLONAL	1	TRUE	1	0.51	2		497	518	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41905124	41905124	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	19	338	0	ENST00000372991.4:c.423G>T	p.Glu141Asp	p.E141D	ENST00000372991	NM_001760.3	141	gaG/gaT	3/5	1	2	FACETS	0.374	0.285	0.478	0.374	0.285	0.478	SUBCLONAL	1	TRUE	1	0.51	2		338	199	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43746228	43746228	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	25	600	0	ENST00000523873.1:c.347A>C	p.His116Pro	p.H116P	ENST00000523873		116	cAc/cCc	4/8	1	2	FACETS	0.43	0.34	0.532	0.43	0.34	0.532	SUBCLONAL	1	TRUE	1	0.51	2		600	228	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553111	106553111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	23	489	1	ENST00000369096.4:c.1076C>T	p.Thr359Met	p.T359M	ENST00000369096	NM_001198.3	359	aCg/aTg	5/7	1	2	FACETS	0.245	0.191	0.308	0.245	0.191	0.308	SUBCLONAL	1	TRUE	1	0.51	2		490	368	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554979	106554979	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	60	448	0	ENST00000369096.4:c.2096T>C	p.Leu699Pro	p.L699P	ENST00000369096	NM_001198.3	699	cTc/cCc	7/7	1	2	FACETS	0.749	0.65	0.856	0.749	0.65	0.856	SUBCLONAL	1	TRUE	1	0.51	2		448	314	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638408	117638408	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	39	422	0	ENST00000368508.3:c.6033G>T	p.Lys2011Asn	p.K2011N	ENST00000368508	NM_002944.2	2011	aaG/aaT	38/43	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.51	2		422	117	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687370	117687370	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs535778217	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	10	368	0	ENST00000368508.3:c.2681G>A	p.Arg894Gln	p.R894Q	ENST00000368508	NM_002944.2	894	cGg/cAg	18/43	1	2	FACETS	0.316	0.215	0.442	0.316	0.215	0.442	SUBCLONAL	1	TRUE	1	0.51	2		368	124	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687404	117687404	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	16	363	0	ENST00000368508.3:c.2647A>C	p.Ile883Leu	p.I883L	ENST00000368508	NM_002944.2	883	Att/Ctt	18/43	1	2	FACETS	0.66	0.496	0.85	0.66	0.496	0.85	SUBCLONAL	1	TRUE	1	0.51	2		363	95	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708139	117708139	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	30	438	0	ENST00000368508.3:c.2038G>A	p.Ala680Thr	p.A680T	ENST00000368508	NM_002944.2	680	Gct/Act	14/43	1	2	FACETS	1	0.84	1	1	0.84	1	CLONAL	1	TRUE	1	0.51	2		438	115	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519472	137519472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	12	357	0	ENST00000367739.4:c.1166C>T	p.Pro389Leu	p.P389L	ENST00000367739	NM_000416.2	389	cCt/cTt	7/7	1	2	FACETS	0.56	0.399	0.752	0.56	0.399	0.752	SUBCLONAL	1	TRUE	1	0.51	2		357	84	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519502	137519502	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	11	372	0	ENST00000367739.4:c.1136C>A	p.Ser379Tyr	p.S379Y	ENST00000367739	NM_000416.2	379	tCt/tAt	7/7	1	2	FACETS	0.372	0.258	0.511	0.372	0.258	0.511	SUBCLONAL	1	TRUE	1	0.51	2		372	116	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997711	149997711	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	23	385	1	ENST00000253339.5:c.2756C>A	p.Pro919His	p.P919H	ENST00000253339		919	cCt/cAt	5/7	1	2	FACETS	0.784	0.621	0.966	0.784	0.621	0.966	CLONAL	1	TRUE	1	0.51	2		386	115	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997774	149997774	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	29	510	0	ENST00000253339.5:c.2693C>A	p.Ala898Asp	p.A898D	ENST00000253339		898	gCt/gAt	5/7	1	2	FACETS	0.31	0.249	0.38	0.31	0.249	0.38	SUBCLONAL	1	TRUE	1	0.51	2		510	367	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004271	150004271	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	19	397	0	ENST00000253339.5:c.1954A>G	p.Lys652Glu	p.K652E	ENST00000253339		652	Aaa/Gaa	3/7	1	2	FACETS	0.955	0.743	1	0.955	0.743	1	CLONAL	1	TRUE	1	0.51	2		397	78	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150022947	150022947	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1377004205	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	48	541	0	ENST00000253339.5:c.316C>T	p.Leu106Phe	p.L106F	ENST00000253339		106	Ctt/Ttt	1/7	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.51	2		541	155	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405944	157405944	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1305375329	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	50	501	0	ENST00000346085.5:c.2186C>A	p.Ser729Tyr	p.S729Y	ENST00000346085	NM_020732.3	729	tCc/tAc	6/20	1	2	FACETS	0.589	0.502	0.683	0.589	0.502	0.683	SUBCLONAL	1	TRUE	1	0.51	2		501	333	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157431654	157431654	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762229592	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	97	572	1	ENST00000346085.5:c.2330C>T	p.Ser777Phe	p.S777F	ENST00000346085	NM_020732.3	777	tCc/tTc	7/20	1	2	FACETS	0.758	0.678	0.842	0.758	0.678	0.842	SUBCLONAL	1	TRUE	1	0.51	2		573	502	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683592	162683592	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	98	498	0	ENST00000366898.1:c.377A>G	p.Asp126Gly	p.D126G	ENST00000366898	NM_004562.2	126	gAc/gGc	3/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.51	2		498	309	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683745	162683745	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	71	606	0	ENST00000366898.1:c.224G>T	p.Arg75Ile	p.R75I	ENST00000366898	NM_004562.2	75	aGa/aTa	3/12	1	2	FACETS	0.821	0.722	0.927	0.821	0.722	0.927	CLONAL	1	TRUE	1	0.51	2		606	339	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6029443	6029443	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	30	425	1	ENST00000265849.7:c.1132C>A	p.Leu378Met	p.L378M	ENST00000265849	NM_000535.5	378	Ctg/Atg	10/15	1	2	FACETS	0.811	0.663	0.974	0.811	0.663	0.974	CLONAL	1	TRUE	1	0.51	2		426	145	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467828	50467829	+	missense_variant	Missense_Mutation	DNP	GC	GC	AT	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	23	454	0	ENST00000331340.3:c.1063_1064delinsAT	p.Ala355Met	p.A355M	ENST00000331340	NM_006060.4	355	GCg/ATg	8/8	1	2	FACETS	0.318	0.248	0.398	0.318	0.248	0.398	SUBCLONAL	1	TRUE	1	0.51	2		454	284	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467870	50467870	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	26	435	0	ENST00000331340.3:c.1105G>T	p.Ala369Ser	p.A369S	ENST00000331340	NM_006060.4	369	Gcc/Tcc	8/8	1	2	FACETS	0.389	0.309	0.48	0.389	0.309	0.48	SUBCLONAL	1	TRUE	1	0.51	2		435	262	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220269	55220269	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	122	852	0	ENST00000275493.2:c.659C>A	p.Ser220Tyr	p.S220Y	ENST00000275493	NM_005228.3	220	tCc/tAc	6/28	1	2	FACETS	0.748	0.677	0.821	0.748	0.677	0.821	SUBCLONAL	1	TRUE	1	0.51	2		852	640	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224488	55224488	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	33	443	0	ENST00000275493.2:c.1170G>T	p.Gln390His	p.Q390H	ENST00000275493	NM_005228.3	390	caG/caT	10/28	1	2	FACETS	0.98	0.813	1	0.98	0.813	1	CLONAL	1	TRUE	1	0.51	2		443	132	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268089	55268089	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1140476	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	89	801	0	ENST00000275493.2:c.2929C>T	p.Arg977Cys	p.R977C	ENST00000275493	NM_005228.3	977	Cgc/Tgc	24/28	1	2	FACETS	0.879	0.785	0.979	0.879	0.785	0.979	CLONAL	1	TRUE	1	0.51	2		801	397	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508460	106508460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	26	243	0	ENST00000359195.3:c.454C>T	p.Arg152Trp	p.R152W	ENST00000359195	NM_002649.2	152	Cgg/Tgg	2/11	1	2	FACETS	0.887	0.715	1	0.887	0.715	1	CLONAL	1	TRUE	1	0.51	2		243	115	SUCCESS
MET	4233	MSKCC	GRCh37	7	116414864	116414864	+	intron_variant	Intron	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	77	685	0	ENST00000397752.3:c.3029-71C>A		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.51	2		685	209	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423456	116423456	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	15	303	0	ENST00000397752.3:c.3731A>C	p.Lys1244Thr	p.K1244T	ENST00000397752	NM_000245.2	1244	aAg/aCg	19/21	1	2	FACETS	0.56	0.415	0.73	0.56	0.415	0.73	SUBCLONAL	1	TRUE	1	0.51	2		303	105	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860030	151860030	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	23	331	2	ENST00000262189.6:c.10632C>A	p.Phe3544Leu	p.F3544L	ENST00000262189	NM_170606.2	3544	ttC/ttA	43/59	1	2	FACETS	1	0.8	1	1	0.8	1	CLONAL	1	TRUE	1	0.51	2		333	90	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874400	151874400	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	11	386	0	ENST00000262189.6:c.8138A>C	p.Asp2713Ala	p.D2713A	ENST00000262189	NM_170606.2	2713	gAt/gCt	38/59	1	2	FACETS	0.634	0.446	0.858	0.634	0.446	0.858	SUBCLONAL	1	TRUE	1	0.51	2		386	68	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879117	151879117	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	27	716	0	ENST00000262189.6:c.5828C>T	p.Ala1943Val	p.A1943V	ENST00000262189	NM_170606.2	1943	gCa/gTa	36/59	1	2	FACETS	0.646	0.519	0.787	0.646	0.519	0.787	SUBCLONAL	1	TRUE	1	0.51	2		716	164	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891172	151891172	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	33	458	0	ENST00000262189.6:c.4582C>A	p.Leu1528Ile	p.L1528I	ENST00000262189	NM_170606.2	1528	Ctt/Att	31/59	1	2	FACETS	0.905	0.749	1	0.905	0.749	1	CLONAL	1	TRUE	1	0.51	2		458	143	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945640	151945640	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	17	782	0	ENST00000262189.6:c.1879G>T	p.Asp627Tyr	p.D627Y	ENST00000262189	NM_170606.2	627	Gac/Tac	14/59	1	2	FACETS	0.388	0.29	0.502	0.388	0.29	0.502	SUBCLONAL	1	TRUE	1	0.51	2		782	172	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945653	151945653	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	22	894	0	ENST00000262189.6:c.1866A>C	p.Glu622Asp	p.E622D	ENST00000262189	NM_170606.2	622	gaA/gaC	14/59	1	2	FACETS	0.464	0.362	0.581	0.464	0.362	0.581	SUBCLONAL	1	TRUE	1	0.51	2		894	186	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133333	38133333	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	37	468	0	ENST00000317025.8:c.4140C>A	p.Phe1380Leu	p.F1380L	ENST00000317025	NM_023034.1	1380	ttC/ttA	24/24	1	2	FACETS	0.623	0.517	0.739	0.623	0.517	0.739	SUBCLONAL	1	TRUE	1	0.51	2		468	233	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38134008	38134008	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753149466	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	45	460	0	ENST00000317025.8:c.3878C>T	p.Ala1293Val	p.A1293V	ENST00000317025	NM_023034.1	1293	gCg/gTg	23/24	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.51	2		460	139	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020482	69020482	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1292060270	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	31	649	0	ENST00000288368.4:c.2854A>G	p.Thr952Ala	p.T952A	ENST00000288368	NM_024870.2	952	Acc/Gcc	24/40	1	2	FACETS	0.844	0.693	1	0.844	0.693	1	CLONAL	1	TRUE	1	0.51	2		649	144	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869620	117869620	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	16	525	2	ENST00000297338.2:c.574C>A	p.Leu192Ile	p.L192I	ENST00000297338	NM_006265.2	192	Cta/Ata	6/14	1	2	FACETS	0.523	0.39	0.677	0.523	0.39	0.677	SUBCLONAL	1	TRUE	1	0.51	2		527	120	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753139	128753139	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	48	282	0	ENST00000377970.2:c.1300T>G	p.Leu434Val	p.L434V	ENST00000377970	NM_002467.4	434	Ttg/Gtg	3/3	1	2	FACETS	0.871	0.762	0.983	1	0.975	1	CLONAL	2	TRUE	1	0.51	2		282	108	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5463023	5463023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	10	298	0	ENST00000381577.3:c.584G>A	p.Ser195Asn	p.S195N	ENST00000381577	NM_014143.3	195	aGc/aAc	4/7	1	2	FACETS	0.49	0.336	0.678	0.49	0.336	0.678	SUBCLONAL	1	TRUE	1	0.51	2		298	80	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340402	8340402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759538026	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	68	485	0	ENST00000356435.5:c.5194C>T	p.Leu1732Phe	p.L1732F	ENST00000356435		1732	Ctc/Ttc	31/35	1	2	FACETS	0.886	0.778	1	0.886	0.778	1	CLONAL	1	TRUE	1	0.51	2		485	301	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449803	8449803	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1407336366	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	33	577	0	ENST00000356435.5:c.3910A>G	p.Ile1304Val	p.I1304V	ENST00000356435		1304	Ata/Gta	23/35	1	2	FACETS	0.563	0.461	0.675	0.563	0.461	0.675	SUBCLONAL	1	TRUE	1	0.51	2		577	230	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524931	8524931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	42	342	0	ENST00000356435.5:c.673G>A	p.Val225Ile	p.V225I	ENST00000356435		225	Gtc/Atc	7/35	1	2	FACETS	0.963	0.816	1	0.963	0.816	1	CLONAL	1	TRUE	1	0.51	2		342	171	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015068	37015068	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	91	627	0	ENST00000358127.4:c.336G>A	p.Trp112Ter	p.W112*	ENST00000358127	NM_001280556.1	112	tgG/tgA	3/10	1	2	FACETS	0.978	0.875	1	0.978	0.875	1	CLONAL	1	TRUE	1	0.51	2		627	365	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606289	93606289	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	71	755	0	ENST00000375746.1:c.109G>T	p.Gly37Trp	p.G37W	ENST00000375746	NM_001174167.1	37	Ggg/Tgg	2/14	1	2	FACETS	0.75	0.659	0.848	0.75	0.659	0.848	SUBCLONAL	1	TRUE	1	0.51	2		755	371	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242255	98242255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs555332902	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	30	543	1	ENST00000331920.6:c.1063G>A	p.Val355Ile	p.V355I	ENST00000331920	NM_000264.3	355	Gtc/Atc	7/24	1	2	FACETS	0.376	0.303	0.458	0.376	0.303	0.458	SUBCLONAL	1	TRUE	1	0.51	2		544	313	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908769	101908769	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	16	318	0	ENST00000374994.4:c.1133A>G	p.Tyr378Cys	p.Y378C	ENST00000374994	NM_004612.2	378	tAc/tGc	7/9	1	2	FACETS	1	0.834	1	1	0.834	1	CLONAL	1	TRUE	1	0.51	2		318	56	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249978	110249978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	79	629	1	ENST00000374672.4:c.697G>A	p.Ala233Thr	p.A233T	ENST00000374672	NM_004235.4	233	Gcg/Acg	3/5	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.51	2		630	260	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750349	133750349	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	56	543	0	ENST00000318560.5:c.1180A>G	p.Thr394Ala	p.T394A	ENST00000318560	NM_005157.4	394	Aca/Gca	7/11	1	2	FACETS	0.776	0.67	0.89	0.776	0.67	0.89	SUBCLONAL	1	TRUE	1	0.51	2		543	283	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760840	133760840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113458739	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	112	771	1	ENST00000318560.5:c.3163G>A	p.Ala1055Thr	p.A1055T	ENST00000318560	NM_005157.4	1055	Gca/Aca	11/11	1	2	FACETS	0.951	0.86	1	0.951	0.86	1	CLONAL	1	TRUE	1	0.51	2		772	462	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797259	135797259	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060505021	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	20	244	0	ENST00000298552.3:c.610C>T	p.Arg204Cys	p.R204C	ENST00000298552	NM_001162426.1	204	Cgt/Tgt	7/23	1	2	FACETS	0.98	0.768	1	0.98	0.768	1	CLONAL	1	TRUE	1	0.51	2		244	80	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293669	137293669	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	52	914	1	ENST00000481739.1:c.220C>A	p.Pro74Thr	p.P74T	ENST00000481739	NM_002957.4	74	Ccc/Acc	2/10	1	2	FACETS	0.377	0.321	0.439	0.377	0.321	0.439	SUBCLONAL	1	TRUE	1	0.51	2		915	541	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395084	139395084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764798860	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	102	758	0	ENST00000277541.6:c.5854G>A	p.Ala1952Thr	p.A1952T	ENST00000277541	NM_017617.3	1952	Gca/Aca	31/34	1	2	FACETS	0.693	0.621	0.769	0.693	0.621	0.769	SUBCLONAL	1	TRUE	1	0.51	2		758	577	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396914	139396914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	29	386	0	ENST00000277541.6:c.5194G>A	p.Ala1732Thr	p.A1732T	ENST00000277541	NM_017617.3	1732	Gcg/Acg	28/34	1	2	FACETS	0.302	0.242	0.37	0.302	0.242	0.37	SUBCLONAL	1	TRUE	1	0.51	2		386	377	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399282	139399282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867637156	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	47	921	1	ENST00000277541.6:c.4861G>A	p.Gly1621Ser	p.G1621S	ENST00000277541	NM_017617.3	1621	Ggc/Agc	26/34	1	2	FACETS	0.261	0.219	0.307	0.261	0.219	0.307	SUBCLONAL	1	TRUE	1	0.51	2		922	707	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403344	139403344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1272970231	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	26	708	0	ENST00000277541.6:c.3149G>A	p.Gly1050Asp	p.G1050D	ENST00000277541	NM_017617.3	1050	gGc/gAc	19/34	1	2	FACETS	0.235	0.185	0.292	0.235	0.185	0.292	SUBCLONAL	1	TRUE	1	0.51	2		708	434	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413993	139413993	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	35	799	0	ENST00000277541.6:c.767A>G	p.Glu256Gly	p.E256G	ENST00000277541	NM_017617.3	256	gAa/gGa	5/34	1	2	FACETS	0.306	0.25	0.368	0.306	0.25	0.368	SUBCLONAL	1	TRUE	1	0.51	2		799	449	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15833832	15833832	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	14	753	0	ENST00000307771.7:c.590G>A	p.Ser197Asn	p.S197N	ENST00000307771	NM_005089.3	197	aGt/aAt	8/11	0.0770245185744091	0	FACETS	0.131	0.095	0.175			1	INDETERMINATE	1	TRUE	0	0.51	0		753	205	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922064	39922064	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	84	830	0	ENST00000378444.4:c.4108C>A	p.Pro1370Thr	p.P1370T	ENST00000378444	NM_001123385.1	1370	Cct/Act	9/15	0.0770245185744091	0	FACETS	0.376	0.334	0.421			1	INDETERMINATE	1	TRUE	0	0.51	0		830	429	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937157	39937157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	110	827	0	ENST00000378444.4:c.26G>A	p.Gly9Glu	p.G9E	ENST00000378444	NM_001123385.1	9	gGg/gAg	2/15	0.0770245185744091	0	FACETS	0.424	0.383	0.468			1	INDETERMINATE	1	TRUE	0	0.51	0		827	498	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918334	44918334	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	36	509	0	ENST00000377967.4:c.959C>A	p.Thr320Lys	p.T320K	ENST00000377967	NM_021140.2	320	aCa/aAa	11/29	0.0770245185744091	0	FACETS	0.744	0.632	0.86			1	INDETERMINATE	1	TRUE	0	0.51	0		509	93	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929164	44929164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757564026	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	51	641	0	ENST00000377967.4:c.2264C>T	p.Thr755Met	p.T755M	ENST00000377967	NM_021140.2	755	aCg/aTg	17/29	0.0770245185744091	0	FACETS	0.505	0.435	0.579			1	INDETERMINATE	1	TRUE	0	0.51	0		641	194	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030553	47030553	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782480608	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	79	693	0	ENST00000377604.3:c.328G>A	p.Glu110Lys	p.E110K	ENST00000377604	NM_001204468.1	110	Gag/Aag	4/24	0.0770245185744091	0	FACETS	0.482	0.428	0.539			1	INDETERMINATE	1	TRUE	0	0.51	0		693	315	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426677	47426677	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	103	705	0	ENST00000377045.4:c.922A>G	p.Ser308Gly	p.S308G	ENST00000377045	NM_001654.4	308	Agt/Ggt	10/16	0.0770245185744091	0	FACETS	0.429	0.386	0.475			1	INDETERMINATE	1	TRUE	0	0.51	0		705	461	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426758	47426758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1206503276	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	120	662	1	ENST00000377045.4:c.1003G>A	p.Val335Met	p.V335M	ENST00000377045	NM_001654.4	335	Gtg/Atg	10/16	0.0770245185744091	0	FACETS	0.382	0.346	0.421			1	INDETERMINATE	1	TRUE	0	0.51	0		663	603	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650559	48650559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1482381233	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	62	835	2	ENST00000376670.3:c.529G>A	p.Gly177Arg	p.G177R	ENST00000376670	NM_002049.3	177	Ggg/Agg	3/6	0.0770245185744091	0	FACETS	0.308	0.267	0.352			1	INDETERMINATE	1	TRUE	0	0.51	0		837	387	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410087	63410087	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	22	754	0	ENST00000330258.3:c.3080A>G	p.His1027Arg	p.H1027R	ENST00000330258	NM_152424.3	1027	cAc/cGc	2/2	0.0770245185744091	0	FACETS	0.116	0.09	0.147			1	INDETERMINATE	1	TRUE	0	0.51	0		754	364	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410891	63410891	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	27	659	0	ENST00000330258.3:c.2276T>C	p.Val759Ala	p.V759A	ENST00000330258	NM_152424.3	759	gTt/gCt	2/2	0.0770245185744091	0	FACETS	0.234	0.187	0.287			1	INDETERMINATE	1	TRUE	0	0.51	0		659	222	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411056	63411056	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768098639	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	72	637	1	ENST00000330258.3:c.2111G>A	p.Arg704His	p.R704H	ENST00000330258	NM_152424.3	704	cGt/cAt	2/2	0.0770245185744091	0	FACETS	0.516	0.456	0.579			1	INDETERMINATE	1	TRUE	0	0.51	0		638	268	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412602	63412602	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	24	702	1	ENST00000330258.3:c.565C>T	p.Gln189Ter	p.Q189*	ENST00000330258	NM_152424.3	189	Caa/Taa	2/2	0.0770245185744091	0	FACETS	0.144	0.113	0.18			1	INDETERMINATE	1	TRUE	0	0.51	0		703	320	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356290	70356290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	97	657	0	ENST00000374080.3:c.5185C>T	p.His1729Tyr	p.H1729Y	ENST00000374080		1729	Cac/Tac	37/45	0.0770245185744091	0	FACETS	0.42	0.376	0.466			1	INDETERMINATE	1	TRUE	0	0.51	0		657	444	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763988	76763988	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	46	779	1	ENST00000373344.5:c.7320G>T	p.Lys2440Asn	p.K2440N	ENST00000373344	NM_000489.3	2440	aaG/aaT	35/35	0.0770245185744091	0	FACETS	0.352	0.299	0.41			1	INDETERMINATE	1	TRUE	0	0.51	0		780	251	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890125	76890125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	10	492	1	ENST00000373344.5:c.4769G>A	p.Cys1590Tyr	p.C1590Y	ENST00000373344	NM_000489.3	1590	tGc/tAc	17/35	0.0770245185744091	0	FACETS	0.1	0.067	0.141			1	INDETERMINATE	1	TRUE	0	0.51	0		493	192	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907796	76907796	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	20	321	1	ENST00000373344.5:c.4365G>T	p.Glu1455Asp	p.E1455D	ENST00000373344	NM_000489.3	1455	gaG/gaT	15/35	0.0770245185744091	0	FACETS	0.384	0.299	0.48			1	INDETERMINATE	1	TRUE	0	0.51	0		322	100	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938596	76938596	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	21	688	0	ENST00000373344.5:c.2152A>G	p.Lys718Glu	p.K718E	ENST00000373344	NM_000489.3	718	Aaa/Gaa	9/35	0.0770245185744091	0	FACETS	0.273	0.212	0.342			1	INDETERMINATE	1	TRUE	0	0.51	0		688	148	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944400	76944400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	10	428	0	ENST00000373344.5:c.505G>A	p.Val169Met	p.V169M	ENST00000373344	NM_000489.3	169	Gtg/Atg	7/35	0.0770245185744091	0	FACETS	0.133	0.09	0.187			1	INDETERMINATE	1	TRUE	0	0.51	0		428	144	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615626	100615626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782467781	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	49	650	1	ENST00000308731.7:c.706C>T	p.Arg236Trp	p.R236W	ENST00000308731	NM_000061.2	236	Cgg/Tgg	8/19	0.0770245185744091	0	FACETS	0.564	0.486	0.646			1	INDETERMINATE	1	TRUE	0	0.51	0		651	167	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195716	123195716	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	44	435	0	ENST00000218089.9:c.1630G>T	p.Gly544Ter	p.G544*	ENST00000218089	NM_001042749.1	544	Gga/Tga	17/35	0.0770245185744091	0	FACETS	0.556	0.475	0.642			1	INDETERMINATE	1	TRUE	0	0.51	0		435	152	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943665	9943665	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	44	598	0	ENST00000330684.3:c.1276A>G	p.Thr426Ala	p.T426A	ENST00000330684	NM_001134407.1	426	Acc/Gcc	5/13	1	2	FACETS	0.493	0.415	0.579	0.493	0.415	0.579	SUBCLONAL	1	TRUE	1	0.51	2		598	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0032593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	11	997	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	1	2	FACETS	0.429	0.295	0.596	0.429	0.295	0.596	SUBCLONAL	1	TRUE	1	0.15	2		997	342	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0032593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	23	730	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	1	2	FACETS	0.699	0.544	0.879	0.699	0.544	0.879	SUBCLONAL	1	TRUE	1	0.15	2		730	439	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0032593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	28	597	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.15	2		597	293	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971209	21971209	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1554654224	NA	P-0032593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	30	307	0	ENST00000304494.5:c.151-2A>G		p.X51_splice	ENST00000304494	NM_000077.4	51			1	2	FACETS	0.962	0.781	1	1	0.957	1	CLONAL	2	TRUE	1	0.15	2		307	208	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0032593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	15	462	1				ENST00000310581	NM_198253.2	-/1132			0.205803299913047	0	FACETS	1	0.867	1			1	CLONAL	1	TRUE	0	0.15	0		463	128	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	26	396	1	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	0.205803299913047	3	FACETS	1	0.89	1	0.601	0.477	0.743	CLONAL	1	TRUE	1	0.15	3		397	310	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928078	178928080	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs587776933	NA	P-0032593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	30	571	0	ENST00000263967.3:c.1359_1361del	p.Glu453del	p.E453del	ENST00000263967	NM_006218.2	452	ttAGAa/tta	8/21	0.205803299913047	3	FACETS	0.817	0.657	1	0.409	0.328	0.5	CLONAL	1	TRUE	1	0.15	3		571	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578513	7578513	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567554121	NA	P-0032593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	14	1049	1	ENST00000269305.4:c.417G>T	p.Lys139Asn	p.K139N	ENST00000269305	NM_001126112.2	139	aaG/aaT	5/11	1	2	FACETS	0.43	0.309	0.577	0.43	0.309	0.577	SUBCLONAL	1	TRUE	1	0.15	2		1050	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0032593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	79	597	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.25	2		597	564	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971209	21971209	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1554654224	NA	P-0032593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	52	307	0	ENST00000304494.5:c.151-2A>G		p.X51_splice	ENST00000304494	NM_000077.4	51			0.292548085831287	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.25	1		307	330	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0032593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	24	462	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.587	0.46	0.733	0.587	0.46	0.733	SUBCLONAL	1	TRUE	1	0.25	2		463	327	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	55	396	1	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.25	2		397	425	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928078	178928080	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs587776933	NA	P-0032593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	84	571	0	ENST00000263967.3:c.1359_1361del	p.Glu453del	p.E453del	ENST00000263967	NM_006218.2	452	ttAGAa/tta	8/21	1	2	FACETS	0.952	0.841	1	0.952	0.841	1	CLONAL	1	TRUE	1	0.25	2		571	706	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624275	89624275	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204910	NA	P-0032601-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	8	468	0	ENST00000371953.3:c.49C>T	p.Gln17Ter	p.Q17*	ENST00000371953	NM_000314.4	17	Caa/Taa	1/9	0.3	1	FACETS	0.083	0.053	0.123	0.083	0.053	0.123	SUBCLONAL	1	FALSE	0	0.3	1		468	545	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622332	1622332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs551790548	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	57	917	0	ENST00000344749.5:c.632C>T	p.Pro211Leu	p.P211L	ENST00000344749	NM_001136139.2	211	cCc/cTc	9/19	1	2	FACETS	0.903	0.774	1	0.903	0.774	1	CLONAL	1	TRUE	1	0.18	2		917	701	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	21	179	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.807	0.622	1	0.807	0.622	1	CLONAL	1	TRUE	1	0.18	2		179	289	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971187	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	32	418	0	ENST00000304494.5:c.171_172delinsTT	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	57	gcCCga/gcTTga	2/3	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.18	2		418	335	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355849	73355849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764982259	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	29	552	1	ENST00000377767.4:c.122G>A	p.Gly41Glu	p.G41E	ENST00000377767	NM_014953.3	41	gGg/gAg	1/21	1	2	FACETS	0.734	0.588	0.9	0.734	0.588	0.9	SUBCLONAL	1	TRUE	1	0.18	2		553	439	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413072	139413072	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	47	678	0	ENST00000277541.6:c.1070T>C	p.Phe357Ser	p.F357S	ENST00000277541	NM_017617.3	357	tTc/tCc	6/34	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.18	2		678	508	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622516	158622516	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906589	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	42	678	0	ENST00000263640.3:c.983G>A	p.Gly328Glu	p.G328E	ENST00000263640	NM_001105.4	328	gGg/gAg	8/11	1	2	FACETS	0.691	0.576	0.82	0.691	0.576	0.82	SUBCLONAL	1	TRUE	1	0.18	2		678	675	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412898	49412898	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519954	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	65	799	0	ENST00000418115.1:c.125A>G	p.Tyr42Cys	p.Y42C	ENST00000418115	NM_001664.2	42	tAt/tGt	2/5	1	2	FACETS	0.874	0.757	1	0.874	0.757	1	CLONAL	1	TRUE	1	0.18	2		799	826	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450712	70450712	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	36	539	0	ENST00000373644.4:c.5552C>T	p.Ser1851Phe	p.S1851F	ENST00000373644	NM_030625.2	1851	tCc/tTc	12/12	1	2	FACETS	0.789	0.648	0.947	0.789	0.648	0.947	CLONAL	1	TRUE	1	0.18	2		539	507	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051163	128051163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	42	674	0	ENST00000285398.2:c.160G>A	p.Asp54Asn	p.D54N	ENST00000285398	NM_000122.1	54	Gat/Aat	2/15	1	2	FACETS	0.744	0.62	0.883	0.744	0.62	0.883	SUBCLONAL	1	TRUE	1	0.18	2		674	627	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257880	19257880	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1266163850	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	60	995	0	ENST00000162023.5:c.506C>T	p.Pro169Leu	p.P169L	ENST00000162023		169	cCc/cTc	9/13	1	2	FACETS	0.866	0.745	0.998	0.866	0.745	0.998	CLONAL	1	TRUE	1	0.18	2		995	770	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845922	156845922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	48	912	1	ENST00000524377.1:c.1552G>A	p.Glu518Lys	p.E518K	ENST00000524377	NM_002529.3	518	Gag/Aag	13/17	1	2	FACETS	0.694	0.585	0.815	0.694	0.585	0.815	SUBCLONAL	1	TRUE	1	0.18	2		913	768	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396248	139396249	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	53	800	2	ENST00000277541.6:c.5589_5590delinsTT	p.Gln1864Ter	p.Q1864*	ENST00000277541	NM_017617.3	1863	ccCCag/ccTTag	30/34	1	2	FACETS	0.878	0.747	1	0.878	0.747	1	CLONAL	1	TRUE	1	0.18	2		802	671	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467778	50467778	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	25	444	0	ENST00000331340.3:c.1013C>T	p.Ser338Phe	p.S338F	ENST00000331340	NM_006060.4	338	tCc/tTc	8/8	1	2	FACETS	0.731	0.576	0.91	0.731	0.576	0.91	CLONAL	1	TRUE	1	0.18	2		444	380	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274310	5274310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	53	710	0	ENST00000357368.4:c.137C>T	p.Ser46Leu	p.S46L	ENST00000357368	NM_002850.3	46	tCg/tTg	3/38	1	2	FACETS	0.872	0.743	1	0.872	0.743	1	CLONAL	1	TRUE	1	0.18	2		710	675	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439578	51439578	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	61	375	0	ENST00000262662.1:c.143G>A	p.Gly48Glu	p.G48E	ENST00000262662		48	gGa/gAa	4/4	1	2	FACETS	0.781	0.676	0.895	1	0.972	1	SUBCLONAL	2	TRUE	1	0.18	2		375	434	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169941	32169941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	49	803	0	ENST00000375023.3:c.3667C>T	p.Leu1223Phe	p.L1223F	ENST00000375023	NM_004557.3	1223	Ctc/Ttc	21/30	1	2	FACETS	0.82	0.693	0.96	0.82	0.693	0.96	CLONAL	1	TRUE	1	0.18	2		803	664	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969941	161969941	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529808032	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	43	482	0	ENST00000366898.1:c.1028C>T	p.Pro343Leu	p.P343L	ENST00000366898	NM_004562.2	343	cCg/cTg	9/12	1	2	FACETS	0.893	0.747	1	0.893	0.747	1	CLONAL	1	TRUE	1	0.18	2		482	535	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433853	78433853	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs368283824	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	69	525	0	ENST00000370768.2:c.246T>G	p.Asn82Lys	p.N82K	ENST00000370768	NM_003902.3	82	aaT/aaG	3/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.18	2		525	574	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166128	118166128	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	52	373	0	ENST00000369448.3:c.638A>T	p.Glu213Val	p.E213V	ENST00000369448	NM_017709.3	213	gAg/gTg	2/2	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.18	2		373	391	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332295	70332295	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	28	422	0	ENST00000373644.4:c.200C>T	p.Pro67Leu	p.P67L	ENST00000373644	NM_030625.2	67	cCc/cTc	2/12	1	2	FACETS	0.701	0.559	0.862	0.701	0.559	0.862	SUBCLONAL	1	TRUE	1	0.18	2		422	444	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922212	100922212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	45	471	0	ENST00000325455.5:c.2300C>T	p.Ser767Phe	p.S767F	ENST00000325455	NM_001202474.3	767	tCc/tTc	5/8	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.18	2		471	445	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981586	101981587	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	10	152	0	ENST00000282441.5:c.7_8delinsTT	p.Pro3Phe	p.P3F	ENST00000282441	NM_001130145.2	3	CCc/TTc	1/9	1	2	FACETS	0.661	0.449	0.928	0.661	0.449	0.928	SUBCLONAL	1	TRUE	1	0.18	2		152	168	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981629	101981629	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1036138787	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	12	108	0	ENST00000282441.5:c.50G>A	p.Gly17Glu	p.G17E	ENST00000282441	NM_001130145.2	17	gGg/gAg	1/9	1	2	FACETS	0.988	0.698	1	0.988	0.698	1	CLONAL	1	TRUE	1	0.18	2		108	135	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119659	108119659	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs876660038	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	14	165	0	ENST00000278616.4:c.1066-1G>A		p.X356_splice	ENST00000278616	NM_000051.3	356			1	2	FACETS	1	0.738	1	1	0.738	1	CLONAL	1	TRUE	1	0.18	2		165	153	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427168	49427169	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	51	897	1	ENST00000301067.7:c.11319_11320delinsTT	p.Gln3774Ter	p.Q3774*	ENST00000301067	NM_003482.3	3773	ccCCag/ccTTag	39/54	1	2	FACETS	0.888	0.754	1	0.888	0.754	1	CLONAL	1	TRUE	1	0.18	2		898	638	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865101	57865101	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	60	955	0	ENST00000228682.2:c.2578C>T	p.Leu860Phe	p.L860F	ENST00000228682	NM_005269.2	860	Ctc/Ttc	12/12	1	2	FACETS	0.829	0.713	0.956	0.829	0.713	0.956	CLONAL	1	TRUE	1	0.18	2		955	804	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541711	120541711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	45	758	0	ENST00000229340.5:c.146C>T	p.Thr49Ile	p.T49I	ENST00000229340	NM_006861.6	49	aCc/aTc	3/6	1	2	FACETS	0.769	0.645	0.907	0.769	0.645	0.907	CLONAL	1	TRUE	1	0.18	2		758	650	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093405	30093405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	41	775	1	ENST00000331968.5:c.1858C>T	p.Pro620Ser	p.P620S	ENST00000331968	NM_002742.2	620	Cca/Tca	13/18	1	2	FACETS	0.657	0.546	0.782	0.657	0.546	0.782	SUBCLONAL	1	TRUE	1	0.18	2		776	693	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993884	72993884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	34	561	0	ENST00000268489.5:c.161G>A	p.Arg54Lys	p.R54K	ENST00000268489	NM_006885.3	54	aGg/aAg	2/10	1	2	FACETS	0.861	0.703	1	0.861	0.703	1	CLONAL	1	TRUE	1	0.18	2		561	439	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578267	+	frameshift_variant	Frame_Shift_Del	DEL	GGATA	GGATA	-	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	46	666	0	ENST00000269305.4:c.582_586del	p.Ile195SerfsTer12	p.I195Sfs*12	ENST00000269305	NM_001126112.2	194	ctTATCCga/ctga	6/11	1	2	FACETS	0.813	0.683	0.956	0.813	0.683	0.956	CLONAL	1	TRUE	1	0.18	2		666	629	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578456	+	frameshift_variant	Frame_Shift_Del	DEL	GCG	GCG	CA	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	61	853	3	ENST00000269305.4:c.474_476delinsTG	p.Met160TrpfsTer10	p.M160Wfs*10	ENST00000269305	NM_001126112.2	158	cgCGCc/cgTGc	5/11	1	2	FACETS	0.811	0.698	0.934	0.811	0.698	0.934	CLONAL	1	TRUE	1	0.18	2		856	836	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615758	1615758	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769351563	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	47	796	1	ENST00000344749.5:c.1513G>A	p.Glu505Lys	p.E505K	ENST00000344749	NM_001136139.2	505	Gag/Aag	17/19	1	2	FACETS	0.838	0.706	0.984	0.838	0.706	0.984	CLONAL	1	TRUE	1	0.18	2		797	623	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295181	15295181	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	61	916	0	ENST00000263388.2:c.2491G>A	p.Gly831Arg	p.G831R	ENST00000263388	NM_000435.2	831	Ggg/Agg	16/33	1	2	FACETS	0.816	0.702	0.94	0.816	0.702	0.94	CLONAL	1	TRUE	1	0.18	2		916	831	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257163	19257163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	36	595	1	ENST00000162023.5:c.800C>T	p.Pro267Leu	p.P267L	ENST00000162023		267	cCt/cTt	12/13	1	2	FACETS	0.847	0.696	1	0.847	0.696	1	CLONAL	1	TRUE	1	0.18	2		596	472	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972866	25972866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	39	680	1	ENST00000435504.4:c.1559C>T	p.Ser520Phe	p.S520F	ENST00000435504		520	tCt/tTt	12/13	1	2	FACETS	0.754	0.624	0.899	0.754	0.624	0.899	SUBCLONAL	1	TRUE	1	0.18	2		681	575	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026521	48026521	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	36	568	0	ENST00000234420.5:c.1399G>T	p.Gly467Cys	p.G467C	ENST00000234420	NM_000179.2	467	Ggc/Tgc	4/10	1	2	FACETS	0.763	0.627	0.917	0.763	0.627	0.917	CLONAL	1	TRUE	1	0.18	2		568	524	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378246	225378246	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	27	355	0	ENST00000264414.4:c.649T>A	p.Phe217Ile	p.F217I	ENST00000264414	NM_003590.4	217	Ttt/Att	5/16	1	2	FACETS	0.893	0.711	1	0.893	0.711	1	CLONAL	1	TRUE	1	0.18	2		355	336	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755552	39755552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	31	517	0	ENST00000288319.7:c.1213G>A	p.Glu405Lys	p.E405K	ENST00000288319	NM_182918.3	405	Gag/Aag	10/10	1	2	FACETS	0.757	0.612	0.922	0.757	0.612	0.922	CLONAL	1	TRUE	1	0.18	2		517	455	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566441	41566442	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	66	490	0	ENST00000263253.7:c.4318_4319delinsTT	p.Pro1440Leu	p.P1440L	ENST00000263253	NM_001429.3	1440	CCa/TTa	27/31	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.18	2		490	513	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713733	30713734	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	20	439	1	ENST00000295754.5:c.1058_1059delinsTT	p.Ser353Phe	p.S353F	ENST00000295754	NM_003242.5	353	tCC/tTT	4/7	1	2	FACETS	0.573	0.437	0.732	0.573	0.437	0.732	SUBCLONAL	1	TRUE	1	0.18	2		440	388	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163685	47163685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370885797	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	32	546	0	ENST00000409792.3:c.2441C>T	p.Pro814Leu	p.P814L	ENST00000409792	NM_014159.6	814	cCt/cTt	3/21	1	2	FACETS	0.797	0.647	0.967	0.797	0.647	0.967	CLONAL	1	TRUE	1	0.18	2		546	446	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934020	49934020	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	60	767	0	ENST00000296474.3:c.2392C>A	p.His798Asn	p.H798N	ENST00000296474	NM_002447.2	798	Cac/Aac	9/20	1	2	FACETS	0.991	0.853	1	0.991	0.853	1	CLONAL	1	TRUE	1	0.18	2		767	673	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090569	71090569	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	44	569	0	ENST00000318789.4:c.779C>T	p.Ser260Phe	p.S260F	ENST00000318789	NM_032682.5	260	tCc/tTc	11/21	1	2	FACETS	0.816	0.684	0.963	0.816	0.684	0.963	CLONAL	1	TRUE	1	0.18	2		569	599	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390077	89390077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	38	377	0	ENST00000336596.2:c.826G>A	p.Gly276Ser	p.G276S	ENST00000336596	NM_005233.5	276	Ggt/Agt	4/17	1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	1	0.18	2		377	411	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413711	138413712	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	26	428	1	ENST00000289153.2:c.1808_1809delinsTT	p.Pro603Leu	p.P603L	ENST00000289153	NM_006219.2	603	cCC/cTT	12/22	1	2	FACETS	0.596	0.471	0.739	0.596	0.471	0.739	SUBCLONAL	1	TRUE	1	0.18	2		429	485	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84384055	84384055	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	32	718	1	ENST00000321945.7:c.797G>A	p.Arg266Lys	p.R266K	ENST00000321945	NM_139076.2	266	aGa/aAa	9/9	1	2	FACETS	0.673	0.546	0.818	0.673	0.546	0.818	SUBCLONAL	1	TRUE	1	0.18	2		719	528	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512440	149512441	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	37	607	1	ENST00000261799.4:c.999_1000delinsTT	p.Arg334Trp	p.R334W	ENST00000261799	NM_002609.3	333	agCCgg/agTTgg	7/23	1	2	FACETS	0.702	0.577	0.841	0.702	0.577	0.841	SUBCLONAL	1	TRUE	1	0.18	2		608	586	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714451	117714451	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1371504833	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	38	513	1	ENST00000368508.3:c.1198A>G	p.Ile400Val	p.I400V	ENST00000368508	NM_002944.2	400	Atc/Gtc	11/43	1	2	FACETS	0.949	0.785	1	0.949	0.785	1	CLONAL	1	TRUE	1	0.18	2		514	445	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683575	162683575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	39	561	0	ENST00000366898.1:c.394C>T	p.Pro132Ser	p.P132S	ENST00000366898	NM_004562.2	132	Cca/Tca	3/12	1	2	FACETS	0.763	0.631	0.91	0.763	0.631	0.91	CLONAL	1	TRUE	1	0.18	2		561	568	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431622	6431622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	36	422	0	ENST00000356142.4:c.175G>A	p.Ala59Thr	p.A59T	ENST00000356142	NM_018890.3	59	Gct/Act	3/7	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.18	2		422	379	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367320	50367320	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	35	368	0	ENST00000331340.3:c.127G>A	p.Gly43Arg	p.G43R	ENST00000331340	NM_006060.4	43	Gga/Aga	3/8	1	2	FACETS	0.977	0.802	1	0.977	0.802	1	CLONAL	1	TRUE	1	0.18	2		368	398	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227845	55227845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	29	367	0	ENST00000275493.2:c.1312C>T	p.Leu438Phe	p.L438F	ENST00000275493	NM_005228.3	438	Ctt/Ttt	12/28	1	2	FACETS	0.91	0.731	1	0.91	0.731	1	CLONAL	1	TRUE	1	0.18	2		367	354	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434613	128434613	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	52	681	0	ENST00000265960.3:c.241A>G	p.Arg81Gly	p.R81G	ENST00000265960	NM_001006617.1	81	Aga/Gga	2/12	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.18	2		681	540	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652314	48652314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1557020571	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	64	463	0	ENST00000376670.3:c.985G>A	p.Gly329Arg	p.G329R	ENST00000376670	NM_002049.3	329	Gga/Aga	6/6	1	1	FACETS	0.801	0.696	0.913	1	0.974	1	CLONAL	2	TRUE	0	0.18	1		463	404	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227995	53227995	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1085307655	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	54	388	0	ENST00000375401.3:c.2319G>A	p.Trp773Ter	p.W773*	ENST00000375401	NM_004187.3	773	tgG/tgA	16/26	1	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.18	1		388	387	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79974801	79974803	+	missense_variant	Missense_Mutation	TNP	CTC	CTC	TTT	novel	NA	P-0032660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	44	693	0	ENST00000265081.6:c.1229_1231delinsTTT	p.Ser410_Arg411delinsPheCys	p.S410_R411delinsFC	ENST00000265081	NM_002439.4	410	tCTCgt/tTTTgt	8/24	1	2	FACETS	0.612	0.511	0.724	0.612	0.511	0.724	SUBCLONAL	1	TRUE	1	0.18	2		693	799	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	23	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.568	0.443	0.712	0.568	0.443	0.712	SUBCLONAL	1	TRUE	1	0.27	2		215	300	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0032675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	43	458	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	0.691	0.578	0.816	0.691	0.578	0.816	SUBCLONAL	1	TRUE	1	0.27	2		458	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0032675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	48	691	2	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	1	2	FACETS	0.443	0.374	0.521	0.443	0.374	0.521	SUBCLONAL	1	TRUE	1	0.27	2		693	802	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098957	178098957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	54	356	0	ENST00000397062.3:c.88C>T	p.Leu30Phe	p.L30F	ENST00000397062	NM_006164.4	30	Ctt/Ttt	2/5	1	2	FACETS	0.701	0.598	0.813	0.701	0.598	0.813	SUBCLONAL	1	TRUE	1	0.27	2		356	571	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395529	116395529	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	37	442	0	ENST00000397752.3:c.1822G>C	p.Glu608Gln	p.E608Q	ENST00000397752	NM_000245.2	608	Gag/Cag	6/21	1	2	FACETS	0.428	0.351	0.513	0.428	0.351	0.513	SUBCLONAL	1	TRUE	1	0.27	2		442	641	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131498	202131498	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	30	333	0	ENST00000358485.4:c.466C>T	p.Gln156Ter	p.Q156*	ENST00000358485	NM_001080125.1	156	Caa/Taa	2/9	1	2	FACETS	0.513	0.413	0.627	0.513	0.413	0.627	SUBCLONAL	1	TRUE	1	0.27	2		333	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0032675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	59	740	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	1	2	FACETS	0.517	0.444	0.598	0.517	0.444	0.598	SUBCLONAL	1	TRUE	1	0.27	2		740	845	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743602	46743602	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	50	642	0	ENST00000371975.4:c.1983G>T	p.Leu661Phe	p.L661F	ENST00000371975	NM_003579.3	661	ttG/ttT	17/18	1	2	FACETS	0.559	0.474	0.654	0.559	0.474	0.654	SUBCLONAL	1	TRUE	1	0.27	2		642	662	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383980	84383980	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	49	638	0	ENST00000321945.7:c.872C>G	p.Ser291Cys	p.S291C	ENST00000321945	NM_139076.2	291	tCt/tGt	9/9	1	2	FACETS	0.454	0.383	0.533	0.454	0.383	0.533	SUBCLONAL	1	TRUE	1	0.27	2		638	799	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541533	187541534	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	30	373	0	ENST00000441802.2:c.6206_6207insA	p.Ile2070HisfsTer7	p.I2070Hfs*7	ENST00000441802	NM_005245.3	2069	gtc/gtAc	10/27	0.3	2	FACETS	0.433	0.348	0.53			1	SUBCLONAL	1	TRUE	NA	0.27	2		373	513	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671730	30671730	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	54	734	0	ENST00000376406.3:c.5230G>A	p.Ala1744Thr	p.A1744T	ENST00000376406	NM_014641.2	1744	Gca/Aca	10/15	1	2	FACETS	0.522	0.444	0.606	0.522	0.444	0.606	SUBCLONAL	1	TRUE	1	0.27	2		734	767	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	206	351	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.429542895699289	4	FACETS	0.862	0.807	0.919	0.862	0.807	0.919	CLONAL	3	TRUE	1	0.429542895699289	4		351	530	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609861	117609861	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	100	719	0	ENST00000368508.3:c.6838G>A	p.Glu2280Lys	p.E2280K	ENST00000368508	NM_002944.2	2280	Gaa/Aaa	43/43	0.331902208554568	1	FACETS	0.569	0.509	0.633	0.569	0.509	0.633	SUBCLONAL	1	TRUE	0	0.429542895699289	1		719	642	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	13	179	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.284	0.203	0.384	0.284	0.203	0.384	SUBCLONAL	1	TRUE	1	0.429542895699289	2		179	213	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	151	705	0	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	1	2	FACETS	0.944	0.864	1	0.944	0.864	1	CLONAL	1	TRUE	1	0.429542895699289	2		705	745	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518175	8518175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1354824749	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	66	453	1	ENST00000356435.5:c.1216G>A	p.Glu406Lys	p.E406K	ENST00000356435		406	Gaa/Aaa	10/35	0.429542895699289	1	FACETS	0.691	0.604	0.785	0.691	0.604	0.785	SUBCLONAL	1	TRUE	0	0.429542895699289	1		454	349	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432368	432368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1362895739	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	44	134	0	ENST00000399788.2:c.2155C>T	p.Arg719Cys	p.R719C	ENST00000399788	NM_001042603.1	719	Cgc/Tgc	16/28	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.429542895699289	2		134	192	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858517	9858517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765370528	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	107	595	0	ENST00000330684.3:c.2884G>A	p.Glu962Lys	p.E962K	ENST00000330684	NM_001134407.1	962	Gaa/Aaa	13/13	1	2	FACETS	0.886	0.798	0.98	0.886	0.798	0.98	CLONAL	1	TRUE	1	0.429542895699289	2		595	562	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544088	18544088	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	19	321	0	ENST00000266497.5:c.1905G>A	p.Met635Ile	p.M635I	ENST00000266497		635	atG/atA	13/31	NA	2	FACETS	0.254	0.192	0.327			1	INDETERMINATE	1	TRUE	NA	0.429542895699289	2		321	348	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124422	94124422	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	40	374	0	ENST00000369303.4:c.161G>A	p.Gly54Glu	p.G54E	ENST00000369303	NM_004440.3	54	gGg/gAg	2/17	0.331902208554568	1	FACETS	0.341	0.283	0.405	0.341	0.283	0.405	SUBCLONAL	1	TRUE	0	0.429542895699289	1		374	429	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812260	212812260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751175543	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	85	313	0	ENST00000342788.4:c.316C>T	p.Arg106Cys	p.R106C	ENST00000342788	NM_005235.2	106	Cgt/Tgt	3/28	0.236963970823561	2	FACETS	1	0.928	1	0.528	0.47	0.589	INDETERMINATE	1	TRUE	0	0.429542895699289	2		313	375	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729613	41729613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs564878978	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	38	501	1	ENST00000242208.4:c.916C>T	p.Arg306Cys	p.R306C	ENST00000242208	NM_002192.2	306	Cgc/Tgc	3/3	1	2	FACETS	0.412	0.341	0.492	0.412	0.341	0.492	SUBCLONAL	1	TRUE	1	0.429542895699289	2		502	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577540	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	rs1555525498	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	80	684	1	ENST00000269305.4:c.741_742delinsTT	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	247	aaCCgg/aaTTgg	7/11	1	2	FACETS	0.668	0.588	0.752	0.668	0.588	0.752	SUBCLONAL	1	TRUE	1	0.429542895699289	2		685	558	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639422	3639422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	33	696	0	ENST00000294008.3:c.4217C>T	p.Ser1406Phe	p.S1406F	ENST00000294008	NM_032444.2	1406	tCc/tTc	12/15	1	2	FACETS	0.27	0.219	0.327	0.27	0.219	0.327	SUBCLONAL	1	TRUE	1	0.429542895699289	2		696	570	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763500	41763500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	35	518	1	ENST00000301178.4:c.2299C>T	p.Arg767Cys	p.R767C	ENST00000301178	NM_021913.4	767	Cgc/Tgc	19/20	1	2	FACETS	0.402	0.33	0.484	0.402	0.33	0.484	SUBCLONAL	1	TRUE	1	0.429542895699289	2		519	405	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306677	41306677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs724159835	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	84	731	0	ENST00000373198.4:c.982C>T	p.Arg328Cys	p.R328C	ENST00000373198	NM_133170.3	328	Cgc/Tgc	7/32	1	2	FACETS	0.669	0.591	0.751	0.669	0.591	0.751	SUBCLONAL	1	TRUE	1	0.429542895699289	2		731	585	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163804	72163804	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	154	416	1	ENST00000357731.5:c.554G>A	p.Gly185Glu	p.G185E	ENST00000357731	NM_173808.2	185	gGa/gAa	4/7	0.236963970823561	2	FACETS	0.798	0.737	0.861	0.798	0.737	0.861	INDETERMINATE	2	TRUE	0	0.429542895699289	2		417	449	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	72	462	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.429542895699289	2		463	260	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435557	18435557	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	16	243	0	ENST00000266497.5:c.542C>T	p.Ser181Phe	p.S181F	ENST00000266497		181	tCc/tTc	1/31	1	2	FACETS	0.305	0.226	0.4	0.305	0.226	0.4	SUBCLONAL	1	TRUE	1	0.429542895699289	2		243	244	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63760038	63760038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868152271	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	41	367	0	ENST00000279873.7:c.691C>T	p.His231Tyr	p.H231Y	ENST00000279873	NM_032199.2	231	Cac/Tac	4/10	0.383087164564422	1	FACETS	0.414	0.346	0.49	0.414	0.346	0.49	SUBCLONAL	1	TRUE	0	0.429542895699289	1		367	362	SUCCESS
AR	367	MSKCC	GRCh37	X	66863145	66863145	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	53	319	0	ENST00000374690.3:c.1664C>T	p.Pro555Leu	p.P555L	ENST00000374690	NM_000044.3	555	cCa/cTa	2/8	0.429542895699289	2	FACETS	0.611	0.522	0.707			1	SUBCLONAL	1	TRUE	NA	0.429542895699289	2		319	404	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230878	66230878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	27	361	0	ENST00000273854.3:c.2093G>A	p.Gly698Glu	p.G698E	ENST00000273854	NM_004439.5	698	gGa/gAa	12/18	1	2	FACETS	0.333	0.264	0.411	0.333	0.264	0.411	SUBCLONAL	1	TRUE	1	0.429542895699289	2		361	378	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916248	9916248	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397518472	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	35	390	1	ENST00000330684.3:c.2041C>T	p.Arg681Ter	p.R681*	ENST00000330684	NM_001134407.1	681	Cga/Tga	10/13	1	2	FACETS	0.359	0.294	0.432	0.359	0.294	0.432	SUBCLONAL	1	TRUE	1	0.429542895699289	2		391	454	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862896	9862896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1198247451	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	37	596	1	ENST00000330684.3:c.2407G>A	p.Glu803Lys	p.E803K	ENST00000330684	NM_001134407.1	803	Gag/Aag	12/13	1	2	FACETS	0.317	0.261	0.38	0.317	0.261	0.38	SUBCLONAL	1	TRUE	1	0.429542895699289	2		597	543	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862939	9862939	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1163381321	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	72	459	0	ENST00000330684.3:c.2364G>A	p.Met788Ile	p.M788I	ENST00000330684	NM_001134407.1	788	atG/atA	12/13	1	2	FACETS	0.832	0.73	0.94	0.832	0.73	0.94	CLONAL	1	TRUE	1	0.429542895699289	2		459	403	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387101	31387101	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1226308460	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	93	577	0	ENST00000328111.2:c.1726C>T	p.Arg576Ter	p.R576*	ENST00000328111	NM_006892.3	576	Cga/Tga	16/23	1	2	FACETS	0.836	0.746	0.932	0.836	0.746	0.932	CLONAL	1	TRUE	1	0.429542895699289	2		577	518	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900353	3900353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374499169	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	41	714	0	ENST00000262367.5:c.743C>T	p.Pro248Leu	p.P248L	ENST00000262367	NM_004380.2	248	cCg/cTg	2/31	1	2	FACETS	0.315	0.262	0.375	0.315	0.262	0.375	SUBCLONAL	1	TRUE	1	0.429542895699289	2		714	606	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858769	9858769	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	27	276	0	ENST00000330684.3:c.2632G>A	p.Glu878Lys	p.E878K	ENST00000330684	NM_001134407.1	878	Gaa/Aaa	13/13	1	2	FACETS	0.441	0.352	0.543	0.441	0.352	0.543	SUBCLONAL	1	TRUE	1	0.429542895699289	2		276	285	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732409	74732409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326283685	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	16	314	0	ENST00000359995.5:c.500G>A	p.Arg167Gln	p.R167Q	ENST00000359995	NM_001195427.1	167	cGa/cAa	2/3	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.429542895699289	NA		314	303	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895656	28895656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	244	522	0	ENST00000282397.4:c.3118G>A	p.Asp1040Asn	p.D1040N	ENST00000282397	NM_002019.4	1040	Gat/Aat	23/30	0.418748378374643	4	FACETS	1	0.973	1	0.71	0.666	0.756	CLONAL	2	TRUE	1	0.429542895699289	4		522	762	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259262	89259262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770780950	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	75	562	1	ENST00000336596.2:c.406C>T	p.Arg136Ter	p.R136*	ENST00000336596	NM_005233.5	136	Cga/Tga	3/17	1	2	FACETS	0.818	0.72	0.922	0.818	0.72	0.922	CLONAL	1	TRUE	1	0.429542895699289	2		563	427	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922294	100922294	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1315135533	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	24	254	0	ENST00000325455.5:c.2218C>T	p.Arg740Ter	p.R740*	ENST00000325455	NM_001202474.3	740	Cga/Tga	5/8	0.279784603210633	3	FACETS	0.359	0.281	0.449	0.18	0.14	0.225	SUBCLONAL	1	TRUE	1	0.429542895699289	3		254	378	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118941	115118941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	18	278	0	ENST00000257566.3:c.400C>T	p.Pro134Ser	p.P134S	ENST00000257566	NM_016569.3	134	Cct/Tct	2/8	0.365058481719109	1	FACETS	0.301	0.227	0.387	0.301	0.227	0.387	SUBCLONAL	1	TRUE	0	0.429542895699289	1		278	219	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325105	123325105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	49	613	0	ENST00000358487.5:c.223G>A	p.Asp75Asn	p.D75N	ENST00000358487	NM_000141.4	75	Gat/Aat	3/18	0.383087164564422	1	FACETS	0.369	0.312	0.431	0.369	0.312	0.431	SUBCLONAL	1	TRUE	0	0.429542895699289	1		613	486	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284880	15284880	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	86	666	0	ENST00000263388.2:c.4735G>A	p.Gly1579Ser	p.G1579S	ENST00000263388	NM_000435.2	1579	Ggc/Agc	25/33	1	2	FACETS	0.737	0.654	0.826	0.737	0.654	0.826	SUBCLONAL	1	TRUE	1	0.429542895699289	2		666	543	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55219001	55219001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	32	364	0	ENST00000275493.2:c.574C>T	p.Pro192Ser	p.P192S	ENST00000275493	NM_005228.3	192	Cca/Tca	5/28	1	2	FACETS	0.454	0.369	0.55	0.454	0.369	0.55	SUBCLONAL	1	TRUE	1	0.429542895699289	2		364	328	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81558939	81558939	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1230091225	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	45	444	2	ENST00000298171.2:c.532G>A	p.Glu178Lys	p.E178K	ENST00000298171	NM_000369.2	178	Gaa/Aaa	6/10	1	2	FACETS	0.447	0.375	0.525	0.447	0.375	0.525	SUBCLONAL	1	TRUE	1	0.429542895699289	2		446	469	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341914	8341914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	38	507	0	ENST00000356435.5:c.4726G>A	p.Glu1576Lys	p.E1576K	ENST00000356435		1576	Gaa/Aaa	29/35	0.429542895699289	1	FACETS	0.332	0.274	0.396	0.332	0.274	0.396	SUBCLONAL	1	TRUE	0	0.429542895699289	1		507	419	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687306	37687306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1172789499	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	43	525	0	ENST00000447079.4:c.4210C>T	p.Arg1404Cys	p.R1404C	ENST00000447079	NM_015083.1	1404	Cgt/Tgt	14/14	1	2	FACETS	0.437	0.366	0.516	0.437	0.366	0.516	SUBCLONAL	1	TRUE	1	0.429542895699289	2		525	458	SUCCESS
APC	324	MSKCC	GRCh37	5	112175118	112175118	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	20	217	0	ENST00000257430.4:c.3827C>T	p.Ser1276Leu	p.S1276L	ENST00000257430	NM_000038.5	1276	tCa/tTa	16/16	0.191910590072447	2	FACETS	0.372	0.285	0.474	0.186	0.142	0.237	INDETERMINATE	1	TRUE	0	0.429542895699289	2		217	250	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308348	15308348	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555730189	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	51	710	0	ENST00000263388.2:c.160C>T	p.Arg54Cys	p.R54C	ENST00000263388	NM_000435.2	54	Cgt/Tgt	2/33	1	2	FACETS	0.394	0.334	0.459	0.394	0.334	0.459	SUBCLONAL	1	TRUE	1	0.429542895699289	2		710	603	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295704	212295704	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745376683	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	56	508	0	ENST00000342788.4:c.2609G>A	p.Gly870Glu	p.G870E	ENST00000342788	NM_005235.2	870	gGa/gAa	21/28	0.236963970823561	2	FACETS	0.465	0.398	0.538	0.232	0.199	0.269	INDETERMINATE	1	TRUE	0	0.429542895699289	2		508	561	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413577	32413577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1037084691	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	30	378	0	ENST00000332351.3:c.1373G>A	p.Arg458Gln	p.R458Q	ENST00000332351	NM_024426.4	458	cGa/cAa	9/10	1	2	FACETS	0.287	0.23	0.351	0.287	0.23	0.351	SUBCLONAL	1	TRUE	1	0.429542895699289	2		378	487	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817882	3817882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757051244	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	74	564	0	ENST00000262367.5:c.3089C>T	p.Ser1030Phe	p.S1030F	ENST00000262367	NM_004380.2	1030	tCc/tTc	16/31	1	2	FACETS	0.524	0.458	0.594	0.524	0.458	0.594	SUBCLONAL	1	TRUE	1	0.429542895699289	2		564	658	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285851	198285851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1360783408	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	174	463	0	ENST00000335508.6:c.202G>A	p.Asp68Asn	p.D68N	ENST00000335508	NM_012433.2	68	Gat/Aat	3/25	0.236963970823561	2	FACETS	0.754	0.699	0.811	0.754	0.699	0.811	INDETERMINATE	2	TRUE	0	0.429542895699289	2		463	537	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512361	149512361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	37	615	0	ENST00000261799.4:c.1079C>T	p.Ser360Phe	p.S360F	ENST00000261799	NM_002609.3	360	tCc/tTc	7/23	0.191910590072447	2	FACETS	0.339	0.279	0.406	0.17	0.139	0.203	INDETERMINATE	1	TRUE	0	0.429542895699289	2		615	508	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264375	30264375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316496668	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	17	252	0	ENST00000322652.5:c.110C>T	p.Ser37Leu	p.S37L	ENST00000322652	NM_015355.2	37	tCg/tTg	1/16	1	2	FACETS	0.442	0.331	0.573	0.442	0.331	0.573	SUBCLONAL	1	TRUE	1	0.429542895699289	2		252	179	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476382	88476382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	34	482	0	ENST00000360948.2:c.1750G>A	p.Asp584Asn	p.D584N	ENST00000360948	NM_001012338.2	584	Gat/Aat	15/19	1	2	FACETS	0.358	0.292	0.432	0.358	0.292	0.432	SUBCLONAL	1	TRUE	1	0.429542895699289	2		482	442	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977620	2977620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	69	880	0	ENST00000396946.4:c.1064G>A	p.Gly355Glu	p.G355E	ENST00000396946	NM_032415.4	355	gGa/gAa	8/25	1	2	FACETS	0.488	0.424	0.556	0.488	0.424	0.556	SUBCLONAL	1	TRUE	1	0.429542895699289	2		880	659	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259231	89259231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	70	416	0	ENST00000336596.2:c.375G>A	p.Met125Ile	p.M125I	ENST00000336596	NM_005233.5	125	atG/atA	3/17	1	2	FACETS	0.825	0.723	0.934	0.825	0.723	0.934	CLONAL	1	TRUE	1	0.429542895699289	2		416	395	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919565	78919565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1307148616	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	30	353	0	ENST00000306801.3:c.3124G>A	p.Asp1042Asn	p.D1042N	ENST00000306801	NM_020761.2	1042	Gac/Aac	26/34	0.383087164564422	1	FACETS	0.339	0.273	0.413	0.339	0.273	0.413	SUBCLONAL	1	TRUE	0	0.429542895699289	1		353	324	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944398	131944398	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs372347288	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	46	175	0	ENST00000265335.6:c.2810A>G	p.Asn937Ser	p.N937S	ENST00000265335		937	aAc/aGc	17/25	0.191910590072447	2	FACETS	0.799	0.678	0.931	0.4	0.339	0.466	INDETERMINATE	1	TRUE	0	0.429542895699289	2		175	268	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955087	93955087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	30	407	1	ENST00000369303.4:c.2811G>A	p.Met937Ile	p.M937I	ENST00000369303	NM_004440.3	937	atG/atA	16/17	0.331902208554568	1	FACETS	0.261	0.21	0.319	0.261	0.21	0.319	SUBCLONAL	1	TRUE	0	0.429542895699289	1		408	420	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233952	133233952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	47	542	0	ENST00000320574.5:c.3442C>T	p.Pro1148Ser	p.P1148S	ENST00000320574	NM_006231.2	1148	Cct/Tct	28/49	0.365058481719109	1	FACETS	0.366	0.308	0.429	0.366	0.308	0.429	SUBCLONAL	1	TRUE	0	0.429542895699289	1		542	470	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016610	12016610	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	31	377	1	ENST00000353533.5:c.746G>A	p.Gly249Asp	p.G249D	ENST00000353533	NM_003010.3	249	gGc/gAc	7/11	1	2	FACETS	0.341	0.276	0.416	0.341	0.276	0.416	SUBCLONAL	1	TRUE	1	0.429542895699289	2		378	423	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42057206	42057206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	109	561	0	ENST00000219905.7:c.7867C>T	p.Leu2623Phe	p.L2623F	ENST00000219905	NM_001164273.1	2623	Ctc/Ttc	23/24	0.383087164564422	1	FACETS	0.859	0.776	0.946	0.859	0.776	0.946	CLONAL	1	TRUE	0	0.429542895699289	1		561	464	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248617	212248617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765120252	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	49	555	0	ENST00000342788.4:c.3650G>A	p.Gly1217Glu	p.G1217E	ENST00000342788	NM_005235.2	1217	gGa/gAa	28/28	0.236963970823561	2	FACETS	0.395	0.334	0.463	0.198	0.167	0.232	INDETERMINATE	1	TRUE	0	0.429542895699289	2		555	577	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348640	89348640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567569519	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	75	898	0	ENST00000301030.4:c.4310C>T	p.Pro1437Leu	p.P1437L	ENST00000301030	NM_001256183.1	1437	cCt/cTt	9/13	0.383087164564422	1	FACETS	0.363	0.318	0.412	0.363	0.318	0.412	SUBCLONAL	1	TRUE	0	0.429542895699289	1		898	755	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650837	93650837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	18	356	0	ENST00000375746.1:c.1763G>A	p.Gly588Glu	p.G588E	ENST00000375746	NM_001174167.1	588	gGa/gAa	13/14	0.429542895699289	1	FACETS	0.184	0.138	0.238	0.184	0.138	0.238	SUBCLONAL	1	TRUE	0	0.429542895699289	1		356	358	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133523	55133523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142492533	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	38	427	1	ENST00000257290.5:c.827C>T	p.Thr276Met	p.T276M	ENST00000257290	NM_006206.4	276	aCg/aTg	6/23	1	2	FACETS	0.347	0.286	0.415	0.347	0.286	0.415	SUBCLONAL	1	TRUE	1	0.429542895699289	2		428	510	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719286	52719286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775654171	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	55	578	1	ENST00000322088.6:c.952C>T	p.Arg318Trp	p.R318W	ENST00000322088	NM_014225.5	318	Cgg/Tgg	8/15	1	2	FACETS	0.428	0.366	0.496	0.428	0.366	0.496	SUBCLONAL	1	TRUE	1	0.429542895699289	2		579	598	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242063	105242063	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369198922	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	50	744	0	ENST00000349310.3:c.361C>T	p.Arg121Trp	p.R121W	ENST00000349310	NM_001014432.1	121	Cgg/Tgg	6/15	1	2	FACETS	0.448	0.38	0.522	0.448	0.38	0.522	SUBCLONAL	1	TRUE	1	0.429542895699289	2		744	520	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573933	18573933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	28	349	0	ENST00000266497.5:c.2251G>A	p.Asp751Asn	p.D751N	ENST00000266497		751	Gat/Aat	15/31	NA	2	FACETS	0.324	0.259	0.399			1	INDETERMINATE	1	TRUE	NA	0.429542895699289	2		349	402	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027169	49027169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751560923	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	39	444	0	ENST00000267163.4:c.1736G>A	p.Arg579Gln	p.R579Q	ENST00000267163	NM_000321.2	579	cGa/cAa	18/27	0.418748378374643	4	FACETS	0.359	0.296	0.429	0.12	0.098	0.143	SUBCLONAL	1	TRUE	1	0.429542895699289	4		444	723	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041017	112041017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	24	364	2	ENST00000368678.4:c.238G>A	p.Gly80Arg	p.G80R	ENST00000368678		80	Gga/Aga	3/13	0.331902208554568	1	FACETS	0.263	0.206	0.328	0.263	0.206	0.328	SUBCLONAL	1	TRUE	0	0.429542895699289	1		366	334	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865537	57865537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	40	718	0	ENST00000228682.2:c.3014G>A	p.Gly1005Glu	p.G1005E	ENST00000228682	NM_005269.2	1005	gGa/gAa	12/12	0.365058481719109	1	FACETS	0.299	0.248	0.356	0.299	0.248	0.356	SUBCLONAL	1	TRUE	0	0.429542895699289	1		718	489	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640985	3640985	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147492092	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	121	905	0	ENST00000294008.3:c.2654C>T	p.Pro885Leu	p.P885L	ENST00000294008	NM_032444.2	885	cCg/cTg	12/15	1	2	FACETS	0.692	0.625	0.763	0.692	0.625	0.763	SUBCLONAL	1	TRUE	1	0.429542895699289	2		905	814	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164779	106164779	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs562667223	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	34	411	0	ENST00000380013.4:c.3647G>A	p.Arg1216Gln	p.R1216Q	ENST00000380013	NM_001127208.2	1216	cGa/cAa	6/11	1	2	FACETS	0.339	0.276	0.409	0.339	0.276	0.409	SUBCLONAL	1	TRUE	1	0.429542895699289	2		411	467	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806564	1806564	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	72	550	0	ENST00000260795.2:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000260795		427	tCc/tTc	9/17	1	2	FACETS	0.723	0.633	0.818	0.723	0.633	0.818	SUBCLONAL	1	TRUE	1	0.429542895699289	2		550	464	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342551	118342551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	36	185	0	ENST00000534358.1:c.677C>T	p.Pro226Leu	p.P226L	ENST00000534358	NM_005933.3	226	cCc/cTc	3/36	0.279784603210633	3	FACETS	0.974	0.808	1	0.487	0.404	0.579	CLONAL	1	TRUE	1	0.429542895699289	3		185	209	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180050958	180050958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781305649	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	45	760	1	ENST00000261937.6:c.1525G>A	p.Glu509Lys	p.E509K	ENST00000261937	NM_182925.4	509	Gag/Aag	11/30	0.429542895699289	1	FACETS	0.285	0.239	0.336	0.285	0.239	0.336	SUBCLONAL	1	TRUE	0	0.429542895699289	1		761	577	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332632	65332632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	27	347	1	ENST00000342505.4:c.907C>T	p.His303Tyr	p.H303Y	ENST00000342505	NM_002227.2	303	Cat/Tat	7/25	0.236963970823561	2	FACETS	0.324	0.257	0.4	0.162	0.128	0.2	INDETERMINATE	1	TRUE	0	0.429542895699289	2		348	388	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182201	99182201	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	183	496	0	ENST00000074304.5:c.2266G>A	p.Asp756Asn	p.D756N	ENST00000074304	NM_001134224.1	756	Gac/Aac	21/26	0.236963970823561	2	FACETS	0.822	0.765	0.881	0.822	0.765	0.881	INDETERMINATE	2	TRUE	0	0.429542895699289	2		496	518	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120366	94120366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1216099858	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	47	280	0	ENST00000369303.4:c.685G>A	p.Glu229Lys	p.E229K	ENST00000369303	NM_004440.3	229	Gag/Aag	3/17	0.331902208554568	1	FACETS	0.577	0.489	0.672	0.577	0.489	0.672	SUBCLONAL	1	TRUE	0	0.429542895699289	1		280	298	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460345	149460345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	28	420	0	ENST00000286301.3:c.292C>T	p.His98Tyr	p.H98Y	ENST00000286301	NM_005211.3	98	Cac/Tac	3/22	0.191910590072447	2	FACETS	0.432	0.346	0.529	0.216	0.173	0.265	INDETERMINATE	1	TRUE	0	0.429542895699289	2		420	302	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827885	40827885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	67	435	0	ENST00000373198.4:c.2543G>A	p.Gly848Glu	p.G848E	ENST00000373198	NM_133170.3	848	gGa/gAa	17/32	1	2	FACETS	0.698	0.608	0.794	0.698	0.608	0.794	SUBCLONAL	1	TRUE	1	0.429542895699289	2		435	447	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588211	69588211	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	31	589	0	ENST00000168712.1:c.487C>T	p.Pro163Ser	p.P163S	ENST00000168712	NM_002007.2	163	Ccc/Tcc	3/3	0.279784603210633	3	FACETS	0.335	0.27	0.408	0.167	0.135	0.204	SUBCLONAL	1	TRUE	1	0.429542895699289	3		589	524	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40864899	40864899	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs746035795	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	71	342	0	ENST00000373198.4:c.2370-1G>A		p.X790_splice	ENST00000373198	NM_133170.3	790			1	2	FACETS	0.839	0.736	0.949	0.839	0.736	0.949	CLONAL	1	TRUE	1	0.429542895699289	2		342	394	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741804	17741804	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	39	264	0	ENST00000250003.3:c.475G>A	p.Gly159Ser	p.G159S	ENST00000250003	NM_002478.4	159	Ggc/Agc	1/3	1	2	FACETS	0.622	0.518	0.737	0.622	0.518	0.737	SUBCLONAL	1	TRUE	1	0.429542895699289	2		264	292	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449496	149449496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	50	624	0	ENST00000286301.3:c.1450G>A	p.Glu484Lys	p.E484K	ENST00000286301	NM_005211.3	484	Gag/Aag	10/22	0.191910590072447	2	FACETS	0.4	0.339	0.467	0.2	0.169	0.234	INDETERMINATE	1	TRUE	0	0.429542895699289	2		624	582	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543689	29543689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	100	599	0	ENST00000389048.3:c.1474G>A	p.Gly492Ser	p.G492S	ENST00000389048	NM_004304.4	492	Ggc/Agc	7/29	0.129015905956431	3	FACETS	0.853	0.763	0.949	0.284	0.254	0.317	INDETERMINATE	1	TRUE	0	0.429542895699289	3		599	663	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435190	18435190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	19	288	0	ENST00000266497.5:c.175G>A	p.Asp59Asn	p.D59N	ENST00000266497		59	Gat/Aat	1/31	1	2	FACETS	0.259	0.196	0.334	0.259	0.196	0.334	SUBCLONAL	1	TRUE	1	0.429542895699289	2		288	341	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519758	176519758	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	26	705	0	ENST00000292408.4:c.1030C>T	p.Gln344Ter	p.Q344*	ENST00000292408	NM_213647.1	344	Cag/Tag	8/18	0.191910590072447	2	FACETS	0.263	0.207	0.326	0.131	0.103	0.163	INDETERMINATE	1	TRUE	0	0.429542895699289	2		705	461	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343259	118343259	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	22	352	0	ENST00000534358.1:c.1385C>T	p.Ser462Leu	p.S462L	ENST00000534358	NM_005933.3	462	tCa/tTa	3/36	0.279784603210633	3	FACETS	0.312	0.241	0.394	0.156	0.12	0.197	SUBCLONAL	1	TRUE	1	0.429542895699289	3		352	399	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11175467	11175467	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	89	510	0	ENST00000361445.4:c.7075G>A	p.Gly2359Arg	p.G2359R	ENST00000361445	NM_004958.3	2359	Ggg/Agg	51/58	0.129015905956431	3	FACETS	0.883	0.785	0.988	0.294	0.261	0.33	INDETERMINATE	1	TRUE	0	0.429542895699289	3		510	570	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099971	27099972	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	34	625	2	ENST00000324856.7:c.3850_3851delinsTT	p.Pro1284Phe	p.P1284F	ENST00000324856	NM_006015.4	1284	CCt/TTt	15/20	0.129015905956431	3	FACETS	0.386	0.315	0.466	0.129	0.105	0.156	INDETERMINATE	1	TRUE	0	0.429542895699289	3		627	498	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106184	27106184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	85	475	0	ENST00000324856.7:c.5795C>T	p.Ala1932Val	p.A1932V	ENST00000324856	NM_006015.4	1932	gCc/gTc	20/20	0.129015905956431	3	FACETS	0.965	0.856	1	0.322	0.285	0.361	INDETERMINATE	1	TRUE	0	0.429542895699289	3		475	498	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436146	51436147	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	21	309	0	ENST00000262662.1:c.106_107delinsAA	p.Gly36Lys	p.G36K	ENST00000262662		36	GGa/AAa	3/4	0.429542895699289	3	FACETS	0.342	0.263	0.435			1	SUBCLONAL	1	TRUE	NA	0.429542895699289	3		309	347	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400815	72400815	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	71	389	0	ENST00000357731.5:c.356C>T	p.Ser119Phe	p.S119F	ENST00000357731	NM_173808.2	119	tCt/tTt	2/7	0.236963970823561	2	FACETS	0.793	0.695	0.898	0.396	0.347	0.449	INDETERMINATE	1	TRUE	0	0.429542895699289	2		389	417	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165986	118165986	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	51	413	1	ENST00000369448.3:c.496G>T	p.Glu166Ter	p.E166*	ENST00000369448	NM_017709.3	166	Gag/Tag	2/2	0.236963970823561	2	FACETS	0.575	0.49	0.668	0.287	0.245	0.334	INDETERMINATE	1	TRUE	0	0.429542895699289	2		414	413	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120469126	120469126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772588398	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	58	334	0	ENST00000256646.2:c.4001C>T	p.Pro1334Leu	p.P1334L	ENST00000256646	NM_024408.3	1334	cCc/cTc	24/34	0.236963970823561	2	FACETS	0.621	0.535	0.714	0.31	0.267	0.357	INDETERMINATE	1	TRUE	0	0.429542895699289	2		334	435	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491097	120491097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	51	456	0	ENST00000256646.2:c.2692G>A	p.Glu898Lys	p.E898K	ENST00000256646	NM_024408.3	898	Gaa/Aaa	17/34	0.236963970823561	2	FACETS	0.523	0.445	0.608	0.262	0.222	0.304	INDETERMINATE	1	TRUE	0	0.429542895699289	2		456	454	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491661	120491661	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	29	297	0	ENST00000256646.2:c.2568T>G	p.Ser856Arg	p.S856R	ENST00000256646	NM_024408.3	856	agT/agG	16/34	0.236963970823561	2	FACETS	0.385	0.309	0.471	0.192	0.154	0.236	INDETERMINATE	1	TRUE	0	0.429542895699289	2		297	351	SUCCESS
FH	2271	MSKCC	GRCh37	1	241665761	241665761	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	86	354	0	ENST00000366560.3:c.1218T>G	p.Asn406Lys	p.N406K	ENST00000366560	NM_000143.3	406	aaT/aaG	8/10	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.429542895699289	2		354	399	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100718	8100718	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568688815	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	28	595	0	ENST00000346208.3:c.692C>T	p.Ser231Phe	p.S231F	ENST00000346208		231	tCc/tTc	3/6	0.383087164564422	1	FACETS	0.243	0.193	0.299	0.243	0.193	0.299	SUBCLONAL	1	TRUE	0	0.429542895699289	1		595	422	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609027	43609027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1483605155	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	28	506	1	ENST00000355710.3:c.1783G>A	p.Glu595Lys	p.E595K	ENST00000355710	NM_020975.4	595	Gag/Aag	10/20	0.383087164564422	1	FACETS	0.329	0.263	0.404	0.329	0.263	0.404	SUBCLONAL	1	TRUE	0	0.429542895699289	1		507	311	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610140	43610140	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1276303673	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	40	725	0	ENST00000355710.3:c.2092G>A	p.Asp698Asn	p.D698N	ENST00000355710	NM_020975.4	698	Gac/Aac	11/20	0.383087164564422	1	FACETS	0.367	0.305	0.436	0.367	0.305	0.436	SUBCLONAL	1	TRUE	0	0.429542895699289	1		725	398	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404783	70404783	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	33	452	0	ENST00000373644.4:c.2297T>C	p.Leu766Ser	p.L766S	ENST00000373644	NM_030625.2	766	tTa/tCa	4/12	0.383087164564422	1	FACETS	0.309	0.251	0.373	0.309	0.251	0.373	SUBCLONAL	1	TRUE	0	0.429542895699289	1		452	391	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446134	70446134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772997622	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	35	481	0	ENST00000373644.4:c.5074G>A	p.Asp1692Asn	p.D1692N	ENST00000373644	NM_030625.2	1692	Gat/Aat	11/12	0.383087164564422	1	FACETS	0.296	0.242	0.356	0.296	0.242	0.356	SUBCLONAL	1	TRUE	0	0.429542895699289	1		481	433	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112769106	112769106	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	51	466	0	ENST00000369452.4:c.1385C>T	p.Ser462Phe	p.S462F	ENST00000369452	NM_007373.3	462	tCc/tTc	7/9	0.383087164564422	1	FACETS	0.433	0.368	0.503	0.433	0.368	0.503	SUBCLONAL	1	TRUE	0	0.429542895699289	1		466	431	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239498	123239498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	47	777	0	ENST00000358487.5:c.2339C>T	p.Ser780Leu	p.S780L	ENST00000358487	NM_000141.4	780	tCa/tTa	18/18	0.383087164564422	1	FACETS	0.293	0.246	0.344	0.293	0.246	0.344	SUBCLONAL	1	TRUE	0	0.429542895699289	1		777	587	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123353226	123353226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	22	359	1	ENST00000358487.5:c.106G>A	p.Glu36Lys	p.E36K	ENST00000358487	NM_000141.4	36	Gaa/Aaa	2/18	0.383087164564422	1	FACETS	0.291	0.226	0.367	0.291	0.226	0.367	SUBCLONAL	1	TRUE	0	0.429542895699289	1		360	276	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417850	32417850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	60	532	0	ENST00000332351.3:c.1202G>A	p.Arg401Lys	p.R401K	ENST00000332351	NM_024426.4	401	aGa/aAa	7/10	1	2	FACETS	0.603	0.521	0.693	0.603	0.521	0.693	SUBCLONAL	1	TRUE	1	0.429542895699289	2		532	463	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996828	100996828	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	113	606	0	ENST00000325455.5:c.1699T>G	p.Cys567Gly	p.C567G	ENST00000325455	NM_001202474.3	567	Tgt/Ggt	2/8	0.279784603210633	3	FACETS	0.965	0.87	1	0.483	0.435	0.533	CLONAL	1	TRUE	1	0.429542895699289	3		606	662	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151774	108151774	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	139	389	0	ENST00000278616.4:c.3455C>T	p.Ser1152Phe	p.S1152F	ENST00000278616	NM_000051.3	1152	tCt/tTt	24/63	0.279784603210633	3	FACETS	1	0.983	1	0.653	0.596	0.712	CLONAL	1	TRUE	1	0.429542895699289	3		389	602	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373218	118373218	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	34	447	0	ENST00000534358.1:c.6611C>T	p.Ser2204Leu	p.S2204L	ENST00000534358	NM_005933.3	2204	tCa/tTa	27/36	0.279784603210633	3	FACETS	0.376	0.307	0.455	0.188	0.153	0.228	SUBCLONAL	1	TRUE	1	0.429542895699289	3		447	511	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374480	118374480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	61	454	0	ENST00000534358.1:c.7873C>T	p.Arg2625Cys	p.R2625C	ENST00000534358	NM_005933.3	2625	Cgt/Tgt	27/36	0.279784603210633	3	FACETS	0.747	0.646	0.856	0.373	0.323	0.428	SUBCLONAL	1	TRUE	1	0.429542895699289	3		454	462	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103402	119103402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1474071047	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	30	306	0	ENST00000264033.4:c.440C>T	p.Pro147Leu	p.P147L	ENST00000264033	NM_005188.3	147	cCt/cTt	2/16	0.279784603210633	3	FACETS	0.442	0.356	0.539	0.221	0.178	0.27	SUBCLONAL	1	TRUE	1	0.429542895699289	3		306	384	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427563	427563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	135	479	0	ENST00000399788.2:c.2606C>T	p.Pro869Leu	p.P869L	ENST00000399788	NM_001042603.1	869	cCa/cTa	19/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.429542895699289	2		479	506	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383363	4383363	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	38	525	0	ENST00000261254.3:c.157C>T	p.Pro53Ser	p.P53S	ENST00000261254	NM_001759.3	53	Ccc/Tcc	1/5	1	2	FACETS	0.411	0.34	0.491	0.411	0.34	0.491	SUBCLONAL	1	TRUE	1	0.429542895699289	2		525	430	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435419	18435419	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	26	296	0	ENST00000266497.5:c.404G>A	p.Gly135Asp	p.G135D	ENST00000266497		135	gGt/gAt	1/31	1	2	FACETS	0.344	0.272	0.426	0.344	0.272	0.426	SUBCLONAL	1	TRUE	1	0.429542895699289	2		296	352	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435666	18435666	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	24	216	0	ENST00000266497.5:c.651G>A	p.Trp217Ter	p.W217*	ENST00000266497		217	tgG/tgA	1/31	1	2	FACETS	0.409	0.321	0.51	0.409	0.321	0.51	SUBCLONAL	1	TRUE	1	0.429542895699289	2		216	273	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420265	49420266	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	88	632	1	ENST00000301067.7:c.15483_15484delinsAA	p.Val5162Met	p.V5162M	ENST00000301067	NM_003482.3	5161	gaGGtg/gaAAtg	48/54	0.365058481719109	1	FACETS	0.654	0.581	0.731	0.654	0.581	0.731	SUBCLONAL	1	TRUE	0	0.429542895699289	1		633	492	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433916	49433916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766114622	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	40	760	1	ENST00000301067.7:c.7637C>T	p.Ser2546Phe	p.S2546F	ENST00000301067	NM_003482.3	2546	tCc/tTc	31/54	0.365058481719109	1	FACETS	0.31	0.257	0.368	0.31	0.257	0.368	SUBCLONAL	1	TRUE	0	0.429542895699289	1		761	472	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445041	49445041	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	80	472	2	ENST00000301067.7:c.2425C>T	p.Gln809Ter	p.Q809*	ENST00000301067	NM_003482.3	809	Cag/Tag	10/54	0.365058481719109	1	FACETS	0.81	0.718	0.907	0.81	0.718	0.907	CLONAL	1	TRUE	0	0.429542895699289	1		474	361	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864723	57864723	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	46	721	0	ENST00000228682.2:c.2200G>A	p.Gly734Arg	p.G734R	ENST00000228682	NM_005269.2	734	Gga/Aga	12/12	0.365058481719109	1	FACETS	0.36	0.303	0.423	0.36	0.303	0.423	SUBCLONAL	1	TRUE	0	0.429542895699289	1		721	467	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864805	57864805	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	41	651	0	ENST00000228682.2:c.2282A>C	p.Tyr761Ser	p.Y761S	ENST00000228682	NM_005269.2	761	tAt/tCt	12/12	0.365058481719109	1	FACETS	0.394	0.329	0.467	0.394	0.329	0.467	SUBCLONAL	1	TRUE	0	0.429542895699289	1		651	380	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536908	120536908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	52	649	2	ENST00000229340.5:c.278C>T	p.Ala93Val	p.A93V	ENST00000229340	NM_006861.6	93	gCc/gTc	4/6	0.365058481719109	1	FACETS	0.405	0.345	0.47	0.405	0.345	0.47	SUBCLONAL	1	TRUE	0	0.429542895699289	1		651	470	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120795644	120795644	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs376073182	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	29	411	0	ENST00000257552.2:c.509A>G	p.His170Arg	p.H170R	ENST00000257552	NM_002442.3	170	cAt/cGt	8/15	0.365058481719109	1	FACETS	0.3	0.24	0.367	0.3	0.24	0.367	SUBCLONAL	1	TRUE	0	0.429542895699289	1		411	354	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225909	133225909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	44	649	0	ENST00000320574.5:c.3988C>T	p.Pro1330Ser	p.P1330S	ENST00000320574	NM_006231.2	1330	Ccg/Tcg	31/49	0.365058481719109	1	FACETS	0.37	0.31	0.436	0.37	0.31	0.436	SUBCLONAL	1	TRUE	0	0.429542895699289	1		649	435	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254169	133254169	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	40	466	0	ENST00000320574.5:c.715C>T	p.His239Tyr	p.H239Y	ENST00000320574	NM_006231.2	239	Cac/Tac	7/49	0.365058481719109	1	FACETS	0.391	0.325	0.464	0.391	0.325	0.464	SUBCLONAL	1	TRUE	0	0.429542895699289	1		466	374	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608322	28608322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	47	627	0	ENST00000241453.7:c.1734G>A	p.Met578Ile	p.M578I	ENST00000241453	NM_004119.2	578	atG/atA	14/24	0.418748378374643	4	FACETS	0.349	0.293	0.411	0.116	0.097	0.137	SUBCLONAL	1	TRUE	1	0.429542895699289	4		627	896	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622418	28622418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	278	359	0	ENST00000241453.7:c.1199G>A	p.Gly400Glu	p.G400E	ENST00000241453	NM_004119.2	400	gGa/gAa	9/24	0.418748378374643	4	FACETS	0.859	0.811	0.907	0.859	0.811	0.907	CLONAL	3	TRUE	1	0.429542895699289	4		359	718	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28883012	28883012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	50	539	0	ENST00000282397.4:c.3688G>A	p.Glu1230Lys	p.E1230K	ENST00000282397	NM_002019.4	1230	Gaa/Aaa	28/30	0.418748378374643	4	FACETS	0.425	0.359	0.497	0.142	0.119	0.166	SUBCLONAL	1	TRUE	1	0.429542895699289	4		539	783	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041745	29041745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1377493987	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	249	407	0	ENST00000282397.4:c.74C>T	p.Ser25Leu	p.S25L	ENST00000282397	NM_002019.4	25	tCa/tTa	2/30	0.418748378374643	4	FACETS	1	0.99	1	0.826	0.777	0.875	CLONAL	2	TRUE	1	0.429542895699289	4		407	669	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912192	32912192	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	86	605	0	ENST00000380152.3:c.3700C>G	p.Leu1234Val	p.L1234V	ENST00000380152		1234	Ctg/Gtg	11/27	0.418748378374643	4	FACETS	0.538	0.474	0.606	0.179	0.158	0.202	SUBCLONAL	1	TRUE	1	0.429542895699289	4		605	1064	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913741	32913742	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	42	376	0	ENST00000380152.3:c.5249_5250delinsTT	p.Ser1750Phe	p.S1750F	ENST00000380152		1750	tCC/tTT	11/27	0.418748378374643	4	FACETS	0.432	0.36	0.513	0.144	0.12	0.171	SUBCLONAL	1	TRUE	1	0.429542895699289	4		376	647	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504501	103504501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1275853625	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	28	287	0	ENST00000355739.4:c.122G>A	p.Gly41Glu	p.G41E	ENST00000355739	NM_000123.3	41	gGa/gAa	2/15	0.418748378374643	4	FACETS	0.346	0.276	0.427	0.115	0.092	0.143	SUBCLONAL	1	TRUE	1	0.429542895699289	4		287	538	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986649	36986650	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TA	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	10	74	0	ENST00000354822.5:c.1039_1040delinsTA	p.Pro347Ter	p.P347*	ENST00000354822	NM_001079668.2	347	CCg/TAg	3/3	1	2	FACETS	0.675	0.465	0.929	0.675	0.465	0.929	SUBCLONAL	1	TRUE	1	0.429542895699289	2		74	69	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675082	40675082	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1307486609	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	51	621	0	ENST00000249776.8:c.46A>C	p.Thr16Pro	p.T16P	ENST00000249776	NM_033286.3	16	Aca/Cca	1/9	0.383087164564422	1	FACETS	0.329	0.279	0.384	0.329	0.279	0.384	SUBCLONAL	1	TRUE	0	0.429542895699289	1		621	567	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675131	40675131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745844593	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	54	661	1	ENST00000249776.8:c.95G>A	p.Arg32Gln	p.R32Q	ENST00000249776	NM_033286.3	32	cGg/cAg	1/9	0.383087164564422	1	FACETS	0.363	0.31	0.421	0.363	0.31	0.421	SUBCLONAL	1	TRUE	0	0.429542895699289	1		662	544	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678334	88678334	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	47	624	0	ENST00000360948.2:c.1202C>T	p.Pro401Leu	p.P401L	ENST00000360948	NM_001012338.2	401	cCa/cTa	9/19	1	2	FACETS	0.462	0.39	0.541	0.462	0.39	0.541	SUBCLONAL	1	TRUE	1	0.429542895699289	2		624	474	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303978	91303978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	61	614	0	ENST00000355112.3:c.1375C>T	p.Pro459Ser	p.P459S	ENST00000355112	NM_000057.2	459	Ccc/Tcc	7/22	1	2	FACETS	0.474	0.409	0.545	0.474	0.409	0.545	SUBCLONAL	1	TRUE	1	0.429542895699289	2		614	599	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131785	2131785	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	30	550	0	ENST00000219476.3:c.3800C>A	p.Pro1267His	p.P1267H	ENST00000219476	NM_000548.3	1267	cCt/cAt	31/42	1	2	FACETS	0.297	0.239	0.364	0.297	0.239	0.364	SUBCLONAL	1	TRUE	1	0.429542895699289	2		550	470	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779316	3779316	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	34	608	1	ENST00000262367.5:c.5732C>T	p.Pro1911Leu	p.P1911L	ENST00000262367	NM_004380.2	1911	cCc/cTc	31/31	1	2	FACETS	0.331	0.27	0.4	0.331	0.27	0.4	SUBCLONAL	1	TRUE	1	0.429542895699289	2		609	478	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857184	9857184	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	56	479	0	ENST00000330684.3:c.4217G>T	p.Arg1406Met	p.R1406M	ENST00000330684	NM_001134407.1	1406	aGg/aTg	13/13	1	2	FACETS	0.705	0.606	0.811	0.705	0.606	0.811	SUBCLONAL	1	TRUE	1	0.429542895699289	2		479	370	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862818	9862818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	78	576	0	ENST00000330684.3:c.2485G>A	p.Ala829Thr	p.A829T	ENST00000330684	NM_001134407.1	829	Gcc/Acc	12/13	1	2	FACETS	0.711	0.626	0.801	0.711	0.626	0.801	SUBCLONAL	1	TRUE	1	0.429542895699289	2		576	511	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844170	68844170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776503962	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	90	620	0	ENST00000261769.5:c.758C>T	p.Thr253Ile	p.T253I	ENST00000261769	NM_004360.3	253	aCc/aTc	6/16	0.383087164564422	1	FACETS	0.708	0.631	0.789	0.708	0.631	0.789	SUBCLONAL	1	TRUE	0	0.429542895699289	1		620	465	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993825	72993825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757494633	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	44	454	0	ENST00000268489.5:c.220C>T	p.Pro74Ser	p.P74S	ENST00000268489	NM_006885.3	74	Ccc/Tcc	2/10	0.383087164564422	1	FACETS	0.603	0.509	0.705	0.603	0.509	0.705	SUBCLONAL	1	TRUE	0	0.429542895699289	1		454	267	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81954867	81954867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757834798	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	101	647	1	ENST00000359376.3:c.2300C>T	p.Pro767Leu	p.P767L	ENST00000359376	NM_002661.3	767	cCg/cTg	21/33	0.383087164564422	1	FACETS	0.718	0.645	0.796	0.718	0.645	0.796	SUBCLONAL	1	TRUE	0	0.429542895699289	1		648	514	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347140	89347140	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762451759	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	20	445	0	ENST00000301030.4:c.5810G>A	p.Gly1937Asp	p.G1937D	ENST00000301030	NM_001256183.1	1937	gGt/gAt	9/13	0.383087164564422	1	FACETS	0.26	0.199	0.332	0.26	0.199	0.332	SUBCLONAL	1	TRUE	0	0.429542895699289	1		445	281	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348932	89348932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	107	804	1	ENST00000301030.4:c.4018C>T	p.Leu1340Phe	p.L1340F	ENST00000301030	NM_001256183.1	1340	Ctc/Ttc	9/13	0.383087164564422	1	FACETS	0.709	0.638	0.783	0.709	0.638	0.783	SUBCLONAL	1	TRUE	0	0.429542895699289	1		805	552	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349759	89349759	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	138	865	0	ENST00000301030.4:c.3191A>T	p.Glu1064Val	p.E1064V	ENST00000301030	NM_001256183.1	1064	gAa/gTa	9/13	0.383087164564422	1	FACETS	0.675	0.615	0.738	0.675	0.615	0.738	SUBCLONAL	1	TRUE	0	0.429542895699289	1		865	747	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349855	89349855	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	145	1014	0	ENST00000301030.4:c.3095C>T	p.Ser1032Phe	p.S1032F	ENST00000301030	NM_001256183.1	1032	tCc/tTc	9/13	0.383087164564422	1	FACETS	0.645	0.589	0.704	0.645	0.589	0.704	SUBCLONAL	1	TRUE	0	0.429542895699289	1		1014	822	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577548	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	106	660	1	ENST00000269305.4:c.733_734delinsTA	p.Gly245Tyr	p.G245Y	ENST00000269305	NM_001126112.2	245	GGc/TAc	7/11	1	2	FACETS	0.929	0.836	1	0.929	0.836	1	CLONAL	1	TRUE	1	0.429542895699289	2		661	531	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004911	16004911	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	59	630	0	ENST00000268712.3:c.2343G>C	p.Glu781Asp	p.E781D	ENST00000268712	NM_006311.3	781	gaG/gaC	20/46	1	2	FACETS	0.438	0.377	0.505	0.438	0.377	0.505	SUBCLONAL	1	TRUE	1	0.429542895699289	2		630	627	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16052790	16052790	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	45	461	0	ENST00000268712.3:c.884G>A	p.Arg295Lys	p.R295K	ENST00000268712	NM_006311.3	295	aGa/aAa	9/46	1	2	FACETS	0.401	0.337	0.473	0.401	0.337	0.473	SUBCLONAL	1	TRUE	1	0.429542895699289	2		461	522	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492752	56492752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	189	609	0	ENST00000407977.2:c.187C>T	p.Leu63Phe	p.L63F	ENST00000407977		63	Ctc/Ttc	2/10	0.236963970823561	2	FACETS	1	0.983	1	0.596	0.552	0.641	INDETERMINATE	1	TRUE	0	0.429542895699289	2		609	738	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414990	56414990	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	63	552	0	ENST00000348428.3:c.2391T>A	p.His797Gln	p.H797Q	ENST00000348428	NM_006785.3	797	caT/caA	17/17	1	2	FACETS	0.512	0.443	0.587	0.512	0.443	0.587	SUBCLONAL	1	TRUE	1	0.429542895699289	2		552	573	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223116	1223117	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	80	599	0	ENST00000326873.7:c.1053_1054delinsAA	p.Asp352Asn	p.D352N	ENST00000326873	NM_000455.4	351	gaGGac/gaAAac	8/10	1	2	FACETS	0.784	0.693	0.882	0.784	0.693	0.882	SUBCLONAL	1	TRUE	1	0.429542895699289	2		599	475	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226890	2226891	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	31	152	0	ENST00000398665.3:c.4370_4371delinsTT	p.Ser1457Phe	p.S1457F	ENST00000398665	NM_032482.2	1457	tCC/tTT	27/28	1	2	FACETS	0.87	0.712	1	0.87	0.712	1	CLONAL	1	TRUE	1	0.429542895699289	2		152	166	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122742	7122742	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	41	693	1	ENST00000302850.5:c.3412C>T	p.Gln1138Ter	p.Q1138*	ENST00000302850	NM_000208.2	1138	Cag/Tag	19/22	1	2	FACETS	0.33	0.274	0.392	0.33	0.274	0.392	SUBCLONAL	1	TRUE	1	0.429542895699289	2		694	579	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122909	7122909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	79	679	0	ENST00000302850.5:c.3350C>T	p.Ser1117Phe	p.S1117F	ENST00000302850	NM_000208.2	1117	tCt/tTt	18/22	1	2	FACETS	0.765	0.675	0.861	0.765	0.675	0.861	SUBCLONAL	1	TRUE	1	0.429542895699289	2		679	481	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125332	7125332	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	99	585	0	ENST00000302850.5:c.3220G>A	p.Glu1074Lys	p.E1074K	ENST00000302850	NM_000208.2	1074	Gag/Aag	17/22	1	2	FACETS	0.933	0.837	1	0.933	0.837	1	CLONAL	1	TRUE	1	0.429542895699289	2		585	494	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184479	7184479	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	45	648	0	ENST00000302850.5:c.822C>A	p.His274Gln	p.H274Q	ENST00000302850	NM_000208.2	274	caC/caA	3/22	1	2	FACETS	0.361	0.302	0.425	0.361	0.302	0.425	SUBCLONAL	1	TRUE	1	0.429542895699289	2		648	581	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250462	10250462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	34	490	0	ENST00000340748.4:c.3790C>T	p.Leu1264Phe	p.L1264F	ENST00000340748		1264	Ctc/Ttc	33/40	1	2	FACETS	0.372	0.303	0.448	0.372	0.303	0.448	SUBCLONAL	1	TRUE	1	0.429542895699289	2		490	426	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250770	10250770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1290055474	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	38	676	2	ENST00000340748.4:c.3710C>T	p.Ser1237Leu	p.S1237L	ENST00000340748		1237	tCg/tTg	32/40	1	2	FACETS	0.324	0.267	0.388	0.324	0.267	0.388	SUBCLONAL	1	TRUE	1	0.429542895699289	2		678	546	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152158	11152158	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	71	483	1	ENST00000358026.2:c.4442A>T	p.Glu1481Val	p.E1481V	ENST00000358026	NM_001128849.1	1481	gAg/gTg	31/36	1	2	FACETS	0.695	0.608	0.788	0.695	0.608	0.788	SUBCLONAL	1	TRUE	1	0.429542895699289	2		484	476	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272119	15272119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	30	478	0	ENST00000263388.2:c.6320C>T	p.Ser2107Phe	p.S2107F	ENST00000263388	NM_000435.2	2107	tCc/tTc	33/33	1	2	FACETS	0.384	0.309	0.468	0.384	0.309	0.468	SUBCLONAL	1	TRUE	1	0.429542895699289	2		478	364	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945921	17945921	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774183456	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	69	795	0	ENST00000458235.1:c.2018G>A	p.Gly673Glu	p.G673E	ENST00000458235	NM_000215.3	673	gGg/gAg	15/24	1	2	FACETS	0.462	0.401	0.527	0.462	0.401	0.527	SUBCLONAL	1	TRUE	1	0.429542895699289	2		795	696	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950352	17950352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	44	725	1	ENST00000458235.1:c.1375G>A	p.Asp459Asn	p.D459N	ENST00000458235	NM_000215.3	459	Gat/Aat	10/24	1	2	FACETS	0.35	0.293	0.414	0.35	0.293	0.414	SUBCLONAL	1	TRUE	1	0.429542895699289	2		726	585	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273029	18273029	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766285678	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	43	672	0	ENST00000222254.8:c.919C>T	p.Pro307Ser	p.P307S	ENST00000222254	NM_005027.3	307	Ccc/Tcc	8/16	1	2	FACETS	0.341	0.285	0.404	0.341	0.285	0.404	SUBCLONAL	1	TRUE	1	0.429542895699289	2		672	587	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256725	19256725	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	30	457	1	ENST00000162023.5:c.988C>T	p.Pro330Ser	p.P330S	ENST00000162023		330	Ccc/Tcc	13/13	1	2	FACETS	0.372	0.3	0.455	0.372	0.3	0.455	SUBCLONAL	1	TRUE	1	0.429542895699289	2		458	375	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213615	36213615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	90	807	1	ENST00000222270.7:c.2717C>T	p.Thr906Ile	p.T906I	ENST00000222270	NM_014727.1	906	aCa/aTa	5/37	1	2	FACETS	0.654	0.58	0.732	0.654	0.58	0.732	SUBCLONAL	1	TRUE	1	0.429542895699289	2		808	641	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867325	45867325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	45	623	2	ENST00000391945.4:c.868G>A	p.Glu290Lys	p.E290K	ENST00000391945	NM_000400.3	290	Gag/Aag	10/23	1	2	FACETS	0.382	0.321	0.45	0.382	0.321	0.45	SUBCLONAL	1	TRUE	1	0.429542895699289	2		625	548	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905488	50905489	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	46	830	1	ENST00000440232.2:c.616_617delinsTT	p.Pro206Phe	p.P206F	ENST00000440232	NM_002691.3	206	CCc/TTc	6/27	1	2	FACETS	0.355	0.298	0.417	0.355	0.298	0.417	SUBCLONAL	1	TRUE	1	0.429542895699289	2		831	604	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085827	16085827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	86	433	0	ENST00000281043.3:c.1003C>T	p.Pro335Ser	p.P335S	ENST00000281043	NM_005378.4	335	Ccc/Tcc	3/3	0.129015905956431	3	FACETS	1	0.978	1	0.477	0.425	0.531	INDETERMINATE	1	TRUE	0	0.429542895699289	3		433	340	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972744	25972744	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1348431069	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	34	459	0	ENST00000435504.4:c.1681C>T	p.Gln561Ter	p.Q561*	ENST00000435504		561	Cag/Tag	12/13	0.129015905956431	3	FACETS	0.398	0.325	0.481	0.133	0.108	0.161	INDETERMINATE	1	TRUE	0	0.429542895699289	3		459	483	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972989	25972989	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	31	399	0	ENST00000435504.4:c.1436C>T	p.Pro479Leu	p.P479L	ENST00000435504		479	cCc/cTc	12/13	0.129015905956431	3	FACETS	0.385	0.311	0.47	0.128	0.103	0.157	INDETERMINATE	1	TRUE	0	0.429542895699289	3		399	455	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029195	26029195	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	72	333	0	ENST00000435504.4:c.155C>T	p.Pro52Leu	p.P52L	ENST00000435504		52	cCt/cTt	4/13	0.129015905956431	3	FACETS	0.943	0.827	1	0.314	0.275	0.356	INDETERMINATE	1	TRUE	0	0.429542895699289	3		333	432	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519825	29519825	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	49	604	0	ENST00000389048.3:c.1746G>A	p.Trp582Ter	p.W582*	ENST00000389048	NM_004304.4	582	tgG/tgA	9/29	0.129015905956431	3	FACETS	0.463	0.392	0.542	0.154	0.13	0.181	INDETERMINATE	1	TRUE	0	0.429542895699289	3		604	598	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940473	29940473	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	23	345	0	ENST00000389048.3:c.758T>A	p.Phe253Tyr	p.F253Y	ENST00000389048	NM_004304.4	253	tTc/tAc	2/29	0.129015905956431	3	FACETS	0.329	0.256	0.414	0.11	0.085	0.138	INDETERMINATE	1	TRUE	0	0.429542895699289	3		345	395	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248692	212248692	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	42	504	0	ENST00000342788.4:c.3575C>T	p.Ser1192Phe	p.S1192F	ENST00000342788	NM_005235.2	1192	tCc/tTc	28/28	0.236963970823561	2	FACETS	0.371	0.309	0.44	0.186	0.154	0.22	INDETERMINATE	1	TRUE	0	0.429542895699289	2		504	527	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251634	212251634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3748961	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	38	526	0	ENST00000342788.4:c.3425G>A	p.Arg1142Gln	p.R1142Q	ENST00000342788	NM_005235.2	1142	cGa/cAa	27/28	0.236963970823561	2	FACETS	0.376	0.311	0.45	0.188	0.155	0.225	INDETERMINATE	1	TRUE	0	0.429542895699289	2		526	470	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285336	212285336	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	29	392	0	ENST00000342788.4:c.2965G>A	p.Gly989Ser	p.G989S	ENST00000342788	NM_005235.2	989	Ggt/Agt	25/28	0.236963970823561	2	FACETS	0.405	0.326	0.496	0.203	0.163	0.248	INDETERMINATE	1	TRUE	0	0.429542895699289	2		392	333	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426711	212426711	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1484741477	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	38	543	0	ENST00000342788.4:c.2404G>A	p.Gly802Ser	p.G802S	ENST00000342788	NM_005235.2	802	Ggc/Agc	20/28	0.236963970823561	2	FACETS	0.323	0.267	0.387	0.162	0.133	0.194	INDETERMINATE	1	TRUE	0	0.429542895699289	2		543	547	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794494	242794494	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	45	643	0	ENST00000334409.5:c.448G>A	p.Glu150Lys	p.E150K	ENST00000334409	NM_005018.2	150	Gaa/Aaa	3/5	0.236963970823561	2	FACETS	0.403	0.338	0.474	0.201	0.169	0.237	INDETERMINATE	1	TRUE	0	0.429542895699289	2		643	520	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525083	9525083	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	59	429	0	ENST00000353224.5:c.1802A>T	p.Lys601Ile	p.K601I	ENST00000353224	NM_177990.2	601	aAa/aTa	8/10	1	2	FACETS	0.656	0.566	0.753	0.656	0.566	0.753	SUBCLONAL	1	TRUE	1	0.429542895699289	2		429	419	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561131	9561131	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1463915700	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	33	387	0	ENST00000353224.5:c.651G>A	p.Trp217Ter	p.W217*	ENST00000353224	NM_177990.2	217	tgG/tgA	4/10	1	2	FACETS	0.388	0.316	0.469	0.388	0.316	0.469	SUBCLONAL	1	TRUE	1	0.429542895699289	2		387	396	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46270974	46270974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	92	496	0	ENST00000371998.3:c.3098C>T	p.Ser1033Phe	p.S1033F	ENST00000371998		1033	tCc/tTc	17/23	1	2	FACETS	0.753	0.67	0.84	0.753	0.67	0.84	SUBCLONAL	1	TRUE	1	0.429542895699289	2		496	569	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321451	62321451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	36	608	0	ENST00000360203.5:c.2153C>T	p.Ala718Val	p.A718V	ENST00000360203	NM_001283009.1	718	gCc/gTc	25/35	1	2	FACETS	0.328	0.269	0.394	0.328	0.269	0.394	SUBCLONAL	1	TRUE	1	0.429542895699289	2		608	511	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764345	39764345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	82	512	1	ENST00000288319.7:c.767G>A	p.Arg256Lys	p.R256K	ENST00000288319	NM_182918.3	256	aGg/aAg	7/10	1	2	FACETS	0.743	0.657	0.835	0.743	0.657	0.835	SUBCLONAL	1	TRUE	1	0.429542895699289	2		513	514	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655229	45655229	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs900588921	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	73	594	0	ENST00000407780.3:c.623C>A	p.Thr208Asn	p.T208N	ENST00000407780	NM_001283052.1	208	aCc/aAc	4/7	1	2	FACETS	0.669	0.586	0.758	0.669	0.586	0.758	SUBCLONAL	1	TRUE	1	0.429542895699289	2		594	508	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422958	12422958	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	47	593	0	ENST00000287820.6:c.448C>T	p.His150Tyr	p.H150Y	ENST00000287820	NM_015869.4	150	Cac/Tac	3/7	1	2	FACETS	0.373	0.315	0.439	0.373	0.315	0.439	SUBCLONAL	1	TRUE	1	0.429542895699289	2		593	586	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49413010	49413011	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	41	621	1	ENST00000418115.1:c.12_13delinsTT	p.Arg5Trp	p.R5W	ENST00000418115	NM_001664.2	4	atCCgg/atTTgg	2/5	1	2	FACETS	0.314	0.261	0.373	0.314	0.261	0.373	SUBCLONAL	1	TRUE	1	0.429542895699289	2		622	608	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960074	134960074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	41	594	0	ENST00000398015.3:c.2431G>A	p.Gly811Arg	p.G811R	ENST00000398015	NM_004441.4	811	Ggg/Agg	13/16	0.270152035660751	1	FACETS	0.263	0.218	0.313	0.263	0.218	0.313	SUBCLONAL	1	TRUE	0	0.429542895699289	1		594	570	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156486	55156486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756581500	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	24	366	0	ENST00000257290.5:c.2887G>A	p.Glu963Lys	p.E963K	ENST00000257290	NM_006206.4	963	Gaa/Aaa	22/23	1	2	FACETS	0.301	0.236	0.377	0.301	0.236	0.377	SUBCLONAL	1	TRUE	1	0.429542895699289	2		366	371	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564452	55564452	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs772836939	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	36	352	0	ENST00000288135.5:c.340C>T	p.Pro114Ser	p.P114S	ENST00000288135	NM_000222.2	114	Cct/Tct	3/21	1	2	FACETS	0.394	0.324	0.473	0.394	0.324	0.473	SUBCLONAL	1	TRUE	1	0.429542895699289	2		352	425	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981566	55981566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	34	283	0	ENST00000263923.4:c.371C>T	p.Pro124Leu	p.P124L	ENST00000263923	NM_002253.2	124	cCa/cTa	4/30	1	2	FACETS	0.456	0.373	0.549	0.456	0.373	0.549	SUBCLONAL	1	TRUE	1	0.429542895699289	2		283	347	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157704	106157704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	24	237	0	ENST00000380013.4:c.2605C>T	p.Pro869Ser	p.P869S	ENST00000380013	NM_001127208.2	869	Cca/Tca	3/11	1	2	FACETS	0.379	0.297	0.473	0.379	0.297	0.473	SUBCLONAL	1	TRUE	1	0.429542895699289	2		237	295	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516867	187516867	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	32	429	0	ENST00000441802.2:c.13114C>T	p.Gln4372Ter	p.Q4372*	ENST00000441802	NM_005245.3	4372	Cag/Tag	26/27	1	2	FACETS	0.334	0.271	0.406	0.334	0.271	0.406	SUBCLONAL	1	TRUE	1	0.429542895699289	2		429	446	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539870	187539870	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	114	419	0	ENST00000441802.2:c.7870G>T	p.Asp2624Tyr	p.D2624Y	ENST00000441802	NM_005245.3	2624	Gat/Tat	10/27	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.429542895699289	2		419	369	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629457	187629457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	90	565	0	ENST00000441802.2:c.1525C>T	p.Pro509Ser	p.P509S	ENST00000441802	NM_005245.3	509	Ccg/Tcg	2/27	1	2	FACETS	0.672	0.596	0.752	0.672	0.596	0.752	SUBCLONAL	1	TRUE	1	0.429542895699289	2		565	624	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176998	56176999	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	93	417	1	ENST00000399503.3:c.2268_2269delinsTT	p.Arg757Cys	p.R757C	ENST00000399503	NM_005921.1	756	ggCCgc/ggTTgc	13/20	1	2	FACETS	0.884	0.789	0.984	0.884	0.789	0.984	CLONAL	1	TRUE	1	0.429542895699289	2		418	490	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755578	57755579	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	25	493	0	ENST00000274289.3:c.208_209delinsAT	p.Ser70Met	p.S70M	ENST00000274289	NM_006622.3	70	TCg/ATg	1/14	0.191910590072447	2	FACETS	0.326	0.257	0.406	0.163	0.128	0.203	INDETERMINATE	1	TRUE	0	0.429542895699289	2		493	357	SUCCESS
APC	324	MSKCC	GRCh37	5	112175984	112175984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767138124	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	23	228	0	ENST00000257430.4:c.4693G>A	p.Asp1565Asn	p.D1565N	ENST00000257430	NM_000038.5	1565	Gat/Aat	16/16	0.191910590072447	2	FACETS	0.407	0.318	0.51	0.204	0.159	0.255	INDETERMINATE	1	TRUE	0	0.429542895699289	2		228	263	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520175	176520176	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	135	858	3	ENST00000292408.4:c.1094_1095delinsTT	p.Ala365Val	p.A365V	ENST00000292408	NM_213647.1	365	gCC/gTT	9/18	0.191910590072447	2	FACETS	1	0.95	1	0.53	0.483	0.579	INDETERMINATE	1	TRUE	0	0.429542895699289	2		861	593	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047646	180047646	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	82	544	1	ENST00000261937.6:c.2369G>A	p.Trp790Ter	p.W790*	ENST00000261937	NM_182925.4	790	tGg/tAg	16/30	0.429542895699289	1	FACETS	0.737	0.653	0.825	0.737	0.653	0.825	SUBCLONAL	1	TRUE	0	0.429542895699289	1		545	407	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271209	26271209	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1318299590	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	52	330	0	ENST00000305910.3:c.404G>A	p.Arg135Lys	p.R135K	ENST00000305910	NM_003534.2	135	aGa/aAa	1/1	1	2	FACETS	0.653	0.558	0.756	0.653	0.558	0.756	SUBCLONAL	1	TRUE	1	0.429542895699289	2		330	371	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181503	32181503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	47	621	0	ENST00000375023.3:c.2282G>A	p.Gly761Glu	p.G761E	ENST00000375023	NM_004557.3	761	gGg/gAg	14/30	1	2	FACETS	0.346	0.291	0.406	0.346	0.291	0.406	SUBCLONAL	1	TRUE	1	0.429542895699289	2		621	633	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181560	32181560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	91	707	0	ENST00000375023.3:c.2225G>A	p.Gly742Asp	p.G742D	ENST00000375023	NM_004557.3	742	gGc/gAc	14/30	1	2	FACETS	0.634	0.563	0.71	0.634	0.563	0.71	SUBCLONAL	1	TRUE	1	0.429542895699289	2		707	668	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185835	32185835	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138825503	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	115	659	0	ENST00000375023.3:c.1561C>T	p.Pro521Ser	p.P521S	ENST00000375023	NM_004557.3	521	Ccc/Tcc	9/30	1	2	FACETS	0.953	0.861	1	0.953	0.861	1	CLONAL	1	TRUE	1	0.429542895699289	2		659	562	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956664	93956664	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	39	406	0	ENST00000369303.4:c.2572C>T	p.Pro858Ser	p.P858S	ENST00000369303	NM_004440.3	858	Ccc/Tcc	15/17	0.331902208554568	1	FACETS	0.345	0.286	0.411	0.345	0.286	0.411	SUBCLONAL	1	TRUE	0	0.429542895699289	1		406	413	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967856	93967856	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	51	506	0	ENST00000369303.4:c.2071C>T	p.His691Tyr	p.H691Y	ENST00000369303	NM_004440.3	691	Cac/Tac	11/17	0.331902208554568	1	FACETS	0.327	0.277	0.381	0.327	0.277	0.381	SUBCLONAL	1	TRUE	0	0.429542895699289	1		506	571	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536230	106536230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	44	448	0	ENST00000369096.4:c.197C>T	p.Pro66Leu	p.P66L	ENST00000369096	NM_001198.3	66	cCc/cTc	2/7	0.331902208554568	1	FACETS	0.346	0.29	0.408	0.346	0.29	0.408	SUBCLONAL	1	TRUE	0	0.429542895699289	1		448	465	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631376	117631376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	40	503	0	ENST00000368508.3:c.6302G>A	p.Gly2101Glu	p.G2101E	ENST00000368508	NM_002944.2	2101	gGa/gAa	40/43	0.331902208554568	1	FACETS	0.311	0.258	0.37	0.311	0.258	0.37	SUBCLONAL	1	TRUE	0	0.429542895699289	1		503	470	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622230	162622230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	75	483	0	ENST00000366898.1:c.467G>A	p.Arg156Lys	p.R156K	ENST00000366898	NM_004562.2	156	aGa/aAa	4/12	0.331902208554568	1	FACETS	0.59	0.518	0.666	0.59	0.518	0.666	SUBCLONAL	1	TRUE	0	0.429542895699289	1		483	465	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954900	2954900	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	31	621	0	ENST00000396946.4:c.2810C>T	p.Ala937Val	p.A937V	ENST00000396946	NM_032415.4	937	gCc/gTc	21/25	1	2	FACETS	0.309	0.249	0.377	0.309	0.249	0.377	SUBCLONAL	1	TRUE	1	0.429542895699289	2		621	467	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962794	2962794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1206291917	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	44	570	1	ENST00000396946.4:c.2114G>A	p.Gly705Asp	p.G705D	ENST00000396946	NM_032415.4	705	gGc/gAc	16/25	1	2	FACETS	0.516	0.433	0.607	0.516	0.433	0.607	SUBCLONAL	1	TRUE	1	0.429542895699289	2		571	397	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371827	116371827	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200740468	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	46	501	0	ENST00000397752.3:c.1306G>A	p.Glu436Lys	p.E436K	ENST00000397752	NM_000245.2	436	Gaa/Aaa	3/21	0.429542895699289	4	FACETS	0.421	0.354	0.496	0.14	0.118	0.166	SUBCLONAL	1	TRUE	1	0.429542895699289	4		501	727	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403212	116403212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	375	541	0	ENST00000397752.3:c.2473G>A	p.Gly825Arg	p.G825R	ENST00000397752	NM_000245.2	825	Ggg/Agg	11/21	0.429542895699289	4	FACETS	0.916	0.873	0.96	0.916	0.873	0.96	CLONAL	3	TRUE	1	0.429542895699289	4		541	908	SUCCESS
MET	4233	MSKCC	GRCh37	7	116409810	116409810	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753911898	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	32	298	0	ENST00000397752.3:c.2695G>A	p.Asp899Asn	p.D899N	ENST00000397752	NM_000245.2	899	Gac/Aac	12/21	0.429542895699289	4	FACETS	0.418	0.339	0.509	0.139	0.113	0.17	SUBCLONAL	1	TRUE	1	0.429542895699289	4		298	509	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29195907	29195907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	72	767	0	ENST00000240100.2:c.691G>A	p.Asp231Asn	p.D231N	ENST00000240100	NM_001394.6	231	Gac/Aac	3/4	1	2	FACETS	0.516	0.45	0.586	0.516	0.45	0.586	SUBCLONAL	1	TRUE	1	0.429542895699289	2		767	650	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56860239	56860239	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	44	510	0	ENST00000519728.1:c.241G>A	p.Asp81Asn	p.D81N	ENST00000519728	NM_002350.3	81	Gac/Aac	4/13	1	2	FACETS	0.498	0.418	0.587	0.498	0.418	0.587	SUBCLONAL	1	TRUE	1	0.429542895699289	2		510	411	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965451	68965451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	96	661	0	ENST00000288368.4:c.1063G>A	p.Ala355Thr	p.A355T	ENST00000288368	NM_024870.2	355	Gct/Act	9/40	1	2	FACETS	0.643	0.573	0.718	0.643	0.573	0.718	SUBCLONAL	1	TRUE	1	0.429542895699289	2		661	695	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5463052	5463052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	34	251	0	ENST00000381577.3:c.613G>A	p.Glu205Lys	p.E205K	ENST00000381577	NM_014143.3	205	Gag/Aag	4/7	0.429542895699289	1	FACETS	0.499	0.41	0.598	0.499	0.41	0.598	SUBCLONAL	1	TRUE	0	0.429542895699289	1		251	249	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400191	139400191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367710569	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	23	678	0	ENST00000277541.6:c.4157C>T	p.Pro1386Leu	p.P1386L	ENST00000277541	NM_017617.3	1386	cCg/cTg	25/34	0.429542895699289	1	FACETS	0.205	0.159	0.258	0.205	0.159	0.258	SUBCLONAL	1	TRUE	0	0.429542895699289	1		678	411	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400218	139400218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	44	686	0	ENST00000277541.6:c.4130C>T	p.Pro1377Leu	p.P1377L	ENST00000277541	NM_017617.3	1377	cCc/cTc	25/34	0.429542895699289	1	FACETS	0.423	0.356	0.498	0.423	0.356	0.498	SUBCLONAL	1	TRUE	0	0.429542895699289	1		686	380	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929343	44929343	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs376391350	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	131	329	0	ENST00000377967.4:c.2443G>T	p.Val815Phe	p.V815F	ENST00000377967	NM_021140.2	815	Gtt/Ttt	17/29	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.429542895699289	1		329	370	SUCCESS
AR	367	MSKCC	GRCh37	X	66766116	66766117	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	139	237	0	ENST00000374690.3:c.1128_1129delinsTT	p.Pro377Ser	p.P377S	ENST00000374690	NM_000044.3	376	ccCCct/ccTTct	1/8	0.429542895699289	2	FACETS	1	0.981	1			1	CLONAL	2	TRUE	NA	0.429542895699289	2		237	276	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617183	100617183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs988577951	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	85	300	0	ENST00000308731.7:c.566C>T	p.Pro189Leu	p.P189L	ENST00000308731	NM_000061.2	189	cCc/cTc	7/19	0.429542895699289	2	FACETS	1	0.951	1			1	CLONAL	1	TRUE	NA	0.429542895699289	2		300	353	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200071	128200071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	49	878	1	ENST00000341105.2:c.1234G>A	p.Glu412Lys	p.E412K	ENST00000341105	NM_032638.4	412	Gag/Aag	6/6	1	2	FACETS	0.326	0.275	0.382	0.326	0.275	0.382	SUBCLONAL	1	TRUE	1	0.429542895699289	2		879	700	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	35	215	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		215	83	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971209	21971209	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0032692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	38	235	0	ENST00000304494.5:c.151-2A>T		p.X51_splice	ENST00000304494	NM_000077.4	51			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		235	86	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624274	89624274	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs587782187	NA	P-0032692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	44	265	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		265	90	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032692-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	47	215	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		215	206	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971209	21971209	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0032692-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	73	235	0	ENST00000304494.5:c.151-2A>T		p.X51_splice	ENST00000304494	NM_000077.4	51			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		235	175	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624274	89624274	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs587782187	NA	P-0032692-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	113	265	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		265	241	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346627	89346627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201509886	NA	P-0032692-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	17	318	0	ENST00000301030.4:c.6323G>A	p.Gly2108Asp	p.G2108D	ENST00000301030	NM_001256183.1	2108	gGc/gAc	9/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		318	217	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102882	71102882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	72	314	0	ENST00000318789.4:c.325C>T	p.Pro109Ser	p.P109S	ENST00000318789	NM_032682.5	109	Ccc/Tcc	8/21	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.580098445434209	2		314	238	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033198	69033198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	255	433	0	ENST00000288368.4:c.3638G>A	p.Arg1213Lys	p.R1213K	ENST00000288368	NM_024870.2	1213	aGg/aAg	30/40	0.202191194009076	6	FACETS	0.967	0.917	1			1	INDETERMINATE	4	TRUE	NA	0.580098445434209	6		433	491	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	74	462	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.580098445434209	2		463	213	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934573	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	251	499	0	ENST00000269305.4:c.722C>A	p.Ser241Tyr	p.S241Y	ENST00000269305	NM_001126112.2	241	tCc/tAc	7/11	0.580098445434209	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.580098445434209	2		499	406	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423632	88423632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1478926904	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	83	370	1	ENST00000360948.2:c.2203C>T	p.Arg735Cys	p.R735C	ENST00000360948	NM_001012338.2	735	Cgc/Tgc	18/19	1	2	FACETS	0.987	0.881	1	0.987	0.881	1	CLONAL	1	TRUE	1	0.580098445434209	2		371	290	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042238	6042238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs116373169	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	110	440	1	ENST00000265849.7:c.383C>T	p.Ser128Leu	p.S128L	ENST00000265849	NM_000535.5	128	tCg/tTg	5/15	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.580098445434209	2		441	367	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107185	11107185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555763975	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	98	441	0	ENST00000358026.2:c.1777G>A	p.Glu593Lys	p.E593K	ENST00000358026	NM_001128849.1	593	Gaa/Aaa	11/36	1	2	FACETS	0.891	0.802	0.985	0.891	0.802	0.985	CLONAL	1	TRUE	1	0.580098445434209	2		441	379	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798881	42798881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	124	613	0	ENST00000575354.2:c.4453C>T	p.Pro1485Ser	p.P1485S	ENST00000575354	NM_015125.3	1485	Ccg/Tcg	19/20	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.580098445434209	2		613	406	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256812	19256812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200233107	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	70	263	0	ENST00000162023.5:c.901G>A	p.Glu301Lys	p.E301K	ENST00000162023		301	Gag/Aag	13/13	1	2	FACETS	0.993	0.878	1	0.993	0.878	1	CLONAL	1	TRUE	1	0.580098445434209	2		263	243	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911104	32911104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	80	331	0	ENST00000380152.3:c.2612C>T	p.Ser871Leu	p.S871L	ENST00000380152		871	tCa/tTa	11/27	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.580098445434209	2		331	227	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184559	7184559	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773115239	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	95	394	0	ENST00000302850.5:c.742G>A	p.Asp248Asn	p.D248N	ENST00000302850	NM_000208.2	248	Gac/Aac	3/22	1	2	FACETS	0.999	0.899	1	0.999	0.899	1	CLONAL	1	TRUE	1	0.580098445434209	2		394	328	SUCCESS
CBL	867	MSKCC	GRCh37	11	119158561	119158561	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	115	356	0	ENST00000264033.4:c.1942-1G>A		p.X648_splice	ENST00000264033	NM_005188.3	648			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.580098445434209	2		356	352	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878458	151878458	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	106	572	0	ENST00000262189.6:c.6487C>T	p.Pro2163Ser	p.P2163S	ENST00000262189	NM_170606.2	2163	Cct/Tct	36/59	1	2	FACETS	0.832	0.751	0.918	0.832	0.751	0.918	CLONAL	1	TRUE	1	0.580098445434209	2		572	439	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78882680	78882680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	112	547	0	ENST00000306801.3:c.2471C>T	p.Pro824Leu	p.P824L	ENST00000306801	NM_020761.2	824	cCa/cTa	21/34	1	2	FACETS	0.946	0.858	1	0.946	0.858	1	CLONAL	1	TRUE	1	0.580098445434209	2		547	408	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350486	89350486	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	103	841	1	ENST00000301030.4:c.2464C>T	p.Gln822Ter	p.Q822*	ENST00000301030	NM_001256183.1	822	Cag/Tag	9/13	1	2	FACETS	0.794	0.715	0.878	0.794	0.715	0.878	SUBCLONAL	1	TRUE	1	0.580098445434209	2		842	447	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157359	106157359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210417590	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	78	356	0	ENST00000380013.4:c.2260G>A	p.Glu754Lys	p.E754K	ENST00000380013	NM_001127208.2	754	Gag/Aag	3/11	1	2	FACETS	0.992	0.883	1	0.992	0.883	1	CLONAL	1	TRUE	1	0.580098445434209	2		356	271	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022646	12022646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	88	421	0	ENST00000396373.4:c.752C>T	p.Ser251Phe	p.S251F	ENST00000396373	NM_001987.4	251	tCc/tTc	5/8	1	2	FACETS	0.892	0.798	0.991	0.892	0.798	0.991	CLONAL	1	TRUE	1	0.580098445434209	2		421	340	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087895	27087895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	123	533	0	ENST00000324856.7:c.2182C>T	p.Pro728Ser	p.P728S	ENST00000324856	NM_006015.4	728	Cca/Tca	6/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.580098445434209	2		533	366	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36931983	36931984	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	105	410	2	ENST00000361632.4:c.2485_2486delinsAA	p.Gly829Lys	p.G829K	ENST00000361632		829	GGg/AAg	16/16	1	2	FACETS	0.973	0.88	1	0.973	0.88	1	CLONAL	1	TRUE	1	0.580098445434209	2		412	372	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685268	89685273	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGGTTT	AGGTTT	-	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	44	250	0	ENST00000371953.3:c.165-2_168del		p.X55_splice	ENST00000371953	NM_000314.4	55		3/9	0.580098445434209	1	FACETS	0.835	0.717	0.958	0.835	0.717	0.958	CLONAL	1	TRUE	0	0.580098445434209	1		250	129	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374108	118374108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555046621	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	108	402	0	ENST00000534358.1:c.7501C>T	p.Pro2501Ser	p.P2501S	ENST00000534358	NM_005933.3	2501	Ccc/Tcc	27/36	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.580098445434209	2		402	290	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49419968	49419968	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	98	382	0	ENST00000301067.7:c.15781C>T	p.Gln5261Ter	p.Q5261*	ENST00000301067	NM_003482.3	5261	Cag/Tag	48/54	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.580098445434209	2		382	305	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557827	21557827	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	124	634	1	ENST00000382592.4:c.2018C>T	p.Thr673Ile	p.T673I	ENST00000382592	NM_014572.2	673	aCc/aTc	5/8	1	2	FACETS	0.942	0.858	1	0.942	0.858	1	CLONAL	1	TRUE	1	0.580098445434209	2		635	454	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058510	42058510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749945071	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	94	341	0	ENST00000219905.7:c.8230C>T	p.Pro2744Ser	p.P2744S	ENST00000219905	NM_001164273.1	2744	Cct/Tct	24/24	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.580098445434209	2		341	281	SUCCESS
BLM	641	MSKCC	GRCh37	15	91333904	91333904	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs575498961	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	108	456	0	ENST00000355112.3:c.2849G>A	p.Gly950Glu	p.G950E	ENST00000355112	NM_000057.2	950	gGa/gAa	15/22	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.580098445434209	2		456	348	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828465	72828465	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765402795	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	95	560	0	ENST00000268489.5:c.8116C>T	p.Pro2706Ser	p.P2706S	ENST00000268489	NM_006885.3	2706	Cca/Tca	9/10	1	2	FACETS	0.811	0.727	0.899	0.811	0.727	0.899	CLONAL	1	TRUE	1	0.580098445434209	2		560	404	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485976	40485976	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	124	524	2	ENST00000264657.5:c.889C>T	p.Pro297Ser	p.P297S	ENST00000264657	NM_139276.2	297	Ccc/Tcc	9/24	1	2	FACETS	0.86	0.783	0.941	0.86	0.783	0.941	CLONAL	1	TRUE	1	0.580098445434209	2		526	497	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78882679	78882680	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	112	546	1	ENST00000306801.3:c.2470_2471delinsTT	p.Pro824Leu	p.P824L	ENST00000306801	NM_020761.2	824	CCa/TTa	21/34	1	2	FACETS	0.944	0.856	1	0.944	0.856	1	CLONAL	1	TRUE	1	0.580098445434209	2		547	409	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211760	36211760	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	105	585	0	ENST00000222270.7:c.1511G>C	p.Gly504Ala	p.G504A	ENST00000222270	NM_014727.1	504	gGa/gCa	3/37	1	2	FACETS	0.914	0.826	1	0.914	0.826	1	CLONAL	1	TRUE	1	0.580098445434209	2		585	396	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905727	50905728	+	missense_variant	Missense_Mutation	DNP	GA	GA	AG	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	123	625	1	ENST00000440232.2:c.775_776delinsAG	p.Asp259Ser	p.D259S	ENST00000440232	NM_002691.3	259	GAc/AGc	7/27	1	2	FACETS	0.998	0.91	1	0.998	0.91	1	CLONAL	1	TRUE	1	0.580098445434209	2		626	425	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253866	30253867	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	102	422	0	ENST00000307677.4:c.587_588delinsAA	p.Gly196Glu	p.G196E	ENST00000307677	NM_138578.1	196	gGG/gAA	3/3	1	2	FACETS	0.95	0.858	1	0.95	0.858	1	CLONAL	1	TRUE	1	0.580098445434209	2		422	370	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022494	31022494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	55	289	0	ENST00000375687.4:c.1979G>A	p.Gly660Asp	p.G660D	ENST00000375687	NM_015338.5	660	gGc/gAc	13/13	1	2	FACETS	0.972	0.845	1	0.972	0.845	1	CLONAL	1	TRUE	1	0.580098445434209	2		289	195	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39729932	39729932	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	106	439	0	ENST00000361337.2:c.1247G>A	p.Trp416Ter	p.W416*	ENST00000361337	NM_003286.2	416	tGg/tAg	13/21	1	2	FACETS	0.942	0.851	1	0.942	0.851	1	CLONAL	1	TRUE	1	0.580098445434209	2		439	388	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944421	40944421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	76	548	0	ENST00000373198.4:c.2081C>T	p.Pro694Leu	p.P694L	ENST00000373198	NM_133170.3	694	cCt/cTt	12/32	1	2	FACETS	0.693	0.612	0.78	0.693	0.612	0.78	SUBCLONAL	1	TRUE	1	0.580098445434209	2		548	378	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37038176	37038177	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	44	174	0	ENST00000231790.2:c.183_184delinsTT	p.Gln62Ter	p.Q62*	ENST00000231790	NM_000249.3	61	atCCaa/atTTaa	2/19	1	2	FACETS	0.919	0.784	1	0.919	0.784	1	CLONAL	1	TRUE	1	0.580098445434209	2		174	165	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215898	142215898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	104	409	1	ENST00000350721.4:c.5695C>T	p.Pro1899Ser	p.P1899S	ENST00000350721	NM_001184.3	1899	Cct/Tct	33/47	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.580098445434209	2		410	330	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998081	169998081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138560118	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	130	567	1	ENST00000295797.4:c.772C>T	p.Arg258Trp	p.R258W	ENST00000295797	NM_002740.5	258	Cgg/Tgg	9/18	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.580098445434209	2		568	420	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189349324	189349324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568702479	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	71	302	0	ENST00000264731.3:c.20G>A	p.Arg7Gln	p.R7Q	ENST00000264731	NM_003722.4	7	cGg/cAg	1/14	1	2	FACETS	0.853	0.752	0.96	0.853	0.752	0.96	CLONAL	1	TRUE	1	0.580098445434209	2		302	287	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111456	56111456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	28	155	0	ENST00000399503.3:c.56C>T	p.Ala19Val	p.A19V	ENST00000399503	NM_005921.1	19	gCt/gTt	1/20	1	2	FACETS	0.791	0.644	0.953	0.791	0.644	0.953	CLONAL	1	TRUE	1	0.580098445434209	2		155	122	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673787	176673787	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	98	379	0	ENST00000439151.2:c.4487C>T	p.Pro1496Leu	p.P1496L	ENST00000439151	NM_022455.4	1496	cCa/cTa	10/23	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.580098445434209	2		379	306	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395883	395883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	75	493	0	ENST00000380956.4:c.440C>T	p.Ser147Phe	p.S147F	ENST00000380956	NM_001195286.1	147	tCc/tTc	4/9	1	2	FACETS	0.798	0.705	0.896	0.798	0.705	0.896	SUBCLONAL	1	TRUE	1	0.580098445434209	2		493	324	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032190	26032191	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	62	312	1	ENST00000244661.2:c.98_99delinsTT	p.Thr33Ile	p.T33I	ENST00000244661	NM_003537.3	33	aCC/aTT	1/1	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.580098445434209	2		313	206	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168655	32168655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	114	491	1	ENST00000375023.3:c.4268C>T	p.Pro1423Leu	p.P1423L	ENST00000375023	NM_004557.3	1423	cCc/cTc	23/30	1	2	FACETS	0.973	0.883	1	0.973	0.883	1	CLONAL	1	TRUE	1	0.580098445434209	2		492	404	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184761	32184761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	104	502	0	ENST00000375023.3:c.1822C>T	p.Pro608Ser	p.P608S	ENST00000375023	NM_004557.3	608	Cca/Tca	11/30	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.580098445434209	2		502	358	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004816	150004816	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	101	530	0	ENST00000253339.5:c.1409G>A	p.Gly470Glu	p.G470E	ENST00000253339		470	gGa/gAa	3/7	1	2	FACETS	0.995	0.898	1	0.995	0.898	1	CLONAL	1	TRUE	1	0.580098445434209	2		530	350	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129133	152129133	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	129	561	0	ENST00000206249.3:c.86C>T	p.Pro29Leu	p.P29L	ENST00000206249	NM_000125.3	29	cCg/cTg	1/8	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.580098445434209	2		561	407	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476855	140476855	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	112	485	0	ENST00000288602.6:c.1551G>A	p.Met517Ile	p.M517I	ENST00000288602	NM_004333.4	517	atG/atA	13/18	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.580098445434209	2		485	339	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072600	5072600	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	72	303	0	ENST00000381652.3:c.1750G>A	p.Asp584Asn	p.D584N	ENST00000381652	NM_004972.3	584	Gat/Aat	13/25	0.580098445434209	2	FACETS	1	0.915	1	0.519	0.46	0.581	CLONAL	1	TRUE	0	0.580098445434209	2		303	239	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465639	8465640	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	97	442	0	ENST00000356435.5:c.3540_3541delinsTT	p.Arg1181Cys	p.R1181C	ENST00000356435		1180	atCCgt/atTTgt	21/35	0.580098445434209	2	FACETS	1	0.917	1	0.51	0.459	0.562	CLONAL	1	TRUE	0	0.580098445434209	2		442	328	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971188	21971190	+	frameshift_variant	Frame_Shift_Del	DEL	GCG	GCG	CA	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	153	289	1	ENST00000304494.5:c.168_170delinsTG	p.Arg58GlufsTer88	p.R58Efs*88	ENST00000304494	NM_000077.4	56	agCGCc/agTGc	2/3	0.580098445434209	2	FACETS	0.916	0.856	0.976	0.916	0.856	0.976	CLONAL	2	TRUE	0	0.580098445434209	2		290	288	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37006506	37006506	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	73	390	0	ENST00000358127.4:c.439C>T	p.Pro147Ser	p.P147S	ENST00000358127	NM_001280556.1	147	Ccc/Tcc	4/10	1	2	FACETS	0.847	0.748	0.952	0.847	0.748	0.952	CLONAL	1	TRUE	1	0.580098445434209	2		390	297	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482167	87482168	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	116	527	1	ENST00000277120.3:c.1454_1455delinsTT	p.Ser485Phe	p.S485F	ENST00000277120		485	tCC/tTT	14/19	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.580098445434209	2		528	393	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128206794	128206794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	69	410	0	ENST00000265960.3:c.1429G>A	p.Glu477Lys	p.E477K	ENST00000265960	NM_001006617.1	477	Gaa/Aaa	11/12	1	2	FACETS	0.777	0.683	0.878	0.777	0.683	0.878	SUBCLONAL	1	TRUE	1	0.580098445434209	2		410	306	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755469	133755469	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	140	538	0	ENST00000318560.5:c.1438C>T	p.Pro480Ser	p.P480S	ENST00000318560	NM_005157.4	480	Ccc/Tcc	9/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.580098445434209	2		538	413	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	83	215	0				ENST00000310581	NM_198253.2	-/1132			0.747798533796482	3	FACETS	1	0.925	1	1	0.925	1	CLONAL	2	TRUE	1	0.787605976923483	3		215	145	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189585728	189585728	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	92	486	0	ENST00000264731.3:c.989G>C	p.Arg330Thr	p.R330T	ENST00000264731	NM_003722.4	330	aGa/aCa	7/14	0.654935509655857	5	FACETS	1	0.962	1	0.391	0.349	0.435	CLONAL	1	TRUE	2	0.787605976923483	5		486	435	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872380	45872380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	136	680	1	ENST00000391945.4:c.131C>T	p.Ser44Leu	p.S44L	ENST00000391945	NM_000400.3	44	tCa/tTa	3/23	0.787605976923483	3	FACETS	1	0.955	1	0.531	0.487	0.577	CLONAL	1	TRUE	1	0.787605976923483	3		681	453	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	14	554	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.787605976923483	4	FACETS	0.156	0.112	0.21	0.078	0.056	0.105	SUBCLONAL	1	TRUE	2	0.787605976923483	4		554	407	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs121913468	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	53	418	0	ENST00000269571.5:c.2305G>C	p.Asp769His	p.D769H	ENST00000269571		769	Gac/Cac	19/27	0.787605976923483	6	FACETS	0.647	0.551	0.751	0.216	0.183	0.251	SUBCLONAL	1	TRUE	3	0.787605976923483	6		418	536	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30061031	30061031	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	22	528	0	ENST00000338641.4:c.863C>G	p.Ser288Ter	p.S288*	ENST00000338641	NM_000268.3	288	tCa/tGa	9/16	0.787605976923483	3	FACETS	0.196	0.151	0.248	0.098	0.075	0.124	SUBCLONAL	1	TRUE	1	0.787605976923483	3		528	397	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514842	103514842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	41	348	0	ENST00000355739.4:c.1343C>T	p.Ser448Leu	p.S448L	ENST00000355739	NM_000123.3	448	tCa/tTa	8/15	0.787605976923483	7	FACETS	0.912	0.762	1	0.182	0.152	0.216	CLONAL	1	TRUE	2	0.787605976923483	7		348	339	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794857	42794857	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	50	616	0	ENST00000575354.2:c.1937G>C	p.Arg646Thr	p.R646T	ENST00000575354	NM_015125.3	646	aGa/aCa	10/20	0.787605976923483	3	FACETS	0.673	0.575	0.778	0.336	0.287	0.389	SUBCLONAL	1	TRUE	1	0.787605976923483	3		616	263	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557837	187557837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs184443677	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	132	593	0	ENST00000441802.2:c.3874G>A	p.Glu1292Lys	p.E1292K	ENST00000441802	NM_005245.3	1292	Gaa/Aaa	5/27	0.579834600764068	3	FACETS	1	0.98	1	0.409	0.375	0.444	CLONAL	1	TRUE	0	0.787605976923483	3		593	381	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379354	225379354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	37	557	1	ENST00000264414.4:c.514G>A	p.Glu172Lys	p.E172K	ENST00000264414	NM_003590.4	172	Gag/Aag	4/16	0.769578673781032	3	FACETS	0.356	0.294	0.425	0.119	0.098	0.142	SUBCLONAL	1	TRUE	0	0.787605976923483	3		558	368	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499483	89499483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1426641543	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	19	497	0	ENST00000336596.2:c.2653C>T	p.Pro885Ser	p.P885S	ENST00000336596	NM_005233.5	885	Ccc/Tcc	15/17	0.602228315140951	6	FACETS	0.336	0.254	0.432	0.112	0.084	0.144	SUBCLONAL	1	TRUE	3	0.787605976923483	6		497	370	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197334	26197334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	75	557	0	ENST00000356476.2:c.145C>A	p.Leu49Met	p.L49M	ENST00000356476		49	Ctg/Atg	1/1	0.787605976923483	4	FACETS	0.822	0.724	0.927	0.411	0.362	0.464	CLONAL	1	TRUE	2	0.787605976923483	4		557	414	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155681	56155681	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	69	361	0	ENST00000399503.3:c.773C>T	p.Ser258Leu	p.S258L	ENST00000399503	NM_005921.1	258	tCa/tTa	3/20	0.747798533796482	3	FACETS	0.954	0.841	1	0.477	0.42	0.537	CLONAL	1	TRUE	1	0.787605976923483	3		361	256	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289947	15289947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779780504	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	110	752	0	ENST00000263388.2:c.3607G>A	p.Glu1203Lys	p.E1203K	ENST00000263388	NM_000435.2	1203	Gag/Aag	22/33	0.409215953997312	5	FACETS	1	0.978	1	0.435	0.393	0.479	INDETERMINATE	1	TRUE	2	0.787605976923483	5		752	467	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878083	48878117	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCCGCCGCTGCCGCCGCGGAACCCCCGGCACCG	CCGCCGCCGCTGCCGCCGCGGAACCCCCGGCACCG	-	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	115	99	0	ENST00000267163.4:c.45_79del	p.Ala16ProfsTer3	p.A16Pfs*3	ENST00000267163	NM_000321.2	12	aCCGCCGCCGCTGCCGCCGCGGAACCCCCGGCACCG/a	1/27	0.669395431230033	4	FACETS	1	0.96	1	1	0.99	1	CLONAL	3	TRUE	2	0.787605976923483	4		99	168	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652777	212652777	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	71	419	0	ENST00000342788.4:c.529C>T	p.Leu177Phe	p.L177F	ENST00000342788	NM_005235.2	177	Ctt/Ttt	4/28	0.769578673781032	3	FACETS	0.907	0.8	1	0.302	0.266	0.34	CLONAL	1	TRUE	0	0.787605976923483	3		419	277	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637199	176637199	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	20	676	0	ENST00000439151.2:c.1799C>G	p.Ser600Ter	p.S600*	ENST00000439151	NM_022455.4	600	tCa/tGa	5/23	0.747798533796482	3	FACETS	0.195	0.149	0.249	0.098	0.074	0.125	SUBCLONAL	1	TRUE	1	0.787605976923483	3		676	363	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414917	78414917	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	22	523	0	ENST00000370768.2:c.1849G>C	p.Glu617Gln	p.E617Q	ENST00000370768	NM_003902.3	617	Gag/Cag	19/20	0.481320718004901	5	FACETS	0.29	0.224	0.367	0.097	0.074	0.123	SUBCLONAL	1	TRUE	2	0.787605976923483	5		523	420	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258970	153258970	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	61	303	0	ENST00000281708.4:c.845C>G	p.Ser282Ter	p.S282*	ENST00000281708	NM_033632.3	282	tCa/tGa	5/12	0.579834600764068	3	FACETS	0.973	0.851	1	0.324	0.283	0.367	CLONAL	1	TRUE	0	0.787605976923483	3		303	222	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213884	2213884	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	114	819	0	ENST00000398665.3:c.1696C>T	p.Gln566Ter	p.Q566*	ENST00000398665	NM_032482.2	566	Caa/Taa	18/28	0.409215953997312	5	FACETS	1	0.952	1	0.363	0.327	0.4	INDETERMINATE	1	TRUE	2	0.787605976923483	5		819	580	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246091297	246091297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758081490	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	80	464	0	ENST00000388985.4:c.638C>T	p.Ser213Leu	p.S213L	ENST00000388985		213	tCg/tTg	7/12	0.787605976923483	3	FACETS	0.787	0.697	0.881	0.393	0.348	0.441	SUBCLONAL	1	TRUE	1	0.787605976923483	3		464	360	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619292	37619292	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	124	399	0	ENST00000447079.4:c.968C>T	p.Ser323Leu	p.S323L	ENST00000447079	NM_015083.1	323	tCg/tTg	1/14	0.787605976923483	6	FACETS	0.943	0.86	1	0.629	0.573	0.686	CLONAL	2	TRUE	3	0.787605976923483	6		399	430	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11114047	11114047	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	32	566	0	ENST00000358026.2:c.1975G>A	p.Glu659Lys	p.E659K	ENST00000358026	NM_001128849.1	659	Gaa/Aaa	13/36	0.409215953997312	5	FACETS	0.509	0.414	0.617	0.17	0.138	0.206	INDETERMINATE	1	TRUE	2	0.787605976923483	5		566	348	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449396	31449396	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	79	506	0	ENST00000344624.3:c.2813G>A	p.Arg938Gln	p.R938Q	ENST00000344624		938	cGg/cAg	19/33	0.747798533796482	3	FACETS	0.926	0.823	1	0.463	0.411	0.517	CLONAL	1	TRUE	1	0.787605976923483	3		506	302	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143370	30143370	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	16	505	0	ENST00000389048.3:c.156G>C	p.Lys52Asn	p.K52N	ENST00000389048	NM_004304.4	52	aaG/aaC	1/29	0.787605976923483	3	FACETS	0.215	0.158	0.282	0.107	0.079	0.141	SUBCLONAL	1	TRUE	1	0.787605976923483	3		505	264	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023087	31023087	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	81	634	0	ENST00000375687.4:c.2572C>T	p.Gln858Ter	p.Q858*	ENST00000375687	NM_015338.5	858	Cag/Tag	13/13	0.787605976923483	6	FACETS	0.974	0.86	1	0.325	0.286	0.366	CLONAL	1	TRUE	3	0.787605976923483	6		634	544	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023183	31023183	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	51	711	0	ENST00000375687.4:c.2668C>G	p.Leu890Val	p.L890V	ENST00000375687	NM_015338.5	890	Ctc/Gtc	13/13	0.787605976923483	6	FACETS	0.512	0.434	0.597	0.171	0.144	0.199	SUBCLONAL	1	TRUE	3	0.787605976923483	6		711	652	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117755	70117755	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	81	652	0	ENST00000245479.2:c.223G>C	p.Glu75Gln	p.E75Q	ENST00000245479	NM_000346.3	75	Gag/Cag	1/3	0.654935509655857	5	FACETS	0.887	0.783	0.997	0.296	0.261	0.333	CLONAL	1	TRUE	2	0.787605976923483	5		652	506	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646346	3646346	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1202254236	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	17	905	0	ENST00000294008.3:c.1732G>C	p.Glu578Gln	p.E578Q	ENST00000294008	NM_032444.2	578	Gag/Cag	8/15	0.397707904998554	3	FACETS	0.189	0.141	0.247	0.095	0.07	0.124	INDETERMINATE	1	TRUE	1	0.787605976923483	3		905	318	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2488113	2488113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756893287	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	17	560	0	ENST00000355716.4:c.10C>T	p.Pro4Ser	p.P4S	ENST00000355716	NM_003820.2	4	Cct/Tct	1/8	0.429678209693089	3	FACETS	0.22	0.164	0.287			1	INDETERMINATE	1	TRUE	NA	0.787605976923483	3		560	273	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317178	11317178	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	82	504	0	ENST00000361445.4:c.316A>G	p.Arg106Gly	p.R106G	ENST00000361445	NM_004958.3	106	Aga/Gga	4/58	0.429678209693089	3	FACETS	0.849	0.754	0.948			1	INDETERMINATE	1	TRUE	NA	0.787605976923483	3		504	342	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317205	11317205	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	71	457	0	ENST00000361445.4:c.289G>T	p.Glu97Ter	p.E97*	ENST00000361445	NM_004958.3	97	Gaa/Taa	4/58	0.429678209693089	3	FACETS	0.945	0.834	1			1	INDETERMINATE	1	TRUE	NA	0.787605976923483	3		457	266	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818349	43818349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	93	807	1	ENST00000372470.3:c.1814C>T	p.Ser605Phe	p.S605F	ENST00000372470	NM_005373.2	605	tCt/tTt	12/12	0.481320718004901	5	FACETS	0.95	0.847	1	0.317	0.282	0.354	CLONAL	1	TRUE	2	0.787605976923483	5		808	542	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248677	59248677	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	123	852	0	ENST00000371222.2:c.66G>C	p.Glu22Asp	p.E22D	ENST00000371222	NM_002228.3	22	gaG/gaC	1/1	0.481320718004901	5	FACETS	1	0.969	1	0.387	0.351	0.425	CLONAL	1	TRUE	2	0.787605976923483	5		852	587	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468118	120468118	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	87	682	0	ENST00000256646.2:c.4321G>A	p.Glu1441Lys	p.E1441K	ENST00000256646	NM_024408.3	1441	Gag/Aag	25/34	0.735020117927312	5	FACETS	1	0.896	1			1	CLONAL	1	TRUE	NA	0.787605976923483	5		682	478	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226595597	226595597	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	61	439	0	ENST00000366794.5:c.34G>C	p.Glu12Gln	p.E12Q	ENST00000366794	NM_001618.3	12	Gag/Cag	1/23	0.787605976923483	3	FACETS	0.758	0.659	0.862	0.379	0.329	0.431	SUBCLONAL	1	TRUE	1	0.787605976923483	3		439	285	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577331	64577331	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	50	722	0	ENST00000312049.6:c.251C>G	p.Ser84Cys	p.S84C	ENST00000312049	NM_130799.2	84	tCt/tGt	2/10	0.787605976923483	4	FACETS	0.594	0.506	0.691	0.297	0.253	0.346	SUBCLONAL	1	TRUE	2	0.787605976923483	4		722	382	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383376	4383376	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	58	502	0	ENST00000261254.3:c.170G>C	p.Arg57Thr	p.R57T	ENST00000261254	NM_001759.3	57	aGa/aCa	1/5	0.37309136775671	5	FACETS	1	0.921	1			1	INDETERMINATE	1	TRUE	NA	0.787605976923483	5		502	294	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125004	46125004	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	51	264	0	ENST00000334344.6:c.191C>T	p.Ser64Phe	p.S64F	ENST00000334344	NM_152641.2	64	tCt/tTt	3/21	0.787605976923483	4	FACETS	0.851	0.729	0.983	0.426	0.364	0.492	CLONAL	1	TRUE	2	0.787605976923483	4		264	272	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865082	57865082	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	58	897	1	ENST00000228682.2:c.2559G>T	p.Gln853His	p.Q853H	ENST00000228682	NM_005269.2	853	caG/caT	12/12	0.787605976923483	4	FACETS	0.429	0.368	0.495	0.214	0.184	0.248	SUBCLONAL	1	TRUE	2	0.787605976923483	4		898	614	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597540	28597540	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	77	674	0	ENST00000241453.7:c.2365C>T	p.Leu789Phe	p.L789F	ENST00000241453	NM_004119.2	789	Ctt/Ttt	19/24	0.669395431230033	4	FACETS	0.689	0.607	0.778	0.345	0.303	0.389	SUBCLONAL	1	TRUE	2	0.787605976923483	4		674	507	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32905150	32905150	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	96	425	0	ENST00000380152.3:c.776G>C	p.Arg259Thr	p.R259T	ENST00000380152		259	aGa/aCa	9/27	0.669395431230033	4	FACETS	1	0.921	1	0.516	0.463	0.573	CLONAL	1	TRUE	2	0.787605976923483	4		425	422	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32918733	32918733	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	21	165	0	ENST00000380152.3:c.6880G>C	p.Asp2294His	p.D2294H	ENST00000380152		2294	Gac/Cac	12/27	0.669395431230033	4	FACETS	0.567	0.44	0.714	0.284	0.22	0.357	SUBCLONAL	1	TRUE	2	0.787605976923483	4		165	168	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134763	41134763	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	31	422	0	ENST00000379561.5:c.865G>A	p.Gly289Arg	p.G289R	ENST00000379561	NM_002015.3	289	Gga/Aga	2/3	0.669395431230033	4	FACETS	0.637	0.518	0.769	0.318	0.259	0.385	SUBCLONAL	1	TRUE	2	0.787605976923483	4		422	221	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881400	48881420	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TATTTTCATTTGGTAGGCTTG	TATTTTCATTTGGTAGGCTTG	-	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	44	166	0	ENST00000267163.4:c.138-16_142del		p.X46_splice	ENST00000267163	NM_000321.2	46		2/27	0.669395431230033	4	FACETS	0.933	0.808	1	0.933	0.808	1	CLONAL	2	TRUE	2	0.787605976923483	4		166	107	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345095	73345095	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs759251654	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	33	361	0	ENST00000377767.4:c.1702C>A	p.His568Asn	p.H568N	ENST00000377767	NM_014953.3	568	Cac/Aac	13/21	0.787605976923483	7	FACETS	0.468	0.38	0.567	0.094	0.076	0.114	SUBCLONAL	1	TRUE	2	0.787605976923483	7		361	532	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437112	110437112	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	11	82	0	ENST00000375856.3:c.1289C>T	p.Ser430Phe	p.S430F	ENST00000375856	NM_003749.2	430	tCc/tTc	1/2	0.787605976923483	7	FACETS	0.417	0.288	0.577	0.083	0.057	0.116	SUBCLONAL	1	TRUE	2	0.787605976923483	7		82	199	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438226	110438226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	37	116	0	ENST00000375856.3:c.175G>A	p.Glu59Lys	p.E59K	ENST00000375856	NM_003749.2	59	Gag/Aag	1/2	0.787605976923483	7	FACETS	0.84	0.702	0.99	0.336	0.281	0.396	CLONAL	2	TRUE	2	0.787605976923483	7		116	166	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991085	41991085	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	107	489	0	ENST00000219905.7:c.2038G>A	p.Asp680Asn	p.D680N	ENST00000219905	NM_001164273.1	680	Gat/Aat	4/24	0.551127922041928	3	FACETS	0.999	0.904	1	0.5	0.452	0.549	CLONAL	1	TRUE	1	0.787605976923483	3		489	379	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059029	42059029	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	44	450	0	ENST00000219905.7:c.8749G>A	p.Ala2917Thr	p.A2917T	ENST00000219905	NM_001164273.1	2917	Gca/Aca	24/24	0.551127922041928	3	FACETS	0.718	0.608	0.836	0.359	0.304	0.418	SUBCLONAL	1	TRUE	1	0.787605976923483	3		450	217	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43738643	43738643	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	93	689	0	ENST00000382044.4:c.2982G>A	p.Met994Ile	p.M994I	ENST00000382044	NM_001141980.1	994	atG/atA	14/28	0.551127922041928	3	FACETS	0.873	0.782	0.968	0.437	0.391	0.484	CLONAL	1	TRUE	1	0.787605976923483	3		689	377	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762067	43762067	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	74	639	0	ENST00000382044.4:c.1378C>T	p.Gln460Ter	p.Q460*	ENST00000382044	NM_001141980.1	460	Cag/Tag	11/28	0.551127922041928	3	FACETS	0.813	0.718	0.914	0.407	0.359	0.457	CLONAL	1	TRUE	1	0.787605976923483	3		639	322	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467239	99467239	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	20	295	0	ENST00000268035.6:c.2620G>C	p.Glu874Gln	p.E874Q	ENST00000268035	NM_000875.3	874	Gag/Cag	12/21	0.551127922041928	3	FACETS	0.557	0.431	0.701	0.279	0.215	0.351	SUBCLONAL	1	TRUE	1	0.787605976923483	3		295	127	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126548	2126548	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	71	748	1	ENST00000219476.3:c.2799C>A	p.Phe933Leu	p.F933L	ENST00000219476	NM_000548.3	933	ttC/ttA	25/42	0.397707904998554	3	FACETS	0.907	0.8	1	0.454	0.4	0.51	INDETERMINATE	1	TRUE	1	0.787605976923483	3		749	277	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961280	15961280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	67	588	0	ENST00000268712.3:c.6109G>A	p.Glu2037Lys	p.E2037K	ENST00000268712	NM_006311.3	2037	Gag/Aag	39/46	0.654935509655857	5	FACETS	0.757	0.66	0.863	0.252	0.22	0.288	SUBCLONAL	1	TRUE	2	0.787605976923483	5		588	490	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983764	15983764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	35	602	3	ENST00000268712.3:c.3358G>A	p.Glu1120Lys	p.E1120K	ENST00000268712	NM_006311.3	1120	Gag/Aag	25/46	0.654935509655857	5	FACETS	0.371	0.304	0.448	0.124	0.101	0.15	SUBCLONAL	1	TRUE	2	0.787605976923483	5		605	522	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16040717	16040717	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	44	255	0	ENST00000268712.3:c.1417G>T	p.Asp473Tyr	p.D473Y	ENST00000268712	NM_006311.3	473	Gat/Tat	14/46	0.654935509655857	5	FACETS	0.886	0.748	1	0.295	0.249	0.346	CLONAL	1	TRUE	2	0.787605976923483	5		255	275	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37856495	37856495	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	82	288	0	ENST00000269571.5:c.4G>C	p.Glu2Gln	p.E2Q	ENST00000269571		2	Gag/Cag	1/27	0.787605976923483	6	FACETS	0.798	0.71	0.891	0.532	0.473	0.594	SUBCLONAL	2	TRUE	3	0.787605976923483	6		288	336	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873661	37873661	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	322	795	0	ENST00000269571.5:c.1826C>G	p.Ser609Cys	p.S609C	ENST00000269571		609	tCc/tGc	15/27	0.787605976923483	6	FACETS	1	0.979	1	0.713	0.674	0.752	CLONAL	2	TRUE	3	0.787605976923483	6		795	985	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234427	41234427	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	194	514	0	ENST00000357654.3:c.4351G>C	p.Glu1451Gln	p.E1451Q	ENST00000357654	NM_007294.3	1451	Gaa/Caa	12/23	0.787605976923483	6	FACETS	1	0.932	1	0.668	0.621	0.716	CLONAL	2	TRUE	3	0.787605976923483	6		514	633	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41247905	41247905	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs879255495	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	81	543	1	ENST00000357654.3:c.628C>T	p.Gln210Ter	p.Q210*	ENST00000357654	NM_007294.3	210	Caa/Taa	9/23	0.787605976923483	6	FACETS	0.747	0.658	0.843	0.249	0.219	0.281	SUBCLONAL	1	TRUE	3	0.787605976923483	6		544	709	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533069	63533069	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	68	635	1	ENST00000307078.5:c.1825C>A	p.Pro609Thr	p.P609T	ENST00000307078	NM_004655.3	609	Ccc/Acc	7/11	0.654935509655857	5	FACETS	0.88	0.768	1	0.293	0.256	0.334	CLONAL	1	TRUE	2	0.787605976923483	5		636	428	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936755	78936755	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	126	817	0	ENST00000306801.3:c.3837C>G	p.Ile1279Met	p.I1279M	ENST00000306801	NM_020761.2	1279	atC/atG	33/34	0.654935509655857	5	FACETS	0.989	0.896	1	0.33	0.298	0.362	CLONAL	1	TRUE	2	0.787605976923483	5		817	706	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745735	745735	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	88	617	0	ENST00000314574.4:c.697C>G	p.Leu233Val	p.L233V	ENST00000314574	NM_005433.3	233	Ctg/Gtg	6/12	0.693684864651253	5	FACETS	0.81	0.718	0.907			1	CLONAL	1	TRUE	NA	0.787605976923483	5		617	602	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591955	48591955	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	14	477	0	ENST00000342988.3:c.1118C>G	p.Thr373Arg	p.T373R	ENST00000342988	NM_005359.5	373	aCa/aGa	9/12	0.787605976923483	3	FACETS	0.249	0.18	0.332	0.125	0.09	0.166	SUBCLONAL	1	TRUE	1	0.787605976923483	3		477	199	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210764	5210764	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	29	830	0	ENST00000357368.4:c.5287G>C	p.Asp1763His	p.D1763H	ENST00000357368	NM_002850.3	1763	Gac/Cac	34/38	0.409215953997312	5	FACETS	0.337	0.27	0.414	0.112	0.09	0.138	INDETERMINATE	1	TRUE	2	0.787605976923483	5		830	476	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097180	11097180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1368858108	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	74	667	1	ENST00000358026.2:c.671C>T	p.Ser224Leu	p.S224L	ENST00000358026	NM_001128849.1	224	tCg/tTg	4/36	0.409215953997312	5	FACETS	1	0.961	1	0.407	0.358	0.458	INDETERMINATE	1	TRUE	2	0.787605976923483	5		668	336	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271823	15271823	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	91	767	0	ENST00000263388.2:c.6616G>C	p.Glu2206Gln	p.E2206Q	ENST00000263388	NM_000435.2	2206	Gag/Cag	33/33	0.409215953997312	5	FACETS	1	0.961	1	0.39	0.348	0.434	INDETERMINATE	1	TRUE	2	0.787605976923483	5		767	431	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965421	18965421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	17	416	0	ENST00000262803.5:c.1168G>A	p.Glu390Lys	p.E390K	ENST00000262803	NM_002911.3	390	Gag/Aag	9/24	0.409215953997312	5	FACETS	0.359	0.268	0.468	0.12	0.089	0.156	INDETERMINATE	1	TRUE	2	0.787605976923483	5		416	262	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190717447	190717447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	82	374	0	ENST00000441310.2:c.766G>A	p.Glu256Lys	p.E256K	ENST00000441310	NM_000534.4	256	Gaa/Aaa	7/13	0.769578673781032	3	FACETS	0.964	0.859	1	0.321	0.286	0.358	CLONAL	1	TRUE	0	0.787605976923483	3		374	301	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719175	190719175	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs760960503	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	62	303	1	ENST00000441310.2:c.1177G>T	p.Asp393Tyr	p.D393Y	ENST00000441310	NM_000534.4	393	Gat/Tat	9/13	0.769578673781032	3	FACETS	1	0.912	1	0.35	0.307	0.395	CLONAL	1	TRUE	0	0.787605976923483	3		304	209	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023498	31023498	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	68	497	0	ENST00000375687.4:c.2983C>G	p.His995Asp	p.H995D	ENST00000375687	NM_015338.5	995	Cac/Gac	13/13	0.787605976923483	6	FACETS	1	0.939	1	0.375	0.328	0.426	CLONAL	1	TRUE	3	0.787605976923483	6		497	395	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386358	31386378	+	inframe_deletion	In_Frame_Del	DEL	TCCCGCAGCGCTGTCATGGCG	TCCCGCAGCGCTGTCATGGCG	-	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	104	667	0	ENST00000328111.2:c.1586_1606del	p.Pro529_Val535del	p.P529_V535del	ENST00000328111	NM_006892.3	528	cTCCCGCAGCGCTGTCATGGCGtc/ctc	15/23	0.787605976923483	6	FACETS	1	0.945	1	0.361	0.323	0.401	CLONAL	1	TRUE	3	0.787605976923483	6		667	628	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161868	47161868	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	96	531	0	ENST00000409792.3:c.4258G>A	p.Glu1420Lys	p.E1420K	ENST00000409792	NM_014159.6	1420	Gag/Aag	3/21	0.602228315140951	6	FACETS	1	0.971	1	0.419	0.374	0.465	CLONAL	1	TRUE	3	0.787605976923483	6		531	500	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149243913	149243913	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	95	466	0	ENST00000360632.3:c.906-1G>A		p.X302_splice	ENST00000360632	NM_015472.4	302			0.654935509655857	5	FACETS	1	0.951	1	0.37	0.331	0.412	CLONAL	1	TRUE	2	0.787605976923483	5		466	474	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539417	187539417	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs747465065	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	43	443	0	ENST00000441802.2:c.8323C>T	p.Gln2775Ter	p.Q2775*	ENST00000441802	NM_005245.3	2775	Cag/Tag	10/27	0.579834600764068	3	FACETS	0.746	0.631	0.87	0.249	0.21	0.29	SUBCLONAL	1	TRUE	0	0.787605976923483	3		443	204	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295298	1295298	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1421284705	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	15	479	0				ENST00000310581	NM_198253.2	-/1132			0.747798533796482	3	FACETS	0.194	0.142	0.258	0.097	0.071	0.129	SUBCLONAL	1	TRUE	1	0.787605976923483	3		479	273	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518732	176518732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs962807397	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	67	793	0	ENST00000292408.4:c.650C>T	p.Ser217Leu	p.S217L	ENST00000292408	NM_213647.1	217	tCg/tTg	6/18	0.747798533796482	3	FACETS	0.565	0.492	0.642	0.282	0.246	0.321	SUBCLONAL	1	TRUE	1	0.787605976923483	3		793	420	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158611	26158611	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	22	355	0	ENST00000289316.2:c.214G>A	p.Glu72Lys	p.E72K	ENST00000289316	NM_138720.2	72	Gag/Aag	1/2	0.787605976923483	4	FACETS	0.452	0.351	0.568	0.226	0.175	0.284	SUBCLONAL	1	TRUE	2	0.787605976923483	4		355	221	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30668382	30668382	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1210657939	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	36	552	0	ENST00000376406.3:c.6130C>T	p.Gln2044Ter	p.Q2044*	ENST00000376406	NM_014641.2	2044	Cag/Tag	15/15	0.787605976923483	4	FACETS	0.43	0.354	0.515	0.215	0.177	0.258	SUBCLONAL	1	TRUE	2	0.787605976923483	4		552	380	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324214	31324214	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs281864614	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	68	528	0	ENST00000412585.2:c.349C>A	p.His117Asn	p.H117N	ENST00000412585	NM_005514.6	117	Cac/Aac	3/8	0.787605976923483	4	FACETS	1	0.915	1	0.527	0.462	0.595	CLONAL	1	TRUE	2	0.787605976923483	4		528	293	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117717416	117717416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	16	394	0	ENST00000368508.3:c.791C>T	p.Ala264Val	p.A264V	ENST00000368508	NM_002944.2	264	gCa/gTa	8/43	0.358020438644297	3	FACETS	0.335	0.249	0.437	0.112	0.083	0.146	INDETERMINATE	1	TRUE	0	0.787605976923483	3		394	169	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016283	150016283	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	97	659	0	ENST00000253339.5:c.423G>C	p.Met141Ile	p.M141I	ENST00000253339		141	atG/atC	2/7	0.358020438644297	3	FACETS	0.86	0.773	0.952	0.287	0.257	0.318	INDETERMINATE	1	TRUE	0	0.787605976923483	3		659	399	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848628	151848628	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	49	308	0	ENST00000262189.6:c.12565G>A	p.Glu4189Lys	p.E4189K	ENST00000262189	NM_170606.2	4189	Gaa/Aaa	50/59	0.787605976923483	4	FACETS	0.824	0.703	0.954	0.412	0.351	0.477	CLONAL	1	TRUE	2	0.787605976923483	4		308	270	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874923	151874923	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	25	404	0	ENST00000262189.6:c.7615C>G	p.Gln2539Glu	p.Q2539E	ENST00000262189	NM_170606.2	2539	Cag/Gag	38/59	0.787605976923483	4	FACETS	0.359	0.283	0.446	0.18	0.141	0.223	SUBCLONAL	1	TRUE	2	0.787605976923483	4		404	316	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864878	117864878	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1169346397	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	234	601	0	ENST00000297338.2:c.1231G>C	p.Asp411His	p.D411H	ENST00000297338	NM_006265.2	411	Gat/Cat	10/14	0.705552028319837	4	FACETS	0.945	0.889	1	0.945	0.889	1	CLONAL	2	TRUE	2	0.787605976923483	4		601	562	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139811033	139811033	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	129	708	0	ENST00000247668.2:c.644C>T	p.Pro215Leu	p.P215L	ENST00000247668	NM_021138.3	215	cCt/cTt	7/11	0.787605976923483	3	FACETS	0.999	0.912	1	0.5	0.456	0.545	CLONAL	1	TRUE	1	0.787605976923483	3		708	457	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934236	39934236	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	51	381	0	ENST00000378444.4:c.363G>C	p.Glu121Asp	p.E121D	ENST00000378444	NM_001123385.1	121	gaG/gaC	4/15	0.735020117927312	2	FACETS	0.412	0.352	0.478			1	SUBCLONAL	1	TRUE	NA	0.787605976923483	2		381	314	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922744	44922745	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AACTCAGTCTCTGGCCAGCAGCCAC	novel	NA	P-0032842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	10	202	0	ENST00000377967.4:c.1607_1631dup	p.Ala546SerfsTer15	p.A546Sfs*15	ENST00000377967	NM_021140.2	535	-/AACTCAGTCTCTGGCCAGCAGCCAC	16/29	0.735020117927312	2	FACETS	0.162	0.109	0.227			1	SUBCLONAL	1	TRUE	NA	0.787605976923483	2		202	157	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913381	NA	P-0032922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	32	219	1	ENST00000304494.5:c.322G>T	p.Asp108Tyr	p.D108Y	ENST00000304494	NM_000077.4	108	Gat/Tat	2/3	1	2	FACETS	0.491	0.398	0.597	0.491	0.398	0.597	SUBCLONAL	1	TRUE	1	0.25	2		220	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0032922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	95	637	0	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	1	2	FACETS	0.8	0.711	0.895	0.8	0.711	0.895	SUBCLONAL	1	TRUE	1	0.25	2		637	950	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597395	10597395	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	118	690	0	ENST00000171111.5:c.1808G>T	p.Gly603Val	p.G603V	ENST00000171111	NM_203500.1	603	gGg/gTg	6/6	0.249581601228451	1	FACETS	0.878	0.791	0.97	0.878	0.791	0.97	CLONAL	1	TRUE	0	0.25	1		690	941	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484596	57484596	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913494	NA	P-0032922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	82	497	0	ENST00000371085.3:c.680A>T	p.Gln227Leu	p.Q227L	ENST00000371085	NM_000516.4	227	cAg/cTg	9/13	1	2	FACETS	0.73	0.642	0.824	0.73	0.642	0.824	SUBCLONAL	1	TRUE	1	0.25	2		497	899	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786868	135786868	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs118203481	NA	P-0032922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	84	421	0	ENST00000298552.3:c.1001C>T	p.Ser334Leu	p.S334L	ENST00000298552	NM_001162426.1	334	tCg/tTg	10/23	1	2	FACETS	0.935	0.825	1	0.935	0.825	1	CLONAL	1	TRUE	1	0.25	2		421	719	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980416	201980416	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	85	557	0	ENST00000359651.3:c.152T>G	p.Leu51Trp	p.L51W	ENST00000359651		51	tTg/tGg	1/8	1	2	FACETS	0.711	0.627	0.802	0.711	0.627	0.802	SUBCLONAL	1	TRUE	1	0.25	2		557	956	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748116	41748116	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	28	106	0	ENST00000226382.2:c.653C>A	p.Pro218His	p.P218H	ENST00000226382	NM_003924.3	218	cCc/cAc	3/3	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.25	2		106	164	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144529	55144529	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	101	508	0	ENST00000257290.5:c.2003G>T	p.Gly668Val	p.G668V	ENST00000257290	NM_006206.4	668	gGc/gTc	15/23	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.25	2		508	721	SUCCESS
APC	324	MSKCC	GRCh37	5	112154846	112154865	+	frameshift_variant	Frame_Shift_Del	DEL	TCCCGGGGCAGTAAAGAGGC	TCCCGGGGCAGTAAAGAGGC	-	novel	NA	P-0032922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	120	557	0	ENST00000257430.4:c.1119_1138del	p.Arg374GlyfsTer16	p.R374Gfs*16	ENST00000257430	NM_000038.5	373	TCCCGGGGCAGTAAAGAGGCt/t	10/16	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.25	2		557	940	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500885	8500885	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	58	574	0	ENST00000356435.5:c.1997C>G	p.Pro666Arg	p.P666R	ENST00000356435		666	cCt/cGt	13/35	1	2	FACETS	0.534	0.457	0.618	0.534	0.457	0.618	SUBCLONAL	1	TRUE	1	0.25	2		574	869	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786887	135786887	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554817388	NA	P-0032922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	77	396	0	ENST00000298552.3:c.982C>T	p.Gln328Ter	p.Q328*	ENST00000298552	NM_001162426.1	328	Cag/Tag	10/23	1	2	FACETS	0.914	0.802	1	0.914	0.802	1	CLONAL	1	TRUE	1	0.25	2		396	674	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317421	1317421	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	48	529	0	ENST00000400841.2:c.644G>T	p.Arg215Leu	p.R215L	ENST00000400841		215	cGg/cTg	5/6	1	2	FACETS	0.485	0.409	0.57	0.485	0.409	0.57	SUBCLONAL	1	TRUE	1	0.25	2		529	791	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	59	188	2	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	0.175889809188831	1	FACETS	0.289	0.248	0.332	0.289	0.248	0.332	INDETERMINATE	1	TRUE	0	0.585468328149877	1		190	494	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	36	290	0	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	1	2	FACETS	0.184	0.15	0.221	0.184	0.15	0.221	SUBCLONAL	1	TRUE	1	0.585468328149877	2		290	670	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	120	341	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.81	0.735	0.888	0.81	0.735	0.888	CLONAL	1	TRUE	1	0.585468328149877	2		341	506	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	38	490	2	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.226	0.186	0.27	0.226	0.186	0.27	SUBCLONAL	1	TRUE	1	0.585468328149877	2		492	575	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	164	953	7	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	0.175889809188831	1	FACETS	0.399	0.365	0.433	0.399	0.365	0.433	INDETERMINATE	1	TRUE	0	0.585468328149877	1		960	994	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	138	701	5	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	0.868	0.794	0.945	0.868	0.794	0.945	CLONAL	1	TRUE	1	0.585468328149877	2		706	543	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	36	705	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.175889809188831	1	FACETS	0.166	0.136	0.2	0.166	0.136	0.2	INDETERMINATE	1	TRUE	0	0.585468328149877	1		705	524	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861149	57861149	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774058977	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	171	560	0	ENST00000228682.2:c.946G>A	p.Glu316Lys	p.E316K	ENST00000228682	NM_005269.2	316	Gaa/Aaa	9/12	0.116934369802768	4	FACETS	1	0.987	1	0.669	0.617	0.723	INDETERMINATE	1	TRUE	2	0.585468328149877	4		560	692	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780872	9780872	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	49	774	0	ENST00000377346.4:c.1594T>C	p.Trp532Arg	p.W532R	ENST00000377346	NM_005026.3	532	Tgg/Cgg	13/24	1	2	FACETS	0.203	0.171	0.238	0.203	0.171	0.238	SUBCLONAL	1	TRUE	1	0.585468328149877	2		774	825	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255248	16255248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752574502	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	131	453	2	ENST00000375759.3:c.2513C>T	p.Thr838Met	p.T838M	ENST00000375759	NM_015001.2	838	aCg/aTg	11/15	1	2	FACETS	0.938	0.857	1	0.938	0.857	1	CLONAL	1	TRUE	1	0.585468328149877	2		455	477	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256124	16256124	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	41	653	0	ENST00000375759.3:c.3389G>T	p.Arg1130Met	p.R1130M	ENST00000375759	NM_015001.2	1130	aGg/aTg	11/15	1	2	FACETS	0.275	0.229	0.327	0.275	0.229	0.327	SUBCLONAL	1	TRUE	1	0.585468328149877	2		653	509	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259754	16259754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747993146	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	52	582	0	ENST00000375759.3:c.7019G>A	p.Arg2340His	p.R2340H	ENST00000375759	NM_015001.2	2340	cGc/cAc	11/15	1	2	FACETS	0.328	0.279	0.381	0.328	0.279	0.381	SUBCLONAL	1	TRUE	1	0.585468328149877	2		582	542	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265804	16265804	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	121	718	0	ENST00000375759.3:c.10877T>C	p.Leu3626Pro	p.L3626P	ENST00000375759	NM_015001.2	3626	cTg/cCg	15/15	1	2	FACETS	0.471	0.425	0.52	0.471	0.425	0.52	SUBCLONAL	1	TRUE	1	0.585468328149877	2		718	877	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097661	27097661	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	161	631	0	ENST00000324856.7:c.3250A>G	p.Thr1084Ala	p.T1084A	ENST00000324856	NM_006015.4	1084	Aca/Gca	12/20	1	2	FACETS	0.732	0.673	0.794	0.732	0.673	0.794	SUBCLONAL	1	TRUE	1	0.585468328149877	2		631	751	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	134	576	3	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	0.75	0.684	0.82	0.75	0.684	0.82	SUBCLONAL	1	TRUE	1	0.585468328149877	2		579	610	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739415	46739415	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377020524	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	45	516	0	ENST00000371975.4:c.1606C>T	p.Arg536Ter	p.R536*	ENST00000371975	NM_003579.3	536	Cga/Tga	14/18	1	2	FACETS	0.273	0.229	0.321	0.273	0.229	0.321	SUBCLONAL	1	TRUE	1	0.585468328149877	2		516	564	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301079	65301079	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	96	344	0	ENST00000342505.4:c.3369G>T	p.Glu1123Asp	p.E1123D	ENST00000342505	NM_002227.2	1123	gaG/gaT	24/25	1	2	FACETS	0.854	0.767	0.945	0.854	0.767	0.945	CLONAL	1	TRUE	1	0.585468328149877	2		344	384	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310468	65310468	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	54	524	0	ENST00000342505.4:c.2220del	p.Gly741AlafsTer30	p.G741Afs*30	ENST00000342505	NM_002227.2	740	ccC/cc	16/25	1	2	FACETS	0.34	0.29	0.394	0.34	0.29	0.394	SUBCLONAL	1	TRUE	1	0.585468328149877	2		524	543	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330611	65330611	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	53	680	0	ENST00000342505.4:c.1035del	p.Lys345AsnfsTer32	p.K345Nfs*32	ENST00000342505	NM_002227.2	345	aaA/aa	8/25	1	2	FACETS	0.297	0.253	0.345	0.297	0.253	0.345	SUBCLONAL	1	TRUE	1	0.585468328149877	2		680	610	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058500	72058500	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1428865181	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	63	649	0	ENST00000357731.5:c.940C>T	p.Pro314Ser	p.P314S	ENST00000357731	NM_173808.2	314	Cct/Tct	6/7	1	2	FACETS	0.408	0.353	0.467	0.408	0.353	0.467	SUBCLONAL	1	TRUE	1	0.585468328149877	2		649	528	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262317	115262317	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	57	585	0	ENST00000438362.2:c.2237T>C	p.Phe746Ser	p.F746S	ENST00000438362	NM_001242891.1	746	tTc/tCc	18/20	1	2	FACETS	0.338	0.29	0.391	0.338	0.29	0.391	SUBCLONAL	1	TRUE	1	0.585468328149877	2		585	576	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275258	115275258	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	49	783	1	ENST00000438362.2:c.1155T>A	p.Asn385Lys	p.N385K	ENST00000438362	NM_001242891.1	385	aaT/aaA	10/20	1	2	FACETS	0.283	0.239	0.331	0.283	0.239	0.331	SUBCLONAL	1	TRUE	1	0.585468328149877	2		784	592	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120493383	120493383	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	41	634	0	ENST00000256646.2:c.2443A>G	p.Ser815Gly	p.S815G	ENST00000256646	NM_024408.3	815	Agt/Ggt	15/34	1	2	FACETS	0.221	0.183	0.262	0.221	0.183	0.262	SUBCLONAL	1	TRUE	1	0.585468328149877	2		634	635	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746002	162746002	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1056323839	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	34	558	0	ENST00000367921.3:c.2125C>T	p.Arg709Ter	p.R709*	ENST00000367921	NM_006182.2	709	Cga/Tga	16/18	0.201782877030459	3	FACETS	0.232	0.189	0.281	0.077	0.063	0.094	INDETERMINATE	1	TRUE	0	0.585468328149877	3		558	646	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163297290	163297290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	37	730	2	ENST00000271452.3:c.136C>T	p.His46Tyr	p.H46Y	ENST00000271452	NM_145697.2	46	Cac/Tac	3/14	0.201782877030459	3	FACETS	0.226	0.185	0.271	0.075	0.061	0.091	INDETERMINATE	1	TRUE	0	0.585468328149877	3		732	724	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306589	163306589	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	46	621	0	ENST00000271452.3:c.386A>G	p.His129Arg	p.H129R	ENST00000271452	NM_145697.2	129	cAc/cGc	6/14	0.201782877030459	3	FACETS	0.295	0.248	0.348	0.098	0.082	0.116	INDETERMINATE	1	TRUE	0	0.585468328149877	3		621	688	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176153769	176153770	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	A	rs34500417	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	32	546	0	ENST00000367669.3:c.466dup	p.Cys156LeufsTer13	p.C156Lfs*13	ENST00000367669	NM_022457.5	156	tgc/tTgc	2/20	0.201782877030459	3	FACETS	0.228	0.184	0.277	0.076	0.061	0.093	INDETERMINATE	1	TRUE	0	0.585468328149877	3		546	621	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107258	193107258	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	30	438	1	ENST00000367435.3:c.467G>A	p.Arg156His	p.R156H	ENST00000367435	NM_024529.4	156	cGt/cAt	6/17	0.201782877030459	3	FACETS	0.241	0.193	0.295	0.08	0.064	0.099	INDETERMINATE	1	TRUE	0	0.585468328149877	3		439	550	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649553	206649553	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147688366	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	51	611	0	ENST00000367120.3:c.388G>A	p.Gly130Ser	p.G130S	ENST00000367120	NM_014002.3	130	Ggc/Agc	6/22	0.201782877030459	3	FACETS	0.298	0.253	0.349	0.099	0.084	0.117	INDETERMINATE	1	TRUE	0	0.585468328149877	3		611	755	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206664179	206664179	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553390150	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	53	540	0	ENST00000367120.3:c.1721A>G	p.His574Arg	p.H574R	ENST00000367120	NM_014002.3	574	cAc/cGc	17/22	0.201782877030459	3	FACETS	0.272	0.231	0.318	0.091	0.077	0.106	INDETERMINATE	1	TRUE	0	0.585468328149877	3		540	859	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097740	8097740	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1436692613	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	65	544	0	ENST00000346208.3:c.122A>G	p.Tyr41Cys	p.Y41C	ENST00000346208		41	tAc/tGc	2/6	1	2	FACETS	0.355	0.307	0.406	0.355	0.307	0.406	SUBCLONAL	1	TRUE	1	0.585468328149877	2		544	626	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63760077	63760077	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	42	355	0	ENST00000279873.7:c.730T>C	p.Phe244Leu	p.F244L	ENST00000279873	NM_032199.2	244	Ttt/Ctt	4/10	1	2	FACETS	0.293	0.245	0.348	0.293	0.245	0.348	SUBCLONAL	1	TRUE	1	0.585468328149877	2		355	489	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333914	70333914	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	22	437	0	ENST00000373644.4:c.1819A>G	p.Thr607Ala	p.T607A	ENST00000373644	NM_030625.2	607	Act/Gct	2/12	1	2	FACETS	0.231	0.178	0.291	0.231	0.178	0.291	SUBCLONAL	1	TRUE	1	0.585468328149877	2		437	326	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653808	89653808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	29	570	0	ENST00000371953.3:c.106G>A	p.Gly36Arg	p.G36R	ENST00000371953	NM_000314.4	36	Gga/Aga	2/9	1	2	FACETS	0.22	0.176	0.27	0.22	0.176	0.27	SUBCLONAL	1	TRUE	1	0.585468328149877	2		570	450	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	21	282	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	0.258	0.199	0.327	0.258	0.199	0.327	SUBCLONAL	1	TRUE	1	0.585468328149877	2		282	278	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421565	32421565	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	45	782	0	ENST00000332351.3:c.1027A>G	p.Asn343Asp	p.N343D	ENST00000332351	NM_024426.4	343	Aac/Gac	6/10	0.175889809188831	1	FACETS	0.149	0.124	0.176	0.149	0.124	0.176	INDETERMINATE	1	TRUE	0	0.585468328149877	1		782	732	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129438	64129438	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	45	687	2	ENST00000334205.4:c.874del	p.Ala292HisfsTer83	p.A292Hfs*83	ENST00000334205	NM_003942.2	290	caG/ca	8/17	0.175889809188831	1	FACETS	0.134	0.111	0.158	0.134	0.111	0.158	INDETERMINATE	1	TRUE	0	0.585468328149877	1		689	814	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103478	77103478	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	85	489	0	ENST00000356341.3:c.88G>T	p.Asp30Tyr	p.D30Y	ENST00000356341	NM_002576.4	30	Gat/Tat	2/15	0.175889809188831	1	FACETS	0.365	0.323	0.41	0.365	0.323	0.41	INDETERMINATE	1	TRUE	0	0.585468328149877	1		489	563	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202742	108202742	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs878853546	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	58	474	0	ENST00000278616.4:c.7766A>G	p.Lys2589Arg	p.K2589R	ENST00000278616	NM_000051.3	2589	aAa/aGa	52/63	0.175889809188831	1	FACETS	0.389	0.336	0.447	0.389	0.336	0.447	INDETERMINATE	1	TRUE	0	0.585468328149877	1		474	360	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376653	118376653	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	110	641	0	ENST00000534358.1:c.10046T>C	p.Met3349Thr	p.M3349T	ENST00000534358	NM_005933.3	3349	aTg/aCg	27/36	0.175889809188831	1	FACETS	0.518	0.467	0.571	0.518	0.467	0.571	INDETERMINATE	1	TRUE	0	0.585468328149877	1		641	513	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	463324	463324	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	37	516	0	ENST00000399788.2:c.947A>G	p.Asp316Gly	p.D316G	ENST00000399788	NM_001042603.1	316	gAc/gGc	8/28	NA	2	FACETS	0.204	0.167	0.244			1	INDETERMINATE	1	TRUE	NA	0.585468328149877	2		516	621	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037382	12037382	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	61	844	0	ENST00000396373.4:c.1013G>A	p.Cys338Tyr	p.C338Y	ENST00000396373	NM_001987.4	338	tGt/tAt	6/8	0.309452475913692	4	FACETS	0.395	0.339	0.455	0.197	0.169	0.228	INDETERMINATE	1	TRUE	2	0.585468328149877	4		844	837	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211462	46211462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	72	320	0	ENST00000334344.6:c.428G>A	p.Arg143His	p.R143H	ENST00000334344	NM_152641.2	143	cGt/cAt	5/21	0.116934369802768	4	FACETS	1	0.971	1	0.675	0.595	0.758	INDETERMINATE	1	TRUE	2	0.585468328149877	4		320	289	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431115	49431115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371869550	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	55	608	1	ENST00000301067.7:c.10024C>T	p.Arg3342Cys	p.R3342C	ENST00000301067	NM_003482.3	3342	Cgc/Tgc	34/54	0.116934369802768	4	FACETS	0.388	0.331	0.451	0.194	0.165	0.226	INDETERMINATE	1	TRUE	2	0.585468328149877	4		609	767	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444809	49444809	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	209	757	2	ENST00000301067.7:c.2657del	p.Pro886LeufsTer44	p.P886Lfs*44	ENST00000301067	NM_003482.3	886	cCt/ct	10/54	0.116934369802768	4	FACETS	1	0.99	1	0.694	0.645	0.744	INDETERMINATE	1	TRUE	2	0.585468328149877	4		759	816	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120796835	120796835	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	61	709	0	ENST00000257552.2:c.424T>C	p.Phe142Leu	p.F142L	ENST00000257552	NM_002442.3	142	Ttt/Ctt	7/15	1	2	FACETS	0.242	0.208	0.279	0.242	0.208	0.279	SUBCLONAL	1	TRUE	1	0.585468328149877	2		709	861	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120805853	120805853	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	59	771	0	ENST00000257552.2:c.225T>G	p.Asp75Glu	p.D75E	ENST00000257552	NM_002442.3	75	gaT/gaG	4/15	1	2	FACETS	0.228	0.195	0.264	0.228	0.195	0.264	SUBCLONAL	1	TRUE	1	0.585468328149877	2		771	885	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986596	36986596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	38	316	0	ENST00000354822.5:c.1093G>A	p.Ala365Thr	p.A365T	ENST00000354822	NM_001079668.2	365	Gcc/Acc	3/3	1	2	FACETS	0.354	0.293	0.422	0.354	0.293	0.422	SUBCLONAL	1	TRUE	1	0.585468328149877	2		316	367	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060991	38060992	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	90	324	0	ENST00000250448.2:c.996_997dup	p.Gln333ProfsTer18	p.Q333Pfs*18	ENST00000250448	NM_004496.3	333	cag/cCCag	2/2	1	2	FACETS	0.899	0.805	0.997	0.899	0.805	0.997	CLONAL	1	TRUE	1	0.585468328149877	2		324	342	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061469	38061469	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	144	524	0	ENST00000250448.2:c.520T>A	p.Ser174Thr	p.S174T	ENST00000250448	NM_004496.3	174	Tcg/Acg	2/2	1	2	FACETS	0.955	0.877	1	0.955	0.877	1	CLONAL	1	TRUE	1	0.585468328149877	2		524	515	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331813	68331813	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	49	619	0	ENST00000487270.1:c.409G>A	p.Ala137Thr	p.A137T	ENST00000487270	NM_133509.3	137	Gct/Act	5/11	1	2	FACETS	0.243	0.205	0.285	0.243	0.205	0.285	SUBCLONAL	1	TRUE	1	0.585468328149877	2		619	689	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961400	41961400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	148	705	0	ENST00000219905.7:c.308G>A	p.Arg103His	p.R103H	ENST00000219905	NM_001164273.1	103	cGc/cAc	2/24	0.175889809188831	1	FACETS	0.647	0.594	0.702	0.647	0.594	0.702	INDETERMINATE	1	TRUE	0	0.585468328149877	1		705	553	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	37	1055	5	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	0.175889809188831	1	FACETS	0.121	0.099	0.146	0.121	0.099	0.146	INDETERMINATE	1	TRUE	0	0.585468328149877	1		1060	737	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457358	67457358	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	41	725	0	ENST00000327367.4:c.332T>C	p.Phe111Ser	p.F111S	ENST00000327367	NM_005902.3	111	tTc/tCc	2/9	0.175889809188831	1	FACETS	0.135	0.111	0.16	0.135	0.111	0.16	INDETERMINATE	1	TRUE	0	0.585468328149877	1		725	736	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347902	347902	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	90	933	0	ENST00000262320.3:c.1604T>C	p.Val535Ala	p.V535A	ENST00000262320	NM_003502.3	535	gTc/gCc	6/11	1	2	FACETS	0.33	0.292	0.37	0.33	0.292	0.37	SUBCLONAL	1	TRUE	1	0.585468328149877	2		933	933	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639471	3639471	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	61	771	0	ENST00000294008.3:c.4168G>T	p.Gly1390Cys	p.G1390C	ENST00000294008	NM_032444.2	1390	Ggt/Tgt	12/15	1	2	FACETS	0.265	0.228	0.305	0.265	0.228	0.305	SUBCLONAL	1	TRUE	1	0.585468328149877	2		771	787	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646304	3646304	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs772185448	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	66	850	0	ENST00000294008.3:c.1774A>G	p.Thr592Ala	p.T592A	ENST00000294008	NM_032444.2	592	Act/Gct	8/15	1	2	FACETS	0.315	0.273	0.361	0.315	0.273	0.361	SUBCLONAL	1	TRUE	1	0.585468328149877	2		850	715	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619248	23619248	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201142	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	147	670	0	ENST00000261584.4:c.3287A>G	p.Asn1096Ser	p.N1096S	ENST00000261584	NM_024675.3	1096	aAc/aGc	12/13	1	2	FACETS	0.685	0.626	0.746	0.685	0.626	0.746	SUBCLONAL	1	TRUE	1	0.585468328149877	2		670	733	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671723	67671723	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	67	681	1	ENST00000264010.4:c.2136del	p.Asn713ThrfsTer8	p.N713Tfs*8	ENST00000264010	NM_006565.3	711	gCc/gc	12/12	0.585468328149877	1	FACETS	0.281	0.244	0.32	0.281	0.244	0.32	SUBCLONAL	1	TRUE	0	0.585468328149877	1		682	577	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976156	7976156	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	56	738	0	ENST00000319144.4:c.2039A>G	p.Asn680Ser	p.N680S	ENST00000319144	NM_001139.2	680	aAc/aGc	15/15	1	2	FACETS	0.235	0.2	0.273	0.235	0.2	0.273	SUBCLONAL	1	TRUE	1	0.585468328149877	2		738	815	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127276	17127276	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	50	704	0	ENST00000285071.4:c.578T>A	p.Val193Asp	p.V193D	ENST00000285071	NM_144997.5	193	gTc/gAc	6/14	1	2	FACETS	0.24	0.202	0.28	0.24	0.202	0.28	SUBCLONAL	1	TRUE	1	0.585468328149877	2		704	713	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667646	29667646	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56013763	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	93	601	0	ENST00000356175.3:c.6982C>T	p.Arg2328Cys	p.R2328C	ENST00000356175	NM_000267.3	2328	Cgt/Tgt	46/57	1	2	FACETS	0.675	0.602	0.751	0.675	0.602	0.751	SUBCLONAL	1	TRUE	1	0.585468328149877	2		601	471	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40364210	40364210	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	39	1053	0	ENST00000293328.3:c.1474-2A>G		p.X492_splice	ENST00000293328	NM_012448.3	492			1	2	FACETS	0.176	0.145	0.21	0.176	0.145	0.21	SUBCLONAL	1	TRUE	1	0.585468328149877	2		1053	759	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876542	59876542	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	36	716	0	ENST00000259008.2:c.1259A>T	p.Asp420Val	p.D420V	ENST00000259008	NM_032043.2	420	gAt/gTt	9/20	1	2	FACETS	0.214	0.175	0.258	0.214	0.175	0.258	SUBCLONAL	1	TRUE	1	0.585468328149877	2		716	574	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554698	63554698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	41	552	0	ENST00000307078.5:c.41G>A	p.Ser14Asn	p.S14N	ENST00000307078	NM_004655.3	14	aGc/aAc	2/11	1	2	FACETS	0.242	0.201	0.288	0.242	0.201	0.288	SUBCLONAL	1	TRUE	1	0.585468328149877	2		552	579	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617679	39617680	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	36	551	0	ENST00000262039.4:c.1869dup	p.Lys624Ter	p.K624*	ENST00000262039	NM_002647.2	621	-/T	17/25	0.175889809188831	1	FACETS	0.199	0.163	0.239	0.199	0.163	0.239	INDETERMINATE	1	TRUE	0	0.585468328149877	1		551	438	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593507	48593507	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1367209662	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	111	437	1	ENST00000342988.3:c.1258C>T	p.Arg420Cys	p.R420C	ENST00000342988	NM_005359.5	420	Cgt/Tgt	10/12	0.175889809188831	1	FACETS	0.573	0.518	0.631	0.573	0.518	0.631	INDETERMINATE	1	TRUE	0	0.585468328149877	1		438	468	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212403	5212403	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs558410776	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	248	838	3	ENST00000357368.4:c.4714C>T	p.Arg1572Trp	p.R1572W	ENST00000357368	NM_002850.3	1572	Cgg/Tgg	31/38	1	2	FACETS	0.972	0.91	1	0.972	0.91	1	CLONAL	1	TRUE	1	0.585468328149877	2		841	872	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599978	10599978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	68	815	1	ENST00000171111.5:c.1598G>A	p.Ser533Asn	p.S533N	ENST00000171111	NM_203500.1	533	aGc/aAc	5/6	1	2	FACETS	0.248	0.215	0.284	0.248	0.215	0.284	SUBCLONAL	1	TRUE	1	0.585468328149877	2		816	936	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974315	18974315	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	95	677	0	ENST00000262803.5:c.2669A>G	p.Asn890Ser	p.N890S	ENST00000262803	NM_002911.3	890	aAc/aGc	19/24	1	2	FACETS	0.477	0.425	0.533	0.477	0.425	0.533	SUBCLONAL	1	TRUE	1	0.585468328149877	2		677	680	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210686	36210686	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	40	643	0	ENST00000222270.7:c.437G>A	p.Gly146Asp	p.G146D	ENST00000222270	NM_014727.1	146	gGt/gAt	3/37	1	2	FACETS	0.175	0.145	0.209	0.175	0.145	0.209	SUBCLONAL	1	TRUE	1	0.585468328149877	2		643	780	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211795	36211795	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	53	911	0	ENST00000222270.7:c.1549del	p.Ser517AlafsTer5	p.S517Afs*5	ENST00000222270	NM_014727.1	516	Aaa/aa	3/37	1	2	FACETS	0.193	0.163	0.225	0.193	0.163	0.225	SUBCLONAL	1	TRUE	1	0.585468328149877	2		911	940	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228964	36228964	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	107	685	0	ENST00000222270.7:c.7744T>C	p.Ser2582Pro	p.S2582P	ENST00000222270	NM_014727.1	2582	Tca/Cca	36/37	1	2	FACETS	0.454	0.407	0.504	0.454	0.407	0.504	SUBCLONAL	1	TRUE	1	0.585468328149877	2		685	805	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794554	42794554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150295260	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	79	873	2	ENST00000575354.2:c.1634C>T	p.Ser545Leu	p.S545L	ENST00000575354	NM_015125.3	545	tCg/tTg	10/20	1	2	FACETS	0.292	0.256	0.331	0.292	0.256	0.331	SUBCLONAL	1	TRUE	1	0.585468328149877	2		875	923	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973154	25973154	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	44	588	0	ENST00000435504.4:c.1271C>A	p.Pro424Gln	p.P424Q	ENST00000435504		424	cCa/cAa	12/13	0.175889809188831	1	FACETS	0.211	0.177	0.25	0.211	0.177	0.25	INDETERMINATE	1	TRUE	0	0.585468328149877	1		588	503	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605218	46605218	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1373712541	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	22	349	0	ENST00000263734.3:c.1435T>A	p.Cys479Ser	p.C479S	ENST00000263734	NM_001430.4	479	Tgc/Agc	10/16	0.585468328149877	1	FACETS	0.391	0.306	0.487	0.391	0.306	0.487	SUBCLONAL	1	TRUE	0	0.585468328149877	1		349	136	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033685	48033685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	39	488	1	ENST00000234420.5:c.3896G>A	p.Gly1299Asp	p.G1299D	ENST00000234420	NM_000179.2	1299	gGc/gAc	9/10	0.585468328149877	1	FACETS	0.322	0.267	0.381	0.322	0.267	0.381	SUBCLONAL	1	TRUE	0	0.585468328149877	1		489	293	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	32	775	0	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	1	2	FACETS	0.186	0.15	0.226	0.186	0.15	0.226	SUBCLONAL	1	TRUE	1	0.585468328149877	2		775	588	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721045	61721045	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	27	595	0	ENST00000401558.2:c.1229T>C	p.Leu410Ser	p.L410S	ENST00000401558	NM_003400.3	410	tTg/tCg	12/25	1	2	FACETS	0.186	0.147	0.23	0.186	0.147	0.23	SUBCLONAL	1	TRUE	1	0.585468328149877	2		595	497	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172064	99172064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	47	657	0	ENST00000074304.5:c.1630C>T	p.Arg544Cys	p.R544C	ENST00000074304	NM_001134224.1	544	Cgt/Tgt	17/26	1	2	FACETS	0.226	0.19	0.266	0.226	0.19	0.266	SUBCLONAL	1	TRUE	1	0.585468328149877	2		657	709	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439482	220439482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	47	614	0	ENST00000243786.2:c.335G>A	p.Arg112Lys	p.R112K	ENST00000243786	NM_002191.3	112	aGa/aAa	2/2	1	2	FACETS	0.286	0.241	0.336	0.286	0.241	0.336	SUBCLONAL	1	TRUE	1	0.585468328149877	2		614	561	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384619	31384619	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	67	718	0	ENST00000328111.2:c.1325del	p.Asn442ThrfsTer148	p.N442Tfs*148	ENST00000328111	NM_006892.3	441	Aaa/aa	13/23	0.292989725964173	1	FACETS	0.206	0.178	0.236	0.206	0.178	0.236	INDETERMINATE	1	TRUE	0	0.585468328149877	1		718	787	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101047	41101047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1480616778	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	158	788	2	ENST00000373198.4:c.1309G>A	p.Ala437Thr	p.A437T	ENST00000373198	NM_133170.3	437	Gcc/Acc	8/32	0.292989725964173	1	FACETS	0.593	0.545	0.642	0.593	0.545	0.642	INDETERMINATE	1	TRUE	0	0.585468328149877	1		790	644	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164602	36164602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	49	544	0	ENST00000300305.3:c.1273C>T	p.Pro425Ser	p.P425S	ENST00000300305		425	Ccg/Tcg	8/8	1	2	FACETS	0.256	0.216	0.299	0.256	0.216	0.299	SUBCLONAL	1	TRUE	1	0.585468328149877	2		544	655	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755705	39755705	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs547051424	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	174	701	1	ENST00000288319.7:c.1060C>T	p.Arg354Trp	p.R354W	ENST00000288319	NM_182918.3	354	Cgg/Tgg	10/10	1	2	FACETS	0.895	0.827	0.965	0.895	0.827	0.965	CLONAL	1	TRUE	1	0.585468328149877	2		702	664	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656872	45656872	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	52	666	1	ENST00000407780.3:c.284A>G	p.Asp95Gly	p.D95G	ENST00000407780	NM_001283052.1	95	gAc/gGc	3/7	1	2	FACETS	0.241	0.204	0.281	0.241	0.204	0.281	SUBCLONAL	1	TRUE	1	0.585468328149877	2		667	738	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940153	49940153	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	70	702	0	ENST00000296474.3:c.890T>A	p.Val297Asp	p.V297D	ENST00000296474	NM_002447.2	297	gTc/gAc	1/20	1	2	FACETS	0.329	0.287	0.376	0.329	0.287	0.376	SUBCLONAL	1	TRUE	1	0.585468328149877	2		702	726	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438572	52438572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201844078	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	54	574	0	ENST00000460680.1:c.1147C>T	p.Arg383Cys	p.R383C	ENST00000460680	NM_004656.3	383	Cgc/Tgc	12/17	1	2	FACETS	0.261	0.222	0.304	0.261	0.222	0.304	SUBCLONAL	1	TRUE	1	0.585468328149877	2		574	706	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928487	69928487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	54	692	0	ENST00000352241.4:c.307C>T	p.Pro103Ser	p.P103S	ENST00000352241	NM_198159.2	103	Ccc/Tcc	2/10	1	2	FACETS	0.21	0.178	0.244	0.21	0.178	0.244	SUBCLONAL	1	TRUE	1	0.585468328149877	2		692	880	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890194	72890194	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	120	526	1	ENST00000325599.8:c.486+2T>C		p.X162_splice	ENST00000325599	NM_018130.2	162			0.40193441872269	1	FACETS	0.881	0.806	0.958	0.881	0.806	0.958	CLONAL	1	TRUE	0	0.585468328149877	1		527	329	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528582	89528582	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033077-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.2882C>A	p.Pro961Gln	p.P961Q	ENST00000336596	NM_005233.5	961	cCa/cAa	17/17	0.40193441872269	1	FACETS	0.231	0.186	0.281	0.231	0.186	0.281	SUBCLONAL	1	TRUE	0	0.585468328149877	1		286	314	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138375111	138375111	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771812474	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	35	487	0	ENST00000289153.2:c.2948G>A	p.Arg983His	p.R983H	ENST00000289153	NM_006219.2	983	cGc/cAc	21/22	0.40193441872269	1	FACETS	0.172	0.14	0.207	0.172	0.14	0.207	SUBCLONAL	1	TRUE	0	0.585468328149877	1		487	492	SUCCESS
ATR	545	MSKCC	GRCh37	3	142172005	142172005	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs911475726	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	59	825	0	ENST00000350721.4:c.7726C>T	p.Pro2576Ser	p.P2576S	ENST00000350721	NM_001184.3	2576	Cca/Tca	46/47	0.40193441872269	1	FACETS	0.22	0.189	0.254	0.22	0.189	0.254	SUBCLONAL	1	TRUE	0	0.585468328149877	1		825	647	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430410	181430410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	42	544	0	ENST00000325404.1:c.262C>T	p.Arg88Trp	p.R88W	ENST00000325404	NM_003106.3	88	Cgg/Tgg	1/1	0.40193441872269	1	FACETS	0.154	0.128	0.183	0.154	0.128	0.183	SUBCLONAL	1	TRUE	0	0.585468328149877	1		544	658	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146476	185146476	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	31	570	0	ENST00000265026.3:c.107A>T	p.Asn36Ile	p.N36I	ENST00000265026	NM_004721.4	36	aAc/aTc	2/14	0.40193441872269	1	FACETS	0.153	0.123	0.187	0.153	0.123	0.187	SUBCLONAL	1	TRUE	0	0.585468328149877	1		570	489	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502386	186502386	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	170	650	0	ENST00000323963.5:c.109G>C	p.Asp37His	p.D37H	ENST00000323963		37	Gat/Cat	3/11	1	2	FACETS	0.931	0.86	1	0.931	0.86	1	CLONAL	1	TRUE	1	0.585468328149877	2		650	624	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803118	1803118	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	36	727	1	ENST00000260795.2:c.470A>G	p.Glu157Gly	p.E157G	ENST00000260795		157	gAg/gGg	4/17	0.175889809188831	1	FACETS	0.129	0.105	0.155	0.129	0.105	0.155	INDETERMINATE	1	TRUE	0	0.585468328149877	1		728	676	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133538	55133538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770343276	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	65	607	0	ENST00000257290.5:c.842C>T	p.Thr281Met	p.T281M	ENST00000257290	NM_006206.4	281	aCg/aTg	6/23	0.175889809188831	1	FACETS	0.248	0.214	0.284	0.248	0.214	0.284	INDETERMINATE	1	TRUE	0	0.585468328149877	1		607	634	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968156	55968156	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	41	642	0	ENST00000263923.4:c.2174G>A	p.Arg725His	p.R725H	ENST00000263923	NM_002253.2	725	cGc/cAc	15/30	0.175889809188831	1	FACETS	0.163	0.135	0.194	0.163	0.135	0.194	INDETERMINATE	1	TRUE	0	0.585468328149877	1		642	609	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557785	187557785	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	33	527	0	ENST00000441802.2:c.3926T>C	p.Val1309Ala	p.V1309A	ENST00000441802	NM_005245.3	1309	gTt/gCt	5/27	0.175889809188831	1	FACETS	0.134	0.108	0.162	0.134	0.108	0.162	INDETERMINATE	1	TRUE	0	0.585468328149877	1		527	597	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31401569	31401570	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	67	799	0	ENST00000344624.3:c.4094_4095del	p.Glu1365AlafsTer3	p.E1365Afs*3	ENST00000344624		1365	gAG/g	33/33	1	2	FACETS	0.352	0.305	0.402	0.352	0.305	0.402	SUBCLONAL	1	TRUE	1	0.585468328149877	2		799	651	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160636	56160636	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	133	382	0	ENST00000399503.3:c.910A>G	p.Thr304Ala	p.T304A	ENST00000399503	NM_005921.1	304	Aca/Gca	4/20	1	2	FACETS	0.975	0.892	1	0.975	0.892	1	CLONAL	1	TRUE	1	0.585468328149877	2		382	466	SUCCESS
APC	324	MSKCC	GRCh37	5	112173515	112173515	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs748046147	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	21	428	0	ENST00000257430.4:c.2224A>G	p.Ile742Val	p.I742V	ENST00000257430	NM_000038.5	742	Att/Gtt	16/16	1	2	FACETS	0.197	0.151	0.25	0.197	0.151	0.25	SUBCLONAL	1	TRUE	1	0.585468328149877	2		428	365	SUCCESS
APC	324	MSKCC	GRCh37	5	112179287	112179287	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1460128902	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	21	480	0	ENST00000257430.4:c.7996A>G	p.Ile2666Val	p.I2666V	ENST00000257430	NM_000038.5	2666	Att/Gtt	16/16	1	2	FACETS	0.188	0.144	0.24	0.188	0.144	0.24	SUBCLONAL	1	TRUE	1	0.585468328149877	2		480	381	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149436870	149436870	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	130	590	0	ENST00000286301.3:c.2299G>T	p.Ala767Ser	p.A767S	ENST00000286301	NM_005211.3	767	Gcc/Tcc	17/22	1	2	FACETS	0.705	0.641	0.772	0.705	0.641	0.772	SUBCLONAL	1	TRUE	1	0.585468328149877	2		590	630	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149498310	149498311	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	41	600	0	ENST00000261799.4:c.2903dup	p.Lys969GlufsTer7	p.K969Efs*7	ENST00000261799	NM_002609.3	968	aag/aaAg	21/23	1	2	FACETS	0.224	0.186	0.267	0.224	0.186	0.267	SUBCLONAL	1	TRUE	1	0.585468328149877	2		600	624	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510165	149510165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs904740973	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	83	806	0	ENST00000261799.4:c.1304G>A	p.Arg435His	p.R435H	ENST00000261799	NM_002609.3	435	cGc/cAc	9/23	1	2	FACETS	0.33	0.29	0.372	0.33	0.29	0.372	SUBCLONAL	1	TRUE	1	0.585468328149877	2		806	860	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271488	26271488	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	28	444	0	ENST00000305910.3:c.125A>G	p.Tyr42Cys	p.Y42C	ENST00000305910	NM_003534.2	42	tAc/tGc	1/1	0.116934369802768	4	FACETS	0.308	0.246	0.38	0.154	0.123	0.19	INDETERMINATE	1	TRUE	2	0.585468328149877	4		444	492	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120293	94120293	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	130	496	0	ENST00000369303.4:c.758A>G	p.Glu253Gly	p.E253G	ENST00000369303	NM_004440.3	253	gAa/gGa	3/17	0.585468328149877	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.585468328149877	1		496	313	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553759	106553759	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1450522672	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	29	439	0	ENST00000369096.4:c.1724A>G	p.Tyr575Cys	p.Y575C	ENST00000369096	NM_001198.3	575	tAc/tGc	5/7	0.585468328149877	1	FACETS	0.164	0.131	0.201	0.164	0.131	0.201	SUBCLONAL	1	TRUE	0	0.585468328149877	1		439	427	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200419	138200419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778025601	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	91	675	0	ENST00000237289.4:c.1837G>A	p.Val613Met	p.V613M	ENST00000237289	NM_001270507.1	613	Gtg/Atg	7/9	1	2	FACETS	0.404	0.358	0.453	0.404	0.358	0.453	SUBCLONAL	1	TRUE	1	0.585468328149877	2		675	769	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265368	152265368	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	36	521	0	ENST00000206249.3:c.821G>T	p.Gly274Val	p.G274V	ENST00000206249	NM_000125.3	274	gGg/gTg	4/8	1	2	FACETS	0.259	0.213	0.312	0.259	0.213	0.312	SUBCLONAL	1	TRUE	1	0.585468328149877	2		521	474	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157488256	157488256	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	34	521	0	ENST00000346085.5:c.2962A>G	p.Ser988Gly	p.S988G	ENST00000346085	NM_020732.3	988	Agc/Ggc	10/20	1	2	FACETS	0.212	0.173	0.257	0.212	0.173	0.257	SUBCLONAL	1	TRUE	1	0.585468328149877	2		521	547	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528016	157528016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751391187	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	178	602	0	ENST00000346085.5:c.5741G>A	p.Arg1914Gln	p.R1914Q	ENST00000346085	NM_020732.3	1914	cGg/cAg	20/20	1	2	FACETS	0.971	0.899	1	0.971	0.899	1	CLONAL	1	TRUE	1	0.585468328149877	2		602	626	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984157	2984157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	40	512	2	ENST00000396946.4:c.373G>A	p.Glu125Lys	p.E125K	ENST00000396946	NM_032415.4	125	Gag/Aag	5/25	1	2	FACETS	0.263	0.218	0.313	0.263	0.218	0.313	SUBCLONAL	1	TRUE	1	0.585468328149877	2		514	520	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81399286	81399286	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	95	686	0	ENST00000222390.5:c.2T>C	p.Met1?	p.M1?	ENST00000222390	NM_000601.4	1	aTg/aCg	1/18	1	2	FACETS	0.379	0.337	0.424	0.379	0.337	0.424	SUBCLONAL	1	TRUE	1	0.585468328149877	2		686	856	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509514	106509514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	50	622	0	ENST00000359195.3:c.1508C>T	p.Thr503Met	p.T503M	ENST00000359195	NM_002649.2	503	aCg/aTg	2/11	1	2	FACETS	0.258	0.218	0.302	0.258	0.218	0.302	SUBCLONAL	1	TRUE	1	0.585468328149877	2		622	662	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846206	128846206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761081288	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	44	768	1	ENST00000249373.3:c.1136C>T	p.Ala379Val	p.A379V	ENST00000249373	NM_005631.4	379	gCg/gTg	5/12	1	2	FACETS	0.197	0.164	0.233	0.197	0.164	0.233	SUBCLONAL	1	TRUE	1	0.585468328149877	2		769	763	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860868	151860868	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	50	617	0	ENST00000262189.6:c.9794A>G	p.Tyr3265Cys	p.Y3265C	ENST00000262189	NM_170606.2	3265	tAt/tGt	43/59	1	2	FACETS	0.243	0.206	0.285	0.243	0.206	0.285	SUBCLONAL	1	TRUE	1	0.585468328149877	2		617	702	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187005	38187005	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	48	885	0	ENST00000317025.8:c.1472A>G	p.Asp491Gly	p.D491G	ENST00000317025	NM_023034.1	491	gAt/gGt	6/24	0.585468328149877	1	FACETS	0.125	0.105	0.148	0.125	0.105	0.148	SUBCLONAL	1	TRUE	0	0.585468328149877	1		885	926	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56860268	56860268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	133	468	0	ENST00000519728.1:c.270G>A	p.Met90Ile	p.M90I	ENST00000519728	NM_002350.3	90	atG/atA	4/13	0.264212582616455	1	FACETS	0.661	0.604	0.72	0.661	0.604	0.72	INDETERMINATE	1	TRUE	0	0.585468328149877	1		468	486	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922493	56922493	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	102	470	0	ENST00000519728.1:c.1363G>A	p.Ala455Thr	p.A455T	ENST00000519728	NM_002350.3	455	Gcc/Acc	13/13	0.264212582616455	1	FACETS	0.437	0.392	0.485	0.437	0.392	0.485	INDETERMINATE	1	TRUE	0	0.585468328149877	1		470	564	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982691	90982691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769420	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	49	505	0	ENST00000265433.3:c.797C>T	p.Pro266Leu	p.P266L	ENST00000265433	NM_002485.4	266	cCg/cTg	7/16	0.509067209066727	3	FACETS	0.305	0.258	0.358			1	SUBCLONAL	1	TRUE	NA	0.585468328149877	3		505	709	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528707	8528707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs545049137	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	132	468	0	ENST00000356435.5:c.425C>T	p.Thr142Met	p.T142M	ENST00000356435		142	aCg/aTg	4/35	0.175889809188831	1	FACETS	0.77	0.706	0.837	0.77	0.706	0.837	INDETERMINATE	1	TRUE	0	0.585468328149877	1		468	414	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971141	21971141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759763964	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	44	368	0	ENST00000304494.5:c.217G>A	p.Ala73Thr	p.A73T	ENST00000304494	NM_000077.4	73	Gcc/Acc	2/3	0.175889809188831	1	FACETS	0.223	0.187	0.264	0.223	0.187	0.264	INDETERMINATE	1	TRUE	0	0.585468328149877	1		368	476	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27203073	27203073	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs759976151	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	33	662	0	ENST00000380036.4:c.2165A>G	p.Asn722Ser	p.N722S	ENST00000380036	NM_000459.3	722	aAc/aGc	13/23	0.175889809188831	1	FACETS	0.133	0.108	0.162	0.133	0.108	0.162	INDETERMINATE	1	TRUE	0	0.585468328149877	1		662	598	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98244295	98244295	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	23	543	0	ENST00000331920.6:c.682A>T	p.Ile228Phe	p.I228F	ENST00000331920	NM_000264.3	228	Att/Ttt	5/24	0.175889809188831	1	FACETS	0.122	0.094	0.153	0.122	0.094	0.153	INDETERMINATE	1	TRUE	0	0.585468328149877	1		543	457	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891282	101891282	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	42	791	0	ENST00000374994.4:c.243T>A	p.Asp81Glu	p.D81E	ENST00000374994	NM_004612.2	81	gaT/gaA	2/9	0.175889809188831	1	FACETS	0.158	0.132	0.188	0.158	0.132	0.188	INDETERMINATE	1	TRUE	0	0.585468328149877	1		791	641	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912101	127912101	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	42	523	0	ENST00000373547.4:c.769T>C	p.Ser257Pro	p.S257P	ENST00000373547	NM_002721.4	257	Tct/Cct	7/7	0.175889809188831	1	FACETS	0.201	0.167	0.238	0.201	0.167	0.238	INDETERMINATE	1	TRUE	0	0.585468328149877	1		523	506	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730247	133730247	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	88	675	0	ENST00000318560.5:c.317del	p.Asn106MetfsTer36	p.N106Mfs*36	ENST00000318560	NM_005157.4	105	Aaa/aa	3/11	0.175889809188831	1	FACETS	0.283	0.25	0.318	0.283	0.25	0.318	INDETERMINATE	1	TRUE	0	0.585468328149877	1		675	752	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772950	135772951	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs118203724	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	30	526	1	ENST00000298552.3:c.2672dup	p.Asn891LysfsTer13	p.N891Kfs*13	ENST00000298552	NM_001162426.1	891	aac/aaAc	21/23	0.175889809188831	1	FACETS	0.145	0.116	0.178	0.145	0.116	0.178	INDETERMINATE	1	TRUE	0	0.585468328149877	1		527	499	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300040	137300040	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	57	748	2	ENST00000481739.1:c.331del	p.Leu111TrpfsTer57	p.L111Wfs*57	ENST00000481739	NM_002957.4	109	Ccc/cc	3/10	0.175889809188831	1	FACETS	0.139	0.118	0.161	0.139	0.118	0.161	INDETERMINATE	1	TRUE	0	0.585468328149877	1		750	992	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417424	139417424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779118023	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	57	729	0	ENST00000277541.6:c.620G>A	p.Arg207His	p.R207H	ENST00000277541	NM_017617.3	207	cGc/cAc	4/34	0.175889809188831	1	FACETS	0.172	0.147	0.199	0.172	0.147	0.199	INDETERMINATE	1	TRUE	0	0.585468328149877	1		729	801	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317487	1317487	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	46	799	0	ENST00000400841.2:c.578T>C	p.Val193Ala	p.V193A	ENST00000400841		193	gTa/gCa	5/6	1	1	FACETS	0.15	0.125	0.177	0.15	0.125	0.177	SUBCLONAL	1	TRUE	0	0.585468328149877	1		799	742	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932408	39932408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	85	439	1	ENST00000378444.4:c.2191C>T	p.Pro731Ser	p.P731S	ENST00000378444	NM_001123385.1	731	Cca/Tca	4/15	1	1	FACETS	0.445	0.395	0.499	0.445	0.395	0.499	SUBCLONAL	1	TRUE	0	0.585468328149877	1		440	461	SUCCESS
AR	367	MSKCC	GRCh37	X	66765934	66765934	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	21	413	0	ENST00000374690.3:c.946T>C	p.Tyr316His	p.Y316H	ENST00000374690	NM_000044.3	316	Tac/Cac	1/8	1	1	FACETS	0.127	0.098	0.162	0.127	0.098	0.162	SUBCLONAL	1	TRUE	0	0.585468328149877	1		413	398	SUCCESS
AR	367	MSKCC	GRCh37	X	66931247	66931247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868669253	NA	P-0033077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	69	227	0	ENST00000374690.3:c.1889G>A	p.Arg630Gln	p.R630Q	ENST00000374690	NM_000044.3	630	cGg/cAg	4/8	1	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.585468328149877	1		227	160	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0033108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	79	736	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.932	0.819	1	0.932	0.819	1	CLONAL	1	FALSE	1	0.212459851362732	2		741	798	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0033108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	38	548	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.793	0.656	0.947	0.793	0.656	0.947	CLONAL	1	FALSE	1	0.212459851362732	2		548	451	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	76	797	3	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.786	0.688	0.892	0.786	0.688	0.892	SUBCLONAL	1	FALSE	1	0.212459851362732	2		800	910	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0033108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	34	537	1	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	0.567	0.463	0.686	0.567	0.463	0.686	SUBCLONAL	1	FALSE	1	0.212459851362732	2		538	564	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654643	67654643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs968244943	NA	P-0033108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	49	649	0	ENST00000264010.4:c.1130G>A	p.Arg377His	p.R377H	ENST00000264010	NM_006565.3	377	cGt/cAt	6/12	1	2	FACETS	0.544	0.459	0.638	0.544	0.459	0.638	SUBCLONAL	1	FALSE	1	0.212459851362732	2		649	848	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0033108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	33	457	1	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.664	0.54	0.803	0.664	0.54	0.803	SUBCLONAL	1	FALSE	1	0.212459851362732	2		458	468	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592108	67592108	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1419325070	NA	P-0033108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	34	312	0	ENST00000274335.5:c.1924C>T	p.Arg642Ter	p.R642*	ENST00000274335		642	Cga/Tga	14/15	1	2	FACETS	0.626	0.511	0.756	0.626	0.511	0.756	SUBCLONAL	1	FALSE	1	0.212459851362732	2		312	511	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0033108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	49	739	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.439	0.37	0.516	0.439	0.37	0.516	SUBCLONAL	1	FALSE	1	0.212459851362732	2		739	1050	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804207	46804207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	65	756	2	ENST00000290295.7:c.800G>A	p.Arg267His	p.R267H	ENST00000290295	NM_006361.5	267	cGc/cAc	2/2	1	2	FACETS	0.688	0.595	0.789	0.688	0.595	0.789	SUBCLONAL	1	FALSE	1	0.212459851362732	2		758	890	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0033108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	59	543	1	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	0.655	0.562	0.757	0.655	0.562	0.757	SUBCLONAL	1	FALSE	1	0.212459851362732	2		544	848	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278343	39278343	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	83	862	1	ENST00000402219.2:c.806T>A	p.Met269Lys	p.M269K	ENST00000402219	NM_005633.3	269	aTg/aAg	6/23	0.16135819342754	2	FACETS	1	0.946	1	0.563	0.497	0.634	CLONAL	1	FALSE	0	0.212459851362732	2		863	694	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3114967	3114967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	47	643	1	ENST00000078429.4:c.502G>A	p.Ala168Thr	p.A168T	ENST00000078429	NM_002067.2	168	Gcc/Acc	4/7	1	2	FACETS	0.55	0.463	0.647	0.55	0.463	0.647	SUBCLONAL	1	FALSE	1	0.212459851362732	2		644	804	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451444	187451444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	51	510	1	ENST00000232014.4:c.38G>A	p.Arg13His	p.R13H	ENST00000232014	NM_001130845.1	13	cGc/cAc	3/10	1	2	FACETS	0.709	0.602	0.828	0.709	0.602	0.828	SUBCLONAL	1	FALSE	1	0.212459851362732	2		511	677	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220069	36220069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1239076295	NA	P-0033108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	55	715	1	ENST00000222270.7:c.4789C>T	p.Arg1597Trp	p.R1597W	ENST00000222270	NM_014727.1	1597	Cgg/Tgg	22/37	1	2	FACETS	0.606	0.516	0.703	0.606	0.516	0.703	SUBCLONAL	1	FALSE	1	0.212459851362732	2		716	855	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158525	26158525	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1222808686	NA	P-0033108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	30	513	0	ENST00000289316.2:c.128A>G	p.Tyr43Cys	p.Y43C	ENST00000289316	NM_138720.2	43	tAc/tGc	1/2	1	2	FACETS	0.544	0.437	0.666	0.544	0.437	0.666	SUBCLONAL	1	FALSE	1	0.212459851362732	2		513	519	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347173	89347173	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	35	509	1	ENST00000301030.4:c.5777del	p.Pro1926ArgfsTer37	p.P1926Rfs*37	ENST00000301030	NM_001256183.1	1926	cCg/cg	9/13	1	2	FACETS	0.557	0.456	0.672	0.557	0.456	0.672	SUBCLONAL	1	FALSE	1	0.212459851362732	2		510	591	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941016	71941016	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	93	791	0	ENST00000298229.2:c.892C>T	p.Gln298Ter	p.Q298*	ENST00000298229	NM_001567.3	298	Cag/Tag	8/28	1	2	FACETS	0.978	0.868	1	0.978	0.868	1	CLONAL	1	FALSE	1	0.212459851362732	2		791	895	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	443552	443552	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs760194850	NA	P-0033108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	24	480	1	ENST00000399788.2:c.1345C>A	p.Pro449Thr	p.P449T	ENST00000399788	NM_001042603.1	449	Cct/Act	11/28	0.212459851362732	1	FACETS	0.475	0.372	0.595	0.475	0.372	0.595	SUBCLONAL	1	FALSE	0	0.212459851362732	1		481	425	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225592	2225592	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	39	655	0	ENST00000326181.6:c.1595A>G	p.Tyr532Cys	p.Y532C	ENST00000326181	NM_032271.2	532	tAc/tGc	17/21	1	2	FACETS	0.538	0.445	0.643	0.538	0.445	0.643	SUBCLONAL	1	FALSE	1	0.212459851362732	2		655	682	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56873512	56873512	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	35	515	0	ENST00000308159.5:c.2216A>G	p.Asp739Gly	p.D739G	ENST00000308159	NM_014669.4	739	gAt/gGt	20/22	1	2	FACETS	0.545	0.445	0.657	0.545	0.445	0.657	SUBCLONAL	1	FALSE	1	0.212459851362732	2		515	605	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40490748	40490748	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0033108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	45	494	0	ENST00000264657.5:c.550+1G>A		p.X184_splice	ENST00000264657	NM_139276.2	184			1	2	FACETS	0.575	0.482	0.678	0.575	0.482	0.678	SUBCLONAL	1	FALSE	1	0.212459851362732	2		494	737	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243896	41243896	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs80356894	NA	P-0033108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	42	678	0	ENST00000357654.3:c.3652A>G	p.Ser1218Gly	p.S1218G	ENST00000357654	NM_007294.3	1218	Agt/Ggt	10/23	1	2	FACETS	0.604	0.503	0.716	0.604	0.503	0.716	SUBCLONAL	1	FALSE	1	0.212459851362732	2		678	655	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78882668	78882668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	62	680	2	ENST00000306801.3:c.2459C>T	p.Ala820Val	p.A820V	ENST00000306801	NM_020761.2	820	gCt/gTt	21/34	1	2	FACETS	0.662	0.57	0.762	0.662	0.57	0.762	SUBCLONAL	1	FALSE	1	0.212459851362732	2		682	882	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656786	45656786	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	62	594	0	ENST00000407780.3:c.370G>T	p.Glu124Ter	p.E124*	ENST00000407780	NM_001283052.1	124	Gag/Tag	3/7	1	2	FACETS	0.798	0.689	0.918	0.798	0.689	0.918	CLONAL	1	FALSE	1	0.212459851362732	2		594	731	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674228	86674228	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	26	506	0	ENST00000274376.6:c.2360T>C	p.Leu787Pro	p.L787P	ENST00000274376	NM_002890.2	787	cTa/cCa	18/25	1	2	FACETS	0.568	0.449	0.704	0.568	0.449	0.704	SUBCLONAL	1	FALSE	1	0.212459851362732	2		506	431	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524318	176524318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	67	719	0	ENST00000292408.4:c.2179C>T	p.His727Tyr	p.H727Y	ENST00000292408	NM_213647.1	727	Cac/Tac	17/18	1	2	FACETS	0.717	0.621	0.82	0.717	0.621	0.82	SUBCLONAL	1	FALSE	1	0.212459851362732	2		719	880	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673814	30673814	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	46	538	0	ENST00000376406.3:c.3146C>A	p.Pro1049His	p.P1049H	ENST00000376406	NM_014641.2	1049	cCc/cAc	10/15	1	2	FACETS	0.637	0.535	0.75	0.637	0.535	0.75	SUBCLONAL	1	FALSE	1	0.212459851362732	2		538	680	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738645	145738645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764549158	NA	P-0033108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	49	578	1	ENST00000428558.2:c.2419C>T	p.Arg807Cys	p.R807C	ENST00000428558	NM_004260.3	807	Cgt/Tgt	15/22	1	2	FACETS	0.754	0.638	0.882	0.754	0.638	0.882	SUBCLONAL	1	FALSE	1	0.212459851362732	2		579	612	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190063	123190063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	41	561	0	ENST00000218089.9:c.1282G>A	p.Ala428Thr	p.A428T	ENST00000218089	NM_001042749.1	428	Gct/Act	14/35	1	2	FACETS	0.725	0.604	0.861	0.725	0.604	0.861	SUBCLONAL	1	FALSE	1	0.212459851362732	2		561	532	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465650	8465650	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763141884	NA	P-0033129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	23	368	0	ENST00000356435.5:c.3530G>T	p.Arg1177Leu	p.R1177L	ENST00000356435		1177	cGc/cTc	21/35	0.269503895819155	1	FACETS	0.423	0.33	0.531	0.423	0.33	0.531	SUBCLONAL	1	TRUE	0	0.269503895819155	1		368	349	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73334699	73334699	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	36	270	0	ENST00000377767.4:c.2761C>T	p.Gln921Ter	p.Q921*	ENST00000377767	NM_014953.3	921	Cag/Tag	20/21	0.269503895819155	1	FACETS	0.758	0.625	0.905	0.758	0.625	0.905	CLONAL	1	TRUE	0	0.269503895819155	1		270	305	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242716	46242716	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	86	325	0	ENST00000334344.6:c.1678G>T	p.Gly560Ter	p.G560*	ENST00000334344	NM_152641.2	560	Gga/Tga	13/21	0.217407236131275	2	FACETS	0.904	0.806	1	0.904	0.806	1	CLONAL	2	TRUE	0	0.269503895819155	2		325	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	119	549	0	ENST00000269305.4:c.848del	p.Arg283ProfsTer62	p.R283Pfs*62	ENST00000269305	NM_001126112.2	283	cGc/cc	8/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.269503895819155	2		549	738	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754666	42754666	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	73	369	1	ENST00000222329.4:c.74G>T	p.Arg25Met	p.R25M	ENST00000222329	NM_006494.2	25	aGg/aTg	2/4	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.269503895819155	2		370	457	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295773	212295773	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	40	435	0	ENST00000342788.4:c.2540G>T	p.Arg847Leu	p.R847L	ENST00000342788	NM_005235.2	847	cGt/cTt	21/28	1	2	FACETS	0.606	0.503	0.72	0.606	0.503	0.72	SUBCLONAL	1	TRUE	1	0.269503895819155	2		435	490	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133579	55133579	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	41	397	0	ENST00000257290.5:c.883G>T	p.Ala295Ser	p.A295S	ENST00000257290	NM_006206.4	295	Gct/Tct	6/23	1	2	FACETS	0.592	0.493	0.702	0.592	0.493	0.702	SUBCLONAL	1	TRUE	1	0.269503895819155	2		397	514	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979642	55979642	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	49	403	0	ENST00000263923.4:c.805C>A	p.His269Asn	p.H269N	ENST00000263923	NM_002253.2	269	Cat/Aat	7/30	0.269503895819155	1	FACETS	0.682	0.579	0.797	0.682	0.579	0.797	SUBCLONAL	1	TRUE	0	0.269503895819155	1		403	461	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249007	+	missense_variant	Missense_Mutation	TNP	GCG	GCG	TTT	novel	NA	P-0033129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	169	421	1	ENST00000275493.2:c.2303_2305delinsTTT	p.Ser768_Val769delinsIleLeu	p.S768_V769delinsIL	ENST00000275493	NM_005228.3	768	aGCGtg/aTTTtg	20/28	0.269503895819155	5	FACETS	0.938	0.866	1	0.703	0.649	0.759	CLONAL	3	TRUE	1	0.269503895819155	5		422	626	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	45	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.973	0.83	1	1	0.978	1	CLONAL	3	TRUE	1	0.167484143552864	2		215	184	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0033364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	79	499	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.167484143552864	3	FACETS	1	0.944	1	0.567	0.497	0.642	CLONAL	1	TRUE	1	0.167484143552864	3		499	902	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913283	NA	P-0033364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	38	366	1	ENST00000263967.3:c.3129G>T	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atT	21/21	0.167484143552864	3	FACETS	1	0.888	1	0.55	0.455	0.657	CLONAL	1	TRUE	1	0.167484143552864	3		367	447	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650756	67650756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	97	649	0	ENST00000264010.4:c.1061C>T	p.Ser354Phe	p.S354F	ENST00000264010	NM_006565.3	354	tCc/tTc	5/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.167484143552864	2		649	791	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587782272	NA	P-0033364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	69	708	0	ENST00000269305.4:c.994-1G>C		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.167484143552864	3	FACETS	0.922	0.805	1	0.922	0.805	1	CLONAL	2	TRUE	1	0.167484143552864	3		708	484	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814667	43814667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	54	409	0	ENST00000372470.3:c.1462G>A	p.Glu488Lys	p.E488K	ENST00000372470	NM_005373.2	488	Gag/Aag	9/12	0.167484143552864	3	FACETS	0.915	0.784	1	0.915	0.784	1	CLONAL	2	TRUE	1	0.167484143552864	3		409	382	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69210676	69210676	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1229293747	NA	P-0033364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	57	507	0	ENST00000462284.1:c.259C>G	p.Leu87Val	p.L87V	ENST00000462284	NM_002392.5	87	Ctt/Gtt	4/11	0.167484143552864	7	FACETS	1	0.962	1	0.35	0.299	0.405	CLONAL	1	TRUE	3	0.167484143552864	7		507	690	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135021	11135021	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	81	827	0	ENST00000358026.2:c.2988C>G	p.Ile996Met	p.I996M	ENST00000358026	NM_001128849.1	996	atC/atG	21/36	1	2	FACETS	0.902	0.797	1	1	0.982	1	CLONAL	2	TRUE	1	0.167484143552864	2		827	536	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530128	212530128	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	41	420	0	ENST00000342788.4:c.1791A>C	p.Leu597Phe	p.L597F	ENST00000342788	NM_005235.2	597	ttA/ttC	15/28	0.167484143552864	6	FACETS	1	0.941	1	0.439	0.366	0.521	CLONAL	1	TRUE	3	0.167484143552864	6		420	496	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295214	1295214	+	upstream_gene_variant	5'Flank	SNP	T	T	G	rs796747192	NA	P-0033364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	11	285	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.787	0.545	1	0.787	0.545	1	CLONAL	1	TRUE	1	0.167484143552864	2		286	167	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806569	1806569	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs182935140	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	133	670	0	ENST00000260795.2:c.1285G>A	p.Ala429Thr	p.A429T	ENST00000260795		429	Gcg/Acg	9/17	1	2	FACETS	0.649	0.59	0.71	0.649	0.59	0.71	SUBCLONAL	1	TRUE	1	0.59	2		670	695	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	44	304	1	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.374	0.314	0.44	0.374	0.314	0.44	SUBCLONAL	1	TRUE	1	0.59	2		305	399	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	123	519	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.778	0.707	0.852	0.778	0.707	0.852	SUBCLONAL	1	TRUE	1	0.59	2		524	536	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	207	736	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.59	2		741	685	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	127	495	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.71	0.645	0.778	0.71	0.645	0.778	SUBCLONAL	1	TRUE	1	0.59	2		497	606	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732996	30732996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893809	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	124	319	0	ENST00000295754.5:c.1609C>T	p.Arg537Cys	p.R537C	ENST00000295754	NM_003242.5	537	Cgc/Tgc	7/7	1	2	FACETS	0.975	0.889	1	0.975	0.889	1	CLONAL	1	TRUE	1	0.59	2		319	431	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467573	66467573	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	85	321	0	ENST00000273854.3:c.696del	p.Lys232AsnfsTer36	p.K232Nfs*36	ENST00000273854	NM_004439.5	232	aaA/aa	3/18	1	2	FACETS	0.873	0.779	0.972	0.873	0.779	0.972	CLONAL	1	TRUE	1	0.59	2		321	330	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	128	548	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.692	0.629	0.758	0.692	0.629	0.758	SUBCLONAL	1	TRUE	1	0.59	2		548	627	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	90	457	0	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	0.807	0.721	0.897	0.807	0.721	0.897	CLONAL	1	TRUE	1	0.59	2		457	378	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538990	23538990	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775943527	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	143	543	0	ENST00000380871.4:c.449C>T	p.Ser150Leu	p.S150L	ENST00000380871	NM_006167.3	150	tCg/tTg	2/2	1	2	FACETS	0.727	0.664	0.792	0.727	0.664	0.792	SUBCLONAL	1	TRUE	1	0.59	2		543	667	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671655	67671655	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1400980130	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	59	444	2	ENST00000264010.4:c.2070del	p.Glu691SerfsTer30	p.E691Sfs*30	ENST00000264010	NM_006565.3	688	gtA/gt	12/12	0.1063980619458	3	FACETS	0.468	0.402	0.539	0.234	0.201	0.27	INDETERMINATE	1	TRUE	1	0.59	3		446	554	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	115	391	1	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.967	0.879	1	0.967	0.879	1	CLONAL	1	TRUE	1	0.59	2		392	403	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	181	930	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.98	0.908	1	0.98	0.908	1	CLONAL	1	TRUE	1	0.59	2		933	626	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	148	797	3	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.626	0.572	0.682	0.626	0.572	0.682	SUBCLONAL	1	TRUE	1	0.59	2		800	802	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	229	683	2	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.941	0.879	1	0.941	0.879	1	CLONAL	1	TRUE	1	0.59	2		685	825	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707684	176707684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	151	404	1	ENST00000439151.2:c.5741G>A	p.Arg1914His	p.R1914H	ENST00000439151	NM_022455.4	1914	cGc/cAc	18/23	1	2	FACETS	0.992	0.913	1	0.992	0.913	1	CLONAL	1	TRUE	1	0.59	2		405	516	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240450	98240450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370354759	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	91	371	0	ENST00000331920.6:c.1234G>A	p.Ala412Thr	p.A412T	ENST00000331920	NM_000264.3	412	Gca/Aca	9/24	1	2	FACETS	0.607	0.541	0.678	0.607	0.541	0.678	SUBCLONAL	1	TRUE	1	0.59	2		371	508	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121256	29121256	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	130	708	0	ENST00000328354.6:c.419G>T	p.Ser140Ile	p.S140I	ENST00000328354	NM_007194.3	140	aGc/aTc	3/15	1	2	FACETS	0.867	0.791	0.947	0.867	0.791	0.947	CLONAL	1	TRUE	1	0.59	2		708	508	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	76	402	7	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.823	0.729	0.923	0.823	0.729	0.923	CLONAL	1	TRUE	1	0.59	2		409	313	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219579	133219579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542430685	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	147	431	0	ENST00000320574.5:c.4555C>T	p.Arg1519Cys	p.R1519C	ENST00000320574	NM_006231.2	1519	Cgc/Tgc	36/49	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.59	2		431	480	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556292	29556292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1251621684	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	183	540	1	ENST00000356175.3:c.2659G>A	p.Ala887Thr	p.A887T	ENST00000356175	NM_000267.3	887	Gca/Aca	21/57	1	2	FACETS	0.988	0.916	1	0.988	0.916	1	CLONAL	1	TRUE	1	0.59	2		541	628	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169092	32169092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs189264181	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	187	614	1	ENST00000375023.3:c.3941C>T	p.Ala1314Val	p.A1314V	ENST00000375023	NM_004557.3	1314	gCc/gTc	22/30	1	2	FACETS	0.932	0.864	1	0.932	0.864	1	CLONAL	1	TRUE	1	0.59	2		615	680	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265314	152265314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781741770	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	79	260	0	ENST00000206249.3:c.767G>A	p.Arg256Gln	p.R256Q	ENST00000206249	NM_000125.3	256	cGa/cAa	4/8	1	2	FACETS	0.956	0.851	1	0.956	0.851	1	CLONAL	1	TRUE	1	0.59	2		260	280	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196695	67196696	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	101	406	0	ENST00000312629.5:c.230dup	p.Tyr78LeufsTer42	p.Y78Lfs*42	ENST00000312629	NM_003952.2	75	aag/aaGg	3/15	1	2	FACETS	0.843	0.759	0.931	0.843	0.759	0.931	CLONAL	1	TRUE	1	0.59	2		406	406	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	202	576	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.59	2		576	660	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108787	2108788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs137854024	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	235	725	0	ENST00000219476.3:c.894dup	p.Val299CysfsTer39	p.V299Cfs*39	ENST00000219476	NM_000548.3	296	-/T	10/42	1	2	FACETS	0.902	0.843	0.963	0.902	0.843	0.963	CLONAL	1	TRUE	1	0.59	2		725	883	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	146	392	1	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.865	0.793	0.94	0.865	0.793	0.94	CLONAL	1	TRUE	1	0.59	2		393	572	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203791	94203791	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs190142346	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	12	202	0	ENST00000323929.3:c.863G>A	p.Arg288His	p.R288H	ENST00000323929	NM_005591.3	288	cGt/cAt	9/20	1	2	FACETS	0.311	0.219	0.421	0.311	0.219	0.421	SUBCLONAL	1	TRUE	1	0.59	2		202	131	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149516607	149516607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148272095	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	197	630	3	ENST00000261799.4:c.4C>T	p.Arg2Trp	p.R2W	ENST00000261799	NM_002609.3	2	Cgg/Tgg	2/23	1	2	FACETS	0.941	0.874	1	0.941	0.874	1	CLONAL	1	TRUE	1	0.59	2		633	710	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229336	36229336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777603343	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	184	510	0	ENST00000222270.7:c.8026G>A	p.Ala2676Thr	p.A2676T	ENST00000222270	NM_014727.1	2676	Gcc/Acc	37/37	1	2	FACETS	0.924	0.856	0.994	0.924	0.856	0.994	CLONAL	1	TRUE	1	0.59	2		510	675	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	30	597	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.261	0.21	0.319	0.261	0.21	0.319	SUBCLONAL	1	TRUE	1	0.59	2		597	389	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687472	37687472	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	25	202	0	ENST00000447079.4:c.4382del	p.Gly1461AlafsTer38	p.G1461Afs*38	ENST00000447079	NM_015083.1	1459	tGg/tg	14/14	1	2	FACETS	0.349	0.276	0.432	0.349	0.276	0.432	SUBCLONAL	1	TRUE	1	0.59	2		202	243	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176338	24176338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	226	613	3	ENST00000263121.7:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000263121	NM_003073.3	377	Cgt/Tgt	9/9	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.59	2		616	706	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845485	128845485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779548739	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	274	758	2	ENST00000249373.3:c.782G>A	p.Arg261His	p.R261H	ENST00000249373	NM_005631.4	261	cGc/cAc	4/12	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.59	2		760	914	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902635	1902635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759803629	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	206	613	0	ENST00000382891.5:c.254G>A	p.Arg85Gln	p.R85Q	ENST00000382891	NM_133335.3	85	cGg/cAg	2/22	1	2	FACETS	0.922	0.858	0.988	0.922	0.858	0.988	CLONAL	1	TRUE	1	0.59	2		613	757	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431115	49431115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371869550	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	174	608	1	ENST00000301067.7:c.10024C>T	p.Arg3342Cys	p.R3342C	ENST00000301067	NM_003482.3	3342	Cgc/Tgc	34/54	1	2	FACETS	0.914	0.845	0.986	0.914	0.845	0.986	CLONAL	1	TRUE	1	0.59	2		609	645	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	256	739	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.847	0.793	0.902	0.847	0.793	0.902	CLONAL	1	TRUE	1	0.59	2		739	1025	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	443491	443491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	97	420	0	ENST00000399788.2:c.1406C>T	p.Pro469Leu	p.P469L	ENST00000399788	NM_001042603.1	469	cCg/cTg	11/28	1	2	FACETS	0.937	0.843	1	0.937	0.843	1	CLONAL	1	TRUE	1	0.59	2		420	351	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273884	18273884	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201531496	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	192	630	0	ENST00000222254.8:c.1217G>A	p.Arg406His	p.R406H	ENST00000222254	NM_005027.3	406	cGc/cAc	10/16	1	2	FACETS	0.942	0.874	1	0.942	0.874	1	CLONAL	1	TRUE	1	0.59	2		630	691	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434367	121434367	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	171	710	1	ENST00000257555.6:c.1136del	p.Pro379LeufsTer5	p.P379Lfs*5	ENST00000257555		377	ctC/ct	6/10	1	2	FACETS	0.896	0.827	0.967	0.896	0.827	0.967	CLONAL	1	TRUE	1	0.59	2		711	647	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457390	67457390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782977	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	186	544	0	ENST00000327367.4:c.364G>A	p.Val122Met	p.V122M	ENST00000327367	NM_005902.3	122	Gtg/Atg	2/9	1	2	FACETS	0.945	0.877	1	0.945	0.877	1	CLONAL	1	TRUE	1	0.59	2		544	667	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106225	2106225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147196739	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	235	686	4	ENST00000219476.3:c.628G>A	p.Ala210Thr	p.A210T	ENST00000219476	NM_000548.3	210	Gcg/Acg	7/42	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.59	2		690	754	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	117	502	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.862	0.782	0.945	0.862	0.782	0.945	CLONAL	1	TRUE	1	0.59	2		502	460	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191005	185191005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	202	751	0	ENST00000265026.3:c.1886C>T	p.Pro629Leu	p.P629L	ENST00000265026	NM_004721.4	629	cCt/cTt	11/14	1	2	FACETS	0.665	0.616	0.716	0.665	0.616	0.716	SUBCLONAL	1	TRUE	1	0.59	2		751	1029	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310820	123310820	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747502397	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	246	570	1	ENST00000358487.5:c.608G>A	p.Arg203His	p.R203H	ENST00000358487	NM_000141.4	203	cGc/cAc	5/18	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.59	2		571	798	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	46	465	1	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	1	2	FACETS	0.256	0.215	0.301	0.256	0.215	0.301	SUBCLONAL	1	TRUE	1	0.59	2		466	609	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638918	176638918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770929380	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	113	496	1	ENST00000439151.2:c.3518G>A	p.Arg1173His	p.R1173H	ENST00000439151	NM_022455.4	1173	cGc/cAc	5/23	1	2	FACETS	0.61	0.55	0.673	0.61	0.55	0.673	SUBCLONAL	1	TRUE	1	0.59	2		497	628	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198389	138198389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751123351	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	88	279	0	ENST00000237289.4:c.982G>A	p.Ala328Thr	p.A328T	ENST00000237289	NM_001270507.1	328	Gca/Aca	6/9	1	2	FACETS	0.763	0.68	0.85	0.763	0.68	0.85	SUBCLONAL	1	TRUE	1	0.59	2		279	391	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216596	108216596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778080	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	36	405	1	ENST00000278616.4:c.8545C>T	p.Arg2849Ter	p.R2849*	ENST00000278616	NM_000051.3	2849	Cga/Tga	58/63	1	2	FACETS	0.484	0.4	0.577	0.484	0.4	0.577	SUBCLONAL	1	TRUE	1	0.59	2		406	252	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504513	103504513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140917545	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	24	308	0	ENST00000355739.4:c.134G>A	p.Arg45His	p.R45H	ENST00000355739	NM_000123.3	45	cGc/cAc	2/15	1	2	FACETS	0.306	0.24	0.381	0.306	0.24	0.381	SUBCLONAL	1	TRUE	1	0.59	2		308	266	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122735	7122735	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772334614	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	256	682	0	ENST00000302850.5:c.3419C>T	p.Ala1140Val	p.A1140V	ENST00000302850	NM_000208.2	1140	gCg/gTg	19/22	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.59	2		682	825	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246486	10246486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1388371493	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	207	594	1	ENST00000340748.4:c.4651C>T	p.Arg1551Trp	p.R1551W	ENST00000340748		1551	Cgg/Tgg	38/40	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.59	2		595	699	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299832	15299832	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465285176	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	244	679	0	ENST00000263388.2:c.1346G>A	p.Arg449His	p.R449H	ENST00000263388	NM_000435.2	449	cGc/cAc	8/33	1	2	FACETS	0.977	0.915	1	0.977	0.915	1	CLONAL	1	TRUE	1	0.59	2		679	847	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251991	8251991	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760736132	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	242	658	1	ENST00000335790.3:c.86G>A	p.Arg29His	p.R29H	ENST00000335790	NM_002315.2	29	cGc/cAc	2/4	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.59	2		659	799	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752375	57752375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777774366	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	28	394	0	ENST00000274289.3:c.1198C>T	p.His400Tyr	p.H400Y	ENST00000274289	NM_006622.3	400	Cat/Tat	9/14	1	2	FACETS	0.339	0.271	0.415	0.339	0.271	0.415	SUBCLONAL	1	TRUE	1	0.59	2		394	280	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001366	29001366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779189056	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	97	301	0	ENST00000282397.4:c.1366G>A	p.Ala456Thr	p.A456T	ENST00000282397	NM_002019.4	456	Gca/Aca	10/30	1	2	FACETS	0.792	0.711	0.878	0.792	0.711	0.878	SUBCLONAL	1	TRUE	1	0.59	2		301	415	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295773	212295773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1299031105	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	24	588	2	ENST00000342788.4:c.2540G>A	p.Arg847His	p.R847H	ENST00000342788	NM_005235.2	847	cGt/cAt	21/28	1	2	FACETS	0.183	0.143	0.229	0.183	0.143	0.229	SUBCLONAL	1	TRUE	1	0.59	2		590	445	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7128960	7128960	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139944962	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	15	322	0	ENST00000302850.5:c.2848G>A	p.Val950Ile	p.V950I	ENST00000302850	NM_000208.2	950	Gtc/Atc	15/22	1	2	FACETS	0.175	0.127	0.232	0.175	0.127	0.232	SUBCLONAL	1	TRUE	1	0.59	2		322	291	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979563	7979563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1221632429	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	151	522	1	ENST00000319144.4:c.1462C>T	p.Arg488Cys	p.R488C	ENST00000319144	NM_001139.2	488	Cgt/Tgt	11/15	1	2	FACETS	0.863	0.793	0.936	0.863	0.793	0.936	CLONAL	1	TRUE	1	0.59	2		523	593	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935633	13935633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756650303	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	165	413	1	ENST00000405192.2:c.1223G>A	p.Arg408His	p.R408H	ENST00000405192	NM_001163147.1	408	cGt/cAt	12/12	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.59	2		414	524	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155627	56155627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768025328	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	104	300	1	ENST00000399503.3:c.719C>T	p.Ala240Val	p.A240V	ENST00000399503	NM_005921.1	240	gCg/gTg	3/20	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.59	2		301	350	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246522	10246522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs919486255	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	168	494	0	ENST00000340748.4:c.4615G>A	p.Val1539Met	p.V1539M	ENST00000340748		1539	Gtg/Atg	38/40	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.59	2		494	520	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066821	77066821	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1319725019	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	156	384	0	ENST00000356341.3:c.664A>G	p.Ile222Val	p.I222V	ENST00000356341	NM_002576.4	222	Att/Gtt	7/15	1	2	FACETS	0.949	0.874	1	0.949	0.874	1	CLONAL	1	TRUE	1	0.59	2		384	557	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805473	1805473	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188723332	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	249	651	0	ENST00000260795.2:c.985G>A	p.Val329Ile	p.V329I	ENST00000260795		329	Gtc/Atc	7/17	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.59	2		651	787	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209514	98209514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781539921	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	111	520	1	ENST00000331920.6:c.4024C>T	p.Arg1342Cys	p.R1342C	ENST00000331920	NM_000264.3	1342	Cgc/Tgc	23/24	1	2	FACETS	0.722	0.652	0.796	0.722	0.652	0.796	SUBCLONAL	1	TRUE	1	0.59	2		521	521	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821594	72821596	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	rs374416547	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	12	108	0	ENST00000268489.5:c.10579_10581del	p.Gly3527del	p.G3527del	ENST00000268489	NM_006885.3	3527	GGC/-	10/10	0.1063980619458	3	FACETS	0.466	0.33	0.63	0.233	0.165	0.315	INDETERMINATE	1	TRUE	1	0.59	3		108	113	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944382	131944382	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs748536322	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	41	221	1	ENST00000265335.6:c.2801del	p.Asn934IlefsTer6	p.N934Ifs*6	ENST00000265335		932	Aaa/aa	17/25	1	2	FACETS	0.92	0.78	1	0.92	0.78	1	CLONAL	1	TRUE	1	0.59	2		222	151	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65323452	65323452	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765489448	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	150	455	0	ENST00000342505.4:c.1345G>A	p.Ala449Thr	p.A449T	ENST00000342505	NM_002227.2	449	Gcc/Acc	10/25	1	2	FACETS	0.898	0.825	0.974	0.898	0.825	0.974	CLONAL	1	TRUE	1	0.59	2		455	566	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132552	11132552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	216	653	2	ENST00000358026.2:c.2768C>T	p.Ala923Val	p.A923V	ENST00000358026	NM_001128849.1	923	gCg/gTg	19/36	1	2	FACETS	0.939	0.875	1	0.939	0.875	1	CLONAL	1	TRUE	1	0.59	2		655	780	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606304	93606304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	172	622	2	ENST00000375746.1:c.124C>T	p.Arg42Cys	p.R42C	ENST00000375746	NM_001174167.1	42	Cgc/Tgc	2/14	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.59	2		624	579	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787731	135787731	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151309813	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	54	519	0	ENST00000298552.3:c.851G>A	p.Arg284His	p.R284H	ENST00000298552	NM_001162426.1	284	cGc/cAc	9/23	1	2	FACETS	0.264	0.225	0.307	0.264	0.225	0.307	SUBCLONAL	1	TRUE	1	0.59	2		519	694	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469038	25469038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775263815	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	230	678	0	ENST00000264709.3:c.1420C>T	p.Arg474Cys	p.R474C	ENST00000264709	NM_175629.2	474	Cgc/Tgc	11/23	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.59	2		678	753	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911520	134911520	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756316035	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	183	481	0	ENST00000398015.3:c.1985G>A	p.Arg662His	p.R662H	ENST00000398015	NM_004441.4	662	cGt/cAt	11/16	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.59	2		481	610	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979661	7979661	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1053727821	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	58	292	0	ENST00000319144.4:c.1364G>A	p.Gly455Asp	p.G455D	ENST00000319144	NM_001139.2	455	gGc/gAc	11/15	1	2	FACETS	0.671	0.581	0.768	0.671	0.581	0.768	SUBCLONAL	1	TRUE	1	0.59	2		292	293	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135777085	135777085	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1331635112	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	180	470	2	ENST00000298552.3:c.2393C>T	p.Thr798Met	p.T798M	ENST00000298552	NM_001162426.1	798	aCg/aTg	19/23	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.59	2		472	608	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990723	7990723	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	120	537	0	ENST00000319144.4:c.38A>T	p.Asp13Val	p.D13V	ENST00000319144	NM_001139.2	13	gAc/gTc	1/15	1	2	FACETS	0.651	0.589	0.716	0.651	0.589	0.716	SUBCLONAL	1	TRUE	1	0.59	2		537	625	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351421	70351421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1474736821	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	259	347	0	ENST00000374080.3:c.4069C>T	p.Arg1357Cys	p.R1357C	ENST00000374080		1357	Cgc/Tgc	29/45	1	1	FACETS	0.78	0.745	0.813	1	0.995	1	SUBCLONAL	2	TRUE	0	0.59	1		347	397	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638555	176638555	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210270412	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	152	557	1	ENST00000439151.2:c.3155G>A	p.Arg1052His	p.R1052H	ENST00000439151	NM_022455.4	1052	cGc/cAc	5/23	1	2	FACETS	0.846	0.777	0.918	0.846	0.777	0.918	CLONAL	1	TRUE	1	0.59	2		558	609	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729271	41729271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749989847	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	132	406	0	ENST00000242208.4:c.1258G>A	p.Val420Met	p.V420M	ENST00000242208	NM_002192.2	420	Gtg/Atg	3/3	1	2	FACETS	0.936	0.856	1	0.936	0.856	1	CLONAL	1	TRUE	1	0.59	2		406	478	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567646	226567647	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1159330096	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	174	534	4	ENST00000366794.5:c.1519dup	p.Ser507LysfsTer14	p.S507Kfs*14	ENST00000366794	NM_001618.3	507	agc/aAgc	10/23	1	2	FACETS	0.933	0.863	1	0.933	0.863	1	CLONAL	1	TRUE	1	0.59	2		538	632	SUCCESS
ATM	472	MSKCC	GRCh37	11	108213967	108213967	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876659872	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	44	319	0	ENST00000278616.4:c.8287C>T	p.Arg2763Ter	p.R2763*	ENST00000278616	NM_000051.3	2763	Cga/Tga	57/63	1	2	FACETS	0.531	0.448	0.622	0.531	0.448	0.622	SUBCLONAL	1	TRUE	1	0.59	2		319	281	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858253	59858253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778133	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	134	538	0	ENST00000259008.2:c.1742G>A	p.Arg581Gln	p.R581Q	ENST00000259008	NM_032043.2	581	cGa/cAa	12/20	1	2	FACETS	0.977	0.894	1	0.977	0.894	1	CLONAL	1	TRUE	1	0.59	2		538	465	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582302	119582302	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	144	426	2	ENST00000316626.5:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000316626		367	Cga/Tga	10/12	1	2	FACETS	0.952	0.873	1	0.952	0.873	1	CLONAL	1	TRUE	1	0.59	2		428	513	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417080	417080	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779176655	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	129	338	1	ENST00000399788.2:c.3470G>A	p.Arg1157His	p.R1157H	ENST00000399788	NM_001042603.1	1157	cGc/cAc	23/28	1	2	FACETS	0.894	0.816	0.976	0.894	0.816	0.976	CLONAL	1	TRUE	1	0.59	2		339	489	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393199	393199	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	45	432	0	ENST00000380956.4:c.47C>T	p.Ala16Val	p.A16V	ENST00000380956	NM_001195286.1	16	gCg/gTg	2/9	1	2	FACETS	0.293	0.246	0.346	0.293	0.246	0.346	SUBCLONAL	1	TRUE	1	0.59	2		432	520	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779578	3779578	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	219	918	1	ENST00000262367.5:c.5470G>A	p.Ala1824Thr	p.A1824T	ENST00000262367	NM_004380.2	1824	Gcc/Acc	31/31	1	2	FACETS	0.704	0.655	0.756	0.704	0.655	0.756	SUBCLONAL	1	TRUE	1	0.59	2		919	1054	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926270	112926270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918457	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	41	619	1	ENST00000351677.2:c.1403C>T	p.Thr468Met	p.T468M	ENST00000351677	NM_002834.3	468	aCg/aTg	12/16	1	2	FACETS	0.188	0.156	0.224	0.188	0.156	0.224	SUBCLONAL	1	TRUE	1	0.59	2		620	739	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983115	111983115	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	123	455	0	ENST00000368678.4:c.1432C>T	p.Arg478Ter	p.R478*	ENST00000368678		478	Cga/Tga	13/13	1	2	FACETS	0.784	0.712	0.859	0.784	0.712	0.859	SUBCLONAL	1	TRUE	1	0.59	2		455	532	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935669	15935669	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	155	363	0	ENST00000268712.3:c.7264C>T	p.Arg2422Ter	p.R2422*	ENST00000268712	NM_006311.3	2422	Cga/Tga	46/46	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.59	2		363	520	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227948	53227948	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	181	347	0	ENST00000375401.3:c.2366G>A	p.Arg789His	p.R789H	ENST00000375401	NM_004187.3	789	cGc/cAc	16/26	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.59	1		347	345	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149973	202149973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1272714323	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	142	437	1	ENST00000358485.4:c.1414C>T	p.Arg472Ter	p.R472*	ENST00000358485	NM_001080125.1	472	Cga/Tga	8/9	1	2	FACETS	0.71	0.648	0.774	0.71	0.648	0.774	SUBCLONAL	1	TRUE	1	0.59	2		438	678	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239843	98239843	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1398130707	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	187	575	1	ENST00000331920.6:c.1489G>A	p.Ala497Thr	p.A497T	ENST00000331920	NM_000264.3	497	Gct/Act	10/24	1	2	FACETS	0.941	0.872	1	0.941	0.872	1	CLONAL	1	TRUE	1	0.59	2		576	674	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272105	15272105	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372833545	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	98	491	0	ENST00000263388.2:c.6334G>A	p.Gly2112Ser	p.G2112S	ENST00000263388	NM_000435.2	2112	Ggt/Agt	33/33	1	2	FACETS	0.634	0.567	0.704	0.634	0.567	0.704	SUBCLONAL	1	TRUE	1	0.59	2		491	524	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575133	48575133	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	56	374	0	ENST00000342988.3:c.330del	p.Lys110AsnfsTer12	p.K110Nfs*12	ENST00000342988	NM_005359.5	109	ctA/ct	3/12	1	2	FACETS	0.655	0.565	0.751	0.655	0.565	0.751	SUBCLONAL	1	TRUE	1	0.59	2		374	290	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312426	91312426	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55880859	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	107	501	0	ENST00000355112.3:c.2371C>T	p.Arg791Cys	p.R791C	ENST00000355112	NM_000057.2	791	Cgt/Tgt	11/22	1	2	FACETS	0.815	0.736	0.898	0.815	0.736	0.898	CLONAL	1	TRUE	1	0.59	2		501	445	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765753	41765753	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761731744	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	101	429	3	ENST00000301178.4:c.2629G>A	p.Ala877Thr	p.A877T	ENST00000301178	NM_021913.4	877	Gct/Act	20/20	1	2	FACETS	0.804	0.723	0.888	0.804	0.723	0.888	CLONAL	1	TRUE	1	0.59	2		432	426	SUCCESS
BLM	641	MSKCC	GRCh37	15	91306337	91306337	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	81	415	1	ENST00000355112.3:c.2024C>T	p.Ala675Val	p.A675V	ENST00000355112	NM_000057.2	675	gCg/gTg	8/22	1	2	FACETS	0.847	0.753	0.946	0.847	0.753	0.946	CLONAL	1	TRUE	1	0.59	2		416	324	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143351	30143351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	30	612	0	ENST00000389048.3:c.175G>A	p.Val59Met	p.V59M	ENST00000389048	NM_004304.4	59	Gtg/Atg	1/29	1	2	FACETS	0.171	0.137	0.21	0.171	0.137	0.21	SUBCLONAL	1	TRUE	1	0.59	2		612	594	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579365	7579365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782461	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	231	608	0	ENST00000269305.4:c.322G>A	p.Gly108Ser	p.G108S	ENST00000269305	NM_001126112.2	108	Ggt/Agt	4/11	1	2	FACETS	0.992	0.928	1	0.992	0.928	1	CLONAL	1	TRUE	1	0.59	2		608	789	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729551	41729551	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1356119994	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	175	593	0	ENST00000242208.4:c.978C>A	p.Phe326Leu	p.F326L	ENST00000242208	NM_002192.2	326	ttC/ttA	3/3	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.59	2		593	593	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274568	198274568	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746956131	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	91	507	0	ENST00000335508.6:c.830C>T	p.Ala277Val	p.A277V	ENST00000335508	NM_012433.2	277	gCg/gTg	7/25	1	2	FACETS	0.44	0.391	0.493	0.44	0.391	0.493	SUBCLONAL	1	TRUE	1	0.59	2		507	701	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518190	8518190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	148	366	0	ENST00000356435.5:c.1201C>T	p.Arg401Trp	p.R401W	ENST00000356435		401	Cgg/Tgg	10/35	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.59	2		366	500	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143232	24143232	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	244	595	4	ENST00000263121.7:c.464G>A	p.Arg155His	p.R155H	ENST00000263121	NM_003073.3	155	cGc/cAc	4/9	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.59	2		599	778	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938239	36938239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199991273	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	259	695	1	ENST00000361632.4:c.722C>T	p.Ala241Val	p.A241V	ENST00000361632		241	gCg/gTg	6/16	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.59	2		696	742	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467731	66467731	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1285001325	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	111	394	0	ENST00000273854.3:c.538G>A	p.Asp180Asn	p.D180N	ENST00000273854	NM_004439.5	180	Gat/Aat	3/18	1	2	FACETS	0.875	0.792	0.961	0.875	0.792	0.961	CLONAL	1	TRUE	1	0.59	2		394	430	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739871	46739871	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769214858	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	105	389	0	ENST00000371975.4:c.1672C>T	p.Arg558Cys	p.R558C	ENST00000371975	NM_003579.3	558	Cgc/Tgc	15/18	1	2	FACETS	0.626	0.562	0.693	0.626	0.562	0.693	SUBCLONAL	1	TRUE	1	0.59	2		389	569	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003202	143003202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766146483	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	34	404	0	ENST00000262992.4:c.2624C>T	p.Ala875Val	p.A875V	ENST00000262992	NM_001101669.1	875	gCg/gTg	23/24	1	2	FACETS	0.284	0.232	0.342	0.284	0.232	0.342	SUBCLONAL	1	TRUE	1	0.59	2		404	406	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350626	15350626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1234699192	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	227	744	1	ENST00000263377.2:c.3289C>T	p.Arg1097Cys	p.R1097C	ENST00000263377	NM_058243.2	1097	Cgt/Tgt	16/20	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.59	2		745	767	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509954	187509954	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs993828603	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	46	361	1	ENST00000441802.2:c.13559C>T	p.Pro4520Leu	p.P4520L	ENST00000441802	NM_005245.3	4520	cCg/cTg	27/27	1	2	FACETS	0.377	0.317	0.442	0.377	0.317	0.442	SUBCLONAL	1	TRUE	1	0.59	2		362	414	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263394	123263394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773245022	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	174	412	0	ENST00000358487.5:c.1349G>A	p.Arg450His	p.R450H	ENST00000358487	NM_000141.4	450	cGc/cAc	10/18	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.59	2		412	580	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794732	120794732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1276733276	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	196	595	2	ENST00000257552.2:c.625G>A	p.Ala209Thr	p.A209T	ENST00000257552	NM_002442.3	209	Gcc/Acc	9/15	1	2	FACETS	0.91	0.845	0.977	0.91	0.845	0.977	CLONAL	1	TRUE	1	0.59	2		597	730	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107749	30107749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760459161	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	141	530	0	ENST00000331968.5:c.931C>T	p.Arg311Cys	p.R311C	ENST00000331968	NM_002742.2	311	Cgt/Tgt	6/18	1	2	FACETS	0.874	0.8	0.95	0.874	0.8	0.95	CLONAL	1	TRUE	1	0.59	2		530	547	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144149	11144149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	67	522	1	ENST00000358026.2:c.3730C>T	p.Arg1244Cys	p.R1244C	ENST00000358026	NM_001128849.1	1244	Cgc/Tgc	26/36	1	2	FACETS	0.368	0.32	0.421	0.368	0.32	0.421	SUBCLONAL	1	TRUE	1	0.59	2		523	617	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038147	128038147	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144012336	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	156	436	0	ENST00000285398.2:c.1403C>T	p.Ala468Val	p.A468V	ENST00000285398	NM_000122.1	468	gCg/gTg	9/15	1	2	FACETS	0.899	0.827	0.974	0.899	0.827	0.974	CLONAL	1	TRUE	1	0.59	2		436	588	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541714	120541714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750190278	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	211	613	0	ENST00000229340.5:c.143G>A	p.Arg48Gln	p.R48Q	ENST00000229340	NM_006861.6	48	cGg/cAg	3/6	1	2	FACETS	0.924	0.861	0.989	0.924	0.861	0.989	CLONAL	1	TRUE	1	0.59	2		613	774	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433507	138433507	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759331142	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	76	474	0	ENST00000289153.2:c.1105G>A	p.Val369Ile	p.V369I	ENST00000289153	NM_006219.2	369	Gta/Ata	7/22	1	2	FACETS	0.944	0.838	1	0.944	0.838	1	CLONAL	1	TRUE	1	0.59	2		474	273	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420745	49420745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768594066	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	172	561	0	ENST00000301067.7:c.15004C>T	p.Arg5002Trp	p.R5002W	ENST00000301067	NM_003482.3	5002	Cgg/Tgg	48/54	1	2	FACETS	0.917	0.847	0.989	0.917	0.847	0.989	CLONAL	1	TRUE	1	0.59	2		561	636	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391832	139391832	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766836819	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	174	704	2	ENST00000277541.6:c.6359G>A	p.Arg2120His	p.R2120H	ENST00000277541	NM_017617.3	2120	cGc/cAc	34/34	1	2	FACETS	0.935	0.864	1	0.935	0.864	1	CLONAL	1	TRUE	1	0.59	2		706	631	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56787287	56787287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267606997	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	98	560	1	ENST00000337432.4:c.773G>A	p.Arg258His	p.R258H	ENST00000337432	NM_058216.2	258	cGt/cAt	5/9	1	2	FACETS	0.721	0.646	0.799	0.721	0.646	0.799	SUBCLONAL	1	TRUE	1	0.59	2		561	461	SUCCESS
APC	324	MSKCC	GRCh37	5	112176555	112176555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771967537	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	52	256	0	ENST00000257430.4:c.5264C>T	p.Ala1755Val	p.A1755V	ENST00000257430	NM_000038.5	1755	gCg/gTg	16/16	1	2	FACETS	0.943	0.815	1	0.943	0.815	1	CLONAL	1	TRUE	1	0.59	2		256	187	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373313	118373313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1335499500	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	33	401	3	ENST00000534358.1:c.6706G>A	p.Ala2236Thr	p.A2236T	ENST00000534358	NM_005933.3	2236	Gct/Act	27/36	1	2	FACETS	0.28	0.228	0.339	0.28	0.228	0.339	SUBCLONAL	1	TRUE	1	0.59	2		404	399	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354324	354324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200716081	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	68	584	0	ENST00000262320.3:c.1234C>T	p.Arg412Trp	p.R412W	ENST00000262320	NM_003502.3	412	Cgg/Tgg	5/11	1	2	FACETS	0.293	0.254	0.335	0.293	0.254	0.335	SUBCLONAL	1	TRUE	1	0.59	2		584	787	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589313	67589313	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	21	190	0	ENST00000274335.5:c.1299+2T>C		p.X433_splice	ENST00000274335		433			1	2	FACETS	0.691	0.542	0.859	0.691	0.542	0.859	SUBCLONAL	1	TRUE	1	0.59	2		190	103	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001431	29001431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	112	235	1	ENST00000282397.4:c.1301C>T	p.Ala434Val	p.A434V	ENST00000282397	NM_002019.4	434	gCc/gTc	10/30	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.59	2		236	354	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128222	30128222	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs527481960	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	182	608	0	ENST00000263025.4:c.1010C>T	p.Thr337Met	p.T337M	ENST00000263025	NM_002746.2	337	aCg/aTg	7/9	0.1063980619458	3	FACETS	1	0.985	1	0.624	0.578	0.671	INDETERMINATE	1	TRUE	1	0.59	3		608	640	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524475	44524475	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	47	279	0	ENST00000291552.4:c.82C>T	p.Arg28Cys	p.R28C	ENST00000291552	NM_006758.2	28	Cgt/Tgt	2/8	1	2	FACETS	0.762	0.651	0.882	0.762	0.651	0.882	SUBCLONAL	1	TRUE	1	0.59	2		279	209	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226589	2226589	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760808115	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	150	697	4	ENST00000398665.3:c.4069C>T	p.Arg1357Cys	p.R1357C	ENST00000398665	NM_032482.2	1357	Cgc/Tgc	27/28	1	2	FACETS	0.693	0.634	0.754	0.693	0.634	0.754	SUBCLONAL	1	TRUE	1	0.59	2		701	734	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248579	8248579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253559924	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	221	678	1	ENST00000335790.3:c.308G>A	p.Arg103Gln	p.R103Q	ENST00000335790	NM_002315.2	103	cGg/cAg	3/4	1	2	FACETS	0.974	0.909	1	0.974	0.909	1	CLONAL	1	TRUE	1	0.59	2		679	769	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937723	44937723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	84	273	0	ENST00000377967.4:c.2911C>T	p.Arg971Cys	p.R971C	ENST00000377967	NM_021140.2	971	Cgt/Tgt	19/29	1	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.59	1		273	183	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14015969	14015969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760327512	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	63	270	0	ENST00000311895.7:c.289C>T	p.Arg97Cys	p.R97C	ENST00000311895	NM_005236.2	97	Cgc/Tgc	2/11	1	2	FACETS	0.865	0.757	0.979	0.865	0.757	0.979	CLONAL	1	TRUE	1	0.59	2		270	247	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349036	70349036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1336321422	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	203	286	0	ENST00000374080.3:c.3548C>T	p.Pro1183Leu	p.P1183L	ENST00000374080		1183	cCg/cTg	25/45	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.59	1		286	390	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259533	55259533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	139	495	0	ENST00000275493.2:c.2591C>T	p.Ala864Val	p.A864V	ENST00000275493	NM_005228.3	864	gCg/gTg	21/28	1	2	FACETS	0.906	0.83	0.985	0.906	0.83	0.985	CLONAL	1	TRUE	1	0.59	2		495	520	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874713	151874713	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	101	397	0	ENST00000262189.6:c.7825C>T	p.Arg2609Ter	p.R2609*	ENST00000262189	NM_170606.2	2609	Cga/Tga	38/59	1	2	FACETS	0.702	0.63	0.777	0.702	0.63	0.777	SUBCLONAL	1	TRUE	1	0.59	2		397	488	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753276	42753276	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756887571	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	98	782	1	ENST00000222329.4:c.988G>A	p.Ala330Thr	p.A330T	ENST00000222329	NM_006494.2	330	Gcc/Acc	4/4	1	2	FACETS	0.368	0.327	0.411	0.368	0.327	0.411	SUBCLONAL	1	TRUE	1	0.59	2		783	903	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599874	10599874	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1356624458	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	240	655	0	ENST00000171111.5:c.1702G>A	p.Val568Ile	p.V568I	ENST00000171111	NM_203500.1	568	Gtc/Atc	5/6	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.59	2		655	806	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213611	36213611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757982914	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	265	711	5	ENST00000222270.7:c.2713G>A	p.Ala905Thr	p.A905T	ENST00000222270	NM_014727.1	905	Gcc/Acc	5/37	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.59	2		716	894	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639874	3639874	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	215	608	0	ENST00000294008.3:c.3765G>A	p.Trp1255Ter	p.W1255*	ENST00000294008	NM_032444.2	1255	tgG/tgA	12/15	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.59	2		608	712	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201693	66201693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142359231	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	117	494	0	ENST00000273854.3:c.2809C>T	p.Arg937Cys	p.R937C	ENST00000273854	NM_004439.5	937	Cgt/Tgt	16/18	1	2	FACETS	0.785	0.712	0.862	0.785	0.712	0.862	SUBCLONAL	1	TRUE	1	0.59	2		494	505	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437361	121437361	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751368921	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	241	701	3	ENST00000257555.6:c.1699G>A	p.Val567Ile	p.V567I	ENST00000257555		567	Gtc/Atc	9/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.59	2		704	765	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31379461	31379461	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	159	555	0	ENST00000328111.2:c.868G>A	p.Ala290Thr	p.A290T	ENST00000328111	NM_006892.3	290	Gcc/Acc	8/23	1	2	FACETS	0.914	0.841	0.988	0.914	0.841	0.988	CLONAL	1	TRUE	1	0.59	2		555	590	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435129	110435129	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	213	592	3	ENST00000375856.3:c.3272del	p.Pro1091ArgfsTer15	p.P1091Rfs*15	ENST00000375856	NM_003749.2	1091	cCg/cg	1/2	1	2	FACETS	0.936	0.873	1	0.936	0.873	1	CLONAL	1	TRUE	1	0.59	2		595	771	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047947	180047947	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	239	678	1	ENST00000261937.6:c.2228C>T	p.Ala743Val	p.A743V	ENST00000261937	NM_182925.4	743	gCg/gTg	15/30	1	2	FACETS	0.974	0.911	1	0.974	0.911	1	CLONAL	1	TRUE	1	0.59	2		679	832	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1978301	1978301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774737951	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	244	678	0	ENST00000382891.5:c.3721G>A	p.Glu1241Lys	p.E1241K	ENST00000382891	NM_133335.3	1241	Gag/Aag	21/22	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.59	2		678	823	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924617	94924617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1433012201	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	167	566	0	ENST00000536441.1:c.293G>A	p.Arg98His	p.R98H	ENST00000536441	NM_144665.3	98	cGc/cAc	3/10	1	2	FACETS	0.835	0.77	0.903	0.835	0.77	0.903	CLONAL	1	TRUE	1	0.59	2		566	678	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964143	28964143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766569666	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	93	394	0	ENST00000282397.4:c.1759G>A	p.Val587Ile	p.V587I	ENST00000282397	NM_002019.4	587	Gtt/Att	13/30	1	2	FACETS	0.873	0.783	0.968	0.873	0.783	0.968	CLONAL	1	TRUE	1	0.59	2		394	361	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739012	145739012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373292946	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	145	556	0	ENST00000428558.2:c.2143C>T	p.Arg715Trp	p.R715W	ENST00000428558	NM_004260.3	715	Cgg/Tgg	13/22	1	2	FACETS	0.676	0.618	0.737	0.676	0.618	0.737	SUBCLONAL	1	TRUE	1	0.59	2		556	727	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261368	16261368	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781561009	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	111	522	3	ENST00000375759.3:c.8633C>T	p.Ala2878Val	p.A2878V	ENST00000375759	NM_015001.2	2878	gCg/gTg	11/15	1	2	FACETS	0.624	0.562	0.689	0.624	0.562	0.689	SUBCLONAL	1	TRUE	1	0.59	2		525	603	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376665	8376665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753080783	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	164	559	0	ENST00000356435.5:c.4448C>T	p.Thr1483Met	p.T1483M	ENST00000356435		1483	aCg/aTg	27/35	1	2	FACETS	0.919	0.847	0.993	0.919	0.847	0.993	CLONAL	1	TRUE	1	0.59	2		559	605	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845523	151845524	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	62	670	0	ENST00000262189.6:c.13488dup	p.Lys4497Ter	p.K4497*	ENST00000262189	NM_170606.2	4496	-/T	52/59	1	2	FACETS	0.311	0.268	0.358	0.311	0.268	0.358	SUBCLONAL	1	TRUE	1	0.59	2		670	676	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422455	47422455	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398289359	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	198	252	0	ENST00000377045.4:c.89G>A	p.Arg30His	p.R30H	ENST00000377045	NM_001654.4	30	cGc/cAc	2/16	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.59	1		252	331	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190344	32190344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146490163	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	99	592	0	ENST00000375023.3:c.395G>A	p.Arg132His	p.R132H	ENST00000375023	NM_004557.3	132	cGc/cAc	3/30	1	2	FACETS	0.591	0.529	0.657	0.591	0.529	0.657	SUBCLONAL	1	TRUE	1	0.59	2		592	568	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923807	72923807	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766702555	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	181	582	1	ENST00000268489.5:c.3271G>A	p.Val1091Ile	p.V1091I	ENST00000268489	NM_006885.3	1091	Gtt/Att	4/10	0.1063980619458	3	FACETS	1	0.985	1	0.629	0.582	0.676	INDETERMINATE	1	TRUE	1	0.59	3		583	632	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986925	36986925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1192440323	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	212	481	1	ENST00000354822.5:c.764C>T	p.Ala255Val	p.A255V	ENST00000354822	NM_001079668.2	255	gCg/gTg	3/3	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.59	2		482	634	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015296	128015296	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772307115	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	127	366	0	ENST00000285398.2:c.2225G>A	p.Arg742Gln	p.R742Q	ENST00000285398	NM_000122.1	742	cGg/cAg	15/15	1	2	FACETS	0.914	0.834	0.998	0.914	0.834	0.998	CLONAL	1	TRUE	1	0.59	2		366	471	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245225	46245225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529386166	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	65	399	1	ENST00000334344.6:c.3319G>A	p.Ala1107Thr	p.A1107T	ENST00000334344	NM_152641.2	1107	Gca/Aca	15/21	1	2	FACETS	0.419	0.363	0.479	0.419	0.363	0.479	SUBCLONAL	1	TRUE	1	0.59	2		400	526	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193476	99193476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	230	622	0	ENST00000074304.5:c.2671C>T	p.Arg891Trp	p.R891W	ENST00000074304	NM_001134224.1	891	Cgg/Tgg	25/26	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.59	2		622	777	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21630862	21630862	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202110155	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	106	496	0	ENST00000421138.2:c.742G>A	p.Ala248Thr	p.A248T	ENST00000421138		248	Gca/Aca	8/16	1	2	FACETS	0.826	0.745	0.91	0.826	0.745	0.91	CLONAL	1	TRUE	1	0.59	2		496	435	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521972	157521972	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs769118968	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	56	355	0	ENST00000346085.5:c.4244A>G	p.Asp1415Gly	p.D1415G	ENST00000346085	NM_020732.3	1415	gAc/gGc	18/20	1	2	FACETS	0.513	0.441	0.591	0.513	0.441	0.591	SUBCLONAL	1	TRUE	1	0.59	2		355	370	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415846	49415846	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886041398	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	97	450	0	ENST00000301067.7:c.16501C>T	p.Arg5501Ter	p.R5501*	ENST00000301067	NM_003482.3	5501	Cga/Tga	53/54	1	2	FACETS	0.575	0.514	0.64	0.575	0.514	0.64	SUBCLONAL	1	TRUE	1	0.59	2		450	572	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288743	33288743	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs533137350	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	164	425	1	ENST00000374542.5:c.809G>A	p.Arg270His	p.R270H	ENST00000374542	NM_001141970.1	270	cGc/cAc	3/8	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.59	2		426	528	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051273	128051273	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	99	517	0	ENST00000285398.2:c.50G>A	p.Arg17Gln	p.R17Q	ENST00000285398	NM_000122.1	17	cGg/cAg	2/15	1	2	FACETS	0.543	0.485	0.604	0.543	0.485	0.604	SUBCLONAL	1	TRUE	1	0.59	2		517	618	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439750	49439750	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs200119692	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	194	489	0	ENST00000301067.7:c.4694C>T	p.Ala1565Val	p.A1565V	ENST00000301067	NM_003482.3	1565	gCg/gTg	18/54	1	2	FACETS	0.93	0.864	0.999	0.93	0.864	0.999	CLONAL	1	TRUE	1	0.59	2		489	707	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845190	151845190	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764910946	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	157	484	0	ENST00000262189.6:c.13822C>T	p.Arg4608Cys	p.R4608C	ENST00000262189	NM_170606.2	4608	Cgc/Tgc	52/59	1	2	FACETS	0.934	0.86	1	0.934	0.86	1	CLONAL	1	TRUE	1	0.59	2		484	570	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353823	40353823	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	247	533	2	ENST00000293328.3:c.2297C>T	p.Ala766Val	p.A766V	ENST00000293328	NM_012448.3	766	gCg/gTg	19/19	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.59	2		535	805	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634731	158634731	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748791232	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	76	395	0	ENST00000263640.3:c.455G>A	p.Arg152His	p.R152H	ENST00000263640	NM_001105.4	152	cGc/cAc	5/11	1	2	FACETS	0.573	0.504	0.646	0.573	0.504	0.646	SUBCLONAL	1	TRUE	1	0.59	2		395	450	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316075	14316075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs566703225	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	16	367	0	ENST00000256196.4:c.350G>A	p.Arg117His	p.R117H	ENST00000256196		117	cGt/cAt	4/6	1	2	FACETS	0.214	0.158	0.281	0.214	0.158	0.281	SUBCLONAL	1	TRUE	1	0.59	2		367	253	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435696	149435696	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1214473761	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	129	575	0	ENST00000286301.3:c.2447G>A	p.Arg816His	p.R816H	ENST00000286301	NM_005211.3	816	cGc/cAc	19/22	1	2	FACETS	0.669	0.608	0.733	0.669	0.608	0.733	SUBCLONAL	1	TRUE	1	0.59	2		575	654	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136051	64136051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	204	567	1	ENST00000334205.4:c.1312G>A	p.Ala438Thr	p.A438T	ENST00000334205	NM_003942.2	438	Gca/Aca	11/17	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.59	2		568	659	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40442026	40442026	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758471182	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	203	687	1	ENST00000345506.4:c.271G>A	p.Ala91Thr	p.A91T	ENST00000345506	NM_003152.3	91	Gcc/Acc	4/20	1	2	FACETS	0.924	0.859	0.99	0.924	0.859	0.99	CLONAL	1	TRUE	1	0.59	2		688	745	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20488470	20488470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147333935	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	52	308	0	ENST00000346618.3:c.1126G>A	p.Ala376Thr	p.A376T	ENST00000346618	NM_001949.4	376	Gct/Act	6/7	1	2	FACETS	0.77	0.663	0.884	0.77	0.663	0.884	SUBCLONAL	1	TRUE	1	0.59	2		308	229	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206851	162206851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769230602	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	122	346	0	ENST00000366898.1:c.824G>A	p.Arg275Gln	p.R275Q	ENST00000366898	NM_004562.2	275	cGg/cAg	7/12	1	2	FACETS	0.936	0.852	1	0.936	0.852	1	CLONAL	1	TRUE	1	0.59	2		346	442	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141549486	141549486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	161	432	1	ENST00000220592.5:c.2102G>A	p.Gly701Glu	p.G701E	ENST00000220592	NM_012154.3	701	gGg/gAg	16/19	1	2	FACETS	0.93	0.857	1	0.93	0.857	1	CLONAL	1	TRUE	1	0.59	2		433	587	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082455	16082455	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	225	661	2	ENST00000281043.3:c.269G>A	p.Ser90Asn	p.S90N	ENST00000281043	NM_005378.4	90	aGc/aAc	2/3	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.59	2		663	754	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166874	32166874	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	244	678	0	ENST00000375023.3:c.4364C>T	p.Ala1455Val	p.A1455V	ENST00000375023	NM_004557.3	1455	gCc/gTc	24/30	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.59	2		678	814	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590452	67590452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	10	167	0	ENST00000274335.5:c.1514G>A	p.Ser505Asn	p.S505N	ENST00000274335		505	aGc/aAc	11/15	1	2	FACETS	0.271	0.184	0.379	0.271	0.184	0.379	SUBCLONAL	1	TRUE	1	0.59	2		167	125	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9770555	9770555	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	247	578	0	ENST00000377346.4:c.42G>T	p.Lys14Asn	p.K14N	ENST00000377346	NM_005026.3	14	aaG/aaT	3/24	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.59	2		578	819	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199670	11199670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766533620	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	199	619	1	ENST00000361445.4:c.4918C>T	p.Arg1640Trp	p.R1640W	ENST00000361445	NM_004958.3	1640	Cgg/Tgg	35/58	1	2	FACETS	0.973	0.905	1	0.973	0.905	1	CLONAL	1	TRUE	1	0.59	2		620	693	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11264747	11264747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	195	563	0	ENST00000361445.4:c.3815C>T	p.Ala1272Val	p.A1272V	ENST00000361445	NM_004958.3	1272	gCc/gTc	26/58	1	2	FACETS	0.914	0.849	0.982	0.914	0.849	0.982	CLONAL	1	TRUE	1	0.59	2		563	723	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11270923	11270923	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs975845561	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	77	452	0	ENST00000361445.4:c.3602G>A	p.Arg1201Gln	p.R1201Q	ENST00000361445	NM_004958.3	1201	cGa/cAa	24/58	1	2	FACETS	0.725	0.641	0.814	0.725	0.641	0.814	SUBCLONAL	1	TRUE	1	0.59	2		452	360	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298093	11298093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	42	393	0	ENST00000361445.4:c.2015G>A	p.Arg672His	p.R672H	ENST00000361445	NM_004958.3	672	cGc/cAc	13/58	1	2	FACETS	0.285	0.238	0.338	0.285	0.238	0.338	SUBCLONAL	1	TRUE	1	0.59	2		393	499	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303178	11303178	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763879621	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	128	414	0	ENST00000361445.4:c.1405G>A	p.Ala469Thr	p.A469T	ENST00000361445	NM_004958.3	469	Gcc/Acc	9/58	1	2	FACETS	0.868	0.791	0.948	0.868	0.791	0.948	CLONAL	1	TRUE	1	0.59	2		414	500	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258227	16258227	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1022665445	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	57	445	0	ENST00000375759.3:c.5492C>T	p.Ala1831Val	p.A1831V	ENST00000375759	NM_015001.2	1831	gCt/gTt	11/15	1	2	FACETS	0.377	0.323	0.435	0.377	0.323	0.435	SUBCLONAL	1	TRUE	1	0.59	2		445	513	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259270	16259270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774668447	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	73	286	0	ENST00000375759.3:c.6535G>A	p.Ala2179Thr	p.A2179T	ENST00000375759	NM_015001.2	2179	Gca/Aca	11/15	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.59	2		286	240	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261983	16261983	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	44	441	0	ENST00000375759.3:c.9248G>T	p.Ser3083Ile	p.S3083I	ENST00000375759	NM_015001.2	3083	aGc/aTc	11/15	1	2	FACETS	0.298	0.25	0.352	0.298	0.25	0.352	SUBCLONAL	1	TRUE	1	0.59	2		441	500	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262442	16262442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371890904	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	16	249	0	ENST00000375759.3:c.9707C>T	p.Thr3236Ile	p.T3236I	ENST00000375759	NM_015001.2	3236	aCa/aTa	11/15	1	2	FACETS	0.216	0.159	0.284	0.216	0.159	0.284	SUBCLONAL	1	TRUE	1	0.59	2		249	251	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263659	16263659	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	120	360	0	ENST00000375759.3:c.10028G>A	p.Gly3343Asp	p.G3343D	ENST00000375759	NM_015001.2	3343	gGc/gAc	12/15	1	2	FACETS	0.948	0.863	1	0.948	0.863	1	CLONAL	1	TRUE	1	0.59	2		360	429	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818396	43818396	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	169	631	0	ENST00000372470.3:c.1861A>G	p.Ile621Val	p.I621V	ENST00000372470	NM_005373.2	621	Att/Gtt	12/12	1	2	FACETS	0.805	0.742	0.87	0.805	0.742	0.87	CLONAL	1	TRUE	1	0.59	2		631	712	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733478	85733478	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	99	415	0	ENST00000370580.1:c.534A>T	p.Glu178Asp	p.E178D	ENST00000370580	NM_003921.4	178	gaA/gaT	3/3	1	2	FACETS	0.831	0.747	0.918	0.831	0.747	0.918	CLONAL	1	TRUE	1	0.59	2		415	404	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466402	120466402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	153	516	0	ENST00000256646.2:c.4717C>T	p.Leu1573Phe	p.L1573F	ENST00000256646	NM_024408.3	1573	Ctc/Ttc	26/34	1	2	FACETS	0.943	0.868	1	0.943	0.868	1	CLONAL	1	TRUE	1	0.59	2		516	550	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483182	120483182	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	34	290	0	ENST00000256646.2:c.3179G>A	p.Cys1060Tyr	p.C1060Y	ENST00000256646	NM_024408.3	1060	tGt/tAt	19/34	1	2	FACETS	0.287	0.235	0.347	0.287	0.235	0.347	SUBCLONAL	1	TRUE	1	0.59	2		290	401	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483322	120483322	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	97	343	0	ENST00000256646.2:c.3039C>A	p.Cys1013Ter	p.C1013*	ENST00000256646	NM_024408.3	1013	tgC/tgA	19/34	1	2	FACETS	0.926	0.833	1	0.926	0.833	1	CLONAL	1	TRUE	1	0.59	2		343	355	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120496192	120496192	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	97	562	0	ENST00000256646.2:c.2339G>T	p.Arg780Met	p.R780M	ENST00000256646	NM_024408.3	780	aGg/aTg	14/34	1	2	FACETS	0.6	0.536	0.667	0.6	0.536	0.667	SUBCLONAL	1	TRUE	1	0.59	2		562	548	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724547	162724547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	48	467	2	ENST00000367921.3:c.319G>A	p.Ala107Thr	p.A107T	ENST00000367921	NM_006182.2	107	Gca/Aca	5/18	1	2	FACETS	0.266	0.225	0.312	0.266	0.225	0.312	SUBCLONAL	1	TRUE	1	0.59	2		469	611	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731095	162731095	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	70	504	0	ENST00000367921.3:c.950C>T	p.Ala317Val	p.A317V	ENST00000367921	NM_006182.2	317	gCc/gTc	9/18	1	2	FACETS	0.399	0.348	0.454	0.399	0.348	0.454	SUBCLONAL	1	TRUE	1	0.59	2		504	595	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117019	193117019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	27	315	0	ENST00000367435.3:c.752C>T	p.Ala251Val	p.A251V	ENST00000367435	NM_024529.4	251	gCa/gTa	8/17	1	2	FACETS	0.218	0.173	0.269	0.218	0.173	0.269	SUBCLONAL	1	TRUE	1	0.59	2		315	420	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193205388	193205388	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	51	396	0	ENST00000367435.3:c.1319A>G	p.Asp440Gly	p.D440G	ENST00000367435	NM_024529.4	440	gAc/gGc	15/17	1	2	FACETS	0.294	0.249	0.342	0.294	0.249	0.342	SUBCLONAL	1	TRUE	1	0.59	2		396	589	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226589935	226589935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1558243852	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	157	491	0	ENST00000366794.5:c.266C>T	p.Ala89Val	p.A89V	ENST00000366794	NM_001618.3	89	gCg/gTg	2/23	1	2	FACETS	0.914	0.842	0.99	0.914	0.842	0.99	CLONAL	1	TRUE	1	0.59	2		491	582	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104389886	104389886	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501117	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	155	392	1	ENST00000369902.3:c.1429G>A	p.Val477Met	p.V477M	ENST00000369902	NM_016169.3	477	Gtg/Atg	12/12	1	2	FACETS	0.928	0.854	1	0.928	0.854	1	CLONAL	1	TRUE	1	0.59	2		393	566	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724281	112724281	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	125	385	0	ENST00000369452.4:c.165G>T	p.Lys55Asn	p.K55N	ENST00000369452	NM_007373.3	55	aaG/aaT	2/9	1	2	FACETS	0.927	0.845	1	0.927	0.845	1	CLONAL	1	TRUE	1	0.59	2		385	457	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	532676	532676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	147	816	0	ENST00000451590.1:c.530G>A	p.Ser177Asn	p.S177N	ENST00000451590	NM_001130442.1	177	aGt/aAt	5/5	1	2	FACETS	0.589	0.538	0.643	0.589	0.538	0.643	SUBCLONAL	1	TRUE	1	0.59	2		816	846	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316397	14316397	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	22	439	0	ENST00000256196.4:c.208G>T	p.Ala70Ser	p.A70S	ENST00000256196		70	Gca/Tca	3/6	1	2	FACETS	0.221	0.171	0.279	0.221	0.171	0.279	SUBCLONAL	1	TRUE	1	0.59	2		439	338	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196682	67196682	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1463411225	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	132	433	0	ENST00000312629.5:c.211C>T	p.Arg71Cys	p.R71C	ENST00000312629	NM_003952.2	71	Cgt/Tgt	3/15	1	2	FACETS	0.986	0.902	1	0.986	0.902	1	CLONAL	1	TRUE	1	0.59	2		433	454	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941313	71941313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs927834612	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	56	546	1	ENST00000298229.2:c.1088G>A	p.Arg363His	p.R363H	ENST00000298229	NM_001567.3	363	cGc/cAc	9/28	1	2	FACETS	0.379	0.325	0.438	0.379	0.325	0.438	SUBCLONAL	1	TRUE	1	0.59	2		547	501	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103416	77103417	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	99	369	0	ENST00000356341.3:c.149dup	p.Lys51GlufsTer13	p.K51Efs*13	ENST00000356341	NM_002576.4	50	aag/aaAg	2/15	1	2	FACETS	0.874	0.786	0.965	0.874	0.786	0.965	CLONAL	1	TRUE	1	0.59	2		369	384	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198403	108198403	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	31	341	0	ENST00000278616.4:c.7007A>G	p.Glu2336Gly	p.E2336G	ENST00000278616	NM_000051.3	2336	gAa/gGa	48/63	1	2	FACETS	0.32	0.259	0.389	0.32	0.259	0.389	SUBCLONAL	1	TRUE	1	0.59	2		341	328	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118368741	118368741	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555044515	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	98	541	0	ENST00000534358.1:c.5755G>A	p.Gly1919Arg	p.G1919R	ENST00000534358	NM_005933.3	1919	Gga/Aga	21/36	1	2	FACETS	0.573	0.512	0.637	0.573	0.512	0.637	SUBCLONAL	1	TRUE	1	0.59	2		541	580	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374115	118374115	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs143525945	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	27	363	0	ENST00000534358.1:c.7508C>A	p.Ala2503Asp	p.A2503D	ENST00000534358	NM_005933.3	2503	gCt/gAt	27/36	1	2	FACETS	0.232	0.184	0.287	0.232	0.184	0.287	SUBCLONAL	1	TRUE	1	0.59	2		363	394	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125513789	125513789	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1433658665	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	87	498	0	ENST00000428830.2:c.917C>T	p.Ala306Val	p.A306V	ENST00000428830	NM_001114121.2	306	gCt/gTt	9/14	1	2	FACETS	0.778	0.694	0.867	0.778	0.694	0.867	SUBCLONAL	1	TRUE	1	0.59	2		498	379	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022832	12022832	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771593728	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	151	482	0	ENST00000396373.4:c.938C>T	p.Ala313Val	p.A313V	ENST00000396373	NM_001987.4	313	gCt/gTt	5/8	1	2	FACETS	0.944	0.868	1	0.944	0.868	1	CLONAL	1	TRUE	1	0.59	2		482	542	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870822	12870822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	16	142	1	ENST00000228872.4:c.49G>A	p.Asp17Asn	p.D17N	ENST00000228872	NM_004064.3	17	Gac/Aac	1/3	1	2	FACETS	0.354	0.263	0.462	0.354	0.263	0.462	SUBCLONAL	1	TRUE	1	0.59	2		143	153	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499767	18499767	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	70	308	0	ENST00000266497.5:c.1622A>G	p.His541Arg	p.H541R	ENST00000266497		541	cAc/cGc	10/31	1	2	FACETS	0.869	0.766	0.978	0.869	0.766	0.978	CLONAL	1	TRUE	1	0.59	2		308	273	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21630754	21630754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	21	338	0	ENST00000421138.2:c.850C>T	p.Pro284Ser	p.P284S	ENST00000421138		284	Cca/Tca	8/16	1	2	FACETS	0.282	0.218	0.358	0.282	0.218	0.358	SUBCLONAL	1	TRUE	1	0.59	2		338	252	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636309	21636309	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	72	355	1	ENST00000421138.2:c.700+1G>A		p.X234_splice	ENST00000421138		234			1	2	FACETS	0.972	0.861	1	0.972	0.861	1	CLONAL	1	TRUE	1	0.59	2		356	251	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427056	49427056	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	118	491	0	ENST00000301067.7:c.11432A>T	p.Gln3811Leu	p.Q3811L	ENST00000301067	NM_003482.3	3811	cAg/cTg	39/54	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.59	2		491	382	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433847	49433847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	204	846	0	ENST00000301067.7:c.7706G>A	p.Gly2569Asp	p.G2569D	ENST00000301067	NM_003482.3	2569	gGc/gAc	31/54	1	2	FACETS	0.726	0.674	0.781	0.726	0.674	0.781	SUBCLONAL	1	TRUE	1	0.59	2		846	952	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435980	49435980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1405791853	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	218	621	0	ENST00000301067.7:c.6001C>T	p.Arg2001Trp	p.R2001W	ENST00000301067	NM_003482.3	2001	Cgg/Tgg	28/54	1	2	FACETS	0.995	0.928	1	0.995	0.928	1	CLONAL	1	TRUE	1	0.59	2		621	743	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487277	56487278	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	62	518	2	ENST00000267101.3:c.1428dup	p.Pro477AlafsTer11	p.P477Afs*11	ENST00000267101	NM_001982.3	475	cgg/cGgg	12/28	1	2	FACETS	0.318	0.275	0.366	0.318	0.275	0.366	SUBCLONAL	1	TRUE	1	0.59	2		520	660	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495610	56495610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs538526313	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	156	457	1	ENST00000267101.3:c.3800G>A	p.Arg1267Gln	p.R1267Q	ENST00000267101	NM_001982.3	1267	cGa/cAa	28/28	1	2	FACETS	0.994	0.916	1	0.994	0.916	1	CLONAL	1	TRUE	1	0.59	2		458	532	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202900	133202900	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	139	458	0	ENST00000320574.5:c.6334C>A	p.Leu2112Met	p.L2112M	ENST00000320574	NM_006231.2	2112	Ctg/Atg	46/49	1	2	FACETS	0.994	0.912	1	0.994	0.912	1	CLONAL	1	TRUE	1	0.59	2		458	474	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215748	133215748	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141519273	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	53	542	0	ENST00000320574.5:c.5515C>T	p.Arg1839Cys	p.R1839C	ENST00000320574	NM_006231.2	1839	Cgc/Tgc	40/49	1	2	FACETS	0.262	0.223	0.305	0.262	0.223	0.305	SUBCLONAL	1	TRUE	1	0.59	2		542	685	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219125	133219125	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	193	578	0	ENST00000320574.5:c.4919A>G	p.Asp1640Gly	p.D1640G	ENST00000320574	NM_006231.2	1640	gAc/gGc	37/49	1	2	FACETS	0.936	0.869	1	0.936	0.869	1	CLONAL	1	TRUE	1	0.59	2		578	699	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233748	133233748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	192	525	0	ENST00000320574.5:c.3556C>T	p.Leu1186Phe	p.L1186F	ENST00000320574	NM_006231.2	1186	Ctc/Ttc	29/49	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.59	2		525	593	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249829	133249829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555228490	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	147	407	2	ENST00000320574.5:c.1394C>T	p.Ala465Val	p.A465V	ENST00000320574	NM_006231.2	465	gCc/gTc	14/49	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.59	2		409	487	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28885802	28885802	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	98	531	0	ENST00000282397.4:c.3560C>A	p.Pro1187His	p.P1187H	ENST00000282397	NM_002019.4	1187	cCt/cAt	27/30	1	2	FACETS	0.879	0.79	0.971	0.879	0.79	0.971	CLONAL	1	TRUE	1	0.59	2		531	378	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964102	28964102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	92	487	0	ENST00000282397.4:c.1800G>A	p.Met600Ile	p.M600I	ENST00000282397	NM_002019.4	600	atG/atA	13/30	1	2	FACETS	0.78	0.697	0.866	0.78	0.697	0.866	SUBCLONAL	1	TRUE	1	0.59	2		487	400	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906627	32906627	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358396	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	37	341	0	ENST00000380152.3:c.1012G>A	p.Ala338Thr	p.A338T	ENST00000380152		338	Gct/Act	10/27	1	2	FACETS	0.804	0.673	0.945	0.804	0.673	0.945	CLONAL	1	TRUE	1	0.59	2		341	156	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942682	48942682	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568421803	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	49	269	0	ENST00000267163.4:c.1069C>T	p.Pro357Ser	p.P357S	ENST00000267163	NM_000321.2	357	Cca/Tca	11/27	1	2	FACETS	0.826	0.709	0.952	0.826	0.709	0.952	CLONAL	1	TRUE	1	0.59	2		269	201	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514012	103514013	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	76	356	0	ENST00000355739.4:c.830_831del	p.Glu277ValfsTer7	p.E277Vfs*7	ENST00000355739	NM_000123.3	276	gtAGag/gtag	7/15	1	2	FACETS	0.847	0.751	0.95	0.847	0.751	0.95	CLONAL	1	TRUE	1	0.59	2		356	304	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871619	35871619	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201191831	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	95	312	0	ENST00000216797.5:c.887C>T	p.Thr296Met	p.T296M	ENST00000216797	NM_020529.2	296	aCg/aTg	5/6	1	2	FACETS	0.868	0.779	0.961	0.868	0.779	0.961	CLONAL	1	TRUE	1	0.59	2		312	371	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061069	38061069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1401881303	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	23	192	0	ENST00000250448.2:c.920C>T	p.Ser307Leu	p.S307L	ENST00000250448	NM_004496.3	307	tCg/tTg	2/2	1	2	FACETS	0.392	0.307	0.489	0.392	0.307	0.489	SUBCLONAL	1	TRUE	1	0.59	2		192	199	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675040	40675040	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	180	501	0	ENST00000249776.8:c.4G>A	p.Ala2Thr	p.A2T	ENST00000249776	NM_033286.3	2	Gcg/Acg	1/9	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.59	2		501	610	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41011037	41011037	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	203	665	1	ENST00000267868.3:c.470C>T	p.Ala157Val	p.A157V	ENST00000267868	NM_002875.4	157	gCc/gTc	6/10	1	2	FACETS	0.88	0.818	0.944	0.88	0.818	0.944	CLONAL	1	TRUE	1	0.59	2		666	782	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991060	41991060	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	50	321	0	ENST00000219905.7:c.2014-1G>T		p.X672_splice	ENST00000219905	NM_001164273.1	672			1	2	FACETS	0.649	0.555	0.751	0.649	0.555	0.751	SUBCLONAL	1	TRUE	1	0.59	2		321	261	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994717	73994717	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	291	763	0	ENST00000318443.5:c.201G>A	p.Trp67Ter	p.W67*	ENST00000318443	NM_001024736.1	67	tgG/tgA	3/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.59	2		763	876	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680683	88680683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	229	610	1	ENST00000360948.2:c.574G>A	p.Ala192Thr	p.A192T	ENST00000360948	NM_001012338.2	192	Gct/Act	6/19	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.59	2		611	741	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347432	91347433	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	79	313	0	ENST00000355112.3:c.3600dup	p.Gln1201ThrfsTer16	p.Q1201Tfs*16	ENST00000355112	NM_000057.2	1198	-/A	19/22	1	2	FACETS	0.996	0.887	1	0.996	0.887	1	CLONAL	1	TRUE	1	0.59	2		313	269	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250917	99250917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1292080642	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	156	466	1	ENST00000268035.6:c.221G>A	p.Arg74His	p.R74H	ENST00000268035	NM_000875.3	74	cGc/cAc	2/21	1	2	FACETS	0.996	0.918	1	0.996	0.918	1	CLONAL	1	TRUE	1	0.59	2		467	531	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456341	99456341	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	114	325	0	ENST00000268035.6:c.1658A>G	p.Asp553Gly	p.D553G	ENST00000268035	NM_000875.3	553	gAc/gGc	8/21	1	2	FACETS	0.966	0.877	1	0.966	0.877	1	CLONAL	1	TRUE	1	0.59	2		325	400	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396172	396172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1161120248	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	142	426	0	ENST00000262320.3:c.854G>A	p.Arg285Gln	p.R285Q	ENST00000262320	NM_003502.3	285	cGg/cAg	2/11	1	2	FACETS	0.967	0.887	1	0.967	0.887	1	CLONAL	1	TRUE	1	0.59	2		426	498	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100432	2100432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397514949	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	179	492	0	ENST00000219476.3:c.170G>A	p.Arg57His	p.R57H	ENST00000219476	NM_000548.3	57	cGc/cAc	3/42	1	2	FACETS	0.979	0.907	1	0.979	0.907	1	CLONAL	1	TRUE	1	0.59	2		492	620	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136814	2136814	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	100	699	0	ENST00000219476.3:c.4931A>G	p.Asp1644Gly	p.D1644G	ENST00000219476	NM_000548.3	1644	gAc/gGc	38/42	1	2	FACETS	0.424	0.378	0.472	0.424	0.378	0.472	SUBCLONAL	1	TRUE	1	0.59	2		699	800	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639032	3639032	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759939338	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	69	630	0	ENST00000294008.3:c.4607C>T	p.Ala1536Val	p.A1536V	ENST00000294008	NM_032444.2	1536	gCt/gTt	12/15	1	2	FACETS	0.339	0.295	0.387	0.339	0.295	0.387	SUBCLONAL	1	TRUE	1	0.59	2		630	690	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642778	3642778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145353518	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	158	668	0	ENST00000294008.3:c.2249C>T	p.Thr750Met	p.T750M	ENST00000294008	NM_032444.2	750	aCg/aTg	11/15	1	2	FACETS	0.652	0.597	0.708	0.652	0.597	0.708	SUBCLONAL	1	TRUE	1	0.59	2		668	822	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658617	3658617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	222	835	0	ENST00000294008.3:c.349G>A	p.Ala117Thr	p.A117T	ENST00000294008	NM_032444.2	117	Gcc/Acc	2/15	1	2	FACETS	0.691	0.643	0.741	0.691	0.643	0.741	SUBCLONAL	1	TRUE	1	0.59	2		835	1089	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779650	3779650	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	208	708	1	ENST00000262367.5:c.5398C>T	p.Arg1800Trp	p.R1800W	ENST00000262367	NM_004380.2	1800	Cgg/Tgg	31/31	1	2	FACETS	0.958	0.892	1	0.958	0.892	1	CLONAL	1	TRUE	1	0.59	2		709	736	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817760	3817760	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1041960106	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	199	574	2	ENST00000262367.5:c.3211G>A	p.Ala1071Thr	p.A1071T	ENST00000262367	NM_004380.2	1071	Gcc/Acc	16/31	1	2	FACETS	0.879	0.817	0.944	0.879	0.817	0.944	CLONAL	1	TRUE	1	0.59	2		576	767	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129408	30129408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200652640	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	125	592	1	ENST00000263025.4:c.620C>T	p.Thr207Met	p.T207M	ENST00000263025	NM_002746.2	207	aCg/aTg	4/9	0.1063980619458	3	FACETS	0.798	0.723	0.876	0.399	0.361	0.438	INDETERMINATE	1	TRUE	1	0.59	3		593	688	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868075	56868075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760057496	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	49	460	1	ENST00000308159.5:c.1573C>T	p.Arg525Trp	p.R525W	ENST00000308159	NM_014669.4	525	Cgg/Tgg	14/22	0.1063980619458	3	FACETS	0.358	0.303	0.419	0.179	0.151	0.21	INDETERMINATE	1	TRUE	1	0.59	3		461	601	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953123	81953123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763556693	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	40	275	1	ENST00000359376.3:c.2089C>T	p.Arg697Trp	p.R697W	ENST00000359376	NM_002661.3	697	Cgg/Tgg	20/33	1	2	FACETS	0.324	0.269	0.385	0.324	0.269	0.385	SUBCLONAL	1	TRUE	1	0.59	2		276	418	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347463	89347463	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	126	519	0	ENST00000301030.4:c.5487G>T	p.Met1829Ile	p.M1829I	ENST00000301030	NM_001256183.1	1829	atG/atT	9/13	1	2	FACETS	0.826	0.752	0.904	0.826	0.752	0.904	CLONAL	1	TRUE	1	0.59	2		519	517	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348079	89348079	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	322	863	3	ENST00000301030.4:c.4871C>T	p.Ala1624Val	p.A1624V	ENST00000301030	NM_001256183.1	1624	gCg/gTg	9/13	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.59	2		866	1044	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349606	89349606	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	230	827	0	ENST00000301030.4:c.3344T>C	p.Ile1115Thr	p.I1115T	ENST00000301030	NM_001256183.1	1115	aTc/aCc	9/13	1	2	FACETS	0.952	0.89	1	0.952	0.89	1	CLONAL	1	TRUE	1	0.59	2		827	819	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357036	89357036	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	138	384	0	ENST00000301030.4:c.598G>A	p.Ala200Thr	p.A200T	ENST00000301030	NM_001256183.1	200	Gca/Aca	6/13	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.59	2		384	402	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849432	89849432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778309	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	250	627	0	ENST00000389301.3:c.1549C>T	p.Arg517Trp	p.R517W	ENST00000389301	NM_000135.2	517	Cgg/Tgg	16/43	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.59	2		627	844	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12043197	12043197	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	58	263	0	ENST00000353533.5:c.1082T>G	p.Leu361Arg	p.L361R	ENST00000353533	NM_003010.3	361	cTt/cGt	10/11	1	2	FACETS	0.812	0.706	0.926	0.812	0.706	0.926	CLONAL	1	TRUE	1	0.59	2		263	242	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16021300	16021300	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	16	330	0	ENST00000268712.3:c.1957del	p.Met653TrpfsTer115	p.M653Wfs*115	ENST00000268712	NM_006311.3	653	Atg/tg	18/46	1	2	FACETS	0.174	0.128	0.229	0.174	0.128	0.229	SUBCLONAL	1	TRUE	1	0.59	2		330	312	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527519	29527519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	130	603	1	ENST00000356175.3:c.968C>T	p.Ala323Val	p.A323V	ENST00000356175	NM_000267.3	323	gCc/gTc	9/57	1	2	FACETS	0.81	0.738	0.885	0.81	0.738	0.885	CLONAL	1	TRUE	1	0.59	2		604	544	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264326	30264326	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	26	70	0	ENST00000322652.5:c.65del	p.Gly22GlufsTer50	p.G22Efs*50	ENST00000322652	NM_015355.2	21	Ggg/gg	1/16	1	2	FACETS	0.699	0.563	0.851	0.699	0.563	0.851	SUBCLONAL	1	TRUE	1	0.59	2		70	126	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428351	33428351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs181695922	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	211	660	0	ENST00000345365.6:c.772G>A	p.Gly258Arg	p.G258R	ENST00000345365	NM_002878.3	258	Ggg/Agg	9/10	1	2	FACETS	0.965	0.9	1	0.965	0.9	1	CLONAL	1	TRUE	1	0.59	2		660	741	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627604	37627604	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs780994234	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	31	482	1	ENST00000447079.4:c.1519G>T	p.Ala507Ser	p.A507S	ENST00000447079	NM_015083.1	507	Gca/Tca	2/14	1	2	FACETS	0.242	0.195	0.294	0.242	0.195	0.294	SUBCLONAL	1	TRUE	1	0.59	2		483	435	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864701	37864701	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	136	598	0	ENST00000269571.5:c.353A>G	p.Asp118Gly	p.D118G	ENST00000269571		118	gAc/gGc	3/27	1	2	FACETS	0.688	0.627	0.752	0.688	0.627	0.752	SUBCLONAL	1	TRUE	1	0.59	2		598	670	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453361	40453361	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372745237	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	220	673	2	ENST00000345506.4:c.1058G>A	p.Arg353His	p.R353H	ENST00000345506	NM_003152.3	353	cGc/cAc	10/20	1	2	FACETS	0.98	0.915	1	0.98	0.915	1	CLONAL	1	TRUE	1	0.59	2		675	761	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40855763	40855763	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	123	552	0	ENST00000428826.2:c.2093C>T	p.Ala698Val	p.A698V	ENST00000428826		698	gCc/gTc	19/21	1	2	FACETS	0.728	0.66	0.798	0.728	0.66	0.798	SUBCLONAL	1	TRUE	1	0.59	2		552	573	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870539	40870539	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	311	570	0	ENST00000428826.2:c.864G>T	p.Glu288Asp	p.E288D	ENST00000428826		288	gaG/gaT	9/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.59	2		570	954	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246305	41246305	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782770	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	96	577	0	ENST00000357654.3:c.1243G>A	p.Val415Ile	p.V415I	ENST00000357654	NM_007294.3	415	Gtt/Att	10/23	1	2	FACETS	0.773	0.693	0.857	0.773	0.693	0.857	SUBCLONAL	1	TRUE	1	0.59	2		577	421	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439918	56439919	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1567876313	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	71	511	0	ENST00000407977.2:c.673dup	p.Arg225ProfsTer34	p.R225Pfs*34	ENST00000407977		225	cgc/cCgc	6/10	1	2	FACETS	0.354	0.309	0.404	0.354	0.309	0.404	SUBCLONAL	1	TRUE	1	0.59	2		511	679	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885994	59885994	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780834054	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	146	557	0	ENST00000259008.2:c.752G>A	p.Arg251His	p.R251H	ENST00000259008	NM_032043.2	251	cGc/cAc	7/20	1	2	FACETS	0.93	0.854	1	0.93	0.854	1	CLONAL	1	TRUE	1	0.59	2		557	532	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511577	66511577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1177674637	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	108	298	0	ENST00000358598.2:c.37C>T	p.Arg13Cys	p.R13C	ENST00000358598	NM_212471.2	13	Cgc/Tgc	2/11	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.59	2		298	364	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375028	45375028	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	22	356	1	ENST00000262160.6:c.815C>T	p.Ala272Val	p.A272V	ENST00000262160	NM_005901.5	272	gCa/gTa	8/11	1	2	FACETS	0.245	0.19	0.31	0.245	0.19	0.31	SUBCLONAL	1	TRUE	1	0.59	2		357	304	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220661	1220661	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	219	760	2	ENST00000326873.7:c.679G>A	p.Gly227Ser	p.G227S	ENST00000326873	NM_000455.4	227	Ggc/Agc	5/10	1	2	FACETS	0.922	0.86	0.986	0.922	0.86	0.986	CLONAL	1	TRUE	1	0.59	2		762	805	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223370	2223370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561499135	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	226	628	0	ENST00000398665.3:c.3481G>A	p.Asp1161Asn	p.D1161N	ENST00000398665	NM_032482.2	1161	Gac/Aac	25/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.59	2		628	708	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3113379	3113379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1170008066	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	238	553	0	ENST00000078429.4:c.373G>A	p.Glu125Lys	p.E125K	ENST00000078429	NM_002067.2	125	Gag/Aag	3/7	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.59	2		553	765	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220059	5220059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265450607	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	115	600	0	ENST00000357368.4:c.3656C>T	p.Thr1219Met	p.T1219M	ENST00000357368	NM_002850.3	1219	aCg/aTg	22/38	1	2	FACETS	0.556	0.501	0.614	0.556	0.501	0.614	SUBCLONAL	1	TRUE	1	0.59	2		600	701	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10257127	10257127	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	220	561	0	ENST00000340748.4:c.2746G>T	p.Asp916Tyr	p.D916Y	ENST00000340748		916	Gac/Tac	27/40	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.59	2		561	653	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10271059	10271059	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	82	530	2	ENST00000340748.4:c.995+1G>A		p.X332_splice	ENST00000340748		332			1	2	FACETS	0.476	0.42	0.536	0.476	0.42	0.536	SUBCLONAL	1	TRUE	1	0.59	2		532	584	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291104	10291104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	261	722	0	ENST00000340748.4:c.367G>A	p.Ala123Thr	p.A123T	ENST00000340748		123	Gca/Aca	4/40	1	2	FACETS	0.979	0.919	1	0.979	0.919	1	CLONAL	1	TRUE	1	0.59	2		722	904	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10305557	10305557	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766984573	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	162	443	0	ENST00000340748.4:c.19C>T	p.Pro7Ser	p.P7S	ENST00000340748		7	Cca/Tca	1/40	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.59	2		443	533	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030281	11030281	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	52	397	0	ENST00000327064.4:c.1031A>G	p.Asp344Gly	p.D344G	ENST00000327064	NM_199141.1	344	gAc/gGc	9/16	1	2	FACETS	0.335	0.285	0.39	0.335	0.285	0.39	SUBCLONAL	1	TRUE	1	0.59	2		397	526	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030635	11030635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	122	501	0	ENST00000327064.4:c.1189G>A	p.Gly397Ser	p.G397S	ENST00000327064	NM_199141.1	397	Ggc/Agc	10/16	1	2	FACETS	0.675	0.611	0.741	0.675	0.611	0.741	SUBCLONAL	1	TRUE	1	0.59	2		501	613	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107024	11107024	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1369374541	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	120	438	1	ENST00000358026.2:c.1729G>A	p.Ala577Thr	p.A577T	ENST00000358026	NM_001128849.1	577	Gcc/Acc	10/36	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.59	2		439	393	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118642	11118642	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	188	560	0	ENST00000358026.2:c.2066A>C	p.Lys689Thr	p.K689T	ENST00000358026	NM_001128849.1	689	aAg/aCg	14/36	1	2	FACETS	0.912	0.845	0.98	0.912	0.845	0.98	CLONAL	1	TRUE	1	0.59	2		560	699	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051598	13051598	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	52	394	2	ENST00000316448.5:c.857A>T	p.Lys286Met	p.K286M	ENST00000316448	NM_004343.3	286	aAg/aTg	7/9	1	2	FACETS	0.3	0.255	0.349	0.3	0.255	0.349	SUBCLONAL	1	TRUE	1	0.59	2		396	588	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298742	15298742	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	228	675	1	ENST00000263388.2:c.1556G>T	p.Gly519Val	p.G519V	ENST00000263388	NM_000435.2	519	gGc/gTc	10/33	1	2	FACETS	0.916	0.855	0.978	0.916	0.855	0.978	CLONAL	1	TRUE	1	0.59	2		676	844	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302837	15302837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	228	724	1	ENST00000263388.2:c.613C>T	p.Pro205Ser	p.P205S	ENST00000263388	NM_000435.2	205	Cca/Tca	4/33	1	2	FACETS	0.93	0.869	0.993	0.93	0.869	0.993	CLONAL	1	TRUE	1	0.59	2		725	831	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951082	17951082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	228	539	0	ENST00000458235.1:c.1211G>A	p.Ser404Asn	p.S404N	ENST00000458235	NM_000215.3	404	aGc/aAc	9/24	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.59	2		539	761	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278056	18278056	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530214511	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	196	666	0	ENST00000222254.8:c.1676G>A	p.Arg559His	p.R559H	ENST00000222254	NM_005027.3	559	cGc/cAc	13/16	1	2	FACETS	0.793	0.735	0.853	0.793	0.735	0.853	SUBCLONAL	1	TRUE	1	0.59	2		666	838	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18964115	18964115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	172	476	0	ENST00000262803.5:c.1112C>T	p.Ala371Val	p.A371V	ENST00000262803	NM_002911.3	371	gCg/gTg	8/24	1	2	FACETS	0.954	0.882	1	0.954	0.882	1	CLONAL	1	TRUE	1	0.59	2		476	611	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974986	18974986	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	138	491	1	ENST00000262803.5:c.2783G>A	p.Arg928His	p.R928H	ENST00000262803	NM_002911.3	928	cGc/cAc	20/24	1	2	FACETS	0.871	0.797	0.948	0.871	0.797	0.948	CLONAL	1	TRUE	1	0.59	2		492	537	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792666	33792666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	77	120	0	ENST00000498907.2:c.655C>T	p.His219Tyr	p.H219Y	ENST00000498907	NM_004364.3	219	Cac/Tac	1/1	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.59	2		120	222	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212095	36212095	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759236542	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	215	681	0	ENST00000222270.7:c.1846C>T	p.Arg616Trp	p.R616W	ENST00000222270	NM_014727.1	616	Cgg/Tgg	3/37	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.59	2		681	689	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216711	36216711	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770209871	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	135	398	0	ENST00000222270.7:c.3877C>T	p.Arg1293Cys	p.R1293C	ENST00000222270	NM_014727.1	1293	Cgc/Tgc	13/37	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.59	2		398	456	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791588	42791588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752629455	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	52	503	1	ENST00000575354.2:c.569G>A	p.Arg190His	p.R190H	ENST00000575354	NM_015125.3	190	cGc/cAc	4/20	1	2	FACETS	0.296	0.252	0.345	0.296	0.252	0.345	SUBCLONAL	1	TRUE	1	0.59	2		504	595	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867575	45867575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777291413	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	215	789	0	ENST00000391945.4:c.733G>A	p.Asp245Asn	p.D245N	ENST00000391945	NM_000400.3	245	Gac/Aac	9/23	1	2	FACETS	0.99	0.924	1	0.99	0.924	1	CLONAL	1	TRUE	1	0.59	2		789	736	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905346	50905346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370292497	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	254	773	0	ENST00000440232.2:c.554C>T	p.Pro185Leu	p.P185L	ENST00000440232	NM_002691.3	185	cCg/cTg	5/27	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.59	2		773	856	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919881	50919881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1410415830	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	147	664	0	ENST00000440232.2:c.2968C>T	p.Arg990Cys	p.R990C	ENST00000440232	NM_002691.3	990	Cgc/Tgc	24/27	1	2	FACETS	0.833	0.764	0.905	0.833	0.764	0.905	CLONAL	1	TRUE	1	0.59	2		664	598	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716241	52716241	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	172	571	1	ENST00000322088.6:c.685G>A	p.Val229Met	p.V229M	ENST00000322088	NM_014225.5	229	Gtg/Atg	6/15	1	2	FACETS	0.945	0.874	1	0.945	0.874	1	CLONAL	1	TRUE	1	0.59	2		572	617	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086205	16086205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761805254	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	132	337	0	ENST00000281043.3:c.1381G>A	p.Ala461Thr	p.A461T	ENST00000281043	NM_005378.4	461	Gct/Act	3/3	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.59	2		337	432	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609593	46609593	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	141	704	0	ENST00000263734.3:c.2317C>A	p.Leu773Met	p.L773M	ENST00000263734	NM_001430.4	773	Ctg/Atg	15/16	1	2	FACETS	0.558	0.508	0.61	0.558	0.508	0.61	SUBCLONAL	1	TRUE	1	0.59	2		704	857	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47596672	47596672	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863224709	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	108	308	0	ENST00000263735.4:c.28G>A	p.Gly10Arg	p.G10R	ENST00000263735	NM_002354.2	10	Ggg/Agg	1/9	1	2	FACETS	0.855	0.773	0.941	0.855	0.773	0.941	CLONAL	1	TRUE	1	0.59	2		308	428	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873374	136873374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	110	439	1	ENST00000241393.3:c.124C>T	p.Pro42Ser	p.P42S	ENST00000241393	NM_003467.2	42	Ccc/Tcc	2/2	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.59	2		440	372	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017736	31017736	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368981019	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	170	433	0	ENST00000375687.4:c.598G>A	p.Gly200Ser	p.G200S	ENST00000375687	NM_015338.5	200	Ggc/Agc	8/13	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.59	2		433	506	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375105	31375105	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1344773962	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	76	651	0	ENST00000328111.2:c.502A>G	p.Ile168Val	p.I168V	ENST00000328111	NM_006892.3	168	Atc/Gtc	6/23	1	2	FACETS	0.336	0.294	0.381	0.336	0.294	0.381	SUBCLONAL	1	TRUE	1	0.59	2		651	767	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39751878	39751878	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	87	369	0	ENST00000361337.2:c.2239A>G	p.Thr747Ala	p.T747A	ENST00000361337	NM_003286.2	747	Acc/Gcc	21/21	1	2	FACETS	0.591	0.525	0.661	0.591	0.525	0.661	SUBCLONAL	1	TRUE	1	0.59	2		369	499	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420011	41420011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773011187	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	124	365	0	ENST00000373198.4:c.310G>A	p.Asp104Asn	p.D104N	ENST00000373198	NM_133170.3	104	Gac/Aac	3/32	1	2	FACETS	0.918	0.836	1	0.918	0.836	1	CLONAL	1	TRUE	1	0.59	2		365	458	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958143	54958143	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	30	464	0	ENST00000312783.6:c.464G>T	p.Ser155Ile	p.S155I	ENST00000312783	NM_198436.1	155	aGc/aTc	6/10	1	2	FACETS	0.247	0.199	0.302	0.247	0.199	0.302	SUBCLONAL	1	TRUE	1	0.59	2		464	411	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326475	62326475	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	275	777	0	ENST00000360203.5:c.3400G>T	p.Asp1134Tyr	p.D1134Y	ENST00000360203	NM_001283009.1	1134	Gac/Tac	33/35	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.59	2		777	930	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39772561	39772561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	85	350	0	ENST00000288319.7:c.680C>T	p.Ala227Val	p.A227V	ENST00000288319	NM_182918.3	227	gCa/gTa	6/10	1	2	FACETS	0.83	0.74	0.925	0.83	0.74	0.925	CLONAL	1	TRUE	1	0.59	2		350	347	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175800	24175800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773457718	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	99	391	1	ENST00000263121.7:c.1028C>T	p.Thr343Met	p.T343M	ENST00000263121	NM_003073.3	343	aCg/aTg	8/9	1	2	FACETS	0.64	0.574	0.711	0.64	0.574	0.711	SUBCLONAL	1	TRUE	1	0.59	2		392	524	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513676	41513676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs996577997	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	60	483	0	ENST00000263253.7:c.580G>A	p.Gly194Ser	p.G194S	ENST00000263253	NM_001429.3	194	Ggt/Agt	2/31	1	2	FACETS	0.356	0.306	0.409	0.356	0.306	0.409	SUBCLONAL	1	TRUE	1	0.59	2		483	572	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573548	41573548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774508702	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	42	651	1	ENST00000263253.7:c.5833G>A	p.Val1945Met	p.V1945M	ENST00000263253	NM_001429.3	1945	Gtg/Atg	31/31	1	2	FACETS	0.213	0.177	0.253	0.213	0.177	0.253	SUBCLONAL	1	TRUE	1	0.59	2		652	668	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421289	12421289	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	216	607	1	ENST00000287820.6:c.169T>C	p.Ser57Pro	p.S57P	ENST00000287820	NM_015869.4	57	Tcc/Ccc	2/7	1	2	FACETS	0.951	0.887	1	0.951	0.887	1	CLONAL	1	TRUE	1	0.59	2		608	770	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165140	47165140	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540015912	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	44	306	0	ENST00000409792.3:c.986G>A	p.Arg329Gln	p.R329Q	ENST00000409792	NM_014159.6	329	cGg/cAg	3/21	1	2	FACETS	0.728	0.617	0.847	0.728	0.617	0.847	SUBCLONAL	1	TRUE	1	0.59	2		306	205	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722238	49722238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369252300	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	148	498	0	ENST00000449682.2:c.1702C>T	p.Arg568Trp	p.R568W	ENST00000449682	NM_020998.3	568	Cgg/Tgg	15/18	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.59	2		498	484	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940997	49940997	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	142	447	0	ENST00000296474.3:c.46C>A	p.Leu16Met	p.L16M	ENST00000296474	NM_002447.2	16	Ctg/Atg	1/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.59	2		447	468	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584583	52584583	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs201088500	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	72	629	1	ENST00000394830.3:c.4430C>A	p.Pro1477His	p.P1477H	ENST00000394830	NM_018313.4	1477	cCt/cAt	29/30	1	2	FACETS	0.302	0.263	0.344	0.302	0.263	0.344	SUBCLONAL	1	TRUE	1	0.59	2		630	809	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643650	52643650	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1376146321	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	254	526	0	ENST00000394830.3:c.2246C>A	p.Ala749Asp	p.A749D	ENST00000394830	NM_018313.4	749	gCt/gAt	17/30	1	2	FACETS	0.922	0.875	0.968	1	0.995	1	CLONAL	2	TRUE	1	0.59	2		526	467	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72881575	72881575	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1040831506	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	138	398	2	ENST00000325599.8:c.544C>T	p.Arg182Ter	p.R182*	ENST00000325599	NM_018130.2	182	Cga/Tga	5/11	1	2	FACETS	0.865	0.791	0.941	0.865	0.791	0.941	CLONAL	1	TRUE	1	0.59	2		400	541	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462291	89462291	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs771851703	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	56	325	0	ENST00000336596.2:c.1763T>C	p.Leu588Ser	p.L588S	ENST00000336596	NM_005233.5	588	tTa/tCa	10/17	1	2	FACETS	0.791	0.685	0.904	0.791	0.685	0.904	CLONAL	1	TRUE	1	0.59	2		325	240	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205164	128205164	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	67	604	0	ENST00000341105.2:c.277C>T	p.Pro93Ser	p.P93S	ENST00000341105	NM_032638.4	93	Ccg/Tcg	3/6	1	2	FACETS	0.35	0.304	0.401	0.35	0.304	0.401	SUBCLONAL	1	TRUE	1	0.59	2		604	648	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242884	142242884	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868817417	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	124	469	0	ENST00000350721.4:c.4103G>A	p.Arg1368Gln	p.R1368Q	ENST00000350721	NM_001184.3	1368	cGa/cAa	22/47	1	2	FACETS	0.832	0.757	0.911	0.832	0.757	0.911	CLONAL	1	TRUE	1	0.59	2		469	505	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269089	142269089	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751341031	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	57	442	0	ENST00000350721.4:c.2861G>A	p.Cys954Tyr	p.C954Y	ENST00000350721	NM_001184.3	954	tGc/tAc	14/47	1	2	FACETS	0.359	0.308	0.415	0.359	0.308	0.415	SUBCLONAL	1	TRUE	1	0.59	2		442	538	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446988	187446988	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139744042	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	207	701	1	ENST00000232014.4:c.1205G>A	p.Arg402His	p.R402H	ENST00000232014	NM_001130845.1	402	cGc/cAc	5/10	1	2	FACETS	0.941	0.876	1	0.941	0.876	1	CLONAL	1	TRUE	1	0.59	2		702	746	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801476	1801476	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs200300532	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	130	670	0	ENST00000260795.2:c.382G>A	p.Ala128Thr	p.A128T	ENST00000260795		128	Gct/Act	3/17	1	2	FACETS	0.651	0.591	0.713	0.651	0.591	0.713	SUBCLONAL	1	TRUE	1	0.59	2		670	677	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807147	1807147	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	218	763	1	ENST00000260795.2:c.1478G>A	p.Gly493Asp	p.G493D	ENST00000260795		493	gGc/gAc	10/17	1	2	FACETS	0.954	0.889	1	0.954	0.889	1	CLONAL	1	TRUE	1	0.59	2		764	775	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1918766	1918766	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	53	254	0	ENST00000382891.5:c.927+2T>C		p.X309_splice	ENST00000382891	NM_133335.3	309			1	2	FACETS	0.603	0.517	0.695	0.603	0.517	0.695	SUBCLONAL	1	TRUE	1	0.59	2		254	298	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748140	41748140	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1442934701	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	108	269	0	ENST00000226382.2:c.629C>T	p.Ala210Val	p.A210V	ENST00000226382	NM_003924.3	210	gCg/gTg	3/3	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.59	2		269	331	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981058	55981058	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	67	419	0	ENST00000263923.4:c.641A>G	p.Tyr214Cys	p.Y214C	ENST00000263923	NM_002253.2	214	tAc/tGc	5/30	1	2	FACETS	0.817	0.717	0.923	0.817	0.717	0.923	CLONAL	1	TRUE	1	0.59	2		419	278	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467937	66467937	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	99	383	0	ENST00000273854.3:c.332A>G	p.Asn111Ser	p.N111S	ENST00000273854	NM_004439.5	111	aAc/aGc	3/18	1	2	FACETS	0.919	0.828	1	0.919	0.828	1	CLONAL	1	TRUE	1	0.59	2		383	365	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535448	66535448	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	121	269	0	ENST00000273854.3:c.13G>A	p.Gly5Arg	p.G5R	ENST00000273854	NM_004439.5	5	Ggg/Agg	1/18	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.59	2		269	323	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155865	106155865	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	101	377	0	ENST00000380013.4:c.766G>A	p.Ala256Thr	p.A256T	ENST00000380013	NM_001127208.2	256	Gct/Act	3/11	1	2	FACETS	0.845	0.761	0.934	0.845	0.761	0.934	CLONAL	1	TRUE	1	0.59	2		377	405	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251901	153251901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	56	492	0	ENST00000281708.4:c.1105G>A	p.Glu369Lys	p.E369K	ENST00000281708	NM_033632.3	369	Gaa/Aaa	7/12	1	2	FACETS	0.586	0.505	0.673	0.586	0.505	0.673	SUBCLONAL	1	TRUE	1	0.59	2		492	324	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527265	187527265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373448625	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	173	465	1	ENST00000441802.2:c.10309G>A	p.Ala3437Thr	p.A3437T	ENST00000441802	NM_005245.3	3437	Gcg/Acg	17/27	1	2	FACETS	0.879	0.812	0.949	0.879	0.812	0.949	CLONAL	1	TRUE	1	0.59	2		466	667	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535398	187535398	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	93	470	0	ENST00000441802.2:c.9176C>T	p.Thr3059Ile	p.T3059I	ENST00000441802	NM_005245.3	3059	aCt/aTt	12/27	1	2	FACETS	0.79	0.707	0.877	0.79	0.707	0.877	SUBCLONAL	1	TRUE	1	0.59	2		470	399	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541412	187541412	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	136	390	0	ENST00000441802.2:c.6328A>G	p.Ser2110Gly	p.S2110G	ENST00000441802	NM_005245.3	2110	Agt/Ggt	10/27	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.59	2		390	437	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584691	187584691	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	63	427	0	ENST00000441802.2:c.3342G>T	p.Gln1114His	p.Q1114H	ENST00000441802	NM_005245.3	1114	caG/caT	3/27	1	2	FACETS	0.373	0.322	0.427	0.373	0.322	0.427	SUBCLONAL	1	TRUE	1	0.59	2		427	573	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31451720	31451720	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	15	287	0	ENST00000344624.3:c.2602C>A	p.His868Asn	p.H868N	ENST00000344624		868	Cat/Aat	18/33	1	2	FACETS	0.19	0.138	0.251	0.19	0.138	0.251	SUBCLONAL	1	TRUE	1	0.59	2		287	268	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31464435	31464435	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1471632102	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	196	721	0	ENST00000344624.3:c.2482del	p.Ile828TyrfsTer7	p.I828Yfs*7	ENST00000344624		828	Ata/ta	17/33	1	2	FACETS	0.913	0.848	0.98	0.913	0.848	0.98	CLONAL	1	TRUE	1	0.59	2		721	728	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515249	31515249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	92	740	2	ENST00000344624.3:c.1136G>A	p.Gly379Asp	p.G379D	ENST00000344624		379	gGc/gAc	5/33	1	2	FACETS	0.377	0.334	0.422	0.377	0.334	0.422	SUBCLONAL	1	TRUE	1	0.59	2		742	828	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38960564	38960564	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	18	217	0	ENST00000357387.3:c.1787C>T	p.Ala596Val	p.A596V	ENST00000357387	NM_152756.3	596	gCc/gTc	20/38	1	2	FACETS	0.285	0.215	0.367	0.285	0.215	0.367	SUBCLONAL	1	TRUE	1	0.59	2		217	214	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80083469	80083469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs963584392	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	134	700	2	ENST00000265081.6:c.2521G>A	p.Ala841Thr	p.A841T	ENST00000265081	NM_002439.4	841	Gct/Act	18/24	1	2	FACETS	0.655	0.596	0.717	0.655	0.596	0.717	SUBCLONAL	1	TRUE	1	0.59	2		702	693	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441360	149441360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	71	686	0	ENST00000286301.3:c.1679G>A	p.Ser560Asn	p.S560N	ENST00000286301	NM_005211.3	560	aGt/aAt	12/22	1	2	FACETS	0.3	0.261	0.343	0.3	0.261	0.343	SUBCLONAL	1	TRUE	1	0.59	2		686	801	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504391	149504391	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752228799	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	151	527	0	ENST00000261799.4:c.1811G>A	p.Arg604His	p.R604H	ENST00000261799	NM_002609.3	604	cGc/cAc	13/23	1	2	FACETS	0.871	0.799	0.944	0.871	0.799	0.944	CLONAL	1	TRUE	1	0.59	2		527	588	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721424	176721424	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	137	415	0	ENST00000439151.2:c.7055G>A	p.Arg2352Lys	p.R2352K	ENST00000439151	NM_022455.4	2352	aGa/aAa	23/23	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.59	2		415	447	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31939990	31939990	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777951037	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	121	558	0	ENST00000375333.2:c.217G>A	p.Ala73Thr	p.A73T	ENST00000375333	NM_032454.1	73	Gct/Act	1/8	1	2	FACETS	0.842	0.765	0.922	0.842	0.765	0.922	CLONAL	1	TRUE	1	0.59	2		558	487	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181576	32181576	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	272	717	0	ENST00000375023.3:c.2209C>T	p.Pro737Ser	p.P737S	ENST00000375023	NM_004557.3	737	Cca/Tca	14/30	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.59	2		717	893	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190578	32190578	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1561951240	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	166	518	0	ENST00000375023.3:c.161C>T	p.Ala54Val	p.A54V	ENST00000375023	NM_004557.3	54	gCc/gTc	3/30	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.59	2		518	543	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797263	32797263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	258	689	0	ENST00000374899.4:c.1846G>A	p.Ala616Thr	p.A616T	ENST00000374899	NM_018833.2	616	Gcc/Acc	11/12	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.59	2		689	871	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800549	32800549	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756271450	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	318	672	0	ENST00000374899.4:c.998G>A	p.Arg333Gln	p.R333Q	ENST00000374899	NM_018833.2	333	cGg/cAg	6/12	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.59	2		672	980	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820249	32820249	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550037204	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	75	550	0	ENST00000354258.4:c.809G>A	p.Arg270His	p.R270H	ENST00000354258	NM_000593.5	270	cGc/cAc	2/11	1	2	FACETS	0.317	0.277	0.36	0.317	0.277	0.36	SUBCLONAL	1	TRUE	1	0.59	2		550	802	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139172	37139172	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	137	350	0	ENST00000373509.5:c.515del	p.Asn172ThrfsTer102	p.N172Tfs*102	ENST00000373509	NM_002648.3	171	gAa/ga	4/6	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.59	2		350	417	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553470	106553470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1361366044	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	97	277	0	ENST00000369096.4:c.1435C>T	p.Leu479Phe	p.L479F	ENST00000369096	NM_001198.3	479	Ctc/Ttc	5/7	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.59	2		277	303	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554865	106554865	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	29	358	0	ENST00000369096.4:c.1982G>A	p.Cys661Tyr	p.C661Y	ENST00000369096	NM_001198.3	661	tGc/tAc	7/7	1	2	FACETS	0.224	0.179	0.275	0.224	0.179	0.275	SUBCLONAL	1	TRUE	1	0.59	2		358	439	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641129	117641129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777678761	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	131	580	1	ENST00000368508.3:c.5842C>T	p.Arg1948Cys	p.R1948C	ENST00000368508	NM_002944.2	1948	Cgt/Tgt	36/43	1	2	FACETS	0.729	0.664	0.798	0.729	0.664	0.798	SUBCLONAL	1	TRUE	1	0.59	2		581	609	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708058	117708058	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	45	365	0	ENST00000368508.3:c.2119G>A	p.Val707Met	p.V707M	ENST00000368508	NM_002944.2	707	Gtg/Atg	14/43	1	2	FACETS	0.737	0.626	0.856	0.737	0.626	0.856	SUBCLONAL	1	TRUE	1	0.59	2		365	207	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200393	138200393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564646155	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	48	432	0	ENST00000237289.4:c.1811C>T	p.Thr604Met	p.T604M	ENST00000237289	NM_001270507.1	604	aCg/aTg	7/9	1	2	FACETS	0.293	0.247	0.343	0.293	0.247	0.343	SUBCLONAL	1	TRUE	1	0.59	2		432	556	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005023	150005023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs914634583	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	43	442	1	ENST00000253339.5:c.1202C>T	p.Thr401Ile	p.T401I	ENST00000253339		401	aCa/aTa	3/7	1	2	FACETS	0.346	0.29	0.409	0.346	0.29	0.409	SUBCLONAL	1	TRUE	1	0.59	2		443	421	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976827	2976827	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	222	688	2	ENST00000396946.4:c.1185G>T	p.Gln395His	p.Q395H	ENST00000396946	NM_032415.4	395	caG/caT	9/25	1	2	FACETS	0.919	0.857	0.982	0.919	0.857	0.982	CLONAL	1	TRUE	1	0.59	2		690	819	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940404	13940404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	141	390	0	ENST00000405192.2:c.1102C>T	p.Arg368Cys	p.R368C	ENST00000405192	NM_001163147.1	368	Cgt/Tgt	11/12	1	2	FACETS	0.941	0.863	1	0.941	0.863	1	CLONAL	1	TRUE	1	0.59	2		390	508	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467718	50467718	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	140	465	0	ENST00000331340.3:c.953C>A	p.Ala318Asp	p.A318D	ENST00000331340	NM_006060.4	318	gCc/gAc	8/8	1	2	FACETS	0.934	0.856	1	0.934	0.856	1	CLONAL	1	TRUE	1	0.59	2		465	508	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223559	55223559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	218	489	1	ENST00000275493.2:c.926G>A	p.Arg309Gln	p.R309Q	ENST00000275493	NM_005228.3	309	cGa/cAa	8/28	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.59	2		490	667	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55225397	55225397	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	167	454	0	ENST00000275493.2:c.1249C>A	p.Leu417Ile	p.L417I	ENST00000275493	NM_005228.3	417	Ctc/Atc	11/28	1	2	FACETS	0.951	0.879	1	0.951	0.879	1	CLONAL	1	TRUE	1	0.59	2		454	595	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233015	55233015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1235180640	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	159	345	0	ENST00000275493.2:c.1765C>T	p.Pro589Ser	p.P589S	ENST00000275493	NM_005228.3	589	Ccc/Tcc	15/28	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.59	2		345	528	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508410	106508410	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	47	205	0	ENST00000359195.3:c.404T>C	p.Ile135Thr	p.I135T	ENST00000359195	NM_002649.2	135	aTc/aCc	2/11	1	2	FACETS	0.895	0.767	1	0.895	0.767	1	CLONAL	1	TRUE	1	0.59	2		205	178	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340302	116340302	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	70	279	1	ENST00000397752.3:c.1168del	p.Tyr390ThrfsTer14	p.Y390Tfs*14	ENST00000397752	NM_000245.2	388	caT/ca	2/21	1	2	FACETS	0.882	0.778	0.992	0.882	0.778	0.992	CLONAL	1	TRUE	1	0.59	2		280	269	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412250	116412250	+	intron_variant	Intron	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	95	672	2	ENST00000397752.3:c.3028+207C>T		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.83	0.744	0.92	0.83	0.744	0.92	CLONAL	1	TRUE	1	0.59	2		674	388	SUCCESS
MET	4233	MSKCC	GRCh37	7	116417488	116417488	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060503533	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	27	337	0	ENST00000397752.3:c.3305G>A	p.Gly1102Asp	p.G1102D	ENST00000397752	NM_000245.2	1102	gGc/gAc	16/21	1	2	FACETS	0.356	0.284	0.438	0.356	0.284	0.438	SUBCLONAL	1	TRUE	1	0.59	2		337	257	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841812	151841812	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	90	294	0	ENST00000262189.6:c.14329C>T	p.Arg4777Trp	p.R4777W	ENST00000262189	NM_170606.2	4777	Cgg/Tgg	55/59	1	2	FACETS	0.884	0.792	0.981	0.884	0.792	0.981	CLONAL	1	TRUE	1	0.59	2		294	345	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845229	151845229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	144	412	2	ENST00000262189.6:c.13783C>T	p.Arg4595Cys	p.R4595C	ENST00000262189	NM_170606.2	4595	Cgc/Tgc	52/59	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.59	2		414	475	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194902	29194902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750523072	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	77	673	2	ENST00000240100.2:c.826G>A	p.Val276Met	p.V276M	ENST00000240100	NM_001394.6	276	Gtg/Atg	4/4	1	2	FACETS	0.301	0.263	0.342	0.301	0.263	0.342	SUBCLONAL	1	TRUE	1	0.59	2		675	867	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29195943	29195943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754443801	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	266	691	0	ENST00000240100.2:c.655G>A	p.Ala219Thr	p.A219T	ENST00000240100	NM_001394.6	219	Gcc/Acc	3/4	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.59	2		691	872	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38173035	38173035	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	120	463	1	ENST00000317025.8:c.2014C>A	p.Pro672Thr	p.P672T	ENST00000317025	NM_023034.1	672	Cct/Act	11/24	1	2	FACETS	0.842	0.765	0.923	0.842	0.765	0.923	CLONAL	1	TRUE	1	0.59	2		464	483	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370751	55370751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	150	412	2	ENST00000297316.4:c.53G>A	p.Ser18Asn	p.S18N	ENST00000297316	NM_022454.3	18	aGc/aAc	1/2	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.59	2		414	472	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864734	68864734	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	167	515	0	ENST00000288368.4:c.105G>T	p.Glu35Asp	p.E35D	ENST00000288368	NM_024870.2	35	gaG/gaT	1/40	1	2	FACETS	0.939	0.867	1	0.939	0.867	1	CLONAL	1	TRUE	1	0.59	2		515	603	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046350	69046350	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	85	440	0	ENST00000288368.4:c.3823G>A	p.Val1275Ile	p.V1275I	ENST00000288368	NM_024870.2	1275	Gtc/Atc	32/40	1	2	FACETS	0.494	0.437	0.555	0.494	0.437	0.555	SUBCLONAL	1	TRUE	1	0.59	2		440	583	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069573	69069573	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	53	372	0	ENST00000288368.4:c.4248A>C	p.Glu1416Asp	p.E1416D	ENST00000288368	NM_024870.2	1416	gaA/gaC	35/40	1	2	FACETS	0.768	0.662	0.881	0.768	0.662	0.881	SUBCLONAL	1	TRUE	1	0.59	2		372	234	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129944	69129944	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1344977730	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	86	239	0	ENST00000288368.4:c.4698G>A	p.Met1566Ile	p.M1566I	ENST00000288368	NM_024870.2	1566	atG/atA	38/40	1	2	FACETS	0.87	0.777	0.968	0.87	0.777	0.968	CLONAL	1	TRUE	1	0.59	2		239	335	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752762	128752762	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	46	228	0	ENST00000377970.2:c.923G>T	p.Ser308Ile	p.S308I	ENST00000377970	NM_002467.4	308	aGc/aTc	3/3	1	2	FACETS	0.611	0.519	0.712	0.611	0.519	0.712	SUBCLONAL	1	TRUE	1	0.59	2		228	255	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752788	128752788	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	24	211	0	ENST00000377970.2:c.949G>A	p.Val317Ile	p.V317I	ENST00000377970	NM_002467.4	317	Gtc/Atc	3/3	1	2	FACETS	0.32	0.252	0.399	0.32	0.252	0.399	SUBCLONAL	1	TRUE	1	0.59	2		211	254	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141567297	141567297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768230647	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	200	529	0	ENST00000220592.5:c.917G>A	p.Cys306Tyr	p.C306Y	ENST00000220592	NM_012154.3	306	tGc/tAc	8/19	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.59	2		529	633	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449746	8449746	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1424143158	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	180	535	0	ENST00000356435.5:c.3967C>T	p.Arg1323Cys	p.R1323C	ENST00000356435		1323	Cgc/Tgc	23/35	1	2	FACETS	0.877	0.811	0.944	0.877	0.811	0.944	CLONAL	1	TRUE	1	0.59	2		535	696	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215865	98215865	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	66	522	0	ENST00000331920.6:c.3344C>A	p.Ala1115Asp	p.A1115D	ENST00000331920	NM_000264.3	1115	gCt/gAt	20/24	1	2	FACETS	0.303	0.262	0.347	0.303	0.262	0.347	SUBCLONAL	1	TRUE	1	0.59	2		522	739	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242740	98242740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	63	543	1	ENST00000331920.6:c.877G>A	p.Asp293Asn	p.D293N	ENST00000331920	NM_000264.3	293	Gac/Aac	6/24	1	2	FACETS	0.314	0.271	0.36	0.314	0.271	0.36	SUBCLONAL	1	TRUE	1	0.59	2		544	681	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128322074	128322074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	105	419	1	ENST00000265960.3:c.686C>T	p.Ala229Val	p.A229V	ENST00000265960	NM_001006617.1	229	gCc/gTc	6/12	1	2	FACETS	0.791	0.713	0.873	0.791	0.713	0.873	SUBCLONAL	1	TRUE	1	0.59	2		420	450	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300944	137300944	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	155	511	1	ENST00000481739.1:c.589G>A	p.Ala197Thr	p.A197T	ENST00000481739	NM_002957.4	197	Gcc/Acc	4/10	1	2	FACETS	0.834	0.766	0.904	0.834	0.766	0.904	CLONAL	1	TRUE	1	0.59	2		512	630	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390759	139390759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779039862	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	257	760	1	ENST00000277541.6:c.7432G>A	p.Ala2478Thr	p.A2478T	ENST00000277541	NM_017617.3	2478	Gca/Aca	34/34	1	2	FACETS	0.993	0.932	1	0.993	0.932	1	CLONAL	1	TRUE	1	0.59	2		761	877	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400281	139400281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs864622727	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	80	661	0	ENST00000277541.6:c.4067G>A	p.Arg1356His	p.R1356H	ENST00000277541	NM_017617.3	1356	cGc/cAc	25/34	1	2	FACETS	0.398	0.35	0.45	0.398	0.35	0.45	SUBCLONAL	1	TRUE	1	0.59	2		661	681	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402735	139402735	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	103	828	1	ENST00000277541.6:c.3274C>A	p.Leu1092Ile	p.L1092I	ENST00000277541	NM_017617.3	1092	Ctt/Att	20/34	1	2	FACETS	0.397	0.355	0.442	0.397	0.355	0.442	SUBCLONAL	1	TRUE	1	0.59	2		829	879	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409841	139409841	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779794980	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	160	823	0	ENST00000277541.6:c.1915G>A	p.Glu639Lys	p.E639K	ENST00000277541	NM_017617.3	639	Gag/Aag	12/34	1	2	FACETS	0.597	0.547	0.649	0.597	0.547	0.649	SUBCLONAL	1	TRUE	1	0.59	2		823	909	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412721	139412721	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	250	730	2	ENST00000277541.6:c.1123G>A	p.Ala375Thr	p.A375T	ENST00000277541	NM_017617.3	375	Gca/Aca	7/34	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.59	2		732	801	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841144	15841144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	122	222	0	ENST00000307771.7:c.1228C>T	p.Arg410Cys	p.R410C	ENST00000307771	NM_005089.3	410	Cgc/Tgc	11/11	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.59	1		222	215	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933028	39933028	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	261	378	0	ENST00000378444.4:c.1571G>A	p.Ser524Asn	p.S524N	ENST00000378444	NM_001123385.1	524	aGc/aAc	4/15	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.59	1		378	426	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934165	39934165	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	229	320	0	ENST00000378444.4:c.434T>C	p.Phe145Ser	p.F145S	ENST00000378444	NM_001123385.1	145	tTc/tCc	4/15	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.59	1		320	379	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44935952	44935952	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	19	162	0	ENST00000377967.4:c.2717del	p.Asn906MetfsTer31	p.N906Mfs*31	ENST00000377967	NM_021140.2	905	Aaa/aa	18/29	1	1	FACETS	0.331	0.254	0.421	0.331	0.254	0.421	SUBCLONAL	1	TRUE	0	0.59	1		162	137	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412545	63412545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772338892	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	190	289	0	ENST00000330258.3:c.622G>A	p.Val208Met	p.V208M	ENST00000330258	NM_152424.3	208	Gtg/Atg	2/2	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.59	1		289	315	SUCCESS
AR	367	MSKCC	GRCh37	X	66765679	66765679	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	238	409	0	ENST00000374690.3:c.691A>G	p.Thr231Ala	p.T231A	ENST00000374690	NM_000044.3	231	Acc/Gcc	1/8	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.59	1		409	442	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939320	76939320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	34	376	0	ENST00000373344.5:c.1428G>T	p.Gln476His	p.Q476H	ENST00000373344	NM_000489.3	476	caG/caT	9/35	1	1	FACETS	0.373	0.307	0.446	0.373	0.307	0.446	SUBCLONAL	1	TRUE	0	0.59	1		376	218	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224544	123224544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1400154883	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	16	290	0	ENST00000218089.9:c.3397C>T	p.Arg1133Trp	p.R1133W	ENST00000218089	NM_001042749.1	1133	Cgg/Tgg	31/35	1	1	FACETS	0.132	0.097	0.173	0.132	0.097	0.173	SUBCLONAL	1	TRUE	0	0.59	1		290	290	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152857973	152857973	+	synonymous_variant	Silent	SNP	C	C	T	rs782152074	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	44	89	0	ENST00000406277.2:c.642G>A	p.Pro214=	p.P214=	ENST00000406277	NM_152274.4	214	ccG/ccA	6/7	1	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.59	1		89	71	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881329	37881332	+	missense_variant	Missense_Mutation	ONP	CTCG	CTCG	ATCA	novel	NA	P-0033425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	142	655	0	ENST00000269571.5:c.2521_2524delinsATCA	p.Leu841_Val842delinsIleIle	p.L841_V842delinsII	ENST00000269571		841	CTCGta/ATCAta	21/27	1	2	FACETS	0.685	0.625	0.747	0.685	0.625	0.747	SUBCLONAL	1	TRUE	1	0.59	2		655	703	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	136	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.706001864801516	2		215	310	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200975	108200975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	190	414	0	ENST00000278616.4:c.7342G>A	p.Asp2448Asn	p.D2448N	ENST00000278616	NM_000051.3	2448	Gat/Aat	50/63	1	2	FACETS	0.941	0.876	1	0.941	0.876	1	CLONAL	1	TRUE	1	0.706001864801516	2		414	572	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913409	NA	P-0033633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	168	301	1	ENST00000349496.5:c.134C>A	p.Ser45Tyr	p.S45Y	ENST00000349496	NM_001904.3	45	tCt/tAt	3/15	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.706001864801516	2		302	469	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193202218	193202238	+	inframe_deletion	In_Frame_Del	DEL	CTGCAATTAGTGTTACAGTAC	CTGCAATTAGTGTTACAGTAC	-	novel	NA	P-0033633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	133	405	0	ENST00000367435.3:c.1252_1272del	p.Ala418_Pro424del	p.A418_P424del	ENST00000367435	NM_024529.4	417	aCTGCAATTAGTGTTACAGTACct/act	14/17	0.706001864801516	3	FACETS	0.608	0.552	0.666	0.304	0.276	0.333	SUBCLONAL	1	TRUE	1	0.706001864801516	3		405	839	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218044	108218044	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519869	NA	P-0033633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	194	372	0	ENST00000278616.4:c.8623A>C	p.Asn2875His	p.N2875H	ENST00000278616	NM_000051.3	2875	Aat/Cat	59/63	1	2	FACETS	0.946	0.881	1	0.946	0.881	1	CLONAL	1	TRUE	1	0.706001864801516	2		372	581	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021187	31021188	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	285	512	1	ENST00000375687.4:c.1187dup	p.Arg397AlafsTer13	p.R397Afs*13	ENST00000375687	NM_015338.5	396	cag/cAag	12/13	1	2	FACETS	0.974	0.919	1	0.974	0.919	1	CLONAL	1	TRUE	1	0.706001864801516	2		513	829	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275342	41275342	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	159	358	1	ENST00000349496.5:c.1508A>C	p.His503Pro	p.H503P	ENST00000349496	NM_001904.3	503	cAc/cCc	9/15	1	2	FACETS	0.933	0.862	1	0.933	0.862	1	CLONAL	1	TRUE	1	0.706001864801516	2		359	483	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438519	52438520	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCATCCTCATCA	novel	NA	P-0033633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	260	682	0	ENST00000460680.1:c.1188_1199dup	p.Asp397_Asp400dup	p.D397_D400dup	ENST00000460680	NM_004656.3	397	gac/gaTGATGAGGATGAc	12/17	1	2	FACETS	0.729	0.684	0.776	0.729	0.684	0.776	SUBCLONAL	1	TRUE	1	0.706001864801516	2		682	1010	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030628	47030628	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	338	340	0	ENST00000377604.3:c.403A>T	p.Met135Leu	p.M135L	ENST00000377604	NM_001204468.1	135	Atg/Ttg	4/24	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.706001864801516	1		340	493	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	45	430	0				ENST00000310581	NM_198253.2	-/1132			0.314282514213794	1	FACETS	0.856	0.735	0.983	1	0.97	1	CLONAL	2	TRUE	0	0.314282514213794	1		430	141	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013719	170013719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388201066	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	174	374	0	ENST00000295797.4:c.1438C>T	p.Arg480Cys	p.R480C	ENST00000295797	NM_002740.5	480	Cgc/Tgc	15/18	1	2	FACETS	0.871	0.805	0.938	1	0.992	1	CLONAL	2	TRUE	1	0.314282514213794	2		374	636	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873660	35873660	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs201559094	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	71	257	0	ENST00000303115.3:c.616C>T	p.Arg206Ter	p.R206*	ENST00000303115	NM_002185.3	206	Cga/Tga	5/8	0.314282514213794	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.314282514213794	1		257	352	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832265	72832265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267604632	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	151	396	0	ENST00000268489.5:c.4316G>A	p.Arg1439Gln	p.R1439Q	ENST00000268489	NM_006885.3	1439	cGa/cAa	9/10	1	2	FACETS	0.92	0.847	0.996	1	0.991	1	CLONAL	2	TRUE	1	0.314282514213794	2		396	522	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426731	47426731	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1452639448	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	227	503	2	ENST00000377045.4:c.976C>T	p.Arg326Ter	p.R326*	ENST00000377045	NM_001654.4	326	Cga/Tga	10/16	1	2	FACETS	1	0.951	1	1	0.994	1	CLONAL	2	TRUE	1	0.314282514213794	2		505	709	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220636	2220636	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768139800	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	190	503	0	ENST00000326181.6:c.253C>T	p.Arg85Cys	p.R85C	ENST00000326181	NM_032271.2	85	Cgc/Tgc	5/21	1	2	FACETS	1	0.97	1	1	0.994	1	CLONAL	2	TRUE	1	0.314282514213794	2		503	563	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546931	9546931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs562732119	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	146	341	0	ENST00000353224.5:c.1091C>T	p.Ser364Leu	p.S364L	ENST00000353224	NM_177990.2	364	tCg/tTg	5/10	1	2	FACETS	0.958	0.881	1	1	0.991	1	CLONAL	2	TRUE	1	0.314282514213794	2		341	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	270	653	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	1	2	FACETS	0.998	0.939	1	1	0.995	1	CLONAL	2	TRUE	1	0.314282514213794	2		653	861	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239513	123239513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1032609119	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	283	805	0	ENST00000358487.5:c.2324C>T	p.Pro775Leu	p.P775L	ENST00000358487	NM_000141.4	775	cCt/cTt	18/18	1	2	FACETS	0.925	0.87	0.98	1	0.995	1	CLONAL	2	TRUE	1	0.314282514213794	2		805	974	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500891	8500891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	179	441	0	ENST00000356435.5:c.1991G>A	p.Gly664Glu	p.G664E	ENST00000356435		664	gGa/gAa	13/35	1	2	FACETS	0.956	0.886	1	1	0.993	1	CLONAL	2	TRUE	1	0.314282514213794	2		441	596	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850341	128850341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121918347	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	230	491	0	ENST00000249373.3:c.1604G>T	p.Trp535Leu	p.W535L	ENST00000249373	NM_005631.4	535	tGg/tTg	9/12	1	2	FACETS	1	0.977	1	1	0.995	1	CLONAL	2	TRUE	1	0.314282514213794	2		491	674	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976476	25976476	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	361	486	0	ENST00000435504.4:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000435504		357	Cga/Tga	11/13	1	2	FACETS	0.929	0.892	0.967	1	0.997	1	CLONAL	4	TRUE	1	0.314282514213794	2		486	618	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696719	47696719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	139	366	0	ENST00000347630.2:c.229G>A	p.Asp77Asn	p.D77N	ENST00000347630	NM_001007230.1	77	Gat/Aat	5/11	1	2	FACETS	0.961	0.882	1	1	0.991	1	CLONAL	2	TRUE	1	0.314282514213794	2		366	460	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622457	28622457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751562024	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	198	478	0	ENST00000241453.7:c.1160G>A	p.Arg387Gln	p.R387Q	ENST00000241453	NM_004119.2	387	cGa/cAa	9/24	1	2	FACETS	0.94	0.875	1	1	0.993	1	CLONAL	2	TRUE	1	0.314282514213794	2		478	670	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139714	55139714	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600186	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	145	321	0	ENST00000257290.5:c.1375G>A	p.Glu459Lys	p.E459K	ENST00000257290	NM_006206.4	459	Gaa/Aaa	10/23	1	2	FACETS	0.947	0.871	1	1	0.991	1	CLONAL	2	TRUE	1	0.314282514213794	2		321	487	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259433	89259433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	203	512	0	ENST00000336596.2:c.577G>A	p.Val193Met	p.V193M	ENST00000336596	NM_005233.5	193	Gtg/Atg	3/17	1	2	FACETS	0.951	0.886	1	1	0.993	1	CLONAL	2	TRUE	1	0.314282514213794	2		512	679	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098576	108098576	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1800054	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	129	300	0	ENST00000278616.4:c.146C>T	p.Ser49Phe	p.S49F	ENST00000278616	NM_000051.3	49	tCc/tTc	3/63	1	2	FACETS	0.944	0.862	1	1	0.99	1	CLONAL	2	TRUE	1	0.314282514213794	2		300	435	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609831	117609831	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	182	600	0	ENST00000368508.3:c.6868G>A	p.Gly2290Ser	p.G2290S	ENST00000368508	NM_002944.2	2290	Ggt/Agt	43/43	0.308254347597006	4	FACETS	0.763	0.703	0.825	0.508	0.469	0.55	SUBCLONAL	2	TRUE	1	0.314282514213794	4		600	998	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852332	63852332	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	179	383	0	ENST00000279873.7:c.3110C>T	p.Ser1037Phe	p.S1037F	ENST00000279873	NM_032199.2	1037	tCc/tTc	10/10	1	2	FACETS	1	0.959	1	1	0.993	1	CLONAL	2	TRUE	1	0.314282514213794	2		383	544	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999621	100999621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	284	771	0	ENST00000325455.5:c.181C>T	p.Pro61Ser	p.P61S	ENST00000325455	NM_001202474.3	61	Cct/Tct	1/8	1	2	FACETS	1	0.955	1	1	0.995	1	CLONAL	2	TRUE	1	0.314282514213794	2		771	890	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759803	133759803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	188	431	0	ENST00000318560.5:c.2126C>T	p.Ser709Phe	p.S709F	ENST00000318560	NM_005157.4	709	tCc/tTc	11/11	1	2	FACETS	1	0.983	1	1	0.994	1	CLONAL	2	TRUE	1	0.314282514213794	2		431	514	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723473	52723473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	214	486	1	ENST00000322088.6:c.1334C>T	p.Ser445Phe	p.S445F	ENST00000322088	NM_014225.5	445	tCc/tTc	11/15	1	2	FACETS	0.983	0.917	1	1	0.994	1	CLONAL	2	TRUE	1	0.314282514213794	2		487	693	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69230522	69230522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	159	337	0	ENST00000462284.1:c.911C>T	p.Ser304Phe	p.S304F	ENST00000462284	NM_002392.5	304	tCc/tTc	10/11	1	2	FACETS	1	0.927	1	1	0.992	1	CLONAL	2	TRUE	1	0.314282514213794	2		337	504	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997433	149997433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	269	574	1	ENST00000253339.5:c.2846C>T	p.Pro949Leu	p.P949L	ENST00000253339		949	cCt/cTt	6/7	0.308254347597006	4	FACETS	0.991	0.929	1	0.661	0.619	0.703	CLONAL	2	TRUE	1	0.314282514213794	4		575	1135	SUCCESS
AR	367	MSKCC	GRCh37	X	66766114	66766114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	148	407	0	ENST00000374690.3:c.1126C>T	p.Pro376Ser	p.P376S	ENST00000374690	NM_000044.3	376	Ccc/Tcc	1/8	1	2	FACETS	0.882	0.81	0.956	1	0.99	1	CLONAL	2	TRUE	1	0.314282514213794	2		407	534	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68292235	68292235	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200355697	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	207	425	1	ENST00000487270.1:c.139C>T	p.Arg47Ter	p.R47*	ENST00000487270	NM_133509.3	47	Cga/Tga	3/11	1	2	FACETS	0.937	0.873	1	1	0.993	1	CLONAL	2	TRUE	1	0.314282514213794	2		426	703	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186711	11186711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	212	437	0	ENST00000361445.4:c.6494C>T	p.Ser2165Phe	p.S2165F	ENST00000361445	NM_004958.3	2165	tCc/tTc	46/58	1	2	FACETS	0.983	0.918	1	1	0.994	1	CLONAL	2	TRUE	1	0.314282514213794	2		437	686	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262543	16262543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	121	321	0	ENST00000375759.3:c.9808C>T	p.Leu3270Phe	p.L3270F	ENST00000375759	NM_015001.2	3270	Ctc/Ttc	11/15	1	2	FACETS	0.985	0.898	1	1	0.99	1	CLONAL	2	TRUE	1	0.314282514213794	2		321	391	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468014	120468014	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	268	574	0	ENST00000256646.2:c.4425T>A	p.Tyr1475Ter	p.Y1475*	ENST00000256646	NM_024408.3	1475	taT/taA	25/34	1	2	FACETS	1	0.973	1	1	0.995	1	CLONAL	2	TRUE	1	0.314282514213794	2		574	808	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390715	118390715	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	148	308	0	ENST00000534358.1:c.11365C>T	p.Arg3789Cys	p.R3789C	ENST00000534358	NM_005933.3	3789	Cgt/Tgt	33/36	1	2	FACETS	1	0.922	1	1	0.992	1	CLONAL	2	TRUE	1	0.314282514213794	2		308	470	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170258	119170258	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	89	265	0	ENST00000264033.4:c.2488A>T	p.Arg830Ter	p.R830*	ENST00000264033	NM_005188.3	830	Aga/Tga	16/16	1	2	FACETS	0.963	0.864	1	1	0.986	1	CLONAL	2	TRUE	1	0.314282514213794	2		265	294	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287415	46287415	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	149	315	0	ENST00000334344.6:c.5274T>G	p.Asp1758Glu	p.D1758E	ENST00000334344	NM_152641.2	1758	gaT/gaG	20/21	1	2	FACETS	0.984	0.905	1	1	0.992	1	CLONAL	2	TRUE	1	0.314282514213794	2		315	482	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422934	49422934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777064703	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	215	525	0	ENST00000301067.7:c.14161C>T	p.Arg4721Cys	p.R4721C	ENST00000301067	NM_003482.3	4721	Cgt/Tgt	44/54	1	2	FACETS	1	0.962	1	1	0.994	1	CLONAL	2	TRUE	1	0.314282514213794	2		525	656	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435122	49435126	+	frameshift_variant	Frame_Shift_Del	DEL	TTCAG	TTCAG	-	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	126	378	0	ENST00000301067.7:c.6427_6431del	p.Leu2143AlafsTer10	p.L2143Afs*10	ENST00000301067	NM_003482.3	2143	CTGAAg/g	31/54	1	2	FACETS	0.905	0.826	0.987	1	0.989	1	CLONAL	2	TRUE	1	0.314282514213794	2		378	443	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123892054	123892054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	143	311	0	ENST00000330479.4:c.863G>A	p.Arg288Lys	p.R288K	ENST00000330479	NM_020382.3	288	aGa/aAa	8/9	1	2	FACETS	1	0.919	1	1	0.991	1	CLONAL	2	TRUE	1	0.314282514213794	2		311	455	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578217	28578217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	181	463	1	ENST00000241453.7:c.2954C>T	p.Ser985Phe	p.S985F	ENST00000241453	NM_004119.2	985	tCt/tTt	24/24	1	2	FACETS	0.927	0.86	0.997	1	0.993	1	CLONAL	2	TRUE	1	0.314282514213794	2		464	621	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73352471	73352471	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	245	563	0	ENST00000377767.4:c.434A>T	p.Asn145Ile	p.N145I	ENST00000377767	NM_014953.3	145	aAt/aTt	3/21	1	2	FACETS	0.967	0.907	1	1	0.995	1	CLONAL	2	TRUE	1	0.314282514213794	2		563	806	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656502	3656502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	320	711	0	ENST00000294008.3:c.733C>T	p.Pro245Ser	p.P245S	ENST00000294008	NM_032444.2	245	Cct/Tct	3/15	1	2	FACETS	1	0.973	1	1	0.996	1	CLONAL	2	TRUE	1	0.314282514213794	2		711	975	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032234	10032235	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	200	534	0	ENST00000330684.3:c.588_589delinsAA	p.Gly197Ser	p.G197S	ENST00000330684	NM_001134407.1	196	gtGGgc/gtAAgc	3/13	1	2	FACETS	0.903	0.839	0.968	1	0.993	1	CLONAL	2	TRUE	1	0.314282514213794	2		534	705	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984858	72984858	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	140	330	0	ENST00000268489.5:c.2726G>A	p.Gly909Asp	p.G909D	ENST00000268489	NM_006885.3	909	gGt/gAt	3/10	1	2	FACETS	0.992	0.911	1	1	0.991	1	CLONAL	2	TRUE	1	0.314282514213794	2		330	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579891	7579891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	223	504	0	ENST00000269305.4:c.22C>T	p.Pro8Ser	p.P8S	ENST00000269305	NM_001126112.2	8	Cct/Tct	2/11	1	2	FACETS	1	0.971	1	1	0.995	1	CLONAL	2	TRUE	1	0.314282514213794	2		504	666	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989339	7989339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	175	496	0	ENST00000319144.4:c.347C>T	p.Ala116Val	p.A116V	ENST00000319144	NM_001139.2	116	gCc/gTc	2/15	1	2	FACETS	0.907	0.839	0.977	1	0.992	1	CLONAL	2	TRUE	1	0.314282514213794	2		496	614	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245948	41245948	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs142074233	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	291	735	0	ENST00000357654.3:c.1600C>T	p.Gln534Ter	p.Q534*	ENST00000357654	NM_007294.3	534	Cag/Tag	10/23	1	2	FACETS	0.932	0.878	0.987	1	0.995	1	CLONAL	2	TRUE	1	0.314282514213794	2		735	994	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533883	63533883	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780894296	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	137	378	0	ENST00000307078.5:c.1271C>T	p.Ser424Phe	p.S424F	ENST00000307078	NM_004655.3	424	tCc/tTc	6/11	1	2	FACETS	0.874	0.8	0.95	1	0.99	1	CLONAL	2	TRUE	1	0.314282514213794	2		378	499	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39595469	39595469	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	153	368	0	ENST00000262039.4:c.1355C>T	p.Ser452Leu	p.S452L	ENST00000262039	NM_002647.2	452	tCa/tTa	12/25	1	2	FACETS	0.991	0.914	1	1	0.992	1	CLONAL	2	TRUE	1	0.314282514213794	2		368	491	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168972	11168972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	185	447	0	ENST00000358026.2:c.4562C>T	p.Pro1521Leu	p.P1521L	ENST00000358026	NM_001128849.1	1521	cCc/cTc	32/36	1	2	FACETS	0.94	0.872	1	1	0.993	1	CLONAL	2	TRUE	1	0.314282514213794	2		447	626	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212195	36212195	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1436747286	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	204	533	0	ENST00000222270.7:c.1946C>T	p.Ala649Val	p.A649V	ENST00000222270	NM_014727.1	649	gCc/gTc	3/37	1	2	FACETS	1	0.978	1	1	0.994	1	CLONAL	2	TRUE	1	0.314282514213794	2		533	584	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213531	36213531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	316	840	2	ENST00000222270.7:c.2633C>T	p.Ala878Val	p.A878V	ENST00000222270	NM_014727.1	878	gCc/gTc	5/37	1	2	FACETS	0.977	0.923	1	1	0.996	1	CLONAL	2	TRUE	1	0.314282514213794	2		842	1029	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483981	212483982	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	114	413	0	ENST00000342788.4:c.2221_2222delinsAA	p.Gly741Lys	p.G741K	ENST00000342788	NM_005235.2	741	GGa/AAa	19/28	1	2	FACETS	0.773	0.7	0.85	1	0.985	1	SUBCLONAL	2	TRUE	1	0.314282514213794	2		413	469	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775521	39775521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	210	532	0	ENST00000288319.7:c.499G>A	p.Glu167Lys	p.E167K	ENST00000288319	NM_182918.3	167	Gaa/Aaa	4/10	1	2	FACETS	0.891	0.83	0.954	1	0.993	1	CLONAL	2	TRUE	1	0.314282514213794	2		532	750	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456467	89456467	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1386464909	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	167	409	0	ENST00000336596.2:c.1643C>T	p.Ser548Leu	p.S548L	ENST00000336596	NM_005233.5	548	tCa/tTa	8/17	1	2	FACETS	0.937	0.866	1	1	0.992	1	CLONAL	2	TRUE	1	0.314282514213794	2		409	567	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199891	128199891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	154	372	0	ENST00000341105.2:c.1414C>T	p.Pro472Ser	p.P472S	ENST00000341105	NM_032638.4	472	Ccg/Tcg	6/6	1	2	FACETS	1	0.943	1	1	0.992	1	CLONAL	2	TRUE	1	0.314282514213794	2		372	477	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447657	187447657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	219	480	1	ENST00000232014.4:c.536C>T	p.Ala179Val	p.A179V	ENST00000232014	NM_001130845.1	179	gCc/gTc	5/10	1	2	FACETS	1	0.978	1	1	0.995	1	CLONAL	2	TRUE	1	0.314282514213794	2		481	634	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517762	187517762	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	110	206	0	ENST00000441802.2:c.12932C>T	p.Pro4311Leu	p.P4311L	ENST00000441802	NM_005245.3	4311	cCa/cTa	25/27	1	2	FACETS	0.842	0.769	0.917	1	0.991	1	CLONAL	3	TRUE	1	0.314282514213794	2		206	277	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629840	187629840	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	242	549	0	ENST00000441802.2:c.1142C>T	p.Pro381Leu	p.P381L	ENST00000441802	NM_005245.3	381	cCt/cTt	2/27	1	2	FACETS	0.94	0.881	1	1	0.994	1	CLONAL	2	TRUE	1	0.314282514213794	2		549	819	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449772	149449772	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1428002377	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	92	477	0	ENST00000286301.3:c.1292G>A	p.Trp431Ter	p.W431*	ENST00000286301	NM_005211.3	431	tGg/tAg	9/22	0.314282514213794	1	FACETS	0.91	0.811	1	0.91	0.811	1	CLONAL	1	TRUE	0	0.314282514213794	1		477	542	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057098	180057098	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773696166	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	117	536	1	ENST00000261937.6:c.521C>T	p.Ser174Leu	p.S174L	ENST00000261937	NM_182925.4	174	tCg/tTg	5/30	0.314282514213794	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.314282514213794	1		537	538	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120708	94120708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	379	425	1	ENST00000369303.4:c.343G>A	p.Val115Ile	p.V115I	ENST00000369303	NM_004440.3	115	Gta/Ata	3/17	0.308254347597006	4	FACETS	1	0.959	1	1	0.995	1	CLONAL	4	TRUE	1	0.314282514213794	4		426	790	SUCCESS
MET	4233	MSKCC	GRCh37	7	116414025	116414025	+	intron_variant	Intron	SNP	C	C	T	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	425	846	2	ENST00000397752.3:c.3029-910C>T		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	1	0.984	1	1	0.997	1	CLONAL	2	TRUE	1	0.314282514213794	2		848	1263	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624435	140624435	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	20	39	0	ENST00000288602.6:c.69G>A	p.Met23Ile	p.M23I	ENST00000288602	NM_004333.4	23	atG/atA	1/18	1	2	FACETS	0.943	0.761	1	1	0.956	1	CLONAL	3	TRUE	1	0.314282514213794	2		39	45	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860539	151860539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	231	547	0	ENST00000262189.6:c.10123C>T	p.Pro3375Ser	p.P3375S	ENST00000262189	NM_170606.2	3375	Cca/Tca	43/59	1	2	FACETS	0.999	0.935	1	1	0.994	1	CLONAL	2	TRUE	1	0.314282514213794	2		547	736	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38314943	38314943	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1259538191	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	221	526	0	ENST00000425967.3:c.121C>T	p.Leu41Phe	p.L41F	ENST00000425967	NM_001174067.1	41	Ctc/Ttc	3/19	1	2	FACETS	0.912	0.851	0.974	1	0.994	1	CLONAL	2	TRUE	1	0.314282514213794	2		526	771	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500780	8500780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	161	340	0	ENST00000356435.5:c.2102C>T	p.Ser701Phe	p.S701F	ENST00000356435		701	tCc/tTc	13/35	1	2	FACETS	1	0.969	1	1	0.993	1	CLONAL	2	TRUE	1	0.314282514213794	2		340	470	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231352	98231353	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	295	578	1	ENST00000331920.6:c.1930_1931delinsTT	p.Pro644Phe	p.P644F	ENST00000331920	NM_000264.3	644	CCc/TTc	14/24	1	2	FACETS	1	0.97	1	1	0.996	1	CLONAL	2	TRUE	1	0.314282514213794	2		579	900	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395129	139395129	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	215	639	0	ENST00000277541.6:c.5809C>G	p.Arg1937Gly	p.R1937G	ENST00000277541	NM_017617.3	1937	Cgc/Ggc	31/34	1	2	FACETS	0.966	0.902	1	1	0.994	1	CLONAL	2	TRUE	1	0.314282514213794	2		639	708	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933583	39933583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778095	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	177	488	0	ENST00000378444.4:c.1016C>T	p.Pro339Leu	p.P339L	ENST00000378444	NM_001123385.1	339	cCg/cTg	4/15	1	2	FACETS	0.91	0.842	0.979	1	0.992	1	CLONAL	2	TRUE	1	0.314282514213794	2		488	619	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941870	44941870	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	180	360	0	ENST00000377967.4:c.3194C>A	p.Ser1065Tyr	p.S1065Y	ENST00000377967	NM_021140.2	1065	tCt/tAt	21/29	1	2	FACETS	0.939	0.87	1	1	0.993	1	CLONAL	2	TRUE	1	0.314282514213794	2		360	610	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430276	47430276	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	241	485	0	ENST00000377045.4:c.1552-1G>A		p.X518_splice	ENST00000377045	NM_001654.4	518			1	2	FACETS	1	0.97	1	1	0.995	1	CLONAL	2	TRUE	1	0.314282514213794	2		485	727	SUCCESS
AR	367	MSKCC	GRCh37	X	66766474	66766474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	146	357	0	ENST00000374690.3:c.1486G>A	p.Asp496Asn	p.D496N	ENST00000374690	NM_000044.3	496	Gac/Aac	1/8	1	2	FACETS	0.978	0.899	1	1	0.991	1	CLONAL	2	TRUE	1	0.314282514213794	2		357	475	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344179	70344179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	151	393	0	ENST00000374080.3:c.1915G>A	p.Asp639Asn	p.D639N	ENST00000374080		639	Gat/Aat	13/45	1	2	FACETS	0.965	0.888	1	1	0.992	1	CLONAL	2	TRUE	1	0.314282514213794	2		393	498	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351450	70351450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	198	510	1	ENST00000374080.3:c.4098G>A	p.Met1366Ile	p.M1366I	ENST00000374080		1366	atG/atA	29/45	1	2	FACETS	0.918	0.854	0.985	1	0.993	1	CLONAL	2	TRUE	1	0.314282514213794	2		511	686	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778880	76778880	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	153	467	0	ENST00000373344.5:c.6700-1G>A		p.X2234_splice	ENST00000373344	NM_000489.3	2234			1	2	FACETS	0.857	0.788	0.928	1	0.99	1	CLONAL	2	TRUE	1	0.314282514213794	2		467	568	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182879	123182879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	160	278	0	ENST00000218089.9:c.844G>A	p.Glu282Lys	p.E282K	ENST00000218089	NM_001042749.1	282	Gaa/Aaa	10/35	1	2	FACETS	0.99	0.915	1	1	0.992	1	CLONAL	2	TRUE	1	0.314282514213794	2		278	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0033715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	181	417	1	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.682000261565304	4	FACETS	0.988	0.947	1	0.988	0.947	1	CLONAL	4	FALSE	0	0.682000261565304	4		418	226	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41525914	41525914	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs773503228	NA	P-0033715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	45	419	0	ENST00000263253.7:c.1189C>T	p.Arg397Ter	p.R397*	ENST00000263253	NM_001429.3	397	Cga/Tga	5/31	0.679174344867464	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	FALSE	0	0.682000261565304	2		419	56	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924980	49924980	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	81	504	0	ENST00000296474.3:c.3963G>T	p.Gln1321His	p.Q1321H	ENST00000296474	NM_002447.2	1321	caG/caT	20/20	0.385777426823031	5	FACETS	0.989	0.885	1	0.659	0.59	0.731	INDETERMINATE	2	FALSE	2	0.682000261565304	5		504	243	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0033836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	166	429	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.267862595344812	3	FACETS	1	0.982	1	0.789	0.733	0.847	CLONAL	2	TRUE	0	0.38	3		429	439	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0033836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	185	179	0				ENST00000310581	NM_198253.2	-/1132			0.299290227092691	6	FACETS	1	0.98	1	0.852	0.793	0.911	CLONAL	3	TRUE	2	0.38	6		179	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0033836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	317	823	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.181971464258117	4	FACETS	0.931	0.883	0.981			1	INDETERMINATE	3	TRUE	NA	0.38	4		823	824	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916248	9916248	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397518472	NA	P-0033836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	38	390	1	ENST00000330684.3:c.2041C>T	p.Arg681Ter	p.R681*	ENST00000330684	NM_001134407.1	681	Cga/Tga	10/13	0.230351287582309	3	FACETS	0.588	0.486	0.701	0.294	0.243	0.351	SUBCLONAL	1	TRUE	1	0.38	3		391	405	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409769	139409769	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	142	813	0	ENST00000277541.6:c.1987G>T	p.Glu663Ter	p.E663*	ENST00000277541	NM_017617.3	663	Gag/Tag	12/34	0.125196469939784	4	FACETS	1	0.984	1	0.673	0.614	0.735	INDETERMINATE	1	TRUE	2	0.38	4		813	766	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510233	120510233	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	176	381	0	ENST00000256646.2:c.1276C>T	p.Pro426Ser	p.P426S	ENST00000256646	NM_024408.3	426	Cct/Tct	8/34	0.299290227092691	3	FACETS	0.885	0.826	0.946	0.885	0.826	0.946	CLONAL	3	TRUE	0	0.38	3		381	415	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822285	72822285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781775682	NA	P-0033836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	120	836	1	ENST00000268489.5:c.9890C>T	p.Ser3297Leu	p.S3297L	ENST00000268489	NM_006885.3	3297	tCg/tTg	10/10	0.230351287582309	3	FACETS	0.95	0.858	1	0.475	0.429	0.524	CLONAL	1	TRUE	1	0.38	3		837	791	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403372	139403372	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375260339	NA	P-0033836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	54	775	2	ENST00000277541.6:c.3121G>A	p.Gly1041Ser	p.G1041S	ENST00000277541	NM_017617.3	1041	Ggc/Agc	19/34	0.125196469939784	4	FACETS	0.522	0.445	0.607	0.261	0.222	0.304	INDETERMINATE	1	TRUE	2	0.38	4		777	751	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224190	36224190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	65	786	0	ENST00000222270.7:c.6740G>A	p.Gly2247Glu	p.G2247E	ENST00000222270	NM_014727.1	2247	gGa/gAa	28/37	1	2	FACETS	0.596	0.517	0.682	0.596	0.517	0.682	SUBCLONAL	1	TRUE	1	0.38	2		786	574	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576147	88576147	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	149	803	1	ENST00000360948.2:c.1526C>T	p.Pro509Leu	p.P509L	ENST00000360948	NM_001012338.2	509	cCt/cTt	13/19	0.230351287582309	3	FACETS	1	0.986	1	0.688	0.63	0.749	CLONAL	1	TRUE	1	0.38	3		804	678	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224158	39224158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	77	301	0	ENST00000402219.2:c.2986C>T	p.Pro996Ser	p.P996S	ENST00000402219	NM_005633.3	996	Ccg/Tcg	19/23	0.235204860474955	3	FACETS	1	0.971	1	0.67	0.592	0.752	CLONAL	1	TRUE	1	0.38	3		301	360	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115601	108115601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56123940	NA	P-0033836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	93	385	0	ENST00000278616.4:c.749G>A	p.Arg250Gln	p.R250Q	ENST00000278616	NM_000051.3	250	cGa/cAa	7/63	0.198969968275407	5	FACETS	0.869	0.777	0.967	0.58	0.518	0.645	INDETERMINATE	2	TRUE	2	0.38	5		385	442	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465551	99465552	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	100	666	2	ENST00000268035.6:c.2376_2377delinsTT	p.Leu793Phe	p.L793F	ENST00000268035	NM_000875.3	792	aaCCtt/aaTTtt	11/21	0.230351287582309	3	FACETS	1	0.962	1	0.58	0.52	0.644	CLONAL	1	TRUE	1	0.38	3		668	540	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15960889	15960889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774844897	NA	P-0033836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	79	346	0	ENST00000268712.3:c.6331C>T	p.His2111Tyr	p.H2111Y	ENST00000268712	NM_006311.3	2111	Cat/Tat	40/46	0.168936763553782	3	FACETS	1	0.974	1	0.693	0.614	0.777	INDETERMINATE	1	TRUE	1	0.38	3		346	357	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223985	36223985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766396530	NA	P-0033836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	93	1033	0	ENST00000222270.7:c.6535C>T	p.Pro2179Ser	p.P2179S	ENST00000222270	NM_014727.1	2179	Cct/Tct	28/37	1	2	FACETS	0.637	0.566	0.713	0.637	0.566	0.713	SUBCLONAL	1	TRUE	1	0.38	2		1033	768	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321118	62321118	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	554	840	0	ENST00000360203.5:c.2041G>A	p.Glu681Lys	p.E681K	ENST00000360203	NM_001283009.1	681	Gag/Aag	24/35	0.299290227092691	6	FACETS	0.965	0.931	0.998	0.804	0.775	0.832	CLONAL	5	TRUE	0	0.38	6		840	1064	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499489	89499489	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	107	457	0	ENST00000336596.2:c.2659A>T	p.Ser887Cys	p.S887C	ENST00000336596	NM_005233.5	887	Agc/Tgc	15/17	0.247932236523647	2	FACETS	1	0.978	1	0.652	0.588	0.718	CLONAL	1	TRUE	0	0.38	2		457	432	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921549	+	missense_variant	Missense_Mutation	DNP	GT	GT	AA	novel	NA	P-0033836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	69	263	0	ENST00000263967.3:c.1030_1031delinsAA	p.Val344Lys	p.V344K	ENST00000263967	NM_006218.2	344	GTg/AAg	5/21	0.125196469939784	4	FACETS	0.832	0.732	0.94	0.832	0.732	0.94	INDETERMINATE	2	TRUE	2	0.38	4		263	301	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146760	185146760	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182047206	NA	P-0033836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	128	724	0	ENST00000265026.3:c.391C>T	p.Leu131Phe	p.L131F	ENST00000265026	NM_004721.4	131	Ctt/Ttt	2/14	0.125196469939784	4	FACETS	1	0.98	1	0.646	0.586	0.709	INDETERMINATE	1	TRUE	2	0.38	4		724	720	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557972	187557972	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	107	474	0	ENST00000441802.2:c.3739C>T	p.Gln1247Ter	p.Q1247*	ENST00000441802	NM_005245.3	1247	Caa/Taa	5/27	0.247932236523647	2	FACETS	1	0.978	1	0.653	0.59	0.72	CLONAL	1	TRUE	0	0.38	2		474	431	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439328	149439329	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	256	798	1	ENST00000286301.3:c.2066_2067delinsTT	p.Pro689Leu	p.P689L	ENST00000286301	NM_005211.3	689	cCC/cTT	15/22	0.271947228397092	3	FACETS	1	0.977	1	0.717	0.675	0.761	CLONAL	2	TRUE	0	0.38	3		799	745	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741986	145741987	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	119	730	0	ENST00000428558.2:c.516_517delinsTT	p.Gln173Ter	p.Q173*	ENST00000428558	NM_004260.3	172	ctCCag/ctTTag	5/22	0.198969968275407	5	FACETS	1	0.982	1	0.463	0.418	0.51	INDETERMINATE	1	TRUE	2	0.38	5		730	708	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399775	139399775	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	151	645	0	ENST00000277541.6:c.4573G>T	p.Glu1525Ter	p.E1525*	ENST00000277541	NM_017617.3	1525	Gaa/Taa	25/34	0.125196469939784	4	FACETS	1	0.988	1	0.743	0.68	0.808	INDETERMINATE	1	TRUE	2	0.38	4		645	738	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019693	123019693	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	114	297	0	ENST00000355640.3:c.181G>T	p.Val61Leu	p.V61L	ENST00000355640		61	Gtg/Ttg	2/7	0.264382211156056	2	FACETS	0.94	0.858	1			1	CLONAL	2	TRUE	NA	0.38	2		297	319	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0033950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	62	429	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.256445689769538	2		429	406	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0033950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	32	351	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.658	0.535	0.798	0.658	0.535	0.798	SUBCLONAL	1	TRUE	1	0.256445689769538	2		351	379	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518175	8518175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1354824749	NA	P-0033950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	46	453	1	ENST00000356435.5:c.1216G>A	p.Glu406Lys	p.E406K	ENST00000356435		406	Gaa/Aaa	10/35	1	2	FACETS	0.867	0.731	1	0.867	0.731	1	CLONAL	1	TRUE	1	0.256445689769538	2		454	414	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971005	21971005	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501270	NA	P-0033950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	44	636	0	ENST00000304494.5:c.353C>T	p.Ala118Val	p.A118V	ENST00000304494	NM_000077.4	118	gCt/gTt	2/3	1	2	FACETS	0.692	0.58	0.816	0.692	0.58	0.816	SUBCLONAL	1	TRUE	1	0.256445689769538	2		636	496	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0033950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	41	462	1				ENST00000310581	NM_198253.2	-/1132			0.256445689769538	1	FACETS	0.955	0.799	1	0.955	0.799	1	CLONAL	1	TRUE	0	0.256445689769538	1		463	292	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273962	10273962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	67	879	0	ENST00000330684.3:c.307G>A	p.Asp103Asn	p.D103N	ENST00000330684	NM_001134407.1	103	Gac/Aac	2/13	1	2	FACETS	0.762	0.661	0.87	0.762	0.661	0.87	SUBCLONAL	1	TRUE	1	0.256445689769538	2		879	686	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061147	38061148	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	31	261	0	ENST00000250448.2:c.841_842delinsAA	p.Gly281Lys	p.G281K	ENST00000250448	NM_004496.3	281	GGa/AAa	2/2	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.256445689769538	2		261	173	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612422	1612422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1312230157	NA	P-0033950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	79	774	0	ENST00000344749.5:c.1597G>A	p.Glu533Lys	p.E533K	ENST00000344749	NM_001136139.2	533	Gag/Aag	18/19	1	2	FACETS	0.865	0.761	0.978	0.865	0.761	0.978	CLONAL	1	TRUE	1	0.256445689769538	2		774	712	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370708	55370708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867226331	NA	P-0033950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	70	495	0	ENST00000297316.4:c.10C>T	p.Pro4Ser	p.P4S	ENST00000297316	NM_022454.3	4	Ccg/Tcg	1/2	0.0863471562518159	4	FACETS	1	0.974	1	0.746	0.652	0.846	INDETERMINATE	1	TRUE	2	0.256445689769538	4		495	460	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	184	458	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.389911913527149	5	FACETS	0.974	0.92	1			1	CLONAL	5	TRUE	NA	0.389911913527149	5		458	307	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	162	316	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.389911913527149	3	FACETS	0.935	0.863	1	0.935	0.863	1	CLONAL	2	TRUE	1	0.389911913527149	3		316	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	197	596	1	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.389911913527149	4	FACETS	0.892	0.828	0.959	0.892	0.828	0.959	CLONAL	2	TRUE	2	0.389911913527149	4		597	787	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980483	7980483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	144	401	0	ENST00000319144.4:c.1100C>T	p.Pro367Leu	p.P367L	ENST00000319144	NM_001139.2	367	cCc/cTc	9/15	0.389911913527149	4	FACETS	0.856	0.783	0.931	0.856	0.783	0.931	CLONAL	2	TRUE	2	0.389911913527149	4		401	600	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956553	93956553	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1035177735	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	129	331	0	ENST00000369303.4:c.2683C>T	p.Arg895Ter	p.R895*	ENST00000369303	NM_004440.3	895	Cga/Tga	15/17	0.389911913527149	4	FACETS	0.997	0.911	1	0.997	0.911	1	CLONAL	2	TRUE	2	0.389911913527149	4		331	461	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	61	462	1				ENST00000310581	NM_198253.2	-/1132			0.389911913527149	3	FACETS	1	0.908	1	1	0.908	1	CLONAL	2	TRUE	1	0.389911913527149	3		463	180	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082466	16082466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	151	491	0	ENST00000281043.3:c.280G>A	p.Glu94Lys	p.E94K	ENST00000281043	NM_005378.4	94	Gag/Aag	2/3	0.380109042875664	4	FACETS	0.881	0.809	0.956	0.881	0.809	0.956	CLONAL	2	TRUE	2	0.389911913527149	4		491	611	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953799	55953799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867819358	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	74	484	0	ENST00000263923.4:c.3637C>T	p.His1213Tyr	p.H1213Y	ENST00000263923	NM_002253.2	1213	Cat/Tat	27/30	0.389911913527149	1	FACETS	0.78	0.686	0.879	0.78	0.686	0.879	SUBCLONAL	1	TRUE	0	0.389911913527149	1		484	392	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32182003	32182003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780829867	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	95	594	2	ENST00000375023.3:c.2051C>T	p.Thr684Met	p.T684M	ENST00000375023	NM_004557.3	684	aCg/aTg	13/30	0.310957271587007	3	FACETS	0.917	0.817	1	0.458	0.408	0.512	CLONAL	1	TRUE	1	0.389911913527149	3		596	635	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672764	30672764	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758481782	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	90	622	0	ENST00000376406.3:c.4196C>T	p.Ser1399Phe	p.S1399F	ENST00000376406	NM_014641.2	1399	tCc/tTc	10/15	0.336241030380556	4	FACETS	0.925	0.821	1	0.462	0.41	0.518	CLONAL	1	TRUE	2	0.389911913527149	4		622	694	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270054	198270054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	69	363	0	ENST00000335508.6:c.1382C>T	p.Ser461Phe	p.S461F	ENST00000335508	NM_012433.2	461	tCt/tTt	10/25	1	2	FACETS	0.922	0.807	1	0.922	0.807	1	CLONAL	1	TRUE	1	0.389911913527149	2		363	384	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257890	19257890	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1386180499	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	149	627	0	ENST00000162023.5:c.496C>T	p.Arg166Cys	p.R166C	ENST00000162023		166	Cgc/Tgc	9/13	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.389911913527149	2		627	664	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428259	49428259	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	96	534	0	ENST00000301067.7:c.10441G>A	p.Glu3481Lys	p.E3481K	ENST00000301067	NM_003482.3	3481	Gag/Aag	37/54	1	2	FACETS	0.966	0.863	1	0.966	0.863	1	CLONAL	1	TRUE	1	0.389911913527149	2		534	510	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46725669	46725669	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765591007	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	193	472	0	ENST00000371975.4:c.305G>A	p.Arg102Lys	p.R102K	ENST00000371975	NM_003579.3	102	aGg/aAg	5/18	0.389911913527149	3	FACETS	0.978	0.91	1	0.978	0.91	1	CLONAL	2	TRUE	1	0.389911913527149	3		472	605	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120493407	120493407	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	161	369	0	ENST00000256646.2:c.2419C>T	p.Gln807Ter	p.Q807*	ENST00000256646	NM_024408.3	807	Caa/Taa	15/34	0.389911913527149	3	FACETS	0.964	0.89	1	0.964	0.89	1	CLONAL	2	TRUE	1	0.389911913527149	3		369	512	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636390	21636390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	70	533	0	ENST00000421138.2:c.620C>T	p.Ala207Val	p.A207V	ENST00000421138		207	gCc/gTc	7/16	1	2	FACETS	0.796	0.696	0.903	0.796	0.696	0.903	CLONAL	1	TRUE	1	0.389911913527149	2		533	451	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448479	49448479	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs941339684	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	78	414	0	ENST00000301067.7:c.232G>A	p.Gly78Arg	p.G78R	ENST00000301067	NM_003482.3	78	Ggg/Agg	3/54	1	2	FACETS	0.887	0.783	0.999	0.887	0.783	0.999	CLONAL	1	TRUE	1	0.389911913527149	2		414	451	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861999	57862000	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	43	264	0	ENST00000228682.2:c.1300_1301delinsAA	p.Gly434Asn	p.G434N	ENST00000228682	NM_005269.2	434	GGt/AAt	10/12	0.310957271587007	3	FACETS	0.951	0.801	1	0.476	0.4	0.558	CLONAL	1	TRUE	1	0.389911913527149	3		264	277	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562338	95562338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	109	331	0	ENST00000393063.1:c.4919G>A	p.Gly1640Asp	p.G1640D	ENST00000393063	NM_030621.3	1640	gGt/gAt	24/28	0.336241030380556	4	FACETS	0.867	0.784	0.955	0.867	0.784	0.955	CLONAL	2	TRUE	2	0.389911913527149	4		331	448	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058680	42058681	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	56	203	1	ENST00000219905.7:c.8400_8401delinsAA	p.Glu2801Lys	p.E2801K	ENST00000219905	NM_001164273.1	2800	gaGGaa/gaAAaa	24/24	0.351126972799554	2	FACETS	0.816	0.712	0.925	0.816	0.712	0.925	CLONAL	2	TRUE	0	0.389911913527149	2		204	176	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631869	90631869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	218	545	1	ENST00000330062.3:c.484C>T	p.Pro162Ser	p.P162S	ENST00000330062	NM_002168.2	162	Cct/Tct	4/11	0.351126972799554	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.389911913527149	2		546	522	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828167	72828167	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	166	528	0	ENST00000268489.5:c.8414T>G	p.Ile2805Ser	p.I2805S	ENST00000268489	NM_006885.3	2805	aTt/aGt	9/10	0.351126972799554	2	FACETS	0.916	0.849	0.984	0.916	0.849	0.984	CLONAL	2	TRUE	0	0.389911913527149	2		528	465	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830036	72830036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	209	545	0	ENST00000268489.5:c.6545C>T	p.Ser2182Phe	p.S2182F	ENST00000268489	NM_006885.3	2182	tCc/tTc	9/10	0.351126972799554	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.389911913527149	2		545	523	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857842	89857842	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367733447	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	209	468	0	ENST00000389301.3:c.1328C>T	p.Ser443Phe	p.S443F	ENST00000389301	NM_000135.2	443	tCt/tTt	14/43	0.351126972799554	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	0	0.389911913527149	2		468	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578192	7578193	+	missense_variant	Missense_Mutation	DNP	GG	GG	AC	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	151	490	1	ENST00000269305.4:c.656_657delinsGT	p.Pro219Arg	p.P219R	ENST00000269305	NM_001126112.2	219	cCC/cGT	6/11	0.389911913527149	4	FACETS	0.786	0.72	0.854	0.786	0.72	0.854	SUBCLONAL	2	TRUE	2	0.389911913527149	4		491	685	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508508	29508508	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1060500245	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	75	217	1	ENST00000356175.3:c.654+1G>A		p.X218_splice	ENST00000356175	NM_000267.3	218			0.389911913527149	3	FACETS	0.842	0.746	0.942	0.842	0.746	0.942	CLONAL	2	TRUE	1	0.389911913527149	3		218	273	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40384105	40384105	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	179	455	0	ENST00000293328.3:c.41C>T	p.Ala14Val	p.A14V	ENST00000293328	NM_012448.3	14	gCc/gTc	2/19	0.389911913527149	3	FACETS	0.933	0.865	1	0.933	0.865	1	CLONAL	2	TRUE	1	0.389911913527149	3		455	588	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554204	63554204	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	239	513	0	ENST00000307078.5:c.535C>T	p.Gln179Ter	p.Q179*	ENST00000307078	NM_004655.3	179	Cag/Tag	2/11	0.389911913527149	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	1	0.389911913527149	3		513	724	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66521928	66521928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	59	239	0	ENST00000358598.2:c.583G>A	p.Gly195Arg	p.G195R	ENST00000358598	NM_212471.2	195	Ggg/Agg	7/11	0.389911913527149	3	FACETS	1	0.941	1	0.58	0.502	0.663	CLONAL	1	TRUE	1	0.389911913527149	3		239	312	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603054	48603054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	75	327	0	ENST00000342988.3:c.1355C>T	p.Ala452Val	p.A452V	ENST00000342988	NM_005359.5	452	gCt/gTt	11/12	1	2	FACETS	0.842	0.74	0.95	0.842	0.74	0.95	CLONAL	1	TRUE	1	0.389911913527149	2		327	457	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222536	2222536	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	58	395	0	ENST00000398665.3:c.3368C>G	p.Ser1123Cys	p.S1123C	ENST00000398665	NM_032482.2	1123	tCt/tGt	24/28	1	2	FACETS	0.697	0.6	0.801	0.697	0.6	0.801	SUBCLONAL	1	TRUE	1	0.389911913527149	2		395	427	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122978	7122978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	101	528	1	ENST00000302850.5:c.3281C>T	p.Ser1094Phe	p.S1094F	ENST00000302850	NM_000208.2	1094	tCc/tTc	18/22	1	2	FACETS	0.906	0.812	1	0.906	0.812	1	CLONAL	1	TRUE	1	0.389911913527149	2		529	572	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7163058	7163058	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	65	421	0	ENST00000302850.5:c.2014G>A	p.Asp672Asn	p.D672N	ENST00000302850	NM_000208.2	672	Gat/Aat	9/22	1	2	FACETS	0.734	0.638	0.838	0.734	0.638	0.838	SUBCLONAL	1	TRUE	1	0.389911913527149	2		421	454	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953930	17953930	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	114	550	0	ENST00000458235.1:c.472G>A	p.Glu158Lys	p.E158K	ENST00000458235	NM_000215.3	158	Gag/Aag	5/24	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.389911913527149	2		550	564	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211612	36211612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	84	409	0	ENST00000222270.7:c.1363G>A	p.Glu455Lys	p.E455K	ENST00000222270	NM_014727.1	455	Gaa/Aaa	3/37	0.389911913527149	3	FACETS	0.94	0.832	1	0.47	0.416	0.528	CLONAL	1	TRUE	1	0.389911913527149	3		409	548	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212263	36212264	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	187	529	1	ENST00000222270.7:c.2014_2015delinsAA	p.Gly672Lys	p.G672K	ENST00000222270	NM_014727.1	672	GGg/AAg	3/37	0.389911913527149	3	FACETS	0.923	0.857	0.991	0.923	0.857	0.991	CLONAL	2	TRUE	1	0.389911913527149	3		530	621	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753531	42753532	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	185	567	2	ENST00000222329.4:c.732_733delinsTT	p.Leu245Phe	p.L245F	ENST00000222329	NM_006494.2	244	ccCCtc/ccTTtc	4/4	0.389911913527149	3	FACETS	0.876	0.813	0.942	0.876	0.813	0.942	CLONAL	2	TRUE	1	0.389911913527149	3		569	647	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044353	128044353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	86	486	0	ENST00000285398.2:c.1268C>T	p.Ala423Val	p.A423V	ENST00000285398	NM_000122.1	423	gCc/gTc	8/15	NA	2	FACETS	0.945	0.839	1			1	INDETERMINATE	1	TRUE	NA	0.389911913527149	2		486	467	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293184	212293184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	66	278	0	ENST00000342788.4:c.2668G>A	p.Glu890Lys	p.E890K	ENST00000342788	NM_005235.2	890	Gag/Aag	22/28	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.389911913527149	2		278	328	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451341	187451341	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	70	271	0	ENST00000232014.4:c.141A>T	p.Lys47Asn	p.K47N	ENST00000232014	NM_001130845.1	47	aaA/aaT	3/10	0.389911913527149	3	FACETS	1	0.959	1	0.611	0.536	0.691	CLONAL	1	TRUE	1	0.389911913527149	3		271	351	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490539	20490539	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	79	403	0	ENST00000346618.3:c.1276C>A	p.Leu426Met	p.L426M	ENST00000346618	NM_001949.4	426	Ctg/Atg	7/7	0.336924185931968	4	FACETS	1	0.934	1			1	CLONAL	1	TRUE	NA	0.389911913527149	4		403	517	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662377	117662378	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	75	376	0	ENST00000368508.3:c.4999_5000delinsTT	p.Pro1667Leu	p.P1667L	ENST00000368508	NM_002944.2	1667	CCa/TTa	30/43	0.389911913527149	3	FACETS	1	0.911	1	0.521	0.458	0.588	CLONAL	1	TRUE	1	0.389911913527149	3		376	441	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92247511	92247511	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	61	187	0	ENST00000265734.4:c.709C>T	p.Leu237Phe	p.L237F	ENST00000265734	NM_001259.6	237	Ctc/Ttc	7/8	0.373981137654939	2	FACETS	0.889	0.782	1	0.889	0.782	1	CLONAL	2	TRUE	0	0.389911913527149	2		187	176	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56911031	56911031	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	164	485	0	ENST00000519728.1:c.1177G>A	p.Glu393Lys	p.E393K	ENST00000519728	NM_002350.3	393	Gaa/Aaa	11/13	0.389911913527149	3	FACETS	0.931	0.86	1	0.931	0.86	1	CLONAL	2	TRUE	1	0.389911913527149	3		485	540	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69103988	69103988	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	121	406	0	ENST00000288368.4:c.4378C>T	p.Pro1460Ser	p.P1460S	ENST00000288368	NM_024870.2	1460	Cca/Tca	36/40	0.389911913527149	3	FACETS	0.845	0.769	0.924	0.845	0.769	0.924	CLONAL	2	TRUE	1	0.389911913527149	3		406	439	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637067	93637067	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	82	347	0	ENST00000375746.1:c.1117G>A	p.Glu373Lys	p.E373K	ENST00000375746	NM_001174167.1	373	Gaa/Aaa	9/14	0.389911913527149	3	FACETS	1	0.927	1	0.355	0.314	0.399	CLONAL	1	TRUE	0	0.389911913527149	3		347	472	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755544	133755545	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	187	345	1	ENST00000318560.5:c.1513_1513+1delinsAA		p.X505_splice	ENST00000318560	NM_005157.4	505		9/11	0.389911913527149	3	FACETS	0.918	0.86	0.978	0.918	0.86	0.978	CLONAL	3	TRUE	0	0.389911913527149	3		346	416	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391917	139391917	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	176	575	1	ENST00000277541.6:c.6274C>T	p.His2092Tyr	p.H2092Y	ENST00000277541	NM_017617.3	2092	Cat/Tat	34/34	0.389911913527149	3	FACETS	0.753	0.696	0.813	0.502	0.464	0.542	SUBCLONAL	2	TRUE	0	0.389911913527149	3		576	716	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410038	139410038	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	62	615	0	ENST00000277541.6:c.1800C>G	p.Cys600Trp	p.C600W	ENST00000277541	NM_017617.3	600	tgC/tgG	11/34	0.389911913527149	3	FACETS	0.537	0.463	0.617	0.179	0.154	0.206	SUBCLONAL	1	TRUE	0	0.389911913527149	3		615	708	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417594	139417598	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGC	GGCGC	AGCA	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	329	610	2	ENST00000277541.6:c.446_450delinsTGCT	p.Cys149LeufsTer128	p.C149Lfs*128	ENST00000277541	NM_017617.3	149	tGCGCC/tTGCT	4/34	0.389911913527149	3	FACETS	1	0.992	1	0.829	0.787	0.871	CLONAL	2	TRUE	0	0.389911913527149	3		612	811	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566525	139566525	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	115	672	0	ENST00000308874.7:c.784G>A	p.Glu262Lys	p.E262K	ENST00000308874		262	Gag/Aag	9/10	0.389911913527149	3	FACETS	0.9	0.811	0.995	0.3	0.27	0.332	CLONAL	1	TRUE	0	0.389911913527149	3		672	783	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227015	53227015	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782562716	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	171	228	0	ENST00000375401.3:c.2560C>T	p.Arg854Trp	p.R854W	ENST00000375401	NM_004187.3	854	Cgg/Tgg	18/26	0.336924185931968	2	FACETS	0.914	0.857	0.97			1	CLONAL	3	TRUE	NA	0.389911913527149	2		228	320	SUCCESS
AR	367	MSKCC	GRCh37	X	66931357	66931358	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	125	212	0	ENST00000374690.3:c.1999_2000delinsAA	p.Gly667Asn	p.G667N	ENST00000374690	NM_000044.3	667	GGc/AAc	4/8	0.336924185931968	2	FACETS	1	0.968	1			1	CLONAL	2	TRUE	NA	0.389911913527149	2		212	291	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512280	120512284	+	stop_gained	Nonsense_Mutation	ONP	CCTCC	CCTCC	GCTCA	novel	NA	P-0033976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	72	429	0	ENST00000256646.2:c.958_962delinsTGAGC	p.Gly320_Gly321delinsTer	p.G320_G321delins*	ENST00000256646	NM_024408.3	320	GGAGGc/TGAGCc	6/34	0.389911913527149	3	FACETS	0.842	0.737	0.955	0.421	0.368	0.478	CLONAL	1	TRUE	1	0.389911913527149	3		429	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	52	593	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.792	0.682	0.911	1	0.97	1	CLONAL	2	FALSE	1	0.278048204482926	2		593	236	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589168	67589168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	37	352	0	ENST00000274335.5:c.1156C>T	p.Arg386Ter	p.R386*	ENST00000274335		386	Cga/Tga	9/15	0.278048204482926	5	FACETS	1	0.95	1			1	CLONAL	1	FALSE	NA	0.278048204482926	5		352	259	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480466	89480466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446890859	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	18	439	0	ENST00000336596.2:c.2303C>T	p.Ser768Leu	p.S768L	ENST00000336596	NM_005233.5	768	tCg/tTg	13/17	1	2	FACETS	0.689	0.521	0.885	0.689	0.521	0.885	SUBCLONAL	1	FALSE	1	0.278048204482926	2		439	188	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546761	9546761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768724288	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	12	314	0	ENST00000353224.5:c.1261G>A	p.Asp421Asn	p.D421N	ENST00000353224	NM_177990.2	421	Gac/Aac	5/10	0.0974760791284044	4	FACETS	1	0.87	1	0.745	0.533	0.996	INDETERMINATE	1	FALSE	2	0.278048204482926	4		314	74	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	34	462	1				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.97	0.809	1			1	INDETERMINATE	2	FALSE	NA	0.278048204482926	2		463	126	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196537	106196537	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	29	485	0	ENST00000380013.4:c.4870C>T	p.Gln1624Ter	p.Q1624*	ENST00000380013	NM_001127208.2	1624	Cag/Tag	11/11	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	1	0.278048204482926	2		485	143	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298606	11298606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199712134	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	53	761	1	ENST00000361445.4:c.1855C>T	p.Arg619Cys	p.R619C	ENST00000361445	NM_004958.3	619	Cgc/Tgc	12/58	0.278048204482926	1	FACETS	0.892	0.773	1	1	0.975	1	CLONAL	2	FALSE	0	0.278048204482926	1		762	184	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289058	33289058	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	91	974	0	ENST00000374542.5:c.494C>T	p.Ser165Phe	p.S165F	ENST00000374542	NM_001141970.1	165	tCc/tTc	3/8	0.278048204482926	5	FACETS	1	0.933	1	0.708	0.631	0.788	CLONAL	2	FALSE	2	0.278048204482926	5		974	437	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372442	55372442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	54	1234	0	ENST00000297316.4:c.1132C>T	p.Pro378Ser	p.P378S	ENST00000297316	NM_022454.3	378	Ccc/Tcc	2/2	1	2	FACETS	0.903	0.782	1	1	0.975	1	CLONAL	2	FALSE	1	0.278048204482926	2		1234	215	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177635	56177635	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs755905626	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	29	495	0	ENST00000399503.3:c.2608C>T	p.Gln870Ter	p.Q870*	ENST00000399503	NM_005921.1	870	Cag/Tag	14/20	0.278048204482926	5	FACETS	1	0.913	1			1	CLONAL	1	FALSE	NA	0.278048204482926	5		495	235	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119595289	119595289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	44	391	0	ENST00000316626.5:c.880C>T	p.Pro294Ser	p.P294S	ENST00000316626		294	Cct/Tct	8/12	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.278048204482926	2		391	238	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149298	119149298	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	53	698	0	ENST00000264033.4:c.1306C>T	p.Pro436Ser	p.P436S	ENST00000264033	NM_005188.3	436	Cct/Tct	9/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.278048204482926	2		698	265	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259689	11259689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	49	654	0	ENST00000361445.4:c.4016G>A	p.Arg1339Lys	p.R1339K	ENST00000361445	NM_004958.3	1339	aGa/aAa	27/58	0.278048204482926	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	0	0.278048204482926	1		654	206	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156157	119156157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	42	671	0	ENST00000264033.4:c.1822C>T	p.Pro608Ser	p.P608S	ENST00000264033	NM_005188.3	608	Ccc/Tcc	11/16	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.278048204482926	2		671	213	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675113	40675113	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	67	948	0	ENST00000249776.8:c.77C>T	p.Pro26Leu	p.P26L	ENST00000249776	NM_033286.3	26	cCa/cTa	1/9	0.0374877161612965	3	FACETS	1	0.967	1	0.678	0.591	0.77	INDETERMINATE	1	FALSE	1	0.278048204482926	3		948	405	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019540	42019540	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	83	750	0	ENST00000219905.7:c.3593T>G	p.Val1198Gly	p.V1198G	ENST00000219905	NM_001164273.1	1198	gTg/gGg	10/24	0.0374877161612965	3	FACETS	0.947	0.842	1	0.947	0.842	1	INDETERMINATE	2	FALSE	1	0.278048204482926	3		750	359	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923465	9923465	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771688818	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	41	651	0	ENST00000330684.3:c.1822C>T	p.Leu608Phe	p.L608F	ENST00000330684	NM_001134407.1	608	Ctt/Ttt	9/13	1	2	FACETS	0.81	0.684	0.947	1	0.963	1	CLONAL	2	FALSE	1	0.278048204482926	2		651	182	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805493	46805493	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	47	869	0	ENST00000290295.7:c.463C>T	p.Pro155Ser	p.P155S	ENST00000290295	NM_006361.5	155	Cct/Tct	1/2	0.221625596149755	3	FACETS	0.944	0.806	1	0.944	0.806	1	CLONAL	2	FALSE	1	0.278048204482926	3		869	204	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15273284	15273284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	37	893	0	ENST00000263388.2:c.5905G>A	p.Asp1969Asn	p.D1969N	ENST00000263388	NM_000435.2	1969	Gat/Aat	32/33	1	2	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	FALSE	1	0.278048204482926	2		893	258	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281608	15281608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	37	1118	2	ENST00000263388.2:c.4765C>T	p.Arg1589Trp	p.R1589W	ENST00000263388	NM_000435.2	1589	Cgg/Tgg	26/33	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	1	0.278048204482926	2		1120	220	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224126	36224126	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763442835	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	50	1013	0	ENST00000222270.7:c.6676C>T	p.Pro2226Ser	p.P2226S	ENST00000222270	NM_014727.1	2226	Ccc/Tcc	28/37	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.278048204482926	2		1013	252	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190742130	190742130	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	32	483	0	ENST00000441310.2:c.2767C>T	p.His923Tyr	p.H923Y	ENST00000441310	NM_000534.4	923	Cat/Tat	13/13	0.0547458475445368	4	FACETS	1	0.939	1	0.7	0.573	0.842	INDETERMINATE	1	FALSE	2	0.278048204482926	4		483	210	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530091	212530091	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	36	423	0	ENST00000342788.4:c.1828C>T	p.Pro610Ser	p.P610S	ENST00000342788	NM_005235.2	610	Cca/Tca	15/28	0.278048204482926	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	0	0.278048204482926	1		423	179	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29090042	29090042	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786203303	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	25	283	0	ENST00000328354.6:c.1439C>T	p.Ala480Val	p.A480V	ENST00000328354	NM_007194.3	480	gCc/gTc	13/15	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	FALSE	1	0.278048204482926	2		283	127	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130460	29130460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	27	770	0	ENST00000328354.6:c.250G>A	p.Glu84Lys	p.E84K	ENST00000328354	NM_007194.3	84	Gaa/Aaa	2/15	1	2	FACETS	0.637	0.507	0.784	0.637	0.507	0.784	SUBCLONAL	1	FALSE	1	0.278048204482926	2		770	305	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458437	12458437	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530007199	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	28	875	0	ENST00000287820.6:c.1054G>A	p.Glu352Lys	p.E352K	ENST00000287820	NM_015869.4	352	Gag/Aag	6/7	1	2	FACETS	0.724	0.581	0.887	0.724	0.581	0.887	SUBCLONAL	1	FALSE	1	0.278048204482926	2		875	278	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713205	30713205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	25	493	0	ENST00000295754.5:c.530G>A	p.Gly177Glu	p.G177E	ENST00000295754	NM_003242.5	177	gGa/gAa	4/7	1	2	FACETS	0.983	0.781	1	0.983	0.781	1	CLONAL	1	FALSE	1	0.278048204482926	2		493	183	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441295	52441295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1559590603	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	33	641	0	ENST00000460680.1:c.475C>T	p.Leu159Phe	p.L159F	ENST00000460680	NM_004656.3	159	Ctt/Ttt	7/17	1	2	FACETS	0.873	0.714	1	0.873	0.714	1	CLONAL	1	FALSE	1	0.278048204482926	2		641	272	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445073	89445073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	19	494	0	ENST00000336596.2:c.1393G>A	p.Gly465Arg	p.G465R	ENST00000336596	NM_005233.5	465	Ggg/Agg	6/17	1	2	FACETS	0.809	0.618	1	0.809	0.618	1	CLONAL	1	FALSE	1	0.278048204482926	2		494	169	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55987310	55987310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	38	585	1	ENST00000263923.4:c.115G>A	p.Asp39Asn	p.D39N	ENST00000263923	NM_002253.2	39	Gac/Aac	2/30	0.278048204482926	0	FACETS	0.851	0.709	1			1	CLONAL	1	FALSE	0	0.278048204482926	0		586	232	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295265	1295265	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	31	667	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.858	0.706	1			1	INDETERMINATE	2	FALSE	NA	0.278048204482926	2		667	130	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177634	56177635	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	29	495	0	ENST00000399503.3:c.2607_2608delinsTT	p.Gln870Ter	p.Q870*	ENST00000399503	NM_005921.1	869	atCCag/atTTag	14/20	0.278048204482926	5	FACETS	1	0.913	1			1	CLONAL	1	FALSE	NA	0.278048204482926	5		495	235	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750468	57750468	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	69	735	0	ENST00000274289.3:c.2000C>T	p.Ser667Leu	p.S667L	ENST00000274289	NM_006622.3	667	tCa/tTa	14/14	0.278048204482926	5	FACETS	0.94	0.823	1			1	CLONAL	2	FALSE	NA	0.278048204482926	5		735	374	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176710827	176710827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587784176	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	16	603	2	ENST00000439151.2:c.6049C>T	p.Arg2017Trp	p.R2017W	ENST00000439151	NM_022455.4	2017	Cgg/Tgg	20/23	0.221625596149755	3	FACETS	0.518	0.383	0.679	0.259	0.191	0.34	SUBCLONAL	1	FALSE	1	0.278048204482926	3		605	253	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553485	106553486	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	29	334	1	ENST00000369096.4:c.1450_1451delinsTT	p.Pro484Phe	p.P484F	ENST00000369096	NM_001198.3	484	CCc/TTc	5/7	0.278048204482926	6	FACETS	1	0.862	1	0.717	0.582	0.865	CLONAL	2	FALSE	3	0.278048204482926	6		335	151	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739824	41739824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	42	691	0	ENST00000242208.4:c.149C>T	p.Ser50Phe	p.S50F	ENST00000242208	NM_002192.2	50	tCt/tTt	2/3	0.221625596149755	3	FACETS	1	0.949	1	0.675	0.567	0.792	CLONAL	1	FALSE	1	0.278048204482926	3		691	255	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846314	128846314	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	25	799	0	ENST00000249373.3:c.1150G>A	p.Asp384Asn	p.D384N	ENST00000249373	NM_005631.4	384	Gac/Aac	6/12	0.221625596149755	3	FACETS	1	0.859	1	0.554	0.439	0.683	CLONAL	1	FALSE	1	0.278048204482926	3		799	185	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331666	8331667	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	67	617	0	ENST00000356435.5:c.5449_5450delinsAT	p.Gly1817Ile	p.G1817I	ENST00000356435		1817	GGa/ATa	33/35	0.0547458475445368	4	FACETS	0.845	0.744	0.951	1	0.964	1	INDETERMINATE	3	FALSE	2	0.278048204482926	4		617	243	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248138	98248139	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	GACTTACTCGTCCTCCAACT	novel	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	58	579	0	ENST00000331920.6:c.395-2_412dup	p.Arg138GlnfsTer6	p.R138Qfs*6	ENST00000331920	NM_000264.3	138	cgt/cAGTTGGAGGACGAGTAAGTCgt	3/24	0.0664721974948275	4	FACETS	1	0.929	1			1	INDETERMINATE	2	FALSE	NA	0.278048204482926	4		579	241	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396812	139396813	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	35	1065	2	ENST00000277541.6:c.5295_5296delinsTT	p.Gln1766Ter	p.Q1766*	ENST00000277541	NM_017617.3	1765	ggCCag/ggTTag	28/34	0.278048204482926	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	FALSE	0	0.278048204482926	1		1067	170	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331666	8331666	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	66	613	0	ENST00000356435.5:c.5450G>T	p.Gly1817Val	p.G1817V	ENST00000356435		1817	gGa/gTa	33/35	0.0547458475445368	4	FACETS	1	0.962	1	1	0.962	1	INDETERMINATE	2	FALSE	2	0.278048204482926	4		613	243	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411734	63411734	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs751544083	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	21	773	0	ENST00000330258.3:c.1433G>T	p.Gly478Val	p.G478V	ENST00000330258	NM_152424.3	478	gGa/gTa	2/2	1	2	FACETS	0.53	0.407	0.674	0.53	0.407	0.674	SUBCLONAL	1	TRUE	1	0.19	2		773	417	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	35	736	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.0810666718303437	0	FACETS	0.802	0.658	0.963			1	INDETERMINATE	1	TRUE	0	0.19	0		741	372	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	53	510	1	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	0.0810666718303437	0	FACETS	1	0.909	1			1	INDETERMINATE	1	TRUE	0	0.19	0		511	416	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349733	15349733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754054879	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	26	653	1	ENST00000263377.2:c.3841C>T	p.Arg1281Trp	p.R1281W	ENST00000263377	NM_058243.2	1281	Cgg/Tgg	19/20	1	2	FACETS	0.636	0.503	0.789	0.636	0.503	0.789	SUBCLONAL	1	TRUE	1	0.19	2		654	430	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	33	504	7	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.862	0.702	1	0.862	0.702	1	CLONAL	1	TRUE	1	0.19	2		511	403	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656280	18656280	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	23	449	1	ENST00000266497.5:c.2959G>T	p.Gly987Ter	p.G987*	ENST00000266497		987	Gga/Tga	21/31	1	2	FACETS	0.698	0.544	0.876	0.698	0.544	0.876	SUBCLONAL	1	TRUE	1	0.19	2		450	347	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86682692	86682692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757298110	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	13	284	0	ENST00000274376.6:c.2897G>A	p.Arg966His	p.R966H	ENST00000274376	NM_002890.2	966	cGt/cAt	23/25	1	2	FACETS	0.585	0.417	0.789	0.585	0.417	0.789	SUBCLONAL	1	TRUE	1	0.19	2		284	234	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696461	47696461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	22	422	0	ENST00000347630.2:c.362G>A	p.Arg121Gln	p.R121Q	ENST00000347630	NM_001007230.1	121	cGg/cAg	6/11	0.0810666718303437	0	FACETS	0.601	0.466	0.758			1	INDETERMINATE	1	TRUE	0	0.19	0		422	312	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882049	36882050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs780753361	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	40	639	0	ENST00000358127.4:c.963dup	p.Ala322ArgfsTer19	p.A322Rfs*19	ENST00000358127	NM_001280556.1	321	-/C	8/10	1	2	FACETS	0.919	0.764	1	0.919	0.764	1	CLONAL	1	TRUE	1	0.19	2		639	458	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698180	47698180	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63751411	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	18	213	0	ENST00000233146.2:c.1738G>T	p.Glu580Ter	p.E580*	ENST00000233146	NM_000251.2	580	Gaa/Taa	11/16	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.19	2		213	141	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198261	185198261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376662287	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	25	439	1	ENST00000265026.3:c.2743C>T	p.Arg915Cys	p.R915C	ENST00000265026	NM_004721.4	915	Cgt/Tgt	13/14	1	2	FACETS	0.591	0.465	0.737	0.591	0.465	0.737	SUBCLONAL	1	TRUE	1	0.19	2		440	445	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512289	120512289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782615247	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	26	449	1	ENST00000256646.2:c.953G>A	p.Arg318His	p.R318H	ENST00000256646	NM_024408.3	318	cGc/cAc	6/34	1	2	FACETS	0.669	0.529	0.83	0.669	0.529	0.83	SUBCLONAL	1	TRUE	1	0.19	2		450	409	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	28	443	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.869	0.696	1	0.869	0.696	1	CLONAL	1	TRUE	1	0.19	2		443	339	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955550	48955550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913304	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	20	353	0	ENST00000267163.4:c.1666C>T	p.Arg556Ter	p.R556*	ENST00000267163	NM_000321.2	556	Cga/Tga	17/27	0.124442880638595	3	FACETS	0.809	0.619	1	0.404	0.309	0.516	CLONAL	1	TRUE	1	0.19	3		353	285	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921606	39921606	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	27	546	0	ENST00000378444.4:c.4214C>T	p.Ser1405Leu	p.S1405L	ENST00000378444	NM_001123385.1	1405	tCg/tTg	10/15	1	2	FACETS	0.698	0.555	0.862	0.698	0.555	0.862	SUBCLONAL	1	TRUE	1	0.19	2		546	407	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950375	17950375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145751599	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	33	669	0	ENST00000458235.1:c.1352G>A	p.Arg451Gln	p.R451Q	ENST00000458235	NM_000215.3	451	cGa/cAa	10/24	1	2	FACETS	0.791	0.644	0.957	0.791	0.644	0.957	CLONAL	1	TRUE	1	0.19	2		669	439	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649922	88649922	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786201038	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	25	470	0	ENST00000372037.3:c.176del	p.Leu59Ter	p.L59*	ENST00000372037	NM_004329.2	57	ccT/cc	4/13	1	2	FACETS	0.895	0.707	1	0.895	0.707	1	CLONAL	1	TRUE	1	0.19	2		470	294	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777792	3777792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200566758	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	61	908	1	ENST00000262367.5:c.7256C>T	p.Ala2419Val	p.A2419V	ENST00000262367	NM_004380.2	2419	gCg/gTg	31/31	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.19	2		909	533	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654642	67654642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	56	478	0	ENST00000264010.4:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000264010	NM_006565.3	377	Cgt/Tgt	6/12	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.19	2		478	560	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208010	5208010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	36	569	0	ENST00000357368.4:c.5701C>T	p.Arg1901Trp	p.R1901W	ENST00000357368	NM_002850.3	1901	Cgg/Tgg	37/38	1	2	FACETS	0.789	0.649	0.948	0.789	0.649	0.948	CLONAL	1	TRUE	1	0.19	2		569	480	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533093	63533093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750354919	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	20	492	0	ENST00000307078.5:c.1801G>A	p.Gly601Ser	p.G601S	ENST00000307078	NM_004655.3	601	Ggc/Agc	7/11	0.0810666718303437	0	FACETS	0.472	0.361	0.604			1	INDETERMINATE	1	TRUE	0	0.19	0		492	361	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144146	11144146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	38	524	1	ENST00000358026.2:c.3727C>T	p.Arg1243Trp	p.R1243W	ENST00000358026	NM_001128849.1	1243	Cgg/Tgg	26/36	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.19	2		525	379	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633259	12633259	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559632360	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	34	545	1	ENST00000251849.4:c.1141G>A	p.Asp381Asn	p.D381N	ENST00000251849	NM_002880.3	381	Gac/Aac	11/17	1	2	FACETS	0.795	0.65	0.959	0.795	0.65	0.959	CLONAL	1	TRUE	1	0.19	2		546	450	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409068	4409068	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	22	266	0	ENST00000261254.3:c.763C>T	p.Leu255Phe	p.L255F	ENST00000261254	NM_001759.3	255	Ctc/Ttc	5/5	1	2	FACETS	0.905	0.703	1	0.905	0.703	1	CLONAL	1	TRUE	1	0.19	2		266	256	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145582	24145582	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555877286	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	41	584	0	ENST00000263121.7:c.601C>T	p.Arg201Ter	p.R201*	ENST00000263121	NM_003073.3	201	Cga/Tga	5/9	0.0810666718303437	0	FACETS	0.876	0.731	1			1	INDETERMINATE	1	TRUE	0	0.19	0		584	399	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692835	89692835	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs57374291	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	14	151	0	ENST00000371953.3:c.319G>T	p.Asp107Tyr	p.D107Y	ENST00000371953	NM_000314.4	107	Gat/Tat	5/9	1	2	FACETS	1	0.796	1	1	0.796	1	CLONAL	1	TRUE	1	0.19	2		151	132	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094479	27094479	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	37	425	0	ENST00000324856.7:c.3187G>T	p.Gly1063Ter	p.G1063*	ENST00000324856	NM_006015.4	1063	Gga/Tga	11/20	1	2	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	1	0.19	2		425	378	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515240	106515240	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs945222564	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	20	295	0	ENST00000359195.3:c.2383G>A	p.Ala795Thr	p.A795T	ENST00000359195	NM_002649.2	795	Gcg/Acg	5/11	0.259933852591637	4	FACETS	0.849	0.65	1	0.425	0.325	0.542	CLONAL	1	TRUE	2	0.19	4		295	295	SUCCESS
ALK	238	MSKCC	GRCh37	2	29450509	29450509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774004991	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	26	768	0	ENST00000389048.3:c.2845G>A	p.Glu949Lys	p.E949K	ENST00000389048	NM_004304.4	949	Gaa/Aaa	17/29	1	2	FACETS	0.538	0.425	0.668	0.538	0.425	0.668	SUBCLONAL	1	TRUE	1	0.19	2		768	509	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525868	148525868	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	25	434	0	ENST00000320356.2:c.589G>T	p.Glu197Ter	p.E197*	ENST00000320356	NM_004456.4	197	Gaa/Taa	6/20	1	2	FACETS	0.707	0.557	0.88	0.707	0.557	0.88	SUBCLONAL	1	TRUE	1	0.19	2		434	372	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915943	127915943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781486938	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	48	517	2	ENST00000373547.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000373547	NM_002721.4	180	Gaa/Aaa	6/7	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.19	2		519	434	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650710	67650710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243010179	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	46	492	1	ENST00000264010.4:c.1015C>T	p.Arg339Trp	p.R339W	ENST00000264010	NM_006565.3	339	Cgg/Tgg	5/12	1	2	FACETS	0.908	0.765	1	0.908	0.765	1	CLONAL	1	TRUE	1	0.19	2		493	533	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940455	29940455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138686378	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	12	271	0	ENST00000389048.3:c.776G>A	p.Arg259His	p.R259H	ENST00000389048	NM_004304.4	259	cGc/cAc	2/29	1	2	FACETS	0.672	0.473	0.916	0.672	0.473	0.916	SUBCLONAL	1	TRUE	1	0.19	2		271	188	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916843	48916843	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	18	311	0	ENST00000267163.4:c.373G>T	p.Glu125Ter	p.E125*	ENST00000267163	NM_000321.2	125	Gaa/Taa	3/27	0.124442880638595	3	FACETS	0.85	0.641	1	0.425	0.32	0.549	CLONAL	1	TRUE	1	0.19	3		311	244	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518038	176518038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111435837	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	23	569	2	ENST00000292408.4:c.536C>T	p.Thr179Met	p.T179M	ENST00000292408	NM_213647.1	179	aCg/aTg	5/18	1	2	FACETS	0.591	0.46	0.742	0.591	0.46	0.742	SUBCLONAL	1	TRUE	1	0.19	2		571	410	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933307	49933307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749037053	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	27	588	0	ENST00000296474.3:c.2803G>A	p.Val935Ile	p.V935I	ENST00000296474	NM_002447.2	935	Gta/Ata	12/20	1	2	FACETS	0.77	0.613	0.95	0.77	0.613	0.95	CLONAL	1	TRUE	1	0.19	2		588	369	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136875627	136875627	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	23	378	0	ENST00000241393.3:c.4G>T	p.Glu2Ter	p.E2*	ENST00000241393	NM_003467.2	2	Gag/Tag	1/2	1	2	FACETS	0.651	0.507	0.818	0.651	0.507	0.818	SUBCLONAL	1	TRUE	1	0.19	2		378	372	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872556	35872556	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	29	401	0	ENST00000216797.5:c.347A>G	p.His116Arg	p.H116R	ENST00000216797	NM_020529.2	116	cAc/cGc	3/6	1	2	FACETS	0.599	0.479	0.735	0.599	0.479	0.735	SUBCLONAL	1	TRUE	1	0.19	2		401	510	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942751	44942751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763592177	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	27	491	0	ENST00000377967.4:c.3331C>T	p.Arg1111Cys	p.R1111C	ENST00000377967	NM_021140.2	1111	Cgt/Tgt	23/29	1	2	FACETS	0.539	0.428	0.667	0.539	0.428	0.667	SUBCLONAL	1	TRUE	1	0.19	2		491	527	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481429	40481429	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs749583802	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	37	465	0	ENST00000264657.5:c.1280A>G	p.Asp427Gly	p.D427G	ENST00000264657	NM_139276.2	427	gAt/gGt	14/24	0.0810666718303437	0	FACETS	0.751	0.62	0.898			1	INDETERMINATE	1	TRUE	0	0.19	0		465	420	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203492	108203492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs138941496	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	16	239	0	ENST00000278616.4:c.7792C>T	p.Arg2598Ter	p.R2598*	ENST00000278616	NM_000051.3	2598	Cga/Tga	53/63	1	2	FACETS	1	0.815	1	1	0.815	1	CLONAL	1	TRUE	1	0.19	2		239	150	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116262	209116263	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs754375602	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	13	281	1	ENST00000345146.2:c.13dup	p.Ile5AsnfsTer13	p.I5Nfs*13	ENST00000345146	NM_005896.2	5	atc/aAtc	3/10	1	2	FACETS	0.72	0.515	0.97	0.72	0.515	0.97	CLONAL	1	TRUE	1	0.19	2		282	190	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094931	11094931	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs563079629	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	25	650	0	ENST00000358026.2:c.104C>T	p.Ser35Leu	p.S35L	ENST00000358026	NM_001128849.1	35	tCg/tTg	2/36	1	2	FACETS	0.696	0.548	0.866	0.696	0.548	0.866	SUBCLONAL	1	TRUE	1	0.19	2		650	378	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784380	9784380	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	30	630	0	ENST00000377346.4:c.2765A>C	p.Lys922Thr	p.K922T	ENST00000377346	NM_005026.3	922	aAg/aCg	22/24	1	2	FACETS	0.726	0.584	0.887	0.726	0.584	0.887	SUBCLONAL	1	TRUE	1	0.19	2		630	435	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56867190	56867190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374772646	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	25	559	0	ENST00000308159.5:c.1409C>T	p.Ala470Val	p.A470V	ENST00000308159	NM_014669.4	470	gCg/gTg	13/22	1	2	FACETS	0.643	0.506	0.801	0.643	0.506	0.801	SUBCLONAL	1	TRUE	1	0.19	2		559	409	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570878	226570878	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1383847803	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	19	428	0	ENST00000366794.5:c.1018C>T	p.Arg340Ter	p.R340*	ENST00000366794	NM_001618.3	340	Cga/Tga	8/23	1	2	FACETS	0.702	0.533	0.9	0.702	0.533	0.9	SUBCLONAL	1	TRUE	1	0.19	2		428	285	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73340147	73340147	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	22	326	0	ENST00000377767.4:c.1933A>G	p.Thr645Ala	p.T645A	ENST00000377767	NM_014953.3	645	Act/Gct	15/21	0.124442880638595	3	FACETS	0.909	0.705	1	0.454	0.352	0.572	CLONAL	1	TRUE	1	0.19	3		326	279	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285669	46285669	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1368075571	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	24	438	0	ENST00000334344.6:c.5029C>T	p.Arg1677Ter	p.R1677*	ENST00000334344	NM_152641.2	1677	Cga/Tga	17/21	1	2	FACETS	0.632	0.495	0.79	0.632	0.495	0.79	SUBCLONAL	1	TRUE	1	0.19	2		438	400	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106879	27106879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	32	473	0	ENST00000324856.7:c.6490C>T	p.Arg2164Trp	p.R2164W	ENST00000324856	NM_006015.4	2164	Cgg/Tgg	20/20	1	2	FACETS	0.842	0.684	1	0.842	0.684	1	CLONAL	1	TRUE	1	0.19	2		473	400	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	16	430	0	ENST00000320574.5:c.1231G>C	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ctg	13/49	1	2	FACETS	0.648	0.479	0.849	0.648	0.479	0.849	SUBCLONAL	1	TRUE	1	0.19	2		430	260	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287986	33287986	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	25	401	0	ENST00000374542.5:c.1267G>A	p.Ala423Thr	p.A423T	ENST00000374542	NM_001141970.1	423	Gca/Aca	5/8	0.124442880638595	3	FACETS	0.997	0.787	1	0.499	0.393	0.619	CLONAL	1	TRUE	1	0.19	3		401	289	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20152085	20152085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	23	229	0	ENST00000379607.5:c.245G>A	p.Arg82Gln	p.R82Q	ENST00000379607	NM_001412.3	82	cGa/cAa	4/7	1	2	FACETS	1	0.822	1	1	0.822	1	CLONAL	1	TRUE	1	0.19	2		229	229	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042400	42042400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	28	459	0	ENST00000219905.7:c.6595G>A	p.Glu2199Lys	p.E2199K	ENST00000219905	NM_001164273.1	2199	Gag/Aag	17/24	1	2	FACETS	0.792	0.633	0.973	0.792	0.633	0.973	CLONAL	1	TRUE	1	0.19	2		459	372	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593563	215593563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782662	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	21	276	1	ENST00000260947.4:c.2171C>T	p.Ala724Val	p.A724V	ENST00000260947	NM_000465.2	724	gCg/gTg	11/11	1	2	FACETS	0.606	0.466	0.769	0.606	0.466	0.769	SUBCLONAL	1	TRUE	1	0.19	2		277	365	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238417	98238417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137903539	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	43	355	0	ENST00000331920.6:c.1627C>T	p.Arg543Cys	p.R543C	ENST00000331920	NM_000264.3	543	Cgc/Tgc	12/24	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.19	2		355	427	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937121	39937121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778129253	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	45	647	0	ENST00000378444.4:c.62G>A	p.Arg21His	p.R21H	ENST00000378444	NM_001123385.1	21	cGc/cAc	2/15	1	2	FACETS	0.944	0.793	1	0.944	0.793	1	CLONAL	1	TRUE	1	0.19	2		647	502	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041629	14041629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777184889	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	29	431	0	ENST00000311895.7:c.2176C>T	p.Arg726Cys	p.R726C	ENST00000311895	NM_005236.2	726	Cgc/Tgc	11/11	1	2	FACETS	0.723	0.58	0.886	0.723	0.58	0.886	SUBCLONAL	1	TRUE	1	0.19	2		431	422	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149982885	149982885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139248642	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	35	483	0	ENST00000253339.5:c.3373C>T	p.Arg1125Cys	p.R1125C	ENST00000253339		1125	Cgc/Tgc	7/7	0.124442880638595	3	FACETS	1	0.861	1	0.529	0.434	0.636	CLONAL	1	TRUE	1	0.19	3		483	381	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348136	89348136	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	55	858	0	ENST00000301030.4:c.4814T>C	p.Met1605Thr	p.M1605T	ENST00000301030	NM_001256183.1	1605	aTg/aCg	9/13	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.19	2		858	500	SUCCESS
RET	5979	MSKCC	GRCh37	10	43598017	43598017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1210452561	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	23	629	0	ENST00000355710.3:c.565C>T	p.Arg189Cys	p.R189C	ENST00000355710	NM_020975.4	189	Cgc/Tgc	3/20	1	2	FACETS	0.618	0.481	0.776	0.618	0.481	0.776	SUBCLONAL	1	TRUE	1	0.19	2		629	392	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120529603	120529603	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782452794	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	36	414	0	ENST00000256646.2:c.854G>A	p.Arg285His	p.R285H	ENST00000256646	NM_024408.3	285	cGc/cAc	5/34	1	2	FACETS	0.753	0.619	0.905	0.753	0.619	0.905	CLONAL	1	TRUE	1	0.19	2		414	503	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347446	91347446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757088548	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	18	336	0	ENST00000355112.3:c.3608C>T	p.Ala1203Val	p.A1203V	ENST00000355112	NM_000057.2	1203	gCg/gTg	19/22	1	2	FACETS	0.773	0.583	0.997	0.773	0.583	0.997	CLONAL	1	TRUE	1	0.19	2		336	245	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62320438	62320438	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752318462	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	44	595	1	ENST00000360203.5:c.1831G>A	p.Ala611Thr	p.A611T	ENST00000360203	NM_001283009.1	611	Gcc/Acc	22/35	1	2	FACETS	0.869	0.728	1	0.869	0.728	1	CLONAL	1	TRUE	1	0.19	2		596	533	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62009575	62009575	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs114330958	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	27	460	0	ENST00000392795.3:c.47C>T	p.Ala16Val	p.A16V	ENST00000392795	NM_001039933.1	16	gCg/gTg	1/6	0.0810666718303437	0	FACETS	0.607	0.483	0.749			1	INDETERMINATE	1	TRUE	0	0.19	0		460	379	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288765	15288765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1317504991	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	11	108	1	ENST00000263388.2:c.3974G>A	p.Arg1325His	p.R1325H	ENST00000263388	NM_000435.2	1325	cGc/cAc	24/33	1	2	FACETS	0.665	0.46	0.919	0.665	0.46	0.919	SUBCLONAL	1	TRUE	1	0.19	2		109	174	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797246	135797246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264782606	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	15	205	0	ENST00000298552.3:c.623G>A	p.Ser208Asn	p.S208N	ENST00000298552	NM_001162426.1	208	aGt/aAt	7/23	1	2	FACETS	0.734	0.538	0.97	0.734	0.538	0.97	CLONAL	1	TRUE	1	0.19	2		205	215	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006604	62006604	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs781172398	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	17	497	0	ENST00000392795.3:c.675G>T	p.Glu225Asp	p.E225D	ENST00000392795	NM_001039933.1	225	gaG/gaT	6/6	0.0810666718303437	0	FACETS	0.478	0.357	0.623			1	INDETERMINATE	1	TRUE	0	0.19	0		497	303	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303059	15303059	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767150916	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	49	773	1	ENST00000263388.2:c.391G>A	p.Gly131Ser	p.G131S	ENST00000263388	NM_000435.2	131	Ggt/Agt	4/33	1	2	FACETS	0.986	0.835	1	0.986	0.835	1	CLONAL	1	TRUE	1	0.19	2		774	523	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349757	15349757	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	25	670	0	ENST00000263377.2:c.3817C>T	p.Arg1273Trp	p.R1273W	ENST00000263377	NM_058243.2	1273	Cgg/Tgg	19/20	1	2	FACETS	0.633	0.498	0.788	0.633	0.498	0.788	SUBCLONAL	1	TRUE	1	0.19	2		670	416	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280136	142280136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369434236	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	32	536	0	ENST00000350721.4:c.1298G>A	p.Arg433His	p.R433H	ENST00000350721	NM_001184.3	433	cGt/cAt	5/47	1	2	FACETS	0.619	0.502	0.753	0.619	0.502	0.753	SUBCLONAL	1	TRUE	1	0.19	2		536	544	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495715	56495715	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	32	443	0	ENST00000267101.3:c.3910del	p.His1304MetfsTer7	p.H1304Mfs*7	ENST00000267101	NM_001982.3	1302	gCc/gc	28/28	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.19	2		443	313	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671934	30671934	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	47	725	0	ENST00000376406.3:c.5026G>T	p.Ala1676Ser	p.A1676S	ENST00000376406	NM_014641.2	1676	Gct/Tct	10/15	0.124442880638595	3	FACETS	1	0.922	1	0.576	0.486	0.675	CLONAL	1	TRUE	1	0.19	3		725	470	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497849	120497849	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	18	410	0	ENST00000256646.2:c.2033G>T	p.Arg678Ile	p.R678I	ENST00000256646	NM_024408.3	678	aGa/aTa	13/34	1	2	FACETS	0.617	0.464	0.798	0.617	0.464	0.798	SUBCLONAL	1	TRUE	1	0.19	2		410	307	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149290	119149290	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140627020	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	31	471	0	ENST00000264033.4:c.1298C>T	p.Pro433Leu	p.P433L	ENST00000264033	NM_005188.3	433	cCg/cTg	9/16	1	2	FACETS	0.699	0.564	0.851	0.699	0.564	0.851	SUBCLONAL	1	TRUE	1	0.19	2		471	467	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721836	176721836	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	33	464	0	ENST00000439151.2:c.7467T>G	p.Ser2489Arg	p.S2489R	ENST00000439151	NM_022455.4	2489	agT/agG	23/23	1	2	FACETS	0.981	0.8	1	0.981	0.8	1	CLONAL	1	TRUE	1	0.19	2		464	354	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742886	17742886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	26	613	0	ENST00000250003.3:c.794C>T	p.Ala265Val	p.A265V	ENST00000250003	NM_002478.4	265	gCg/gTg	3/3	1	2	FACETS	0.746	0.591	0.924	0.746	0.591	0.924	CLONAL	1	TRUE	1	0.19	2		613	367	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99181170	99181170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759905070	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	21	492	2	ENST00000074304.5:c.2111G>A	p.Arg704His	p.R704H	ENST00000074304	NM_001134224.1	704	cGc/cAc	20/26	1	2	FACETS	0.539	0.414	0.685	0.539	0.414	0.685	SUBCLONAL	1	TRUE	1	0.19	2		494	410	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432829	432829	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326148362	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	29	461	0	ENST00000399788.2:c.2087G>A	p.Arg696Gln	p.R696Q	ENST00000399788	NM_001042603.1	696	cGg/cAg	15/28	1	2	FACETS	0.853	0.685	1	0.853	0.685	1	CLONAL	1	TRUE	1	0.19	2		461	358	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940441	49940441	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1338633573	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	31	628	0	ENST00000296474.3:c.602C>T	p.Ser201Phe	p.S201F	ENST00000296474	NM_002447.2	201	tCc/tTc	1/20	1	2	FACETS	0.706	0.571	0.86	0.706	0.571	0.86	SUBCLONAL	1	TRUE	1	0.19	2		628	462	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39240688	39240688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	15	410	1	ENST00000402219.2:c.2080C>T	p.Arg694Trp	p.R694W	ENST00000402219	NM_005633.3	694	Cgg/Tgg	13/23	1	2	FACETS	0.605	0.442	0.801	0.605	0.442	0.801	SUBCLONAL	1	TRUE	1	0.19	2		411	261	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026616	48026616	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	20	422	0	ENST00000234420.5:c.1494G>T	p.Lys498Asn	p.K498N	ENST00000234420	NM_000179.2	498	aaG/aaT	4/10	1	2	FACETS	0.681	0.521	0.869	0.681	0.521	0.869	SUBCLONAL	1	TRUE	1	0.19	2		422	309	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059347	42059347	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	33	353	0	ENST00000219905.7:c.9067T>C	p.Ser3023Pro	p.S3023P	ENST00000219905	NM_001164273.1	3023	Tca/Cca	24/24	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.19	2		353	278	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939537	76939537	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	33	685	0	ENST00000373344.5:c.1211A>G	p.Lys404Arg	p.K404R	ENST00000373344	NM_000489.3	404	aAg/aGg	9/35	1	2	FACETS	0.819	0.667	0.991	0.819	0.667	0.991	CLONAL	1	TRUE	1	0.19	2		685	424	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43742126	43742126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1193943585	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	46	610	0	ENST00000523873.1:c.115G>A	p.Glu39Lys	p.E39K	ENST00000523873		39	Gaa/Aaa	2/8	0.124442880638595	3	FACETS	1	0.896	1	0.542	0.456	0.637	CLONAL	1	TRUE	1	0.19	3		610	489	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963878	2963878	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	19	517	0	ENST00000396946.4:c.1929C>A	p.Phe643Leu	p.F643L	ENST00000396946	NM_032415.4	643	ttC/ttA	15/25	1	2	FACETS	0.557	0.422	0.716	0.557	0.422	0.716	SUBCLONAL	1	TRUE	1	0.19	2		517	359	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603092	48603092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786201798	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	30	458	0	ENST00000342988.3:c.1393G>A	p.Val465Met	p.V465M	ENST00000342988	NM_005359.5	465	Gtg/Atg	11/12	1	2	FACETS	0.716	0.576	0.875	0.716	0.576	0.875	SUBCLONAL	1	TRUE	1	0.19	2		458	441	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272374	15272374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778080758	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	32	835	0	ENST00000263388.2:c.6065G>A	p.Arg2022His	p.R2022H	ENST00000263388	NM_000435.2	2022	cGc/cAc	33/33	1	2	FACETS	0.659	0.534	0.801	0.659	0.534	0.801	SUBCLONAL	1	TRUE	1	0.19	2		835	511	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896539	78896539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	39	711	0	ENST00000306801.3:c.2536C>T	p.Arg846Trp	p.R846W	ENST00000306801	NM_020761.2	846	Cgg/Tgg	22/34	0.0810666718303437	0	FACETS	0.688	0.57	0.82			1	INDETERMINATE	1	TRUE	0	0.19	0		711	483	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964206	28964206	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	13	346	1	ENST00000282397.4:c.1696del	p.Met566CysfsTer8	p.M566Cfs*8	ENST00000282397	NM_002019.4	566	Atg/tg	13/30	0.3	0	FACETS	0.476	0.339	0.642			1	SUBCLONAL	1	TRUE	0	0.19	0		347	233	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280637	41280637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753246841	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	25	582	0	ENST00000349496.5:c.2150G>A	p.Arg717His	p.R717H	ENST00000349496	NM_001904.3	717	cGt/cAt	15/15	1	2	FACETS	0.611	0.48	0.761	0.611	0.48	0.761	SUBCLONAL	1	TRUE	1	0.19	2		582	431	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646257	23646257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142103232	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	30	599	1	ENST00000261584.4:c.1610C>T	p.Ser537Leu	p.S537L	ENST00000261584	NM_024675.3	537	tCg/tTg	4/13	1	2	FACETS	0.736	0.593	0.899	0.736	0.593	0.899	SUBCLONAL	1	TRUE	1	0.19	2		600	429	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061634	38061634	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764371648	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	16	352	0	ENST00000250448.2:c.355C>T	p.Gln119Ter	p.Q119*	ENST00000250448	NM_004496.3	119	Cag/Tag	2/2	1	2	FACETS	0.855	0.634	1	0.855	0.634	1	CLONAL	1	TRUE	1	0.19	2		352	197	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513165	106513165	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs778461029	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	18	326	0	ENST00000359195.3:c.2069G>T	p.Arg690Ile	p.R690I	ENST00000359195	NM_002649.2	690	aGa/aTa	4/11	0.259933852591637	4	FACETS	0.808	0.609	1	0.404	0.304	0.522	CLONAL	1	TRUE	2	0.19	4		326	279	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218350	36218350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1454713201	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	47	737	0	ENST00000222270.7:c.4129G>A	p.Glu1377Lys	p.E1377K	ENST00000222270	NM_014727.1	1377	Gag/Aag	16/37	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.19	2		737	491	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644532	3644532	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	32	733	0	ENST00000294008.3:c.2082G>C	p.Gln694His	p.Q694H	ENST00000294008	NM_032444.2	694	caG/caC	10/15	1	2	FACETS	0.699	0.567	0.849	0.699	0.567	0.849	SUBCLONAL	1	TRUE	1	0.19	2		733	482	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124201	2124201	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs767252128	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	31	496	1	ENST00000219476.3:c.2356C>T	p.Arg786Cys	p.R786C	ENST00000219476	NM_000548.3	786	Cgc/Tgc	22/42	1	2	FACETS	0.93	0.753	1	0.93	0.753	1	CLONAL	1	TRUE	1	0.19	2		497	351	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168740	56168740	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	23	400	0	ENST00000399503.3:c.1594C>T	p.Arg532Ter	p.R532*	ENST00000399503	NM_005921.1	532	Cga/Tga	9/20	1	2	FACETS	0.568	0.442	0.715	0.568	0.442	0.715	SUBCLONAL	1	TRUE	1	0.19	2		400	426	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868298	37868298	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs532077147	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	17	402	0	ENST00000269571.5:c.1019G>A	p.Arg340Gln	p.R340Q	ENST00000269571		340	cGa/cAa	8/27	0.0810666718303437	0	FACETS	0.449	0.334	0.585			1	INDETERMINATE	1	TRUE	0	0.19	0		402	323	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541733	120541733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	32	523	0	ENST00000229340.5:c.124G>A	p.Gly42Arg	p.G42R	ENST00000229340	NM_006861.6	42	Gga/Aga	3/6	1	2	FACETS	0.767	0.622	0.931	0.767	0.622	0.931	CLONAL	1	TRUE	1	0.19	2		523	439	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870336	155870336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs938749530	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	34	445	1	ENST00000368323.3:c.503G>A	p.Arg168His	p.R168H	ENST00000368323	NM_006912.5	168	cGc/cAc	6/6	1	2	FACETS	0.96	0.785	1	0.96	0.785	1	CLONAL	1	TRUE	1	0.19	2		446	373	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133958	38133958	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	37	688	0	ENST00000317025.8:c.3928C>T	p.Arg1310Ter	p.R1310*	ENST00000317025	NM_023034.1	1310	Cga/Tga	23/24	1	2	FACETS	0.792	0.652	0.948	0.792	0.652	0.948	CLONAL	1	TRUE	1	0.19	2		688	492	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73995386	73995386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs184115783	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	19	415	0	ENST00000318443.5:c.692C>T	p.Ala231Val	p.A231V	ENST00000318443	NM_001024736.1	231	gCg/gTg	4/10	1	2	FACETS	0.781	0.594	1	0.781	0.594	1	CLONAL	1	TRUE	1	0.19	2		415	256	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817865	3817865	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	44	623	0	ENST00000262367.5:c.3106A>G	p.Thr1036Ala	p.T1036A	ENST00000262367	NM_004380.2	1036	Aca/Gca	16/31	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.19	2		623	399	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785686	50785686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763792744	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	41	503	0	ENST00000398568.2:c.676G>A	p.Glu226Lys	p.E226K	ENST00000398568	NM_001042412.1	226	Gaa/Aaa	4/18	1	2	FACETS	0.82	0.683	0.974	0.82	0.683	0.974	CLONAL	1	TRUE	1	0.19	2		503	526	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073649	8073649	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	31	405	0	ENST00000377482.5:c.1010G>T	p.Ser337Ile	p.S337I	ENST00000377482	NM_018948.3	337	aGc/aTc	4/4	1	2	FACETS	0.863	0.699	1	0.863	0.699	1	CLONAL	1	TRUE	1	0.19	2		405	378	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776652	9776652	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	50	590	0	ENST00000377346.4:c.755G>T	p.Gly252Val	p.G252V	ENST00000377346	NM_005026.3	252	gGc/gTc	6/24	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.19	2		590	415	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294198	11294198	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	28	415	0	ENST00000361445.4:c.2331+2T>C		p.X777_splice	ENST00000361445	NM_004958.3	777			1	2	FACETS	0.819	0.655	1	0.819	0.655	1	CLONAL	1	TRUE	1	0.19	2		415	360	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294241	11294241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	33	465	0	ENST00000361445.4:c.2290G>A	p.Ala764Thr	p.A764T	ENST00000361445	NM_004958.3	764	Gcc/Acc	14/58	1	2	FACETS	0.868	0.708	1	0.868	0.708	1	CLONAL	1	TRUE	1	0.19	2		465	400	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202726	16202726	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	17	318	0	ENST00000375759.3:c.434A>C	p.Glu145Ala	p.E145A	ENST00000375759	NM_015001.2	145	gAa/gCa	3/15	1	2	FACETS	0.563	0.419	0.733	0.563	0.419	0.733	SUBCLONAL	1	TRUE	1	0.19	2		318	318	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256796	16256796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	20	648	0	ENST00000375759.3:c.4061G>A	p.Ser1354Asn	p.S1354N	ENST00000375759	NM_015001.2	1354	aGt/aAt	11/15	1	2	FACETS	0.58	0.443	0.741	0.58	0.443	0.741	SUBCLONAL	1	TRUE	1	0.19	2		648	363	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259393	16259393	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	16	293	0	ENST00000375759.3:c.6658G>A	p.Gly2220Ser	p.G2220S	ENST00000375759	NM_015001.2	2220	Ggc/Agc	11/15	1	2	FACETS	0.806	0.597	1	0.806	0.597	1	CLONAL	1	TRUE	1	0.19	2		293	209	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259726	16259726	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	26	393	1	ENST00000375759.3:c.6991G>T	p.Gly2331Trp	p.G2331W	ENST00000375759	NM_015001.2	2331	Ggg/Tgg	11/15	1	2	FACETS	0.977	0.776	1	0.977	0.776	1	CLONAL	1	TRUE	1	0.19	2		394	280	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260240	16260240	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	16	375	0	ENST00000375759.3:c.7505T>G	p.Ile2502Ser	p.I2502S	ENST00000375759	NM_015001.2	2502	aTc/aGc	11/15	1	2	FACETS	0.671	0.496	0.88	0.671	0.496	0.88	SUBCLONAL	1	TRUE	1	0.19	2		375	251	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22417932	22417932	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	27	232	0	ENST00000344548.3:c.498G>T	p.Lys166Asn	p.K166N	ENST00000344548	NM_001039802.1	166	aaG/aaT	7/7	1	2	FACETS	1	0.807	1	1	0.807	1	CLONAL	1	TRUE	1	0.19	2		232	281	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885709	23885709	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	39	648	0	ENST00000374561.5:c.209T>C	p.Leu70Pro	p.L70P	ENST00000374561	NM_002167.4	70	cTa/cCa	1/3	1	2	FACETS	0.802	0.664	0.956	0.802	0.664	0.956	CLONAL	1	TRUE	1	0.19	2		648	512	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885774	23885774	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	48	547	0	ENST00000374561.5:c.144C>A	p.Tyr48Ter	p.Y48*	ENST00000374561	NM_002167.4	48	taC/taA	1/3	1	2	FACETS	0.977	0.826	1	0.977	0.826	1	CLONAL	1	TRUE	1	0.19	2		547	517	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935271	36935271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs767301627	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	39	766	0	ENST00000361632.4:c.1456A>G	p.Thr486Ala	p.T486A	ENST00000361632		486	Acg/Gcg	10/16	1	2	FACETS	0.769	0.636	0.917	0.769	0.636	0.917	CLONAL	1	TRUE	1	0.19	2		766	534	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818320	43818320	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	36	643	0	ENST00000372470.3:c.1785G>T	p.Gln595His	p.Q595H	ENST00000372470	NM_005373.2	595	caG/caT	12/12	1	2	FACETS	0.788	0.647	0.946	0.788	0.647	0.946	CLONAL	1	TRUE	1	0.19	2		643	481	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818436	43818436	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	41	464	0	ENST00000372470.3:c.1901A>G	p.Gln634Arg	p.Q634R	ENST00000372470	NM_005373.2	634	cAg/cGg	12/12	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.19	2		464	385	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521586	46521586	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	36	583	0	ENST00000262741.5:c.822A>C	p.Lys274Asn	p.K274N	ENST00000262741	NM_003629.3	274	aaA/aaC	7/10	1	2	FACETS	0.844	0.694	1	0.844	0.694	1	CLONAL	1	TRUE	1	0.19	2		583	449	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743868	46743868	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	52	581	1	ENST00000371975.4:c.2158C>A	p.Leu720Ile	p.L720I	ENST00000371975	NM_003579.3	720	Ctc/Atc	18/18	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.19	2		582	366	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248697	59248697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748223511	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	50	773	2	ENST00000371222.2:c.46G>A	p.Ala16Thr	p.A16T	ENST00000371222	NM_002228.3	16	Gcc/Acc	1/1	1	2	FACETS	0.914	0.775	1	0.914	0.775	1	CLONAL	1	TRUE	1	0.19	2		775	576	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335120	65335120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774843930	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	29	463	0	ENST00000342505.4:c.521G>A	p.Arg174Gln	p.R174Q	ENST00000342505	NM_002227.2	174	cGa/cAa	6/25	1	2	FACETS	0.759	0.609	0.93	0.759	0.609	0.93	CLONAL	1	TRUE	1	0.19	2		463	402	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263308	115263308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	52	564	0	ENST00000438362.2:c.2042G>A	p.Gly681Asp	p.G681D	ENST00000438362	NM_001242891.1	681	gGc/gAc	17/20	1	2	FACETS	0.977	0.832	1	0.977	0.832	1	CLONAL	1	TRUE	1	0.19	2		564	560	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649554	206649554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	32	399	0	ENST00000367120.3:c.389G>A	p.Gly130Asp	p.G130D	ENST00000367120	NM_014002.3	130	gGc/gAc	6/22	1	2	FACETS	0.8	0.649	0.97	0.8	0.649	0.97	CLONAL	1	TRUE	1	0.19	2		399	421	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226564921	226564921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	35	508	1	ENST00000366794.5:c.1829C>T	p.Ala610Val	p.A610V	ENST00000366794	NM_001618.3	610	gCc/gTc	13/23	1	2	FACETS	0.769	0.63	0.926	0.769	0.63	0.926	CLONAL	1	TRUE	1	0.19	2		509	479	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667486	241667486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	11	250	0	ENST00000366560.3:c.964G>A	p.Val322Ile	p.V322I	ENST00000366560	NM_000143.3	322	Gtt/Att	7/10	1	2	FACETS	0.565	0.39	0.782	0.565	0.39	0.782	SUBCLONAL	1	TRUE	1	0.19	2		250	205	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675403	241675403	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	12	394	0	ENST00000366560.3:c.419T>C	p.Val140Ala	p.V140A	ENST00000366560	NM_000143.3	140	gTa/gCa	4/10	1	2	FACETS	0.554	0.389	0.757	0.554	0.389	0.757	SUBCLONAL	1	TRUE	1	0.19	2		394	228	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608394	43608394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	31	877	0	ENST00000355710.3:c.1742G>A	p.Cys581Tyr	p.C581Y	ENST00000355710	NM_020975.4	581	tGc/tAc	9/20	1	2	FACETS	0.6	0.484	0.731	0.6	0.484	0.731	SUBCLONAL	1	TRUE	1	0.19	2		877	544	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609098	43609098	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	25	658	0	ENST00000355710.3:c.1854C>A	p.Cys618Ter	p.C618*	ENST00000355710	NM_020975.4	618	tgC/tgA	10/20	1	2	FACETS	0.562	0.442	0.701	0.562	0.442	0.701	SUBCLONAL	1	TRUE	1	0.19	2		658	468	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404662	70404662	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	18	456	0	ENST00000373644.4:c.2176T>C	p.Phe726Leu	p.F726L	ENST00000373644	NM_030625.2	726	Ttt/Ctt	4/12	1	2	FACETS	0.561	0.421	0.725	0.561	0.421	0.725	SUBCLONAL	1	TRUE	1	0.19	2		456	338	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32449551	32449551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	25	626	0	ENST00000332351.3:c.823G>A	p.Asp275Asn	p.D275N	ENST00000332351	NM_024426.4	275	Gac/Aac	3/10	1	2	FACETS	0.577	0.454	0.719	0.577	0.454	0.719	SUBCLONAL	1	TRUE	1	0.19	2		626	456	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577343	64577343	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	43	571	0	ENST00000312049.6:c.239T>C	p.Val80Ala	p.V80A	ENST00000312049	NM_130799.2	80	gTg/gCg	2/10	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.19	2		571	367	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202094	67202094	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	33	652	0	ENST00000312629.5:c.1197G>T	p.Lys399Asn	p.K399N	ENST00000312629	NM_003952.2	399	aaG/aaT	14/15	1	2	FACETS	0.692	0.563	0.838	0.692	0.563	0.838	SUBCLONAL	1	TRUE	1	0.19	2		652	502	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943995	71943995	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	43	643	0	ENST00000298229.2:c.1928A>C	p.Lys643Thr	p.K643T	ENST00000298229	NM_001567.3	643	aAg/aCg	16/28	1	2	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	1	0.19	2		643	446	SUCCESS
EED	8726	MSKCC	GRCh37	11	85975273	85975273	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759722952	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	20	276	0	ENST00000263360.6:c.694G>A	p.Val232Ile	p.V232I	ENST00000263360	NM_003797.3	232	Gta/Ata	7/12	1	2	FACETS	0.711	0.544	0.907	0.711	0.544	0.907	CLONAL	1	TRUE	1	0.19	2		276	296	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192587	94192587	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	27	557	0	ENST00000323929.3:c.1487A>G	p.Lys496Arg	p.K496R	ENST00000323929	NM_005591.3	496	aAa/aGa	13/20	1	2	FACETS	0.718	0.571	0.886	0.718	0.571	0.886	SUBCLONAL	1	TRUE	1	0.19	2		557	396	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94211957	94211957	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	18	492	0	ENST00000323929.3:c.488A>G	p.Asp163Gly	p.D163G	ENST00000323929	NM_005591.3	163	gAc/gGc	6/20	1	2	FACETS	0.567	0.427	0.734	0.567	0.427	0.734	SUBCLONAL	1	TRUE	1	0.19	2		492	334	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195481	102195481	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	34	418	0	ENST00000263464.3:c.241A>C	p.Ser81Arg	p.S81R	ENST00000263464	NM_001165.4	81	Agt/Cgt	2/9	1	2	FACETS	0.906	0.741	1	0.906	0.741	1	CLONAL	1	TRUE	1	0.19	2		418	395	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102196203	102196203	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	31	340	1	ENST00000263464.3:c.860G>A	p.Ser287Asn	p.S287N	ENST00000263464	NM_001165.4	287	aGt/aAt	3/9	1	2	FACETS	0.977	0.792	1	0.977	0.792	1	CLONAL	1	TRUE	1	0.19	2		341	334	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344141	118344141	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	42	532	1	ENST00000534358.1:c.2267G>T	p.Arg756Met	p.R756M	ENST00000534358	NM_005933.3	756	aGg/aTg	3/36	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.19	2		533	358	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359343	118359343	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	30	215	0	ENST00000534358.1:c.4347A>C	p.Gln1449His	p.Q1449H	ENST00000534358	NM_005933.3	1449	caA/caC	11/36	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.19	2		215	295	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376920	118376920	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782425634	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	22	296	0	ENST00000534358.1:c.10313C>T	p.Thr3438Met	p.T3438M	ENST00000534358	NM_005933.3	3438	aCg/aTg	27/36	1	2	FACETS	1	0.78	1	1	0.78	1	CLONAL	1	TRUE	1	0.19	2		296	231	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148507	119148507	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	33	395	0	ENST00000264033.4:c.1048A>G	p.Thr350Ala	p.T350A	ENST00000264033	NM_005188.3	350	Act/Gct	7/16	1	2	FACETS	0.888	0.724	1	0.888	0.724	1	CLONAL	1	TRUE	1	0.19	2		395	391	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125513729	125513729	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	26	477	0	ENST00000428830.2:c.857C>A	p.Ser286Tyr	p.S286Y	ENST00000428830	NM_001114121.2	286	tCt/tAt	9/14	1	2	FACETS	0.632	0.5	0.784	0.632	0.5	0.784	SUBCLONAL	1	TRUE	1	0.19	2		477	433	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514413	125514413	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	33	316	0	ENST00000428830.2:c.1108T>C	p.Trp370Arg	p.W370R	ENST00000428830	NM_001114121.2	370	Tgg/Cgg	11/14	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.19	2		316	274	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402099	402100	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	39	597	0	ENST00000399788.2:c.4691dup	p.Lys1565GlufsTer10	p.K1565Efs*10	ENST00000399788	NM_001042603.1	1564	aag/aaAg	27/28	1	2	FACETS	0.992	0.823	1	0.992	0.823	1	CLONAL	1	TRUE	1	0.19	2		597	414	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419064	419064	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	32	469	1	ENST00000399788.2:c.3283G>T	p.Glu1095Ter	p.E1095*	ENST00000399788	NM_001042603.1	1095	Gaa/Taa	22/28	1	2	FACETS	0.931	0.756	1	0.931	0.756	1	CLONAL	1	TRUE	1	0.19	2		470	362	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025974	1025974	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	25	367	1	ENST00000358495.3:c.556G>T	p.Val186Leu	p.V186L	ENST00000358495	NM_134424.2	186	Gtg/Ttg	8/12	1	2	FACETS	0.914	0.722	1	0.914	0.722	1	CLONAL	1	TRUE	1	0.19	2		368	288	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636360	21636360	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	25	591	2	ENST00000421138.2:c.650C>A	p.Ala217Asp	p.A217D	ENST00000421138		217	gCt/gAt	7/16	1	2	FACETS	0.578	0.455	0.721	0.578	0.455	0.721	SUBCLONAL	1	TRUE	1	0.19	2		593	455	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123669	46123669	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	28	257	0	ENST00000334344.6:c.50T>C	p.Leu17Pro	p.L17P	ENST00000334344	NM_152641.2	17	cTc/cCc	1/21	1	2	FACETS	0.979	0.784	1	0.979	0.784	1	CLONAL	1	TRUE	1	0.19	2		257	301	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416445	49416445	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	38	532	0	ENST00000301067.7:c.16266G>A	p.Met5422Ile	p.M5422I	ENST00000301067	NM_003482.3	5422	atG/atA	51/54	1	2	FACETS	1	0.83	1	1	0.83	1	CLONAL	1	TRUE	1	0.19	2		532	399	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424504	49424504	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	24	485	0	ENST00000301067.7:c.13719del	p.Phe4573LeufsTer19	p.F4573Lfs*19	ENST00000301067	NM_003482.3	4573	ttT/tt	41/54	1	2	FACETS	0.643	0.503	0.804	0.643	0.503	0.804	SUBCLONAL	1	TRUE	1	0.19	2		485	393	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427056	49427056	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	14	481	0	ENST00000301067.7:c.11432A>G	p.Gln3811Arg	p.Q3811R	ENST00000301067	NM_003482.3	3811	cAg/cGg	39/54	1	2	FACETS	0.594	0.429	0.794	0.594	0.429	0.794	SUBCLONAL	1	TRUE	1	0.19	2		481	248	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427192	49427192	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	36	722	0	ENST00000301067.7:c.11296A>C	p.Asn3766His	p.N3766H	ENST00000301067	NM_003482.3	3766	Aac/Cac	39/54	1	2	FACETS	0.995	0.819	1	0.995	0.819	1	CLONAL	1	TRUE	1	0.19	2		722	381	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431253	49431253	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	22	458	0	ENST00000301067.7:c.9886T>C	p.Ser3296Pro	p.S3296P	ENST00000301067	NM_003482.3	3296	Tct/Cct	34/54	1	2	FACETS	0.887	0.689	1	0.887	0.689	1	CLONAL	1	TRUE	1	0.19	2		458	261	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444004	49444004	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	32	509	0	ENST00000301067.7:c.3367G>T	p.Ala1123Ser	p.A1123S	ENST00000301067	NM_003482.3	1123	Gcc/Tcc	11/54	1	2	FACETS	0.91	0.74	1	0.91	0.74	1	CLONAL	1	TRUE	1	0.19	2		509	370	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491651	56491651	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	40	435	0	ENST00000267101.3:c.2543T>C	p.Val848Ala	p.V848A	ENST00000267101	NM_001982.3	848	gTt/gCt	21/28	1	2	FACETS	1	0.838	1	1	0.838	1	CLONAL	1	TRUE	1	0.19	2		435	418	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495686	56495686	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	41	468	0	ENST00000267101.3:c.3876G>T	p.Met1292Ile	p.M1292I	ENST00000267101	NM_001982.3	1292	atG/atT	28/28	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.19	2		468	340	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218185	69218185	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	26	443	1	ENST00000462284.1:c.401A>G	p.His134Arg	p.H134R	ENST00000462284	NM_002392.5	134	cAc/cGc	6/11	1	2	FACETS	0.866	0.687	1	0.866	0.687	1	CLONAL	1	TRUE	1	0.19	2		444	316	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222710	69222710	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1387843274	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	35	362	0	ENST00000462284.1:c.683C>T	p.Pro228Leu	p.P228L	ENST00000462284	NM_002392.5	228	cCg/cTg	8/11	1	2	FACETS	1	0.839	1	1	0.839	1	CLONAL	1	TRUE	1	0.19	2		362	360	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915497	112915497	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	30	518	0	ENST00000351677.2:c.896A>C	p.Glu299Ala	p.E299A	ENST00000351677	NM_002834.3	299	gAg/gCg	8/16	1	2	FACETS	0.814	0.656	0.993	0.814	0.656	0.993	CLONAL	1	TRUE	1	0.19	2		518	388	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794785	120794785	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375135447	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	45	753	1	ENST00000257552.2:c.572C>T	p.Ser191Leu	p.S191L	ENST00000257552	NM_002442.3	191	tCg/tTg	9/15	1	2	FACETS	0.876	0.735	1	0.876	0.735	1	CLONAL	1	TRUE	1	0.19	2		754	541	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120796811	120796811	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	39	569	0	ENST00000257552.2:c.448C>T	p.Arg150Ter	p.R150*	ENST00000257552	NM_002442.3	150	Cga/Tga	7/15	1	2	FACETS	1	0.833	1	1	0.833	1	CLONAL	1	TRUE	1	0.19	2		569	409	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225624	133225624	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	37	582	0	ENST00000320574.5:c.4040T>G	p.Leu1347Arg	p.L1347R	ENST00000320574	NM_006231.2	1347	cTg/cGg	32/49	1	2	FACETS	0.971	0.802	1	0.971	0.802	1	CLONAL	1	TRUE	1	0.19	2		582	401	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226017	133226017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770966534	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	37	627	3	ENST00000320574.5:c.3880C>T	p.Arg1294Cys	p.R1294C	ENST00000320574	NM_006231.2	1294	Cgt/Tgt	31/49	1	2	FACETS	0.774	0.638	0.927	0.774	0.638	0.927	CLONAL	1	TRUE	1	0.19	2		630	503	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257252	133257252	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1468404698	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	22	444	0	ENST00000320574.5:c.226A>G	p.Lys76Glu	p.K76E	ENST00000320574	NM_006231.2	76	Aag/Gag	3/49	1	2	FACETS	0.713	0.552	0.899	0.713	0.552	0.899	SUBCLONAL	1	TRUE	1	0.19	2		444	325	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896477	28896477	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	18	329	0	ENST00000282397.4:c.2973G>T	p.Lys991Asn	p.K991N	ENST00000282397	NM_002019.4	991	aaG/aaT	22/30	0.3	0	FACETS	0.49	0.369	0.634			1	SUBCLONAL	1	TRUE	0	0.19	0		329	313	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907486	32907486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769698255	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	24	242	0	ENST00000380152.3:c.1871C>T	p.Ala624Val	p.A624V	ENST00000380152		624	gCt/gTt	10/27	0.124442880638595	3	FACETS	1	0.907	1	0.656	0.517	0.814	CLONAL	1	TRUE	1	0.19	3		242	211	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972449	32972449	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	26	579	0	ENST00000380152.3:c.9799A>C	p.Lys3267Gln	p.K3267Q	ENST00000380152		3267	Aag/Cag	27/27	0.124442880638595	3	FACETS	0.644	0.509	0.8	0.322	0.254	0.4	SUBCLONAL	1	TRUE	1	0.19	3		579	465	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134960	41134960	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	19	327	0	ENST00000379561.5:c.668T>G	p.Phe223Cys	p.F223C	ENST00000379561	NM_002015.3	223	tTc/tGc	2/3	0.124442880638595	3	FACETS	0.869	0.661	1	0.435	0.33	0.557	CLONAL	1	TRUE	1	0.19	3		327	252	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349453	73349453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	35	508	0	ENST00000377767.4:c.883G>A	p.Glu295Lys	p.E295K	ENST00000377767	NM_014953.3	295	Gag/Aag	6/21	0.124442880638595	3	FACETS	0.875	0.717	1	0.438	0.358	0.527	CLONAL	1	TRUE	1	0.19	3		508	461	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506163	103506163	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	16	246	0	ENST00000355739.4:c.321G>T	p.Glu107Asp	p.E107D	ENST00000355739	NM_000123.3	107	gaG/gaT	3/15	0.124442880638595	3	FACETS	0.72	0.533	0.944	0.36	0.266	0.472	CLONAL	1	TRUE	1	0.19	3		246	256	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514924	103514924	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	15	272	0	ENST00000355739.4:c.1425A>C	p.Gln475His	p.Q475H	ENST00000355739	NM_000123.3	475	caA/caC	8/15	0.124442880638595	3	FACETS	0.745	0.545	0.985	0.373	0.272	0.493	CLONAL	1	TRUE	1	0.19	3		272	232	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061382	38061382	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	27	600	0	ENST00000250448.2:c.607C>A	p.Leu203Ile	p.L203I	ENST00000250448	NM_004496.3	203	Ctc/Atc	2/2	1	2	FACETS	0.633	0.503	0.782	0.633	0.503	0.782	SUBCLONAL	1	TRUE	1	0.19	2		600	449	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95577754	95577754	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	14	289	0	ENST00000393063.1:c.2156C>A	p.Thr719Asn	p.T719N	ENST00000393063	NM_030621.3	719	aCt/aAt	15/28	1	2	FACETS	0.542	0.391	0.725	0.542	0.391	0.725	SUBCLONAL	1	TRUE	1	0.19	2		289	272	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005368	42005368	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	27	358	0	ENST00000219905.7:c.3104C>A	p.Pro1035His	p.P1035H	ENST00000219905	NM_001164273.1	1035	cCt/cAt	9/24	1	2	FACETS	0.897	0.714	1	0.897	0.714	1	CLONAL	1	TRUE	1	0.19	2		358	317	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42026776	42026776	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	31	370	0	ENST00000219905.7:c.3900T>G	p.Asp1300Glu	p.D1300E	ENST00000219905	NM_001164273.1	1300	gaT/gaG	12/24	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.19	2		370	248	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43700201	43700201	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	40	446	0	ENST00000382044.4:c.5686A>C	p.Ile1896Leu	p.I1896L	ENST00000382044	NM_001141980.1	1896	Atc/Ctc	27/28	1	2	FACETS	0.972	0.809	1	0.972	0.809	1	CLONAL	1	TRUE	1	0.19	2		446	433	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724448	43724448	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	57	778	0	ENST00000382044.4:c.3619A>G	p.Ser1207Gly	p.S1207G	ENST00000382044	NM_001141980.1	1207	Agt/Ggt	17/28	1	2	FACETS	0.985	0.845	1	0.985	0.845	1	CLONAL	1	TRUE	1	0.19	2		778	609	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43772121	43772121	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	51	708	1	ENST00000382044.4:c.594G>T	p.Glu198Asp	p.E198D	ENST00000382044	NM_001141980.1	198	gaG/gaT	6/28	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.19	2		709	501	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007788	45007788	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	26	425	0	ENST00000558401.1:c.235G>T	p.Asp79Tyr	p.D79Y	ENST00000558401	NM_004048.2	79	Gac/Tac	2/4	1	2	FACETS	0.612	0.484	0.76	0.612	0.484	0.76	SUBCLONAL	1	TRUE	1	0.19	2		425	447	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472496	88472496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	23	550	0	ENST00000360948.2:c.2059G>A	p.Val687Ile	p.V687I	ENST00000360948	NM_001012338.2	687	Gtt/Att	16/19	1	2	FACETS	0.544	0.423	0.684	0.544	0.423	0.684	SUBCLONAL	1	TRUE	1	0.19	2		550	445	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630422	90630422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	28	544	0	ENST00000330062.3:c.889G>A	p.Val297Ile	p.V297I	ENST00000330062	NM_002168.2	297	Gtc/Atc	7/11	1	2	FACETS	0.698	0.558	0.859	0.698	0.558	0.859	SUBCLONAL	1	TRUE	1	0.19	2		544	422	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90634832	90634832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	23	466	0	ENST00000330062.3:c.160G>A	p.Asp54Asn	p.D54N	ENST00000330062	NM_002168.2	54	Gat/Aat	2/11	1	2	FACETS	0.574	0.446	0.722	0.574	0.446	0.722	SUBCLONAL	1	TRUE	1	0.19	2		466	422	SUCCESS
BLM	641	MSKCC	GRCh37	15	91334031	91334031	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	26	367	0	ENST00000355112.3:c.2976C>A	p.Phe992Leu	p.F992L	ENST00000355112	NM_000057.2	992	ttC/ttA	15/22	1	2	FACETS	0.819	0.649	1	0.819	0.649	1	CLONAL	1	TRUE	1	0.19	2		367	334	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251224	99251224	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	25	471	1	ENST00000268035.6:c.528G>T	p.Lys176Asn	p.K176N	ENST00000268035	NM_000875.3	176	aaG/aaT	2/21	1	2	FACETS	0.75	0.591	0.932	0.75	0.591	0.932	CLONAL	1	TRUE	1	0.19	2		472	351	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478055	99478055	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	16	332	0	ENST00000268035.6:c.2959T>C	p.Tyr987His	p.Y987H	ENST00000268035	NM_000875.3	987	Tac/Cac	16/21	1	2	FACETS	0.591	0.436	0.776	0.591	0.436	0.776	SUBCLONAL	1	TRUE	1	0.19	2		332	285	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127693	2127693	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768241596	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	27	422	0	ENST00000219476.3:c.2932C>T	p.Arg978Cys	p.R978C	ENST00000219476	NM_000548.3	978	Cgc/Tgc	26/42	1	2	FACETS	0.738	0.587	0.911	0.738	0.587	0.911	CLONAL	1	TRUE	1	0.19	2		422	385	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134353	2134353	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	39	733	0	ENST00000219476.3:c.4130A>G	p.Gln1377Arg	p.Q1377R	ENST00000219476	NM_000548.3	1377	cAg/cGg	34/42	1	2	FACETS	0.782	0.647	0.932	0.782	0.647	0.932	CLONAL	1	TRUE	1	0.19	2		733	525	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647930	3647930	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs774436086	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	51	751	0	ENST00000294008.3:c.1234A>G	p.Lys412Glu	p.K412E	ENST00000294008	NM_032444.2	412	Aag/Gag	6/15	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.19	2		751	511	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3651021	3651021	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	31	478	0	ENST00000294008.3:c.1122G>T	p.Gln374His	p.Q374H	ENST00000294008	NM_032444.2	374	caG/caT	5/15	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.19	2		478	282	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038694	14038694	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	22	200	0	ENST00000311895.7:c.2017+2T>C		p.X673_splice	ENST00000311895	NM_005236.2	673			1	2	FACETS	0.759	0.589	0.957	0.759	0.589	0.957	CLONAL	1	TRUE	1	0.19	2		200	305	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647073	23647073	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	48	772	1	ENST00000261584.4:c.794T>C	p.Ile265Thr	p.I265T	ENST00000261584	NM_024675.3	265	aTt/aCt	4/13	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.19	2		773	458	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785717	50785717	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	42	540	0	ENST00000398568.2:c.707T>C	p.Val236Ala	p.V236A	ENST00000398568	NM_001042412.1	236	gTt/gCt	4/18	1	2	FACETS	0.9	0.752	1	0.9	0.752	1	CLONAL	1	TRUE	1	0.19	2		540	491	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50820836	50820836	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	16	351	0	ENST00000398568.2:c.2011G>T	p.Gly671Ter	p.G671*	ENST00000398568	NM_001042412.1	671	Gga/Tga	12/18	1	2	FACETS	0.653	0.483	0.856	0.653	0.483	0.856	SUBCLONAL	1	TRUE	1	0.19	2		351	258	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56872974	56872974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	12	335	0	ENST00000308159.5:c.2129C>T	p.Ala710Val	p.A710V	ENST00000308159	NM_014669.4	710	gCt/gTt	19/22	1	2	FACETS	0.574	0.403	0.784	0.574	0.403	0.784	SUBCLONAL	1	TRUE	1	0.19	2		335	220	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644931	67644931	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	31	464	1	ENST00000264010.4:c.196C>A	p.Leu66Met	p.L66M	ENST00000264010	NM_006565.3	66	Ctg/Atg	3/12	1	2	FACETS	0.954	0.773	1	0.954	0.773	1	CLONAL	1	TRUE	1	0.19	2		465	342	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671720	67671720	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	23	458	0	ENST00000264010.4:c.2129A>C	p.Asp710Ala	p.D710A	ENST00000264010	NM_006565.3	710	gAt/gCt	12/12	1	2	FACETS	0.734	0.572	0.921	0.734	0.572	0.921	CLONAL	1	TRUE	1	0.19	2		458	330	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829135	72829135	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs770938985	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	23	588	0	ENST00000268489.5:c.7446G>T	p.Gln2482His	p.Q2482H	ENST00000268489	NM_006885.3	2482	caG/caT	9/10	1	2	FACETS	0.637	0.496	0.801	0.637	0.496	0.801	SUBCLONAL	1	TRUE	1	0.19	2		588	380	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72833998	72833998	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	32	422	0	ENST00000268489.5:c.3895A>G	p.Ser1299Gly	p.S1299G	ENST00000268489	NM_006885.3	1299	Agc/Ggc	8/10	1	2	FACETS	0.715	0.58	0.868	0.715	0.58	0.868	SUBCLONAL	1	TRUE	1	0.19	2		422	471	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845598	72845598	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1303587779	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	32	608	0	ENST00000268489.5:c.3742G>A	p.Val1248Met	p.V1248M	ENST00000268489	NM_006885.3	1248	Gtg/Atg	7/10	1	2	FACETS	0.658	0.533	0.799	0.658	0.533	0.799	SUBCLONAL	1	TRUE	1	0.19	2		608	512	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81904523	81904523	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	14	328	0	ENST00000359376.3:c.631T>C	p.Phe211Leu	p.F211L	ENST00000359376	NM_002661.3	211	Ttt/Ctt	7/33	1	2	FACETS	0.737	0.533	0.982	0.737	0.533	0.982	CLONAL	1	TRUE	1	0.19	2		328	200	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350878	89350878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1336431815	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	26	875	1	ENST00000301030.4:c.2072G>A	p.Arg691His	p.R691H	ENST00000301030	NM_001256183.1	691	cGc/cAc	9/13	1	2	FACETS	0.722	0.572	0.895	0.722	0.572	0.895	SUBCLONAL	1	TRUE	1	0.19	2		876	379	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877132	89877132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372691338	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	40	372	0	ENST00000389301.3:c.505G>A	p.Glu169Lys	p.E169K	ENST00000389301	NM_000135.2	169	Gaa/Aaa	5/43	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.19	2		372	294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579526	7579526	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	42	709	0	ENST00000269305.4:c.161T>C	p.Phe54Ser	p.F54S	ENST00000269305	NM_001126112.2	54	tTc/tCc	4/11	0.0810666718303437	0	FACETS	0.807	0.674	0.954			1	INDETERMINATE	1	TRUE	0	0.19	0		709	444	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983251	7983251	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	21	375	2	ENST00000319144.4:c.763G>A	p.Ala255Thr	p.A255T	ENST00000319144	NM_001139.2	255	Gcc/Acc	7/15	0.0810666718303437	0	FACETS	0.635	0.489	0.804			1	INDETERMINATE	1	TRUE	0	0.19	0		377	282	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110180	8110180	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1482688018	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	44	447	0	ENST00000585124.1:c.425A>G	p.Asn142Ser	p.N142S	ENST00000585124	NM_004217.3	142	aAc/aGc	6/9	0.0810666718303437	0	FACETS	1	0.843	1			1	INDETERMINATE	1	TRUE	0	0.19	0		447	374	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974921	15974921	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	27	454	0	ENST00000268712.3:c.3954T>G	p.Ile1318Met	p.I1318M	ENST00000268712	NM_006311.3	1318	atT/atG	30/46	0.0810666718303437	0	FACETS	0.586	0.466	0.723			1	INDETERMINATE	1	TRUE	0	0.19	0		454	393	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496961	29496961	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	22	350	0	ENST00000356175.3:c.532G>T	p.Glu178Ter	p.E178*	ENST00000356175	NM_000267.3	178	Gaa/Taa	5/57	0.0810666718303437	0	FACETS	0.736	0.571	0.925			1	INDETERMINATE	1	TRUE	0	0.19	0		350	255	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586048	29586048	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1555618634	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	14	365	0	ENST00000356175.3:c.4270-2A>G		p.X1424_splice	ENST00000356175	NM_000267.3	1424			0.0810666718303437	0	FACETS	0.444	0.32	0.593			1	INDETERMINATE	1	TRUE	0	0.19	0		365	269	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657513	29657513	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	15	322	0	ENST00000356175.3:c.5746T>C	p.Ser1916Pro	p.S1916P	ENST00000356175	NM_000267.3	1916	Tct/Cct	38/57	0.0810666718303437	0	FACETS	0.633	0.464	0.835			1	INDETERMINATE	1	TRUE	0	0.19	0		322	202	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29701166	29701166	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	17	288	0	ENST00000356175.3:c.8450T>C	p.Ile2817Thr	p.I2817T	ENST00000356175	NM_000267.3	2817	aTc/aCc	57/57	0.0810666718303437	0	FACETS	0.468	0.348	0.609			1	INDETERMINATE	1	TRUE	0	0.19	0		288	310	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618452	37618452	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	30	366	0	ENST00000447079.4:c.128A>G	p.Lys43Arg	p.K43R	ENST00000447079	NM_015083.1	43	aAg/aGg	1/14	0.0810666718303437	0	FACETS	0.833	0.673	1			1	INDETERMINATE	1	TRUE	0	0.19	0		366	307	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627640	37627640	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	29	550	0	ENST00000447079.4:c.1555G>T	p.Glu519Ter	p.E519*	ENST00000447079	NM_015083.1	519	Gaa/Taa	2/14	0.0810666718303437	0	FACETS	0.663	0.532	0.812			1	INDETERMINATE	1	TRUE	0	0.19	0		550	373	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676276	37676276	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	38	544	0	ENST00000447079.4:c.3031G>T	p.Ala1011Ser	p.A1011S	ENST00000447079	NM_015083.1	1011	Gct/Tct	11/14	0.0810666718303437	0	FACETS	0.812	0.672	0.968			1	INDETERMINATE	1	TRUE	0	0.19	0		544	399	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686900	37686900	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	35	367	0	ENST00000447079.4:c.3804G>T	p.Glu1268Asp	p.E1268D	ENST00000447079	NM_015083.1	1268	gaG/gaT	14/14	0.0810666718303437	0	FACETS	0.8	0.657	0.961			1	INDETERMINATE	1	TRUE	0	0.19	0		367	373	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687382	37687382	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1167681980	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	24	391	0	ENST00000447079.4:c.4286C>A	p.Ser1429Tyr	p.S1429Y	ENST00000447079	NM_015083.1	1429	tCt/tAt	14/14	0.0810666718303437	0	FACETS	0.622	0.488	0.777			1	INDETERMINATE	1	TRUE	0	0.19	0		391	329	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512431	38512431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	30	732	1	ENST00000254066.5:c.1342C>T	p.Leu448Phe	p.L448F	ENST00000254066	NM_000964.3	448	Ctc/Ttc	9/9	0.0810666718303437	0	FACETS	0.583	0.469	0.712			1	INDETERMINATE	1	TRUE	0	0.19	0		733	439	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40460314	40460314	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	36	446	0	ENST00000345506.4:c.2025G>T	p.Lys675Asn	p.K675N	ENST00000345506	NM_003152.3	675	aaG/aaT	17/20	0.0810666718303437	0	FACETS	0.777	0.639	0.931			1	INDETERMINATE	1	TRUE	0	0.19	0		446	395	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40871171	40871171	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	28	587	0	ENST00000428826.2:c.719T>C	p.Ile240Thr	p.I240T	ENST00000428826		240	aTt/aCt	8/21	0.0810666718303437	0	FACETS	0.571	0.456	0.703			1	INDETERMINATE	1	TRUE	0	0.19	0		587	418	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40879669	40879669	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	26	416	0	ENST00000428826.2:c.230A>G	p.His77Arg	p.H77R	ENST00000428826		77	cAc/cGc	4/21	0.0810666718303437	0	FACETS	0.704	0.558	0.87			1	INDETERMINATE	1	TRUE	0	0.19	0		416	315	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244366	41244366	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	47	818	0	ENST00000357654.3:c.3182T>C	p.Ile1061Thr	p.I1061T	ENST00000357654	NM_007294.3	1061	aTa/aCa	10/23	0.0810666718303437	0	FACETS	1	0.936	1			1	INDETERMINATE	1	TRUE	0	0.19	0		818	331	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244481	41244481	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	26	678	0	ENST00000357654.3:c.3067G>T	p.Val1023Leu	p.V1023L	ENST00000357654	NM_007294.3	1023	Gtg/Ttg	10/23	0.0810666718303437	0	FACETS	0.815	0.647	1			1	INDETERMINATE	1	TRUE	0	0.19	0		678	272	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245387	41245387	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	37	741	0	ENST00000357654.3:c.2161T>A	p.Phe721Ile	p.F721I	ENST00000357654	NM_007294.3	721	Ttt/Att	10/23	0.0810666718303437	0	FACETS	0.995	0.823	1			1	INDETERMINATE	1	TRUE	0	0.19	0		741	317	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678191	58678191	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	64	717	0	ENST00000305921.3:c.416G>A	p.Cys139Tyr	p.C139Y	ENST00000305921	NM_003620.3	139	tGc/tAc	1/6	0.0810666718303437	0	FACETS	0.783	0.677	0.898			1	INDETERMINATE	1	TRUE	0	0.19	0		717	697	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760679	59760679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765545033	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	22	560	0	ENST00000259008.2:c.3728G>A	p.Gly1243Asp	p.G1243D	ENST00000259008	NM_032043.2	1243	gGc/gAc	20/20	0.0810666718303437	0	FACETS	0.632	0.49	0.796			1	INDETERMINATE	1	TRUE	0	0.19	0		560	297	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821888	59821888	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	33	478	0	ENST00000259008.2:c.2162A>G	p.Lys721Arg	p.K721R	ENST00000259008	NM_032043.2	721	aAg/aGg	15/20	0.0810666718303437	0	FACETS	0.693	0.564	0.838			1	INDETERMINATE	1	TRUE	0	0.19	0		478	406	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63537620	63537620	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748459029	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	32	610	0	ENST00000307078.5:c.1012C>T	p.His338Tyr	p.H338Y	ENST00000307078	NM_004655.3	338	Cat/Tat	4/11	0.0810666718303437	0	FACETS	0.563	0.456	0.683			1	INDETERMINATE	1	TRUE	0	0.19	0		610	485	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554732	63554732	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	26	332	0	ENST00000307078.5:c.7A>C	p.Ser3Arg	p.S3R	ENST00000307078	NM_004655.3	3	Agc/Cgc	2/11	0.0810666718303437	0	FACETS	0.783	0.622	0.968			1	INDETERMINATE	1	TRUE	0	0.19	0		332	283	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756806	756806	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	22	457	0	ENST00000314574.4:c.22G>T	p.Glu8Ter	p.E8*	ENST00000314574	NM_005433.3	8	Gaa/Taa	2/12	1	2	FACETS	0.695	0.539	0.877	0.695	0.539	0.877	SUBCLONAL	1	TRUE	1	0.19	2		457	333	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39537622	39537622	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	24	303	0	ENST00000262039.4:c.156G>T	p.Glu52Asp	p.E52D	ENST00000262039	NM_002647.2	52	gaG/gaT	2/25	1	2	FACETS	0.805	0.631	1	0.805	0.631	1	CLONAL	1	TRUE	1	0.19	2		303	314	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56401545	56401545	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	19	370	0	ENST00000348428.3:c.1407C>A	p.Asp469Glu	p.D469E	ENST00000348428	NM_006785.3	469	gaC/gaA	12/17	1	2	FACETS	0.619	0.47	0.795	0.619	0.47	0.795	SUBCLONAL	1	TRUE	1	0.19	2		370	323	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414979	56414979	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	28	533	0	ENST00000348428.3:c.2380G>A	p.Ala794Thr	p.A794T	ENST00000348428	NM_006785.3	794	Gct/Act	17/17	1	2	FACETS	0.717	0.573	0.882	0.717	0.573	0.882	SUBCLONAL	1	TRUE	1	0.19	2		533	411	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191063	2191063	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	26	404	0	ENST00000398665.3:c.317T>C	p.Leu106Pro	p.L106P	ENST00000398665	NM_032482.2	106	cTc/cCc	5/28	1	2	FACETS	1	0.799	1	1	0.799	1	CLONAL	1	TRUE	1	0.19	2		404	272	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217000	2217000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772792385	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	43	691	0	ENST00000398665.3:c.2455G>A	p.Val819Met	p.V819M	ENST00000398665	NM_032482.2	819	Gtg/Atg	21/28	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.19	2		691	437	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217916	2217916	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs759690350	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	35	595	0	ENST00000398665.3:c.2690C>T	p.Ala897Val	p.A897V	ENST00000398665	NM_032482.2	897	gCg/gTg	22/28	1	2	FACETS	0.813	0.666	0.978	0.813	0.666	0.978	CLONAL	1	TRUE	1	0.19	2		595	453	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117488	4117488	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	23	441	1	ENST00000262948.5:c.232C>A	p.Leu78Met	p.L78M	ENST00000262948	NM_030662.3	78	Ctg/Atg	2/11	1	2	FACETS	1	0.819	1	1	0.819	1	CLONAL	1	TRUE	1	0.19	2		442	230	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231504	5231504	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	22	565	0	ENST00000357368.4:c.1972T>C	p.Tyr658His	p.Y658H	ENST00000357368	NM_002850.3	658	Tac/Cac	14/38	1	2	FACETS	0.529	0.409	0.669	0.529	0.409	0.669	SUBCLONAL	1	TRUE	1	0.19	2		565	438	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247842	10247842	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	45	732	0	ENST00000340748.4:c.4360A>G	p.Lys1454Glu	p.K1454E	ENST00000340748		1454	Aag/Gag	36/40	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.19	2		732	460	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251844	10251844	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	42	615	0	ENST00000340748.4:c.3283A>C	p.Ser1095Arg	p.S1095R	ENST00000340748		1095	Agc/Cgc	30/40	1	2	FACETS	0.935	0.781	1	0.935	0.781	1	CLONAL	1	TRUE	1	0.19	2		615	473	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10283801	10283801	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1211520360	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	57	562	0	ENST00000340748.4:c.685A>G	p.Thr229Ala	p.T229A	ENST00000340748		229	Acg/Gcg	8/40	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.19	2		562	468	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10284572	10284572	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	20	358	1	ENST00000340748.4:c.610A>T	p.Arg204Ter	p.R204*	ENST00000340748		204	Aga/Tga	7/40	1	2	FACETS	0.819	0.627	1	0.819	0.627	1	CLONAL	1	TRUE	1	0.19	2		359	257	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10292754	10292754	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	22	318	0	ENST00000340748.4:c.81-1G>T		p.X27_splice	ENST00000340748		27			1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.19	2		318	189	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599919	10599919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375390113	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	46	580	0	ENST00000171111.5:c.1657C>T	p.Arg553Trp	p.R553W	ENST00000171111	NM_203500.1	553	Cgg/Tgg	5/6	1	2	FACETS	0.931	0.784	1	0.931	0.784	1	CLONAL	1	TRUE	1	0.19	2		580	520	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602455	10602455	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	30	611	0	ENST00000171111.5:c.1123T>C	p.Tyr375His	p.Y375H	ENST00000171111	NM_203500.1	375	Tac/Cac	3/6	1	2	FACETS	0.761	0.613	0.929	0.761	0.613	0.929	CLONAL	1	TRUE	1	0.19	2		611	415	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610676	10610676	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	20	440	1	ENST00000171111.5:c.34del	p.Ala12ProfsTer20	p.A12Pfs*20	ENST00000171111	NM_203500.1	12	Gcc/cc	2/6	1	2	FACETS	0.614	0.469	0.784	0.614	0.469	0.784	SUBCLONAL	1	TRUE	1	0.19	2		441	343	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170789	11170789	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370639203	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	24	557	0	ENST00000358026.2:c.4933C>T	p.Arg1645Trp	p.R1645W	ENST00000358026	NM_001128849.1	1645	Cgg/Tgg	35/36	1	2	FACETS	0.579	0.453	0.725	0.579	0.453	0.725	SUBCLONAL	1	TRUE	1	0.19	2		557	436	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272261	15272261	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	26	642	0	ENST00000263388.2:c.6178T>C	p.Ser2060Pro	p.S2060P	ENST00000263388	NM_000435.2	2060	Tcc/Ccc	33/33	1	2	FACETS	0.713	0.564	0.883	0.713	0.564	0.883	SUBCLONAL	1	TRUE	1	0.19	2		642	384	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288867	15288867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	21	161	0	ENST00000263388.2:c.3872G>A	p.Arg1291His	p.R1291H	ENST00000263388	NM_000435.2	1291	cGc/cAc	24/33	1	2	FACETS	0.86	0.664	1	0.86	0.664	1	CLONAL	1	TRUE	1	0.19	2		161	257	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295717	15295717	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1186782199	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	33	608	0	ENST00000263388.2:c.2410G>T	p.Gly804Cys	p.G804C	ENST00000263388	NM_000435.2	804	Ggc/Tgc	15/33	1	2	FACETS	0.895	0.73	1	0.895	0.73	1	CLONAL	1	TRUE	1	0.19	2		608	388	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384974	17384974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765161255	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	31	734	2	ENST00000359435.4:c.524C>T	p.Thr175Met	p.T175M	ENST00000359435	NM_001033549.1	175	aCg/aTg	5/9	1	2	FACETS	0.745	0.602	0.907	0.745	0.602	0.907	CLONAL	1	TRUE	1	0.19	2		736	438	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273084	18273084	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	27	576	0	ENST00000222254.8:c.974T>C	p.Leu325Pro	p.L325P	ENST00000222254	NM_005027.3	325	cTg/cCg	8/16	1	2	FACETS	0.859	0.684	1	0.859	0.684	1	CLONAL	1	TRUE	1	0.19	2		576	331	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18960882	18960882	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	38	439	0	ENST00000262803.5:c.462-2A>G		p.X154_splice	ENST00000262803	NM_002911.3	154			1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.19	2		439	372	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216453	36216453	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs765902603	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	45	746	0	ENST00000222270.7:c.3716A>G	p.Gln1239Arg	p.Q1239R	ENST00000222270	NM_014727.1	1239	cAg/cGg	12/37	1	2	FACETS	0.787	0.66	0.927	0.787	0.66	0.927	CLONAL	1	TRUE	1	0.19	2		746	602	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748524	40748524	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	42	767	1	ENST00000392038.2:c.358A>G	p.Met120Val	p.M120V	ENST00000392038	NM_001626.4	120	Atg/Gtg	5/14	1	2	FACETS	0.989	0.826	1	0.989	0.826	1	CLONAL	1	TRUE	1	0.19	2		768	447	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748856	41748856	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781747516	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	24	553	0	ENST00000301178.4:c.1381G>A	p.Ala461Thr	p.A461T	ENST00000301178	NM_021913.4	461	Gct/Act	11/20	1	2	FACETS	0.529	0.413	0.662	0.529	0.413	0.662	SUBCLONAL	1	TRUE	1	0.19	2		553	478	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383159	42383159	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs370313642	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	45	537	0	ENST00000221972.3:c.179A>G	p.Asn60Ser	p.N60S	ENST00000221972	NM_021601.3	60	aAc/aGc	2/5	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.19	2		537	450	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797404	42797404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748515698	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	33	627	0	ENST00000575354.2:c.3766C>T	p.Arg1256Trp	p.R1256W	ENST00000575354	NM_015125.3	1256	Cgg/Tgg	15/20	1	2	FACETS	0.789	0.643	0.955	0.789	0.643	0.955	CLONAL	1	TRUE	1	0.19	2		627	440	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725143	47725143	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	47	659	0	ENST00000449228.1:c.601A>G	p.Thr201Ala	p.T201A	ENST00000449228	NM_001127240.2	201	Acc/Gcc	4/4	1	2	FACETS	0.926	0.782	1	0.926	0.782	1	CLONAL	1	TRUE	1	0.19	2		659	534	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52705240	52705240	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	20	448	0	ENST00000322088.6:c.122C>A	p.Ala41Asp	p.A41D	ENST00000322088	NM_014225.5	41	gCc/gAc	2/15	1	2	FACETS	0.564	0.431	0.721	0.564	0.431	0.721	SUBCLONAL	1	TRUE	1	0.19	2		448	373	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966037	25966037	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	37	742	0	ENST00000435504.4:c.3169G>T	p.Gly1057Ter	p.G1057*	ENST00000435504		1057	Gga/Tga	13/13	1	2	FACETS	0.879	0.725	1	0.879	0.725	1	CLONAL	1	TRUE	1	0.19	2		742	443	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416499	29416499	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	29	721	1	ENST00000389048.3:c.4454C>A	p.Pro1485His	p.P1485H	ENST00000389048	NM_004304.4	1485	cCt/cAt	29/29	1	2	FACETS	0.579	0.464	0.711	0.579	0.464	0.711	SUBCLONAL	1	TRUE	1	0.19	2		722	527	SUCCESS
ALK	238	MSKCC	GRCh37	2	29436853	29436853	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	20	347	0	ENST00000389048.3:c.3740A>G	p.His1247Arg	p.H1247R	ENST00000389048	NM_004304.4	1247	cAc/cGc	24/29	1	2	FACETS	0.571	0.436	0.729	0.571	0.436	0.729	SUBCLONAL	1	TRUE	1	0.19	2		347	369	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250221	39250221	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	32	821	0	ENST00000402219.2:c.1348C>A	p.Leu450Ile	p.L450I	ENST00000402219	NM_005633.3	450	Ctt/Att	10/23	1	2	FACETS	0.693	0.562	0.842	0.693	0.562	0.842	SUBCLONAL	1	TRUE	1	0.19	2		821	486	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705476	47705476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs386833406	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	12	362	0	ENST00000233146.2:c.2276G>A	p.Gly759Glu	p.G759E	ENST00000233146	NM_000251.2	759	gGa/gAa	14/16	1	2	FACETS	0.529	0.371	0.723	0.529	0.371	0.723	SUBCLONAL	1	TRUE	1	0.19	2		362	239	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705508	47705508	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs63750684	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	23	377	0	ENST00000233146.2:c.2308A>G	p.Ile770Val	p.I770V	ENST00000233146	NM_000251.2	770	Att/Gtt	14/16	1	2	FACETS	0.815	0.636	1	0.815	0.636	1	CLONAL	1	TRUE	1	0.19	2		377	297	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096540	178096540	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs370697150	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	25	340	0	ENST00000397062.3:c.791A>G	p.Asn264Ser	p.N264S	ENST00000397062	NM_006164.4	264	aAc/aGc	5/5	1	2	FACETS	0.774	0.61	0.962	0.774	0.61	0.962	CLONAL	1	TRUE	1	0.19	2		340	340	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136256	202136256	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	34	536	0	ENST00000358485.4:c.500T>A	p.Ile167Asn	p.I167N	ENST00000358485	NM_001080125.1	167	aTt/aAt	3/9	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.19	2		536	317	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288900	212288900	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	19	292	0	ENST00000342788.4:c.2846T>G	p.Val949Gly	p.V949G	ENST00000342788	NM_005235.2	949	gTt/gGt	23/28	1	2	FACETS	0.702	0.533	0.9	0.702	0.533	0.9	SUBCLONAL	1	TRUE	1	0.19	2		292	285	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812203	212812203	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	15	376	0	ENST00000342788.4:c.373A>G	p.Lys125Glu	p.K125E	ENST00000342788	NM_005235.2	125	Aaa/Gaa	3/28	1	2	FACETS	0.585	0.427	0.774	0.585	0.427	0.774	SUBCLONAL	1	TRUE	1	0.19	2		376	270	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662181	227662181	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	30	569	0	ENST00000305123.5:c.1274T>C	p.Phe425Ser	p.F425S	ENST00000305123	NM_005544.2	425	tTc/tCc	1/2	1	2	FACETS	0.822	0.663	1	0.822	0.663	1	CLONAL	1	TRUE	1	0.19	2		569	384	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793387	242793387	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	30	690	0	ENST00000334409.5:c.690G>A	p.Trp230Ter	p.W230*	ENST00000334409	NM_005018.2	230	tgG/tgA	5/5	1	2	FACETS	0.679	0.546	0.83	0.679	0.546	0.83	SUBCLONAL	1	TRUE	1	0.19	2		690	465	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525017	9525017	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	11	284	0	ENST00000353224.5:c.1868A>G	p.Glu623Gly	p.E623G	ENST00000353224	NM_177990.2	623	gAg/gGg	8/10	1	2	FACETS	0.559	0.386	0.774	0.559	0.386	0.774	SUBCLONAL	1	TRUE	1	0.19	2		284	207	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021615	31021615	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	18	435	0	ENST00000375687.4:c.1614G>T	p.Lys538Asn	p.K538N	ENST00000375687	NM_015338.5	538	aaG/aaT	12/13	1	2	FACETS	0.581	0.437	0.752	0.581	0.437	0.752	SUBCLONAL	1	TRUE	1	0.19	2		435	326	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024426	31024426	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	28	599	1	ENST00000375687.4:c.3915del	p.Phe1305LeufsTer145	p.F1305Lfs*145	ENST00000375687	NM_015338.5	1304	cTt/ct	13/13	1	2	FACETS	0.764	0.61	0.938	0.764	0.61	0.938	CLONAL	1	TRUE	1	0.19	2		600	386	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024843	31024843	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	27	586	0	ENST00000375687.4:c.4328A>C	p.Lys1443Thr	p.K1443T	ENST00000375687	NM_015338.5	1443	aAg/aCg	13/13	1	2	FACETS	0.682	0.542	0.842	0.682	0.542	0.842	SUBCLONAL	1	TRUE	1	0.19	2		586	417	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39690033	39690033	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	17	156	0	ENST00000361337.2:c.59-1G>T		p.X20_splice	ENST00000361337	NM_003286.2	20			1	2	FACETS	0.932	0.698	1	0.932	0.698	1	CLONAL	1	TRUE	1	0.19	2		156	192	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728820	39728820	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	18	305	0	ENST00000361337.2:c.1100A>G	p.His367Arg	p.H367R	ENST00000361337	NM_003286.2	367	cAc/cGc	12/21	1	2	FACETS	0.588	0.443	0.761	0.588	0.443	0.761	SUBCLONAL	1	TRUE	1	0.19	2		305	322	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757422	40757422	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	29	533	0	ENST00000373198.4:c.2876C>A	p.Ser959Tyr	p.S959Y	ENST00000373198	NM_133170.3	959	tCt/tAt	20/32	1	2	FACETS	0.656	0.526	0.805	0.656	0.526	0.805	SUBCLONAL	1	TRUE	1	0.19	2		533	465	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256431	46256431	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs72645252	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	44	427	0	ENST00000371998.3:c.659G>T	p.Arg220Ile	p.R220I	ENST00000371998		220	aGa/aTa	7/23	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.19	2		427	424	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262366	46262366	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200506500	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	15	447	0	ENST00000371998.3:c.950G>A	p.Arg317His	p.R317H	ENST00000371998		317	cGt/cAt	9/23	1	2	FACETS	0.598	0.437	0.792	0.598	0.437	0.792	SUBCLONAL	1	TRUE	1	0.19	2		447	264	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264799	46264799	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	24	373	0	ENST00000371998.3:c.1669A>G	p.Thr557Ala	p.T557A	ENST00000371998		557	Acc/Gcc	12/23	1	2	FACETS	0.896	0.704	1	0.896	0.704	1	CLONAL	1	TRUE	1	0.19	2		373	282	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281730	46281730	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	31	578	0	ENST00000371998.3:c.4177G>A	p.Val1393Met	p.V1393M	ENST00000371998		1393	Gtg/Atg	22/23	1	2	FACETS	0.728	0.589	0.887	0.728	0.589	0.887	SUBCLONAL	1	TRUE	1	0.19	2		578	448	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319390	62319390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149952845	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	56	741	3	ENST00000360203.5:c.1582G>A	p.Ala528Thr	p.A528T	ENST00000360203	NM_001283009.1	528	Gcg/Acg	18/35	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.19	2		744	498	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091734	29091734	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	12	204	0	ENST00000328354.6:c.1223T>C	p.Val408Ala	p.V408A	ENST00000328354	NM_007194.3	408	gTg/gCg	11/15	0.0810666718303437	0	FACETS	0.793	0.561	1			1	INDETERMINATE	1	TRUE	0	0.19	0		204	129	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130623	29130623	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	28	457	0	ENST00000328354.6:c.87A>C	p.Gln29His	p.Q29H	ENST00000328354	NM_007194.3	29	caA/caC	2/15	0.0810666718303437	0	FACETS	0.587	0.468	0.721			1	INDETERMINATE	1	TRUE	0	0.19	0		457	407	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546008	41546008	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	56	694	0	ENST00000263253.7:c.2623T>C	p.Ser875Pro	p.S875P	ENST00000263253	NM_001429.3	875	Tcc/Ccc	14/31	0.0810666718303437	0	FACETS	0.918	0.787	1			1	INDETERMINATE	1	TRUE	0	0.19	0		694	520	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546126	41546126	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	34	378	1	ENST00000263253.7:c.2741C>A	p.Pro914His	p.P914H	ENST00000263253	NM_001429.3	914	cCt/cAt	14/31	0.0810666718303437	0	FACETS	0.765	0.626	0.921			1	INDETERMINATE	1	TRUE	0	0.19	0		379	379	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546198	41546198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	24	264	0	ENST00000263253.7:c.2813C>T	p.Thr938Ile	p.T938I	ENST00000263253	NM_001429.3	938	aCt/aTt	14/31	0.0810666718303437	0	FACETS	0.914	0.719	1			1	INDETERMINATE	1	TRUE	0	0.19	0		264	224	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551029	41551029	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	33	369	0	ENST00000263253.7:c.3173T>C	p.Leu1058Pro	p.L1058P	ENST00000263253	NM_001429.3	1058	cTg/cCg	17/31	0.0810666718303437	0	FACETS	0.773	0.63	0.933			1	INDETERMINATE	1	TRUE	0	0.19	0		369	364	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553179	41553179	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	32	376	0	ENST00000263253.7:c.3268T>G	p.Phe1090Val	p.F1090V	ENST00000263253	NM_001429.3	1090	Ttt/Gtt	18/31	0.0810666718303437	0	FACETS	1	0.921	1			1	INDETERMINATE	1	TRUE	0	0.19	0		376	217	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089140	37089140	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	19	460	1	ENST00000231790.2:c.1862T>C	p.Met621Thr	p.M621T	ENST00000231790	NM_000249.3	621	aTg/aCg	16/19	1	2	FACETS	0.625	0.474	0.803	0.625	0.474	0.803	SUBCLONAL	1	TRUE	1	0.19	2		461	320	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182026	38182026	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	30	451	0	ENST00000396334.3:c.650T>C	p.Val217Ala	p.V217A	ENST00000396334	NM_002468.4	217	gTc/gCc	3/5	1	2	FACETS	0.689	0.555	0.843	0.689	0.555	0.843	SUBCLONAL	1	TRUE	1	0.19	2		451	458	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098936	47098936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	42	507	0	ENST00000409792.3:c.6338G>A	p.Arg2113His	p.R2113H	ENST00000409792	NM_014159.6	2113	cGc/cAc	15/21	1	2	FACETS	0.78	0.65	0.924	0.78	0.65	0.924	CLONAL	1	TRUE	1	0.19	2		507	567	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162122	47162122	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537154191	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	19	455	0	ENST00000409792.3:c.4004G>A	p.Arg1335His	p.R1335H	ENST00000409792	NM_014159.6	1335	cGt/cAt	3/21	1	2	FACETS	0.746	0.567	0.957	0.746	0.567	0.957	CLONAL	1	TRUE	1	0.19	2		455	268	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164980	47164980	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	20	342	0	ENST00000409792.3:c.1146A>C	p.Lys382Asn	p.K382N	ENST00000409792	NM_014159.6	382	aaA/aaC	3/21	1	2	FACETS	0.835	0.64	1	0.835	0.64	1	CLONAL	1	TRUE	1	0.19	2		342	252	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165759	47165759	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	35	559	0	ENST00000409792.3:c.367A>G	p.Thr123Ala	p.T123A	ENST00000409792	NM_014159.6	123	Acc/Gcc	3/21	1	2	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	TRUE	1	0.19	2		559	353	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165955	47165955	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	50	467	0	ENST00000409792.3:c.171A>C	p.Lys57Asn	p.K57N	ENST00000409792	NM_014159.6	57	aaA/aaC	3/21	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.19	2		467	435	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936105	49936105	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	34	513	0	ENST00000296474.3:c.1565T>C	p.Ile522Thr	p.I522T	ENST00000296474	NM_002447.2	522	aTc/aCc	4/20	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.19	2		513	322	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936341	49936341	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	26	473	0	ENST00000296474.3:c.1507A>G	p.Ser503Gly	p.S503G	ENST00000296474	NM_002447.2	503	Agt/Ggt	3/20	1	2	FACETS	0.756	0.599	0.936	0.756	0.599	0.936	CLONAL	1	TRUE	1	0.19	2		473	362	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939816	49939816	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	46	661	0	ENST00000296474.3:c.1227C>A	p.Asn409Lys	p.N409K	ENST00000296474	NM_002447.2	409	aaC/aaA	1/20	1	2	FACETS	0.965	0.812	1	0.965	0.812	1	CLONAL	1	TRUE	1	0.19	2		661	502	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712585	52712585	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	48	428	0	ENST00000394830.3:c.167C>T	p.Thr56Ile	p.T56I	ENST00000394830	NM_018313.4	56	aCc/aTc	3/30	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.19	2		428	403	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582343	119582343	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	24	371	0	ENST00000316626.5:c.1058T>C	p.Phe353Ser	p.F353S	ENST00000316626		353	tTt/tCt	10/12	1	2	FACETS	0.538	0.42	0.673	0.538	0.42	0.673	SUBCLONAL	1	TRUE	1	0.19	2		371	470	SUCCESS
ATR	545	MSKCC	GRCh37	3	142204082	142204082	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	26	474	0	ENST00000350721.4:c.6121del	p.Tyr2041ThrfsTer9	p.Y2041Tfs*9	ENST00000350721	NM_001184.3	2041	Tac/ac	36/47	1	2	FACETS	0.641	0.507	0.795	0.641	0.507	0.795	SUBCLONAL	1	TRUE	1	0.19	2		474	427	SUCCESS
ATR	545	MSKCC	GRCh37	3	142253959	142253959	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	28	339	1	ENST00000350721.4:c.3908C>A	p.Ala1303Asp	p.A1303D	ENST00000350721	NM_001184.3	1303	gCt/gAt	21/47	1	2	FACETS	0.79	0.632	0.971	0.79	0.632	0.971	CLONAL	1	TRUE	1	0.19	2		340	373	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374929	149374929	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	59	586	0	ENST00000360632.3:c.165G>T	p.Glu55Asp	p.E55D	ENST00000360632	NM_015472.4	55	gaG/gaT	2/7	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.19	2		586	480	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185169179	185169179	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs930308945	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	22	377	0	ENST00000265026.3:c.1274C>T	p.Ser425Phe	p.S425F	ENST00000265026	NM_004721.4	425	tCt/tTt	7/14	1	2	FACETS	0.735	0.57	0.927	0.735	0.57	0.927	CLONAL	1	TRUE	1	0.19	2		377	315	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503756	186503756	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	38	486	0	ENST00000323963.5:c.433A>G	p.Met145Val	p.M145V	ENST00000323963		145	Atg/Gtg	5/11	1	2	FACETS	0.873	0.722	1	0.873	0.722	1	CLONAL	1	TRUE	1	0.19	2		486	458	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807999	1807999	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	24	786	0	ENST00000260795.2:c.1975A>G	p.Lys659Glu	p.K659E	ENST00000260795		659	Aag/Gag	14/17	1	2	FACETS	0.54	0.422	0.676	0.54	0.422	0.676	SUBCLONAL	1	TRUE	1	0.19	2		786	468	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1959759	1959759	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	20	188	0	ENST00000382891.5:c.2981T>C	p.Ile994Thr	p.I994T	ENST00000382891	NM_133335.3	994	aTc/aCc	16/22	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.19	2		188	174	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129839	55129839	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs762935664	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	16	443	0	ENST00000257290.5:c.373G>T	p.Asp125Tyr	p.D125Y	ENST00000257290	NM_006206.4	125	Gat/Tat	4/23	1	2	FACETS	0.679	0.502	0.89	0.679	0.502	0.89	SUBCLONAL	1	TRUE	1	0.19	2		443	248	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158290	106158290	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	13	297	0	ENST00000380013.4:c.3194del	p.Leu1065Ter	p.L1065*	ENST00000380013	NM_001127208.2	1064	gTt/gt	3/11	1	2	FACETS	0.55	0.392	0.742	0.55	0.392	0.742	SUBCLONAL	1	TRUE	1	0.19	2		297	249	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143043305	143043305	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	35	374	0	ENST00000262992.4:c.2111T>C	p.Val704Ala	p.V704A	ENST00000262992	NM_001101669.1	704	gTg/gCg	19/24	1	2	FACETS	0.873	0.716	1	0.873	0.716	1	CLONAL	1	TRUE	1	0.19	2		374	422	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542848	187542848	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751475602	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	17	419	0	ENST00000441802.2:c.4892C>T	p.Ala1631Val	p.A1631V	ENST00000441802	NM_005245.3	1631	gCg/gTg	10/27	1	2	FACETS	0.68	0.508	0.885	0.68	0.508	0.885	SUBCLONAL	1	TRUE	1	0.19	2		419	263	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508815	31508815	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	33	538	0	ENST00000344624.3:c.1500A>C	p.Glu500Asp	p.E500D	ENST00000344624		500	gaA/gaC	7/33	1	2	FACETS	0.548	0.445	0.665	0.548	0.445	0.665	SUBCLONAL	1	TRUE	1	0.19	2		538	634	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31511250	31511250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767118229	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	43	683	0	ENST00000344624.3:c.1324C>T	p.Arg442Cys	p.R442C	ENST00000344624		442	Cgt/Tgt	6/33	1	2	FACETS	0.898	0.751	1	0.898	0.751	1	CLONAL	1	TRUE	1	0.19	2		683	504	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31521263	31521263	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	49	537	0	ENST00000344624.3:c.914G>T	p.Arg305Met	p.R305M	ENST00000344624		305	aGg/aTg	3/33	1	2	FACETS	0.839	0.709	0.981	0.839	0.709	0.981	CLONAL	1	TRUE	1	0.19	2		537	615	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526788	31526788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	34	626	0	ENST00000344624.3:c.252del	p.Met85CysfsTer23	p.M85Cfs*23	ENST00000344624		84	ccC/cc	2/33	1	2	FACETS	0.768	0.627	0.927	0.768	0.627	0.927	CLONAL	1	TRUE	1	0.19	2		626	466	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685239	86685239	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	18	238	0	ENST00000274376.6:c.2955G>T	p.Glu985Asp	p.E985D	ENST00000274376	NM_002890.2	985	gaG/gaT	24/25	1	2	FACETS	0.702	0.529	0.906	0.702	0.529	0.906	CLONAL	1	TRUE	1	0.19	2		238	270	SUCCESS
APC	324	MSKCC	GRCh37	5	112176510	112176510	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	20	278	0	ENST00000257430.4:c.5219C>A	p.Pro1740His	p.P1740H	ENST00000257430	NM_000038.5	1740	cCt/cAt	16/16	1	2	FACETS	0.988	0.759	1	0.988	0.759	1	CLONAL	1	TRUE	1	0.19	2		278	213	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131972818	131972818	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	10	234	0	ENST00000265335.6:c.3401A>C	p.Lys1134Thr	p.K1134T	ENST00000265335		1134	aAa/aCa	22/25	1	2	FACETS	0.605	0.41	0.849	0.605	0.41	0.849	SUBCLONAL	1	TRUE	1	0.19	2		234	174	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149434884	149434884	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	23	543	0	ENST00000286301.3:c.2570C>A	p.Pro857His	p.P857H	ENST00000286301	NM_005211.3	857	cCt/cAt	20/22	1	2	FACETS	0.632	0.492	0.794	0.632	0.492	0.794	SUBCLONAL	1	TRUE	1	0.19	2		543	383	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435801	149435801	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1365494031	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	29	570	0	ENST00000286301.3:c.2423A>G	p.Asn808Ser	p.N808S	ENST00000286301	NM_005211.3	808	aAc/aGc	18/22	1	2	FACETS	0.68	0.545	0.834	0.68	0.545	0.834	SUBCLONAL	1	TRUE	1	0.19	2		570	449	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500505	149500505	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	24	586	0	ENST00000261799.4:c.2532C>A	p.Asp844Glu	p.D844E	ENST00000261799	NM_002609.3	844	gaC/gaA	18/23	1	2	FACETS	0.536	0.419	0.672	0.536	0.419	0.672	SUBCLONAL	1	TRUE	1	0.19	2		586	471	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513266	149513266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373131428	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	28	512	0	ENST00000261799.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000261799	NM_002609.3	273	Cgc/Tgc	6/23	1	2	FACETS	0.678	0.541	0.834	0.678	0.541	0.834	SUBCLONAL	1	TRUE	1	0.19	2		512	435	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518811	176518811	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs201851606	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	33	520	0	ENST00000292408.4:c.727+2T>C		p.X243_splice	ENST00000292408	NM_213647.1	243			1	2	FACETS	0.949	0.774	1	0.949	0.774	1	CLONAL	1	TRUE	1	0.19	2		520	366	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637099	176637099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1168342939	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	40	533	0	ENST00000439151.2:c.1699A>G	p.Ser567Gly	p.S567G	ENST00000439151	NM_022455.4	567	Agt/Ggt	5/23	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.19	2		533	384	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048745	180048745	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	45	749	0	ENST00000261937.6:c.1817T>G	p.Leu606Arg	p.L606R	ENST00000261937	NM_182925.4	606	cTt/cGt	13/30	1	2	FACETS	0.931	0.782	1	0.931	0.782	1	CLONAL	1	TRUE	1	0.19	2		749	509	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393271	393271	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	28	527	0	ENST00000380956.4:c.119T>C	p.Leu40Pro	p.L40P	ENST00000380956	NM_001195286.1	40	cTg/cCg	2/9	0.3	4	FACETS	1	0.839	1			1	CLONAL	1	TRUE	NA	0.19	4		527	332	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681607	30681607	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	46	467	0	ENST00000376406.3:c.490T>G	p.Leu164Val	p.L164V	ENST00000376406	NM_014641.2	164	Ttg/Gtg	3/15	0.124442880638595	3	FACETS	1	0.917	1	0.571	0.481	0.671	CLONAL	1	TRUE	1	0.19	3		467	464	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31947237	31947237	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	61	593	0	ENST00000375333.2:c.722A>C	p.Lys241Thr	p.K241T	ENST00000375333	NM_032454.1	241	aAa/aCa	5/8	0.124442880638595	3	FACETS	1	0.962	1	0.671	0.579	0.77	CLONAL	1	TRUE	1	0.19	3		593	524	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165275	32165275	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	56	738	0	ENST00000375023.3:c.4853C>A	p.Pro1618His	p.P1618H	ENST00000375023	NM_004557.3	1618	cCt/cAt	27/30	0.124442880638595	3	FACETS	1	0.951	1	0.633	0.542	0.731	CLONAL	1	TRUE	1	0.19	3		738	510	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185039	32185039	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	24	490	0	ENST00000375023.3:c.1629C>A	p.Phe543Leu	p.F543L	ENST00000375023	NM_004557.3	543	ttC/ttA	10/30	0.124442880638595	3	FACETS	0.811	0.636	1	0.406	0.318	0.507	CLONAL	1	TRUE	1	0.19	3		490	341	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813534	32813534	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	34	381	0	ENST00000354258.4:c.2249A>G	p.Glu750Gly	p.E750G	ENST00000354258	NM_000593.5	750	gAg/gGg	11/11	0.124442880638595	3	FACETS	1	0.915	1	0.607	0.497	0.729	CLONAL	1	TRUE	1	0.19	3		381	323	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287626	33287626	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	41	523	0	ENST00000374542.5:c.1471G>T	p.Asp491Tyr	p.D491Y	ENST00000374542	NM_001141970.1	491	Gat/Tat	6/8	0.124442880638595	3	FACETS	1	0.917	1	0.583	0.486	0.691	CLONAL	1	TRUE	1	0.19	3		523	405	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908158	41908158	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	43	651	0	ENST00000372991.4:c.364G>A	p.Glu122Lys	p.E122K	ENST00000372991	NM_001760.3	122	Gaa/Aaa	2/5	0.124442880638595	3	FACETS	0.911	0.762	1	0.456	0.381	0.539	CLONAL	1	TRUE	1	0.19	3		651	544	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553699	106553699	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	15	270	0	ENST00000369096.4:c.1664A>G	p.Asn555Ser	p.N555S	ENST00000369096	NM_001198.3	555	aAc/aGc	5/7	0.124442880638595	3	FACETS	0.613	0.448	0.812	0.307	0.224	0.406	SUBCLONAL	1	TRUE	1	0.19	3		270	282	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020778	112020778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747153794	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	20	316	1	ENST00000368678.4:c.793C>T	p.Arg265Cys	p.R265C	ENST00000368678		265	Cgt/Tgt	8/13	0.124442880638595	3	FACETS	0.692	0.529	0.884	0.346	0.264	0.442	SUBCLONAL	1	TRUE	1	0.19	3		317	333	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192540	138192540	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	47	346	0	ENST00000237289.4:c.176A>G	p.Gln59Arg	p.Q59R	ENST00000237289	NM_001270507.1	59	cAg/cGg	2/9	0.124442880638595	3	FACETS	1	0.898	1	0.543	0.458	0.636	CLONAL	1	TRUE	1	0.19	3		346	499	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001122	150001122	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	30	446	1	ENST00000253339.5:c.2482G>T	p.Asp828Tyr	p.D828Y	ENST00000253339		828	Gat/Tat	4/7	0.124442880638595	3	FACETS	1	0.869	1	0.551	0.444	0.671	CLONAL	1	TRUE	1	0.19	3		447	314	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001230	150001230	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	39	523	0	ENST00000253339.5:c.2374A>G	p.Ser792Gly	p.S792G	ENST00000253339		792	Agc/Ggc	4/7	0.124442880638595	3	FACETS	1	0.947	1	0.696	0.579	0.826	CLONAL	1	TRUE	1	0.19	3		523	323	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004958	150004958	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs756388991	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	34	426	0	ENST00000253339.5:c.1267A>G	p.Asn423Asp	p.N423D	ENST00000253339		423	Aac/Gac	3/7	0.124442880638595	3	FACETS	1	0.945	1	0.726	0.596	0.871	CLONAL	1	TRUE	1	0.19	3		426	270	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129331	152129331	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	38	504	1	ENST00000206249.3:c.284G>T	p.Gly95Val	p.G95V	ENST00000206249	NM_000125.3	95	gGg/gTg	1/8	0.124442880638595	3	FACETS	1	0.891	1	0.553	0.458	0.659	CLONAL	1	TRUE	1	0.19	3		505	396	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502194	157502194	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	21	398	0	ENST00000346085.5:c.3227A>G	p.Tyr1076Cys	p.Y1076C	ENST00000346085	NM_020732.3	1076	tAc/tGc	12/20	0.124442880638595	3	FACETS	0.642	0.494	0.815	0.321	0.247	0.408	SUBCLONAL	1	TRUE	1	0.19	3		398	377	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528421	157528421	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	35	583	0	ENST00000346085.5:c.6146T>G	p.Leu2049Trp	p.L2049W	ENST00000346085	NM_020732.3	2049	tTg/tGg	20/20	0.124442880638595	3	FACETS	0.823	0.674	0.991	0.412	0.337	0.496	CLONAL	1	TRUE	1	0.19	3		583	490	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954892	2954892	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	35	555	0	ENST00000396946.4:c.2818C>A	p.Leu940Ile	p.L940I	ENST00000396946	NM_032415.4	940	Ctc/Atc	21/25	1	2	FACETS	0.851	0.697	1	0.851	0.697	1	CLONAL	1	TRUE	1	0.19	2		555	433	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523564	106523564	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	19	252	0	ENST00000359195.3:c.2716G>A	p.Val906Ile	p.V906I	ENST00000359195	NM_002649.2	906	Gtc/Atc	8/11	0.259933852591637	4	FACETS	0.768	0.583	0.986	0.384	0.291	0.493	CLONAL	1	TRUE	2	0.19	4		252	310	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412026	116412026	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	31	690	0	ENST00000397752.3:c.3011G>A	p.Arg1004Gln	p.R1004Q	ENST00000397752	NM_000245.2	1004	cGa/cAa	14/21	1	2	FACETS	0.738	0.597	0.899	0.738	0.597	0.899	SUBCLONAL	1	TRUE	1	0.19	2		690	442	SUCCESS
MET	4233	MSKCC	GRCh37	7	116413074	116413074	+	intron_variant	Intron	SNP	G	G	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	28	655	1	ENST00000397752.3:c.3028+1031G>A		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.19	2		656	237	SUCCESS
MET	4233	MSKCC	GRCh37	7	116413267	116413267	+	intron_variant	Intron	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	44	696	0	ENST00000397752.3:c.3028+1224T>C		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.983	0.825	1	0.983	0.825	1	CLONAL	1	TRUE	1	0.19	2		696	471	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423427	116423427	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	25	315	0	ENST00000397752.3:c.3702C>A	p.Tyr1234Ter	p.Y1234*	ENST00000397752	NM_000245.2	1234	taC/taA	19/21	1	2	FACETS	0.933	0.737	1	0.933	0.737	1	CLONAL	1	TRUE	1	0.19	2		315	282	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846019	128846019	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	34	645	0	ENST00000249373.3:c.949A>G	p.Ile317Val	p.I317V	ENST00000249373	NM_005631.4	317	Atc/Gtc	5/12	1	2	FACETS	0.719	0.586	0.868	0.719	0.586	0.868	SUBCLONAL	1	TRUE	1	0.19	2		645	498	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140500160	140500160	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	30	725	0	ENST00000288602.6:c.980+2T>C		p.X327_splice	ENST00000288602	NM_004333.4	327			1	2	FACETS	0.551	0.443	0.675	0.551	0.443	0.675	SUBCLONAL	1	TRUE	1	0.19	2		725	573	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512079	148512079	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs768512235	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	37	372	0	ENST00000320356.2:c.1599G>T	p.Gln533His	p.Q533H	ENST00000320356	NM_004456.4	533	caG/caT	14/20	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.19	2		372	370	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543617	148543617	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	53	462	0	ENST00000320356.2:c.191G>T	p.Arg64Met	p.R64M	ENST00000320356	NM_004456.4	64	aGg/aTg	3/20	1	2	FACETS	0.897	0.764	1	0.897	0.764	1	CLONAL	1	TRUE	1	0.19	2		462	622	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848601	151848601	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	21	256	0	ENST00000262189.6:c.12592T>C	p.Cys4198Arg	p.C4198R	ENST00000262189	NM_170606.2	4198	Tgt/Cgt	50/59	1	2	FACETS	0.656	0.505	0.832	0.656	0.505	0.832	SUBCLONAL	1	TRUE	1	0.19	2		256	337	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151893008	151893008	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	28	334	0	ENST00000262189.6:c.4362A>T	p.Lys1454Asn	p.K1454N	ENST00000262189	NM_170606.2	1454	aaA/aaT	28/59	1	2	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	TRUE	1	0.19	2		334	279	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960210	151960210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761700904	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	12	203	1	ENST00000262189.6:c.1190C>T	p.Ser397Leu	p.S397L	ENST00000262189	NM_170606.2	397	tCg/tTg	9/59	1	2	FACETS	1	0.845	1	1	0.845	1	CLONAL	1	TRUE	1	0.19	2		204	94	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38148066	38148066	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	44	565	0	ENST00000317025.8:c.3045A>C	p.Arg1015Ser	p.R1015S	ENST00000317025	NM_023034.1	1015	agA/agC	17/24	1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	1	0.19	2		565	458	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205329	38205329	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	49	902	2	ENST00000317025.8:c.361C>T	p.Pro121Ser	p.P121S	ENST00000317025	NM_023034.1	121	Cca/Tca	2/24	1	2	FACETS	0.863	0.73	1	0.863	0.73	1	CLONAL	1	TRUE	1	0.19	2		904	598	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285950	38285950	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	18	363	0	ENST00000425967.3:c.461C>A	p.Ala154Asp	p.A154D	ENST00000425967	NM_001174067.1	154	gCt/gAt	5/19	1	2	FACETS	0.846	0.638	1	0.846	0.638	1	CLONAL	1	TRUE	1	0.19	2		363	224	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931847	68931847	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	23	514	0	ENST00000288368.4:c.277G>T	p.Glu93Ter	p.E93*	ENST00000288368	NM_024870.2	93	Gaa/Taa	3/40	1	2	FACETS	0.601	0.468	0.755	0.601	0.468	0.755	SUBCLONAL	1	TRUE	1	0.19	2		514	403	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028086	69028086	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	35	480	0	ENST00000288368.4:c.3245G>T	p.Ser1082Ile	p.S1082I	ENST00000288368	NM_024870.2	1082	aGc/aTc	26/40	1	2	FACETS	0.905	0.742	1	0.905	0.742	1	CLONAL	1	TRUE	1	0.19	2		480	407	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117870594	117870594	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	13	315	0	ENST00000297338.2:c.478T>C	p.Phe160Leu	p.F160L	ENST00000297338	NM_006265.2	160	Ttt/Ctt	5/14	1	2	FACETS	0.639	0.456	0.862	0.639	0.456	0.862	SUBCLONAL	1	TRUE	1	0.19	2		315	214	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542163	141542163	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324425100	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	25	510	2	ENST00000220592.5:c.2560C>T	p.Arg854Cys	p.R854C	ENST00000220592	NM_012154.3	854	Cgc/Tgc	19/19	1	2	FACETS	0.707	0.557	0.88	0.707	0.557	0.88	SUBCLONAL	1	TRUE	1	0.19	2		512	372	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141557714	141557714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	34	537	0	ENST00000220592.5:c.1601G>A	p.Arg534His	p.R534H	ENST00000220592	NM_012154.3	534	cGc/cAc	13/19	1	2	FACETS	0.819	0.669	0.988	0.819	0.669	0.988	CLONAL	1	TRUE	1	0.19	2		537	437	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5081808	5081808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	32	239	0	ENST00000381652.3:c.2518G>A	p.Asp840Asn	p.D840N	ENST00000381652	NM_004972.3	840	Gat/Aat	19/25	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.19	2		239	275	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521325	8521325	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1335469081	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	29	451	0	ENST00000356435.5:c.913A>G	p.Met305Val	p.M305V	ENST00000356435		305	Atg/Gtg	9/35	1	2	FACETS	0.9	0.724	1	0.9	0.724	1	CLONAL	1	TRUE	1	0.19	2		451	339	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015057	37015057	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	31	515	1	ENST00000358127.4:c.347A>T	p.Asp116Val	p.D116V	ENST00000358127	NM_001280556.1	116	gAc/gTc	3/10	1	2	FACETS	0.635	0.512	0.774	0.635	0.512	0.774	SUBCLONAL	1	TRUE	1	0.19	2		516	514	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212151	98212151	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	18	241	0	ENST00000331920.6:c.3521T>G	p.Leu1174Arg	p.L1174R	ENST00000331920	NM_000264.3	1174	cTt/cGt	21/24	1	2	FACETS	0.564	0.424	0.73	0.564	0.424	0.73	SUBCLONAL	1	TRUE	1	0.19	2		241	336	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220572	98220572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377120922	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	29	231	1	ENST00000331920.6:c.2891C>T	p.Pro964Leu	p.P964L	ENST00000331920	NM_000264.3	964	cCg/cTg	18/24	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.19	2		232	232	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240431	98240431	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	23	395	0	ENST00000331920.6:c.1253A>C	p.Lys418Thr	p.K418T	ENST00000331920	NM_000264.3	418	aAg/aCg	9/24	1	2	FACETS	0.55	0.428	0.692	0.55	0.428	0.692	SUBCLONAL	1	TRUE	1	0.19	2		395	440	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248064	98248064	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	55	577	0	ENST00000331920.6:c.487A>G	p.Lys163Glu	p.K163E	ENST00000331920	NM_000264.3	163	Aaa/Gaa	3/24	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.19	2		577	431	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891178	101891178	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	19	363	0	ENST00000374994.4:c.139A>G	p.Thr47Ala	p.T47A	ENST00000374994	NM_004612.2	47	Act/Gct	2/9	1	2	FACETS	0.526	0.399	0.677	0.526	0.399	0.677	SUBCLONAL	1	TRUE	1	0.19	2		363	380	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778092	135778092	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	34	556	0	ENST00000298552.3:c.2291T>C	p.Leu764Pro	p.L764P	ENST00000298552	NM_001162426.1	764	cTc/cCc	18/23	1	2	FACETS	0.699	0.57	0.844	0.699	0.57	0.844	SUBCLONAL	1	TRUE	1	0.19	2		556	512	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781119	135781119	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	20	564	0	ENST00000298552.3:c.1846G>T	p.Ala616Ser	p.A616S	ENST00000298552	NM_001162426.1	616	Gcc/Tcc	15/23	1	2	FACETS	0.557	0.425	0.712	0.557	0.425	0.712	SUBCLONAL	1	TRUE	1	0.19	2		564	378	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786489	135786489	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	19	390	0	ENST00000298552.3:c.1041G>T	p.Trp347Cys	p.W347C	ENST00000298552	NM_001162426.1	347	tgG/tgT	11/23	1	2	FACETS	0.621	0.471	0.798	0.621	0.471	0.798	SUBCLONAL	1	TRUE	1	0.19	2		390	322	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390609	139390609	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	41	846	0	ENST00000277541.6:c.7582A>G	p.Asn2528Asp	p.N2528D	ENST00000277541	NM_017617.3	2528	Aac/Gac	34/34	1	2	FACETS	0.767	0.638	0.91	0.767	0.638	0.91	CLONAL	1	TRUE	1	0.19	2		846	563	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412293	139412293	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	36	688	0	ENST00000277541.6:c.1352T>C	p.Ile451Thr	p.I451T	ENST00000277541	NM_017617.3	451	aTc/aCc	8/34	1	2	FACETS	0.703	0.577	0.845	0.703	0.577	0.845	SUBCLONAL	1	TRUE	1	0.19	2		688	539	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1331470	1331470	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	26	488	1	ENST00000400841.2:c.58G>A	p.Ala20Thr	p.A20T	ENST00000400841		20	Gct/Act	1/6	1	2	FACETS	0.789	0.625	0.976	0.789	0.625	0.976	CLONAL	1	TRUE	1	0.19	2		489	347	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913271	39913271	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	24	434	0	ENST00000378444.4:c.4844A>T	p.Asp1615Val	p.D1615V	ENST00000378444	NM_001123385.1	1615	gAt/gTt	14/15	1	2	FACETS	0.818	0.642	1	0.818	0.642	1	CLONAL	1	TRUE	1	0.19	2		434	309	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921435	39921435	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	22	449	0	ENST00000378444.4:c.4385C>A	p.Ala1462Asp	p.A1462D	ENST00000378444	NM_001123385.1	1462	gCt/gAt	10/15	1	2	FACETS	0.55	0.425	0.695	0.55	0.425	0.695	SUBCLONAL	1	TRUE	1	0.19	2		449	421	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932570	39932570	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	35	787	0	ENST00000378444.4:c.2029G>T	p.Gly677Ter	p.G677*	ENST00000378444	NM_001123385.1	677	Gga/Tga	4/15	1	2	FACETS	0.857	0.702	1	0.857	0.702	1	CLONAL	1	TRUE	1	0.19	2		787	430	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424728	47424728	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs779625869	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	50	487	0	ENST00000377045.4:c.536T>C	p.Leu179Ser	p.L179S	ENST00000377045	NM_001654.4	179	tTg/tCg	6/16	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.19	2		487	489	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224145	53224145	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	43	747	0	ENST00000375401.3:c.3406T>C	p.Ser1136Pro	p.S1136P	ENST00000375401	NM_004187.3	1136	Tct/Cct	22/26	1	2	FACETS	0.893	0.747	1	0.893	0.747	1	CLONAL	1	TRUE	1	0.19	2		747	507	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53241054	53241054	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	29	483	1	ENST00000375401.3:c.1157A>C	p.Glu386Ala	p.E386A	ENST00000375401	NM_004187.3	386	gAg/gCg	9/26	1	2	FACETS	0.631	0.505	0.774	0.631	0.505	0.774	SUBCLONAL	1	TRUE	1	0.19	2		484	484	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907661	76907661	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	30	575	0	ENST00000373344.5:c.4500G>T	p.Glu1500Asp	p.E1500D	ENST00000373344	NM_000489.3	1500	gaG/gaT	15/35	1	2	FACETS	0.726	0.584	0.887	0.726	0.584	0.887	SUBCLONAL	1	TRUE	1	0.19	2		575	435	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952065	76952065	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	14	410	0	ENST00000373344.5:c.370G>T	p.Gly124Cys	p.G124C	ENST00000373344	NM_000489.3	124	Ggt/Tgt	5/35	1	2	FACETS	0.624	0.451	0.834	0.624	0.451	0.834	SUBCLONAL	1	TRUE	1	0.19	2		410	236	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	131	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.447062379196911	2		215	475	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0034468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	149	380	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.447062379196911	2		380	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578195	7578197	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0034468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	238	673	0	ENST00000269305.4:c.652_654del	p.Val218del	p.V218del	ENST00000269305	NM_001126112.2	218	GTG/-	6/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.447062379196911	2		673	1042	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0034468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	187	606	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			1	2	FACETS	0.971	0.897	1	0.971	0.897	1	CLONAL	1	TRUE	1	0.447062379196911	2		606	862	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229256	36229256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	504	774	0	ENST00000222270.7:c.7946G>A	p.Arg2649His	p.R2649H	ENST00000222270	NM_014727.1	2649	cGc/cAc	37/37	0.445534067606972	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.447062379196911	3		774	1348	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942754	68942754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569463208	NA	P-0034468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	125	445	0	ENST00000288368.4:c.566G>A	p.Arg189Gln	p.R189Q	ENST00000288368	NM_024870.2	189	cGg/cAg	6/40	0.447062379196911	3	FACETS	1	0.923	1	0.51	0.462	0.56	CLONAL	1	TRUE	1	0.447062379196911	3		445	671	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444166	49444166	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	233	821	0	ENST00000301067.7:c.3205G>T	p.Glu1069Ter	p.E1069*	ENST00000301067	NM_003482.3	1069	Gag/Tag	11/54	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.447062379196911	2		821	1028	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63545656	63545656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	75	463	0	ENST00000307078.5:c.938C>T	p.Ser313Phe	p.S313F	ENST00000307078	NM_004655.3	313	tCc/tTc	3/11	0.208669359200292	3	FACETS	0.59	0.516	0.669	0.197	0.172	0.223	INDETERMINATE	1	TRUE	0	0.447062379196911	3		463	696	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80150126	80150126	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	52	451	1	ENST00000265081.6:c.2991C>A	p.Phe997Leu	p.F997L	ENST00000265081	NM_002439.4	997	ttC/ttA	21/24	1	2	FACETS	0.368	0.313	0.429	0.368	0.313	0.429	SUBCLONAL	1	TRUE	1	0.447062379196911	2		452	632	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0034594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	183	458	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.752918664595101	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.752918664595101	1		458	274	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0034594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	100	462	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.929	0.841	1	0.929	0.841	1	CLONAL	1	TRUE	1	0.752918664595101	2		463	286	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710594	117710594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768790336	NA	P-0034594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	94	250	0	ENST00000368508.3:c.1678C>T	p.Arg560Cys	p.R560C	ENST00000368508	NM_002944.2	560	Cgc/Tgc	12/43	0.752918664595101	1	FACETS	0.992	0.914	1	0.992	0.914	1	CLONAL	1	TRUE	0	0.752918664595101	1		250	157	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690816	89690817	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0034594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	125	305	0	ENST00000371953.3:c.224dup	p.His75GlnfsTer3	p.H75Qfs*3	ENST00000371953	NM_000314.4	75	cat/cAat	4/9	0.752918664595101	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.752918664595101	1		305	207	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755708	39755708	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	41	589	0	ENST00000288319.7:c.1057G>C	p.Glu353Gln	p.E353Q	ENST00000288319	NM_182918.3	353	Gag/Cag	10/10	1	2	FACETS	0.2	0.166	0.238	0.2	0.166	0.238	SUBCLONAL	1	TRUE	1	0.752918664595101	2		589	545	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339491	81339491	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs772388735	NA	P-0034594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	181	450	0	ENST00000222390.5:c.1513A>G	p.Ile505Val	p.I505V	ENST00000222390	NM_000601.4	505	Ata/Gta	13/18	0.438056826323749	3	FACETS	1	0.983	1	0.597	0.554	0.641	INDETERMINATE	1	TRUE	1	0.752918664595101	3		450	554	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	50	738	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.82	0.706	0.94	0.82	0.706	0.94	CLONAL	1	TRUE	1	0.652324328169863	2		738	187	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983463	90983463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	35	249	0	ENST00000265433.3:c.640G>A	p.Gly214Arg	p.G214R	ENST00000265433	NM_002485.4	214	Gga/Aga	6/16	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.652324328169863	2		249	104	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245026	133245026	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs5744800	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	50	863	0	ENST00000320574.5:c.2089C>T	p.Pro697Ser	p.P697S	ENST00000320574	NM_006231.2	697	Ccc/Tcc	19/49	1	2	FACETS	0.856	0.739	0.981	0.856	0.739	0.981	CLONAL	1	TRUE	1	0.652324328169863	2		863	179	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033352	48033352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750949	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	78	338	0	ENST00000234420.5:c.3656C>T	p.Thr1219Ile	p.T1219I	ENST00000234420	NM_000179.2	1219	aCt/aTt	8/10	0.652324328169863	3	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	TRUE	1	0.652324328169863	3		338	154	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	32	529	1	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	1	2	FACETS	0.486	0.397	0.584	0.486	0.397	0.584	SUBCLONAL	1	TRUE	1	0.652324328169863	2		530	202	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584501	189584501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908849	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	71	336	0	ENST00000264731.3:c.797G>A	p.Arg266Gln	p.R266Q	ENST00000264731	NM_003722.4	266	cGa/cAa	6/14	0.404144500413878	3	FACETS	0.962	0.865	1	0.962	0.865	1	CLONAL	2	TRUE	1	0.652324328169863	3		336	150	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	43	462	1				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.896	1			1	INDETERMINATE	1	TRUE	NA	0.652324328169863	2		463	125	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259559	16259559	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	61	543	0	ENST00000375759.3:c.6824C>T	p.Thr2275Ile	p.T2275I	ENST00000375759	NM_015001.2	2275	aCt/aTt	11/15	0.344310312954456	3	FACETS	1	0.957	1	0.611	0.535	0.69	INDETERMINATE	1	TRUE	1	0.652324328169863	3		543	203	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885772	23885772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	127	700	1	ENST00000374561.5:c.146C>T	p.Ser49Phe	p.S49F	ENST00000374561	NM_002167.4	49	tCc/tTc	1/3	0.344310312954456	3	FACETS	0.967	0.894	1	0.967	0.894	1	INDETERMINATE	2	TRUE	1	0.652324328169863	3		701	267	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598895	28598895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774449109	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	84	791	0	ENST00000253063.3:c.455C>T	p.Ala152Val	p.A152V	ENST00000253063	NM_031459.4	152	gCc/gTc	4/10	0.344310312954456	3	FACETS	0.858	0.775	0.943	0.858	0.775	0.943	INDETERMINATE	2	TRUE	1	0.652324328169863	3		791	199	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439677	51439677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	81	459	0	ENST00000262662.1:c.242G>A	p.Gly81Asp	p.G81D	ENST00000262662		81	gGt/gAt	4/4	0.652324328169863	3	FACETS	1	0.95	1	0.56	0.499	0.624	CLONAL	1	TRUE	1	0.652324328169863	3		459	294	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439890	51439890	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	132	388	0	ENST00000262662.1:c.455T>A	p.Val152Asp	p.V152D	ENST00000262662		152	gTt/gAt	4/4	0.652324328169863	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.652324328169863	3		388	251	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248568	59248568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	108	824	1	ENST00000371222.2:c.175G>A	p.Asp59Asn	p.D59N	ENST00000371222	NM_002228.3	59	Gac/Aac	1/1	0.652324328169863	3	FACETS	1	0.98	1	0.655	0.595	0.718	CLONAL	1	TRUE	1	0.652324328169863	3		825	335	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551957	150551957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1012747207	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	88	507	1	ENST00000369026.2:c.50G>A	p.Gly17Glu	p.G17E	ENST00000369026	NM_021960.4	17	gGg/gAg	1/3	0.607331942014389	4	FACETS	0.899	0.809	0.991			1	CLONAL	2	TRUE	NA	0.652324328169863	4		508	248	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838383	156838383	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	115	799	1	ENST00000524377.1:c.661G>A	p.Gly221Ser	p.G221S	ENST00000524377	NM_002529.3	221	Ggc/Agc	6/17	0.344310312954456	3	FACETS	0.931	0.856	1	0.931	0.856	1	INDETERMINATE	2	TRUE	1	0.652324328169863	3		800	251	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843506	156843506	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1434897221	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	87	818	0	ENST00000524377.1:c.932C>T	p.Pro311Leu	p.P311L	ENST00000524377	NM_002529.3	311	cCg/cTg	8/17	0.344310312954456	3	FACETS	0.921	0.835	1	0.921	0.835	1	INDETERMINATE	2	TRUE	1	0.652324328169863	3		818	192	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851285	156851285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778520978	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	96	738	1	ENST00000524377.1:c.2242C>T	p.Arg748Trp	p.R748W	ENST00000524377	NM_002529.3	748	Cgg/Tgg	17/17	0.344310312954456	3	FACETS	0.856	0.778	0.935	0.856	0.778	0.935	INDETERMINATE	2	TRUE	1	0.652324328169863	3		739	228	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518500	204518500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	39	313	0	ENST00000367182.3:c.1163C>T	p.Pro388Leu	p.P388L	ENST00000367182	NM_001278516.1	388	cCc/cTc	11/11	0.344310312954456	3	FACETS	1	0.955	1	0.695	0.592	0.805	INDETERMINATE	1	TRUE	1	0.652324328169863	3		313	114	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612116	43612116	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	69	445	0	ENST00000355710.3:c.2221G>A	p.Ala741Thr	p.A741T	ENST00000355710	NM_020975.4	741	Gca/Aca	12/20	0.465517616082022	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.652324328169863	1		445	110	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298105	123298105	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	85	580	0	ENST00000358487.5:c.748+1G>A		p.X250_splice	ENST00000358487	NM_000141.4	250			0.652324328169863	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.652324328169863	1		580	133	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154841	2154841	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	69	873	0	ENST00000434045.2:c.380G>A	p.Cys127Tyr	p.C127Y	ENST00000434045	NM_001127598.1	127	tGt/tAt	4/5	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.652324328169863	2		873	193	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251945	8251945	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	115	890	0	ENST00000335790.3:c.132G>A	p.Trp44Ter	p.W44*	ENST00000335790	NM_002315.2	44	tgG/tgA	2/4	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.652324328169863	2		890	260	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127961	64127961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	93	736	0	ENST00000334205.4:c.359G>A	p.Gly120Asp	p.G120D	ENST00000334205	NM_003942.2	120	gGc/gAc	4/17	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.652324328169863	2		736	233	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577136	64577136	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	66	783	0	ENST00000312049.6:c.445+1G>A		p.X149_splice	ENST00000312049	NM_130799.2	149			1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.652324328169863	2		783	186	SUCCESS
EED	8726	MSKCC	GRCh37	11	85968638	85968638	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	33	203	0	ENST00000263360.6:c.634G>A	p.Asp212Asn	p.D212N	ENST00000263360	NM_003797.3	212	Gat/Aat	6/12	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.652324328169863	2		203	93	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195566	102195566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	48	360	1	ENST00000263464.3:c.326C>T	p.Ser109Phe	p.S109F	ENST00000263464	NM_001165.4	109	tCt/tTt	2/9	1	2	FACETS	0.861	0.74	0.989	0.861	0.74	0.989	CLONAL	1	TRUE	1	0.652324328169863	2		361	171	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195760	102195760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	48	332	0	ENST00000263464.3:c.520C>T	p.Leu174Phe	p.L174F	ENST00000263464	NM_001165.4	174	Ctt/Ttt	2/9	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.652324328169863	2		332	143	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206672	108206672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	35	337	0	ENST00000278616.4:c.8252C>T	p.Thr2751Ile	p.T2751I	ENST00000278616	NM_000051.3	2751	aCt/aTt	56/63	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.652324328169863	2		337	100	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363838	118363838	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	51	470	0	ENST00000534358.1:c.5071G>A	p.Gly1691Arg	p.G1691R	ENST00000534358	NM_005933.3	1691	Gga/Aga	16/36	1	2	FACETS	0.936	0.811	1	0.936	0.811	1	CLONAL	1	TRUE	1	0.652324328169863	2		470	167	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372432	118372432	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	37	534	1	ENST00000534358.1:c.6365C>T	p.Pro2122Leu	p.P2122L	ENST00000534358	NM_005933.3	2122	cCt/cTt	26/36	1	2	FACETS	0.766	0.643	0.9	0.766	0.643	0.9	SUBCLONAL	1	TRUE	1	0.652324328169863	2		535	148	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435220	18435220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201018498	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	94	259	0	ENST00000266497.5:c.205C>T	p.Pro69Ser	p.P69S	ENST00000266497		69	Cca/Tca	1/31	0.499789728717317	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.652324328169863	3		259	167	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242619	46242619	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	25	204	0	ENST00000334344.6:c.1581G>A	p.Trp527Ter	p.W527*	ENST00000334344	NM_152641.2	527	tgG/tgA	13/21	0.499789728717317	3	FACETS	1	0.914	1	0.627	0.509	0.755	CLONAL	1	TRUE	1	0.652324328169863	3		204	81	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49419970	49419970	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	10	529	0	ENST00000301067.7:c.15779C>T	p.Pro5260Leu	p.P5260L	ENST00000301067	NM_003482.3	5260	cCc/cTc	48/54	0.499789728717317	3	FACETS	0.221	0.149	0.311	0.11	0.074	0.156	SUBCLONAL	1	TRUE	1	0.652324328169863	3		529	184	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420039	49420039	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	72	697	1	ENST00000301067.7:c.15710G>A	p.Gly5237Glu	p.G5237E	ENST00000301067	NM_003482.3	5237	gGg/gAg	48/54	0.499789728717317	3	FACETS	1	0.952	1	0.574	0.508	0.644	CLONAL	1	TRUE	1	0.652324328169863	3		698	255	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431711	49431711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	82	786	0	ENST00000301067.7:c.9428C>T	p.Pro3143Leu	p.P3143L	ENST00000301067	NM_003482.3	3143	cCc/cTc	34/54	0.499789728717317	3	FACETS	1	0.974	1	0.654	0.585	0.725	CLONAL	1	TRUE	1	0.652324328169863	3		786	255	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488291	56488291	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	50	641	0	ENST00000267101.3:c.1810C>T	p.Pro604Ser	p.P604S	ENST00000267101	NM_001982.3	604	Cca/Tca	15/28	0.499789728717317	3	FACETS	1	0.888	1	0.519	0.446	0.596	CLONAL	1	TRUE	1	0.652324328169863	3		641	196	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784095	120784095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	83	918	0	ENST00000257552.2:c.890C>T	p.Pro297Leu	p.P297L	ENST00000257552	NM_002442.3	297	cCa/cTa	13/15	1	2	FACETS	0.925	0.827	1	0.925	0.827	1	CLONAL	1	TRUE	1	0.652324328169863	2		918	275	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218778	133218778	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	62	698	0	ENST00000320574.5:c.5158G>A	p.Gly1720Ser	p.G1720S	ENST00000320574	NM_006231.2	1720	Ggc/Agc	38/49	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.652324328169863	2		698	161	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263856	133263856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241114520	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	81	262	1	ENST00000320574.5:c.46G>A	p.Asp16Asn	p.D16N	ENST00000320574	NM_006231.2	16	Gat/Aat	1/49	1	2	FACETS	0.839	0.764	0.913	1	0.985	1	CLONAL	2	TRUE	1	0.652324328169863	2		263	148	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913021	32913021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	69	376	1	ENST00000380152.3:c.4529C>T	p.Pro1510Leu	p.P1510L	ENST00000380152		1510	cCc/cTc	11/27	0.499789728717317	3	FACETS	0.816	0.727	0.906	0.816	0.727	0.906	CLONAL	2	TRUE	1	0.652324328169863	3		377	172	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030348	49030348	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	26	223	0	ENST00000267163.4:c.1823C>T	p.Ser608Phe	p.S608F	ENST00000267163	NM_000321.2	608	tCt/tTt	19/27	0.499789728717317	3	FACETS	1	0.933	1	0.686	0.561	0.819	CLONAL	1	TRUE	1	0.652324328169863	3		223	77	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437067	110437067	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	53	84	0	ENST00000375856.3:c.1334C>T	p.Pro445Leu	p.P445L	ENST00000375856	NM_003749.2	445	cCc/cTc	1/2	0.348560961517666	3	FACETS	1	0.967	1			1	INDETERMINATE	2	TRUE	NA	0.652324328169863	3		84	87	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30102133	30102133	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	43	386	0	ENST00000331968.5:c.1334G>A	p.Arg445Lys	p.R445K	ENST00000331968	NM_002742.2	445	aGa/aAa	9/18	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.652324328169863	2		386	129	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194796	30194796	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	72	607	0	ENST00000331968.5:c.349G>A	p.Val117Met	p.V117M	ENST00000331968	NM_002742.2	117	Gtg/Atg	2/18	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.652324328169863	2		607	202	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986781	36986781	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	20	144	1	ENST00000354822.5:c.908G>A	p.Gly303Asp	p.G303D	ENST00000354822	NM_001079668.2	303	gGt/gAt	3/3	1	2	FACETS	0.889	0.7	1	0.889	0.7	1	CLONAL	1	TRUE	1	0.652324328169863	2		145	69	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574351	95574351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906934	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	24	188	0	ENST00000393063.1:c.2516C>T	p.Ser839Phe	p.S839F	ENST00000393063	NM_030621.3	839	tCt/tTt	17/28	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.652324328169863	2		188	67	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713226	43713226	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	43	732	0	ENST00000382044.4:c.4247C>T	p.Thr1416Ile	p.T1416I	ENST00000382044	NM_001141980.1	1416	aCc/aTc	20/28	0.203904830039417	0	FACETS	0.259	0.219	0.301			1	INDETERMINATE	1	TRUE	0	0.652324328169863	0		732	177	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631632	90631632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1202254907	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	50	688	0	ENST00000330062.3:c.637C>T	p.Pro213Ser	p.P213S	ENST00000330062	NM_002168.2	213	Ccc/Tcc	5/11	1	2	FACETS	0.866	0.747	0.992	0.866	0.747	0.992	CLONAL	1	TRUE	1	0.652324328169863	2		688	177	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121855	2121855	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	71	493	2	ENST00000219476.3:c.2017G>A	p.Ala673Thr	p.A673T	ENST00000219476	NM_000548.3	673	Gcg/Acg	19/42	0.652324328169863	1	FACETS	0.789	0.732	0.84	1	0.986	1	SUBCLONAL	2	TRUE	0	0.652324328169863	1		495	93	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121936	2121936	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	64	725	0	ENST00000219476.3:c.2097+1G>A		p.X699_splice	ENST00000219476	NM_000548.3	699			0.652324328169863	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.652324328169863	1		725	111	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860743	3860743	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs989859922	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	59	544	0	ENST00000262367.5:c.836C>T	p.Pro279Leu	p.P279L	ENST00000262367	NM_004380.2	279	cCc/cTc	3/31	0.652324328169863	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.652324328169863	1		544	111	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828208	50828208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	49	600	0	ENST00000398568.2:c.2546G>A	p.Gly849Asp	p.G849D	ENST00000398568	NM_001042412.1	849	gGc/gAc	17/18	0.253303443574687	1	FACETS	0.713	0.618	0.812	0.713	0.618	0.812	INDETERMINATE	1	TRUE	0	0.652324328169863	1		600	142	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063332	67063332	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	44	248	0	ENST00000412916.2:c.22C>T	p.Gln8Ter	p.Q8*	ENST00000412916		8	Cag/Tag	1/6	0.253303443574687	1	FACETS	0.784	0.676	0.895	0.784	0.676	0.895	INDETERMINATE	1	TRUE	0	0.652324328169863	1		248	116	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829202	72829202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1468327978	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	61	901	0	ENST00000268489.5:c.7379C>T	p.Pro2460Leu	p.P2460L	ENST00000268489	NM_006885.3	2460	cCc/cTc	9/10	0.652324328169863	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.652324328169863	1		901	116	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349322	89349322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	63	936	0	ENST00000301030.4:c.3628G>A	p.Asp1210Asn	p.D1210N	ENST00000301030	NM_001256183.1	1210	Gat/Aat	9/13	0.652324328169863	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.652324328169863	1		936	112	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	65	706	0	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.652324328169863	2		706	172	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578502	7578502	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	11	843	0	ENST00000269305.4:c.428T>C	p.Val143Ala	p.V143A	ENST00000269305	NM_001126112.2	143	gTg/gCg	5/11	1	2	FACETS	0.175	0.12	0.242	0.175	0.12	0.242	SUBCLONAL	1	TRUE	1	0.652324328169863	2		843	193	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982853	7982853	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	76	658	0	ENST00000319144.4:c.932G>A	p.Gly311Glu	p.G311E	ENST00000319144	NM_001139.2	311	gGg/gAg	8/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.652324328169863	2		658	188	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983179	7983179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	42	701	0	ENST00000319144.4:c.835C>T	p.Arg279Cys	p.R279C	ENST00000319144	NM_001139.2	279	Cgc/Tgc	7/15	1	2	FACETS	0.749	0.634	0.871	0.749	0.634	0.871	SUBCLONAL	1	TRUE	1	0.652324328169863	2		701	172	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16056652	16056652	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	28	173	0	ENST00000268712.3:c.789+1G>A		p.X263_splice	ENST00000268712	NM_006311.3	263			1	2	FACETS	0.987	0.812	1	0.987	0.812	1	CLONAL	1	TRUE	1	0.652324328169863	2		173	87	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16062105	16062105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	63	523	0	ENST00000268712.3:c.701G>A	p.Ser234Asn	p.S234N	ENST00000268712	NM_006311.3	234	aGt/aAt	6/46	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.652324328169863	2		523	165	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881075	37881075	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	93	828	1	ENST00000269571.5:c.2404C>T	p.Pro802Ser	p.P802S	ENST00000269571		802	Ccc/Tcc	20/27	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.652324328169863	2		829	223	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677927	58677927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	64	321	0	ENST00000305921.3:c.152C>T	p.Pro51Leu	p.P51L	ENST00000305921	NM_003620.3	51	cCg/cTg	1/6	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.652324328169863	2		321	157	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761063	59761063	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1419933310	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	40	409	0	ENST00000259008.2:c.3344C>T	p.Ser1115Phe	p.S1115F	ENST00000259008	NM_032043.2	1115	tCc/tTc	20/20	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.652324328169863	2		409	104	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763512	59763512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149529390	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	30	338	0	ENST00000259008.2:c.2590G>A	p.Val864Ile	p.V864I	ENST00000259008	NM_032043.2	864	Gta/Ata	19/20	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.652324328169863	2		338	84	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118885	70118885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	69	612	0	ENST00000245479.2:c.457C>T	p.Pro153Ser	p.P153S	ENST00000245479	NM_000346.3	153	Ccc/Tcc	2/3	1	2	FACETS	0.949	0.839	1	0.949	0.839	1	CLONAL	1	TRUE	1	0.652324328169863	2		612	223	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414805	56414805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	48	634	1	ENST00000348428.3:c.2206C>T	p.Pro736Ser	p.P736S	ENST00000348428	NM_006785.3	736	Cct/Tct	17/17	0.199974716719056	3	FACETS	1	0.925	1	0.561	0.482	0.645	INDETERMINATE	1	TRUE	1	0.652324328169863	3		635	174	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221280	1221280	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	20	735	1	ENST00000326873.7:c.803G>A	p.Gly268Glu	p.G268E	ENST00000326873	NM_000455.4	268	gGg/gAg	6/10	0.179791908265556	2	FACETS	0.285	0.219	0.363	0.143	0.109	0.182	INDETERMINATE	1	TRUE	0	0.652324328169863	2		736	215	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615722	1615722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	60	828	0	ENST00000344749.5:c.1549G>A	p.Glu517Lys	p.E517K	ENST00000344749	NM_001136139.2	517	Gag/Aag	17/19	0.179791908265556	2	FACETS	0.915	0.801	1	0.458	0.4	0.518	INDETERMINATE	1	TRUE	0	0.652324328169863	2		828	201	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244137	5244137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747264114	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	48	858	0	ENST00000357368.4:c.1345G>A	p.Glu449Lys	p.E449K	ENST00000357368	NM_002850.3	449	Gag/Aag	11/38	0.368431889440751	1	FACETS	0.59	0.508	0.678	0.59	0.508	0.678	INDETERMINATE	1	TRUE	0	0.652324328169863	1		858	168	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125410	7125410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	61	918	0	ENST00000302850.5:c.3142G>A	p.Gly1048Ser	p.G1048S	ENST00000302850	NM_000208.2	1048	Ggt/Agt	17/22	0.368431889440751	1	FACETS	0.63	0.552	0.712	0.63	0.552	0.712	INDETERMINATE	1	TRUE	0	0.652324328169863	1		918	200	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7152795	7152795	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	48	733	0	ENST00000302850.5:c.2173G>A	p.Glu725Lys	p.E725K	ENST00000302850	NM_000208.2	725	Gag/Aag	10/22	0.368431889440751	1	FACETS	0.713	0.617	0.814	0.713	0.617	0.814	INDETERMINATE	1	TRUE	0	0.652324328169863	1		733	139	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101905	11101905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771446534	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	13	771	0	ENST00000358026.2:c.1325G>A	p.Ser442Asn	p.S442N	ENST00000358026	NM_001128849.1	442	aGc/aAc	8/36	0.368431889440751	1	FACETS	0.176	0.125	0.236	0.176	0.125	0.236	INDETERMINATE	1	TRUE	0	0.652324328169863	1		771	153	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144462	11144462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775157286	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	68	682	0	ENST00000358026.2:c.3794G>A	p.Gly1265Asp	p.G1265D	ENST00000358026	NM_001128849.1	1265	gGc/gAc	27/36	1	2	FACETS	0.862	0.759	0.969	0.862	0.759	0.969	CLONAL	1	TRUE	1	0.652324328169863	2		682	242	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152237	11152237	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	42	526	1	ENST00000358026.2:c.4520+1G>A		p.X1507_splice	ENST00000358026	NM_001128849.1	1507			1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.652324328169863	2		527	119	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281290	15281290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	71	710	1	ENST00000263388.2:c.4966G>A	p.Val1656Ile	p.V1656I	ENST00000263388	NM_000435.2	1656	Gtc/Atc	27/33	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.652324328169863	2		711	188	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303102	15303102	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	46	928	0	ENST00000263388.2:c.348C>G	p.Asp116Glu	p.D116E	ENST00000263388	NM_000435.2	116	gaC/gaG	4/33	1	2	FACETS	0.784	0.67	0.905	0.784	0.67	0.905	CLONAL	1	TRUE	1	0.652324328169863	2		928	180	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349775	15349775	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1323126971	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	71	726	0	ENST00000263377.2:c.3799G>A	p.Asp1267Asn	p.D1267N	ENST00000263377	NM_058243.2	1267	Gat/Aat	19/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.652324328169863	2		726	184	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350202	15350202	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	61	882	1	ENST00000263377.2:c.3576+1G>A		p.X1192_splice	ENST00000263377	NM_058243.2	1192			1	2	FACETS	0.839	0.733	0.95	0.839	0.733	0.95	CLONAL	1	TRUE	1	0.652324328169863	2		883	223	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367885	15367885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753457206	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	35	801	0	ENST00000263377.2:c.1441G>A	p.Ala481Thr	p.A481T	ENST00000263377	NM_058243.2	481	Gcc/Acc	8/20	1	2	FACETS	0.506	0.418	0.603	0.506	0.418	0.603	SUBCLONAL	1	TRUE	1	0.652324328169863	2		801	212	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945786	17945786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	48	690	0	ENST00000458235.1:c.2074G>A	p.Ala692Thr	p.A692T	ENST00000458235	NM_000215.3	692	Gcc/Acc	16/24	1	2	FACETS	0.908	0.782	1	0.908	0.782	1	CLONAL	1	TRUE	1	0.652324328169863	2		690	162	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214664	36214664	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	62	587	0	ENST00000222270.7:c.3090G>A	p.Trp1030Ter	p.W1030*	ENST00000222270	NM_014727.1	1030	tgG/tgA	8/37	1	2	FACETS	0.955	0.839	1	0.955	0.839	1	CLONAL	1	TRUE	1	0.652324328169863	2		587	199	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793484	42793484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780297917	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	89	730	5	ENST00000575354.2:c.1286C>T	p.Ala429Val	p.A429V	ENST00000575354	NM_015125.3	429	gCg/gTg	8/20	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.652324328169863	2		735	251	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795310	42795310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	11	748	0	ENST00000575354.2:c.2390G>A	p.Gly797Asp	p.G797D	ENST00000575354	NM_015125.3	797	gGt/gAt	10/20	1	2	FACETS	0.157	0.108	0.218	0.157	0.108	0.218	SUBCLONAL	1	TRUE	1	0.652324328169863	2		748	215	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795781	42795781	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	22	806	1	ENST00000575354.2:c.2770G>A	p.Val924Met	p.V924M	ENST00000575354	NM_015125.3	924	Gtg/Atg	11/20	1	2	FACETS	0.275	0.214	0.346	0.275	0.214	0.346	SUBCLONAL	1	TRUE	1	0.652324328169863	2		807	245	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796999	42796999	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs972439778	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	60	892	0	ENST00000575354.2:c.3457C>T	p.Pro1153Ser	p.P1153S	ENST00000575354	NM_015125.3	1153	Ccc/Tcc	14/20	1	2	FACETS	0.825	0.72	0.935	0.825	0.72	0.935	CLONAL	1	TRUE	1	0.652324328169863	2		892	223	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798888	42798888	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	62	861	0	ENST00000575354.2:c.4459+1G>A		p.X1487_splice	ENST00000575354	NM_015125.3	1487			1	2	FACETS	0.901	0.79	1	0.901	0.79	1	CLONAL	1	TRUE	1	0.652324328169863	2		861	211	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905560	50905560	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	18	868	0	ENST00000440232.2:c.688G>A	p.Gly230Ser	p.G230S	ENST00000440232	NM_002691.3	230	Ggc/Agc	6/27	1	2	FACETS	0.253	0.191	0.326	0.253	0.191	0.326	SUBCLONAL	1	TRUE	1	0.652324328169863	2		868	218	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714631	52714631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	66	756	0	ENST00000322088.6:c.389C>T	p.Pro130Leu	p.P130L	ENST00000322088	NM_014225.5	130	cCg/cTg	4/15	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.652324328169863	2		756	184	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469539	25469539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1401774585	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	129	824	1	ENST00000264709.3:c.1229C>T	p.Ala410Val	p.A410V	ENST00000264709	NM_175629.2	410	gCc/gTc	10/23	0.199974716719056	3	FACETS	0.914	0.843	0.985	0.914	0.843	0.985	INDETERMINATE	2	TRUE	1	0.652324328169863	3		825	287	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698160	47698160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	24	140	0	ENST00000233146.2:c.1718C>T	p.Ala573Val	p.A573V	ENST00000233146	NM_000251.2	573	gCc/gTc	11/16	0.652324328169863	3	FACETS	0.904	0.722	1	0.452	0.361	0.553	CLONAL	1	TRUE	1	0.652324328169863	3		140	108	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027764	48027764	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	56	316	1	ENST00000234420.5:c.2642G>A	p.Gly881Asp	p.G881D	ENST00000234420	NM_000179.2	881	gGt/gAt	4/10	0.652324328169863	3	FACETS	0.78	0.685	0.878	0.78	0.685	0.878	SUBCLONAL	2	TRUE	1	0.652324328169863	3		317	146	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147760	61147760	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	44	180	1	ENST00000295025.8:c.1070G>A	p.Gly357Glu	p.G357E	ENST00000295025	NM_002908.2	357	gGa/gAa	10/11	0.652324328169863	3	FACETS	1	0.905	1	1	0.905	1	CLONAL	2	TRUE	1	0.652324328169863	3		181	86	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158655938	158655938	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	25	265	0	ENST00000263640.3:c.67+1G>A		p.X23_splice	ENST00000263640	NM_001105.4	23			0.465109459740539	4	FACETS	0.989	0.791	1	0.495	0.395	0.605	CLONAL	1	TRUE	2	0.652324328169863	4		265	128	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543847	212543847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	99	420	0	ENST00000342788.4:c.1552G>A	p.Asp518Asn	p.D518N	ENST00000342788	NM_005235.2	518	Gac/Aac	13/28	0.199974716719056	3	FACETS	0.972	0.889	1	0.972	0.889	1	INDETERMINATE	2	TRUE	1	0.652324328169863	3		420	207	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593620	215593620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	13	507	0	ENST00000260947.4:c.2114G>A	p.Arg705Lys	p.R705K	ENST00000260947	NM_000465.2	705	aGa/aAa	11/11	0.199974716719056	3	FACETS	0.222	0.158	0.3	0.111	0.079	0.15	INDETERMINATE	1	TRUE	1	0.652324328169863	3		507	238	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225367786	225367786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	36	268	0	ENST00000264414.4:c.1381G>A	p.Glu461Lys	p.E461K	ENST00000264414	NM_003590.4	461	Gaa/Aaa	10/16	0.199974716719056	3	FACETS	0.904	0.773	1	0.904	0.773	1	INDETERMINATE	2	TRUE	1	0.652324328169863	3		268	81	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662551	227662551	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	94	587	0	ENST00000305123.5:c.904C>T	p.Arg302Ter	p.R302*	ENST00000305123	NM_005544.2	302	Cga/Tga	1/2	0.199974716719056	3	FACETS	1	0.98	1	0.687	0.62	0.757	INDETERMINATE	1	TRUE	1	0.652324328169863	3		587	278	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309577	30309577	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	91	745	0	ENST00000307677.4:c.445G>A	p.Ala149Thr	p.A149T	ENST00000307677	NM_138578.1	149	Gca/Aca	2/3	0.591726867931355	2	FACETS	1	0.93	1	0.521	0.469	0.574	CLONAL	1	TRUE	0	0.652324328169863	2		745	268	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46276103	46276103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	49	534	0	ENST00000371998.3:c.3539G>A	p.Gly1180Asp	p.G1180D	ENST00000371998		1180	gGc/gAc	18/23	0.591726867931355	2	FACETS	0.884	0.762	1	0.442	0.381	0.507	CLONAL	1	TRUE	0	0.652324328169863	2		534	170	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279910	46279910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	62	784	1	ENST00000371998.3:c.3836C>T	p.Ala1279Val	p.A1279V	ENST00000371998		1279	gCc/gTc	20/23	0.591726867931355	2	FACETS	1	0.88	1	0.5	0.44	0.563	CLONAL	1	TRUE	0	0.652324328169863	2		785	190	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945588	54945588	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	37	599	0	ENST00000312783.6:c.982C>T	p.Pro328Ser	p.P328S	ENST00000312783	NM_198436.1	328	Cct/Tct	9/10	0.591726867931355	2	FACETS	1	0.882	1	0.525	0.445	0.61	CLONAL	1	TRUE	0	0.652324328169863	2		599	108	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484459	57484459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	10	575	0	ENST00000371085.3:c.640G>A	p.Val214Met	p.V214M	ENST00000371085	NM_000516.4	214	Gtg/Atg	8/13	0.591726867931355	2	FACETS	0.216	0.146	0.303	0.108	0.073	0.152	SUBCLONAL	1	TRUE	0	0.652324328169863	2		575	142	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62320864	62320864	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	92	815	0	ENST00000360203.5:c.1888G>A	p.Gly630Arg	p.G630R	ENST00000360203	NM_001283009.1	630	Ggg/Agg	23/35	0.591726867931355	2	FACETS	1	0.939	1	0.528	0.476	0.582	CLONAL	1	TRUE	0	0.652324328169863	2		815	267	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145595	24145595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	62	693	0	ENST00000263121.7:c.614C>T	p.Thr205Ile	p.T205I	ENST00000263121	NM_003073.3	205	aCc/aTc	5/9	0.253303443574687	1	FACETS	0.776	0.686	0.87	0.776	0.686	0.87	INDETERMINATE	1	TRUE	0	0.652324328169863	1		693	165	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536226	41536226	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	10	509	0	ENST00000263253.7:c.1843G>A	p.Val615Ile	p.V615I	ENST00000263253	NM_001429.3	615	Gtt/Att	9/31	0.253303443574687	1	FACETS	0.151	0.102	0.211	0.151	0.102	0.211	INDETERMINATE	1	TRUE	0	0.652324328169863	1		509	137	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551097	41551097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	52	598	0	ENST00000263253.7:c.3241C>T	p.Pro1081Ser	p.P1081S	ENST00000263253	NM_001429.3	1081	Cct/Tct	17/31	0.253303443574687	1	FACETS	0.676	0.587	0.769	0.676	0.587	0.769	INDETERMINATE	1	TRUE	0	0.652324328169863	1		598	159	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574047	41574047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	66	611	1	ENST00000263253.7:c.6332C>T	p.Pro2111Leu	p.P2111L	ENST00000263253	NM_001429.3	2111	cCa/cTa	31/31	0.253303443574687	1	FACETS	0.915	0.817	1	0.915	0.817	1	INDETERMINATE	1	TRUE	0	0.652324328169863	1		612	149	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574740	41574740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	65	905	1	ENST00000263253.7:c.7025C>T	p.Pro2342Leu	p.P2342L	ENST00000263253	NM_001429.3	2342	cCa/cTa	31/31	0.253303443574687	1	FACETS	0.643	0.566	0.723	0.643	0.566	0.723	INDETERMINATE	1	TRUE	0	0.652324328169863	1		906	209	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090485	37090485	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	42	455	0	ENST00000231790.2:c.2080G>A	p.Glu694Lys	p.E694K	ENST00000231790	NM_000249.3	694	Gag/Aag	18/19	1	2	FACETS	0.998	0.853	1	0.998	0.853	1	CLONAL	1	TRUE	1	0.652324328169863	2		455	129	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623236	52623236	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1232278552	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	44	399	0	ENST00000394830.3:c.2815G>A	p.Gly939Ser	p.G939S	ENST00000394830	NM_018313.4	939	Ggc/Agc	19/30	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.652324328169863	2		399	134	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71019951	71019951	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	29	250	0	ENST00000318789.4:c.1658C>T	p.Pro553Leu	p.P553L	ENST00000318789	NM_032682.5	553	cCt/cTt	19/21	1	2	FACETS	1	0.844	1	1	0.844	1	CLONAL	1	TRUE	1	0.652324328169863	2		250	87	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114566	73114566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	24	149	0	ENST00000356692.5:c.947G>A	p.Arg316Lys	p.R316K	ENST00000356692		316	aGa/aAa	9/9	1	2	FACETS	1	0.827	1	1	0.827	1	CLONAL	1	TRUE	1	0.652324328169863	2		149	72	SUCCESS
ATR	545	MSKCC	GRCh37	3	142259768	142259768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	32	362	0	ENST00000350721.4:c.3559G>A	p.Asp1187Asn	p.D1187N	ENST00000350721	NM_001184.3	1187	Gat/Aat	18/47	1	2	FACETS	0.732	0.605	0.871	0.732	0.605	0.871	SUBCLONAL	1	TRUE	1	0.652324328169863	2		362	134	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447672	187447672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	97	630	0	ENST00000232014.4:c.521G>A	p.Gly174Glu	p.G174E	ENST00000232014	NM_001130845.1	174	gGg/gAg	5/10	0.404144500413878	3	FACETS	0.896	0.816	0.977	0.896	0.816	0.977	CLONAL	2	TRUE	1	0.652324328169863	3		630	220	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806629	1806629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61735104	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	24	779	0	ENST00000260795.2:c.1345C>T	p.Pro449Ser	p.P449S	ENST00000260795		449	Ccc/Tcc	9/17	1	2	FACETS	0.324	0.255	0.403	0.324	0.255	0.403	SUBCLONAL	1	TRUE	1	0.652324328169863	2		779	227	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1956935	1956935	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	58	812	0	ENST00000382891.5:c.2386G>A	p.Asp796Asn	p.D796N	ENST00000382891	NM_133335.3	796	Gat/Aat	13/22	1	2	FACETS	0.956	0.836	1	0.956	0.836	1	CLONAL	1	TRUE	1	0.652324328169863	2		812	186	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979602	55979602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	61	517	0	ENST00000263923.4:c.845G>A	p.Gly282Glu	p.G282E	ENST00000263923	NM_002253.2	282	gGg/gAg	7/30	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.652324328169863	2		517	147	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99823094	99823094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	42	289	0	ENST00000280892.6:c.118G>A	p.Glu40Lys	p.E40K	ENST00000280892	NM_001130678.1	40	Gag/Aag	2/7	0.344310312954456	3	FACETS	0.854	0.737	0.974	0.854	0.737	0.974	INDETERMINATE	2	TRUE	1	0.652324328169863	3		289	100	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628154	187628154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	45	743	0	ENST00000441802.2:c.2828G>A	p.Gly943Glu	p.G943E	ENST00000441802	NM_005245.3	943	gGa/gAa	2/27	1	2	FACETS	0.784	0.669	0.907	0.784	0.669	0.907	CLONAL	1	TRUE	1	0.652324328169863	2		743	176	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515583	31515583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	46	257	0	ENST00000344624.3:c.1036C>T	p.Pro346Ser	p.P346S	ENST00000344624		346	Cca/Tca	4/33	NA	2	FACETS	0.766	0.672	0.861			1	INDETERMINATE	2	TRUE	NA	0.652324328169863	2		257	92	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871169	35871169	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	24	271	0	ENST00000303115.3:c.391G>A	p.Ala131Thr	p.A131T	ENST00000303115	NM_002185.3	131	Gct/Act	4/8	0.199974716719056	3	FACETS	1	0.844	1	0.53	0.425	0.645	INDETERMINATE	1	TRUE	1	0.652324328169863	3		271	92	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	29	175	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	0.199974716719056	3	FACETS	1	0.934	1	0.662	0.547	0.785	INDETERMINATE	1	TRUE	1	0.652324328169863	3		175	89	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721157	176721157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373571733	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	10	472	1	ENST00000439151.2:c.6788C>T	p.Ser2263Leu	p.S2263L	ENST00000439151	NM_022455.4	2263	tCg/tTg	23/23	NA	2	FACETS	0.232	0.158	0.325			1	INDETERMINATE	1	TRUE	NA	0.652324328169863	2		473	132	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036912	180036912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	68	677	0	ENST00000261937.6:c.3800G>A	p.Gly1267Asp	p.G1267D	ENST00000261937	NM_182925.4	1267	gGc/gAc	28/30	NA	2	FACETS	1	0.891	1			1	INDETERMINATE	1	TRUE	NA	0.652324328169863	2		677	207	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041097	180041097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	100	879	0	ENST00000261937.6:c.3302G>A	p.Gly1101Glu	p.G1101E	ENST00000261937	NM_182925.4	1101	gGg/gAg	24/30	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	1	TRUE	NA	0.652324328169863	2		879	252	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057731	180057731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	71	740	0	ENST00000261937.6:c.224G>A	p.Ser75Asn	p.S75N	ENST00000261937	NM_182925.4	75	aGc/aAc	3/30	NA	2	FACETS	1	0.902	1			1	INDETERMINATE	1	TRUE	NA	0.652324328169863	2		740	214	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402660	20402660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777566535	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	34	440	0	ENST00000346618.3:c.197C>T	p.Ser66Phe	p.S66F	ENST00000346618	NM_001949.4	66	tCc/tTc	1/7	NA	2	FACETS	0.766	0.637	0.906			1	INDETERMINATE	1	TRUE	NA	0.652324328169863	2		440	136	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672807	30672807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774434419	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	52	876	0	ENST00000376406.3:c.4153C>T	p.Pro1385Ser	p.P1385S	ENST00000376406	NM_014641.2	1385	Cct/Tct	10/15	1	2	FACETS	0.911	0.789	1	0.911	0.789	1	CLONAL	1	TRUE	1	0.652324328169863	2		876	175	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818747	32818747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	75	707	0	ENST00000354258.4:c.1204C>T	p.Pro402Ser	p.P402S	ENST00000354258	NM_000593.5	402	Ccc/Tcc	4/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.652324328169863	2		707	206	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41904362	41904362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201272551	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	78	706	0	ENST00000372991.4:c.646G>A	p.Gly216Ser	p.G216S	ENST00000372991	NM_001760.3	216	Ggt/Agt	4/5	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.652324328169863	2		706	200	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64286804	64286804	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	49	287	0	ENST00000370651.3:c.19C>T	p.Pro7Ser	p.P7S	ENST00000370651	NM_003463.4	7	Cca/Tca	2/6	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.652324328169863	2		287	124	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020862	112020862	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	29	270	0	ENST00000368678.4:c.709G>A	p.Gly237Ser	p.G237S	ENST00000368678		237	Ggt/Agt	8/13	1	2	FACETS	0.917	0.755	1	0.917	0.755	1	CLONAL	1	TRUE	1	0.652324328169863	2		270	97	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631320	117631320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	42	478	0	ENST00000368508.3:c.6358G>A	p.Glu2120Lys	p.E2120K	ENST00000368508	NM_002944.2	2120	Gaa/Aaa	40/43	1	2	FACETS	0.947	0.808	1	0.947	0.808	1	CLONAL	1	TRUE	1	0.652324328169863	2		478	136	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099110	157099110	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	40	169	0	ENST00000346085.5:c.47C>T	p.Ala16Val	p.A16V	ENST00000346085	NM_020732.3	16	gCc/gTc	1/20	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.652324328169863	2		169	119	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976867	2976867	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs776851896	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	35	622	0	ENST00000396946.4:c.1145C>T	p.Ala382Val	p.A382V	ENST00000396946	NM_032415.4	382	gCc/gTc	9/25	0.652324328169863	3	FACETS	0.799	0.663	0.949	0.4	0.331	0.475	CLONAL	1	TRUE	1	0.652324328169863	3		622	178	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977621	2977621	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	62	875	0	ENST00000396946.4:c.1063G>A	p.Gly355Arg	p.G355R	ENST00000396946	NM_032415.4	355	Gga/Aga	8/25	0.652324328169863	3	FACETS	0.894	0.779	1	0.447	0.389	0.508	CLONAL	1	TRUE	1	0.652324328169863	3		875	282	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975450	13975450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	72	483	0	ENST00000405192.2:c.437C>T	p.Ser146Phe	p.S146F	ENST00000405192	NM_001163147.1	146	tCc/tTc	7/12	0.652324328169863	4	FACETS	1	0.971	1	0.449	0.396	0.504	CLONAL	1	TRUE	1	0.652324328169863	4		483	271	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455153	50455153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	59	327	0	ENST00000331340.3:c.700G>A	p.Gly234Ser	p.G234S	ENST00000331340	NM_006060.4	234	Ggc/Agc	6/8	0.652324328169863	4	FACETS	0.869	0.763	0.979	0.579	0.508	0.653	CLONAL	2	TRUE	1	0.652324328169863	4		327	172	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220272	55220272	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	69	854	0	ENST00000275493.2:c.662G>A	p.Gly221Glu	p.G221E	ENST00000275493	NM_005228.3	221	gGg/gAg	6/28	0.368617299366889	4	FACETS	1	0.928	1			1	INDETERMINATE	1	TRUE	NA	0.652324328169863	4		854	323	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513171	106513171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771600769	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	41	335	0	ENST00000359195.3:c.2075G>A	p.Gly692Asp	p.G692D	ENST00000359195	NM_002649.2	692	gGt/gAt	4/11	0.652324328169863	4	FACETS	1	0.881	1	0.351	0.296	0.412	CLONAL	1	TRUE	1	0.652324328169863	4		335	197	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829068	128829068	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs925643027	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	13	10	0	ENST00000249373.3:c.76C>T	p.Pro26Ser	p.P26S	ENST00000249373	NM_005631.4	26	Ccg/Tcg	1/12	0.652324328169863	4	FACETS	0.844	0.651	1	0.844	0.651	1	CLONAL	3	TRUE	1	0.652324328169863	4		10	26	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846073	128846073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	21	928	0	ENST00000249373.3:c.1003C>T	p.Leu335Phe	p.L335F	ENST00000249373	NM_005631.4	335	Ctc/Ttc	5/12	0.652324328169863	4	FACETS	0.316	0.243	0.401	0.105	0.081	0.134	SUBCLONAL	1	TRUE	1	0.652324328169863	4		928	337	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845502	151845502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	55	704	0	ENST00000262189.6:c.13510C>T	p.Pro4504Ser	p.P4504S	ENST00000262189	NM_170606.2	4504	Ccc/Tcc	52/59	0.613927844515871	4	FACETS	1	0.89	1	0.345	0.298	0.396	CLONAL	1	TRUE	1	0.652324328169863	4		704	269	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864349	151864349	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	47	560	0	ENST00000262189.6:c.9632C>T	p.Ala3211Val	p.A3211V	ENST00000262189	NM_170606.2	3211	gCc/gTc	42/59	0.613927844515871	4	FACETS	0.972	0.827	1	0.324	0.275	0.376	CLONAL	1	TRUE	1	0.652324328169863	4		560	245	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877048	151877048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	62	507	0	ENST00000262189.6:c.7313C>T	p.Pro2438Leu	p.P2438L	ENST00000262189	NM_170606.2	2438	cCc/cTc	37/59	0.613927844515871	4	FACETS	1	0.955	1	0.406	0.354	0.461	CLONAL	1	TRUE	1	0.652324328169863	4		507	258	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878185	151878185	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1174385764	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	58	737	0	ENST00000262189.6:c.6760G>A	p.Ala2254Thr	p.A2254T	ENST00000262189	NM_170606.2	2254	Gca/Aca	36/59	0.613927844515871	4	FACETS	1	0.937	1	0.38	0.329	0.433	CLONAL	1	TRUE	1	0.652324328169863	4		737	258	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879061	151879061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs965807663	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	92	696	0	ENST00000262189.6:c.5884C>T	p.Pro1962Ser	p.P1962S	ENST00000262189	NM_170606.2	1962	Ccc/Tcc	36/59	0.613927844515871	4	FACETS	0.914	0.825	1	0.609	0.55	0.67	CLONAL	2	TRUE	1	0.652324328169863	4		696	255	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205092	38205092	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	25	550	0	ENST00000317025.8:c.598del	p.Ser200AlafsTer20	p.S200Afs*20	ENST00000317025	NM_023034.1	200	Agc/gc	2/24	1	2	FACETS	0.59	0.471	0.721	0.59	0.471	0.721	SUBCLONAL	1	TRUE	1	0.652324328169863	2		550	130	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965824	90965824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	27	269	0	ENST00000265433.3:c.1493C>T	p.Pro498Leu	p.P498L	ENST00000265433	NM_002485.4	498	cCc/cTc	11/16	1	2	FACETS	0.796	0.647	0.958	0.796	0.647	0.958	CLONAL	1	TRUE	1	0.652324328169863	2		269	104	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993035	90993035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	50	292	0	ENST00000265433.3:c.407G>A	p.Gly136Glu	p.G136E	ENST00000265433	NM_002485.4	136	gGa/gAa	4/16	1	2	FACETS	0.891	0.769	1	0.891	0.769	1	CLONAL	1	TRUE	1	0.652324328169863	2		292	172	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868476	117868476	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	52	415	0	ENST00000297338.2:c.866C>T	p.Thr289Ile	p.T289I	ENST00000297338	NM_006265.2	289	aCc/aTc	8/14	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.652324328169863	2		415	136	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054784	5054784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765196728	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	39	272	0	ENST00000381652.3:c.836C>T	p.Pro279Leu	p.P279L	ENST00000381652	NM_004972.3	279	cCt/cTt	7/25	0.344310312954456	3	FACETS	1	0.951	1	0.672	0.571	0.778	INDETERMINATE	1	TRUE	1	0.652324328169863	3		272	118	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	72	365	0	ENST00000304494.5:c.262G>A	p.Glu88Lys	p.E88K	ENST00000304494	NM_000077.4	88	Gag/Aag	2/3	0.344310312954456	3	FACETS	0.879	0.805	0.95	1	0.98	1	INDETERMINATE	3	TRUE	1	0.652324328169863	3		365	111	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537177	80537177	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	33	427	0	ENST00000286548.4:c.221G>A	p.Gly74Asp	p.G74D	ENST00000286548	NM_002072.3	74	gGc/gAc	2/7	0.344310312954456	3	FACETS	1	0.83	1	0.501	0.415	0.594	INDETERMINATE	1	TRUE	1	0.652324328169863	3		427	134	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912102	127912102	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	61	298	0	ENST00000373547.4:c.768G>A	p.Trp256Ter	p.W256*	ENST00000373547	NM_002721.4	256	tgG/tgA	7/7	0.344310312954456	3	FACETS	1	0.913	1	1	0.913	1	INDETERMINATE	2	TRUE	1	0.652324328169863	3		298	121	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399470	139399470	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	75	802	1	ENST00000277541.6:c.4673G>A	p.Gly1558Glu	p.G1558E	ENST00000277541	NM_017617.3	1558	gGg/gAg	26/34	0.344310312954456	3	FACETS	1	0.923	1	0.528	0.467	0.591	INDETERMINATE	1	TRUE	1	0.652324328169863	3		803	289	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15840920	15840920	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	29	148	0	ENST00000307771.7:c.1004C>T	p.Pro335Leu	p.P335L	ENST00000307771	NM_005089.3	335	cCc/cTc	11/11	1	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.652324328169863	1		148	48	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921391	39921391	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	49	220	0	ENST00000378444.4:c.4428+1G>A		p.X1476_splice	ENST00000378444	NM_001123385.1	1476			1	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.652324328169863	1		220	73	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039332	47039332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	88	445	0	ENST00000377604.3:c.955G>A	p.Ala319Thr	p.A319T	ENST00000377604	NM_001204468.1	319	Gcc/Acc	10/24	1	1	FACETS	0.758	0.706	0.805	1	0.988	1	SUBCLONAL	2	TRUE	0	0.652324328169863	1		445	120	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412380	63412380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	69	443	0	ENST00000330258.3:c.787G>A	p.Glu263Lys	p.E263K	ENST00000330258	NM_152424.3	263	Gag/Aag	2/2	1	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.652324328169863	1		443	125	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412541	63412541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	51	389	0	ENST00000330258.3:c.626G>A	p.Ser209Asn	p.S209N	ENST00000330258	NM_152424.3	209	aGc/aAc	2/2	1	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.652324328169863	1		389	82	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345564	70345564	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	44	355	0	ENST00000374080.3:c.2422+1G>A		p.X808_splice	ENST00000374080		808			1	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.652324328169863	1		355	66	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611944	100611944	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	10	263	0	ENST00000308731.7:c.1178-1G>A		p.X393_splice	ENST00000308731	NM_000061.2	393			1	1	FACETS	0.265	0.182	0.366	0.265	0.182	0.366	SUBCLONAL	1	TRUE	0	0.652324328169863	1		263	78	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184049	123184049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556521622	NA	P-0034618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	53	175	0	ENST00000218089.9:c.907G>A	p.Glu303Lys	p.E303K	ENST00000218089	NM_001042749.1	303	Gaa/Aaa	11/35	1	1	FACETS	0.771	0.705	0.831	1	0.981	1	SUBCLONAL	2	TRUE	0	0.652324328169863	1		175	71	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910686	32910686	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034632-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	86	675	0	ENST00000380152.3:c.2194G>T	p.Glu732Ter	p.E732*	ENST00000380152		732	Gag/Tag	11/27	1	2	FACETS	0.763	0.677	0.854	1	0.979	1	SUBCLONAL	2	FALSE	1	0.233435880633453	2		675	483	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319920	8319920	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034632-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	108	491	0	ENST00000356435.5:c.5581T>A	p.Leu1861Met	p.L1861M	ENST00000356435		1861	Ttg/Atg	34/35	0.233435880633453	1	FACETS	1	0.967	1	1	0.99	1	CLONAL	2	FALSE	0	0.233435880633453	1		491	355	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38064107	38064107	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034632-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	55	429	0	ENST00000250448.2:c.71A>T	p.Glu24Val	p.E24V	ENST00000250448	NM_004496.3	24	gAg/gTg	1/2	1	2	FACETS	0.939	0.804	1	0.939	0.804	1	CLONAL	1	FALSE	1	0.233435880633453	2		429	502	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224130	36224130	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034632-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	129	840	0	ENST00000222270.7:c.6680C>G	p.Thr2227Arg	p.T2227R	ENST00000222270	NM_014727.1	2227	aCg/aGg	28/37	1	2	FACETS	0.904	0.823	0.99	1	0.989	1	CLONAL	2	FALSE	1	0.233435880633453	2		840	611	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0034697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	329	288	0	ENST00000304494.5:c.151-1G>A		p.X51_splice	ENST00000304494	NM_000077.4	51			0.313143043901754	2	FACETS	0.919	0.896	0.941	1	0.997	1	CLONAL	6	FALSE	0	0.313143043901754	2		288	381	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317926	8317926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	366	337	0	ENST00000356435.5:c.5687C>T	p.Ser1896Phe	p.S1896F	ENST00000356435		1896	tCc/tTc	35/35	0.313143043901754	2	FACETS	0.948	0.927	0.967	1	0.997	1	CLONAL	6	FALSE	0	0.313143043901754	2		337	411	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0034697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	402	462	1				ENST00000310581	NM_198253.2	-/1132			0.313143043901754	5	FACETS	0.937	0.902	0.972	1	0.996	1	CLONAL	6	FALSE	1	0.313143043901754	5		463	671	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683713	162683713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747891099	NA	P-0034697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	354	549	0	ENST00000366898.1:c.256G>A	p.Asp86Asn	p.D86N	ENST00000366898	NM_004562.2	86	Gac/Aac	3/12	0.283156881025676	2	FACETS	0.889	0.851	0.926	1	0.996	1	CLONAL	4	FALSE	0	0.313143043901754	2		549	636	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546086	29546086	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057518134	NA	P-0034697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	356	361	0	ENST00000356175.3:c.1591C>T	p.Gln531Ter	p.Q531*	ENST00000356175	NM_000267.3	531	Caa/Taa	14/57	0.30351540445172	4	FACETS	0.916	0.877	0.955	1	0.996	1	CLONAL	5	FALSE	1	0.313143043901754	4		361	652	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352660	118352660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	213	439	0	ENST00000534358.1:c.3865C>T	p.Pro1289Ser	p.P1289S	ENST00000534358	NM_005933.3	1289	Cca/Tca	7/36	0.313143043901754	5	FACETS	0.908	0.847	0.971	0.681	0.635	0.728	CLONAL	3	FALSE	1	0.313143043901754	5		439	734	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118361916	118361916	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	74	220	0	ENST00000534358.1:c.4702T>C	p.Phe1568Leu	p.F1568L	ENST00000534358	NM_005933.3	1568	Ttc/Ctc	14/36	0.313143043901754	5	FACETS	0.802	0.705	0.906	0.401	0.352	0.453	CLONAL	2	FALSE	1	0.313143043901754	5		220	433	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118368754	118368754	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	453	474	0	ENST00000534358.1:c.5768A>T	p.Asn1923Ile	p.N1923I	ENST00000534358	NM_005933.3	1923	aAt/aTt	21/36	0.313143043901754	5	FACETS	0.931	0.898	0.964	1	0.996	1	CLONAL	6	FALSE	1	0.313143043901754	5		474	761	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926910	112926910	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	429	564	0	ENST00000351677.2:c.1530G>T	p.Gln510His	p.Q510H	ENST00000351677	NM_002834.3	510	caG/caT	13/16	0.30351540445172	4	FACETS	0.962	0.926	0.998	1	0.997	1	CLONAL	5	FALSE	1	0.313143043901754	4		564	748	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118820	115118821	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0034697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	155	471	1	ENST00000257566.3:c.520_521delinsCT	p.Gly174Leu	p.G174L	ENST00000257566	NM_016569.3	174	GGt/CTt	2/8	0.30351540445172	4	FACETS	0.894	0.82	0.971	0.596	0.547	0.648	CLONAL	2	FALSE	1	0.313143043901754	4		472	727	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022938	33022938	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1191361049	NA	P-0034697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	272	391	0	ENST00000300177.4:c.47G>A	p.Gly16Glu	p.G16E	ENST00000300177	NM_001191322.1	16	gGg/gAg	2/2	0.313143043901754	7	FACETS	0.904	0.854	0.955	1	0.986	1	CLONAL	5	FALSE	3	0.313143043901754	7		391	685	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996081	73996081	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	715	884	0	ENST00000318443.5:c.815C>T	p.Pro272Leu	p.P272L	ENST00000318443	NM_001024736.1	272	cCc/cTc	5/10	0.313143043901754	7	FACETS	1	0.993	1	1	0.997	1	CLONAL	5	FALSE	3	0.313143043901754	7		884	1503	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679365	29679366	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0034697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	178	380	2	ENST00000356175.3:c.7485_7486delinsTT	p.Arg2496Ter	p.R2496*	ENST00000356175	NM_000267.3	2495	ccCCga/ccTTga	50/57	0.30351540445172	4	FACETS	1	0.982	1	0.796	0.737	0.857	CLONAL	2	FALSE	1	0.313143043901754	4		382	625	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480411	89480411	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	362	347	0	ENST00000336596.2:c.2248C>T	p.Arg750Trp	p.R750W	ENST00000336596	NM_005233.5	750	Cgg/Tgg	13/17	0.313143043901754	8	FACETS	0.956	0.912	1	1	0.995	1	CLONAL	6	FALSE	4	0.313143043901754	8		347	782	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747861	41747861	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	171	515	2	ENST00000226382.2:c.908G>A	p.Gly303Asp	p.G303D	ENST00000226382	NM_003924.3	303	gGt/gAt	3/3	0.313143043901754	2	FACETS	0.953	0.882	1	0.953	0.882	1	CLONAL	2	FALSE	0	0.313143043901754	2		517	573	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945119	38945119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	175	338	1	ENST00000357387.3:c.4685C>T	p.Pro1562Leu	p.P1562L	ENST00000357387	NM_152756.3	1562	cCt/cTt	35/38	0.313143043901754	5	FACETS	0.949	0.879	1	0.712	0.659	0.766	CLONAL	3	FALSE	1	0.313143043901754	5		339	577	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522561	176522561	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs865779136	NA	P-0034697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	308	683	3	ENST00000292408.4:c.1658C>T	p.Ala553Val	p.A553V	ENST00000292408	NM_213647.1	553	gCc/gTc	13/18	0.313143043901754	5	FACETS	0.941	0.888	0.995	0.706	0.666	0.746	CLONAL	3	FALSE	1	0.313143043901754	5		686	1024	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680438	30680438	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	1445	580	0	ENST00000376406.3:c.1281G>A	p.Trp427Ter	p.W427*	ENST00000376406	NM_014641.2	427	tgG/tgA	5/15	0.313143043901754	16	FACETS	0.983	0.968	0.998			1	CLONAL	16	FALSE	NA	0.313143043901754	16		580	1873	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781150	161781150	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752418689	NA	P-0034697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	455	710	1	ENST00000366898.1:c.1255C>T	p.Pro419Ser	p.P419S	ENST00000366898	NM_004562.2	419	Ccc/Tcc	11/12	0.283156881025676	2	FACETS	0.897	0.864	0.93	1	0.997	1	CLONAL	4	FALSE	0	0.313143043901754	2		711	810	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980720	70980720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	459	530	2	ENST00000276594.2:c.748C>T	p.Pro250Ser	p.P250S	ENST00000276594	NM_024504.3	250	Cca/Tca	3/8	0.313143043901754	5	FACETS	1	0.986	1	1	0.996	1	CLONAL	5	FALSE	1	0.313143043901754	5		532	823	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389286	8389286	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs868721731	NA	P-0034697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	564	709	0	ENST00000356435.5:c.4332G>A	p.Trp1444Ter	p.W1444*	ENST00000356435		1444	tgG/tgA	26/35	0.313143043901754	2	FACETS	1	0.995	1	1	0.998	1	CLONAL	5	FALSE	0	0.313143043901754	2		709	675	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0034818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	348	691	2	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	NA	2	FACETS	1	0.972	1			1	INDETERMINATE	2	FALSE	NA	0.495079390639885	2		693	687	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0034818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	324	566	1	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	0.437349607946453	4	FACETS	0.988	0.935	1	0.988	0.935	1	CLONAL	2	FALSE	2	0.495079390639885	4		567	990	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808870	1808870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs560280646	NA	P-0034818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	696	796	2	ENST00000260795.2:c.2302G>A	p.Glu768Lys	p.E768K	ENST00000260795		768	Gag/Aag	17/17	0.495079390639885	5	FACETS	1	0.995	1			1	CLONAL	3	FALSE	NA	0.495079390639885	5		798	1413	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123681	46123682	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGAG	novel	NA	P-0034818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	144	226	0	ENST00000334344.6:c.64_67dup	p.Leu23ArgfsTer14	p.L23Rfs*14	ENST00000334344	NM_152641.2	21	gac/gaCGAGc	1/21	0.437349607946453	4	FACETS	0.984	0.905	1	0.984	0.905	1	CLONAL	2	FALSE	2	0.495079390639885	4		226	442	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434426	110434426	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	258	660	0	ENST00000375856.3:c.3975C>G	p.Phe1325Leu	p.F1325L	ENST00000375856	NM_003749.2	1325	ttC/ttG	1/2	0.402800876359191	3	FACETS	0.921	0.867	0.976	0.614	0.578	0.651	CLONAL	2	FALSE	0	0.495079390639885	3		660	706	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792651	33792651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	68	69	0	ENST00000498907.2:c.670C>T	p.His224Tyr	p.H224Y	ENST00000498907	NM_004364.3	224	Cac/Tac	1/1	0.169255579377471	6	FACETS	0.84	0.742	0.942	0.84	0.742	0.942	INDETERMINATE	3	FALSE	3	0.495079390639885	6		69	217	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123687	46123687	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	146	228	0	ENST00000334344.6:c.68T>G	p.Leu23Arg	p.L23R	ENST00000334344	NM_152641.2	23	cTg/cGg	1/21	0.437349607946453	4	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	FALSE	2	0.495079390639885	4		228	425	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219118	94219118	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	24	351	0	ENST00000323929.3:c.286G>A	p.Asp96Asn	p.D96N	ENST00000323929	NM_005591.3	96	Gat/Aat	4/20	0.492867208320819	2	FACETS	0.413	0.324	0.513	0.206	0.162	0.257	SUBCLONAL	1	FALSE	0	0.495079390639885	2		351	235	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0034868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	106	424	0	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.264408135954362	2		424	572	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865500	57865500	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	49	395	0	ENST00000228682.2:c.2981del	p.Pro994HisfsTer26	p.P994Hfs*26	ENST00000228682	NM_005269.2	993	Ccc/cc	12/12	1	2	FACETS	0.681	0.577	0.796	0.681	0.577	0.796	SUBCLONAL	1	TRUE	1	0.264408135954362	2		395	544	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923714	72923714	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	39	402	0	ENST00000268489.5:c.3364C>T	p.Gln1122Ter	p.Q1122*	ENST00000268489	NM_006885.3	1122	Cag/Tag	4/10	1	2	FACETS	0.552	0.457	0.659	0.552	0.457	0.659	SUBCLONAL	1	TRUE	1	0.264408135954362	2		402	534	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10259590	10259590	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	83	424	0	ENST00000340748.4:c.2642A>G	p.Lys881Arg	p.K881R	ENST00000340748		881	aAa/aGa	26/40	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.264408135954362	2		424	618	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428433	72428433	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	68	395	0	ENST00000477973.2:c.571G>T	p.Val191Phe	p.V191F	ENST00000477973	NM_012234.5	191	Gtt/Ttt	2/4	1	2	FACETS	0.942	0.821	1	0.942	0.821	1	CLONAL	1	TRUE	1	0.264408135954362	2		395	546	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629358	187629358	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	73	415	0	ENST00000441802.2:c.1624G>T	p.Asp542Tyr	p.D542Y	ENST00000441802	NM_005245.3	542	Gac/Tac	2/27	0.264408135954362	1	FACETS	0.835	0.731	0.947	0.835	0.731	0.947	CLONAL	1	TRUE	0	0.264408135954362	1		415	574	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638804	176638804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1021852466	NA	P-0034868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	82	353	0	ENST00000439151.2:c.3404C>T	p.Pro1135Leu	p.P1135L	ENST00000439151	NM_022455.4	1135	cCa/cTa	5/23	0.264408135954362	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.264408135954362	1		353	504	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527741	157527742	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0034868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	39	319	0	ENST00000346085.5:c.5471dup	p.Asp1825Ter	p.D1825*	ENST00000346085	NM_020732.3	1822	-/G	20/20	1	2	FACETS	0.686	0.569	0.817	0.686	0.569	0.817	SUBCLONAL	1	TRUE	1	0.264408135954362	2		319	430	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971053	21971054	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0034868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	98	302	0	ENST00000304494.5:c.303_304dup	p.Ala102GlyfsTer45	p.A102Gfs*45	ENST00000304494	NM_000077.4	102	gcg/gGGcg	2/3	0.196677431329709	2	FACETS	0.866	0.777	0.959	0.866	0.777	0.959	CLONAL	2	TRUE	0	0.264408135954362	2		302	428	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030518	47030518	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	16	199	0	ENST00000377604.3:c.293G>A	p.Arg98Gln	p.R98Q	ENST00000377604	NM_001204468.1	98	cGa/cAa	4/24	1	1	FACETS	0.331	0.244	0.436	0.331	0.244	0.436	SUBCLONAL	1	TRUE	0	0.264408135954362	1		199	317	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	118	529	3	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.412	0.371	0.455	0.412	0.371	0.455	SUBCLONAL	1	TRUE	1	0.667497706789241	2		532	859	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	153	341	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.91	0.838	0.983	0.91	0.838	0.983	CLONAL	1	TRUE	1	0.667497706789241	2		341	504	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	406	510	1	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	1	2	FACETS	1	0.989	1	1	0.997	1	CLONAL	2	TRUE	1	0.667497706789241	2		511	577	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	228	433	0	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.667497706789241	2		433	653	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033753	48033753	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1553333707	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	92	233	0	ENST00000234420.5:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000234420	NM_000179.2	1322	Gaa/Taa	9/10	1	2	FACETS	0.91	0.818	1	0.91	0.818	1	CLONAL	1	TRUE	1	0.667497706789241	2		233	303	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187560905	187560905	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1302189943	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	159	332	0	ENST00000441802.2:c.3613C>T	p.Arg1205Ter	p.R1205*	ENST00000441802	NM_005245.3	1205	Cga/Tga	4/27	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.667497706789241	2		332	442	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416952	416953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs771545848	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	175	386	4	ENST00000399788.2:c.3597dup	p.Gly1200ArgfsTer7	p.G1200Rfs*7	ENST00000399788	NM_001042603.1	1199	-/A	23/28	1	2	FACETS	0.89	0.824	0.958	0.89	0.824	0.958	CLONAL	1	TRUE	1	0.667497706789241	2		390	589	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	54	196	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.722	0.624	0.827	0.722	0.624	0.827	SUBCLONAL	1	TRUE	1	0.667497706789241	2		196	224	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213953	2213953	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759408599	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	248	441	1	ENST00000326181.6:c.32G>A	p.Arg11His	p.R11H	ENST00000326181	NM_032271.2	11	cGc/cAc	2/21	1	2	FACETS	0.978	0.918	1	0.978	0.918	1	CLONAL	1	TRUE	1	0.667497706789241	2		442	760	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	105	923	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.331	0.296	0.369	0.331	0.296	0.369	SUBCLONAL	1	TRUE	1	0.667497706789241	2		923	950	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	191	406	1	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.667497706789241	2		407	550	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17349218	17349218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747518441	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	157	314	0	ENST00000375499.3:c.650G>A	p.Arg217His	p.R217H	ENST00000375499	NM_003000.2	217	cGc/cAc	7/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.667497706789241	2		314	429	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687472	37687472	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	36	202	0	ENST00000447079.4:c.4382del	p.Gly1461AlafsTer38	p.G1461Afs*38	ENST00000447079	NM_015083.1	1459	tGg/tg	14/14	1	2	FACETS	0.355	0.292	0.424	0.355	0.292	0.424	SUBCLONAL	1	TRUE	1	0.667497706789241	2		202	304	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149973	202149973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1272714323	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	286	437	1	ENST00000358485.4:c.1414C>T	p.Arg472Ter	p.R472*	ENST00000358485	NM_001080125.1	472	Cga/Tga	8/9	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.667497706789241	2		438	730	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005368	42005368	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	30	358	0	ENST00000219905.7:c.3104C>A	p.Pro1035His	p.P1035H	ENST00000219905	NM_001164273.1	1035	cCt/cAt	9/24	1	2	FACETS	0.179	0.144	0.22	0.179	0.144	0.22	SUBCLONAL	1	TRUE	1	0.667497706789241	2		358	501	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098936	47098936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	268	507	0	ENST00000409792.3:c.6338G>A	p.Arg2113His	p.R2113H	ENST00000409792	NM_014159.6	2113	cGc/cAc	15/21	1	2	FACETS	0.982	0.924	1	0.982	0.924	1	CLONAL	1	TRUE	1	0.667497706789241	2		507	818	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	68	175	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.667497706789241	2		175	173	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099424	157099426	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	rs754060642	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	69	212	0	ENST00000346085.5:c.363_365del	p.Gln131del	p.Q131del	ENST00000346085	NM_020732.3	121	CAA/-	1/20	1	2	FACETS	0.644	0.565	0.728	0.644	0.565	0.728	SUBCLONAL	1	TRUE	1	0.667497706789241	2		212	321	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40743956	40743956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773553776	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	212	419	0	ENST00000392038.2:c.751C>T	p.Arg251Trp	p.R251W	ENST00000392038	NM_001626.4	251	Cgg/Tgg	9/14	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.667497706789241	2		419	590	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4090688	4090688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1003521922	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	110	594	0	ENST00000262948.5:c.1111C>T	p.Arg371Trp	p.R371W	ENST00000262948	NM_030662.3	371	Cgg/Tgg	11/11	1	2	FACETS	0.343	0.307	0.38	0.343	0.307	0.38	SUBCLONAL	1	TRUE	1	0.667497706789241	2		594	962	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004217	150004217	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1431439182	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	46	251	0	ENST00000253339.5:c.2008C>T	p.Arg670Trp	p.R670W	ENST00000253339		670	Cgg/Tgg	3/7	1	2	FACETS	0.387	0.327	0.453	0.387	0.327	0.453	SUBCLONAL	1	TRUE	1	0.667497706789241	2		251	356	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096498	178096498	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs375627384	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	135	276	0	ENST00000397062.3:c.833A>G	p.Asn278Ser	p.N278S	ENST00000397062	NM_006164.4	278	aAc/aGc	5/5	1	2	FACETS	0.991	0.91	1	0.991	0.91	1	CLONAL	1	TRUE	1	0.667497706789241	2		276	408	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670048	86670048	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	121	303	0	ENST00000274376.6:c.1845T>G	p.Tyr615Ter	p.Y615*	ENST00000274376	NM_002890.2	615	taT/taG	14/25	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.667497706789241	2		303	333	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133701	2133701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45517319	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	94	475	1	ENST00000219476.3:c.3889G>A	p.Ala1297Thr	p.A1297T	ENST00000219476	NM_000548.3	1297	Gcc/Acc	33/42	1	2	FACETS	0.373	0.331	0.417	0.373	0.331	0.417	SUBCLONAL	1	TRUE	1	0.667497706789241	2		476	756	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238995	5238995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	56	511	0	ENST00000357368.4:c.1784C>T	p.Ala595Val	p.A595V	ENST00000357368	NM_002850.3	595	gCg/gTg	13/38	1	2	FACETS	0.225	0.192	0.261	0.225	0.192	0.261	SUBCLONAL	1	TRUE	1	0.667497706789241	2		511	747	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386335	31386335	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	302	511	0	ENST00000328111.2:c.1560G>T	p.Glu520Asp	p.E520D	ENST00000328111	NM_006892.3	520	gaG/gaT	15/23	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.667497706789241	2		511	846	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206711	36206711	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757570529	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	229	595	0	ENST00000300305.3:c.801G>A	p.Met267Ile	p.M267I	ENST00000300305		267	atG/atA	6/8	1	2	FACETS	0.871	0.814	0.929	0.871	0.814	0.929	CLONAL	1	TRUE	1	0.667497706789241	2		595	788	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127688	2127688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779832805	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	209	454	0	ENST00000219476.3:c.2927G>A	p.Arg976Gln	p.R976Q	ENST00000219476	NM_000548.3	976	cGg/cAg	26/42	1	2	FACETS	0.978	0.913	1	0.978	0.913	1	CLONAL	1	TRUE	1	0.667497706789241	2		454	640	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046342	180046342	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768185411	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	300	520	2	ENST00000261937.6:c.2672G>A	p.Arg891His	p.R891H	ENST00000261937	NM_182925.4	891	cGc/cAc	19/30	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.667497706789241	2		522	761	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798836	42798836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	108	596	0	ENST00000575354.2:c.4408C>T	p.Arg1470Cys	p.R1470C	ENST00000575354	NM_015125.3	1470	Cgc/Tgc	19/20	1	2	FACETS	0.356	0.319	0.396	0.356	0.319	0.396	SUBCLONAL	1	TRUE	1	0.667497706789241	2		596	908	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726525	46726525	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28363218	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	179	343	0	ENST00000371975.4:c.604C>T	p.Arg202Cys	p.R202C	ENST00000371975	NM_003579.3	202	Cgc/Tgc	7/18	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.667497706789241	2		343	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138729528	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	250	512	0	ENST00000269305.4:c.523C>T	p.Arg175Cys	p.R175C	ENST00000269305	NM_001126112.2	175	Cgc/Tgc	5/11	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.667497706789241	2		512	747	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527697	157527697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745372243	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	219	432	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	0.667497706789241	2		432	656	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755666	39755666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	263	496	0	ENST00000288319.7:c.1099C>T	p.Arg367Cys	p.R367C	ENST00000288319	NM_182918.3	367	Cgc/Tgc	10/10	1	2	FACETS	0.951	0.894	1	0.951	0.894	1	CLONAL	1	TRUE	1	0.667497706789241	2		496	829	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909491	50909491	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139557851	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	60	644	1	ENST00000440232.2:c.1295G>A	p.Arg432Gln	p.R432Q	ENST00000440232	NM_002691.3	432	cGg/cAg	11/27	1	2	FACETS	0.179	0.153	0.207	0.179	0.153	0.207	SUBCLONAL	1	TRUE	1	0.667497706789241	2		645	1006	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780711	9780711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs545136223	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	251	551	1	ENST00000377346.4:c.1513G>A	p.Glu505Lys	p.E505K	ENST00000377346	NM_005026.3	505	Gag/Aag	12/24	1	2	FACETS	0.967	0.908	1	0.967	0.908	1	CLONAL	1	TRUE	1	0.667497706789241	2		552	778	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972893	32972893	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	94	161	1	ENST00000380152.3:c.10248del	p.Lys3416AsnfsTer11	p.K3416Nfs*11	ENST00000380152		3415	Aaa/aa	27/27	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.667497706789241	2		162	215	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411489	63411489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200798538	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	117	695	0	ENST00000330258.3:c.1678C>T	p.Arg560Trp	p.R560W	ENST00000330258	NM_152424.3	560	Cgg/Tgg	2/2	1	2	FACETS	0.399	0.359	0.441	0.399	0.359	0.441	SUBCLONAL	1	TRUE	1	0.667497706789241	2		695	879	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256696	46256696	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768977330	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	203	377	0	ENST00000371998.3:c.752G>A	p.Arg251His	p.R251H	ENST00000371998		251	cGc/cAc	8/23	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.667497706789241	2		377	560	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518250	8518250	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	64	276	0	ENST00000356435.5:c.1141G>A	p.Ala381Thr	p.A381T	ENST00000356435		381	Gct/Act	10/35	1	2	FACETS	0.444	0.385	0.507	0.444	0.385	0.507	SUBCLONAL	1	TRUE	1	0.667497706789241	2		276	432	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612170	189612170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793283	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	36	442	0	ENST00000264731.3:c.1922C>T	p.Ala641Val	p.A641V	ENST00000264731	NM_003722.4	641	gCt/gTt	14/14	1	2	FACETS	0.173	0.141	0.208	0.173	0.141	0.208	SUBCLONAL	1	TRUE	1	0.667497706789241	2		442	624	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254166	133254166	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs371882716	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	27	340	0	ENST00000320574.5:c.718G>A	p.Val240Met	p.V240M	ENST00000320574	NM_006231.2	240	Gtg/Atg	7/49	1	2	FACETS	0.163	0.129	0.202	0.163	0.129	0.202	SUBCLONAL	1	TRUE	1	0.667497706789241	2		340	497	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15967421	15967421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766158799	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	246	378	0	ENST00000268712.3:c.5182C>T	p.Arg1728Trp	p.R1728W	ENST00000268712	NM_006311.3	1728	Cgg/Tgg	35/46	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.667497706789241	2		378	716	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97873817	97873817	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	206	447	2	ENST00000289081.3:c.1257del	p.Thr420ArgfsTer27	p.T420Rfs*27	ENST00000289081	NM_000136.2	419	ccC/cc	13/15	1	2	FACETS	0.867	0.807	0.928	0.867	0.807	0.928	CLONAL	1	TRUE	1	0.667497706789241	2		449	712	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552837	106552837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1399614609	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	38	517	0	ENST00000369096.4:c.802C>T	p.Arg268Cys	p.R268C	ENST00000369096	NM_001198.3	268	Cgt/Tgt	5/7	1	2	FACETS	0.151	0.124	0.181	0.151	0.124	0.181	SUBCLONAL	1	TRUE	1	0.667497706789241	2		517	754	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226047	133226047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753426630	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	290	526	0	ENST00000320574.5:c.3850C>T	p.Arg1284Trp	p.R1284W	ENST00000320574	NM_006231.2	1284	Cgg/Tgg	31/49	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.667497706789241	2		526	799	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748503	43748503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs769957944	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	53	268	0	ENST00000523873.1:c.457C>T	p.Arg153Ter	p.R153*	ENST00000523873		153	Cga/Tga	6/8	1	2	FACETS	0.376	0.321	0.436	0.376	0.321	0.436	SUBCLONAL	1	TRUE	1	0.667497706789241	2		268	422	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727513	88727513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374069724	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	38	355	0	ENST00000360948.2:c.266G>A	p.Arg89His	p.R89H	ENST00000360948	NM_001012338.2	89	cGc/cAc	3/19	1	2	FACETS	0.171	0.141	0.205	0.171	0.141	0.205	SUBCLONAL	1	TRUE	1	0.667497706789241	2		355	666	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548269	41548269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	21	207	0	ENST00000263253.7:c.3061del	p.Thr1021LeufsTer3	p.T1021Lfs*3	ENST00000263253	NM_001429.3	1019	ttA/tt	16/31	1	2	FACETS	0.192	0.147	0.244	0.192	0.147	0.244	SUBCLONAL	1	TRUE	1	0.667497706789241	2		207	328	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655272	45655272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764295138	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	346	586	0	ENST00000407780.3:c.580C>T	p.Arg194Trp	p.R194W	ENST00000407780	NM_001283052.1	194	Cgg/Tgg	4/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.667497706789241	2		586	988	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934365	81934365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200919414	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	37	414	0	ENST00000359376.3:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000359376	NM_002661.3	448	Cgg/Tgg	14/33	1	2	FACETS	0.18	0.148	0.217	0.18	0.148	0.217	SUBCLONAL	1	TRUE	1	0.667497706789241	2		414	615	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015725	112015725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376486970	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	80	394	0	ENST00000368678.4:c.1117G>A	p.Ala373Thr	p.A373T	ENST00000368678		373	Gca/Aca	11/13	1	2	FACETS	0.382	0.336	0.431	0.382	0.336	0.431	SUBCLONAL	1	TRUE	1	0.667497706789241	2		394	628	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683175	88683175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1418504897	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	21	275	0	ENST00000372037.3:c.1385C>T	p.Pro462Leu	p.P462L	ENST00000372037	NM_004329.2	462	cCg/cTg	12/13	1	2	FACETS	0.15	0.115	0.191	0.15	0.115	0.191	SUBCLONAL	1	TRUE	1	0.667497706789241	2		275	420	SUCCESS
APC	324	MSKCC	GRCh37	5	112176011	112176011	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	20	217	0	ENST00000257430.4:c.4720A>G	p.Ile1574Val	p.I1574V	ENST00000257430	NM_000038.5	1574	Ata/Gta	16/16	1	2	FACETS	0.21	0.161	0.268	0.21	0.161	0.268	SUBCLONAL	1	TRUE	1	0.667497706789241	2		217	285	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27213538	27213538	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	202	385	0	ENST00000380036.4:c.2938del	p.Ile980Ter	p.I980*	ENST00000380036	NM_000459.3	978	gcA/gc	18/23	1	2	FACETS	0.979	0.913	1	0.979	0.913	1	CLONAL	1	TRUE	1	0.667497706789241	2		385	618	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573978	41573978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	88	428	0	ENST00000263253.7:c.6263G>A	p.Arg2088Gln	p.R2088Q	ENST00000263253	NM_001429.3	2088	cGg/cAg	31/31	1	2	FACETS	0.365	0.323	0.41	0.365	0.323	0.41	SUBCLONAL	1	TRUE	1	0.667497706789241	2		428	723	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880988	37880988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772054394	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	67	554	0	ENST00000269571.5:c.2317G>A	p.Val773Met	p.V773M	ENST00000269571		773	Gtg/Atg	20/27	1	2	FACETS	0.235	0.204	0.27	0.235	0.204	0.27	SUBCLONAL	1	TRUE	1	0.667497706789241	2		554	853	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843515	156843515	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368769883	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	286	568	1	ENST00000524377.1:c.941G>A	p.Arg314His	p.R314H	ENST00000524377	NM_002529.3	314	cGc/cAc	8/17	0.642947367549425	3	FACETS	1	0.966	1	0.519	0.488	0.551	CLONAL	1	TRUE	1	0.667497706789241	3		569	1101	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158116	27158116	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1302331916	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	178	323	0	ENST00000380036.4:c.340C>T	p.Arg114Ter	p.R114*	ENST00000380036	NM_000459.3	114	Cga/Tga	2/23	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.667497706789241	2		323	512	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998128	169998128	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs753143066	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	48	537	2	ENST00000295797.4:c.826del	p.Thr276GlnfsTer7	p.T276Qfs*7	ENST00000295797	NM_002740.5	273	ttA/tt	9/18	1	2	FACETS	0.171	0.144	0.202	0.171	0.144	0.202	SUBCLONAL	1	TRUE	1	0.667497706789241	2		539	839	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941264	71941264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772985547	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	257	569	0	ENST00000298229.2:c.1039C>T	p.Arg347Trp	p.R347W	ENST00000298229	NM_001567.3	347	Cgg/Tgg	9/28	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.667497706789241	2		569	737	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107227	27107227	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	207	353	1	ENST00000324856.7:c.6842del	p.Leu2281Ter	p.L2281*	ENST00000324856	NM_006015.4	2280	Ttt/tt	20/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.667497706789241	2		354	589	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541588	29541588	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1555612289	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	80	192	0	ENST00000356175.3:c.1514del	p.Lys505SerfsTer21	p.K505Sfs*21	ENST00000356175	NM_000267.3	504	ccA/cc	13/57	1	2	FACETS	0.963	0.86	1	0.963	0.86	1	CLONAL	1	TRUE	1	0.667497706789241	2		192	249	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152357809	152357809	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	167	327	0	ENST00000359321.1:c.98C>A	p.Ala33Asp	p.A33D	ENST00000359321	NM_005431.1	33	gCt/gAt	2/3	1	2	FACETS	0.878	0.811	0.947	0.878	0.811	0.947	CLONAL	1	TRUE	1	0.667497706789241	2		327	570	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137075	64137075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	316	500	1	ENST00000334205.4:c.1586G>A	p.Arg529His	p.R529H	ENST00000334205	NM_003942.2	529	cGc/cAc	13/17	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.667497706789241	2		501	803	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671770	67671770	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1192224462	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	109	381	1	ENST00000264010.4:c.2179C>T	p.Arg727Trp	p.R727W	ENST00000264010	NM_006565.3	727	Cgg/Tgg	12/12	1	2	FACETS	0.456	0.41	0.505	0.456	0.41	0.505	SUBCLONAL	1	TRUE	1	0.667497706789241	2		382	716	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996755	100996757	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	139	325	0	ENST00000325455.5:c.1770_1772del	p.Phe591del	p.F591del	ENST00000325455	NM_001202474.3	590	ttCTTt/ttt	2/8	1	2	FACETS	0.992	0.911	1	0.992	0.911	1	CLONAL	1	TRUE	1	0.667497706789241	2		325	420	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279790	46279790	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776910504	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	232	377	0	ENST00000371998.3:c.3716G>A	p.Arg1239Gln	p.R1239Q	ENST00000371998		1239	cGa/cAa	20/23	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.667497706789241	2		377	618	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46727055	46727055	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	204	425	0	ENST00000371975.4:c.889G>A	p.Glu297Lys	p.E297K	ENST00000371975	NM_003579.3	297	Gag/Aag	8/18	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.667497706789241	2		425	554	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101910	11101910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550815250	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	346	511	1	ENST00000358026.2:c.1330C>T	p.Arg444Cys	p.R444C	ENST00000358026	NM_001128849.1	444	Cgc/Tgc	8/36	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.667497706789241	2		512	937	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707758	176707758	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064796690	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	70	285	0	ENST00000439151.2:c.5815C>T	p.Arg1939Cys	p.R1939C	ENST00000439151	NM_022455.4	1939	Cgc/Tgc	18/23	1	2	FACETS	0.387	0.338	0.44	0.387	0.338	0.44	SUBCLONAL	1	TRUE	1	0.667497706789241	2		285	542	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339110	65339111	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	230	454	2	ENST00000342505.4:c.425dup	p.Ile143AspfsTer9	p.I143Dfs*9	ENST00000342505	NM_002227.2	142	aag/aaAg	5/25	1	2	FACETS	0.999	0.936	1	0.999	0.936	1	CLONAL	1	TRUE	1	0.667497706789241	2		456	690	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921618	39921618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201959477	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	203	426	0	ENST00000378444.4:c.4202C>T	p.Pro1401Leu	p.P1401L	ENST00000378444	NM_001123385.1	1401	cCg/cTg	10/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.667497706789241	2		426	568	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211899	36211899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	387	750	5	ENST00000222270.7:c.1656del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	550	gaC/ga	3/37	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.667497706789241	2		755	1149	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68878170	68878170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138522390	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	132	263	0	ENST00000487270.1:c.883G>A	p.Ala295Thr	p.A295T	ENST00000487270	NM_133509.3	295	Gca/Aca	9/11	1	2	FACETS	0.933	0.854	1	0.933	0.854	1	CLONAL	1	TRUE	1	0.667497706789241	2		263	424	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433722	49433722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572359740	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	92	683	0	ENST00000301067.7:c.7831C>T	p.Arg2611Cys	p.R2611C	ENST00000301067	NM_003482.3	2611	Cgc/Tgc	31/54	1	2	FACETS	0.278	0.247	0.313	0.278	0.247	0.313	SUBCLONAL	1	TRUE	1	0.667497706789241	2		683	990	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879364	151879364	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765915364	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	190	369	0	ENST00000262189.6:c.5581C>T	p.Arg1861Trp	p.R1861W	ENST00000262189	NM_170606.2	1861	Cgg/Tgg	36/59	1	2	FACETS	0.967	0.899	1	0.967	0.899	1	CLONAL	1	TRUE	1	0.667497706789241	2		369	589	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212857	27212857	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs906836493	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	238	529	1	ENST00000380036.4:c.2839G>A	p.Asp947Asn	p.D947N	ENST00000380036	NM_000459.3	947	Gac/Aac	17/23	1	2	FACETS	0.932	0.873	0.992	0.932	0.873	0.992	CLONAL	1	TRUE	1	0.667497706789241	2		530	765	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431665	6431665	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	287	547	0	ENST00000356142.4:c.218C>T	p.Pro73Leu	p.P73L	ENST00000356142	NM_018890.3	73	cCg/cTg	3/7	1	2	FACETS	0.996	0.94	1	0.996	0.94	1	CLONAL	1	TRUE	1	0.667497706789241	2		547	863	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641468	18641468	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372430045	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	113	259	0	ENST00000266497.5:c.2467G>A	p.Ala823Thr	p.A823T	ENST00000266497		823	Gcc/Acc	17/31	1	2	FACETS	0.891	0.809	0.976	0.891	0.809	0.976	CLONAL	1	TRUE	1	0.667497706789241	2		259	380	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306549	163306549	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753469318	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	157	343	0	ENST00000271452.3:c.346C>T	p.Arg116Trp	p.R116W	ENST00000271452	NM_145697.2	116	Cgg/Tgg	6/14	0.642947367549425	3	FACETS	1	0.961	1	0.536	0.493	0.581	CLONAL	1	TRUE	1	0.667497706789241	3		343	585	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520202	176520202	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763979974	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	349	694	1	ENST00000292408.4:c.1121C>T	p.Ala374Val	p.A374V	ENST00000292408	NM_213647.1	374	gCg/gTg	9/18	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.667497706789241	2		695	997	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578415	7578415	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1131691021	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	266	529	0	ENST00000269305.4:c.515T>C	p.Val172Ala	p.V172A	ENST00000269305	NM_001126112.2	172	gTt/gCt	5/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.667497706789241	2		529	778	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642782	3642782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753926402	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	112	539	0	ENST00000294008.3:c.2245C>T	p.Arg749Cys	p.R749C	ENST00000294008	NM_032444.2	749	Cgc/Tgc	11/15	1	2	FACETS	0.38	0.341	0.421	0.38	0.341	0.421	SUBCLONAL	1	TRUE	1	0.667497706789241	2		539	883	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057879	27057879	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	305	651	0	ENST00000324856.7:c.1587G>T	p.Gln529His	p.Q529H	ENST00000324856	NM_006015.4	529	caG/caT	3/20	1	2	FACETS	0.92	0.869	0.973	0.92	0.869	0.973	CLONAL	1	TRUE	1	0.667497706789241	2		651	993	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806600	1806600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529493162	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	280	575	0	ENST00000260795.2:c.1316G>A	p.Arg439His	p.R439H	ENST00000260795		439	cGc/cAc	9/17	1	2	FACETS	0.934	0.88	0.99	0.934	0.88	0.99	CLONAL	1	TRUE	1	0.667497706789241	2		575	898	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64290050	64290050	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs546134768	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	75	435	1	ENST00000370651.3:c.493G>A	p.Gly165Ser	p.G165S	ENST00000370651	NM_003463.4	165	Ggt/Agt	6/6	1	2	FACETS	0.369	0.323	0.418	0.369	0.323	0.418	SUBCLONAL	1	TRUE	1	0.667497706789241	2		436	609	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99169415	99169415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs909251709	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	135	286	0	ENST00000074304.5:c.1345G>A	p.Ala449Thr	p.A449T	ENST00000074304	NM_001134224.1	449	Gcc/Acc	15/26	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.667497706789241	2		286	381	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298137	15298137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200317373	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	321	596	1	ENST00000263388.2:c.1619C>T	p.Thr540Met	p.T540M	ENST00000263388	NM_000435.2	540	aCg/aTg	11/33	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.667497706789241	2		597	925	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948755	71948755	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1565399032	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	263	550	1	ENST00000298229.2:c.3470del	p.Gly1157AspfsTer45	p.G1157Dfs*45	ENST00000298229	NM_001567.3	1156	cGg/cg	26/28	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.667497706789241	2		551	782	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225997	53225997	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781878921	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	300	644	1	ENST00000375401.3:c.2852G>A	p.Arg951Gln	p.R951Q	ENST00000375401	NM_004187.3	951	cGa/cAa	19/26	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.667497706789241	2		645	882	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333089	70333089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	270	548	1	ENST00000373644.4:c.994G>A	p.Ala332Thr	p.A332T	ENST00000373644	NM_030625.2	332	Gca/Aca	2/12	1	2	FACETS	0.991	0.933	1	0.991	0.933	1	CLONAL	1	TRUE	1	0.667497706789241	2		549	816	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176490	123176490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	86	198	0	ENST00000218089.9:c.457G>A	p.Asp153Asn	p.D153N	ENST00000218089	NM_001042749.1	153	Gat/Aat	7/35	1	2	FACETS	0.856	0.766	0.95	0.856	0.766	0.95	CLONAL	1	TRUE	1	0.667497706789241	2		198	301	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915579	131915579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28903087	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	57	168	0	ENST00000265335.6:c.577C>T	p.Arg193Trp	p.R193W	ENST00000265335		193	Cgg/Tgg	5/25	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.667497706789241	2		168	165	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779704	3779704	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567263529	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	283	529	0	ENST00000262367.5:c.5344G>A	p.Ala1782Thr	p.A1782T	ENST00000262367	NM_004380.2	1782	Gcg/Acg	31/31	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.667497706789241	2		529	820	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724611	162724611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149507401	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	175	334	0	ENST00000367921.3:c.383G>A	p.Arg128His	p.R128H	ENST00000367921	NM_006182.2	128	cGc/cAc	5/18	0.642947367549425	3	FACETS	1	0.945	1	0.513	0.474	0.554	CLONAL	1	TRUE	1	0.667497706789241	3		334	681	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95596505	95596505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745802492	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	24	171	0	ENST00000393063.1:c.463G>A	p.Ala155Thr	p.A155T	ENST00000393063	NM_030621.3	155	Gcc/Acc	6/28	1	2	FACETS	0.371	0.292	0.46	0.371	0.292	0.46	SUBCLONAL	1	TRUE	1	0.667497706789241	2		171	194	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555911	226555911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	236	341	0	ENST00000366794.5:c.2266G>A	p.Asp756Asn	p.D756N	ENST00000366794	NM_001618.3	756	Gac/Aac	16/23	0.642947367549425	3	FACETS	1	0.973	1	0.537	0.502	0.573	CLONAL	1	TRUE	1	0.667497706789241	3		341	878	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481405	140481405	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397507473	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	185	304	0	ENST00000288602.6:c.1403T>C	p.Phe468Ser	p.F468S	ENST00000288602	NM_004333.4	468	tTt/tCt	11/18	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.667497706789241	2		304	500	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073784	8073784	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	140	285	0	ENST00000377482.5:c.875G>T	p.Arg292Ile	p.R292I	ENST00000377482	NM_018948.3	292	aGa/aTa	4/4	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.667497706789241	2		285	397	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073845	8073845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	45	263	0	ENST00000377482.5:c.814G>A	p.Ala272Thr	p.A272T	ENST00000377482	NM_018948.3	272	Gct/Act	4/4	1	2	FACETS	0.333	0.28	0.391	0.333	0.28	0.391	SUBCLONAL	1	TRUE	1	0.667497706789241	2		263	405	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11276280	11276280	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	48	287	0	ENST00000361445.4:c.3042G>T	p.Gln1014His	p.Q1014H	ENST00000361445	NM_004958.3	1014	caG/caT	20/58	1	2	FACETS	0.394	0.334	0.46	0.394	0.334	0.46	SUBCLONAL	1	TRUE	1	0.667497706789241	2		287	365	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298605	11298605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	228	460	0	ENST00000361445.4:c.1856G>A	p.Arg619His	p.R619H	ENST00000361445	NM_004958.3	619	cGc/cAc	12/58	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.667497706789241	2		460	673	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202960	16202960	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	186	372	0	ENST00000375759.3:c.668A>G	p.Asp223Gly	p.D223G	ENST00000375759	NM_015001.2	223	gAt/gGt	3/15	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.667497706789241	2		372	534	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057951	27057951	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	298	515	1	ENST00000324856.7:c.1659G>T	p.Gln553His	p.Q553H	ENST00000324856	NM_006015.4	553	caG/caT	3/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.667497706789241	2		516	810	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099388	27099388	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	228	375	0	ENST00000324856.7:c.3625C>A	p.Pro1209Thr	p.P1209T	ENST00000324856	NM_006015.4	1209	Cct/Act	14/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.667497706789241	2		375	660	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101326	27101326	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	261	451	0	ENST00000324856.7:c.4608T>G	p.Asp1536Glu	p.D1536E	ENST00000324856	NM_006015.4	1536	gaT/gaG	18/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.667497706789241	2		451	700	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101513	27101513	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	304	539	0	ENST00000324856.7:c.4795A>G	p.Thr1599Ala	p.T1599A	ENST00000324856	NM_006015.4	1599	Acc/Gcc	18/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.667497706789241	2		539	859	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805768	43805768	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	83	504	0	ENST00000372470.3:c.824C>A	p.Pro275His	p.P275H	ENST00000372470	NM_005373.2	275	cCt/cAt	5/12	1	2	FACETS	0.338	0.298	0.381	0.338	0.298	0.381	SUBCLONAL	1	TRUE	1	0.667497706789241	2		504	736	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332725	65332725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	168	318	0	ENST00000342505.4:c.814G>A	p.Ala272Thr	p.A272T	ENST00000342505	NM_002227.2	272	Gct/Act	7/25	1	2	FACETS	0.979	0.907	1	0.979	0.907	1	CLONAL	1	TRUE	1	0.667497706789241	2		318	514	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332823	65332823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	66	308	1	ENST00000342505.4:c.716G>A	p.Arg239Gln	p.R239Q	ENST00000342505	NM_002227.2	239	cGg/cAg	7/25	1	2	FACETS	0.456	0.397	0.519	0.456	0.397	0.519	SUBCLONAL	1	TRUE	1	0.667497706789241	2		309	434	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429363	78429363	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	214	355	0	ENST00000370768.2:c.1079G>T	p.Gly360Val	p.G360V	ENST00000370768	NM_003902.3	360	gGa/gTa	13/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.667497706789241	2		355	592	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261316	115261316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	27	336	0	ENST00000438362.2:c.2405G>A	p.Arg802His	p.R802H	ENST00000438362	NM_001242891.1	802	cGc/cAc	19/20	1	2	FACETS	0.164	0.13	0.203	0.164	0.13	0.203	SUBCLONAL	1	TRUE	1	0.667497706789241	2		336	494	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120463021	120463021	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	21	307	0	ENST00000256646.2:c.5311-1G>T		p.X1771_splice	ENST00000256646	NM_024408.3	1771			1	2	FACETS	0.162	0.124	0.206	0.162	0.124	0.206	SUBCLONAL	1	TRUE	1	0.667497706789241	2		307	388	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731140	162731140	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752360996	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	199	377	0	ENST00000367921.3:c.995G>A	p.Arg332Gln	p.R332Q	ENST00000367921	NM_006182.2	332	cGg/cAg	9/18	0.642947367549425	3	FACETS	1	0.942	1	0.508	0.471	0.545	CLONAL	1	TRUE	1	0.667497706789241	3		377	783	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054999	176054999	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	169	405	1	ENST00000367669.3:c.1054A>G	p.Thr352Ala	p.T352A	ENST00000367669	NM_022457.5	352	Acg/Gcg	10/20	0.642947367549425	3	FACETS	0.941	0.867	1	0.47	0.433	0.509	CLONAL	1	TRUE	1	0.667497706789241	3		406	718	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983073	201983073	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs775686420	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	269	482	0	ENST00000359651.3:c.922T>C	p.Ser308Pro	p.S308P	ENST00000359651		308	Tcc/Ccc	7/8	0.642947367549425	3	FACETS	1	0.949	1	0.506	0.475	0.538	CLONAL	1	TRUE	1	0.667497706789241	3		482	1062	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653804	206653804	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	224	462	1	ENST00000367120.3:c.1355C>T	p.Ala452Val	p.A452V	ENST00000367120	NM_014002.3	452	gCc/gTc	13/22	0.642947367549425	3	FACETS	0.965	0.899	1	0.482	0.449	0.516	CLONAL	1	TRUE	1	0.667497706789241	3		463	928	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88672001	88672001	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	231	488	0	ENST00000372037.3:c.535T>C	p.Tyr179His	p.Y179H	ENST00000372037	NM_004329.2	179	Tat/Cat	8/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.667497706789241	2		488	627	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624249	89624294	+	frameshift_variant	Frame_Shift_Del	DEL	TCGTTAGCAGAAACAAAAGGAGATATCAAGAGGATGGATTCGACTT	TCGTTAGCAGAAACAAAAGGAGATATCAAGAGGATGGATTCGACTT	-	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	97	172	0	ENST00000371953.3:c.23_68del	p.Ile8LysfsTer3	p.I8Kfs*3	ENST00000371953	NM_000314.4	8	aTCGTTAGCAGAAACAAAAGGAGATATCAAGAGGATGGATTCGACTTa/aa	1/9	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.667497706789241	2		172	267	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154369	2154369	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	318	682	0	ENST00000434045.2:c.559C>T	p.Pro187Ser	p.P187S	ENST00000434045	NM_001127598.1	187	Cct/Tct	5/5	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.667497706789241	2		682	908	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196997	67196997	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	45	274	0	ENST00000312629.5:c.241-1G>T		p.X81_splice	ENST00000312629	NM_003952.2	81			1	2	FACETS	0.337	0.284	0.396	0.337	0.284	0.396	SUBCLONAL	1	TRUE	1	0.667497706789241	2		274	400	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941304	71941304	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372182741	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	78	487	0	ENST00000298229.2:c.1079C>T	p.Thr360Met	p.T360M	ENST00000298229	NM_001567.3	360	aCg/aTg	9/28	1	2	FACETS	0.357	0.313	0.404	0.357	0.313	0.404	SUBCLONAL	1	TRUE	1	0.667497706789241	2		487	655	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946480	71946480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	256	445	0	ENST00000298229.2:c.2644C>T	p.Arg882Cys	p.R882C	ENST00000298229	NM_001567.3	882	Cgt/Tgt	23/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.667497706789241	2		445	728	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155098	108155098	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	140	372	0	ENST00000278616.4:c.3894del	p.Phe1298LeufsTer51	p.F1298Lfs*51	ENST00000278616	NM_000051.3	1297	taT/ta	26/63	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.667497706789241	2		372	387	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375636	118375636	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	25	302	0	ENST00000534358.1:c.9029C>A	p.Pro3010His	p.P3010H	ENST00000534358	NM_005933.3	3010	cCt/cAt	27/36	1	2	FACETS	0.166	0.13	0.207	0.166	0.13	0.207	SUBCLONAL	1	TRUE	1	0.667497706789241	2		302	451	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394823	394823	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	138	327	0	ENST00000399788.2:c.4872C>A	p.Asp1624Glu	p.D1624E	ENST00000399788	NM_001042603.1	1624	gaC/gaA	28/28	1	2	FACETS	0.948	0.87	1	0.948	0.87	1	CLONAL	1	TRUE	1	0.667497706789241	2		327	436	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992167	11992167	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777976357	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	29	345	0	ENST00000396373.4:c.257C>T	p.Thr86Met	p.T86M	ENST00000396373	NM_001987.4	86	aCg/aTg	3/8	1	2	FACETS	0.174	0.139	0.214	0.174	0.139	0.214	SUBCLONAL	1	TRUE	1	0.667497706789241	2		345	499	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499658	18499658	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	176	380	0	ENST00000266497.5:c.1513T>C	p.Phe505Leu	p.F505L	ENST00000266497		505	Ttt/Ctt	10/31	1	2	FACETS	0.903	0.836	0.971	0.903	0.836	0.971	CLONAL	1	TRUE	1	0.667497706789241	2		380	584	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21626490	21626490	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	195	400	0	ENST00000421138.2:c.1442A>G	p.Asp481Gly	p.D481G	ENST00000421138		481	gAc/gGc	13/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.667497706789241	2		400	534	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230433	46230434	+	missense_variant	Missense_Mutation	DNP	CT	CT	AC	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	63	267	0	ENST00000334344.6:c.767_768delinsAC	p.Ser256Tyr	p.S256Y	ENST00000334344	NM_152641.2	256	tCT/tAC	7/21	1	2	FACETS	0.425	0.368	0.486	0.425	0.368	0.486	SUBCLONAL	1	TRUE	1	0.667497706789241	2		267	444	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480543	50480543	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147034181	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	171	343	1	ENST00000394963.4:c.413G>A	p.Arg138His	p.R138H	ENST00000394963	NM_003076.4	138	cGt/cAt	4/13	1	2	FACETS	0.993	0.92	1	0.993	0.92	1	CLONAL	1	TRUE	1	0.667497706789241	2		344	516	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478878	56478878	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	309	619	0	ENST00000267101.3:c.334G>T	p.Asp112Tyr	p.D112Y	ENST00000267101	NM_001982.3	112	Gat/Tat	3/28	1	2	FACETS	0.997	0.942	1	0.997	0.942	1	CLONAL	1	TRUE	1	0.667497706789241	2		619	929	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495609	56495609	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs745487835	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	181	406	0	ENST00000267101.3:c.3799C>T	p.Arg1267Ter	p.R1267*	ENST00000267101	NM_001982.3	1267	Cga/Tga	28/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.667497706789241	2		406	499	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69229674	69229674	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	186	390	0	ENST00000462284.1:c.750G>T	p.Gln250His	p.Q250H	ENST00000462284	NM_002392.5	250	caG/caT	9/11	1	2	FACETS	0.986	0.917	1	0.986	0.917	1	CLONAL	1	TRUE	1	0.667497706789241	2		390	565	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233088	69233088	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	38	289	0	ENST00000462284.1:c.953A>G	p.Asn318Ser	p.N318S	ENST00000462284	NM_002392.5	318	aAt/aGt	11/11	1	2	FACETS	0.309	0.255	0.368	0.309	0.255	0.368	SUBCLONAL	1	TRUE	1	0.667497706789241	2		289	369	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437173	121437173	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	145	639	0	ENST00000257555.6:c.1604G>A	p.Ser535Asn	p.S535N	ENST00000257555		535	aGc/aAc	8/10	1	2	FACETS	0.411	0.375	0.45	0.411	0.375	0.45	SUBCLONAL	1	TRUE	1	0.667497706789241	2		639	1056	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123875258	123875258	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	45	115	0	ENST00000330479.4:c.214G>T	p.Glu72Ter	p.E72*	ENST00000330479	NM_020382.3	72	Gaa/Taa	3/9	1	2	FACETS	0.95	0.815	1	0.95	0.815	1	CLONAL	1	TRUE	1	0.667497706789241	2		115	142	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252325	133252325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	165	349	0	ENST00000320574.5:c.1102G>A	p.Asp368Asn	p.D368N	ENST00000320574	NM_006231.2	368	Gac/Aac	11/49	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.667497706789241	2		349	485	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562086	21562086	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	469	788	2	ENST00000382592.4:c.1833G>T	p.Glu611Asp	p.E611D	ENST00000382592	NM_014572.2	611	gaG/gaT	4/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.667497706789241	2		790	1340	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588620	28588620	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	35	299	0	ENST00000241453.7:c.2828del	p.Leu943Ter	p.L943*	ENST00000241453	NM_004119.2	943	tTa/ta	23/24	1	2	FACETS	0.196	0.16	0.236	0.196	0.16	0.236	SUBCLONAL	1	TRUE	1	0.667497706789241	2		299	536	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623877	28623877	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	188	427	0	ENST00000241453.7:c.777A>C	p.Gln259His	p.Q259H	ENST00000241453	NM_004119.2	259	caA/caC	7/24	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.667497706789241	2		427	516	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913989	32913989	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	114	368	0	ENST00000380152.3:c.5497A>G	p.Asn1833Asp	p.N1833D	ENST00000380152		1833	Aat/Gat	11/27	1	2	FACETS	0.913	0.83	0.999	0.913	0.83	0.999	CLONAL	1	TRUE	1	0.667497706789241	2		368	374	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915043	32915043	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1216313735	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	143	390	0	ENST00000380152.3:c.6551A>G	p.Gln2184Arg	p.Q2184R	ENST00000380152		2184	cAg/cGg	11/27	1	2	FACETS	0.972	0.894	1	0.972	0.894	1	CLONAL	1	TRUE	1	0.667497706789241	2		390	441	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133865	41133865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751994432	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	46	271	0	ENST00000379561.5:c.1763G>A	p.Gly588Asp	p.G588D	ENST00000379561	NM_002015.3	588	gGc/gAc	2/3	1	2	FACETS	0.376	0.317	0.44	0.376	0.317	0.44	SUBCLONAL	1	TRUE	1	0.667497706789241	2		271	367	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528246	103528246	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	33	133	0	ENST00000355739.4:c.3554A>G	p.Lys1185Arg	p.K1185R	ENST00000355739	NM_000123.3	1185	aAa/aGa	15/15	1	2	FACETS	0.462	0.379	0.554	0.462	0.379	0.554	SUBCLONAL	1	TRUE	1	0.667497706789241	2		133	214	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436439	110436439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	53	703	0	ENST00000375856.3:c.1962G>A	p.Met654Ile	p.M654I	ENST00000375856	NM_003749.2	654	atG/atA	1/2	1	2	FACETS	0.168	0.143	0.197	0.168	0.143	0.197	SUBCLONAL	1	TRUE	1	0.667497706789241	2		703	943	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100070	30100070	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs778250867	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	263	539	1	ENST00000331968.5:c.1550A>T	p.Asn517Ile	p.N517I	ENST00000331968	NM_002742.2	517	aAc/aTc	10/18	1	2	FACETS	0.991	0.932	1	0.991	0.932	1	CLONAL	1	TRUE	1	0.667497706789241	2		540	795	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557422	95557422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1426678586	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	190	338	0	ENST00000393063.1:c.5552G>A	p.Arg1851His	p.R1851H	ENST00000393063	NM_030621.3	1851	cGt/cAt	27/28	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.667497706789241	2		338	539	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562862	95562862	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	133	285	0	ENST00000393063.1:c.4395G>T	p.Lys1465Asn	p.K1465N	ENST00000393063	NM_030621.3	1465	aaG/aaT	24/28	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.667497706789241	2		285	388	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570351	95570351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	168	300	0	ENST00000393063.1:c.3382G>A	p.Val1128Ile	p.V1128I	ENST00000393063	NM_030621.3	1128	Gtc/Atc	22/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.667497706789241	2		300	459	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643773	38643773	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	67	593	0	ENST00000299084.4:c.1243C>A	p.Pro415Thr	p.P415T	ENST00000299084	NM_152594.2	415	Cca/Aca	7/7	1	2	FACETS	0.204	0.176	0.234	0.204	0.176	0.234	SUBCLONAL	1	TRUE	1	0.667497706789241	2		593	985	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021547	42021547	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	94	399	1	ENST00000219905.7:c.3843G>T	p.Lys1281Asn	p.K1281N	ENST00000219905	NM_001164273.1	1281	aaG/aaT	11/24	1	2	FACETS	0.424	0.377	0.474	0.424	0.377	0.474	SUBCLONAL	1	TRUE	1	0.667497706789241	2		400	664	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712793	43712793	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770333392	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	48	556	0	ENST00000382044.4:c.4391G>A	p.Arg1464His	p.R1464H	ENST00000382044	NM_001141980.1	1464	cGt/cAt	21/28	1	2	FACETS	0.176	0.148	0.207	0.176	0.148	0.207	SUBCLONAL	1	TRUE	1	0.667497706789241	2		556	816	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724658	43724658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755481776	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	298	652	0	ENST00000382044.4:c.3409C>T	p.Arg1137Trp	p.R1137W	ENST00000382044	NM_001141980.1	1137	Cgg/Tgg	17/28	1	2	FACETS	0.958	0.904	1	0.958	0.904	1	CLONAL	1	TRUE	1	0.667497706789241	2		652	932	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74000686	74000686	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	267	522	0	ENST00000318443.5:c.1376C>A	p.Pro459His	p.P459H	ENST00000318443	NM_001024736.1	459	cCt/cAt	7/10	1	2	FACETS	0.993	0.934	1	0.993	0.934	1	CLONAL	1	TRUE	1	0.667497706789241	2		522	806	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799265	88799265	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	228	419	1	ENST00000360948.2:c.120G>T	p.Lys40Asn	p.K40N	ENST00000360948	NM_001012338.2	40	aaG/aaT	2/19	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.667497706789241	2		420	583	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346837	91346837	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	21	265	0	ENST00000355112.3:c.3445C>A	p.Leu1149Met	p.L1149M	ENST00000355112	NM_000057.2	1149	Ctg/Atg	18/22	1	2	FACETS	0.151	0.115	0.192	0.151	0.115	0.192	SUBCLONAL	1	TRUE	1	0.667497706789241	2		265	418	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251001	99251001	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	80	398	0	ENST00000268035.6:c.305A>G	p.Asn102Ser	p.N102S	ENST00000268035	NM_000875.3	102	aAc/aGc	2/21	1	2	FACETS	0.428	0.377	0.482	0.428	0.377	0.482	SUBCLONAL	1	TRUE	1	0.667497706789241	2		398	560	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347111	347111	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	385	762	0	ENST00000262320.3:c.1900C>T	p.Gln634Ter	p.Q634*	ENST00000262320	NM_003502.3	634	Cag/Tag	7/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.667497706789241	2		762	1101	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106228	2106228	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	287	506	0	ENST00000219476.3:c.631T>C	p.Ser211Pro	p.S211P	ENST00000219476	NM_000548.3	211	Tcc/Ccc	7/42	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.667497706789241	2		506	824	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110744	2110744	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	130	707	0	ENST00000219476.3:c.1049G>T	p.Arg350Met	p.R350M	ENST00000219476	NM_000548.3	350	aGg/aTg	11/42	1	2	FACETS	0.424	0.384	0.466	0.424	0.384	0.466	SUBCLONAL	1	TRUE	1	0.667497706789241	2		707	918	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122297	2122297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45517215	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	323	661	0	ENST00000219476.3:c.2153G>A	p.Arg718His	p.R718H	ENST00000219476	NM_000548.3	718	cGc/cAc	20/42	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.667497706789241	2		661	954	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639236	3639236	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs574214196	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	330	601	0	ENST00000294008.3:c.4403G>A	p.Arg1468His	p.R1468H	ENST00000294008	NM_032444.2	1468	cGc/cAc	12/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.667497706789241	2		601	915	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801746	3801746	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1005189041	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	206	379	0	ENST00000262367.5:c.3760G>A	p.Asp1254Asn	p.D1254N	ENST00000262367	NM_004380.2	1254	Gac/Aac	20/31	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.667497706789241	2		379	579	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823816	3823816	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371771785	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	78	471	0	ENST00000262367.5:c.2399C>T	p.Pro800Leu	p.P800L	ENST00000262367	NM_004380.2	800	cCg/cTg	13/31	1	2	FACETS	0.361	0.317	0.408	0.361	0.317	0.408	SUBCLONAL	1	TRUE	1	0.667497706789241	2		471	648	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032323	10032323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	165	351	0	ENST00000330684.3:c.500G>T	p.Trp167Leu	p.W167L	ENST00000330684	NM_001134407.1	167	tGg/tTg	3/13	1	2	FACETS	0.935	0.864	1	0.935	0.864	1	CLONAL	1	TRUE	1	0.667497706789241	2		351	529	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041914	14041914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	65	273	0	ENST00000311895.7:c.2461C>T	p.Pro821Ser	p.P821S	ENST00000311895	NM_005236.2	821	Cca/Tca	11/11	1	2	FACETS	0.484	0.422	0.552	0.484	0.422	0.552	SUBCLONAL	1	TRUE	1	0.667497706789241	2		273	402	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041930	14041930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141790888	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	61	268	0	ENST00000311895.7:c.2477C>T	p.Ala826Val	p.A826V	ENST00000311895	NM_005236.2	826	gCg/gTg	11/11	1	2	FACETS	0.48	0.415	0.549	0.48	0.415	0.549	SUBCLONAL	1	TRUE	1	0.667497706789241	2		268	381	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632692	23632692	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	173	294	0	ENST00000261584.4:c.3104T>G	p.Ile1035Ser	p.I1035S	ENST00000261584	NM_024675.3	1035	aTt/aGt	10/13	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.667497706789241	2		294	493	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67646008	67646008	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	178	287	0	ENST00000264010.4:c.937del	p.Asn314ThrfsTer19	p.N314Tfs*19	ENST00000264010	NM_006565.3	312	caC/ca	4/12	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.667497706789241	2		287	501	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853296	68853296	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746481984	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	232	375	0	ENST00000261769.5:c.1679C>T	p.Thr560Met	p.T560M	ENST00000261769	NM_004360.3	560	aCg/aTg	11/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.667497706789241	2		375	630	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828060	72828060	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	380	728	1	ENST00000268489.5:c.8521G>T	p.Ala2841Ser	p.A2841S	ENST00000268489	NM_006885.3	2841	Gca/Tca	9/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.667497706789241	2		729	1134	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984384	72984384	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	216	360	0	ENST00000268489.5:c.3200G>T	p.Ser1067Ile	p.S1067I	ENST00000268489	NM_006885.3	1067	aGc/aTc	3/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.667497706789241	2		360	633	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81957132	81957132	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1567534502	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	216	479	1	ENST00000359376.3:c.2350C>T	p.Arg784Ter	p.R784*	ENST00000359376	NM_002661.3	784	Cga/Tga	22/33	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.667497706789241	2		480	549	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89828418	89828418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	195	409	0	ENST00000389301.3:c.2791G>A	p.Asp931Asn	p.D931N	ENST00000389301	NM_000135.2	931	Gac/Aac	29/43	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.667497706789241	2		409	574	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573979	7573979	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	306	541	0	ENST00000269305.4:c.1048C>A	p.Leu350Ile	p.L350I	ENST00000269305	NM_001126112.2	350	Ctc/Atc	10/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.667497706789241	2		541	791	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578182	7578182	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	252	431	0	ENST00000269305.4:c.667C>A	p.Pro223Thr	p.P223T	ENST00000269305	NM_001126112.2	223	Cct/Act	6/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.667497706789241	2		431	718	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110176	8110176	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	221	415	0	ENST00000585124.1:c.429T>G	p.Tyr143Ter	p.Y143*	ENST00000585124	NM_004217.3	143	taT/taG	6/9	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.667497706789241	2		415	634	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556392	29556392	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199474775	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	213	443	0	ENST00000356175.3:c.2759T>C	p.Leu920Pro	p.L920P	ENST00000356175	NM_000267.3	920	cTg/cCg	21/57	1	2	FACETS	0.951	0.888	1	0.951	0.888	1	CLONAL	1	TRUE	1	0.667497706789241	2		443	671	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560200	29560200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	114	234	0	ENST00000356175.3:c.3677C>A	p.Ala1226Asp	p.A1226D	ENST00000356175	NM_000267.3	1226	gCt/gAt	27/57	1	2	FACETS	0.911	0.828	0.997	0.911	0.828	0.997	CLONAL	1	TRUE	1	0.667497706789241	2		234	375	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619187	37619187	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	57	338	0	ENST00000447079.4:c.863G>T	p.Ser288Ile	p.S288I	ENST00000447079	NM_015083.1	288	aGc/aTc	1/14	1	2	FACETS	0.349	0.299	0.402	0.349	0.299	0.402	SUBCLONAL	1	TRUE	1	0.667497706789241	2		338	490	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883965	37883965	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762062043	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	260	502	1	ENST00000269571.5:c.3436C>T	p.Arg1146Trp	p.R1146W	ENST00000269571		1146	Cgg/Tgg	27/27	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.667497706789241	2		503	727	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38504716	38504716	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	219	424	0	ENST00000254066.5:c.327G>T	p.Lys109Asn	p.K109N	ENST00000254066	NM_000964.3	109	aaG/aaT	3/9	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.667497706789241	2		424	621	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441476	40441476	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	249	510	0	ENST00000345506.4:c.47G>A	p.Arg16His	p.R16H	ENST00000345506	NM_003152.3	16	cGc/cAc	3/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.667497706789241	2		510	682	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441528	40441528	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	51	642	0	ENST00000345506.4:c.99C>A	p.Tyr33Ter	p.Y33*	ENST00000345506	NM_003152.3	33	taC/taA	3/20	1	2	FACETS	0.162	0.137	0.19	0.162	0.137	0.19	SUBCLONAL	1	TRUE	1	0.667497706789241	2		642	942	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481441	40481441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113994137	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	178	410	0	ENST00000264657.5:c.1268G>A	p.Arg423Gln	p.R423Q	ENST00000264657	NM_139276.2	423	cGa/cAa	14/24	1	2	FACETS	0.848	0.785	0.913	0.848	0.785	0.913	CLONAL	1	TRUE	1	0.667497706789241	2		410	629	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485932	40485932	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	99	513	1	ENST00000264657.5:c.933G>T	p.Glu311Asp	p.E311D	ENST00000264657	NM_139276.2	311	gaG/gaT	9/24	1	2	FACETS	0.38	0.339	0.424	0.38	0.339	0.424	SUBCLONAL	1	TRUE	1	0.667497706789241	2		514	780	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40490819	40490819	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	42	290	0	ENST00000264657.5:c.480G>T	p.Gln160His	p.Q160H	ENST00000264657	NM_139276.2	160	caG/caT	6/24	1	2	FACETS	0.272	0.227	0.323	0.272	0.227	0.323	SUBCLONAL	1	TRUE	1	0.667497706789241	2		290	462	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688798	47688798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	142	216	0	ENST00000347630.2:c.502G>A	p.Val168Ile	p.V168I	ENST00000347630	NM_001007230.1	168	Gtc/Atc	7/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.667497706789241	2		216	405	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435855	56435855	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	179	410	0	ENST00000407977.2:c.1282C>A	p.Pro428Thr	p.P428T	ENST00000407977		428	Cct/Act	9/10	1	2	FACETS	0.999	0.927	1	0.999	0.927	1	CLONAL	1	TRUE	1	0.667497706789241	2		410	537	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56811549	56811549	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs577852020	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	68	334	0	ENST00000337432.4:c.1097G>A	p.Arg366Gln	p.R366Q	ENST00000337432	NM_058216.2	366	cGg/cAg	9/9	1	2	FACETS	0.413	0.36	0.471	0.413	0.36	0.471	SUBCLONAL	1	TRUE	1	0.667497706789241	2		334	493	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59770793	59770793	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	35	275	0	ENST00000259008.2:c.2573C>A	p.Ser858Tyr	p.S858Y	ENST00000259008	NM_032043.2	858	tCt/tAt	18/20	1	2	FACETS	0.301	0.247	0.362	0.301	0.247	0.362	SUBCLONAL	1	TRUE	1	0.667497706789241	2		275	348	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78704375	78704375	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	141	311	0	ENST00000306801.3:c.523A>G	p.Ile175Val	p.I175V	ENST00000306801	NM_020761.2	175	Atc/Gtc	5/34	1	2	FACETS	0.907	0.832	0.983	0.907	0.832	0.983	CLONAL	1	TRUE	1	0.667497706789241	2		311	466	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724503	724503	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	61	307	0	ENST00000314574.4:c.1553C>T	p.Thr518Ile	p.T518I	ENST00000314574	NM_005433.3	518	aCa/aTa	12/12	1	2	FACETS	0.386	0.334	0.443	0.386	0.334	0.443	SUBCLONAL	1	TRUE	1	0.667497706789241	2		307	473	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39542530	39542530	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753063601	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	131	284	0	ENST00000262039.4:c.334G>A	p.Asp112Asn	p.D112N	ENST00000262039	NM_002647.2	112	Gat/Aat	3/25	1	2	FACETS	0.89	0.814	0.969	0.89	0.814	0.969	CLONAL	1	TRUE	1	0.667497706789241	2		284	441	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390334	56390334	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	111	259	0	ENST00000348428.3:c.1073A>C	p.Lys358Thr	p.K358T	ENST00000348428	NM_006785.3	358	aAg/aCg	10/17	1	2	FACETS	0.914	0.83	1	0.914	0.83	1	CLONAL	1	TRUE	1	0.667497706789241	2		259	364	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7141726	7141726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs565092654	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	272	514	0	ENST00000302850.5:c.2644G>A	p.Val882Met	p.V882M	ENST00000302850	NM_000208.2	882	Gtg/Atg	13/22	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.667497706789241	2		514	758	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7141791	7141791	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	42	481	0	ENST00000302850.5:c.2579A>G	p.Glu860Gly	p.E860G	ENST00000302850	NM_000208.2	860	gAa/gGa	13/22	1	2	FACETS	0.177	0.147	0.21	0.177	0.147	0.21	SUBCLONAL	1	TRUE	1	0.667497706789241	2		481	711	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246943	10246943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749413587	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	113	448	0	ENST00000340748.4:c.4462G>A	p.Ala1488Thr	p.A1488T	ENST00000340748		1488	Gca/Aca	37/40	1	2	FACETS	0.465	0.419	0.514	0.465	0.419	0.514	SUBCLONAL	1	TRUE	1	0.667497706789241	2		448	728	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051113	13051113	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	75	397	0	ENST00000316448.5:c.549G>T	p.Glu183Asp	p.E183D	ENST00000316448	NM_004343.3	183	gaG/gaT	5/9	1	2	FACETS	0.378	0.331	0.429	0.378	0.331	0.429	SUBCLONAL	1	TRUE	1	0.667497706789241	2		397	594	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298041	15298041	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	162	669	1	ENST00000263388.2:c.1715C>A	p.Pro572His	p.P572H	ENST00000263388	NM_000435.2	572	cCt/cAt	11/33	1	2	FACETS	0.465	0.426	0.506	0.465	0.426	0.506	SUBCLONAL	1	TRUE	1	0.667497706789241	2		670	1044	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302610	15302611	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1412990396	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	144	656	0	ENST00000263388.2:c.747dup	p.Thr250AspfsTer10	p.T250Dfs*10	ENST00000263388	NM_000435.2	249	-/G	5/33	1	2	FACETS	0.406	0.369	0.444	0.406	0.369	0.444	SUBCLONAL	1	TRUE	1	0.667497706789241	2		656	1064	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354106	15354106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	235	693	0	ENST00000263377.2:c.2774C>T	p.Ser925Phe	p.S925F	ENST00000263377	NM_058243.2	925	tCc/tTc	14/20	1	2	FACETS	0.934	0.875	0.995	0.934	0.875	0.995	CLONAL	1	TRUE	1	0.667497706789241	2		693	754	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366150	15366150	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1305265035	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	253	453	1	ENST00000263377.2:c.2005C>T	p.Arg669Cys	p.R669C	ENST00000263377	NM_058243.2	669	Cgc/Tgc	10/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.667497706789241	2		454	706	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943365	17943365	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	310	493	0	ENST00000458235.1:c.2643T>G	p.Asp881Glu	p.D881E	ENST00000458235	NM_000215.3	881	gaT/gaG	19/24	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.667497706789241	2		493	757	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945688	17945688	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	218	480	0	ENST00000458235.1:c.2172G>T	p.Met724Ile	p.M724I	ENST00000458235	NM_000215.3	724	atG/atT	16/24	1	2	FACETS	0.897	0.838	0.958	0.897	0.838	0.958	CLONAL	1	TRUE	1	0.667497706789241	2		480	728	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273238	18273238	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	208	355	0	ENST00000222254.8:c.1031T>C	p.Leu344Pro	p.L344P	ENST00000222254	NM_005027.3	344	cTc/cCc	9/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.667497706789241	2		355	594	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18956828	18956828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759056334	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	234	415	0	ENST00000262803.5:c.271G>A	p.Asp91Asn	p.D91N	ENST00000262803	NM_002911.3	91	Gac/Aac	2/24	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.667497706789241	2		415	680	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18972899	18972899	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	87	540	0	ENST00000262803.5:c.2538G>T	p.Glu846Asp	p.E846D	ENST00000262803	NM_002911.3	846	gaG/gaT	18/24	1	2	FACETS	0.337	0.298	0.379	0.337	0.298	0.379	SUBCLONAL	1	TRUE	1	0.667497706789241	2		540	774	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210722	36210722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201092669	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	283	516	1	ENST00000222270.7:c.473C>T	p.Thr158Met	p.T158M	ENST00000222270	NM_014727.1	158	aCg/aTg	3/37	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.667497706789241	2		517	824	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212581	36212581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	347	721	2	ENST00000222270.7:c.2332G>A	p.Ala778Thr	p.A778T	ENST00000222270	NM_014727.1	778	Gcg/Acg	3/37	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.667497706789241	2		723	976	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754708	41754708	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	246	474	0	ENST00000301178.4:c.1694C>A	p.Ala565Asp	p.A565D	ENST00000301178	NM_021913.4	565	gCt/gAt	14/20	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.667497706789241	2		474	731	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752749	42752749	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	127	631	0	ENST00000222329.4:c.1515G>T	p.Glu505Asp	p.E505D	ENST00000222329	NM_006494.2	505	gaG/gaT	4/4	1	2	FACETS	0.432	0.391	0.476	0.432	0.391	0.476	SUBCLONAL	1	TRUE	1	0.667497706789241	2		631	880	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791539	42791539	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	297	558	1	ENST00000575354.2:c.520C>A	p.Leu174Ile	p.L174I	ENST00000575354	NM_015125.3	174	Ctc/Atc	4/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.667497706789241	2		559	813	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791775	42791775	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745501361	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	250	493	0	ENST00000575354.2:c.661C>T	p.Arg221Cys	p.R221C	ENST00000575354	NM_015125.3	221	Cgt/Tgt	5/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.667497706789241	2		493	664	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798337	42798337	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	263	503	0	ENST00000575354.2:c.4208C>A	p.Ala1403Glu	p.A1403E	ENST00000575354	NM_015125.3	1403	gCa/gAa	18/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.667497706789241	2		503	757	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724364	52724364	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	152	318	0	ENST00000322088.6:c.1496T>C	p.Met499Thr	p.M499T	ENST00000322088	NM_014225.5	499	aTg/aCg	12/15	1	2	FACETS	0.953	0.878	1	0.953	0.878	1	CLONAL	1	TRUE	1	0.667497706789241	2		318	478	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965610	25965610	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	298	471	0	ENST00000435504.4:c.3596C>T	p.Pro1199Leu	p.P1199L	ENST00000435504		1199	cCc/cTc	13/13	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.667497706789241	2		471	839	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101081	26101081	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	62	408	1	ENST00000435504.4:c.11del	p.Lys4ArgfsTer18	p.K4Rfs*18	ENST00000435504		4	aAg/ag	1/13	1	2	FACETS	0.359	0.31	0.412	0.359	0.31	0.412	SUBCLONAL	1	TRUE	1	0.667497706789241	2		409	517	SUCCESS
ALK	238	MSKCC	GRCh37	2	29450540	29450540	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	276	472	0	ENST00000389048.3:c.2816-2A>G		p.X939_splice	ENST00000389048	NM_004304.4	939			1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.667497706789241	2		472	716	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630379	47630379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750966	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	241	459	0	ENST00000233146.2:c.49G>A	p.Val17Ile	p.V17I	ENST00000233146	NM_000251.2	17	Gtc/Atc	1/16	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.667497706789241	2		459	709	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635624	47635624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553350175	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	255	445	0	ENST00000233146.2:c.296G>A	p.Arg99Lys	p.R99K	ENST00000233146	NM_000251.2	99	aGa/aAa	2/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.667497706789241	2		445	731	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170937	99170937	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	218	364	0	ENST00000074304.5:c.1566G>A	p.Trp522Ter	p.W522*	ENST00000074304	NM_001134224.1	522	tgG/tgA	16/26	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.667497706789241	2		364	622	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182103	99182103	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	147	231	0	ENST00000074304.5:c.2168G>T	p.Gly723Val	p.G723V	ENST00000074304	NM_001134224.1	723	gGg/gTg	21/26	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.667497706789241	2		231	360	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038178	128038178	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747124421	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	192	329	0	ENST00000285398.2:c.1372G>A	p.Val458Met	p.V458M	ENST00000285398	NM_000122.1	458	Gtg/Atg	9/15	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.667497706789241	2		329	558	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273113	198273113	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	207	470	0	ENST00000335508.6:c.1097A>G	p.Asn366Ser	p.N366S	ENST00000335508	NM_012433.2	366	aAc/aGc	8/25	1	2	FACETS	0.997	0.931	1	0.997	0.931	1	CLONAL	1	TRUE	1	0.667497706789241	2		470	622	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136311	202136311	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	223	464	0	ENST00000358485.4:c.555G>T	p.Glu185Asp	p.E185D	ENST00000358485	NM_001080125.1	185	gaG/gaT	3/9	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.667497706789241	2		464	629	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209108254	209108254	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	33	415	0	ENST00000345146.2:c.595A>T	p.Met199Leu	p.M199L	ENST00000345146	NM_005896.2	199	Atg/Ttg	6/10	1	2	FACETS	0.159	0.129	0.193	0.159	0.129	0.193	SUBCLONAL	1	TRUE	1	0.667497706789241	2		415	622	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812322	212812322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	92	212	0	ENST00000342788.4:c.254G>A	p.Gly85Asp	p.G85D	ENST00000342788	NM_005235.2	85	gGc/gAc	3/28	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.667497706789241	2		212	271	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660201	227660201	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	289	620	0	ENST00000305123.5:c.3254C>T	p.Ala1085Val	p.A1085V	ENST00000305123	NM_005544.2	1085	gCc/gTc	1/2	1	2	FACETS	0.98	0.924	1	0.98	0.924	1	CLONAL	1	TRUE	1	0.667497706789241	2		620	884	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46252826	46252826	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	54	133	0	ENST00000371998.3:c.255A>C	p.Gln85His	p.Q85H	ENST00000371998		85	caA/caC	4/23	1	2	FACETS	0.909	0.79	1	0.909	0.79	1	CLONAL	1	TRUE	1	0.667497706789241	2		133	178	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46266392	46266392	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	15	266	0	ENST00000371998.3:c.2377G>A	p.Gly793Arg	p.G793R	ENST00000371998		793	Gga/Aga	13/23	1	2	FACETS	0.178	0.13	0.236	0.178	0.13	0.236	SUBCLONAL	1	TRUE	1	0.667497706789241	2		266	252	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62305391	62305391	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	262	526	0	ENST00000360203.5:c.864G>T	p.Lys288Asn	p.K288N	ENST00000360203	NM_001283009.1	288	aaG/aaT	10/35	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.667497706789241	2		526	764	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319084	62319084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773057452	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	49	559	0	ENST00000360203.5:c.1442C>T	p.Thr481Met	p.T481M	ENST00000360203	NM_001283009.1	481	aCg/aTg	17/35	1	2	FACETS	0.161	0.136	0.19	0.161	0.136	0.19	SUBCLONAL	1	TRUE	1	0.667497706789241	2		559	910	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62320883	62320883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200847054	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	350	635	0	ENST00000360203.5:c.1907C>T	p.Thr636Met	p.T636M	ENST00000360203	NM_001283009.1	636	aCg/aTg	23/35	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.667497706789241	2		635	958	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324257	62324257	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	46	619	0	ENST00000360203.5:c.2752G>T	p.Ala918Ser	p.A918S	ENST00000360203	NM_001283009.1	918	Gcc/Tcc	29/35	1	2	FACETS	0.151	0.126	0.179	0.151	0.126	0.179	SUBCLONAL	1	TRUE	1	0.667497706789241	2		619	912	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326795	62326795	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768665929	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	325	614	1	ENST00000360203.5:c.3614C>T	p.Ser1205Phe	p.S1205F	ENST00000360203	NM_001283009.1	1205	tCc/tTc	34/35	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.667497706789241	2		615	933	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145515	24145515	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	93	489	1	ENST00000263121.7:c.534G>T	p.Glu178Asp	p.E178D	ENST00000263121	NM_003073.3	178	gaG/gaT	5/9	1	2	FACETS	0.382	0.339	0.427	0.382	0.339	0.427	SUBCLONAL	1	TRUE	1	0.667497706789241	2		490	730	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054251	30054251	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1386029079	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	196	398	0	ENST00000338641.4:c.673C>T	p.Arg225Trp	p.R225W	ENST00000338641	NM_000268.3	225	Cgg/Tgg	7/16	1	2	FACETS	0.985	0.918	1	0.985	0.918	1	CLONAL	1	TRUE	1	0.667497706789241	2		398	596	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523573	41523573	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	229	469	0	ENST00000263253.7:c.989C>A	p.Ala330Asp	p.A330D	ENST00000263253	NM_001429.3	330	gCt/gAt	4/31	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.667497706789241	2		469	631	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553339	41553339	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	220	408	0	ENST00000263253.7:c.3428C>A	p.Ser1143Tyr	p.S1143Y	ENST00000263253	NM_001429.3	1143	tCc/tAc	18/31	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.667497706789241	2		408	609	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574893	41574893	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	241	411	0	ENST00000263253.7:c.7178T>C	p.Leu2393Pro	p.L2393P	ENST00000263253	NM_001429.3	2393	cTg/cCg	31/31	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.667497706789241	2		411	709	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626032	12626032	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1382398408	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	187	280	0	ENST00000251849.4:c.1928C>T	p.Pro643Leu	p.P643L	ENST00000251849	NM_002880.3	643	cCg/cTg	17/17	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.667497706789241	2		280	477	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626104	12626104	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	167	253	0	ENST00000251849.4:c.1856G>T	p.Ser619Ile	p.S619I	ENST00000251849	NM_002880.3	619	aGc/aTc	17/17	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.667497706789241	2		253	480	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729897	30729897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516839	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	42	245	0	ENST00000295754.5:c.1418C>T	p.Pro473Leu	p.P473L	ENST00000295754	NM_003242.5	473	cCa/cTa	6/7	1	2	FACETS	0.305	0.254	0.36	0.305	0.254	0.36	SUBCLONAL	1	TRUE	1	0.667497706789241	2		245	413	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397763	49397763	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	283	500	0	ENST00000418115.1:c.461T>C	p.Phe154Ser	p.F154S	ENST00000418115	NM_001664.2	154	tTt/tCt	5/5	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.667497706789241	2		500	842	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412890	49412890	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	277	538	0	ENST00000418115.1:c.133G>T	p.Asp45Tyr	p.D45Y	ENST00000418115	NM_001664.2	45	Gat/Tat	2/5	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.667497706789241	2		538	741	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924833	49924833	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	48	658	0	ENST00000296474.3:c.4110G>T	p.Glu1370Asp	p.E1370D	ENST00000296474	NM_002447.2	1370	gaG/gaT	20/20	1	2	FACETS	0.152	0.128	0.179	0.152	0.128	0.179	SUBCLONAL	1	TRUE	1	0.667497706789241	2		658	947	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935107	49935107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370774556	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	61	383	0	ENST00000296474.3:c.1892G>A	p.Arg631Gln	p.R631Q	ENST00000296474	NM_002447.2	631	cGg/cAg	6/20	1	2	FACETS	0.346	0.299	0.398	0.346	0.299	0.398	SUBCLONAL	1	TRUE	1	0.667497706789241	2		383	528	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935997	49935997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	310	503	1	ENST00000296474.3:c.1673G>A	p.Cys558Tyr	p.C558Y	ENST00000296474	NM_002447.2	558	tGt/tAt	4/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.667497706789241	2		504	835	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939848	49939848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750979879	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	300	533	2	ENST00000296474.3:c.1195G>A	p.Asp399Asn	p.D399N	ENST00000296474	NM_002447.2	399	Gac/Aac	1/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.667497706789241	2		535	833	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643641	52643641	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	67	434	0	ENST00000394830.3:c.2255T>C	p.Leu752Pro	p.L752P	ENST00000394830	NM_018313.4	752	cTa/cCa	17/30	1	2	FACETS	0.311	0.27	0.356	0.311	0.27	0.356	SUBCLONAL	1	TRUE	1	0.667497706789241	2		434	645	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71008537	71008537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	130	211	0	ENST00000318789.4:c.1895C>T	p.Pro632Leu	p.P632L	ENST00000318789	NM_032682.5	632	cCt/cTt	21/21	1	2	FACETS	0.986	0.903	1	0.986	0.903	1	CLONAL	1	TRUE	1	0.667497706789241	2		211	395	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259485	89259485	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761263727	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	203	382	0	ENST00000336596.2:c.629C>T	p.Ala210Val	p.A210V	ENST00000336596	NM_005233.5	210	gCt/gTt	3/17	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.667497706789241	2		382	572	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967204	134967204	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	172	299	0	ENST00000398015.3:c.2543A>T	p.Asp848Val	p.D848V	ENST00000398015	NM_004441.4	848	gAc/gTc	14/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.667497706789241	2		299	486	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403636	138403636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	144	343	0	ENST00000289153.2:c.2146C>T	p.Leu716Phe	p.L716F	ENST00000289153	NM_006219.2	716	Ctc/Ttc	15/22	1	2	FACETS	0.928	0.853	1	0.928	0.853	1	CLONAL	1	TRUE	1	0.667497706789241	2		343	465	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431047	181431047	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	271	464	0	ENST00000325404.1:c.899G>A	p.Ser300Asn	p.S300N	ENST00000325404	NM_003106.3	300	aGc/aAc	1/1	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.667497706789241	2		464	727	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443304	187443304	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1042221684	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	162	229	0	ENST00000232014.4:c.1822G>A	p.Gly608Arg	p.G608R	ENST00000232014	NM_001130845.1	608	Gga/Aga	8/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.667497706789241	2		229	426	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957419	1957419	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	166	363	2	ENST00000382891.5:c.2523del		p.X841_splice	ENST00000382891	NM_133335.3	841			1	2	FACETS	0.966	0.894	1	0.966	0.894	1	CLONAL	1	TRUE	1	0.667497706789241	2		365	515	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749524	41749524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1192207345	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	224	460	0	ENST00000226382.2:c.271G>A	p.Gly91Ser	p.G91S	ENST00000226382	NM_003924.3	91	Ggc/Agc	2/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.667497706789241	2		460	628	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146559	55146559	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	175	320	0	ENST00000257290.5:c.2233A>G	p.Met745Val	p.M745V	ENST00000257290	NM_006206.4	745	Atg/Gtg	16/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.667497706789241	2		320	480	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55974036	55974036	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	159	327	0	ENST00000263923.4:c.1280C>A	p.Ser427Tyr	p.S427Y	ENST00000263923	NM_002253.2	427	tCt/tAt	10/30	1	2	FACETS	0.89	0.821	0.962	0.89	0.821	0.962	CLONAL	1	TRUE	1	0.667497706789241	2		327	535	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522472	187522472	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749669933	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	264	484	0	ENST00000441802.2:c.11591C>T	p.Thr3864Met	p.T3864M	ENST00000441802	NM_005245.3	3864	aCg/aTg	21/27	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.667497706789241	2		484	748	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535396	187535396	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	35	400	1	ENST00000441802.2:c.9178T>C	p.Tyr3060His	p.Y3060H	ENST00000441802	NM_005245.3	3060	Tac/Cac	12/27	1	2	FACETS	0.175	0.143	0.211	0.175	0.143	0.211	SUBCLONAL	1	TRUE	1	0.667497706789241	2		401	600	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629781	187629781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1470996737	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	42	476	0	ENST00000441802.2:c.1201G>A	p.Val401Ile	p.V401I	ENST00000441802	NM_005245.3	401	Gtt/Att	2/27	1	2	FACETS	0.178	0.148	0.211	0.178	0.148	0.211	SUBCLONAL	1	TRUE	1	0.667497706789241	2		476	708	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279521	1279521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1353891039	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	313	647	1	ENST00000310581.5:c.2015G>A	p.Arg672His	p.R672H	ENST00000310581	NM_198253.2	672	cGc/cAc	5/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.667497706789241	2		648	868	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295364	1295364	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	162	287	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.667497706789241	2		287	435	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178037	56178037	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	24	313	0	ENST00000399503.3:c.3010C>T	p.His1004Tyr	p.H1004Y	ENST00000399503	NM_005921.1	1004	Cat/Tat	14/20	1	2	FACETS	0.157	0.122	0.197	0.157	0.122	0.197	SUBCLONAL	1	TRUE	1	0.667497706789241	2		313	459	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189494	56189494	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373075979	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	58	299	0	ENST00000399503.3:c.4526G>A	p.Arg1509His	p.R1509H	ENST00000399503	NM_005921.1	1509	cGt/cAt	20/20	1	2	FACETS	0.352	0.302	0.406	0.352	0.302	0.406	SUBCLONAL	1	TRUE	1	0.667497706789241	2		299	494	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752780	57752780	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	148	230	0	ENST00000274289.3:c.1148A>C	p.Asp383Ala	p.D383A	ENST00000274289	NM_006622.3	383	gAc/gCc	8/14	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.667497706789241	2		230	403	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755746	57755746	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	282	507	0	ENST00000274289.3:c.41G>T	p.Ser14Ile	p.S14I	ENST00000274289	NM_006622.3	14	aGc/aTc	1/14	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.667497706789241	2		507	762	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79966069	79966069	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs558080525	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	189	380	0	ENST00000265081.6:c.733G>T	p.Asp245Tyr	p.D245Y	ENST00000265081	NM_002439.4	245	Gat/Tat	4/24	1	2	FACETS	0.963	0.896	1	0.963	0.896	1	CLONAL	1	TRUE	1	0.667497706789241	2		380	588	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627257	86627257	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	146	274	0	ENST00000274376.6:c.632G>T	p.Arg211Leu	p.R211L	ENST00000274376	NM_002890.2	211	cGg/cTg	2/25	1	2	FACETS	0.919	0.845	0.995	0.919	0.845	0.995	CLONAL	1	TRUE	1	0.667497706789241	2		274	476	SUCCESS
APC	324	MSKCC	GRCh37	5	112176096	112176096	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	137	296	0	ENST00000257430.4:c.4805C>A	p.Pro1602His	p.P1602H	ENST00000257430	NM_000038.5	1602	cCt/cAt	16/16	1	2	FACETS	0.946	0.868	1	0.946	0.868	1	CLONAL	1	TRUE	1	0.667497706789241	2		296	434	SUCCESS
APC	324	MSKCC	GRCh37	5	112176456	112176456	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1175970075	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	102	241	0	ENST00000257430.4:c.5165A>G	p.Asp1722Gly	p.D1722G	ENST00000257430	NM_000038.5	1722	gAt/gGt	16/16	1	2	FACETS	0.98	0.887	1	0.98	0.887	1	CLONAL	1	TRUE	1	0.667497706789241	2		241	312	SUCCESS
APC	324	MSKCC	GRCh37	5	112178237	112178237	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	133	320	0	ENST00000257430.4:c.6946C>T	p.Pro2316Ser	p.P2316S	ENST00000257430	NM_000038.5	2316	Cca/Tca	16/16	1	2	FACETS	0.974	0.893	1	0.974	0.893	1	CLONAL	1	TRUE	1	0.667497706789241	2		320	409	SUCCESS
APC	324	MSKCC	GRCh37	5	112178387	112178387	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	56	257	0	ENST00000257430.4:c.7096T>C	p.Tyr2366His	p.Y2366H	ENST00000257430	NM_000038.5	2366	Tat/Cat	16/16	1	2	FACETS	0.478	0.411	0.55	0.478	0.411	0.55	SUBCLONAL	1	TRUE	1	0.667497706789241	2		257	351	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131930572	131930572	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	86	166	0	ENST00000265335.6:c.1805C>A	p.Ala602Asp	p.A602D	ENST00000265335		602	gCt/gAt	12/25	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.667497706789241	2		166	248	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131951696	131951696	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	62	154	0	ENST00000265335.6:c.3038T>C	p.Ile1013Thr	p.I1013T	ENST00000265335		1013	aTa/aCa	20/25	1	2	FACETS	0.958	0.842	1	0.958	0.842	1	CLONAL	1	TRUE	1	0.667497706789241	2		154	194	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515210	149515210	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	264	572	1	ENST00000261799.4:c.272C>A	p.Thr91Asn	p.T91N	ENST00000261799	NM_002609.3	91	aCt/aAt	3/23	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.667497706789241	2		573	765	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518767	176518767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755103491	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	232	535	0	ENST00000292408.4:c.685G>A	p.Ala229Thr	p.A229T	ENST00000292408	NM_213647.1	229	Gct/Act	6/18	1	2	FACETS	0.939	0.879	1	0.939	0.879	1	CLONAL	1	TRUE	1	0.667497706789241	2		535	740	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638344	176638344	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	272	485	0	ENST00000439151.2:c.2948del	p.Gly983ValfsTer57	p.G983Vfs*57	ENST00000439151	NM_022455.4	982	Ggg/gg	5/23	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.667497706789241	2		485	797	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638971	176638971	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	248	381	0	ENST00000439151.2:c.3571C>T	p.Leu1191Phe	p.L1191F	ENST00000439151	NM_022455.4	1191	Ctt/Ttt	5/23	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.667497706789241	2		381	695	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047610	180047610	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1368938536	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	188	359	0	ENST00000261937.6:c.2405G>T	p.Arg802Met	p.R802M	ENST00000261937	NM_182925.4	802	aGg/aTg	16/30	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.667497706789241	2		359	523	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180050947	180050947	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	60	603	0	ENST00000261937.6:c.1536G>T	p.Glu512Asp	p.E512D	ENST00000261937	NM_182925.4	512	gaG/gaT	11/30	1	2	FACETS	0.192	0.164	0.222	0.192	0.164	0.222	SUBCLONAL	1	TRUE	1	0.667497706789241	2		603	938	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401554	401554	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	159	309	0	ENST00000380956.4:c.876C>A	p.Phe292Leu	p.F292L	ENST00000380956	NM_001195286.1	292	ttC/ttA	7/9	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.667497706789241	2		309	445	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20488420	20488420	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	167	306	1	ENST00000346618.3:c.1076G>T	p.Ser359Ile	p.S359I	ENST00000346618	NM_001949.4	359	aGt/aTt	6/7	NA	2	FACETS	1	0.93	1			1	INDETERMINATE	1	TRUE	NA	0.667497706789241	2		307	498	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056108	26056108	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	93	403	0	ENST00000343677.2:c.549G>T	p.Lys183Asn	p.K183N	ENST00000343677	NM_005319.3	183	aaG/aaT	1/1	1	2	FACETS	0.433	0.385	0.484	0.433	0.385	0.484	SUBCLONAL	1	TRUE	1	0.667497706789241	2		403	643	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839945	27839945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	244	573	0	ENST00000328488.2:c.149G>A	p.Arg50His	p.R50H	ENST00000328488	NM_003533.2	50	cGc/cAc	1/1	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.667497706789241	2		573	698	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858362	27858362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	209	410	0	ENST00000359303.2:c.209G>A	p.Arg70His	p.R70H	ENST00000359303	NM_003535.2	70	cGc/cAc	1/1	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.667497706789241	2		410	592	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672468	30672468	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	339	558	0	ENST00000376406.3:c.4492G>A	p.Ala1498Thr	p.A1498T	ENST00000376406	NM_014641.2	1498	Gct/Act	10/15	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.667497706789241	2		558	903	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31939995	31939995	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	33	441	1	ENST00000375333.2:c.220+2T>C		p.X74_splice	ENST00000375333	NM_032454.1	74			1	2	FACETS	0.165	0.133	0.2	0.165	0.133	0.2	SUBCLONAL	1	TRUE	1	0.667497706789241	2		442	600	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109311953	109311953	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	94	423	0	ENST00000436639.2:c.1319T>C	p.Ile440Thr	p.I440T	ENST00000436639	NM_014454.2	440	aTt/aCt	8/10	1	2	FACETS	0.429	0.382	0.48	0.429	0.382	0.48	SUBCLONAL	1	TRUE	1	0.667497706789241	2		423	656	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041051	112041051	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	174	342	0	ENST00000368678.4:c.204C>A	p.Asn68Lys	p.N68K	ENST00000368678		68	aaC/aaA	3/13	1	2	FACETS	0.987	0.916	1	0.987	0.916	1	CLONAL	1	TRUE	1	0.667497706789241	2		342	528	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642443	117642443	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1348779301	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	146	564	1	ENST00000368508.3:c.5756C>T	p.Ala1919Val	p.A1919V	ENST00000368508	NM_002944.2	1919	gCt/gTt	35/43	1	2	FACETS	0.518	0.473	0.566	0.518	0.473	0.566	SUBCLONAL	1	TRUE	1	0.667497706789241	2		565	844	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704501	117704501	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	66	278	0	ENST00000368508.3:c.2475G>T	p.Gln825His	p.Q825H	ENST00000368508	NM_002944.2	825	caG/caT	16/43	1	2	FACETS	0.434	0.377	0.494	0.434	0.377	0.494	SUBCLONAL	1	TRUE	1	0.667497706789241	2		278	456	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710519	117710519	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	54	110	0	ENST00000368508.3:c.1753G>T	p.Gly585Ter	p.G585*	ENST00000368508	NM_002944.2	585	Gga/Tga	12/43	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.667497706789241	2		110	145	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196945	138196945	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	120	230	0	ENST00000237289.4:c.607C>A	p.Leu203Ile	p.L203I	ENST00000237289	NM_001270507.1	203	Ctc/Atc	4/9	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.667497706789241	2		230	281	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129155	152129155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	229	598	1	ENST00000206249.3:c.108G>T	p.Glu36Asp	p.E36D	ENST00000206249	NM_000125.3	36	gaG/gaT	1/8	1	2	FACETS	0.905	0.847	0.965	0.905	0.847	0.965	CLONAL	1	TRUE	1	0.667497706789241	2		599	758	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099193	157099193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	219	408	0	ENST00000346085.5:c.130G>A	p.Ala44Thr	p.A44T	ENST00000346085	NM_020732.3	44	Gca/Aca	1/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.667497706789241	2		408	621	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959178	2959178	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	121	507	1	ENST00000396946.4:c.2338C>A	p.Leu780Met	p.L780M	ENST00000396946	NM_032415.4	780	Ctg/Atg	18/25	1	2	FACETS	0.408	0.368	0.45	0.408	0.368	0.45	SUBCLONAL	1	TRUE	1	0.667497706789241	2		508	889	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983916	2983916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	346	642	0	ENST00000396946.4:c.614C>T	p.Ala205Val	p.A205V	ENST00000396946	NM_032415.4	205	gCc/gTc	5/25	1	2	FACETS	0.944	0.895	0.995	0.944	0.895	0.995	CLONAL	1	TRUE	1	0.667497706789241	2		642	1098	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026480	6026480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876659769	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	166	260	0	ENST00000265849.7:c.1916G>A	p.Ser639Asn	p.S639N	ENST00000265849	NM_000535.5	639	aGt/aAt	11/15	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.667497706789241	2		260	495	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221755	55221755	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	233	453	0	ENST00000275493.2:c.799C>A	p.Leu267Ile	p.L267I	ENST00000275493	NM_005228.3	267	Ctc/Atc	7/28	1	2	FACETS	0.976	0.915	1	0.976	0.915	1	CLONAL	1	TRUE	1	0.667497706789241	2		453	715	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223527	55223527	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	288	558	0	ENST00000275493.2:c.894T>G	p.Asn298Lys	p.N298K	ENST00000275493	NM_005228.3	298	aaT/aaG	8/28	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.667497706789241	2		558	804	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374430	81374430	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	145	291	0	ENST00000222390.5:c.632G>A	p.Cys211Tyr	p.C211Y	ENST00000222390	NM_000601.4	211	tGc/tAc	6/18	1	2	FACETS	0.955	0.878	1	0.955	0.878	1	CLONAL	1	TRUE	1	0.667497706789241	2		291	455	SUCCESS
MET	4233	MSKCC	GRCh37	7	116414544	116414544	+	intron_variant	Intron	SNP	T	T	C	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	303	650	0	ENST00000397752.3:c.3029-391T>C		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.667497706789241	2		650	846	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151871280	151871280	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	35	378	0	ENST00000262189.6:c.9310C>A	p.Leu3104Ile	p.L3104I	ENST00000262189	NM_170606.2	3104	Ctt/Att	39/59	1	2	FACETS	0.176	0.144	0.213	0.176	0.144	0.213	SUBCLONAL	1	TRUE	1	0.667497706789241	2		378	595	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873340	151873340	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	165	249	0	ENST00000262189.6:c.9198G>T	p.Gln3066His	p.Q3066H	ENST00000262189	NM_170606.2	3066	caG/caT	38/59	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.667497706789241	2		249	447	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151947030	151947030	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	143	315	0	ENST00000262189.6:c.1744G>A	p.Val582Ile	p.V582I	ENST00000262189	NM_170606.2	582	Gtc/Atc	13/59	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.667497706789241	2		315	393	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132849	152132849	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	83	463	0	ENST00000262189.6:c.23G>T	p.Ser8Ile	p.S8I	ENST00000262189	NM_170606.2	8	aGc/aTc	1/59	1	2	FACETS	0.375	0.331	0.422	0.375	0.331	0.422	SUBCLONAL	1	TRUE	1	0.667497706789241	2		463	663	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29195949	29195949	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	292	589	0	ENST00000240100.2:c.649C>A	p.Leu217Met	p.L217M	ENST00000240100	NM_001394.6	217	Ctg/Atg	3/4	1	2	FACETS	0.981	0.925	1	0.981	0.925	1	CLONAL	1	TRUE	1	0.667497706789241	2		589	892	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133295	38133295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	112	412	0	ENST00000317025.8:c.4178C>T	p.Ala1393Val	p.A1393V	ENST00000317025	NM_023034.1	1393	gCc/gTc	24/24	1	2	FACETS	0.473	0.426	0.523	0.473	0.426	0.523	SUBCLONAL	1	TRUE	1	0.667497706789241	2		412	709	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38153343	38153343	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	121	450	0	ENST00000317025.8:c.2886G>T	p.Gln962His	p.Q962H	ENST00000317025	NM_023034.1	962	caG/caT	16/24	1	2	FACETS	0.446	0.403	0.492	0.446	0.403	0.492	SUBCLONAL	1	TRUE	1	0.667497706789241	2		450	812	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277205	38277205	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	82	506	0	ENST00000425967.3:c.1223T>G	p.Ile408Ser	p.I408S	ENST00000425967	NM_001174067.1	408	aTc/aGc	10/19	1	2	FACETS	0.327	0.288	0.369	0.327	0.288	0.369	SUBCLONAL	1	TRUE	1	0.667497706789241	2		506	751	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56854541	56854541	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	130	276	0	ENST00000519728.1:c.123G>T	p.Gln41His	p.Q41H	ENST00000519728	NM_002350.3	41	caG/caT	2/13	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.667497706789241	2		276	378	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141568606	141568606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750164894	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	85	428	0	ENST00000220592.5:c.856C>T	p.Arg286Trp	p.R286W	ENST00000220592	NM_012154.3	286	Cgg/Tgg	7/19	1	2	FACETS	0.384	0.339	0.431	0.384	0.339	0.431	SUBCLONAL	1	TRUE	1	0.667497706789241	2		428	664	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090823	5090823	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	18	202	0	ENST00000381652.3:c.2974del	p.Ile992LeufsTer6	p.I992Lfs*6	ENST00000381652	NM_004972.3	991	Aaa/aa	22/25	1	2	FACETS	0.266	0.2	0.342	0.266	0.2	0.342	SUBCLONAL	1	TRUE	1	0.667497706789241	2		202	203	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460555	8460555	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	47	273	0	ENST00000356435.5:c.3731G>T	p.Ser1244Ile	p.S1244I	ENST00000356435		1244	aGc/aTc	22/35	1	2	FACETS	0.316	0.267	0.371	0.316	0.267	0.371	SUBCLONAL	1	TRUE	1	0.667497706789241	2		273	445	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27220053	27220053	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	179	393	0	ENST00000380036.4:c.3110C>T	p.Thr1037Ile	p.T1037I	ENST00000380036	NM_000459.3	1037	aCa/aTa	21/23	1	2	FACETS	0.982	0.912	1	0.982	0.912	1	CLONAL	1	TRUE	1	0.667497706789241	2		393	546	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923371	36923371	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	40	454	0	ENST00000358127.4:c.891G>C	p.Gln297His	p.Q297H	ENST00000358127	NM_001280556.1	297	caG/caC	7/10	1	2	FACETS	0.173	0.143	0.206	0.173	0.143	0.206	SUBCLONAL	1	TRUE	1	0.667497706789241	2		454	693	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624627	93624627	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	113	205	0	ENST00000375746.1:c.717+1G>A		p.X239_splice	ENST00000375746	NM_001174167.1	239			1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.667497706789241	2		205	335	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900356	101900356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	116	233	0	ENST00000374994.4:c.790G>A	p.Ala264Thr	p.A264T	ENST00000374994	NM_004612.2	264	Gca/Aca	4/9	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.667497706789241	2		233	325	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101910008	101910008	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	84	175	0	ENST00000374994.4:c.1328A>C	p.Lys443Thr	p.K443T	ENST00000374994	NM_004612.2	443	aAa/aCa	8/9	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.667497706789241	2		175	239	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248156	110248156	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	170	327	0	ENST00000374672.4:c.1316G>A	p.Arg439His	p.R439H	ENST00000374672	NM_004235.4	439	cGc/cAc	5/5	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.667497706789241	2		327	499	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738249	133738249	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	99	378	0	ENST00000318560.5:c.649G>A	p.Ala217Thr	p.A217T	ENST00000318560	NM_005157.4	217	Gcc/Acc	4/11	1	2	FACETS	0.527	0.471	0.586	0.527	0.471	0.586	SUBCLONAL	1	TRUE	1	0.667497706789241	2		378	563	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759758	133759758	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1307730338	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	182	395	0	ENST00000318560.5:c.2081C>A	p.Thr694Asn	p.T694N	ENST00000318560	NM_005157.4	694	aCc/aAc	11/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.667497706789241	2		395	516	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404322	139404322	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	133	562	2	ENST00000277541.6:c.2832G>T	p.Glu944Asp	p.E944D	ENST00000277541	NM_017617.3	944	gaG/gaT	18/34	1	2	FACETS	0.428	0.388	0.47	0.428	0.388	0.47	SUBCLONAL	1	TRUE	1	0.667497706789241	2		564	931	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15833835	15833835	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	101	458	0	ENST00000307771.7:c.593C>A	p.Pro198His	p.P198H	ENST00000307771	NM_005089.3	198	cCt/cAt	8/11	1	2	FACETS	0.376	0.336	0.419	0.376	0.336	0.419	SUBCLONAL	1	TRUE	1	0.667497706789241	2		458	805	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932533	39932533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	274	592	0	ENST00000378444.4:c.2066G>A	p.Gly689Asp	p.G689D	ENST00000378444	NM_001123385.1	689	gGc/gAc	4/15	1	2	FACETS	0.962	0.906	1	0.962	0.906	1	CLONAL	1	TRUE	1	0.667497706789241	2		592	853	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833962	44833962	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	205	454	0	ENST00000377967.4:c.384+2T>C		p.X128_splice	ENST00000377967	NM_021140.2	128			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.667497706789241	2		454	583	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041602	47041602	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	305	523	0	ENST00000377604.3:c.1827T>G	p.Asp609Glu	p.D609E	ENST00000377604	NM_001204468.1	609	gaT/gaG	17/24	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.667497706789241	2		523	724	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430720	47430720	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	86	524	0	ENST00000377045.4:c.1687-2A>G		p.X563_splice	ENST00000377045	NM_001654.4	563			1	2	FACETS	0.362	0.32	0.408	0.362	0.32	0.408	SUBCLONAL	1	TRUE	1	0.667497706789241	2		524	711	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225997	53225998	+	stop_gained	Nonsense_Mutation	DNP	CG	CG	TA	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	300	644	1	ENST00000375401.3:c.2851_2852delinsTA	p.Arg951Ter	p.R951*	ENST00000375401	NM_004187.3	951	CGa/TAa	19/26	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.667497706789241	2		645	884	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409767	63409767	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	122	252	0	ENST00000330258.3:c.3400G>T	p.Ala1134Ser	p.A1134S	ENST00000330258	NM_152424.3	1134	Gcc/Tcc	2/2	1	2	FACETS	0.945	0.862	1	0.945	0.862	1	CLONAL	1	TRUE	1	0.667497706789241	2		252	387	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411069	63411069	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	200	481	0	ENST00000330258.3:c.2098C>T	p.Pro700Ser	p.P700S	ENST00000330258	NM_152424.3	700	Cct/Tct	2/2	1	2	FACETS	0.865	0.804	0.927	0.865	0.804	0.927	CLONAL	1	TRUE	1	0.667497706789241	2		481	693	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345945	70345945	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	194	463	0	ENST00000374080.3:c.2482G>T	p.Asp828Tyr	p.D828Y	ENST00000374080		828	Gat/Tat	18/45	1	2	FACETS	0.915	0.851	0.981	0.915	0.851	0.981	CLONAL	1	TRUE	1	0.667497706789241	2		463	635	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76777770	76777770	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	87	433	2	ENST00000373344.5:c.6946C>A	p.Leu2316Met	p.L2316M	ENST00000373344	NM_000489.3	2316	Ctg/Atg	32/35	1	2	FACETS	0.396	0.35	0.444	0.396	0.35	0.444	SUBCLONAL	1	TRUE	1	0.667497706789241	2		435	659	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019861	123019861	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	34	452	1	ENST00000355640.3:c.349G>T	p.Val117Phe	p.V117F	ENST00000355640		117	Gtt/Ttt	2/7	1	2	FACETS	0.154	0.125	0.187	0.154	0.125	0.187	SUBCLONAL	1	TRUE	1	0.667497706789241	2		453	661	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020174	123020174	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	293	546	0	ENST00000355640.3:c.662G>A	p.Arg221Lys	p.R221K	ENST00000355640		221	aGg/aAg	2/7	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.667497706789241	2		546	814	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123040919	123040919	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	59	311	0	ENST00000355640.3:c.1382T>G	p.Val461Gly	p.V461G	ENST00000355640		461	gTt/gGt	7/7	1	2	FACETS	0.4	0.345	0.46	0.4	0.345	0.46	SUBCLONAL	1	TRUE	1	0.667497706789241	2		311	442	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225998	53225998	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	300	644	1	ENST00000375401.3:c.2851C>T	p.Arg951Ter	p.R951*	ENST00000375401	NM_004187.3	951	Cga/Tga	19/26	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.667497706789241	2		645	884	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230433	46230433	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	63	266	0	ENST00000334344.6:c.767C>A	p.Ser256Tyr	p.S256Y	ENST00000334344	NM_152641.2	256	tCt/tAt	7/21	1	2	FACETS	0.427	0.37	0.488	0.427	0.37	0.488	SUBCLONAL	1	TRUE	1	0.667497706789241	2		266	442	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	50	290	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.765	0.663	0.872	1	0.969	1	SUBCLONAL	2	TRUE	1	0.430147013877646	2		290	152	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	53	445	9	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.430147013877646	2		454	175	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	40	420	2	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	1	2	FACETS	0.676	0.565	0.799	0.676	0.565	0.799	SUBCLONAL	1	TRUE	1	0.430147013877646	2		422	275	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	109	519	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.886	0.808	0.966	1	0.988	1	CLONAL	2	TRUE	1	0.430147013877646	2		524	286	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857296	9857296	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567275428	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	31	559	0	ENST00000330684.3:c.4105C>T	p.His1369Tyr	p.H1369Y	ENST00000330684	NM_001134407.1	1369	Cac/Tac	13/13	1	2	FACETS	0.613	0.499	0.741	0.613	0.499	0.741	SUBCLONAL	1	TRUE	1	0.430147013877646	2		559	235	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427974	49427974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	76	703	1	ENST00000301067.7:c.10616G>A	p.Arg3539Gln	p.R3539Q	ENST00000301067	NM_003482.3	3539	cGg/cAg	38/54	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.430147013877646	2		704	254	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045714	26045714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	21	262	0	ENST00000540144.1:c.76G>A	p.Ala26Thr	p.A26T	ENST00000540144	NM_003531.2	26	Gcc/Acc	1/1	0.208489092606192	4	FACETS	1	0.841	1	0.367	0.286	0.458	INDETERMINATE	1	TRUE	1	0.430147013877646	4		262	127	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026708	48026708	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786201964	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	51	421	0	ENST00000234420.5:c.1586G>A	p.Gly529Asp	p.G529D	ENST00000234420	NM_000179.2	529	gGt/gAt	4/10	0.31770096190722	0	FACETS	0.772	0.668	0.883			1	SUBCLONAL	1	TRUE	0	0.430147013877646	0		421	175	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	100	508	12	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	0.31770096190722	0	FACETS	0.64	0.586	0.695			1	SUBCLONAL	2	TRUE	0	0.430147013877646	0		520	207	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435868	110435868	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754439736	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	18	519	0	ENST00000375856.3:c.2533C>T	p.Pro845Ser	p.P845S	ENST00000375856	NM_003749.2	845	Cca/Tca	1/2	0.354048583745509	3	FACETS	0.726	0.552	0.929	0.363	0.276	0.465	CLONAL	1	TRUE	1	0.430147013877646	3		519	140	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909713	50909713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397514632	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	83	788	0	ENST00000440232.2:c.1433G>A	p.Ser478Asn	p.S478N	ENST00000440232	NM_002691.3	478	aGc/aAc	12/27	1	2	FACETS	0.818	0.734	0.904	1	0.983	1	CLONAL	2	TRUE	1	0.430147013877646	2		788	236	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732924	30732924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	34	298	0	ENST00000295754.5:c.1537G>A	p.Val513Met	p.V513M	ENST00000295754	NM_003242.5	513	Gtg/Atg	7/7	1	2	FACETS	0.864	0.714	1	0.864	0.714	1	CLONAL	1	TRUE	1	0.430147013877646	2		298	183	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	30	374	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.83	0.676	1	0.83	0.676	1	CLONAL	1	TRUE	1	0.430147013877646	2		374	168	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461173	120461173	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	44	385	0	ENST00000256646.2:c.5785C>A	p.Leu1929Met	p.L1929M	ENST00000256646	NM_024408.3	1929	Ctg/Atg	32/34	1	2	FACETS	0.809	0.683	0.945	0.809	0.683	0.945	CLONAL	1	TRUE	1	0.430147013877646	2		385	253	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	26	447	1	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	1	2	FACETS	0.601	0.479	0.739	0.601	0.479	0.739	SUBCLONAL	1	TRUE	1	0.430147013877646	2		448	201	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610608	52610609	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	37	574	0	ENST00000394830.3:c.3564dup	p.Glu1189ArgfsTer6	p.E1189Rfs*6	ENST00000394830	NM_018313.4	1188	-/A	23/30	1	2	FACETS	0.708	0.588	0.841	0.708	0.588	0.841	SUBCLONAL	1	TRUE	1	0.430147013877646	2		574	243	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374480	118374480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	70	454	0	ENST00000534358.1:c.7873C>T	p.Arg2625Cys	p.R2625C	ENST00000534358	NM_005933.3	2625	Cgt/Tgt	27/36	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.430147013877646	2		454	246	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317178	11317178	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	33	504	0	ENST00000361445.4:c.316A>G	p.Arg106Gly	p.R106G	ENST00000361445	NM_004958.3	106	Aga/Gga	4/58	0.362898603513773	1	FACETS	0.547	0.449	0.657	0.547	0.449	0.657	SUBCLONAL	1	TRUE	0	0.430147013877646	1		504	220	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2492096	2492097	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs772088410	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	67	582	0	ENST00000355716.4:c.500dup	p.Thr169AspfsTer65	p.T169Dfs*65	ENST00000355716	NM_003820.2	165	tgc/tgCc	5/8	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.430147013877646	2		582	245	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075573	8075573	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	44	547	0	ENST00000377482.5:c.107G>T	p.Ser36Ile	p.S36I	ENST00000377482	NM_018948.3	36	aGt/aTt	2/4	NA	2	FACETS	0.741	0.625	0.868			1	INDETERMINATE	1	TRUE	NA	0.430147013877646	2		547	276	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784896	9784896	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	35	676	0	ENST00000377346.4:c.2899C>A	p.Leu967Met	p.L967M	ENST00000377346	NM_005026.3	967	Ctg/Atg	23/24	NA	2	FACETS	0.67	0.552	0.8			1	INDETERMINATE	1	TRUE	NA	0.430147013877646	2		676	243	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187068	11187068	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	82	499	0	ENST00000361445.4:c.6350A>G	p.Gln2117Arg	p.Q2117R	ENST00000361445	NM_004958.3	2117	cAg/cGg	45/58	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.430147013877646	2		499	277	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187864	11187864	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	41	453	0	ENST00000361445.4:c.6034-1G>T		p.X2012_splice	ENST00000361445	NM_004958.3	2012			NA	2	FACETS	0.912	0.768	1			1	INDETERMINATE	1	TRUE	NA	0.430147013877646	2		453	209	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294323	11294323	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	41	505	0	ENST00000361445.4:c.2209-1G>T		p.X737_splice	ENST00000361445	NM_004958.3	737			0.362898603513773	1	FACETS	0.618	0.519	0.727	0.618	0.519	0.727	SUBCLONAL	1	TRUE	0	0.430147013877646	1		505	242	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307962	11307962	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	42	486	0	ENST00000361445.4:c.1030G>T	p.Gly344Ter	p.G344*	ENST00000361445	NM_004958.3	344	Gga/Tga	7/58	0.362898603513773	1	FACETS	0.557	0.468	0.655	0.557	0.468	0.655	SUBCLONAL	1	TRUE	0	0.430147013877646	1		486	275	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255464	16255464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	52	457	0	ENST00000375759.3:c.2729C>T	p.Ser910Phe	p.S910F	ENST00000375759	NM_015001.2	910	tCt/tTt	11/15	1	2	FACETS	0.825	0.707	0.952	0.825	0.707	0.952	CLONAL	1	TRUE	1	0.430147013877646	2		457	293	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261251	16261251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1188801107	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	43	488	0	ENST00000375759.3:c.8516C>T	p.Pro2839Leu	p.P2839L	ENST00000375759	NM_015001.2	2839	cCg/cTg	11/15	1	2	FACETS	0.823	0.694	0.963	0.823	0.694	0.963	CLONAL	1	TRUE	1	0.430147013877646	2		488	243	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261744	16261744	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	28	550	0	ENST00000375759.3:c.9012del	p.Ser3006AlafsTer16	p.S3006Afs*16	ENST00000375759	NM_015001.2	3003	tcG/tc	11/15	1	2	FACETS	0.592	0.476	0.722	0.592	0.476	0.722	SUBCLONAL	1	TRUE	1	0.430147013877646	2		550	220	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088789	27088789	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	41	487	1	ENST00000324856.7:c.2398G>A	p.Gly800Arg	p.G800R	ENST00000324856	NM_006015.4	800	Ggg/Agg	7/20	1	2	FACETS	0.791	0.664	0.93	0.791	0.664	0.93	CLONAL	1	TRUE	1	0.430147013877646	2		488	241	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101405	27101405	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1484432441	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	38	494	0	ENST00000324856.7:c.4687C>T	p.Pro1563Ser	p.P1563S	ENST00000324856	NM_006015.4	1563	Ccc/Tcc	18/20	1	2	FACETS	0.866	0.723	1	0.866	0.723	1	CLONAL	1	TRUE	1	0.430147013877646	2		494	204	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107006	27107006	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	32	505	0	ENST00000324856.7:c.6617C>T	p.Thr2206Ile	p.T2206I	ENST00000324856	NM_006015.4	2206	aCa/aTa	20/20	1	2	FACETS	0.715	0.585	0.86	0.715	0.585	0.86	SUBCLONAL	1	TRUE	1	0.430147013877646	2		505	208	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36945038	36945038	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	34	669	0	ENST00000361632.4:c.60del	p.Gly21GlufsTer83	p.G21Efs*83	ENST00000361632		20	ccC/cc	2/16	1	2	FACETS	0.559	0.458	0.671	0.559	0.458	0.671	SUBCLONAL	1	TRUE	1	0.430147013877646	2		669	283	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46527599	46527599	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	44	454	0	ENST00000262741.5:c.764+2T>C		p.X255_splice	ENST00000262741	NM_003629.3	255			1	2	FACETS	0.772	0.652	0.903	0.772	0.652	0.903	CLONAL	1	TRUE	1	0.430147013877646	2		454	265	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739403	46739403	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	34	483	0	ENST00000371975.4:c.1594C>A	p.Leu532Met	p.L532M	ENST00000371975	NM_003579.3	532	Ctg/Atg	14/18	1	2	FACETS	0.577	0.473	0.692	0.577	0.473	0.692	SUBCLONAL	1	TRUE	1	0.430147013877646	2		483	274	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306996	65306997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	73	419	5	ENST00000342505.4:c.2580dup	p.Pro861ThrfsTer4	p.P861Tfs*4	ENST00000342505	NM_002227.2	860	-/A	19/25	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.430147013877646	2		424	235	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313359	65313359	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	84	447	1	ENST00000342505.4:c.1756-1G>T		p.X586_splice	ENST00000342505	NM_002227.2	586			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.430147013877646	2		448	263	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058505	72058505	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	50	477	0	ENST00000357731.5:c.935T>A	p.Leu312His	p.L312H	ENST00000357731	NM_173808.2	312	cTt/cAt	6/7	1	2	FACETS	0.788	0.673	0.913	0.788	0.673	0.913	CLONAL	1	TRUE	1	0.430147013877646	2		477	295	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429330	78429330	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	53	575	0	ENST00000370768.2:c.1112del	p.Gly371AspfsTer20	p.G371Dfs*20	ENST00000370768	NM_003902.3	371	gGa/ga	13/20	1	2	FACETS	0.702	0.601	0.811	0.702	0.601	0.811	SUBCLONAL	1	TRUE	1	0.430147013877646	2		575	351	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430035	78430035	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	22	312	0	ENST00000370768.2:c.844A>G	p.Ile282Val	p.I282V	ENST00000370768	NM_003902.3	282	Att/Gtt	11/20	1	2	FACETS	0.609	0.475	0.761	0.609	0.475	0.761	SUBCLONAL	1	TRUE	1	0.430147013877646	2		312	168	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273140	115273140	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	39	519	0	ENST00000438362.2:c.1318A>G	p.Thr440Ala	p.T440A	ENST00000438362	NM_001242891.1	440	Act/Gct	11/20	1	2	FACETS	0.627	0.522	0.743	0.627	0.522	0.743	SUBCLONAL	1	TRUE	1	0.430147013877646	2		519	289	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280598	115280598	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	51	594	1	ENST00000438362.2:c.433C>T	p.Arg145Ter	p.R145*	ENST00000438362	NM_001242891.1	145	Cga/Tga	4/20	1	2	FACETS	0.748	0.639	0.866	0.748	0.639	0.866	SUBCLONAL	1	TRUE	1	0.430147013877646	2		595	317	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282457	115282457	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	45	527	0	ENST00000438362.2:c.193G>T	p.Gly65Cys	p.G65C	ENST00000438362	NM_001242891.1	65	Ggt/Tgt	3/20	1	2	FACETS	0.742	0.627	0.867	0.742	0.627	0.867	SUBCLONAL	1	TRUE	1	0.430147013877646	2		527	282	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120460367	120460367	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	51	513	0	ENST00000256646.2:c.5948G>T	p.Trp1983Leu	p.W1983L	ENST00000256646	NM_024408.3	1983	tGg/tTg	33/34	1	2	FACETS	0.878	0.752	1	0.878	0.752	1	CLONAL	1	TRUE	1	0.430147013877646	2		513	270	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120478097	120478097	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs138122751	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	53	430	0	ENST00000256646.2:c.3653G>A	p.Arg1218Gln	p.R1218Q	ENST00000256646	NM_024408.3	1218	cGg/cAg	22/34	1	2	FACETS	0.813	0.698	0.938	0.813	0.698	0.938	CLONAL	1	TRUE	1	0.430147013877646	2		430	303	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874149	155874149	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1251455206	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	44	613	0	ENST00000368323.3:c.382C>T	p.Pro128Ser	p.P128S	ENST00000368323	NM_006912.5	128	Cct/Tct	5/6	1	2	FACETS	0.718	0.605	0.841	0.718	0.605	0.841	SUBCLONAL	1	TRUE	1	0.430147013877646	2		613	285	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846279	156846279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368806213	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	48	726	1	ENST00000524377.1:c.1720C>T	p.Arg574Cys	p.R574C	ENST00000524377	NM_002529.3	574	Cgc/Tgc	14/17	1	2	FACETS	0.833	0.709	0.967	0.833	0.709	0.967	CLONAL	1	TRUE	1	0.430147013877646	2		727	268	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724529	162724529	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	78	535	0	ENST00000367921.3:c.301G>A	p.Gly101Arg	p.G101R	ENST00000367921	NM_006182.2	101	Ggg/Agg	5/18	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.430147013877646	2		535	263	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729618	162729618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381891916	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	42	490	0	ENST00000367921.3:c.704G>A	p.Gly235Asp	p.G235D	ENST00000367921	NM_006182.2	235	gGt/gAt	8/18	1	2	FACETS	0.669	0.561	0.787	0.669	0.561	0.787	SUBCLONAL	1	TRUE	1	0.430147013877646	2		490	292	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741999	162741999	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	43	477	1	ENST00000367921.3:c.1690A>T	p.Thr564Ser	p.T564S	ENST00000367921	NM_006182.2	564	Act/Tct	13/18	1	2	FACETS	0.8	0.674	0.936	0.8	0.674	0.936	CLONAL	1	TRUE	1	0.430147013877646	2		478	250	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748401	162748401	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	37	502	0	ENST00000367921.3:c.2315C>T	p.Ala772Val	p.A772V	ENST00000367921	NM_006182.2	772	gCc/gTc	17/18	1	2	FACETS	0.765	0.635	0.907	0.765	0.635	0.907	CLONAL	1	TRUE	1	0.430147013877646	2		502	225	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317611	163317611	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	22	291	0	ENST00000271452.3:c.1007C>T	p.Thr336Ile	p.T336I	ENST00000271452	NM_145697.2	336	aCt/aTt	12/14	1	2	FACETS	0.696	0.545	0.867	0.696	0.545	0.867	SUBCLONAL	1	TRUE	1	0.430147013877646	2		291	147	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958556	175958556	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	52	520	0	ENST00000367669.3:c.1789G>T	p.Gly597Ter	p.G597*	ENST00000367669	NM_022457.5	597	Gga/Tga	16/20	1	2	FACETS	0.889	0.763	1	0.889	0.763	1	CLONAL	1	TRUE	1	0.430147013877646	2		520	272	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117013	193117013	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	39	380	0	ENST00000367435.3:c.750del	p.Phe250LeufsTer7	p.F250Lfs*7	ENST00000367435	NM_024529.4	249	aTt/at	8/17	1	2	FACETS	0.684	0.57	0.81	0.684	0.57	0.81	SUBCLONAL	1	TRUE	1	0.430147013877646	2		380	265	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578183	226578183	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	38	523	0	ENST00000366794.5:c.545A>C	p.Lys182Thr	p.K182T	ENST00000366794	NM_001618.3	182	aAg/aCg	4/23	1	2	FACETS	0.755	0.629	0.894	0.755	0.629	0.894	SUBCLONAL	1	TRUE	1	0.430147013877646	2		523	234	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670393	246670393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	30	417	0	ENST00000388985.4:c.127G>A	p.Gly43Arg	p.G43R	ENST00000388985		43	Ggg/Agg	1/12	1	2	FACETS	0.955	0.781	1	0.955	0.781	1	CLONAL	1	TRUE	1	0.430147013877646	2		417	146	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115832	8115832	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	67	567	0	ENST00000346208.3:c.1178C>G	p.Pro393Arg	p.P393R	ENST00000346208		393	cCg/cGg	6/6	0.300142853067812	3	FACETS	1	0.963	1	0.635	0.557	0.718	CLONAL	1	TRUE	1	0.430147013877646	3		567	298	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601828	43601828	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	46	492	0	ENST00000355710.3:c.872C>T	p.Thr291Ile	p.T291I	ENST00000355710	NM_020975.4	291	aCc/aTc	5/20	0.300142853067812	3	FACETS	1	0.893	1	0.533	0.452	0.62	CLONAL	1	TRUE	1	0.430147013877646	3		492	244	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604628	43604628	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	33	641	1	ENST00000355710.3:c.1213C>T	p.Pro405Ser	p.P405S	ENST00000355710	NM_020975.4	405	Ccc/Tcc	6/20	0.300142853067812	3	FACETS	0.731	0.598	0.879	0.366	0.299	0.44	SUBCLONAL	1	TRUE	1	0.430147013877646	3		642	255	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619159	43619159	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	82	573	0	ENST00000355710.3:c.2842G>T	p.Gly948Trp	p.G948W	ENST00000355710	NM_020975.4	948	Ggg/Tgg	17/20	0.300142853067812	3	FACETS	0.942	0.843	1	0.942	0.843	1	CLONAL	2	TRUE	1	0.430147013877646	3		573	246	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851312	63851312	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	47	576	0	ENST00000279873.7:c.2090C>T	p.Ser697Phe	p.S697F	ENST00000279873	NM_032199.2	697	tCc/tTc	10/10	0.300142853067812	3	FACETS	0.876	0.744	1	0.438	0.372	0.511	CLONAL	1	TRUE	1	0.430147013877646	3		576	303	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692769	89692769	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	88	449	0	ENST00000371953.3:c.254-1G>T		p.X85_splice	ENST00000371953	NM_000314.4	85			1	2	FACETS	0.922	0.832	1	1	0.986	1	CLONAL	2	TRUE	1	0.430147013877646	2		449	222	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692885	89692885	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	55	319	0	ENST00000371953.3:c.369C>A	p.His123Gln	p.H123Q	ENST00000371953	NM_000314.4	123	caC/caA	5/9	1	2	FACETS	0.888	0.779	1	1	0.977	1	CLONAL	2	TRUE	1	0.430147013877646	2		319	144	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692958	89692958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660321	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	61	487	0	ENST00000371953.3:c.442G>A	p.Ala148Thr	p.A148T	ENST00000371953	NM_000314.4	148	Gca/Aca	5/9	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.430147013877646	2		487	249	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925378	114925378	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	54	649	2	ENST00000543371.1:c.1456G>T	p.Asp486Tyr	p.D486Y	ENST00000543371	NM_001198531.1	486	Gat/Tat	14/14	1	2	FACETS	0.91	0.783	1	0.91	0.783	1	CLONAL	1	TRUE	1	0.430147013877646	2		651	276	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256195	123256195	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	30	428	0	ENST00000358487.5:c.1714C>A	p.Leu572Ile	p.L572I	ENST00000358487	NM_000141.4	572	Ctc/Atc	13/18	1	2	FACETS	0.62	0.502	0.751	0.62	0.502	0.751	SUBCLONAL	1	TRUE	1	0.430147013877646	2		428	225	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417914	32417914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765218093	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	48	544	0	ENST00000332351.3:c.1138C>T	p.Arg380Trp	p.R380W	ENST00000332351	NM_024426.4	380	Cgg/Tgg	7/10	1	2	FACETS	0.886	0.755	1	0.886	0.755	1	CLONAL	1	TRUE	1	0.430147013877646	2		544	252	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32449604	32449604	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs372225738	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	38	490	0	ENST00000332351.3:c.770G>A	p.Gly257Asp	p.G257D	ENST00000332351	NM_024426.4	257	gGt/gAt	3/10	1	2	FACETS	0.955	0.799	1	0.955	0.799	1	CLONAL	1	TRUE	1	0.430147013877646	2		490	185	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575448	64575448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878855195	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	44	660	0	ENST00000312049.6:c.569G>A	p.Gly190Glu	p.G190E	ENST00000312049	NM_130799.2	190	gGg/gAg	3/10	1	2	FACETS	0.755	0.637	0.883	0.755	0.637	0.883	SUBCLONAL	1	TRUE	1	0.430147013877646	2		660	271	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941215	71941215	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	41	781	2	ENST00000298229.2:c.990G>T	p.Gln330His	p.Q330H	ENST00000298229	NM_001567.3	330	caG/caT	9/28	1	2	FACETS	0.681	0.57	0.802	0.681	0.57	0.802	SUBCLONAL	1	TRUE	1	0.430147013877646	2		783	280	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946340	71946340	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	42	727	1	ENST00000298229.2:c.2504G>T	p.Gly835Val	p.G835V	ENST00000298229	NM_001567.3	835	gGg/gTg	23/28	1	2	FACETS	0.697	0.586	0.82	0.697	0.586	0.82	SUBCLONAL	1	TRUE	1	0.430147013877646	2		728	280	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948185	71948185	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1008622934	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	42	799	1	ENST00000298229.2:c.2897C>A	p.Ala966Asp	p.A966D	ENST00000298229	NM_001567.3	966	gCt/gAt	26/28	1	2	FACETS	0.666	0.559	0.784	0.666	0.559	0.784	SUBCLONAL	1	TRUE	1	0.430147013877646	2		800	293	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94224025	94224025	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	89	529	0	ENST00000323929.3:c.127A>T	p.Ile43Phe	p.I43F	ENST00000323929	NM_005591.3	43	Att/Ttt	3/20	1	2	FACETS	0.799	0.719	0.881	1	0.983	1	SUBCLONAL	2	TRUE	1	0.430147013877646	2		529	259	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94224041	94224041	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	85	527	0	ENST00000323929.3:c.111del	p.Phe37LeufsTer2	p.F37Lfs*2	ENST00000323929	NM_005591.3	37	ttT/tt	3/20	1	2	FACETS	0.763	0.684	0.845	1	0.981	1	SUBCLONAL	2	TRUE	1	0.430147013877646	2		527	259	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962543	100962544	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	44	626	1	ENST00000325455.5:c.1853dup	p.Asn618LysfsTer8	p.N618Kfs*8	ENST00000325455	NM_001202474.3	618	aac/aaAc	3/8	1	2	FACETS	0.635	0.535	0.745	0.635	0.535	0.745	SUBCLONAL	1	TRUE	1	0.430147013877646	2		627	322	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999546	100999546	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868723861	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	39	862	6	ENST00000325455.5:c.256G>A	p.Ala86Thr	p.A86T	ENST00000325455	NM_001202474.3	86	Gca/Aca	1/8	1	2	FACETS	0.714	0.596	0.844	0.714	0.596	0.844	SUBCLONAL	1	TRUE	1	0.430147013877646	2		868	254	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207515	102207515	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	39	485	0	ENST00000263464.3:c.1604C>A	p.Pro535His	p.P535H	ENST00000263464	NM_001165.4	535	cCc/cAc	8/9	1	2	FACETS	0.689	0.575	0.816	0.689	0.575	0.816	SUBCLONAL	1	TRUE	1	0.430147013877646	2		485	263	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124663	108124663	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs201762714	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	100	513	0	ENST00000278616.4:c.2021A>G	p.His674Arg	p.H674R	ENST00000278616	NM_000051.3	674	cAc/cGc	13/63	1	2	FACETS	1	0.913	1	1	0.989	1	CLONAL	2	TRUE	1	0.430147013877646	2		513	232	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129720	108129721	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	53	577	0	ENST00000278616.4:c.2387dup	p.Asn796LysfsTer2	p.N796Kfs*2	ENST00000278616	NM_000051.3	795	cca/ccAa	16/63	1	2	FACETS	0.89	0.765	1	0.89	0.765	1	CLONAL	1	TRUE	1	0.430147013877646	2		577	277	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142067	108142067	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	54	590	1	ENST00000278616.4:c.3011G>T	p.Ser1004Ile	p.S1004I	ENST00000278616	NM_000051.3	1004	aGc/aTc	20/63	1	2	FACETS	0.951	0.82	1	0.951	0.82	1	CLONAL	1	TRUE	1	0.430147013877646	2		591	264	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204642	108204642	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs747448699	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	63	316	0	ENST00000278616.4:c.7957A>G	p.Ile2653Val	p.I2653V	ENST00000278616	NM_000051.3	2653	Att/Gtt	54/63	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.430147013877646	2		316	202	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216620	108216620	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	45	383	0	ENST00000278616.4:c.8569G>T	p.Ala2857Ser	p.A2857S	ENST00000278616	NM_000051.3	2857	Gct/Tct	58/63	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.430147013877646	2		383	200	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343232	118343232	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	54	389	0	ENST00000534358.1:c.1361del	p.Pro454ArgfsTer113	p.P454Rfs*113	ENST00000534358	NM_005933.3	453	gCc/gc	3/36	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.430147013877646	2		389	250	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343659	118343660	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	37	496	0	ENST00000534358.1:c.1790dup	p.Leu597PhefsTer22	p.L597Ffs*22	ENST00000534358	NM_005933.3	595	-/T	3/36	1	2	FACETS	0.654	0.542	0.778	0.654	0.542	0.778	SUBCLONAL	1	TRUE	1	0.430147013877646	2		496	263	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344405	118344405	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	45	293	0	ENST00000534358.1:c.2531A>G	p.Gln844Arg	p.Q844R	ENST00000534358	NM_005933.3	844	cAg/cGg	3/36	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.430147013877646	2		293	151	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359383	118359383	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	46	456	0	ENST00000534358.1:c.4388del	p.Asn1463ThrfsTer123	p.N1463Tfs*123	ENST00000534358	NM_005933.3	1463	Aac/ac	11/36	1	2	FACETS	0.895	0.76	1	0.895	0.76	1	CLONAL	1	TRUE	1	0.430147013877646	2		456	239	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373151	118373151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	65	402	1	ENST00000534358.1:c.6544G>A	p.Gly2182Ser	p.G2182S	ENST00000534358	NM_005933.3	2182	Ggt/Agt	27/36	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.430147013877646	2		403	229	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375790	118375790	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	41	484	0	ENST00000534358.1:c.9183G>T	p.Gln3061His	p.Q3061H	ENST00000534358	NM_005933.3	3061	caG/caT	27/36	1	2	FACETS	0.714	0.598	0.841	0.714	0.598	0.841	SUBCLONAL	1	TRUE	1	0.430147013877646	2		484	267	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376607	118376607	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	32	429	1	ENST00000534358.1:c.10000G>A	p.Val3334Met	p.V3334M	ENST00000534358	NM_005933.3	3334	Gtg/Atg	27/36	1	2	FACETS	0.564	0.459	0.68	0.564	0.459	0.68	SUBCLONAL	1	TRUE	1	0.430147013877646	2		430	264	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103402	119103402	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	42	321	0	ENST00000264033.4:c.440C>A	p.Pro147His	p.P147H	ENST00000264033	NM_005188.3	147	cCt/cAt	2/16	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.430147013877646	2		321	176	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125513732	125513732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1314732435	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	44	523	0	ENST00000428830.2:c.860C>T	p.Pro287Leu	p.P287L	ENST00000428830	NM_001114121.2	287	cCc/cTc	9/14	1	2	FACETS	0.761	0.642	0.89	0.761	0.642	0.89	SUBCLONAL	1	TRUE	1	0.430147013877646	2		523	269	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416632	416632	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	54	366	0	ENST00000399788.2:c.3918T>A	p.Asn1306Lys	p.N1306K	ENST00000399788	NM_001042603.1	1306	aaT/aaA	23/28	1	2	FACETS	0.81	0.696	0.933	0.81	0.696	0.933	CLONAL	1	TRUE	1	0.430147013877646	2		366	310	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416753	416753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	31	368	1	ENST00000399788.2:c.3797C>T	p.Thr1266Ile	p.T1266I	ENST00000399788	NM_001042603.1	1266	aCa/aTa	23/28	1	2	FACETS	0.611	0.497	0.738	0.611	0.497	0.738	SUBCLONAL	1	TRUE	1	0.430147013877646	2		369	236	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427457	427457	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	73	684	0	ENST00000399788.2:c.2712G>T	p.Leu904Phe	p.L904F	ENST00000399788	NM_001042603.1	904	ttG/ttT	19/28	1	2	FACETS	0.962	0.847	1	0.962	0.847	1	CLONAL	1	TRUE	1	0.430147013877646	2		684	353	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	430161	430161	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	36	289	0	ENST00000399788.2:c.2541G>T	p.Lys847Asn	p.K847N	ENST00000399788	NM_001042603.1	847	aaG/aaT	18/28	1	2	FACETS	0.813	0.674	0.965	0.813	0.674	0.965	CLONAL	1	TRUE	1	0.430147013877646	2		289	206	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438057	438057	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	42	489	0	ENST00000399788.2:c.1912G>T	p.Glu638Ter	p.E638*	ENST00000399788	NM_001042603.1	638	Gaa/Taa	14/28	1	2	FACETS	0.664	0.557	0.782	0.664	0.557	0.782	SUBCLONAL	1	TRUE	1	0.430147013877646	2		489	294	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475167	475167	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	59	621	0	ENST00000399788.2:c.470T>C	p.Leu157Pro	p.L157P	ENST00000399788	NM_001042603.1	157	cTt/cCt	4/28	1	2	FACETS	0.99	0.86	1	0.99	0.86	1	CLONAL	1	TRUE	1	0.430147013877646	2		621	277	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383382	4383382	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	26	506	0	ENST00000261254.3:c.176T>C	p.Val59Ala	p.V59A	ENST00000261254	NM_001759.3	59	gTg/gCg	1/5	1	2	FACETS	0.728	0.582	0.892	0.728	0.582	0.892	SUBCLONAL	1	TRUE	1	0.430147013877646	2		506	166	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022904	12022904	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	41	662	0	ENST00000396373.4:c.1009+1G>T		p.X337_splice	ENST00000396373	NM_001987.4	337			1	2	FACETS	0.611	0.511	0.721	0.611	0.511	0.721	SUBCLONAL	1	TRUE	1	0.430147013877646	2		662	312	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491482	18491482	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	41	329	0	ENST00000266497.5:c.1395G>T	p.Glu465Asp	p.E465D	ENST00000266497		465	gaG/gaT	8/31	1	2	FACETS	0.844	0.709	0.99	0.844	0.709	0.99	CLONAL	1	TRUE	1	0.430147013877646	2		329	226	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499762	18499762	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	47	326	0	ENST00000266497.5:c.1617G>T	p.Trp539Cys	p.W539C	ENST00000266497		539	tgG/tgT	10/31	1	2	FACETS	0.95	0.81	1	0.95	0.81	1	CLONAL	1	TRUE	1	0.430147013877646	2		326	230	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641388	18641389	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1229278001	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	19	253	0	ENST00000266497.5:c.2393dup	p.Asn798LysfsTer5	p.N798Kfs*5	ENST00000266497		796	cta/ctAa	17/31	1	2	FACETS	0.749	0.576	0.946	0.749	0.576	0.946	CLONAL	1	TRUE	1	0.430147013877646	2		253	118	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650589	18650589	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs558256965	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	36	604	1	ENST00000266497.5:c.2800C>T	p.Gln934Ter	p.Q934*	ENST00000266497		934	Cag/Tag	20/31	1	2	FACETS	0.689	0.57	0.82	0.689	0.57	0.82	SUBCLONAL	1	TRUE	1	0.430147013877646	2		605	243	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658389	18658390	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	30	396	1	ENST00000266497.5:c.3199dup	p.Arg1067LysfsTer38	p.R1067Kfs*38	ENST00000266497		1065	ata/atAa	22/31	1	2	FACETS	0.623	0.505	0.755	0.623	0.505	0.755	SUBCLONAL	1	TRUE	1	0.430147013877646	2		397	224	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800873	18800873	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	45	470	0	ENST00000266497.5:c.4249A>G	p.Thr1417Ala	p.T1417A	ENST00000266497		1417	Act/Gct	31/31	1	2	FACETS	0.942	0.8	1	0.942	0.8	1	CLONAL	1	TRUE	1	0.430147013877646	2		470	222	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636509	21636509	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs773801667	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	55	406	1	ENST00000421138.2:c.502-1G>T		p.X168_splice	ENST00000421138		168			1	2	FACETS	0.814	0.712	0.921	1	0.975	1	CLONAL	2	TRUE	1	0.430147013877646	2		407	157	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644451	21644451	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	27	331	0	ENST00000421138.2:c.214+2T>C		p.X72_splice	ENST00000421138		72			1	2	FACETS	0.717	0.576	0.876	0.717	0.576	0.876	SUBCLONAL	1	TRUE	1	0.430147013877646	2		331	175	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945067	31945067	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	34	662	0	ENST00000340398.3:c.34A>G	p.Thr12Ala	p.T12A	ENST00000340398	NM_001013699.2	12	Acc/Gcc	1/1	1	2	FACETS	0.62	0.509	0.743	0.62	0.509	0.743	SUBCLONAL	1	TRUE	1	0.430147013877646	2		662	255	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244335	46244335	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1433339453	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	48	489	0	ENST00000334344.6:c.2429C>T	p.Ala810Val	p.A810V	ENST00000334344	NM_152641.2	810	gCa/gTa	15/21	1	2	FACETS	0.72	0.612	0.838	0.72	0.612	0.838	SUBCLONAL	1	TRUE	1	0.430147013877646	2		489	310	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245312	46245312	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760671052	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	36	488	0	ENST00000334344.6:c.3406C>T	p.Pro1136Ser	p.P1136S	ENST00000334344	NM_152641.2	1136	Ccc/Tcc	15/21	1	2	FACETS	0.689	0.57	0.82	0.689	0.57	0.82	SUBCLONAL	1	TRUE	1	0.430147013877646	2		488	243	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285562	46285562	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs79280775	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	31	283	1	ENST00000334344.6:c.4923-1G>T		p.X1641_splice	ENST00000334344	NM_152641.2	1641			1	2	FACETS	0.912	0.747	1	0.912	0.747	1	CLONAL	1	TRUE	1	0.430147013877646	2		284	158	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298803	46298803	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	27	389	0	ENST00000334344.6:c.5451del	p.Glu1817AspfsTer22	p.E1817Dfs*22	ENST00000334344	NM_152641.2	1817	gAa/ga	21/21	1	2	FACETS	0.606	0.486	0.743	0.606	0.486	0.743	SUBCLONAL	1	TRUE	1	0.430147013877646	2		389	207	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415828	49415828	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	40	432	0	ENST00000301067.7:c.16519G>A	p.Glu5507Lys	p.E5507K	ENST00000301067	NM_003482.3	5507	Gag/Aag	53/54	1	2	FACETS	0.762	0.638	0.898	0.762	0.638	0.898	SUBCLONAL	1	TRUE	1	0.430147013877646	2		432	244	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416416	49416416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123734	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	49	643	1	ENST00000301067.7:c.16295G>A	p.Arg5432Gln	p.R5432Q	ENST00000301067	NM_003482.3	5432	cGg/cAg	51/54	1	2	FACETS	0.817	0.696	0.947	0.817	0.696	0.947	CLONAL	1	TRUE	1	0.430147013877646	2		644	279	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422666	49422666	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	35	671	4	ENST00000301067.7:c.14327A>G	p.Lys4776Arg	p.K4776R	ENST00000301067	NM_003482.3	4776	aAg/aGg	45/54	1	2	FACETS	0.573	0.471	0.686	0.573	0.471	0.686	SUBCLONAL	1	TRUE	1	0.430147013877646	2		675	284	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422961	49422961	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	32	662	0	ENST00000301067.7:c.14134G>T	p.Glu4712Ter	p.E4712*	ENST00000301067	NM_003482.3	4712	Gag/Tag	44/54	1	2	FACETS	0.583	0.476	0.704	0.583	0.476	0.704	SUBCLONAL	1	TRUE	1	0.430147013877646	2		662	255	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431726	49431726	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	43	675	0	ENST00000301067.7:c.9413C>A	p.Thr3138Asn	p.T3138N	ENST00000301067	NM_003482.3	3138	aCc/aAc	34/54	1	2	FACETS	0.757	0.638	0.888	0.757	0.638	0.888	SUBCLONAL	1	TRUE	1	0.430147013877646	2		675	264	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431947	49431947	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	88	815	0	ENST00000301067.7:c.9192T>A	p.Asp3064Glu	p.D3064E	ENST00000301067	NM_003482.3	3064	gaT/gaA	34/54	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.430147013877646	2		815	273	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434384	49434384	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866926540	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	34	635	0	ENST00000301067.7:c.7169C>T	p.Pro2390Leu	p.P2390L	ENST00000301067	NM_003482.3	2390	cCg/cTg	31/54	1	2	FACETS	0.67	0.551	0.802	0.67	0.551	0.802	SUBCLONAL	1	TRUE	1	0.430147013877646	2		635	236	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442994	49442994	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	33	483	0	ENST00000301067.7:c.3914G>T	p.Ser1305Ile	p.S1305I	ENST00000301067	NM_003482.3	1305	aGc/aTc	12/54	1	2	FACETS	0.564	0.461	0.679	0.564	0.461	0.679	SUBCLONAL	1	TRUE	1	0.430147013877646	2		483	272	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445168	49445168	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	41	646	1	ENST00000301067.7:c.2298G>T	p.Glu766Asp	p.E766D	ENST00000301067	NM_003482.3	766	gaG/gaT	10/54	1	2	FACETS	0.822	0.69	0.965	0.822	0.69	0.965	CLONAL	1	TRUE	1	0.430147013877646	2		647	232	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445430	49445430	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	81	811	3	ENST00000301067.7:c.2036C>A	p.Pro679His	p.P679H	ENST00000301067	NM_003482.3	679	cCc/cAc	10/54	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.430147013877646	2		814	271	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50482318	50482318	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	69	450	0	ENST00000394963.4:c.669A>C	p.Lys223Asn	p.K223N	ENST00000394963	NM_003076.4	223	aaA/aaC	6/13	1	2	FACETS	0.782	0.694	0.875	1	0.978	1	SUBCLONAL	2	TRUE	1	0.430147013877646	2		450	205	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861199	57861199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774006233	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	54	484	0	ENST00000228682.2:c.996G>A	p.Met332Ile	p.M332I	ENST00000228682	NM_005269.2	332	atG/atA	9/12	1	2	FACETS	0.981	0.846	1	0.981	0.846	1	CLONAL	1	TRUE	1	0.430147013877646	2		484	256	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864144	57864144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs544591554	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	41	569	1	ENST00000228682.2:c.1621C>T	p.Arg541Cys	p.R541C	ENST00000228682	NM_005269.2	541	Cgc/Tgc	12/12	1	2	FACETS	0.706	0.592	0.832	0.706	0.592	0.832	SUBCLONAL	1	TRUE	1	0.430147013877646	2		570	270	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864571	57864571	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	36	678	0	ENST00000228682.2:c.2048C>A	p.Ser683Tyr	p.S683Y	ENST00000228682	NM_005269.2	683	tCt/tAt	12/12	1	2	FACETS	0.667	0.551	0.794	0.667	0.551	0.794	SUBCLONAL	1	TRUE	1	0.430147013877646	2		678	251	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865140	57865140	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	33	792	0	ENST00000228682.2:c.2617C>A	p.Leu873Ile	p.L873I	ENST00000228682	NM_005269.2	873	Ctt/Att	12/12	1	2	FACETS	0.575	0.47	0.691	0.575	0.47	0.691	SUBCLONAL	1	TRUE	1	0.430147013877646	2		792	267	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222592	69222592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555187172	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	50	467	1	ENST00000462284.1:c.565C>T	p.Arg189Cys	p.R189C	ENST00000462284	NM_002392.5	189	Cgc/Tgc	8/11	1	2	FACETS	0.901	0.771	1	0.901	0.771	1	CLONAL	1	TRUE	1	0.430147013877646	2		468	258	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112884148	112884149	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	39	475	0	ENST00000351677.2:c.89dup	p.Leu30PhefsTer5	p.L30Ffs*5	ENST00000351677	NM_002834.3	28	agt/agTt	2/16	1	2	FACETS	0.84	0.702	0.989	0.84	0.702	0.989	CLONAL	1	TRUE	1	0.430147013877646	2		475	216	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924348	112924348	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	39	552	0	ENST00000351677.2:c.1294C>A	p.Pro432Thr	p.P432T	ENST00000351677	NM_002834.3	432	Cct/Act	11/16	1	2	FACETS	0.768	0.642	0.907	0.768	0.642	0.907	CLONAL	1	TRUE	1	0.430147013877646	2		552	236	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120791129	120791129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375034852	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	56	590	1	ENST00000257552.2:c.706G>A	p.Ala236Thr	p.A236T	ENST00000257552	NM_002442.3	236	Gcc/Acc	10/15	1	2	FACETS	0.917	0.792	1	0.917	0.792	1	CLONAL	1	TRUE	1	0.430147013877646	2		591	284	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202894	133202894	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	31	500	0	ENST00000320574.5:c.6340del	p.Leu2114TrpfsTer9	p.L2114Wfs*9	ENST00000320574	NM_006231.2	2114	Ctg/tg	46/49	1	2	FACETS	0.593	0.482	0.717	0.593	0.482	0.717	SUBCLONAL	1	TRUE	1	0.430147013877646	2		500	243	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212559	133212559	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	38	556	2	ENST00000320574.5:c.5730C>A	p.Cys1910Ter	p.C1910*	ENST00000320574	NM_006231.2	1910	tgC/tgA	42/49	1	2	FACETS	0.736	0.613	0.872	0.736	0.613	0.872	SUBCLONAL	1	TRUE	1	0.430147013877646	2		558	240	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235963	133235963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	98	595	0	ENST00000320574.5:c.3193G>A	p.Gly1065Arg	p.G1065R	ENST00000320574	NM_006231.2	1065	Gga/Aga	26/49	1	2	FACETS	0.788	0.713	0.866	1	0.985	1	SUBCLONAL	2	TRUE	1	0.430147013877646	2		595	289	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237677	133237677	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	33	679	0	ENST00000320574.5:c.2938C>T	p.Gln980Ter	p.Q980*	ENST00000320574	NM_006231.2	980	Cag/Tag	25/49	1	2	FACETS	0.624	0.511	0.749	0.624	0.511	0.749	SUBCLONAL	1	TRUE	1	0.430147013877646	2		679	246	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257866	133257866	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	49	411	0	ENST00000320574.5:c.63-1G>T		p.X21_splice	ENST00000320574	NM_006231.2	21			1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.430147013877646	2		411	216	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549492	21549492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	47	462	0	ENST00000382592.4:c.2784G>A	p.Trp928Ter	p.W928*	ENST00000382592	NM_014572.2	928	tgG/tgA	8/8	1	2	FACETS	0.731	0.62	0.851	0.731	0.62	0.851	SUBCLONAL	1	TRUE	1	0.430147013877646	2		462	299	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21553937	21553937	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	24	382	1	ENST00000382592.4:c.2666-1G>T		p.X889_splice	ENST00000382592	NM_014572.2	889			1	2	FACETS	0.575	0.454	0.713	0.575	0.454	0.713	SUBCLONAL	1	TRUE	1	0.430147013877646	2		383	194	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562886	21562886	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	33	669	0	ENST00000382592.4:c.1033C>T	p.Gln345Ter	p.Q345*	ENST00000382592	NM_014572.2	345	Cag/Tag	4/8	1	2	FACETS	0.629	0.515	0.756	0.629	0.515	0.756	SUBCLONAL	1	TRUE	1	0.430147013877646	2		669	244	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563002	21563002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748263686	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	41	673	0	ENST00000382592.4:c.917C>T	p.Pro306Leu	p.P306L	ENST00000382592	NM_014572.2	306	cCc/cTc	4/8	1	2	FACETS	0.815	0.684	0.957	0.815	0.684	0.957	CLONAL	1	TRUE	1	0.430147013877646	2		673	234	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28611372	28611372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	40	607	1	ENST00000241453.7:c.1259C>T	p.Ala420Val	p.A420V	ENST00000241453	NM_004119.2	420	gCa/gTa	10/24	1	2	FACETS	0.679	0.567	0.802	0.679	0.567	0.802	SUBCLONAL	1	TRUE	1	0.430147013877646	2		608	274	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893590	28893590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752645756	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	47	441	0	ENST00000282397.4:c.3256G>A	p.Gly1086Arg	p.G1086R	ENST00000282397	NM_002019.4	1086	Gga/Aga	24/30	1	2	FACETS	0.967	0.824	1	0.967	0.824	1	CLONAL	1	TRUE	1	0.430147013877646	2		441	226	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005345	29005345	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs762663070	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	97	674	0	ENST00000282397.4:c.916A>G	p.Lys306Glu	p.K306E	ENST00000282397	NM_002019.4	306	Aaa/Gaa	7/30	1	2	FACETS	0.803	0.726	0.882	1	0.985	1	CLONAL	2	TRUE	1	0.430147013877646	2		674	281	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008291	29008291	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs777429596	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	49	465	0	ENST00000282397.4:c.580A>G	p.Ile194Val	p.I194V	ENST00000282397	NM_002019.4	194	Ata/Gta	5/30	1	2	FACETS	0.893	0.763	1	0.893	0.763	1	CLONAL	1	TRUE	1	0.430147013877646	2		465	255	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041755	29041755	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	33	403	0	ENST00000282397.4:c.65-1G>T		p.X22_splice	ENST00000282397	NM_002019.4	22			1	2	FACETS	0.741	0.609	0.888	0.741	0.609	0.888	SUBCLONAL	1	TRUE	1	0.430147013877646	2		403	207	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906858	32906858	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	80	507	0	ENST00000380152.3:c.1243C>T	p.His415Tyr	p.H415Y	ENST00000380152		415	Cat/Tat	10/27	1	2	FACETS	0.759	0.678	0.843	1	0.98	1	SUBCLONAL	2	TRUE	1	0.430147013877646	2		507	245	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912902	32912902	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	37	383	0	ENST00000380152.3:c.4410A>G	p.Ile1470Met	p.I1470M	ENST00000380152		1470	atA/atG	11/27	1	2	FACETS	0.771	0.641	0.915	0.771	0.641	0.915	CLONAL	1	TRUE	1	0.430147013877646	2		383	223	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930564	32930564	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	28	267	1	ENST00000380152.3:c.7436-1G>T		p.X2479_splice	ENST00000380152		2479			1	2	FACETS	0.789	0.637	0.958	0.789	0.637	0.958	CLONAL	1	TRUE	1	0.430147013877646	2		268	165	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133674	41133674	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	35	354	0	ENST00000379561.5:c.1954T>C	p.Trp652Arg	p.W652R	ENST00000379561	NM_002015.3	652	Tgg/Cgg	2/3	1	2	FACETS	0.757	0.625	0.902	0.757	0.625	0.902	CLONAL	1	TRUE	1	0.430147013877646	2		354	215	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881430	48881430	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	63	196	0	ENST00000267163.4:c.152A>G	p.Glu51Gly	p.E51G	ENST00000267163	NM_000321.2	51	gAa/gGa	2/27	1	2	FACETS	0.91	0.806	1	1	0.981	1	CLONAL	2	TRUE	1	0.430147013877646	2		196	161	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050919	49050919	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	33	390	0	ENST00000267163.4:c.2603C>A	p.Pro868His	p.P868H	ENST00000267163	NM_000321.2	868	cCt/cAt	25/27	1	2	FACETS	0.731	0.6	0.875	0.731	0.6	0.875	SUBCLONAL	1	TRUE	1	0.430147013877646	2		390	210	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281734	49281734	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	64	775	0	ENST00000282018.3:c.781C>A	p.Leu261Met	p.L261M	ENST00000282018	NM_020377.2	261	Ctg/Atg	1/1	1	2	FACETS	0.91	0.793	1	0.91	0.793	1	CLONAL	1	TRUE	1	0.430147013877646	2		775	327	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337683	73337684	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	29	343	1	ENST00000377767.4:c.2032dup	p.Ile678AsnfsTer3	p.I678Nfs*3	ENST00000377767	NM_014953.3	678	att/aAtt	16/21	1	2	FACETS	0.762	0.617	0.923	0.762	0.617	0.923	CLONAL	1	TRUE	1	0.430147013877646	2		344	177	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103513867	103513867	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	36	318	0	ENST00000355739.4:c.683A>T	p.Asp228Val	p.D228V	ENST00000355739	NM_000123.3	228	gAc/gTc	7/15	0.354048583745509	3	FACETS	0.904	0.749	1	0.452	0.374	0.538	CLONAL	1	TRUE	1	0.430147013877646	3		318	225	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519075	103519075	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs899478069	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	35	567	1	ENST00000355739.4:c.2413G>A	p.Gly805Arg	p.G805R	ENST00000355739	NM_000123.3	805	Gga/Aga	11/15	0.354048583745509	3	FACETS	0.732	0.603	0.876	0.366	0.301	0.438	SUBCLONAL	1	TRUE	1	0.430147013877646	3		568	270	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436077	110436077	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	30	716	0	ENST00000375856.3:c.2324T>A	p.Val775Asp	p.V775D	ENST00000375856	NM_003749.2	775	gTc/gAc	1/2	0.354048583745509	3	FACETS	0.757	0.613	0.917	0.378	0.306	0.459	CLONAL	1	TRUE	1	0.430147013877646	3		716	224	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436207	110436207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	24	484	0	ENST00000375856.3:c.2194C>T	p.Pro732Ser	p.P732S	ENST00000375856	NM_003749.2	732	Ccc/Tcc	1/2	0.354048583745509	3	FACETS	0.753	0.595	0.933	0.377	0.297	0.467	CLONAL	1	TRUE	1	0.430147013877646	3		484	180	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107707	30107707	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	46	626	0	ENST00000331968.5:c.973A>G	p.Thr325Ala	p.T325A	ENST00000331968	NM_002742.2	325	Acc/Gcc	6/18	1	2	FACETS	0.723	0.612	0.843	0.723	0.612	0.843	SUBCLONAL	1	TRUE	1	0.430147013877646	2		626	296	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987211	36987211	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	40	593	0	ENST00000354822.5:c.478G>A	p.Gly160Ser	p.G160S	ENST00000354822	NM_001079668.2	160	Ggc/Agc	3/3	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.430147013877646	2		593	172	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40993319	40993319	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	32	462	0	ENST00000267868.3:c.145G>A	p.Val49Met	p.V49M	ENST00000267868	NM_002875.4	49	Gtg/Atg	3/10	0.430147013877646	1	FACETS	0.642	0.526	0.769	0.642	0.526	0.769	SUBCLONAL	1	TRUE	0	0.430147013877646	1		462	182	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989076	41989076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	49	504	0	ENST00000219905.7:c.1868G>A	p.Cys623Tyr	p.C623Y	ENST00000219905	NM_001164273.1	623	tGt/tAt	3/24	0.430147013877646	1	FACETS	0.784	0.671	0.906	0.784	0.671	0.906	CLONAL	1	TRUE	0	0.430147013877646	1		504	228	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034852	42034852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1349365358	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	48	532	0	ENST00000219905.7:c.4694C>T	p.Thr1565Ile	p.T1565I	ENST00000219905	NM_001164273.1	1565	aCa/aTa	15/24	0.430147013877646	1	FACETS	0.782	0.668	0.905	0.782	0.668	0.905	CLONAL	1	TRUE	0	0.430147013877646	1		532	224	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040877	42040877	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	49	554	0	ENST00000219905.7:c.5255C>A	p.Pro1752His	p.P1752H	ENST00000219905	NM_001164273.1	1752	cCt/cAt	16/24	0.430147013877646	1	FACETS	0.788	0.674	0.91	0.788	0.674	0.91	CLONAL	1	TRUE	0	0.430147013877646	1		554	227	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041692	42041692	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	49	515	0	ENST00000219905.7:c.5887G>A	p.Val1963Ile	p.V1963I	ENST00000219905	NM_001164273.1	1963	Gtt/Att	17/24	0.430147013877646	1	FACETS	0.872	0.748	1	0.872	0.748	1	CLONAL	1	TRUE	0	0.430147013877646	1		515	205	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720315	43720315	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	111	692	0	ENST00000382044.4:c.3727C>A	p.Arg1243Ser	p.R1243S	ENST00000382044	NM_001141980.1	1243	Cgt/Agt	18/28	0.430147013877646	1	FACETS	0.782	0.716	0.849	1	0.987	1	SUBCLONAL	2	TRUE	0	0.430147013877646	1		692	259	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628267	90628267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1466352839	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	34	755	0	ENST00000330062.3:c.1144C>T	p.Arg382Trp	p.R382W	ENST00000330062	NM_002168.2	382	Cgg/Tgg	9/11	0.430147013877646	1	FACETS	0.537	0.442	0.643	0.537	0.442	0.643	SUBCLONAL	1	TRUE	0	0.430147013877646	1		755	231	SUCCESS
BLM	641	MSKCC	GRCh37	15	91298098	91298098	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	37	365	0	ENST00000355112.3:c.1017A>C	p.Lys339Asn	p.K339N	ENST00000355112	NM_000057.2	339	aaA/aaC	5/22	0.430147013877646	1	FACETS	0.646	0.537	0.765	0.646	0.537	0.765	SUBCLONAL	1	TRUE	0	0.430147013877646	1		365	209	SUCCESS
BLM	641	MSKCC	GRCh37	15	91326139	91326139	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs367543039	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	37	369	0	ENST00000355112.3:c.2643G>A	p.Trp881Ter	p.W881*	ENST00000355112	NM_000057.2	881	tgG/tgA	13/22	0.430147013877646	1	FACETS	0.718	0.599	0.849	0.718	0.599	0.849	SUBCLONAL	1	TRUE	0	0.430147013877646	1		369	188	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467863	99467863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	28	365	0	ENST00000268035.6:c.2732C>T	p.Ser911Phe	p.S911F	ENST00000268035	NM_000875.3	911	tCt/tTt	13/21	0.430147013877646	1	FACETS	0.552	0.445	0.672	0.552	0.445	0.672	SUBCLONAL	1	TRUE	0	0.430147013877646	1		365	185	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500382	99500382	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	36	634	0	ENST00000268035.6:c.3815C>A	p.Pro1272His	p.P1272H	ENST00000268035	NM_000875.3	1272	cCt/cAt	21/21	0.430147013877646	1	FACETS	0.589	0.488	0.701	0.589	0.488	0.701	SUBCLONAL	1	TRUE	0	0.430147013877646	1		634	223	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500577	99500577	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs759627092	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	32	458	0	ENST00000268035.6:c.4010G>T	p.Arg1337Leu	p.R1337L	ENST00000268035	NM_000875.3	1337	cGc/cTc	21/21	0.430147013877646	1	FACETS	0.652	0.535	0.782	0.652	0.535	0.782	SUBCLONAL	1	TRUE	0	0.430147013877646	1		458	179	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122868	2122868	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs45517221	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	35	570	0	ENST00000219476.3:c.2239C>A	p.Leu747Met	p.L747M	ENST00000219476	NM_000548.3	747	Ctg/Atg	21/42	1	2	FACETS	0.717	0.592	0.855	0.717	0.592	0.855	SUBCLONAL	1	TRUE	1	0.430147013877646	2		570	227	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124319	2124319	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	39	814	0	ENST00000219476.3:c.2474T>A	p.Val825Asp	p.V825D	ENST00000219476	NM_000548.3	825	gTt/gAt	22/42	1	2	FACETS	0.731	0.61	0.864	0.731	0.61	0.864	SUBCLONAL	1	TRUE	1	0.430147013877646	2		814	248	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130340	2130340	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	53	626	0	ENST00000219476.3:c.3572C>T	p.Thr1191Ile	p.T1191I	ENST00000219476	NM_000548.3	1191	aCc/aTc	30/42	1	2	FACETS	0.998	0.859	1	0.998	0.859	1	CLONAL	1	TRUE	1	0.430147013877646	2		626	247	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2218117	2218117	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	46	747	0	ENST00000326181.6:c.179C>A	p.Pro60His	p.P60H	ENST00000326181	NM_032271.2	60	cCc/cAc	4/21	1	2	FACETS	0.887	0.754	1	0.887	0.754	1	CLONAL	1	TRUE	1	0.430147013877646	2		747	241	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225386	2225386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139483392	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	49	675	0	ENST00000326181.6:c.1471G>A	p.Val491Met	p.V491M	ENST00000326181	NM_032271.2	491	Gtg/Atg	16/21	1	2	FACETS	0.757	0.645	0.879	0.757	0.645	0.879	SUBCLONAL	1	TRUE	1	0.430147013877646	2		675	301	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639380	3639380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	38	688	1	ENST00000294008.3:c.4259C>T	p.Pro1420Leu	p.P1420L	ENST00000294008	NM_032444.2	1420	cCa/cTa	12/15	1	2	FACETS	0.682	0.567	0.809	0.682	0.567	0.809	SUBCLONAL	1	TRUE	1	0.430147013877646	2		689	259	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032171	10032171	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs387906637	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	50	750	0	ENST00000330684.3:c.652C>T	p.Gln218Ter	p.Q218*	ENST00000330684	NM_001134407.1	218	Cag/Tag	3/13	1	2	FACETS	0.75	0.64	0.869	0.75	0.64	0.869	SUBCLONAL	1	TRUE	1	0.430147013877646	2		750	310	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14015887	14015887	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	31	242	0	ENST00000311895.7:c.208-1G>T		p.X70_splice	ENST00000311895	NM_005236.2	70			1	2	FACETS	0.89	0.728	1	0.89	0.728	1	CLONAL	1	TRUE	1	0.430147013877646	2		242	162	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038621	14038621	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	32	346	0	ENST00000311895.7:c.1946G>T	p.Arg649Ile	p.R649I	ENST00000311895	NM_005236.2	649	aGa/aTa	10/11	1	2	FACETS	0.639	0.521	0.769	0.639	0.521	0.769	SUBCLONAL	1	TRUE	1	0.430147013877646	2		346	233	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641344	23641344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555460478	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	42	712	0	ENST00000261584.4:c.2131G>A	p.Val711Ile	p.V711I	ENST00000261584	NM_024675.3	711	Gtt/Att	5/13	1	2	FACETS	0.74	0.622	0.869	0.74	0.622	0.869	SUBCLONAL	1	TRUE	1	0.430147013877646	2		712	264	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828297	50828297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767180517	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	105	523	0	ENST00000398568.2:c.2635G>A	p.Asp879Asn	p.D879N	ENST00000398568	NM_001042412.1	879	Gat/Aat	17/18	1	2	FACETS	0.775	0.703	0.849	1	0.985	1	SUBCLONAL	2	TRUE	1	0.430147013877646	2		523	315	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655395	67655395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	44	558	0	ENST00000264010.4:c.1258G>A	p.Gly420Ser	p.G420S	ENST00000264010	NM_006565.3	420	Ggt/Agt	7/12	1	2	FACETS	0.766	0.647	0.896	0.766	0.647	0.896	SUBCLONAL	1	TRUE	1	0.430147013877646	2		558	267	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835660	68835660	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	45	627	0	ENST00000261769.5:c.251C>A	p.Thr84Lys	p.T84K	ENST00000261769	NM_004360.3	84	aCa/aAa	3/16	1	2	FACETS	0.747	0.632	0.873	0.747	0.632	0.873	SUBCLONAL	1	TRUE	1	0.430147013877646	2		627	280	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867295	68867295	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	100	537	0	ENST00000261769.5:c.2542C>A	p.Leu848Met	p.L848M	ENST00000261769	NM_004360.3	848	Ctg/Atg	16/16	1	2	FACETS	0.76	0.687	0.835	1	0.984	1	SUBCLONAL	2	TRUE	1	0.430147013877646	2		537	306	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822557	72822557	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	26	511	0	ENST00000268489.5:c.9618G>T	p.Gln3206His	p.Q3206H	ENST00000268489	NM_006885.3	3206	caG/caT	10/10	1	2	FACETS	0.691	0.552	0.847	0.691	0.552	0.847	SUBCLONAL	1	TRUE	1	0.430147013877646	2		511	175	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827427	72827428	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	47	710	0	ENST00000268489.5:c.9153dup	p.Val3052SerfsTer2	p.V3052Sfs*2	ENST00000268489	NM_006885.3	3051	-/A	9/10	1	2	FACETS	0.748	0.635	0.872	0.748	0.635	0.872	SUBCLONAL	1	TRUE	1	0.430147013877646	2		710	292	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831172	72831172	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	37	559	0	ENST00000268489.5:c.5409del	p.Ser1804ValfsTer10	p.S1804Vfs*10	ENST00000268489	NM_006885.3	1803	ccC/cc	9/10	1	2	FACETS	0.723	0.6	0.858	0.723	0.6	0.858	SUBCLONAL	1	TRUE	1	0.430147013877646	2		559	238	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984430	72984430	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	41	678	2	ENST00000268489.5:c.3154C>A	p.Leu1052Met	p.L1052M	ENST00000268489	NM_006885.3	1052	Ctg/Atg	3/10	1	2	FACETS	0.635	0.532	0.75	0.635	0.532	0.75	SUBCLONAL	1	TRUE	1	0.430147013877646	2		680	300	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991503	72991503	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	46	829	0	ENST00000268489.5:c.2542C>A	p.Leu848Met	p.L848M	ENST00000268489	NM_006885.3	848	Ctg/Atg	2/10	1	2	FACETS	0.658	0.557	0.769	0.658	0.557	0.769	SUBCLONAL	1	TRUE	1	0.430147013877646	2		829	325	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991698	72991698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775988108	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	38	482	0	ENST00000268489.5:c.2347G>A	p.Ala783Thr	p.A783T	ENST00000268489	NM_006885.3	783	Gca/Aca	2/10	1	2	FACETS	0.826	0.689	0.975	0.826	0.689	0.975	CLONAL	1	TRUE	1	0.430147013877646	2		482	214	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992417	72992417	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	53	858	0	ENST00000268489.5:c.1628T>C	p.Leu543Pro	p.L543P	ENST00000268489	NM_006885.3	543	cTg/cCg	2/10	1	2	FACETS	0.686	0.588	0.794	0.686	0.588	0.794	SUBCLONAL	1	TRUE	1	0.430147013877646	2		858	359	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993872	72993872	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	38	512	0	ENST00000268489.5:c.173A>T	p.Asn58Ile	p.N58I	ENST00000268489	NM_006885.3	58	aAt/aTt	2/10	1	2	FACETS	0.775	0.646	0.917	0.775	0.646	0.917	CLONAL	1	TRUE	1	0.430147013877646	2		512	228	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925195	81925195	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	64	483	0	ENST00000359376.3:c.986C>T	p.Thr329Met	p.T329M	ENST00000359376	NM_002661.3	329	aCg/aTg	11/33	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.430147013877646	2		483	236	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953145	81953145	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	48	388	0	ENST00000359376.3:c.2111T>C	p.Leu704Pro	p.L704P	ENST00000359376	NM_002661.3	704	cTg/cCg	20/33	1	2	FACETS	0.815	0.693	0.946	0.815	0.693	0.946	CLONAL	1	TRUE	1	0.430147013877646	2		388	274	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81960686	81960686	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	22	410	0	ENST00000359376.3:c.2418-1G>A		p.X806_splice	ENST00000359376	NM_002661.3	806			1	2	FACETS	0.568	0.443	0.711	0.568	0.443	0.711	SUBCLONAL	1	TRUE	1	0.430147013877646	2		410	180	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81971483	81971483	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	50	424	0	ENST00000359376.3:c.3173A>T	p.Lys1058Met	p.K1058M	ENST00000359376	NM_002661.3	1058	aAg/aTg	28/33	1	2	FACETS	0.998	0.855	1	0.998	0.855	1	CLONAL	1	TRUE	1	0.430147013877646	2		424	233	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346777	89346777	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	28	395	0	ENST00000301030.4:c.6173C>A	p.Pro2058His	p.P2058H	ENST00000301030	NM_001256183.1	2058	cCt/cAt	9/13	1	2	FACETS	0.731	0.59	0.889	0.731	0.59	0.889	SUBCLONAL	1	TRUE	1	0.430147013877646	2		395	178	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348038	89348038	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs113527563	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	44	966	0	ENST00000301030.4:c.4912C>G	p.Pro1638Ala	p.P1638A	ENST00000301030	NM_001256183.1	1638	Cct/Gct	9/13	1	2	FACETS	0.662	0.558	0.776	0.662	0.558	0.776	SUBCLONAL	1	TRUE	1	0.430147013877646	2		966	309	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350431	89350431	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149776253	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	54	818	1	ENST00000301030.4:c.2519G>A	p.Arg840Gln	p.R840Q	ENST00000301030	NM_001256183.1	840	cGg/cAg	9/13	1	2	FACETS	0.745	0.64	0.859	0.745	0.64	0.859	SUBCLONAL	1	TRUE	1	0.430147013877646	2		819	337	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89815123	89815123	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	81	550	0	ENST00000389301.3:c.3292G>T	p.Glu1098Ter	p.E1098*	ENST00000389301	NM_000135.2	1098	Gaa/Taa	33/43	1	2	FACETS	0.759	0.679	0.843	1	0.98	1	SUBCLONAL	2	TRUE	1	0.430147013877646	2		550	248	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831311	89831311	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs899634878	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	50	542	0	ENST00000389301.3:c.2765A>G	p.Glu922Gly	p.E922G	ENST00000389301	NM_000135.2	922	gAg/gGg	28/43	1	2	FACETS	0.827	0.707	0.958	0.827	0.707	0.958	CLONAL	1	TRUE	1	0.430147013877646	2		542	281	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838103	89838103	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	85	574	0	ENST00000389301.3:c.2134G>T	p.Glu712Ter	p.E712*	ENST00000389301	NM_000135.2	712	Gag/Tag	23/43	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.430147013877646	2		574	285	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217667	7217667	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	43	552	1	ENST00000380728.2:c.260del	p.Phe87SerfsTer22	p.F87Sfs*22	ENST00000380728		87	tTc/tc	4/11	1	2	FACETS	0.752	0.633	0.881	0.752	0.633	0.881	SUBCLONAL	1	TRUE	1	0.430147013877646	2		553	266	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577138	7577138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780075	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	79	512	0	ENST00000269305.4:c.800G>A	p.Arg267Gln	p.R267Q	ENST00000269305	NM_001126112.2	267	cGg/cAg	8/11	1	2	FACETS	0.753	0.672	0.837	1	0.98	1	SUBCLONAL	2	TRUE	1	0.430147013877646	2		512	244	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1555525367	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	27	444	0	ENST00000269305.4:c.783-1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	0.621	0.498	0.761	0.621	0.498	0.761	SUBCLONAL	1	TRUE	1	0.430147013877646	2		444	202	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs878854073	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	36	532	0	ENST00000269305.4:c.673-1G>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			1	2	FACETS	0.618	0.51	0.737	0.618	0.51	0.737	SUBCLONAL	1	TRUE	1	0.430147013877646	2		532	271	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984293	7984293	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	29	556	1	ENST00000319144.4:c.436T>C	p.Trp146Arg	p.W146R	ENST00000319144	NM_001139.2	146	Tgg/Cgg	4/15	1	2	FACETS	0.621	0.502	0.755	0.621	0.502	0.755	SUBCLONAL	1	TRUE	1	0.430147013877646	2		557	217	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108250	8108250	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	107	568	0	ENST00000585124.1:c.974C>T	p.Pro325Leu	p.P325L	ENST00000585124	NM_004217.3	325	cCt/cTt	9/9	1	2	FACETS	0.832	0.757	0.909	1	0.987	1	CLONAL	2	TRUE	1	0.430147013877646	2		568	299	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15960997	15960997	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	90	440	1	ENST00000268712.3:c.6223C>T	p.Gln2075Ter	p.Q2075*	ENST00000268712	NM_006311.3	2075	Cag/Tag	40/46	1	2	FACETS	0.764	0.687	0.843	1	0.982	1	SUBCLONAL	2	TRUE	1	0.430147013877646	2		441	274	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973493	15973493	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	81	368	0	ENST00000268712.3:c.4499A>G	p.Asn1500Ser	p.N1500S	ENST00000268712	NM_006311.3	1500	aAc/aGc	31/46	1	2	FACETS	0.815	0.73	0.903	1	0.982	1	CLONAL	2	TRUE	1	0.430147013877646	2		368	231	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973623	15973624	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	45	468	1	ENST00000268712.3:c.4368_4369insA	p.Ser1457IlefsTer4	p.S1457Ifs*4	ENST00000268712	NM_006311.3	1456	-/A	31/46	1	2	FACETS	0.719	0.608	0.841	0.719	0.608	0.841	SUBCLONAL	1	TRUE	1	0.430147013877646	2		469	291	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029445	16029446	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	98	541	2	ENST00000268712.3:c.1584dup	p.Glu529ArgfsTer7	p.E529Rfs*7	ENST00000268712	NM_006311.3	528	-/A	15/46	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.430147013877646	2		543	314	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556280	29556280	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	49	587	0	ENST00000356175.3:c.2647T>C	p.Ser883Pro	p.S883P	ENST00000356175	NM_000267.3	883	Tca/Cca	21/57	1	2	FACETS	0.762	0.649	0.884	0.762	0.649	0.884	SUBCLONAL	1	TRUE	1	0.430147013877646	2		587	299	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663652	29663652	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	32	435	0	ENST00000356175.3:c.6085-1G>T		p.X2029_splice	ENST00000356175	NM_000267.3	2029			1	2	FACETS	0.737	0.603	0.885	0.737	0.603	0.885	SUBCLONAL	1	TRUE	1	0.430147013877646	2		435	202	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618483	37618483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	43	480	0	ENST00000447079.4:c.159G>A	p.Met53Ile	p.M53I	ENST00000447079	NM_015083.1	53	atG/atA	1/14	1	2	FACETS	0.905	0.764	1	0.905	0.764	1	CLONAL	1	TRUE	1	0.430147013877646	2		480	221	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619260	37619260	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	29	395	0	ENST00000447079.4:c.936C>A	p.Ser312Arg	p.S312R	ENST00000447079	NM_015083.1	312	agC/agA	1/14	1	2	FACETS	0.61	0.493	0.742	0.61	0.493	0.742	SUBCLONAL	1	TRUE	1	0.430147013877646	2		395	221	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627730	37627730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763665826	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	53	730	0	ENST00000447079.4:c.1645C>T	p.Pro549Ser	p.P549S	ENST00000447079	NM_015083.1	549	Ccc/Tcc	2/14	1	2	FACETS	0.893	0.767	1	0.893	0.767	1	CLONAL	1	TRUE	1	0.430147013877646	2		730	276	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650924	37650924	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	42	469	0	ENST00000447079.4:c.2396C>T	p.Ala799Val	p.A799V	ENST00000447079	NM_015083.1	799	gCa/gTa	5/14	1	2	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	TRUE	1	0.430147013877646	2		469	195	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37856539	37856540	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	32	354	0	ENST00000269571.5:c.54dup	p.Gly19ArgfsTer91	p.G19Rfs*91	ENST00000269571		16	-/C	1/27	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.430147013877646	2		354	134	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359576	40359576	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	87	500	0	ENST00000293328.3:c.2077G>A	p.Ala693Thr	p.A693T	ENST00000293328	NM_012448.3	693	Gct/Act	16/19	0.362898603513773	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.430147013877646	1		500	267	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40443988	40443988	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	59	508	0	ENST00000345506.4:c.286-2A>G		p.X96_splice	ENST00000345506	NM_003152.3	96			0.362898603513773	1	FACETS	0.979	0.854	1	0.979	0.854	1	CLONAL	1	TRUE	0	0.430147013877646	1		508	220	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243487	41243487	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	55	658	0	ENST00000357654.3:c.4061A>T	p.Asn1354Ile	p.N1354I	ENST00000357654	NM_007294.3	1354	aAt/aTt	10/23	0.362898603513773	1	FACETS	0.648	0.557	0.745	0.648	0.557	0.745	SUBCLONAL	1	TRUE	0	0.430147013877646	1		658	310	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243932	41243932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	101	649	1	ENST00000357654.3:c.3616G>A	p.Ala1206Thr	p.A1206T	ENST00000357654	NM_007294.3	1206	Gcc/Acc	10/23	0.362898603513773	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.430147013877646	1		650	291	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244818	41244818	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	105	782	0	ENST00000357654.3:c.2730del	p.Gly911GlufsTer89	p.G911Efs*89	ENST00000357654	NM_007294.3	910	caA/ca	10/23	0.362898603513773	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.430147013877646	1		782	270	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245087	41245087	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	52	826	0	ENST00000357654.3:c.2461G>T	p.Asp821Tyr	p.D821Y	ENST00000357654	NM_007294.3	821	Gat/Tat	10/23	0.362898603513773	1	FACETS	0.563	0.482	0.652	0.563	0.482	0.652	SUBCLONAL	1	TRUE	0	0.430147013877646	1		826	337	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246282	41246282	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	47	609	0	ENST00000357654.3:c.1266T>A	p.Tyr422Ter	p.Y422*	ENST00000357654	NM_007294.3	422	taT/taA	10/23	0.362898603513773	1	FACETS	0.645	0.548	0.75	0.645	0.548	0.75	SUBCLONAL	1	TRUE	0	0.430147013877646	1		609	266	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758286312	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	56	621	0	ENST00000407977.2:c.349C>T	p.Arg117Cys	p.R117C	ENST00000407977		117	Cgc/Tgc	3/10	1	2	FACETS	0.907	0.783	1	0.907	0.783	1	CLONAL	1	TRUE	1	0.430147013877646	2		621	287	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740629	58740629	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	39	579	0	ENST00000305921.3:c.1534A>C	p.Asn512His	p.N512H	ENST00000305921	NM_003620.3	512	Aat/Cat	6/6	0.330731520347077	1	FACETS	0.591	0.493	0.698	0.591	0.493	0.698	SUBCLONAL	1	TRUE	0	0.430147013877646	1		579	241	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760660	59760660	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	57	524	0	ENST00000259008.2:c.3747G>T	p.Lys1249Asn	p.K1249N	ENST00000259008	NM_032043.2	1249	aaG/aaT	20/20	0.330731520347077	1	FACETS	0.825	0.716	0.943	0.825	0.716	0.943	CLONAL	1	TRUE	0	0.430147013877646	1		524	252	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926535	59926535	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	35	651	0	ENST00000259008.2:c.462del	p.Gln155LysfsTer2	p.Q155Kfs*2	ENST00000259008	NM_032043.2	154	ttT/tt	5/20	0.330731520347077	1	FACETS	0.478	0.394	0.572	0.478	0.394	0.572	SUBCLONAL	1	TRUE	0	0.430147013877646	1		651	267	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59934491	59934491	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs777068696	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	50	542	0	ENST00000259008.2:c.307G>T	p.Gly103Ter	p.G103*	ENST00000259008	NM_032043.2	103	Gga/Tga	4/20	0.330731520347077	1	FACETS	0.647	0.553	0.749	0.647	0.553	0.749	SUBCLONAL	1	TRUE	0	0.430147013877646	1		542	282	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530029	63530029	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	59	443	0	ENST00000307078.5:c.2405+1G>A		p.X802_splice	ENST00000307078	NM_004655.3	802			0.330731520347077	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.430147013877646	1		443	166	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66522016	66522016	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1568698504	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	35	271	0	ENST00000358598.2:c.671G>A	p.Trp224Ter	p.W224*	ENST00000358598	NM_212471.2	224	tGg/tAg	7/11	1	2	FACETS	0.736	0.608	0.878	0.736	0.608	0.878	SUBCLONAL	1	TRUE	1	0.430147013877646	2		271	221	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796094	78796094	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	30	435	1	ENST00000306801.3:c.988del	p.Arg330GlyfsTer28	p.R330Gfs*28	ENST00000306801	NM_020761.2	328	ctC/ct	8/34	1	2	FACETS	0.694	0.563	0.839	0.694	0.563	0.839	SUBCLONAL	1	TRUE	1	0.430147013877646	2		436	201	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899281	78899281	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	42	486	1	ENST00000306801.3:c.2919+1G>A		p.X973_splice	ENST00000306801	NM_020761.2	973			1	2	FACETS	0.775	0.652	0.91	0.775	0.652	0.91	CLONAL	1	TRUE	1	0.430147013877646	2		487	252	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743290	743290	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	41	605	0	ENST00000314574.4:c.850G>T	p.Gly284Ter	p.G284*	ENST00000314574	NM_005433.3	284	Gga/Tga	7/12	0.330731520347077	1	FACETS	0.578	0.484	0.68	0.578	0.484	0.68	SUBCLONAL	1	TRUE	0	0.430147013877646	1		605	259	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39620668	39620668	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	92	473	0	ENST00000262039.4:c.2066C>A	p.Pro689His	p.P689H	ENST00000262039	NM_002647.2	689	cCt/cAt	19/25	0.330731520347077	1	FACETS	0.803	0.73	0.878	1	0.985	1	CLONAL	2	TRUE	0	0.430147013877646	1		473	209	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584806	48584806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370176106	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	34	418	0	ENST00000342988.3:c.884C>T	p.Pro295Leu	p.P295L	ENST00000342988	NM_005359.5	295	cCg/cTg	7/12	0.330731520347077	1	FACETS	0.47	0.386	0.564	0.47	0.386	0.564	SUBCLONAL	1	TRUE	0	0.430147013877646	1		418	264	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	43	541	0	ENST00000342988.3:c.1067C>A	p.Pro356His	p.P356H	ENST00000342988	NM_005359.5	356	cCt/cAt	9/12	0.330731520347077	1	FACETS	0.668	0.564	0.781	0.668	0.564	0.781	SUBCLONAL	1	TRUE	0	0.430147013877646	1		541	235	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985722	60985722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	18	193	1	ENST00000333681.4:c.178G>A	p.Ala60Thr	p.A60T	ENST00000333681		60	Gcc/Acc	2/3	0.330731520347077	1	FACETS	0.966	0.748	1	0.966	0.748	1	CLONAL	1	TRUE	0	0.430147013877646	1		194	68	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226606	1226606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253803683	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	53	448	0	ENST00000326873.7:c.1262G>A	p.Ser421Asn	p.S421N	ENST00000326873	NM_000455.4	421	aGc/aAc	9/10	1	2	FACETS	0.811	0.707	0.919	1	0.974	1	CLONAL	2	TRUE	1	0.430147013877646	2		448	152	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2194560	2194560	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1444512111	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	71	429	0	ENST00000398665.3:c.635A>C	p.Lys212Thr	p.K212T	ENST00000398665	NM_032482.2	212	aAg/aCg	7/28	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.430147013877646	2		429	228	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211173	2211173	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	32	735	0	ENST00000398665.3:c.1427T>C	p.Leu476Pro	p.L476P	ENST00000398665	NM_032482.2	476	cTg/cCg	15/28	1	2	FACETS	0.722	0.591	0.868	0.722	0.591	0.868	SUBCLONAL	1	TRUE	1	0.430147013877646	2		735	206	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222254	2222254	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	46	726	0	ENST00000398665.3:c.3086C>A	p.Pro1029His	p.P1029H	ENST00000398665	NM_032482.2	1029	cCc/cAc	24/28	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.430147013877646	2		726	210	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223375	2223376	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	40	598	0	ENST00000398665.3:c.3492dup	p.Val1165ArgfsTer28	p.V1165Rfs*28	ENST00000398665	NM_032482.2	1162	-/C	25/28	1	2	FACETS	0.753	0.63	0.888	0.753	0.63	0.888	SUBCLONAL	1	TRUE	1	0.430147013877646	2		598	247	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110315	3110315	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	67	531	0	ENST00000078429.4:c.305A>G	p.Lys102Arg	p.K102R	ENST00000078429	NM_002067.2	102	aAg/aGg	2/7	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.430147013877646	2		531	231	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121089	3121089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	38	672	1	ENST00000078429.4:c.992C>T	p.Ala331Val	p.A331V	ENST00000078429	NM_002067.2	331	gCc/gTc	7/7	1	2	FACETS	0.81	0.676	0.958	0.81	0.676	0.958	CLONAL	1	TRUE	1	0.430147013877646	2		673	218	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267754	7267754	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	61	612	0	ENST00000302850.5:c.254C>A	p.Thr85Asn	p.T85N	ENST00000302850	NM_000208.2	85	aCt/aAt	2/22	1	2	FACETS	0.903	0.785	1	0.903	0.785	1	CLONAL	1	TRUE	1	0.430147013877646	2		612	314	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248552	10248552	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1323856557	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	34	671	1	ENST00000340748.4:c.4201C>T	p.Arg1401Trp	p.R1401W	ENST00000340748		1401	Cgg/Tgg	35/40	1	2	FACETS	0.764	0.629	0.912	0.764	0.629	0.912	CLONAL	1	TRUE	1	0.430147013877646	2		672	207	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265406	10265406	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	48	643	0	ENST00000340748.4:c.1640A>T	p.Glu547Val	p.E547V	ENST00000340748		547	gAg/gTg	20/40	1	2	FACETS	0.713	0.606	0.83	0.713	0.606	0.83	SUBCLONAL	1	TRUE	1	0.430147013877646	2		643	313	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10305521	10305521	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	17	496	0	ENST00000340748.4:c.55T>C	p.Ser19Pro	p.S19P	ENST00000340748		19	Tcg/Ccg	1/40	1	2	FACETS	0.693	0.524	0.889	0.693	0.524	0.889	SUBCLONAL	1	TRUE	1	0.430147013877646	2		496	114	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610243	10610243	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	64	719	0	ENST00000171111.5:c.467T>C	p.Met156Thr	p.M156T	ENST00000171111	NM_203500.1	156	aTg/aCg	2/6	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.430147013877646	2		719	240	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11018721	11018721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748146066	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	51	625	0	ENST00000327064.4:c.353G>A	p.Cys118Tyr	p.C118Y	ENST00000327064	NM_199141.1	118	tGt/tAt	3/16	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.430147013877646	2		625	233	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031222	11031222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	40	663	0	ENST00000327064.4:c.1307G>A	p.Gly436Glu	p.G436E	ENST00000327064	NM_199141.1	436	gGg/gAg	11/16	1	2	FACETS	0.732	0.612	0.864	0.732	0.612	0.864	SUBCLONAL	1	TRUE	1	0.430147013877646	2		663	254	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113714	11113714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	38	498	0	ENST00000358026.2:c.1822G>A	p.Glu608Lys	p.E608K	ENST00000358026	NM_001128849.1	608	Gag/Aag	12/36	1	2	FACETS	0.73	0.608	0.865	0.73	0.608	0.865	SUBCLONAL	1	TRUE	1	0.430147013877646	2		498	242	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168942	11168942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057523566	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	49	420	0	ENST00000358026.2:c.4532G>A	p.Arg1511His	p.R1511H	ENST00000358026	NM_001128849.1	1511	cGt/cAt	32/36	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.430147013877646	2		420	181	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170480	11170480	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	35	622	0	ENST00000358026.2:c.4786del	p.Ile1596SerfsTer32	p.I1596Sfs*32	ENST00000358026	NM_001128849.1	1595	Aaa/aa	34/36	1	2	FACETS	0.633	0.522	0.757	0.633	0.522	0.757	SUBCLONAL	1	TRUE	1	0.430147013877646	2		622	257	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050961	13050961	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	44	478	2	ENST00000316448.5:c.492G>T	p.Lys164Asn	p.K164N	ENST00000316448	NM_004343.3	164	aaG/aaT	4/9	1	2	FACETS	0.793	0.67	0.927	0.793	0.67	0.927	CLONAL	1	TRUE	1	0.430147013877646	2		480	258	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054352	13054352	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	62	483	0	ENST00000316448.5:c.962T>C	p.Val321Ala	p.V321A	ENST00000316448	NM_004343.3	321	gTc/gCc	8/9	1	2	FACETS	0.977	0.851	1	0.977	0.851	1	CLONAL	1	TRUE	1	0.430147013877646	2		483	295	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376268	15376268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536634033	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	32	581	0	ENST00000263377.2:c.746C>T	p.Thr249Met	p.T249M	ENST00000263377	NM_058243.2	249	aCg/aTg	5/20	1	2	FACETS	0.641	0.524	0.772	0.641	0.524	0.772	SUBCLONAL	1	TRUE	1	0.430147013877646	2		581	232	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17389660	17389660	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	65	511	0	ENST00000359435.4:c.793T>G	p.Phe265Val	p.F265V	ENST00000359435	NM_001033549.1	265	Ttt/Gtt	9/9	1	2	FACETS	0.791	0.699	0.887	1	0.977	1	SUBCLONAL	2	TRUE	1	0.430147013877646	2		511	191	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951077	17951077	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	25	570	0	ENST00000458235.1:c.1216C>T	p.Gln406Ter	p.Q406*	ENST00000458235	NM_000215.3	406	Cag/Tag	9/24	1	2	FACETS	0.578	0.458	0.714	0.578	0.458	0.714	SUBCLONAL	1	TRUE	1	0.430147013877646	2		570	201	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273092	18273092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	40	564	0	ENST00000222254.8:c.982G>A	p.Ala328Thr	p.A328T	ENST00000222254	NM_005027.3	328	Gct/Act	8/16	1	2	FACETS	0.762	0.638	0.898	0.762	0.638	0.898	SUBCLONAL	1	TRUE	1	0.430147013877646	2		564	244	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279284	18279284	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	28	415	0	ENST00000222254.8:c.1737-1G>T		p.X579_splice	ENST00000222254	NM_005027.3	579			1	2	FACETS	0.664	0.535	0.809	0.664	0.535	0.809	SUBCLONAL	1	TRUE	1	0.430147013877646	2		415	196	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212521	36212521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	32	792	0	ENST00000222270.7:c.2272C>T	p.Pro758Ser	p.P758S	ENST00000222270	NM_014727.1	758	Cca/Tca	3/37	1	2	FACETS	0.633	0.517	0.763	0.633	0.517	0.763	SUBCLONAL	1	TRUE	1	0.430147013877646	2		792	235	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212537	36212537	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs370359238	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	37	805	0	ENST00000222270.7:c.2288C>A	p.Pro763Gln	p.P763Q	ENST00000222270	NM_014727.1	763	cCg/cAg	3/37	1	2	FACETS	0.635	0.526	0.755	0.635	0.526	0.755	SUBCLONAL	1	TRUE	1	0.430147013877646	2		805	271	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213573	36213573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1236115722	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	98	865	0	ENST00000222270.7:c.2675G>A	p.Arg892His	p.R892H	ENST00000222270	NM_014727.1	892	cGc/cAc	5/37	1	2	FACETS	0.901	0.817	0.986	1	0.987	1	CLONAL	2	TRUE	1	0.430147013877646	2		865	253	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222811	36222811	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	36	648	0	ENST00000222270.7:c.5444del	p.Pro1815GlnfsTer80	p.P1815Qfs*80	ENST00000222270	NM_014727.1	1814	Ccc/cc	27/37	1	2	FACETS	0.741	0.613	0.881	0.741	0.613	0.881	SUBCLONAL	1	TRUE	1	0.430147013877646	2		648	226	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223962	36223962	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	36	791	1	ENST00000222270.7:c.6512G>T	p.Gly2171Val	p.G2171V	ENST00000222270	NM_014727.1	2171	gGg/gTg	28/37	1	2	FACETS	0.609	0.503	0.726	0.609	0.503	0.726	SUBCLONAL	1	TRUE	1	0.430147013877646	2		792	275	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224039	36224039	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	46	809	0	ENST00000222270.7:c.6589C>A	p.Leu2197Met	p.L2197M	ENST00000222270	NM_014727.1	2197	Ctg/Atg	28/37	1	2	FACETS	0.767	0.65	0.894	0.767	0.65	0.894	SUBCLONAL	1	TRUE	1	0.430147013877646	2		809	279	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748585	40748585	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	33	541	0	ENST00000392038.2:c.297G>A	p.Trp99Ter	p.W99*	ENST00000392038	NM_001626.4	99	tgG/tgA	5/14	1	2	FACETS	0.745	0.612	0.892	0.745	0.612	0.892	SUBCLONAL	1	TRUE	1	0.430147013877646	2		541	206	SUCCESS
AXL	558	MSKCC	GRCh37	19	41736887	41736887	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	34	642	0	ENST00000301178.4:c.602C>T	p.Ser201Phe	p.S201F	ENST00000301178	NM_021913.4	201	tCc/tTc	5/20	1	2	FACETS	0.76	0.626	0.908	0.76	0.626	0.908	CLONAL	1	TRUE	1	0.430147013877646	2		642	208	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383075	42383075	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	52	363	2	ENST00000221972.3:c.95C>T	p.Ala32Val	p.A32V	ENST00000221972	NM_021601.3	32	gCc/gTc	2/5	1	2	FACETS	0.756	0.656	0.86	1	0.97	1	SUBCLONAL	2	TRUE	1	0.430147013877646	2		365	160	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383153	42383153	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	42	633	0	ENST00000221972.3:c.173G>T	p.Ser58Ile	p.S58I	ENST00000221972	NM_021601.3	58	aGc/aTc	2/5	1	2	FACETS	0.74	0.622	0.869	0.74	0.622	0.869	SUBCLONAL	1	TRUE	1	0.430147013877646	2		633	264	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795269	42795269	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	51	638	0	ENST00000575354.2:c.2349G>T	p.Gln783His	p.Q783H	ENST00000575354	NM_015125.3	783	caG/caT	10/20	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.430147013877646	2		638	236	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795886	42795886	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1568520020	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	97	749	0	ENST00000575354.2:c.2880del	p.Ser961AlafsTer6	p.S961Afs*6	ENST00000575354	NM_015125.3	959	Ccc/cc	11/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.430147013877646	2		749	307	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798348	42798348	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	37	647	0	ENST00000575354.2:c.4219C>T	p.Pro1407Ser	p.P1407S	ENST00000575354	NM_015125.3	1407	Ccc/Tcc	18/20	1	2	FACETS	0.748	0.621	0.887	0.748	0.621	0.887	SUBCLONAL	1	TRUE	1	0.430147013877646	2		647	230	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858035	45858035	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	97	656	0	ENST00000391945.4:c.1618A>G	p.Thr540Ala	p.T540A	ENST00000391945	NM_000400.3	540	Acc/Gcc	17/23	1	2	FACETS	0.993	0.904	1	1	0.988	1	CLONAL	2	TRUE	1	0.430147013877646	2		656	227	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867068	45867068	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	30	569	1	ENST00000391945.4:c.1051C>T	p.Gln351Ter	p.Q351*	ENST00000391945	NM_000400.3	351	Cag/Tag	11/23	1	2	FACETS	0.802	0.653	0.967	0.802	0.653	0.967	CLONAL	1	TRUE	1	0.430147013877646	2		570	174	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902244	50902244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	58	743	0	ENST00000440232.2:c.136G>A	p.Ala46Thr	p.A46T	ENST00000440232	NM_002691.3	46	Gca/Aca	2/27	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.430147013877646	2		743	239	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905055	50905055	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568618739	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	30	527	0	ENST00000440232.2:c.337G>A	p.Gly113Arg	p.G113R	ENST00000440232	NM_002691.3	113	Ggg/Agg	4/27	1	2	FACETS	0.674	0.547	0.816	0.674	0.547	0.816	SUBCLONAL	1	TRUE	1	0.430147013877646	2		527	207	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52709251	52709252	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	42	486	0	ENST00000322088.6:c.205_206insA	p.Leu69HisfsTer55	p.L69Hfs*55	ENST00000322088	NM_014225.5	69	ctg/cAtg	3/15	1	2	FACETS	0.794	0.668	0.931	0.794	0.668	0.931	CLONAL	1	TRUE	1	0.430147013877646	2		486	246	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52709254	52709254	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	36	475	2	ENST00000322088.6:c.208G>T	p.Ala70Ser	p.A70S	ENST00000322088	NM_014225.5	70	Gca/Tca	3/15	1	2	FACETS	0.68	0.563	0.81	0.68	0.563	0.81	SUBCLONAL	1	TRUE	1	0.430147013877646	2		477	246	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464544	25464544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368961181	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	37	648	0	ENST00000264709.3:c.1969G>A	p.Val657Met	p.V657M	ENST00000264709	NM_175629.2	657	Gtg/Atg	17/23	1	2	FACETS	0.688	0.571	0.818	0.688	0.571	0.818	SUBCLONAL	1	TRUE	1	0.430147013877646	2		648	250	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467446	25467446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	39	624	0	ENST00000264709.3:c.1630C>T	p.Arg544Cys	p.R544C	ENST00000264709	NM_175629.2	544	Cgt/Tgt	14/23	1	2	FACETS	0.746	0.623	0.882	0.746	0.623	0.882	SUBCLONAL	1	TRUE	1	0.430147013877646	2		624	243	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451823	29451823	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	61	595	1	ENST00000389048.3:c.2742del	p.Trp915GlyfsTer24	p.W915Gfs*24	ENST00000389048	NM_004304.4	914	ggG/gg	16/29	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.430147013877646	2		596	216	SUCCESS
ALK	238	MSKCC	GRCh37	2	29541264	29541264	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	48	359	0	ENST00000389048.3:c.1553C>T	p.Ala518Val	p.A518V	ENST00000389048	NM_004304.4	518	gCt/gTt	8/29	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.430147013877646	2		359	183	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46602874	46602874	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	53	662	0	ENST00000263734.3:c.932C>T	p.Ala311Val	p.A311V	ENST00000263734	NM_001430.4	311	gCa/gTa	8/16	0.359575936743278	0	FACETS	0.605	0.522	0.695			1	SUBCLONAL	1	TRUE	0	0.430147013877646	0		662	232	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145714	61145714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	40	380	0	ENST00000295025.8:c.826G>A	p.Asp276Asn	p.D276N	ENST00000295025	NM_002908.2	276	Gat/Aat	7/11	1	2	FACETS	0.816	0.684	0.96	0.816	0.684	0.96	CLONAL	1	TRUE	1	0.430147013877646	2		380	228	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61711149	61711149	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	46	471	0	ENST00000401558.2:c.2600C>A	p.Pro867Gln	p.P867Q	ENST00000401558	NM_003400.3	867	cCa/cAa	21/25	1	2	FACETS	0.986	0.839	1	0.986	0.839	1	CLONAL	1	TRUE	1	0.430147013877646	2		471	217	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61722619	61722619	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	70	371	0	ENST00000401558.2:c.1018del	p.Arg340AspfsTer2	p.R340Dfs*2	ENST00000401558	NM_003400.3	340	Aga/ga	11/25	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.430147013877646	2		371	231	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61760939	61760939	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	53	537	0	ENST00000401558.2:c.94G>A	p.Val32Met	p.V32M	ENST00000401558	NM_003400.3	32	Gtg/Atg	2/25	1	2	FACETS	0.982	0.845	1	0.982	0.845	1	CLONAL	1	TRUE	1	0.430147013877646	2		537	251	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919560	96919560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756910411	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	41	519	0	ENST00000258439.3:c.703G>A	p.Ala235Thr	p.A235T	ENST00000258439	NM_001193304.2	235	Gct/Act	4/4	1	2	FACETS	0.878	0.739	1	0.878	0.739	1	CLONAL	1	TRUE	1	0.430147013877646	2		519	217	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881498	111881498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	38	510	0	ENST00000393256.3:c.176G>A	p.Ser59Asn	p.S59N	ENST00000393256	NM_006538.4	59	aGc/aAc	2/4	1	2	FACETS	0.636	0.528	0.754	0.636	0.528	0.754	SUBCLONAL	1	TRUE	1	0.430147013877646	2		510	278	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617532	158617532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	60	467	0	ENST00000263640.3:c.1124G>A	p.Arg375His	p.R375H	ENST00000263640	NM_001105.4	375	cGt/cAt	9/11	1	2	FACETS	0.754	0.653	0.863	0.754	0.653	0.863	SUBCLONAL	1	TRUE	1	0.430147013877646	2		467	370	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095797	178095797	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	53	588	0	ENST00000397062.3:c.1534C>T	p.Gln512Ter	p.Q512*	ENST00000397062	NM_006164.4	512	Cag/Tag	5/5	1	2	FACETS	0.941	0.809	1	0.941	0.809	1	CLONAL	1	TRUE	1	0.430147013877646	2		588	262	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096543	178096543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	28	404	0	ENST00000397062.3:c.788C>T	p.Pro263Leu	p.P263L	ENST00000397062	NM_006164.4	263	cCc/cTc	5/5	1	2	FACETS	0.671	0.54	0.817	0.671	0.54	0.817	SUBCLONAL	1	TRUE	1	0.430147013877646	2		404	194	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190670376	190670376	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs760336651	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	42	366	0	ENST00000441310.2:c.316-2A>G		p.X106_splice	ENST00000441310	NM_000534.4	106			1	2	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	TRUE	1	0.430147013877646	2		366	195	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198263207	198263207	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	58	475	0	ENST00000335508.6:c.3112C>A	p.Leu1038Ile	p.L1038I	ENST00000335508	NM_012433.2	1038	Ctt/Att	21/25	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.430147013877646	2		475	250	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202123034	202123034	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	39	424	0	ENST00000358485.4:c.80C>A	p.Pro27His	p.P27H	ENST00000358485	NM_001080125.1	27	cCt/cAt	1/9	1	2	FACETS	0.684	0.57	0.81	0.684	0.57	0.81	SUBCLONAL	1	TRUE	1	0.430147013877646	2		424	265	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141587	202141587	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	43	360	0	ENST00000358485.4:c.878del	p.Gly293AspfsTer4	p.G293Dfs*4	ENST00000358485	NM_001080125.1	292	cGg/cg	7/9	1	2	FACETS	0.952	0.805	1	0.952	0.805	1	CLONAL	1	TRUE	1	0.430147013877646	2		360	210	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151300	202151300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768375470	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	35	481	0	ENST00000358485.4:c.1600G>A	p.Val534Ile	p.V534I	ENST00000358485	NM_001080125.1	534	Gtc/Atc	9/9	1	2	FACETS	0.592	0.487	0.708	0.592	0.487	0.708	SUBCLONAL	1	TRUE	1	0.430147013877646	2		481	275	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735477	204735477	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	47	492	0	ENST00000302823.3:c.278A>T	p.Asn93Ile	p.N93I	ENST00000302823	NM_005214.4	93	aAt/aTt	2/4	1	2	FACETS	0.837	0.712	0.973	0.837	0.712	0.973	CLONAL	1	TRUE	1	0.430147013877646	2		492	261	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736204	204736205	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	41	411	0	ENST00000302823.3:c.565dup	p.Met189AsnfsTer24	p.M189Nfs*24	ENST00000302823	NM_005214.4	187	-/A	3/4	1	2	FACETS	0.836	0.703	0.982	0.836	0.703	0.982	CLONAL	1	TRUE	1	0.430147013877646	2		411	228	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209101872	209101872	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	47	463	0	ENST00000345146.2:c.1176G>T	p.Leu392Phe	p.L392F	ENST00000345146	NM_005896.2	392	ttG/ttT	10/10	1	2	FACETS	0.942	0.803	1	0.942	0.803	1	CLONAL	1	TRUE	1	0.430147013877646	2		463	232	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104728	209104728	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	44	264	0	ENST00000345146.2:c.851-1G>T		p.X284_splice	ENST00000345146	NM_005896.2	284			1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.430147013877646	2		264	203	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576881	212576881	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	38	459	0	ENST00000342788.4:c.1018G>T	p.Gly340Ter	p.G340*	ENST00000342788	NM_005235.2	340	Gga/Tga	9/28	1	2	FACETS	0.81	0.676	0.958	0.81	0.676	0.958	CLONAL	1	TRUE	1	0.430147013877646	2		459	218	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578331	212578331	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	40	447	0	ENST00000342788.4:c.926C>A	p.Pro309His	p.P309H	ENST00000342788	NM_005235.2	309	cCt/cAt	8/28	1	2	FACETS	0.838	0.702	0.986	0.838	0.702	0.986	CLONAL	1	TRUE	1	0.430147013877646	2		447	222	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645448	215645448	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	95	709	0	ENST00000260947.4:c.1150T>A	p.Ser384Thr	p.S384T	ENST00000260947	NM_000465.2	384	Tcc/Acc	4/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.430147013877646	2		709	295	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645751	215645751	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	46	637	0	ENST00000260947.4:c.847G>A	p.Ala283Thr	p.A283T	ENST00000260947	NM_000465.2	283	Gct/Act	4/11	1	2	FACETS	0.842	0.715	0.98	0.842	0.715	0.98	CLONAL	1	TRUE	1	0.430147013877646	2		637	254	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646084	215646085	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs746325928	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	58	678	1	ENST00000260947.4:c.513dup	p.Asp172ArgfsTer10	p.D172Rfs*10	ENST00000260947	NM_000465.2	171	-/A	4/11	1	2	FACETS	0.94	0.814	1	0.94	0.814	1	CLONAL	1	TRUE	1	0.430147013877646	2		679	287	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439938	220439938	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	44	808	0	ENST00000243786.2:c.791G>T	p.Arg264Ile	p.R264I	ENST00000243786	NM_002191.3	264	aGa/aTa	2/2	1	2	FACETS	0.822	0.694	0.96	0.822	0.694	0.96	CLONAL	1	TRUE	1	0.430147013877646	2		808	249	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755078884	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	58	542	0	ENST00000305123.5:c.1103C>T	p.Pro368Leu	p.P368L	ENST00000305123	NM_005544.2	368	cCg/cTg	1/2	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.430147013877646	2		542	184	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663068	227663070	+	frameshift_variant	Frame_Shift_Del	DEL	CGC	CGC	AG	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	41	557	3	ENST00000305123.5:c.385_387delinsCT	p.Ala129LeufsTer21	p.A129Lfs*21	ENST00000305123	NM_005544.2	129	GCG/CT	1/2	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.430147013877646	2		560	162	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663070	227663070	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	41	547	0	ENST00000305123.5:c.385del	p.Ala129ArgfsTer21	p.A129Rfs*21	ENST00000305123	NM_005544.2	129	Gcg/cg	1/2	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.430147013877646	2		547	162	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546967	9546968	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	35	395	0	ENST00000353224.5:c.1054dup	p.Arg352LysfsTer79	p.R352Kfs*79	ENST00000353224	NM_177990.2	352	agg/aAgg	5/10	1	2	FACETS	0.75	0.62	0.894	0.75	0.62	0.894	SUBCLONAL	1	TRUE	1	0.430147013877646	2		395	217	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561455	9561455	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	119	554	0	ENST00000353224.5:c.327T>A	p.Asp109Glu	p.D109E	ENST00000353224	NM_177990.2	109	gaT/gaA	4/10	1	2	FACETS	0.777	0.709	0.847	1	0.987	1	SUBCLONAL	2	TRUE	1	0.430147013877646	2		554	356	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624973	9624973	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	19	255	0	ENST00000353224.5:c.4T>A	p.Phe2Ile	p.F2I	ENST00000353224	NM_177990.2	2	Ttt/Att	3/10	1	2	FACETS	0.605	0.463	0.769	0.605	0.463	0.769	SUBCLONAL	1	TRUE	1	0.430147013877646	2		255	146	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016162	31016162	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	45	547	0	ENST00000375687.4:c.408T>A	p.Cys136Ter	p.C136*	ENST00000375687	NM_015338.5	136	tgT/tgA	6/13	1	2	FACETS	0.742	0.627	0.867	0.742	0.627	0.867	SUBCLONAL	1	TRUE	1	0.430147013877646	2		547	282	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023835	31023835	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	36	645	0	ENST00000375687.4:c.3320T>A	p.Leu1107His	p.L1107H	ENST00000375687	NM_015338.5	1107	cTt/cAt	13/13	1	2	FACETS	0.611	0.505	0.729	0.611	0.505	0.729	SUBCLONAL	1	TRUE	1	0.430147013877646	2		645	274	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024805	31024805	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	34	657	0	ENST00000375687.4:c.4293del	p.Ser1432ProfsTer18	p.S1432Pfs*18	ENST00000375687	NM_015338.5	1430	ctC/ct	13/13	1	2	FACETS	0.592	0.486	0.71	0.592	0.486	0.71	SUBCLONAL	1	TRUE	1	0.430147013877646	2		657	267	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388713	31388713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	43	595	0	ENST00000328111.2:c.1978G>A	p.Ala660Thr	p.A660T	ENST00000328111	NM_006892.3	660	Gcc/Acc	18/23	1	2	FACETS	0.823	0.694	0.963	0.823	0.694	0.963	CLONAL	1	TRUE	1	0.430147013877646	2		595	243	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030004	36030004	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	44	599	0	ENST00000358208.4:c.1040-1G>T		p.X347_splice	ENST00000358208		347			1	2	FACETS	0.842	0.712	0.983	0.842	0.712	0.983	CLONAL	1	TRUE	1	0.430147013877646	2		599	243	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030982	36030982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	42	585	0	ENST00000358208.4:c.1261G>A	p.Ala421Thr	p.A421T	ENST00000358208		421	Gcg/Acg	10/12	1	2	FACETS	0.804	0.676	0.943	0.804	0.676	0.943	CLONAL	1	TRUE	1	0.430147013877646	2		585	243	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39725870	39725870	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	82	375	1	ENST00000361337.2:c.741G>A	p.Met247Ile	p.M247I	ENST00000361337	NM_003286.2	247	atG/atA	10/21	1	2	FACETS	0.912	0.82	1	1	0.985	1	CLONAL	2	TRUE	1	0.430147013877646	2		376	209	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741444	39741444	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	37	321	0	ENST00000361337.2:c.1331A>T	p.Tyr444Phe	p.Y444F	ENST00000361337	NM_003286.2	444	tAc/tTc	14/21	1	2	FACETS	0.732	0.608	0.869	0.732	0.608	0.869	SUBCLONAL	1	TRUE	1	0.430147013877646	2		321	235	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713373	40713373	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	69	626	0	ENST00000373198.4:c.4142A>T	p.Lys1381Met	p.K1381M	ENST00000373198	NM_133170.3	1381	aAg/aTg	30/32	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.430147013877646	2		626	246	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419846	41419846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	41	358	0	ENST00000373198.4:c.475C>T	p.His159Tyr	p.H159Y	ENST00000373198	NM_133170.3	159	Cat/Tat	3/32	1	2	FACETS	0.811	0.681	0.953	0.811	0.681	0.953	CLONAL	1	TRUE	1	0.430147013877646	2		358	235	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264965	46264965	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	36	454	0	ENST00000371998.3:c.1835C>A	p.Pro612His	p.P612H	ENST00000371998		612	cCt/cAt	12/23	1	2	FACETS	0.747	0.619	0.888	0.747	0.619	0.888	SUBCLONAL	1	TRUE	1	0.430147013877646	2		454	224	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485416	57485416	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1418870137	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	36	367	0	ENST00000371085.3:c.998G>A	p.Arg333His	p.R333H	ENST00000371085	NM_000516.4	333	cGc/cAc	12/13	1	2	FACETS	0.646	0.534	0.77	0.646	0.534	0.77	SUBCLONAL	1	TRUE	1	0.430147013877646	2		367	259	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62320462	62320462	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	38	539	0	ENST00000360203.5:c.1855T>C	p.Phe619Leu	p.F619L	ENST00000360203	NM_001283009.1	619	Ttc/Ctc	22/35	1	2	FACETS	0.724	0.603	0.858	0.724	0.603	0.858	SUBCLONAL	1	TRUE	1	0.430147013877646	2		539	244	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62322170	62322170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	64	576	2	ENST00000360203.5:c.2426C>T	p.Ala809Val	p.A809V	ENST00000360203	NM_001283009.1	809	gCc/gTc	27/35	1	2	FACETS	0.827	0.73	0.926	1	0.978	1	CLONAL	2	TRUE	1	0.430147013877646	2		578	180	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324205	62324205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	52	710	1	ENST00000360203.5:c.2700G>A	p.Met900Ile	p.M900I	ENST00000360203	NM_001283009.1	900	atG/atA	29/35	1	2	FACETS	0.879	0.754	1	0.879	0.754	1	CLONAL	1	TRUE	1	0.430147013877646	2		711	275	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231876	36231877	+	splice_acceptor_variant	Splice_Site	INS	-	-	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	32	421	0	ENST00000300305.3:c.509-2_509-1insT		p.X170_splice	ENST00000300305		170			1	2	FACETS	0.715	0.585	0.86	0.715	0.585	0.86	SUBCLONAL	1	TRUE	1	0.430147013877646	2		421	208	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44527577	44527577	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	32	439	0	ENST00000291552.4:c.28G>T	p.Gly10Cys	p.G10C	ENST00000291552	NM_006758.2	10	Ggc/Tgc	1/8	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.430147013877646	2		439	107	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091749	29091749	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1435731482	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	15	279	0	ENST00000328354.6:c.1208G>T	p.Gly403Val	p.G403V	ENST00000328354	NM_007194.3	403	gGg/gTg	11/15	1	2	FACETS	0.652	0.482	0.85	0.652	0.482	0.85	SUBCLONAL	1	TRUE	1	0.430147013877646	2		279	107	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29106022	29106022	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	45	444	0	ENST00000328354.6:c.818A>G	p.Glu273Gly	p.E273G	ENST00000328354	NM_007194.3	273	gAa/gGa	7/15	1	2	FACETS	0.745	0.63	0.87	0.745	0.63	0.87	SUBCLONAL	1	TRUE	1	0.430147013877646	2		444	281	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30061043	30061043	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	41	436	0	ENST00000338641.4:c.875T>C	p.Val292Ala	p.V292A	ENST00000338641	NM_000268.3	292	gTt/gCt	9/16	1	2	FACETS	0.706	0.592	0.832	0.706	0.592	0.832	SUBCLONAL	1	TRUE	1	0.430147013877646	2		436	270	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37628018	37628018	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	34	541	0	ENST00000249071.6:c.242G>A	p.Cys81Tyr	p.C81Y	ENST00000249071	NM_002872.4	81	tGc/tAc	4/7	1	2	FACETS	0.779	0.642	0.93	0.779	0.642	0.93	CLONAL	1	TRUE	1	0.430147013877646	2		541	203	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574140	41574140	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	45	486	1	ENST00000263253.7:c.6425G>T	p.Arg2142Met	p.R2142M	ENST00000263253	NM_001429.3	2142	aGg/aTg	31/31	1	2	FACETS	0.955	0.811	1	0.955	0.811	1	CLONAL	1	TRUE	1	0.430147013877646	2		487	219	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12393125	12393125	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	54	625	0	ENST00000287820.6:c.34C>A	p.Pro12Thr	p.P12T	ENST00000287820	NM_015869.4	12	Cca/Aca	1/7	1	2	FACETS	0.747	0.641	0.862	0.747	0.641	0.862	SUBCLONAL	1	TRUE	1	0.430147013877646	2		625	336	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458316	12458316	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	63	652	0	ENST00000287820.6:c.933G>T	p.Gln311His	p.Q311H	ENST00000287820	NM_015869.4	311	caG/caT	6/7	1	2	FACETS	0.864	0.752	0.984	0.864	0.752	0.984	CLONAL	1	TRUE	1	0.430147013877646	2		652	339	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626351	12626352	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	38	598	0	ENST00000251849.4:c.1797dup	p.Pro600SerfsTer8	p.P600Sfs*8	ENST00000251849	NM_002880.3	599	-/T	16/17	1	2	FACETS	0.62	0.515	0.736	0.62	0.515	0.736	SUBCLONAL	1	TRUE	1	0.430147013877646	2		598	285	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691842	30691842	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	46	419	0	ENST00000295754.5:c.344A>T	p.Asp115Val	p.D115V	ENST00000295754	NM_003242.5	115	gAt/gTt	3/7	1	2	FACETS	0.852	0.723	0.992	0.852	0.723	0.992	CLONAL	1	TRUE	1	0.430147013877646	2		419	251	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691872	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs79375991	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	147	413	23	ENST00000295754.5:c.383del	p.Lys128SerfsTer35	p.K128Sfs*35	ENST00000295754	NM_003242.5	125	gAa/ga	3/7	1	2	FACETS	0.904	0.847	0.961	1	0.994	1	CLONAL	3	TRUE	1	0.430147013877646	2		436	252	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182023	38182023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	57	597	0	ENST00000396334.3:c.647G>A	p.Cys216Tyr	p.C216Y	ENST00000396334	NM_002468.4	216	tGt/tAt	3/5	1	2	FACETS	0.95	0.822	1	0.95	0.822	1	CLONAL	1	TRUE	1	0.430147013877646	2		597	279	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103819	47103819	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	48	491	0	ENST00000409792.3:c.6127G>A	p.Asp2043Asn	p.D2043N	ENST00000409792	NM_014159.6	2043	Gat/Aat	14/21	1	2	FACETS	0.875	0.746	1	0.875	0.746	1	CLONAL	1	TRUE	1	0.430147013877646	2		491	255	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162680	47162680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757222335	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	50	532	0	ENST00000409792.3:c.3446G>A	p.Ser1149Asn	p.S1149N	ENST00000409792	NM_014159.6	1149	aGt/aAt	3/21	1	2	FACETS	0.802	0.685	0.928	0.802	0.685	0.928	CLONAL	1	TRUE	1	0.430147013877646	2		532	290	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163377	47163377	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	85	468	0	ENST00000409792.3:c.2749del	p.Ser917ValfsTer5	p.S917Vfs*5	ENST00000409792	NM_014159.6	917	Agt/gt	3/21	1	2	FACETS	0.763	0.684	0.845	1	0.981	1	SUBCLONAL	2	TRUE	1	0.430147013877646	2		468	259	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164475	47164475	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	93	408	0	ENST00000409792.3:c.1651A>G	p.Ser551Gly	p.S551G	ENST00000409792	NM_014159.6	551	Agt/Ggt	3/21	1	2	FACETS	0.996	0.905	1	1	0.988	1	CLONAL	2	TRUE	1	0.430147013877646	2		408	217	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165492	47165492	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368670205	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	39	581	0	ENST00000409792.3:c.634G>A	p.Val212Met	p.V212M	ENST00000409792	NM_014159.6	212	Gtg/Atg	3/21	1	2	FACETS	0.623	0.519	0.738	0.623	0.519	0.738	SUBCLONAL	1	TRUE	1	0.430147013877646	2		581	291	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165581	47165581	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	44	686	0	ENST00000409792.3:c.545C>A	p.Thr182Asn	p.T182N	ENST00000409792	NM_014159.6	182	aCt/aAt	3/21	1	2	FACETS	0.605	0.509	0.711	0.605	0.509	0.711	SUBCLONAL	1	TRUE	1	0.430147013877646	2		686	338	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933177	49933177	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	33	545	0	ENST00000296474.3:c.2933T>C	p.Phe978Ser	p.F978S	ENST00000296474	NM_002447.2	978	tTc/tCc	12/20	1	2	FACETS	0.72	0.591	0.863	0.72	0.591	0.863	SUBCLONAL	1	TRUE	1	0.430147013877646	2		545	213	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598140	52598140	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	53	615	0	ENST00000394830.3:c.3726G>T	p.Gln1242His	p.Q1242H	ENST00000394830	NM_018313.4	1242	caG/caT	24/30	1	2	FACETS	0.941	0.809	1	0.941	0.809	1	CLONAL	1	TRUE	1	0.430147013877646	2		615	262	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643375	52643375	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	74	489	0	ENST00000394830.3:c.2521C>T	p.Gln841Ter	p.Q841*	ENST00000394830	NM_018313.4	841	Caa/Taa	17/30	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.430147013877646	2		489	293	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102824	71102824	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	44	383	0	ENST00000318789.4:c.383T>C	p.Val128Ala	p.V128A	ENST00000318789	NM_032682.5	128	gTt/gCt	8/21	1	2	FACETS	0.763	0.644	0.893	0.763	0.644	0.893	SUBCLONAL	1	TRUE	1	0.430147013877646	2		383	268	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427651	72427651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	57	440	0	ENST00000477973.2:c.839C>T	p.Ala280Val	p.A280V	ENST00000477973	NM_012234.5	280	gCa/gTa	4/4	1	2	FACETS	0.872	0.753	0.999	0.872	0.753	0.999	CLONAL	1	TRUE	1	0.430147013877646	2		440	304	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259614	89259614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	96	362	0	ENST00000336596.2:c.758C>T	p.Pro253Leu	p.P253L	ENST00000336596	NM_005233.5	253	cCc/cTc	3/17	1	2	FACETS	0.789	0.712	0.867	1	0.984	1	SUBCLONAL	2	TRUE	1	0.430147013877646	2		362	283	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480484	89480484	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	29	331	0	ENST00000336596.2:c.2321A>G	p.Asp774Gly	p.D774G	ENST00000336596	NM_005233.5	774	gAc/gGc	13/17	1	2	FACETS	0.61	0.493	0.742	0.61	0.493	0.742	SUBCLONAL	1	TRUE	1	0.430147013877646	2		331	221	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119721060	119721060	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	58	511	0	ENST00000316626.5:c.115A>T	p.Thr39Ser	p.T39S	ENST00000316626		39	Aca/Tca	2/12	1	2	FACETS	0.917	0.794	1	0.917	0.794	1	CLONAL	1	TRUE	1	0.430147013877646	2		511	294	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880965	134880965	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	61	527	0	ENST00000398015.3:c.1528A>G	p.Thr510Ala	p.T510A	ENST00000398015	NM_004441.4	510	Act/Gct	7/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.430147013877646	2		527	225	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138431131	138431131	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	35	410	0	ENST00000289153.2:c.1318T>C	p.Trp440Arg	p.W440R	ENST00000289153	NM_006219.2	440	Tgg/Cgg	8/22	1	2	FACETS	0.736	0.608	0.878	0.736	0.608	0.878	SUBCLONAL	1	TRUE	1	0.430147013877646	2		410	221	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433399	138433399	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	51	665	0	ENST00000289153.2:c.1213del	p.Tyr405MetfsTer7	p.Y405Mfs*7	ENST00000289153	NM_006219.2	405	Tat/at	7/22	1	2	FACETS	0.916	0.785	1	0.916	0.785	1	CLONAL	1	TRUE	1	0.430147013877646	2		665	259	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665183	138665183	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	26	678	0	ENST00000330315.3:c.382T>A	p.Trp128Arg	p.W128R	ENST00000330315	NM_023067.3	128	Tgg/Agg	1/1	1	2	FACETS	0.687	0.549	0.842	0.687	0.549	0.842	SUBCLONAL	1	TRUE	1	0.430147013877646	2		678	176	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665462	138665462	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	28	541	0	ENST00000330315.3:c.103G>T	p.Gly35Cys	p.G35C	ENST00000330315	NM_023067.3	35	Ggc/Tgc	1/1	1	2	FACETS	0.74	0.597	0.899	0.74	0.597	0.899	SUBCLONAL	1	TRUE	1	0.430147013877646	2		541	176	SUCCESS
ATR	545	MSKCC	GRCh37	3	142168281	142168281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	50	426	0	ENST00000350721.4:c.7925C>T	p.Pro2642Leu	p.P2642L	ENST00000350721	NM_001184.3	2642	cCa/cTa	47/47	1	2	FACETS	0.867	0.742	1	0.867	0.742	1	CLONAL	1	TRUE	1	0.430147013877646	2		426	268	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217584	142217584	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	34	516	0	ENST00000350721.4:c.5413G>T	p.Gly1805Ter	p.G1805*	ENST00000350721	NM_001184.3	1805	Gga/Tga	32/47	1	2	FACETS	0.696	0.573	0.833	0.696	0.573	0.833	SUBCLONAL	1	TRUE	1	0.430147013877646	2		516	227	SUCCESS
ATR	545	MSKCC	GRCh37	3	142224079	142224079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761194898	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	36	592	0	ENST00000350721.4:c.5098C>T	p.Pro1700Ser	p.P1700S	ENST00000350721	NM_001184.3	1700	Cca/Tca	29/47	1	2	FACETS	0.634	0.524	0.756	0.634	0.524	0.756	SUBCLONAL	1	TRUE	1	0.430147013877646	2		592	264	SUCCESS
ATR	545	MSKCC	GRCh37	3	142257439	142257439	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	39	380	0	ENST00000350721.4:c.3610G>T	p.Asp1204Tyr	p.D1204Y	ENST00000350721	NM_001184.3	1204	Gat/Tat	19/47	1	2	FACETS	0.868	0.726	1	0.868	0.726	1	CLONAL	1	TRUE	1	0.430147013877646	2		380	209	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149290773	149290774	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	43	464	0	ENST00000360632.3:c.445dup	p.Ile149AsnfsTer8	p.I149Nfs*8	ENST00000360632	NM_015472.4	149	atc/aAtc	3/7	1	2	FACETS	0.735	0.619	0.862	0.735	0.619	0.862	SUBCLONAL	1	TRUE	1	0.430147013877646	2		464	272	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998127	169998128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs753143066	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	41	633	6	ENST00000295797.4:c.826dup	p.Thr276AsnfsTer16	p.T276Nfs*16	ENST00000295797	NM_002740.5	273	tta/ttAa	9/18	1	2	FACETS	0.669	0.56	0.788	0.669	0.56	0.788	SUBCLONAL	1	TRUE	1	0.430147013877646	2		639	285	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170002304	170002304	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	16	170	0	ENST00000295797.4:c.1123A>G	p.Ile375Val	p.I375V	ENST00000295797	NM_002740.5	375	Att/Gtt	12/18	1	2	FACETS	0.875	0.659	1	0.875	0.659	1	CLONAL	1	TRUE	1	0.430147013877646	2		170	85	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928101	178928101	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	84	528	0	ENST00000263967.3:c.1379G>A	p.Gly460Asp	p.G460D	ENST00000263967	NM_006218.2	460	gGt/gAt	8/21	1	2	FACETS	0.831	0.746	0.918	1	0.984	1	CLONAL	2	TRUE	1	0.430147013877646	2		528	235	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430452	181430452	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	26	635	1	ENST00000325404.1:c.304A>G	p.Met102Val	p.M102V	ENST00000325404	NM_003106.3	102	Atg/Gtg	1/1	1	2	FACETS	0.568	0.452	0.698	0.568	0.452	0.698	SUBCLONAL	1	TRUE	1	0.430147013877646	2		636	213	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502362	186502362	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	91	400	0	ENST00000323963.5:c.85A>G	p.Asn29Asp	p.N29D	ENST00000323963		29	Aat/Gat	3/11	0.300142853067812	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	1	0.430147013877646	3		400	239	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444640	187444640	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	54	506	0	ENST00000232014.4:c.1587G>T	p.Glu529Asp	p.E529D	ENST00000232014	NM_001130845.1	529	gaG/gaT	7/10	0.300142853067812	3	FACETS	1	0.937	1	0.58	0.5	0.666	CLONAL	1	TRUE	1	0.430147013877646	3		506	263	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447385	187447385	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	47	680	0	ENST00000232014.4:c.808C>T	p.Arg270Ter	p.R270*	ENST00000232014	NM_001130845.1	270	Cga/Tga	5/10	0.300142853067812	3	FACETS	0.876	0.744	1	0.438	0.372	0.511	CLONAL	1	TRUE	1	0.430147013877646	3		680	303	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447552	187447552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs911074942	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	88	515	0	ENST00000232014.4:c.641G>A	p.Arg214Gln	p.R214Q	ENST00000232014	NM_001130845.1	214	cGg/cAg	5/10	0.300142853067812	3	FACETS	1	0.913	1	1	0.913	1	CLONAL	2	TRUE	1	0.430147013877646	3		515	245	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590742	189590742	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	91	539	0	ENST00000264731.3:c.1307G>A	p.Arg436Lys	p.R436K	ENST00000264731	NM_003722.4	436	aGg/aAg	10/14	0.300142853067812	3	FACETS	0.974	0.878	1	0.974	0.878	1	CLONAL	2	TRUE	1	0.430147013877646	3		539	264	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808856	1808856	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	42	685	0	ENST00000260795.2:c.2288T>C	p.Leu763Pro	p.L763P	ENST00000260795		763	cTg/cCg	17/17	1	2	FACETS	0.838	0.706	0.982	0.838	0.706	0.982	CLONAL	1	TRUE	1	0.430147013877646	2		685	233	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1918709	1918709	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	34	342	0	ENST00000382891.5:c.876del	p.Lys292AsnfsTer20	p.K292Nfs*20	ENST00000382891	NM_133335.3	291	gAa/ga	4/22	1	2	FACETS	0.67	0.551	0.802	0.67	0.551	0.802	SUBCLONAL	1	TRUE	1	0.430147013877646	2		342	236	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1941480	1941480	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	37	443	0	ENST00000382891.5:c.1856C>A	p.Pro619His	p.P619H	ENST00000382891	NM_133335.3	619	cCt/cAt	9/22	1	2	FACETS	0.649	0.538	0.772	0.649	0.538	0.772	SUBCLONAL	1	TRUE	1	0.430147013877646	2		443	265	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957915	1957915	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	50	339	0	ENST00000382891.5:c.2881G>A	p.Ala961Thr	p.A961T	ENST00000382891	NM_133335.3	961	Gca/Aca	15/22	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.430147013877646	2		339	188	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1976686	1976686	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	56	628	0	ENST00000382891.5:c.3469G>A	p.Gly1157Arg	p.G1157R	ENST00000382891	NM_133335.3	1157	Ggg/Agg	19/22	1	2	FACETS	0.845	0.729	0.971	0.845	0.729	0.971	CLONAL	1	TRUE	1	0.430147013877646	2		628	308	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141132	55141132	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	98	392	0	ENST00000257290.5:c.1778T>C	p.Leu593Pro	p.L593P	ENST00000257290	NM_006206.4	593	cTa/cCa	12/23	1	2	FACETS	0.897	0.814	0.982	1	0.987	1	CLONAL	2	TRUE	1	0.430147013877646	2		392	254	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594228	55594228	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	69	525	1	ENST00000288135.5:c.1931T>C	p.Leu644Pro	p.L644P	ENST00000288135	NM_000222.2	644	cTg/cCg	13/21	1	2	FACETS	0.806	0.715	0.9	1	0.979	1	CLONAL	2	TRUE	1	0.430147013877646	2		526	199	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594289	55594289	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	47	508	0	ENST00000288135.5:c.1990+2T>C		p.X664_splice	ENST00000288135	NM_000222.2	664			1	2	FACETS	0.822	0.698	0.955	0.822	0.698	0.955	CLONAL	1	TRUE	1	0.430147013877646	2		508	266	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964423	55964423	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	32	483	0	ENST00000263923.4:c.2390T>C	p.Leu797Pro	p.L797P	ENST00000263923	NM_002253.2	797	cTg/cCg	17/30	1	2	FACETS	0.57	0.465	0.688	0.57	0.465	0.688	SUBCLONAL	1	TRUE	1	0.430147013877646	2		483	261	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157335	106157336	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	34	391	0	ENST00000380013.4:c.2241dup	p.Leu748IlefsTer6	p.L748Ifs*6	ENST00000380013	NM_001127208.2	746	caa/cAaa	3/11	1	2	FACETS	0.709	0.583	0.848	0.709	0.583	0.848	SUBCLONAL	1	TRUE	1	0.430147013877646	2		391	223	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190830	106190830	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	44	526	0	ENST00000380013.4:c.4108G>T	p.Gly1370Trp	p.G1370W	ENST00000380013	NM_001127208.2	1370	Ggg/Tgg	9/11	1	2	FACETS	0.718	0.605	0.841	0.718	0.605	0.841	SUBCLONAL	1	TRUE	1	0.430147013877646	2		526	285	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197493	106197493	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	30	320	0	ENST00000380013.4:c.5826G>T	p.Gln1942His	p.Q1942H	ENST00000380013	NM_001127208.2	1942	caG/caT	11/11	1	2	FACETS	0.655	0.531	0.793	0.655	0.531	0.793	SUBCLONAL	1	TRUE	1	0.430147013877646	2		320	213	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197553	106197554	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	38	381	0	ENST00000380013.4:c.5887dup	p.Thr1963AsnfsTer52	p.T1963Nfs*52	ENST00000380013	NM_001127208.2	1962	-/A	11/11	1	2	FACETS	0.727	0.605	0.861	0.727	0.605	0.861	SUBCLONAL	1	TRUE	1	0.430147013877646	2		381	243	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247348	153247348	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	29	300	0	ENST00000281708.4:c.1454T>G	p.Val485Gly	p.V485G	ENST00000281708	NM_033632.3	485	gTt/gGt	10/12	1	2	FACETS	0.671	0.542	0.814	0.671	0.542	0.814	SUBCLONAL	1	TRUE	1	0.430147013877646	2		300	201	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518153	187518153	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	43	514	0	ENST00000441802.2:c.12541G>A	p.Glu4181Lys	p.E4181K	ENST00000441802	NM_005245.3	4181	Gaa/Aaa	25/27	1	2	FACETS	0.813	0.685	0.951	0.813	0.685	0.951	CLONAL	1	TRUE	1	0.430147013877646	2		514	246	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534484	187534484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748020206	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	40	283	1	ENST00000441802.2:c.9242C>T	p.Thr3081Met	p.T3081M	ENST00000441802	NM_005245.3	3081	aCg/aTg	13/27	1	2	FACETS	0.857	0.719	1	0.857	0.719	1	CLONAL	1	TRUE	1	0.430147013877646	2		284	217	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538976	187538976	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	45	558	0	ENST00000441802.2:c.8764A>C	p.Ile2922Leu	p.I2922L	ENST00000441802	NM_005245.3	2922	Atc/Ctc	10/27	1	2	FACETS	0.717	0.606	0.838	0.717	0.606	0.838	SUBCLONAL	1	TRUE	1	0.430147013877646	2		558	292	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540935	187540935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	38	369	0	ENST00000441802.2:c.6805G>A	p.Val2269Met	p.V2269M	ENST00000441802	NM_005245.3	2269	Gtg/Atg	10/27	1	2	FACETS	0.762	0.634	0.901	0.762	0.634	0.901	CLONAL	1	TRUE	1	0.430147013877646	2		369	232	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557208	187557208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	38	436	0	ENST00000441802.2:c.4154C>T	p.Pro1385Leu	p.P1385L	ENST00000441802	NM_005245.3	1385	cCt/cTt	6/27	1	2	FACETS	0.707	0.588	0.837	0.707	0.588	0.837	SUBCLONAL	1	TRUE	1	0.430147013877646	2		436	250	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628407	187628407	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	61	782	0	ENST00000441802.2:c.2575T>C	p.Tyr859His	p.Y859H	ENST00000441802	NM_005245.3	859	Tac/Cac	2/27	1	2	FACETS	0.711	0.615	0.814	0.711	0.615	0.814	SUBCLONAL	1	TRUE	1	0.430147013877646	2		782	399	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629391	187629391	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	119	644	1	ENST00000441802.2:c.1591C>T	p.Pro531Ser	p.P531S	ENST00000441802	NM_005245.3	531	Cct/Tct	2/27	1	2	FACETS	0.762	0.695	0.831	1	0.986	1	SUBCLONAL	2	TRUE	1	0.430147013877646	2		645	363	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410867	31410867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	61	564	0	ENST00000344624.3:c.3653C>T	p.Ala1218Val	p.A1218V	ENST00000344624		1218	gCg/gTg	28/33	1	2	FACETS	0.852	0.739	0.972	0.852	0.739	0.972	CLONAL	1	TRUE	1	0.430147013877646	2		564	333	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31422952	31422952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	60	604	0	ENST00000344624.3:c.3361G>A	p.Val1121Ile	p.V1121I	ENST00000344624		1121	Gtt/Att	26/33	1	2	FACETS	0.982	0.854	1	0.982	0.854	1	CLONAL	1	TRUE	1	0.430147013877646	2		604	284	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526684	31526684	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	39	737	0	ENST00000344624.3:c.356C>A	p.Pro119His	p.P119H	ENST00000344624		119	cCc/cAc	2/33	1	2	FACETS	0.708	0.591	0.838	0.708	0.591	0.838	SUBCLONAL	1	TRUE	1	0.430147013877646	2		737	256	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35857163	35857163	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	18	339	0	ENST00000303115.3:c.82+2T>C		p.X28_splice	ENST00000303115	NM_002185.3	28			1	2	FACETS	0.562	0.426	0.719	0.562	0.426	0.719	SUBCLONAL	1	TRUE	1	0.430147013877646	2		339	149	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874580	35874580	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	45	580	0	ENST00000303115.3:c.736A>C	p.Ser246Arg	p.S246R	ENST00000303115	NM_002185.3	246	Agc/Cgc	6/8	1	2	FACETS	0.769	0.651	0.898	0.769	0.651	0.898	SUBCLONAL	1	TRUE	1	0.430147013877646	2		580	272	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958932	38958932	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	28	227	0	ENST00000357387.3:c.2180C>T	p.Ala727Val	p.A727V	ENST00000357387	NM_152756.3	727	gCc/gTc	23/38	1	2	FACETS	0.957	0.777	1	0.957	0.777	1	CLONAL	1	TRUE	1	0.430147013877646	2		227	136	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178257	56178258	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	59	357	0	ENST00000399503.3:c.3236dup	p.Asn1079LysfsTer2	p.N1079Kfs*2	ENST00000399503	NM_005921.1	1077	tca/tcAa	14/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.430147013877646	2		357	211	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750769	57750769	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	97	445	0	ENST00000274289.3:c.1835T>C	p.Leu612Pro	p.L612P	ENST00000274289	NM_006622.3	612	cTa/cCa	13/14	1	2	FACETS	0.891	0.808	0.976	1	0.987	1	CLONAL	2	TRUE	1	0.430147013877646	2		445	253	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569766	67569766	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	40	372	0	ENST00000274335.5:c.428-1G>T		p.X143_splice	ENST00000274335		143			1	2	FACETS	0.842	0.706	0.99	0.842	0.706	0.99	CLONAL	1	TRUE	1	0.430147013877646	2		372	221	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588995	67588996	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	41	317	0	ENST00000274335.5:c.1090dup	p.Met364AsnfsTer4	p.M364Nfs*4	ENST00000274335		362	-/A	8/15	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.430147013877646	2		317	183	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	39	293	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	0.84	0.702	0.989	0.84	0.702	0.989	CLONAL	1	TRUE	1	0.430147013877646	2		293	216	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80063751	80063751	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	80	417	0	ENST00000265081.6:c.1897-1G>A		p.X633_splice	ENST00000265081	NM_002439.4	633			1	2	FACETS	0.857	0.768	0.948	1	0.983	1	CLONAL	2	TRUE	1	0.430147013877646	2		417	217	SUCCESS
APC	324	MSKCC	GRCh37	5	112111360	112111360	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	29	189	0	ENST00000257430.4:c.457A>C	p.Lys153Gln	p.K153Q	ENST00000257430	NM_000038.5	153	Aag/Cag	5/16	1	2	FACETS	0.899	0.731	1	0.899	0.731	1	CLONAL	1	TRUE	1	0.430147013877646	2		189	150	SUCCESS
APC	324	MSKCC	GRCh37	5	112116493	112116493	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	46	251	0	ENST00000257430.4:c.539del	p.Leu180TyrfsTer5	p.L180Yfs*5	ENST00000257430	NM_000038.5	180	Tta/ta	6/16	1	2	FACETS	0.823	0.71	0.94	1	0.97	1	CLONAL	2	TRUE	1	0.430147013877646	2		251	130	SUCCESS
APC	324	MSKCC	GRCh37	5	112137060	112137060	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	33	367	0	ENST00000257430.4:c.814G>T	p.Ala272Ser	p.A272S	ENST00000257430	NM_000038.5	272	Gca/Tca	8/16	1	2	FACETS	0.597	0.489	0.718	0.597	0.489	0.718	SUBCLONAL	1	TRUE	1	0.430147013877646	2		367	257	SUCCESS
APC	324	MSKCC	GRCh37	5	112176291	112176291	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	38	330	2	ENST00000257430.4:c.5000A>T	p.Asn1667Ile	p.N1667I	ENST00000257430	NM_000038.5	1667	aAt/aTt	16/16	1	2	FACETS	0.822	0.685	0.971	0.822	0.685	0.971	CLONAL	1	TRUE	1	0.430147013877646	2		332	215	SUCCESS
APC	324	MSKCC	GRCh37	5	112177341	112177341	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	42	343	0	ENST00000257430.4:c.6050C>T	p.Thr2017Ile	p.T2017I	ENST00000257430	NM_000038.5	2017	aCc/aTc	16/16	1	2	FACETS	0.778	0.654	0.913	0.778	0.654	0.913	CLONAL	1	TRUE	1	0.430147013877646	2		343	251	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927650	131927650	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	84	318	0	ENST00000265335.6:c.1722del	p.Lys574AsnfsTer24	p.K574Nfs*24	ENST00000265335		573	Aaa/aa	11/25	1	2	FACETS	1	0.951	1	1	0.988	1	CLONAL	2	TRUE	1	0.430147013877646	2		318	181	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131938996	131938996	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	39	272	0	ENST00000265335.6:c.2212A>C	p.Ser738Arg	p.S738R	ENST00000265335		738	Agc/Cgc	14/25	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.430147013877646	2		272	121	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439313	149439313	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	40	646	0	ENST00000286301.3:c.2082G>T	p.Glu694Asp	p.E694D	ENST00000286301	NM_005211.3	694	gaG/gaT	15/22	1	2	FACETS	0.781	0.654	0.92	0.781	0.654	0.92	CLONAL	1	TRUE	1	0.430147013877646	2		646	238	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149465968	149465968	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	47	796	0	ENST00000286301.3:c.23T>C	p.Leu8Pro	p.L8P	ENST00000286301	NM_005211.3	8	cTc/cCc	2/22	1	2	FACETS	0.888	0.756	1	0.888	0.756	1	CLONAL	1	TRUE	1	0.430147013877646	2		796	246	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495446	149495446	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	35	764	0	ENST00000261799.4:c.3201G>T	p.Gln1067His	p.Q1067H	ENST00000261799	NM_002609.3	1067	caG/caT	23/23	1	2	FACETS	0.651	0.537	0.778	0.651	0.537	0.778	SUBCLONAL	1	TRUE	1	0.430147013877646	2		764	250	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502765	149502765	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	72	489	2	ENST00000261799.4:c.2024-1G>T		p.X675_splice	ENST00000261799	NM_002609.3	675			1	2	FACETS	0.771	0.685	0.861	1	0.979	1	SUBCLONAL	2	TRUE	1	0.430147013877646	2		491	217	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518058	176518058	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	51	667	0	ENST00000292408.4:c.557del	p.Lys186ArgfsTer25	p.K186Rfs*25	ENST00000292408	NM_213647.1	186	Aag/ag	5/18	1	2	FACETS	0.753	0.643	0.871	0.753	0.643	0.871	SUBCLONAL	1	TRUE	1	0.430147013877646	2		667	315	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519663	176519663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	47	632	0	ENST00000292408.4:c.935G>A	p.Ser312Asn	p.S312N	ENST00000292408	NM_213647.1	312	aGc/aAc	8/18	1	2	FACETS	0.896	0.762	1	0.896	0.762	1	CLONAL	1	TRUE	1	0.430147013877646	2		632	244	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631187	176631187	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	38	486	0	ENST00000439151.2:c.1130G>A	p.Trp377Ter	p.W377*	ENST00000439151	NM_022455.4	377	tGg/tAg	4/23	1	2	FACETS	0.674	0.561	0.8	0.674	0.561	0.8	SUBCLONAL	1	TRUE	1	0.430147013877646	2		486	262	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638085	176638085	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	66	636	0	ENST00000439151.2:c.2685T>A	p.Ser895Arg	p.S895R	ENST00000439151	NM_022455.4	895	agT/agA	5/23	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.430147013877646	2		636	298	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720840	176720840	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	40	495	0	ENST00000439151.2:c.6471G>A	p.Trp2157Ter	p.W2157*	ENST00000439151	NM_022455.4	2157	tgG/tgA	23/23	1	2	FACETS	0.718	0.6	0.847	0.718	0.6	0.847	SUBCLONAL	1	TRUE	1	0.430147013877646	2		495	259	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722110	176722110	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	87	427	0	ENST00000439151.2:c.7741A>G	p.Lys2581Glu	p.K2581E	ENST00000439151	NM_022455.4	2581	Aag/Gag	23/23	1	2	FACETS	0.769	0.691	0.85	1	0.982	1	SUBCLONAL	2	TRUE	1	0.430147013877646	2		427	263	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036960	180036960	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	104	643	0	ENST00000261937.6:c.3752G>T	p.Arg1251Met	p.R1251M	ENST00000261937	NM_182925.4	1251	aGg/aTg	28/30	1	2	FACETS	0.952	0.868	1	1	0.989	1	CLONAL	2	TRUE	1	0.430147013877646	2		643	254	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397241	397241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	21	276	0	ENST00000380956.4:c.626C>T	p.Ala209Val	p.A209V	ENST00000380956	NM_001195286.1	209	gCt/gTt	5/9	NA	3	FACETS	0.746	0.579	0.937			1	INDETERMINATE	1	TRUE	NA	0.430147013877646	3		276	159	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20486929	20486929	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	29	312	0	ENST00000346618.3:c.894T>A	p.Tyr298Ter	p.Y298*	ENST00000346618	NM_001949.4	298	taT/taA	5/7	NA	3	FACETS	0.719	0.58	0.874			1	INDETERMINATE	1	TRUE	NA	0.430147013877646	3		312	228	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056260	26056260	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	45	568	0	ENST00000343677.2:c.397G>A	p.Gly133Arg	p.G133R	ENST00000343677	NM_005319.3	133	Ggg/Agg	1/1	0.208489092606192	4	FACETS	1	0.932	1	0.397	0.336	0.464	INDETERMINATE	1	TRUE	1	0.430147013877646	4		568	251	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056349	26056349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201295771	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	37	438	2	ENST00000343677.2:c.308G>A	p.Gly103Asp	p.G103D	ENST00000343677	NM_005319.3	103	gGc/gAc	1/1	0.208489092606192	4	FACETS	1	0.85	1	0.342	0.283	0.406	INDETERMINATE	1	TRUE	1	0.430147013877646	4		440	240	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056568	26056568	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	24	252	0	ENST00000343677.2:c.89del	p.Gly30ValfsTer33	p.G30Vfs*33	ENST00000343677	NM_005319.3	30	gGt/gt	1/1	0.208489092606192	4	FACETS	0.997	0.79	1	0.332	0.263	0.411	INDETERMINATE	1	TRUE	1	0.430147013877646	4		252	160	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158709	26158709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs752085869	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	23	261	0	ENST00000289316.2:c.316del	p.Glu106SerfsTer29	p.E106Sfs*29	ENST00000289316	NM_138720.2	104	ccG/cc	1/2	0.208489092606192	4	FACETS	0.944	0.756	1	0.629	0.504	0.766	INDETERMINATE	2	TRUE	1	0.430147013877646	4		261	81	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225384	26225384	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	13	155	0	ENST00000360408.1:c.2T>C	p.Met1?	p.M1?	ENST00000360408	NM_003532.2	1	aTg/aCg	1/1	0.208489092606192	4	FACETS	0.8	0.577	1	0.267	0.192	0.356	INDETERMINATE	1	TRUE	1	0.430147013877646	4		155	108	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30676084	30676084	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	32	418	0	ENST00000376406.3:c.2272A>T	p.Arg758Ter	p.R758*	ENST00000376406	NM_014641.2	758	Aga/Tga	8/15	1	2	FACETS	0.598	0.487	0.72	0.598	0.487	0.72	SUBCLONAL	1	TRUE	1	0.430147013877646	2		418	249	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681829	30681829	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs774216207	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	37	580	2	ENST00000376406.3:c.268C>T	p.Arg90Ter	p.R90*	ENST00000376406	NM_014641.2	90	Cga/Tga	3/15	1	2	FACETS	0.63	0.522	0.75	0.63	0.522	0.75	SUBCLONAL	1	TRUE	1	0.430147013877646	2		582	273	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172069	32172069	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	42	735	0	ENST00000375023.3:c.2963G>T	p.Gly988Val	p.G988V	ENST00000375023	NM_004557.3	988	gGa/gTa	19/30	1	2	FACETS	0.737	0.619	0.866	0.737	0.619	0.866	SUBCLONAL	1	TRUE	1	0.430147013877646	2		735	265	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180262	32180262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	39	501	0	ENST00000375023.3:c.2669C>T	p.Ala890Val	p.A890V	ENST00000375023	NM_004557.3	890	gCa/gTa	17/30	1	2	FACETS	0.824	0.689	0.972	0.824	0.689	0.972	CLONAL	1	TRUE	1	0.430147013877646	2		501	220	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813386	32813386	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	50	820	0	ENST00000354258.4:c.2397G>A	p.Met799Ile	p.M799I	ENST00000354258	NM_000593.5	799	atG/atA	11/11	1	2	FACETS	0.67	0.571	0.778	0.67	0.571	0.778	SUBCLONAL	1	TRUE	1	0.430147013877646	2		820	347	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813402	32813402	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	116	799	0	ENST00000354258.4:c.2381G>A	p.Gly794Glu	p.G794E	ENST00000354258	NM_000593.5	794	gGg/gAg	11/11	1	2	FACETS	0.793	0.723	0.865	1	0.987	1	SUBCLONAL	2	TRUE	1	0.430147013877646	2		799	340	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32814886	32814886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	60	726	0	ENST00000354258.4:c.2179G>A	p.Asp727Asn	p.D727N	ENST00000354258	NM_000593.5	727	Gat/Aat	10/11	1	2	FACETS	0.779	0.675	0.892	0.779	0.675	0.892	SUBCLONAL	1	TRUE	1	0.430147013877646	2		726	358	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790819	89790819	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	20	634	4	ENST00000336032.3:c.211del	p.Gln71SerfsTer112	p.Q71Sfs*112	ENST00000336032	NM_006813.2	69	aCc/ac	1/2	1	2	FACETS	0.669	0.517	0.843	0.669	0.517	0.843	SUBCLONAL	1	TRUE	1	0.430147013877646	2		638	139	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793754	89793755	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	41	425	0	ENST00000336032.3:c.827dup	p.Glu277GlyfsTer9	p.E277Gfs*9	ENST00000336032	NM_006813.2	275	caa/cAaa	2/2	1	2	FACETS	0.753	0.632	0.886	0.753	0.632	0.886	SUBCLONAL	1	TRUE	1	0.430147013877646	2		425	253	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956685	93956685	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	39	358	1	ENST00000369303.4:c.2551G>T	p.Glu851Ter	p.E851*	ENST00000369303	NM_004440.3	851	Gaa/Taa	15/17	1	2	FACETS	0.847	0.709	0.999	0.847	0.709	0.999	CLONAL	1	TRUE	1	0.430147013877646	2		359	214	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553015	106553015	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	99	591	0	ENST00000369096.4:c.984del	p.Ile329PhefsTer49	p.I329Ffs*49	ENST00000369096	NM_001198.3	327	tCc/tc	5/7	1	2	FACETS	0.906	0.823	0.991	1	0.987	1	CLONAL	2	TRUE	1	0.430147013877646	2		591	254	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109322549	109322549	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1243042829	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	56	661	0	ENST00000436639.2:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000436639	NM_014454.2	163	tAt/tGt	3/10	1	2	FACETS	0.711	0.612	0.819	0.711	0.612	0.819	SUBCLONAL	1	TRUE	1	0.430147013877646	2		661	366	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015699	112015699	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	47	533	0	ENST00000368678.4:c.1143G>T	p.Met381Ile	p.M381I	ENST00000368678		381	atG/atT	11/13	1	2	FACETS	0.769	0.653	0.896	0.769	0.653	0.896	SUBCLONAL	1	TRUE	1	0.430147013877646	2		533	284	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710947	117710947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767371570	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	38	385	0	ENST00000368508.3:c.1325G>A	p.Arg442Gln	p.R442Q	ENST00000368508	NM_002944.2	442	cGg/cAg	12/43	1	2	FACETS	0.758	0.632	0.897	0.758	0.632	0.897	SUBCLONAL	1	TRUE	1	0.430147013877646	2		385	233	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714459	117714459	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1459296351	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	74	462	0	ENST00000368508.3:c.1190G>A	p.Cys397Tyr	p.C397Y	ENST00000368508	NM_002944.2	397	tGc/tAc	11/43	1	2	FACETS	0.815	0.727	0.907	1	0.981	1	CLONAL	2	TRUE	1	0.430147013877646	2		462	211	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525524	137525524	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	50	601	0	ENST00000367739.4:c.491A>G	p.Glu164Gly	p.E164G	ENST00000367739	NM_000416.2	164	gAa/gGa	4/7	1	2	FACETS	0.901	0.771	1	0.901	0.771	1	CLONAL	1	TRUE	1	0.430147013877646	2		601	258	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200456	138200456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	42	484	1	ENST00000237289.4:c.1874C>T	p.Thr625Ile	p.T625I	ENST00000237289	NM_001270507.1	625	aCa/aTa	7/9	1	2	FACETS	0.807	0.679	0.946	0.807	0.679	0.946	CLONAL	1	TRUE	1	0.430147013877646	2		485	242	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149982876	149982876	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	38	455	0	ENST00000253339.5:c.3382G>T	p.Val1128Leu	p.V1128L	ENST00000253339		1128	Gta/Tta	7/7	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.430147013877646	2		455	167	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099825	157099825	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	26	441	0	ENST00000346085.5:c.762A>T	p.Gln254His	p.Q254H	ENST00000346085	NM_020732.3	254	caA/caT	1/20	1	2	FACETS	0.828	0.664	1	0.828	0.664	1	CLONAL	1	TRUE	1	0.430147013877646	2		441	146	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405795	157405795	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	58	309	0	ENST00000346085.5:c.2038-1G>T		p.X680_splice	ENST00000346085	NM_020732.3	680			1	2	FACETS	0.827	0.726	0.932	1	0.976	1	CLONAL	2	TRUE	1	0.430147013877646	2		309	163	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405974	157405974	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	47	523	0	ENST00000346085.5:c.2216C>A	p.Pro739His	p.P739H	ENST00000346085	NM_020732.3	739	cCt/cAt	6/20	1	2	FACETS	0.751	0.637	0.874	0.751	0.637	0.874	SUBCLONAL	1	TRUE	1	0.430147013877646	2		523	291	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157406036	157406036	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	52	351	0	ENST00000346085.5:c.2278C>T	p.Pro760Ser	p.P760S	ENST00000346085	NM_020732.3	760	Cca/Tca	6/20	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.430147013877646	2		351	222	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521942	157521942	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	43	433	0	ENST00000346085.5:c.4214A>G	p.Asn1405Ser	p.N1405S	ENST00000346085	NM_020732.3	1405	aAc/aGc	18/20	1	2	FACETS	0.893	0.754	1	0.893	0.754	1	CLONAL	1	TRUE	1	0.430147013877646	2		433	224	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527806	157527806	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	39	423	0	ENST00000346085.5:c.5531G>T	p.Arg1844Met	p.R1844M	ENST00000346085	NM_020732.3	1844	aGg/aTg	20/20	1	2	FACETS	0.81	0.677	0.955	0.81	0.677	0.955	CLONAL	1	TRUE	1	0.430147013877646	2		423	224	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528599	157528599	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	61	658	0	ENST00000346085.5:c.6324G>T	p.Gln2108His	p.Q2108H	ENST00000346085	NM_020732.3	2108	caG/caT	20/20	1	2	FACETS	0.909	0.79	1	0.909	0.79	1	CLONAL	1	TRUE	1	0.430147013877646	2		658	312	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959019	2959019	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	35	607	0	ENST00000396946.4:c.2497C>T	p.Pro833Ser	p.P833S	ENST00000396946	NM_032415.4	833	Ccc/Tcc	18/25	0.330731520347077	1	FACETS	0.548	0.452	0.654	0.548	0.452	0.654	SUBCLONAL	1	TRUE	0	0.430147013877646	1		607	233	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962345	2962345	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	82	691	1	ENST00000396946.4:c.2192G>T	p.Cys731Phe	p.C731F	ENST00000396946	NM_032415.4	731	tGc/tTc	17/25	0.330731520347077	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.430147013877646	1		692	260	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978390	2978390	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	89	784	0	ENST00000396946.4:c.940G>A	p.Glu314Lys	p.E314K	ENST00000396946	NM_032415.4	314	Gag/Aag	7/25	0.330731520347077	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.430147013877646	1		784	267	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026430	6026430	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	35	196	0	ENST00000265849.7:c.1966G>T	p.Glu656Ter	p.E656*	ENST00000265849	NM_000535.5	656	Gaa/Taa	11/15	0.330731520347077	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.430147013877646	1		196	93	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026725	6026725	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	88	619	0	ENST00000265849.7:c.1671T>G	p.Asp557Glu	p.D557E	ENST00000265849	NM_000535.5	557	gaT/gaG	11/15	0.330731520347077	1	FACETS	0.845	0.767	0.924	1	0.986	1	CLONAL	2	TRUE	0	0.430147013877646	1		619	190	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426866	6426866	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	105	577	0	ENST00000356142.4:c.59T>C	p.Leu20Pro	p.L20P	ENST00000356142	NM_018890.3	20	cTg/cCg	2/7	0.330731520347077	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.430147013877646	1		577	286	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358966	81358966	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	42	556	0	ENST00000222390.5:c.995A>C	p.Gln332Pro	p.Q332P	ENST00000222390	NM_000601.4	332	cAg/cCg	8/18	1	2	FACETS	0.751	0.631	0.882	0.751	0.631	0.882	SUBCLONAL	1	TRUE	1	0.430147013877646	2		556	260	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508319	106508319	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1429946228	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	32	318	0	ENST00000359195.3:c.313C>T	p.Gln105Ter	p.Q105*	ENST00000359195	NM_002649.2	105	Cag/Tag	2/11	1	2	FACETS	0.87	0.714	1	0.87	0.714	1	CLONAL	1	TRUE	1	0.430147013877646	2		318	171	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509633	106509633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	41	478	0	ENST00000359195.3:c.1627G>A	p.Val543Ile	p.V543I	ENST00000359195	NM_002649.2	543	Gtt/Att	2/11	1	2	FACETS	0.627	0.525	0.74	0.627	0.525	0.74	SUBCLONAL	1	TRUE	1	0.430147013877646	2		478	304	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545697	106545698	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	88	577	0	ENST00000359195.3:c.3179dup	p.Asn1060LysfsTer2	p.N1060Kfs*2	ENST00000359195	NM_002649.2	1058	-/A	11/11	1	2	FACETS	0.772	0.694	0.853	1	0.982	1	SUBCLONAL	2	TRUE	1	0.430147013877646	2		577	265	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339643	116339643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766944441	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	56	424	0	ENST00000397752.3:c.505C>T	p.Pro169Ser	p.P169S	ENST00000397752	NM_000245.2	169	Ccc/Tcc	2/21	1	2	FACETS	0.994	0.859	1	0.994	0.859	1	CLONAL	1	TRUE	1	0.430147013877646	2		424	262	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339841	116339841	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	60	548	0	ENST00000397752.3:c.703A>G	p.Ile235Val	p.I235V	ENST00000397752	NM_000245.2	235	Att/Gtt	2/21	1	2	FACETS	0.965	0.839	1	0.965	0.839	1	CLONAL	1	TRUE	1	0.430147013877646	2		548	289	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395436	116395436	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	30	499	0	ENST00000397752.3:c.1729G>T	p.Gly577Ter	p.G577*	ENST00000397752	NM_000245.2	577	Gga/Tga	6/21	1	2	FACETS	0.589	0.477	0.714	0.589	0.477	0.714	SUBCLONAL	1	TRUE	1	0.430147013877646	2		499	237	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412710	116412710	+	intron_variant	Intron	SNP	T	T	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	59	873	0	ENST00000397752.3:c.3028+667T>C		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.764	0.661	0.876	0.764	0.661	0.876	SUBCLONAL	1	TRUE	1	0.430147013877646	2		873	359	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418859	116418859	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	78	329	0	ENST00000397752.3:c.3370T>A	p.Phe1124Ile	p.F1124I	ENST00000397752	NM_000245.2	1124	Ttt/Att	17/21	1	2	FACETS	0.778	0.695	0.865	1	0.98	1	SUBCLONAL	2	TRUE	1	0.430147013877646	2		329	233	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845476	128845476	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	63	763	0	ENST00000249373.3:c.773A>T	p.Asn258Ile	p.N258I	ENST00000249373	NM_005631.4	258	aAc/aTc	4/12	1	2	FACETS	0.954	0.832	1	0.954	0.832	1	CLONAL	1	TRUE	1	0.430147013877646	2		763	307	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846428	128846428	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	35	434	1	ENST00000249373.3:c.1264G>A	p.Gly422Arg	p.G422R	ENST00000249373	NM_005631.4	422	Gga/Aga	6/12	1	2	FACETS	0.73	0.603	0.87	0.73	0.603	0.87	SUBCLONAL	1	TRUE	1	0.430147013877646	2		435	223	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851536	128851536	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1031386726	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	50	662	0	ENST00000249373.3:c.1861C>T	p.His621Tyr	p.H621Y	ENST00000249373	NM_005631.4	621	Cat/Tat	11/12	1	2	FACETS	0.833	0.712	0.964	0.833	0.712	0.964	CLONAL	1	TRUE	1	0.430147013877646	2		662	279	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148507433	148507433	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	56	480	0	ENST00000320356.2:c.2021T>C	p.Leu674Ser	p.L674S	ENST00000320356	NM_004456.4	674	tTg/tCg	17/20	1	2	FACETS	0.943	0.815	1	0.943	0.815	1	CLONAL	1	TRUE	1	0.430147013877646	2		480	276	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515176	148515176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1390180981	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	48	361	1	ENST00000320356.2:c.1033G>A	p.Ala345Thr	p.A345T	ENST00000320356	NM_004456.4	345	Gct/Act	10/20	1	2	FACETS	0.889	0.758	1	0.889	0.758	1	CLONAL	1	TRUE	1	0.430147013877646	2		362	251	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845684	151845684	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	95	620	0	ENST00000262189.6:c.13328A>G	p.Gln4443Arg	p.Q4443R	ENST00000262189	NM_170606.2	4443	cAg/cGg	52/59	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.430147013877646	2		620	308	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859911	151859911	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	71	469	0	ENST00000262189.6:c.10751del	p.Gly3584AspfsTer13	p.G3584Dfs*13	ENST00000262189	NM_170606.2	3584	gGa/ga	43/59	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.430147013877646	2		469	223	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874012	151874013	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	39	592	1	ENST00000262189.6:c.8525dup	p.Asn2842LysfsTer2	p.N2842Kfs*2	ENST00000262189	NM_170606.2	2842	aat/aaAt	38/59	1	2	FACETS	0.659	0.549	0.781	0.659	0.549	0.781	SUBCLONAL	1	TRUE	1	0.430147013877646	2		593	275	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877959	151877959	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	43	404	0	ENST00000262189.6:c.6986G>A	p.Gly2329Glu	p.G2329E	ENST00000262189	NM_170606.2	2329	gGa/gAa	36/59	1	2	FACETS	0.917	0.775	1	0.917	0.775	1	CLONAL	1	TRUE	1	0.430147013877646	2		404	218	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878862	151878862	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778364715	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	112	604	0	ENST00000262189.6:c.6083G>A	p.Arg2028Gln	p.R2028Q	ENST00000262189	NM_170606.2	2028	cGa/cAa	36/59	1	2	FACETS	0.796	0.725	0.87	1	0.987	1	SUBCLONAL	2	TRUE	1	0.430147013877646	2		604	327	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891651	151891651	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	51	289	0	ENST00000262189.6:c.4381A>G	p.Ile1461Val	p.I1461V	ENST00000262189	NM_170606.2	1461	Att/Gtt	29/59	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.430147013877646	2		289	168	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055745	152055745	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	81	543	3	ENST00000262189.6:c.177del	p.Thr61LeufsTer44	p.T61Lfs*44	ENST00000262189	NM_170606.2	59	ggG/gg	2/59	1	2	FACETS	0.788	0.705	0.874	1	0.982	1	SUBCLONAL	2	TRUE	1	0.430147013877646	2		546	239	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538933	23538933	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	40	655	0	ENST00000380871.4:c.506A>G	p.Lys169Arg	p.K169R	ENST00000380871	NM_006167.3	169	aAg/aGg	2/2	0.300142853067812	3	FACETS	0.683	0.569	0.808	0.341	0.284	0.404	SUBCLONAL	1	TRUE	1	0.430147013877646	3		655	331	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194729	29194729	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	89	778	1	ENST00000240100.2:c.999G>T	p.Gln333His	p.Q333H	ENST00000240100	NM_001394.6	333	caG/caT	4/4	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.430147013877646	2		779	282	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38173059	38173059	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	46	400	0	ENST00000317025.8:c.1990G>T	p.Gly664Cys	p.G664C	ENST00000317025	NM_023034.1	664	Ggc/Tgc	11/24	1	2	FACETS	0.899	0.764	1	0.899	0.764	1	CLONAL	1	TRUE	1	0.430147013877646	2		400	238	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271244	38271244	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	36	706	0	ENST00000425967.3:c.2464G>T	p.Gly822Trp	p.G822W	ENST00000425967	NM_001174067.1	822	Ggg/Tgg	19/19	1	2	FACETS	0.656	0.543	0.782	0.656	0.543	0.782	SUBCLONAL	1	TRUE	1	0.430147013877646	2		706	255	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38314969	38314969	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	54	707	0	ENST00000425967.3:c.95C>A	p.Thr32Asn	p.T32N	ENST00000425967	NM_001174067.1	32	aCt/aAt	3/19	1	2	FACETS	0.93	0.801	1	0.93	0.801	1	CLONAL	1	TRUE	1	0.430147013877646	2		707	270	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370975	55370975	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	39	607	0	ENST00000297316.4:c.277C>A	p.Leu93Met	p.L93M	ENST00000297316	NM_022454.3	93	Ctg/Atg	1/2	1	2	FACETS	0.778	0.65	0.919	0.778	0.65	0.919	CLONAL	1	TRUE	1	0.430147013877646	2		607	233	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371002	55371002	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	26	530	1	ENST00000297316.4:c.304C>A	p.Leu102Met	p.L102M	ENST00000297316	NM_022454.3	102	Ctg/Atg	1/2	1	2	FACETS	0.587	0.468	0.722	0.587	0.468	0.722	SUBCLONAL	1	TRUE	1	0.430147013877646	2		531	206	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372230	55372230	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	32	434	0	ENST00000297316.4:c.920G>A	p.Gly307Asp	p.G307D	ENST00000297316	NM_022454.3	307	gGc/gAc	2/2	1	2	FACETS	0.924	0.76	1	0.924	0.76	1	CLONAL	1	TRUE	1	0.430147013877646	2		434	161	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372287	55372288	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1170462661	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	29	578	0	ENST00000297316.4:c.983dup	p.Gly331ArgfsTer34	p.G331Rfs*34	ENST00000297316	NM_022454.3	326	cac/caCc	2/2	1	2	FACETS	0.681	0.551	0.827	0.681	0.551	0.827	SUBCLONAL	1	TRUE	1	0.430147013877646	2		578	198	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922580	56922580	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	99	518	0	ENST00000519728.1:c.1450G>A	p.Ala484Thr	p.A484T	ENST00000519728	NM_002350.3	484	Gca/Aca	13/13	1	2	FACETS	0.791	0.716	0.869	1	0.985	1	SUBCLONAL	2	TRUE	1	0.430147013877646	2		518	291	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69011988	69011988	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	65	705	0	ENST00000288368.4:c.2625A>T	p.Glu875Asp	p.E875D	ENST00000288368	NM_024870.2	875	gaA/gaT	23/40	1	2	FACETS	0.908	0.792	1	0.908	0.792	1	CLONAL	1	TRUE	1	0.430147013877646	2		705	333	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030790	69030790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	32	393	0	ENST00000288368.4:c.3332G>A	p.Cys1111Tyr	p.C1111Y	ENST00000288368	NM_024870.2	1111	tGc/tAc	27/40	1	2	FACETS	0.63	0.515	0.759	0.63	0.515	0.759	SUBCLONAL	1	TRUE	1	0.430147013877646	2		393	236	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058565	69058616	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCATCCTGTTCTTTTTGCACAAGGTAAACTGTTTCTCTTTTGATGGCTGCTA	TCATCCTGTTCTTTTTGCACAAGGTAAACTGTTTCTCTTTTGATGGCTGCTA	GATATTTAATAGTATATTACTTCCTAAAATAAGGATATGCTAGATGG	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	85	682	2	ENST00000288368.4:c.4209_4231+29delinsGATATTTAATAGTATATTACTTCCTAAAATAAGGATATGCTAGATGG		p.X1403_splice	ENST00000288368	NM_024870.2	1403		34/40	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.430147013877646	2		684	285	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958479	90958480	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs780235686	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	36	507	0	ENST00000265433.3:c.1958dup	p.Leu654AlafsTer5	p.L654Afs*5	ENST00000265433	NM_002485.4	653	aag/aaAg	13/16	1	2	FACETS	0.768	0.636	0.912	0.768	0.636	0.912	CLONAL	1	TRUE	1	0.430147013877646	2		507	218	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751043	128751043	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	58	545	0	ENST00000377970.2:c.580C>T	p.Gln194Ter	p.Q194*	ENST00000377970	NM_002467.4	194	Cag/Tag	2/3	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.430147013877646	2		545	222	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141583031	141583031	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	51	604	1	ENST00000220592.5:c.216G>T	p.Arg72Ser	p.R72S	ENST00000220592	NM_012154.3	72	agG/agT	3/19	1	2	FACETS	0.869	0.744	1	0.869	0.744	1	CLONAL	1	TRUE	1	0.430147013877646	2		605	273	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738379	145738379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	46	687	0	ENST00000428558.2:c.2606G>A	p.Gly869Asp	p.G869D	ENST00000428558	NM_004260.3	869	gGt/gAt	16/22	1	2	FACETS	0.839	0.712	0.976	0.839	0.712	0.976	CLONAL	1	TRUE	1	0.430147013877646	2		687	255	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741607	145741607	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	43	750	0	ENST00000428558.2:c.896C>A	p.Pro299Gln	p.P299Q	ENST00000428558	NM_004260.3	299	cCa/cAa	5/22	1	2	FACETS	0.743	0.626	0.871	0.743	0.626	0.871	SUBCLONAL	1	TRUE	1	0.430147013877646	2		750	269	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486205	8486205	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	31	425	0	ENST00000356435.5:c.2612T>A	p.Leu871His	p.L871H	ENST00000356435		871	cTt/cAt	17/35	1	2	FACETS	0.707	0.576	0.852	0.707	0.576	0.852	SUBCLONAL	1	TRUE	1	0.430147013877646	2		425	204	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499748	8499748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	44	628	0	ENST00000356435.5:c.2221C>T	p.His741Tyr	p.H741Y	ENST00000356435		741	Cat/Tat	14/35	1	2	FACETS	0.588	0.494	0.69	0.588	0.494	0.69	SUBCLONAL	1	TRUE	1	0.430147013877646	2		628	348	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518185	8518185	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	38	421	0	ENST00000356435.5:c.1206del	p.Pro403LeufsTer7	p.P403Lfs*7	ENST00000356435		402	ggG/gg	10/35	1	2	FACETS	0.749	0.623	0.886	0.749	0.623	0.886	SUBCLONAL	1	TRUE	1	0.430147013877646	2		421	236	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8526627	8526627	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	76	399	0	ENST00000356435.5:c.568G>T	p.Gly190Ter	p.G190*	ENST00000356435		190	Gga/Tga	6/35	1	2	FACETS	0.875	0.782	0.97	1	0.983	1	CLONAL	2	TRUE	1	0.430147013877646	2		399	202	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971119	21971120	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	65	530	0	ENST00000304494.5:c.238dup	p.Arg80ProfsTer40	p.R80Pfs*40	ENST00000304494	NM_000077.4	80	cga/cCga	2/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.430147013877646	2		530	211	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212833	27212833	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	58	708	0	ENST00000380036.4:c.2815C>T	p.Gln939Ter	p.Q939*	ENST00000380036	NM_000459.3	939	Cag/Tag	17/23	1	2	FACETS	0.859	0.743	0.983	0.859	0.743	0.983	CLONAL	1	TRUE	1	0.430147013877646	2		708	314	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966649	36966649	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	40	514	0	ENST00000358127.4:c.677del	p.Gly226GlufsTer52	p.G226Efs*52	ENST00000358127	NM_001280556.1	226	gGa/ga	6/10	1	2	FACETS	0.756	0.633	0.891	0.756	0.633	0.891	SUBCLONAL	1	TRUE	1	0.430147013877646	2		514	246	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635172	87635172	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	33	512	0	ENST00000277120.3:c.2224A>G	p.Met742Val	p.M742V	ENST00000277120		742	Atg/Gtg	18/19	1	2	FACETS	0.564	0.461	0.679	0.564	0.461	0.679	SUBCLONAL	1	TRUE	1	0.430147013877646	2		512	272	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637126	93637127	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	35	403	0	ENST00000375746.1:c.1181dup	p.Val395SerfsTer16	p.V395Sfs*16	ENST00000375746	NM_001174167.1	392	-/A	9/14	1	2	FACETS	0.654	0.539	0.781	0.654	0.539	0.781	SUBCLONAL	1	TRUE	1	0.430147013877646	2		403	249	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209521	98209521	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	42	554	0	ENST00000331920.6:c.4017G>A	p.Trp1339Ter	p.W1339*	ENST00000331920	NM_000264.3	1339	tgG/tgA	23/24	1	2	FACETS	0.934	0.788	1	0.934	0.788	1	CLONAL	1	TRUE	1	0.430147013877646	2		554	209	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904843	101904843	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	99	398	0	ENST00000374994.4:c.831G>A	p.Trp277Ter	p.W277*	ENST00000374994	NM_004612.2	277	tgG/tgA	5/9	1	2	FACETS	0.889	0.807	0.973	1	0.987	1	CLONAL	2	TRUE	1	0.430147013877646	2		398	259	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730443	133730443	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	39	437	0	ENST00000318560.5:c.509G>T	p.Arg170Met	p.R170M	ENST00000318560	NM_005157.4	170	aGg/aTg	3/11	1	2	FACETS	0.792	0.662	0.934	0.792	0.662	0.934	CLONAL	1	TRUE	1	0.430147013877646	2		437	229	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133748300	133748300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	86	559	0	ENST00000318560.5:c.961G>A	p.Gly321Arg	p.G321R	ENST00000318560	NM_005157.4	321	Ggg/Agg	6/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.430147013877646	2		559	273	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753826	133753826	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	52	609	0	ENST00000318560.5:c.1295T>A	p.Ile432Asn	p.I432N	ENST00000318560	NM_005157.4	432	aTt/aAt	8/11	1	2	FACETS	0.857	0.735	0.989	0.857	0.735	0.989	CLONAL	1	TRUE	1	0.430147013877646	2		609	282	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755989	133755989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	54	512	0	ENST00000318560.5:c.1616C>T	p.Ala539Val	p.A539V	ENST00000318560	NM_005157.4	539	gCa/gTa	10/11	1	2	FACETS	0.92	0.792	1	0.92	0.792	1	CLONAL	1	TRUE	1	0.430147013877646	2		512	273	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760511	133760511	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	38	702	0	ENST00000318560.5:c.2834C>A	p.Ala945Asp	p.A945D	ENST00000318560	NM_005157.4	945	gCt/gAt	11/11	1	2	FACETS	0.758	0.632	0.897	0.758	0.632	0.897	SUBCLONAL	1	TRUE	1	0.430147013877646	2		702	233	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815627	139815627	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	45	591	0	ENST00000247668.2:c.1098G>T	p.Gln366His	p.Q366H	ENST00000247668	NM_021138.3	366	caG/caT	9/11	1	2	FACETS	0.769	0.651	0.898	0.769	0.651	0.898	SUBCLONAL	1	TRUE	1	0.430147013877646	2		591	272	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934126	39934127	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	45	335	0	ENST00000378444.4:c.472dup	p.Ser158LysfsTer28	p.S158Kfs*28	ENST00000378444	NM_001123385.1	158	agt/aAgt	4/15	1	1	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	0	0.430147013877646	1		335	162	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44935949	44935949	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	38	203	0	ENST00000377967.4:c.2710G>T	p.Gly904Cys	p.G904C	ENST00000377967	NM_021140.2	904	Ggt/Tgt	18/29	1	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.430147013877646	1		203	97	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044872	47044872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	34	421	0	ENST00000377604.3:c.2198G>A	p.Ser733Asn	p.S733N	ENST00000377604	NM_001204468.1	733	aGc/aAc	20/24	1	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.430147013877646	1		421	107	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409931	63409931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	34	206	0	ENST00000330258.3:c.3236G>A	p.Gly1079Asp	p.G1079D	ENST00000330258	NM_152424.3	1079	gGc/gAc	2/2	1	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.430147013877646	1		206	102	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410936	63410936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs189503587	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	99	357	0	ENST00000330258.3:c.2231C>T	p.Ala744Val	p.A744V	ENST00000330258	NM_152424.3	744	gCc/gTc	2/2	1	1	FACETS	1	0.977	1	1	0.991	1	CLONAL	2	TRUE	0	0.430147013877646	1		357	157	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412174	63412174	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	17	482	0	ENST00000330258.3:c.993A>G	p.Ile331Met	p.I331M	ENST00000330258	NM_152424.3	331	atA/atG	2/2	1	1	FACETS	0.521	0.393	0.67	0.521	0.393	0.67	SUBCLONAL	1	TRUE	0	0.430147013877646	1		482	119	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413082	63413082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138399473	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	26	372	0	ENST00000330258.3:c.85G>A	p.Ala29Thr	p.A29T	ENST00000330258	NM_152424.3	29	Gcc/Acc	2/2	1	1	FACETS	0.612	0.49	0.749	0.612	0.49	0.749	SUBCLONAL	1	TRUE	0	0.430147013877646	1		372	155	SUCCESS
AR	367	MSKCC	GRCh37	X	66766444	66766444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1219527157	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	46	145	0	ENST00000374690.3:c.1456C>T	p.Pro486Ser	p.P486S	ENST00000374690	NM_000044.3	486	Ccc/Tcc	1/8	1	1	FACETS	0.999	0.919	1	1	0.983	1	CLONAL	3	TRUE	0	0.430147013877646	1		145	56	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814280	76814280	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	44	196	1	ENST00000373344.5:c.6364C>A	p.Leu2122Ile	p.L2122I	ENST00000373344	NM_000489.3	2122	Cta/Ata	29/35	1	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.430147013877646	1		197	129	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849320	76849320	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	39	206	0	ENST00000373344.5:c.5957-1G>T		p.X1986_splice	ENST00000373344	NM_000489.3	1986			1	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.430147013877646	1		206	115	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937371	76937371	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	78	294	0	ENST00000373344.5:c.3377A>G	p.Asp1126Gly	p.D1126G	ENST00000373344	NM_000489.3	1126	gAt/gGt	9/35	1	1	FACETS	0.912	0.849	0.971	1	0.989	1	CLONAL	3	TRUE	0	0.430147013877646	1		294	104	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939178	76939178	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1255976123	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	22	330	0	ENST00000373344.5:c.1570G>A	p.Val524Ile	p.V524I	ENST00000373344	NM_000489.3	524	Gtt/Att	9/35	1	1	FACETS	0.595	0.466	0.74	0.595	0.466	0.74	SUBCLONAL	1	TRUE	0	0.430147013877646	1		330	135	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939798	76939798	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	107	311	1	ENST00000373344.5:c.950C>A	p.Pro317Gln	p.P317Q	ENST00000373344	NM_000489.3	317	cCa/cAa	9/35	1	1	FACETS	1	0.985	1	1	0.992	1	CLONAL	2	TRUE	0	0.430147013877646	1		312	157	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611814	100611814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	47	313	0	ENST00000308731.7:c.1307C>T	p.Ser436Phe	p.S436F	ENST00000308731	NM_000061.2	436	tCc/tTc	14/19	1	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.430147013877646	1		313	150	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615075	100615075	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	126	291	0	ENST00000308731.7:c.839+1G>T		p.X280_splice	ENST00000308731	NM_000061.2	280			1	1	FACETS	0.876	0.825	0.924	1	0.993	1	CLONAL	3	TRUE	0	0.430147013877646	1		291	175	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171465	123171465	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	31	240	0	ENST00000218089.9:c.377G>A	p.Gly126Asp	p.G126D	ENST00000218089	NM_001042749.1	126	gGc/gAc	6/35	1	1	FACETS	1	0.835	1	1	0.835	1	CLONAL	1	TRUE	0	0.430147013877646	1		240	112	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0035316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	328	772	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	0.999	0.95	1			1	INDETERMINATE	2	TRUE	NA	0.439097602182801	2		772	748	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299836	15299836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	253	648	0	ENST00000263388.2:c.1342G>A	p.Asp448Asn	p.D448N	ENST00000263388	NM_000435.2	448	Gac/Aac	8/33	0.439097602182801	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.439097602182801	1		648	621	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508059	106508059	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs142380460	NA	P-0035316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	79	210	0	ENST00000359195.3:c.53G>T	p.Arg18Leu	p.R18L	ENST00000359195	NM_002649.2	18	cGa/cTa	2/11	0.316776031802168	2	FACETS	1	0.962	1	0.598	0.531	0.668	CLONAL	1	TRUE	0	0.439097602182801	2		210	301	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738293	190738293	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	46	360	0	ENST00000441310.2:c.2545G>T	p.Asp849Tyr	p.D849Y	ENST00000441310	NM_000534.4	849	Gat/Tat	12/13	0.289003102690275	3	FACETS	0.578	0.487	0.678	0.289	0.243	0.339	SUBCLONAL	1	TRUE	1	0.439097602182801	3		360	442	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664557	29664557	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	141	502	0	ENST00000356175.3:c.6536C>A	p.Thr2179Lys	p.T2179K	ENST00000356175	NM_000267.3	2179	aCa/aAa	42/57	0.31268997392944	3	FACETS	1	0.973	1	0.58	0.53	0.633	CLONAL	1	TRUE	1	0.439097602182801	3		502	675	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38506139	38506139	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	241	496	0	ENST00000254066.5:c.431G>A	p.Arg144Gln	p.R144Q	ENST00000254066	NM_000964.3	144	cGa/cAa	4/9	0.215451532127712	3	FACETS	0.872	0.817	0.927	0.872	0.817	0.927	INDETERMINATE	2	TRUE	1	0.439097602182801	3		496	768	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207119	1207122	+	frameshift_variant	Frame_Shift_Del	DEL	GGAG	GGAG	-	novel	NA	P-0035316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	256	724	0	ENST00000326873.7:c.207_210del	p.Glu70ArgfsTer25	p.E70Rfs*25	ENST00000326873	NM_000455.4	69	tcGGAG/tc	1/10	0.439097602182801	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.439097602182801	1		724	782	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176521304	176522326	+	splice_region_variant,intron_variant	Splice_Region	DEL	CTCCCAGCCCAAGGATTGTGGAAAGTGCCTGGCTCATAGTCAGGGCTCAATAAATCTTCACCACTGGGGTGATGATGATGAGAAGAATTTGGTGTGACAGGCTTGATATCCTGTGTCAGCATTAGTCTGTGTCAGCTTTGACTTCACATCTCCTTGTCAGCCTCACAGGCCCTCTACCTCCTTCCTTATGGTTCCCCCCAGACACACCCTCAGCCTCCCTTGGACCCTCCCTAGGTCTGCCCCCCACGTCCACTGCTGTAGGAGGACAGCCCTTCTGCTTGCACCCAGGCCCAGCCCCGGGGTGCTCTTGCTGGGCACTCCTGCACCCCACCCATCAGGGCCTCTCCTTGCAGTTCCCCAGCCCCCTCTGCAAGAATGGCCTCCACTGCTCTTCTGCTCCTCCCCTCCTCTCTACACAGCTGGGGCCACCTGGTGCTCCCTGGGAGGCAGGGATTGAGAAATGCACATTGTGTCATTGGCCCAGGGCCACAGGTCAGCCCCAGGGGCTCAGCCAGAGAAGCCAAAGCAGCCTTCTTCCCAAGCTCCCCGGCTGCACCCGGCCTGCCGCCAGCTCCCTGAATTCCCAGGCCAGTTGGAAGCCAGGCCCTGGTCAAACAGACCCCAGGGCGCCAGCCTGCTTTCCGCACCCAGAAGCTCTGACCCCATGCGGGGACTACCGCTGACCCCTCCAGCGGCAGCTTCCTTCCTTCCTTCCTGCTCCGAGCTCTTCCCCTCTCTCCTGTGTCCTGGGCCTGCCCGCTGGAAGGCCTGCCTCTTAGATCCTTGATACAGTTGCATCCTTGCAACTGCTGTGACAGGCAGGGTGTGACCCACTGCTCTGTTTCCCACAAGACGAACCTGAGGTTCAGAGACGCTAGGAGACTTTTTCAAGGCCACACAGCCTAGCAAGGATTCAGCCCTAGACCTACGTAGCCCTGGTCCAGTGCTGCTTGTCCTGCACCTGCCTCTGCATGCTCCCTCGTGCAGTTGGAGGGCAGCCTCTTCACCCCGTCTGCTGCCCTT	CTCCCAGCCCAAGGATTGTGGAAAGTGCCTGGCTCATAGTCAGGGCTCAATAAATCTTCACCACTGGGGTGATGATGATGAGAAGAATTTGGTGTGACAGGCTTGATATCCTGTGTCAGCATTAGTCTGTGTCAGCTTTGACTTCACATCTCCTTGTCAGCCTCACAGGCCCTCTACCTCCTTCCTTATGGTTCCCCCCAGACACACCCTCAGCCTCCCTTGGACCCTCCCTAGGTCTGCCCCCCACGTCCACTGCTGTAGGAGGACAGCCCTTCTGCTTGCACCCAGGCCCAGCCCCGGGGTGCTCTTGCTGGGCACTCCTGCACCCCACCCATCAGGGCCTCTCCTTGCAGTTCCCCAGCCCCCTCTGCAAGAATGGCCTCCACTGCTCTTCTGCTCCTCCCCTCCTCTCTACACAGCTGGGGCCACCTGGTGCTCCCTGGGAGGCAGGGATTGAGAAATGCACATTGTGTCATTGGCCCAGGGCCACAGGTCAGCCCCAGGGGCTCAGCCAGAGAAGCCAAAGCAGCCTTCTTCCCAAGCTCCCCGGCTGCACCCGGCCTGCCGCCAGCTCCCTGAATTCCCAGGCCAGTTGGAAGCCAGGCCCTGGTCAAACAGACCCCAGGGCGCCAGCCTGCTTTCCGCACCCAGAAGCTCTGACCCCATGCGGGGACTACCGCTGACCCCTCCAGCGGCAGCTTCCTTCCTTCCTTCCTGCTCCGAGCTCTTCCCCTCTCTCCTGTGTCCTGGGCCTGCCCGCTGGAAGGCCTGCCTCTTAGATCCTTGATACAGTTGCATCCTTGCAACTGCTGTGACAGGCAGGGTGTGACCCACTGCTCTGTTTCCCACAAGACGAACCTGAGGTTCAGAGACGCTAGGAGACTTTTTCAAGGCCACACAGCCTAGCAAGGATTCAGCCCTAGACCTACGTAGCCCTGGTCCAGTGCTGCTTGTCCTGCACCTGCCTCTGCATGCTCCCTCGTGCAGTTGGAGGGCAGCCTCTTCACCCCGTCTGCTGCCCTT	-	novel	NA	P-0035316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	26	1	0	ENST00000292408.4:c.1519+528_1520-5del		p.X507_splice	ENST00000292408	NM_213647.1	507			0.404559119127618	2	FACETS	0.175	0.138	0.218	0.088	0.069	0.109	SUBCLONAL	1	TRUE	0	0.439097602182801	2		1	676	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729255	41729255	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	83	470	0	ENST00000242208.4:c.1274G>C	p.Cys425Ser	p.C425S	ENST00000242208	NM_002192.2	425	tGc/tCc	3/3	0.289003102690275	3	FACETS	0.691	0.61	0.778	0.346	0.305	0.389	SUBCLONAL	1	TRUE	1	0.439097602182801	3		470	667	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509637	106509637	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs766453335	NA	P-0035316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	218	466	0	ENST00000359195.3:c.1631G>T	p.Arg544Leu	p.R544L	ENST00000359195	NM_002649.2	544	cGa/cTa	2/11	0.316776031802168	2	FACETS	0.822	0.77	0.875	0.822	0.77	0.875	CLONAL	2	TRUE	0	0.439097602182801	2		466	604	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90995060	90995060	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	55	426	0	ENST00000265433.3:c.61G>T	p.Gly21Cys	p.G21C	ENST00000265433	NM_002485.4	21	Ggc/Tgc	2/16	0.439097602182801	5	FACETS	0.557	0.475	0.647	0.139	0.118	0.162	SUBCLONAL	1	TRUE	1	0.439097602182801	5		426	746	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751075	128751076	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0035316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1418	141	542	0	ENST00000377970.2:c.613dup	p.Asp205GlyfsTer53	p.D205Gfs*53	ENST00000377970	NM_002467.4	204	-/G	2/3	0.439097602182801	7	FACETS	0.864	0.784	0.949			1	CLONAL	1	TRUE	NA	0.439097602182801	7		542	1559	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376651	8376651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	111	572	1	ENST00000356435.5:c.4462G>A	p.Val1488Met	p.V1488M	ENST00000356435		1488	Gtg/Atg	27/35	0.439097602182801	1	FACETS	0.824	0.744	0.907	0.824	0.744	0.907	CLONAL	1	TRUE	0	0.439097602182801	1		573	479	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152857997	152857997	+	synonymous_variant	Silent	SNP	G	G	A	rs201983563	NA	P-0035316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	107	123	0	ENST00000406277.2:c.618C>T	p.Pro206=	p.P206=	ENST00000406277	NM_152274.4	206	ccC/ccT	6/7	1	1	FACETS	0.98	0.905	1	1	0.99	1	CLONAL	2	TRUE	0	0.439097602182801	1		123	194	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435312	56435312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139405076	NA	P-0035665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1338	120	797	1	ENST00000407977.2:c.1825C>T	p.Arg609Trp	p.R609W	ENST00000407977		609	Cgg/Tgg	9/10	0.928739009815215	1	FACETS	0.095	0.085	0.106	0.095	0.085	0.106	SUBCLONAL	1	TRUE	0	0.928739009815215	1		798	1458	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681102	37681102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1337640463	NA	P-0035665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	347	616	0	ENST00000447079.4:c.3271C>T	p.Pro1091Ser	p.P1091S	ENST00000447079	NM_015083.1	1091	Cct/Tct	12/14	0.928739009815215	1	FACETS	0.356	0.337	0.376	0.356	0.337	0.376	SUBCLONAL	1	TRUE	0	0.928739009815215	1		616	1123	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164505	36164505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	31	656	0	ENST00000300305.3:c.1370G>A	p.Gly457Asp	p.G457D	ENST00000300305		457	gGc/gAc	8/8	0.454861484820088	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.928739009815215	0		656	488	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670703	134670703	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	394	665	0	ENST00000398015.3:c.614T>A	p.Val205Glu	p.V205E	ENST00000398015	NM_004441.4	205	gTg/gAg	3/16	1	2	FACETS	0.543	0.515	0.572	0.543	0.515	0.572	SUBCLONAL	1	TRUE	1	0.928739009815215	2		665	1562	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231202	142231202	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	300	592	0	ENST00000350721.4:c.4752G>C	p.Met1584Ile	p.M1584I	ENST00000350721	NM_001184.3	1584	atG/atC	27/47	1	2	FACETS	0.523	0.492	0.555	0.523	0.492	0.555	SUBCLONAL	1	TRUE	1	0.928739009815215	2		592	1236	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681102	37681102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1337640463	NA	P-0035665-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	44	616	0	ENST00000447079.4:c.3271C>T	p.Pro1091Ser	p.P1091S	ENST00000447079	NM_015083.1	1091	Cct/Tct	12/14	0.3	1	FACETS	0.609	0.509	0.72	0.609	0.509	0.72	SUBCLONAL	1	TRUE	0	0.17	1		616	778	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670703	134670703	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035665-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	71	665	0	ENST00000398015.3:c.614T>A	p.Val205Glu	p.V205E	ENST00000398015	NM_004441.4	205	gTg/gAg	3/16	1	2	FACETS	0.799	0.695	0.912	0.799	0.695	0.912	CLONAL	1	TRUE	1	0.17	2		665	1045	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231202	142231202	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035665-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	51	592	0	ENST00000350721.4:c.4752G>C	p.Met1584Ile	p.M1584I	ENST00000350721	NM_001184.3	1584	atG/atC	27/47	1	2	FACETS	0.733	0.622	0.857	0.733	0.622	0.857	SUBCLONAL	1	TRUE	1	0.17	2		592	818	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792755	33792757	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs746430067	NA	P-0035665-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	13	80	0	ENST00000498907.2:c.564_566del	p.Pro189del	p.P189del	ENST00000498907	NM_004364.3	188	ccGCCc/ccc	1/1	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.17	2		80	104	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317422	1317422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759127718	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	260	585	0	ENST00000400841.2:c.643C>T	p.Arg215Trp	p.R215W	ENST00000400841		215	Cgg/Tgg	5/6	1	1	FACETS	0.602	0.567	0.638	0.602	0.567	0.638	SUBCLONAL	1	TRUE	0	0.758552893314745	1		585	707	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518175	8518175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1354824749	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	277	453	1	ENST00000356435.5:c.1216G>A	p.Glu406Lys	p.E406K	ENST00000356435		406	Gaa/Aaa	10/35	0.739765040823127	3	FACETS	0.986	0.926	1	0.493	0.463	0.523	CLONAL	1	TRUE	1	0.758552893314745	3		454	1022	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286791	212286791	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	234	461	0	ENST00000342788.4:c.2905G>A	p.Glu969Lys	p.E969K	ENST00000342788	NM_005235.2	969	Gaa/Aaa	24/28	1	2	FACETS	0.869	0.814	0.925	0.869	0.814	0.925	CLONAL	1	TRUE	1	0.758552893314745	2		461	710	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66518954	66518954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	216	425	0	ENST00000358598.2:c.235G>A	p.Glu79Lys	p.E79K	ENST00000358598	NM_212471.2	79	Gag/Aag	3/11	1	2	FACETS	0.956	0.895	1	0.956	0.895	1	CLONAL	1	TRUE	1	0.758552893314745	2		425	596	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206910	102206910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776938400	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	235	388	0	ENST00000263464.3:c.1538C>T	p.Ser513Phe	p.S513F	ENST00000263464	NM_001165.4	513	tCt/tTt	7/9	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.758552893314745	2		388	605	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721003	176721003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	248	515	1	ENST00000439151.2:c.6634C>T	p.Pro2212Ser	p.P2212S	ENST00000439151	NM_022455.4	2212	Cct/Tct	23/23	1	2	FACETS	0.98	0.922	1	0.98	0.922	1	CLONAL	1	TRUE	1	0.758552893314745	2		516	667	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1268	464	1004	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	0.758552893314745	3	FACETS	0.974	0.929	1	0.487	0.464	0.511	CLONAL	1	TRUE	1	0.758552893314745	3		1004	1732	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	186	462	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.945	0.88	1	0.945	0.88	1	CLONAL	1	TRUE	1	0.758552893314745	2		463	519	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462975	120462975	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1435723160	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	235	505	1	ENST00000256646.2:c.5356C>T	p.Arg1786Ter	p.R1786*	ENST00000256646	NM_024408.3	1786	Cga/Tga	30/34	1	2	FACETS	0.921	0.864	0.979	0.921	0.864	0.979	CLONAL	1	TRUE	1	0.758552893314745	2		506	673	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259262	89259262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770780950	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	241	562	1	ENST00000336596.2:c.406C>T	p.Arg136Ter	p.R136*	ENST00000336596	NM_005233.5	136	Cga/Tga	3/17	1	2	FACETS	0.956	0.898	1	0.956	0.898	1	CLONAL	1	TRUE	1	0.758552893314745	2		563	665	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49413010	49413011	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	252	621	1	ENST00000418115.1:c.12_13delinsTT	p.Arg5Trp	p.R5W	ENST00000418115	NM_001664.2	4	atCCgg/atTTgg	2/5	1	2	FACETS	0.847	0.796	0.9	0.847	0.796	0.9	CLONAL	1	TRUE	1	0.758552893314745	2		622	784	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489225	2489225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	259	784	0	ENST00000355716.4:c.130G>A	p.Glu44Lys	p.E44K	ENST00000355716	NM_003820.2	44	Gag/Aag	2/8	1	2	FACETS	0.887	0.834	0.941	0.887	0.834	0.941	CLONAL	1	TRUE	1	0.758552893314745	2		784	770	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099839	27099839	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	207	456	0	ENST00000324856.7:c.3718C>T	p.Pro1240Ser	p.P1240S	ENST00000324856	NM_006015.4	1240	Cca/Tca	15/20	1	2	FACETS	0.987	0.923	1	0.987	0.923	1	CLONAL	1	TRUE	1	0.758552893314745	2		456	553	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101338	27101339	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	272	684	1	ENST00000324856.7:c.4620_4621delinsTT	p.His1541Tyr	p.H1541Y	ENST00000324856	NM_006015.4	1540	aaCCac/aaTTac	18/20	1	2	FACETS	0.901	0.849	0.954	0.901	0.849	0.954	CLONAL	1	TRUE	1	0.758552893314745	2		685	796	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462982	120462983	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	208	520	0	ENST00000256646.2:c.5348_5349delinsTT	p.Pro1783Leu	p.P1783L	ENST00000256646	NM_024408.3	1783	cCC/cTT	30/34	1	2	FACETS	0.868	0.81	0.927	0.868	0.81	0.927	CLONAL	1	TRUE	1	0.758552893314745	2		520	632	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226561934	226561934	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	254	498	0	ENST00000366794.5:c.2063A>G	p.Glu688Gly	p.E688G	ENST00000366794	NM_001618.3	688	gAg/gGg	14/23	1	2	FACETS	0.992	0.934	1	0.992	0.934	1	CLONAL	1	TRUE	1	0.758552893314745	2		498	675	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736316	243736316	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	198	377	0	ENST00000263826.5:c.731C>T	p.Ser244Phe	p.S244F	ENST00000263826	NM_005465.4	244	tCt/tTt	8/13	1	2	FACETS	0.842	0.784	0.901	0.842	0.784	0.901	CLONAL	1	TRUE	1	0.758552893314745	2		377	620	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100403	8100403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	800	759	0	ENST00000346208.3:c.377C>T	p.Ser126Phe	p.S126F	ENST00000346208		126	tCc/tTc	3/6	0.739765040823127	3	FACETS	0.993	0.965	1	0.993	0.965	1	CLONAL	2	TRUE	1	0.758552893314745	3		759	1465	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263976	104263976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766666529	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	421	315	0	ENST00000369902.3:c.67C>T	p.Pro23Ser	p.P23S	ENST00000369902	NM_016169.3	23	Ccc/Tcc	1/12	0.739765040823127	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	1	0.758552893314745	3		315	646	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912110	114912110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	205	407	2	ENST00000543371.1:c.1180G>A	p.Glu394Lys	p.E394K	ENST00000543371	NM_001198531.1	394	Gaa/Aaa	11/14	0.739765040823127	3	FACETS	0.938	0.872	1	0.469	0.436	0.503	CLONAL	1	TRUE	1	0.758552893314745	3		409	795	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589800	69589800	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759707481	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	38	53	0	ENST00000168712.1:c.53C>T	p.Ala18Val	p.A18V	ENST00000168712	NM_002007.2	18	gCc/gTc	1/3	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.758552893314745	2		53	86	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77070046	77070046	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	258	497	0	ENST00000356341.3:c.494C>T	p.Ser165Phe	p.S165F	ENST00000356341	NM_002576.4	165	tCt/tTt	6/15	1	2	FACETS	0.982	0.925	1	0.982	0.925	1	CLONAL	1	TRUE	1	0.758552893314745	2		497	693	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435018	18435018	+	start_lost	Translation_Start_Site	SNP	G	G	T	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	147	275	0	ENST00000266497.5:c.3G>T	p.Met1?	p.M1?	ENST00000266497		1	atG/atT	1/31	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.758552893314745	2		275	380	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433631	49433631	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	457	1187	0	ENST00000301067.7:c.7922C>T	p.Pro2641Leu	p.P2641L	ENST00000301067	NM_003482.3	2641	cCt/cTt	31/54	1	2	FACETS	0.958	0.915	1	0.958	0.915	1	CLONAL	1	TRUE	1	0.758552893314745	2		1187	1258	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434711	49434711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	385	868	1	ENST00000301067.7:c.6842C>T	p.Ser2281Phe	p.S2281F	ENST00000301067	NM_003482.3	2281	tCc/tTc	31/54	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.758552893314745	2		869	992	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444201	49444201	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	428	930	0	ENST00000301067.7:c.3170C>T	p.Pro1057Leu	p.P1057L	ENST00000301067	NM_003482.3	1057	cCc/cTc	11/54	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.758552893314745	2		930	1058	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856004	111856004	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	258	615	0	ENST00000341259.2:c.55C>T	p.Pro19Ser	p.P19S	ENST00000341259	NM_005475.2	19	Ccg/Tcg	2/8	1	2	FACETS	0.955	0.899	1	0.955	0.899	1	CLONAL	1	TRUE	1	0.758552893314745	2		615	712	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257848	133257848	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	244	471	1	ENST00000320574.5:c.80C>T	p.Ser27Phe	p.S27F	ENST00000320574	NM_006231.2	27	tCc/tTc	2/49	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.758552893314745	2		472	602	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975658	26975658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	187	385	0	ENST00000381527.3:c.1166G>A	p.Gly389Glu	p.G389E	ENST00000381527	NM_001260.1	389	gGg/gAg	12/13	0.344830832714651	1	FACETS	0.57	0.53	0.61	0.57	0.53	0.61	INDETERMINATE	1	TRUE	0	0.758552893314745	1		385	537	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572070	95572070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	347	707	0	ENST00000393063.1:c.3038C>T	p.Pro1013Leu	p.P1013L	ENST00000393063	NM_030621.3	1013	cCt/cTt	20/28	1	2	FACETS	0.921	0.874	0.969	0.921	0.874	0.969	CLONAL	1	TRUE	1	0.758552893314745	2		707	993	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95595855	95595855	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	250	558	1	ENST00000393063.1:c.688C>T	p.Leu230Phe	p.L230F	ENST00000393063	NM_030621.3	230	Ctt/Ttt	7/28	1	2	FACETS	0.9	0.846	0.956	0.9	0.846	0.956	CLONAL	1	TRUE	1	0.758552893314745	2		559	732	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675097	40675097	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	429	787	0	ENST00000249776.8:c.61G>A	p.Glu21Lys	p.E21K	ENST00000249776	NM_033286.3	21	Gag/Aag	1/9	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.758552893314745	2		787	1087	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43730612	43730613	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	207	429	1	ENST00000382044.4:c.3100_3101delinsTT	p.Pro1034Phe	p.P1034F	ENST00000382044	NM_001141980.1	1034	CCc/TTc	16/28	1	2	FACETS	0.916	0.855	0.977	0.916	0.855	0.977	CLONAL	1	TRUE	1	0.758552893314745	2		430	596	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43783936	43783936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1027436739	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	300	565	0	ENST00000382044.4:c.302C>T	p.Ser101Phe	p.S101F	ENST00000382044	NM_001141980.1	101	tCt/tTt	4/28	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.758552893314745	2		565	766	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477145	67477145	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	307	570	0	ENST00000327367.4:c.952C>T	p.Pro318Ser	p.P318S	ENST00000327367	NM_005902.3	318	Ccc/Tcc	7/9	1	2	FACETS	0.953	0.902	1	0.953	0.902	1	CLONAL	1	TRUE	1	0.758552893314745	2		570	849	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817894	3817894	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	259	606	0	ENST00000262367.5:c.3077T>G	p.Leu1026Trp	p.L1026W	ENST00000262367	NM_004380.2	1026	tTg/tGg	16/31	1	2	FACETS	0.951	0.895	1	0.951	0.895	1	CLONAL	1	TRUE	1	0.758552893314745	2		606	718	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923309	9923309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	295	615	0	ENST00000330684.3:c.1978G>A	p.Asp660Asn	p.D660N	ENST00000330684	NM_001134407.1	660	Gac/Aac	9/13	1	2	FACETS	0.936	0.884	0.988	0.936	0.884	0.988	CLONAL	1	TRUE	1	0.758552893314745	2		615	831	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984890	9984890	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465126724	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	300	617	0	ENST00000330684.3:c.1075C>T	p.Pro359Ser	p.P359S	ENST00000330684	NM_001134407.1	359	Ccc/Tcc	4/13	1	2	FACETS	0.929	0.879	0.981	0.929	0.879	0.981	CLONAL	1	TRUE	1	0.758552893314745	2		617	851	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031912	10031912	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	324	704	0	ENST00000330684.3:c.911C>T	p.Ser304Phe	p.S304F	ENST00000330684	NM_001134407.1	304	tCt/tTt	3/13	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.758552893314745	2		704	845	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129372	30129372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	268	614	0	ENST00000263025.4:c.656C>T	p.Ser219Phe	p.S219F	ENST00000263025	NM_002746.2	219	tCc/tTc	4/9	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.758552893314745	2		614	705	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134434	30134435	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	292	672	1	ENST00000263025.4:c.96_97delinsAA	p.Gly33Arg	p.G33R	ENST00000263025	NM_002746.2	32	aaGGgg/aaAAgg	1/9	1	2	FACETS	0.952	0.899	1	0.952	0.899	1	CLONAL	1	TRUE	1	0.758552893314745	2		673	809	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984850	72984850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765294332	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	213	488	0	ENST00000268489.5:c.2734C>T	p.Pro912Ser	p.P912S	ENST00000268489	NM_006885.3	912	Ccc/Tcc	3/10	1	2	FACETS	0.975	0.913	1	0.975	0.913	1	CLONAL	1	TRUE	1	0.758552893314745	2		488	576	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337278	89337279	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	277	622	0	ENST00000301030.4:c.7752_7753delinsTT	p.Arg2585Cys	p.R2585C	ENST00000301030	NM_001256183.1	2584	gcCCgc/gcTTgc	12/13	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.758552893314745	2		622	682	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341583	89341583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1336341769	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	201	464	0	ENST00000301030.4:c.7487C>T	p.Ser2496Phe	p.S2496F	ENST00000301030	NM_001256183.1	2496	tCc/tTc	10/13	1	2	FACETS	0.983	0.919	1	0.983	0.919	1	CLONAL	1	TRUE	1	0.758552893314745	2		464	539	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350110	89350110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	409	885	1	ENST00000301030.4:c.2840C>T	p.Ala947Val	p.A947V	ENST00000301030	NM_001256183.1	947	gCc/gTc	9/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.758552893314745	2		886	1076	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352474	89352474	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	292	733	0	ENST00000301030.4:c.865T>A	p.Tyr289Asn	p.Y289N	ENST00000301030	NM_001256183.1	289	Tac/Aac	8/13	1	2	FACETS	0.962	0.909	1	0.962	0.909	1	CLONAL	1	TRUE	1	0.758552893314745	2		733	800	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577059	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AT	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	354	882	0	ENST00000269305.4:c.879_880delinsAT	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	293	ggGGag/ggATag	8/11	1	2	FACETS	0.992	0.943	1	0.992	0.943	1	CLONAL	1	TRUE	1	0.758552893314745	2		882	941	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577567	7577567	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	299	666	0	ENST00000269305.4:c.714T>A	p.Cys238Ter	p.C238*	ENST00000269305	NM_001126112.2	238	tgT/tgA	7/11	1	2	FACETS	0.998	0.944	1	0.998	0.944	1	CLONAL	1	TRUE	1	0.758552893314745	2		666	790	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588784	29588784	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555619019	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	212	357	1	ENST00000356175.3:c.4570T>C	p.Tyr1524His	p.Y1524H	ENST00000356175	NM_000267.3	1524	Tac/Cac	34/57	1	2	FACETS	0.965	0.903	1	0.965	0.903	1	CLONAL	1	TRUE	1	0.758552893314745	2		358	579	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881620	37881621	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	310	733	2	ENST00000269571.5:c.2690_2691delinsAA	p.Arg897Gln	p.R897Q	ENST00000269571		897	cGG/cAA	22/27	1	2	FACETS	0.923	0.873	0.973	0.923	0.873	0.973	CLONAL	1	TRUE	1	0.758552893314745	2		735	886	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510599	38510599	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	238	681	0	ENST00000254066.5:c.853A>T	p.Thr285Ser	p.T285S	ENST00000254066	NM_000964.3	285	Acc/Tcc	7/9	1	2	FACETS	0.873	0.818	0.928	0.873	0.818	0.928	CLONAL	1	TRUE	1	0.758552893314745	2		681	719	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40477071	40477072	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	195	480	0	ENST00000264657.5:c.1373_1374delinsTT	p.Ser458Phe	p.S458F	ENST00000264657	NM_139276.2	458	tCC/tTT	16/24	1	2	FACETS	0.974	0.909	1	0.974	0.909	1	CLONAL	1	TRUE	1	0.758552893314745	2		480	528	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805673	46805673	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	321	793	0	ENST00000290295.7:c.283A>G	p.Ser95Gly	p.S95G	ENST00000290295	NM_006361.5	95	Agc/Ggc	1/2	1	2	FACETS	0.997	0.945	1	0.997	0.945	1	CLONAL	1	TRUE	1	0.758552893314745	2		793	849	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435135	56435135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746854614	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	374	720	0	ENST00000407977.2:c.2002C>T	p.Arg668Trp	p.R668W	ENST00000407977		668	Cgg/Tgg	9/10	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.758552893314745	2		720	877	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39593533	39593533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	145	314	0	ENST00000262039.4:c.1298C>T	p.Ser433Phe	p.S433F	ENST00000262039	NM_002647.2	433	tCt/tTt	11/25	1	2	FACETS	0.963	0.888	1	0.963	0.888	1	CLONAL	1	TRUE	1	0.758552893314745	2		314	397	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226394	2226394	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	339	975	1	ENST00000398665.3:c.3874C>T	p.Pro1292Ser	p.P1292S	ENST00000398665	NM_032482.2	1292	Ccc/Tcc	27/28	1	2	FACETS	0.915	0.867	0.963	0.915	0.867	0.963	CLONAL	1	TRUE	1	0.758552893314745	2		976	977	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220105	5220105	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750841016	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	253	628	0	ENST00000357368.4:c.3610G>A	p.Val1204Met	p.V1204M	ENST00000357368	NM_002850.3	1204	Gtg/Atg	22/38	1	2	FACETS	0.961	0.904	1	0.961	0.904	1	CLONAL	1	TRUE	1	0.758552893314745	2		628	694	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244247	5244248	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	246	700	0	ENST00000357368.4:c.1234_1235delinsTT	p.Pro412Phe	p.P412F	ENST00000357368	NM_002850.3	412	CCc/TTc	11/38	1	2	FACETS	0.89	0.835	0.945	0.89	0.835	0.945	CLONAL	1	TRUE	1	0.758552893314745	2		700	729	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252760	10252760	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	302	626	1	ENST00000340748.4:c.3205C>T	p.Pro1069Ser	p.P1069S	ENST00000340748		1069	Ccc/Tcc	29/40	1	2	FACETS	0.97	0.918	1	0.97	0.918	1	CLONAL	1	TRUE	1	0.758552893314745	2		627	821	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100046	11100047	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	254	652	0	ENST00000358026.2:c.1172_1173delinsTT	p.Ser391Phe	p.S391F	ENST00000358026	NM_001128849.1	391	tCC/tTT	7/36	1	2	FACETS	0.888	0.835	0.943	0.888	0.835	0.943	CLONAL	1	TRUE	1	0.758552893314745	2		652	754	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130271	11130271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	207	464	0	ENST00000358026.2:c.2510C>T	p.Ser837Phe	p.S837F	ENST00000358026	NM_001128849.1	837	tCc/tTc	18/36	1	2	FACETS	0.978	0.915	1	0.978	0.915	1	CLONAL	1	TRUE	1	0.758552893314745	2		464	558	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295807	15295807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1160299759	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	409	905	0	ENST00000263388.2:c.2320C>T	p.Pro774Ser	p.P774S	ENST00000263388	NM_000435.2	774	Ccc/Tcc	15/33	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.758552893314745	2		905	995	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222931	36222931	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202092778	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	421	991	0	ENST00000222270.7:c.5560C>T	p.Pro1854Ser	p.P1854S	ENST00000222270	NM_014727.1	1854	Cct/Tct	27/37	1	2	FACETS	0.928	0.885	0.972	0.928	0.885	0.972	CLONAL	1	TRUE	1	0.758552893314745	2		991	1196	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224566	36224566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	402	1008	0	ENST00000222270.7:c.7028C>T	p.Pro2343Leu	p.P2343L	ENST00000222270	NM_014727.1	2343	cCc/cTc	29/37	1	2	FACETS	0.945	0.9	0.99	0.945	0.9	0.99	CLONAL	1	TRUE	1	0.758552893314745	2		1008	1122	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973154	25973154	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1038333577	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	283	525	1	ENST00000435504.4:c.1271C>T	p.Pro424Leu	p.P424L	ENST00000435504		424	cCa/cTa	12/13	0.758552893314745	3	FACETS	1	0.942	1	0.501	0.471	0.531	CLONAL	1	TRUE	1	0.758552893314745	3		526	1028	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754973	29754973	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	243	451	0	ENST00000389048.3:c.962T>A	p.Leu321His	p.L321H	ENST00000389048	NM_004304.4	321	cTc/cAc	4/29	0.758552893314745	3	FACETS	0.922	0.863	0.984	0.461	0.431	0.492	CLONAL	1	TRUE	1	0.758552893314745	3		451	958	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026206	48026206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	168	419	0	ENST00000234420.5:c.1084C>T	p.Pro362Ser	p.P362S	ENST00000234420	NM_000179.2	362	Cct/Tct	4/10	1	2	FACETS	0.989	0.918	1	0.989	0.918	1	CLONAL	1	TRUE	1	0.758552893314745	2		419	448	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158636923	158636923	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773459224	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	286	516	0	ENST00000263640.3:c.257C>T	p.Ser86Phe	p.S86F	ENST00000263640	NM_001105.4	86	tCc/tTc	4/11	1	2	FACETS	0.952	0.899	1	0.952	0.899	1	CLONAL	1	TRUE	1	0.758552893314745	2		516	792	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113155	209113155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371567806	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	203	369	0	ENST00000345146.2:c.352C>T	p.Pro118Ser	p.P118S	ENST00000345146	NM_005896.2	118	Ccc/Tcc	4/10	1	2	FACETS	0.91	0.85	0.972	0.91	0.85	0.972	CLONAL	1	TRUE	1	0.758552893314745	2		369	588	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488679	212488679	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752771315	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	281	549	0	ENST00000342788.4:c.2170C>T	p.Leu724Phe	p.L724F	ENST00000342788	NM_005235.2	724	Ctt/Ttt	18/28	1	2	FACETS	0.889	0.839	0.941	0.889	0.839	0.941	CLONAL	1	TRUE	1	0.758552893314745	2		549	833	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422407	225422407	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	309	579	0	ENST00000264414.4:c.233G>A	p.Arg78Lys	p.R78K	ENST00000264414	NM_003590.4	78	aGa/aAa	2/16	NA	2	FACETS	1	0.947	1			1	INDETERMINATE	1	TRUE	NA	0.758552893314745	2		579	815	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793310	242793310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	341	870	0	ENST00000334409.5:c.767G>A	p.Gly256Glu	p.G256E	ENST00000334409	NM_005018.2	256	gGa/gAa	5/5	NA	2	FACETS	0.98	0.931	1			1	INDETERMINATE	1	TRUE	NA	0.758552893314745	2		870	917	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525054	9525055	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	208	440	2	ENST00000353224.5:c.1830_1831delinsAA	p.Met610_Ala611delinsIleThr	p.M610_A611delinsIT	ENST00000353224	NM_177990.2	610	atGGcc/atAAcc	8/10	1	2	FACETS	0.949	0.887	1	0.949	0.887	1	CLONAL	1	TRUE	1	0.758552893314745	2		442	578	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546788	9546788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772481025	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	199	386	0	ENST00000353224.5:c.1234C>T	p.Pro412Ser	p.P412S	ENST00000353224	NM_177990.2	412	Ccg/Tcg	5/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.758552893314745	2		386	444	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29083962	29083962	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs200432447	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	29	117	0	ENST00000328354.6:c.1555C>T	p.Arg519Ter	p.R519*	ENST00000328354	NM_007194.3	519	Cga/Tga	15/15	1	2	FACETS	0.538	0.438	0.649	0.538	0.438	0.649	SUBCLONAL	1	TRUE	1	0.758552893314745	2		117	142	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546201	41546201	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	172	377	0	ENST00000263253.7:c.2816C>T	p.Pro939Leu	p.P939L	ENST00000263253	NM_001429.3	939	cCa/cTa	14/31	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.758552893314745	2		377	425	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602746	55602746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	281	567	0	ENST00000288135.5:c.2567G>A	p.Gly856Glu	p.G856E	ENST00000288135	NM_000222.2	856	gGg/gAg	18/21	1	2	FACETS	0.975	0.92	1	0.975	0.92	1	CLONAL	1	TRUE	1	0.758552893314745	2		567	760	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143033782	143033782	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	282	500	0	ENST00000262992.4:c.2189C>T	p.Pro730Leu	p.P730L	ENST00000262992	NM_001101669.1	730	cCt/cTt	20/24	0.758552893314745	1	FACETS	0.97	0.925	1	0.97	0.925	1	CLONAL	1	TRUE	0	0.758552893314745	1		500	476	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143352393	143352393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1322547312	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	372	608	0	ENST00000262992.4:c.20G>A	p.Gly7Glu	p.G7E	ENST00000262992	NM_001101669.1	7	gGg/gAg	2/24	0.758552893314745	1	FACETS	0.959	0.92	0.997	0.959	0.92	0.997	CLONAL	1	TRUE	0	0.758552893314745	1		608	635	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630816	187630816	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373030986	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	353	641	0	ENST00000441802.2:c.166C>T	p.Pro56Ser	p.P56S	ENST00000441802	NM_005245.3	56	Cct/Tct	2/27	0.758552893314745	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.758552893314745	1		641	578	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401691	401691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	198	571	0	ENST00000380956.4:c.1013G>A	p.Gly338Glu	p.G338E	ENST00000380956	NM_001195286.1	338	gGg/gAg	7/9	1	2	FACETS	0.879	0.819	0.94	0.879	0.819	0.94	CLONAL	1	TRUE	1	0.758552893314745	2		571	594	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120729	94120729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	344	568	0	ENST00000369303.4:c.322G>A	p.Asp108Asn	p.D108N	ENST00000369303	NM_004440.3	108	Gat/Aat	3/17	1	2	FACETS	0.977	0.928	1	0.977	0.928	1	CLONAL	1	TRUE	1	0.758552893314745	2		568	928	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041031	112041031	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	218	471	0	ENST00000368678.4:c.224C>T	p.Thr75Ile	p.T75I	ENST00000368678		75	aCc/aTc	3/13	1	2	FACETS	0.956	0.896	1	0.956	0.896	1	CLONAL	1	TRUE	1	0.758552893314745	2		471	601	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631302	117631302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138376257	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	300	462	1	ENST00000368508.3:c.6376C>T	p.Arg2126Trp	p.R2126W	ENST00000368508	NM_002944.2	2126	Cgg/Tgg	40/43	1	2	FACETS	0.999	0.945	1	0.999	0.945	1	CLONAL	1	TRUE	1	0.758552893314745	2		463	792	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678077	117678077	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs199725375	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	148	344	0	ENST00000368508.3:c.3856C>T	p.Arg1286Cys	p.R1286C	ENST00000368508	NM_002944.2	1286	Cgc/Tgc	25/43	1	2	FACETS	0.867	0.799	0.937	0.867	0.799	0.937	CLONAL	1	TRUE	1	0.758552893314745	2		344	450	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679142	117679142	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	250	460	0	ENST00000368508.3:c.3679A>C	p.Thr1227Pro	p.T1227P	ENST00000368508	NM_002944.2	1227	Aca/Cca	24/43	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.758552893314745	2		460	646	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527399	137527399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	230	424	0	ENST00000367739.4:c.247C>T	p.His83Tyr	p.H83Y	ENST00000367739	NM_000416.2	83	Cat/Tat	3/7	1	2	FACETS	0.964	0.905	1	0.964	0.905	1	CLONAL	1	TRUE	1	0.758552893314745	2		424	629	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983127	149983127	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	374	800	0	ENST00000253339.5:c.3131C>T	p.Pro1044Leu	p.P1044L	ENST00000253339		1044	cCt/cTt	7/7	1	2	FACETS	0.986	0.938	1	0.986	0.938	1	CLONAL	1	TRUE	1	0.758552893314745	2		800	1000	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332882	152332882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	287	539	0	ENST00000206249.3:c.1188G>A	p.Met396Ile	p.M396I	ENST00000206249	NM_000125.3	396	atG/atA	5/8	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.758552893314745	2		539	754	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528180	157528180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	349	671	0	ENST00000346085.5:c.5905C>T	p.Pro1969Ser	p.P1969S	ENST00000346085	NM_020732.3	1969	Cca/Tca	20/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.758552893314745	2		671	822	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509354	106509354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1562954993	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	241	598	0	ENST00000359195.3:c.1348C>T	p.Pro450Ser	p.P450S	ENST00000359195	NM_002649.2	450	Ccc/Tcc	2/11	1	2	FACETS	0.883	0.828	0.938	0.883	0.828	0.938	CLONAL	1	TRUE	1	0.758552893314745	2		598	720	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509799	106509799	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	328	666	0	ENST00000359195.3:c.1793G>A	p.Trp598Ter	p.W598*	ENST00000359195	NM_002649.2	598	tGg/tAg	2/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.758552893314745	2		666	766	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106510002	106510002	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs995519902	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	264	586	0	ENST00000359195.3:c.1995+1G>A		p.X665_splice	ENST00000359195	NM_002649.2	665			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.758552893314745	2		586	637	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520111	106520111	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	77	243	1	ENST00000359195.3:c.2538+1G>A		p.X846_splice	ENST00000359195	NM_002649.2	846			1	2	FACETS	0.672	0.596	0.753	0.672	0.596	0.753	SUBCLONAL	1	TRUE	1	0.758552893314745	2		244	302	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436102	116436102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	331	557	0	ENST00000397752.3:c.4097C>T	p.Pro1366Leu	p.P1366L	ENST00000397752	NM_000245.2	1366	cCt/cTt	21/21	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.758552893314745	2		557	755	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515118	148515118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757601923	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	313	536	0	ENST00000320356.2:c.1091C>T	p.Pro364Leu	p.P364L	ENST00000320356	NM_004456.4	364	cCc/cTc	10/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.758552893314745	2		536	798	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843737	151843737	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	242	399	0	ENST00000262189.6:c.13978G>A	p.Gly4660Arg	p.G4660R	ENST00000262189	NM_170606.2	4660	Gga/Aga	53/59	1	2	FACETS	0.937	0.88	0.995	0.937	0.88	0.995	CLONAL	1	TRUE	1	0.758552893314745	2		399	681	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879384	151879384	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	278	549	0	ENST00000262189.6:c.5561C>T	p.Pro1854Leu	p.P1854L	ENST00000262189	NM_170606.2	1854	cCt/cTt	36/59	1	2	FACETS	0.959	0.905	1	0.959	0.905	1	CLONAL	1	TRUE	1	0.758552893314745	2		549	764	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561431	141561432	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	168	442	1	ENST00000220592.5:c.1373_1374delinsTT	p.Pro458Leu	p.P458L	ENST00000220592	NM_012154.3	458	cCC/cTT	11/19	1	2	FACETS	0.888	0.822	0.955	0.888	0.822	0.955	CLONAL	1	TRUE	1	0.758552893314745	2		443	499	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319931	8319931	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	234	352	0	ENST00000356435.5:c.5570T>A	p.Leu1857Gln	p.L1857Q	ENST00000356435		1857	cTa/cAa	34/35	0.739765040823127	3	FACETS	1	0.953	1	0.511	0.478	0.546	CLONAL	1	TRUE	1	0.758552893314745	3		352	832	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331718	8331718	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	207	482	0	ENST00000356435.5:c.5398G>C	p.Val1800Leu	p.V1800L	ENST00000356435		1800	Gta/Cta	33/35	0.739765040823127	3	FACETS	0.858	0.797	0.921	0.429	0.398	0.461	CLONAL	1	TRUE	1	0.758552893314745	3		482	877	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180289	27180289	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	370	674	0	ENST00000380036.4:c.953A>T	p.Asn318Ile	p.N318I	ENST00000380036	NM_000459.3	318	aAc/aTc	7/23	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.758552893314745	2		674	940	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342767	87342767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	253	455	0	ENST00000277120.3:c.1052C>T	p.Pro351Leu	p.P351L	ENST00000277120		351	cCc/cTc	9/19	0.758552893314745	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.758552893314745	1		455	410	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650109	93650109	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	316	555	0	ENST00000375746.1:c.1660G>A	p.Asp554Asn	p.D554N	ENST00000375746	NM_001174167.1	554	Gat/Aat	12/14	0.758552893314745	1	FACETS	0.976	0.934	1	0.976	0.934	1	CLONAL	1	TRUE	0	0.758552893314745	1		555	530	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268833	98268833	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	226	357	0	ENST00000331920.6:c.250C>T	p.Gln84Ter	p.Q84*	ENST00000331920	NM_000264.3	84	Cag/Tag	2/24	0.621673601048548	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.758552893314745	1		357	353	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250139	110250139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs965501282	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	281	651	1	ENST00000374672.4:c.536C>T	p.Pro179Leu	p.P179L	ENST00000374672	NM_004235.4	179	cCc/cTc	3/5	0.758552893314745	1	FACETS	0.97	0.926	1	0.97	0.926	1	CLONAL	1	TRUE	0	0.758552893314745	1		652	474	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797272	135797272	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	16	242	0	ENST00000298552.3:c.597del	p.Phe199LeufsTer11	p.F199Lfs*11	ENST00000298552	NM_001162426.1	199	ttC/tt	7/23	0.758552893314745	1	FACETS	0.105	0.077	0.138	0.105	0.077	0.138	SUBCLONAL	1	TRUE	0	0.758552893314745	1		242	249	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797304	135797307	+	frameshift_variant	Frame_Shift_Del	DEL	GAAA	GAAA	-	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	32	250	0	ENST00000298552.3:c.562_565del	p.Phe188IlefsTer21	p.F188Ifs*21	ENST00000298552	NM_001162426.1	188	TTTCat/at	7/23	0.758552893314745	1	FACETS	0.217	0.177	0.262	0.217	0.177	0.262	SUBCLONAL	1	TRUE	0	0.758552893314745	1		250	241	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797309	135797310	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTGC	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	22	255	0	ENST00000298552.3:c.556_559dup	p.Leu187ArgfsTer32	p.L187Rfs*32	ENST00000298552	NM_001162426.1	187	ctc/cGCACtc	7/23	0.758552893314745	1	FACETS	0.148	0.114	0.186	0.148	0.114	0.186	SUBCLONAL	1	TRUE	0	0.758552893314745	1		255	244	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933836	39933836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	384	393	0	ENST00000378444.4:c.763C>T	p.Pro255Ser	p.P255S	ENST00000378444	NM_001123385.1	255	Ccc/Tcc	4/15	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.758552893314745	1		393	495	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499706	8499706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	285	665	0	ENST00000356435.5:c.2263G>A	p.Glu755Lys	p.E755K	ENST00000356435		755	Gaa/Aaa	14/35	0.806043485663711	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.806043485663711	1		665	399	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	277	316	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.793175504696792	3	FACETS	1	0.967	1	0.52	0.489	0.551	CLONAL	1	TRUE	1	0.806043485663711	3		316	928	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279680	123279680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	138	308	0	ENST00000358487.5:c.752G>A	p.Arg251Gln	p.R251Q	ENST00000358487	NM_000141.4	251	cGa/cAa	7/18	1	2	FACETS	0.906	0.834	0.979	0.906	0.834	0.979	CLONAL	1	TRUE	1	0.806043485663711	2		308	378	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	184	173	1				ENST00000310581	NM_198253.2	-/1132			0.806043485663711	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.806043485663711	1		174	252	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956771	68956771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774302685	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	427	644	2	ENST00000288368.4:c.889C>T	p.Arg297Cys	p.R297C	ENST00000288368	NM_024870.2	297	Cgt/Tgt	8/40	0.227857837036822	3	FACETS	0.807	0.773	0.841	0.807	0.773	0.841	INDETERMINATE	2	TRUE	1	0.806043485663711	3		646	921	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979556	2979556	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	417	475	0	ENST00000396946.4:c.691C>T	p.Gln231Ter	p.Q231*	ENST00000396946	NM_032415.4	231	Cag/Tag	6/25	0.793175504696792	3	FACETS	0.959	0.921	0.996	0.959	0.921	0.996	CLONAL	2	TRUE	1	0.806043485663711	3		475	757	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879807	123879807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755330697	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	411	412	0	ENST00000330479.4:c.503G>A	p.Arg168Gln	p.R168Q	ENST00000330479	NM_020382.3	168	cGa/cAa	4/9	0.806043485663711	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.806043485663711	2		412	495	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032257	26032257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	123	277	0	ENST00000244661.2:c.32C>T	p.Ser11Phe	p.S11F	ENST00000244661	NM_003537.3	11	tCc/tTc	1/1	0.806043485663711	3	FACETS	1	0.955	1	0.537	0.49	0.585	CLONAL	1	TRUE	1	0.806043485663711	3		277	399	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380017	116380017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752842662	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	533	555	0	ENST00000397752.3:c.1406G>A	p.Arg469Gln	p.R469Q	ENST00000397752	NM_000245.2	469	cGa/cAa	4/21	0.793175504696792	3	FACETS	0.976	0.942	1	0.976	0.942	1	CLONAL	2	TRUE	1	0.806043485663711	3		555	951	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	217	462	1				ENST00000310581	NM_198253.2	-/1132			0.806043485663711	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.806043485663711	1		463	316	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964333	70964333	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	213	351	0	ENST00000276594.2:c.1695G>A	p.Met565Ile	p.M565I	ENST00000276594	NM_024504.3	565	atG/atA	8/8	0.227857837036822	3	FACETS	1	0.993	1	0.749	0.703	0.795	INDETERMINATE	1	TRUE	1	0.806043485663711	3		351	495	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926270	112926270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918457	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	652	619	1	ENST00000351677.2:c.1403C>T	p.Thr468Met	p.T468M	ENST00000351677	NM_002834.3	468	aCg/aTg	12/16	0.806043485663711	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.806043485663711	2		620	802	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1023835002	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	250	529	0	ENST00000558401.1:c.1A>G	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Gtg	1/4	0.750832139761723	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.806043485663711	1		529	364	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562981	29562981	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs376576925	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	288	666	1	ENST00000356175.3:c.3916C>T	p.Arg1306Ter	p.R1306*	ENST00000356175	NM_000267.3	1306	Cga/Tga	29/57	1	2	FACETS	0.997	0.943	1	0.997	0.943	1	CLONAL	1	TRUE	1	0.806043485663711	2		667	717	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679274	29679274	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	154	338	0	ENST00000356175.3:c.7395-1G>A		p.X2465_splice	ENST00000356175	NM_000267.3	2465			1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.806043485663711	2		338	377	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043904	180043904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56082504	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	584	797	2	ENST00000261937.6:c.3092G>A	p.Arg1031Gln	p.R1031Q	ENST00000261937	NM_182925.4	1031	cGa/cAa	22/30	0.806043485663711	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.806043485663711	2		799	710	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211050	55211050	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17289589	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	277	599	0	ENST00000275493.2:c.293G>A	p.Arg98Gln	p.R98Q	ENST00000275493	NM_005228.3	98	cGa/cAa	3/28	0.793175504696792	3	FACETS	1	0.958	1	0.511	0.481	0.543	CLONAL	1	TRUE	1	0.806043485663711	3		599	943	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091207	29091207	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137853011	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	154	170	0	ENST00000328354.6:c.1283C>T	p.Ser428Phe	p.S428F	ENST00000328354	NM_007194.3	428	tCt/tTt	12/15	0.793175504696792	3	FACETS	0.968	0.906	1	0.968	0.906	1	CLONAL	2	TRUE	1	0.806043485663711	3		170	277	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249824	110249824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	316	839	0	ENST00000374672.4:c.851C>T	p.Ser284Leu	p.S284L	ENST00000374672	NM_004235.4	284	tCg/tTg	3/5	1	2	FACETS	0.968	0.918	1	0.968	0.918	1	CLONAL	1	TRUE	1	0.806043485663711	2		839	810	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955959	55955959	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	245	480	0	ENST00000263923.4:c.3203C>T	p.Pro1068Leu	p.P1068L	ENST00000263923	NM_002253.2	1068	cCt/cTt	24/30	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.806043485663711	2		480	581	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1976665	1976665	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	270	681	0	ENST00000382891.5:c.3448A>G	p.Thr1150Ala	p.T1150A	ENST00000382891	NM_133335.3	1150	Acc/Gcc	19/22	1	2	FACETS	0.846	0.797	0.896	0.846	0.797	0.896	CLONAL	1	TRUE	1	0.806043485663711	2		681	792	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688747	47688747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	219	371	1	ENST00000347630.2:c.553C>T	p.Arg185Trp	p.R185W	ENST00000347630	NM_001007230.1	185	Cgg/Tgg	7/11	1	2	FACETS	0.95	0.891	1	0.95	0.891	1	CLONAL	1	TRUE	1	0.806043485663711	2		372	572	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425230	49425230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199797812	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	420	1009	1	ENST00000301067.7:c.13258C>T	p.Arg4420Trp	p.R4420W	ENST00000301067	NM_003482.3	4420	Cgg/Tgg	39/54	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.806043485663711	2		1010	1020	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348802	118348802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	159	312	0	ENST00000534358.1:c.3455C>T	p.Ser1152Leu	p.S1152L	ENST00000534358	NM_005933.3	1152	tCg/tTg	5/36	0.806043485663711	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.806043485663711	1		312	220	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971155	21971155	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	210	561	0	ENST00000304494.5:c.203del	p.Ala68GlyfsTer78	p.A68Gfs*78	ENST00000304494	NM_000077.4	68	gCg/gg	2/3	0.806043485663711	1	FACETS	0.984	0.937	1	0.984	0.937	1	CLONAL	1	TRUE	0	0.806043485663711	1		561	316	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737121	162737121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	468	540	0	ENST00000367921.3:c.1265G>A	p.Arg422Lys	p.R422K	ENST00000367921	NM_006182.2	422	aGg/aAg	11/18	0.793175504696792	3	FACETS	0.962	0.926	0.997	0.962	0.926	0.997	CLONAL	2	TRUE	1	0.806043485663711	3		540	847	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741336	17741336	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	314	747	0	ENST00000250003.3:c.7C>A	p.Leu3Ile	p.L3I	ENST00000250003	NM_002478.4	3	Cta/Ata	1/3	0.806043485663711	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.806043485663711	1		747	449	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77069965	77069965	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	271	652	0	ENST00000356341.3:c.575C>T	p.Pro192Leu	p.P192L	ENST00000356341	NM_002576.4	192	cCa/cTa	6/15	1	2	FACETS	0.961	0.907	1	0.961	0.907	1	CLONAL	1	TRUE	1	0.806043485663711	2		652	700	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195697	102195697	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	205	432	1	ENST00000263464.3:c.457G>A	p.Asp153Asn	p.D153N	ENST00000263464	NM_001165.4	153	Gat/Aat	2/9	0.806043485663711	1	FACETS	0.992	0.944	1	0.992	0.944	1	CLONAL	1	TRUE	0	0.806043485663711	1		433	306	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211467	46211470	+	frameshift_variant	Frame_Shift_Del	DEL	AGTT	AGTT	-	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	128	252	0	ENST00000334344.6:c.434_437del	p.Ser145MetfsTer69	p.S145Mfs*69	ENST00000334344	NM_152641.2	145	AGTTat/at	5/21	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.806043485663711	2		252	311	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244386	46244386	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	183	503	0	ENST00000334344.6:c.2481del	p.Gln827HisfsTer22	p.Q827Hfs*22	ENST00000334344	NM_152641.2	827	cAa/ca	15/21	1	2	FACETS	0.91	0.847	0.974	0.91	0.847	0.974	CLONAL	1	TRUE	1	0.806043485663711	2		503	499	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857965	9857965	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	293	637	1	ENST00000330684.3:c.3436G>A	p.Asp1146Asn	p.D1146N	ENST00000330684	NM_001134407.1	1146	Gac/Aac	13/13	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.806043485663711	2		638	715	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349203	11349203	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	78	175	0	ENST00000332029.2:c.133G>A	p.Val45Ile	p.V45I	ENST00000332029	NM_003745.1	45	Gtc/Atc	2/2	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.806043485663711	2		175	182	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828294	72828294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	258	623	0	ENST00000268489.5:c.8287G>A	p.Asp2763Asn	p.D2763N	ENST00000268489	NM_006885.3	2763	Gat/Aat	9/10	1	2	FACETS	0.994	0.938	1	0.994	0.938	1	CLONAL	1	TRUE	1	0.806043485663711	2		623	644	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216439	7216439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	233	629	0	ENST00000380728.2:c.809C>T	p.Ser270Phe	p.S270F	ENST00000380728		270	tCt/tTt	10/11	1	2	FACETS	0.869	0.815	0.924	0.869	0.815	0.924	CLONAL	1	TRUE	1	0.806043485663711	2		629	665	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587415	29587415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1265291141	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	204	443	0	ENST00000356175.3:c.4396C>T	p.Pro1466Ser	p.P1466S	ENST00000356175	NM_000267.3	1466	Cct/Tct	33/57	1	2	FACETS	0.893	0.834	0.953	0.893	0.834	0.953	CLONAL	1	TRUE	1	0.806043485663711	2		443	567	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348433	56348433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	151	311	0	ENST00000348428.3:c.241G>A	p.Val81Ile	p.V81I	ENST00000348428	NM_006785.3	81	Gta/Ata	2/17	0.806043485663711	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.806043485663711	1		311	202	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727874	41727874	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767554708	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	371	890	0	ENST00000301178.4:c.499G>A	p.Glu167Lys	p.E167K	ENST00000301178	NM_021913.4	167	Gag/Aag	4/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.806043485663711	2		890	895	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972795	25972795	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	261	604	0	ENST00000435504.4:c.1630G>A	p.Ala544Thr	p.A544T	ENST00000435504		544	Gcg/Acg	12/13	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.806043485663711	2		604	645	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101085	26101085	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	216	534	0	ENST00000435504.4:c.7G>T	p.Glu3Ter	p.E3*	ENST00000435504		3	Gaa/Taa	1/13	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.806043485663711	2		534	527	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182589	99182589	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	216	547	0	ENST00000074304.5:c.2392C>T	p.Leu798Phe	p.L798F	ENST00000074304	NM_001134224.1	798	Ctc/Ttc	22/26	1	2	FACETS	0.939	0.879	0.999	0.939	0.879	0.999	CLONAL	1	TRUE	1	0.806043485663711	2		547	571	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713377	40713377	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1417250081	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	295	758	0	ENST00000373198.4:c.4138G>A	p.Glu1380Lys	p.E1380K	ENST00000373198	NM_133170.3	1380	Gag/Aag	30/32	1	2	FACETS	0.944	0.893	0.996	0.944	0.893	0.996	CLONAL	1	TRUE	1	0.806043485663711	2		758	775	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730871	40730871	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	287	766	1	ENST00000373198.4:c.3664C>T	p.His1222Tyr	p.H1222Y	ENST00000373198	NM_133170.3	1222	Cat/Tat	27/32	1	2	FACETS	0.968	0.915	1	0.968	0.915	1	CLONAL	1	TRUE	1	0.806043485663711	2		767	736	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125494	47125494	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	249	574	1	ENST00000409792.3:c.5776C>T	p.Gln1926Ter	p.Q1926*	ENST00000409792	NM_014159.6	1926	Caa/Taa	12/21	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.806043485663711	2		575	606	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164690	47164690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	172	393	0	ENST00000409792.3:c.1436C>T	p.Ser479Phe	p.S479F	ENST00000409792	NM_014159.6	479	tCt/tTt	3/21	1	2	FACETS	0.968	0.9	1	0.968	0.9	1	CLONAL	1	TRUE	1	0.806043485663711	2		393	441	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670621	134670621	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	377	937	0	ENST00000398015.3:c.532C>T	p.Gln178Ter	p.Q178*	ENST00000398015	NM_004441.4	178	Cag/Tag	3/16	0.806043485663711	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.806043485663711	1		937	549	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921514	178921514	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	164	402	0	ENST00000263967.3:c.996T>G	p.Ser332Arg	p.S332R	ENST00000263967	NM_006218.2	332	agT/agG	5/21	1	2	FACETS	0.946	0.878	1	0.946	0.878	1	CLONAL	1	TRUE	1	0.806043485663711	2		402	430	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442814	187442814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	255	561	1	ENST00000232014.4:c.1892C>T	p.Pro631Leu	p.P631L	ENST00000232014	NM_001130845.1	631	cCc/cTc	9/10	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.806043485663711	2		562	622	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955073	55955073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	254	539	1	ENST00000263923.4:c.3472G>A	p.Glu1158Lys	p.E1158K	ENST00000263923	NM_002253.2	1158	Gaa/Aaa	26/30	1	2	FACETS	0.994	0.937	1	0.994	0.937	1	CLONAL	1	TRUE	1	0.806043485663711	2		540	634	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84403388	84403388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	228	396	0	ENST00000321945.7:c.97C>T	p.Leu33Phe	p.L33F	ENST00000321945	NM_139076.2	33	Ctt/Ttt	2/9	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.806043485663711	2		396	531	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196610	106196610	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	240	516	0	ENST00000380013.4:c.4943C>T	p.Ser1648Phe	p.S1648F	ENST00000380013	NM_001127208.2	1648	tCc/tTc	11/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.806043485663711	2		516	552	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538860	187538860	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	110	232	0	ENST00000441802.2:c.8878+2T>C		p.X2960_splice	ENST00000441802	NM_005245.3	2960			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.806043485663711	2		232	251	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638816	176638816	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	592	596	0	ENST00000439151.2:c.3416C>T	p.Ser1139Phe	p.S1139F	ENST00000439151	NM_022455.4	1139	tCt/tTt	5/23	0.806043485663711	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.806043485663711	2		596	713	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680200	30680200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	430	931	0	ENST00000376406.3:c.1519G>A	p.Gly507Arg	p.G507R	ENST00000376406	NM_014641.2	507	Ggg/Agg	5/15	0.806043485663711	3	FACETS	1	0.978	1	0.522	0.497	0.548	CLONAL	1	TRUE	1	0.806043485663711	3		931	1433	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967994	93967994	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	205	436	0	ENST00000369303.4:c.1933G>C	p.Gly645Arg	p.G645R	ENST00000369303	NM_004440.3	645	Ggt/Cgt	11/17	0.806043485663711	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.806043485663711	1		436	303	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359036	81359036	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	443	586	1	ENST00000222390.5:c.925C>T	p.Gln309Ter	p.Q309*	ENST00000222390	NM_000601.4	309	Caa/Taa	8/18	0.793175504696792	3	FACETS	0.942	0.905	0.978	0.942	0.905	0.978	CLONAL	2	TRUE	1	0.806043485663711	3		587	819	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878259	151878259	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	336	656	0	ENST00000262189.6:c.6686T>C	p.Ile2229Thr	p.I2229T	ENST00000262189	NM_170606.2	2229	aTt/aCt	36/59	0.793175504696792	3	FACETS	0.995	0.941	1	0.497	0.47	0.525	CLONAL	1	TRUE	1	0.806043485663711	3		656	1176	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934209	68934270	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CATAGGTTAAAATTGCAGAATGGTGAATAAAATGACTAATTTATTCTTACATGAATTCACAG	CATAGGTTAAAATTGCAGAATGGTGAATAAAATGACTAATTTATTCTTACATGAATTCACAG	ACATACAGTAACACATAAATATACACTTACCA	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	95	283	2	ENST00000288368.4:c.337-62_337-1delinsACATACAGTAACACATAAATATACACTTACCA		p.X113_splice	ENST00000288368	NM_024870.2	113			0.227857837036822	3	FACETS	0.848	0.761	0.94	0.424	0.38	0.47	INDETERMINATE	1	TRUE	1	0.806043485663711	3		285	390	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992747	68992747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	280	635	0	ENST00000288368.4:c.1712G>A	p.Gly571Glu	p.G571E	ENST00000288368	NM_024870.2	571	gGa/gAa	16/40	0.227857837036822	3	FACETS	1	0.994	1	0.724	0.685	0.764	INDETERMINATE	1	TRUE	1	0.806043485663711	3		635	673	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69103956	69103956	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	235	507	0	ENST00000288368.4:c.4347-1G>A		p.X1449_splice	ENST00000288368	NM_024870.2	1449			0.227857837036822	3	FACETS	1	0.989	1	0.621	0.582	0.66	INDETERMINATE	1	TRUE	1	0.806043485663711	3		507	659	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460424	8460424	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	112	291	0	ENST00000356435.5:c.3862C>T	p.Leu1288Phe	p.L1288F	ENST00000356435		1288	Ctt/Ttt	22/35	0.806043485663711	1	FACETS	0.999	0.934	1	0.999	0.934	1	CLONAL	1	TRUE	0	0.806043485663711	1		291	166	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971155	21971157	+	frameshift_variant	Frame_Shift_Del	DEL	GCG	GCG	CT	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	192	579	1	ENST00000304494.5:c.201_203delinsAG	p.Ala68GlyfsTer78	p.A68Gfs*78	ENST00000304494	NM_000077.4	67	ggCGCg/ggAGg	2/3	0.806043485663711	1	FACETS	0.9	0.851	0.948	0.9	0.851	0.948	CLONAL	1	TRUE	0	0.806043485663711	1		580	316	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971157	21971157	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	192	561	1	ENST00000579755.1:c.244C>A	p.Arg82Ser	p.R82S	ENST00000579755		82	Cgc/Agc	2/3	0.806043485663711	1	FACETS	0.991	0.941	1	0.991	0.941	1	CLONAL	1	TRUE	0	0.806043485663711	1		562	287	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0035869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	110	230	0				ENST00000310581	NM_198253.2	-/1132			0.3	4	FACETS	1	0.938	1	0.696	0.631	0.763	CLONAL	2	TRUE	1	0.4	4		230	369	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971138	21971138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760640852	NA	P-0035869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	36	338	0	ENST00000304494.5:c.220G>A	p.Asp74Asn	p.D74N	ENST00000304494	NM_000077.4	74	Gac/Aac	2/3	0.215964191248674	1	FACETS	0.335	0.275	0.402	0.335	0.275	0.402	INDETERMINATE	1	TRUE	0	0.4	1		338	430	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28929495	NA	P-0035869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	121	595	0	ENST00000275493.2:c.2155G>A	p.Gly719Ser	p.G719S	ENST00000275493	NM_005228.3	719	Ggc/Agc	18/28	0.171419301828502	3	FACETS	0.838	0.757	0.924	0.419	0.378	0.462	INDETERMINATE	1	TRUE	1	0.4	3		595	866	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0035869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	93	536	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.171419301828502	3	FACETS	0.705	0.626	0.789	0.352	0.313	0.395	INDETERMINATE	1	TRUE	1	0.4	3		536	792	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041721	29041721	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	66	516	0	ENST00000282397.4:c.98A>C	p.Glu33Ala	p.E33A	ENST00000282397	NM_002019.4	33	gAa/gCa	2/30	1	2	FACETS	0.434	0.376	0.497	0.434	0.376	0.497	SUBCLONAL	1	TRUE	1	0.4	2		516	760	SUCCESS
BTK	695	MSKCC	GRCh37	X	100612572	100612572	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0035869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	60	565	0	ENST00000308731.7:c.1103-1G>T		p.X368_splice	ENST00000308731	NM_000061.2	368			1	2	FACETS	0.428	0.368	0.493	0.428	0.368	0.493	SUBCLONAL	1	TRUE	1	0.4	2		565	701	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	40	215	0				ENST00000310581	NM_198253.2	-/1132			0.502973367093144	3	FACETS	0.858	0.719	1	0.429	0.359	0.505	CLONAL	1	TRUE	1	0.502973367093144	3		215	232	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0036201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	264	730	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.490612984233313	2	FACETS	0.949	0.899	0.999	0.949	0.899	0.999	CLONAL	2	TRUE	0	0.502973367093144	2		730	553	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12647737	12647737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773051648	NA	P-0036201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	58	343	0	ENST00000251849.4:c.643C>T	p.Arg215Cys	p.R215C	ENST00000251849	NM_002880.3	215	Cgt/Tgt	6/17	0.502973367093144	3	FACETS	0.992	0.859	1	0.496	0.429	0.567	CLONAL	1	TRUE	1	0.502973367093144	3		343	291	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870888	12870888	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	86	274	0	ENST00000228872.4:c.115G>T	p.Glu39Ter	p.E39*	ENST00000228872	NM_004064.3	39	Gaa/Taa	1/3	0.502973367093144	5	FACETS	0.843	0.751	0.939	0.562	0.501	0.626	CLONAL	2	TRUE	2	0.502973367093144	5		274	356	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358571	67358571	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	159	459	0	ENST00000327367.4:c.79G>T	p.Glu27Ter	p.E27*	ENST00000327367	NM_005902.3	27	Gag/Tag	1/9	0.502973367093144	2	FACETS	0.976	0.91	1	0.976	0.91	1	CLONAL	2	TRUE	0	0.502973367093144	2		459	324	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664541	29664541	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	241	538	0	ENST00000356175.3:c.6520G>T	p.Glu2174Ter	p.E2174*	ENST00000356175	NM_000267.3	2174	Gag/Tag	42/57	0.48296663245599	4	FACETS	0.981	0.92	1	0.981	0.92	1	CLONAL	2	TRUE	2	0.502973367093144	4		538	734	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684058	29684058	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	212	540	1	ENST00000356175.3:c.7756G>T	p.Glu2586Ter	p.E2586*	ENST00000356175	NM_000267.3	2586	Gaa/Taa	52/57	0.48296663245599	4	FACETS	0.922	0.86	0.985	0.922	0.86	0.985	CLONAL	2	TRUE	2	0.502973367093144	4		541	687	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685577	29685578	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTGTGCAGAGTGTGGTGTACCATGAAGAATCCCCACCACAATACCAAACATCTTACCTGCAAAG	novel	NA	P-0036201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	70	554	0	ENST00000356175.3:c.7989_8050+2dup		p.I2663fs	ENST00000356175	NM_000267.3	2663	att/aTTGTGCAGAGTGTGGTGTACCATGAAGAATCCCCACCACAATACCAAACATCTTACCTGCAAAGtt	54/57	0.48296663245599	4	FACETS	0.584	0.509	0.666	0.292	0.254	0.333	SUBCLONAL	1	TRUE	2	0.502973367093144	4		554	716	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763218	59763218	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	341	574	0	ENST00000259008.2:c.2884A>G	p.Ile962Val	p.I962V	ENST00000259008	NM_032043.2	962	Att/Gtt	19/20	0.479960301196111	5	FACETS	0.996	0.948	1	0.996	0.948	1	CLONAL	3	TRUE	2	0.502973367093144	5		574	796	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543864	212543864	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	134	345	0	ENST00000342788.4:c.1535G>T	p.Cys512Phe	p.C512F	ENST00000342788	NM_005235.2	512	tGt/tTt	13/28	0.11661483951855	3	FACETS	1	0.923	1			1	INDETERMINATE	2	TRUE	NA	0.502973367093144	3		345	333	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123104	5123104	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	193	505	0	ENST00000381652.3:c.3160A>T	p.Ser1054Cys	p.S1054C	ENST00000381652	NM_004972.3	1054	Agt/Tgt	23/25	0.472497806798106	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	0	0.502973367093144	2		505	383	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971109	21971121	+	frameshift_variant	Frame_Shift_Del	DEL	GTGCACGGGTCGG	GTGCACGGGTCGG	-	novel	NA	P-0036201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	111	378	0	ENST00000304494.5:c.237_249del	p.Arg80ThrfsTer62	p.R80Tfs*62	ENST00000304494	NM_000077.4	79	acCCGACCCGTGCAC/ac	2/3	0.472497806798106	2	FACETS	0.777	0.71	0.846	0.777	0.71	0.846	SUBCLONAL	2	TRUE	0	0.502973367093144	2		378	284	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0036260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	124	288	0	ENST00000304494.5:c.151-1G>A		p.X51_splice	ENST00000304494	NM_000077.4	51			0.674182576299524	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.674182576299524	1		288	224	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729162	66729162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519732	NA	P-0036260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	299	668	0	ENST00000307102.5:c.370C>T	p.Pro124Ser	p.P124S	ENST00000307102	NM_002755.3	124	Ccg/Tcg	3/11	0.674182576299524	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.674182576299524	1		668	517	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18439842	18439842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	76	366	0	ENST00000266497.5:c.740C>T	p.Ser247Phe	p.S247F	ENST00000266497		247	tCt/tTt	2/31	1	2	FACETS	0.829	0.736	0.927	0.829	0.736	0.927	CLONAL	1	TRUE	1	0.674182576299524	2		366	272	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0036260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	218	641	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.989	0.925	1	0.989	0.925	1	CLONAL	1	TRUE	1	0.674182576299524	2		641	654	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0036260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	58	462	1				ENST00000310581	NM_198253.2	-/1132			0.674182576299524	1	FACETS	0.7	0.614	0.789	0.7	0.614	0.789	SUBCLONAL	1	TRUE	0	0.674182576299524	1		463	163	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0036260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	220	516	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	0.674182576299524	1	FACETS	0.919	0.865	0.972	0.919	0.865	0.972	CLONAL	1	TRUE	0	0.674182576299524	1		516	471	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085635	16085635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	96	445	0	ENST00000281043.3:c.811G>A	p.Glu271Lys	p.E271K	ENST00000281043	NM_005378.4	271	Gaa/Aaa	3/3	1	2	FACETS	0.916	0.826	1	0.916	0.826	1	CLONAL	1	TRUE	1	0.674182576299524	2		445	311	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274897	41274897	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	266	514	0	ENST00000349496.5:c.1147T>C	p.Trp383Arg	p.W383R	ENST00000349496	NM_001904.3	383	Tgg/Cgg	8/15	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.674182576299524	2		514	645	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962530	100962530	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752817186	NA	P-0036260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	136	555	0	ENST00000325455.5:c.1867C>T	p.Arg623Cys	p.R623C	ENST00000325455	NM_001202474.3	623	Cgc/Tgc	3/8	0.516036326241905	1	FACETS	0.514	0.47	0.56	0.514	0.47	0.56	SUBCLONAL	1	TRUE	0	0.674182576299524	1		555	520	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961796	55961796	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	90	470	0	ENST00000263923.4:c.2765G>A	p.Gly922Glu	p.G922E	ENST00000263923	NM_002253.2	922	gGa/gAa	20/30	1	2	FACETS	0.809	0.725	0.897	0.809	0.725	0.897	CLONAL	1	TRUE	1	0.674182576299524	2		470	330	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247617	123247617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	88	462	0	ENST00000358487.5:c.1874G>A	p.Arg625Gln	p.R625Q	ENST00000358487	NM_000141.4	625	cGa/cAa	14/18	1	2	FACETS	0.859	0.769	0.952	0.859	0.769	0.952	CLONAL	1	TRUE	1	0.674182576299524	2		462	304	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246511	41246511	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	220	729	0	ENST00000357654.3:c.1037C>T	p.Pro346Leu	p.P346L	ENST00000357654	NM_007294.3	346	cCc/cTc	10/23	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.674182576299524	2		729	639	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858448	9858448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	99	552	0	ENST00000330684.3:c.2953C>T	p.Pro985Ser	p.P985S	ENST00000330684	NM_001134407.1	985	Cct/Tct	13/13	1	2	FACETS	0.753	0.677	0.832	0.753	0.677	0.832	SUBCLONAL	1	TRUE	1	0.674182576299524	2		552	390	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268938	115268938	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1379534757	NA	P-0036260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	176	450	2	ENST00000438362.2:c.1672C>T	p.Arg558Cys	p.R558C	ENST00000438362	NM_001242891.1	558	Cgt/Tgt	14/20	1	2	FACETS	0.958	0.888	1	0.958	0.888	1	CLONAL	1	TRUE	1	0.674182576299524	2		452	545	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518368	204518368	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	138	473	0	ENST00000367182.3:c.1031C>T	p.Ser344Phe	p.S344F	ENST00000367182	NM_001278516.1	344	tCt/tTt	11/11	1	2	FACETS	0.975	0.895	1	0.975	0.895	1	CLONAL	1	TRUE	1	0.674182576299524	2		473	420	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871000	12871000	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121917832	NA	P-0036260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	119	335	0	ENST00000228872.4:c.227G>A	p.Trp76Ter	p.W76*	ENST00000228872	NM_004064.3	76	tGg/tAg	1/3	NA	2	FACETS	0.944	0.861	1			1	INDETERMINATE	1	TRUE	NA	0.674182576299524	2		335	374	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041744	42041744	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1379312041	NA	P-0036260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	193	417	0	ENST00000219905.7:c.5939A>G	p.Glu1980Gly	p.E1980G	ENST00000219905	NM_001164273.1	1980	gAa/gGa	17/24	0.674182576299524	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.674182576299524	1		417	324	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858238	9858238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	115	465	0	ENST00000330684.3:c.3163G>A	p.Glu1055Lys	p.E1055K	ENST00000330684	NM_001134407.1	1055	Gag/Aag	13/13	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.674182576299524	2		465	334	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40451847	40451847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	34	78	0	ENST00000345506.4:c.629C>T	p.Ser210Phe	p.S210F	ENST00000345506	NM_003152.3	210	tCt/tTt	7/20	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.674182576299524	2		78	92	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971186	18971188	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	novel	NA	P-0036260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	211	635	0	ENST00000262803.5:c.2243_2245del	p.Phe748del	p.F748del	ENST00000262803	NM_002911.3	747	TTC/-	16/24	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.674182576299524	2		635	617	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546793	9546793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	82	332	0	ENST00000353224.5:c.1229C>T	p.Thr410Ile	p.T410I	ENST00000353224	NM_177990.2	410	aCc/aTc	5/10	0.193022478405315	3	FACETS	1	0.936	1	0.358	0.319	0.399	INDETERMINATE	1	TRUE	0	0.674182576299524	3		332	303	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958902	38958902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	77	292	0	ENST00000357387.3:c.2210G>A	p.Arg737Lys	p.R737K	ENST00000357387	NM_152756.3	737	aGg/aAg	23/38	0.134006720312849	3	FACETS	1	0.979	1	0.727	0.65	0.806	INDETERMINATE	1	TRUE	1	0.674182576299524	3		292	210	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931459	131931459	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	79	385	0	ENST00000265335.6:c.2164A>G	p.Lys722Glu	p.K722E	ENST00000265335		722	Aag/Gag	13/25	0.34703323093215	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.674182576299524	0		385	279	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674237	117674237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs928456849	NA	P-0036260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	184	584	0	ENST00000368508.3:c.4237G>A	p.Gly1413Arg	p.G1413R	ENST00000368508	NM_002944.2	1413	Gga/Aga	26/43	0.669028667408624	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.674182576299524	1		584	354	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069049	5069052	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs759468230	NA	P-0036260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	49	301	0	ENST00000381652.3:c.1356_1359del	p.Cys452Ter	p.C452*	ENST00000381652	NM_004972.3	452	TGTTtg/tg	11/25	0.674182576299524	1	FACETS	0.845	0.739	0.954	0.845	0.739	0.954	CLONAL	1	TRUE	0	0.674182576299524	1		301	114	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376048	8376048	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	106	351	0	ENST00000356435.5:c.4549A>C	p.Thr1517Pro	p.T1517P	ENST00000356435		1517	Acc/Ccc	28/35	0.674182576299524	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.674182576299524	1		351	197	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396293	139396293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	173	738	0	ENST00000277541.6:c.5545G>A	p.Asp1849Asn	p.D1849N	ENST00000277541	NM_017617.3	1849	Gat/Aat	30/34	1	2	FACETS	0.987	0.915	1	0.987	0.915	1	CLONAL	1	TRUE	1	0.674182576299524	2		738	520	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	255	215	0				ENST00000310581	NM_198253.2	-/1132			0.702294829421928	4	FACETS	0.9	0.856	0.943	1	0.994	1	CLONAL	3	TRUE	2	0.752655251817465	4		215	440	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692881	89692881	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	358	335	0	ENST00000371953.3:c.365T>A	p.Ile122Asn	p.I122N	ENST00000371953	NM_000314.4	122	aTt/aAt	5/9	0.752655251817465	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.752655251817465	3		335	422	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958595	175958595	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	330	402	0	ENST00000367669.3:c.1750G>C	p.Asp584His	p.D584H	ENST00000367669	NM_022457.5	584	Gat/Cat	16/20	0.752655251817465	2	FACETS	0.987	0.954	1	0.987	0.954	1	CLONAL	2	TRUE	0	0.752655251817465	2		402	444	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526447	66526447	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	70	500	0	ENST00000358598.2:c.1003C>G	p.Arg335Gly	p.R335G	ENST00000358598	NM_212471.2	335	Cgt/Ggt	11/11	0.752655251817465	4	FACETS	0.308	0.268	0.353	0.154	0.134	0.177	SUBCLONAL	1	TRUE	2	0.752655251817465	4		500	1057	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295172	1295172	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0036290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	206	144	0				ENST00000310581	NM_198253.2	-/1132			0.702294829421928	4	FACETS	0.893	0.845	0.941	1	0.992	1	CLONAL	3	TRUE	2	0.752655251817465	4		144	358	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141517	11141517	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036400-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	252	781	0	ENST00000358026.2:c.3494T>A	p.Leu1165His	p.L1165H	ENST00000358026	NM_001128849.1	1165	cTc/cAc	25/36	0.457761573288434	1	FACETS	0.582	0.548	0.615	0.582	0.548	0.615	INDETERMINATE	1	TRUE	0	0.841139865421864	1		781	597	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	144	380	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.400969177091812	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.400969177091812	1		380	507	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805735	43805735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	207	688	0	ENST00000372470.3:c.791C>T	p.Ser264Phe	p.S264F	ENST00000372470	NM_005373.2	264	tCc/tTc	5/12	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.400969177091812	2		688	929	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574004	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	367	852	1	ENST00000269305.4:c.1023_1024delinsTT	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	341	ttCCga/ttTTga	10/11	1	2	FACETS	0.939	0.893	0.985	1	0.996	1	CLONAL	2	TRUE	1	0.400969177091812	2		853	975	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024225	31024225	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749636650	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	165	668	0	ENST00000375687.4:c.3710C>T	p.Ser1237Phe	p.S1237F	ENST00000375687	NM_015338.5	1237	tCc/tTc	13/13	1	2	FACETS	0.963	0.884	1	0.963	0.884	1	CLONAL	1	TRUE	1	0.400969177091812	2		668	855	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967135	25967135	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	122	571	0	ENST00000435504.4:c.2071C>T	p.Pro691Ser	p.P691S	ENST00000435504		691	Cca/Tca	13/13	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.400969177091812	2		571	602	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965761	25965761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377352572	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	208	863	0	ENST00000435504.4:c.3445C>T	p.Arg1149Cys	p.R1149C	ENST00000435504		1149	Cgt/Tgt	13/13	1	2	FACETS	0.961	0.891	1	0.961	0.891	1	CLONAL	1	TRUE	1	0.400969177091812	2		863	1080	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	121	462	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.400969177091812	2		463	532	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354106	15354106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	136	693	0	ENST00000263377.2:c.2774C>T	p.Ser925Phe	p.S925F	ENST00000263377	NM_058243.2	925	tCc/tTc	14/20	1	2	FACETS	0.832	0.757	0.911	0.832	0.757	0.911	CLONAL	1	TRUE	1	0.400969177091812	2		693	815	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979539	55979539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	138	707	0	ENST00000263923.4:c.908G>A	p.Gly303Glu	p.G303E	ENST00000263923	NM_002253.2	303	gGa/gAa	7/30	0.400969177091812	1	FACETS	0.802	0.732	0.876	0.802	0.732	0.876	CLONAL	1	TRUE	0	0.400969177091812	1		707	686	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578505	7578505	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779196500	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	249	908	0	ENST00000269305.4:c.425C>T	p.Pro142Leu	p.P142L	ENST00000269305	NM_001126112.2	142	cCt/cTt	5/11	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.400969177091812	2		908	1237	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120377	94120377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	96	471	0	ENST00000369303.4:c.674C>T	p.Ser225Phe	p.S225F	ENST00000369303	NM_004440.3	225	tCc/tTc	3/17	1	2	FACETS	0.969	0.867	1	0.969	0.867	1	CLONAL	1	TRUE	1	0.400969177091812	2		471	494	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441322	149441322	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376280561	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	178	785	0	ENST00000286301.3:c.1717G>A	p.Glu573Lys	p.E573K	ENST00000286301	NM_005211.3	573	Gag/Aag	12/22	1	2	FACETS	0.887	0.817	0.96	0.887	0.817	0.96	CLONAL	1	TRUE	1	0.400969177091812	2		785	1001	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527676	103527676	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756730021	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	68	277	0	ENST00000355739.4:c.2984C>T	p.Ser995Phe	p.S995F	ENST00000355739	NM_000123.3	995	tCc/tTc	15/15	1	2	FACETS	0.888	0.776	1	0.888	0.776	1	CLONAL	1	TRUE	1	0.400969177091812	2		277	382	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076731	72076731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	171	639	0	ENST00000357731.5:c.766G>A	p.Glu256Lys	p.E256K	ENST00000357731	NM_173808.2	256	Gaa/Aaa	5/7	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.400969177091812	2		639	820	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725507	162725507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773159664	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	152	748	0	ENST00000367921.3:c.619G>A	p.Gly207Ser	p.G207S	ENST00000367921	NM_006182.2	207	Ggt/Agt	7/18	1	2	FACETS	0.831	0.76	0.906	0.831	0.76	0.906	CLONAL	1	TRUE	1	0.400969177091812	2		748	912	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347764	89347764	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1353936075	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	151	740	0	ENST00000301030.4:c.5186C>T	p.Ala1729Val	p.A1729V	ENST00000301030	NM_001256183.1	1729	gCc/gTc	9/13	1	2	FACETS	0.955	0.874	1	0.955	0.874	1	CLONAL	1	TRUE	1	0.400969177091812	2		740	789	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202740	16202740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	142	479	0	ENST00000375759.3:c.448G>A	p.Gly150Arg	p.G150R	ENST00000375759	NM_015001.2	150	Gga/Aga	3/15	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.400969177091812	2		479	694	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260455	16260455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	143	567	0	ENST00000375759.3:c.7720C>T	p.Pro2574Ser	p.P2574S	ENST00000375759	NM_015001.2	2574	Ccg/Tcg	11/15	1	2	FACETS	0.989	0.904	1	0.989	0.904	1	CLONAL	1	TRUE	1	0.400969177091812	2		567	721	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933729	36933729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375011831	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	204	797	0	ENST00000361632.4:c.1670G>A	p.Ser557Asn	p.S557N	ENST00000361632		557	aGc/aAc	12/16	1	2	FACETS	0.949	0.88	1	0.949	0.88	1	CLONAL	1	TRUE	1	0.400969177091812	2		797	1072	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471676	120471676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1557808434	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	124	567	1	ENST00000256646.2:c.3815C>T	p.Pro1272Leu	p.P1272L	ENST00000256646	NM_024408.3	1272	cCc/cTc	23/34	1	2	FACETS	0.896	0.812	0.985	0.896	0.812	0.985	CLONAL	1	TRUE	1	0.400969177091812	2		568	690	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491090	120491090	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	138	591	0	ENST00000256646.2:c.2699C>T	p.Pro900Leu	p.P900L	ENST00000256646	NM_024408.3	900	cCa/cTa	17/34	1	2	FACETS	0.956	0.871	1	0.956	0.871	1	CLONAL	1	TRUE	1	0.400969177091812	2		591	720	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512179	120512179	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781979575	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	105	555	1	ENST00000256646.2:c.1063G>A	p.Asp355Asn	p.D355N	ENST00000256646	NM_024408.3	355	Gac/Aac	6/34	1	2	FACETS	0.856	0.768	0.948	0.856	0.768	0.948	CLONAL	1	TRUE	1	0.400969177091812	2		556	612	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112764503	112764503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	158	530	0	ENST00000369452.4:c.1112C>T	p.Pro371Leu	p.P371L	ENST00000369452	NM_007373.3	371	cCa/cTa	5/9	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.400969177091812	2		530	704	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137086	64137086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	191	709	0	ENST00000334205.4:c.1597C>T	p.Pro533Ser	p.P533S	ENST00000334205	NM_003942.2	533	Ccg/Tcg	13/17	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.400969177091812	2		709	876	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998178	100998178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1452692847	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	89	434	0	ENST00000325455.5:c.1624C>T	p.Leu542Phe	p.L542F	ENST00000325455	NM_001202474.3	542	Ctc/Ttc	1/8	1	2	FACETS	0.844	0.75	0.943	0.844	0.75	0.943	CLONAL	1	TRUE	1	0.400969177091812	2		434	526	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115723	108115723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	72	328	0	ENST00000278616.4:c.871C>T	p.His291Tyr	p.H291Y	ENST00000278616	NM_000051.3	291	Cat/Tat	7/63	1	2	FACETS	0.898	0.788	1	0.898	0.788	1	CLONAL	1	TRUE	1	0.400969177091812	2		328	400	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371767	118371767	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	138	477	0	ENST00000534358.1:c.6224T>G	p.Val2075Gly	p.V2075G	ENST00000534358	NM_005933.3	2075	gTg/gGg	25/36	1	2	FACETS	0.989	0.902	1	0.989	0.902	1	CLONAL	1	TRUE	1	0.400969177091812	2		477	696	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373470	118373470	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	121	500	0	ENST00000534358.1:c.6863C>T	p.Ser2288Phe	p.S2288F	ENST00000534358	NM_005933.3	2288	tCt/tTt	27/36	1	2	FACETS	0.924	0.837	1	0.924	0.837	1	CLONAL	1	TRUE	1	0.400969177091812	2		500	653	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375707	118375707	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	172	629	0	ENST00000534358.1:c.9100C>T	p.Leu3034Phe	p.L3034F	ENST00000534358	NM_005933.3	3034	Ctt/Ttt	27/36	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.400969177091812	2		629	756	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285828	46285828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	135	519	1	ENST00000334344.6:c.5096G>A	p.Gly1699Glu	p.G1699E	ENST00000334344	NM_152641.2	1699	gGa/gAa	18/21	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.400969177091812	2		520	650	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120802537	120802537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	158	651	1	ENST00000257552.2:c.289C>T	p.Pro97Ser	p.P97S	ENST00000257552	NM_002442.3	97	Cct/Tct	5/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.400969177091812	2		652	702	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416731	121416731	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	174	870	1	ENST00000257555.6:c.160C>T	p.Arg54Ter	p.R54*	ENST00000257555		54	Cga/Tga	1/10	1	2	FACETS	0.899	0.828	0.974	0.899	0.828	0.974	CLONAL	1	TRUE	1	0.400969177091812	2		871	965	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001453	29001453	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	71	280	0	ENST00000282397.4:c.1279A>C	p.Lys427Gln	p.K427Q	ENST00000282397	NM_002019.4	427	Aaa/Caa	10/30	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.400969177091812	2		280	351	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001987	29001987	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	154	637	1	ENST00000282397.4:c.1178A>T	p.Lys393Met	p.K393M	ENST00000282397	NM_002019.4	393	aAg/aTg	9/30	1	2	FACETS	0.874	0.8	0.951	0.874	0.8	0.951	CLONAL	1	TRUE	1	0.400969177091812	2		638	879	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105594	30105594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	215	889	0	ENST00000331968.5:c.1092G>A	p.Met364Ile	p.M364I	ENST00000331968	NM_002742.2	364	atG/atA	7/18	1	2	FACETS	0.974	0.905	1	0.974	0.905	1	CLONAL	1	TRUE	1	0.400969177091812	2		889	1101	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843626	3843626	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1311466278	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	132	566	1	ENST00000262367.5:c.977C>T	p.Ser326Phe	p.S326F	ENST00000262367	NM_004380.2	326	tCt/tTt	4/31	1	2	FACETS	0.909	0.827	0.996	0.909	0.827	0.996	CLONAL	1	TRUE	1	0.400969177091812	2		567	724	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827268	72827269	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	169	779	1	ENST00000268489.5:c.9312_9313delinsTT	p.Pro3105Ser	p.P3105S	ENST00000268489	NM_006885.3	3104	acCCct/acTTct	9/10	1	2	FACETS	0.905	0.832	0.982	0.905	0.832	0.982	CLONAL	1	TRUE	1	0.400969177091812	2		780	931	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877462	89877462	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	134	655	1	ENST00000389301.3:c.301C>T	p.Gln101Ter	p.Q101*	ENST00000389301	NM_000135.2	101	Caa/Taa	4/43	1	2	FACETS	0.869	0.79	0.952	0.869	0.79	0.952	CLONAL	1	TRUE	1	0.400969177091812	2		656	769	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627697	37627697	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	214	777	0	ENST00000447079.4:c.1612C>T	p.Pro538Ser	p.P538S	ENST00000447079	NM_015083.1	538	Cct/Tct	2/14	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.400969177091812	2		777	1038	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118942	70118942	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	341	746	0	ENST00000245479.2:c.514T>C	p.Tyr172His	p.Y172H	ENST00000245479	NM_000346.3	172	Tac/Cac	2/3	0.400969177091812	3	FACETS	0.929	0.88	0.979	0.929	0.88	0.979	CLONAL	2	TRUE	1	0.400969177091812	3		746	1099	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727987	78727987	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	98	371	0	ENST00000306801.3:c.830+2T>G		p.X277_splice	ENST00000306801	NM_020761.2	277			0.400969177091812	3	FACETS	0.978	0.874	1	0.489	0.437	0.544	CLONAL	1	TRUE	1	0.400969177091812	3		371	600	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857756	78857756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	146	736	0	ENST00000306801.3:c.1826C>T	p.Ser609Phe	p.S609F	ENST00000306801	NM_020761.2	609	tCc/tTc	16/34	0.400969177091812	3	FACETS	0.898	0.819	0.982	0.449	0.409	0.491	CLONAL	1	TRUE	1	0.400969177091812	3		736	973	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793234	33793235	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	61	130	1	ENST00000498907.2:c.86_87delinsTT	p.Ala29Val	p.A29V	ENST00000498907	NM_004364.3	29	gCC/gTT	1/1	1	2	FACETS	0.805	0.707	0.907	1	0.976	1	CLONAL	2	TRUE	1	0.400969177091812	2		131	189	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158594069	158594069	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	136	567	0	ENST00000263640.3:c.1504C>T	p.Leu502Phe	p.L502F	ENST00000263640	NM_001105.4	502	Ctc/Ttc	11/11	1	2	FACETS	0.901	0.82	0.986	0.901	0.82	0.986	CLONAL	1	TRUE	1	0.400969177091812	2		567	753	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149779	202149779	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	193	876	0	ENST00000358485.4:c.1220T>G	p.Leu407Arg	p.L407R	ENST00000358485	NM_001080125.1	407	cTt/cGt	8/9	1	2	FACETS	0.996	0.921	1	0.996	0.921	1	CLONAL	1	TRUE	1	0.400969177091812	2		876	967	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376300	225376300	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	81	353	0	ENST00000264414.4:c.655-1G>A		p.X219_splice	ENST00000264414	NM_003590.4	219			1	2	FACETS	0.929	0.822	1	0.929	0.822	1	CLONAL	1	TRUE	1	0.400969177091812	2		353	435	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023372	31023372	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759572953	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	154	663	0	ENST00000375687.4:c.2857C>T	p.Leu953Phe	p.L953F	ENST00000375687	NM_015338.5	953	Ctt/Ttt	13/13	1	2	FACETS	0.93	0.852	1	0.93	0.852	1	CLONAL	1	TRUE	1	0.400969177091812	2		663	826	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419926	41419927	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	140	588	1	ENST00000373198.4:c.394_395delinsAA	p.Gly132Lys	p.G132K	ENST00000373198	NM_133170.3	132	GGg/AAg	3/32	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.400969177091812	2		589	608	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933494	49933494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	186	926	1	ENST00000296474.3:c.2696C>T	p.Thr899Ile	p.T899I	ENST00000296474	NM_002447.2	899	aCc/aTc	11/20	0.400969177091812	1	FACETS	0.869	0.803	0.937	0.869	0.803	0.937	CLONAL	1	TRUE	0	0.400969177091812	1		927	854	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259325	89259325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	125	621	0	ENST00000336596.2:c.469C>T	p.Leu157Phe	p.L157F	ENST00000336596	NM_005233.5	157	Ctt/Ttt	3/17	1	2	FACETS	0.902	0.818	0.991	0.902	0.818	0.991	CLONAL	1	TRUE	1	0.400969177091812	2		621	691	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188180	142188180	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	102	398	0	ENST00000350721.4:c.6551A>C	p.Lys2184Thr	p.K2184T	ENST00000350721	NM_001184.3	2184	aAg/aCg	38/47	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.400969177091812	2		398	477	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602924	55602924	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	90	445	0	ENST00000288135.5:c.2634G>T	p.Lys878Asn	p.K878N	ENST00000288135	NM_000222.2	878	aaG/aaT	19/21	0.400969177091812	1	FACETS	0.762	0.679	0.85	0.762	0.679	0.85	SUBCLONAL	1	TRUE	0	0.400969177091812	1		445	471	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526595	31526595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	139	609	0	ENST00000344624.3:c.445C>T	p.Pro149Ser	p.P149S	ENST00000344624		149	Ccc/Tcc	2/33	1	2	FACETS	0.96	0.876	1	0.96	0.876	1	CLONAL	1	TRUE	1	0.400969177091812	2		609	722	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323247	31323247	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	116	436	0	ENST00000412585.2:c.742C>T	p.Gln248Ter	p.Q248*	ENST00000412585	NM_005514.6	248	Caa/Taa	4/8	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.400969177091812	2		436	578	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178639	32178640	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	171	772	1	ENST00000375023.3:c.2754_2755delinsTT	p.Pro919Ser	p.P919S	ENST00000375023	NM_004557.3	918	tgCCcc/tgTTcc	18/30	1	2	FACETS	0.941	0.866	1	0.941	0.866	1	CLONAL	1	TRUE	1	0.400969177091812	2		773	906	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467624	50467624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758404349	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	74	362	0	ENST00000331340.3:c.859G>A	p.Gly287Ser	p.G287S	ENST00000331340	NM_006060.4	287	Ggc/Agc	8/8	1	2	FACETS	0.828	0.727	0.935	0.828	0.727	0.935	CLONAL	1	TRUE	1	0.400969177091812	2		362	446	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273053	55273053	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	153	681	0	ENST00000275493.2:c.3376C>T	p.Gln1126Ter	p.Q1126*	ENST00000275493	NM_005228.3	1126	Cag/Tag	28/28	1	2	FACETS	0.863	0.79	0.94	0.863	0.79	0.94	CLONAL	1	TRUE	1	0.400969177091812	2		681	884	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970963	70970963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	234	887	0	ENST00000276594.2:c.1298C>T	p.Pro433Leu	p.P433L	ENST00000276594	NM_024504.3	433	cCc/cTc	6/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.400969177091812	2		887	1104	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375969	8375969	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	94	397	0	ENST00000356435.5:c.4628C>G	p.Pro1543Arg	p.P1543R	ENST00000356435		1543	cCt/cGt	28/35	0.400969177091812	1	FACETS	0.872	0.78	0.968	0.872	0.78	0.968	CLONAL	1	TRUE	0	0.400969177091812	1		397	430	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499735	8499735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	167	768	0	ENST00000356435.5:c.2234G>A	p.Arg745Lys	p.R745K	ENST00000356435		745	aGa/aAa	14/35	0.400969177091812	1	FACETS	0.892	0.821	0.965	0.892	0.821	0.965	CLONAL	1	TRUE	0	0.400969177091812	1		768	747	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224140	98224140	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs1064796618	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	177	374	0	ENST00000331920.6:c.2701C>T	p.Gln901Ter	p.Q901*	ENST00000331920	NM_000264.3	901	Cag/Tag	16/24	0.400969177091812	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.400969177091812	2		374	431	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295320	1295321	+	upstream_gene_variant	5'Flank	DEL	CC	CC	T	novel	NA	P-0036435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	110	532	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.868	0.781	0.96	0.868	0.781	0.96	CLONAL	1	TRUE	1	0.400969177091812	2		532	632	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0036512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	437	598	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.268429858591507	6	FACETS	0.99	0.948	1			1	CLONAL	5	TRUE	NA	0.268429858591507	6		598	1011	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0036512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	117	462	1				ENST00000310581	NM_198253.2	-/1132			0.268429858591507	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.268429858591507	3		463	447	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28605671	28605671	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	102	500	0	ENST00000253063.3:c.1275C>G	p.Ile425Met	p.I425M	ENST00000253063	NM_031459.4	425	atC/atG	9/10	0.268429858591507	3	FACETS	1	0.979	1	0.695	0.623	0.772	CLONAL	1	TRUE	1	0.268429858591507	3		500	620	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	461475	461475	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs998253161	NA	P-0036512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	59	419	0	ENST00000399788.2:c.1045C>T	p.Arg349Ter	p.R349*	ENST00000399788	NM_001042603.1	349	Cga/Tga	9/28	1	2	FACETS	0.92	0.793	1	0.92	0.793	1	CLONAL	1	TRUE	1	0.268429858591507	2		419	478	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281177	15281202	+	frameshift_variant	Frame_Shift_Del	DEL	CCGGCCCTTGTGACCAGAGGCCACGT	CCGGCCCTTGTGACCAGAGGCCACGT	-	novel	NA	P-0036512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	78	752	0	ENST00000263388.2:c.5054_5079del	p.Asp1685AlafsTer18	p.D1685Afs*18	ENST00000263388	NM_000435.2	1685	gACGTGGCCTCTGGTCACAAGGGCCGG/g	27/33	0.268429858591507	3	FACETS	0.678	0.594	0.769	0.339	0.297	0.385	SUBCLONAL	1	TRUE	1	0.268429858591507	3		752	972	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295176	1295176	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1475402448	NA	P-0036512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	82	190	0				ENST00000310581	NM_198253.2	-/1132			0.268429858591507	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.268429858591507	3		190	300	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0036680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	96	179	0				ENST00000310581	NM_198253.2	-/1132			0.151476566473459	2	FACETS	1	0.974	1	0.626	0.564	0.691	INDETERMINATE	1	TRUE	0	0.470071928966061	2		179	326	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971088	21971088	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	254	581	0	ENST00000304494.5:c.270C>G	p.Phe90Leu	p.F90L	ENST00000304494	NM_000077.4	90	ttC/ttG	2/3	0.470071928966061	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.470071928966061	2		581	487	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944512	40944512	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	54	684	0	ENST00000373198.4:c.1990T>G	p.Phe664Val	p.F664V	ENST00000373198	NM_133170.3	664	Ttt/Gtt	12/32	1	2	FACETS	0.488	0.417	0.565	0.488	0.417	0.565	SUBCLONAL	1	TRUE	1	0.470071928966061	2		684	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0036680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	136	736	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.470071928966061	2		736	539	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903688	114903688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	173	542	0	ENST00000543371.1:c.692C>T	p.Pro231Leu	p.P231L	ENST00000543371	NM_001198531.1	231	cCa/cTa	7/14	0.470071928966061	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.470071928966061	1		542	468	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37034025	37034025	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	137	396	0	ENST00000358127.4:c.4G>A	p.Asp2Asn	p.D2N	ENST00000358127	NM_001280556.1	2	Gat/Aat	1/10	NA	2	FACETS	0.976	0.891	1			1	INDETERMINATE	1	TRUE	NA	0.470071928966061	2		396	597	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910932	32910932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	64	462	0	ENST00000380152.3:c.2440C>T	p.Pro814Ser	p.P814S	ENST00000380152		814	Ccc/Tcc	11/27	1	2	FACETS	0.651	0.566	0.743	0.651	0.566	0.743	SUBCLONAL	1	TRUE	1	0.470071928966061	2		462	418	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434747	49434747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	165	782	0	ENST00000301067.7:c.6806C>T	p.Ser2269Phe	p.S2269F	ENST00000301067	NM_003482.3	2269	tCc/tTc	31/54	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.470071928966061	2		782	570	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026709	6026709	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587778618	NA	P-0036680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	231	780	1	ENST00000265849.7:c.1687C>T	p.Arg563Ter	p.R563*	ENST00000265849	NM_000535.5	563	Cga/Tga	11/15	0.147547369663504	4	FACETS	0.79	0.738	0.845	0.79	0.738	0.845	INDETERMINATE	2	TRUE	2	0.470071928966061	4		781	914	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958620	38958620	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	100	271	1	ENST00000357387.3:c.2345C>T	p.Ala782Val	p.A782V	ENST00000357387	NM_152756.3	782	gCc/gTc	24/38	0.151476566473459	2	FACETS	1	0.964	1	0.577	0.519	0.636	INDETERMINATE	1	TRUE	0	0.470071928966061	2		272	369	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720796	89720796	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1064793345	NA	P-0036680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	45	229	0	ENST00000371953.3:c.947T>C	p.Leu316Pro	p.L316P	ENST00000371953	NM_000314.4	316	cTa/cCa	8/9	0.470071928966061	1	FACETS	0.544	0.461	0.636	0.544	0.461	0.636	SUBCLONAL	1	TRUE	0	0.470071928966061	1		229	269	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249229	133249229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	122	632	0	ENST00000320574.5:c.1670C>T	p.Pro557Leu	p.P557L	ENST00000320574	NM_006231.2	557	cCt/cTt	15/49	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.470071928966061	2		632	402	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060818	38060818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	148	939	0	ENST00000250448.2:c.1171G>A	p.Asp391Asn	p.D391N	ENST00000250448	NM_004496.3	391	Gac/Aac	2/2	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.470071928966061	2		939	607	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386384	31386384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771223602	NA	P-0036680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	159	717	0	ENST00000328111.2:c.1609C>T	p.Arg537Trp	p.R537W	ENST00000328111	NM_006892.3	537	Cgg/Tgg	15/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.470071928966061	2		717	605	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932600	49932600	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	66	607	0	ENST00000296474.3:c.3271G>A	p.Gly1091Ser	p.G1091S	ENST00000296474	NM_002447.2	1091	Ggc/Agc	14/20	1	2	FACETS	0.707	0.617	0.805	0.707	0.617	0.805	SUBCLONAL	1	TRUE	1	0.470071928966061	2		607	397	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21968236	21968236	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1060501271	NA	P-0036680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	242	363	0	ENST00000304494.5:c.463C>G	p.Pro155Ala	p.P155A	ENST00000304494	NM_000077.4	155	Ccc/Gcc	3/3	0.470071928966061	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.470071928966061	2		363	448	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169603	27169603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	157	756	1	ENST00000380036.4:c.604G>A	p.Ala202Thr	p.A202T	ENST00000380036	NM_000459.3	202	Gcc/Acc	4/23	0.470071928966061	2	FACETS	0.975	0.896	1	0.488	0.448	0.529	CLONAL	1	TRUE	0	0.470071928966061	2		757	685	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409055	139409055	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	247	942	2	ENST00000277541.6:c.2114C>T	p.Pro705Leu	p.P705L	ENST00000277541	NM_017617.3	705	cCc/cTc	13/34	1	2	FACETS	0.752	0.706	0.798	1	0.993	1	SUBCLONAL	2	TRUE	1	0.470071928966061	2		944	699	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	540	215	0				ENST00000310581	NM_198253.2	-/1132			0.746880876788907	4	FACETS	1	0.975	1			1	CLONAL	3	TRUE	NA	0.803530460920735	4		215	804	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945093	31945093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	331	650	0	ENST00000340398.3:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000340398	NM_001013699.2	3	cGa/cAa	1/1	1	2	FACETS	0.94	0.892	0.989	0.94	0.892	0.989	CLONAL	1	TRUE	1	0.803530460920735	2		650	876	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	295	510	1	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	1	2	FACETS	0.982	0.929	1	0.982	0.929	1	CLONAL	1	TRUE	1	0.803530460920735	2		511	748	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805735	43805735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	409	688	0	ENST00000372470.3:c.791C>T	p.Ser264Phe	p.S264F	ENST00000372470	NM_005373.2	264	tCc/tTc	5/12	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.803530460920735	2		688	981	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561263	9561263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769939031	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	255	346	1	ENST00000353224.5:c.519G>A	p.Met173Ile	p.M173I	ENST00000353224	NM_177990.2	173	atG/atA	4/10	1	2	FACETS	0.915	0.861	0.969	0.915	0.861	0.969	CLONAL	1	TRUE	1	0.803530460920735	2		347	694	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242451	55242451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	214	410	0	ENST00000275493.2:c.2221C>T	p.Pro741Ser	p.P741S	ENST00000275493	NM_005228.3	741	Ccc/Tcc	19/28	0.538897470519101	4	FACETS	1	0.975	1	0.367	0.341	0.393	CLONAL	1	TRUE	1	0.803530460920735	4		410	873	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903687	114903687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	263	526	1	ENST00000543371.1:c.691C>T	p.Pro231Ser	p.P231S	ENST00000543371	NM_001198531.1	231	Cca/Tca	7/14	1	2	FACETS	0.941	0.887	0.995	0.941	0.887	0.995	CLONAL	1	TRUE	1	0.803530460920735	2		527	696	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609925	81609925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772490052	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	375	356	1	ENST00000298171.2:c.1523C>T	p.Ser508Leu	p.S508L	ENST00000298171	NM_000369.2	508	tCg/tTg	10/10	0.794593418799224	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.803530460920735	2		357	453	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984854	9984854	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149344082	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	275	556	0	ENST00000330684.3:c.1111G>A	p.Glu371Lys	p.E371K	ENST00000330684	NM_001134407.1	371	Gaa/Aaa	4/13	0.549543367405246	1	FACETS	0.686	0.65	0.722	0.686	0.65	0.722	SUBCLONAL	1	TRUE	0	0.803530460920735	1		556	597	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278101	142278101	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1488897339	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	267	407	0	ENST00000350721.4:c.1724A>G	p.Tyr575Cys	p.Y575C	ENST00000350721	NM_001184.3	575	tAt/tGt	7/47	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.803530460920735	2		407	642	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497317	149497317	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	184	606	0	ENST00000261799.4:c.3001C>T	p.Pro1001Ser	p.P1001S	ENST00000261799	NM_002609.3	1001	Ccc/Tcc	22/23	0.265908393194984	1	FACETS	0.413	0.382	0.444	0.413	0.382	0.444	INDETERMINATE	1	TRUE	0	0.803530460920735	1		606	664	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578400	7578400	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs751477326	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	401	681	0	ENST00000269305.4:c.530C>G	p.Pro177Arg	p.P177R	ENST00000269305	NM_001126112.2	177	cCc/cGc	5/11	0.803530460920735	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.803530460920735	1		681	583	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770597	40770597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761441812	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	252	543	0	ENST00000373198.4:c.2785G>A	p.Asp929Asn	p.D929N	ENST00000373198	NM_133170.3	929	Gat/Aat	19/32	1	2	FACETS	0.947	0.892	1	0.947	0.892	1	CLONAL	1	TRUE	1	0.803530460920735	2		543	662	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268059	55268059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	554	758	0	ENST00000275493.2:c.2899G>A	p.Glu967Lys	p.E967K	ENST00000275493	NM_005228.3	967	Gaa/Aaa	24/28	0.538897470519101	4	FACETS	0.788	0.756	0.82	0.525	0.504	0.547	SUBCLONAL	2	TRUE	1	0.803530460920735	4		758	1578	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523348	9523348	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	216	400	0	ENST00000353224.5:c.1889G>A	p.Gly630Glu	p.G630E	ENST00000353224	NM_177990.2	630	gGg/gAg	9/10	1	2	FACETS	0.952	0.892	1	0.952	0.892	1	CLONAL	1	TRUE	1	0.803530460920735	2		400	565	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670813	134670813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765851482	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	232	467	0	ENST00000398015.3:c.724G>A	p.Gly242Arg	p.G242R	ENST00000398015	NM_004441.4	242	Ggg/Agg	3/16	1	2	FACETS	0.907	0.851	0.963	0.907	0.851	0.963	CLONAL	1	TRUE	1	0.803530460920735	2		467	637	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40447674	40447674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1439727336	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	95	617	0	ENST00000345506.4:c.413C>T	p.Ser138Phe	p.S138F	ENST00000345506	NM_003152.3	138	tCc/tTc	6/20	1	2	FACETS	0.271	0.24	0.303	0.271	0.24	0.303	SUBCLONAL	1	TRUE	1	0.803530460920735	2		617	874	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562641	29562641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854562	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	323	510	0	ENST00000356175.3:c.3721C>T	p.Arg1241Ter	p.R1241*	ENST00000356175	NM_000267.3	1241	Cga/Tga	28/57	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.803530460920735	2		510	801	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874636	35874636	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	261	438	2	ENST00000303115.3:c.792G>A	p.Trp264Ter	p.W264*	ENST00000303115	NM_002185.3	264	tgG/tgA	6/8	0.803530460920735	5	FACETS	0.967	0.904	1	0.242	0.226	0.259	CLONAL	1	TRUE	1	0.803530460920735	5		440	1481	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472522	88472522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55890138	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	327	633	1	ENST00000360948.2:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000360948	NM_001012338.2	678	cGa/cAa	16/19	0.351624935327701	3	FACETS	1	0.993	1	0.66	0.626	0.695	INDETERMINATE	1	TRUE	1	0.803530460920735	3		634	864	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584423	39584423	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	223	401	0	ENST00000262039.4:c.1088C>T	p.Ser363Phe	p.S363F	ENST00000262039	NM_002647.2	363	tCc/tTc	10/25	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.803530460920735	2		401	533	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367239	50367239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1045233686	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	322	235	0	ENST00000331340.3:c.46G>A	p.Glu16Lys	p.E16K	ENST00000331340	NM_006060.4	16	Gaa/Aaa	3/8	0.538897470519101	4	FACETS	0.859	0.821	0.896	0.859	0.821	0.896	CLONAL	3	TRUE	1	0.803530460920735	4		235	561	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058731	180058731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	261	817	0	ENST00000261937.6:c.106G>A	p.Glu36Lys	p.E36K	ENST00000261937	NM_182925.4	36	Gag/Aag	2/30	0.265908393194984	1	FACETS	0.451	0.424	0.48	0.451	0.424	0.48	INDETERMINATE	1	TRUE	0	0.803530460920735	1		817	861	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511630	46511630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773472193	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	296	572	0	ENST00000262741.5:c.1147C>T	p.Arg383Cys	p.R383C	ENST00000262741	NM_003629.3	383	Cgt/Tgt	9/10	1	2	FACETS	0.993	0.94	1	0.993	0.94	1	CLONAL	1	TRUE	1	0.803530460920735	2		572	742	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086016	16086016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057517770	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	49	489	1	ENST00000281043.3:c.1192C>T	p.Arg398Trp	p.R398W	ENST00000281043	NM_005378.4	398	Cgg/Tgg	3/3	NA	2	FACETS	0.174	0.146	0.204			1	INDETERMINATE	1	TRUE	NA	0.803530460920735	2		490	702	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913492	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	305	555	0	ENST00000286548.4:c.626A>G	p.Gln209Arg	p.Q209R	ENST00000286548	NM_002072.3	209	cAa/cGa	5/7	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.803530460920735	2		555	681	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812196	212812196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	214	343	0	ENST00000342788.4:c.380G>A	p.Gly127Glu	p.G127E	ENST00000342788	NM_005235.2	127	gGa/gAa	3/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.803530460920735	2		343	484	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331724	8331724	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs763525789	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	211	369	0	ENST00000356435.5:c.5392C>T	p.Arg1798Ter	p.R1798*	ENST00000356435		1798	Cga/Tga	33/35	0.803530460920735	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.803530460920735	1		369	293	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860908	151860908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	41	354	1	ENST00000262189.6:c.9754C>T	p.Arg3252Cys	p.R3252C	ENST00000262189	NM_170606.2	3252	Cgt/Tgt	43/59	1	2	FACETS	0.17	0.141	0.202	0.17	0.141	0.202	SUBCLONAL	1	TRUE	1	0.803530460920735	2		355	602	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197392	106197392	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	165	315	0	ENST00000380013.4:c.5725G>A	p.Glu1909Lys	p.E1909K	ENST00000380013	NM_001127208.2	1909	Gag/Aag	11/11	0.427987378091973	1	FACETS	0.768	0.718	0.817	0.768	0.718	0.817	INDETERMINATE	1	TRUE	0	0.803530460920735	1		315	320	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40447715	40447715	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	383	643	1	ENST00000345506.4:c.454C>T	p.Arg152Ter	p.R152*	ENST00000345506	NM_003152.3	152	Cga/Tga	6/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.803530460920735	2		644	901	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264782	46264782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	209	427	0	ENST00000371998.3:c.1652C>T	p.Ser551Phe	p.S551F	ENST00000371998		551	tCt/tTt	12/23	1	2	FACETS	0.916	0.857	0.976	0.916	0.857	0.976	CLONAL	1	TRUE	1	0.803530460920735	2		427	568	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11308073	11308073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749298128	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	524	780	0	ENST00000361445.4:c.919G>A	p.Gly307Arg	p.G307R	ENST00000361445	NM_004958.3	307	Gga/Aga	7/58	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.803530460920735	2		780	1248	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265351	16265351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	387	650	0	ENST00000375759.3:c.10843C>T	p.Pro3615Ser	p.P3615S	ENST00000375759	NM_015001.2	3615	Ccc/Tcc	14/15	1	2	FACETS	0.957	0.911	1	0.957	0.911	1	CLONAL	1	TRUE	1	0.803530460920735	2		650	1007	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165800	118165800	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	245	404	1	ENST00000369448.3:c.310G>A	p.Glu104Lys	p.E104K	ENST00000369448	NM_017709.3	104	Gaa/Aaa	2/2	1	2	FACETS	0.995	0.937	1	0.995	0.937	1	CLONAL	1	TRUE	1	0.803530460920735	2		405	613	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193202130	193202130	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	129	261	0	ENST00000367435.3:c.1162C>T	p.Pro388Ser	p.P388S	ENST00000367435	NM_024529.4	388	Cca/Tca	14/17	1	2	FACETS	0.902	0.828	0.978	0.902	0.828	0.978	CLONAL	1	TRUE	1	0.803530460920735	2		261	356	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405508	70405508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	60	595	0	ENST00000373644.4:c.3022C>T	p.Pro1008Ser	p.P1008S	ENST00000373644	NM_030625.2	1008	Cca/Tca	4/12	1	2	FACETS	0.194	0.166	0.224	0.194	0.166	0.224	SUBCLONAL	1	TRUE	1	0.803530460920735	2		595	771	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258102	123258102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868142351	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	230	489	0	ENST00000358487.5:c.1579G>A	p.Asp527Asn	p.D527N	ENST00000358487	NM_000141.4	527	Gac/Aac	12/18	1	2	FACETS	0.929	0.872	0.987	0.929	0.872	0.987	CLONAL	1	TRUE	1	0.803530460920735	2		489	616	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316103	14316103	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	146	300	1	ENST00000256196.4:c.322C>T	p.Gln108Ter	p.Q108*	ENST00000256196		108	Caa/Taa	4/6	1	2	FACETS	0.925	0.854	0.997	0.925	0.854	0.997	CLONAL	1	TRUE	1	0.803530460920735	2		301	393	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946982	71946982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	463	865	0	ENST00000298229.2:c.2831C>T	p.Pro944Leu	p.P944L	ENST00000298229	NM_001567.3	944	cCc/cTc	25/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.803530460920735	2		865	1103	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206760	102206760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	338	508	0	ENST00000263464.3:c.1388C>T	p.Pro463Leu	p.P463L	ENST00000263464	NM_001165.4	463	cCa/cTa	7/9	0.803530460920735	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.803530460920735	1		508	500	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165787	108165787	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	167	302	0	ENST00000278616.4:c.4909+1G>C		p.X1637_splice	ENST00000278616	NM_000051.3	1637			0.803530460920735	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.803530460920735	1		302	240	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362557	118362557	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	348	499	0	ENST00000534358.1:c.4918G>T	p.Glu1640Ter	p.E1640*	ENST00000534358	NM_005933.3	1640	Gaa/Taa	15/36	0.803530460920735	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.803530460920735	1		499	490	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435228	18435228	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs746772476	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	143	304	0	ENST00000266497.5:c.213G>A	p.Trp71Ter	p.W71*	ENST00000266497		71	tgG/tgA	1/31	1	2	FACETS	0.944	0.871	1	0.944	0.871	1	CLONAL	1	TRUE	1	0.803530460920735	2		304	377	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644484	18644484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	218	423	0	ENST00000266497.5:c.2662G>A	p.Asp888Asn	p.D888N	ENST00000266497		888	Gat/Aat	18/31	1	2	FACETS	0.92	0.861	0.979	0.92	0.861	0.979	CLONAL	1	TRUE	1	0.803530460920735	2		423	590	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658337	18658337	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	235	536	1	ENST00000266497.5:c.3142T>A	p.Phe1048Ile	p.F1048I	ENST00000266497		1048	Ttt/Att	22/31	1	2	FACETS	0.885	0.83	0.94	0.885	0.83	0.94	CLONAL	1	TRUE	1	0.803530460920735	2		537	661	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944931	31944931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	185	307	0	ENST00000340398.3:c.170C>T	p.Ser57Leu	p.S57L	ENST00000340398	NM_001013699.2	57	tCg/tTg	1/1	1	2	FACETS	0.978	0.912	1	0.978	0.912	1	CLONAL	1	TRUE	1	0.803530460920735	2		307	471	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865752	57865752	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144663837	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	379	719	0	ENST00000228682.2:c.3229C>T	p.Pro1077Ser	p.P1077S	ENST00000228682	NM_005269.2	1077	Ccc/Tcc	12/12	0.389743833941571	1	FACETS	0.773	0.74	0.806	0.773	0.74	0.806	INDETERMINATE	1	TRUE	0	0.803530460920735	1		719	730	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120863	115120863	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	133	470	0	ENST00000257566.3:c.143C>T	p.Pro48Leu	p.P48L	ENST00000257566	NM_016569.3	48	cCc/cTc	1/8	0.389743833941571	1	FACETS	0.476	0.436	0.517	0.476	0.436	0.517	INDETERMINATE	1	TRUE	0	0.803530460920735	1		470	416	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669514	88669514	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	321	411	0	ENST00000360948.2:c.1384T>C	p.Phe462Leu	p.F462L	ENST00000360948	NM_001012338.2	462	Ttt/Ctt	12/19	0.351624935327701	3	FACETS	0.801	0.762	0.84	0.801	0.762	0.84	INDETERMINATE	2	TRUE	1	0.803530460920735	3		411	699	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642712	3642712	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs933623617	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	249	552	0	ENST00000294008.3:c.2315C>T	p.Ser772Phe	p.S772F	ENST00000294008	NM_032444.2	772	tCc/tTc	11/15	0.549543367405246	1	FACETS	0.697	0.659	0.735	0.697	0.659	0.735	SUBCLONAL	1	TRUE	0	0.803530460920735	1		552	532	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829439	72829439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs961357704	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	55	634	0	ENST00000268489.5:c.7142C>T	p.Ser2381Phe	p.S2381F	ENST00000268489	NM_006885.3	2381	tCc/tTc	9/10	0.803530460920735	1	FACETS	0.148	0.126	0.171	0.148	0.126	0.171	SUBCLONAL	1	TRUE	0	0.803530460920735	1		634	555	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832424	72832424	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	162	419	0	ENST00000268489.5:c.4157C>T	p.Ala1386Val	p.A1386V	ENST00000268489	NM_006885.3	1386	gCc/gTc	9/10	0.803530460920735	1	FACETS	0.6	0.557	0.644	0.6	0.557	0.644	SUBCLONAL	1	TRUE	0	0.803530460920735	1		419	402	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992819	72992819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370750954	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	140	516	0	ENST00000268489.5:c.1226C>T	p.Ser409Leu	p.S409L	ENST00000268489	NM_006885.3	409	tCg/tTg	2/10	0.803530460920735	1	FACETS	0.556	0.512	0.601	0.556	0.512	0.601	SUBCLONAL	1	TRUE	0	0.803530460920735	1		516	375	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012149	16012149	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	344	542	0	ENST00000268712.3:c.2133T>G	p.Asp711Glu	p.D711E	ENST00000268712	NM_006311.3	711	gaT/gaG	19/46	0.803530460920735	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.803530460920735	1		542	504	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321596	30321596	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs751277924	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	243	455	0	ENST00000322652.5:c.1451G>T	p.Gly484Val	p.G484V	ENST00000322652	NM_015355.2	484	gGt/gTt	13/16	1	2	FACETS	0.901	0.847	0.957	0.901	0.847	0.957	CLONAL	1	TRUE	1	0.803530460920735	2		455	671	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40371830	40371830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	473	773	0	ENST00000293328.3:c.581C>T	p.Pro194Leu	p.P194L	ENST00000293328	NM_012448.3	194	cCc/cTc	6/19	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.803530460920735	2		773	1079	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119795	70119795	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	357	628	0	ENST00000245479.2:c.797C>G	p.Pro266Arg	p.P266R	ENST00000245479	NM_000346.3	266	cCc/cGc	3/3	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.803530460920735	2		628	807	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211158	2211158	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	393	884	1	ENST00000398665.3:c.1412C>T	p.Ser471Phe	p.S471F	ENST00000398665	NM_032482.2	471	tCc/tTc	15/28	0.370909564177794	1	FACETS	0.621	0.593	0.65	0.621	0.593	0.65	INDETERMINATE	1	TRUE	0	0.803530460920735	1		885	942	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243912	5243912	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	154	460	0	ENST00000357368.4:c.1570G>A	p.Val524Met	p.V524M	ENST00000357368	NM_002850.3	524	Gtg/Atg	11/38	0.370909564177794	1	FACETS	0.505	0.466	0.545	0.505	0.466	0.545	INDETERMINATE	1	TRUE	0	0.803530460920735	1		460	454	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354228	15354229	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	362	881	4	ENST00000263377.2:c.2651_2652delinsTT	p.Pro884Leu	p.P884L	ENST00000263377	NM_058243.2	884	cCC/cTT	14/20	0.370909564177794	1	FACETS	0.514	0.488	0.54	0.514	0.488	0.54	INDETERMINATE	1	TRUE	0	0.803530460920735	1		885	1049	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355233	15355233	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	326	775	1	ENST00000263377.2:c.2390C>T	p.Pro797Leu	p.P797L	ENST00000263377	NM_058243.2	797	cCc/cTc	13/20	0.370909564177794	1	FACETS	0.594	0.564	0.625	0.594	0.564	0.625	INDETERMINATE	1	TRUE	0	0.803530460920735	1		776	817	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355362	15355362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	87	572	0	ENST00000263377.2:c.2261C>T	p.Pro754Leu	p.P754L	ENST00000263377	NM_058243.2	754	cCc/cTc	13/20	0.370909564177794	1	FACETS	0.236	0.209	0.265	0.236	0.209	0.265	INDETERMINATE	1	TRUE	0	0.803530460920735	1		572	548	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308125	30308126	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	205	600	0	ENST00000262643.3:c.262_263delinsTT	p.Pro88Leu	p.P88L	ENST00000262643	NM_001238.2	88	CCa/TTa	5/12	0.370909564177794	1	FACETS	0.447	0.416	0.479	0.447	0.416	0.479	INDETERMINATE	1	TRUE	0	0.803530460920735	1		600	683	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216191	36216191	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	349	719	0	ENST00000222270.7:c.3599C>T	p.Pro1200Leu	p.P1200L	ENST00000222270	NM_014727.1	1200	cCc/cTc	11/37	0.370909564177794	1	FACETS	0.622	0.591	0.652	0.622	0.591	0.652	INDETERMINATE	1	TRUE	0	0.803530460920735	1		719	836	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224755	36224755	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	332	940	0	ENST00000222270.7:c.7141C>T	p.Gln2381Ter	p.Q2381*	ENST00000222270	NM_014727.1	2381	Cag/Tag	30/37	0.370909564177794	1	FACETS	0.481	0.455	0.507	0.481	0.455	0.507	INDETERMINATE	1	TRUE	0	0.803530460920735	1		940	1028	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085861	16085861	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	194	439	0	ENST00000281043.3:c.1037C>T	p.Pro346Leu	p.P346L	ENST00000281043	NM_005378.4	346	cCa/cTa	3/3	NA	2	FACETS	0.886	0.826	0.947			1	INDETERMINATE	1	TRUE	NA	0.803530460920735	2		439	545	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158595041	158595041	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1262652803	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	234	390	1	ENST00000263640.3:c.1306C>T	p.Pro436Ser	p.P436S	ENST00000263640	NM_001105.4	436	Ccc/Tcc	10/11	1	2	FACETS	0.996	0.936	1	0.996	0.936	1	CLONAL	1	TRUE	1	0.803530460920735	2		391	585	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568861	212568861	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	259	480	0	ENST00000342788.4:c.1257C>A	p.Asn419Lys	p.N419K	ENST00000342788	NM_005235.2	419	aaC/aaA	11/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.803530460920735	2		480	619	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37637660	37637660	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	415	766	1	ENST00000249071.6:c.74C>T	p.Thr25Ile	p.T25I	ENST00000249071	NM_002872.4	25	aCc/aTc	2/7	1	2	FACETS	0.964	0.921	1	0.964	0.921	1	CLONAL	1	TRUE	1	0.803530460920735	2		767	1071	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573182	41573182	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2007	252	696	0	ENST00000263253.7:c.5467C>T	p.Gln1823Ter	p.Q1823*	ENST00000263253	NM_001429.3	1823	Cag/Tag	31/31	0.803530460920735	6	FACETS	0.724	0.674	0.776			1	SUBCLONAL	1	TRUE	NA	0.803530460920735	6		696	2259	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574011	41574011	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1606	179	491	0	ENST00000263253.7:c.6296C>T	p.Pro2099Leu	p.P2099L	ENST00000263253	NM_001429.3	2099	cCc/cTc	31/31	0.803530460920735	6	FACETS	0.651	0.597	0.707			1	SUBCLONAL	1	TRUE	NA	0.803530460920735	6		491	1785	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280717	41280717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	332	611	0	ENST00000349496.5:c.2230C>T	p.Pro744Ser	p.P744S	ENST00000349496	NM_001904.3	744	Cct/Tct	15/15	1	2	FACETS	0.996	0.946	1	0.996	0.946	1	CLONAL	1	TRUE	1	0.803530460920735	2		611	830	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247511	71247511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	267	490	0	ENST00000318789.4:c.22G>A	p.Glu8Lys	p.E8K	ENST00000318789	NM_032682.5	8	Gag/Aag	6/21	1	2	FACETS	0.97	0.915	1	0.97	0.915	1	CLONAL	1	TRUE	1	0.803530460920735	2		490	685	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72866526	72866526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	171	269	0	ENST00000325599.8:c.737C>T	p.Ser246Phe	p.S246F	ENST00000325599	NM_018130.2	246	tCt/tTt	7/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.803530460920735	2		269	405	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204854	128204854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1200135021	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	481	869	0	ENST00000341105.2:c.587C>T	p.Ser196Phe	p.S196F	ENST00000341105	NM_032638.4	196	tCt/tTt	3/6	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.803530460920735	2		869	1126	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461597	138461597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369650319	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	259	456	0	ENST00000289153.2:c.424G>A	p.Asp142Asn	p.D142N	ENST00000289153	NM_006219.2	142	Gat/Aat	3/22	1	2	FACETS	0.947	0.892	1	0.947	0.892	1	CLONAL	1	TRUE	1	0.803530460920735	2		456	681	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275358	142275358	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	238	487	0	ENST00000350721.4:c.1945C>T	p.Leu649Phe	p.L649F	ENST00000350721	NM_001184.3	649	Ctt/Ttt	9/47	1	2	FACETS	0.936	0.879	0.993	0.936	0.879	0.993	CLONAL	1	TRUE	1	0.803530460920735	2		487	633	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919282	178919282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	122	221	0	ENST00000263967.3:c.767G>A	p.Gly256Glu	p.G256E	ENST00000263967	NM_006218.2	256	gGa/gAa	4/21	1	2	FACETS	0.86	0.787	0.936	0.86	0.787	0.936	CLONAL	1	TRUE	1	0.803530460920735	2		221	353	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952063	178952063	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	215	389	0	ENST00000263967.3:c.3118A>C	p.Met1040Leu	p.M1040L	ENST00000263967	NM_006218.2	1040	Atg/Ctg	21/21	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.803530460920735	2		389	519	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604203	189604203	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	286	517	0	ENST00000264731.3:c.1370C>A	p.Ser457Tyr	p.S457Y	ENST00000264731	NM_003722.4	457	tCt/tAt	11/14	1	2	FACETS	0.958	0.906	1	0.958	0.906	1	CLONAL	1	TRUE	1	0.803530460920735	2		517	743	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946135	55946136	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	172	331	1	ENST00000263923.4:c.4043_4044delinsAA	p.Gly1348Glu	p.G1348E	ENST00000263923	NM_002253.2	1348	gGG/gAA	30/30	NA	2	FACETS	0.915	0.85	0.981			1	INDETERMINATE	1	TRUE	NA	0.803530460920735	2		332	468	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286281	66286281	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	157	367	0	ENST00000273854.3:c.1405C>T	p.Pro469Ser	p.P469S	ENST00000273854	NM_004439.5	469	Cca/Tca	6/18	0.427987378091973	1	FACETS	0.774	0.723	0.825	0.774	0.723	0.825	INDETERMINATE	1	TRUE	0	0.803530460920735	1		367	302	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196370	106196370	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	103	337	0	ENST00000380013.4:c.4703C>T	p.Pro1568Leu	p.P1568L	ENST00000380013	NM_001127208.2	1568	cCa/cTa	11/11	0.427987378091973	1	FACETS	0.337	0.303	0.373	0.337	0.303	0.373	INDETERMINATE	1	TRUE	0	0.803530460920735	1		337	455	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524527	187524527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	687	706	0	ENST00000441802.2:c.11153C>T	p.Ser3718Phe	p.S3718F	ENST00000441802	NM_005245.3	3718	tCc/tTc	19/27	0.520807980191648	3	FACETS	0.916	0.887	0.944	0.916	0.887	0.944	CLONAL	2	TRUE	1	0.803530460920735	3		706	1309	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264687	1264687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1403	271	744	0	ENST00000310581.5:c.2675C>T	p.Pro892Leu	p.P892L	ENST00000310581	NM_198253.2	892	cCt/cTt	11/16	0.746880876788907	4	FACETS	0.727	0.679	0.776			1	SUBCLONAL	1	TRUE	NA	0.803530460920735	4		744	1674	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149453057	149453057	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	170	334	0	ENST00000286301.3:c.890-1G>A		p.X297_splice	ENST00000286301	NM_005211.3	297			0.265908393194984	1	FACETS	0.607	0.565	0.65	0.607	0.565	0.65	INDETERMINATE	1	TRUE	0	0.803530460920735	1		334	417	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500461	149500461	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	293	542	0	ENST00000261799.4:c.2576C>T	p.Ser859Phe	p.S859F	ENST00000261799	NM_002609.3	859	tCc/tTc	18/23	0.265908393194984	1	FACETS	0.647	0.613	0.681	0.647	0.613	0.681	INDETERMINATE	1	TRUE	0	0.803530460920735	1		542	674	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522570	176522570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	279	725	0	ENST00000292408.4:c.1667G>A	p.Gly556Glu	p.G556E	ENST00000292408	NM_213647.1	556	gGa/gAa	13/18	0.265908393194984	1	FACETS	0.485	0.457	0.514	0.485	0.457	0.514	INDETERMINATE	1	TRUE	0	0.803530460920735	1		725	856	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043479	180043479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	225	593	0	ENST00000261937.6:c.3107G>A	p.Arg1036Lys	p.R1036K	ENST00000261937	NM_182925.4	1036	aGa/aAa	23/30	0.265908393194984	1	FACETS	0.459	0.429	0.49	0.459	0.429	0.49	INDETERMINATE	1	TRUE	0	0.803530460920735	1		593	730	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048892	180048892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	84	955	0	ENST00000261937.6:c.1670G>A	p.Gly557Asp	p.G557D	ENST00000261937	NM_182925.4	557	gGc/gAc	13/30	0.265908393194984	1	FACETS	0.111	0.097	0.125	0.111	0.097	0.125	INDETERMINATE	1	TRUE	0	0.803530460920735	1		955	1131	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956652	93956652	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	254	470	0	ENST00000369303.4:c.2584C>T	p.Pro862Ser	p.P862S	ENST00000369303	NM_004440.3	862	Cca/Tca	15/17	0.803530460920735	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.803530460920735	1		470	361	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120505	94120505	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	52	420	0	ENST00000369303.4:c.546C>G	p.Phe182Leu	p.F182L	ENST00000369303	NM_004440.3	182	ttC/ttG	3/17	0.803530460920735	1	FACETS	0.247	0.211	0.286	0.247	0.211	0.286	SUBCLONAL	1	TRUE	0	0.803530460920735	1		420	313	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968322	2968322	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779888619	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	855	697	0	ENST00000396946.4:c.1664G>A	p.Arg555Gln	p.R555Q	ENST00000396946	NM_032415.4	555	cGg/cAg	13/25	0.538897470519101	4	FACETS	0.893	0.87	0.917	0.893	0.87	0.917	CLONAL	3	TRUE	1	0.803530460920735	4		697	1432	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026897	6026897	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	270	323	0	ENST00000265849.7:c.1499C>T	p.Ser500Phe	p.S500F	ENST00000265849	NM_000535.5	500	tCc/tTc	11/15	0.538897470519101	4	FACETS	0.856	0.808	0.905	0.571	0.538	0.604	CLONAL	2	TRUE	1	0.803530460920735	4		323	708	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444480	50444480	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	144	286	0	ENST00000331340.3:c.410G>A	p.Arg137Lys	p.R137K	ENST00000331340	NM_006060.4	137	aGa/aAa	4/8	0.538897470519101	4	FACETS	1	0.949	1	0.35	0.32	0.382	CLONAL	1	TRUE	1	0.803530460920735	4		286	615	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856028	151856028	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144222590	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	366	564	0	ENST00000262189.6:c.11590C>T	p.Arg3864Cys	p.R3864C	ENST00000262189	NM_170606.2	3864	Cgc/Tgc	44/59	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.803530460920735	2		564	835	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152009020	152009020	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	63	371	0	ENST00000262189.6:c.602C>T	p.Pro201Leu	p.P201L	ENST00000262189	NM_170606.2	201	cCt/cTt	5/59	1	2	FACETS	0.309	0.267	0.354	0.309	0.267	0.354	SUBCLONAL	1	TRUE	1	0.803530460920735	2		371	508	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370834	55370834	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	311	635	0	ENST00000297316.4:c.136G>A	p.Gly46Ser	p.G46S	ENST00000297316	NM_022454.3	46	Ggc/Agc	1/2	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.803530460920735	2		635	773	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127923143	127923143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	53	539	0	ENST00000373547.4:c.214C>T	p.Pro72Ser	p.P72S	ENST00000373547	NM_002721.4	72	Cct/Tct	3/7	1	2	FACETS	0.159	0.135	0.185	0.159	0.135	0.185	SUBCLONAL	1	TRUE	1	0.803530460920735	2		539	831	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314956	1314956	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	337	564	0	ENST00000400841.2:c.705T>G	p.Ile235Met	p.I235M	ENST00000400841		235	atT/atG	6/6	1	1	FACETS	0.588	0.558	0.618	0.588	0.558	0.618	SUBCLONAL	1	TRUE	0	0.803530460920735	1		564	854	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932309	39932309	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	615	499	0	ENST00000378444.4:c.2290T>C	p.Phe764Leu	p.F764L	ENST00000378444	NM_001123385.1	764	Ttt/Ctt	4/15	1	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.803530460920735	1		499	723	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611096	100611096	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	388	353	0	ENST00000308731.7:c.1510G>A	p.Asp504Asn	p.D504N	ENST00000308731	NM_000061.2	504	Gat/Aat	15/19	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.803530460920735	1		353	478	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504162	123504162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	61	247	0	ENST00000371139.4:c.338G>A	p.Gly113Asp	p.G113D	ENST00000371139	NM_001114937.2	113	gGt/gAt	3/4	1	1	FACETS	0.323	0.281	0.368	0.323	0.281	0.368	SUBCLONAL	1	TRUE	0	0.803530460920735	1		247	281	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860061	152860061	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	198	358	0	ENST00000406277.2:c.367G>T	p.Glu123Ter	p.E123*	ENST00000406277	NM_152274.4	123	Gag/Tag	5/7	1		FACETS		0.967	1				CLONAL	1	TRUE	0	0.803530460920735	1		358	289	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0037116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	178	351	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.368004759996158	3	FACETS	0.967	0.897	1	0.967	0.897	1	CLONAL	2	TRUE	1	0.368004759996158	3		351	592	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0037116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	78	430	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.762	0.671	0.86	0.762	0.671	0.86	SUBCLONAL	1	TRUE	1	0.368004759996158	2		430	556	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904821	101904821	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	95	319	0	ENST00000374994.4:c.809A>T	p.Asn270Ile	p.N270I	ENST00000374994	NM_004612.2	270	aAt/aTt	5/9	0.278745654057803	1	FACETS	0.848	0.758	0.943	0.848	0.758	0.943	CLONAL	1	TRUE	0	0.368004759996158	1		319	497	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219242	133219242	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	147	711	0	ENST00000320574.5:c.4802C>G	p.Pro1601Arg	p.P1601R	ENST00000320574	NM_006231.2	1601	cCt/cGt	37/49	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.368004759996158	2		711	791	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980810	40980810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	144	599	0	ENST00000373198.4:c.1676G>A	p.Gly559Glu	p.G559E	ENST00000373198	NM_133170.3	559	gGg/gAg	10/32	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.368004759996158	2		599	774	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971161	21971162	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGAGCA	novel	NA	P-0037116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	77	511	0	ENST00000304494.5:c.191_196dup	p.Leu64_Leu65dup	p.L64_L65dup	ENST00000304494	NM_000077.4	64	cac/cTGCTCCac	2/3	0.368004759996158	1	FACETS	0.78	0.687	0.878	0.78	0.687	0.878	SUBCLONAL	1	TRUE	0	0.368004759996158	1		511	438	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	102	380	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.233707890860871	1	FACETS	0.988	0.891	1	1	0.988	1	CLONAL	2	TRUE	0	0.233707890860871	1		380	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	52	616	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	0.549	0.466	0.641	0.549	0.466	0.641	SUBCLONAL	1	TRUE	1	0.233707890860871	2		617	810	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	104	596	1	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	TRUE	1	0.233707890860871	2		597	760	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	198	179	0				ENST00000310581	NM_198253.2	-/1132			0.233707890860871	6	FACETS	1	0.943	1	1	0.943	1	CLONAL	5	TRUE	1	0.233707890860871	6		179	493	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418372	139418372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	119	725	0	ENST00000277541.6:c.200C>T	p.Pro67Leu	p.P67L	ENST00000277541	NM_017617.3	67	cCc/cTc	3/34	0.233707890860871	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.233707890860871	1		725	800	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170837530	170837530	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs776815873	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	16	110	0	ENST00000296930.5:c.847-1G>T		p.X283_splice	ENST00000296930	NM_002520.6	283			1	2	FACETS	1	0.836	1	1	0.836	1	CLONAL	1	TRUE	1	0.233707890860871	2		110	117	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488228	56488228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	99	514	0	ENST00000267101.3:c.1747C>T	p.Pro583Ser	p.P583S	ENST00000267101	NM_001982.3	583	Ccc/Tcc	15/28	0.00946665858936102	3	FACETS	1	0.98	1	0.729	0.651	0.811	INDETERMINATE	1	TRUE	1	0.233707890860871	3		514	649	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481417	140481417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913348	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	67	373	0	ENST00000288602.6:c.1391G>A	p.Gly464Glu	p.G464E	ENST00000288602	NM_004333.4	464	gGa/gAa	11/18	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.233707890860871	2		373	481	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812261	43812261	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	39	484	0	ENST00000372470.3:c.1126C>T	p.His376Tyr	p.H376Y	ENST00000372470	NM_005373.2	376	Cac/Tac	7/12	0.177440754080855	3	FACETS	0.556	0.459	0.664	0.278	0.229	0.332	SUBCLONAL	1	TRUE	1	0.233707890860871	3		484	671	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739837	41739837	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	79	438	0	ENST00000242208.4:c.136G>A	p.Asp46Asn	p.D46N	ENST00000242208	NM_002192.2	46	Gat/Aat	2/3	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.233707890860871	2		438	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577527	7577527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	123	625	0	ENST00000269305.4:c.754C>T	p.Leu252Phe	p.L252F	ENST00000269305	NM_001126112.2	252	Ctc/Ttc	7/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.233707890860871	2		625	736	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355233	81355233	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	54	265	0	ENST00000222390.5:c.1141C>T	p.Pro381Ser	p.P381S	ENST00000222390	NM_000601.4	381	Cca/Tca	9/18	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.233707890860871	2		265	434	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502444	186502444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	81	344	0	ENST00000323963.5:c.167C>T	p.Pro56Leu	p.P56L	ENST00000323963		56	cCt/cTt	3/11	0.177440754080855	3	FACETS	0.762	0.673	0.857	0.762	0.673	0.857	SUBCLONAL	2	TRUE	1	0.233707890860871	3		344	508	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794728	42794728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769275790	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	47	620	0	ENST00000575354.2:c.1808C>T	p.Pro603Leu	p.P603L	ENST00000575354	NM_015125.3	603	cCc/cTc	10/20	0.233707890860871	1	FACETS	0.659	0.556	0.773	0.659	0.556	0.773	SUBCLONAL	1	TRUE	0	0.233707890860871	1		620	539	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038684	14038684	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56129764	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	60	211	1	ENST00000311895.7:c.2009G>A	p.Arg670Gln	p.R670Q	ENST00000311895	NM_005236.2	670	cGg/cAg	10/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.233707890860871	2		212	349	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965749	93965749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	28	199	0	ENST00000369303.4:c.2179G>A	p.Asp727Asn	p.D727N	ENST00000369303	NM_004440.3	727	Gat/Aat	13/17	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.233707890860871	2		199	195	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644720	134644720	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1240367222	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	94	405	0	ENST00000398015.3:c.121G>A	p.Gly41Arg	p.G41R	ENST00000398015	NM_004441.4	41	Ggg/Agg	2/16	0.177440754080855	3	FACETS	1	0.963	1	0.597	0.531	0.668	CLONAL	1	TRUE	1	0.233707890860871	3		405	752	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16235913	16235913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	45	415	0	ENST00000375759.3:c.979G>A	p.Glu327Lys	p.E327K	ENST00000375759	NM_015001.2	327	Gaa/Aaa	4/15	1	2	FACETS	0.542	0.455	0.64	0.542	0.455	0.64	SUBCLONAL	1	TRUE	1	0.233707890860871	2		415	710	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204515974	204515974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs560966150	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	54	237	0	ENST00000367182.3:c.872G>A	p.Ser291Asn	p.S291N	ENST00000367182	NM_001278516.1	291	aGt/aAt	10/11	0.233707890860871	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.233707890860871	1		237	351	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332118	70332118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778536892	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	12	156	0	ENST00000373644.4:c.23G>A	p.Arg8Lys	p.R8K	ENST00000373644	NM_030625.2	8	aGg/aAg	2/12	1	2	FACETS	0.499	0.35	0.681	0.499	0.35	0.681	SUBCLONAL	1	TRUE	1	0.233707890860871	2		156	206	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21630824	21630824	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	77	441	0	ENST00000421138.2:c.780C>A	p.His260Gln	p.H260Q	ENST00000421138		260	caC/caA	8/16	0.233707890860871	1	FACETS	0.77	0.675	0.872	0.77	0.675	0.872	SUBCLONAL	1	TRUE	0	0.233707890860871	1		441	756	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434022	49434022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	68	633	0	ENST00000301067.7:c.7531C>T	p.Pro2511Ser	p.P2511S	ENST00000301067	NM_003482.3	2511	Cca/Tca	31/54	0.00946665858936102	3	FACETS	1	0.949	1	0.591	0.514	0.673	INDETERMINATE	1	TRUE	1	0.233707890860871	3		633	550	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491645	56491645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	88	467	0	ENST00000267101.3:c.2537G>A	p.Ser846Asn	p.S846N	ENST00000267101	NM_001982.3	846	aGt/aAt	21/28	0.00946665858936102	3	FACETS	1	0.97	1	0.648	0.574	0.727	INDETERMINATE	1	TRUE	1	0.233707890860871	3		467	649	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435838	110435838	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	48	435	0	ENST00000375856.3:c.2563G>A	p.Gly855Arg	p.G855R	ENST00000375856	NM_003749.2	855	Ggg/Agg	1/2	1	2	FACETS	0.859	0.727	1	0.859	0.727	1	CLONAL	1	TRUE	1	0.233707890860871	2		435	478	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708503	43708504	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	91	646	1	ENST00000382044.4:c.4792_4793delinsAA	p.Gly1598Lys	p.G1598K	ENST00000382044	NM_001141980.1	1598	GGa/AAa	22/28	0.233707890860871	1	FACETS	0.941	0.835	1	0.941	0.835	1	CLONAL	1	TRUE	0	0.233707890860871	1		647	731	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210482	5210483	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	63	479	0	ENST00000357368.4:c.5484_5485delinsTT	p.Arg1829Trp	p.R1829W	ENST00000357368	NM_002850.3	1828	gcCCgg/gcTTgg	35/38	0.233707890860871	1	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	0	0.233707890860871	1		479	472	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354182	15354182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	78	638	0	ENST00000263377.2:c.2698C>T	p.Leu900Phe	p.L900F	ENST00000263377	NM_058243.2	900	Ctc/Ttc	14/20	0.233707890860871	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.233707890860871	1		638	523	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982400	25982400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	60	285	0	ENST00000435504.4:c.890G>A	p.Gly297Glu	p.G297E	ENST00000435504		297	gGa/gAa	9/13	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.233707890860871	2		285	473	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462566	29462566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	74	538	0	ENST00000389048.3:c.2335G>A	p.Gly779Arg	p.G779R	ENST00000389048	NM_004304.4	779	Gga/Aga	13/29	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.233707890860871	2		538	505	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212615376	212615376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	29	364	0	ENST00000342788.4:c.610C>T	p.His204Tyr	p.H204Y	ENST00000342788	NM_005235.2	204	Cat/Tat	5/28	1	2	FACETS	0.442	0.354	0.543	0.442	0.354	0.543	SUBCLONAL	1	TRUE	1	0.233707890860871	2		364	561	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22153418	22153418	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	52	252	0	ENST00000215832.6:c.493-1G>A		p.X165_splice	ENST00000215832	NM_002745.4	165			1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.233707890860871	2		252	367	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165139	47165140	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	36	296	0	ENST00000409792.3:c.986_987delinsAA	p.Arg329Gln	p.R329Q	ENST00000409792	NM_014159.6	329	cGG/cAA	3/21	0.233707890860871	1	FACETS	0.958	0.791	1	0.958	0.791	1	CLONAL	1	TRUE	0	0.233707890860871	1		296	284	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917544	178917544	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1382877640	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	63	345	0	ENST00000263967.3:c.419G>A	p.Arg140Gln	p.R140Q	ENST00000263967	NM_006218.2	140	cGa/cAa	3/21	0.177440754080855	3	FACETS	1	0.946	1	0.593	0.513	0.679	CLONAL	1	TRUE	1	0.233707890860871	3		345	508	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750474	41750474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	54	404	0	ENST00000226382.2:c.154G>A	p.Gly52Arg	p.G52R	ENST00000226382	NM_003924.3	52	Ggg/Agg	1/3	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.233707890860871	2		404	448	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521192	187521192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749936232	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	90	565	1	ENST00000441802.2:c.11963C>T	p.Pro3988Leu	p.P3988L	ENST00000441802	NM_005245.3	3988	cCt/cTt	22/27	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.233707890860871	2		566	640	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628142	187628142	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	94	579	1	ENST00000441802.2:c.2840del	p.Met947SerfsTer3	p.M947Sfs*3	ENST00000441802	NM_005245.3	947	aTg/ag	2/27	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.233707890860871	2		580	767	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189403	56189403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	100	568	0	ENST00000399503.3:c.4435C>T	p.Pro1479Ser	p.P1479S	ENST00000399503	NM_005921.1	1479	Cct/Tct	20/20	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.233707890860871	2		568	775	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176715886	176715886	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	72	445	0	ENST00000439151.2:c.6218G>T	p.Gly2073Val	p.G2073V	ENST00000439151	NM_022455.4	2073	gGa/gTa	21/23	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.233707890860871	2		445	608	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672253	30672253	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	63	666	0	ENST00000376406.3:c.4707A>C	p.Glu1569Asp	p.E1569D	ENST00000376406	NM_014641.2	1569	gaA/gaC	10/15	0.233707890860871	5	FACETS	0.699	0.603	0.805	0.233	0.201	0.269	SUBCLONAL	1	TRUE	2	0.233707890860871	5		666	1041	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955164	93955164	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	34	347	0	ENST00000369303.4:c.2734A>G	p.Ser912Gly	p.S912G	ENST00000369303	NM_004440.3	912	Agc/Ggc	16/17	1	2	FACETS	0.613	0.5	0.739	0.613	0.5	0.739	SUBCLONAL	1	TRUE	1	0.233707890860871	2		347	475	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198343	138198344	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	50	282	1	ENST00000237289.4:c.936_937delinsTT	p.Pro313Ser	p.P313S	ENST00000237289	NM_001270507.1	312	atCCcc/atTTcc	6/9	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.233707890860871	2		283	380	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514974	148514974	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	82	355	0	ENST00000320356.2:c.1235C>T	p.Ser412Phe	p.S412F	ENST00000320356	NM_004456.4	412	tCc/tTc	10/20	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.233707890860871	2		355	632	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27218799	27218800	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	83	566	2	ENST00000380036.4:c.3087_3088delinsAA	p.Trp1029_Glu1030delinsTer	p.W1029_E1030delins*	ENST00000380036	NM_000459.3	1029	tgGGag/tgAAag	20/23	0.233707890860871	1	FACETS	0.929	0.82	1	0.929	0.82	1	CLONAL	1	TRUE	0	0.233707890860871	1		568	675	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412312	139412312	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	51	649	0	ENST00000277541.6:c.1333A>C	p.Thr445Pro	p.T445P	ENST00000277541	NM_017617.3	445	Acg/Ccg	8/34	0.233707890860871	1	FACETS	0.506	0.429	0.591	0.506	0.429	0.591	SUBCLONAL	1	TRUE	0	0.233707890860871	1		649	762	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228328	53228329	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0037166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	43	499	0	ENST00000375401.3:c.2073_2074delinsAA	p.Ala692Thr	p.A692T	ENST00000375401	NM_004187.3	691	gaGGct/gaAAct	15/26	0.233707890860871	0	FACETS	0.595	0.498	0.702			1	SUBCLONAL	1	TRUE	0	0.233707890860871	0		499	474	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	126	215	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.896	0.823	0.97			1	INDETERMINATE	1	TRUE	NA	0.876162143739369	2		215	321	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0037437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	334	380	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.828313778347971	2	FACETS	0.972	0.947	0.996	0.972	0.947	0.996	CLONAL	2	TRUE	0	0.876162143739369	2		380	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0037437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	410	636	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.826488567071842	2	FACETS	0.923	0.898	0.946	0.923	0.898	0.946	CLONAL	2	TRUE	0	0.876162143739369	2		636	507	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0037437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	296	354	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.832058632692117	2	FACETS	0.985	0.958	1	0.985	0.958	1	CLONAL	2	TRUE	0	0.876162143739369	2		354	343	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284946	15284946	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	937	783	0	ENST00000263388.2:c.4669C>T	p.Pro1557Ser	p.P1557S	ENST00000263388	NM_000435.2	1557	Cct/Tct	25/33	0.829498396964611	3	FACETS	0.993	0.981	1	0.993	0.981	1	CLONAL	3	TRUE	0	0.876162143739369	3		783	1032	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100949	27100949	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	584	557	0	ENST00000324856.7:c.4231C>T	p.Gln1411Ter	p.Q1411*	ENST00000324856	NM_006015.4	1411	Cag/Tag	18/20	0.829498396964611	3	FACETS	0.97	0.953	0.986	0.97	0.953	0.986	CLONAL	3	TRUE	0	0.876162143739369	3		557	659	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606553	93606553	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267602311	NA	P-0037437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	391	645	0	ENST00000375746.1:c.373G>A	p.Glu125Lys	p.E125K	ENST00000375746	NM_001174167.1	125	Gaa/Aaa	2/14	0.828313778347971	2	FACETS	0.945	0.921	0.969	0.945	0.921	0.969	CLONAL	2	TRUE	0	0.876162143739369	2		645	472	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858947	57858947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	286	711	0	ENST00000228682.2:c.443C>T	p.Ser148Phe	p.S148F	ENST00000228682	NM_005269.2	148	tCc/tTc	5/12	0.832058632692117	2	FACETS	0.912	0.862	0.962	0.456	0.431	0.481	CLONAL	1	TRUE	0	0.876162143739369	2		711	716	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526176	189526176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747354750	NA	P-0037437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	245	591	1	ENST00000264731.3:c.440C>T	p.Ser147Leu	p.S147L	ENST00000264731	NM_003722.4	147	tCg/tTg	4/14	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.876162143739369	2		592	557	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556190	29556190	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	91	144	0	ENST00000356175.3:c.2557C>T	p.Gln853Ter	p.Q853*	ENST00000356175	NM_000267.3	853	Cag/Tag	21/57	0.826488567071842	2	FACETS	0.927	0.874	0.974	0.927	0.874	0.974	CLONAL	2	TRUE	0	0.876162143739369	2		144	112	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528952	157528952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1263114512	NA	P-0037437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	430	453	0	ENST00000346085.5:c.6677C>T	p.Ser2226Leu	p.S2226L	ENST00000346085	NM_020732.3	2226	tCg/tTg	20/20	0.830974612054048	2	FACETS	0.978	0.955	0.998	0.978	0.955	0.998	CLONAL	2	TRUE	0	0.876162143739369	2		453	502	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459299	120459299	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	416	365	0	ENST00000256646.2:c.6046C>T	p.Leu2016Phe	p.L2016F	ENST00000256646	NM_024408.3	2016	Ctt/Ttt	34/34	0.829498396964611	3	FACETS	0.977	0.957	0.995	0.977	0.957	0.995	CLONAL	3	TRUE	0	0.876162143739369	3		365	466	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060638	38060638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764112817	NA	P-0037437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	338	851	0	ENST00000250448.2:c.1351G>A	p.Glu451Lys	p.E451K	ENST00000250448	NM_004496.3	451	Gag/Aag	2/2	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.876162143739369	2		851	761	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829182	72829182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	221	570	0	ENST00000268489.5:c.7399C>T	p.Pro2467Ser	p.P2467S	ENST00000268489	NM_006885.3	2467	Ccc/Tcc	9/10	0.807003320657094	3	FACETS	0.962	0.898	1	0.481	0.449	0.514	CLONAL	1	TRUE	1	0.876162143739369	3		570	754	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437157	220437158	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0037437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	586	825	0	ENST00000243786.2:c.61_62delinsAT	p.Gly21Met	p.G21M	ENST00000243786	NM_002191.3	21	GGg/ATg	1/2	0.826488567071842	2	FACETS	0.937	0.916	0.956	0.937	0.916	0.956	CLONAL	2	TRUE	0	0.876162143739369	2		825	714	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437158	220437158	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	586	815	0	ENST00000243786.2:c.62G>T	p.Gly21Val	p.G21V	ENST00000243786	NM_002191.3	21	gGg/gTg	1/2	0.826488567071842	2	FACETS	0.937	0.916	0.956	0.937	0.916	0.956	CLONAL	2	TRUE	0	0.876162143739369	2		815	714	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561012	9561012	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	383	348	0	ENST00000353224.5:c.770G>A	p.Trp257Ter	p.W257*	ENST00000353224	NM_177990.2	257	tGg/tAg	4/10	0.857358561302114	5	FACETS	0.918	0.887	0.949	1	0.995	1	CLONAL	4	TRUE	2	0.876162143739369	5		348	551	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400152	41400152	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	422	481	1	ENST00000373198.4:c.607G>A	p.Val203Met	p.V203M	ENST00000373198	NM_133170.3	203	Gtg/Atg	5/32	0.857358561302114	5	FACETS	0.885	0.848	0.921	0.885	0.848	0.921	CLONAL	3	TRUE	2	0.876162143739369	5		482	840	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265096	46265096	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	327	385	0	ENST00000371998.3:c.1966C>T	p.Pro656Ser	p.P656S	ENST00000371998		656	Ccc/Tcc	12/23	0.857358561302114	5	FACETS	0.921	0.879	0.963	0.921	0.879	0.963	CLONAL	3	TRUE	2	0.876162143739369	5		385	625	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62293290	62293290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	564	447	0	ENST00000360203.5:c.389C>T	p.Ser130Phe	p.S130F	ENST00000360203	NM_001283009.1	130	tCc/tTc	4/35	0.857358561302114	5	FACETS	0.924	0.892	0.956	0.924	0.892	0.956	CLONAL	3	TRUE	2	0.876162143739369	5		447	1075	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670415	30670415	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	472	551	0	ENST00000376406.3:c.6017G>A	p.Gly2006Glu	p.G2006E	ENST00000376406	NM_014641.2	2006	gGa/gAa	14/15	0.830974612054048	2	FACETS	0.996	0.975	1	0.996	0.975	1	CLONAL	2	TRUE	0	0.876162143739369	2		551	541	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005903	69005903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	515	453	1	ENST00000288368.4:c.2314C>T	p.His772Tyr	p.H772Y	ENST00000288368	NM_024870.2	772	Cac/Tac	21/40	0.876162143739369	3	FACETS	0.949	0.93	0.967	0.949	0.93	0.967	CLONAL	3	TRUE	0	0.876162143739369	3		454	594	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639890	93639891	+	missense_variant	Missense_Mutation	DNP	GA	GA	AC	novel	NA	P-0037437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	144	229	0	ENST00000375746.1:c.1219_1220delinsAC	p.Glu407Thr	p.E407T	ENST00000375746	NM_001174167.1	407	GAg/ACg	10/14	0.828313778347971	2	FACETS	0.888	0.845	0.928	0.888	0.845	0.928	CLONAL	2	TRUE	0	0.876162143739369	2		229	185	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639891	93639891	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	144	229	0	ENST00000375746.1:c.1220A>C	p.Glu407Ala	p.E407A	ENST00000375746	NM_001174167.1	407	gAg/gCg	10/14	0.828313778347971	2	FACETS	0.888	0.845	0.928	0.888	0.845	0.928	CLONAL	2	TRUE	0	0.876162143739369	2		229	185	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437157	220437157	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	580	825	0	ENST00000243786.2:c.61G>A	p.Gly21Arg	p.G21R	ENST00000243786	NM_002191.3	21	Ggg/Agg	1/2	0.826488567071842	2	FACETS	0.936	0.916	0.956	0.936	0.916	0.956	CLONAL	2	TRUE	0	0.876162143739369	2		825	707	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639890	93639890	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	143	227	0	ENST00000375746.1:c.1219G>A	p.Glu407Lys	p.E407K	ENST00000375746	NM_001174167.1	407	Gag/Aag	10/14	0.828313778347971	2	FACETS	0.892	0.849	0.932	0.892	0.849	0.932	CLONAL	2	TRUE	0	0.876162143739369	2		227	183	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	25	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	FALSE	1	0.235338539626944	2		215	171	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098815	178098815	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	200	564	0	ENST00000397062.3:c.230A>G	p.Asp77Gly	p.D77G	ENST00000397062	NM_006164.4	77	gAt/gGt	2/5	0.235338539626944	3	FACETS	0.827	0.765	0.891			1	CLONAL	2	FALSE	NA	0.235338539626944	3		564	1149	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961186	41961187	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0037488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	40	418	1	ENST00000219905.7:c.94_95delinsTT	p.Gly32Leu	p.G32L	ENST00000219905	NM_001164273.1	32	GGa/TTa	2/24	0.191394632970667	1	FACETS	0.521	0.432	0.62	0.521	0.432	0.62	SUBCLONAL	1	FALSE	0	0.235338539626944	1		419	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577617	7578217	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAACACAGGCCCAAGATGAGGCCAGTGCGCCTTGGGGAGACCTGTGGCAAGCAGGGGAGGCCTTTTTTTTTTTTTTTTGAGATGGAATCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGTGATCTCAGCTCACTGCAAGCTCCACCGCCCAGGTTCACGCCATTCTCCTTCCTCAGCCTCCCGAGTAGCTGGGACTACAGGTGCCCAGCACCACGCCCGGCTAATTTTTTTTTGTATTTTTCAGTAGAGACGGGGTTTCACCGTTAGCCAGGATGGTCTCGATCTCCCAACCTCGTGATCCGCCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACTGCGCCCAGCCAAGCAGGGGAGGCCCTTAGCCTCTGTAAGCTTCAGTTTTTTCAACTGTGCAATAGTTAAACCCATTTACTTTGCACATCTCATGGGGTTATAGGGAGGTCAAATAAGCAGCAGGAGAAAGCCCCCCTACTGCTCACCTGGAGGGCCACTGACAACCACCCTTAACCCCTCCTCCCAGAGACCCCAGTTGCAAACCAGACCTCAGGCGGCTCATAGGGCACCACCACACTATGTCGAAAAG	TAACACAGGCCCAAGATGAGGCCAGTGCGCCTTGGGGAGACCTGTGGCAAGCAGGGGAGGCCTTTTTTTTTTTTTTTTGAGATGGAATCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGTGATCTCAGCTCACTGCAAGCTCCACCGCCCAGGTTCACGCCATTCTCCTTCCTCAGCCTCCCGAGTAGCTGGGACTACAGGTGCCCAGCACCACGCCCGGCTAATTTTTTTTTGTATTTTTCAGTAGAGACGGGGTTTCACCGTTAGCCAGGATGGTCTCGATCTCCCAACCTCGTGATCCGCCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACTGCGCCCAGCCAAGCAGGGGAGGCCCTTAGCCTCTGTAAGCTTCAGTTTTTTCAACTGTGCAATAGTTAAACCCATTTACTTTGCACATCTCATGGGGTTATAGGGAGGTCAAATAAGCAGCAGGAGAAAGCCCCCCTACTGCTCACCTGGAGGGCCACTGACAACCACCCTTAACCCCTCCTCCCAGAGACCCCAGTTGCAAACCAGACCTCAGGCGGCTCATAGGGCACCACCACACTATGTCGAAAAG	-	novel	NA	P-0037488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	89	385	0	ENST00000269305.4:c.632_673-9del		p.X211_splice	ENST00000269305	NM_001126112.2	211		6/11	0.170630369992954	2	FACETS	1	0.97	1	0.638	0.566	0.714	CLONAL	1	FALSE	0	0.235338539626944	2		385	593	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919754	96919754	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	112	459	0	ENST00000258439.3:c.509A>C	p.Tyr170Ser	p.Y170S	ENST00000258439	NM_001193304.2	170	tAt/tCt	4/4	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.235338539626944	2		459	817	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248740	212248740	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	51	366	0	ENST00000342788.4:c.3527A>G	p.Lys1176Arg	p.K1176R	ENST00000342788	NM_005235.2	1176	aAa/aGa	28/28	1	2	FACETS	0.883	0.751	1	0.883	0.751	1	CLONAL	1	FALSE	1	0.235338539626944	2		366	491	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231077	98231077	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	112	508	0	ENST00000331920.6:c.2206G>A	p.Ala736Thr	p.A736T	ENST00000331920	NM_000264.3	736	Gct/Act	14/24	0.170630369992954	2	FACETS	1	0.979	1	0.669	0.602	0.74	CLONAL	1	FALSE	0	0.235338539626944	2		508	711	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	40	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.268588692841832	2		215	225	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0037516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	46	199	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.268588692841832	2		199	291	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913381	NA	P-0037516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	58	219	1	ENST00000304494.5:c.322G>T	p.Asp108Tyr	p.D108Y	ENST00000304494	NM_000077.4	108	Gat/Tat	2/3	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.268588692841832	2		220	298	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546643	9546643	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	51	374	1	ENST00000353224.5:c.1379C>T	p.Thr460Ile	p.T460I	ENST00000353224	NM_177990.2	460	aCc/aTc	5/10	1	2	FACETS	0.896	0.763	1	0.896	0.763	1	CLONAL	1	TRUE	1	0.268588692841832	2		375	424	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0037539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	145	462	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.608875196886124	2		463	403	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015039	37015039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs185643174	NA	P-0037539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	237	509	1	ENST00000358127.4:c.365G>A	p.Arg122Gln	p.R122Q	ENST00000358127	NM_001280556.1	122	cGg/cAg	3/10	0.608875196886124	2	FACETS	1	0.946	1	0.506	0.473	0.539	CLONAL	1	TRUE	0	0.608875196886124	2		510	770	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436341	52436341	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1440748203	NA	P-0037539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	256	659	1	ENST00000460680.1:c.2153G>A	p.Arg718Gln	p.R718Q	ENST00000460680	NM_004656.3	718	cGg/cAg	17/17	0.11534885123403	4	FACETS	0.842	0.791	0.895	0.842	0.791	0.895	INDETERMINATE	2	TRUE	2	0.608875196886124	4		660	803	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55225427	55225427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11270	3880	372	0	ENST00000275493.2:c.1279C>T	p.Arg427Cys	p.R427C	ENST00000275493	NM_005228.3	427	Cgc/Tgc	11/28	0.608875196886124	46	FACETS	1	0.99	1			1	CLONAL	12	TRUE	NA	0.608875196886124	46		372	15150	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692920	89692921	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0037539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	158	525	0	ENST00000371953.3:c.405_406insAA	p.Cys136AsnfsTer12	p.C136Nfs*12	ENST00000371953	NM_000314.4	135	ata/atAAa	5/9	0.608875196886124	1	FACETS	0.992	0.922	1	0.992	0.922	1	CLONAL	1	TRUE	0	0.608875196886124	1		525	364	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220968	55221758	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGCTGCCCCAGCGGGCTCTGAGCAGCACTGGAGGGTACAGGTCAGAAGCGTCTTGGAAGTCCTGGAGACGCCAAGGCTGGTGGATGTGACTCCTGGAGTGGGAGCTGGTGTGACGAAGCCCTTCCTAAGACTAAATCCAGAGCACTCTGTGGTTTCAGAGAAGATTCCTAAATTCCAGAGTTTGGACCCAGACCCAGGAATTGTGACTTGGTTGGCCTGAGCTGTTTCTAATGTGAGCCCCAGGGAGAAGACTGTGCGTGGGGTTGGTCCTAGGAAAAGCCCTCGCTGTATTGGGTCTGGCTCCTTTACACGGCATTGTTCTAGCAAGGCTTTCTGCCATTCAGCAATACATTATAAAATATACCCTCAATTGTACTTTATAAGGGAAGCCCAATGTCCTTTATAAGGGAAATTAAACATAATTTCATTCCATAGTCACCGCTATAATGTGTGAACTCCATCATCTATACGTTAGTAAACAGACGTATTTTTATCATAATCCATAAATTATGATAGGTGGGACAGTGCACCTAAGAAAAAAATGGACTTTTTAGAGAAGGGTCTTTCTGACTCTGCAGAGGGCGCCAGCTGGGTTTTCCCACACTAGTGGAACACTAGGCTGCAAAGACAGTAACTTGGGCTTTCTGACGGGAGTCAACACCGTGCTGCGCTTCCTCCGTGTGTGGCGCTGAGTGTACTTACCTCACTTGCCCAGCGTGTCCTCTCTCCTCCATAGGTCTGCCGCAAATTCCGAGACGAAGCCACGTGCAAGGACACCTGCCCCCCACTCA	TGCTGCCCCAGCGGGCTCTGAGCAGCACTGGAGGGTACAGGTCAGAAGCGTCTTGGAAGTCCTGGAGACGCCAAGGCTGGTGGATGTGACTCCTGGAGTGGGAGCTGGTGTGACGAAGCCCTTCCTAAGACTAAATCCAGAGCACTCTGTGGTTTCAGAGAAGATTCCTAAATTCCAGAGTTTGGACCCAGACCCAGGAATTGTGACTTGGTTGGCCTGAGCTGTTTCTAATGTGAGCCCCAGGGAGAAGACTGTGCGTGGGGTTGGTCCTAGGAAAAGCCCTCGCTGTATTGGGTCTGGCTCCTTTACACGGCATTGTTCTAGCAAGGCTTTCTGCCATTCAGCAATACATTATAAAATATACCCTCAATTGTACTTTATAAGGGAAGCCCAATGTCCTTTATAAGGGAAATTAAACATAATTTCATTCCATAGTCACCGCTATAATGTGTGAACTCCATCATCTATACGTTAGTAAACAGACGTATTTTTATCATAATCCATAAATTATGATAGGTGGGACAGTGCACCTAAGAAAAAAATGGACTTTTTAGAGAAGGGTCTTTCTGACTCTGCAGAGGGCGCCAGCTGGGTTTTCCCACACTAGTGGAACACTAGGCTGCAAAGACAGTAACTTGGGCTTTCTGACGGGAGTCAACACCGTGCTGCGCTTCCTCCGTGTGTGGCGCTGAGTGTACTTACCTCACTTGCCCAGCGTGTCCTCTCTCCTCCATAGGTCTGCCGCAAATTCCGAGACGAAGCCACGTGCAAGGACACCTGCCCCCCACTCA	-	novel	NA	P-0037539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	674	0	0	ENST00000275493.2:c.747+615_806del		p.X249_splice	ENST00000275493	NM_005228.3	249		7/28	0.608875196886124	46	FACETS	0.989	0.977	1			1	CLONAL	45	TRUE	NA	0.608875196886124	46		0	716	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	76	215	0				ENST00000310581	NM_198253.2	-/1132			0.254501727547704	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	3	TRUE	1	0.278775395969867	4		215	206	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0037719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	42	188	2	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.278775395969867	2		190	228	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0037719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	83	923	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.889	0.784	1	0.889	0.784	1	CLONAL	1	TRUE	1	0.278775395969867	2		923	670	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0037719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	90	721	0	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.278775395969867	2		721	502	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266605	198266605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	41	310	0	ENST00000335508.6:c.2231C>T	p.Ala744Val	p.A744V	ENST00000335508	NM_012433.2	744	gCt/gTt	16/25	1	2	FACETS	0.865	0.723	1	0.865	0.723	1	CLONAL	1	TRUE	1	0.278775395969867	2		310	340	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058732	42058732	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	33	209	0	ENST00000219905.7:c.8452G>T	p.Asp2818Tyr	p.D2818Y	ENST00000219905	NM_001164273.1	2818	Gat/Tat	24/24	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.278775395969867	2		209	206	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212365	36212365	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	87	591	2	ENST00000222270.7:c.2116C>T	p.Arg706Ter	p.R706*	ENST00000222270	NM_014727.1	706	Cga/Tga	3/37	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.278775395969867	2		593	618	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136344	202136344	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	49	369	0	ENST00000358485.4:c.588G>A	p.Met196Ile	p.M196I	ENST00000358485	NM_001080125.1	196	atG/atA	3/9	1	2	FACETS	0.853	0.724	0.995	0.853	0.724	0.995	CLONAL	1	TRUE	1	0.278775395969867	2		369	412	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391409	139391409	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	78	592	0	ENST00000277541.6:c.6782del	p.Gly2261AlafsTer34	p.G2261Afs*34	ENST00000277541	NM_017617.3	2261	gGc/gc	34/34	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.278775395969867	2		592	511	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	143	215	0				ENST00000310581	NM_198253.2	-/1132			0.514961816223367	1	FACETS	0.782	0.717	0.85	0.782	0.717	0.85	SUBCLONAL	1	FALSE	0	0.517156411845486	1		215	524	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0037745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	527	598	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.517156411845486	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	FALSE	0	0.517156411845486	2		598	984	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784077	120784077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1210006090	NA	P-0037745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	239	790	1	ENST00000257552.2:c.908G>A	p.Arg303His	p.R303H	ENST00000257552	NM_002442.3	303	cGc/cAc	13/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.517156411845486	2		791	857	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224232	55224232	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	263	474	0	ENST00000275493.2:c.1013A>G	p.Asn338Ser	p.N338S	ENST00000275493	NM_005228.3	338	aAc/aGc	9/28	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	1	0.517156411845486	2		474	762	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339169	70339256	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCTTCCCCCTTCCCCTAAGGAAAAAACAACTAAACGCCGCTTTCCTGCCTCAGGATGAACTGACGGCCTTGAATGTAAAACAAGGTT	CCCTTCCCCCTTCCCCTAAGGAAAAAACAACTAAACGCCGCTTTCCTGCCTCAGGATGAACTGACGGCCTTGAATGTAAAACAAGGTT	-	novel	NA	P-0037745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	169	396	0	ENST00000374080.3:c.100-54_133del		p.X34_splice	ENST00000374080		34		2/45	0.517156411845486	1	FACETS	0.985	0.913	1	0.985	0.913	1	CLONAL	1	FALSE	0	0.517156411845486	1		396	492	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0037808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	106	380	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.238363849237833	2	FACETS	0.837	0.758	0.92	1	0.976	1	CLONAL	3	TRUE	0	0.238363849237833	2		380	354	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0037808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	73	462	1				ENST00000310581	NM_198253.2	-/1132			0.207893266930184	3	FACETS	1	0.905	1	1	0.905	1	CLONAL	3	TRUE	0	0.238363849237833	3		463	224	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003136	42003137	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0037808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	31	588	0	ENST00000219905.7:c.2678dup	p.Val894CysfsTer19	p.V894Cfs*19	ENST00000219905	NM_001164273.1	891	-/C	8/24	1	2	FACETS	0.42	0.339	0.513	0.42	0.339	0.513	SUBCLONAL	1	TRUE	1	0.238363849237833	2		588	619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577971	7578178	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCAGCCAAGCAGGGGAGGCCCTTAGCCTCTGTAAGCTTCAGTTTTTTCAACTGTGCAATAGTTAAACCCATTTACTTTGCACATCTCATGGGGTTATAGGGAGGTCAAATAAGCAGCAGGAGAAAGCCCCCCTACTGCTCACCTGGAGGGCCACTGACAACCACCCTTAACCCCTCCTCCCAGAGACCCCAGTTGCAAACCAGACCT	CCCAGCCAAGCAGGGGAGGCCCTTAGCCTCTGTAAGCTTCAGTTTTTTCAACTGTGCAATAGTTAAACCCATTTACTTTGCACATCTCATGGGGTTATAGGGAGGTCAAATAAGCAGCAGGAGAAAGCCCCCCTACTGCTCACCTGGAGGGCCACTGACAACCACCCTTAACCCCTCCTCCCAGAGACCCCAGTTGCAAACCAGACCT	-	novel	NA	P-0037808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	83	91	0	ENST00000269305.4:c.671_672+206del		p.X224_splice	ENST00000269305	NM_001126112.2	224		6/11	0.188405915783693	2	FACETS	0.948	0.888	1	1	0.99	1	CLONAL	7	TRUE	0	0.238363849237833	2		91	105	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409073	139409074	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CATT	novel	NA	P-0037808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	141	862	0	ENST00000277541.6:c.2092_2095dup	p.Gly699GlufsTer19	p.G699Efs*19	ENST00000277541	NM_017617.3	699	ggc/gAATGgc	13/34	0.238363849237833	2	FACETS	0.782	0.714	0.855	0.782	0.714	0.855	SUBCLONAL	2	TRUE	0	0.238363849237833	2		862	756	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	66	215	0				ENST00000310581	NM_198253.2	-/1132			0.339451698698408	1	FACETS	1	0.954	1	1	0.954	1	INDETERMINATE	1	TRUE	0	0.648082788616832	1		215	124	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0037873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	86	380	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.648082788616832	2		380	200	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587118	189587118	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761885185	NA	P-0037873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	37	271	0	ENST00000264731.3:c.1135C>T	p.Arg379Cys	p.R379C	ENST00000264731	NM_003722.4	379	Cgt/Tgt	9/14	0.60123585387987	1	FACETS	0.839	0.761	0.905	1	0.976	1	CLONAL	2	TRUE	0	0.648082788616832	1		271	46	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995569	68995569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775560862	NA	P-0037873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	46	430	1	ENST00000288368.4:c.1973C>T	p.Ser658Leu	p.S658L	ENST00000288368	NM_024870.2	658	tCg/tTg	18/40	0.648082788616832	4	FACETS	1	0.894	1	0.354	0.301	0.412	CLONAL	1	TRUE	1	0.648082788616832	4		431	220	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606921	47606921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	24	266	0	ENST00000263735.4:c.671C>T	p.Ser224Phe	p.S224F	ENST00000263735	NM_002354.2	224	tCc/tTc	7/9	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.648082788616832	2		266	65	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971116	21971116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552823	NA	P-0037873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	100	501	1	ENST00000304494.5:c.242C>T	p.Pro81Leu	p.P81L	ENST00000304494	NM_000077.4	81	cCc/cTc	2/3	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.648082788616832	2		502	285	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321372	1321372	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1319865856	NA	P-0037873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	71	456	1	ENST00000400841.2:c.383C>T	p.Ser128Leu	p.S128L	ENST00000400841		128	tCg/tTg	4/6	0.287541973117992	1	FACETS	0.771	0.687	0.859	0.771	0.687	0.859	INDETERMINATE	1	TRUE	0	0.648082788616832	1		457	192	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281660	49281660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61735175	NA	P-0037873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	70	601	1	ENST00000282018.3:c.707C>T	p.Ser236Leu	p.S236L	ENST00000282018	NM_020377.2	236	tCg/tTg	1/1	0.43115627112206	1	FACETS	0.83	0.74	0.922	0.83	0.74	0.922	CLONAL	1	TRUE	0	0.648082788616832	1		602	176	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169552	27169552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	60	539	0	ENST00000380036.4:c.553G>A	p.Asp185Asn	p.D185N	ENST00000380036	NM_000459.3	185	Gat/Aat	4/23	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.648082788616832	2		539	151	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970945	70970945	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1242917883	NA	P-0037873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	209	574	2	ENST00000276594.2:c.1316G>A	p.Arg439Gln	p.R439Q	ENST00000276594	NM_024504.3	439	cGa/cAa	6/8	0.648082788616832	4	FACETS	1	0.951	1	1	0.951	1	CLONAL	3	TRUE	1	0.648082788616832	4		576	353	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526781	31526781	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	50	525	0	ENST00000344624.3:c.259C>T	p.Pro87Ser	p.P87S	ENST00000344624		87	Ccg/Tcg	2/33	0.339451698698408	1	FACETS	0.555	0.478	0.637	0.555	0.478	0.637	INDETERMINATE	1	TRUE	0	0.648082788616832	1		525	188	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31468137	31468137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	49	450	1	ENST00000344624.3:c.2275C>T	p.Arg759Cys	p.R759C	ENST00000344624		759	Cgt/Tgt	15/33	0.339451698698408	1	FACETS	0.946	0.829	1	0.946	0.829	1	INDETERMINATE	1	TRUE	0	0.648082788616832	1		451	108	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700292	117700292	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	27	374	0	ENST00000368508.3:c.2527G>A	p.Gly843Arg	p.G843R	ENST00000368508	NM_002944.2	843	Ggg/Agg	17/43	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.648082788616832	2		374	69	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846208	156846208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	74	583	0	ENST00000524377.1:c.1649C>T	p.Ser550Phe	p.S550F	ENST00000524377	NM_002529.3	550	tCc/tTc	14/17	0.261091240217966	3	FACETS	1	0.968	1	0.633	0.562	0.706	INDETERMINATE	1	TRUE	1	0.648082788616832	3		583	239	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380792	118380792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	22	256	0	ENST00000534358.1:c.11030C>T	p.Ser3677Phe	p.S3677F	ENST00000534358	NM_005933.3	3677	tCc/tTc	30/36	0.648082788616832	1	FACETS	1	0.837	1	1	0.837	1	CLONAL	1	TRUE	0	0.648082788616832	1		256	45	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549165	21549165	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	52	642	1	ENST00000382592.4:c.3111T>A	p.Phe1037Leu	p.F1037L	ENST00000382592	NM_014572.2	1037	ttT/ttA	8/8	0.43115627112206	1	FACETS	0.524	0.452	0.601	0.524	0.452	0.601	SUBCLONAL	1	TRUE	0	0.648082788616832	1		643	207	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586021	29586072	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTATTTATAACCCTGTTTTATTGTGTAGATACTTCAGAGTATTGCCAATCA	ATTATTTATAACCCTGTTTTATTGTGTAGATACTTCAGAGTATTGCCAATCA	-	novel	NA	P-0037873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	14	163	0	ENST00000356175.3:c.4270-29_4292del		p.X1424_splice	ENST00000356175	NM_000267.3	1424		32/57	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.648082788616832	2		163	30	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586057	29586057	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786204157	NA	P-0037873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	10	221	0	ENST00000356175.3:c.4277A>G	p.Gln1426Arg	p.Q1426R	ENST00000356175	NM_000267.3	1426	cAg/cGg	32/57	1	2	FACETS	0.908	0.643	1	0.908	0.643	1	CLONAL	1	TRUE	1	0.648082788616832	2		221	34	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031207	11031208	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0037873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	86	633	1	ENST00000327064.4:c.1292_1293delinsAA	p.Gly431Glu	p.G431E	ENST00000327064	NM_199141.1	431	gGG/gAA	11/16	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.648082788616832	2		634	263	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213263	39213263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	71	626	0	ENST00000402219.2:c.3704C>T	p.Pro1235Leu	p.P1235L	ENST00000402219	NM_005633.3	1235	cCt/cTt	23/23	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.648082788616832	2		626	214	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872458	136872458	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	14	179	0	ENST00000241393.3:c.1040C>T	p.Ser347Leu	p.S347L	ENST00000241393	NM_003467.2	347	tCa/tTa	2/2	1	2	FACETS	0.847	0.633	1	0.847	0.633	1	CLONAL	1	TRUE	1	0.648082788616832	2		179	51	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016164	31016164	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1285138418	NA	P-0037873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	45	354	0	ENST00000375687.4:c.410C>G	p.Ser137Cys	p.S137C	ENST00000375687	NM_015338.5	137	tCt/tGt	6/13	0.42044083571346	3	FACETS	1	0.927	1	0.571	0.488	0.659	CLONAL	1	TRUE	1	0.648082788616832	3		354	161	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475551	12475552	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0037873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	55	413	1	ENST00000287820.6:c.1425_1426delinsAA	p.Glu476Lys	p.E476K	ENST00000287820	NM_015869.4	475	acGGaa/acAAaa	7/7	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.648082788616832	2		414	134	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729971	30729972	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0037873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	30	294	0	ENST00000295754.5:c.1492_1493delinsTT	p.Pro498Leu	p.P498L	ENST00000295754	NM_003242.5	498	CCa/TTa	6/7	1	2	FACETS	0.691	0.566	0.828	0.691	0.566	0.828	SUBCLONAL	1	TRUE	1	0.648082788616832	2		294	134	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191131	185191131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1445224231	NA	P-0037873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	42	443	0	ENST00000265026.3:c.2012G>A	p.Arg671Lys	p.R671K	ENST00000265026	NM_004721.4	671	aGg/aAg	11/14	0.60123585387987	1	FACETS	0.903	0.781	1	0.903	0.781	1	CLONAL	1	TRUE	0	0.648082788616832	1		443	97	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55974015	55974015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	18	479	0	ENST00000263923.4:c.1301C>T	p.Ser434Phe	p.S434F	ENST00000263923	NM_002253.2	434	tCc/tTc	10/30	0.287541973117992	1	FACETS	0.305	0.232	0.389	0.305	0.232	0.389	INDETERMINATE	1	TRUE	0	0.648082788616832	1		479	123	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322439	31322439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	56	360	0	ENST00000412585.2:c.1016G>A	p.Gly339Glu	p.G339E	ENST00000412585	NM_005514.6	339	gGa/gAa	6/8	0.648082788616832	3	FACETS	0.946	0.819	1	0.473	0.409	0.54	CLONAL	1	TRUE	1	0.648082788616832	3		360	242	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166857	32166857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	108	669	0	ENST00000375023.3:c.4381G>A	p.Ala1461Thr	p.A1461T	ENST00000375023	NM_004557.3	1461	Gcc/Acc	24/30	0.648082788616832	3	FACETS	0.987	0.892	1	0.494	0.446	0.544	CLONAL	1	TRUE	1	0.648082788616832	3		669	447	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540158	23540158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	59	303	0	ENST00000380871.4:c.245C>T	p.Ala82Val	p.A82V	ENST00000380871	NM_006167.3	82	gCc/gTc	1/2	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.648082788616832	2		303	147	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27173333	27173333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	51	506	0	ENST00000380036.4:c.874G>A	p.Gly292Ser	p.G292S	ENST00000380036	NM_000459.3	292	Ggc/Agc	6/23	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.648082788616832	2		506	151	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356227	70356227	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1195049407	NA	P-0037873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	102	661	0	ENST00000374080.3:c.5122G>A	p.Val1708Ile	p.V1708I	ENST00000374080		1708	Gtc/Atc	37/45	0.287541973117992	1	FACETS	0.848	0.772	0.925	0.848	0.772	0.925	INDETERMINATE	1	TRUE	0	0.648082788616832	1		661	251	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776313	76776313	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	29	476	0	ENST00000373344.5:c.7153A>G	p.Lys2385Glu	p.K2385E	ENST00000373344	NM_000489.3	2385	Aaa/Gaa	34/35	0.287541973117992	1	FACETS	0.508	0.416	0.609	0.508	0.416	0.609	INDETERMINATE	1	TRUE	0	0.648082788616832	1		476	119	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	20	215	0				ENST00000310581	NM_198253.2	-/1132			0.222066188695727	3	FACETS	0.475	0.363	0.605	0.237	0.181	0.303	SUBCLONAL	1	TRUE	1	0.348158392758662	3		215	284	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0037954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	127	772	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.932	0.844	1	0.932	0.844	1	CLONAL	1	TRUE	1	0.348158392758662	2		772	783	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971124	21971125	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0037954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	19	304	0	ENST00000304494.5:c.233_234del	p.Leu78HisfsTer41	p.L78Hfs*41	ENST00000304494	NM_000077.4	78	cTC/c	2/3	1	2	FACETS	0.307	0.233	0.395	0.307	0.233	0.395	SUBCLONAL	1	TRUE	1	0.348158392758662	2		304	355	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910684	29910684	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs41542016	NA	P-0037954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	60	962	1	ENST00000376809.5:c.224G>A	p.Trp75Ter	p.W75*	ENST00000376809	NM_002116.7	75	tGg/tAg	2/8	1	2	FACETS	0.318	0.273	0.368	0.318	0.273	0.368	SUBCLONAL	1	TRUE	1	0.348158392758662	2		963	1084	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435726	110435726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	21	136	0	ENST00000375856.3:c.2675G>A	p.Arg892His	p.R892H	ENST00000375856	NM_003749.2	892	cGc/cAc	1/2	1	2	FACETS	0.606	0.469	0.764	0.606	0.469	0.764	SUBCLONAL	1	TRUE	1	0.348158392758662	2		136	199	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524937	187524958	+	frameshift_variant	Frame_Shift_Del	DEL	ACTGTAGGTTAGAGTATCATAC	ACTGTAGGTTAGAGTATCATAC	-	novel	NA	P-0037954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	104	579	0	ENST00000441802.2:c.10722_10743del	p.Tyr3575SerfsTer18	p.Y3575Sfs*18	ENST00000441802	NM_005245.3	3574	gtGTATGATACTCTAACCTACAGT/gt	19/27	1	2	FACETS	0.696	0.623	0.774	0.696	0.623	0.774	SUBCLONAL	1	TRUE	1	0.348158392758662	2		579	858	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412608	139412608	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	51	591	0	ENST00000277541.6:c.1236C>G	p.Asp412Glu	p.D412E	ENST00000277541	NM_017617.3	412	gaC/gaG	7/34	1	2	FACETS	0.441	0.374	0.515	0.441	0.374	0.515	SUBCLONAL	1	TRUE	1	0.348158392758662	2		591	664	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	62	215	0				ENST00000310581	NM_198253.2	-/1132			0.24378625581565	3	FACETS	0.879	0.761	1	0.44	0.38	0.504	CLONAL	1	TRUE	1	0.325354700437163	3		215	504	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796990	45796990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	72	601	0	ENST00000450313.1:c.1340C>T	p.Ser447Phe	p.S447F	ENST00000450313	NM_012222.2	447	tCt/tTt	14/16	1	2	FACETS	0.659	0.575	0.749	0.659	0.575	0.749	SUBCLONAL	1	TRUE	1	0.325354700437163	2		601	672	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243801039	243801039	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	29	292	0	ENST00000263826.5:c.435G>A	p.Met145Ile	p.M145I	ENST00000263826	NM_005465.4	145	atG/atA	5/13	0.24378625581565	3	FACETS	0.987	0.798	1	0.493	0.399	0.6	CLONAL	1	TRUE	1	0.325354700437163	3		292	210	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115960	8115960	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	71	340	0	ENST00000346208.3:c.1306del	p.Ser436ProfsTer39	p.S436Pfs*39	ENST00000346208		436	Tcc/cc	6/6	1	2	FACETS	0.979	0.857	1	0.979	0.857	1	CLONAL	1	TRUE	1	0.325354700437163	2		340	446	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742448	17742448	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0038145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	69	574	0	ENST00000250003.3:c.631-1G>A		p.X211_splice	ENST00000250003	NM_002478.4	211			0.312991432533792	3	FACETS	0.675	0.587	0.77	0.225	0.195	0.257	SUBCLONAL	1	TRUE	0	0.325354700437163	3		574	731	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436408	49436408	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1426177890	NA	P-0038145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	125	572	0	ENST00000301067.7:c.5803C>G	p.Leu1935Val	p.L1935V	ENST00000301067	NM_003482.3	1935	Ctg/Gtg	27/54	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.325354700437163	2		572	686	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445068	49445068	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	138	641	0	ENST00000301067.7:c.2398C>T	p.Gln800Ter	p.Q800*	ENST00000301067	NM_003482.3	800	Cag/Tag	10/54	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.325354700437163	2		641	721	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105505	30105505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772494452	NA	P-0038145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	78	495	0	ENST00000331968.5:c.1181G>A	p.Arg394Lys	p.R394K	ENST00000331968	NM_002742.2	394	aGa/aAa	7/18	0.24378625581565	3	FACETS	0.793	0.696	0.897	0.396	0.348	0.449	SUBCLONAL	1	TRUE	1	0.325354700437163	3		495	703	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0038145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	378	883	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.325354700437163	2	FACETS	0.989	0.939	1	0.989	0.939	1	CLONAL	2	TRUE	0	0.325354700437163	2		883	1175	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40486059	40486059	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0038145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	58	441	0	ENST00000264657.5:c.806C>G	p.Ser269Ter	p.S269*	ENST00000264657	NM_139276.2	269	tCa/tGa	9/24	0.325354700437163	3	FACETS	0.684	0.587	0.79	0.342	0.293	0.395	SUBCLONAL	1	TRUE	1	0.325354700437163	3		441	606	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245840	41245840	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	82	509	0	ENST00000357654.3:c.1708C>G	p.Pro570Ala	p.P570A	ENST00000357654	NM_007294.3	570	Cca/Gca	10/23	0.325354700437163	3	FACETS	1	0.959	1	0.594	0.526	0.668	CLONAL	1	TRUE	1	0.325354700437163	3		509	493	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770029	56770029	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	165	480	1	ENST00000337432.4:c.25G>T	p.Glu9Ter	p.E9*	ENST00000337432	NM_058216.2	9	Gaa/Taa	1/9	0.23739087597418	3	FACETS	1	0.965	1	0.717	0.663	0.774	CLONAL	2	TRUE	0	0.325354700437163	3		481	548	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972747	25972747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757702270	NA	P-0038145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	61	348	0	ENST00000435504.4:c.1678G>A	p.Asp560Asn	p.D560N	ENST00000435504		560	Gat/Aat	12/13	1	2	FACETS	0.839	0.726	0.961	0.839	0.726	0.961	CLONAL	1	TRUE	1	0.325354700437163	2		348	447	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513190	41513190	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0038145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	50	358	0	ENST00000263253.7:c.95-1G>C		p.X32_splice	ENST00000263253	NM_001429.3	32			1	2	FACETS	0.849	0.723	0.986	0.849	0.723	0.986	CLONAL	1	TRUE	1	0.325354700437163	2		358	362	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295187	1295187	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0038145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	61	313	1				ENST00000310581	NM_198253.2	-/1132			0.24378625581565	3	FACETS	1	0.879	1	0.508	0.439	0.582	CLONAL	1	TRUE	1	0.325354700437163	3		314	429	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295252	1295252	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0038145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	69	427	0				ENST00000310581	NM_198253.2	-/1132			0.24378625581565	3	FACETS	0.898	0.783	1	0.449	0.391	0.511	CLONAL	1	TRUE	1	0.325354700437163	3		427	549	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295264	1295264	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs562120871	NA	P-0038145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	75	440	0				ENST00000310581	NM_198253.2	-/1132			0.24378625581565	3	FACETS	0.929	0.815	1	0.465	0.407	0.526	CLONAL	1	TRUE	1	0.325354700437163	3		440	577	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439357	149439357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	98	669	0	ENST00000286301.3:c.2038G>A	p.Glu680Lys	p.E680K	ENST00000286301	NM_005211.3	680	Gag/Aag	15/22	1	2	FACETS	0.852	0.76	0.95	0.852	0.76	0.95	CLONAL	1	TRUE	1	0.325354700437163	2		669	707	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912194	127912194	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	56	198	0	ENST00000373547.4:c.676C>G	p.His226Asp	p.H226D	ENST00000373547	NM_002721.4	226	Cat/Gat	7/7	0.312991432533792	3	FACETS	1	0.957	1	0.824	0.721	0.931	CLONAL	2	TRUE	0	0.325354700437163	3		198	162	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801050	135801050	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	196	424	0	ENST00000298552.3:c.287T>A	p.Val96Asp	p.V96D	ENST00000298552	NM_001162426.1	96	gTc/gAc	5/23	0.312991432533792	3	FACETS	0.928	0.867	0.99	0.928	0.867	0.99	CLONAL	3	TRUE	0	0.325354700437163	3		424	503	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341249	70341249	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	153	499	0	ENST00000374080.3:c.808G>A	p.Asp270Asn	p.D270N	ENST00000374080		270	Gat/Aat	6/45	0.239406990737245	2	FACETS	0.864	0.795	0.936	0.864	0.795	0.936	CLONAL	2	TRUE	0	0.325354700437163	2		499	544	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	109	215	0				ENST00000310581	NM_198253.2	-/1132			0.230497578724513	1	FACETS	0.923	0.837	1	0.923	0.837	1	INDETERMINATE	1	TRUE	0	0.501508799157147	1		215	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0038250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	750	745	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	0.501508799157147	2		745	1267	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934152	48934152	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0038250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	89	256	0	ENST00000267163.4:c.608-1G>A		p.X203_splice	ENST00000267163	NM_000321.2	203			0.501508799157147	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.501508799157147	1		256	239	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197400	26197400	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	127	331	0	ENST00000356476.2:c.79C>T	p.Arg27Ter	p.R27*	ENST00000356476		27	Cga/Tga	1/1	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.501508799157147	2		331	506	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087386	27087386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	231	566	0	ENST00000324856.7:c.1960G>A	p.Glu654Lys	p.E654K	ENST00000324856	NM_006015.4	654	Gaa/Aaa	5/20	0.501508799157147	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.501508799157147	1		566	665	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880537	155880537	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1373221300	NA	P-0038250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	215	560	0	ENST00000368323.3:c.16C>G	p.Arg6Gly	p.R6G	ENST00000368323	NM_006912.5	6	Cgc/Ggc	2/6	0.230497578724513	1	FACETS	0.761	0.709	0.815	0.761	0.709	0.815	INDETERMINATE	1	TRUE	0	0.501508799157147	1		560	844	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440574	49440581	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CTGGGGCA	CTGGGGCA	TTGGGCC	novel	NA	P-0038250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	114	603	1	ENST00000301067.7:c.4237-8_4237-1delinsGGCCCAA		p.X1413_splice	ENST00000301067	NM_003482.3	1413			1	2	FACETS	0.516	0.464	0.571	0.516	0.464	0.571	SUBCLONAL	1	TRUE	1	0.501508799157147	2		604	881	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41011040	41011040	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	272	574	0	ENST00000267868.3:c.473T>A	p.Met158Lys	p.M158K	ENST00000267868	NM_002875.4	158	aTg/aAg	6/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.501508799157147	2		574	953	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639843	3639843	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	81	589	0	ENST00000294008.3:c.3796A>G	p.Ser1266Gly	p.S1266G	ENST00000294008	NM_032444.2	1266	Agc/Ggc	12/15	0.501508799157147	1	FACETS	0.332	0.292	0.375	0.332	0.292	0.375	SUBCLONAL	1	TRUE	0	0.501508799157147	1		589	729	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984770	72984770	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	84	603	0	ENST00000268489.5:c.2814C>A	p.Asn938Lys	p.N938K	ENST00000268489	NM_006885.3	938	aaC/aaA	3/10	0.283199084591399	2	FACETS	0.396	0.349	0.446	0.198	0.174	0.223	INDETERMINATE	1	TRUE	0	0.501508799157147	2		603	847	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885974	59885974	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	120	413	0	ENST00000259008.2:c.772C>T	p.Gln258Ter	p.Q258*	ENST00000259008	NM_032043.2	258	Cag/Tag	7/20	0.230497578724513	1	FACETS	0.504	0.456	0.555	0.504	0.456	0.555	INDETERMINATE	1	TRUE	0	0.501508799157147	1		413	711	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774966	73774966	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	86	305	0	ENST00000254810.4:c.207G>C	p.Gln69His	p.Q69H	ENST00000254810	NM_005324.3	69	caG/caC	3/4	0.230497578724513	1	FACETS	0.494	0.438	0.554	0.494	0.438	0.554	INDETERMINATE	1	TRUE	0	0.501508799157147	1		305	520	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604632	48604632	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0038250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	95	225	0	ENST00000342988.3:c.1454C>G	p.Ser485Ter	p.S485*	ENST00000342988	NM_005359.5	485	tCa/tGa	12/12	0.501508799157147	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.501508799157147	1		225	277	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906835	50906835	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	302	549	0	ENST00000440232.2:c.1223C>T	p.Ser408Phe	p.S408F	ENST00000440232	NM_002691.3	408	tCt/tTt	10/27	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.501508799157147	2		549	889	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25990551	25990551	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	202	438	0	ENST00000435504.4:c.676C>T	p.Gln226Ter	p.Q226*	ENST00000435504		226	Caa/Taa	8/13	0.230497578724513	1	FACETS	0.913	0.85	0.977	0.913	0.85	0.977	INDETERMINATE	1	TRUE	0	0.501508799157147	1		438	661	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309886	30309886	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	203	530	0	ENST00000307677.4:c.136G>C	p.Glu46Gln	p.E46Q	ENST00000307677	NM_138578.1	46	Gag/Cag	2/3	1	2	FACETS	0.907	0.841	0.974	0.907	0.841	0.974	CLONAL	1	TRUE	1	0.501508799157147	2		530	893	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405870	49405870	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	210	482	0	ENST00000418115.1:c.268G>T	p.Asp90Tyr	p.D90Y	ENST00000418115	NM_001664.2	90	Gat/Tat	3/5	0.501508799157147	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.501508799157147	1		482	569	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31464356	31464356	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1559205	NA	P-0038250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	247	594	0	ENST00000344624.3:c.2561C>T	p.Ser854Phe	p.S854F	ENST00000344624		854	tCt/tTt	17/33	0.230497578724513	1	FACETS	0.848	0.795	0.903	0.848	0.795	0.903	INDETERMINATE	1	TRUE	0	0.501508799157147	1		594	870	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562826	176562826	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	244	468	0	ENST00000439151.2:c.722G>C	p.Arg241Thr	p.R241T	ENST00000439151	NM_022455.4	241	aGa/aCa	2/23	0.230497578724513	1	FACETS	0.926	0.869	0.986	0.926	0.869	0.986	INDETERMINATE	1	TRUE	0	0.501508799157147	1		468	787	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737811	145737811	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	311	696	0	ENST00000428558.2:c.3019C>G	p.Leu1007Val	p.L1007V	ENST00000428558	NM_004260.3	1007	Ctc/Gtc	18/22	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.501508799157147	2		696	1139	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741138	145741164	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GATGTCTCACCTGGCCGGGGACACTGG	GATGTCTCACCTGGCCGGGGACACTGG	-	novel	NA	P-0038250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	249	437	0	ENST00000428558.2:c.1242_1258+10del		p.X414_splice	ENST00000428558	NM_004260.3	414		6/22	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.501508799157147	2		437	754	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93640057	93640057	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	57	216	0	ENST00000375746.1:c.1386G>C	p.Gln462His	p.Q462H	ENST00000375746	NM_001174167.1	462	caG/caC	10/14	1	2	FACETS	0.824	0.713	0.942	0.824	0.713	0.942	CLONAL	1	TRUE	1	0.501508799157147	2		216	276	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	128	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.748964495528342	2		215	331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0038265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	51	772	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.158138103485311	2	FACETS	0.185	0.157	0.216	0.093	0.078	0.108	INDETERMINATE	1	TRUE	0	0.748964495528342	2		772	736	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0038265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	189	529	1	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.158138103485311	2	FACETS	0.609	0.563	0.656	0.304	0.281	0.328	INDETERMINATE	1	TRUE	0	0.748964495528342	2		530	829	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761014	59761017	+	frameshift_variant	Frame_Shift_Del	DEL	ATAG	ATAG	-	rs778664039	NA	P-0038265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	245	390	0	ENST00000259008.2:c.3390_3393del	p.Tyr1131LeufsTer18	p.Y1131Lfs*18	ENST00000259008	NM_032043.2	1130	atCTAT/at	20/20	0.158138103485311	2	FACETS	1	0.991	1	0.625	0.591	0.66	INDETERMINATE	1	TRUE	0	0.748964495528342	2		390	523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578466	7578466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	384	533	0	ENST00000269305.4:c.464C>T	p.Thr155Ile	p.T155I	ENST00000269305	NM_001126112.2	155	aCc/aTc	5/11	0.158138103485311	2	FACETS	1	0.993	1	0.595	0.568	0.623	INDETERMINATE	1	TRUE	0	0.748964495528342	2		533	861	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653842	89653842	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057518425	NA	P-0038265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	87	336	0	ENST00000371953.3:c.140G>A	p.Arg47Lys	p.R47K	ENST00000371953	NM_000314.4	47	aGg/aAg	2/9	0.748964495528342	1	FACETS	0.532	0.477	0.589	0.532	0.477	0.589	SUBCLONAL	1	TRUE	0	0.748964495528342	1		336	273	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888165	112888165	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397507510	NA	P-0038265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	246	501	0	ENST00000351677.2:c.181G>C	p.Asp61His	p.D61H	ENST00000351677	NM_002834.3	61	Gat/Cat	3/16	1	2	FACETS	0.991	0.932	1	0.991	0.932	1	CLONAL	1	TRUE	1	0.748964495528342	2		501	663	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661949	29661950	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs863224835	NA	P-0038265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	230	347	0	ENST00000356175.3:c.5844_5845del	p.Arg1949SerfsTer6	p.R1949Sfs*6	ENST00000356175	NM_000267.3	1948	cAA/c	39/57	0.158138103485311	2	FACETS	1	0.983	1	0.557	0.524	0.591	INDETERMINATE	1	TRUE	0	0.748964495528342	2		347	551	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591239	67591250	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTTTTTCAGGTG	GTTTTTCAGGTG	-	novel	NA	P-0038265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	126	377	0	ENST00000274335.5:c.1746-6_1751del		p.X582_splice	ENST00000274335		582		13/15	1	2	FACETS	0.731	0.667	0.798	0.731	0.667	0.798	SUBCLONAL	1	TRUE	1	0.748964495528342	2		377	460	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994299	21994299	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	45	372	0	ENST00000579755.1:c.32T>G	p.Ile11Ser	p.I11S	ENST00000579755		11	aTt/aGt	1/3	0.681615205812485		FACETS		NA	1				NA	1	TRUE	0	0.748964495528342	0		372	166	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410762	63410762	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	250	507	1	ENST00000330258.3:c.2405A>G	p.Glu802Gly	p.E802G	ENST00000330258	NM_152424.3	802	gAg/gGg	2/2	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.748964495528342	2		508	650	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174395	11174395	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	121	820	0	ENST00000361445.4:c.7280T>G	p.Leu2427Arg	p.L2427R	ENST00000361445	NM_004958.3	2427	cTg/cGg	53/58	0.38932381467298	1	FACETS	0.93	0.844	1	0.93	0.844	1	CLONAL	1	TRUE	0	0.38932381467298	1		820	538	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66737033	66737033	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	230	585	0	ENST00000307102.5:c.556A>T	p.Ile186Phe	p.I186F	ENST00000307102	NM_002755.3	186	Atc/Ttc	5/11	0.38932381467298	3	FACETS	0.976	0.914	1	0.976	0.914	1	CLONAL	2	TRUE	1	0.38932381467298	3		585	723	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	93	215	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		215	261	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954181	48954261	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTTTCAGGAAGAAGAACGATTATCCATTCAAAATTTTAGGTAAATTTTTTACTTTTAGTAAAAAATTTTTTTCTTTTTAT	TGTTTCAGGAAGAAGAACGATTATCCATTCAAAATTTTAGGTAAATTTTTTACTTTTAGTAAAAAATTTTTTTCTTTTTAT	-	novel	NA	P-0038316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	66	233	0	ENST00000267163.4:c.1390-8_1422-40del		p.X464_splice	ENST00000267163	NM_000321.2	464		15/27	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		233	136	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	130	215	0				ENST00000310581	NM_198253.2	-/1132			0.418169750518829	5	FACETS	1	0.973	1	0.774	0.708	0.842	CLONAL	2	TRUE	2	0.434323545124284	5		215	426	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0038330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	147	499	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.434323545124284	4	FACETS	1	0.977	1	0.402	0.367	0.438	CLONAL	1	TRUE	1	0.434323545124284	4		499	806	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0038330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	294	413	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.434323545124284	4	FACETS	0.97	0.92	1	0.97	0.92	1	CLONAL	3	TRUE	1	0.434323545124284	4		413	667	SUCCESS
AXL	558	MSKCC	GRCh37	19	41749547	41749547	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	372	536	0	ENST00000301178.4:c.1472G>C	p.Arg491Thr	p.R491T	ENST00000301178	NM_021913.4	491	aGa/aCa	12/20	0.221674059394783	5	FACETS	0.85	0.807	0.893	0.85	0.807	0.893	INDETERMINATE	3	TRUE	2	0.434323545124284	5		536	1110	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6048638	6048638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	278	597	0	ENST00000265849.7:c.13G>A	p.Glu5Lys	p.E5K	ENST00000265849	NM_000535.5	5	Gag/Aag	1/15	0.221674059394783	5	FACETS	1	0.982	1	0.74	0.696	0.785	INDETERMINATE	2	TRUE	2	0.434323545124284	5		597	952	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275399	142275399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202162034	NA	P-0038330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	80	348	1	ENST00000350721.4:c.1904G>A	p.Arg635Gln	p.R635Q	ENST00000350721	NM_001184.3	635	cGa/cAa	9/47	0.434323545124284	4	FACETS	0.988	0.871	1	0.329	0.29	0.371	CLONAL	1	TRUE	1	0.434323545124284	4		349	535	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160488	108160488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730881369	NA	P-0038330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	262	437	0	ENST00000278616.4:c.4396C>T	p.Arg1466Ter	p.R1466*	ENST00000278616	NM_000051.3	1466	Cga/Tga	29/63	0.434323545124284	2	FACETS	0.965	0.911	1	0.965	0.911	1	CLONAL	2	TRUE	0	0.434323545124284	2		437	625	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010560	48010560	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587779920	NA	P-0038330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	133	259	0	ENST00000234420.5:c.188C>G	p.Ser63Cys	p.S63C	ENST00000234420	NM_000179.2	63	tCc/tGc	1/10	0.271210286566775	6	FACETS	1	0.912	1			1	CLONAL	2	TRUE	NA	0.434323545124284	6		259	572	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478902	56478902	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	2036	725	0	ENST00000267101.3:c.358A>G	p.Met120Val	p.M120V	ENST00000267101	NM_001982.3	120	Atg/Gtg	3/28	0.434323545124284	7	FACETS	1	0.998	1			1	CLONAL	7	TRUE	NA	0.434323545124284	7		725	2628	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412634	63412634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753930754	NA	P-0038330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	152	297	0	ENST00000330258.3:c.533G>A	p.Arg178His	p.R178H	ENST00000330258	NM_152424.3	178	cGt/cAt	2/2	1	1	FACETS	0.833	0.774	0.892	1	0.991	1	CLONAL	2	TRUE	0	0.434323545124284	1		297	329	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439718	51439718	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	104	337	0	ENST00000262662.1:c.283G>A	p.Asp95Asn	p.D95N	ENST00000262662		95	Gat/Aat	4/4	0.434323545124284	5	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.434323545124284	5		337	611	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771504	112771504	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	264	463	0	ENST00000369452.4:c.1677G>C	p.Gln559His	p.Q559H	ENST00000369452	NM_007373.3	559	caG/caC	9/9	0.227879225307601	2	FACETS	0.84	0.791	0.889	0.84	0.791	0.889	INDETERMINATE	2	TRUE	0	0.434323545124284	2		463	724	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211548	46211548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	48	275	2	ENST00000334344.6:c.514G>A	p.Glu172Lys	p.E172K	ENST00000334344	NM_152641.2	172	Gaa/Aaa	5/21	0.434323545124284	4	FACETS	0.719	0.608	0.84	0.24	0.202	0.28	SUBCLONAL	1	TRUE	1	0.434323545124284	4		277	441	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26971342	26971342	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	41	281	0	ENST00000381527.3:c.913G>C	p.Asp305His	p.D305H	ENST00000381527	NM_001260.1	305	Gat/Cat	9/13	0.434323545124284	3	FACETS	0.753	0.63	0.889	0.251	0.21	0.297	SUBCLONAL	1	TRUE	0	0.434323545124284	3		281	305	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701248	43701248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773338141	NA	P-0038330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	114	494	0	ENST00000382044.4:c.5447G>A	p.Arg1816Gln	p.R1816Q	ENST00000382044	NM_001141980.1	1816	cGa/cAa	26/28	0.434323545124284	4	FACETS	0.813	0.731	0.9	0.271	0.243	0.3	CLONAL	1	TRUE	1	0.434323545124284	4		494	926	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50818257	50818257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	233	310	0	ENST00000398568.2:c.1835C>G	p.Ser612Cys	p.S612C	ENST00000398568	NM_001042412.1	612	tCt/tGt	11/18	0.271210286566775	6	FACETS	1	0.958	1			1	CLONAL	3	TRUE	NA	0.434323545124284	6		310	651	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78599493	78599493	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	355	439	0	ENST00000306801.3:c.165G>A	p.Met55Ile	p.M55I	ENST00000306801	NM_020761.2	55	atG/atA	2/34	0.434323545124284	5	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	2	0.434323545124284	5		439	790	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372117	45372117	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	116	537	0	ENST00000262160.6:c.1052G>C	p.Ser351Thr	p.S351T	ENST00000262160	NM_005901.5	351	aGt/aCt	9/11	0.271210286566775	6	FACETS	0.872	0.784	0.965			1	CLONAL	1	TRUE	NA	0.434323545124284	6		537	1145	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110624	4110624	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	169	643	0	ENST00000262948.5:c.333C>G	p.Ile111Met	p.I111M	ENST00000262948	NM_030662.3	111	atC/atG	3/11	0.425672429927865	3	FACETS	0.972	0.893	1	0.486	0.446	0.527	CLONAL	1	TRUE	1	0.434323545124284	3		643	975	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871990	45871990	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	309	536	0	ENST00000391945.4:c.258G>C	p.Glu86Asp	p.E86D	ENST00000391945	NM_000400.3	86	gaG/gaC	5/23	0.221674059394783	5	FACETS	1	0.99	1	0.795	0.751	0.84	INDETERMINATE	2	TRUE	2	0.434323545124284	5		536	985	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660333	227660333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	42	477	0	ENST00000305123.5:c.3122C>T	p.Ser1041Phe	p.S1041F	ENST00000305123	NM_005544.2	1041	tCt/tTt	1/2	0.434323545124284	2	FACETS	0.399	0.333	0.472	0.199	0.166	0.236	SUBCLONAL	1	TRUE	0	0.434323545124284	2		477	485	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184618	185184618	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	86	305	0	ENST00000265026.3:c.1510G>C	p.Glu504Gln	p.E504Q	ENST00000265026	NM_004721.4	504	Gag/Cag	10/14	0.434323545124284	4	FACETS	1	0.956	1	0.386	0.343	0.433	CLONAL	1	TRUE	1	0.434323545124284	4		305	490	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955887	55955887	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	112	386	0	ENST00000263923.4:c.3275G>C	p.Gly1092Ala	p.G1092A	ENST00000263923	NM_002253.2	1092	gGt/gCt	24/30	0.434323545124284	4	FACETS	1	0.924	1	0.344	0.309	0.381	CLONAL	1	TRUE	1	0.434323545124284	4		386	717	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032230	26032230	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	56	341	0	ENST00000244661.2:c.59A>C	p.Gln20Pro	p.Q20P	ENST00000244661	NM_003537.3	20	cAg/cCg	1/1	0.434323545124284	4	FACETS	0.734	0.629	0.848	0.245	0.209	0.283	SUBCLONAL	1	TRUE	1	0.434323545124284	4		341	504	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412064	116412064	+	intron_variant	Intron	SNP	C	C	G	novel	NA	P-0038330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	156	687	0	ENST00000397752.3:c.3028+21C>G		p.*1010*	ENST00000397752	NM_000245.2	-/1390			0.425672429927865	3	FACETS	0.887	0.811	0.966	0.443	0.405	0.483	CLONAL	1	TRUE	1	0.434323545124284	3		687	986	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418227	139418228	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0038330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	445	809	1	ENST00000277541.6:c.344dup	p.Thr116HisfsTer27	p.T116Hfs*27	ENST00000277541	NM_017617.3	115	ggc/ggGc	3/34	0.434323545124284	2	FACETS	0.962	0.921	1	0.962	0.921	1	CLONAL	2	TRUE	0	0.434323545124284	2		810	1065	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790000	40790000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159843	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	197	500	0	ENST00000373198.4:c.2731G>A	p.Glu911Lys	p.E911K	ENST00000373198	NM_133170.3	911	Gaa/Aaa	18/32	0.843609827229772	1	FACETS	0.464	0.434	0.495	0.464	0.434	0.495	SUBCLONAL	1	TRUE	0	0.925421067513927	1		500	493	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40864381	40864381	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	374	694	0	ENST00000428826.2:c.1327C>T	p.Arg443Ter	p.R443*	ENST00000428826		443	Cga/Tga	12/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.925421067513927	2		694	807	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	180	462	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.987	0.923	1	0.987	0.923	1	CLONAL	1	TRUE	1	0.925421067513927	2		463	394	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156480	106156480	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	220	408	0	ENST00000380013.4:c.1381C>T	p.Gln461Ter	p.Q461*	ENST00000380013	NM_001127208.2	461	Cag/Tag	3/11	1	2	FACETS	0.962	0.905	1	0.962	0.905	1	CLONAL	1	TRUE	1	0.925421067513927	2		408	494	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717678	89717678	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554825200	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	683	466	0	ENST00000371953.3:c.703G>T	p.Glu235Ter	p.E235*	ENST00000371953	NM_000314.4	235	Gaa/Taa	7/9	0.925421067513927	2	FACETS	0.995	0.981	1	0.995	0.981	1	CLONAL	2	TRUE	0	0.925421067513927	2		466	742	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550494	29550497	+	frameshift_variant	Frame_Shift_Del	DEL	TAAC	TAAC	-	rs786202782	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	164	262	0	ENST00000356175.3:c.1756_1759del	p.Thr586ValfsTer18	p.T586Vfs*18	ENST00000356175	NM_000267.3	585	tTAACt/tt	16/57	1	2	FACETS	0.982	0.915	1	0.982	0.915	1	CLONAL	1	TRUE	1	0.925421067513927	2		262	361	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411831	63411831	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	350	364	0	ENST00000330258.3:c.1336C>T	p.Pro446Ser	p.P446S	ENST00000330258	NM_152424.3	446	Cct/Tct	2/2	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.925421067513927	1		364	376	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29686022	29686022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	176	324	0	ENST00000356175.3:c.8086C>T	p.Pro2696Ser	p.P2696S	ENST00000356175	NM_000267.3	2696	Ccg/Tcg	55/57	1	2	FACETS	0.946	0.883	1	0.946	0.883	1	CLONAL	1	TRUE	1	0.925421067513927	2		324	402	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638338	117638338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	196	382	0	ENST00000368508.3:c.6103C>T	p.Leu2035Phe	p.L2035F	ENST00000368508	NM_002944.2	2035	Ctt/Ttt	38/43	1	2	FACETS	0.866	0.81	0.923	0.866	0.81	0.923	CLONAL	1	TRUE	1	0.925421067513927	2		382	489	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868605	37868605	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775972596	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	287	447	0	ENST00000269571.5:c.1052G>A	p.Arg351Gln	p.R351Q	ENST00000269571		351	cGa/cAa	9/27	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.925421067513927	2		447	596	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076955	41076955	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs724159838	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	215	459	1	ENST00000373198.4:c.1465C>T	p.Pro489Ser	p.P489S	ENST00000373198	NM_133170.3	489	Cct/Tct	9/32	0.843609827229772	1	FACETS	0.523	0.492	0.555	0.523	0.492	0.555	SUBCLONAL	1	TRUE	0	0.925421067513927	1		460	477	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28880827	28880827	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368266056	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	229	520	1	ENST00000282397.4:c.3803C>T	p.Ser1268Leu	p.S1268L	ENST00000282397	NM_002019.4	1268	tCg/tTg	29/30	0.343601181506767	3	FACETS	0.943	0.881	1			1	INDETERMINATE	1	TRUE	NA	0.925421067513927	3		521	768	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379868	17379868	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765555081	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	433	681	1	ENST00000359435.4:c.253C>T	p.Arg85Trp	p.R85W	ENST00000359435	NM_001033549.1	85	Cgg/Tgg	2/9	1	2	FACETS	0.964	0.923	1	0.964	0.923	1	CLONAL	1	TRUE	1	0.925421067513927	2		682	971	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500885	8500885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1193645875	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	226	514	0	ENST00000356435.5:c.1997C>T	p.Pro666Leu	p.P666L	ENST00000356435		666	cCt/cTt	13/35	0.925421067513927	1	FACETS	0.983	0.951	1	0.983	0.951	1	CLONAL	1	TRUE	0	0.925421067513927	1		514	267	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435662	18435662	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	153	278	0	ENST00000266497.5:c.647T>G	p.Met216Arg	p.M216R	ENST00000266497		216	aTg/aGg	1/31	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.925421067513927	2		278	300	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691157	18691157	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	209	403	0	ENST00000266497.5:c.3268C>A	p.Gln1090Lys	p.Q1090K	ENST00000266497		1090	Cag/Aag	23/31	1	2	FACETS	0.916	0.859	0.974	0.916	0.859	0.974	CLONAL	1	TRUE	1	0.925421067513927	2		403	493	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476390	88476390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	167	462	0	ENST00000360948.2:c.1742C>T	p.Ala581Val	p.A581V	ENST00000360948	NM_001012338.2	581	gCc/gTc	15/19	NA	2	FACETS	0.749	0.694	0.805			1	INDETERMINATE	1	TRUE	NA	0.925421067513927	2		462	482	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678470	88678470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1307510401	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	257	615	0	ENST00000360948.2:c.1066G>A	p.Gly356Arg	p.G356R	ENST00000360948	NM_001012338.2	356	Gga/Aga	9/19	NA	2	FACETS	0.948	0.895	1			1	INDETERMINATE	1	TRUE	NA	0.925421067513927	2		615	586	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122953	2122953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	312	592	1	ENST00000219476.3:c.2324C>T	p.Ser775Phe	p.S775F	ENST00000219476	NM_000548.3	775	tCt/tTt	21/42	0.794519032759769	3	FACETS	1	0.963	1	0.512	0.484	0.541	CLONAL	1	TRUE	1	0.925421067513927	3		593	963	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2218126	2218126	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	777	703	0	ENST00000326181.6:c.188C>T	p.Ser63Phe	p.S63F	ENST00000326181	NM_032271.2	63	tCc/tTc	4/21	0.794519032759769	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.925421067513927	3		703	1205	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858619	9858619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	231	492	0	ENST00000330684.3:c.2782G>A	p.Gly928Ser	p.G928S	ENST00000330684	NM_001134407.1	928	Ggt/Agt	13/13	0.794519032759769	3	FACETS	1	0.97	1	0.528	0.495	0.563	CLONAL	1	TRUE	1	0.925421067513927	3		492	691	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032387	10032387	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555455835	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	166	385	0	ENST00000330684.3:c.436C>T	p.Gln146Ter	p.Q146*	ENST00000330684	NM_001134407.1	146	Cag/Tag	3/13	0.794519032759769	3	FACETS	0.99	0.916	1	0.495	0.458	0.534	CLONAL	1	TRUE	1	0.925421067513927	3		385	530	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29482978	29483036	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTTTTTTTCTTTTTTTTTCAGCTTCCAATAAAAACAGGACAGCAGAACACACATACC	TTTTTTTTTTCTTTTTTTTTCAGCTTCCAATAAAAACAGGACAGCAGAACACACATACC	-	novel	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	159	205	0	ENST00000356175.3:c.61-23_96del		p.X21_splice	ENST00000356175	NM_000267.3	21		2/57	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.925421067513927	2		205	298	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753491	42753491	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749536161	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	487	712	0	ENST00000222329.4:c.773C>T	p.Ser258Phe	p.S258F	ENST00000222329	NM_006494.2	258	tCc/tTc	4/4	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.925421067513927	2		712	1004	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249743	39249743	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	281	423	0	ENST00000402219.2:c.1826T>C	p.Leu609Pro	p.L609P	ENST00000402219	NM_005633.3	609	cTt/cCt	10/23	NA	2	FACETS	0.95	0.9	1			1	INDETERMINATE	1	TRUE	NA	0.925421067513927	2		423	639	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421260	12421260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772234905	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	499	556	2	ENST00000287820.6:c.140C>T	p.Ser47Phe	p.S47F	ENST00000287820	NM_015869.4	47	tCc/tTc	2/7	0.411832852954028	3	FACETS	0.879	0.848	0.911	0.879	0.848	0.911	INDETERMINATE	2	TRUE	1	0.925421067513927	3		558	897	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499367	89499367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	233	398	1	ENST00000336596.2:c.2537C>T	p.Pro846Leu	p.P846L	ENST00000336596	NM_005233.5	846	cCc/cTc	15/17	0.794519032759769	3	FACETS	1	0.988	1	0.6	0.563	0.637	CLONAL	1	TRUE	1	0.925421067513927	3		399	614	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582096	189582096	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	244	467	0	ENST00000264731.3:c.655C>G	p.Pro219Ala	p.P219A	ENST00000264731	NM_003722.4	219	Cct/Gct	5/14	1	2	FACETS	0.975	0.92	1	0.975	0.92	1	CLONAL	1	TRUE	1	0.925421067513927	2		467	541	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957774	1957774	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	348	602	2	ENST00000382891.5:c.2740G>A	p.Glu914Lys	p.E914K	ENST00000382891	NM_133335.3	914	Gag/Aag	15/22	0.323341390806845	1	FACETS	0.473	0.45	0.497	0.473	0.45	0.497	INDETERMINATE	1	TRUE	0	0.925421067513927	1		604	854	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156043	106156043	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	181	333	0	ENST00000380013.4:c.944C>T	p.Ser315Phe	p.S315F	ENST00000380013	NM_001127208.2	315	tCc/tTc	3/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.925421067513927	2		333	381	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520447	176520447	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765902714	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	339	640	1	ENST00000292408.4:c.1292C>T	p.Ser431Phe	p.S431F	ENST00000292408	NM_213647.1	431	tCc/tTc	10/18	1	2	FACETS	0.986	0.939	1	0.986	0.939	1	CLONAL	1	TRUE	1	0.925421067513927	2		641	743	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402692	20402692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343489714	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	210	388	2	ENST00000346618.3:c.229G>A	p.Gly77Ser	p.G77S	ENST00000346618	NM_001949.4	77	Ggc/Agc	1/7	0.705547302103779	3	FACETS	0.919	0.857	0.984			1	CLONAL	1	TRUE	NA	0.925421067513927	3		390	722	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527731	157527731	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	332	538	0	ENST00000346085.5:c.5456G>T	p.Trp1819Leu	p.W1819L	ENST00000346085	NM_020732.3	1819	tGg/tTg	20/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.925421067513927	2		538	703	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729739	41729739	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	218	455	0	ENST00000242208.4:c.790G>A	p.Glu264Lys	p.E264K	ENST00000242208	NM_002192.2	264	Gaa/Aaa	3/3	0.385153841400086	1	FACETS	0.518	0.487	0.549	0.518	0.487	0.549	INDETERMINATE	1	TRUE	0	0.925421067513927	1		455	489	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104700	69104700	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149428879	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	300	541	0	ENST00000288368.4:c.4544C>T	p.Ser1515Leu	p.S1515L	ENST00000288368	NM_024870.2	1515	tCg/tTg	37/40	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.925421067513927	2		541	639	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760687	133760687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	386	771	1	ENST00000318560.5:c.3010C>T	p.Pro1004Ser	p.P1004S	ENST00000318560	NM_005157.4	1004	Cct/Tct	11/11	1	2	FACETS	0.964	0.921	1	0.964	0.921	1	CLONAL	1	TRUE	1	0.925421067513927	2		772	865	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510816	120510816	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	47	482	0	ENST00000256646.2:c.1148C>T	p.Pro383Leu	p.P383L	ENST00000256646	NM_024408.3	383	cCt/cTt	7/34	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.332008247542503	2		482	232	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	37	462	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.782	0.648	0.931	0.782	0.648	0.931	CLONAL	1	TRUE	1	0.332008247542503	2		463	285	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151774	108151774	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	17	389	0	ENST00000278616.4:c.3455C>T	p.Ser1152Phe	p.S1152F	ENST00000278616	NM_000051.3	1152	tCt/tTt	24/63	1	2	FACETS	0.711	0.535	0.917	0.711	0.535	0.917	CLONAL	1	TRUE	1	0.332008247542503	2		389	144	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138944	64138944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	52	402	0	ENST00000334205.4:c.2311C>T	p.Pro771Ser	p.P771S	ENST00000334205	NM_003942.2	771	Ccc/Tcc	17/17	1	2	FACETS	0.941	0.805	1	0.941	0.805	1	CLONAL	1	TRUE	1	0.332008247542503	2		402	333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064794618	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	106	820	0	ENST00000269305.4:c.159G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgG/tgA	4/11	0.290895068007914	2	FACETS	0.792	0.716	0.872	0.792	0.716	0.872	SUBCLONAL	2	TRUE	0	0.332008247542503	2		820	403	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539951	187539951	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs777631605	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	32	467	0	ENST00000441802.2:c.7789C>T	p.Arg2597Ter	p.R2597*	ENST00000441802	NM_005245.3	2597	Cga/Tga	10/27	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.332008247542503	2		467	172	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286196	66286196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	19	387	1	ENST00000273854.3:c.1490G>A	p.Gly497Glu	p.G497E	ENST00000273854	NM_004439.5	497	gGa/gAa	6/18	1	2	FACETS	0.954	0.733	1	0.954	0.733	1	CLONAL	1	TRUE	1	0.332008247542503	2		388	120	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993500	72993500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1234634202	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	76	765	0	ENST00000268489.5:c.545G>A	p.Gly182Glu	p.G182E	ENST00000268489	NM_006885.3	182	gGg/gAg	2/10	1	2	FACETS	0.853	0.749	0.963	0.853	0.749	0.963	CLONAL	1	TRUE	1	0.332008247542503	2		765	537	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959121	2959121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778152	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	72	619	0	ENST00000396946.4:c.2395G>A	p.Asp799Asn	p.D799N	ENST00000396946	NM_032415.4	799	Gat/Aat	18/25	1	2	FACETS	0.775	0.677	0.879	0.775	0.677	0.879	SUBCLONAL	1	TRUE	1	0.332008247542503	2		619	560	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537076	41537076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	14	382	0	ENST00000263253.7:c.1903G>A	p.Glu635Lys	p.E635K	ENST00000263253	NM_001429.3	635	Gag/Aag	10/31	1	2	FACETS	0.835	0.611	1	0.835	0.611	1	CLONAL	1	TRUE	1	0.332008247542503	2		382	101	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955096	55955096	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	48	579	0	ENST00000263923.4:c.3449G>A	p.Arg1150Lys	p.R1150K	ENST00000263923	NM_002253.2	1150	aGa/aAa	26/30	1	2	FACETS	0.674	0.571	0.787	0.674	0.571	0.787	SUBCLONAL	1	TRUE	1	0.332008247542503	2		579	429	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980352	201980352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	35	795	0	ENST00000359651.3:c.88C>T	p.Pro30Ser	p.P30S	ENST00000359651		30	Ccc/Tcc	1/8	1	2	FACETS	0.409	0.335	0.493	0.409	0.335	0.493	SUBCLONAL	1	TRUE	1	0.332008247542503	2		795	515	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522425	187522425	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	20	481	0	ENST00000441802.2:c.11638G>A	p.Glu3880Lys	p.E3880K	ENST00000441802	NM_005245.3	3880	Gag/Aag	21/27	1	2	FACETS	0.658	0.506	0.834	0.658	0.506	0.834	SUBCLONAL	1	TRUE	1	0.332008247542503	2		481	183	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218848	36218848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774736378	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	71	926	0	ENST00000222270.7:c.4459C>T	p.Arg1487Cys	p.R1487C	ENST00000222270	NM_014727.1	1487	Cgc/Tgc	18/37	1	2	FACETS	0.745	0.651	0.847	0.745	0.651	0.847	SUBCLONAL	1	TRUE	1	0.332008247542503	2		926	574	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518415	204518415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs913129198	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	23	538	0	ENST00000367182.3:c.1078C>T	p.Pro360Ser	p.P360S	ENST00000367182	NM_001278516.1	360	Cct/Tct	11/11	1	2	FACETS	0.882	0.695	1	0.882	0.695	1	CLONAL	1	TRUE	1	0.332008247542503	2		538	157	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246498734	246498734	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	52	641	0	ENST00000388985.4:c.271A>T	p.Lys91Ter	p.K91*	ENST00000388985		91	Aaa/Taa	3/12	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.332008247542503	2		641	284	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392038	118392038	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	43	590	0	ENST00000534358.1:c.11549G>A	p.Arg3850Lys	p.R3850K	ENST00000534358	NM_005933.3	3850	aGa/aAa	35/36	1	2	FACETS	0.783	0.657	0.92	0.783	0.657	0.92	CLONAL	1	TRUE	1	0.332008247542503	2		590	331	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49419988	49419988	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	54	640	0	ENST00000301067.7:c.15761T>G	p.Val5254Gly	p.V5254G	ENST00000301067	NM_003482.3	5254	gTc/gGc	48/54	1	2	FACETS	0.803	0.688	0.928	0.803	0.688	0.928	CLONAL	1	TRUE	1	0.332008247542503	2		640	405	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446049	49446049	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	51	926	0	ENST00000301067.7:c.1417G>T	p.Glu473Ter	p.E473*	ENST00000301067	NM_003482.3	473	Gaa/Taa	10/54	1	2	FACETS	0.472	0.4	0.551	0.472	0.4	0.551	SUBCLONAL	1	TRUE	1	0.332008247542503	2		926	651	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514814	103514814	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	27	430	0	ENST00000355739.4:c.1315G>C	p.Gly439Arg	p.G439R	ENST00000355739	NM_000123.3	439	Gga/Cga	8/15	1	2	FACETS	0.672	0.537	0.825	0.672	0.537	0.825	SUBCLONAL	1	TRUE	1	0.332008247542503	2		430	242	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986782	36986782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	35	120	1	ENST00000354822.5:c.907G>A	p.Gly303Ser	p.G303S	ENST00000354822	NM_001079668.2	303	Ggt/Agt	3/3	1	2	FACETS	0.868	0.716	1	0.868	0.716	1	CLONAL	1	TRUE	1	0.332008247542503	2		121	243	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003267	42003267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	27	624	0	ENST00000219905.7:c.2804G>A	p.Gly935Glu	p.G935E	ENST00000219905	NM_001164273.1	935	gGa/gAa	8/24	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.332008247542503	2		624	147	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708449	43708449	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	34	614	0	ENST00000382044.4:c.4847T>C	p.Leu1616Pro	p.L1616P	ENST00000382044	NM_001141980.1	1616	cTt/cCt	22/28	1	2	FACETS	0.999	0.824	1	0.999	0.824	1	CLONAL	1	TRUE	1	0.332008247542503	2		614	205	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43773191	43773191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764794131	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	23	540	0	ENST00000382044.4:c.401C>T	p.Pro134Leu	p.P134L	ENST00000382044	NM_001141980.1	134	cCt/cTt	5/28	1	2	FACETS	0.84	0.66	1	0.84	0.66	1	CLONAL	1	TRUE	1	0.332008247542503	2		540	165	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830471	72830472	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	46	583	2	ENST00000268489.5:c.6109_6110delinsTT	p.Pro2037Leu	p.P2037L	ENST00000268489	NM_006885.3	2037	CCa/TTa	9/10	1	2	FACETS	0.952	0.807	1	0.952	0.807	1	CLONAL	1	TRUE	1	0.332008247542503	2		585	291	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353797	40353798	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	66	688	1	ENST00000293328.3:c.2322_2323delinsTT	p.Arg775Trp	p.R775W	ENST00000293328	NM_012448.3	774	ggCCgg/ggTTgg	19/19	0.212243356432535	1	FACETS	0.484	0.42	0.554	0.484	0.42	0.554	SUBCLONAL	1	TRUE	0	0.332008247542503	1		689	685	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481454	40481454	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	45	616	0	ENST00000264657.5:c.1255G>T	p.Gly419Trp	p.G419W	ENST00000264657	NM_139276.2	419	Ggg/Tgg	14/24	0.212243356432535	1	FACETS	0.816	0.69	0.953	0.816	0.69	0.953	CLONAL	1	TRUE	0	0.332008247542503	1		616	277	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59820492	59820492	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	14	390	0	ENST00000259008.2:c.2261G>C	p.Gly754Ala	p.G754A	ENST00000259008	NM_032043.2	754	gGa/gCa	16/20	0.212243356432535	1	FACETS	0.463	0.336	0.614	0.463	0.336	0.614	SUBCLONAL	1	TRUE	0	0.332008247542503	1		390	152	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532640	63532640	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	44	780	1	ENST00000307078.5:c.1939G>A	p.Glu647Lys	p.E647K	ENST00000307078	NM_004655.3	647	Gag/Aag	8/11	0.212243356432535	1	FACETS	0.492	0.413	0.58	0.492	0.413	0.58	SUBCLONAL	1	TRUE	0	0.332008247542503	1		781	449	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099252	4099252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	61	810	1	ENST00000262948.5:c.866G>A	p.Gly289Glu	p.G289E	ENST00000262948	NM_030662.3	289	gGa/gAa	7/11	1	2	FACETS	0.759	0.656	0.871	0.759	0.656	0.871	SUBCLONAL	1	TRUE	1	0.332008247542503	2		811	484	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39233561	39233562	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	33	419	0	ENST00000402219.2:c.2782_2783delinsTT	p.Pro928Phe	p.P928F	ENST00000402219	NM_005633.3	928	CCt/TTt	17/23	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.332008247542503	2		419	159	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593581	215593581	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs773166130	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	31	425	0	ENST00000260947.4:c.2153A>T	p.Asn718Ile	p.N718I	ENST00000260947	NM_000465.2	718	aAt/aTt	11/11	1	2	FACETS	0.658	0.533	0.797	0.658	0.533	0.797	SUBCLONAL	1	TRUE	1	0.332008247542503	2		425	284	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023328	31023328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	35	686	1	ENST00000375687.4:c.2813C>T	p.Pro938Leu	p.P938L	ENST00000375687	NM_015338.5	938	cCt/cTt	13/13	1	2	FACETS	0.657	0.54	0.787	0.657	0.54	0.787	SUBCLONAL	1	TRUE	1	0.332008247542503	2		687	321	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748165	41748165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	32	467	0	ENST00000226382.2:c.604C>T	p.Pro202Ser	p.P202S	ENST00000226382	NM_003924.3	202	Ccc/Tcc	3/3	1	2	FACETS	0.63	0.513	0.762	0.63	0.513	0.762	SUBCLONAL	1	TRUE	1	0.332008247542503	2		467	306	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286280	66286280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372519544	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	13	300	0	ENST00000273854.3:c.1406C>T	p.Pro469Leu	p.P469L	ENST00000273854	NM_004439.5	469	cCa/cTa	6/18	1	2	FACETS	0.699	0.503	0.933	0.699	0.503	0.933	SUBCLONAL	1	TRUE	1	0.332008247542503	2		300	112	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157387	106157387	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	13	398	0	ENST00000380013.4:c.2288C>T	p.Pro763Leu	p.P763L	ENST00000380013	NM_001127208.2	763	cCc/cTc	3/11	1	2	FACETS	0.88	0.636	1	0.88	0.636	1	CLONAL	1	TRUE	1	0.332008247542503	2		398	89	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43745276	43745277	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	56	800	2	ENST00000523873.1:c.189_190delinsAA	p.Glu64Lys	p.E64K	ENST00000523873		63	caGGag/caAAag	3/8	1	2	FACETS	0.716	0.614	0.827	0.716	0.614	0.827	SUBCLONAL	1	TRUE	1	0.332008247542503	2		802	471	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346626	81346626	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	26	361	0	ENST00000222390.5:c.1327C>T	p.Pro443Ser	p.P443S	ENST00000222390	NM_000601.4	443	Cca/Tca	11/18	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.332008247542503	2		361	138	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92244471	92244472	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	35	344	1	ENST00000265734.4:c.963_964delinsAA	p.Glu322Lys	p.E322K	ENST00000265734	NM_001259.6	321	tcGGag/tcAAag	8/8	1	2	FACETS	0.667	0.548	0.8	0.667	0.548	0.8	SUBCLONAL	1	TRUE	1	0.332008247542503	2		345	316	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477858	140477858	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	18	560	0	ENST00000288602.6:c.1450A>T	p.Met484Leu	p.M484L	ENST00000288602	NM_004333.4	484	Atg/Ttg	12/18	1	2	FACETS	0.642	0.486	0.823	0.642	0.486	0.823	SUBCLONAL	1	TRUE	1	0.332008247542503	2		560	169	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194682	29194682	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	62	851	0	ENST00000240100.2:c.1046C>T	p.Pro349Leu	p.P349L	ENST00000240100	NM_001394.6	349	cCc/cTc	4/4	0.266230073385579	2	FACETS	0.663	0.573	0.761	0.332	0.286	0.381	SUBCLONAL	1	TRUE	0	0.332008247542503	2		851	563	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518139	8518139	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	79	548	0	ENST00000356435.5:c.1252T>A	p.Ser418Thr	p.S418T	ENST00000356435		418	Tcc/Acc	10/35	0.320854394434566	1	FACETS	0.966	0.854	1	0.966	0.854	1	CLONAL	1	TRUE	0	0.332008247542503	1		548	411	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971157	21971163	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGTGG	GCCGTGG	ACCGT	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	62	445	1	ENST00000304494.5:c.195_201delinsACGGT	p.His66ArgfsTer53	p.H66Rfs*53	ENST00000304494	NM_000077.4	65	ctCCACGGC/ctACGGT	2/3	0.320854394434566	1	FACETS	0.88	0.764	1	0.88	0.764	1	CLONAL	1	TRUE	0	0.332008247542503	1		446	354	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907752	76907752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	28	521	0	ENST00000373344.5:c.4409C>T	p.Ser1470Phe	p.S1470F	ENST00000373344	NM_000489.3	1470	tCc/tTc	15/35	1	2	FACETS	0.664	0.533	0.812	0.664	0.533	0.812	SUBCLONAL	1	TRUE	1	0.332008247542503	2		521	254	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200049	123200049	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	17	345	0	ENST00000218089.9:c.2121T>A	p.Asp707Glu	p.D707E	ENST00000218089	NM_001042749.1	707	gaT/gaA	22/35	1	2	FACETS	0.898	0.679	1	0.898	0.679	1	CLONAL	1	TRUE	1	0.332008247542503	2		345	114	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202413	123202413	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0038413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	25	425	0	ENST00000218089.9:c.2266-1G>A		p.X756_splice	ENST00000218089	NM_001042749.1	756			1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.332008247542503	2		425	103	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	65	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.721	0.625	0.824	0.721	0.625	0.824	SUBCLONAL	1	TRUE	1	0.32563155024952	2		215	554	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0038861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	128	446	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.323020194007746	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	2	TRUE	0	0.32563155024952	2		446	390	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971194	21971194	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	69	413	0	ENST00000304494.5:c.164del	p.Gly55AlafsTer91	p.G55Afs*91	ENST00000304494	NM_000077.4	55	gGc/gc	2/3	0.32563155024952	1	FACETS	0.934	0.817	1	0.934	0.817	1	CLONAL	1	TRUE	0	0.32563155024952	1		413	380	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0038861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	142	754	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.32563155024952	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.32563155024952	1		754	638	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120855	115120855	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1565862637	NA	P-0038861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	70	476	0	ENST00000257566.3:c.151G>A	p.Ala51Thr	p.A51T	ENST00000257566	NM_016569.3	51	Gcg/Acg	1/8	0.3166842241456	3	FACETS	0.998	0.872	1	0.333	0.29	0.378	CLONAL	1	TRUE	0	0.32563155024952	3		476	501	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260956	16260957	+	missense_variant	Missense_Mutation	DNP	GT	GT	CA	novel	NA	P-0038861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	91	386	0	ENST00000375759.3:c.8221_8222delinsCA	p.Val2741His	p.V2741H	ENST00000375759	NM_015001.2	2741	GTc/CAc	11/15	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.32563155024952	2		386	534	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575439	64575439	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	99	523	0	ENST00000312049.6:c.578C>A	p.Thr193Lys	p.T193K	ENST00000312049	NM_130799.2	193	aCa/aAa	3/10	1	2	FACETS	0.782	0.697	0.871	0.782	0.697	0.871	SUBCLONAL	1	TRUE	1	0.32563155024952	2		523	778	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4387959	4387959	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	160	499	0	ENST00000261254.3:c.445T>C	p.Trp149Arg	p.W149R	ENST00000261254	NM_001759.3	149	Tgg/Cgg	3/5	0.323020194007746	2	FACETS	0.884	0.815	0.955	0.884	0.815	0.955	CLONAL	2	TRUE	0	0.32563155024952	2		499	556	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435261	18435261	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764478238	NA	P-0038861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	108	337	0	ENST00000266497.5:c.246C>A	p.His82Gln	p.H82Q	ENST00000266497		82	caC/caA	1/31	0.323020194007746	2	FACETS	0.914	0.828	1	0.914	0.828	1	CLONAL	2	TRUE	0	0.32563155024952	2		337	363	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727523	88727524	+	missense_variant	Missense_Mutation	DNP	CT	CT	TA	novel	NA	P-0038861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	66	406	0	ENST00000360948.2:c.255_256delinsTA	p.Glu86Lys	p.E86K	ENST00000360948	NM_001012338.2	85	atAGag/atTAag	3/19	0.32563155024952	1	FACETS	0.808	0.704	0.92	0.808	0.704	0.92	CLONAL	1	TRUE	0	0.32563155024952	1		406	420	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99472854	99472855	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	93	444	1	ENST00000268035.6:c.2852dup	p.Leu951PhefsTer10	p.L951Ffs*10	ENST00000268035	NM_000875.3	950	-/T	14/21	0.32563155024952	1	FACETS	0.889	0.793	0.991	0.889	0.793	0.991	CLONAL	1	TRUE	0	0.32563155024952	1		445	538	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223986	2223986	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	146	605	0	ENST00000326181.6:c.1200G>T	p.Trp400Cys	p.W400C	ENST00000326181	NM_032271.2	400	tgG/tgT	13/21	1	2	FACETS	0.978	0.892	1	0.978	0.892	1	CLONAL	1	TRUE	1	0.32563155024952	2		605	917	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39573270	39573270	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	91	360	1	ENST00000262039.4:c.751G>T	p.Glu251Ter	p.E251*	ENST00000262039	NM_002647.2	251	Gaa/Taa	7/25	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.32563155024952	2		361	535	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158637007	158637007	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	79	481	0	ENST00000263640.3:c.173G>T	p.Ser58Ile	p.S58I	ENST00000263640	NM_001105.4	58	aGc/aTc	4/11	1	2	FACETS	0.809	0.712	0.912	0.809	0.712	0.912	CLONAL	1	TRUE	1	0.32563155024952	2		481	600	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805749	32805749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1446442425	NA	P-0038861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	107	640	1	ENST00000374899.4:c.262C>T	p.Arg88Cys	p.R88C	ENST00000374899	NM_018833.2	88	Cgt/Tgt	2/12	1	2	FACETS	0.928	0.833	1	0.928	0.833	1	CLONAL	1	TRUE	1	0.32563155024952	2		641	708	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410494	139410494	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	118	691	0	ENST00000277541.6:c.1608del	p.Cys537AlafsTer94	p.C537Afs*94	ENST00000277541	NM_017617.3	536	ccC/cc	10/34	0.32563155024952	1	FACETS	0.75	0.676	0.828	0.75	0.676	0.828	SUBCLONAL	1	TRUE	0	0.32563155024952	1		691	809	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763908	76763927	+	frameshift_variant	Frame_Shift_Del	DEL	ATACCACCAGCCACTGGCTG	ATACCACCAGCCACTGGCTG	-	novel	NA	P-0038861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	80	266	0	ENST00000373344.5:c.7381_7400del	p.Gln2461AlafsTer30	p.Q2461Afs*30	ENST00000373344	NM_000489.3	2461	CAGCCAGTGGCTGGTGGTATg/g	35/35	1	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.32563155024952	1		266	289	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260956	16260956	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs559925121	NA	P-0038861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	88	381	0	ENST00000375759.3:c.8221G>C	p.Val2741Leu	p.V2741L	ENST00000375759	NM_015001.2	2741	Gtc/Ctc	11/15	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.32563155024952	2		381	534	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	155	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.814	0.749	0.882	1	0.99	1	CLONAL	2	TRUE	1	0.326066673955666	2		215	584	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	213	458	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.240649424996563	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.326066673955666	3		458	689	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	108	316	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.0991248980098025	4	FACETS	1	0.961	1	1	0.961	1	INDETERMINATE	2	TRUE	2	0.326066673955666	4		316	393	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	120	779	1	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	1	2	FACETS	0.735	0.663	0.812	0.735	0.663	0.812	SUBCLONAL	1	TRUE	1	0.326066673955666	2		780	1001	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748170	41748170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs964285984	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	61	329	0	ENST00000226382.2:c.599C>T	p.Pro200Leu	p.P200L	ENST00000226382	NM_003924.3	200	cCc/cTc	3/3	1	2	FACETS	0.615	0.531	0.708	0.615	0.531	0.708	SUBCLONAL	1	TRUE	1	0.326066673955666	2		329	608	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522148	157522148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	88	438	0	ENST00000346085.5:c.4420C>T	p.Pro1474Ser	p.P1474S	ENST00000346085	NM_020732.3	1474	Ccc/Tcc	18/20	0.326066673955666	3	FACETS	0.749	0.663	0.842	0.25	0.221	0.281	SUBCLONAL	1	TRUE	0	0.326066673955666	3		438	838	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561418	9561418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	76	456	0	ENST00000353224.5:c.364G>A	p.Glu122Lys	p.E122K	ENST00000353224	NM_177990.2	122	Gaa/Aaa	4/10	0.0991248980098025	4	FACETS	0.785	0.688	0.891	0.393	0.344	0.446	INDETERMINATE	1	TRUE	2	0.326066673955666	4		456	787	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120714	94120714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	39	319	0	ENST00000369303.4:c.337C>T	p.Pro113Ser	p.P113S	ENST00000369303	NM_004440.3	113	Cct/Tct	3/17	0.326066673955666	3	FACETS	0.601	0.498	0.716	0.2	0.166	0.239	SUBCLONAL	1	TRUE	0	0.326066673955666	3		319	463	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55974015	55974015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	156	479	0	ENST00000263923.4:c.1301C>T	p.Ser434Phe	p.S434F	ENST00000263923	NM_002253.2	434	tCc/tTc	10/30	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.326066673955666	2		479	659	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11175483	11175484	+	missense_variant	Missense_Mutation	DNP	GA	GA	AC	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	166	390	2	ENST00000361445.4:c.7058_7059delinsGT	p.Ile2353Ser	p.I2353S	ENST00000361445	NM_004958.3	2353	aTC/aGT	51/58	0.326066673955666	5	FACETS	0.81	0.744	0.879	0.54	0.496	0.586	CLONAL	2	TRUE	2	0.326066673955666	5		392	936	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294237	11294237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	294	452	1	ENST00000361445.4:c.2294C>T	p.Pro765Leu	p.P765L	ENST00000361445	NM_004958.3	765	cCc/cTc	14/58	0.326066673955666	5	FACETS	0.889	0.838	0.941	0.889	0.838	0.941	CLONAL	3	TRUE	2	0.326066673955666	5		453	1007	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263715	16263716	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	86	367	1	ENST00000375759.3:c.10084_10085delinsTT	p.Pro3362Phe	p.P3362F	ENST00000375759	NM_015001.2	3362	CCt/TTt	12/15	0.326066673955666	5	FACETS	0.87	0.768	0.979	0.29	0.256	0.327	CLONAL	1	TRUE	2	0.326066673955666	5		368	903	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107183	27107183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	179	400	0	ENST00000324856.7:c.6794C>T	p.Pro2265Leu	p.P2265L	ENST00000324856	NM_006015.4	2265	cCg/cTg	20/20	0.326066673955666	5	FACETS	0.945	0.872	1	0.63	0.581	0.681	CLONAL	2	TRUE	2	0.326066673955666	5		400	865	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115272956	115272956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1178464540	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	46	467	0	ENST00000438362.2:c.1417C>T	p.Arg473Cys	p.R473C	ENST00000438362	NM_001242891.1	473	Cgt/Tgt	12/20	0.326066673955666	3	FACETS	0.701	0.591	0.823	0.351	0.295	0.412	SUBCLONAL	1	TRUE	1	0.326066673955666	3		467	468	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849818	156849818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761967383	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	84	442	2	ENST00000524377.1:c.2074C>T	p.Arg692Cys	p.R692C	ENST00000524377	NM_002529.3	692	Cgc/Tgc	16/17	0.326066673955666	3	FACETS	0.726	0.641	0.818	0.363	0.32	0.409	SUBCLONAL	1	TRUE	1	0.326066673955666	3		444	825	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206647779	206647779	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	89	407	0	ENST00000367120.3:c.193C>T	p.Gln65Ter	p.Q65*	ENST00000367120	NM_014002.3	65	Cag/Tag	4/22	0.326066673955666	3	FACETS	0.723	0.64	0.812	0.362	0.32	0.406	SUBCLONAL	1	TRUE	1	0.326066673955666	3		407	878	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652340	206652341	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	113	541	1	ENST00000367120.3:c.1047_1048delinsTT	p.Gln350Ter	p.Q350*	ENST00000367120	NM_014002.3	349	caCCag/caTTag	10/22	0.326066673955666	3	FACETS	0.805	0.723	0.891	0.402	0.361	0.446	CLONAL	1	TRUE	1	0.326066673955666	3		542	1002	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927445	245927445	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	133	355	0	ENST00000388985.4:c.1083T>G	p.Phe361Leu	p.F361L	ENST00000388985		361	ttT/ttG	11/12	0.326066673955666	3	FACETS	0.793	0.723	0.867	0.793	0.723	0.867	SUBCLONAL	2	TRUE	1	0.326066673955666	3		355	598	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333513	70333513	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	74	406	0	ENST00000373644.4:c.1418C>T	p.Ser473Leu	p.S473L	ENST00000373644	NM_030625.2	473	tCa/tTa	2/12	1	2	FACETS	0.799	0.7	0.905	0.799	0.7	0.905	CLONAL	1	TRUE	1	0.326066673955666	2		406	568	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451255	70451255	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	211	508	0	ENST00000373644.4:c.6095C>T	p.Pro2032Leu	p.P2032L	ENST00000373644	NM_030625.2	2032	cCt/cTt	12/12	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.326066673955666	2		508	880	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925409	114925410	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	94	545	1	ENST00000543371.1:c.1487_1488delinsTT	p.Ser496Phe	p.S496F	ENST00000543371	NM_001198531.1	496	tCC/tTT	14/14	1	2	FACETS	0.682	0.606	0.764	0.682	0.606	0.764	SUBCLONAL	1	TRUE	1	0.326066673955666	2		546	845	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456586	32456586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	58	78	0	ENST00000332351.3:c.306G>A	p.Trp102Ter	p.W102*	ENST00000332351	NM_024426.4	102	tgG/tgA	1/10	1	2	FACETS	0.898	0.784	1	1	0.977	1	CLONAL	2	TRUE	1	0.326066673955666	2		78	198	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574534	64574534	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	247	491	0	ENST00000312049.6:c.861G>T	p.Glu287Asp	p.E287D	ENST00000312049	NM_130799.2	287	gaG/gaT	6/10	1	2	FACETS	0.788	0.738	0.84	1	0.993	1	SUBCLONAL	2	TRUE	1	0.326066673955666	2		491	961	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200209	67200209	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	124	510	1	ENST00000312629.5:c.517T>A	p.Phe173Ile	p.F173I	ENST00000312629	NM_003952.2	173	Ttc/Atc	7/15	1	2	FACETS	0.759	0.686	0.837	0.759	0.686	0.837	SUBCLONAL	1	TRUE	1	0.326066673955666	2		511	1002	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588835	69588835	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	86	540	0	ENST00000168712.1:c.401G>A	p.Arg134Gln	p.R134Q	ENST00000168712	NM_002007.2	134	cGg/cAg	2/3	1	2	FACETS	0.572	0.505	0.644	0.572	0.505	0.644	SUBCLONAL	1	TRUE	1	0.326066673955666	2		540	922	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940160	71940160	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514509	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	109	573	0	ENST00000298229.2:c.545C>T	p.Ser182Leu	p.S182L	ENST00000298229	NM_001567.3	182	tCg/tTg	5/28	1	2	FACETS	0.767	0.688	0.851	0.767	0.688	0.851	SUBCLONAL	1	TRUE	1	0.326066673955666	2		573	872	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204679	108204679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	17	130	0	ENST00000278616.4:c.7994C>T	p.Pro2665Leu	p.P2665L	ENST00000278616	NM_000051.3	2665	cCt/cTt	54/63	0.326066673955666	1	FACETS	0.71	0.535	0.912	0.71	0.535	0.912	CLONAL	1	TRUE	0	0.326066673955666	1		130	123	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149009	119149009	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	90	327	0	ENST00000264033.4:c.1227+2T>C		p.X409_splice	ENST00000264033	NM_005188.3	409			NA	2	FACETS	0.798	0.714	0.885			1	INDETERMINATE	2	TRUE	NA	0.326066673955666	2		327	346	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244850	46244850	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	207	466	0	ENST00000334344.6:c.2945del	p.Asn982ThrfsTer28	p.N982Tfs*28	ENST00000334344	NM_152641.2	982	Aac/ac	15/21	0.0991248980098025	4	FACETS	1	0.947	1	1	0.947	1	INDETERMINATE	2	TRUE	2	0.326066673955666	4		466	824	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415840	49415840	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	65	322	0	ENST00000301067.7:c.16507C>T	p.Pro5503Ser	p.P5503S	ENST00000301067	NM_003482.3	5503	Ccc/Tcc	53/54	0.0991248980098025	4	FACETS	0.892	0.773	1	0.446	0.386	0.51	INDETERMINATE	1	TRUE	2	0.326066673955666	4		322	593	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861264	57861264	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	108	419	0	ENST00000228682.2:c.1061G>A	p.Arg354Gln	p.R354Q	ENST00000228682	NM_005269.2	354	cGg/cAg	9/12	0.0991248980098025	4	FACETS	1	0.938	1	0.532	0.477	0.591	INDETERMINATE	1	TRUE	2	0.326066673955666	4		419	825	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233594	69233594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	29	216	0	ENST00000462284.1:c.1459C>T	p.Pro487Ser	p.P487S	ENST00000462284	NM_002392.5	487	Cca/Tca	11/11	0.0991248980098025	4	FACETS	0.831	0.669	1	0.415	0.334	0.507	INDETERMINATE	1	TRUE	2	0.326066673955666	4		216	284	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120882	115120883	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	158	412	1	ENST00000257566.3:c.123_124delinsTT	p.Pro42Ser	p.P42S	ENST00000257566	NM_016569.3	41	ttCCcc/ttTTcc	1/8	0.326066673955666	3	FACETS	0.941	0.866	1	0.941	0.866	1	CLONAL	2	TRUE	1	0.326066673955666	3		413	599	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202759	133202760	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	162	459	0	ENST00000320574.5:c.6474_6475delinsTT	p.Arg2159Cys	p.R2159C	ENST00000320574	NM_006231.2	2158	tgCCgc/tgTTgc	46/49	0.326066673955666	3	FACETS	1	0.984	1	0.646	0.593	0.702	CLONAL	1	TRUE	1	0.326066673955666	3		459	894	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589330	28589330	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	97	301	0	ENST00000241453.7:c.2717T>G	p.Phe906Cys	p.F906C	ENST00000241453	NM_004119.2	906	tTt/tGt	22/24	0.235192758898944	2	FACETS	0.806	0.725	0.891	0.806	0.725	0.891	CLONAL	2	TRUE	0	0.326066673955666	2		301	369	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623897	28623897	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	32	272	0	ENST00000241453.7:c.757C>T	p.Pro253Ser	p.P253S	ENST00000241453	NM_004119.2	253	Cct/Tct	7/24	0.235192758898944	2	FACETS	0.798	0.651	0.962	0.399	0.325	0.481	CLONAL	1	TRUE	0	0.326066673955666	2		272	246	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937539	32937539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	59	422	0	ENST00000380152.3:c.8200C>T	p.Pro2734Ser	p.P2734S	ENST00000380152		2734	Cct/Tct	18/27	0.235192758898944	2	FACETS	0.647	0.557	0.746	0.324	0.278	0.373	SUBCLONAL	1	TRUE	0	0.326066673955666	2		422	559	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039240	49039241	+	missense_variant	Missense_Mutation	DNP	CC	CC	GT	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	92	313	0	ENST00000267163.4:c.2318_2319delinsGT	p.Ser773Cys	p.S773C	ENST00000267163	NM_000321.2	773	tCC/tGT	22/27	0.235192758898944	2	FACETS	0.763	0.683	0.846	0.763	0.683	0.846	SUBCLONAL	2	TRUE	0	0.326066673955666	2		313	370	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061358	38061358	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	108	452	1	ENST00000250448.2:c.631C>T	p.Gln211Ter	p.Q211*	ENST00000250448	NM_004496.3	211	Cag/Tag	2/2	0.235192758898944	2	FACETS	0.82	0.735	0.909	0.41	0.367	0.455	CLONAL	1	TRUE	0	0.326066673955666	2		453	808	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707915	43707916	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	107	515	1	ENST00000382044.4:c.4965_4966delinsTT	p.Arg1656Ter	p.R1656*	ENST00000382044	NM_001141980.1	1655	acCCga/acTTga	23/28	1	2	FACETS	0.638	0.571	0.709	0.638	0.571	0.709	SUBCLONAL	1	TRUE	1	0.326066673955666	2		516	1029	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483927	88483927	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	110	531	0	ENST00000360948.2:c.1643C>T	p.Ala548Val	p.A548V	ENST00000360948	NM_001012338.2	548	gCc/gTc	14/19	1	2	FACETS	0.839	0.754	0.93	0.839	0.754	0.93	CLONAL	1	TRUE	1	0.326066673955666	2		531	804	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633189	3633189	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	285	674	0	ENST00000294008.3:c.5062C>T	p.Pro1688Ser	p.P1688S	ENST00000294008	NM_032444.2	1688	Cca/Tca	14/15	1	2	FACETS	0.831	0.782	0.881	1	0.994	1	CLONAL	2	TRUE	1	0.326066673955666	2		674	1052	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640245	3640245	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	71	646	0	ENST00000294008.3:c.3394G>A	p.Asp1132Asn	p.D1132N	ENST00000294008	NM_032444.2	1132	Gac/Aac	12/15	1	2	FACETS	0.443	0.386	0.506	0.443	0.386	0.506	SUBCLONAL	1	TRUE	1	0.326066673955666	2		646	982	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656572	3656573	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	91	567	1	ENST00000294008.3:c.662_663delinsTT	p.Pro221Leu	p.P221L	ENST00000294008	NM_032444.2	221	cCC/cTT	3/15	1	2	FACETS	0.583	0.517	0.655	0.583	0.517	0.655	SUBCLONAL	1	TRUE	1	0.326066673955666	2		568	957	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860696	3860696	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	196	480	0	ENST00000262367.5:c.883C>G	p.Pro295Ala	p.P295A	ENST00000262367	NM_004380.2	295	Ccc/Gcc	3/31	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.326066673955666	2		480	869	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645174	67645174	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs933470800	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	193	471	0	ENST00000264010.4:c.439C>T	p.Leu147Phe	p.L147F	ENST00000264010	NM_006565.3	147	Ctt/Ttt	3/12	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.326066673955666	2		471	803	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844242	68844242	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	53	367	0	ENST00000261769.5:c.830C>T	p.Pro277Leu	p.P277L	ENST00000261769	NM_004360.3	277	cCa/cTa	6/16	1	2	FACETS	0.636	0.543	0.738	0.636	0.543	0.738	SUBCLONAL	1	TRUE	1	0.326066673955666	2		367	511	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822139	72822139	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	78	420	0	ENST00000268489.5:c.10036C>T	p.Pro3346Ser	p.P3346S	ENST00000268489	NM_006885.3	3346	Cct/Tct	10/10	1	2	FACETS	0.623	0.547	0.705	0.623	0.547	0.705	SUBCLONAL	1	TRUE	1	0.326066673955666	2		420	768	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350107	89350107	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	120	532	0	ENST00000301030.4:c.2843G>T	p.Gly948Val	p.G948V	ENST00000301030	NM_001256183.1	948	gGg/gTg	9/13	1	2	FACETS	0.764	0.689	0.844	0.764	0.689	0.844	SUBCLONAL	1	TRUE	1	0.326066673955666	2		532	963	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578396	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	242	439	0	ENST00000269305.4:c.534_535delinsTT	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	178	caCCat/caTTat	5/11	0.275611672552481	3	FACETS	1	0.982	1	0.749	0.702	0.797	CLONAL	2	TRUE	0	0.326066673955666	3		439	768	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653191	29653191	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	56	263	0	ENST00000356175.3:c.5126C>T	p.Thr1709Ile	p.T1709I	ENST00000356175	NM_000267.3	1709	aCc/aTc	36/57	0.275611672552481	3	FACETS	0.771	0.661	0.891	0.257	0.22	0.297	SUBCLONAL	1	TRUE	0	0.326066673955666	3		263	518	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682531	37682531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	228	285	0	ENST00000447079.4:c.3722C>T	p.Pro1241Leu	p.P1241L	ENST00000447079	NM_015083.1	1241	cCc/cTc	13/14	0.275611672552481	3	FACETS	0.91	0.854	0.966	0.91	0.854	0.966	CLONAL	3	TRUE	0	0.326066673955666	3		285	596	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40379600	40379600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	116	621	0	ENST00000293328.3:c.232G>A	p.Glu78Lys	p.E78K	ENST00000293328	NM_012448.3	78	Gaa/Aaa	3/19	0.275611672552481	3	FACETS	0.848	0.763	0.938	0.283	0.254	0.313	CLONAL	1	TRUE	0	0.326066673955666	3		621	976	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743374	743374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	62	284	0	ENST00000314574.4:c.766C>T	p.Pro256Ser	p.P256S	ENST00000314574	NM_005433.3	256	Cca/Tca	7/12	0.240649424996563	3	FACETS	0.779	0.673	0.894	0.389	0.336	0.447	SUBCLONAL	1	TRUE	1	0.326066673955666	3		284	568	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222853	5222853	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	176	428	0	ENST00000357368.4:c.2950C>T	p.Pro984Ser	p.P984S	ENST00000357368	NM_002850.3	984	Ccg/Tcg	18/38	0.290857650788167	2	FACETS	0.841	0.778	0.906	0.841	0.778	0.906	CLONAL	2	TRUE	0	0.326066673955666	2		428	642	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229613	5229614	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	25	65	1	ENST00000357368.4:c.2237_2238delinsTT	p.Pro746Leu	p.P746L	ENST00000357368	NM_002850.3	746	cCC/cTT	15/38	0.290857650788167	2	FACETS	1	0.857	1	0.548	0.437	0.671	CLONAL	1	TRUE	0	0.326066673955666	2		66	140	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937692	17937692	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	313	440	0	ENST00000458235.1:c.3235G>A	p.Ala1079Thr	p.A1079T	ENST00000458235	NM_000215.3	1079	Gcc/Acc	24/24	0.079032643390857	6	FACETS	0.959	0.905	1	0.959	0.905	1	INDETERMINATE	3	TRUE	3	0.326066673955666	6		440	1103	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943625	17943625	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	137	546	0	ENST00000458235.1:c.2464C>G	p.Leu822Val	p.L822V	ENST00000458235	NM_000215.3	822	Ctc/Gtc	18/24	0.079032643390857	6	FACETS	1	0.953	1	0.36	0.326	0.396	INDETERMINATE	1	TRUE	3	0.326066673955666	6		546	1285	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792558	33792558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	19	57	0	ENST00000498907.2:c.763G>A	p.Gly255Arg	p.G255R	ENST00000498907	NM_004364.3	255	Ggg/Agg	1/1	0.287998975811769	5	FACETS	0.923	0.704	1	0.308	0.234	0.393	CLONAL	1	TRUE	2	0.326066673955666	5		57	188	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223262	36223262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1267	264	623	1	ENST00000222270.7:c.5812C>T	p.Gln1938Ter	p.Q1938*	ENST00000222270	NM_014727.1	1938	Cag/Tag	28/37	0.287998975811769	5	FACETS	0.787	0.736	0.841	0.525	0.49	0.561	SUBCLONAL	2	TRUE	2	0.326066673955666	5		624	1531	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224583	36224583	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1462118687	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	228	560	0	ENST00000222270.7:c.7045C>T	p.Pro2349Ser	p.P2349S	ENST00000222270	NM_014727.1	2349	Cct/Tct	29/37	0.287998975811769	5	FACETS	0.885	0.823	0.948	0.59	0.549	0.632	CLONAL	2	TRUE	2	0.326066673955666	5		560	1177	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762437	41762437	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs905260458	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	203	441	0	ENST00000301178.4:c.2117G>A	p.Gly706Glu	p.G706E	ENST00000301178	NM_021913.4	706	gGa/gAa	18/20	0.287998975811769	5	FACETS	0.891	0.825	0.958	0.594	0.55	0.639	CLONAL	2	TRUE	2	0.326066673955666	5		441	1041	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082766	16082766	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	22	80	0	ENST00000281043.3:c.580C>T	p.Pro194Ser	p.P194S	ENST00000281043	NM_005378.4	194	Ccc/Tcc	2/3	0.0991248980098025	4	FACETS	0.771	0.6	0.969	0.386	0.3	0.485	INDETERMINATE	1	TRUE	2	0.326066673955666	4		80	232	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609603	46609603	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1449817007	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	102	564	0	ENST00000263734.3:c.2327C>T	p.Pro776Leu	p.P776L	ENST00000263734	NM_001430.4	776	cCc/cTc	15/16	0.0991248980098025	4	FACETS	0.827	0.738	0.922	0.414	0.369	0.461	INDETERMINATE	1	TRUE	2	0.326066673955666	4		564	1003	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61722741	61722742	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	57	270	1	ENST00000401558.2:c.895_896delinsTT	p.Pro299Phe	p.P299F	ENST00000401558	NM_003400.3	299	CCt/TTt	11/25	0.0991248980098025	4	FACETS	1	0.966	1	0.715	0.618	0.821	INDETERMINATE	1	TRUE	2	0.326066673955666	4		271	324	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732564	190732564	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	44	303	0	ENST00000441310.2:c.2382A>T	p.Lys794Asn	p.K794N	ENST00000441310	NM_000534.4	794	aaA/aaT	11/13	0.0991248980098025	4	FACETS	0.81	0.686	0.944	0.81	0.686	0.944	INDETERMINATE	2	TRUE	2	0.326066673955666	4		303	221	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483981	212483981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	22	301	0	ENST00000342788.4:c.2222G>A	p.Gly741Glu	p.G741E	ENST00000342788	NM_005235.2	741	gGa/gAa	19/28	0.0991248980098025	4	FACETS	1	0.806	1	0.517	0.404	0.647	INDETERMINATE	1	TRUE	2	0.326066673955666	4		301	173	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543575	9543575	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	152	355	0	ENST00000353224.5:c.1579G>C	p.Glu527Gln	p.E527Q	ENST00000353224	NM_177990.2	527	Gaa/Caa	6/10	0.0991248980098025	4	FACETS	0.904	0.829	0.982	0.904	0.829	0.982	INDETERMINATE	2	TRUE	2	0.326066673955666	4		355	684	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561261	9561261	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	130	334	0	ENST00000353224.5:c.521A>G	p.Lys174Arg	p.K174R	ENST00000353224	NM_177990.2	174	aAa/aGa	4/10	0.0991248980098025	4	FACETS	0.826	0.751	0.904	0.826	0.751	0.904	INDETERMINATE	2	TRUE	2	0.326066673955666	4		334	640	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944449	40944449	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	141	441	0	ENST00000373198.4:c.2053A>C	p.Lys685Gln	p.K685Q	ENST00000373198	NM_133170.3	685	Aag/Cag	12/32	0.0991248980098025	4	FACETS	1	0.986	1	0.731	0.667	0.799	INDETERMINATE	1	TRUE	2	0.326066673955666	4		441	784	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101018	41101018	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	137	453	0	ENST00000373198.4:c.1338C>G	p.His446Gln	p.H446Q	ENST00000373198	NM_133170.3	446	caC/caG	8/32	0.0991248980098025	4	FACETS	1	0.984	1	0.697	0.635	0.763	INDETERMINATE	1	TRUE	2	0.326066673955666	4		453	799	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306689	41306689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868376470	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	87	482	0	ENST00000373198.4:c.970G>A	p.Glu324Lys	p.E324K	ENST00000373198	NM_133170.3	324	Gaa/Aaa	7/32	0.0991248980098025	4	FACETS	0.834	0.738	0.938	0.417	0.369	0.469	INDETERMINATE	1	TRUE	2	0.326066673955666	4		482	848	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321174	62321175	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	198	516	1	ENST00000360203.5:c.2097_2098delinsTT	p.Arg700Trp	p.R700W	ENST00000360203	NM_001283009.1	699	atCCgg/atTTgg	24/35	0.0991248980098025	4	FACETS	0.779	0.721	0.839	0.779	0.721	0.839	INDETERMINATE	2	TRUE	2	0.326066673955666	4		517	1034	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755558	39755558	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756534988	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	86	420	0	ENST00000288319.7:c.1207C>T	p.Pro403Ser	p.P403S	ENST00000288319	NM_182918.3	403	Ccc/Tcc	10/10	1	2	FACETS	0.826	0.731	0.927	0.826	0.731	0.927	CLONAL	1	TRUE	1	0.326066673955666	2		420	639	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536160	41536160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	111	374	0	ENST00000263253.7:c.1777C>T	p.Pro593Ser	p.P593S	ENST00000263253	NM_001429.3	593	Cct/Tct	9/31	0.326066673955666	3	FACETS	1	0.98	1	0.683	0.615	0.753	CLONAL	1	TRUE	1	0.326066673955666	3		374	580	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713511	30713511	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	209	402	0	ENST00000295754.5:c.836T>G	p.Phe279Cys	p.F279C	ENST00000295754	NM_003242.5	279	tTt/tGt	4/7	0.276786508414187	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	2	0.326066673955666	4		402	794	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026979	71026979	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1553668386	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	67	359	0	ENST00000318789.4:c.1348G>A	p.Ala450Thr	p.A450T	ENST00000318789	NM_032682.5	450	Gca/Aca	15/21	0.276786508414187	4	FACETS	0.727	0.63	0.831	0.363	0.315	0.416	SUBCLONAL	1	TRUE	2	0.326066673955666	4		359	750	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096135	71096135	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1553709881	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	138	265	0	ENST00000318789.4:c.622C>T	p.Gln208Ter	p.Q208*	ENST00000318789	NM_032682.5	208	Cag/Tag	10/21	0.276786508414187	4	FACETS	0.881	0.804	0.961	0.881	0.804	0.961	CLONAL	2	TRUE	2	0.326066673955666	4		265	637	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968335	134968335	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	120	401	0	ENST00000398015.3:c.2846+2T>G		p.X949_splice	ENST00000398015	NM_004441.4	949			0.235310207506386	2	FACETS	0.821	0.747	0.899	0.821	0.747	0.899	CLONAL	2	TRUE	0	0.326066673955666	2		401	448	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146382	185146382	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	68	201	0	ENST00000265026.3:c.13C>T	p.Gln5Ter	p.Q5*	ENST00000265026	NM_004721.4	5	Cag/Tag	2/14	0.235310207506386	2	FACETS	1	0.974	1	0.745	0.654	0.84	CLONAL	1	TRUE	0	0.326066673955666	2		201	280	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153598	55153598	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	88	307	0	ENST00000257290.5:c.2564C>T	p.Thr855Ile	p.T855I	ENST00000257290	NM_006206.4	855	aCc/aTc	19/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.326066673955666	2		307	417	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561711	55561711	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55755457	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	42	229	1	ENST00000288135.5:c.101C>T	p.Pro34Leu	p.P34L	ENST00000288135	NM_000222.2	34	cCg/cTg	2/21	1	2	FACETS	0.603	0.504	0.713	0.603	0.504	0.713	SUBCLONAL	1	TRUE	1	0.326066673955666	2		230	427	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55974019	55974019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	58	471	0	ENST00000263923.4:c.1297G>A	p.Asp433Asn	p.D433N	ENST00000263923	NM_002253.2	433	Gat/Aat	10/30	1	2	FACETS	0.558	0.479	0.645	0.558	0.479	0.645	SUBCLONAL	1	TRUE	1	0.326066673955666	2		471	637	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268207	153268207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	42	214	0	ENST00000281708.4:c.601C>T	p.Pro201Ser	p.P201S	ENST00000281708	NM_033632.3	201	Cca/Tca	4/12	1	2	FACETS	0.676	0.566	0.798	0.676	0.566	0.798	SUBCLONAL	1	TRUE	1	0.326066673955666	2		214	381	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628121	187628122	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	130	508	2	ENST00000441802.2:c.2860_2861delinsTT	p.Pro954Phe	p.P954F	ENST00000441802	NM_005245.3	954	CCt/TTt	2/27	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.326066673955666	2		510	704	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294079	1294079	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	123	659	2	ENST00000310581.5:c.922C>T	p.Pro308Ser	p.P308S	ENST00000310581	NM_198253.2	308	Cca/Tca	2/16	1	2	FACETS	0.677	0.61	0.747	0.677	0.61	0.747	SUBCLONAL	1	TRUE	1	0.326066673955666	2		661	1115	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873675	35873675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	35	273	0	ENST00000303115.3:c.631C>T	p.His211Tyr	p.H211Y	ENST00000303115	NM_002185.3	211	Cac/Tac	5/8	1	2	FACETS	0.534	0.438	0.642	0.534	0.438	0.642	SUBCLONAL	1	TRUE	1	0.326066673955666	2		273	402	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967280	38967280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770728330	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	25	242	1	ENST00000357387.3:c.1201C>T	p.Arg401Cys	p.R401C	ENST00000357387	NM_152756.3	401	Cgt/Tgt	14/38	1	2	FACETS	0.564	0.445	0.699	0.564	0.445	0.699	SUBCLONAL	1	TRUE	1	0.326066673955666	2		243	272	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435605	149435605	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	113	388	0	ENST00000286301.3:c.2538G>A	p.Trp846Ter	p.W846*	ENST00000286301	NM_005211.3	846	tgG/tgA	19/22	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.326066673955666	2		388	654	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515316	149515316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	88	509	0	ENST00000261799.4:c.166G>A	p.Gly56Ser	p.G56S	ENST00000261799	NM_002609.3	56	Ggt/Agt	3/23	1	2	FACETS	0.756	0.67	0.848	0.756	0.67	0.848	SUBCLONAL	1	TRUE	1	0.326066673955666	2		509	714	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041095	180041096	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	99	518	0	ENST00000261937.6:c.3303_3304delinsAA	p.Val1102Met	p.V1102M	ENST00000261937	NM_182925.4	1101	ggGGtg/ggAAtg	24/30	1	2	FACETS	0.77	0.687	0.858	0.77	0.687	0.858	SUBCLONAL	1	TRUE	1	0.326066673955666	2		518	789	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032031	26032031	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	52	311	0	ENST00000244661.2:c.258G>C	p.Gln86His	p.Q86H	ENST00000244661	NM_003537.3	86	caG/caC	1/1	0.240649424996563	3	FACETS	0.751	0.64	0.873	0.375	0.32	0.437	SUBCLONAL	1	TRUE	1	0.326066673955666	3		311	494	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250469	26250469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766551981	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	72	430	0	ENST00000446824.2:c.365C>T	p.Pro122Leu	p.P122L	ENST00000446824	NM_021018.2	122	cCc/cTc	1/1	0.240649424996563	3	FACETS	0.702	0.612	0.798	0.351	0.306	0.399	SUBCLONAL	1	TRUE	1	0.326066673955666	3		430	732	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815867	32815868	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	166	399	0	ENST00000354258.4:c.1748_1749delinsAA	p.Gly583Glu	p.G583E	ENST00000354258	NM_000593.5	583	gGG/gAA	8/11	0.240649424996563	3	FACETS	0.765	0.704	0.829	0.765	0.704	0.829	SUBCLONAL	2	TRUE	1	0.326066673955666	3		399	774	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790684	89790684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1279886870	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	105	536	0	ENST00000336032.3:c.71C>T	p.Ser24Phe	p.S24F	ENST00000336032	NM_006813.2	24	tCc/tTc	1/2	0.240649424996563	3	FACETS	0.654	0.584	0.728	0.327	0.292	0.364	SUBCLONAL	1	TRUE	1	0.326066673955666	3		536	1146	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969117	93969117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	44	248	0	ENST00000369303.4:c.1879G>A	p.Glu627Lys	p.E627K	ENST00000369303	NM_004440.3	627	Gag/Aag	10/17	0.326066673955666	3	FACETS	0.71	0.596	0.836	0.237	0.198	0.279	SUBCLONAL	1	TRUE	0	0.326066673955666	3		248	442	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068099	94068099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767281324	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	30	216	0	ENST00000369303.4:c.863C>T	p.Ser288Phe	p.S288F	ENST00000369303	NM_004440.3	288	tCt/tTt	4/17	0.326066673955666	3	FACETS	0.578	0.466	0.706	0.193	0.155	0.236	SUBCLONAL	1	TRUE	0	0.326066673955666	3		216	370	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647493	117647493	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1441561770	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	107	308	0	ENST00000368508.3:c.5451G>A	p.Trp1817Ter	p.W1817*	ENST00000368508	NM_002944.2	1817	tgG/tgA	33/43	0.326066673955666	3	FACETS	0.922	0.84	1	0.922	0.84	1	CLONAL	3	TRUE	0	0.326066673955666	3		308	276	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117650544	117650544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1192695384	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	175	422	0	ENST00000368508.3:c.5314G>A	p.Glu1772Lys	p.E1772K	ENST00000368508	NM_002944.2	1772	Gag/Aag	32/43	0.326066673955666	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	3	TRUE	0	0.326066673955666	3		422	394	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729384	41729384	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	193	445	0	ENST00000242208.4:c.1145G>A	p.Ser382Asn	p.S382N	ENST00000242208	NM_002192.2	382	aGc/aAc	3/3	0.0991248980098025	4	FACETS	0.942	0.873	1	0.942	0.873	1	INDETERMINATE	2	TRUE	2	0.326066673955666	4		445	833	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729516	41729516	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	178	447	0	ENST00000242208.4:c.1013G>A	p.Trp338Ter	p.W338*	ENST00000242208	NM_002192.2	338	tGg/tAg	3/3	0.0991248980098025	4	FACETS	0.832	0.767	0.899	0.832	0.767	0.899	INDETERMINATE	2	TRUE	2	0.326066673955666	4		447	870	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346551	81346551	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444026216	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	34	232	0	ENST00000222390.5:c.1402C>T	p.Arg468Cys	p.R468C	ENST00000222390	NM_000601.4	468	Cgt/Tgt	11/18	0.276786508414187	4	FACETS	0.772	0.632	0.93	0.386	0.316	0.465	CLONAL	1	TRUE	2	0.326066673955666	4		232	358	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346668	81346668	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	89	196	0	ENST00000222390.5:c.1285G>T	p.Glu429Ter	p.E429*	ENST00000222390	NM_000601.4	429	Gaa/Taa	11/18	0.276786508414187	4	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	2	0.326066673955666	4		196	329	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508442	106508442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	45	250	0	ENST00000359195.3:c.436G>A	p.Glu146Lys	p.E146K	ENST00000359195	NM_002649.2	146	Gag/Aag	2/11	0.276786508414187	4	FACETS	0.88	0.741	1	0.44	0.37	0.517	CLONAL	1	TRUE	2	0.326066673955666	4		250	416	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513263	106513263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	155	263	0	ENST00000359195.3:c.2167G>A	p.Gly723Ser	p.G723S	ENST00000359195	NM_002649.2	723	Ggc/Agc	4/11	0.276786508414187	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	2	0.326066673955666	4		263	569	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850885	128850885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61740964	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	208	520	0	ENST00000249373.3:c.1732G>A	p.Glu578Lys	p.E578K	ENST00000249373	NM_005631.4	578	Gag/Aag	10/12	0.276786508414187	4	FACETS	0.81	0.752	0.871	0.81	0.752	0.871	CLONAL	2	TRUE	2	0.326066673955666	4		520	1044	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372112	55372112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1385441707	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	160	308	0	ENST00000297316.4:c.802G>A	p.Gly268Ser	p.G268S	ENST00000297316	NM_022454.3	268	Ggt/Agt	2/2	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.326066673955666	2		308	703	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70967623	70967623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	50	360	0	ENST00000276594.2:c.1400G>A	p.Gly467Glu	p.G467E	ENST00000276594	NM_024504.3	467	gGg/gAg	7/8	1	2	FACETS	0.831	0.708	0.966	0.831	0.708	0.966	CLONAL	1	TRUE	1	0.326066673955666	2		360	369	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559293	141559293	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	137	488	0	ENST00000220592.5:c.1508C>T	p.Pro503Leu	p.P503L	ENST00000220592	NM_012154.3	503	cCc/cTc	12/19	1	2	FACETS	0.852	0.774	0.934	0.852	0.774	0.934	CLONAL	1	TRUE	1	0.326066673955666	2		488	986	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331589	8331589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	36	315	1	ENST00000356435.5:c.5527C>T	p.His1843Tyr	p.H1843Y	ENST00000356435		1843	Cat/Tat	33/35	0.240649424996563	3	FACETS	0.628	0.516	0.753	0.314	0.258	0.377	SUBCLONAL	1	TRUE	1	0.326066673955666	3		316	409	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471012	8471012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	43	268	0	ENST00000356435.5:c.3487G>A	p.Glu1163Lys	p.E1163K	ENST00000356435		1163	Gaa/Aaa	20/35	0.240649424996563	3	FACETS	0.956	0.803	1	0.478	0.401	0.562	CLONAL	1	TRUE	1	0.326066673955666	3		268	321	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27217686	27217686	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	133	374	0	ENST00000380036.4:c.2992G>A	p.Gly998Arg	p.G998R	ENST00000380036	NM_000459.3	998	Gga/Aga	19/23	0.326066673955666	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.326066673955666	1		374	512	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412493	80412493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514698	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	56	283	0	ENST00000286548.4:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000286548	NM_002072.3	183	cGa/cAa	4/7	0.0991248980098025	4	FACETS	0.828	0.71	0.958	0.414	0.355	0.479	INDETERMINATE	1	TRUE	2	0.326066673955666	4		283	550	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209703	98209703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	129	494	0	ENST00000331920.6:c.3835C>T	p.Pro1279Ser	p.P1279S	ENST00000331920	NM_000264.3	1279	Ccc/Tcc	23/24	0.0991248980098025	4	FACETS	0.929	0.841	1	0.465	0.42	0.512	INDETERMINATE	1	TRUE	2	0.326066673955666	4		494	1129	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760457	133760457	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	206	536	0	ENST00000318560.5:c.2780T>G	p.Val927Gly	p.V927G	ENST00000318560	NM_005157.4	927	gTc/gGc	11/11	0.0991248980098025	4	FACETS	0.886	0.822	0.951	0.886	0.822	0.951	INDETERMINATE	2	TRUE	2	0.326066673955666	4		536	946	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760897	133760897	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs996624163	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	229	524	0	ENST00000318560.5:c.3220A>G	p.Ile1074Val	p.I1074V	ENST00000318560	NM_005157.4	1074	Atc/Gtc	11/11	0.0991248980098025	4	FACETS	0.854	0.796	0.915	0.854	0.796	0.915	INDETERMINATE	2	TRUE	2	0.326066673955666	4		524	1090	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913182	39913182	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	82	163	0	ENST00000378444.4:c.4933C>G	p.Pro1645Ala	p.P1645A	ENST00000378444	NM_001123385.1	1645	Ccc/Gcc	14/15	1	1	FACETS	0.822	0.735	0.912	1	0.982	1	CLONAL	2	TRUE	0	0.326066673955666	1		163	256	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120882	115120882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1337484837	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	154	412	0	ENST00000257566.3:c.124C>T	p.Pro42Ser	p.P42S	ENST00000257566	NM_016569.3	42	Ccc/Tcc	1/8	0.326066673955666	3	FACETS	0.929	0.854	1	0.929	0.854	1	CLONAL	2	TRUE	1	0.326066673955666	3		412	591	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28624292	28624292	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	24	371	0	ENST00000241453.7:c.682G>A	p.Asp228Asn	p.D228N	ENST00000241453	NM_004119.2	228	Gac/Aac	6/24	0.235192758898944	2	FACETS	0.393	0.307	0.491	0.196	0.153	0.246	SUBCLONAL	1	TRUE	0	0.326066673955666	2		371	375	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0039026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	405	628	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.38005211620921	1	FACETS	0.83	0.794	0.866	0.83	0.794	0.866	INDETERMINATE	1	TRUE	0	0.712840935731761	1		628	881	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295176	1295176	+	upstream_gene_variant	5'Flank	SNP	G	G	C	novel	NA	P-0039026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	133	287	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.904	0.828	0.981	0.904	0.828	0.981	CLONAL	1	TRUE	1	0.712840935731761	2		287	413	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295215	1295215	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0039026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	162	360	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.977	0.905	1	0.977	0.905	1	CLONAL	1	TRUE	1	0.712840935731761	2		361	465	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171462	123171462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	46	310	0	ENST00000218089.9:c.374C>T	p.Ser125Leu	p.S125L	ENST00000218089	NM_001042749.1	125	tCa/tTa	6/35	0.482538872594743	1	FACETS	0.399	0.34	0.463	0.399	0.34	0.463	SUBCLONAL	1	TRUE	0	0.712840935731761	1		310	208	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142982	30142982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1229550831	NA	P-0039026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	374	874	0	ENST00000389048.3:c.544G>A	p.Glu182Lys	p.E182K	ENST00000389048	NM_004304.4	182	Gaa/Aaa	1/29	0.337298131209605	2	FACETS	0.987	0.939	1	0.494	0.469	0.518	INDETERMINATE	1	TRUE	0	0.712840935731761	2		874	1063	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056181	27056181	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	240	450	0	ENST00000324856.7:c.1177C>T	p.Gln393Ter	p.Q393*	ENST00000324856	NM_006015.4	393	Cag/Tag	2/20	0.38005211620921	1	FACETS	0.815	0.768	0.861	0.815	0.768	0.861	INDETERMINATE	1	TRUE	0	0.712840935731761	1		450	532	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988327	36988327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	126	465	1	ENST00000354822.5:c.326C>T	p.Ser109Leu	p.S109L	ENST00000354822	NM_001079668.2	109	tCg/tTg	2/3	1	2	FACETS	0.542	0.492	0.595	0.542	0.492	0.595	SUBCLONAL	1	TRUE	1	0.712840935731761	2		466	652	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714369	40714369	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs775489787	NA	P-0039026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	79	345	0	ENST00000373198.4:c.4028G>A	p.Arg1343Gln	p.R1343Q	ENST00000373198	NM_133170.3	1343	cGg/cAg	29/32	1	2	FACETS	0.504	0.445	0.567	0.504	0.445	0.567	SUBCLONAL	1	TRUE	1	0.712840935731761	2		345	440	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101080	27101081	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	162	745	0	ENST00000324856.7:c.4365dup	p.Pro1456SerfsTer35	p.P1456Sfs*35	ENST00000324856	NM_006015.4	1454	-/T	18/20	0.38005211620921	1	FACETS	0.37	0.339	0.401	0.37	0.339	0.401	INDETERMINATE	1	TRUE	0	0.712840935731761	1		745	791	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295181	1295181	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1195843544	NA	P-0039026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	137	285	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.902	0.828	0.979	0.902	0.828	0.979	CLONAL	1	TRUE	1	0.712840935731761	2		285	426	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753318	57753318	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	38	328	0	ENST00000274289.3:c.806T>G	p.Val269Gly	p.V269G	ENST00000274289	NM_006622.3	269	gTa/gGa	6/14	0.38005211620921	1	FACETS	0.285	0.237	0.337	0.285	0.237	0.337	INDETERMINATE	1	TRUE	0	0.712840935731761	1		328	241	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179072	123179072	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	122	543	0	ENST00000218089.9:c.521G>T	p.Ser174Ile	p.S174I	ENST00000218089	NM_001042749.1	174	aGt/aTt	8/35	0.482538872594743	1	FACETS	0.555	0.506	0.605	0.555	0.506	0.605	SUBCLONAL	1	TRUE	0	0.712840935731761	1		543	397	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609828	117609828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	124	433	0	ENST00000368508.3:c.6871C>T	p.Pro2291Ser	p.P2291S	ENST00000368508	NM_002944.2	2291	Cct/Tct	43/43	0.21958813984625	4	FACETS	0.927	0.839	1	0.463	0.419	0.509	INDETERMINATE	1	TRUE	2	0.619046423125393	4		433	700	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984848	9984848	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	116	359	1	ENST00000330684.3:c.1117G>A	p.Glu373Lys	p.E373K	ENST00000330684	NM_001134407.1	373	Gaa/Aaa	4/13	0.197589374596131	2	FACETS	0.695	0.629	0.765	0.348	0.314	0.383	INDETERMINATE	1	TRUE	0	0.619046423125393	2		360	539	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	145	179	0				ENST00000310581	NM_198253.2	-/1132			0.21958813984625	4	FACETS	1	0.951	1	1	0.951	1	INDETERMINATE	2	TRUE	2	0.619046423125393	4		179	365	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875648	35875648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	70	266	0	ENST00000303115.3:c.835C>T	p.His279Tyr	p.H279Y	ENST00000303115	NM_002185.3	279	Cat/Tat	7/8	0.21958813984625	4	FACETS	0.808	0.707	0.917	0.404	0.353	0.459	INDETERMINATE	1	TRUE	2	0.619046423125393	4		266	453	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911436	39911436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437936868	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	115	463	0	ENST00000378444.4:c.5194G>A	p.Glu1732Lys	p.E1732K	ENST00000378444	NM_001123385.1	1732	Gaa/Aaa	15/15	1	2	FACETS	0.609	0.55	0.671	0.609	0.55	0.671	SUBCLONAL	1	TRUE	1	0.619046423125393	2		463	610	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259565	89259565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139652107	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	89	281	0	ENST00000336596.2:c.709G>A	p.Glu237Lys	p.E237K	ENST00000336596	NM_005233.5	237	Gaa/Aaa	3/17	0.21958813984625	4	FACETS	0.887	0.788	0.991	0.443	0.394	0.496	INDETERMINATE	1	TRUE	2	0.619046423125393	4		281	525	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317926	8317926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	58	337	0	ENST00000356435.5:c.5687C>T	p.Ser1896Phe	p.S1896F	ENST00000356435		1896	tCc/tTc	35/35	0.30142364741596	1	FACETS	0.317	0.273	0.365	0.317	0.273	0.365	INDETERMINATE	1	TRUE	0	0.619046423125393	1		337	408	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561263	9561263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769939031	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	92	346	1	ENST00000353224.5:c.519G>A	p.Met173Ile	p.M173I	ENST00000353224	NM_177990.2	173	atG/atA	4/10	0.21958813984625	4	FACETS	0.732	0.651	0.819	0.366	0.325	0.41	INDETERMINATE	1	TRUE	2	0.619046423125393	4		347	657	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677780	47677780	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1052158260	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	102	390	0	ENST00000347630.2:c.1085C>T	p.Pro362Leu	p.P362L	ENST00000347630	NM_001007230.1	362	cCt/cTt	11/11	1	2	FACETS	0.529	0.474	0.587	0.529	0.474	0.587	SUBCLONAL	1	TRUE	1	0.619046423125393	2		390	623	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923328	9923328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	138	492	0	ENST00000330684.3:c.1959G>A	p.Met653Ile	p.M653I	ENST00000330684	NM_001134407.1	653	atG/atA	9/13	0.197589374596131	2	FACETS	0.736	0.672	0.802	0.368	0.336	0.401	INDETERMINATE	1	TRUE	0	0.619046423125393	2		492	606	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068238	30068238	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	70	322	1	ENST00000331968.5:c.2161C>T	p.Pro721Ser	p.P721S	ENST00000331968	NM_002742.2	721	Cct/Tct	15/18	1	2	FACETS	0.536	0.469	0.608	0.536	0.469	0.608	SUBCLONAL	1	TRUE	1	0.619046423125393	2		323	422	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547022	9547022	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs58486349	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	83	224	0	ENST00000353224.5:c.1000G>A	p.Asp334Asn	p.D334N	ENST00000353224	NM_177990.2	334	Gat/Aat	5/10	0.21958813984625	4	FACETS	1	0.973	1	0.658	0.586	0.734	INDETERMINATE	1	TRUE	2	0.619046423125393	4		224	330	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604319	189604319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	102	389	0	ENST00000264731.3:c.1486C>T	p.Pro496Ser	p.P496S	ENST00000264731	NM_003722.4	496	Cct/Tct	11/14	0.21958813984625	4	FACETS	0.843	0.755	0.936	0.421	0.377	0.468	INDETERMINATE	1	TRUE	2	0.619046423125393	4		389	633	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546761	9546761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768724288	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	210	314	0	ENST00000353224.5:c.1261G>A	p.Asp421Asn	p.D421N	ENST00000353224	NM_177990.2	421	Gac/Aac	5/10	0.21958813984625	4	FACETS	0.977	0.915	1	0.977	0.915	1	INDETERMINATE	2	TRUE	2	0.619046423125393	4		314	562	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	187	462	1				ENST00000310581	NM_198253.2	-/1132			0.21958813984625	4	FACETS	1	0.983	1	1	0.983	1	INDETERMINATE	2	TRUE	2	0.619046423125393	4		463	427	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922294	100922294	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1315135533	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	59	254	0	ENST00000325455.5:c.2218C>T	p.Arg740Ter	p.R740*	ENST00000325455	NM_001202474.3	740	Cga/Tga	5/8	0.342336129333357	2	FACETS	0.887	0.774	1	0.443	0.387	0.503	INDETERMINATE	1	TRUE	0	0.619046423125393	2		254	215	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622418	28622418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	76	359	0	ENST00000241453.7:c.1199G>A	p.Gly400Glu	p.G400E	ENST00000241453	NM_004119.2	400	gGa/gAa	9/24	0.21958813984625	4	FACETS	0.762	0.669	0.86	0.381	0.334	0.43	INDETERMINATE	1	TRUE	2	0.619046423125393	4		359	522	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526781	31526781	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	159	525	0	ENST00000344624.3:c.259C>T	p.Pro87Ser	p.P87S	ENST00000344624		87	Ccg/Tcg	2/33	0.21958813984625	4	FACETS	1	0.939	1	0.514	0.471	0.558	INDETERMINATE	1	TRUE	2	0.619046423125393	4		525	809	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959121	2959121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778152	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	176	619	0	ENST00000396946.4:c.2395G>A	p.Asp799Asn	p.D799N	ENST00000396946	NM_032415.4	799	Gat/Aat	18/25	0.21958813984625	4	FACETS	0.948	0.873	1	0.474	0.436	0.513	INDETERMINATE	1	TRUE	2	0.619046423125393	4		619	971	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508121	106508121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	133	188	1	ENST00000359195.3:c.115C>T	p.Pro39Ser	p.P39S	ENST00000359195	NM_002649.2	39	Ccc/Tcc	2/11	0.21958813984625	4	FACETS	0.906	0.832	0.982	0.906	0.832	0.982	INDETERMINATE	2	TRUE	2	0.619046423125393	4		189	384	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120612003	120612004	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	rs372504208	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	10	17	0	ENST00000256646.2:c.17_18del	p.Pro6ArgfsTer27	p.P6Rfs*27	ENST00000256646	NM_024408.3	6	cCC/c	1/34	0.406390661254719	4	FACETS	0.793	0.562	1	0.793	0.562	1	CLONAL	2	TRUE	2	0.619046423125393	4		17	33	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955949	55955949	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	106	367	0	ENST00000263923.4:c.3213G>A	p.Trp1071Ter	p.W1071*	ENST00000263923	NM_002253.2	1071	tgG/tgA	24/30	0.21958813984625	4	FACETS	0.923	0.829	1	0.461	0.414	0.511	INDETERMINATE	1	TRUE	2	0.619046423125393	4		367	601	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376626	8376626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772303653	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	84	353	2	ENST00000356435.5:c.4487G>A	p.Arg1496Gln	p.R1496Q	ENST00000356435		1496	cGa/cAa	27/35	0.30142364741596	1	FACETS	0.431	0.382	0.482	0.431	0.382	0.482	INDETERMINATE	1	TRUE	0	0.619046423125393	1		355	435	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508805	106508805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762805000	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	118	468	0	ENST00000359195.3:c.799G>A	p.Glu267Lys	p.E267K	ENST00000359195	NM_002649.2	267	Gaa/Aaa	2/11	0.21958813984625	4	FACETS	0.802	0.723	0.884	0.401	0.361	0.442	INDETERMINATE	1	TRUE	2	0.619046423125393	4		468	770	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812522	43812522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	149	542	0	ENST00000372470.3:c.1225G>A	p.Glu409Lys	p.E409K	ENST00000372470	NM_005373.2	409	Gag/Aag	8/12	1	2	FACETS	0.698	0.639	0.759	0.698	0.639	0.759	SUBCLONAL	1	TRUE	1	0.619046423125393	2		542	690	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801074	135801074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	71	376	0	ENST00000298552.3:c.263C>T	p.Ser88Phe	p.S88F	ENST00000298552	NM_001162426.1	88	tCc/tTc	5/23	0.284365409704459	2	FACETS	0.503	0.44	0.57	0.252	0.22	0.285	INDETERMINATE	1	TRUE	0	0.619046423125393	2		376	456	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285793	46285793	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	252	298	1	ENST00000334344.6:c.5062-1G>A		p.X1688_splice	ENST00000334344	NM_152641.2	1688			0.619046423125393	2	FACETS	0.99	0.944	1	0.99	0.944	1	CLONAL	2	TRUE	0	0.619046423125393	2		299	411	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562870	21562870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1047262994	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	126	465	0	ENST00000382592.4:c.1049C>T	p.Pro350Leu	p.P350L	ENST00000382592	NM_014572.2	350	cCc/cTc	4/8	0.21958813984625	4	FACETS	0.808	0.731	0.888	0.404	0.365	0.444	INDETERMINATE	1	TRUE	2	0.619046423125393	4		465	816	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930342	39930342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	145	460	0	ENST00000378444.4:c.3122C>T	p.Ser1041Phe	p.S1041F	ENST00000378444	NM_001123385.1	1041	tCc/tTc	6/15	1	2	FACETS	0.658	0.601	0.717	0.658	0.601	0.717	SUBCLONAL	1	TRUE	1	0.619046423125393	2		460	712	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488718	212488718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267599191	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	154	437	0	ENST00000342788.4:c.2131C>T	p.Arg711Cys	p.R711C	ENST00000342788	NM_005235.2	711	Cgt/Tgt	18/28	0.323431676329365	2	FACETS	0.942	0.868	1	0.471	0.434	0.51	INDETERMINATE	1	TRUE	0	0.619046423125393	2		437	528	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55962398	55962398	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	86	298	0	ENST00000263923.4:c.2726G>A	p.Gly909Glu	p.G909E	ENST00000263923	NM_002253.2	909	gGa/gAa	19/30	0.21958813984625	4	FACETS	0.87	0.772	0.975	0.435	0.386	0.488	INDETERMINATE	1	TRUE	2	0.619046423125393	4		298	517	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435772	110435772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	51	53	0	ENST00000375856.3:c.2629C>T	p.Pro877Ser	p.P877S	ENST00000375856	NM_003749.2	877	Ccg/Tcg	1/2	0.21958813984625	4	FACETS	0.967	0.842	1	0.967	0.842	1	INDETERMINATE	2	TRUE	2	0.619046423125393	4		53	138	SUCCESS
ALK	238	MSKCC	GRCh37	2	29473990	29473990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	91	609	0	ENST00000389048.3:c.2185C>T	p.Pro729Ser	p.P729S	ENST00000389048	NM_004304.4	729	Cca/Tca	12/29	0.313854402580802	2	FACETS	0.395	0.35	0.442	0.197	0.175	0.221	INDETERMINATE	1	TRUE	0	0.619046423125393	2		609	745	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422086	81422086	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	120	463	0	ENST00000298171.2:c.62G>A	p.Gly21Glu	p.G21E	ENST00000298171	NM_000369.2	21	gGa/gAa	1/10	1	2	FACETS	0.587	0.53	0.645	0.587	0.53	0.645	SUBCLONAL	1	TRUE	1	0.619046423125393	2		463	661	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700235	117700235	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	88	384	0	ENST00000368508.3:c.2584C>T	p.Leu862Phe	p.L862F	ENST00000368508	NM_002944.2	862	Ctt/Ttt	17/43	0.21958813984625	4	FACETS	0.815	0.723	0.912	0.407	0.361	0.456	INDETERMINATE	1	TRUE	2	0.619046423125393	4		384	565	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406293	406293	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	115	416	0	ENST00000399788.2:c.4148C>T	p.Ser1383Phe	p.S1383F	ENST00000399788	NM_001042603.1	1383	tCc/tTc	25/28	0.197589374596131	2	FACETS	0.676	0.611	0.744	0.338	0.305	0.372	INDETERMINATE	1	TRUE	0	0.619046423125393	2		416	550	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184333	7184333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	140	510	0	ENST00000302850.5:c.968C>T	p.Ser323Phe	p.S323F	ENST00000302850	NM_000208.2	323	tCc/tTc	3/22	0.197589374596131	2	FACETS	0.684	0.625	0.747	0.342	0.312	0.374	INDETERMINATE	1	TRUE	0	0.619046423125393	2		510	661	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217393	123217393	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1569520230	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	77	285	1	ENST00000218089.9:c.3047G>A	p.Arg1016Lys	p.R1016K	ENST00000218089	NM_001042749.1	1016	aGa/aAa	29/35	1	2	FACETS	0.838	0.743	0.937	0.838	0.743	0.937	CLONAL	1	TRUE	1	0.619046423125393	2		286	297	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455536	189455536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	151	355	0	ENST00000264731.3:c.70G>A	p.Glu24Lys	p.E24K	ENST00000264731	NM_003722.4	24	Gaa/Aaa	2/14	0.21958813984625	4	FACETS	0.938	0.866	1	0.938	0.866	1	INDETERMINATE	2	TRUE	2	0.619046423125393	4		355	421	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367944	15367944	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	182	703	0	ENST00000263377.2:c.1382C>T	p.Pro461Leu	p.P461L	ENST00000263377	NM_058243.2	461	cCt/cTt	8/20	0.197589374596131	2	FACETS	0.675	0.623	0.729	0.338	0.311	0.365	INDETERMINATE	1	TRUE	0	0.619046423125393	2		703	871	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478758	57478758	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137854539	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	84	287	0	ENST00000371085.3:c.344C>T	p.Pro115Leu	p.P115L	ENST00000371085	NM_000516.4	115	cCc/cTc	5/13	0.21958813984625	4	FACETS	0.73	0.645	0.82	0.365	0.322	0.41	INDETERMINATE	1	TRUE	2	0.619046423125393	4		287	602	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436605	8436605	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201031030	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	41	313	0	ENST00000356435.5:c.4073C>T	p.Ser1358Phe	p.S1358F	ENST00000356435		1358	tCc/tTc	24/35	0.30142364741596	1	FACETS	0.359	0.301	0.422	0.359	0.301	0.422	INDETERMINATE	1	TRUE	0	0.619046423125393	1		313	255	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625110	69625110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782454437	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	118	608	1	ENST00000334134.2:c.683C>T	p.Ser228Leu	p.S228L	ENST00000334134	NM_005247.2	228	tCg/tTg	3/3	0.197589374596131	2	FACETS	0.57	0.515	0.628	0.285	0.257	0.314	INDETERMINATE	1	TRUE	0	0.619046423125393	2		609	669	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499707	8499707	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	68	413	0	ENST00000356435.5:c.2262G>A	p.Met754Ile	p.M754I	ENST00000356435		754	atG/atA	14/35	0.30142364741596	1	FACETS	0.296	0.257	0.337	0.296	0.257	0.337	INDETERMINATE	1	TRUE	0	0.619046423125393	1		413	513	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546784	9546784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1252319558	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	196	328	0	ENST00000353224.5:c.1238C>T	p.Pro413Leu	p.P413L	ENST00000353224	NM_177990.2	413	cCg/cTg	5/10	0.21958813984625	4	FACETS	0.876	0.816	0.938	0.876	0.816	0.938	INDETERMINATE	2	TRUE	2	0.619046423125393	4		328	585	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968102	68968102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	39	391	0	ENST00000288368.4:c.1131G>A	p.Met377Ile	p.M377I	ENST00000288368	NM_024870.2	377	atG/atA	10/40	0.314698281437382	3	FACETS	0.346	0.286	0.412	0.173	0.143	0.206	INDETERMINATE	1	TRUE	1	0.619046423125393	3		391	477	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524996	8524996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	55	270	0	ENST00000356435.5:c.608G>A	p.Gly203Glu	p.G203E	ENST00000356435		203	gGa/gAa	7/35	0.30142364741596	1	FACETS	0.352	0.302	0.405	0.352	0.302	0.405	INDETERMINATE	1	TRUE	0	0.619046423125393	1		270	349	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872881	136872881	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	116	335	0	ENST00000241393.3:c.617T>C	p.Val206Ala	p.V206A	ENST00000241393	NM_003467.2	206	gTt/gCt	2/2	0.323431676329365	2	FACETS	0.868	0.788	0.951	0.434	0.394	0.476	INDETERMINATE	1	TRUE	0	0.619046423125393	2		335	432	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748519	43748519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267601048	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	120	354	0	ENST00000523873.1:c.473C>T	p.Ser158Phe	p.S158F	ENST00000523873		158	tCc/tTc	6/8	0.21958813984625	4	FACETS	0.902	0.815	0.993	0.451	0.407	0.497	INDETERMINATE	1	TRUE	2	0.619046423125393	4		354	696	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10259681	10259681	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	97	354	0	ENST00000340748.4:c.2551C>T	p.Pro851Ser	p.P851S	ENST00000340748		851	Ccc/Tcc	26/40	0.197589374596131	2	FACETS	0.638	0.571	0.709	0.319	0.285	0.355	INDETERMINATE	1	TRUE	0	0.619046423125393	2		354	491	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757459	40757459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303277916	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	152	488	0	ENST00000373198.4:c.2839C>T	p.Arg947Trp	p.R947W	ENST00000373198	NM_133170.3	947	Cgg/Tgg	20/32	0.21958813984625	4	FACETS	0.917	0.839	0.999	0.459	0.419	0.5	INDETERMINATE	1	TRUE	2	0.619046423125393	4		488	867	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926910	112926910	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397507550	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	384	430	0	ENST00000351677.2:c.1530G>C	p.Gln510His	p.Q510H	ENST00000351677	NM_002834.3	510	caG/caC	13/16	0.619046423125393	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.619046423125393	2		430	596	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591712	38591713	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	157	395	0	ENST00000299084.4:c.177dup	p.Ile60TyrfsTer18	p.I60Yfs*18	ENST00000299084	NM_152594.2	57	-/T	2/7	0.619046423125393	1	FACETS	0.934	0.867	1	0.934	0.867	1	CLONAL	1	TRUE	0	0.619046423125393	1		395	375	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992692	68992692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529924687	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	53	401	0	ENST00000288368.4:c.1657G>A	p.Glu553Lys	p.E553K	ENST00000288368	NM_024870.2	553	Gaa/Aaa	16/40	0.314698281437382	3	FACETS	0.556	0.476	0.644	0.278	0.238	0.322	INDETERMINATE	1	TRUE	1	0.619046423125393	3		401	403	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946286	55946286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751241917	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	82	236	0	ENST00000263923.4:c.3893G>A	p.Gly1298Asp	p.G1298D	ENST00000263923	NM_002253.2	1298	gGc/gAc	30/30	0.21958813984625	4	FACETS	0.92	0.815	1	0.46	0.407	0.517	INDETERMINATE	1	TRUE	2	0.619046423125393	4		236	466	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306763	41306763	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	93	369	0	ENST00000373198.4:c.896C>T	p.Ala299Val	p.A299V	ENST00000373198	NM_133170.3	299	gCt/gTt	7/32	0.21958813984625	4	FACETS	0.837	0.746	0.934	0.419	0.373	0.467	INDETERMINATE	1	TRUE	2	0.619046423125393	4		369	581	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210120	55210120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	76	365	0	ENST00000275493.2:c.230C>T	p.Ser77Phe	p.S77F	ENST00000275493	NM_005228.3	77	tCc/tTc	2/28	0.21958813984625	4	FACETS	0.718	0.63	0.811	0.359	0.315	0.406	INDETERMINATE	1	TRUE	2	0.619046423125393	4		365	554	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101604	27101604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	138	688	0	ENST00000324856.7:c.4886C>T	p.Pro1629Leu	p.P1629L	ENST00000324856	NM_006015.4	1629	cCt/cTt	18/20	1	2	FACETS	0.514	0.468	0.563	0.514	0.468	0.563	SUBCLONAL	1	TRUE	1	0.619046423125393	2		688	867	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800963	243800963	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1402272180	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	58	407	0	ENST00000263826.5:c.511G>A	p.Gly171Arg	p.G171R	ENST00000263826	NM_005465.4	171	Gga/Aga	5/13	0.222823058206259	5	FACETS	0.837	0.721	0.962			1	INDETERMINATE	1	TRUE	NA	0.619046423125393	5		407	432	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609021	43609021	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878855059	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	73	534	0	ENST00000355710.3:c.1777G>A	p.Gly593Arg	p.G593R	ENST00000355710	NM_020975.4	593	Gga/Aga	10/20	0.493693755086897	1	FACETS	0.286	0.25	0.325	0.286	0.25	0.325	SUBCLONAL	1	TRUE	0	0.619046423125393	1		534	569	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332627	70332627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	57	444	0	ENST00000373644.4:c.532C>T	p.Pro178Ser	p.P178S	ENST00000373644	NM_030625.2	178	Ccc/Tcc	2/12	0.493693755086897	1	FACETS	0.235	0.201	0.271	0.235	0.201	0.271	SUBCLONAL	1	TRUE	0	0.619046423125393	1		444	542	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405100	70405100	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	41	395	0	ENST00000373644.4:c.2614C>G	p.Pro872Ala	p.P872A	ENST00000373644	NM_030625.2	872	Ccc/Gcc	4/12	0.493693755086897	1	FACETS	0.183	0.152	0.217	0.183	0.152	0.217	SUBCLONAL	1	TRUE	0	0.619046423125393	1		395	500	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325107	123325107	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	117	552	0	ENST00000358487.5:c.221A>C	p.Lys74Thr	p.K74T	ENST00000358487	NM_000141.4	74	aAg/aCg	3/18	0.493693755086897	1	FACETS	0.433	0.391	0.477	0.433	0.391	0.477	SUBCLONAL	1	TRUE	0	0.619046423125393	1		552	603	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137313	64137313	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	151	488	0	ENST00000334205.4:c.1745C>G	p.Ala582Gly	p.A582G	ENST00000334205	NM_003942.2	582	gCg/gGg	14/17	0.197589374596131	2	FACETS	0.671	0.615	0.73	0.336	0.307	0.365	INDETERMINATE	1	TRUE	0	0.619046423125393	2		488	727	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77069965	77069965	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	121	380	0	ENST00000356341.3:c.575C>A	p.Pro192Gln	p.P192Q	ENST00000356341	NM_002576.4	192	cCa/cAa	6/15	0.197589374596131	2	FACETS	0.636	0.576	0.699	0.318	0.288	0.35	INDETERMINATE	1	TRUE	0	0.619046423125393	2		380	615	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102196084	102196085	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	22	227	0	ENST00000263464.3:c.845dup	p.Tyr282Ter	p.Y282*	ENST00000263464	NM_001165.4	282	tat/tAat	2/9	0.342336129333357	2	FACETS	0.261	0.203	0.329	0.131	0.101	0.165	INDETERMINATE	1	TRUE	0	0.619046423125393	2		227	272	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347518	118347518	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	89	327	0	ENST00000534358.1:c.3157-2A>T		p.X1053_splice	ENST00000534358	NM_005933.3	1053			0.342336129333357	2	FACETS	0.773	0.69	0.86	0.386	0.345	0.43	INDETERMINATE	1	TRUE	0	0.619046423125393	2		327	372	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118361941	118361941	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	50	202	0	ENST00000534358.1:c.4727A>G	p.Tyr1576Cys	p.Y1576C	ENST00000534358	NM_005933.3	1576	tAt/tGt	14/36	0.342336129333357	2	FACETS	0.646	0.553	0.746	0.323	0.276	0.373	INDETERMINATE	1	TRUE	0	0.619046423125393	2		202	250	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118367051	118367051	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	52	355	0	ENST00000534358.1:c.5633T>C	p.Leu1878Ser	p.L1878S	ENST00000534358	NM_005933.3	1878	tTa/tCa	20/36	0.342336129333357	2	FACETS	0.37	0.315	0.43	0.185	0.157	0.215	INDETERMINATE	1	TRUE	0	0.619046423125393	2		355	454	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118378287	118378287	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	306	521	1	ENST00000534358.1:c.10798G>T	p.Glu3600Ter	p.E3600*	ENST00000534358	NM_005933.3	3600	Gag/Tag	28/36	0.342336129333357	2	FACETS	0.785	0.746	0.823	0.785	0.746	0.823	INDETERMINATE	2	TRUE	0	0.619046423125393	2		522	630	SUCCESS
CBL	867	MSKCC	GRCh37	11	119158620	119158620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	131	426	0	ENST00000264033.4:c.2000C>T	p.Ser667Phe	p.S667F	ENST00000264033	NM_005188.3	667	tCc/tTc	12/16	0.342336129333357	2	FACETS	0.764	0.696	0.835	0.382	0.348	0.418	INDETERMINATE	1	TRUE	0	0.619046423125393	2		426	554	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402016	402016	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	157	334	0	ENST00000399788.2:c.4775C>T	p.Pro1592Leu	p.P1592L	ENST00000399788	NM_001042603.1	1592	cCc/cTc	27/28	0.197589374596131	2	FACETS	1	0.935	1	0.507	0.468	0.548	INDETERMINATE	1	TRUE	0	0.619046423125393	2		334	500	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88428956	88428956	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	69	235	0	ENST00000360948.2:c.2144C>T	p.Pro715Leu	p.P715L	ENST00000360948	NM_001012338.2	715	cCa/cTa	17/19	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.619046423125393	2		235	192	SUCCESS
BLM	641	MSKCC	GRCh37	15	91308589	91308589	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	66	433	0	ENST00000355112.3:c.2138T>C	p.Ile713Thr	p.I713T	ENST00000355112	NM_000057.2	713	aTt/aCt	9/22	1	2	FACETS	0.407	0.353	0.465	0.407	0.353	0.465	SUBCLONAL	1	TRUE	1	0.619046423125393	2		433	524	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81962178	81962178	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	99	445	0	ENST00000359376.3:c.2530C>T	p.Pro844Ser	p.P844S	ENST00000359376	NM_002661.3	844	Ccc/Tcc	24/33	0.17642449119249	0	FACETS	0.261	0.234	0.29			1	INDETERMINATE	1	TRUE	0	0.619046423125393	0		445	466	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122342	17122343	+	missense_variant	Missense_Mutation	DNP	GT	GT	AC	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	75	358	1	ENST00000285071.4:c.1052_1053inv	p.His351Arg	p.H351R	ENST00000285071	NM_144997.5	351	cAC/cGT	9/14	1	2	FACETS	0.475	0.417	0.537	0.475	0.417	0.537	SUBCLONAL	1	TRUE	1	0.619046423125393	2		359	510	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223162	41223162	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs773524529	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	88	476	0	ENST00000357654.3:c.4769T>C	p.Val1590Ala	p.V1590A	ENST00000357654	NM_007294.3	1590	gTt/gCt	15/23	1	2	FACETS	0.426	0.377	0.478	0.426	0.377	0.478	SUBCLONAL	1	TRUE	1	0.619046423125393	2		476	668	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119849	70119849	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	98	594	0	ENST00000245479.2:c.851C>T	p.Ser284Phe	p.S284F	ENST00000245479	NM_000346.3	284	tCc/tTc	3/3	1	2	FACETS	0.396	0.353	0.442	0.396	0.353	0.442	SUBCLONAL	1	TRUE	1	0.619046423125393	2		594	799	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743091	743091	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	87	486	0	ENST00000314574.4:c.887G>A	p.Trp296Ter	p.W296*	ENST00000314574	NM_005433.3	296	tGg/tAg	8/12	0.307993828423297	3	FACETS	0.729	0.647	0.816	0.364	0.323	0.408	INDETERMINATE	1	TRUE	1	0.619046423125393	3		486	505	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290234	15290234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257366364	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	183	658	0	ENST00000263388.2:c.3401G>A	p.Gly1134Glu	p.G1134E	ENST00000263388	NM_000435.2	1134	gGg/gAg	21/33	0.197589374596131	2	FACETS	0.634	0.585	0.685	0.317	0.292	0.343	INDETERMINATE	1	TRUE	0	0.619046423125393	2		658	932	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951115	17951115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	158	642	1	ENST00000458235.1:c.1178G>A	p.Gly393Asp	p.G393D	ENST00000458235	NM_000215.3	393	gGc/gAc	9/24	0.197589374596131	2	FACETS	0.621	0.569	0.675	0.311	0.284	0.338	INDETERMINATE	1	TRUE	0	0.619046423125393	2		643	822	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18972840	18972840	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	147	468	1	ENST00000262803.5:c.2479G>A	p.Asp827Asn	p.D827N	ENST00000262803	NM_002911.3	827	Gac/Aac	18/24	0.197589374596131	2	FACETS	0.661	0.605	0.72	0.331	0.302	0.36	INDETERMINATE	1	TRUE	0	0.619046423125393	2		469	718	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221702	36221702	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	187	696	0	ENST00000222270.7:c.5371del	p.Glu1791SerfsTer104	p.E1791Sfs*104	ENST00000222270	NM_014727.1	1791	Gag/ag	26/37	0.21958813984625	4	FACETS	0.852	0.786	0.921	0.426	0.393	0.461	INDETERMINATE	1	TRUE	2	0.619046423125393	4		696	1148	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907669	111907669	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1279964032	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	59	374	0	ENST00000393256.3:c.443T>C	p.Ile148Thr	p.I148T	ENST00000393256	NM_006538.4	148	aTc/aCc	3/4	0.323431676329365	2	FACETS	0.41	0.353	0.472	0.205	0.176	0.236	INDETERMINATE	1	TRUE	0	0.619046423125393	2		374	465	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546901	9546901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs924744761	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	275	398	0	ENST00000353224.5:c.1121C>T	p.Pro374Leu	p.P374L	ENST00000353224	NM_177990.2	374	cCg/cTg	5/10	0.21958813984625	4	FACETS	0.939	0.886	0.993	0.939	0.886	0.993	INDETERMINATE	2	TRUE	2	0.619046423125393	4		398	766	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735472	40735472	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	295	575	0	ENST00000373198.4:c.3401G>T	p.Cys1134Phe	p.C1134F	ENST00000373198	NM_133170.3	1134	tGc/tTc	25/32	0.21958813984625	4	FACETS	0.838	0.79	0.886	0.838	0.79	0.886	INDETERMINATE	2	TRUE	2	0.619046423125393	4		575	921	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100950	41100951	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	134	476	1	ENST00000373198.4:c.1405_1406delinsAA	p.Gly469Asn	p.G469N	ENST00000373198	NM_133170.3	469	GGc/AAc	8/32	0.21958813984625	4	FACETS	0.871	0.791	0.954	0.435	0.395	0.477	INDETERMINATE	1	TRUE	2	0.619046423125393	4		477	805	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39774502	39774502	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769456407	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	97	409	0	ENST00000288319.7:c.650G>A	p.Arg217Gln	p.R217Q	ENST00000288319	NM_182918.3	217	cGg/cAg	5/10	1	2	FACETS	0.531	0.474	0.591	0.531	0.474	0.591	SUBCLONAL	1	TRUE	1	0.619046423125393	2		409	590	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526100	189526100	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	128	514	1	ENST00000264731.3:c.364C>T	p.Gln122Ter	p.Q122*	ENST00000264731	NM_003722.4	122	Cag/Tag	4/14	0.21958813984625	4	FACETS	0.765	0.693	0.841	0.383	0.346	0.421	INDETERMINATE	1	TRUE	2	0.619046423125393	4		515	875	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584539	189584539	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	82	339	0	ENST00000264731.3:c.835C>A	p.Pro279Thr	p.P279T	ENST00000264731	NM_003722.4	279	Ccc/Acc	6/14	0.21958813984625	4	FACETS	0.709	0.626	0.798	0.354	0.313	0.399	INDETERMINATE	1	TRUE	2	0.619046423125393	4		339	605	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99823034	99823034	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	134	228	0	ENST00000280892.6:c.178C>A	p.Gln60Lys	p.Q60K	ENST00000280892	NM_001130678.1	60	Cag/Aag	2/7	0.21958813984625	4	FACETS	0.793	0.726	0.862	0.793	0.726	0.862	INDETERMINATE	2	TRUE	2	0.619046423125393	4		228	442	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522448	187522448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757311451	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	121	382	0	ENST00000441802.2:c.11615G>A	p.Arg3872Gln	p.R3872Q	ENST00000441802	NM_005245.3	3872	cGa/cAa	21/27	0.21958813984625	4	FACETS	0.947	0.858	1	0.474	0.429	0.521	INDETERMINATE	1	TRUE	2	0.619046423125393	4		382	668	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873729	35873729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774177784	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	66	256	0	ENST00000303115.3:c.685C>T	p.Pro229Ser	p.P229S	ENST00000303115	NM_002185.3	229	Cca/Tca	5/8	0.21958813984625	4	FACETS	0.951	0.83	1	0.476	0.415	0.54	INDETERMINATE	1	TRUE	2	0.619046423125393	4		256	363	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80160639	80160639	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	89	459	0	ENST00000265081.6:c.3008C>T	p.Ser1003Phe	p.S1003F	ENST00000265081	NM_002439.4	1003	tCc/tTc	22/24	0.21958813984625	4	FACETS	0.725	0.643	0.812	0.363	0.321	0.406	INDETERMINATE	1	TRUE	2	0.619046423125393	4		459	642	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517545	176517545	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	170	807	0	ENST00000292408.4:c.246G>A	p.Trp82Ter	p.W82*	ENST00000292408	NM_213647.1	82	tgG/tgA	3/18	0.21958813984625	4	FACETS	0.814	0.747	0.883	0.407	0.373	0.442	INDETERMINATE	1	TRUE	2	0.619046423125393	4		807	1093	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057749	180057749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs574248675	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	152	545	1	ENST00000261937.6:c.206C>T	p.Ala69Val	p.A69V	ENST00000261937	NM_182925.4	69	gCc/gTc	3/30	0.21958813984625	4	FACETS	0.914	0.836	0.995	0.457	0.418	0.498	INDETERMINATE	1	TRUE	2	0.619046423125393	4		546	870	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197259	26197259	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	80	378	0	ENST00000356476.2:c.220G>A	p.Glu74Lys	p.E74K	ENST00000356476		74	Gag/Aag	1/1	0.21958813984625	4	FACETS	0.659	0.58	0.743	0.329	0.29	0.372	INDETERMINATE	1	TRUE	2	0.619046423125393	4		378	635	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672858	30672858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	183	662	0	ENST00000376406.3:c.4102C>T	p.Pro1368Ser	p.P1368S	ENST00000376406	NM_014641.2	1368	Cct/Tct	10/15	0.21958813984625	4	FACETS	0.937	0.864	1	0.468	0.432	0.506	INDETERMINATE	1	TRUE	2	0.619046423125393	4		662	1022	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161807873	161807873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	103	359	0	ENST00000366898.1:c.1120G>A	p.Glu374Lys	p.E374K	ENST00000366898	NM_004562.2	374	Gaa/Aaa	10/12	0.21958813984625	4	FACETS	0.939	0.842	1	0.469	0.421	0.52	INDETERMINATE	1	TRUE	2	0.619046423125393	4		359	574	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6031670	6031670	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781358	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	90	485	0	ENST00000265849.7:c.922G>A	p.Glu308Lys	p.E308K	ENST00000265849	NM_000535.5	308	Gag/Aag	9/15	0.21958813984625	4	FACETS	0.675	0.599	0.757	0.338	0.299	0.379	INDETERMINATE	1	TRUE	2	0.619046423125393	4		485	697	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975379	13975379	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	222	376	0	ENST00000405192.2:c.508C>T	p.Pro170Ser	p.P170S	ENST00000405192	NM_001163147.1	170	Cct/Tct	7/12	0.21958813984625	4	FACETS	0.886	0.83	0.944	0.886	0.83	0.944	INDETERMINATE	2	TRUE	2	0.619046423125393	4		376	655	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395437	116395437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	157	373	0	ENST00000397752.3:c.1730G>A	p.Gly577Glu	p.G577E	ENST00000397752	NM_000245.2	577	gGa/gAa	6/21	0.21958813984625	4	FACETS	0.794	0.732	0.858	0.794	0.732	0.858	INDETERMINATE	2	TRUE	2	0.619046423125393	4		373	517	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411885	116411885	+	intron_variant	Intron	SNP	C	C	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	209	704	0	ENST00000397752.3:c.2888-18C>T		p.*963*	ENST00000397752	NM_000245.2	-/1390			0.21958813984625	4	FACETS	0.963	0.893	1	0.482	0.446	0.518	INDETERMINATE	1	TRUE	2	0.619046423125393	4		704	1135	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851390	151851390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	147	512	0	ENST00000262189.6:c.12101C>T	p.Ser4034Phe	p.S4034F	ENST00000262189	NM_170606.2	4034	tCc/tTc	47/59	0.21958813984625	4	FACETS	0.92	0.84	1	0.46	0.42	0.502	INDETERMINATE	1	TRUE	2	0.619046423125393	4		512	836	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931830	68931830	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	38	474	0	ENST00000288368.4:c.260T>G	p.Phe87Cys	p.F87C	ENST00000288368	NM_024870.2	87	tTc/tGc	3/40	0.314698281437382	3	FACETS	0.279	0.23	0.334	0.14	0.115	0.167	INDETERMINATE	1	TRUE	1	0.619046423125393	3		474	576	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942732	68942732	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	37	304	0	ENST00000288368.4:c.544G>A	p.Glu182Lys	p.E182K	ENST00000288368	NM_024870.2	182	Gag/Aag	6/40	0.314698281437382	3	FACETS	0.352	0.29	0.421	0.176	0.145	0.211	INDETERMINATE	1	TRUE	1	0.619046423125393	3		304	445	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968209	68968209	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	101	495	0	ENST00000288368.4:c.1238G>A	p.Ser413Asn	p.S413N	ENST00000288368	NM_024870.2	413	aGc/aAc	10/40	0.314698281437382	3	FACETS	0.732	0.655	0.812	0.366	0.327	0.406	INDETERMINATE	1	TRUE	1	0.619046423125393	3		495	584	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404537	8404537	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	24	155	0	ENST00000356435.5:c.4210G>A	p.Gly1404Arg	p.G1404R	ENST00000356435		1404	Ggg/Agg	25/35	0.30142364741596	1	FACETS	0.311	0.246	0.385	0.311	0.246	0.385	INDETERMINATE	1	TRUE	0	0.619046423125393	1		155	172	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404567	8404567	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	33	187	0	ENST00000356435.5:c.4180C>T	p.His1394Tyr	p.H1394Y	ENST00000356435		1394	Cat/Tat	25/35	0.30142364741596	1	FACETS	0.323	0.264	0.388	0.323	0.264	0.388	INDETERMINATE	1	TRUE	0	0.619046423125393	1		187	228	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449821	8449821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754699635	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	85	354	0	ENST00000356435.5:c.3892G>A	p.Asp1298Asn	p.D1298N	ENST00000356435		1298	Gac/Aac	23/35	0.30142364741596	1	FACETS	0.429	0.381	0.48	0.429	0.381	0.48	INDETERMINATE	1	TRUE	0	0.619046423125393	1		354	442	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500850	8500850	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1168246256	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	84	398	0	ENST00000356435.5:c.2032G>A	p.Glu678Lys	p.E678K	ENST00000356435		678	Gaa/Aaa	13/35	0.30142364741596	1	FACETS	0.441	0.391	0.494	0.441	0.391	0.494	INDETERMINATE	1	TRUE	0	0.619046423125393	1		398	425	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517925	8517925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	68	266	0	ENST00000356435.5:c.1466C>T	p.Ser489Phe	p.S489F	ENST00000356435		489	tCt/tTt	10/35	0.30142364741596	1	FACETS	0.449	0.393	0.508	0.449	0.393	0.508	INDETERMINATE	1	TRUE	0	0.619046423125393	1		266	338	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518020	8518020	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	78	328	0	ENST00000356435.5:c.1371G>A	p.Met457Ile	p.M457I	ENST00000356435		457	atG/atA	10/35	0.30142364741596	1	FACETS	0.414	0.366	0.466	0.414	0.366	0.466	INDETERMINATE	1	TRUE	0	0.619046423125393	1		328	420	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197546	27197546	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	115	470	0	ENST00000380036.4:c.1858A>G	p.Lys620Glu	p.K620E	ENST00000380036	NM_000459.3	620	Aag/Gag	12/23	0.284365409704459	2	FACETS	0.611	0.552	0.674	0.306	0.276	0.337	INDETERMINATE	1	TRUE	0	0.619046423125393	2		470	608	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27209136	27209136	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	183	390	0	ENST00000380036.4:c.2593G>T	p.Asp865Tyr	p.D865Y	ENST00000380036	NM_000459.3	865	Gat/Tat	16/23	0.284365409704459	2	FACETS	1	0.989	1	0.657	0.613	0.702	INDETERMINATE	1	TRUE	0	0.619046423125393	2		390	450	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87356837	87356837	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	55	323	0	ENST00000277120.3:c.1190A>T	p.Tyr397Phe	p.Y397F	ENST00000277120		397	tAt/tTt	10/19	0.284365409704459	2	FACETS	0.676	0.583	0.775	0.338	0.291	0.388	INDETERMINATE	1	TRUE	0	0.619046423125393	2		323	263	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931687	39931687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	164	573	0	ENST00000378444.4:c.2912G>A	p.Gly971Asp	p.G971D	ENST00000378444	NM_001123385.1	971	gGt/gAt	4/15	1	2	FACETS	0.68	0.625	0.737	0.68	0.625	0.737	SUBCLONAL	1	TRUE	1	0.619046423125393	2		573	779	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934433	39934433	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	150	381	0	ENST00000378444.4:c.166G>A	p.Val56Met	p.V56M	ENST00000378444	NM_001123385.1	56	Gtg/Atg	4/15	1	2	FACETS	0.911	0.837	0.987	0.911	0.837	0.987	CLONAL	1	TRUE	1	0.619046423125393	2		381	532	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223347	53223347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	81	559	0	ENST00000375401.3:c.4012G>A	p.Glu1338Lys	p.E1338K	ENST00000375401	NM_004187.3	1338	Gag/Aag	23/26	1	2	FACETS	0.333	0.292	0.376	0.333	0.292	0.376	SUBCLONAL	1	TRUE	1	0.619046423125393	2		559	787	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413151	63413151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	129	481	0	ENST00000330258.3:c.16G>A	p.Asp6Asn	p.D6N	ENST00000330258	NM_152424.3	6	Gat/Aat	2/2	1	2	FACETS	0.638	0.58	0.699	0.638	0.58	0.699	SUBCLONAL	1	TRUE	1	0.619046423125393	2		481	653	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814312	76814312	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	58	225	0	ENST00000373344.5:c.6332G>A	p.Arg2111Gln	p.R2111Q	ENST00000373344	NM_000489.3	2111	cGa/cAa	29/35	1	2	FACETS	0.829	0.721	0.943	0.829	0.721	0.943	CLONAL	1	TRUE	1	0.619046423125393	2		225	226	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937521	76937521	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	33	351	0	ENST00000373344.5:c.3227del	p.Ser1076PhefsTer42	p.S1076Ffs*42	ENST00000373344	NM_000489.3	1076	tCt/tt	9/35	1	2	FACETS	0.363	0.296	0.437	0.363	0.296	0.437	SUBCLONAL	1	TRUE	1	0.619046423125393	2		351	294	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812335	212812335	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	75	285	0	ENST00000342788.4:c.241C>T	p.Arg81Ter	p.R81*	ENST00000342788	NM_005235.2	81	Cga/Tga	3/28	1	2	FACETS	0.837	0.737	0.943	0.837	0.737	0.943	CLONAL	1	TRUE	1	0.458307934354483	2		285	391	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777894	NA	P-0039281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	152	700	0	ENST00000361445.4:c.6644C>T	p.Ser2215Phe	p.S2215F	ENST00000361445	NM_004958.3	2215	tCt/tTt	47/58	1	2	FACETS	0.892	0.817	0.97	0.892	0.817	0.97	CLONAL	1	TRUE	1	0.458307934354483	2		700	744	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0039281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	103	462	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.965	0.868	1	0.965	0.868	1	CLONAL	1	TRUE	1	0.458307934354483	2		463	466	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900288	101900288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111854391	NA	P-0039281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	65	361	0	ENST00000374994.4:c.722C>T	p.Ser241Leu	p.S241L	ENST00000374994	NM_004612.2	241	tCg/tTg	4/9	0.458307934354483	1	FACETS	0.51	0.443	0.581	0.51	0.443	0.581	SUBCLONAL	1	TRUE	0	0.458307934354483	1		361	429	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508904	106508904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	107	562	3	ENST00000359195.3:c.898G>A	p.Gly300Arg	p.G300R	ENST00000359195	NM_002649.2	300	Gga/Aga	2/11	0.450946594687441	3	FACETS	0.87	0.781	0.963	0.435	0.39	0.482	CLONAL	1	TRUE	1	0.458307934354483	3		565	660	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645607	215645607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553622313	NA	P-0039281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	38	546	0	ENST00000260947.4:c.991C>T	p.Pro331Ser	p.P331S	ENST00000260947	NM_000465.2	331	Ccc/Tcc	4/11	1	2	FACETS	0.235	0.193	0.282	0.235	0.193	0.282	SUBCLONAL	1	TRUE	1	0.458307934354483	2		546	706	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904872	101904872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863223832	NA	P-0039281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	23	390	0	ENST00000374994.4:c.860C>T	p.Ser287Phe	p.S287F	ENST00000374994	NM_004612.2	287	tCc/tTc	5/9	0.458307934354483	1	FACETS	0.219	0.17	0.276	0.219	0.17	0.276	SUBCLONAL	1	TRUE	0	0.458307934354483	1		390	353	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127420	55127420	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	138	680	1	ENST00000257290.5:c.208G>A	p.Glu70Lys	p.E70K	ENST00000257290	NM_006206.4	70	Gaa/Aaa	3/23	1	2	FACETS	0.788	0.718	0.862	0.788	0.718	0.862	SUBCLONAL	1	TRUE	1	0.458307934354483	2		681	764	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100511	8100511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	178	744	2	ENST00000346208.3:c.485C>T	p.Ser162Phe	p.S162F	ENST00000346208		162	tCc/tTc	3/6	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.458307934354483	2		746	731	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937185	76937185	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	110	476	0	ENST00000373344.5:c.3563C>T	p.Ser1188Phe	p.S1188F	ENST00000373344	NM_000489.3	1188	tCc/tTc	9/35	1	2	FACETS	0.847	0.763	0.935	0.847	0.763	0.935	CLONAL	1	TRUE	1	0.458307934354483	2		476	567	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426073	47426073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	175	772	0	ENST00000377045.4:c.593C>T	p.Pro198Leu	p.P198L	ENST00000377045	NM_001654.4	198	cCc/cTc	7/16	1	2	FACETS	0.974	0.899	1	0.974	0.899	1	CLONAL	1	TRUE	1	0.458307934354483	2		772	784	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43772141	43772141	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	130	743	0	ENST00000382044.4:c.574C>T	p.Pro192Ser	p.P192S	ENST00000382044	NM_001141980.1	192	Cca/Tca	6/28	1	2	FACETS	0.65	0.589	0.714	0.65	0.589	0.714	SUBCLONAL	1	TRUE	1	0.458307934354483	2		743	873	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141562	11141562	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	132	635	2	ENST00000358026.2:c.3539C>T	p.Pro1180Leu	p.P1180L	ENST00000358026	NM_001128849.1	1180	cCt/cTt	25/36	1	2	FACETS	0.837	0.761	0.917	0.837	0.761	0.917	CLONAL	1	TRUE	1	0.458307934354483	2		637	688	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645679	12645679	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	87	335	0	ENST00000251849.4:c.790C>T	p.His264Tyr	p.H264Y	ENST00000251849	NM_002880.3	264	Cac/Tac	7/17	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.458307934354483	2		335	377	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878508	151878508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	367	692	0	ENST00000262189.6:c.6437C>T	p.Ser2146Phe	p.S2146F	ENST00000262189	NM_170606.2	2146	tCc/tTc	36/59	0.450946594687441	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.458307934354483	3		692	955	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275824	38275824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	159	736	1	ENST00000425967.3:c.1445C>T	p.Ser482Phe	p.S482F	ENST00000425967	NM_001174067.1	482	tCc/tTc	11/19	1	2	FACETS	0.924	0.848	1	0.924	0.848	1	CLONAL	1	TRUE	1	0.458307934354483	2		737	751	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229572	98229572	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0039281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	108	462	1	ENST00000331920.6:c.2386A>T	p.Lys796Ter	p.K796*	ENST00000331920	NM_000264.3	796	Aaa/Taa	15/24	0.458307934354483	1	FACETS	0.899	0.813	0.989	0.899	0.813	0.989	CLONAL	1	TRUE	0	0.458307934354483	1		463	404	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006869	47006869	+	5_prime_UTR_variant	5'UTR	SNP	C	C	T	novel	NA	P-0039281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	173	762	0	ENST00000377604.3:c.-12C>T		p.*4*	ENST00000377604	NM_001204468.1	-/852		2/24	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.458307934354483	2		762	729	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874399	76874400	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0039281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	67	382	1	ENST00000373344.5:c.5322_5323delinsAA	p.Glu1775Lys	p.E1775K	ENST00000373344	NM_000489.3	1774	aaGGag/aaAAag	21/35	1	2	FACETS	0.582	0.507	0.664	0.582	0.507	0.664	SUBCLONAL	1	TRUE	1	0.458307934354483	2		383	502	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615121	100615121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	127	550	0	ENST00000308731.7:c.794C>T	p.Pro265Leu	p.P265L	ENST00000308731	NM_000061.2	265	cCt/cTt	9/19	1	2	FACETS	0.91	0.827	0.997	0.91	0.827	0.997	CLONAL	1	TRUE	1	0.458307934354483	2		550	609	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	82	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.969	0.859	1	0.969	0.859	1	CLONAL	1	TRUE	1	0.404920202280012	2		215	418	SUCCESS
BLM	641	MSKCC	GRCh37	15	91290720	91290720	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs139282091	NA	P-0039287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	58	291	0	ENST00000355112.3:c.98C>T	p.Ser33Leu	p.S33L	ENST00000355112	NM_000057.2	33	tCa/tTa	2/22	1	2	FACETS	0.85	0.735	0.975	0.85	0.735	0.975	CLONAL	1	TRUE	1	0.404920202280012	2		291	337	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612073	189612073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142762485	NA	P-0039287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	137	538	0	ENST00000264731.3:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000264731	NM_003722.4	609	Gaa/Aaa	14/14	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.404920202280012	2		538	617	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0039287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	105	423	1	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	0.948	0.852	1	0.948	0.852	1	CLONAL	1	TRUE	1	0.404920202280012	2		424	547	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003205	143003205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751420268	NA	P-0039287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	80	387	0	ENST00000262992.4:c.2621G>A	p.Arg874Gln	p.R874Q	ENST00000262992	NM_001101669.1	874	cGa/cAa	23/24	1	2	FACETS	0.834	0.736	0.937	0.834	0.736	0.937	CLONAL	1	TRUE	1	0.404920202280012	2		387	474	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554566	29554566	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	55	247	0	ENST00000356175.3:c.2351G>A	p.Trp784Ter	p.W784*	ENST00000356175	NM_000267.3	784	tGg/tAg	20/57	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.404920202280012	2		247	261	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735593	204735593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	99	415	0	ENST00000302823.3:c.394G>A	p.Glu132Lys	p.E132K	ENST00000302823	NM_005214.4	132	Gag/Aag	2/4	1	2	FACETS	0.998	0.895	1	0.998	0.895	1	CLONAL	1	TRUE	1	0.404920202280012	2		415	490	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625670	1625670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167586863	NA	P-0039287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	200	625	1	ENST00000344749.5:c.404C>T	p.Pro135Leu	p.P135L	ENST00000344749	NM_001136139.2	135	cCc/cTc	7/19	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.404920202280012	2		626	787	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637034	93637034	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	118	515	0	ENST00000375746.1:c.1084G>A	p.Glu362Lys	p.E362K	ENST00000375746	NM_001174167.1	362	Gag/Aag	9/14	1	2	FACETS	0.894	0.808	0.984	0.894	0.808	0.984	CLONAL	1	TRUE	1	0.404920202280012	2		515	652	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074309	8074309	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	120	481	0	ENST00000377482.5:c.350A>T	p.Lys117Ile	p.K117I	ENST00000377482	NM_018948.3	117	aAa/aTa	4/4	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.404920202280012	2		481	550	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161326518	161326518	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	56	235	0	ENST00000367975.2:c.293C>T	p.Ser98Phe	p.S98F	ENST00000367975	NM_003001.3	98	tCt/tTt	5/6	1	2	FACETS	0.816	0.703	0.938	0.816	0.703	0.938	CLONAL	1	TRUE	1	0.404920202280012	2		235	339	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428237	49428237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	186	626	1	ENST00000301067.7:c.10463C>T	p.Ser3488Phe	p.S3488F	ENST00000301067	NM_003482.3	3488	tCc/tTc	37/54	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.404920202280012	2		627	750	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610503	81610503	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	87	376	0	ENST00000298171.2:c.2101C>G	p.Arg701Gly	p.R701G	ENST00000298171	NM_000369.2	701	Cgc/Ggc	10/10	1	2	FACETS	0.903	0.802	1	0.903	0.802	1	CLONAL	1	TRUE	1	0.404920202280012	2		376	476	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569957	95569957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	85	418	0	ENST00000393063.1:c.3776C>T	p.Ala1259Val	p.A1259V	ENST00000393063	NM_030621.3	1259	gCc/gTc	22/28	1	2	FACETS	0.869	0.771	0.974	0.869	0.771	0.974	CLONAL	1	TRUE	1	0.404920202280012	2		418	483	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131644	2131644	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	144	710	1	ENST00000219476.3:c.3659C>T	p.Ser1220Phe	p.S1220F	ENST00000219476	NM_000548.3	1220	tCc/tTc	31/42	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.404920202280012	2		711	698	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81902868	81902868	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	156	502	0	ENST00000359376.3:c.529G>A	p.Val177Met	p.V177M	ENST00000359376	NM_002661.3	177	Gtg/Atg	6/33	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.404920202280012	2		502	659	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867579	78867579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	141	583	1	ENST00000306801.3:c.2315C>T	p.Pro772Leu	p.P772L	ENST00000306801	NM_020761.2	772	cCc/cTc	20/34	0.404920202280012	3	FACETS	0.982	0.894	1	0.491	0.447	0.537	CLONAL	1	TRUE	1	0.404920202280012	3		584	853	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985467	60985467	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	136	649	1	ENST00000333681.4:c.433G>A	p.Gly145Arg	p.G145R	ENST00000333681		145	Ggg/Agg	2/3	1	2	FACETS	0.995	0.907	1	0.995	0.907	1	CLONAL	1	TRUE	1	0.404920202280012	2		650	675	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223641	36223641	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	161	769	0	ENST00000222270.7:c.6191T>C	p.Val2064Ala	p.V2064A	ENST00000222270	NM_014727.1	2064	gTg/gCg	28/37	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.404920202280012	2		769	779	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441470	52441470	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	86	431	0	ENST00000460680.1:c.382G>A	p.Gly128Arg	p.G128R	ENST00000460680	NM_004656.3	128	Gga/Aga	6/17	0.404920202280012	1	FACETS	0.933	0.832	1	0.933	0.832	1	CLONAL	1	TRUE	0	0.404920202280012	1		431	363	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920526	134920526	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	116	402	0	ENST00000398015.3:c.2341T>G	p.Ser781Ala	p.S781A	ENST00000398015	NM_004441.4	781	Tcc/Gcc	12/16	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.404920202280012	2		402	532	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157906	106157906	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	115	322	0	ENST00000380013.4:c.2807G>T	p.Ser936Ile	p.S936I	ENST00000380013	NM_001127208.2	936	aGt/aTt	3/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.404920202280012	2		322	423	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426417	47426417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	124	696	0	ENST00000377045.4:c.760C>T	p.Pro254Ser	p.P254S	ENST00000377045	NM_001654.4	254	Ccc/Tcc	9/16	1	2	FACETS	0.909	0.824	0.998	0.909	0.824	0.998	CLONAL	1	TRUE	1	0.404920202280012	2		696	674	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152864439	152864439	+	synonymous_variant	Silent	SNP	C	C	T	novel	NA	P-0039287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	59	137	0	ENST00000406277.2:c.87G>A	p.Ala29=	p.A29=	ENST00000406277	NM_152274.4	29	gcG/gcA	3/7	1		FACETS		0.948	1				CLONAL	1	TRUE	1	0.404920202280012	2		137	246	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148875	119148876	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0039426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	119	269	0	ENST00000264033.4:c.1096-1_1096delinsAA		p.X366_splice	ENST00000264033	NM_005188.3	366		8/16	0.226280801907178	0	FACETS	0.841	0.776	0.906			1	CLONAL	4	TRUE	0	0.226280801907178	0		269	242	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0039426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	165	173	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.941	0.881	1	1	0.995	1	CLONAL	5	TRUE	1	0.226280801907178	2		174	310	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556367	29556367	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	257	456	1	ENST00000356175.3:c.2734C>T	p.Gln912Ter	p.Q912*	ENST00000356175	NM_000267.3	912	Caa/Taa	21/57	0.226280801907178	5	FACETS	0.951	0.893	1			1	CLONAL	4	TRUE	NA	0.226280801907178	5		457	800	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29197692	29197692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747088146	NA	P-0039426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	488	717	1	ENST00000240100.2:c.502C>T	p.Pro168Ser	p.P168S	ENST00000240100	NM_001394.6	168	Cca/Tca	2/4	0.137766848704115	4	FACETS	1	0.976	1	1	0.997	1	CLONAL	4	TRUE	2	0.226280801907178	4		718	1286	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0039426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	220	462	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.984	1	1	0.996	1	CLONAL	4	TRUE	1	0.226280801907178	2		463	434	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556877	29556877	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	164	230	0	ENST00000356175.3:c.2875C>T	p.Gln959Ter	p.Q959*	ENST00000356175	NM_000267.3	959	Caa/Taa	22/57	0.226280801907178	5	FACETS	0.949	0.882	1			1	CLONAL	5	TRUE	NA	0.226280801907178	5		230	409	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545150	41545150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1352652949	NA	P-0039426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	316	498	0	ENST00000263253.7:c.2350C>T	p.Pro784Ser	p.P784S	ENST00000263253	NM_001429.3	784	Ccg/Tcg	13/31	0.226280801907178	9	FACETS	1	0.945	1			1	CLONAL	4	TRUE	NA	0.226280801907178	9		498	1249	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718148	117718148	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs747794595	NA	P-0039426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	242	512	0	ENST00000368508.3:c.709C>T	p.Gln237Ter	p.Q237*	ENST00000368508	NM_002944.2	237	Caa/Taa	7/43	0.226280801907178	0	FACETS	0.794	0.754	0.833			1	SUBCLONAL	5	TRUE	0	0.226280801907178	0		512	417	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305355	65305355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	120	504	0	ENST00000342505.4:c.2773G>A	p.Glu925Lys	p.E925K	ENST00000342505	NM_002227.2	925	Gaa/Aaa	20/25	0.226280801907178	2	FACETS	0.991	0.899	1	0.991	0.899	1	CLONAL	2	TRUE	0	0.226280801907178	2		504	535	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226558156	226558158	+	missense_variant	Missense_Mutation	TNP	GGA	GGA	AAG	novel	NA	P-0039426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	303	542	0	ENST00000366794.5:c.2131_2133delinsCTT	p.Ser711Leu	p.S711L	ENST00000366794	NM_001618.3	711	TCC/CTT	15/23	0.226280801907178	5	FACETS	1	0.98	1	1	0.994	1	CLONAL	4	TRUE	2	0.226280801907178	5		542	836	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612047	43612047	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	349	872	1	ENST00000355710.3:c.2152G>A	p.Glu718Lys	p.E718K	ENST00000355710	NM_020975.4	718	Gaa/Aaa	12/20	0.201688772839581	0	FACETS	0.913	0.869	0.959			1	CLONAL	3	TRUE	0	0.226280801907178	0		873	871	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70411609	70411609	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	101	338	0	ENST00000373644.4:c.4283T>C	p.Val1428Ala	p.V1428A	ENST00000373644	NM_030625.2	1428	gTt/gCt	5/12	0.155967893593595	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	2	TRUE	0	0.226280801907178	2		338	444	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609600	81609601	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0039426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	242	546	1	ENST00000298171.2:c.1198_1199delinsTT	p.Pro400Phe	p.P400F	ENST00000298171	NM_000369.2	400	CCc/TTc	10/10	0.137766848704115	4	FACETS	0.944	0.886	1	1	0.995	1	CLONAL	4	TRUE	2	0.226280801907178	4		547	695	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325845	30325846	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0039426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	163	347	1	ENST00000322652.5:c.2043_2044delinsTT	p.Arg682Cys	p.R682C	ENST00000322652	NM_015355.2	681	ctCCgt/ctTTgt	16/16	0.226280801907178	5	FACETS	0.931	0.861	1			1	CLONAL	4	TRUE	NA	0.226280801907178	5		348	518	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272326	15272326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs545621067	NA	P-0039426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	322	738	1	ENST00000263388.2:c.6113G>A	p.Gly2038Asp	p.G2038D	ENST00000263388	NM_000435.2	2038	gGc/gAc	33/33	1	2	FACETS	0.966	0.914	1	1	0.997	1	CLONAL	3	TRUE	1	0.226280801907178	2		739	982	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349922	15349922	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	341	673	0	ENST00000263377.2:c.3730C>T	p.Gln1244Ter	p.Q1244*	ENST00000263377	NM_058243.2	1244	Cag/Tag	18/20	1	2	FACETS	1	0.966	1	1	0.997	1	CLONAL	3	TRUE	1	0.226280801907178	2		673	981	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355314	15355314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745730200	NA	P-0039426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	170	340	0	ENST00000263377.2:c.2309C>T	p.Pro770Leu	p.P770L	ENST00000263377	NM_058243.2	770	cCg/cTg	13/20	1	2	FACETS	0.945	0.875	1	1	0.994	1	CLONAL	3	TRUE	1	0.226280801907178	2		340	530	SUCCESS
AXL	558	MSKCC	GRCh37	19	41749583	41749583	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	365	746	0	ENST00000301178.4:c.1508C>T	p.Ser503Phe	p.S503F	ENST00000301178	NM_021913.4	503	tCc/tTc	12/20	1	2	FACETS	1	0.986	1	1	0.997	1	CLONAL	3	TRUE	1	0.226280801907178	2		746	986	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762436	41762436	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	314	685	0	ENST00000301178.4:c.2116G>A	p.Gly706Arg	p.G706R	ENST00000301178	NM_021913.4	706	Gga/Aga	18/20	1	2	FACETS	1	0.98	1	1	0.997	1	CLONAL	3	TRUE	1	0.226280801907178	2		685	866	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456531	29456531	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1263111905	NA	P-0039426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	177	584	0	ENST00000389048.3:c.2387G>A	p.Gly796Glu	p.G796E	ENST00000389048	NM_004304.4	796	gGa/gAa	14/29	NA	2	FACETS	1	0.95	1			1	INDETERMINATE	2	TRUE	NA	0.226280801907178	2		584	754	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149510	61149510	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs772883337	NA	P-0039426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	199	311	0	ENST00000295025.8:c.1700T>C	p.Phe567Ser	p.F567S	ENST00000295025	NM_002908.2	567	tTc/tCc	11/11	0.226280801907178	2	FACETS	0.979	0.918	1	1	0.994	1	CLONAL	4	TRUE	0	0.226280801907178	2		311	449	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872725	136872725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	112	443	0	ENST00000241393.3:c.773G>A	p.Gly258Glu	p.G258E	ENST00000241393	NM_003467.2	258	gGg/gAg	2/2	NA	2	FACETS	0.934	0.843	1			1	INDETERMINATE	2	TRUE	NA	0.226280801907178	2		443	530	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944448	40944448	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	261	503	0	ENST00000373198.4:c.2054A>G	p.Lys685Arg	p.K685R	ENST00000373198	NM_133170.3	685	aAg/aGg	12/32	0.226280801907178	0	FACETS	0.941	0.895	0.988			1	CLONAL	4	TRUE	0	0.226280801907178	0		503	474	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604332	189604332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763644058	NA	P-0039426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	198	372	0	ENST00000264731.3:c.1499G>A	p.Gly500Glu	p.G500E	ENST00000264731	NM_003722.4	500	gGa/gAa	11/14	0.214706293824237	4	FACETS	0.994	0.928	1	1	0.994	1	CLONAL	4	TRUE	2	0.226280801907178	4		372	540	SUCCESS
APC	324	MSKCC	GRCh37	5	112179744	112179744	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	129	299	2	ENST00000257430.4:c.8453C>T	p.Ser2818Phe	p.S2818F	ENST00000257430	NM_000038.5	2818	tCc/tTc	16/16	0.226280801907178	3	FACETS	0.961	0.879	1	1	0.986	1	CLONAL	3	TRUE	1	0.226280801907178	3		301	440	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056122	26056123	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0039426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	300	431	0	ENST00000343677.2:c.534_535delinsAA	p.Val179Ile	p.V179I	ENST00000343677	NM_005319.3	178	aaGGtt/aaAAtt	1/1	0.226280801907178	9	FACETS	0.983	0.925	1	0.561	0.528	0.595	CLONAL	4	TRUE	2	0.226280801907178	9		431	1209	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981886	70981887	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0039426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	278	787	1	ENST00000276594.2:c.209_210delinsTT	p.Pro70Leu	p.P70L	ENST00000276594	NM_024504.3	70	cCC/cTT	2/8	1	2	FACETS	0.993	0.936	1	1	0.996	1	CLONAL	3	TRUE	1	0.226280801907178	2		788	825	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923700	39923700	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372187961	NA	P-0039426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	481	380	0	ENST00000378444.4:c.3391C>T	p.Arg1131Trp	p.R1131W	ENST00000378444	NM_001123385.1	1131	Cgg/Tgg	7/15	0.226280801907178	2	FACETS	1	0.993	1			1	CLONAL	6	TRUE	NA	0.226280801907178	2		380	657	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226558157	226558157	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	297	535	0	ENST00000366794.5:c.2132C>T	p.Ser711Phe	p.S711F	ENST00000366794	NM_001618.3	711	tCc/tTc	15/23	0.226280801907178	5	FACETS	1	0.974	1	1	0.993	1	CLONAL	4	TRUE	2	0.226280801907178	5		535	836	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	78	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.518057040517802	2		215	271	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	143	458	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.518057040517802	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.518057040517802	1		458	350	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	137	390	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.20879002984533	5	FACETS	1	0.976	1	0.774	0.711	0.838	INDETERMINATE	2	TRUE	2	0.518057040517802	5		390	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	148	772	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.473364882773635	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.518057040517802	1		772	421	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961761	55961761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	95	457	0	ENST00000263923.4:c.2800G>A	p.Glu934Lys	p.E934K	ENST00000263923	NM_002253.2	934	Gaa/Aaa	20/30	1	2	FACETS	0.955	0.857	1	0.955	0.857	1	CLONAL	1	TRUE	1	0.518057040517802	2		457	384	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947466	38947466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	76	327	0	ENST00000357387.3:c.4214G>A	p.Arg1405Gln	p.R1405Q	ENST00000357387	NM_152756.3	1405	cGa/cAa	32/38	1	2	FACETS	0.876	0.774	0.983	0.876	0.774	0.983	CLONAL	1	TRUE	1	0.518057040517802	2		327	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578400	7578400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751477326	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	148	732	0	ENST00000269305.4:c.530C>T	p.Pro177Leu	p.P177L	ENST00000269305	NM_001126112.2	177	cCc/cTc	5/11	0.473364882773635	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.518057040517802	1		732	411	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022297	31022297	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	90	492	0	ENST00000375687.4:c.1786del	p.Arg596GlyfsTer107	p.R596Gfs*107	ENST00000375687	NM_015338.5	594	tgC/tg	13/13	1	2	FACETS	0.877	0.784	0.976	0.877	0.784	0.976	CLONAL	1	TRUE	1	0.518057040517802	2		492	396	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805719	43805719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528834914	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	119	654	0	ENST00000372470.3:c.775G>A	p.Glu259Lys	p.E259K	ENST00000372470	NM_005373.2	259	Gaa/Aaa	5/12	1	2	FACETS	0.837	0.758	0.919	0.837	0.758	0.919	CLONAL	1	TRUE	1	0.518057040517802	2		654	549	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975495	13975495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1003578447	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	74	365	0	ENST00000405192.2:c.392G>A	p.Gly131Glu	p.G131E	ENST00000405192	NM_001163147.1	131	gGa/gAa	7/12	1	2	FACETS	0.907	0.801	1	0.907	0.801	1	CLONAL	1	TRUE	1	0.518057040517802	2		365	315	SUCCESS
ATR	545	MSKCC	GRCh37	3	142286928	142286928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751709684	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	65	363	1	ENST00000350721.4:c.128G>A	p.Arg43Gln	p.R43Q	ENST00000350721	NM_001184.3	43	cGg/cAg	2/47	1	2	FACETS	0.642	0.559	0.731	0.642	0.559	0.731	SUBCLONAL	1	TRUE	1	0.518057040517802	2		364	391	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397721	139397721	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	312	798	0	ENST00000277541.6:c.5080C>T	p.Gln1694Ter	p.Q1694*	ENST00000277541	NM_017617.3	1694	Cag/Tag	27/34	0.518057040517802	3	FACETS	0.983	0.933	1	0.983	0.933	1	CLONAL	2	TRUE	1	0.518057040517802	3		798	771	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956528	93956528	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	74	333	0	ENST00000369303.4:c.2708C>T	p.Pro903Leu	p.P903L	ENST00000369303	NM_004440.3	903	cCc/cTc	15/17	1	2	FACETS	0.922	0.814	1	0.922	0.814	1	CLONAL	1	TRUE	1	0.518057040517802	2		333	310	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715688	30715688	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893807	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	74	329	0	ENST00000295754.5:c.1346C>T	p.Ser449Phe	p.S449F	ENST00000295754	NM_003242.5	449	tCc/tTc	5/7	0.468839503151676	1	FACETS	0.764	0.676	0.856	0.764	0.676	0.856	SUBCLONAL	1	TRUE	0	0.518057040517802	1		329	277	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780675	9780675	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	163	785	0	ENST00000377346.4:c.1477G>A	p.Glu493Lys	p.E493K	ENST00000377346	NM_005026.3	493	Gag/Aag	12/24	1	2	FACETS	0.996	0.917	1	0.996	0.917	1	CLONAL	1	TRUE	1	0.518057040517802	2		785	632	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258365	16258365	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769126178	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	153	641	0	ENST00000375759.3:c.5630G>A	p.Arg1877Lys	p.R1877K	ENST00000375759	NM_015001.2	1877	aGg/aAg	11/15	1	2	FACETS	0.962	0.884	1	0.962	0.884	1	CLONAL	1	TRUE	1	0.518057040517802	2		641	614	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65316507	65316507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	139	433	0	ENST00000342505.4:c.1735C>T	p.Leu579Phe	p.L579F	ENST00000342505	NM_002227.2	579	Ctc/Ttc	12/25	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.518057040517802	2		433	483	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491093	120491095	+	frameshift_variant	Frame_Shift_Del	DEL	CAT	CAT	TA	novel	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	113	515	1	ENST00000256646.2:c.2694_2696delinsTA	p.Glu898AspfsTer33	p.E898Dfs*33	ENST00000256646	NM_024408.3	898	gaATGt/gaTAt	17/34	1	2	FACETS	0.922	0.835	1	0.922	0.835	1	CLONAL	1	TRUE	1	0.518057040517802	2		516	473	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43733737	43733737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1280487265	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	118	452	0	ENST00000382044.4:c.3085G>A	p.Glu1029Lys	p.E1029K	ENST00000382044	NM_001141980.1	1029	Gag/Aag	15/28	1	2	FACETS	0.943	0.856	1	0.943	0.856	1	CLONAL	1	TRUE	1	0.518057040517802	2		452	483	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343620	343620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	179	804	0	ENST00000262320.3:c.2054C>T	p.Pro685Leu	p.P685L	ENST00000262320	NM_003502.3	685	cCc/cTc	8/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.518057040517802	2		804	657	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829327	72829328	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	104	651	3	ENST00000268489.5:c.7253_7254delinsTT	p.Thr2418Ile	p.T2418I	ENST00000268489	NM_006885.3	2418	aCC/aTT	9/10	1	2	FACETS	0.803	0.722	0.888	0.803	0.722	0.888	CLONAL	1	TRUE	1	0.518057040517802	2		654	500	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314613	30314613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	75	642	0	ENST00000262643.3:c.1162C>T	p.Pro388Ser	p.P388S	ENST00000262643	NM_001238.2	388	Cct/Tct	12/12	1	2	FACETS	0.468	0.41	0.53	0.468	0.41	0.53	SUBCLONAL	1	TRUE	1	0.518057040517802	2		642	619	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211781	36211781	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	178	899	1	ENST00000222270.7:c.1532C>T	p.Pro511Leu	p.P511L	ENST00000222270	NM_014727.1	511	cCc/cTc	3/37	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.518057040517802	2		900	668	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022298	31022300	+	frameshift_variant	Frame_Shift_Del	DEL	CCC	CCC	TT	novel	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	90	498	0	ENST00000375687.4:c.1783_1785delinsTT	p.Pro595PhefsTer108	p.P595Ffs*108	ENST00000375687	NM_015338.5	595	CCC/TT	13/13	1	2	FACETS	0.889	0.794	0.988	0.889	0.794	0.988	CLONAL	1	TRUE	1	0.518057040517802	2		498	391	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739001	40739001	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	125	590	0	ENST00000373198.4:c.3283G>T	p.Glu1095Ter	p.E1095*	ENST00000373198	NM_133170.3	1095	Gaa/Taa	24/32	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.518057040517802	2		590	421	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62323117	62323118	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	127	644	2	ENST00000360203.5:c.2579_2580delinsTT	p.Ser860Phe	p.S860F	ENST00000360203	NM_001283009.1	860	tCC/tTT	28/35	1	2	FACETS	0.936	0.852	1	0.936	0.852	1	CLONAL	1	TRUE	1	0.518057040517802	2		646	524	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278162	142278162	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	131	501	0	ENST00000350721.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000350721	NM_001184.3	555	Cag/Tag	7/47	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.518057040517802	2		501	453	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139739	55139739	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	120	491	0	ENST00000257290.5:c.1400A>G	p.Asn467Ser	p.N467S	ENST00000257290	NM_006206.4	467	aAc/aGc	10/23	1	2	FACETS	0.969	0.88	1	0.969	0.88	1	CLONAL	1	TRUE	1	0.518057040517802	2		491	478	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268220	153268221	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	43	251	1	ENST00000281708.4:c.587_588delinsTT	p.Thr196Ile	p.T196I	ENST00000281708	NM_033632.3	196	aCC/aTT	4/12	1	2	FACETS	0.651	0.549	0.763	0.651	0.549	0.763	SUBCLONAL	1	TRUE	1	0.518057040517802	2		252	255	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554935	187554936	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	100	451	0	ENST00000441802.2:c.4225_4226delinsAA	p.Gly1409Lys	p.G1409K	ENST00000441802	NM_005245.3	1409	GGa/AAa	7/27	0.518057040517802	1	FACETS	0.851	0.769	0.937	0.851	0.769	0.937	CLONAL	1	TRUE	0	0.518057040517802	1		451	336	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630306	187630307	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	138	562	0	ENST00000441802.2:c.675_676delinsAA	p.Asp226Asn	p.D226N	ENST00000441802	NM_005245.3	225	gcGGac/gcAAac	2/27	0.518057040517802	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.518057040517802	1		562	378	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187546	32187546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	161	633	0	ENST00000375023.3:c.1333C>T	p.Pro445Ser	p.P445S	ENST00000375023	NM_004557.3	445	Ccc/Tcc	8/30	1	2	FACETS	0.91	0.837	0.986	0.91	0.837	0.986	CLONAL	1	TRUE	1	0.518057040517802	2		633	683	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192508	138192509	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	91	444	0	ENST00000237289.4:c.144_145delinsAA	p.Glu49Lys	p.E49K	ENST00000237289	NM_001270507.1	48	ctGGaa/ctAAaa	2/9	1	2	FACETS	0.733	0.654	0.818	0.733	0.654	0.818	SUBCLONAL	1	TRUE	1	0.518057040517802	2		444	479	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157454242	157454242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	107	549	0	ENST00000346085.5:c.2452C>T	p.Pro818Ser	p.P818S	ENST00000346085	NM_020732.3	818	Cct/Tct	8/20	1	2	FACETS	0.781	0.703	0.863	0.781	0.703	0.863	SUBCLONAL	1	TRUE	1	0.518057040517802	2		549	529	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358960	81358960	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	102	503	0	ENST00000222390.5:c.1001C>T	p.Pro334Leu	p.P334L	ENST00000222390	NM_000601.4	334	cCt/cTt	8/18	1	2	FACETS	0.97	0.874	1	0.97	0.874	1	CLONAL	1	TRUE	1	0.518057040517802	2		503	406	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738171	133738171	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	144	530	0	ENST00000318560.5:c.571C>G	p.Arg191Gly	p.R191G	ENST00000318560	NM_005157.4	191	Cgc/Ggc	4/11	0.518057040517802	3	FACETS	1	0.934	1	0.512	0.468	0.558	CLONAL	1	TRUE	1	0.518057040517802	3		530	683	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491095	120491095	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	113	510	0	ENST00000256646.2:c.2694del	p.Glu898AspfsTer33	p.E898Dfs*33	ENST00000256646	NM_024408.3	898	gaA/ga	17/34	1	2	FACETS	0.926	0.838	1	0.926	0.838	1	CLONAL	1	TRUE	1	0.518057040517802	2		510	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0040118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	382	593	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.321089939223969	4	FACETS	0.938	0.899	0.977	0.704	0.674	0.733	INDETERMINATE	3	TRUE	0	0.59851280423518	4		593	725	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665310	176665310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758774947	NA	P-0040118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	224	412	0	ENST00000439151.2:c.3994G>A	p.Glu1332Lys	p.E1332K	ENST00000439151	NM_022455.4	1332	Gag/Aag	7/23	0.458207689746776	4	FACETS	1	0.988	1	0.596	0.561	0.631	CLONAL	2	TRUE	0	0.59851280423518	4		412	502	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446203	187446203	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	116	699	0	ENST00000232014.4:c.1485del	p.Thr496ArgfsTer94	p.T496Rfs*94	ENST00000232014	NM_001130845.1	495	ccC/cc	6/10	0.59851280423518	5	FACETS	0.8	0.721	0.885	0.267	0.24	0.295	SUBCLONAL	1	TRUE	2	0.59851280423518	5		699	919	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497359	149497359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397509382	NA	P-0040118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	178	640	1	ENST00000261799.4:c.2959C>T	p.Arg987Trp	p.R987W	ENST00000261799	NM_002609.3	987	Cgg/Tgg	22/23	0.458207689746776	4	FACETS	0.857	0.795	0.92	0.428	0.397	0.46	CLONAL	2	TRUE	0	0.59851280423518	4		641	555	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681568	117681569	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0040118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	33	280	1	ENST00000368508.3:c.3382-1_3382delinsTT		p.X1128_splice	ENST00000368508	NM_002944.2	1128		22/43	0.487493625550786	3	FACETS	0.618	0.506	0.741	0.206	0.168	0.247	SUBCLONAL	1	TRUE	0	0.59851280423518	3		281	232	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	40	215	0				ENST00000310581	NM_198253.2	-/1132			0.203081081401261	3	FACETS	0.433	0.36	0.513	0.216	0.18	0.257	INDETERMINATE	1	TRUE	1	0.654090111602018	3		215	375	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0040388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	148	281	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	0.654090111602018	2		281	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0040388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	155	738	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.473	0.432	0.515	0.473	0.432	0.515	SUBCLONAL	1	TRUE	1	0.654090111602018	2		738	1003	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0040388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	100	462	1				ENST00000310581	NM_198253.2	-/1132			0.203081081401261	3	FACETS	0.962	0.865	1	0.481	0.432	0.532	INDETERMINATE	1	TRUE	1	0.654090111602018	3		463	422	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909629	76909629	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs919106518	NA	P-0040388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	53	516	0	ENST00000373344.5:c.4276C>T	p.Arg1426Ter	p.R1426*	ENST00000373344	NM_000489.3	1426	Cga/Tga	14/35	1	2	FACETS	0.236	0.201	0.275	0.236	0.201	0.275	SUBCLONAL	1	TRUE	1	0.654090111602018	2		516	686	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795255	42795255	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	69	817	0	ENST00000575354.2:c.2335C>T	p.Gln779Ter	p.Q779*	ENST00000575354	NM_015125.3	779	Cag/Tag	10/20	0.654090111602018	1	FACETS	0.279	0.243	0.318	0.279	0.243	0.318	SUBCLONAL	1	TRUE	0	0.654090111602018	1		817	509	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273140	55273140	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	203	637	1	ENST00000275493.2:c.3463G>T	p.Ala1155Ser	p.A1155S	ENST00000275493	NM_005228.3	1155	Gcc/Tcc	28/28	1	2	FACETS	0.647	0.599	0.695	0.647	0.599	0.695	SUBCLONAL	1	TRUE	1	0.654090111602018	2		638	960	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	73	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.478929960853984	2		215	302	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	94	380	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.419453121241114	1	FACETS	0.672	0.601	0.747	0.672	0.601	0.747	SUBCLONAL	1	TRUE	0	0.478929960853984	1		380	444	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444255	49444255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	171	1007	0	ENST00000301067.7:c.3116C>T	p.Pro1039Leu	p.P1039L	ENST00000301067	NM_003482.3	1039	cCt/cTt	11/54	1	2	FACETS	0.6	0.55	0.651	0.6	0.55	0.651	SUBCLONAL	1	TRUE	1	0.478929960853984	2		1007	1191	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577537	7577538	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	129	702	0	ENST00000269305.4:c.743_744delinsAA	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGG/cAA	7/11	1	2	FACETS	0.608	0.551	0.668	0.608	0.551	0.668	SUBCLONAL	1	TRUE	1	0.478929960853984	2		702	886	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182050	11182050	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	109	580	0	ENST00000361445.4:c.6796C>T	p.Arg2266Cys	p.R2266C	ENST00000361445	NM_004958.3	2266	Cgc/Tgc	48/58	1	2	FACETS	0.667	0.6	0.739	0.667	0.6	0.739	SUBCLONAL	1	TRUE	1	0.478929960853984	2		580	682	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472522	88472522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55890138	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	112	633	1	ENST00000360948.2:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000360948	NM_001012338.2	678	cGa/cAa	16/19	1	2	FACETS	0.564	0.507	0.625	0.564	0.507	0.625	SUBCLONAL	1	TRUE	1	0.478929960853984	2		634	829	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572534	95572534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555370340	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	34	285	0	ENST00000393063.1:c.2831G>A	p.Arg944Gln	p.R944Q	ENST00000393063	NM_030621.3	944	cGa/cAa	19/28	1	2	FACETS	0.475	0.389	0.571	0.475	0.389	0.571	SUBCLONAL	1	TRUE	1	0.478929960853984	2		285	299	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199839	108199839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779861	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	42	238	1	ENST00000278616.4:c.7181C>T	p.Ser2394Leu	p.S2394L	ENST00000278616	NM_000051.3	2394	tCa/tTa	49/63	1	2	FACETS	0.581	0.487	0.684	0.581	0.487	0.684	SUBCLONAL	1	TRUE	1	0.478929960853984	2		239	302	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458525	120458525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369659944	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	140	683	0	ENST00000256646.2:c.6820C>T	p.Pro2274Ser	p.P2274S	ENST00000256646	NM_024408.3	2274	Cca/Tca	34/34	1	2	FACETS	0.766	0.698	0.837	0.766	0.698	0.837	SUBCLONAL	1	TRUE	1	0.478929960853984	2		683	763	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325367	1325367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750085547	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	74	523	0	ENST00000400841.2:c.308C>T	p.Thr103Met	p.T103M	ENST00000400841		103	aCg/aTg	3/6	1	2	FACETS	0.45	0.394	0.511	0.45	0.394	0.511	SUBCLONAL	1	TRUE	1	0.478929960853984	2		523	686	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273251	198273251	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	54	525	0	ENST00000335508.6:c.959G>A	p.Gly320Glu	p.G320E	ENST00000335508	NM_012433.2	320	gGa/gAa	8/25	1	2	FACETS	0.318	0.27	0.369	0.318	0.27	0.369	SUBCLONAL	1	TRUE	1	0.478929960853984	2		525	710	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863659	68863659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782162	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	130	622	0	ENST00000261769.5:c.2398C>T	p.Arg800Cys	p.R800C	ENST00000261769	NM_004360.3	800	Cgc/Tgc	15/16	1	2	FACETS	0.628	0.569	0.689	0.628	0.569	0.689	SUBCLONAL	1	TRUE	1	0.478929960853984	2		622	865	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132732	152132732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	98	282	0	ENST00000262189.6:c.140C>T	p.Pro47Leu	p.P47L	ENST00000262189	NM_170606.2	47	cCt/cTt	1/59	1	2	FACETS	0.865	0.776	0.96	0.865	0.776	0.96	CLONAL	1	TRUE	1	0.478929960853984	2		282	473	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182134	11182134	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	189	775	1	ENST00000361445.4:c.6712G>A	p.Gly2238Ser	p.G2238S	ENST00000361445	NM_004958.3	2238	Ggc/Agc	48/58	1	2	FACETS	0.758	0.7	0.819	0.758	0.7	0.819	SUBCLONAL	1	TRUE	1	0.478929960853984	2		776	1041	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307162	65307162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1295294134	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	77	398	0	ENST00000342505.4:c.2526G>A	p.Met842Ile	p.M842I	ENST00000342505	NM_002227.2	842	atG/atA	18/25	1	2	FACETS	0.659	0.58	0.743	0.659	0.58	0.743	SUBCLONAL	1	TRUE	1	0.478929960853984	2		398	488	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468238	120468238	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	123	748	0	ENST00000256646.2:c.4201C>T	p.Gln1401Ter	p.Q1401*	ENST00000256646	NM_024408.3	1401	Cag/Tag	25/34	1	2	FACETS	0.601	0.543	0.662	0.601	0.543	0.662	SUBCLONAL	1	TRUE	1	0.478929960853984	2		748	855	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841421	156841421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	82	518	0	ENST00000524377.1:c.724G>A	p.Gly242Arg	p.G242R	ENST00000524377	NM_002529.3	242	Ggg/Agg	7/17	1	2	FACETS	0.538	0.474	0.606	0.538	0.474	0.606	SUBCLONAL	1	TRUE	1	0.478929960853984	2		518	637	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333624	70333624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	76	508	0	ENST00000373644.4:c.1529C>T	p.Ala510Val	p.A510V	ENST00000373644	NM_030625.2	510	gCt/gTt	2/12	1	2	FACETS	0.583	0.512	0.66	0.583	0.512	0.66	SUBCLONAL	1	TRUE	1	0.478929960853984	2		508	544	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413568	32413568	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1421664466	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	90	446	0	ENST00000332351.3:c.1382C>T	p.Ser461Phe	p.S461F	ENST00000332351	NM_024426.4	461	tCc/tTc	9/10	1	2	FACETS	0.612	0.544	0.685	0.612	0.544	0.685	SUBCLONAL	1	TRUE	1	0.478929960853984	2		446	614	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121723	108121723	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	73	528	0	ENST00000278616.4:c.1531A>G	p.Ile511Val	p.I511V	ENST00000278616	NM_000051.3	511	Ata/Gta	10/63	1	2	FACETS	0.466	0.407	0.529	0.466	0.407	0.529	SUBCLONAL	1	TRUE	1	0.478929960853984	2		528	654	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446108	49446108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	154	861	1	ENST00000301067.7:c.1358C>T	p.Pro453Leu	p.P453L	ENST00000301067	NM_003482.3	453	cCt/cTt	10/54	1	2	FACETS	0.612	0.559	0.667	0.612	0.559	0.667	SUBCLONAL	1	TRUE	1	0.478929960853984	2		862	1051	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906487	32906487	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	44	349	0	ENST00000380152.3:c.872T>G	p.Leu291Arg	p.L291R	ENST00000380152		291	cTa/cGa	10/27	1	2	FACETS	0.4	0.336	0.472	0.4	0.336	0.472	SUBCLONAL	1	TRUE	1	0.478929960853984	2		349	459	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713292	43713292	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	179	1072	1	ENST00000382044.4:c.4181G>A	p.Gly1394Glu	p.G1394E	ENST00000382044	NM_001141980.1	1394	gGg/gAg	20/28	1	2	FACETS	0.644	0.593	0.698	0.644	0.593	0.698	SUBCLONAL	1	TRUE	1	0.478929960853984	2		1073	1160	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662336	67662336	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	102	556	0	ENST00000264010.4:c.1582T>C	p.Cys528Arg	p.C528R	ENST00000264010	NM_006565.3	528	Tgc/Cgc	9/12	1	2	FACETS	0.633	0.566	0.703	0.633	0.566	0.703	SUBCLONAL	1	TRUE	1	0.478929960853984	2		556	673	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357111	89357111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	147	730	0	ENST00000301030.4:c.523G>A	p.Ala175Thr	p.A175T	ENST00000301030	NM_001256183.1	175	Gcc/Acc	6/13	1	2	FACETS	0.627	0.572	0.685	0.627	0.572	0.685	SUBCLONAL	1	TRUE	1	0.478929960853984	2		730	979	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805349	89805349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs566927763	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	99	622	0	ENST00000389301.3:c.4201C>T	p.Leu1401Phe	p.L1401F	ENST00000389301	NM_000135.2	1401	Ctt/Ttt	42/43	1	2	FACETS	0.552	0.493	0.615	0.552	0.493	0.615	SUBCLONAL	1	TRUE	1	0.478929960853984	2		622	749	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882990	89882990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	32	132	2	ENST00000389301.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000389301	NM_000135.2	12	Ggc/Agc	1/43	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.478929960853984	NA		134	247	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577125	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	122	759	0	ENST00000269305.4:c.813_814delinsAA	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	271	gaGGtg/gaAAtg	8/11	1	2	FACETS	0.543	0.49	0.599	0.543	0.49	0.599	SUBCLONAL	1	TRUE	1	0.478929960853984	2		759	939	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075212	16075212	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	87	410	0	ENST00000268712.3:c.340G>A	p.Val114Ile	p.V114I	ENST00000268712	NM_006311.3	114	Gtt/Att	4/46	1	2	FACETS	0.655	0.581	0.733	0.655	0.581	0.733	SUBCLONAL	1	TRUE	1	0.478929960853984	2		410	555	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354218	15354218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1216396543	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	177	867	3	ENST00000263377.2:c.2662C>T	p.Pro888Ser	p.P888S	ENST00000263377	NM_058243.2	888	Cca/Tca	14/20	1	2	FACETS	0.642	0.59	0.696	0.642	0.59	0.696	SUBCLONAL	1	TRUE	1	0.478929960853984	2		870	1152	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741864	40741864	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	151	752	0	ENST00000392038.2:c.1108C>T	p.Pro370Ser	p.P370S	ENST00000392038	NM_001626.4	370	Ccg/Tcg	11/14	1	2	FACETS	0.724	0.662	0.789	0.724	0.662	0.789	SUBCLONAL	1	TRUE	1	0.478929960853984	2		752	871	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249738	39249738	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	49	386	0	ENST00000402219.2:c.1831G>A	p.Glu611Lys	p.E611K	ENST00000402219	NM_005633.3	611	Gag/Aag	10/23	1	2	FACETS	0.485	0.411	0.566	0.485	0.411	0.566	SUBCLONAL	1	TRUE	1	0.478929960853984	2		386	422	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920689	96920690	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	40	528	1	ENST00000258439.3:c.290_291delinsTT	p.Ala97Val	p.A97V	ENST00000258439	NM_001193304.2	97	gCC/gTT	3/4	1	2	FACETS	0.306	0.254	0.364	0.306	0.254	0.364	SUBCLONAL	1	TRUE	1	0.478929960853984	2		529	546	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634747	158634747	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1267861432	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	69	328	1	ENST00000263640.3:c.439C>T	p.Arg147Ter	p.R147*	ENST00000263640	NM_001105.4	147	Cga/Tga	5/11	1	2	FACETS	0.635	0.554	0.721	0.635	0.554	0.721	SUBCLONAL	1	TRUE	1	0.478929960853984	2		329	454	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031219	36031220	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	190	762	1	ENST00000358208.4:c.1338_1339delinsAA	p.Asp447Asn	p.D447N	ENST00000358208		446	tcGGac/tcAAac	11/12	1	2	FACETS	0.789	0.729	0.851	0.789	0.729	0.851	SUBCLONAL	1	TRUE	1	0.478929960853984	2		763	1006	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457806	149457806	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1561936512	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	96	518	0	ENST00000286301.3:c.598C>T	p.Pro200Ser	p.P200S	ENST00000286301	NM_005211.3	200	Cca/Tca	5/22	1	2	FACETS	0.754	0.673	0.838	0.754	0.673	0.838	SUBCLONAL	1	TRUE	1	0.478929960853984	2		518	532	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675928	30675928	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	134	769	0	ENST00000376406.3:c.2428G>T	p.Val810Leu	p.V810L	ENST00000376406	NM_014641.2	810	Gtg/Ttg	8/15	1	2	FACETS	0.546	0.495	0.6	0.546	0.495	0.6	SUBCLONAL	1	TRUE	1	0.478929960853984	2		769	1025	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165359	32165360	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	140	806	2	ENST00000375023.3:c.4768_4769delinsTT	p.Pro1590Phe	p.P1590F	ENST00000375023	NM_004557.3	1590	CCc/TTc	27/30	1	2	FACETS	0.574	0.522	0.629	0.574	0.522	0.629	SUBCLONAL	1	TRUE	1	0.478929960853984	2		808	1019	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974149	2974149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	138	643	0	ENST00000396946.4:c.1456G>A	p.Asp486Asn	p.D486N	ENST00000396946	NM_032415.4	486	Gac/Aac	10/25	1	2	FACETS	0.656	0.596	0.718	0.656	0.596	0.718	SUBCLONAL	1	TRUE	1	0.478929960853984	2		643	879	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752830	128752830	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs184271012	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	185	317	0	ENST00000377970.2:c.991C>T	p.Arg331Trp	p.R331W	ENST00000377970	NM_002467.4	331	Cgg/Tgg	3/3	0.478929960853984	3	FACETS	0.903	0.84	0.968	0.903	0.84	0.968	CLONAL	2	TRUE	1	0.478929960853984	3		317	530	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98244323	98244324	+	splice_acceptor_variant	Splice_Site	DNP	CT	CT	TA	novel	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	54	459	1	ENST00000331920.6:c.655-2_655-1delinsTA		p.X219_splice	ENST00000331920	NM_000264.3	219			1	2	FACETS	0.47	0.402	0.544	0.47	0.402	0.544	SUBCLONAL	1	TRUE	1	0.478929960853984	2		460	480	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397721	139397722	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	139	837	1	ENST00000277541.6:c.5079_5080delinsTT	p.Gln1694Ter	p.Q1694*	ENST00000277541	NM_017617.3	1693	ttCCag/ttTTag	27/34	1	2	FACETS	0.55	0.499	0.603	0.55	0.499	0.603	SUBCLONAL	1	TRUE	1	0.478929960853984	2		838	1056	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405681	139405682	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	218	1041	0	ENST00000277541.6:c.2509_2510delinsTT	p.Pro837Phe	p.P837F	ENST00000277541	NM_017617.3	837	CCc/TTc	16/34	1	2	FACETS	0.735	0.682	0.789	0.735	0.682	0.789	SUBCLONAL	1	TRUE	1	0.478929960853984	2		1041	1239	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405724	139405724	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	168	908	0	ENST00000277541.6:c.2468-1G>A		p.X823_splice	ENST00000277541	NM_017617.3	823			1	2	FACETS	0.659	0.605	0.716	0.659	0.605	0.716	SUBCLONAL	1	TRUE	1	0.478929960853984	2		908	1064	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793277	139793277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	168	819	0	ENST00000247668.2:c.85G>A	p.Glu29Lys	p.E29K	ENST00000247668	NM_021138.3	29	Gaa/Aaa	2/11	1	2	FACETS	0.723	0.664	0.785	0.723	0.664	0.785	SUBCLONAL	1	TRUE	1	0.478929960853984	2		819	970	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032582	47032583	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	136	730	1	ENST00000377604.3:c.488_489delinsAA	p.Arg163Gln	p.R163Q	ENST00000377604	NM_001204468.1	163	cGG/cAA	5/24	1	2	FACETS	0.582	0.528	0.638	0.582	0.528	0.638	SUBCLONAL	1	TRUE	1	0.478929960853984	2		731	976	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426402	47426402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	132	780	0	ENST00000377045.4:c.745G>A	p.Gly249Ser	p.G249S	ENST00000377045	NM_001654.4	249	Ggt/Agt	9/16	1	2	FACETS	0.652	0.592	0.716	0.652	0.592	0.716	SUBCLONAL	1	TRUE	1	0.478929960853984	2		780	845	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226156	53226157	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	137	718	1	ENST00000375401.3:c.2692_2693delinsTT	p.Pro898Leu	p.P898L	ENST00000375401	NM_004187.3	898	CCa/TTa	19/26	1	2	FACETS	0.669	0.608	0.733	0.669	0.608	0.733	SUBCLONAL	1	TRUE	1	0.478929960853984	2		719	855	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250029	53250029	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	113	677	0	ENST00000375401.3:c.220G>A	p.Glu74Lys	p.E74K	ENST00000375401	NM_004187.3	74	Gag/Aag	2/26	1	2	FACETS	0.555	0.498	0.614	0.555	0.498	0.614	SUBCLONAL	1	TRUE	1	0.478929960853984	2		677	851	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504138	123504138	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	54	477	0	ENST00000371139.4:c.314A>G	p.Lys105Arg	p.K105R	ENST00000371139	NM_001114937.2	105	aAg/aGg	3/4	1	2	FACETS	0.45	0.385	0.522	0.45	0.385	0.522	SUBCLONAL	1	TRUE	1	0.478929960853984	2		477	501	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0040523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	263	772	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.428714578320508	3	FACETS	1	0.985	1			1	CLONAL	2	TRUE	NA	0.694378725757233	3		772	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0040523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	9	721	0	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	0.428714578320508	3	FACETS	0.082	0.054	0.119			1	SUBCLONAL	1	TRUE	NA	0.694378725757233	3		721	425	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432664	29432664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113994087	NA	P-0040523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	8	720	1	ENST00000389048.3:c.3824G>A	p.Arg1275Gln	p.R1275Q	ENST00000389048	NM_004304.4	1275	cGa/cAa	25/29	0.694378725757233	1	FACETS	0.04	0.025	0.059	0.04	0.025	0.059	SUBCLONAL	1	TRUE	0	0.694378725757233	1		721	379	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791757	42791757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568504941	NA	P-0040523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	8	847	2	ENST00000575354.2:c.643C>T	p.Arg215Trp	p.R215W	ENST00000575354	NM_015125.3	215	Cgg/Tgg	5/20	0.287228774887547	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.694378725757233	0		849	305	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221726	22221726	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	11	78	0	ENST00000215832.6:c.5C>T	p.Ala2Val	p.A2V	ENST00000215832	NM_002745.4	2	gCg/gTg	1/9	0.411059950550311	1	FACETS	0.099	0.068	0.138	0.099	0.068	0.138	INDETERMINATE	1	TRUE	0	0.694378725757233	1		78	208	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336099	73336099	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	15	329	0	ENST00000377767.4:c.2304del	p.Ser769LeufsTer36	p.S769Lfs*36	ENST00000377767	NM_014953.3	768	gcG/gc	17/21	0.593571911884049	2	FACETS	0.758	0.572	0.966	0.379	0.286	0.483	CLONAL	1	TRUE	0	0.694378725757233	2		329	57	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158429	26158429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	70	900	1	ENST00000289316.2:c.32C>T	p.Pro11Leu	p.P11L	ENST00000289316	NM_138720.2	11	cCa/cTa	1/2	0.65308136374007	4	FACETS	0.484	0.421	0.552	0.121	0.105	0.138	SUBCLONAL	1	TRUE	0	0.694378725757233	4		901	706	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289314	33289314	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs779943557	NA	P-0040523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	51	581	2	ENST00000374542.5:c.238G>C	p.Asp80His	p.D80H	ENST00000374542	NM_001141970.1	80	Gac/Cac	3/8	0.432919558712919	4	FACETS	0.505	0.429	0.588	0.126	0.107	0.147	SUBCLONAL	1	TRUE	0	0.694378725757233	4		583	493	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273111	55273111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	39	824	0	ENST00000275493.2:c.3434C>T	p.Thr1145Ile	p.T1145I	ENST00000275493	NM_005228.3	1145	aCc/aTc	28/28	0.296411712862739	2	FACETS	0.351	0.292	0.417	0.176	0.146	0.209	INDETERMINATE	1	TRUE	0	0.694378725757233	2		824	320	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399471	139399471	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751810380	NA	P-0040523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	61	983	0	ENST00000277541.6:c.4672G>A	p.Gly1558Arg	p.G1558R	ENST00000277541	NM_017617.3	1558	Ggg/Agg	26/34	0.660900013655633	2	FACETS	0.166	0.142	0.192	0.083	0.071	0.096	SUBCLONAL	1	TRUE	0	0.694378725757233	2		983	1058	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	426	779	1	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.663209215852228	2		780	1202	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983275	149983275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	191	434	0	ENST00000253339.5:c.2983C>T	p.Arg995Cys	p.R995C	ENST00000253339		995	Cgc/Tgc	7/7	1	2	FACETS	0.911	0.847	0.978	0.911	0.847	0.978	CLONAL	1	TRUE	1	0.663209215852228	2		434	632	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509438	106509438	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748511834	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	251	530	0	ENST00000359195.3:c.1432G>A	p.Gly478Arg	p.G478R	ENST00000359195	NM_002649.2	478	Gga/Aga	2/11	1	2	FACETS	0.986	0.926	1	0.986	0.926	1	CLONAL	1	TRUE	1	0.663209215852228	2		530	768	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230691	46230691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424958105	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	144	320	0	ENST00000334344.6:c.940C>T	p.Arg314Cys	p.R314C	ENST00000334344	NM_152641.2	314	Cgt/Tgt	8/21	1	2	FACETS	0.963	0.886	1	0.963	0.886	1	CLONAL	1	TRUE	1	0.663209215852228	2		320	451	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601944	43601944	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1172318035	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	402	723	0	ENST00000355710.3:c.988C>T	p.Arg330Trp	p.R330W	ENST00000355710	NM_020975.4	330	Cgg/Tgg	5/20	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	1	TRUE	NA	0.663209215852228	2		723	1170	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406105	70406105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	218	492	0	ENST00000373644.4:c.3619C>T	p.Pro1207Ser	p.P1207S	ENST00000373644	NM_030625.2	1207	Cct/Tct	4/12	1	2	FACETS	0.942	0.88	1	0.942	0.88	1	CLONAL	1	TRUE	1	0.663209215852228	2		492	698	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196349	106196349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	102	259	1	ENST00000380013.4:c.4682C>T	p.Ser1561Phe	p.S1561F	ENST00000380013	NM_001127208.2	1561	tCt/tTt	11/11	1	2	FACETS	0.836	0.754	0.921	0.836	0.754	0.921	CLONAL	1	TRUE	1	0.663209215852228	2		260	368	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835741	68835741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567501376	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	236	589	1	ENST00000261769.5:c.332C>T	p.Ser111Phe	p.S111F	ENST00000261769	NM_004360.3	111	tCc/tTc	3/16	1	2	FACETS	0.884	0.827	0.942	0.884	0.827	0.942	CLONAL	1	TRUE	1	0.663209215852228	2		590	805	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117707020	117707020	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	134	378	0	ENST00000368508.3:c.2130G>A	p.Met710Ile	p.M710I	ENST00000368508	NM_002944.2	710	atG/atA	15/43	NA	2	FACETS	0.825	0.754	0.898			1	INDETERMINATE	1	TRUE	NA	0.663209215852228	2		378	490	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831350	89831350	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	279	501	0	ENST00000389301.3:c.2726C>T	p.Ser909Phe	p.S909F	ENST00000389301	NM_000135.2	909	tCt/tTt	28/43	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.663209215852228	2		501	823	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231707	66231707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1211795184	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	90	350	1	ENST00000273854.3:c.1993G>A	p.Glu665Lys	p.E665K	ENST00000273854	NM_004439.5	665	Gaa/Aaa	11/18	1	2	FACETS	0.848	0.76	0.94	0.848	0.76	0.94	CLONAL	1	TRUE	1	0.663209215852228	2		351	320	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811741	102811741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769928521	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	257	490	0	ENST00000307046.8:c.443G>A	p.Arg148Lys	p.R148K	ENST00000307046	NM_001111285.1	148	aGa/aAa	4/4	1	2	FACETS	0.99	0.93	1	0.99	0.93	1	CLONAL	1	TRUE	1	0.663209215852228	2		490	783	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	761	462	1				ENST00000310581	NM_198253.2	-/1132			0.663209215852228	6	FACETS	1	0.995	1	1	0.995	1	CLONAL	5	TRUE	1	0.663209215852228	6		463	1013	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554204	63554204	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	221	513	0	ENST00000307078.5:c.535C>T	p.Gln179Ter	p.Q179*	ENST00000307078	NM_004655.3	179	Cag/Tag	2/11	1	2	FACETS	0.85	0.793	0.908	0.85	0.793	0.908	CLONAL	1	TRUE	1	0.663209215852228	2		513	784	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	262	576	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.6177494979224	1	FACETS	0.906	0.857	0.955	0.906	0.857	0.955	CLONAL	1	TRUE	0	0.663209215852228	1		577	583	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920503	134920503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	224	534	0	ENST00000398015.3:c.2318C>T	p.Thr773Ile	p.T773I	ENST00000398015	NM_004441.4	773	aCc/aTc	12/16	1	2	FACETS	0.925	0.865	0.987	0.925	0.865	0.987	CLONAL	1	TRUE	1	0.663209215852228	2		534	730	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609994	81609994	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750198847	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	135	256	2	ENST00000298171.2:c.1592G>A	p.Arg531Gln	p.R531Q	ENST00000298171	NM_000369.2	531	cGg/cAg	10/10	1	2	FACETS	0.962	0.883	1	0.962	0.883	1	CLONAL	1	TRUE	1	0.663209215852228	2		258	423	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892164	9892164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776791010	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	215	421	0	ENST00000330684.3:c.2326G>A	p.Asp776Asn	p.D776N	ENST00000330684	NM_001134407.1	776	Gac/Aac	11/13	1	2	FACETS	0.933	0.871	0.996	0.933	0.871	0.996	CLONAL	1	TRUE	1	0.663209215852228	2		421	695	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259493	89259493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1293200426	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	181	338	0	ENST00000336596.2:c.637C>T	p.Pro213Ser	p.P213S	ENST00000336596	NM_005233.5	213	Cca/Tca	3/17	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.663209215852228	2		338	541	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133761036	133761036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1456042173	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	316	594	3	ENST00000318560.5:c.3359C>T	p.Ser1120Leu	p.S1120L	ENST00000318560	NM_005157.4	1120	tCg/tTg	11/11	0.663209215852228	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.663209215852228	1		597	604	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735422	204735422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	159	328	0	ENST00000302823.3:c.223C>T	p.Arg75Trp	p.R75W	ENST00000302823	NM_005214.4	75	Cgg/Tgg	2/4	0.6177494979224	1	FACETS	0.9	0.838	0.963	0.9	0.838	0.963	CLONAL	1	TRUE	0	0.663209215852228	1		328	356	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818714	170818714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	174	352	0	ENST00000296930.5:c.263C>T	p.Ser88Phe	p.S88F	ENST00000296930	NM_002520.6	88	tCc/tTc	4/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.663209215852228	2		352	499	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713514	30713514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	212	417	0	ENST00000295754.5:c.839C>T	p.Pro280Leu	p.P280L	ENST00000295754	NM_003242.5	280	cCc/cTc	4/7	1	2	FACETS	0.95	0.887	1	0.95	0.887	1	CLONAL	1	TRUE	1	0.663209215852228	2		417	673	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830919	72830919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	205	461	0	ENST00000268489.5:c.5662G>A	p.Glu1888Lys	p.E1888K	ENST00000268489	NM_006885.3	1888	Gaa/Aaa	9/10	1	2	FACETS	0.983	0.917	1	0.983	0.917	1	CLONAL	1	TRUE	1	0.663209215852228	2		461	629	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131787	2131787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1020561347	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	282	546	0	ENST00000219476.3:c.3802C>T	p.Arg1268Cys	p.R1268C	ENST00000219476	NM_000548.3	1268	Cgc/Tgc	31/42	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.663209215852228	2		546	850	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066618	94066618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	166	374	0	ENST00000369303.4:c.1141C>T	p.Pro381Ser	p.P381S	ENST00000369303	NM_004440.3	381	Ccc/Tcc	5/17	1	2	FACETS	0.902	0.834	0.972	0.902	0.834	0.972	CLONAL	1	TRUE	1	0.663209215852228	2		374	555	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741578	145741578	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554902528	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	402	801	1	ENST00000428558.2:c.925C>T	p.Gln309Ter	p.Q309*	ENST00000428558	NM_004260.3	309	Cag/Tag	5/22	1	2	FACETS	0.978	0.93	1	0.978	0.93	1	CLONAL	1	TRUE	1	0.663209215852228	2		802	1240	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362506	40362506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561888537	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	224	441	1	ENST00000293328.3:c.1690C>T	p.Pro564Ser	p.P564S	ENST00000293328	NM_012448.3	564	Cca/Tca	14/19	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.663209215852228	2		442	644	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156523	55156523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	192	401	0	ENST00000257290.5:c.2924C>T	p.Pro975Leu	p.P975L	ENST00000257290	NM_006206.4	975	cCt/cTt	22/23	1	2	FACETS	0.975	0.907	1	0.975	0.907	1	CLONAL	1	TRUE	1	0.663209215852228	2		401	594	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163802	152163802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	174	398	1	ENST00000206249.3:c.523G>A	p.Ala175Thr	p.A175T	ENST00000206249	NM_000125.3	175	Gct/Act	2/8	1	2	FACETS	0.906	0.839	0.975	0.906	0.839	0.975	CLONAL	1	TRUE	1	0.663209215852228	2		399	579	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068396	16068396	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150910818	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	10	41	0	ENST00000268712.3:c.515C>T	p.Ser172Leu	p.S172L	ENST00000268712	NM_006311.3	172	tCa/tTa	5/46	0.6177494979224	1	FACETS	0.325	0.224	0.446	0.325	0.224	0.446	SUBCLONAL	1	TRUE	0	0.663209215852228	1		41	62	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212114	36212114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	303	514	0	ENST00000222270.7:c.1865C>T	p.Pro622Leu	p.P622L	ENST00000222270	NM_014727.1	622	cCc/cTc	3/37	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.663209215852228	2		514	840	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164709	36164709	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1350744261	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	351	620	0	ENST00000300305.3:c.1166C>T	p.Ser389Leu	p.S389L	ENST00000300305		389	tCg/tTg	8/8	1	2	FACETS	0.996	0.945	1	0.996	0.945	1	CLONAL	1	TRUE	1	0.663209215852228	2		620	1063	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121525	108121525	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	199	338	0	ENST00000278616.4:c.1333C>T	p.Gln445Ter	p.Q445*	ENST00000278616	NM_000051.3	445	Caa/Taa	10/63	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.663209215852228	2		338	571	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932976	49932976	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	273	559	0	ENST00000296474.3:c.2968C>T	p.Pro990Ser	p.P990S	ENST00000296474	NM_002447.2	990	Cct/Tct	13/20	1	2	FACETS	0.986	0.928	1	0.986	0.928	1	CLONAL	1	TRUE	1	0.663209215852228	2		559	835	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741825	17741825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs548800810	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	122	226	0	ENST00000250003.3:c.496G>A	p.Asp166Asn	p.D166N	ENST00000250003	NM_002478.4	166	Gac/Aac	1/3	1	2	FACETS	0.997	0.911	1	0.997	0.911	1	CLONAL	1	TRUE	1	0.663209215852228	2		226	369	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412118	63412118	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	346	391	0	ENST00000330258.3:c.1049G>A	p.Arg350Lys	p.R350K	ENST00000330258	NM_152424.3	350	aGa/aAa	2/2	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.663209215852228	1		391	517	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068441	16068441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	33	71	0	ENST00000268712.3:c.470C>T	p.Ser157Phe	p.S157F	ENST00000268712	NM_006311.3	157	tCc/tTc	5/46	0.6177494979224	1	FACETS	0.554	0.461	0.655	0.554	0.461	0.655	SUBCLONAL	1	TRUE	0	0.663209215852228	1		71	120	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606651	29606651	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760717114	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	228	459	0	ENST00000389048.3:c.1229G>A	p.Gly410Glu	p.G410E	ENST00000389048	NM_004304.4	410	gGa/gAa	5/29	1	2	FACETS	0.96	0.899	1	0.96	0.899	1	CLONAL	1	TRUE	1	0.663209215852228	2		459	716	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436643	49436643	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	290	508	0	ENST00000301067.7:c.5663C>T	p.Ser1888Phe	p.S1888F	ENST00000301067	NM_003482.3	1888	tCc/tTc	26/54	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.663209215852228	2		508	855	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182068	11182068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	218	505	0	ENST00000361445.4:c.6778C>T	p.Leu2260Phe	p.L2260F	ENST00000361445	NM_004958.3	2260	Ctt/Ttt	48/58	1	2	FACETS	0.942	0.88	1	0.942	0.88	1	CLONAL	1	TRUE	1	0.663209215852228	2		505	698	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62009599	62009599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	321	632	0	ENST00000392795.3:c.23C>T	p.Pro8Leu	p.P8L	ENST00000392795	NM_001039933.1	8	cCt/cTt	1/6	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.663209215852228	2		632	950	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124474	94124474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	82	309	0	ENST00000369303.4:c.109G>A	p.Asp37Asn	p.D37N	ENST00000369303	NM_004440.3	37	Gat/Aat	2/17	1	2	FACETS	0.85	0.758	0.946	0.85	0.758	0.946	CLONAL	1	TRUE	1	0.663209215852228	2		309	291	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775598	9775598	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	206	462	0	ENST00000377346.4:c.142-1G>A		p.X48_splice	ENST00000377346	NM_005026.3	48			1	2	FACETS	0.943	0.879	1	0.943	0.879	1	CLONAL	1	TRUE	1	0.663209215852228	2		462	659	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932884	36932884	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	308	633	1	ENST00000361632.4:c.1987C>T	p.Pro663Ser	p.P663S	ENST00000361632		663	Cca/Tca	15/16	1	2	FACETS	0.902	0.851	0.953	0.902	0.851	0.953	CLONAL	1	TRUE	1	0.663209215852228	2		634	1030	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166644	118166644	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	120	234	0	ENST00000369448.3:c.1154C>T	p.Pro385Leu	p.P385L	ENST00000369448	NM_017709.3	385	cCt/cTt	2/2	1	2	FACETS	0.935	0.853	1	0.935	0.853	1	CLONAL	1	TRUE	1	0.663209215852228	2		234	387	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551793	150551793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	50	74	0	ENST00000369026.2:c.214G>A	p.Asp72Asn	p.D72N	ENST00000369026	NM_021960.4	72	Gac/Aac	1/3	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.663209215852228	2		74	133	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740131	162740131	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	185	423	1	ENST00000367921.3:c.1333C>T	p.Leu445Phe	p.L445F	ENST00000367921	NM_006182.2	445	Ctt/Ttt	12/18	1	2	FACETS	0.957	0.889	1	0.957	0.889	1	CLONAL	1	TRUE	1	0.663209215852228	2		424	583	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163295959	163295959	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	151	405	0	ENST00000271452.3:c.118C>T	p.Pro40Ser	p.P40S	ENST00000271452	NM_145697.2	40	Cca/Tca	2/14	1	2	FACETS	0.953	0.878	1	0.953	0.878	1	CLONAL	1	TRUE	1	0.663209215852228	2		405	478	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716236	243716236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	138	377	0	ENST00000263826.5:c.958G>A	p.Asp320Asn	p.D320N	ENST00000263826	NM_005465.4	320	Gat/Aat	10/13	1	2	FACETS	0.986	0.906	1	0.986	0.906	1	CLONAL	1	TRUE	1	0.663209215852228	2		377	422	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243801011	243801011	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	102	333	0	ENST00000263826.5:c.463G>A	p.Gly155Ser	p.G155S	ENST00000263826	NM_005465.4	155	Ggt/Agt	5/13	1	2	FACETS	0.85	0.767	0.936	0.85	0.767	0.936	CLONAL	1	TRUE	1	0.663209215852228	2		333	362	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132791	64132791	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	275	559	0	ENST00000334205.4:c.925C>A	p.Leu309Met	p.L309M	ENST00000334205	NM_003942.2	309	Ctg/Atg	9/17	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.663209215852228	2		559	812	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939813	71939814	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	322	732	1	ENST00000298229.2:c.440_441delinsTT	p.Ser147Phe	p.S147F	ENST00000298229	NM_001567.3	147	tCC/tTT	4/28	1	2	FACETS	0.892	0.843	0.942	0.892	0.843	0.942	CLONAL	1	TRUE	1	0.663209215852228	2		733	1089	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962563	100962563	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	174	407	0	ENST00000325455.5:c.1834G>A	p.Asp612Asn	p.D612N	ENST00000325455	NM_001202474.3	612	Gat/Aat	3/8	1	2	FACETS	0.917	0.85	0.987	0.917	0.85	0.987	CLONAL	1	TRUE	1	0.663209215852228	2		407	572	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343883	118343883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	175	328	0	ENST00000534358.1:c.2009C>T	p.Ser670Phe	p.S670F	ENST00000534358	NM_005933.3	670	tCt/tTt	3/36	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.663209215852228	2		328	508	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037443	12037444	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	224	426	1	ENST00000396373.4:c.1074_1075delinsTT	p.Arg359Ter	p.R359*	ENST00000396373	NM_001987.4	358	atCCga/atTTga	6/8	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.663209215852228	2		427	675	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945094	31945094	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771332167	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	254	577	4	ENST00000340398.3:c.7C>T	p.Arg3Ter	p.R3*	ENST00000340398	NM_001013699.2	3	Cga/Tga	1/1	1	2	FACETS	0.933	0.876	0.991	0.933	0.876	0.991	CLONAL	1	TRUE	1	0.663209215852228	2		581	821	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427471	49427471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	290	681	1	ENST00000301067.7:c.11017C>T	p.Leu3673Phe	p.L3673F	ENST00000301067	NM_003482.3	3673	Ctt/Ttt	39/54	1	2	FACETS	0.87	0.82	0.922	0.87	0.82	0.922	CLONAL	1	TRUE	1	0.663209215852228	2		682	1005	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865840	57865840	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	157	399	0	ENST00000228682.2:c.3317C>T	p.Ala1106Val	p.A1106V	ENST00000228682	NM_005269.2	1106	gCc/gTc	12/12	1	2	FACETS	0.853	0.786	0.923	0.853	0.786	0.923	CLONAL	1	TRUE	1	0.663209215852228	2		399	555	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856350	111856350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762113777	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	42	54	1	ENST00000341259.2:c.401C>T	p.Ser134Phe	p.S134F	ENST00000341259	NM_005475.2	134	tCc/tTc	2/8	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.663209215852228	2		55	120	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112892448	112892448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	165	385	0	ENST00000351677.2:c.606G>A	p.Met202Ile	p.M202I	ENST00000351677	NM_002834.3	202	atG/atA	5/16	1	2	FACETS	0.873	0.806	0.942	0.873	0.806	0.942	CLONAL	1	TRUE	1	0.663209215852228	2		385	570	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202713	133202713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555301177	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	212	458	0	ENST00000320574.5:c.6521C>T	p.Ser2174Phe	p.S2174F	ENST00000320574	NM_006231.2	2174	tCc/tTc	46/49	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.663209215852228	2		458	621	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557441	21557441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	218	442	0	ENST00000382592.4:c.2404G>A	p.Asp802Asn	p.D802N	ENST00000382592	NM_014572.2	802	Gat/Aat	5/8	1	2	FACETS	0.965	0.902	1	0.965	0.902	1	CLONAL	1	TRUE	1	0.663209215852228	2		442	681	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28908188	28908188	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770523274	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	165	359	0	ENST00000282397.4:c.2567G>A	p.Arg856Gln	p.R856Q	ENST00000282397	NM_002019.4	856	cGg/cAg	18/30	1	2	FACETS	0.865	0.799	0.934	0.865	0.799	0.934	CLONAL	1	TRUE	1	0.663209215852228	2		359	575	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281893	49281893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	229	488	0	ENST00000282018.3:c.940G>A	p.Asp314Asn	p.D314N	ENST00000282018	NM_020377.2	314	Gac/Aac	1/1	1	2	FACETS	0.933	0.873	0.995	0.933	0.873	0.995	CLONAL	1	TRUE	1	0.663209215852228	2		488	740	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337646	73337646	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	87	162	0	ENST00000377767.4:c.2070del	p.Lys690AsnfsTer47	p.K690Nfs*47	ENST00000377767	NM_014953.3	690	aaA/aa	16/21	1	2	FACETS	0.961	0.862	1	0.961	0.862	1	CLONAL	1	TRUE	1	0.663209215852228	2		162	273	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643441	38643441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	207	419	0	ENST00000299084.4:c.911C>T	p.Ser304Leu	p.S304L	ENST00000299084	NM_152594.2	304	tCa/tTa	7/7	1	2	FACETS	0.896	0.834	0.958	0.896	0.834	0.958	CLONAL	1	TRUE	1	0.663209215852228	2		419	697	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041728	42041728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	170	318	0	ENST00000219905.7:c.5923C>T	p.Pro1975Ser	p.P1975S	ENST00000219905	NM_001164273.1	1975	Cca/Tca	17/24	1	2	FACETS	0.988	0.915	1	0.988	0.915	1	CLONAL	1	TRUE	1	0.663209215852228	2		318	519	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669502	88669502	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	184	352	0	ENST00000360948.2:c.1396G>A	p.Gly466Ser	p.G466S	ENST00000360948	NM_001012338.2	466	Ggt/Agt	12/19	1	2	FACETS	0.931	0.864	1	0.931	0.864	1	CLONAL	1	TRUE	1	0.663209215852228	2		352	596	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639279	3639279	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	308	730	0	ENST00000294008.3:c.4360C>T	p.Pro1454Ser	p.P1454S	ENST00000294008	NM_032444.2	1454	Ccc/Tcc	12/15	1	2	FACETS	0.94	0.888	0.993	0.94	0.888	0.993	CLONAL	1	TRUE	1	0.663209215852228	2		730	988	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801806	3801806	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	168	345	0	ENST00000262367.5:c.3700T>A	p.Tyr1234Asn	p.Y1234N	ENST00000262367	NM_004380.2	1234	Tat/Aat	20/31	1	2	FACETS	0.938	0.868	1	0.938	0.868	1	CLONAL	1	TRUE	1	0.663209215852228	2		345	540	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823810	3823810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	218	566	1	ENST00000262367.5:c.2405C>T	p.Ser802Phe	p.S802F	ENST00000262367	NM_004380.2	802	tCc/tTc	13/31	1	2	FACETS	0.865	0.807	0.925	0.865	0.807	0.925	CLONAL	1	TRUE	1	0.663209215852228	2		567	760	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943649	9943649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	272	640	0	ENST00000330684.3:c.1292G>A	p.Arg431Lys	p.R431K	ENST00000330684	NM_001134407.1	431	aGg/aAg	5/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.663209215852228	2		640	776	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641514	23641514	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	201	511	0	ENST00000261584.4:c.1961T>A	p.Ile654Asn	p.I654N	ENST00000261584	NM_024675.3	654	aTt/aAt	5/13	1	2	FACETS	0.861	0.801	0.923	0.861	0.801	0.923	CLONAL	1	TRUE	1	0.663209215852228	2		511	704	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644847	67644847	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	235	500	0	ENST00000264010.4:c.112T>C	p.Cys38Arg	p.C38R	ENST00000264010	NM_006565.3	38	Tgc/Cgc	3/12	1	2	FACETS	0.983	0.921	1	0.983	0.921	1	CLONAL	1	TRUE	1	0.663209215852228	2		500	721	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89846364	89846364	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	232	519	0	ENST00000389301.3:c.1628C>T	p.Pro543Leu	p.P543L	ENST00000389301	NM_000135.2	543	cCc/cTc	18/43	1	2	FACETS	0.949	0.889	1	0.949	0.889	1	CLONAL	1	TRUE	1	0.663209215852228	2		519	737	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559894	29559894	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	109	195	0	ENST00000356175.3:c.3491C>T	p.Ser1164Phe	p.S1164F	ENST00000356175	NM_000267.3	1164	tCc/tTc	26/57	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.663209215852228	2		195	327	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441463	40441464	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	245	639	0	ENST00000345506.4:c.34_35delinsAA	p.Gly12Lys	p.G12K	ENST00000345506	NM_003152.3	12	GGa/AAa	3/20	1	2	FACETS	0.924	0.866	0.983	0.924	0.866	0.983	CLONAL	1	TRUE	1	0.663209215852228	2		639	800	SUCCESS
YES1	7525	MSKCC	GRCh37	18	742996	742996	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	190	389	0	ENST00000314574.4:c.982A>G	p.Arg328Gly	p.R328G	ENST00000314574	NM_005433.3	328	Aga/Gga	8/12	1	2	FACETS	0.936	0.87	1	0.936	0.87	1	CLONAL	1	TRUE	1	0.663209215852228	2		389	612	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10267073	10267073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	138	350	0	ENST00000340748.4:c.1345C>T	p.Leu449Phe	p.L449F	ENST00000340748		449	Ctt/Ttt	17/40	1	2	FACETS	0.858	0.786	0.932	0.858	0.786	0.932	CLONAL	1	TRUE	1	0.663209215852228	2		350	485	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098437	11098437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555755005	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	174	343	0	ENST00000358026.2:c.955C>T	p.Pro319Ser	p.P319S	ENST00000358026	NM_001128849.1	319	Cca/Tca	6/36	1	2	FACETS	0.986	0.915	1	0.986	0.915	1	CLONAL	1	TRUE	1	0.663209215852228	2		343	532	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302436	15302436	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	400	738	0	ENST00000263388.2:c.835C>T	p.Gln279Ter	p.Q279*	ENST00000263388	NM_000435.2	279	Cag/Tag	6/33	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.663209215852228	2		738	1136	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350014	15350015	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	375	871	0	ENST00000263377.2:c.3637_3638delinsTT	p.Pro1213Phe	p.P1213F	ENST00000263377	NM_058243.2	1213	CCc/TTc	18/20	1	2	FACETS	0.916	0.87	0.964	0.916	0.87	0.964	CLONAL	1	TRUE	1	0.663209215852228	2		871	1234	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727878	41727878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	361	707	0	ENST00000301178.4:c.503C>T	p.Pro168Leu	p.P168L	ENST00000301178	NM_021913.4	168	cCc/cTc	4/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.663209215852228	2		707	1083	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383095	42383095	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555843453	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	209	544	0	ENST00000221972.3:c.115C>T	p.Pro39Ser	p.P39S	ENST00000221972	NM_021601.3	39	Cca/Tca	2/5	1	2	FACETS	0.9	0.839	0.963	0.9	0.839	0.963	CLONAL	1	TRUE	1	0.663209215852228	2		544	700	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753199	42753200	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	330	721	0	ENST00000222329.4:c.1064_1065delinsTT	p.Pro355Leu	p.P355L	ENST00000222329	NM_006494.2	355	cCC/cTT	4/4	1	2	FACETS	0.93	0.88	0.981	0.93	0.88	0.981	CLONAL	1	TRUE	1	0.663209215852228	2		721	1070	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470970	25470970	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	371	636	0	ENST00000264709.3:c.791C>T	p.Pro264Leu	p.P264L	ENST00000264709	NM_175629.2	264	cCc/cTc	7/23	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.663209215852228	2		636	1029	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578324	212578325	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	101	361	2	ENST00000342788.4:c.932_933delinsTT	p.Ser311Phe	p.S311F	ENST00000342788	NM_005235.2	311	tCC/tTT	8/28	0.6177494979224	1	FACETS	0.838	0.763	0.914	0.838	0.763	0.914	CLONAL	1	TRUE	0	0.663209215852228	1		363	243	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587234	212587234	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	124	329	0	ENST00000342788.4:c.767G>T	p.Gly256Val	p.G256V	ENST00000342788	NM_005235.2	256	gGa/gTa	7/28	0.6177494979224	1	FACETS	0.95	0.877	1	0.95	0.877	1	CLONAL	1	TRUE	0	0.663209215852228	1		329	263	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419971	41419971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	261	514	1	ENST00000373198.4:c.350C>T	p.Pro117Leu	p.P117L	ENST00000373198	NM_133170.3	117	cCa/cTa	3/32	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.663209215852228	2		515	783	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485395	57485395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	142	235	0	ENST00000371085.3:c.977C>T	p.Pro326Leu	p.P326L	ENST00000371085	NM_000516.4	326	cCc/cTc	12/13	1	2	FACETS	0.984	0.905	1	0.984	0.905	1	CLONAL	1	TRUE	1	0.663209215852228	2		235	435	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144872	47144872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	175	386	0	ENST00000409792.3:c.4881G>A	p.Met1627Ile	p.M1627I	ENST00000409792	NM_014159.6	1627	atG/atA	7/21	1	2	FACETS	0.954	0.885	1	0.954	0.885	1	CLONAL	1	TRUE	1	0.663209215852228	2		386	553	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163317	47163317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781674299	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	153	300	0	ENST00000409792.3:c.2809C>T	p.Pro937Ser	p.P937S	ENST00000409792	NM_014159.6	937	Cct/Tct	3/21	1	2	FACETS	0.942	0.868	1	0.942	0.868	1	CLONAL	1	TRUE	1	0.663209215852228	2		300	490	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72897392	72897392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	225	435	0	ENST00000325599.8:c.100G>A	p.Glu34Lys	p.E34K	ENST00000325599	NM_018130.2	34	Gag/Aag	1/11	1	2	FACETS	0.965	0.903	1	0.965	0.903	1	CLONAL	1	TRUE	1	0.663209215852228	2		435	703	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582349	119582349	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	174	261	0	ENST00000316626.5:c.1052C>T	p.Ser351Leu	p.S351L	ENST00000316626		351	tCa/tTa	10/12	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.663209215852228	2		261	508	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825364	134825364	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1423406836	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	184	423	0	ENST00000398015.3:c.880C>T	p.Pro294Ser	p.P294S	ENST00000398015	NM_004441.4	294	Cct/Tct	4/16	1	2	FACETS	0.823	0.763	0.886	0.823	0.763	0.886	CLONAL	1	TRUE	1	0.663209215852228	2		423	674	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805521	1805521	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1315257038	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	336	697	0	ENST00000260795.2:c.1033A>G	p.Ile345Val	p.I345V	ENST00000260795		345	Att/Gtt	7/17	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.663209215852228	2		697	1002	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094828	143094828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	150	302	0	ENST00000262992.4:c.1316C>T	p.Ser439Phe	p.S439F	ENST00000262992	NM_001101669.1	439	tCt/tTt	14/24	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.663209215852228	2		302	441	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295304	1295304	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1185	169	362	2				ENST00000310581	NM_198253.2	-/1132			0.663209215852228	6	FACETS	0.876	0.803	0.952	0.175	0.16	0.191	CLONAL	1	TRUE	1	0.663209215852228	6		364	1354	SUCCESS
APC	324	MSKCC	GRCh37	5	112173339	112173339	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	99	268	0	ENST00000257430.4:c.2048C>A	p.Thr683Asn	p.T683N	ENST00000257430	NM_000038.5	683	aCt/aAt	16/16	1	2	FACETS	0.939	0.848	1	0.939	0.848	1	CLONAL	1	TRUE	1	0.663209215852228	2		268	318	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149447826	149447826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	258	625	2	ENST00000286301.3:c.1578G>A	p.Met526Ile	p.M526I	ENST00000286301	NM_005211.3	526	atG/atA	11/22	1	2	FACETS	0.893	0.839	0.949	0.893	0.839	0.949	CLONAL	1	TRUE	1	0.663209215852228	2		627	871	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163338	32163338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	446	839	0	ENST00000375023.3:c.5888C>T	p.Ser1963Phe	p.S1963F	ENST00000375023	NM_004557.3	1963	tCc/tTc	30/30	1	2	FACETS	0.991	0.946	1	0.991	0.946	1	CLONAL	1	TRUE	1	0.663209215852228	2		839	1357	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163449	32163449	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	343	652	0	ENST00000375023.3:c.5777A>G	p.Asn1926Ser	p.N1926S	ENST00000375023	NM_004557.3	1926	aAc/aGc	30/30	1	2	FACETS	0.975	0.924	1	0.975	0.924	1	CLONAL	1	TRUE	1	0.663209215852228	2		652	1061	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120579	94120579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	153	301	0	ENST00000369303.4:c.472G>A	p.Gly158Ser	p.G158S	ENST00000369303	NM_004440.3	158	Ggt/Agt	3/17	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.663209215852228	2		301	423	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001379	150001379	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	196	427	0	ENST00000253339.5:c.2225T>G	p.Leu742Arg	p.L742R	ENST00000253339		742	cTt/cGt	4/7	1	2	FACETS	0.998	0.93	1	0.998	0.93	1	CLONAL	1	TRUE	1	0.663209215852228	2		427	592	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528450	157528450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	252	522	1	ENST00000346085.5:c.6175C>T	p.Pro2059Ser	p.P2059S	ENST00000346085	NM_020732.3	2059	Ccg/Tcg	20/20	1	2	FACETS	0.966	0.907	1	0.966	0.907	1	CLONAL	1	TRUE	1	0.663209215852228	2		523	787	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128848632	128848632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	319	703	0	ENST00000249373.3:c.1297C>T	p.His433Tyr	p.H433Y	ENST00000249373	NM_005631.4	433	Cac/Tac	7/12	1	2	FACETS	0.973	0.92	1	0.973	0.92	1	CLONAL	1	TRUE	1	0.663209215852228	2		703	989	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492910	8492910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767627241	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	203	434	0	ENST00000356435.5:c.2419G>A	p.Gly807Arg	p.G807R	ENST00000356435		807	Gga/Aga	16/35	0.663209215852228	1	FACETS	0.949	0.892	1	0.949	0.892	1	CLONAL	1	TRUE	0	0.663209215852228	1		434	431	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238318	98238319	+	stop_gained,splice_region_variant	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	194	345	0	ENST00000331920.6:c.1725_1726delinsTT	p.Gln576Ter	p.Q576*	ENST00000331920	NM_000264.3	575	ctCCag/ctTTag	12/24	0.663209215852228	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.663209215852228	1		345	363	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904961	101904961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	129	254	0	ENST00000374994.4:c.949C>T	p.His317Tyr	p.H317Y	ENST00000374994	NM_004612.2	317	Cac/Tac	5/9	0.663209215852228	1	FACETS	0.952	0.881	1	0.952	0.881	1	CLONAL	1	TRUE	0	0.663209215852228	1		254	273	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939186	76939187	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	183	276	0	ENST00000373344.5:c.1561_1562delinsTT	p.Pro521Phe	p.P521F	ENST00000373344	NM_000489.3	521	CCt/TTt	9/35	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.663209215852228	1		276	305	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199975	128199976	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	A	novel	NA	P-0040867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	312	610	0	ENST00000341105.2:c.1329_1330delinsT	p.Pro444ArgfsTer33	p.P444Rfs*33	ENST00000341105	NM_032638.4	443	ctCCcg/ctTcg	6/6	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.663209215852228	2		610	931	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097101	11097101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1195533596	NA	P-0041060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	56	762	1	ENST00000358026.2:c.592G>A	p.Asp198Asn	p.D198N	ENST00000358026	NM_001128849.1	198	Gac/Aac	4/36	0.485589731524554	1	FACETS	0.257	0.219	0.298	0.257	0.219	0.298	SUBCLONAL	1	TRUE	0	0.485589731524554	1		763	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0041060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	369	515	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.485589731524554	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.485589731524554	2		515	712	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313222	30313222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	52	546	0	ENST00000262643.3:c.916C>T	p.His306Tyr	p.H306Y	ENST00000262643	NM_001238.2	306	Cat/Tat	10/12	1	2	FACETS	0.376	0.319	0.437	0.376	0.319	0.437	SUBCLONAL	1	TRUE	1	0.485589731524554	2		546	570	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858370	9858370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760522909	NA	P-0041060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	55	435	0	ENST00000330684.3:c.3031C>T	p.Arg1011Trp	p.R1011W	ENST00000330684	NM_001134407.1	1011	Cgg/Tgg	13/13	0.246445946353718	1	FACETS	0.449	0.385	0.518	0.449	0.385	0.518	INDETERMINATE	1	TRUE	0	0.485589731524554	1		435	382	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932055	36932055	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	155	629	0	ENST00000361632.4:c.2414del	p.Pro805GlnfsTer45	p.P805Qfs*45	ENST00000361632		805	cCa/ca	16/16	1	2	FACETS	0.895	0.821	0.972	0.895	0.821	0.972	CLONAL	1	TRUE	1	0.485589731524554	2		629	713	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804989	43804989	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	80	411	0	ENST00000372470.3:c.439C>G	p.Pro147Ala	p.P147A	ENST00000372470	NM_005373.2	147	Cca/Gca	4/12	1	2	FACETS	0.703	0.621	0.79	0.703	0.621	0.79	SUBCLONAL	1	TRUE	1	0.485589731524554	2		411	469	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117746745	117746746	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	113	325	0	ENST00000368508.3:c.74dup	p.Gln26AlafsTer7	p.Q26Afs*7	ENST00000368508	NM_002944.2	25	gtg/gtTg	1/43	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.485589731524554	2		325	440	SUCCESS
AR	367	MSKCC	GRCh37	X	66766381	66766381	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	74	99	0	ENST00000374690.3:c.1393G>T	p.Gly465Cys	p.G465C	ENST00000374690	NM_000044.3	465	Ggc/Tgc	1/8	0.485589731524554	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.485589731524554	1		99	176	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	129	351	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.488381152363497	3	FACETS	0.904	0.829	0.981	0.904	0.829	0.981	CLONAL	2	TRUE	1	0.487651131732156	3		351	364	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	85	290	0	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.487651131732156	2		290	341	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	301	519	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.966	1	1	0.996	1	CLONAL	2	TRUE	1	0.487651131732156	2		524	606	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	179	530	7	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.996	0.921	1	0.996	0.921	1	CLONAL	1	TRUE	1	0.487651131732156	2		537	737	SUCCESS
APC	324	MSKCC	GRCh37	5	112175952	112175952	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587783031	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	73	209	1	ENST00000257430.4:c.4666del	p.Thr1556LeufsTer9	p.T1556Lfs*9	ENST00000257430	NM_000038.5	1554	gAa/ga	16/16	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.487651131732156	2		210	292	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	136	417	2	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	0.19604824644947	3	FACETS	1	0.976	1	0.599	0.547	0.654	INDETERMINATE	1	TRUE	1	0.487651131732156	3		419	579	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	111	504	7	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	0.260534689398314	1	FACETS	0.77	0.697	0.847	0.77	0.697	0.847	INDETERMINATE	1	TRUE	0	0.487651131732156	1		511	447	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38631981	38631981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1255149646	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	108	515	2	ENST00000299084.4:c.471del	p.Gln158SerfsTer16	p.Q158Sfs*16	ENST00000299084	NM_152594.2	156	cTt/ct	5/7	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.487651131732156	2		517	439	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384651	31384651	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	241	751	2	ENST00000328111.2:c.1359del	p.Leu454SerfsTer136	p.L454Sfs*136	ENST00000328111	NM_006892.3	451	gaG/ga	13/23	1	2	FACETS	0.983	0.919	1	0.983	0.919	1	CLONAL	1	TRUE	1	0.487651131732156	2		753	1005	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900984	114900984	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778855667	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	60	579	0	ENST00000543371.1:c.598del	p.Leu200SerfsTer25	p.L200Sfs*25	ENST00000543371	NM_001198531.1	198	caC/ca	6/14	0.487651131732156	2	FACETS	0.27	0.231	0.311	0.135	0.115	0.156	SUBCLONAL	1	TRUE	0	0.487651131732156	2		579	913	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	121	348	1	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	0.296643060348971	4	FACETS	1	0.916	1	1	0.916	1	CLONAL	2	TRUE	2	0.487651131732156	4		349	368	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508257	106508257	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766854286	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	99	337	1	ENST00000359195.3:c.251C>T	p.Ala84Val	p.A84V	ENST00000359195	NM_002649.2	84	gCg/gTg	2/11	0.488381152363497	3	FACETS	0.88	0.787	0.978	0.44	0.393	0.489	CLONAL	1	TRUE	1	0.487651131732156	3		338	574	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81957132	81957132	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1567534502	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	166	479	1	ENST00000359376.3:c.2350C>T	p.Arg784Ter	p.R784*	ENST00000359376	NM_002661.3	784	Cga/Tga	22/33	1	2	FACETS	0.933	0.859	1	0.933	0.859	1	CLONAL	1	TRUE	1	0.487651131732156	2		480	730	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256205	16256205	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	164	539	1	ENST00000375759.3:c.3475del	p.Ile1159LeufsTer28	p.I1159Lfs*28	ENST00000375759	NM_015001.2	1157	gAa/ga	11/15	1	2	FACETS	0.985	0.907	1	0.985	0.907	1	CLONAL	1	TRUE	1	0.487651131732156	2		540	683	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599302	28599302	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	311	729	2	ENST00000253063.3:c.748G>A	p.Gly250Arg	p.G250R	ENST00000253063	NM_031459.4	250	Ggg/Agg	5/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.487651131732156	2		731	1124	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36824368	36824368	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	196	573	0	ENST00000373129.3:c.168A>C	p.Lys56Asn	p.K56N	ENST00000373129	NM_032017.1	56	aaA/aaC	4/12	1	2	FACETS	0.977	0.906	1	0.977	0.906	1	CLONAL	1	TRUE	1	0.487651131732156	2		573	823	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843599	156843599	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770090356	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	298	815	0	ENST00000524377.1:c.1025G>A	p.Arg342Gln	p.R342Q	ENST00000524377	NM_002529.3	342	cGg/cAg	8/17	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.487651131732156	2		815	1166	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	155	266	1	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	0.487651131732156	2	FACETS	0.949	0.883	1	0.949	0.883	1	CLONAL	2	TRUE	0	0.487651131732156	2		267	335	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692826	89692826	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	63	161	0	ENST00000371953.3:c.313del	p.Cys105ValfsTer8	p.C105Vfs*8	ENST00000371953	NM_000314.4	104	Ttt/tt	5/9	0.487651131732156	2	FACETS	0.964	0.86	1	0.964	0.86	1	CLONAL	2	TRUE	0	0.487651131732156	2		161	134	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946901	71946901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748853590	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	242	802	0	ENST00000298229.2:c.2750G>A	p.Arg917His	p.R917H	ENST00000298229	NM_001567.3	917	cGc/cAc	25/28	1	2	FACETS	0.951	0.888	1	0.951	0.888	1	CLONAL	1	TRUE	1	0.487651131732156	2		802	1044	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924639	94924639	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781016923	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	96	648	0	ENST00000536441.1:c.271C>T	p.Arg91Trp	p.R91W	ENST00000536441	NM_144665.3	91	Cgg/Tgg	3/10	1	2	FACETS	0.477	0.424	0.533	0.477	0.424	0.533	SUBCLONAL	1	TRUE	1	0.487651131732156	2		648	826	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125499317	125499317	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	75	326	0	ENST00000428830.2:c.386G>T	p.Arg129Met	p.R129M	ENST00000428830	NM_001114121.2	129	aGg/aTg	5/14	1	2	FACETS	0.999	0.883	1	0.999	0.883	1	CLONAL	1	TRUE	1	0.487651131732156	2		326	308	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425184	49425184	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	377	859	0	ENST00000301067.7:c.13304C>T	p.Ala4435Val	p.A4435V	ENST00000301067	NM_003482.3	4435	gCc/gTc	39/54	0.129225934474003	3	FACETS	0.764	0.725	0.804	0.764	0.725	0.804	INDETERMINATE	2	TRUE	1	0.487651131732156	3		859	1258	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432396	49432396	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783729	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	341	828	0	ENST00000301067.7:c.8743C>T	p.Arg2915Ter	p.R2915*	ENST00000301067	NM_003482.3	2915	Cga/Tga	34/54	0.129225934474003	3	FACETS	0.766	0.725	0.807	0.766	0.725	0.807	INDETERMINATE	2	TRUE	1	0.487651131732156	3		828	1136	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856521	111856521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	154	348	0	ENST00000341259.2:c.572C>T	p.Pro191Leu	p.P191L	ENST00000341259	NM_005475.2	191	cCg/cTg	2/8	0.129225934474003	3	FACETS	1	0.982	1	0.624	0.573	0.677	INDETERMINATE	1	TRUE	1	0.487651131732156	3		348	629	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794796	120794797	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	312	875	0	ENST00000257552.2:c.560dup	p.Glu188GlyfsTer191	p.E188Gfs*191	ENST00000257552	NM_002442.3	187	aag/aaAg	9/15	0.129225934474003	3	FACETS	1	0.989	1	0.604	0.569	0.64	INDETERMINATE	1	TRUE	1	0.487651131732156	3		875	1318	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209298	133209298	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060500809	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	240	692	1	ENST00000320574.5:c.6088del	p.Ala2030ProfsTer18	p.A2030Pfs*18	ENST00000320574	NM_006231.2	2030	Gcc/cc	44/49	0.129225934474003	3	FACETS	1	0.985	1	0.587	0.548	0.627	INDETERMINATE	1	TRUE	1	0.487651131732156	3		693	1043	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28674632	28674632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	44	36	0	ENST00000241453.7:c.16C>T	p.Arg6Cys	p.R6C	ENST00000241453	NM_004119.2	6	Cgc/Tgc	1/24	0.296643060348971	4	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	2	0.487651131732156	4		36	118	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061649	38061649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	129	339	0	ENST00000250448.2:c.340G>A	p.Gly114Ser	p.G114S	ENST00000250448	NM_004496.3	114	Ggc/Agc	2/2	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.487651131732156	2		339	402	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95563031	95563031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776416084	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	101	259	0	ENST00000393063.1:c.4226C>T	p.Ala1409Val	p.A1409V	ENST00000393063	NM_030621.3	1409	gCg/gTg	24/28	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.487651131732156	2		259	413	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028622	42028622	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	189	570	0	ENST00000219905.7:c.4160A>G	p.Asn1387Ser	p.N1387S	ENST00000219905	NM_001164273.1	1387	aAc/aGc	13/24	1	2	FACETS	0.981	0.909	1	0.981	0.909	1	CLONAL	1	TRUE	1	0.487651131732156	2		570	790	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423598	88423598	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	169	574	0	ENST00000360948.2:c.2237A>C	p.Lys746Thr	p.K746T	ENST00000360948	NM_001012338.2	746	aAg/aCg	18/19	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.487651131732156	2		574	661	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56867253	56867253	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1161606833	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	198	381	0	ENST00000308159.5:c.1472A>G	p.His491Arg	p.H491R	ENST00000308159	NM_014669.4	491	cAt/cGt	13/22	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.487651131732156	2		381	628	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655343	67655343	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	92	333	0	ENST00000264010.4:c.1208-2A>G		p.X403_splice	ENST00000264010	NM_006565.3	403			NA	2	FACETS	0.985	0.882	1			1	INDETERMINATE	1	TRUE	NA	0.487651131732156	2		333	383	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828251	72828251	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	177	611	0	ENST00000268489.5:c.8330G>A	p.Ser2777Asn	p.S2777N	ENST00000268489	NM_006885.3	2777	aGt/aAt	9/10	NA	2	FACETS	0.905	0.835	0.978			1	INDETERMINATE	1	TRUE	NA	0.487651131732156	2		611	802	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993013	72993014	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	240	847	0	ENST00000268489.5:c.1031dup	p.Asn344LysfsTer13	p.N344Kfs*13	ENST00000268489	NM_006885.3	344	aac/aaAc	2/10	1	2	FACETS	0.976	0.911	1	0.976	0.911	1	CLONAL	1	TRUE	1	0.487651131732156	2		847	1009	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119703	17119703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	80	468	0	ENST00000285071.4:c.1291C>T	p.Leu431Phe	p.L431F	ENST00000285071	NM_144997.5	431	Ctc/Ttc	11/14	1	2	FACETS	0.5	0.44	0.565	0.5	0.44	0.565	SUBCLONAL	1	TRUE	1	0.487651131732156	2		468	656	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883774	37883774	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	285	809	1	ENST00000269571.5:c.3391del	p.Leu1131Ter	p.L1131*	ENST00000269571		1129	gCc/gc	26/27	1	2	FACETS	0.982	0.923	1	0.982	0.923	1	CLONAL	1	TRUE	1	0.487651131732156	2		810	1190	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804246	46804246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	260	727	1	ENST00000290295.7:c.761G>A	p.Ser254Asn	p.S254N	ENST00000290295	NM_006361.5	254	aGc/aAc	2/2	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.487651131732156	2		728	1060	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740450	58740450	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	156	570	0	ENST00000305921.3:c.1357del	p.Ser453GlnfsTer4	p.S453Qfs*4	ENST00000305921	NM_003620.3	452	gTt/gt	6/6	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.487651131732156	2		570	564	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573505	48573506	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	50	270	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	0.487651131732156	2		270	186	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575209	48575209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767326	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	47	258	0	ENST00000342988.3:c.403C>T	p.Arg135Ter	p.R135*	ENST00000342988	NM_005359.5	135	Cga/Tga	3/12	1	2	FACETS	0.762	0.648	0.885	0.762	0.648	0.885	SUBCLONAL	1	TRUE	1	0.487651131732156	2		258	253	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231539	5231539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760884281	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	121	618	1	ENST00000357368.4:c.1937C>T	p.Thr646Met	p.T646M	ENST00000357368	NM_002850.3	646	aCg/aTg	14/38	0.238523859866648	3	FACETS	0.681	0.615	0.752	0.227	0.205	0.251	INDETERMINATE	1	TRUE	0	0.487651131732156	3		619	906	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260127	10260127	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	129	617	0	ENST00000340748.4:c.2538+2T>C		p.X846_splice	ENST00000340748		846			0.238523859866648	3	FACETS	0.695	0.629	0.764	0.232	0.209	0.255	INDETERMINATE	1	TRUE	0	0.487651131732156	3		617	947	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303246	15303246	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	142	881	0	ENST00000263388.2:c.282G>T	p.Gln94His	p.Q94H	ENST00000263388	NM_000435.2	94	caG/caT	3/33	0.238523859866648	3	FACETS	0.573	0.521	0.628	0.191	0.173	0.21	INDETERMINATE	1	TRUE	0	0.487651131732156	3		881	1264	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943456	17943456	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs770825375	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	138	764	0	ENST00000458235.1:c.2552T>C	p.Leu851Pro	p.L851P	ENST00000458235	NM_000215.3	851	cTg/cCg	19/24	0.238523859866648	3	FACETS	0.603	0.548	0.662	0.201	0.182	0.221	INDETERMINATE	1	TRUE	0	0.487651131732156	3		764	1167	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950470	17950470	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs765549264	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	135	685	0	ENST00000458235.1:c.1257C>A	p.Asn419Lys	p.N419K	ENST00000458235	NM_000215.3	419	aaC/aaA	10/24	0.238523859866648	3	FACETS	0.653	0.592	0.717	0.218	0.197	0.239	INDETERMINATE	1	TRUE	0	0.487651131732156	3		685	1055	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213376	36213376	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	296	885	1	ENST00000222270.7:c.2571+2T>C		p.X857_splice	ENST00000222270	NM_014727.1	857			0.238523859866648	3	FACETS	1	0.981	1	0.367	0.345	0.39	INDETERMINATE	1	TRUE	0	0.487651131732156	3		886	1371	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229237	36229237	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	66	689	0	ENST00000222270.7:c.7927A>G	p.Met2643Val	p.M2643V	ENST00000222270	NM_014727.1	2643	Atg/Gtg	37/37	0.238523859866648	3	FACETS	0.325	0.281	0.373	0.108	0.093	0.125	INDETERMINATE	1	TRUE	0	0.487651131732156	3		689	1036	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753887	42753887	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	542	797	2	ENST00000222329.4:c.377del	p.Gly126ValfsTer145	p.G126Vfs*145	ENST00000222329	NM_006494.2	126	gGt/gt	4/4	0.238523859866648	3	FACETS	1	0.991	1	0.73	0.701	0.758	INDETERMINATE	2	TRUE	0	0.487651131732156	3		799	1263	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50916773	50916773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	351	625	2	ENST00000440232.2:c.2245G>A	p.Ala749Thr	p.A749T	ENST00000440232	NM_002691.3	749	Gcc/Acc	18/27	0.238523859866648	3	FACETS	1	0.981	1	0.705	0.671	0.74	INDETERMINATE	2	TRUE	0	0.487651131732156	3		627	846	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661129	227661129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781654199	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	65	774	1	ENST00000305123.5:c.2326C>T	p.Arg776Cys	p.R776C	ENST00000305123	NM_005544.2	776	Cgc/Tgc	1/2	1	2	FACETS	0.238	0.206	0.274	0.238	0.206	0.274	SUBCLONAL	1	TRUE	1	0.487651131732156	2		775	1118	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827961	40827961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757952832	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	210	506	0	ENST00000373198.4:c.2467G>A	p.Ala823Thr	p.A823T	ENST00000373198	NM_133170.3	823	Gcc/Acc	17/32	0.488381152363497	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.487651131732156	1		506	566	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845396	42845396	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775404304	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	237	670	0	ENST00000398585.3:c.866G>A	p.Arg289His	p.R289H	ENST00000398585	NM_001135099.1	289	cGc/cAc	9/14	0.260534689398314	1	FACETS	0.921	0.862	0.981	0.921	0.862	0.981	INDETERMINATE	1	TRUE	0	0.487651131732156	1		670	798	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167562	24167562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769023941	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	220	608	0	ENST00000263121.7:c.946C>T	p.Arg316Trp	p.R316W	ENST00000263121	NM_003073.3	316	Cgg/Tgg	7/9	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.487651131732156	2		608	872	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574736	41574737	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	296	858	0	ENST00000263253.7:c.7025dup	p.Gln2343ThrfsTer36	p.Q2343Tfs*36	ENST00000263253	NM_001429.3	2341	tcc/tCcc	31/31	1	2	FACETS	0.971	0.913	1	0.971	0.913	1	CLONAL	1	TRUE	1	0.487651131732156	2		858	1250	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090057	37090057	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	61	559	0	ENST00000231790.2:c.1946C>A	p.Pro649His	p.P649H	ENST00000231790	NM_000249.3	649	cCt/cAt	17/19	1	2	FACETS	0.371	0.32	0.427	0.371	0.32	0.427	SUBCLONAL	1	TRUE	1	0.487651131732156	2		559	674	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99823088	99823088	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	96	390	0	ENST00000280892.6:c.124del	p.Thr42ArgfsTer41	p.T42Rfs*41	ENST00000280892	NM_001130678.1	42	Acg/cg	2/7	1	2	FACETS	0.944	0.847	1	0.944	0.847	1	CLONAL	1	TRUE	1	0.487651131732156	2		390	417	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197300	106197300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776598022	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	57	333	0	ENST00000380013.4:c.5633G>A	p.Arg1878His	p.R1878H	ENST00000380013	NM_001127208.2	1878	cGt/cAt	11/11	1	2	FACETS	0.497	0.427	0.574	0.497	0.427	0.574	SUBCLONAL	1	TRUE	1	0.487651131732156	2		333	470	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963111	38963111	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377753143	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	47	235	0	ENST00000357387.3:c.1433G>A	p.Arg478His	p.R478H	ENST00000357387	NM_152756.3	478	cGc/cAc	17/38	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.487651131732156	2		235	159	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	65	341	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.913	0.799	1	0.913	0.799	1	CLONAL	1	TRUE	1	0.487651131732156	2		341	292	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288620	33288620	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	90	392	0	ENST00000374542.5:c.932T>G	p.Leu311Arg	p.L311R	ENST00000374542	NM_001141970.1	311	cTc/cGc	3/8	0.433089802464189	3	FACETS	0.63	0.559	0.706	0.21	0.186	0.236	SUBCLONAL	1	TRUE	0	0.487651131732156	3		392	729	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420001	152420001	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763337967	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	185	534	3	ENST00000206249.3:c.1688C>T	p.Thr563Met	p.T563M	ENST00000206249	NM_000125.3	563	aCg/aTg	8/8	0.488381152363497	3	FACETS	0.884	0.816	0.956	0.442	0.408	0.478	CLONAL	1	TRUE	1	0.487651131732156	3		537	1067	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099427	157099432	+	inframe_deletion	In_Frame_Del	DEL	CAGCAG	CAGCAG	-	rs587779744	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	57	313	0	ENST00000346085.5:c.381_386del	p.Gln130_Gln131del	p.Q130_Q131del	ENST00000346085	NM_020732.3	122	CAGCAG/-	1/20	0.488381152363497	3	FACETS	0.457	0.392	0.529	0.229	0.196	0.265	SUBCLONAL	1	TRUE	1	0.487651131732156	3		313	636	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521969	157521969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs530430137	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	54	549	0	ENST00000346085.5:c.4241C>T	p.Pro1414Leu	p.P1414L	ENST00000346085	NM_020732.3	1414	cCg/cTg	18/20	0.488381152363497	3	FACETS	0.272	0.231	0.317	0.136	0.115	0.159	SUBCLONAL	1	TRUE	1	0.487651131732156	3		549	1014	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266558	55266558	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	149	420	0	ENST00000275493.2:c.2848+2T>C		p.X950_splice	ENST00000275493	NM_005228.3	950			0.488381152363497	3	FACETS	0.942	0.861	1	0.471	0.43	0.513	CLONAL	1	TRUE	1	0.487651131732156	3		420	807	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545783	106545783	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	202	474	0	ENST00000359195.3:c.3260T>C	p.Phe1087Ser	p.F1087S	ENST00000359195	NM_002649.2	1087	tTt/tCt	11/11	0.488381152363497	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	1	0.487651131732156	3		474	508	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930087	68930087	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	108	315	0	ENST00000288368.4:c.148T>G	p.Leu50Val	p.L50V	ENST00000288368	NM_024870.2	50	Tta/Gta	2/40	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.487651131732156	2		315	358	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249593	110249593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754379894	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	366	908	1	ENST00000374672.4:c.1082C>T	p.Pro361Leu	p.P361L	ENST00000374672	NM_004235.4	361	cCg/cTg	3/5	0.314007028146778	3	FACETS	1	0.991	1	0.605	0.572	0.638	CLONAL	1	TRUE	1	0.487651131732156	3		909	1544	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128419934	128419934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	37	471	1	ENST00000265960.3:c.494G>A	p.Gly165Asp	p.G165D	ENST00000265960	NM_001006617.1	165	gGc/gAc	4/12	0.314007028146778	3	FACETS	0.4	0.329	0.479	0.2	0.164	0.24	SUBCLONAL	1	TRUE	1	0.487651131732156	3		472	472	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128420046	128420047	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	124	596	0	ENST00000265960.3:c.381dup	p.Ser128IlefsTer28	p.S128Ifs*28	ENST00000265960	NM_001006617.1	127	-/A	4/12	0.314007028146778	3	FACETS	0.97	0.88	1	0.485	0.44	0.533	CLONAL	1	TRUE	1	0.487651131732156	3		596	652	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413899	139413899	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	361	598	0	ENST00000277541.6:c.861G>A	p.Trp287Ter	p.W287*	ENST00000277541	NM_017617.3	287	tgG/tgA	5/34	0.314007028146778	3	FACETS	0.932	0.886	0.979	0.932	0.886	0.979	CLONAL	2	TRUE	1	0.487651131732156	3		598	988	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20153856	20153857	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	87	366	0	ENST00000379607.5:c.203dup	p.Val69GlyfsTer19	p.V69Gfs*19	ENST00000379607	NM_001412.3	68	aag/aaAg	3/7	1	2	FACETS	0.894	0.797	0.997	0.894	0.797	0.997	CLONAL	1	TRUE	1	0.487651131732156	2		366	399	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0041530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	36	446	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.755	0.622	0.904	0.755	0.622	0.904	CLONAL	1	TRUE	1	0.27319829485676	2		446	349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577497	7577497	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0041530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	97	743	0	ENST00000269305.4:c.782+2T>C		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.267507010294753	1	FACETS	0.615	0.547	0.688	0.615	0.547	0.688	SUBCLONAL	1	TRUE	0	0.27319829485676	1		743	997	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900207	101900207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	24	411	0	ENST00000374994.4:c.641G>A	p.Gly214Asp	p.G214D	ENST00000374994	NM_004612.2	214	gGt/gAt	4/9	0.267507010294753	1	FACETS	0.632	0.497	0.786	0.632	0.497	0.786	SUBCLONAL	1	TRUE	0	0.27319829485676	1		411	240	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0041536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	101	390	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.91	0.818	1	0.91	0.818	1	CLONAL	1	TRUE	1	0.483564210048391	2		390	459	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0041536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	160	462	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.483564210048391	2		463	512	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223582	55223582	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6690	1854	806	0	ENST00000275493.2:c.949G>C	p.Glu317Gln	p.E317Q	ENST00000275493	NM_005228.3	317	Gag/Cag	8/28	0.483564210048391	32	FACETS	1	0.994	1	0.231	0.225	0.238	CLONAL	7	TRUE	0	0.483564210048391	32		806	8544	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736166	204736166	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	41	364	4	ENST00000302823.3:c.529del	p.Tyr177IlefsTer10	p.Y177Ifs*10	ENST00000302823	NM_005214.4	175	Ttt/tt	3/4	0.137235655920728	5	FACETS	0.877	0.73	1	0.292	0.243	0.347	INDETERMINATE	1	TRUE	2	0.26959474073114	5		368	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0041658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	258	759	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.212553696645966	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.26959474073114	2		759	847	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346465	89346465	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753900347	NA	P-0041658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	86	805	0	ENST00000301030.4:c.6485C>T	p.Pro2162Leu	p.P2162L	ENST00000301030	NM_001256183.1	2162	cCt/cTt	9/13	0.2583628887376	2	FACETS	1	0.919	1	0.524	0.464	0.588	CLONAL	1	TRUE	0	0.26959474073114	2		805	609	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021368	31021412	+	inframe_deletion	In_Frame_Del	DEL	CTGACCCAGCAGGGCTGAGCAGTCCCCATCTGCCAGGCACATCCT	CTGACCCAGCAGGGCTGAGCAGTCCCCATCTGCCAGGCACATCCT	-	novel	NA	P-0041658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	55	605	0	ENST00000375687.4:c.1370_1414del	p.Asp457_Ser471del	p.D457_S471del	ENST00000375687	NM_015338.5	456	aCTGACCCAGCAGGGCTGAGCAGTCCCCATCTGCCAGGCACATCCTct/act	12/13	0.217099221746754	3	FACETS	0.903	0.773	1	0.451	0.386	0.522	CLONAL	1	TRUE	1	0.26959474073114	3		605	513	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207451	29207510	+	inframe_deletion	In_Frame_Del	DEL	GGCGCGCGGGCTGCGCTCGTCGTAGACGATGACCGCCGAGTAGAGGCCGGAGCGCAAGCG	GGCGCGCGGGCTGCGCTCGTCGTAGACGATGACCGCCGAGTAGAGGCCGGAGCGCAAGCG	-	novel	NA	P-0041658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	47	652	0	ENST00000240100.2:c.286_345del	p.Arg96_Ala115del	p.R96_A115del	ENST00000240100	NM_001394.6	96	CGCTTGCGCTCCGGCCTCTACTCGGCGGTCATCGTCTACGACGAGCGCAGCCCGCGCGCC/-	1/4	0.142580900810888	3	FACETS	0.686	0.578	0.805	0.343	0.289	0.403	INDETERMINATE	1	TRUE	1	0.26959474073114	3		652	577	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0041664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	115	446	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.699	0.631	0.769	0.699	0.631	0.769	SUBCLONAL	1	TRUE	1	0.573569413005658	2		446	574	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0041664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	311	467	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.573569413005658	2	FACETS	0.928	0.886	0.971	0.928	0.886	0.971	CLONAL	2	TRUE	0	0.573569413005658	2		467	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578378	7578395	+	inframe_deletion	In_Frame_Del	DEL	ATCTGAGCAGCGCTCATG	ATCTGAGCAGCGCTCATG	-	novel	NA	P-0041664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	154	731	0	ENST00000269305.4:c.535_552del	p.His179_Asp184del	p.H179_D184del	ENST00000269305	NM_001126112.2	179	CATGAGCGCTGCTCAGAT/-	5/11	0.573569413005658	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.573569413005658	1		731	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0041667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	564	1018	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	1	2	FACETS	0.995	0.959	1	0.995	0.959	1	CLONAL	1	TRUE	1	0.93825206303582	2		1018	1208	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0041667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	106	346	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	0.816	0.743	0.89	0.816	0.743	0.89	CLONAL	1	TRUE	1	0.93825206303582	2		346	277	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692890	89692890	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	118	402	0	ENST00000371953.3:c.374A>T	p.Lys125Ile	p.K125I	ENST00000371953	NM_000314.4	125	aAa/aTa	5/9	0.93825206303582	1	FACETS	0.997	0.956	1	0.997	0.956	1	CLONAL	1	TRUE	0	0.93825206303582	1		402	134	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371743	55371743	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	293	656	1	ENST00000297316.4:c.433G>T	p.Val145Leu	p.V145L	ENST00000297316	NM_022454.3	145	Gtg/Ttg	2/2	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.93825206303582	2		657	621	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128432128	128432128	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	39	306	0	ENST00000265960.3:c.318T>G	p.Ile106Met	p.I106M	ENST00000265960	NM_001006617.1	106	atT/atG	3/12	1	2	FACETS	0.272	0.226	0.322	0.272	0.226	0.322	SUBCLONAL	1	TRUE	1	0.93825206303582	2		306	306	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0041672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	215	763	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	0.151745723053725	4	FACETS	0.884	0.824	0.945	0.884	0.824	0.945	INDETERMINATE	2	TRUE	2	0.469896583320321	4		763	761	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907822	76907822	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	26	216	1	ENST00000373344.5:c.4339G>T	p.Glu1447Ter	p.E1447*	ENST00000373344	NM_000489.3	1447	Gag/Tag	15/35	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.469896583320321	2		217	80	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	96	683	2	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	0.151745723053725	4	FACETS	0.858	0.772	0.948	0.858	0.772	0.948	INDETERMINATE	2	TRUE	2	0.469896583320321	4		685	350	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469945	25469945	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767236033	NA	P-0041672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	226	838	3	ENST00000264709.3:c.1097G>A	p.Arg366His	p.R366H	ENST00000264709	NM_175629.2	366	cGc/cAc	9/23	0.151745723053725	4	FACETS	0.923	0.863	0.985	0.923	0.863	0.985	INDETERMINATE	2	TRUE	2	0.469896583320321	4		841	766	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023589	27023590	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTCCCCGAGAGGTGGCA	novel	NA	P-0041672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	40	521	0	ENST00000324856.7:c.700_716dup	p.Gly240ArgfsTer129	p.G240Rfs*129	ENST00000324856	NM_006015.4	232	agc/agCTCCCCGAGAGGTGGCAc	1/20	0.151745723053725	4	FACETS	0.466	0.387	0.555	0.233	0.193	0.278	INDETERMINATE	1	TRUE	2	0.469896583320321	4		521	537	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690797	89690801	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TTTTA	TTTTA	-	rs1564828909	NA	P-0041674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	66	336	0	ENST00000371953.3:c.210-6_210-2del		p.X70_splice	ENST00000371953	NM_000314.4	70			0.384911069594733	1	FACETS	0.982	0.861	1	0.982	0.861	1	CLONAL	1	TRUE	0	0.384911069594733	1		336	282	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985730	60985730	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	39	242	0	ENST00000333681.4:c.170C>A	p.Pro57His	p.P57H	ENST00000333681		57	cCc/cAc	2/3	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.384911069594733	2		242	154	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752979	128752979	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	63	562	0	ENST00000377970.2:c.1140G>C	p.Gln380His	p.Q380H	ENST00000377970	NM_002467.4	380	caG/caC	3/3	1	2	FACETS	0.688	0.596	0.787	0.688	0.596	0.787	SUBCLONAL	1	TRUE	1	0.384911069594733	2		562	476	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	386	215	0				ENST00000310581	NM_198253.2	-/1132			0.327095452587077	3	FACETS	1	0.991	1	0.758	0.723	0.792	CLONAL	2	TRUE	0	0.482363859580402	3		215	874	SUCCESS
ATM	472	MSKCC	GRCh37	11	108225575	108225575	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	81	353	0	ENST00000278616.4:c.8824C>T	p.Gln2942Ter	p.Q2942*	ENST00000278616	NM_000051.3	2942	Cag/Tag	61/63	0.475495969165459	1	FACETS	0.94	0.839	1	0.94	0.839	1	CLONAL	1	TRUE	0	0.482363859580402	1		353	271	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875055	151875055	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	34	167	0	ENST00000262189.6:c.7483C>T	p.Gln2495Ter	p.Q2495*	ENST00000262189	NM_170606.2	2495	Caa/Taa	38/59	1	2	FACETS	0.716	0.59	0.854	0.716	0.59	0.854	SUBCLONAL	1	TRUE	1	0.482363859580402	2		167	197	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312408	91312408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	68	382	0	ENST00000355112.3:c.2353G>A	p.Glu785Lys	p.E785K	ENST00000355112	NM_000057.2	785	Gag/Aag	11/22	0.451448659383981	1	FACETS	0.65	0.57	0.736	0.65	0.57	0.736	SUBCLONAL	1	TRUE	0	0.482363859580402	1		382	329	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166279	118166279	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	26	382	0	ENST00000369448.3:c.789C>G	p.Ile263Met	p.I263M	ENST00000369448	NM_017709.3	263	atC/atG	2/2	0.222582667125348	2	FACETS	0.252	0.199	0.313	0.126	0.099	0.157	INDETERMINATE	1	TRUE	0	0.482363859580402	2		382	427	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466528	120466528	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	56	603	0	ENST00000256646.2:c.4591G>A	p.Gly1531Arg	p.G1531R	ENST00000256646	NM_024408.3	1531	Ggg/Agg	26/34	0.222582667125348	2	FACETS	0.273	0.233	0.318	0.137	0.116	0.159	INDETERMINATE	1	TRUE	0	0.482363859580402	2		603	849	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426715	49426715	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	108	336	0	ENST00000301067.7:c.11773C>T	p.Gln3925Ter	p.Q3925*	ENST00000301067	NM_003482.3	3925	Caa/Taa	39/54	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.482363859580402	2		336	446	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26911703	26911703	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0041700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	25	172	0	ENST00000381527.3:c.129-1G>A		p.X43_splice	ENST00000381527	NM_001260.1	43			NA	2	FACETS	1	0.888	1			1	INDETERMINATE	1	TRUE	NA	0.482363859580402	2		172	90	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256925	41256925	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	97	458	0	ENST00000357654.3:c.261del	p.Ile89SerfsTer30	p.I89Sfs*30	ENST00000357654	NM_007294.3	87	ttG/tt	5/23	1	2	FACETS	0.784	0.701	0.871	0.784	0.701	0.871	SUBCLONAL	1	TRUE	1	0.482363859580402	2		458	513	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276837	15276837	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	80	815	0	ENST00000263388.2:c.5428G>C	p.Glu1810Gln	p.E1810Q	ENST00000263388	NM_000435.2	1810	Gag/Cag	30/33	0.430946126501817	1	FACETS	0.25	0.219	0.283	0.25	0.219	0.283	SUBCLONAL	1	TRUE	0	0.482363859580402	1		815	1007	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698192	47698192	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1236208777	NA	P-0041700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	14	202	0	ENST00000233146.2:c.1750A>G	p.Ile584Val	p.I584V	ENST00000233146	NM_000251.2	584	Att/Gtt	11/16	0.257613579836845	2	FACETS	0.354	0.257	0.471	0.177	0.128	0.236	INDETERMINATE	1	TRUE	0	0.482363859580402	2		202	164	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719442	190719442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	27	248	0	ENST00000441310.2:c.1444G>A	p.Glu482Lys	p.E482K	ENST00000441310	NM_000534.4	482	Gag/Aag	9/13	0.260967058500724	1	FACETS	0.559	0.45	0.68	0.559	0.45	0.68	INDETERMINATE	1	TRUE	0	0.482363859580402	1		248	152	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143029249	143029249	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1389881866	NA	P-0041700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	63	176	0	ENST00000262992.4:c.2371G>A	p.Asp791Asn	p.D791N	ENST00000262992	NM_001101669.1	791	Gat/Aat	21/24	0.482363859580402	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.482363859580402	1		176	187	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922749	44922749	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0041700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	126	198	0	ENST00000377967.4:c.1610C>G	p.Ser537Ter	p.S537*	ENST00000377967	NM_021140.2	537	tCa/tGa	16/29	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.482363859580402	1		198	286	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039901	47039901	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	270	414	0	ENST00000377604.3:c.1244C>A	p.Ser415Ter	p.S415*	ENST00000377604	NM_001204468.1	415	tCa/tAa	12/24	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.482363859580402	1		414	654	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210315	123210315	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0041700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	54	116	0	ENST00000218089.9:c.2667T>A	p.Tyr889Ter	p.Y889*	ENST00000218089	NM_001042749.1	889	taT/taA	26/35	1	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.482363859580402	1		116	121	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0041703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	124	354	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.336600512449731	5	FACETS	1	0.926	1	0.681	0.618	0.746	CLONAL	2	TRUE	2	0.336600512449731	5		354	543	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962854	2962854	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	293	759	2	ENST00000396946.4:c.2054del	p.Gly685AlafsTer31	p.G685Afs*31	ENST00000396946	NM_032415.4	685	gGc/gc	16/25	0.13889399764135	4	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.336600512449731	4		761	966	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215258	142215258	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	146	503	0	ENST00000350721.4:c.5843G>T	p.Gly1948Val	p.G1948V	ENST00000350721	NM_001184.3	1948	gGg/gTg	34/47	0.187382769595988	4	FACETS	0.928	0.85	1	0.928	0.85	1	INDETERMINATE	2	TRUE	2	0.336600512449731	4		503	625	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028883	47028883	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	130	570	0	ENST00000377604.3:c.187G>T	p.Glu63Ter	p.E63*	ENST00000377604	NM_001204468.1	63	Gag/Tag	3/24	0.321905182027799	2	FACETS	0.864	0.79	0.941	0.864	0.79	0.941	CLONAL	2	TRUE	0	0.336600512449731	2		570	447	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199325	16199325	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	38	286	0	ENST00000375759.3:c.98A>G	p.Glu33Gly	p.E33G	ENST00000375759	NM_015001.2	33	gAa/gGa	2/15	0.2917368090146	3	FACETS	0.879	0.73	1	0.44	0.365	0.523	CLONAL	1	TRUE	1	0.336600512449731	3		286	300	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426751	121426751	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	164	658	0	ENST00000257555.6:c.442C>G	p.Leu148Val	p.L148V	ENST00000257555		148	Ctc/Gtc	2/10	0.321905182027799	2	FACETS	0.813	0.75	0.879	0.813	0.75	0.879	CLONAL	2	TRUE	0	0.336600512449731	2		658	599	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865753	56865753	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0041703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	107	214	0	ENST00000308159.5:c.1086-1G>T		p.X362_splice	ENST00000308159	NM_014669.4	362			0.222991667862229	5	FACETS	1	0.933	1	1	0.933	1	CLONAL	3	TRUE	2	0.336600512449731	5		214	309	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575113	48575113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	45	346	0	ENST00000342988.3:c.307G>A	p.Asp103Asn	p.D103N	ENST00000342988	NM_005359.5	103	Gat/Aat	3/12	1	2	FACETS	0.836	0.705	0.978	0.836	0.705	0.978	CLONAL	1	TRUE	1	0.336600512449731	2		346	320	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353828	15353828	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	161	469	0	ENST00000263377.2:c.3052C>A	p.Gln1018Lys	p.Q1018K	ENST00000263377	NM_058243.2	1018	Cag/Aag	14/20	0.31309028255093	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.336600512449731	2		469	448	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47604202	47604202	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	52	360	1	ENST00000263735.4:c.541A>G	p.Ile181Val	p.I181V	ENST00000263735	NM_002354.2	181	Atc/Gtc	5/9	0.2917368090146	3	FACETS	0.916	0.782	1	0.458	0.391	0.531	CLONAL	1	TRUE	1	0.336600512449731	3		361	394	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024355	31024355	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	151	536	0	ENST00000375687.4:c.3840C>G	p.Ile1280Met	p.I1280M	ENST00000375687	NM_015338.5	1280	atC/atG	13/13	0.111193053546101	4	FACETS	0.996	0.914	1	0.996	0.914	1	INDETERMINATE	2	TRUE	2	0.336600512449731	4		536	602	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331961	81331961	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	35	264	0	ENST00000222390.5:c.2123G>T	p.Arg708Leu	p.R708L	ENST00000222390	NM_000601.4	708	cGa/cTa	18/18	0.2917368090146	3	FACETS	0.976	0.805	1	0.488	0.402	0.583	CLONAL	1	TRUE	1	0.336600512449731	3		264	249	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332021	81332021	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	85	316	0	ENST00000222390.5:c.2063T>G	p.Leu688Arg	p.L688R	ENST00000222390	NM_000601.4	688	cTt/cGt	18/18	0.2917368090146	3	FACETS	0.925	0.826	1	0.925	0.826	1	CLONAL	2	TRUE	1	0.336600512449731	3		316	319	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0041715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	40	930	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.765	0.634	0.912	0.765	0.634	0.912	CLONAL	1	TRUE	1	0.15	2		933	697	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0041715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	22	683	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.472	0.364	0.599	0.472	0.364	0.599	SUBCLONAL	1	TRUE	1	0.15	2		683	621	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0041715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	20	576	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.561	0.428	0.719	0.561	0.428	0.719	SUBCLONAL	1	TRUE	1	0.15	2		576	475	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870942	12870942	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	25	438	0	ENST00000228872.4:c.169C>T	p.Gln57Ter	p.Q57*	ENST00000228872	NM_004064.3	57	Cag/Tag	1/3	1	2	FACETS	0.864	0.68	1	0.864	0.68	1	CLONAL	1	TRUE	1	0.15	2		438	386	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466025	69466026	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGA	novel	NA	P-0041715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	44	1023	0	ENST00000227507.2:c.866_868dup	p.Asp289dup	p.D289dup	ENST00000227507	NM_053056.2	289	acc/acCGAc	5/5	1	2	FACETS	0.667	0.557	0.789	0.667	0.557	0.789	SUBCLONAL	1	TRUE	1	0.15	2		1023	880	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624228	89624251	+	start_lost,inframe_deletion	Translation_Start_Site	DEL	TGACAGCCATCATCAAAGAGATCG	TGACAGCCATCATCAAAGAGATCG	-	novel	NA	P-0041715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	11	221	0	ENST00000371953.3:c.3_26del	p.MetThrAlaIleIleLysGluIleVal1_?9	p.MTAIIKEIV1_?9	ENST00000371953	NM_000314.4	1	aTGACAGCCATCATCAAAGAGATCGtt/att	1/9	1	2	FACETS	1	0.766	1	1	0.766	1	CLONAL	1	TRUE	1	0.15	2		221	130	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0041732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	259	772	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.3	0	FACETS	0.598	0.566	0.63			1	INDETERMINATE	1	TRUE	0	0.62	0		772	531	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0041732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	297	366	0	ENST00000374080.3:c.3670C>T	p.Leu1224Phe	p.L1224F	ENST00000374080		1224	Ctc/Ttc	26/45	0.126778087739928	2	FACETS	0.927	0.885	0.968			1	INDETERMINATE	2	TRUE	NA	0.62	2		366	517	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640564	3640564	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	73	826	1	ENST00000294008.3:c.3075G>T	p.Trp1025Cys	p.W1025C	ENST00000294008	NM_032444.2	1025	tgG/tgT	12/15	1	2	FACETS	0.295	0.258	0.336	0.295	0.258	0.336	SUBCLONAL	1	TRUE	1	0.62	2		827	797	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032071	26032071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	26	397	0	ENST00000244661.2:c.218G>A	p.Arg73Gln	p.R73Q	ENST00000244661	NM_003537.3	73	cGa/cAa	1/1	1	2	FACETS	0.165	0.13	0.205	0.165	0.13	0.205	SUBCLONAL	1	TRUE	1	0.62	2		397	508	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0041828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	62	599	1	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.209631859110729	2	FACETS	0.7	0.605	0.805	0.35	0.302	0.403	SUBCLONAL	1	TRUE	0	0.27658870442831	2		600	640	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0041828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	49	536	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.12361882106524	4	FACETS	1	0.856	1	0.505	0.428	0.589	INDETERMINATE	1	TRUE	2	0.27658870442831	4		536	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574005	7574005	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	52	879	0	ENST00000269305.4:c.1022T>G	p.Phe341Cys	p.F341C	ENST00000269305	NM_001126112.2	341	tTc/tGc	10/11	1	2	FACETS	0.618	0.526	0.72	0.618	0.526	0.72	SUBCLONAL	1	TRUE	1	0.27658870442831	2		879	608	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971144	21971154	+	frameshift_variant	Frame_Shift_Del	DEL	AGTTGGGCTCC	AGTTGGGCTCC	GGT	novel	NA	P-0041828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	25	458	2	ENST00000304494.5:c.204_214delinsACC	p.Glu69ProfsTer48	p.E69Pfs*48	ENST00000304494	NM_000077.4	68	gcGGAGCCCAACTgc/gcACCgc	2/3	1	2	FACETS	0.491	0.387	0.611	0.491	0.387	0.611	SUBCLONAL	1	TRUE	1	0.27658870442831	2		460	368	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057874	27057874	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	265	794	0	ENST00000324856.7:c.1582C>T	p.Gln528Ter	p.Q528*	ENST00000324856	NM_006015.4	528	Cag/Tag	3/20	0.588963406042829	1	FACETS	0.892	0.841	0.944	0.892	0.841	0.944	CLONAL	1	TRUE	0	0.588963406042829	1		794	712	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676218	29676219	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0041854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	64	365	0	ENST00000356175.3:c.7208_7209del	p.Arg2403LysfsTer3	p.R2403Kfs*3	ENST00000356175	NM_000267.3	2403	AGa/a	48/57	0.588963406042829	1	FACETS	0.734	0.645	0.826	0.734	0.645	0.826	SUBCLONAL	1	TRUE	0	0.588963406042829	1		365	209	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38942978	38942978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	59	322	0	ENST00000357387.3:c.5009G>A	p.Arg1670Gln	p.R1670Q	ENST00000357387	NM_152756.3	1670	cGg/cAg	37/38	1	2	FACETS	0.679	0.589	0.776	0.679	0.589	0.776	SUBCLONAL	1	TRUE	1	0.588963406042829	2		322	295	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052684	42052684	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0041854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	172	593	0	ENST00000219905.7:c.7355T>A	p.Leu2452Ter	p.L2452*	ENST00000219905	NM_001164273.1	2452	tTa/tAa	20/24	0.588963406042829	1	FACETS	0.902	0.838	0.967	0.902	0.838	0.967	CLONAL	1	TRUE	0	0.588963406042829	1		593	457	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	143	354	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.526908603317922	3	FACETS	0.816	0.751	0.882	0.816	0.751	0.882	CLONAL	2	TRUE	1	0.532209586029738	3		354	417	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	166	519	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.532209586029738	2		524	612	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	227	736	5	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	0.532209586029738	2		741	773	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	74	320	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	0.532209586029738	2	FACETS	0.79	0.696	0.889	0.395	0.348	0.445	SUBCLONAL	1	TRUE	0	0.532209586029738	2		321	352	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	52	304	1	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	0.587	0.502	0.679	0.587	0.502	0.679	SUBCLONAL	1	TRUE	1	0.532209586029738	2		305	333	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003782	45003782	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs752758095	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	170	457	0	ENST00000558401.1:c.38T>C	p.Leu13Pro	p.L13P	ENST00000558401	NM_004048.2	13	cTc/cCc	1/4	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.532209586029738	2		457	426	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	224	683	2	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.532209586029738	2		685	802	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272337	15272337	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs771517374	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	255	747	5	ENST00000263388.2:c.6102del	p.Gly2035ValfsTer50	p.G2035Vfs*50	ENST00000263388	NM_000435.2	2034	ccC/cc	33/33	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.532209586029738	2		752	915	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007332	143007332	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	83	335	0	ENST00000262992.4:c.2452del	p.Arg818GlufsTer4	p.R818Efs*4	ENST00000262992	NM_001101669.1	818	Aga/ga	22/24	1	2	FACETS	0.901	0.802	1	0.901	0.802	1	CLONAL	1	TRUE	1	0.532209586029738	2		335	346	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	73	302	1	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.976	0.863	1	0.976	0.863	1	CLONAL	1	TRUE	1	0.532209586029738	2		303	281	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	147	543	1	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	0.79	0.723	0.86	0.79	0.723	0.86	SUBCLONAL	1	TRUE	1	0.532209586029738	2		544	699	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434367	121434367	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	185	710	1	ENST00000257555.6:c.1136del	p.Pro379LeufsTer5	p.P379Lfs*5	ENST00000257555		377	ctC/ct	6/10	0.526908603317922	3	FACETS	0.945	0.873	1	0.473	0.436	0.511	CLONAL	1	TRUE	1	0.532209586029738	3		711	931	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161907	47161907	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	76	351	0	ENST00000409792.3:c.4219del	p.Arg1407GlyfsTer5	p.R1407Gfs*5	ENST00000409792	NM_014159.6	1407	Agg/gg	3/21	0.532209586029738	2	FACETS	0.732	0.646	0.824	0.366	0.323	0.412	SUBCLONAL	1	TRUE	0	0.532209586029738	2		351	390	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913837	32913837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359507	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	90	442	1	ENST00000380152.3:c.5351del	p.Asn1784ThrfsTer7	p.N1784Tfs*7	ENST00000380152		1782	cAa/ca	11/27	1	2	FACETS	0.914	0.817	1	0.914	0.817	1	CLONAL	1	TRUE	1	0.532209586029738	2		443	370	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024001	27024002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	25	41	0	ENST00000324856.7:c.1113dup	p.Gln372AlafsTer28	p.Q372Afs*28	ENST00000324856	NM_006015.4	369	-/G	1/20	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.532209586029738	2		41	88	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641389	18641389	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1229278001	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	38	198	1	ENST00000266497.5:c.2393del	p.Asn798MetfsTer16	p.N798Mfs*16	ENST00000266497		796	ctA/ct	17/31	0.526908603317922	3	FACETS	0.909	0.759	1	0.454	0.379	0.536	CLONAL	1	TRUE	1	0.532209586029738	3		199	199	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857895	9857895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761399460	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	196	593	2	ENST00000330684.3:c.3506G>A	p.Arg1169Gln	p.R1169Q	ENST00000330684	NM_001134407.1	1169	cGg/cAg	13/13	1	2	FACETS	0.999	0.928	1	0.999	0.928	1	CLONAL	1	TRUE	1	0.532209586029738	2		595	737	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165213	47165213	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	61	269	0	ENST00000409792.3:c.913del	p.Thr305GlnfsTer35	p.T305Qfs*35	ENST00000409792	NM_014159.6	305	Aca/ca	3/21	0.532209586029738	2	FACETS	0.875	0.763	0.994	0.437	0.381	0.497	CLONAL	1	TRUE	0	0.532209586029738	2		269	262	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545939	41545939	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	247	736	0	ENST00000263253.7:c.2554C>T	p.Gln852Ter	p.Q852*	ENST00000263253	NM_001429.3	852	Cag/Tag	14/31	1	2	FACETS	0.984	0.921	1	0.984	0.921	1	CLONAL	1	TRUE	1	0.532209586029738	2		736	943	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683223	88683223	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113849804	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	111	498	0	ENST00000372037.3:c.1433G>A	p.Arg478His	p.R478H	ENST00000372037	NM_004329.2	478	cGt/cAt	12/13	1	2	FACETS	0.979	0.887	1	0.979	0.887	1	CLONAL	1	TRUE	1	0.532209586029738	2		498	426	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553588	106553588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753673199	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	134	398	0	ENST00000369096.4:c.1553C>T	p.Thr518Met	p.T518M	ENST00000369096	NM_001198.3	518	aCg/aTg	5/7	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.532209586029738	2		398	475	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057744	180057744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138831198	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	208	717	0	ENST00000261937.6:c.211G>A	p.Gly71Arg	p.G71R	ENST00000261937	NM_182925.4	71	Gga/Aga	3/30	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.532209586029738	2		717	725	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265479	152265479	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766779326	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	149	545	0	ENST00000206249.3:c.932C>T	p.Thr311Met	p.T311M	ENST00000206249	NM_000125.3	311	aCg/aTg	4/8	1	2	FACETS	0.939	0.862	1	0.939	0.862	1	CLONAL	1	TRUE	1	0.532209586029738	2		545	596	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246532	41246532	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357569	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	113	630	4	ENST00000357654.3:c.1016del	p.Lys339ArgfsTer2	p.K339Rfs*2	ENST00000357654	NM_007294.3	339	aAg/ag	10/23	1	2	FACETS	0.821	0.742	0.904	0.821	0.742	0.904	CLONAL	1	TRUE	1	0.532209586029738	2		634	517	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795609	42795609	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	212	795	2	ENST00000575354.2:c.2694del	p.Ala900ProfsTer24	p.A900Pfs*24	ENST00000575354	NM_015125.3	897	Ccc/cc	10/20	1	2	FACETS	0.852	0.792	0.914	0.852	0.792	0.914	CLONAL	1	TRUE	1	0.532209586029738	2		797	935	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332152	70332153	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1196853334	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	61	227	3	ENST00000373644.4:c.65dup	p.Lys23GlufsTer37	p.K23Efs*37	ENST00000373644	NM_030625.2	19	-/A	2/12	1	2	FACETS	0.796	0.692	0.906	0.796	0.692	0.906	CLONAL	1	TRUE	1	0.532209586029738	2		230	288	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733375	85733377	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs587776637	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	106	430	0	ENST00000370580.1:c.635_637del	p.Glu212del	p.E212del	ENST00000370580	NM_003921.4	212	gAAGga/gga	3/3	1	2	FACETS	0.929	0.838	1	0.929	0.838	1	CLONAL	1	TRUE	1	0.532209586029738	2		430	429	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399278	139399278	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778271353	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	273	666	2	ENST00000277541.6:c.4865G>A	p.Arg1622His	p.R1622H	ENST00000277541	NM_017617.3	1622	cGc/cAc	26/34	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.532209586029738	2		668	916	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652397	48652397	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	189	405	4	ENST00000376670.3:c.1073del	p.Pro358GlnfsTer74	p.P358Qfs*74	ENST00000376670	NM_002049.3	356	ggC/gg	6/6	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.532209586029738	1		409	390	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	147	562	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	0.903	0.827	0.981	0.903	0.827	0.981	CLONAL	1	TRUE	1	0.532209586029738	2		562	612	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686962	37686962	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	175	525	1	ENST00000447079.4:c.3871del	p.Gln1291ArgfsTer3	p.Q1291Rfs*3	ENST00000447079	NM_015083.1	1289	gCc/gc	14/14	1	2	FACETS	0.999	0.924	1	0.999	0.924	1	CLONAL	1	TRUE	1	0.532209586029738	2		526	658	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658869	3658869	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780117582	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	129	570	0	ENST00000294008.3:c.97G>A	p.Asp33Asn	p.D33N	ENST00000294008	NM_032444.2	33	Gac/Aac	2/15	1	2	FACETS	0.845	0.769	0.924	0.845	0.769	0.924	CLONAL	1	TRUE	1	0.532209586029738	2		570	574	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513037	106513037	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765837588	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	57	211	0	ENST00000359195.3:c.2051G>A	p.Arg684His	p.R684H	ENST00000359195	NM_002649.2	684	cGt/cAt	3/11	1	2	FACETS	0.843	0.731	0.963	0.843	0.731	0.963	CLONAL	1	TRUE	1	0.532209586029738	2		211	254	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271304	18271304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs553673157	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	240	722	1	ENST00000222254.8:c.346G>A	p.Glu116Lys	p.E116K	ENST00000222254	NM_005027.3	116	Gag/Aag	3/16	1	2	FACETS	0.952	0.89	1	0.952	0.89	1	CLONAL	1	TRUE	1	0.532209586029738	2		723	947	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732820	44732820	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	76	283	0	ENST00000377967.4:c.23T>C	p.Leu8Pro	p.L8P	ENST00000377967	NM_021140.2	8	cTc/cCc	1/29	1	1	FACETS	0.539	0.475	0.607	0.539	0.475	0.607	SUBCLONAL	1	TRUE	0	0.532209586029738	1		283	389	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434356	121434356	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	193	667	3	ENST00000257555.6:c.1124del	p.Gly375AlafsTer9	p.G375Afs*9	ENST00000257555		374	Ggg/gg	6/10	0.526908603317922	3	FACETS	1	0.965	1	0.535	0.495	0.576	CLONAL	1	TRUE	1	0.532209586029738	3		670	858	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776086	9776086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1250682190	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	197	715	4	ENST00000377346.4:c.550C>T	p.Arg184Trp	p.R184W	ENST00000377346	NM_005026.3	184	Cgg/Tgg	5/24	1	2	FACETS	0.905	0.839	0.973	0.905	0.839	0.973	CLONAL	1	TRUE	1	0.532209586029738	2		719	818	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37637694	37637694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1461567991	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	183	694	1	ENST00000249071.6:c.40G>A	p.Val14Met	p.V14M	ENST00000249071	NM_002872.4	14	Gtg/Atg	2/7	1	2	FACETS	0.863	0.798	0.93	0.863	0.798	0.93	CLONAL	1	TRUE	1	0.532209586029738	2		695	797	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133898	41133898	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	107	352	0	ENST00000379561.5:c.1730del	p.Gly577AlafsTer5	p.G577Afs*5	ENST00000379561	NM_002015.3	577	gGc/gc	2/3	1	2	FACETS	0.976	0.882	1	0.976	0.882	1	CLONAL	1	TRUE	1	0.532209586029738	2		352	412	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619031	37619031	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	185	612	0	ENST00000447079.4:c.707G>A	p.Ser236Asn	p.S236N	ENST00000447079	NM_015083.1	236	aGc/aAc	1/14	1	2	FACETS	0.999	0.925	1	0.999	0.925	1	CLONAL	1	TRUE	1	0.532209586029738	2		612	696	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436102	49436102	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	65	418	0	ENST00000301067.7:c.5879del	p.Gly1960AlafsTer87	p.G1960Afs*87	ENST00000301067	NM_003482.3	1960	gGc/gc	28/54	0.526908603317922	3	FACETS	0.636	0.553	0.727	0.318	0.276	0.364	SUBCLONAL	1	TRUE	1	0.532209586029738	3		418	486	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121604	2121604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746677177	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	225	758	0	ENST00000219476.3:c.1933G>A	p.Val645Ile	p.V645I	ENST00000219476	NM_000548.3	645	Gtc/Atc	18/42	1	2	FACETS	0.959	0.894	1	0.959	0.894	1	CLONAL	1	TRUE	1	0.532209586029738	2		758	882	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2189772	2189772	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	280	761	0	ENST00000398665.3:c.242C>T	p.Ala81Val	p.A81V	ENST00000398665	NM_032482.2	81	gCc/gTc	4/28	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.532209586029738	2		761	994	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318754	163318755	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	98	349	0	ENST00000271452.3:c.1150dup	p.Arg384LysfsTer6	p.R384Kfs*6	ENST00000271452	NM_145697.2	382	gaa/gAaa	13/14	0.371096822725892	3	FACETS	1	0.903	1	0.504	0.451	0.559	CLONAL	1	TRUE	1	0.532209586029738	3		349	463	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760724	133760724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778935845	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	240	885	0	ENST00000318560.5:c.3047G>A	p.Arg1016His	p.R1016H	ENST00000318560	NM_005157.4	1016	cGc/cAc	11/11	1	2	FACETS	0.912	0.852	0.974	0.912	0.852	0.974	CLONAL	1	TRUE	1	0.532209586029738	2		885	989	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605204	46605204	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1459319402	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	102	335	6	ENST00000263734.3:c.1421G>C	p.Ser474Thr	p.S474T	ENST00000263734	NM_001430.4	474	aGc/aCc	10/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.532209586029738	2		341	314	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67132621	67132623	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	rs761606770	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	92	474	0	ENST00000412916.2:c.508_510del	p.Gln170del	p.Q170del	ENST00000412916		168	agACAa/aga	6/6	1	2	FACETS	0.696	0.62	0.775	0.696	0.62	0.775	SUBCLONAL	1	TRUE	1	0.532209586029738	2		474	497	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748369	162748369	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	29	293	0	ENST00000367921.3:c.2284-1G>T		p.X762_splice	ENST00000367921	NM_006182.2	762			0.371096822725892	3	FACETS	0.444	0.357	0.542	0.222	0.178	0.271	SUBCLONAL	1	TRUE	1	0.532209586029738	3		293	311	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006078	22006078	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	179	385	0	ENST00000276925.6:c.325C>T	p.Arg109Cys	p.R109C	ENST00000276925	NM_004936.3	109	Cgc/Tgc	2/2	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.532209586029738	2		385	565	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974816	15974816	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	42	372	0	ENST00000268712.3:c.4059G>C	p.Glu1353Asp	p.E1353D	ENST00000268712	NM_006311.3	1353	gaG/gaC	30/46	1	2	FACETS	0.407	0.34	0.481	0.407	0.34	0.481	SUBCLONAL	1	TRUE	1	0.532209586029738	2		372	388	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272356	38272356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	160	596	1	ENST00000425967.3:c.2011G>A	p.Ala671Thr	p.A671T	ENST00000425967	NM_001174067.1	671	Gca/Aca	15/19	1	2	FACETS	0.925	0.851	1	0.925	0.851	1	CLONAL	1	TRUE	1	0.532209586029738	2		597	650	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317061	11317061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	162	562	1	ENST00000361445.4:c.433G>A	p.Val145Met	p.V145M	ENST00000361445	NM_004958.3	145	Gtg/Atg	4/58	1	2	FACETS	0.96	0.884	1	0.96	0.884	1	CLONAL	1	TRUE	1	0.532209586029738	2		563	634	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598307	28598307	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	265	828	1	ENST00000253063.3:c.279C>A	p.Phe93Leu	p.F93L	ENST00000253063	NM_031459.4	93	ttC/ttA	3/10	1	2	FACETS	0.94	0.882	1	0.94	0.882	1	CLONAL	1	TRUE	1	0.532209586029738	2		829	1059	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276732	115276732	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	81	305	0	ENST00000438362.2:c.727T>G	p.Phe243Val	p.F243V	ENST00000438362	NM_001242891.1	243	Ttt/Gtt	8/20	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.532209586029738	2		305	286	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748368	162748369	+	splice_acceptor_variant	Splice_Site	DNP	AG	AG	GT	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	29	292	1	ENST00000367921.3:c.2284-2_2284-1delinsGT		p.X762_splice	ENST00000367921	NM_006182.2	762			0.371096822725892	3	FACETS	0.444	0.357	0.542	0.222	0.178	0.271	SUBCLONAL	1	TRUE	1	0.532209586029738	3		293	311	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981563	201981565	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TGG	TGG	-	rs995289305	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	301	805	0	ENST00000359651.3:c.478+1_478+3del		p.X160_splice	ENST00000359651		160		3/8	0.371096822725892	3	FACETS	0.782	0.738	0.826	0.782	0.738	0.826	SUBCLONAL	2	TRUE	1	0.532209586029738	3		805	916	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981825	201981825	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	112	844	0	ENST00000359651.3:c.536A>G	p.Tyr179Cys	p.Y179C	ENST00000359651		179	tAc/tGc	4/8	0.371096822725892	3	FACETS	0.47	0.421	0.521	0.235	0.21	0.261	SUBCLONAL	1	TRUE	1	0.532209586029738	3		844	1135	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944287	206944287	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs150423829	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	88	474	0	ENST00000423557.1:c.343A>T	p.Asn115Tyr	p.N115Y	ENST00000423557	NM_000572.2	115	Aac/Tac	3/5	0.371096822725892	3	FACETS	0.568	0.503	0.638	0.284	0.251	0.319	SUBCLONAL	1	TRUE	1	0.532209586029738	3		474	737	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670369	246670369	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	113	408	0	ENST00000388985.4:c.151C>T	p.Arg51Cys	p.R51C	ENST00000388985		51	Cgc/Tgc	1/12	0.371096822725892	3	FACETS	0.698	0.628	0.772	0.349	0.314	0.386	SUBCLONAL	1	TRUE	1	0.532209586029738	3		408	770	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851679	63851679	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	174	527	1	ENST00000279873.7:c.2461del	p.His821IlefsTer61	p.H821Ifs*61	ENST00000279873	NM_032199.2	819	ctC/ct	10/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.532209586029738	2		528	601	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333879	70333879	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	72	350	0	ENST00000373644.4:c.1784A>T	p.Glu595Val	p.E595V	ENST00000373644	NM_030625.2	595	gAa/gTa	2/12	1	2	FACETS	0.82	0.722	0.924	0.82	0.722	0.924	CLONAL	1	TRUE	1	0.532209586029738	2		350	330	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710984	114710984	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773516884	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	185	380	0	ENST00000543371.1:c.208C>T	p.Pro70Ser	p.P70S	ENST00000543371	NM_001198531.1	70	Cct/Tct	2/14	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.532209586029738	2		380	585	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589630	69589630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	55	104	0	ENST00000168712.1:c.223G>A	p.Asp75Asn	p.D75N	ENST00000168712	NM_002007.2	75	Gac/Aac	1/3	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.532209586029738	2		104	170	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186814	108186814	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	79	417	0	ENST00000278616.4:c.6172T>A	p.Ser2058Thr	p.S2058T	ENST00000278616	NM_000051.3	2058	Tca/Aca	42/63	1	2	FACETS	0.719	0.635	0.808	0.719	0.635	0.808	SUBCLONAL	1	TRUE	1	0.532209586029738	2		417	413	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344627	118344627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	46	420	0	ENST00000534358.1:c.2753G>A	p.Gly918Asp	p.G918D	ENST00000534358	NM_005933.3	918	gGt/gAt	3/36	1	2	FACETS	0.383	0.323	0.45	0.383	0.323	0.45	SUBCLONAL	1	TRUE	1	0.532209586029738	2		420	451	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025564	1025564	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	223	717	0	ENST00000358495.3:c.811C>T	p.Arg271Trp	p.R271W	ENST00000358495	NM_134424.2	271	Cgg/Tgg	9/12	0.508838406309824	3	FACETS	1	0.941	1	0.506	0.471	0.543	CLONAL	1	TRUE	1	0.532209586029738	3		717	1048	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489040	56489040	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	125	411	0	ENST00000267101.3:c.1860-1G>T		p.X620_splice	ENST00000267101	NM_001982.3	620			0.526908603317922	3	FACETS	1	0.923	1	0.509	0.462	0.558	CLONAL	1	TRUE	1	0.532209586029738	3		411	584	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858642	57858642	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751408248	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	134	521	0	ENST00000228682.2:c.380G>A	p.Gly127Asp	p.G127D	ENST00000228682	NM_005269.2	127	gGc/gAc	4/12	0.526908603317922	3	FACETS	0.884	0.805	0.968	0.442	0.402	0.484	CLONAL	1	TRUE	1	0.532209586029738	3		521	721	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240971	133240971	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	150	581	0	ENST00000320574.5:c.2546T>C	p.Leu849Pro	p.L849P	ENST00000320574	NM_006231.2	849	cTg/cCg	22/49	0.526908603317922	3	FACETS	0.859	0.785	0.936	0.429	0.392	0.468	CLONAL	1	TRUE	1	0.532209586029738	3		581	831	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303446	91303446	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	104	358	0	ENST00000355112.3:c.1157T>C	p.Ile386Thr	p.I386T	ENST00000355112	NM_000057.2	386	aTt/aCt	6/22	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.532209586029738	2		358	376	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347480	91347480	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	137	509	0	ENST00000355112.3:c.3642G>T	p.Met1214Ile	p.M1214I	ENST00000355112	NM_000057.2	1214	atG/atT	19/22	1	2	FACETS	0.876	0.8	0.955	0.876	0.8	0.955	CLONAL	1	TRUE	1	0.532209586029738	2		509	588	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110806	2110806	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45469099	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	209	634	0	ENST00000219476.3:c.1111C>T	p.Gln371Ter	p.Q371*	ENST00000219476	NM_000548.3	371	Cag/Tag	11/42	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.532209586029738	2		634	726	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658869	3658870	+	missense_variant	Missense_Mutation	DNP	CT	CT	TC	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	129	576	0	ENST00000294008.3:c.96_97delinsGA	p.Asp33Asn	p.D33N	ENST00000294008	NM_032444.2	32	gaAGac/gaGAac	2/15	1	2	FACETS	0.843	0.767	0.922	0.843	0.767	0.922	CLONAL	1	TRUE	1	0.532209586029738	2		576	575	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808042	3808042	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	48	340	0	ENST00000262367.5:c.3377T>A	p.Phe1126Tyr	p.F1126Y	ENST00000262367	NM_004380.2	1126	tTt/tAt	18/31	1	2	FACETS	0.439	0.372	0.513	0.439	0.372	0.513	SUBCLONAL	1	TRUE	1	0.532209586029738	2		340	411	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646303	23646303	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	151	578	1	ENST00000261584.4:c.1564C>A	p.Pro522Thr	p.P522T	ENST00000261584	NM_024675.3	522	Cca/Aca	4/13	1	2	FACETS	0.972	0.892	1	0.972	0.892	1	CLONAL	1	TRUE	1	0.532209586029738	2		579	584	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836979	89836979	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	230	650	2	ENST00000389301.3:c.2215C>A	p.Pro739Thr	p.P739T	ENST00000389301	NM_000135.2	739	Ccg/Acg	24/43	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.532209586029738	2		652	805	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131333	17131333	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	250	772	0	ENST00000285071.4:c.119G>T	p.Gly40Val	p.G40V	ENST00000285071	NM_144997.5	40	gGc/gTc	4/14	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.532209586029738	2		772	896	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372032	45372032	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	98	401	0	ENST00000262160.6:c.1135+2T>C		p.X379_splice	ENST00000262160	NM_005901.5	379			0.371096822725892	3	FACETS	1	0.977	1	0.651	0.586	0.719	CLONAL	1	TRUE	1	0.532209586029738	3		401	358	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961574	18961574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	185	608	1	ENST00000262803.5:c.707G>A	p.Arg236His	p.R236H	ENST00000262803	NM_002911.3	236	cGc/cAc	5/24	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.532209586029738	2		609	677	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921115	50921115	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	197	581	0	ENST00000440232.2:c.3235T>A	p.Phe1079Ile	p.F1079I	ENST00000440232	NM_002691.3	1079	Ttc/Atc	27/27	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.532209586029738	2		581	690	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754856	29754856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	152	424	0	ENST00000389048.3:c.1079G>A	p.Arg360Lys	p.R360K	ENST00000389048	NM_004304.4	360	aGg/aAg	4/29	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.532209586029738	2		424	508	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877375	40877375	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	161	527	0	ENST00000373198.4:c.2321T>G	p.Leu774Arg	p.L774R	ENST00000373198	NM_133170.3	774	cTc/cGc	15/32	0.508838406309824	3	FACETS	1	0.938	1	0.512	0.47	0.555	CLONAL	1	TRUE	1	0.532209586029738	3		527	748	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324156	62324158	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGG	AGG	-	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	153	600	0	ENST00000360203.5:c.2656_2658del		p.X886_splice	ENST00000360203	NM_001283009.1	886		29/35	0.508838406309824	3	FACETS	0.899	0.823	0.978	0.449	0.411	0.489	CLONAL	1	TRUE	1	0.532209586029738	3		600	810	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42842589	42842590	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs771443342	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	244	652	0	ENST00000398585.3:c.1267dup	p.Ala423GlyfsTer21	p.A423Gfs*21	ENST00000398585	NM_001135099.1	423	gcc/gGcc	11/14	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.532209586029738	2		652	884	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641731	12641731	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	153	489	0	ENST00000251849.4:c.910G>T	p.Gly304Cys	p.G304C	ENST00000251849	NM_002880.3	304	Ggc/Tgc	9/17	0.532209586029738	2	FACETS	0.8	0.733	0.869	0.4	0.366	0.435	SUBCLONAL	1	TRUE	0	0.532209586029738	2		489	719	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275240	41275240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	123	327	0	ENST00000349496.5:c.1406G>A	p.Arg469His	p.R469H	ENST00000349496	NM_001904.3	469	cGt/cAt	9/15	0.532209586029738	2	FACETS	1	0.957	1	0.541	0.493	0.591	CLONAL	1	TRUE	0	0.532209586029738	2		327	427	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442539	52442539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572063023	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	103	488	0	ENST00000460680.1:c.206C>T	p.Thr69Met	p.T69M	ENST00000460680	NM_004656.3	69	aCg/aTg	4/17	0.532209586029738	2	FACETS	0.666	0.598	0.739	0.333	0.299	0.37	SUBCLONAL	1	TRUE	0	0.532209586029738	2		488	581	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431007	181431007	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760688357	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	227	712	0	ENST00000325404.1:c.859G>A	p.Ala287Thr	p.A287T	ENST00000325404	NM_003106.3	287	Gcc/Acc	1/1	1	2	FACETS	0.982	0.916	1	0.982	0.916	1	CLONAL	1	TRUE	1	0.532209586029738	2		712	869	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182681778	182681778	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1460834002	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	127	445	0	ENST00000292782.4:c.280G>A	p.Ala94Thr	p.A94T	ENST00000292782	NM_020640.2	94	Gca/Aca	3/7	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.532209586029738	2		445	455	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447621	187447621	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778230721	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	142	652	2	ENST00000232014.4:c.572C>T	p.Pro191Leu	p.P191L	ENST00000232014	NM_001130845.1	191	cCg/cTg	5/10	1	2	FACETS	0.784	0.716	0.854	0.784	0.716	0.854	SUBCLONAL	1	TRUE	1	0.532209586029738	2		654	681	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590666	189590666	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	87	421	0	ENST00000264731.3:c.1231T>A	p.Tyr411Asn	p.Y411N	ENST00000264731	NM_003722.4	411	Tat/Aat	10/14	1	2	FACETS	0.903	0.806	1	0.903	0.806	1	CLONAL	1	TRUE	1	0.532209586029738	2		421	362	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902622	1902622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	230	713	0	ENST00000382891.5:c.241G>A	p.Asp81Asn	p.D81N	ENST00000382891	NM_133335.3	81	Gat/Aat	2/22	1	2	FACETS	0.953	0.889	1	0.953	0.889	1	CLONAL	1	TRUE	1	0.532209586029738	2		713	907	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521105	187521105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	137	439	1	ENST00000441802.2:c.12050G>A	p.Cys4017Tyr	p.C4017Y	ENST00000441802	NM_005245.3	4017	tGc/tAc	22/27	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.532209586029738	2		440	513	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409427	31409427	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1195955783	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	81	348	0	ENST00000344624.3:c.3680C>T	p.Ala1227Val	p.A1227V	ENST00000344624		1227	gCg/gTg	29/33	1	2	FACETS	0.982	0.874	1	0.982	0.874	1	CLONAL	1	TRUE	1	0.532209586029738	2		348	310	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170866	56170866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	74	251	0	ENST00000399503.3:c.1694G>A	p.Gly565Glu	p.G565E	ENST00000399503	NM_005921.1	565	gGa/gAa	10/20	1	2	FACETS	0.874	0.772	0.983	0.874	0.772	0.983	CLONAL	1	TRUE	1	0.532209586029738	2		251	318	SUCCESS
APC	324	MSKCC	GRCh37	5	112170646	112170646	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs587783035	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	68	246	0	ENST00000257430.4:c.1744-2A>T		p.X582_splice	ENST00000257430	NM_000038.5	582			1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.532209586029738	2		246	248	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953766	131953766	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	47	226	0	ENST00000265335.6:c.3169C>T	p.His1057Tyr	p.H1057Y	ENST00000265335		1057	Cat/Tat	21/25	1	2	FACETS	0.73	0.621	0.847	0.73	0.621	0.847	SUBCLONAL	1	TRUE	1	0.532209586029738	2		226	242	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158725	26158725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752165028	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	117	439	0	ENST00000289316.2:c.328C>T	p.His110Tyr	p.H110Y	ENST00000289316	NM_138720.2	110	Cac/Tac	1/2	1	2	FACETS	0.839	0.76	0.922	0.839	0.76	0.922	CLONAL	1	TRUE	1	0.532209586029738	2		439	524	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163228	32163228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	197	881	0	ENST00000375023.3:c.5998G>A	p.Glu2000Lys	p.E2000K	ENST00000375023	NM_004557.3	2000	Gag/Aag	30/30	1	2	FACETS	0.871	0.808	0.937	0.871	0.808	0.937	CLONAL	1	TRUE	1	0.532209586029738	2		881	850	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168946	32168946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	211	875	0	ENST00000375023.3:c.4087G>A	p.Ala1363Thr	p.A1363T	ENST00000375023	NM_004557.3	1363	Gca/Aca	22/30	1	2	FACETS	0.896	0.833	0.961	0.896	0.833	0.961	CLONAL	1	TRUE	1	0.532209586029738	2		875	885	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242488	55242488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559717059	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	109	409	0	ENST00000275493.2:c.2258C>T	p.Pro753Leu	p.P753L	ENST00000275493	NM_005228.3	753	cCg/cTg	19/28	1	2	FACETS	0.9	0.813	0.991	0.9	0.813	0.991	CLONAL	1	TRUE	1	0.532209586029738	2		409	455	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515137	148515137	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	162	447	0	ENST00000320356.2:c.1072C>A	p.Arg358Ser	p.R358S	ENST00000320356	NM_004456.4	358	Cgc/Agc	10/20	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.532209586029738	2		447	597	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205015	38205016	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	147	572	0	ENST00000317025.8:c.674dup	p.Asn225LysfsTer2	p.N225Kfs*2	ENST00000317025	NM_023034.1	225	aat/aaAt	2/24	1	2	FACETS	0.992	0.91	1	0.992	0.91	1	CLONAL	1	TRUE	1	0.532209586029738	2		572	557	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964415	70964415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777306806	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	134	426	2	ENST00000276594.2:c.1613G>A	p.Arg538His	p.R538H	ENST00000276594	NM_024504.3	538	cGt/cAt	8/8	1	2	FACETS	0.97	0.886	1	0.97	0.886	1	CLONAL	1	TRUE	1	0.532209586029738	2		428	519	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090566	5090566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	88	284	0	ENST00000381652.3:c.2882G>A	p.Cys961Tyr	p.C961Y	ENST00000381652	NM_004972.3	961	tGc/tAc	21/25	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.532209586029738	2		284	276	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27203007	27203007	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	131	513	0	ENST00000380036.4:c.2099A>G	p.Lys700Arg	p.K700R	ENST00000380036	NM_000459.3	700	aAg/aGg	13/23	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.532209586029738	2		513	488	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139563044	139563044	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	241	791	0	ENST00000308874.7:c.116C>A	p.Pro39His	p.P39H	ENST00000308874		39	cCt/cAt	4/10	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.532209586029738	2		791	897	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933540	39933540	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	204	350	0	ENST00000378444.4:c.1059del	p.Tyr354ThrfsTer24	p.Y354Tfs*24	ENST00000378444	NM_001123385.1	353	acC/ac	4/15	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.532209586029738	1		350	412	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748368	162748368	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0041855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	29	286	0	ENST00000367921.3:c.2284-2A>G		p.X762_splice	ENST00000367921	NM_006182.2	762			0.371096822725892	3	FACETS	0.449	0.361	0.549	0.225	0.18	0.275	SUBCLONAL	1	TRUE	1	0.532209586029738	3		286	307	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	39	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.288821859278774	2		215	244	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521544	8521544	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	97	514	1	ENST00000356435.5:c.694C>T	p.Arg232Cys	p.R232C	ENST00000356435		232	Cgc/Tgc	9/35	0.288821859278774	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.288821859278774	1		515	537	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900288	101900288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111854391	NA	P-0041869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	51	361	0	ENST00000374994.4:c.722C>T	p.Ser241Leu	p.S241L	ENST00000374994	NM_004612.2	241	tCg/tTg	4/9	0.288821859278774	1	FACETS	0.617	0.524	0.718	0.617	0.524	0.718	SUBCLONAL	1	TRUE	0	0.288821859278774	1		361	490	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741608	145741608	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1319378486	NA	P-0041869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	117	1026	0	ENST00000428558.2:c.895C>T	p.Pro299Ser	p.P299S	ENST00000428558	NM_004260.3	299	Cca/Tca	5/22	0.165722699310364	3	FACETS	0.836	0.752	0.925	0.418	0.376	0.463	INDETERMINATE	1	TRUE	1	0.288821859278774	3		1026	1109	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428005	49428005	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	176	778	0	ENST00000301067.7:c.10585G>C	p.Glu3529Gln	p.E3529Q	ENST00000301067	NM_003482.3	3529	Gag/Cag	38/54	0.165722699310364	3	FACETS	1	0.988	1	0.709	0.653	0.768	INDETERMINATE	1	TRUE	1	0.288821859278774	3		778	983	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197348	94197348	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	38	381	0	ENST00000323929.3:c.1156G>A	p.Val386Met	p.V386M	ENST00000323929	NM_005591.3	386	Gtg/Atg	11/20	0.165722699310364	3	FACETS	0.418	0.345	0.501	0.209	0.172	0.251	INDETERMINATE	1	TRUE	1	0.288821859278774	3		381	720	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427997	49427997	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	166	761	0	ENST00000301067.7:c.10593G>C	p.Gln3531His	p.Q3531H	ENST00000301067	NM_003482.3	3531	caG/caC	38/54	0.165722699310364	3	FACETS	1	0.986	1	0.687	0.63	0.745	INDETERMINATE	1	TRUE	1	0.288821859278774	3		761	958	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805448	46805448	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1335165337	NA	P-0041869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	213	949	1	ENST00000290295.7:c.508C>T	p.Gln170Ter	p.Q170*	ENST00000290295	NM_006361.5	170	Cag/Tag	1/2	0.165722699310364	3	FACETS	1	0.991	1	0.745	0.691	0.801	INDETERMINATE	1	TRUE	1	0.288821859278774	3		950	1133	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221956	1221956	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	129	798	0	ENST00000326873.7:c.871G>C	p.Glu291Gln	p.E291Q	ENST00000326873	NM_000455.4	291	Gag/Cag	7/10	1	2	FACETS	0.998	0.904	1	0.998	0.904	1	CLONAL	1	TRUE	1	0.288821859278774	2		798	895	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913554	39913554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	86	594	0	ENST00000378444.4:c.4774G>A	p.Asp1592Asn	p.D1592N	ENST00000378444	NM_001123385.1	1592	Gat/Aat	13/15	1	2	FACETS	0.873	0.773	0.981	0.873	0.773	0.981	CLONAL	1	TRUE	1	0.288821859278774	2		594	682	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0041900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	70	429	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.189740442833604	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.31	1		429	328	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0041900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	44	446	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.498	0.417	0.588	0.498	0.417	0.588	SUBCLONAL	1	TRUE	1	0.31	2		446	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0041900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	84	923	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.189740442833604	1	FACETS	0.707	0.624	0.795	0.707	0.624	0.795	SUBCLONAL	1	TRUE	0	0.31	1		923	648	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216516	36216516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771120688	NA	P-0041900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	196	1028	0	ENST00000222270.7:c.3779G>A	p.Arg1260His	p.R1260H	ENST00000222270	NM_014727.1	1260	cGt/cAt	12/37	1	2	FACETS	0.8	0.742	0.86	1	0.992	1	SUBCLONAL	2	TRUE	1	0.31	2		1028	790	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0041949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	106	351	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.442672336496755	2		351	450	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0041950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	218	534	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.271423636043555	4	FACETS	1	0.988	1	0.813	0.764	0.863	INDETERMINATE	2	TRUE	1	0.544500143559346	4		534	507	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3795330	3795330	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	87	429	1	ENST00000262367.5:c.3862C>T	p.Arg1288Trp	p.R1288W	ENST00000262367	NM_004380.2	1288	Cgg/Tgg	22/31	0.544500143559346	3	FACETS	0.771	0.685	0.864	0.386	0.342	0.432	SUBCLONAL	1	TRUE	1	0.544500143559346	3		430	527	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553609	29553609	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759679443	NA	P-0041950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	66	403	1	ENST00000356175.3:c.2158C>T	p.Arg720Trp	p.R720W	ENST00000356175	NM_000267.3	720	Cgg/Tgg	18/57	0.271423636043555	4	FACETS	1	0.955	1	0.403	0.352	0.456	INDETERMINATE	1	TRUE	1	0.544500143559346	4		404	310	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953792	55953792	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	60	516	0	ENST00000263923.4:c.3644A>G	p.Asp1215Gly	p.D1215G	ENST00000263923	NM_002253.2	1215	gAc/gGc	27/30	0.544500143559346	3	FACETS	0.658	0.569	0.755	0.329	0.284	0.378	SUBCLONAL	1	TRUE	1	0.544500143559346	3		516	426	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876445	35876445	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs368172701	NA	P-0041950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	104	710	0	ENST00000303115.3:c.1237A>T	p.Ser413Cys	p.S413C	ENST00000303115	NM_002185.3	413	Agc/Tgc	8/8	0.481249135894282	3	FACETS	0.929	0.835	1	0.465	0.417	0.514	CLONAL	1	TRUE	1	0.544500143559346	3		710	523	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518042	8518042	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	27	433	0	ENST00000356435.5:c.1349G>T	p.Gly450Val	p.G450V	ENST00000356435		450	gGa/gTa	10/35	0.544500143559346	3	FACETS	0.306	0.243	0.377	0.153	0.121	0.189	SUBCLONAL	1	TRUE	1	0.544500143559346	3		433	413	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637711	52637711	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	31	351	1	ENST00000394830.3:c.2605C>T	p.Gln869Ter	p.Q869*	ENST00000394830	NM_018313.4	869	Cag/Tag	18/30	1	2	FACETS	1	0.839	1	1	0.839	1	CLONAL	1	TRUE	1	0.19	2		352	314	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183692	10183693	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs869025615	NA	P-0041961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	53	658	0	ENST00000256474.2:c.163dup	p.Glu55GlyfsTer77	p.E55Gfs*77	ENST00000256474	NM_000551.3	54	atg/atGg	1/3	1	2	FACETS	0.998	0.851	1	0.998	0.851	1	CLONAL	1	TRUE	1	0.19	2		658	559	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	151	215	0				ENST00000310581	NM_198253.2	-/1132			0.50846065543619	6	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	FALSE	3	0.50846065543619	6		215	343	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0041970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	222	427	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.50846065543619	5	FACETS	0.99	0.931	1			1	CLONAL	3	FALSE	NA	0.50846065543619	5		427	518	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95597910	95597910	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0041970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	142	423	0	ENST00000393063.1:c.374C>G	p.Ser125Ter	p.S125*	ENST00000393063	NM_030621.3	125	tCa/tGa	5/28	0.503369064258435	4	FACETS	0.928	0.853	1	0.928	0.853	1	CLONAL	2	FALSE	2	0.50846065543619	4		423	454	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41552995	41553257	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAATATCTCTGTAAACTAATATTTAAAGAAGTGATGGACATCAGTCACCTCTTGGGGAATATAGACAGGCCAGAAACTAAAACACTGCCTGGAAAATTAACAATGATAATGGATGATACTCCATCTCCCGTAAAAATAGTGAGACTTGAGTAATGTTTGATGTCACTTGTCTTTCTAGGATTACTTTGATATTGTGAAGAGCCCCATGGATCTTTCTACCATTAAGAGGAAGTTAGACACTGGACAGTATCAGGAGCCCTGGC	TAATATCTCTGTAAACTAATATTTAAAGAAGTGATGGACATCAGTCACCTCTTGGGGAATATAGACAGGCCAGAAACTAAAACACTGCCTGGAAAATTAACAATGATAATGGATGATACTCCATCTCCCGTAAAAATAGTGAGACTTGAGTAATGTTTGATGTCACTTGTCTTTCTAGGATTACTTTGATATTGTGAAGAGCCCCATGGATCTTTCTACCATTAAGAGGAAGTTAGACACTGGACAGTATCAGGAGCCCTGGC	-	novel	NA	P-0041970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	104	46	0	ENST00000263253.7:c.3262-178_3346del		p.X1088_splice	ENST00000263253	NM_001429.3	1088		18/31	0.31367507364972	4	FACETS	0.928	0.875	0.976	1	0.992	1	CLONAL	5	FALSE	2	0.50846065543619	4		46	133	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922747	44922751	+	frameshift_variant	Frame_Shift_Del	DEL	CTCAG	CTCAG	-	novel	NA	P-0041970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	167	234	0	ENST00000377967.4:c.1608_1612del	p.Ser537LeufsTer14	p.S537Lfs*14	ENST00000377967	NM_021140.2	536	aaCTCAGtc/aatc	16/29	0.418325237610559	2	FACETS	0.869	0.822	0.915			1	CLONAL	3	FALSE	NA	0.50846065543619	2		234	252	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0041979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	48	376	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	0.3	4	FACETS	0.872	0.739	1			1	CLONAL	2	TRUE	NA	0.18	4		376	361	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0041979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	14	512	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.197334491854144	4	FACETS	0.408	0.293	0.548	0.204	0.146	0.274	SUBCLONAL	1	TRUE	2	0.18	4		512	450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	26	676	0	ENST00000269305.4:c.811G>C	p.Glu271Gln	p.E271Q	ENST00000269305	NM_001126112.2	271	Gag/Cag	8/11	0.256227270426427	4	FACETS	0.764	0.604	0.948	0.382	0.302	0.474	CLONAL	1	TRUE	2	0.18	4		676	446	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749389	41749389	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	14	350	0	ENST00000226382.2:c.406G>A	p.Asp136Asn	p.D136N	ENST00000226382	NM_003924.3	136	Gac/Aac	2/3	0.128667207686032	1	FACETS	1	0.799	1	1	0.799	1	CLONAL	1	TRUE	0	0.18	1		350	126	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467924	50467924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	10	517	0	ENST00000331340.3:c.1159G>A	p.Glu387Lys	p.E387K	ENST00000331340	NM_006060.4	387	Gag/Aag	8/8	1	2	FACETS	0.635	0.43	0.891	0.635	0.43	0.891	SUBCLONAL	1	TRUE	1	0.18	2		517	175	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609791	28609791	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146341559	NA	P-0041979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	12	454	0	ENST00000241453.7:c.1438G>A	p.Glu480Lys	p.E480K	ENST00000241453	NM_004119.2	480	Gaa/Aaa	12/24	0.197334491854144	0	FACETS	0.509	0.357	0.695			1	SUBCLONAL	1	TRUE	0	0.18	0		454	215	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446420	70446420	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0041979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	19	406	0	ENST00000373644.4:c.5360C>G	p.Ser1787Ter	p.S1787*	ENST00000373644	NM_030625.2	1787	tCa/tGa	11/12	0.197334491854144	3	FACETS	0.728	0.552	0.935	0.364	0.276	0.468	CLONAL	1	TRUE	1	0.18	3		406	316	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849901	151849901	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	21	414	0	ENST00000262189.6:c.12415C>T	p.Arg4139Ter	p.R4139*	ENST00000262189	NM_170606.2	4139	Cga/Tga	49/59	0.197334491854144	4	FACETS	0.748	0.575	0.95	0.374	0.287	0.475	CLONAL	1	TRUE	2	0.18	4		414	368	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144442	58144442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373619077	NA	P-0041979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	39	281	0	ENST00000257904.6:c.629G>A	p.Arg210Gln	p.R210Q	ENST00000257904	NM_000075.3	210	cGa/cAa	5/8	0.256227270426427	4	FACETS	1	0.902	1	0.566	0.469	0.674	CLONAL	1	TRUE	2	0.18	4		281	452	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426526	49426526	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	66	952	0	ENST00000301067.7:c.11962C>T	p.Gln3988Ter	p.Q3988*	ENST00000301067	NM_003482.3	3988	Cag/Tag	39/54	0.500532629005747	4	FACETS	1	0.948	1	0.597	0.517	0.683	CLONAL	1	TRUE	2	0.18	4		952	725	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660066	12660066	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	23	389	0	ENST00000251849.4:c.155C>G	p.Ser52Cys	p.S52C	ENST00000251849	NM_002880.3	52	tCt/tGt	2/17	0.256227270426427	4	FACETS	0.826	0.644	1	0.413	0.322	0.519	CLONAL	1	TRUE	2	0.18	4		389	365	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612798	228612798	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	19	579	0	ENST00000366696.1:c.229C>G	p.Gln77Glu	p.Q77E	ENST00000366696	NM_003493.2	77	Cag/Gag	1/1	0.3	1	FACETS	0.582	0.441	0.748	0.582	0.441	0.748	SUBCLONAL	1	TRUE	0	0.18	1		579	330	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273916	10273916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	23	802	1	ENST00000330684.3:c.353C>T	p.Ser118Phe	p.S118F	ENST00000330684	NM_001134407.1	118	tCc/tTc	2/13	0.3	0	FACETS	0.966	0.756	1			1	CLONAL	1	TRUE	0	0.18	0		803	217	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47679339	47679339	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	42	360	0	ENST00000347630.2:c.868G>A	p.Glu290Lys	p.E290K	ENST00000347630	NM_001007230.1	290	Gag/Aag	10/11	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.18	2		360	428	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772367	56772367	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	28	365	0	ENST00000337432.4:c.221G>C	p.Arg74Thr	p.R74T	ENST00000337432	NM_058216.2	74	aGa/aCa	2/9	1	2	FACETS	0.871	0.697	1	0.871	0.697	1	CLONAL	1	TRUE	1	0.18	2		365	357	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641447	47641447	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	19	316	0	ENST00000233146.2:c.832G>C	p.Glu278Gln	p.E278Q	ENST00000233146	NM_000251.2	278	Gaa/Caa	5/16	0.3	2	FACETS	0.558	0.423	0.718			1	SUBCLONAL	1	TRUE	NA	0.18	2		316	378	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519521	137519521	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	16	297	0	ENST00000367739.4:c.1117C>G	p.Pro373Ala	p.P373A	ENST00000367739	NM_000416.2	373	Cca/Gca	7/7	0.3	8	FACETS	0.875	0.646	1			1	CLONAL	1	TRUE	NA	0.18	8		297	313	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509413	46509413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772733484	NA	P-0041985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	293	485	0	ENST00000262741.5:c.1318C>T	p.His440Tyr	p.H440Y	ENST00000262741	NM_003629.3	440	Cac/Tac	10/10	0.738844880097352	3	FACETS	0.94	0.885	0.997			1	CLONAL	1	TRUE	NA	0.81747555599511	3		485	1074	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	442	759	0	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.81747555599511	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.81747555599511	1		759	611	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912519	32912519	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1405264241	NA	P-0041985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	137	268	0	ENST00000380152.3:c.4031del	p.Asn1344MetfsTer30	p.N1344Mfs*30	ENST00000380152		1343	Aaa/aa	11/27	0.81747555599511	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.81747555599511	1		268	194	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647679	2647679	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	255	469	0	ENST00000342085.4:c.1582C>G	p.Pro528Ala	p.P528A	ENST00000342085	NM_002613.4	528	Ccc/Gcc	14/14	0.81747555599511	3	FACETS	0.936	0.877	0.996	0.468	0.438	0.498	CLONAL	1	TRUE	1	0.81747555599511	3		469	939	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280726	41280726	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	197	440	0	ENST00000349496.5:c.2239G>A	p.Asp747Asn	p.D747N	ENST00000349496	NM_001904.3	747	Gac/Aac	15/15	1	2	FACETS	0.92	0.859	0.982	0.92	0.859	0.982	CLONAL	1	TRUE	1	0.81747555599511	2		440	524	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539942	187539957	+	frameshift_variant	Frame_Shift_Del	DEL	TGGTTGCTCGAAATTG	TGGTTGCTCGAAATTG	-	novel	NA	P-0041985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	140	319	0	ENST00000441802.2:c.7783_7798del	p.Gln2595AsnfsTer4	p.Q2595Nfs*4	ENST00000441802	NM_005245.3	2595	CAATTTCGAGCAACCAaa/aa	10/27	0.81747555599511	1	FACETS	0.912	0.856	0.967	0.912	0.856	0.967	CLONAL	1	TRUE	0	0.81747555599511	1		319	222	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0041989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	49	446	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.763	0.648	0.888	0.763	0.648	0.888	SUBCLONAL	1	TRUE	1	0.340797312266537	2		446	377	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970971	21970971	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	166	536	0	ENST00000304494.5:c.387C>A	p.Tyr129Ter	p.Y129*	ENST00000304494	NM_000077.4	129	taC/taA	2/3	0.339361977819473	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.340797312266537	1		536	774	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573563	48573564	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs786203560	NA	P-0041989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	20	214	0	ENST00000342988.3:c.153dup	p.Asp52ArgfsTer2	p.D52Rfs*2	ENST00000342988	NM_005359.5	49	-/A	2/12	0.319493868087207	1	FACETS	0.437	0.335	0.555	0.437	0.335	0.555	SUBCLONAL	1	TRUE	0	0.340797312266537	1		214	223	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284969	15284969	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	199	743	0	ENST00000263388.2:c.4646C>T	p.Ala1549Val	p.A1549V	ENST00000263388	NM_000435.2	1549	gCg/gTg	25/33	1	2	FACETS	0.974	0.901	1	0.974	0.901	1	CLONAL	1	TRUE	1	0.340797312266537	2		743	1199	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653782	89653782	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	rs886041877	NA	P-0041989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	41	189	0	ENST00000371953.3:c.80A>C	p.Tyr27Ser	p.Y27S	ENST00000371953	NM_000314.4	27	tAt/tCt	2/9	0.340797312266537	1	FACETS	0.92	0.774	1	0.92	0.774	1	CLONAL	1	TRUE	0	0.340797312266537	1		189	217	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858431	9858431	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	146	452	0	ENST00000330684.3:c.2970G>C	p.Glu990Asp	p.E990D	ENST00000330684	NM_001134407.1	990	gaG/gaC	13/13	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.340797312266537	2		452	723	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14031675	14031675	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	44	321	0	ENST00000311895.7:c.1864G>T	p.Ala622Ser	p.A622S	ENST00000311895	NM_005236.2	622	Gct/Tct	9/11	1	2	FACETS	0.519	0.435	0.611	0.519	0.435	0.611	SUBCLONAL	1	TRUE	1	0.340797312266537	2		321	498	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961110	55961110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	149	547	0	ENST00000263923.4:c.2830C>T	p.Arg944Ter	p.R944*	ENST00000263923	NM_002253.2	944	Cga/Tga	21/30	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.340797312266537	2		547	862	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253911	NA	P-0042099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	13	572	0	ENST00000269305.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000269305	NM_001126112.2	180	Gag/Aag	5/11	1	2	FACETS	0.057	0.04	0.078	0.057	0.04	0.078	SUBCLONAL	1	TRUE	1	0.736415132673133	2		572	620	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218084	108218084	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs760955058	NA	P-0042099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	35	236	0	ENST00000278616.4:c.8663T>C	p.Ile2888Thr	p.I2888T	ENST00000278616	NM_000051.3	2888	aTa/aCa	59/63	1	2	FACETS	0.255	0.209	0.306	0.255	0.209	0.306	SUBCLONAL	1	TRUE	1	0.736415132673133	2		236	373	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602688	10602688	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	341	699	1	ENST00000171111.5:c.890G>T	p.Cys297Phe	p.C297F	ENST00000171111	NM_203500.1	297	tGc/tTc	3/6	0.736415132673133	1	FACETS	0.974	0.932	1	0.974	0.932	1	CLONAL	1	TRUE	0	0.736415132673133	1		700	601	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197885	123197885	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	77	158	0	ENST00000218089.9:c.2009A>C	p.Glu670Ala	p.E670A	ENST00000218089	NM_001042749.1	670	gAa/gCa	20/35	1	1	FACETS	0.569	0.508	0.634	0.569	0.508	0.634	SUBCLONAL	1	TRUE	0	0.736415132673133	1		158	232	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807376	36807376	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	258	576	0	ENST00000373129.3:c.1288C>G	p.Gln430Glu	p.Q430E	ENST00000373129	NM_032017.1	430	Cag/Gag	12/12	1	2	FACETS	0.98	0.923	1	0.98	0.923	1	CLONAL	1	TRUE	1	0.736415132673133	2		576	715	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63810698	63810698	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	180	271	0	ENST00000279873.7:c.785G>C	p.Arg262Thr	p.R262T	ENST00000279873	NM_032199.2	262	aGa/aCa	5/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.736415132673133	2		271	456	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858792	9858792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	23	184	0	ENST00000330684.3:c.2609G>A	p.Cys870Tyr	p.C870Y	ENST00000330684	NM_001134407.1	870	tGc/tAc	13/13	1	2	FACETS	0.349	0.274	0.435	0.349	0.274	0.435	SUBCLONAL	1	TRUE	1	0.736415132673133	2		184	179	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508802	29508803	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	GGTAAGGATAC	novel	NA	P-0042099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	70	272	0	ENST00000356175.3:c.730+1_730+11dup		p.-243fs	ENST00000356175	NM_000267.3	243	-/GGTAAGGATAC	7/57	0.717622742360619	1	FACETS	0.448	0.395	0.504	0.448	0.395	0.504	SUBCLONAL	1	TRUE	0	0.736415132673133	1		272	268	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78858861	78858861	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	191	726	0	ENST00000306801.3:c.1896G>C	p.Glu632Asp	p.E632D	ENST00000306801	NM_020761.2	632	gaG/gaC	17/34	1	2	FACETS	0.637	0.59	0.686	0.637	0.59	0.686	SUBCLONAL	1	TRUE	1	0.736415132673133	2		726	814	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157480	106157481	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0042099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	115	228	0	ENST00000380013.4:c.2383dup	p.Ser795LysfsTer7	p.S795Kfs*7	ENST00000380013	NM_001127208.2	794	tca/tcAa	3/11	1	2	FACETS	0.913	0.832	0.997	0.913	0.832	0.997	CLONAL	1	TRUE	1	0.736415132673133	2		228	342	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226193	53226193	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	249	299	0	ENST00000375401.3:c.2656G>T	p.Glu886Ter	p.E886*	ENST00000375401	NM_004187.3	886	Gag/Tag	19/26	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.736415132673133	1		299	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0042104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	375	754	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.273564975038734	2	FACETS	0.87	0.825	0.917	0.87	0.825	0.917	CLONAL	2	TRUE	0	0.28703533151528	2		754	1501	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945665	151945665	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	143	540	0	ENST00000262189.6:c.1854G>T	p.Gln618His	p.Q618H	ENST00000262189	NM_170606.2	618	caG/caT	14/59	0.28703533151528	1	FACETS	0.869	0.791	0.951	0.869	0.791	0.951	CLONAL	1	TRUE	0	0.28703533151528	1		540	982	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941684	48941684	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000828-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	28	207	0	ENST00000267163.4:c.994G>C	p.Asp332His	p.D332H	ENST00000267163	NM_000321.2	332	Gat/Cat	10/27	0.232522050293219	1	FACETS	0.621	0.496	0.762	0.621	0.496	0.762	SUBCLONAL	1	TRUE	0	0.232522050293219	1		207	343	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-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	130	579	0	ENST00000269305.4:c.559+35_568del		p.X187_splice	ENST00000269305	NM_001126112.2	187		6/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.232522050293219	2		579	935	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42384966	42384966	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001101-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	250	578	0	ENST00000221972.3:c.600G>C	p.Glu200Asp	p.E200D	ENST00000221972	NM_021601.3	200	gaG/gaC	5/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		578	481	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0002386-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	64	374	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.548130016925163	4	FACETS	0.862	0.75	0.982	0.431	0.375	0.491	CLONAL	1	TRUE	2	0.65829259899625	4		374	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0002386-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	312	654	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.368933500213254	5	FACETS	0.966	0.936	0.995	0.966	0.936	0.995	INDETERMINATE	5	TRUE	0	0.65829259899625	5		656	390	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0002386-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	83	257	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.65829259899625	2		257	239	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239225	105239225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002386-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	74	441	0	ENST00000349310.3:c.1162C>T	p.Pro388Ser	p.P388S	ENST00000349310	NM_001014432.1	388	Ccc/Tcc	12/15	0.56561063421993	4	FACETS	1	0.946	1	0.565	0.498	0.635	CLONAL	1	TRUE	2	0.65829259899625	4		441	330	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939600	76939601	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002386-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	201	400	0	ENST00000373344.5:c.1147dup	p.Ile383AsnfsTer11	p.I383Nfs*11	ENST00000373344	NM_000489.3	383	atc/aAtc	9/35	0.57034575464855	3	FACETS	0.858	0.804	0.913	0.858	0.804	0.913	CLONAL	2	TRUE	1	0.65829259899625	3		400	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0002386-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	200	654	2	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	3	TRUE	NA	0.237311216721562	2		656	502	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0002386-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	140	257	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.225980959897033	1	FACETS	0.919	0.84	1	1	0.99	1	CLONAL	2	TRUE	0	0.237311216721562	1		257	566	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939600	76939601	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002386-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	138	400	0	ENST00000373344.5:c.1147dup	p.Ile383AsnfsTer11	p.I383Nfs*11	ENST00000373344	NM_000489.3	383	atc/aAtc	9/35	0.176166605591935	0	FACETS	0.651	0.594	0.711			1	SUBCLONAL	2	TRUE	0	0.237311216721562	0		400	681	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246438	53246438	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002386-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	99	333	0	ENST00000375401.3:c.544G>T	p.Asp182Tyr	p.D182Y	ENST00000375401	NM_004187.3	182	Gat/Tat	5/26	0.212962603232331	3	FACETS	0.764	0.68	0.855			1	SUBCLONAL	1	TRUE	NA	0.237311216721562	3		333	1221	SUCCESS
AR	367	MSKCC	GRCh37	X	66765854	66765854	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs956270286	NA	P-0002386-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	54	298	0	ENST00000374690.3:c.866A>G	p.Glu289Gly	p.E289G	ENST00000374690	NM_000044.3	289	gAa/gGa	1/8	0.176166605591935	0	FACETS	0.372	0.317	0.434			1	SUBCLONAL	1	TRUE	0	0.237311216721562	0		298	932	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0003322-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	102	521	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.397061694988679	1	FACETS	0.852	0.766	0.942	0.852	0.766	0.942	CLONAL	1	TRUE	0	0.415243685166243	1		521	457	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913385	NA	P-0003322-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	71	336	0	ENST00000304494.5:c.247C>G	p.His83Asp	p.H83D	ENST00000304494	NM_000077.4	83	Cac/Gac	2/3	0.415243685166243	1	FACETS	0.909	0.801	1	0.909	0.801	1	CLONAL	1	TRUE	0	0.415243685166243	1		336	298	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242483	55242506	+	inframe_deletion	In_Frame_Del	DEL	ATCTCCGAAAGCCAACAAGGAAAT	ATCTCCGAAAGCCAACAAGGAAAT	-	rs727504232	NA	P-0003322-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	959	332	0	ENST00000275493.2:c.2253_2276del	p.Ser752_Ile759del	p.S752_I759del	ENST00000275493	NM_005228.3	751	acATCTCCGAAAGCCAACAAGGAAATc/acc	19/28	0.415243685166243	19	FACETS	1	0.984	1			1	CLONAL	16	TRUE	NA	0.415243685166243	19		332	1301	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104386990	104386990	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003322-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	35	235	1	ENST00000369902.3:c.1355C>A	p.Ser452Tyr	p.S452Y	ENST00000369902	NM_016169.3	452	tCt/tAt	11/12	1	2	FACETS	0.484	0.398	0.581	0.484	0.398	0.581	SUBCLONAL	1	TRUE	1	0.415243685166243	2		236	348	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343201	118343201	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003322-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	25	271	0	ENST00000534358.1:c.1327T>G	p.Leu443Val	p.L443V	ENST00000534358	NM_005933.3	443	Tta/Gta	3/36	0.166029678806469	2	FACETS	0.444	0.351	0.551	0.222	0.175	0.276	INDETERMINATE	1	TRUE	0	0.415243685166243	2		271	271	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566283	141566283	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003322-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	31	289	0	ENST00000220592.5:c.1129G>A	p.Glu377Lys	p.E377K	ENST00000220592	NM_012154.3	377	Gaa/Aaa	9/19	0.13441613731121	4	FACETS	0.587	0.475	0.713	0.293	0.237	0.357	INDETERMINATE	1	TRUE	2	0.415243685166243	4		289	360	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	245	846	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.686576740714095	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.686576740714095	1		846	435	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779704	3779704	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567263529	NA	P-0004896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	296	609	0	ENST00000262367.5:c.5344G>A	p.Ala1782Thr	p.A1782T	ENST00000262367	NM_004380.2	1782	Gcg/Acg	31/31	0.641687478514119	3	FACETS	1	0.989	1			1	CLONAL	1	TRUE	NA	0.686576740714095	3		609	977	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898812	134898812	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368385190	NA	P-0004896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	20	259	0	ENST00000398015.3:c.1870G>A	p.Val624Ile	p.V624I	ENST00000398015	NM_004441.4	624	Gtc/Atc	10/16	1	2	FACETS	0.165	0.126	0.211	0.165	0.126	0.211	SUBCLONAL	1	TRUE	1	0.686576740714095	2		259	353	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224550	123224550	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	229	467	0	ENST00000218089.9:c.3403G>T	p.Glu1135Ter	p.E1135*	ENST00000218089	NM_001042749.1	1135	Gag/Tag	31/35	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.686576740714095	2		467	646	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0005264-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	373	598	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.398210018939442	9	FACETS	1	0.976	1			1	CLONAL	5	TRUE	NA	0.398210018939442	9		598	865	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0005264-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	77	846	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.398210018939442	9	FACETS	1	0.954	1			1	CLONAL	1	TRUE	NA	0.398210018939442	9		847	778	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300206	15300206	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005264-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	69	747	0	ENST00000263388.2:c.1070G>T	p.Ser357Ile	p.S357I	ENST00000263388	NM_000435.2	357	aGc/aTc	7/33	0.398210018939442	3	FACETS	1	0.902	1	0.518	0.453	0.588	CLONAL	1	TRUE	1	0.398210018939442	3		747	401	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006890	47006891	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005264-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	155	414	0	ENST00000377604.3:c.13dup	p.Arg5LysfsTer7	p.R5Kfs*7	ENST00000377604	NM_001204468.1	4	gaa/gAaa	2/24	0.352258102894736	2	FACETS	0.874	0.816	0.931			1	CLONAL	3	TRUE	NA	0.398210018939442	2		414	297	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249091	55249091	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519861	NA	P-0005264-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	74	717	0	ENST00000275493.2:c.2389T>A	p.Cys797Ser	p.C797S	ENST00000275493	NM_005228.3	797	Tgc/Agc	20/28	0.398210018939442	9	FACETS	1	0.929	1			1	CLONAL	1	TRUE	NA	0.398210018939442	9		717	814	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281344	49281344	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202077345	NA	P-0005264-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	75	765	0	ENST00000282018.3:c.391G>A	p.Val131Met	p.V131M	ENST00000282018	NM_020377.2	131	Gtg/Atg	1/1	0.398210018939442	2	FACETS	0.966	0.851	1	0.483	0.425	0.544	CLONAL	1	TRUE	0	0.398210018939442	2		765	390	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198272802	198272802	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745511585	NA	P-0005264-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	58	464	0	ENST00000335508.6:c.1159C>T	p.Arg387Trp	p.R387W	ENST00000335508	NM_012433.2	387	Cgg/Tgg	9/25	0.394057587641648	4	FACETS	0.928	0.799	1	0.464	0.399	0.534	CLONAL	1	TRUE	2	0.398210018939442	4		464	439	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	87	395	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.648779251010235	2		395	208	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888210	112888210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121918464	NA	P-0005361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	19	442	0	ENST00000351677.2:c.226G>A	p.Glu76Lys	p.E76K	ENST00000351677	NM_002834.3	76	Gag/Aag	3/16	NA	2	FACETS	0.067	0.05	0.087			1	INDETERMINATE	1	TRUE	NA	0.648779251010235	2		442	877	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653807	89653807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554893782	NA	P-0005361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	322	299	0	ENST00000371953.3:c.105G>A	p.Met35Ile	p.M35I	ENST00000371953	NM_000314.4	35	atG/atA	2/9	0.648779251010235	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.648779251010235	1		299	653	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572404	41572404	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs139310551	NA	P-0005361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	306	443	2	ENST00000263253.7:c.4933C>T	p.Arg1645Ter	p.R1645*	ENST00000263253	NM_001429.3	1645	Cga/Tga	30/31	0.642676080436601	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.648779251010235	1		445	522	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894899	101894899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs539413187	NA	P-0006466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	70	142	1	ENST00000374994.4:c.452G>A	p.Arg151His	p.R151H	ENST00000374994	NM_004612.2	151	cGc/cAc	3/9	0.517854957505631	2	FACETS	0.259	0.225	0.295			1	SUBCLONAL	1	TRUE	NA	0.85	2		143	637	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86676377	86676377	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	129	66	0	ENST00000274376.6:c.2655G>T	p.Trp885Cys	p.W885C	ENST00000274376	NM_002890.2	885	tgG/tgT	20/25	0.517854957505631	2	FACETS	0.525	0.478	0.575			1	SUBCLONAL	1	TRUE	NA	0.85	2		66	578	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575089	64575089	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	66	236	0	ENST00000312049.6:c.718G>C	p.Val240Leu	p.V240L	ENST00000312049	NM_130799.2	240	Gtg/Ctg	4/10	0.517854957505631	2	FACETS	0.144	0.124	0.165			1	SUBCLONAL	1	TRUE	NA	0.85	2		236	1081	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223491	53223491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	62	75	0	ENST00000375401.3:c.3868G>A	p.Gly1290Ser	p.G1290S	ENST00000375401	NM_004187.3	1290	Ggc/Agc	23/26	0.517854957505631	3	FACETS	0.426	0.368	0.488			1	SUBCLONAL	1	TRUE	NA	0.85	3		75	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577113	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CTCTCCCAGGACAGGCA	CTCTCCCAGGACAGGCA	-	novel	NA	P-0006466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	251	197	0	ENST00000269305.4:c.825_841del	p.Cys275Ter	p.C275*	ENST00000269305	NM_001126112.2	275	tgTGCCTGTCCTGGGAGAGac/tgac	8/11	0.517854957505631	1	FACETS	0.49	0.461	0.52	0.49	0.461	0.52	SUBCLONAL	1	TRUE	0	0.85	1		197	693	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0006609-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	193	447	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	2	TRUE	NA	0.547616051270012	2		447	342	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0007690-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	406	626	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	0.445822523837238	2	FACETS	0.76	0.733	0.786	0.76	0.733	0.786	INDETERMINATE	2	TRUE	0	0.870300368758242	2		626	614	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437503	52437522	+	frameshift_variant	Frame_Shift_Del	DEL	AGATCACGGACAGCACGGTT	AGATCACGGACAGCACGGTT	-	novel	NA	P-0007690-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	290	396	0	ENST00000460680.1:c.1639_1658del	p.Asn547GlyfsTer13	p.N547Gfs*13	ENST00000460680	NM_004656.3	547	AACCGTGCTGTCCGTGATCTg/g	13/17	0.870300368758242	2	FACETS	0.998	0.971	1	0.998	0.971	1	CLONAL	2	TRUE	0	0.870300368758242	2		396	334	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435395	56435396	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGGC	novel	NA	P-0008232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	243	728	0	ENST00000407977.2:c.1737_1741dup	p.Pro581ArgfsTer121	p.P581Rfs*121	ENST00000407977		581	cct/cGCCTCct	9/10	1	2	FACETS	0.76	0.71	0.812	0.76	0.71	0.812	SUBCLONAL	1	TRUE	1	0.583558473227426	2		728	1096	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0008440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	112	441	2	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.423453496004901	2		443	522	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220428	1220428	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	193	719	0	ENST00000326873.7:c.521A>G	p.His174Arg	p.H174R	ENST00000326873	NM_000455.4	174	cAc/cGc	4/10	0.423453496004901	1	FACETS	0.998	0.926	1	0.998	0.926	1	CLONAL	1	TRUE	0	0.423453496004901	1		719	720	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132399	11132399	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0008440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	163	656	0	ENST00000358026.2:c.2617-2A>T		p.X873_splice	ENST00000358026	NM_001128849.1	873			0.423453496004901	1	FACETS	0.914	0.842	0.989	0.914	0.842	0.989	CLONAL	1	TRUE	0	0.423453496004901	1		656	664	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965240	25965240	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	176	514	0	ENST00000435504.4:c.3966G>T	p.Gln1322His	p.Q1322H	ENST00000435504		1322	caG/caT	13/13	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.423453496004901	2		514	719	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0010980-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	114	441	2	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.36141747876834	3	FACETS	1	0.983	1	0.688	0.626	0.754	CLONAL	1	TRUE	1	0.549723783502973	3		443	384	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845854	72845855	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010980-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	135	475	0	ENST00000268489.5:c.3612dup	p.Pro1205SerfsTer11	p.P1205Sfs*11	ENST00000268489	NM_006885.3	1204	-/T	6/10	1	2	FACETS	0.781	0.712	0.853	0.781	0.712	0.853	SUBCLONAL	1	TRUE	1	0.549723783502973	2		475	629	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222987	1222987	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010980-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	357	677	0	ENST00000326873.7:c.924G>T	p.Trp308Cys	p.W308C	ENST00000326873	NM_000455.4	308	tgG/tgT	8/10	0.549723783502973	2	FACETS	0.956	0.915	0.998	0.956	0.915	0.998	CLONAL	2	TRUE	0	0.549723783502973	2		677	679	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602737	10602737	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010980-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	432	744	1	ENST00000171111.5:c.841C>A	p.Leu281Met	p.L281M	ENST00000171111	NM_203500.1	281	Ctg/Atg	3/6	0.537371830726943	2	FACETS	0.917	0.88	0.954	0.917	0.88	0.954	CLONAL	2	TRUE	0	0.549723783502973	2		745	857	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098601	11098601	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0010980-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	389	640	0	ENST00000358026.2:c.1118+1G>T		p.X373_splice	ENST00000358026	NM_001128849.1	373			0.537371830726943	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.549723783502973	2		640	703	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662958	227662958	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010980-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	170	689	0	ENST00000305123.5:c.497T>C	p.Val166Ala	p.V166A	ENST00000305123	NM_005544.2	166	gTg/gCg	1/2	0.248362395267896	3	FACETS	0.787	0.723	0.854	0.262	0.241	0.285	INDETERMINATE	1	TRUE	0	0.549723783502973	3		689	1002	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164513	47164513	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010980-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	78	295	0	ENST00000409792.3:c.1613G>T	p.Gly538Val	p.G538V	ENST00000409792	NM_014159.6	538	gGa/gTa	3/21	1	2	FACETS	0.915	0.812	1	0.915	0.812	1	CLONAL	1	TRUE	1	0.549723783502973	2		295	310	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288645	33288645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs865973372	NA	P-0010980-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	235	336	0	ENST00000374542.5:c.907G>A	p.Gly303Ser	p.G303S	ENST00000374542	NM_001141970.1	303	Ggc/Agc	3/8	0.549723783502973	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.549723783502973	3		336	511	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11552822	NA	P-0010980-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	165	640	0	ENST00000304494.5:c.250G>T	p.Asp84Tyr	p.D84Y	ENST00000304494	NM_000077.4	84	Gac/Tac	2/3	0.549723783502973	1	FACETS	0.953	0.883	1	0.953	0.883	1	CLONAL	1	TRUE	0	0.549723783502973	1		640	457	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430406	47430406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010980-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	55	559	0	ENST00000377045.4:c.1681C>T	p.Pro561Ser	p.P561S	ENST00000377045	NM_001654.4	561	Ccc/Tcc	15/16	1	2	FACETS	0.3	0.256	0.348	0.3	0.256	0.348	SUBCLONAL	1	TRUE	1	0.549723783502973	2		559	668	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411922	63411922	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010980-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	313	849	0	ENST00000330258.3:c.1245G>T	p.Met415Ile	p.M415I	ENST00000330258	NM_152424.3	415	atG/atT	2/2	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.549723783502973	2		849	1039	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011202-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	38	395	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.833	0.691	0.992	0.833	0.691	0.992	CLONAL	1	TRUE	1	0.265160296638994	2		395	344	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239940	53239940	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011202-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	82	357	0	ENST00000375401.3:c.1501T>C	p.Trp501Arg	p.W501R	ENST00000375401	NM_004187.3	501	Tgg/Cgg	11/26	1	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.265160296638994	1		357	363	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874942	151874942	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011202-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	72	422	0	ENST00000262189.6:c.7596T>G	p.Asn2532Lys	p.N2532K	ENST00000262189	NM_170606.2	2532	aaT/aaG	38/59	0.265160296638994	3	FACETS	0.994	0.868	1	0.497	0.434	0.565	CLONAL	1	TRUE	1	0.265160296638994	3		422	619	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0012598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	133	598	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.299757101458451	3	FACETS	1	0.984	1	0.699	0.636	0.765	CLONAL	1	TRUE	1	0.316256188077587	3		598	697	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554933	106554933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	31	269	0	ENST00000369096.4:c.2050G>A	p.Glu684Lys	p.E684K	ENST00000369096	NM_001198.3	684	Gag/Aag	7/7	1	2	FACETS	0.333	0.269	0.407	0.333	0.269	0.407	SUBCLONAL	1	TRUE	1	0.316256188077587	2		269	588	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427996	49427997	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0012598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	36	237	0	ENST00000301067.7:c.10593_10594del	p.Gln3531HisfsTer24	p.Q3531Hfs*24	ENST00000301067	NM_003482.3	3531	caGAtt/catt	38/54	1	2	FACETS	0.386	0.316	0.464	0.386	0.316	0.464	SUBCLONAL	1	TRUE	1	0.316256188077587	2		237	590	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319952	8319952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1460608894	NA	P-0012743-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	133	223	0	ENST00000356435.5:c.5549G>A	p.Arg1850Lys	p.R1850K	ENST00000356435		1850	aGa/aAa	34/35	0.691456606886079	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.691456606886079	1		223	235	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460538	8460538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs772029273	NA	P-0012743-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	196	414	0	ENST00000356435.5:c.3748G>T	p.Val1250Leu	p.V1250L	ENST00000356435		1250	Gtg/Ttg	22/35	0.691456606886079	1	FACETS	0.961	0.904	1	0.961	0.904	1	CLONAL	1	TRUE	0	0.691456606886079	1		414	386	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820133	139820133	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0012743-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	488	479	0	ENST00000247668.2:c.1288-2A>C		p.X430_splice	ENST00000247668	NM_021138.3	430			0.691456606886079	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.691456606886079	2		479	686	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41203080	41203080	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs80357112	NA	P-0012743-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	278	589	0	ENST00000357654.3:c.5332G>T	p.Asp1778Tyr	p.D1778Y	ENST00000357654	NM_007294.3	1778	Gat/Tat	20/23	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.691456606886079	2		589	799	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0012743-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	295	590	0	ENST00000269305.4:c.97-1G>A		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.691456606886079	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.691456606886079	1		590	510	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992729	68992729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779079528	NA	P-0012743-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	314	537	0	ENST00000288368.4:c.1694C>T	p.Ser565Leu	p.S565L	ENST00000288368	NM_024870.2	565	tCg/tTg	16/40	1	2	FACETS	0.919	0.869	0.971	0.919	0.869	0.971	CLONAL	1	TRUE	1	0.691456606886079	2		537	988	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636747	2636747	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012743-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	311	579	0	ENST00000342085.4:c.1196C>G	p.Ala399Gly	p.A399G	ENST00000342085	NM_002613.4	399	gCc/gGc	11/14	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.691456606886079	2		579	827	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0013079-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	257	678	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.247485340183274	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.253767849438438	2		678	952	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578466	7578466	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786202752	NA	P-0013079-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	163	777	0	ENST00000269305.4:c.464C>A	p.Thr155Asn	p.T155N	ENST00000269305	NM_001126112.2	155	aCc/aAc	5/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.253767849438438	2		777	1052	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266225	198266225	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013079-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	69	464	0	ENST00000335508.6:c.2395G>C	p.Asp799His	p.D799H	ENST00000335508	NM_012433.2	799	Gat/Cat	17/25	1	2	FACETS	0.814	0.709	0.928	0.814	0.709	0.928	CLONAL	1	TRUE	1	0.253767849438438	2		464	668	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562710	29562710	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs863224660	NA	P-0013079-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	101	516	2	ENST00000356175.3:c.3790G>T	p.Glu1264Ter	p.E1264*	ENST00000356175	NM_000267.3	1264	Gaa/Taa	28/57	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.253767849438438	2		518	671	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10273394	10273397	+	frameshift_variant	Frame_Shift_Del	DEL	TTCT	TTCT	-	novel	NA	P-0013079-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	63	581	1	ENST00000340748.4:c.906_909del	p.Lys302AsnfsTer5	p.K302Nfs*5	ENST00000340748		302	aaAGAA/aa	12/40	1	2	FACETS	0.606	0.522	0.696	0.606	0.522	0.696	SUBCLONAL	1	TRUE	1	0.253767849438438	2		582	820	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970901	21970901	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs45476696	NA	P-0013079-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	109	776	0	ENST00000304494.5:c.457G>T	p.Asp153Tyr	p.D153Y	ENST00000304494	NM_000077.4	153	Gac/Tac	2/3	1	2	FACETS	0.869	0.779	0.964	0.869	0.779	0.964	CLONAL	1	TRUE	1	0.253767849438438	2		776	989	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63699949	63699949	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013079-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	51	272	0	ENST00000279873.7:c.284T>A	p.Val95Asp	p.V95D	ENST00000279873	NM_032199.2	95	gTc/gAc	3/10	1	2	FACETS	0.855	0.728	0.995	0.855	0.728	0.995	CLONAL	1	TRUE	1	0.253767849438438	2		272	470	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427700	49427700	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013079-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	110	721	0	ENST00000301067.7:c.10788del	p.Asn3597ThrfsTer61	p.N3597Tfs*61	ENST00000301067	NM_003482.3	3596	cgG/cg	39/54	1	2	FACETS	0.888	0.797	0.986	0.888	0.797	0.986	CLONAL	1	TRUE	1	0.253767849438438	2		721	976	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56811492	56811492	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013079-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	138	448	1	ENST00000337432.4:c.1040G>T	p.Arg347Ile	p.R347I	ENST00000337432	NM_058216.2	347	aGa/aTa	9/9	0.247485340183274	2	FACETS	0.813	0.741	0.888	0.813	0.741	0.888	CLONAL	2	TRUE	0	0.253767849438438	2		449	669	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47601064	47601064	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013079-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	124	616	0	ENST00000263735.4:c.302A>G	p.Glu101Gly	p.E101G	ENST00000263735	NM_002354.2	101	gAg/gGg	3/9	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.253767849438438	2		616	771	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960100	151960100	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0013079-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	139	359	0	ENST00000262189.6:c.1299+1G>A		p.X433_splice	ENST00000262189	NM_170606.2	433			0.247370130267791	3	FACETS	0.997	0.911	1			1	CLONAL	2	TRUE	NA	0.253767849438438	3		359	619	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593618	55593662	+	inframe_deletion	In_Frame_Del	DEL	GAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTT	GAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTT	-	novel	NA	P-0014184-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	173	578	0	ENST00000288135.5:c.1684_1728del	p.Glu562_Leu576del	p.E562_L576del	ENST00000288135	NM_000222.2	562	GAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTT/-	11/21	1	2	FACETS	0.836	0.774	0.899	0.836	0.774	0.899	CLONAL	1	TRUE	1	0.753882786430299	2		578	549	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893613	28893613	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	74	442	0	ENST00000282397.4:c.3233C>T	p.Thr1078Ile	p.T1078I	ENST00000282397	NM_002019.4	1078	aCc/aTc	24/30	0.363291715880982	3	FACETS	0.686	0.6	0.778	0.343	0.3	0.389	SUBCLONAL	1	FALSE	1	0.363291715880982	3		442	702	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579386	7579390	+	frameshift_variant	Frame_Shift_Del	DEL	TCTGG	TCTGG	-	novel	NA	P-0014975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	309	417	0	ENST00000269305.4:c.297_301del	p.Gln100AsnfsTer47	p.Q100Nfs*47	ENST00000269305	NM_001126112.2	99	tcCCAGAaa/tcaa	4/11	0.283520904336403	3	FACETS	1	0.99	1	0.789	0.747	0.832	CLONAL	2	FALSE	0	0.363291715880982	3		417	849	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231719	66231719	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs762252936	NA	P-0014975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	61	272	2	ENST00000273854.3:c.1981C>A	p.Gln661Lys	p.Q661K	ENST00000273854	NM_004439.5	661	Caa/Aaa	11/18	0.363291715880982	5	FACETS	1	0.965	1	0.344	0.298	0.394	CLONAL	1	FALSE	1	0.363291715880982	5		274	377	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839726	27839726	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs761339099	NA	P-0014975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	78	373	1	ENST00000328488.2:c.368A>G	p.Lys123Arg	p.K123R	ENST00000328488	NM_003533.2	123	aAa/aGa	1/1	0.28916756006419	4	FACETS	0.743	0.652	0.841	0.248	0.217	0.281	SUBCLONAL	1	FALSE	1	0.363291715880982	4		374	788	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55087032	55087032	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	85	287	0	ENST00000275493.2:c.62C>G	p.Ala21Gly	p.A21G	ENST00000275493	NM_005228.3	21	gCg/gGg	1/28	0.363291715880982	4	FACETS	0.981	0.868	1	0.327	0.289	0.368	CLONAL	1	FALSE	1	0.363291715880982	4		287	650	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848642	151848649	+	frameshift_variant	Frame_Shift_Del	DEL	CTAGAATC	CTAGAATC	-	novel	NA	P-0014975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	35	230	0	ENST00000262189.6:c.12544_12551del	p.Asp4182SerfsTer18	p.D4182Sfs*18	ENST00000262189	NM_170606.2	4182	GATTCTAGt/t	50/59	0.363291715880982	5	FACETS	0.64	0.524	0.77	0.213	0.174	0.257	SUBCLONAL	1	FALSE	2	0.363291715880982	5		230	465	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771786	135771786	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	270	544	1	ENST00000298552.3:c.3331A>G	p.Ser1111Gly	p.S1111G	ENST00000298552	NM_001162426.1	1111	Agt/Ggt	23/23	0.363291715880982	3	FACETS	0.864	0.812	0.919	0.864	0.812	0.919	CLONAL	2	FALSE	1	0.363291715880982	3		545	1016	SUCCESS
AR	367	MSKCC	GRCh37	X	66931516	66931516	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	101	442	1	ENST00000374690.3:c.2158G>A	p.Ala720Thr	p.A720T	ENST00000374690	NM_000044.3	720	Gcc/Acc	4/8	0.363291715880982	3	FACETS	0.813	0.726	0.906	0.407	0.363	0.453	CLONAL	1	FALSE	1	0.363291715880982	3		443	808	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015463-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	74	395	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.758	0.664	0.861	0.758	0.664	0.861	SUBCLONAL	1	TRUE	1	0.285277853450974	2		395	684	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0015463-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	58	411	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.285277853450974	3	FACETS	0.809	0.701	0.925	0.809	0.701	0.925	CLONAL	2	TRUE	1	0.285277853450974	3		411	287	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0015463-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	20	365	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	0.489	0.374	0.623	0.489	0.374	0.623	SUBCLONAL	1	TRUE	1	0.285277853450974	2		365	287	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829040	128829042	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	rs570242755	NA	P-0015463-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	11	41	0	ENST00000249373.3:c.67_69del	p.Leu23del	p.L23del	ENST00000249373	NM_005631.4	16	ggGCTg/ggg	1/12	0.285277853450974	3	FACETS	0.643	0.446	0.885	0.322	0.223	0.443	SUBCLONAL	1	TRUE	1	0.285277853450974	3		41	137	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482926	140482927	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs777474487	NA	P-0015463-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	50	500	1	ENST00000288602.6:c.1208dup	p.Ala404CysfsTer9	p.A404Cfs*9	ENST00000288602	NM_004333.4	403	cct/ccCt	10/18	0.285277853450974	3	FACETS	0.493	0.417	0.577	0.247	0.208	0.289	SUBCLONAL	1	TRUE	1	0.285277853450974	3		501	812	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231410	46231410	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0015463-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	27	393	0	ENST00000334344.6:c.1250C>G	p.Ser417Ter	p.S417*	ENST00000334344	NM_152641.2	417	tCa/tGa	10/21	1	2	FACETS	0.683	0.545	0.84	0.683	0.545	0.84	SUBCLONAL	1	TRUE	1	0.285277853450974	2		393	277	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883794	37883794	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs746595697	NA	P-0015463-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	138	781	0	ENST00000269571.5:c.3406C>T	p.Gln1136Ter	p.Q1136*	ENST00000269571		1136	Cag/Tag	26/27	1	2	FACETS	0.868	0.788	0.952	0.868	0.788	0.952	CLONAL	1	TRUE	1	0.285277853450974	2		781	1115	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233110	46233110	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0015463-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	25	206	0	ENST00000334344.6:c.1331-2A>C		p.X444_splice	ENST00000334344	NM_152641.2	444			1	2	FACETS	0.656	0.519	0.814	0.656	0.519	0.814	SUBCLONAL	1	TRUE	1	0.285277853450974	2		206	267	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926888	112926888	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397507546	NA	P-0015581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	47	135	0	ENST00000351677.2:c.1508G>T	p.Gly503Val	p.G503V	ENST00000351677	NM_002834.3	503	gGg/gTg	13/16	1	2	FACETS	0.173	0.145	0.204	0.173	0.145	0.204	SUBCLONAL	1	TRUE	1	0.877152113217222	2		135	619	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	257	395	0				ENST00000310581	NM_198253.2	-/1132			0.279163716464263	3	FACETS	0.993	0.935	1	1	0.993	1	CLONAL	3	TRUE	1	0.279163716464263	3		395	704	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0016163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	402	739	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.216732296630184	2	FACETS	0.966	0.918	1	0.966	0.918	1	CLONAL	2	TRUE	0	0.279163716464263	2		740	1490	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222268	2222553	+	splice_acceptor_variant,splice_donor_variant,frameshift_variant,stop_lost,intron_variant	Splice_Site	DEL	CTTCATCCACTGCCGGCACGGCTGCCGGGTAGCGGGCAGCGGGAAGCCCCCCATCTTTGAGGTGGACCCCCGAGGGTGCCCCTTCACCATCAAGCTCAGCGCCCGGAAGTAAGTGCCCCTCCCTGGGCACCTCTGCCTCCCTGGGGGCTGCTTCTCAGGGCTCTGGCTGAGGCCTCCCCGCATCCCGCCCTGGCACAGGGACCACGAGGGCAGCTGTGACTACAGGCCTGTGCGGTGTCCCAACAACCCCAGCTGCCCCCCGCTGCTCAGGATGAACCTGGAGGCC	CTTCATCCACTGCCGGCACGGCTGCCGGGTAGCGGGCAGCGGGAAGCCCCCCATCTTTGAGGTGGACCCCCGAGGGTGCCCCTTCACCATCAAGCTCAGCGCCCGGAAGTAAGTGCCCCTCCCTGGGCACCTCTGCCTCCCTGGGGGCTGCTTCTCAGGGCTCTGGCTGAGGCCTCCCCGCATCCCGCCCTGGCACAGGGACCACGAGGGCAGCTGTGACTACAGGCCTGTGCGGTGTCCCAACAACCCCAGCTGCCCCCCGCTGCTCAGGATGAACCTGGAGGCC	-	novel	NA	P-0016163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1295	76	598	0	ENST00000326181.6:c.553_748del		p.X185_splice	ENST00000326181	NM_032271.2	185	ctCTTCATCCACTGCCGGCACGGCTGCCGGGTAGCGGGCAGCGGGAAGCCCCCCATCTTTGAGGTGGACCCCCGAGGGTGCCCCTTCACCATCAAGCTCAGCGCCCGGAAGTAAGTGCCCCTCCCTGGGCACCTCTGCCTCCCTGGGGGCTGCTTCTCAGGGCTCTGGCTGAGGCCTCCCCGCATCCCGCCCTGGCACAGGGACCACGAGGGCAGCTGTGACTACAGGCCTGTGCGGTGTCCCAACAACCCCAGCTGCCCCCCGCTGCTCAGGATGAACCTGGAGGCC/ct	8-9/21	1	2	FACETS	0.397	0.347	0.452	0.397	0.347	0.452	SUBCLONAL	1	TRUE	1	0.279163716464263	2		598	1371	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0016389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	101	266	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.269486505582621	4	FACETS	0.802	0.719	0.891			1	CLONAL	2	TRUE	NA	0.269486505582621	4		266	593	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566556	41566556	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756061989	NA	P-0016389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	73	221	0	ENST00000263253.7:c.4433G>A	p.Arg1478His	p.R1478H	ENST00000263253	NM_001429.3	1478	cGt/cAt	27/31	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.269486505582621	2		221	369	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912181	114912181	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	82	357	0	ENST00000543371.1:c.1251G>T	p.Trp417Cys	p.W417C	ENST00000543371	NM_001198531.1	417	tgG/tgT	11/14	0.269486505582621	3	FACETS	1	0.933	1	0.542	0.478	0.611	CLONAL	1	TRUE	1	0.269486505582621	3		357	637	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358554	67358556	+	frameshift_variant	Frame_Shift_Del	DEL	GCG	GCG	AA	novel	NA	P-0016389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	104	224	2	ENST00000327367.4:c.62_64delinsAA	p.Gly21GlufsTer95	p.G21Efs*95	ENST00000327367	NM_005902.3	21	gGCGag/gAAag	1/9	0.266022286213595	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	2	TRUE	0	0.269486505582621	2		226	384	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374909	45374909	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	117	251	0	ENST00000262160.6:c.934T>G	p.Cys312Gly	p.C312G	ENST00000262160	NM_005901.5	312	Tgc/Ggc	8/11	0.266022286213595	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.269486505582621	2		251	391	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931678	39931678	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	152	377	0	ENST00000378444.4:c.2921G>C	p.Gly974Ala	p.G974A	ENST00000378444	NM_001123385.1	974	gGt/gCt	4/15	0.22357110561276	3	FACETS	0.983	0.902	1			1	CLONAL	2	TRUE	NA	0.269486505582621	3		377	651	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199841	108199841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	179	234	0	ENST00000278616.4:c.7183G>A	p.Asp2395Asn	p.D2395N	ENST00000278616	NM_000051.3	2395	Gat/Aat	49/63	0.8232738675391	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	0	0.8232738675391	1		234	250	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	748	63	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.302311244017023	6	FACETS	0.992	0.96	1	0.992	0.96	1	CLONAL	5	TRUE	1	0.302311244017023	6		63	1601	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922227	100922227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	140	301	0	ENST00000325455.5:c.2285G>A	p.Gly762Asp	p.G762D	ENST00000325455	NM_001202474.3	762	gGt/gAt	5/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.302311244017023	2		301	847	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577088	7577088	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1204379654	NA	P-0016623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1429	374	669	0	ENST00000269305.4:c.850A>C	p.Thr284Pro	p.T284P	ENST00000269305	NM_001126112.2	284	Aca/Cca	8/11	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.302311244017023	2		669	1803	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	103	63	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.274870632723773	1	FACETS	0.658	0.594	0.726	0.658	0.594	0.726	INDETERMINATE	1	FALSE	0	0.573609768917419	1		63	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0016778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	167	276	0	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	0.573609768917419	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	0	0.573609768917419	1		276	379	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959057	28959057	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	60	211	1	ENST00000282397.4:c.2081G>T	p.Trp694Leu	p.W694L	ENST00000282397	NM_002019.4	694	tGg/tTg	14/30	0.560740358958887	5	FACETS	0.819	0.707	0.941	0.205	0.176	0.236	CLONAL	1	FALSE	1	0.573609768917419	5		212	475	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5246051	5246051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	65	92	0	ENST00000357368.4:c.724C>T	p.Arg242Cys	p.R242C	ENST00000357368	NM_002850.3	242	Cgc/Tgc	10/38	NA	2	FACETS	0.882	0.773	0.997			1	INDETERMINATE	1	FALSE	NA	0.573609768917419	2		92	257	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281358	15281358	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375474414	NA	P-0016778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	199	196	3	ENST00000263388.2:c.4898C>T	p.Pro1633Leu	p.P1633L	ENST00000263388	NM_000435.2	1633	cCg/cTg	27/33	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.573609768917419	2		199	596	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721792	176721792	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	86	216	0	ENST00000439151.2:c.7423G>T	p.Val2475Phe	p.V2475F	ENST00000439151	NM_022455.4	2475	Gtc/Ttc	23/23	1	2	FACETS	0.906	0.809	1	0.906	0.809	1	CLONAL	1	FALSE	1	0.573609768917419	2		216	331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0017005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	369	547	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.874010452962294	1	FACETS	0.964	0.934	0.994	0.964	0.934	0.994	CLONAL	1	TRUE	0	0.874010452962294	1		548	493	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224492	108224492	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0017005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	104	141	0	ENST00000278616.4:c.8672-1G>A		p.X2891_splice	ENST00000278616	NM_000051.3	2891			NA	2	FACETS	0.952	0.868	1			1	INDETERMINATE	1	TRUE	NA	0.874010452962294	2		141	250	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814248	76814270	+	frameshift_variant	Frame_Shift_Del	DEL	TACTCGATTAGCAGCTACCAGAT	TACTCGATTAGCAGCTACCAGAT	G	novel	NA	P-0017009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	97	232	0	ENST00000373344.5:c.6374_6396delinsC	p.Asn2125ThrfsTer35	p.N2125Tfs*35	ENST00000373344	NM_000489.3	2125	aATCTGGTAGCTGCTAATCGAGTA/aC	29/35	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.319757316050131	2		232	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934573	NA	P-0017053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	145	384	0	ENST00000269305.4:c.722C>A	p.Ser241Tyr	p.S241Y	ENST00000269305	NM_001126112.2	241	tCc/tAc	7/11	0.285188115227746	1	FACETS	1	0.959	1	1	0.991	1	CLONAL	2	TRUE	0	0.14	1		384	886	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220691	1220691	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs878853247	NA	P-0017053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	60	368	0	ENST00000326873.7:c.709G>T	p.Asp237Tyr	p.D237Y	ENST00000326873	NM_000455.4	237	Gac/Tac	5/10	1	2	FACETS	0.85	0.73	0.982	0.85	0.73	0.982	CLONAL	1	TRUE	1	0.14	2		368	1008	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056296	27056296	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs572680423	NA	P-0017053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	40	205	0	ENST00000324856.7:c.1292C>T	p.Pro431Leu	p.P431L	ENST00000324856	NM_006015.4	431	cCg/cTg	2/20	1	2	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	TRUE	1	0.14	2		205	560	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105587	30105587	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	80	498	0	ENST00000331968.5:c.1099G>C	p.Asp367His	p.D367H	ENST00000331968	NM_002742.2	367	Gat/Cat	7/18	1	2	FACETS	0.971	0.852	1	0.971	0.852	1	CLONAL	1	TRUE	1	0.14	2		498	1177	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219385	1219397	+	frameshift_variant	Frame_Shift_Del	DEL	AGCGTTTCCCAGT	AGCGTTTCCCAGT	-	novel	NA	P-0017053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	48	293	0	ENST00000326873.7:c.437_449del	p.Lys146SerfsTer11	p.K146Sfs*11	ENST00000326873	NM_000455.4	146	aAGCGTTTCCCAGTg/ag	3/10	1	2	FACETS	0.892	0.752	1	0.892	0.752	1	CLONAL	1	TRUE	1	0.14	2		293	769	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0017200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	273	505	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.230059620484206	3	FACETS	1	0.983	1	0.733	0.692	0.775	INDETERMINATE	2	TRUE	0	0.422380316336436	3		505	712	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0017200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	575	355	9	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	0.32053992272745	4	FACETS	0.993	0.961	1			1	CLONAL	4	TRUE	NA	0.422380316336436	4		364	975	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0017200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	130	330	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	NA	2	FACETS	0.905	0.823	0.992			1	INDETERMINATE	1	TRUE	NA	0.422380316336436	2		330	680	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589588	67589590	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0017200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	80	318	2	ENST00000274335.5:c.1351_1353del	p.Glu451del	p.E451del	ENST00000274335		451	GAA/-	10/15	1	2	FACETS	0.726	0.64	0.817	0.726	0.64	0.817	SUBCLONAL	1	TRUE	1	0.422380316336436	2		320	522	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242742	46242742	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0017319-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	59	271	0	ENST00000334344.6:c.1704T>A	p.Tyr568Ter	p.Y568*	ENST00000334344	NM_152641.2	568	taT/taA	13/21	0.733760943163799	3	FACETS	1	0.962	1	0.421	0.369	0.475	CLONAL	1	FALSE	0	0.739226151337473	3		271	173	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577521	7577521	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017319-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	97	686	0	ENST00000269305.4:c.760A>T	p.Ile254Phe	p.I254F	ENST00000269305	NM_001126112.2	254	Atc/Ttc	7/11	NA	2	FACETS	0.911	0.847	0.972			1	INDETERMINATE	2	FALSE	NA	0.739226151337473	2		686	144	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772349	56772349	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017319-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	49	403	0	ENST00000337432.4:c.203G>T	p.Cys68Phe	p.C68F	ENST00000337432	NM_058216.2	68	tGt/tTt	2/9	0.739226151337473	3	FACETS	1	0.94	1	0.586	0.506	0.67	CLONAL	1	FALSE	1	0.739226151337473	3		403	155	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28929495	NA	P-0017319-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	227	594	0	ENST00000275493.2:c.2155G>T	p.Gly719Cys	p.G719C	ENST00000275493	NM_005228.3	719	Ggc/Tgc	18/28	0.739226151337473	6	FACETS	0.917	0.868	0.965	0.917	0.868	0.965	CLONAL	4	FALSE	2	0.739226151337473	6		594	415	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0017319-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	253	522	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.739226151337473	6	FACETS	0.902	0.856	0.948	0.902	0.856	0.948	CLONAL	4	FALSE	2	0.739226151337473	6		522	470	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0017438-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	239	531	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.56925471158507	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	2	0.577109637856651	4		531	608	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665752	29665755	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1555535032	NA	P-0017438-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	188	401	1	ENST00000356175.3:c.6789_6792del	p.Tyr2264ThrfsTer5	p.Y2264Tfs*5	ENST00000356175	NM_000267.3	2263	ACTTac/ac	45/57	0.577109637856651	3	FACETS	0.897	0.847	0.945	0.897	0.847	0.945	CLONAL	3	TRUE	0	0.577109637856651	3		402	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577560	7577560	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520002	NA	P-0017438-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	491	593	0	ENST00000269305.4:c.721T>G	p.Ser241Ala	p.S241A	ENST00000269305	NM_001126112.2	241	Tcc/Gcc	7/11	0.577109637856651	3	FACETS	0.992	0.96	1	0.992	0.96	1	CLONAL	3	TRUE	0	0.577109637856651	3		593	737	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0017629-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	110	360	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.3	1	FACETS	0.681	0.61	0.757	0.681	0.61	0.757	SUBCLONAL	1	TRUE	0	0.24	1		360	1184	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842641	68842641	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017629-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	103	430	0	ENST00000261769.5:c.577A>C	p.Thr193Pro	p.T193P	ENST00000261769	NM_004360.3	193	Act/Cct	5/16	0.162899068525779	1	FACETS	0.697	0.623	0.777	0.697	0.623	0.777	SUBCLONAL	1	TRUE	0	0.24	1		430	1083	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93953227	93953227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017629-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	88	407	0	ENST00000369303.4:c.2914G>A	p.Gly972Ser	p.G972S	ENST00000369303	NM_004440.3	972	Ggt/Agt	17/17	1	2	FACETS	0.734	0.649	0.826	0.734	0.649	0.826	SUBCLONAL	1	TRUE	1	0.24	2		407	999	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959106	2959106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs895214237	NA	P-0017629-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1262	175	345	1	ENST00000396946.4:c.2410C>T	p.Arg804Cys	p.R804C	ENST00000396946	NM_032415.4	804	Cgt/Tgt	18/25	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.24	2		346	1437	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0017664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	70	40	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		40	155	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553290	106553290	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	95	27	0	ENST00000369096.4:c.1255G>A	p.Gly419Ser	p.G419S	ENST00000369096	NM_001198.3	419	Ggc/Agc	5/7	0.3	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		27	413	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852242	128852242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140172891	NA	P-0017664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	100	57	0	ENST00000249373.3:c.2314C>T	p.Arg772Cys	p.R772C	ENST00000249373	NM_005631.4	772	Cgc/Tgc	12/12	0.3	4	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	4		57	878	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972485	81972485	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1462	289	136	0	ENST00000359376.3:c.3278A>T	p.Glu1093Val	p.E1093V	ENST00000359376	NM_002661.3	1093	gAg/gTg	29/33	0.3	3	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	3		136	1751	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578237	7578245	+	inframe_deletion	In_Frame_Del	DEL	CTCCACACG	CTCCACACG	-	novel	NA	P-0017664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	310	65	0	ENST00000269305.4:c.604_612del	p.Arg202_Glu204del	p.R202_E204del	ENST00000269305	NM_001126112.2	202	CGTGTGGAG/-	6/11	0.3	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		65	619	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645739	215645739	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	106	33	0	ENST00000260947.4:c.859G>C	p.Glu287Gln	p.E287Q	ENST00000260947	NM_000465.2	287	Gag/Cag	4/11	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		33	261	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750758	39750758	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	306	16	0	ENST00000361337.2:c.2158A>G	p.Lys720Glu	p.K720E	ENST00000361337	NM_003286.2	720	Aaa/Gaa	20/21	0.3	6	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	6		16	483	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0017736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	71	233	2	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	0.396087160909572	2		235	262	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0017736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	56	141	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.396087160909572	2		141	230	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685307	89685307	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123317	NA	P-0017736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	28	87	0	ENST00000371953.3:c.202T>C	p.Tyr68His	p.Y68H	ENST00000371953	NM_000314.4	68	Tac/Cac	3/9	0.274601488444649	0	FACETS	0.678	0.551	0.817			1	SUBCLONAL	1	TRUE	0	0.396087160909572	0		87	126	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471712	120471712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs75423398	NA	P-0017736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	108	281	0	ENST00000256646.2:c.3779G>A	p.Arg1260His	p.R1260H	ENST00000256646	NM_024408.3	1260	cGt/cAt	23/34	0.276466126560146	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.396087160909572	1		281	398	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235935	108235935	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770641163	NA	P-0017736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	42	144	0	ENST00000278616.4:c.8977C>T	p.Arg2993Ter	p.R2993*	ENST00000278616	NM_000051.3	2993	Cga/Tga	62/63	1	2	FACETS	0.947	0.798	1	0.947	0.798	1	CLONAL	1	TRUE	1	0.396087160909572	2		144	224	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206594	108206594	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555128314	NA	P-0017736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	43	143	0	ENST00000278616.4:c.8174A>G	p.Asp2725Gly	p.D2725G	ENST00000278616	NM_000051.3	2725	gAt/gGt	56/63	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.396087160909572	2		143	196	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045912	143045912	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	28	89	1	ENST00000262992.4:c.1722G>T	p.Glu574Asp	p.E574D	ENST00000262992	NM_001101669.1	574	gaG/gaT	17/24	0.274601488444649	0	FACETS	0.776	0.633	0.932			1	CLONAL	1	TRUE	0	0.396087160909572	0		90	110	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31495463	31495463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	91	285	0	ENST00000344624.3:c.1685G>A	p.Arg562His	p.R562H	ENST00000344624		562	cGt/cAt	9/33	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.396087160909572	2		285	377	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589585	67589586	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATGAAT	novel	NA	P-0017736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	11	153	0	ENST00000274335.5:c.1351_1356dup	p.Glu451_Tyr452dup	p.E451_Y452dup	ENST00000274335		451	cat/cATGAATat	10/15	1	2	FACETS	0.283	0.196	0.392	0.283	0.196	0.392	SUBCLONAL	1	TRUE	1	0.396087160909572	2		153	196	SUCCESS
APC	324	MSKCC	GRCh37	5	112175663	112175663	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	72	171	0	ENST00000257430.4:c.4373del	p.Pro1458LeufsTer15	p.P1458Lfs*15	ENST00000257430	NM_000038.5	1458	Cct/ct	16/16	1	2	FACETS	0.757	0.671	0.848	1	0.977	1	SUBCLONAL	2	TRUE	1	0.396087160909572	2		171	240	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002837	69002837	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	30	141	0	ENST00000288368.4:c.2137C>A	p.Leu713Ile	p.L713I	ENST00000288368	NM_024870.2	713	Ctt/Att	20/40	0.242863362345553	3	FACETS	0.799	0.648	0.969	0.4	0.324	0.485	CLONAL	1	TRUE	1	0.396087160909572	3		141	227	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0017817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	299	598	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.539573494489685	5	FACETS	0.751	0.706	0.797	0.501	0.471	0.532	SUBCLONAL	2	TRUE	2	0.539549717298445	5		598	1335	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190321	32190321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1033015617	NA	P-0017817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	143	561	0	ENST00000375023.3:c.418C>T	p.Arg140Cys	p.R140C	ENST00000375023	NM_004557.3	140	Cgc/Tgc	3/30	0.469767643061281	3	FACETS	0.975	0.891	1	0.488	0.445	0.532	CLONAL	1	TRUE	1	0.539549717298445	3		561	690	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843614	156843614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs797045060	NA	P-0017817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	182	725	0	ENST00000524377.1:c.1040G>A	p.Arg347His	p.R347H	ENST00000524377	NM_002529.3	347	cGc/cAc	8/17	0.388009055221679	5	FACETS	0.881	0.811	0.955	0.294	0.27	0.319	CLONAL	1	TRUE	2	0.539549717298445	5		725	1385	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624530	21624530	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	96	463	0	ENST00000421138.2:c.1499T>C	p.Leu500Pro	p.L500P	ENST00000421138		500	cTg/cCg	14/16	0.392762950648679	4	FACETS	0.68	0.605	0.759	0.34	0.302	0.38	SUBCLONAL	1	TRUE	2	0.539549717298445	4		463	806	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110566	4110566	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	160	695	0	ENST00000262948.5:c.391G>T	p.Val131Leu	p.V131L	ENST00000262948	NM_030662.3	131	Gtg/Ttg	3/11	0.460906195774877	3	FACETS	0.808	0.741	0.879	0.404	0.37	0.44	CLONAL	1	TRUE	1	0.539549717298445	3		695	932	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226549185	226549185	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	118	409	0	ENST00000366794.5:c.3021C>G	p.Phe1007Leu	p.F1007L	ENST00000366794	NM_001618.3	1007	ttC/ttG	23/23	0.539573494489685	5	FACETS	0.851	0.767	0.94	0.284	0.255	0.314	CLONAL	1	TRUE	2	0.539549717298445	5		409	930	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76931731	76931731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	38	336	0	ENST00000373344.5:c.3799C>T	p.Pro1267Ser	p.P1267S	ENST00000373344	NM_000489.3	1267	Cct/Tct	10/35	1	2	FACETS	0.289	0.239	0.346	0.289	0.239	0.346	SUBCLONAL	1	TRUE	1	0.539549717298445	2		336	487	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044930	47044930	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	163	786	0	ENST00000377604.3:c.2256G>T	p.Lys752Asn	p.K752N	ENST00000377604	NM_001204468.1	752	aaG/aaT	20/24	1	2	FACETS	0.613	0.562	0.667	0.613	0.562	0.667	SUBCLONAL	1	TRUE	1	0.539549717298445	2		786	985	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0017896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	134	505	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.971	0.893	1	0.971	0.893	1	CLONAL	1	TRUE	1	0.76	2		505	363	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0017896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	483	900	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	1	2	FACETS	0.954	0.912	0.995	0.954	0.912	0.995	CLONAL	1	TRUE	1	0.76	2		900	1333	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0017896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	10	531	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.082	0.055	0.117	0.082	0.055	0.117	SUBCLONAL	1	TRUE	1	0.76	2		531	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0017935-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	203	355	9	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	0.288311029090598	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	0	0.288311029090598	1		364	920	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711874	89711874	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs786204862	NA	P-0017935-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	121	424	0	ENST00000371953.3:c.493-1G>A		p.X165_splice	ENST00000371953	NM_000314.4	165			0.288311029090598	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	0	0.288311029090598	1		424	632	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0018055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	321	332	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.388614792248366	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.422453821417662	2		332	741	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACAACCCCC	rs397517115	NA	P-0018055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	231	232	0	ENST00000275493.2:c.2311_2319dup	p.Asn771_His773dup	p.N771_H773dup	ENST00000275493	NM_005228.3	771	gac/gACAACCCCCac	20/28	0.422453821417662	4	FACETS	0.809	0.754	0.864	0.809	0.754	0.864	CLONAL	2	TRUE	2	0.422453821417662	4		232	962	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163804	72163804	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	98	155	0	ENST00000357731.5:c.554G>A	p.Gly185Glu	p.G185E	ENST00000357731	NM_173808.2	185	gGa/gAa	4/7	0.422453821417662	3	FACETS	0.935	0.836	1	0.468	0.418	0.52	CLONAL	1	TRUE	1	0.422453821417662	3		155	601	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176132989	176132989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	124	223	0	ENST00000367669.3:c.604G>A	p.Glu202Lys	p.E202K	ENST00000367669	NM_022457.5	202	Gaa/Aaa	4/20	0.255212216018524	5	FACETS	1	0.934	1	0.347	0.314	0.383	CLONAL	1	TRUE	2	0.422453821417662	5		223	920	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137528128	137528128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	177	195	2	ENST00000367739.4:c.172G>A	p.Val58Ile	p.V58I	ENST00000367739	NM_000416.2	58	Gtt/Att	2/7	0.422453821417662	3	FACETS	0.95	0.882	1	0.95	0.882	1	CLONAL	2	TRUE	1	0.422453821417662	3		197	534	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346623	81346623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	86	153	0	ENST00000222390.5:c.1330G>A	p.Asp444Asn	p.D444N	ENST00000222390	NM_000601.4	444	Gat/Aat	11/18	0.255212216018524	5	FACETS	0.981	0.868	1	0.327	0.289	0.368	CLONAL	1	TRUE	2	0.422453821417662	5		153	678	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981671	70981671	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779542728	NA	P-0018055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	453	342	0	ENST00000276594.2:c.425C>T	p.Pro142Leu	p.P142L	ENST00000276594	NM_024504.3	142	cCg/cTg	2/8	0.296961236942235	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	2	0.422453821417662	4		342	1331	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061213	38061213	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018181-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	53	529	0	ENST00000250448.2:c.776A>C	p.Tyr259Ser	p.Y259S	ENST00000250448	NM_004496.3	259	tAc/tCc	2/2	0.210533866290849	18	FACETS	1	0.896	1			1	CLONAL	3	FALSE	NA	0.210533866290849	18		529	425	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267360	198267360	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs374250186	NA	P-0018181-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	61	585	0	ENST00000335508.6:c.1997A>C	p.Lys666Thr	p.K666T	ENST00000335508	NM_012433.2	666	aAg/aCg	14/25	0.149325326459788	4	FACETS	1	0.894	1	1	0.974	1	CLONAL	3	FALSE	2	0.210533866290849	4		585	228	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100312	27100312	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018181-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	231	702	0	ENST00000324856.7:c.4024C>T	p.Gln1342Ter	p.Q1342*	ENST00000324856	NM_006015.4	1342	Cag/Tag	17/20	0.210533866290849	8	FACETS	1	0.976	1	1	0.99	1	CLONAL	8	FALSE	1	0.210533866290849	8		702	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0018202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	387	937	1	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	0.583532261422319	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.583532261422319	2		938	643	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54956538	54956538	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	115	310	0	ENST00000312783.6:c.656A>T	p.Tyr219Phe	p.Y219F	ENST00000312783	NM_198436.1	219	tAt/tTt	7/10	0.583532261422319	4	FACETS	1	0.919	1	0.51	0.46	0.562	CLONAL	1	TRUE	2	0.583532261422319	4		310	612	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430947	181430947	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	312	306	1	ENST00000325404.1:c.799G>T	p.Ala267Ser	p.A267S	ENST00000325404	NM_003106.3	267	Gcc/Tcc	1/1	0.579371903952499	5	FACETS	1	0.961	1	0.681	0.643	0.719	CLONAL	2	TRUE	2	0.583532261422319	5		307	982	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517532	176517532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200146267	NA	P-0018202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	140	358	0	ENST00000292408.4:c.233G>A	p.Arg78His	p.R78H	ENST00000292408	NM_213647.1	78	cGt/cAt	3/18	0.583532261422319	3	FACETS	0.894	0.816	0.976	0.447	0.408	0.488	CLONAL	1	TRUE	1	0.583532261422319	3		358	693	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395736	45395736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	10	188	0	ENST00000262160.6:c.398G>A	p.Arg133His	p.R133H	ENST00000262160	NM_005901.5	133	cGc/cAc	4/11	0.397050041683979	1	FACETS	0.262	0.178	0.368	0.262	0.178	0.368	SUBCLONAL	1	TRUE	0	0.397050041683979	1		188	154	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519985	NA	P-0018218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	197	506	0	ENST00000269305.4:c.857A>C	p.Glu286Ala	p.E286A	ENST00000269305	NM_001126112.2	286	gAa/gCa	8/11	0.397050041683979	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.397050041683979	1		506	612	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023647	27023648	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCTC	novel	NA	P-0018218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	76	221	0	ENST00000324856.7:c.759_762dup	p.Ser255LeufsTer146	p.S255Lfs*146	ENST00000324856	NM_006015.4	251	-/CCTC	1/20	1	2	FACETS	0.892	0.786	1	0.892	0.786	1	CLONAL	1	TRUE	1	0.397050041683979	2		221	429	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63829540	63829540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	35	226	0	ENST00000279873.7:c.1183C>T	p.Arg395Cys	p.R395C	ENST00000279873	NM_032199.2	395	Cgc/Tgc	8/10	1	2	FACETS	0.7	0.577	0.836	0.7	0.577	0.836	SUBCLONAL	1	TRUE	1	0.397050041683979	2		226	252	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495133	56495133	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	335	50	1	ENST00000267101.3:c.3490A>T	p.Thr1164Ser	p.T1164S	ENST00000267101	NM_001982.3	1164	Aca/Tca	27/28	1	2	FACETS	1	0.989	1	1	0.997	1	CLONAL	2	TRUE	1	0.397050041683979	2		51	744	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78829307	78829307	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	34	335	0	ENST00000306801.3:c.1358T>C	p.Leu453Pro	p.L453P	ENST00000306801	NM_020761.2	453	cTt/cCt	12/34	0.331995382817333	4	FACETS	0.358	0.291	0.433			1	SUBCLONAL	1	TRUE	NA	0.397050041683979	4		335	669	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372095	45372095	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	14	258	0	ENST00000262160.6:c.1074G>T	p.Gln358His	p.Q358H	ENST00000262160	NM_005901.5	358	caG/caT	9/11	0.397050041683979	1	FACETS	0.246	0.177	0.328	0.246	0.177	0.328	SUBCLONAL	1	TRUE	0	0.397050041683979	1		258	230	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132501	11132501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	148	359	0	ENST00000358026.2:c.2717G>A	p.Arg906His	p.R906H	ENST00000358026	NM_001128849.1	906	cGc/cAc	19/36	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.397050041683979	2		359	685	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245352	153245353	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0018218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	244	79	0	ENST00000281708.4:c.1838_1839del	p.Cys613PhefsTer30	p.C613Ffs*30	ENST00000281708	NM_033632.3	613	tGT/t	11/12	0.397050041683979	2	FACETS	1	0.985	1	1	0.995	1	CLONAL	3	TRUE	0	0.397050041683979	2		79	379	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175215	+	frameshift_variant	Frame_Shift_Del	DEL	AAAA	AAAA	-	rs863224457	NA	P-0018218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	50	116	0	ENST00000257430.4:c.3921_3924del	p.Ile1307MetfsTer13	p.I1307Mfs*13	ENST00000257430	NM_000038.5	1307	atAAAA/at	16/16	0.397050041683979	2	FACETS	0.961	0.837	1	0.961	0.837	1	CLONAL	2	TRUE	0	0.397050041683979	2		116	131	SUCCESS
AR	367	MSKCC	GRCh37	X	66765478	66765478	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	68	307	0	ENST00000374690.3:c.490T>A	p.Leu164Met	p.L164M	ENST00000374690	NM_000044.3	164	Ttg/Atg	1/8	1	2	FACETS	0.526	0.457	0.601	0.526	0.457	0.601	SUBCLONAL	1	TRUE	1	0.397050041683979	2		307	651	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0018345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	596	665	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.717601570073395	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.717601570073395	1		665	987	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699360	47699360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	207	410	2	ENST00000347630.2:c.148G>A	p.Glu50Lys	p.E50K	ENST00000347630	NM_001007230.1	50	Gaa/Aaa	4/11	0.717601570073395	2	FACETS	0.919	0.874	0.962	0.919	0.874	0.962	CLONAL	2	TRUE	0	0.717601570073395	2		412	314	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913351	NA	P-0018345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	131	329	1	ENST00000288602.6:c.1397G>A	p.Gly466Glu	p.G466E	ENST00000288602	NM_004333.4	466	gGa/gAa	11/18	0.223746233307835	1	FACETS	0.736	0.678	0.795	0.736	0.678	0.795	INDETERMINATE	1	TRUE	0	0.717601570073395	1		330	318	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692902	89692902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909218	NA	P-0018345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	80	348	2	ENST00000371953.3:c.386G>A	p.Gly129Glu	p.G129E	ENST00000371953	NM_000314.4	129	gGa/gAa	5/9	1	2	FACETS	0.811	0.722	0.903	0.811	0.722	0.903	CLONAL	1	TRUE	1	0.717601570073395	2		350	275	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711910	89711925	+	frameshift_variant	Frame_Shift_Del	DEL	TTATTATAGCTACCTG	TTATTATAGCTACCTG	-	novel	NA	P-0018345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	47	420	0	ENST00000371953.3:c.531_546del	p.Tyr177Ter	p.Y177*	ENST00000371953	NM_000314.4	176	taTTATTATAGCTACCTG/ta	6/9	1	2	FACETS	0.455	0.386	0.53	0.455	0.386	0.53	SUBCLONAL	1	TRUE	1	0.717601570073395	2		420	288	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497527	125497527	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	46	223	2	ENST00000428830.2:c.91A>G	p.Thr31Ala	p.T31A	ENST00000428830	NM_001114121.2	31	Act/Gct	3/14	NA	2	FACETS	0.737	0.63	0.85			1	INDETERMINATE	1	TRUE	NA	0.717601570073395	2		225	174	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236086	108236086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782292	NA	P-0018349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	108	564	0	ENST00000278616.4:c.9022C>T	p.Arg3008Cys	p.R3008C	ENST00000278616	NM_000051.3	3008	Cgt/Tgt	63/63	0.369475255472051	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.369475255472051	1		564	428	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313454	30313454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1304746106	NA	P-0018349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	147	580	1	ENST00000262643.3:c.1054G>A	p.Val352Ile	p.V352I	ENST00000262643	NM_001238.2	352	Gtc/Atc	11/12	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.369475255472051	2		581	751	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0018442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	197	130	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.78	0.727	0.835	1	0.992	1	SUBCLONAL	2	TRUE	1	0.414519833169879	2		130	609	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0018442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	297	587	2	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.405581612253676	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.414519833169879	1		589	978	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1976665	1976665	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	145	436	0	ENST00000382891.5:c.3448A>G	p.Thr1150Ala	p.T1150A	ENST00000382891	NM_133335.3	1150	Acc/Gcc	19/22	1	2	FACETS	0.834	0.761	0.91	0.834	0.761	0.91	CLONAL	1	TRUE	1	0.414519833169879	2		436	839	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270110	66270110	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs913058482	NA	P-0018442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	168	319	0	ENST00000273854.3:c.1772G>C	p.Gly591Ala	p.G591A	ENST00000273854	NM_004439.5	591	gGc/gCc	8/18	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.414519833169879	2		319	741	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106861	27106861	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	124	189	0	ENST00000324856.7:c.6472C>T	p.Arg2158Ter	p.R2158*	ENST00000324856	NM_006015.4	2158	Cga/Tga	20/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.243050695900137	2		189	772	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs863224499	NA	P-0018443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	237	355	0	ENST00000269305.4:c.672+1G>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			1	2	FACETS	0.756	0.704	0.81	1	0.992	1	SUBCLONAL	2	TRUE	1	0.243050695900137	2		355	1290	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949720	151949720	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	83	188	0	ENST00000262189.6:c.1380C>A	p.Tyr460Ter	p.Y460*	ENST00000262189	NM_170606.2	460	taC/taA	10/59	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.243050695900137	2		188	493	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0018484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	195	314	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.379955767387649	1	FACETS	0.672	0.63	0.715	0.672	0.63	0.715	INDETERMINATE	1	TRUE	0	0.798090990299117	1		315	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577544	7577544	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587780074	NA	P-0018484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	595	382	0	ENST00000269305.4:c.737T>C	p.Met246Thr	p.M246T	ENST00000269305	NM_001126112.2	246	aTg/aCg	7/11	0.798090990299117	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.798090990299117	1		382	857	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341452	70341452	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556334519	NA	P-0018484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	575	415	0	ENST00000374080.3:c.887G>A	p.Arg296Gln	p.R296Q	ENST00000374080		296	cGg/cAg	7/45	0.379955767387649	1	FACETS	0.711	0.685	0.737	0.711	0.685	0.737	INDETERMINATE	1	TRUE	0	0.798090990299117	1		415	1218	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555193	226555193	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	316	226	0	ENST00000366794.5:c.2394A>C	p.Lys798Asn	p.K798N	ENST00000366794	NM_001618.3	798	aaA/aaC	17/23	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		226	688	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112764493	112764493	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	345	216	0	ENST00000369452.4:c.1102A>G	p.Asn368Asp	p.N368D	ENST00000369452	NM_007373.3	368	Aac/Gac	5/9	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		216	691	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17940931	17940931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	332	412	0	ENST00000458235.1:c.3193G>A	p.Ala1065Thr	p.A1065T	ENST00000458235	NM_000215.3	1065	Gcc/Acc	23/24	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		412	1146	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0018716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	198	686	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.353334098299613	1	FACETS	0.789	0.73	0.851	0.789	0.73	0.851	SUBCLONAL	1	TRUE	0	0.353334098299613	1		686	1169	SUCCESS
APC	324	MSKCC	GRCh37	5	112175476	112175476	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	183	69	0	ENST00000257430.4:c.4188del	p.Phe1396LeufsTer19	p.F1396Lfs*19	ENST00000257430	NM_000038.5	1395	agT/ag	16/16	1	2	FACETS	0.786	0.728	0.845	1	0.991	1	SUBCLONAL	2	TRUE	1	0.353334098299613	2		69	659	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0018716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	358	43	1	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	NA	2	FACETS	0.918	0.871	0.966			1	INDETERMINATE	2	TRUE	NA	0.353334098299613	2		44	1104	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	314	173	0	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.353334098299613	2		173	1186	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805740	43805740	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367877736	NA	P-0018716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	82	342	0	ENST00000372470.3:c.796G>A	p.Gly266Ser	p.G266S	ENST00000372470	NM_005373.2	266	Ggt/Agt	5/12	0.157532906398168	1	FACETS	0.387	0.34	0.438	0.387	0.34	0.438	INDETERMINATE	1	TRUE	0	0.353334098299613	1		342	987	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690829	89690829	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	36	273	0	ENST00000371953.3:c.236C>G	p.Ala79Gly	p.A79G	ENST00000371953	NM_000314.4	79	gCc/gGc	4/9	0.230266415751843	1	FACETS	0.34	0.279	0.408	0.34	0.279	0.408	SUBCLONAL	1	TRUE	0	0.353334098299613	1		273	494	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584756	48584757	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	488	221	1	ENST00000342988.3:c.836dup	p.Asn279LysfsTer29	p.N279Kfs*29	ENST00000342988	NM_005359.5	278	-/A	7/12	0.353334098299613	1	FACETS	0.809	0.774	0.845	1	0.997	1	CLONAL	2	TRUE	0	0.353334098299613	1		222	1405	SUCCESS
APC	324	MSKCC	GRCh37	5	112174391	112174391	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	71	137	0	ENST00000257430.4:c.3100G>T	p.Glu1034Ter	p.E1034*	ENST00000257430	NM_000038.5	1034	Gag/Tag	16/16	1	2	FACETS	0.846	0.74	0.959	0.846	0.74	0.959	CLONAL	1	TRUE	1	0.353334098299613	2		137	475	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483033	29483034	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018976-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	149	339	0	ENST00000356175.3:c.94dup	p.Thr32AsnfsTer6	p.T32Nfs*6	ENST00000356175	NM_000267.3	31	-/A	2/57	0.75141895371615	1	FACETS	0.951	0.893	1	0.951	0.893	1	CLONAL	1	TRUE	0	0.784175498467766	1		339	243	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71161724	71161724	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018976-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	160	388	0	ENST00000318789.4:c.245A>T	p.Lys82Ile	p.K82I	ENST00000318789	NM_032682.5	82	aAa/aTa	7/21	1	2	FACETS	0.932	0.863	1	0.932	0.863	1	CLONAL	1	TRUE	1	0.784175498467766	2		388	438	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0019280-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	155	377	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.99	0.911	1	0.99	0.911	1	CLONAL	1	TRUE	1	0.550099659760048	2		377	569	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152033	55152033	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763325080	NA	P-0019280-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	145	480	2	ENST00000257290.5:c.2465G>A	p.Arg822His	p.R822H	ENST00000257290	NM_006206.4	822	cGc/cAc	18/23	1	2	FACETS	0.841	0.77	0.915	0.841	0.77	0.915	CLONAL	1	TRUE	1	0.550099659760048	2		482	627	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277160	38277160	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019280-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	86	661	0	ENST00000425967.3:c.1268G>C	p.Gly423Ala	p.G423A	ENST00000425967	NM_001174067.1	423	gGg/gCg	10/19	1	2	FACETS	0.398	0.351	0.448	0.398	0.351	0.448	SUBCLONAL	1	TRUE	1	0.550099659760048	2		661	786	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152033	55152033	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763325080	NA	P-0019280-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	236	480	2	ENST00000257290.5:c.2465G>A	p.Arg822His	p.R822H	ENST00000257290	NM_006206.4	822	cGc/cAc	18/23	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.641603352252906	2		482	673	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107047	11107047	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019280-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	145	368	0	ENST00000358026.2:c.1752G>T	p.Lys584Asn	p.K584N	ENST00000358026	NM_001128849.1	584	aaG/aaT	10/36	0.641603352252906	3	FACETS	0.949	0.869	1	0.475	0.434	0.517	CLONAL	1	TRUE	1	0.641603352252906	3		368	629	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0019280-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	116	468	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.999	0.91	1	0.999	0.91	1	CLONAL	1	TRUE	1	0.641603352252906	2		468	362	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731599	47731599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019280-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	17	35	0	ENST00000449228.1:c.193G>A	p.Gly65Ser	p.G65S	ENST00000449228	NM_001127240.2	65	Ggt/Agt	2/4	1	2	FACETS	0.707	0.54	0.894	0.707	0.54	0.894	SUBCLONAL	1	TRUE	1	0.641603352252906	2		35	75	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0019327-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	348	726	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	NA	2	FACETS	0.972	0.933	1			1	INDETERMINATE	2	TRUE	NA	0.638241115371386	2		726	561	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560466	95560466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886037724	NA	P-0019327-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	123	302	2	ENST00000393063.1:c.5123G>A	p.Gly1708Glu	p.G1708E	ENST00000393063	NM_030621.3	1708	gGa/gAa	25/28	0.601445965274143	5	FACETS	0.925	0.836	1			1	CLONAL	1	TRUE	NA	0.638241115371386	5		304	816	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176105677	176105677	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	127	201	0	ENST00000367669.3:c.838G>A	p.Glu280Lys	p.E280K	ENST00000367669	NM_022457.5	280	Gaa/Aaa	7/20	0.857725566409294	4	FACETS	0.749	0.68	0.823	0.187	0.17	0.206	SUBCLONAL	1	TRUE	0	0.857725566409294	4		201	734	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574673	64574677	+	frameshift_variant	Frame_Shift_Del	DEL	AGAGC	AGAGC	-	novel	NA	P-0019367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	308	256	1	ENST00000312049.6:c.798_802del	p.Leu267Ter	p.L267*	ENST00000312049	NM_130799.2	266	ctGCTCTat/ctat	5/10	0.857725566409294	2	FACETS	0.995	0.944	1	0.497	0.472	0.523	CLONAL	1	TRUE	0	0.857725566409294	2		257	722	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444752	49444752	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1240	257	447	1	ENST00000301067.7:c.2714A>T	p.Glu905Val	p.E905V	ENST00000301067	NM_003482.3	905	gAa/gTa	10/54	0.365964877716539	3	FACETS	0.572	0.534	0.611	0.286	0.267	0.306	INDETERMINATE	1	TRUE	1	0.857725566409294	3		448	1497	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164914	123164914	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	72	184	0	ENST00000218089.9:c.227A>T	p.Gln76Leu	p.Q76L	ENST00000218089	NM_001042749.1	76	cAg/cTg	5/35	0.857725566409294	3	FACETS	0.433	0.379	0.492	0.217	0.189	0.246	SUBCLONAL	1	TRUE	1	0.857725566409294	3		184	554	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042728	42042728	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019738-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	234	184	0	ENST00000219905.7:c.6923A>G	p.Asp2308Gly	p.D2308G	ENST00000219905	NM_001164273.1	2308	gAt/gGt	17/24	1	2	FACETS	0.998	0.936	1	0.998	0.936	1	CLONAL	1	TRUE	1	0.72613628861739	2		184	646	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799249	88799249	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774269690	NA	P-0019738-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	328	296	0	ENST00000360948.2:c.136C>T	p.Arg46Trp	p.R46W	ENST00000360948	NM_001012338.2	46	Cgg/Tgg	2/19	1	2	FACETS	0.984	0.933	1	0.984	0.933	1	CLONAL	1	TRUE	1	0.72613628861739	2		296	918	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	251	63	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.185086111845669	4	FACETS	0.836	0.79	0.882	1	0.991	1	INDETERMINATE	3	TRUE	2	0.577173953431391	4		63	547	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0020032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	124	307	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	0.206551111876616	2	FACETS	1	0.946	1	0.525	0.479	0.573	INDETERMINATE	1	TRUE	0	0.577173953431391	2		307	409	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239419	105239419	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	331	700	0	ENST00000349310.3:c.968A>G	p.Asp323Gly	p.D323G	ENST00000349310	NM_001014432.1	323	gAc/gGc	12/15	0.577173953431391	1	FACETS	0.765	0.734	0.796	1	0.996	1	SUBCLONAL	2	TRUE	0	0.577173953431391	1		700	533	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446294	70446294	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144991411	NA	P-0020032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	250	371	2	ENST00000373644.4:c.5234C>T	p.Thr1745Met	p.T1745M	ENST00000373644	NM_030625.2	1745	aCg/aTg	11/12	0.185086111845669	4	FACETS	0.789	0.739	0.839	0.789	0.739	0.839	INDETERMINATE	2	TRUE	2	0.577173953431391	4		373	866	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737061	162737061	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753126978	NA	P-0020032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	460	276	0	ENST00000367921.3:c.1205T>C	p.Ile402Thr	p.I402T	ENST00000367921	NM_006182.2	402	aTt/aCt	11/18	0.535584145528313	4	FACETS	0.971	0.934	1	1	0.996	1	CLONAL	3	TRUE	2	0.577173953431391	4		276	863	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714135	43714135	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	140	363	0	ENST00000382044.4:c.4018G>T	p.Gly1340Ter	p.G1340*	ENST00000382044	NM_001141980.1	1340	Gga/Tga	19/28	0.263277323236287	1	FACETS	0.494	0.45	0.539	0.494	0.45	0.539	INDETERMINATE	1	TRUE	0	0.577173953431391	1		363	699	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020563	14020567	+	frameshift_variant	Frame_Shift_Del	DEL	GGAAA	GGAAA	TTC	novel	NA	P-0020032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	142	240	1	ENST00000311895.7:c.534_538delinsTTC	p.Glu179SerfsTer31	p.E179Sfs*31	ENST00000311895	NM_005236.2	178	gtGGAAAga/gtTTCga	3/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.577173953431391	2		241	449	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	24	81	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.43	2		81	97	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	31	315	2	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.806	0.658	0.969	0.806	0.658	0.969	CLONAL	1	TRUE	1	0.43	2		317	179	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665752	29665755	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1555535032	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	13	401	1	ENST00000356175.3:c.6789_6792del	p.Tyr2264ThrfsTer5	p.Y2264Tfs*5	ENST00000356175	NM_000267.3	2263	ACTTac/ac	45/57	1	2	FACETS	0.393	0.281	0.527	0.393	0.281	0.527	SUBCLONAL	1	TRUE	1	0.43	2		402	154	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101402	27101402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	154	313	0	ENST00000324856.7:c.4689del	p.Met1564Ter	p.M1564*	ENST00000324856	NM_006015.4	1562	Ccc/cc	18/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.43	2		313	532	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161907	47161907	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	13	132	0	ENST00000409792.3:c.4219del	p.Arg1407GlyfsTer5	p.R1407Gfs*5	ENST00000409792	NM_014159.6	1407	Agg/gg	3/21	1	2	FACETS	0.346	0.247	0.465	0.346	0.247	0.465	SUBCLONAL	1	TRUE	1	0.43	2		132	175	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	57	396	1	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.345	0.295	0.4	0.345	0.295	0.4	SUBCLONAL	1	TRUE	1	0.43	2		397	768	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	126	405	3	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	2	FACETS	0.852	0.773	0.935	0.852	0.773	0.935	CLONAL	1	TRUE	1	0.43	2		408	688	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	12	235	1	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.809	0.58	1	0.809	0.58	1	CLONAL	1	TRUE	1	0.43	2		236	69	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039347	47039347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	56	622	1	ENST00000377604.3:c.970G>A	p.Ala324Thr	p.A324T	ENST00000377604	NM_001204468.1	324	Gcg/Acg	10/24	1	2	FACETS	0.329	0.281	0.382	0.329	0.281	0.382	SUBCLONAL	1	TRUE	1	0.43	2		623	791	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850705	63850705	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs201178069	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	13	125	0	ENST00000279873.7:c.1489del	p.Ile497Ter	p.I497*	ENST00000279873	NM_032199.2	495	Aaa/aa	10/10	1	2	FACETS	0.358	0.256	0.481	0.358	0.256	0.481	SUBCLONAL	1	TRUE	1	0.43	2		125	169	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238958	5238958	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	63	276	0	ENST00000357368.4:c.1821del	p.Val608TrpfsTer30	p.V608Wfs*30	ENST00000357368	NM_002850.3	607	ccC/cc	13/38	1	2	FACETS	0.538	0.465	0.616	0.538	0.465	0.616	SUBCLONAL	1	TRUE	1	0.43	2		276	545	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37038192	37038192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750206	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	26	77	0	ENST00000231790.2:c.199G>A	p.Gly67Arg	p.G67R	ENST00000231790	NM_000249.3	67	Ggg/Agg	2/19	1	2	FACETS	0.889	0.714	1	0.889	0.714	1	CLONAL	1	TRUE	1	0.43	2		77	136	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	87	430	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.952	0.847	1	0.952	0.847	1	CLONAL	1	TRUE	1	0.43	2		430	425	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230892	53230892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	122	481	1	ENST00000375401.3:c.1901G>A	p.Arg634His	p.R634H	ENST00000375401	NM_004187.3	634	cGc/cAc	14/26	1	2	FACETS	0.837	0.758	0.92	0.837	0.758	0.92	CLONAL	1	TRUE	1	0.43	2		482	678	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	24	159	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	0.49	0.385	0.609	0.49	0.385	0.609	SUBCLONAL	1	TRUE	1	0.43	2		159	228	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	39	186	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	0.759	0.634	0.896	0.759	0.634	0.896	SUBCLONAL	1	TRUE	1	0.43	2		186	239	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007332	143007332	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	12	146	2	ENST00000262992.4:c.2452del	p.Arg818GlufsTer4	p.R818Efs*4	ENST00000262992	NM_001101669.1	818	Aga/ga	22/24	1	2	FACETS	0.365	0.257	0.496	0.365	0.257	0.496	SUBCLONAL	1	TRUE	1	0.43	2		148	153	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	55	624	0	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.268	0.228	0.311	0.268	0.228	0.311	SUBCLONAL	1	TRUE	1	0.43	2		624	956	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111131	193111131	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	29	122	0	ENST00000367435.3:c.664C>T	p.Arg222Ter	p.R222*	ENST00000367435	NM_024529.4	222	Cga/Tga	7/17	1	2	FACETS	0.899	0.731	1	0.899	0.731	1	CLONAL	1	TRUE	1	0.43	2		122	150	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	39	182	2	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.907	0.76	1	0.907	0.76	1	CLONAL	1	TRUE	1	0.43	2		184	200	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101751	71101751	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	18	79	0	ENST00000318789.4:c.447del	p.Lys149AsnfsTer57	p.K149Nfs*57	ENST00000318789	NM_032682.5	149	aaA/aa	9/21	1	2	FACETS	0.805	0.615	1	0.805	0.615	1	CLONAL	1	TRUE	1	0.43	2		79	104	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794441	42794441	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	62	695	2	ENST00000575354.2:c.1526del	p.Pro509HisfsTer14	p.P509Hfs*14	ENST00000575354	NM_015125.3	507	cgC/cg	10/20	1	2	FACETS	0.272	0.233	0.313	0.272	0.233	0.313	SUBCLONAL	1	TRUE	1	0.43	2		697	1062	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564823	41564823	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	83	188	0	ENST00000263253.7:c.4124G>T	p.Gly1375Val	p.G1375V	ENST00000263253	NM_001429.3	1375	gGc/gTc	25/31	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.43	2		188	285	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137784	64137784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	266	781	0	ENST00000334205.4:c.1885C>T	p.Arg629Cys	p.R629C	ENST00000334205	NM_003942.2	629	Cgc/Tgc	15/17	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.43	2		781	1217	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508239	106508239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	101	189	0	ENST00000359195.3:c.233C>T	p.Ala78Val	p.A78V	ENST00000359195	NM_002649.2	78	gCg/gTg	2/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.43	2		189	354	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128029004	128029004	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1385827451	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	64	224	2	ENST00000285398.2:c.1853C>T	p.Pro618Leu	p.P618L	ENST00000285398	NM_000122.1	618	cCg/cTg	12/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.43	2		226	228	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138915	64138915	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	60	475	2	ENST00000334205.4:c.2287del	p.Arg763AlafsTer21	p.R763Afs*21	ENST00000334205	NM_003942.2	761	gCc/gc	17/17	1	2	FACETS	0.304	0.261	0.351	0.304	0.261	0.351	SUBCLONAL	1	TRUE	1	0.43	2		477	918	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755426	39755427	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	26	247	1	ENST00000288319.7:c.1338dup	p.Ala447CysfsTer19	p.A447Cfs*19	ENST00000288319	NM_182918.3	446	-/T	10/10	1	2	FACETS	0.391	0.31	0.484	0.391	0.31	0.484	SUBCLONAL	1	TRUE	1	0.43	2		248	309	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098396	11098396	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138097741	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	82	666	0	ENST00000358026.2:c.914C>T	p.Pro305Leu	p.P305L	ENST00000358026	NM_001128849.1	305	cCg/cTg	6/36	1	2	FACETS	0.306	0.269	0.347	0.306	0.269	0.347	SUBCLONAL	1	TRUE	1	0.43	2		666	1246	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905324	50905324	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	55	717	2	ENST00000440232.2:c.537del	p.Arg180GlyfsTer3	p.R180Gfs*3	ENST00000440232	NM_002691.3	178	Ggg/gg	5/27	1	2	FACETS	0.236	0.201	0.275	0.236	0.201	0.275	SUBCLONAL	1	TRUE	1	0.43	2		719	1083	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910273	50910273	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555791349	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	194	633	3	ENST00000440232.2:c.1528G>A	p.Val510Met	p.V510M	ENST00000440232	NM_002691.3	510	Gtg/Atg	13/27	1	2	FACETS	0.908	0.84	0.978	0.908	0.84	0.978	CLONAL	1	TRUE	1	0.43	2		636	994	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521525	46521525	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	62	231	0	ENST00000262741.5:c.883del	p.Met295Ter	p.M295*	ENST00000262741	NM_003629.3	295	Atg/tg	7/10	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.43	2		231	265	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647685	2647685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	122	378	2	ENST00000342085.4:c.1588G>A	p.Gly530Arg	p.G530R	ENST00000342085	NM_002613.4	530	Ggg/Agg	14/14	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.43	2		380	526	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466022	69466022	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	64	583	0	ENST00000227507.2:c.860C>A	p.Pro287His	p.P287H	ENST00000227507	NM_053056.2	287	cCc/cAc	5/5	1	2	FACETS	0.277	0.238	0.318	0.277	0.238	0.318	SUBCLONAL	1	TRUE	1	0.43	2		583	1076	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784064	120784064	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	231	679	0	ENST00000257552.2:c.921C>A	p.Phe307Leu	p.F307L	ENST00000257552	NM_002442.3	307	ttC/ttA	13/15	1	2	FACETS	0.932	0.868	0.998	0.932	0.868	0.998	CLONAL	1	TRUE	1	0.43	2		679	1153	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7120689	7120689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568426700	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	65	388	0	ENST00000302850.5:c.3601C>T	p.Arg1201Trp	p.R1201W	ENST00000302850	NM_000208.2	1201	Cgg/Tgg	20/22	1	2	FACETS	0.679	0.591	0.775	0.679	0.591	0.775	SUBCLONAL	1	TRUE	1	0.43	2		388	445	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944132	71944134	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs746559845	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	93	365	0	ENST00000298229.2:c.1967_1969del	p.Ser656del	p.S656del	ENST00000298229	NM_001567.3	655	atCTCc/atc	17/28	1	2	FACETS	0.892	0.796	0.993	0.892	0.796	0.993	CLONAL	1	TRUE	1	0.43	2		365	485	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644874	67644874	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	52	208	0	ENST00000264010.4:c.143del	p.Gly48ValfsTer14	p.G48Vfs*14	ENST00000264010	NM_006565.3	47	Ggg/gg	3/12	1	2	FACETS	0.995	0.856	1	0.995	0.856	1	CLONAL	1	TRUE	1	0.43	2		208	243	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265285	46265285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1447875218	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	13	96	0	ENST00000371998.3:c.2155G>A	p.Gly719Arg	p.G719R	ENST00000371998		719	Gga/Aga	12/23	1	2	FACETS	0.393	0.281	0.527	0.393	0.281	0.527	SUBCLONAL	1	TRUE	1	0.43	2		96	154	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216189	36216189	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	79	452	0	ENST00000222270.7:c.3602del	p.Pro1201ArgfsTer154	p.P1201Rfs*154	ENST00000222270	NM_014727.1	1199	ggC/gg	11/37	1	2	FACETS	0.526	0.462	0.594	0.526	0.462	0.594	SUBCLONAL	1	TRUE	1	0.43	2		452	699	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980265	201980265	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	29	201	0	ENST00000359651.3:c.1A>G	p.Met1?	p.M1?	ENST00000359651		1	Atg/Gtg	1/8	1	2	FACETS	0.467	0.375	0.57	0.467	0.375	0.57	SUBCLONAL	1	TRUE	1	0.43	2		201	289	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63816997	63816997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	21	85	0	ENST00000279873.7:c.968C>T	p.Ala323Val	p.A323V	ENST00000279873	NM_032199.2	323	gCc/gTc	6/10	1	2	FACETS	0.921	0.722	1	0.921	0.722	1	CLONAL	1	TRUE	1	0.43	2		85	106	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845594	63845594	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	15	98	0	ENST00000279873.7:c.1335del	p.Lys445AsnfsTer34	p.K445Nfs*34	ENST00000279873	NM_032199.2	445	Aaa/aa	9/10	1	2	FACETS	0.549	0.405	0.719	0.549	0.405	0.719	SUBCLONAL	1	TRUE	1	0.43	2		98	127	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717719	89717720	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs780264945	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	43	123	0	ENST00000371953.3:c.750_751del	p.Cys250TrpfsTer2	p.C250Wfs*2	ENST00000371953	NM_000314.4	248	ccTGtg/cctg	7/9	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.43	2		123	155	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925402	114925402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748822481	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	78	438	4	ENST00000543371.1:c.1485del	p.Ser496ProfsTer5	p.S496Pfs*5	ENST00000543371	NM_001198531.1	494	Ccc/cc	14/14	1	2	FACETS	0.574	0.504	0.649	0.574	0.504	0.649	SUBCLONAL	1	TRUE	1	0.43	2		442	632	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946429	71946429	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs764768551	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	147	566	0	ENST00000298229.2:c.2593A>G	p.Asn865Asp	p.N865D	ENST00000298229	NM_001567.3	865	Aat/Gat	23/28	1	2	FACETS	0.897	0.82	0.978	0.897	0.82	0.978	CLONAL	1	TRUE	1	0.43	2		566	762	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375057	118375057	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	10	127	0	ENST00000534358.1:c.8454del	p.Ser2819ProfsTer14	p.S2819Pfs*14	ENST00000534358	NM_005933.3	2817	aCc/ac	27/36	1	2	FACETS	0.249	0.168	0.35	0.249	0.168	0.35	SUBCLONAL	1	TRUE	1	0.43	2		127	187	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444378	49444378	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	39	370	0	ENST00000301067.7:c.2993del	p.Pro998LeufsTer2	p.P998Lfs*2	ENST00000301067	NM_003482.3	998	cCt/ct	11/54	1	2	FACETS	0.354	0.293	0.423	0.354	0.293	0.423	SUBCLONAL	1	TRUE	1	0.43	2		370	512	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518988	103518988	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	20	264	0	ENST00000355739.4:c.2326C>A	p.Leu776Met	p.L776M	ENST00000355739	NM_000123.3	776	Ctg/Atg	11/15	1	2	FACETS	0.247	0.188	0.316	0.247	0.188	0.316	SUBCLONAL	1	TRUE	1	0.43	2		264	377	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060955	38060955	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	34	241	0	ENST00000250448.2:c.1034del	p.Gly345AlafsTer5	p.G345Afs*5	ENST00000250448	NM_004496.3	345	gGc/gc	2/2	1	2	FACETS	0.323	0.264	0.391	0.323	0.264	0.391	SUBCLONAL	1	TRUE	1	0.43	2		241	489	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456306	99456306	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	72	195	0	ENST00000268035.6:c.1623G>T	p.Gln541His	p.Q541H	ENST00000268035	NM_000875.3	541	caG/caT	8/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.43	2		195	288	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500476	99500476	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	147	474	0	ENST00000268035.6:c.3913del	p.Leu1305TrpfsTer45	p.L1305Wfs*45	ENST00000268035	NM_000875.3	1303	gtC/gt	21/21	1	2	FACETS	0.85	0.777	0.927	0.85	0.777	0.927	CLONAL	1	TRUE	1	0.43	2		474	804	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655410	67655410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	17	235	0	ENST00000264010.4:c.1273C>T	p.His425Tyr	p.H425Y	ENST00000264010	NM_006565.3	425	Cac/Tac	7/12	1	2	FACETS	0.314	0.234	0.408	0.314	0.234	0.408	SUBCLONAL	1	TRUE	1	0.43	2		235	252	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942085	81942085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767040629	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	65	277	2	ENST00000359376.3:c.1622C>T	p.Thr541Met	p.T541M	ENST00000359376	NM_002661.3	541	aCg/aTg	17/33	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.43	2		279	288	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217432	7217432	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	206	58	0	ENST00000380728.2:c.364G>A	p.Val122Ile	p.V122I	ENST00000380728		122	Gtt/Att	5/11	1	2	FACETS	0.84	0.793	0.887	1	0.995	1	CLONAL	3	TRUE	1	0.43	2		58	380	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980507	7980507	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	234	49	0	ENST00000319144.4:c.1076G>A	p.Ser359Asn	p.S359N	ENST00000319144	NM_001139.2	359	aGc/aAc	9/15	1	2	FACETS	0.872	0.827	0.917	1	0.996	1	CLONAL	3	TRUE	1	0.43	2		49	416	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857633	78857633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	197	533	0	ENST00000306801.3:c.1703A>G	p.Asp568Gly	p.D568G	ENST00000306801	NM_020761.2	568	gAc/gGc	16/34	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.43	2		533	793	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191174	2191174	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	52	530	0	ENST00000398665.3:c.428T>C	p.Leu143Pro	p.L143P	ENST00000398665	NM_032482.2	143	cTg/cCg	5/28	1	2	FACETS	0.357	0.303	0.416	0.357	0.303	0.416	SUBCLONAL	1	TRUE	1	0.43	2		530	678	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210524	5210524	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1432193218	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	30	423	0	ENST00000357368.4:c.5443A>G	p.Met1815Val	p.M1815V	ENST00000357368	NM_002850.3	1815	Atg/Gtg	35/38	1	2	FACETS	0.258	0.207	0.316	0.258	0.207	0.316	SUBCLONAL	1	TRUE	1	0.43	2		423	540	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950388	17950388	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	45	545	1	ENST00000458235.1:c.1339del	p.His447ThrfsTer18	p.H447Tfs*18	ENST00000458235	NM_000215.3	447	Cac/ac	10/24	1	2	FACETS	0.258	0.216	0.305	0.258	0.216	0.305	SUBCLONAL	1	TRUE	1	0.43	2		546	812	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273026	18273026	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	232	596	4	ENST00000222254.8:c.921del	p.Lys308ArgfsTer33	p.K308Rfs*33	ENST00000222254	NM_005027.3	306	Ccc/cc	8/16	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.43	2		600	914	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794474	42794474	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	87	675	0	ENST00000575354.2:c.1555del	p.Asp519IlefsTer4	p.D519Ifs*4	ENST00000575354	NM_015125.3	518	ccG/cc	10/20	1	2	FACETS	0.371	0.327	0.418	0.371	0.327	0.418	SUBCLONAL	1	TRUE	1	0.43	2		675	1091	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212615400	212615400	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	41	156	1	ENST00000342788.4:c.586C>A	p.Arg196Ser	p.R196S	ENST00000342788	NM_005235.2	196	Cgt/Agt	5/28	1	2	FACETS	0.733	0.615	0.863	0.733	0.615	0.863	SUBCLONAL	1	TRUE	1	0.43	2		157	260	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164566	36164566	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	157	377	0	ENST00000300305.3:c.1309A>G	p.Thr437Ala	p.T437A	ENST00000300305		437	Acc/Gcc	8/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.43	2		377	681	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537109	41537110	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	41	128	0	ENST00000263253.7:c.1941dup	p.Arg648ThrfsTer27	p.R648Tfs*27	ENST00000263253	NM_001429.3	646	gaa/gAaa	10/31	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.43	2		128	150	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12393112	12393112	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	55	186	0	ENST00000287820.6:c.21T>A	p.Asp7Glu	p.D7E	ENST00000287820	NM_015869.4	7	gaT/gaA	1/7	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.43	2		186	239	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403497	138403497	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	57	179	0	ENST00000289153.2:c.2285T>C	p.Leu762Pro	p.L762P	ENST00000289153	NM_006219.2	762	cTg/cCg	15/22	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.43	2		179	226	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518017	187518017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs553450953	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	11	167	0	ENST00000441802.2:c.12677C>T	p.Ala4226Val	p.A4226V	ENST00000441802	NM_005245.3	4226	gCt/gTt	25/27	1	2	FACETS	0.281	0.194	0.389	0.281	0.194	0.389	SUBCLONAL	1	TRUE	1	0.43	2		167	182	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540069	187540069	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	36	151	0	ENST00000441802.2:c.7671A>T	p.Glu2557Asp	p.E2557D	ENST00000441802	NM_005245.3	2557	gaA/gaT	10/27	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.43	2		151	152	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176700715	176700715	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	37	143	0	ENST00000439151.2:c.5556del	p.Glu1853SerfsTer2	p.E1853Sfs*2	ENST00000439151	NM_022455.4	1851	cAa/ca	17/23	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.43	2		143	157	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109311861	109311861	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1016537660	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	14	181	0	ENST00000436639.2:c.1411A>G	p.Met471Val	p.M471V	ENST00000436639	NM_014454.2	471	Atg/Gtg	8/10	1	2	FACETS	0.27	0.195	0.361	0.27	0.195	0.361	SUBCLONAL	1	TRUE	1	0.43	2		181	241	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100246	157100246	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773467188	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	12	79	0	ENST00000346085.5:c.1183G>A	p.Ala395Thr	p.A395T	ENST00000346085	NM_020732.3	395	Gcc/Acc	1/20	1	2	FACETS	0.256	0.18	0.35	0.256	0.18	0.35	SUBCLONAL	1	TRUE	1	0.43	2		79	218	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335658	81335658	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	21	139	0	ENST00000222390.5:c.1702T>C	p.Ser568Pro	p.S568P	ENST00000222390	NM_000601.4	568	Tcc/Ccc	15/18	1	2	FACETS	0.474	0.367	0.598	0.474	0.367	0.598	SUBCLONAL	1	TRUE	1	0.43	2		139	206	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38178604	38178606	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	44	190	0	ENST00000317025.8:c.1793_1795del	p.Lys598del	p.K598del	ENST00000317025	NM_023034.1	598	aAGAtc/atc	8/24	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.43	2		190	200	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69000005	69000005	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561299451	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	34	219	0	ENST00000288368.4:c.2074C>T	p.Arg692Trp	p.R692W	ENST00000288368	NM_024870.2	692	Cgg/Tgg	19/40	1	2	FACETS	0.618	0.507	0.74	0.618	0.507	0.74	SUBCLONAL	1	TRUE	1	0.43	2		219	256	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974678	21974678	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs587778189	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	41	348	0	ENST00000304494.5:c.149A>C	p.Gln50Pro	p.Q50P	ENST00000304494	NM_000077.4	50	cAg/cCg	1/3	1	2	FACETS	0.325	0.27	0.386	0.325	0.27	0.386	SUBCLONAL	1	TRUE	1	0.43	2		348	587	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240399	98240399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377546733	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	99	300	0	ENST00000331920.6:c.1285G>A	p.Asp429Asn	p.D429N	ENST00000331920	NM_000264.3	429	Gac/Aac	9/24	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.43	2		300	422	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969405	44969405	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	67	176	0	ENST00000377967.4:c.4087C>T	p.Arg1363Ter	p.R1363*	ENST00000377967	NM_021140.2	1363	Cga/Tga	28/29	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.43	2		176	245	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518569	69518569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	47	450	5	ENST00000294312.3:c.76G>A	p.Ala26Thr	p.A26T	ENST00000294312	NM_005117.2	26	Gcc/Acc	1/3	1	2	FACETS	0.262	0.22	0.309	0.262	0.22	0.309	SUBCLONAL	1	TRUE	1	0.43	2		455	833	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36824388	36824388	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	58	480	0	ENST00000373129.3:c.148G>C	p.Val50Leu	p.V50L	ENST00000373129	NM_032017.1	50	Gtg/Ctg	4/12	1	2	FACETS	0.766	0.656	0.886	0.766	0.656	0.886	SUBCLONAL	1	TRUE	1	0.17	2		480	891	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983132	201983133	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	104	376	0	ENST00000359651.3:c.983dup	p.Leu329AlafsTer142	p.L329Afs*142	ENST00000359651		327	-/A	7/8	0.195668665105928	3	FACETS	0.868	0.777	0.964	0.868	0.777	0.964	CLONAL	2	TRUE	1	0.17	3		376	765	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404752	70404752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376909245	NA	P-0020460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	45	216	2	ENST00000373644.4:c.2266G>A	p.Val756Ile	p.V756I	ENST00000373644	NM_030625.2	756	Gta/Ata	4/12	1	2	FACETS	0.859	0.721	1	0.859	0.721	1	CLONAL	1	TRUE	1	0.17	2		218	616	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712002	89712002	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	15	94	0	ENST00000371953.3:c.620G>A	p.Ser207Asn	p.S207N	ENST00000371953	NM_000314.4	207	aGt/aAt	6/9	1	2	FACETS	0.676	0.494	0.895	0.676	0.494	0.895	SUBCLONAL	1	TRUE	1	0.17	2		94	261	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476310	88476310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760692815	NA	P-0020460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	92	438	0	ENST00000360948.2:c.1822G>A	p.Gly608Ser	p.G608S	ENST00000360948	NM_001012338.2	608	Ggc/Agc	15/19	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.17	2		438	819	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846036	68846036	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0020460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	139	402	0	ENST00000261769.5:c.1009-2A>G		p.X337_splice	ENST00000261769	NM_004360.3	337			0.185587402926318	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	0	0.17	2		402	797	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61708417	61709439	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CTGCAAATCAAAACACAATGATTAAATAATGATTTATTTTTCCCCCGAGACAGAGTATTGCTCTGTCACCAGGCTGGAGTACAGTGGCATGATCTCTGCTCACTGTAATCTCTGCCTCCCGGGTTCAAGACATTCTCCTGCCTCAGCGTCCCAATAATGTTTTTTTTTTTTAATCAAGAATTTTTTTTTAATTTTTGAGACAAAGTTTTGCTCGTTTACCAGGTTGGAGTACAATCGCACAATCGCGGCTCACCGCAACCTCTGAAGCTATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGATTACAGGCATGCACCACCATGCCCGGCTAATTTGTATTTTTAGTAGAGACAGGGTTTCTCCATGTTGGTCAGGCAAATCTCAAACTCCTGACCTCAGGTAATCTGCCCGCCTAGGCCTCCCAAAGTGCTTGGATTACAGGCGTTTGCCACCGTGCCCAGCCTTTTTATTTTTTGAGACAGTCTTGCTCTGTCACCCACACTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAACCTCTGCCTCCTGGGTTCAAGCAGTTCTCCCCCTCAGCCTCCCAAGTAGCTGGGATTTCAGGCACCCACCACCATGCCCAACTAATTTTTTGTATTTTTAGTAGAAACGGGGTTTCACCATCTTGGCCAGGCTGGTCTTGAACTCCTGACCTTGTGATTCACCCACCTCAGCCTCCCAAAGTGTTGGGATTACAGTCATGAGCCACCGTGCGTGGCCTTTTTTTTTTTTTTTTTTTTTTTGCTTTTTTAAAGAGGCAGGGTCTCACTCTATCACCCAGGCTGGTGTACAGTGGTGCGATCATAGCTCACTGCAGTCTTAAACTCCAGGATGCAAACAACCCTCTCGCCTCAGCCTCTCCAACAGCTGGTCCTACAGATGCATACCACTTCTGACTACTTTTTTTTTTGTAGAGACGGGATCTTGTTTTGTTGTCTAGGTTGGTCTCCAACTTTTGGGCCCAAGCAATCCTCCCACCTTAGGCTTCCC	CTGCAAATCAAAACACAATGATTAAATAATGATTTATTTTTCCCCCGAGACAGAGTATTGCTCTGTCACCAGGCTGGAGTACAGTGGCATGATCTCTGCTCACTGTAATCTCTGCCTCCCGGGTTCAAGACATTCTCCTGCCTCAGCGTCCCAATAATGTTTTTTTTTTTTAATCAAGAATTTTTTTTTAATTTTTGAGACAAAGTTTTGCTCGTTTACCAGGTTGGAGTACAATCGCACAATCGCGGCTCACCGCAACCTCTGAAGCTATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGATTACAGGCATGCACCACCATGCCCGGCTAATTTGTATTTTTAGTAGAGACAGGGTTTCTCCATGTTGGTCAGGCAAATCTCAAACTCCTGACCTCAGGTAATCTGCCCGCCTAGGCCTCCCAAAGTGCTTGGATTACAGGCGTTTGCCACCGTGCCCAGCCTTTTTATTTTTTGAGACAGTCTTGCTCTGTCACCCACACTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAACCTCTGCCTCCTGGGTTCAAGCAGTTCTCCCCCTCAGCCTCCCAAGTAGCTGGGATTTCAGGCACCCACCACCATGCCCAACTAATTTTTTGTATTTTTAGTAGAAACGGGGTTTCACCATCTTGGCCAGGCTGGTCTTGAACTCCTGACCTTGTGATTCACCCACCTCAGCCTCCCAAAGTGTTGGGATTACAGTCATGAGCCACCGTGCGTGGCCTTTTTTTTTTTTTTTTTTTTTTTGCTTTTTTAAAGAGGCAGGGTCTCACTCTATCACCCAGGCTGGTGTACAGTGGTGCGATCATAGCTCACTGCAGTCTTAAACTCCAGGATGCAAACAACCCTCTCGCCTCAGCCTCTCCAACAGCTGGTCCTACAGATGCATACCACTTCTGACTACTTTTTTTTTTGTAGAGACGGGATCTTGTTTTGTTGTCTAGGTTGGTCTCCAACTTTTGGGCCCAAGCAATCCTCCCACCTTAGGCTTCCC	-	novel	NA	P-0020460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	183	38	0	ENST00000401558.2:c.2972+76_2973-1del		p.X991_splice	ENST00000401558	NM_003400.3	991			0.195668665105928	3	FACETS	1	0.971	1	1	0.991	1	CLONAL	3	TRUE	1	0.17	3		38	711	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61709673	61710089	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACCTGTTGATAAGAAGAAAATTATTAACTCCAAAATGTAATATAACTATAGATCTTAGCGTTTTTTTTTGTTTTGTTTTTTTTTTTTAGACGGAGTCTCGCTCTGTCACCCAAGCTGGAATGCCGTGGCGCAATCTTAGTTCACTGCAACCTCTGCCTCCTCGGTCCAAGCCATTCTCCTGCCTCAGCCTCCCGAATAGGTGGGATTGCAATCACATGCCACCATGCCCAGTATTTTTATTGTATCTTTTATTTTTTTATGGTATTTTTAGTACAGACAGTTTCACCATGGTGGCCAGGCTGTTCTCGAACTCCTGACCTCATAATCTCCCCGCCTCGACCTCCCAAAGTGCTGGGATTATAGGCGTGAGGCCCTGTGCCCAGCTGGCACTTAACATTTAAATCGTATTAAATTCTT	ACCTGTTGATAAGAAGAAAATTATTAACTCCAAAATGTAATATAACTATAGATCTTAGCGTTTTTTTTTGTTTTGTTTTTTTTTTTTAGACGGAGTCTCGCTCTGTCACCCAAGCTGGAATGCCGTGGCGCAATCTTAGTTCACTGCAACCTCTGCCTCCTCGGTCCAAGCCATTCTCCTGCCTCAGCCTCCCGAATAGGTGGGATTGCAATCACATGCCACCATGCCCAGTATTTTTATTGTATCTTTTATTTTTTTATGGTATTTTTAGTACAGACAGTTTCACCATGGTGGCCAGGCTGTTCTCGAACTCCTGACCTCATAATCTCCCCGCCTCGACCTCCCAAAGTGCTGGGATTATAGGCGTGAGGCCCTGTGCCCAGCTGGCACTTAACATTTAAATCGTATTAAATTCTT	-	novel	NA	P-0020460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	22	103	0	ENST00000401558.2:c.2812+3_2814del		p.X938_splice	ENST00000401558	NM_003400.3	938		23/25	0.195668665105928	3	FACETS	0.996	0.773	1	0.498	0.386	0.627	CLONAL	1	TRUE	1	0.17	3		103	282	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61710226	61711070	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTAAAAGACATAGAATACCAATGGAAAGTTACTACAGACTGACAGCACTCATGATAGTATTTAGCTCTTATCAAAGTATTCTGAATCTAACCCTGTTCTCCCTTTTTTTTGGGATGATGACTAATAATTACTTGCATAAGGTTTCTTAAATTAATAATGGAATACAACTATATCCAATGCTGGCTTACTTATAAATTATAATAAGTTGTGTGAGAGCTAAACTGTGAAGATGTAAAGGCATAAAGATCATATAATGGACTTTGGGGACTTGTGGGGAAGGGCAGGAGTGGGTGAGGGATAAGACTACACATAAGGTGGAGTTCATACACATGAGGGATAAGACTACACATAAAGTAGAGTTCATACTGCTCACATGACAGGTGCACCAAAATCTCAGAAATCACCACTGAAGAACTTATTCATGTAACCAAAAACCACCTGTTCCCCAAAAACTATTGAAATAAAAAAAGAACCTCATGAATATTTTTTAAAAGCCTATGGGAAAAAAATTACAATCTAAGTTATGACTATTACCACCCTTTCACCATTTCTGAAAGCTCAGCTGATTCTATATGAACTTCTACAACATCACTACCCAGTAGAACTTTGTATTACGCAAACCAATTATTACTAGGCCGCTCTCCCCATAACTCAATTCTGCCTATGGACTCACTTGGAGTGGAGTGGAACAGTTGATTAAACTGCTTATAGGATTTTCTCAGATGTTCATATATGTAATTCACACACTCAAAACTCTGAACAAGTAATACCTTCCTATGTACAATTAACTATATTTGTATTTTTGGATTGGCAGGCAAATGAATAAAAGAACATCTTTTATTTA	CCTAAAAGACATAGAATACCAATGGAAAGTTACTACAGACTGACAGCACTCATGATAGTATTTAGCTCTTATCAAAGTATTCTGAATCTAACCCTGTTCTCCCTTTTTTTTGGGATGATGACTAATAATTACTTGCATAAGGTTTCTTAAATTAATAATGGAATACAACTATATCCAATGCTGGCTTACTTATAAATTATAATAAGTTGTGTGAGAGCTAAACTGTGAAGATGTAAAGGCATAAAGATCATATAATGGACTTTGGGGACTTGTGGGGAAGGGCAGGAGTGGGTGAGGGATAAGACTACACATAAGGTGGAGTTCATACACATGAGGGATAAGACTACACATAAAGTAGAGTTCATACTGCTCACATGACAGGTGCACCAAAATCTCAGAAATCACCACTGAAGAACTTATTCATGTAACCAAAAACCACCTGTTCCCCAAAAACTATTGAAATAAAAAAAGAACCTCATGAATATTTTTTAAAAGCCTATGGGAAAAAAATTACAATCTAAGTTATGACTATTACCACCCTTTCACCATTTCTGAAAGCTCAGCTGATTCTATATGAACTTCTACAACATCACTACCCAGTAGAACTTTGTATTACGCAAACCAATTATTACTAGGCCGCTCTCCCCATAACTCAATTCTGCCTATGGACTCACTTGGAGTGGAGTGGAACAGTTGATTAAACTGCTTATAGGATTTTCTCAGATGTTCATATATGTAATTCACACACTCAAAACTCTGAACAAGTAATACCTTCCTATGTACAATTAACTATATTTGTATTTTTGGATTGGCAGGCAAATGAATAAAAGAACATCTTTTATTTA	-	novel	NA	P-0020460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	46	189	0	ENST00000401558.2:c.2677+2_2678del		p.X893_splice	ENST00000401558	NM_003400.3	893		22/25	0.195668665105928	3	FACETS	1	0.842	1	0.5	0.421	0.588	CLONAL	1	TRUE	1	0.17	3		189	587	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61713087	61713087	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	30	138	0	ENST00000401558.2:c.2324A>G	p.Asn775Ser	p.N775S	ENST00000401558	NM_003400.3	775	aAt/aGt	20/25	0.195668665105928	3	FACETS	1	0.855	1	0.536	0.432	0.654	CLONAL	1	TRUE	1	0.17	3		138	357	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715405	61715720	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACCTACAAAACAGAATCAAATGGAATCTAATTTTACCACTAAACTTATACAGTGGTACTCAGGTGTACATTAGATGCAATTCCATTTTACCATTAAAAAGTTTAAAGCCAAAAGTTCACAAAATTTATTGGGAAAATAAGCTTTAAGACTAATTTTAAAAGGGAAAGGTACACTTAACTGTTTTAAATATGTCTAGGGTCATTTGGGAAATGGGAGGTCTGATTTAAATCTGTAAAAAACATCAAATGTTTGACTTAAGGCAGTAGAAGAGAAGTGGTTTGTTTATACTGCATTGTGTAAGAAATCAGAATCACCT	ACCTACAAAACAGAATCAAATGGAATCTAATTTTACCACTAAACTTATACAGTGGTACTCAGGTGTACATTAGATGCAATTCCATTTTACCATTAAAAAGTTTAAAGCCAAAAGTTCACAAAATTTATTGGGAAAATAAGCTTTAAGACTAATTTTAAAAGGGAAAGGTACACTTAACTGTTTTAAATATGTCTAGGGTCATTTGGGAAATGGGAGGTCTGATTTAAATCTGTAAAAAACATCAAATGTTTGACTTAAGGCAGTAGAAGAGAAGTGGTTTGTTTATACTGCATTGTGTAAGAAATCAGAATCACCT	-	novel	NA	P-0020460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	50	182	0	ENST00000401558.2:c.2206+3_2208del		p.X736_splice	ENST00000401558	NM_003400.3	736		19/25	0.195668665105928	3	FACETS	1	0.875	1	0.518	0.439	0.605	CLONAL	1	TRUE	1	0.17	3		182	616	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719334	61719459	+	splice_donor_variant,splice_acceptor_variant,intron_variant	Splice_Site	DEL	CTAACAAGACAAAAATATTCATTTATTTTGTCCTGGACTCCATCATGGGTCTCTAACAAGACAAAAACATTCATTTATTTTCTTCAATAAAAATAAAAGCAAAATATAGTAAAGAAAGAGATTTAC	CTAACAAGACAAAAATATTCATTTATTTTGTCCTGGACTCCATCATGGGTCTCTAACAAGACAAAAACATTCATTTATTTTCTTCAATAAAAATAAAAGCAAAATATAGTAAAGAAAGAGATTTAC	-	novel	NA	P-0020460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	33	172	0	ENST00000401558.2:c.1723+1_1724-1del		p.X575_splice	ENST00000401558	NM_003400.3	575			0.195668665105928	3	FACETS	0.848	0.689	1	0.424	0.344	0.513	CLONAL	1	TRUE	1	0.17	3		172	497	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719616	61719700	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTGTAAATAAGACAAATTTGTATTATTTATTGTAACAACATAATACTTATTTAGCAATTCTAATTCATACCTATCCCTTGCATA	CCTGTAAATAAGACAAATTTGTATTATTTATTGTAACAACATAATACTTATTTAGCAATTCTAATTCATACCTATCCCTTGCATA	-	novel	NA	P-0020460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	53	163	0	ENST00000401558.2:c.1566+2_1567del		p.X522_splice	ENST00000401558	NM_003400.3	522		15/25	0.195668665105928	3	FACETS	1	0.938	1	0.599	0.51	0.696	CLONAL	1	TRUE	1	0.17	3		163	565	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719884	61720049	+	splice_acceptor_variant,splice_donor_variant,intron_variant	Splice_Site	DEL	CTACAAAGAAAAACATGGTTTCAAATGCAAATAATGAGCAGAATTTTATTGATGAGTAACAATACATTTAGAAAATATTTAGAAACTACAAGTACATTTCCTAAAATGTATTTCCACCCCAGAATAGATTTATAAAGGTAAAGATTAACAGTATTTATTAACTTAC	CTACAAAGAAAAACATGGTTTCAAATGCAAATAATGAGCAGAATTTTATTGATGAGTAACAATACATTTAGAAAATATTTAGAAACTACAAGTACATTTCCTAAAATGTATTTCCACCCCAGAATAGATTTATAAAGGTAAAGATTAACAGTATTTATTAACTTAC	-	novel	NA	P-0020460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	49	195	0	ENST00000401558.2:c.1384+1_1385-1del		p.X462_splice	ENST00000401558	NM_003400.3	462			0.195668665105928	3	FACETS	1	0.934	1	0.599	0.507	0.7	CLONAL	1	TRUE	1	0.17	3		195	522	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61720187	61721026	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACCTATACTCAACAATATATCAATCAAGAAAAAAATCGTTAGATCACTGAAATCATTAGTGTAGAAGCTTAGTTAAAAACAAACAAAACCAAAAAAACCACAAGCCAGCCATGTGTAGGGATTCATGCCTATAATTCCAACTATTCCGGAGGGCCGAGGCAAAAAGAACTGTTGTGGCCAGGAATTTGAGAGCAGCTTGAGCAACACAAAATGACACCCAATCTCTAAAACAATAAAAATACTGGGGCTTAAAGCACAACAGAAAAAACTATGTAAATATAAATGAAGTAAAACTAAAAAATTTAAAATTTGCTAGGCATGGTGGTGTGTGCCTGCAACCAATTACTTGGGAGGCTGACACAAGAGAATTGCTTTAGTCTAGGAGTTCAAGATTGTAGTGAGCTATGACCACGCCACTGCACTCCAACCTGAGCCACAGAGCAAGACCCTGTCTCCAAAAGAAAAAATTTTTTTTCACTGTAATTCTACAAAAATGGCTTTATAATTATTTAAGTGTGTTTTAATGTGATTTTTTTAACCAACTTCTGTTACAGGAGTTTCCTGTGTCTCATTCCTAGACTCTGGTTTAGTAGATTGGCAGGTGGCCAATGAATTTGCCTAACGAAATCACAACCAATGTTGATACTGAGAGAAGGACCACACTCTTGAGAATCAAGGTTCTAGACTCAACTCCTTTCATGTTCTAGTTTTCCACACTCATGGAGAAGTTGTTGGGTTCTCTTTTTATAGCTAATTTATTTACACAGATTAGAAGTATTTGGATTCAGACCTCAAAACCACAGTATGCAACAGGAAGAACACTCAACCAACCGCTCTGTT	ACCTATACTCAACAATATATCAATCAAGAAAAAAATCGTTAGATCACTGAAATCATTAGTGTAGAAGCTTAGTTAAAAACAAACAAAACCAAAAAAACCACAAGCCAGCCATGTGTAGGGATTCATGCCTATAATTCCAACTATTCCGGAGGGCCGAGGCAAAAAGAACTGTTGTGGCCAGGAATTTGAGAGCAGCTTGAGCAACACAAAATGACACCCAATCTCTAAAACAATAAAAATACTGGGGCTTAAAGCACAACAGAAAAAACTATGTAAATATAAATGAAGTAAAACTAAAAAATTTAAAATTTGCTAGGCATGGTGGTGTGTGCCTGCAACCAATTACTTGGGAGGCTGACACAAGAGAATTGCTTTAGTCTAGGAGTTCAAGATTGTAGTGAGCTATGACCACGCCACTGCACTCCAACCTGAGCCACAGAGCAAGACCCTGTCTCCAAAAGAAAAAATTTTTTTTCACTGTAATTCTACAAAAATGGCTTTATAATTATTTAAGTGTGTTTTAATGTGATTTTTTTAACCAACTTCTGTTACAGGAGTTTCCTGTGTCTCATTCCTAGACTCTGGTTTAGTAGATTGGCAGGTGGCCAATGAATTTGCCTAACGAAATCACAACCAATGTTGATACTGAGAGAAGGACCACACTCTTGAGAATCAAGGTTCTAGACTCAACTCCTTTCATGTTCTAGTTTTCCACACTCATGGAGAAGTTGTTGGGTTCTCTTTTTATAGCTAATTTATTTACACAGATTAGAAGTATTTGGATTCAGACCTCAAAACCACAGTATGCAACAGGAAGAACACTCAACCAACCGCTCTGTT	-	novel	NA	P-0020460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	55	206	0	ENST00000401558.2:c.1245+3_1247del		p.X415_splice	ENST00000401558	NM_003400.3	415		13/25	0.195668665105928	3	FACETS	1	0.937	1	0.59	0.504	0.684	CLONAL	1	TRUE	1	0.17	3		206	595	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729932	30729932	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	41	283	1	ENST00000295754.5:c.1453G>T	p.Glu485Ter	p.E485*	ENST00000295754	NM_003242.5	485	Gaa/Taa	6/7	1	2	FACETS	0.948	0.789	1	0.948	0.789	1	CLONAL	1	TRUE	1	0.17	2		284	509	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985587	2985587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064795280	NA	P-0020460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	30	190	0	ENST00000396946.4:c.224G>A	p.Arg75Gln	p.R75Q	ENST00000396946	NM_032415.4	75	cGg/cAg	4/25	0.195668665105928	3	FACETS	0.785	0.631	0.959	0.392	0.315	0.48	CLONAL	1	TRUE	1	0.17	3		190	488	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638542	176638542	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	243	564	0	ENST00000439151.2:c.3142T>G	p.Leu1048Val	p.L1048V	ENST00000439151	NM_022455.4	1048	Tta/Gta	5/23	0.685813898773708	3	FACETS	0.872	0.815	0.932	0.436	0.407	0.466	CLONAL	1	TRUE	1	0.685813898773708	3		564	1091	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302643	15302643	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	338	765	0	ENST00000263388.2:c.715G>T	p.Asp239Tyr	p.D239Y	ENST00000263388	NM_000435.2	239	Gac/Tac	5/33	1	2	FACETS	0.926	0.877	0.975	0.926	0.877	0.975	CLONAL	1	TRUE	1	0.685813898773708	2		765	1065	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216479	36216479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	358	784	0	ENST00000222270.7:c.3742C>T	p.Arg1248Cys	p.R1248C	ENST00000222270	NM_014727.1	1248	Cgc/Tgc	12/37	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.685813898773708	2		784	1035	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331667	8331667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147793450	NA	P-0020567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	110	416	2	ENST00000356435.5:c.5449G>A	p.Gly1817Arg	p.G1817R	ENST00000356435		1817	Gga/Aga	33/35	0.683638387635054	3	FACETS	0.545	0.489	0.603	0.272	0.244	0.302	SUBCLONAL	1	TRUE	1	0.685813898773708	3		418	791	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	13	233	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		235	184	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs17849781	NA	P-0020805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	64	182	0	ENST00000269305.4:c.832C>G	p.Pro278Ala	p.P278A	ENST00000269305	NM_001126112.2	278	Cct/Gct	8/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		182	510	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971209	21971209	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0020805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	106	81	0	ENST00000304494.5:c.151-2A>C		p.X51_splice	ENST00000304494	NM_000077.4	51			0.240253796878587	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		81	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0020904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	72	872	1	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.179112704712887	3	FACETS	0.973	0.848	1	0.486	0.424	0.554	CLONAL	1	TRUE	1	0.17	3		873	945	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913351	NA	P-0020904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	28	240	0	ENST00000288602.6:c.1397G>T	p.Gly466Val	p.G466V	ENST00000288602	NM_004333.4	466	gGa/gTa	11/18	1	2	FACETS	0.598	0.477	0.737	0.598	0.477	0.737	SUBCLONAL	1	TRUE	1	0.17	2		240	551	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602413	10602413	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	60	849	0	ENST00000171111.5:c.1165G>T	p.Asp389Tyr	p.D389Y	ENST00000171111	NM_203500.1	389	Gac/Tac	3/6	1	2	FACETS	0.795	0.683	0.917	0.795	0.683	0.917	CLONAL	1	TRUE	1	0.17	2		849	888	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041116	42041116	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780889520	NA	P-0020904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	39	613	0	ENST00000219905.7:c.5494C>T	p.Arg1832Trp	p.R1832W	ENST00000219905	NM_001164273.1	1832	Cgg/Tgg	16/24	0.179112704712887	3	FACETS	0.719	0.595	0.859	0.36	0.297	0.43	SUBCLONAL	1	TRUE	1	0.17	3		613	692	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838362	156838362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372041586	NA	P-0020904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	65	939	1	ENST00000524377.1:c.640C>T	p.Arg214Trp	p.R214W	ENST00000524377	NM_002529.3	214	Cgg/Tgg	6/17	0.179112704712887	3	FACETS	0.859	0.743	0.986	0.429	0.371	0.493	CLONAL	1	TRUE	1	0.17	3		940	966	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17743054	17743054	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0020904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	38	722	0	ENST00000250003.3:c.962G>C	p.Ter321SerextTer33	p.*321Sext*33	ENST00000250003	NM_002478.4	321	tGa/tCa	3/3	1	2	FACETS	0.65	0.536	0.778	0.65	0.536	0.778	SUBCLONAL	1	TRUE	1	0.17	2		722	688	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444304	49444304	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	82	981	0	ENST00000301067.7:c.3067C>A	p.Gln1023Lys	p.Q1023K	ENST00000301067	NM_003482.3	1023	Cag/Aag	11/54	1	2	FACETS	0.88	0.774	0.995	0.88	0.774	0.995	CLONAL	1	TRUE	1	0.17	2		981	1096	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444475	49444475	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	49	735	0	ENST00000301067.7:c.2896del	p.Asp966ThrfsTer34	p.D966Tfs*34	ENST00000301067	NM_003482.3	966	Gac/ac	11/54	1	2	FACETS	0.673	0.569	0.79	0.673	0.569	0.79	SUBCLONAL	1	TRUE	1	0.17	2		735	856	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863482	57863482	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0020904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	37	493	0	ENST00000228682.2:c.1576+1G>T		p.X526_splice	ENST00000228682	NM_005269.2	526			1	2	FACETS	0.704	0.579	0.845	0.704	0.579	0.845	SUBCLONAL	1	TRUE	1	0.17	2		493	618	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865257	57865257	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1253674081	NA	P-0020904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	52	769	0	ENST00000228682.2:c.2734G>C	p.Gly912Arg	p.G912R	ENST00000228682	NM_005269.2	912	Ggt/Cgt	12/12	1	2	FACETS	0.671	0.569	0.783	0.671	0.569	0.783	SUBCLONAL	1	TRUE	1	0.17	2		769	912	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857919	9857919	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	42	691	0	ENST00000330684.3:c.3482G>T	p.Gly1161Val	p.G1161V	ENST00000330684	NM_001134407.1	1161	gGg/gTg	13/13	0.179112704712887	3	FACETS	0.655	0.545	0.778	0.328	0.272	0.389	SUBCLONAL	1	TRUE	1	0.17	3		691	818	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58700968	58700968	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	136	714	0	ENST00000305921.3:c.559G>A	p.Val187Ile	p.V187I	ENST00000305921	NM_003620.3	187	Gta/Ata	2/6	0.25512123461115	3	FACETS	0.901	0.819	0.988	0.901	0.819	0.988	CLONAL	2	TRUE	1	0.17	3		714	963	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120182	70120182	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1301255636	NA	P-0020904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	54	499	0	ENST00000245479.2:c.1184C>T	p.Thr395Met	p.T395M	ENST00000245479	NM_000346.3	395	aCg/aTg	3/3	0.25512123461115	3	FACETS	1	0.945	1	0.617	0.526	0.715	CLONAL	1	TRUE	1	0.17	3		499	559	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250094	39250094	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	55	629	0	ENST00000402219.2:c.1475A>C	p.Glu492Ala	p.E492A	ENST00000402219	NM_005633.3	492	gAa/gCa	10/23	0.179112704712887	3	FACETS	0.983	0.84	1	0.492	0.42	0.571	CLONAL	1	TRUE	1	0.17	3		629	714	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139654	202139654	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	35	387	0	ENST00000358485.4:c.815G>C	p.Arg272Thr	p.R272T	ENST00000358485	NM_001080125.1	272	aGa/aCa	6/9	0.179112704712887	4	FACETS	0.954	0.781	1	0.477	0.39	0.575	CLONAL	1	TRUE	2	0.17	4		387	505	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295808	212295808	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	48	515	0	ENST00000342788.4:c.2505A>T	p.Glu835Asp	p.E835D	ENST00000342788	NM_005235.2	835	gaA/gaT	21/28	0.179112704712887	4	FACETS	0.888	0.749	1	0.444	0.374	0.521	CLONAL	1	TRUE	2	0.17	4		515	744	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827976	40827976	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	41	600	2	ENST00000373198.4:c.2452G>T	p.Gly818Trp	p.G818W	ENST00000373198	NM_133170.3	818	Ggg/Tgg	17/32	0.25512123461115	3	FACETS	0.771	0.64	0.916	0.385	0.32	0.458	CLONAL	1	TRUE	1	0.17	3		602	679	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269117	142269117	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	36	408	0	ENST00000350721.4:c.2833C>G	p.Gln945Glu	p.Q945E	ENST00000350721	NM_001184.3	945	Cag/Gag	14/47	0.179112704712887	3	FACETS	0.693	0.568	0.834	0.347	0.284	0.417	SUBCLONAL	1	TRUE	1	0.17	3		408	663	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99823085	99823085	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	26	382	0	ENST00000280892.6:c.127G>C	p.Glu43Gln	p.E43Q	ENST00000280892	NM_001130678.1	43	Gaa/Caa	2/7	0.179112704712887	3	FACETS	0.664	0.525	0.824	0.332	0.262	0.412	SUBCLONAL	1	TRUE	1	0.17	3		382	500	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540194	187540194	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	36	621	0	ENST00000441802.2:c.7546A>T	p.Thr2516Ser	p.T2516S	ENST00000441802	NM_005245.3	2516	Act/Tct	10/27	0.25512123461115	3	FACETS	0.678	0.556	0.816	0.339	0.278	0.408	SUBCLONAL	1	TRUE	1	0.17	3		621	678	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56879313	56879313	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	144	794	0	ENST00000519728.1:c.830T>G	p.Leu277Arg	p.L277R	ENST00000519728	NM_002350.3	277	cTg/cGg	9/13	1	2	FACETS	0.814	0.742	0.891	1	0.988	1	CLONAL	2	TRUE	1	0.17	2		794	1040	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801127	135801127	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs118203353	NA	P-0020904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	24	313	0	ENST00000298552.3:c.211-1G>A		p.X71_splice	ENST00000298552	NM_001162426.1	71			1	2	FACETS	0.704	0.551	0.881	0.704	0.551	0.881	SUBCLONAL	1	TRUE	1	0.17	2		313	401	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430758	47430758	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	57	438	0	ENST00000377045.4:c.1723C>G	p.Pro575Ala	p.P575A	ENST00000377045	NM_001654.4	575	Ccc/Gcc	16/16	1	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.17	1		438	478	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938665	76938665	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	39	339	0	ENST00000373344.5:c.2083G>A	p.Val695Met	p.V695M	ENST00000373344	NM_000489.3	695	Gtg/Atg	9/35	1	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.17	1		339	318	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224776	123224776	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	90	285	1	ENST00000218089.9:c.3540G>A	p.Met1180Ile	p.M1180I	ENST00000218089	NM_001042749.1	1180	atG/atA	32/35	1	1	FACETS	1	0.968	1	1	0.988	1	CLONAL	2	TRUE	0	0.17	1		286	397	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161807867	161807867	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	35	607	0	ENST00000366898.1:c.1126del	p.Glu376SerfsTer59	p.E376Sfs*59	ENST00000366898	NM_004562.2	376	Gag/ag	10/12	1	2	FACETS	0.649	0.531	0.783	0.649	0.531	0.783	SUBCLONAL	1	TRUE	1	0.17	2		607	634	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0021087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	39	531	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.595	0.493	0.709	0.595	0.493	0.709	SUBCLONAL	1	TRUE	1	0.29	2		531	452	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126552	2126552	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	50	440	0	ENST00000219476.3:c.2803G>T	p.Ala935Ser	p.A935S	ENST00000219476	NM_000548.3	935	Gcc/Tcc	25/42	1	2	FACETS	0.527	0.447	0.616	0.527	0.447	0.616	SUBCLONAL	1	TRUE	1	0.29	2		440	654	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62297431	62297433	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	AGG	AGG	-	novel	NA	P-0021087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	244	33	0	ENST00000360203.5:c.613_614+1del		p.X205_splice	ENST00000360203	NM_001283009.1	205		7/35	1	2	FACETS	1	0.974	1	1	0.995	1	CLONAL	2	TRUE	1	0.29	2		33	784	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412899	49412899	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	19	466	0	ENST00000418115.1:c.124T>C	p.Tyr42His	p.Y42H	ENST00000418115	NM_001664.2	42	Tat/Cat	2/5	0.3	1	FACETS	0.141	0.106	0.182	0.141	0.106	0.182	SUBCLONAL	1	TRUE	0	0.29	1		466	796	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936089	178936089	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	40	341	0	ENST00000263967.3:c.1631C>G	p.Thr544Ser	p.T544S	ENST00000263967	NM_006218.2	544	aCt/aGt	10/21	1	2	FACETS	0.542	0.45	0.645	0.542	0.45	0.645	SUBCLONAL	1	TRUE	1	0.29	2		341	509	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437281	52437282	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	T	novel	NA	P-0021087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	34	391	0	ENST00000460680.1:c.1762_1763delinsA	p.Pro588LysfsTer29	p.P588Kfs*29	ENST00000460680	NM_004656.3	588	CCa/Aa	14/17	0.3	1	FACETS	0.352	0.287	0.426	0.352	0.287	0.426	SUBCLONAL	1	TRUE	0	0.29	1		391	569	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100201	27100201	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	128	469	2	ENST00000324856.7:c.3997C>T	p.Gln1333Ter	p.Q1333*	ENST00000324856	NM_006015.4	1333	Cag/Tag	16/20	0.182871189800685	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.182871189800685	2		471	641	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54956569	54956569	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	167	590	0	ENST00000312783.6:c.625A>C	p.Ile209Leu	p.I209L	ENST00000312783	NM_198436.1	209	Att/Ctt	7/10	0.182871189800685	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.182871189800685	4		590	943	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000087	30000087	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	203	725	0	ENST00000338641.4:c.100G>T	p.Glu34Ter	p.E34*	ENST00000338641	NM_000268.3	34	Gag/Tag	1/16	0.182871189800685	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.182871189800685	2		725	902	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578188	7578188	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201592	NA	P-0021343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	483	341	0	ENST00000269305.4:c.661G>T	p.Glu221Ter	p.E221*	ENST00000269305	NM_001126112.2	221	Gag/Tag	6/11	NA	2	FACETS	0.859	0.834	0.883			1	INDETERMINATE	2	TRUE	NA	0.850951872866603	2		341	661	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101118	41101118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751886972	NA	P-0021343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	167	727	3	ENST00000373198.4:c.1238C>T	p.Ala413Val	p.A413V	ENST00000373198	NM_133170.3	413	gCg/gTg	8/32	0.850951872866603	5	FACETS	0.915	0.841	0.994	0.305	0.28	0.332	CLONAL	1	TRUE	2	0.850951872866603	5		730	976	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504507	103504507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758174644	NA	P-0021343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	287	403	2	ENST00000355739.4:c.128G>A	p.Arg43Gln	p.R43Q	ENST00000355739	NM_000123.3	43	cGg/cAg	2/15	0.757192322570378	2	FACETS	0.815	0.782	0.846	0.815	0.782	0.846	CLONAL	2	TRUE	0	0.850951872866603	2		405	414	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626982	14627276	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTTGAAAAGCAAAAGGACAGCATTAGATGGAAGCTGGCTCAAGAGGCTCAGCTCTTGCCCAGAGGCCGTCTGCCATAGATAAGACCCATCAGGCCTCTGCAGCTAAGACCTGGCCCCCAAATCTACACGTCCCCACCACGAAAGCTCCACAACAGCGCCCTGGTCAGTCCTGTTCACTGTTGTGCCCCAAGCCTGGCACGCACCACACACCCCAACACATTGGTTCAGCAAATACTAAACTGCTTCAAAAAGCAGCCATCGCCCTCTACAGACACCGCCCCACCTGGCACCTTA	CCTTGAAAAGCAAAAGGACAGCATTAGATGGAAGCTGGCTCAAGAGGCTCAGCTCTTGCCCAGAGGCCGTCTGCCATAGATAAGACCCATCAGGCCTCTGCAGCTAAGACCTGGCCCCCAAATCTACACGTCCCCACCACGAAAGCTCCACAACAGCGCCCTGGTCAGTCCTGTTCACTGTTGTGCCCCAAGCCTGGCACGCACCACACACCCCAACACATTGGTTCAGCAAATACTAAACTGCTTCAAAAAGCAGCCATCGCCCTCTACAGACACCGCCCCACCTGGCACCTTA	-	novel	NA	P-0021343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	114	914	0	ENST00000254322.2:c.792+2_793del		p.X264_splice	ENST00000254322	NM_006145.1	264		3/3	1	2	FACETS	0.273	0.245	0.302	0.273	0.245	0.302	SUBCLONAL	1	TRUE	1	0.850951872866603	2		914	983	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791599	42791599	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	586	696	0	ENST00000575354.2:c.580A>C	p.Lys194Gln	p.K194Q	ENST00000575354	NM_015125.3	194	Aag/Cag	4/20	0.850951872866603	5	FACETS	0.961	0.928	0.993	0.961	0.928	0.993	CLONAL	3	TRUE	2	0.850951872866603	5		696	1088	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970899	21970899	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0021343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	566	916	0	ENST00000304494.5:c.457+2T>A		p.X153_splice	ENST00000304494	NM_000077.4	153			0.742718191238481	2	FACETS	0.923	0.9	0.944	0.923	0.9	0.944	CLONAL	2	TRUE	0	0.850951872866603	2		916	721	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397742	139397742	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	456	842	0	ENST00000277541.6:c.5059C>T	p.Gln1687Ter	p.Q1687*	ENST00000277541	NM_017617.3	1687	Cag/Tag	27/34	0.742718191238481	2	FACETS	0.919	0.894	0.943	0.919	0.894	0.943	CLONAL	2	TRUE	0	0.850951872866603	2		842	583	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0021371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	472	798	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.992	0.952	1	0.992	0.952	1	CLONAL	1	TRUE	1	0.903537443884129	2		800	1053	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0021371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	215	505	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.983	0.924	1	0.983	0.924	1	CLONAL	1	TRUE	1	0.903537443884129	2		505	484	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675571	86675571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1561325048	NA	P-0021371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	118	245	2	ENST00000274376.6:c.2513del	p.Asn838MetfsTer4	p.N838Mfs*4	ENST00000274376	NM_002890.2	836	gAa/ga	19/25	1	2	FACETS	0.907	0.832	0.984	0.907	0.832	0.984	CLONAL	1	TRUE	1	0.903537443884129	2		247	288	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664989	138664989	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	259	43	0	ENST00000330315.3:c.576del	p.Lys193SerfsTer78	p.K193Sfs*78	ENST00000330315	NM_023067.3	192	ccC/cc	1/1	1	2	FACETS	0.89	0.84	0.941	0.89	0.84	0.941	CLONAL	1	TRUE	1	0.903537443884129	2		43	644	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913527	NA	P-0021371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	356	170	0	ENST00000311936.3:c.436G>C	p.Ala146Pro	p.A146P	ENST00000311936	NM_004985.3	146	Gca/Cca	4/5	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.903537443884129	2		170	603	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134568	2134569	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs397514939	NA	P-0021371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	452	502	0	ENST00000219476.3:c.4351dup	p.Arg1451ProfsTer73	p.R1451Pfs*73	ENST00000219476	NM_000548.3	1449	tcc/tCcc	34/42	1	2	FACETS	0.897	0.858	0.935	0.897	0.858	0.935	CLONAL	1	TRUE	1	0.903537443884129	2		502	1116	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134251	11134251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1218643327	NA	P-0021371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	351	434	1	ENST00000358026.2:c.2917C>T	p.Arg973Trp	p.R973W	ENST00000358026	NM_001128849.1	973	Cgg/Tgg	20/36	1	2	FACETS	0.885	0.842	0.929	0.885	0.842	0.929	CLONAL	1	TRUE	1	0.903537443884129	2		435	878	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301111	65301111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370434553	NA	P-0021371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	195	262	1	ENST00000342505.4:c.3337C>T	p.Arg1113Cys	p.R1113C	ENST00000342505	NM_002227.2	1113	Cgc/Tgc	24/25	1	2	FACETS	0.845	0.789	0.902	0.845	0.789	0.902	CLONAL	1	TRUE	1	0.903537443884129	2		263	511	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954321	48954321	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	209	327	0	ENST00000267163.4:c.1446del	p.His483IlefsTer12	p.H483Ifs*12	ENST00000267163	NM_000321.2	481	aTt/at	16/27	1	2	FACETS	0.812	0.759	0.865	0.812	0.759	0.865	CLONAL	1	TRUE	1	0.903537443884129	2		327	570	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	569	605	0	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.96	0.924	0.996	0.96	0.924	0.996	CLONAL	1	TRUE	1	0.903537443884129	2		605	1312	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444987	49444987	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	392	372	1	ENST00000301067.7:c.2479del	p.Gln827AsnfsTer103	p.Q827Nfs*103	ENST00000301067	NM_003482.3	827	Caa/aa	10/54	1	2	FACETS	0.974	0.93	1	0.974	0.93	1	CLONAL	1	TRUE	1	0.903537443884129	2		373	891	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106037	8106037	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	299	394	1	ENST00000346208.3:c.857C>T	p.Ala286Val	p.A286V	ENST00000346208		286	gCc/gTc	4/6	1	2	FACETS	0.931	0.882	0.98	0.931	0.882	0.98	CLONAL	1	TRUE	1	0.903537443884129	2		395	711	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624306	89624306	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0021371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	300	538	1	ENST00000371953.3:c.79+1G>A		p.X27_splice	ENST00000371953	NM_000314.4	27			1	2	FACETS	0.835	0.79	0.881	0.835	0.79	0.881	CLONAL	1	TRUE	1	0.903537443884129	2		539	795	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692920	89692920	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs370795352	NA	P-0021371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	173	321	0	ENST00000371953.3:c.404T>A	p.Ile135Lys	p.I135K	ENST00000371953	NM_000314.4	135	aTa/aAa	5/9	1	2	FACETS	0.878	0.817	0.94	0.878	0.817	0.94	CLONAL	1	TRUE	1	0.903537443884129	2		321	436	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693010	89693010	+	splice_donor_variant	Splice_Site	DEL	T	T	-	rs1060500124	NA	P-0021371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	105	184	0	ENST00000371953.3:c.492+2del		p.X164_splice	ENST00000371953	NM_000314.4	164			1	2	FACETS	0.911	0.831	0.993	0.911	0.831	0.993	CLONAL	1	TRUE	1	0.903537443884129	2		184	255	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534781	18534781	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	337	480	1	ENST00000266497.5:c.1839G>T	p.Trp613Cys	p.W613C	ENST00000266497		613	tgG/tgT	12/31	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.903537443884129	2		481	699	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945055	31945055	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868513155	NA	P-0021371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	434	514	0	ENST00000340398.3:c.46G>A	p.Ala16Thr	p.A16T	ENST00000340398	NM_001013699.2	16	Gcc/Acc	1/1	1	2	FACETS	0.92	0.88	0.961	0.92	0.88	0.961	CLONAL	1	TRUE	1	0.903537443884129	2		514	1044	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3634833	3634833	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	626	537	0	ENST00000294008.3:c.4676C>T	p.Pro1559Leu	p.P1559L	ENST00000294008	NM_032444.2	1559	cCc/cTc	13/15	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.903537443884129	2		537	1282	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660490	67660490	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	332	417	0	ENST00000264010.4:c.1390G>T	p.Glu464Ter	p.E464*	ENST00000264010	NM_006565.3	464	Gag/Tag	8/12	1	2	FACETS	0.972	0.925	1	0.972	0.925	1	CLONAL	1	TRUE	1	0.903537443884129	2		417	756	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41276100	41276100	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	87	467	0	ENST00000357654.3:c.14C>G	p.Ala5Gly	p.A5G	ENST00000357654	NM_007294.3	5	gCt/gGt	2/23	1	2	FACETS	0.26	0.23	0.292	0.26	0.23	0.292	SUBCLONAL	1	TRUE	1	0.903537443884129	2		467	741	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418346	139418346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532574807	NA	P-0021371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	621	628	0	ENST00000277541.6:c.226G>A	p.Val76Met	p.V76M	ENST00000277541	NM_017617.3	76	Gtg/Atg	3/34	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.903537443884129	2		628	1326	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665752	29665755	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1555535032	NA	P-0021464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	286	401	1	ENST00000356175.3:c.6789_6792del	p.Tyr2264ThrfsTer5	p.Y2264Tfs*5	ENST00000356175	NM_000267.3	2263	ACTTac/ac	45/57	0.872457314637261	2	FACETS	0.919	0.893	0.943	0.919	0.893	0.943	CLONAL	2	TRUE	0	0.929062567089605	2		402	335	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0021499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	166	365	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	0.252897933129987	3	FACETS	0.846	0.788	0.905	1	0.987	1	CLONAL	3	TRUE	1	0.421086111677203	3		365	376	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023151	27023179	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	-	novel	NA	P-0021499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	163	98	0	ENST00000324856.7:c.267_295del	p.Ser90ProfsTer11	p.S90Pfs*11	ENST00000324856	NM_006015.4	86	gGCGGAGCCGGCAGCGGCGGCGGGCCCGGC/g	1/20	1	2	FACETS	0.86	0.806	0.914	1	0.994	1	CLONAL	3	TRUE	1	0.421086111677203	2		98	300	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023440	27023440	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	370	265	1	ENST00000324856.7:c.546del	p.Ala183ArgfsTer49	p.A183Rfs*49	ENST00000324856	NM_006015.4	182	gcA/gc	1/20	1	2	FACETS	1	0.988	1	1	0.997	1	CLONAL	2	TRUE	1	0.421086111677203	2		266	797	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779728	3779728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	306	376	0	ENST00000262367.5:c.5320C>T	p.Arg1774Cys	p.R1774C	ENST00000262367	NM_004380.2	1774	Cgc/Tgc	31/31	1	2	FACETS	1	0.993	1	1	0.996	1	CLONAL	2	TRUE	1	0.421086111677203	2		376	592	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88678953	88678953	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021806-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	109	306	0	ENST00000372037.3:c.893G>A	p.Gly298Asp	p.G298D	ENST00000372037	NM_004329.2	298	gGt/gAt	10/13	1	2	FACETS	0.99	0.898	1	0.99	0.898	1	CLONAL	1	TRUE	1	0.596777538858377	2		306	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0021969-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	352	204	0	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.392686182607596	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.392686182607596	3		204	946	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276788	15276788	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021969-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1224	304	245	0	ENST00000263388.2:c.5477G>T	p.Cys1826Phe	p.C1826F	ENST00000263388	NM_000435.2	1826	tGc/tTc	30/33	0.392686182607596	5	FACETS	0.805	0.757	0.855	0.537	0.504	0.57	CLONAL	2	TRUE	2	0.392686182607596	5		245	1528	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730916	40730916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765075213	NA	P-0021969-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	70	190	1	ENST00000373198.4:c.3619C>T	p.Arg1207Cys	p.R1207C	ENST00000373198	NM_133170.3	1207	Cgt/Tgt	27/32	0.347170445073008	4	FACETS	0.529	0.46	0.604	0.176	0.153	0.202	SUBCLONAL	1	TRUE	1	0.392686182607596	4		191	939	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472652	88472652	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021969-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	55	136	0	ENST00000360948.2:c.1903G>C	p.Asp635His	p.D635H	ENST00000360948	NM_001012338.2	635	Gat/Cat	16/19	0.352200037696059	4	FACETS	0.766	0.656	0.887	0.383	0.328	0.444	SUBCLONAL	1	TRUE	2	0.392686182607596	4		136	509	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967476	38967476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021969-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	65	144	0	ENST00000357387.3:c.1114G>A	p.Glu372Lys	p.E372K	ENST00000357387	NM_152756.3	372	Gag/Aag	13/38	0.308355880675474	5	FACETS	0.797	0.691	0.913	0.266	0.23	0.305	CLONAL	1	TRUE	2	0.392686182607596	5		144	660	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030338	11030340	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0021969-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	128	177	0	ENST00000327064.4:c.1091_1093del	p.Glu364del	p.E364del	ENST00000327064	NM_199141.1	363	aAAGaa/aaa	9/16	0.392686182607596	5	FACETS	0.937	0.848	1	0.312	0.282	0.344	CLONAL	1	TRUE	2	0.392686182607596	5		177	1105	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910405	29910405	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0021969-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1473	95	292	0	ENST00000376809.5:c.73+2T>G		p.X25_splice	ENST00000376809	NM_002116.7	25			0.352200037696059	4	FACETS	0.43	0.381	0.482	0.215	0.19	0.241	SUBCLONAL	1	TRUE	2	0.392686182607596	4		292	1568	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367780	15367780	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021969-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1244	113	256	0	ENST00000263377.2:c.1546G>C	p.Glu516Gln	p.E516Q	ENST00000263377	NM_058243.2	516	Gag/Cag	8/20	0.392686182607596	5	FACETS	0.674	0.604	0.748	0.225	0.201	0.25	SUBCLONAL	1	TRUE	2	0.392686182607596	5		256	1357	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660663	227660663	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021969-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	228	237	0	ENST00000305123.5:c.2792C>A	p.Pro931His	p.P931H	ENST00000305123	NM_005544.2	931	cCc/cAc	1/2	0.255207993981823	2	FACETS	1	0.991	1	0.7	0.653	0.747	CLONAL	1	TRUE	0	0.392686182607596	2		237	830	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445005	89445005	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021969-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	53	140	0	ENST00000336596.2:c.1325C>A	p.Thr442Lys	p.T442K	ENST00000336596	NM_005233.5	442	aCg/aAg	6/17	0.392686182607596	3	FACETS	0.553	0.471	0.643	0.276	0.235	0.322	SUBCLONAL	1	TRUE	1	0.392686182607596	3		140	584	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950753	38950753	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021969-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	29	91	0	ENST00000357387.3:c.3197A>T	p.Glu1066Val	p.E1066V	ENST00000357387	NM_152756.3	1066	gAa/gTa	31/38	0.308355880675474	5	FACETS	0.567	0.455	0.695	0.189	0.151	0.232	SUBCLONAL	1	TRUE	2	0.392686182607596	5		91	414	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138654	37138654	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021969-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	108	207	0	ENST00000373509.5:c.188C>A	p.Pro63Gln	p.P63Q	ENST00000373509	NM_002648.3	63	cCg/cAg	2/6	0.352200037696059	4	FACETS	0.727	0.651	0.808	0.363	0.325	0.404	SUBCLONAL	1	TRUE	2	0.392686182607596	4		207	1054	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877926	151877926	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1394961873	NA	P-0021969-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	140	102	0	ENST00000262189.6:c.7019C>G	p.Ser2340Cys	p.S2340C	ENST00000262189	NM_170606.2	2340	tCt/tGt	36/59	0.352200037696059	4	FACETS	0.806	0.737	0.878	0.806	0.737	0.878	CLONAL	2	TRUE	2	0.392686182607596	4		102	616	SUCCESS
AR	367	MSKCC	GRCh37	X	66765686	66765686	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021969-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	158	143	0	ENST00000374690.3:c.698C>G	p.Ser233Cys	p.S233C	ENST00000374690	NM_000044.3	233	tCt/tGt	1/8	0.392686182607596	2	FACETS	0.924	0.847	1			1	CLONAL	1	TRUE	NA	0.392686182607596	2		143	871	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0021991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	142	63	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.205790759103946	5	FACETS	1	0.981	1	0.828	0.76	0.898	INDETERMINATE	2	TRUE	2	0.367241676777306	5		63	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0021991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	226	607	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.365863899409082	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.367241676777306	2		607	598	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0021991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	192	88	1	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	0.367241676777306	3	FACETS	0.973	0.912	1	1	0.992	1	CLONAL	3	TRUE	1	0.367241676777306	3		89	424	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256145	16256145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	56	347	0	ENST00000375759.3:c.3410G>A	p.Arg1137His	p.R1137H	ENST00000375759	NM_015001.2	1137	cGt/cAt	11/15	0.365863899409082	2	FACETS	0.571	0.489	0.66	0.286	0.244	0.33	SUBCLONAL	1	TRUE	0	0.367241676777306	2		347	534	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929077	44929077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2230018	NA	P-0021991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	149	151	2	ENST00000377967.4:c.2177C>T	p.Thr726Met	p.T726M	ENST00000377967	NM_021140.2	726	aCg/aTg	17/29	0.367241676777306	2	FACETS	0.867	0.806	0.928			1	CLONAL	3	TRUE	NA	0.367241676777306	2		153	312	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431257	49431267	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCTGGGCAG	GGCCTGGGCAG	-	novel	NA	P-0021991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	98	242	0	ENST00000301067.7:c.9872_9882del	p.Pro3291HisfsTer6	p.P3291Hfs*6	ENST00000301067	NM_003482.3	3291	cCTGCCCAGGCC/c	34/54	0.205790759103946	5	FACETS	0.762	0.682	0.847	0.508	0.454	0.565	INDETERMINATE	2	TRUE	2	0.367241676777306	5		242	543	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468397	89468398	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1467832547	NA	P-0021991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	96	184	0	ENST00000336596.2:c.1938dup	p.Glu647ArgfsTer7	p.E647Rfs*7	ENST00000336596	NM_005233.5	644	tca/tcAa	11/17	0.205790759103946	5	FACETS	1	0.96	1	0.759	0.682	0.839	INDETERMINATE	2	TRUE	2	0.367241676777306	5		184	356	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911546	114911546	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	108	315	0	ENST00000543371.1:c.1064A>G	p.Asn355Ser	p.N355S	ENST00000543371	NM_001198531.1	355	aAt/aGt	10/14	0.272110164499046	3	FACETS	0.763	0.689	0.841	0.763	0.689	0.841	SUBCLONAL	2	TRUE	1	0.367241676777306	3		315	456	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0022107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	105	233	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.325335728160138	3	FACETS	1	0.979	1	0.689	0.619	0.762	CLONAL	1	TRUE	1	0.325335728160138	3		235	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579372	7579372	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	176	595	0	ENST00000269305.4:c.315del	p.Ser106AlafsTer17	p.S106Afs*17	ENST00000269305	NM_001126112.2	105	ggC/gg	4/11	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.325335728160138	2		595	1075	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240171	41240171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1291996842	NA	P-0022108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	64	58	3	ENST00000379561.5:c.179C>T	p.Ser60Leu	p.S60L	ENST00000379561	NM_002015.3	60	tCg/tTg	1/3	0.503248726605527	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.503248726605527	1		61	127	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252156	226252156	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	30	73	0	ENST00000366813.1:c.104G>T	p.Gly35Val	p.G35V	ENST00000366813		35	gGg/gTg	1/3	1	2	FACETS	0.939	0.77	1	0.939	0.77	1	CLONAL	1	TRUE	1	0.503248726605527	2		73	127	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0022108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	244	229	0	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	0.471172273827901	2	FACETS	1	0.992	1	0.714	0.671	0.758	CLONAL	1	TRUE	0	0.503248726605527	2		229	679	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039497	49039497	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0022108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	155	223	0	ENST00000267163.4:c.2482A>T	p.Arg828Ter	p.R828*	ENST00000267163	NM_000321.2	828	Aga/Tga	23/27	0.503248726605527	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.503248726605527	1		223	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577524	7577524	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022143-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	669	630	0	ENST00000269305.4:c.757A>C	p.Thr253Pro	p.T253P	ENST00000269305	NM_001126112.2	253	Acc/Ccc	7/11	0.544965143398837	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.544965143398837	2		630	1153	SUCCESS
APC	324	MSKCC	GRCh37	5	112176863	112176863	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1270783041	NA	P-0022143-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	124	198	0	ENST00000257430.4:c.5572C>T	p.Arg1858Ter	p.R1858*	ENST00000257430	NM_000038.5	1858	Cga/Tga	16/16	0.43420860013269	1	FACETS	0.849	0.775	0.925	0.849	0.775	0.925	CLONAL	1	TRUE	0	0.544965143398837	1		198	390	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556727	41556727	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0022143-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	155	358	1	ENST00000263253.7:c.3671+1G>A		p.X1224_splice	ENST00000263253	NM_001429.3	1224			0.544965143398837	2	FACETS	0.966	0.888	1	0.483	0.444	0.523	CLONAL	1	TRUE	0	0.544965143398837	2		359	589	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335690	81335690	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022143-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	324	479	0	ENST00000222390.5:c.1670G>T	p.Gly557Val	p.G557V	ENST00000222390	NM_000601.4	557	gGa/gTa	15/18	0.439857687371732	6	FACETS	1	0.946	1			1	CLONAL	2	TRUE	NA	0.544965143398837	6		479	1240	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604648	48604649	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGTGTTG	novel	NA	P-0022143-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	132	235	0	ENST00000342988.3:c.1471_1477dup	p.Asp493GlyfsTer3	p.D493Gfs*3	ENST00000342988	NM_005359.5	490	-/GGTGTTG	12/12	0.543018224648776	1	FACETS	0.879	0.806	0.954	0.879	0.806	0.954	CLONAL	1	TRUE	0	0.544965143398837	1		235	401	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349966	15349966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022143-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1277	422	780	1	ENST00000263377.2:c.3686G>A	p.Arg1229His	p.R1229H	ENST00000263377	NM_058243.2	1229	cGc/cAc	18/20	0.544965143398837	3	FACETS	1	0.99	1	0.58	0.551	0.61	CLONAL	1	TRUE	1	0.544965143398837	3		781	1699	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192454	138192454	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1324617507	NA	P-0022143-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	140	333	0	ENST00000237289.4:c.90T>A	p.Phe30Leu	p.F30L	ENST00000237289	NM_001270507.1	30	ttT/ttA	2/9	0.544965143398837	3	FACETS	0.892	0.813	0.974	0.446	0.406	0.487	CLONAL	1	TRUE	1	0.544965143398837	3		333	733	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022337-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	19	374	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.675	0.516	0.86	0.675	0.516	0.86	SUBCLONAL	1	TRUE	1	0.335051818882885	2		374	168	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984825	72984825	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022337-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	13	682	2	ENST00000268489.5:c.2759G>A	p.Gly920Glu	p.G920E	ENST00000268489	NM_006885.3	920	gGg/gAg	3/10	1	2	FACETS	0.488	0.349	0.656	0.488	0.349	0.656	SUBCLONAL	1	TRUE	1	0.335051818882885	2		684	159	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	37	63	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.290855724521667	2	FACETS	1	0.861	1	0.514	0.431	0.604	INDETERMINATE	1	TRUE	0	0.499476999529043	2		63	144	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0022382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	62	103	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.466591740554663	3	FACETS	0.892	0.8	0.982	0.892	0.8	0.982	CLONAL	3	TRUE	0	0.499476999529043	3		103	116	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936564	49936564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199940178	NA	P-0022382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	157	591	3	ENST00000296474.3:c.1363C>T	p.Arg455Cys	p.R455C	ENST00000296474	NM_002447.2	455	Cgc/Tgc	2/20	1	2	FACETS	0.814	0.747	0.885	0.814	0.747	0.885	CLONAL	1	TRUE	1	0.499476999529043	2		594	772	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574035	7574035	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0022382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	353	507	1	ENST00000269305.4:c.994-2A>T		p.X332_splice	ENST00000269305	NM_001126112.2	332			NA	2	FACETS	0.897	0.855	0.939			1	INDETERMINATE	2	TRUE	NA	0.499476999529043	2		508	788	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912094	114912095	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0022382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	34	283	0	ENST00000543371.1:c.1164_1165delinsTT	p.Trp388_His389delinsCysTyr	p.W388_H389delinsCY	ENST00000543371	NM_001198531.1	388	tgGCat/tgTTat	11/14	0.290855724521667	2	FACETS	0.337	0.275	0.406	0.168	0.137	0.203	INDETERMINATE	1	TRUE	0	0.499476999529043	2		283	404	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280288	1280288	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	104	800	0	ENST00000310581.5:c.1935C>A	p.Phe645Leu	p.F645L	ENST00000310581	NM_198253.2	645	ttC/ttA	4/16	1	2	FACETS	0.342	0.305	0.382	0.342	0.305	0.382	SUBCLONAL	1	TRUE	1	0.499476999529043	2		800	1217	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336634	81336634	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	60	92	0	ENST00000222390.5:c.1588C>A	p.Leu530Ile	p.L530I	ENST00000222390	NM_000601.4	530	Ctt/Att	14/18	0.405796449855637	3	FACETS	1	0.906	1	1	0.906	1	CLONAL	2	TRUE	1	0.499476999529043	3		92	146	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0022426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	575	891	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	0.639239404463971	4	FACETS	0.978	0.94	1			1	CLONAL	2	FALSE	NA	0.639239404463971	4		891	1507	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600042	10600042	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs148641376	NA	P-0022426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	209	789	0	ENST00000171111.5:c.1534G>A	p.Val512Ile	p.V512I	ENST00000171111	NM_203500.1	512	Gtc/Atc	5/6	1	2	FACETS	0.87	0.81	0.931	0.87	0.81	0.931	CLONAL	1	FALSE	1	0.639239404463971	2		789	752	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1555525367	NA	P-0022426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	374	279	0	ENST00000269305.4:c.783-1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.510278394959639	3	FACETS	1	0.994	1	0.809	0.777	0.841	CLONAL	2	FALSE	0	0.639239404463971	3		279	636	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491295	2491295	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	502	933	0	ENST00000355716.4:c.338G>C	p.Arg113Thr	p.R113T	ENST00000355716	NM_003820.2	113	aGg/aCg	4/8	0.639239404463971	3	FACETS	0.969	0.932	1	0.969	0.932	1	CLONAL	2	FALSE	1	0.639239404463971	3		933	1069	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	59	63	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.390831425904757	1	FACETS	0.65	0.562	0.745	0.65	0.562	0.745	SUBCLONAL	1	TRUE	0	0.409144798326125	1		63	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757274881	NA	P-0022517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	288	1161	3	ENST00000269305.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	144	Cag/Tag	5/11	0.409144798326125	1	FACETS	0.926	0.87	0.984	0.926	0.87	0.984	CLONAL	1	TRUE	0	0.409144798326125	1		1164	1209	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866393	37866393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	195	734	0	ENST00000269571.5:c.698C>T	p.Thr233Ile	p.T233I	ENST00000269571		233	aCt/aTt	6/27	1	2	FACETS	0.853	0.788	0.92	0.853	0.788	0.92	CLONAL	1	TRUE	1	0.409144798326125	2		734	1118	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245317	46245318	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1555155252	NA	P-0022517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	125	321	0	ENST00000334344.6:c.3411_3412del	p.Gly1139SerfsTer20	p.G1139Sfs*20	ENST00000334344	NM_152641.2	1137	tcAGgg/tcgg	15/21	0.390831425904757	1	FACETS	0.905	0.823	0.991	0.905	0.823	0.991	CLONAL	1	TRUE	0	0.409144798326125	1		321	537	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281824	142281825	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCAGGACTCTT	novel	NA	P-0022517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	71	142	0	ENST00000350721.4:c.409_419dup	p.Ile141ArgfsTer28	p.I141Rfs*28	ENST00000350721	NM_001184.3	140	gct/gcAAGAGTCCTGCt	4/47	1	2	FACETS	0.817	0.716	0.925	0.817	0.716	0.925	CLONAL	1	TRUE	1	0.409144798326125	2		142	425	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022642-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	350	395	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		395	964	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	64	395	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.394069581758532	2		395	258	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0022682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	114	1543	0	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	0.391394124327666	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.394069581758532	1		1543	418	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056352	26056352	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	63	287	0	ENST00000343677.2:c.305C>G	p.Ser102Cys	p.S102C	ENST00000343677	NM_005319.3	102	tCt/tGt	1/1	0.117716210685008	4	FACETS	1	0.952	1	0.607	0.528	0.693	INDETERMINATE	1	TRUE	2	0.394069581758532	4		287	367	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345252	73345252	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	96	375	0	ENST00000377767.4:c.1637C>G	p.Ser546Cys	p.S546C	ENST00000377767	NM_014953.3	546	tCt/tGt	12/21	0.117716210685008	4	FACETS	1	0.977	1	0.685	0.612	0.761	INDETERMINATE	1	TRUE	2	0.394069581758532	4		375	496	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539712	187539749	+	frameshift_variant	Frame_Shift_Del	DEL	CACAGCTCTAACAAAGAAAGTGAAGAATTCATTTTCCA	CACAGCTCTAACAAAGAAAGTGAAGAATTCATTTTCCA	-	novel	NA	P-0022682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	81	318	0	ENST00000441802.2:c.7991_8028del	p.Leu2664Ter	p.L2664*	ENST00000441802	NM_005245.3	2664	tTGGAAAATGAATTCTTCACTTTCTTTGTTAGAGCTGTG/t	10/27	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.394069581758532	2		318	402	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557767	187557767	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	72	261	0	ENST00000441802.2:c.3944C>A	p.Ser1315Ter	p.S1315*	ENST00000441802	NM_005245.3	1315	tCa/tAa	5/27	1	2	FACETS	0.923	0.81	1	0.923	0.81	1	CLONAL	1	TRUE	1	0.394069581758532	2		261	396	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	126	395	0				ENST00000310581	NM_198253.2	-/1132			0.211445415009072	2	FACETS	0.915	0.831	1	0.915	0.831	1	CLONAL	2	TRUE	0	0.211445415009072	2		395	651	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137323819	137323819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	95	550	0	ENST00000481739.1:c.1112G>A	p.Arg371His	p.R371H	ENST00000481739	NM_002957.4	371	cGc/cAc	8/10	0.148272988295415	2	FACETS	0.979	0.87	1	0.489	0.435	0.548	CLONAL	1	TRUE	0	0.211445415009072	2		550	918	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0022698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	127	428	0	ENST00000269305.4:c.920-2A>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.148272988295415	2	FACETS	0.779	0.706	0.856	0.779	0.706	0.856	SUBCLONAL	2	TRUE	0	0.211445415009072	2		428	771	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170011224	170011224	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	62	376	0	ENST00000295797.4:c.1345G>C	p.Gly449Arg	p.G449R	ENST00000295797	NM_002740.5	449	Gga/Cga	14/18	0.151632336324762	3	FACETS	0.904	0.78	1	0.452	0.39	0.52	CLONAL	1	TRUE	1	0.211445415009072	3		376	717	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69143588	69143588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150821816	NA	P-0022698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	29	290	0	ENST00000288368.4:c.4796C>T	p.Pro1599Leu	p.P1599L	ENST00000288368	NM_024870.2	1599	cCa/cTa	40/40	0.178912252995032	3	FACETS	0.613	0.491	0.752	0.306	0.245	0.376	SUBCLONAL	1	TRUE	1	0.211445415009072	3		290	495	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0022797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	78	463	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.285136221139078	2	FACETS	1	0.978	1	0.748	0.664	0.835	CLONAL	1	TRUE	0	0.366031303987199	2		463	285	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0022797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	81	301	1	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	0.366031303987199	2		302	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577144	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs879253942	NA	P-0022797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	176	1000	0	ENST00000269305.4:c.794T>C	p.Leu265Pro	p.L265P	ENST00000269305	NM_001126112.2	265	cTg/cCg	8/11	0.215682236319402	2	FACETS	0.811	0.751	0.873	0.811	0.751	0.873	INDETERMINATE	2	TRUE	0	0.366031303987199	2		1000	593	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385182	41385182	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367872006	NA	P-0022797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	129	1215	0	ENST00000373198.4:c.779G>A	p.Arg260Gln	p.R260Q	ENST00000373198	NM_133170.3	260	cGg/cAg	6/32	0.357856851351497	4	FACETS	1	0.982	1	0.676	0.614	0.742	CLONAL	1	TRUE	2	0.366031303987199	4		1215	712	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190742037	190742037	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	39	693	0	ENST00000441310.2:c.2674T>G	p.Leu892Val	p.L892V	ENST00000441310	NM_000534.4	892	Tta/Gta	13/13	1	2	FACETS	0.644	0.535	0.764	0.644	0.535	0.764	SUBCLONAL	1	TRUE	1	0.366031303987199	2		693	331	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972009	55972009	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	45	653	0	ENST00000263923.4:c.1635C>A	p.Phe545Leu	p.F545L	ENST00000263923	NM_002253.2	545	ttC/ttA	12/30	0.366031303987199	1	FACETS	0.47	0.396	0.553	0.47	0.396	0.553	SUBCLONAL	1	TRUE	0	0.366031303987199	1		653	427	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920388	134920388	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	42	898	0	ENST00000398015.3:c.2203C>A	p.Leu735Met	p.L735M	ENST00000398015	NM_004441.4	735	Ctg/Atg	12/16	0.366031303987199	3	FACETS	0.429	0.357	0.509	0.214	0.178	0.255	SUBCLONAL	1	TRUE	1	0.366031303987199	3		898	633	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224189	98224189	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	202	184	0	ENST00000331920.6:c.2652del	p.Tyr884Ter	p.Y884*	ENST00000331920	NM_000264.3	884	taC/ta	16/24	0.465858104646569	2	FACETS	0.891	0.835	0.948	0.891	0.835	0.948	CLONAL	2	TRUE	0	0.471279658738994	2		184	481	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	90	63	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.823	0.73	0.921	1	0.982	1	CLONAL	2	FALSE	1	0.159941186374493	2		63	684	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097687	27097688	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	102	147	0	ENST00000324856.7:c.3281dup	p.Gln1095AlafsTer10	p.Q1095Afs*10	ENST00000324856	NM_006015.4	1092	-/A	12/20	1	2	FACETS	0.881	0.788	0.979	1	0.985	1	CLONAL	2	FALSE	1	0.159941186374493	2		147	724	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011096	12011103	+	splice_region_variant,intron_variant	Splice_Region	DEL	TTATTTTA	TTATTTTA	-	novel	NA	P-0022988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	43	43	0	ENST00000353533.5:c.514-10_514-3del		p.X172_splice	ENST00000353533	NM_003010.3	172			0.142701457992489	3	FACETS	0.785	0.658	0.924	0.785	0.658	0.924	CLONAL	2	FALSE	1	0.159941186374493	3		43	370	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677801	47677801	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	77	270	0	ENST00000347630.2:c.1064C>G	p.Ser355Cys	p.S355C	ENST00000347630	NM_001007230.1	355	tCt/tGt	11/11	0.142701457992489	3	FACETS	0.887	0.78	1	0.887	0.78	1	CLONAL	2	FALSE	1	0.159941186374493	3		270	586	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0022994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	45	330	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.677	0.568	0.797	0.677	0.568	0.797	SUBCLONAL	1	TRUE	1	0.25	2		330	532	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112043	115112043	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372029833	NA	P-0022994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	46	412	1	ENST00000257566.3:c.1697C>T	p.Ala566Val	p.A566V	ENST00000257566	NM_016569.3	566	gCg/gTg	7/8	1	2	FACETS	0.603	0.507	0.71	0.603	0.507	0.71	SUBCLONAL	1	TRUE	1	0.25	2		413	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577501	7577501	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	rs1427471466	NA	P-0022994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	74	407	1	ENST00000269305.4:c.780del	p.Ser261ValfsTer84	p.S261Vfs*84	ENST00000269305	NM_001126112.2	260	tcC/tc	7/11	1	2	FACETS	0.937	0.82	1	0.937	0.82	1	CLONAL	1	TRUE	1	0.25	2		408	632	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380350	14380350	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	20	151	0	ENST00000256196.4:c.67G>T	p.Gly23Cys	p.G23C	ENST00000256196		23	Ggc/Tgc	1/6	1	2	FACETS	0.623	0.477	0.793	0.623	0.477	0.793	SUBCLONAL	1	TRUE	1	0.25	2		151	257	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0023038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	158	129	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	0.813326668055571	5	FACETS	1	0.958	1	0.7	0.648	0.752	CLONAL	2	TRUE	2	0.813326668055571	5		129	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577576	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	novel	NA	P-0023038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	684	744	0	ENST00000269305.4:c.703_705dup	p.Asn235dup	p.N235dup	ENST00000269305	NM_001126112.2	235	-/AAC	7/11	0.811273878669919	2	FACETS	0.909	0.887	0.93	0.909	0.887	0.93	CLONAL	2	TRUE	0	0.813326668055571	2		744	925	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	12	395	0				ENST00000310581	NM_198253.2	-/1132			0.184414403542423	1	FACETS	1	0.816	1	1	0.816	1	CLONAL	1	TRUE	0	0.184129667782316	1		395	97	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0023288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	29	174	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.184129667782316	2		174	278	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056263	26056263	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	48	131	0	ENST00000343677.2:c.394G>T	p.Val132Phe	p.V132F	ENST00000343677	NM_005319.3	132	Gtt/Ttt	1/1	0.182581056206382	4	FACETS	1	0.937	1	0.61	0.516	0.714	CLONAL	1	TRUE	2	0.184129667782316	4		131	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138729528	NA	P-0023289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	765	326	0	ENST00000269305.4:c.523C>G	p.Arg175Gly	p.R175G	ENST00000269305	NM_001126112.2	175	Cgc/Ggc	5/11	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	2	FALSE	NA	0.729017204913146	2		326	1025	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954331	48954333	+	inframe_deletion	In_Frame_Del	DEL	GTC	GTC	-	novel	NA	P-0023289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	196	363	0	ENST00000267163.4:c.1452_1454del	p.Met484_Ser485delinsIle	p.M484_S485delinsI	ENST00000267163	NM_000321.2	484	atGTCt/att	16/27	0.729017204913146	1	FACETS	0.921	0.867	0.975	0.921	0.867	0.975	CLONAL	1	FALSE	0	0.729017204913146	1		363	371	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469043	25469043	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1227182180	NA	P-0023289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	348	461	0	ENST00000264709.3:c.1415A>G	p.Asp472Gly	p.D472G	ENST00000264709	NM_175629.2	472	gAt/gGt	11/23	1	2	FACETS	0.96	0.911	1	0.96	0.911	1	CLONAL	1	FALSE	1	0.729017204913146	2		461	995	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938385	76938385	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0023289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	302	506	0	ENST00000373344.5:c.2363C>G	p.Ser788Ter	p.S788*	ENST00000373344	NM_000489.3	788	tCa/tGa	9/35	1	2	FACETS	0.948	0.896	1	0.948	0.896	1	CLONAL	1	FALSE	1	0.729017204913146	2		506	874	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	144	63	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.762	0.697	0.83	1	0.988	1	SUBCLONAL	2	TRUE	1	0.28	2		63	675	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0023290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	200	499	0	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	0.18818613695099	2	FACETS	1	0.988	1	0.672	0.622	0.724	CLONAL	1	TRUE	0	0.28	2		499	1063	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0023292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	496	262	8	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	0.497335255998883	5	FACETS	1	0.992	1			1	CLONAL	5	TRUE	NA	0.535394201368455	5		270	640	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335633	81335633	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	96	138	0	ENST00000222390.5:c.1727G>A	p.Gly576Glu	p.G576E	ENST00000222390	NM_000601.4	576	gGa/gAa	15/18	0.535394201368455	5	FACETS	1	0.981	1	0.492	0.441	0.546	CLONAL	1	TRUE	2	0.535394201368455	5		138	438	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736551	85736564	+	frameshift_variant	Frame_Shift_Del	DEL	GATTTTCTCACACA	GATTTTCTCACACA	-	novel	NA	P-0023292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	51	82	0	ENST00000370580.1:c.83_96del	p.Leu28HisfsTer3	p.L28Hfs*3	ENST00000370580	NM_003921.4	28	cTGTGTGAGAAAATC/c	2/3	0.471424150219793	4	FACETS	1	0.956	1	0.653	0.561	0.751	CLONAL	1	TRUE	2	0.535394201368455	4		82	224	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69203041	69203042	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	191	134	0	ENST00000462284.1:c.69dup	p.Gln24ThrfsTer12	p.Q24Tfs*12	ENST00000462284	NM_002392.5	23	tca/tcAa	2/11	0.52994806218912	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.535394201368455	4		134	527	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741945	40741945	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	198	509	13	ENST00000392038.2:c.1027A>T	p.Met343Leu	p.M343L	ENST00000392038	NM_001626.4	343	Atg/Ttg	11/14	0.295819112483855	5	FACETS	1	0.949	1	0.683	0.635	0.732	INDETERMINATE	2	TRUE	2	0.535394201368455	5		522	651	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876100	35876100	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	68	68	1	ENST00000303115.3:c.892T>C	p.Phe298Leu	p.F298L	ENST00000303115	NM_002185.3	298	Ttc/Ctc	8/8	0.471424150219793	4	FACETS	0.859	0.758	0.964	0.859	0.758	0.964	CLONAL	2	TRUE	2	0.535394201368455	4		69	227	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410708	63410708	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	129	210	1	ENST00000330258.3:c.2459G>T	p.Gly820Val	p.G820V	ENST00000330258	NM_152424.3	820	gGc/gTc	2/2	NA	2	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.535394201368455	2		211	433	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	15	63	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.285768865056954	1	FACETS	0.833	0.616	1	0.833	0.616	1	CLONAL	1	TRUE	0	0.285768865056954	1		63	108	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0023293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	35	547	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	0.988	0.815	1	0.988	0.815	1	CLONAL	1	TRUE	1	0.285768865056954	2		548	248	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441147	149441147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	47	566	1	ENST00000286301.3:c.1765G>A	p.Gly589Arg	p.G589R	ENST00000286301	NM_005211.3	589	Gga/Aga	13/22	0.495323542447326	1	FACETS	0.139	0.117	0.163	0.139	0.117	0.163	INDETERMINATE	1	TRUE	0	0.902005175045906	1		567	411	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807934	3807934	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148166625	NA	P-0023380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	266	516	0	ENST00000262367.5:c.3485A>G	p.Asn1162Ser	p.N1162S	ENST00000262367	NM_004380.2	1162	aAc/aGc	18/31	1	2	FACETS	0.843	0.795	0.891	0.843	0.795	0.891	CLONAL	1	TRUE	1	0.902005175045906	2		516	700	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213353	36213353	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	826	272	0	ENST00000222270.7:c.2550A>T	p.Glu850Asp	p.E850D	ENST00000222270	NM_014727.1	850	gaA/gaT	4/37	0.902083269077291	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.902005175045906	1		272	880	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259113	36259377	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCCCACCACCCTCTCCGGGCCAGTACCTTGAAAGCGATGGGCAGGGTCTTGTTGCAGCGCCAGTGCGTAGGCAGCACGGAGCAGAGGAAGTTGGGGCTGTCGGTGCGCACCAGCTCGCCCGGGTGGTCGGCCAGCACCTCCACCATGCTGCGGTCGCCGCTCCTCAGCTTGCCGGCCAGGGCAGCGCCGGCGTCCGGGGCGCCCAGCGGCAACGCCTCGCTCATCTTGCCTGGGCTCAGCGCGGTGGAAGGCGGCGTGAAGCGG	CTCCCACCACCCTCTCCGGGCCAGTACCTTGAAAGCGATGGGCAGGGTCTTGTTGCAGCGCCAGTGCGTAGGCAGCACGGAGCAGAGGAAGTTGGGGCTGTCGGTGCGCACCAGCTCGCCCGGGTGGTCGGCCAGCACCTCCACCATGCTGCGGTCGCCGCTCCTCAGCTTGCCGGCCAGGGCAGCGCCGGCGTCCGGGGCGCCCAGCGGCAACGCCTCGCTCATCTTGCCTGGGCTCAGCGCGGTGGAAGGCGGCGTGAAGCGG	-	novel	NA	P-0023380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	199	441	0	ENST00000300305.3:c.114_351+27del		p.X38_splice	ENST00000300305		38		3/8	0.413269188391062	1	FACETS	0.767	0.727	0.806	0.767	0.727	0.806	INDETERMINATE	1	TRUE	0	0.902005175045906	1		441	316	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31483712	31483712	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1561231356	NA	P-0023380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	64	280	1	ENST00000344624.3:c.2020C>T	p.Pro674Ser	p.P674S	ENST00000344624		674	Ccc/Tcc	13/33	0.342828748435006	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.902005175045906	0		281	162	SUCCESS
MET	4233	MSKCC	GRCh37	7	116409711	116409711	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	60	180	0	ENST00000397752.3:c.2596G>C	p.Asp866His	p.D866H	ENST00000397752	NM_000245.2	866	Gac/Cac	12/21	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.902005175045906	2		180	129	SUCCESS
AR	367	MSKCC	GRCh37	X	66766144	66766144	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	2454	249	0	ENST00000374690.3:c.1156C>G	p.Arg386Gly	p.R386G	ENST00000374690	NM_000044.3	386	Cgc/Ggc	1/8	0.902005175045906	12	FACETS	1	0.999	1			1	CLONAL	12	TRUE	NA	0.902005175045906	12		249	2478	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023523-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	236	395	0				ENST00000310581	NM_198253.2	-/1132			0.309112560438862	4	FACETS	1	0.973	1			1	CLONAL	2	TRUE	NA	0.497556094811162	4		395	668	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0023523-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	435	798	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.0767860253110489	6	FACETS	1	0.991	1			1	INDETERMINATE	4	TRUE	NA	0.497556094811162	6		800	791	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267698	198267698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023523-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	191	378	0	ENST00000335508.6:c.1781G>A	p.Arg594Gln	p.R594Q	ENST00000335508	NM_012433.2	594	cGa/cAa	13/25	0.497688694166555	3	FACETS	0.988	0.923	1	0.988	0.923	1	CLONAL	2	TRUE	1	0.497556094811162	3		378	485	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711908	89711910	+	inframe_deletion	In_Frame_Del	DEL	TAT	TAT	-	rs587780711	NA	P-0023523-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	157	519	0	ENST00000371953.3:c.532_534del	p.Tyr178del	p.Y178del	ENST00000371953	NM_000314.4	176	TAT/-	6/9	0.497556094811162	2	FACETS	1	0.989	1	0.729	0.674	0.784	CLONAL	1	TRUE	0	0.497556094811162	2		519	433	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877308	28877308	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023523-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	64	400	0	ENST00000282397.4:c.4013T>C	p.Ile1338Thr	p.I1338T	ENST00000282397	NM_002019.4	1338	aTc/aCc	30/30	0.497688694166555	3	FACETS	0.682	0.592	0.779	0.341	0.296	0.39	SUBCLONAL	1	TRUE	1	0.497556094811162	3		400	471	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56870541	56870541	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023523-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	222	379	0	ENST00000308159.5:c.1811A>G	p.Asp604Gly	p.D604G	ENST00000308159	NM_014669.4	604	gAc/gGc	17/22	0.497688694166555	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.497556094811162	3		379	501	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244025	5244025	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023523-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	257	826	0	ENST00000357368.4:c.1457C>A	p.Thr486Asn	p.T486N	ENST00000357368	NM_002850.3	486	aCc/aAc	11/38	0.12806288942891	6	FACETS	0.827	0.773	0.883			1	INDETERMINATE	2	TRUE	NA	0.497556094811162	6		826	1246	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755329	39755329	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023523-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	134	423	0	ENST00000288319.7:c.1436A>G	p.Tyr479Cys	p.Y479C	ENST00000288319	NM_182918.3	479	tAc/tGc	10/10	0.307286180289855	4	FACETS	0.78	0.713	0.85	0.78	0.713	0.85	SUBCLONAL	2	TRUE	2	0.497556094811162	4		423	517	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243484	46243484	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	105	106	0	ENST00000334344.6:c.1837C>T	p.Gln613Ter	p.Q613*	ENST00000334344	NM_152641.2	613	Cag/Tag	14/21	0.51612653054211	3	FACETS	0.871	0.802	0.939	0.871	0.802	0.939	CLONAL	3	TRUE	0	0.51612653054211	3		106	196	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412095	63412095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852217	NA	P-0023565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	348	182	1	ENST00000330258.3:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000330258	NM_152424.3	358	Cga/Tga	2/2	0.2362436640137	2	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.51612653054211	2		183	583	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100041	157100055	+	inframe_deletion	In_Frame_Del	DEL	AGGAGGAGCAGGAGC	AGGAGGAGCAGGAGC	-	rs773423003	NA	P-0023565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	52	34	2	ENST00000346085.5:c.993_1007del	p.Gly333_Gly337del	p.G333_G337del	ENST00000346085	NM_020732.3	326	ggAGGAGGAGCAGGAGCa/gga	1/20	0.512728493457417	4	FACETS	0.804	0.695	0.919			1	CLONAL	2	TRUE	NA	0.51612653054211	4		36	190	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100049	157100049	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1256773336	NA	P-0023565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	40	17	0	ENST00000346085.5:c.986C>G	p.Ala329Gly	p.A329G	ENST00000346085	NM_020732.3	329	gCa/gGa	1/20	0.512728493457417	4	FACETS	1	0.946	1			1	CLONAL	1	TRUE	NA	0.51612653054211	4		17	178	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578527	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0023565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	549	739	1	ENST00000269305.4:c.402_403dup	p.Cys135PhefsTer36	p.C135Ffs*36	ENST00000269305	NM_001126112.2	135	tgc/tTTgc	5/11	NA	2	FACETS	0.973	0.938	1			1	INDETERMINATE	2	TRUE	NA	0.51612653054211	2		740	1093	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972889	55972890	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	73	167	0	ENST00000263923.4:c.1500dup	p.Lys501Ter	p.K501*	ENST00000263923	NM_002253.2	500	-/T	11/30	0.2362436640137	4	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.51612653054211	4		167	309	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348978	70348978	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	96	242	0	ENST00000374080.3:c.3490G>T	p.Asp1164Tyr	p.D1164Y	ENST00000374080		1164	Gac/Tac	25/45	0.2362436640137	2	FACETS	0.79	0.707	0.877			1	INDETERMINATE	1	TRUE	NA	0.51612653054211	2		242	471	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0023910-T09-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	186	598	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.647226357539693	3	FACETS	0.917	0.871	0.963	0.917	0.871	0.963	CLONAL	3	TRUE	0	0.63925499025235	3		598	279	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0023910-T09-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	34	846	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.647226357539693	3	FACETS	0.469	0.385	0.564	0.156	0.128	0.188	SUBCLONAL	1	TRUE	0	0.63925499025235	3		847	299	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445007	89445007	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023910-T09-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	61	620	0	ENST00000336596.2:c.1327A>G	p.Ile443Val	p.I443V	ENST00000336596	NM_005233.5	443	Att/Gtt	6/17	0.647226357539693	3	FACETS	1	0.915	1	0.531	0.464	0.603	CLONAL	1	TRUE	1	0.63925499025235	3		620	237	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280314	1280314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561203868	NA	P-0023910-T09-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	404	1290	0	ENST00000310581.5:c.1909G>A	p.Asp637Asn	p.D637N	ENST00000310581	NM_198253.2	637	Gac/Aac	4/16	0.63925499025235	8	FACETS	1	0.971	1			1	CLONAL	5	TRUE	NA	0.63925499025235	8		1290	728	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241704	55241704	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023910-T09-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	31	840	0	ENST00000275493.2:c.2152C>G	p.Leu718Val	p.L718V	ENST00000275493	NM_005228.3	718	Ctg/Gtg	18/28	0.647226357539693	3	FACETS	0.414	0.336	0.503	0.138	0.112	0.168	SUBCLONAL	1	TRUE	0	0.63925499025235	3		840	309	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241705	55241705	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023910-T09-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	25	846	1	ENST00000275493.2:c.2153T>A	p.Leu718Gln	p.L718Q	ENST00000275493	NM_005228.3	718	cTg/cAg	18/28	0.647226357539693	3	FACETS	0.333	0.262	0.414	0.111	0.087	0.138	SUBCLONAL	1	TRUE	0	0.63925499025235	3		847	310	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039380	47039380	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0023910-T09-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	200	1037	0	ENST00000377604.3:c.1003A>T	p.Lys335Ter	p.K335*	ENST00000377604	NM_001204468.1	335	Aag/Tag	10/24	0.63823063090519	2	FACETS	0.884	0.853	0.912	1	0.994	1	CLONAL	3	TRUE	0	0.63925499025235	2		1037	236	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	267	673	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.341217439663966	3	FACETS	0.944	0.887	1	0.944	0.887	1	CLONAL	2	TRUE	1	0.378883578301888	3		673	888	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	255	735	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.283065161788116	5	FACETS	1	0.973	1	0.712	0.667	0.759	CLONAL	2	TRUE	2	0.378883578301888	5		735	988	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254672	16254672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	198	555	0	ENST00000375759.3:c.1937C>T	p.Ser646Phe	p.S646F	ENST00000375759	NM_015001.2	646	tCc/tTc	11/15	0.378883578301888	3	FACETS	0.824	0.766	0.885	0.824	0.766	0.885	CLONAL	2	TRUE	1	0.378883578301888	3		555	754	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818207	43818207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	238	533	0	ENST00000372470.3:c.1672G>A	p.Asp558Asn	p.D558N	ENST00000372470	NM_005373.2	558	Gat/Aat	12/12	0.283065161788116	5	FACETS	0.876	0.821	0.932	0.876	0.821	0.932	CLONAL	3	TRUE	2	0.378883578301888	5		533	750	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120508075	120508076	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	118	331	0	ENST00000256646.2:c.1681_1681+1delinsAA		p.X561_splice	ENST00000256646	NM_024408.3	561		10/34	0.283065161788116	5	FACETS	1	0.97	1	0.77	0.7	0.842	CLONAL	2	TRUE	2	0.378883578301888	5		331	423	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162742024	162742024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	41	446	1	ENST00000367921.3:c.1715G>A	p.Gly572Glu	p.G572E	ENST00000367921	NM_006182.2	572	gGa/gAa	13/18	0.242279349593262	3	FACETS	0.523	0.436	0.621	0.174	0.145	0.207	SUBCLONAL	1	TRUE	0	0.378883578301888	3		447	492	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193121567	193121567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	30	249	0	ENST00000367435.3:c.965C>T	p.Ser322Phe	p.S322F	ENST00000367435	NM_024529.4	322	tCt/tTt	10/17	0.271922899259664	5	FACETS	0.923	0.747	1	0.308	0.249	0.374	CLONAL	1	TRUE	2	0.378883578301888	5		249	269	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649611	206649611	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	221	710	0	ENST00000367120.3:c.446G>A	p.Gly149Glu	p.G149E	ENST00000367120	NM_014002.3	149	gGg/gAg	6/22	0.271922899259664	5	FACETS	0.917	0.853	0.982	0.611	0.569	0.655	CLONAL	2	TRUE	2	0.378883578301888	5		710	998	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612629	228612629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	251	634	0	ENST00000366696.1:c.398G>A	p.Gly133Glu	p.G133E	ENST00000366696	NM_003493.2	133	gGg/gAg	1/1	0.271922899259664	5	FACETS	0.87	0.817	0.925	0.87	0.817	0.925	CLONAL	3	TRUE	2	0.378883578301888	5		634	796	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246021924	246021924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	183	603	0	ENST00000388985.4:c.950C>T	p.Ser317Phe	p.S317F	ENST00000388985		317	tCt/tTt	10/12	0.271922899259664	5	FACETS	0.936	0.865	1	0.624	0.577	0.673	CLONAL	2	TRUE	2	0.378883578301888	5		603	809	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405581	70405582	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	178	507	2	ENST00000373644.4:c.3095_3096delinsTT	p.Ser1032Phe	p.S1032F	ENST00000373644	NM_030625.2	1032	tCC/tTT	4/12	0.378883578301888	5	FACETS	1	0.985	1			1	CLONAL	2	TRUE	NA	0.378883578301888	5		509	594	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88672134	88672134	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	188	717	0	ENST00000372037.3:c.668C>T	p.Pro223Leu	p.P223L	ENST00000372037	NM_004329.2	223	cCt/cTt	8/13	0.378883578301888	5	FACETS	1	0.982	1			1	CLONAL	2	TRUE	NA	0.378883578301888	5		717	657	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112769505	112769505	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	98	572	0	ENST00000369452.4:c.1457T>A	p.Leu486His	p.L486H	ENST00000369452	NM_007373.3	486	cTt/cAt	8/9	0.378883578301888	3	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.378883578301888	3		572	473	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047325	77047325	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	64	382	0	ENST00000356341.3:c.1219G>T	p.Asp407Tyr	p.D407Y	ENST00000356341	NM_002576.4	407	Gac/Tac	13/15	0.378883578301888	4	FACETS	0.998	0.866	1	0.333	0.288	0.38	CLONAL	1	TRUE	1	0.378883578301888	4		382	467	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909855	100909855	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	81	197	0	ENST00000325455.5:c.2794A>T	p.Lys932Ter	p.K932*	ENST00000325455	NM_001202474.3	932	Aaa/Taa	8/8	0.378883578301888	4	FACETS	0.951	0.864	1	1	0.977	1	CLONAL	4	TRUE	1	0.378883578301888	4		197	155	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192078	108192078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200431631	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	291	475	0	ENST00000278616.4:c.6503C>T	p.Ser2168Leu	p.S2168L	ENST00000278616	NM_000051.3	2168	tCg/tTg	45/63	0.378883578301888	4	FACETS	0.939	0.888	0.99	0.939	0.888	0.99	CLONAL	3	TRUE	1	0.378883578301888	4		475	752	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342452	118342452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	32	316	0	ENST00000534358.1:c.578C>T	p.Pro193Leu	p.P193L	ENST00000534358	NM_005933.3	193	cCa/cTa	3/36	0.378883578301888	4	FACETS	0.681	0.554	0.824	0.227	0.184	0.275	SUBCLONAL	1	TRUE	1	0.378883578301888	4		316	342	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390342	118390342	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	257	515	0	ENST00000534358.1:c.11156G>C	p.Gly3719Ala	p.G3719A	ENST00000534358	NM_005933.3	3719	gGt/gCt	32/36	0.378883578301888	4	FACETS	0.908	0.855	0.961	0.908	0.855	0.961	CLONAL	3	TRUE	1	0.378883578301888	4		515	687	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420955	49420955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	197	547	0	ENST00000301067.7:c.14794C>T	p.Pro4932Ser	p.P4932S	ENST00000301067	NM_003482.3	4932	Ccc/Tcc	48/54	0.271922899259664	5	FACETS	1	0.941	1	0.677	0.628	0.728	CLONAL	2	TRUE	2	0.378883578301888	5		547	803	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434804	49434804	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	277	808	1	ENST00000301067.7:c.6749C>T	p.Pro2250Leu	p.P2250L	ENST00000301067	NM_003482.3	2250	cCc/cTc	31/54	0.271922899259664	5	FACETS	1	0.941	1	0.668	0.627	0.71	CLONAL	2	TRUE	2	0.378883578301888	5		809	1144	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28979939	28979939	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	107	456	1	ENST00000282397.4:c.1529C>A	p.Ala510Glu	p.A510E	ENST00000282397	NM_002019.4	510	gCa/gAa	11/30	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.378883578301888	2		457	460	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281980	49281980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777806801	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	114	624	0	ENST00000282018.3:c.1027G>A	p.Glu343Lys	p.E343K	ENST00000282018	NM_020377.2	343	Gaa/Aaa	1/1	1	2	FACETS	0.898	0.81	0.991	0.898	0.81	0.991	CLONAL	1	TRUE	1	0.378883578301888	2		624	670	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100220	30100220	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866059930	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	107	397	0	ENST00000331968.5:c.1400C>T	p.Pro467Leu	p.P467L	ENST00000331968	NM_002742.2	467	cCt/cTt	10/18	0.295821580638381	4	FACETS	0.923	0.834	1	0.923	0.834	1	CLONAL	2	TRUE	2	0.378883578301888	4		397	422	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560227	95560227	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	82	254	0	ENST00000393063.1:c.5362G>T	p.Glu1788Ter	p.E1788*	ENST00000393063	NM_030621.3	1788	Gag/Tag	25/28	0.295821580638381	4	FACETS	0.93	0.828	1	0.93	0.828	1	CLONAL	2	TRUE	2	0.378883578301888	4		254	321	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675068	40675068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	204	765	1	ENST00000249776.8:c.32G>A	p.Arg11Lys	p.R11K	ENST00000249776	NM_033286.3	11	aGa/aAa	1/9	0.271922899259664	5	FACETS	0.809	0.75	0.87	0.539	0.5	0.58	CLONAL	2	TRUE	2	0.378883578301888	5		766	1044	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675103	40675103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	307	810	1	ENST00000249776.8:c.67G>A	p.Asp23Asn	p.D23N	ENST00000249776	NM_033286.3	23	Gat/Aat	1/9	0.271922899259664	5	FACETS	1	0.987	1	0.765	0.722	0.81	CLONAL	2	TRUE	2	0.378883578301888	5		811	1107	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961963	41961963	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs753015602	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	138	494	0	ENST00000219905.7:c.871C>G	p.Arg291Gly	p.R291G	ENST00000219905	NM_001164273.1	291	Cgg/Ggg	2/24	0.271922899259664	5	FACETS	1	0.918	1	0.669	0.612	0.729	CLONAL	2	TRUE	2	0.378883578301888	5		494	569	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713232	43713232	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	300	812	0	ENST00000382044.4:c.4241C>T	p.Thr1414Ile	p.T1414I	ENST00000382044	NM_001141980.1	1414	aCt/aTt	20/28	0.271922899259664	5	FACETS	1	0.988	1	0.785	0.74	0.832	CLONAL	2	TRUE	2	0.378883578301888	5		812	1054	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724691	43724691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	210	662	0	ENST00000382044.4:c.3376G>A	p.Val1126Met	p.V1126M	ENST00000382044	NM_001141980.1	1126	Gtg/Atg	17/28	0.271922899259664	5	FACETS	0.99	0.921	1	0.66	0.614	0.708	CLONAL	2	TRUE	2	0.378883578301888	5		662	878	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032279	10032279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	167	567	0	ENST00000330684.3:c.544G>A	p.Glu182Lys	p.E182K	ENST00000330684	NM_001134407.1	182	Gaa/Aaa	3/13	0.378883578301888	5	FACETS	0.845	0.777	0.916	0.563	0.518	0.611	CLONAL	2	TRUE	2	0.378883578301888	5		567	818	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133274	30133275	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	277	693	2	ENST00000263025.4:c.223_224delinsTT	p.Pro75Phe	p.P75F	ENST00000263025	NM_002746.2	75	CCc/TTc	2/9	0.378883578301888	5	FACETS	1	0.985	1	0.758	0.712	0.804	CLONAL	2	TRUE	2	0.378883578301888	5		695	1009	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827964	72827964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768307205	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	280	743	1	ENST00000268489.5:c.8617G>A	p.Glu2873Lys	p.E2873K	ENST00000268489	NM_006885.3	2873	Gaa/Aaa	9/10	0.341217439663966	3	FACETS	0.999	0.941	1	0.999	0.941	1	CLONAL	2	TRUE	1	0.378883578301888	3		744	880	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828755	72828755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	70	549	0	ENST00000268489.5:c.7826C>T	p.Ser2609Phe	p.S2609F	ENST00000268489	NM_006885.3	2609	tCc/tTc	9/10	0.341217439663966	3	FACETS	0.703	0.613	0.801	0.352	0.306	0.401	SUBCLONAL	1	TRUE	1	0.378883578301888	3		549	625	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81979779	81979780	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	109	407	0	ENST00000359376.3:c.3482-1_3482delinsAA		p.X1161_splice	ENST00000359376	NM_002661.3	1161		31/33	0.341217439663966	3	FACETS	1	0.983	1	0.737	0.666	0.812	CLONAL	1	TRUE	1	0.378883578301888	3		407	464	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110133	8110133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	174	530	0	ENST00000585124.1:c.472C>T	p.Pro158Ser	p.P158S	ENST00000585124	NM_004217.3	158	Ccc/Tcc	6/9	0.341217439663966	3	FACETS	0.814	0.752	0.878	0.814	0.752	0.878	CLONAL	2	TRUE	1	0.378883578301888	3		530	671	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012211	16012211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1391053845	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	125	345	1	ENST00000268712.3:c.2071C>T	p.Arg691Cys	p.R691C	ENST00000268712	NM_006311.3	691	Cgt/Tgt	19/46	0.378883578301888	5	FACETS	1	0.963	1	0.739	0.673	0.807	CLONAL	2	TRUE	2	0.378883578301888	5		346	467	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245740	41245740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	75	567	0	ENST00000357654.3:c.1808C>T	p.Ser603Leu	p.S603L	ENST00000357654	NM_007294.3	603	tCa/tTa	10/23	0.283065161788116	5	FACETS	0.925	0.811	1	0.308	0.27	0.35	CLONAL	1	TRUE	2	0.378883578301888	5		567	671	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245861	41245861	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs80356898	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	118	520	0	ENST00000357654.3:c.1687C>T	p.Gln563Ter	p.Q563*	ENST00000357654	NM_007294.3	563	Cag/Tag	10/23	0.283065161788116	5	FACETS	0.874	0.791	0.96	0.583	0.527	0.64	CLONAL	2	TRUE	2	0.378883578301888	5		520	559	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435090	56435090	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	235	734	0	ENST00000407977.2:c.2047C>T	p.His683Tyr	p.H683Y	ENST00000407977		683	Cat/Tat	9/10	0.283065161788116	5	FACETS	1	0.945	1	0.676	0.631	0.722	CLONAL	2	TRUE	2	0.378883578301888	5		734	960	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774769	73774769	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	210	502	0	ENST00000254810.4:c.318A>T	p.Glu106Asp	p.E106D	ENST00000254810	NM_005324.3	106	gaA/gaT	4/4	0.283065161788116	5	FACETS	1	0.93	1	0.667	0.62	0.715	CLONAL	2	TRUE	2	0.378883578301888	5		502	869	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621863	1621864	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	112	740	0	ENST00000344749.5:c.928_929delinsTT	p.Pro310Phe	p.P310F	ENST00000344749	NM_001136139.2	310	CCt/TTt	11/19	0.378883578301888	3	FACETS	0.885	0.795	0.979	0.442	0.397	0.49	CLONAL	1	TRUE	1	0.378883578301888	3		740	795	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222055	2222055	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	127	822	0	ENST00000398665.3:c.2887G>A	p.Ala963Thr	p.A963T	ENST00000398665	NM_032482.2	963	Gcc/Acc	24/28	0.378883578301888	3	FACETS	0.871	0.788	0.958	0.435	0.394	0.479	CLONAL	1	TRUE	1	0.378883578301888	3		822	916	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222277	2222277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	175	835	0	ENST00000398665.3:c.3109C>T	p.Pro1037Ser	p.P1037S	ENST00000398665	NM_032482.2	1037	Cct/Tct	24/28	0.378883578301888	3	FACETS	1	0.975	1	0.569	0.524	0.617	CLONAL	1	TRUE	1	0.378883578301888	3		835	965	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226643	2226643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269354910	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	294	781	1	ENST00000398665.3:c.4123G>A	p.Gly1375Ser	p.G1375S	ENST00000398665	NM_032482.2	1375	Ggc/Agc	27/28	0.378883578301888	3	FACETS	0.975	0.919	1	0.975	0.919	1	CLONAL	2	TRUE	1	0.378883578301888	3		782	947	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118977	3118977	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	271	845	0	ENST00000078429.4:c.661G>A	p.Glu221Lys	p.E221K	ENST00000078429	NM_002067.2	221	Gag/Aag	5/7	0.378883578301888	3	FACETS	0.942	0.886	1	0.942	0.886	1	CLONAL	2	TRUE	1	0.378883578301888	3		845	903	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223192	5223192	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	137	809	0	ENST00000357368.4:c.2611G>A	p.Gly871Ser	p.G871S	ENST00000357368	NM_002850.3	871	Ggc/Agc	18/38	0.378883578301888	3	FACETS	0.985	0.896	1	0.493	0.448	0.54	CLONAL	1	TRUE	1	0.378883578301888	3		809	873	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117082	7117083	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	83	577	0	ENST00000302850.5:c.4133_4134delinsAA	p.Arg1378Gln	p.R1378Q	ENST00000302850	NM_000208.2	1378	cGG/cAA	22/22	0.378883578301888	3	FACETS	0.729	0.643	0.821	0.364	0.321	0.411	SUBCLONAL	1	TRUE	1	0.378883578301888	3		577	715	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051148	13051148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	102	547	0	ENST00000316448.5:c.584C>T	p.Ser195Phe	p.S195F	ENST00000316448	NM_004343.3	195	tCc/tTc	5/9	0.295821580638381	4	FACETS	0.905	0.809	1	0.453	0.404	0.504	CLONAL	1	TRUE	2	0.378883578301888	4		547	820	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271561	15271561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	147	958	1	ENST00000263388.2:c.6878C>T	p.Pro2293Leu	p.P2293L	ENST00000263388	NM_000435.2	2293	cCc/cTc	33/33	0.295821580638381	4	FACETS	0.964	0.878	1	0.482	0.439	0.527	CLONAL	1	TRUE	2	0.378883578301888	4		959	1110	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291528	15291528	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	242	683	0	ENST00000263388.2:c.3106C>T	p.Arg1036Ter	p.R1036*	ENST00000263388	NM_000435.2	1036	Cga/Tga	19/33	0.295821580638381	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	2	0.378883578301888	4		683	860	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384937	17384937	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	121	870	1	ENST00000359435.4:c.487C>T	p.Pro163Ser	p.P163S	ENST00000359435	NM_001033549.1	163	Ccc/Tcc	5/9	0.295821580638381	4	FACETS	0.858	0.773	0.947	0.429	0.386	0.474	CLONAL	1	TRUE	2	0.378883578301888	4		871	1027	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943518	17943518	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	92	641	0	ENST00000458235.1:c.2491-1G>C		p.X831_splice	ENST00000458235	NM_000215.3	831			0.295821580638381	4	FACETS	0.892	0.792	0.998	0.446	0.396	0.499	CLONAL	1	TRUE	2	0.378883578301888	4		641	751	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274165	18274166	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	216	680	0	ENST00000222254.8:c.1383_1384delinsTT	p.Gln462Ter	p.Q462*	ENST00000222254	NM_005027.3	461	gaCCag/gaTTag	11/16	0.295821580638381	4	FACETS	0.948	0.883	1	0.948	0.883	1	CLONAL	2	TRUE	2	0.378883578301888	4		680	829	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867730	45867730	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	326	831	1	ENST00000391945.4:c.670G>A	p.Glu224Lys	p.E224K	ENST00000391945	NM_000400.3	224	Gaa/Aaa	8/23	0.378883578301888	4	FACETS	0.955	0.902	1	0.955	0.902	1	CLONAL	2	TRUE	2	0.378883578301888	4		832	1242	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50143285	50143286	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGTCCCCGGGCCCA	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	44	245	0	ENST00000246792.3:c.57_70dup	p.Pro24LeufsTer27	p.P24Lfs*27	ENST00000246792	NM_006270.3	24	ccc/cTGGGCCCGGGGACCcc	1/6	0.378883578301888	4	FACETS	0.77	0.647	0.906	0.385	0.323	0.453	CLONAL	1	TRUE	2	0.378883578301888	4		245	416	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902172	50902172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779418268	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	241	805	0	ENST00000440232.2:c.64C>T	p.Leu22Phe	p.L22F	ENST00000440232	NM_002691.3	22	Ctc/Ttc	2/27	0.378883578301888	4	FACETS	0.961	0.899	1	0.961	0.899	1	CLONAL	2	TRUE	2	0.378883578301888	4		805	913	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966630	25966630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	78	556	0	ENST00000435504.4:c.2576C>T	p.Ala859Val	p.A859V	ENST00000435504		859	gCa/gTa	13/13	0.365443051315667	5	FACETS	0.674	0.591	0.764			1	SUBCLONAL	1	TRUE	NA	0.378883578301888	5		556	958	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143035	30143036	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	481	836	0	ENST00000389048.3:c.490_491delinsAA	p.Gly164Lys	p.G164K	ENST00000389048	NM_004304.4	164	GGg/AAg	1/29	0.378883578301888	6	FACETS	1	0.992	1	0.856	0.82	0.894	CLONAL	3	TRUE	2	0.378883578301888	6		836	1303	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222264	39222264	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1281786941	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	147	410	0	ENST00000402219.2:c.3346A>G	p.Ser1116Gly	p.S1116G	ENST00000402219	NM_005633.3	1116	Agc/Ggc	20/23	0.378883578301888	6	FACETS	0.97	0.888	1	0.485	0.444	0.528	CLONAL	2	TRUE	2	0.378883578301888	6		410	703	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426669	212426669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	213	522	0	ENST00000342788.4:c.2446G>A	p.Gly816Arg	p.G816R	ENST00000342788	NM_005235.2	816	Gga/Aga	20/28	0.378883578301888	3	FACETS	1	0.988	1	0.824	0.772	0.877	CLONAL	2	TRUE	0	0.378883578301888	3		522	541	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566709	212566709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	143	268	0	ENST00000342788.4:c.1472G>A	p.Arg491Lys	p.R491K	ENST00000342788	NM_005235.2	491	aGa/aAa	12/28	0.378883578301888	3	FACETS	0.978	0.908	1	0.978	0.908	1	CLONAL	3	TRUE	0	0.378883578301888	3		268	306	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546694	9546694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs942131023	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	173	357	0	ENST00000353224.5:c.1328G>A	p.Gly443Glu	p.G443E	ENST00000353224	NM_177990.2	443	gGa/gAa	5/10	0.378883578301888	5	FACETS	0.87	0.806	0.935	0.87	0.806	0.935	CLONAL	3	TRUE	2	0.378883578301888	5		357	549	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39706274	39706274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	104	246	0	ENST00000361337.2:c.332C>T	p.Ser111Phe	p.S111F	ENST00000361337	NM_003286.2	111	tCt/tTt	5/21	0.378883578301888	5	FACETS	0.965	0.869	1	0.643	0.579	0.711	CLONAL	2	TRUE	2	0.378883578301888	5		246	446	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714425	40714426	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	193	510	3	ENST00000373198.4:c.3971_3972delinsTT	p.Ser1324Phe	p.S1324F	ENST00000373198	NM_133170.3	1324	tCC/tTT	29/32	0.378883578301888	5	FACETS	1	0.963	1	0.706	0.655	0.759	CLONAL	2	TRUE	2	0.378883578301888	5		513	754	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29083962	29083962	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs200432447	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	34	127	0	ENST00000328354.6:c.1555C>T	p.Arg519Ter	p.R519*	ENST00000328354	NM_007194.3	519	Cga/Tga	15/15	0.378883578301888	5	FACETS	0.984	0.818	1	0.656	0.545	0.777	CLONAL	2	TRUE	2	0.378883578301888	5		127	143	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47079163	47079163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	109	581	0	ENST00000409792.3:c.7343C>T	p.Pro2448Leu	p.P2448L	ENST00000409792	NM_014159.6	2448	cCc/cTc	18/21	1	2	FACETS	0.956	0.86	1	0.956	0.86	1	CLONAL	1	TRUE	1	0.378883578301888	2		581	602	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162908	47162908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	66	415	0	ENST00000409792.3:c.3218C>T	p.Pro1073Leu	p.P1073L	ENST00000409792	NM_014159.6	1073	cCa/cTa	3/21	1	2	FACETS	0.889	0.775	1	0.889	0.775	1	CLONAL	1	TRUE	1	0.378883578301888	2		415	392	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163793	47163793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	55	408	0	ENST00000409792.3:c.2333C>T	p.Pro778Leu	p.P778L	ENST00000409792	NM_014159.6	778	cCa/cTa	3/21	1	2	FACETS	0.731	0.628	0.844	0.731	0.628	0.844	SUBCLONAL	1	TRUE	1	0.378883578301888	2		408	397	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199890	128199890	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779338723	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	97	458	0	ENST00000341105.2:c.1415C>T	p.Pro472Leu	p.P472L	ENST00000341105	NM_032638.4	472	cCg/cTg	6/6	0.378883578301888	4	FACETS	0.899	0.801	1	0.3	0.267	0.335	CLONAL	1	TRUE	1	0.378883578301888	4		458	785	SUCCESS
ATR	545	MSKCC	GRCh37	3	142254994	142254994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	38	269	0	ENST00000350721.4:c.3775C>T	p.Pro1259Ser	p.P1259S	ENST00000350721	NM_001184.3	1259	Cca/Tca	20/47	0.378883578301888	3	FACETS	1	0.944	1	0.666	0.558	0.784	CLONAL	1	TRUE	1	0.378883578301888	3		269	179	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683491	182683491	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	122	464	0	ENST00000292782.4:c.54C>A	p.Phe18Leu	p.F18L	ENST00000292782	NM_020640.2	18	ttC/ttA	2/7	0.378883578301888	3	FACETS	0.882	0.804	0.964	0.882	0.804	0.964	CLONAL	2	TRUE	1	0.378883578301888	3		464	434	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801486	1801486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766911583	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	146	858	4	ENST00000260795.2:c.392C>T	p.Ser131Leu	p.S131L	ENST00000260795		131	tCg/tTg	3/17	0.341217439663966	3	FACETS	0.808	0.736	0.884	0.404	0.368	0.442	CLONAL	1	TRUE	1	0.378883578301888	3		862	1134	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127487	55127487	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759729258	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	185	565	1	ENST00000257290.5:c.275C>T	p.Ala92Val	p.A92V	ENST00000257290	NM_006206.4	92	gCg/gTg	3/23	0.341217439663966	3	FACETS	0.941	0.874	1	0.941	0.874	1	CLONAL	2	TRUE	1	0.378883578301888	3		566	617	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161339	55161339	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	77	475	0	ENST00000257290.5:c.3170C>T	p.Ser1057Phe	p.S1057F	ENST00000257290	NM_006206.4	1057	tCc/tTc	23/23	0.341217439663966	3	FACETS	0.963	0.848	1	0.482	0.424	0.543	CLONAL	1	TRUE	1	0.378883578301888	3		475	502	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564515	55564515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754738766	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	74	458	0	ENST00000288135.5:c.403C>T	p.Arg135Cys	p.R135C	ENST00000288135	NM_000222.2	135	Cgc/Tgc	3/21	0.341217439663966	3	FACETS	0.805	0.706	0.912	0.403	0.353	0.456	CLONAL	1	TRUE	1	0.378883578301888	3		458	577	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602982	55602982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	95	351	0	ENST00000288135.5:c.2692G>A	p.Glu898Lys	p.E898K	ENST00000288135	NM_000222.2	898	Gaa/Aaa	19/21	0.341217439663966	3	FACETS	0.869	0.782	0.961	0.869	0.782	0.961	CLONAL	2	TRUE	1	0.378883578301888	3		351	343	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972864	55972864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866807777	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	70	356	0	ENST00000263923.4:c.1526G>A	p.Gly509Glu	p.G509E	ENST00000263923	NM_002253.2	509	gGa/gAa	11/30	0.341217439663966	3	FACETS	0.79	0.696	0.89	0.79	0.696	0.89	SUBCLONAL	2	TRUE	1	0.378883578301888	3		356	278	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213909	66213909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	44	367	0	ENST00000273854.3:c.2521C>T	p.Pro841Ser	p.P841S	ENST00000273854	NM_004439.5	841	Cca/Tca	15/18	0.341217439663966	3	FACETS	0.883	0.744	1	0.441	0.372	0.518	CLONAL	1	TRUE	1	0.378883578301888	3		367	313	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213917	66213917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	41	355	0	ENST00000273854.3:c.2513G>A	p.Gly838Glu	p.G838E	ENST00000273854	NM_004439.5	838	gGa/gAa	15/18	0.341217439663966	3	FACETS	0.891	0.746	1	0.445	0.373	0.525	CLONAL	1	TRUE	1	0.378883578301888	3		355	289	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467380	66467380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	35	199	0	ENST00000273854.3:c.889G>A	p.Glu297Lys	p.E297K	ENST00000273854	NM_004439.5	297	Gag/Aag	3/18	0.341217439663966	3	FACETS	0.931	0.768	1	0.466	0.384	0.556	CLONAL	1	TRUE	1	0.378883578301888	3		199	236	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467661	66467661	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	48	364	0	ENST00000273854.3:c.608G>A	p.Gly203Glu	p.G203E	ENST00000273854	NM_004439.5	203	gGa/gAa	3/18	0.341217439663966	3	FACETS	0.842	0.714	0.981	0.421	0.357	0.491	CLONAL	1	TRUE	1	0.378883578301888	3		364	358	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156918	106156918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778708	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	141	422	1	ENST00000380013.4:c.1819G>A	p.Gly607Arg	p.G607R	ENST00000380013	NM_001127208.2	607	Gga/Aga	3/11	0.341217439663966	3	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	1	0.378883578301888	3		423	435	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057081	180057081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139378654	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	290	782	0	ENST00000261937.6:c.538G>A	p.Gly180Arg	p.G180R	ENST00000261937	NM_182925.4	180	Ggg/Agg	5/30	0.378883578301888	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.378883578301888	4		782	983	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056296	26056296	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	97	453	1	ENST00000343677.2:c.361A>T	p.Lys121Ter	p.K121*	ENST00000343677	NM_005319.3	121	Aaa/Taa	1/1	0.378883578301888	3	FACETS	0.849	0.757	0.947	0.425	0.378	0.474	CLONAL	1	TRUE	1	0.378883578301888	3		454	717	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672308	30672308	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767273130	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	141	767	0	ENST00000376406.3:c.4652C>T	p.Pro1551Leu	p.P1551L	ENST00000376406	NM_014641.2	1551	cCc/cTc	10/15	0.378883578301888	3	FACETS	0.956	0.87	1	0.478	0.435	0.523	CLONAL	1	TRUE	1	0.378883578301888	3		767	926	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188823	32188823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs8192585	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	250	804	1	ENST00000375023.3:c.731C>T	p.Ser244Leu	p.S244L	ENST00000375023	NM_004557.3	244	tCg/tTg	4/30	0.378883578301888	3	FACETS	0.937	0.878	0.996	0.937	0.878	0.996	CLONAL	2	TRUE	1	0.378883578301888	3		805	838	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798504	32798505	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	313	791	1	ENST00000374899.4:c.1351_1352delinsTT	p.Pro451Leu	p.P451L	ENST00000374899	NM_018833.2	451	CCa/TTa	8/12	0.378883578301888	4	FACETS	1	0.987	1	0.759	0.717	0.802	CLONAL	2	TRUE	1	0.378883578301888	4		792	1000	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964384	93964384	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	41	376	0	ENST00000369303.4:c.2513G>A	p.Trp838Ter	p.W838*	ENST00000369303	NM_004440.3	838	tGg/tAg	14/17	0.341217439663966	3	FACETS	0.731	0.611	0.864	0.366	0.305	0.432	SUBCLONAL	1	TRUE	1	0.378883578301888	3		376	352	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982061	93982061	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	58	392	0	ENST00000369303.4:c.1404T>A	p.His468Gln	p.H468Q	ENST00000369303	NM_004440.3	468	caT/caA	6/17	0.341217439663966	3	FACETS	0.867	0.747	0.997	0.434	0.373	0.499	CLONAL	1	TRUE	1	0.378883578301888	3		392	420	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117632225	117632225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	114	533	1	ENST00000368508.3:c.6191C>T	p.Ser2064Leu	p.S2064L	ENST00000368508	NM_002944.2	2064	tCa/tTa	39/43	0.341217439663966	3	FACETS	0.828	0.751	0.909	0.828	0.751	0.909	CLONAL	2	TRUE	1	0.378883578301888	3		534	432	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662429	117662429	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	111	472	0	ENST00000368508.3:c.4948C>T	p.Pro1650Ser	p.P1650S	ENST00000368508	NM_002944.2	1650	Cct/Tct	30/43	0.341217439663966	3	FACETS	0.846	0.766	0.929	0.846	0.766	0.929	CLONAL	2	TRUE	1	0.378883578301888	3		472	412	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678055	117678055	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	42	379	0	ENST00000368508.3:c.3878C>T	p.Ser1293Phe	p.S1293F	ENST00000368508	NM_002944.2	1293	tCc/tTc	25/43	0.341217439663966	3	FACETS	0.73	0.611	0.862	0.365	0.305	0.431	SUBCLONAL	1	TRUE	1	0.378883578301888	3		379	361	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725462	117725462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	132	432	0	ENST00000368508.3:c.419G>A	p.Gly140Glu	p.G140E	ENST00000368508	NM_002944.2	140	gGa/gAa	5/43	0.341217439663966	3	FACETS	0.895	0.818	0.974	0.895	0.818	0.974	CLONAL	2	TRUE	1	0.378883578301888	3		432	463	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415612	152415612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	93	620	0	ENST00000206249.3:c.1462C>T	p.His488Tyr	p.H488Y	ENST00000206249	NM_000125.3	488	Cac/Tac	7/8	0.378883578301888	4	FACETS	0.883	0.784	0.987			1	CLONAL	1	TRUE	NA	0.378883578301888	4		620	767	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522553	157522553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	112	696	0	ENST00000346085.5:c.4825C>T	p.Pro1609Ser	p.P1609S	ENST00000346085	NM_020732.3	1609	Cct/Tct	18/20	0.378883578301888	4	FACETS	0.815	0.732	0.904			1	CLONAL	1	TRUE	NA	0.378883578301888	4		696	1000	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984094	2984094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	142	481	0	ENST00000396946.4:c.436G>A	p.Asp146Asn	p.D146N	ENST00000396946	NM_032415.4	146	Gac/Aac	5/25	0.365443051315667	5	FACETS	0.911	0.833	0.993			1	CLONAL	2	TRUE	NA	0.378883578301888	5		481	645	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729807	41729807	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756546726	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	142	405	0	ENST00000242208.4:c.722G>A	p.Arg241Gln	p.R241Q	ENST00000242208	NM_002192.2	241	cGg/cAg	3/3	0.295821580638381	4	FACETS	0.941	0.862	1	0.941	0.862	1	CLONAL	2	TRUE	2	0.378883578301888	4		405	549	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367239	50367239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1045233686	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	111	343	0	ENST00000331340.3:c.46G>A	p.Glu16Lys	p.E16K	ENST00000331340	NM_006060.4	16	Gaa/Aaa	3/8	0.295821580638381	4	FACETS	0.914	0.827	1	0.914	0.827	1	CLONAL	2	TRUE	2	0.378883578301888	4		343	442	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851483	151851483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	282	486	0	ENST00000262189.6:c.12008C>T	p.Pro4003Leu	p.P4003L	ENST00000262189	NM_170606.2	4003	cCc/cTc	47/59	0.378883578301888	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	3	TRUE	1	0.378883578301888	4		486	676	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874754	151874754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775427298	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	287	398	0	ENST00000262189.6:c.7784C>T	p.Pro2595Leu	p.P2595L	ENST00000262189	NM_170606.2	2595	cCc/cTc	38/59	0.378883578301888	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	1	0.378883578301888	4		398	647	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879204	151879204	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	77	514	0	ENST00000262189.6:c.5741T>C	p.Phe1914Ser	p.F1914S	ENST00000262189	NM_170606.2	1914	tTt/tCt	36/59	0.378883578301888	4	FACETS	0.767	0.673	0.868	0.256	0.224	0.29	SUBCLONAL	1	TRUE	1	0.378883578301888	4		514	731	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949713	151949713	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	39	419	0	ENST00000262189.6:c.1387C>T	p.Gln463Ter	p.Q463*	ENST00000262189	NM_170606.2	463	Cag/Tag	10/59	0.378883578301888	4	FACETS	0.516	0.427	0.616	0.172	0.142	0.206	SUBCLONAL	1	TRUE	1	0.378883578301888	4		419	550	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285602	38285602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	48	376	0	ENST00000425967.3:c.551C>T	p.Pro184Leu	p.P184L	ENST00000425967	NM_001174067.1	184	cCa/cTa	6/19	0.286095948637984	3	FACETS	0.905	0.769	1			1	CLONAL	1	TRUE	NA	0.378883578301888	3		376	333	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950469	68950469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	93	440	0	ENST00000288368.4:c.781C>T	p.Gln261Ter	p.Q261*	ENST00000288368	NM_024870.2	261	Caa/Taa	7/40	0.351706091624959	4	FACETS	1	0.974	1	0.441	0.393	0.491	CLONAL	1	TRUE	1	0.378883578301888	4		440	512	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542592	141542593	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	82	643	0	ENST00000220592.5:c.2393_2394delinsTT	p.Ser798Phe	p.S798F	ENST00000220592	NM_012154.3	798	tCC/tTT	18/19	0.351706091624959	4	FACETS	0.786	0.693	0.887	0.262	0.231	0.296	SUBCLONAL	1	TRUE	1	0.378883578301888	4		643	759	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006089	22006089	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376104829	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	209	602	0	ENST00000276925.6:c.314G>A	p.Arg105Gln	p.R105Q	ENST00000276925	NM_004936.3	105	cGg/cAg	2/2	0.353144677454126	2	FACETS	0.897	0.838	0.957	0.897	0.838	0.957	CLONAL	2	TRUE	0	0.378883578301888	2		602	615	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606448	93606448	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	135	774	0	ENST00000375746.1:c.268C>T	p.His90Tyr	p.H90Y	ENST00000375746	NM_001174167.1	90	Cac/Tac	2/14	0.378883578301888	3	FACETS	1	0.946	1	0.528	0.48	0.578	CLONAL	1	TRUE	1	0.378883578301888	3		774	803	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238318	98238318	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	153	390	0	ENST00000331920.6:c.1726C>T	p.Gln576Ter	p.Q576*	ENST00000331920	NM_000264.3	576	Cag/Tag	12/24	0.378883578301888	3	FACETS	0.91	0.837	0.984	0.91	0.837	0.984	CLONAL	2	TRUE	1	0.378883578301888	3		390	528	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242871	98242871	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	60	315	0	ENST00000331920.6:c.747-1G>A		p.X249_splice	ENST00000331920	NM_000264.3	249			0.378883578301888	3	FACETS	0.895	0.773	1	0.447	0.386	0.513	CLONAL	1	TRUE	1	0.378883578301888	3		315	421	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249984	110249984	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs61749200	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	182	632	0	ENST00000374672.4:c.691C>G	p.Leu231Val	p.L231V	ENST00000374672	NM_004235.4	231	Ctg/Gtg	3/5	0.378883578301888	3	FACETS	0.874	0.809	0.94	0.874	0.809	0.94	CLONAL	2	TRUE	1	0.378883578301888	3		632	654	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128322026	128322026	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	242	702	1	ENST00000265960.3:c.734T>C	p.Phe245Ser	p.F245S	ENST00000265960	NM_001006617.1	245	tTc/tCc	6/12	0.378883578301888	3	FACETS	0.902	0.845	0.961	0.902	0.845	0.961	CLONAL	2	TRUE	1	0.378883578301888	3		703	842	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417634	139417634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749786734	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	257	806	3	ENST00000277541.6:c.410C>T	p.Ser137Leu	p.S137L	ENST00000277541	NM_017617.3	137	tCg/tTg	4/34	0.378883578301888	3	FACETS	0.854	0.8	0.908	0.854	0.8	0.908	CLONAL	2	TRUE	1	0.378883578301888	3		809	945	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314906	1314906	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	66	434	0	ENST00000400841.2:c.755G>A	p.Trp252Ter	p.W252*	ENST00000400841		252	tGg/tAg	6/6	1	1	FACETS	0.623	0.543	0.71	0.623	0.543	0.71	SUBCLONAL	1	TRUE	0	0.378883578301888	1		434	453	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258744	115258744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434596	NA	P-0024145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	20	244	0	ENST00000369535.4:c.38G>A	p.Gly13Asp	p.G13D	ENST00000369535	NM_002524.4	13	gGt/gAt	2/7	1	2	FACETS	0.27	0.206	0.345	0.27	0.206	0.345	SUBCLONAL	1	TRUE	1	0.44976732090963	2		244	329	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440948	56440948	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	142	400	1	ENST00000407977.2:c.389G>A	p.Gly130Asp	p.G130D	ENST00000407977		130	gGt/gAt	4/10	0.44976732090963	1	FACETS	0.735	0.671	0.801	0.735	0.671	0.801	SUBCLONAL	1	TRUE	0	0.44976732090963	1		401	666	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0024146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	366	572	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.683608337178827	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.683608337178827	1		572	636	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	290	505	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.123261633758176	4	FACETS	1	0.985	1	1	0.985	1	INDETERMINATE	2	TRUE	2	0.683608337178827	4		505	648	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470011	25470011	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs749817324	NA	P-0024146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	262	326	0	ENST00000264709.3:c.1031T>C	p.Leu344Pro	p.L344P	ENST00000264709	NM_175629.2	344	cTg/cCg	9/23	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.683608337178827	2		326	708	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435827	56435827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140873038	NA	P-0024146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	33	335	0	ENST00000407977.2:c.1310G>A	p.Arg437Gln	p.R437Q	ENST00000407977		437	cGg/cAg	9/10	0.306517363950828	3	FACETS	0.213	0.173	0.259	0.107	0.086	0.13	INDETERMINATE	1	TRUE	1	0.683608337178827	3		335	607	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606122	47606122	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	232	427	0	ENST00000263735.4:c.586G>T	p.Val196Phe	p.V196F	ENST00000263735	NM_002354.2	196	Gtt/Ttt	6/9	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.683608337178827	2		427	602	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225449693	225449693	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0024146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	20	297	1	ENST00000264414.4:c.34A>T	p.Lys12Ter	p.K12*	ENST00000264414	NM_003590.4	12	Aag/Tag	1/16	1	2	FACETS	0.159	0.121	0.204	0.159	0.121	0.204	SUBCLONAL	1	TRUE	1	0.683608337178827	2		298	367	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577523	7577524	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	74	693	0	ENST00000269305.4:c.757dup	p.Thr253AsnfsTer11	p.T253Nfs*11	ENST00000269305	NM_001126112.2	253	acc/aAcc	7/11	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.17	2		693	835	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441441	40441441	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	33	173	0	ENST00000345506.4:c.12G>C	p.Trp4Cys	p.W4C	ENST00000345506	NM_003152.3	4	tgG/tgC	3/20	1	2	FACETS	0.649	0.527	0.787	0.649	0.527	0.787	SUBCLONAL	1	TRUE	1	0.17	2		173	598	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398288	+	missense_variant	Missense_Mutation	ONP	CCAGC	CCAGC	ACATG	novel	NA	P-0024147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	51	222	0	ENST00000311936.3:c.31_35delinsCATGT	p.Ala11_Gly12delinsHisVal	p.A11_G12delinsHV	ENST00000311936	NM_004985.3	11	GCTGGt/CATGTt	2/5	1	2	FACETS	0.997	0.846	1	0.997	0.846	1	CLONAL	1	TRUE	1	0.17	2		222	602	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0024148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	63	419	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.691	0.598	0.791	0.691	0.598	0.791	SUBCLONAL	1	TRUE	1	0.349493820535817	2		420	522	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0024148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	53	301	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.349493820535817	2		302	281	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349689	70349689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs979229015	NA	P-0024148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	88	320	1	ENST00000374080.3:c.3851G>A	p.Arg1284His	p.R1284H	ENST00000374080		1284	cGc/cAc	27/45	1	2	FACETS	0.862	0.765	0.966	0.862	0.765	0.966	CLONAL	1	TRUE	1	0.349493820535817	2		321	584	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884875	134884875	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368240835	NA	P-0024148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	114	383	0	ENST00000398015.3:c.1651G>A	p.Val551Met	p.V551M	ENST00000398015	NM_004441.4	551	Gtg/Atg	8/16	0.349493820535817	3	FACETS	0.931	0.838	1			1	CLONAL	1	TRUE	NA	0.349493820535817	3		383	823	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380302	25380303	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0024148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	181	49	0	ENST00000311936.3:c.155dup	p.Asp54GlyfsTer33	p.D54Gfs*33	ENST00000311936	NM_004985.3	52	ctc/ctTc	3/5	1	2	FACETS	1	0.972	1	1	0.994	1	CLONAL	2	TRUE	1	0.349493820535817	2		49	477	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476388	88476388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374759890	NA	P-0024148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	116	315	0	ENST00000360948.2:c.1744C>T	p.Arg582Trp	p.R582W	ENST00000360948	NM_001012338.2	582	Cgg/Tgg	15/19	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.349493820535817	2		315	633	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268089	153268090	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	56	186	0	ENST00000281708.4:c.718dup	p.Met240AsnfsTer16	p.M240Nfs*16	ENST00000281708	NM_033632.3	240	atg/aAtg	4/12	1	2	FACETS	0.828	0.712	0.954	0.828	0.712	0.954	CLONAL	1	TRUE	1	0.349493820535817	2		186	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0024149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	178	686	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.402800032404032	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.402800032404032	2		686	394	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057817	27057817	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	130	342	0	ENST00000324856.7:c.1525C>A	p.Pro509Thr	p.P509T	ENST00000324856	NM_006015.4	509	Cca/Aca	3/20	0.402800032404032	6	FACETS	1	0.974	1			1	CLONAL	2	TRUE	NA	0.402800032404032	6		342	494	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727441	66727441	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519728	NA	P-0024149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	102	185	0	ENST00000307102.5:c.157T>A	p.Phe53Ile	p.F53I	ENST00000307102	NM_002755.3	53	Ttt/Att	2/11	0.27002588746257	5	FACETS	0.846	0.766	0.93	0.846	0.766	0.93	CLONAL	3	TRUE	2	0.402800032404032	5		185	320	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024340-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	199	395	0				ENST00000310581	NM_198253.2	-/1132			0.524377372341748	6	FACETS	0.984	0.914	1	0.492	0.457	0.529	CLONAL	2	TRUE	2	0.524377372341748	6		395	790	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981529	201981530	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0024340-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	361	851	0	ENST00000359651.3:c.445dup	p.Ala149GlyfsTer12	p.A149Gfs*12	ENST00000359651		148	atg/atGg	3/8	0.524377372341748	4	FACETS	0.865	0.82	0.911	0.865	0.82	0.911	CLONAL	2	TRUE	2	0.524377372341748	4		851	1213	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268483	46268483	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs778964948	NA	P-0024340-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	332	381	0	ENST00000371998.3:c.2870C>G	p.Ser957Cys	p.S957C	ENST00000371998		957	tCt/tGt	15/23	0.524377372341748	6	FACETS	0.974	0.929	1	0.974	0.929	1	CLONAL	4	TRUE	2	0.524377372341748	6		381	666	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347548	118347548	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024340-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	92	468	0	ENST00000534358.1:c.3185C>A	p.Ser1062Tyr	p.S1062Y	ENST00000534358	NM_005933.3	1062	tCt/tAt	4/36	0.472060865166178	1	FACETS	0.704	0.63	0.781	0.704	0.63	0.781	SUBCLONAL	1	TRUE	0	0.524377372341748	1		468	368	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347646	118347646	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024340-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	114	566	0	ENST00000534358.1:c.3283G>T	p.Ala1095Ser	p.A1095S	ENST00000534358	NM_005933.3	1095	Gcc/Tcc	4/36	0.472060865166178	1	FACETS	0.844	0.767	0.924	0.844	0.767	0.924	CLONAL	1	TRUE	0	0.524377372341748	1		566	380	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59793424	59793424	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1261005517	NA	P-0024340-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	18	344	0	ENST00000259008.2:c.2380G>T	p.Val794Phe	p.V794F	ENST00000259008	NM_032043.2	794	Gtt/Ttt	17/20	0.524377372341748	6	FACETS	0.454	0.341	0.587	0.113	0.085	0.147	SUBCLONAL	1	TRUE	2	0.524377372341748	6		344	310	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224572	36224572	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024340-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1239	73	991	1	ENST00000222270.7:c.7034G>A	p.Gly2345Glu	p.G2345E	ENST00000222270	NM_014727.1	2345	gGg/gAg	29/37	0.524377372341748	4	FACETS	0.323	0.281	0.369	0.162	0.14	0.185	SUBCLONAL	1	TRUE	2	0.524377372341748	4		992	1312	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067139	143067139	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1217385988	NA	P-0024340-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	54	386	0	ENST00000262992.4:c.1574G>T	p.Trp525Leu	p.W525L	ENST00000262992	NM_001101669.1	525	tGg/tTg	16/24	0.469449128626347	4	FACETS	0.61	0.521	0.707	0.305	0.26	0.354	SUBCLONAL	1	TRUE	2	0.524377372341748	4		386	515	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31493394	31493394	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024340-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	79	343	0	ENST00000344624.3:c.1762A>T	p.Arg588Trp	p.R588W	ENST00000344624		588	Agg/Tgg	10/33	0.524377372341748	6	FACETS	1	0.951	1	0.289	0.254	0.326	CLONAL	1	TRUE	2	0.524377372341748	6		343	534	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340429	8340429	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024340-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	95	527	0	ENST00000356435.5:c.5167G>T	p.Glu1723Ter	p.E1723*	ENST00000356435		1723	Gag/Tag	31/35	0.524377372341748	5	FACETS	0.725	0.644	0.811	0.242	0.214	0.271	SUBCLONAL	1	TRUE	2	0.524377372341748	5		527	893	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0024430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	22	374	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.235948827715243	2		374	135	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0024430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	73	262	0	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.235948827715243	2		262	519	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920413	134920413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1338928289	NA	P-0024430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	84	351	1	ENST00000398015.3:c.2228G>A	p.Arg743Gln	p.R743Q	ENST00000398015	NM_004441.4	743	cGg/cAg	12/16	1	2	FACETS	0.844	0.744	0.951	0.844	0.744	0.951	CLONAL	1	TRUE	1	0.235948827715243	2		352	844	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398262	25398262	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913538	NA	P-0024430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	26	105	0	ENST00000311936.3:c.57G>T	p.Leu19Phe	p.L19F	ENST00000311936	NM_004985.3	19	ttG/ttT	2/5	NA	2	FACETS	0.878	0.698	1			1	INDETERMINATE	1	TRUE	NA	0.235948827715243	2		105	251	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510561	38510561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1457382271	NA	P-0024430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	90	283	2	ENST00000254066.5:c.815G>A	p.Arg272Gln	p.R272Q	ENST00000254066	NM_000964.3	272	cGg/cAg	7/9	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.235948827715243	2		285	656	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740668	58740668	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs759850701	NA	P-0024430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	60	155	0	ENST00000305921.3:c.1573G>T	p.Glu525Ter	p.E525*	ENST00000305921	NM_003620.3	525	Gaa/Taa	6/6	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.235948827715243	2		155	421	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992720	68992720	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs182978151	NA	P-0024430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	129	43	0	ENST00000288368.4:c.1685G>A	p.Arg562His	p.R562H	ENST00000288368	NM_024870.2	562	cGt/cAt	16/40	1	2	FACETS	0.896	0.82	0.974	1	0.992	1	CLONAL	3	TRUE	1	0.235948827715243	2		43	407	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205170	61205170	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	173	66	0	ENST00000301761.2:c.110G>A	p.Gly37Asp	p.G37D	ENST00000301761	NM_017841.2	37	gGt/gAt	2/4	1	2	FACETS	1	0.98	1	1	0.993	1	CLONAL	2	TRUE	1	0.235948827715243	2		66	623	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656600	3656600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs575953567	NA	P-0024430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1214	121	541	2	ENST00000294008.3:c.635G>A	p.Arg212Gln	p.R212Q	ENST00000294008	NM_032444.2	212	cGa/cAa	3/15	0.235948827715243	3	FACETS	0.859	0.773	0.95	0.429	0.386	0.475	CLONAL	1	TRUE	1	0.235948827715243	3		543	1335	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664450	29664451	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	55	128	0	ENST00000356175.3:c.6432dup	p.Gly2145TrpfsTer3	p.G2145Wfs*3	ENST00000356175	NM_000267.3	2143	-/T	42/57	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.235948827715243	2		128	438	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684022	29684023	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0024430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	32	115	0	ENST00000356175.3:c.7721_7722del	p.Lys2574SerfsTer5	p.K2574Sfs*5	ENST00000356175	NM_000267.3	2574	AAa/a	52/57	1	2	FACETS	0.976	0.795	1	0.976	0.795	1	CLONAL	1	TRUE	1	0.235948827715243	2		115	278	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167538	24167538	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	85	460	0	ENST00000263121.7:c.922G>T	p.Val308Phe	p.V308F	ENST00000263121	NM_003073.3	308	Gtc/Ttc	7/9	0.235948827715243	3	FACETS	0.826	0.729	0.931	0.275	0.243	0.311	CLONAL	1	TRUE	0	0.235948827715243	3		460	975	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070871	30070871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs74315503	NA	P-0024430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	78	470	0	ENST00000338641.4:c.1387G>A	p.Glu463Lys	p.E463K	ENST00000338641	NM_000268.3	463	Gag/Aag	13/16	0.235948827715243	3	FACETS	0.724	0.634	0.821	0.241	0.211	0.274	SUBCLONAL	1	TRUE	0	0.235948827715243	3		470	1021	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0024502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	336	798	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.589508785369699	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.589508785369699	2		800	553	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0024502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	203	411	1	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.393553337882304	3	FACETS	0.993	0.932	1			1	CLONAL	2	TRUE	NA	0.589508785369699	3		412	449	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0024502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	155	210	1	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	0.589508785369699	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	1	0.589508785369699	3		211	331	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710517	114710517	+	start_lost	Translation_Start_Site	SNP	T	T	A	novel	NA	P-0024502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	32	231	0	ENST00000543371.1:c.2T>A	p.Met1?	p.M1?	ENST00000543371	NM_001198531.1	1	aTg/aAg	1/14	0.267565355606755	2	FACETS	0.416	0.339	0.502	0.208	0.169	0.251	INDETERMINATE	1	TRUE	0	0.589508785369699	2		231	261	SUCCESS
APC	324	MSKCC	GRCh37	5	112175770	112175770	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	44	177	0	ENST00000257430.4:c.4480del	p.Glu1494LysfsTer13	p.E1494Kfs*13	ENST00000257430	NM_000038.5	1493	acG/ac	16/16	0.589508785369699	3	FACETS	0.826	0.699	0.964	0.413	0.349	0.482	CLONAL	1	TRUE	1	0.589508785369699	3		177	234	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478788	56478788	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	142	341	0	ENST00000267101.3:c.244G>C	p.Glu82Gln	p.E82Q	ENST00000267101	NM_001982.3	82	Gaa/Caa	3/28	0.393553337882304	3	FACETS	1	0.923	1			1	CLONAL	1	TRUE	NA	0.589508785369699	3		341	618	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285902	39285902	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	33	339	1	ENST00000402219.2:c.257C>A	p.Ala86Glu	p.A86E	ENST00000402219	NM_005633.3	86	gCa/gAa	3/23	0.589508785369699	3	FACETS	0.33	0.269	0.4	0.165	0.134	0.2	SUBCLONAL	1	TRUE	1	0.589508785369699	3		340	439	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523114	176523114	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	136	460	1	ENST00000292408.4:c.1878G>A	p.Met626Ile	p.M626I	ENST00000292408	NM_213647.1	626	atG/atA	14/18	0.260222818424893	4	FACETS	1	0.981	1	0.33	0.299	0.362	CLONAL	1	TRUE	0	0.26	4		461	999	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982071	70982071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	50	356	0	ENST00000276594.2:c.25G>A	p.Ala9Thr	p.A9T	ENST00000276594	NM_024504.3	9	Gcc/Acc	2/8	0.297710618932816	8	FACETS	0.859	0.727	1	0.143	0.121	0.168	CLONAL	1	TRUE	2	0.26	8		356	797	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050303	176050303	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	32	182	0	ENST00000367669.3:c.1262C>G	p.Ser421Cys	p.S421C	ENST00000367669	NM_022457.5	421	tCc/tGc	11/20	0.297710618932816	5	FACETS	0.659	0.534	0.801	0.165	0.133	0.201	SUBCLONAL	1	TRUE	1	0.26	5		182	519	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123888136	123888136	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	66	165	0	ENST00000330479.4:c.614G>C	p.Arg205Thr	p.R205T	ENST00000330479	NM_020382.3	205	aGa/aCa	6/9	0.00735919243851457	3	FACETS	0.755	0.658	0.858	0.755	0.658	0.858	INDETERMINATE	2	TRUE	1	0.26	3		165	380	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541521	29541521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1004943800	NA	P-0024505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	53	222	0	ENST00000356175.3:c.1445C>T	p.Thr482Ile	p.T482I	ENST00000356175	NM_000267.3	482	aCa/aTa	13/57	0.297710618932816	5	FACETS	0.808	0.688	0.941	0.269	0.229	0.314	CLONAL	1	TRUE	2	0.26	5		222	701	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798136	42798136	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	90	448	0	ENST00000575354.2:c.4090G>C	p.Glu1364Gln	p.E1364Q	ENST00000575354	NM_015125.3	1364	Gag/Cag	17/20	0.297710618932816	6	FACETS	0.887	0.785	0.998	0.148	0.13	0.167	CLONAL	1	TRUE	0	0.26	6		448	1186	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180554	56180554	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	67	169	0	ENST00000399503.3:c.3883A>G	p.Ile1295Val	p.I1295V	ENST00000399503	NM_005921.1	1295	Ata/Gta	16/20	0.260222818424893	4	FACETS	1	0.96	1	0.319	0.277	0.364	CLONAL	1	TRUE	0	0.26	4		169	509	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165854	118165854	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	91	302	0	ENST00000369448.3:c.364G>C	p.Glu122Gln	p.E122Q	ENST00000369448	NM_017709.3	122	Gag/Cag	2/2	1	2	FACETS	0.841	0.752	0.935	0.841	0.752	0.935	CLONAL	1	TRUE	1	0.546658616062749	2		302	396	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713371	43713371	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs749486979	NA	P-0024632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	174	621	1	ENST00000382044.4:c.4102C>T	p.Pro1368Ser	p.P1368S	ENST00000382044	NM_001141980.1	1368	Cct/Tct	20/28	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.546658616062749	2		622	591	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719234	61719234	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	120	326	0	ENST00000401558.2:c.1823T>C	p.Met608Thr	p.M608T	ENST00000401558	NM_003400.3	608	aTg/aCg	16/25	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.546658616062749	2		326	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0024779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	213	621	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.53006490318759	2		622	785	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0024779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	170	292	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	1	2	FACETS	0.981	0.905	1	0.981	0.905	1	CLONAL	1	TRUE	1	0.53006490318759	2		292	654	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856364	111856364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	24	82	0	ENST00000341259.2:c.415C>T	p.Arg139Cys	p.R139C	ENST00000341259	NM_005475.2	139	Cgc/Tgc	2/8	0.259233627823255	1	FACETS	0.421	0.333	0.52	0.421	0.333	0.52	INDETERMINATE	1	TRUE	0	0.53006490318759	1		82	158	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176104150	176104150	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	67	223	0	ENST00000367669.3:c.964C>T	p.His322Tyr	p.H322Y	ENST00000367669	NM_022457.5	322	Cac/Tac	8/20	0.259233627823255	1	FACETS	0.706	0.621	0.797	0.706	0.621	0.797	INDETERMINATE	1	TRUE	0	0.53006490318759	1		223	263	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104268957	104268957	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	271	321	1	ENST00000369902.3:c.214A>T	p.Ser72Cys	p.S72C	ENST00000369902	NM_016169.3	72	Agc/Tgc	2/12	0.53006490318759	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.53006490318759	1		322	543	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5081728	5081728	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	139	92	0	ENST00000381652.3:c.2438A>G	p.Tyr813Cys	p.Y813C	ENST00000381652	NM_004972.3	813	tAt/tGt	19/25	0.53006490318759	3	FACETS	0.941	0.88	1	0.941	0.88	1	CLONAL	3	TRUE	0	0.53006490318759	3		92	235	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441973	52441973	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs775451516	NA	P-0024780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	108	342	1	ENST00000460680.1:c.375+1G>A		p.X125_splice	ENST00000460680	NM_004656.3	125			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		343	321	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024797-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	1107	395	0				ENST00000310581	NM_198253.2	-/1132			0.805235901130965	6	FACETS	1	0.983	1	1	0.983	1	CLONAL	5	TRUE	1	0.805235901130965	6		395	1435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0024797-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	805	798	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.805235901130965	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.805235901130965	2		800	979	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934194	48934194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024797-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	155	358	0	ENST00000267163.4:c.649C>T	p.Gln217Ter	p.Q217*	ENST00000267163	NM_000321.2	217	Cag/Tag	7/27	0.791678659578491	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.805235901130965	1		358	228	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438587	49438587	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024797-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	412	856	0	ENST00000301067.7:c.4903del	p.Gly1636AlafsTer86	p.G1636Afs*86	ENST00000301067	NM_003482.3	1635	Ctt/tt	19/54	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.805235901130965	2		856	966	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095002	11095002	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1315494799	NA	P-0024797-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	533	1250	1	ENST00000358026.2:c.175C>T	p.Gln59Ter	p.Q59*	ENST00000358026	NM_001128849.1	59	Cag/Tag	2/36	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.805235901130965	2		1251	1290	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39074468	39074468	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1031851536	NA	P-0024797-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1289	303	606	0	ENST00000357387.3:c.12C>G	p.Ile4Met	p.I4M	ENST00000357387	NM_152756.3	4	atC/atG	1/38	0.805235901130965	6	FACETS	1	0.99	1	0.247	0.232	0.263	CLONAL	1	TRUE	1	0.805235901130965	6		606	1592	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165730	108165730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765759912	NA	P-0024797-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	185	356	0	ENST00000278616.4:c.4853G>A	p.Arg1618Gln	p.R1618Q	ENST00000278616	NM_000051.3	1618	cGa/cAa	32/63	1	2	FACETS	0.932	0.868	0.997	0.932	0.868	0.997	CLONAL	1	TRUE	1	0.805235901130965	2		356	493	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030499	47030500	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0024797-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	36	546	1	ENST00000377604.3:c.274_275delinsTT	p.Gly92Phe	p.G92F	ENST00000377604	NM_001204468.1	92	GGc/TTc	4/24	1	1	FACETS	0.079	0.064	0.095	0.079	0.064	0.095	SUBCLONAL	1	TRUE	0	0.805235901130965	1		547	679	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0024868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	221	374	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.635925426220931	4	FACETS	0.98	0.941	1	0.98	0.941	1	CLONAL	4	TRUE	0	0.639302013161638	4		374	289	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101468	27101468	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	133	407	0	ENST00000324856.7:c.4750C>T	p.Gln1584Ter	p.Q1584*	ENST00000324856	NM_006015.4	1584	Cag/Tag	18/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.639302013161638	2		407	396	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711908	89711908	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	83	333	0	ENST00000371953.3:c.526del	p.Tyr176IlefsTer7	p.Y176Ifs*7	ENST00000371953	NM_000314.4	176	Tat/at	6/9	1	2	FACETS	0.773	0.701	0.844	1	0.984	1	SUBCLONAL	2	TRUE	1	0.639302013161638	2		333	168	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121687	108121687	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555071075	NA	P-0024868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	74	352	0	ENST00000278616.4:c.1495C>T	p.Gln499Ter	p.Q499*	ENST00000278616	NM_000051.3	499	Caa/Taa	10/63	0.639302013161638	1	FACETS	0.955	0.858	1	0.955	0.858	1	CLONAL	1	TRUE	0	0.639302013161638	1		352	165	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268140	153268140	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	132	279	0	ENST00000281708.4:c.668G>C	p.Arg223Pro	p.R223P	ENST00000281708	NM_033632.3	223	cGc/cCc	4/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.639302013161638	2		279	364	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922739	44922739	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	66	236	0	ENST00000377967.4:c.1600C>A	p.Pro534Thr	p.P534T	ENST00000377967	NM_021140.2	534	Cct/Act	16/29	0.639302013161638	1	FACETS	0.831	0.738	0.927	0.831	0.738	0.927	CLONAL	1	TRUE	0	0.639302013161638	1		236	169	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913343	NA	P-0024955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	114	213	0	ENST00000269305.4:c.817C>A	p.Arg273Ser	p.R273S	ENST00000269305	NM_001126112.2	273	Cgt/Agt	8/11	0.254272874443923	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.254272874443923	1		213	538	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134959989	134959989	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0024955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	25	90	0	ENST00000398015.3:c.2347-1G>A		p.X783_splice	ENST00000398015	NM_004441.4	783			0.254272874443923	3	FACETS	0.682	0.538	0.847	0.341	0.269	0.424	SUBCLONAL	1	TRUE	1	0.254272874443923	3		90	325	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41197729	41197729	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs80357258	NA	P-0024955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	117	235	0	ENST00000357654.3:c.5558A>G	p.Tyr1853Cys	p.Y1853C	ENST00000357654	NM_007294.3	1853	tAc/tGc	23/23	0.254272874443923	1	FACETS	0.954	0.867	1	1	0.989	1	CLONAL	2	TRUE	0	0.254272874443923	1		235	421	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031113	11031161	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	ATGACCGTGTGGCTGTCCACAGCCCCGACAGAGCCCCTGACCCACTGGT	ATGACCGTGTGGCTGTCCACAGCCCCGACAGAGCCCCTGACCCACTGGT	-	novel	NA	P-0024955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	30	186	0	ENST00000327064.4:c.1199_1247del	p.Met400ThrfsTer54	p.M400Tfs*54	ENST00000327064	NM_199141.1	400	ATGACCGTGTGGCTGTCCACAGCCCCGACAGAGCCCCTGACCCACTGGTac/ac	11/16	NA	2	FACETS	0.456	0.367	0.558			1	INDETERMINATE	1	TRUE	NA	0.254272874443923	2		186	517	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0024957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	665	447	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.601528934756959	6	FACETS	1	0.994	1			1	CLONAL	4	TRUE	NA	0.601528934756959	6		447	1115	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548886	29548886	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs953440640	NA	P-0024957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	56	516	0	ENST00000356175.3:c.1660C>T	p.Gln554Ter	p.Q554*	ENST00000356175	NM_000267.3	554	Cag/Tag	15/57	0.589423009718533	2	FACETS	0.383	0.328	0.443	0.192	0.164	0.222	SUBCLONAL	1	TRUE	0	0.601528934756959	2		516	486	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006627	62006627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1063625	NA	P-0024957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	116	612	0	ENST00000392795.3:c.652G>A	p.Glu218Lys	p.E218K	ENST00000392795	NM_001039933.1	218	Gaa/Aaa	6/6	0.589423009718533	2	FACETS	0.557	0.502	0.614	0.278	0.251	0.307	SUBCLONAL	1	TRUE	0	0.601528934756959	2		612	693	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245376	46245376	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0024957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	127	451	0	ENST00000334344.6:c.3470C>G	p.Ser1157Ter	p.S1157*	ENST00000334344	NM_152641.2	1157	tCa/tGa	15/21	NA	2	FACETS	0.862	0.785	0.941			1	INDETERMINATE	1	TRUE	NA	0.601528934756959	2		451	490	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917679	94917679	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369321677	NA	P-0024957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	153	722	0	ENST00000536441.1:c.842C>T	p.Ala281Val	p.A281V	ENST00000536441	NM_144665.3	281	gCg/gTg	6/10	0.601528934756959	3	FACETS	0.897	0.822	0.975	0.448	0.411	0.488	CLONAL	1	TRUE	1	0.601528934756959	3		722	738	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233225	69233225	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	321	59	0	ENST00000462284.1:c.1090G>C	p.Asp364His	p.D364H	ENST00000462284	NM_002392.5	364	Gat/Cat	11/11	0.564530359548741	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	2	0.601528934756959	4		59	748	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99452120	99452120	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	26	277	0	ENST00000268035.6:c.1454G>C	p.Arg485Thr	p.R485T	ENST00000268035	NM_000875.3	485	aGa/aCa	6/21	1	2	FACETS	0.26	0.206	0.323	0.26	0.206	0.323	SUBCLONAL	1	TRUE	1	0.601528934756959	2		277	332	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640119	3640119	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	427	821	0	ENST00000294008.3:c.3520G>T	p.Asp1174Tyr	p.D1174Y	ENST00000294008	NM_032444.2	1174	Gat/Tat	12/15	0.601528934756959	3	FACETS	0.935	0.894	0.975	0.935	0.894	0.975	CLONAL	2	TRUE	1	0.601528934756959	3		821	988	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830577	72830577	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	103	581	0	ENST00000268489.5:c.6004C>G	p.Gln2002Glu	p.Q2002E	ENST00000268489	NM_006885.3	2002	Caa/Gaa	9/10	0.601528934756959	3	FACETS	0.638	0.571	0.709	0.319	0.285	0.355	SUBCLONAL	1	TRUE	1	0.601528934756959	3		581	698	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578514	7578537	+	inframe_deletion	In_Frame_Del	DEL	TTGGCCAGTTGGCAAAACATCTTG	TTGGCCAGTTGGCAAAACATCTTG	-	novel	NA	P-0024957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	436	794	1	ENST00000269305.4:c.393_416del	p.Asn131_Ala138del	p.N131_A138del	ENST00000269305	NM_001126112.2	131	aaCAAGATGTTTTGCCAACTGGCCAAg/aag	5/11	0.589423009718533	2	FACETS	0.849	0.815	0.883	0.849	0.815	0.883	CLONAL	2	TRUE	0	0.601528934756959	2		795	854	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684041	29684041	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0024957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	99	639	0	ENST00000356175.3:c.7739C>G	p.Ser2580Ter	p.S2580*	ENST00000356175	NM_000267.3	2580	tCa/tGa	52/57	0.589423009718533	2	FACETS	0.666	0.597	0.739	0.333	0.298	0.37	SUBCLONAL	1	TRUE	0	0.601528934756959	2		639	494	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794764	42794764	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568514291	NA	P-0024957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	114	501	1	ENST00000575354.2:c.1844C>T	p.Ser615Leu	p.S615L	ENST00000575354	NM_015125.3	615	tCa/tTa	10/20	0.601528934756959	3	FACETS	0.692	0.624	0.765	0.346	0.312	0.383	SUBCLONAL	1	TRUE	1	0.601528934756959	3		502	712	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470914	25470914	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	138	567	0	ENST00000264709.3:c.847G>T	p.Glu283Ter	p.E283*	ENST00000264709	NM_175629.2	283	Gag/Tag	7/23	0.527781368954961	4	FACETS	0.71	0.645	0.778			1	SUBCLONAL	1	TRUE	NA	0.601528934756959	4		567	1035	SUCCESS
REL	5966	MSKCC	GRCh37	2	61148931	61148931	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	319	74	0	ENST00000295025.8:c.1121G>C	p.Arg374Thr	p.R374T	ENST00000295025	NM_002908.2	374	aGa/aCa	11/11	0.601528934756959	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.601528934756959	3		74	687	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483994	212483997	+	frameshift_variant	Frame_Shift_Del	DEL	AAAT	AAAT	-	novel	NA	P-0024957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	89	403	0	ENST00000342788.4:c.2206_2209del	p.Ile736GlyfsTer8	p.I736Gfs*8	ENST00000342788	NM_005235.2	736	ATTTgg/gg	19/28	0.584996471198551	2	FACETS	0.964	0.864	1	0.482	0.432	0.534	CLONAL	1	TRUE	0	0.601528934756959	2		403	307	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561335	9561335	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	105	476	0	ENST00000353224.5:c.447G>C	p.Lys149Asn	p.K149N	ENST00000353224	NM_177990.2	149	aaG/aaC	4/10	0.564530359548741	4	FACETS	0.708	0.634	0.786	0.354	0.317	0.393	SUBCLONAL	1	TRUE	2	0.601528934756959	4		476	790	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750453	57750453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	100	524	0	ENST00000274289.3:c.2015G>A	p.Arg672Gln	p.R672Q	ENST00000274289	NM_006622.3	672	cGa/cAa	14/14	0.601528934756959	3	FACETS	0.83	0.744	0.921	0.415	0.372	0.461	CLONAL	1	TRUE	1	0.601528934756959	3		524	521	SUCCESS
APC	324	MSKCC	GRCh37	5	112176877	112176877	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	93	424	0	ENST00000257430.4:c.5586G>C	p.Leu1862Phe	p.L1862F	ENST00000257430	NM_000038.5	1862	ttG/ttC	16/16	0.442691051019525	2	FACETS	0.789	0.706	0.875	0.394	0.353	0.438	SUBCLONAL	1	TRUE	0	0.601528934756959	2		424	392	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637685	176637685	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	148	585	0	ENST00000439151.2:c.2285C>G	p.Ser762Cys	p.S762C	ENST00000439151	NM_022455.4	762	tCc/tGc	5/23	0.572337039714867	3	FACETS	0.833	0.762	0.908	0.417	0.381	0.454	CLONAL	1	TRUE	1	0.601528934756959	3		585	768	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647406	117647406	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	136	690	0	ENST00000368508.3:c.5538G>C	p.Glu1846Asp	p.E1846D	ENST00000368508	NM_002944.2	1846	gaG/gaC	33/43	0.601528934756959	1	FACETS	0.876	0.806	0.947	0.876	0.806	0.947	CLONAL	1	TRUE	0	0.601528934756959	1		690	361	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100219	157100219	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	26	78	3	ENST00000346085.5:c.1156G>A	p.Gly386Arg	p.G386R	ENST00000346085	NM_020732.3	386	Ggg/Agg	1/20	0.550247320741312	1	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	0	0.601528934756959	1		81	58	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050770	5050770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	135	498	0	ENST00000381652.3:c.553G>A	p.Asp185Asn	p.D185N	ENST00000381652	NM_004972.3	185	Gat/Aat	6/25	0.589427609358589	1	FACETS	0.94	0.866	1	0.94	0.866	1	CLONAL	1	TRUE	0	0.601528934756959	1		498	334	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819731	170819731	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1030167696	NA	P-0024957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	21	97	0	ENST00000296930.5:c.370G>C	p.Glu124Gln	p.E124Q	ENST00000296930	NM_002520.6	124	Gag/Cag	5/11	0.572337039714867	3	FACETS	0.744	0.581	0.929	0.372	0.29	0.465	CLONAL	1	TRUE	1	0.601528934756959	3		97	122	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0024958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	161	798	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.235115193223591	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.235115193223591	2		800	642	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0024958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	85	191	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	0.235115193223591	3	FACETS	0.951	0.845	1	0.951	0.845	1	CLONAL	2	TRUE	1	0.235115193223591	3		191	425	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0024958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	86	196	1	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	0.235115193223591	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	1	0.235115193223591	3		197	368	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443482	49443482	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	135	277	0	ENST00000301067.7:c.3889C>G	p.Arg1297Gly	p.R1297G	ENST00000301067	NM_003482.3	1297	Cgt/Ggt	11/54	0.235115193223591	3	FACETS	1	0.921	1	1	0.921	1	CLONAL	2	TRUE	1	0.235115193223591	3		277	635	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89791115	89791115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	10	77	0	ENST00000336032.3:c.502C>T	p.Arg168Trp	p.R168W	ENST00000336032	NM_006813.2	168	Cgg/Tgg	1/2	0.235115193223591	3	FACETS	0.478	0.323	0.672	0.239	0.161	0.336	SUBCLONAL	1	TRUE	1	0.235115193223591	3		77	199	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576848	7576873	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTACCTGAAGGGTGAAATATTCTCC	AGTACCTGAAGGGTGAAATATTCTCC	-	novel	NA	P-0024984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	37	241	0	ENST00000269305.4:c.973_993+5del		p.X325_splice	ENST00000269305	NM_001126112.2	325		9/11	1	2	FACETS	0.595	0.49	0.714	0.595	0.49	0.714	SUBCLONAL	1	TRUE	1	0.21	2		241	592	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657653	37657653	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	46	240	0	ENST00000447079.4:c.2570A>G	p.His857Arg	p.H857R	ENST00000447079	NM_015083.1	857	cAt/cGt	6/14	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.21	2		240	427	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158358	106158358	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	18	172	0	ENST00000380013.4:c.3259T>A	p.Ser1087Thr	p.S1087T	ENST00000380013	NM_001127208.2	1087	Tct/Act	3/11	1	2	FACETS	0.486	0.365	0.629	0.486	0.365	0.629	SUBCLONAL	1	TRUE	1	0.21	2		172	353	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921430	39921430	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	136	197	0	ENST00000378444.4:c.4390G>A	p.Glu1464Lys	p.E1464K	ENST00000378444	NM_001123385.1	1464	Gag/Aag	10/15	0.752156555129004	1	FACETS	0.861	0.8	0.922	0.861	0.8	0.922	CLONAL	1	TRUE	0	0.752156555129004	1		197	262	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	39	395	0				ENST00000310581	NM_198253.2	-/1132			0.46073718532452	3	FACETS	0.641	0.533	0.76	0.32	0.266	0.38	SUBCLONAL	1	TRUE	1	0.46073718532452	3		395	325	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577524	7577524	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	110	359	0	ENST00000269305.4:c.757A>G	p.Thr253Ala	p.T253A	ENST00000269305	NM_001126112.2	253	Acc/Gcc	7/11	0.434414586935204	1	FACETS	0.988	0.896	1	0.988	0.896	1	CLONAL	1	TRUE	0	0.46073718532452	1		359	372	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117313	108117720	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTACACTAGTTGAAGGAACTCGTAATATTTTTCTCTTAGGCCAGAAAAAGGCATACGGAGAACTTGGTCCTCATATGAAAGAGGGAACATATTAATTGTATTTGCCTCAGGTGGGAGAATAAATTGGAGAAAGACAGATTTTAGGTCAGAATATGGAAGAAATTTATAAGAAACACAGTTATCTAAATGTAAAATGGACAGTTATGAAATAGAGTTTGTCAAGGATCTTGTCAGAAGAGGCATTAGTACTGAATGGAAGGTTGGACCAGGTGTCTTCTAACGCTGATGCAGCTTGACAGCTGAATAATTTTGTGGGAGCTAGCAGTGTAAACAGAGTACATACATAAAAATTACATTTTAATTTTTTGGATTACAGGTGCTTATGAATCAACAAAATGGAGAAGTA	TTTTACACTAGTTGAAGGAACTCGTAATATTTTTCTCTTAGGCCAGAAAAAGGCATACGGAGAACTTGGTCCTCATATGAAAGAGGGAACATATTAATTGTATTTGCCTCAGGTGGGAGAATAAATTGGAGAAAGACAGATTTTAGGTCAGAATATGGAAGAAATTTATAAGAAACACAGTTATCTAAATGTAAAATGGACAGTTATGAAATAGAGTTTGTCAAGGATCTTGTCAGAAGAGGCATTAGTACTGAATGGAAGGTTGGACCAGGTGTCTTCTAACGCTGATGCAGCTTGACAGCTGAATAATTTTGTGGGAGCTAGCAGTGTAAACAGAGTACATACATAAAAATTACATTTTAATTTTTTGGATTACAGGTGCTTATGAATCAACAAAATGGAGAAGTA	-	novel	NA	P-0025388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4	43	0	0	ENST00000278616.4:c.902-373_936del		p.X301_splice	ENST00000278616	NM_000051.3	301		8/63	0.319584779458677	5	FACETS	0.959	0.9	1	1	0.982	1	CLONAL	7	TRUE	2	0.46073718532452	5		0	47	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936098	178936098	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	193	281	0	ENST00000263967.3:c.1640A>C	p.Glu547Ala	p.E547A	ENST00000263967	NM_006218.2	547	gAg/gCg	10/21	0.306060327721657	4	FACETS	0.897	0.833	0.963	0.897	0.833	0.963	CLONAL	2	TRUE	2	0.46073718532452	4		281	682	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0025391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	99	314	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.745	0.666	0.829	0.745	0.666	0.829	SUBCLONAL	1	TRUE	1	0.400945929383079	2		315	663	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26911760	26911760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	116	220	0	ENST00000381527.3:c.185C>T	p.Ser62Leu	p.S62L	ENST00000381527	NM_001260.1	62	tCg/tTg	2/13	1	2	FACETS	0.83	0.749	0.916	0.83	0.749	0.916	CLONAL	1	TRUE	1	0.400945929383079	2		220	697	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795187	42795187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377759151	NA	P-0025391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	184	573	0	ENST00000575354.2:c.2267C>T	p.Ala756Val	p.A756V	ENST00000575354	NM_015125.3	756	gCg/gTg	10/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.400945929383079	2		573	814	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542576	187542576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	158	450	0	ENST00000441802.2:c.5164C>T	p.Gln1722Ter	p.Q1722*	ENST00000441802	NM_005245.3	1722	Cag/Tag	10/27	1	2	FACETS	0.98	0.899	1	0.98	0.899	1	CLONAL	1	TRUE	1	0.400945929383079	2		450	804	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489568	56489568	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	122	375	0	ENST00000267101.3:c.2033G>T	p.Arg678Met	p.R678M	ENST00000267101	NM_001982.3	678	aGg/aTg	17/28	1	2	FACETS	0.82	0.742	0.903	0.82	0.742	0.903	CLONAL	1	TRUE	1	0.400945929383079	2		375	742	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349179	89349180	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	rs886039477	NA	P-0025391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1283	345	808	0	ENST00000301030.4:c.3770_3771del	p.Lys1257ArgfsTer25	p.K1257Rfs*25	ENST00000301030	NM_001256183.1	1257	aAA/a	9/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.400945929383079	2		808	1628	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741894	40741894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs930976777	NA	P-0025391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	162	522	2	ENST00000392038.2:c.1078G>A	p.Glu360Lys	p.E360K	ENST00000392038	NM_001626.4	360	Gag/Aag	11/14	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.400945929383079	2		524	764	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516954	187516954	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1261546277	NA	P-0025391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	152	405	0	ENST00000441802.2:c.13027C>T	p.Leu4343Phe	p.L4343F	ENST00000441802	NM_005245.3	4343	Ctt/Ttt	26/27	1	2	FACETS	0.996	0.913	1	0.996	0.913	1	CLONAL	1	TRUE	1	0.400945929383079	2		405	761	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630135	187630135	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	239	472	0	ENST00000441802.2:c.847C>T	p.Gln283Ter	p.Q283*	ENST00000441802	NM_005245.3	283	Cag/Tag	2/27	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.400945929383079	2		472	980	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79974857	79974857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	169	433	0	ENST00000265081.6:c.1285C>T	p.Pro429Ser	p.P429S	ENST00000265081	NM_002439.4	429	Cct/Tct	8/24	0.400945929383079	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.400945929383079	1		433	671	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279639	18279639	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781445775	NA	P-0025391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	166	480	0	ENST00000222254.8:c.1912G>A	p.Gly638Ser	p.G638S	ENST00000222254	NM_005027.3	638	Ggc/Agc	15/16	1	2	FACETS	0.999	0.918	1	0.999	0.918	1	CLONAL	1	TRUE	1	0.400945929383079	2		480	829	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0025393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	127	174	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	1	0.927	1	1	0.99	1	CLONAL	2	TRUE	1	0.249200079701251	2		174	500	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699369	47699369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	202	297	1	ENST00000347630.2:c.139G>A	p.Glu47Lys	p.E47K	ENST00000347630	NM_001007230.1	47	Gaa/Aaa	4/11	1	2	FACETS	1	0.963	1	1	0.994	1	CLONAL	2	TRUE	1	0.249200079701251	2		298	769	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100833	27100846	+	frameshift_variant	Frame_Shift_Del	DEL	CAATGGATGGCACA	CAATGGATGGCACA	ACG	novel	NA	P-0025393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	152	253	1	ENST00000324856.7:c.4115_4128delinsACG	p.Pro1372HisfsTer69	p.P1372Hfs*69	ENST00000324856	NM_006015.4	1372	cCAATGGATGGCACA/cACG	18/20	1	2	FACETS	0.949	0.87	1	1	0.991	1	CLONAL	2	TRUE	1	0.249200079701251	2		254	643	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845562	151845562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	137	421	0	ENST00000262189.6:c.13450C>T	p.His4484Tyr	p.H4484Y	ENST00000262189	NM_170606.2	4484	Cac/Tac	52/59	0.249200079701251	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.249200079701251	1		421	832	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0025463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	128	798	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.172250884618662	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.264652268742644	1		800	770	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663299	227663301	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs753296153	NA	P-0025463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	71	245	2	ENST00000305123.5:c.154_156del	p.Lys52del	p.K52del	ENST00000305123	NM_005544.2	52	AAG/-	1/2	1	2	FACETS	0.865	0.755	0.984	0.865	0.755	0.984	CLONAL	1	TRUE	1	0.264652268742644	2		247	620	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249451	153249451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	177	148	1	ENST00000281708.4:c.1327C>T	p.Leu443Phe	p.L443F	ENST00000281708	NM_033632.3	443	Ctc/Ttc	9/12	0.260639066713046	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.264652268742644	2		149	641	SUCCESS
APC	324	MSKCC	GRCh37	5	112103071	112103071	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	48	105	0	ENST00000257430.4:c.406G>T	p.Glu136Ter	p.E136*	ENST00000257430	NM_000038.5	136	Gaa/Taa	4/16	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.264652268742644	2		105	349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0025545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	753	577	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			NA	2	FACETS	1	0.996	1			1	INDETERMINATE	2	TRUE	NA	0.766926572153752	2		577	922	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425121	49425121	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555187461	NA	P-0025545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	224	478	0	ENST00000301067.7:c.13367C>G	p.Ser4456Ter	p.S4456*	ENST00000301067	NM_003482.3	4456	tCa/tGa	39/54	1	2	FACETS	0.959	0.899	1	0.959	0.899	1	CLONAL	1	TRUE	1	0.766926572153752	2		478	609	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244451	41244451	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs273899698	NA	P-0025545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	328	456	0	ENST00000357654.3:c.3097G>T	p.Glu1033Ter	p.E1033*	ENST00000357654	NM_007294.3	1033	Gaa/Taa	10/23	0.766926572153752	2	FACETS	0.979	0.946	1	0.979	0.946	1	CLONAL	2	TRUE	0	0.766926572153752	2		456	437	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15273329	15273329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1761	236	420	0	ENST00000263388.2:c.5860G>A	p.Ala1954Thr	p.A1954T	ENST00000263388	NM_000435.2	1954	Gcc/Acc	32/33	0.766926572153752	7	FACETS	0.899	0.835	0.966			1	CLONAL	1	TRUE	NA	0.766926572153752	7		420	1997	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741993	40741993	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	75	383	0	ENST00000392038.2:c.979T>A	p.Tyr327Asn	p.Y327N	ENST00000392038	NM_001626.4	327	Tat/Aat	11/14	1	2	FACETS	0.368	0.323	0.417	0.368	0.323	0.417	SUBCLONAL	1	TRUE	1	0.766926572153752	2		383	531	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031971	26031971	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	264	314	0	ENST00000244661.2:c.318G>C	p.Glu106Asp	p.E106D	ENST00000244661	NM_003537.3	106	gaG/gaC	1/1	0.766926572153752	5	FACETS	0.966	0.91	1	0.644	0.606	0.683	CLONAL	2	TRUE	2	0.766926572153752	5		314	766	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0025687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	426	94	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.278878384885063	5	FACETS	0.961	0.92	1	0.961	0.92	1	CLONAL	4	TRUE	1	0.347630730423876	5		94	970	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0025687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	302	135	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	1	2	FACETS	0.874	0.83	0.918	1	0.996	1	CLONAL	3	TRUE	1	0.347630730423876	2		135	663	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	190	541	1	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.347630730423876	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.347630730423876	1		542	894	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795544	42795544	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs940815613	NA	P-0025687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	230	669	0	ENST00000575354.2:c.2624A>G	p.Lys875Arg	p.K875R	ENST00000575354	NM_015125.3	875	aAa/aGa	10/20	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.347630730423876	2		669	1284	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0025699-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	119	332	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.425078174125141	1	FACETS	0.9	0.817	0.987	0.9	0.817	0.987	CLONAL	1	TRUE	0	0.425078174125141	1		332	490	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0025699-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	120	793	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.380651299551436	4	FACETS	0.878	0.798	0.962	0.878	0.798	0.962	CLONAL	2	TRUE	2	0.425078174125141	4		793	458	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412493	80412493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514698	NA	P-0025699-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	22	69	0	ENST00000286548.4:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000286548	NM_002072.3	183	cGa/cAa	4/7	0.425078174125141	1	FACETS	0.308	0.239	0.387	0.308	0.239	0.387	SUBCLONAL	1	TRUE	0	0.425078174125141	1		69	265	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870257	155870257	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025699-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	108	140	0	ENST00000368323.3:c.582G>T	p.Glu194Asp	p.E194D	ENST00000368323	NM_006912.5	194	gaG/gaT	6/6	0.425078174125141	3	FACETS	1	0.96	1	0.564	0.508	0.623	CLONAL	1	TRUE	1	0.425078174125141	3		140	546	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176153806	176153806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1366705437	NA	P-0025699-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	77	80	0	ENST00000367669.3:c.430G>A	p.Glu144Lys	p.E144K	ENST00000367669	NM_022457.5	144	Gaa/Aaa	2/20	0.425078174125141	3	FACETS	1	0.973	1	0.68	0.602	0.762	CLONAL	1	TRUE	1	0.425078174125141	3		80	323	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690810	89690810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025699-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	46	64	0	ENST00000371953.3:c.217G>A	p.Glu73Lys	p.E73K	ENST00000371953	NM_000314.4	73	Gaa/Aaa	4/9	1	2	FACETS	0.958	0.815	1	0.958	0.815	1	CLONAL	1	TRUE	1	0.425078174125141	2		64	226	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602532	10602532	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1237235830	NA	P-0025699-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	101	161	0	ENST00000171111.5:c.1046A>G	p.Asp349Gly	p.D349G	ENST00000171111	NM_203500.1	349	gAc/gGc	3/6	1	2	FACETS	0.866	0.776	0.96	0.866	0.776	0.96	CLONAL	1	TRUE	1	0.425078174125141	2		161	549	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531867	41531867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025699-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	190	130	0	ENST00000263253.7:c.1579C>T	p.Leu527Phe	p.L527F	ENST00000263253	NM_001429.3	527	Ctt/Ttt	7/31	0.425078174125141	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.425078174125141	2		130	374	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023387	27023387	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025699-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	56	68	0	ENST00000324856.7:c.493G>A	p.Ala165Thr	p.A165T	ENST00000324856	NM_006015.4	165	Gcg/Acg	1/20	0.425078174125141	2	FACETS	0.724	0.623	0.833	0.362	0.311	0.417	SUBCLONAL	1	TRUE	0	0.425078174125141	2		68	364	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555728	21555731	+	frameshift_variant	Frame_Shift_Del	DEL	AGTT	AGTT	-	novel	NA	P-0025731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	111	489	0	ENST00000382592.4:c.2539_2542del	p.Asn847ValfsTer7	p.N847Vfs*7	ENST00000382592	NM_014572.2	847	AACTgt/gt	6/8	0.349767090333265	1	FACETS	0.882	0.795	0.973	0.882	0.795	0.973	CLONAL	1	TRUE	0	0.349767090333265	1		489	594	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115279454	115279454	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	15	269	0	ENST00000438362.2:c.563C>A	p.Thr188Asn	p.T188N	ENST00000438362	NM_001242891.1	188	aCc/aAc	6/20	0.227437223566051	1	FACETS	0.207	0.151	0.274	0.207	0.151	0.274	INDETERMINATE	1	TRUE	0	0.50947688210096	1		269	212	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654775	29654776	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1555533628	NA	P-0025737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	79	217	0	ENST00000356175.3:c.5466dup	p.Lys1823GlnfsTer18	p.K1823Qfs*18	ENST00000356175	NM_000267.3	1822	acc/aCcc	37/57	0.379403334797586	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.50947688210096	1		217	212	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0025772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	20	505	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.285	0.218	0.363	0.285	0.218	0.363	SUBCLONAL	1	TRUE	1	0.548913209180798	2		505	256	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0025772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	89	101	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.548913209180798	2		101	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0025772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	285	582	3	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.548913209180798	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.548913209180798	1		585	648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0025772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	45	559	0	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	0.548913209180798	1	FACETS	0.255	0.214	0.3	0.255	0.214	0.3	SUBCLONAL	1	TRUE	0	0.548913209180798	1		559	466	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604665	48604665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660045	NA	P-0025772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	24	112	0	ENST00000342988.3:c.1487G>A	p.Arg496His	p.R496H	ENST00000342988	NM_005359.5	496	cGt/cAt	12/12	0.548913209180798	1	FACETS	0.257	0.202	0.32	0.257	0.202	0.32	SUBCLONAL	1	TRUE	0	0.548913209180798	1		112	247	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591901	48591901	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	77	96	0	ENST00000342988.3:c.1064A>T	p.Asp355Val	p.D355V	ENST00000342988	NM_005359.5	355	gAc/gTc	9/12	0.548913209180798	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.548913209180798	1		96	178	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214022	36214022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	425	454	0	ENST00000222270.7:c.2848C>T	p.Arg950Trp	p.R950W	ENST00000222270	NM_014727.1	950	Cgg/Tgg	6/37	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.548913209180798	2		454	1260	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474619	138474619	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	90	86	0	ENST00000289153.2:c.374A>C	p.Lys125Thr	p.K125T	ENST00000289153	NM_006219.2	125	aAa/aCa	2/22	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.548913209180798	2		86	225	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519454	176519454	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	336	425	0	ENST00000292408.4:c.860T>C	p.Ile287Thr	p.I287T	ENST00000292408	NM_213647.1	287	aTc/aCc	7/18	1	2	FACETS	0.959	0.907	1	0.959	0.907	1	CLONAL	1	TRUE	1	0.548913209180798	2		425	1276	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594258	55594258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913523	NA	P-0025989-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	100	558	0	ENST00000288135.5:c.1961T>C	p.Val654Ala	p.V654A	ENST00000288135	NM_000222.2	654	gTg/gCg	13/21	1	2	FACETS	0.26	0.232	0.29	0.26	0.232	0.29	SUBCLONAL	1	TRUE	1	0.906769216383208	2		558	848	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578237	7578237	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025989-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	564	843	1	ENST00000269305.4:c.612G>C	p.Glu204Asp	p.E204D	ENST00000269305	NM_001126112.2	204	gaG/gaC	6/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.906769216383208	2		844	1213	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593594	55593647	+	inframe_deletion	In_Frame_Del	DEL	GAAGTACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATA	GAAGTACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATA	-	novel	NA	P-0025989-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	276	495	0	ENST00000288135.5:c.1662_1715del	p.Glu554_Ile571del	p.E554_I571del	ENST00000288135	NM_000222.2	554	GAAGTACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATA/-	11/21	1	2	FACETS	0.985	0.933	1	0.985	0.933	1	CLONAL	1	TRUE	1	0.906769216383208	2		495	618	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	318	395	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.94	0.893	0.987	0.94	0.893	0.987	CLONAL	1	TRUE	1	0.932196343142234	2		395	726	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197011	123197011	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	293	238	0	ENST00000218089.9:c.1777C>G	p.Gln593Glu	p.Q593E	ENST00000218089	NM_001042749.1	593	Cag/Gag	19/35	NA	2	FACETS	0.978	0.928	1			1	INDETERMINATE	1	TRUE	NA	0.932196343142234	2		238	643	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653781	89653781	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs786204914	NA	P-0026048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	143	145	0	ENST00000371953.3:c.80-1G>C		p.X27_splice	ENST00000371953	NM_000314.4	27			0.932196343142234	1	FACETS	0.91	0.867	0.949	0.91	0.867	0.949	CLONAL	1	TRUE	0	0.932196343142234	1		145	180	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378630	25378630	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	234	248	0	ENST00000311936.3:c.368G>T	p.Arg123Ile	p.R123I	ENST00000311936	NM_004985.3	123	aGa/aTa	4/5	1	2	FACETS	0.913	0.859	0.967	0.913	0.859	0.967	CLONAL	1	TRUE	1	0.932196343142234	2		248	550	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922825	44922838	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTGGGCAGCCTT	CCCTGGGCAGCCTT	-	novel	NA	P-0026048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	324	210	1	ENST00000377967.4:c.1686_1699del	p.Pro563GlyfsTer13	p.P563Gfs*13	ENST00000377967	NM_021140.2	562	tgCCCTGGGCAGCCTTtg/tgtg	16/29	0.932196343142234	1	FACETS	0.987	0.962	1	0.987	0.962	1	CLONAL	1	TRUE	0	0.932196343142234	1		211	376	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0026050-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	11311	691	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.796334402916591	26	FACETS	1	0.999	1			1	CLONAL	25	TRUE	NA	0.796334402916591	26		691	11879	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850801	63850801	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026050-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	189	503	0	ENST00000279873.7:c.1579G>T	p.Glu527Ter	p.E527*	ENST00000279873	NM_032199.2	527	Gag/Tag	10/10	0.785807622610662	4	FACETS	1	0.983	1	0.301	0.279	0.324	CLONAL	1	TRUE	0	0.796334402916591	4		503	708	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914526	32914526	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026050-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	421	608	0	ENST00000380152.3:c.6034T>C	p.Ser2012Pro	p.S2012P	ENST00000380152		2012	Tcc/Ccc	11/27	0.267062917760359	6	FACETS	1	0.992	1	0.856	0.821	0.89	INDETERMINATE	3	TRUE	2	0.796334402916591	6		608	801	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040903	42040903	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026050-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	659	632	2	ENST00000219905.7:c.5281C>T	p.Arg1761Ter	p.R1761*	ENST00000219905	NM_001164273.1	1761	Cga/Tga	16/24	0.796334402916591	3	FACETS	0.929	0.909	0.949	0.929	0.909	0.949	CLONAL	3	TRUE	0	0.796334402916591	3		634	830	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781345	3781345	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026050-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	656	913	1	ENST00000262367.5:c.5020A>G	p.Lys1674Glu	p.K1674E	ENST00000262367	NM_004380.2	1674	Aag/Gag	30/31	0.796334402916591	5	FACETS	0.99	0.953	1	0.66	0.635	0.685	CLONAL	2	TRUE	2	0.796334402916591	5		914	1826	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579585	7579585	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026050-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	991	632	1	ENST00000269305.4:c.102del	p.Leu35CysfsTer9	p.L35Cfs*9	ENST00000269305	NM_001126112.2	34	ccC/cc	4/11	0.796334402916591	4	FACETS	0.952	0.937	0.966			1	CLONAL	4	TRUE	NA	0.796334402916591	4		633	1174	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265138	5265138	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026050-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	1031	963	1	ENST00000357368.4:c.449G>T	p.Arg150Leu	p.R150L	ENST00000357368	NM_002850.3	150	cGg/cTg	5/38	0.770505127490926	4	FACETS	0.934	0.919	0.948	0.934	0.919	0.948	CLONAL	4	TRUE	0	0.796334402916591	4		964	1245	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391196	89391196	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs144998277	NA	P-0026050-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	316	492	0	ENST00000336596.2:c.1262C>A	p.Pro421Gln	p.P421Q	ENST00000336596	NM_005233.5	421	cCa/cAa	5/17	0.72942101774506	4	FACETS	0.907	0.86	0.954	0.907	0.86	0.954	CLONAL	2	TRUE	2	0.796334402916591	4		492	786	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607157	189607157	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026050-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1216	304	754	0	ENST00000264731.3:c.1536G>A	p.Met512Ile	p.M512I	ENST00000264731	NM_003722.4	512	atG/atA	12/14	0.776920757137516	5	FACETS	1	0.981	1	0.276	0.259	0.293	CLONAL	1	TRUE	1	0.796334402916591	5		754	1520	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512360	149512361	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0026050-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	410	764	1	ENST00000261799.4:c.1079_1080delinsAA	p.Ser360Ter	p.S360*	ENST00000261799	NM_002609.3	360	tCC/tAA	7/23	0.796334402916591	4	FACETS	1	0.993	1	0.587	0.563	0.611	CLONAL	2	TRUE	0	0.796334402916591	4		765	788	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878233	151878233	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs762198582	NA	P-0026050-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1243	621	634	0	ENST00000262189.6:c.6712A>G	p.Met2238Val	p.M2238V	ENST00000262189	NM_170606.2	2238	Atg/Gtg	36/59	0.796334402916591	8	FACETS	0.945	0.908	0.982			1	CLONAL	3	TRUE	NA	0.796334402916591	8		634	1864	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579584	7579585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0026633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	70	109	0	ENST00000269305.4:c.101_102dup	p.Leu35ProfsTer10	p.L35Pfs*10	ENST00000269305	NM_001126112.2	34	-/CC	4/11	0.159756260415641	1	FACETS	1	0.978	1	1	0.978	1	INDETERMINATE	1	TRUE	0	0.54	1		109	137	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10277306	10277306	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	125	280	2	ENST00000340748.4:c.811C>A	p.Gln271Lys	p.Q271K	ENST00000340748		271	Cag/Aag	10/40	0.282654066852099	1	FACETS	0.553	0.502	0.607	0.553	0.502	0.607	INDETERMINATE	1	TRUE	0	0.54	1		282	611	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729978	30729978	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	10	151	0	ENST00000295754.5:c.1499T>G	p.Ile500Ser	p.I500S	ENST00000295754	NM_003242.5	500	aTt/aGt	6/7	0.196485330412206	1	FACETS	0.145	0.098	0.203	0.145	0.098	0.203	INDETERMINATE	1	TRUE	0	0.54	1		151	187	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268796	41268796	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	17	59	0	ENST00000349496.5:c.1034A>G	p.Lys345Arg	p.K345R	ENST00000349496	NM_001904.3	345	aAg/aGg	7/15	0.196485330412206	1	FACETS	0.707	0.543	0.889	0.707	0.543	0.889	INDETERMINATE	1	TRUE	0	0.54	1		59	65	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934297	49934297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1487887311	NA	P-0026633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	187	17	0	ENST00000296474.3:c.2210C>T	p.Ala737Val	p.A737V	ENST00000296474	NM_002447.2	737	gCc/gTc	8/20	0.196485330412206	1	FACETS	1	0.981	1	1	0.981	1	INDETERMINATE	1	TRUE	0	0.54	1		17	446	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204693	128204693	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	77	208	0	ENST00000341105.2:c.748C>A	p.Pro250Thr	p.P250T	ENST00000341105	NM_032638.4	250	Ccc/Acc	3/6	0.196485330412206	1	FACETS	0.6	0.531	0.673	0.6	0.531	0.673	INDETERMINATE	1	TRUE	0	0.54	1		208	347	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868926	117868926	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	12	46	0	ENST00000297338.2:c.773A>T	p.Gln258Leu	p.Q258L	ENST00000297338	NM_006265.2	258	cAg/cTg	7/14	NA	2	FACETS	0.577	0.412	0.773			1	INDETERMINATE	1	TRUE	NA	0.54	2		46	77	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123499639	123499639	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	15	54	0	ENST00000371139.4:c.166G>T	p.Val56Leu	p.V56L	ENST00000371139	NM_001114937.2	56	Gtg/Ttg	2/4	1	1	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	0	0.54	1		54	30	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576899	7576900	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	304	222	0	ENST00000269305.4:c.946_947insT	p.Pro316LeufsTer21	p.P316Lfs*21	ENST00000269305	NM_001126112.2	316	ccc/cTcc	9/11	0.597894083030205	1	FACETS	0.97	0.92	1	0.97	0.92	1	CLONAL	1	TRUE	0	0.597894083030205	1		222	735	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112603	2112603	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs397515301	NA	P-0026636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	386	366	0	ENST00000219476.3:c.1361+2T>C		p.X454_splice	ENST00000219476	NM_000548.3	454			0.597894083030205	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.597894083030205	1		366	828	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221613	36221613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1736	253	490	1	ENST00000222270.7:c.5282C>T	p.Ser1761Phe	p.S1761F	ENST00000222270	NM_014727.1	1761	tCc/tTc	26/37	0.386801504584261	3	FACETS	0.553	0.515	0.592	0.276	0.257	0.296	SUBCLONAL	1	TRUE	1	0.597894083030205	3		491	1989	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021283	31021283	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886041975	NA	P-0026636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	354	278	2	ENST00000375687.4:c.1282C>T	p.Gln428Ter	p.Q428*	ENST00000375687	NM_015338.5	428	Cag/Tag	12/13	0.591347963324823	3	FACETS	1	0.984	1	0.549	0.519	0.58	CLONAL	1	TRUE	1	0.597894083030205	3		280	1400	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0026720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1162	280	665	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.242371056069608	2	FACETS	1	0.98	1	0.553	0.519	0.589	CLONAL	1	TRUE	0	0.350852022969496	2		665	1442	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254819	16254819	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	115	413	0	ENST00000375759.3:c.2084A>G	p.Tyr695Cys	p.Y695C	ENST00000375759	NM_015001.2	695	tAt/tGt	11/15	1	2	FACETS	0.785	0.707	0.868	0.785	0.707	0.868	SUBCLONAL	1	TRUE	1	0.350852022969496	2		413	835	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165701	108165701	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	63	201	0	ENST00000278616.4:c.4824G>T	p.Leu1608Phe	p.L1608F	ENST00000278616	NM_000051.3	1608	ttG/ttT	32/63	0.154293883746118	2	FACETS	0.958	0.832	1	0.479	0.416	0.546	INDETERMINATE	1	TRUE	0	0.350852022969496	2		201	375	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127723	2127723	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763047420	NA	P-0026720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	45	297	1	ENST00000219476.3:c.2962C>T	p.Arg988Cys	p.R988C	ENST00000219476	NM_000548.3	988	Cgc/Tgc	26/42	1	2	FACETS	0.379	0.318	0.448	0.379	0.318	0.448	SUBCLONAL	1	TRUE	1	0.350852022969496	2		298	676	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435170	56435171	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0026720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	201	348	0	ENST00000407977.2:c.1966dup	p.Arg656LysfsTer91	p.R656Kfs*91	ENST00000407977		656	agg/aAgg	9/10	0.242371056069608	2	FACETS	1	0.989	1	0.684	0.634	0.734	CLONAL	1	TRUE	0	0.350852022969496	2		348	838	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795213	42795213	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	72	448	1	ENST00000575354.2:c.2293G>T	p.Val765Leu	p.V765L	ENST00000575354	NM_015125.3	765	Gtg/Ttg	10/20	1	2	FACETS	0.402	0.35	0.459	0.402	0.35	0.459	SUBCLONAL	1	TRUE	1	0.350852022969496	2		449	1020	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867449	35867449	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	72	170	1	ENST00000303115.3:c.263T>A	p.Leu88Gln	p.L88Q	ENST00000303115	NM_002185.3	88	cTa/cAa	3/8	0.278305580638328	2	FACETS	0.996	0.874	1	0.498	0.437	0.563	CLONAL	1	TRUE	0	0.350852022969496	2		171	412	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511254	157511254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747374301	NA	P-0026720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	60	372	2	ENST00000346085.5:c.3772G>A	p.Ala1258Thr	p.A1258T	ENST00000346085	NM_020732.3	1258	Gcc/Acc	15/20	NA	2	FACETS	0.409	0.351	0.472			1	INDETERMINATE	1	TRUE	NA	0.350852022969496	2		374	837	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0027045-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	105	374	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.675472756981829	2		374	299	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577527	7577531	+	frameshift_variant	Frame_Shift_Del	DEL	GGATG	GGATG	-	novel	NA	P-0027045-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	314	686	0	ENST00000269305.4:c.750_754del	p.Ile251HisfsTer11	p.I251Hfs*11	ENST00000269305	NM_001126112.2	250	ccCATCCtc/cctc	7/11	0.675472756981829	2	FACETS	0.995	0.957	1	0.995	0.957	1	CLONAL	2	TRUE	0	0.675472756981829	2		686	467	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677209	29677210	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0027045-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	183	291	0	ENST00000356175.3:c.7268_7269del	p.Thr2423SerfsTer3	p.T2423Sfs*3	ENST00000356175	NM_000267.3	2423	ACa/a	49/57	0.675472756981829	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.675472756981829	2		291	261	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509665	106509665	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027045-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	135	612	1	ENST00000359195.3:c.1659G>T	p.Lys553Asn	p.K553N	ENST00000359195	NM_002649.2	553	aaG/aaT	2/11	1	2	FACETS	0.954	0.875	1	0.954	0.875	1	CLONAL	1	TRUE	1	0.675472756981829	2		613	419	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90996768	90996768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	134	235	0	ENST00000265433.3:c.22G>A	p.Ala8Thr	p.A8T	ENST00000265433	NM_002485.4	8	Gcg/Acg	1/16	0.662493477726029	7	FACETS	1	0.969	1	0.23	0.209	0.253	CLONAL	1	TRUE	2	0.662493477726029	7		235	934	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732969	30732969	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	105	241	0	ENST00000295754.5:c.1582C>G	p.Arg528Gly	p.R528G	ENST00000295754	NM_003242.5	528	Cgt/Ggt	7/7	0.366860969087813	3	FACETS	1	0.969	1	0.588	0.532	0.646	INDETERMINATE	1	TRUE	1	0.662493477726029	3		241	359	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416200	29416200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	41	324	0	ENST00000389048.3:c.4753G>A	p.Gly1585Ser	p.G1585S	ENST00000389048	NM_004304.4	1585	Ggc/Agc	29/29	0.19480632260784	5	FACETS	0.471	0.392	0.559			1	INDETERMINATE	1	TRUE	NA	0.662493477726029	5		324	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs1202793339	NA	P-0027125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	326	305	0	ENST00000269305.4:c.560-1G>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.662493477726029	2		305	434	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205831	108205831	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	64	160	0	ENST00000278616.4:c.8146G>C	p.Val2716Leu	p.V2716L	ENST00000278616	NM_000051.3	2716	Gtt/Ctt	55/63	0.662493477726029	3	FACETS	0.623	0.541	0.711	0.311	0.27	0.356	SUBCLONAL	1	TRUE	1	0.662493477726029	3		160	413	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998910	11998910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444656785	NA	P-0027125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	82	111	0	ENST00000353533.5:c.412G>A	p.Asp138Asn	p.D138N	ENST00000353533	NM_003010.3	138	Gat/Aat	4/11	0.662493477726029	5	FACETS	0.783	0.691	0.882			1	SUBCLONAL	1	TRUE	NA	0.662493477726029	5		111	630	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867693	45867693	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	163	496	0	ENST00000391945.4:c.707C>T	p.Ala236Val	p.A236V	ENST00000391945	NM_000400.3	236	gCc/gTc	8/23	0.662493477726029	4	FACETS	0.794	0.728	0.863	0.265	0.242	0.288	SUBCLONAL	1	TRUE	1	0.662493477726029	4		496	1030	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576554	67576554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	182	118	0	ENST00000274335.5:c.833C>T	p.Ala278Val	p.A278V	ENST00000274335		278	gCc/gTc	5/15	0.662493477726029	3	FACETS	0.757	0.705	0.81	0.757	0.705	0.81	SUBCLONAL	2	TRUE	1	0.662493477726029	3		118	483	SUCCESS
APC	324	MSKCC	GRCh37	5	112178934	112178934	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	108	179	0	ENST00000257430.4:c.7643A>T	p.Lys2548Ile	p.K2548I	ENST00000257430	NM_000038.5	2548	aAa/aTa	16/16	0.662493477726029	4	FACETS	1	0.915	1	0.508	0.458	0.562	CLONAL	1	TRUE	2	0.662493477726029	4		179	533	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0027140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	218	505	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.764	0.715	0.813	1	0.993	1	SUBCLONAL	2	TRUE	1	0.476632795848448	2		505	599	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412095	63412095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852217	NA	P-0027140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	347	182	1	ENST00000330258.3:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000330258	NM_152424.3	358	Cga/Tga	2/2	0.214597355465199	2	FACETS	0.928	0.893	0.962			1	INDETERMINATE	3	TRUE	NA	0.476632795848448	2		183	523	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0027140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	136	285	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.476632795848448	2		285	479	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0027140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	111	226	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	0.476632795848448	2		226	403	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029453	16029454	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0027140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	213	334	2	ENST00000268712.3:c.1576_1577del	p.Glu526LysfsTer9	p.E526Kfs*9	ENST00000268712	NM_006311.3	526	GAa/a	15/46	1	2	FACETS	0.769	0.72	0.819	1	0.992	1	SUBCLONAL	2	TRUE	1	0.476632795848448	2		336	581	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729743	162729743	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	221	248	1	ENST00000367921.3:c.829C>T	p.Arg277Cys	p.R277C	ENST00000367921	NM_006182.2	277	Cgc/Tgc	8/18	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.476632795848448	2		249	663	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118990	70118990	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	379	339	0	ENST00000245479.2:c.562G>T	p.Glu188Ter	p.E188*	ENST00000245479	NM_000346.3	188	Gag/Tag	2/3	1	2	FACETS	0.761	0.724	0.798	1	0.995	1	SUBCLONAL	2	TRUE	1	0.476632795848448	2		339	1045	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953237	81953237	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs963117904	NA	P-0027140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	155	214	0	ENST00000359376.3:c.2203G>A	p.Val735Met	p.V735M	ENST00000359376	NM_002661.3	735	Gtg/Atg	20/33	0.124234814350917	4	FACETS	1	0.927	1	1	0.927	1	INDETERMINATE	2	TRUE	2	0.476632795848448	4		214	478	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784902	9784902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs551657853	NA	P-0027140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	331	331	0	ENST00000377346.4:c.2905C>T	p.Arg969Cys	p.R969C	ENST00000377346	NM_005026.3	969	Cgc/Tgc	23/24	1	2	FACETS	0.76	0.72	0.8	1	0.995	1	SUBCLONAL	2	TRUE	1	0.476632795848448	2		331	914	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711316	114711317	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0027140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	247	387	0	ENST00000543371.1:c.332_333dup	p.Thr112Ter	p.T112*	ENST00000543371	NM_001198531.1	111	ctg/cTGtg	3/14	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.476632795848448	2		387	693	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288380	21288380	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	234	366	0	ENST00000354336.3:c.625C>T	p.Gln209Ter	p.Q209*	ENST00000354336	NM_005207.3	209	Caa/Taa	2/3	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.476632795848448	2		366	760	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49399991	49399991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	246	338	2	ENST00000418115.1:c.346G>A	p.Gly116Arg	p.G116R	ENST00000418115	NM_001664.2	116	Ggg/Agg	4/5	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.476632795848448	2		340	725	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750435	57750435	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1326371047	NA	P-0027140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	143	248	0	ENST00000274289.3:c.2033A>G	p.Asn678Ser	p.N678S	ENST00000274289	NM_006622.3	678	aAc/aGc	14/14	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.476632795848448	2		248	470	SUCCESS
APC	324	MSKCC	GRCh37	5	112174386	112174386	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	62	121	1	ENST00000257430.4:c.3095C>A	p.Ser1032Ter	p.S1032*	ENST00000257430	NM_000038.5	1032	tCa/tAa	16/16	1	2	FACETS	0.761	0.671	0.853	1	0.975	1	SUBCLONAL	2	TRUE	1	0.476632795848448	2		122	171	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739816	41739816	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	187	190	0	ENST00000242208.4:c.157G>A	p.Glu53Lys	p.E53K	ENST00000242208	NM_002192.2	53	Gag/Aag	2/3	0.476632795848448	4	FACETS	1	0.989	1	0.466	0.431	0.502	CLONAL	1	TRUE	1	0.476632795848448	4		190	829	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372278	55372278	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1379606008	NA	P-0027140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	304	206	0	ENST00000297316.4:c.968A>G	p.His323Arg	p.H323R	ENST00000297316	NM_022454.3	323	cAc/cGc	2/2	0.188606363262195	5	FACETS	0.891	0.844	0.94	0.891	0.844	0.94	INDETERMINATE	3	TRUE	2	0.476632795848448	5		206	818	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0027253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	681	937	1	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	0.563096836534475	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.570285278571225	3		938	987	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346198	70346198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	262	182	0	ENST00000374080.3:c.2549G>A	p.Arg850Gln	p.R850Q	ENST00000374080		850	cGg/cAg	19/45	0.406215109931226	2	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.570285278571225	2		182	392	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409016	139409016	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	710	415	0	ENST00000277541.6:c.2153A>G	p.Asn718Ser	p.N718S	ENST00000277541	NM_017617.3	718	aAt/aGt	13/34	0.511953344185209	3	FACETS	0.971	0.945	0.997	0.971	0.945	0.997	CLONAL	3	TRUE	0	0.570285278571225	3		415	1098	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73350221	73350221	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	28	102	0	ENST00000377767.4:c.664G>A	p.Glu222Lys	p.E222K	ENST00000377767	NM_014953.3	222	Gaa/Aaa	5/21	0.458618621976967	1	FACETS	0.949	0.786	1	0.949	0.786	1	CLONAL	1	TRUE	0	0.570285278571225	1		102	74	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	364646	364647	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	377	389	1	ENST00000262320.3:c.915dup	p.Val306CysfsTer45	p.V306Cfs*45	ENST00000262320	NM_003502.3	305	-/T	3/11	0.484438830089521	4	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	2	0.570285278571225	4		390	1037	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640561	3640561	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	212	401	0	ENST00000294008.3:c.3078G>T	p.Gln1026His	p.Q1026H	ENST00000294008	NM_032444.2	1026	caG/caT	12/15	0.484438830089521	4	FACETS	0.906	0.84	0.974	0.453	0.42	0.487	CLONAL	1	TRUE	2	0.570285278571225	4		401	1289	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566424	41566424	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	162	100	0	ENST00000263253.7:c.4301A>T	p.His1434Leu	p.H1434L	ENST00000263253	NM_001429.3	1434	cAt/cTt	27/31	0.51267084448902	5	FACETS	1	0.975	1			1	CLONAL	2	TRUE	NA	0.570285278571225	5		100	469	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709496	176709497	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	98	157	0	ENST00000439151.2:c.5925dup	p.Ile1976TyrfsTer3	p.I1976Yfs*3	ENST00000439151	NM_022455.4	1975	ctt/cTtt	19/23	0.515111679593416	2	FACETS	1	0.98	1	0.671	0.609	0.735	CLONAL	1	TRUE	0	0.570285278571225	2		157	256	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0027349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	686	683	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.55932141770741	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.55932141770741	2		683	1106	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246009	46246009	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	42	130	1	ENST00000334344.6:c.4103A>T	p.Asp1368Val	p.D1368V	ENST00000334344	NM_152641.2	1368	gAt/gTt	15/21	0.509306272370411	4	FACETS	0.714	0.598	0.841			1	SUBCLONAL	1	TRUE	NA	0.55932141770741	4		131	328	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309742	30309742	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	357	174	0	ENST00000307677.4:c.280G>C	p.Gly94Arg	p.G94R	ENST00000307677	NM_138578.1	94	Ggc/Cgc	2/3	0.55932141770741	3	FACETS	1	0.995	1	0.748	0.71	0.787	CLONAL	1	TRUE	1	0.55932141770741	3		174	1092	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902422	1902422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	171	532	0	ENST00000382891.5:c.41G>A	p.Ser14Asn	p.S14N	ENST00000382891	NM_133335.3	14	aGt/aAt	2/22	0.55932141770741	2	FACETS	0.746	0.687	0.807	0.373	0.343	0.404	SUBCLONAL	1	TRUE	0	0.55932141770741	2		532	820	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521050	187521050	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0027349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	91	190	2	ENST00000441802.2:c.12103+2T>A		p.X4035_splice	ENST00000441802	NM_005245.3	4035			0.55932141770741	1	FACETS	0.862	0.776	0.95	0.862	0.776	0.95	CLONAL	1	TRUE	0	0.55932141770741	1		192	272	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285524	38285524	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	231	545	0	ENST00000425967.3:c.629C>A	p.Pro210His	p.P210H	ENST00000425967	NM_001174067.1	210	cCt/cAt	6/19	0.55932141770741	3	FACETS	0.917	0.854	0.982	0.458	0.427	0.491	CLONAL	1	TRUE	1	0.55932141770741	3		545	1153	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341235	8341235	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	44	125	0	ENST00000356435.5:c.4981T>A	p.Phe1661Ile	p.F1661I	ENST00000356435		1661	Ttt/Att	30/35	0.55932141770741	3	FACETS	0.709	0.598	0.83	0.354	0.299	0.415	SUBCLONAL	1	TRUE	1	0.55932141770741	3		125	284	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417483	139417483	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	1079	797	2	ENST00000277541.6:c.561del	p.Leu188PhefsTer89	p.L188Ffs*89	ENST00000277541	NM_017617.3	187	ggG/gg	4/34	0.55932141770741	3	FACETS	0.936	0.914	0.957	0.936	0.914	0.957	CLONAL	3	TRUE	0	0.55932141770741	3		799	1759	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613381	100613381	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	171	192	0	ENST00000308731.7:c.1019C>T	p.Pro340Leu	p.P340L	ENST00000308731	NM_000061.2	340	cCt/cTt	12/19	0.55932141770741	3	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.55932141770741	3		192	646	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900339	3900340	+	frameshift_variant	Frame_Shift_Ins	INS	GA	GA	CCCC	novel	NA	P-0027349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	443	498	1	ENST00000262367.5:c.756_757delinsGGGG	p.His253GlyfsTer5	p.H253Gfs*5	ENST00000262367	NM_004380.2	252	ggTCac/ggGGGGac	2/31	0.55932141770741	2	FACETS	0.965	0.928	1	0.965	0.928	1	CLONAL	2	TRUE	0	0.55932141770741	2		499	821	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0027355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	33	94	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.844	0.697	1	0.844	0.697	1	CLONAL	1	TRUE	1	0.49506866326162	2		94	158	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0027355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	220	621	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.49506866326162	1	FACETS	0.869	0.811	0.928	0.869	0.811	0.928	CLONAL	1	TRUE	0	0.49506866326162	1		622	770	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0027355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	33	40	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.49506866326162	2	FACETS	0.939	0.799	1	0.939	0.799	1	CLONAL	2	TRUE	0	0.49506866326162	2		40	71	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714176	43714176	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	189	470	2	ENST00000382044.4:c.3977T>A	p.Leu1326His	p.L1326H	ENST00000382044	NM_001141980.1	1326	cTc/cAc	19/28	1	2	FACETS	0.84	0.777	0.906	0.84	0.777	0.906	CLONAL	1	TRUE	1	0.49506866326162	2		472	909	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573537	48573537	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	20	55	0	ENST00000342988.3:c.121G>T	p.Glu41Ter	p.E41*	ENST00000342988	NM_005359.5	41	Gaa/Taa	2/12	0.49506866326162	1	FACETS	0.59	0.459	0.738	0.59	0.459	0.738	SUBCLONAL	1	TRUE	0	0.49506866326162	1		55	103	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575677	48575677	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs377767329	NA	P-0027355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	10	86	0	ENST00000342988.3:c.437T>G	p.Leu146Ter	p.L146*	ENST00000342988	NM_005359.5	146	tTa/tGa	4/12	0.49506866326162	1	FACETS	0.195	0.132	0.273	0.195	0.132	0.273	SUBCLONAL	1	TRUE	0	0.49506866326162	1		86	156	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968235	2968235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1188731718	NA	P-0027355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	307	639	1	ENST00000396946.4:c.1751G>A	p.Arg584His	p.R584H	ENST00000396946	NM_032415.4	584	cGc/cAc	13/25	0.166463659485414	3	FACETS	1	0.985	1	0.567	0.533	0.601	INDETERMINATE	1	TRUE	1	0.49506866326162	3		640	1365	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	111	63	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.704	0.637	0.775	0.704	0.637	0.775	SUBCLONAL	1	TRUE	1	0.697304985944346	2		63	452	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0027356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	288	210	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	2	TRUE	NA	0.697304985944346	2		210	407	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	800	615	1	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.672159804932349	2	FACETS	0.961	0.937	0.984	0.961	0.937	0.984	CLONAL	2	TRUE	0	0.697304985944346	2		616	1194	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970914	79970915	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587776701	NA	P-0027356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	203	477	5	ENST00000265081.6:c.1148dup	p.Asn385GlnfsTer19	p.N385Qfs*19	ENST00000265081	NM_002439.4	380	-/A	7/24	NA	2	FACETS	0.705	0.655	0.757			1	INDETERMINATE	1	TRUE	NA	0.697304985944346	2		482	826	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459183	120459183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	457	435	2	ENST00000256646.2:c.6162G>A	p.Met2054Ile	p.M2054I	ENST00000256646	NM_024408.3	2054	atG/atA	34/34	0.697304985944346	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.697304985944346	1		437	754	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120616	115120616	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0027356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	432	697	1	ENST00000257566.3:c.389+1G>A		p.X130_splice	ENST00000257566	NM_016569.3	130			1	2	FACETS	0.958	0.913	1	0.958	0.913	1	CLONAL	1	TRUE	1	0.697304985944346	2		698	1294	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275750	41275750	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1210247690	NA	P-0027356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	329	435	0	ENST00000349496.5:c.1645C>T	p.Arg549Cys	p.R549C	ENST00000349496	NM_001904.3	549	Cgc/Tgc	10/15	1	2	FACETS	0.894	0.845	0.943	0.894	0.845	0.943	CLONAL	1	TRUE	1	0.697304985944346	2		435	1056	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	143	63	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.826	0.752	0.904	0.826	0.752	0.904	CLONAL	1	TRUE	1	0.33998204053494	2		63	1018	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971101	21971101	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	109	266	3	ENST00000579755.1:c.300C>A	p.Cys100Ter	p.C100*	ENST00000579755		100	tgC/tgA	2/3	0.33998204053494	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.33998204053494	1		269	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057520000	NA	P-0027407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	297	587	0	ENST00000269305.4:c.452C>G	p.Pro151Arg	p.P151R	ENST00000269305	NM_001126112.2	151	cCc/cGc	5/11	0.33998204053494	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.33998204053494	1		587	1146	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779220	3779220	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780545388	NA	P-0027407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	116	223	3	ENST00000262367.5:c.5828C>T	p.Pro1943Leu	p.P1943L	ENST00000262367	NM_004380.2	1943	cCg/cTg	31/31	1	2	FACETS	0.753	0.683	0.826	1	0.985	1	SUBCLONAL	2	TRUE	1	0.33998204053494	2		226	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027813-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	154	551	0	ENST00000269305.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	336	Gag/Tag	10/11	0.298955859655591	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.33	1		551	595	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155365	47155365	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0027813-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	73	357	0	ENST00000409792.3:c.4715+1G>T		p.X1572_splice	ENST00000409792	NM_014159.6	1572			0.304800314721067	1	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	0	0.33	1		357	366	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089776	27089777	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	TT	novel	NA	P-0027813-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	72	455	1	ENST00000324856.7:c.2732_2732+1delinsTT		p.X911_splice	ENST00000324856	NM_006015.4	911		8/20	0.304800314721067	1	FACETS	0.804	0.705	0.911	0.804	0.705	0.911	CLONAL	1	TRUE	0	0.33	1		456	453	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109730	115109731	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0027813-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	125	687	0	ENST00000257566.3:c.2147dup	p.Ala717GlyfsTer13	p.A717Gfs*13	ENST00000257566	NM_016569.3	716	gcg/gcCg	8/8	0.208526297704999	1	FACETS	0.861	0.78	0.946	0.861	0.78	0.946	CLONAL	1	TRUE	0	0.33	1		687	735	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609769	28609769	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027813-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	103	572	0	ENST00000241453.7:c.1460C>A	p.Ala487Asp	p.A487D	ENST00000241453	NM_004119.2	487	gCt/gAt	12/24	0.215496769209767	3	FACETS	1	0.944	1	0.54	0.484	0.6	CLONAL	1	TRUE	1	0.33	3		572	673	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032207	10032207	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027813-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	67	630	2	ENST00000330684.3:c.616C>A	p.Leu206Met	p.L206M	ENST00000330684	NM_001134407.1	206	Ctg/Atg	3/13	1	2	FACETS	0.527	0.457	0.603	0.527	0.457	0.603	SUBCLONAL	1	TRUE	1	0.33	2		632	771	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129968	55129968	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027813-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	113	515	0	ENST00000257290.5:c.502G>T	p.Val168Leu	p.V168L	ENST00000257290	NM_006206.4	168	Gta/Tta	4/23	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.33	2		515	660	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31939814	31939814	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027813-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	60	677	0	ENST00000375333.2:c.41A>G	p.Gln14Arg	p.Q14R	ENST00000375333	NM_032454.1	14	cAg/cGg	1/8	1	2	FACETS	0.515	0.443	0.594	0.515	0.443	0.594	SUBCLONAL	1	TRUE	1	0.33	2		677	706	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714627	52714627	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027813-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	58	605	0	ENST00000322088.6:c.385G>C	p.Val129Leu	p.V129L	ENST00000322088	NM_014225.5	129	Gtg/Ctg	4/15	0.208526297704999	1	FACETS	0.452	0.388	0.522	0.452	0.388	0.522	SUBCLONAL	1	TRUE	0	0.33	1		605	649	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	36	395	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.945	0.778	1	0.945	0.778	1	CLONAL	1	FALSE	1	0.208277544511271	2		395	366	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1555525367	NA	P-0027827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	53	279	0	ENST00000269305.4:c.783-1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.208277544511271	1	FACETS	0.706	0.601	0.821	0.706	0.601	0.821	SUBCLONAL	1	FALSE	0	0.208277544511271	1		279	646	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693003	89693003	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs786204900	NA	P-0027827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	28	196	1	ENST00000371953.3:c.491del	p.Lys164ArgfsTer3	p.K164Rfs*3	ENST00000371953	NM_000314.4	163	Aaa/aa	5/9	1	2	FACETS	0.745	0.595	0.915	0.745	0.595	0.915	CLONAL	1	FALSE	1	0.208277544511271	2		197	361	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770575	40770575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1294592345	NA	P-0027827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	100	272	0	ENST00000373198.4:c.2807G>A	p.Arg936Gln	p.R936Q	ENST00000373198	NM_133170.3	936	cGa/cAa	19/32	0.198973827743997	3	FACETS	0.775	0.693	0.862	0.775	0.693	0.862	SUBCLONAL	2	FALSE	1	0.208277544511271	3		272	684	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590761	95590761	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	43	168	0	ENST00000393063.1:c.1148T>A	p.Ile383Asn	p.I383N	ENST00000393063	NM_030621.3	383	aTc/aAc	9/28	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	1	0.208277544511271	2		168	342	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144076	11144077	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0027827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	78	308	3	ENST00000358026.2:c.3658_3659dup	p.Lys1221ThrfsTer9	p.K1221Tfs*9	ENST00000358026	NM_001128849.1	1219	-/TA	26/36	1	2	FACETS	0.818	0.717	0.926	0.818	0.717	0.926	CLONAL	1	FALSE	1	0.208277544511271	2		311	916	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0027870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	287	582	3	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	NA	2	FACETS	0.915	0.865	0.965			1	INDETERMINATE	2	TRUE	NA	0.417811306152046	2		585	751	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997802	149997803	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	TCCACATCGACAGCTTGAGGGATCCCCCCATTCATTACTGAAA	novel	NA	P-0027870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	58	378	0	ENST00000253339.5:c.2622_2664dup	p.Asp889PhefsTer3	p.D889Ffs*3	ENST00000253339		888	-/TTTCAGTAATGAATGGGGGGATCCCTCAAGCTGTCGATGTGGA	5/7	0.391631458431385	1	FACETS	0.393	0.337	0.453	0.393	0.337	0.453	SUBCLONAL	1	TRUE	0	0.417811306152046	1		378	559	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971145	21971159	+	inframe_deletion	In_Frame_Del	DEL	GTTGGGCTCCGCGCC	GTTGGGCTCCGCGCC	-	novel	NA	P-0027870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	348	56	0	ENST00000304494.5:c.199_213del	p.Gly67_Asn71del	p.G67_N71del	ENST00000304494	NM_000077.4	67	GGCGCGGAGCCCAAC/-	2/3	0.409490655914429	1	FACETS	0.961	0.917	1	1	0.996	1	CLONAL	2	TRUE	0	0.417811306152046	1		56	686	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0027872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	229	438	2	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.493220918853921	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.493220918853921	1		440	615	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424707	49424717	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCTGACCCC	GCCCTGACCCC	-	novel	NA	P-0027872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	185	400	0	ENST00000301067.7:c.13630_13640del	p.Gly4544GlnfsTer27	p.G4544Qfs*27	ENST00000301067	NM_003482.3	4544	GGGGTCAGGGCc/c	40/54	1	2	FACETS	0.952	0.881	1	0.952	0.881	1	CLONAL	1	TRUE	1	0.493220918853921	2		400	788	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239960	53239961	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	462	101	0	ENST00000375401.3:c.1480dup	p.Ile494AsnfsTer23	p.I494Nfs*23	ENST00000375401	NM_004187.3	494	atc/aAtc	11/26	0.29725692977422	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.493220918853921	1		101	1283	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891563	151891563	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	177	262	0	ENST00000262189.6:c.4469G>A	p.Gly1490Glu	p.G1490E	ENST00000262189	NM_170606.2	1490	gGg/gAg	29/59	1	2	FACETS	0.939	0.874	1	0.939	0.874	1	CLONAL	1	TRUE	1	0.828411396986587	2		262	455	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0028340-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	99	233	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.832	0.745	0.923	0.832	0.745	0.923	CLONAL	1	TRUE	1	0.451757646637502	2		235	527	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691922	30691922	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028340-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	261	367	0	ENST00000295754.5:c.424G>T	p.Glu142Ter	p.E142*	ENST00000295754	NM_003242.5	142	Gag/Tag	3/7	0.446023645776573	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.451757646637502	2		367	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028382-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	76	417	0	ENST00000269305.4:c.584del	p.Ile195ThrfsTer52	p.I195Tfs*52	ENST00000269305	NM_001126112.2	195	aTc/ac	6/11	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.19980502542648	2		417	679	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251913	153251913	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028382-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	66	311	0	ENST00000281708.4:c.1093T>C	p.Trp365Arg	p.W365R	ENST00000281708	NM_033632.3	365	Tgg/Cgg	7/12	0.19980502542648	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.19980502542648	1		311	501	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993149	72993149	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028382-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	82	550	0	ENST00000268489.5:c.896C>T	p.Thr299Ile	p.T299I	ENST00000268489	NM_006885.3	299	aCc/aTc	2/10	0.19980502542648	1	FACETS	0.865	0.762	0.976	0.865	0.762	0.976	CLONAL	1	TRUE	0	0.19980502542648	1		550	854	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317426	1317426	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028382-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	33	364	0	ENST00000400841.2:c.639G>C	p.Glu213Asp	p.E213D	ENST00000400841		213	gaG/gaC	5/6	1	1	FACETS	0.56	0.455	0.678	0.56	0.455	0.678	SUBCLONAL	1	TRUE	0	0.19980502542648	1		364	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0028415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	1074	621	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.663388009944075	3	FACETS	0.98	0.961	0.998	0.98	0.961	0.998	CLONAL	3	TRUE	0	0.683893387923929	3		622	1434	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306676	41306676	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754008236	NA	P-0028415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	614	518	6	ENST00000373198.4:c.983G>A	p.Arg328His	p.R328H	ENST00000373198	NM_133170.3	328	cGc/cAc	7/32	0.628348428961564	4	FACETS	0.936	0.901	0.972	0.936	0.901	0.972	CLONAL	2	TRUE	2	0.683893387923929	4		524	1615	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998127	169998128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs753143066	NA	P-0028415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	327	500	7	ENST00000295797.4:c.826dup	p.Thr276AsnfsTer16	p.T276Nfs*16	ENST00000295797	NM_002740.5	273	tta/ttAa	9/18	0.300430917277317	3	FACETS	1	0.982	1	0.544	0.514	0.575	INDETERMINATE	1	TRUE	1	0.683893387923929	3		507	1179	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913878	32913878	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	52	209	0	ENST00000380152.3:c.5386G>C	p.Asp1796His	p.D1796H	ENST00000380152		1796	Gat/Cat	11/27	0.683893387923929	3	FACETS	0.287	0.243	0.334	0.143	0.121	0.167	SUBCLONAL	1	TRUE	1	0.683893387923929	3		209	712	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89862408	89862408	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	349	495	1	ENST00000389301.3:c.912del	p.His305ThrfsTer6	p.H305Tfs*6	ENST00000389301	NM_000135.2	304	ggA/gg	11/43	0.682375333098057	2	FACETS	0.979	0.929	1	0.49	0.464	0.516	CLONAL	1	TRUE	0	0.683893387923929	2		496	1042	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388054	31388054	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs576798456	NA	P-0028415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	234	348	1	ENST00000328111.2:c.1855G>A	p.Glu619Lys	p.E619K	ENST00000328111	NM_006892.3	619	Gag/Aag	17/23	0.628348428961564	4	FACETS	1	0.952	1	0.513	0.478	0.549	CLONAL	1	TRUE	2	0.683893387923929	4		349	1123	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950724	79950725	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCGCAGCGC	rs1554066076	NA	P-0028416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	19	123	0	ENST00000265081.6:c.181_189dup	p.Ala61_Pro63dup	p.A61_P63dup	ENST00000265081	NM_002439.4	61	gcc/gCCGCAGCGCcc	1/24	1	2	FACETS	0.309	0.235	0.395	0.309	0.235	0.395	SUBCLONAL	1	FALSE	1	0.578121245319774	2		123	213	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321697	30321697	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	126	342	0	ENST00000322652.5:c.1552G>T	p.Gly518Ter	p.G518*	ENST00000322652	NM_015355.2	518	Gga/Tga	13/16	0.458475908191007	0	FACETS		NA	1			1	NA	2	FALSE	0	0.578121245319774	0		342	167	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0028417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	52	509	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	1	2	FACETS	0.452	0.384	0.528	0.452	0.384	0.528	SUBCLONAL	1	TRUE	1	0.27	2		509	852	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546721	9546721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	28	178	1	ENST00000353224.5:c.1301C>T	p.Ala434Val	p.A434V	ENST00000353224	NM_177990.2	434	gCg/gTg	5/10	0.239735822921719	3	FACETS	0.613	0.49	0.754	0.307	0.245	0.377	SUBCLONAL	1	TRUE	1	0.27	3		179	384	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286827	33286827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	101	235	0	ENST00000374542.5:c.2110G>A	p.Ala704Thr	p.A704T	ENST00000374542	NM_001141970.1	704	Gcc/Acc	7/8	1	2	FACETS	0.353	0.315	0.393	0.353	0.315	0.393	SUBCLONAL	1	TRUE	1	0.797329629310396	2		235	718	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165538	47165539	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGTGGAGGC	novel	NA	P-0028418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	118	237	0	ENST00000409792.3:c.579_587dup	p.Pro194_Pro196dup	p.P194_P196dup	ENST00000409792	NM_014159.6	194	cct/ccGCCTCCACCt	3/21	0.797329629310396	1	FACETS	0.748	0.69	0.806	0.748	0.69	0.806	SUBCLONAL	1	TRUE	0	0.797329629310396	1		237	238	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933546	36933546	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	67	565	0	ENST00000361632.4:c.1741T>A	p.Ser581Thr	p.S581T	ENST00000361632		581	Tcc/Acc	13/16	0.102739580527076	3	FACETS	0.39	0.338	0.446			1	INDETERMINATE	1	TRUE	NA	0.573286784231366	3		565	771	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752393	55752393	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	81	587	0	ENST00000284073.2:c.851A>T	p.Asp284Val	p.D284V	ENST00000284073	NM_138962.2	284	gAt/gTt	12/14	0.573286784231366	3	FACETS	0.442	0.389	0.5	0.221	0.194	0.25	SUBCLONAL	1	TRUE	1	0.573286784231366	3		587	822	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210688	36210688	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	30	424	0	ENST00000222270.7:c.439C>G	p.Arg147Gly	p.R147G	ENST00000222270	NM_014727.1	147	Cga/Gga	3/37	0.103088627907141	5	FACETS	0.365	0.293	0.447			1	INDETERMINATE	1	TRUE	NA	0.573286784231366	5		424	533	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0029308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	93	242	1	ENST00000311936.3:c.34_35delinsTT	p.Gly12Phe	p.G12F	ENST00000311936	NM_004985.3	12	GGt/TTt	2/5	0.219907811941485	4	FACETS	0.844	0.755	0.937	0.844	0.755	0.937	CLONAL	3	TRUE	1	0.218388659100713	4		243	410	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913179	39913179	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	40	239	1	ENST00000378444.4:c.4936del	p.Leu1646SerfsTer28	p.L1646Sfs*28	ENST00000378444	NM_001123385.1	1646	Ctc/tc	14/15	1	2	FACETS	0.776	0.645	0.922	0.776	0.645	0.922	CLONAL	1	TRUE	1	0.218388659100713	2		240	472	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225462	26225462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	39	157	0	ENST00000360408.1:c.80G>A	p.Arg27His	p.R27H	ENST00000360408	NM_003532.2	27	cGc/cAc	1/1	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.218388659100713	2		157	312	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274734	123274734	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029327-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	199	552	0	ENST00000358487.5:c.1184T>A	p.Val395Asp	p.V395D	ENST00000358487	NM_000141.4	395	gTc/gAc	9/18	0.316233587352269	1	FACETS	0.801	0.747	0.856	0.801	0.747	0.856	INDETERMINATE	1	TRUE	0	0.594798459409498	1		552	587	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362446	40362447	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1202978138	NA	P-0029327-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	179	555	0	ENST00000293328.3:c.1749dup	p.His584ThrfsTer8	p.H584Tfs*8	ENST00000293328	NM_012448.3	583	-/A	14/19	1	2	FACETS	0.881	0.815	0.949	0.881	0.815	0.949	CLONAL	1	TRUE	1	0.594798459409498	2		555	683	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245350	41245350	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029327-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	110	588	0	ENST00000357654.3:c.2198A>G	p.Glu733Gly	p.E733G	ENST00000357654	NM_007294.3	733	gAg/gGg	10/23	1	2	FACETS	0.5	0.449	0.554	0.5	0.449	0.554	SUBCLONAL	1	TRUE	1	0.594798459409498	2		588	740	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163641	32163641	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029327-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	210	558	0	ENST00000375023.3:c.5585G>T	p.Arg1862Leu	p.R1862L	ENST00000375023	NM_004557.3	1862	cGg/cTg	30/30	0.316233587352269	1	FACETS	0.845	0.79	0.901	0.845	0.79	0.901	INDETERMINATE	1	TRUE	0	0.594798459409498	1		558	587	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390280	139390774	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	CAGAATAGATAAAAGTTTCTACCTGGGGCCAGATAAAACAGTACATATAAATAAAAAGGCAGTGTTTCTGTGTAAAATAAAAGTACATAAATAAATACTAAAAAAAATTAAAATCCTCGTTCTTATTTTGTATAAAAACATGTGTTTTAAAAAGGCTCCTCTGGTCGGCCCTGGCATCCACAGAGCGCACACAGACGCCCGAAGGCTTGGGAAAGGAAGCCGGGGTCTCGTGGGGCGCGCCGTTTACTTGAAGGCCTCCGGAATGCGGGCGATCTGGGACTGCATGCTGGTGGGAGGGCTGGAGACGCCCTCGGACCAGTCGGAGACGTTGGAATGCGGGGACGAGCTGGACCACTGGTCAGGGGACTCAGGGGACGGGGTGAGGAAGGGGTGCTCAGGCACCTGTAGCTGGTGGCTGGGGGTGTTGTCCACAGGCGAGGAGTAGCTGTGCTGCGAGGGGGGCGTCAGGAACTGGGCTGCGGTCACGGGTGGGAC	CAGAATAGATAAAAGTTTCTACCTGGGGCCAGATAAAACAGTACATATAAATAAAAAGGCAGTGTTTCTGTGTAAAATAAAAGTACATAAATAAATACTAAAAAAAATTAAAATCCTCGTTCTTATTTTGTATAAAAACATGTGTTTTAAAAAGGCTCCTCTGGTCGGCCCTGGCATCCACAGAGCGCACACAGACGCCCGAAGGCTTGGGAAAGGAAGCCGGGGTCTCGTGGGGCGCGCCGTTTACTTGAAGGCCTCCGGAATGCGGGCGATCTGGGACTGCATGCTGGTGGGAGGGCTGGAGACGCCCTCGGACCAGTCGGAGACGTTGGAATGCGGGGACGAGCTGGACCACTGGTCAGGGGACTCAGGGGACGGGGTGAGGAAGGGGTGCTCAGGCACCTGTAGCTGGTGGCTGGGGGTGTTGTCCACAGGCGAGGAGTAGCTGTGCTGCGAGGGGGGCGTCAGGAACTGGGCTGCGGTCACGGGTGGGAC	-	novel	NA	P-0029327-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	581	45	0	ENST00000277541.6:c.7417_*243del		p.*2473*	ENST00000277541	NM_017617.3	2473		34/34	0.480387522867966	4	FACETS	0.981	0.966	0.995	1	0.998	1	CLONAL	5	TRUE	0	0.594798459409498	4		45	635	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397717	139397717	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029327-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	675	772	0	ENST00000277541.6:c.5084G>T	p.Ser1695Ile	p.S1695I	ENST00000277541	NM_017617.3	1695	aGt/aTt	27/34	0.480387522867966	4	FACETS	0.934	0.904	0.964	0.7	0.678	0.723	CLONAL	3	TRUE	0	0.594798459409498	4		772	1292	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399125	139399125	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029327-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	147	736	1	ENST00000277541.6:c.5018G>T	p.Gly1673Val	p.G1673V	ENST00000277541	NM_017617.3	1673	gGc/gTc	26/34	0.480387522867966	4	FACETS	0.669	0.609	0.731	0.167	0.152	0.183	SUBCLONAL	1	TRUE	0	0.594798459409498	4		737	1179	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505637	186505652	+	frameshift_variant	Frame_Shift_Del	DEL	GATCTACCTACCAATC	GATCTACCTACCAATC	-	novel	NA	P-0029327-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	33	274	0	ENST00000323963.5:c.1046_1061del	p.Asp349ValfsTer21	p.D349Vfs*21	ENST00000323963		349	GATCTACCTACCAATCgt/gt	10/11	1	2	FACETS	0.338	0.276	0.408	0.338	0.276	0.408	SUBCLONAL	1	TRUE	1	0.594798459409498	2		274	328	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838327	156838331	+	protein_altering_variant	In_Frame_Del	DEL	ATGCC	ATGCC	CA	novel	NA	P-0029327-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	109	840	1	ENST00000524377.1:c.605_609delinsCA	p.Asn202_Ala203delinsThr	p.N202_A203delinsT	ENST00000524377	NM_002529.3	202	aATGCC/aCA	6/17	0.328210986357813	1	FACETS	0.347	0.311	0.384	0.347	0.311	0.384	INDETERMINATE	1	TRUE	0	0.594798459409498	1		841	743	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647173	23647173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029327-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	141	627	15	ENST00000261584.4:c.694G>A	p.Gly232Ser	p.G232S	ENST00000261584	NM_024675.3	232	Ggt/Agt	4/13	0.594798459409498	2	FACETS	0.616	0.561	0.673	0.308	0.28	0.337	SUBCLONAL	1	TRUE	0	0.594798459409498	2		642	770	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005134	150005146	+	frameshift_variant	Frame_Shift_Del	DEL	GGGACAACATTTT	GGGACAACATTTT	-	novel	NA	P-0029437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	424	265	0	ENST00000253339.5:c.1079_1091del	p.Gln360LeufsTer5	p.Q360Lfs*5	ENST00000253339		360	cAAAATGTTGTCCCt/ct	3/7	0.891729316614872	2	FACETS	0.947	0.925	0.968	0.947	0.925	0.968	CLONAL	2	TRUE	0	0.891729316614872	2		265	502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0029517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	463	385	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.282609915507549	1	FACETS	1	0.996	1	1	0.996	1	INDETERMINATE	1	TRUE	0	0.657095111571459	1		385	762	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222343	53222343	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	25	204	0	ENST00000375401.3:c.4489G>C	p.Glu1497Gln	p.E1497Q	ENST00000375401	NM_004187.3	1497	Gag/Cag	26/26	1	1	FACETS	0.131	0.103	0.163	0.131	0.103	0.163	SUBCLONAL	1	TRUE	0	0.657095111571459	1		204	390	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054665	13054665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150264068	NA	P-0029517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	57	301	0	ENST00000316448.5:c.1192G>A	p.Glu398Lys	p.E398K	ENST00000316448	NM_004343.3	398	Gag/Aag	9/9	1	2	FACETS	0.268	0.23	0.31	0.268	0.23	0.31	SUBCLONAL	1	TRUE	1	0.657095111571459	2		301	647	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374909	149374909	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	74	310	0	ENST00000360632.3:c.185C>G	p.Ser62Trp	p.S62W	ENST00000360632	NM_015472.4	62	tCg/tGg	2/7	0.657095111571459	3	FACETS	0.395	0.345	0.449	0.132	0.115	0.15	SUBCLONAL	1	TRUE	0	0.657095111571459	3		310	758	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231165	142231165	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	112	333	0	ENST00000350721.4:c.4789C>T	p.Gln1597Ter	p.Q1597*	ENST00000350721	NM_001184.3	1597	Cag/Tag	27/47	0.657095111571459	3	FACETS	0.464	0.416	0.515	0.155	0.138	0.172	SUBCLONAL	1	TRUE	0	0.657095111571459	3		333	976	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199451	16199451	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	161	225	0	ENST00000375759.3:c.224G>T	p.Arg75Leu	p.R75L	ENST00000375759	NM_015001.2	75	cGc/cTc	2/15	0.657095111571459	1	FACETS	0.991	0.925	1	0.991	0.925	1	CLONAL	1	TRUE	0	0.657095111571459	1		225	332	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865272	57865272	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	107	381	0	ENST00000228682.2:c.2749G>A	p.Asp917Asn	p.D917N	ENST00000228682	NM_005269.2	917	Gat/Aat	12/12	1	2	FACETS	0.436	0.391	0.484	0.436	0.391	0.484	SUBCLONAL	1	TRUE	1	0.657095111571459	2		381	747	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988452	41988452	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0029517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	229	325	0	ENST00000219905.7:c.1244C>G	p.Ser415Ter	p.S415*	ENST00000219905	NM_001164273.1	415	tCa/tGa	3/24	0.585408274123263	1	FACETS	0.963	0.908	1	0.963	0.908	1	CLONAL	1	TRUE	0	0.657095111571459	1		325	486	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989112	41989112	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	299	374	0	ENST00000219905.7:c.1904C>G	p.Ser635Cys	p.S635C	ENST00000219905	NM_001164273.1	635	tCt/tGt	3/24	0.585408274123263	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.657095111571459	1		374	581	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059467	42059467	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1469421247	NA	P-0029517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	197	88	1	ENST00000219905.7:c.9187G>A	p.Ala3063Thr	p.A3063T	ENST00000219905	NM_001164273.1	3063	Gca/Aca	24/24	0.585408274123263	1	FACETS	0.934	0.876	0.993	0.934	0.876	0.993	CLONAL	1	TRUE	0	0.657095111571459	1		89	431	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820737	3820737	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	201	450	1	ENST00000262367.5:c.2714C>A	p.Ser905Ter	p.S905*	ENST00000262367	NM_004380.2	905	tCa/tAa	14/31	0.322706032209064	1	FACETS	0.473	0.439	0.509	0.473	0.439	0.509	INDETERMINATE	1	TRUE	0	0.657095111571459	1		451	868	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843558	3843558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	72	311	1	ENST00000262367.5:c.1045G>A	p.Glu349Lys	p.E349K	ENST00000262367	NM_004380.2	349	Gaa/Aaa	4/31	0.322706032209064	1	FACETS	0.258	0.225	0.293	0.258	0.225	0.293	INDETERMINATE	1	TRUE	0	0.657095111571459	1		312	570	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857808	9857808	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	85	278	0	ENST00000330684.3:c.3593C>G	p.Ser1198Cys	p.S1198C	ENST00000330684	NM_001134407.1	1198	tCc/tGc	13/13	0.322706032209064	1	FACETS	0.352	0.312	0.395	0.352	0.312	0.395	INDETERMINATE	1	TRUE	0	0.657095111571459	1		278	493	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56862982	56862982	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	94	258	0	ENST00000308159.5:c.888C>G	p.Phe296Leu	p.F296L	ENST00000308159	NM_014669.4	296	ttC/ttG	9/22	0.532081403466765	3	FACETS	0.535	0.476	0.598	0.267	0.238	0.299	SUBCLONAL	1	TRUE	1	0.657095111571459	3		258	711	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226469	41226469	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	358	132	0	ENST00000357654.3:c.4554G>C	p.Gln1518His	p.Q1518H	ENST00000357654	NM_007294.3	1518	caG/caC	14/23	0.322706032209064	1	FACETS	0.802	0.763	0.842	0.802	0.763	0.842	INDETERMINATE	1	TRUE	0	0.657095111571459	1		132	912	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170435	11170435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	109	273	0	ENST00000358026.2:c.4738G>A	p.Glu1580Lys	p.E1580K	ENST00000358026	NM_001128849.1	1580	Gaa/Aaa	34/36	1	2	FACETS	0.486	0.436	0.538	0.486	0.436	0.538	SUBCLONAL	1	TRUE	1	0.657095111571459	2		273	683	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050910	13050910	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	289	86	0	ENST00000316448.5:c.441C>G	p.Ile147Met	p.I147M	ENST00000316448	NM_004343.3	147	atC/atG	4/9	1	2	FACETS	0.977	0.922	1	0.977	0.922	1	CLONAL	1	TRUE	1	0.657095111571459	2		86	900	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054656	13054656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	303	56	0	ENST00000316448.5:c.1183G>A	p.Glu395Lys	p.E395K	ENST00000316448	NM_004343.3	395	Gag/Aag	9/9	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.657095111571459	2		56	915	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279629	18279629	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	47	351	0	ENST00000222254.8:c.1902G>C	p.Glu634Asp	p.E634D	ENST00000222254	NM_005027.3	634	gaG/gaC	15/16	1	2	FACETS	0.173	0.145	0.204	0.173	0.145	0.204	SUBCLONAL	1	TRUE	1	0.657095111571459	2		351	827	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383199	42383199	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	123	336	0	ENST00000221972.3:c.219C>G	p.Asn73Lys	p.N73K	ENST00000221972	NM_021601.3	73	aaC/aaG	2/5	1	2	FACETS	0.457	0.413	0.503	0.457	0.413	0.503	SUBCLONAL	1	TRUE	1	0.657095111571459	2		336	820	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309652	30309652	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1343127692	NA	P-0029517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	322	120	0	ENST00000307677.4:c.370G>C	p.Glu124Gln	p.E124Q	ENST00000307677	NM_138578.1	124	Gaa/Caa	2/3	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.657095111571459	2		120	964	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547996	41547996	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	260	368	2	ENST00000263253.7:c.2977C>T	p.Gln993Ter	p.Q993*	ENST00000263253	NM_001429.3	993	Cag/Tag	15/31	0.367665095895384	1	FACETS	0.762	0.718	0.807	0.762	0.718	0.807	INDETERMINATE	1	TRUE	0	0.657095111571459	1		370	697	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103827	47103827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1244929991	NA	P-0029517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	143	284	0	ENST00000409792.3:c.6119G>A	p.Arg2040Gln	p.R2040Q	ENST00000409792	NM_014159.6	2040	cGa/cAa	14/21	0.657095111571459	1	FACETS	0.786	0.725	0.847	0.786	0.725	0.847	SUBCLONAL	1	TRUE	0	0.657095111571459	1		284	372	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474668	138474668	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	132	329	0	ENST00000289153.2:c.325C>G	p.Leu109Val	p.L109V	ENST00000289153	NM_006219.2	109	Ctc/Gtc	2/22	0.657095111571459	3	FACETS	0.605	0.549	0.664	0.202	0.183	0.222	SUBCLONAL	1	TRUE	0	0.657095111571459	3		329	882	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998020	169998020	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	119	377	0	ENST00000295797.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000295797	NM_002740.5	237	atG/atT	9/18	0.657095111571459	3	FACETS	0.466	0.42	0.516	0.155	0.14	0.172	SUBCLONAL	1	TRUE	0	0.657095111571459	3		377	1032	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164071	106164071	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	121	178	0	ENST00000380013.4:c.3581C>G	p.Pro1194Arg	p.P1194R	ENST00000380013	NM_001127208.2	1194	cCt/cGt	5/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.657095111571459	2		178	332	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099212	157099212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1226326033	NA	P-0029517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	273	46	0	ENST00000346085.5:c.149C>T	p.Ser50Phe	p.S50F	ENST00000346085	NM_020732.3	50	tCc/tTc	1/20	0.322706032209064	1	FACETS	0.809	0.764	0.854	0.809	0.764	0.854	INDETERMINATE	1	TRUE	0	0.657095111571459	1		46	690	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020509	69020509	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	153	370	2	ENST00000288368.4:c.2881C>T	p.Gln961Ter	p.Q961*	ENST00000288368	NM_024870.2	961	Cag/Tag	24/40	1	2	FACETS	0.731	0.671	0.793	0.731	0.671	0.793	SUBCLONAL	1	TRUE	1	0.657095111571459	2		372	637	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97869493	97869493	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	322	274	0	ENST00000289081.3:c.1388C>T	p.Ser463Leu	p.S463L	ENST00000289081	NM_000136.2	463	tCa/tTa	14/15	0.655217878937495	2	FACETS	1	0.995	1	0.738	0.703	0.773	CLONAL	1	TRUE	0	0.657095111571459	2		274	664	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0029518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	97	63	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.8	0.724	0.879	1	0.985	1	SUBCLONAL	2	TRUE	1	0.442407793331388	2		63	274	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0029518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	80	461	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.442407793331388	2		461	342	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0029518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	70	101	1	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.439874247658937	3	FACETS	1	0.958	1	0.606	0.532	0.684	CLONAL	1	TRUE	1	0.442407793331388	3		102	319	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589147	67589147	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	31	44	0	ENST00000274335.5:c.1135A>G	p.Lys379Glu	p.K379E	ENST00000274335		379	Aaa/Gaa	9/15	1	2	FACETS	0.966	0.793	1	0.966	0.793	1	CLONAL	1	TRUE	1	0.442407793331388	2		44	145	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370985	55370985	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	201	290	0	ENST00000297316.4:c.287C>G	p.Ala96Gly	p.A96G	ENST00000297316	NM_022454.3	96	gCc/gGc	1/2	0.439874247658937	3	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	1	0.442407793331388	3		290	551	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088664	27088664	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	295	107	0	ENST00000324856.7:c.2273del	p.Gln758ArgfsTer75	p.Q758Rfs*75	ENST00000324856	NM_006015.4	758	cAg/cg	7/20	1	2	FACETS	0.891	0.844	0.94	1	0.995	1	CLONAL	2	TRUE	1	0.442407793331388	2		107	748	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094361	27094361	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	278	95	0	ENST00000324856.7:c.3069G>T	p.Trp1023Cys	p.W1023C	ENST00000324856	NM_006015.4	1023	tgG/tgT	11/20	1	2	FACETS	1	0.948	1	1	0.996	1	CLONAL	2	TRUE	1	0.442407793331388	2		95	628	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653846	89653846	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs762518389	NA	P-0029518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	76	93	0	ENST00000371953.3:c.144C>G	p.Asn48Lys	p.N48K	ENST00000371953	NM_000314.4	48	aaC/aaG	2/9	0.439874247658937	3	FACETS	1	0.977	1	0.736	0.653	0.824	CLONAL	1	TRUE	1	0.442407793331388	3		93	285	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808569	1808569	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	105	372	0	ENST00000260795.2:c.2182C>G	p.Arg728Gly	p.R728G	ENST00000260795		728	Cgg/Ggg	16/17	1	2	FACETS	0.934	0.841	1	0.934	0.841	1	CLONAL	1	TRUE	1	0.442407793331388	2		372	508	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407481	139407481	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779375653	NA	P-0029518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	71	314	0	ENST00000277541.6:c.2459C>T	p.Pro820Leu	p.P820L	ENST00000277541	NM_017617.3	820	cCc/cTc	15/34	1	2	FACETS	0.836	0.733	0.945	0.836	0.733	0.945	CLONAL	1	TRUE	1	0.442407793331388	2		314	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764146326	NA	P-0029528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	90	870	0	ENST00000269305.4:c.841G>T	p.Asp281Tyr	p.D281Y	ENST00000269305	NM_001126112.2	281	Gac/Tac	8/11	0.230076846168558	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.18	1		870	759	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314932	1314932	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	24	510	0	ENST00000400841.2:c.729G>T	p.Met243Ile	p.M243I	ENST00000400841		243	atG/atT	6/6	1	1	FACETS	0.557	0.435	0.697	0.557	0.435	0.697	SUBCLONAL	1	TRUE	0	0.18	1		510	436	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509630	29509630	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	43	533	0	ENST00000356175.3:c.835G>T	p.Glu279Ter	p.E279*	ENST00000356175	NM_000267.3	279	Gaa/Taa	8/57	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.18	2		533	390	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102083	27102083	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	85	684	1	ENST00000324856.7:c.5009G>T	p.Trp1670Leu	p.W1670L	ENST00000324856	NM_006015.4	1670	tGg/tTg	19/20	0.139866125856258	3	FACETS	1	0.977	1	0.745	0.658	0.838	CLONAL	1	TRUE	1	0.18	3		685	691	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838398	156838398	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	103	919	0	ENST00000524377.1:c.676G>T	p.Gly226Cys	p.G226C	ENST00000524377	NM_002529.3	226	Ggc/Tgc	6/17	0.139866125856258	3	FACETS	1	0.975	1	0.661	0.591	0.737	CLONAL	1	TRUE	1	0.18	3		919	943	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163310201	163310201	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	452	41	0	ENST00000271452.3:c.654G>C	p.Glu218Asp	p.E218D	ENST00000271452	NM_145697.2	218	gaG/gaC	9/14	0.3	1	FACETS	1	0.988	1	1	0.998	1	CLONAL	6	TRUE	0	0.18	1		41	723	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115928	8115928	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	62	542	0	ENST00000346208.3:c.1274C>A	p.Pro425Gln	p.P425Q	ENST00000346208		425	cCa/cAa	6/6	0.230076846168558	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.18	1		542	517	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518491	69518491	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	430	45	2	ENST00000294312.3:c.154C>A	p.Pro52Thr	p.P52T	ENST00000294312	NM_005117.2	52	Ccc/Acc	1/3	1	2	FACETS	1	0.979	1	1	0.998	1	CLONAL	6	TRUE	1	0.18	2		47	776	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005294	29005294	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	458	18	0	ENST00000282397.4:c.967A>C	p.Asn323His	p.N323H	ENST00000282397	NM_002019.4	323	Aac/Cac	7/30	0.170191682775115	0	FACETS	0.907	0.874	0.939			1	CLONAL	6	TRUE	0	0.18	0		18	767	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021449	42021449	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	555	60	0	ENST00000219905.7:c.3745G>T	p.Glu1249Ter	p.E1249*	ENST00000219905	NM_001164273.1	1249	Gag/Tag	11/24	1	2	FACETS	1	0.992	1	1	0.998	1	CLONAL	6	TRUE	1	0.18	2		60	957	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663729	29663729	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	546	46	0	ENST00000356175.3:c.6163del	p.Asp2055MetfsTer6	p.D2055Mfs*6	ENST00000356175	NM_000267.3	2054	tGg/tg	41/57	1	2	FACETS	0.987	0.953	1	1	0.998	1	CLONAL	6	TRUE	1	0.18	2		46	1024	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212252719	212252719	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0029528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	208	11	0	ENST00000342788.4:c.3136-2A>T		p.X1046_splice	ENST00000342788	NM_005235.2	1046			1	2	FACETS	0.971	0.921	1	1	0.996	1	CLONAL	7	TRUE	1	0.18	2		11	340	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967226	134967226	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	624	48	1	ENST00000398015.3:c.2565G>T	p.Gln855His	p.Q855H	ENST00000398015	NM_004441.4	855	caG/caT	14/16	0.3	1	FACETS	0.937	0.907	0.967	1	0.998	1	CLONAL	6	TRUE	0	0.18	1		49	1122	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374727	149374727	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	51	608	0	ENST00000360632.3:c.367G>T	p.Glu123Ter	p.E123*	ENST00000360632	NM_015472.4	123	Gag/Tag	2/7	1	2	FACETS	0.872	0.74	1	0.872	0.74	1	CLONAL	1	TRUE	1	0.18	2		608	650	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184724	32184724	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	723	41	1	ENST00000375023.3:c.1859C>T	p.Thr620Ile	p.T620I	ENST00000375023	NM_004557.3	620	aCa/aTa	11/30	1	2	FACETS	0.94	0.91	0.969			1	CLONAL	6	TRUE	1	0.18	2		42	1425	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099547	157099547	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	23	170	0	ENST00000346085.5:c.484G>T	p.Ala162Ser	p.A162S	ENST00000346085	NM_020732.3	162	Gcc/Tcc	1/20	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.18	2		170	211	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372526	55372526	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	1066	55	1	ENST00000297316.4:c.1216G>T	p.Val406Leu	p.V406L	ENST00000297316	NM_022454.3	406	Gta/Tta	2/2	1	2	FACETS	0.932	0.91	0.954			1	CLONAL	7	TRUE	1	0.18	2		56	1816	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395174	139395174	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	975	79	0	ENST00000277541.6:c.5764A>T	p.Asn1922Tyr	p.N1922Y	ENST00000277541	NM_017617.3	1922	Aac/Tac	31/34	1	2	FACETS	1	0.993	1			1	CLONAL	6	TRUE	1	0.18	2		79	1716	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411375	63411375	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	31	393	0	ENST00000330258.3:c.1792G>T	p.Ala598Ser	p.A598S	ENST00000330258	NM_152424.3	598	Gcc/Tcc	2/2	1	1	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	TRUE	0	0.18	1		393	301	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	11	133	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.380607149006406	1	FACETS	0.467	0.327	0.636	0.467	0.327	0.636	SUBCLONAL	1	FALSE	0	0.441939968880081	1		133	83	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	86	686	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.14059629465604	0	FACETS	0.597	0.532	0.665			1	INDETERMINATE	1	FALSE	0	0.441939968880081	0		686	364	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17117087	17117087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764899882	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	433	77	0	ENST00000285071.4:c.1622C>T	p.Ala541Val	p.A541V	ENST00000285071	NM_144997.5	541	gCg/gTg	14/14	0.14059629465604	0	FACETS	0.71	0.683	0.737			1	INDETERMINATE	2	FALSE	0	0.441939968880081	0		77	770	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	74	475	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.14059629465604	0	FACETS	0.385	0.337	0.435			1	INDETERMINATE	1	FALSE	0	0.441939968880081	0		478	486	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	102	555	6	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.799	0.716	0.886	0.799	0.716	0.886	SUBCLONAL	1	FALSE	1	0.441939968880081	2		561	578	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339111	65339111	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	36	316	3	ENST00000342505.4:c.425del	p.Lys142ArgfsTer26	p.K142Rfs*26	ENST00000342505	NM_002227.2	142	aAg/ag	5/25	1	2	FACETS	0.727	0.603	0.865	0.727	0.603	0.865	SUBCLONAL	1	FALSE	1	0.441939968880081	2		319	224	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196213	106196213	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs370735654	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	18	134	0	ENST00000380013.4:c.4546C>T	p.Arg1516Ter	p.R1516*	ENST00000380013	NM_001127208.2	1516	Cga/Tga	11/11	1	2	FACETS	0.578	0.439	0.739	0.578	0.439	0.739	SUBCLONAL	1	FALSE	1	0.441939968880081	2		134	141	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	33	411	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.821	0.675	0.98	0.821	0.675	0.98	CLONAL	1	FALSE	1	0.441939968880081	2		411	182	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721164	176721165	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1562308992	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	32	315	0	ENST00000439151.2:c.6801dup	p.Ala2268SerfsTer13	p.A2268Sfs*13	ENST00000439151	NM_022455.4	2265	-/A	23/23	1	2	FACETS	0.667	0.545	0.803	0.667	0.545	0.803	SUBCLONAL	1	FALSE	1	0.441939968880081	2		315	217	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828772	3828772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	22	443	1	ENST00000262367.5:c.1870C>T	p.Arg624Cys	p.R624C	ENST00000262367	NM_004380.2	624	Cgc/Tgc	9/31	0.221552316876246	1	FACETS	0.257	0.199	0.324	0.257	0.199	0.324	INDETERMINATE	1	FALSE	0	0.441939968880081	1		444	302	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567647	226567647	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	40	322	2	ENST00000366794.5:c.1519del	p.Ser507AlafsTer17	p.S507Afs*17	ENST00000366794	NM_001618.3	507	Agc/gc	10/23	1	2	FACETS	0.595	0.497	0.704	0.595	0.497	0.704	SUBCLONAL	1	FALSE	1	0.441939968880081	2		324	304	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989562	85989562	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs767548896	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	27	211	0	ENST00000263360.6:c.1321C>T	p.Arg441Ter	p.R441*	ENST00000263360	NM_003797.3	441	Cga/Tga	12/12	1	2	FACETS	0.614	0.492	0.751	0.614	0.492	0.751	SUBCLONAL	1	FALSE	1	0.441939968880081	2		211	199	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	30	385	1	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	0.221552316876246	1	FACETS	0.412	0.333	0.5	0.412	0.333	0.5	INDETERMINATE	1	FALSE	0	0.441939968880081	1		386	257	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942751	44942751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763592177	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	56	191	1	ENST00000377967.4:c.3331C>T	p.Arg1111Cys	p.R1111C	ENST00000377967	NM_021140.2	1111	Cgt/Tgt	23/29	1	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	0	0.441939968880081	1		192	166	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953826	131953826	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs368980595	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	16	240	0	ENST00000265335.6:c.3229C>T	p.Arg1077Ter	p.R1077*	ENST00000265335		1077	Cga/Tga	21/25	1	2	FACETS	0.51	0.38	0.663	0.51	0.38	0.663	SUBCLONAL	1	FALSE	1	0.441939968880081	2		240	142	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852243	128852243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149170801	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	90	470	0	ENST00000249373.3:c.2315G>A	p.Arg772His	p.R772H	ENST00000249373	NM_005631.4	772	cGc/cAc	12/12	1	2	FACETS	0.843	0.751	0.941	0.843	0.751	0.941	CLONAL	1	FALSE	1	0.441939968880081	2		470	483	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446317	29446317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768123237	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	104	458	0	ENST00000389048.3:c.3250C>T	p.Arg1084Cys	p.R1084C	ENST00000389048	NM_004304.4	1084	Cgc/Tgc	20/29	1	2	FACETS	0.898	0.807	0.994	0.898	0.807	0.994	CLONAL	1	FALSE	1	0.441939968880081	2		458	524	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30946592	30946594	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs752094508	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	137	226	0	ENST00000375687.4:c.25_27del	p.Lys9del	p.K9del	ENST00000375687	NM_015338.5	5	cAGAag/cag	1/13	1	2	FACETS	0.939	0.857	1	0.939	0.857	1	CLONAL	1	FALSE	1	0.441939968880081	2		226	660	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	103	646	4	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.652	0.584	0.724	0.652	0.584	0.724	SUBCLONAL	1	FALSE	1	0.441939968880081	2		650	715	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630855	187630855	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560660262	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	35	366	0	ENST00000441802.2:c.127G>A	p.Val43Met	p.V43M	ENST00000441802	NM_005245.3	43	Gtg/Atg	2/27	1	2	FACETS	0.593	0.489	0.709	0.593	0.489	0.709	SUBCLONAL	1	FALSE	1	0.441939968880081	2		366	267	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	278	601	0	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.821	0.775	0.868	1	0.995	1	CLONAL	2	FALSE	1	0.441939968880081	2		601	766	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201089	108201089	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779865	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	32	237	0	ENST00000278616.4:c.7456C>T	p.Arg2486Ter	p.R2486*	ENST00000278616	NM_000051.3	2486	Cga/Tga	50/63	1	2	FACETS	0.842	0.691	1	0.842	0.691	1	CLONAL	1	FALSE	1	0.441939968880081	2		237	172	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184411	7184411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375845481	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	131	495	1	ENST00000302850.5:c.890G>A	p.Arg297Gln	p.R297Q	ENST00000302850	NM_000208.2	297	cGg/cAg	3/22	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.441939968880081	2		496	553	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321686	62321686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777844293	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	462	108	1	ENST00000360203.5:c.2305C>T	p.Arg769Cys	p.R769C	ENST00000360203	NM_001283009.1	769	Cgt/Tgt	26/35	1	2	FACETS	1	0.989	1	1	0.997	1	CLONAL	2	FALSE	1	0.441939968880081	2		109	963	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024682	11024682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	61	357	1	ENST00000327064.4:c.799C>T	p.Arg267Cys	p.R267C	ENST00000327064	NM_199141.1	267	Cgc/Tgc	6/16	1	2	FACETS	0.76	0.659	0.869	0.76	0.659	0.869	SUBCLONAL	1	FALSE	1	0.441939968880081	2		358	363	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444681	187444681	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373425354	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	28	207	1	ENST00000232014.4:c.1546G>A	p.Gly516Arg	p.G516R	ENST00000232014	NM_001130845.1	516	Ggg/Agg	7/10	1	2	FACETS	0.609	0.49	0.743	0.609	0.49	0.743	SUBCLONAL	1	FALSE	1	0.441939968880081	2		208	208	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864117	57864117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749783306	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	94	324	0	ENST00000228682.2:c.1594C>T	p.Arg532Cys	p.R532C	ENST00000228682	NM_005269.2	532	Cgc/Tgc	12/12	1	2	FACETS	0.715	0.637	0.797	0.715	0.637	0.797	SUBCLONAL	1	FALSE	1	0.441939968880081	2		324	595	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243502	41243502	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357345	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	35	468	1	ENST00000357654.3:c.4046C>T	p.Thr1349Met	p.T1349M	ENST00000357654	NM_007294.3	1349	aCg/aTg	10/23	0.14059629465604	0	FACETS	0.44	0.364	0.523			1	INDETERMINATE	1	FALSE	0	0.441939968880081	0		469	201	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260194	16260194	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1557761571	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	57	357	1	ENST00000375759.3:c.7464del	p.Ile2489SerfsTer10	p.I2489Sfs*10	ENST00000375759	NM_015001.2	2487	Ggg/gg	11/15	1	2	FACETS	0.693	0.597	0.797	0.693	0.597	0.797	SUBCLONAL	1	FALSE	1	0.441939968880081	2		358	372	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721713	176721713	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	26	331	0	ENST00000439151.2:c.7349del	p.Asn2450IlefsTer6	p.N2450Ifs*6	ENST00000439151	NM_022455.4	2448	tcA/tc	23/23	1	2	FACETS	0.636	0.508	0.781	0.636	0.508	0.781	SUBCLONAL	1	FALSE	1	0.441939968880081	2		331	185	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420913	49420913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756017412	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	85	449	1	ENST00000301067.7:c.14836G>A	p.Val4946Ile	p.V4946I	ENST00000301067	NM_003482.3	4946	Gtc/Atc	48/54	1	2	FACETS	0.595	0.526	0.669	0.595	0.526	0.669	SUBCLONAL	1	FALSE	1	0.441939968880081	2		450	646	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196092	138196092	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200740561	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	42	226	0	ENST00000237289.4:c.406C>T	p.Arg136Cys	p.R136C	ENST00000237289	NM_001270507.1	136	Cgc/Tgc	3/9	1	2	FACETS	0.819	0.69	0.96	0.819	0.69	0.96	CLONAL	1	FALSE	1	0.441939968880081	2		226	232	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450805	70450805	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759636615	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	45	334	0	ENST00000373644.4:c.5645C>T	p.Thr1882Met	p.T1882M	ENST00000373644	NM_030625.2	1882	aCg/aTg	12/12	0.380607149006406	1	FACETS	0.551	0.465	0.644	0.551	0.465	0.644	SUBCLONAL	1	FALSE	0	0.441939968880081	1		334	288	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121571	108121571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781841	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	43	364	0	ENST00000278616.4:c.1379C>T	p.Thr460Met	p.T460M	ENST00000278616	NM_000051.3	460	aCg/aTg	10/63	1	2	FACETS	0.69	0.581	0.81	0.69	0.581	0.81	SUBCLONAL	1	FALSE	1	0.441939968880081	2		364	282	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160402	108160402	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	23	236	0	ENST00000278616.4:c.4310G>T	p.Arg1437Ile	p.R1437I	ENST00000278616	NM_000051.3	1437	aGa/aTa	29/63	1	2	FACETS	0.703	0.554	0.872	0.703	0.554	0.872	SUBCLONAL	1	FALSE	1	0.441939968880081	2		236	148	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552744	18552744	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	42	323	0	ENST00000266497.5:c.2155T>C	p.Ser719Pro	p.S719P	ENST00000266497		719	Tct/Cct	14/31	1	2	FACETS	0.872	0.735	1	0.872	0.735	1	CLONAL	1	FALSE	1	0.441939968880081	2		323	218	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418361	49418361	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1555185217	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	45	259	0	ENST00000301067.7:c.16052G>A	p.Arg5351Gln	p.R5351Q	ENST00000301067	NM_003482.3	5351	cGg/cAg	50/54	1	2	FACETS	0.882	0.748	1	0.882	0.748	1	CLONAL	1	FALSE	1	0.441939968880081	2		259	231	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484048	50484048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1319486448	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	51	397	1	ENST00000394963.4:c.898C>T	p.Arg300Cys	p.R300C	ENST00000394963	NM_003076.4	300	Cgc/Tgc	8/13	1	2	FACETS	0.622	0.53	0.722	0.622	0.53	0.722	SUBCLONAL	1	FALSE	1	0.441939968880081	2		398	371	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031828	10031828	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	83	430	0	ENST00000330684.3:c.995A>G	p.His332Arg	p.H332R	ENST00000330684	NM_001134407.1	332	cAc/cGc	3/13	0.221552316876246	1	FACETS	0.655	0.58	0.734	0.655	0.58	0.734	INDETERMINATE	1	FALSE	0	0.441939968880081	1		430	447	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828807	72828807	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	52	371	0	ENST00000268489.5:c.7774del	p.Ala2592ProfsTer20	p.A2592Pfs*20	ENST00000268489	NM_006885.3	2592	Gcc/cc	9/10	0.221552316876246	1	FACETS	0.77	0.663	0.886	0.77	0.663	0.886	INDETERMINATE	1	FALSE	0	0.441939968880081	1		371	238	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347878	89347878	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763039848	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	65	403	1	ENST00000301030.4:c.5072C>T	p.Ala1691Val	p.A1691V	ENST00000301030	NM_001256183.1	1691	gCg/gTg	9/13	0.221552316876246	1	FACETS	0.746	0.652	0.847	0.746	0.652	0.847	INDETERMINATE	1	FALSE	0	0.441939968880081	1		404	307	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321668	30321668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1468359813	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	50	408	0	ENST00000322652.5:c.1523G>A	p.Arg508His	p.R508H	ENST00000322652	NM_015355.2	508	cGc/cAc	13/16	0.14059629465604	0	FACETS	0.402	0.343	0.467			1	INDETERMINATE	1	FALSE	0	0.441939968880081	0		408	314	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554687	63554687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	28	312	0	ENST00000307078.5:c.52C>T	p.Arg18Cys	p.R18C	ENST00000307078	NM_004655.3	18	Cgt/Tgt	2/11	0.14059629465604	0	FACETS	0.187	0.149	0.23			1	INDETERMINATE	1	FALSE	0	0.441939968880081	0		312	378	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379781	17379781	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758868685	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	158	630	0	ENST00000359435.4:c.166G>A	p.Ala56Thr	p.A56T	ENST00000359435	NM_001033549.1	56	Gcc/Acc	2/9	1	2	FACETS	0.778	0.713	0.846	0.778	0.713	0.846	SUBCLONAL	1	FALSE	1	0.441939968880081	2		630	919	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974395	18974395	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1322079562	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	96	388	2	ENST00000262803.5:c.2749C>T	p.Arg917Trp	p.R917W	ENST00000262803	NM_002911.3	917	Cgg/Tgg	19/24	1	2	FACETS	0.839	0.75	0.933	0.839	0.75	0.933	CLONAL	1	FALSE	1	0.441939968880081	2		390	518	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62303912	62303912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866782181	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	80	406	1	ENST00000360203.5:c.703C>T	p.Arg235Cys	p.R235C	ENST00000360203	NM_001283009.1	235	Cgc/Tgc	9/35	1	2	FACETS	0.842	0.745	0.945	0.842	0.745	0.945	CLONAL	1	FALSE	1	0.441939968880081	2		407	430	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723041	49723041	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	40	217	0	ENST00000449682.2:c.1375C>A	p.Leu459Met	p.L459M	ENST00000449682	NM_020998.3	459	Ctg/Atg	11/18	1	2	FACETS	0.761	0.637	0.896	0.761	0.637	0.896	SUBCLONAL	1	FALSE	1	0.441939968880081	2		217	238	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932981	49932981	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	44	473	0	ENST00000296474.3:c.2963T>C	p.Val988Ala	p.V988A	ENST00000296474	NM_002447.2	988	gTt/gCt	13/20	1	2	FACETS	0.751	0.634	0.879	0.751	0.634	0.879	SUBCLONAL	1	FALSE	1	0.441939968880081	2		473	265	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592121	55592121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	50	330	0	ENST00000288135.5:c.1445C>T	p.Ala482Val	p.A482V	ENST00000288135	NM_000222.2	482	gCa/gTa	9/21	1	2	FACETS	0.927	0.794	1	0.927	0.794	1	CLONAL	1	FALSE	1	0.441939968880081	2		330	244	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233618	233618	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	20	221	0	ENST00000264932.6:c.922A>G	p.Thr308Ala	p.T308A	ENST00000264932	NM_004168.2	308	Acg/Gcg	8/15	1	2	FACETS	0.984	0.768	1	0.984	0.768	1	CLONAL	1	FALSE	1	0.441939968880081	2		221	92	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206854	162206854	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	49	356	0	ENST00000366898.1:c.821A>T	p.Asp274Val	p.D274V	ENST00000366898	NM_004562.2	274	gAt/gTt	7/12	1	2	FACETS	0.689	0.586	0.8	0.689	0.586	0.8	SUBCLONAL	1	FALSE	1	0.441939968880081	2		356	322	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545698	106545698	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	59	396	0	ENST00000359195.3:c.3179del	p.Asn1060MetfsTer48	p.N1060Mfs*48	ENST00000359195	NM_002649.2	1059	Aaa/aa	11/11	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	FALSE	1	0.441939968880081	2		396	249	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829084	128829084	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	16	35	0	ENST00000249373.3:c.92C>T	p.Ala31Val	p.A31V	ENST00000249373	NM_005631.4	31	gCc/gTc	1/12	1	2	FACETS	0.345	0.255	0.451	0.345	0.255	0.451	SUBCLONAL	1	FALSE	1	0.441939968880081	2		35	210	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285748	87285748	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1440777069	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	115	368	1	ENST00000277120.3:c.85G>A	p.Ala29Thr	p.A29T	ENST00000277120		29	Gct/Act	2/19	1	2	FACETS	0.891	0.805	0.981	0.891	0.805	0.981	CLONAL	1	FALSE	1	0.441939968880081	2		369	584	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97873825	97873825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140687953	NA	P-0029817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	114	466	0	ENST00000289081.3:c.1249G>A	p.Glu417Lys	p.E417K	ENST00000289081	NM_000136.2	417	Gaa/Aaa	13/15	1	2	FACETS	0.775	0.698	0.855	0.775	0.698	0.855	SUBCLONAL	1	FALSE	1	0.441939968880081	2		466	666	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	62	233	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.241513772089876	1	FACETS	0.863	0.746	0.99	0.863	0.746	0.99	CLONAL	1	TRUE	0	0.241513772089876	1		235	523	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0029996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	227	81	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.241513772089876	1	FACETS	1	0.982	1	1	0.995	1	CLONAL	2	TRUE	0	0.241513772089876	1		81	730	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579388	7579422	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGAAGGGACAGAAGATGACAGGGGCCAGGAGGG	TGGGAAGGGACAGAAGATGACAGGGGCCAGGAGGG	-	novel	NA	P-0029996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	103	349	0	ENST00000269305.4:c.265_299del	p.Pro89GlufsTer48	p.P89Efs*48	ENST00000269305	NM_001126112.2	89	CCCTCCTGGCCCCTGTCATCTTCTGTCCCTTCCCAg/g	4/11	1	2	FACETS	0.949	0.848	1	0.949	0.848	1	CLONAL	1	TRUE	1	0.241513772089876	2		349	899	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0030304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	48	739	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.309895114662509	1	FACETS	0.221	0.186	0.26	0.221	0.186	0.26	SUBCLONAL	1	TRUE	0	0.402526607590153	1		740	861	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0030304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	252	683	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.309895114662509	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.402526607590153	1		683	944	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251754	212251754	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	180	261	0	ENST00000342788.4:c.3305T>G	p.Phe1102Cys	p.F1102C	ENST00000342788	NM_005235.2	1102	tTt/tGt	27/28	0.347502792385248	2	FACETS	1	0.989	1	0.711	0.659	0.765	CLONAL	1	TRUE	0	0.402526607590153	2		261	629	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436231	110436231	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs902033010	NA	P-0030304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	25	184	0	ENST00000375856.3:c.2170G>A	p.Gly724Arg	p.G724R	ENST00000375856	NM_003749.2	724	Ggg/Agg	1/2	0.172398660316711	2	FACETS	0.251	0.197	0.314	0.126	0.098	0.157	INDETERMINATE	1	TRUE	0	0.402526607590153	2		184	494	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89825000	89825000	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	154	345	0	ENST00000389301.3:c.2966T>A	p.Met989Lys	p.M989K	ENST00000389301	NM_000135.2	989	aTg/aAg	30/43	0.182549401130571	4	FACETS	0.996	0.91	1			1	INDETERMINATE	1	TRUE	NA	0.402526607590153	4		345	1078	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860547	45860547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150865508	NA	P-0030304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	69	472	0	ENST00000391945.4:c.1460G>A	p.Arg487Gln	p.R487Q	ENST00000391945	NM_000400.3	487	cGg/cAg	15/23	0.227331435181417	2	FACETS	0.368	0.32	0.421	0.184	0.16	0.211	INDETERMINATE	1	TRUE	0	0.402526607590153	2		472	931	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005842	69005842	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	244	123	0	ENST00000288368.4:c.2253A>C	p.Gln751His	p.Q751H	ENST00000288368	NM_024870.2	751	caA/caC	21/40	0.227331435181417	2	FACETS	0.958	0.901	1	0.958	0.901	1	INDETERMINATE	2	TRUE	0	0.402526607590153	2		123	633	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249606	110249606	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	92	502	2	ENST00000374672.4:c.1069C>T	p.Gln357Ter	p.Q357*	ENST00000374672	NM_004235.4	357	Cag/Tag	3/5	0.402526607590153	1	FACETS	0.357	0.316	0.401	0.357	0.316	0.401	SUBCLONAL	1	TRUE	0	0.402526607590153	1		504	1023	SUCCESS
AR	367	MSKCC	GRCh37	X	66942711	66942711	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	120	216	0	ENST00000374690.3:c.2492T>C	p.Leu831Pro	p.L831P	ENST00000374690	NM_000044.3	831	cTt/cCt	7/8	0.312555986409924	0	FACETS	0.904	0.824	0.987			1	CLONAL	1	TRUE	NA	0.402526607590153	0		216	394	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592099	67592099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	355	269	0	ENST00000274335.5:c.1915C>T	p.Arg639Ter	p.R639*	ENST00000274335		639	Cga/Tga	14/15	NA	2	FACETS	0.984	0.958	1			1	INDETERMINATE	2	TRUE	NA	0.861325638106334	2		269	419	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070543	67070543	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	163	254	0	ENST00000412916.2:c.167C>A	p.Ala56Asp	p.A56D	ENST00000412916		56	gCt/gAt	3/6	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.861325638106334	2		254	359	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827572	72827574	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs751017331	NA	P-0030521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	354	740	0	ENST00000268489.5:c.9007_9009del	p.Lys3003del	p.K3003del	ENST00000268489	NM_006885.3	3003	AAG/-	9/10	1	2	FACETS	0.912	0.868	0.958	0.912	0.868	0.958	CLONAL	1	TRUE	1	0.861325638106334	2		740	901	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942754	68942754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569463208	NA	P-0030521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	273	498	0	ENST00000288368.4:c.566G>A	p.Arg189Gln	p.R189Q	ENST00000288368	NM_024870.2	189	cGg/cAg	6/40	1	2	FACETS	0.928	0.877	0.98	0.928	0.877	0.98	CLONAL	1	TRUE	1	0.861325638106334	2		498	683	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180463	94180463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867533770	NA	P-0030521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	291	495	0	ENST00000323929.3:c.1705G>A	p.Gly569Arg	p.G569R	ENST00000323929	NM_005591.3	569	Gga/Aga	15/20	1	2	FACETS	0.901	0.852	0.95	0.901	0.852	0.95	CLONAL	1	TRUE	1	0.861325638106334	2		495	750	SUCCESS
APC	324	MSKCC	GRCh37	5	112176799	112176799	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	379	353	0	ENST00000257430.4:c.5509del	p.Ser1837ValfsTer26	p.S1837Vfs*26	ENST00000257430	NM_000038.5	1836	ggA/gg	16/16	NA	2	FACETS	0.998	0.974	1			1	INDETERMINATE	2	TRUE	NA	0.861325638106334	2		353	441	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499733	8499733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	330	568	1	ENST00000356435.5:c.2236G>A	p.Gly746Arg	p.G746R	ENST00000356435		746	Gga/Aga	14/35	1	2	FACETS	0.982	0.934	1	0.982	0.934	1	CLONAL	1	TRUE	1	0.861325638106334	2		569	780	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0030554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	41	441	2	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.296159478993392	3	FACETS	1	0.883	1	1	0.883	1	CLONAL	2	TRUE	1	0.325720753364983	3		443	140	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0030554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	212	249	1	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	0.325720753364983	2	FACETS	0.875	0.815	0.936	0.875	0.815	0.936	CLONAL	2	TRUE	0	0.325720753364983	2		250	744	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281629	49281629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749662416	NA	P-0030554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	331	307	0	ENST00000282018.3:c.676C>T	p.Arg226Trp	p.R226W	ENST00000282018	NM_020377.2	226	Cgg/Tgg	1/1	0.325720753364983	6	FACETS	0.993	0.943	1	0.993	0.943	1	CLONAL	4	TRUE	2	0.325720753364983	6		307	845	SUCCESS
APC	324	MSKCC	GRCh37	5	112175748	112175760	+	frameshift_variant	Frame_Shift_Del	DEL	ATACTTTATTACA	ATACTTTATTACA	-	novel	NA	P-0030554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	48	100	0	ENST00000257430.4:c.4457_4469del	p.Asp1486ValfsTer17	p.D1486Vfs*17	ENST00000257430	NM_000038.5	1486	gATACTTTATTACAt/gt	16/16	0.325720753364983	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	0	0.325720753364983	2		100	134	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0030556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	383	43	1	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	1	2	FACETS	0.889	0.848	0.93	1	0.997	1	CLONAL	4	FALSE	1	0.23723869854564	2		44	908	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207162	1207162	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs137853076	NA	P-0030556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	149	645	0	ENST00000326873.7:c.250A>T	p.Lys84Ter	p.K84*	ENST00000326873	NM_000455.4	84	Aag/Tag	1/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.23723869854564	2		645	1063	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs80338963	NA	P-0030556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	42	303	0	ENST00000342988.3:c.1081C>A	p.Arg361Ser	p.R361S	ENST00000342988	NM_005359.5	361	Cgc/Agc	9/12	1	2	FACETS	0.864	0.722	1	0.864	0.722	1	CLONAL	1	FALSE	1	0.23723869854564	2		303	410	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508235	106508235	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1448416221	NA	P-0030585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	79	209	0	ENST00000359195.3:c.229C>T	p.Arg77Ter	p.R77*	ENST00000359195	NM_002649.2	77	Cga/Tga	2/11	0.225287100473543	4	FACETS	0.826	0.731	0.927	0.826	0.731	0.927	CLONAL	2	TRUE	2	0.341089360257082	4		209	376	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807420	36807447	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCCCAGCCGTCGCACCGGTGGTGCGC	TGGCCCAGCCGTCGCACCGGTGGTGCGC	-	novel	NA	P-0030585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	227	498	0	ENST00000373129.3:c.1217_1244del	p.Ser406ThrfsTer6	p.S406Tfs*6	ENST00000373129	NM_032017.1	406	aGCGCACCACCGGTGCGACGGCTGGGCCAc/ac	12/12	NA	2	FACETS	0.939	0.878	1			1	INDETERMINATE	2	TRUE	NA	0.341089360257082	2		498	709	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166347	118166347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219813462	NA	P-0030585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	67	284	0	ENST00000369448.3:c.857G>A	p.Arg286Lys	p.R286K	ENST00000369448	NM_017709.3	286	aGg/aAg	2/2	0.341089360257082	3	FACETS	0.933	0.812	1	0.466	0.406	0.532	CLONAL	1	TRUE	1	0.341089360257082	3		284	493	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914938	32914939	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TAAA	novel	NA	P-0030585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	166	366	0	ENST00000380152.3:c.6447_6450dup	p.Val2151Ter	p.V2151*	ENST00000380152		2149	att/atTAAAt	11/27	0.340783422128972	3	FACETS	0.942	0.876	1	0.942	0.876	1	CLONAL	3	TRUE	0	0.341089360257082	3		366	403	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847296	68847318	+	frameshift_variant	Frame_Shift_Del	DEL	CCCAGCGTGGGAGGCTGTATACA	CCCAGCGTGGGAGGCTGTATACA	-	novel	NA	P-0030585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	233	430	0	ENST00000261769.5:c.1220_1242del	p.Pro407HisfsTer4	p.P407Hfs*4	ENST00000261769	NM_004360.3	406	acCCCAGCGTGGGAGGCTGTATACAcc/accc	9/16	NA	2	FACETS	1	0.94	1			1	INDETERMINATE	2	TRUE	NA	0.341089360257082	2		430	681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573991	7574135	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CATTCAGCTCTCGGAACATCTCGAAGCGCTCACGCCCACGGATCTGCAGCAACAGAGGAGGGGGAGAAGTAAGTATATACACAGTACCTGAGTTAAAAGATGGTTCAAGTTACAATTGTTTGACTTTATGACGGTACAAAAGCAA	CATTCAGCTCTCGGAACATCTCGAAGCGCTCACGCCCACGGATCTGCAGCAACAGAGGAGGGGGAGAAGTAAGTATATACACAGTACCTGAGTTAAAAGATGGTTCAAGTTACAATTGTTTGACTTTATGACGGTACAAAAGCAA	-	novel	NA	P-0030585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	141	491	0	ENST00000269305.4:c.994-102_1036del		p.X332_splice	ENST00000269305	NM_001126112.2	332		10/11	0.274817292622436	2	FACETS	1	0.975	1	0.589	0.537	0.643	CLONAL	1	TRUE	0	0.341089360257082	2		491	702	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945789	17945789	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	201	502	1	ENST00000458235.1:c.2071G>T	p.Val691Leu	p.V691L	ENST00000458235	NM_000215.3	691	Gtg/Ttg	16/24	NA	2	FACETS	0.845	0.787	0.906			1	INDETERMINATE	2	TRUE	NA	0.341089360257082	2		503	697	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0030706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	158	691	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.272697181551883	4	FACETS	0.782	0.718	0.849	0.782	0.718	0.849	SUBCLONAL	2	TRUE	2	0.37	4		691	748	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757274881	NA	P-0030706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	71	1161	3	ENST00000269305.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	144	Cag/Tag	5/11	1	2	FACETS	0.47	0.41	0.536	0.47	0.41	0.536	SUBCLONAL	1	TRUE	1	0.37	2		1164	816	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	142	395	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		395	431	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0030998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	197	598	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.184525446545909	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	FALSE	2	0.24682642669009	4		598	914	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0030998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	71	679	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.24682642669009	1	FACETS	0.722	0.63	0.822	0.722	0.63	0.822	SUBCLONAL	1	FALSE	0	0.24682642669009	1		679	698	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909214	41909214	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1333	91	768	0	ENST00000372991.4:c.174G>C	p.Lys58Asn	p.K58N	ENST00000372991	NM_001760.3	58	aaG/aaC	1/5	0.24682642669009	3	FACETS	0.582	0.514	0.654	0.194	0.171	0.218	SUBCLONAL	1	FALSE	0	0.24682642669009	3		768	1424	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909235	41909235	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1320	83	736	0	ENST00000372991.4:c.153G>C	p.Glu51Asp	p.E51D	ENST00000372991	NM_001760.3	51	gaG/gaC	1/5	0.24682642669009	3	FACETS	0.539	0.473	0.609	0.18	0.157	0.203	SUBCLONAL	1	FALSE	0	0.24682642669009	3		736	1403	SUCCESS
BTK	695	MSKCC	GRCh37	X	100604886	100604886	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	21	308	0	ENST00000308731.7:c.1967A>T	p.Asp656Val	p.D656V	ENST00000308731	NM_000061.2	656	gAt/gTt	19/19	1	2	FACETS	0.411	0.316	0.523	0.411	0.316	0.523	SUBCLONAL	1	FALSE	1	0.24682642669009	2		308	414	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909320	41909320	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	51	590	0	ENST00000372991.4:c.68G>C	p.Gly23Ala	p.G23A	ENST00000372991	NM_001760.3	23	gGg/gCg	1/5	0.24682642669009	3	FACETS	0.501	0.424	0.586	0.167	0.141	0.196	SUBCLONAL	1	FALSE	0	0.24682642669009	3		590	927	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0031041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	370	233	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.552199687292091	3	FACETS	0.839	0.804	0.874	1	0.994	1	CLONAL	3	FALSE	1	0.551722258066835	3		235	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0031041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	575	759	1	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.551722258066835	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	FALSE	0	0.551722258066835	2		760	1021	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971077	21971077	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	453	228	0	ENST00000304494.5:c.281T>G	p.Leu94Arg	p.L94R	ENST00000304494	NM_000077.4	94	cTg/cGg	2/3	0.479507321283119	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	FALSE	0	0.551722258066835	2		228	678	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100374	27100374	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0031041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	294	583	0	ENST00000324856.7:c.4086T>G	p.Tyr1362Ter	p.Y1362*	ENST00000324856	NM_006015.4	1362	taT/taG	17/20	0.290216125882427	3	FACETS	0.826	0.781	0.872	0.826	0.781	0.872	INDETERMINATE	2	FALSE	1	0.551722258066835	3		583	823	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031900	10031900	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	78	548	0	ENST00000330684.3:c.923A>G	p.Glu308Gly	p.E308G	ENST00000330684	NM_001134407.1	308	gAg/gGg	3/13	0.293316060494285	4	FACETS	0.499	0.438	0.566	0.125	0.109	0.142	INDETERMINATE	1	FALSE	0	0.551722258066835	4		548	879	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99204063	99204063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	77	350	0	ENST00000074304.5:c.2926G>A	p.Glu976Lys	p.E976K	ENST00000074304	NM_001134224.1	976	Gaa/Aaa	26/26	0.457041193471719	4	FACETS	0.704	0.619	0.796	0.352	0.309	0.398	SUBCLONAL	1	FALSE	2	0.551722258066835	4		350	615	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409892	63409892	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	136	347	0	ENST00000330258.3:c.3275C>A	p.Pro1092His	p.P1092H	ENST00000330258	NM_152424.3	1092	cCt/cAt	2/2	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.551722258066835	2		347	390	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	211	63	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.995	0.924	1	0.995	0.924	1	CLONAL	1	TRUE	1	0.418196529905293	2		63	1014	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0031187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	229	798	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.418196529905293	1	FACETS	0.966	0.901	1	0.966	0.901	1	CLONAL	1	TRUE	0	0.418196529905293	1		800	897	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0031187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	377	135	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	1	2	FACETS	0.933	0.889	0.978	1	0.996	1	CLONAL	2	TRUE	1	0.418196529905293	2		135	966	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0031187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	162	415	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	0.418196529905293	1	FACETS	0.963	0.887	1	0.963	0.887	1	CLONAL	1	TRUE	0	0.418196529905293	1		415	636	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383357	42383357	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs782709381	NA	P-0031187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	161	575	0	ENST00000221972.3:c.377G>A	p.Arg126His	p.R126H	ENST00000221972	NM_021601.3	126	cGc/cAc	2/5	0.418196529905293	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.418196529905293	1		575	604	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911099	29911100	+	stop_gained	Nonsense_Mutation	DNP	TC	TC	AA	novel	NA	P-0031187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	165	562	1	ENST00000376809.5:c.398_399delinsAA	p.Phe133Ter	p.F133*	ENST00000376809	NM_002116.7	133	tTC/tAA	3/8	0.418196529905293	1	FACETS	0.931	0.858	1	0.931	0.858	1	CLONAL	1	TRUE	0	0.418196529905293	1		563	670	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0031340-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	182	470	1	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.442402866495832	7	FACETS	0.967	0.902	1			1	CLONAL	4	TRUE	NA	0.442402866495832	7		471	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138729528	NA	P-0031340-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	295	326	0	ENST00000269305.4:c.523C>G	p.Arg175Gly	p.R175G	ENST00000269305	NM_001126112.2	175	Cgc/Ggc	5/11	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.442402866495832	2		326	576	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040679	47040679	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031340-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	272	469	0	ENST00000377604.3:c.1314C>A	p.Tyr438Ter	p.Y438*	ENST00000377604	NM_001204468.1	438	taC/taA	13/24	0.410170049144088	2	FACETS	1	0.964	1			1	CLONAL	3	TRUE	NA	0.442402866495832	2		469	407	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527348	187527348	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs184300563	NA	P-0031340-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	70	508	0	ENST00000441802.2:c.10226C>T	p.Thr3409Met	p.T3409M	ENST00000441802	NM_005245.3	3409	aCg/aTg	17/27	1	2	FACETS	0.865	0.758	0.978	0.865	0.758	0.978	CLONAL	1	TRUE	1	0.442402866495832	2		508	366	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860875	151860875	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031340-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	118	368	0	ENST00000262189.6:c.9787G>A	p.Glu3263Lys	p.E3263K	ENST00000262189	NM_170606.2	3263	Gaa/Aaa	43/59	0.442402866495832	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.442402866495832	3		368	272	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856002	45856002	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0031340-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	112	635	0	ENST00000391945.4:c.1902+2T>A		p.X634_splice	ENST00000391945	NM_000400.3	634			0.442402866495832	3	FACETS	0.989	0.892	1	0.495	0.446	0.546	CLONAL	1	TRUE	1	0.442402866495832	3		635	625	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	33	395	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.779	0.638	0.935	0.779	0.638	0.935	CLONAL	1	TRUE	1	0.344588475335772	2		395	246	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503838	149503838	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs864309711	NA	P-0031354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	149	330	0	ENST00000261799.4:c.1998C>G	p.Asn666Lys	p.N666K	ENST00000261799	NM_002609.3	666	aaC/aaG	14/23	0.344588475335772	3	FACETS	0.886	0.814	0.961	0.886	0.814	0.961	CLONAL	2	TRUE	1	0.344588475335772	3		330	572	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967229	93967229	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	103	229	0	ENST00000369303.4:c.2123T>C	p.Met708Thr	p.M708T	ENST00000369303	NM_004440.3	708	aTg/aCg	12/17	0.344588475335772	2	FACETS	0.955	0.865	1	0.955	0.865	1	CLONAL	2	TRUE	0	0.344588475335772	2		229	313	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219336	1219336	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	146	749	0	ENST00000326873.7:c.388G>T	p.Glu130Ter	p.E130*	ENST00000326873	NM_000455.4	130	Gag/Tag	3/10	0.430867211029117	1	FACETS	0.855	0.783	0.93	0.855	0.783	0.93	CLONAL	1	TRUE	0	0.430867211029117	1		749	622	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0031393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	103	242	1	ENST00000311936.3:c.34_35delinsTT	p.Gly12Phe	p.G12F	ENST00000311936	NM_004985.3	12	GGt/TTt	2/5	1	2	FACETS	0.976	0.877	1	0.976	0.877	1	CLONAL	1	TRUE	1	0.430867211029117	2		243	490	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610285	10610285	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	195	942	2	ENST00000171111.5:c.425C>T	p.Thr142Met	p.T142M	ENST00000171111	NM_203500.1	142	aCg/aTg	2/6	0.430867211029117	1	FACETS	0.962	0.893	1	0.962	0.893	1	CLONAL	1	TRUE	0	0.430867211029117	1		944	738	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026115	71026115	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs797045584	NA	P-0031393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	183	412	0	ENST00000318789.4:c.1507C>T	p.Arg503Ter	p.R503*	ENST00000318789	NM_032682.5	503	Cga/Tga	17/21	0.430867211029117	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.430867211029117	1		412	474	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105508	30105508	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	106	642	0	ENST00000331968.5:c.1178A>T	p.Asn393Ile	p.N393I	ENST00000331968	NM_002742.2	393	aAc/aTc	7/18	1	2	FACETS	0.791	0.71	0.876	0.791	0.71	0.876	SUBCLONAL	1	TRUE	1	0.430867211029117	2		642	622	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312944	30312944	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	130	541	0	ENST00000262643.3:c.747G>T	p.Trp249Cys	p.W249C	ENST00000262643	NM_001238.2	249	tgG/tgT	9/12	1	2	FACETS	0.972	0.884	1	0.972	0.884	1	CLONAL	1	TRUE	1	0.430867211029117	2		541	621	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685307	86685307	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	44	178	0	ENST00000274376.6:c.3023A>G	p.Glu1008Gly	p.E1008G	ENST00000274376	NM_002890.2	1008	gAa/gGa	24/25	1	2	FACETS	0.88	0.745	1	0.88	0.745	1	CLONAL	1	TRUE	1	0.430867211029117	2		178	232	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039686	47039686	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	159	436	0	ENST00000377604.3:c.1138G>T	p.Glu380Ter	p.E380*	ENST00000377604	NM_001204468.1	380	Gag/Tag	11/24	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.430867211029117	1		436	398	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	39	63	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.807	0.68	0.943	0.807	0.68	0.943	CLONAL	1	TRUE	1	0.64	2		63	151	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	83	115	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.64	2		116	229	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	75	103	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.64	2		103	192	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	41	76	0	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.909	0.772	1	0.909	0.772	1	CLONAL	1	TRUE	1	0.64	2		76	141	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007635	45007635	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	23	33	0	ENST00000558401.1:c.82C>T	p.Gln28Ter	p.Q28*	ENST00000558401	NM_004048.2	28	Cag/Tag	2/4	1	2	FACETS	0.877	0.702	1	0.877	0.702	1	CLONAL	1	TRUE	1	0.64	2		33	82	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	28	52	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	0.634	0.514	0.766	0.634	0.514	0.766	SUBCLONAL	1	TRUE	1	0.64	2		52	138	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	211	351	1	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.826	0.769	0.885	0.826	0.769	0.885	CLONAL	1	TRUE	1	0.64	2		352	798	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390585	139390585	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111627256	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	387	498	2	ENST00000277541.6:c.7606G>A	p.Val2536Ile	p.V2536I	ENST00000277541	NM_017617.3	2536	Gtc/Atc	34/34	1	2	FACETS	0.993	0.944	1	0.993	0.944	1	CLONAL	1	TRUE	1	0.64	2		500	1218	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593507	48593507	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1367209662	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	42	70	0	ENST00000342988.3:c.1258C>T	p.Arg420Cys	p.R420C	ENST00000342988	NM_005359.5	420	Cgt/Tgt	10/12	0.3	2	FACETS	0.791	0.671	0.919			1	INDETERMINATE	1	TRUE	NA	0.64	2		70	166	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242662	46242662	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	25	51	0	ENST00000334344.6:c.1624C>T	p.Arg542Ter	p.R542*	ENST00000334344	NM_152641.2	542	Cga/Tga	13/21	1	2	FACETS	0.679	0.545	0.828	0.679	0.545	0.828	SUBCLONAL	1	TRUE	1	0.64	2		51	115	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	209	142	1	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	0.995	1	CLONAL	2	TRUE	1	0.64	2		143	304	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007619	45007619	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs111482205	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	21	22	0	ENST00000558401.1:c.68-2A>G		p.X23_splice	ENST00000558401	NM_004048.2	23			1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.64	2		22	55	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117594	70117594	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	240	312	1	ENST00000245479.2:c.66del	p.Ser23AlafsTer38	p.S23Afs*38	ENST00000245479	NM_000346.3	21	gCc/gc	1/3	1	2	FACETS	0.919	0.861	0.979	0.919	0.861	0.979	CLONAL	1	TRUE	1	0.64	2		313	816	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933640	39933640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780396086	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	181	227	0	ENST00000378444.4:c.959C>T	p.Ala320Val	p.A320V	ENST00000378444	NM_001123385.1	320	gCg/gTg	4/15	0.3	2	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.64	2		227	532	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257102	19257102	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	147	239	1	ENST00000162023.5:c.861del	p.Ala288ProfsTer?	p.A288Pfs*?	ENST00000162023		287	ccC/cc	12/13	1	2	FACETS	0.775	0.71	0.842	0.775	0.71	0.842	SUBCLONAL	1	TRUE	1	0.64	2		240	593	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028638	12028638	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	48	54	0	ENST00000353533.5:c.841C>T	p.Arg281Ter	p.R281*	ENST00000353533	NM_003010.3	281	Cga/Tga	8/11	1	2	FACETS	0.785	0.673	0.905	0.785	0.673	0.905	CLONAL	1	TRUE	1	0.64	2		54	191	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812317	212812317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143662416	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	34	42	0	ENST00000342788.4:c.259G>A	p.Val87Met	p.V87M	ENST00000342788	NM_005235.2	87	Gtg/Atg	3/28	1	2	FACETS	0.984	0.824	1	0.984	0.824	1	CLONAL	1	TRUE	1	0.64	2		42	108	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983363	15983363	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	27	62	0	ENST00000268712.3:c.3416T>C	p.Ile1139Thr	p.I1139T	ENST00000268712	NM_006311.3	1139	aTa/aCa	26/46	1	2	FACETS	0.76	0.617	0.917	0.76	0.617	0.917	CLONAL	1	TRUE	1	0.64	2		62	111	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856377	111856377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	117	127	1	ENST00000341259.2:c.428G>A	p.Arg143His	p.R143H	ENST00000341259	NM_005475.2	143	cGc/cAc	2/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.64	2		128	328	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625159	69625159	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554980306	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	280	365	1	ENST00000334134.2:c.634C>T	p.Arg212Trp	p.R212W	ENST00000334134	NM_005247.2	212	Cgg/Tgg	3/3	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.64	2		366	789	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	231	377	1	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	1	2	FACETS	0.774	0.722	0.827	0.774	0.722	0.827	SUBCLONAL	1	TRUE	1	0.64	2		378	933	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5239002	5239002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775100072	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	316	474	0	ENST00000357368.4:c.1777C>T	p.Arg593Cys	p.R593C	ENST00000357368	NM_002850.3	593	Cgc/Tgc	13/38	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.64	2		474	924	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247358	71247358	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	29	277	0	ENST00000318789.4:c.175C>T	p.Gln59Ter	p.Q59*	ENST00000318789	NM_032682.5	59	Caa/Taa	6/21	1	2	FACETS	0.176	0.14	0.216	0.176	0.14	0.216	SUBCLONAL	1	TRUE	1	0.64	2		277	516	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655272	45655272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764295138	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	206	323	2	ENST00000407780.3:c.580C>T	p.Arg194Trp	p.R194W	ENST00000407780	NM_001283052.1	194	Cgg/Tgg	4/7	1	2	FACETS	0.866	0.806	0.928	0.866	0.806	0.928	CLONAL	1	TRUE	1	0.64	2		325	743	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735351	204735351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759766975	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	77	104	0	ENST00000302823.3:c.152G>A	p.Arg51Gln	p.R51Q	ENST00000302823	NM_005214.4	51	cGa/cAa	2/4	1	2	FACETS	0.853	0.758	0.954	0.853	0.758	0.954	CLONAL	1	TRUE	1	0.64	2		104	282	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120783952	120783952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754954103	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	118	336	0	ENST00000257552.2:c.1033G>A	p.Gly345Ser	p.G345S	ENST00000257552	NM_002442.3	345	Ggc/Agc	13/15	1	2	FACETS	0.431	0.389	0.476	0.431	0.389	0.476	SUBCLONAL	1	TRUE	1	0.64	2		336	855	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	81	141	7	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.931	0.83	1	0.931	0.83	1	CLONAL	1	TRUE	1	0.64	2		148	272	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374298	138374298	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	78	125	0	ENST00000289153.2:c.3146T>G	p.Leu1049Arg	p.L1049R	ENST00000289153	NM_006219.2	1049	cTc/cGc	22/22	1	2	FACETS	0.983	0.876	1	0.983	0.876	1	CLONAL	1	TRUE	1	0.64	2		125	248	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627218	37627218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375280392	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	62	109	0	ENST00000447079.4:c.1133G>A	p.Arg378His	p.R378H	ENST00000447079	NM_015083.1	378	cGc/cAc	2/14	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.64	2		109	190	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440420	49440420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1474346582	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	201	375	1	ENST00000301067.7:c.4390G>A	p.Val1464Ile	p.V1464I	ENST00000301067	NM_003482.3	1464	Gtc/Atc	15/54	1	2	FACETS	0.795	0.738	0.853	0.795	0.738	0.853	SUBCLONAL	1	TRUE	1	0.64	2		376	790	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216642	36216642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1276578109	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	268	385	0	ENST00000222270.7:c.3808C>T	p.Arg1270Cys	p.R1270C	ENST00000222270	NM_014727.1	1270	Cgc/Tgc	13/37	1	2	FACETS	0.958	0.901	1	0.958	0.901	1	CLONAL	1	TRUE	1	0.64	2		385	874	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983281	149983281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749247753	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	19	93	0	ENST00000253339.5:c.2977G>A	p.Glu993Lys	p.E993K	ENST00000253339		993	Gaa/Aaa	7/7	1	2	FACETS	0.341	0.26	0.435	0.341	0.26	0.435	SUBCLONAL	1	TRUE	1	0.64	2		93	174	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849153	156849153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	138	207	0	ENST00000524377.1:c.2045G>A	p.Arg682His	p.R682H	ENST00000524377	NM_002529.3	682	cGt/cAt	15/17	1	2	FACETS	0.923	0.847	1	0.923	0.847	1	CLONAL	1	TRUE	1	0.64	2		207	467	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164136	108164137	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	23	55	0	ENST00000278616.4:c.4713dup	p.Lys1572Ter	p.K1572*	ENST00000278616	NM_000051.3	1570	gtt/gTtt	31/63	1	2	FACETS	0.712	0.566	0.873	0.712	0.566	0.873	SUBCLONAL	1	TRUE	1	0.64	2		55	101	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431159	49431159	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs771174318	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	287	384	0	ENST00000301067.7:c.9980A>G	p.Gln3327Arg	p.Q3327R	ENST00000301067	NM_003482.3	3327	cAg/cGg	34/54	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.64	2		384	897	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40993362	40993362	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	34	46	0	ENST00000267868.3:c.188T>A	p.Ile63Asn	p.I63N	ENST00000267868	NM_002875.4	63	aTt/aAt	3/10	1	2	FACETS	0.857	0.715	1	0.857	0.715	1	CLONAL	1	TRUE	1	0.64	2		46	124	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112990	2112990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	330	485	1	ENST00000219476.3:c.1379C>T	p.Ala460Val	p.A460V	ENST00000219476	NM_000548.3	460	gCc/gTc	14/42	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.64	2		486	939	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134470	2134470	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	338	445	0	ENST00000219476.3:c.4247C>T	p.Ala1416Val	p.A1416V	ENST00000219476	NM_000548.3	1416	gCc/gTc	34/42	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.64	2		445	1000	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828083	3828083	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	174	309	0	ENST00000262367.5:c.2042A>G	p.Asn681Ser	p.N681S	ENST00000262367	NM_004380.2	681	aAc/aGc	10/31	1	2	FACETS	0.843	0.779	0.909	0.843	0.779	0.909	CLONAL	1	TRUE	1	0.64	2		309	645	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128490	30128490	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	124	218	0	ENST00000263025.4:c.892A>G	p.Lys298Glu	p.K298E	ENST00000263025	NM_002746.2	298	Aag/Gag	6/9	1	2	FACETS	0.77	0.701	0.843	0.77	0.701	0.843	SUBCLONAL	1	TRUE	1	0.64	2		218	503	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805076	89805076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1047662111	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	328	370	0	ENST00000389301.3:c.4301C>T	p.Ala1434Val	p.A1434V	ENST00000389301	NM_000135.2	1434	gCc/gTc	43/43	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.64	2		370	934	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40457658	40457658	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	217	315	0	ENST00000345506.4:c.1411C>A	p.His471Asn	p.H471N	ENST00000345506	NM_003152.3	471	Cac/Aac	13/20	1	2	FACETS	0.877	0.818	0.938	0.877	0.818	0.938	CLONAL	1	TRUE	1	0.64	2		315	773	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593486	48593486	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	82	69	0	ENST00000342988.3:c.1237T>C	p.Tyr413His	p.Y413H	ENST00000342988	NM_005359.5	413	Tac/Cac	10/12	0.3	2	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.64	2		69	217	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211706	5211706	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757375502	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	176	295	0	ENST00000357368.4:c.5129G>A	p.Arg1710His	p.R1710H	ENST00000357368	NM_002850.3	1710	cGc/cAc	33/38	1	2	FACETS	0.896	0.829	0.964	0.896	0.829	0.964	CLONAL	1	TRUE	1	0.64	2		295	614	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125388	7125388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	320	441	1	ENST00000302850.5:c.3164C>T	p.Ala1055Val	p.A1055V	ENST00000302850	NM_000208.2	1055	gCg/gTg	17/22	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.64	2		442	993	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383692	42383692	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202097187	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	257	351	0	ENST00000221972.3:c.467C>T	p.Ala156Val	p.A156V	ENST00000221972	NM_021601.3	156	gCg/gTg	3/5	1	2	FACETS	0.885	0.831	0.942	0.885	0.831	0.942	CLONAL	1	TRUE	1	0.64	2		351	907	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637354	47637354	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs63750214	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	88	116	0	ENST00000233146.2:c.488T>A	p.Val163Asp	p.V163D	ENST00000233146	NM_000251.2	163	gTt/gAt	3/16	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.64	2		116	273	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439517	220439517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142156311	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	43	284	0	ENST00000243786.2:c.370C>T	p.Arg124Cys	p.R124C	ENST00000243786	NM_002191.3	124	Cgc/Tgc	2/2	1	2	FACETS	0.197	0.164	0.233	0.197	0.164	0.233	SUBCLONAL	1	TRUE	1	0.64	2		284	683	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538355	9538355	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	38	50	0	ENST00000353224.5:c.1643T>A	p.Val548Asp	p.V548D	ENST00000353224	NM_177990.2	548	gTc/gAc	7/10	1	2	FACETS	0.69	0.578	0.812	0.69	0.578	0.812	SUBCLONAL	1	TRUE	1	0.64	2		50	172	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62320979	62320979	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	177	254	0	ENST00000360203.5:c.2003G>A	p.Gly668Asp	p.G668D	ENST00000360203	NM_001283009.1	668	gGc/gAc	23/35	1	2	FACETS	0.904	0.837	0.973	0.904	0.837	0.973	CLONAL	1	TRUE	1	0.64	2		254	612	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157048	106157048	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	15	111	0	ENST00000380013.4:c.1949A>G	p.His650Arg	p.H650R	ENST00000380013	NM_001127208.2	650	cAt/cGt	3/11	1	2	FACETS	0.175	0.127	0.232	0.175	0.127	0.232	SUBCLONAL	1	TRUE	1	0.64	2		111	268	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164887	106164887	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	209	237	0	ENST00000380013.4:c.3755T>C	p.Leu1252Pro	p.L1252P	ENST00000380013	NM_001127208.2	1252	cTg/cCg	6/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.64	2		237	573	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681703	30681703	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs534669744	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	131	163	0	ENST00000376406.3:c.394C>T	p.Arg132Cys	p.R132C	ENST00000376406	NM_014641.2	132	Cgc/Tgc	3/15	1	2	FACETS	0.869	0.794	0.947	0.869	0.794	0.947	CLONAL	1	TRUE	1	0.64	2		163	471	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165237	32165237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1425032163	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	181	262	0	ENST00000375023.3:c.4891G>A	p.Val1631Met	p.V1631M	ENST00000375023	NM_004557.3	1631	Gtg/Atg	27/30	1	2	FACETS	0.752	0.695	0.811	0.752	0.695	0.811	SUBCLONAL	1	TRUE	1	0.64	2		262	752	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29197752	29197752	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	168	265	0	ENST00000240100.2:c.442G>C	p.Glu148Gln	p.E148Q	ENST00000240100	NM_001394.6	148	Gag/Cag	2/4	1	2	FACETS	0.908	0.839	0.979	0.908	0.839	0.979	CLONAL	1	TRUE	1	0.64	2		265	578	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372146	55372146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	179	306	0	ENST00000297316.4:c.836C>T	p.Ala279Val	p.A279V	ENST00000297316	NM_022454.3	279	gCg/gTg	2/2	1	2	FACETS	0.84	0.777	0.905	0.84	0.777	0.905	CLONAL	1	TRUE	1	0.64	2		306	666	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739485	145739485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772074149	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	61	367	1	ENST00000428558.2:c.1885C>T	p.Arg629Trp	p.R629W	ENST00000428558	NM_004260.3	629	Cgg/Tgg	12/22	1	2	FACETS	0.228	0.196	0.263	0.228	0.196	0.263	SUBCLONAL	1	TRUE	1	0.64	2		368	837	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389304	8389304	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	14	91	0	ENST00000356435.5:c.4314C>A	p.Asp1438Glu	p.D1438E	ENST00000356435		1438	gaC/gaA	26/35	1	2	FACETS	0.217	0.156	0.289	0.217	0.156	0.289	SUBCLONAL	1	TRUE	1	0.64	2		91	202	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391212	139391212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751007903	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	261	410	0	ENST00000277541.6:c.6979C>T	p.Arg2327Trp	p.R2327W	ENST00000277541	NM_017617.3	2327	Cgg/Tgg	34/34	1	2	FACETS	0.921	0.864	0.978	0.921	0.864	0.978	CLONAL	1	TRUE	1	0.64	2		410	886	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401008	139401008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763098618	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	284	435	0	ENST00000277541.6:c.3985G>A	p.Ala1329Thr	p.A1329T	ENST00000277541	NM_017617.3	1329	Gcc/Acc	24/34	1	2	FACETS	0.96	0.905	1	0.96	0.905	1	CLONAL	1	TRUE	1	0.64	2		435	924	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793259	139793259	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	224	376	1	ENST00000247668.2:c.67C>A	p.Leu23Ile	p.L23I	ENST00000247668	NM_021138.3	23	Ctc/Atc	2/11	1	2	FACETS	0.793	0.739	0.848	0.793	0.739	0.848	SUBCLONAL	1	TRUE	1	0.64	2		377	883	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240811	53240811	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	117	21	0	ENST00000375401.3:c.1269G>T	p.Lys423Asn	p.K423N	ENST00000375401	NM_004187.3	423	aaG/aaT	10/26	0.3	2	FACETS	0.988	0.9	1			1	INDETERMINATE	1	TRUE	NA	0.64	2		21	370	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	99	379	0	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	0.799	0.718	0.884	0.799	0.718	0.884	SUBCLONAL	1	TRUE	1	0.6	2		379	413	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	169	315	2	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.861	0.807	0.916	1	0.993	1	CLONAL	2	TRUE	1	0.6	2		317	327	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	40	555	6	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.266	0.221	0.317	0.266	0.221	0.317	SUBCLONAL	1	TRUE	1	0.6	2		561	501	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	188	605	0	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.6	2		605	612	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	216	646	4	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.928	0.865	0.992	0.928	0.865	0.992	CLONAL	1	TRUE	1	0.6	2		650	776	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	11	295	1	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS	0.159	0.11	0.221	0.159	0.11	0.221	SUBCLONAL	1	TRUE	1	0.6	2		296	230	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	170	535	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.984	0.91	1	0.984	0.91	1	CLONAL	1	TRUE	1	0.6	2		535	576	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	75	267	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.98	0.871	1	0.98	0.871	1	CLONAL	1	TRUE	1	0.6	2		267	255	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	90	394	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.673	0.6	0.75	0.673	0.6	0.75	SUBCLONAL	1	TRUE	1	0.6	2		394	446	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796883	42796883	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	174	608	1	ENST00000575354.2:c.3347del	p.Pro1116GlnfsTer45	p.P1116Qfs*45	ENST00000575354	NM_015125.3	1114	gCc/gc	14/20	1	2	FACETS	0.861	0.795	0.928	0.861	0.795	0.928	CLONAL	1	TRUE	1	0.6	2		609	674	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	105	495	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.923	0.835	1	0.923	0.835	1	CLONAL	1	TRUE	1	0.6	2		495	379	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	313	338	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	0.997	1	CLONAL	2	TRUE	1	0.6	2		338	494	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310914	123310914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	144	377	0	ENST00000358487.5:c.514G>A	p.Ala172Thr	p.A172T	ENST00000358487	NM_000141.4	172	Gcc/Acc	5/18	1	2	FACETS	0.907	0.832	0.985	0.907	0.832	0.985	CLONAL	1	TRUE	1	0.6	2		377	529	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720712	89720712	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	21	79	0	ENST00000371953.3:c.867del	p.Val290Ter	p.V290*	ENST00000371953	NM_000314.4	288	gAa/ga	8/9	1	2	FACETS	0.805	0.634	0.994	0.805	0.634	0.994	CLONAL	1	TRUE	1	0.6	2		79	87	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606814	43606814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746512075	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	149	566	0	ENST00000355710.3:c.1423C>T	p.Arg475Trp	p.R475W	ENST00000355710	NM_020975.4	475	Cgg/Tgg	7/20	1	2	FACETS	0.92	0.845	0.997	0.92	0.845	0.997	CLONAL	1	TRUE	1	0.6	2		566	540	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910549	29910549	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45585732	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	247	20	2	ENST00000376809.5:c.89G>A	p.Arg30Lys	p.R30K	ENST00000376809	NM_002116.7	30	aGg/aAg	2/8	0.0825343750246759	3	FACETS	1	0.98	1	1	0.98	1	INDETERMINATE	2	TRUE	1	0.6	3		22	499	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884218	37884218	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	117	464	0	ENST00000269571.5:c.3694del	p.Ala1232LeufsTer70	p.A1232Lfs*70	ENST00000269571		1230	cGg/cg	27/27	1	2	FACETS	0.707	0.639	0.777	0.707	0.639	0.777	SUBCLONAL	1	TRUE	1	0.6	2		464	552	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	97	373	0	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.932	0.839	1	0.932	0.839	1	CLONAL	1	TRUE	1	0.6	2		373	347	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137832	64137832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753090599	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	212	671	1	ENST00000334205.4:c.1933G>A	p.Glu645Lys	p.E645K	ENST00000334205	NM_003942.2	645	Gag/Aag	15/17	1	2	FACETS	0.983	0.917	1	0.983	0.917	1	CLONAL	1	TRUE	1	0.6	2		672	719	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023186	31023186	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774520876	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	110	591	0	ENST00000375687.4:c.2671G>A	p.Val891Ile	p.V891I	ENST00000375687	NM_015338.5	891	Gtt/Att	13/13	1	2	FACETS	0.845	0.764	0.929	0.845	0.764	0.929	CLONAL	1	TRUE	1	0.6	2		591	434	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345769	152345769	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs759063323	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	12	266	0	ENST00000359321.1:c.801del	p.Lys267AsnfsTer30	p.K267Nfs*30	ENST00000359321	NM_005431.1	267	aaA/aa	3/3	1	2	FACETS	0.208	0.146	0.284	0.208	0.146	0.284	SUBCLONAL	1	TRUE	1	0.6	2		266	192	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061219	38061219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	25	395	0	ENST00000250448.2:c.770G>A	p.Gly257Asp	p.G257D	ENST00000250448	NM_004496.3	257	gGc/gAc	2/2	1	2	FACETS	0.174	0.136	0.217	0.174	0.136	0.217	SUBCLONAL	1	TRUE	1	0.6	2		395	479	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101086	41101086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776769442	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	141	398	0	ENST00000373198.4:c.1270G>A	p.Val424Met	p.V424M	ENST00000373198	NM_133170.3	424	Gtg/Atg	8/32	1	2	FACETS	0.948	0.869	1	0.948	0.869	1	CLONAL	1	TRUE	1	0.6	2		398	496	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276958	123276958	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	90	268	0	ENST00000358487.5:c.959C>T	p.Thr320Met	p.T320M	ENST00000358487	NM_000141.4	320	aCg/aTg	8/18	1	2	FACETS	0.952	0.854	1	0.952	0.854	1	CLONAL	1	TRUE	1	0.6	2		268	315	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786734	3786734	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	154	491	0	ENST00000262367.5:c.4477del	p.Ile1493TyrfsTer57	p.I1493Yfs*57	ENST00000262367	NM_004380.2	1493	Ata/ta	27/31	1	2	FACETS	0.901	0.828	0.975	0.901	0.828	0.975	CLONAL	1	TRUE	1	0.6	2		491	570	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95596408	95596408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775207591	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	54	329	0	ENST00000393063.1:c.560G>A	p.Arg187Gln	p.R187Q	ENST00000393063	NM_030621.3	187	cGa/cAa	6/28	1	2	FACETS	0.766	0.661	0.878	0.766	0.661	0.878	SUBCLONAL	1	TRUE	1	0.6	2		329	235	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752695	42752695	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1366176199	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	150	451	2	ENST00000222329.4:c.1569del	p.Leu525SerfsTer6	p.L525Sfs*6	ENST00000222329	NM_006494.2	523	ggG/gg	4/4	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.6	2		453	498	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	159	503	2	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	0.0825343750246759	3	FACETS	1	0.976	1	0.577	0.531	0.624	INDETERMINATE	1	TRUE	1	0.6	3		505	597	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576819	67576819	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs367669362	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	59	322	0	ENST00000274335.5:c.901C>T	p.Arg301Ter	p.R301*	ENST00000274335		301	Cga/Tga	6/15	1	2	FACETS	0.894	0.78	1	0.894	0.78	1	CLONAL	1	TRUE	1	0.6	2		322	220	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934531	9934531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	26	332	0	ENST00000330684.3:c.1624G>A	p.Gly542Ser	p.G542S	ENST00000330684	NM_001134407.1	542	Ggc/Agc	7/13	1	2	FACETS	0.228	0.18	0.283	0.228	0.18	0.283	SUBCLONAL	1	TRUE	1	0.6	2		332	380	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258944	16258944	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	156	650	0	ENST00000375759.3:c.6215del	p.Asn2072ThrfsTer14	p.N2072Tfs*14	ENST00000375759	NM_015001.2	2070	gAa/ga	11/15	1	2	FACETS	0.802	0.737	0.87	0.802	0.737	0.87	CLONAL	1	TRUE	1	0.6	2		650	648	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231215	98231215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750970743	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	155	467	0	ENST00000331920.6:c.2068G>A	p.Val690Ile	p.V690I	ENST00000331920	NM_000264.3	690	Gtc/Atc	14/24	1	2	FACETS	0.786	0.722	0.853	0.786	0.722	0.853	SUBCLONAL	1	TRUE	1	0.6	2		467	657	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400267	139400267	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	141	513	0	ENST00000277541.6:c.4081G>A	p.Gly1361Ser	p.G1361S	ENST00000277541	NM_017617.3	1361	Ggc/Agc	25/34	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.6	2		513	458	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741678	17741678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	30	294	0	ENST00000250003.3:c.349C>T	p.Arg117Cys	p.R117C	ENST00000250003	NM_002478.4	117	Cgc/Tgc	1/3	1	2	FACETS	0.184	0.148	0.226	0.184	0.148	0.226	SUBCLONAL	1	TRUE	1	0.6	2		294	543	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435774	110435774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1428455100	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	83	97	0	ENST00000375856.3:c.2627G>A	p.Arg876His	p.R876H	ENST00000375856	NM_003749.2	876	cGc/cAc	1/2	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.6	2		97	192	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981921	70981921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	190	514	1	ENST00000276594.2:c.175G>A	p.Ala59Thr	p.A59T	ENST00000276594	NM_024504.3	59	Gca/Aca	2/8	1	2	FACETS	0.918	0.852	0.986	0.918	0.852	0.986	CLONAL	1	TRUE	1	0.6	2		515	690	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15280905	15280905	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	168	468	0	ENST00000263388.2:c.5191C>T	p.Arg1731Trp	p.R1731W	ENST00000263388	NM_000435.2	1731	Cgg/Tgg	28/33	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.6	2		468	523	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560482	95560482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878855272	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	110	366	0	ENST00000393063.1:c.5107C>T	p.Arg1703Cys	p.R1703C	ENST00000393063	NM_030621.3	1703	Cgc/Tgc	25/28	1	2	FACETS	0.901	0.816	0.989	0.901	0.816	0.989	CLONAL	1	TRUE	1	0.6	2		366	407	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527703	157527703	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554237318	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	208	458	0	ENST00000346085.5:c.5428C>T	p.Gln1810Ter	p.Q1810*	ENST00000346085	NM_020732.3	1810	Cag/Tag	20/20	0.0825343750246759	3	FACETS	1	0.986	1	0.613	0.571	0.657	INDETERMINATE	1	TRUE	1	0.6	3		458	735	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259062	16259063	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	127	456	0	ENST00000375759.3:c.6331dup	p.Glu2111GlyfsTer12	p.E2111Gfs*12	ENST00000375759	NM_015001.2	2109	-/G	11/15	1	2	FACETS	0.842	0.767	0.92	0.842	0.767	0.92	CLONAL	1	TRUE	1	0.6	2		456	503	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429279	78429279	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	78	351	0	ENST00000370768.2:c.1163C>T	p.Thr388Ile	p.T388I	ENST00000370768	NM_003902.3	388	aCt/aTt	13/20	1	2	FACETS	0.734	0.65	0.824	0.734	0.65	0.824	SUBCLONAL	1	TRUE	1	0.6	2		351	354	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451273	70451273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	192	548	0	ENST00000373644.4:c.6113G>A	p.Arg2038His	p.R2038H	ENST00000373644	NM_030625.2	2038	cGt/cAt	12/12	1	2	FACETS	0.891	0.827	0.958	0.891	0.827	0.958	CLONAL	1	TRUE	1	0.6	2		548	718	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692838	89692839	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	30	161	0	ENST00000371953.3:c.324dup	p.Asp109Ter	p.D109*	ENST00000371953	NM_000314.4	108	ctt/cTtt	5/9	1	2	FACETS	0.935	0.77	1	0.935	0.77	1	CLONAL	1	TRUE	1	0.6	2		161	107	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156651	2156651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	161	504	0	ENST00000434045.2:c.271G>A	p.Gly91Arg	p.G91R	ENST00000434045	NM_001127598.1	91	Ggg/Agg	3/5	1	2	FACETS	0.94	0.867	1	0.94	0.867	1	CLONAL	1	TRUE	1	0.6	2		504	571	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625162	69625162	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554980307	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	146	519	0	ENST00000334134.2:c.631C>T	p.Arg211Trp	p.R211W	ENST00000334134	NM_005247.2	211	Cgg/Tgg	3/3	1	2	FACETS	0.869	0.797	0.944	0.869	0.797	0.944	CLONAL	1	TRUE	1	0.6	2		519	560	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170528	108170528	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	16	434	1	ENST00000278616.4:c.5093A>G	p.Lys1698Arg	p.K1698R	ENST00000278616	NM_000051.3	1698	aAg/aGg	34/63	1	2	FACETS	0.214	0.158	0.281	0.214	0.158	0.281	SUBCLONAL	1	TRUE	1	0.6	2		435	249	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427023	49427023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1270374784	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	108	400	0	ENST00000301067.7:c.11465G>A	p.Gly3822Asp	p.G3822D	ENST00000301067	NM_003482.3	3822	gGc/gAc	39/54	0.0825343750246759	3	FACETS	1	0.983	1	0.703	0.638	0.77	INDETERMINATE	1	TRUE	1	0.6	3		400	333	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431178	49431178	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs793888512	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	176	470	0	ENST00000301067.7:c.9961C>T	p.Arg3321Ter	p.R3321*	ENST00000301067	NM_003482.3	3321	Cga/Tga	34/54	0.0825343750246759	3	FACETS	1	0.989	1	0.688	0.638	0.74	INDETERMINATE	1	TRUE	1	0.6	3		470	554	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120819	115120819	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	77	364	0	ENST00000257566.3:c.187C>G	p.Pro63Ala	p.P63A	ENST00000257566	NM_016569.3	63	Ccg/Gcg	1/8	0.0825343750246759	3	FACETS	1	0.962	1	0.6	0.533	0.671	INDETERMINATE	1	TRUE	1	0.6	3		364	278	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609813	81609813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs925961475	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	109	261	0	ENST00000298171.2:c.1411G>A	p.Ala471Thr	p.A471T	ENST00000298171	NM_000369.2	471	Gcc/Acc	10/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.6	2		261	323	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569939	95569939	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	87	327	0	ENST00000393063.1:c.3794C>T	p.Thr1265Ile	p.T1265I	ENST00000393063	NM_030621.3	1265	aCa/aTa	22/28	1	2	FACETS	0.924	0.826	1	0.924	0.826	1	CLONAL	1	TRUE	1	0.6	2		327	314	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643536	38643536	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373477920	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	83	530	0	ENST00000299084.4:c.1006G>A	p.Val336Ile	p.V336I	ENST00000299084	NM_152594.2	336	Gta/Ata	7/7	0.135154276832324	1	FACETS	0.573	0.51	0.639	0.573	0.51	0.639	INDETERMINATE	1	TRUE	0	0.6	1		530	338	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423659	88423659	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs766284968	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	50	294	0	ENST00000360948.2:c.2176G>A	p.Val726Met	p.V726M	ENST00000360948	NM_001012338.2	726	Gtg/Atg	18/19	0.135154276832324	1	FACETS	0.449	0.384	0.519	0.449	0.384	0.519	INDETERMINATE	1	TRUE	0	0.6	1		294	260	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136268	2136268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	177	505	0	ENST00000219476.3:c.4738del	p.Arg1580GlyfsTer5	p.R1580Gfs*5	ENST00000219476	NM_000548.3	1579	ggC/gg	37/42	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.6	2		505	560	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81968056	81968058	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	102	374	0	ENST00000359376.3:c.2766_2768del	p.Lys922del	p.K922del	ENST00000359376	NM_002661.3	921	gAGAag/gag	26/33	1	2	FACETS	0.731	0.657	0.809	0.731	0.657	0.809	SUBCLONAL	1	TRUE	1	0.6	2		374	465	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81968074	81968074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	129	426	0	ENST00000359376.3:c.2780C>T	p.Ala927Val	p.A927V	ENST00000359376	NM_002661.3	927	gCc/gTc	26/33	1	2	FACETS	0.885	0.807	0.965	0.885	0.807	0.965	CLONAL	1	TRUE	1	0.6	2		426	486	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127351	17127351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759556434	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	194	527	1	ENST00000285071.4:c.503G>A	p.Arg168His	p.R168H	ENST00000285071	NM_144997.5	168	cGc/cAc	6/14	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.6	2		528	630	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883114	37883114	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749454186	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	172	551	1	ENST00000269571.5:c.3017G>A	p.Arg1006His	p.R1006H	ENST00000269571		1006	cGc/cAc	25/27	1	2	FACETS	0.965	0.893	1	0.965	0.893	1	CLONAL	1	TRUE	1	0.6	2		552	594	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40364003	40364003	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	255	689	0	ENST00000293328.3:c.1679G>T	p.Arg560Met	p.R560M	ENST00000293328	NM_012448.3	560	aGg/aTg	13/19	1	2	FACETS	0.923	0.865	0.982	0.923	0.865	0.982	CLONAL	1	TRUE	1	0.6	2		689	921	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221243	1221243	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	160	524	0	ENST00000326873.7:c.766G>C	p.Glu256Gln	p.E256Q	ENST00000326873	NM_000455.4	256	Gaa/Caa	6/10	1	2	FACETS	0.853	0.786	0.924	0.853	0.786	0.924	CLONAL	1	TRUE	1	0.6	2		524	625	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220901	36220901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	193	50	0	ENST00000222270.7:c.4951G>A	p.Val1651Met	p.V1651M	ENST00000222270	NM_014727.1	1651	Gtg/Atg	23/37	1	2	FACETS	1	0.968	1	1	0.995	1	CLONAL	2	TRUE	1	0.6	2		50	312	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856394	45856394	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	236	503	1	ENST00000391945.4:c.1778G>A	p.Gly593Glu	p.G593E	ENST00000391945	NM_000400.3	593	gGg/gAg	19/23	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.6	2		504	655	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867013	45867013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	102	392	2	ENST00000391945.4:c.1106G>A	p.Arg369His	p.R369H	ENST00000391945	NM_000400.3	369	cGc/cAc	11/23	1	2	FACETS	0.821	0.74	0.907	0.821	0.74	0.907	CLONAL	1	TRUE	1	0.6	2		394	414	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693886	47693886	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	68	415	0	ENST00000233146.2:c.1600del	p.Arg534ValfsTer9	p.R534Vfs*9	ENST00000233146	NM_000251.2	534	Cgt/gt	10/16	0.135154276832324	0	FACETS	0.312	0.273	0.352			1	INDETERMINATE	1	TRUE	0	0.6	0		415	291	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47709917	47709917	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs267608020	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	308	62	0	ENST00000233146.2:c.2635-1G>C		p.X879_splice	ENST00000233146	NM_000251.2	879			0.135154276832324	0	FACETS		NA	1			1	INDETERMINATE	2	TRUE	0	0.6	0		62	462	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023050	48023050	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553411396	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	70	294	0	ENST00000234420.5:c.475G>A	p.Ala159Thr	p.A159T	ENST00000234420	NM_000179.2	159	Gcc/Acc	3/10	0.135154276832324	0	FACETS	0.31	0.272	0.35			1	INDETERMINATE	1	TRUE	0	0.6	0		294	301	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660400	227660400	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	104	379	0	ENST00000305123.5:c.3055A>T	p.Ile1019Phe	p.I1019F	ENST00000305123	NM_005544.2	1019	Att/Ttt	1/2	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.6	2		379	325	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024162	31024162	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	163	513	0	ENST00000375687.4:c.3647T>C	p.Val1216Ala	p.V1216A	ENST00000375687	NM_015338.5	1216	gTg/gCg	13/13	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.6	2		513	489	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39763604	39763605	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	74	304	0	ENST00000288319.7:c.847dup	p.Thr283AsnfsTer2	p.T283Nfs*2	ENST00000288319	NM_182918.3	283	act/aAct	8/10	1	2	FACETS	0.851	0.752	0.954	0.851	0.752	0.954	CLONAL	1	TRUE	1	0.6	2		304	290	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660103	12660103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772390935	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	93	422	2	ENST00000251849.4:c.118C>T	p.Arg40Cys	p.R40C	ENST00000251849	NM_002880.3	40	Cgc/Tgc	2/17	1	2	FACETS	0.795	0.712	0.882	0.795	0.712	0.882	SUBCLONAL	1	TRUE	1	0.6	2		424	390	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098880	47098880	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	134	567	0	ENST00000409792.3:c.6394C>G	p.Arg2132Gly	p.R2132G	ENST00000409792	NM_014159.6	2132	Cgg/Ggg	15/21	1	2	FACETS	0.641	0.583	0.701	0.641	0.583	0.701	SUBCLONAL	1	TRUE	1	0.6	2		567	697	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939853	49939853	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	271	623	1	ENST00000296474.3:c.1190G>A	p.Gly397Asp	p.G397D	ENST00000296474	NM_002447.2	397	gGc/gAc	1/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.6	2		624	888	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521703	89521703	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	106	356	0	ENST00000336596.2:c.2780A>G	p.His927Arg	p.H927R	ENST00000336596	NM_005233.5	927	cAc/cGc	16/17	1	2	FACETS	0.913	0.825	1	0.913	0.825	1	CLONAL	1	TRUE	1	0.6	2		356	387	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526074	189526074	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	143	370	0	ENST00000264731.3:c.338A>T	p.Asn113Ile	p.N113I	ENST00000264731	NM_003722.4	113	aAc/aTc	4/14	1	2	FACETS	0.862	0.79	0.937	0.862	0.79	0.937	CLONAL	1	TRUE	1	0.6	2		370	553	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541754	187541754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147571313	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	87	317	0	ENST00000441802.2:c.5986G>A	p.Glu1996Lys	p.E1996K	ENST00000441802	NM_005245.3	1996	Gaa/Aaa	10/27	1	2	FACETS	0.993	0.89	1	0.993	0.89	1	CLONAL	1	TRUE	1	0.6	2		317	292	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254486	1254486	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1345598002	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	110	492	0	ENST00000310581.5:c.3292A>G	p.Thr1098Ala	p.T1098A	ENST00000310581	NM_198253.2	1098	Aca/Gca	15/16	1	2	FACETS	0.719	0.649	0.793	0.719	0.649	0.793	SUBCLONAL	1	TRUE	1	0.6	2		492	510	SUCCESS
APC	324	MSKCC	GRCh37	5	112177907	112177907	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	315	14	0	ENST00000257430.4:c.6616A>G	p.Asn2206Asp	p.N2206D	ENST00000257430	NM_000038.5	2206	Aat/Gat	16/16	1	2	FACETS	0.949	0.907	0.991	1	0.996	1	CLONAL	2	TRUE	1	0.6	2		14	553	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435636	149435636	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	134	507	0	ENST00000286301.3:c.2507G>A	p.Ser836Asn	p.S836N	ENST00000286301	NM_005211.3	836	aGc/aAc	19/22	1	2	FACETS	0.785	0.716	0.857	0.785	0.716	0.857	SUBCLONAL	1	TRUE	1	0.6	2		507	569	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709464	176709464	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs587784163	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	40	310	0	ENST00000439151.2:c.5893-2A>G		p.X1965_splice	ENST00000439151	NM_022455.4	1965			1	2	FACETS	0.713	0.6	0.836	0.713	0.6	0.836	SUBCLONAL	1	TRUE	1	0.6	2		310	187	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839812	27839812	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	178	450	0	ENST00000328488.2:c.282G>T	p.Gln94His	p.Q94H	ENST00000328488	NM_003533.2	94	caG/caT	1/1	0.0825343750246759	3	FACETS	1	0.987	1	0.645	0.597	0.694	INDETERMINATE	1	TRUE	1	0.6	3		450	598	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026810	6026810	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658794	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	93	285	0	ENST00000265849.7:c.1586C>T	p.Ser529Leu	p.S529L	ENST00000265849	NM_000535.5	529	tCg/tTg	11/15	1	2	FACETS	0.904	0.811	1	0.904	0.811	1	CLONAL	1	TRUE	1	0.6	2		285	343	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843381	128843381	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	130	476	0	ENST00000249373.3:c.488G>C	p.Trp163Ser	p.W163S	ENST00000249373	NM_005631.4	163	tGg/tCg	2/12	1	2	FACETS	0.851	0.777	0.929	0.851	0.777	0.929	CLONAL	1	TRUE	1	0.6	2		476	509	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752956	128752956	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	134	359	1	ENST00000377970.2:c.1117A>G	p.Thr373Ala	p.T373A	ENST00000377970	NM_002467.4	373	Aca/Gca	3/3	1	2	FACETS	0.967	0.885	1	0.967	0.885	1	CLONAL	1	TRUE	1	0.6	2		360	462	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639896	93639896	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	19	253	0	ENST00000375746.1:c.1225A>G	p.Asn409Asp	p.N409D	ENST00000375746	NM_001174167.1	409	Aat/Gat	10/14	1	2	FACETS	0.249	0.189	0.32	0.249	0.189	0.32	SUBCLONAL	1	TRUE	1	0.6	2		253	254	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781133	135781133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	120	451	1	ENST00000298552.3:c.1832C>T	p.Ala611Val	p.A611V	ENST00000298552	NM_001162426.1	611	gCa/gTa	15/23	1	2	FACETS	0.837	0.76	0.917	0.837	0.76	0.917	CLONAL	1	TRUE	1	0.6	2		452	478	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139563052	139563052	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	148	491	0	ENST00000308874.7:c.124G>C	p.Glu42Gln	p.E42Q	ENST00000308874		42	Gag/Cag	4/10	1	2	FACETS	0.814	0.746	0.884	0.814	0.746	0.884	CLONAL	1	TRUE	1	0.6	2		491	606	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342382	70342382	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	169	467	0	ENST00000374080.3:c.1273G>A	p.Glu425Lys	p.E425K	ENST00000374080		425	Gag/Aag	9/45	1	2	FACETS	0.893	0.824	0.964	0.893	0.824	0.964	CLONAL	1	TRUE	1	0.6	2		467	631	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849172	76849173	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0031501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	42	329	0	ENST00000373344.5:c.6103dup	p.Asp2035GlyfsTer2	p.D2035Gfs*2	ENST00000373344	NM_000489.3	2035	gat/gGat	26/35	1	2	FACETS	0.664	0.56	0.776	0.664	0.56	0.776	SUBCLONAL	1	TRUE	1	0.6	2		329	211	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0031502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	14	323	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.246638990860217	1	FACETS	0.565	0.41	0.752	0.565	0.41	0.752	SUBCLONAL	1	FALSE	0	0.246638990860217	1		323	176	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0031502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	45	535	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.161325335903894	1	FACETS	0.557	0.468	0.657	0.557	0.468	0.657	SUBCLONAL	1	FALSE	0	0.246638990860217	1		535	574	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100847	27100848	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0031502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	18	447	0	ENST00000324856.7:c.4129_4130insC	p.Tyr1377SerfsTer68	p.Y1377Sfs*68	ENST00000324856	NM_006015.4	1377	tat/tCat	18/20	1	2	FACETS	0.479	0.36	0.619	0.479	0.36	0.619	SUBCLONAL	1	FALSE	1	0.246638990860217	2		447	305	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433394	49433394	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783727	NA	P-0031503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	264	587	2	ENST00000301067.7:c.8053C>T	p.Arg2685Ter	p.R2685*	ENST00000301067	NM_003482.3	2685	Cga/Tga	32/54	0.753858017785727	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.753858017785727	3		589	460	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262201	16262201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	75	191	0	ENST00000375759.3:c.9466C>T	p.Pro3156Ser	p.P3156S	ENST00000375759	NM_015001.2	3156	Ccc/Tcc	11/15	NA	2	FACETS	1	0.934	1			1	INDETERMINATE	2	TRUE	NA	0.753858017785727	2		191	99	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626789	14626789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs532564939	NA	P-0031503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	246	531	0	ENST00000254322.2:c.986C>T	p.Thr329Ile	p.T329I	ENST00000254322	NM_006145.1	329	aCa/aTa	3/3	0.176674859592981	6	FACETS	0.903	0.851	0.956	0.903	0.851	0.956	INDETERMINATE	3	TRUE	3	0.753858017785727	6		531	604	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25459843	25459843	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1174921909	NA	P-0031503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	450	525	0	ENST00000264709.3:c.2440G>T	p.Glu814Ter	p.E814*	ENST00000264709	NM_175629.2	814	Gag/Tag	21/23	0.753858017785727	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	0	0.753858017785727	3		525	546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0031579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	306	654	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.449233904985187	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.449233904985187	1		656	766	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780224	9780224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368722127	NA	P-0031579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	92	499	4	ENST00000377346.4:c.1394C>T	p.Thr465Met	p.T465M	ENST00000377346	NM_005026.3	465	aCg/aTg	11/24	0.305423453002651	1	FACETS	0.396	0.352	0.444	0.396	0.352	0.444	SUBCLONAL	1	TRUE	0	0.449233904985187	1		503	801	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380276	+	missense_variant	Missense_Mutation	DNP	TT	TT	GA	novel	NA	P-0031579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	390	195	0	ENST00000311936.3:c.182_183delinsTC	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAA/cTC	3/5	1	2	FACETS	0.878	0.837	0.919	1	0.996	1	CLONAL	2	TRUE	1	0.449233904985187	2		195	989	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68758619	68758619	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	166	380	0	ENST00000487270.1:c.775A>T	p.Ile259Phe	p.I259F	ENST00000487270	NM_133509.3	259	Att/Ttt	8/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.449233904985187	2		380	636	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0031579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	122	228	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.449233904985187	2		228	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0031662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	360	683	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.736778363666269	2		683	893	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913476	NA	P-0031662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	174	358	0	ENST00000358487.5:c.1647T>G	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaG	12/18	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.736778363666269	2		358	417	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419951	41419951	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	268	451	0	ENST00000373198.4:c.370G>A	p.Val124Met	p.V124M	ENST00000373198	NM_133170.3	124	Gtg/Atg	3/32	0.729391739056737	3	FACETS	0.934	0.876	0.993	0.467	0.438	0.497	CLONAL	1	TRUE	1	0.736778363666269	3		451	1066	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028790	47028790	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	205	273	0	ENST00000377604.3:c.94C>T	p.Arg32Ter	p.R32*	ENST00000377604	NM_001204468.1	32	Cga/Tga	3/24	1	1	FACETS	0.735	0.689	0.782	0.735	0.689	0.782	SUBCLONAL	1	TRUE	0	0.736778363666269	1		273	478	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339230	70339230	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	269	268	0	ENST00000374080.3:c.107T>C	p.Leu36Pro	p.L36P	ENST00000374080		36	cTg/cCg	2/45	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.736778363666269	1		268	370	SUCCESS
FH	2271	MSKCC	GRCh37	1	241672078	241672078	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	73	232	0	ENST00000366560.3:c.563A>G	p.Asn188Ser	p.N188S	ENST00000366560	NM_000143.3	188	aAt/aGt	5/10	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.736778363666269	2		232	196	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106049	8106049	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	287	439	0	ENST00000346208.3:c.869A>G	p.Tyr290Cys	p.Y290C	ENST00000346208		290	tAt/tGt	4/6	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.736778363666269	2		439	749	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724795	112724795	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	73	237	0	ENST00000369452.4:c.679A>G	p.Ile227Val	p.I227V	ENST00000369452	NM_007373.3	227	Att/Gtt	2/9	1	2	FACETS	0.826	0.732	0.923	0.826	0.732	0.923	CLONAL	1	TRUE	1	0.736778363666269	2		237	240	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942902	15942904	+	inframe_deletion	In_Frame_Del	DEL	ATA	ATA	-	novel	NA	P-0031662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	376	182	0	ENST00000268712.3:c.6798_6800del	p.Ile2267del	p.I2267del	ENST00000268712	NM_006311.3	2266	atTATc/atc	44/46	1	2	FACETS	0.783	0.751	0.814	1	0.996	1	SUBCLONAL	2	TRUE	1	0.736778363666269	2		182	652	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026555	48026555	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1343978618	NA	P-0031662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	338	94	0	ENST00000234420.5:c.1433A>G	p.Tyr478Cys	p.Y478C	ENST00000234420	NM_000179.2	478	tAt/tGt	4/10	1	2	FACETS	0.78	0.747	0.813	1	0.996	1	SUBCLONAL	2	TRUE	1	0.736778363666269	2		94	588	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839738	27839738	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	170	418	0	ENST00000328488.2:c.356C>G	p.Thr119Ser	p.T119S	ENST00000328488	NM_003533.2	119	aCt/aGt	1/1	1	2	FACETS	0.818	0.757	0.881	0.818	0.757	0.881	CLONAL	1	TRUE	1	0.736778363666269	2		418	564	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942035	44942035	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0031662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	85	147	0	ENST00000377967.4:c.3284+1G>A		p.X1095_splice	ENST00000377967	NM_021140.2	1095			1	1	FACETS		NA	1	1	0.99	1	NA	2	TRUE	0	0.736778363666269	1		147	96	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0031747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1194	114	233	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.336868232563323	3	FACETS	0.605	0.542	0.671			1	SUBCLONAL	1	TRUE	NA	0.336868232563323	3		235	1308	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488657	212488657	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374970657	NA	P-0031747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	36	370	0	ENST00000342788.4:c.2192C>T	p.Thr731Met	p.T731M	ENST00000342788	NM_005235.2	731	aCg/aTg	18/28	1	2	FACETS	0.319	0.261	0.384	0.319	0.261	0.384	SUBCLONAL	1	TRUE	1	0.336868232563323	2		370	671	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218478	1218479	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0031747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	131	385	1	ENST00000326873.7:c.354_355del	p.Tyr118Ter	p.Y118*	ENST00000326873	NM_000455.4	118	tAC/t	2/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.336868232563323	2		386	694	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221270	1221271	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0031747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	136	450	0	ENST00000326873.7:c.795_796del	p.Asn266HisfsTer18	p.N266Hfs*18	ENST00000326873	NM_000455.4	265	GAg/g	6/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.336868232563323	2		450	690	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871037	12871037	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031755-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	179	405	0	ENST00000228872.4:c.264del	p.Tyr89ThrfsTer30	p.Y89Tfs*30	ENST00000228872	NM_004064.3	88	taC/ta	1/3	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.726004345715449	2		405	477	SUCCESS
APC	324	MSKCC	GRCh37	5	112164575	112164575	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031755-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	127	305	0	ENST00000257430.4:c.1649A>G	p.Asn550Ser	p.N550S	ENST00000257430	NM_000038.5	550	aAt/aGt	14/16	0.726004345715449	3	FACETS	0.958	0.872	1	0.479	0.436	0.523	CLONAL	1	TRUE	1	0.726004345715449	3		305	498	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0031862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	71	505	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.167965209990606	3	FACETS	0.881	0.773	0.996	0.294	0.257	0.332	INDETERMINATE	1	TRUE	0	0.522792949354983	3		505	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0031862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	136	692	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.42069571335189	2	FACETS	1	0.923	1	0.505	0.462	0.55	CLONAL	1	TRUE	0	0.522792949354983	2		692	515	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771344	68771344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555509646	NA	P-0031862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	64	397	2	ENST00000261769.5:c.26C>T	p.Ser9Leu	p.S9L	ENST00000261769	NM_004360.3	9	tCg/tTg	1/16	0.522792949354983	1	FACETS	0.895	0.788	1	0.895	0.788	1	CLONAL	1	TRUE	0	0.522792949354983	1		399	202	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152009018	152009018	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	53	323	0	ENST00000262189.6:c.604C>T	p.Gln202Ter	p.Q202*	ENST00000262189	NM_170606.2	202	Cag/Tag	5/59	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.522792949354983	2		323	179	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17359597	17359597	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	70	500	0	ENST00000375499.3:c.244G>T	p.Glu82Ter	p.E82*	ENST00000375499	NM_003000.2	82	Gaa/Taa	3/8	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.522792949354983	2		500	254	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175996780	175996780	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	54	518	0	ENST00000367669.3:c.1657G>A	p.Glu553Lys	p.E553K	ENST00000367669	NM_022457.5	553	Gag/Aag	15/20	1	2	FACETS	0.601	0.515	0.693	0.601	0.515	0.693	SUBCLONAL	1	TRUE	1	0.522792949354983	2		518	344	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699410	47699410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	38	349	0	ENST00000347630.2:c.98C>T	p.Ser33Phe	p.S33F	ENST00000347630	NM_001007230.1	33	tCc/tTc	4/11	0.47929066184601	3	FACETS	0.562	0.466	0.669	0.281	0.233	0.335	SUBCLONAL	1	TRUE	1	0.522792949354983	3		349	326	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25990467	25990467	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	51	454	0	ENST00000435504.4:c.760G>C	p.Glu254Gln	p.E254Q	ENST00000435504		254	Gag/Cag	8/13	0.270758783410212	2	FACETS	0.655	0.56	0.757	0.327	0.28	0.379	INDETERMINATE	1	TRUE	0	0.522792949354983	2		454	298	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938311	76938311	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	15	504	0	ENST00000373344.5:c.2437G>C	p.Glu813Gln	p.E813Q	ENST00000373344	NM_000489.3	813	Gag/Cag	9/35	0.522792949354983	1	FACETS	0.149	0.109	0.198	0.149	0.109	0.198	SUBCLONAL	1	TRUE	0	0.522792949354983	1		504	284	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	198	395	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.783713678270498	2		395	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0032063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	342	944	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.783713678270498	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.783713678270498	1		945	503	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0032063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	18063	586	1	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.783713678270498	28	FACETS	1	0.999	1	0.98	0.978	0.982	CLONAL	27	TRUE	0	0.783713678270498	28		587	18799	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843410	128843410	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143083812	NA	P-0032063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	191	623	0	ENST00000249373.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000249373	NM_005631.4	173	Cgc/Tgc	2/12	0.149882271135918	3	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.783713678270498	3		623	593	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923342	9923342	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397514557	NA	P-0032100-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	43	597	0	ENST00000330684.3:c.1945C>G	p.Leu649Val	p.L649V	ENST00000330684	NM_001134407.1	649	Ctg/Gtg	9/13	0.376685073862559	4	FACETS	1	0.876	1	0.522	0.44	0.611	CLONAL	1	TRUE	2	0.532526619430691	4		597	237	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117383	115117383	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032100-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	151	379	0	ENST00000257566.3:c.791del	p.Pro264LeufsTer18	p.P264Lfs*18	ENST00000257566	NM_016569.3	264	cCt/ct	4/8	0.532526619430691	8	FACETS	1	0.945	1			1	CLONAL	3	TRUE	NA	0.532526619430691	8		379	476	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845659	68845660	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0032100-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	244	695	1	ENST00000261769.5:c.907_908del	p.Thr303HisfsTer7	p.T303Hfs*7	ENST00000261769	NM_004360.3	302	tAC/t	7/16	0.532526619430691	2	FACETS	0.851	0.814	0.887	1	0.993	1	CLONAL	3	TRUE	0	0.532526619430691	2		696	359	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349199	15349199	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032100-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	23	466	0	ENST00000263377.2:c.4078A>T	p.Asn1360Tyr	p.N1360Y	ENST00000263377	NM_058243.2	1360	Aat/Tat	20/20	0.532526619430691	3	FACETS	0.706	0.555	0.876	0.353	0.277	0.438	SUBCLONAL	1	TRUE	1	0.532526619430691	3		466	155	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196433	106196433	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs368705448	NA	P-0032100-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	30	389	0	ENST00000380013.4:c.4766A>G	p.Tyr1589Cys	p.Y1589C	ENST00000380013	NM_001127208.2	1589	tAt/tGt	11/11	1	2	FACETS	0.736	0.601	0.885	0.736	0.601	0.885	SUBCLONAL	1	TRUE	1	0.532526619430691	2		389	153	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570311	87570311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1285612169	NA	P-0032100-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	88	643	1	ENST00000277120.3:c.2051C>T	p.Ala684Val	p.A684V	ENST00000277120		684	gCg/gTg	17/19	0.355353139401762	5	FACETS	0.929	0.831	1	0.619	0.554	0.687	CLONAL	2	TRUE	2	0.532526619430691	5		644	320	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606469	93606469	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032100-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	42	811	0	ENST00000375746.1:c.289G>C	p.Asp97His	p.D97H	ENST00000375746	NM_001174167.1	97	Gat/Cat	2/14	0.355353139401762	5	FACETS	1	0.909	1	0.374	0.314	0.439	CLONAL	1	TRUE	2	0.532526619430691	5		811	253	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	246	63	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.343273222901083	2	FACETS	0.928	0.871	0.987	0.928	0.871	0.987	CLONAL	2	TRUE	0	0.343273222901083	2		63	772	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0032128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	405	193	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.343273222901083	3	FACETS	0.912	0.866	0.958	0.912	0.866	0.958	CLONAL	2	TRUE	1	0.343273222901083	3		193	1516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0032128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	193	621	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.343273222901083	1	FACETS	0.996	0.922	1	0.996	0.922	1	CLONAL	1	TRUE	0	0.343273222901083	1		622	935	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729875	30729875	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0032128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	207	248	0	ENST00000295754.5:c.1397-1G>C		p.X466_splice	ENST00000295754	NM_003242.5	466			0.343273222901083	2	FACETS	0.903	0.842	0.965	0.903	0.842	0.965	CLONAL	2	TRUE	0	0.343273222901083	2		248	668	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260150	149260150	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	170	394	0	ENST00000360632.3:c.743G>C	p.Arg248Pro	p.R248P	ENST00000360632	NM_015472.4	248	cGa/cCa	4/7	0.259648024278949	3	FACETS	1	0.951	1	0.524	0.481	0.569	CLONAL	1	TRUE	1	0.343273222901083	3		394	1107	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0032180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	20	441	2	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.627528309502994	1	FACETS	0.157	0.12	0.2	0.157	0.12	0.2	SUBCLONAL	1	TRUE	0	0.627528309502994	1		443	279	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0032180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	24	235	1	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.627528309502994	NA		236	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0032180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	546	662	0	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	0.351164650271853	2	FACETS	0.998	0.966	1	0.998	0.966	1	INDETERMINATE	2	TRUE	0	0.627528309502994	2		662	872	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673787	37673787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1300041019	NA	P-0032180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	71	400	1	ENST00000447079.4:c.2941C>T	p.Arg981Cys	p.R981C	ENST00000447079	NM_015083.1	981	Cgt/Tgt	10/14	0.627528309502994	3	FACETS	0.301	0.262	0.344	0.1	0.087	0.115	SUBCLONAL	1	TRUE	0	0.627528309502994	3		401	987	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762839	40762839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1407888862	NA	P-0032180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	50	182	2	ENST00000392038.2:c.169G>A	p.Val57Ile	p.V57I	ENST00000392038	NM_001626.4	57	Gta/Ata	3/14	0.245372667838097	3	FACETS	0.33	0.279	0.385	0.165	0.139	0.193	INDETERMINATE	1	TRUE	1	0.627528309502994	3		184	635	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870961	12870962	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	21	123	0	ENST00000228872.4:c.192dup	p.Gln65SerfsTer60	p.Q65Sfs*60	ENST00000228872	NM_004064.3	63	gat/gaTt	1/3	0.627528309502994	1	FACETS	0.205	0.158	0.259	0.205	0.158	0.259	SUBCLONAL	1	TRUE	0	0.627528309502994	1		123	224	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954957	2954957	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	79	375	0	ENST00000396946.4:c.2753G>A	p.Arg918Gln	p.R918Q	ENST00000396946	NM_032415.4	918	cGg/cAg	21/25	1	2	FACETS	0.252	0.221	0.286	0.252	0.221	0.286	SUBCLONAL	1	TRUE	1	0.627528309502994	2		375	998	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913836	32913837	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359507	NA	P-0032180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	18	183	0	ENST00000380152.3:c.5351dup	p.Asn1784LysfsTer3	p.N1784Kfs*3	ENST00000380152		1782	caa/cAaa	11/27	0.627528309502994	2	FACETS	0.18	0.135	0.233	0.09	0.067	0.117	SUBCLONAL	1	TRUE	0	0.627528309502994	2		183	319	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096132	2096133	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs763525759	NA	P-0032180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	68	296	1	ENST00000219066.1:c.374dup	p.Val127GlyfsTer43	p.V127Gfs*43	ENST00000219066	NM_002528.5	125	cca/ccCa	2/6	1	2	FACETS	0.295	0.256	0.338	0.295	0.256	0.338	SUBCLONAL	1	TRUE	1	0.627528309502994	2		297	734	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425810	49425812	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs777996753	NA	P-0032180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	47	266	0	ENST00000301067.7:c.12676_12678del	p.Leu4226del	p.L4226del	ENST00000301067	NM_003482.3	4226	CTC/-	39/54	1	2	FACETS	0.28	0.236	0.329	0.28	0.236	0.329	SUBCLONAL	1	TRUE	1	0.627528309502994	2		266	535	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56477621	56477621	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	67	336	0	ENST00000267101.3:c.169G>C	p.Glu57Gln	p.E57Q	ENST00000267101	NM_001982.3	57	Gag/Cag	2/28	1	2	FACETS	0.272	0.236	0.312	0.272	0.236	0.312	SUBCLONAL	1	TRUE	1	0.627528309502994	2		336	784	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861257	57861257	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	43	248	0	ENST00000228682.2:c.1054C>T	p.Gln352Ter	p.Q352*	ENST00000228682	NM_005269.2	352	Cag/Tag	9/12	1	2	FACETS	0.241	0.201	0.285	0.241	0.201	0.285	SUBCLONAL	1	TRUE	1	0.627528309502994	2		248	569	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134239	41134239	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	25	214	0	ENST00000379561.5:c.1389G>T	p.Lys463Asn	p.K463N	ENST00000379561	NM_002015.3	463	aaG/aaT	2/3	0.627528309502994	2	FACETS	0.201	0.158	0.25	0.1	0.079	0.125	SUBCLONAL	1	TRUE	0	0.627528309502994	2		214	397	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2089994	2089994	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0032180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	90	406	0	ENST00000219066.1:c.870T>A	p.Cys290Ter	p.C290*	ENST00000219066	NM_002528.5	290	tgT/tgA	6/6	1	2	FACETS	0.308	0.273	0.347	0.308	0.273	0.347	SUBCLONAL	1	TRUE	1	0.627528309502994	2		406	930	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2224050	2224050	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0032180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	65	302	0	ENST00000326181.6:c.1263+1G>A		p.X421_splice	ENST00000326181	NM_032271.2	421			1	2	FACETS	0.276	0.239	0.317	0.276	0.239	0.317	SUBCLONAL	1	TRUE	1	0.627528309502994	2		302	750	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351136	89351136	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749017226	NA	P-0032180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	78	288	0	ENST00000301030.4:c.1814C>T	p.Ser605Leu	p.S605L	ENST00000301030	NM_001256183.1	605	tCg/tTg	9/13	1	2	FACETS	0.343	0.301	0.388	0.343	0.301	0.388	SUBCLONAL	1	TRUE	1	0.627528309502994	2		288	725	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032514	12032514	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	38	209	0	ENST00000353533.5:c.950T>C	p.Leu317Pro	p.L317P	ENST00000353533	NM_003010.3	317	cTa/cCa	9/11	0.351164650271853	2	FACETS	0.359	0.298	0.428	0.18	0.149	0.214	INDETERMINATE	1	TRUE	0	0.627528309502994	2		209	337	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281383	142281383	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	106	353	0	ENST00000350721.4:c.861A>C	p.Gln287His	p.Q287H	ENST00000350721	NM_001184.3	287	caA/caC	4/47	0.512376399335441	3	FACETS	0.583	0.523	0.647	0.292	0.261	0.324	SUBCLONAL	1	TRUE	1	0.627528309502994	3		353	761	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672770	86672770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	196	13	0	ENST00000274376.6:c.2257G>A	p.Ala753Thr	p.A753T	ENST00000274376	NM_002890.2	753	Gcc/Acc	17/25	0.410221864711958	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.627528309502994	1		13	425	SUCCESS
APC	324	MSKCC	GRCh37	5	112179821	112179821	+	stop_lost	Nonstop_Mutation	SNP	T	T	G	novel	NA	P-0032180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	82	13	0	ENST00000257430.4:c.8530T>G	p.Ter2844GluextTer27	p.*2844Eext*27	ENST00000257430	NM_000038.5	2844	Taa/Gaa	16/16	0.410221864711958	1	FACETS	0.687	0.614	0.763	0.687	0.614	0.763	SUBCLONAL	1	TRUE	0	0.627528309502994	1		13	261	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249008	55249009	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGG	novel	NA	P-0032180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	63	200	0	ENST00000275493.2:c.2308_2309insGGG	p.Val769_Asp770insGly	p.V769_D770insG	ENST00000275493	NM_005228.3	769	gtg/gtGGGg	20/28	0.504237549761674	3	FACETS	0.405	0.35	0.465			1	SUBCLONAL	1	TRUE	NA	0.627528309502994	3		200	651	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151847985	151847985	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	27	160	0	ENST00000262189.6:c.12774G>T	p.Lys4258Asn	p.K4258N	ENST00000262189	NM_170606.2	4258	aaG/aaT	51/59	0.410221864711958	1	FACETS	0.224	0.178	0.275	0.224	0.178	0.275	SUBCLONAL	1	TRUE	0	0.627528309502994	1		160	264	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814756	139814756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376884527	NA	P-0032180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	58	262	1	ENST00000247668.2:c.749C>T	p.Ser250Leu	p.S250L	ENST00000247668	NM_021138.3	250	tCg/tTg	8/11	NA	2	FACETS	0.277	0.237	0.32			1	INDETERMINATE	1	TRUE	NA	0.627528309502994	2		263	668	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321316	1321316	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	43	201	0	ENST00000400841.2:c.439C>A	p.Leu147Ile	p.L147I	ENST00000400841		147	Ctc/Atc	4/6	0.627528309502994	1	FACETS	0.241	0.202	0.284	0.241	0.202	0.284	SUBCLONAL	1	TRUE	0	0.627528309502994	1		201	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0032616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	130	559	0	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	0.557240425409742	1	FACETS	0.999	0.918	1	0.999	0.918	1	CLONAL	1	TRUE	0	0.557240425409742	1		559	337	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252376	133252376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759414746	NA	P-0032616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	130	376	0	ENST00000320574.5:c.1051G>A	p.Val351Ile	p.V351I	ENST00000320574	NM_006231.2	351	Gtc/Atc	11/49	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.557240425409742	2		376	418	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727490	88727490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1222179640	NA	P-0032616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	277	496	1	ENST00000360948.2:c.289G>A	p.Val97Met	p.V97M	ENST00000360948	NM_001012338.2	97	Gtg/Atg	3/19	0.506642539172419	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.557240425409742	3		497	597	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750702	128750702	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	122	461	0	ENST00000377970.2:c.239G>T	p.Arg80Leu	p.R80L	ENST00000377970	NM_002467.4	80	cGc/cTc	2/3	1	2	FACETS	0.991	0.902	1	0.991	0.902	1	CLONAL	1	TRUE	1	0.557240425409742	2		461	442	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974727	21974744	+	inframe_deletion	In_Frame_Del	DEL	CCTCCAGCAGCGCCCGCA	CCTCCAGCAGCGCCCGCA	-	novel	NA	P-0032616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	47	296	0	ENST00000304494.5:c.83_100del	p.Val28_Glu33del	p.V28_E33del	ENST00000304494	NM_000077.4	28	gTGCGGGCGCTGCTGGAGGcg/gcg	1/3	0.557240425409742	1	FACETS	0.68	0.582	0.784	0.68	0.582	0.784	SUBCLONAL	1	TRUE	0	0.557240425409742	1		296	179	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057520007	NA	P-0032618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	327	417	0	ENST00000269305.4:c.614A>C	p.Tyr205Ser	p.Y205S	ENST00000269305	NM_001126112.2	205	tAt/tCt	6/11	0.567231294381201	2	FACETS	0.954	0.912	0.997	0.954	0.912	0.997	CLONAL	2	TRUE	0	0.567231294381201	2		417	604	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685309	89685309	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	75	220	0	ENST00000371953.3:c.204C>A	p.Tyr68Ter	p.Y68*	ENST00000371953	NM_000314.4	68	taC/taA	3/9	0.567231294381201	3	FACETS	0.891	0.812	0.968	0.891	0.812	0.968	CLONAL	3	TRUE	0	0.567231294381201	3		220	127	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38631998	38631998	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	160	405	0	ENST00000299084.4:c.484G>C	p.Val162Leu	p.V162L	ENST00000299084	NM_152594.2	162	Gtt/Ctt	5/7	0.567231294381201	2	FACETS	0.873	0.815	0.931	0.873	0.815	0.931	CLONAL	2	TRUE	0	0.567231294381201	2		405	323	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989705	15989706	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0032618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	242	272	0	ENST00000268712.3:c.3067_3068del	p.Arg1023AlafsTer47	p.R1023Afs*47	ENST00000268712	NM_006311.3	1023	CGg/g	23/46	0.567231294381201	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.567231294381201	2		272	384	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52677360	52677360	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0032618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	119	305	0	ENST00000394830.3:c.900-1G>C		p.X300_splice	ENST00000394830	NM_018313.4	300			0.567231294381201	4	FACETS	1	0.919	1	0.339	0.307	0.374	CLONAL	1	TRUE	1	0.567231294381201	4		305	646	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467402	66467402	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	103	209	0	ENST00000273854.3:c.867C>A	p.Cys289Ter	p.C289*	ENST00000273854	NM_004439.5	289	tgC/tgA	3/18	0.561964224882473	2	FACETS	0.931	0.856	1	0.931	0.856	1	CLONAL	2	TRUE	0	0.567231294381201	2		209	195	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79974854	79974854	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	42	375	0	ENST00000265081.6:c.1282C>T	p.Leu428Phe	p.L428F	ENST00000265081	NM_002439.4	428	Ctt/Ttt	8/24	0.186327211268097	3	FACETS	0.357	0.298	0.423	0.119	0.099	0.141	INDETERMINATE	1	TRUE	0	0.567231294381201	3		375	532	SUCCESS
APC	324	MSKCC	GRCh37	5	112174189	112174190	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTCAGTAG	novel	NA	P-0032618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	79	260	0	ENST00000257430.4:c.2899_2906dup	p.Ser969ArgfsTer14	p.S969Rfs*14	ENST00000257430	NM_000038.5	966	-/GTCAGTAG	16/16	0.186327211268097	3	FACETS	0.788	0.704	0.874	0.525	0.469	0.583	INDETERMINATE	2	TRUE	0	0.567231294381201	3		260	227	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162159	38162159	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	33	330	0	ENST00000317025.8:c.2557C>T	p.Arg853Trp	p.R853W	ENST00000317025	NM_023034.1	853	Cgg/Tgg	14/24	0.564566223736297	1	FACETS	0.329	0.269	0.396	0.329	0.269	0.396	SUBCLONAL	1	TRUE	0	0.567231294381201	1		330	253	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090497	5090497	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1346944271	NA	P-0032618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	44	162	0	ENST00000381652.3:c.2813G>A	p.Arg938Gln	p.R938Q	ENST00000381652	NM_004972.3	938	cGa/cAa	21/25	0.144629143144307	6	FACETS	1	0.899	1	0.712	0.608	0.823	INDETERMINATE	2	TRUE	3	0.567231294381201	6		162	155	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0032621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	333	665	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.461847149523141	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.5132034759716	1		665	932	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0032621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	105	314	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.809	0.728	0.894	0.809	0.728	0.894	CLONAL	1	TRUE	1	0.5132034759716	2		315	506	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947827	178947827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	16	198	1	ENST00000263967.3:c.2702G>T	p.Cys901Phe	p.C901F	ENST00000263967	NM_006218.2	901	tGt/tTt	19/21	1	2	FACETS	0.145	0.106	0.191	0.145	0.106	0.191	SUBCLONAL	1	TRUE	1	0.5132034759716	2		199	430	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575149	48575149	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	113	188	0	ENST00000342988.3:c.343T>A	p.Cys115Ser	p.C115S	ENST00000342988	NM_005359.5	115	Tgt/Agt	3/12	0.5132034759716	1	FACETS	0.989	0.901	1	0.989	0.901	1	CLONAL	1	TRUE	0	0.5132034759716	1		188	331	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970902	55970902	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	187	391	0	ENST00000263923.4:c.1895C>A	p.Ala632Glu	p.A632E	ENST00000263923	NM_002253.2	632	gCa/gAa	13/30	1	2	FACETS	0.899	0.831	0.968	0.899	0.831	0.968	CLONAL	1	TRUE	1	0.5132034759716	2		391	811	SUCCESS
APC	324	MSKCC	GRCh37	5	112164584	112164584	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs863225318	NA	P-0032621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	162	178	0	ENST00000257430.4:c.1658G>A	p.Trp553Ter	p.W553*	ENST00000257430	NM_000038.5	553	tGg/tAg	14/16	0.5132034759716	2	FACETS	0.918	0.856	0.98	0.918	0.856	0.98	CLONAL	2	TRUE	0	0.5132034759716	2		178	344	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0032622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	15	26	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.313418489706645	1	FACETS	0.569	0.428	0.727	0.569	0.428	0.727	INDETERMINATE	1	TRUE	0	0.610433474344397	1		26	60	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	94	309	0	ENST00000269305.4:c.376T>C	p.Tyr126His	p.Y126H	ENST00000269305	NM_001126112.2	126	Tac/Cac	5/11	0.610433474344397	1	FACETS	0.991	0.9	1	0.991	0.9	1	CLONAL	1	TRUE	0	0.610433474344397	1		309	216	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	75	63	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.91	0.801	1	0.91	0.801	1	CLONAL	1	TRUE	1	0.392510977644904	2		63	420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0032638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	180	686	1	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.392510977644904	1	FACETS	0.965	0.892	1	0.965	0.892	1	CLONAL	1	TRUE	0	0.392510977644904	1		687	764	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574348	41574348	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	455	102	0	ENST00000263253.7:c.6633C>A	p.Phe2211Leu	p.F2211L	ENST00000263253	NM_001429.3	2211	ttC/ttA	31/31	1	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	1	0.392510977644904	2		102	1021	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32905134	32905134	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	77	319	0	ENST00000380152.3:c.760G>T	p.Glu254Ter	p.E254*	ENST00000380152		254	Gaa/Taa	9/27	0.392510977644904	1	FACETS	0.802	0.708	0.902	0.802	0.708	0.902	CLONAL	1	TRUE	0	0.392510977644904	1		319	393	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2089926	2089926	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	novel	NA	P-0032638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	106	365	0	ENST00000219066.1:c.938G>C	p.Ter313SerextTer?	p.*313Sext*?	ENST00000219066	NM_002528.5	313	tGa/tCa	6/6	0.241067567846401	3	FACETS	0.967	0.868	1			1	CLONAL	1	TRUE	NA	0.392510977644904	3		365	668	SUCCESS
APC	324	MSKCC	GRCh37	5	112102912	112102939	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGGAGTAAAACTGCGGTCAAAAATGT	CCTGGAGTAAAACTGCGGTCAAAAATGT	-	novel	NA	P-0032638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	49	207	0	ENST00000257430.4:c.249_276del	p.Gly84SerfsTer32	p.G84Sfs*32	ENST00000257430	NM_000038.5	83	CCTGGAGTAAAACTGCGGTCAAAAATGTcc/cc	4/16	0.392510977644904	1	FACETS	0.861	0.737	0.995	0.861	0.737	0.995	CLONAL	1	TRUE	0	0.392510977644904	1		207	233	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564645	139564645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	190	667	2	ENST00000308874.7:c.434G>T	p.Arg145Met	p.R145M	ENST00000308874		145	aGg/aTg	7/10	1	2	FACETS	0.949	0.877	1	0.949	0.877	1	CLONAL	1	TRUE	1	0.392510977644904	2		669	1020	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584436	52584436	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0032638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	98	326	0	ENST00000394830.3:c.4576+1G>T		p.X1526_splice	ENST00000394830	NM_018313.4	1526			0.35182976216394	1	FACETS	0.927	0.832	1	0.927	0.832	1	CLONAL	1	TRUE	0	0.392510977644904	1		326	433	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124336	2124336	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	112	314	0	ENST00000219476.3:c.2491A>C	p.Thr831Pro	p.T831P	ENST00000219476	NM_000548.3	831	Acg/Ccg	22/42	1	2	FACETS	0.417	0.375	0.461	0.417	0.375	0.461	SUBCLONAL	1	TRUE	1	0.808169232296352	2		314	665	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486107	29486107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567816119	NA	P-0033042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	128	135	0	ENST00000356175.3:c.284C>T	p.Ala95Val	p.A95V	ENST00000356175	NM_000267.3	95	gCt/gTt	3/57	0.787353056355344	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.808169232296352	1		135	186	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0033157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	32	379	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.13	2		379	399	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933521	36933521	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	20	194	0	ENST00000361632.4:c.1766G>T	p.Gly589Val	p.G589V	ENST00000361632		589	gGc/gTc	13/16	1	2	FACETS	0.791	0.604	1	0.791	0.604	1	CLONAL	1	TRUE	1	0.13	2		194	389	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246205	41246220	+	frameshift_variant	Frame_Shift_Del	DEL	TGAACTCTTTCACTTT	TGAACTCTTTCACTTT	-	novel	NA	P-0033157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	39	223	0	ENST00000357654.3:c.1328_1343del	p.Lys443ThrfsTer5	p.K443Tfs*5	ENST00000357654	NM_007294.3	443	aAAAGTGAAAGAGTTCAc/ac	10/23	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.13	2		223	412	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033219-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	446	846	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.616162451062464	2	FACETS	0.969	0.934	1	0.969	0.934	1	CLONAL	2	TRUE	0	0.623973188581062	2		846	738	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578469	+	frameshift_variant	Frame_Shift_Del	DEL	CGGACGCGGGTGC	CGGACGCGGGTGC	-	novel	NA	P-0033219-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	561	1029	0	ENST00000269305.4:c.461_473del	p.Gly154AlafsTer12	p.G154Afs*12	ENST00000269305	NM_001126112.2	154	gGCACCCGCGTCCGc/gc	5/11	0.616162451062464	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.623973188581062	2		1029	869	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874012	151874012	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033219-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	185	738	0	ENST00000262189.6:c.8526T>G	p.Asn2842Lys	p.N2842K	ENST00000262189	NM_170606.2	2842	aaT/aaG	38/59	0.605890569927662	3	FACETS	0.909	0.84	0.98	0.454	0.42	0.49	CLONAL	1	TRUE	1	0.623973188581062	3		738	856	SUCCESS
APC	324	MSKCC	GRCh37	5	112176863	112176863	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1270783041	NA	P-0033225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	117	198	0	ENST00000257430.4:c.5572C>T	p.Arg1858Ter	p.R1858*	ENST00000257430	NM_000038.5	1858	Cga/Tga	16/16	0.845787096151583	2	FACETS	0.979	0.932	1	0.979	0.932	1	CLONAL	2	TRUE	0	0.847640692478286	2		198	141	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0033225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	231	607	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.841290908226742	3	FACETS	0.88	0.822	0.94	0.44	0.411	0.47	CLONAL	1	TRUE	1	0.847640692478286	3		607	882	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0033225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	835	1543	0	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	0.841290908226742	3	FACETS	0.988	0.961	1	0.988	0.961	1	CLONAL	2	TRUE	1	0.847640692478286	3		1543	1420	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054650	13054658	+	inframe_deletion	In_Frame_Del	DEL	GAGGATGAG	GAGGATGAG	-	rs550353351	NA	P-0033225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	473	426	1	ENST00000316448.5:c.1191_1199del	p.Glu398_Asp400del	p.E398_D400del	ENST00000316448	NM_004343.3	393	GAGGATGAG/-	9/9	0.845305877960828	4	FACETS	1	0.987	1	0.773	0.75	0.796	CLONAL	3	TRUE	0	0.847640692478286	4		427	667	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522568	106522568	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs754441790	NA	P-0033225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	44	154	0	ENST00000359195.3:c.2545C>T	p.Arg849Ter	p.R849*	ENST00000359195	NM_002649.2	849	Cga/Tga	7/11	0.841290908226742	3	FACETS	0.936	0.799	1	0.468	0.399	0.541	CLONAL	1	TRUE	1	0.847640692478286	3		154	158	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5563193	5563193	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	144	215	0	ENST00000397747.3:c.798G>C	p.Lys266Asn	p.K266N	ENST00000397747	NM_025239.3	266	aaG/aaC	6/7	0.842530596237888	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.847640692478286	2		215	163	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16097870	16097870	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs76145228	NA	P-0033225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	13	175	2	ENST00000268712.3:c.14G>T	p.Gly5Val	p.G5V	ENST00000268712	NM_006311.3	5	gGt/gTt	2/46	0.841290908226742	3	FACETS	0.24	0.171	0.323	0.12	0.085	0.162	SUBCLONAL	1	TRUE	1	0.847640692478286	3		177	182	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205689	38205689	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0033225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	142	376	0	ENST00000317025.8:c.1A>G	p.Met1?	p.M1?	ENST00000317025	NM_023034.1	1	Atg/Gtg	2/24	0.841290908226742	3	FACETS	1	0.961	1	0.537	0.494	0.582	CLONAL	1	TRUE	1	0.847640692478286	3		376	444	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0033315-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	725	470	1	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.635168581793168	13	FACETS	1	0.986	1	0.721	0.698	0.743	CLONAL	7	TRUE	3	0.635168581793168	13		471	1423	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941068	36941068	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779487638	NA	P-0033315-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	216	494	0	ENST00000361632.4:c.271C>T	p.His91Tyr	p.H91Y	ENST00000361632		91	Cac/Tac	3/16	1	2	FACETS	0.949	0.885	1	0.949	0.885	1	CLONAL	1	TRUE	1	0.635168581793168	2		494	717	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925123	81925123	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033315-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	377	452	0	ENST00000359376.3:c.914A>C	p.Lys305Thr	p.K305T	ENST00000359376	NM_002661.3	305	aAg/aCg	11/33	0.634343581995461	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.635168581793168	2		452	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578246	7578247	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033315-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	443	494	0	ENST00000269305.4:c.602dup	p.Leu201PhefsTer8	p.L201Ffs*8	ENST00000269305	NM_001126112.2	201	ttg/ttTg	6/11	0.631797057314042	2	FACETS	0.967	0.933	1	0.967	0.933	1	CLONAL	2	TRUE	0	0.635168581793168	2		494	721	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978973	25978973	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033315-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	235	358	0	ENST00000435504.4:c.950A>G	p.Asp317Gly	p.D317G	ENST00000435504		317	gAt/gGt	10/13	0.635168581793168	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.635168581793168	3		358	427	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971147	21971225	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCTGCCCATCATCATGACCTGCCAGAGAGAACAGAA	TGGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCTGCCCATCATCATGACCTGCCAGAGAGAACAGAA	-	novel	NA	P-0033315-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	148	323	0	ENST00000304494.5:c.151-18_211del		p.X51_splice	ENST00000304494	NM_000077.4	51		2/3	0.635168581793168	2	FACETS	1	0.987	1	0.658	0.61	0.708	CLONAL	1	TRUE	0	0.635168581793168	2		323	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0033419-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	256	798	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.295385041508502	2	FACETS	0.841	0.788	0.895	0.841	0.788	0.895	CLONAL	2	TRUE	0	0.31	2		800	982	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033419-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	92	395	0	ENST00000397062.3:c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	NM_006164.4	34	Cga/Gga	2/5	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.31	2		395	520	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106892	27106900	+	inframe_deletion	In_Frame_Del	DEL	TGGTACTGC	TGGTACTGC	-	novel	NA	P-0033419-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	199	681	0	ENST00000324856.7:c.6506_6514del	p.Val2169_Leu2171del	p.V2169_L2171del	ENST00000324856	NM_006015.4	2168	gTGGTACTGCtg/gtg	20/20	0.19783762492709	2	FACETS	0.819	0.76	0.879	0.819	0.76	0.879	CLONAL	2	TRUE	0	0.31	2		681	784	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220706	2220706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033419-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	105	607	0	ENST00000326181.6:c.323C>T	p.Ser108Leu	p.S108L	ENST00000326181	NM_032271.2	108	tCa/tTa	5/21	0.295385041508502	1	FACETS	0.907	0.814	1	0.907	0.814	1	CLONAL	1	TRUE	0	0.31	1		607	631	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830178	72830178	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033419-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	156	586	0	ENST00000268489.5:c.6403C>G	p.Gln2135Glu	p.Q2135E	ENST00000268489	NM_006885.3	2135	Cag/Gag	9/10	0.248108300784187	3	FACETS	0.751	0.689	0.816	0.751	0.689	0.816	SUBCLONAL	2	TRUE	1	0.31	3		586	774	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468423	89468423	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0033419-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	128	396	0	ENST00000336596.2:c.1957A>T	p.Lys653Ter	p.K653*	ENST00000336596	NM_005233.5	653	Aag/Tag	11/17	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.31	2		396	598	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754812	57754813	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0033419-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	51	310	0	ENST00000274289.3:c.377_378del	p.Lys126AsnfsTer2	p.K126Nfs*2	ENST00000274289	NM_006622.3	126	aAG/a	2/14	0.248108300784187	3	FACETS	0.846	0.72	0.984	0.423	0.36	0.492	CLONAL	1	TRUE	1	0.31	3		310	449	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522577	157522577	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554236027	NA	P-0033419-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	350	889	1	ENST00000346085.5:c.4849C>T	p.Gln1617Ter	p.Q1617*	ENST00000346085	NM_020732.3	1617	Caa/Taa	18/20	0.244810085155017	2	FACETS	0.964	0.913	1	0.964	0.913	1	CLONAL	2	TRUE	0	0.31	2		890	1171	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041332	47041351	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTTCCCCTCACCCCCTAGCT	GTTCCCCTCACCCCCTAGCT	-	novel	NA	P-0033419-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	155	416	0	ENST00000377604.3:c.1694-12_1701del		p.X565_splice	ENST00000377604	NM_001204468.1	565		16/24	1	1	FACETS	0.88	0.812	0.95	1	0.991	1	CLONAL	2	TRUE	0	0.31	1		416	480	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0033518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	46	233	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.936	0.793	1	0.936	0.793	1	CLONAL	1	TRUE	1	0.327645136552528	2		235	300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0033518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	50	178	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.289396140497105	1	FACETS	0.703	0.599	0.817	0.703	0.599	0.817	SUBCLONAL	1	TRUE	0	0.327645136552528	1		178	363	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765694	41765694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61737385	NA	P-0033518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	63	215	2	ENST00000301178.4:c.2570C>T	p.Ala857Val	p.A857V	ENST00000301178	NM_021913.4	857	gCg/gTg	20/20	1	2	FACETS	0.716	0.62	0.82	0.716	0.62	0.82	SUBCLONAL	1	TRUE	1	0.327645136552528	2		217	537	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056153	26056153	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs534420299	NA	P-0033519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	159	327	0	ENST00000343677.2:c.504G>C	p.Lys168Asn	p.K168N	ENST00000343677	NM_005319.3	168	aaG/aaC	1/1	0.535047191552072	3	FACETS	0.893	0.819	0.97	0.298	0.273	0.324	CLONAL	1	TRUE	0	0.535047191552072	3		327	844	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23625413	23625413	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs886039619	NA	P-0033519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	37	140	0	ENST00000261584.4:c.3114-1G>A		p.X1038_splice	ENST00000261584	NM_024675.3	1038			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.535047191552072	NA		140	156	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412309	139412309	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	203	256	1	ENST00000277541.6:c.1336G>T	p.Gly446Cys	p.G446C	ENST00000277541	NM_017617.3	446	Ggc/Tgc	8/34	0.190395286214706	6	FACETS	0.854	0.792	0.918			1	INDETERMINATE	2	TRUE	NA	0.535047191552072	6		257	920	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852623	63852623	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	101	276	0	ENST00000279873.7:c.3401C>A	p.Pro1134Gln	p.P1134Q	ENST00000279873	NM_032199.2	1134	cCg/cAg	10/10	1	2	FACETS	0.868	0.78	0.96	0.868	0.78	0.96	CLONAL	1	TRUE	1	0.535047191552072	2		276	435	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624262	89624274	+	frameshift_variant	Frame_Shift_Del	DEL	CAAAAGGAGATAT	CAAAAGGAGATAT	-	novel	NA	P-0033519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	69	124	0	ENST00000371953.3:c.39_51del	p.Arg15MetfsTer5	p.R15Mfs*5	ENST00000371953	NM_000314.4	12	aaCAAAAGGAGATAT/aa	1/9	0.535047191552072	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.535047191552072	1		124	148	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788574	3788584	+	frameshift_variant	Frame_Shift_Del	DEL	ATACTCTAAAT	ATACTCTAAAT	-	novel	NA	P-0033519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	39	103	0	ENST00000262367.5:c.4370_4380del	p.Tyr1457CysfsTer18	p.Y1457Cfs*18	ENST00000262367	NM_004380.2	1457	tATTTAGAGTAT/t	26/31	0.535047191552072	3	FACETS	0.868	0.726	1			1	CLONAL	1	TRUE	NA	0.535047191552072	3		103	213	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032077	10032077	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs759019028	NA	P-0033519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	100	249	0	ENST00000330684.3:c.746C>G	p.Thr249Ser	p.T249S	ENST00000330684	NM_001134407.1	249	aCc/aGc	3/13	0.535047191552072	3	FACETS	0.84	0.752	0.933			1	CLONAL	1	TRUE	NA	0.535047191552072	3		249	564	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745840	745840	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs34580680	NA	P-0033519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	52	176	0	ENST00000314574.4:c.592A>G	p.Ile198Val	p.I198V	ENST00000314574	NM_005433.3	198	Att/Gtt	6/12	0.535047191552072	3	FACETS	0.948	0.814	1	0.474	0.407	0.546	CLONAL	1	TRUE	1	0.535047191552072	3		176	260	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022496	31022496	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs991997701	NA	P-0033519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	75	110	0	ENST00000375687.4:c.1981A>G	p.Arg661Gly	p.R661G	ENST00000375687	NM_015338.5	661	Aga/Gga	13/13	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.535047191552072	2		110	246	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964440	55964440	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0033519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	76	204	0	ENST00000263923.4:c.2374-1G>A		p.X792_splice	ENST00000263923	NM_002253.2	792			1	2	FACETS	0.986	0.875	1	0.986	0.875	1	CLONAL	1	TRUE	1	0.535047191552072	2		204	288	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972043	55972043	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	171	329	0	ENST00000263923.4:c.1601A>C	p.Asn534Thr	p.N534T	ENST00000263923	NM_002253.2	534	aAc/aCc	12/30	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.535047191552072	2		329	558	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069059	5069059	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	28	84	0	ENST00000381652.3:c.1364C>G	p.Thr455Arg	p.T455R	ENST00000381652	NM_004972.3	455	aCa/aGa	11/25	1	2	FACETS	0.858	0.698	1	0.858	0.698	1	CLONAL	1	TRUE	1	0.535047191552072	2		84	122	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0033608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	47	301	1	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	0.4425595622246	2		302	243	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0033608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	77	103	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.4425595622246	2	FACETS	0.845	0.756	0.936	0.845	0.756	0.936	CLONAL	2	TRUE	0	0.4425595622246	2		103	206	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0033608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	528	654	3	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.4425595622246	2	FACETS	0.918	0.881	0.955	0.918	0.881	0.955	CLONAL	2	TRUE	0	0.4425595622246	2		657	1300	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445091	89445091	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	54	175	0	ENST00000336596.2:c.1411G>A	p.Glu471Lys	p.E471K	ENST00000336596	NM_005233.5	471	Gag/Aag	6/17	0.4425595622246	2	FACETS	0.79	0.679	0.91	0.395	0.339	0.455	CLONAL	1	TRUE	0	0.4425595622246	2		175	309	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100975	41100975	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	481	337	1	ENST00000373198.4:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000373198	NM_133170.3	461	Cga/Tga	8/32	0.398234258491594	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.4425595622246	3		338	1200	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578188	7578188	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201592	NA	P-0033652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	528	341	0	ENST00000269305.4:c.661G>T	p.Glu221Ter	p.E221*	ENST00000269305	NM_001126112.2	221	Gag/Tag	6/11	0.509569388475907	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.509569388475907	3		341	824	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871758	12871758	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0033652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	77	59	0	ENST00000228872.4:c.476-1G>T		p.X159_splice	ENST00000228872	NM_004064.3	159			0.477360272456745	4	FACETS	0.975	0.869	1	0.975	0.869	1	CLONAL	2	TRUE	2	0.509569388475907	4		59	234	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2957003	2957003	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	270	194	0	ENST00000396946.4:c.2624A>G	p.Glu875Gly	p.E875G	ENST00000396946	NM_032415.4	875	gAa/gGa	20/25	0.509569388475907	5	FACETS	0.89	0.84	0.941	0.89	0.84	0.941	CLONAL	3	TRUE	2	0.509569388475907	5		194	700	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508277	106508277	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1390175513	NA	P-0033652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	55	164	0	ENST00000359195.3:c.271C>G	p.Leu91Val	p.L91V	ENST00000359195	NM_002649.2	91	Ctg/Gtg	2/11	0.509569388475907	3	FACETS	0.928	0.799	1	0.464	0.399	0.533	CLONAL	1	TRUE	1	0.509569388475907	3		164	292	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073755	8073756	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0033740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	108	284	0	ENST00000377482.5:c.903dup	p.Ser302ValfsTer10	p.S302Vfs*10	ENST00000377482	NM_018948.3	301	-/G	4/4	NA	2	FACETS	1	0.942	1			1	INDETERMINATE	2	TRUE	NA	0.28198598879569	2		284	363	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633568	69633568	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	50	212	0	ENST00000334134.2:c.134G>C	p.Arg45Pro	p.R45P	ENST00000334134	NM_005247.2	45	cGc/cCc	1/3	0.280684609836221	4	FACETS	1	0.945	1	0.415	0.353	0.483	CLONAL	1	TRUE	1	0.28198598879569	4		212	365	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999210	100999210	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	253	485	0	ENST00000325455.5:c.592C>A	p.Pro198Thr	p.P198T	ENST00000325455	NM_001202474.3	198	Ccg/Acg	1/8	0.280684609836221	4	FACETS	0.991	0.931	1	0.991	0.931	1	CLONAL	3	TRUE	1	0.28198598879569	4		485	774	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0033740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	38	411	1	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.275206162362076	3	FACETS	0.72	0.596	0.859	0.36	0.298	0.43	SUBCLONAL	1	TRUE	1	0.28198598879569	3		412	427	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2105515	2105515	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	91	441	0	ENST00000219476.3:c.594G>T	p.Met198Ile	p.M198I	ENST00000219476	NM_000548.3	198	atG/atT	6/42	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.28198598879569	2		441	584	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602745	10602745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1040740503	NA	P-0033740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	245	623	1	ENST00000171111.5:c.833C>T	p.Pro278Leu	p.P278L	ENST00000171111	NM_203500.1	278	cCg/cTg	3/6	0.28198598879569	2	FACETS	0.971	0.909	1	0.971	0.909	1	CLONAL	2	TRUE	0	0.28198598879569	2		624	895	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135067	11135067	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	187	549	1	ENST00000358026.2:c.3034C>T	p.Gln1012Ter	p.Q1012*	ENST00000358026	NM_001128849.1	1012	Cag/Tag	21/36	0.28198598879569	2	FACETS	0.97	0.899	1	0.97	0.899	1	CLONAL	2	TRUE	0	0.28198598879569	2		550	684	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284978	15284978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	207	574	1	ENST00000263388.2:c.4637G>A	p.Arg1546His	p.R1546H	ENST00000263388	NM_000435.2	1546	cGc/cAc	25/33	0.28198598879569	2	FACETS	0.977	0.91	1	0.977	0.91	1	CLONAL	2	TRUE	0	0.28198598879569	2		575	751	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910623	50910623	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	177	477	0	ENST00000440232.2:c.1726G>C	p.Glu576Gln	p.E576Q	ENST00000440232	NM_002691.3	576	Gag/Cag	14/27	0.28198598879569	2	FACETS	0.899	0.831	0.97	0.899	0.831	0.97	CLONAL	2	TRUE	0	0.28198598879569	2		477	698	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397769	49397769	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	37	484	0	ENST00000418115.1:c.455G>T	p.Gly152Val	p.G152V	ENST00000418115	NM_001664.2	152	gGc/gTc	5/5	0.281119629673322	2	FACETS	0.396	0.325	0.475	0.198	0.162	0.238	SUBCLONAL	1	TRUE	0	0.28198598879569	2		484	663	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274791	142274791	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	108	402	0	ENST00000350721.4:c.2269C>T	p.Gln757Ter	p.Q757*	ENST00000350721	NM_001184.3	757	Caa/Taa	10/47	0.28198598879569	3	FACETS	0.98	0.885	1	0.98	0.885	1	CLONAL	2	TRUE	1	0.28198598879569	3		402	446	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749554	41749554	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0033740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	156	429	0	ENST00000226382.2:c.242-1G>T		p.X81_splice	ENST00000226382	NM_003924.3	81			0.103526268414785	5	FACETS	0.899	0.827	0.973	0.674	0.62	0.73	INDETERMINATE	3	TRUE	1	0.28198598879569	5		429	584	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971022	55971023	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0033740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	158	474	2	ENST00000263923.4:c.1774_1775delinsAA	p.Pro592Lys	p.P592K	ENST00000263923	NM_002253.2	592	CCa/AAa	13/30	0.103526268414785	5	FACETS	0.852	0.784	0.922	0.639	0.588	0.692	INDETERMINATE	3	TRUE	1	0.28198598879569	5		476	624	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515306	149515306	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	80	471	0	ENST00000261799.4:c.176C>A	p.Pro59Gln	p.P59Q	ENST00000261799	NM_002609.3	59	cCg/cAg	3/23	0.103526268414785	5	FACETS	1	0.955	1	0.296	0.26	0.334	INDETERMINATE	1	TRUE	1	0.28198598879569	5		471	683	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951891	2951891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	99	501	1	ENST00000396946.4:c.3059C>A	p.Thr1020Lys	p.T1020K	ENST00000396946	NM_032415.4	1020	aCg/aAg	23/25	NA	2	FACETS	0.953	0.851	1			1	INDETERMINATE	1	TRUE	NA	0.28198598879569	2		502	737	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963866	2963866	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0033740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	60	348	0	ENST00000396946.4:c.1940+1G>T		p.X647_splice	ENST00000396946	NM_032415.4	647			0.28198598879569	3	FACETS	0.893	0.769	1	0.446	0.384	0.513	CLONAL	1	TRUE	1	0.28198598879569	3		348	544	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069158	5069158	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0033740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	108	396	0	ENST00000381652.3:c.1463C>G	p.Ser488Ter	p.S488*	ENST00000381652	NM_004972.3	488	tCa/tGa	11/25	0.28198598879569	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	2	TRUE	0	0.28198598879569	2		396	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0033826-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	652	850	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.733522949780812	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.733522949780812	2		850	834	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626123	12626123	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs80338797	NA	P-0033826-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	177	464	0	ENST00000251849.4:c.1837C>G	p.Leu613Val	p.L613V	ENST00000251849	NM_002880.3	613	Cta/Gta	17/17	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.733522949780812	2		464	472	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033826-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	156	205	0	ENST00000256196.4:c.68G>A	p.Gly23Asp	p.G23D	ENST00000256196		23	gGc/gAc	1/6	0.733522949780812	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.733522949780812	1		205	248	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37665987	37665987	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033826-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	178	441	0	ENST00000447079.4:c.2639T>C	p.Leu880Pro	p.L880P	ENST00000447079	NM_015083.1	880	cTt/cCt	7/14	1	2	FACETS	0.977	0.908	1	0.977	0.908	1	CLONAL	1	TRUE	1	0.733522949780812	2		441	497	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229024	36229024	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	102	286	0	ENST00000222270.7:c.7804A>G	p.Ile2602Val	p.I2602V	ENST00000222270	NM_014727.1	2602	Atc/Gtc	36/37	NA	2	FACETS	0.57	0.51	0.635			1	INDETERMINATE	1	TRUE	NA	0.452671039395796	2		286	790	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0034614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	109	353	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.30473990362384	1	FACETS	0.974	0.877	1	0.974	0.877	1	CLONAL	1	TRUE	0	0.31	1		353	610	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0034614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	72	466	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	0.818	0.722	0.919	1	0.979	1	CLONAL	2	TRUE	1	0.31	2		466	284	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0034614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	78	301	1	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.31	2		302	415	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952093	178952093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs2108429932	NA	P-0034614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	70	147	0	ENST00000263967.3:c.3148G>A	p.Gly1050Ser	p.G1050S	ENST00000263967	NM_006218.2	1050	Ggc/Agc	21/21	0.220590596576844	3	FACETS	0.781	0.686	0.882	0.781	0.686	0.882	SUBCLONAL	2	TRUE	1	0.31	3		147	334	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589019	67589020	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0034614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	33	104	0	ENST00000274335.5:c.1111dup	p.Thr371AsnfsTer8	p.T371Nfs*8	ENST00000274335		370	-/A	8/15	1	2	FACETS	1	0.824	1	1	0.824	1	CLONAL	1	TRUE	1	0.31	2		104	212	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319920	8319920	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034632-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	15	239	0	ENST00000356435.5:c.5581T>A	p.Leu1861Met	p.L1861M	ENST00000356435		1861	Ttg/Atg	34/35	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		239	293	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0034712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	98	468	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.881	0.793	0.972			1	INDETERMINATE	1	FALSE	NA	0.641421935119627	2		468	347	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711894	89711894	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786204865	NA	P-0034712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	214	456	0	ENST00000371953.3:c.512A>G	p.Gln171Arg	p.Q171R	ENST00000371953	NM_000314.4	171	cAg/cGg	6/9	0.641421935119627	1	FACETS	0.919	0.864	0.976	0.919	0.864	0.976	CLONAL	1	FALSE	0	0.641421935119627	1		456	493	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367887	15367887	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs754887182	NA	P-0034712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	169	625	0	ENST00000263377.2:c.1439T>C	p.Val480Ala	p.V480A	ENST00000263377	NM_058243.2	480	gTg/gCg	8/20	0.184870954616962	0	FACETS	0.321	0.296	0.346			1	INDETERMINATE	1	FALSE	0	0.641421935119627	0		625	589	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203559	108203588	+	inframe_deletion	In_Frame_Del	DEL	TTGAGGCACTTTGTGATGCTTATATTATAT	TTGAGGCACTTTGTGATGCTTATATTATAT	-	novel	NA	P-0034784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	70	325	0	ENST00000278616.4:c.7860_7889del	p.Glu2621_Leu2630del	p.E2621_L2630del	ENST00000278616	NM_000051.3	2620	gTTGAGGCACTTTGTGATGCTTATATTATATta/gta	53/63	0.442952694399275	1	FACETS	0.762	0.669	0.86	0.762	0.669	0.86	SUBCLONAL	1	TRUE	0	0.442952694399275	1		325	323	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322658	30322658	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0034784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	82	401	0	ENST00000322652.5:c.1671T>A	p.Tyr557Ter	p.Y557*	ENST00000322652	NM_015355.2	557	taT/taA	14/16	1	2	FACETS	0.595	0.525	0.67	0.595	0.525	0.67	SUBCLONAL	1	TRUE	1	0.442952694399275	2		401	622	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878118	151878119	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0034784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	105	350	0	ENST00000262189.6:c.6826_6827del	p.Pro2276Ter	p.P2276*	ENST00000262189	NM_170606.2	2276	CCt/t	36/59	0.442952694399275	1	FACETS	0.914	0.825	1	0.914	0.825	1	CLONAL	1	TRUE	0	0.442952694399275	1		350	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0034885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	340	601	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.572034715464542	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.733410607473817	1		601	581	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330639	65330639	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	125	354	1	ENST00000342505.4:c.1007del	p.Lys336ArgfsTer6	p.K336Rfs*6	ENST00000342505	NM_002227.2	336	aAg/ag	8/25	0.733410607473817	1	FACETS	0.467	0.426	0.511	0.467	0.426	0.511	SUBCLONAL	1	TRUE	0	0.733410607473817	1		355	462	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907186	32907187	+	missense_variant	Missense_Mutation	DNP	TG	TG	AT	novel	NA	P-0034885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	99	306	0	ENST00000380152.3:c.1571_1572delinsAT	p.Met524Asn	p.M524N	ENST00000380152		524	aTG/aAT	10/27	0.671502050375733	3	FACETS	0.551	0.492	0.613	0.184	0.164	0.205	SUBCLONAL	1	TRUE	0	0.733410607473817	3		306	670	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066795	30066795	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs778162256	NA	P-0034885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	150	464	0	ENST00000331968.5:c.2336G>T	p.Gly779Val	p.G779V	ENST00000331968	NM_002742.2	779	gGc/gTc	16/18	0.165232526136852	3	FACETS	0.725	0.663	0.789	0.363	0.331	0.395	INDETERMINATE	1	TRUE	1	0.733410607473817	3		464	771	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633498	3633498	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	182	619	0	ENST00000294008.3:c.4753C>A	p.Pro1585Thr	p.P1585T	ENST00000294008	NM_032444.2	1585	Cct/Act	14/15	0.385768080812337	1	FACETS	0.375	0.346	0.405	0.375	0.346	0.405	INDETERMINATE	1	TRUE	0	0.733410607473817	1		619	839	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664850	29664851	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0034885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	261	297	0	ENST00000356175.3:c.6595_6596del	p.Ile2199SerfsTer21	p.I2199Sfs*21	ENST00000356175	NM_000267.3	2198	gAT/g	43/57	0.572034715464542	1	FACETS	0.969	0.922	1	0.969	0.922	1	CLONAL	1	TRUE	0	0.733410607473817	1		297	465	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184471	7184471	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	332	618	0	ENST00000302850.5:c.830A>G	p.Asp277Gly	p.D277G	ENST00000302850	NM_000208.2	277	gAc/gGc	3/22	0.733410607473817	1	FACETS	0.956	0.914	0.997	0.956	0.914	0.997	CLONAL	1	TRUE	0	0.733410607473817	1		618	600	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55963885	55963885	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	166	465	0	ENST00000263923.4:c.2558C>A	p.Ala853Asp	p.A853D	ENST00000263923	NM_002253.2	853	gCc/gAc	18/30	NA	2	FACETS	0.549	0.505	0.596			1	INDETERMINATE	1	TRUE	NA	0.733410607473817	2		465	824	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530329	187530346	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCACTTACCGTTTCTCGG	TCACTTACCGTTTCTCGG	-	novel	NA	P-0034885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	115	245	0	ENST00000441802.2:c.10197_10206+8del		p.X3399_splice	ENST00000441802	NM_005245.3	3399		16/27	0.733410607473817	1	FACETS	0.867	0.8	0.935	0.867	0.8	0.935	CLONAL	1	TRUE	0	0.733410607473817	1		245	229	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631839	90631839	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519906	NA	P-0034936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	71	519	0	ENST00000330062.3:c.514A>T	p.Arg172Trp	p.R172W	ENST00000330062	NM_002168.2	172	Agg/Tgg	4/11	1	2	FACETS	0.94	0.822	1	0.94	0.822	1	CLONAL	1	TRUE	1	0.284942712039358	2		519	530	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0034971-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	59	458	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.228068267010687	4	FACETS	1	0.925	1	1	0.925	1	INDETERMINATE	2	TRUE	2	0.440121377539626	4		458	179	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911579	134911579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs959853730	NA	P-0034971-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	95	739	1	ENST00000398015.3:c.2044C>T	p.Arg682Cys	p.R682C	ENST00000398015	NM_004441.4	682	Cgc/Tgc	11/16	0.228068267010687	4	FACETS	0.769	0.69	0.853	0.769	0.69	0.853	INDETERMINATE	2	TRUE	2	0.440121377539626	4		740	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578175	7578175	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0034971-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	202	919	0	ENST00000269305.4:c.672+2T>G		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.440121377539626	1	FACETS	0.795	0.746	0.845	1	0.993	1	SUBCLONAL	2	TRUE	0	0.440121377539626	1		919	450	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023662	27023662	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034971-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	81	468	0	ENST00000324856.7:c.768C>G	p.Ser256Arg	p.S256R	ENST00000324856	NM_006015.4	256	agC/agG	1/20	0.364732049412645	3	FACETS	0.74	0.652	0.834	0.37	0.326	0.417	SUBCLONAL	1	TRUE	1	0.440121377539626	3		468	607	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190806	106190806	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034971-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	39	691	0	ENST00000380013.4:c.4084C>G	p.Leu1362Val	p.L1362V	ENST00000380013	NM_001127208.2	1362	Ctg/Gtg	9/11	1	2	FACETS	0.511	0.424	0.607	0.511	0.424	0.607	SUBCLONAL	1	TRUE	1	0.440121377539626	2		691	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs786201057	NA	P-0035218-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	104	725	0	ENST00000269305.4:c.374C>G	p.Thr125Arg	p.T125R	ENST00000269305	NM_001126112.2	125	aCg/aGg	4/11	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.24	2		725	816	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921744	111921744	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035218-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	81	542	0	ENST00000393256.3:c.533A>G	p.His178Arg	p.H178R	ENST00000393256	NM_006538.4	178	cAc/cGc	4/4	1	2	FACETS	0.962	0.847	1	0.962	0.847	1	CLONAL	1	TRUE	1	0.24	2		542	702	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966640	36966640	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035218-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	41	719	0	ENST00000358127.4:c.686T>G	p.Phe229Cys	p.F229C	ENST00000358127	NM_001280556.1	229	tTc/tGc	6/10	1	2	FACETS	0.446	0.37	0.531	0.446	0.37	0.531	SUBCLONAL	1	TRUE	1	0.24	2		719	766	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs770248150	NA	P-0121442-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	282	623	9	ENST00000311936.3:c.351A>T	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaT	4/5	0.381071238084441	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	NA	1	0.381071238084441	4		632	638	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0035740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	162	230	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.974	0.904	1	0.974	0.904	1	CLONAL	1	TRUE	1	0.797775194158625	2		230	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	577	480	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	2	TRUE	NA	0.797775194158625	2		480	713	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584513	48584514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs377767334	NA	P-0035740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	189	237	0	ENST00000342988.3:c.692dup	p.Ser232GlnfsTer3	p.S232Qfs*3	ENST00000342988	NM_005359.5	229	ctg/ctGg	6/12	0.771947174453964	1	FACETS	0.937	0.887	0.986	0.937	0.887	0.986	CLONAL	1	TRUE	0	0.797775194158625	1		237	304	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857833	9857833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765522252	NA	P-0035740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	67	419	0	ENST00000330684.3:c.3568C>T	p.His1190Tyr	p.H1190Y	ENST00000330684	NM_001134407.1	1190	Cac/Tac	13/13	1	2	FACETS	0.235	0.203	0.269	0.235	0.203	0.269	SUBCLONAL	1	TRUE	1	0.797775194158625	2		419	716	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197399	26197399	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	139	232	0	ENST00000356476.2:c.80G>C	p.Arg27Pro	p.R27P	ENST00000356476		27	cGa/cCa	1/1	0.794831270641073	1	FACETS	0.983	0.924	1	0.983	0.924	1	CLONAL	1	TRUE	0	0.797775194158625	1		232	213	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131978054	131978055	+	frameshift_variant,stop_retained_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	314	146	0	ENST00000265335.6:c.*3dup		p.*1313fs	ENST00000265335		1313	taa/tAaa	25/25	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.797775194158625	2		146	673	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508713	106508713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750113758	NA	P-0035740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	211	318	0	ENST00000359195.3:c.707C>T	p.Ser236Leu	p.S236L	ENST00000359195	NM_002649.2	236	tCa/tTa	2/11	1	2	FACETS	0.936	0.876	0.997	0.936	0.876	0.997	CLONAL	1	TRUE	1	0.797775194158625	2		318	565	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944734	31944734	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	28	48	0	ENST00000340398.3:c.367G>C	p.Asp123His	p.D123H	ENST00000340398	NM_001013699.2	123	Gac/Cac	1/1	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.797775194158625	2		48	55	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323001	31323001	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0035741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	589	300	0	ENST00000412585.2:c.896-1G>C		p.X299_splice	ENST00000412585	NM_005514.6	299			0.545523931126117	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.545523931126117	2		300	910	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969477	44969480	+	frameshift_variant	Frame_Shift_Del	DEL	TATG	TATG	-	novel	NA	P-0035741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	95	290	0	ENST00000377967.4:c.4159_4162del	p.Tyr1387ThrfsTer5	p.Y1387Tfs*5	ENST00000377967	NM_021140.2	1387	TATGac/ac	28/29	1	2	FACETS	0.998	0.897	1	0.998	0.897	1	CLONAL	1	TRUE	1	0.545523931126117	2		290	349	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183867	10183867	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	176	243	1	ENST00000256474.2:c.336C>A	p.Tyr112Ter	p.Y112*	ENST00000256474	NM_000551.3	112	taC/taA	1/3	0.264851470967389	2	FACETS	0.889	0.823	0.956	0.889	0.823	0.956	CLONAL	2	FALSE	0	0.345700636616101	2		244	573	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720732	89720732	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	11	105	0	ENST00000371953.3:c.883del	p.Leu295TyrfsTer12	p.L295Yfs*12	ENST00000371953	NM_000314.4	295	Cta/ta	8/9	0.317426085383167	3	FACETS	1	0.727	1	0.346	0.242	0.469	CLONAL	1	FALSE	0	0.345700636616101	3		105	72	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122367	17122367	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	250	142	0	ENST00000285071.4:c.1028T>C	p.Leu343Pro	p.L343P	ENST00000285071	NM_144997.5	343	cTg/cCg	9/14	1	2	FACETS	0.925	0.868	0.983	1	0.995	1	CLONAL	2	FALSE	1	0.345700636616101	2		142	782	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871987	45871988	+	missense_variant	Missense_Mutation	DNP	AA	AA	TT	novel	NA	P-0035744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	159	324	0	ENST00000391945.4:c.260_261inv	p.Leu87Gln	p.L87Q	ENST00000391945	NM_000400.3	87	cTT/cAA	5/23	0.174736741409572	5	FACETS	0.919	0.844	0.997	0.613	0.562	0.665	INDETERMINATE	2	FALSE	2	0.345700636616101	5		324	760	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270535	98270535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs199976372	NA	P-0035744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	166	62	0	ENST00000331920.6:c.109G>T	p.Gly37Trp	p.G37W	ENST00000331920	NM_000264.3	37	Ggg/Tgg	1/24	1	2	FACETS	0.996	0.923	1	1	0.993	1	CLONAL	2	FALSE	1	0.345700636616101	2		62	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0035757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	262	679	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.277709845292915	2	FACETS	0.962	0.902	1	0.962	0.902	1	CLONAL	2	TRUE	0	0.277709845292915	2		679	981	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0035757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	108	330	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	NA	2	FACETS	0.751	0.673	0.835			1	INDETERMINATE	1	TRUE	NA	0.277709845292915	2		330	1035	SUCCESS
BLM	641	MSKCC	GRCh37	15	91352424	91352424	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	53	430	0	ENST00000355112.3:c.3809A>G	p.Lys1270Arg	p.K1270R	ENST00000355112	NM_000057.2	1270	aAa/aGa	20/22	0.277709845292915	4	FACETS	0.701	0.596	0.815	0.234	0.198	0.272	SUBCLONAL	1	TRUE	1	0.277709845292915	4		430	696	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953354	17953354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	156	916	0	ENST00000458235.1:c.632G>A	p.Arg211Lys	p.R211K	ENST00000458235	NM_000215.3	211	aGg/aAg	6/24	0.245450704293006	3	FACETS	0.983	0.898	1	0.491	0.449	0.536	CLONAL	1	TRUE	1	0.277709845292915	3		916	1302	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807098	1807098	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1515	144	866	0	ENST00000260795.2:c.1429C>T	p.Pro477Ser	p.P477S	ENST00000260795		477	Ccc/Tcc	10/17	0.277709845292915	7	FACETS	1	0.946	1			1	CLONAL	1	TRUE	NA	0.277709845292915	7		866	1659	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633842	86633842	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	20	383	0	ENST00000274376.6:c.951G>T	p.Trp317Cys	p.W317C	ENST00000274376	NM_002890.2	317	tgG/tgT	5/25	0.277709845292915	2	FACETS	0.652	0.5	0.828	0.326	0.25	0.414	SUBCLONAL	1	TRUE	0	0.277709845292915	2		383	221	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942761	68942761	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	201	562	0	ENST00000288368.4:c.573C>A	p.His191Gln	p.H191Q	ENST00000288368	NM_024870.2	191	caC/caA	6/40	0.245450704293006	3	FACETS	0.966	0.897	1	0.966	0.897	1	CLONAL	2	TRUE	1	0.277709845292915	3		562	853	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0035781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	65	233	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.211926074165765	3	FACETS	0.774	0.673	0.883	0.774	0.673	0.883	SUBCLONAL	2	TRUE	1	0.211926074165765	3		235	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0035781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	56	654	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.211926074165765	1	FACETS	0.801	0.686	0.927	0.801	0.686	0.927	CLONAL	1	TRUE	0	0.211926074165765	1		656	590	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107135	27107136	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	106	403	0	ENST00000324856.7:c.6747dup	p.Glu2250ArgfsTer28	p.E2250Rfs*28	ENST00000324856	NM_006015.4	2249	tca/tcAa	20/20	1	2	FACETS	0.798	0.716	0.884	1	0.984	1	SUBCLONAL	2	TRUE	1	0.211926074165765	2		403	627	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584603	48584603	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	30	261	0	ENST00000342988.3:c.776del	p.Thr259IlefsTer77	p.T259Ifs*77	ENST00000342988	NM_005359.5	259	aCt/at	6/12	0.208027938703483	1	FACETS	0.57	0.459	0.697	0.57	0.459	0.697	SUBCLONAL	1	TRUE	0	0.211926074165765	1		261	444	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913078	44913078	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	28	167	0	ENST00000377967.4:c.753G>A	p.Trp251Ter	p.W251*	ENST00000377967	NM_021140.2	251	tgG/tgA	10/29	1	2	FACETS	0.844	0.676	1	0.844	0.676	1	CLONAL	1	TRUE	1	0.211926074165765	2		167	313	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918608	44918609	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0035781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	55	349	1	ENST00000377967.4:c.1091_1092delinsTT	p.Ser364Phe	p.S364F	ENST00000377967	NM_021140.2	364	tCC/tTT	12/29	1	2	FACETS	0.859	0.735	0.996	0.859	0.735	0.996	CLONAL	1	TRUE	1	0.211926074165765	2		350	604	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	32	395	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.83	1	1	0.83	1	CLONAL	1	TRUE	1	0.17	2		395	368	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0036098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	47	374	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	0.898	0.756	1	0.898	0.756	1	CLONAL	1	TRUE	1	0.17	2		374	616	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004922	150004922	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	38	325	0	ENST00000253339.5:c.1303C>T	p.Gln435Ter	p.Q435*	ENST00000253339		435	Cag/Tag	3/7	1	2	FACETS	0.691	0.57	0.827	0.691	0.57	0.827	SUBCLONAL	1	TRUE	1	0.17	2		325	647	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541913	187541913	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs755889337	NA	P-0036098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	59	366	0	ENST00000441802.2:c.5827C>T	p.Gln1943Ter	p.Q1943*	ENST00000441802	NM_005245.3	1943	Cag/Tag	10/27	1	2	FACETS	0.825	0.708	0.953	0.825	0.708	0.953	CLONAL	1	TRUE	1	0.17	2		366	841	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247247	153247247	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	39	267	0	ENST00000281708.4:c.1555T>G	p.Tyr519Asp	p.Y519D	ENST00000281708	NM_033632.3	519	Tat/Gat	10/12	1	2	FACETS	0.942	0.781	1	0.942	0.781	1	CLONAL	1	TRUE	1	0.17	2		267	487	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808856	3808856	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	45	302	0	ENST00000262367.5:c.3368del	p.Pro1123GlnfsTer7	p.P1123Qfs*7	ENST00000262367	NM_004380.2	1123	cCa/ca	17/31	1	2	FACETS	0.835	0.701	0.984	0.835	0.701	0.984	CLONAL	1	TRUE	1	0.17	2		302	634	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845880	151845880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	80	475	0	ENST00000262189.6:c.13132G>A	p.Glu4378Lys	p.E4378K	ENST00000262189	NM_170606.2	4378	Gaa/Aaa	52/59	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.17	2		475	929	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912664	NA	P-0036576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	127	389	0	ENST00000269305.4:c.1010G>C	p.Arg337Pro	p.R337P	ENST00000269305	NM_001126112.2	337	cGc/cCc	10/11	0.202971898356056	2	FACETS	0.829	0.753	0.909	0.829	0.753	0.909	CLONAL	2	TRUE	0	0.235930188752592	2		389	649	SUCCESS
APC	324	MSKCC	GRCh37	5	112151291	112151291	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs876660765	NA	P-0036576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	35	114	0	ENST00000257430.4:c.933+1G>A		p.X311_splice	ENST00000257430	NM_000038.5	311			1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.235930188752592	2		114	221	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942599	71942599	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1420082156	NA	P-0036576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	108	267	0	ENST00000298229.2:c.1555G>A	p.Glu519Lys	p.E519K	ENST00000298229	NM_001567.3	519	Gag/Aag	13/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.235930188752592	2		267	654	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515418	103515418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	14	103	0	ENST00000355739.4:c.1919C>T	p.Pro640Leu	p.P640L	ENST00000355739	NM_000123.3	640	cCa/cTa	8/15	0.235930188752592	3	FACETS	0.68	0.493	0.906	0.34	0.246	0.453	SUBCLONAL	1	TRUE	1	0.235930188752592	3		103	195	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750403	41750403	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	209	33	0	ENST00000226382.2:c.225C>A	p.Ser75Arg	p.S75R	ENST00000226382	NM_003924.3	75	agC/agA	1/3	1	2	FACETS	0.993	0.928	1	1	0.995	1	CLONAL	3	TRUE	1	0.235930188752592	2		33	595	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0036670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	126	466	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.83031610098508	2		466	289	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593268	67593268	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	TTGTT	novel	NA	P-0036670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	20	538	0	ENST00000274335.5:c.2014delinsTTGTT	p.Ile672LeufsTer16	p.I672Lfs*16	ENST00000274335		672	Ata/TTGTTta	15/15	1	2	FACETS	0.12	0.092	0.154	0.12	0.092	0.154	SUBCLONAL	1	TRUE	1	0.83031610098508	2		538	400	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0036671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	369	944	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.804198489276715	2		945	874	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131118	55131118	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139913632	NA	P-0036671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	286	879	1	ENST00000257290.5:c.661C>T	p.Leu221Phe	p.L221F	ENST00000257290	NM_006206.4	221	Ctt/Ttt	5/23	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.804198489276715	2		880	653	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252155	226252155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553260624	NA	P-0036671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	147	65	0	ENST00000366813.1:c.103G>A	p.Gly35Arg	p.G35R	ENST00000366813		35	Ggg/Agg	1/3	1	2	FACETS	0.785	0.737	0.831	1	0.992	1	SUBCLONAL	2	TRUE	1	0.804198489276715	2		65	233	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579390	7579393	+	frameshift_variant	Frame_Shift_Del	DEL	GGAA	GGAA	-	rs730882015	NA	P-0036671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	301	906	0	ENST00000269305.4:c.294_297del	p.Ser99ArgfsTer23	p.S99Rfs*23	ENST00000269305	NM_001126112.2	98	ccTTCC/cc	4/11	1	2	FACETS	0.915	0.866	0.965	0.915	0.866	0.965	CLONAL	1	TRUE	1	0.804198489276715	2		906	818	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938003	76938006	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	novel	NA	P-0036671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	278	479	0	ENST00000373344.5:c.2742_2745del	p.Ser915LeufsTer54	p.S915Lfs*54	ENST00000373344	NM_000489.3	914	gcAAGT/gc	9/35	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.804198489276715	1		479	389	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430735	181430735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	329	870	1	ENST00000325404.1:c.587C>T	p.Pro196Leu	p.P196L	ENST00000325404	NM_003106.3	196	cCc/cTc	1/1	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.804198489276715	2		871	784	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131131	55131131	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	290	844	1	ENST00000257290.5:c.674A>C	p.Tyr225Ser	p.Y225S	ENST00000257290	NM_006206.4	225	tAt/tCt	5/23	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.804198489276715	2		845	644	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972965	68972965	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	222	751	1	ENST00000288368.4:c.1290A>T	p.Glu430Asp	p.E430D	ENST00000288368	NM_024870.2	430	gaA/gaT	11/40	1	2	FACETS	0.923	0.865	0.982	0.923	0.865	0.982	CLONAL	1	TRUE	1	0.804198489276715	2		752	598	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0036673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	294	621	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.77302326348842	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.77302326348842	1		622	465	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105594	27105607	+	frameshift_variant	Frame_Shift_Del	DEL	GGTGGGTGACCCAG	GGTGGGTGACCCAG	-	novel	NA	P-0036673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	205	685	0	ENST00000324856.7:c.5206_5219del	p.Val1736ThrfsTer15	p.V1736Tfs*15	ENST00000324856	NM_006015.4	1735	gaGGTGGGTGACCCAGga/gaga	20/20	0.763000937990505	1	FACETS	0.971	0.921	1	0.971	0.921	1	CLONAL	1	TRUE	0	0.77302326348842	1		685	335	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299072	15299072	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs376728138	NA	P-0036673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	261	786	0	ENST00000263388.2:c.1466A>G	p.Asn489Ser	p.N489S	ENST00000263388	NM_000435.2	489	aAt/aGt	9/33	1	2	FACETS	0.909	0.855	0.963	0.909	0.855	0.963	CLONAL	1	TRUE	1	0.77302326348842	2		786	743	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469071	25469071	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	376	1180	0	ENST00000264709.3:c.1387G>C	p.Glu463Gln	p.E463Q	ENST00000264709	NM_175629.2	463	Gag/Cag	11/23	0.77302326348842	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.77302326348842	1		1180	584	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838096	89838096	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1054636249	NA	P-0036674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	19	191	0	ENST00000389301.3:c.2141G>A	p.Arg714Gln	p.R714Q	ENST00000389301	NM_000135.2	714	cGg/cAg	23/43	1	2	FACETS	1	0.77	1	1	0.77	1	CLONAL	1	TRUE	1	0.234414862433966	2		191	161	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578381	7578431	+	inframe_deletion	In_Frame_Del	DEL	TGAGCAGCGCTCATGGTGGGGGCAGCGCCTCACAACCTCCGTCATGTGCTG	TGAGCAGCGCTCATGGTGGGGGCAGCGCCTCACAACCTCCGTCATGTGCTG	-	novel	NA	P-0036674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	33	224	0	ENST00000269305.4:c.499_549del	p.Gln167_Ser183del	p.Q167_S183del	ENST00000269305	NM_001126112.2	167	CAGCACATGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCA/-	5/11	0.234414862433966	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.234414862433966	1		224	195	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0036751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	824	654	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.909708869470695	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.940420462359775	3		656	1245	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0036751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	470	523	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.909708869470695	3	FACETS	0.966	0.922	1	0.483	0.461	0.505	CLONAL	1	TRUE	1	0.940420462359775	3		523	1522	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs199469669	NA	P-0036751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	292	349	0	ENST00000374080.3:c.130G>C	p.Gly44Arg	p.G44R	ENST00000374080		44	Ggt/Cgt	2/45	1	2	FACETS	0.894	0.846	0.941	0.894	0.846	0.941	CLONAL	1	TRUE	1	0.940420462359775	2		349	695	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239300	105239300	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs372502847	NA	P-0036751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	433	387	0	ENST00000349310.3:c.1087A>G	p.Met363Val	p.M363V	ENST00000349310	NM_001014432.1	363	Atg/Gtg	12/15	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.940420462359775	2		387	838	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855028	76855029	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0036751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	341	255	0	ENST00000373344.5:c.5807_5808del	p.Lys1936ArgfsTer5	p.K1936Rfs*5	ENST00000373344	NM_000489.3	1936	aAG/a	25/35	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.940420462359775	2		255	707	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0037113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	92	449	1	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	0.2	2		450	692	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0037113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	77	716	1	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	1	2	FACETS	0.929	0.814	1	0.929	0.814	1	CLONAL	1	TRUE	1	0.2	2		717	829	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944946	31944946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	30	484	1	ENST00000340398.3:c.155G>A	p.Arg52His	p.R52H	ENST00000340398	NM_001013699.2	52	cGt/cAt	1/1	1	2	FACETS	0.525	0.422	0.643	0.525	0.422	0.643	SUBCLONAL	1	TRUE	1	0.2	2		485	571	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651978	36651979	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0037113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	52	796	0	ENST00000244741.5:c.102_103del	p.Cys34Ter	p.C34*	ENST00000244741	NM_000389.4	34	TGt/t	2/3	1	2	FACETS	0.669	0.568	0.78	0.669	0.568	0.78	SUBCLONAL	1	TRUE	1	0.2	2		796	777	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544167	18544167	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	62	338	0	ENST00000266497.5:c.1984C>T	p.Gln662Ter	p.Q662*	ENST00000266497		662	Cag/Tag	13/31	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.2	2		338	555	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346890	89346898	+	inframe_deletion	In_Frame_Del	DEL	GGCGGGAGG	GGCGGGAGG	-	rs775221712	NA	P-0037113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	18	396	1	ENST00000301030.4:c.6052_6060del	p.Pro2018_Ala2020del	p.P2018_A2020del	ENST00000301030	NM_001256183.1	2018	CCTCCCGCC/-	9/13	1	2	FACETS	0.7	0.528	0.904	0.7	0.528	0.904	SUBCLONAL	1	TRUE	1	0.2	2		397	257	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094470	27094470	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	96	511	0	ENST00000324856.7:c.3178G>T	p.Glu1060Ter	p.E1060*	ENST00000324856	NM_006015.4	1060	Gag/Tag	11/20	0.268199252326374	2	FACETS	0.758	0.676	0.845	0.758	0.676	0.845	SUBCLONAL	2	TRUE	0	0.2	2		511	633	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497678	125497678	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	48	451	0	ENST00000428830.2:c.242A>G	p.Tyr81Cys	p.Y81C	ENST00000428830	NM_001114121.2	81	tAt/tGt	3/14	0.265755195172395	1	FACETS	0.587	0.495	0.689	0.587	0.495	0.689	SUBCLONAL	1	TRUE	0	0.2	1		451	736	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527404	137527404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	37	351	0	ENST00000367739.4:c.242C>T	p.Ser81Phe	p.S81F	ENST00000367739	NM_000416.2	81	tCt/tTt	3/7	1	2	FACETS	0.695	0.573	0.833	0.695	0.573	0.833	SUBCLONAL	1	TRUE	1	0.2	2		351	532	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0037292-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	229	233	2	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	0.995	1	CLONAL	2	TRUE	1	0.420108545452655	2		235	520	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0037292-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	163	461	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.420108545452655	2		461	754	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0037292-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	91	338	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	1	2	FACETS	0.989	0.883	1	0.989	0.883	1	CLONAL	1	TRUE	1	0.420108545452655	2		338	438	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037292-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	221	505	0	ENST00000206249.3:c.1607T>A	p.Leu536His	p.L536H	ENST00000206249	NM_000125.3	536	cTc/cAc	8/8	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.420108545452655	2		505	785	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916929	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519931	NA	P-0037292-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	107	405	0	ENST00000263967.3:c.316G>C	p.Gly106Arg	p.G106R	ENST00000263967	NM_006218.2	106	Ggc/Cgc	2/21	1	2	FACETS	0.862	0.775	0.954	0.862	0.775	0.954	CLONAL	1	TRUE	1	0.420108545452655	2		405	591	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246445	105246445	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037292-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	362	608	0	ENST00000349310.3:c.155T>G	p.Leu52Arg	p.L52R	ENST00000349310	NM_001014432.1	52	cTc/cGc	4/15	0.420108545452655	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.420108545452655	2		608	830	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217654	7217654	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037292-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	116	380	0	ENST00000380728.2:c.273G>T	p.Lys91Asn	p.K91N	ENST00000380728		91	aaG/aaT	4/11	1	2	FACETS	0.879	0.794	0.969	0.879	0.794	0.969	CLONAL	1	TRUE	1	0.420108545452655	2		380	628	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748896	41748896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs545871181	NA	P-0037292-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	83	571	0	ENST00000301178.4:c.1421G>A	p.Arg474Gln	p.R474Q	ENST00000301178	NM_021913.4	474	cGg/cAg	11/20	1	2	FACETS	0.446	0.393	0.503	0.446	0.393	0.503	SUBCLONAL	1	TRUE	1	0.420108545452655	2		571	886	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50815230	50815230	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037292-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	182	566	0	ENST00000398568.2:c.1583C>A	p.Ala528Glu	p.A528E	ENST00000398568	NM_001042412.1	528	gCg/gAg	9/18	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.420108545452655	2		566	741	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209101817	209101817	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037292-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	124	364	0	ENST00000345146.2:c.1231C>G	p.Gln411Glu	p.Q411E	ENST00000345146	NM_005896.2	411	Cag/Gag	10/10	1	2	FACETS	0.925	0.839	1	0.925	0.839	1	CLONAL	1	TRUE	1	0.420108545452655	2		364	638	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182679076	182679076	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037292-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	53	295	1	ENST00000292782.4:c.458G>T	p.Arg153Leu	p.R153L	ENST00000292782	NM_020640.2	153	cGa/cTa	4/7	1	2	FACETS	0.539	0.46	0.625	0.539	0.46	0.625	SUBCLONAL	1	TRUE	1	0.420108545452655	2		296	468	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680197	30680197	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037292-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	214	644	0	ENST00000376406.3:c.1522A>T	p.Ile508Phe	p.I508F	ENST00000376406	NM_014641.2	508	Atc/Ttc	5/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.420108545452655	2		644	917	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190557	32190557	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753044693	NA	P-0037292-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	223	672	0	ENST00000375023.3:c.182C>T	p.Thr61Met	p.T61M	ENST00000375023	NM_004557.3	61	aCg/aTg	3/30	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.420108545452655	2		672	1020	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037331-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	337	63	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.352773863889832	5	FACETS	0.971	0.929	1	0.971	0.929	1	CLONAL	5	TRUE	0	0.352773863889832	5		63	602	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0037331-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	74	283	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	0.958	0.842	1	0.958	0.842	1	CLONAL	1	TRUE	1	0.352773863889832	2		283	438	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100183	27100183	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1421112233	NA	P-0037331-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	155	390	0	ENST00000324856.7:c.3979C>T	p.Gln1327Ter	p.Q1327*	ENST00000324856	NM_006015.4	1327	Cag/Tag	16/20	0.333700905051449	2	FACETS	0.863	0.796	0.933	0.863	0.796	0.933	CLONAL	2	TRUE	0	0.352773863889832	2		390	509	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575080	48575080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037331-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	50	259	0	ENST00000342988.3:c.274C>T	p.His92Tyr	p.H92Y	ENST00000342988	NM_005359.5	92	Cat/Tat	3/12	1	2	FACETS	0.756	0.643	0.879	0.756	0.643	0.879	SUBCLONAL	1	TRUE	1	0.352773863889832	2		259	375	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472523	88472523	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1419472052	NA	P-0037331-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	115	539	0	ENST00000360948.2:c.2032C>T	p.Arg678Ter	p.R678*	ENST00000360948	NM_001012338.2	678	Cga/Tga	16/19	0.352773863889832	3	FACETS	0.952	0.857	1	0.476	0.428	0.526	CLONAL	1	TRUE	1	0.352773863889832	3		539	806	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651532	52651532	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037331-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	81	319	0	ENST00000394830.3:c.1564C>T	p.Arg522Ter	p.R522*	ENST00000394830	NM_018313.4	522	Cga/Tga	15/30	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.352773863889832	2		319	439	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176330	24176330	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037331-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	141	619	0	ENST00000263121.7:c.1121G>C	p.Arg374Pro	p.R374P	ENST00000263121	NM_003073.3	374	cGg/cCg	9/9	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.352773863889832	2		619	785	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727152	41727153	+	splice_donor_variant	Splice_Site	DNP	GT	GT	AA	novel	NA	P-0037331-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	91	465	0	ENST00000301178.4:c.409+1_409+2delinsAA		p.X137_splice	ENST00000301178	NM_021913.4	137			0.352773863889832	3	FACETS	0.774	0.687	0.867	0.387	0.343	0.434	SUBCLONAL	1	TRUE	1	0.352773863889832	3		465	784	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408864	41408864	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037331-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	78	343	0	ENST00000373198.4:c.562C>A	p.Pro188Thr	p.P188T	ENST00000373198	NM_133170.3	188	Cca/Aca	4/32	0.352773863889832	3	FACETS	0.819	0.72	0.926	0.41	0.36	0.463	CLONAL	1	TRUE	1	0.352773863889832	3		343	635	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-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	83	185	0	ENST00000274335.5:c.1104_1358del		p.X368_splice	ENST00000274335		368	tATACTCTTACACTAAGGTAAGCCAGGGAATATAGCTGAAATTAGGGTTTTGGGCTGATATTAAAACATATTTCCTTATTCCAAAATGTTAATACCTTTATTTTTATATTGTTTTTACAGGAAAGGGGGAAATAACAAATTAATCAAAATATTTCATCGAGATGGGAAATATGGCTTCTCTGACCCATTAACCTTCAGTTCTGTGGTTGAATTAATAAACCACTACCGGAATGAATCTCTAGCTCAGTATAATCCCAAATTGGATGTGAAATTACTTTATCCAGTATCCAAATACCAACAGGTAATAAAAACTGAATGAATTATCCAGTTACGATGTTTAGACAAGATCCTTTTAATACTTAGAAAACATTTGAAGCAGATGAATTACATGTAATCAAGTCTAAAAAACTTGACACTCGTAATTACATAATTGCAATTTTAAAGATGTTTCCATGTCAGCTATTTTGTTAAACAATTGTTATTTGATTAAATACCTTATCCATTGAATTTATTTTAATCTTTCTAGGATCAAGTTGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAac/tac	8-10/15	0.352773863889832	3	FACETS	0.86	0.766	0.958	0.86	0.766	0.958	CLONAL	2	TRUE	1	0.352773863889832	3		185	322	SUCCESS
APC	324	MSKCC	GRCh37	5	112174979	112174979	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs863225344	NA	P-0037331-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	41	146	0	ENST00000257430.4:c.3688C>T	p.Gln1230Ter	p.Q1230*	ENST00000257430	NM_000038.5	1230	Cag/Tag	16/16	0.352773863889832	4	FACETS	1	0.876	1	0.528	0.441	0.622	CLONAL	1	TRUE	2	0.352773863889832	4		146	298	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38139056	38139056	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037331-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	88	383	0	ENST00000317025.8:c.3547G>T	p.Glu1183Ter	p.E1183*	ENST00000317025	NM_023034.1	1183	Gaa/Taa	20/24	1	2	FACETS	0.843	0.748	0.944	0.843	0.748	0.944	CLONAL	1	TRUE	1	0.352773863889832	2		383	592	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0037340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	73	233	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.160144154055048	2	FACETS	0.652	0.571	0.739	0.326	0.285	0.37	INDETERMINATE	1	TRUE	0	0.42148961037994	2		235	531	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0037340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	124	374	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.313991130564015	2	FACETS	0.77	0.704	0.839	0.77	0.704	0.839	SUBCLONAL	2	TRUE	0	0.42148961037994	2		374	382	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0037340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	218	411	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA	2	FACETS	1	0.957	1			1	INDETERMINATE	2	TRUE	NA	0.42148961037994	2		411	506	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0037340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	162	262	0	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	0.313991130564015	2	FACETS	0.776	0.718	0.837	0.776	0.718	0.837	SUBCLONAL	2	TRUE	0	0.42148961037994	2		262	495	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546725	9546725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210292896	NA	P-0037340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	93	409	0	ENST00000353224.5:c.1297C>T	p.Arg433Trp	p.R433W	ENST00000353224	NM_177990.2	433	Cgg/Tgg	5/10	0.308643565790269	3	FACETS	0.786	0.705	0.87	0.786	0.705	0.87	SUBCLONAL	2	TRUE	1	0.42148961037994	3		409	340	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5206828	5206828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1326058191	NA	P-0037340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	101	727	2	ENST00000357368.4:c.5804C>T	p.Ala1935Val	p.A1935V	ENST00000357368	NM_002850.3	1935	gCg/gTg	38/38	1	2	FACETS	0.667	0.597	0.743	0.667	0.597	0.743	SUBCLONAL	1	TRUE	1	0.42148961037994	2		729	718	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812249	212812249	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	85	320	0	ENST00000342788.4:c.327A>C	p.Lys109Asn	p.K109N	ENST00000342788	NM_005235.2	109	aaA/aaC	3/28	0.313991130564015	2	FACETS	1	0.953	1	0.565	0.503	0.63	CLONAL	1	TRUE	0	0.42148961037994	2		320	357	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225365173	225365173	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180155404	NA	P-0037340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	158	361	0	ENST00000264414.4:c.1517G>A	p.Arg506Gln	p.R506Q	ENST00000264414	NM_003590.4	506	cGg/cAg	11/16	0.313991130564015	2	FACETS	1	0.989	1	0.742	0.685	0.801	CLONAL	1	TRUE	0	0.42148961037994	2		361	505	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800205	32800211	+	frameshift_variant	Frame_Shift_Del	DEL	TCAGCAT	TCAGCAT	AG	novel	NA	P-0037340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	56	477	1	ENST00000374899.4:c.1171_1177delinsCT	p.Met391LeufsTer90	p.M391Lfs*90	ENST00000374899	NM_018833.2	391	ATGCTGAgc/CTgc	7/12	1	2	FACETS	0.604	0.518	0.697	0.604	0.518	0.697	SUBCLONAL	1	TRUE	1	0.42148961037994	2		478	440	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450301	50450301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770551610	NA	P-0037340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	80	608	1	ENST00000331340.3:c.485G>A	p.Arg162Gln	p.R162Q	ENST00000331340	NM_006060.4	162	cGg/cAg	5/8	0.42148961037994	3	FACETS	0.576	0.506	0.651	0.288	0.253	0.326	SUBCLONAL	1	TRUE	1	0.42148961037994	3		609	798	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531904	41531904	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	78	478	0	ENST00000263253.7:c.1616C>A	p.Ser539Tyr	p.S539Y	ENST00000263253	NM_001429.3	539	tCt/tAt	7/31	1	2	FACETS	0.736	0.648	0.829	0.736	0.648	0.829	SUBCLONAL	1	TRUE	1	0.42148961037994	2		478	503	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467810	66467810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370146960	NA	P-0037340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	49	326	0	ENST00000273854.3:c.459G>A	p.Met153Ile	p.M153I	ENST00000273854	NM_004439.5	153	atG/atA	3/18	1	2	FACETS	0.639	0.543	0.744	0.639	0.543	0.744	SUBCLONAL	1	TRUE	1	0.42148961037994	2		326	364	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037874	49037874	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037356-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	60	217	0	ENST00000267163.4:c.2114T>A	p.Met705Lys	p.M705K	ENST00000267163	NM_000321.2	705	aTg/aAg	21/27	0.308179416887806	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.350014780677983	1		217	256	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632591	3632653	+	inframe_deletion	In_Frame_Del	DEL	CTGTGTCCGCCGCCTGCACGGCTGCCTGCGAGGCACTGACCTCCCCCTCGCCCTCCTCTTCAC	CTGTGTCCGCCGCCTGCACGGCTGCCTGCGAGGCACTGACCTCCCCCTCGCCCTCCTCTTCAC	-	novel	NA	P-0037356-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	54	727	0	ENST00000294008.3:c.5195_5257del	p.Gly1732_Thr1752del	p.G1732_T1752del	ENST00000294008	NM_032444.2	1732	gGTGAAGAGGAGGGCGAGGGGGAGGTCAGTGCCTCGCAGGCAGCCGTGCAGGCGGCGGACACAGac/gac	15/15	0.207327967255298	3	FACETS	0.421	0.358	0.49	0.21	0.179	0.245	INDETERMINATE	1	TRUE	1	0.350014780677983	3		727	862	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578289	7578289	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037356-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	159	596	0	ENST00000269305.4:c.560del	p.Gly187ValfsTer60	p.G187Vfs*60	ENST00000269305	NM_001126112.2	187	gGt/gt	6/11	0.24387875928299	2	FACETS	0.779	0.718	0.843	0.779	0.718	0.843	SUBCLONAL	2	TRUE	0	0.350014780677983	2		596	583	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0037356-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	60	486	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.350014780677983	3	FACETS	0.659	0.568	0.759	0.33	0.284	0.38	SUBCLONAL	1	TRUE	1	0.350014780677983	3		486	611	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981951	70981951	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037356-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	244	826	1	ENST00000276594.2:c.145G>A	p.Asp49Asn	p.D49N	ENST00000276594	NM_024504.3	49	Gac/Aac	2/8	0.193276375993845	2	FACETS	0.784	0.734	0.836	0.784	0.734	0.836	INDETERMINATE	2	TRUE	0	0.350014780677983	2		827	889	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465659	8465659	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037356-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	45	301	0	ENST00000356435.5:c.3521C>A	p.Ser1174Tyr	p.S1174Y	ENST00000356435		1174	tCt/tAt	21/35	0.350014780677983	1	FACETS	0.717	0.606	0.838	0.717	0.606	0.838	SUBCLONAL	1	TRUE	0	0.350014780677983	1		301	296	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141052	55141066	+	inframe_deletion	In_Frame_Del	DEL	CCCAGATGGACATGA	CCCAGATGGACATGA	-	novel	NA	P-0037453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	45	184	0	ENST00000257290.5:c.1698_1712del	p.Ser566_Glu571delinsArg	p.S566_E571delinsR	ENST00000257290	NM_006206.4	566	agCCCAGATGGACATGAa/aga	12/23	1	2	FACETS	0.515	0.432	0.608	0.515	0.432	0.608	SUBCLONAL	1	TRUE	1	0.260994171664266	2		184	669	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776634	9776634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756020651	NA	P-0037453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	81	265	0	ENST00000377346.4:c.737G>A	p.Arg246Lys	p.R246K	ENST00000377346	NM_005026.3	246	aGg/aAg	6/24	1	2	FACETS	0.735	0.646	0.83	0.735	0.646	0.83	SUBCLONAL	1	TRUE	1	0.260994171664266	2		265	845	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162475145	162475145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748352072	NA	P-0037453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	38	190	0	ENST00000366898.1:c.596C>T	p.Pro199Leu	p.P199L	ENST00000366898	NM_004562.2	199	cCa/cTa	5/12	1	2	FACETS	0.392	0.323	0.47	0.392	0.323	0.47	SUBCLONAL	1	TRUE	1	0.260994171664266	2		190	742	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467693	50467693	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	48	173	0	ENST00000331340.3:c.928G>A	p.Val310Met	p.V310M	ENST00000331340	NM_006060.4	310	Gtg/Atg	8/8	0.178589968555992	3	FACETS	0.503	0.424	0.591	0.251	0.212	0.296	SUBCLONAL	1	TRUE	1	0.260994171664266	3		173	827	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0037453-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	428	301	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.708087143914911	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.892810821557584	4		302	891	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037453-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	123	151	0	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	0.892810821557584	1	FACETS	0.936	0.884	0.984	0.936	0.884	0.984	CLONAL	1	TRUE	0	0.892810821557584	1		151	163	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519990	NA	P-0037453-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	480	232	0	ENST00000269305.4:c.796G>C	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Cga	8/11	0.892810821557584	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.892810821557584	2		232	529	SUCCESS
APC	324	MSKCC	GRCh37	5	112175760	112175760	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037453-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	159	143	0	ENST00000257430.4:c.4469del	p.His1490LeufsTer17	p.H1490Lfs*17	ENST00000257430	NM_000038.5	1490	cAt/ct	16/16	1	2	FACETS	0.989	0.92	1	0.989	0.92	1	CLONAL	1	TRUE	1	0.892810821557584	2		143	360	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595822	52595822	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037453-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	266	546	0	ENST00000394830.3:c.4093T>C	p.Trp1365Arg	p.W1365R	ENST00000394830	NM_018313.4	1365	Tgg/Cgg	26/30	0.846590814572911	4	FACETS	1	0.99	1	0.634	0.596	0.674	CLONAL	1	TRUE	2	0.892810821557584	4		546	889	SUCCESS
APC	324	MSKCC	GRCh37	5	112174677	112174678	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0037453-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	132	155	0	ENST00000257430.4:c.3389_3390del	p.Cys1130SerfsTer4	p.C1130Sfs*4	ENST00000257430	NM_000038.5	1129	tTG/t	16/16	1	2	FACETS	0.918	0.846	0.992	0.918	0.846	0.992	CLONAL	1	TRUE	1	0.892810821557584	2		155	322	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	230	395	0				ENST00000310581	NM_198253.2	-/1132			0.352169388307538	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	2	0.390467724575259	4		395	748	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0037465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	276	650	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.299845691748561	2	FACETS	0.828	0.779	0.877	0.828	0.779	0.877	CLONAL	2	TRUE	0	0.390467724575259	2		650	854	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477837	140477851	+	inframe_deletion	In_Frame_Del	DEL	TAGGTGCTGTCACAT	TAGGTGCTGTCACAT	-	novel	NA	P-0037465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	203	541	0	ENST00000288602.6:c.1457_1471del	p.Asn486_Pro490del	p.N486_P490del	ENST00000288602	NM_004333.4	486	aATGTGACAGCACCTAca/aca	12/18	0.298069472271542	4	FACETS	0.889	0.826	0.954	0.593	0.551	0.636	CLONAL	2	TRUE	1	0.390467724575259	4		541	813	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256243	16256243	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	111	611	0	ENST00000375759.3:c.3508C>G	p.Arg1170Gly	p.R1170G	ENST00000375759	NM_015001.2	1170	Cga/Gga	11/15	1	2	FACETS	0.81	0.729	0.896	0.81	0.729	0.896	CLONAL	1	TRUE	1	0.390467724575259	2		611	702	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982329	201982330	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0037465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	153	739	0	ENST00000359651.3:c.710dup	p.Asp239GlyfsTer62	p.D239Gfs*62	ENST00000359651		236	-/A	6/8	1	2	FACETS	0.786	0.718	0.857	0.786	0.718	0.857	SUBCLONAL	1	TRUE	1	0.390467724575259	2		739	997	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405688	139405688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377353441	NA	P-0037465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	294	858	0	ENST00000277541.6:c.2503C>T	p.Pro835Ser	p.P835S	ENST00000277541	NM_017617.3	835	Ccc/Tcc	16/34	0.390467724575259	3	FACETS	1	0.992	1	0.458	0.43	0.486	CLONAL	1	TRUE	0	0.390467724575259	3		858	1311	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0037699-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	70	468	0				ENST00000310581	NM_198253.2	-/1132			0.350784328637573	1	FACETS	1	0.919	1	1	0.985	1	CLONAL	2	FALSE	0	0.350021576822773	1		468	160	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0037699-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	85	638	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.191746464994971	5	FACETS	0.895	0.801	0.992	0.895	0.801	0.992	INDETERMINATE	3	FALSE	2	0.350021576822773	5		639	276	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937422	178937422	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037699-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	60	283	0	ENST00000263967.3:c.1810T>C	p.Cys604Arg	p.C604R	ENST00000263967	NM_006218.2	604	Tgt/Cgt	12/21	0.143193513444418	5	FACETS	1	0.948	1	1	0.948	1	INDETERMINATE	3	FALSE	2	0.350021576822773	5		283	153	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0037926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	493	468	0				ENST00000310581	NM_198253.2	-/1132			0.376052256099701	7	FACETS	1	0.971	1	1	0.971	1	CLONAL	4	FALSE	3	0.376052256099701	7		468	1252	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0037926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	303	735	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.376052256099701	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	FALSE	1	0.376052256099701	3		735	934	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161310391	161310391	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	103	419	0	ENST00000367975.2:c.187C>T	p.Leu63Phe	p.L63F	ENST00000367975	NM_003001.3	63	Ctt/Ttt	4/6	0.376052256099701	6	FACETS	1	0.931	1	0.522	0.469	0.577	CLONAL	2	FALSE	2	0.376052256099701	6		419	460	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951110	48951110	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	72	296	1	ENST00000267163.4:c.1272C>A	p.Tyr424Ter	p.Y424*	ENST00000267163	NM_000321.2	424	taC/taA	13/27	0.368163943180241	3	FACETS	0.93	0.834	1	0.93	0.834	1	CLONAL	3	FALSE	0	0.376052256099701	3		297	163	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244664	41244664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80356955	NA	P-0037926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	46	726	1	ENST00000357654.3:c.2884G>A	p.Glu962Lys	p.E962K	ENST00000357654	NM_007294.3	962	Gaa/Aaa	10/23	0.376052256099701	3	FACETS	0.865	0.731	1	0.433	0.365	0.506	CLONAL	1	FALSE	1	0.376052256099701	3		727	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577069	7577070	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0037926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	364	830	0	ENST00000269305.4:c.868dup	p.Arg290ProfsTer16	p.R290Pfs*16	ENST00000269305	NM_001126112.2	290	cgc/cCgc	8/11	0.376052256099701	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	FALSE	0	0.376052256099701	2		830	942	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245487	41245487	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	68	960	0	ENST00000357654.3:c.2061G>C	p.Gln687His	p.Q687H	ENST00000357654	NM_007294.3	687	caG/caC	10/23	0.376052256099701	3	FACETS	0.916	0.799	1	0.458	0.399	0.521	CLONAL	1	FALSE	1	0.376052256099701	3		960	469	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0038074-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	96	233	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.887	0.794	0.985	0.887	0.794	0.985	CLONAL	1	TRUE	1	0.458446246179802	2		235	472	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591888	48591888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519739	NA	P-0038074-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	74	402	0	ENST00000342988.3:c.1051G>A	p.Asp351Asn	p.D351N	ENST00000342988	NM_005359.5	351	Gat/Aat	9/12	0.424892789149758	1	FACETS	0.594	0.522	0.67	0.594	0.522	0.67	SUBCLONAL	1	TRUE	0	0.458446246179802	1		402	419	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114767	108114767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1196611507	NA	P-0038074-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	37	414	0	ENST00000278616.4:c.584C>T	p.Thr195Ile	p.T195I	ENST00000278616	NM_000051.3	195	aCc/aTc	6/63	0.33186745894201	1	FACETS	0.298	0.246	0.357	0.298	0.246	0.357	SUBCLONAL	1	TRUE	0	0.458446246179802	1		414	417	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864537	57864537	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038074-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	210	698	0	ENST00000228682.2:c.2014G>T	p.Gly672Ter	p.G672*	ENST00000228682	NM_005269.2	672	Gga/Tga	12/12	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.458446246179802	2		698	870	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937424	32937434	+	frameshift_variant	Frame_Shift_Del	DEL	ATTGAGCGCAA	ATTGAGCGCAA	-	novel	NA	P-0038074-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	191	432	0	ENST00000380152.3:c.8087_8097del	p.Leu2696TyrfsTer3	p.L2696Yfs*3	ENST00000380152		2695	tcATTGAGCGCAAat/tcat	18/27	0.296888685921789	3	FACETS	0.908	0.845	0.972	0.908	0.845	0.972	CLONAL	2	TRUE	1	0.458446246179802	3		432	564	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438169	56438169	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038074-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	196	711	0	ENST00000407977.2:c.824G>T	p.Cys275Phe	p.C275F	ENST00000407977		275	tGt/tTt	7/10	1	2	FACETS	0.942	0.872	1	0.942	0.872	1	CLONAL	1	TRUE	1	0.458446246179802	2		711	908	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604721	48604721	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038074-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	31	372	0	ENST00000342988.3:c.1543A>G	p.Arg515Gly	p.R515G	ENST00000342988	NM_005359.5	515	Aga/Gga	12/12	0.424892789149758	1	FACETS	0.306	0.247	0.372	0.306	0.247	0.372	SUBCLONAL	1	TRUE	0	0.458446246179802	1		372	341	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978838	13978838	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038074-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	81	412	0	ENST00000405192.2:c.269A>C	p.Lys90Thr	p.K90T	ENST00000405192	NM_001163147.1	90	aAa/aCa	6/12	1	2	FACETS	0.646	0.57	0.727	0.646	0.57	0.727	SUBCLONAL	1	TRUE	1	0.458446246179802	2		412	547	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878052	151878052	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038074-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	31	362	0	ENST00000262189.6:c.6893C>A	p.Pro2298His	p.P2298H	ENST00000262189	NM_170606.2	2298	cCc/cAc	36/59	1	2	FACETS	0.28	0.226	0.341	0.28	0.226	0.341	SUBCLONAL	1	TRUE	1	0.458446246179802	2		362	483	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412605	63412605	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038074-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	57	583	0	ENST00000330258.3:c.562G>T	p.Glu188Ter	p.E188*	ENST00000330258	NM_152424.3	188	Gag/Tag	2/2	1	2	FACETS	0.354	0.303	0.41	0.354	0.303	0.41	SUBCLONAL	1	TRUE	1	0.458446246179802	2		583	703	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0038086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	678	679	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.54398898723213	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.54398898723213	3		679	947	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404534	70404534	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	54	438	0	ENST00000373644.4:c.2048A>G	p.Gln683Arg	p.Q683R	ENST00000373644	NM_030625.2	683	cAa/cGa	4/12	0.226617803369143	5	FACETS	0.545	0.464	0.633	0.182	0.154	0.211	INDETERMINATE	1	TRUE	2	0.54398898723213	5		438	662	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056170	26056170	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	43	488	0	ENST00000343677.2:c.487G>T	p.Ala163Ser	p.A163S	ENST00000343677	NM_005319.3	163	Gcg/Tcg	1/1	0.54398898723213	3	FACETS	0.36	0.301	0.426	0.18	0.15	0.213	SUBCLONAL	1	TRUE	1	0.54398898723213	3		488	558	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412682	139412682	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1290954710	NA	P-0038086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	201	851	0	ENST00000277541.6:c.1162G>A	p.Asp388Asn	p.D388N	ENST00000277541	NM_017617.3	388	Gac/Aac	7/34	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.54398898723213	2		851	687	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0038110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	78	233	2	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	0.316880406517439	2		235	452	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610229	10610229	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	156	951	0	ENST00000171111.5:c.481A>G	p.Met161Val	p.M161V	ENST00000171111	NM_203500.1	161	Atg/Gtg	2/6	0.316880406517439	1	FACETS	0.927	0.849	1	0.927	0.849	1	CLONAL	1	TRUE	0	0.316880406517439	1		951	894	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220707	1220707	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	157	731	1	ENST00000326873.7:c.725G>T	p.Gly242Val	p.G242V	ENST00000326873	NM_000455.4	242	gGg/gTg	5/10	0.316880406517439	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.316880406517439	1		732	743	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	463295	463295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1361134161	NA	P-0038110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	80	424	0	ENST00000399788.2:c.976C>T	p.Pro326Ser	p.P326S	ENST00000399788	NM_001042603.1	326	Cca/Tca	8/28	1	2	FACETS	0.94	0.829	1	0.94	0.829	1	CLONAL	1	TRUE	1	0.316880406517439	2		424	537	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106888	11106888	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0038110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	138	701	1	ENST00000358026.2:c.1594-1G>A		p.X532_splice	ENST00000358026	NM_001128849.1	532			0.316880406517439	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.316880406517439	1		702	624	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439543	220439543	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	120	661	0	ENST00000243786.2:c.396G>C	p.Trp132Cys	p.W132C	ENST00000243786	NM_002191.3	132	tgG/tgC	2/2	1	2	FACETS	0.964	0.87	1	0.964	0.87	1	CLONAL	1	TRUE	1	0.316880406517439	2		661	786	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096094	71096094	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	55	200	0	ENST00000318789.4:c.663A>T	p.Gln221His	p.Q221H	ENST00000318789	NM_032682.5	221	caA/caT	10/21	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.316880406517439	2		200	326	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266631	142266631	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	87	322	1	ENST00000350721.4:c.3293C>T	p.Ala1098Val	p.A1098V	ENST00000350721	NM_001184.3	1098	gCc/gTc	16/47	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.316880406517439	2		323	439	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729843	41729843	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	91	313	1	ENST00000242208.4:c.686G>T	p.Arg229Leu	p.R229L	ENST00000242208	NM_002192.2	229	cGg/cTg	3/3	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.316880406517439	2		314	503	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0038126-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	70	458	0	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	0.575224660682447	2		458	186	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0038126-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	38	133	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.287632639692356	1	FACETS	1	0.896	1	1	0.896	1	INDETERMINATE	1	TRUE	0	0.575224660682447	1		133	89	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409841	139409841	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779794980	NA	P-0038126-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	33	741	0	ENST00000277541.6:c.1915G>A	p.Glu639Lys	p.E639K	ENST00000277541	NM_017617.3	639	Gag/Aag	12/34	0.287632639692356	1	FACETS	0.256	0.209	0.309	0.256	0.209	0.309	INDETERMINATE	1	TRUE	0	0.575224660682447	1		741	319	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858407	89858407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757760966	NA	P-0038126-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	111	642	0	ENST00000389301.3:c.1153C>T	p.His385Tyr	p.H385Y	ENST00000389301	NM_000135.2	385	Cac/Tac	13/43	0.575224660682447	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.575224660682447	1		642	254	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579529	7579529	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658483	NA	P-0038188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	326	946	0	ENST00000269305.4:c.158G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tGg/tAg	4/11	0.373608674289421	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.522422618051756	1		946	840	SUCCESS
APC	324	MSKCC	GRCh37	5	112175346	112175350	+	frameshift_variant	Frame_Shift_Del	DEL	TTGAA	TTGAA	-	novel	NA	P-0038188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	89	399	0	ENST00000257430.4:c.4057_4061del	p.Glu1353PhefsTer20	p.E1353Ffs*20	ENST00000257430	NM_000038.5	1352	gTTGAA/g	16/16	0.522422618051756	1	FACETS	0.983	0.885	1	0.983	0.885	1	CLONAL	1	TRUE	0	0.522422618051756	1		399	256	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355325	81355325	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750575553	NA	P-0038188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	31	338	0	ENST00000222390.5:c.1049G>A	p.Arg350Gln	p.R350Q	ENST00000222390	NM_000601.4	350	cGa/cAa	9/18	1	2	FACETS	0.638	0.521	0.768	0.638	0.521	0.768	SUBCLONAL	1	TRUE	1	0.522422618051756	2		338	186	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39317393	39317393	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	87	745	1	ENST00000373001.3:c.793G>T	p.Val265Phe	p.V265F	ENST00000373001	NM_022157.3	265	Gtc/Ttc	5/7	0.304359815770518	1	FACETS	0.932	0.837	1	0.932	0.837	1	INDETERMINATE	1	TRUE	0	0.522422618051756	1		746	264	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554724	63554725	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATAG	novel	NA	P-0038188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	201	647	0	ENST00000307078.5:c.11_14dup	p.Met5IlefsTer16	p.M5Ifs*16	ENST00000307078	NM_004655.3	5	atg/atCTATg	2/11	0.264182036848142	1	FACETS	0.793	0.737	0.85	0.793	0.737	0.85	INDETERMINATE	1	TRUE	0	0.522422618051756	1		647	717	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62293296	62293296	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs762587175	NA	P-0038188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	349	611	1	ENST00000360203.5:c.395G>A	p.Arg132Gln	p.R132Q	ENST00000360203	NM_001283009.1	132	cGg/cAg	4/35	0.486129393237193	5	FACETS	0.854	0.808	0.902	0.427	0.404	0.451	CLONAL	2	TRUE	1	0.522422618051756	5		612	1395	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937011	76937011	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0038188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	26	379	0	ENST00000373344.5:c.3736+1G>T		p.X1246_splice	ENST00000373344	NM_000489.3	1246			0.467113952423583	3	FACETS	1	0.838	1	0.523	0.421	0.635	CLONAL	1	TRUE	1	0.522422618051756	3		379	120	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0038214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	122	301	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.842	0.768	0.919	1	0.991	1	CLONAL	3	TRUE	1	0.241450401383812	2		302	400	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0038214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	76	601	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.241450401383812	1	FACETS	0.799	0.7	0.905	0.799	0.7	0.905	CLONAL	1	TRUE	0	0.241450401383812	1		601	693	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224498	108224498	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	38	176	0	ENST00000278616.4:c.8677G>C	p.Ala2893Pro	p.A2893P	ENST00000278616	NM_000051.3	2893	Gct/Cct	60/63	0.295760286246018	5	FACETS	0.998	0.855	1	0.998	0.855	1	CLONAL	4	TRUE	1	0.31	5		176	90	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336625	81336625	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs527951814	NA	P-0038215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	22	170	0	ENST00000222390.5:c.1597C>T	p.Arg533Ter	p.R533*	ENST00000222390	NM_000601.4	533	Cga/Tga	14/18	0.295760286246018	6	FACETS	1	0.922	1	0.498	0.389	0.621	CLONAL	1	TRUE	3	0.31	6		170	154	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0038323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	154	411	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.677946283974417	3	FACETS	0.916	0.852	0.98	0.916	0.852	0.98	CLONAL	2	TRUE	1	0.677946283974417	3		411	332	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794062	42794062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	147	681	1	ENST00000575354.2:c.1423G>A	p.Glu475Lys	p.E475K	ENST00000575354	NM_015125.3	475	Gag/Aag	9/20	1	2	FACETS	0.887	0.815	0.96	0.887	0.815	0.96	CLONAL	1	TRUE	1	0.677946283974417	2		682	489	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0038369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	94	759	1	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.3	1	FACETS	0.774	0.689	0.865	0.774	0.689	0.865	SUBCLONAL	1	FALSE	0	0.3	1		760	688	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682384	37682384	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	108	556	0	ENST00000447079.4:c.3575del	p.Ala1192GlufsTer23	p.A1192Efs*23	ENST00000447079	NM_015083.1	1192	gCa/ga	13/14	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.3	2		556	545	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216504	36216504	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	63	959	1	ENST00000222270.7:c.3767G>A	p.Gly1256Glu	p.G1256E	ENST00000222270	NM_014727.1	1256	gGa/gAa	12/37	0.114454681557941	4	FACETS	0.694	0.599	0.797			1	INDETERMINATE	1	FALSE	NA	0.3	4		960	787	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922756	44922838	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCCAGCAGCCACAGCTTGCTCTGACCAGAGTGCCTAGCGTCTCTCAGCCTGGAGTCCGTCCTGCCTGCCCTGGGCAGCCTT	TGGCCAGCAGCCACAGCTTGCTCTGACCAGAGTGCCTAGCGTCTCTCAGCCTGGAGTCCGTCCTGCCTGCCCTGGGCAGCCTT	-	novel	NA	P-0038369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	18	190	0	ENST00000377967.4:c.1623_1705del	p.Gln542TrpfsTer11	p.Q542Wfs*11	ENST00000377967	NM_021140.2	539	tcTGGCCAGCAGCCACAGCTTGCTCTGACCAGAGTGCCTAGCGTCTCTCAGCCTGGAGTCCGTCCTGCCTGCCCTGGGCAGCCTTtg/tctg	16/29	0.3	2	FACETS	0.368	0.277	0.476			1	SUBCLONAL	1	FALSE	NA	0.3	2		190	326	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247516	123247516	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519795	NA	P-0038419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	60	577	0	ENST00000358487.5:c.1975A>G	p.Lys659Glu	p.K659E	ENST00000358487	NM_000141.4	659	Aag/Gag	14/18	1	2	FACETS	0.521	0.449	0.6	0.521	0.449	0.6	SUBCLONAL	1	TRUE	1	0.373052931415122	2		577	617	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0038419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	235	676	1	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.293243162787164	2	FACETS	0.932	0.874	0.991	0.932	0.874	0.991	CLONAL	2	TRUE	0	0.373052931415122	2		677	676	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027647	48027647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	56	364	0	ENST00000234420.5:c.2525C>T	p.Ala842Val	p.A842V	ENST00000234420	NM_000179.2	842	gCt/gTt	4/10	0.345545273812833	4	FACETS	0.808	0.693	0.934	0.269	0.231	0.312	CLONAL	1	TRUE	1	0.373052931415122	4		364	510	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750749	128750750	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0038419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	96	791	0	ENST00000377970.2:c.286_287delinsAT	p.Ser96Ile	p.S96I	ENST00000377970	NM_002467.4	96	TCc/ATc	2/3	0.373052931415122	5	FACETS	0.809	0.719	0.905	0.27	0.239	0.302	CLONAL	1	TRUE	2	0.373052931415122	5		791	992	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0038449-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	128	566	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.220543092147957	2		566	1006	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56839443	56839443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778313837	NA	P-0038449-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	64	414	1	ENST00000308159.5:c.388C>T	p.Arg130Trp	p.R130W	ENST00000308159	NM_014669.4	130	Cgg/Tgg	5/22	0.220543092147957	1	FACETS	0.721	0.624	0.827	0.721	0.624	0.827	SUBCLONAL	1	FALSE	0	0.220543092147957	1		415	716	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165719	185165719	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038449-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	36	280	0	ENST00000265026.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000265026	NM_004721.4	332	Gaa/Aaa	5/14	1	2	FACETS	0.554	0.455	0.666	0.554	0.455	0.666	SUBCLONAL	1	FALSE	1	0.220543092147957	2		280	589	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845562	151845562	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038449-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	107	524	2	ENST00000262189.6:c.13450C>A	p.His4484Asn	p.H4484N	ENST00000262189	NM_170606.2	4484	Cac/Aac	52/59	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.220543092147957	2		526	899	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845685	151845685	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038449-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	128	411	0	ENST00000262189.6:c.13327C>T	p.Gln4443Ter	p.Q4443*	ENST00000262189	NM_170606.2	4443	Cag/Tag	52/59	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.220543092147957	2		411	834	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0038522-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	430	872	1	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.395376527557523	3	FACETS	0.843	0.807	0.878	0.843	0.807	0.878	CLONAL	3	TRUE	0	0.465538784349775	3		873	901	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852064	63852064	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038522-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	68	542	2	ENST00000279873.7:c.2842C>T	p.Arg948Ter	p.R948*	ENST00000279873	NM_032199.2	948	Cga/Tga	10/10	1	2	FACETS	0.526	0.458	0.6	0.526	0.458	0.6	SUBCLONAL	1	TRUE	1	0.465538784349775	2		544	555	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37856497	37856497	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038522-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	21	377	0	ENST00000269571.5:c.6G>T	p.Glu2Asp	p.E2D	ENST00000269571		2	gaG/gaT	1/27	0.465538784349775	1	FACETS	0.171	0.131	0.218	0.171	0.131	0.218	SUBCLONAL	1	TRUE	0	0.465538784349775	1		377	404	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446977	187446977	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038522-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	100	703	0	ENST00000232014.4:c.1216C>G	p.Arg406Gly	p.R406G	ENST00000232014	NM_001130845.1	406	Cga/Gga	5/10	0.451530065663324	2	FACETS	0.634	0.566	0.705	0.317	0.283	0.353	SUBCLONAL	1	TRUE	0	0.465538784349775	2		703	678	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056601	26056601	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs751693792	NA	P-0038522-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	25	230	0	ENST00000343677.2:c.56C>A	p.Pro19His	p.P19H	ENST00000343677	NM_005319.3	19	cCt/cAt	1/1	0.28450726838225	1	FACETS	0.383	0.303	0.474	0.383	0.303	0.474	SUBCLONAL	1	TRUE	0	0.465538784349775	1		230	215	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681121	30681121	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038522-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	42	286	0	ENST00000376406.3:c.598G>C	p.Gly200Arg	p.G200R	ENST00000376406	NM_014641.2	200	Ggg/Cgg	5/15	0.28450726838225	1	FACETS	0.468	0.392	0.551	0.468	0.392	0.551	SUBCLONAL	1	TRUE	0	0.465538784349775	1		286	296	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133320	38133321	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038522-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	61	432	0	ENST00000317025.8:c.4152dup	p.Phe1385IlefsTer3	p.F1385Ifs*3	ENST00000317025	NM_023034.1	1384	-/A	24/24	0.418941966039511	1	FACETS	0.442	0.382	0.507	0.442	0.382	0.507	SUBCLONAL	1	TRUE	0	0.465538784349775	1		432	455	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0038526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	22	531	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.332916431923732	3	FACETS	0.243	0.188	0.309	0.122	0.094	0.155	SUBCLONAL	1	TRUE	1	0.362554133349226	3		531	589	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574032	7574032	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	147	564	0	ENST00000269305.4:c.995T>G	p.Ile332Ser	p.I332S	ENST00000269305	NM_001126112.2	332	aTc/aGc	10/11	0.362554133349226	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.362554133349226	1		564	492	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244508	41244509	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0038526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	137	520	0	ENST00000357654.3:c.3039_3040del	p.Glu1013AspfsTer4	p.E1013Dfs*4	ENST00000357654	NM_007294.3	1013	gaAAtg/gatg	10/23	0.362554133349226	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.362554133349226	1		520	542	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275843	38275843	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	100	532	0	ENST00000425967.3:c.1426C>G	p.Arg476Gly	p.R476G	ENST00000425967	NM_001174067.1	476	Cgg/Ggg	11/19	1	2	FACETS	0.903	0.808	1	0.903	0.808	1	CLONAL	1	TRUE	1	0.362554133349226	2		532	611	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0038533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	28	101	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.363307758237109	2		101	132	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0038533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	39	258	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.976	0.816	1	0.976	0.816	1	CLONAL	1	TRUE	1	0.363307758237109	2		258	220	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587781702	NA	P-0038533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	98	261	0	ENST00000269305.4:c.920-1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.363307758237109	1	FACETS	0.999	0.896	1	0.999	0.896	1	CLONAL	1	TRUE	0	0.363307758237109	1		261	442	SUCCESS
APC	324	MSKCC	GRCh37	5	112175759	112175759	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1554085898	NA	P-0038533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	30	62	0	ENST00000257430.4:c.4468del	p.His1490IlefsTer17	p.H1490Ifs*17	ENST00000257430	NM_000038.5	1490	Cat/at	16/16	1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	1	0.363307758237109	2		62	158	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575148	48575148	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0038533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	27	84	0	ENST00000342988.3:c.342T>A	p.Tyr114Ter	p.Y114*	ENST00000342988	NM_005359.5	114	taT/taA	3/12	0.363307758237109	1	FACETS	0.981	0.794	1	0.981	0.794	1	CLONAL	1	TRUE	0	0.363307758237109	1		84	124	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0038546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	26	233	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.369216187824153	4	FACETS	0.94	0.767	1	0.94	0.767	1	CLONAL	2	FALSE	2	0.490592244857563	4		235	84	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0038546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	72	547	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.487750310986059	3	FACETS	0.977	0.859	1	0.489	0.429	0.552	CLONAL	1	FALSE	1	0.490592244857563	3		548	374	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0038546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	15	283	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.490592244857563	3	FACETS	0.846	0.629	1	0.423	0.314	0.549	CLONAL	1	FALSE	1	0.490592244857563	3		283	90	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0038546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	10	258	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.490592244857563	3	FACETS	0.529	0.361	0.735	0.264	0.18	0.368	SUBCLONAL	1	FALSE	1	0.490592244857563	3		258	96	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819605	81819605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199972098	NA	P-0038546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	16	379	1	ENST00000359376.3:c.11C>T	p.Thr4Met	p.T4M	ENST00000359376	NM_002661.3	4	aCg/aTg	2/33	0.487750310986059	3	FACETS	0.615	0.459	0.799	0.308	0.229	0.4	SUBCLONAL	1	FALSE	1	0.490592244857563	3		380	132	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11313971	11313971	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	26	502	0	ENST00000361445.4:c.765G>A	p.Met255Ile	p.M255I	ENST00000361445	NM_004958.3	255	atG/atA	6/58	0.3759463650366	3	FACETS	0.587	0.467	0.722	0.293	0.233	0.361	SUBCLONAL	1	FALSE	1	0.490592244857563	3		502	225	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578404	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0038554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	459	560	1	ENST00000269305.4:c.526_527delinsCT	p.Cys176Leu	p.C176L	ENST00000269305	NM_001126112.2	176	TGc/CTc	5/11	0.906094336875479	2	FACETS	0.982	0.964	0.998	0.982	0.964	0.998	CLONAL	2	TRUE	0	0.925794313473221	2		561	505	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272410	38272410	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121909628	NA	P-0038554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	132	341	0	ENST00000425967.3:c.1957C>G	p.Arg653Gly	p.R653G	ENST00000425967	NM_001174067.1	653	Cga/Gga	15/19	0.925803505567407	1	FACETS	0.912	0.866	0.954	0.912	0.866	0.954	CLONAL	1	TRUE	0	0.925794313473221	1		341	168	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0038564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	47	277	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.139954603514878	4	FACETS	1	0.945	1	1	0.945	1	INDETERMINATE	2	TRUE	2	0.787619832357418	4		277	93	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271747	15271747	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs773656789	NA	P-0038564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	39	1158	0	ENST00000263388.2:c.6692del	p.Pro2231GlnfsTer15	p.P2231Qfs*15	ENST00000263388	NM_000435.2	2231	cCa/ca	33/33	1	2	FACETS	0.396	0.33	0.468	0.396	0.33	0.468	SUBCLONAL	1	TRUE	1	0.787619832357418	2		1158	250	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857391	68857398	+	frameshift_variant	Frame_Shift_Del	DEL	GACCAAGT	GACCAAGT	-	novel	NA	P-0038564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	92	629	0	ENST00000261769.5:c.2031_2038del	p.Gln677HisfsTer8	p.Q677Hfs*8	ENST00000261769	NM_004360.3	676	GACCAAGTg/g	13/16	0.787619832357418	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.787619832357418	1		629	120	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181858	56181858	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	94	392	0	ENST00000399503.3:c.4082A>G	p.His1361Arg	p.H1361R	ENST00000399503	NM_005921.1	1361	cAt/cGt	17/20	0.787624171265948	4	FACETS	1	0.93	1			1	CLONAL	2	TRUE	NA	0.787619832357418	4		392	208	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939107	131939107	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	56	552	0	ENST00000265335.6:c.2323T>A	p.Leu775Met	p.L775M	ENST00000265335		775	Ttg/Atg	14/25	0.260803821848971	4	FACETS	0.921	0.811	1	0.921	0.811	1	INDETERMINATE	2	TRUE	2	0.787619832357418	4		552	138	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038614-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	73	63	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.229681934798343	2		63	623	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0038614-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	74	419	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.938	0.821	1	0.938	0.821	1	CLONAL	1	TRUE	1	0.229681934798343	2		420	687	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110063	115110063	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0038614-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	98	936	1	ENST00000257566.3:c.1815C>G	p.Tyr605Ter	p.Y605*	ENST00000257566	NM_016569.3	605	taC/taG	8/8	1	2	FACETS	0.855	0.761	0.955	0.855	0.761	0.955	CLONAL	1	TRUE	1	0.229681934798343	2		937	998	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986960	36986961	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0038614-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	62	659	0	ENST00000354822.5:c.728_729delinsTT	p.Arg243Leu	p.R243L	ENST00000354822	NM_001079668.2	243	cGC/cTT	3/3	1	2	FACETS	0.703	0.606	0.809	0.703	0.606	0.809	SUBCLONAL	1	TRUE	1	0.229681934798343	2		659	768	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101099	27101099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	43	575	1	ENST00000324856.7:c.4381C>T	p.Arg1461Ter	p.R1461*	ENST00000324856	NM_006015.4	1461	Cga/Tga	18/20	1	2	FACETS	0.811	0.678	0.959	0.811	0.678	0.959	CLONAL	1	TRUE	1	0.19	2		576	558	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849586	68849586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567508990	NA	P-0038635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	41	277	0	ENST00000261769.5:c.1489G>A	p.Glu497Lys	p.E497K	ENST00000261769	NM_004360.3	497	Gag/Aag	10/16	NA	2	FACETS	1	0.884	1			1	INDETERMINATE	1	TRUE	NA	0.19	2		277	401	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420076	49420076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	51	288	0	ENST00000301067.7:c.15673C>T	p.Arg5225Cys	p.R5225C	ENST00000301067	NM_003482.3	5225	Cgc/Tgc	48/54	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.19	2		288	532	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420098	49420098	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	50	269	0	ENST00000301067.7:c.15651G>T	p.Trp5217Cys	p.W5217C	ENST00000301067	NM_003482.3	5217	tgG/tgT	48/54	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.19	2		269	514	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349942	70349942	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	61	399	0	ENST00000374080.3:c.3925G>A	p.Asp1309Asn	p.D1309N	ENST00000374080		1309	Gac/Aac	28/45	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.19	2		399	596	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578462	7578478	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGGTGCCGGGCGGGG	GCGGGTGCCGGGCGGGG	-	novel	NA	P-0038646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	466	925	0	ENST00000269305.4:c.452_468del	p.Pro151ArgfsTer24	p.P151Rfs*24	ENST00000269305	NM_001126112.2	151	cCCCCGCCCGGCACCCGC/c	5/11	0.510860331155274	3	FACETS	0.988	0.956	1	0.988	0.956	1	CLONAL	3	TRUE	0	0.578533317917007	3		925	701	SUCCESS
APC	324	MSKCC	GRCh37	5	112173873	112173873	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	71	376	0	ENST00000257430.4:c.2582G>A	p.Gly861Asp	p.G861D	ENST00000257430	NM_000038.5	861	gGc/gAc	16/16	1	2	FACETS	0.753	0.662	0.849	0.753	0.662	0.849	SUBCLONAL	1	TRUE	1	0.578533317917007	2		376	326	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139155	37139155	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	18	623	0	ENST00000373509.5:c.495C>G	p.His165Gln	p.H165Q	ENST00000373509	NM_002648.3	165	caC/caG	4/6	0.578533317917007	3	FACETS	1	0.791	1	0.514	0.396	0.647	CLONAL	1	TRUE	1	0.578533317917007	3		623	78	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574030	7574030	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	419	778	0	ENST00000269305.4:c.997del	p.Arg333ValfsTer12	p.R333Vfs*12	ENST00000269305	NM_001126112.2	333	Cgt/gt	10/11	0.813258956033539	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.813258956033539	2		778	485	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266730	18266730	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	202	786	0	ENST00000222254.8:c.41C>G	p.Pro14Arg	p.P14R	ENST00000222254	NM_005027.3	14	cCg/cGg	2/16	0.466191878588293	2	FACETS	1	0.938	1	0.505	0.469	0.541	CLONAL	1	TRUE	0	0.528151811070479	2		786	758	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574020	7574021	+	inframe_insertion	In_Frame_Ins	INS	-	-	CACGCC	novel	NA	P-0038745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	514	760	0	ENST00000269305.4:c.1001_1006dup	p.Gly334_Arg335dup	p.G334_R335dup	ENST00000269305	NM_001126112.2	334	gag/gGGCGTGag	10/11	0.514859317812532	3	FACETS	1	0.995	1	0.803	0.773	0.833	CLONAL	2	TRUE	0	0.528151811070479	3		760	1021	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0038791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	151	277	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.533043516905955	3	FACETS	0.949	0.879	1	0.949	0.879	1	CLONAL	2	TRUE	1	0.533043516905955	3		277	378	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273944	10273944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	222	701	2	ENST00000330684.3:c.325G>A	p.Val109Ile	p.V109I	ENST00000330684	NM_001134407.1	109	Gta/Ata	2/13	0.533043516905955	3	FACETS	1	0.939	1	0.505	0.469	0.541	CLONAL	1	TRUE	1	0.533043516905955	3		703	1045	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412698	63412698	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	149	550	0	ENST00000330258.3:c.469G>C	p.Glu157Gln	p.E157Q	ENST00000330258	NM_152424.3	157	Gag/Cag	2/2	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.533043516905955	2		550	538	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087952	27087958	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCAAG	GCCCAAG	-	novel	NA	P-0038791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	421	404	1	ENST00000324856.7:c.2239_2245del	p.Ala747IlefsTer84	p.A747Ifs*84	ENST00000324856	NM_006015.4	747	GCCCAAGat/at	6/20	0.529041033199721	3	FACETS	0.981	0.945	1	0.981	0.945	1	CLONAL	3	TRUE	0	0.533043516905955	3		405	680	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383285	4383285	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	127	410	0	ENST00000261254.3:c.79C>A	p.Leu27Met	p.L27M	ENST00000261254	NM_001759.3	27	Ctg/Atg	1/5	0.533043516905955	3	FACETS	0.977	0.887	1	0.488	0.443	0.535	CLONAL	1	TRUE	1	0.533043516905955	3		410	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	104	620	0	ENST00000269305.4:c.569del	p.Pro190LeufsTer57	p.P190Lfs*57	ENST00000269305	NM_001126112.2	190	cCt/ct	6/11	1	2	FACETS	0.722	0.646	0.804	0.722	0.646	0.804	SUBCLONAL	1	FALSE	1	0.3	2		620	960	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754506	42754506	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	176	848	0	ENST00000222329.4:c.234C>A	p.Tyr78Ter	p.Y78*	ENST00000222329	NM_006494.2	78	taC/taA	2/4	0.242099392687517	3	FACETS	1	0.964	1	0.543	0.499	0.589	CLONAL	1	FALSE	1	0.3	3		848	1242	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828497	72828497	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	46	701	2	ENST00000268489.5:c.8084G>A	p.Arg2695Gln	p.R2695Q	ENST00000268489	NM_006885.3	2695	cGg/cAg	9/10	1	2	FACETS	0.356	0.299	0.42	0.356	0.299	0.42	SUBCLONAL	1	FALSE	1	0.3	2		703	861	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239419	105239419	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038831-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	30	700	0	ENST00000349310.3:c.968A>G	p.Asp323Gly	p.D323G	ENST00000349310	NM_001014432.1	323	gAc/gGc	12/15	1	2	FACETS	0.393	0.316	0.481	0.393	0.316	0.481	SUBCLONAL	1	TRUE	1	0.3	2		700	509	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680608	30680608	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2075015	NA	P-0038831-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	75	531	0	ENST00000376406.3:c.1111G>A	p.Glu371Lys	p.E371K	ENST00000376406	NM_014641.2	371	Gag/Aag	5/15	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.3	2		531	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0038851-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	330	621	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.512529537530926	3	FACETS	1	0.963	1	0.677	0.644	0.712	CLONAL	2	FALSE	0	0.512529537530926	3		622	796	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654646	67654646	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038851-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	243	445	0	ENST00000264010.4:c.1133C>A	p.Pro378Gln	p.P378Q	ENST00000264010	NM_006565.3	378	cCg/cAg	6/12	0.358627417145793	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	FALSE	1	0.512529537530926	3		445	577	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202843	128202843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038857-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	454	639	0	ENST00000341105.2:c.877C>T	p.Arg293Trp	p.R293W	ENST00000341105	NM_032638.4	293	Cgg/Tgg	4/6	0.84833116230331	5	FACETS	0.994	0.95	1	0.497	0.475	0.519	CLONAL	2	FALSE	1	0.84833116230331	5		639	1224	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665419	117665419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376021394	NA	P-0038857-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	83	216	0	ENST00000368508.3:c.4328C>T	p.Ala1443Val	p.A1443V	ENST00000368508	NM_002944.2	1443	gCg/gTg	27/43	0.840777255075642	4	FACETS	0.988	0.878	1	0.247	0.219	0.276	CLONAL	1	FALSE	0	0.84833116230331	4		216	366	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403235	213403235	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038857-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	332	511	1	ENST00000342788.4:c.20T>G	p.Leu7Arg	p.L7R	ENST00000342788	NM_005235.2	7	cTt/cGt	1/28	0.84833116230331	5	FACETS	0.943	0.894	0.993	0.629	0.596	0.662	CLONAL	2	FALSE	2	0.84833116230331	5		512	943	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256541	115256541	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038857-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	224	574	0	ENST00000369535.4:c.170del	p.Asp57ValfsTer11	p.D57Vfs*11	ENST00000369535	NM_002524.4	57	gAt/gt	3/7	0.84833116230331	4	FACETS	0.881	0.82	0.944	0.294	0.273	0.315	CLONAL	1	FALSE	1	0.84833116230331	4		574	1108	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510802	120510802	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1273608383	NA	P-0038857-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	158	418	0	ENST00000256646.2:c.1162G>A	p.Ala388Thr	p.A388T	ENST00000256646	NM_024408.3	388	Gca/Aca	7/34	0.84833116230331	4	FACETS	0.853	0.783	0.927			1	CLONAL	1	FALSE	NA	0.84833116230331	4		418	807	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32918727	32918727	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038857-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	110	216	0	ENST00000380152.3:c.6874G>A	p.Glu2292Lys	p.E2292K	ENST00000380152		2292	Gaa/Aaa	12/27	0.84833116230331	3	FACETS	0.957	0.885	1	0.957	0.885	1	CLONAL	2	FALSE	1	0.84833116230331	3		216	193	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578365	7578398	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTCACCATCGCTATCTGAGCAGCGCTCATGGTG	GCTCACCATCGCTATCTGAGCAGCGCTCATGGTG	-	novel	NA	P-0038857-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	790	594	0	ENST00000269305.4:c.532_559+6del		p.X178_splice	ENST00000269305	NM_001126112.2	178		5/11	0.84833116230331	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	FALSE	0	0.84833116230331	3		594	878	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245963	5245963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1490066505	NA	P-0038857-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	719	835	1	ENST00000357368.4:c.812C>T	p.Ser271Leu	p.S271L	ENST00000357368	NM_002850.3	271	tCg/tTg	10/38	0.84833116230331	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	FALSE	0	0.84833116230331	2		836	831	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483976	212483976	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038857-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	246	401	0	ENST00000342788.4:c.2227A>C	p.Thr743Pro	p.T743P	ENST00000342788	NM_005235.2	743	Act/Cct	19/28	0.84833116230331	5	FACETS	1	0.95	1	0.674	0.634	0.715	CLONAL	2	FALSE	2	0.84833116230331	5		401	652	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211705	36211705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758411036	NA	P-0038857-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	81	712	0	ENST00000222270.7:c.1456C>T	p.Arg486Trp	p.R486W	ENST00000222270	NM_014727.1	486	Cgg/Tgg	3/37	0.777172209716664	4	FACETS	0.315	0.277	0.357	0.158	0.138	0.179	SUBCLONAL	1	FALSE	2	0.84833116230331	4		712	1119	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021329	31021329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038857-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	157	533	0	ENST00000375687.4:c.1328C>T	p.Ala443Val	p.A443V	ENST00000375687	NM_015338.5	443	gCc/gTc	12/13	0.84833116230331	5	FACETS	0.748	0.684	0.815	0.249	0.228	0.272	SUBCLONAL	1	FALSE	2	0.84833116230331	5		533	1125	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	174	395	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.825	0.764	0.889	0.825	0.764	0.889	CLONAL	1	TRUE	1	0.69	2		395	611	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0038900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	360	609	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	0.189247889705682	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.69	0		609	897	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2107145	2107145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373818076	NA	P-0038968-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	59	897	1	ENST00000219476.3:c.814G>A	p.Ala272Thr	p.A272T	ENST00000219476	NM_000548.3	272	Gcc/Acc	9/42	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		898	890	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0038997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	522	582	3	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.912978148902359	2	FACETS	0.986	0.969	1	0.986	0.969	1	CLONAL	2	TRUE	0	0.91606149833444	2		585	578	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662412	227662412	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	369	623	0	ENST00000305123.5:c.1043G>A	p.Ser348Asn	p.S348N	ENST00000305123	NM_005544.2	348	aGt/aAt	1/2	0.825062649353446	3	FACETS	1	0.996	1	0.742	0.708	0.775	CLONAL	1	TRUE	1	0.91606149833444	3		623	792	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433495	138433495	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	98	417	0	ENST00000289153.2:c.1117G>T	p.Val373Leu	p.V373L	ENST00000289153	NM_006219.2	373	Gta/Tta	7/22	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.91606149833444	2		417	207	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860670	151860670	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	177	508	0	ENST00000262189.6:c.9992G>C	p.Ser3331Thr	p.S3331T	ENST00000262189	NM_170606.2	3331	aGt/aCt	43/59	0.91606149833444	5	FACETS	0.907	0.835	0.981	0.227	0.208	0.246	CLONAL	1	TRUE	1	0.91606149833444	5		508	1012	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	93	314	0	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	0.888	0.796	0.986	0.888	0.796	0.986	CLONAL	1	TRUE	1	0.53	2		314	395	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	126	394	0	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.53	2		394	467	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	298	368	20	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	1	2	FACETS	0.942	0.896	0.988	1	0.996	1	CLONAL	2	TRUE	1	0.53	2		388	597	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	58	205	0	ENST00000256196.4:c.68G>A	p.Gly23Asp	p.G23D	ENST00000256196		23	gGc/gAc	1/6	1	2	FACETS	0.839	0.728	0.957	0.839	0.728	0.957	CLONAL	1	TRUE	1	0.53	2		205	261	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	90	235	1	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.898	0.803	0.999	0.898	0.803	0.999	CLONAL	1	TRUE	1	0.53	2		236	378	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794441	42794441	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	214	695	2	ENST00000575354.2:c.1526del	p.Pro509HisfsTer14	p.P509Hfs*14	ENST00000575354	NM_015125.3	507	cgC/cg	10/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.53	2		697	784	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	198	617	2	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.53	2		619	642	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259042	16259043	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	160	490	0	ENST00000375759.3:c.6313dup	p.Ala2105GlyfsTer18	p.A2105Gfs*18	ENST00000375759	NM_015001.2	2103	agg/aGgg	11/15	1	2	FACETS	0.988	0.91	1	0.988	0.91	1	CLONAL	1	TRUE	1	0.53	2		490	611	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	141	433	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.903	0.826	0.983	0.903	0.826	0.983	CLONAL	1	TRUE	1	0.53	2		433	589	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553478	29553478	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781807	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	194	426	0	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	0.53	2		426	636	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148544345	148544345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	202	440	0	ENST00000320356.2:c.46C>T	p.Arg16Trp	p.R16W	ENST00000320356	NM_004456.4	16	Cgg/Tgg	2/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.53	2		440	707	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693002	89693003	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	81	394	0	ENST00000371953.3:c.491dup	p.Val166SerfsTer14	p.V166Sfs*14	ENST00000371953	NM_000314.4	162	-/A	5/9	1	2	FACETS	0.638	0.564	0.717	0.638	0.564	0.717	SUBCLONAL	1	TRUE	1	0.53	2		394	479	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046289	128046289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746827111	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	157	406	0	ENST00000285398.2:c.974G>A	p.Arg325Gln	p.R325Q	ENST00000285398	NM_000122.1	325	cGa/cAa	7/15	1	2	FACETS	0.999	0.92	1	0.999	0.92	1	CLONAL	1	TRUE	1	0.53	2		406	593	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155778	106155779	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs759055581	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	117	367	0	ENST00000380013.4:c.685dup	p.Thr229AsnfsTer25	p.T229Nfs*25	ENST00000380013	NM_001127208.2	227	gaa/gAaa	3/11	1	2	FACETS	0.854	0.774	0.938	0.854	0.774	0.938	CLONAL	1	TRUE	1	0.53	2		367	517	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966231	25966231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781134057	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	166	506	0	ENST00000435504.4:c.2975C>T	p.Ala992Val	p.A992V	ENST00000435504		992	gCg/gTg	13/13	1	2	FACETS	0.985	0.908	1	0.985	0.908	1	CLONAL	1	TRUE	1	0.53	2		506	636	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148526849	148526849	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	139	365	0	ENST00000320356.2:c.455del	p.Asn152IlefsTer15	p.N152Ifs*15	ENST00000320356	NM_004456.4	152	aAt/at	5/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.53	2		365	491	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145635	11145635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	186	526	0	ENST00000358026.2:c.3997C>T	p.Arg1333Trp	p.R1333W	ENST00000358026	NM_001128849.1	1333	Cgg/Tgg	29/36	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.53	2		526	662	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	163	589	6	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.53	2		595	615	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15836766	15836766	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	157	366	0	ENST00000307771.7:c.827+1G>A		p.X276_splice	ENST00000307771	NM_005089.3	276			1	2	FACETS	0.91	0.836	0.986	0.91	0.836	0.986	CLONAL	1	TRUE	1	0.53	2		366	651	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112892399	112892399	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764663951	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	119	418	0	ENST00000351677.2:c.557G>A	p.Arg186Gln	p.R186Q	ENST00000351677	NM_002834.3	186	cGg/cAg	5/16	1	2	FACETS	0.811	0.734	0.89	0.811	0.734	0.89	CLONAL	1	TRUE	1	0.53	2		418	554	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977952	131977952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201810	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	121	303	0	ENST00000265335.6:c.3835C>T	p.Arg1279Cys	p.R1279C	ENST00000265335		1279	Cgt/Tgt	25/25	1	2	FACETS	0.83	0.753	0.911	0.83	0.753	0.911	CLONAL	1	TRUE	1	0.53	2		303	550	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481659	56481659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140656187	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	244	560	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	0.53	2		560	789	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84384746	84384747	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	98	243	0	ENST00000321945.7:c.696dup	p.Val233SerfsTer5	p.V233Sfs*5	ENST00000321945	NM_139076.2	232	-/A	8/9	1	2	FACETS	0.906	0.814	1	0.906	0.814	1	CLONAL	1	TRUE	1	0.53	2		243	408	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163226	32163226	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	194	571	1	ENST00000375023.3:c.6000G>T	p.Glu2000Asp	p.E2000D	ENST00000375023	NM_004557.3	2000	gaG/gaT	30/30	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.53	2		572	719	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468193	120468193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	172	603	1	ENST00000256646.2:c.4246G>A	p.Ala1416Thr	p.A1416T	ENST00000256646	NM_024408.3	1416	Gca/Aca	25/34	1	2	FACETS	0.98	0.906	1	0.98	0.906	1	CLONAL	1	TRUE	1	0.53	2		604	662	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263973	104263974	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	57	282	0	ENST00000369902.3:c.70_71dup	p.Ala25ArgfsTer72	p.A25Rfs*72	ENST00000369902	NM_016169.3	22	gcc/gCCcc	1/12	1	2	FACETS	0.739	0.639	0.847	0.739	0.639	0.847	SUBCLONAL	1	TRUE	1	0.53	2		282	291	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375045	118375045	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	118	370	0	ENST00000534358.1:c.8438T>A	p.Val2813Asp	p.V2813D	ENST00000534358	NM_005933.3	2813	gTc/gAc	27/36	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.53	2		370	436	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445100	49445100	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	46	585	0	ENST00000301067.7:c.2366C>T	p.Ser789Phe	p.S789F	ENST00000301067	NM_003482.3	789	tCc/tTc	10/54	1	2	FACETS	0.274	0.23	0.323	0.274	0.23	0.323	SUBCLONAL	1	TRUE	1	0.53	2		585	633	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120535126	120535126	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	192	409	0	ENST00000229340.5:c.529G>T	p.Ala177Ser	p.A177S	ENST00000229340	NM_006861.6	177	Gca/Tca	6/6	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.53	2		409	639	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562535	21562535	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	24	77	0	ENST00000382592.4:c.1384C>T	p.His462Tyr	p.H462Y	ENST00000382592	NM_014572.2	462	Cac/Tac	4/8	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.53	2		77	81	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346896	73346896	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	97	216	0	ENST00000377767.4:c.1321del	p.His441IlefsTer24	p.H441Ifs*24	ENST00000377767	NM_014953.3	441	Cat/at	9/21	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.53	2		216	355	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2090213	2090213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147559648	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	197	566	0	ENST00000219066.1:c.736G>A	p.Ala246Thr	p.A246T	ENST00000219066	NM_002528.5	246	Gcc/Acc	5/6	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.53	2		566	694	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223493	2223493	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	222	551	0	ENST00000326181.6:c.1024G>A	p.Glu342Lys	p.E342K	ENST00000326181	NM_032271.2	342	Gaa/Aaa	11/21	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.53	2		551	692	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118323	17118323	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	194	548	0	ENST00000285071.4:c.1514T>A	p.Val505Asp	p.V505D	ENST00000285071	NM_144997.5	505	gTc/gAc	13/14	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.53	2		548	705	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214734	36214734	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	131	465	0	ENST00000222270.7:c.3163del	p.Arg1055GlyfsTer127	p.R1055Gfs*127	ENST00000222270	NM_014727.1	1054	Ccc/cc	8/37	1	2	FACETS	0.983	0.897	1	0.983	0.897	1	CLONAL	1	TRUE	1	0.53	2		465	503	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726652	41726652	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	168	622	2	ENST00000301178.4:c.197A>G	p.Glu66Gly	p.E66G	ENST00000301178	NM_021913.4	66	gAg/gGg	2/20	1	2	FACETS	0.86	0.792	0.931	0.86	0.792	0.931	CLONAL	1	TRUE	1	0.53	2		624	737	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795007	42795007	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200405570	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	228	650	1	ENST00000575354.2:c.2087G>A	p.Arg696Gln	p.R696Q	ENST00000575354	NM_015125.3	696	cGg/cAg	10/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.53	2		651	722	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086101	16086101	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	158	475	0	ENST00000281043.3:c.1277C>T	p.Ala426Val	p.A426V	ENST00000281043	NM_005378.4	426	gCc/gTc	3/3	1	2	FACETS	0.984	0.906	1	0.984	0.906	1	CLONAL	1	TRUE	1	0.53	2		475	606	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566889	212566889	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	74	194	0	ENST00000342788.4:c.1292G>A	p.Gly431Asp	p.G431D	ENST00000342788	NM_005235.2	431	gGc/gAc	12/28	1	2	FACETS	0.976	0.864	1	0.976	0.864	1	CLONAL	1	TRUE	1	0.53	2		194	286	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39713141	39713141	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	92	199	1	ENST00000361337.2:c.552del	p.Val185PhefsTer36	p.V185Ffs*36	ENST00000361337	NM_003286.2	183	Aaa/aa	8/21	1	2	FACETS	0.962	0.862	1	0.962	0.862	1	CLONAL	1	TRUE	1	0.53	2		200	361	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042526	37042530	+	frameshift_variant	Frame_Shift_Del	DEL	CTATG	CTATG	TATA	novel	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	217	397	1	ENST00000231790.2:c.288_292delinsTATA	p.Tyr97IlefsTer11	p.Y97Ifs*11	ENST00000231790	NM_000249.3	96	acCTATGgc/acTATAgc	3/19	0.528711615110362	2	FACETS	0.862	0.811	0.913	0.862	0.811	0.913	CLONAL	2	TRUE	0	0.53	2		398	475	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293637	1293637	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	167	589	0	ENST00000310581.5:c.1364A>G	p.His455Arg	p.H455R	ENST00000310581	NM_198253.2	455	cAc/cGc	2/16	1	2	FACETS	0.997	0.92	1	0.997	0.92	1	CLONAL	1	TRUE	1	0.53	2		589	632	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117630085	117630085	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	34	272	0	ENST00000368508.3:c.6441del	p.Phe2147LeufsTer4	p.F2147Lfs*4	ENST00000368508	NM_002944.2	2147	ttT/tt	41/43	1	2	FACETS	0.338	0.276	0.407	0.338	0.276	0.407	SUBCLONAL	1	TRUE	1	0.53	2		272	380	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90947826	90947826	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	85	257	0	ENST00000265433.3:c.2249del	p.Leu750Ter	p.L750*	ENST00000265433	NM_002485.4	750	tTa/ta	16/16	1	2	FACETS	0.93	0.829	1	0.93	0.829	1	CLONAL	1	TRUE	1	0.53	2		257	345	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0039045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	177	365	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.646045361900626	2		365	513	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101099	27101099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	584	575	1	ENST00000324856.7:c.4381C>T	p.Arg1461Ter	p.R1461*	ENST00000324856	NM_006015.4	1461	Cga/Tga	18/20	0.646045361900626	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.646045361900626	2		576	839	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25536832	25536832	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781229619	NA	P-0039045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	146	433	0	ENST00000264709.3:c.22G>A	p.Gly8Ser	p.G8S	ENST00000264709	NM_175629.2	8	Ggc/Agc	2/23	1	2	FACETS	0.663	0.606	0.722	0.663	0.606	0.722	SUBCLONAL	1	TRUE	1	0.646045361900626	2		433	682	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710609	40710609	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0039045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	117	480	0	ENST00000373198.4:c.4242T>A	p.Cys1414Ter	p.C1414*	ENST00000373198	NM_133170.3	1414	tgT/tgA	31/32	1	2	FACETS	0.47	0.424	0.519	0.47	0.424	0.519	SUBCLONAL	1	TRUE	1	0.646045361900626	2		480	770	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577523	7577524	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	336	693	0	ENST00000269305.4:c.757dup	p.Thr253AsnfsTer11	p.T253Nfs*11	ENST00000269305	NM_001126112.2	253	acc/aAcc	7/11	0.646035264547833	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.646035264547833	2		693	512	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992223	11992223	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	40	374	0	ENST00000396373.4:c.313C>G	p.Arg105Gly	p.R105G	ENST00000396373	NM_001987.4	105	Cga/Gga	3/8	0.646035264547833	3	FACETS	0.408	0.339	0.484	0.204	0.169	0.242	SUBCLONAL	1	TRUE	1	0.646035264547833	3		374	402	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164821	36164821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1397164331	NA	P-0039180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	180	874	0	ENST00000300305.3:c.1054G>A	p.Ala352Thr	p.A352T	ENST00000300305		352	Gcc/Acc	8/8	0.646035264547833	3	FACETS	1	0.93	1	0.503	0.465	0.542	CLONAL	1	TRUE	1	0.646035264547833	3		874	733	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0039191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	151	411	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.353798913804123	3	FACETS	0.96	0.884	1	0.96	0.884	1	CLONAL	2	TRUE	1	0.353798913804123	3		411	523	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573427	48573433	+	frameshift_variant	Frame_Shift_Del	DEL	TGTCTAT	TGTCTAT	-	novel	NA	P-0039191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	20	181	0	ENST00000342988.3:c.12_18del	p.Met4IlefsTer12	p.M4Ifs*12	ENST00000342988	NM_005359.5	4	aTGTCTATt/at	2/12	0.316821158528703	1	FACETS	0.694	0.537	0.875	0.694	0.537	0.875	SUBCLONAL	1	TRUE	0	0.353798913804123	1		181	134	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456502	29456502	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	184	587	0	ENST00000389048.3:c.2416C>G	p.Arg806Gly	p.R806G	ENST00000389048	NM_004304.4	806	Cgt/Ggt	14/29	0.650994839459735	5	FACETS	1	0.946	1	0.344	0.317	0.372	CLONAL	1	TRUE	2	0.757860226958682	5		587	1006	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437055	110437055	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	90	79	0	ENST00000375856.3:c.1346C>T	p.Ser449Leu	p.S449L	ENST00000375856	NM_003749.2	449	tCg/tTg	1/2	0.757860226958682	8	FACETS	0.906	0.814	1			1	CLONAL	3	TRUE	NA	0.757860226958682	8		79	286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578226	7578249	+	inframe_deletion	In_Frame_Del	DEL	TCATCCAAATACTCCACACGCAAA	TCATCCAAATACTCCACACGCAAA	-	novel	NA	P-0039242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	451	640	0	ENST00000269305.4:c.600_623del	p.Leu201_Asp208del	p.L201_D208del	ENST00000269305	NM_001126112.2	200	aaTTTGCGTGTGGAGTATTTGGATGAc/aac	6/11	0.523717091177996	3	FACETS	0.996	0.972	1			1	CLONAL	3	TRUE	NA	0.757860226958682	3		640	549	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40457698	40457698	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	166	509	0	ENST00000345506.4:c.1451G>A	p.Trp484Ter	p.W484*	ENST00000345506	NM_003152.3	484	tGg/tAg	13/20	NA	2	FACETS	1	0.944	1			1	INDETERMINATE	1	TRUE	NA	0.757860226958682	2		509	430	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55729466	55729466	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	399	632	0	ENST00000284073.2:c.734C>A	p.Pro245Gln	p.P245Q	ENST00000284073	NM_138962.2	245	cCa/cAa	11/14	0.757860226958682	3	FACETS	0.98	0.94	1			1	CLONAL	2	TRUE	NA	0.757860226958682	3		632	741	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004964	150004970	+	frameshift_variant	Frame_Shift_Del	DEL	GTTCCAT	GTTCCAT	-	novel	NA	P-0039242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	147	325	0	ENST00000253339.5:c.1255_1261del	p.Met419TyrfsTer40	p.M419Yfs*40	ENST00000253339		419	ATGGAACta/ta	3/7	0.757860226958682	2	FACETS	0.915	0.864	0.963	0.915	0.864	0.963	CLONAL	2	TRUE	0	0.757860226958682	2		325	212	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0039288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	44	621	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.362	0.303	0.428	0.362	0.303	0.428	SUBCLONAL	1	TRUE	1	0.354284032784111	2		622	686	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039420-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	65	395	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.639	0.555	0.73			1	INDETERMINATE	1	TRUE	NA	0.394962811435638	2		395	515	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576919	7576919	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039420-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	132	606	0	ENST00000269305.4:c.927del	p.Asn310ThrfsTer35	p.N310Tfs*35	ENST00000269305	NM_001126112.2	309	ccC/cc	9/11	0.394962811435638	1	FACETS	0.949	0.866	1	0.949	0.866	1	CLONAL	1	TRUE	0	0.394962811435638	1		606	565	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870853	12870853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500190	NA	P-0039420-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	61	259	0	ENST00000228872.4:c.80C>T	p.Ser27Leu	p.S27L	ENST00000228872	NM_004064.3	27	tCg/tTg	1/3	0.381734284669135	1	FACETS	0.911	0.794	1	0.911	0.794	1	CLONAL	1	TRUE	0	0.394962811435638	1		259	272	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870872	12870872	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039420-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	73	282	0	ENST00000228872.4:c.99C>A	p.Phe33Leu	p.F33L	ENST00000228872	NM_004064.3	33	ttC/ttA	1/3	0.381734284669135	1	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	0	0.394962811435638	1		282	292	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141570495	141570496	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0039420-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	144	664	1	ENST00000220592.5:c.632_633delinsTT	p.Trp211Phe	p.W211F	ENST00000220592	NM_012154.3	211	tGG/tTT	5/19	1	2	FACETS	0.993	0.908	1	0.993	0.908	1	CLONAL	1	TRUE	1	0.394962811435638	2		665	734	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814186	76814186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039420-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	63	168	0	ENST00000373344.5:c.6458G>A	p.Arg2153His	p.R2153H	ENST00000373344	NM_000489.3	2153	cGc/cAc	29/35	1	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.394962811435638	1		168	195	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0039422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	369	589	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.43599761493152	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	3	TRUE	0	0.449457729872817	3		589	667	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314611	30314613	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0039422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	259	617	1	ENST00000262643.3:c.1163_1165del	p.Pro388del	p.P388del	ENST00000262643	NM_001238.2	387	tCTCct/tct	12/12	0.359972826860627	5	FACETS	0.831	0.778	0.886	0.554	0.518	0.591	CLONAL	2	TRUE	2	0.449457729872817	5		618	1161	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280011	18280011	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	102	527	1	ENST00000222254.8:c.2094C>A	p.His698Gln	p.H698Q	ENST00000222254	NM_005027.3	698	caC/caA	16/16	0.359972826860627	5	FACETS	0.968	0.866	1	0.323	0.288	0.359	CLONAL	1	TRUE	2	0.449457729872817	5		528	785	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538997	187538997	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	79	520	0	ENST00000441802.2:c.8743C>G	p.Pro2915Ala	p.P2915A	ENST00000441802	NM_005245.3	2915	Cca/Gca	10/27	0.447284224467756	2	FACETS	0.74	0.653	0.833	0.37	0.326	0.417	SUBCLONAL	1	TRUE	0	0.449457729872817	2		520	475	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	42	233	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.496	0.414	0.588	0.496	0.414	0.588	SUBCLONAL	1	TRUE	1	0.33	2		235	513	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882019	NA	P-0039456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	83	544	0	ENST00000269305.4:c.455dup	p.Pro153AlafsTer28	p.P153Afs*28	ENST00000269305	NM_001126112.2	152	ccg/ccCg	5/11	1	2	FACETS	0.735	0.649	0.828	0.735	0.649	0.828	SUBCLONAL	1	TRUE	1	0.33	2		544	684	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107136	27107137	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0039456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	60	441	0	ENST00000324856.7:c.6749_6750del	p.Glu2250ValfsTer27	p.E2250Vfs*27	ENST00000324856	NM_006015.4	2249	tcAGag/tcag	20/20	1	2	FACETS	0.616	0.531	0.709	0.616	0.531	0.709	SUBCLONAL	1	TRUE	1	0.33	2		441	590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578196	7578196	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555525743	NA	P-0039511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	284	866	0	ENST00000269305.4:c.653T>G	p.Val218Gly	p.V218G	ENST00000269305	NM_001126112.2	218	gTg/gGg	6/11	NA	2	FACETS	0.895	0.843	0.949			1	INDETERMINATE	2	TRUE	NA	0.334924534771679	2		866	947	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039523-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	255	233	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.201863260763794	3	FACETS	0.9	0.849	0.952	0.6	0.566	0.635	INDETERMINATE	2	TRUE	0	0.576450911142538	3		235	633	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0039523-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	516	683	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.576450911142538	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.576450911142538	1		683	1052	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707579	176707579	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039523-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	46	421	0	ENST00000439151.2:c.5636T>C	p.Ile1879Thr	p.I1879T	ENST00000439151	NM_022455.4	1879	aTt/aCt	18/23	0.556411281927242	2	FACETS	0.18	0.151	0.212	0.09	0.075	0.106	SUBCLONAL	1	TRUE	0	0.576450911142538	2		421	887	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0039552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	73	441	2	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.984	0.861	1	0.984	0.861	1	CLONAL	1	TRUE	1	0.246164351599572	2		443	603	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792731	33792732	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCGGGT	rs762459325	NA	P-0039552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	52	11	1	ENST00000498907.2:c.584_589dup	p.His195_Pro196dup	p.H195_P196dup	ENST00000498907	NM_004364.3	195	ccg/cACCCGCcg	1/1	0.246164351599572	1	FACETS	1	0.926	1	1	0.983	1	CLONAL	3	TRUE	0	0.246164351599572	1		12	115	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0039552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	100	744	3	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.246164351599572	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.246164351599572	1		747	663	SUCCESS
AR	367	MSKCC	GRCh37	X	66766357	66766401	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	-	novel	NA	P-0039552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	16	68	0	ENST00000374690.3:c.1376_1420del	p.Gly459_Gly473del	p.G459_G473del	ENST00000374690	NM_000044.3	457	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC/-	1/8	1	2	FACETS	0.903	0.672	1	0.903	0.672	1	CLONAL	1	TRUE	1	0.246164351599572	2		68	144	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0039615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	405	798	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.547685623223455	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.547685623223455	2		800	726	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532577	63532577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774732785	NA	P-0039615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	306	958	0	ENST00000307078.5:c.2002G>A	p.Gly668Arg	p.G668R	ENST00000307078	NM_004655.3	668	Ggg/Agg	8/11	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.547685623223455	2		958	861	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42861470	42861470	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	430	695	0	ENST00000398585.3:c.400G>A	p.Gly134Arg	p.G134R	ENST00000398585	NM_001135099.1	134	Gga/Aga	4/14	0.206236593955745	5	FACETS	1	0.993	1	0.695	0.667	0.723	INDETERMINATE	3	TRUE	0	0.547685623223455	5		695	823	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940118	49940118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776047479	NA	P-0039615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	346	877	2	ENST00000296474.3:c.925C>T	p.Arg309Trp	p.R309W	ENST00000296474	NM_002447.2	309	Cgg/Tgg	1/20	0.547685623223455	3	FACETS	0.994	0.946	1	0.994	0.946	1	CLONAL	2	TRUE	1	0.547685623223455	3		879	810	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920142	1920142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748673417	NA	P-0039615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	178	932	0	ENST00000382891.5:c.1202G>A	p.Arg401Gln	p.R401Q	ENST00000382891	NM_133335.3	401	cGg/cAg	5/22	0.15121536845334	6	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.547685623223455	6		932	1084	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711883	89711886	+	frameshift_variant	Frame_Shift_Del	DEL	TATT	TATT	-	novel	NA	P-0039648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	201	364	0	ENST00000371953.3:c.501_504del	p.Ile168ProfsTer14	p.I168Pfs*14	ENST00000371953	NM_000314.4	167	acTATT/ac	6/9	0.645763288442181	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.645763288442181	1		364	383	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946199	71946201	+	inframe_deletion	In_Frame_Del	DEL	CAG	CAG	-	novel	NA	P-0039648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	301	631	0	ENST00000298229.2:c.2457_2459del	p.Gln819del	p.Q819del	ENST00000298229	NM_001567.3	819	CAG/-	22/28	0.645763288442181	1	FACETS	0.906	0.859	0.953	0.906	0.859	0.953	CLONAL	1	TRUE	0	0.645763288442181	1		631	697	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878076	48878087	+	inframe_deletion	In_Frame_Del	DEL	GCCGCCACCGCC	GCCGCCACCGCC	-	novel	NA	P-0039648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	364	125	0	ENST00000267163.4:c.33_44del	p.Thr12_Ala15del	p.T12_A15del	ENST00000267163	NM_000321.2	10	GCCGCCACCGCC/-	1/27	0.645763288442181	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.645763288442181	2		125	546	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434556	110434557	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCT	novel	NA	P-0039648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	188	437	0	ENST00000375856.3:c.3842_3844dup	p.Lys1281dup	p.K1281dup	ENST00000375856	NM_003749.2	1281	agc/aAGAgc	1/2	0.645763288442181	3	FACETS	0.809	0.748	0.873	0.405	0.374	0.437	CLONAL	1	TRUE	1	0.645763288442181	3		437	952	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873716	35873717	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATCT	novel	NA	P-0039648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	303	454	1	ENST00000216797.5:c.131_134dup	p.Met45IlefsTer42	p.M45Ifs*42	ENST00000216797	NM_020529.2	45	atg/atAGATg	1/6	1	2	FACETS	0.86	0.811	0.911	0.86	0.811	0.911	CLONAL	1	TRUE	1	0.645763288442181	2		455	1091	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437508	56437508	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0039648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	278	540	0	ENST00000407977.2:c.952+2T>A		p.X318_splice	ENST00000407977		318			0.645763288442181	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.645763288442181	1		540	577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0039660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	36	654	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.58	0.475	0.698	0.58	0.475	0.698	SUBCLONAL	1	TRUE	1	0.17	2		656	730	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0039668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	109	531	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	0.346947893354393	2		531	570	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857502	68857503	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	112	410	0	ENST00000261769.5:c.2139dup	p.Leu714SerfsTer34	p.L714Sfs*34	ENST00000261769	NM_004360.3	713	att/aTtt	13/16	0.346947893354393	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.346947893354393	1		410	462	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231872	36231872	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	139	436	0	ENST00000300305.3:c.512A>T	p.Lys171Ile	p.K171I	ENST00000300305		171	aAa/aTa	5/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.346947893354393	2		436	581	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945391	151945392	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0039668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	250	464	0	ENST00000262189.6:c.2127_2128del	p.Cys710SerfsTer2	p.C710Sfs*2	ENST00000262189	NM_170606.2	709	ttATgt/ttgt	14/59	0.346947893354393	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.346947893354393	3		464	730	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0039831-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	25	247	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.927	0.747	1	0.927	0.747	1	CLONAL	1	TRUE	1	0.555899395514367	2		247	97	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696708	47696708	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039831-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	69	420	2	ENST00000347630.2:c.240C>G	p.Ser80Arg	p.S80R	ENST00000347630	NM_001007230.1	80	agC/agG	5/11	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.555899395514367	2		422	241	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519886	NA	P-0039831-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	93	358	0	ENST00000349496.5:c.97T>G	p.Ser33Ala	p.S33A	ENST00000349496	NM_001904.3	33	Tct/Gct	3/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.555899395514367	2		358	286	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105967	27105967	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039831-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	128	527	1	ENST00000324856.7:c.5578G>T	p.Glu1860Ter	p.E1860*	ENST00000324856	NM_006015.4	1860	Gag/Tag	20/20	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.555899395514367	2		528	432	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0039859-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	472	486	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.468576387346616	5	FACETS	1	0.992	1	0.874	0.843	0.904	CLONAL	4	TRUE	0	0.468576387346616	5		486	785	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0039859-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	720	937	1	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	0.468576387346616	3	FACETS	0.949	0.92	0.977	0.949	0.92	0.977	CLONAL	3	TRUE	0	0.468576387346616	3		938	1333	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57470669	57470669	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039859-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	67	313	0	ENST00000371085.3:c.142G>T	p.Ala48Ser	p.A48S	ENST00000371085	NM_000516.4	48	Gct/Tct	2/13	0.468576387346616	7	FACETS	0.702	0.609	0.804	0.176	0.152	0.201	SUBCLONAL	1	TRUE	3	0.468576387346616	7		313	884	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708981	117708981	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039859-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	118	607	0	ENST00000368508.3:c.1976C>G	p.Pro659Arg	p.P659R	ENST00000368508	NM_002944.2	659	cCc/cGc	13/43	0.458170451182908	2	FACETS	0.852	0.771	0.937	0.426	0.385	0.469	CLONAL	1	TRUE	0	0.468576387346616	2		607	591	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258178	16258178	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039859-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	185	665	0	ENST00000375759.3:c.5443G>C	p.Asp1815His	p.D1815H	ENST00000375759	NM_015001.2	1815	Gat/Cat	11/15	0.468576387346616	3	FACETS	1	0.937	1	0.339	0.312	0.366	CLONAL	1	TRUE	0	0.468576387346616	3		665	959	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191480	10191480	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913346	NA	P-0039883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	87	468	0	ENST00000256474.2:c.473T>C	p.Leu158Pro	p.L158P	ENST00000256474	NM_000551.3	158	cTg/cCg	3/3	0.415647138480363	1	FACETS	0.802	0.714	0.895	0.802	0.714	0.895	CLONAL	1	TRUE	0	0.41928465120971	1		468	409	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36024706	36024706	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	78	720	0	ENST00000358208.4:c.695A>C	p.Tyr232Ser	p.Y232S	ENST00000358208		232	tAc/tCc	6/12	0.163636672436329	2	FACETS	0.618	0.543	0.698	0.309	0.271	0.349	INDETERMINATE	1	TRUE	0	0.41928465120971	2		720	602	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52677343	52677343	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	88	489	0	ENST00000394830.3:c.916del	p.Ala306LeufsTer5	p.A306Lfs*5	ENST00000394830	NM_018313.4	306	Gct/ct	10/30	0.415647138480363	1	FACETS	0.707	0.629	0.79	0.707	0.629	0.79	SUBCLONAL	1	TRUE	0	0.41928465120971	1		489	469	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842308	151842308	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	81	405	0	ENST00000262189.6:c.14104G>T	p.Ala4702Ser	p.A4702S	ENST00000262189	NM_170606.2	4702	Gcc/Tcc	54/59	1	2	FACETS	0.764	0.675	0.859	0.764	0.675	0.859	SUBCLONAL	1	TRUE	1	0.41928465120971	2		405	506	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904897	101904897	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	33	422	0	ENST00000374994.4:c.885C>A	p.Tyr295Ter	p.Y295*	ENST00000374994	NM_004612.2	295	taC/taA	5/9	0.41928465120971	1	FACETS	0.287	0.233	0.347	0.287	0.233	0.347	SUBCLONAL	1	TRUE	0	0.41928465120971	1		422	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0039907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	516	521	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.380911916939527	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	4	TRUE	0	0.380911916939527	4		521	914	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794118	242794118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758277335	NA	P-0039907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	167	381	1	ENST00000334409.5:c.610C>T	p.Arg204Cys	p.R204C	ENST00000334409	NM_005018.2	204	Cgc/Tgc	4/5	0.380911916939527	3	FACETS	1	0.971	1	0.559	0.514	0.607	CLONAL	1	TRUE	1	0.380911916939527	3		382	933	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0039907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	19	38	0	ENST00000267163.4:c.1215+1G>T		p.X405_splice	ENST00000267163	NM_000321.2	405			0.380911916939527	2	FACETS	0.907	0.716	1	0.907	0.716	1	CLONAL	2	TRUE	0	0.380911916939527	2		38	55	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717720	89717720	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	126	172	2	ENST00000371953.3:c.745del	p.Val249CysfsTer7	p.V249Cfs*7	ENST00000371953	NM_000314.4	249	Gtg/tg	7/9	0.380911916939527	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.380911916939527	2		174	298	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200844	67200844	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	357	135	2	ENST00000312629.5:c.832A>G	p.Met278Val	p.M278V	ENST00000312629	NM_003952.2	278	Atg/Gtg	10/15	0.36597303984573	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.380911916939527	3		137	1004	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468540	89468540	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	73	79	0	ENST00000336596.2:c.2074A>T	p.Ser692Cys	p.S692C	ENST00000336596	NM_005233.5	692	Agt/Tgt	11/17	0.380911916939527	2	FACETS	0.949	0.846	1	0.949	0.846	1	CLONAL	2	TRUE	0	0.380911916939527	2		79	202	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968262	134968262	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	293	340	0	ENST00000398015.3:c.2776del	p.Val926SerfsTer21	p.V926Sfs*21	ENST00000398015	NM_004441.4	925	atG/at	15/16	0.380911916939527	6	FACETS	1	0.951	1	0.507	0.476	0.539	CLONAL	2	TRUE	2	0.380911916939527	6		340	1337	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664680	138664680	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	42	71	0	ENST00000330315.3:c.885C>A	p.His295Gln	p.H295Q	ENST00000330315	NM_023067.3	295	caC/caA	1/1	0.380911916939527	6	FACETS	0.929	0.784	1	0.465	0.392	0.544	CLONAL	2	TRUE	2	0.380911916939527	6		71	209	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0039908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	262	598	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.262214751528752	4	FACETS	1	0.944	1	1	0.944	1	CLONAL	3	TRUE	1	0.262214751528752	4		598	837	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0039908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	223	662	0	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	0.262214751528752	2	FACETS	0.982	0.916	1	0.982	0.916	1	CLONAL	2	TRUE	0	0.262214751528752	2		662	866	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0039948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	203	654	3	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	NA	2	FACETS	0.895	0.833	0.958			1	INDETERMINATE	2	TRUE	NA	0.328786538367458	2		657	690	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115279473	115279473	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	44	359	0	ENST00000438362.2:c.544G>T	p.Val182Leu	p.V182L	ENST00000438362	NM_001242891.1	182	Gtg/Ttg	6/20	1	2	FACETS	0.913	0.77	1	0.913	0.77	1	CLONAL	1	TRUE	1	0.328786538367458	2		359	293	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646116	215646116	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	56	491	1	ENST00000260947.4:c.482C>T	p.Ala161Val	p.A161V	ENST00000260947	NM_000465.2	161	gCt/gTt	4/11	0.19253917830629	3	FACETS	0.967	0.831	1	0.484	0.415	0.558	INDETERMINATE	1	TRUE	1	0.328786538367458	3		492	410	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0039994-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	472	735	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.580962362289789	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.580962362289789	3		735	645	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0039994-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	448	692	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.08535533821235	3	FACETS	0.957	0.925	0.989			1	INDETERMINATE	3	TRUE	NA	0.580962362289789	3		692	693	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126686	5126686	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039994-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	46	336	0	ENST00000381652.3:c.3294C>G	p.Ile1098Met	p.I1098M	ENST00000381652	NM_004972.3	1098	atC/atG	25/25	0.580962362289789	2	FACETS	0.478	0.404	0.559	0.239	0.202	0.28	SUBCLONAL	1	TRUE	0	0.580962362289789	2		336	331	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551085	41551085	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039994-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	182	620	1	ENST00000263253.7:c.3229C>T	p.Gln1077Ter	p.Q1077*	ENST00000263253	NM_001429.3	1077	Caa/Taa	17/31	0.370568437131598	3	FACETS	1	0.985	1	0.617	0.572	0.664	CLONAL	1	TRUE	1	0.580962362289789	3		621	655	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420927	49420928	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0039994-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	230	636	0	ENST00000301067.7:c.14821_14822del	p.Leu4941GlyfsTer2	p.L4941Gfs*2	ENST00000301067	NM_003482.3	4941	TTg/g	48/54	0.151190648912008	6	FACETS	0.889	0.834	0.945	0.889	0.834	0.945	INDETERMINATE	3	TRUE	3	0.580962362289789	6		636	642	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299836	15299836	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039994-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	369	772	2	ENST00000263388.2:c.1342G>T	p.Asp448Tyr	p.D448Y	ENST00000263388	NM_000435.2	448	Gac/Tac	8/33	0.285981285132744	3	FACETS	1	0.992	1	0.773	0.74	0.806	INDETERMINATE	2	TRUE	0	0.580962362289789	3		774	707	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292751	62292751	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039994-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	247	649	0	ENST00000360203.5:c.203C>T	p.Ser68Phe	p.S68F	ENST00000360203	NM_001283009.1	68	tCt/tTt	3/35	0.285981285132744	3	FACETS	1	0.985	1	0.739	0.699	0.779	INDETERMINATE	2	TRUE	0	0.580962362289789	3		649	495	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31511180	31511180	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755611158	NA	P-0039994-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	658	637	0	ENST00000344624.3:c.1394C>T	p.Pro465Leu	p.P465L	ENST00000344624		465	cCg/cTg	6/33	0.580962362289789	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	1	0.580962362289789	4		637	1139	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250145	110250145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039994-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	236	655	1	ENST00000374672.4:c.530C>T	p.Ser177Phe	p.S177F	ENST00000374672	NM_004235.4	177	tCc/tTc	3/5	0.580962362289789	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.580962362289789	2		656	373	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015233	128015233	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0039994-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	72	549	0	ENST00000285398.2:c.2288C>G	p.Ser763Ter	p.S763*	ENST00000285398	NM_000122.1	763	tCa/tGa	15/15	0.580750434889055	3	FACETS	0.473	0.413	0.538	0.237	0.206	0.269	SUBCLONAL	1	TRUE	1	0.580962362289789	3		549	676	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180394	38180394	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039994-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	24	646	0	ENST00000396334.3:c.242C>G	p.Ala81Gly	p.A81G	ENST00000396334	NM_002468.4	81	gCg/gGg	1/5	0.580750434889055	3	FACETS	0.223	0.174	0.279	0.111	0.087	0.14	SUBCLONAL	1	TRUE	1	0.580962362289789	3		646	479	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643728	52643728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039994-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	58	575	0	ENST00000394830.3:c.2168C>T	p.Ser723Phe	p.S723F	ENST00000394830	NM_018313.4	723	tCt/tTt	17/30	0.295206103391505	2	FACETS	0.409	0.352	0.472	0.205	0.176	0.236	INDETERMINATE	1	TRUE	0	0.580962362289789	2		575	488	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662381	117662381	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039994-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	188	522	0	ENST00000368508.3:c.4996G>C	p.Val1666Leu	p.V1666L	ENST00000368508	NM_002944.2	1666	Gtt/Ctt	30/43	0.213027909708447	4	FACETS	0.864	0.803	0.927	0.864	0.803	0.927	INDETERMINATE	2	TRUE	2	0.580962362289789	4		522	592	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0040045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	127	468	0				ENST00000310581	NM_198253.2	-/1132			0.368258736051853	2	FACETS	1	0.983	1	0.652	0.596	0.709	CLONAL	1	TRUE	0	0.50743871164923	2		468	384	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736907	736907	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs986350587	NA	P-0040045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	57	396	0	ENST00000314574.4:c.1192C>T	p.Arg398Trp	p.R398W	ENST00000314574	NM_005433.3	398	Cgg/Tgg	10/12	0.390111345307298	2	FACETS	0.453	0.389	0.523	0.226	0.194	0.262	SUBCLONAL	1	TRUE	0	0.50743871164923	2		396	496	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107151	27107151	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0040045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	146	388	0	ENST00000324856.7:c.6762C>G	p.Tyr2254Ter	p.Y2254*	ENST00000324856	NM_006015.4	2254	taC/taG	20/20	0.390436927197963	3	FACETS	1	0.971	1	0.378	0.346	0.412	CLONAL	1	TRUE	0	0.50743871164923	3		388	636	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40456672	40456672	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0040045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	544	134	0	ENST00000345506.4:c.1380+2T>G		p.X460_splice	ENST00000345506	NM_003152.3	460			0.224986305453688	3	FACETS	0.855	0.825	0.885	0.855	0.825	0.885	INDETERMINATE	3	TRUE	0	0.50743871164923	3		134	1048	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754631	42754695	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGCTCCAGGATAAAGTGCCACAGCTGGATCTGCCTTGAGCCAGGGGACGACTCTGGCTTGTAG	GCAGCTCCAGGATAAAGTGCCACAGCTGGATCTGCCTTGAGCCAGGGGACGACTCTGGCTTGTAG	-	novel	NA	P-0040045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	57	681	0	ENST00000222329.4:c.45_109del	p.Tyr16AlafsTer24	p.Y16Afs*24	ENST00000222329	NM_006494.2	15	gcCTACAAGCCAGAGTCGTCCCCTGGCTCAAGGCAGATCCAGCTGTGGCACTTTATCCTGGAGCTGCtg/gctg	2/4	NA	2	FACETS	0.366	0.314	0.424			1	INDETERMINATE	1	TRUE	NA	0.50743871164923	2		681	613	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597463	52597464	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0040045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	112	345	0	ENST00000394830.3:c.3846dup	p.Lys1283GlufsTer8	p.K1283Efs*8	ENST00000394830	NM_018313.4	1282	-/G	25/30	0.50743871164923	2	FACETS	1	0.972	1	0.59	0.536	0.647	CLONAL	1	TRUE	0	0.50743871164923	2		345	374	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204926	128204927	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0040045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	1210	173	2	ENST00000341105.2:c.514_515delinsAA	p.Gly172Asn	p.G172N	ENST00000341105	NM_032638.4	172	GGc/AAc	3/6	0.390436927197963	3	FACETS	0.997	0.975	1	0.997	0.975	1	CLONAL	3	TRUE	0	0.50743871164923	3		175	2000	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187423	32187423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	184	823	1	ENST00000375023.3:c.1456C>T	p.Pro486Ser	p.P486S	ENST00000375023	NM_004557.3	486	Cca/Tca	8/30	0.34794479148299	3	FACETS	1	0.983	1	0.607	0.561	0.654	CLONAL	1	TRUE	1	0.50743871164923	3		824	749	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864347	151864347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	388	118	1	ENST00000262189.6:c.9634C>T	p.Leu3212Phe	p.L3212F	ENST00000262189	NM_170606.2	3212	Ctt/Ttt	42/59	0.285961527348808	3	FACETS	1	0.984	1	0.712	0.679	0.744	INDETERMINATE	2	TRUE	0	0.50743871164923	3		119	898	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606587	93606587	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs865783333	NA	P-0040045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	419	108	0	ENST00000375746.1:c.407G>A	p.Trp136Ter	p.W136*	ENST00000375746	NM_001174167.1	136	tGg/tAg	2/14	0.368258736051853	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.50743871164923	2		108	761	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0040227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	151	523	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.248538594113992	2		523	1046	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460354	149460354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437040009	NA	P-0040227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	67	483	0	ENST00000286301.3:c.283G>A	p.Ala95Thr	p.A95T	ENST00000286301	NM_005211.3	95	Gcc/Acc	3/22	0.248538594113992	0	FACETS	0.827	0.72	0.942			1	CLONAL	1	FALSE	0	0.248538594113992	0		483	490	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163642	32163642	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs775494392	NA	P-0040227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	50	352	0	ENST00000375023.3:c.5584C>G	p.Arg1862Gly	p.R1862G	ENST00000375023	NM_004557.3	1862	Cgg/Ggg	30/30	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	FALSE	1	0.248538594113992	2		352	348	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40367115	40367115	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	28	447	0	ENST00000397332.2:c.82G>A	p.Gly28Arg	p.G28R	ENST00000397332	NM_001033082.2	28	Gga/Aga	2/3	0.248538594113992	1	FACETS	0.424	0.338	0.523	0.424	0.338	0.523	SUBCLONAL	1	FALSE	0	0.248538594113992	1		447	465	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097802	8097802	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1320708723	NA	P-0040227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	79	627	0	ENST00000346208.3:c.184C>T	p.Pro62Ser	p.P62S	ENST00000346208		62	Ccc/Tcc	2/6	0.248538594113992	1	FACETS	0.794	0.698	0.897	0.794	0.698	0.897	SUBCLONAL	1	FALSE	0	0.248538594113992	1		627	701	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266560	115266560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	58	544	0	ENST00000438362.2:c.1955G>A	p.Arg652Lys	p.R652K	ENST00000438362	NM_001242891.1	652	aGg/aAg	16/20	0.248538594113992	1	FACETS	0.627	0.538	0.724	0.627	0.538	0.724	SUBCLONAL	1	FALSE	0	0.248538594113992	1		544	652	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416809	416809	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	74	405	0	ENST00000399788.2:c.3741G>T	p.Gln1247His	p.Q1247H	ENST00000399788	NM_001042603.1	1247	caG/caT	23/28	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.248538594113992	2		405	498	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443958	49443958	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	101	763	1	ENST00000301067.7:c.3413del	p.Gly1138AspfsTer26	p.G1138Dfs*26	ENST00000301067	NM_003482.3	1138	gGa/ga	11/54	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	FALSE	1	0.248538594113992	2		764	780	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	99	651	0	ENST00000269305.4:c.610del	p.Glu204SerfsTer43	p.E204Sfs*43	ENST00000269305	NM_001126112.2	204	Gag/ag	6/11	1	2	FACETS	0.907	0.809	1	0.907	0.809	1	CLONAL	1	FALSE	1	0.248538594113992	2		651	878	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3113380	3113380	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	79	700	0	ENST00000078429.4:c.374A>T	p.Glu125Val	p.E125V	ENST00000078429	NM_002067.2	125	gAg/gTg	3/7	1	2	FACETS	0.778	0.683	0.88	0.778	0.683	0.88	SUBCLONAL	1	FALSE	1	0.248538594113992	2		700	817	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610394	10610394	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	47	751	0	ENST00000171111.5:c.316G>A	p.Val106Ile	p.V106I	ENST00000171111	NM_203500.1	106	Gtc/Atc	2/6	1	2	FACETS	0.419	0.352	0.493	0.419	0.352	0.493	SUBCLONAL	1	FALSE	1	0.248538594113992	2		751	903	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292540	15292540	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	83	801	0	ENST00000263388.2:c.2639C>A	p.Ala880Asp	p.A880D	ENST00000263388	NM_000435.2	880	gCc/gAc	17/33	1	2	FACETS	0.723	0.637	0.816	0.723	0.637	0.816	SUBCLONAL	1	FALSE	1	0.248538594113992	2		801	924	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056341	180056341	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	105	806	1	ENST00000261937.6:c.903C>A	p.Ser301Arg	p.S301R	ENST00000261937	NM_182925.4	301	agC/agA	7/30	0.248538594113992	0	FACETS	0.908	0.814	1			1	CLONAL	1	FALSE	0	0.248538594113992	0		807	699	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863315	56863315	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	65	482	0	ENST00000519728.1:c.459C>A	p.Phe153Leu	p.F153L	ENST00000519728	NM_002350.3	153	ttC/ttA	6/13	1	2	FACETS	0.739	0.64	0.846	0.739	0.64	0.846	SUBCLONAL	1	FALSE	1	0.248538594113992	2		482	708	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974698	21974699	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0040227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	65	374	0	ENST00000304494.5:c.128_129del	p.Ser43IlefsTer76	p.S43Ifs*76	ENST00000304494	NM_000077.4	43	aGT/a	1/3	0.248538594113992	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	FALSE	0	0.248538594113992	1		374	411	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405686	139405687	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	110	890	0	ENST00000277541.6:c.2504_2505insT	p.Ser836GlnfsTer16	p.S836Qfs*16	ENST00000277541	NM_017617.3	835	ccc/ccTc	16/34	1	2	FACETS	0.947	0.849	1	0.947	0.849	1	CLONAL	1	FALSE	1	0.248538594113992	2		890	935	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	102	316	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	0.263406541948065	3	FACETS	1	0.983	1	0.704	0.639	0.77	INDETERMINATE	1	TRUE	1	0.719184079359651	3		316	274	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0040305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	87	419	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.29	2		420	562	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0040305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	120	301	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.273470585728141	3	FACETS	0.865	0.784	0.949	0.865	0.784	0.949	CLONAL	2	TRUE	1	0.29	3		302	548	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	19	411	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.224	0.169	0.29	0.224	0.169	0.29	SUBCLONAL	1	TRUE	1	0.29	2		411	584	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099338	193099338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	49	271	0	ENST00000367435.3:c.272G>A	p.Arg91Gln	p.R91Q	ENST00000367435	NM_024529.4	91	cGa/cAa	3/17	1	2	FACETS	0.613	0.519	0.717	0.613	0.519	0.717	SUBCLONAL	1	TRUE	1	0.29	2		271	551	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129817	30129817	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	36	457	0	ENST00000263025.4:c.396G>T	p.Leu132Phe	p.L132F	ENST00000263025	NM_002746.2	132	ttG/ttT	3/9	1	2	FACETS	0.455	0.373	0.547	0.455	0.373	0.547	SUBCLONAL	1	TRUE	1	0.29	2		457	546	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	35	63	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	0.441116181872194	2		63	113	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	12	32	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	0.8	0.573	1	0.8	0.573	1	CLONAL	1	TRUE	1	0.441116181872194	2		32	68	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119780	70119781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0040353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	94	134	0	ENST00000245479.2:c.788dup	p.Arg264GlnfsTer32	p.R264Qfs*32	ENST00000245479	NM_000346.3	261	gag/gaGg	3/3	1	2	FACETS	0.829	0.74	0.923	0.829	0.74	0.923	CLONAL	1	TRUE	1	0.441116181872194	2		134	514	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006224	22006224	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	93	134	0	ENST00000276925.6:c.179G>A	p.Arg60His	p.R60H	ENST00000276925	NM_004936.3	60	cGc/cAc	2/2	1	2	FACETS	0.976	0.873	1	0.976	0.873	1	CLONAL	1	TRUE	1	0.441116181872194	2		134	432	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304295	91304295	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	21	37	0	ENST00000355112.3:c.1692T>G	p.Asp564Glu	p.D564E	ENST00000355112	NM_000057.2	564	gaT/gaG	7/22	1	2	FACETS	0.982	0.771	1	0.982	0.771	1	CLONAL	1	TRUE	1	0.441116181872194	2		37	97	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222235	2222235	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	161	260	0	ENST00000326181.6:c.519C>A	p.Asn173Lys	p.N173K	ENST00000326181	NM_032271.2	173	aaC/aaA	8/21	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.441116181872194	2		260	726	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835704	68835704	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	86	135	0	ENST00000261769.5:c.295T>G	p.Leu99Val	p.L99V	ENST00000261769	NM_004360.3	99	Ttg/Gtg	3/16	1	2	FACETS	0.997	0.888	1	0.997	0.888	1	CLONAL	1	TRUE	1	0.441116181872194	2		135	391	SUCCESS
APC	324	MSKCC	GRCh37	5	112173588	112173930	+	frameshift_variant	Frame_Shift_Del	DEL	CTCAGCACTTATCAGAAACTTTTGACAATATAGACAATTTAAGTCCCAAGGCATCTCATCGTAGTAAGCAGAGACACAAGCAAAGTCTCTATGGTGATTATGTTTTTGACACCAATCGACATGATGATAATAGGTCAGACAATTTTAATACTGGCAACATGACTGTCCTTTCACCATATTTGAATACTACAGTGTTACCCAGCTCCTCTTCATCAAGAGGAAGCTTAGATAGTTCTCGTTCTGAAAAAGATAGAAGTTTGGAGAGAGAACGCGGAATTGGTCTAGGCAACTACCATCCAGCAACAGAAAATCCAGGAACTTCTTCAAAGCGAGGTTTGCAGAT	CTCAGCACTTATCAGAAACTTTTGACAATATAGACAATTTAAGTCCCAAGGCATCTCATCGTAGTAAGCAGAGACACAAGCAAAGTCTCTATGGTGATTATGTTTTTGACACCAATCGACATGATGATAATAGGTCAGACAATTTTAATACTGGCAACATGACTGTCCTTTCACCATATTTGAATACTACAGTGTTACCCAGCTCCTCTTCATCAAGAGGAAGCTTAGATAGTTCTCGTTCTGAAAAAGATAGAAGTTTGGAGAGAGAACGCGGAATTGGTCTAGGCAACTACCATCCAGCAACAGAAAATCCAGGAACTTCTTCAAAGCGAGGTTTGCAGAT	-	novel	NA	P-0040353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	17	21	0	ENST00000257430.4:c.2300_2642del	p.Gln767ProfsTer35	p.Q767Pfs*35	ENST00000257430	NM_000038.5	766	gCTCAGCACTTATCAGAAACTTTTGACAATATAGACAATTTAAGTCCCAAGGCATCTCATCGTAGTAAGCAGAGACACAAGCAAAGTCTCTATGGTGATTATGTTTTTGACACCAATCGACATGATGATAATAGGTCAGACAATTTTAATACTGGCAACATGACTGTCCTTTCACCATATTTGAATACTACAGTGTTACCCAGCTCCTCTTCATCAAGAGGAAGCTTAGATAGTTCTCGTTCTGAAAAAGATAGAAGTTTGGAGAGAGAACGCGGAATTGGTCTAGGCAACTACCATCCAGCAACAGAAAATCCAGGAACTTCTTCAAAGCGAGGTTTGCAGATc/gc	16/16	1	2	FACETS	0.94	0.716	1	0.94	0.716	1	CLONAL	1	TRUE	1	0.441116181872194	2		21	82	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44921968	44921971	+	frameshift_variant	Frame_Shift_Del	DEL	AGTT	AGTT	-	novel	NA	P-0040353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	24	56	0	ENST00000377967.4:c.1502_1505del	p.Gln501LeufsTer3	p.Q501Lfs*3	ENST00000377967	NM_021140.2	501	cAGTTt/ct	15/29	NA	2	FACETS	0.98	0.782	1			1	INDETERMINATE	1	TRUE	NA	0.441116181872194	2		56	111	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0040369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	150	233	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.126037342061458	4	FACETS	0.94	0.87	1	1	0.99	1	CLONAL	5	TRUE	1	0.202430041661385	4		235	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0040369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	142	379	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.170605319456037	3	FACETS	1	0.976	1	0.795	0.726	0.866	CLONAL	2	TRUE	0	0.202430041661385	3		379	648	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	141	408	0	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	0.126037342061458	4	FACETS	0.838	0.766	0.914	0.838	0.766	0.914	CLONAL	3	TRUE	1	0.202430041661385	4		408	666	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439948	56439948	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	199	432	0	ENST00000407977.2:c.644C>A	p.Ala215Asp	p.A215D	ENST00000407977		215	gCt/gAt	6/10	0.164778083040305	4	FACETS	0.959	0.89	1	1	0.99	1	CLONAL	3	TRUE	2	0.202430041661385	4		432	822	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971116	21971117	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0040369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	131	275	0	ENST00000304494.5:c.241_242delinsAA	p.Pro81Asn	p.P81N	ENST00000304494	NM_000077.4	81	CCc/AAc	2/3	0.202430041661385	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.202430041661385	2		275	540	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497691	120497691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	51	551	0	ENST00000256646.2:c.2191C>T	p.His731Tyr	p.H731Y	ENST00000256646	NM_024408.3	731	Cat/Tat	13/34	0.792572162373917	1	FACETS	0.155	0.131	0.181	0.155	0.131	0.181	SUBCLONAL	1	TRUE	0	0.807214436895861	1		551	486	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572267	41572267	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040422-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	118	714	0	ENST00000263253.7:c.4796del	p.Arg1599ProfsTer25	p.R1599Pfs*25	ENST00000263253	NM_001429.3	1599	cGc/cc	30/31	1	2	FACETS	0.786	0.71	0.865	1	0.985	1	SUBCLONAL	2	TRUE	1	0.23	2		714	653	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0040443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	246	654	3	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.577305171953053	1	FACETS	0.953	0.897	1	0.953	0.897	1	CLONAL	1	TRUE	0	0.577305171953053	1		657	636	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0040443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	190	478	0	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	0.577305171953053	1	FACETS	0.909	0.848	0.972	0.909	0.848	0.972	CLONAL	1	TRUE	0	0.577305171953053	1		478	515	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686341	30686341	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	132	362	0	ENST00000295754.5:c.197C>T	p.Ser66Phe	p.S66F	ENST00000295754	NM_003242.5	66	tCc/tTc	2/7	0.577305171953053	1	FACETS	0.858	0.788	0.931	0.858	0.788	0.931	CLONAL	1	TRUE	0	0.577305171953053	1		362	379	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021784	71021784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553663084	NA	P-0040443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	122	239	0	ENST00000318789.4:c.1574G>A	p.Arg525Gln	p.R525Q	ENST00000318789	NM_032682.5	525	cGa/cAa	18/21	0.577305171953053	1	FACETS	0.973	0.893	1	0.973	0.893	1	CLONAL	1	TRUE	0	0.577305171953053	1		239	309	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100750	8100750	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs11567901	NA	P-0040443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	220	726	0	ENST00000346208.3:c.724G>T	p.Gly242Cys	p.G242C	ENST00000346208		242	Ggc/Tgc	3/6	1	2	FACETS	0.886	0.826	0.948	0.886	0.826	0.948	CLONAL	1	TRUE	1	0.577305171953053	2		726	860	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857785	9857785	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	204	479	1	ENST00000330684.3:c.3616C>G	p.Arg1206Gly	p.R1206G	ENST00000330684	NM_001134407.1	1206	Cga/Gga	13/13	0.577305171953053	1	FACETS	0.982	0.919	1	0.982	0.919	1	CLONAL	1	TRUE	0	0.577305171953053	1		480	512	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379773	17379773	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	387	886	0	ENST00000359435.4:c.158G>T	p.Gly53Val	p.G53V	ENST00000359435	NM_001033549.1	53	gGt/gTt	2/9	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.577305171953053	2		886	1258	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564849	41564849	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	252	501	0	ENST00000263253.7:c.4150G>T	p.Asp1384Tyr	p.D1384Y	ENST00000263253	NM_001429.3	1384	Gac/Tac	25/31	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.577305171953053	2		501	818	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120591	94120591	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	147	308	0	ENST00000369303.4:c.460A>T	p.Ser154Cys	p.S154C	ENST00000369303	NM_004440.3	154	Agt/Tgt	3/17	0.229625431175807	3	FACETS	1	0.927	1	0.506	0.464	0.551	INDETERMINATE	1	TRUE	1	0.577305171953053	3		308	648	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950476	68950476	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	118	387	1	ENST00000288368.4:c.788G>T	p.Arg263Leu	p.R263L	ENST00000288368	NM_024870.2	263	cGg/cTg	7/40	1	2	FACETS	0.686	0.62	0.755	0.686	0.62	0.755	SUBCLONAL	1	TRUE	1	0.577305171953053	2		388	596	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0040443-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	543	683	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.687685741340931	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.687685741340931	2		683	691	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841000	15841000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754101239	NA	P-0040443-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	150	299	0	ENST00000307771.7:c.1084G>A	p.Glu362Lys	p.E362K	ENST00000307771	NM_005089.3	362	Gaa/Aaa	11/11	1	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.687685741340931	1		299	252	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339003	225339003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040443-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	168	337	0	ENST00000264414.4:c.2266C>T	p.Arg756Ter	p.R756*	ENST00000264414	NM_003590.4	756	Cga/Tga	16/16	0.687685741340931	2	FACETS	1	0.984	1	0.603	0.561	0.646	CLONAL	1	TRUE	0	0.687685741340931	2		337	405	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096337	2096337	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040443-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	65	712	0	ENST00000219066.1:c.170G>C	p.Arg57Pro	p.R57P	ENST00000219066	NM_002528.5	57	cGt/cCt	2/6	0.687685741340931	2	FACETS	0.313	0.272	0.359	0.157	0.136	0.18	SUBCLONAL	1	TRUE	0	0.687685741340931	2		712	603	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99809065	99809065	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040443-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	90	191	0	ENST00000280892.6:c.320C>G	p.Pro107Arg	p.P107R	ENST00000280892	NM_001130678.1	107	cCt/cGt	4/7	0.456822336943221	1	FACETS	0.725	0.654	0.797	0.725	0.654	0.797	SUBCLONAL	1	TRUE	0	0.687685741340931	1		191	237	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878394	151878394	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040443-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	290	602	0	ENST00000262189.6:c.6551C>G	p.Ser2184Cys	p.S2184C	ENST00000262189	NM_170606.2	2184	tCt/tGt	36/59	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.687685741340931	NA		602	646	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878742	151878742	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040443-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	155	370	0	ENST00000262189.6:c.6203C>A	p.Ser2068Tyr	p.S2068Y	ENST00000262189	NM_170606.2	2068	tCt/tAt	36/59	0.53416553348623	5	FACETS	1	0.985	1	0.83	0.77	0.89	CLONAL	2	TRUE	2	0.687685741340931	5		370	368	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878808	151878808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040443-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	218	418	0	ENST00000262189.6:c.6137C>T	p.Pro2046Leu	p.P2046L	ENST00000262189	NM_170606.2	2046	cCa/cTa	36/59	0.53416553348623	5	FACETS	0.86	0.809	0.913	0.86	0.809	0.913	CLONAL	3	TRUE	2	0.687685741340931	5		418	499	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542692	141542692	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040443-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	48	567	0	ENST00000220592.5:c.2294A>G	p.Tyr765Cys	p.Y765C	ENST00000220592	NM_012154.3	765	tAt/tGt	18/19	0.495863269390179	4	FACETS	0.272	0.229	0.32	0.136	0.114	0.16	SUBCLONAL	1	TRUE	2	0.687685741340931	4		567	865	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0040443-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	397	673	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.701166910248652	2	FACETS	0.982	0.949	1	0.982	0.949	1	CLONAL	2	TRUE	0	0.710591230596195	2		673	569	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911116	29911116	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs199474504	NA	P-0040443-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	246	695	0	ENST00000376809.5:c.415C>T	p.Gln139Ter	p.Q139*	ENST00000376809	NM_002116.7	139	Cag/Tag	3/8	0.710591230596195	3	FACETS	1	0.99	1	0.635	0.596	0.675	CLONAL	1	TRUE	1	0.710591230596195	3		695	739	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143332	108143332	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs774935453	NA	P-0040443-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	112	358	0	ENST00000278616.4:c.3151G>C	p.Glu1051Gln	p.E1051Q	ENST00000278616	NM_000051.3	1051	Gag/Cag	21/63	0.6825488769149	2	FACETS	0.911	0.829	0.996	0.456	0.414	0.498	CLONAL	1	TRUE	0	0.710591230596195	2		358	346	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190890	185190890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs979026761	NA	P-0040443-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2289	184	711	0	ENST00000265026.3:c.1771C>T	p.Arg591Cys	p.R591C	ENST00000265026	NM_004721.4	591	Cgc/Tgc	11/14	0.710591230596195	9	FACETS	0.73	0.67	0.793			1	SUBCLONAL	1	TRUE	NA	0.710591230596195	9		711	2473	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77060319	77060319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040443-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	94	214	2	ENST00000356341.3:c.850G>A	p.Val284Met	p.V284M	ENST00000356341	NM_002576.4	284	Gtg/Atg	9/15	0.6825488769149	2	FACETS	1	0.936	1	0.523	0.473	0.574	CLONAL	1	TRUE	0	0.710591230596195	2		216	253	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446430	49446431	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040443-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	292	572	0	ENST00000301067.7:c.1174dup	p.Cys392LeufsTer24	p.C392Lfs*24	ENST00000301067	NM_003482.3	392	tgc/tTgc	9/54	0.353467768850218	6	FACETS	0.85	0.804	0.898	0.85	0.804	0.898	INDETERMINATE	3	TRUE	3	0.710591230596195	6		572	780	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46611749	46611749	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040443-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	209	673	0	ENST00000263734.3:c.2563A>G	p.Thr855Ala	p.T855A	ENST00000263734	NM_001430.4	855	Acg/Gcg	16/16	0.505281323914132	4	FACETS	1	0.96	1	0.524	0.486	0.563	CLONAL	1	TRUE	2	0.710591230596195	4		673	960	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665134	138665134	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1228381934	NA	P-0040443-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	134	443	0	ENST00000330315.3:c.431G>C	p.Arg144Pro	p.R144P	ENST00000330315	NM_023067.3	144	cGg/cCg	1/1	0.710591230596195	6	FACETS	1	0.951	1			1	CLONAL	1	TRUE	NA	0.710591230596195	6		443	853	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808337	99808337	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040443-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	87	380	0	ENST00000280892.6:c.352A>T	p.Ile118Phe	p.I118F	ENST00000280892	NM_001130678.1	118	Att/Ttt	5/7	1	2	FACETS	0.684	0.61	0.761	0.684	0.61	0.761	SUBCLONAL	1	TRUE	1	0.710591230596195	2		380	358	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460552	8460552	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040443-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	134	382	0	ENST00000356435.5:c.3734C>G	p.Pro1245Arg	p.P1245R	ENST00000356435		1245	cCt/cGt	22/35	0.674790319278366	3	FACETS	1	0.964	1	0.366	0.335	0.399	CLONAL	1	TRUE	0	0.710591230596195	3		382	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0040443-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	547	652	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.676893616155628	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.676893616155628	2		652	793	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	441049	441049	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs913417551	NA	P-0040443-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	291	445	0	ENST00000399788.2:c.1709A>G	p.Tyr570Cys	p.Y570C	ENST00000399788	NM_001042603.1	570	tAt/tGt	13/28	0.651472247622353	3	FACETS	1	0.992	1	0.435	0.41	0.46	CLONAL	1	TRUE	0	0.676893616155628	3		445	882	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49430984	49430985	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040443-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	538	606	0	ENST00000301067.7:c.10154dup	p.Met3385IlefsTer38	p.M3385Ifs*38	ENST00000301067	NM_003482.3	3385	atg/atTg	34/54	0.651472247622353	3	FACETS	0.961	0.935	0.986	0.961	0.935	0.986	CLONAL	3	TRUE	0	0.676893616155628	3		606	738	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032179	26032179	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040443-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	167	417	0	ENST00000244661.2:c.110A>T	p.Lys37Ile	p.K37I	ENST00000244661	NM_003537.3	37	aAa/aTa	1/1	0.349086820105998	3	FACETS	1	0.989	1	0.7	0.648	0.752	INDETERMINATE	1	TRUE	1	0.676893616155628	3		417	472	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	94	395	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.624282806414134	2		395	227	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0040454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	103	411	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	TRUE	1	0.624282806414134	2		411	301	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176329	24176329	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1568963596	NA	P-0040454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	266	866	1	ENST00000263121.7:c.1120C>T	p.Arg374Trp	p.R374W	ENST00000263121	NM_003073.3	374	Cgg/Tgg	9/9	0.624282806414134	1	FACETS	0.963	0.91	1	0.963	0.91	1	CLONAL	1	TRUE	0	0.624282806414134	1		867	609	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332934	70332934	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	216	759	0	ENST00000373644.4:c.839T>G	p.Leu280Arg	p.L280R	ENST00000373644	NM_030625.2	280	cTt/cGt	2/12	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.624282806414134	2		759	681	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602581	10602581	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	213	809	0	ENST00000171111.5:c.997G>T	p.Gly333Cys	p.G333C	ENST00000171111	NM_203500.1	333	Ggc/Tgc	3/6	1	2	FACETS	0.781	0.732	0.83	1	0.993	1	SUBCLONAL	2	TRUE	1	0.519655486573777	2		809	525	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003545	42003545	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs765013304	NA	P-0040473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	34	418	0	ENST00000219905.7:c.3082C>G	p.Gln1028Glu	p.Q1028E	ENST00000219905	NM_001164273.1	1028	Caa/Gaa	8/24	1	2	FACETS	0.395	0.323	0.476	0.395	0.323	0.476	SUBCLONAL	1	TRUE	1	0.519655486573777	2		418	331	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36024580	36024580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	99	822	0	ENST00000358208.4:c.569C>T	p.Ser190Leu	p.S190L	ENST00000358208		190	tCa/tTa	6/12	1	2	FACETS	0.545	0.487	0.607	0.545	0.487	0.607	SUBCLONAL	1	TRUE	1	0.519655486573777	2		822	699	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221975	1221975	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	157	745	0	ENST00000326873.7:c.890G>T	p.Arg297Met	p.R297M	ENST00000326873	NM_000455.4	297	aGg/aTg	7/10	0.519655486573777	1	FACETS	0.886	0.817	0.956	0.886	0.817	0.956	CLONAL	1	TRUE	0	0.519655486573777	1		745	505	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161492	2161492	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753098162	NA	P-0040473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	42	652	0	ENST00000434045.2:c.35C>T	p.Ala12Val	p.A12V	ENST00000434045	NM_001127598.1	12	gCc/gTc	2/5	NA	2	FACETS	0.241	0.201	0.287			1	INDETERMINATE	1	TRUE	NA	0.519655486573777	2		652	670	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953133	81953133	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	76	338	0	ENST00000359376.3:c.2099G>T	p.Arg700Leu	p.R700L	ENST00000359376	NM_002661.3	700	cGg/cTg	20/33	1	2	FACETS	0.85	0.751	0.955	0.85	0.751	0.955	CLONAL	1	TRUE	1	0.519655486573777	2		338	344	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325810	30325810	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	80	338	0	ENST00000322652.5:c.2008A>G	p.Ser670Gly	p.S670G	ENST00000322652	NM_015355.2	670	Agc/Ggc	16/16	1	2	FACETS	0.959	0.852	1	0.959	0.852	1	CLONAL	1	TRUE	1	0.519655486573777	2		338	321	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40861956	40861956	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0040473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	27	394	0	ENST00000428826.2:c.1402-1G>A		p.X468_splice	ENST00000428826		468			1	2	FACETS	0.275	0.218	0.339	0.275	0.218	0.339	SUBCLONAL	1	TRUE	1	0.519655486573777	2		394	378	SUCCESS
APC	324	MSKCC	GRCh37	5	112175211	112175211	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	57	239	0	ENST00000257430.4:c.3920T>G	p.Ile1307Arg	p.I1307R	ENST00000257430	NM_000038.5	1307	aTa/aGa	16/16	1	2	FACETS	0.946	0.821	1	0.946	0.821	1	CLONAL	1	TRUE	1	0.519655486573777	2		239	232	SUCCESS
APC	324	MSKCC	GRCh37	5	112175226	112175226	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	64	248	0	ENST00000257430.4:c.3935G>T	p.Gly1312Val	p.G1312V	ENST00000257430	NM_000038.5	1312	gGa/gTa	16/16	1	2	FACETS	0.962	0.843	1	0.962	0.843	1	CLONAL	1	TRUE	1	0.519655486573777	2		248	256	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31939840	31939840	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	136	805	2	ENST00000375333.2:c.67C>T	p.Arg23Trp	p.R23W	ENST00000375333	NM_032454.1	23	Cgg/Tgg	1/8	0.519655486573777	3	FACETS	0.692	0.628	0.759	0.346	0.314	0.38	SUBCLONAL	1	TRUE	1	0.519655486573777	3		807	953	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100003	157100003	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	20	52	1	ENST00000346085.5:c.940G>A	p.Gly314Ser	p.G314S	ENST00000346085	NM_020732.3	314	Ggc/Agc	1/20	0.519655486573777	1	FACETS	1	0.795	1	1	0.795	1	CLONAL	1	TRUE	0	0.519655486573777	1		53	57	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0040473-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	156	441	2	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.484607812797952	2		443	625	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249456	153249456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040473-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	192	523	0	ENST00000281708.4:c.1322G>A	p.Arg441Gln	p.R441Q	ENST00000281708	NM_033632.3	441	cGg/cAg	9/12	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.484607812797952	2		523	769	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441821	49441821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202217665	NA	P-0040473-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	187	646	0	ENST00000301067.7:c.4163G>A	p.Arg1388Gln	p.R1388Q	ENST00000301067	NM_003482.3	1388	cGg/cAg	14/54	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.484607812797952	2		646	643	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938457	76938457	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040473-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	171	518	0	ENST00000373344.5:c.2291del	p.Leu764CysfsTer4	p.L764Cfs*4	ENST00000373344	NM_000489.3	764	tTg/tg	9/35	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.484607812797952	2		518	695	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602878	10602878	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040473-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	392	983	0	ENST00000171111.5:c.700C>G	p.Arg234Gly	p.R234G	ENST00000171111	NM_203500.1	234	Cgg/Ggg	3/6	0.484607812797952	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.484607812797952	2		983	785	SUCCESS
ATM	472	MSKCC	GRCh37	11	108128334	108128334	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs730881347	NA	P-0040473-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	120	289	0	ENST00000278616.4:c.2376+1G>A		p.X792_splice	ENST00000278616	NM_000051.3	792			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.484607812797952	2		289	426	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165703	108165703	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1316363133	NA	P-0040473-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	111	384	0	ENST00000278616.4:c.4826C>G	p.Thr1609Arg	p.T1609R	ENST00000278616	NM_000051.3	1609	aCa/aGa	32/63	1	2	FACETS	0.888	0.802	0.978	0.888	0.802	0.978	CLONAL	1	TRUE	1	0.484607812797952	2		384	516	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993995	72993995	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040473-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	176	786	0	ENST00000268489.5:c.50del	p.Gly17ValfsTer37	p.G17Vfs*37	ENST00000268489	NM_006885.3	17	gGt/gt	2/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.484607812797952	2		786	650	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207064	1207065	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGGG	novel	NA	P-0040473-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	185	896	0	ENST00000326873.7:c.154_157dup	p.Asp53GlyfsTer111	p.D53Gfs*111	ENST00000326873	NM_000455.4	51	atg/atGGGGg	1/10	0.484607812797952	2	FACETS	1	0.989	1	0.689	0.641	0.739	CLONAL	1	TRUE	0	0.484607812797952	2		896	554	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584459	187584459	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040473-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	73	328	0	ENST00000441802.2:c.3574A>G	p.Lys1192Glu	p.K1192E	ENST00000441802	NM_005245.3	1192	Aaa/Gaa	3/27	1	2	FACETS	0.939	0.828	1	0.939	0.828	1	CLONAL	1	TRUE	1	0.484607812797952	2		328	321	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5467850	5467850	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040473-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	105	347	0	ENST00000381577.3:c.861G>T	p.Leu287Phe	p.L287F	ENST00000381577	NM_014143.3	287	ttG/ttT	7/7	1	2	FACETS	0.93	0.838	1	0.93	0.838	1	CLONAL	1	TRUE	1	0.484607812797952	2		347	466	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500899	8500899	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040473-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	124	517	0	ENST00000356435.5:c.1983G>C	p.Glu661Asp	p.E661D	ENST00000356435		661	gaG/gaC	13/35	1	2	FACETS	0.849	0.77	0.931	0.849	0.77	0.931	CLONAL	1	TRUE	1	0.484607812797952	2		517	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0040475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	239	744	3	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.594474340314308	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	0	0.594474340314308	1		747	506	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649051	37649051	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	436	478	0	ENST00000447079.4:c.2156G>A	p.Trp719Ter	p.W719*	ENST00000447079	NM_015083.1	719	tGg/tAg	4/14	0.298941322863453	4	FACETS	0.897	0.867	0.926			1	INDETERMINATE	4	FALSE	NA	0.594474340314308	4		478	652	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56367679	56367679	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs775872427	NA	P-0040475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	211	70	0	ENST00000348428.3:c.505A>G	p.Asn169Asp	p.N169D	ENST00000348428	NM_006785.3	169	Aat/Gat	4/17	0.594474340314308	1	FACETS	0.799	0.762	0.836	1	0.994	1	SUBCLONAL	2	FALSE	0	0.594474340314308	1		70	312	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005886	69005886	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	530	65	0	ENST00000288368.4:c.2297A>G	p.Glu766Gly	p.E766G	ENST00000288368	NM_024870.2	766	gAa/gGa	21/40	0.206124945985632	4	FACETS	0.998	0.963	1	0.998	0.963	1	INDETERMINATE	3	FALSE	1	0.594474340314308	4		65	950	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578204	7578204	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520001	NA	P-0040476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	132	782	0	ENST00000269305.4:c.645T>G	p.Ser215Arg	p.S215R	ENST00000269305	NM_001126112.2	215	agT/agG	6/11	0.244763888871834	2	FACETS	1	0.98	1	0.635	0.579	0.695	CLONAL	1	TRUE	0	0.350915899726778	2		782	592	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965710	18965710	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	149	714	0	ENST00000262803.5:c.1288T>C	p.Phe430Leu	p.F430L	ENST00000262803	NM_002911.3	430	Ttt/Ctt	10/24	1	2	FACETS	0.797	0.732	0.863	1	0.989	1	SUBCLONAL	2	TRUE	1	0.350915899726778	2		714	533	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156902	89156902	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	43	511	0	ENST00000336596.2:c.4G>A	p.Asp2Asn	p.D2N	ENST00000336596	NM_005233.5	2	Gat/Aat	1/17	0.226015953966301	3	FACETS	0.477	0.398	0.564	0.238	0.199	0.282	SUBCLONAL	1	TRUE	1	0.350915899726778	3		511	604	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76764059	76764059	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	52	330	0	ENST00000373344.5:c.7249C>T	p.Gln2417Ter	p.Q2417*	ENST00000373344	NM_000489.3	2417	Cag/Tag	35/35	1	1	FACETS	0.776	0.664	0.897	0.776	0.664	0.897	SUBCLONAL	1	TRUE	0	0.350915899726778	1		330	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0040504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	385	547	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.737628275762881	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.773195249292675	1		548	605	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609934	81609934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369995834	NA	P-0040504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	31	346	0	ENST00000298171.2:c.1532C>T	p.Thr511Met	p.T511M	ENST00000298171	NM_000369.2	511	aCg/aTg	10/10	0.392538099443804	1	FACETS	0.125	0.101	0.153	0.125	0.101	0.153	INDETERMINATE	1	TRUE	0	0.773195249292675	1		346	393	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647301	23647301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	94	611	0	ENST00000261584.4:c.566G>A	p.Arg189Lys	p.R189K	ENST00000261584	NM_024675.3	189	aGa/aAa	4/13	0.773195249292675	1	FACETS	0.248	0.22	0.277	0.248	0.22	0.277	SUBCLONAL	1	TRUE	0	0.773195249292675	1		611	602	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161807867	161807867	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	16	446	0	ENST00000366898.1:c.1126G>T	p.Glu376Ter	p.E376*	ENST00000366898	NM_004562.2	376	Gag/Tag	10/12	0.773195249292675	1	FACETS	0.094	0.069	0.124	0.094	0.069	0.124	SUBCLONAL	1	TRUE	0	0.773195249292675	1		446	269	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0040511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	486	441	2	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.630474807772164	4	FACETS	0.883	0.855	0.909			1	CLONAL	4	TRUE	NA	0.630474807772164	4		443	712	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087555	27087555	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1171422700	NA	P-0040511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	79	688	1	ENST00000324856.7:c.2129G>T	p.Arg710Leu	p.R710L	ENST00000324856	NM_006015.4	710	cGc/cTc	5/20	0.33857995516992	2	FACETS	0.392	0.344	0.442	0.196	0.172	0.221	INDETERMINATE	1	TRUE	0	0.630474807772164	2		689	640	SUCCESS
FH	2271	MSKCC	GRCh37	1	241665804	241665804	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	110	477	0	ENST00000366560.3:c.1175T>C	p.Val392Ala	p.V392A	ENST00000366560	NM_000143.3	392	gTt/gCt	8/10	0.618678036975467	3	FACETS	0.773	0.696	0.853	0.258	0.232	0.285	SUBCLONAL	1	TRUE	0	0.630474807772164	3		477	594	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912720	100912720	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	51	434	0	ENST00000325455.5:c.2602C>G	p.Gln868Glu	p.Q868E	ENST00000325455	NM_001202474.3	868	Cag/Gag	7/8	0.478422031456432	1	FACETS	0.259	0.221	0.302	0.259	0.221	0.302	SUBCLONAL	1	TRUE	0	0.630474807772164	1		434	427	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435461	18435461	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	158	281	0	ENST00000266497.5:c.446C>A	p.Thr149Lys	p.T149K	ENST00000266497		149	aCa/aAa	1/31	0.374147254941882	3	FACETS	1	0.975	1	0.728	0.68	0.775	INDETERMINATE	2	TRUE	0	0.630474807772164	3		281	302	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112892484	112892484	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	48	373	0	ENST00000351677.2:c.642G>C	p.Gln214His	p.Q214H	ENST00000351677	NM_002834.3	214	caG/caC	5/16	0.360875901771452	3	FACETS	0.419	0.354	0.49	0.14	0.118	0.164	INDETERMINATE	1	TRUE	0	0.630474807772164	3		373	478	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528066	103528066	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	195	379	1	ENST00000355739.4:c.3374G>T	p.Ser1125Ile	p.S1125I	ENST00000355739	NM_000123.3	1125	aGt/aTt	15/15	0.379502901957023	2	FACETS	0.777	0.73	0.824	0.777	0.73	0.824	SUBCLONAL	2	TRUE	0	0.630474807772164	2		380	398	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436252	110436252	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	38	378	0	ENST00000375856.3:c.2149G>T	p.Gly717Cys	p.G717C	ENST00000375856	NM_003749.2	717	Ggc/Tgc	1/2	0.379502901957023	2	FACETS	0.432	0.359	0.513	0.216	0.179	0.257	SUBCLONAL	1	TRUE	0	0.630474807772164	2		378	279	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0040511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	317	749	1	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.584446559725986	2	FACETS	0.943	0.903	0.983	0.943	0.903	0.983	CLONAL	2	TRUE	0	0.630474807772164	2		750	533	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523051	25523051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	93	740	0	ENST00000264709.3:c.134C>T	p.Ala45Val	p.A45V	ENST00000264709	NM_175629.2	45	gCa/gTa	3/23	0.288559887705004	3	FACETS	0.462	0.41	0.517	0.154	0.136	0.173	INDETERMINATE	1	TRUE	0	0.630474807772164	3		740	840	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010532	48010532	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	119	593	0	ENST00000234420.5:c.162del	p.Pro55LeufsTer26	p.P55Lfs*26	ENST00000234420	NM_000179.2	54	Ggg/gg	1/10	0.630474807772164	3	FACETS	0.789	0.714	0.868	0.395	0.357	0.434	SUBCLONAL	1	TRUE	1	0.630474807772164	3		593	629	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662127	227662127	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs745943416	NA	P-0040511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	217	702	0	ENST00000305123.5:c.1328G>T	p.Arg443Leu	p.R443L	ENST00000305123	NM_005544.2	443	cGc/cTc	1/2	0.630474807772164	2	FACETS	1	0.989	1	0.629	0.59	0.669	CLONAL	1	TRUE	0	0.630474807772164	2		702	547	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448529	89448529	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	226	503	0	ENST00000336596.2:c.1493G>T	p.Ser498Ile	p.S498I	ENST00000336596	NM_005233.5	498	aGc/aTc	7/17	0.33857995516992	2	FACETS	1	0.992	1	0.703	0.661	0.745	INDETERMINATE	1	TRUE	0	0.630474807772164	2		503	510	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244091	153244091	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	250	458	0	ENST00000281708.4:c.2066G>T	p.Arg689Leu	p.R689L	ENST00000281708	NM_033632.3	689	cGg/cTg	12/12	0.368155773177312	2	FACETS	0.842	0.798	0.885	0.842	0.798	0.885	INDETERMINATE	2	TRUE	0	0.630474807772164	2		458	471	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876137	35876138	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0040511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	222	512	1	ENST00000303115.3:c.929_930delinsTT	p.Arg310Ile	p.R310I	ENST00000303115	NM_002185.3	310	aGG/aTT	8/8	0.630474807772164	6	FACETS	0.806	0.75	0.863	0.403	0.375	0.432	CLONAL	2	TRUE	2	0.630474807772164	6		513	988	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180951	32180951	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	326	686	1	ENST00000375023.3:c.2399C>A	p.Pro800Gln	p.P800Q	ENST00000375023	NM_004557.3	800	cCg/cAg	15/30	0.227160853206598	2	FACETS	0.83	0.792	0.868	0.83	0.792	0.868	INDETERMINATE	2	TRUE	0	0.630474807772164	2		687	623	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730031	41730032	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0040511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	203	613	0	ENST00000242208.4:c.497_498delinsAT	p.Arg166Asn	p.R166N	ENST00000242208	NM_002192.2	166	aGG/aAT	3/3	0.595451925509832	3	FACETS	0.758	0.708	0.808	0.758	0.708	0.808	SUBCLONAL	2	TRUE	1	0.630474807772164	3		613	559	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287391	38287391	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763858257	NA	P-0040511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	187	615	2	ENST00000425967.3:c.266G>A	p.Arg89Gln	p.R89Q	ENST00000425967	NM_001174067.1	89	cGg/cAg	4/19	0.630474807772164	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.630474807772164	1		617	364	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372550	55372550	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	228	797	0	ENST00000297316.4:c.1240G>C	p.Val414Leu	p.V414L	ENST00000297316	NM_022454.3	414	Gtg/Ctg	2/2	0.369264903139348	6	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.630474807772164	6		797	1216	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376683	8376683	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	57	558	1	ENST00000356435.5:c.4430A>T	p.His1477Leu	p.H1477L	ENST00000356435		1477	cAc/cTc	27/35	0.474044298130608	1	FACETS	0.293	0.251	0.337	0.293	0.251	0.337	SUBCLONAL	1	TRUE	0	0.630474807772164	1		559	423	SUCCESS
AR	367	MSKCC	GRCh37	X	66942741	66942741	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs9332969	NA	P-0040511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	89	269	0	ENST00000374690.3:c.2522G>T	p.Arg841Leu	p.R841L	ENST00000374690	NM_000044.3	841	cGt/cTt	7/8	1	1	FACETS	0.957	0.868	1	0.957	0.868	1	CLONAL	1	TRUE	0	0.630474807772164	1		269	202	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs17849781	NA	P-0040519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	483	182	0	ENST00000269305.4:c.832C>G	p.Pro278Ala	p.P278A	ENST00000269305	NM_001126112.2	278	Cct/Gct	8/11	1	2	FACETS	1	0.993	1	1	0.998	1	CLONAL	2	TRUE	1	0.579579824837415	2		182	759	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133574	55133574	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373948582	NA	P-0040519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	174	165	0	ENST00000257290.5:c.878G>A	p.Arg293His	p.R293H	ENST00000257290	NM_006206.4	293	cGc/cAc	6/23	0.579579824837415	3	FACETS	1	0.985	1	0.627	0.579	0.675	CLONAL	1	TRUE	1	0.579579824837415	3		165	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0040520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	315	686	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.69797370871733	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.734651514659831	2		686	423	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0040520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	237	663	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	0.424879096608071	5	FACETS	0.954	0.902	1	0.954	0.902	1	INDETERMINATE	3	TRUE	2	0.734651514659831	5		663	474	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589619	67589621	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0040520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	102	228	0	ENST00000274335.5:c.1382_1384del	p.Arg461_Glu462delinsGln	p.R461_E462delinsQ	ENST00000274335		461	cGAGaa/caa	10/15	0.666722147842265	3	FACETS	1	0.984	1	0.733	0.667	0.801	CLONAL	1	TRUE	1	0.734651514659831	3		228	259	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780071	NA	P-0040528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	62	804	0	ENST00000269305.4:c.580C>T	p.Leu194Phe	p.L194F	ENST00000269305	NM_001126112.2	194	Ctt/Ttt	6/11	1	2	FACETS	0.998	0.863	1	0.998	0.863	1	CLONAL	1	TRUE	1	0.230513156215606	2		804	539	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0040528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	89	860	2	ENST00000397752.3:c.3028+1G>A		p.X1010_splice	ENST00000397752	NM_000245.2	1010			1	2	FACETS	0.798	0.71	0.891	1	0.981	1	SUBCLONAL	2	TRUE	1	0.230513156215606	2		862	484	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696430	47696430	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	120	613	0	ENST00000347630.2:c.393G>C	p.Trp131Cys	p.W131C	ENST00000347630	NM_001007230.1	131	tgG/tgC	6/11	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.33	2		613	703	SUCCESS
APC	324	MSKCC	GRCh37	5	112175650	112175651	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	35	391	0	ENST00000257430.4:c.4364dup	p.Asn1455LysfsTer2	p.N1455Kfs*2	ENST00000257430	NM_000038.5	1453	-/A	16/16	1	2	FACETS	0.598	0.49	0.717	0.598	0.49	0.717	SUBCLONAL	1	TRUE	1	0.33	2		391	355	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	113	63	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.379073759268167	3	FACETS	0.93	0.837	1	0.465	0.418	0.514	CLONAL	1	TRUE	1	0.380119458921991	3		63	761	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604701	48604701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555687572	NA	P-0040531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	251	569	0	ENST00000342988.3:c.1523G>A	p.Gly508Asp	p.G508D	ENST00000342988	NM_005359.5	508	gGc/gAc	12/12	0.379073759268167	3	FACETS	0.913	0.856	0.971	0.913	0.856	0.971	CLONAL	2	TRUE	1	0.380119458921991	3		569	861	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427250	49427251	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGC	rs760816616	NA	P-0040531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	129	994	0	ENST00000301067.7:c.11235_11237dup	p.Gln3745dup	p.Q3745dup	ENST00000301067	NM_003482.3	3745	cac/caGCAc	39/54	0.379073759268167	3	FACETS	0.652	0.589	0.718	0.326	0.294	0.359	SUBCLONAL	1	TRUE	1	0.380119458921991	3		994	1239	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47700117	47700117	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	132	622	0	ENST00000347630.2:c.56C>G	p.Ala19Gly	p.A19G	ENST00000347630	NM_001007230.1	19	gCt/gGt	3/11	0.37277425459681	2	FACETS	0.896	0.814	0.982	0.448	0.407	0.491	CLONAL	1	TRUE	0	0.380119458921991	2		622	775	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212311	36212311	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	238	1138	0	ENST00000222270.7:c.2062C>T	p.Pro688Ser	p.P688S	ENST00000222270	NM_014727.1	688	Cca/Tca	3/37	0.380119458921991	2	FACETS	1	0.947	1	0.509	0.475	0.545	CLONAL	1	TRUE	0	0.380119458921991	2		1138	1229	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62290777	62290777	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	202	428	0	ENST00000360203.5:c.22G>A	p.Gly8Ser	p.G8S	ENST00000360203	NM_001283009.1	8	Ggt/Agt	2/35	0.380119458921991	5	FACETS	1	0.972	1	0.725	0.674	0.778	CLONAL	2	TRUE	2	0.380119458921991	5		428	767	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602314	10602314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1503	83	1057	0	ENST00000171111.5:c.1264G>A	p.Asp422Asn	p.D422N	ENST00000171111	NM_203500.1	422	Gat/Aat	3/6	1	2	FACETS	0.162	0.142	0.184	0.162	0.142	0.184	SUBCLONAL	1	TRUE	1	0.646692326402094	2		1057	1586	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572549	64572549	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs104894260	NA	P-0040534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	477	868	2	ENST00000312049.6:c.1307G>A	p.Trp436Ter	p.W436*	ENST00000312049	NM_130799.2	436	tGg/tAg	9/10	0.646692326402094	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.646692326402094	1		870	982	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888697	76888697	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	222	283	0	ENST00000373344.5:c.5132C>T	p.Pro1711Leu	p.P1711L	ENST00000373344	NM_000489.3	1711	cCa/cTa	19/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.646692326402094	1		283	339	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0040536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	56	233	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.812	0.694	0.94	0.812	0.694	0.94	CLONAL	1	TRUE	1	0.2	2		235	690	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	97	585	1	ENST00000269305.4:c.859G>T	p.Glu287Ter	p.E287*	ENST00000269305	NM_001126112.2	287	Gag/Tag	8/11	0.295106487789113	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.2	1		586	841	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0040536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	75	653	0	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	0.295106487789113	1	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	0	0.2	1		653	644	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799345	88799637	+	splice_donor_variant,splice_acceptor_variant,start_lost,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	GCCAGAAACTACACTTGGCTGGGCAAAGAGAGACATCCATCTCCGATCGCTGCTTCTAAAAAAGAGGAGGAGGAGAGGAGAGGGGGGTGGGGTGGGGGGAGTGGGGAGAGCAGGGGGGGAAGGAAACAAAGACGGCGAGGGAGGGGGGAAGGGGGAGGGGGGGCCTCTGCCTTTGAAACGCCGAGCGATCAGATGCAAAATCCTTCAGCGTCTGAAACCATCGCGGACGCCGCCGCCGCCGCCGCCGCCGCCGGGTGGGAGCCGCGAGGAGCGCCTAGTGGCGCGGTCTGCCG	GCCAGAAACTACACTTGGCTGGGCAAAGAGAGACATCCATCTCCGATCGCTGCTTCTAAAAAAGAGGAGGAGGAGAGGAGAGGGGGGTGGGGTGGGGGGAGTGGGGAGAGCAGGGGGGGAAGGAAACAAAGACGGCGAGGGAGGGGGGAAGGGGGAGGGGGGGCCTCTGCCTTTGAAACGCCGAGCGATCAGATGCAAAATCCTTCAGCGTCTGAAACCATCGCGGACGCCGCCGCCGCCGCCGCCGCCGCCGGGTGGGAGCCGCGAGGAGCGCCTAGTGGCGCGGTCTGCCG	-	novel	NA	P-0040536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	31	521	0	ENST00000360948.2:c.-138_40del		p.X46_splice	ENST00000360948	NM_001012338.2	46		1-2/19	0.178694774400485	2	FACETS	0.573	0.462	0.699	0.287	0.231	0.35	SUBCLONAL	1	TRUE	0	0.2	2		521	541	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207135	1207136	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGC	novel	NA	P-0040536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	78	841	0	ENST00000326873.7:c.225_226insCGG	p.Arg75dup	p.R75dup	ENST00000326873	NM_000455.4	75	agg/aGGCgg	1/10	0.259919005493405	0	FACETS	0.68	0.596	0.77			1	SUBCLONAL	1	TRUE	0	0.2	0		841	918	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610189	10610189	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	128	823	0	ENST00000171111.5:c.521del	p.Phe174SerfsTer56	p.F174Sfs*56	ENST00000171111	NM_203500.1	174	tTc/tc	2/6	0.295106487789113	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.2	1		823	859	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180671	32180671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	57	751	0	ENST00000375023.3:c.2456C>A	p.Ala819Glu	p.A819E	ENST00000375023	NM_004557.3	819	gCa/gAa	16/30	0.189655403401465	3	FACETS	0.736	0.63	0.852	0.368	0.315	0.426	SUBCLONAL	1	TRUE	1	0.2	3		751	852	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5055762	5055762	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	51	375	0	ENST00000381652.3:c.1030A>G	p.Ile344Val	p.I344V	ENST00000381652	NM_004972.3	344	Atc/Gtc	8/25	0.295106487789113	1	FACETS	0.681	0.578	0.795	0.681	0.578	0.795	SUBCLONAL	1	TRUE	0	0.2	1		375	674	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0040537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	165	654	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.616814411136671	1	FACETS	0.865	0.802	0.928	0.865	0.802	0.928	CLONAL	1	TRUE	0	0.616814411136671	1		656	428	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229407	36229407	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	158	667	0	ENST00000222270.7:c.8097C>G	p.Asn2699Lys	p.N2699K	ENST00000222270	NM_014727.1	2699	aaC/aaG	37/37	1	2	FACETS	0.908	0.837	0.982	0.908	0.837	0.982	CLONAL	1	TRUE	1	0.616814411136671	2		667	564	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	84	395	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.337235668054557	2		395	419	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0040540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3280	69	568	0	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.337235668054557	21	FACETS	0.514	0.444	0.59	0.026	0.022	0.03	SUBCLONAL	1	TRUE	1	0.337235668054557	21		568	3349	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235329	235329	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749309213	NA	P-0040540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	125	874	0	ENST00000264932.6:c.1135C>T	p.Arg379Cys	p.R379C	ENST00000264932	NM_004168.2	379	Cgc/Tgc	9/15	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.337235668054557	2		874	733	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3277	72	568	0	ENST00000275493.2:c.1793G>A	p.Gly598Glu	p.G598E	ENST00000275493	NM_005228.3	598	gGa/gAa	15/28	0.337235668054557	21	FACETS	0.536	0.465	0.613	0.027	0.023	0.031	SUBCLONAL	1	TRUE	1	0.337235668054557	21		568	3349	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720807	89720822	+	frameshift_variant	Frame_Shift_Del	DEL	TTAACAAAAAATGATC	TTAACAAAAAATGATC	-	novel	NA	P-0040540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	62	438	0	ENST00000371953.3:c.960_975del	p.Asn323GlnfsTer16	p.N323Qfs*16	ENST00000371953	NM_000314.4	320	TTAACAAAAAATGATCtt/tt	8/9	0.337235668054557	1	FACETS	0.813	0.706	0.929	0.813	0.706	0.929	CLONAL	1	TRUE	0	0.337235668054557	1		438	376	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913351	NA	P-0040552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	71	240	0	ENST00000288602.6:c.1397G>T	p.Gly466Val	p.G466V	ENST00000288602	NM_004333.4	466	gGa/gTa	11/18	0.152566557481967	4	FACETS	0.916	0.8	1	0.458	0.4	0.52	INDETERMINATE	1	TRUE	2	0.371151445482047	4		240	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574035	7574035	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs867389695	NA	P-0040552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	78	359	0	ENST00000269305.4:c.994-2A>G		p.X332_splice	ENST00000269305	NM_001126112.2	332			1	2	FACETS	0.662	0.582	0.748	0.662	0.582	0.748	SUBCLONAL	1	TRUE	1	0.371151445482047	2		359	635	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730882	40730882	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	99	447	0	ENST00000373198.4:c.3653T>C	p.Leu1218Pro	p.L1218P	ENST00000373198	NM_133170.3	1218	cTg/cCg	27/32	1	2	FACETS	0.664	0.592	0.74	0.664	0.592	0.74	SUBCLONAL	1	TRUE	1	0.371151445482047	2		447	804	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741608	17741608	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	23	219	0	ENST00000250003.3:c.279C>A	p.Cys93Ter	p.C93*	ENST00000250003	NM_002478.4	93	tgC/tgA	1/3	1	2	FACETS	0.276	0.214	0.348	0.276	0.214	0.348	SUBCLONAL	1	TRUE	1	0.371151445482047	2		219	449	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795172	42795172	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	78	624	0	ENST00000575354.2:c.2252G>T	p.Gly751Val	p.G751V	ENST00000575354	NM_015125.3	751	gGc/gTc	10/20	1	2	FACETS	0.425	0.372	0.482	0.425	0.372	0.482	SUBCLONAL	1	TRUE	1	0.371151445482047	2		624	990	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912898	50912898	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	75	529	0	ENST00000440232.2:c.2129A>T	p.Lys710Met	p.K710M	ENST00000440232	NM_002691.3	710	aAg/aTg	17/27	1	2	FACETS	0.451	0.394	0.513	0.451	0.394	0.513	SUBCLONAL	1	TRUE	1	0.371151445482047	2		529	896	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272795	142272795	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	35	244	0	ENST00000350721.4:c.2404G>T	p.Val802Leu	p.V802L	ENST00000350721	NM_001184.3	802	Gta/Tta	11/47	0.371151445482047	3	FACETS	0.341	0.278	0.411	0.17	0.139	0.206	SUBCLONAL	1	TRUE	1	0.371151445482047	3		244	656	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31422988	31422988	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	54	366	0	ENST00000344624.3:c.3325G>T	p.Glu1109Ter	p.E1109*	ENST00000344624		1109	Gag/Tag	26/33	1	2	FACETS	0.396	0.338	0.461	0.396	0.338	0.461	SUBCLONAL	1	TRUE	1	0.371151445482047	2		366	734	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987236	2987236	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1554276629	NA	P-0040552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	37	363	0	ENST00000396946.4:c.193A>G	p.Met65Val	p.M65V	ENST00000396946	NM_032415.4	65	Atg/Gtg	3/25	0.152566557481967	4	FACETS	0.403	0.331	0.484	0.202	0.165	0.242	INDETERMINATE	1	TRUE	2	0.371151445482047	4		363	678	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335062	81335062	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	80	224	0	ENST00000222390.5:c.1765G>C	p.Val589Leu	p.V589L	ENST00000222390	NM_000601.4	589	Gtc/Ctc	16/18	0.152566557481967	4	FACETS	1	0.965	1	0.625	0.552	0.703	INDETERMINATE	1	TRUE	2	0.371151445482047	4		224	473	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852090	128852090	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	123	536	0	ENST00000249373.3:c.2162C>T	p.Ala721Val	p.A721V	ENST00000249373	NM_005631.4	721	gCt/gTt	12/12	0.152566557481967	4	FACETS	0.765	0.69	0.845	0.382	0.345	0.423	INDETERMINATE	1	TRUE	2	0.371151445482047	4		536	1188	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868980	117868980	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	36	234	0	ENST00000297338.2:c.719G>T	p.Gly240Val	p.G240V	ENST00000297338	NM_006265.2	240	gGt/gTt	7/14	0.115887067235454	5	FACETS	0.63	0.518	0.757	0.158	0.129	0.19	INDETERMINATE	1	TRUE	1	0.371151445482047	5		234	479	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045137	47045137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556782140	NA	P-0040552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	61	481	0	ENST00000377604.3:c.2378G>A	p.Arg793Gln	p.R793Q	ENST00000377604	NM_001204468.1	793	cGa/cAa	21/24	0.22994185560175	1	FACETS	0.372	0.32	0.428	0.372	0.32	0.428	SUBCLONAL	1	TRUE	0	0.371151445482047	1		481	720	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650592	48650592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	40	541	1	ENST00000376670.3:c.562C>A	p.Pro188Thr	p.P188T	ENST00000376670	NM_002049.3	188	Ccc/Acc	3/6	0.22994185560175	1	FACETS	0.237	0.196	0.283	0.237	0.196	0.283	SUBCLONAL	1	TRUE	0	0.371151445482047	1		542	741	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281339	49281339	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	770	890	0	ENST00000282018.3:c.386T>A	p.Leu129Gln	p.L129Q	ENST00000282018	NM_020377.2	129	cTg/cAg	1/1	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.862455899395249	2		890	1659	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779812	3779812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567263703	NA	P-0040573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	654	839	0	ENST00000262367.5:c.5236G>A	p.Gly1746Arg	p.G1746R	ENST00000262367	NM_004380.2	1746	Ggg/Agg	31/31	1	2	FACETS	0.916	0.883	0.949	0.916	0.883	0.949	CLONAL	1	TRUE	1	0.862455899395249	2		839	1656	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443485	52443585	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTGTCTTCCCTAAGGGGCCCTGTTCTCTGGGACCTTCCCCAGCACTCTGGGTGTAAGGGGCAGCCCTGGTGTACAGCCACTCACCCCTGACATTTGCTCT	ACTGTCTTCCCTAAGGGGCCCTGTTCTCTGGGACCTTCCCCAGCACTCTGGGTGTAAGGGGCAGCCCTGGTGTACAGCCACTCACCCCTGACATTTGCTCT	-	novel	NA	P-0040573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	323	237	0	ENST00000460680.1:c.107_122+85del		p.X36_splice	ENST00000460680	NM_004656.3	36		3/17	0.862455899395249	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.862455899395249	1		237	362	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398902	398938	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGCATAAGGTCTGCCGAAGCCTTGGCGTTCTCAGGTG	AGCATAAGGTCTGCCGAAGCCTTGGCGTTCTCAGGTG	-	novel	NA	P-0040573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	247	552	0	ENST00000380956.4:c.714_745+5del		p.X238_splice	ENST00000380956	NM_001195286.1	238		6/9	0.83072020178147	3	FACETS	0.594	0.554	0.636	0.297	0.277	0.318	SUBCLONAL	1	TRUE	1	0.862455899395249	3		552	1380	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0040578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	228	571	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.324165533368055	2	FACETS	0.873	0.817	0.93	0.873	0.817	0.93	CLONAL	2	TRUE	0	0.374297131814532	2		571	698	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281491	49281491	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	126	520	0	ENST00000282018.3:c.538C>A	p.Gln180Lys	p.Q180K	ENST00000282018	NM_020377.2	180	Cag/Aag	1/1	1	2	FACETS	0.93	0.843	1	0.93	0.843	1	CLONAL	1	TRUE	1	0.374297131814532	2		520	724	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307779	11307779	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	174	451	0	ENST00000361445.4:c.1128G>C	p.Trp376Cys	p.W376C	ENST00000361445	NM_004958.3	376	tgG/tgC	8/58	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.374297131814532	2		451	641	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163791	72163791	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	57	359	1	ENST00000357731.5:c.567C>A	p.Asp189Glu	p.D189E	ENST00000357731	NM_173808.2	189	gaC/gaA	4/7	0.339315792807023	3	FACETS	1	0.863	1	0.501	0.431	0.576	CLONAL	1	TRUE	1	0.374297131814532	3		360	361	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88678959	88678959	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	14	226	0	ENST00000372037.3:c.899G>T	p.Gly300Val	p.G300V	ENST00000372037	NM_004329.2	300	gGt/gTt	10/13	0.347329739503172	2	FACETS	0.303	0.219	0.405	0.151	0.109	0.203	SUBCLONAL	1	TRUE	0	0.374297131814532	2		226	247	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636336	21636336	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	97	458	0	ENST00000421138.2:c.674G>T	p.Ser225Ile	p.S225I	ENST00000421138		225	aGt/aTt	7/16	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.374297131814532	2		458	505	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244076	46244076	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs748108135	NA	P-0040578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	45	426	0	ENST00000334344.6:c.2170C>A	p.Pro724Thr	p.P724T	ENST00000334344	NM_152641.2	724	Ccc/Acc	15/21	1	2	FACETS	0.421	0.353	0.496	0.421	0.353	0.496	SUBCLONAL	1	TRUE	1	0.374297131814532	2		426	571	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560464	95560464	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	316	385	0	ENST00000393063.1:c.5125G>T	p.Asp1709Tyr	p.D1709Y	ENST00000393063	NM_030621.3	1709	Gat/Tat	25/28	0.359301102311651	3	FACETS	0.956	0.909	1	0.956	0.909	1	CLONAL	3	TRUE	0	0.374297131814532	3		385	699	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467754	99467754	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	42	244	0	ENST00000268035.6:c.2623G>T	p.Asp875Tyr	p.D875Y	ENST00000268035	NM_000875.3	875	Gat/Tat	13/21	0.190059652522871	5	FACETS	0.701	0.585	0.83	0.234	0.195	0.277	INDETERMINATE	1	TRUE	2	0.374297131814532	5		244	500	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813855	50813855	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	47	581	0	ENST00000398568.2:c.1409G>T	p.Gly470Val	p.G470V	ENST00000398568	NM_001042412.1	470	gGc/gTc	8/18	1	2	FACETS	0.272	0.228	0.32	0.272	0.228	0.32	SUBCLONAL	1	TRUE	1	0.374297131814532	2		581	924	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579361	7579363	+	inframe_deletion	In_Frame_Del	DEL	AAA	AAA	-	rs1567555808	NA	P-0040578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	52	713	0	ENST00000269305.4:c.324_326del	p.Phe109del	p.F109del	ENST00000269305	NM_001126112.2	108	ggTTTc/ggc	4/11	0.324165533368055	2	FACETS	0.267	0.226	0.312	0.134	0.113	0.156	SUBCLONAL	1	TRUE	0	0.374297131814532	2		713	1040	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243573	41243573	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	196	488	0	ENST00000357654.3:c.3975G>T	p.Arg1325Ser	p.R1325S	ENST00000357654	NM_007294.3	1325	agG/agT	10/23	0.324165533368055	2	FACETS	0.803	0.747	0.861	0.803	0.747	0.861	CLONAL	2	TRUE	0	0.374297131814532	2		488	652	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533090	63533090	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	67	599	1	ENST00000307078.5:c.1804G>T	p.Gly602Ter	p.G602*	ENST00000307078	NM_004655.3	602	Gga/Tga	7/11	0.180823794451581	2	FACETS	0.428	0.371	0.49	0.214	0.185	0.245	INDETERMINATE	1	TRUE	0	0.374297131814532	2		600	836	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29099497	29099497	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	102	222	0	ENST00000328354.6:c.904G>T	p.Glu302Ter	p.E302*	ENST00000328354	NM_007194.3	302	Gaa/Taa	8/15	0.374297131814532	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.374297131814532	2		222	255	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202850	128202850	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1179739809	NA	P-0040578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	359	505	0	ENST00000341105.2:c.872-2A>G		p.X291_splice	ENST00000341105	NM_032638.4	291			0.339315792807023	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.374297131814532	3		505	1055	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149498320	149498320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	141	582	0	ENST00000261799.4:c.2894G>T	p.Gly965Val	p.G965V	ENST00000261799	NM_002609.3	965	gGt/gTt	21/23	0.34441806475538	2	FACETS	0.9	0.82	0.984	0.45	0.41	0.492	CLONAL	1	TRUE	0	0.374297131814532	2		582	837	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161807896	161807896	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	130	313	0	ENST00000366898.1:c.1097G>C	p.Arg366Pro	p.R366P	ENST00000366898	NM_004562.2	366	cGg/cCg	10/12	0.347329739503172	2	FACETS	0.831	0.76	0.904	0.831	0.76	0.904	CLONAL	2	TRUE	0	0.374297131814532	2		313	418	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6037052	6037052	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs201395630	NA	P-0040578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	180	279	0	ENST00000265849.7:c.708G>T	p.Leu236Phe	p.L236F	ENST00000265849	NM_000535.5	236	ttG/ttT	7/15	0.339315792807023	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.374297131814532	3		279	483	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339928	116339928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	118	289	0	ENST00000397752.3:c.790G>A	p.Val264Ile	p.V264I	ENST00000397752	NM_000245.2	264	Gtc/Atc	2/21	0.174752164035094	2	FACETS	0.847	0.772	0.925	0.847	0.772	0.925	INDETERMINATE	2	TRUE	0	0.374297131814532	2		289	372	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37006479	37006479	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	110	213	0	ENST00000358127.4:c.466C>A	p.His156Asn	p.H156N	ENST00000358127	NM_001280556.1	156	Cac/Aac	4/10	0.374297131814532	1	FACETS	0.758	0.69	0.828	1	0.986	1	SUBCLONAL	2	TRUE	0	0.374297131814532	1		213	315	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101909962	101909963	+	missense_variant	Missense_Mutation	DNP	TA	TA	AT	novel	NA	P-0040578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	12	156	0	ENST00000374994.4:c.1282_1283delinsAT	p.Tyr428Ile	p.Y428I	ENST00000374994	NM_004612.2	428	TAt/ATt	8/9	0.374297131814532	1	FACETS	0.32	0.225	0.435	0.32	0.225	0.435	SUBCLONAL	1	TRUE	0	0.374297131814532	1		156	163	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302957	15302998	+	frameshift_variant	Frame_Shift_Del	DEL	CCACCCGGCACTCATCCACGTCGCTTCGGCAGCTGCGGCCCT	CCACCCGGCACTCATCCACGTCGCTTCGGCAGCTGCGGCCCT	A	novel	NA	P-0040578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	120	813	0	ENST00000263388.2:c.452_493delinsT	p.Gln151LeufsTer2	p.Q151Lfs*2	ENST00000263388	NM_000435.2	151	cAGGGCCGCAGCTGCCGAAGCGACGTGGATGAGTGCCGGGTGGgt/cTgt	4/33	0.374297131814532	1	FACETS	0.545	0.491	0.601	0.545	0.491	0.601	SUBCLONAL	1	TRUE	0	0.374297131814532	1		813	957	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657674	37657674	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	182	530	0	ENST00000447079.4:c.2591A>T	p.Asn864Ile	p.N864I	ENST00000447079	NM_015083.1	864	aAc/aTc	6/14	0.256085044258426	0	FACETS	0.813	0.773	0.852			1	CLONAL	5	FALSE	0	0.256085044258426	0		530	260	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690810	89690813	+	frameshift_variant	Frame_Shift_Del	DEL	GAAA	GAAA	-	novel	NA	P-0040580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	405	344	0	ENST00000371953.3:c.219_222del	p.Glu73AspfsTer25	p.E73Dfs*25	ENST00000371953	NM_000314.4	73	GAAAga/ga	4/9	0.87951280164279	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.87951280164279	1		344	476	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817750	3817757	+	frameshift_variant	Frame_Shift_Del	DEL	GACTGAGA	GACTGAGA	AAC	novel	NA	P-0040580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	230	703	1	ENST00000262367.5:c.3214_3221delinsGTT	p.Ser1072ValfsTer13	p.S1072Vfs*13	ENST00000262367	NM_004380.2	1072	TCTCAGTCa/GTTa	16/31	0.87951280164279	1	FACETS	0.554	0.521	0.587	0.554	0.521	0.587	SUBCLONAL	1	TRUE	0	0.87951280164279	1		704	529	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817762	3817766	+	missense_variant	Missense_Mutation	ONP	GTGCC	GTGCC	AACGG	novel	NA	P-0040580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	43	729	1	ENST00000262367.5:c.3205_3209delinsCCGTT	p.Gly1069_Thr1070delinsProLeu	p.G1069_T1070delinsPL	ENST00000262367	NM_004380.2	1069	GGCACa/CCGTTa	16/31	0.87951280164279	1	FACETS	0.096	0.08	0.114	0.096	0.08	0.114	SUBCLONAL	1	TRUE	0	0.87951280164279	1		730	568	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250851	153250852	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAA	novel	NA	P-0040580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	395	477	0	ENST00000281708.4:c.1206_1208dup	p.Thr402_Leu403insPhe	p.T402_L403insF	ENST00000281708	NM_033632.3	403	tta/ttTTTa	8/12	0.87951280164279	1	FACETS	0.959	0.929	0.987	0.959	0.929	0.987	CLONAL	1	TRUE	0	0.87951280164279	1		477	525	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622141	117622141	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	38	304	0	ENST00000368508.3:c.6729del	p.Phe2243LeufsTer8	p.F2243Lfs*8	ENST00000368508	NM_002944.2	2243	ttT/tt	42/43	0.87951280164279	1	FACETS	0.116	0.096	0.139	0.116	0.096	0.139	SUBCLONAL	1	TRUE	0	0.87951280164279	1		304	416	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025533	1025533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1489679789	NA	P-0040581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	175	882	0	ENST00000358495.3:c.842C>T	p.Thr281Met	p.T281M	ENST00000358495	NM_134424.2	281	aCg/aTg	9/12	0.676094446419562	3	FACETS	0.564	0.518	0.611	0.188	0.172	0.204	SUBCLONAL	1	TRUE	0	0.761245139931173	3		882	1126	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	198	63	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.542899109850219	4	FACETS	0.905	0.844	0.968	0.905	0.844	0.968	CLONAL	2	TRUE	2	0.592428552450935	4		63	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577567	7577567	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920789	NA	P-0040582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	217	771	0	ENST00000269305.4:c.714T>G	p.Cys238Trp	p.C238W	ENST00000269305	NM_001126112.2	238	tgT/tgG	7/11	0.572594548441208	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.592428552450935	1		771	457	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041630	14041630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368096448	NA	P-0040582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	159	571	0	ENST00000311895.7:c.2177G>A	p.Arg726His	p.R726H	ENST00000311895	NM_005236.2	726	cGc/cAc	11/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.592428552450935	2		571	507	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659599	88659599	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	363	745	0	ENST00000372037.3:c.382A>G	p.Asn128Asp	p.N128D	ENST00000372037	NM_004329.2	128	Aat/Gat	6/13	0.592428552450935	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.592428552450935	2		745	596	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974769	21974787	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCCGTGGCCAGCCAGTC	CGGCCGTGGCCAGCCAGTC	-	novel	NA	P-0040582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	161	274	1	ENST00000304494.5:c.40_58del	p.Asp14ArgfsTer6	p.D14Rfs*6	ENST00000304494	NM_000077.4	14	GACTGGCTGGCCACGGCCGcg/cg	1/3	0.585325178492004	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.592428552450935	2		275	259	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342374	70342374	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752746769	NA	P-0040582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	221	397	0	ENST00000374080.3:c.1265G>A	p.Arg422Gln	p.R422Q	ENST00000374080		422	cGg/cAg	9/45	1	1	FACETS	0.777	0.74	0.813	1	0.994	1	SUBCLONAL	2	TRUE	0	0.592428552450935	1		397	338	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676268	37676268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	1246	616	0	ENST00000447079.4:c.3023G>A	p.Arg1008Gln	p.R1008Q	ENST00000447079	NM_015083.1	1008	cGg/cAg	11/14	0.348260956651757	6	FACETS	0.976	0.966	0.985			1	INDETERMINATE	7	TRUE	NA	0.594051326340211	6		616	1344	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344782	118344783	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	158	342	0	ENST00000534358.1:c.2914dup	p.Thr972AsnfsTer26	p.T972Nfs*26	ENST00000534358	NM_005933.3	970	gaa/gAaa	3/36	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.594051326340211	2		342	431	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726609	41726609	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	399	733	0	ENST00000301178.4:c.154G>A	p.Gly52Ser	p.G52S	ENST00000301178	NM_021913.4	52	Ggc/Agc	2/20	NA	2	FACETS	0.76	0.726	0.794			1	INDETERMINATE	2	TRUE	NA	0.594051326340211	2		733	884	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778045	27778045	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs900372657	NA	P-0040588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	574	478	0	ENST00000369163.2:c.194A>G	p.Lys65Arg	p.K65R	ENST00000369163	NM_003536.2	65	aAg/aGg	1/1	0.593279419130752	4	FACETS	1	0.994	1			1	CLONAL	3	TRUE	NA	0.594051326340211	4		478	930	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0040591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	89	233	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.212271502275438	2		235	590	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743943	40743943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs763964405	NA	P-0040591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	54	512	6	ENST00000373198.4:c.3052C>T	p.Arg1018Ter	p.R1018*	ENST00000373198	NM_133170.3	1018	Cga/Tga	23/32	1	2	FACETS	0.874	0.746	1	0.874	0.746	1	CLONAL	1	TRUE	1	0.212271502275438	2		518	582	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0040591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	119	881	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.212271502275438	2		881	927	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0040591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	27	403	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	0.164206795148983	2	FACETS	0.57	0.453	0.705	0.285	0.226	0.353	SUBCLONAL	1	TRUE	0	0.212271502275438	2		403	446	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276714	15276714	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376590511	NA	P-0040591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	83	979	0	ENST00000263388.2:c.5551C>T	p.Arg1851Cys	p.R1851C	ENST00000263388	NM_000435.2	1851	Cgt/Tgt	30/33	1	2	FACETS	0.827	0.728	0.933	0.827	0.728	0.933	CLONAL	1	TRUE	1	0.212271502275438	2		979	946	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555299	226555299	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	35	513	0	ENST00000366794.5:c.2288A>G	p.Glu763Gly	p.E763G	ENST00000366794	NM_001618.3	763	gAa/gGa	17/23	0.212271502275438	2	FACETS	0.53	0.433	0.639	0.265	0.216	0.32	SUBCLONAL	1	TRUE	0	0.212271502275438	2		513	622	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246667	46246684	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTGGTCCCGCAGGTAAG	TGTGGTCCCGCAGGTAAG	-	novel	NA	P-0040591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	15	200	0	ENST00000334344.6:c.4762_4773+6del		p.X1588_splice	ENST00000334344	NM_152641.2	1588		15/21	1	2	FACETS	0.689	0.505	0.91	0.689	0.505	0.91	SUBCLONAL	1	TRUE	1	0.212271502275438	2		200	205	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0040592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	42	233	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.171903359596745	3	FACETS	0.659	0.549	0.781	0.329	0.274	0.391	SUBCLONAL	1	TRUE	1	0.23	3		235	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0040592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	69	683	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	0.634	0.551	0.725	0.634	0.551	0.725	SUBCLONAL	1	TRUE	1	0.23	2		683	946	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220707	1220707	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	105	731	1	ENST00000326873.7:c.725G>T	p.Gly242Val	p.G242V	ENST00000326873	NM_000455.4	242	gGg/gTg	5/10	1	2	FACETS	0.965	0.863	1	0.965	0.863	1	CLONAL	1	TRUE	1	0.23	2		732	946	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500891	8500891	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	75	568	0	ENST00000356435.5:c.1991G>T	p.Gly664Val	p.G664V	ENST00000356435		664	gGa/gTa	13/35	1	2	FACETS	0.837	0.733	0.95	0.837	0.733	0.95	CLONAL	1	TRUE	1	0.23	2		568	779	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412656	63412656	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	55	769	0	ENST00000330258.3:c.511G>T	p.Gly171Cys	p.G171C	ENST00000330258	NM_152424.3	171	Ggc/Tgc	2/2	1	2	FACETS	0.507	0.432	0.59	0.507	0.432	0.59	SUBCLONAL	1	TRUE	1	0.23	2		769	943	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858095	152858095	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	77	962	0	ENST00000406277.2:c.520del	p.Asp174ThrfsTer170	p.D174Tfs*170	ENST00000406277	NM_152274.4	174	Gac/ac	6/7	1	2	FACETS	0.579	0.506	0.657	0.579	0.506	0.657	SUBCLONAL	1	TRUE	1	0.23	2		962	1157	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654857	29654857	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	41	292	0	ENST00000356175.3:c.5546G>T	p.Arg1849Leu	p.R1849L	ENST00000356175	NM_000267.3	1849	cGg/cTg	37/57	1	2	FACETS	0.983	0.825	1	0.983	0.825	1	CLONAL	1	TRUE	1	0.343320492439075	2		292	243	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148948	119148948	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs267606707	NA	P-0040594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	74	523	0	ENST00000264033.4:c.1168G>T	p.Asp390Tyr	p.D390Y	ENST00000264033	NM_005188.3	390	Gat/Tat	8/16	0.343320492439075	1	FACETS	0.854	0.751	0.964	0.854	0.751	0.964	CLONAL	1	TRUE	0	0.343320492439075	1		523	418	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250912	10250912	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	152	793	0	ENST00000340748.4:c.3568G>C	p.Asp1190His	p.D1190H	ENST00000340748		1190	Gac/Cac	32/40	1	2	FACETS	0.945	0.864	1	0.945	0.864	1	CLONAL	1	TRUE	1	0.343320492439075	2		793	937	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175796	24175796	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	131	706	0	ENST00000263121.7:c.1024A>G	p.Asn342Asp	p.N342D	ENST00000263121	NM_003073.3	342	Aac/Gac	8/9	0.132376713810558	5	FACETS	1	0.972	1	0.296	0.268	0.326	INDETERMINATE	1	TRUE	1	0.343320492439075	5		706	975	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058603	47058603	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	103	654	0	ENST00000409792.3:c.7675G>C	p.Glu2559Gln	p.E2559Q	ENST00000409792	NM_014159.6	2559	Gag/Cag	21/21	1	2	FACETS	0.784	0.702	0.872	0.784	0.702	0.872	SUBCLONAL	1	TRUE	1	0.343320492439075	2		654	765	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670907	30670907	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	136	917	0	ENST00000376406.3:c.5839A>T	p.Ile1947Phe	p.I1947F	ENST00000376406	NM_014641.2	1947	Att/Ttt	12/15	0.270143615166541	4	FACETS	0.815	0.739	0.895	0.272	0.246	0.299	CLONAL	1	TRUE	1	0.343320492439075	4		917	1306	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670910	30670911	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	136	909	0	ENST00000376406.3:c.5835_5836insA	p.Pro1946ThrfsTer22	p.P1946Tfs*22	ENST00000376406	NM_014641.2	1945	-/A	12/15	0.270143615166541	4	FACETS	0.812	0.736	0.892	0.271	0.245	0.298	CLONAL	1	TRUE	1	0.343320492439075	4		909	1311	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564767	139564767	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	273	930	2	ENST00000308874.7:c.556G>A	p.Ala186Thr	p.A186T	ENST00000308874		186	Gcc/Acc	7/10	0.333810710959369	2	FACETS	0.835	0.785	0.887	0.835	0.785	0.887	CLONAL	2	TRUE	0	0.343320492439075	2		932	952	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624274	89624274	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs587782187	NA	P-0040595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	53	523	0	ENST00000371953.3:c.48T>A	p.Tyr16Ter	p.Y16*	ENST00000371953	NM_000314.4	16	taT/taA	1/9	0.585668927718556	1	FACETS	0.977	0.857	1	0.977	0.857	1	CLONAL	1	TRUE	0	0.585668927718556	1		523	131	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190405	32190405	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765988217	NA	P-0040595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	59	994	0	ENST00000375023.3:c.334G>A	p.Glu112Lys	p.E112K	ENST00000375023	NM_004557.3	112	Gag/Aag	3/30	0.126730865072893	4	FACETS	1	0.951	1	0.605	0.526	0.69	INDETERMINATE	1	TRUE	2	0.585668927718556	4		994	264	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577104	7577106	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0040595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	111	918	0	ENST00000269305.4:c.832_834del	p.Pro278del	p.P278del	ENST00000269305	NM_001126112.2	278	CCT/-	8/11	0.585668927718556	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.585668927718556	1		918	248	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0040597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	522	654	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.584591989927576	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.584591989927576	2		656	884	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88651917	88651917	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	87	517	0	ENST00000372037.3:c.264A>C	p.Glu88Asp	p.E88D	ENST00000372037	NM_004329.2	88	gaA/gaC	5/13	0.584591989927576	3	FACETS	0.517	0.457	0.581	0.258	0.228	0.291	SUBCLONAL	1	TRUE	1	0.584591989927576	3		517	744	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061257	38061257	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	567	825	0	ENST00000250448.2:c.732G>A	p.Trp244Ter	p.W244*	ENST00000250448	NM_004496.3	244	tgG/tgA	2/2	0.510647086786548	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.584591989927576	4		825	1439	SUCCESS
APC	324	MSKCC	GRCh37	5	112162944	112162944	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	194	367	0	ENST00000257430.4:c.1548+1del		p.K516fs	ENST00000257430	NM_000038.5	516	aaG/aa	12/16	0.584591989927576	2	FACETS	0.932	0.878	0.986	0.932	0.878	0.986	CLONAL	2	TRUE	0	0.584591989927576	2		367	356	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508137	106508137	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	78	324	0	ENST00000359195.3:c.131T>C	p.Leu44Pro	p.L44P	ENST00000359195	NM_002649.2	44	cTg/cCg	2/11	1	2	FACETS	0.855	0.759	0.957	0.855	0.759	0.957	CLONAL	1	TRUE	1	0.584591989927576	2		324	312	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189093	38189093	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	192	573	0	ENST00000317025.8:c.921A>T	p.Glu307Asp	p.E307D	ENST00000317025	NM_023034.1	307	gaA/gaT	5/24	0.584591989927576	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.584591989927576	1		573	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0040602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	406	547	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.345076863569939	5	FACETS	1	0.99	1	0.758	0.723	0.794	INDETERMINATE	2	TRUE	2	0.626372204869218	5		548	1105	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934874	NA	P-0040602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	476	513	0	ENST00000269305.4:c.451C>G	p.Pro151Ala	p.P151A	ENST00000269305	NM_001126112.2	151	Ccc/Gcc	5/11	0.345076863569939	5	FACETS	1	0.994	1	0.803	0.769	0.837	INDETERMINATE	2	TRUE	2	0.626372204869218	5		513	1224	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714657	52714657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	158	386	2	ENST00000322088.6:c.415G>A	p.Asp139Asn	p.D139N	ENST00000322088	NM_014225.5	139	Gac/Aac	4/15	0.626372204869218	4	FACETS	0.776	0.71	0.845			1	SUBCLONAL	1	TRUE	NA	0.626372204869218	4		388	1057	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692910	89692910	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	314	344	0	ENST00000371953.3:c.394G>T	p.Gly132Cys	p.G132C	ENST00000371953	NM_000314.4	132	Ggt/Tgt	5/9	0.623943840287854	3	FACETS	0.997	0.961	1	0.997	0.961	1	CLONAL	3	TRUE	0	0.626372204869218	3		344	440	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098959	178098959	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519921	NA	P-0040602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	164	158	0	ENST00000397062.3:c.86A>G	p.Asp29Gly	p.D29G	ENST00000397062	NM_006164.4	29	gAt/gGt	2/5	0.620470763723104	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.626372204869218	3		158	304	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255277	16255277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	485	339	0	ENST00000375759.3:c.2542C>T	p.Pro848Ser	p.P848S	ENST00000375759	NM_015001.2	848	Cct/Tct	11/15	0.625122611628779	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.626372204869218	3		339	655	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955449	48955450	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	221	213	0	ENST00000267163.4:c.1568dup	p.Leu523PhefsTer5	p.L523Ffs*5	ENST00000267163	NM_000321.2	522	aat/aaTt	17/27	0.625122611628779	3	FACETS	0.984	0.94	1	0.984	0.94	1	CLONAL	3	TRUE	0	0.626372204869218	3		213	314	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132580	11132580	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	225	414	0	ENST00000358026.2:c.2796C>G	p.Ile932Met	p.I932M	ENST00000358026	NM_001128849.1	932	atC/atG	19/36	0.620470763723104	3	FACETS	0.995	0.928	1	0.498	0.464	0.533	CLONAL	1	TRUE	1	0.626372204869218	3		414	948	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0040603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	47	184	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	1	2	FACETS	0.943	0.799	1	0.943	0.799	1	CLONAL	1	TRUE	1	0.272993487008474	2		184	365	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426582	49426582	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	133	493	0	ENST00000301067.7:c.11906A>T	p.Gln3969Leu	p.Q3969L	ENST00000301067	NM_003482.3	3969	cAg/cTg	39/54	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.272993487008474	2		493	959	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249239	133249239	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	108	427	0	ENST00000320574.5:c.1660A>G	p.Ser554Gly	p.S554G	ENST00000320574	NM_006231.2	554	Agc/Ggc	15/49	1	2	FACETS	0.863	0.773	0.958	0.863	0.773	0.958	CLONAL	1	TRUE	1	0.272993487008474	2		427	917	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29068917	29068917	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	56	216	0	ENST00000282397.4:c.64G>A	p.Gly22Arg	p.G22R	ENST00000282397	NM_002019.4	22	Gga/Aga	1/30	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.272993487008474	2		216	393	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637652	52637662	+	frameshift_variant	Frame_Shift_Del	DEL	TGAAAGAAGAA	TGAAAGAAGAA	-	novel	NA	P-0040603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	81	256	0	ENST00000394830.3:c.2654_2664del	p.Ile885ThrfsTer12	p.I885Tfs*12	ENST00000394830	NM_018313.4	885	aTTCTTCTTTCA/a	18/30	0.272993487008474	1	FACETS	0.949	0.838	1	0.949	0.838	1	CLONAL	1	TRUE	0	0.272993487008474	1		256	540	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056055	26056055	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	78	288	0	ENST00000343677.2:c.602A>C	p.Lys201Thr	p.K201T	ENST00000343677	NM_005319.3	201	aAg/aCg	1/1	0.241483286730936	4	FACETS	0.951	0.835	1	0.475	0.417	0.538	CLONAL	1	TRUE	2	0.272993487008474	4		288	765	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39935740	39935740	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	88	172	0	ENST00000378444.4:c.132A>C	p.Glu44Asp	p.E44D	ENST00000378444	NM_001123385.1	44	gaA/gaC	3/15	1	1	FACETS	0.756	0.675	0.842	1	0.98	1	SUBCLONAL	2	TRUE	0	0.272993487008474	1		172	368	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0040607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	53	411	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.150135700675679	2	FACETS	1	0.936	1	0.588	0.503	0.681	CLONAL	1	TRUE	0	0.232837674687871	2		411	387	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383707	42383707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782414774	NA	P-0040607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	54	556	0	ENST00000221972.3:c.482C>T	p.Thr161Met	p.T161M	ENST00000221972	NM_021601.3	161	aCg/aTg	3/5	1	2	FACETS	0.776	0.662	0.9	0.776	0.662	0.9	SUBCLONAL	1	TRUE	1	0.232837674687871	2		556	598	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822609	72822609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771122441	NA	P-0040607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	51	567	0	ENST00000268489.5:c.9566C>T	p.Ala3189Val	p.A3189V	ENST00000268489	NM_006885.3	3189	gCg/gTg	10/10	NA	3	FACETS	0.849	0.721	0.99	0.425	0.36	0.495	INDETERMINATE	1	TRUE	1	0.232837674687871	3		567	576	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032377	10032377	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1348316426	NA	P-0040607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	24	426	0	ENST00000330684.3:c.446C>T	p.Ala149Val	p.A149V	ENST00000330684	NM_001134407.1	149	gCg/gTg	3/13	0.232837674687871	1	FACETS	0.519	0.407	0.648	0.519	0.407	0.648	SUBCLONAL	1	TRUE	0	0.232837674687871	1		426	351	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439922	56439923	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCGGCACCGGATGC	novel	NA	P-0040607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	71	587	0	ENST00000407977.2:c.656_669dup	p.Pro224AlafsTer200	p.P224Afs*200	ENST00000407977		223	-/GCATCCGGTGCCGC	6/10	1	2	FACETS	0.866	0.756	0.986	0.866	0.756	0.986	CLONAL	1	TRUE	1	0.232837674687871	2		587	704	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591924	48591924	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	37	410	0	ENST00000342988.3:c.1087T>G	p.Cys363Gly	p.C363G	ENST00000342988	NM_005359.5	363	Tgt/Ggt	9/12	0.232837674687871	1	FACETS	0.731	0.604	0.874	0.731	0.604	0.874	SUBCLONAL	1	TRUE	0	0.232837674687871	1		410	384	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164671	36164671	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	76	677	0	ENST00000300305.3:c.1204T>G	p.Ser402Ala	p.S402A	ENST00000300305		402	Tcc/Gcc	8/8	1	2	FACETS	0.815	0.714	0.924	0.815	0.714	0.924	CLONAL	1	TRUE	1	0.232837674687871	2		677	801	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0040608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	38	335	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.438	0.361	0.524	0.438	0.361	0.524	SUBCLONAL	1	TRUE	1	0.29	2		335	598	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936083	178936083	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519927	NA	P-0040608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	40	444	0	ENST00000263967.3:c.1625A>T	p.Glu542Val	p.E542V	ENST00000263967	NM_006218.2	542	gAa/gTa	10/21	1	2	FACETS	0.584	0.485	0.695	0.584	0.485	0.695	SUBCLONAL	1	TRUE	1	0.29	2		444	472	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671558	30671558	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755871425	NA	P-0040608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	62	603	1	ENST00000376406.3:c.5402C>T	p.Pro1801Leu	p.P1801L	ENST00000376406	NM_014641.2	1801	cCg/cTg	10/15	1	2	FACETS	0.452	0.389	0.521	0.452	0.389	0.521	SUBCLONAL	1	TRUE	1	0.29	2		604	946	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690848	89690848	+	splice_donor_variant	Splice_Site	SNP	T	T	A	rs1224040268	NA	P-0040608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	23	298	0	ENST00000371953.3:c.253+2T>A		p.X85_splice	ENST00000371953	NM_000314.4	85			1	2	FACETS	0.4	0.311	0.502	0.4	0.311	0.502	SUBCLONAL	1	TRUE	1	0.29	2		298	397	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690795	89690803	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTTTTAGT	TCTTTTAGT	A	novel	NA	P-0040608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	24	282	0	ENST00000371953.3:c.210-8_210delinsA		p.X70_splice	ENST00000371953	NM_000314.4	70		4/9	1	2	FACETS	0.49	0.384	0.612	0.49	0.384	0.612	SUBCLONAL	1	TRUE	1	0.29	2		282	338	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521361	187521373	+	frameshift_variant	Frame_Shift_Del	DEL	TATGAACTTGGTC	TATGAACTTGGTC	GG	novel	NA	P-0040609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	191	585	1	ENST00000441802.2:c.11782_11794delinsCC	p.Asp3928ProfsTer17	p.D3928Pfs*17	ENST00000441802	NM_005245.3	3928	GACCAAGTTCATAct/CCct	22/27	1	2	FACETS	0.937	0.868	1	0.937	0.868	1	CLONAL	1	TRUE	1	0.545245668169468	2		586	748	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850328	128850329	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0040609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	244	721	3	ENST00000249373.3:c.1591_1592delinsAA	p.Ala531Asn	p.A531N	ENST00000249373	NM_005631.4	531	GCc/AAc	9/12	1	2	FACETS	0.899	0.84	0.959	0.899	0.84	0.959	CLONAL	1	TRUE	1	0.545245668169468	2		724	996	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151866304	151866304	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	54	384	0	ENST00000262189.6:c.9484C>A	p.Pro3162Thr	p.P3162T	ENST00000262189	NM_170606.2	3162	Cct/Act	41/59	1	2	FACETS	0.783	0.675	0.898	0.783	0.675	0.898	SUBCLONAL	1	TRUE	1	0.545245668169468	2		384	253	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176334	24176351	+	inframe_deletion	In_Frame_Del	DEL	GAGGCGTCTTGCCAACAC	GAGGCGTCTTGCCAACAC	-	novel	NA	P-0040609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	263	735	0	ENST00000263121.7:c.1126_1143del	p.Arg376_Thr381del	p.R376_T381del	ENST00000263121	NM_003073.3	375	atGAGGCGTCTTGCCAACACg/atg	9/9	1	2	FACETS	0.828	0.775	0.882	0.828	0.775	0.882	CLONAL	1	TRUE	1	0.545245668169468	2		735	1165	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597401	10597401	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	322	786	0	ENST00000171111.5:c.1802G>T	p.Arg601Leu	p.R601L	ENST00000171111	NM_203500.1	601	cGg/cTg	6/6	0.342408636629744	3	FACETS	0.861	0.814	0.908	0.861	0.814	0.908	CLONAL	2	FALSE	1	0.465405826518182	3		786	991	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022532	12022532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	106	707	0	ENST00000396373.4:c.638C>T	p.Ser213Phe	p.S213F	ENST00000396373	NM_001987.4	213	tCc/tTc	5/8	0.465405826518182	4	FACETS	0.683	0.611	0.759	0.341	0.305	0.38	SUBCLONAL	1	FALSE	2	0.465405826518182	4		707	978	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0040612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	231	488	0	ENST00000269305.4:c.673-2A>C		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.341423552761122	3	FACETS	1	0.988	1	0.792	0.746	0.838	CLONAL	2	FALSE	0	0.465405826518182	3		488	515	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974720	21974721	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs398123152	NA	P-0040612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	189	405	0	ENST00000304494.5:c.106dup	p.Ala36GlyfsTer8	p.A36Gfs*8	ENST00000304494	NM_000077.4	36	gcg/gGcg	1/3	0.423004417397617	3	FACETS	1	0.981	1	0.753	0.704	0.803	CLONAL	2	FALSE	0	0.465405826518182	3		405	443	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634747	158634747	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1267861432	NA	P-0040612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	28	405	0	ENST00000263640.3:c.439C>T	p.Arg147Ter	p.R147*	ENST00000263640	NM_001105.4	147	Cga/Tga	5/11	0.342408636629744	3	FACETS	0.32	0.255	0.395	0.16	0.127	0.198	SUBCLONAL	1	FALSE	1	0.465405826518182	3		405	463	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4388017	4388017	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	152	501	0	ENST00000261254.3:c.503C>A	p.Pro168His	p.P168H	ENST00000261254	NM_001759.3	168	cCc/cAc	3/5	0.343482340077652	4	FACETS	0.794	0.729	0.861			1	SUBCLONAL	2	FALSE	NA	0.465405826518182	4		501	603	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715666	18715666	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	100	324	0	ENST00000266497.5:c.3497C>A	p.Pro1166His	p.P1166H	ENST00000266497		1166	cCt/cAt	25/31	NA	2	FACETS	1	0.969	1			1	INDETERMINATE	1	FALSE	NA	0.465405826518182	2		324	362	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442528	49442529	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0040612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	170	485	0	ENST00000301067.7:c.4044dup	p.Ser1349GlnfsTer2	p.S1349Qfs*2	ENST00000301067	NM_003482.3	1348	-/C	13/54	0.305998747336566	5	FACETS	0.86	0.793	0.93	0.574	0.529	0.62	CLONAL	2	FALSE	2	0.465405826518182	5		485	721	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95556929	95556929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	84	576	0	ENST00000393063.1:c.5675G>A	p.Gly1892Asp	p.G1892D	ENST00000393063	NM_030621.3	1892	gGt/gAt	28/28	0.465405826518182	3	FACETS	0.7	0.618	0.787	0.35	0.309	0.394	SUBCLONAL	1	FALSE	1	0.465405826518182	3		576	636	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964751	15964751	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	80	569	0	ENST00000268712.3:c.5845G>A	p.Glu1949Lys	p.E1949K	ENST00000268712	NM_006311.3	1949	Gaa/Aaa	37/46	0.341423552761122	3	FACETS	0.587	0.516	0.663	0.196	0.172	0.221	SUBCLONAL	1	FALSE	0	0.465405826518182	3		569	722	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600333	10600333	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	115	629	0	ENST00000171111.5:c.1522A>C	p.Ser508Arg	p.S508R	ENST00000171111	NM_203500.1	508	Agc/Cgc	4/6	0.342408636629744	3	FACETS	0.83	0.748	0.916	0.415	0.374	0.458	CLONAL	1	FALSE	1	0.465405826518182	3		629	734	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99162534	99162534	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	75	280	0	ENST00000074304.5:c.1052C>T	p.Ser351Leu	p.S351L	ENST00000074304	NM_001134224.1	351	tCa/tTa	12/26	0.342408636629744	3	FACETS	1	0.957	1	0.593	0.524	0.666	CLONAL	1	FALSE	1	0.465405826518182	3		280	335	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535345	187535345	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	259	453	0	ENST00000441802.2:c.9229G>C	p.Gly3077Arg	p.G3077R	ENST00000441802	NM_005245.3	3077	Ggt/Cgt	12/27	0.389126701166571	3	FACETS	0.931	0.884	0.979	0.931	0.884	0.979	CLONAL	3	FALSE	0	0.465405826518182	3		453	491	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554917	187554917	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs750458666	NA	P-0040612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	292	541	0	ENST00000441802.2:c.4244A>G	p.Lys1415Arg	p.K1415R	ENST00000441802	NM_005245.3	1415	aAa/aGa	7/27	0.389126701166571	3	FACETS	0.932	0.888	0.977	0.932	0.888	0.977	CLONAL	3	FALSE	0	0.465405826518182	3		541	553	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665292	176665292	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	68	462	0	ENST00000439151.2:c.3976C>G	p.Gln1326Glu	p.Q1326E	ENST00000439151	NM_022455.4	1326	Cag/Gag	7/23	0.465405826518182	3	FACETS	0.591	0.514	0.674			1	SUBCLONAL	1	FALSE	NA	0.465405826518182	3		462	610	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148516774	148516774	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	59	317	0	ENST00000320356.2:c.913C>G	p.His305Asp	p.H305D	ENST00000320356	NM_004456.4	305	Cat/Gat	9/20	0.409852008875256	5	FACETS	0.765	0.658	0.881	0.255	0.219	0.294	SUBCLONAL	1	FALSE	2	0.465405826518182	5		317	563	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38178602	38178602	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	185	464	0	ENST00000317025.8:c.1797C>G	p.Ile599Met	p.I599M	ENST00000317025	NM_023034.1	599	atC/atG	8/24	0.411067661378683	2	FACETS	0.793	0.739	0.849	0.793	0.739	0.849	SUBCLONAL	2	FALSE	0	0.465405826518182	2		464	501	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341940	8341940	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1360063110	NA	P-0040612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	220	373	0	ENST00000356435.5:c.4700A>T	p.Asp1567Val	p.D1567V	ENST00000356435		1567	gAt/gTt	29/35	0.423004417397617	3	FACETS	0.881	0.831	0.931	0.881	0.831	0.931	CLONAL	3	FALSE	0	0.465405826518182	3		373	441	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	305	395	0				ENST00000310581	NM_198253.2	-/1132			0.472998763839111	1	FACETS	0.764	0.729	0.798	0.764	0.729	0.798	INDETERMINATE	1	TRUE	0	0.848249807739201	1		395	542	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302906	15302906	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28933697	NA	P-0040613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	238	746	1	ENST00000263388.2:c.544C>T	p.Arg182Cys	p.R182C	ENST00000263388	NM_000435.2	182	Cgc/Tgc	4/33	1	2	FACETS	0.48	0.447	0.514	0.48	0.447	0.514	SUBCLONAL	1	TRUE	1	0.848249807739201	2		747	1169	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359364	118359364	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	236	396	0	ENST00000534358.1:c.4368C>G	p.His1456Gln	p.H1456Q	ENST00000534358	NM_005933.3	1456	caC/caG	11/36	1	2	FACETS	0.935	0.879	0.992	0.935	0.879	0.992	CLONAL	1	TRUE	1	0.848249807739201	2		396	595	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0040617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	358	626	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	0.7998623116518	2		626	825	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0040617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	162	286	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.7998623116518	2		286	396	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555733	21555736	+	protein_altering_variant	In_Frame_Del	DEL	GACA	GACA	C	novel	NA	P-0040617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	344	557	0	ENST00000382592.4:c.2534_2537delinsG	p.Val845_Ser846delinsGly	p.V845_S846delinsG	ENST00000382592	NM_014572.2	845	gTGTCt/gGt	6/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.7998623116518	2		557	831	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0040620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	75	374	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.45	2		374	323	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0040620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	119	487	0	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	0.0875346589741133	0	FACETS	0.609	0.552	0.667			1	INDETERMINATE	1	TRUE	0	0.45	0		487	478	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562821	95562821	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1218181729	NA	P-0040620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	59	368	0	ENST00000393063.1:c.4436A>G	p.Tyr1479Cys	p.Y1479C	ENST00000393063	NM_030621.3	1479	tAt/tGt	24/28	1	2	FACETS	0.947	0.822	1	0.947	0.822	1	CLONAL	1	TRUE	1	0.45	2		368	277	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273398	38273398	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	170	864	0	ENST00000425967.3:c.1937C>T	p.Ala646Val	p.A646V	ENST00000425967	NM_001174067.1	646	gCc/gTc	14/19	0.0875346589741133	0	FACETS	0.619	0.571	0.669			1	INDETERMINATE	1	TRUE	0	0.45	0		864	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0040642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	280	686	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.643314534473583	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.647139585935338	1		686	567	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110623	4110623	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201129499	NA	P-0040642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	207	553	1	ENST00000262948.5:c.334C>T	p.Arg112Trp	p.R112W	ENST00000262948	NM_030662.3	112	Cgg/Tgg	3/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.647139585935338	2		554	615	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0040642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	84	210	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	1	2	FACETS	0.947	0.848	1	0.947	0.848	1	CLONAL	1	TRUE	1	0.647139585935338	2		210	274	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256751	16256751	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199784733	NA	P-0040642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	145	529	1	ENST00000375759.3:c.4016G>A	p.Arg1339His	p.R1339H	ENST00000375759	NM_015001.2	1339	cGt/cAt	11/15	0.434673199244817	1	FACETS	0.7	0.645	0.757	0.7	0.645	0.757	SUBCLONAL	1	TRUE	0	0.647139585935338	1		530	433	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965421	18965421	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	81	369	0	ENST00000262803.5:c.1168G>C	p.Glu390Gln	p.E390Q	ENST00000262803	NM_002911.3	390	Gag/Cag	9/24	1	2	FACETS	0.715	0.635	0.8	0.715	0.635	0.8	SUBCLONAL	1	TRUE	1	0.647139585935338	2		369	350	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89869687	89869687	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	73	510	0	ENST00000389301.3:c.772G>C	p.Glu258Gln	p.E258Q	ENST00000389301	NM_000135.2	258	Gag/Cag	8/43	0.299280986325558	3	FACETS	0.354	0.309	0.403	0.118	0.103	0.135	INDETERMINATE	1	TRUE	0	0.647139585935338	3		510	843	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18963805	18963806	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0040642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	22	356	0	ENST00000262803.5:c.982_983del	p.Asn328HisfsTer10	p.N328Hfs*10	ENST00000262803	NM_002911.3	328	AAc/c	7/24	1	2	FACETS	0.183	0.142	0.232	0.183	0.142	0.232	SUBCLONAL	1	TRUE	1	0.647139585935338	2		356	371	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827951	40827951	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	94	500	0	ENST00000373198.4:c.2477C>A	p.Pro826His	p.P826H	ENST00000373198	NM_133170.3	826	cCc/cAc	17/32	0.647139585935338	4	FACETS	0.507	0.45	0.568	0.169	0.15	0.19	SUBCLONAL	1	TRUE	1	0.647139585935338	4		500	943	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535306	66535306	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	186	536	0	ENST00000273854.3:c.155C>T	p.Thr52Ile	p.T52I	ENST00000273854	NM_004439.5	52	aCc/aTc	1/18	0.434673199244817	1	FACETS	0.817	0.762	0.873	0.817	0.762	0.873	CLONAL	1	TRUE	0	0.647139585935338	1		536	476	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740356	145740356	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	284	695	0	ENST00000428558.2:c.1584G>T	p.Leu528Phe	p.L528F	ENST00000428558	NM_004260.3	528	ttG/ttT	9/22	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.647139585935338	2		695	781	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0040643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	153	621	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.30278637563913	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.29	1		622	679	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127733	64127733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	59	634	1	ENST00000334205.4:c.226G>A	p.Ala76Thr	p.A76T	ENST00000334205	NM_003942.2	76	Gcc/Acc	3/17	0.30278637563913	4	FACETS	0.832	0.715	0.959	0.277	0.238	0.32	CLONAL	1	TRUE	1	0.29	4		635	631	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405992	70405992	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	58	604	1	ENST00000373644.4:c.3506A>C	p.Gln1169Pro	p.Q1169P	ENST00000373644	NM_030625.2	1169	cAa/cCa	4/12	1	2	FACETS	0.574	0.492	0.663	0.574	0.492	0.663	SUBCLONAL	1	TRUE	1	0.29	2		605	697	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627592	14627592	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	98	483	0	ENST00000254322.2:c.478C>A	p.Gln160Lys	p.Q160K	ENST00000254322	NM_006145.1	160	Caa/Aaa	2/3	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.29	2		483	615	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0040644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	588	530	1	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.457490104847551	3	FACETS	1	0.987	1			1	CLONAL	3	TRUE	NA	0.560392280317961	3		531	871	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453412	40453435	+	inframe_deletion	In_Frame_Del	DEL	AGGCCACCATCATCAGTGAGCAGC	AGGCCACCATCATCAGTGAGCAGC	-	novel	NA	P-0040644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	640	174	0	ENST00000345506.4:c.1115_1138del	p.Thr372_Ala379del	p.T372_A379del	ENST00000345506	NM_003152.3	370	aAGGCCACCATCATCAGTGAGCAGCag/aag	10/20	1	2	FACETS	0.926	0.896	0.957	1	0.998	1	CLONAL	2	TRUE	1	0.560392280317961	2		174	1233	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0040652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	258	374	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.798310503445689	2		374	545	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16041510	16041510	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0040652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	78	187	0	ENST00000268712.3:c.1369A>T	p.Lys457Ter	p.K457*	ENST00000268712	NM_006311.3	457	Aaa/Taa	13/46	0.389399426967145	1	FACETS	0.498	0.444	0.553	0.498	0.444	0.553	INDETERMINATE	1	TRUE	0	0.798310503445689	1		187	236	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0040656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	157	798	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.288662767685345	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	0	0.33502390116674	2		800	467	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0040656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	87	233	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.114319926409694	4	FACETS	1	0.911	1	0.682	0.609	0.758	INDETERMINATE	2	TRUE	1	0.33502390116674	4		233	339	SUCCESS
APC	324	MSKCC	GRCh37	5	112174973	112174973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085227	NA	P-0040656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	175	70	0	ENST00000257430.4:c.3682C>T	p.Gln1228Ter	p.Q1228*	ENST00000257430	NM_000038.5	1228	Cag/Tag	16/16	0.33502390116674	3	FACETS	0.968	0.919	1	1	0.994	1	CLONAL	5	TRUE	0	0.33502390116674	3		70	252	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43766907	43766907	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765177854	NA	P-0040656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	64	207	0	ENST00000382044.4:c.1144G>A	p.Val382Ile	p.V382I	ENST00000382044	NM_001141980.1	382	Gtt/Att	10/28	0.313273159724676	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	2	TRUE	0	0.33502390116674	2		207	187	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561217	9561217	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	28	333	0	ENST00000353224.5:c.565A>G	p.Lys189Glu	p.K189E	ENST00000353224	NM_177990.2	189	Aaa/Gaa	4/10	0.33502390116674	7	FACETS	0.606	0.483	0.746	0.121	0.096	0.15	SUBCLONAL	1	TRUE	2	0.33502390116674	7		333	507	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41554496	41554496	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0040656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	320	101	0	ENST00000263253.7:c.3582C>G	p.Tyr1194Ter	p.Y1194*	ENST00000263253	NM_001429.3	1194	taC/taG	19/31	0.33502390116674	3	FACETS	0.916	0.874	0.957	1	0.996	1	CLONAL	4	TRUE	1	0.33502390116674	3		101	609	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405927	157405928	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0040656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	115	443	0	ENST00000346085.5:c.2170dup	p.Ala724GlyfsTer39	p.A724Gfs*39	ENST00000346085	NM_020732.3	723	-/G	6/20	0.106331754754449	5	FACETS	1	0.969	1	0.776	0.704	0.851	INDETERMINATE	2	TRUE	2	0.33502390116674	5		443	443	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968137	68968137	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	46	449	0	ENST00000288368.4:c.1166T>A	p.Met389Lys	p.M389K	ENST00000288368	NM_024870.2	389	aTg/aAg	10/40	0.33502390116674	7	FACETS	0.869	0.731	1	0.217	0.182	0.256	CLONAL	1	TRUE	3	0.33502390116674	7		449	581	SUCCESS
APC	324	MSKCC	GRCh37	5	112157650	112157650	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1060503333	NA	P-0040668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	10	358	0	ENST00000257430.4:c.1370C>A	p.Ser457Ter	p.S457*	ENST00000257430	NM_000038.5	457	tCa/tAa	11/16	0.72741247637752	1	FACETS	0.175	0.119	0.244	0.175	0.119	0.244	SUBCLONAL	1	TRUE	0	0.72741247637752	1		358	100	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920217	1920217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200784805	NA	P-0040668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	165	651	0	ENST00000382891.5:c.1277C>T	p.Thr426Met	p.T426M	ENST00000382891	NM_133335.3	426	aCg/aTg	5/22	1	2	FACETS	0.688	0.634	0.744	0.688	0.634	0.744	SUBCLONAL	1	TRUE	1	0.72741247637752	2		651	659	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248394	59248394	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	84	367	0	ENST00000371222.2:c.349G>T	p.Ala117Ser	p.A117S	ENST00000371222	NM_002228.3	117	Gcc/Tcc	1/1	1	2	FACETS	0.704	0.628	0.784	0.704	0.628	0.784	SUBCLONAL	1	TRUE	1	0.72741247637752	2		367	328	SUCCESS
APC	324	MSKCC	GRCh37	5	112175643	112175643	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554085817	NA	P-0040668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	52	327	0	ENST00000257430.4:c.4353del	p.Val1452TyrfsTer21	p.V1452Yfs*21	ENST00000257430	NM_000038.5	1451	gAa/ga	16/16	0.72741247637752	1	FACETS	0.674	0.589	0.762	0.674	0.589	0.762	SUBCLONAL	1	TRUE	0	0.72741247637752	1		327	135	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426016	49426017	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTGTT	novel	NA	P-0040668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	139	803	0	ENST00000301067.7:c.12467_12471dup	p.Pro4158AsnfsTer5	p.P4158Nfs*5	ENST00000301067	NM_003482.3	4157	-/AACAG	39/54	1	2	FACETS	0.519	0.472	0.567	0.519	0.472	0.567	SUBCLONAL	1	TRUE	1	0.72741247637752	2		803	737	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935063	49935063	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1268792118	NA	P-0040668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	108	716	0	ENST00000296474.3:c.1936G>T	p.Gly646Cys	p.G646C	ENST00000296474	NM_002447.2	646	Ggc/Tgc	6/20	1	2	FACETS	0.356	0.319	0.395	0.356	0.319	0.395	SUBCLONAL	1	TRUE	1	0.72741247637752	2		716	835	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0040676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	130	621	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.401	0.363	0.441	0.401	0.363	0.441	SUBCLONAL	1	TRUE	1	0.65	2		622	997	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755606	39755606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	53	665	0	ENST00000288319.7:c.1159G>A	p.Ala387Thr	p.A387T	ENST00000288319	NM_182918.3	387	Gcc/Acc	10/10	1	2	FACETS	0.221	0.187	0.257	0.221	0.187	0.257	SUBCLONAL	1	TRUE	1	0.65	2		665	739	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756622	756622	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749885349	NA	P-0040676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	49	625	1	ENST00000314574.4:c.206C>T	p.Thr69Met	p.T69M	ENST00000314574	NM_005433.3	69	aCg/aTg	2/12	1	2	FACETS	0.21	0.177	0.246	0.21	0.177	0.246	SUBCLONAL	1	TRUE	1	0.65	2		626	719	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227679	36227681	+	inframe_deletion	In_Frame_Del	DEL	CGA	CGA	-	novel	NA	P-0040676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	65	791	0	ENST00000222270.7:c.7248_7250del	p.Phe2416_Glu2417delinsLeu	p.F2416_E2417delinsL	ENST00000222270	NM_014727.1	2416	ttCGAg/ttg	31/37	1	2	FACETS	0.214	0.185	0.246	0.214	0.185	0.246	SUBCLONAL	1	TRUE	1	0.65	2		791	933	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027887	48027887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752839086	NA	P-0040683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	36	358	0	ENST00000234420.5:c.2765G>A	p.Arg922Gln	p.R922Q	ENST00000234420	NM_000179.2	922	cGa/cAa	4/10	0.241400104323893	5	FACETS	0.846	0.7	1	0.564	0.467	0.672	CLONAL	2	TRUE	2	0.241400104323893	5		358	240	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612890	228612890	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	74	571	2	ENST00000366696.1:c.137C>A	p.Thr46Lys	p.T46K	ENST00000366696	NM_003493.2	46	aCg/aAg	1/1	0.241400104323893	5	FACETS	0.934	0.821	1	0.623	0.547	0.704	CLONAL	2	TRUE	2	0.241400104323893	5		573	447	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683697	162683697	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528661586	NA	P-0040684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	71	473	0	ENST00000366898.1:c.272C>T	p.Ala91Val	p.A91V	ENST00000366898	NM_004562.2	91	gCg/gTg	3/12	0.513760533472675	2	FACETS	0.404	0.352	0.459	0.202	0.176	0.23	SUBCLONAL	1	TRUE	0	0.546160298609347	2		473	644	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578525	7578525	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519976	NA	P-0040684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	336	683	0	ENST00000269305.4:c.405C>G	p.Cys135Trp	p.C135W	ENST00000269305	NM_001126112.2	135	tgC/tgG	5/11	0.546160298609347	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.546160298609347	1		683	844	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242475	+	protein_altering_variant	In_Frame_Del	DEL	GAATTAAGAG	GAATTAAGAG	C	novel	NA	P-0040684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	388	420	1	ENST00000275493.2:c.2236_2245delinsC	p.Glu746_Glu749delinsGln	p.E746_E749delinsQ	ENST00000275493	NM_005228.3	746	GAATTAAGAGaa/Caa	19/28	0.546160298609347	4	FACETS	0.953	0.907	1	0.636	0.604	0.667	CLONAL	2	TRUE	1	0.546160298609347	4		421	1152	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367345	50367345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	64	427	0	ENST00000331340.3:c.152G>A	p.Arg51Lys	p.R51K	ENST00000331340	NM_006060.4	51	aGa/aAa	3/8	0.546160298609347	4	FACETS	0.315	0.271	0.362	0.105	0.09	0.121	SUBCLONAL	1	TRUE	1	0.546160298609347	4		427	1151	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534710	18534710	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	32	392	0	ENST00000266497.5:c.1768C>G	p.Leu590Val	p.L590V	ENST00000266497		590	Ctc/Gtc	12/31	0.546160298609347	1	FACETS	0.154	0.124	0.187	0.154	0.124	0.187	SUBCLONAL	1	TRUE	0	0.546160298609347	1		392	554	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058213	42058213	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	49	266	0	ENST00000219905.7:c.7933T>G	p.Leu2645Val	p.L2645V	ENST00000219905	NM_001164273.1	2645	Tta/Gta	24/24	0.199749600587973	1	FACETS	0.354	0.301	0.413	0.354	0.301	0.413	INDETERMINATE	1	TRUE	0	0.546160298609347	1		266	368	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0040685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	72	273	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.369668183533496	1	FACETS	0.482	0.423	0.546	0.482	0.423	0.546	SUBCLONAL	1	TRUE	0	0.54242806089185	1		273	401	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0040685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	126	366	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	0.907	0.826	0.992	0.907	0.826	0.992	CLONAL	1	TRUE	1	0.54242806089185	2		366	512	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119884	70119884	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	44	537	1	ENST00000245479.2:c.886C>T	p.Gln296Ter	p.Q296*	ENST00000245479	NM_000346.3	296	Cag/Tag	3/3	0.429801347567429	1	FACETS	0.174	0.145	0.206	0.174	0.145	0.206	SUBCLONAL	1	TRUE	0	0.54242806089185	1		538	679	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469956	157469956	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	177	493	1	ENST00000346085.5:c.2754del	p.Ser919ValfsTer20	p.S919Vfs*20	ENST00000346085	NM_020732.3	917	aCc/ac	9/20	0.369668183533496	1	FACETS	0.749	0.693	0.807	0.749	0.693	0.807	SUBCLONAL	1	TRUE	0	0.54242806089185	1		494	635	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933481	100933481	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	38	180	0	ENST00000325455.5:c.1909C>G	p.Arg637Gly	p.R637G	ENST00000325455	NM_001202474.3	637	Cga/Gga	4/8	1	2	FACETS	0.601	0.501	0.712	0.601	0.501	0.712	SUBCLONAL	1	TRUE	1	0.54242806089185	2		180	233	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577113	7577114	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0040685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	268	640	0	ENST00000269305.4:c.824dup	p.Cys275TrpfsTer31	p.C275Wfs*31	ENST00000269305	NM_001126112.2	275	tgt/tgGt	8/11	0.528520433918308	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.54242806089185	1		640	712	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489513	40489513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1221396883	NA	P-0040685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	54	536	0	ENST00000264657.5:c.737G>A	p.Arg246Gln	p.R246Q	ENST00000264657	NM_139276.2	246	cGg/cAg	8/24	NA	2	FACETS	0.23	0.196	0.268			1	INDETERMINATE	1	TRUE	NA	0.54242806089185	2		536	865	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1555525367	NA	P-0040689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	140	279	0	ENST00000269305.4:c.783-1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.412378235028378	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.412378235028378	1		279	458	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982094	201982095	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	98	667	0	ENST00000359651.3:c.619dup	p.Ser207PhefsTer10	p.S207Ffs*10	ENST00000359651		206	-/T	5/8	0.4101964086144	1	FACETS	0.541	0.483	0.603	0.541	0.483	0.603	SUBCLONAL	1	TRUE	0	0.412378235028378	1		667	697	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604671	48604671	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0040689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	62	377	0	ENST00000342988.3:c.1493T>G	p.Leu498Ter	p.L498*	ENST00000342988	NM_005359.5	498	tTa/tGa	12/12	0.407097698363489	1	FACETS	0.918	0.801	1	0.918	0.801	1	CLONAL	1	TRUE	0	0.412378235028378	1		377	260	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420057	152420057	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	75	506	0	ENST00000206249.3:c.1744T>C	p.Tyr582His	p.Y582H	ENST00000206249	NM_000125.3	582	Tat/Cat	8/8	0.4101964086144	1	FACETS	0.764	0.673	0.86	0.764	0.673	0.86	SUBCLONAL	1	TRUE	0	0.412378235028378	1		506	378	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974675	21974675	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1060501265	NA	P-0040689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	108	465	0	ENST00000304494.5:c.150+2T>C		p.X50_splice	ENST00000304494	NM_000077.4	50			0.369937367123289	0	FACETS	0.773	0.7	0.85			1	SUBCLONAL	1	TRUE	0	0.412378235028378	0		465	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0040690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	291	673	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.415572111525723	2	FACETS	0.952	0.902	1	0.952	0.902	1	CLONAL	2	TRUE	0	0.429185190308959	2		673	712	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821930	59821930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200313471	NA	P-0040690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	68	367	0	ENST00000259008.2:c.2120G>A	p.Arg707His	p.R707H	ENST00000259008	NM_032043.2	707	cGt/cAt	15/20	0.368650611087397	4	FACETS	0.826	0.72	0.942	0.207	0.18	0.236	CLONAL	1	TRUE	0	0.429185190308959	4		367	548	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36022635	36022635	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	154	638	0	ENST00000358208.4:c.508A>G	p.Asn170Asp	p.N170D	ENST00000358208		170	Aac/Gac	5/12	0.429583967052623	3	FACETS	1	0.951	1	0.528	0.483	0.574	CLONAL	1	TRUE	1	0.429185190308959	3		638	826	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858260	27858272	+	frameshift_variant	Frame_Shift_Del	DEL	AGACCCACCAGAT	AGACCCACCAGAT	-	novel	NA	P-0040690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	192	577	0	ENST00000359303.2:c.299_311del	p.Tyr100SerfsTer?	p.Y100Sfs*?	ENST00000359303	NM_003535.2	100	tATCTGGTGGGTCTc/tc	1/1	0.429583967052623	4	FACETS	0.794	0.736	0.855	0.794	0.736	0.855	SUBCLONAL	2	TRUE	2	0.429185190308959	4		577	805	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902290	151902290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301632462	NA	P-0040690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	54	114	0	ENST00000262189.6:c.3862C>T	p.Arg1288Trp	p.R1288W	ENST00000262189	NM_170606.2	1288	Cgg/Tgg	25/59	0.429185190308959	6	FACETS	0.779	0.67	0.897	0.26	0.223	0.299	SUBCLONAL	2	TRUE	0	0.429185190308959	6		114	300	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0040693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	343	626	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	0.735390111174085	2		626	924	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442495	52442569	+	inframe_deletion	In_Frame_Del	DEL	GGGCAAAGAACATGTTATTCACAATATCATCATCAATCACGGACGTATCATCCACCAAGGTAGAGACCTTTCGCC	GGGCAAAGAACATGTTATTCACAATATCATCATCAATCACGGACGTATCATCCACCAAGGTAGAGACCTTTCGCC	-	novel	NA	P-0040693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	74	465	0	ENST00000460680.1:c.176_250del	p.Arg59_Ala83del	p.R59_A83del	ENST00000460680	NM_004656.3	59	cGGCGAAAGGTCTCTACCTTGGTGGATGATACGTCCGTGATTGATGATGATATTGTGAATAACATGTTCTTTGCCCac/cac	4/17	0.735390111174085	1	FACETS	0.515	0.457	0.576	0.515	0.457	0.576	SUBCLONAL	1	TRUE	0	0.735390111174085	1		465	247	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	261	63	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	1	0.978	1			1	INDETERMINATE	2	TRUE	NA	0.422245278466192	2		63	580	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0040694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	205	509	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.422245278466192	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.422245278466192	1		509	584	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955538	48955538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913303	NA	P-0040694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	210	411	1	ENST00000267163.4:c.1654C>T	p.Arg552Ter	p.R552*	ENST00000267163	NM_000321.2	552	Cga/Tga	17/27	0.422245278466192	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.422245278466192	2		412	471	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984016	2984016	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	266	691	0	ENST00000396946.4:c.514G>T	p.Glu172Ter	p.E172*	ENST00000396946	NM_032415.4	172	Gag/Tag	5/25	0.422245278466192	3	FACETS	0.945	0.89	1	0.945	0.89	1	CLONAL	2	TRUE	1	0.422245278466192	3		691	807	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733527	85733527	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200837308	NA	P-0040694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	50	498	1	ENST00000370580.1:c.485C>T	p.Thr162Met	p.T162M	ENST00000370580	NM_003921.4	162	aCg/aTg	3/3	0.422245278466192	3	FACETS	0.422	0.357	0.493	0.211	0.178	0.247	SUBCLONAL	1	TRUE	1	0.422245278466192	3		499	680	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	244006426	244006426	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0040694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	277	581	0	ENST00000263826.5:c.46+1G>T		p.X16_splice	ENST00000263826	NM_005465.4	16			0.422245278466192	2	FACETS	0.963	0.911	1	0.963	0.911	1	CLONAL	2	TRUE	0	0.422245278466192	2		581	681	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913492	32913492	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs397507346	NA	P-0040694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	127	571	0	ENST00000380152.3:c.5000C>G	p.Ser1667Ter	p.S1667*	ENST00000380152		1667	tCa/tGa	11/27	0.422245278466192	2	FACETS	0.958	0.87	1	0.479	0.435	0.525	CLONAL	1	TRUE	0	0.422245278466192	2		571	628	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246584	41246584	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	294	699	0	ENST00000357654.3:c.964G>T	p.Ala322Ser	p.A322S	ENST00000357654	NM_007294.3	322	Gct/Tct	10/23	0.422245278466192	2	FACETS	0.968	0.917	1	0.968	0.917	1	CLONAL	2	TRUE	0	0.422245278466192	2		699	719	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152220	99152220	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1451177166	NA	P-0040694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	81	403	0	ENST00000074304.5:c.299G>C	p.Ser100Thr	p.S100T	ENST00000074304	NM_001134224.1	100	aGt/aCt	6/26	1	2	FACETS	0.931	0.825	1	0.931	0.825	1	CLONAL	1	TRUE	1	0.422245278466192	2		403	412	SUCCESS
APC	324	MSKCC	GRCh37	5	112174211	112174212	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0040694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	133	490	1	ENST00000257430.4:c.2920_2921delinsTT	p.Gly974Phe	p.G974F	ENST00000257430	NM_000038.5	974	GGt/TTt	16/16	0.354392377345202	2	FACETS	0.754	0.691	0.818	0.754	0.691	0.818	SUBCLONAL	2	TRUE	0	0.422245278466192	2		491	418	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005873	69005873	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	54	517	0	ENST00000288368.4:c.2284G>T	p.Glu762Ter	p.E762*	ENST00000288368	NM_024870.2	762	Gag/Tag	21/40	0.422245278466192	2	FACETS	0.447	0.382	0.519	0.224	0.191	0.26	SUBCLONAL	1	TRUE	0	0.422245278466192	2		517	572	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252155	226252155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	21	144	0	ENST00000366813.1:c.103G>T	p.Gly35Trp	p.G35W	ENST00000366813		35	Ggg/Tgg	1/3	1	2	FACETS	0.893	0.707	1	1	0.94	1	CLONAL	2	TRUE	1	0.317939136440521	2		144	74	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109319907	109319907	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	10	649	0	ENST00000436639.2:c.781G>T	p.Ala261Ser	p.A261S	ENST00000436639	NM_014454.2	261	Gca/Tca	5/10	0.133682856211734	0	FACETS	0.228	0.154	0.321			1	INDETERMINATE	1	TRUE	0	0.317939136440521	0		649	188	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0040696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	102	531	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.324125074425681	3	FACETS	0.906	0.811	1	0.453	0.405	0.504	CLONAL	1	TRUE	1	0.350847096392865	3		531	754	SUCCESS
BLM	641	MSKCC	GRCh37	15	91328178	91328178	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	121	485	0	ENST00000355112.3:c.2690C>T	p.Ser897Phe	p.S897F	ENST00000355112	NM_000057.2	897	tCc/tTc	14/22	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.350847096392865	2		485	606	SUCCESS
AR	367	MSKCC	GRCh37	X	66765325	66765325	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	148	819	0	ENST00000374690.3:c.337G>T	p.Glu113Ter	p.E113*	ENST00000374690	NM_000044.3	113	Gaa/Taa	1/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.350847096392865	2		819	778	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023191	27023191	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	31	145	0	ENST00000324856.7:c.298del	p.Leu100Ter	p.L100*	ENST00000324856	NM_006015.4	99	gaC/ga	1/20	0.350847096392865	1	FACETS	0.889	0.727	1	0.889	0.727	1	CLONAL	1	TRUE	0	0.350847096392865	1		145	164	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103508437	103508437	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	80	306	0	ENST00000355739.4:c.503G>C	p.Arg168Thr	p.R168T	ENST00000355739	NM_000123.3	168	aGa/aCa	5/15	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.350847096392865	2		306	451	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434824	110434824	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767707896	NA	P-0040696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	117	686	3	ENST00000375856.3:c.3577G>A	p.Gly1193Ser	p.G1193S	ENST00000375856	NM_003749.2	1193	Ggc/Agc	1/2	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.350847096392865	2		689	617	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005077	150005077	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	98	552	0	ENST00000253339.5:c.1148G>C	p.Gly383Ala	p.G383A	ENST00000253339		383	gGa/gCa	3/7	1	2	FACETS	0.895	0.8	0.996	0.895	0.8	0.996	CLONAL	1	TRUE	1	0.350847096392865	2		552	624	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0040699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	46	747	0	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	1	2	FACETS	0.616	0.518	0.726	0.616	0.518	0.726	SUBCLONAL	1	TRUE	1	0.222077246466492	2		747	672	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	37	444	0	ENST00000257430.4:c.4199del	p.Ser1400Ter	p.S1400*	ENST00000257430	NM_000038.5	1400	tCg/tg	16/16	0.222077246466492	1	FACETS	0.657	0.541	0.786	0.657	0.541	0.786	SUBCLONAL	1	TRUE	0	0.222077246466492	1		444	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912654	NA	P-0040699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	71	828	3	ENST00000269305.4:c.469G>A	p.Val157Ile	p.V157I	ENST00000269305	NM_001126112.2	157	Gtc/Atc	5/11	1	2	FACETS	0.717	0.624	0.817	0.717	0.624	0.817	SUBCLONAL	1	TRUE	1	0.222077246466492	2		831	892	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	161	441	2	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.974	0.903	1	0.974	0.903	1	CLONAL	1	TRUE	1	0.76884464301688	2		443	430	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	193	315	2	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.94	0.877	1	0.94	0.877	1	CLONAL	1	TRUE	1	0.76884464301688	2		317	534	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	57	101	1	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.206	0.176	0.239	0.206	0.176	0.239	SUBCLONAL	1	TRUE	1	0.76884464301688	2		102	720	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965666	90965666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	80	64	0	ENST00000265433.3:c.1651del	p.Arg551GlyfsTer8	p.R551Gfs*8	ENST00000265433	NM_002485.4	551	Agg/gg	11/16	1	2	FACETS	0.553	0.49	0.62	0.553	0.49	0.62	SUBCLONAL	1	TRUE	1	0.76884464301688	2		64	376	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415537	152415537	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519714	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	227	97	0	ENST00000206249.3:c.1387T>C	p.Ser463Pro	p.S463P	ENST00000206249	NM_000125.3	463	Tcc/Ccc	7/8	1	2	FACETS	0.865	0.809	0.921	0.865	0.809	0.921	CLONAL	1	TRUE	1	0.76884464301688	2		97	683	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610608	52610609	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	123	105	0	ENST00000394830.3:c.3564dup	p.Glu1189ArgfsTer6	p.E1189Rfs*6	ENST00000394830	NM_018313.4	1188	-/A	23/30	1	2	FACETS	0.63	0.572	0.69	0.63	0.572	0.69	SUBCLONAL	1	TRUE	1	0.76884464301688	2		105	508	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154242	2154242	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755455183	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	222	151	1	ENST00000434045.2:c.686del	p.Pro229GlnfsTer27	p.P229Qfs*27	ENST00000434045	NM_001127598.1	229	cCa/ca	5/5	1	2	FACETS	0.71	0.663	0.759	0.71	0.663	0.759	SUBCLONAL	1	TRUE	1	0.76884464301688	2		152	813	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	151	76	0	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.708	0.65	0.767	0.708	0.65	0.767	SUBCLONAL	1	TRUE	1	0.76884464301688	2		76	555	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991757	72991758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760959844	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	85	66	0	ENST00000268489.5:c.2287dup	p.Glu763GlyfsTer26	p.E763Gfs*26	ENST00000268489	NM_006885.3	763	gag/gGag	2/10	1	2	FACETS	0.533	0.473	0.596	0.533	0.473	0.596	SUBCLONAL	1	TRUE	1	0.76884464301688	2		66	415	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	201	555	6	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.729	0.678	0.782	0.729	0.678	0.782	SUBCLONAL	1	TRUE	1	0.76884464301688	2		561	717	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339110	65339111	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	160	115	0	ENST00000342505.4:c.425dup	p.Ile143AspfsTer9	p.I143Dfs*9	ENST00000342505	NM_002227.2	142	aag/aaAg	5/25	1	2	FACETS	0.646	0.595	0.7	0.646	0.595	0.7	SUBCLONAL	1	TRUE	1	0.76884464301688	2		115	644	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231107	53231107	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	86	124	0	ENST00000375401.3:c.1795del	p.Arg599ValfsTer60	p.R599Vfs*60	ENST00000375401	NM_004187.3	599	Cgt/gt	13/26	1	2	FACETS	0.239	0.211	0.269	0.239	0.211	0.269	SUBCLONAL	1	TRUE	1	0.76884464301688	2		124	936	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943379	71943379	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1165709765	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	255	116	0	ENST00000298229.2:c.1711C>T	p.Arg571Trp	p.R571W	ENST00000298229	NM_001567.3	571	Cgg/Tgg	14/28	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.76884464301688	2		116	662	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37622730	37622730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758461304	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	214	109	0	ENST00000249071.6:c.562G>A	p.Ala188Thr	p.A188T	ENST00000249071	NM_002872.4	188	Gcc/Acc	6/7	1	2	FACETS	0.59	0.549	0.633	0.59	0.549	0.633	SUBCLONAL	1	TRUE	1	0.76884464301688	2		109	943	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426973	49426973	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1565778024	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	157	128	0	ENST00000301067.7:c.11515del	p.Gln3839SerfsTer42	p.Q3839Sfs*42	ENST00000301067	NM_003482.3	3839	Cag/ag	39/54	1	2	FACETS	0.56	0.514	0.608	0.56	0.514	0.608	SUBCLONAL	1	TRUE	1	0.76884464301688	2		128	729	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162750028	162750028	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771898787	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	117	59	0	ENST00000367921.3:c.2560G>A	p.Asp854Asn	p.D854N	ENST00000367921	NM_006182.2	854	Gac/Aac	18/18	0.76884464301688	3	FACETS	0.535	0.482	0.59	0.267	0.241	0.295	SUBCLONAL	1	TRUE	1	0.76884464301688	3		59	788	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156734	20156734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	192	64	0	ENST00000379607.5:c.23G>A	p.Gly8Glu	p.G8E	ENST00000379607	NM_001412.3	8	gGa/gAa	2/7	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.76884464301688	2		64	457	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129438	64129438	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	231	134	0	ENST00000334205.4:c.874del	p.Ala292HisfsTer83	p.A292Hfs*83	ENST00000334205	NM_003942.2	290	caG/ca	8/17	1	2	FACETS	0.663	0.619	0.709	0.663	0.619	0.709	SUBCLONAL	1	TRUE	1	0.76884464301688	2		134	906	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295278	1295278	+	upstream_gene_variant	5'Flank	SNP	C	C	T	rs914835735	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	193	67	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.914	0.852	0.978	0.914	0.852	0.978	CLONAL	1	TRUE	1	0.76884464301688	2		68	549	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023542	27023542	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	33	70	0	ENST00000324856.7:c.651del	p.Asn218ThrfsTer14	p.N218Tfs*14	ENST00000324856	NM_006015.4	216	taC/ta	1/20	1	2	FACETS	0.141	0.114	0.171	0.141	0.114	0.171	SUBCLONAL	1	TRUE	1	0.76884464301688	2		70	610	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448552	89448552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	275	123	0	ENST00000336596.2:c.1516G>A	p.Val506Ile	p.V506I	ENST00000336596	NM_005233.5	506	Gta/Ata	7/17	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.76884464301688	2		123	711	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22413164	22413164	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	90	50	0	ENST00000344548.3:c.291G>A	p.Trp97Ter	p.W97*	ENST00000344548	NM_001039802.1	97	tgG/tgA	6/7	1	2	FACETS	0.607	0.542	0.675	0.607	0.542	0.675	SUBCLONAL	1	TRUE	1	0.76884464301688	2		50	386	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246027124	246027125	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	159	137	0	ENST00000388985.4:c.877dup	p.Ile293AsnfsTer2	p.I293Nfs*2	ENST00000388985		293	att/aAtt	9/12	0.76884464301688	3	FACETS	0.547	0.501	0.596	0.274	0.25	0.298	SUBCLONAL	1	TRUE	1	0.76884464301688	3		137	1046	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653814	89653814	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	252	84	0	ENST00000371953.3:c.113del	p.Pro38LeufsTer16	p.P38Lfs*16	ENST00000371953	NM_000314.4	38	Cct/ct	2/9	0.741688146827882	2	FACETS	0.978	0.941	1	0.978	0.941	1	CLONAL	2	TRUE	0	0.76884464301688	2		84	335	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118354904	118354904	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	126	67	0	ENST00000534358.1:c.4093C>A	p.Pro1365Thr	p.P1365T	ENST00000534358	NM_005933.3	1365	Cca/Aca	9/36	1	2	FACETS	0.674	0.614	0.737	0.674	0.614	0.737	SUBCLONAL	1	TRUE	1	0.76884464301688	2		67	486	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480009	50480010	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1302818922	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	213	113	0	ENST00000394963.4:c.249dup	p.Asn84GlufsTer47	p.N84Efs*47	ENST00000394963	NM_003076.4	81	-/G	2/13	1	2	FACETS	0.693	0.645	0.742	0.693	0.645	0.742	SUBCLONAL	1	TRUE	1	0.76884464301688	2		113	800	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650714	67650714	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	346	103	0	ENST00000264010.4:c.1019A>T	p.His340Leu	p.H340L	ENST00000264010	NM_006565.3	340	cAt/cTt	5/12	1	2	FACETS	0.953	0.905	1	0.953	0.905	1	CLONAL	1	TRUE	1	0.76884464301688	2		103	944	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645379	215645379	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	69	123	0	ENST00000260947.4:c.1219G>C	p.Val407Leu	p.V407L	ENST00000260947	NM_000465.2	407	Gtg/Ctg	4/11	1	2	FACETS	0.288	0.25	0.328	0.288	0.25	0.328	SUBCLONAL	1	TRUE	1	0.76884464301688	2		123	624	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439722	220439722	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	206	139	0	ENST00000243786.2:c.575C>A	p.Pro192His	p.P192H	ENST00000243786	NM_002191.3	192	cCc/cAc	2/2	1	2	FACETS	0.604	0.561	0.649	0.604	0.561	0.649	SUBCLONAL	1	TRUE	1	0.76884464301688	2		139	887	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368471	225368471	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	78	75	0	ENST00000264414.4:c.1275del	p.Asp426MetfsTer29	p.D426Mfs*29	ENST00000264414	NM_003590.4	425	aaA/aa	9/16	1	2	FACETS	0.431	0.38	0.485	0.431	0.38	0.485	SUBCLONAL	1	TRUE	1	0.76884464301688	2		75	471	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30954230	30954230	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	59	80	0	ENST00000375687.4:c.101T>A	p.Ile34Asn	p.I34N	ENST00000375687	NM_015338.5	34	aTt/aAt	2/13	1	2	FACETS	0.315	0.271	0.362	0.315	0.271	0.362	SUBCLONAL	1	TRUE	1	0.76884464301688	2		80	488	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691871	30691871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1389197358	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	49	72	0	ENST00000295754.5:c.373G>A	p.Glu125Lys	p.E125K	ENST00000295754	NM_003242.5	125	Gaa/Aaa	3/7	1	2	FACETS	0.271	0.23	0.317	0.271	0.23	0.317	SUBCLONAL	1	TRUE	1	0.76884464301688	2		72	470	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1919891	1919892	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	93	104	0	ENST00000382891.5:c.953dup	p.Leu318PhefsTer64	p.L318Ffs*64	ENST00000382891	NM_133335.3	317	-/T	5/22	1	2	FACETS	0.393	0.349	0.439	0.393	0.349	0.439	SUBCLONAL	1	TRUE	1	0.76884464301688	2		104	616	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152102	55152102	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs777679907	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	247	133	0	ENST00000257290.5:c.2534A>G	p.His845Arg	p.H845R	ENST00000257290	NM_006206.4	845	cAt/cGt	18/23	1	2	FACETS	0.724	0.678	0.771	0.724	0.678	0.771	SUBCLONAL	1	TRUE	1	0.76884464301688	2		133	888	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249468	153249468	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	182	139	0	ENST00000281708.4:c.1310del	p.Gly437AspfsTer61	p.G437Dfs*61	ENST00000281708	NM_033632.3	437	gGa/ga	9/12	1	2	FACETS	0.955	0.888	1	0.955	0.888	1	CLONAL	1	TRUE	1	0.76884464301688	2		139	496	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589549	67589572	+	inframe_deletion	In_Frame_Del	DEL	AAAGAAGATAATATTGAAGCTGTA	AAAGAAGATAATATTGAAGCTGTA	-	novel	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	56	62	0	ENST00000274335.5:c.1312_1335del	p.Lys438_Val445del	p.K438_V445del	ENST00000274335		438	AAAGAAGATAATATTGAAGCTGTA/-	10/15	1	2	FACETS	0.694	0.603	0.79	0.694	0.603	0.79	SUBCLONAL	1	TRUE	1	0.76884464301688	2		62	210	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509711	106509711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	160	134	0	ENST00000359195.3:c.1705G>A	p.Ala569Thr	p.A569T	ENST00000359195	NM_002649.2	569	Gca/Aca	2/11	1	2	FACETS	0.713	0.657	0.771	0.713	0.657	0.771	SUBCLONAL	1	TRUE	1	0.76884464301688	2		134	584	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412766	63412766	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	51	125	0	ENST00000330258.3:c.401A>G	p.His134Arg	p.H134R	ENST00000330258	NM_152424.3	134	cAt/cGt	2/2	1	2	FACETS	0.18	0.152	0.21	0.18	0.152	0.21	SUBCLONAL	1	TRUE	1	0.76884464301688	2		125	738	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608282	100608282	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	73	144	0	ENST00000308731.7:c.1808A>C	p.Asn603Thr	p.N603T	ENST00000308731	NM_000061.2	603	aAc/aCc	18/19	1	2	FACETS	0.224	0.195	0.255	0.224	0.195	0.255	SUBCLONAL	1	TRUE	1	0.76884464301688	2		144	849	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391421	139391421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377112509	NA	P-0040729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	18	648	0	ENST00000277541.6:c.6770C>T	p.Ala2257Val	p.A2257V	ENST00000277541	NM_017617.3	2257	gCg/gTg	34/34	0.250864150125477	1	FACETS	0.38	0.286	0.492	0.38	0.286	0.492	SUBCLONAL	1	TRUE	0	0.250864150125477	1		648	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578408	7578411	+	frameshift_variant	Frame_Shift_Del	DEL	CCTC	CCTC	-	novel	NA	P-0040729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	55	566	0	ENST00000269305.4:c.519_522del	p.Arg174AlafsTer72	p.R174Afs*72	ENST00000269305	NM_001126112.2	173	gtGAGG/gt	5/11	0.250864150125477	1	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	0	0.250864150125477	1		566	363	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508919	106508919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748229046	NA	P-0040738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	115	518	0	ENST00000359195.3:c.913G>A	p.Val305Met	p.V305M	ENST00000359195	NM_002649.2	305	Gtg/Atg	2/11	0.710764728141277	6	FACETS	0.862	0.776	0.954	0.216	0.194	0.239	CLONAL	1	TRUE	2	0.710764728141277	6		518	909	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675238	40675239	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0040738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	208	660	1	ENST00000249776.8:c.202_203delinsTT	p.Ala68Phe	p.A68F	ENST00000249776	NM_033286.3	68	GCt/TTt	1/9	0.708654593736468	3	FACETS	0.981	0.912	1	0.49	0.456	0.526	CLONAL	1	TRUE	1	0.710764728141277	3		661	809	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243859016	243859016	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs397514606	NA	P-0040739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	13	178	0	ENST00000263826.5:c.49G>A	p.Glu17Lys	p.E17K	ENST00000263826	NM_005465.4	17	Gaa/Aaa	2/13	1	2	FACETS	0.69	0.503	0.907	0.69	0.503	0.907	SUBCLONAL	1	TRUE	1	0.570557683090613	2		178	66	SUCCESS
APC	324	MSKCC	GRCh37	5	112176020	112176020	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	46	190	0	ENST00000257430.4:c.4729G>T	p.Glu1577Ter	p.E1577*	ENST00000257430	NM_000038.5	1577	Gaa/Taa	16/16	0.501156315348641	1	FACETS	0.96	0.832	1	0.96	0.832	1	CLONAL	1	TRUE	0	0.570557683090613	1		190	120	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100286	8100286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241255776	NA	P-0040739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	159	501	0	ENST00000346208.3:c.260C>T	p.Pro87Leu	p.P87L	ENST00000346208		87	cCg/cTg	3/6	1	2	FACETS	0.86	0.791	0.932	0.86	0.791	0.932	CLONAL	1	TRUE	1	0.570557683090613	2		501	648	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907380	32907381	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs397507606	NA	P-0040739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	23	223	0	ENST00000380152.3:c.1765_1766del	p.Lys589ValfsTer7	p.K589Vfs*7	ENST00000380152		589	AAg/g	10/27	0.570557683090613	1	FACETS	0.64	0.511	0.782	0.64	0.511	0.782	SUBCLONAL	1	TRUE	0	0.570557683090613	1		223	90	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47596687	47596688	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0040739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	94	281	1	ENST00000263735.4:c.43_44delinsTT	p.Ala15Leu	p.A15L	ENST00000263735	NM_002354.2	15	GCg/TTg	1/9	1	2	FACETS	0.798	0.714	0.886	0.798	0.714	0.886	SUBCLONAL	1	TRUE	1	0.570557683090613	2		282	413	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848025	151848046	+	frameshift_variant	Frame_Shift_Del	DEL	AGAATAAAGCAGTTATTACTAC	AGAATAAAGCAGTTATTACTAC	-	novel	NA	P-0040739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	38	196	0	ENST00000262189.6:c.12713_12734del	p.Cys4238PhefsTer25	p.C4238Ffs*25	ENST00000262189	NM_170606.2	4238	tGTAGTAATAACTGCTTTATTCTt/tt	51/59	1	2	FACETS	0.951	0.801	1	0.951	0.801	1	CLONAL	1	TRUE	1	0.570557683090613	2		196	140	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939047	48939047	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs775381228	NA	P-0040741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	18	173	0	ENST00000267163.4:c.879C>A	p.Phe293Leu	p.F293L	ENST00000267163	NM_000321.2	293	ttC/ttA	9/27	1	2	FACETS	0.874	0.657	1	0.874	0.657	1	CLONAL	1	TRUE	1	0.13	2		173	317	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127916015	127916015	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	25	256	0	ENST00000373547.4:c.466G>A	p.Asp156Asn	p.D156N	ENST00000373547	NM_002721.4	156	Gat/Aat	6/7	1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	1	0.13	2		256	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0040747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	50	670	1	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	1	2	FACETS	0.534	0.452	0.624	0.534	0.452	0.624	SUBCLONAL	1	TRUE	1	0.29	2		671	646	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233223	46233235	+	frameshift_variant	Frame_Shift_Del	DEL	TTAGGCCACAAGC	TTAGGCCACAAGC	-	novel	NA	P-0040747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	30	284	0	ENST00000334344.6:c.1443_1455del	p.Arg482Ter	p.R482*	ENST00000334344	NM_152641.2	481	aTTAGGCCACAAGCt/at	11/21	1	2	FACETS	0.58	0.467	0.707	0.58	0.467	0.707	SUBCLONAL	1	TRUE	1	0.29	2		284	357	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685511	29685511	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	165	211	0	ENST00000356175.3:c.7921G>C	p.Asp2641His	p.D2641H	ENST00000356175	NM_000267.3	2641	Gac/Cac	54/57	0.626411478772536	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.675069644091237	1		211	322	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944427	40944427	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	233	465	0	ENST00000373198.4:c.2075A>T	p.Asn692Ile	p.N692I	ENST00000373198	NM_133170.3	692	aAc/aTc	12/32	NA	2	FACETS	0.887	0.83	0.946			1	INDETERMINATE	1	TRUE	NA	0.675069644091237	2		465	778	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259036	153259036	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	82	124	0	ENST00000281708.4:c.779G>A	p.Cys260Tyr	p.C260Y	ENST00000281708	NM_033632.3	260	tGt/tAt	5/12	0.675069644091237	1	FACETS	0.894	0.808	0.981	0.894	0.808	0.981	CLONAL	1	TRUE	0	0.675069644091237	1		124	180	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577521	7577521	+	frameshift_variant	Frame_Shift_Ins	INS	T	T	CG	novel	NA	P-0040748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	313	666	0	ENST00000269305.4:c.760delinsCG	p.Ile254ArgfsTer10	p.I254Rfs*10	ENST00000269305	NM_001126112.2	254	Atc/CGtc	7/11	0.675069644091237	1	FACETS	0.874	0.83	0.918	0.874	0.83	0.918	CLONAL	1	TRUE	0	0.675069644091237	1		666	703	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711879	89711879	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	61	483	0	ENST00000371953.3:c.497T>G	p.Val166Gly	p.V166G	ENST00000371953	NM_000314.4	166	gTa/gGa	6/9	0.264208185939189	3	FACETS	0.86	0.745	0.984			1	INDETERMINATE	1	TRUE	NA	0.451685059595278	3		483	385	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829029	72829029	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	82	853	0	ENST00000268489.5:c.7552C>T	p.Gln2518Ter	p.Q2518*	ENST00000268489	NM_006885.3	2518	Caa/Taa	9/10	0.245357442218904	2	FACETS	0.461	0.406	0.52	0.23	0.203	0.26	INDETERMINATE	1	TRUE	0	0.451685059595278	2		853	788	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578438	7578440	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0040754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	389	938	0	ENST00000269305.4:c.490_492del	p.Lys164del	p.K164del	ENST00000269305	NM_001126112.2	164	AAG/-	5/11	0.358692844199368	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.451685059595278	2		938	790	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624296	89624296	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs786201995	NA	P-0040762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	67	631	0	ENST00000371953.3:c.70G>C	p.Asp24His	p.D24H	ENST00000371953	NM_000314.4	24	Gac/Cac	1/9	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.14	2		631	858	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	49	619	0	ENST00000347630.2:c.397T>C	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	Ttc/Ctc	6/11	1	2	FACETS	0.991	0.837	1	0.991	0.837	1	CLONAL	1	TRUE	1	0.13	2		619	761	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0040764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	14	414	0	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	1	2	FACETS	0.43	0.309	0.577	0.43	0.309	0.577	SUBCLONAL	1	TRUE	1	0.13	2		414	501	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0040765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	59	257	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.74	0.64	0.846	0.74	0.64	0.846	SUBCLONAL	1	TRUE	1	0.486433125190784	2		257	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0040765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	377	673	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.846	0.806	0.886	1	0.996	1	CLONAL	2	TRUE	1	0.486433125190784	2		673	916	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591086	67591086	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	41	251	0	ENST00000274335.5:c.1679A>G	p.Asp560Gly	p.D560G	ENST00000274335		560	gAc/gGc	12/15	1	2	FACETS	0.448	0.374	0.531	0.448	0.374	0.531	SUBCLONAL	1	TRUE	1	0.486433125190784	2		251	376	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974783	21974783	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658556	NA	P-0040765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	58	202	0	ENST00000304494.5:c.44G>A	p.Trp15Ter	p.W15*	ENST00000304494	NM_000077.4	15	tGg/tAg	1/3	0.486433125190784	1	FACETS	0.96	0.839	1	0.96	0.839	1	CLONAL	1	TRUE	0	0.486433125190784	1		202	188	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092993	27092993	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0040765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	109	379	0	ENST00000324856.7:c.2924T>G	p.Leu975Ter	p.L975*	ENST00000324856	NM_006015.4	975	tTa/tGa	10/20	1	2	FACETS	0.872	0.786	0.962	0.872	0.786	0.962	CLONAL	1	TRUE	1	0.486433125190784	2		379	514	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434638	110434638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	194	759	2	ENST00000375856.3:c.3763G>A	p.Ala1255Thr	p.A1255T	ENST00000375856	NM_003749.2	1255	Gcc/Acc	1/2	1	2	FACETS	0.932	0.863	1	0.932	0.863	1	CLONAL	1	TRUE	1	0.486433125190784	2		761	856	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371804	116371804	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	41	400	0	ENST00000397752.3:c.1283A>G	p.Asp428Gly	p.D428G	ENST00000397752	NM_000245.2	428	gAc/gGc	3/21	0.265662733301561	3	FACETS	0.334	0.277	0.397	0.167	0.138	0.199	INDETERMINATE	1	TRUE	1	0.486433125190784	3		400	628	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250062	110250062	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1312725159	NA	P-0040765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	212	760	0	ENST00000374672.4:c.613C>T	p.Arg205Trp	p.R205W	ENST00000374672	NM_004235.4	205	Cgg/Tgg	3/5	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.486433125190784	2		760	845	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938814	76938814	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0040765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	150	585	0	ENST00000373344.5:c.1934C>G	p.Ser645Ter	p.S645*	ENST00000373344	NM_000489.3	645	tCa/tGa	9/35	1	2	FACETS	0.889	0.814	0.966	0.889	0.814	0.966	CLONAL	1	TRUE	1	0.486433125190784	2		585	694	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0040767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	78	230	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.451	0.398	0.507	0.451	0.398	0.507	SUBCLONAL	1	TRUE	1	0.844003641407867	2		230	410	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717624	89717624	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	87	326	0	ENST00000371953.3:c.649G>T	p.Val217Phe	p.V217F	ENST00000371953	NM_000314.4	217	Gtc/Ttc	7/9	1	2	FACETS	0.472	0.42	0.527	0.472	0.42	0.527	SUBCLONAL	1	TRUE	1	0.844003641407867	2		326	437	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685309	89685309	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs773176120	NA	P-0040767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	38	190	0	ENST00000371953.3:c.204C>G	p.Tyr68Ter	p.Y68*	ENST00000371953	NM_000314.4	68	taC/taG	3/9	1	2	FACETS	0.421	0.351	0.497	0.421	0.351	0.497	SUBCLONAL	1	TRUE	1	0.844003641407867	2		190	214	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101006	27101006	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	190	599	0	ENST00000324856.7:c.4288C>T	p.Gln1430Ter	p.Q1430*	ENST00000324856	NM_006015.4	1430	Cag/Tag	18/20	1	2	FACETS	0.521	0.482	0.562	0.521	0.482	0.562	SUBCLONAL	1	TRUE	1	0.844003641407867	2		599	864	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118936	70118936	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866706988	NA	P-0040767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	362	754	0	ENST00000245479.2:c.508C>A	p.Pro170Thr	p.P170T	ENST00000245479	NM_000346.3	170	Ccg/Acg	2/3	0.418655909904948	2	FACETS	0.871	0.828	0.915	0.435	0.414	0.458	INDETERMINATE	1	TRUE	0	0.844003641407867	2		754	985	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485713	40485713	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	193	499	0	ENST00000264657.5:c.1027G>T	p.Val343Phe	p.V343F	ENST00000264657	NM_139276.2	343	Gtc/Ttc	10/24	1	2	FACETS	0.57	0.528	0.613	0.57	0.528	0.613	SUBCLONAL	1	TRUE	1	0.844003641407867	2		499	803	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591110	67591136	+	inframe_deletion	In_Frame_Del	DEL	CAGACCTTATCCAGCTGAGAAAGACGA	CAGACCTTATCCAGCTGAGAAAGACGA	-	novel	NA	P-0040767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	25	272	0	ENST00000274335.5:c.1703_1729del	p.Pro568_Thr576del	p.P568_T576del	ENST00000274335		568	cCAGACCTTATCCAGCTGAGAAAGACGAga/cga	12/15	1	2	FACETS	0.241	0.19	0.299	0.241	0.19	0.299	SUBCLONAL	1	TRUE	1	0.844003641407867	2		272	246	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128432171	128432171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1477195100	NA	P-0040767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	45	321	0	ENST00000265960.3:c.275G>A	p.Arg92Gln	p.R92Q	ENST00000265960	NM_001006617.1	92	cGa/cAa	3/12	1	2	FACETS	0.311	0.262	0.365	0.311	0.262	0.365	SUBCLONAL	1	TRUE	1	0.844003641407867	2		321	343	SUCCESS
APC	324	MSKCC	GRCh37	5	112163677	112163677	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0040768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	52	233	0	ENST00000257430.4:c.1600A>T	p.Lys534Ter	p.K534*	ENST00000257430	NM_000038.5	534	Aaa/Taa	13/16	1	2	FACETS	0.72	0.619	0.828	0.72	0.619	0.828	SUBCLONAL	1	TRUE	1	0.589676171979757	2		233	245	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0040768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	319	276	0	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	0.530274423709759	2	FACETS	0.964	0.922	1	0.964	0.922	1	CLONAL	2	TRUE	0	0.589676171979757	2		276	561	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	228	424	1	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	0.0589908954285187	6	FACETS	0.955	0.897	1	0.955	0.897	1	INDETERMINATE	3	TRUE	3	0.589676171979757	6		425	588	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154812	2154812	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	192	897	0	ENST00000434045.2:c.409G>C	p.Glu137Gln	p.E137Q	ENST00000434045	NM_001127598.1	137	Gag/Cag	4/5	0.460458096164122	3	FACETS	0.991	0.918	1	0.495	0.459	0.534	CLONAL	1	TRUE	1	0.589676171979757	3		897	851	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435436	18435436	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	25	286	0	ENST00000266497.5:c.421T>A	p.Phe141Ile	p.F141I	ENST00000266497		141	Ttc/Atc	1/31	0.537862162007466	3	FACETS	0.563	0.447	0.695	0.282	0.223	0.348	SUBCLONAL	1	TRUE	1	0.589676171979757	3		286	195	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719424	190719424	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	37	218	0	ENST00000441310.2:c.1426G>C	p.Asp476His	p.D476H	ENST00000441310	NM_000534.4	476	Gat/Cat	9/13	0.537834240664419	3	FACETS	0.956	0.799	1	0.478	0.399	0.563	CLONAL	1	TRUE	1	0.589676171979757	3		218	170	SUCCESS
APC	324	MSKCC	GRCh37	5	112173452	112173452	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	27	256	0	ENST00000257430.4:c.2161G>T	p.Gly721Ter	p.G721*	ENST00000257430	NM_000038.5	721	Gga/Tga	16/16	1	2	FACETS	0.498	0.399	0.608	0.498	0.399	0.608	SUBCLONAL	1	TRUE	1	0.589676171979757	2		256	184	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0040769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	438	441	2	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.764014056017529	3	FACETS	0.934	0.909	0.958	0.934	0.909	0.958	CLONAL	3	TRUE	0	0.790162840176542	3		443	552	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273306	55273306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35918369	NA	P-0040769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	427	538	0	ENST00000275493.2:c.3629C>T	p.Ala1210Val	p.A1210V	ENST00000275493	NM_005228.3	1210	gCa/gTa	28/28	0.609735784140423	4	FACETS	0.914	0.874	0.955	0.914	0.874	0.955	CLONAL	2	TRUE	2	0.790162840176542	4		538	1058	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0040769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	935	1045	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.772042224356777	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.790162840176542	2		1045	1182	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612068	43612068	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	336	900	0	ENST00000355710.3:c.2173G>T	p.Val725Phe	p.V725F	ENST00000355710	NM_020975.4	725	Gtt/Ttt	12/20	0.760396714706921	3	FACETS	0.913	0.862	0.964	0.456	0.431	0.482	CLONAL	1	TRUE	1	0.790162840176542	3		900	1300	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156689	2156689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	307	934	0	ENST00000434045.2:c.233G>A	p.Cys78Tyr	p.C78Y	ENST00000434045	NM_001127598.1	78	tGc/tAc	3/5	0.790162840176542	1	FACETS	0.604	0.572	0.636	0.604	0.572	0.636	SUBCLONAL	1	TRUE	0	0.790162840176542	1		934	778	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125513723	125513723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	343	478	1	ENST00000428830.2:c.851C>T	p.Ser284Leu	p.S284L	ENST00000428830	NM_001114121.2	284	tCa/tTa	9/14	0.772675868080359	3	FACETS	1	0.994	1	0.691	0.656	0.725	CLONAL	1	TRUE	1	0.790162840176542	3		479	877	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488689	212488689	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	207	558	0	ENST00000342788.4:c.2160G>T	p.Arg720Ser	p.R720S	ENST00000342788	NM_005235.2	720	agG/agT	18/28	1	2	FACETS	0.885	0.827	0.945	0.885	0.827	0.945	CLONAL	1	TRUE	1	0.790162840176542	2		558	592	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	125	395	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		395	733	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0040793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	124	411	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		411	766	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586470	189586470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147148566	NA	P-0040805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	281	533	0	ENST00000264731.3:c.1094C>T	p.Ser365Leu	p.S365L	ENST00000264731	NM_003722.4	365	tCg/tTg	8/14	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.813379921854612	2		533	670	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885956	59885956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28997569	NA	P-0040805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1271	285	630	1	ENST00000259008.2:c.790C>T	p.Arg264Trp	p.R264W	ENST00000259008	NM_032043.2	264	Cgg/Tgg	7/20	0.813379921854612	4	FACETS	0.817	0.766	0.87	0.272	0.255	0.29	CLONAL	1	TRUE	1	0.813379921854612	4		631	1556	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980769	40980769	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	289	664	0	ENST00000373198.4:c.1717G>A	p.Gly573Ser	p.G573S	ENST00000373198	NM_133170.3	573	Ggc/Agc	10/32	1	2	FACETS	0.908	0.858	0.958	0.908	0.858	0.958	CLONAL	1	TRUE	1	0.813379921854612	2		664	783	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288119	21288119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148491827	NA	P-0040805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	228	559	0	ENST00000354336.3:c.364G>A	p.Glu122Lys	p.E122K	ENST00000354336	NM_005207.3	122	Gaa/Aaa	2/3	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	1	TRUE	NA	0.813379921854612	2		559	526	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71947006	71947006	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	401	1055	0	ENST00000298229.2:c.2855C>T	p.Pro952Leu	p.P952L	ENST00000298229	NM_001567.3	952	cCc/cTc	25/28	0.101466098946348	5	FACETS	1	0.985	1			1	INDETERMINATE	2	TRUE	NA	0.813379921854612	5		1055	1022	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964230	28964230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	98	270	0	ENST00000282397.4:c.1672G>A	p.Gly558Arg	p.G558R	ENST00000282397	NM_002019.4	558	Ggg/Agg	13/30	1	2	FACETS	0.886	0.802	0.972	0.886	0.802	0.972	CLONAL	1	TRUE	1	0.813379921854612	2		270	272	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730766	40730766	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	203	587	0	ENST00000373198.4:c.3769G>A	p.Asp1257Asn	p.D1257N	ENST00000373198	NM_133170.3	1257	Gat/Aat	27/32	1	2	FACETS	0.87	0.812	0.928	0.87	0.812	0.928	CLONAL	1	TRUE	1	0.813379921854612	2		587	574	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55154980	55154980	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1435679141	NA	P-0040805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	187	532	0	ENST00000257290.5:c.2689C>T	p.Pro897Ser	p.P897S	ENST00000257290	NM_006206.4	897	Ccc/Tcc	20/23	1	2	FACETS	0.781	0.725	0.837	0.781	0.725	0.837	SUBCLONAL	1	TRUE	1	0.813379921854612	2		532	589	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68982119	68982119	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	222	584	0	ENST00000288368.4:c.1493G>A	p.Arg498Lys	p.R498K	ENST00000288368	NM_024870.2	498	aGa/aAa	13/40	0.264980379005729	1	FACETS	0.48	0.449	0.512	0.48	0.449	0.512	INDETERMINATE	1	TRUE	0	0.813379921854612	1		584	675	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0040807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	286	505	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.851	0.805	0.897	1	0.995	1	CLONAL	2	TRUE	1	0.487187528657983	2		505	690	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0040807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	171	592	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.487187528657983	2		592	548	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971037	21971037	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs772527888	NA	P-0040807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	169	590	0	ENST00000579755.1:c.364C>T	p.Arg122Ter	p.R122*	ENST00000579755		122	Cga/Tga	2/3	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.487187528657983	2		590	604	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871807	12871807	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	133	353	0	ENST00000228872.4:c.524C>A	p.Ser175Ter	p.S175*	ENST00000228872	NM_004064.3	175	tCa/tAa	2/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.487187528657983	2		353	438	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056089	26056089	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1018305284	NA	P-0040807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	170	457	0	ENST00000343677.2:c.568G>A	p.Ala190Thr	p.A190T	ENST00000343677	NM_005319.3	190	Gct/Act	1/1	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.487187528657983	2		457	531	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458146	120458146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587654671	NA	P-0040807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	230	755	0	ENST00000256646.2:c.7199G>A	p.Arg2400Gln	p.R2400Q	ENST00000256646	NM_024408.3	2400	cGa/cAa	34/34	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.487187528657983	2		755	730	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438093	438093	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	193	461	0	ENST00000399788.2:c.1876T>A	p.Cys626Ser	p.C626S	ENST00000399788	NM_001042603.1	626	Tgc/Agc	14/28	0.290476635809946	1	FACETS	1	0.973	1	1	0.973	1	INDETERMINATE	1	TRUE	0	0.487187528657983	1		461	551	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	94	63	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.821	0.731	0.917	0.821	0.731	0.917	CLONAL	1	TRUE	1	0.338333250931724	2		63	677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0040808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	191	621	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.338333250931724	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.338333250931724	1		622	927	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201798	152201798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761613029	NA	P-0040808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	66	337	2	ENST00000206249.3:c.652G>A	p.Asp218Asn	p.D218N	ENST00000206249	NM_000125.3	218	Gac/Aac	3/8	1	2	FACETS	0.776	0.674	0.885	0.776	0.674	0.885	SUBCLONAL	1	TRUE	1	0.338333250931724	2		339	503	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922980	44922983	+	frameshift_variant	Frame_Shift_Del	DEL	CACT	CACT	-	novel	NA	P-0040808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	190	306	0	ENST00000377967.4:c.1846_1849del	p.Thr616TyrfsTer8	p.T616Yfs*8	ENST00000377967	NM_021140.2	614	gCACTc/gc	16/29	1	1	FACETS	0.877	0.817	0.938	1	0.993	1	CLONAL	2	TRUE	0	0.338333250931724	1		306	532	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141552	11141552	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	195	787	0	ENST00000358026.2:c.3529G>T	p.Asp1177Tyr	p.D1177Y	ENST00000358026	NM_001128849.1	1177	Gac/Tac	25/36	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.338333250931724	2		787	991	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141611	202141611	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1360228191	NA	P-0040808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	87	450	0	ENST00000358485.4:c.899A>G	p.Asn300Ser	p.N300S	ENST00000358485	NM_001080125.1	300	aAt/aGt	7/9	1	2	FACETS	0.725	0.642	0.815	0.725	0.642	0.815	SUBCLONAL	1	TRUE	1	0.338333250931724	2		450	709	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938790	178938790	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	52	467	0	ENST00000263967.3:c.2032A>G	p.Lys678Glu	p.K678E	ENST00000263967	NM_006218.2	678	Aaa/Gaa	14/21	1	2	FACETS	0.404	0.343	0.471	0.404	0.343	0.471	SUBCLONAL	1	TRUE	1	0.338333250931724	2		467	761	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938812	178938812	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	37	318	0	ENST00000263967.3:c.2054G>T	p.Gly685Val	p.G685V	ENST00000263967	NM_006218.2	685	gGc/gTc	14/21	1	2	FACETS	0.433	0.357	0.519	0.433	0.357	0.519	SUBCLONAL	1	TRUE	1	0.338333250931724	2		318	505	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0040809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	134	233	2	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	0.532568696296819	2		235	463	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0040809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	198	468	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.532568696296819	2		468	503	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0040809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	224	505	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	TRUE	1	0.532568696296819	2		505	601	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106058	8106058	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	234	558	0	ENST00000346208.3:c.878T>A	p.Met293Lys	p.M293K	ENST00000346208		293	aTg/aAg	4/6	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.532568696296819	2		558	659	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038526	47038526	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	323	356	2	ENST00000377604.3:c.688C>T	p.Arg230Ter	p.R230*	ENST00000377604	NM_001204468.1	230	Cga/Tga	8/24	1	1	FACETS	1	0.988	1	1	0.997	1	CLONAL	2	TRUE	0	0.532568696296819	1		358	425	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171462	123171462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	109	211	0	ENST00000218089.9:c.374C>T	p.Ser125Leu	p.S125L	ENST00000218089	NM_001042749.1	125	tCa/tTa	6/35	1	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.532568696296819	1		211	261	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553266	41553266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759315982	NA	P-0040809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	107	583	0	ENST00000263253.7:c.3355G>A	p.Asp1119Asn	p.D1119N	ENST00000263253	NM_001429.3	1119	Gat/Aat	18/31	1	2	FACETS	0.523	0.469	0.581	0.523	0.469	0.581	SUBCLONAL	1	TRUE	1	0.532568696296819	2		583	768	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724314	117724314	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	111	567	0	ENST00000368508.3:c.565C>T	p.His189Tyr	p.H189Y	ENST00000368508	NM_002944.2	189	Cat/Tat	6/43	1	2	FACETS	0.635	0.572	0.702	0.635	0.572	0.702	SUBCLONAL	1	TRUE	1	0.532568696296819	2		567	656	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401492	401492	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752393433	NA	P-0040809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	173	441	0	ENST00000380956.4:c.814G>A	p.Glu272Lys	p.E272K	ENST00000380956	NM_001195286.1	272	Gag/Aag	7/9	1	2	FACETS	0.818	0.763	0.874	1	0.992	1	CLONAL	2	TRUE	1	0.532568696296819	2		441	397	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418643	49418643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs936142615	NA	P-0040809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	240	538	1	ENST00000301067.7:c.15871G>A	p.Glu5291Lys	p.E5291K	ENST00000301067	NM_003482.3	5291	Gag/Aag	49/54	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.532568696296819	2		539	675	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938406	44938406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	190	212	0	ENST00000377967.4:c.2954C>T	p.Ser985Phe	p.S985F	ENST00000377967	NM_021140.2	985	tCt/tTt	20/29	1	1	FACETS	1	0.978	1	1	0.995	1	CLONAL	2	TRUE	0	0.532568696296819	1		212	252	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554367	141554367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	989	856	0	ENST00000220592.5:c.1784G>A	p.Gly595Glu	p.G595E	ENST00000220592	NM_012154.3	595	gGa/gAa	14/19	0.532568696296819	6	FACETS	0.958	0.932	0.984	0.958	0.932	0.984	CLONAL	4	TRUE	2	0.532568696296819	6		856	2001	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087533	27087534	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0040809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	333	756	0	ENST00000324856.7:c.2108_2109del	p.Pro703ArgfsTer113	p.P703Rfs*113	ENST00000324856	NM_006015.4	703	CCc/c	5/20	0.472654717868218	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.532568696296819	1		756	741	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012342	176012342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	218	436	0	ENST00000367669.3:c.1592C>T	p.Ser531Leu	p.S531L	ENST00000367669	NM_022457.5	531	tCa/tTa	14/20	0.143616802583597	3	FACETS	0.939	0.881	0.998	0.939	0.881	0.998	INDETERMINATE	2	TRUE	1	0.532568696296819	3		436	552	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258095	123258095	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	202	473	0	ENST00000358487.5:c.1586C>G	p.Ser529Cys	p.S529C	ENST00000358487	NM_000141.4	529	tCt/tGt	12/18	1	2	FACETS	0.797	0.747	0.848	1	0.993	1	SUBCLONAL	2	TRUE	1	0.532568696296819	2		473	476	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589630	69589630	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs922987433	NA	P-0040809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	66	201	0	ENST00000168712.1:c.223G>T	p.Asp75Tyr	p.D75Y	ENST00000168712	NM_002007.2	75	Gac/Tac	1/3	1	2	FACETS	0.873	0.765	0.987	0.873	0.765	0.987	CLONAL	1	TRUE	1	0.532568696296819	2		201	284	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076696	102076696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	233	568	0	ENST00000282441.5:c.875G>A	p.Gly292Glu	p.G292E	ENST00000282441	NM_001130145.2	292	gGa/gAa	5/9	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.532568696296819	2		568	597	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351569	89351569	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1397102513	NA	P-0040809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	330	810	0	ENST00000301030.4:c.1381G>C	p.Glu461Gln	p.E461Q	ENST00000301030	NM_001256183.1	461	Gaa/Caa	9/13	0.143616802583597	3	FACETS	0.94	0.892	0.988	0.94	0.892	0.988	INDETERMINATE	2	TRUE	1	0.532568696296819	3		810	835	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158626928	158626928	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	245	571	0	ENST00000263640.3:c.742G>C	p.Glu248Gln	p.E248Q	ENST00000263640	NM_001105.4	248	Gaa/Caa	7/11	0.491241818234269	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.532568696296819	1		571	483	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548252	41548252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	43	373	0	ENST00000263253.7:c.3040G>A	p.Glu1014Lys	p.E1014K	ENST00000263253	NM_001429.3	1014	Gag/Aag	16/31	1	2	FACETS	0.429	0.36	0.506	0.429	0.36	0.506	SUBCLONAL	1	TRUE	1	0.532568696296819	2		373	376	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696154	52696154	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1261727399	NA	P-0040809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	276	553	0	ENST00000394830.3:c.523G>A	p.Glu175Lys	p.E175K	ENST00000394830	NM_018313.4	175	Gaa/Aaa	5/30	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.532568696296819	2		553	743	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920280	1920280	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1306925576	NA	P-0040809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	147	722	0	ENST00000382891.5:c.1340C>A	p.Ser447Tyr	p.S447Y	ENST00000382891	NM_133335.3	447	tCc/tAc	5/22	1	2	FACETS	0.715	0.654	0.779	0.715	0.654	0.779	SUBCLONAL	1	TRUE	1	0.532568696296819	2		722	772	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84384672	84384672	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	229	457	0	ENST00000321945.7:c.771G>C	p.Arg257Ser	p.R257S	ENST00000321945	NM_139076.2	257	agG/agC	8/9	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.532568696296819	2		457	625	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950602	79950602	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	76	495	0	ENST00000265081.6:c.56C>A	p.Ala19Glu	p.A19E	ENST00000265081	NM_002439.4	19	gCg/gAg	1/24	1	2	FACETS	0.459	0.402	0.52	0.459	0.402	0.52	SUBCLONAL	1	TRUE	1	0.532568696296819	2		495	622	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554797	106554797	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	62	317	0	ENST00000369096.4:c.1914G>C	p.Lys638Asn	p.K638N	ENST00000369096	NM_001198.3	638	aaG/aaC	7/7	1	2	FACETS	0.699	0.608	0.797	0.699	0.608	0.797	SUBCLONAL	1	TRUE	1	0.532568696296819	2		317	333	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223553	55223553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	95	692	1	ENST00000275493.2:c.920G>A	p.Cys307Tyr	p.C307Y	ENST00000275493	NM_005228.3	307	tGc/tAc	8/28	1	2	FACETS	0.5	0.445	0.559	0.5	0.445	0.559	SUBCLONAL	1	TRUE	1	0.532568696296819	2		693	713	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	241	903	0	ENST00000267101.3:c.310G>C	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ctg	3/28	0.257003290756624	4	FACETS	0.952	0.889	1	0.952	0.889	1	CLONAL	2	FALSE	2	0.293421555316197	4		903	1116	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73342969	73342969	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	68	383	0	ENST00000377767.4:c.1837C>G	p.Leu613Val	p.L613V	ENST00000377767	NM_014953.3	613	Ctg/Gtg	14/21	0.25571501359641	3	FACETS	0.901	0.784	1	0.45	0.392	0.514	CLONAL	1	FALSE	1	0.293421555316197	3		383	590	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0040814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	255	229	2	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	0.863236313144862	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.863236313144862	1		231	324	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148890	119148890	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs754168206	NA	P-0040814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	87	296	0	ENST00000264033.4:c.1110A>C	p.Leu370Phe	p.L370F	ENST00000264033	NM_005188.3	370	ttA/ttC	8/16	1	2	FACETS	0.459	0.408	0.513	0.459	0.408	0.513	SUBCLONAL	1	TRUE	1	0.863236313144862	2		296	439	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175850	176175850	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	215	316	1	ENST00000367669.3:c.265C>T	p.His89Tyr	p.H89Y	ENST00000367669	NM_022457.5	89	Cac/Tac	1/20	0.488549750047872	1	FACETS	0.833	0.791	0.873	0.833	0.791	0.873	INDETERMINATE	1	TRUE	0	0.863236313144862	1		317	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577606	7577606	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	rs1567550076	NA	P-0040814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	310	534	0	ENST00000269305.4:c.675del	p.Gly226AlafsTer21	p.G226Afs*21	ENST00000269305	NM_001126112.2	225	gtT/gt	7/11	0.850645141866456	1	FACETS	0.922	0.887	0.955	0.922	0.887	0.955	CLONAL	1	TRUE	0	0.863236313144862	1		534	443	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162123	47162123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1216047088	NA	P-0040816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	22	393	0	ENST00000409792.3:c.4003C>T	p.Arg1335Cys	p.R1335C	ENST00000409792	NM_014159.6	1335	Cgt/Tgt	3/21	1	2	FACETS	0.261	0.202	0.33	0.261	0.202	0.33	SUBCLONAL	1	TRUE	1	0.472966785711658	2		393	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0040832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	1003	798	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.883521313083441	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.900149793424956	2		800	1110	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013719	170013719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388201066	NA	P-0040832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	234	451	1	ENST00000295797.4:c.1438C>T	p.Arg480Cys	p.R480C	ENST00000295797	NM_002740.5	480	Cgc/Tgc	15/18	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.900149793424956	2		452	509	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430411	78430412	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	243	447	0	ENST00000370768.2:c.756dup	p.Glu253ArgfsTer5	p.E253Rfs*5	ENST00000370768	NM_003902.3	252	-/A	10/20	0.900149793424956	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.900149793424956	1		447	296	SUCCESS
APC	324	MSKCC	GRCh37	5	112173723	112173723	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0040832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	185	360	0	ENST00000257430.4:c.2432C>G	p.Ser811Ter	p.S811*	ENST00000257430	NM_000038.5	811	tCa/tGa	16/16	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.900149793424956	2		360	406	SUCCESS
APC	324	MSKCC	GRCh37	5	112175256	112175266	+	frameshift_variant	Frame_Shift_Del	DEL	AAGTTCCAGCA	AAGTTCCAGCA	-	novel	NA	P-0040832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	121	264	0	ENST00000257430.4:c.3965_3975del	p.Glu1322GlyfsTer6	p.E1322Gfs*6	ENST00000257430	NM_000038.5	1322	gAAGTTCCAGCA/g	16/16	1	2	FACETS	0.825	0.755	0.896	0.825	0.755	0.896	CLONAL	1	TRUE	1	0.900149793424956	2		264	326	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964483	93964483	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	52	495	0	ENST00000369303.4:c.2414C>A	p.Pro805His	p.P805H	ENST00000369303	NM_004440.3	805	cCc/cAc	14/17	1	2	FACETS	0.202	0.172	0.236	0.202	0.172	0.236	SUBCLONAL	1	TRUE	1	0.900149793424956	2		495	571	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0040835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	27	304	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	0.294	0.233	0.364	0.294	0.233	0.364	SUBCLONAL	1	TRUE	1	0.361752946267101	2		304	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0040835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	175	657	0	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	0.361752946267101	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.361752946267101	1		657	749	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023380	27023390	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCGCCGCGG	CGCCGCCGCGG	-	novel	NA	P-0040842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	51	472	0	ENST00000324856.7:c.487_497del	p.Ala163ArgfsTer233	p.A163Rfs*233	ENST00000324856	NM_006015.4	162	gcCGCCGCCGCGGcc/gccc	1/20	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.16	2		472	637	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153552	108153552	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0040842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	52	385	0	ENST00000278616.4:c.3692T>A	p.Leu1231Ter	p.L1231*	ENST00000278616	NM_000051.3	1231	tTa/tAa	25/63	1	2	FACETS	0.927	0.788	1	0.927	0.788	1	CLONAL	1	TRUE	1	0.16	2		385	701	SUCCESS
ATM	472	MSKCC	GRCh37	11	108225540	108225540	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1060501572	NA	P-0040842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	51	407	0	ENST00000278616.4:c.8789G>T	p.Cys2930Phe	p.C2930F	ENST00000278616	NM_000051.3	2930	tGc/tTc	61/63	1	2	FACETS	0.859	0.729	1	0.859	0.729	1	CLONAL	1	TRUE	1	0.16	2		407	742	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43699761	43699776	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGCAATATCTGCAAGG	AGCAATATCTGCAAGG	-	novel	NA	P-0040842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	56	525	0	ENST00000382044.4:c.5747-8_5754del		p.X1916_splice	ENST00000382044	NM_001141980.1	1916		28/28	1	2	FACETS	0.913	0.78	1	0.913	0.78	1	CLONAL	1	TRUE	1	0.16	2		525	767	SUCCESS
APC	324	MSKCC	GRCh37	5	112174112	112174112	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	180	390	0	ENST00000257430.4:c.2821G>T	p.Glu941Ter	p.E941*	ENST00000257430	NM_000038.5	941	Gaa/Taa	16/16	0.530882784151714	2	FACETS	0.876	0.821	0.931	0.876	0.821	0.931	CLONAL	2	TRUE	0	0.564690224760328	2		390	364	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0040844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	735	621	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.533740057371689	3	FACETS	0.954	0.928	0.98	0.954	0.928	0.98	CLONAL	3	TRUE	0	0.564690224760328	3		622	1166	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0040844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	116	233	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.81	0.734	0.89	0.81	0.734	0.89	CLONAL	1	TRUE	1	0.564690224760328	2		233	507	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016310	150016310	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	208	492	0	ENST00000253339.5:c.396del	p.Ala133GlnfsTer9	p.A133Qfs*9	ENST00000253339		132	gaA/ga	2/7	1	2	FACETS	0.906	0.848	0.966	0.906	0.848	0.966	CLONAL	1	TRUE	1	0.813782388577954	2		492	564	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552927	106552927	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776111636	NA	P-0040852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	32	792	1	ENST00000369096.4:c.892G>A	p.Val298Ile	p.V298I	ENST00000369096	NM_001198.3	298	Gtt/Att	5/7	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	FALSE	1	0.238903129774232	2		793	196	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400830	72400830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	17	246	0	ENST00000357731.5:c.341G>A	p.Gly114Asp	p.G114D	ENST00000357731	NM_173808.2	114	gGc/gAc	2/7	1	2	FACETS	0.8	0.608	1	1	0.914	1	CLONAL	2	FALSE	1	0.238903129774232	2		246	89	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165007	47165010	+	frameshift_variant	Frame_Shift_Del	DEL	TCTG	TCTG	-	rs752743762	NA	P-0040852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	22	267	0	ENST00000409792.3:c.1116_1119del	p.Asp372GlufsTer111	p.D372Efs*111	ENST00000409792	NM_014159.6	372	gaCAGA/ga	3/21	0.238903129774232	1	FACETS	1	0.842	1	1	0.96	1	CLONAL	3	FALSE	0	0.238903129774232	1		267	52	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439780	52439780	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0040852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	26	470	1	ENST00000460680.1:c.931+1G>C		p.X311_splice	ENST00000460680	NM_004656.3	311			0.238903129774232	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	FALSE	0	0.238903129774232	1		471	142	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180783	106180783	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	15	238	0	ENST00000380013.4:c.3811T>C	p.Cys1271Arg	p.C1271R	ENST00000380013	NM_001127208.2	1271	Tgc/Cgc	7/11	1	2	FACETS	1	0.826	1	1	0.826	1	CLONAL	1	FALSE	1	0.238903129774232	2		238	108	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934347	68934347	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	24	554	0	ENST00000288368.4:c.413A>T	p.Lys138Ile	p.K138I	ENST00000288368	NM_024870.2	138	aAa/aTa	4/40	0.165450814347714	3	FACETS	0.879	0.699	1	0.586	0.466	0.72	CLONAL	2	FALSE	0	0.238903129774232	3		554	128	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0040857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	187	257	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.294201851487178	4	FACETS	1	0.975	1	1	0.994	1	CLONAL	5	FALSE	1	0.294201851487178	4		257	311	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0040857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	813	686	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.294201851487178	6	FACETS	1	0.997	1	1	0.999	1	CLONAL	10	FALSE	0	0.294201851487178	6		686	854	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448592	89448592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543425684	NA	P-0040857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	203	493	2	ENST00000336596.2:c.1556C>T	p.Thr519Met	p.T519M	ENST00000336596	NM_005233.5	519	aCg/aTg	7/17	0.294201851487178	4	FACETS	1	0.971	1	0.724	0.673	0.778	CLONAL	2	FALSE	1	0.294201851487178	4		495	822	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	215	641	0	ENST00000397752.3:c.3028G>A	p.Asp1010Asn	p.D1010N	ENST00000397752	NM_000245.2	1010	Gat/Aat	14/21	0.294201851487178	5	FACETS	1	0.984	1	0.795	0.74	0.852	CLONAL	2	FALSE	2	0.294201851487178	5		641	883	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165602	118165602	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs921184290	NA	P-0040857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	128	428	0	ENST00000369448.3:c.112C>T	p.Arg38Ter	p.R38*	ENST00000369448	NM_017709.3	38	Cga/Tga	2/2	0.294201851487178	6	FACETS	1	0.978	1	0.826	0.751	0.903	CLONAL	2	FALSE	3	0.294201851487178	6		428	558	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521730	89521730	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	121	412	0	ENST00000336596.2:c.2807A>C	p.Glu936Ala	p.E936A	ENST00000336596	NM_005233.5	936	gAg/gCg	16/17	0.294201851487178	4	FACETS	0.867	0.785	0.953	0.578	0.523	0.635	CLONAL	2	FALSE	1	0.294201851487178	4		412	614	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973877	131973881	+	frameshift_variant	Frame_Shift_Del	DEL	GCCTT	GCCTT	-	novel	NA	P-0040857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	21	367	0	ENST00000265335.6:c.3581_3585del	p.Ala1194GlyfsTer24	p.A1194Gfs*24	ENST00000265335		1194	GCCTTg/g	23/25	NA	2	FACETS	0.473	0.364	0.599			1	INDETERMINATE	1	FALSE	NA	0.294201851487178	2		367	302	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939568	76939568	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	331	262	0	ENST00000373344.5:c.1180del	p.Ala394LeufsTer20	p.A394Lfs*20	ENST00000373344	NM_000489.3	394	Gct/ct	9/35	0.294201851487178	3	FACETS	1	0.993	1			1	CLONAL	7	FALSE	NA	0.294201851487178	3		262	357	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs199469672	NA	P-0040859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	25	324	0	ENST00000374080.3:c.131G>C	p.Gly44Ala	p.G44A	ENST00000374080		44	gGt/gCt	2/45	1	1	FACETS	0.986	0.777	1	0.986	0.777	1	CLONAL	1	TRUE	0	0.14	1		324	337	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0040859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	8	323	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.315	0.202	0.463	0.315	0.202	0.463	SUBCLONAL	1	TRUE	1	0.14	2		323	363	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227982	53227982	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1556840029	NA	P-0040859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	27	432	1	ENST00000375401.3:c.2332C>T	p.Arg778Ter	p.R778*	ENST00000375401	NM_004187.3	778	Cga/Tga	16/26	1	1	FACETS	1	0.809	1	1	0.809	1	CLONAL	1	TRUE	0	0.14	1		433	353	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396482	139396482	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	53	890	1	ENST00000277541.6:c.5443del	p.Asp1815ThrfsTer72	p.D1815Tfs*72	ENST00000277541	NM_017617.3	1815	Gac/ac	29/34	1	2	FACETS	0.995	0.847	1	0.995	0.847	1	CLONAL	1	TRUE	1	0.14	2		891	761	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305244	39305244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770232749	NA	P-0040859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	35	551	0	ENST00000373001.3:c.1181C>T	p.Thr394Met	p.T394M	ENST00000373001	NM_022157.3	394	aCg/aTg	7/7	1	2	FACETS	0.898	0.735	1	0.898	0.735	1	CLONAL	1	TRUE	1	0.14	2		551	557	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	181	395	0				ENST00000310581	NM_198253.2	-/1132			0.295512005851869	2	FACETS	0.903	0.838	0.97	0.452	0.419	0.485	INDETERMINATE	1	FALSE	0	0.694400191489895	2		395	577	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160227	22160227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	104	107	0	ENST00000215832.6:c.404G>A	p.Arg135Lys	p.R135K	ENST00000215832	NM_002745.4	135	aGa/aAa	3/9	0.28657289563859	2	FACETS	0.772	0.697	0.85	0.386	0.348	0.425	INDETERMINATE	1	FALSE	0	0.694400191489895	2		107	388	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492752	56492752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	58	187	0	ENST00000407977.2:c.187C>T	p.Leu63Phe	p.L63F	ENST00000407977		63	Ctc/Ttc	2/10	0.541351689468887	3	FACETS	0.268	0.23	0.311	0.089	0.076	0.104	SUBCLONAL	1	FALSE	0	0.694400191489895	3		187	839	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468039	120468039	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	230	235	0	ENST00000256646.2:c.4400C>G	p.Ser1467Cys	p.S1467C	ENST00000256646	NM_024408.3	1467	tCc/tGc	25/34	0.243844660635899	2	FACETS	0.754	0.704	0.806	0.377	0.352	0.403	INDETERMINATE	1	FALSE	0	0.694400191489895	2		235	878	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984339	201984340	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0040890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	545	193	0	ENST00000359651.3:c.1005dup	p.Tyr336LeufsTer135	p.Y336Lfs*135	ENST00000359651		335	tac/taCc	8/8	0.560742609561282	4	FACETS	1	0.995	1	0.816	0.786	0.845	CLONAL	2	FALSE	1	0.694400191489895	4		193	1087	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	338199	338199	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	52	303	0	ENST00000262320.3:c.2512G>C	p.Glu838Gln	p.E838Q	ENST00000262320	NM_003502.3	838	Gag/Cag	11/11	0.295512005851869	2	FACETS	0.15	0.127	0.176	0.075	0.063	0.088	INDETERMINATE	1	FALSE	0	0.694400191489895	2		303	997	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878254	151878254	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	183	199	0	ENST00000262189.6:c.6691G>C	p.Glu2231Gln	p.E2231Q	ENST00000262189	NM_170606.2	2231	Gag/Cag	36/59	0.295512005851869	2	FACETS	0.648	0.599	0.699	0.324	0.299	0.35	INDETERMINATE	1	FALSE	0	0.694400191489895	2		199	813	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929114	44929115	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	242	224	0	ENST00000377967.4:c.2216dup	p.Asn739LysfsTer11	p.N739Kfs*11	ENST00000377967	NM_021140.2	738	-/A	17/29	NA	2	FACETS	0.976	0.916	1			1	INDETERMINATE	1	FALSE	NA	0.694400191489895	2		224	714	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0040913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	253	588	1	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.0876324760446443	5	FACETS	0.901	0.867	0.933			1	INDETERMINATE	5	TRUE	NA	0.679000861885188	5		589	334	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829292	72829292	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	842	668	0	ENST00000268489.5:c.7289C>T	p.Pro2430Leu	p.P2430L	ENST00000268489	NM_006885.3	2430	cCa/cTa	9/10	0.679000861885188	8	FACETS	1	0.982	1			1	CLONAL	6	TRUE	NA	0.679000861885188	8		668	1246	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917744	151917748	+	frameshift_variant	Frame_Shift_Del	DEL	AACTG	AACTG	-	novel	NA	P-0040913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	22	96	0	ENST00000262189.6:c.3572_3576del	p.Thr1191AsnfsTer21	p.T1191Nfs*21	ENST00000262189	NM_170606.2	1191	aCAGTT/a	23/59	0.679000861885188	2	FACETS	1	0.813	1	0.506	0.407	0.612	CLONAL	1	TRUE	0	0.679000861885188	2		96	64	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509436	106509436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200175951	NA	P-0040921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	204	556	1	ENST00000359195.3:c.1430G>A	p.Arg477His	p.R477H	ENST00000359195	NM_002649.2	477	cGt/cAt	2/11	0.340632592181442	5	FACETS	1	0.958	1	0.52	0.484	0.557	CLONAL	2	TRUE	1	0.45222538711135	5		557	728	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591076	67591076	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	109	296	0	ENST00000274335.5:c.1669C>T	p.Arg557Ter	p.R557*	ENST00000274335		557	Cga/Tga	12/15	0.45222538711135	2	FACETS	0.934	0.854	1	0.934	0.854	1	CLONAL	2	TRUE	0	0.45222538711135	2		296	258	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679033	117679033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	44	349	0	ENST00000368508.3:c.3788C>T	p.Pro1263Leu	p.P1263L	ENST00000368508	NM_002944.2	1263	cCc/cTc	24/43	1	2	FACETS	0.688	0.58	0.805	0.688	0.58	0.805	SUBCLONAL	1	TRUE	1	0.45222538711135	2		349	283	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288489	15288489	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	78	266	0	ENST00000263388.2:c.4250G>T	p.Cys1417Phe	p.C1417F	ENST00000263388	NM_000435.2	1417	tGc/tTc	24/33	0.344215717672486	5	FACETS	0.905	0.802	1	0.603	0.535	0.675	CLONAL	2	TRUE	2	0.45222538711135	5		266	320	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579584	7579651	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGGGGACTGTAGATGGGTGAAAAGAGCAGTCAGAGGACCAGGTCCTCAGCCCCCCAGCCCCCCAGCC	AGGGGGACTGTAGATGGGTGAAAAGAGCAGTCAGAGGACCAGGTCCTCAGCCCCCCAGCCCCCCAGCC	-	novel	NA	P-0040921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	257	506	0	ENST00000269305.4:c.96+49_103del		p.X32_splice	ENST00000269305	NM_001126112.2	32		4/11	0.45222538711135	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.45222538711135	2		506	477	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874549	35874549	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0040921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	154	387	0	ENST00000303115.3:c.707-2A>T		p.X236_splice	ENST00000303115	NM_002185.3	236			0.22310111312185	5	FACETS	0.884	0.817	0.952	0.884	0.817	0.952	INDETERMINATE	3	TRUE	2	0.45222538711135	5		387	431	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176593	56176593	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	163	349	0	ENST00000399503.3:c.2143G>T	p.Gly715Ter	p.G715*	ENST00000399503	NM_005921.1	715	Gga/Tga	12/20	0.45222538711135	2	FACETS	0.998	0.93	1	0.998	0.93	1	CLONAL	2	TRUE	0	0.45222538711135	2		349	361	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100312	157100312	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	70	234	0	ENST00000346085.5:c.1249C>G	p.Pro417Ala	p.P417A	ENST00000346085	NM_020732.3	417	Ccg/Gcg	1/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.45222538711135	2		234	243	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486301	8486301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	70	317	0	ENST00000356435.5:c.2516C>T	p.Ala839Val	p.A839V	ENST00000356435		839	gCt/gTt	17/35	0.45222538711135	2	FACETS	1	0.937	1	0.551	0.485	0.62	CLONAL	1	TRUE	0	0.45222538711135	2		317	281	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0040923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	78	592	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.919	0.814	1	0.919	0.814	1	CLONAL	1	TRUE	1	0.508417622342341	2		592	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0040923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	271	702	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.508417622342341	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.508417622342341	1		702	659	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0040923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	90	427	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.508417622342341	1	FACETS	0.83	0.744	0.92	0.83	0.744	0.92	CLONAL	1	TRUE	0	0.508417622342341	1		427	318	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655380	67655380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	99	497	0	ENST00000264010.4:c.1243C>T	p.Arg415Trp	p.R415W	ENST00000264010	NM_006565.3	415	Cgg/Tgg	7/12	1	2	FACETS	0.841	0.755	0.932	0.841	0.755	0.932	CLONAL	1	TRUE	1	0.508417622342341	2		497	463	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225474	26225474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	105	352	0	ENST00000360408.1:c.92C>T	p.Pro31Leu	p.P31L	ENST00000360408	NM_003532.2	31	cCg/cTg	1/1	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.508417622342341	2		352	373	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971127	55971127	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	132	547	0	ENST00000263923.4:c.1670C>A	p.Pro557His	p.P557H	ENST00000263923	NM_002253.2	557	cCt/cAt	13/30	1	2	FACETS	0.905	0.825	0.988	0.905	0.825	0.988	CLONAL	1	TRUE	1	0.508417622342341	2		547	574	SUCCESS
APC	324	MSKCC	GRCh37	5	112175145	112175146	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	57	204	0	ENST00000257430.4:c.3855dup	p.Glu1286Ter	p.E1286*	ENST00000257430	NM_000038.5	1285	gat/gaTt	16/16	0.508417622342341	2	FACETS	0.843	0.744	0.944	0.843	0.744	0.944	CLONAL	2	TRUE	0	0.508417622342341	2		204	133	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722030	176722030	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	51	458	0	ENST00000439151.2:c.7661A>G	p.Gln2554Arg	p.Q2554R	ENST00000439151	NM_022455.4	2554	cAg/cGg	23/23	0.508417622342341	2	FACETS	0.531	0.452	0.616	0.265	0.226	0.308	SUBCLONAL	1	TRUE	0	0.508417622342341	2		458	378	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928994	44928998	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCT	CCTCT	-	novel	NA	P-0040923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	152	504	0	ENST00000377967.4:c.2100_2104del	p.Ser701HisfsTer27	p.S701Hfs*27	ENST00000377967	NM_021140.2	698	caCCTCTcc/cacc	17/29	1	2	FACETS	0.913	0.837	0.991	0.913	0.837	0.991	CLONAL	1	TRUE	1	0.508417622342341	2		504	655	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913517	NA	P-0040924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	199	397	0	ENST00000288135.5:c.1676T>G	p.Val559Gly	p.V559G	ENST00000288135	NM_000222.2	559	gTt/gGt	11/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.653908005759414	2		397	568	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	374	63	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.491632020226551	6	FACETS	1	0.991	1	0.86	0.82	0.899	CLONAL	3	TRUE	2	0.535628737402831	6		63	841	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579317	7579317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	251	547	0	ENST00000269305.4:c.370del	p.Cys124AlafsTer46	p.C124Afs*46	ENST00000269305	NM_001126112.2	124	Tgc/gc	4/11	0.384537247534281	2	FACETS	0.775	0.73	0.819	0.775	0.73	0.819	SUBCLONAL	2	TRUE	0	0.535628737402831	2		547	605	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562190	21562190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	715	810	1	ENST00000382592.4:c.1729C>T	p.Pro577Ser	p.P577S	ENST00000382592	NM_014572.2	577	Ccc/Tcc	4/8	0.535628737402831	3	FACETS	0.939	0.913	0.966	0.939	0.913	0.966	CLONAL	3	TRUE	0	0.535628737402831	3		811	1201	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974773	21974775	+	inframe_deletion	In_Frame_Del	DEL	CGT	CGT	-	novel	NA	P-0040925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	43	300	0	ENST00000304494.5:c.52_54del	p.Thr18del	p.T18del	ENST00000304494	NM_000077.4	18	ACG/-	1/3	0.486652139046873	1	FACETS	0.552	0.467	0.644	0.552	0.467	0.644	SUBCLONAL	1	TRUE	0	0.535628737402831	1		300	213	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197697	123197698	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GC	GC	TT	novel	NA	P-0040925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	42	277	1	ENST00000218089.9:c.1822-1_1822delinsTT		p.X608_splice	ENST00000218089	NM_001042749.1	608		20/35	0.473473771492357	3	FACETS	0.581	0.487	0.686	0.291	0.243	0.343	SUBCLONAL	1	TRUE	1	0.535628737402831	3		278	342	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0040938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	144	505	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	0.276125678281258	2		505	877	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059260	27059260	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	134	681	0	ENST00000324856.7:c.1897C>T	p.Gln633Ter	p.Q633*	ENST00000324856	NM_006015.4	633	Cag/Tag	4/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.276125678281258	2		681	827	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0040938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	121	242	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.276125678281258	2		242	587	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs371769427	NA	P-0040938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	95	426	0	ENST00000291552.4:c.101C>A	p.Ser34Tyr	p.S34Y	ENST00000291552	NM_006758.2	34	tCt/tAt	2/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.276125678281258	2		426	527	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653800	89653800	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1554893771	NA	P-0040938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	107	462	0	ENST00000371953.3:c.98T>C	p.Ile33Thr	p.I33T	ENST00000371953	NM_000314.4	33	aTt/aCt	2/9	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.276125678281258	2		462	608	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720669	89720669	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	60	290	0	ENST00000371953.3:c.820T>G	p.Trp274Gly	p.W274G	ENST00000371953	NM_000314.4	274	Tgg/Ggg	8/9	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.276125678281258	2		290	430	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111002	193111002	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	71	264	0	ENST00000367435.3:c.535G>A	p.Val179Met	p.V179M	ENST00000367435	NM_024529.4	179	Gtg/Atg	7/17	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.276125678281258	2		264	353	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480123	50480123	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	59	639	0	ENST00000394963.4:c.359del	p.Asn120ThrfsTer43	p.N120Tfs*43	ENST00000394963	NM_003076.4	119	cgA/cg	2/13	1	2	FACETS	0.575	0.494	0.664	0.575	0.494	0.664	SUBCLONAL	1	TRUE	1	0.276125678281258	2		639	743	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47708005	47708006	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs63751618	NA	P-0040938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	58	441	0	ENST00000233146.2:c.2633_2634del	p.Glu878AlafsTer3	p.E878Afs*3	ENST00000233146	NM_000251.2	877	AGa/a	15/16	1	2	FACETS	0.791	0.68	0.912	0.791	0.68	0.912	CLONAL	1	TRUE	1	0.276125678281258	2		441	531	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151615	55151615	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	125	750	0	ENST00000257290.5:c.2401C>G	p.Gln801Glu	p.Q801E	ENST00000257290	NM_006206.4	801	Caa/Gaa	17/23	1	2	FACETS	0.951	0.86	1	0.951	0.86	1	CLONAL	1	TRUE	1	0.276125678281258	2		750	952	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64289229	64289229	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	133	546	0	ENST00000370651.3:c.397A>G	p.Ile133Val	p.I133V	ENST00000370651	NM_003463.4	133	Ata/Gta	5/6	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.276125678281258	2		546	771	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575609	55575613	+	frameshift_variant	Frame_Shift_Del	DEL	CTAAC	CTAAC	A	novel	NA	P-0040938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	79	496	0	ENST00000288135.5:c.1135_1139delinsA	p.Leu379ArgfsTer3	p.L379Rfs*3	ENST00000288135	NM_000222.2	379	CTAACg/Ag	7/21	1	2	FACETS	0.878	0.772	0.991	0.878	0.772	0.991	CLONAL	1	TRUE	1	0.276125678281258	2		496	652	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0040946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	52	760	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.787	0.67	0.916	0.787	0.67	0.916	CLONAL	1	FALSE	1	0.240591471238922	2		760	549	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771828	135771828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779599439	NA	P-0040946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	49	870	0	ENST00000298552.3:c.3289C>T	p.Arg1097Cys	p.R1097C	ENST00000298552	NM_001162426.1	1097	Cgt/Tgt	23/23	0.240591471238922	1	FACETS	0.748	0.634	0.873	0.748	0.634	0.873	SUBCLONAL	1	FALSE	0	0.240591471238922	1		870	479	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112569	115112569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180836314	NA	P-0040946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	66	1089	3	ENST00000257566.3:c.1171G>A	p.Asp391Asn	p.D391N	ENST00000257566	NM_016569.3	391	Gac/Aac	7/8	0.103708858109141	0	FACETS	0.65	0.564	0.743			1	INDETERMINATE	1	FALSE	0	0.240591471238922	0		1092	641	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651994	36651995	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0040946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	66	704	0	ENST00000244741.5:c.119dup	p.Cys41LeufsTer7	p.C41Lfs*7	ENST00000244741	NM_000389.4	39	gcg/gcGg	2/3	1	2	FACETS	0.872	0.757	0.997	0.872	0.757	0.997	CLONAL	1	FALSE	1	0.240591471238922	2		704	629	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169760	11169760	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	37	729	0	ENST00000361445.4:c.7393G>C	p.Glu2465Gln	p.E2465Q	ENST00000361445	NM_004958.3	2465	Gag/Cag	55/58	0.240591471238922	1	FACETS	0.587	0.484	0.703	0.587	0.484	0.703	SUBCLONAL	1	FALSE	0	0.240591471238922	1		729	461	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49430981	49430985	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCA	TGGCA	-	novel	NA	P-0040946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	70	701	0	ENST00000301067.7:c.10154_10158del	p.Met3385ThrfsTer36	p.M3385Tfs*36	ENST00000301067	NM_003482.3	3385	aTGCCA/a	34/54	1	2	FACETS	0.996	0.869	1	0.996	0.869	1	CLONAL	1	FALSE	1	0.240591471238922	2		701	584	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225367711	225367711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	50	537	0	ENST00000264414.4:c.1456G>A	p.Glu486Lys	p.E486K	ENST00000264414	NM_003590.4	486	Gaa/Aaa	10/16	1	2	FACETS	0.87	0.738	1	0.87	0.738	1	CLONAL	1	FALSE	1	0.240591471238922	2		537	478	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385179	41385179	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	51	944	0	ENST00000373198.4:c.782G>A	p.Ser261Asn	p.S261N	ENST00000373198	NM_133170.3	261	aGc/aAc	6/32	1	2	FACETS	0.71	0.603	0.828	0.71	0.603	0.828	SUBCLONAL	1	FALSE	1	0.240591471238922	2		944	597	SUCCESS
ATR	545	MSKCC	GRCh37	3	142241645	142241645	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	37	554	0	ENST00000350721.4:c.4191G>C	p.Leu1397Phe	p.L1397F	ENST00000350721	NM_001184.3	1397	ttG/ttC	23/47	1	2	FACETS	0.715	0.59	0.856	0.715	0.59	0.856	SUBCLONAL	1	FALSE	1	0.240591471238922	2		554	430	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535348	187535348	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	37	594	0	ENST00000441802.2:c.9226A>T	p.Thr3076Ser	p.T3076S	ENST00000441802	NM_005245.3	3076	Aca/Tca	12/27	1	2	FACETS	0.661	0.545	0.792	0.661	0.545	0.792	SUBCLONAL	1	FALSE	1	0.240591471238922	2		594	465	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782186	135782187	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	28	606	0	ENST00000298552.3:c.1369dup	p.Ser457LysfsTer2	p.S457Kfs*2	ENST00000298552	NM_001162426.1	457	agt/aAgt	14/23	0.240591471238922	1	FACETS	0.676	0.541	0.829	0.676	0.541	0.829	SUBCLONAL	1	FALSE	0	0.240591471238922	1		606	303	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938522	44938522	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	44	338	0	ENST00000377967.4:c.3070G>T	p.Glu1024Ter	p.E1024*	ENST00000377967	NM_021140.2	1024	Gaa/Taa	20/29	1	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	0	0.240591471238922	1		338	270	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295192	1295192	+	upstream_gene_variant	5'Flank	INS	C	C	AACGGAAAGGAAGGGGAGGGGCT	novel	NA	P-0040946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	15	337	0				ENST00000310581	NM_198253.2	-/1132			0.129669027806419	0	FACETS	0.371	0.271	0.492			1	INDETERMINATE	1	FALSE	0	0.240591471238922	0		337	255	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0040947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	291	654	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.368665621626366	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	FALSE	0	0.368665621626366	2		656	784	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091448	193091448	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	288	644	0	ENST00000367435.3:c.118T>G	p.Tyr40Asp	p.Y40D	ENST00000367435	NM_024529.4	40	Tat/Gat	1/17	0.368665621626366	3	FACETS	0.87	0.823	0.917	1	0.993	1	CLONAL	3	FALSE	1	0.368665621626366	3		644	709	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983120	201983121	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0040947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	380	910	1	ENST00000359651.3:c.970_971dup	p.Met324IlefsTer2	p.M324Ifs*2	ENST00000359651		323	-/AT	7/8	0.368665621626366	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	FALSE	1	0.368665621626366	3		911	1140	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295788	212295788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1412193732	NA	P-0040947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	83	697	0	ENST00000342788.4:c.2525G>A	p.Arg842Gln	p.R842Q	ENST00000342788	NM_005235.2	842	cGg/cAg	21/28	0.336543143160292	3	FACETS	1	0.979	1	0.745	0.662	0.832	CLONAL	1	FALSE	1	0.368665621626366	3		697	358	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0040955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	328	759	0	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	0.595269285817295	4	FACETS	1	0.978	1	0.356	0.336	0.377	CLONAL	1	TRUE	1	0.879736322333932	4		759	1311	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0040955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	1001	683	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.595269285817295	4	FACETS	0.931	0.91	0.951	0.931	0.91	0.951	CLONAL	3	TRUE	1	0.879736322333932	4		683	1532	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572527	41572527	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	42	644	0	ENST00000263253.7:c.5056T>G	p.Cys1686Gly	p.C1686G	ENST00000263253	NM_001429.3	1686	Tgt/Ggt	30/31	0.879736322333932	2	FACETS	0.122	0.101	0.145	0.061	0.05	0.073	SUBCLONAL	1	TRUE	0	0.879736322333932	2		644	784	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069572	69069572	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	80	409	0	ENST00000288368.4:c.4247A>C	p.Glu1416Ala	p.E1416A	ENST00000288368	NM_024870.2	1416	gAa/gCa	35/40	0.580067213445919	3	FACETS	0.495	0.437	0.558	0.248	0.218	0.279	SUBCLONAL	1	TRUE	1	0.879736322333932	3		409	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578177	7578177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs267605076	NA	P-0040965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	226	749	0	ENST00000269305.4:c.672G>T	p.Glu224Asp	p.E224D	ENST00000269305	NM_001126112.2	224	gaG/gaT	6/11	0.453478070295219	3	FACETS	1	0.987	1	0.761	0.719	0.803	CLONAL	2	FALSE	0	0.590930376845738	3		749	434	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731202	162731202	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs766637472	NA	P-0040965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	40	448	1	ENST00000367921.3:c.1057G>T	p.Ala353Ser	p.A353S	ENST00000367921	NM_006182.2	353	Gca/Tca	9/18	0.523985585925262	3	FACETS	0.486	0.404	0.576	0.243	0.202	0.288	SUBCLONAL	1	FALSE	1	0.590930376845738	3		449	361	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222987	1222987	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	170	677	0	ENST00000326873.7:c.924G>T	p.Trp308Cys	p.W308C	ENST00000326873	NM_000455.4	308	tgG/tgT	8/10	0.511014738542766	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.511014738542766	1		677	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0040984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	181	722	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.511014738542766	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.511014738542766	1		722	481	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	93	701	0	ENST00000267101.3:c.273G>A	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atA	3/28	1	2	FACETS	0.586	0.522	0.655	0.586	0.522	0.655	SUBCLONAL	1	TRUE	1	0.511014738542766	2		701	621	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624949	9624949	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	74	268	0	ENST00000353224.5:c.28G>A	p.Glu10Lys	p.E10K	ENST00000353224	NM_177990.2	10	Gaa/Aaa	3/10	1	2	FACETS	0.985	0.871	1	0.985	0.871	1	CLONAL	1	TRUE	1	0.511014738542766	2		268	294	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406445	70406445	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	174	747	0	ENST00000373644.4:c.3959G>T	p.Arg1320Leu	p.R1320L	ENST00000373644	NM_030625.2	1320	cGg/cTg	4/12	0.511014738542766	4	FACETS	0.94	0.864	1			1	CLONAL	1	TRUE	NA	0.511014738542766	4		747	1095	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801794	3801794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	109	512	0	ENST00000262367.5:c.3712G>A	p.Glu1238Lys	p.E1238K	ENST00000262367	NM_004380.2	1238	Gag/Aag	20/31	1	2	FACETS	0.825	0.744	0.91	0.825	0.744	0.91	CLONAL	1	TRUE	1	0.511014738542766	2		512	517	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222249	2222249	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	228	1005	0	ENST00000398665.3:c.3082del	p.Leu1028CysfsTer40	p.L1028Cfs*40	ENST00000398665	NM_032482.2	1027	gaC/ga	24/28	0.511014738542766	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.511014738542766	1		1005	624	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610338	10610338	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	239	943	3	ENST00000171111.5:c.372del	p.Ile125LeufsTer32	p.I125Lfs*32	ENST00000171111	NM_203500.1	124	tcC/tc	2/6	0.511014738542766	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.511014738542766	1		946	649	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546715	9546715	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	74	375	0	ENST00000353224.5:c.1307T>A	p.Leu436Gln	p.L436Q	ENST00000353224	NM_177990.2	436	cTg/cAg	5/10	1	2	FACETS	0.943	0.834	1	0.943	0.834	1	CLONAL	1	TRUE	1	0.511014738542766	2		375	307	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444673	187444673	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	119	392	0	ENST00000232014.4:c.1554C>G	p.Phe518Leu	p.F518L	ENST00000232014	NM_001130845.1	518	ttC/ttG	7/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.511014738542766	2		392	403	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207021	1207021	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913324	NA	P-0040984-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	138	784	0	ENST00000326873.7:c.109C>T	p.Gln37Ter	p.Q37*	ENST00000326873	NM_000455.4	37	Cag/Tag	1/10	0.321869795810698	1	FACETS	0.88	0.802	0.962	0.88	0.802	0.962	CLONAL	1	TRUE	0	0.358474655301546	1		784	718	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0040984-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	82	369	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.20381082103713	2	FACETS	0.949	0.84	1	0.475	0.42	0.533	INDETERMINATE	1	TRUE	0	0.358474655301546	2		369	482	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727455	66727455	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs869025608	NA	P-0040984-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	148	487	1	ENST00000307102.5:c.171G>T	p.Lys57Asn	p.K57N	ENST00000307102	NM_002755.3	57	aaG/aaT	2/11	0.209722654240419	3	FACETS	1	0.988	1	0.746	0.683	0.811	INDETERMINATE	1	TRUE	1	0.358474655301546	3		488	653	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602698	10602698	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040984-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	158	749	0	ENST00000171111.5:c.880G>T	p.Asp294Tyr	p.D294Y	ENST00000171111	NM_203500.1	294	Gac/Tac	3/6	0.321869795810698	1	FACETS	0.831	0.761	0.903	0.831	0.761	0.903	CLONAL	1	TRUE	0	0.358474655301546	1		749	871	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994779	73994779	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040984-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	201	701	0	ENST00000318443.5:c.263C>G	p.Ala88Gly	p.A88G	ENST00000318443	NM_001024736.1	88	gCc/gGc	3/10	0.209722654240419	3	FACETS	0.833	0.773	0.894	0.833	0.773	0.894	INDETERMINATE	2	TRUE	1	0.358474655301546	3		701	794	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0040994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	63	531	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.814	0.713	0.92	1	0.976	1	CLONAL	2	TRUE	1	0.336618395661331	2		531	230	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106687	27106687	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	114	709	0	ENST00000324856.7:c.6298C>T	p.Gln2100Ter	p.Q2100*	ENST00000324856	NM_006015.4	2100	Cag/Tag	20/20	0.0872793380844101	3	FACETS	0.982	0.884	1	0.491	0.442	0.543	INDETERMINATE	1	TRUE	1	0.336618395661331	3		709	806	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325945	65325945	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	20	404	0	ENST00000342505.4:c.1177G>T	p.Glu393Ter	p.E393*	ENST00000342505	NM_002227.2	393	Gaa/Taa	9/25	0.336618395661331	1	FACETS	0.253	0.193	0.324	0.253	0.193	0.324	SUBCLONAL	1	TRUE	0	0.336618395661331	1		404	390	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844139	68844139	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	89	657	0	ENST00000261769.5:c.727G>T	p.Glu243Ter	p.E243*	ENST00000261769	NM_004360.3	243	Gag/Tag	6/16	0.336618395661331	1	FACETS	0.861	0.765	0.962	0.861	0.765	0.962	CLONAL	1	TRUE	0	0.336618395661331	1		657	511	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164995	47165003	+	inframe_deletion	In_Frame_Del	DEL	ATATTTATC	ATATTTATC	-	novel	NA	P-0040994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	33	318	0	ENST00000409792.3:c.1123_1131del	p.Asp375_Tyr377del	p.D375_Y377del	ENST00000409792	NM_014159.6	375	GATAAATAT/-	3/21	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.336618395661331	2		318	163	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026871	71026871	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	53	282	0	ENST00000318789.4:c.1351G>C	p.Asp451His	p.D451H	ENST00000318789	NM_032682.5	451	Gat/Cat	16/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.336618395661331	2		282	227	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169993022	169993022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	21	316	0	ENST00000295797.4:c.652C>T	p.Pro218Ser	p.P218S	ENST00000295797	NM_002740.5	218	Cca/Tca	8/18	1	2	FACETS	0.885	0.689	1	0.885	0.689	1	CLONAL	1	TRUE	1	0.336618395661331	2		316	141	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0040995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	228	751	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	0.412420698235715	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.506690620723452	1		751	536	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856060	45856060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913024	NA	P-0040995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	132	720	3	ENST00000391945.4:c.1846C>T	p.Arg616Trp	p.R616W	ENST00000391945	NM_000400.3	616	Cgg/Tgg	20/23	1	2	FACETS	0.684	0.621	0.75	0.684	0.621	0.75	SUBCLONAL	1	TRUE	1	0.506690620723452	2		723	762	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0040997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	405	806	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.338876485937241	3	FACETS	0.933	0.89	0.975	0.933	0.89	0.975	CLONAL	3	TRUE	0	0.338876485937241	3		806	999	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599322	55599322	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	137	529	0	ENST00000288135.5:c.2448C>A	p.Asp816Glu	p.D816E	ENST00000288135	NM_000222.2	816	gaC/gaA	17/21	0.333276856261813	2	FACETS	0.844	0.773	0.917	0.844	0.773	0.917	CLONAL	2	TRUE	0	0.338876485937241	2		529	479	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438192	49438192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	169	862	0	ENST00000301067.7:c.5077C>T	p.Arg1693Trp	p.R1693W	ENST00000301067	NM_003482.3	1693	Cgg/Tgg	20/54	0.338876485937241	3	FACETS	1	0.97	1	0.557	0.511	0.605	CLONAL	1	TRUE	1	0.338876485937241	3		862	1047	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57569945	57569945	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	82	346	0	ENST00000316660.6:c.126del	p.Leu43Ter	p.L43*	ENST00000316660	NM_021127.2	42	cTt/ct	2/2	0.196711494476913	2	FACETS	1	0.963	1	0.605	0.536	0.678	INDETERMINATE	1	TRUE	0	0.338876485937241	2		346	400	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933688	36933688	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	106	1084	0	ENST00000361632.4:c.1711A>C	p.Asn571His	p.N571H	ENST00000361632		571	Aac/Cac	12/16	0.169453295125997	4	FACETS	0.737	0.659	0.821	0.369	0.329	0.411	INDETERMINATE	1	TRUE	2	0.338876485937241	4		1084	1136	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119799	108119799	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	36	296	0	ENST00000278616.4:c.1205A>T	p.Lys402Met	p.K402M	ENST00000278616	NM_000051.3	402	aAg/aTg	9/63	0.316054626248145	4	FACETS	0.604	0.496	0.725	0.302	0.248	0.363	SUBCLONAL	1	TRUE	2	0.338876485937241	4		296	471	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435783	110435783	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	66	462	0	ENST00000375856.3:c.2618G>T	p.Ser873Ile	p.S873I	ENST00000375856	NM_003749.2	873	aGc/aTc	1/2	0.255941906380835	2	FACETS	1	0.9	1	0.518	0.452	0.589	CLONAL	1	TRUE	0	0.338876485937241	2		462	376	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391214	89391214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs530556931	NA	P-0040997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	41	404	1	ENST00000336596.2:c.1280C>T	p.Ala427Val	p.A427V	ENST00000336596	NM_005233.5	427	gCg/gTg	5/17	0.290142059136895	3	FACETS	0.522	0.434	0.62	0.261	0.217	0.31	SUBCLONAL	1	TRUE	1	0.338876485937241	3		405	542	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322442	31322442	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	77	562	0	ENST00000412585.2:c.1013G>T	p.Gly338Val	p.G338V	ENST00000412585	NM_005514.6	338	gGt/gTt	6/8	0.338876485937241	3	FACETS	0.699	0.613	0.792	0.233	0.204	0.264	SUBCLONAL	1	TRUE	0	0.338876485937241	3		562	760	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981372	68981372	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0040997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	35	341	0	ENST00000288368.4:c.1443+1G>T		p.X481_splice	ENST00000288368	NM_024870.2	481			0.210531797349141	4	FACETS	0.728	0.597	0.874	0.364	0.298	0.437	SUBCLONAL	1	TRUE	2	0.338876485937241	4		341	380	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0040997-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	434	806	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.502072448427506	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.504635525595107	2		806	846	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599322	55599322	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040997-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	163	529	0	ENST00000288135.5:c.2448C>A	p.Asp816Glu	p.D816E	ENST00000288135	NM_000222.2	816	gaC/gaA	17/21	0.447745877191699	2	FACETS	0.859	0.799	0.919	0.859	0.799	0.919	CLONAL	2	TRUE	0	0.504635525595107	2		529	376	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438192	49438192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040997-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	138	862	0	ENST00000301067.7:c.5077C>T	p.Arg1693Trp	p.R1693W	ENST00000301067	NM_003482.3	1693	Cgg/Tgg	20/54	0.164770871565455	2	FACETS	0.603	0.548	0.661	0.302	0.274	0.331	INDETERMINATE	1	TRUE	0	0.504635525595107	2		862	907	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57569945	57569945	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040997-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	203	346	0	ENST00000316660.6:c.126del	p.Leu43Ter	p.L43*	ENST00000316660	NM_021127.2	42	cTt/ct	2/2	0.502072448427506	2	FACETS	0.949	0.892	1	0.949	0.892	1	CLONAL	2	TRUE	0	0.504635525595107	2		346	424	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847368	68847369	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAC	novel	NA	P-0040997-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	125	582	1	ENST00000261769.5:c.1294_1296dup	p.Asn432dup	p.N432dup	ENST00000261769	NM_004360.3	432	-/AAC	9/16	NA	2	FACETS	0.622	0.563	0.685			1	INDETERMINATE	1	TRUE	NA	0.504635525595107	2		583	796	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651664	48651664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040997-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	57	347	0	ENST00000376670.3:c.830C>T	p.Pro277Leu	p.P277L	ENST00000376670	NM_002049.3	277	cCc/cTc	5/6	1	1	FACETS	0.302	0.258	0.349	0.302	0.258	0.349	SUBCLONAL	1	TRUE	0	0.504635525595107	1		347	560	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602581	10602581	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	198	809	0	ENST00000171111.5:c.997G>T	p.Gly333Cys	p.G333C	ENST00000171111	NM_203500.1	333	Ggc/Tgc	3/6	0.477329376183809	1	FACETS	0.976	0.909	1	0.976	0.909	1	CLONAL	1	FALSE	0	0.477329376183809	1		809	647	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0041007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	59	353	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.962	0.836	1	0.962	0.836	1	CLONAL	1	FALSE	1	0.477329376183809	2		353	257	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46733165	46733165	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	170	451	0	ENST00000371975.4:c.926A>T	p.Tyr309Phe	p.Y309F	ENST00000371975	NM_003579.3	309	tAc/tTc	9/18	0.477329376183809	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	0	0.477329376183809	1		451	451	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40477043	40477043	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	142	446	0	ENST00000264657.5:c.1402T>G	p.Cys468Gly	p.C468G	ENST00000264657	NM_139276.2	468	Tgt/Ggt	16/24	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	FALSE	1	0.477329376183809	2		446	583	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374890	45374890	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	41	474	0	ENST00000262160.6:c.953A>G	p.Asn318Ser	p.N318S	ENST00000262160	NM_005901.5	318	aAt/aGt	8/11	0.365763147080399	1	FACETS	0.334	0.279	0.396	0.334	0.279	0.396	SUBCLONAL	1	FALSE	0	0.477329376183809	1		474	391	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220375	1220413	+	inframe_deletion	In_Frame_Del	DEL	CTTCTGTCAGCTGATTGACGGCCTGGAGTACCTGCATAG	CTTCTGTCAGCTGATTGACGGCCTGGAGTACCTGCATAG	-	novel	NA	P-0041007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	128	581	0	ENST00000326873.7:c.469_507del	p.Phe157_Ser169del	p.F157_S169del	ENST00000326873	NM_000455.4	156	taCTTCTGTCAGCTGATTGACGGCCTGGAGTACCTGCATAGc/tac	4/10	0.477329376183809	1	FACETS	0.878	0.801	0.958	0.878	0.801	0.958	CLONAL	1	FALSE	0	0.477329376183809	1		581	465	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876508	35876508	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	92	476	0	ENST00000303115.3:c.1300G>T	p.Gly434Cys	p.G434C	ENST00000303115	NM_002185.3	434	Ggt/Tgt	8/8	0.225008426046057	1	FACETS	0.62	0.554	0.691	0.62	0.554	0.691	INDETERMINATE	1	FALSE	0	0.477329376183809	1		476	473	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522604	106522604	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	58	349	0	ENST00000359195.3:c.2581G>T	p.Asp861Tyr	p.D861Y	ENST00000359195	NM_002649.2	861	Gat/Tat	7/11	1	2	FACETS	0.835	0.723	0.955	0.835	0.723	0.955	CLONAL	1	FALSE	1	0.477329376183809	2		349	291	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0121544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	133	43	1	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	1	2	FACETS		NA	1			1	NA	NA	NA	1	NA	2		44	596	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455587	189455587	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0121544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	52	444	0	ENST00000264731.3:c.121T>A	p.Ser41Thr	p.S41T	ENST00000264731	NM_003722.4	41	Tcc/Acc	2/14	1	2	FACETS		NA	1			1	NA	NA	NA	1	NA	2		444	557	SUCCESS
APC	324	MSKCC	GRCh37	5	112154827	112154828	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs387906237	NA	P-0041014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	78	509	0	ENST00000257430.4:c.1100_1101del	p.Ser367CysfsTer10	p.S367Cfs*10	ENST00000257430	NM_000038.5	366	gaCTct/gact	10/16	0.317782766758029	1	FACETS	0.996	0.88	1	0.996	0.88	1	CLONAL	1	TRUE	0	0.33372470371349	1		509	391	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175857	24175859	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs875989800	NA	P-0041014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	70	634	0	ENST00000263121.7:c.1091_1093del	p.Lys364del	p.K364del	ENST00000263121	NM_003073.3	362	gAGAag/gag	8/9	0.33372470371349	1	FACETS	0.77	0.673	0.873	0.77	0.673	0.873	SUBCLONAL	1	TRUE	0	0.33372470371349	1		634	454	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221947	1221947	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0041014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	109	907	0	ENST00000326873.7:c.863-1G>T		p.X288_splice	ENST00000326873	NM_000455.4	288			0.33372470371349	1	FACETS	0.86	0.773	0.951	0.86	0.773	0.951	CLONAL	1	TRUE	0	0.33372470371349	1		907	633	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711973	89711975	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	rs1064793244	NA	P-0041014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	42	313	0	ENST00000371953.3:c.595_597del	p.Met199del	p.M199del	ENST00000371953	NM_000314.4	197	aaGATg/aag	6/9	1	2	FACETS	0.839	0.704	0.987	0.839	0.704	0.987	CLONAL	1	TRUE	1	0.33372470371349	2		313	300	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81939091	81939091	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0041014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	80	606	0	ENST00000359376.3:c.1446C>G	p.Tyr482Ter	p.Y482*	ENST00000359376	NM_002661.3	482	taC/taG	15/33	1	2	FACETS	0.873	0.77	0.984	0.873	0.77	0.984	CLONAL	1	TRUE	1	0.33372470371349	2		606	549	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602676	10602690	+	frameshift_variant	Frame_Shift_Del	DEL	AGGTAGTCCTTGCAG	AGGTAGTCCTTGCAG	TA	novel	NA	P-0041014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	109	870	3	ENST00000171111.5:c.888_902delinsTA	p.Cys297ArgfsTer16	p.C297Rfs*16	ENST00000171111	NM_203500.1	296	cgCTGCAAGGACTACCTg/cgTAg	3/6	0.33372470371349	1	FACETS	0.889	0.8	0.983	0.889	0.8	0.983	CLONAL	1	TRUE	0	0.33372470371349	1		873	612	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778800	76778800	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	56	247	0	ENST00000373344.5:c.6779A>T	p.His2260Leu	p.H2260L	ENST00000373344	NM_000489.3	2260	cAc/cTc	31/35	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.33372470371349	2		247	316	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0041022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	86	447	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.533634446098178	3	FACETS	0.89	0.814	0.964	0.89	0.814	0.964	CLONAL	3	TRUE	0	0.533634446098178	3		447	153	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	78	846	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.528630062224767	4	FACETS	1	0.971	1	0.661	0.586	0.741	CLONAL	1	TRUE	2	0.533634446098178	4		846	339	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508955	106508955	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759136884	NA	P-0041022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	36	435	0	ENST00000359195.3:c.949G>A	p.Glu317Lys	p.E317K	ENST00000359195	NM_002649.2	317	Gag/Aag	2/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.533634446098178	NA		435	209	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248401	212248401	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1365124530	NA	P-0041022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	36	256	0	ENST00000342788.4:c.3866C>T	p.Ser1289Phe	p.S1289F	ENST00000342788	NM_005235.2	1289	tCc/tTc	28/28	0.533634446098178	3	FACETS	1	0.856	1	0.515	0.429	0.608	CLONAL	1	TRUE	1	0.533634446098178	3		256	166	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883959	37883959	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138611862	NA	P-0041022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	92	676	0	ENST00000269571.5:c.3430G>C	p.Asp1144His	p.D1144H	ENST00000269571		1144	Gat/Cat	27/27	0.533634446098178	2	FACETS	0.866	0.788	0.945	0.866	0.788	0.945	CLONAL	2	TRUE	0	0.533634446098178	2		676	199	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210474	2210474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	40	723	1	ENST00000398665.3:c.1081G>A	p.Glu361Lys	p.E361K	ENST00000398665	NM_032482.2	361	Gag/Aag	13/28	0.128605132097306	3	FACETS	0.848	0.711	0.998	0.283	0.237	0.333	INDETERMINATE	1	TRUE	0	0.533634446098178	3		724	224	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033959	48033959	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	24	298	0	ENST00000234420.5:c.4043A>G	p.Glu1348Gly	p.E1348G	ENST00000234420	NM_000179.2	1348	gAa/gGa	10/10	0.238208486834898	4	FACETS	1	0.85	1	0.543	0.432	0.667	INDETERMINATE	1	TRUE	2	0.533634446098178	4		298	127	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160564	56160564	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	44	216	0	ENST00000399503.3:c.838C>A	p.Gln280Lys	p.Q280K	ENST00000399503	NM_005921.1	280	Cag/Aag	4/20	0.522936081730556	5	FACETS	1	0.93	1	0.571	0.49	0.656	CLONAL	2	TRUE	1	0.533634446098178	5		216	130	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178367	56178400	+	frameshift_variant	Frame_Shift_Del	DEL	ACCCCAGTAGAGGAGAAATGCAGATTAGATGTCA	ACCCCAGTAGAGGAGAAATGCAGATTAGATGTCA	-	novel	NA	P-0041022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	26	279	0	ENST00000399503.3:c.3341_3374del	p.Thr1114IlefsTer23	p.T1114Ifs*23	ENST00000399503	NM_005921.1	1114	ACCCCAGTAGAGGAGAAATGCAGATTAGATGTCAat/at	14/20	0.533634446098178	3	FACETS	0.807	0.646	0.986	0.403	0.323	0.493	CLONAL	1	TRUE	1	0.533634446098178	3		279	153	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140500172	140500172	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	68	691	1	ENST00000288602.6:c.970G>T	p.Asp324Tyr	p.D324Y	ENST00000288602	NM_004333.4	324	Gac/Tac	7/18	0.450505008642517	3	FACETS	0.897	0.785	1	0.448	0.392	0.508	CLONAL	1	TRUE	1	0.533634446098178	3		692	360	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0041032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	40	726	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	1	2	FACETS	0.897	0.743	1	0.897	0.743	1	CLONAL	1	TRUE	1	0.11	2		726	811	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641718	12641718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs5746220	NA	P-0041032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	41	445	0	ENST00000251849.4:c.923C>T	p.Pro308Leu	p.P308L	ENST00000251849	NM_002880.3	308	cCg/cTg	9/17	1	2	FACETS	0.971	0.806	1	0.971	0.806	1	CLONAL	1	TRUE	1	0.11	2		445	768	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988440	41988440	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781303112	NA	P-0041032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	34	542	0	ENST00000219905.7:c.1232C>T	p.Thr411Met	p.T411M	ENST00000219905	NM_001164273.1	411	aCg/aTg	3/24	1	2	FACETS	1	0.821	1	1	0.821	1	CLONAL	1	TRUE	1	0.11	2		542	614	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842659	68842672	+	frameshift_variant	Frame_Shift_Del	DEL	ACACCCCCTGTTGG	ACACCCCCTGTTGG	-	novel	NA	P-0041032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	42	660	0	ENST00000261769.5:c.595_608del	p.Thr199CysfsTer5	p.T199Cfs*5	ENST00000261769	NM_004360.3	199	ACACCCCCTGTTGGt/t	5/16	1	2	FACETS	0.91	0.757	1	0.91	0.757	1	CLONAL	1	TRUE	1	0.11	2		660	839	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0041033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	26	63	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.95	0.752	1	0.95	0.752	1	CLONAL	1	TRUE	1	0.12	2		63	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0041033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	55	683	3	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	1	2	FACETS	0.994	0.848	1	0.994	0.848	1	CLONAL	1	TRUE	1	0.12	2		686	922	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0041039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	33	63	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.875	0.715	1	0.875	0.715	1	CLONAL	1	TRUE	1	0.27741093478801	2		63	272	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0041039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	27	242	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	0.814	0.651	0.999	0.814	0.651	0.999	CLONAL	1	TRUE	1	0.27741093478801	2		242	239	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221334	1221338	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TGAAA	TGAAA	-	novel	NA	P-0041039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	42	537	0	ENST00000326873.7:c.857_861del	p.Leu286ArgfsTer4	p.L286Rfs*4	ENST00000326873	NM_000455.4	286	cTGAAA/c	6/10	NA	2	FACETS	0.937	0.786	1			1	INDETERMINATE	1	TRUE	NA	0.27741093478801	2		537	323	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133162	38133164	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	novel	NA	P-0041039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	17	408	0	ENST00000317025.8:c.4309_4311del	p.Glu1437del	p.E1437del	ENST00000317025	NM_023034.1	1437	GAA/-	24/24	1	2	FACETS	0.454	0.339	0.591	0.454	0.339	0.591	SUBCLONAL	1	TRUE	1	0.27741093478801	2		408	270	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248196	110248196	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	26	331	0	ENST00000374672.4:c.1276T>G	p.Tyr426Asp	p.Y426D	ENST00000374672	NM_004235.4	426	Tac/Gac	5/5	1	2	FACETS	0.759	0.603	0.936	0.759	0.603	0.936	CLONAL	1	TRUE	1	0.27741093478801	2		331	247	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602572	10602572	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	62	734	1	ENST00000171111.5:c.1006C>T	p.Arg336Ter	p.R336*	ENST00000171111	NM_203500.1	336	Cga/Tga	3/6	0.283660996529912	3	FACETS	0.926	0.801	1	0.463	0.4	0.531	CLONAL	1	TRUE	1	0.289863101891528	3		735	529	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	136	395	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.578826839665896	2		395	394	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922328	178922328	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	69	494	0	ENST00000263967.3:c.1097C>G	p.Pro366Arg	p.P366R	ENST00000263967	NM_006218.2	366	cCc/cGc	6/21	1	2	FACETS	0.921	0.811	1	0.921	0.811	1	CLONAL	1	TRUE	1	0.578826839665896	2		494	259	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	82	395	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.978	0.867	1	0.978	0.867	1	CLONAL	1	TRUE	1	0.391610412583259	2		395	428	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922328	178922328	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	103	494	0	ENST00000263967.3:c.1097C>G	p.Pro366Arg	p.P366R	ENST00000263967	NM_006218.2	366	cCc/cGc	6/21	1	2	FACETS	0.831	0.745	0.922	0.831	0.745	0.922	CLONAL	1	TRUE	1	0.391610412583259	2		494	633	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262612	16262612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	101	515	0	ENST00000375759.3:c.9877G>A	p.Val3293Met	p.V3293M	ENST00000375759	NM_015001.2	3293	Gtg/Atg	11/15	1	2	FACETS	0.91	0.815	1	0.91	0.815	1	CLONAL	1	TRUE	1	0.391610412583259	2		515	567	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162068	47162068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	84	435	0	ENST00000409792.3:c.4058C>T	p.Ser1353Phe	p.S1353F	ENST00000409792	NM_014159.6	1353	tCc/tTc	3/21	1	2	FACETS	0.846	0.75	0.949	0.846	0.75	0.949	CLONAL	1	TRUE	1	0.391610412583259	2		435	507	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	140	774	2	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	0.370287581924079	1	FACETS	0.776	0.708	0.848	0.776	0.708	0.848	SUBCLONAL	1	TRUE	0	0.391610412583259	1		776	741	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523145	176523145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746619070	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	151	856	4	ENST00000292408.4:c.1909G>A	p.Val637Ile	p.V637I	ENST00000292408	NM_213647.1	637	Gtc/Atc	14/18	1	2	FACETS	0.919	0.841	1	0.919	0.841	1	CLONAL	1	TRUE	1	0.391610412583259	2		860	839	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920413	134920413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1338928289	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	120	351	1	ENST00000398015.3:c.2228G>A	p.Arg743Gln	p.R743Q	ENST00000398015	NM_004441.4	743	cGg/cAg	12/16	1	2	FACETS	0.892	0.807	0.982	0.892	0.807	0.982	CLONAL	1	TRUE	1	0.391610412583259	2		352	687	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346233	152346233	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1438202364	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	156	588	0	ENST00000359321.1:c.337G>A	p.Gly113Arg	p.G113R	ENST00000359321	NM_005431.1	113	Gga/Aga	3/3	0.377986158339099	4	FACETS	1	0.951	1	0.353	0.322	0.385	CLONAL	1	TRUE	1	0.391610412583259	4		588	1048	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557570	21557570	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756702960	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	133	827	0	ENST00000382592.4:c.2275C>T	p.Arg759Trp	p.R759W	ENST00000382592	NM_014572.2	759	Cgg/Tgg	5/8	1	2	FACETS	0.93	0.846	1	0.93	0.846	1	CLONAL	1	TRUE	1	0.391610412583259	2		827	730	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557912	21557912	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757472527	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	117	513	1	ENST00000382592.4:c.1933C>T	p.Arg645Trp	p.R645W	ENST00000382592	NM_014572.2	645	Cgg/Tgg	5/8	1	2	FACETS	0.98	0.886	1	0.98	0.886	1	CLONAL	1	TRUE	1	0.391610412583259	2		514	610	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309117	137309117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1383908613	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	183	1094	3	ENST00000481739.1:c.724G>A	p.Val242Met	p.V242M	ENST00000481739	NM_002957.4	242	Gtg/Atg	5/10	1	2	FACETS	0.913	0.842	0.987	0.913	0.842	0.987	CLONAL	1	TRUE	1	0.391610412583259	2		1097	1024	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284937	15284937	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1275632781	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	176	1011	4	ENST00000263388.2:c.4678C>T	p.Arg1560Trp	p.R1560W	ENST00000263388	NM_000435.2	1560	Cgg/Tgg	25/33	1	2	FACETS	0.905	0.833	0.98	0.905	0.833	0.98	CLONAL	1	TRUE	1	0.391610412583259	2		1015	993	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846380	128846380	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757620819	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	152	742	0	ENST00000249373.3:c.1216G>A	p.Ala406Thr	p.A406T	ENST00000249373	NM_005631.4	406	Gcc/Acc	6/12	0.377986158339099	4	FACETS	1	0.922	1	0.337	0.307	0.368	CLONAL	1	TRUE	1	0.391610412583259	4		742	1069	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913277	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	89	363	0	ENST00000263967.3:c.3145G>A	p.Gly1049Ser	p.G1049S	ENST00000263967	NM_006218.2	1049	Ggt/Agt	21/21	1	2	FACETS	0.928	0.826	1	0.928	0.826	1	CLONAL	1	TRUE	1	0.391610412583259	2		363	490	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244218	5244218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781558493	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	163	804	0	ENST00000357368.4:c.1264G>A	p.Gly422Ser	p.G422S	ENST00000357368	NM_002850.3	422	Ggc/Agc	11/38	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.391610412583259	2		804	751	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298639	11298639	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	149	657	0	ENST00000361445.4:c.1822G>A	p.Asp608Asn	p.D608N	ENST00000361445	NM_004958.3	608	Gat/Aat	12/58	1	2	FACETS	0.988	0.904	1	0.988	0.904	1	CLONAL	1	TRUE	1	0.391610412583259	2		657	770	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073403	8073403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	104	551	1	ENST00000377482.5:c.1256G>A	p.Gly419Glu	p.G419E	ENST00000377482	NM_018948.3	419	gGa/gAa	4/4	1	2	FACETS	0.778	0.697	0.863	0.778	0.697	0.863	SUBCLONAL	1	TRUE	1	0.391610412583259	2		552	683	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430390	78430390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367853057	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	119	520	1	ENST00000370768.2:c.778G>A	p.Gly260Ser	p.G260S	ENST00000370768	NM_003902.3	260	Ggt/Agt	10/20	1	2	FACETS	0.869	0.786	0.958	0.869	0.786	0.958	CLONAL	1	TRUE	1	0.391610412583259	2		521	699	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631144	69631144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554981085	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	165	895	2	ENST00000334134.2:c.268G>A	p.Gly90Ser	p.G90S	ENST00000334134	NM_005247.2	90	Ggt/Agt	2/3	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.391610412583259	2		897	800	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999086	100999086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	137	797	0	ENST00000325455.5:c.716G>A	p.Gly239Asp	p.G239D	ENST00000325455	NM_001202474.3	239	gGc/gAc	1/8	1	2	FACETS	0.987	0.899	1	0.987	0.899	1	CLONAL	1	TRUE	1	0.391610412583259	2		797	709	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366447	118366447	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	108	449	1	ENST00000534358.1:c.5396C>T	p.Pro1799Leu	p.P1799L	ENST00000534358	NM_005933.3	1799	cCt/cTt	19/36	1	2	FACETS	0.983	0.885	1	0.983	0.885	1	CLONAL	1	TRUE	1	0.391610412583259	2		450	561	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022766	12022766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs72550787	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	98	569	0	ENST00000396373.4:c.872G>A	p.Arg291Lys	p.R291K	ENST00000396373	NM_001987.4	291	aGg/aAg	5/8	1	2	FACETS	0.943	0.844	1	0.943	0.844	1	CLONAL	1	TRUE	1	0.391610412583259	2		569	531	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439747	49439747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	109	737	0	ENST00000301067.7:c.4697C>T	p.Pro1566Leu	p.P1566L	ENST00000301067	NM_003482.3	1566	cCt/cTt	18/54	1	2	FACETS	0.741	0.666	0.821	0.741	0.666	0.821	SUBCLONAL	1	TRUE	1	0.391610412583259	2		737	751	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209252	133209252	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	145	877	0	ENST00000320574.5:c.6134C>T	p.Pro2045Leu	p.P2045L	ENST00000320574	NM_006231.2	2045	cCc/cTc	44/49	1	2	FACETS	0.969	0.885	1	0.969	0.885	1	CLONAL	1	TRUE	1	0.391610412583259	2		877	764	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964008	28964008	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	68	456	0	ENST00000282397.4:c.1894G>A	p.Gly632Ser	p.G632S	ENST00000282397	NM_002019.4	632	Ggc/Agc	13/30	1	2	FACETS	0.75	0.654	0.853	0.75	0.654	0.853	SUBCLONAL	1	TRUE	1	0.391610412583259	2		456	463	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914305	32914305	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	94	530	0	ENST00000380152.3:c.5813G>A	p.Gly1938Glu	p.G1938E	ENST00000380152		1938	gGa/gAa	11/27	1	2	FACETS	0.927	0.827	1	0.927	0.827	1	CLONAL	1	TRUE	1	0.391610412583259	2		530	518	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352695	68352695	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	84	366	1	ENST00000487270.1:c.562G>A	p.Val188Ile	p.V188I	ENST00000487270	NM_133509.3	188	Gtt/Att	6/11	1	2	FACETS	0.844	0.748	0.947	0.844	0.748	0.947	CLONAL	1	TRUE	1	0.391610412583259	2		367	508	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961208	41961208	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757411884	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	86	416	0	ENST00000219905.7:c.116G>A	p.Gly39Glu	p.G39E	ENST00000219905	NM_001164273.1	39	gGa/gAa	2/24	1	2	FACETS	0.81	0.718	0.908	0.81	0.718	0.908	CLONAL	1	TRUE	1	0.391610412583259	2		416	542	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134271	2134271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	145	1005	0	ENST00000219476.3:c.4048G>A	p.Glu1350Lys	p.E1350K	ENST00000219476	NM_000548.3	1350	Gag/Aag	34/42	1	2	FACETS	0.872	0.796	0.952	0.872	0.796	0.952	CLONAL	1	TRUE	1	0.391610412583259	2		1005	849	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020613	14020613	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	93	350	0	ENST00000311895.7:c.584G>A	p.Arg195Lys	p.R195K	ENST00000311895	NM_005236.2	195	aGg/aAg	3/11	1	2	FACETS	0.905	0.807	1	0.905	0.807	1	CLONAL	1	TRUE	1	0.391610412583259	2		350	525	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864565	56864565	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	120	553	0	ENST00000308159.5:c.1053G>A	p.Trp351Ter	p.W351*	ENST00000308159	NM_014669.4	351	tgG/tgA	10/22	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.391610412583259	2		553	608	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554606	63554606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	115	686	0	ENST00000307078.5:c.133G>A	p.Val45Ile	p.V45I	ENST00000307078	NM_004655.3	45	Gtc/Atc	2/11	1	2	FACETS	0.941	0.85	1	0.941	0.85	1	CLONAL	1	TRUE	1	0.391610412583259	2		686	624	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222422	2222422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	142	806	1	ENST00000398665.3:c.3254G>A	p.Arg1085Lys	p.R1085K	ENST00000398665	NM_032482.2	1085	aGg/aAg	24/28	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.391610412583259	2		807	703	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051676	13051676	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	134	630	0	ENST00000316448.5:c.935G>A	p.Gly312Asp	p.G312D	ENST00000316448	NM_004343.3	312	gGc/gAc	7/9	1	2	FACETS	0.96	0.873	1	0.96	0.873	1	CLONAL	1	TRUE	1	0.391610412583259	2		630	713	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276648	15276648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749429793	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	189	926	3	ENST00000263388.2:c.5617C>T	p.Arg1873Cys	p.R1873C	ENST00000263388	NM_000435.2	1873	Cgc/Tgc	30/33	1	2	FACETS	0.983	0.908	1	0.983	0.908	1	CLONAL	1	TRUE	1	0.391610412583259	2		929	982	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350499	15350499	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1352931938	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	131	826	1	ENST00000263377.2:c.3416G>A	p.Ser1139Asn	p.S1139N	ENST00000263377	NM_058243.2	1139	aGc/aAc	16/20	1	2	FACETS	0.875	0.794	0.959	0.875	0.794	0.959	CLONAL	1	TRUE	1	0.391610412583259	2		827	765	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15364962	15364962	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	125	584	0	ENST00000263377.2:c.2158+1G>A		p.X720_splice	ENST00000263377	NM_058243.2	720			1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.391610412583259	2		584	629	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224587	36224587	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1437261281	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	171	1190	0	ENST00000222270.7:c.7049G>A	p.Gly2350Glu	p.G2350E	ENST00000222270	NM_014727.1	2350	gGg/gAg	29/37	1	2	FACETS	0.903	0.83	0.979	0.903	0.83	0.979	CLONAL	1	TRUE	1	0.391610412583259	2		1190	967	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705544	47705545	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	72	437	0	ENST00000233146.2:c.2344_2345del	p.Thr782ProfsTer4	p.T782Pfs*4	ENST00000233146	NM_000251.2	782	ACc/c	14/16	0.101308396326356	4	FACETS	0.958	0.839	1	0.479	0.419	0.544	INDETERMINATE	1	TRUE	2	0.391610412583259	4		437	534	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47709984	47709984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	100	447	0	ENST00000233146.2:c.2701G>A	p.Glu901Lys	p.E901K	ENST00000233146	NM_000251.2	901	Gaa/Aaa	16/16	0.101308396326356	4	FACETS	1	0.967	1	0.602	0.539	0.669	INDETERMINATE	1	TRUE	2	0.391610412583259	4		447	590	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170882	99170882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	128	875	1	ENST00000074304.5:c.1511C>T	p.Thr504Ile	p.T504I	ENST00000074304	NM_001134224.1	504	aCc/aTc	16/26	1	2	FACETS	0.831	0.753	0.912	0.831	0.753	0.912	CLONAL	1	TRUE	1	0.391610412583259	2		876	787	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038183	128038183	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	113	533	0	ENST00000285398.2:c.1367C>T	p.Thr456Ile	p.T456I	ENST00000285398	NM_000122.1	456	aCc/aTc	9/15	1	2	FACETS	0.834	0.751	0.921	0.834	0.751	0.921	CLONAL	1	TRUE	1	0.391610412583259	2		533	692	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096273	178096273	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	100	517	0	ENST00000397062.3:c.1058G>A	p.Ser353Asn	p.S353N	ENST00000397062	NM_006164.4	353	aGt/aAt	5/5	1	2	FACETS	0.854	0.764	0.949	0.854	0.764	0.949	CLONAL	1	TRUE	1	0.391610412583259	2		517	598	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651282	45651282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	177	817	0	ENST00000407780.3:c.743G>A	p.Ser248Asn	p.S248N	ENST00000407780	NM_001283052.1	248	aGt/aAt	5/7	1	2	FACETS	0.975	0.899	1	0.975	0.899	1	CLONAL	1	TRUE	1	0.391610412583259	2		817	927	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725046	49725046	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371656831	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	191	907	2	ENST00000449682.2:c.298C>T	p.His100Tyr	p.H100Y	ENST00000449682	NM_020998.3	100	Cac/Tac	3/18	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.391610412583259	2		909	895	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961118	55961125	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTGGTCTA	TTGGTCTA	-	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	127	574	0	ENST00000263923.4:c.2818-3_2822del		p.X940_splice	ENST00000263923	NM_002253.2	940		21/30	1	2	FACETS	0.879	0.797	0.965	0.879	0.797	0.965	CLONAL	1	TRUE	1	0.391610412583259	2		574	738	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628014	187628014	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	150	721	0	ENST00000441802.2:c.2968G>A	p.Asp990Asn	p.D990N	ENST00000441802	NM_005245.3	990	Gac/Aac	2/27	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.391610412583259	2		721	741	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294607	1294607	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	127	637	1	ENST00000310581.5:c.394C>T	p.Arg132Trp	p.R132W	ENST00000310581	NM_198253.2	132	Cgg/Tgg	2/16	1	2	FACETS	0.958	0.87	1	0.958	0.87	1	CLONAL	1	TRUE	1	0.391610412583259	2		638	677	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564764	86564764	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	172	984	0	ENST00000274376.6:c.496G>A	p.Glu166Lys	p.E166K	ENST00000274376	NM_002890.2	166	Gag/Aag	1/25	1	2	FACETS	0.88	0.809	0.954	0.88	0.809	0.954	CLONAL	1	TRUE	1	0.391610412583259	2		984	998	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459798	149459798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	157	839	0	ENST00000286301.3:c.409G>A	p.Gly137Ser	p.G137S	ENST00000286301	NM_005211.3	137	Ggc/Agc	4/22	1	2	FACETS	0.935	0.856	1	0.935	0.856	1	CLONAL	1	TRUE	1	0.391610412583259	2		839	858	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017579	112017579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	138	594	1	ENST00000368678.4:c.934G>A	p.Ala312Thr	p.A312T	ENST00000368678		312	Gcg/Acg	9/13	1	2	FACETS	0.938	0.855	1	0.938	0.855	1	CLONAL	1	TRUE	1	0.391610412583259	2		595	751	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686285	117686285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1366263868	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	89	358	1	ENST00000368508.3:c.3056C>T	p.Thr1019Ile	p.T1019I	ENST00000368508	NM_002944.2	1019	aCt/aTt	20/43	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.391610412583259	2		359	449	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469814	157469814	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	185	808	0	ENST00000346085.5:c.2608C>T	p.Pro870Ser	p.P870S	ENST00000346085	NM_020732.3	870	Cca/Tca	9/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.391610412583259	2		808	874	SUCCESS
MET	4233	MSKCC	GRCh37	7	116409846	116409846	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	72	308	0	ENST00000397752.3:c.2730+1G>A		p.X910_splice	ENST00000397752	NM_000245.2	910			0.377986158339099	4	FACETS	1	0.9	1	0.344	0.301	0.39	CLONAL	1	TRUE	1	0.391610412583259	4		308	496	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140549945	140549945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	111	391	0	ENST00000288602.6:c.206G>A	p.Gly69Asp	p.G69D	ENST00000288602	NM_004333.4	69	gGt/gAt	2/18	0.377986158339099	4	FACETS	0.936	0.841	1	0.312	0.28	0.346	CLONAL	1	TRUE	1	0.391610412583259	4		391	843	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540341	23540341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	96	518	0	ENST00000380871.4:c.62C>T	p.Thr21Ile	p.T21I	ENST00000380871	NM_006167.3	21	aCc/aTc	1/2	1	2	FACETS	0.925	0.827	1	0.925	0.827	1	CLONAL	1	TRUE	1	0.391610412583259	2		518	530	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272144	38272144	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	46	692	1	ENST00000425967.3:c.2074C>T	p.Arg692Ter	p.R692*	ENST00000425967	NM_001174067.1	692	Cga/Tga	16/19	1	2	FACETS	0.312	0.262	0.368	0.312	0.262	0.368	SUBCLONAL	1	TRUE	1	0.391610412583259	2		693	753	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561472	141561472	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	131	667	0	ENST00000220592.5:c.1333G>A	p.Gly445Ser	p.G445S	ENST00000220592	NM_012154.3	445	Ggc/Agc	11/19	1	2	FACETS	0.909	0.826	0.996	0.909	0.826	0.996	CLONAL	1	TRUE	1	0.391610412583259	2		667	736	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041063-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	164	395	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.971	0.902	1	0.971	0.902	1	CLONAL	1	TRUE	1	0.831866949863668	2		395	406	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922328	178922328	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041063-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	194	494	0	ENST00000263967.3:c.1097C>G	p.Pro366Arg	p.P366R	ENST00000263967	NM_006218.2	366	cCc/cGc	6/21	1	2	FACETS	0.906	0.845	0.967	0.906	0.845	0.967	CLONAL	1	TRUE	1	0.831866949863668	2		494	515	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0041075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	247	43	1	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.334601594105363	2		44	655	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591888	48591888	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519739	NA	P-0041075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	86	480	0	ENST00000342988.3:c.1051G>C	p.Asp351His	p.D351H	ENST00000342988	NM_005359.5	351	Gat/Cat	9/12	0.334601594105363	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.334601594105363	1		480	367	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988555	41988555	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	91	558	0	ENST00000219905.7:c.1349del	p.Pro450HisfsTer12	p.P450Hfs*12	ENST00000219905	NM_001164273.1	449	agC/ag	3/24	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.334601594105363	2		558	527	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657370	29657370	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	77	609	0	ENST00000356175.3:c.5603A>T	p.Glu1868Val	p.E1868V	ENST00000356175	NM_000267.3	1868	gAg/gTg	38/57	1	2	FACETS	0.919	0.809	1	0.919	0.809	1	CLONAL	1	TRUE	1	0.334601594105363	2		609	501	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046386	128046386	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	87	460	0	ENST00000285398.2:c.877del	p.Ala293GlnfsTer18	p.A293Qfs*18	ENST00000285398	NM_000122.1	293	Gca/ca	7/15	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.334601594105363	2		460	499	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47108609	47108609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0041075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	79	296	0	ENST00000409792.3:c.6061-1G>C		p.X2021_splice	ENST00000409792	NM_014159.6	2021			0.334601594105363	2	FACETS	0.941	0.839	1	0.941	0.839	1	CLONAL	2	TRUE	0	0.334601594105363	2		296	251	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027114	71027114	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs756765084	NA	P-0041075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	84	584	0	ENST00000318789.4:c.1213C>G	p.His405Asp	p.H405D	ENST00000318789	NM_032682.5	405	Cat/Gat	15/21	1	2	FACETS	0.864	0.764	0.971	0.864	0.764	0.971	CLONAL	1	TRUE	1	0.334601594105363	2		584	581	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280188	142280188	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	97	524	0	ENST00000350721.4:c.1246C>A	p.Gln416Lys	p.Q416K	ENST00000350721	NM_001184.3	416	Caa/Aaa	5/47	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.334601594105363	2		524	479	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936070	178936070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	36	415	0	ENST00000263967.3:c.1612G>A	p.Asp538Asn	p.D538N	ENST00000263967	NM_006218.2	538	Gat/Aat	10/21	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.334601594105363	2		415	205	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233660	233660	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	44	115	0	ENST00000264932.6:c.964C>T	p.Gln322Ter	p.Q322*	ENST00000264932	NM_004168.2	322	Caa/Taa	8/15	1	2	FACETS	0.865	0.739	0.999	1	0.969	1	CLONAL	2	TRUE	1	0.334601594105363	2		115	152	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460555	149460555	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	117	788	0	ENST00000286301.3:c.82C>G	p.Pro28Ala	p.P28A	ENST00000286301	NM_005211.3	28	Cct/Gct	3/22	1	2	FACETS	0.948	0.855	1	0.948	0.855	1	CLONAL	1	TRUE	1	0.334601594105363	2		788	738	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950455	68950455	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	55	452	0	ENST00000288368.4:c.767C>G	p.Ser256Cys	p.S256C	ENST00000288368	NM_024870.2	256	tCt/tGt	7/40	1	2	FACETS	0.884	0.759	1	0.884	0.759	1	CLONAL	1	TRUE	1	0.334601594105363	2		452	372	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460567	8460567	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	75	374	0	ENST00000356435.5:c.3719T>A	p.Met1240Lys	p.M1240K	ENST00000356435		1240	aTg/aAg	22/35	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.334601594105363	2		374	346	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0041102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	110	639	2	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	0.352884116340291	4	FACETS	0.87	0.781	0.963	0.435	0.39	0.482	CLONAL	1	FALSE	2	0.483683399779198	4		641	776	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604796	48604798	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0041102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	46	449	0	ENST00000342988.3:c.1619_1621del	p.Leu540del	p.L540del	ENST00000342988	NM_005359.5	540	CTT/-	12/12	0.483683399779198	2	FACETS	1	0.933	1	0.58	0.497	0.668	CLONAL	1	FALSE	0	0.483683399779198	2		449	164	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307172	65307172	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	42	573	0	ENST00000342505.4:c.2516G>A	p.Arg839Gln	p.R839Q	ENST00000342505	NM_002227.2	839	cGa/cAa	18/25	0.352884116340291	4	FACETS	0.776	0.65	0.915	0.388	0.325	0.458	CLONAL	1	FALSE	2	0.483683399779198	4		573	332	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692779	89692780	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	24	532	0	ENST00000371953.3:c.264dup	p.Pro89SerfsTer3	p.P89Sfs*3	ENST00000371953	NM_000314.4	88	tat/taTt	5/9	0.484254329748675	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	2	FALSE	0	0.483683399779198	2		532	47	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475046	40475046	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	143	754	0	ENST00000264657.5:c.1864A>G	p.Thr622Ala	p.T622A	ENST00000264657	NM_139276.2	622	Act/Gct	20/24	0.222687549935192	0	FACETS	0.858	0.791	0.926			1	CLONAL	3	TRUE	0	0.222687549935192	0		754	388	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871068	12871068	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	125	425	0	ENST00000228872.4:c.295T>A	p.Cys99Ser	p.C99S	ENST00000228872	NM_004064.3	99	Tgc/Agc	1/3	0.146791172711933	3	FACETS	1	0.948	1	1	0.988	1	CLONAL	3	TRUE	1	0.222687549935192	3		425	395	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701142	43701142	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0041103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	127	669	0	ENST00000382044.4:c.5553T>A	p.Tyr1851Ter	p.Y1851*	ENST00000382044	NM_001141980.1	1851	taT/taA	26/28	0.222687549935192	1	FACETS	1	0.959	1	1	0.991	1	CLONAL	2	TRUE	0	0.222687549935192	1		669	466	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732399	74732399	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	157	542	0	ENST00000359995.5:c.510G>T	p.Lys170Asn	p.K170N	ENST00000359995	NM_001195427.1	170	aaG/aaT	2/3	0.222687549935192	1	FACETS	1	0.962	1	1	0.992	1	CLONAL	2	TRUE	0	0.222687549935192	1		542	583	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0041107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	27	468	0				ENST00000310581	NM_198253.2	-/1132			0.283859181086773	1	FACETS	0.629	0.502	0.773	0.629	0.502	0.773	SUBCLONAL	1	FALSE	0	0.282338625038789	1		468	261	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0041107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	277	941	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.283859181086773	4	FACETS	0.873	0.821	0.926	0.873	0.821	0.926	CLONAL	3	FALSE	1	0.282338625038789	4		941	961	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039161	49039161	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	137	333	0	ENST00000267163.4:c.2239G>T	p.Glu747Ter	p.E747*	ENST00000267163	NM_000321.2	747	Gag/Tag	22/27	0.282338625038789	8	FACETS	1	0.975	1	0.478	0.435	0.523	CLONAL	2	FALSE	3	0.282338625038789	8		333	750	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	148	285	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	0.283859181086773	2	FACETS	0.979	0.906	1			1	CLONAL	3	FALSE	NA	0.282338625038789	2		285	357	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972418	32972418	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	340	753	0	ENST00000380152.3:c.9768G>C	p.Glu3256Asp	p.E3256D	ENST00000380152		3256	gaG/gaC	27/27	0.282338625038789	8	FACETS	0.988	0.935	1	0.79	0.748	0.833	CLONAL	4	FALSE	3	0.282338625038789	8		753	1126	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916748	48916758	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAGAAAAAG	AAAAGAAAAAG	-	novel	NA	P-0041107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	165	453	0	ENST00000267163.4:c.278_288del	p.Gln93ArgfsTer13	p.Q93Rfs*13	ENST00000267163	NM_000321.2	93	cAAAAGAAAAAG/c	3/27	0.282338625038789	8	FACETS	0.991	0.912	1	0.595	0.547	0.644	CLONAL	3	FALSE	3	0.282338625038789	8		453	726	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098999	178098999	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	103	297	0	ENST00000397062.3:c.46G>C	p.Asp16His	p.D16H	ENST00000397062	NM_006164.4	16	Gac/Cac	2/5	0.283859181086773	5	FACETS	1	0.952	1	0.733	0.66	0.811	CLONAL	2	FALSE	2	0.282338625038789	5		297	472	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289223	33289223	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	197	703	0	ENST00000374542.5:c.329C>G	p.Ser110Cys	p.S110C	ENST00000374542	NM_001141970.1	110	tCt/tGt	3/8	0.282338625038789	11	FACETS	0.944	0.873	1	0.472	0.436	0.509	CLONAL	3	FALSE	5	0.282338625038789	11		703	1119	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527432	137527432	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	28	343	0	ENST00000367739.4:c.214G>A	p.Glu72Lys	p.E72K	ENST00000367739	NM_000416.2	72	Gaa/Aaa	3/7	0.282338625038789	5	FACETS	0.543	0.433	0.669			1	SUBCLONAL	1	FALSE	NA	0.282338625038789	5		343	520	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38135837	38135837	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	138	591	0	ENST00000317025.8:c.3854G>C	p.Gly1285Ala	p.G1285A	ENST00000317025	NM_023034.1	1285	gGa/gCa	22/24	0.282338625038789	5	FACETS	0.86	0.783	0.941			1	CLONAL	2	FALSE	NA	0.282338625038789	5		591	809	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038759	47038759	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs868971914	NA	P-0041107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	128	535	0	ENST00000377604.3:c.766C>T	p.Gln256Ter	p.Q256*	ENST00000377604	NM_001204468.1	256	Cag/Tag	9/24	0.283859181086773	2	FACETS	0.835	0.765	0.906			1	CLONAL	3	FALSE	NA	0.282338625038789	2		535	362	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236086	108236086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782292	NA	P-0041108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	141	564	0	ENST00000278616.4:c.9022C>T	p.Arg3008Cys	p.R3008C	ENST00000278616	NM_000051.3	3008	Cgt/Tgt	63/63	0.187244067704866	2	FACETS	0.906	0.826	0.99	0.906	0.826	0.99	CLONAL	2	FALSE	0	0.187244067704866	2		564	831	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208046	5208046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142977438	NA	P-0041108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1314	98	779	0	ENST00000357368.4:c.5665G>A	p.Val1889Ile	p.V1889I	ENST00000357368	NM_002850.3	1889	Gtc/Atc	37/38	1	2	FACETS	0.741	0.659	0.83	0.741	0.659	0.83	SUBCLONAL	1	FALSE	1	0.187244067704866	2		779	1412	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728500	190728500	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	82	501	0	ENST00000441310.2:c.1888C>G	p.Arg630Gly	p.R630G	ENST00000441310	NM_000534.4	630	Cga/Gga	10/13	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.187244067704866	2		501	592	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	155	395	0				ENST00000310581	NM_198253.2	-/1132			0.176324288329754	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		395	349	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0041117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	115	411	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		411	382	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151892994	151892994	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0041118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	66	233	0	ENST00000262189.6:c.4376C>G	p.Ser1459Ter	p.S1459*	ENST00000262189	NM_170606.2	1459	tCa/tGa	28/59	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.574353803832326	2		233	199	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849484	68849484	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	151	659	1	ENST00000261769.5:c.1387G>C	p.Glu463Gln	p.E463Q	ENST00000261769	NM_004360.3	463	Gag/Cag	10/16	0.293942326924683	1	FACETS	1	0.931	1	1	0.931	1	INDETERMINATE	1	TRUE	0	0.574353803832326	1		660	373	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144612	119144612	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs767162260	NA	P-0041118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	41	405	0	ENST00000264033.4:c.625C>G	p.Leu209Val	p.L209V	ENST00000264033	NM_005188.3	209	Cta/Gta	4/16	1	2	FACETS	0.453	0.379	0.535	0.453	0.379	0.535	SUBCLONAL	1	TRUE	1	0.574353803832326	2		405	315	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051204	128051204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1251238422	NA	P-0041118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	127	713	1	ENST00000285398.2:c.119C>T	p.Ser40Leu	p.S40L	ENST00000285398	NM_000122.1	40	tCg/tTg	2/15	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.574353803832326	2		714	430	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21968242	21968242	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0041118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	96	396	0	ENST00000304494.5:c.458-1G>C		p.X153_splice	ENST00000304494	NM_000077.4	153			0.571768959902844	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.574353803832326	1		396	229	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748582	43748582	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	176	944	0	ENST00000382044.4:c.2224G>T	p.Glu742Ter	p.E742*	ENST00000382044	NM_001141980.1	742	Gaa/Taa	12/28	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.574353803832326	2		944	604	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332307	70332307	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	117	468	1	ENST00000373644.4:c.212G>T	p.Arg71Ile	p.R71I	ENST00000373644	NM_030625.2	71	aGa/aTa	2/12	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.574353803832326	2		469	386	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443534	49443534	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	115	697	0	ENST00000301067.7:c.3837C>G	p.Ile1279Met	p.I1279M	ENST00000301067	NM_003482.3	1279	atC/atG	11/54	1	2	FACETS	0.923	0.837	1	0.923	0.837	1	CLONAL	1	TRUE	1	0.574353803832326	2		697	434	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443583	49443583	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0041118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	126	789	0	ENST00000301067.7:c.3788C>G	p.Ser1263Ter	p.S1263*	ENST00000301067	NM_003482.3	1263	tCa/tGa	11/54	1	2	FACETS	0.905	0.824	0.988	0.905	0.824	0.988	CLONAL	1	TRUE	1	0.574353803832326	2		789	485	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966987	25966987	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	130	834	0	ENST00000435504.4:c.2219C>T	p.Thr740Met	p.T740M	ENST00000435504		740	aCg/aTg	13/13	1	2	FACETS	0.869	0.792	0.949	0.869	0.792	0.949	CLONAL	1	TRUE	1	0.574353803832326	2		834	521	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99136536	99136536	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781317145	NA	P-0041118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	122	789	1	ENST00000074304.5:c.25C>T	p.Arg9Cys	p.R9C	ENST00000074304	NM_001134224.1	9	Cgc/Tgc	3/26	1	2	FACETS	0.926	0.842	1	0.926	0.842	1	CLONAL	1	TRUE	1	0.574353803832326	2		790	459	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156003	106156003	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	36	316	0	ENST00000380013.4:c.904G>C	p.Asp302His	p.D302H	ENST00000380013	NM_001127208.2	302	Gat/Cat	3/11	1	2	FACETS	0.379	0.312	0.453	0.379	0.312	0.453	SUBCLONAL	1	TRUE	1	0.574353803832326	2		316	331	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287454	33287475	+	frameshift_variant	Frame_Shift_Del	DEL	TTGCTTTCAGCATCTATGCTGG	TTGCTTTCAGCATCTATGCTGG	-	novel	NA	P-0041118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	113	654	0	ENST00000374542.5:c.1622_1643del	p.Ser541LeufsTer8	p.S541Lfs*8	ENST00000374542	NM_001141970.1	541	tCCAGCATAGATGCTGAAAGCAAt/tt	6/8	1	2	FACETS	0.867	0.785	0.952	0.867	0.785	0.952	CLONAL	1	TRUE	1	0.574353803832326	2		654	454	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058521	69058521	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	86	600	0	ENST00000288368.4:c.4165G>C	p.Glu1389Gln	p.E1389Q	ENST00000288368	NM_024870.2	1389	Gaa/Caa	34/40	1	2	FACETS	0.711	0.633	0.795	0.711	0.633	0.795	SUBCLONAL	1	TRUE	1	0.574353803832326	2		600	421	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864071	97864071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55939573	NA	P-0041118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	132	631	1	ENST00000289081.3:c.1595G>A	p.Arg532Lys	p.R532K	ENST00000289081	NM_000136.2	532	aGa/aAa	15/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.574353803832326	2		632	415	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0041120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	72	63	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.815	0.715	0.922	0.815	0.715	0.922	CLONAL	1	TRUE	1	0.408153069253574	2		63	433	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0041120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	83	368	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.408153069253574	2		368	405	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0041120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	100	103	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.408153069253574	2		103	455	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435297	110435302	+	inframe_deletion	In_Frame_Del	DEL	GGCGGT	GGCGGT	-	rs761851705	NA	P-0041120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	91	194	0	ENST00000375856.3:c.3099_3104del	p.Pro1035_Pro1036del	p.P1035_P1036del	ENST00000375856	NM_003749.2	1033	ccACCGCCg/ccg	1/2	0.385752728898229	3	FACETS	0.78	0.699	0.865	0.78	0.699	0.865	SUBCLONAL	2	TRUE	1	0.408153069253574	3		194	344	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619223	43619223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	124	635	0	ENST00000355710.3:c.2906G>A	p.Arg969Gln	p.R969Q	ENST00000355710	NM_020975.4	969	cGg/cAg	17/20	0.207603075305753	1	FACETS	0.774	0.702	0.849	0.774	0.702	0.849	INDETERMINATE	1	TRUE	0	0.408153069253574	1		635	625	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222823	5222823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201423065	NA	P-0041120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	185	619	1	ENST00000357368.4:c.2980G>A	p.Ala994Thr	p.A994T	ENST00000357368	NM_002850.3	994	Gcg/Acg	18/38	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.408153069253574	2		620	763	SUCCESS
APC	324	MSKCC	GRCh37	5	112102032	112102035	+	frameshift_variant	Frame_Shift_Del	DEL	AAAC	AAAC	-	rs587781694	NA	P-0041120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	38	299	0	ENST00000257430.4:c.147_150del	p.Lys49AsnfsTer20	p.K49Nfs*20	ENST00000257430	NM_000038.5	49	AAACaa/aa	3/16	1	2	FACETS	0.73	0.607	0.865	0.73	0.607	0.865	SUBCLONAL	1	TRUE	1	0.408153069253574	2		299	255	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324622	31324622	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	99	569	0	ENST00000412585.2:c.186del	p.Ser62ArgfsTer15	p.S62Rfs*15	ENST00000412585	NM_005514.6	62	agC/ag	2/8	1	2	FACETS	0.829	0.742	0.922	0.829	0.742	0.922	CLONAL	1	TRUE	1	0.408153069253574	2		569	585	SUCCESS
AR	367	MSKCC	GRCh37	X	66765217	66765217	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555969528	NA	P-0041120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	73	352	1	ENST00000374690.3:c.229C>T	p.Gln77Ter	p.Q77*	ENST00000374690	NM_000044.3	77	Cag/Tag	1/8	0.385752728898229	3	FACETS	0.997	0.876	1	0.499	0.437	0.564	CLONAL	1	TRUE	1	0.408153069253574	3		353	432	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0041125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	64	441	2	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.719	0.622	0.824	0.719	0.622	0.824	SUBCLONAL	1	TRUE	1	0.28	2		443	636	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477807	140477807	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs180177038	NA	P-0041125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	84	511	0	ENST00000288602.6:c.1501G>A	p.Glu501Lys	p.E501K	ENST00000288602	NM_004333.4	501	Gaa/Aaa	12/18	1	2	FACETS	0.739	0.652	0.833	0.739	0.652	0.833	SUBCLONAL	1	TRUE	1	0.28	2		511	812	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11291488	11291488	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	66	497	0	ENST00000361445.4:c.2518G>T	p.Ala840Ser	p.A840S	ENST00000361445	NM_004958.3	840	Gct/Tct	17/58	1	2	FACETS	0.742	0.644	0.849	0.742	0.644	0.849	SUBCLONAL	1	TRUE	1	0.28	2		497	635	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097657	8097657	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	70	432	0	ENST00000346208.3:c.39C>A	p.His13Gln	p.H13Q	ENST00000346208		13	caC/caA	2/6	1	2	FACETS	0.943	0.824	1	0.943	0.824	1	CLONAL	1	TRUE	1	0.28	2		432	530	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759849	63759849	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0041125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	33	325	0	ENST00000279873.7:c.503-1G>C		p.X168_splice	ENST00000279873	NM_032199.2	168			1	2	FACETS	0.532	0.433	0.644	0.532	0.433	0.644	SUBCLONAL	1	TRUE	1	0.28	2		325	443	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794889	242794889	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	132	937	0	ENST00000334409.5:c.320A>T	p.His107Leu	p.H107L	ENST00000334409	NM_005018.2	107	cAc/cTc	2/5	1	2	FACETS	0.821	0.744	0.903	0.821	0.744	0.903	CLONAL	1	TRUE	1	0.28	2		937	1148	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133621	55133621	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	76	502	0	ENST00000257290.5:c.925G>T	p.Val309Phe	p.V309F	ENST00000257290	NM_006206.4	309	Gtc/Ttc	6/23	1	2	FACETS	0.847	0.743	0.959	0.847	0.743	0.959	CLONAL	1	TRUE	1	0.28	2		502	641	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149447870	149447870	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1169	118	977	0	ENST00000286301.3:c.1534G>T	p.Glu512Ter	p.E512*	ENST00000286301	NM_005211.3	512	Gag/Tag	11/22	1	2	FACETS	0.655	0.589	0.725	0.655	0.589	0.725	SUBCLONAL	1	TRUE	1	0.28	2		977	1287	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545811	106545811	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	65	448	0	ENST00000359195.3:c.3288A>T	p.Gln1096His	p.Q1096H	ENST00000359195	NM_002649.2	1096	caA/caT	11/11	1	2	FACETS	0.805	0.698	0.92	0.805	0.698	0.92	CLONAL	1	TRUE	1	0.28	2		448	577	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404368	139404368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	137	949	0	ENST00000277541.6:c.2786C>T	p.Ala929Val	p.A929V	ENST00000277541	NM_017617.3	929	gCc/gTc	18/34	1	2	FACETS	0.73	0.662	0.802	0.73	0.662	0.802	SUBCLONAL	1	TRUE	1	0.28	2		949	1340	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0041125-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	56	441	2	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.220879312970753	2		443	507	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023805	27023805	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041125-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	62	358	0	ENST00000324856.7:c.911C>A	p.Ser304Ter	p.S304*	ENST00000324856	NM_006015.4	304	tCg/tAg	1/20	0.220879312970753	1	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	0	0.220879312970753	1		358	496	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521724	89521724	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041125-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	65	320	0	ENST00000336596.2:c.2801G>T	p.Gly934Val	p.G934V	ENST00000336596	NM_005233.5	934	gGt/gTt	16/17	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.220879312970753	2		320	493	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828071	72828071	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041125-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	91	649	0	ENST00000268489.5:c.8510C>G	p.Ser2837Cys	p.S2837C	ENST00000268489	NM_006885.3	2837	tCt/tGt	9/10	1	2	FACETS	0.911	0.808	1	0.911	0.808	1	CLONAL	1	TRUE	1	0.220879312970753	2		649	904	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539741	187539741	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041125-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	48	329	0	ENST00000441802.2:c.7999G>T	p.Glu2667Ter	p.E2667*	ENST00000441802	NM_005245.3	2667	Gaa/Taa	10/27	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.220879312970753	2		329	415	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980310	201980310	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041125-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	60	569	0	ENST00000359651.3:c.46A>T	p.Ser16Cys	p.S16C	ENST00000359651		16	Agt/Tgt	1/8	0.153747997126476	3	FACETS	0.638	0.548	0.737	0.213	0.182	0.246	SUBCLONAL	1	TRUE	0	0.220879312970753	3		569	945	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432863	432863	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041125-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	31	366	0	ENST00000399788.2:c.2053C>A	p.Leu685Ile	p.L685I	ENST00000399788	NM_001042603.1	685	Ctc/Atc	15/28	0.220879312970753	1	FACETS	0.414	0.334	0.505	0.414	0.334	0.505	SUBCLONAL	1	TRUE	0	0.220879312970753	1		366	603	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445303	49445303	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041125-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	52	740	0	ENST00000301067.7:c.2163G>T	p.Glu721Asp	p.E721D	ENST00000301067	NM_003482.3	721	gaG/gaT	10/54	1	2	FACETS	0.541	0.459	0.632	0.541	0.459	0.632	SUBCLONAL	1	TRUE	1	0.220879312970753	2		740	870	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893672	28893672	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0041125-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	32	282	0	ENST00000282397.4:c.3175-1G>C		p.X1059_splice	ENST00000282397	NM_002019.4	1059			1	2	FACETS	0.688	0.558	0.835	0.688	0.558	0.835	SUBCLONAL	1	TRUE	1	0.220879312970753	2		282	421	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95599738	95599738	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041125-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	40	325	0	ENST00000393063.1:c.58G>T	p.Ala20Ser	p.A20S	ENST00000393063	NM_030621.3	20	Gct/Tct	3/28	0.0561149394788136	3	FACETS	0.902	0.75	1	0.451	0.375	0.536	INDETERMINATE	1	TRUE	1	0.220879312970753	3		325	446	SUCCESS
YES1	7525	MSKCC	GRCh37	18	747928	747928	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041125-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	51	308	0	ENST00000314574.4:c.462G>T	p.Gln154His	p.Q154H	ENST00000314574	NM_005433.3	154	caG/caT	4/12	0.0561149394788136	3	FACETS	0.992	0.843	1	0.496	0.421	0.578	INDETERMINATE	1	TRUE	1	0.220879312970753	3		308	517	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867739	45867739	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041125-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	98	730	0	ENST00000391945.4:c.661G>T	p.Val221Leu	p.V221L	ENST00000391945	NM_000400.3	221	Gtg/Ttg	8/23	0.220879312970753	1	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	0	0.220879312970753	1		730	785	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157749	106157749	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041125-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	32	193	0	ENST00000380013.4:c.2650C>T	p.Gln884Ter	p.Q884*	ENST00000380013	NM_001127208.2	884	Caa/Taa	3/11	1	2	FACETS	1	0.83	1	1	0.83	1	CLONAL	1	TRUE	1	0.220879312970753	2		193	284	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839744	27839744	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041125-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	73	479	0	ENST00000328488.2:c.350G>T	p.Arg117Leu	p.R117L	ENST00000328488	NM_003533.2	117	cGc/cTc	1/1	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.220879312970753	2		479	629	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92244531	92244531	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041125-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	57	289	0	ENST00000265734.4:c.904G>T	p.Asp302Tyr	p.D302Y	ENST00000265734	NM_001259.6	302	Gac/Tac	8/8	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.220879312970753	2		289	485	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908773	101908773	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041125-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	42	242	0	ENST00000374994.4:c.1137G>C	p.Met379Ile	p.M379I	ENST00000374994	NM_004612.2	379	atG/atC	7/9	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.220879312970753	2		242	314	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040779	47040779	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041125-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	100	665	0	ENST00000377604.3:c.1416del	p.Asp474IlefsTer11	p.D474Ifs*11	ENST00000377604	NM_001204468.1	472	Aaa/aa	13/24	0.220879312970753	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.220879312970753	1		665	681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0041150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	449	868	4	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	NA	2	FACETS	0.981	0.944	1			1	INDETERMINATE	2	TRUE	NA	0.584769965592791	2		872	783	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778083	3778083	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	253	1226	0	ENST00000262367.5:c.6965C>T	p.Ser2322Leu	p.S2322L	ENST00000262367	NM_004380.2	2322	tCa/tTa	31/31	1	2	FACETS	0.965	0.904	1	0.965	0.904	1	CLONAL	1	TRUE	1	0.584769965592791	2		1226	897	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898765	134898765	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	117	449	0	ENST00000398015.3:c.1823G>T	p.Arg608Leu	p.R608L	ENST00000398015	NM_004441.4	608	cGg/cTg	10/16	0.554285386736166	3	FACETS	1	0.924	1	0.511	0.463	0.561	CLONAL	1	TRUE	1	0.584769965592791	3		449	506	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167753	185167753	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0041150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	179	620	0	ENST00000265026.3:c.1076C>G	p.Ser359Ter	p.S359*	ENST00000265026	NM_004721.4	359	tCa/tGa	6/14	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.584769965592791	2		620	564	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604340	189604340	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	114	446	0	ENST00000264731.3:c.1507A>G	p.Ile503Val	p.I503V	ENST00000264731	NM_003722.4	503	Att/Gtt	11/14	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.584769965592791	2		446	385	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938364	76938364	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	288	663	0	ENST00000373344.5:c.2384del	p.Gly795AlafsTer8	p.G795Afs*8	ENST00000373344	NM_000489.3	795	gGc/gc	9/35	0.584769965592791	2	FACETS	0.977	0.932	1	0.977	0.932	1	CLONAL	2	TRUE	0	0.584769965592791	2		663	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0041163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	127	618	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.617626376977943	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	0	0.589122353853027	1		618	294	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120535161	120535161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	86	488	1	ENST00000229340.5:c.494C>T	p.Thr165Met	p.T165M	ENST00000229340	NM_006861.6	165	aCg/aTg	6/6	NA	2	FACETS	0.684	0.608	0.764			1	INDETERMINATE	1	FALSE	NA	0.589122353853027	2		489	427	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108059	30108059	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	99	697	1	ENST00000331968.5:c.748C>A	p.Gln250Lys	p.Q250K	ENST00000331968	NM_002742.2	250	Caa/Aaa	5/18	0.521939083737867	2	FACETS	0.739	0.663	0.818	0.369	0.331	0.409	SUBCLONAL	1	FALSE	0	0.589122353853027	2		698	455	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423486	116423486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45454696	NA	P-0041163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	58	382	0	ENST00000397752.3:c.3761G>A	p.Ser1254Asn	p.S1254N	ENST00000397752	NM_000245.2	1254	aGt/aAt	19/21	0.597522640950165	3	FACETS	0.761	0.657	0.872	0.38	0.328	0.436	SUBCLONAL	1	FALSE	1	0.589122353853027	3		382	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577129	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519986	NA	P-0041165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	429	682	0	ENST00000269305.4:c.809T>C	p.Phe270Ser	p.F270S	ENST00000269305	NM_001126112.2	270	tTt/tCt	8/11	0.8769283653521	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.881026654782605	2		682	474	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735635	204735635	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	281	434	0	ENST00000302823.3:c.436G>T	p.Gly146Ter	p.G146*	ENST00000302823	NM_005214.4	146	Gga/Tga	2/4	0.881026654782605	3	FACETS	0.969	0.925	1	0.969	0.925	1	CLONAL	2	TRUE	1	0.881026654782605	3		434	474	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332738	65332738	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	268	460	4	ENST00000342505.4:c.801G>T	p.Lys267Asn	p.K267N	ENST00000342505	NM_002227.2	267	aaG/aaT	7/25	0.323350521411858	6	FACETS	0.935	0.885	0.986	0.701	0.663	0.739	INDETERMINATE	3	TRUE	2	0.881026654782605	6		464	599	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934244	48934244	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	198	404	0	ENST00000267163.4:c.699del	p.Met233IlefsTer31	p.M233Ifs*31	ENST00000267163	NM_000321.2	233	atG/at	7/27	0.8769283653521	2	FACETS	0.944	0.91	0.976	0.944	0.91	0.976	CLONAL	2	TRUE	0	0.881026654782605	2		404	238	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455613	189455613	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	289	508	4	ENST00000264731.3:c.147C>A	p.Phe49Leu	p.F49L	ENST00000264731	NM_003722.4	49	ttC/ttA	2/14	0.792783931636013	4	FACETS	0.995	0.944	1	0.995	0.944	1	CLONAL	2	TRUE	2	0.881026654782605	4		512	620	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197779	66197779	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	403	403	2	ENST00000273854.3:c.2920C>A	p.Leu974Ile	p.L974I	ENST00000273854	NM_004439.5	974	Cta/Ata	17/18	0.840026097116485	3	FACETS	0.968	0.947	0.986	0.968	0.947	0.986	CLONAL	3	TRUE	0	0.881026654782605	3		405	454	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948296	31948296	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	380	777	5	ENST00000375333.2:c.884C>T	p.Ala295Val	p.A295V	ENST00000375333	NM_032454.1	295	gCt/gTt	6/8	0.792783931636013	4	FACETS	0.988	0.944	1	0.988	0.944	1	CLONAL	2	TRUE	2	0.881026654782605	4		782	821	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255773	16255773	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745325343	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	148	453	0	ENST00000375759.3:c.3038G>A	p.Arg1013His	p.R1013H	ENST00000375759	NM_015001.2	1013	cGc/cAc	11/15	1	2	FACETS	1	0.973	1	1	0.992	1	CLONAL	2	TRUE	1	0.33	2		453	401	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599897	28599897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145754239	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	180	655	0	ENST00000253063.3:c.779C>T	p.Ala260Val	p.A260V	ENST00000253063	NM_031459.4	260	gCg/gTg	6/10	1	2	FACETS	1	0.976	1	1	0.994	1	CLONAL	2	TRUE	1	0.33	2		655	493	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363231	40363231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768216635	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	95	542	0	ENST00000397332.2:c.998C>T	p.Ala333Val	p.A333V	ENST00000397332	NM_001033082.2	333	gCg/gTg	3/3	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.33	2		542	527	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406655	70406655	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	34	588	2	ENST00000373644.4:c.4169G>T	p.Ser1390Ile	p.S1390I	ENST00000373644	NM_030625.2	1390	aGt/aTt	4/12	0.273869825844014	3	FACETS	0.405	0.33	0.49			1	SUBCLONAL	1	TRUE	NA	0.33	3		590	593	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200122	67200122	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780978333	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	212	642	0	ENST00000312629.5:c.509C>T	p.Thr170Met	p.T170M	ENST00000312629	NM_003952.2	170	aCg/aTg	6/15	1	2	FACETS	1	0.973	1	1	0.994	1	CLONAL	2	TRUE	1	0.33	2		642	598	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202635	67202635	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202063609	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	171	594	0	ENST00000312629.5:c.1444C>T	p.Arg482Cys	p.R482C	ENST00000312629	NM_003952.2	482	Cgc/Tgc	15/15	1	2	FACETS	1	0.951	1	1	0.993	1	CLONAL	2	TRUE	1	0.33	2		594	502	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641389	18641389	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1229278001	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	90	227	1	ENST00000266497.5:c.2393del	p.Asn798MetfsTer16	p.N798Mfs*16	ENST00000266497		796	ctA/ct	17/31	0.0892785354859775	3	FACETS	1	0.967	1	1	0.967	1	INDETERMINATE	2	TRUE	1	0.33	3		228	269	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434502	49434502	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	196	726	0	ENST00000301067.7:c.7051G>T	p.Glu2351Ter	p.E2351*	ENST00000301067	NM_003482.3	2351	Gag/Tag	31/54	0.0892785354859775	3	FACETS	0.875	0.817	0.935	1	0.989	1	INDETERMINATE	3	TRUE	1	0.33	3		726	527	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	90	659	1	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	0.0892785354859775	3	FACETS	1	0.969	1	0.629	0.56	0.702	INDETERMINATE	1	TRUE	1	0.33	3		660	505	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856392	111856392	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868066223	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	75	241	1	ENST00000341259.2:c.443G>A	p.Arg148His	p.R148H	ENST00000341259	NM_005475.2	148	cGc/cAc	2/8	0.3	1	FACETS	0.883	0.787	0.981	1	0.983	1	CLONAL	2	TRUE	0	0.33	1		242	215	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926270	112926270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918457	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	170	492	1	ENST00000351677.2:c.1403C>T	p.Thr468Met	p.T468M	ENST00000351677	NM_002834.3	468	aCg/aTg	12/16	0.3	1	FACETS	0.964	0.896	1	1	0.993	1	CLONAL	2	TRUE	0	0.33	1		493	446	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435057	110435057	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1449182090	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	244	781	0	ENST00000375856.3:c.3344C>T	p.Ser1115Leu	p.S1115L	ENST00000375856	NM_003749.2	1115	tCg/tTg	1/2	0.0304815228867676	3	FACETS	1	0.988	1	1	0.988	1	INDETERMINATE	2	TRUE	1	0.33	3		781	707	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435136	110435136	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs780127725	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	241	726	0	ENST00000375856.3:c.3265G>C	p.Ala1089Pro	p.A1089P	ENST00000375856	NM_003749.2	1089	Gcc/Ccc	1/2	0.0304815228867676	3	FACETS	1	0.989	1	1	0.989	1	INDETERMINATE	2	TRUE	1	0.33	3		726	684	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021365	42021365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs984878518	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	147	359	0	ENST00000219905.7:c.3661C>T	p.Arg1221Trp	p.R1221W	ENST00000219905	NM_001164273.1	1221	Cgg/Tgg	11/24	1	2	FACETS	1	0.983	1	1	0.993	1	CLONAL	2	TRUE	1	0.33	2		359	365	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465624	99465624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771088781	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	130	541	0	ENST00000268035.6:c.2449G>A	p.Ala817Thr	p.A817T	ENST00000268035	NM_000875.3	817	Gcc/Acc	11/21	1	2	FACETS	0.975	0.893	1	1	0.99	1	CLONAL	2	TRUE	1	0.33	2		541	404	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830755	3830755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	105	471	0	ENST00000262367.5:c.1801C>T	p.Arg601Trp	p.R601W	ENST00000262367	NM_004380.2	601	Cgg/Tgg	8/31	1	2	FACETS	0.933	0.845	1	1	0.988	1	CLONAL	2	TRUE	1	0.33	2		471	341	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041941	14041941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	113	371	0	ENST00000311895.7:c.2488G>A	p.Ala830Thr	p.A830T	ENST00000311895	NM_005236.2	830	Gcc/Acc	11/11	1	2	FACETS	1	0.968	1	1	0.99	1	CLONAL	2	TRUE	1	0.33	2		371	303	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56871638	56871638	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs199837299	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	22	424	1	ENST00000308159.5:c.2018G>A	p.Arg673Gln	p.R673Q	ENST00000308159	NM_014669.4	673	cGg/cAg	18/22	1	2	FACETS	0.404	0.313	0.51	0.404	0.313	0.51	SUBCLONAL	1	TRUE	1	0.33	2		425	330	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	91	393	1	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	1	0.915	1	1	0.987	1	CLONAL	2	TRUE	1	0.33	2		394	271	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831707	72831707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1313031657	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	151	608	0	ENST00000268489.5:c.4874G>A	p.Arg1625Gln	p.R1625Q	ENST00000268489	NM_006885.3	1625	cGg/cAg	9/10	1	2	FACETS	1	0.972	1	1	0.993	1	CLONAL	2	TRUE	1	0.33	2		608	412	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40451823	40451823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374346157	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	111	446	1	ENST00000345506.4:c.605C>T	p.Thr202Met	p.T202M	ENST00000345506	NM_003152.3	202	aCg/aTg	7/20	1	2	FACETS	0.981	0.892	1	1	0.989	1	CLONAL	2	TRUE	1	0.33	2		447	343	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55729499	55729499	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772529843	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	240	781	1	ENST00000284073.2:c.767C>T	p.Ala256Val	p.A256V	ENST00000284073	NM_138962.2	256	gCg/gTg	11/14	1	2	FACETS	1	0.989	1	1	0.995	1	CLONAL	2	TRUE	1	0.33	2		782	593	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919507	78919507	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	29	622	0	ENST00000306801.3:c.3069del	p.Gly1024AlafsTer6	p.G1024Afs*6	ENST00000306801	NM_020761.2	1022	aaC/aa	26/34	0.274414944093325	0	FACETS	0.282	0.226	0.346			1	SUBCLONAL	1	TRUE	0	0.33	0		622	417	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096021	11096021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778890805	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	228	801	3	ENST00000358026.2:c.295C>T	p.Arg99Trp	p.R99W	ENST00000358026	NM_001128849.1	99	Cgg/Tgg	3/36	1	2	FACETS	1	0.985	1	1	0.995	1	CLONAL	2	TRUE	1	0.33	2		804	601	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097604	11097604	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	188	757	0	ENST00000358026.2:c.788del	p.Pro263GlnfsTer40	p.P263Qfs*40	ENST00000358026	NM_001128849.1	262	Ccc/cc	5/36	1	2	FACETS	0.989	0.92	1	1	0.993	1	CLONAL	2	TRUE	1	0.33	2		757	576	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141492	11141492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	163	765	0	ENST00000358026.2:c.3469C>T	p.Arg1157Trp	p.R1157W	ENST00000358026	NM_001128849.1	1157	Cgg/Tgg	25/36	1	2	FACETS	1	0.939	1	1	0.993	1	CLONAL	2	TRUE	1	0.33	2		765	486	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152070	11152070	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772153816	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	196	597	0	ENST00000358026.2:c.4354G>A	p.Gly1452Ser	p.G1452S	ENST00000358026	NM_001128849.1	1452	Ggc/Agc	31/36	1	2	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	1	0.33	2		597	487	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753149	42753151	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs199960550	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	172	695	4	ENST00000222329.4:c.1113_1115del	p.Ser373del	p.S373del	ENST00000222329	NM_006494.2	371	tcTTCc/tcc	4/4	0.0304815228867676	3	FACETS	1	0.953	1	1	0.953	1	INDETERMINATE	2	TRUE	1	0.33	3		699	584	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086076	16086076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760647298	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	164	653	0	ENST00000281043.3:c.1252G>A	p.Ala418Thr	p.A418T	ENST00000281043	NM_005378.4	418	Gcc/Acc	3/3	1	2	FACETS	1	0.954	1	1	0.993	1	CLONAL	2	TRUE	1	0.33	2		653	477	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702239	47702239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	187	269	0	ENST00000233146.2:c.1835C>A	p.Ser612Ter	p.S612*	ENST00000233146	NM_000251.2	612	tCa/tAa	12/16	1	2	FACETS	1	0.985	1	1	0.995	1	CLONAL	4	TRUE	1	0.33	2		269	261	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945359	54945359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	71	557	0	ENST00000312783.6:c.1067C>T	p.Ala356Val	p.A356V	ENST00000312783	NM_198436.1	356	gCc/gTc	10/10	0.3	1	FACETS	0.807	0.707	0.915	0.807	0.707	0.915	CLONAL	1	TRUE	0	0.33	1		557	445	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	177	708	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	1	2	FACETS	1	0.97	1	1	0.993	1	CLONAL	2	TRUE	1	0.33	2		708	497	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400009	49400009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2107830267	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	228	647	2	ENST00000418115.1:c.328G>A	p.Val110Met	p.V110M	ENST00000418115	NM_001664.2	110	Gtg/Atg	4/5	1	2	FACETS	1	0.967	1	1	0.995	1	CLONAL	2	TRUE	1	0.33	2		649	659	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014202	70014202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143537610	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	215	729	2	ENST00000394351.3:c.1063G>A	p.Gly355Arg	p.G355R	ENST00000394351	NM_000248.3	355	Gga/Aga	9/9	1	2	FACETS	1	0.961	1	1	0.994	1	CLONAL	2	TRUE	1	0.33	2		731	627	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027014	71027014	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	205	541	0	ENST00000318789.4:c.1313G>A	p.Arg438Gln	p.R438Q	ENST00000318789	NM_032682.5	438	cGg/cAg	15/21	1	2	FACETS	1	0.968	1	1	0.994	1	CLONAL	2	TRUE	1	0.33	2		541	586	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	198	600	1	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	0.871	0.816	0.927	1	0.995	1	CLONAL	3	TRUE	1	0.33	2		601	459	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806119	1806119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931614	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	263	815	0	ENST00000260795.2:c.1138G>A	p.Gly380Arg	p.G380R	ENST00000260795		380	Ggg/Agg	8/17	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.33	2		815	655	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515165	149515165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs544478083	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	203	675	0	ENST00000261799.4:c.317G>A	p.Arg106His	p.R106H	ENST00000261799	NM_002609.3	106	cGt/cAt	3/23	0.3	1	FACETS	0.911	0.851	0.972	1	0.993	1	CLONAL	2	TRUE	0	0.33	1		675	564	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225647	26225647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746543899	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	240	515	0	ENST00000360408.1:c.265G>A	p.Ala89Thr	p.A89T	ENST00000360408	NM_003532.2	89	Gcg/Acg	1/1	0.3	5	FACETS	1	0.967	1	1	0.993	1	CLONAL	3	TRUE	3	0.33	5		515	693	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912306	29912306	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761593088	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	204	640	0	ENST00000376809.5:c.925G>A	p.Val309Met	p.V309M	ENST00000376809	NM_002116.7	309	Gtg/Atg	5/8	0.0304815228867676	3	FACETS	1	0.979	1	1	0.979	1	INDETERMINATE	2	TRUE	1	0.33	3		640	643	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552891	106552891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771056895	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	309	747	0	ENST00000369096.4:c.856C>T	p.Arg286Cys	p.R286C	ENST00000369096	NM_001198.3	286	Cgt/Tgt	5/7	0.0304815228867676	3	FACETS	1	0.986	1	1	0.986	1	INDETERMINATE	2	TRUE	1	0.33	3		747	971	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845415	151845415	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	209	633	0	ENST00000262189.6:c.13597C>T	p.Arg4533Ter	p.R4533*	ENST00000262189	NM_170606.2	4533	Cga/Tga	52/59	1	2	FACETS	1	0.981	1	1	0.995	1	CLONAL	2	TRUE	1	0.33	2		633	562	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162117	38162117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115403388	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	183	530	0	ENST00000317025.8:c.2599G>A	p.Val867Ile	p.V867I	ENST00000317025	NM_023034.1	867	Gtt/Att	14/24	1	2	FACETS	1	0.946	1	1	0.993	1	CLONAL	2	TRUE	1	0.33	2		530	543	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460448	8460448	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	178	488	0	ENST00000356435.5:c.3838A>T	p.Ile1280Phe	p.I1280F	ENST00000356435		1280	Atc/Ttc	22/35	1	2	FACETS	1	0.977	1	1	0.994	1	CLONAL	2	TRUE	1	0.33	2		488	484	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212182	98212182	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371346118	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	115	361	1	ENST00000331920.6:c.3490G>A	p.Val1164Ile	p.V1164I	ENST00000331920	NM_000264.3	1164	Gtt/Att	21/24	1	2	FACETS	1	0.931	1	1	0.99	1	CLONAL	2	TRUE	1	0.33	2		362	340	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911649	39911649	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	33	553	1	ENST00000378444.4:c.4981C>T	p.Arg1661Ter	p.R1661*	ENST00000378444	NM_001123385.1	1661	Cga/Tga	15/15	0.3	1	FACETS	0.399	0.324	0.482	0.399	0.324	0.482	SUBCLONAL	1	TRUE	0	0.33	1		554	419	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922973	44922973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	231	669	1	ENST00000377967.4:c.1834C>T	p.Arg612Ter	p.R612*	ENST00000377967	NM_021140.2	612	Cga/Tga	16/29	0.3	1	FACETS	0.986	0.926	1	1	0.995	1	CLONAL	2	TRUE	0	0.33	1		670	593	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349973	70349973	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1421325265	NA	P-0041166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	219	718	0	ENST00000374080.3:c.3956G>A	p.Arg1319His	p.R1319H	ENST00000374080		1319	cGc/cAc	28/45	0.3	1	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	0	0.33	1		718	479	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642443	117642443	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	72	701	1	ENST00000368508.3:c.5756C>A	p.Ala1919Asp	p.A1919D	ENST00000368508	NM_002944.2	1919	gCt/gAt	35/43	0.143812922966065	4	FACETS	1	0.973	1	0.714	0.628	0.806	INDETERMINATE	1	NA	2	0.402725693211499	4		702	351	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0121488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	84	487	0	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	0.320818299318789	6	FACETS	1	0.964	1	0.311	0.274	0.35	CLONAL	1	NA	2	0.320818299318789	6		487	692	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642443	117642443	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	129	701	1	ENST00000368508.3:c.5756C>A	p.Ala1919Asp	p.A1919D	ENST00000368508	NM_002944.2	1919	gCt/gAt	35/43	0.316923950453045	3	FACETS	1	0.981	1	0.659	0.598	0.723	CLONAL	1	NA	1	0.320818299318789	3		702	708	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859427	57859427	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	66	695	0	ENST00000228682.2:c.572G>T	p.Arg191Leu	p.R191L	ENST00000228682	NM_005269.2	191	cGg/cTg	6/12	0.320818299318789	4	FACETS	0.837	0.727	0.958	0.419	0.363	0.479	CLONAL	1	NA	2	0.320818299318789	4		695	649	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	88	395	0				ENST00000310581	NM_198253.2	-/1132			0.257808303468628	3	FACETS	1	0.97	1	0.627	0.559	0.699	CLONAL	1	TRUE	1	0.426675463177628	3		395	399	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015230	128015230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs189511674	NA	P-0041172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	305	610	0	ENST00000285398.2:c.2291C>T	p.Ser764Leu	p.S764L	ENST00000285398	NM_000122.1	764	tCg/tTg	15/15	1	2	FACETS	0.834	0.789	0.88	1	0.995	1	CLONAL	2	TRUE	1	0.426675463177628	2		610	857	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578433	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555526101	NA	P-0041172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	522	832	0	ENST00000269305.4:c.497C>G	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	166	tCa/tGa	5/11	0.427257737887046	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	TRUE	0	0.426675463177628	3		832	981	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39074230	39074230	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	98	454	0	ENST00000357387.3:c.80C>G	p.Pro27Arg	p.P27R	ENST00000357387	NM_152756.3	27	cCg/cGg	2/38	0.257808303468628	3	FACETS	1	0.944	1	0.541	0.484	0.601	CLONAL	1	TRUE	1	0.426675463177628	3		454	515	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126686	5126686	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	131	336	0	ENST00000381652.3:c.3294C>G	p.Ile1098Met	p.I1098M	ENST00000381652	NM_004972.3	1098	atC/atG	25/25	0.426675463177628	16	FACETS	1	0.959	1			1	CLONAL	2	TRUE	NA	0.426675463177628	16		336	1107	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910659	50910659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746649739	NA	P-0041172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	167	706	1	ENST00000440232.2:c.1762G>A	p.Glu588Lys	p.E588K	ENST00000440232	NM_002691.3	588	Gag/Aag	14/27	0.158438387810693	6	FACETS	1	0.986	1	0.459	0.421	0.499	INDETERMINATE	1	TRUE	3	0.426675463177628	6		707	1053	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022445	31022445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs533988689	NA	P-0041172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	24	295	0	ENST00000375687.4:c.1930G>A	p.Gly644Arg	p.G644R	ENST00000375687	NM_015338.5	644	Ggg/Agg	13/13	0.12176802544593	5	FACETS	0.508	0.398	0.635	0.169	0.132	0.212	INDETERMINATE	1	TRUE	2	0.426675463177628	5		295	363	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1941437	1941437	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	269	636	0	ENST00000382891.5:c.1813A>C	p.Thr605Pro	p.T605P	ENST00000382891	NM_133335.3	605	Acg/Ccg	9/22	0.427257737887046	3	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	1	0.426675463177628	3		636	764	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001483	150001483	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	106	502	0	ENST00000253339.5:c.2121G>C	p.Lys707Asn	p.K707N	ENST00000253339		707	aaG/aaC	4/7	0.400519767377804	3	FACETS	1	0.969	1	0.596	0.536	0.658	CLONAL	1	TRUE	1	0.426675463177628	3		502	506	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050800	5050800	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1491	474	462	0	ENST00000381652.3:c.583C>G	p.Gln195Glu	p.Q195E	ENST00000381652	NM_004972.3	195	Caa/Gaa	6/25	0.426675463177628	16	FACETS	0.902	0.859	0.945			1	CLONAL	5	TRUE	NA	0.426675463177628	16		462	1965	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050829	5050829	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1366	389	404	0	ENST00000381652.3:c.612C>G	p.Ile204Met	p.I204M	ENST00000381652	NM_004972.3	204	atC/atG	6/25	0.426675463177628	16	FACETS	1	0.971	1			1	CLONAL	4	TRUE	NA	0.426675463177628	16		404	1755	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922709	44922709	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	196	206	0	ENST00000377967.4:c.1571del	p.Pro524LeufsTer24	p.P524Lfs*24	ENST00000377967	NM_021140.2	524	Cct/ct	16/29	0.426675463177628	2	FACETS	0.87	0.821	0.919			1	CLONAL	3	TRUE	NA	0.426675463177628	2		206	352	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518261	8518261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371051836	NA	P-0041175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	53	350	0	ENST00000356435.5:c.1130G>A	p.Arg377His	p.R377H	ENST00000356435		377	cGc/cAc	10/35	1	2	FACETS	0.729	0.624	0.844	0.729	0.624	0.844	SUBCLONAL	1	TRUE	1	0.390641224844817	2		350	372	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729995	47729995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	86	538	0	ENST00000449228.1:c.394C>T	p.Leu132Phe	p.L132F	ENST00000449228	NM_001127240.2	132	Ctc/Ttc	3/4	1	2	FACETS	0.814	0.722	0.912	0.814	0.722	0.912	CLONAL	1	TRUE	1	0.390641224844817	2		538	541	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0041185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	63	222	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.629610054076281	1	FACETS	0.852	0.754	0.952	0.852	0.754	0.952	CLONAL	1	TRUE	0	0.629610054076281	1		222	161	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696688	47696688	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519971	NA	P-0041185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	97	442	0	ENST00000347630.2:c.260A>G	p.Tyr87Cys	p.Y87C	ENST00000347630	NM_001007230.1	87	tAc/tGc	5/11	1	2	FACETS	0.703	0.631	0.78	0.703	0.631	0.78	SUBCLONAL	1	TRUE	1	0.629610054076281	2		442	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0041186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	108	686	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.323441528508908	4	FACETS	0.94	0.848	1	0.627	0.565	0.691	CLONAL	2	FALSE	1	0.323441528508908	4		686	470	SUCCESS
ATM	472	MSKCC	GRCh37	11	108168020	108168020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752459491	NA	P-0041186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	18	215	1	ENST00000278616.4:c.4916C>T	p.Pro1639Leu	p.P1639L	ENST00000278616	NM_000051.3	1639	cCg/cTg	33/63	0.323441528508908	6	FACETS	0.873	0.659	1	0.291	0.219	0.375	CLONAL	1	FALSE	3	0.323441528508908	6		216	210	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	24	337	0	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	0.323441528508908	3	FACETS	1	0.873	1	0.575	0.455	0.709	CLONAL	1	FALSE	1	0.323441528508908	3		337	150	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193787	106193787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749210253	NA	P-0041186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	17	257	0	ENST00000380013.4:c.4249G>A	p.Val1417Ile	p.V1417I	ENST00000380013	NM_001127208.2	1417	Gtt/Att	10/11	0.316724801157329	3	FACETS	0.664	0.497	0.859	0.332	0.248	0.43	SUBCLONAL	1	FALSE	1	0.323441528508908	3		257	184	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0041190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	123	193	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.332462164278254	3	FACETS	0.778	0.704	0.857	0.389	0.352	0.429	SUBCLONAL	1	TRUE	1	0.461372088557984	3		193	843	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363489	40363489	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749442938	NA	P-0041190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	121	656	0	ENST00000397332.2:c.740G>A	p.Arg247His	p.R247H	ENST00000397332	NM_001033082.2	247	cGt/cAt	3/3	0.332462164278254	3	FACETS	0.768	0.694	0.847	0.384	0.347	0.424	SUBCLONAL	1	TRUE	1	0.461372088557984	3		656	840	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023747	27023747	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	109	509	0	ENST00000324856.7:c.853G>T	p.Gly285Ter	p.G285*	ENST00000324856	NM_006015.4	285	Gga/Tga	1/20	0.332462164278254	3	FACETS	0.972	0.875	1	0.486	0.437	0.538	CLONAL	1	TRUE	1	0.461372088557984	3		509	598	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949156	44949156	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	95	455	0	ENST00000377967.4:c.3717G>T	p.Trp1239Cys	p.W1239C	ENST00000377967	NM_021140.2	1239	tgG/tgT	25/29	0.223924328712337	4	FACETS	0.848	0.755	0.946	0.424	0.377	0.473	INDETERMINATE	1	TRUE	2	0.461372088557984	4		455	710	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115947	8115962	+	frameshift_variant	Frame_Shift_Del	DEL	ACCACACCACCCCTCC	ACCACACCACCCCTCC	-	novel	NA	P-0041190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	65	462	0	ENST00000346208.3:c.1294_1309del	p.Pro432AlafsTer38	p.P432Afs*38	ENST00000346208		431	ggACCACACCACCCCTCC/gg	6/6	0.228558876765887	3	FACETS	0.629	0.546	0.72			1	INDETERMINATE	1	TRUE	NA	0.461372088557984	3		462	551	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663237	227663237	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs764972527	NA	P-0041190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	131	720	0	ENST00000305123.5:c.218A>G	p.Asn73Ser	p.N73S	ENST00000305123	NM_005544.2	73	aAc/aGc	1/2	0.332462164278254	3	FACETS	0.778	0.706	0.855	0.389	0.353	0.428	SUBCLONAL	1	TRUE	1	0.461372088557984	3		720	898	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	123	395	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		395	300	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103525659	103525661	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0041192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	34	450	0	ENST00000355739.4:c.2931_2933del	p.Phe978del	p.F978del	ENST00000355739	NM_000123.3	977	cTGTtt/ctt	14/15	0.0918264463794332	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		450	422	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040723	47040723	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	23	501	0	ENST00000377604.3:c.1360del	p.Leu454SerfsTer31	p.L454Sfs*31	ENST00000377604	NM_001204468.1	453	tCc/tc	13/24	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	0	NA	2		501	328	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121913370	NA	P-0041197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	15	271	0	ENST00000288602.6:c.1742A>G	p.Asn581Ser	p.N581S	ENST00000288602	NM_004333.4	581	aAt/aGt	15/18	1	2	FACETS	0.779	0.57	1	0.779	0.57	1	CLONAL	1	TRUE	1	0.18	2		271	214	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267480	198267480	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	41	437	0	ENST00000335508.6:c.1877A>G	p.Asn626Ser	p.N626S	ENST00000335508	NM_012433.2	626	aAc/aGc	14/25	1	2	FACETS	0.961	0.801	1	0.961	0.801	1	CLONAL	1	TRUE	1	0.18	2		437	474	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28624238	28624238	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	38	580	0	ENST00000241453.7:c.736A>G	p.Thr246Ala	p.T246A	ENST00000241453	NM_004119.2	246	Aca/Gca	6/24	1	2	FACETS	0.838	0.692	1	0.838	0.692	1	CLONAL	1	TRUE	1	0.18	2		580	504	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220706	1220706	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	56	714	0	ENST00000326873.7:c.724G>C	p.Gly242Arg	p.G242R	ENST00000326873	NM_000455.4	242	Ggg/Cgg	5/10	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.18	2		714	500	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610149	10610166	+	inframe_deletion	In_Frame_Del	DEL	GATGCCGATGGCATTGCT	GATGCCGATGGCATTGCT	-	novel	NA	P-0041197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	91	896	0	ENST00000171111.5:c.544_561del	p.Ser182_Ile187del	p.S182_I187del	ENST00000171111	NM_203500.1	182	AGCAATGCCATCGGCATC/-	2/6	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.18	2		896	734	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379763	17379763	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	75	994	0	ENST00000359435.4:c.148G>T	p.Glu50Ter	p.E50*	ENST00000359435	NM_001033549.1	50	Gag/Tag	2/9	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.18	2		994	690	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281487	198281488	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATC	novel	NA	P-0041197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	35	523	0	ENST00000335508.6:c.643_644insGAT	p.Lys214_Leu215insArg	p.K214_L215insR	ENST00000335508	NM_012433.2	215	cta/cGATta	6/25	1	2	FACETS	0.622	0.509	0.75	0.622	0.509	0.75	SUBCLONAL	1	TRUE	1	0.18	2		523	625	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426647	212426647	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	39	574	0	ENST00000342788.4:c.2468G>T	p.Trp823Leu	p.W823L	ENST00000342788	NM_005235.2	823	tGg/tTg	20/28	1	2	FACETS	0.781	0.646	0.931	0.781	0.646	0.931	CLONAL	1	TRUE	1	0.18	2		574	555	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673085	30673085	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	55	666	0	ENST00000376406.3:c.3875G>T	p.Arg1292Leu	p.R1292L	ENST00000376406	NM_014641.2	1292	cGg/cTg	10/15	0.156521427295929	3	FACETS	1	0.954	1	0.649	0.556	0.751	CLONAL	1	TRUE	1	0.18	3		666	513	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0041199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	168	411	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.75267497477818	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.75267497477818	3		411	294	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740117	162740117	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	156	99	0	ENST00000367921.3:c.1321del	p.Met441Ter	p.M441*	ENST00000367921	NM_006182.2	440	gAa/ga	12/18	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.75267497477818	2		99	392	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622171	43622171	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1233945445	NA	P-0041199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	113	107	0	ENST00000355710.3:c.3187+1G>A		p.X1063_splice	ENST00000355710	NM_020975.4	1063			0.75267497477818	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.75267497477818	1		107	181	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575070	64575070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	271	183	0	ENST00000312049.6:c.737C>T	p.Ser246Phe	p.S246F	ENST00000312049	NM_130799.2	246	tCc/tTc	4/10	1	2	FACETS	0.951	0.897	1	0.951	0.897	1	CLONAL	1	TRUE	1	0.75267497477818	2		183	757	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459718	40459718	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	257	152	0	ENST00000345506.4:c.1883C>T	p.Thr628Ile	p.T628I	ENST00000345506	NM_003152.3	628	aCc/aTc	16/20	1	2	FACETS	0.858	0.806	0.911	0.858	0.806	0.911	CLONAL	1	TRUE	1	0.75267497477818	2		152	796	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739811	41739811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	208	151	0	ENST00000242208.4:c.162G>A	p.Met54Ile	p.M54I	ENST00000242208	NM_002192.2	54	atG/atA	2/3	1	2	FACETS	0.973	0.91	1	0.973	0.91	1	CLONAL	1	TRUE	1	0.75267497477818	2		151	568	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15838370	15838370	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	164	62	0	ENST00000307771.7:c.868C>G	p.Arg290Gly	p.R290G	ENST00000307771	NM_005089.3	290	Cga/Gga	10/11	0.456077173719268	1	FACETS	0.704	0.655	0.754	0.704	0.655	0.754	SUBCLONAL	1	TRUE	0	0.75267497477818	1		62	386	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0041212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	46	301	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.697	0.586	0.819	0.697	0.586	0.819	SUBCLONAL	1	TRUE	1	0.23	2		302	574	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390170	89390170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148593404	NA	P-0041212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	48	357	0	ENST00000336596.2:c.919G>A	p.Glu307Lys	p.E307K	ENST00000336596	NM_005233.5	307	Gag/Aag	4/17	1	2	FACETS	0.803	0.679	0.939	0.803	0.679	0.939	CLONAL	1	TRUE	1	0.23	2		357	520	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591909	+	inframe_deletion	In_Frame_Del	DEL	CTTCTG	CTTCTG	-	novel	NA	P-0041212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	50	485	0	ENST00000342988.3:c.1067_1072del	p.Pro356_Gly358delinsArg	p.P356_G358delinsR	ENST00000342988	NM_005359.5	356	cCTTCTGga/cga	9/12	1	2	FACETS	0.651	0.551	0.761	0.651	0.551	0.761	SUBCLONAL	1	TRUE	1	0.23	2		485	668	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400817	72400817	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0041240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	31	389	0	ENST00000357731.5:c.354T>A	p.Cys118Ter	p.C118*	ENST00000357731	NM_173808.2	118	tgT/tgA	2/7	1	2	FACETS	0.799	0.653	0.962	0.799	0.653	0.962	CLONAL	1	FALSE	1	0.421589202382949	2		389	184	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0041253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	104	374	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.237185945377189	4	FACETS	0.99	0.895	1	0.99	0.895	1	CLONAL	2	TRUE	2	0.391902772655046	4		374	373	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	72	395	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.391902772655046	2		395	321	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0041253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	106	760	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.391902772655046	2		760	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0041253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	169	872	1	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.391902772655046	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.391902772655046	1		873	596	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117319	115117319	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	78	335	0	ENST00000257566.3:c.855G>C	p.Gln285His	p.Q285H	ENST00000257566	NM_016569.3	285	caG/caC	4/8	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.391902772655046	2		335	383	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551393	141551393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	146	723	1	ENST00000220592.5:c.1904G>A	p.Arg635Gln	p.R635Q	ENST00000220592	NM_012154.3	635	cGg/cAg	15/19	0.391902772655046	3	FACETS	0.966	0.882	1	0.483	0.441	0.528	CLONAL	1	TRUE	1	0.391902772655046	3		724	922	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432622	78432622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	89	392	0	ENST00000370768.2:c.361G>A	p.Glu121Lys	p.E121K	ENST00000370768	NM_003902.3	121	Gaa/Aaa	6/20	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.391902772655046	2		392	446	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352684	118352684	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	119	581	0	ENST00000534358.1:c.3889C>T	p.Gln1297Ter	p.Q1297*	ENST00000534358	NM_005933.3	1297	Cag/Tag	7/36	0.391902772655046	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.391902772655046	1		581	485	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178136	142178136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	94	340	0	ENST00000350721.4:c.7282C>T	p.Leu2428Phe	p.L2428F	ENST00000350721	NM_001184.3	2428	Ctc/Ttc	43/47	0.237185945377189	4	FACETS	0.976	0.877	1	0.976	0.877	1	CLONAL	2	TRUE	2	0.391902772655046	4		340	342	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170827158	170827158	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	63	332	0	ENST00000296930.5:c.526G>A	p.Asp176Asn	p.D176N	ENST00000296930	NM_002520.6	176	Gat/Aat	7/11	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.391902772655046	2		332	300	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191804	123191805	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1392503050	NA	P-0041253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	84	399	0	ENST00000218089.9:c.1400dup	p.Phe468LeufsTer5	p.F468Lfs*5	ENST00000218089	NM_001042749.1	465	gtt/gTtt	15/35	0.391902772655046	1	FACETS	0.963	0.857	1	0.963	0.857	1	CLONAL	1	TRUE	0	0.391902772655046	1		399	358	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	136	395	0				ENST00000310581	NM_198253.2	-/1132			0.212828091139421	5	FACETS	1	0.978	1	0.795	0.73	0.863	INDETERMINATE	2	TRUE	2	0.461591763988703	5		395	418	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274897	41274897	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	262	501	0	ENST00000349496.5:c.1147T>C	p.Trp383Arg	p.W383R	ENST00000349496	NM_001904.3	383	Tgg/Cgg	8/15	0.461591763988703	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.461591763988703	3		501	660	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577510	7577519	+	frameshift_variant	Frame_Shift_Del	DEL	CAGTGTGATG	CAGTGTGATG	-	novel	NA	P-0041268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	286	632	0	ENST00000269305.4:c.762_771del	p.Ile254MetfsTer88	p.I254Mfs*88	ENST00000269305	NM_001126112.2	254	atCATCACACTG/at	7/11	0.461591763988703	2	FACETS	0.867	0.82	0.914	0.867	0.82	0.914	CLONAL	2	TRUE	0	0.461591763988703	2		632	715	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176581	56176581	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0041268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	220	494	0	ENST00000399503.3:c.2131A>T	p.Lys711Ter	p.K711*	ENST00000399503	NM_005921.1	711	Aaa/Taa	12/20	0.212828091139421	5	FACETS	1	0.983	1	0.769	0.719	0.821	INDETERMINATE	2	TRUE	2	0.461591763988703	5		494	699	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0041270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	182	301	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.884	0.818	0.951	0.884	0.818	0.951	CLONAL	1	TRUE	1	0.607648913659009	2		302	678	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467748	50467748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	112	572	0	ENST00000331340.3:c.983G>A	p.Arg328His	p.R328H	ENST00000331340	NM_006060.4	328	cGc/cAc	8/8	0.328924760668016	1	FACETS	0.407	0.366	0.449	0.407	0.366	0.449	INDETERMINATE	1	TRUE	0	0.607648913659009	1		572	631	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0041272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	196	798	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.275883477274654	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	0	0.277225594846875	2		800	691	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0041272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	151	141	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.277225594846875	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.277225594846875	2		141	478	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649566	206649566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1464747771	NA	P-0041273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	94	759	1	ENST00000367120.3:c.401G>A	p.Arg134His	p.R134H	ENST00000367120	NM_014002.3	134	cGc/cAc	6/22	NA	3	FACETS	0.896	0.798	1			1	INDETERMINATE	1	TRUE	NA	0.362884308559245	3		760	683	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28631592	28631592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	32	195	0	ENST00000241453.7:c.376G>T	p.Val126Phe	p.V126F	ENST00000241453	NM_004119.2	126	Gtt/Ttt	4/24	1	2	FACETS	0.5	0.406	0.605	0.5	0.406	0.605	SUBCLONAL	1	TRUE	1	0.362884308559245	2		195	353	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719618	61719618	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0041273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	83	98	0	ENST00000401558.2:c.1567-2A>T		p.X523_splice	ENST00000401558	NM_003400.3	523			0.179289328794807	4	FACETS	0.928	0.826	1	0.928	0.826	1	INDETERMINATE	2	TRUE	2	0.362884308559245	4		98	336	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070859	30070859	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	82	684	1	ENST00000338641.4:c.1375C>T	p.Gln459Ter	p.Q459*	ENST00000338641	NM_000268.3	459	Cag/Tag	13/16	0.362884308559245	1	FACETS	0.811	0.718	0.91	0.811	0.718	0.91	CLONAL	1	TRUE	0	0.362884308559245	1		685	456	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611219	100611219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781792640	NA	P-0041287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	73	166	0	ENST00000308731.7:c.1387G>A	p.Val463Ile	p.V463I	ENST00000308731	NM_000061.2	463	Gtc/Atc	15/19	1	1	FACETS	0.849	0.749	0.954	1	0.98	1	CLONAL	2	TRUE	0	0.25	1		166	301	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0041287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	39	806	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	1	2	FACETS	0.398	0.329	0.476	0.398	0.329	0.476	SUBCLONAL	1	TRUE	1	0.25	2		806	783	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615713	1615714	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0041287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	107	727	0	ENST00000344749.5:c.1557_1558delinsTT	p.Lys519_Glu520delinsAsnTer	p.K519_E520delinsN*	ENST00000344749	NM_001136139.2	519	aaGGag/aaTTag	17/19	0.166314581651189	1	FACETS	0.792	0.709	0.88	0.792	0.709	0.88	SUBCLONAL	1	TRUE	0	0.25	1		727	946	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579349	7579349	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1567555667	NA	P-0041289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	810	637	0	ENST00000269305.4:c.338T>G	p.Phe113Cys	p.F113C	ENST00000269305	NM_001126112.2	113	tTc/tGc	4/11	0.726350378547148	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.726350378547148	3		637	988	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470549	25470549	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	392	685	0	ENST00000264709.3:c.925C>T	p.Arg309Cys	p.R309C	ENST00000264709	NM_175629.2	309	Cgc/Tgc	8/23	0.726350378547148	3	FACETS	1	0.987	1	0.556	0.528	0.585	CLONAL	1	TRUE	1	0.726350378547148	3		685	1323	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814568	43814568	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	303	424	0	ENST00000372470.3:c.1363T>C	p.Ser455Pro	p.S455P	ENST00000372470	NM_005373.2	455	Tct/Cct	9/12	0.522965174700394	6	FACETS	0.986	0.93	1			1	CLONAL	2	TRUE	NA	0.726350378547148	6		424	1038	SUCCESS
EED	8726	MSKCC	GRCh37	11	85967525	85967525	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	11	278	0	ENST00000263360.6:c.523A>T	p.Ile175Leu	p.I175L	ENST00000263360	NM_003797.3	175	Ata/Tta	5/12	0.726350378547148	2	FACETS	0.166	0.115	0.23	0.083	0.057	0.115	SUBCLONAL	1	TRUE	0	0.726350378547148	2		278	182	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195788	102195788	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	31	292	0	ENST00000263464.3:c.548T>C	p.Phe183Ser	p.F183S	ENST00000263464	NM_001165.4	183	tTt/tCt	2/9	0.726350378547148	2	FACETS	0.308	0.25	0.374	0.154	0.125	0.187	SUBCLONAL	1	TRUE	0	0.726350378547148	2		292	277	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285700	46285700	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	92	288	0	ENST00000334344.6:c.5060A>C	p.Gln1687Pro	p.Q1687P	ENST00000334344	NM_152641.2	1687	cAg/cCg	17/21	0.726350378547148	4	FACETS	1	0.955	1			1	CLONAL	1	TRUE	NA	0.726350378547148	4		288	388	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781211	3781211	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	147	627	0	ENST00000262367.5:c.5154G>A	p.Trp1718Ter	p.W1718*	ENST00000262367	NM_004380.2	1718	tgG/tgA	30/31	0.726350378547148	3	FACETS	0.477	0.434	0.522	0.159	0.144	0.174	SUBCLONAL	1	TRUE	0	0.726350378547148	3		627	1157	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647569	23647569	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs61756147	NA	P-0041289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	165	482	0	ENST00000261584.4:c.298C>G	p.Leu100Val	p.L100V	ENST00000261584	NM_024675.3	100	Ctt/Gtt	4/13	0.726350378547148	3	FACETS	1	0.986	1	0.427	0.395	0.459	CLONAL	1	TRUE	0	0.726350378547148	3		482	484	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827716	72827722	+	frameshift_variant	Frame_Shift_Del	DEL	ATTGGTC	ATTGGTC	-	novel	NA	P-0041289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	217	449	0	ENST00000268489.5:c.8859_8865del	p.Met2953IlefsTer4	p.M2953Ifs*4	ENST00000268489	NM_006885.3	2953	atGACCAAT/at	9/10	0.719796932616563	2	FACETS	1	0.992	1	0.685	0.646	0.725	CLONAL	1	TRUE	0	0.726350378547148	2		449	436	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81892767	81892767	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	48	272	0	ENST00000359376.3:c.478A>T	p.Ser160Cys	p.S160C	ENST00000359376	NM_002661.3	160	Agc/Tgc	5/33	0.726350378547148	1	FACETS	0.61	0.528	0.696	0.61	0.528	0.696	SUBCLONAL	1	TRUE	0	0.726350378547148	1		272	138	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245821	41245821	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	132	435	0	ENST00000357654.3:c.1727A>C	p.Lys576Thr	p.K576T	ENST00000357654	NM_007294.3	576	aAa/aCa	10/23	0.701216008258906	2	FACETS	0.982	0.927	1	0.982	0.927	1	CLONAL	2	TRUE	0	0.726350378547148	2		435	185	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38954925	38954925	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	21	239	0	ENST00000357387.3:c.2648A>T	p.Tyr883Phe	p.Y883F	ENST00000357387	NM_152756.3	883	tAt/tTt	27/38	0.726350378547148	3	FACETS	0.575	0.448	0.72	0.192	0.149	0.24	SUBCLONAL	1	TRUE	0	0.726350378547148	3		239	137	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878107	151878107	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	112	416	0	ENST00000262189.6:c.6838G>T	p.Gly2280Ter	p.G2280*	ENST00000262189	NM_170606.2	2280	Gga/Tga	36/59	0.726350378547148	3	FACETS	0.724	0.653	0.798	0.241	0.217	0.266	SUBCLONAL	1	TRUE	0	0.726350378547148	3		416	581	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250052	53250052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372636870	NA	P-0041289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	116	564	0	ENST00000375401.3:c.197C>T	p.Thr66Ile	p.T66I	ENST00000375401	NM_004187.3	66	aCc/aTc	2/26	0.697705491961348	2	FACETS	0.557	0.504	0.614	0.279	0.252	0.307	SUBCLONAL	1	TRUE	0	0.726350378547148	2		564	573	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0041297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	18	505	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.761	0.576	0.977	1	0.907	1	CLONAL	2	TRUE	1	0.13	2		505	182	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0041297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	38	441	2	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.196401579056244	3	FACETS	1	0.886	1	1	0.886	1	CLONAL	2	TRUE	1	0.13	3		443	286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0041297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	33	692	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	0.699	0.568	0.849	0.699	0.568	0.849	SUBCLONAL	1	TRUE	1	0.13	2		692	726	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491716	120491716	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	17	291	0	ENST00000256646.2:c.2513C>T	p.Ser838Phe	p.S838F	ENST00000256646	NM_024408.3	838	tCc/tTc	16/34	1	2	FACETS	0.807	0.602	1	0.807	0.602	1	CLONAL	1	TRUE	1	0.13	2		291	324	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084144	47084144	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	25	428	0	ENST00000409792.3:c.7145C>G	p.Ser2382Cys	p.S2382C	ENST00000409792	NM_014159.6	2382	tCt/tGt	17/21	1	2	FACETS	0.827	0.651	1	0.827	0.651	1	CLONAL	1	TRUE	1	0.13	2		428	465	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164010	47164010	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	13	231	0	ENST00000409792.3:c.2116G>T	p.Glu706Ter	p.E706*	ENST00000409792	NM_014159.6	706	Gaa/Taa	3/21	1	2	FACETS	1	0.732	1	1	0.732	1	CLONAL	1	TRUE	1	0.13	2		231	195	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249236	133249236	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	37	522	0	ENST00000320574.5:c.1663G>T	p.Asp555Tyr	p.D555Y	ENST00000320574	NM_006231.2	555	Gat/Tat	15/49	1	2	FACETS	0.944	0.777	1	0.944	0.777	1	CLONAL	1	TRUE	1	0.13	2		522	603	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196068	67196068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	43	512	0	ENST00000312629.5:c.52G>A	p.Glu18Lys	p.E18K	ENST00000312629	NM_003952.2	18	Gag/Aag	1/15	1	2	FACETS	0.93	0.777	1	0.93	0.777	1	CLONAL	1	TRUE	1	0.13	2		512	711	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225976	133225976	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	55	695	0	ENST00000320574.5:c.3921C>G	p.Ile1307Met	p.I1307M	ENST00000320574	NM_006231.2	1307	atC/atG	31/49	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.13	2		695	778	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780604	56780604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	17	428	0	ENST00000337432.4:c.619C>T	p.His207Tyr	p.H207Y	ENST00000337432	NM_058216.2	207	Cat/Tat	4/9	1	2	FACETS	0.833	0.621	1	0.833	0.621	1	CLONAL	1	TRUE	1	0.13	2		428	314	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627280	14627280	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	43	801	0	ENST00000254322.2:c.790G>A	p.Glu264Lys	p.E264K	ENST00000254322	NM_006145.1	264	Gag/Aag	2/3	1	2	FACETS	0.773	0.645	0.916	0.773	0.645	0.916	CLONAL	1	TRUE	1	0.13	2		801	856	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627553	14627553	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	35	513	0	ENST00000254322.2:c.517G>C	p.Glu173Gln	p.E173Q	ENST00000254322	NM_006145.1	173	Gaa/Caa	2/3	1	2	FACETS	0.94	0.769	1	0.94	0.769	1	CLONAL	1	TRUE	1	0.13	2		513	573	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1918624	1918624	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	24	371	0	ENST00000382891.5:c.787C>G	p.His263Asp	p.H263D	ENST00000382891	NM_133335.3	263	Cac/Gac	4/22	1	2	FACETS	0.914	0.716	1	0.914	0.716	1	CLONAL	1	TRUE	1	0.13	2		371	404	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250644	26250644	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	31	510	0	ENST00000446824.2:c.190C>A	p.Arg64Ser	p.R64S	ENST00000446824	NM_021018.2	64	Cgc/Agc	1/1	1	2	FACETS	0.796	0.642	0.971	0.796	0.642	0.971	CLONAL	1	TRUE	1	0.13	2		510	599	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005194	150005194	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	20	342	0	ENST00000253339.5:c.1031G>C	p.Arg344Thr	p.R344T	ENST00000253339		344	aGa/aCa	3/7	1	2	FACETS	0.85	0.649	1	0.85	0.649	1	CLONAL	1	TRUE	1	0.13	2		342	362	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864299	151864299	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	19	362	0	ENST00000262189.6:c.9682G>C	p.Glu3228Gln	p.E3228Q	ENST00000262189	NM_170606.2	3228	Gag/Cag	42/59	1	2	FACETS	0.828	0.628	1	0.828	0.628	1	CLONAL	1	TRUE	1	0.13	2		362	353	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933488	39933488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	35	628	0	ENST00000378444.4:c.1111G>A	p.Ala371Thr	p.A371T	ENST00000378444	NM_001123385.1	371	Gcc/Acc	4/15	1	2	FACETS	0.778	0.636	0.939	0.778	0.636	0.939	CLONAL	1	TRUE	1	0.13	2		628	692	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159754	20159754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	176	556	0	ENST00000379607.5:c.5C>T	p.Pro2Leu	p.P2L	ENST00000379607	NM_001412.3	2	cCc/cTc	1/7	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.789622390927986	2		556	443	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0041305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	113	486	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.177924630831531	5	FACETS	0.888	0.801	0.98	0.888	0.801	0.98	CLONAL	3	TRUE	2	0.177924630831531	5		486	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578529	7578529	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs780442292	NA	P-0041305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	119	969	0	ENST00000269305.4:c.401T>G	p.Phe134Cys	p.F134C	ENST00000269305	NM_001126112.2	134	tTt/tGt	5/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.177924630831531	2		969	1071	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888165	112888165	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397507510	NA	P-0041307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	63	664	1	ENST00000351677.2:c.181G>T	p.Asp61Tyr	p.D61Y	ENST00000351677	NM_002834.3	61	Gat/Tat	3/16	0.6365850805193	3	FACETS	0.77	0.67	0.877	0.257	0.223	0.293	SUBCLONAL	1	FALSE	0	0.6365850805193	3		665	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576851	7576851	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0041307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	193	583	0	ENST00000269305.4:c.993+2T>C		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.460151577305295	3	FACETS	1	0.982	1	0.74	0.697	0.783	CLONAL	2	FALSE	0	0.6365850805193	3		583	360	SUCCESS
APC	324	MSKCC	GRCh37	5	112176027	112176030	+	frameshift_variant	Frame_Shift_Del	DEL	TTAT	TTAT	-	novel	NA	P-0041307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	58	313	0	ENST00000257430.4:c.4738_4741del	p.Ile1580LeufsTer69	p.I1580Lfs*69	ENST00000257430	NM_000038.5	1579	aTTATt/at	16/16	0.616046880432257	3	FACETS	0.785	0.691	0.882	0.785	0.691	0.882	SUBCLONAL	2	FALSE	1	0.6365850805193	3		313	153	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682806	190682806	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	14	323	0	ENST00000441310.2:c.482C>A	p.Thr161Asn	p.T161N	ENST00000441310	NM_000534.4	161	aCt/aAt	5/13	0.6365850805193	3	FACETS	0.339	0.246	0.451	0.17	0.123	0.226	SUBCLONAL	1	FALSE	1	0.6365850805193	3		323	171	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84384653	84384653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	54	495	0	ENST00000321945.7:c.790G>A	p.Ala264Thr	p.A264T	ENST00000321945	NM_139076.2	264	Gca/Aca	8/9	0.137388823645898	5	FACETS	1	0.947	1	0.305	0.262	0.351	INDETERMINATE	1	FALSE	1	0.6365850805193	5		495	272	SUCCESS
APC	324	MSKCC	GRCh37	5	112174269	112174279	+	frameshift_variant	Frame_Shift_Del	DEL	AGTTTTGCAGT	AGTTTTGCAGT	-	novel	NA	P-0041307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	12	320	0	ENST00000257430.4:c.2978_2988del	p.Lys993IlefsTer11	p.K993Ifs*11	ENST00000257430	NM_000038.5	993	aAGTTTTGCAGT/a	16/16	0.616046880432257	3	FACETS	0.398	0.281	0.539	0.199	0.14	0.27	SUBCLONAL	1	FALSE	1	0.6365850805193	3		320	125	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93953197	93953197	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	34	392	0	ENST00000369303.4:c.2944C>A	p.Gln982Lys	p.Q982K	ENST00000369303	NM_004440.3	982	Cag/Aag	17/17	0.6365850805193	4	FACETS	0.791	0.651	0.946	0.396	0.325	0.473	CLONAL	1	FALSE	2	0.6365850805193	4		392	221	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0041322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	30	503	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.713	0.573	0.872	0.713	0.573	0.872	SUBCLONAL	1	TRUE	1	0.15	2		503	561	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678541	88678541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145157285	NA	P-0041322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	21	350	0	ENST00000360948.2:c.995C>T	p.Thr332Met	p.T332M	ENST00000360948	NM_001012338.2	332	aCg/aTg	9/19	1	2	FACETS	0.886	0.682	1	0.886	0.682	1	CLONAL	1	TRUE	1	0.15	2		350	316	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572717	141572717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1015925954	NA	P-0041322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	34	387	0	ENST00000220592.5:c.353C>T	p.Thr118Met	p.T118M	ENST00000220592	NM_012154.3	118	aCg/aTg	4/19	1	2	FACETS	0.948	0.774	1	0.948	0.774	1	CLONAL	1	TRUE	1	0.15	2		387	478	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0041324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	22	233	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.115791216038591	3	FACETS	0.593	0.46	0.749	0.297	0.23	0.375	INDETERMINATE	1	TRUE	1	0.24	3		235	346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0041324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	56	686	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.506	0.432	0.588	0.506	0.432	0.588	SUBCLONAL	1	TRUE	1	0.24	2		686	922	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023007	27023008	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGC	rs587779737	NA	P-0041324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	19	4	0	ENST00000324856.7:c.126_128dup	p.Ala45dup	p.A45dup	ENST00000324856	NM_006015.4	45	gag/gaGGCg	1/20	1	2	FACETS	0.977	0.773	1	1	0.952	1	CLONAL	3	TRUE	1	0.24	2		4	54	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253208	133253208	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764254754	NA	P-0041351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	163	257	1	ENST00000320574.5:c.833C>T	p.Thr278Met	p.T278M	ENST00000320574	NM_006231.2	278	aCg/aTg	9/49	0.887901356886198	2	FACETS	0.884	0.821	0.948	0.442	0.41	0.474	CLONAL	1	TRUE	0	0.890785661097622	2		258	414	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502246	186502246	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	182	160	0	ENST00000323963.5:c.55G>T	p.Asp19Tyr	p.D19Y	ENST00000323963		19	Gac/Tac	2/11	0.359315449952358	4	FACETS	1	0.944	1	1	0.944	1	INDETERMINATE	2	TRUE	2	0.890785661097622	4		160	383	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339871	116339871	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs780411452	NA	P-0041351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	109	186	0	ENST00000397752.3:c.733T>C	p.Tyr245His	p.Y245H	ENST00000397752	NM_000245.2	245	Tac/Cac	2/21	1	2	FACETS	0.827	0.753	0.902	0.827	0.753	0.902	CLONAL	1	TRUE	1	0.890785661097622	2		186	296	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0041355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	376	233	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.882	0.839	0.925	1	0.996	1	CLONAL	2	FALSE	1	0.420513371376391	2		235	1014	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435251	49435251	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	142	954	0	ENST00000301067.7:c.6302C>T	p.Ala2101Val	p.A2101V	ENST00000301067	NM_003482.3	2101	gCc/gTc	31/54	1	2	FACETS	0.737	0.672	0.806	0.737	0.672	0.806	SUBCLONAL	1	FALSE	1	0.420513371376391	2		954	916	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059142	42059142	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	106	521	0	ENST00000219905.7:c.8864del	p.Pro2955LeufsTer15	p.P2955Lfs*15	ENST00000219905	NM_001164273.1	2954	ctC/ct	24/24	1	2	FACETS	0.891	0.801	0.985	0.891	0.801	0.985	CLONAL	1	FALSE	1	0.420513371376391	2		521	566	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778066	27778066	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	106	760	0	ENST00000369163.2:c.215T>A	p.Val72Glu	p.V72E	ENST00000369163	NM_003536.2	72	gTg/gAg	1/1	1	2	FACETS	0.742	0.666	0.823	0.742	0.666	0.823	SUBCLONAL	1	FALSE	1	0.420513371376391	2		760	679	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978470	70978470	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	75	438	0	ENST00000276594.2:c.1183G>T	p.Glu395Ter	p.E395*	ENST00000276594	NM_024504.3	395	Gag/Tag	5/8	1	2	FACETS	0.874	0.77	0.986	0.874	0.77	0.986	CLONAL	1	FALSE	1	0.420513371376391	2		438	408	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443695	29443695	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs863225281	NA	P-0121576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	60	482	0	ENST00000389048.3:c.3522C>A	p.Phe1174Leu	p.F1174L	ENST00000389048	NM_004304.4	1174	ttC/ttA	23/29	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	NA	1	0.385476076405047	2		482	249	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115269618	115269620	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs745372505	NA	P-0121576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	20	641	0	ENST00000438362.2:c.1586_1588del	p.Pro529del	p.P529del	ENST00000438362	NM_001242891.1	529	cCTCaa/caa	13/20	1	2	FACETS	0.345	0.263	0.44	0.345	0.263	0.44	SUBCLONAL	1	NA	1	0.385476076405047	2		641	301	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385355	4385355	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0121576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	24	365	0	ENST00000261254.3:c.380C>G	p.Thr127Ser	p.T127S	ENST00000261254	NM_001759.3	127	aCc/aGc	2/5	0.164766884436602	0	FACETS	0.437	0.345	0.541			1	INDETERMINATE	1	NA	0	0.385476076405047	0		365	175	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050399	13050399	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	53	570	0	ENST00000316448.5:c.351G>T	p.Leu117Phe	p.L117F	ENST00000316448	NM_004343.3	117	ttG/ttT	3/9	0.164766884436602	0	FACETS	0.591	0.507	0.681			1	INDETERMINATE	1	NA	0	0.385476076405047	0		570	286	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144122	11144122	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	338	835	1	ENST00000358026.2:c.3703G>T	p.Asp1235Tyr	p.D1235Y	ENST00000358026	NM_001128849.1	1235	Gac/Tac	26/36	0.816710046147359	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.816710046147359	1		836	467	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542729	187542729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776147642	NA	P-0041360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	60	540	0	ENST00000441802.2:c.5011G>A	p.Glu1671Lys	p.E1671K	ENST00000441802	NM_005245.3	1671	Gaa/Aaa	10/27	1	2	FACETS	0.314	0.271	0.361	0.314	0.271	0.361	SUBCLONAL	1	TRUE	1	0.816710046147359	2		540	468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587781702	NA	P-0041363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	295	691	0	ENST00000269305.4:c.920-1G>C		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.669525140515332	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.669525140515332	1		691	528	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240767	55240767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770193776	NA	P-0041363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	324	822	0	ENST00000275493.2:c.2011C>T	p.Arg671Cys	p.R671C	ENST00000275493	NM_005228.3	671	Cgc/Tgc	17/28	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.669525140515332	2		822	920	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938654	76938655	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	158	248	0	ENST00000373344.5:c.2093dup	p.Asp699GlyfsTer2	p.D699Gfs*2	ENST00000373344	NM_000489.3	698	aag/aaAg	9/35	0.302876414542764	1	FACETS	0.816	0.757	0.875	0.816	0.757	0.875	INDETERMINATE	1	TRUE	0	0.669525140515332	1		248	385	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562837	95562837	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	52	217	0	ENST00000393063.1:c.4420A>G	p.Thr1474Ala	p.T1474A	ENST00000393063	NM_030621.3	1474	Acc/Gcc	24/28	0.669525140515332	1	FACETS	0.65	0.565	0.739	0.65	0.565	0.739	SUBCLONAL	1	TRUE	0	0.669525140515332	1		217	159	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155439	106155439	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	50	257	0	ENST00000380013.4:c.340C>A	p.Gln114Lys	p.Q114K	ENST00000380013	NM_001127208.2	114	Caa/Aaa	3/11	1	2	FACETS	0.292	0.247	0.341	0.292	0.247	0.341	SUBCLONAL	1	TRUE	1	0.669525140515332	2		257	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0041364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	197	900	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.37310056485856	1	FACETS	0.832	0.77	0.896	0.832	0.77	0.896	CLONAL	1	TRUE	0	0.37310056485856	1		900	1033	SUCCESS
APC	324	MSKCC	GRCh37	5	112174112	112174112	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	157	390	0	ENST00000257430.4:c.2821G>T	p.Glu941Ter	p.E941*	ENST00000257430	NM_000038.5	941	Gaa/Taa	16/16	0.292608983383895	3	FACETS	0.896	0.826	0.969	0.896	0.826	0.969	CLONAL	2	TRUE	1	0.37310056485856	3		390	557	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332875	152332875	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1131692059	NA	P-0041364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	101	421	0	ENST00000206249.3:c.1181G>A	p.Arg394His	p.R394H	ENST00000206249	NM_000125.3	394	cGc/cAc	5/8	1	2	FACETS	0.862	0.772	0.958	0.862	0.772	0.958	CLONAL	1	TRUE	1	0.37310056485856	2		421	628	SUCCESS
APC	324	MSKCC	GRCh37	5	112175476	112175476	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	77	69	0	ENST00000257430.4:c.4188del	p.Phe1396LeufsTer19	p.F1396Lfs*19	ENST00000257430	NM_000038.5	1395	agT/ag	16/16	0.292608983383895	3	FACETS	0.829	0.728	0.937	0.414	0.364	0.469	CLONAL	1	TRUE	1	0.37310056485856	3		69	591	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56787223	56787223	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770637624	NA	P-0041364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	118	407	0	ENST00000337432.4:c.709C>T	p.Arg237Ter	p.R237*	ENST00000337432	NM_058216.2	237	Cga/Tga	5/9	1	2	FACETS	0.923	0.834	1	0.923	0.834	1	CLONAL	1	TRUE	1	0.37310056485856	2		407	685	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578412	7578412	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519747	NA	P-0041368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	580	721	2	ENST00000269305.4:c.518T>A	p.Val173Glu	p.V173E	ENST00000269305	NM_001126112.2	173	gTg/gAg	5/11	0.480217936850533	3	FACETS	0.999	0.968	1	0.999	0.968	1	CLONAL	3	TRUE	0	0.517880584229894	3		723	941	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097265	178097265	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	278	476	0	ENST00000397062.3:c.449A>G	p.His150Arg	p.H150R	ENST00000397062	NM_006164.4	150	cAc/cGc	4/5	0.161553784275797	5	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.517880584229894	5		476	797	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0041370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	81	374	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.966	0.861	1	0.966	0.861	1	CLONAL	1	TRUE	1	0.580380896684849	2		374	289	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842405	68842405	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	192	462	0	ENST00000261769.5:c.466T>G	p.Trp156Gly	p.W156G	ENST00000261769	NM_004360.3	156	Tgg/Ggg	4/16	0.580380896684849	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.580380896684849	1		462	468	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536269	106536269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1427730094	NA	P-0041370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	166	380	0	ENST00000369096.4:c.236C>T	p.Ala79Val	p.A79V	ENST00000369096	NM_001198.3	79	gCg/gTg	2/7	1	2	FACETS	0.966	0.892	1	0.966	0.892	1	CLONAL	1	TRUE	1	0.580380896684849	2		380	592	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023559	27023560	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	180	595	0	ENST00000324856.7:c.671dup	p.Pro225AlafsTer175	p.P225Afs*175	ENST00000324856	NM_006015.4	222	tac/taCc	1/20	1	2	FACETS	0.86	0.795	0.929	0.86	0.795	0.929	CLONAL	1	TRUE	1	0.517161495521063	2		595	809	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	45	379	0	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	0.309	0.259	0.364	0.309	0.259	0.364	SUBCLONAL	1	TRUE	1	0.517161495521063	2		379	564	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	144	482	5	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.84	0.768	0.915	0.84	0.768	0.915	CLONAL	1	TRUE	1	0.517161495521063	2		487	663	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748084	72748084	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	116	474	0	ENST00000357731.5:c.94C>A	p.Leu32Ile	p.L32I	ENST00000357731	NM_173808.2	32	Ctc/Atc	1/7	1	2	FACETS	0.878	0.795	0.965	0.878	0.795	0.965	CLONAL	1	TRUE	1	0.517161495521063	2		474	511	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736510	85736511	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs387906351	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	29	197	1	ENST00000370580.1:c.136dup	p.Ile46AsnfsTer4	p.I46Nfs*4	ENST00000370580	NM_003921.4	46	ata/aAta	2/3	1	2	FACETS	0.357	0.287	0.437	0.357	0.287	0.437	SUBCLONAL	1	TRUE	1	0.517161495521063	2		198	314	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880270	155880270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	117	369	0	ENST00000368323.3:c.134G>A	p.Arg45Gln	p.R45Q	ENST00000368323	NM_006912.5	45	cGa/cAa	3/6	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.517161495521063	2		369	431	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652330	206652330	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	159	639	2	ENST00000367120.3:c.1042del	p.Arg348AspfsTer32	p.R348Dfs*32	ENST00000367120	NM_014002.3	346	gCc/gc	10/22	1	2	FACETS	0.677	0.621	0.736	0.677	0.621	0.736	SUBCLONAL	1	TRUE	1	0.517161495521063	2		641	908	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570803	226570803	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774530658	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	127	509	0	ENST00000366794.5:c.1093G>A	p.Val365Met	p.V365M	ENST00000366794	NM_001618.3	365	Gtg/Atg	8/23	1	2	FACETS	0.746	0.678	0.819	0.746	0.678	0.819	SUBCLONAL	1	TRUE	1	0.517161495521063	2		509	658	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	173	81	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	1	0.981	1	1	0.994	1	CLONAL	2	TRUE	1	0.517161495521063	2		81	302	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154241	2154242	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755455183	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	124	709	2	ENST00000434045.2:c.686dup	p.Glu230ArgfsTer50	p.E230Rfs*50	ENST00000434045	NM_001127598.1	229	cca/ccCa	5/5	1	2	FACETS	0.655	0.593	0.72	0.655	0.593	0.72	SUBCLONAL	1	TRUE	1	0.517161495521063	2		711	732	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	45	314	0	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	0.289	0.242	0.34	0.289	0.242	0.34	SUBCLONAL	1	TRUE	1	0.517161495521063	2		314	603	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466001	69466001	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	143	748	5	ENST00000227507.2:c.839A>T	p.Glu280Val	p.E280V	ENST00000227507	NM_053056.2	280	gAg/gTg	5/5	1	2	FACETS	0.679	0.619	0.741	0.679	0.619	0.741	SUBCLONAL	1	TRUE	1	0.517161495521063	2		753	815	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942053	71942053	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	70	664	1	ENST00000298229.2:c.1322del	p.Asn441ThrfsTer2	p.N441Tfs*2	ENST00000298229	NM_001567.3	439	ccA/cc	12/28	1	2	FACETS	0.355	0.309	0.405	0.355	0.309	0.405	SUBCLONAL	1	TRUE	1	0.517161495521063	2		665	762	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999549	100999549	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	222	846	1	ENST00000325455.5:c.253G>T	p.Gly85Cys	p.G85C	ENST00000325455	NM_001202474.3	85	Ggc/Tgc	1/8	1	2	FACETS	0.995	0.928	1	0.995	0.928	1	CLONAL	1	TRUE	1	0.517161495521063	2		847	863	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435229	18435229	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	51	254	0	ENST00000266497.5:c.214G>T	p.Asp72Tyr	p.D72Y	ENST00000266497		72	Gac/Tac	1/31	NA	2	FACETS	0.636	0.544	0.736			1	INDETERMINATE	1	TRUE	NA	0.517161495521063	2		254	310	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	152	813	2	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.12811788322355	5	FACETS	1	0.954	1	0.355	0.324	0.388	INDETERMINATE	1	TRUE	2	0.517161495521063	5		815	979	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436028	49436029	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	92	516	0	ENST00000301067.7:c.5952dup	p.Thr1985HisfsTer8	p.T1985Hfs*8	ENST00000301067	NM_003482.3	1984	-/C	28/54	0.12811788322355	5	FACETS	0.928	0.825	1	0.309	0.275	0.346	INDETERMINATE	1	TRUE	2	0.517161495521063	5		516	681	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482606	56482606	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	202	635	0	ENST00000267101.3:c.1063A>G	p.Thr355Ala	p.T355A	ENST00000267101	NM_001982.3	355	Acc/Gcc	9/28	0.12811788322355	5	FACETS	1	0.991	1	0.492	0.456	0.529	INDETERMINATE	1	TRUE	2	0.517161495521063	5		635	940	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913558	32913559	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359479	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	142	287	0	ENST00000380152.3:c.5073dup	p.Trp1692MetfsTer3	p.W1692Mfs*3	ENST00000380152		1689	gca/gcAa	11/27	0.517161495521063	3	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	1	0.517161495521063	3		287	344	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972893	32972893	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	130	251	1	ENST00000380152.3:c.10248del	p.Lys3416AsnfsTer11	p.K3416Nfs*11	ENST00000380152		3415	Aaa/aa	27/27	0.517161495521063	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.517161495521063	3		252	297	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337683	73337684	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	16	174	2	ENST00000377767.4:c.2032dup	p.Ile678AsnfsTer3	p.I678Nfs*3	ENST00000377767	NM_014953.3	678	att/aAtt	16/21	0.517161495521063	3	FACETS	0.313	0.231	0.41	0.156	0.115	0.205	SUBCLONAL	1	TRUE	1	0.517161495521063	3		176	249	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	184	283	6	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	0.517161495521063	3	FACETS	0.961	0.896	1	0.961	0.896	1	CLONAL	2	TRUE	1	0.517161495521063	3		289	466	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242096	105242096	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	199	687	1	ENST00000349310.3:c.328C>A	p.Leu110Ile	p.L110I	ENST00000349310	NM_001014432.1	110	Ctc/Atc	6/15	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.517161495521063	2		688	760	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032383	42032383	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs17677991	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	153	422	0	ENST00000219905.7:c.4567C>A	p.Pro1523Thr	p.P1523T	ENST00000219905	NM_001164273.1	1523	Cca/Aca	14/24	1	2	FACETS	0.993	0.912	1	0.993	0.912	1	CLONAL	1	TRUE	1	0.517161495521063	2		422	596	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	178	702	3	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	1	2	FACETS	0.968	0.895	1	0.968	0.895	1	CLONAL	1	TRUE	1	0.517161495521063	2		705	711	SUCCESS
B2M	567	MSKCC	GRCh37	15	45008535	45008536	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	24	183	0	ENST00000558401.1:c.355_356del	p.Met119ValfsTer8	p.M119Vfs*8	ENST00000558401	NM_004048.2	119	ATg/g	3/4	1	2	FACETS	0.314	0.246	0.391	0.314	0.246	0.391	SUBCLONAL	1	TRUE	1	0.517161495521063	2		183	296	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996257	73996257	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775475628	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	20	94	0	ENST00000318443.5:c.991C>T	p.Arg331Cys	p.R331C	ENST00000318443	NM_001024736.1	331	Cgt/Tgt	5/10	1	2	FACETS	0.684	0.531	0.858	0.684	0.531	0.858	SUBCLONAL	1	TRUE	1	0.517161495521063	2		94	113	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396605	396605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	55	526	0	ENST00000262320.3:c.421G>A	p.Ala141Thr	p.A141T	ENST00000262320	NM_003502.3	141	Gcg/Acg	2/11	1	2	FACETS	0.32	0.273	0.371	0.32	0.273	0.371	SUBCLONAL	1	TRUE	1	0.517161495521063	2		526	665	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641018	3641018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150402424	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	163	870	0	ENST00000294008.3:c.2621G>A	p.Gly874Asp	p.G874D	ENST00000294008	NM_032444.2	874	gGc/gAc	12/15	1	2	FACETS	0.681	0.625	0.739	0.681	0.625	0.739	SUBCLONAL	1	TRUE	1	0.517161495521063	2		870	926	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	134	429	2	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.517161495521063	2		431	442	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645947	67645947	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	201	496	0	ENST00000264010.4:c.875G>T	p.Arg292Ile	p.R292I	ENST00000264010	NM_006565.3	292	aGa/aTa	4/12	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.517161495521063	2		496	720	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671680	67671680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201916739	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	184	521	1	ENST00000264010.4:c.2089G>A	p.Ala697Thr	p.A697T	ENST00000264010	NM_006565.3	697	Gca/Aca	12/12	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.517161495521063	2		522	668	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857491	68857491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	161	445	0	ENST00000261769.5:c.2126C>T	p.Ala709Val	p.A709V	ENST00000261769	NM_004360.3	709	gCc/gTc	13/16	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.517161495521063	2		445	592	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944302	81944302	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	90	520	0	ENST00000359376.3:c.1911C>A	p.Asn637Lys	p.N637K	ENST00000359376	NM_002661.3	637	aaC/aaA	18/33	1	2	FACETS	0.551	0.489	0.617	0.551	0.489	0.617	SUBCLONAL	1	TRUE	1	0.517161495521063	2		520	632	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973566	15973566	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	141	293	0	ENST00000268712.3:c.4426T>C	p.Tyr1476His	p.Y1476H	ENST00000268712	NM_006311.3	1476	Tat/Cat	31/46	0.517161495521063	2	FACETS	1	0.97	1	0.562	0.516	0.61	CLONAL	1	TRUE	0	0.517161495521063	2		293	485	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17117087	17117087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764899882	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	63	77	0	ENST00000285071.4:c.1622C>T	p.Ala541Val	p.A541V	ENST00000285071	NM_144997.5	541	gCg/gTg	14/14	0.517161495521063	2	FACETS	0.35	0.302	0.402	0.175	0.151	0.201	SUBCLONAL	1	TRUE	0	0.517161495521063	2		77	696	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	154	394	0	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	0.517161495521063	2	FACETS	0.941	0.864	1	0.47	0.432	0.51	CLONAL	1	TRUE	0	0.517161495521063	2		394	633	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618715	37618716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	210	472	1	ENST00000447079.4:c.397dup	p.Ser133LysfsTer24	p.S133Kfs*24	ENST00000447079	NM_015083.1	131	gaa/gAaa	1/14	0.517161495521063	2	FACETS	1	0.985	1	0.6	0.559	0.641	CLONAL	1	TRUE	0	0.517161495521063	2		473	677	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	199	481	0	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	0.517161495521063	2	FACETS	1	0.979	1	0.564	0.525	0.605	CLONAL	1	TRUE	0	0.517161495521063	2		481	682	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677756	47677756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1235434281	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	39	380	1	ENST00000347630.2:c.1109G>A	p.Arg370His	p.R370H	ENST00000347630	NM_001007230.1	370	cGc/cAc	11/11	0.517161495521063	2	FACETS	0.288	0.238	0.343	0.144	0.119	0.172	SUBCLONAL	1	TRUE	0	0.517161495521063	2		381	524	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	456	475	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.517161495521063	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.517161495521063	2		478	841	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857650	78857650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184854653	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	208	631	0	ENST00000306801.3:c.1720C>T	p.Arg574Cys	p.R574C	ENST00000306801	NM_020761.2	574	Cgc/Tgc	16/34	0.517161495521063	2	FACETS	1	0.971	1	0.538	0.501	0.577	CLONAL	1	TRUE	0	0.517161495521063	2		631	747	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15273306	15273307	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	144	685	0	ENST00000263388.2:c.5882dup	p.Asn1961LysfsTer5	p.N1961Kfs*5	ENST00000263388	NM_000435.2	1961	aat/aaAt	32/33	1	2	FACETS	0.677	0.618	0.74	0.677	0.618	0.74	SUBCLONAL	1	TRUE	1	0.517161495521063	2		685	822	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288678	15288678	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	14	13	0	ENST00000263388.2:c.4061C>A	p.Pro1354Gln	p.P1354Q	ENST00000263388	NM_000435.2	1354	cCg/cAg	24/33	1	2	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	TRUE	1	0.517161495521063	2		13	46	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955112	17955112	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755706305	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	230	805	5	ENST00000458235.1:c.115del	p.Gln39SerfsTer108	p.Q39Sfs*108	ENST00000458235	NM_000215.3	39	Cag/ag	2/24	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.517161495521063	2		810	887	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211909	36211909	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	72	826	0	ENST00000222270.7:c.1664del	p.Pro555GlnfsTer50	p.P555Qfs*50	ENST00000222270	NM_014727.1	554	Ccc/cc	3/37	1	2	FACETS	0.259	0.225	0.295	0.259	0.225	0.295	SUBCLONAL	1	TRUE	1	0.517161495521063	2		826	1076	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224340	36224340	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1568382485	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	130	731	2	ENST00000222270.7:c.6895del	p.Arg2299GlyfsTer26	p.R2299Gfs*26	ENST00000222270	NM_014727.1	2297	gCc/gc	28/37	1	2	FACETS	0.571	0.518	0.628	0.571	0.518	0.628	SUBCLONAL	1	TRUE	1	0.517161495521063	2		733	880	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140309	50140309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755565332	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	188	453	0	ENST00000246792.3:c.232C>T	p.Arg78Trp	p.R78W	ENST00000246792	NM_006270.3	78	Cgg/Tgg	2/6	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.517161495521063	2		453	636	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	55	701	6	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	0.322	0.275	0.374	0.322	0.275	0.374	SUBCLONAL	1	TRUE	1	0.517161495521063	2		707	660	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082827	16082827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	39	43	0	ENST00000281043.3:c.641C>T	p.Ala214Val	p.A214V	ENST00000281043	NM_005378.4	214	gCg/gTg	2/3	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.517161495521063	2		43	116	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015074	27015074	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	100	461	0	ENST00000335756.4:c.176A>G	p.His59Arg	p.H59R	ENST00000335756	NM_001809.3	59	cAc/cGc	2/5	1	2	FACETS	0.684	0.613	0.76	0.684	0.613	0.76	SUBCLONAL	1	TRUE	1	0.517161495521063	2		461	565	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39233658	39233658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	58	250	0	ENST00000402219.2:c.2686C>T	p.Arg896Cys	p.R896C	ENST00000402219	NM_005633.3	896	Cgc/Tgc	17/23	1	2	FACETS	0.771	0.667	0.882	0.771	0.667	0.882	SUBCLONAL	1	TRUE	1	0.517161495521063	2		250	291	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149930	99149930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766419021	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	191	535	1	ENST00000074304.5:c.242C>T	p.Thr81Met	p.T81M	ENST00000074304	NM_001134224.1	81	aCg/aTg	5/26	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.517161495521063	2		536	687	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589892	212589892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	119	484	0	ENST00000342788.4:c.650G>A	p.Cys217Tyr	p.C217Y	ENST00000342788	NM_005235.2	217	tGt/tAt	6/28	1	2	FACETS	0.809	0.733	0.889	0.809	0.733	0.889	CLONAL	1	TRUE	1	0.517161495521063	2		484	569	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215674224	215674224	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	129	662	0	ENST00000260947.4:c.70C>A	p.Pro24Thr	p.P24T	ENST00000260947	NM_000465.2	24	Ccc/Acc	1/11	1	2	FACETS	0.649	0.588	0.712	0.649	0.588	0.712	SUBCLONAL	1	TRUE	1	0.517161495521063	2		662	769	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437198	220437198	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	165	866	0	ENST00000243786.2:c.102G>T	p.Arg34Ser	p.R34S	ENST00000243786	NM_002191.3	34	agG/agT	1/2	1	2	FACETS	0.652	0.599	0.709	0.652	0.599	0.709	SUBCLONAL	1	TRUE	1	0.517161495521063	2		866	978	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	122	589	3	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	1	2	FACETS	0.718	0.65	0.789	0.718	0.65	0.789	SUBCLONAL	1	TRUE	1	0.517161495521063	2		592	657	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663109	227663109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910703300	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	159	582	0	ENST00000305123.5:c.346C>T	p.Arg116Cys	p.R116C	ENST00000305123	NM_005544.2	116	Cgt/Tgt	1/2	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.517161495521063	2		582	602	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017747	31017749	+	inframe_deletion	In_Frame_Del	DEL	CAG	CAG	-	rs745311249	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	94	529	3	ENST00000375687.4:c.619_621del	p.Ser207del	p.S207del	ENST00000375687	NM_015338.5	203	tcCAGc/tcc	8/13	0.517161495521063	3	FACETS	0.612	0.544	0.684	0.306	0.272	0.342	SUBCLONAL	1	TRUE	1	0.517161495521063	3		532	748	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319725	62319725	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	180	642	1	ENST00000360203.5:c.1708C>A	p.Leu570Met	p.L570M	ENST00000360203	NM_001283009.1	570	Ctg/Atg	20/35	0.517161495521063	3	FACETS	0.76	0.699	0.823	0.38	0.349	0.412	SUBCLONAL	1	TRUE	1	0.517161495521063	3		643	1153	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038263	30038263	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771572024	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	110	320	1	ENST00000338641.4:c.436G>A	p.Val146Ile	p.V146I	ENST00000338641	NM_000268.3	146	Gtc/Atc	4/16	1	2	FACETS	0.971	0.878	1	0.971	0.878	1	CLONAL	1	TRUE	1	0.517161495521063	2		321	438	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37092061	37092061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	115	405	0	ENST00000231790.2:c.2188C>T	p.Pro730Ser	p.P730S	ENST00000231790	NM_000249.3	730	Cct/Tct	19/19	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.517161495521063	2		405	436	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103755	47103756	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	138	415	0	ENST00000409792.3:c.6190_6191del	p.Asp2064ProfsTer8	p.D2064Pfs*8	ENST00000409792	NM_014159.6	2064	GAc/c	14/21	1	2	FACETS	0.933	0.853	1	0.933	0.853	1	CLONAL	1	TRUE	1	0.517161495521063	2		415	572	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936111	49936111	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	66	588	0	ENST00000296474.3:c.1559T>C	p.Val520Ala	p.V520A	ENST00000296474	NM_002447.2	520	gTa/gCa	4/20	1	2	FACETS	0.383	0.332	0.438	0.383	0.332	0.438	SUBCLONAL	1	TRUE	1	0.517161495521063	2		588	667	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144618	55144618	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	137	360	0	ENST00000257290.5:c.2092C>A	p.Pro698Thr	p.P698T	ENST00000257290	NM_006206.4	698	Cca/Aca	15/23	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.517161495521063	2		360	397	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	92	115	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.646	0.575	0.721	0.646	0.575	0.721	SUBCLONAL	1	TRUE	1	0.517161495521063	2		116	551	SUCCESS
APC	324	MSKCC	GRCh37	5	112170863	112170863	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1114167569	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	77	381	0	ENST00000257430.4:c.1958+1G>A		p.X653_splice	ENST00000257430	NM_000038.5	653			1	2	FACETS	0.769	0.679	0.865	0.769	0.679	0.865	SUBCLONAL	1	TRUE	1	0.517161495521063	2		381	387	SUCCESS
APC	324	MSKCC	GRCh37	5	112175651	112175651	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	40	282	0	ENST00000257430.4:c.4364del	p.Asn1455IlefsTer18	p.N1455Ifs*18	ENST00000257430	NM_000038.5	1454	Aaa/aa	16/16	1	2	FACETS	0.496	0.413	0.587	0.496	0.413	0.587	SUBCLONAL	1	TRUE	1	0.517161495521063	2		282	312	SUCCESS
APC	324	MSKCC	GRCh37	5	112177411	112177411	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	12	225	2	ENST00000257430.4:c.6120G>T	p.Gln2040His	p.Q2040H	ENST00000257430	NM_000038.5	2040	caG/caT	16/16	1	2	FACETS	0.208	0.146	0.285	0.208	0.146	0.285	SUBCLONAL	1	TRUE	1	0.517161495521063	2		227	223	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131945083	131945083	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	21	170	1	ENST00000265335.6:c.3031C>T	p.Gln1011Ter	p.Q1011*	ENST00000265335		1011	Cag/Tag	19/25	1	2	FACETS	0.352	0.271	0.444	0.352	0.271	0.444	SUBCLONAL	1	TRUE	1	0.517161495521063	2		171	231	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131972883	131972883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs535261113	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	112	269	0	ENST00000265335.6:c.3466C>T	p.Arg1156Cys	p.R1156C	ENST00000265335		1156	Cgt/Tgt	22/25	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.517161495521063	2		269	425	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721358	176721358	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	103	424	0	ENST00000439151.2:c.6989G>A	p.Ser2330Asn	p.S2330N	ENST00000439151	NM_022455.4	2330	aGc/aAc	23/23	1	2	FACETS	0.651	0.583	0.722	0.651	0.583	0.722	SUBCLONAL	1	TRUE	1	0.517161495521063	2		424	612	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324917	31324917	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	43	438	0	ENST00000412585.2:c.19del	p.Arg7GlufsTer13	p.R7Efs*13	ENST00000412585	NM_005514.6	7	Cga/ga	1/8	1	2	FACETS	0.266	0.222	0.315	0.266	0.222	0.315	SUBCLONAL	1	TRUE	1	0.517161495521063	2		438	626	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188223	32188223	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	201	633	0	ENST00000375023.3:c.1118G>T	p.Arg373Leu	p.R373L	ENST00000375023	NM_004557.3	373	cGg/cTg	6/30	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.517161495521063	2		633	751	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967908	93967908	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	104	448	0	ENST00000369303.4:c.2019A>T	p.Glu673Asp	p.E673D	ENST00000369303	NM_004440.3	673	gaA/gaT	11/17	1	2	FACETS	0.96	0.866	1	0.96	0.866	1	CLONAL	1	TRUE	1	0.517161495521063	2		448	419	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405953	157405954	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1554294674	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	106	457	0	ENST00000346085.5:c.2201dup	p.Ser736IlefsTer27	p.S736Ifs*27	ENST00000346085	NM_020732.3	732	ccg/ccGg	6/20	1	2	FACETS	0.583	0.523	0.647	0.583	0.523	0.647	SUBCLONAL	1	TRUE	1	0.517161495521063	2		457	703	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	241	642	4	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	0.252584129535748	3	FACETS	1	0.992	1	0.7	0.655	0.746	INDETERMINATE	1	TRUE	1	0.517161495521063	3		646	838	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940404	13940404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	85	271	0	ENST00000405192.2:c.1102C>T	p.Arg368Cys	p.R368C	ENST00000405192	NM_001163147.1	368	Cgt/Tgt	11/12	0.252584129535748	3	FACETS	1	0.96	1	0.584	0.52	0.651	INDETERMINATE	1	TRUE	1	0.517161495521063	3		271	354	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455126	50455126	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	57	350	2	ENST00000331340.3:c.673A>G	p.Asn225Asp	p.N225D	ENST00000331340	NM_006060.4	225	Aac/Gac	6/8	0.252584129535748	3	FACETS	0.662	0.57	0.762	0.331	0.285	0.381	INDETERMINATE	1	TRUE	1	0.517161495521063	3		352	419	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850880	128850880	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs577512487	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	191	625	0	ENST00000249373.3:c.1727G>A	p.Arg576Gln	p.R576Q	ENST00000249373	NM_005631.4	576	cGg/cAg	10/12	0.252584129535748	3	FACETS	1	0.986	1	0.626	0.58	0.673	INDETERMINATE	1	TRUE	1	0.517161495521063	3		625	743	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845238	151845238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	86	375	0	ENST00000262189.6:c.13774G>A	p.Ala4592Thr	p.A4592T	ENST00000262189	NM_170606.2	4592	Gcc/Acc	52/59	0.252584129535748	3	FACETS	0.835	0.741	0.935	0.418	0.37	0.468	INDETERMINATE	1	TRUE	1	0.517161495521063	3		375	501	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	166	368	20	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	0.252584129535748	3	FACETS	1	0.978	1	1	0.978	1	INDETERMINATE	2	TRUE	1	0.517161495521063	3		388	361	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891191	151891191	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	152	439	0	ENST00000262189.6:c.4563A>C	p.Glu1521Asp	p.E1521D	ENST00000262189	NM_170606.2	1521	gaA/gaC	31/59	0.252584129535748	3	FACETS	1	0.981	1	0.617	0.566	0.669	INDETERMINATE	1	TRUE	1	0.517161495521063	3		439	600	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69050740	69050740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	39	199	0	ENST00000288368.4:c.4075C>T	p.Pro1359Ser	p.P1359S	ENST00000288368	NM_024870.2	1359	Cct/Tct	33/40	0.517161495521063	3	FACETS	0.765	0.639	0.904	0.255	0.213	0.302	CLONAL	1	TRUE	0	0.517161495521063	3		199	248	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554345	141554345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748399150	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	94	828	3	ENST00000220592.5:c.1806del	p.Ala603ProfsTer92	p.A603Pfs*92	ENST00000220592	NM_012154.3	602	ccC/cc	14/19	0.517161495521063	3	FACETS	0.362	0.321	0.406	0.121	0.107	0.136	SUBCLONAL	1	TRUE	0	0.517161495521063	3		831	1264	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141557572	141557572	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	150	710	0	ENST00000220592.5:c.1743G>T	p.Gln581His	p.Q581H	ENST00000220592	NM_012154.3	581	caG/caT	13/19	0.517161495521063	3	FACETS	0.687	0.627	0.75	0.229	0.209	0.25	SUBCLONAL	1	TRUE	0	0.517161495521063	3		710	1063	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994328	21994328	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	156	448	0	ENST00000579755.1:c.3G>A	p.Met1?	p.M1?	ENST00000579755		1	atG/atA	1/3	0.517161495521063		FACETS		0.984	1				CLONAL	1	TRUE	1	0.517161495521063	3		448	595	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430668	80430668	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	28	354	0	ENST00000286548.4:c.340C>T	p.Arg114Ter	p.R114*	ENST00000286548	NM_002072.3	114	Cga/Tga	3/7	0.517161495521063	3	FACETS	0.267	0.213	0.329	0.134	0.106	0.165	SUBCLONAL	1	TRUE	1	0.517161495521063	3		354	510	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139563016	139563016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760679475	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	224	683	0	ENST00000308874.7:c.88G>A	p.Val30Met	p.V30M	ENST00000308874		30	Gtg/Atg	4/10	0.517161495521063	3	FACETS	1	0.945	1	0.509	0.474	0.546	CLONAL	1	TRUE	1	0.517161495521063	3		683	1071	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	172	624	7	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	0.517161495521063	3	FACETS	0.782	0.718	0.848	0.391	0.359	0.424	SUBCLONAL	1	TRUE	1	0.517161495521063	3		631	1071	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361086	70361097	+	inframe_deletion	In_Frame_Del	DEL	CAGCAACAGCAA	CAGCAACAGCAA	-	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	79	170	0	ENST00000374080.3:c.6279_6290del	p.Gln2112_Gln2115del	p.Q2112_Q2115del	ENST00000374080		2092	CAGCAACAGCAA/-	43/45	1	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.517161495521063	1		170	181	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361800	70361800	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	123	357	0	ENST00000374080.3:c.6476A>G	p.Gln2159Arg	p.Q2159R	ENST00000374080		2159	cAa/cGa	44/45	1	1	FACETS	0.762	0.693	0.833	0.762	0.693	0.833	SUBCLONAL	1	TRUE	0	0.517161495521063	1		357	463	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0041383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	164	63	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.248127256159659	2	FACETS	0.86	0.795	0.927	0.86	0.795	0.927	CLONAL	2	FALSE	0	0.355042266796064	2		63	537	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0041383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	154	505	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.320772189635663	3	FACETS	0.915	0.842	0.991	0.61	0.561	0.661	CLONAL	2	FALSE	0	0.355042266796064	3		505	558	SUCCESS
APC	324	MSKCC	GRCh37	5	112175101	112175101	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs587783033	NA	P-0041383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	34	213	0	ENST00000257430.4:c.3814del	p.Ser1272GlnfsTer16	p.S1272Qfs*16	ENST00000257430	NM_000038.5	1270	tgT/tg	16/16	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	FALSE	1	0.355042266796064	2		213	181	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842468	68842468	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1555515232	NA	P-0041383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	66	496	0	ENST00000261769.5:c.529C>T	p.Gln177Ter	p.Q177*	ENST00000261769	NM_004360.3	177	Cag/Tag	4/16	0.221450203893881	3	FACETS	0.865	0.752	0.987	0.433	0.376	0.494	CLONAL	1	FALSE	1	0.355042266796064	3		496	506	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976556	18976577	+	frameshift_variant	Frame_Shift_Del	DEL	AGCCCGGCCTCTCCCAGCCGGA	AGCCCGGCCTCTCCCAGCCGGA	TGCCC	novel	NA	P-0041383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	67	749	2	ENST00000262803.5:c.3206_3227delinsTGCCC	p.Gln1069LeufsTer11	p.Q1069Lfs*11	ENST00000262803	NM_002911.3	1069	cAGCCCGGCCTCTCCCAGCCGGAg/cTGCCCg	22/24	1	2	FACETS	0.505	0.438	0.577	0.505	0.438	0.577	SUBCLONAL	1	FALSE	1	0.355042266796064	2		751	748	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508823	31508823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	150	580	0	ENST00000344624.3:c.1492G>A	p.Asp498Asn	p.D498N	ENST00000344624		498	Gac/Aac	7/33	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.355042266796064	2		580	720	SUCCESS
APC	324	MSKCC	GRCh37	5	112175903	112175903	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	24	238	0	ENST00000257430.4:c.4612G>T	p.Glu1538Ter	p.E1538*	ENST00000257430	NM_000038.5	1538	Gaa/Taa	16/16	1	2	FACETS	0.615	0.484	0.764	0.615	0.484	0.764	SUBCLONAL	1	FALSE	1	0.355042266796064	2		238	220	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0041421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	419	411	1	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.458819698093677	4	FACETS	0.978	0.943	1			1	CLONAL	4	TRUE	NA	0.458819698093677	4		412	681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0041421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	319	204	0	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.457628320743939	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.458819698093677	2		204	668	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79965953	79965953	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0041421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	66	434	0	ENST00000265081.6:c.617C>G	p.Ser206Ter	p.S206*	ENST00000265081	NM_002439.4	206	tCa/tGa	4/24	0.253335550886939	3	FACETS	0.496	0.43	0.568	0.165	0.143	0.19	INDETERMINATE	1	TRUE	0	0.458819698093677	3		434	713	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162198	38162198	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs773662274	NA	P-0041421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	228	471	0	ENST00000317025.8:c.2518G>C	p.Val840Leu	p.V840L	ENST00000317025	NM_023034.1	840	Gta/Cta	14/24	0.255190638899574	2	FACETS	0.858	0.806	0.911	0.858	0.806	0.911	INDETERMINATE	2	TRUE	0	0.458819698093677	2		471	579	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231783	36231783	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057519748	NA	P-0041430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	9	433	0	ENST00000300305.3:c.601C>T	p.Arg201Ter	p.R201*	ENST00000300305		201	Cga/Tga	5/8	0.21006716397277	4	FACETS	0.295	0.194	0.425	0.098	0.064	0.142	SUBCLONAL	1	FALSE	1	0.21006716397277	4		433	351	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646922	37646922	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	50	405	0	ENST00000447079.4:c.2048del	p.Pro683GlnfsTer70	p.P683Qfs*70	ENST00000447079	NM_015083.1	682	Ccc/cc	3/14	0.21006716397277	0	FACETS	0.95	0.827	1			1	CLONAL	3	FALSE	0	0.21006716397277	0		405	132	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99482508	99482508	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	118	415	0	ENST00000268035.6:c.3376C>A	p.Leu1126Ile	p.L1126I	ENST00000268035	NM_000875.3	1126	Ctc/Atc	18/21	0.155078571320071	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	FALSE	1	0.21006716397277	3		415	570	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144107	11144107	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	72	608	0	ENST00000358026.2:c.3688C>G	p.Gln1230Glu	p.Q1230E	ENST00000358026	NM_001128849.1	1230	Cag/Gag	26/36	1	2	FACETS	0.89	0.782	1	1	0.98	1	CLONAL	2	FALSE	1	0.21006716397277	2		608	385	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005240	150005240	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	53	305	0	ENST00000253339.5:c.985C>G	p.Pro329Ala	p.P329A	ENST00000253339		329	Cca/Gca	3/7	0.21006716397277	3	FACETS	1	0.936	1	1	0.98	1	CLONAL	4	FALSE	1	0.21006716397277	3		305	126	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566524	41566525	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	47	458	1	ENST00000263253.7:c.4408dup	p.Met1470AsnfsTer3	p.M1470Nfs*3	ENST00000263253	NM_001429.3	1467	-/A	27/31	NA	2	FACETS	0.572	0.483	0.672			1	INDETERMINATE	1	TRUE	NA	0.294829911814077	2		459	557	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526211	31526211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs553006501	NA	P-0041438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	190	1059	0	ENST00000344624.3:c.829C>T	p.Arg277Cys	p.R277C	ENST00000344624		277	Cgc/Tgc	2/33	0.294829911814077	3	FACETS	1	0.975	1	0.566	0.522	0.612	CLONAL	1	TRUE	1	0.294829911814077	3		1059	1307	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165321	47165321	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	38	321	0	ENST00000409792.3:c.805C>T	p.Gln269Ter	p.Q269*	ENST00000409792	NM_014159.6	269	Caa/Taa	3/21	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.294829911814077	2		321	237	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20152079	20152079	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	12	203	0	ENST00000379607.5:c.251A>G	p.Tyr84Cys	p.Y84C	ENST00000379607	NM_001412.3	84	tAc/tGc	4/7	0.235841450043917	0	FACETS	0.302	0.212	0.412			1	SUBCLONAL	1	TRUE	NA	0.294829911814077	0		203	190	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307484	118307484	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	48	642	0	ENST00000534358.1:c.257C>G	p.Ser86Trp	p.S86W	ENST00000534358	NM_005933.3	86	tCg/tGg	1/36	1	2	FACETS	0.414	0.349	0.486	0.414	0.349	0.486	SUBCLONAL	1	TRUE	1	0.294829911814077	2		642	786	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0041460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	227	94	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.489018032432806	2	FACETS	0.807	0.759	0.854	0.807	0.759	0.854	CLONAL	2	TRUE	0	0.548489282642869	2		94	513	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221830	55221830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150549265	NA	P-0041460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	191	960	0	ENST00000275493.2:c.874G>A	p.Val292Met	p.V292M	ENST00000275493	NM_005228.3	292	Gtg/Atg	7/28	0.548489282642869	1	FACETS	0.947	0.882	1	0.947	0.882	1	CLONAL	1	TRUE	0	0.548489282642869	1		960	534	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78426105	78426105	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	117	601	0	ENST00000370768.2:c.1420C>G	p.Pro474Ala	p.P474A	ENST00000370768	NM_003902.3	474	Cct/Gct	15/20	1	2	FACETS	0.906	0.822	0.994	0.906	0.822	0.994	CLONAL	1	TRUE	1	0.548489282642869	2		601	471	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847221	68847221	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555515863	NA	P-0041460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	143	609	0	ENST00000261769.5:c.1145del	p.Gly382ValfsTer11	p.G382Vfs*11	ENST00000261769	NM_004360.3	381	aaG/aa	9/16	1	2	FACETS	0.959	0.878	1	0.959	0.878	1	CLONAL	1	TRUE	1	0.548489282642869	2		609	544	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842594	68842595	+	splice_acceptor_variant	Splice_Site	DEL	AG	AG	-	novel	NA	P-0041460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	162	567	0	ENST00000261769.5:c.532-1_532del		p.X178_splice	ENST00000261769	NM_004360.3	178			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.548489282642869	2		567	538	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0041468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	727	447	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.930483239726504	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.931853823390841	2		447	779	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954300	48954300	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1461382798	NA	P-0041468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	198	243	0	ENST00000267163.4:c.1422-1G>A		p.X474_splice	ENST00000267163	NM_000321.2	474			0.931853823390841	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.931853823390841	1		243	220	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0041468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	465	571	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.931853823390841	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.931853823390841	1		571	505	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023107	1023107	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	472	581	0	ENST00000358495.3:c.1148C>G	p.Ser383Cys	p.S383C	ENST00000358495	NM_134424.2	383	tCt/tGt	11/12	1	2	FACETS	0.986	0.947	1	0.986	0.947	1	CLONAL	1	TRUE	1	0.931853823390841	2		581	1027	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436175	56436175	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	374	584	0	ENST00000407977.2:c.962del	p.Ser321TyrfsTer98	p.S321Yfs*98	ENST00000407977		321	tCa/ta	9/10	0.931853823390841	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.931853823390841	1		584	424	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72897455	72897455	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	311	485	0	ENST00000325599.8:c.37G>T	p.Asp13Tyr	p.D13Y	ENST00000325599	NM_018130.2	13	Gac/Tac	1/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.931853823390841	2		485	657	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0041482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	203	572	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	1	2	FACETS	0.793	0.735	0.852	1	0.992	1	SUBCLONAL	2	TRUE	1	0.268443194791766	2		572	954	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627582	14627582	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1329417226	NA	P-0041482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	98	473	0	ENST00000254322.2:c.488C>T	p.Pro163Leu	p.P163L	ENST00000254322	NM_006145.1	163	cCa/cTa	2/3	0.227745045222305	2	FACETS	0.991	0.884	1	0.495	0.442	0.552	CLONAL	1	TRUE	0	0.268443194791766	2		473	737	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286959	33286959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs967799519	NA	P-0041482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	81	502	0	ENST00000374542.5:c.1978G>A	p.Gly660Arg	p.G660R	ENST00000374542	NM_001141970.1	660	Ggg/Agg	7/8	0.213595542755739	4	FACETS	0.745	0.654	0.842	0.372	0.327	0.421	SUBCLONAL	1	TRUE	2	0.268443194791766	4		502	1028	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56852643	56852643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs966758586	NA	P-0041525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	127	439	0	ENST00000308159.5:c.557C>T	p.Ala186Val	p.A186V	ENST00000308159	NM_014669.4	186	gCg/gTg	6/22	0.632707498844457	3	FACETS	0.736	0.667	0.808			1	SUBCLONAL	1	TRUE	NA	0.632707498844457	3		439	718	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579401	7579401	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	384	563	0	ENST00000269305.4:c.286del	p.Ser96LeufsTer27	p.S96Lfs*27	ENST00000269305	NM_001126112.2	96	Tct/ct	4/11	NA	2	FACETS	0.974	0.937	1			1	INDETERMINATE	2	TRUE	NA	0.632707498844457	2		563	623	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443860	49443860	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	179	605	1	ENST00000301067.7:c.3511G>T	p.Glu1171Ter	p.E1171*	ENST00000301067	NM_003482.3	1171	Gaa/Taa	11/54	0.632707498844457	3	FACETS	0.863	0.796	0.932	0.432	0.398	0.466	CLONAL	1	TRUE	1	0.632707498844457	3		606	863	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444379	49444392	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGGACAGGCTCA	GGGGGACAGGCTCA	-	novel	NA	P-0041525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	446	477	0	ENST00000301067.7:c.2979_2992del	p.Glu994TyrfsTer69	p.E994Yfs*69	ENST00000301067	NM_003482.3	993	ccTGAGCCTGTCCCCCct/ccct	11/54	0.632707498844457	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.632707498844457	3		477	868	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799315	88799315	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	316	436	0	ENST00000360948.2:c.70G>C	p.Asp24His	p.D24H	ENST00000360948	NM_001012338.2	24	Gac/Cac	2/19	0.632707498844457	3	FACETS	0.992	0.944	1	0.992	0.944	1	CLONAL	2	TRUE	1	0.632707498844457	3		436	663	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660490	67660490	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	69	361	0	ENST00000264010.4:c.1390G>C	p.Glu464Gln	p.E464Q	ENST00000264010	NM_006565.3	464	Gag/Cag	8/12	0.632707498844457	3	FACETS	0.492	0.429	0.561			1	SUBCLONAL	1	TRUE	NA	0.632707498844457	3		361	583	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029171	26029171	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	114	339	0	ENST00000435504.4:c.179T>C	p.Leu60Pro	p.L60P	ENST00000435504		60	cTt/cCt	4/13	0.632707498844457	3	FACETS	0.9	0.814	0.99	0.45	0.407	0.495	CLONAL	1	TRUE	1	0.632707498844457	3		339	527	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379414	225379414	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	104	581	0	ENST00000264414.4:c.454G>T	p.Val152Leu	p.V152L	ENST00000264414	NM_003590.4	152	Gta/Tta	4/16	0.267360546857313	3	FACETS	0.935	0.841	1	0.467	0.42	0.516	INDETERMINATE	1	TRUE	1	0.632707498844457	3		581	463	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324580	62324580	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs574134304	NA	P-0041525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	193	535	2	ENST00000360203.5:c.2936G>A	p.Arg979Gln	p.R979Q	ENST00000360203	NM_001283009.1	979	cGg/cAg	30/35	0.511191070268026	4	FACETS	1	0.939	1			1	CLONAL	1	TRUE	NA	0.632707498844457	4		537	980	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242762	66242762	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	66	268	0	ENST00000273854.3:c.1810G>T	p.Gly604Trp	p.G604W	ENST00000273854	NM_004439.5	604	Ggg/Tgg	9/18	0.632707498844457	2	FACETS	0.538	0.469	0.612	0.269	0.234	0.306	SUBCLONAL	1	TRUE	0	0.632707498844457	2		268	388	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151216560	151216560	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	83	144	0	ENST00000262187.5:c.38G>T	p.Gly13Val	p.G13V	ENST00000262187	NM_005614.3	13	gGc/gTc	1/8	0.632707498844457	3	FACETS	1	0.97	1	0.626	0.559	0.695	CLONAL	1	TRUE	1	0.632707498844457	3		144	276	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0041543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	197	233	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.320194702295697	4	FACETS	0.851	0.792	0.912			1	CLONAL	3	TRUE	NA	0.320194702295697	4		235	636	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0041543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	358	1029	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.309562149261245	2	FACETS	0.929	0.881	0.979	0.929	0.881	0.979	CLONAL	2	TRUE	0	0.320194702295697	2		1029	1203	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400777	72400777	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	75	268	0	ENST00000357731.5:c.394C>A	p.His132Asn	p.H132N	ENST00000357731	NM_173808.2	132	Cat/Aat	2/7	0.320194702295697	3	FACETS	0.857	0.758	0.962	0.857	0.758	0.962	CLONAL	2	TRUE	1	0.320194702295697	3		268	317	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910346	29910346	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	149	836	0	ENST00000376809.5:c.19del	p.Arg7GlufsTer13	p.R7Efs*13	ENST00000376809	NM_002116.7	6	Ccc/cc	1/8	0.320194702295697	3	FACETS	1	0.937	1	0.517	0.471	0.564	CLONAL	1	TRUE	1	0.320194702295697	3		836	1045	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468453	89468453	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	71	355	0	ENST00000336596.2:c.1987C>A	p.Gln663Lys	p.Q663K	ENST00000336596	NM_005233.5	663	Cag/Aag	11/17	0.318527526543254	3	FACETS	0.766	0.673	0.864	0.766	0.673	0.864	SUBCLONAL	2	TRUE	1	0.320194702295697	3		355	336	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376322	118376322	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	183	551	0	ENST00000534358.1:c.9715C>G	p.Pro3239Ala	p.P3239A	ENST00000534358	NM_005933.3	3239	Ccc/Gcc	27/36	0.320194702295697	5	FACETS	1	0.97	1	0.729	0.674	0.786	CLONAL	2	TRUE	2	0.320194702295697	5		551	774	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549328	21549328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760446066	NA	P-0041543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	136	845	2	ENST00000382592.4:c.2948G>A	p.Arg983Gln	p.R983Q	ENST00000382592	NM_014572.2	983	cGg/cAg	8/8	1	2	FACETS	0.971	0.883	1	0.971	0.883	1	CLONAL	1	TRUE	1	0.320194702295697	2		847	875	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374908	45374908	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	215	523	0	ENST00000262160.6:c.935G>T	p.Cys312Phe	p.C312F	ENST00000262160	NM_005901.5	312	tGc/tTc	8/11	0.320194702295697	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.320194702295697	4		523	795	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029193	26029193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	40	358	0	ENST00000435504.4:c.157C>T	p.Leu53Phe	p.L53F	ENST00000435504		53	Ctt/Ttt	4/13	0.320194702295697	3	FACETS	0.743	0.618	0.882	0.372	0.309	0.441	SUBCLONAL	1	TRUE	1	0.320194702295697	3		358	390	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645839	215645839	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	106	595	0	ENST00000260947.4:c.759G>T	p.Gln253His	p.Q253H	ENST00000260947	NM_000465.2	253	caG/caT	4/11	0.320194702295697	3	FACETS	1	0.951	1	0.551	0.494	0.611	CLONAL	1	TRUE	1	0.320194702295697	3		595	697	SUCCESS
ATR	545	MSKCC	GRCh37	3	142211993	142211993	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	41	375	0	ENST00000350721.4:c.6059C>G	p.Ala2020Gly	p.A2020G	ENST00000350721	NM_001184.3	2020	gCa/gGa	35/47	0.318527526543254	3	FACETS	0.726	0.606	0.86	0.363	0.303	0.43	SUBCLONAL	1	TRUE	1	0.320194702295697	3		375	409	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969991	161969991	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	239	768	0	ENST00000366898.1:c.978G>T	p.Gln326His	p.Q326H	ENST00000366898	NM_004562.2	326	caG/caT	9/12	0.320194702295697	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.320194702295697	2		768	704	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0041546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	14	620	1	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		621	490	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	45	395	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.69	0.584	0.806	0.69	0.584	0.806	SUBCLONAL	1	TRUE	1	0.499479124706969	2		395	261	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0041578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	203	777	0	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	0.500018864734321	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.499479124706969	1		777	479	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872380	45872380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	49	745	0	ENST00000391945.4:c.131C>T	p.Ser44Leu	p.S44L	ENST00000391945	NM_000400.3	44	tCa/tTa	3/23	0.414999716704715	1	FACETS	0.3	0.254	0.35	0.3	0.254	0.35	SUBCLONAL	1	TRUE	0	0.499479124706969	1		745	491	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774148	56774148	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	155	523	1	ENST00000337432.4:c.499G>A	p.Asp167Asn	p.D167N	ENST00000337432	NM_058216.2	167	Gat/Aat	3/9	0.0947319369061237	4	FACETS	0.764	0.702	0.828	0.764	0.702	0.828	INDETERMINATE	2	TRUE	2	0.499479124706969	4		524	609	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908238	41908238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	216	815	0	ENST00000372991.4:c.284G>A	p.Arg95Gln	p.R95Q	ENST00000372991	NM_001760.3	95	cGa/cAa	2/5	0.154314022788825	2	FACETS	1	0.99	1	0.666	0.623	0.711	INDETERMINATE	1	TRUE	0	0.499479124706969	2		815	649	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676254	29676254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659856	NA	P-0041578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	97	302	0	ENST00000356175.3:c.7243G>A	p.Val2415Met	p.V2415M	ENST00000356175	NM_000267.3	2415	Gtg/Atg	48/57	0.500018864734321	5	FACETS	1	0.966	1	0.399	0.356	0.444	CLONAL	1	TRUE	2	0.499479124706969	5		302	568	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075565	8075565	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	104	396	0	ENST00000377482.5:c.115G>C	p.Glu39Gln	p.E39Q	ENST00000377482	NM_018948.3	39	Gag/Cag	2/4	0.255350704917686	1	FACETS	0.944	0.855	1	0.944	0.855	1	INDETERMINATE	1	TRUE	0	0.499479124706969	1		396	331	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107144	27107169	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTGTACGAATCACGGCTGTTGGAC	CTCTGTACGAATCACGGCTGTTGGAC	-	novel	NA	P-0041578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	58	549	0	ENST00000324856.7:c.6755_6780del	p.Thr2252AsnfsTer17	p.T2252Nfs*17	ENST00000324856	NM_006015.4	2252	aCTCTGTACGAATCACGGCTGTTGGAC/a	20/20	0.255350704917686	1	FACETS	0.429	0.37	0.494	0.429	0.37	0.494	INDETERMINATE	1	TRUE	0	0.499479124706969	1		549	406	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850754	63850754	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	57	448	0	ENST00000279873.7:c.1532G>C	p.Arg511Thr	p.R511T	ENST00000279873	NM_032199.2	511	aGa/aCa	10/10	1	2	FACETS	0.615	0.53	0.707	0.615	0.53	0.707	SUBCLONAL	1	TRUE	1	0.499479124706969	2		448	371	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445199	49445199	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	257	785	1	ENST00000301067.7:c.2267C>T	p.Pro756Leu	p.P756L	ENST00000301067	NM_003482.3	756	cCt/cTt	10/54	0.387974498549825	3	FACETS	0.903	0.85	0.957	0.903	0.85	0.957	CLONAL	2	TRUE	1	0.499479124706969	3		786	712	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865735	57865735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	119	719	0	ENST00000228682.2:c.3212C>T	p.Ser1071Phe	p.S1071F	ENST00000228682	NM_005269.2	1071	tCt/tTt	12/12	0.387974498549825	3	FACETS	0.932	0.843	1	0.466	0.421	0.513	CLONAL	1	TRUE	1	0.499479124706969	3		719	639	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590941	95590941	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	38	273	0	ENST00000393063.1:c.968G>C	p.Gly323Ala	p.G323A	ENST00000393063	NM_030621.3	323	gGa/gCa	9/28	0.154314022788825	2	FACETS	0.564	0.468	0.669	0.282	0.234	0.335	INDETERMINATE	1	TRUE	0	0.499479124706969	2		273	270	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483875	88483875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs140982180	NA	P-0041578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	135	659	0	ENST00000360948.2:c.1695C>A	p.Asp565Glu	p.D565E	ENST00000360948	NM_001012338.2	565	gaC/gaA	14/19	0.41211212761622	1	FACETS	0.874	0.8	0.95	0.874	0.8	0.95	CLONAL	1	TRUE	0	0.499479124706969	1		659	464	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640404	3640404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373231418	NA	P-0041578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	68	937	1	ENST00000294008.3:c.3235C>T	p.Pro1079Ser	p.P1079S	ENST00000294008	NM_032444.2	1079	Cca/Tca	12/15	0.41211212761622	1	FACETS	0.333	0.29	0.38	0.333	0.29	0.38	SUBCLONAL	1	TRUE	0	0.499479124706969	1		938	613	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004622	16004622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	131	508	0	ENST00000268712.3:c.2632G>A	p.Asp878Asn	p.D878N	ENST00000268712	NM_006311.3	878	Gat/Aat	20/46	0.500018864734321	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.499479124706969	1		508	326	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59878621	59878621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555607637	NA	P-0041578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	64	304	0	ENST00000259008.2:c.1133G>A	p.Arg378Lys	p.R378K	ENST00000259008	NM_032043.2	378	aGg/aAg	8/20	0.0947319369061237	4	FACETS	1	0.965	1	0.663	0.579	0.752	INDETERMINATE	1	TRUE	2	0.499479124706969	4		304	290	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46603762	46603762	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	193	689	0	ENST00000263734.3:c.1119C>G	p.Ile373Met	p.I373M	ENST00000263734	NM_001430.4	373	atC/atG	9/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.499479124706969	2		689	662	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561342	9561342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	58	462	0	ENST00000353224.5:c.440G>A	p.Arg147Lys	p.R147K	ENST00000353224	NM_177990.2	147	aGg/aAg	4/10	0.425640558081433	1	FACETS	0.581	0.503	0.665	0.581	0.503	0.665	SUBCLONAL	1	TRUE	0	0.499479124706969	1		462	300	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46252810	46252810	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	41	224	0	ENST00000371998.3:c.239G>C	p.Arg80Pro	p.R80P	ENST00000371998		80	cGt/cCt	4/23	0.226272384020829	2	FACETS	0.595	0.498	0.701	0.297	0.249	0.351	INDETERMINATE	1	TRUE	0	0.499479124706969	2		224	276	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252978	36252983	+	inframe_deletion	In_Frame_Del	DEL	AGTGCC	AGTGCC	-	novel	NA	P-0041578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	101	357	0	ENST00000300305.3:c.379_384del	p.Gly127_Thr128del	p.G127_T128del	ENST00000300305		127	GGCACT/-	4/8	1	2	FACETS	0.938	0.844	1	0.938	0.844	1	CLONAL	1	TRUE	1	0.499479124706969	2		357	431	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803126	1803126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867329149	NA	P-0041578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	89	840	0	ENST00000260795.2:c.478G>A	p.Asp160Asn	p.D160N	ENST00000260795		160	Gac/Aac	4/17	0.328411799549273	1	FACETS	0.507	0.451	0.567	0.507	0.451	0.567	SUBCLONAL	1	TRUE	0	0.499479124706969	1		840	527	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177816	56177816	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	64	346	0	ENST00000399503.3:c.2789G>C	p.Arg930Thr	p.R930T	ENST00000399503	NM_005921.1	930	aGa/aCa	14/20	0.500018864734321	1	FACETS	0.825	0.724	0.932	0.825	0.724	0.932	CLONAL	1	TRUE	0	0.499479124706969	1		346	233	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197319	26197319	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	71	541	0	ENST00000356476.2:c.160C>T	p.Arg54Cys	p.R54C	ENST00000356476		54	Cgc/Tgc	1/1	0.154314022788825	2	FACETS	0.727	0.638	0.822	0.364	0.319	0.411	INDETERMINATE	1	TRUE	0	0.499479124706969	2		541	391	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33290667	33290667	+	5_prime_UTR_variant	5'UTR	SNP	C	C	T	novel	NA	P-0041578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	85	649	0	ENST00000374542.5:c.-81G>A		p.*27*	ENST00000374542	NM_001141970.1	-/740		1/8	0.154314022788825	2	FACETS	0.726	0.644	0.813	0.363	0.322	0.407	INDETERMINATE	1	TRUE	0	0.499479124706969	2		649	469	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	176	395	0				ENST00000310581	NM_198253.2	-/1132			0.223398863820072	3	FACETS	1	0.95	1	0.68	0.635	0.725	INDETERMINATE	2	TRUE	0	0.583683320779947	3		395	382	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433847	78433848	+	splice_donor_variant	Splice_Site	DEL	AC	AC	-	rs1477051807	NA	P-0041579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	99	306	0	ENST00000370768.2:c.250+1_250+2del		p.X84_splice	ENST00000370768	NM_003902.3	84			0.300141130803293	1	FACETS	0.852	0.771	0.935	0.852	0.771	0.935	INDETERMINATE	1	TRUE	0	0.583683320779947	1		306	282	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0041579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3618	209	735	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.583683320779947	16	FACETS	0.952	0.878	1			1	CLONAL	1	TRUE	NA	0.583683320779947	16		735	3827	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544703	65544703	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs387906650	NA	P-0041579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	78	742	0	ENST00000358664.4:c.223C>T	p.Arg75Ter	p.R75*	ENST00000358664	NM_002382.4	75	Cga/Tga	4/5	0.327201326768466	1	FACETS	0.306	0.269	0.346	0.306	0.269	0.346	INDETERMINATE	1	TRUE	0	0.583683320779947	1		742	619	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044453	47044453	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0041579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	216	381	0	ENST00000377604.3:c.1951-1G>C		p.X651_splice	ENST00000377604	NM_001204468.1	651			1	1	FACETS	0.809	0.77	0.846	1	0.995	1	CLONAL	2	TRUE	0	0.583683320779947	1		381	324	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530147	212530147	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1287533544	NA	P-0041579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	34	343	0	ENST00000342788.4:c.1772A>G	p.Glu591Gly	p.E591G	ENST00000342788	NM_005235.2	591	gAa/gGa	15/28	0.300141130803293	1	FACETS	0.222	0.181	0.267	0.222	0.181	0.267	INDETERMINATE	1	TRUE	0	0.583683320779947	1		343	372	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196857	108196857	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	201	360	0	ENST00000278616.4:c.6880G>A	p.Glu2294Lys	p.E2294K	ENST00000278616	NM_000051.3	2294	Gaa/Aaa	47/63	0.583683320779947	2	FACETS	0.962	0.908	1	0.962	0.908	1	CLONAL	2	TRUE	0	0.583683320779947	2		360	358	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376338	118376338	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0041579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	339	615	0	ENST00000534358.1:c.9731C>G	p.Ser3244Ter	p.S3244*	ENST00000534358	NM_005933.3	3244	tCa/tGa	27/36	0.583683320779947	2	FACETS	0.995	0.953	1	0.995	0.953	1	CLONAL	2	TRUE	0	0.583683320779947	2		615	584	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295176	1295176	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1475402448	NA	P-0041579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	142	308	0				ENST00000310581	NM_198253.2	-/1132			0.223398863820072	3	FACETS	1	0.959	1	0.698	0.648	0.749	INDETERMINATE	2	TRUE	0	0.583683320779947	3		308	300	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206647692	206647692	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	56	508	0	ENST00000367120.3:c.106G>A	p.Ala36Thr	p.A36T	ENST00000367120	NM_014002.3	36	Gct/Act	4/22	1	2	FACETS	0.425	0.364	0.49	0.425	0.364	0.49	SUBCLONAL	1	TRUE	1	0.583683320779947	2		508	452	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63819044	63819044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	46	210	0	ENST00000279873.7:c.1091G>A	p.Gly364Glu	p.G364E	ENST00000279873	NM_032199.2	364	gGa/gAa	7/10	NA	2	FACETS	0.911	0.78	1			1	INDETERMINATE	1	TRUE	NA	0.583683320779947	2		210	173	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175516	108175516	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	31	389	0	ENST00000278616.4:c.5611A>T	p.Thr1871Ser	p.T1871S	ENST00000278616	NM_000051.3	1871	Acc/Tcc	37/63	0.583683320779947	2	FACETS	0.238	0.192	0.29	0.119	0.096	0.145	SUBCLONAL	1	TRUE	0	0.583683320779947	2		389	447	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376161	118376161	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	292	594	0	ENST00000534358.1:c.9554C>T	p.Ser3185Leu	p.S3185L	ENST00000534358	NM_005933.3	3185	tCa/tTa	27/36	0.583683320779947	2	FACETS	0.997	0.951	1	0.997	0.951	1	CLONAL	2	TRUE	0	0.583683320779947	2		594	502	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649225	23649225	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	118	391	1	ENST00000261584.4:c.157G>T	p.Glu53Ter	p.E53*	ENST00000261584	NM_024675.3	53	Gaa/Taa	3/13	0.339614446300373	1	FACETS	0.721	0.656	0.788	0.721	0.656	0.788	INDETERMINATE	1	TRUE	0	0.583683320779947	1		392	397	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942932	15942932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	81	497	0	ENST00000268712.3:c.6770C>T	p.Pro2257Leu	p.P2257L	ENST00000268712	NM_006311.3	2257	cCt/cTt	44/46	0.339614446300373	1	FACETS	0.446	0.394	0.5	0.446	0.394	0.5	INDETERMINATE	1	TRUE	0	0.583683320779947	1		497	441	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879650	37879650	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	3400	839	0	ENST00000269571.5:c.2025C>G	p.Ile675Met	p.I675M	ENST00000269571		675	atC/atG	17/27	0.583683320779947	16	FACETS	1	0.998	1			1	CLONAL	15	TRUE	NA	0.583683320779947	16		839	3881	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14628978	14628978	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	137	613	0	ENST00000254322.2:c.184G>C	p.Glu62Gln	p.E62Q	ENST00000254322	NM_006145.1	62	Gag/Cag	1/3	0.339614446300373	1	FACETS	0.656	0.6	0.714	0.656	0.6	0.714	INDETERMINATE	1	TRUE	0	0.583683320779947	1		613	507	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84403385	84403385	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	105	391	0	ENST00000321945.7:c.100C>G	p.Leu34Val	p.L34V	ENST00000321945	NM_139076.2	34	Ctt/Gtt	2/9	1	2	FACETS	0.873	0.788	0.962	0.873	0.788	0.962	CLONAL	1	TRUE	1	0.583683320779947	2		391	412	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295217	1295217	+	upstream_gene_variant	5'Flank	SNP	G	G	C	novel	NA	P-0041579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	175	388	0				ENST00000310581	NM_198253.2	-/1132			0.223398863820072	3	FACETS	1	0.959	1	0.69	0.645	0.736	INDETERMINATE	2	TRUE	0	0.583683320779947	3		388	374	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334845	81334845	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	53	416	0	ENST00000222390.5:c.1871A>C	p.Asn624Thr	p.N624T	ENST00000222390	NM_000601.4	624	aAc/aCc	17/18	1	2	FACETS	0.437	0.373	0.506	0.437	0.373	0.506	SUBCLONAL	1	TRUE	1	0.583683320779947	2		416	416	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139411752	139411752	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	265	942	0	ENST00000277541.6:c.1527C>G	p.Ile509Met	p.I509M	ENST00000277541	NM_017617.3	509	atC/atG	9/34	0.339614446300373	1	FACETS	0.943	0.889	0.997	0.943	0.889	0.997	INDETERMINATE	1	TRUE	0	0.583683320779947	1		942	682	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044544	47044544	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	274	461	0	ENST00000377604.3:c.2041G>A	p.Asp681Asn	p.D681N	ENST00000377604	NM_001204468.1	681	Gat/Aat	18/24	1	1	FACETS	0.829	0.795	0.862	1	0.996	1	CLONAL	2	TRUE	0	0.583683320779947	1		461	401	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044840	47044840	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0041579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	334	457	0	ENST00000377604.3:c.2167-1G>A		p.X723_splice	ENST00000377604	NM_001204468.1	723			1	1	FACETS	0.851	0.82	0.881	1	0.997	1	CLONAL	2	TRUE	0	0.583683320779947	1		457	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0041580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	206	739	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.310976352467852	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.310976352467852	1		740	892	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5462858	5462858	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747598352	NA	P-0041580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	46	62	0	ENST00000381577.3:c.419G>C	p.Arg140Thr	p.R140T	ENST00000381577	NM_014143.3	140	aGa/aCa	4/7	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.310976352467852	2		62	286	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62316900	62316900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1417269541	NA	P-0041580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	157	207	1	ENST00000360203.5:c.1216G>A	p.Glu406Lys	p.E406K	ENST00000360203	NM_001283009.1	406	Gag/Aag	15/35	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.310976352467852	2		208	871	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267858	46267858	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	110	184	2	ENST00000371998.3:c.2619C>G	p.Ile873Met	p.I873M	ENST00000371998		873	atC/atG	14/23	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.310976352467852	2		186	650	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023414	27023414	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	144	184	0	ENST00000324856.7:c.520G>T	p.Gly174Cys	p.G174C	ENST00000324856	NM_006015.4	174	Ggc/Tgc	1/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.310976352467852	2		184	646	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243801045	243801045	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0041580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	34	113	0	ENST00000263826.5:c.430-1G>C		p.X144_splice	ENST00000263826	NM_005465.4	144			0.310976352467852	3	FACETS	0.862	0.707	1	0.431	0.353	0.518	CLONAL	1	TRUE	1	0.310976352467852	3		113	293	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945424	71945424	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs781377268	NA	P-0041580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	146	248	3	ENST00000298229.2:c.2312C>G	p.Ser771Cys	p.S771C	ENST00000298229	NM_001567.3	771	tCt/tGt	20/28	0.310976352467852	1	FACETS	0.986	0.901	1	0.986	0.901	1	CLONAL	1	TRUE	0	0.310976352467852	1		251	804	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427852	49427852	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	89	208	0	ENST00000301067.7:c.10738C>T	p.Gln3580Ter	p.Q3580*	ENST00000301067	NM_003482.3	3580	Cag/Tag	38/54	0.310976352467852	1	FACETS	0.77	0.683	0.862	0.77	0.683	0.862	SUBCLONAL	1	TRUE	0	0.310976352467852	1		208	628	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955517	48955517	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	58	114	0	ENST00000267163.4:c.1633G>C	p.Glu545Gln	p.E545Q	ENST00000267163	NM_000321.2	545	Gaa/Caa	17/27	0.310976352467852	1	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	0	0.310976352467852	1		114	301	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347099	347099	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	166	256	0	ENST00000262320.3:c.1912G>C	p.Glu638Gln	p.E638Q	ENST00000262320	NM_003502.3	638	Gag/Cag	7/11	0.310976352467852	1	FACETS	0.873	0.801	0.948	0.873	0.801	0.948	CLONAL	1	TRUE	0	0.310976352467852	1		256	1033	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110251	3110251	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	235	237	0	ENST00000078429.4:c.241C>T	p.Gln81Ter	p.Q81*	ENST00000078429	NM_002067.2	81	Cag/Tag	2/7	0.243356025716325	2	FACETS	0.829	0.774	0.885	0.829	0.774	0.885	CLONAL	2	TRUE	0	0.310976352467852	2		237	912	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200062	128200062	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	159	307	0	ENST00000341105.2:c.1243G>C	p.Glu415Gln	p.E415Q	ENST00000341105	NM_032638.4	415	Gag/Cag	6/6	0.298503775965597	3	FACETS	0.902	0.825	0.983	0.301	0.275	0.328	CLONAL	1	TRUE	0	0.310976352467852	3		307	1310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0041592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	361	673	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.708336334555079	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.708336334555079	1		673	648	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141870	108141870	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	191	336	0	ENST00000278616.4:c.2918T>A	p.Leu973Gln	p.L973Q	ENST00000278616	NM_000051.3	973	cTa/cAa	19/63	1	2	FACETS	0.965	0.898	1	0.965	0.898	1	CLONAL	1	TRUE	1	0.708336334555079	2		336	559	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142082	108142082	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	231	427	0	ENST00000278616.4:c.3026A>C	p.Glu1009Ala	p.E1009A	ENST00000278616	NM_000051.3	1009	gAg/gCg	20/63	1	2	FACETS	0.886	0.83	0.944	0.886	0.83	0.944	CLONAL	1	TRUE	1	0.708336334555079	2		427	736	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620601	52620602	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0041592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	272	409	0	ENST00000394830.3:c.3151_3152del	p.Trp1051AspfsTer30	p.W1051Dfs*30	ENST00000394830	NM_018313.4	1051	TGg/g	21/30	0.708336334555079	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.708336334555079	1		409	485	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828126	243828126	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	372	390	0	ENST00000263826.5:c.232C>A	p.Gln78Lys	p.Q78K	ENST00000263826	NM_005465.4	78	Cag/Aag	3/13	0.494068559378906	5	FACETS	1	0.971	1			1	CLONAL	2	TRUE	NA	0.823409411556924	5		390	982	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405356	70405356	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	312	530	0	ENST00000373644.4:c.2870C>A	p.Pro957Gln	p.P957Q	ENST00000373644	NM_030625.2	957	cCa/cAa	4/12	1	2	FACETS	0.934	0.885	0.984	0.934	0.885	0.984	CLONAL	1	TRUE	1	0.823409411556924	2		530	811	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222369	39222369	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	377	634	0	ENST00000402219.2:c.3241A>G	p.Asn1081Asp	p.N1081D	ENST00000402219	NM_005633.3	1081	Aat/Gat	20/23	0.823409411556924	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.823409411556924	1		634	517	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840051	27840051	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	230	373	0	ENST00000328488.2:c.43A>G	p.Lys15Glu	p.K15E	ENST00000328488	NM_003533.2	15	Aaa/Gaa	1/1	0.293606689855989	3	FACETS	0.795	0.749	0.841	0.795	0.749	0.841	INDETERMINATE	2	TRUE	1	0.823409411556924	3		373	496	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675400	30675400	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	96	545	0	ENST00000376406.3:c.2956T>C	p.Ser986Pro	p.S986P	ENST00000376406	NM_014641.2	986	Tct/Cct	8/15	0.293606689855989	3	FACETS	0.41	0.365	0.459	0.205	0.182	0.23	INDETERMINATE	1	TRUE	1	0.823409411556924	3		545	802	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441988	52441999	+	inframe_deletion	In_Frame_Del	DEL	CCTTGGTGAAGT	CCTTGGTGAAGT	-	novel	NA	P-0041613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	99	436	0	ENST00000460680.1:c.350_361del	p.Asp117_Lys120del	p.D117_K120del	ENST00000460680	NM_004656.3	117	gACTTCACCAAGGgt/ggt	5/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		436	478	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557601	21557602	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATGT	novel	NA	P-0041613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	120	644	0	ENST00000382592.4:c.2240_2243dup	p.Pro749HisfsTer18	p.P749Hfs*18	ENST00000382592	NM_014572.2	748	atc/atACATc	5/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		644	487	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007693	45007693	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	53	347	0	ENST00000558401.1:c.140del	p.Val47GlyfsTer14	p.V47Gfs*14	ENST00000558401	NM_004048.2	47	gTg/gg	2/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		347	213	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441980	52441980	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	96	414	0	ENST00000460680.1:c.369C>G	p.Ser123Arg	p.S123R	ENST00000460680	NM_004656.3	123	agC/agG	5/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		414	441	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0041628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	18	374	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.776	0.584	1	0.776	0.584	1	CLONAL	1	TRUE	1	0.17	2		374	273	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720868	89720871	+	frameshift_variant	Frame_Shift_Del	DEL	ATTT	ATTT	-	novel	NA	P-0041628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	23	390	0	ENST00000371953.3:c.1019_1022del	p.Asn340IlefsTer3	p.N340Ifs*3	ENST00000371953	NM_000314.4	340	aATTTt/at	8/9	1	2	FACETS	0.599	0.466	0.753	0.599	0.466	0.753	SUBCLONAL	1	TRUE	1	0.17	2		390	452	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061115	38061133	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGGCCGCCCTTGGCGCC	CAGGGCCGCCCTTGGCGCC	-	novel	NA	P-0041628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	18	246	0	ENST00000250448.2:c.856_874del	p.Gly286ArgfsTer29	p.G286Rfs*29	ENST00000250448	NM_004496.3	286	GGCGCCAAGGGCGGCCCTGag/ag	2/2	0.161816577300558	3	FACETS	1	0.882	1	0.656	0.497	0.843	CLONAL	1	TRUE	1	0.17	3		246	175	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0041629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	388	63	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.329286444133671	5	FACETS	1	0.981	1	1	0.981	1	INDETERMINATE	3	TRUE	2	0.61452296108572	5		63	776	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0041629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	119	505	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.535376391601917	3	FACETS	0.97	0.88	1	0.485	0.44	0.532	CLONAL	1	TRUE	1	0.61452296108572	3		505	522	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574253	95574253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149242330	NA	P-0041629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	103	267	0	ENST00000393063.1:c.2614G>A	p.Ala872Thr	p.A872T	ENST00000393063	NM_030621.3	872	Gct/Act	17/28	0.535376391601917	3	FACETS	1	0.944	1	0.534	0.481	0.59	CLONAL	1	TRUE	1	0.61452296108572	3		267	410	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43772110	43772110	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	153	728	1	ENST00000382044.4:c.605C>A	p.Ser202Ter	p.S202*	ENST00000382044	NM_001141980.1	202	tCa/tAa	6/28	1	2	FACETS	0.649	0.595	0.706	0.649	0.595	0.706	SUBCLONAL	1	TRUE	1	0.61452296108572	2		729	767	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272394	11272394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	105	417	0	ENST00000361445.4:c.3536C>T	p.Ser1179Leu	p.S1179L	ENST00000361445	NM_004958.3	1179	tCa/tTa	23/58	NA	2	FACETS	0.778	0.702	0.859			1	INDETERMINATE	1	TRUE	NA	0.61452296108572	2		417	439	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909943	100909943	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1472322408	NA	P-0041629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	267	377	0	ENST00000325455.5:c.2706T>A	p.Ser902Arg	p.S902R	ENST00000325455	NM_001202474.3	902	agT/agA	8/8	0.489567830657264	4	FACETS	0.857	0.812	0.901	0.857	0.812	0.901	CLONAL	3	TRUE	1	0.61452296108572	4		377	546	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	459939	459939	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	133	463	1	ENST00000399788.2:c.1156C>T	p.Pro386Ser	p.P386S	ENST00000399788	NM_001042603.1	386	Ccc/Tcc	10/28	0.492815771233702	3	FACETS	0.869	0.791	0.951			1	CLONAL	1	TRUE	NA	0.61452296108572	3		464	651	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492543	50492543	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	290	642	0	ENST00000394963.4:c.1439A>C	p.Glu480Ala	p.E480A	ENST00000394963	NM_003076.4	480	gAg/gCg	12/13	0.329286444133671	5	FACETS	0.979	0.923	1	0.653	0.615	0.691	INDETERMINATE	2	TRUE	2	0.61452296108572	5		642	926	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239805	41239805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	315	636	1	ENST00000379561.5:c.545C>T	p.Thr182Met	p.T182M	ENST00000379561	NM_002015.3	182	aCg/aTg	1/3	0.442136622440771	4	FACETS	0.879	0.831	0.927	0.879	0.831	0.927	CLONAL	2	TRUE	2	0.61452296108572	4		637	942	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046517	30046517	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	135	562	1	ENST00000331968.5:c.2666C>A	p.Ala889Asp	p.A889D	ENST00000331968	NM_002742.2	889	gCt/gAt	18/18	0.535376391601917	3	FACETS	0.865	0.788	0.945	0.433	0.394	0.473	CLONAL	1	TRUE	1	0.61452296108572	3		563	664	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066958	30066958	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	99	380	0	ENST00000331968.5:c.2173C>A	p.Leu725Ile	p.L725I	ENST00000331968	NM_002742.2	725	Ctt/Att	16/18	0.535376391601917	3	FACETS	0.881	0.79	0.977	0.441	0.395	0.489	CLONAL	1	TRUE	1	0.61452296108572	3		380	478	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675127	40675127	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	178	787	0	ENST00000249776.8:c.91T>A	p.Tyr31Asn	p.Y31N	ENST00000249776	NM_033286.3	31	Tac/Aac	1/9	1	2	FACETS	0.76	0.702	0.821	0.76	0.702	0.821	SUBCLONAL	1	TRUE	1	0.61452296108572	2		787	762	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041429	42041429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	149	529	0	ENST00000219905.7:c.5624C>T	p.Ser1875Leu	p.S1875L	ENST00000219905	NM_001164273.1	1875	tCa/tTa	17/24	1	2	FACETS	0.891	0.819	0.966	0.891	0.819	0.966	CLONAL	1	TRUE	1	0.61452296108572	2		529	544	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779676	3779676	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	286	642	0	ENST00000262367.5:c.5372del	p.Ser1791CysfsTer8	p.S1791Cfs*8	ENST00000262367	NM_004380.2	1791	tCg/tg	31/31	0.44664750887675	5	FACETS	0.877	0.825	0.93	0.585	0.55	0.62	CLONAL	2	TRUE	2	0.61452296108572	5		642	1020	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992511	72992511	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	516	779	0	ENST00000268489.5:c.1534G>T	p.Gly512Trp	p.G512W	ENST00000268489	NM_006885.3	512	Ggg/Tgg	2/10	0.328202057003279	3	FACETS	0.882	0.853	0.91			1	INDETERMINATE	3	TRUE	NA	0.61452296108572	3		779	830	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1206987	1206987	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	351	687	0	ENST00000326873.7:c.75C>A	p.Phe25Leu	p.F25L	ENST00000326873	NM_000455.4	25	ttC/ttA	1/10	0.513424355786204	3	FACETS	0.923	0.879	0.967	0.923	0.879	0.967	CLONAL	2	TRUE	1	0.61452296108572	3		687	809	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303041	15303041	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	385	820	2	ENST00000263388.2:c.409G>T	p.Gly137Trp	p.G137W	ENST00000263388	NM_000435.2	137	Ggg/Tgg	4/33	0.513424355786204	3	FACETS	0.881	0.84	0.922	0.881	0.84	0.922	CLONAL	2	TRUE	1	0.61452296108572	3		822	930	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462300	89462300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	86	366	0	ENST00000336596.2:c.1772C>T	p.Pro591Leu	p.P591L	ENST00000336596	NM_005233.5	591	cCa/cTa	10/17	0.535376391601917	3	FACETS	0.839	0.746	0.938	0.42	0.373	0.469	CLONAL	1	TRUE	1	0.61452296108572	3		366	436	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106512982	106512982	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	127	187	1	ENST00000359195.3:c.1996G>C	p.Ala666Pro	p.A666P	ENST00000359195	NM_002649.2	666	Gct/Cct	3/11	0.535376391601917	3	FACETS	0.871	0.802	0.942	0.871	0.802	0.942	CLONAL	2	TRUE	1	0.61452296108572	3		188	310	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380987	116380987	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	156	514	0	ENST00000397752.3:c.1609C>T	p.Gln537Ter	p.Q537*	ENST00000397752	NM_000245.2	537	Cag/Tag	5/21	0.535376391601917	3	FACETS	0.87	0.798	0.945	0.435	0.399	0.473	CLONAL	1	TRUE	1	0.61452296108572	3		514	763	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835970	151835970	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	179	406	0	ENST00000262189.6:c.14554del	p.Ala4852HisfsTer9	p.A4852Hfs*9	ENST00000262189	NM_170606.2	4852	Gca/ca	58/59	0.535376391601917	3	FACETS	1	0.989	1	0.694	0.644	0.745	CLONAL	1	TRUE	1	0.61452296108572	3		406	549	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211538	98211538	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	271	552	0	ENST00000331920.6:c.3617G>T	p.Arg1206Leu	p.R1206L	ENST00000331920	NM_000264.3	1206	cGc/cTc	22/24	0.513424355786204	3	FACETS	0.922	0.872	0.973	0.922	0.872	0.973	CLONAL	2	TRUE	1	0.61452296108572	3		552	625	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793310	139793310	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	161	713	0	ENST00000247668.2:c.118G>T	p.Val40Phe	p.V40F	ENST00000247668	NM_021138.3	40	Gtc/Ttc	2/11	0.513424355786204	3	FACETS	0.85	0.78	0.922	0.425	0.39	0.461	CLONAL	1	TRUE	1	0.61452296108572	3		713	806	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42840342	42840342	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs570454392	NA	P-0041631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	70	432	0	ENST00000398585.3:c.1406G>A	p.Gly469Glu	p.G469E	ENST00000398585	NM_001135099.1	469	gGg/gAg	12/14	1	2	FACETS	0.963	0.841	1	0.963	0.841	1	CLONAL	1	TRUE	1	0.28	2		432	519	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510698	120510704	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ACCCATG	ACCCATG	-	novel	NA	P-0041631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	162	452	0	ENST00000256646.2:c.1260_1264+2del		p.X420_splice	ENST00000256646	NM_024408.3	420		7/34	0.302407396842566	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.28	2		452	518	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623562	43623562	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	90	302	2	ENST00000355710.3:c.3190A>G	p.Met1064Val	p.M1064V	ENST00000355710	NM_020975.4	1064	Atg/Gtg	20/20	0.216326160005129	5	FACETS	1	0.945	1	0.73	0.651	0.812	CLONAL	2	TRUE	2	0.28	5		304	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577069	7577069	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	247	764	0	ENST00000269305.4:c.869del	p.Arg290ProfsTer55	p.R290Pfs*55	ENST00000269305	NM_001126112.2	290	cGc/cc	8/11	0.302407396842566	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.28	2		764	837	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128028921	128028921	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000328-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	191	561	0	ENST00000285398.2:c.1936G>C	p.Ala646Pro	p.A646P	ENST00000285398	NM_000122.1	646	Gct/Cct	12/15	0.308815098616828	4	FACETS	0.831	0.768	0.896	0.831	0.768	0.896	CLONAL	2	TRUE	2	0.308815098616828	4		561	974	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587386	29587386	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0000328-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	456	432	1	ENST00000356175.3:c.4368-1G>A		p.X1456_splice	ENST00000356175	NM_000267.3	1456			0.281944686902737	4	FACETS	0.876	0.839	0.914	0.876	0.839	0.914	CLONAL	4	TRUE	0	0.308815098616828	4		433	1103	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604603	48604632	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTCTTCCAAATCTTTTCTGTTAGGTCTGTC	GTCTTCCAAATCTTTTCTGTTAGGTCTGTC	-	novel	NA	P-0000328-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	26	161	0	ENST00000342988.3:c.1448-23_1454del		p.X483_splice	ENST00000342988	NM_005359.5	483		12/12	0.146150105291246	3	FACETS	0.563	0.446	0.698			1	INDETERMINATE	1	TRUE	NA	0.308815098616828	3		161	345	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088807	27088807	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	27	659	0	ENST00000324856.7:c.2416C>T	p.Gln806Ter	p.Q806*	ENST00000324856	NM_006015.4	806	Caa/Taa	7/20	1	2	FACETS	0.735	0.584	0.909	0.735	0.584	0.909	CLONAL	1	TRUE	1	0.16	2		659	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578195	7578197	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0000369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	59	1026	0	ENST00000269305.4:c.652_654del	p.Val218del	p.V218del	ENST00000269305	NM_001126112.2	218	GTG/-	6/11	1	2	FACETS	0.994	0.854	1	0.994	0.854	1	CLONAL	1	TRUE	1	0.16	2		1026	742	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842752	68842752	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1567504977	NA	P-0000369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	41	549	1	ENST00000261769.5:c.687+1G>A		p.X229_splice	ENST00000261769	NM_004360.3	229			1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.16	2		550	397	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295247	1295247	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0000369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	34	544	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	0.931	0.761	1	0.931	0.761	1	CLONAL	1	TRUE	0	0.16	1		544	420	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338669	70338669	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000382-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	201	1086	0	ENST00000374080.3:c.65C>A	p.Pro22His	p.P22H	ENST00000374080		22	cCc/cAc	1/45	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.613622423833449	2		1086	450	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355262	81355262	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000382-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	98	553	0	ENST00000222390.5:c.1112A>T	p.Asn371Ile	p.N371I	ENST00000222390	NM_000601.4	371	aAc/aTc	9/18	0.156523513534595	5	FACETS	1	0.976	1	0.439	0.393	0.487	INDETERMINATE	1	TRUE	2	0.613622423833449	5		553	466	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509418	106509418	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000382-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	80	689	0	ENST00000359195.3:c.1412A>T	p.His471Leu	p.H471L	ENST00000359195	NM_002649.2	471	cAc/cTc	2/11	0.156523513534595	5	FACETS	1	0.884	1	0.334	0.294	0.376	INDETERMINATE	1	TRUE	2	0.613622423833449	5		689	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000382-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	143	305	0	ENST00000269305.4:c.517G>C	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ctg	5/11	0.588044020078529	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.613622423833449	2		305	203	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243453	41243453	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000382-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	35	925	0	ENST00000357654.3:c.4095A>C	p.Leu1365Phe	p.L1365F	ENST00000357654	NM_007294.3	1365	ttA/ttC	10/23	0.271932751173557	3	FACETS	0.259	0.211	0.312	0.129	0.105	0.156	INDETERMINATE	1	TRUE	1	0.613622423833449	3		925	576	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533700	63533700	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000382-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	53	441	0	ENST00000307078.5:c.1454G>C	p.Gly485Ala	p.G485A	ENST00000307078	NM_004655.3	485	gGc/gCc	6/11	0.271932751173557	3	FACETS	0.981	0.847	1	0.491	0.423	0.563	INDETERMINATE	1	TRUE	1	0.613622423833449	3		441	230	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696425	47696425	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519967	NA	P-0000615-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	181	402	0	ENST00000347630.2:c.398T>G	p.Phe133Cys	p.F133C	ENST00000347630	NM_001007230.1	133	tTc/tGc	6/11	0.143049202239954	1	FACETS	0.971	0.894	1	0.971	0.894	1	INDETERMINATE	1	TRUE	0	0.27	1		402	1194	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081618	143081618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000909-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	61	316	0	ENST00000262992.4:c.1456C>T	p.Pro486Ser	p.P486S	ENST00000262992	NM_001101669.1	486	Ccc/Tcc	15/24	1	2	FACETS	0.706	0.61	0.809	0.706	0.61	0.809	SUBCLONAL	1	TRUE	1	0.377512356836675	2		316	458	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032209	26032209	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000909-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	17	80	0	ENST00000244661.2:c.80G>A	p.Arg27His	p.R27H	ENST00000244661	NM_003537.3	27	cGc/cAc	1/1	1	2	FACETS	0.613	0.461	0.79	0.613	0.461	0.79	SUBCLONAL	1	TRUE	1	0.377512356836675	2		80	147	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0000964-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	27	182	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.232503989170147	0	FACETS	0.865	0.693	1			1	CLONAL	1	TRUE	0	0.232503989170147	0		182	206	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0000964-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	55	392	0	ENST00000262160.6:c.1391C>G	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tGa	11/11	0.232503989170147	0	FACETS	0.979	0.841	1			1	CLONAL	1	TRUE	0	0.232503989170147	0		392	371	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524757	187524757	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs748428503	NA	P-0000964-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	57	355	0	ENST00000441802.2:c.10923C>A	p.His3641Gln	p.H3641Q	ENST00000441802	NM_005245.3	3641	caC/caA	19/27	1	2	FACETS	0.995	0.854	1	0.995	0.854	1	CLONAL	1	TRUE	1	0.232503989170147	2		355	493	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257841	16257842	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0000964-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	32	209	0	ENST00000375759.3:c.5111dup	p.Gly1705ArgfsTer6	p.G1705Rfs*6	ENST00000375759	NM_015001.2	1702	-/C	11/15	0.232503989170147	0	FACETS	1	0.864	1			1	CLONAL	1	TRUE	0	0.232503989170147	0		209	198	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914715	32914719	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGT	AAAGT	-	novel	NA	P-0000964-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	127	415	0	ENST00000380152.3:c.6223_6227del	p.Lys2075Ter	p.K2075*	ENST00000380152		2075	AAAGTt/t	11/27	1	2	FACETS	1	0.954	1	1	0.991	1	CLONAL	2	TRUE	1	0.232503989170147	2		415	509	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0000964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	12	182	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.250422287498132	1	FACETS	0.434	0.305	0.593	0.434	0.305	0.593	SUBCLONAL	1	TRUE	0	0.250422287498132	1		182	193	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0000964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	22	392	0	ENST00000262160.6:c.1391C>G	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tGa	11/11	1	2	FACETS	0.505	0.391	0.637	0.505	0.391	0.637	SUBCLONAL	1	TRUE	1	0.250422287498132	2		392	348	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524757	187524757	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs748428503	NA	P-0000964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	30	355	0	ENST00000441802.2:c.10923C>A	p.His3641Gln	p.H3641Q	ENST00000441802	NM_005245.3	3641	caC/caA	19/27	1	2	FACETS	0.418	0.336	0.512	0.418	0.336	0.512	SUBCLONAL	1	TRUE	1	0.250422287498132	2		355	573	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257841	16257842	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0000964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	22	209	0	ENST00000375759.3:c.5111dup	p.Gly1705ArgfsTer6	p.G1705Rfs*6	ENST00000375759	NM_015001.2	1702	-/C	11/15	0.219170247033489	1	FACETS	0.507	0.393	0.64	0.507	0.393	0.64	SUBCLONAL	1	TRUE	0	0.250422287498132	1		209	303	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914715	32914719	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGT	AAAGT	-	novel	NA	P-0000964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	29	415	0	ENST00000380152.3:c.6223_6227del	p.Lys2075Ter	p.K2075*	ENST00000380152		2075	AAAGTt/t	11/27	0.219170247033489	1	FACETS	0.472	0.379	0.579	0.472	0.379	0.579	SUBCLONAL	1	TRUE	0	0.250422287498132	1		415	429	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0000964-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	138	529	0	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.853	0.777	0.933	0.853	0.777	0.933	CLONAL	1	TRUE	1	0.429473401392521	2		529	753	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000964-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	41	269	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.471	0.393	0.558	0.471	0.393	0.558	SUBCLONAL	1	TRUE	1	0.429473401392521	2		269	405	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0000964-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	113	182	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.429473401392521	1	FACETS	0.935	0.847	1	0.935	0.847	1	CLONAL	1	TRUE	0	0.429473401392521	1		182	442	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0000964-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	199	668	3	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.916	0.848	0.986	0.916	0.848	0.986	CLONAL	1	TRUE	1	0.429473401392521	2		671	1012	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151843	108151843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000964-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	49	460	1	ENST00000278616.4:c.3524C>T	p.Ala1175Val	p.A1175V	ENST00000278616	NM_000051.3	1175	gCc/gTc	24/63	1	2	FACETS	0.311	0.263	0.365	0.311	0.263	0.365	SUBCLONAL	1	TRUE	1	0.429473401392521	2		461	733	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0000964-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	157	392	0	ENST00000262160.6:c.1391C>G	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tGa	11/11	0.429473401392521	1	FACETS	0.8	0.734	0.868	0.8	0.734	0.868	SUBCLONAL	1	TRUE	0	0.429473401392521	1		392	718	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524757	187524757	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs748428503	NA	P-0000964-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	183	355	0	ENST00000441802.2:c.10923C>A	p.His3641Gln	p.H3641Q	ENST00000441802	NM_005245.3	3641	caC/caA	19/27	1	2	FACETS	0.943	0.87	1	0.943	0.87	1	CLONAL	1	TRUE	1	0.429473401392521	2		355	904	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257841	16257842	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0000964-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	115	209	0	ENST00000375759.3:c.5111dup	p.Gly1705ArgfsTer6	p.G1705Rfs*6	ENST00000375759	NM_015001.2	1702	-/C	11/15	0.429473401392521	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.429473401392521	1		209	413	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914715	32914719	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGT	AAAGT	-	novel	NA	P-0000964-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1328	372	415	0	ENST00000380152.3:c.6223_6227del	p.Lys2075Ter	p.K2075*	ENST00000380152		2075	AAAGTt/t	11/27	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.429473401392521	2		415	1700	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577563	7577563	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1567549584	NA	P-0000964-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	192	621	0	ENST00000269305.4:c.718A>G	p.Ser240Gly	p.S240G	ENST00000269305	NM_001126112.2	240	Agt/Ggt	7/11	0.429473401392521	1	FACETS	0.999	0.927	1	0.999	0.927	1	CLONAL	1	TRUE	0	0.429473401392521	1		621	703	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239419	105239419	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000964-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	204	533	0	ENST00000349310.3:c.968A>G	p.Asp323Gly	p.D323G	ENST00000349310	NM_001014432.1	323	gAc/gGc	12/15	0.196162278432407	2	FACETS	1	0.99	1	0.696	0.649	0.746	INDETERMINATE	1	TRUE	0	0.429473401392521	2		533	682	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199945	138199945	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000964-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	95	358	0	ENST00000237289.4:c.1368del	p.Pro457LeufsTer20	p.P457Lfs*20	ENST00000237289	NM_001270507.1	455	Ggg/gg	7/9	1	2	FACETS	0.972	0.87	1	0.972	0.87	1	CLONAL	1	TRUE	1	0.429473401392521	2		358	455	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729711	162729711	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1356127876	NA	P-0000964-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	67	655	0	ENST00000367921.3:c.797A>G	p.Asn266Ser	p.N266S	ENST00000367921	NM_006182.2	266	aAt/aGt	8/18	1	2	FACETS	0.375	0.325	0.429	0.375	0.325	0.429	SUBCLONAL	1	TRUE	1	0.429473401392521	2		655	832	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373433	118373433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000964-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	157	565	1	ENST00000534358.1:c.6826G>A	p.Val2276Ile	p.V2276I	ENST00000534358	NM_005933.3	2276	Gta/Ata	27/36	1	2	FACETS	0.919	0.842	0.998	0.919	0.842	0.998	CLONAL	1	TRUE	1	0.429473401392521	2		566	796	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457640	67457640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs863223759	NA	P-0000964-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	216	730	1	ENST00000327367.4:c.455del	p.Pro152HisfsTer34	p.P152Hfs*34	ENST00000327367	NM_005902.3	150	ttC/tt	3/9	0.429473401392521	1	FACETS	0.928	0.864	0.994	0.928	0.864	0.994	CLONAL	1	TRUE	0	0.429473401392521	1		731	851	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647685	2647685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000964-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	277	765	1	ENST00000342085.4:c.1588G>A	p.Gly530Arg	p.G530R	ENST00000342085	NM_002613.4	530	Ggg/Agg	14/14	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.429473401392521	2		766	1160	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821193	72821193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200911275	NA	P-0000964-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	244	878	2	ENST00000268489.5:c.10982C>T	p.Ser3661Leu	p.S3661L	ENST00000268489	NM_006885.3	3661	tCg/tTg	10/10	1	2	FACETS	0.922	0.861	0.986	0.922	0.861	0.986	CLONAL	1	TRUE	1	0.429473401392521	2		880	1232	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984813	11984830	+	frameshift_variant	Frame_Shift_Del	DEL	TCCACAAACCAAGTGGGC	TCCACAAACCAAGTGGGC	CAGTT	novel	NA	P-0000964-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	122	474	1	ENST00000353533.5:c.359_376delinsCAGTT	p.Val120AlafsTer4	p.V120Afs*4	ENST00000353533	NM_003010.3	120	gTCCACAAACCAAGTGGGCaa/gCAGTTaa	3/11	0.429473401392521	1	FACETS	0.765	0.694	0.84	0.765	0.694	0.84	SUBCLONAL	1	TRUE	0	0.429473401392521	1		475	583	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5207953	5207953	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000964-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	196	814	2	ENST00000357368.4:c.5758C>T	p.Pro1920Ser	p.P1920S	ENST00000357368	NM_002850.3	1920	Ccg/Tcg	37/38	1	2	FACETS	0.902	0.835	0.972	0.902	0.835	0.972	CLONAL	1	TRUE	1	0.429473401392521	2		816	1012	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99136567	99136567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761184076	NA	P-0000964-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	192	549	1	ENST00000074304.5:c.56G>A	p.Arg19Gln	p.R19Q	ENST00000074304	NM_001134224.1	19	cGg/cAg	3/26	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.429473401392521	2		550	877	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256430	46256430	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000964-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1188	291	964	0	ENST00000371998.3:c.658A>G	p.Arg220Gly	p.R220G	ENST00000371998		220	Aga/Gga	7/23	1	2	FACETS	0.916	0.86	0.974	0.916	0.86	0.974	CLONAL	1	TRUE	1	0.429473401392521	2		964	1479	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574911	41574911	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000964-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	177	587	0	ENST00000263253.7:c.7196A>G	p.Asn2399Ser	p.N2399S	ENST00000263253	NM_001429.3	2399	aAc/aGc	31/31	1	2	FACETS	0.897	0.827	0.97	0.897	0.827	0.97	CLONAL	1	TRUE	1	0.429473401392521	2		587	919	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014298	70014298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142372494	NA	P-0000964-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1348	291	925	1	ENST00000394351.3:c.1159G>A	p.Gly387Ser	p.G387S	ENST00000394351	NM_000248.3	387	Ggt/Agt	9/9	0.345057807421704	3	FACETS	1	0.942	1			1	CLONAL	1	TRUE	NA	0.429473401392521	3		926	1639	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217580	142217580	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000964-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	86	528	1	ENST00000350721.4:c.5417A>G	p.Gln1806Arg	p.Q1806R	ENST00000350721	NM_001184.3	1806	cAg/cGg	32/47	0.338158165995953	3	FACETS	0.498	0.44	0.562	0.249	0.22	0.281	SUBCLONAL	1	TRUE	1	0.429473401392521	3		529	976	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260648	1260648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000964-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	161	656	0	ENST00000310581.5:c.2911C>T	p.Arg971Cys	p.R971C	ENST00000310581	NM_198253.2	971	Cgt/Tgt	12/16	1	2	FACETS	0.797	0.73	0.866	0.797	0.73	0.866	SUBCLONAL	1	TRUE	1	0.429473401392521	2		656	941	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38946635	38946635	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000964-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	75	419	0	ENST00000357387.3:c.4334T>A	p.Phe1445Tyr	p.F1445Y	ENST00000357387	NM_152756.3	1445	tTt/tAt	33/38	1	2	FACETS	0.523	0.458	0.593	0.523	0.458	0.593	SUBCLONAL	1	TRUE	1	0.429473401392521	2		419	668	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150449	157150449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779142775	NA	P-0000964-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	217	678	1	ENST00000346085.5:c.1631C>T	p.Pro544Leu	p.P544L	ENST00000346085	NM_020732.3	544	cCg/cTg	2/20	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.429473401392521	2		679	1003	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683689	162683689	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs770930242	NA	P-0000964-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	85	617	0	ENST00000366898.1:c.280G>T	p.Gly94Cys	p.G94C	ENST00000366898	NM_004562.2	94	Ggc/Tgc	3/12	1	2	FACETS	0.483	0.426	0.544	0.483	0.426	0.544	SUBCLONAL	1	TRUE	1	0.429473401392521	2		617	820	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397775	139397775	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1261408162	NA	P-0000964-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	111	397	0	ENST00000277541.6:c.5026G>A	p.Val1676Ile	p.V1676I	ENST00000277541	NM_017617.3	1676	Gtc/Atc	27/34	1	2	FACETS	0.841	0.757	0.928	0.841	0.757	0.928	CLONAL	1	TRUE	1	0.429473401392521	2		397	615	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190321	32190321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1033015617	NA	P-0001092-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	65	135	0	ENST00000375023.3:c.418C>T	p.Arg140Cys	p.R140C	ENST00000375023	NM_004557.3	140	Cgc/Tgc	3/30	0.655695208904111	4	FACETS	0.639	0.554	0.73	0.319	0.277	0.365	SUBCLONAL	1	FALSE	2	0.655695208904111	4		135	514	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681426	88681426	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001092-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	230	192	1	ENST00000372037.3:c.1316A>G	p.Glu439Gly	p.E439G	ENST00000372037	NM_004329.2	439	gAg/gGg	11/13	0.289962874486268	5	FACETS	1	0.96	1	0.688	0.645	0.732	INDETERMINATE	2	FALSE	2	0.655695208904111	5		193	674	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445023	49445023	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001092-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	107	71	0	ENST00000301067.7:c.2443C>A	p.Leu815Met	p.L815M	ENST00000301067	NM_003482.3	815	Ctg/Atg	10/54	0.655695208904111	3	FACETS	0.856	0.783	0.931	0.856	0.783	0.931	CLONAL	2	FALSE	1	0.655695208904111	3		71	253	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577561	7577561	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs764342812	NA	P-0001092-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	228	214	0	ENST00000269305.4:c.720T>G	p.Ser240Arg	p.S240R	ENST00000269305	NM_001126112.2	240	agT/agG	7/11	0.599507906522259	2	FACETS	0.859	0.814	0.903	0.859	0.814	0.903	CLONAL	2	FALSE	0	0.655695208904111	2		214	405	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419958	41419958	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001092-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	241	394	1	ENST00000373198.4:c.363C>A	p.Asn121Lys	p.N121K	ENST00000373198	NM_133170.3	121	aaC/aaA	3/32	0.655695208904111	3	FACETS	1	0.951	1	0.51	0.477	0.544	CLONAL	1	FALSE	1	0.655695208904111	3		395	957	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266080	41266097	+	inframe_deletion	In_Frame_Del	DEL	AGCAACAGTCTTACCTGG	AGCAACAGTCTTACCTGG	-	novel	NA	P-0001092-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	122	224	0	ENST00000349496.5:c.78_95del	p.Gln26_Asp32delinsHis	p.Q26_D32delinsH	ENST00000349496	NM_001904.3	26	cAGCAACAGTCTTACCTGGac/cac	3/15	0.484948960182532	4	FACETS	0.616	0.556	0.68			1	SUBCLONAL	1	FALSE	NA	0.655695208904111	4		224	1000	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243777010	243777010	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200428825	NA	P-0001624-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	277	398	0	ENST00000263826.5:c.659G>A	p.Arg220His	p.R220H	ENST00000263826	NM_005465.4	220	cGt/cAt	7/13	NA	2	FACETS	1	0.95	1			1	INDETERMINATE	1	TRUE	NA	0.693624953503028	2		398	792	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149614	202149614	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001624-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	166	452	0	ENST00000358485.4:c.1055A>G	p.Tyr352Cys	p.Y352C	ENST00000358485	NM_001080125.1	352	tAt/tGt	8/9	0.684929874248518	2	FACETS	0.753	0.694	0.813	0.376	0.347	0.407	SUBCLONAL	1	TRUE	0	0.693624953503028	2		452	636	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436393	52436393	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1244342890	NA	P-0001624-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	184	398	1	ENST00000460680.1:c.2101C>T	p.Arg701Cys	p.R701C	ENST00000460680	NM_004656.3	701	Cgc/Tgc	17/17	0.685212690687698	2	FACETS	0.984	0.915	1	0.492	0.457	0.528	CLONAL	1	TRUE	0	0.693624953503028	2		399	539	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637555	52637555	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001624-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	286	411	0	ENST00000394830.3:c.2761C>T	p.Arg921Ter	p.R921*	ENST00000394830	NM_018313.4	921	Cga/Tga	18/30	0.685212690687698	2	FACETS	0.912	0.86	0.966	0.456	0.43	0.483	CLONAL	1	TRUE	0	0.693624953503028	2		411	904	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638151	176638151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001624-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	189	315	0	ENST00000439151.2:c.2751G>A	p.Met917Ile	p.M917I	ENST00000439151	NM_022455.4	917	atG/atA	5/23	0.693624953503028	3	FACETS	0.979	0.907	1	0.489	0.453	0.527	CLONAL	1	TRUE	1	0.693624953503028	3		315	750	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038454	180038454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772928672	NA	P-0001624-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	153	324	0	ENST00000261937.6:c.3563C>T	p.Pro1188Leu	p.P1188L	ENST00000261937	NM_182925.4	1188	cCg/cTg	27/30	0.693624953503028	3	FACETS	1	0.968	1	0.549	0.505	0.595	CLONAL	1	TRUE	1	0.693624953503028	3		324	541	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200387	138200387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760531232	NA	P-0001624-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	229	276	1	ENST00000237289.4:c.1805C>T	p.Thr602Met	p.T602M	ENST00000237289	NM_001270507.1	602	aCg/aTg	7/9	0.693624953503028	1	FACETS	0.908	0.857	0.959	0.908	0.857	0.959	CLONAL	1	TRUE	0	0.693624953503028	1		277	475	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58142357	58142357	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761577371	NA	P-0001624-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	285	353	0	ENST00000257904.6:c.863G>A	p.Arg288Gln	p.R288Q	ENST00000257904	NM_000075.3	288	cGa/cAa	8/8	0.671874866099643	4	FACETS	1	0.98	1	0.55	0.516	0.584	CLONAL	1	TRUE	2	0.693624953503028	4		353	1266	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118598	17118598	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41419545	NA	P-0001636-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	326	58	713	0	ENST00000285071.4:c.1333G>A	p.Ala445Thr	p.A445T	ENST00000285071	NM_144997.5	445	Gca/Aca	12/14	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.249888188499084	2		713	384	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0001718-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	46	531	0	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	0.0654292146008639	4	FACETS	0.38	0.319	0.447	0.19	0.159	0.224	INDETERMINATE	1	TRUE	2	0.540993265491519	4		531	690	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0001718-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	154	636	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.541	0.494	0.59	0.541	0.494	0.59	SUBCLONAL	1	TRUE	1	0.540993265491519	2		636	1052	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692893	89692893	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001718-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	127	308	0	ENST00000371953.3:c.377C>A	p.Ala126Asp	p.A126D	ENST00000371953	NM_000314.4	126	gCt/gAt	5/9	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.540993265491519	2		308	414	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772294	68772316	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	GAGGCCGCGTCCTGGGCAGAGGT	GAGGCCGCGTCCTGGGCAGAGGT	-	novel	NA	P-0001718-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	111	583	0	ENST00000261769.5:c.147_163+6del		p.X49_splice	ENST00000261769	NM_004360.3	49		2/16	0.540993265491519	1	FACETS	0.647	0.584	0.711	0.647	0.584	0.711	SUBCLONAL	1	TRUE	0	0.540993265491519	1		583	463	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138729528	NA	P-0002116-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	42	250	0	ENST00000269305.4:c.523C>G	p.Arg175Gly	p.R175G	ENST00000269305	NM_001126112.2	175	Cgc/Ggc	5/11	0.262048429659826	2	FACETS	0.921	0.78	1	0.921	0.78	1	CLONAL	2	FALSE	0	0.262048429659826	2		250	174	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263715	16263715	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002116-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	44	203	0	ENST00000375759.3:c.10084C>G	p.Pro3362Ala	p.P3362A	ENST00000375759	NM_015001.2	3362	Cct/Gct	12/15	0.262048429659826	5	FACETS	0.896	0.757	1	0.597	0.505	0.699	CLONAL	2	FALSE	2	0.262048429659826	5		203	261	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440266	52440286	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TACCTGCTGCAGAGCCTCTAG	TACCTGCTGCAGAGCCTCTAG	-	novel	NA	P-0002116-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	38	285	0	ENST00000460680.1:c.766_783+3del		p.X256_splice	ENST00000460680	NM_004656.3	256		9/17	0.362792641953443	3	FACETS	1	0.896	1	0.556	0.461	0.661	CLONAL	1	FALSE	1	0.262048429659826	3		285	295	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431394	121431394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193922598	NA	P-0002273-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	110	302	2	ENST00000257555.6:c.598C>T	p.Arg200Trp	p.R200W	ENST00000257555		200	Cgg/Tgg	3/10	0.2057245090153	5	FACETS	1	0.933	1	0.693	0.627	0.762	INDETERMINATE	2	TRUE	2	0.378766238980253	5		304	438	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680740	88680740	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002273-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	81	449	0	ENST00000360948.2:c.517C>G	p.Leu173Val	p.L173V	ENST00000360948	NM_001012338.2	173	Ctc/Gtc	6/19	0.291920927057269	4	FACETS	1	0.927	1	0.356	0.314	0.401	CLONAL	1	TRUE	1	0.378766238980253	4		449	552	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123639	108123639	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002273-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	77	245	0	ENST00000278616.4:c.1898+1del		p.C633fs	ENST00000278616	NM_000051.3	633	tGt/tt	12/63	0.226134308156651	4	FACETS	1	0.953	1	1	0.953	1	INDETERMINATE	2	TRUE	2	0.378766238980253	4		245	247	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431394	121431394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193922598	NA	P-0002273-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	61	302	2	ENST00000257555.6:c.598C>T	p.Arg200Trp	p.R200W	ENST00000257555		200	Cgg/Tgg	3/10	NA	2	FACETS	1	0.88	1			1	INDETERMINATE	2	FALSE	NA	0.333198958599913	2		304	183	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123639	108123639	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002273-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	109	245	0	ENST00000278616.4:c.1898+1del		p.C633fs	ENST00000278616	NM_000051.3	633	tGt/tt	12/63	0.260452095287173	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	FALSE	2	0.333198958599913	4		245	359	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526184	189526184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762371837	NA	P-0002273-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	36	468	1	ENST00000264731.3:c.448G>A	p.Ala150Thr	p.A150T	ENST00000264731	NM_003722.4	150	Gca/Aca	4/14	0.333198958599913	5	FACETS	0.898	0.739	1	0.299	0.246	0.359	CLONAL	1	FALSE	2	0.333198958599913	5		469	361	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0002311-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	82	157	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.174049210483363	3	FACETS	1	0.91	1	0.516	0.457	0.579	INDETERMINATE	1	TRUE	1	0.414242262498329	3		157	463	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17129492	17129492	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002311-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	190	374	0	ENST00000285071.4:c.394G>A	p.Glu132Lys	p.E132K	ENST00000285071	NM_144997.5	132	Gag/Aag	5/14	1	2	FACETS	0.996	0.921	1	0.996	0.921	1	CLONAL	1	TRUE	1	0.414242262498329	2		374	921	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057988	27057988	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002311-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	210	312	0	ENST00000324856.7:c.1696C>T	p.Gln566Ter	p.Q566*	ENST00000324856	NM_006015.4	566	Cag/Tag	3/20	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.414242262498329	2		312	981	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085800	16085800	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002311-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	96	387	0	ENST00000281043.3:c.976A>C	p.Ile326Leu	p.I326L	ENST00000281043	NM_005378.4	326	Atc/Ctc	3/3	1	2	FACETS	0.45	0.4	0.504	0.45	0.4	0.504	SUBCLONAL	1	TRUE	1	0.414242262498329	2		387	1030	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067374	37067374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002311-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	197	382	0	ENST00000231790.2:c.1285G>A	p.Glu429Lys	p.E429K	ENST00000231790	NM_000249.3	429	Gag/Aag	12/19	1	2	FACETS	0.886	0.819	0.955	0.886	0.819	0.955	CLONAL	1	TRUE	1	0.414242262498329	2		382	1074	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161718	47161718	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002311-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1259	301	551	0	ENST00000409792.3:c.4408C>T	p.Pro1470Ser	p.P1470S	ENST00000409792	NM_014159.6	1470	Cca/Tca	3/21	1	2	FACETS	0.932	0.875	0.99	0.932	0.875	0.99	CLONAL	1	TRUE	1	0.414242262498329	2		551	1560	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281551	142281551	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002311-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	252	447	0	ENST00000350721.4:c.693G>C	p.Gln231His	p.Q231H	ENST00000350721	NM_001184.3	231	caG/caC	4/47	1	2	FACETS	0.911	0.851	0.974	0.911	0.851	0.974	CLONAL	1	TRUE	1	0.414242262498329	2		447	1335	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665487	176665487	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002311-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	167	398	0	ENST00000439151.2:c.4171G>T	p.Glu1391Ter	p.E1391*	ENST00000439151	NM_022455.4	1391	Gaa/Taa	7/23	0.414242262498329	1	FACETS	0.795	0.731	0.861	0.795	0.731	0.861	SUBCLONAL	1	TRUE	0	0.414242262498329	1		398	804	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978788	13978788	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002311-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1447	268	496	0	ENST00000405192.2:c.319C>T	p.Gln107Ter	p.Q107*	ENST00000405192	NM_001163147.1	107	Cag/Tag	6/12	0.223503038362188	3	FACETS	0.911	0.851	0.972	0.304	0.283	0.324	INDETERMINATE	1	TRUE	0	0.414242262498329	3		496	1715	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624301	89624301	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002311-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	188	243	0	ENST00000371953.3:c.75G>C	p.Leu25Phe	p.L25F	ENST00000371953	NM_000314.4	25	ttG/ttC	1/9	1	2	FACETS	0.922	0.851	0.995	0.922	0.851	0.995	CLONAL	1	TRUE	1	0.414242262498329	2		243	985	SUCCESS
ATM	472	MSKCC	GRCh37	11	108214089	108214089	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002311-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	202	345	0	ENST00000278616.4:c.8409G>C	p.Lys2803Asn	p.K2803N	ENST00000278616	NM_000051.3	2803	aaG/aaC	57/63	1	2	FACETS	0.922	0.854	0.992	0.922	0.854	0.992	CLONAL	1	TRUE	1	0.414242262498329	2		345	1058	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12043942	12043942	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002311-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	226	421	0	ENST00000396373.4:c.1321G>A	p.Glu441Lys	p.E441K	ENST00000396373	NM_001987.4	441	Gag/Aag	8/8	1	2	FACETS	0.922	0.858	0.989	0.922	0.858	0.989	CLONAL	1	TRUE	1	0.414242262498329	2		421	1183	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240981	133240981	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002311-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	104	464	0	ENST00000320574.5:c.2536G>C	p.Ala846Pro	p.A846P	ENST00000320574	NM_006231.2	846	Gca/Cca	22/49	1	2	FACETS	0.445	0.397	0.496	0.445	0.397	0.496	SUBCLONAL	1	TRUE	1	0.414242262498329	2		464	1128	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762959	40762959	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs387906659	NA	P-0002311-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	153	283	0	ENST00000392038.2:c.49G>A	p.Glu17Lys	p.E17K	ENST00000392038	NM_001626.4	17	Gaa/Aaa	3/14	1	2	FACETS	0.904	0.828	0.984	0.904	0.828	0.984	CLONAL	1	TRUE	1	0.414242262498329	2		283	817	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918502	44918502	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002311-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	360	332	0	ENST00000377967.4:c.985C>T	p.Gln329Ter	p.Q329*	ENST00000377967	NM_021140.2	329	Cag/Tag	12/29	1	1	FACETS	0.772	0.735	0.81	1	0.995	1	SUBCLONAL	2	TRUE	0	0.414242262498329	1		332	892	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651970	36651980	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGCGACTGT	GCCGCGACTGT	-	novel	NA	P-0002311-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	226	337	0	ENST00000244741.5:c.93_103del	p.Ser31ArgfsTer13	p.S31Rfs*13	ENST00000244741	NM_000389.4	31	aGCCGCGACTGT/a	2/3	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.414242262498329	2		337	1013	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346583	81346583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002334-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	98	572	0	ENST00000222390.5:c.1370C>T	p.Pro457Leu	p.P457L	ENST00000222390	NM_000601.4	457	cCa/cTa	11/18	0.138173196231519	3	FACETS	1	0.979	1	0.697	0.624	0.774	INDETERMINATE	1	FALSE	1	0.319649022727562	3		572	510	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346583	81346583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002334-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	250	572	0	ENST00000222390.5:c.1370C>T	p.Pro457Leu	p.P457L	ENST00000222390	NM_000601.4	457	cCa/cTa	11/18	1	2	FACETS	0.88	0.828	0.933	0.88	0.828	0.933	CLONAL	1	TRUE	1	0.838962680738986	2		572	677	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692811	89692811	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002334-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	11	309	0	ENST00000371953.3:c.295G>T	p.Glu99Ter	p.E99*	ENST00000371953	NM_000314.4	99	Gaa/Taa	5/9	0.838962680738986	1	FACETS	0.076	0.052	0.105	0.076	0.052	0.105	SUBCLONAL	1	TRUE	0	0.838962680738986	1		309	201	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844170	68844170	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002334-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	422	732	0	ENST00000261769.5:c.758C>G	p.Thr253Ser	p.T253S	ENST00000261769	NM_004360.3	253	aCc/aGc	6/16	0.838962680738986	1	FACETS	0.948	0.917	0.979	0.948	0.917	0.979	CLONAL	1	TRUE	0	0.838962680738986	1		732	616	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832391	72832391	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002334-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	301	462	1	ENST00000268489.5:c.4190del	p.His1397LeufsTer28	p.H1397Lfs*28	ENST00000268489	NM_006885.3	1397	cAt/ct	9/10	0.838962680738986	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.838962680738986	1		463	391	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182309	38182309	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002726-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	85	384	0	ENST00000396334.3:c.745C>T	p.Gln249Ter	p.Q249*	ENST00000396334	NM_002468.4	249	Cag/Tag	4/5	0.336368843525468	4	FACETS	0.996	0.88	1	0.498	0.44	0.56	CLONAL	1	TRUE	2	0.339915072574207	4		384	673	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747975	41747975	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002726-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	23	141	0	ENST00000226382.2:c.794C>G	p.Ala265Gly	p.A265G	ENST00000226382	NM_003924.3	265	gCg/gGg	3/3	0.336339849747668	3	FACETS	0.9	0.707	1	0.45	0.353	0.56	CLONAL	1	TRUE	1	0.339915072574207	3		141	176	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31939867	31939919	+	protein_altering_variant	In_Frame_Del	DEL	AAGGAGGTTGACACCAACGTGGCCACCGGCGCCCCTCCACGCCGCCAACGAGT	AAGGAGGTTGACACCAACGTGGCCACCGGCGCCCCTCCACGCCGCCAACGAGT	CC	novel	NA	P-0002726-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	210	672	3	ENST00000375333.2:c.94_146delinsCC	p.Lys32_Val49delinsPro	p.K32_V49delinsP	ENST00000375333	NM_032454.1	32	AAGGAGGTTGACACCAACGTGGCCACCGGCGCCCCTCCACGCCGCCAACGAGTc/CCc	1/8	0.339915072574207	6	FACETS	0.902	0.836	0.97	0.451	0.418	0.485	CLONAL	2	TRUE	2	0.339915072574207	6		675	1151	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415555	152415555	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002726-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	102	542	0	ENST00000206249.3:c.1405C>G	p.Leu469Val	p.L469V	ENST00000206249	NM_000125.3	469	Ctg/Gtg	7/8	0.339915072574207	6	FACETS	1	0.924	1	0.261	0.232	0.291	CLONAL	1	TRUE	2	0.339915072574207	6		542	967	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099756	157099756	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002726-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	41	193	0	ENST00000346085.5:c.693T>G	p.Asn231Lys	p.N231K	ENST00000346085	NM_020732.3	231	aaT/aaG	1/20	0.339915072574207	6	FACETS	1	0.867	1	0.261	0.218	0.309	CLONAL	1	TRUE	2	0.339915072574207	6		193	388	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	17	635	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.814	0.621	1			1	INDETERMINATE	1	TRUE	NA	0.521921986997946	2		635	80	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469672	NA	P-0003361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	206	533	0	ENST00000374080.3:c.131G>A	p.Gly44Asp	p.G44D	ENST00000374080		44	gGt/gAt	2/45	0.37584812401943	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.521921986997946	1		533	574	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144907	47144907	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	49	277	0	ENST00000409792.3:c.4846G>C	p.Asp1616His	p.D1616H	ENST00000409792	NM_014159.6	1616	Gat/Cat	7/21	NA	2	FACETS	0.408	0.346	0.477			1	INDETERMINATE	1	TRUE	NA	0.521921986997946	2		277	460	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510611	38510611	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	72	470	0	ENST00000254066.5:c.865G>A	p.Gly289Arg	p.G289R	ENST00000254066	NM_000964.3	289	Ggg/Agg	7/9	0.241496819652783	4	FACETS	0.647	0.565	0.735			1	INDETERMINATE	1	TRUE	NA	0.521921986997946	4		470	649	SUCCESS
AR	367	MSKCC	GRCh37	X	66765206	66765206	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	56	221	0	ENST00000374690.3:c.218A>T	p.Gln73Leu	p.Q73L	ENST00000374690	NM_000044.3	73	cAg/cTg	1/8	0.37584812401943	1	FACETS	0.718	0.623	0.818	0.718	0.623	0.818	SUBCLONAL	1	TRUE	0	0.521921986997946	1		221	221	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643725	52643725	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	82	251	0	ENST00000394830.3:c.2171T>C	p.Met724Thr	p.M724T	ENST00000394830	NM_018313.4	724	aTg/aCg	17/30	0.512735545609204	1	FACETS	0.925	0.828	1	0.925	0.828	1	CLONAL	1	TRUE	0	0.512735545609204	1		251	257	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919902	50919902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368319533	NA	P-0003568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	98	460	0	ENST00000440232.2:c.2989G>A	p.Gly997Ser	p.G997S	ENST00000440232	NM_002691.3	997	Ggc/Agc	24/27	0.500743421719387	1	FACETS	0.756	0.68	0.835	0.756	0.68	0.835	SUBCLONAL	1	TRUE	0	0.512735545609204	1		460	376	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243884	53243884	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	112	280	0	ENST00000375401.3:c.1109del	p.Lys370SerfsTer60	p.K370Sfs*60	ENST00000375401	NM_004187.3	370	aAg/ag	8/26	0.256025363265914	0	FACETS	0.876	0.804	0.948			1	INDETERMINATE	1	TRUE	NA	0.512735545609204	0		280	243	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188193	10188200	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GATAGGTC	GATAGGTC	T	novel	NA	P-0003568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	89	313	0	ENST00000256474.2:c.341-5_343delinsT		p.X114_splice	ENST00000256474	NM_000551.3	114		2/3	0.479707596177785	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.512735545609204	1		313	229	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204507340	204507340	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	36	328	0	ENST00000367182.3:c.415A>T	p.Ser139Cys	p.S139C	ENST00000367182	NM_001278516.1	139	Agt/Tgt	7/11	0.27447874139559	4	FACETS	1	0.94	1	0.68	0.561	0.813	CLONAL	1	TRUE	2	0.21	4		328	305	SUCCESS
RET	5979	MSKCC	GRCh37	10	43613880	43613880	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	19	326	0	ENST00000355710.3:c.2344G>A	p.Val782Ile	p.V782I	ENST00000355710	NM_020975.4	782	Gtc/Atc	13/20	0.141029172228576	4	FACETS	1	0.829	1	0.556	0.423	0.71	CLONAL	1	TRUE	2	0.21	4		326	197	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061147	38061203	+	inframe_deletion	In_Frame_Del	DEL	CCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTGG	CCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTGG	-	novel	NA	P-0004063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	27	28	0	ENST00000250448.2:c.786_842del	p.Gln263_Gly281del	p.Q263_G281del	ENST00000250448	NM_004496.3	262	cgCCAGAAGCGCTTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGa/cga	2/2	0.201030993654472	4	FACETS	1	0.886	1	1	0.969	1	CLONAL	6	TRUE	2	0.21	4		28	49	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911655	32911655	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	68	523	0	ENST00000380152.3:c.3164del	p.Asn1055IlefsTer5	p.N1055Ifs*5	ENST00000380152		1055	Aat/at	11/27	0.3	1	FACETS	0.889	0.779	1	1	0.979	1	CLONAL	2	TRUE	0	0.21	1		523	326	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615625	100615625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147036606	NA	P-0004445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	131	446	0	ENST00000308731.7:c.707G>A	p.Arg236Gln	p.R236Q	ENST00000308731	NM_000061.2	236	cGg/cAg	8/19	0.1725885289331	1	FACETS	0.496	0.45	0.545	0.496	0.45	0.545	INDETERMINATE	1	TRUE	0	0.454432297112767	1		446	898	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40478210	40478210	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	131	339	0	ENST00000264657.5:c.1289T>A	p.Leu430Gln	p.L430Q	ENST00000264657	NM_139276.2	430	cTg/cAg	15/24	1	2	FACETS	0.755	0.685	0.828	0.755	0.685	0.828	SUBCLONAL	1	TRUE	1	0.454432297112767	2		339	764	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	131	624	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.35733736891348	2		624	663	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187838	11187838	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	105	500	0	ENST00000361445.4:c.6059C>G	p.Ala2020Gly	p.A2020G	ENST00000361445	NM_004958.3	2020	gCc/gGc	44/58	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.35733736891348	2		500	581	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56477631	56477631	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	156	604	0	ENST00000267101.3:c.179T>A	p.Met60Lys	p.M60K	ENST00000267101	NM_001982.3	60	aTg/aAg	2/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.35733736891348	2		604	677	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41542803	41542803	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	39	415	0	ENST00000263253.7:c.2114G>C	p.Arg705Pro	p.R705P	ENST00000263253	NM_001429.3	705	cGa/cCa	11/31	1	2	FACETS	0.371	0.307	0.443	0.371	0.307	0.443	SUBCLONAL	1	TRUE	1	0.35733736891348	2		415	588	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840044	27840044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	71	369	0	ENST00000328488.2:c.50C>T	p.Pro17Leu	p.P17L	ENST00000328488	NM_003533.2	17	cCg/cTg	1/1	1	2	FACETS	0.972	0.852	1	0.972	0.852	1	CLONAL	1	TRUE	1	0.35733736891348	2		369	409	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0004539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	28	444	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.17	0.135	0.21	0.17	0.135	0.21	SUBCLONAL	1	TRUE	1	0.542911948235956	2		444	606	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200963	108200963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	112	376	0	ENST00000278616.4:c.7330G>A	p.Glu2444Lys	p.E2444K	ENST00000278616	NM_000051.3	2444	Gag/Aag	50/63	1	2	FACETS	0.839	0.758	0.923	0.839	0.758	0.923	CLONAL	1	TRUE	1	0.542911948235956	2		376	492	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838432	156838432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55909005	NA	P-0004539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	138	278	0	ENST00000524377.1:c.710C>T	p.Thr237Met	p.T237M	ENST00000524377	NM_002529.3	237	aCg/aTg	6/17	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.542911948235956	2		278	470	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202123079	202123079	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	91	243	0	ENST00000358485.4:c.125C>A	p.Ala42Glu	p.A42E	ENST00000358485	NM_001080125.1	42	gCg/gAg	1/9	1	2	FACETS	0.878	0.785	0.975	0.878	0.785	0.975	CLONAL	1	TRUE	1	0.542911948235956	2		243	382	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729099	66729104	+	inframe_deletion	In_Frame_Del	DEL	ATCAAA	ATCAAA	-	novel	NA	P-0004554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	299	490	0	ENST00000307102.5:c.307_312del	p.Ile103_Lys104del	p.I103_K104del	ENST00000307102	NM_002755.3	103	ATCAAA/-	3/11	1	2	FACETS	0.954	0.9	1	0.954	0.9	1	CLONAL	1	TRUE	1	0.652335618685082	2		490	961	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624262	89624263	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587776671	NA	P-0004554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	36	157	0	ENST00000371953.3:c.40dup	p.Arg14LysfsTer30	p.R14Kfs*30	ENST00000371953	NM_000314.4	12	-/A	1/9	0.652335618685082	1	FACETS	0.383	0.318	0.455	0.383	0.318	0.455	SUBCLONAL	1	TRUE	0	0.652335618685082	1		157	194	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0004554-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	52	272	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	0.686816022065215	2	FACETS	0.419	0.358	0.486	0.21	0.179	0.243	SUBCLONAL	1	TRUE	0	0.686816022065215	2		272	361	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729099	66729104	+	inframe_deletion	In_Frame_Del	DEL	ATCAAA	ATCAAA	-	novel	NA	P-0004554-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	331	490	0	ENST00000307102.5:c.307_312del	p.Ile103_Lys104del	p.I103_K104del	ENST00000307102	NM_002755.3	103	ATCAAA/-	3/11	0.145705781104167	6	FACETS	0.921	0.875	0.968	0.921	0.875	0.968	INDETERMINATE	3	TRUE	3	0.686816022065215	6		490	828	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0004589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	201	656	4	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.307442907214066	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.310547855418661	2		660	605	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0004589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	115	425	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.310547855418661	3	FACETS	0.878	0.796	0.965	0.878	0.796	0.965	CLONAL	2	TRUE	1	0.310547855418661	3		426	487	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089863	5089863	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	97	275	0	ENST00000381652.3:c.2761G>A	p.Gly921Ser	p.G921S	ENST00000381652	NM_004972.3	921	Ggt/Agt	20/25	0.310547855418661	3	FACETS	1	0.978	1	0.461	0.412	0.512	CLONAL	1	TRUE	0	0.310547855418661	3		275	522	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143462	30143462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	17	95	0	ENST00000389048.3:c.64G>A	p.Gly22Arg	p.G22R	ENST00000389048	NM_004304.4	22	Ggg/Agg	1/29	0.310547855418661	3	FACETS	0.703	0.527	0.91	0.234	0.175	0.304	CLONAL	1	TRUE	0	0.310547855418661	3		95	180	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293475	1293475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554042799	NA	P-0004589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	51	393	0	ENST00000310581.5:c.1526C>T	p.Thr509Met	p.T509M	ENST00000310581	NM_198253.2	509	aCg/aTg	2/16	0.310547855418661	3	FACETS	0.72	0.612	0.839	0.36	0.306	0.42	SUBCLONAL	1	TRUE	1	0.310547855418661	3		393	527	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341937	8341937	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	70	336	0	ENST00000356435.5:c.4703C>T	p.Ala1568Val	p.A1568V	ENST00000356435		1568	gCc/gTc	29/35	0.310547855418661	3	FACETS	1	0.942	1	0.379	0.331	0.43	CLONAL	1	TRUE	0	0.310547855418661	3		336	458	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440680	56440680	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs759809905	NA	P-0004589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	70	530	0	ENST00000407977.2:c.538C>G	p.Gln180Glu	p.Q180E	ENST00000407977		180	Caa/Gaa	5/10	0.310547855418661	7	FACETS	0.678	0.589	0.775			1	SUBCLONAL	1	TRUE	NA	0.310547855418661	7		530	1181	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561022	9561022	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1200639374	NA	P-0004589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	68	321	0	ENST00000353224.5:c.760G>C	p.Glu254Gln	p.E254Q	ENST00000353224	NM_177990.2	254	Gaa/Caa	4/10	0.277630587164462	5	FACETS	0.897	0.779	1	0.299	0.259	0.342	CLONAL	1	TRUE	2	0.310547855418661	5		321	716	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739099	40739099	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	65	261	0	ENST00000373198.4:c.3185G>T	p.Arg1062Leu	p.R1062L	ENST00000373198	NM_133170.3	1062	cGc/cTc	24/32	0.277630587164462	5	FACETS	1	0.956	1	0.415	0.36	0.474	CLONAL	1	TRUE	2	0.310547855418661	5		261	493	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347238	70347238	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	86	516	1	ENST00000374080.3:c.2902G>C	p.Glu968Gln	p.E968Q	ENST00000374080		968	Gag/Cag	21/45	0.310547855418661	3	FACETS	0.777	0.686	0.874	0.388	0.343	0.437	SUBCLONAL	1	TRUE	1	0.310547855418661	3		517	824	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93640057	93640057	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	103	486	0	ENST00000375746.1:c.1386G>T	p.Gln462His	p.Q462H	ENST00000375746	NM_001174167.1	462	caG/caT	10/14	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.430867999565288	2		486	470	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911564	101911564	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	170	688	0	ENST00000374994.4:c.1489C>T	p.Gln497Ter	p.Q497*	ENST00000374994	NM_004612.2	497	Caa/Taa	9/9	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.430867999565288	2		688	767	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717699	89717699	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554825210	NA	P-0005751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	118	551	0	ENST00000371953.3:c.724G>T	p.Glu242Ter	p.E242*	ENST00000371953	NM_000314.4	242	Gag/Tag	7/9	0.430867999565288	1	FACETS	0.811	0.735	0.891	0.811	0.735	0.891	CLONAL	1	TRUE	0	0.430867999565288	1		551	530	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657025	45657025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542311532	NA	P-0005751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	115	634	1	ENST00000407780.3:c.131G>A	p.Arg44His	p.R44H	ENST00000407780	NM_001283052.1	44	cGt/cAt	3/7	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.430867999565288	2		635	512	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191571	10191571	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1559429829	NA	P-0005751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	138	784	0	ENST00000256474.2:c.565del	p.Glu189LysfsTer13	p.E189Kfs*13	ENST00000256474	NM_000551.3	188	ctG/ct	3/3	0.430867999565288	1	FACETS	0.856	0.782	0.933	0.856	0.782	0.933	CLONAL	1	TRUE	0	0.430867999565288	1		784	587	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651363	52651363	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	161	819	0	ENST00000394830.3:c.1733del	p.Asp578AlafsTer9	p.D578Afs*9	ENST00000394830	NM_018313.4	578	gAc/gc	15/30	0.339953169742143	0	FACETS	0.704	0.649	0.762			1	SUBCLONAL	1	TRUE	0	0.430867999565288	0		819	604	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231140	53231148	+	inframe_deletion	In_Frame_Del	DEL	GGTTTGTGC	GGTTTGTGC	-	novel	NA	P-0005751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	154	405	0	ENST00000375401.3:c.1754_1762del	p.Arg585_Asn587del	p.R585_N587del	ENST00000375401	NM_004187.3	585	cGCACAAACCag/cag	13/26	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.430867999565288	1		405	392	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129681	47129682	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	C	novel	NA	P-0005751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	137	801	0	ENST00000409792.3:c.5198_5199delinsG	p.Asn1733SerfsTer9	p.N1733Sfs*9	ENST00000409792	NM_014159.6	1733	aAC/aG	10/21	0.430867999565288	1	FACETS	0.815	0.744	0.889	0.815	0.744	0.889	CLONAL	1	TRUE	0	0.430867999565288	1		801	612	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589535	67589535	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0005806-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	309	289	0	ENST00000274335.5:c.1300-2A>T		p.X434_splice	ENST00000274335		434			0.556644997611049	6	FACETS	0.953	0.92	0.985			1	CLONAL	5	TRUE	NA	0.827641284068078	6		289	416	SUCCESS
APC	324	MSKCC	GRCh37	5	112174751	112174753	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs386833391	NA	P-0005806-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	31	477	2	ENST00000257430.4:c.3468_3470del	p.Glu1157del	p.E1157del	ENST00000257430	NM_000038.5	1154	GAA/-	16/16	0.635830505210704	1	FACETS	0.185	0.15	0.224	0.185	0.15	0.224	SUBCLONAL	1	TRUE	0	0.827641284068078	1		479	237	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs967461896	NA	P-0006357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	271	293	0	ENST00000269305.4:c.526T>C	p.Cys176Arg	p.C176R	ENST00000269305	NM_001126112.2	176	Tgc/Cgc	5/11	0.518818361371013	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.518818361371013	2		293	478	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037972	49037972	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0006357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	333	377	0	ENST00000267163.4:c.2211+1G>A		p.X737_splice	ENST00000267163	NM_000321.2	737			0.485008889082736	3	FACETS	0.865	0.826	0.903	0.865	0.826	0.903	CLONAL	3	TRUE	0	0.518818361371013	3		377	623	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162904	47162904	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs757432733	NA	P-0006357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	107	486	0	ENST00000409792.3:c.3222G>T	p.Lys1074Asn	p.K1074N	ENST00000409792	NM_014159.6	1074	aaG/aaT	3/21	0.234757673227356	5	FACETS	0.777	0.696	0.863	0.259	0.232	0.288	INDETERMINATE	1	TRUE	2	0.518818361371013	5		486	944	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425833	49425833	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	37	368	0	ENST00000301067.7:c.12655C>T	p.Gln4219Ter	p.Q4219*	ENST00000301067	NM_003482.3	4219	Cag/Tag	39/54	0.41073126640485	3	FACETS	0.254	0.208	0.305			1	SUBCLONAL	1	TRUE	NA	0.518818361371013	3		368	708	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215285	123215285	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	172	293	0	ENST00000218089.9:c.2831C>G	p.Thr944Arg	p.T944R	ENST00000218089	NM_001042749.1	944	aCa/aGa	28/35	0.346530887752838	2	FACETS	0.853	0.787	0.923			1	CLONAL	1	TRUE	NA	0.518818361371013	2		293	777	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006760-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	167	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.189829915111682	3	FACETS	1	0.987	1	0.706	0.648	0.767	CLONAL	1	TRUE	1	0.24502298276537	3		473	1083	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509049	106509049	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1281619231	NA	P-0006760-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	142	618	1	ENST00000359195.3:c.1043G>T	p.Ser348Ile	p.S348I	ENST00000359195	NM_002649.2	348	aGt/aTt	2/11	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.24502298276537	2		619	1145	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573996	7573996	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006760-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	219	922	0	ENST00000269305.4:c.1031T>A	p.Leu344Gln	p.L344Q	ENST00000269305	NM_001126112.2	344	cTg/cAg	10/11	0.24502298276537	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.24502298276537	1		922	1340	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006760-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	441	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.29825933851156	5	FACETS	0.975	0.929	1	0.975	0.929	1	CLONAL	3	TRUE	2	0.29825933851156	5		473	1463	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509049	106509049	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1281619231	NA	P-0006760-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	196	618	1	ENST00000359195.3:c.1043G>T	p.Ser348Ile	p.S348I	ENST00000359195	NM_002649.2	348	aGt/aTt	2/11	0.287863740678969	3	FACETS	0.818	0.758	0.881	0.818	0.758	0.881	CLONAL	2	TRUE	1	0.29825933851156	3		619	923	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573996	7573996	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006760-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	344	922	0	ENST00000269305.4:c.1031T>A	p.Leu344Gln	p.L344Q	ENST00000269305	NM_001126112.2	344	cTg/cAg	10/11	0.29400138902754	2	FACETS	0.856	0.809	0.904	0.856	0.809	0.904	CLONAL	2	TRUE	0	0.29825933851156	2		922	1348	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519886	NA	P-0006856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	378	331	0	ENST00000349496.5:c.97T>C	p.Ser33Pro	p.S33P	ENST00000349496	NM_001904.3	33	Tct/Cct	3/15	0.82918861195781	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.85716306322977	1		331	498	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664915	138664915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs797044527	NA	P-0006856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	128	127	0	ENST00000330315.3:c.650C>T	p.Ser217Phe	p.S217F	ENST00000330315	NM_023067.3	217	tCc/tTc	1/1	0.856767696212901	3	FACETS	1	0.94	1	0.518	0.473	0.564	CLONAL	1	TRUE	1	0.85716306322977	3		127	412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577512	7577512	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	396	340	0	ENST00000269305.4:c.769C>G	p.Leu257Val	p.L257V	ENST00000269305	NM_001126112.2	257	Ctg/Gtg	7/11	0.82918861195781	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.85716306322977	1		340	505	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941665	48941666	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0006856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	519	237	2	ENST00000267163.4:c.976_977del	p.Leu326Ter	p.L326*	ENST00000267163	NM_000321.2	325	taTCtt/tatt	10/27	0.842065920579855	2	FACETS	0.898	0.875	0.921	0.898	0.875	0.921	CLONAL	2	TRUE	0	0.85716306322977	2		239	674	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519886	NA	P-0006856-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	547	331	0	ENST00000349496.5:c.97T>C	p.Ser33Pro	p.S33P	ENST00000349496	NM_001904.3	33	Tct/Cct	3/15	0.88462151699106	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.894175895535842	1		331	647	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664915	138664915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs797044527	NA	P-0006856-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	128	127	0	ENST00000330315.3:c.650C>T	p.Ser217Phe	p.S217F	ENST00000330315	NM_023067.3	217	tCc/tTc	1/1	0.894175895535842	3	FACETS	1	0.976	1	0.588	0.54	0.638	CLONAL	1	TRUE	1	0.894175895535842	3		127	352	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577512	7577512	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006856-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	496	340	0	ENST00000269305.4:c.769C>G	p.Leu257Val	p.L257V	ENST00000269305	NM_001126112.2	257	Ctg/Gtg	7/11	0.894175895535842	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.894175895535842	1		340	606	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941665	48941666	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0006856-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	627	237	2	ENST00000267163.4:c.976_977del	p.Leu326Ter	p.L326*	ENST00000267163	NM_000321.2	325	taTCtt/tatt	10/27	0.894175895535842	2	FACETS	0.992	0.975	1	0.992	0.975	1	CLONAL	2	TRUE	0	0.894175895535842	2		239	707	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623167	52623167	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	331	471	4	ENST00000394830.3:c.2884G>T	p.Asp962Tyr	p.D962Y	ENST00000394830	NM_018313.4	962	Gat/Tat	19/30	0.673825007556121	1	FACETS	0.867	0.825	0.91	0.867	0.825	0.91	CLONAL	1	TRUE	0	0.673825007556121	1		475	751	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032031	26032031	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	603	1020	0	ENST00000244661.2:c.258G>C	p.Gln86His	p.Q86H	ENST00000244661	NM_003537.3	86	caG/caC	1/1	0.673825007556121	1	FACETS	0.833	0.802	0.864	0.833	0.802	0.864	CLONAL	1	TRUE	0	0.673825007556121	1		1020	1425	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258715	16258715	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	368	543	0	ENST00000375759.3:c.5980G>T	p.Gly1994Ter	p.G1994*	ENST00000375759	NM_015001.2	1994	Gga/Tga	11/15	0.673825007556121	1	FACETS	0.852	0.812	0.892	0.852	0.812	0.892	CLONAL	1	TRUE	0	0.673825007556121	1		543	850	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666622	206666622	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	343	506	0	ENST00000367120.3:c.1956G>T	p.Gln652His	p.Q652H	ENST00000367120	NM_014002.3	652	caG/caT	20/22	1	2	FACETS	0.885	0.837	0.933	0.885	0.837	0.933	CLONAL	1	TRUE	1	0.673825007556121	2		506	1151	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161801	47161801	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	410	509	0	ENST00000409792.3:c.4325C>A	p.Ser1442Ter	p.S1442*	ENST00000409792	NM_014159.6	1442	tCa/tAa	3/21	0.673825007556121	1	FACETS	0.878	0.84	0.917	0.878	0.84	0.917	CLONAL	1	TRUE	0	0.673825007556121	1		509	919	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720978	119720978	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	300	461	0	ENST00000316626.5:c.197C>A	p.Ser66Ter	p.S66*	ENST00000316626		66	tCa/tAa	2/12	1	2	FACETS	0.871	0.822	0.922	0.871	0.822	0.922	CLONAL	1	TRUE	1	0.673825007556121	2		461	1022	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814883	139814883	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	605	849	1	ENST00000247668.2:c.876G>T	p.Glu292Asp	p.E292D	ENST00000247668	NM_021138.3	292	gaG/gaT	8/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.673825007556121	2		850	1781	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717661	89717661	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	231	362	0	ENST00000371953.3:c.686C>A	p.Ser229Ter	p.S229*	ENST00000371953	NM_000314.4	229	tCa/tAa	7/9	0.673825007556121	1	FACETS	0.878	0.827	0.929	0.878	0.827	0.929	CLONAL	1	TRUE	0	0.673825007556121	1		362	518	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514107	69514107	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	404	504	1	ENST00000294312.3:c.574C>A	p.Leu192Met	p.L192M	ENST00000294312	NM_005117.2	192	Ctg/Atg	3/3	0.673825007556121	1	FACETS	0.921	0.882	0.961	0.921	0.882	0.961	CLONAL	1	TRUE	0	0.673825007556121	1		505	863	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190748	108190748	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1339238483	NA	P-0007046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	163	326	0	ENST00000278616.4:c.6415G>T	p.Glu2139Ter	p.E2139*	ENST00000278616	NM_000051.3	2139	Gaa/Taa	44/63	0.673825007556121	1	FACETS	0.899	0.837	0.96	0.899	0.837	0.96	CLONAL	1	TRUE	0	0.673825007556121	1		326	357	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914094	32914094	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs80358781	NA	P-0007046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	346	756	0	ENST00000380152.3:c.5602G>T	p.Asp1868Tyr	p.D1868Y	ENST00000380152		1868	Gac/Tac	11/27	0.673825007556121	1	FACETS	0.896	0.854	0.938	0.896	0.854	0.938	CLONAL	1	TRUE	0	0.673825007556121	1		756	760	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434817	110434817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	259	438	0	ENST00000375856.3:c.3584G>A	p.Gly1195Glu	p.G1195E	ENST00000375856	NM_003749.2	1195	gGa/gAa	1/2	0.673825007556121	1	FACETS	0.934	0.884	0.984	0.934	0.884	0.984	CLONAL	1	TRUE	0	0.673825007556121	1		438	546	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994824	73994824	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	156	176	0	ENST00000318443.5:c.308G>T	p.Gly103Val	p.G103V	ENST00000318443	NM_001024736.1	103	gGc/gTc	3/10	1	2	FACETS	0.93	0.858	1	0.93	0.858	1	CLONAL	1	TRUE	1	0.673825007556121	2		176	498	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354348	354348	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	324	427	1	ENST00000262320.3:c.1210G>T	p.Glu404Ter	p.E404*	ENST00000262320	NM_003502.3	404	Gag/Tag	5/11	0.673825007556121	1	FACETS	0.96	0.915	1	0.96	0.915	1	CLONAL	1	TRUE	0	0.673825007556121	1		428	664	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842438	68842438	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	310	461	0	ENST00000261769.5:c.499G>T	p.Glu167Ter	p.E167*	ENST00000261769	NM_004360.3	167	Gaa/Taa	4/16	0.673825007556121	1	FACETS	0.934	0.889	0.98	0.934	0.889	0.98	CLONAL	1	TRUE	0	0.673825007556121	1		461	653	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81960731	81960731	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	571	646	1	ENST00000359376.3:c.2462C>A	p.Ser821Tyr	p.S821Y	ENST00000359376	NM_002661.3	821	tCc/tAc	23/33	0.673825007556121	1	FACETS	0.947	0.913	0.981	0.947	0.913	0.981	CLONAL	1	TRUE	0	0.673825007556121	1		647	1187	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108203	8108203	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	393	566	2	ENST00000585124.1:c.1021C>A	p.Gln341Lys	p.Q341K	ENST00000585124	NM_004217.3	341	Caa/Aaa	9/9	0.673825007556121	1	FACETS	0.886	0.847	0.926	0.886	0.847	0.926	CLONAL	1	TRUE	0	0.673825007556121	1		568	873	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533489	63533489	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	300	412	0	ENST00000307078.5:c.1665C>A	p.Cys555Ter	p.C555*	ENST00000307078	NM_004655.3	555	tgC/tgA	6/11	0.673825007556121	1	FACETS	0.876	0.831	0.921	0.876	0.831	0.921	CLONAL	1	TRUE	0	0.673825007556121	1		412	674	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604775	48604775	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	330	396	1	ENST00000342988.3:c.1597C>A	p.Leu533Ile	p.L533I	ENST00000342988	NM_005359.5	533	Ctc/Atc	12/12	0.673825007556121	1	FACETS	0.94	0.895	0.984	0.94	0.895	0.984	CLONAL	1	TRUE	0	0.673825007556121	1		397	691	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793388	42793388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1044700149	NA	P-0007046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	228	386	0	ENST00000575354.2:c.1190C>T	p.Ala397Val	p.A397V	ENST00000575354	NM_015125.3	397	gCt/gTt	8/20	1	2	FACETS	0.974	0.912	1	0.974	0.912	1	CLONAL	1	TRUE	1	0.673825007556121	2		386	695	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538341	9538341	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	327	521	0	ENST00000353224.5:c.1657C>A	p.Leu553Met	p.L553M	ENST00000353224	NM_177990.2	553	Ctg/Atg	7/10	0.673825007556121	1	FACETS	0.882	0.839	0.925	0.882	0.839	0.925	CLONAL	1	TRUE	0	0.673825007556121	1		521	730	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508612	38508626	+	inframe_deletion	In_Frame_Del	DEL	GGACATTGACCTCTG	GGACATTGACCTCTG	-	novel	NA	P-0007046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	439	599	0	ENST00000254066.5:c.665_679del	p.Ile222_Asp226del	p.I222_D226del	ENST00000254066	NM_000964.3	220	ctGGACATTGACCTCTGg/ctg	6/9	0.673825007556121	1	FACETS	0.898	0.861	0.936	0.898	0.861	0.936	CLONAL	1	TRUE	0	0.673825007556121	1		599	962	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526435	66526438	+	frameshift_variant	Frame_Shift_Del	DEL	ATGA	ATGA	-	novel	NA	P-0007046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	280	269	0	ENST00000358598.2:c.993_996del	p.Met331IlefsTer14	p.M331Ifs*14	ENST00000358598	NM_212471.2	331	ATGAat/at	11/11	0.673825007556121	1	FACETS	0.979	0.93	1	0.979	0.93	1	CLONAL	1	TRUE	0	0.673825007556121	1		269	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0007164-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1279	130	656	4	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.177208441079192	2		660	1409	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593597	55593597	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007164-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	70	1039	0	ENST00000288135.5:c.1663G>A	p.Val555Ile	p.V555I	ENST00000288135	NM_000222.2	555	Gta/Ata	11/21	1	2	FACETS	0.72	0.626	0.823	0.72	0.626	0.823	SUBCLONAL	1	TRUE	1	0.177208441079192	2		1039	1097	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119702	70119702	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007164-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	68	1079	0	ENST00000245479.2:c.704C>G	p.Pro235Arg	p.P235R	ENST00000245479	NM_000346.3	235	cCg/cGg	3/3	1	2	FACETS	0.611	0.529	0.7	0.611	0.529	0.7	SUBCLONAL	1	TRUE	1	0.177208441079192	2		1079	1257	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250948	10250948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1255153711	NA	P-0007164-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	89	783	1	ENST00000340748.4:c.3532C>T	p.Arg1178Trp	p.R1178W	ENST00000340748		1178	Cgg/Tgg	32/40	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.177208441079192	2		784	973	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391070	139391080	+	frameshift_variant	Frame_Shift_Del	DEL	GCCAGCCGGGT	GCCAGCCGGGT	-	novel	NA	P-0007164-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	59	795	0	ENST00000277541.6:c.7111_7121del	p.Thr2371HisfsTer132	p.T2371Hfs*132	ENST00000277541	NM_017617.3	2371	ACCCGGCTGGCc/c	34/34	0.177208441079192	3	FACETS	0.765	0.656	0.884	0.382	0.328	0.442	SUBCLONAL	1	TRUE	1	0.177208441079192	3		795	948	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0007168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	419	549	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.636579802457136	1	FACETS	0.954	0.914	0.995	0.954	0.914	0.995	CLONAL	1	TRUE	0	0.656840412261634	1		549	898	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417865	138417865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	282	364	0	ENST00000289153.2:c.1654G>A	p.Glu552Lys	p.E552K	ENST00000289153	NM_006219.2	552	Gaa/Aaa	11/22	1	2	FACETS	0.888	0.836	0.941	0.888	0.836	0.941	CLONAL	1	TRUE	1	0.656840412261634	2		364	967	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576822	212576822	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0007168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	244	355	0	ENST00000342788.4:c.1077T>A	p.Cys359Ter	p.C359*	ENST00000342788	NM_005235.2	359	tgT/tgA	9/28	1	2	FACETS	0.901	0.844	0.959	0.901	0.844	0.959	CLONAL	1	TRUE	1	0.656840412261634	2		355	825	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427568	72427568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs912857100	NA	P-0007168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	140	323	0	ENST00000477973.2:c.922G>A	p.Asp308Asn	p.D308N	ENST00000477973	NM_012234.5	308	Gac/Aac	4/4	1	2	FACETS	0.459	0.417	0.502	0.459	0.417	0.502	SUBCLONAL	1	TRUE	1	0.656840412261634	2		323	929	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710597	114710597	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	513	651	0	ENST00000543371.1:c.82G>T	p.Glu28Ter	p.E28*	ENST00000543371	NM_001198531.1	28	Gag/Tag	1/14	1	2	FACETS	0.967	0.925	1	0.967	0.925	1	CLONAL	1	TRUE	1	0.656840412261634	2		651	1615	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3824628	3824628	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1607	171	457	1	ENST00000262367.5:c.2225G>T	p.Arg742Leu	p.R742L	ENST00000262367	NM_004380.2	742	cGt/cTt	12/31	0.511444462037471	3	FACETS	0.389	0.356	0.424			1	SUBCLONAL	1	TRUE	NA	0.656840412261634	3		458	1778	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593491	48593494	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	rs80338965	NA	P-0007168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	301	328	0	ENST00000342988.3:c.1245_1248del	p.Asp415GlufsTer20	p.D415Efs*20	ENST00000342988	NM_005359.5	414	ttAGAC/tt	10/12	0.656840412261634	1	FACETS	0.904	0.858	0.95	0.904	0.858	0.95	CLONAL	1	TRUE	0	0.656840412261634	1		328	681	SUCCESS
APC	324	MSKCC	GRCh37	5	112173472	112173473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	611	436	0	ENST00000257430.4:c.2183dup	p.Asn728LysfsTer6	p.N728Kfs*6	ENST00000257430	NM_000038.5	727	-/A	16/16	0.656840412261634	2	FACETS	0.875	0.847	0.903	0.875	0.847	0.903	CLONAL	2	TRUE	0	0.656840412261634	2		436	1063	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0007267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	627	577	1	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.543737279794312	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.566091609384525	2		578	1080	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474396	40474396	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	381	765	1	ENST00000264657.5:c.2005C>A	p.Pro669Thr	p.P669T	ENST00000264657	NM_139276.2	669	Cca/Aca	21/24	0.566091609384525	1	FACETS	0.93	0.885	0.975	0.93	0.885	0.975	CLONAL	1	TRUE	0	0.566091609384525	1		766	1038	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0007310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	53	656	4	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.442	0.376	0.516	0.442	0.376	0.516	SUBCLONAL	1	TRUE	1	0.25	2		660	959	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163431	47163431	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0007310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	44	259	0	ENST00000409792.3:c.2695A>T	p.Lys899Ter	p.K899*	ENST00000409792	NM_014159.6	899	Aaa/Taa	3/21	1	2	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	1	0.25	2		259	349	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414839	78414839	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0007310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	28	255	0	ENST00000370768.2:c.1926+1G>A		p.X642_splice	ENST00000370768	NM_003902.3	642			1	2	FACETS	0.418	0.333	0.515	0.418	0.333	0.515	SUBCLONAL	1	TRUE	1	0.25	2		255	536	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830761	156830761	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	13	53	0	ENST00000524377.1:c.35G>A	p.Trp12Ter	p.W12*	ENST00000524377	NM_002529.3	12	tGg/tAg	1/17	1	2	FACETS	0.788	0.575	1	1	0.889	1	CLONAL	2	TRUE	1	0.25	2		53	66	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191562	10191562	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	91	373	2	ENST00000256474.2:c.555C>A	p.Tyr185Ter	p.Y185*	ENST00000256474	NM_000551.3	185	taC/taA	3/3	1	2	FACETS	0.978	0.869	1	0.978	0.869	1	CLONAL	1	TRUE	1	0.25	2		375	744	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984906	55984906	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	47	320	0	ENST00000263923.4:c.223G>T	p.Glu75Ter	p.E75*	ENST00000263923	NM_002253.2	75	Gag/Tag	3/30	1	2	FACETS	0.53	0.446	0.623	0.53	0.446	0.623	SUBCLONAL	1	TRUE	1	0.25	2		320	709	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508315	106508315	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	19	111	0	ENST00000359195.3:c.309G>T	p.Lys103Asn	p.K103N	ENST00000359195	NM_002649.2	103	aaG/aaT	2/11	1	2	FACETS	0.502	0.381	0.644	0.502	0.381	0.644	SUBCLONAL	1	TRUE	1	0.25	2		111	303	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883692	37883692	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	142	449	2	ENST00000269571.5:c.3304C>T	p.Pro1102Ser	p.P1102S	ENST00000269571		1102	Ccc/Tcc	26/27	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.25	2		451	862	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443757	52443778	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCCTGGGTGGGGCGACAAGAG	GGCCTGGGTGGGGCGACAAGAG	-	novel	NA	P-0007310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	45	248	0	ENST00000460680.1:c.38-19_40del		p.X13_splice	ENST00000460680	NM_004656.3	13		2/17	1	2	FACETS	0.893	0.752	1	0.893	0.752	1	CLONAL	1	TRUE	1	0.25	2		248	403	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641769	12641769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007531-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	105	475	0	ENST00000251849.4:c.872C>T	p.Ser291Leu	p.S291L	ENST00000251849	NM_002880.3	291	tCa/tTa	9/17	1	2	FACETS	0.607	0.543	0.676	0.607	0.543	0.676	SUBCLONAL	1	TRUE	1	0.337800255114439	2		475	1024	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737092	145737092	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007531-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	204	443	0	ENST00000428558.2:c.3474G>T	p.Arg1158Ser	p.R1158S	ENST00000428558	NM_004260.3	1158	agG/agT	21/22	0.129605871773671	3	FACETS	0.776	0.72	0.833	0.517	0.48	0.556	INDETERMINATE	2	TRUE	0	0.337800255114439	3		443	910	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123260349	123260349	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007531-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	124	532	0	ENST00000358487.5:c.1552A>T	p.Met518Leu	p.M518L	ENST00000358487	NM_000141.4	518	Atg/Ttg	11/18	1	2	FACETS	0.661	0.597	0.73	0.661	0.597	0.73	SUBCLONAL	1	TRUE	1	0.337800255114439	2		532	1110	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212567	133212567	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007531-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	100	582	0	ENST00000320574.5:c.5722T>G	p.Ser1908Ala	p.S1908A	ENST00000320574	NM_006231.2	1908	Tct/Gct	42/49	1	2	FACETS	0.617	0.55	0.688	0.617	0.55	0.688	SUBCLONAL	1	TRUE	1	0.337800255114439	2		582	960	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560193	29560193	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007531-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	77	381	0	ENST00000356175.3:c.3670G>T	p.Ala1224Ser	p.A1224S	ENST00000356175	NM_000267.3	1224	Gcg/Tcg	27/57	1	2	FACETS	0.666	0.584	0.753	0.666	0.584	0.753	SUBCLONAL	1	TRUE	1	0.337800255114439	2		381	685	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123499658	123499658	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007531-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	154	787	0	ENST00000371139.4:c.185G>T	p.Gly62Val	p.G62V	ENST00000371139	NM_001114937.2	62	gGt/gTt	2/4	0.337800255114439	1	FACETS	0.671	0.613	0.732	0.671	0.613	0.732	SUBCLONAL	1	TRUE	0	0.337800255114439	1		787	1129	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566125	95566126	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0007531-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	53	298	0	ENST00000393063.1:c.4197dup	p.Asp1400ArgfsTer2	p.D1400Rfs*2	ENST00000393063	NM_030621.3	1399	-/A	23/28	1	2	FACETS	0.567	0.484	0.659	0.567	0.484	0.659	SUBCLONAL	1	TRUE	1	0.337800255114439	2		298	553	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245609	46245612	+	frameshift_variant	Frame_Shift_Del	DEL	CCCC	CCCC	-	novel	NA	P-0007531-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	73	491	0	ENST00000334344.6:c.3704_3707del	p.Pro1235HisfsTer7	p.P1235Hfs*7	ENST00000334344	NM_152641.2	1235	CCCCca/ca	15/21	1	2	FACETS	0.515	0.449	0.585	0.515	0.449	0.585	SUBCLONAL	1	TRUE	1	0.337800255114439	2		491	840	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914484	32914491	+	frameshift_variant	Frame_Shift_Del	DEL	CAAGTGTT	CAAGTGTT	AATATC	novel	NA	P-0007531-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1407	167	1126	0	ENST00000380152.3:c.5992_5999delinsAATATC	p.Gln1998AsnfsTer4	p.Q1998Nfs*4	ENST00000380152		1998	CAAGTGTTt/AATATCt	11/27	0.236592783125056	2	FACETS	0.628	0.575	0.684	0.314	0.287	0.342	SUBCLONAL	1	TRUE	0	0.337800255114439	2		1126	1574	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985587	2985587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064795280	NA	P-0007531-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	59	351	0	ENST00000396946.4:c.224G>A	p.Arg75Gln	p.R75Q	ENST00000396946	NM_032415.4	75	cGg/cAg	4/25	1	2	FACETS	0.475	0.407	0.548	0.475	0.407	0.548	SUBCLONAL	1	TRUE	1	0.337800255114439	2		351	736	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879048	151879060	+	frameshift_variant	Frame_Shift_Del	DEL	GGTTTTGCATAGG	GGTTTTGCATAGG	-	novel	NA	P-0007531-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	85	504	0	ENST00000262189.6:c.5885_5897del	p.Pro1962LeufsTer8	p.P1962Lfs*8	ENST00000262189	NM_170606.2	1962	cCCTATGCAAAACCt/ct	36/59	1	2	FACETS	0.629	0.555	0.708	0.629	0.555	0.708	SUBCLONAL	1	TRUE	1	0.337800255114439	2		504	800	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088681	27088682	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0007531-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	60	602	1	ENST00000324856.7:c.2296dup	p.Gln766ProfsTer51	p.Q766Pfs*51	ENST00000324856	NM_006015.4	764	tcc/tCcc	7/20	0.307845038385988	1	FACETS	0.283	0.243	0.328	0.283	0.243	0.328	SUBCLONAL	1	TRUE	0	0.337800255114439	1		603	1042	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0007533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	85	92	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.724506608961238	1	FACETS	0.875	0.796	0.955	0.875	0.796	0.955	CLONAL	1	TRUE	0	0.724506608961238	1		92	171	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426070	138426070	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	442	485	0	ENST00000289153.2:c.1461T>A	p.Asn487Lys	p.N487K	ENST00000289153	NM_006219.2	487	aaT/aaA	9/22	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.724506608961238	2		485	1176	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23625405	23625405	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1175812630	NA	P-0007533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	376	447	0	ENST00000261584.4:c.3121A>G	p.Lys1041Glu	p.K1041E	ENST00000261584	NM_024675.3	1041	Aaa/Gaa	11/13	1	2	FACETS	0.991	0.943	1	0.991	0.943	1	CLONAL	1	TRUE	1	0.724506608961238	2		447	1047	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577408	64577408	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008043-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	161	413	0	ENST00000312049.6:c.174del	p.Glu60SerfsTer59	p.E60Sfs*59	ENST00000312049	NM_130799.2	58	gtT/gt	2/10	0.360960412328673	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.360960412328673	1		413	709	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0008157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	187	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.19446204934319	4	FACETS	0.878	0.813	0.945	0.878	0.813	0.945	INDETERMINATE	2	TRUE	2	0.403475653639223	4		473	741	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0008157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	123	189	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	0.403475653639223	1	FACETS	0.938	0.852	1	0.938	0.852	1	CLONAL	1	TRUE	0	0.403475653639223	1		189	519	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523560	106523560	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	110	206	0	ENST00000359195.3:c.2712T>G	p.Asp904Glu	p.D904E	ENST00000359195	NM_002649.2	904	gaT/gaG	8/11	1	2	FACETS	0.903	0.813	0.997	0.903	0.813	0.997	CLONAL	1	TRUE	1	0.403475653639223	2		206	604	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56872929	56872929	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0008157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	110	432	0	ENST00000308159.5:c.2084T>A	p.Leu695Ter	p.L695*	ENST00000308159	NM_014669.4	695	tTg/tAg	19/22	0.403475653639223	2	FACETS	0.461	0.412	0.512	0.23	0.206	0.256	SUBCLONAL	1	TRUE	0	0.403475653639223	2		432	1184	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420093	41420093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	43	125	0	ENST00000373198.4:c.228G>A	p.Met76Ile	p.M76I	ENST00000373198	NM_133170.3	76	atG/atA	3/32	1	2	FACETS	0.517	0.433	0.61	0.517	0.433	0.61	SUBCLONAL	1	TRUE	1	0.403475653639223	2		125	412	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0008387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	69	453	4	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	1	0.954	1	1	0.984	1	CLONAL	2	FALSE	1	0.19473397546187	2		457	299	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0008387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	22	629	1	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	0.164827955701805	0	FACETS	1	0.889	1			1	CLONAL	1	FALSE	0	0.19473397546187	0		630	147	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022403	31022425	+	frameshift_variant	Frame_Shift_Del	DEL	CACCACTGCCATAGAGAGGCGGC	CACCACTGCCATAGAGAGGCGGC	-	rs766433101	NA	P-0008387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	12	321	0	ENST00000375687.4:c.1900_1922del	p.Glu635ArgfsTer15	p.E635Rfs*15	ENST00000375687	NM_015338.5	630	CACCACTGCCATAGAGAGGCGGCc/c	13/13	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	FALSE	1	0.19473397546187	2		321	90	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263998	16263998	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145947516	NA	P-0008387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	33	821	0	ENST00000375759.3:c.10367C>T	p.Pro3456Leu	p.P3456L	ENST00000375759	NM_015001.2	3456	cCg/cTg	12/15	0.147309498590493	1	FACETS	0.784	0.645	0.939	1	0.951	1	CLONAL	2	FALSE	0	0.19473397546187	1		821	195	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028085	48028085	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs115386788	NA	P-0008387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	26	633	3	ENST00000234420.5:c.2963G>A	p.Arg988His	p.R988H	ENST00000234420	NM_000179.2	988	cGc/cAc	4/10	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	FALSE	1	0.19473397546187	2		636	214	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184613	185184613	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs1337362918	NA	P-0008387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	37	849	0	ENST00000265026.3:c.1506-1G>T		p.X502_splice	ENST00000265026	NM_004721.4	502			0.19473397546187	3	FACETS	0.956	0.795	1	0.956	0.795	1	CLONAL	2	FALSE	1	0.19473397546187	3		849	218	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961056	55961056	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1312670638	NA	P-0008387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	23	610	0	ENST00000263923.4:c.2884C>T	p.Arg962Cys	p.R962C	ENST00000263923	NM_002253.2	962	Cgc/Tgc	21/30	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	FALSE	1	0.19473397546187	2		610	169	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527289	187527289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747735486	NA	P-0008387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	25	419	0	ENST00000441802.2:c.10285G>A	p.Asp3429Asn	p.D3429N	ENST00000441802	NM_005245.3	3429	Gat/Aat	17/27	NA	2	FACETS	0.792	0.631	0.974			1	INDETERMINATE	2	FALSE	NA	0.19473397546187	2		419	162	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630815	187630815	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	35	705	1	ENST00000441802.2:c.167C>T	p.Pro56Leu	p.P56L	ENST00000441802	NM_005245.3	56	cCt/cTt	2/27	NA	2	FACETS	0.755	0.623	0.901			1	INDETERMINATE	2	FALSE	NA	0.19473397546187	2		706	238	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968290	2968290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	19	723	0	ENST00000396946.4:c.1696G>A	p.Glu566Lys	p.E566K	ENST00000396946	NM_032415.4	566	Gag/Aag	13/25	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	FALSE	1	0.19473397546187	2		723	159	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935664	13935664	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	42	483	0	ENST00000405192.2:c.1192C>A	p.Leu398Ile	p.L398I	ENST00000405192	NM_001163147.1	398	Ctt/Att	12/12	0.19473397546187	5	FACETS	0.914	0.766	1	0.609	0.511	0.717	CLONAL	2	FALSE	2	0.19473397546187	5		483	305	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878884	117878884	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	51	994	0	ENST00000297338.2:c.85A>G	p.Lys29Glu	p.K29E	ENST00000297338	NM_006265.2	29	Aaa/Gaa	2/14	0.19473397546187	7	FACETS	0.823	0.7	0.958	0.412	0.35	0.479	CLONAL	2	FALSE	3	0.19473397546187	7		994	473	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126778	5126778	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	33	514	0	ENST00000381652.3:c.3386A>G	p.Asn1129Ser	p.N1129S	ENST00000381652	NM_004972.3	1129	aAc/aGc	25/25	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	1	0.19473397546187	2		514	231	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133729624	133729624	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	22	485	0	ENST00000318560.5:c.253G>T	p.Gly85Cys	p.G85C	ENST00000318560	NM_005157.4	85	Ggt/Tgt	2/11	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	FALSE	1	0.19473397546187	2		485	181	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852155	63852155	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	22	433	0	ENST00000279873.7:c.2933C>A	p.Pro978His	p.P978H	ENST00000279873	NM_032199.2	978	cCt/cAt	10/10	0.19473397546187	8	FACETS	0.973	0.759	1			1	CLONAL	2	FALSE	NA	0.19473397546187	8		433	184	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450757	70450757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752525372	NA	P-0008387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	25	478	0	ENST00000373644.4:c.5597C>T	p.Ala1866Val	p.A1866V	ENST00000373644	NM_030625.2	1866	gCa/gTa	12/12	1	2	FACETS	0.813	0.647	0.999	1	0.939	1	CLONAL	2	FALSE	1	0.19473397546187	2		478	158	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252002	133252002	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	22	658	0	ENST00000320574.5:c.1208T>C	p.Ile403Thr	p.I403T	ENST00000320574	NM_006231.2	403	aTc/aCc	12/49	0.164827955701805	0	FACETS	1	0.903	1			1	CLONAL	1	FALSE	0	0.19473397546187	0		658	139	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133772	41133772	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745385825	NA	P-0008387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	31	1119	1	ENST00000379561.5:c.1856G>A	p.Arg619Gln	p.R619Q	ENST00000379561	NM_002015.3	619	cGg/cAg	2/3	0.187663356716571	0	FACETS	0.704	0.575	0.847			1	SUBCLONAL	2	FALSE	0	0.19473397546187	0		1120	182	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988838	41988838	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	33	1241	1	ENST00000219905.7:c.1630C>A	p.Pro544Thr	p.P544T	ENST00000219905	NM_001164273.1	544	Ccc/Acc	3/24	0.19473397546187	0	FACETS	0.714	0.587	0.855			1	SUBCLONAL	2	FALSE	0	0.19473397546187	0		1242	191	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346252	89346252	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	23	619	1	ENST00000301030.4:c.6698G>T	p.Gly2233Val	p.G2233V	ENST00000301030	NM_001256183.1	2233	gGg/gTg	9/13	0.19473397546187	0	FACETS	0.699	0.552	0.865			1	SUBCLONAL	2	FALSE	0	0.19473397546187	0		620	136	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612253	1612253	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	16	802	0	ENST00000344749.5:c.1766T>C	p.Leu589Pro	p.L589P	ENST00000344749	NM_001136139.2	589	cTg/cCg	18/19	0.164827955701805	0	FACETS	0.9	0.67	1			1	CLONAL	1	FALSE	0	0.19473397546187	0		802	147	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061226	38061237	+	inframe_deletion	In_Frame_Del	DEL	CGAACATGTTGC	CGAACATGTTGC	-	novel	NA	P-0008387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	74	468	1	ENST00000250448.2:c.752_763del	p.Gly251_Phe254del	p.G251_F254del	ENST00000250448	NM_004496.3	251	gGCAACATGTTCGag/gag	2/2	0.19473397546187	3	FACETS	1	0.947	1	1	0.986	1	CLONAL	4	FALSE	1	0.19473397546187	3		469	190	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0008522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	26	425	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.460291220658594	2	FACETS	0.246	0.194	0.305	0.123	0.097	0.153	SUBCLONAL	1	TRUE	0	0.46723278739493	2		426	453	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189847	11189847	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	49	441	0	ENST00000361445.4:c.5662T>A	p.Phe1888Ile	p.F1888I	ENST00000361445	NM_004958.3	1888	Ttc/Atc	40/58	1	2	FACETS	0.273	0.23	0.32	0.273	0.23	0.32	SUBCLONAL	1	TRUE	1	0.46723278739493	2		441	768	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441255	52441255	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	66	472	0	ENST00000460680.1:c.515G>A	p.Ser172Asn	p.S172N	ENST00000460680	NM_004656.3	172	aGc/aAc	7/17	0.46723278739493	1	FACETS	0.324	0.28	0.37	0.324	0.28	0.37	SUBCLONAL	1	TRUE	0	0.46723278739493	1		472	669	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056152	27056152	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	131	389	1	ENST00000324856.7:c.1148C>T	p.Pro383Leu	p.P383L	ENST00000324856	NM_006015.4	383	cCa/cTa	2/20	1	2	FACETS	0.878	0.798	0.96	0.878	0.798	0.96	CLONAL	1	TRUE	1	0.46723278739493	2		390	639	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727829	41727829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs545028002	NA	P-0008522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1422	92	677	1	ENST00000301178.4:c.454G>A	p.Ala152Thr	p.A152T	ENST00000301178	NM_021913.4	152	Gcc/Acc	4/20	1	2	FACETS	0.26	0.23	0.293	0.26	0.23	0.293	SUBCLONAL	1	TRUE	1	0.46723278739493	2		678	1514	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40761100	40761101	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATGACTGTGGTCCACTGCAGGCAGCGT	novel	NA	P-0008522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	57	448	0	ENST00000392038.2:c.225_251dup	p.Arg76_Ile84dup	p.R76_I84dup	ENST00000392038	NM_001626.4	76	atc/atACGCTGCCTGCAGTGGACCACAGTCATc	4/14	1	2	FACETS	0.235	0.201	0.273	0.235	0.201	0.273	SUBCLONAL	1	TRUE	1	0.46723278739493	2		448	1037	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246144	46246144	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	85	376	0	ENST00000334344.6:c.4240del	p.Arg1414GlufsTer8	p.R1414Efs*8	ENST00000334344	NM_152641.2	1413	gAa/ga	15/21	1	2	FACETS	0.933	0.83	1	0.933	0.83	1	CLONAL	1	TRUE	1	0.46723278739493	2		376	390	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183717	10183721	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGC	GCTGC	-	novel	NA	P-0008522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	161	443	0	ENST00000256474.2:c.189_193del	p.Arg64GlyfsTer66	p.R64Gfs*66	ENST00000256474	NM_000551.3	62	gtGCTGCgc/gtgc	1/3	0.46723278739493	1	FACETS	0.906	0.835	0.979	0.906	0.835	0.979	CLONAL	1	TRUE	0	0.46723278739493	1		443	583	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057222	30057222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	76	473	0	ENST00000338641.4:c.704G>A	p.Gly235Glu	p.G235E	ENST00000338641	NM_000268.3	235	gGa/gAa	8/16	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		473	752	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439900	52439901	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	TCAGC	novel	NA	P-0008755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	42	311	0	ENST00000460680.1:c.807_811dup	p.Ile271SerfsTer2	p.I271Sfs*2	ENST00000460680	NM_004656.3	271	att/aGCTGAtt	10/17	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		311	738	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0008818-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	49	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.818	0.69	0.96	0.818	0.69	0.96	CLONAL	1	TRUE	1	0.12	2		473	998	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0008818-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	53	470	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	1	2	FACETS	0.822	0.698	0.958	0.822	0.698	0.958	CLONAL	1	TRUE	1	0.12	2		470	1075	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971107	21971107	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008818-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	28	275	0	ENST00000304494.5:c.251A>T	p.Asp84Val	p.D84V	ENST00000304494	NM_000077.4	84	gAc/gTc	2/3	1	2	FACETS	0.876	0.698	1	0.876	0.698	1	CLONAL	1	TRUE	1	0.12	2		275	533	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0008818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	118	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.247002630625899	1	FACETS	0.936	0.844	1	0.936	0.844	1	CLONAL	1	TRUE	0	0.267901730403836	1		473	815	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0008818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	227	470	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.247002630625899	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.267901730403836	1		470	1187	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971107	21971107	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	94	275	0	ENST00000304494.5:c.251A>T	p.Asp84Val	p.D84V	ENST00000304494	NM_000077.4	84	gAc/gTc	2/3	0.267901730403836	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	0	0.267901730403836	1		275	595	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162308	47162308	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	46	540	0	ENST00000409792.3:c.3818A>G	p.Gln1273Arg	p.Q1273R	ENST00000409792	NM_014159.6	1273	cAa/cGa	3/21	0.247002630625899	1	FACETS	0.555	0.467	0.652	0.555	0.467	0.652	SUBCLONAL	1	TRUE	0	0.267901730403836	1		540	536	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829039	128829040	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs570242755	NA	P-0008844-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	20	18	0	ENST00000249373.3:c.67_69dup	p.Leu23dup	p.L23dup	ENST00000249373	NM_005631.4	23	ggg/ggGCTg	1/12	1	2	FACETS	0.999	0.788	1	1	0.954	1	CLONAL	3	TRUE	1	0.196292671924182	2		18	68	SUCCESS
H3C13	653604	MSKCC	GRCh37	1	149784837	149784837	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008844-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	100	450	0	ENST00000331491.1:c.400G>A	p.Glu134Lys	p.E134K	ENST00000331491	NM_001123375.2	134	Gag/Aag	1/1	1	2	FACETS	0.92	0.82	1	0.92	0.82	1	CLONAL	1	TRUE	1	0.196292671924182	2		450	1107	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66781586	66781586	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008844-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	140	449	0	ENST00000307102.5:c.994C>G	p.Leu332Val	p.L332V	ENST00000307102	NM_002755.3	332	Ctg/Gtg	9/11	0.198375441890231	3	FACETS	1	0.977	1	0.62	0.563	0.68	CLONAL	1	TRUE	1	0.196292671924182	3		449	1263	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198265	185198276	+	inframe_deletion	In_Frame_Del	DEL	TGAAGACTCAGA	TGAAGACTCAGA	-	novel	NA	P-0008844-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	110	334	0	ENST00000265026.3:c.2749_2760del	p.Lys917_Met920del	p.K917_M920del	ENST00000265026	NM_004721.4	916	gTGAAGACTCAGAtg/gtg	13/14	0.198375441890231	3	FACETS	1	0.977	1	0.658	0.59	0.73	CLONAL	1	TRUE	1	0.196292671924182	3		334	935	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0008844-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	106	403	0	ENST00000311936.3:c.180_181delinsAA	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggAAaa	3/5	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.196292671924182	2		403	1055	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0008879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	93	580	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.232494438470764	2		580	629	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	695	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	1	0.997	1			1	INDETERMINATE	1	TRUE	NA	0.877356403425832	2		473	1211	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0009045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	568	542	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.865461654902125	1	FACETS	0.982	0.958	1	0.982	0.958	1	CLONAL	1	TRUE	0	0.877356403425832	1		543	740	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0009090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	25	286	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	1	2	FACETS	0.675	0.53	0.844	0.675	0.53	0.844	SUBCLONAL	1	TRUE	1	0.11	2		286	673	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0009107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	25	463	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.3	2	FACETS	1	0.867	1			1	CLONAL	1	TRUE	NA	0.22	2		463	201	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	8	406	0	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	1	2	FACETS	0.505	0.326	0.736	0.505	0.326	0.736	SUBCLONAL	1	TRUE	1	0.22	2		406	144	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0009107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	23	388	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.179507655524505	3	FACETS	1	0.894	1	0.627	0.492	0.781	CLONAL	1	TRUE	1	0.22	3		388	185	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524525	187524525	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	19	524	1	ENST00000441802.2:c.11155G>T	p.Val3719Leu	p.V3719L	ENST00000441802	NM_005245.3	3719	Gtg/Ttg	19/27	0.179507655524505	1	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	0	0.22	1		525	125	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524784	187524784	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	16	473	0	ENST00000441802.2:c.10896A>T	p.Arg3632Ser	p.R3632S	ENST00000441802	NM_005245.3	3632	agA/agT	19/27	0.179507655524505	1	FACETS	0.731	0.543	0.954	0.731	0.543	0.954	CLONAL	1	TRUE	0	0.22	1		473	177	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467829	50467829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	19	250	0	ENST00000331340.3:c.1064C>T	p.Ala355Val	p.A355V	ENST00000331340	NM_006060.4	355	gCg/gTg	8/8	0.179507655524505	3	FACETS	1	0.893	1	0.67	0.513	0.851	CLONAL	1	TRUE	1	0.22	3		250	143	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591880	48591880	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	23	515	0	ENST00000342988.3:c.1044del	p.Thr349LeufsTer35	p.T349Lfs*35	ENST00000342988	NM_005359.5	348	gTt/gt	9/12	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.22	2		515	155	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287893	33287893	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	90	547	0	ENST00000374542.5:c.1360G>T	p.Glu454Ter	p.E454*	ENST00000374542	NM_001141970.1	454	Gaa/Taa	5/8	0.548288549527203	4	FACETS	0.934	0.865	1	1	0.982	1	CLONAL	4	TRUE	1	0.548288549527203	4		547	136	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850861	128850861	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs775441067	NA	P-0009153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	30	504	1	ENST00000249373.3:c.1708G>T	p.Ala570Ser	p.A570S	ENST00000249373	NM_005631.4	570	Gcc/Tcc	10/12	0.336791756451038	5	FACETS	1	0.863	1	0.7	0.579	0.828	CLONAL	2	TRUE	2	0.548288549527203	5		505	95	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574692	64574692	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0009153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	67	401	0	ENST00000312049.6:c.784-1G>T		p.X262_splice	ENST00000312049	NM_130799.2	262			0.548288549527203	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.548288549527203	2		401	104	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061592	38061592	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	15	129	1	ENST00000250448.2:c.397G>A	p.Ala133Thr	p.A133T	ENST00000250448	NM_004496.3	133	Gcc/Acc	2/2	0.420367078861866	5	FACETS	1	0.877	1	0.449	0.335	0.579	CLONAL	1	TRUE	2	0.548288549527203	5		130	74	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595852	52595853	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0009257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1584	263	477	0	ENST00000394830.3:c.4062_4063del	p.Phe1354LeufsTer15	p.F1354Lfs*15	ENST00000394830	NM_018313.4	1354	ttCGgg/ttgg	26/30	0.252366060185555	1	FACETS	0.915	0.854	0.979	0.915	0.854	0.979	CLONAL	1	TRUE	0	0.26924381421057	1		477	1847	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155399	47155399	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	280	497	0	ENST00000409792.3:c.4682G>C	p.Gly1561Ala	p.G1561A	ENST00000409792	NM_014159.6	1561	gGc/gCc	5/21	0.407748274796942	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.407748274796942	1		497	889	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239642	53239642	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	386	314	0	ENST00000375401.3:c.1700T>G	p.Leu567Arg	p.L567R	ENST00000375401	NM_004187.3	567	cTt/cGt	12/26	1	1	FACETS	0.964	0.922	1	1	0.997	1	CLONAL	2	TRUE	0	0.407748274796942	1		314	782	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702609	52702609	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	141	405	0	ENST00000394830.3:c.289del	p.Ile97SerfsTer5	p.I97Sfs*5	ENST00000394830	NM_018313.4	97	Atc/tc	4/30	0.407748274796942	1	FACETS	0.968	0.886	1	0.968	0.886	1	CLONAL	1	TRUE	0	0.407748274796942	1		405	569	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101100	27101100	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1257406381	NA	P-0009374-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	296	516	1	ENST00000324856.7:c.4382G>A	p.Arg1461Gln	p.R1461Q	ENST00000324856	NM_006015.4	1461	cGa/cAa	18/20	0.567731622728301	2	FACETS	1	0.956	1	0.508	0.479	0.538	CLONAL	1	TRUE	0	0.578798470625981	2		517	1006	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248360	59248360	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009374-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	83	195	0	ENST00000371222.2:c.383C>A	p.Pro128His	p.P128H	ENST00000371222	NM_002228.3	128	cCc/cAc	1/1	0.567731622728301	2	FACETS	0.902	0.804	1	0.451	0.402	0.503	CLONAL	1	TRUE	0	0.578798470625981	2		195	318	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246130	41246130	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs80357057	NA	P-0009374-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	214	599	0	ENST00000357654.3:c.1418A>G	p.Asn473Ser	p.N473S	ENST00000357654	NM_007294.3	473	aAc/aGc	10/23	0.417214511770748	3	FACETS	0.858	0.797	0.922			1	CLONAL	1	TRUE	NA	0.578798470625981	3		599	1111	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371708	225371708	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	84	403	0	ENST00000264414.4:c.896T>G	p.Met299Arg	p.M299R	ENST00000264414	NM_003590.4	299	aTg/aGg	7/16	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.23	2		403	721	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216476	108216477	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587782558	NA	P-0009420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	30	379	0	ENST00000278616.4:c.8432dup	p.Ser2812ValfsTer3	p.S2812Vfs*3	ENST00000278616	NM_000051.3	2809	caa/cAaa	58/63	1	2	FACETS	0.445	0.358	0.545	0.445	0.358	0.545	SUBCLONAL	1	TRUE	1	0.23	2		379	586	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190742011	190742011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377603311	NA	P-0009420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	51	396	0	ENST00000441310.2:c.2648G>A	p.Arg883His	p.R883H	ENST00000441310	NM_000534.4	883	cGt/cAt	13/13	1	2	FACETS	0.706	0.599	0.824	0.706	0.599	0.824	SUBCLONAL	1	TRUE	1	0.23	2		396	628	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420269	88420269	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	63	357	0	ENST00000360948.2:c.2417G>T	p.Cys806Phe	p.C806F	ENST00000360948	NM_001012338.2	806	tGc/tTc	19/19	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.23	2		357	529	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	29	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	0.907	0.726	1			1	INDETERMINATE	1	TRUE	NA	0.12	2		473	533	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030367	49030368	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0009911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	31	332	0	ENST00000267163.4:c.1848dup	p.Gly617ArgfsTer36	p.G617Rfs*36	ENST00000267163	NM_000321.2	614	-/A	19/27	1	2	FACETS	1	0.819	1	1	0.819	1	CLONAL	1	TRUE	1	0.12	2		332	509	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726677	41726677	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	54	484	0	ENST00000301178.4:c.222G>C	p.Gln74His	p.Q74H	ENST00000301178	NM_021913.4	74	caG/caC	2/20	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.12	2		484	726	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578493	7578500	+	frameshift_variant	Frame_Shift_Del	DEL	CACAGCTG	CACAGCTG	-	novel	NA	P-0009911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	48	427	0	ENST00000269305.4:c.430_437del	p.Gln144GlyfsTer2	p.Q144Gfs*2	ENST00000269305	NM_001126112.2	144	CAGCTGTGg/g	5/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.12	2		427	607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1555525585	NA	P-0009979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	177	653	0	ENST00000269305.4:c.673-2A>G		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.667744013784886	1	FACETS	0.883	0.826	0.941	0.883	0.826	0.941	CLONAL	1	TRUE	0	0.68817734417363	1		653	382	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0010128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	769	744	2	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	0.52343661835475	3	FACETS	0.979	0.953	1	0.979	0.953	1	CLONAL	3	TRUE	0	0.52343661835475	3		746	1262	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125509	47125509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	109	755	1	ENST00000409792.3:c.5761G>T	p.Glu1921Ter	p.E1921*	ENST00000409792	NM_014159.6	1921	Gaa/Taa	12/21	0.522766484245891	2	FACETS	0.823	0.742	0.908	0.412	0.371	0.454	CLONAL	1	TRUE	0	0.52343661835475	2		756	506	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164304	47164304	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	90	435	0	ENST00000409792.3:c.1822G>T	p.Glu608Ter	p.E608*	ENST00000409792	NM_014159.6	608	Gaa/Taa	3/21	0.522766484245891	2	FACETS	1	0.94	1	0.536	0.48	0.594	CLONAL	1	TRUE	0	0.52343661835475	2		435	321	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509951	187509951	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	336	484	2	ENST00000441802.2:c.13562C>A	p.Pro4521Gln	p.P4521Q	ENST00000441802	NM_005245.3	4521	cCa/cAa	27/27	0.45000640012245	4	FACETS	0.878	0.831	0.926	0.878	0.831	0.926	CLONAL	2	TRUE	2	0.52343661835475	4		486	1114	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982132	93982132	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs749130416	NA	P-0010128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	136	586	3	ENST00000369303.4:c.1333C>A	p.Gln445Lys	p.Q445K	ENST00000369303	NM_004440.3	445	Caa/Aaa	6/17	0.52343661835475	3	FACETS	1	0.925	1	0.339	0.309	0.37	CLONAL	1	TRUE	0	0.52343661835475	3		589	645	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117730772	117730772	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	291	899	0	ENST00000368508.3:c.262G>T	p.Glu88Ter	p.E88*	ENST00000368508	NM_002944.2	88	Gaa/Taa	4/43	0.52343661835475	3	FACETS	0.952	0.9	1	0.635	0.6	0.669	CLONAL	2	TRUE	0	0.52343661835475	3		899	737	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811685	102811685	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	620	910	0	ENST00000307046.8:c.499G>T	p.Ala167Ser	p.A167S	ENST00000307046	NM_001111285.1	167	Gca/Tca	4/4	0.403793193043082	5	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	2	0.52343661835475	5		910	1366	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035203	42035203	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	411	1120	0	ENST00000219905.7:c.5045C>A	p.Ser1682Tyr	p.S1682Y	ENST00000219905	NM_001164273.1	1682	tCt/tAt	15/24	0.52343661835475	3	FACETS	0.903	0.861	0.945	0.903	0.861	0.945	CLONAL	2	TRUE	1	0.52343661835475	3		1120	1097	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135293	2135293	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	250	652	0	ENST00000219476.3:c.4632G>T	p.Lys1544Asn	p.K1544N	ENST00000219476	NM_000548.3	1544	aaG/aaT	36/42	0.52343661835475	3	FACETS	0.917	0.856	0.98	0.306	0.285	0.327	CLONAL	1	TRUE	0	0.52343661835475	3		652	1314	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858746	9858746	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	82	444	0	ENST00000330684.3:c.2655C>A	p.Phe885Leu	p.F885L	ENST00000330684	NM_001134407.1	885	ttC/ttA	13/13	0.52343661835475	3	FACETS	0.905	0.801	1	0.302	0.267	0.338	CLONAL	1	TRUE	0	0.52343661835475	3		444	437	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696704	47696704	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	112	518	0	ENST00000347630.2:c.244G>T	p.Asp82Tyr	p.D82Y	ENST00000347630	NM_001007230.1	82	Gat/Tat	5/11	0.52343661835475	2	FACETS	0.962	0.871	1	0.481	0.435	0.529	CLONAL	1	TRUE	0	0.52343661835475	2		518	445	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953891	17953891	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	620	665	0	ENST00000458235.1:c.511G>T	p.Ala171Ser	p.A171S	ENST00000458235	NM_000215.3	171	Gcc/Tcc	5/24	0.45000640012245	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.52343661835475	4		665	1726	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15822268	15822268	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs767518633	NA	P-0010128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	132	759	0	ENST00000307771.7:c.347G>T	p.Arg116Met	p.R116M	ENST00000307771	NM_005089.3	116	aGg/aTg	5/11	0.52343661835475	3	FACETS	0.819	0.744	0.898	0.409	0.372	0.449	CLONAL	1	TRUE	1	0.52343661835475	3		759	777	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814187	76814187	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	241	886	0	ENST00000373344.5:c.6457C>A	p.Arg2153Ser	p.R2153S	ENST00000373344	NM_000489.3	2153	Cgc/Agc	29/35	0.52343661835475	3	FACETS	0.81	0.76	0.861	0.81	0.76	0.861	CLONAL	2	TRUE	1	0.52343661835475	3		886	717	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504086	123504086	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	91	511	0	ENST00000371139.4:c.262C>A	p.Gln88Lys	p.Q88K	ENST00000371139	NM_001114937.2	88	Cag/Aag	3/4	0.449827831613039	4	FACETS	0.905	0.805	1			1	CLONAL	1	TRUE	NA	0.52343661835475	4		511	585	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118382665	118382665	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0010128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	145	486	0	ENST00000534358.1:c.11072-1G>T		p.X3691_splice	ENST00000534358	NM_005933.3	3691			0.52343661835475	2	FACETS	0.829	0.768	0.891	0.829	0.768	0.891	CLONAL	2	TRUE	0	0.52343661835475	2		486	334	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63700065	63700065	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	15	275	0	ENST00000279873.7:c.400T>A	p.Leu134Met	p.L134M	ENST00000279873	NM_032199.2	134	Ttg/Atg	3/10	0.45000640012245	4	FACETS	0.326	0.238	0.432	0.163	0.119	0.216	SUBCLONAL	1	TRUE	2	0.52343661835475	4		275	268	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945085	31945085	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1537	298	793	2	ENST00000340398.3:c.16C>A	p.Gln6Lys	p.Q6K	ENST00000340398	NM_001013699.2	6	Cag/Aag	1/1	0.403793193043082	5	FACETS	1	0.981	1	0.369	0.346	0.393	CLONAL	1	TRUE	2	0.52343661835475	5		795	1835	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245166	46245166	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs776757244	NA	P-0010128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	60	487	0	ENST00000334344.6:c.3260C>A	p.Pro1087His	p.P1087H	ENST00000334344	NM_152641.2	1087	cCt/cAt	15/21	0.403793193043082	5	FACETS	0.538	0.463	0.621	0.179	0.154	0.207	SUBCLONAL	1	TRUE	2	0.52343661835475	5		487	760	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0010128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	1082	744	2	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	0.811264847691128	3	FACETS	0.977	0.965	0.989	0.977	0.965	0.989	CLONAL	3	TRUE	0	0.878692795175088	3		746	1209	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125509	47125509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	173	755	1	ENST00000409792.3:c.5761G>T	p.Glu1921Ter	p.E1921*	ENST00000409792	NM_014159.6	1921	Gaa/Taa	12/21	0.858138071441404	2	FACETS	0.924	0.861	0.989	0.462	0.43	0.495	CLONAL	1	TRUE	0	0.878692795175088	2		756	426	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164304	47164304	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	174	435	0	ENST00000409792.3:c.1822G>T	p.Glu608Ter	p.E608*	ENST00000409792	NM_014159.6	608	Gaa/Taa	3/21	0.858138071441404	2	FACETS	0.852	0.792	0.913	0.426	0.396	0.457	CLONAL	1	TRUE	0	0.878692795175088	2		435	465	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509951	187509951	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	177	484	2	ENST00000441802.2:c.13562C>A	p.Pro4521Gln	p.P4521Q	ENST00000441802	NM_005245.3	4521	cCa/cAa	27/27	0.878692795175088	3	FACETS	1	0.957	1	0.522	0.484	0.562	CLONAL	1	TRUE	1	0.878692795175088	3		486	555	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982132	93982132	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs749130416	NA	P-0010128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	200	586	3	ENST00000369303.4:c.1333C>A	p.Gln445Lys	p.Q445K	ENST00000369303	NM_004440.3	445	Caa/Aaa	6/17	0.859162150268736	3	FACETS	1	0.945	1	0.339	0.316	0.363	CLONAL	1	TRUE	0	0.878692795175088	3		589	644	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117730772	117730772	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	578	899	0	ENST00000368508.3:c.262G>T	p.Glu88Ter	p.E88*	ENST00000368508	NM_002944.2	88	Gaa/Taa	4/43	0.859162150268736	3	FACETS	0.968	0.937	0.999	0.645	0.625	0.666	CLONAL	2	TRUE	0	0.878692795175088	3		899	978	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811685	102811685	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	850	910	0	ENST00000307046.8:c.499G>T	p.Ala167Ser	p.A167S	ENST00000307046	NM_001111285.1	167	Gca/Tca	4/4	0.878692795175088	4	FACETS	0.942	0.919	0.965	0.942	0.919	0.965	CLONAL	3	TRUE	1	0.878692795175088	4		910	1286	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035203	42035203	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	645	1120	0	ENST00000219905.7:c.5045C>A	p.Ser1682Tyr	p.S1682Y	ENST00000219905	NM_001164273.1	1682	tCt/tAt	15/24	0.85087013436664	3	FACETS	0.923	0.894	0.951	0.923	0.894	0.951	CLONAL	2	TRUE	1	0.878692795175088	3		1120	1145	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135293	2135293	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	278	652	0	ENST00000219476.3:c.4632G>T	p.Lys1544Asn	p.K1544N	ENST00000219476	NM_000548.3	1544	aaG/aaT	36/42	0.865979429320631	3	FACETS	0.977	0.92	1	0.326	0.306	0.346	CLONAL	1	TRUE	0	0.878692795175088	3		652	932	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858746	9858746	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	124	444	0	ENST00000330684.3:c.2655C>A	p.Phe885Leu	p.F885L	ENST00000330684	NM_001134407.1	885	ttC/ttA	13/13	0.297028531292086	5	FACETS	0.808	0.737	0.88			1	INDETERMINATE	2	TRUE	NA	0.878692795175088	5		444	405	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696704	47696704	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	255	518	0	ENST00000347630.2:c.244G>T	p.Asp82Tyr	p.D82Y	ENST00000347630	NM_001007230.1	82	Gat/Tat	5/11	0.852674361162856	2	FACETS	0.966	0.912	1	0.483	0.456	0.51	CLONAL	1	TRUE	0	0.878692795175088	2		518	601	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953891	17953891	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	620	665	0	ENST00000458235.1:c.511G>T	p.Ala171Ser	p.A171S	ENST00000458235	NM_000215.3	171	Gcc/Tcc	5/24	0.657472198274584	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	2	0.878692795175088	4		665	1305	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15822268	15822268	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs767518633	NA	P-0010128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	251	759	0	ENST00000307771.7:c.347G>T	p.Arg116Met	p.R116M	ENST00000307771	NM_005089.3	116	aGg/aTg	5/11	0.261826434415773	5	FACETS	0.759	0.712	0.808			1	INDETERMINATE	2	TRUE	NA	0.878692795175088	5		759	872	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814187	76814187	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	552	886	0	ENST00000373344.5:c.6457C>A	p.Arg2153Ser	p.R2153S	ENST00000373344	NM_000489.3	2153	Cgc/Agc	29/35	0.85087013436664	3	FACETS	0.966	0.934	0.997	0.966	0.934	0.997	CLONAL	2	TRUE	1	0.878692795175088	3		886	936	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504086	123504086	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	285	511	0	ENST00000371139.4:c.262C>A	p.Gln88Lys	p.Q88K	ENST00000371139	NM_001114937.2	88	Cag/Aag	3/4	0.803013053643436	4	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.878692795175088	4		511	1122	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362010	118362010	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	152	289	0	ENST00000534358.1:c.4796G>T	p.Cys1599Phe	p.C1599F	ENST00000534358	NM_005933.3	1599	tGt/tTt	14/36	0.878692795175088	3	FACETS	0.912	0.839	0.988	0.304	0.279	0.33	CLONAL	1	TRUE	0	0.878692795175088	3		289	546	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118382665	118382665	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0010128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	546	486	0	ENST00000534358.1:c.11072-1G>T		p.X3691_splice	ENST00000534358	NM_005933.3	3691			0.878692795175088	3	FACETS	0.971	0.954	0.987	0.971	0.954	0.987	CLONAL	3	TRUE	0	0.878692795175088	3		486	614	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910629	32910629	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	45	527	0	ENST00000380152.3:c.2137C>A	p.Gln713Lys	p.Q713K	ENST00000380152		713	Cag/Aag	11/27	0.867932933406878	1	FACETS	0.165	0.139	0.194	0.165	0.139	0.194	SUBCLONAL	1	TRUE	0	0.878692795175088	1		527	348	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965444	18965444	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	156	317	0	ENST00000262803.5:c.1191C>A	p.Ser397Arg	p.S397R	ENST00000262803	NM_002911.3	397	agC/agA	9/24	0.657472198274584	4	FACETS	0.918	0.842	0.996	0.459	0.421	0.498	CLONAL	1	TRUE	2	0.878692795175088	4		317	727	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228610	36228610	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	299	619	1	ENST00000222270.7:c.7624G>T	p.Glu2542Ter	p.E2542*	ENST00000222270	NM_014727.1	2542	Gag/Tag	34/37	0.869722937796371	3	FACETS	0.921	0.868	0.975	0.46	0.434	0.488	CLONAL	1	TRUE	1	0.878692795175088	3		620	1064	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961018	79961018	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	245	529	0	ENST00000265081.6:c.415G>T	p.Glu139Ter	p.E139*	ENST00000265081	NM_002439.4	139	Gaa/Taa	3/24	0.878692795175088	3	FACETS	0.945	0.886	1	0.473	0.443	0.504	CLONAL	1	TRUE	1	0.878692795175088	3		529	849	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553065	106553065	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	305	549	4	ENST00000369096.4:c.1030G>T	p.Asp344Tyr	p.D344Y	ENST00000369096	NM_001198.3	344	Gac/Tac	5/7	0.859162150268736	3	FACETS	1	0.959	1	0.34	0.321	0.36	CLONAL	1	TRUE	0	0.878692795175088	3		553	980	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157529008	157529008	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	226	249	0	ENST00000346085.5:c.6733C>A	p.Gln2245Lys	p.Q2245K	ENST00000346085	NM_020732.3	2245	Cag/Aag	20/20	0.836545568713092	4	FACETS	0.864	0.812	0.917	0.432	0.406	0.459	CLONAL	2	TRUE	0	0.878692795175088	4		249	559	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342822	87342822	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	229	478	1	ENST00000277120.3:c.1107G>T	p.Lys369Asn	p.K369N	ENST00000277120		369	aaG/aaT	9/19	0.820536839170186	4	FACETS	1	0.933	1	0.5	0.466	0.535	CLONAL	1	TRUE	2	0.878692795175088	4		479	979	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0010196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	159	366	2	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.393224938324865	2		368	710	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67646013	67646014	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs1470210640	NA	P-0010196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	64	194	2	ENST00000264010.4:c.950_951del	p.Thr317ArgfsTer91	p.T317Rfs*91	ENST00000264010	NM_006565.3	314	aAC/a	4/12	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.393224938324865	2		196	284	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	132	285	0	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	0.393224938324865	2		285	569	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0010196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	250	377	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.393224938324865	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.393224938324865	2		377	531	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0010196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	101	366	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.996	0.893	1	0.996	0.893	1	CLONAL	1	TRUE	1	0.393224938324865	2		366	516	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	125	407	2	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.878	0.796	0.965	0.878	0.796	0.965	CLONAL	1	TRUE	1	0.393224938324865	2		409	724	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0010196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1317	27	679	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.102	0.08	0.127	0.102	0.08	0.127	SUBCLONAL	1	TRUE	1	0.393224938324865	2		679	1344	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556463	29556463	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1567849208	NA	P-0010196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	67	235	0	ENST00000356175.3:c.2835del	p.Phe945LeufsTer9	p.F945Lfs*9	ENST00000356175	NM_000267.3	944	Ttt/tt	21/57	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.393224938324865	2		235	317	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910372	29910372	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs41548119	NA	P-0010196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	142	480	2	ENST00000376809.5:c.46del	p.Ala16ProfsTer4	p.A16Pfs*4	ENST00000376809	NM_002116.7	14	tcG/tc	1/8	1	2	FACETS	0.871	0.794	0.952	0.871	0.794	0.952	CLONAL	1	TRUE	1	0.393224938324865	2		482	829	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347484	91347484	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	203	551	4	ENST00000355112.3:c.3651del	p.Lys1217AsnfsTer62	p.K1217Nfs*62	ENST00000355112	NM_000057.2	1216	Aaa/aa	19/22	1	2	FACETS	0.97	0.899	1	0.97	0.899	1	CLONAL	1	TRUE	1	0.393224938324865	2		555	1064	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508791	106508791	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	141	342	1	ENST00000359195.3:c.785C>T	p.Pro262Leu	p.P262L	ENST00000359195	NM_002649.2	262	cCc/cTc	2/11	1	2	FACETS	0.931	0.849	1	0.931	0.849	1	CLONAL	1	TRUE	1	0.393224938324865	2		343	770	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117774	70117774	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	276	592	0	ENST00000245479.2:c.242T>C	p.Leu81Pro	p.L81P	ENST00000245479	NM_000346.3	81	cTc/cCc	1/3	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.393224938324865	2		592	1101	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166329	118166329	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	135	376	0	ENST00000369448.3:c.839A>G	p.Asp280Gly	p.D280G	ENST00000369448	NM_017709.3	280	gAc/gGc	2/2	1	2	FACETS	0.992	0.904	1	0.992	0.904	1	CLONAL	1	TRUE	1	0.393224938324865	2		376	692	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506368	120506368	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	106	355	0	ENST00000256646.2:c.1744G>T	p.Gly582Cys	p.G582C	ENST00000256646	NM_024408.3	582	Ggt/Tgt	11/34	1	2	FACETS	0.875	0.786	0.969	0.875	0.786	0.969	CLONAL	1	TRUE	1	0.393224938324865	2		355	616	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198272735	198272735	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	177	545	0	ENST00000335508.6:c.1226C>A	p.Pro409Gln	p.P409Q	ENST00000335508	NM_012433.2	409	cCa/cAa	9/25	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.393224938324865	2		545	879	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119642220	119642220	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	97	348	0	ENST00000316626.5:c.477G>T	p.Lys159Asn	p.K159N	ENST00000316626		159	aaG/aaT	4/12	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.393224938324865	2		348	474	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160740	56160740	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	120	404	0	ENST00000399503.3:c.1014C>A	p.Tyr338Ter	p.Y338*	ENST00000399503	NM_005921.1	338	taC/taA	4/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.393224938324865	2		404	549	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127920621	127920621	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	341	1037	0	ENST00000373547.4:c.278T>C	p.Phe93Ser	p.F93S	ENST00000373547	NM_002721.4	93	tTc/tCc	4/7	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.393224938324865	2		1037	1501	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139562736	139562736	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0010196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	285	624	0	ENST00000308874.7:c.2T>C	p.Met1?	p.M1?	ENST00000308874		1	aTg/aCg	3/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.393224938324865	2		624	1110	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852217	63852217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	150	316	0	ENST00000279873.7:c.2995C>T	p.Arg999Trp	p.R999W	ENST00000279873	NM_032199.2	999	Cgg/Tgg	10/10	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.393224938324865	2		316	709	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202782	133202782	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1330402168	NA	P-0010196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	158	393	0	ENST00000320574.5:c.6452A>G	p.Tyr2151Cys	p.Y2151C	ENST00000320574	NM_006231.2	2151	tAc/tGc	46/49	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.393224938324865	2		393	804	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987000	36987000	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	134	377	0	ENST00000354822.5:c.689T>C	p.Leu230Pro	p.L230P	ENST00000354822	NM_001079668.2	230	cTg/cCg	3/3	1	2	FACETS	0.978	0.89	1	0.978	0.89	1	CLONAL	1	TRUE	1	0.393224938324865	2		377	697	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90633798	90633798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	219	418	0	ENST00000330062.3:c.286G>A	p.Val96Ile	p.V96I	ENST00000330062	NM_002168.2	96	Gtc/Atc	3/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.393224938324865	2		418	925	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992354	72992354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770703902	NA	P-0010196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1715	453	1083	3	ENST00000268489.5:c.1691C>T	p.Ala564Val	p.A564V	ENST00000268489	NM_006885.3	564	gCg/gTg	2/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.393224938324865	2		1086	2168	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665110	29665110	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658541	NA	P-0010196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	69	305	0	ENST00000356175.3:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000356175	NM_000267.3	2237	Cga/Tga	44/57	1	2	FACETS	0.938	0.822	1	0.938	0.822	1	CLONAL	1	TRUE	1	0.393224938324865	2		305	374	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864589	37864589	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1235532423	NA	P-0010196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	40	300	0	ENST00000269571.5:c.241C>T	p.Gln81Ter	p.Q81*	ENST00000269571		81	Cag/Tag	3/27	1	2	FACETS	0.316	0.262	0.377	0.316	0.262	0.377	SUBCLONAL	1	TRUE	1	0.393224938324865	2		300	644	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220701	1220701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	180	418	0	ENST00000326873.7:c.719C>T	p.Ser240Leu	p.S240L	ENST00000326873	NM_000455.4	240	tCg/tTg	5/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.393224938324865	2		418	811	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210485	5210485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	137	389	0	ENST00000357368.4:c.5482G>A	p.Ala1828Thr	p.A1828T	ENST00000357368	NM_002850.3	1828	Gcc/Acc	35/38	1	2	FACETS	0.85	0.773	0.93	0.85	0.773	0.93	CLONAL	1	TRUE	1	0.393224938324865	2		389	820	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223105	5223105	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	147	357	0	ENST00000357368.4:c.2698A>G	p.Thr900Ala	p.T900A	ENST00000357368	NM_002850.3	900	Acg/Gcg	18/38	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.393224938324865	2		357	687	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273491	5273491	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	194	514	0	ENST00000357368.4:c.341G>T	p.Gly114Val	p.G114V	ENST00000357368	NM_002850.3	114	gGg/gTg	4/38	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.393224938324865	2		514	861	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289872	15289872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142798406	NA	P-0010196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	97	327	1	ENST00000263388.2:c.3682G>A	p.Gly1228Arg	p.G1228R	ENST00000263388	NM_000435.2	1228	Gga/Aga	22/33	1	2	FACETS	0.753	0.672	0.839	0.753	0.672	0.839	SUBCLONAL	1	TRUE	1	0.393224938324865	2		328	655	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15374340	15374340	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	213	460	0	ENST00000263377.2:c.1232A>C	p.Glu411Ala	p.E411A	ENST00000263377	NM_058243.2	411	gAg/gCg	7/20	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.393224938324865	2		460	1076	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491299	2491300	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0010196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	42	300	0	ENST00000355716.4:c.345_346del	p.Asn116ArgfsTer117	p.N116Rfs*117	ENST00000355716	NM_003820.2	114	acAGag/acag	4/8	1	2	FACETS	0.321	0.267	0.381	0.321	0.267	0.381	SUBCLONAL	1	TRUE	1	0.393224938324865	2		300	666	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988339	36988340	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0010196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	36	113	0	ENST00000354822.5:c.313dup	p.Val105GlyfsTer334	p.V105Gfs*334	ENST00000354822	NM_001079668.2	105	gtg/gGtg	2/3	1	2	FACETS	0.939	0.78	1	0.939	0.78	1	CLONAL	1	TRUE	1	0.393224938324865	2		113	195	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256950	16256950	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	149	506	1	ENST00000375759.3:c.4220del	p.Leu1407TyrfsTer2	p.L1407Yfs*2	ENST00000375759	NM_015001.2	1405	tcT/tc	11/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.393224938324865	2		507	710	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0010208-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	57	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.107980634077272	3	FACETS	0.855	0.733	0.987	0.427	0.366	0.494	INDETERMINATE	1	TRUE	1	0.259905155691283	3		473	580	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0010208-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	73	580	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.787	0.687	0.894	0.787	0.687	0.894	SUBCLONAL	1	TRUE	1	0.259905155691283	2		580	714	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023202	27023202	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010208-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	41	279	0	ENST00000324856.7:c.308C>A	p.Ser103Ter	p.S103*	ENST00000324856	NM_006015.4	103	tCg/tAg	1/20	0.259905155691283	1	FACETS	0.477	0.397	0.567	0.477	0.397	0.567	SUBCLONAL	1	TRUE	0	0.259905155691283	1		279	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0010214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	572	519	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.477868049012528	1	FACETS	0.789	0.767	0.811	1	0.998	1	SUBCLONAL	2	TRUE	0	0.617092756178252	1		519	812	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460432	8460432	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	142	366	0	ENST00000356435.5:c.3854T>A	p.Ile1285Asn	p.I1285N	ENST00000356435		1285	aTt/aAt	22/35	0.629626875319957	1	FACETS	0.569	0.521	0.619	0.569	0.521	0.619	SUBCLONAL	1	TRUE	0	0.617092756178252	1		366	559	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861245	57861245	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1460787785	NA	P-0010214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	229	578	0	ENST00000228682.2:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000228682	NM_005269.2	348	Cga/Tga	9/12	NA	2	FACETS	0.617	0.575	0.662			1	INDETERMINATE	1	TRUE	NA	0.617092756178252	2		578	1202	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375291	15375291	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	308	441	0	ENST00000263377.2:c.1136C>G	p.Pro379Arg	p.P379R	ENST00000263377	NM_058243.2	379	cCt/cGt	6/20	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.617092756178252	2		441	781	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0010262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	101	554	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.15	2		554	1079	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380262	25380263	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACTGTACTCCTCTTG	novel	NA	P-0010262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	76	433	0	ENST00000311936.3:c.181_195dup	p.Gln61_Ser65dup	p.Q61_S65dup	ENST00000311936	NM_004985.3	61	-/CAAGAGGAGTACAGT	3/5	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.15	2		433	966	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-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	82	595	0	ENST00000301067.7:c.14643+189_14781del		p.X4881_splice	ENST00000301067	NM_003482.3	4881		48/54	0.610705090880996	3	FACETS	0.448	0.394	0.505	0.224	0.197	0.253	SUBCLONAL	1	TRUE	1	0.657788404972658	3		595	740	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060846	38060864	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTGCCAAGCCGTGTGCC	GGGTGCCAAGCCGTGTGCC	-	novel	NA	P-0010315-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	147	808	1	ENST00000250448.2:c.1125_1143del	p.Ala376ThrfsTer7	p.A376Tfs*7	ENST00000250448	NM_004496.3	375	ccGGCACACGGCTTGGCACCC/cc	2/2	0.417732340512912	4	FACETS	0.748	0.682	0.817	0.374	0.341	0.409	SUBCLONAL	1	TRUE	2	0.657788404972658	4		809	991	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117711004	117711004	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs752178140	NA	P-0010315-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	31	202	0	ENST00000368508.3:c.1268T>C	p.Val423Ala	p.V423A	ENST00000368508	NM_002944.2	423	gTc/gCc	12/43	0.657788404972658	4	FACETS	0.444	0.359	0.539	0.148	0.119	0.18	SUBCLONAL	1	TRUE	1	0.657788404972658	4		202	352	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0010393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	35	634	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.223065208603014	1	FACETS	0.53	0.434	0.639	0.53	0.434	0.639	SUBCLONAL	1	TRUE	0	0.223065208603014	1		635	526	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586502	189586502	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757536818	NA	P-0010393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	19	232	0	ENST00000264731.3:c.1126C>T	p.Arg376Cys	p.R376C	ENST00000264731	NM_003722.4	376	Cgc/Tgc	8/14	0.197792233899188	3	FACETS	0.802	0.61	1	0.401	0.305	0.514	CLONAL	1	TRUE	1	0.223065208603014	3		232	236	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898711	134898711	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	30	522	0	ENST00000398015.3:c.1769G>T	p.Gly590Val	p.G590V	ENST00000398015	NM_004441.4	590	gGg/gTg	10/16	0.197792233899188	3	FACETS	0.837	0.675	1	0.419	0.337	0.511	CLONAL	1	TRUE	1	0.223065208603014	3		522	357	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250515	110250515	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	16	194	0	ENST00000374672.4:c.160C>G	p.Leu54Val	p.L54V	ENST00000374672	NM_004235.4	54	Ctt/Gtt	3/5	0.201975251268451	2	FACETS	0.81	0.602	1	0.405	0.301	0.529	CLONAL	1	TRUE	0	0.223065208603014	2		194	177	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154880	2154880	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761163170	NA	P-0010393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	67	530	1	ENST00000434045.2:c.341G>A	p.Arg114His	p.R114H	ENST00000434045	NM_001127598.1	114	cGt/cAt	4/5	1	2	FACETS	0.577	0.5	0.661	0.577	0.5	0.661	SUBCLONAL	1	TRUE	1	0.223065208603014	2		531	1041	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240003	53240003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868978693	NA	P-0010393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	22	347	1	ENST00000375401.3:c.1438C>T	p.Pro480Ser	p.P480S	ENST00000375401	NM_004187.3	480	Ccg/Tcg	11/26	1	1	FACETS	0.715	0.556	0.899	0.715	0.556	0.899	SUBCLONAL	1	TRUE	0	0.223065208603014	1		348	245	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	347	592	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	0.8	2		593	788	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161293426	161293426	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs201286421	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	71	473	1	ENST00000367975.2:c.43C>T	p.Arg15Ter	p.R15*	ENST00000367975	NM_003001.3	15	Cga/Tga	2/6	1	2	FACETS	0.211	0.183	0.241	0.211	0.183	0.241	SUBCLONAL	1	TRUE	1	0.8	2		474	842	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	294	453	4	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.911	0.861	0.962	0.911	0.861	0.962	CLONAL	1	TRUE	1	0.8	2		457	807	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906394	50906394	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556862476	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	258	731	2	ENST00000440232.2:c.1055G>A	p.Arg352His	p.R352H	ENST00000440232	NM_002691.3	352	cGc/cAc	9/27	1	2	FACETS	0.635	0.595	0.676	0.635	0.595	0.676	SUBCLONAL	1	TRUE	1	0.8	2		733	1016	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845580	151845580	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1287135873	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	416	651	1	ENST00000262189.6:c.13432C>T	p.Arg4478Ter	p.R4478*	ENST00000262189	NM_170606.2	4478	Cga/Tga	52/59	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.8	2		652	962	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	240	832	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.609	0.568	0.65	0.609	0.568	0.65	SUBCLONAL	1	TRUE	1	0.8	2		834	986	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157431662	157431662	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147784000	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	379	627	0	ENST00000346085.5:c.2338G>A	p.Ala780Thr	p.A780T	ENST00000346085	NM_020732.3	780	Gcc/Acc	7/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.8	2		627	936	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144113	11144113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	547	755	1	ENST00000358026.2:c.3694G>A	p.Gly1232Ser	p.G1232S	ENST00000358026	NM_001128849.1	1232	Ggc/Agc	26/36	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.8	2		756	1193	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	93	333	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	0.556	0.497	0.618	0.556	0.497	0.618	SUBCLONAL	1	TRUE	1	0.8	2		333	418	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543828	212543828	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371593463	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	311	536	1	ENST00000342788.4:c.1571G>A	p.Arg524His	p.R524H	ENST00000342788	NM_005235.2	524	cGc/cAc	13/28	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.8	2		537	742	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549883	187549883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs186220887	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	92	452	0	ENST00000441802.2:c.4358G>A	p.Arg1453His	p.R1453H	ENST00000441802	NM_005245.3	1453	cGt/cAt	8/27	1	2	FACETS	0.327	0.29	0.366	0.327	0.29	0.366	SUBCLONAL	1	TRUE	1	0.8	2		452	704	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790455	3790455	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783490	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	344	568	0	ENST00000262367.5:c.4078C>T	p.Arg1360Ter	p.R1360*	ENST00000262367	NM_004380.2	1360	Cga/Tga	24/31	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.8	2		568	849	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828005	72828005	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373169458	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	465	792	0	ENST00000268489.5:c.8576C>T	p.Thr2859Met	p.T2859M	ENST00000268489	NM_006885.3	2859	aCg/aTg	9/10	1	2	FACETS	0.964	0.922	1	0.964	0.922	1	CLONAL	1	TRUE	1	0.8	2		792	1206	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092948	29092948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201206424	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	343	554	0	ENST00000328354.6:c.1036C>T	p.Arg346Cys	p.R346C	ENST00000328354	NM_007194.3	346	Cgt/Tgt	10/15	1	2	FACETS	0.969	0.921	1	0.969	0.921	1	CLONAL	1	TRUE	1	0.8	2		554	885	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220015	5220015	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866165812	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	548	847	0	ENST00000357368.4:c.3700C>T	p.Arg1234Trp	p.R1234W	ENST00000357368	NM_002850.3	1234	Cgg/Tgg	22/38	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.8	2		847	1199	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341976	8341976	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs377463668	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	88	299	0	ENST00000356435.5:c.4664C>T	p.Ala1555Val	p.A1555V	ENST00000356435		1555	gCg/gTg	29/35	1	2	FACETS	0.443	0.393	0.495	0.443	0.393	0.495	SUBCLONAL	1	TRUE	1	0.8	2		299	497	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435726	110435726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	328	427	0	ENST00000375856.3:c.2675G>A	p.Arg892His	p.R892H	ENST00000375856	NM_003749.2	892	cGc/cAc	1/2	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.8	2		427	697	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039404	47039404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556778215	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	387	365	0	ENST00000377604.3:c.1027C>T	p.Arg343Cys	p.R343C	ENST00000377604	NM_001204468.1	343	Cgc/Tgc	10/24	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.8	1		365	459	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211899	36211899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	288	942	4	ENST00000222270.7:c.1656del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	550	gaC/ga	3/37	1	2	FACETS	0.587	0.551	0.623	0.587	0.551	0.623	SUBCLONAL	1	TRUE	1	0.8	2		946	1227	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420660	49420660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	379	635	0	ENST00000301067.7:c.15089G>A	p.Arg5030His	p.R5030H	ENST00000301067	NM_003482.3	5030	cGt/cAt	48/54	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.8	2		635	878	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836804	151836804	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	123	546	2	ENST00000262189.6:c.14416C>T	p.Arg4806Ter	p.R4806*	ENST00000262189	NM_170606.2	4806	Cga/Tga	56/59	1	2	FACETS	0.38	0.343	0.418	0.38	0.343	0.418	SUBCLONAL	1	TRUE	1	0.8	2		548	810	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021818	71021818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs869025203	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	65	211	0	ENST00000318789.4:c.1540C>T	p.Arg514Cys	p.R514C	ENST00000318789	NM_032682.5	514	Cgt/Tgt	18/21	1	2	FACETS	0.451	0.393	0.514	0.451	0.393	0.514	SUBCLONAL	1	TRUE	1	0.8	2		211	360	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527551	41527551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs533244094	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	381	569	0	ENST00000263253.7:c.1442C>T	p.Pro481Leu	p.P481L	ENST00000263253	NM_001429.3	481	cCg/cTg	6/31	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.8	2		569	949	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396743	139396743	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1198855127	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	231	716	1	ENST00000277541.6:c.5365G>A	p.Glu1789Lys	p.E1789K	ENST00000277541	NM_017617.3	1789	Gag/Aag	28/34	1	2	FACETS	0.578	0.538	0.618	0.578	0.538	0.618	SUBCLONAL	1	TRUE	1	0.8	2		717	1000	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438647	49438647	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	418	671	0	ENST00000301067.7:c.4843C>T	p.Arg1615Ter	p.R1615*	ENST00000301067	NM_003482.3	1615	Cga/Tga	19/54	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.8	2		671	960	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098425	11098425	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	278	475	2	ENST00000358026.2:c.947del	p.Pro316LeufsTer10	p.P316Lfs*10	ENST00000358026	NM_001128849.1	315	Ccc/cc	6/36	1	2	FACETS	0.96	0.907	1	0.96	0.907	1	CLONAL	1	TRUE	1	0.8	2		477	724	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957835	1957835	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388626156	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	64	643	1	ENST00000382891.5:c.2801C>T	p.Ala934Val	p.A934V	ENST00000382891	NM_133335.3	934	gCg/gTg	15/22	1	2	FACETS	0.162	0.139	0.187	0.162	0.139	0.187	SUBCLONAL	1	TRUE	1	0.8	2		644	988	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322615	39322615	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	146	647	0	ENST00000373001.3:c.377C>A	p.Pro126Gln	p.P126Q	ENST00000373001	NM_022157.3	126	cCa/cAa	2/7	1	2	FACETS	0.394	0.359	0.431	0.394	0.359	0.431	SUBCLONAL	1	TRUE	1	0.8	2		647	926	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322727	39322727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764801643	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	331	540	0	ENST00000373001.3:c.265G>A	p.Glu89Lys	p.E89K	ENST00000373001	NM_022157.3	89	Gag/Aag	2/7	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.8	2		540	826	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202549	67202549	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs529774605	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	176	709	0	ENST00000312629.5:c.1358C>T	p.Pro453Leu	p.P453L	ENST00000312629	NM_003952.2	453	cCg/cTg	15/15	1	2	FACETS	0.419	0.385	0.454	0.419	0.385	0.454	SUBCLONAL	1	TRUE	1	0.8	2		709	1050	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941049	71941049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373511105	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	312	740	2	ENST00000298229.2:c.925G>A	p.Val309Met	p.V309M	ENST00000298229	NM_001567.3	309	Gtg/Atg	8/28	1	2	FACETS	0.67	0.632	0.709	0.67	0.632	0.709	SUBCLONAL	1	TRUE	1	0.8	2		742	1164	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076692	102076692	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	164	502	2	ENST00000282441.5:c.871C>T	p.Gln291Ter	p.Q291*	ENST00000282441	NM_001130145.2	291	Cag/Tag	5/9	1	2	FACETS	0.555	0.51	0.601	0.555	0.51	0.601	SUBCLONAL	1	TRUE	1	0.8	2		504	739	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164046	108164046	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	38	175	0	ENST00000278616.4:c.4618G>A	p.Asp1540Asn	p.D1540N	ENST00000278616	NM_000051.3	1540	Gac/Aac	31/63	1	2	FACETS	0.285	0.236	0.34	0.285	0.236	0.34	SUBCLONAL	1	TRUE	1	0.8	2		175	333	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856049	111856049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	222	612	0	ENST00000341259.2:c.100G>A	p.Ala34Thr	p.A34T	ENST00000341259	NM_005475.2	34	Gcc/Acc	2/8	1	2	FACETS	0.629	0.586	0.673	0.629	0.586	0.673	SUBCLONAL	1	TRUE	1	0.8	2		612	883	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202758	133202758	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373092830	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	201	592	1	ENST00000320574.5:c.6476G>A	p.Arg2159His	p.R2159H	ENST00000320574	NM_006231.2	2159	cGc/cAc	46/49	1	2	FACETS	0.56	0.519	0.602	0.56	0.519	0.602	SUBCLONAL	1	TRUE	1	0.8	2		593	898	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108043	30108043	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762349599	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	374	604	0	ENST00000331968.5:c.764G>A	p.Arg255Gln	p.R255Q	ENST00000331968	NM_002742.2	255	cGa/cAa	5/18	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.8	2		604	902	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059448	42059449	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	123	361	0	ENST00000219905.7:c.9168_9169insT	p.Gly3057TrpfsTer25	p.G3057Wfs*25	ENST00000219905	NM_001164273.1	3056	-/T	24/24	1	2	FACETS	0.527	0.478	0.579	0.527	0.478	0.579	SUBCLONAL	1	TRUE	1	0.8	2		361	583	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226345	2226345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	308	785	3	ENST00000326181.6:c.1958G>A	p.Arg653Gln	p.R653Q	ENST00000326181	NM_032271.2	653	cGg/cAg	20/21	1	2	FACETS	0.644	0.607	0.683	0.644	0.607	0.683	SUBCLONAL	1	TRUE	1	0.8	2		788	1195	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857415	68857415	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1407001897	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	378	663	0	ENST00000261769.5:c.2050A>G	p.Ser684Gly	p.S684G	ENST00000261769	NM_004360.3	684	Agc/Ggc	13/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.8	2		663	936	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89335005	89335005	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	27	82	0	ENST00000301030.4:c.7873C>T	p.Gln2625Ter	p.Q2625*	ENST00000301030	NM_001256183.1	2625	Cag/Tag	13/13	1	2	FACETS	0.469	0.378	0.57	0.469	0.378	0.57	SUBCLONAL	1	TRUE	1	0.8	2		82	144	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369474	40369474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	88	568	0	ENST00000293328.3:c.1178G>A	p.Ser393Asn	p.S393N	ENST00000293328	NM_012448.3	393	aGt/aAt	10/19	1	2	FACETS	0.256	0.226	0.288	0.256	0.226	0.288	SUBCLONAL	1	TRUE	1	0.8	2		568	858	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532556	63532556	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765149006	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	65	721	0	ENST00000307078.5:c.2023C>T	p.Arg675Cys	p.R675C	ENST00000307078	NM_004655.3	675	Cgt/Tgt	8/11	1	2	FACETS	0.163	0.141	0.188	0.163	0.141	0.188	SUBCLONAL	1	TRUE	1	0.8	2		721	995	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2193702	2193702	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	414	678	0	ENST00000398665.3:c.508G>A	p.Val170Met	p.V170M	ENST00000398665	NM_032482.2	170	Gtg/Atg	6/28	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.8	2		678	1009	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227863	36227863	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1568384928	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	181	942	0	ENST00000222270.7:c.7348C>T	p.Arg2450Ter	p.R2450*	ENST00000222270	NM_014727.1	2450	Cga/Tga	32/37	1	2	FACETS	0.394	0.363	0.427	0.394	0.363	0.427	SUBCLONAL	1	TRUE	1	0.8	2		942	1148	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46611698	46611698	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770192015	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	194	767	0	ENST00000263734.3:c.2512G>A	p.Glu838Lys	p.E838K	ENST00000263734	NM_001430.4	838	Gaa/Aaa	16/16	1	2	FACETS	0.428	0.395	0.462	0.428	0.395	0.462	SUBCLONAL	1	TRUE	1	0.8	2		767	1133	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439585	220439585	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	353	519	0	ENST00000243786.2:c.438T>A	p.Asn146Lys	p.N146K	ENST00000243786	NM_002191.3	146	aaT/aaA	2/2	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.8	2		519	848	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721845	49721845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	20	104	0	ENST00000449682.2:c.1918G>A	p.Val640Ile	p.V640I	ENST00000449682	NM_020998.3	640	Gtc/Atc	17/18	1	2	FACETS	0.365	0.282	0.46	0.365	0.282	0.46	SUBCLONAL	1	TRUE	1	0.8	2		104	137	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582193	189582193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1198643405	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	191	505	0	ENST00000264731.3:c.752G>A	p.Arg251His	p.R251H	ENST00000264731	NM_003722.4	251	cGt/cAt	5/14	1	2	FACETS	0.638	0.591	0.686	0.638	0.591	0.686	SUBCLONAL	1	TRUE	1	0.8	2		505	749	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509346	149509346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753978428	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	313	415	1	ENST00000261799.4:c.1553C>T	p.Thr518Met	p.T518M	ENST00000261799	NM_002609.3	518	aCg/aTg	10/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.8	2		416	734	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707675	176707675	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	170	485	0	ENST00000439151.2:c.5732G>A	p.Cys1911Tyr	p.C1911Y	ENST00000439151	NM_022455.4	1911	tGc/tAc	18/23	1	2	FACETS	0.579	0.534	0.626	0.579	0.534	0.626	SUBCLONAL	1	TRUE	1	0.8	2		485	734	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722347	176722347	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	108	523	2	ENST00000439151.2:c.7978C>T	p.Gln2660Ter	p.Q2660*	ENST00000439151	NM_022455.4	2660	Cag/Tag	23/23	1	2	FACETS	0.326	0.293	0.362	0.326	0.293	0.362	SUBCLONAL	1	TRUE	1	0.8	2		525	827	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187467	32187467	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1255759249	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	223	725	0	ENST00000375023.3:c.1412G>A	p.Arg471His	p.R471H	ENST00000375023	NM_004557.3	471	cGt/cAt	8/30	1	2	FACETS	0.513	0.477	0.55	0.513	0.477	0.55	SUBCLONAL	1	TRUE	1	0.8	2		725	1087	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864815	117864815	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	159	515	0	ENST00000297338.2:c.1294C>T	p.Gln432Ter	p.Q432*	ENST00000297338	NM_006265.2	432	Cag/Tag	10/14	1	2	FACETS	0.554	0.509	0.601	0.554	0.509	0.601	SUBCLONAL	1	TRUE	1	0.8	2		515	717	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864882	117864882	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	94	561	0	ENST00000297338.2:c.1227G>T	p.Glu409Asp	p.E409D	ENST00000297338	NM_006265.2	409	gaG/gaT	10/14	1	2	FACETS	0.3	0.267	0.336	0.3	0.267	0.336	SUBCLONAL	1	TRUE	1	0.8	2		561	783	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650170	93650170	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs201765057	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	126	511	1	ENST00000375746.1:c.1721G>A	p.Arg574Gln	p.R574Q	ENST00000375746	NM_001174167.1	574	cGa/cAa	12/14	1	2	FACETS	0.51	0.463	0.559	0.51	0.463	0.559	SUBCLONAL	1	TRUE	1	0.8	2		512	618	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300924	137300924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	165	749	1	ENST00000481739.1:c.569G>A	p.Cys190Tyr	p.C190Y	ENST00000481739	NM_002957.4	190	tGc/tAc	4/10	1	2	FACETS	0.386	0.353	0.419	0.386	0.353	0.419	SUBCLONAL	1	TRUE	1	0.8	2		750	1070	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0010422-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	473	345	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.395308564962106	3	FACETS	0.981	0.943	1	0.981	0.943	1	CLONAL	3	TRUE	0	0.402666410354525	3		345	959	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010422-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	168	276	0	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	0.405671459353796	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.402666410354525	1		276	462	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70355083	70355083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779481901	NA	P-0010422-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	641	358	0	ENST00000374080.3:c.5005G>A	p.Asp1669Asn	p.D1669N	ENST00000374080		1669	Gat/Aat	36/45	0.405671459353796	2	FACETS	0.891	0.862	0.92			1	CLONAL	3	TRUE	NA	0.402666410354525	2		358	1191	SUCCESS
APC	324	MSKCC	GRCh37	5	112175143	112175143	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010422-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	116	195	0	ENST00000257430.4:c.3852A>T	p.Glu1284Asp	p.E1284D	ENST00000257430	NM_000038.5	1284	gaA/gaT	16/16	0.405671459353796	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.402666410354525	1		195	329	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056263	26056263	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs139623473	NA	P-0010422-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1489	212	476	0	ENST00000343677.2:c.394G>C	p.Val132Leu	p.V132L	ENST00000343677	NM_005319.3	132	Gtt/Ctt	1/1	0.405671459353796	4	FACETS	0.868	0.804	0.936	0.434	0.402	0.468	CLONAL	1	TRUE	2	0.402666410354525	4		476	1701	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006224	22006224	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010422-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	143	163	0	ENST00000276925.6:c.179del	p.Arg60ProfsTer105	p.R60Pfs*105	ENST00000276925	NM_004936.3	60	cGc/cc	2/2	0.368499593515187	4	FACETS	0.89	0.815	0.967	0.89	0.815	0.967	CLONAL	2	TRUE	2	0.402666410354525	4		163	560	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710609	114710609	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010422-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2087	394	959	0	ENST00000543371.1:c.94del	p.Ser32ProfsTer10	p.S32Pfs*10	ENST00000543371	NM_001198531.1	32	Tcc/cc	1/14	0.405671459353796	3	FACETS	0.948	0.896	1	0.474	0.448	0.5	CLONAL	1	TRUE	1	0.402666410354525	3		959	2481	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	430	463	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.42224341357975	4	FACETS	1	0.993	1	0.859	0.827	0.892	CLONAL	3	TRUE	0	0.501585691396084	4		463	749	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057520006	NA	P-0010452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	368	457	0	ENST00000269305.4:c.821T>A	p.Val274Asp	p.V274D	ENST00000269305	NM_001126112.2	274	gTt/gAt	8/11	0.386414194777112	2	FACETS	0.914	0.872	0.956	0.914	0.872	0.956	CLONAL	2	TRUE	0	0.501585691396084	2		457	803	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176710866	176710866	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	226	605	0	ENST00000439151.2:c.6088C>G	p.Gln2030Glu	p.Q2030E	ENST00000439151	NM_022455.4	2030	Cag/Gag	20/23	0.426619191966686	3	FACETS	0.885	0.823	0.949	0.442	0.411	0.475	CLONAL	1	TRUE	1	0.501585691396084	3		605	1274	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456396	32456396	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	143	356	1	ENST00000332351.3:c.496G>A	p.Gly166Ser	p.G166S	ENST00000332351	NM_024426.4	166	Ggc/Agc	1/10	0.32483651289933	3	FACETS	0.893	0.814	0.975			1	CLONAL	1	TRUE	NA	0.501585691396084	3		357	799	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864396	57864396	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768202810	NA	P-0010452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1375	219	776	2	ENST00000228682.2:c.1873G>A	p.Glu625Lys	p.E625K	ENST00000228682	NM_005269.2	625	Gag/Aag	12/12	0.471257867308557	4	FACETS	0.823	0.763	0.885	0.206	0.19	0.222	CLONAL	1	TRUE	0	0.501585691396084	4		778	1594	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506670	103506670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1372959301	NA	P-0010452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	172	382	1	ENST00000355739.4:c.413G>A	p.Arg138Gln	p.R138Q	ENST00000355739	NM_000123.3	138	cGa/cAa	4/15	0.457066629269224	5	FACETS	1	0.969	1	0.277	0.254	0.301	CLONAL	1	TRUE	1	0.501585691396084	5		383	1084	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610608	52610609	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	103	596	0	ENST00000394830.3:c.3564dup	p.Glu1189ArgfsTer6	p.E1189Rfs*6	ENST00000394830	NM_018313.4	1188	-/A	23/30	0.791392663984343	1	FACETS	0.3	0.269	0.333	0.3	0.269	0.333	SUBCLONAL	1	TRUE	0	0.791392663984343	1		596	524	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176338	24176338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	18	324	2	ENST00000263121.7:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000263121	NM_003073.3	377	Cgt/Tgt	9/9	0.791392663984343	1	FACETS	0.062	0.046	0.081	0.062	0.046	0.081	SUBCLONAL	1	TRUE	0	0.791392663984343	1		326	444	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183797	10183797	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs5030807	NA	P-0010561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	182	234	0	ENST00000256474.2:c.266T>C	p.Leu89Pro	p.L89P	ENST00000256474	NM_000551.3	89	cTc/cCc	1/3	0.791392663984343	1	FACETS	0.968	0.916	1	0.968	0.916	1	CLONAL	1	TRUE	0	0.791392663984343	1		234	287	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584582	52584583	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0010561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	171	633	0	ENST00000394830.3:c.4430_4431del	p.Pro1477ArgfsTer31	p.P1477Rfs*31	ENST00000394830	NM_018313.4	1477	cCT/c	29/30	0.791392663984343	1	FACETS	0.34	0.313	0.369	0.34	0.313	0.369	SUBCLONAL	1	TRUE	0	0.791392663984343	1		633	767	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578485	7578485	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1064793929	NA	P-0010594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	94	420	0	ENST00000269305.4:c.445del	p.Ser149ProfsTer21	p.S149Pfs*21	ENST00000269305	NM_001126112.2	149	Tcc/cc	5/11	0.313435442393142	3	FACETS	1	0.938	1	0.539	0.48	0.601	CLONAL	1	TRUE	1	0.313435442393142	3		420	644	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556079	29556079	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886041347	NA	P-0010594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	22	271	0	ENST00000356175.3:c.2446C>T	p.Arg816Ter	p.R816*	ENST00000356175	NM_000267.3	816	Cga/Tga	21/57	0.313435442393142	3	FACETS	0.445	0.344	0.562	0.222	0.172	0.281	SUBCLONAL	1	TRUE	1	0.313435442393142	3		271	365	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997733	149997733	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	81	364	0	ENST00000253339.5:c.2734G>C	p.Gly912Arg	p.G912R	ENST00000253339		912	Ggg/Cgg	5/7	0.313435442393142	3	FACETS	0.884	0.779	0.997			1	CLONAL	1	TRUE	NA	0.313435442393142	3		364	676	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0010604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	254	519	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.310062009719977	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.310062009719977	1		519	1020	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254839	16254839	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	106	487	1	ENST00000375759.3:c.2104C>T	p.Arg702Ter	p.R702*	ENST00000375759	NM_015001.2	702	Cga/Tga	11/15	0.310062009719977	3	FACETS	0.652	0.583	0.726	0.326	0.291	0.363	SUBCLONAL	1	TRUE	1	0.310062009719977	3		488	1211	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690301	117690301	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	106	390	0	ENST00000369458.3:c.828C>G	p.Ser276Arg	p.S276R	ENST00000369458	NM_024626.3	276	agC/agG	5/6	0.310062009719977	1	FACETS	0.784	0.703	0.87	0.784	0.703	0.87	SUBCLONAL	1	TRUE	0	0.310062009719977	1		390	737	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068097	94068097	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1447	112	664	0	ENST00000369303.4:c.865C>G	p.Gln289Glu	p.Q289E	ENST00000369303	NM_004440.3	289	Caa/Gaa	4/17	0.310062009719977	3	FACETS	0.535	0.479	0.595	0.178	0.159	0.199	SUBCLONAL	1	TRUE	0	0.310062009719977	3		664	1559	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390919	139390934	+	frameshift_variant	Frame_Shift_Del	DEL	TGCTGAGCTCACGCCA	TGCTGAGCTCACGCCA	-	novel	NA	P-0010604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	91	356	0	ENST00000277541.6:c.7257_7272del	p.Gly2420ProfsTer10	p.G2420Pfs*10	ENST00000277541	NM_017617.3	2419	ctTGGCGTGAGCTCAGCA/ct	34/34	0.310062009719977	1	FACETS	0.651	0.578	0.729	0.651	0.578	0.729	SUBCLONAL	1	TRUE	0	0.310062009719977	1		356	762	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0010804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	18	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.569	0.426	0.739	0.569	0.426	0.739	SUBCLONAL	1	TRUE	1	0.09	2		473	703	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0010804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	23	580	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.658	0.51	0.83	0.658	0.51	0.83	SUBCLONAL	1	TRUE	1	0.09	2		580	777	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412233	139412233	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs753964476	NA	P-0010865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	238	477	0	ENST00000277541.6:c.1412T>C	p.Ile471Thr	p.I471T	ENST00000277541	NM_017617.3	471	aTt/aCt	8/34	0.555818589926793	3	FACETS	1	0.988	1	0.626	0.586	0.668	CLONAL	1	TRUE	1	0.555640779918974	3		477	874	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0010865-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	229	444	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.41191372218956	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.511816617376686	3		444	549	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412233	139412233	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs753964476	NA	P-0010865-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	276	477	0	ENST00000277541.6:c.1412T>C	p.Ile471Thr	p.I471T	ENST00000277541	NM_017617.3	471	aTt/aCt	8/34	1	2	FACETS	0.96	0.911	1	1	0.996	1	CLONAL	2	TRUE	1	0.511816617376686	2		477	562	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123199797	123199797	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0011218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	50	232	0	ENST00000218089.9:c.2096+1G>A		p.X699_splice	ENST00000218089	NM_001042749.1	699			1	1	FACETS	0.515	0.437	0.6	0.515	0.437	0.6	SUBCLONAL	1	TRUE	0	0.32	1		232	510	SUCCESS
FH	2271	MSKCC	GRCh37	1	241676938	241676980	+	frameshift_variant	Frame_Shift_Del	DEL	TTGGATCAAGACCATAATCCTGGTTTACTTCAGCGGCCGCTCG	TTGGATCAAGACCATAATCCTGGTTTACTTCAGCGGCCGCTCG	-	novel	NA	P-0011218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	129	559	0	ENST00000366560.3:c.301_343del	p.Ala102LeufsTer5	p.A102Lfs*5	ENST00000366560	NM_000143.3	101	CGAGCGGCCGCTGAAGTAAACCAGGATTATGGTCTTGATCCAAag/ag	3/10	0.3	1	FACETS	0.583	0.527	0.642	0.583	0.527	0.642	SUBCLONAL	1	TRUE	0	0.32	1		559	1161	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907621	76907621	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	414	317	0	ENST00000373344.5:c.4540C>T	p.Arg1514Ter	p.R1514*	ENST00000373344	NM_000489.3	1514	Cga/Tga	15/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.692350138454517	1		317	586	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143129616	143129616	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1306172586	NA	P-0011479-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	184	279	0	ENST00000262992.4:c.1034A>G	p.His345Arg	p.H345R	ENST00000262992	NM_001101669.1	345	cAt/cGt	12/24	1	2	FACETS	0.699	0.645	0.755	0.699	0.645	0.755	SUBCLONAL	1	TRUE	1	0.531229177645928	2		279	991	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286530	33286530	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011479-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	126	148	0	ENST00000374542.5:c.2213A>T	p.Asp738Val	p.D738V	ENST00000374542	NM_001141970.1	738	gAc/gTc	8/8	0.531229177645928	1	FACETS	0.764	0.697	0.834	0.764	0.697	0.834	SUBCLONAL	1	TRUE	0	0.531229177645928	1		148	456	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	111	330	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.99	0.892	1	0.99	0.892	1	CLONAL	1	TRUE	1	0.359854277590832	2		330	623	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	98	257	1	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.359854277590832	2		258	541	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	20	385	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.234	0.178	0.299	0.234	0.178	0.299	SUBCLONAL	1	TRUE	1	0.359854277590832	2		385	476	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	300	453	4	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.76	0.716	0.805	1	0.994	1	SUBCLONAL	2	TRUE	1	0.359854277590832	2		457	1097	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	159	338	2	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.359854277590832	2		340	793	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935322	36935323	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs747437399	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	134	432	2	ENST00000361632.4:c.1404dup	p.Ser469GlnfsTer5	p.S469Qfs*5	ENST00000361632		468	-/C	10/16	1	2	FACETS	0.827	0.751	0.908	0.827	0.751	0.908	CLONAL	1	TRUE	1	0.359854277590832	2		434	900	SUCCESS
B2M	567	MSKCC	GRCh37	15	45008529	45008529	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	154	329	0	ENST00000558401.1:c.349C>T	p.Arg117Ter	p.R117*	ENST00000558401	NM_004048.2	117	Cga/Tga	3/4	1	2	FACETS	0.94	0.86	1	0.94	0.86	1	CLONAL	1	TRUE	1	0.359854277590832	2		329	911	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151289	202151290	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	185	453	0	ENST00000358485.4:c.1596dup	p.Leu533ThrfsTer6	p.L533Tfs*6	ENST00000358485	NM_001080125.1	530	aga/agAa	9/9	1	2	FACETS	0.956	0.882	1	0.956	0.882	1	CLONAL	1	TRUE	1	0.359854277590832	2		453	1075	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385221	41385221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375454640	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	176	326	1	ENST00000373198.4:c.740G>A	p.Arg247His	p.R247H	ENST00000373198	NM_133170.3	247	cGc/cAc	6/32	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.359854277590832	2		327	847	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	152	383	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.947	0.866	1	0.947	0.866	1	CLONAL	1	TRUE	1	0.359854277590832	2		383	892	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	230	637	2	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	0.909	0.845	0.975	0.909	0.845	0.975	CLONAL	1	TRUE	1	0.359854277590832	2		639	1406	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	118	257	0	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.359854277590832	2		257	651	SUCCESS
APC	324	MSKCC	GRCh37	5	112173689	112173690	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	102	261	0	ENST00000257430.4:c.2403dup	p.Asp802Ter	p.D802*	ENST00000257430	NM_000038.5	800	gtt/gTtt	16/16	1	2	FACETS	0.864	0.774	0.96	0.864	0.774	0.96	CLONAL	1	TRUE	1	0.359854277590832	2		261	656	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106803	27106804	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	115	263	0	ENST00000324856.7:c.6420dup	p.Phe2141LeufsTer9	p.F2141Lfs*9	ENST00000324856	NM_006015.4	2138	-/C	20/20	1	2	FACETS	0.877	0.79	0.968	0.877	0.79	0.968	CLONAL	1	TRUE	1	0.359854277590832	2		263	729	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074255	8074255	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1263	271	746	2	ENST00000377482.5:c.404del	p.Asn135ThrfsTer40	p.N135Tfs*40	ENST00000377482	NM_018948.3	135	aAc/ac	4/4	1	2	FACETS	0.982	0.919	1	0.982	0.919	1	CLONAL	1	TRUE	1	0.359854277590832	2		748	1534	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156012	99156012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293996326	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	169	378	0	ENST00000074304.5:c.692G>A	p.Arg231His	p.R231H	ENST00000074304	NM_001134224.1	231	cGc/cAc	10/26	1	2	FACETS	0.954	0.876	1	0.954	0.876	1	CLONAL	1	TRUE	1	0.359854277590832	2		378	985	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298480	11298480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780622659	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	129	337	0	ENST00000361445.4:c.1981G>A	p.Val661Ile	p.V661I	ENST00000361445	NM_004958.3	661	Gta/Ata	12/58	1	2	FACETS	0.934	0.847	1	0.934	0.847	1	CLONAL	1	TRUE	1	0.359854277590832	2		337	768	SUCCESS
ATR	545	MSKCC	GRCh37	3	142232477	142232477	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs754602382	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	81	235	0	ENST00000350721.4:c.4507C>T	p.Arg1503Ter	p.R1503*	ENST00000350721	NM_001184.3	1503	Cga/Tga	26/47	1	2	FACETS	0.932	0.824	1	0.932	0.824	1	CLONAL	1	TRUE	1	0.359854277590832	2		235	483	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979442	2979442	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	164	434	0	ENST00000396946.4:c.805C>G	p.Leu269Val	p.L269V	ENST00000396946	NM_032415.4	269	Ctg/Gtg	6/25	0.359827265723483	2	FACETS	0.917	0.841	0.996	0.458	0.42	0.498	CLONAL	1	TRUE	0	0.359854277590832	2		434	994	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223600	55223600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761844164	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	139	274	1	ENST00000275493.2:c.967G>A	p.Val323Ile	p.V323I	ENST00000275493	NM_005228.3	323	Gtc/Atc	8/28	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.359854277590832	2		275	671	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90971041	90971041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200297914	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	120	280	0	ENST00000265433.3:c.1036G>A	p.Val346Met	p.V346M	ENST00000265433	NM_002485.4	346	Gtg/Atg	9/16	1	2	FACETS	0.839	0.758	0.925	0.839	0.758	0.925	CLONAL	1	TRUE	1	0.359854277590832	2		280	795	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633406	8633406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	160	371	4	ENST00000356435.5:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000356435		88	cGg/cAg	3/35	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.359854277590832	2		375	844	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572246	64572246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	48	383	2	ENST00000312049.6:c.1393G>A	p.Ala465Thr	p.A465T	ENST00000312049	NM_130799.2	465	Gcc/Acc	10/10	1	2	FACETS	0.324	0.273	0.381	0.324	0.273	0.381	SUBCLONAL	1	TRUE	1	0.359854277590832	2		385	823	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202217	108202217	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876660422	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	87	229	0	ENST00000278616.4:c.7562A>G	p.Tyr2521Cys	p.Y2521C	ENST00000278616	NM_000051.3	2521	tAc/tGc	51/63	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.359854277590832	2		229	425	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209056	133209056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	131	307	0	ENST00000320574.5:c.6175C>T	p.Leu2059Phe	p.L2059F	ENST00000320574	NM_006231.2	2059	Ctc/Ttc	45/49	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.359854277590832	2		307	646	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14015892	14015892	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	73	188	0	ENST00000311895.7:c.212A>G	p.Tyr71Cys	p.Y71C	ENST00000311895	NM_005236.2	71	tAt/tGt	2/11	1	2	FACETS	0.797	0.699	0.903	0.797	0.699	0.903	CLONAL	1	TRUE	1	0.359854277590832	2		188	509	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553564	29553564	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	26	162	0	ENST00000356175.3:c.2113G>T	p.Val705Phe	p.V705F	ENST00000356175	NM_000267.3	705	Gtt/Ttt	18/57	1	2	FACETS	0.394	0.312	0.488	0.394	0.312	0.488	SUBCLONAL	1	TRUE	1	0.359854277590832	2		162	367	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510626	38510626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	165	394	0	ENST00000254066.5:c.880C>T	p.Arg294Trp	p.R294W	ENST00000254066	NM_000964.3	294	Cgg/Tgg	7/9	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.359854277590832	2		394	872	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857747	59857747	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	110	278	0	ENST00000259008.2:c.1810A>G	p.Asn604Asp	p.N604D	ENST00000259008	NM_032043.2	604	Aat/Gat	13/20	1	2	FACETS	0.98	0.882	1	0.98	0.882	1	CLONAL	1	TRUE	1	0.359854277590832	2		278	624	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383208	42383208	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	215	528	1	ENST00000221972.3:c.228G>A	p.Trp76Ter	p.W76*	ENST00000221972	NM_021601.3	76	tgG/tgA	2/5	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.359854277590832	2		529	1158	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909523	50909523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	219	497	0	ENST00000440232.2:c.1327C>T	p.Arg443Trp	p.R443W	ENST00000440232	NM_002691.3	443	Cgg/Tgg	11/27	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.359854277590832	2		497	1048	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980762	40980762	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	119	345	0	ENST00000373198.4:c.1724G>T	p.Gly575Val	p.G575V	ENST00000373198	NM_133170.3	575	gGg/gTg	10/32	1	2	FACETS	0.837	0.756	0.923	0.837	0.756	0.923	CLONAL	1	TRUE	1	0.359854277590832	2		345	790	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655272	45655272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764295138	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	133	263	1	ENST00000407780.3:c.580C>T	p.Arg194Trp	p.R194W	ENST00000407780	NM_001283052.1	194	Cgg/Tgg	4/7	1	2	FACETS	0.982	0.892	1	0.982	0.892	1	CLONAL	1	TRUE	1	0.359854277590832	2		264	753	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317539	1317539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	181	410	0	ENST00000400841.2:c.526G>A	p.Asp176Asn	p.D176N	ENST00000400841		176	Gat/Aat	5/6	1	1	FACETS	0.85	0.783	0.919	0.85	0.783	0.919	CLONAL	1	TRUE	0	0.359854277590832	1		410	971	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349002	70349002	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	36	250	0	ENST00000374080.3:c.3514A>G	p.Thr1172Ala	p.T1172A	ENST00000374080		1172	Acc/Gcc	25/45	1	1	FACETS	0.258	0.211	0.311	0.258	0.211	0.311	SUBCLONAL	1	TRUE	0	0.359854277590832	1		250	636	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202632	108202632	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	105	213	1	ENST00000278616.4:c.7660del	p.His2554IlefsTer10	p.H2554Ifs*10	ENST00000278616	NM_000051.3	2552	caC/ca	52/63	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.359854277590832	2		214	498	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967191	134967191	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs754939903	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	65	213	0	ENST00000398015.3:c.2534del	p.Pro845HisfsTer34	p.P845Hfs*34	ENST00000398015	NM_004441.4	844	Ccc/cc	14/16	1	2	FACETS	0.83	0.722	0.947	0.83	0.722	0.947	CLONAL	1	TRUE	1	0.359854277590832	2		213	435	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271746	15271747	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs773656789	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	110	325	0	ENST00000263388.2:c.6692dup	p.Ala2233GlyfsTer9	p.A2233Gfs*9	ENST00000263388	NM_000435.2	2231	cca/ccCa	33/33	1	2	FACETS	0.921	0.828	1	0.921	0.828	1	CLONAL	1	TRUE	1	0.359854277590832	2		325	664	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574697	41574698	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	180	557	0	ENST00000263253.7:c.6986dup	p.Arg2330LysfsTer49	p.R2330Kfs*49	ENST00000263253	NM_001429.3	2328	tcc/tCcc	31/31	1	2	FACETS	0.902	0.831	0.977	0.902	0.831	0.977	CLONAL	1	TRUE	1	0.359854277590832	2		557	1109	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739733	41739734	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	212	524	0	ENST00000242208.4:c.239dup	p.Ala81GlyfsTer26	p.A81Gfs*26	ENST00000242208	NM_002192.2	80	aag/aaAg	2/3	1	2	FACETS	0.976	0.905	1	0.976	0.905	1	CLONAL	1	TRUE	1	0.359854277590832	2		524	1207	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022296	31022297	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0011540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	176	403	0	ENST00000375687.4:c.1786dup	p.Arg596ProfsTer23	p.R596Pfs*23	ENST00000375687	NM_015338.5	594	tgc/tgCc	13/13	1	2	FACETS	0.961	0.884	1	0.961	0.884	1	CLONAL	1	TRUE	1	0.359854277590832	2		403	1018	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937175	39937175	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	239	800	1	ENST00000378444.4:c.8C>T	p.Ser3Leu	p.S3L	ENST00000378444	NM_001123385.1	3	tCa/tTa	2/15	0.549898376183417	4	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.693714944992702	4		801	1006	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544646	65544646	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	158	591	0	ENST00000358664.4:c.280C>G	p.Leu94Val	p.L94V	ENST00000358664	NM_002382.4	94	Ctt/Gtt	4/5	0.368727697025723	6	FACETS	1	0.982	1	0.42	0.385	0.457	INDETERMINATE	1	TRUE	3	0.693714944992702	6		591	863	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11318569	11318569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	152	712	0	ENST00000361445.4:c.244G>A	p.Glu82Lys	p.E82K	ENST00000361445	NM_004958.3	82	Gag/Aag	3/58	0.693746975033016	3	FACETS	0.976	0.896	1	0.488	0.448	0.529	CLONAL	1	TRUE	1	0.693714944992702	3		712	605	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691762	30691762	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	113	634	0	ENST00000295754.5:c.264G>C	p.Trp88Cys	p.W88C	ENST00000295754	NM_003242.5	88	tgG/tgC	3/7	0.693714944992702	2	FACETS	0.842	0.764	0.922	0.421	0.382	0.461	CLONAL	1	TRUE	0	0.693714944992702	2		634	387	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138375076	138375076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778509272	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	306	753	1	ENST00000289153.2:c.2983C>T	p.Arg995Trp	p.R995W	ENST00000289153	NM_006219.2	995	Cgg/Tgg	21/22	0.693746975033016	4	FACETS	0.886	0.839	0.935	0.591	0.559	0.623	CLONAL	2	TRUE	1	0.693714944992702	4		754	843	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138407735	138407735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	163	597	0	ENST00000289153.2:c.2118G>A	p.Met706Ile	p.M706I	ENST00000289153	NM_006219.2	706	atG/atA	14/22	0.693746975033016	4	FACETS	0.995	0.914	1	0.332	0.304	0.36	CLONAL	1	TRUE	1	0.693714944992702	4		597	800	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526176	189526176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747354750	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	214	807	1	ENST00000264731.3:c.440C>T	p.Ser147Leu	p.S147L	ENST00000264731	NM_003722.4	147	tCg/tTg	4/14	0.693746975033016	4	FACETS	0.921	0.855	0.989	0.307	0.285	0.33	CLONAL	1	TRUE	1	0.693714944992702	4		808	1135	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590777	189590777	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs868749966	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	153	635	0	ENST00000264731.3:c.1342C>T	p.Gln448Ter	p.Q448*	ENST00000264731	NM_003722.4	448	Cag/Tag	10/14	0.693746975033016	4	FACETS	0.98	0.898	1	0.327	0.299	0.356	CLONAL	1	TRUE	1	0.693714944992702	4		635	762	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131951784	131951784	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	96	693	0	ENST00000265335.6:c.3126G>C	p.Leu1042Phe	p.L1042F	ENST00000265335		1042	ttG/ttC	20/25	0.693746975033016	3	FACETS	0.761	0.681	0.845			1	SUBCLONAL	1	TRUE	NA	0.693714944992702	3		693	490	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722036	176722036	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	123	418	0	ENST00000439151.2:c.7667C>G	p.Ser2556Ter	p.S2556*	ENST00000439151	NM_022455.4	2556	tCa/tGa	23/23	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.693714944992702	NA		418	509	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6027082	6027082	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	67	314	0	ENST00000265849.7:c.1314G>C	p.Lys438Asn	p.K438N	ENST00000265849	NM_000535.5	438	aaG/aaC	11/15	0.671588321018607	3	FACETS	0.949	0.834	1	0.475	0.417	0.536	CLONAL	1	TRUE	1	0.693714944992702	3		314	274	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1039023	1039023	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	236	891	0	ENST00000358495.3:c.310T>G	p.Tyr104Asp	p.Y104D	ENST00000358495	NM_134424.2	104	Tac/Gac	5/12	0.693746975033016	3	FACETS	1	0.968	1	0.528	0.493	0.563	CLONAL	1	TRUE	1	0.693714944992702	3		891	868	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18439842	18439842	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	106	633	1	ENST00000266497.5:c.740C>A	p.Ser247Tyr	p.S247Y	ENST00000266497		247	tCt/tAt	2/31	0.693746975033016	3	FACETS	1	0.94	1	0.528	0.477	0.581	CLONAL	1	TRUE	1	0.693714944992702	3		634	390	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231183	46231183	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs772564527	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	84	453	0	ENST00000334344.6:c.1103G>C	p.Arg368Thr	p.R368T	ENST00000334344	NM_152641.2	368	aGa/aCa	9/21	0.646260896224666	5	FACETS	1	0.964	1			1	CLONAL	1	TRUE	NA	0.693714944992702	5		453	406	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858764	9858764	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	64	227	0	ENST00000330684.3:c.2637G>C	p.Lys879Asn	p.K879N	ENST00000330684	NM_001134407.1	879	aaG/aaC	13/13	0.671588321018607	3	FACETS	1	0.943	1	0.565	0.496	0.637	CLONAL	1	TRUE	1	0.693714944992702	3		227	220	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771344	68771344	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	120	315	0	ENST00000261769.5:c.26C>G	p.Ser9Trp	p.S9W	ENST00000261769	NM_004360.3	9	tCg/tGg	1/16	0.671588321018607	3	FACETS	0.817	0.751	0.885	0.817	0.751	0.885	CLONAL	2	TRUE	1	0.693714944992702	3		315	285	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243913	41243913	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs886038021	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	181	758	0	ENST00000357654.3:c.3635C>G	p.Ser1212Ter	p.S1212*	ENST00000357654	NM_007294.3	1212	tCa/tGa	10/23	NA	2	FACETS	1	0.935	1			1	INDETERMINATE	1	TRUE	NA	0.693714944992702	2		758	519	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637864	39637864	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	94	546	0	ENST00000262039.4:c.2281G>C	p.Asp761His	p.D761H	ENST00000262039	NM_002647.2	761	Gac/Cac	22/25	0.177984946499926	3	FACETS	1	0.964	1	0.579	0.521	0.64	INDETERMINATE	1	TRUE	1	0.693714944992702	3		546	315	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946813	17946813	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	191	812	0	ENST00000458235.1:c.1834C>A	p.Leu612Met	p.L612M	ENST00000458235	NM_000215.3	612	Ctg/Atg	14/24	0.651951250433595	4	FACETS	0.882	0.815	0.952			1	CLONAL	1	TRUE	NA	0.693714944992702	4		812	1057	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024121	31024121	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	196	815	0	ENST00000375687.4:c.3606G>C	p.Lys1202Asn	p.K1202N	ENST00000375687	NM_015338.5	1202	aaG/aaC	13/13	0.654156855377115	4	FACETS	0.989	0.915	1	0.494	0.457	0.533	CLONAL	1	TRUE	2	0.693714944992702	4		815	968	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410001	63410001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	73	406	0	ENST00000330258.3:c.3166G>A	p.Asp1056Asn	p.D1056N	ENST00000330258	NM_152424.3	1056	Gat/Aat	2/2	0.549898376183417	4	FACETS	0.608	0.532	0.69			1	SUBCLONAL	1	TRUE	NA	0.693714944992702	4		406	586	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205041	123205041	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	107	471	0	ENST00000218089.9:c.2401C>G	p.Gln801Glu	p.Q801E	ENST00000218089	NM_001042749.1	801	Cag/Gag	25/35	0.693746975033016	3	FACETS	1	0.979	1	0.647	0.588	0.709	CLONAL	1	TRUE	1	0.693714944992702	3		471	321	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726555	46726555	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	166	517	0	ENST00000371975.4:c.634G>C	p.Asp212His	p.D212H	ENST00000371975	NM_003579.3	212	Gac/Cac	7/18	0.693746975033016	3	FACETS	1	0.973	1	0.56	0.517	0.604	CLONAL	1	TRUE	1	0.693714944992702	3		517	576	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443562	49443562	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	174	719	1	ENST00000301067.7:c.3809C>A	p.Ser1270Ter	p.S1270*	ENST00000301067	NM_003482.3	1270	tCa/tAa	11/54	0.646260896224666	5	FACETS	1	0.927	1			1	CLONAL	1	TRUE	NA	0.693714944992702	5		720	1016	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562404	95562404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377205344	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	165	541	1	ENST00000393063.1:c.4853C>T	p.Ser1618Leu	p.S1618L	ENST00000393063	NM_030621.3	1618	tCa/tTa	24/28	0.368727697025723	6	FACETS	0.793	0.73	0.859	0.529	0.487	0.573	INDETERMINATE	2	TRUE	3	0.693714944992702	6		542	716	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582095	95582095	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	120	496	0	ENST00000393063.1:c.1816G>T	p.Asp606Tyr	p.D606Y	ENST00000393063	NM_030621.3	606	Gat/Tat	12/28	0.368727697025723	6	FACETS	1	0.967	1	0.385	0.348	0.424	INDETERMINATE	1	TRUE	3	0.693714944992702	6		496	715	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775007	73775007	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	104	340	0	ENST00000254810.4:c.166C>G	p.Gln56Glu	p.Q56E	ENST00000254810	NM_005324.3	56	Cag/Gag	3/4	0.693746975033016	5	FACETS	0.882	0.79	0.979	0.294	0.263	0.327	CLONAL	1	TRUE	2	0.693714944992702	5		340	694	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142830	7142830	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1908	119	411	0	ENST00000302850.5:c.2539G>T	p.Glu847Ter	p.E847*	ENST00000302850	NM_000208.2	847	Gaa/Taa	12/22	0.693714944992702	14	FACETS	0.874	0.785	0.969			1	CLONAL	1	TRUE	NA	0.693714944992702	14		411	2027	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10283851	10283851	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	54	654	0	ENST00000340748.4:c.636-1G>C		p.X212_splice	ENST00000340748		212			0.539969096521135	3	FACETS	0.336	0.286	0.39			1	SUBCLONAL	1	TRUE	NA	0.693714944992702	3		654	624	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303185	15303185	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	rs1401657793	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1408	215	868	1	ENST00000263388.2:c.340+3G>A		p.X114_splice	ENST00000263388	NM_000435.2	114			0.693714944992702	6	FACETS	0.912	0.845	0.982			1	CLONAL	1	TRUE	NA	0.693714944992702	6		869	1623	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792245	33792245	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	149	578	0	ENST00000498907.2:c.1076G>C	p.Ter359SerextTer36	p.*359Sext*36	ENST00000498907	NM_004364.3	359	tGa/tCa	1/1	0.671588321018607	3	FACETS	0.974	0.894	1	0.487	0.447	0.529	CLONAL	1	TRUE	1	0.693714944992702	3		578	594	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211603	36211603	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	68	640	0	ENST00000222270.7:c.1354G>C	p.Glu452Gln	p.E452Q	ENST00000222270	NM_014727.1	452	Gag/Cag	3/37	0.671588321018607	3	FACETS	0.422	0.367	0.482	0.211	0.183	0.241	SUBCLONAL	1	TRUE	1	0.693714944992702	3		640	625	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009087	27009087	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	65	217	1	ENST00000335756.4:c.23G>T	p.Arg8Leu	p.R8L	ENST00000335756	NM_001809.3	8	cGa/cTa	1/5	0.671588321018607	3	FACETS	0.914	0.801	1	0.457	0.4	0.518	CLONAL	1	TRUE	1	0.693714944992702	3		218	276	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264838	46264838	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	187	739	2	ENST00000371998.3:c.1708C>A	p.Pro570Thr	p.P570T	ENST00000371998		570	Cct/Act	12/23	0.654156855377115	4	FACETS	1	0.977	1	0.567	0.525	0.611	CLONAL	1	TRUE	2	0.693714944992702	4		741	805	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164445	36164445	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	52	208	0	ENST00000300305.3:c.1430G>A	p.Trp477Ter	p.W477*	ENST00000300305		477	tGg/tAg	8/8	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.693714944992702	NA		208	217	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818336	170818336	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	132	757	0	ENST00000296930.5:c.166G>C	p.Glu56Gln	p.E56Q	ENST00000296930	NM_002520.6	56	Gag/Cag	3/11	0.693746975033016	3	FACETS	0.849	0.773	0.928	0.424	0.386	0.464	CLONAL	1	TRUE	1	0.693714944992702	3		757	604	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813376	32813376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	240	958	0	ENST00000354258.4:c.2407C>T	p.Pro803Ser	p.P803S	ENST00000354258	NM_000593.5	803	Cct/Tct	11/11	0.693746975033016	3	FACETS	0.879	0.821	0.939	0.44	0.41	0.47	CLONAL	1	TRUE	1	0.693714944992702	3		958	1060	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709198	117709198	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	84	480	0	ENST00000368508.3:c.1760-1G>A		p.X587_splice	ENST00000368508	NM_002944.2	587			1	2	FACETS	0.807	0.721	0.898	0.807	0.721	0.898	CLONAL	1	TRUE	1	0.693714944992702	2		480	300	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137524722	137524722	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	128	781	2	ENST00000367739.4:c.647C>T	p.Ser216Leu	p.S216L	ENST00000367739	NM_000416.2	216	tCa/tTa	5/7	0.216787253529007	3	FACETS	1	0.964	1	0.552	0.504	0.602	INDETERMINATE	1	TRUE	1	0.693714944992702	3		783	450	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265405	152265405	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	102	450	0	ENST00000206249.3:c.858G>C	p.Met286Ile	p.M286I	ENST00000206249	NM_000125.3	286	atG/atC	4/8	0.216787253529007	3	FACETS	0.943	0.849	1	0.472	0.424	0.521	INDETERMINATE	1	TRUE	1	0.693714944992702	3		450	420	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874425	151874425	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	93	587	0	ENST00000262189.6:c.8113G>C	p.Glu2705Gln	p.E2705Q	ENST00000262189	NM_170606.2	2705	Gag/Cag	38/59	0.693746975033016	4	FACETS	0.827	0.737	0.922	0.276	0.245	0.308	CLONAL	1	TRUE	1	0.693714944992702	4		587	549	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880094	151880094	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	124	708	0	ENST00000262189.6:c.5230G>C	p.Glu1744Gln	p.E1744Q	ENST00000262189	NM_170606.2	1744	Gaa/Caa	35/59	0.693746975033016	4	FACETS	1	0.953	1	0.359	0.326	0.394	CLONAL	1	TRUE	1	0.693714944992702	4		708	562	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891193	151891193	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	248	674	0	ENST00000262189.6:c.4561G>T	p.Glu1521Ter	p.E1521*	ENST00000262189	NM_170606.2	1521	Gaa/Taa	31/59	0.693746975033016	4	FACETS	0.831	0.78	0.882	0.554	0.52	0.588	CLONAL	2	TRUE	1	0.693714944992702	4		674	729	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27190584	27190610	+	inframe_deletion	In_Frame_Del	DEL	TCATCAACATCAGCTCTGAGCCTTACT	TCATCAACATCAGCTCTGAGCCTTACT	-	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	174	971	0	ENST00000380036.4:c.1386_1412del	p.Ile463_Phe471del	p.I463_F471del	ENST00000380036	NM_000459.3	462	gTCATCAACATCAGCTCTGAGCCTTACTtt/gtt	10/23	1	2	FACETS	0.943	0.874	1	0.943	0.874	1	CLONAL	1	TRUE	1	0.693714944992702	2		971	532	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125437	7125437	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3475	205	1000	0	ENST00000302850.5:c.3115G>C	p.Glu1039Gln	p.E1039Q	ENST00000302850	NM_000208.2	1039	Gag/Cag	17/22	0.693714944992702	14	FACETS	0.829	0.764	0.897			1	CLONAL	1	TRUE	NA	0.693714944992702	14		1000	3680	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410688	63410688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	58	855	1	ENST00000330258.3:c.2479G>A	p.Glu827Lys	p.E827K	ENST00000330258	NM_152424.3	827	Gag/Aag	2/2	0.549898376183417	4	FACETS	0.265	0.227	0.308			1	SUBCLONAL	1	TRUE	NA	0.693714944992702	4		856	1067	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872900	136872900	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012040-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1524	314	650	0	ENST00000241393.3:c.598C>G	p.Gln200Glu	p.Q200E	ENST00000241393	NM_003467.2	200	Cag/Gag	2/2	0.132514108727562	4	FACETS	1	0.993	1	0.722	0.678	0.767	INDETERMINATE	1	TRUE	2	0.31	4		650	1838	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437906	52437906	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0012040-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	206	588	1	ENST00000460680.1:c.1255A>T	p.Lys419Ter	p.K419*	ENST00000460680	NM_004656.3	419	Aag/Tag	13/17	0.3	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.31	1		589	989	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137271	64137271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012040-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	134	329	0	ENST00000334205.4:c.1703C>T	p.Thr568Met	p.T568M	ENST00000334205	NM_003942.2	568	aCg/aTg	14/17	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.31	2		329	725	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191510	10191510	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012040-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	95	265	0	ENST00000256474.2:c.503del	p.Ser168ThrfsTer2	p.S168Tfs*2	ENST00000256474	NM_000551.3	168	aGc/ac	3/3	0.3	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.31	1		265	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0012105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	308	385	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.772457459429771	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.772457459429771	1		385	443	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617459	158617459	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0012105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	646	816	0	ENST00000263640.3:c.1197T>G	p.Tyr399Ter	p.Y399*	ENST00000263640	NM_001105.4	399	taT/taG	9/11	0.268070124481751	1	FACETS	0.664	0.641	0.689	0.664	0.641	0.689	INDETERMINATE	1	TRUE	0	0.772457459429771	1		816	1545	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151833936	151833936	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	179	372	0	ENST00000262189.6:c.14717G>C	p.Cys4906Ser	p.C4906S	ENST00000262189	NM_170606.2	4906	tGc/tCc	59/59	0.568171096103755	3	FACETS	0.541	0.497	0.586			1	SUBCLONAL	1	TRUE	NA	0.772457459429771	3		372	1188	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	208	463	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.269300692016464	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.344386820394576	3		463	658	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057520005	NA	P-0012143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	227	761	0	ENST00000269305.4:c.820G>C	p.Val274Leu	p.V274L	ENST00000269305	NM_001126112.2	274	Gtt/Ctt	8/11	0.28826830994006	2	FACETS	0.761	0.71	0.813	0.761	0.71	0.813	SUBCLONAL	2	TRUE	0	0.344386820394576	2		761	866	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158141	47158141	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	274	720	0	ENST00000409792.3:c.4558T>C	p.Cys1520Arg	p.C1520R	ENST00000409792	NM_014159.6	1520	Tgt/Cgt	4/21	0.278036246945561	4	FACETS	0.9	0.844	0.957			1	CLONAL	2	TRUE	NA	0.344386820394576	4		720	1189	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103510691	103510691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	196	400	0	ENST00000355739.4:c.595G>A	p.Glu199Lys	p.E199K	ENST00000355739	NM_000123.3	199	Gaa/Aaa	6/15	0.243527134429479	3	FACETS	1	0.975	1	0.733	0.682	0.784	CLONAL	2	TRUE	0	0.344386820394576	3		400	607	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347538	91347538	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	99	485	0	ENST00000355112.3:c.3700G>A	p.Gly1234Ser	p.G1234S	ENST00000355112	NM_000057.2	1234	Ggt/Agt	19/22	0.269300692016464	3	FACETS	0.796	0.71	0.887	0.398	0.355	0.444	SUBCLONAL	1	TRUE	1	0.344386820394576	3		485	847	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087050	27087401	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTGCCTGTAATCCCAGCCACTCGGGAGGCTGAGGCAGGAGAATTGCTTGAACCCAGGAGTCAGAGGTTGCGATGAGCCGAGACGTGCCATTGCACTCCAGCCTGGGCAACGAGTGAAACACTGTCTCAAAAAAAAAAATTTTTTTTTTTAATAAAAATAGTATCATGACTAAAGAACGTGTGTGATGTATTTGCTCTTGGTTGTTTAAGGAAAATGCTAAGCAAGTAGTAGGATTATTGAAAGTAGAATCTTTCTGCCTAATATTACTAATCCATGTTCTTATATATATGTTCTAGGATCTATCTGGTTCAATAGATGACCTCCCCATGGGGACAGAAGGAGCTCTGAGTC	CTTGCCTGTAATCCCAGCCACTCGGGAGGCTGAGGCAGGAGAATTGCTTGAACCCAGGAGTCAGAGGTTGCGATGAGCCGAGACGTGCCATTGCACTCCAGCCTGGGCAACGAGTGAAACACTGTCTCAAAAAAAAAAATTTTTTTTTTTAATAAAAATAGTATCATGACTAAAGAACGTGTGTGATGTATTTGCTCTTGGTTGTTTAAGGAAAATGCTAAGCAAGTAGTAGGATTATTGAAAGTAGAATCTTTCTGCCTAATATTACTAATCCATGTTCTTATATATATGTTCTAGGATCTATCTGGTTCAATAGATGACCTCCCCATGGGGACAGAAGGAGCTCTGAGTC	-	novel	NA	P-0012143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2	66	2	0	ENST00000324856.7:c.1921-295_1977del		p.X641_splice	ENST00000324856	NM_006015.4	641		5/20	0.269300692016464	3	FACETS		NA	1	1	0.989	1	NA	7	TRUE	1	0.344386820394576	3		2	68	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133278	30133313	+	inframe_deletion	In_Frame_Del	DEL	TGATCTTCTTGATGGCCACGCGAGTCTTGCGCACGT	TGATCTTCTTGATGGCCACGCGAGTCTTGCGCACGT	-	novel	NA	P-0012143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	275	903	0	ENST00000263025.4:c.185_220del	p.His62_Ser74delinsArg	p.H62_S74delinsR	ENST00000263025	NM_002746.2	62	cACGTGCGCAAGACTCGCGTGGCCATCAAGAAGATCAgc/cgc	2/9	0.220524808986463	3	FACETS	0.755	0.708	0.804			1	SUBCLONAL	2	TRUE	NA	0.344386820394576	3		903	1239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0012274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	315	634	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.5659895757205	2	FACETS	0.953	0.91	0.996	0.953	0.91	0.996	CLONAL	2	TRUE	0	0.5659895757205	2		635	584	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191532	10191532	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	127	434	0	ENST00000256474.2:c.525C>A	p.Tyr175Ter	p.Y175*	ENST00000256474	NM_000551.3	175	taC/taA	3/3	0.5659895757205	1	FACETS	0.987	0.907	1	0.987	0.907	1	CLONAL	1	TRUE	0	0.5659895757205	1		434	326	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027076	48027076	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1553413323	NA	P-0012274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	292	458	1	ENST00000234420.5:c.1954G>T	p.Gly652Trp	p.G652W	ENST00000234420	NM_000179.2	652	Ggg/Tgg	4/10	0.5659895757205	4	FACETS	0.94	0.894	0.986	0.94	0.894	0.986	CLONAL	3	TRUE	1	0.5659895757205	4		459	573	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058654	47058654	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	157	604	0	ENST00000409792.3:c.7624G>T	p.Glu2542Ter	p.E2542*	ENST00000409792	NM_014159.6	2542	Gag/Tag	21/21	0.5659895757205	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.5659895757205	1		604	393	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859410	151859410	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	120	540	1	ENST00000262189.6:c.11252G>T	p.Cys3751Phe	p.C3751F	ENST00000262189	NM_170606.2	3751	tGt/tTt	43/59	0.553598503368054	3	FACETS	0.862	0.78	0.948	0.431	0.39	0.474	CLONAL	1	TRUE	1	0.5659895757205	3		541	631	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634443	23634443	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	231	510	0	ENST00000261584.4:c.2843T>G	p.Phe948Cys	p.F948C	ENST00000261584	NM_024675.3	948	tTt/tGt	9/13	0.272026685732811	5	FACETS	1	0.978	1	0.728	0.682	0.775	INDETERMINATE	2	TRUE	2	0.5659895757205	5		510	691	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866607	37866607	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	144	536	0	ENST00000269571.5:c.774C>A	p.Phe258Leu	p.F258L	ENST00000269571		258	ttC/ttA	7/27	0.489560075302519	3	FACETS	1	0.963	1			1	CLONAL	1	TRUE	NA	0.5659895757205	3		536	597	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651549	52651549	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	91	458	0	ENST00000394830.3:c.1547del	p.Lys516ArgfsTer3	p.K516Rfs*3	ENST00000394830	NM_018313.4	516	aAg/ag	15/30	0.5659895757205	1	FACETS	0.985	0.891	1	0.985	0.891	1	CLONAL	1	TRUE	0	0.5659895757205	1		458	234	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578507	7578507	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519977	NA	P-0012305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	267	464	0	ENST00000269305.4:c.423C>G	p.Cys141Trp	p.C141W	ENST00000269305	NM_001126112.2	141	tgC/tgG	5/11	0.415237648416075	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	0	0.415237648416075	1		464	896	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715979	52715979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786205227	NA	P-0012305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	151	586	1	ENST00000322088.6:c.544C>T	p.Arg182Trp	p.R182W	ENST00000322088	NM_014225.5	182	Cgg/Tgg	5/15	0.415237648416075	1	FACETS	0.572	0.522	0.625	0.572	0.522	0.625	SUBCLONAL	1	FALSE	0	0.415237648416075	1		587	1007	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411531	63411531	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1373726900	NA	P-0012305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	294	717	0	ENST00000330258.3:c.1636T>G	p.Leu546Val	p.L546V	ENST00000330258	NM_152424.3	546	Ttg/Gtg	2/2	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.415237648416075	2		717	1364	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591127	67591129	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0012305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	160	378	0	ENST00000274335.5:c.1721_1723del	p.Arg574del	p.R574del	ENST00000274335		574	AGA/-	12/15	0.415237648416075	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	0	0.415237648416075	1		378	553	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183771	10183771	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	101	383	1	ENST00000256474.2:c.240T>A	p.Ser80Arg	p.S80R	ENST00000256474	NM_000551.3	80	agT/agA	1/3	0.460513014755289	1	FACETS	0.87	0.784	0.96	0.87	0.784	0.96	CLONAL	1	FALSE	0	0.460513014755289	1		384	388	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	103	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.154154758670473	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.12	3		473	802	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0012556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	25	555	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	1	2	FACETS	0.866	0.681	1	0.866	0.681	1	CLONAL	1	TRUE	1	0.12	2		555	481	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151947027	151947027	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	29	597	0	ENST00000262189.6:c.1747C>A	p.His583Asn	p.H583N	ENST00000262189	NM_170606.2	583	Cac/Aac	13/59	1	2	FACETS	0.846	0.678	1	0.846	0.678	1	CLONAL	1	TRUE	1	0.12	2		597	571	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992127	72992127	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	62	1018	1	ENST00000268489.5:c.1918G>T	p.Val640Leu	p.V640L	ENST00000268489	NM_006885.3	640	Gtg/Ttg	2/10	0.154154758670473	1	FACETS	0.762	0.658	0.876	1	0.97	1	SUBCLONAL	2	TRUE	0	0.12	1		1019	637	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793161	33793161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777090929	NA	P-0012556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	19	507	0	ENST00000498907.2:c.160G>A	p.Gly54Ser	p.G54S	ENST00000498907	NM_004364.3	54	Ggc/Agc	1/1	1	2	FACETS	0.965	0.732	1	0.965	0.732	1	CLONAL	1	TRUE	1	0.12	2		507	328	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921606	39921606	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	71	467	0	ENST00000378444.4:c.4214C>G	p.Ser1405Trp	p.S1405W	ENST00000378444	NM_001123385.1	1405	tCg/tGg	10/15	1	1	FACETS	1	0.897	1	1	0.986	1	CLONAL	3	TRUE	0	0.12	1		467	362	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	391	821	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.989	0.941	1	0.989	0.941	1	CLONAL	1	TRUE	1	0.71	2		823	1114	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	174	384	2	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	0.825	0.764	0.888	0.825	0.764	0.888	CLONAL	1	TRUE	1	0.71	2		386	594	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	379	828	0	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	1	2	FACETS	0.96	0.913	1	0.96	0.913	1	CLONAL	1	TRUE	1	0.71	2		828	1112	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	323	676	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	1	2	FACETS	0.943	0.892	0.994	0.943	0.892	0.994	CLONAL	1	TRUE	1	0.71	2		676	965	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911144	40911144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776134993	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	308	807	0	ENST00000373198.4:c.2161C>T	p.Arg721Cys	p.R721C	ENST00000373198	NM_133170.3	721	Cgt/Tgt	13/32	1	2	FACETS	0.899	0.849	0.95	0.899	0.849	0.95	CLONAL	1	TRUE	1	0.71	2		807	965	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111958593	111958593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555186772	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	239	403	0	ENST00000375549.3:c.65G>A	p.Arg22Gln	p.R22Q	ENST00000375549	NM_003002.3	22	cGa/cAa	2/4	1	2	FACETS	0.984	0.924	1	0.984	0.924	1	CLONAL	1	TRUE	1	0.71	2		403	684	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721223	176721223	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	153	371	0	ENST00000439151.2:c.6854G>T	p.Arg2285Ile	p.R2285I	ENST00000439151	NM_022455.4	2285	aGa/aTa	23/23	1	2	FACETS	0.958	0.884	1	0.958	0.884	1	CLONAL	1	TRUE	1	0.71	2		371	450	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	323	671	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	0.992	0.94	1	0.992	0.94	1	CLONAL	1	TRUE	1	0.71	2		671	917	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089730	27089730	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	142	336	0	ENST00000324856.7:c.2686G>T	p.Glu896Ter	p.E896*	ENST00000324856	NM_006015.4	896	Gaa/Taa	8/20	1	2	FACETS	0.844	0.775	0.915	0.844	0.775	0.915	CLONAL	1	TRUE	1	0.71	2		336	474	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224793	123224793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	352	910	1	ENST00000218089.9:c.3557G>A	p.Arg1186Gln	p.R1186Q	ENST00000218089	NM_001042749.1	1186	cGa/cAa	32/35	0.139858357351509	1	FACETS	0.538	0.51	0.567	0.538	0.51	0.567	INDETERMINATE	1	TRUE	0	0.71	1		911	1188	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919244	48919244	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913296	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	306	399	0	ENST00000267163.4:c.409G>T	p.Glu137Ter	p.E137*	ENST00000267163	NM_000321.2	137	Gaa/Taa	4/27	1	2	FACETS	0.881	0.844	0.918	1	0.996	1	CLONAL	2	TRUE	1	0.71	2		399	489	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280031	66280031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867811974	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	254	561	0	ENST00000273854.3:c.1658G>A	p.Arg553Gln	p.R553Q	ENST00000273854	NM_004439.5	553	cGa/cAa	7/18	0.139858357351509	1	FACETS	0.602	0.566	0.64	0.602	0.566	0.64	INDETERMINATE	1	TRUE	0	0.71	1		561	766	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951847	2951847	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868687398	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	277	745	0	ENST00000396946.4:c.3103G>A	p.Glu1035Lys	p.E1035K	ENST00000396946	NM_032415.4	1035	Gaa/Aaa	23/25	1	2	FACETS	0.687	0.645	0.73	0.687	0.645	0.73	SUBCLONAL	1	TRUE	1	0.71	2		745	1136	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637141	176637141	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	140	423	0	ENST00000439151.2:c.1741G>T	p.Glu581Ter	p.E581*	ENST00000439151	NM_022455.4	581	Gaa/Taa	5/23	1	2	FACETS	0.565	0.515	0.617	0.565	0.515	0.617	SUBCLONAL	1	TRUE	1	0.71	2		423	698	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131412	202131412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339962485	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	293	548	0	ENST00000358485.4:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000358485	NM_001080125.1	127	cGa/cAa	2/9	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.71	2		548	757	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091386	193091386	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	316	618	0	ENST00000367435.3:c.56T>C	p.Val19Ala	p.V19A	ENST00000367435	NM_024529.4	19	gTg/gCg	1/17	1	2	FACETS	0.957	0.906	1	0.957	0.906	1	CLONAL	1	TRUE	1	0.71	2		618	930	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249457	153249457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	286	598	2	ENST00000281708.4:c.1321C>T	p.Arg441Trp	p.R441W	ENST00000281708	NM_033632.3	441	Cgg/Tgg	9/12	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.71	2		600	803	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562982	29562982	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1306237220	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	311	826	2	ENST00000356175.3:c.3917G>A	p.Arg1306Gln	p.R1306Q	ENST00000356175	NM_000267.3	1306	cGa/cAa	29/57	1	2	FACETS	0.898	0.848	0.948	0.898	0.848	0.948	CLONAL	1	TRUE	1	0.71	2		828	976	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050416	128050416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1453017999	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	177	441	0	ENST00000285398.2:c.241G>A	p.Asp81Asn	p.D81N	ENST00000285398	NM_000122.1	81	Gat/Aat	3/15	1	2	FACETS	0.827	0.766	0.89	0.827	0.766	0.89	CLONAL	1	TRUE	1	0.71	2		441	603	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760714	133760714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755821709	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	287	636	1	ENST00000318560.5:c.3037C>T	p.Arg1013Trp	p.R1013W	ENST00000318560	NM_005157.4	1013	Cgg/Tgg	11/11	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.71	2		637	806	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624245	89624245	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554890335	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	89	136	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	0.92	1	CLONAL	1	TRUE	1	0.71	2		136	245	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5462858	5462858	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	191	361	0	ENST00000381577.3:c.419G>T	p.Arg140Ile	p.R140I	ENST00000381577	NM_014143.3	140	aGa/aTa	4/7	1	2	FACETS	0.978	0.911	1	0.978	0.911	1	CLONAL	1	TRUE	1	0.71	2		361	550	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743948	41743948	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751738506	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	371	762	1	ENST00000301178.4:c.883C>T	p.Arg295Trp	p.R295W	ENST00000301178	NM_021913.4	295	Cgg/Tgg	7/20	1	2	FACETS	0.916	0.87	0.963	0.916	0.87	0.963	CLONAL	1	TRUE	1	0.71	2		763	1141	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874616	151874616	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	212	555	0	ENST00000262189.6:c.7922C>A	p.Ser2641Ter	p.S2641*	ENST00000262189	NM_170606.2	2641	tCa/tAa	38/59	1	2	FACETS	0.768	0.715	0.822	0.768	0.715	0.822	SUBCLONAL	1	TRUE	1	0.71	2		555	778	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255598	16255598	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	298	562	0	ENST00000375759.3:c.2863G>A	p.Glu955Lys	p.E955K	ENST00000375759	NM_015001.2	955	Gaa/Aaa	11/15	1	2	FACETS	0.943	0.891	0.997	0.943	0.891	0.997	CLONAL	1	TRUE	1	0.71	2		562	890	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965013	25965013	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs190294224	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	308	615	0	ENST00000435504.4:c.4193C>T	p.Ser1398Leu	p.S1398L	ENST00000435504		1398	tCg/tTg	13/13	1	2	FACETS	0.959	0.906	1	0.959	0.906	1	CLONAL	1	TRUE	1	0.71	2		615	905	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026290	48026290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147737737	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	228	557	1	ENST00000234420.5:c.1168G>A	p.Asp390Asn	p.D390N	ENST00000234420	NM_000179.2	390	Gat/Aat	4/10	1	2	FACETS	0.924	0.865	0.984	0.924	0.865	0.984	CLONAL	1	TRUE	1	0.71	2		558	695	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149872	99149872	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs777176771	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	260	510	0	ENST00000074304.5:c.184C>T	p.Arg62Ter	p.R62*	ENST00000074304	NM_001134224.1	62	Cga/Tga	5/26	1	2	FACETS	0.913	0.858	0.969	0.913	0.858	0.969	CLONAL	1	TRUE	1	0.71	2		510	802	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095644	178095644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763240080	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	403	852	1	ENST00000397062.3:c.1687G>A	p.Glu563Lys	p.E563K	ENST00000397062	NM_006164.4	563	Gaa/Aaa	5/5	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.71	2		853	1118	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719589	190719589	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	146	361	0	ENST00000441310.2:c.1591A>C	p.Asn531His	p.N531H	ENST00000441310	NM_000534.4	531	Aat/Cat	9/13	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.71	2		361	411	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265007	198265007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773349667	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	196	509	0	ENST00000335508.6:c.2870G>A	p.Arg957Gln	p.R957Q	ENST00000335508	NM_012433.2	957	cGa/cAa	19/25	1	2	FACETS	0.861	0.801	0.923	0.861	0.801	0.923	CLONAL	1	TRUE	1	0.71	2		509	641	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149880	202149880	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	243	555	1	ENST00000358485.4:c.1321G>T	p.Glu441Ter	p.E441*	ENST00000358485	NM_001080125.1	441	Gaa/Taa	8/9	1	2	FACETS	0.916	0.86	0.974	0.916	0.86	0.974	CLONAL	1	TRUE	1	0.71	2		556	747	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927478	49927478	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	408	969	2	ENST00000296474.3:c.3826C>A	p.Leu1276Met	p.L1276M	ENST00000296474	NM_002447.2	1276	Ctg/Atg	19/20	1	2	FACETS	0.899	0.856	0.943	0.899	0.856	0.943	CLONAL	1	TRUE	1	0.71	2		971	1278	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664459	138664459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	178	383	0	ENST00000330315.3:c.1106C>T	p.Ala369Val	p.A369V	ENST00000330315	NM_023067.3	369	gCg/gTg	1/1	1	2	FACETS	0.981	0.912	1	0.981	0.912	1	CLONAL	1	TRUE	1	0.71	2		383	511	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916669	178916669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	383	961	0	ENST00000263967.3:c.56G>T	p.Arg19Ile	p.R19I	ENST00000263967	NM_006218.2	19	aGa/aTa	2/21	1	2	FACETS	0.968	0.92	1	0.968	0.92	1	CLONAL	1	TRUE	1	0.71	2		961	1115	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178943780	178943780	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	203	503	0	ENST00000263967.3:c.2447T>G	p.Ile816Ser	p.I816S	ENST00000263967	NM_006218.2	816	aTt/aGt	17/21	1	2	FACETS	0.909	0.848	0.972	0.909	0.848	0.972	CLONAL	1	TRUE	1	0.71	2		503	629	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167750	185167750	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	405	831	0	ENST00000265026.3:c.1073C>A	p.Ser358Tyr	p.S358Y	ENST00000265026	NM_004721.4	358	tCt/tAt	6/14	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.71	2		831	1091	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455593	189455593	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	273	524	0	ENST00000264731.3:c.127A>C	p.Ser43Arg	p.S43R	ENST00000264731	NM_003722.4	43	Agc/Cgc	2/14	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.71	2		524	756	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593706	55593706	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	130	344	0	ENST00000288135.5:c.1772T>G	p.Phe591Cys	p.F591C	ENST00000288135	NM_000222.2	591	tTt/tGt	11/21	0.139858357351509	1	FACETS	0.615	0.564	0.668	0.615	0.564	0.668	INDETERMINATE	1	TRUE	0	0.71	1		344	384	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976831	55976831	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	274	589	1	ENST00000263923.4:c.1081G>A	p.Glu361Lys	p.E361K	ENST00000263923	NM_002253.2	361	Gaa/Aaa	8/30	0.139858357351509	1	FACETS	0.604	0.569	0.64	0.604	0.569	0.64	INDETERMINATE	1	TRUE	0	0.71	1		590	824	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003187	143003187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	244	461	1	ENST00000262992.4:c.2639G>A	p.Arg880Lys	p.R880K	ENST00000262992	NM_001101669.1	880	aGa/aAa	23/24	1	2	FACETS	0.949	0.891	1	0.949	0.891	1	CLONAL	1	TRUE	1	0.71	2		462	724	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143226689	143226689	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs149208667	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	178	439	0	ENST00000262992.4:c.425G>A	p.Arg142Gln	p.R142Q	ENST00000262992	NM_001101669.1	142	cGa/cAa	7/24	1	2	FACETS	0.863	0.8	0.928	0.863	0.8	0.928	CLONAL	1	TRUE	1	0.71	2		439	581	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944635	38944635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	185	480	1	ENST00000357387.3:c.4826G>A	p.Arg1609His	p.R1609H	ENST00000357387	NM_152756.3	1609	cGt/cAt	36/38	1	2	FACETS	0.987	0.918	1	0.987	0.918	1	CLONAL	1	TRUE	1	0.71	2		481	528	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176614	56176614	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	173	413	0	ENST00000399503.3:c.2164G>T	p.Glu722Ter	p.E722*	ENST00000399503	NM_005921.1	722	Gaa/Taa	12/20	1	2	FACETS	0.944	0.876	1	0.944	0.876	1	CLONAL	1	TRUE	1	0.71	2		413	516	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184116	56184116	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	200	562	1	ENST00000399503.3:c.4321G>T	p.Glu1441Ter	p.E1441*	ENST00000399503	NM_005921.1	1441	Gaa/Taa	19/20	1	2	FACETS	0.832	0.774	0.892	0.832	0.774	0.892	CLONAL	1	TRUE	1	0.71	2		563	677	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564743	86564743	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	308	799	0	ENST00000274376.6:c.475C>G	p.Leu159Val	p.L159V	ENST00000274376	NM_002890.2	159	Ctg/Gtg	1/25	1	2	FACETS	0.884	0.834	0.934	0.884	0.834	0.934	CLONAL	1	TRUE	1	0.71	2		799	982	SUCCESS
APC	324	MSKCC	GRCh37	5	112176686	112176686	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	217	471	0	ENST00000257430.4:c.5395T>G	p.Leu1799Val	p.L1799V	ENST00000257430	NM_000038.5	1799	Tta/Gta	16/16	1	2	FACETS	0.938	0.877	1	0.938	0.877	1	CLONAL	1	TRUE	1	0.71	2		471	652	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923733	131923733	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	193	488	0	ENST00000265335.6:c.1003G>T	p.Glu335Ter	p.E335*	ENST00000265335		335	Gaa/Taa	7/25	1	2	FACETS	0.867	0.806	0.929	0.867	0.806	0.929	CLONAL	1	TRUE	1	0.71	2		488	627	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680248	30680248	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	382	848	0	ENST00000376406.3:c.1471C>T	p.Pro491Ser	p.P491S	ENST00000376406	NM_014641.2	491	Cct/Tct	5/15	1	2	FACETS	0.96	0.913	1	0.96	0.913	1	CLONAL	1	TRUE	1	0.71	2		848	1121	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662766	117662766	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	145	321	0	ENST00000368508.3:c.4699A>C	p.Thr1567Pro	p.T1567P	ENST00000368508	NM_002944.2	1567	Act/Cct	29/43	1	2	FACETS	0.937	0.863	1	0.937	0.863	1	CLONAL	1	TRUE	1	0.71	2		321	436	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700229	117700229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	225	621	0	ENST00000368508.3:c.2590G>A	p.Gly864Arg	p.G864R	ENST00000368508	NM_002944.2	864	Gga/Aga	17/43	1	2	FACETS	0.848	0.793	0.905	0.848	0.793	0.905	CLONAL	1	TRUE	1	0.71	2		621	747	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706908	117706908	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	350	688	0	ENST00000368508.3:c.2242G>T	p.Ala748Ser	p.A748S	ENST00000368508	NM_002944.2	748	Gca/Tca	15/43	1	2	FACETS	0.995	0.944	1	0.995	0.944	1	CLONAL	1	TRUE	1	0.71	2		688	991	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001524	150001524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	166	433	0	ENST00000253339.5:c.2080C>T	p.Arg694Cys	p.R694C	ENST00000253339		694	Cgt/Tgt	4/7	1	2	FACETS	0.808	0.746	0.871	0.808	0.746	0.871	CLONAL	1	TRUE	1	0.71	2		433	579	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265314	152265314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781741770	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	215	453	0	ENST00000206249.3:c.767G>A	p.Arg256Gln	p.R256Q	ENST00000206249	NM_000125.3	256	cGa/cAa	4/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.71	2		453	538	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508337	106508337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760070255	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	68	181	0	ENST00000359195.3:c.331G>A	p.Asp111Asn	p.D111N	ENST00000359195	NM_002649.2	111	Gac/Aac	2/11	1	2	FACETS	0.921	0.815	1	0.921	0.815	1	CLONAL	1	TRUE	1	0.71	2		181	208	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850260	128850260	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	340	723	1	ENST00000249373.3:c.1523A>T	p.Glu508Val	p.E508V	ENST00000249373	NM_005631.4	508	gAg/gTg	9/12	1	2	FACETS	0.879	0.833	0.927	0.879	0.833	0.927	CLONAL	1	TRUE	1	0.71	2		724	1089	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477859	140477859	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs727504375	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	296	700	0	ENST00000288602.6:c.1449A>C	p.Lys483Asn	p.K483N	ENST00000288602	NM_004333.4	483	aaA/aaC	12/18	1	2	FACETS	0.948	0.895	1	0.948	0.895	1	CLONAL	1	TRUE	1	0.71	2		700	880	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346224	152346224	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	455	1043	0	ENST00000359321.1:c.346T>G	p.Phe116Val	p.F116V	ENST00000359321	NM_005431.1	116	Ttt/Gtt	3/3	1	2	FACETS	0.9	0.859	0.942	0.9	0.859	0.942	CLONAL	1	TRUE	1	0.71	2		1043	1424	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606787	43606787	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	257	687	0	ENST00000355710.3:c.1396T>G	p.Phe466Val	p.F466V	ENST00000355710	NM_020975.4	466	Ttt/Gtt	7/20	1	2	FACETS	0.892	0.838	0.947	0.892	0.838	0.947	CLONAL	1	TRUE	1	0.71	2		687	812	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850948	63850948	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	240	503	0	ENST00000279873.7:c.1726G>T	p.Glu576Ter	p.E576*	ENST00000279873	NM_032199.2	576	Gaa/Taa	10/10	1	2	FACETS	0.97	0.91	1	0.97	0.91	1	CLONAL	1	TRUE	1	0.71	2		503	697	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450814	70450814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776722537	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	172	480	2	ENST00000373644.4:c.5654C>T	p.Ser1885Leu	p.S1885L	ENST00000373644	NM_030625.2	1885	tCg/tTg	12/12	1	2	FACETS	0.935	0.867	1	0.935	0.867	1	CLONAL	1	TRUE	1	0.71	2		482	518	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451264	70451264	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	354	740	0	ENST00000373644.4:c.6104A>G	p.His2035Arg	p.H2035R	ENST00000373644	NM_030625.2	2035	cAc/cGc	12/12	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.71	2		740	984	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624289	89624289	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	181	300	0	ENST00000371953.3:c.63C>A	p.Phe21Leu	p.F21L	ENST00000371953	NM_000314.4	21	ttC/ttA	1/9	1	2	FACETS	0.962	0.894	1	0.962	0.894	1	CLONAL	1	TRUE	1	0.71	2		300	530	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098516	108098516	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs147009251	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	77	275	0	ENST00000278616.4:c.86A>C	p.Lys29Thr	p.K29T	ENST00000278616	NM_000051.3	29	aAa/aCa	3/63	1	2	FACETS	0.62	0.548	0.696	0.62	0.548	0.696	SUBCLONAL	1	TRUE	1	0.71	2		275	350	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115747	108115747	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	95	242	0	ENST00000278616.4:c.895G>T	p.Glu299Ter	p.E299*	ENST00000278616	NM_000051.3	299	Gaa/Taa	7/63	1	2	FACETS	0.916	0.827	1	0.916	0.827	1	CLONAL	1	TRUE	1	0.71	2		242	292	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123576	108123576	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	174	379	0	ENST00000278616.4:c.1835T>G	p.Leu612Arg	p.L612R	ENST00000278616	NM_000051.3	612	cTt/cGt	12/63	1	2	FACETS	0.937	0.869	1	0.937	0.869	1	CLONAL	1	TRUE	1	0.71	2		379	523	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198480	108198480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	108	373	0	ENST00000278616.4:c.7084G>T	p.Glu2362Ter	p.E2362*	ENST00000278616	NM_000051.3	2362	Gaa/Taa	48/63	1	2	FACETS	0.651	0.588	0.718	0.651	0.588	0.718	SUBCLONAL	1	TRUE	1	0.71	2		373	467	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242690	46242690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1423871055	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	170	461	1	ENST00000334344.6:c.1652C>T	p.Ser551Leu	p.S551L	ENST00000334344	NM_152641.2	551	tCg/tTg	13/21	1	2	FACETS	0.909	0.842	0.978	0.909	0.842	0.978	CLONAL	1	TRUE	1	0.71	2		462	527	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418362	49418362	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs940848278	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	170	352	0	ENST00000301067.7:c.16051C>T	p.Arg5351Trp	p.R5351W	ENST00000301067	NM_003482.3	5351	Cgg/Tgg	50/54	1	2	FACETS	0.882	0.816	0.949	0.882	0.816	0.949	CLONAL	1	TRUE	1	0.71	2		352	543	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144824	58144824	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1340574386	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	288	647	0	ENST00000257904.6:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000257904	NM_000075.3	135	tGc/tAc	4/8	1	2	FACETS	0.859	0.81	0.91	0.859	0.81	0.91	CLONAL	1	TRUE	1	0.71	2		647	944	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212572	133212572	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	259	581	0	ENST00000320574.5:c.5717C>A	p.Ser1906Tyr	p.S1906Y	ENST00000320574	NM_006231.2	1906	tCt/tAt	42/49	1	2	FACETS	0.927	0.872	0.984	0.927	0.872	0.984	CLONAL	1	TRUE	1	0.71	2		581	787	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95598942	95598942	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	233	500	0	ENST00000393063.1:c.217A>G	p.Ile73Val	p.I73V	ENST00000393063	NM_030621.3	73	Att/Gtt	4/28	1	2	FACETS	0.936	0.877	0.996	0.936	0.877	0.996	CLONAL	1	TRUE	1	0.71	2		500	701	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358576	67358576	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	122	736	1	ENST00000327367.4:c.84G>T	p.Glu28Asp	p.E28D	ENST00000327367	NM_005902.3	28	gaG/gaT	1/9	1	2	FACETS	0.303	0.273	0.335	0.303	0.273	0.335	SUBCLONAL	1	TRUE	1	0.71	2		737	1133	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892306	9892306	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	109	359	0	ENST00000330684.3:c.2184C>A	p.Phe728Leu	p.F728L	ENST00000330684	NM_001134407.1	728	ttC/ttA	11/13	1	2	FACETS	0.693	0.626	0.763	0.693	0.626	0.763	SUBCLONAL	1	TRUE	1	0.71	2		359	443	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637562	23637562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374736398	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	265	536	1	ENST00000261584.4:c.2743G>A	p.Ala915Thr	p.A915T	ENST00000261584	NM_024675.3	915	Gca/Aca	7/13	1	2	FACETS	0.981	0.924	1	0.981	0.924	1	CLONAL	1	TRUE	1	0.71	2		537	761	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58701094	58701094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	557	1235	0	ENST00000305921.3:c.685G>A	p.Glu229Lys	p.E229K	ENST00000305921	NM_003620.3	229	Gaa/Aaa	2/6	1	2	FACETS	0.95	0.912	0.99	0.95	0.912	0.99	CLONAL	1	TRUE	1	0.71	2		1235	1651	SUCCESS
AR	367	MSKCC	GRCh37	X	66905917	66905917	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	313	908	0	ENST00000374690.3:c.1834T>G	p.Cys612Gly	p.C612G	ENST00000374690	NM_000044.3	612	Tgt/Ggt	3/8	0.139858357351509	1	FACETS	0.594	0.562	0.627	0.594	0.562	0.627	INDETERMINATE	1	TRUE	0	0.71	1		908	957	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211869	123211869	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	391	964	0	ENST00000218089.9:c.2736A>C	p.Lys912Asn	p.K912N	ENST00000218089	NM_001042749.1	912	aaA/aaC	27/35	0.139858357351509	1	FACETS	0.71	0.676	0.743	0.71	0.676	0.743	INDETERMINATE	1	TRUE	0	0.71	1		964	1001	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879966	44879970	+	frameshift_variant	Frame_Shift_Del	DEL	TAGTT	TAGTT	-	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	210	678	0	ENST00000377967.4:c.557_561del	p.Ser186LysfsTer9	p.S186Kfs*9	ENST00000377967	NM_021140.2	185	tcTAGTTta/tcta	6/29	0.139858357351509	1	FACETS	0.528	0.492	0.566	0.528	0.492	0.566	INDETERMINATE	1	TRUE	0	0.71	1		678	722	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628345	86628345	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	191	529	1	ENST00000274376.6:c.715del	p.Tyr239ThrfsTer14	p.Y239Tfs*14	ENST00000274376	NM_002890.2	238	gaT/ga	3/25	1	2	FACETS	0.926	0.862	0.992	0.926	0.862	0.992	CLONAL	1	TRUE	1	0.71	2		530	581	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183872	10183872	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs730882032	NA	P-0013078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	34	125	0	ENST00000256474.2:c.340+1G>A		p.X114_splice	ENST00000256474	NM_000551.3	114			0.237047848702057	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.237047848702057	1		125	212	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643943	52643943	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	53	268	1	ENST00000394830.3:c.1953del	p.Lys651AsnfsTer5	p.K651Nfs*5	ENST00000394830	NM_018313.4	651	aaA/aa	17/30	0.237047848702057	1	FACETS	0.998	0.854	1	0.998	0.854	1	CLONAL	1	TRUE	0	0.237047848702057	1		269	395	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197444	106197444	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1316795626	NA	P-0013078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	135	589	0	ENST00000380013.4:c.5777G>A	p.Arg1926His	p.R1926H	ENST00000380013	NM_001127208.2	1926	cGt/cAt	11/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.237047848702057	2		589	1040	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805241	43805241	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0013081-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	43	423	0	ENST00000372470.3:c.690+1G>C		p.X230_splice	ENST00000372470	NM_005373.2	230			1	2	FACETS	0.948	0.792	1	0.948	0.792	1	CLONAL	1	TRUE	1	0.16	2		423	567	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846285	156846285	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013081-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	46	586	0	ENST00000524377.1:c.1726T>G	p.Phe576Val	p.F576V	ENST00000524377	NM_002529.3	576	Ttc/Gtc	14/17	1	2	FACETS	0.72	0.604	0.848	0.72	0.604	0.848	SUBCLONAL	1	TRUE	1	0.16	2		586	799	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426815	121426815	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013081-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	50	516	0	ENST00000257555.6:c.506A>G	p.Lys169Arg	p.K169R	ENST00000257555		169	aAg/aGg	2/10	1	2	FACETS	0.898	0.761	1	0.898	0.761	1	CLONAL	1	TRUE	1	0.16	2		516	696	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267781	7267781	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013081-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	27	294	0	ENST00000302850.5:c.227T>C	p.Leu76Pro	p.L76P	ENST00000302850	NM_000208.2	76	cTc/cCc	2/22	1	2	FACETS	0.823	0.655	1	0.823	0.655	1	CLONAL	1	TRUE	1	0.16	2		294	410	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225449678	225449681	+	frameshift_variant	Frame_Shift_Del	DEL	GCAT	GCAT	-	novel	NA	P-0013081-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	401	707	0	ENST00000264414.4:c.46_49del	p.Met16GlyfsTer7	p.M16Gfs*7	ENST00000264414	NM_003590.4	16	ATGCgg/gg	1/16	0.118232953640334	5	FACETS	0.901	0.857	0.947	1	0.989	1	CLONAL	5	TRUE	1	0.16	5		707	1379	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244990	41244993	+	protein_altering_variant	In_Frame_Del	DEL	TCAA	TCAA	C	novel	NA	P-0013081-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	51	600	0	ENST00000357654.3:c.2555_2558delinsG	p.Leu852_Asp853delinsArg	p.L852_D853delinsR	ENST00000357654	NM_007294.3	852	cTTGAt/cGt	10/23	1	2	FACETS	0.871	0.739	1	0.871	0.739	1	CLONAL	1	TRUE	1	0.16	2		600	732	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0013106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	81	1124	1	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.608	0.536	0.685	0.608	0.536	0.685	SUBCLONAL	1	TRUE	1	0.436848912314768	2		1125	610	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037486	12037486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1259	132	511	0	ENST00000396373.4:c.1117C>T	p.Pro373Ser	p.P373S	ENST00000396373	NM_001987.4	373	Ccc/Tcc	6/8	0.381559664553595	5	FACETS	0.719	0.651	0.792			1	SUBCLONAL	1	TRUE	NA	0.436848912314768	5		511	1391	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163720	32163720	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	105	415	0	ENST00000375023.3:c.5506G>C	p.Glu1836Gln	p.E1836Q	ENST00000375023	NM_004557.3	1836	Gag/Cag	30/30	0.436848912314768	3	FACETS	0.692	0.619	0.769	0.346	0.309	0.385	SUBCLONAL	1	TRUE	1	0.436848912314768	3		415	847	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880244	155880244	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	475	589	0	ENST00000368323.3:c.160A>T	p.Ile54Phe	p.I54F	ENST00000368323	NM_006912.5	54	Att/Ttt	3/6	0.293816402265136	3	FACETS	0.968	0.925	1	0.645	0.617	0.674	CLONAL	2	TRUE	0	0.436848912314768	3		589	1369	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645922	215645922	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs876659965	NA	P-0013106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1314	445	1010	0	ENST00000260947.4:c.676G>C	p.Asp226His	p.D226H	ENST00000260947	NM_000465.2	226	Gat/Cat	4/11	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.436848912314768	2		1010	1759	SUCCESS
ATR	545	MSKCC	GRCh37	3	142253924	142253924	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	160	473	0	ENST00000350721.4:c.3943C>T	p.Gln1315Ter	p.Q1315*	ENST00000350721	NM_001184.3	1315	Cag/Tag	21/47	NA	2	FACETS	0.752	0.689	0.818			1	INDETERMINATE	1	TRUE	NA	0.436848912314768	2		473	974	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272776	142272776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1247295642	NA	P-0013106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	186	643	1	ENST00000350721.4:c.2423C>T	p.Thr808Ile	p.T808I	ENST00000350721	NM_001184.3	808	aCt/aTt	11/47	NA	2	FACETS	0.707	0.651	0.764			1	INDETERMINATE	1	TRUE	NA	0.436848912314768	2		644	1205	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	240515	240515	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	12	71	0	ENST00000264932.6:c.1475C>G	p.Ser492Cys	p.S492C	ENST00000264932	NM_004168.2	492	tCt/tGt	11/15	0.436848912314768	1	FACETS	0.452	0.321	0.609	0.452	0.321	0.609	SUBCLONAL	1	TRUE	0	0.436848912314768	1		71	95	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989514	85989514	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1324	204	767	0	ENST00000263360.6:c.1273C>G	p.Leu425Val	p.L425V	ENST00000263360	NM_003797.3	425	Ctt/Gtt	12/12	1	2	FACETS	0.611	0.565	0.66	0.611	0.565	0.66	SUBCLONAL	1	TRUE	1	0.436848912314768	2		767	1528	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832751	3832751	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1337	195	725	1	ENST00000262367.5:c.1507C>T	p.Gln503Ter	p.Q503*	ENST00000262367	NM_004380.2	503	Cag/Tag	6/31	NA	2	FACETS	0.583	0.537	0.63			1	INDETERMINATE	1	TRUE	NA	0.436848912314768	2		726	1532	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032120	10032120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	114	776	0	ENST00000330684.3:c.703G>A	p.Glu235Lys	p.E235K	ENST00000330684	NM_001134407.1	235	Gag/Aag	3/13	0.339800570022174	1	FACETS	0.362	0.325	0.401	0.362	0.325	0.401	SUBCLONAL	1	TRUE	0	0.436848912314768	1		776	1127	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041626	14041626	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1349	172	829	0	ENST00000311895.7:c.2173G>C	p.Glu725Gln	p.E725Q	ENST00000311895	NM_005236.2	725	Gag/Cag	11/11	0.178606289943359	3	FACETS	0.631	0.578	0.686			1	INDETERMINATE	1	TRUE	NA	0.436848912314768	3		829	1521	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828615	72828615	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1778	246	1279	0	ENST00000268489.5:c.7966C>T	p.Leu2656Phe	p.L2656F	ENST00000268489	NM_006885.3	2656	Ctc/Ttc	9/10	0.255644766409525	1	FACETS	0.435	0.404	0.467	0.435	0.404	0.467	INDETERMINATE	1	TRUE	0	0.436848912314768	1		1279	2024	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917056	50917056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2972	214	1116	1	ENST00000440232.2:c.2308G>A	p.Glu770Lys	p.E770K	ENST00000440232	NM_002691.3	770	Gag/Aag	19/27	0.396522341901134	5	FACETS	0.509	0.47	0.55			1	SUBCLONAL	1	TRUE	NA	0.436848912314768	5		1117	3186	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160227	22160227	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs797044892	NA	P-0013106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	159	719	0	ENST00000215832.6:c.404G>C	p.Arg135Thr	p.R135T	ENST00000215832	NM_002745.4	135	aGa/aCa	3/9	0.436848912314768	1	FACETS	0.522	0.478	0.569	0.522	0.478	0.569	SUBCLONAL	1	TRUE	0	0.436848912314768	1		719	1090	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	145	463	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.885	0.808	0.966	0.885	0.808	0.966	CLONAL	1	TRUE	1	0.391993407040937	2		463	836	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155138	108155138	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200976093	NA	P-0013167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	154	511	1	ENST00000278616.4:c.3931C>T	p.Gln1311Ter	p.Q1311*	ENST00000278616	NM_000051.3	1311	Caa/Taa	26/63	1	2	FACETS	0.961	0.88	1	0.961	0.88	1	CLONAL	1	TRUE	1	0.391993407040937	2		512	818	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822351	72822351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs62639993	NA	P-0013177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1322	103	1076	2	ENST00000268489.5:c.9824C>T	p.Pro3275Leu	p.P3275L	ENST00000268489	NM_006885.3	3275	cCg/cTg	10/10	0.25760607764559	5	FACETS	0.538	0.479	0.6	0.179	0.159	0.2	INDETERMINATE	1	TRUE	2	0.450661725814603	5		1078	1425	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793280	33793280	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1007915253	NA	P-0013177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	31	343	1	ENST00000498907.2:c.41C>A	p.Pro14Gln	p.P14Q	ENST00000498907	NM_004364.3	14	cCg/cAg	1/1	0.25760607764559	5	FACETS	0.501	0.405	0.611	0.167	0.135	0.204	INDETERMINATE	1	TRUE	2	0.450661725814603	5		344	460	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937516	76937516	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	365	262	0	ENST00000373344.5:c.3232G>T	p.Glu1078Ter	p.E1078*	ENST00000373344	NM_000489.3	1078	Gag/Tag	9/35	0.423380294975904	2	FACETS	1	0.986	1			1	CLONAL	3	TRUE	NA	0.450661725814603	2		262	519	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624274	89624274	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs587782187	NA	P-0013245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	14	273	0	ENST00000371953.3:c.48T>A	p.Tyr16Ter	p.Y16*	ENST00000371953	NM_000314.4	16	taT/taA	1/9	1	2	FACETS	0.498	0.36	0.663	0.498	0.36	0.663	SUBCLONAL	1	TRUE	1	0.29	2		273	194	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437694	49437694	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	261	942	4	ENST00000301067.7:c.5276G>A	p.Arg1759His	p.R1759H	ENST00000301067	NM_003482.3	1759	cGc/cAc	22/54	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.29	2		946	1242	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013395-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	220	463	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.214208755540276	2	FACETS	0.968	0.901	1	0.968	0.901	1	CLONAL	2	TRUE	0	0.248974364657156	2		463	913	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0013395-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	240	592	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	1	2	FACETS	0.811	0.756	0.867	1	0.993	1	CLONAL	2	TRUE	1	0.248974364657156	2		592	1189	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291527	15291527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756527298	NA	P-0013395-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	187	720	0	ENST00000263388.2:c.3107G>A	p.Arg1036Gln	p.R1036Q	ENST00000263388	NM_000435.2	1036	cGa/cAa	19/33	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.248974364657156	2		720	1174	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181926	38181926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1559484615	NA	P-0013395-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	55	575	1	ENST00000396334.3:c.550G>A	p.Asp184Asn	p.D184N	ENST00000396334	NM_002468.4	184	Gac/Aac	3/5	1	2	FACETS	0.456	0.389	0.531	0.456	0.389	0.531	SUBCLONAL	1	TRUE	1	0.248974364657156	2		576	968	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332882	152332882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013395-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	224	607	0	ENST00000206249.3:c.1188G>A	p.Met396Ile	p.M396I	ENST00000206249	NM_000125.3	396	atG/atA	5/8	1	2	FACETS	0.762	0.709	0.818	1	0.992	1	SUBCLONAL	2	TRUE	1	0.248974364657156	2		607	1180	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101014	27101028	+	inframe_deletion	In_Frame_Del	DEL	CAATGCCTATCCTGC	CAATGCCTATCCTGC	-	novel	NA	P-0013395-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	202	677	0	ENST00000324856.7:c.4298_4312del	p.Asn1433_Ala1437del	p.N1433_A1437del	ENST00000324856	NM_006015.4	1432	ggCAATGCCTATCCTGCc/ggc	18/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.248974364657156	2		677	1235	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0013401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	690	883	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.556903684254716	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.863756899019134	1		883	863	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913403	NA	P-0013401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	220	662	2	ENST00000349496.5:c.110C>A	p.Ser37Tyr	p.S37Y	ENST00000349496	NM_001904.3	37	tCt/tAt	3/15	0.275483211567169	2	FACETS	0.568	0.529	0.608	0.284	0.264	0.304	INDETERMINATE	1	TRUE	0	0.863756899019134	2		664	897	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633320	8633320	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866980874	NA	P-0013401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	667	853	3	ENST00000356435.5:c.349C>T	p.Arg117Trp	p.R117W	ENST00000356435		117	Cgg/Tgg	3/35	0.275483211567169	2	FACETS	1	0.997	1	0.652	0.632	0.672	INDETERMINATE	1	TRUE	0	0.863756899019134	2		856	1184	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745623	162745623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs572243397	NA	P-0013401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	152	512	0	ENST00000367921.3:c.2038C>T	p.Arg680Cys	p.R680C	ENST00000367921	NM_006182.2	680	Cgc/Tgc	15/18	0.205843686298706	5	FACETS	0.76	0.694	0.829	0.253	0.231	0.277	INDETERMINATE	1	TRUE	2	0.863756899019134	5		512	1063	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971252	15971252	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs118021690	NA	P-0013401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	384	472	0	ENST00000268712.3:c.4697C>T	p.Thr1566Met	p.T1566M	ENST00000268712	NM_006311.3	1566	aCg/aTg	32/46	0.275483211567169	2	FACETS	1	0.995	1	0.644	0.618	0.67	INDETERMINATE	1	TRUE	0	0.863756899019134	2		472	690	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	207	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.505846746227845	5	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	2	0.505846746227845	5		473	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0013565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	154	705	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.505846746227845	1	FACETS	0.815	0.763	0.867	1	0.992	1	CLONAL	2	TRUE	0	0.505846746227845	1		705	279	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0013615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	615	656	4	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.697468776649202	2	FACETS	0.927	0.901	0.952	0.927	0.901	0.952	CLONAL	2	FALSE	0	0.729402235334481	2		660	910	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656879	45656879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370218763	NA	P-0013615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	451	531	0	ENST00000407780.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000407780	NM_001283052.1	93	Cgg/Tgg	3/7	NA	2	FACETS	0.954	0.924	0.983			1	INDETERMINATE	2	FALSE	NA	0.729402235334481	2		531	648	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033844	49033844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853294	NA	P-0013615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	556	557	0	ENST00000267163.4:c.1981C>T	p.Arg661Trp	p.R661W	ENST00000267163	NM_000321.2	661	Cgg/Tgg	20/27	0.697468776649202	2	FACETS	0.873	0.846	0.9	0.873	0.846	0.9	CLONAL	2	FALSE	0	0.729402235334481	2		557	873	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047283	77047283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs972319037	NA	P-0013615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	305	731	0	ENST00000356341.3:c.1261C>T	p.Arg421Trp	p.R421W	ENST00000356341	NM_002576.4	421	Cgg/Tgg	13/15	0.729402235334481	3	FACETS	0.919	0.865	0.974	0.306	0.288	0.325	CLONAL	1	FALSE	0	0.729402235334481	3		731	1242	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191506	10191506	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs5030820	NA	P-0013615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	617	495	0	ENST00000256474.2:c.499C>T	p.Arg167Trp	p.R167W	ENST00000256474	NM_000551.3	167	Cgg/Tgg	3/3	0.729402235334481	3	FACETS	0.922	0.899	0.944	0.922	0.899	0.944	CLONAL	3	FALSE	0	0.729402235334481	3		495	835	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137244	64137244	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774562817	NA	P-0013615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	699	489	1	ENST00000334205.4:c.1676C>T	p.Pro559Leu	p.P559L	ENST00000334205	NM_003942.2	559	cCg/cTg	14/17	0.729402235334481	3	FACETS	0.983	0.962	1	0.983	0.962	1	CLONAL	3	FALSE	0	0.729402235334481	3		490	887	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336625	81336625	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs527951814	NA	P-0013615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	293	641	0	ENST00000222390.5:c.1597C>T	p.Arg533Ter	p.R533*	ENST00000222390	NM_000601.4	533	Cga/Tga	14/18	0.697468776649202	2	FACETS	0.89	0.839	0.941	0.445	0.419	0.471	CLONAL	1	FALSE	0	0.729402235334481	2		641	903	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0013615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	751	609	2	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	0.729402235334481	3	FACETS	0.866	0.844	0.887	0.866	0.844	0.887	CLONAL	3	FALSE	0	0.729402235334481	3		611	1082	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006641	62006641	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149266494	NA	P-0013615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	556	667	0	ENST00000392795.3:c.638C>T	p.Thr213Met	p.T213M	ENST00000392795	NM_001039933.1	213	aCg/aTg	6/6	0.706219609889758	2	FACETS	0.954	0.927	0.98	0.954	0.927	0.98	CLONAL	2	FALSE	0	0.729402235334481	2		667	799	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272266	15272266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1363323415	NA	P-0013615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	113	327	0	ENST00000263388.2:c.6173C>T	p.Ser2058Leu	p.S2058L	ENST00000263388	NM_000435.2	2058	tCg/tTg	33/33	0.618652802818389	4	FACETS	0.821	0.74	0.906	0.41	0.37	0.453	CLONAL	1	FALSE	2	0.729402235334481	4		327	653	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805672	89805672	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs17227396	NA	P-0013615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	291	613	1	ENST00000389301.3:c.4036G>A	p.Ala1346Thr	p.A1346T	ENST00000389301	NM_000135.2	1346	Gcg/Acg	41/43	0.706219609889758	2	FACETS	1	0.969	1	0.517	0.489	0.546	CLONAL	1	FALSE	0	0.729402235334481	2		614	771	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463536	25463536	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1418039680	NA	P-0013615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	589	635	2	ENST00000264709.3:c.2146G>A	p.Val716Ile	p.V716I	ENST00000264709	NM_175629.2	716	Gtc/Atc	18/23	NA	2	FACETS	0.918	0.891	0.943			1	INDETERMINATE	2	FALSE	NA	0.729402235334481	2		637	880	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298578	11298578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146049556	NA	P-0013615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	275	506	2	ENST00000361445.4:c.1883G>A	p.Arg628His	p.R628H	ENST00000361445	NM_004958.3	628	cGc/cAc	12/58	NA	2	FACETS	1	0.966	1			1	INDETERMINATE	1	FALSE	NA	0.729402235334481	2		508	731	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218979	193218979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500011	NA	P-0013615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	295	516	2	ENST00000367435.3:c.1537C>T	p.Arg513Trp	p.R513W	ENST00000367435	NM_024529.4	513	Cgg/Tgg	16/17	0.697468776649202	2	FACETS	0.912	0.861	0.964	0.456	0.43	0.482	CLONAL	1	FALSE	0	0.729402235334481	2		518	887	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946224	81946224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755569519	NA	P-0013615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	612	673	4	ENST00000359376.3:c.1957C>T	p.Arg653Cys	p.R653C	ENST00000359376	NM_002661.3	653	Cgc/Tgc	19/33	0.706219609889758	2	FACETS	0.972	0.946	0.997	0.972	0.946	0.997	CLONAL	2	FALSE	0	0.729402235334481	2		677	863	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223080	5223080	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1020631416	NA	P-0013615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	48	419	1	ENST00000357368.4:c.2723G>A	p.Arg908Gln	p.R908Q	ENST00000357368	NM_002850.3	908	cGg/cAg	18/38	0.618652802818389	4	FACETS	0.298	0.251	0.35	0.149	0.125	0.175	SUBCLONAL	1	FALSE	2	0.729402235334481	4		420	763	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265154	10265154	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	201	466	0	ENST00000340748.4:c.1786C>T	p.Arg596Ter	p.R596*	ENST00000340748		596	Cga/Tga	21/40	0.618652802818389	4	FACETS	1	0.949	1	0.514	0.476	0.553	CLONAL	1	FALSE	2	0.729402235334481	4		466	927	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10283800	10283800	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143598088	NA	P-0013615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1422	420	785	0	ENST00000340748.4:c.686C>T	p.Thr229Met	p.T229M	ENST00000340748		229	aCg/aTg	8/40	0.618652802818389	4	FACETS	1	0.984	1	0.541	0.513	0.569	CLONAL	1	FALSE	2	0.729402235334481	4		785	1842	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353897	15353897	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777912948	NA	P-0013615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	333	399	0	ENST00000263377.2:c.2983C>T	p.Arg995Trp	p.R995W	ENST00000263377	NM_058243.2	995	Cgg/Tgg	14/20	0.618652802818389	4	FACETS	0.881	0.836	0.927	0.881	0.836	0.927	CLONAL	2	FALSE	2	0.729402235334481	4		399	896	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42385015	42385015	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	628	689	1	ENST00000221972.3:c.649A>C	p.Asn217His	p.N217H	ENST00000221972	NM_021601.3	217	Aac/Cac	5/5	0.618652802818389	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	FALSE	2	0.729402235334481	4		690	1452	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890222	72890222	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs199551642	NA	P-0013615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	582	599	1	ENST00000325599.8:c.460C>T	p.Arg154Ter	p.R154*	ENST00000325599	NM_018130.2	154	Cga/Tga	4/11	0.729402235334481	3	FACETS	0.916	0.883	0.948	0.611	0.589	0.632	CLONAL	2	FALSE	0	0.729402235334481	3		600	1189	SUCCESS
APC	324	MSKCC	GRCh37	5	112173357	112173357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	290	655	0	ENST00000257430.4:c.2066C>T	p.Ala689Val	p.A689V	ENST00000257430	NM_000038.5	689	gCa/gTa	16/16	0.729402235334481	4	FACETS	1	0.968	1	0.523	0.491	0.556	CLONAL	1	FALSE	2	0.729402235334481	4		655	1315	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722149	176722149	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146010779	NA	P-0013615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	177	465	1	ENST00000439151.2:c.7780G>A	p.Ala2594Thr	p.A2594T	ENST00000439151	NM_022455.4	2594	Gcc/Acc	23/23	0.729402235334481	4	FACETS	0.889	0.819	0.962	0.445	0.409	0.481	CLONAL	1	FALSE	2	0.729402235334481	4		466	944	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500833	8500834	+	missense_variant	Missense_Mutation	DNP	GT	GT	TA	novel	NA	P-0013615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	188	569	0	ENST00000356435.5:c.2048_2049delinsTA	p.Tyr683Leu	p.Y683L	ENST00000356435		683	tAC/tTA	13/35	0.717628667527096	3	FACETS	0.708	0.654	0.764	0.354	0.327	0.382	SUBCLONAL	1	FALSE	1	0.729402235334481	3		569	994	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039407	47039407	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	265	696	1	ENST00000377604.3:c.1030G>A	p.Gly344Ser	p.G344S	ENST00000377604	NM_001204468.1	344	Ggc/Agc	10/24	0.729402235334481	1	FACETS	0.856	0.812	0.901	0.856	0.812	0.901	CLONAL	1	FALSE	0	0.729402235334481	1		697	539	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717713	89717714	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0013631-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	88	400	0	ENST00000371953.3:c.739_740dup	p.Leu247PhefsTer10	p.L247Ffs*10	ENST00000371953	NM_000314.4	246	-/TT	7/9	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.26	2		400	641	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720820	89720838	+	frameshift_variant	Frame_Shift_Del	DEL	ATCTTGACAAAGCAAATAA	ATCTTGACAAAGCAAATAA	-	novel	NA	P-0013631-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	13	182	0	ENST00000371953.3:c.972_990del	p.Asp324GlufsTer14	p.D324Efs*14	ENST00000371953	NM_000314.4	324	gATCTTGACAAAGCAAATAAa/ga	8/9	1	2	FACETS	0.448	0.32	0.605	0.448	0.32	0.605	SUBCLONAL	1	TRUE	1	0.26	2		182	223	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782702	135782702	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013631-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	108	616	2	ENST00000298552.3:c.1319A>G	p.Asn440Ser	p.N440S	ENST00000298552	NM_001162426.1	440	aAt/aGt	13/23	1	2	FACETS	0.832	0.745	0.924	0.832	0.745	0.924	CLONAL	1	TRUE	1	0.26	2		618	999	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314896	1314896	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs756815530	NA	P-0013631-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	97	504	0	ENST00000400841.2:c.765G>A	p.Trp255Ter	p.W255*	ENST00000400841		255	tgG/tgA	6/6	1	1	FACETS	0.776	0.692	0.867	0.776	0.692	0.867	SUBCLONAL	1	TRUE	0	0.26	1		504	836	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	27	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.121	0.096	0.15	0.121	0.096	0.15	SUBCLONAL	1	TRUE	1	0.64	2		473	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	259	584	1	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	0.64	2		585	684	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748583	40748583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444440253	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	191	565	2	ENST00000373198.4:c.2933C>T	p.Ala978Val	p.A978V	ENST00000373198	NM_133170.3	978	gCg/gTg	21/32	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.64	2		567	549	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850705	63850705	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs201178069	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	109	631	1	ENST00000279873.7:c.1489del	p.Ile497Ter	p.I497*	ENST00000279873	NM_032199.2	495	Aaa/aa	10/10	1	2	FACETS	0.534	0.48	0.591	0.534	0.48	0.591	SUBCLONAL	1	TRUE	1	0.64	2		632	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	275	705	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.64	2		705	691	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238944	5238944	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs946180785	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	26	428	0	ENST00000357368.4:c.1835G>A	p.Arg612His	p.R612H	ENST00000357368	NM_002850.3	612	cGc/cAc	13/38	0.161389291406258	0	FACETS	0.108	0.086	0.134			1	INDETERMINATE	1	TRUE	0	0.64	0		428	270	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	37	603	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.229	0.189	0.275	0.229	0.189	0.275	SUBCLONAL	1	TRUE	1	0.64	2		604	504	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573977	41573977	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201569846	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	112	518	0	ENST00000263253.7:c.6262C>T	p.Arg2088Trp	p.R2088W	ENST00000263253	NM_001429.3	2088	Cgg/Tgg	31/31	1	2	FACETS	0.864	0.784	0.948	0.864	0.784	0.948	CLONAL	1	TRUE	1	0.64	2		518	405	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600407	10600407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867398451	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	46	787	2	ENST00000171111.5:c.1448G>A	p.Arg483His	p.R483H	ENST00000171111	NM_203500.1	483	cGc/cAc	4/6	1	2	FACETS	0.168	0.14	0.198	0.168	0.14	0.198	SUBCLONAL	1	TRUE	1	0.64	2		789	857	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228306	228306	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775143272	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	19	220	0	ENST00000264932.6:c.628C>T	p.Arg210Ter	p.R210*	ENST00000264932	NM_004168.2	210	Cga/Tga	6/15	1	2	FACETS	0.292	0.223	0.374	0.292	0.223	0.374	SUBCLONAL	1	TRUE	1	0.64	2		220	203	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457243	25457243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377577594	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	13	449	0	ENST00000264709.3:c.2644C>T	p.Arg882Cys	p.R882C	ENST00000264709	NM_175629.2	882	Cgc/Tgc	23/23	1	2	FACETS	0.081	0.057	0.111	0.081	0.057	0.111	SUBCLONAL	1	TRUE	1	0.64	2		449	501	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288666	33288666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	84	401	0	ENST00000374542.5:c.886G>A	p.Ala296Thr	p.A296T	ENST00000374542	NM_001141970.1	296	Gca/Aca	3/8	1	2	FACETS	0.622	0.552	0.696	0.622	0.552	0.696	SUBCLONAL	1	TRUE	1	0.64	2		401	422	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310820	123310820	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747502397	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	140	725	2	ENST00000358487.5:c.608G>A	p.Arg203His	p.R203H	ENST00000358487	NM_000141.4	203	cGc/cAc	5/18	1	2	FACETS	0.608	0.555	0.665	0.608	0.555	0.665	SUBCLONAL	1	TRUE	1	0.64	2		727	719	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346592	81346592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764869064	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	221	711	0	ENST00000222390.5:c.1361C>T	p.Thr454Met	p.T454M	ENST00000222390	NM_000601.4	454	aCg/aTg	11/18	1	2	FACETS	0.943	0.881	1	0.943	0.881	1	CLONAL	1	TRUE	1	0.64	2		711	732	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714532	52714532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	170	544	0	ENST00000322088.6:c.290C>T	p.Ala97Val	p.A97V	ENST00000322088	NM_014225.5	97	gCc/gTc	4/15	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.64	2		544	525	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261155	16261155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1032279699	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	35	343	0	ENST00000375759.3:c.8420G>A	p.Arg2807His	p.R2807H	ENST00000375759	NM_015001.2	2807	cGt/cAt	11/15	1	2	FACETS	0.323	0.265	0.387	0.323	0.265	0.387	SUBCLONAL	1	TRUE	1	0.64	2		343	339	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519818	29519818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772496459	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	176	628	2	ENST00000389048.3:c.1753G>A	p.Ala585Thr	p.A585T	ENST00000389048	NM_004304.4	585	Gcc/Acc	9/29	1	2	FACETS	0.891	0.825	0.96	0.891	0.825	0.96	CLONAL	1	TRUE	1	0.64	2		630	617	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450300	50450300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	32	617	0	ENST00000331340.3:c.484C>T	p.Arg162Trp	p.R162W	ENST00000331340	NM_006060.4	162	Cgg/Tgg	5/8	1	2	FACETS	0.196	0.159	0.239	0.196	0.159	0.239	SUBCLONAL	1	TRUE	1	0.64	2		617	509	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164601	36164601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	41	421	0	ENST00000300305.3:c.1274C>T	p.Pro425Leu	p.P425L	ENST00000300305		425	cCg/cTg	8/8	1	2	FACETS	0.366	0.306	0.433	0.366	0.306	0.433	SUBCLONAL	1	TRUE	1	0.64	2		421	350	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294045	1294045	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1213662764	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	179	782	0	ENST00000310581.5:c.956C>T	p.Thr319Met	p.T319M	ENST00000310581	NM_198253.2	319	aCg/aTg	2/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.64	2		782	507	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140829	37140829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	206	609	0	ENST00000373509.5:c.665C>T	p.Ser222Leu	p.S222L	ENST00000373509	NM_002648.3	222	tCg/tTg	5/6	1	2	FACETS	0.997	0.929	1	0.997	0.929	1	CLONAL	1	TRUE	1	0.64	2		609	646	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420101	420101	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	239	716	1	ENST00000399788.2:c.3166C>T	p.Arg1056Trp	p.R1056W	ENST00000399788	NM_001042603.1	1056	Cgg/Tgg	21/28	0.3	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.64	2		717	682	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085972	16085972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs998174759	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	30	480	0	ENST00000281043.3:c.1148G>A	p.Arg383His	p.R383H	ENST00000281043	NM_005378.4	383	cGc/cAc	3/3	1	2	FACETS	0.202	0.162	0.247	0.202	0.162	0.247	SUBCLONAL	1	TRUE	1	0.64	2		480	465	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149590	61149590	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	28	476	0	ENST00000295025.8:c.1780G>T	p.Asp594Tyr	p.D594Y	ENST00000295025	NM_002908.2	594	Gat/Tat	11/11	1	2	FACETS	0.188	0.149	0.232	0.188	0.149	0.232	SUBCLONAL	1	TRUE	1	0.64	2		476	466	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240789	55240789	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138193597	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	177	462	1	ENST00000275493.2:c.2033C>T	p.Thr678Met	p.T678M	ENST00000275493	NM_005228.3	678	aCg/aTg	17/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.64	2		463	476	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779715	3779715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1220965943	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	20	387	0	ENST00000262367.5:c.5333C>T	p.Ser1778Leu	p.S1778L	ENST00000262367	NM_004380.2	1778	tCg/tTg	31/31	1	2	FACETS	0.197	0.15	0.252	0.197	0.15	0.252	SUBCLONAL	1	TRUE	1	0.64	2		387	317	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026752	48026752	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	154	460	1	ENST00000234420.5:c.1630G>T	p.Glu544Ter	p.E544*	ENST00000234420	NM_000179.2	544	Gaa/Taa	4/10	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.64	2		461	473	SUCCESS
APC	324	MSKCC	GRCh37	5	112174212	112174212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	222	704	0	ENST00000257430.4:c.2921G>A	p.Gly974Asp	p.G974D	ENST00000257430	NM_000038.5	974	gGt/gAt	16/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.64	2		704	648	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907683	111907683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146318804	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	47	730	1	ENST00000393256.3:c.457C>T	p.Arg153Trp	p.R153W	ENST00000393256	NM_006538.4	153	Cgg/Tgg	3/4	0.161389291406258	4	FACETS	0.267	0.224	0.314	0.133	0.112	0.157	INDETERMINATE	1	TRUE	2	0.64	4		731	903	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210728	2210728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745700742	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	222	707	1	ENST00000398665.3:c.1225C>T	p.Arg409Cys	p.R409C	ENST00000398665	NM_032482.2	409	Cgc/Tgc	14/28	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.64	2		708	659	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936072	44936072	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1135401809	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	171	362	1	ENST00000377967.4:c.2832+1G>A		p.X944_splice	ENST00000377967	NM_021140.2	944			1	1	FACETS	0.878	0.817	0.939	0.878	0.817	0.939	CLONAL	1	TRUE	0	0.64	1		363	414	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051011	180051011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146167161	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	40	706	1	ENST00000261937.6:c.1472C>T	p.Ala491Val	p.A491V	ENST00000261937	NM_182925.4	491	gCg/gTg	11/30	1	2	FACETS	0.234	0.194	0.278	0.234	0.194	0.278	SUBCLONAL	1	TRUE	1	0.64	2		707	535	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993849	72993849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758323451	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	127	667	2	ENST00000268489.5:c.196G>A	p.Ala66Thr	p.A66T	ENST00000268489	NM_006885.3	66	Gcg/Acg	2/10	1	2	FACETS	0.735	0.669	0.804	0.735	0.669	0.804	SUBCLONAL	1	TRUE	1	0.64	2		669	540	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105667	11105667	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555762188	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	165	437	0	ENST00000358026.2:c.1583G>A	p.Arg528Gln	p.R528Q	ENST00000358026	NM_001128849.1	528	cGg/cAg	9/36	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.64	2		437	439	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101829	11101829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	28	536	0	ENST00000358026.2:c.1249C>T	p.Arg417Cys	p.R417C	ENST00000358026	NM_001128849.1	417	Cgc/Tgc	8/36	1	2	FACETS	0.186	0.148	0.23	0.186	0.148	0.23	SUBCLONAL	1	TRUE	1	0.64	2		536	470	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49724798	49724798	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs138710044	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	14	72	0	ENST00000449682.2:c.469A>C	p.Lys157Gln	p.K157Q	ENST00000449682	NM_020998.3	157	Aag/Cag	4/18	1	2	FACETS	0.684	0.506	0.886	0.684	0.506	0.886	SUBCLONAL	1	TRUE	1	0.64	2		72	64	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933640	39933640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780396086	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	28	302	0	ENST00000378444.4:c.959C>T	p.Ala320Val	p.A320V	ENST00000378444	NM_001123385.1	320	gCg/gTg	4/15	1	1	FACETS	0.263	0.211	0.322	0.263	0.211	0.322	SUBCLONAL	1	TRUE	0	0.64	1		302	226	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715678	30715678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039551	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	50	573	0	ENST00000295754.5:c.1336G>A	p.Asp446Asn	p.D446N	ENST00000295754	NM_003242.5	446	Gat/Aat	5/7	1	2	FACETS	0.257	0.218	0.301	0.257	0.218	0.301	SUBCLONAL	1	TRUE	1	0.64	2		573	607	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206815	36206815	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765528082	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	27	362	2	ENST00000300305.3:c.697C>T	p.Arg233Cys	p.R233C	ENST00000300305		233	Cgc/Tgc	6/8	1	2	FACETS	0.231	0.183	0.285	0.231	0.183	0.285	SUBCLONAL	1	TRUE	1	0.64	2		364	366	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443576	29443576	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750194005	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	46	614	1	ENST00000389048.3:c.3641G>A	p.Arg1214His	p.R1214H	ENST00000389048	NM_004304.4	1214	cGc/cAc	23/29	1	2	FACETS	0.247	0.208	0.291	0.247	0.208	0.291	SUBCLONAL	1	TRUE	1	0.64	2		615	581	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136847	55136847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	66	726	0	ENST00000257290.5:c.1169G>A	p.Gly390Asp	p.G390D	ENST00000257290	NM_006206.4	390	gGc/gAc	8/23	1	2	FACETS	0.265	0.229	0.304	0.265	0.229	0.304	SUBCLONAL	1	TRUE	1	0.64	2		726	779	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713738	30713738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893813	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	84	375	0	ENST00000295754.5:c.1063G>A	p.Ala355Thr	p.A355T	ENST00000295754	NM_003242.5	355	Gcc/Acc	4/7	1	2	FACETS	0.698	0.621	0.78	0.698	0.621	0.78	SUBCLONAL	1	TRUE	1	0.64	2		375	376	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435612	110435612	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1240327417	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	14	178	2	ENST00000375856.3:c.2789G>A	p.Arg930His	p.R930H	ENST00000375856	NM_003749.2	930	cGc/cAc	1/2	1	2	FACETS	0.238	0.172	0.317	0.238	0.172	0.317	SUBCLONAL	1	TRUE	1	0.64	2		180	184	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055755	152055755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1403418496	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	36	576	0	ENST00000262189.6:c.167G>A	p.Arg56Gln	p.R56Q	ENST00000262189	NM_170606.2	56	cGa/cAa	2/59	1	2	FACETS	0.197	0.161	0.237	0.197	0.161	0.237	SUBCLONAL	1	TRUE	1	0.64	2		576	572	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44520566	44520566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	216	483	1	ENST00000291552.4:c.196C>T	p.Arg66Cys	p.R66C	ENST00000291552	NM_006758.2	66	Cgc/Tgc	3/8	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.64	2		484	647	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400005	139400005	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1479377696	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	180	570	0	ENST00000277541.6:c.4343C>T	p.Ala1448Val	p.A1448V	ENST00000277541	NM_017617.3	1448	gCg/gTg	25/34	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.64	2		570	506	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420253	49420253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758730277	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	48	680	0	ENST00000301067.7:c.15496G>A	p.Ala5166Thr	p.A5166T	ENST00000301067	NM_003482.3	5166	Gct/Act	48/54	1	2	FACETS	0.214	0.18	0.251	0.214	0.18	0.251	SUBCLONAL	1	TRUE	1	0.64	2		680	701	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158382	108158382	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781785	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	213	523	1	ENST00000278616.4:c.4049C>T	p.Thr1350Met	p.T1350M	ENST00000278616	NM_000051.3	1350	aCg/aTg	27/63	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.64	2		524	611	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654553	29654553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876657714	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	44	574	0	ENST00000356175.3:c.5242C>T	p.Arg1748Ter	p.R1748*	ENST00000356175	NM_000267.3	1748	Cga/Tga	37/57	1	2	FACETS	0.194	0.162	0.23	0.194	0.162	0.23	SUBCLONAL	1	TRUE	1	0.64	2		574	708	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739881	145739881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764297840	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	116	619	3	ENST00000428558.2:c.1649C>T	p.Ala550Val	p.A550V	ENST00000428558	NM_004260.3	550	gCg/gTg	10/22	1	2	FACETS	0.618	0.558	0.68	0.618	0.558	0.68	SUBCLONAL	1	TRUE	1	0.64	2		622	587	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914722	39914722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	42	439	0	ENST00000378444.4:c.4640G>A	p.Arg1547Gln	p.R1547Q	ENST00000378444	NM_001123385.1	1547	cGa/cAa	12/15	1	1	FACETS	0.208	0.173	0.246	0.208	0.173	0.246	SUBCLONAL	1	TRUE	0	0.64	1		439	429	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267797	7267797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	69	410	1	ENST00000302850.5:c.211G>A	p.Glu71Lys	p.E71K	ENST00000302850	NM_000208.2	71	Gaa/Aaa	2/22	1	2	FACETS	0.55	0.481	0.624	0.55	0.481	0.624	SUBCLONAL	1	TRUE	1	0.64	2		411	392	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610694	52610694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753432959	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	179	511	1	ENST00000394830.3:c.3479G>A	p.Arg1160Gln	p.R1160Q	ENST00000394830	NM_018313.4	1160	cGa/cAa	23/30	1	2	FACETS	0.969	0.899	1	0.969	0.899	1	CLONAL	1	TRUE	1	0.64	2		512	577	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240695	55240695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764359156	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	38	677	2	ENST00000275493.2:c.1939G>A	p.Ala647Thr	p.A647T	ENST00000275493	NM_005228.3	647	Gcc/Acc	17/28	1	2	FACETS	0.197	0.162	0.236	0.197	0.162	0.236	SUBCLONAL	1	TRUE	1	0.64	2		679	602	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273974	10273974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773569899	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	294	756	1	ENST00000330684.3:c.295G>A	p.Val99Met	p.V99M	ENST00000330684	NM_001134407.1	99	Gtg/Atg	2/13	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.64	2		757	652	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038876	12038876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	60	575	1	ENST00000396373.4:c.1169C>T	p.Thr390Ile	p.T390I	ENST00000396373	NM_001987.4	390	aCc/aTc	7/8	1	2	FACETS	0.242	0.208	0.279	0.242	0.208	0.279	SUBCLONAL	1	TRUE	1	0.64	2		576	775	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254522	1254522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	29	675	0	ENST00000310581.5:c.3256C>T	p.Arg1086Cys	p.R1086C	ENST00000310581	NM_198253.2	1086	Cgt/Tgt	15/16	1	2	FACETS	0.184	0.147	0.226	0.184	0.147	0.226	SUBCLONAL	1	TRUE	1	0.64	2		675	492	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112422	115112422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775182377	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	28	428	2	ENST00000257566.3:c.1318G>A	p.Ala440Thr	p.A440T	ENST00000257566	NM_016569.3	440	Gcc/Acc	7/8	1	2	FACETS	0.237	0.189	0.292	0.237	0.189	0.292	SUBCLONAL	1	TRUE	1	0.64	2		430	369	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589618	67589618	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519838	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	118	308	0	ENST00000274335.5:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000274335		461	Cga/Tga	10/15	1	2	FACETS	0.953	0.868	1	0.953	0.868	1	CLONAL	1	TRUE	1	0.64	2		308	387	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048632	180048632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	78	389	2	ENST00000261937.6:c.1930G>A	p.Ala644Thr	p.A644T	ENST00000261937	NM_182925.4	644	Gcg/Acg	13/30	1	2	FACETS	0.717	0.635	0.804	0.717	0.635	0.804	SUBCLONAL	1	TRUE	1	0.64	2		391	340	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989563	85989563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1363668348	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	208	520	1	ENST00000263360.6:c.1322G>A	p.Arg441Gln	p.R441Q	ENST00000263360	NM_003797.3	441	cGa/cAa	12/12	0.134266970954408	1	FACETS	0.669	0.624	0.715	0.669	0.624	0.715	INDETERMINATE	1	TRUE	0	0.64	1		521	661	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533778	63533778	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368525111	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	37	551	2	ENST00000307078.5:c.1376G>A	p.Arg459His	p.R459H	ENST00000307078	NM_004655.3	459	cGc/cAc	6/11	1	2	FACETS	0.248	0.204	0.297	0.248	0.204	0.297	SUBCLONAL	1	TRUE	1	0.64	2		553	466	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563383	21563383	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	56	789	1	ENST00000382592.4:c.536C>T	p.Ser179Leu	p.S179L	ENST00000382592	NM_014572.2	179	tCg/tTg	4/8	1	2	FACETS	0.265	0.226	0.307	0.265	0.226	0.307	SUBCLONAL	1	TRUE	1	0.64	2		790	661	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533556	63533556	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147716924	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	46	756	0	ENST00000307078.5:c.1598C>T	p.Ala533Val	p.A533V	ENST00000307078	NM_004655.3	533	gCg/gTg	6/11	1	2	FACETS	0.224	0.188	0.264	0.224	0.188	0.264	SUBCLONAL	1	TRUE	1	0.64	2		756	642	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610522	81610522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368452281	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	261	662	2	ENST00000298171.2:c.2120G>A	p.Arg707Gln	p.R707Q	ENST00000298171	NM_000369.2	707	cGg/cAg	10/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.64	2		664	694	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306960	65306960	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	48	708	1	ENST00000342505.4:c.2617C>T	p.Arg873Cys	p.R873C	ENST00000342505	NM_002227.2	873	Cgc/Tgc	19/25	1	2	FACETS	0.248	0.209	0.291	0.248	0.209	0.291	SUBCLONAL	1	TRUE	1	0.64	2		709	605	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372669	81372669	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs764746019	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	206	627	1	ENST00000222390.5:c.865G>A	p.Ala289Thr	p.A289T	ENST00000222390	NM_000601.4	289	Gct/Act	7/18	1	2	FACETS	0.983	0.916	1	0.983	0.916	1	CLONAL	1	TRUE	1	0.64	2		628	655	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444519	187444519	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	55	694	0	ENST00000232014.4:c.1708G>A	p.Gly570Ser	p.G570S	ENST00000232014	NM_001130845.1	570	Ggt/Agt	7/10	1	2	FACETS	0.248	0.211	0.288	0.248	0.211	0.288	SUBCLONAL	1	TRUE	1	0.64	2		694	694	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214637	5214637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757423838	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	175	714	3	ENST00000357368.4:c.4429C>T	p.Arg1477Cys	p.R1477C	ENST00000357368	NM_002850.3	1477	Cgt/Tgt	29/38	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.64	2		717	531	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72873637	72873637	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	228	585	0	ENST00000325599.8:c.665A>C	p.Lys222Thr	p.K222T	ENST00000325599	NM_018130.2	222	aAa/aCa	6/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.64	2		585	670	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710554	40710554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746059787	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	154	519	0	ENST00000373198.4:c.4297C>T	p.Arg1433Cys	p.R1433C	ENST00000373198	NM_133170.3	1433	Cgt/Tgt	31/32	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.64	2		519	473	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117749	115117749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs554364556	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	45	691	0	ENST00000257566.3:c.686C>T	p.Thr229Met	p.T229M	ENST00000257566	NM_016569.3	229	aCg/aTg	3/8	1	2	FACETS	0.2	0.167	0.236	0.2	0.167	0.236	SUBCLONAL	1	TRUE	1	0.64	2		691	703	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650879	37650879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs191899574	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	44	700	3	ENST00000447079.4:c.2351G>A	p.Arg784Gln	p.R784Q	ENST00000447079	NM_015083.1	784	cGa/cAa	5/14	1	2	FACETS	0.187	0.156	0.221	0.187	0.156	0.221	SUBCLONAL	1	TRUE	1	0.64	2		703	736	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763488	41763488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746364612	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	36	716	0	ENST00000301178.4:c.2287C>T	p.Arg763Cys	p.R763C	ENST00000301178	NM_021913.4	763	Cgc/Tgc	19/20	1	2	FACETS	0.178	0.145	0.214	0.178	0.145	0.214	SUBCLONAL	1	TRUE	1	0.64	2		716	633	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244115	133244115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200825008	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	47	619	4	ENST00000320574.5:c.2293C>T	p.Arg765Cys	p.R765C	ENST00000320574	NM_006231.2	765	Cgt/Tgt	20/49	1	2	FACETS	0.212	0.178	0.25	0.212	0.178	0.25	SUBCLONAL	1	TRUE	1	0.64	2		623	692	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801025	1801025	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140087676	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	134	647	0	ENST00000260795.2:c.154G>A	p.Gly52Ser	p.G52S	ENST00000260795		52	Ggc/Agc	2/17	1	2	FACETS	0.958	0.878	1	0.958	0.878	1	CLONAL	1	TRUE	1	0.64	2		647	437	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584747	187584747	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1358297166	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	25	479	2	ENST00000441802.2:c.3286C>T	p.Arg1096Ter	p.R1096*	ENST00000441802	NM_005245.3	1096	Cga/Tga	3/27	1	2	FACETS	0.16	0.126	0.2	0.16	0.126	0.2	SUBCLONAL	1	TRUE	1	0.64	2		481	487	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480443	57480443	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	148	332	0	ENST00000371085.3:c.438C>A	p.Phe146Leu	p.F146L	ENST00000371085	NM_000516.4	146	ttC/ttA	6/13	1	2	FACETS	0.964	0.887	1	0.964	0.887	1	CLONAL	1	TRUE	1	0.64	2		332	480	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190705	11190705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369088781	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	81	709	2	ENST00000361445.4:c.5494G>A	p.Ala1832Thr	p.A1832T	ENST00000361445	NM_004958.3	1832	Gcc/Acc	39/58	1	2	FACETS	0.403	0.355	0.454	0.403	0.355	0.454	SUBCLONAL	1	TRUE	1	0.64	2		711	628	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190746	11190746	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs563143860	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	254	645	0	ENST00000361445.4:c.5453G>A	p.Arg1818His	p.R1818H	ENST00000361445	NM_004958.3	1818	cGt/cAt	39/58	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.64	2		645	631	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300515	11300515	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	80	751	0	ENST00000361445.4:c.1631C>A	p.Ser544Tyr	p.S544Y	ENST00000361445	NM_004958.3	544	tCc/tAc	11/58	1	2	FACETS	0.357	0.314	0.403	0.357	0.314	0.403	SUBCLONAL	1	TRUE	1	0.64	2		751	701	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258019	16258019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	27	474	0	ENST00000375759.3:c.5284C>T	p.Pro1762Ser	p.P1762S	ENST00000375759	NM_015001.2	1762	Cca/Tca	11/15	1	2	FACETS	0.168	0.133	0.209	0.168	0.133	0.209	SUBCLONAL	1	TRUE	1	0.64	2		474	501	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261085	16261085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146051974	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	112	322	1	ENST00000375759.3:c.8350C>T	p.Arg2784Trp	p.R2784W	ENST00000375759	NM_015001.2	2784	Cgg/Tgg	11/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.64	2		323	292	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099936	27099936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773264329	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	112	652	2	ENST00000324856.7:c.3815C>T	p.Ala1272Val	p.A1272V	ENST00000324856	NM_006015.4	1272	gCg/gTg	15/20	1	2	FACETS	0.629	0.568	0.694	0.629	0.568	0.694	SUBCLONAL	1	TRUE	1	0.64	2		654	556	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101205	27101205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773031590	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	30	658	1	ENST00000324856.7:c.4487C>T	p.Thr1496Ile	p.T1496I	ENST00000324856	NM_006015.4	1496	aCc/aTc	18/20	1	2	FACETS	0.159	0.127	0.195	0.159	0.127	0.195	SUBCLONAL	1	TRUE	1	0.64	2		659	590	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809476	36809476	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	27	453	2	ENST00000373129.3:c.989C>T	p.Ala330Val	p.A330V	ENST00000373129	NM_032017.1	330	gCc/gTc	10/12	1	2	FACETS	0.179	0.142	0.222	0.179	0.142	0.222	SUBCLONAL	1	TRUE	1	0.64	2		455	471	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937680	36937680	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	68	783	0	ENST00000361632.4:c.1058A>G	p.Gln353Arg	p.Q353R	ENST00000361632		353	cAg/cGg	8/16	1	2	FACETS	0.298	0.259	0.341	0.298	0.259	0.341	SUBCLONAL	1	TRUE	1	0.64	2		783	713	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805760	43805760	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	34	747	0	ENST00000372470.3:c.816G>C	p.Trp272Cys	p.W272C	ENST00000372470	NM_005373.2	272	tgG/tgC	5/12	1	2	FACETS	0.173	0.141	0.21	0.173	0.141	0.21	SUBCLONAL	1	TRUE	1	0.64	2		747	613	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814630	43814630	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	103	617	1	ENST00000372470.3:c.1425C>A	p.Ser475Arg	p.S475R	ENST00000372470	NM_005373.2	475	agC/agA	9/12	1	2	FACETS	0.66	0.593	0.73	0.66	0.593	0.73	SUBCLONAL	1	TRUE	1	0.64	2		618	488	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818246	43818246	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	48	839	1	ENST00000372470.3:c.1711C>A	p.Leu571Ile	p.L571I	ENST00000372470	NM_005373.2	571	Ctc/Atc	12/12	1	2	FACETS	0.204	0.171	0.239	0.204	0.171	0.239	SUBCLONAL	1	TRUE	1	0.64	2		840	737	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795024	45795024	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	50	678	0	ENST00000450313.1:c.1604C>A	p.Ser535Tyr	p.S535Y	ENST00000450313	NM_012222.2	535	tCt/tAt	16/16	1	2	FACETS	0.223	0.188	0.261	0.223	0.188	0.261	SUBCLONAL	1	TRUE	1	0.64	2		678	701	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799228	45799228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	36	476	1	ENST00000450313.1:c.205G>A	p.Ala69Thr	p.A69T	ENST00000450313	NM_012222.2	69	Gcc/Acc	3/16	1	2	FACETS	0.242	0.198	0.291	0.242	0.198	0.291	SUBCLONAL	1	TRUE	1	0.64	2		477	465	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439764	51439764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	39	457	0	ENST00000262662.1:c.329C>T	p.Ala110Val	p.A110V	ENST00000262662		110	gCt/gTt	4/4	1	2	FACETS	0.219	0.181	0.261	0.219	0.181	0.261	SUBCLONAL	1	TRUE	1	0.64	2		457	557	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305370	65305370	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771621700	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	239	812	1	ENST00000342505.4:c.2758G>A	p.Ala920Thr	p.A920T	ENST00000342505	NM_002227.2	920	Gct/Act	20/25	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.64	2		813	729	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428582	78428582	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	36	554	2	ENST00000370768.2:c.1217C>A	p.Ser406Tyr	p.S406Y	ENST00000370768	NM_003902.3	406	tCt/tAt	14/20	1	2	FACETS	0.181	0.148	0.218	0.181	0.148	0.218	SUBCLONAL	1	TRUE	1	0.64	2		556	622	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736474	85736474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	335	921	0	ENST00000370580.1:c.173G>A	p.Arg58Gln	p.R58Q	ENST00000370580	NM_003921.4	58	cGa/cAa	2/3	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.64	2		921	984	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117712794	117712794	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	160	490	0	ENST00000369458.3:c.33-1G>T		p.X11_splice	ENST00000369458	NM_024626.3	11			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.64	2		490	471	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166118	118166118	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	46	629	0	ENST00000369448.3:c.628G>A	p.Val210Met	p.V210M	ENST00000369448	NM_017709.3	210	Gtg/Atg	2/2	1	2	FACETS	0.265	0.223	0.312	0.265	0.223	0.312	SUBCLONAL	1	TRUE	1	0.64	2		629	542	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120457988	120457988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587616520	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	29	459	3	ENST00000256646.2:c.7357C>T	p.Arg2453Trp	p.R2453W	ENST00000256646	NM_024408.3	2453	Cgg/Tgg	34/34	1	2	FACETS	0.208	0.166	0.255	0.208	0.166	0.255	SUBCLONAL	1	TRUE	1	0.64	2		462	436	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464428	120464428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	19	412	0	ENST00000256646.2:c.5218C>T	p.Leu1740Phe	p.L1740F	ENST00000256646	NM_024408.3	1740	Ctc/Ttc	29/34	1	2	FACETS	0.162	0.123	0.209	0.162	0.123	0.209	SUBCLONAL	1	TRUE	1	0.64	2		412	366	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471608	120471608	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	33	474	0	ENST00000256646.2:c.3883G>A	p.Ala1295Thr	p.A1295T	ENST00000256646	NM_024408.3	1295	Gcc/Acc	23/34	1	2	FACETS	0.2	0.162	0.243	0.2	0.162	0.243	SUBCLONAL	1	TRUE	1	0.64	2		474	515	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837949	156837949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150271893	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	28	625	3	ENST00000524377.1:c.482G>A	p.Arg161His	p.R161H	ENST00000524377	NM_002529.3	161	cGc/cAc	5/17	1	2	FACETS	0.167	0.133	0.206	0.167	0.133	0.206	SUBCLONAL	1	TRUE	1	0.64	2		628	524	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175846	176175846	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	47	171	0	ENST00000367669.3:c.269G>A	p.Ser90Asn	p.S90N	ENST00000367669	NM_022457.5	90	aGc/aAc	1/20	1	2	FACETS	0.821	0.703	0.946	0.821	0.703	0.946	CLONAL	1	TRUE	1	0.64	2		171	179	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651132	206651132	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	49	710	0	ENST00000367120.3:c.742G>T	p.Gly248Cys	p.G248C	ENST00000367120	NM_014002.3	248	Ggt/Tgt	8/22	1	2	FACETS	0.257	0.217	0.301	0.257	0.217	0.301	SUBCLONAL	1	TRUE	1	0.64	2		710	595	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253359	226253359	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	130	380	0	ENST00000366813.1:c.131C>A	p.Pro44His	p.P44H	ENST00000366813		44	cCt/cAt	2/3	1	2	FACETS	0.809	0.738	0.883	0.809	0.738	0.883	CLONAL	1	TRUE	1	0.64	2		380	502	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226549742	226549742	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs201340386	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	257	702	0	ENST00000366794.5:c.2891T>C	p.Leu964Pro	p.L964P	ENST00000366794	NM_001618.3	964	cTg/cCg	22/23	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.64	2		702	650	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570760	226570760	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	131	391	0	ENST00000366794.5:c.1136C>A	p.Ala379Asp	p.A379D	ENST00000366794	NM_001618.3	379	gCt/gAt	8/23	1	2	FACETS	0.97	0.888	1	0.97	0.888	1	CLONAL	1	TRUE	1	0.64	2		391	422	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850937	63850937	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	25	505	0	ENST00000279873.7:c.1715A>G	p.Asp572Gly	p.D572G	ENST00000279873	NM_032199.2	572	gAc/gGc	10/10	1	2	FACETS	0.164	0.129	0.205	0.164	0.129	0.205	SUBCLONAL	1	TRUE	1	0.64	2		505	476	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851872	63851872	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	48	429	0	ENST00000279873.7:c.2650C>A	p.Leu884Ile	p.L884I	ENST00000279873	NM_032199.2	884	Ctc/Atc	10/10	1	2	FACETS	0.328	0.277	0.384	0.328	0.277	0.384	SUBCLONAL	1	TRUE	1	0.64	2		429	457	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332615	70332615	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	108	507	0	ENST00000373644.4:c.520G>A	p.Gly174Ser	p.G174S	ENST00000373644	NM_030625.2	174	Ggt/Agt	2/12	1	2	FACETS	0.804	0.726	0.884	0.804	0.726	0.884	CLONAL	1	TRUE	1	0.64	2		507	420	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405194	70405194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1169743622	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	136	368	0	ENST00000373644.4:c.2708C>T	p.Ala903Val	p.A903V	ENST00000373644	NM_030625.2	903	gCc/gTc	4/12	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.64	2		368	412	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910884	114910884	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	44	883	0	ENST00000543371.1:c.1001+2T>C		p.X334_splice	ENST00000543371	NM_001198531.1	334			1	2	FACETS	0.167	0.14	0.198	0.167	0.14	0.198	SUBCLONAL	1	TRUE	1	0.64	2		883	821	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925702	114925702	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	56	1092	0	ENST00000543371.1:c.1780C>A	p.Leu594Met	p.L594M	ENST00000543371	NM_001198531.1	594	Ctg/Atg	14/14	1	2	FACETS	0.159	0.135	0.185	0.159	0.135	0.185	SUBCLONAL	1	TRUE	1	0.64	2		1092	1100	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123246908	123246908	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	130	596	0	ENST00000358487.5:c.2017G>T	p.Glu673Ter	p.E673*	ENST00000358487	NM_000141.4	673	Gaa/Taa	15/18	1	2	FACETS	0.633	0.575	0.693	0.633	0.575	0.693	SUBCLONAL	1	TRUE	1	0.64	2		596	642	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417808	32417808	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	22	458	0	ENST00000332351.3:c.1244A>G	p.His415Arg	p.H415R	ENST00000332351	NM_024426.4	415	cAc/cGc	7/10	1	2	FACETS	0.178	0.137	0.225	0.178	0.137	0.225	SUBCLONAL	1	TRUE	1	0.64	2		458	386	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417908	32417908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1412336417	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	59	620	2	ENST00000332351.3:c.1144G>A	p.Ala382Thr	p.A382T	ENST00000332351	NM_024426.4	382	Gca/Aca	7/10	1	2	FACETS	0.281	0.241	0.324	0.281	0.241	0.324	SUBCLONAL	1	TRUE	1	0.64	2		622	657	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456335	32456335	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	97	643	0	ENST00000332351.3:c.557G>A	p.Ser186Asn	p.S186N	ENST00000332351	NM_024426.4	186	aGc/aAc	1/10	1	2	FACETS	0.804	0.723	0.889	0.804	0.723	0.889	CLONAL	1	TRUE	1	0.64	2		643	377	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132907	64132907	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	36	754	2	ENST00000334205.4:c.1046del	p.Pro349HisfsTer26	p.P349Hfs*26	ENST00000334205	NM_003942.2	347	agC/ag	9/17	1	2	FACETS	0.158	0.129	0.191	0.158	0.129	0.191	SUBCLONAL	1	TRUE	1	0.64	2		756	711	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69456140	69456140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	43	695	1	ENST00000227507.2:c.59C>T	p.Ala20Val	p.A20V	ENST00000227507	NM_053056.2	20	gCc/gTc	1/5	1	2	FACETS	0.181	0.151	0.215	0.181	0.151	0.215	SUBCLONAL	1	TRUE	1	0.64	2		696	742	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180558	94180558	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	52	509	0	ENST00000323929.3:c.1610C>A	p.Ala537Asp	p.A537D	ENST00000323929	NM_005591.3	537	gCt/gAt	15/20	0.134266970954408	1	FACETS	0.211	0.179	0.246	0.211	0.179	0.246	INDETERMINATE	1	TRUE	0	0.64	1		509	524	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219112	94219112	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659583	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	26	425	0	ENST00000323929.3:c.292T>C	p.Ser98Pro	p.S98P	ENST00000323929	NM_005591.3	98	Tca/Cca	4/20	0.134266970954408	1	FACETS	0.119	0.094	0.148	0.119	0.094	0.148	INDETERMINATE	1	TRUE	0	0.64	1		425	465	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998798	100998798	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	40	851	0	ENST00000325455.5:c.1004C>A	p.Ala335Asp	p.A335D	ENST00000325455	NM_001202474.3	335	gCt/gAt	1/8	0.134266970954408	1	FACETS	0.145	0.12	0.173	0.145	0.12	0.173	INDETERMINATE	1	TRUE	0	0.64	1		851	586	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114714	108114714	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	137	367	0	ENST00000278616.4:c.531A>C	p.Lys177Asn	p.K177N	ENST00000278616	NM_000051.3	177	aaA/aaC	6/63	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.64	2		367	419	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121756	108121756	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	177	460	2	ENST00000278616.4:c.1564G>T	p.Glu522Ter	p.E522*	ENST00000278616	NM_000051.3	522	Gaa/Taa	10/63	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.64	2		462	515	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151843	108151843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	152	460	1	ENST00000278616.4:c.3524C>T	p.Ala1175Val	p.A1175V	ENST00000278616	NM_000051.3	1175	gCc/gTc	24/63	1	2	FACETS	0.833	0.766	0.903	0.833	0.766	0.903	CLONAL	1	TRUE	1	0.64	2		461	570	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153509	108153509	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	33	599	0	ENST00000278616.4:c.3649C>A	p.Leu1217Met	p.L1217M	ENST00000278616	NM_000051.3	1217	Ctg/Atg	25/63	1	2	FACETS	0.179	0.145	0.218	0.179	0.145	0.218	SUBCLONAL	1	TRUE	1	0.64	2		599	575	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348807	118348807	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555038090	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	44	660	0	ENST00000534358.1:c.3460C>T	p.Arg1154Trp	p.R1154W	ENST00000534358	NM_005933.3	1154	Cgg/Tgg	5/36	1	2	FACETS	0.169	0.141	0.2	0.169	0.141	0.2	SUBCLONAL	1	TRUE	1	0.64	2		660	813	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375676	118375676	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	216	703	1	ENST00000534358.1:c.9069G>T	p.Gln3023His	p.Q3023H	ENST00000534358	NM_005933.3	3023	caG/caT	27/36	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.64	2		704	629	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392771	118392771	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	47	655	0	ENST00000534358.1:c.11803C>T	p.Arg3935Cys	p.R3935C	ENST00000534358	NM_005933.3	3935	Cgt/Tgt	36/36	1	2	FACETS	0.244	0.205	0.286	0.244	0.205	0.286	SUBCLONAL	1	TRUE	1	0.64	2		655	603	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125523656	125523656	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	45	523	0	ENST00000428830.2:c.1249A>C	p.Thr417Pro	p.T417P	ENST00000428830	NM_001114121.2	417	Act/Cct	12/14	1	2	FACETS	0.279	0.234	0.329	0.279	0.234	0.329	SUBCLONAL	1	TRUE	1	0.64	2		523	504	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	493201	493201	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	33	551	1	ENST00000399788.2:c.362G>T	p.Ser121Ile	p.S121I	ENST00000399788	NM_001042603.1	121	aGc/aTc	3/28	0.3	2	FACETS	0.175	0.142	0.213			1	INDETERMINATE	1	TRUE	NA	0.64	2		552	589	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552672	18552672	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	139	741	0	ENST00000266497.5:c.2083C>A	p.Leu695Met	p.L695M	ENST00000266497		695	Ctg/Atg	14/31	1	2	FACETS	0.591	0.539	0.646	0.591	0.539	0.646	SUBCLONAL	1	TRUE	1	0.64	2		741	735	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945024	31945024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	97	860	1	ENST00000340398.3:c.77C>T	p.Ala26Val	p.A26V	ENST00000340398	NM_001013699.2	26	gCc/gTc	1/1	1	2	FACETS	0.425	0.378	0.474	0.425	0.378	0.474	SUBCLONAL	1	TRUE	1	0.64	2		861	714	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243879	46243879	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1467228632	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	186	561	0	ENST00000334344.6:c.1973A>G	p.Gln658Arg	p.Q658R	ENST00000334344	NM_152641.2	658	cAa/cGa	15/21	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.64	2		561	565	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244981	46244981	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	266	828	1	ENST00000334344.6:c.3075G>T	p.Gln1025His	p.Q1025H	ENST00000334344	NM_152641.2	1025	caG/caT	15/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.64	2		829	757	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246488	46246488	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761166036	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	85	594	1	ENST00000334344.6:c.4582G>A	p.Ala1528Thr	p.A1528T	ENST00000334344	NM_152641.2	1528	Gca/Aca	15/21	1	2	FACETS	0.346	0.306	0.39	0.346	0.306	0.39	SUBCLONAL	1	TRUE	1	0.64	2		595	767	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254727	46254728	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	98	499	0	ENST00000334344.6:c.4922dup	p.Trp1642ValfsTer15	p.W1642Vfs*15	ENST00000334344	NM_152641.2	1639	-/A	16/21	1	2	FACETS	0.574	0.513	0.637	0.574	0.513	0.637	SUBCLONAL	1	TRUE	1	0.64	2		499	534	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425035	49425035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	52	767	0	ENST00000301067.7:c.13453G>A	p.Ala4485Thr	p.A4485T	ENST00000301067	NM_003482.3	4485	Gct/Act	39/54	1	2	FACETS	0.212	0.18	0.248	0.212	0.18	0.248	SUBCLONAL	1	TRUE	1	0.64	2		767	766	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433243	49433243	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	192	648	0	ENST00000301067.7:c.8204G>A	p.Gly2735Asp	p.G2735D	ENST00000301067	NM_003482.3	2735	gGc/gAc	32/54	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.64	2		648	565	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437681	49437681	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	51	927	0	ENST00000301067.7:c.5289A>C	p.Lys1763Asn	p.K1763N	ENST00000301067	NM_003482.3	1763	aaA/aaC	22/54	1	2	FACETS	0.165	0.14	0.194	0.165	0.14	0.194	SUBCLONAL	1	TRUE	1	0.64	2		927	963	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442997	49442997	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760202783	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	134	383	0	ENST00000301067.7:c.3911G>A	p.Arg1304His	p.R1304H	ENST00000301067	NM_003482.3	1304	cGc/cAc	12/54	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.64	2		383	417	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445511	49445511	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776778856	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	35	488	1	ENST00000301067.7:c.1955G>A	p.Arg652His	p.R652H	ENST00000301067	NM_003482.3	652	cGc/cAc	10/54	1	2	FACETS	0.229	0.187	0.276	0.229	0.187	0.276	SUBCLONAL	1	TRUE	1	0.64	2		489	478	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479968	50479968	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	230	682	0	ENST00000394963.4:c.202C>T	p.Arg68Ter	p.R68*	ENST00000394963	NM_003076.4	68	Cga/Tga	2/13	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.64	2		682	619	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480071	50480071	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	34	569	0	ENST00000394963.4:c.305G>T	p.Arg102Ile	p.R102I	ENST00000394963	NM_003076.4	102	aGa/aTa	2/13	1	2	FACETS	0.166	0.135	0.201	0.166	0.135	0.201	SUBCLONAL	1	TRUE	1	0.64	2		569	639	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492537	50492537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750026102	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	43	680	1	ENST00000394963.4:c.1433G>A	p.Arg478Gln	p.R478Q	ENST00000394963	NM_003076.4	478	cGa/cAa	12/13	1	2	FACETS	0.174	0.144	0.206	0.174	0.144	0.206	SUBCLONAL	1	TRUE	1	0.64	2		681	774	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495587	56495587	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	100	520	0	ENST00000267101.3:c.3777C>A	p.Asp1259Glu	p.D1259E	ENST00000267101	NM_001982.3	1259	gaC/gaA	28/28	1	2	FACETS	0.652	0.585	0.723	0.652	0.585	0.723	SUBCLONAL	1	TRUE	1	0.64	2		520	479	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856622	111856622	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs926306195	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	108	277	0	ENST00000341259.2:c.673C>T	p.Arg225Cys	p.R225C	ENST00000341259	NM_005475.2	225	Cgc/Tgc	2/8	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.64	2		277	335	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536689	120536689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	51	930	1	ENST00000229340.5:c.403G>A	p.Ala135Thr	p.A135T	ENST00000229340	NM_006861.6	135	Gcc/Acc	5/6	1	2	FACETS	0.176	0.149	0.206	0.176	0.149	0.206	SUBCLONAL	1	TRUE	1	0.64	2		931	904	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416740	121416740	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	126	774	0	ENST00000257555.6:c.169C>A	p.Leu57Met	p.L57M	ENST00000257555		57	Ctg/Atg	1/10	1	2	FACETS	0.717	0.652	0.785	0.717	0.652	0.785	SUBCLONAL	1	TRUE	1	0.64	2		774	549	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426784	121426784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765432081	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	228	684	2	ENST00000257555.6:c.475C>T	p.Arg159Trp	p.R159W	ENST00000257555		159	Cgg/Tgg	2/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.64	2		686	672	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219117	133219117	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	138	709	0	ENST00000320574.5:c.4927C>A	p.Leu1643Met	p.L1643M	ENST00000320574	NM_006231.2	1643	Ctg/Atg	37/49	1	2	FACETS	0.727	0.664	0.793	0.727	0.664	0.793	SUBCLONAL	1	TRUE	1	0.64	2		709	593	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235981	133235981	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555225670	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	39	687	1	ENST00000320574.5:c.3175C>T	p.Arg1059Cys	p.R1059C	ENST00000320574	NM_006231.2	1059	Cgc/Tgc	26/49	1	2	FACETS	0.2	0.165	0.239	0.2	0.165	0.239	SUBCLONAL	1	TRUE	1	0.64	2		688	610	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245067	133245067	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	21	405	1	ENST00000320574.5:c.2048A>G	p.Tyr683Cys	p.Y683C	ENST00000320574	NM_006231.2	683	tAc/tGc	19/49	1	2	FACETS	0.188	0.144	0.238	0.188	0.144	0.238	SUBCLONAL	1	TRUE	1	0.64	2		406	350	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253151	133253151	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	170	573	0	ENST00000320574.5:c.890C>A	p.Ser297Tyr	p.S297Y	ENST00000320574	NM_006231.2	297	tCc/tAc	9/49	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.64	2		573	515	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557863	21557863	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	116	647	2	ENST00000382592.4:c.1982C>T	p.Ala661Val	p.A661V	ENST00000382592	NM_014572.2	661	gCc/gTc	5/8	1	2	FACETS	0.632	0.571	0.695	0.632	0.571	0.695	SUBCLONAL	1	TRUE	1	0.64	2		649	574	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562678	21562678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754388230	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	80	271	0	ENST00000382592.4:c.1241C>T	p.Pro414Leu	p.P414L	ENST00000382592	NM_014572.2	414	cCg/cTg	4/8	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.64	2		271	234	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563083	21563083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779402447	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	128	574	0	ENST00000382592.4:c.836C>T	p.Thr279Met	p.T279M	ENST00000382592	NM_014572.2	279	aCg/aTg	4/8	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.64	2		574	381	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578214	28578214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778369	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	51	644	1	ENST00000241453.7:c.2957C>T	p.Pro986Leu	p.P986L	ENST00000241453	NM_004119.2	986	cCg/cTg	24/24	1	2	FACETS	0.24	0.203	0.28	0.24	0.203	0.28	SUBCLONAL	1	TRUE	1	0.64	2		645	665	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008029	29008029	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	40	663	3	ENST00000282397.4:c.740C>A	p.Thr247Asn	p.T247N	ENST00000282397	NM_002019.4	247	aCt/aAt	6/30	1	2	FACETS	0.178	0.147	0.212	0.178	0.147	0.212	SUBCLONAL	1	TRUE	1	0.64	2		666	703	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912346	32912346	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359406	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	43	771	0	ENST00000380152.3:c.3860del	p.Asn1287IlefsTer6	p.N1287Ifs*6	ENST00000380152		1285	gAa/ga	11/27	1	2	FACETS	0.205	0.171	0.243	0.205	0.171	0.243	SUBCLONAL	1	TRUE	1	0.64	2		771	656	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912580	32912580	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	349	950	0	ENST00000380152.3:c.4088A>C	p.Asn1363Thr	p.N1363T	ENST00000380152		1363	aAc/aCc	11/27	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.64	2		950	958	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48921993	48921993	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	136	390	1	ENST00000267163.4:c.533G>T	p.Ser178Ile	p.S178I	ENST00000267163	NM_000321.2	178	aGc/aTc	5/27	1	2	FACETS	0.916	0.839	0.995	0.916	0.839	0.995	CLONAL	1	TRUE	1	0.64	2		391	464	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951063	48951063	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	85	395	0	ENST00000267163.4:c.1225G>T	p.Val409Leu	p.V409L	ENST00000267163	NM_000321.2	409	Gtg/Ttg	13/27	1	2	FACETS	0.606	0.538	0.678	0.606	0.538	0.678	SUBCLONAL	1	TRUE	1	0.64	2		395	438	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73352477	73352477	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs765842209	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	50	599	0	ENST00000377767.4:c.428A>G	p.Asp143Gly	p.D143G	ENST00000377767	NM_014953.3	143	gAc/gGc	3/21	1	2	FACETS	0.193	0.163	0.226	0.193	0.163	0.226	SUBCLONAL	1	TRUE	1	0.64	2		599	809	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436189	110436189	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1360944265	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	196	514	0	ENST00000375856.3:c.2212G>A	p.Glu738Lys	p.E738K	ENST00000375856	NM_003749.2	738	Gag/Aag	1/2	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.64	2		514	556	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436429	110436429	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	23	589	2	ENST00000375856.3:c.1972C>T	p.Pro658Ser	p.P658S	ENST00000375856	NM_003749.2	658	Ccc/Tcc	1/2	1	2	FACETS	0.161	0.125	0.203	0.161	0.125	0.203	SUBCLONAL	1	TRUE	1	0.64	2		591	447	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061304	38061304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	168	737	3	ENST00000250448.2:c.685G>A	p.Val229Ile	p.V229I	ENST00000250448	NM_004496.3	229	Gtc/Atc	2/2	1	2	FACETS	0.887	0.819	0.957	0.887	0.819	0.957	CLONAL	1	TRUE	1	0.64	2		740	592	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061333	38061333	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	136	759	1	ENST00000250448.2:c.656G>A	p.Arg219His	p.R219H	ENST00000250448	NM_004496.3	219	cGc/cAc	2/2	1	2	FACETS	0.697	0.636	0.761	0.697	0.636	0.761	SUBCLONAL	1	TRUE	1	0.64	2		760	610	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061774	38061774	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	23	519	1	ENST00000250448.2:c.215G>A	p.Gly72Asp	p.G72D	ENST00000250448	NM_004496.3	72	gGc/gAc	2/2	1	2	FACETS	0.182	0.141	0.229	0.182	0.141	0.229	SUBCLONAL	1	TRUE	1	0.64	2		520	395	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560376	95560376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	31	475	1	ENST00000393063.1:c.5213C>T	p.Ala1738Val	p.A1738V	ENST00000393063	NM_030621.3	1738	gCc/gTc	25/28	1	2	FACETS	0.192	0.155	0.234	0.192	0.155	0.234	SUBCLONAL	1	TRUE	1	0.64	2		476	505	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570203	95570203	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	37	570	1	ENST00000393063.1:c.3530G>A	p.Gly1177Asp	p.G1177D	ENST00000393063	NM_030621.3	1177	gGt/gAt	22/28	1	2	FACETS	0.178	0.146	0.213	0.178	0.146	0.213	SUBCLONAL	1	TRUE	1	0.64	2		571	651	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572076	95572076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772243498	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	50	665	3	ENST00000393063.1:c.3032C>T	p.Ala1011Val	p.A1011V	ENST00000393063	NM_030621.3	1011	gCg/gTg	20/28	1	2	FACETS	0.19	0.161	0.223	0.19	0.161	0.223	SUBCLONAL	1	TRUE	1	0.64	2		668	821	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239875	105239875	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1458420660	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	163	592	3	ENST00000349310.3:c.745C>T	p.Arg249Trp	p.R249W	ENST00000349310	NM_001014432.1	249	Cgg/Tgg	10/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.64	2		595	437	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023314	33023314	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	107	1015	0	ENST00000300177.4:c.423C>A	p.Cys141Ter	p.C141*	ENST00000300177	NM_001191322.1	141	tgC/tgA	2/2	1	2	FACETS	0.397	0.356	0.441	0.397	0.356	0.441	SUBCLONAL	1	TRUE	1	0.64	2		1015	842	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028774	42028774	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	262	934	1	ENST00000219905.7:c.4312G>T	p.Asp1438Tyr	p.D1438Y	ENST00000219905	NM_001164273.1	1438	Gat/Tat	13/24	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.64	2		935	775	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052590	42052590	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	76	851	0	ENST00000219905.7:c.7261T>C	p.Phe2421Leu	p.F2421L	ENST00000219905	NM_001164273.1	2421	Ttt/Ctt	20/24	1	2	FACETS	0.235	0.206	0.268	0.235	0.206	0.268	SUBCLONAL	1	TRUE	1	0.64	2		851	1009	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058672	42058672	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	51	948	2	ENST00000219905.7:c.8392G>T	p.Ala2798Ser	p.A2798S	ENST00000219905	NM_001164273.1	2798	Gct/Tct	24/24	1	2	FACETS	0.192	0.162	0.224	0.192	0.162	0.224	SUBCLONAL	1	TRUE	1	0.64	2		950	832	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457295	67457295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886038803	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	185	608	2	ENST00000327367.4:c.269G>A	p.Arg90His	p.R90H	ENST00000327367	NM_005902.3	90	cGc/cAc	2/9	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.64	2		610	521	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628529	90628529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1220662107	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	42	747	4	ENST00000330062.3:c.1058G>A	p.Arg353His	p.R353H	ENST00000330062	NM_002168.2	353	cGc/cAc	8/11	1	2	FACETS	0.196	0.163	0.233	0.196	0.163	0.233	SUBCLONAL	1	TRUE	1	0.64	2		751	669	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630377	90630377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	227	662	2	ENST00000330062.3:c.934G>A	p.Asp312Asn	p.D312N	ENST00000330062	NM_002168.2	312	Gac/Aac	7/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.64	2		664	615	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631833	90631833	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	26	454	0	ENST00000330062.3:c.520G>A	p.Ala174Thr	p.A174T	ENST00000330062	NM_002168.2	174	Gcc/Acc	4/11	1	2	FACETS	0.179	0.141	0.223	0.179	0.141	0.223	SUBCLONAL	1	TRUE	1	0.64	2		454	453	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459948	99459948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	54	639	0	ENST00000268035.6:c.2044G>A	p.Glu682Lys	p.E682K	ENST00000268035	NM_000875.3	682	Gag/Aag	10/21	1	2	FACETS	0.314	0.268	0.365	0.314	0.268	0.365	SUBCLONAL	1	TRUE	1	0.64	2		639	537	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99486236	99486236	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	129	612	0	ENST00000268035.6:c.3542C>A	p.Pro1181His	p.P1181H	ENST00000268035	NM_000875.3	1181	cCt/cAt	19/21	1	2	FACETS	0.736	0.67	0.804	0.736	0.67	0.804	SUBCLONAL	1	TRUE	1	0.64	2		612	548	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343500	343500	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1316816500	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	226	714	0	ENST00000262320.3:c.2174C>T	p.Pro725Leu	p.P725L	ENST00000262320	NM_003502.3	725	cCc/cTc	8/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.64	2		714	572	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347819	347819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746435850	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	26	759	3	ENST00000262320.3:c.1687G>A	p.Ala563Thr	p.A563T	ENST00000262320	NM_003502.3	563	Gcc/Acc	6/11	1	2	FACETS	0.167	0.131	0.207	0.167	0.131	0.207	SUBCLONAL	1	TRUE	1	0.64	2		762	487	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104321	2104321	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	38	626	0	ENST00000219476.3:c.361G>T	p.Ala121Ser	p.A121S	ENST00000219476	NM_000548.3	121	Gcc/Tcc	5/42	1	2	FACETS	0.203	0.167	0.243	0.203	0.167	0.243	SUBCLONAL	1	TRUE	1	0.64	2		626	585	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134462	2134462	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	34	735	1	ENST00000219476.3:c.4239G>T	p.Glu1413Asp	p.E1413D	ENST00000219476	NM_000548.3	1413	gaG/gaT	34/42	1	2	FACETS	0.18	0.146	0.218	0.18	0.146	0.218	SUBCLONAL	1	TRUE	1	0.64	2		736	590	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226081	2226081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	46	760	2	ENST00000326181.6:c.1778G>A	p.Arg593Gln	p.R593Q	ENST00000326181	NM_032271.2	593	cGg/cAg	19/21	1	2	FACETS	0.245	0.206	0.288	0.245	0.206	0.288	SUBCLONAL	1	TRUE	1	0.64	2		762	587	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781321	3781321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200112956	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	30	682	0	ENST00000262367.5:c.5044C>T	p.Arg1682Cys	p.R1682C	ENST00000262367	NM_004380.2	1682	Cgc/Tgc	30/31	1	2	FACETS	0.169	0.135	0.207	0.169	0.135	0.207	SUBCLONAL	1	TRUE	1	0.64	2		682	556	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900680	3900680	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	49	449	0	ENST00000262367.5:c.416G>T	p.Ser139Ile	p.S139I	ENST00000262367	NM_004380.2	139	aGc/aTc	2/31	1	2	FACETS	0.368	0.312	0.429	0.368	0.312	0.429	SUBCLONAL	1	TRUE	1	0.64	2		449	416	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274037	10274037	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	54	752	1	ENST00000330684.3:c.232G>A	p.Asp78Asn	p.D78N	ENST00000330684	NM_001134407.1	78	Gac/Aac	2/13	1	2	FACETS	0.291	0.249	0.338	0.291	0.249	0.338	SUBCLONAL	1	TRUE	1	0.64	2		753	579	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020532	14020532	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	181	702	0	ENST00000311895.7:c.503C>A	p.Ala168Asp	p.A168D	ENST00000311895	NM_005236.2	168	gCt/gAt	3/11	1	2	FACETS	0.721	0.666	0.777	0.721	0.666	0.777	SUBCLONAL	1	TRUE	1	0.64	2		702	785	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029222	14029222	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	146	651	0	ENST00000311895.7:c.1433C>A	p.Ala478Asp	p.A478D	ENST00000311895	NM_005236.2	478	gCt/gAt	8/11	1	2	FACETS	0.646	0.591	0.704	0.646	0.591	0.704	SUBCLONAL	1	TRUE	1	0.64	2		651	706	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128105	30128105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	36	825	1	ENST00000263025.4:c.1024G>A	p.Ala342Thr	p.A342T	ENST00000263025	NM_002746.2	342	Gcc/Acc	8/9	1	2	FACETS	0.181	0.148	0.218	0.181	0.148	0.218	SUBCLONAL	1	TRUE	1	0.64	2		826	621	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129729	30129729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1430679556	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	51	1202	0	ENST00000263025.4:c.484G>A	p.Val162Met	p.V162M	ENST00000263025	NM_002746.2	162	Gtg/Atg	3/9	1	2	FACETS	0.182	0.153	0.213	0.182	0.153	0.213	SUBCLONAL	1	TRUE	1	0.64	2		1202	878	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868112	56868112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374706761	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	181	830	0	ENST00000308159.5:c.1610G>A	p.Arg537Gln	p.R537Q	ENST00000308159	NM_014669.4	537	cGg/cAg	14/22	1	2	FACETS	0.696	0.643	0.751	0.696	0.643	0.751	SUBCLONAL	1	TRUE	1	0.64	2		830	813	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662324	67662324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767996920	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	170	605	0	ENST00000264010.4:c.1570G>A	p.Ala524Thr	p.A524T	ENST00000264010	NM_006565.3	524	Gcc/Acc	9/12	1	2	FACETS	0.977	0.904	1	0.977	0.904	1	CLONAL	1	TRUE	1	0.64	2		605	544	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844236	68844236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	27	479	0	ENST00000261769.5:c.824C>T	p.Ala275Val	p.A275V	ENST00000261769	NM_004360.3	275	gCt/gTt	6/16	1	2	FACETS	0.185	0.147	0.229	0.185	0.147	0.229	SUBCLONAL	1	TRUE	1	0.64	2		479	456	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923683	72923683	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	42	892	0	ENST00000268489.5:c.3395A>G	p.Asp1132Gly	p.D1132G	ENST00000268489	NM_006885.3	1132	gAc/gGc	4/10	1	2	FACETS	0.181	0.15	0.215	0.181	0.15	0.215	SUBCLONAL	1	TRUE	1	0.64	2		892	726	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993861	72993861	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756319969	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	39	683	3	ENST00000268489.5:c.184G>A	p.Ala62Thr	p.A62T	ENST00000268489	NM_006885.3	62	Gcg/Acg	2/10	1	2	FACETS	0.221	0.182	0.264	0.221	0.182	0.264	SUBCLONAL	1	TRUE	1	0.64	2		686	552	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819695	81819695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs537204469	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	102	901	5	ENST00000359376.3:c.101G>A	p.Arg34His	p.R34H	ENST00000359376	NM_002661.3	34	cGc/cAc	2/33	1	2	FACETS	0.421	0.376	0.468	0.421	0.376	0.468	SUBCLONAL	1	TRUE	1	0.64	2		906	758	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347584	89347584	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1048947362	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	187	1015	2	ENST00000301030.4:c.5366G>A	p.Arg1789His	p.R1789H	ENST00000301030	NM_001256183.1	1789	cGc/cAc	9/13	1	2	FACETS	0.723	0.669	0.779	0.723	0.669	0.779	SUBCLONAL	1	TRUE	1	0.64	2		1017	808	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349738	89349738	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	304	1168	2	ENST00000301030.4:c.3212G>A	p.Gly1071Asp	p.G1071D	ENST00000301030	NM_001256183.1	1071	gGc/gAc	9/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.64	2		1170	905	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350366	89350366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	157	984	0	ENST00000301030.4:c.2584G>T	p.Val862Leu	p.V862L	ENST00000301030	NM_001256183.1	862	Gtg/Ttg	9/13	1	2	FACETS	0.613	0.562	0.667	0.613	0.562	0.667	SUBCLONAL	1	TRUE	1	0.64	2		984	800	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351578	89351578	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	167	1123	2	ENST00000301030.4:c.1372C>T	p.Arg458Ter	p.R458*	ENST00000301030	NM_001256183.1	458	Cga/Tga	9/13	1	2	FACETS	0.656	0.604	0.711	0.656	0.604	0.711	SUBCLONAL	1	TRUE	1	0.64	2		1125	795	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351812	89351812	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	67	1120	0	ENST00000301030.4:c.1138T>G	p.Phe380Val	p.F380V	ENST00000301030	NM_001256183.1	380	Ttt/Gtt	9/13	1	2	FACETS	0.256	0.222	0.294	0.256	0.222	0.294	SUBCLONAL	1	TRUE	1	0.64	2		1120	817	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89837014	89837014	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1425954290	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	176	679	1	ENST00000389301.3:c.2180G>A	p.Cys727Tyr	p.C727Y	ENST00000389301	NM_000135.2	727	tGt/tAt	24/43	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.64	2		680	534	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882948	89882948	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	16	192	0	ENST00000389301.3:c.76C>A	p.Leu26Met	p.L26M	ENST00000389301	NM_000135.2	26	Ctg/Atg	1/43	1	2	FACETS	0.214	0.158	0.28	0.214	0.158	0.28	SUBCLONAL	1	TRUE	1	0.64	2		192	234	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216739	7216739	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	57	850	0	ENST00000380728.2:c.684G>T	p.Gln228His	p.Q228H	ENST00000380728		228	caG/caT	8/11	1	2	FACETS	0.184	0.157	0.213	0.184	0.157	0.213	SUBCLONAL	1	TRUE	1	0.64	2		850	969	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980394	7980394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs562084711	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	33	584	2	ENST00000319144.4:c.1189G>A	p.Ala397Thr	p.A397T	ENST00000319144	NM_001139.2	397	Gcc/Acc	9/15	1	2	FACETS	0.186	0.151	0.226	0.186	0.151	0.226	SUBCLONAL	1	TRUE	1	0.64	2		586	553	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980512	7980512	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	25	406	0	ENST00000319144.4:c.1072-1G>T		p.X358_splice	ENST00000319144	NM_001139.2	358			1	2	FACETS	0.171	0.134	0.213	0.171	0.134	0.213	SUBCLONAL	1	TRUE	1	0.64	2		406	457	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965201	15965201	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	21	117	0	ENST00000268712.3:c.5395C>A	p.Pro1799Thr	p.P1799T	ENST00000268712	NM_006311.3	1799	Cct/Act	37/46	1	2	FACETS	0.625	0.489	0.777	0.625	0.489	0.777	SUBCLONAL	1	TRUE	1	0.64	2		117	105	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15967388	15967388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776176516	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	211	600	0	ENST00000268712.3:c.5215C>T	p.Arg1739Trp	p.R1739W	ENST00000268712	NM_006311.3	1739	Cgg/Tgg	35/46	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.64	2		600	618	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973577	15973577	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	43	538	0	ENST00000268712.3:c.4415G>T	p.Ser1472Ile	p.S1472I	ENST00000268712	NM_006311.3	1472	aGc/aTc	31/46	1	2	FACETS	0.217	0.181	0.257	0.217	0.181	0.257	SUBCLONAL	1	TRUE	1	0.64	2		538	620	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068300	16068300	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	54	135	0	ENST00000268712.3:c.611A>C	p.Lys204Thr	p.K204T	ENST00000268712	NM_006311.3	204	aAg/aCg	5/46	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.64	2		135	125	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653259	29653259	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	115	330	0	ENST00000356175.3:c.5194G>T	p.Val1732Phe	p.V1732F	ENST00000356175	NM_000267.3	1732	Gtt/Ttt	36/57	1	2	FACETS	0.946	0.86	1	0.946	0.86	1	CLONAL	1	TRUE	1	0.64	2		330	380	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663445	29663445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567616695	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	227	581	1	ENST00000356175.3:c.6038C>T	p.Thr2013Ile	p.T2013I	ENST00000356175	NM_000267.3	2013	aCt/aTt	40/57	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.64	2		582	671	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428254	33428254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773883374	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	109	573	0	ENST00000345365.6:c.869G>A	p.Arg290Gln	p.R290Q	ENST00000345365	NM_002878.3	290	cGg/cAg	9/10	1	2	FACETS	0.658	0.593	0.726	0.658	0.593	0.726	SUBCLONAL	1	TRUE	1	0.64	2		573	518	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33446562	33446562	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	33	771	0	ENST00000345365.6:c.71G>T	p.Arg24Met	p.R24M	ENST00000345365	NM_002878.3	24	aGg/aTg	1/10	1	2	FACETS	0.172	0.14	0.209	0.172	0.14	0.209	SUBCLONAL	1	TRUE	1	0.64	2		771	598	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627917	37627917	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	48	648	2	ENST00000447079.4:c.1832C>A	p.Thr611Asn	p.T611N	ENST00000447079	NM_015083.1	611	aCt/aAt	2/14	1	2	FACETS	0.2	0.169	0.235	0.2	0.169	0.235	SUBCLONAL	1	TRUE	1	0.64	2		650	749	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649006	37649006	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	127	370	0	ENST00000447079.4:c.2111T>G	p.Ile704Ser	p.I704S	ENST00000447079	NM_015083.1	704	aTt/aGt	4/14	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.64	2		370	397	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687445	37687445	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	153	477	0	ENST00000447079.4:c.4349C>T	p.Ala1450Val	p.A1450V	ENST00000447079	NM_015083.1	1450	gCc/gTc	14/14	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.64	2		477	429	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872857	37872857	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs756686824	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	123	478	1	ENST00000269571.5:c.1736C>T	p.Pro579Leu	p.P579L	ENST00000269571		579	cCg/cTg	14/27	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.64	2		479	353	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883732	37883732	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	32	762	0	ENST00000269571.5:c.3344A>G	p.Asp1115Gly	p.D1115G	ENST00000269571		1115	gAc/gGc	26/27	1	2	FACETS	0.162	0.13	0.197	0.162	0.13	0.197	SUBCLONAL	1	TRUE	1	0.64	2		762	619	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510644	38510644	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	229	760	3	ENST00000254066.5:c.898G>A	p.Ala300Thr	p.A300T	ENST00000254066	NM_000964.3	300	Gct/Act	7/9	1	2	FACETS	0.99	0.926	1	0.99	0.926	1	CLONAL	1	TRUE	1	0.64	2		763	723	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359648	40359648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1339796170	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	75	1017	0	ENST00000293328.3:c.2005G>A	p.Val669Met	p.V669M	ENST00000293328	NM_012448.3	669	Gtg/Atg	16/19	1	2	FACETS	0.218	0.19	0.248	0.218	0.19	0.248	SUBCLONAL	1	TRUE	1	0.64	2		1017	1076	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40458299	40458299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757085900	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	127	484	1	ENST00000345506.4:c.1514C>T	p.Pro505Leu	p.P505L	ENST00000345506	NM_003152.3	505	cCg/cTg	14/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.64	2		485	331	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243988	41243988	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80356975	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	59	583	1	ENST00000357654.3:c.3560G>A	p.Ser1187Asn	p.S1187N	ENST00000357654	NM_007294.3	1187	aGc/aAc	10/23	1	2	FACETS	0.307	0.264	0.354	0.307	0.264	0.354	SUBCLONAL	1	TRUE	1	0.64	2		584	601	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245753	41245753	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	37	641	0	ENST00000357654.3:c.1795A>G	p.Asn599Asp	p.N599D	ENST00000357654	NM_007294.3	599	Aat/Gat	10/23	1	2	FACETS	0.181	0.149	0.218	0.181	0.149	0.218	SUBCLONAL	1	TRUE	1	0.64	2		641	638	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804373	46804373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145059285	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	48	707	0	ENST00000290295.7:c.634G>A	p.Ala212Thr	p.A212T	ENST00000290295	NM_006361.5	212	Gcc/Acc	2/2	1	2	FACETS	0.278	0.235	0.326	0.278	0.235	0.326	SUBCLONAL	1	TRUE	1	0.64	2		707	539	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56801431	56801431	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779834376	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	344	752	0	ENST00000337432.4:c.935G>A	p.Arg312Gln	p.R312Q	ENST00000337432	NM_058216.2	312	cGg/cAg	7/9	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.64	2		752	869	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58701089	58701089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	66	1082	1	ENST00000305921.3:c.680G>A	p.Arg227Gln	p.R227Q	ENST00000305921	NM_003620.3	227	cGa/cAa	2/6	1	2	FACETS	0.182	0.157	0.21	0.182	0.157	0.21	SUBCLONAL	1	TRUE	1	0.64	2		1083	1131	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740417	58740417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770633028	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	180	908	1	ENST00000305921.3:c.1322G>A	p.Arg441His	p.R441H	ENST00000305921	NM_003620.3	441	cGt/cAt	6/6	1	2	FACETS	0.583	0.537	0.63	0.583	0.537	0.63	SUBCLONAL	1	TRUE	1	0.64	2		909	965	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740808	58740808	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	90	976	3	ENST00000305921.3:c.1713G>T	p.Gln571His	p.Q571H	ENST00000305921	NM_003620.3	571	caG/caT	6/6	1	2	FACETS	0.303	0.268	0.34	0.303	0.268	0.34	SUBCLONAL	1	TRUE	1	0.64	2		979	929	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761303	59761303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367816363	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	51	671	2	ENST00000259008.2:c.3104G>A	p.Arg1035His	p.R1035H	ENST00000259008	NM_032043.2	1035	cGt/cAt	20/20	1	2	FACETS	0.217	0.184	0.254	0.217	0.184	0.254	SUBCLONAL	1	TRUE	1	0.64	2		673	735	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532631	63532631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148419444	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	41	435	2	ENST00000307078.5:c.1948C>T	p.Arg650Cys	p.R650C	ENST00000307078	NM_004655.3	650	Cgc/Tgc	8/11	1	2	FACETS	0.295	0.246	0.35	0.295	0.246	0.35	SUBCLONAL	1	TRUE	1	0.64	2		437	434	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774746	73774746	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	53	308	0	ENST00000254810.4:c.341A>C	p.His114Pro	p.H114P	ENST00000254810	NM_005324.3	114	cAc/cCc	4/4	1	2	FACETS	0.511	0.438	0.59	0.511	0.438	0.59	SUBCLONAL	1	TRUE	1	0.64	2		308	324	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681695	78681695	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	205	686	0	ENST00000306801.3:c.403A>G	p.Thr135Ala	p.T135A	ENST00000306801	NM_020761.2	135	Acg/Gcg	4/34	1	2	FACETS	0.935	0.871	1	0.935	0.871	1	CLONAL	1	TRUE	1	0.64	2		686	685	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743294	743294	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	289	796	1	ENST00000314574.4:c.846del	p.Lys282AsnfsTer2	p.K282Nfs*2	ENST00000314574	NM_005433.3	282	aaA/aa	7/12	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.64	2		797	873	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584468	39584468	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253032956	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	43	553	0	ENST00000262039.4:c.1133G>A	p.Arg378His	p.R378H	ENST00000262039	NM_002647.2	378	cGt/cAt	10/25	1	2	FACETS	0.211	0.176	0.25	0.211	0.176	0.25	SUBCLONAL	1	TRUE	1	0.64	2		553	637	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612377	1612377	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753978381	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	49	864	2	ENST00000344749.5:c.1642C>T	p.Arg548Cys	p.R548C	ENST00000344749	NM_001136139.2	548	Cgc/Tgc	18/19	1	2	FACETS	0.207	0.175	0.243	0.207	0.175	0.243	SUBCLONAL	1	TRUE	1	0.64	2		866	738	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226457	2226457	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1168808555	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	96	519	0	ENST00000398665.3:c.3937G>A	p.Ala1313Thr	p.A1313T	ENST00000398665	NM_032482.2	1313	Gcc/Acc	27/28	1	2	FACETS	0.714	0.64	0.792	0.714	0.64	0.792	SUBCLONAL	1	TRUE	1	0.64	2		519	420	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110188	3110188	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587777021	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	102	618	1	ENST00000078429.4:c.178C>T	p.Arg60Cys	p.R60C	ENST00000078429	NM_002067.2	60	Cgc/Tgc	2/7	1	2	FACETS	0.587	0.527	0.651	0.587	0.527	0.651	SUBCLONAL	1	TRUE	1	0.64	2		619	543	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115024	3115024	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	97	685	0	ENST00000078429.4:c.559A>G	p.Thr187Ala	p.T187A	ENST00000078429	NM_002067.2	187	Acc/Gcc	4/7	1	2	FACETS	0.629	0.563	0.698	0.629	0.563	0.698	SUBCLONAL	1	TRUE	1	0.64	2		685	482	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115036	3115036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1317391449	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	164	694	0	ENST00000078429.4:c.571G>A	p.Glu191Lys	p.E191K	ENST00000078429	NM_002067.2	191	Gag/Aag	4/7	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.64	2		694	509	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208335	5208335	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148478353	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	205	704	3	ENST00000357368.4:c.5555C>T	p.Ser1852Leu	p.S1852L	ENST00000357368	NM_002850.3	1852	tCg/tTg	36/38	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.64	2		707	523	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212259	5212259	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	79	505	0	ENST00000357368.4:c.4772C>T	p.Ala1591Val	p.A1591V	ENST00000357368	NM_002850.3	1591	gCc/gTc	32/38	1	2	FACETS	0.771	0.685	0.863	0.771	0.685	0.863	SUBCLONAL	1	TRUE	1	0.64	2		505	320	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214612	5214612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139132124	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	27	725	2	ENST00000357368.4:c.4454C>T	p.Ala1485Val	p.A1485V	ENST00000357368	NM_002850.3	1485	gCg/gTg	29/38	1	2	FACETS	0.159	0.126	0.198	0.159	0.126	0.198	SUBCLONAL	1	TRUE	1	0.64	2		727	529	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5260834	5260834	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	35	474	0	ENST00000357368.4:c.578-1G>T		p.X193_splice	ENST00000357368	NM_002850.3	193			0.161389291406258	0	FACETS	0.1	0.082	0.121			1	INDETERMINATE	1	TRUE	0	0.64	0		474	394	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7126663	7126663	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	51	486	0	ENST00000302850.5:c.2946-1G>A		p.X982_splice	ENST00000302850	NM_000208.2	982			0.161389291406258	0	FACETS	0.13	0.11	0.151			1	INDETERMINATE	1	TRUE	0	0.64	0		486	443	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170638	7170638	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	217	839	0	ENST00000302850.5:c.1393G>T	p.Glu465Ter	p.E465*	ENST00000302850	NM_000208.2	465	Gaa/Taa	6/22	0.161389291406258	0	FACETS	0.384	0.359	0.41			1	INDETERMINATE	1	TRUE	0	0.64	0		839	635	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267883	7267883	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	19	251	0	ENST00000302850.5:c.125A>C	p.Asn42Thr	p.N42T	ENST00000302850	NM_000208.2	42	aAc/aCc	2/22	1	2	FACETS	0.217	0.165	0.279	0.217	0.165	0.279	SUBCLONAL	1	TRUE	1	0.64	2		251	273	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247932	10247932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1365871222	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	28	368	1	ENST00000340748.4:c.4270C>T	p.Arg1424Cys	p.R1424C	ENST00000340748		1424	Cgc/Tgc	36/40	1	2	FACETS	0.331	0.266	0.406	0.331	0.266	0.406	SUBCLONAL	1	TRUE	1	0.64	2		369	264	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250470	10250470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774073234	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	34	670	1	ENST00000340748.4:c.3782G>A	p.Arg1261Gln	p.R1261Q	ENST00000340748		1261	cGg/cAg	33/40	1	2	FACETS	0.169	0.137	0.205	0.169	0.137	0.205	SUBCLONAL	1	TRUE	1	0.64	2		671	629	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262506	10262506	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	217	609	0	ENST00000340748.4:c.1989G>T	p.Glu663Asp	p.E663D	ENST00000340748		663	gaG/gaT	22/40	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.64	2		609	660	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105678	11105678	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	88	398	1	ENST00000358026.2:c.1593+1G>A		p.X531_splice	ENST00000358026	NM_001128849.1	531			1	2	FACETS	0.698	0.622	0.778	0.698	0.622	0.778	SUBCLONAL	1	TRUE	1	0.64	2		399	394	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276289	15276289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755817475	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	137	578	2	ENST00000263388.2:c.5705G>A	p.Arg1902His	p.R1902H	ENST00000263388	NM_000435.2	1902	cGc/cAc	31/33	1	2	FACETS	0.752	0.687	0.82	0.752	0.687	0.82	SUBCLONAL	1	TRUE	1	0.64	2		580	569	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15280904	15280904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1251693132	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	33	702	1	ENST00000263388.2:c.5192G>A	p.Arg1731Gln	p.R1731Q	ENST00000263388	NM_000435.2	1731	cGg/cAg	28/33	1	2	FACETS	0.177	0.144	0.215	0.177	0.144	0.215	SUBCLONAL	1	TRUE	1	0.64	2		703	582	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15280944	15280944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	32	781	0	ENST00000263388.2:c.5152G>A	p.Ala1718Thr	p.A1718T	ENST00000263388	NM_000435.2	1718	Gcc/Acc	28/33	1	2	FACETS	0.156	0.126	0.19	0.156	0.126	0.19	SUBCLONAL	1	TRUE	1	0.64	2		781	640	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288871	15288871	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	70	273	0	ENST00000263388.2:c.3868G>A	p.Ala1290Thr	p.A1290T	ENST00000263388	NM_000435.2	1290	Gcg/Acg	24/33	1	2	FACETS	0.708	0.622	0.799	0.708	0.622	0.799	SUBCLONAL	1	TRUE	1	0.64	2		273	309	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299950	15299950	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	30	588	0	ENST00000263388.2:c.1228A>G	p.Asn410Asp	p.N410D	ENST00000263388	NM_000435.2	410	Aac/Gac	8/33	1	2	FACETS	0.181	0.145	0.221	0.181	0.145	0.221	SUBCLONAL	1	TRUE	1	0.64	2		588	519	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302604	15302604	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115836330	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	193	766	3	ENST00000263388.2:c.754G>A	p.Val252Met	p.V252M	ENST00000263388	NM_000435.2	252	Gtg/Atg	5/33	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.64	2		769	592	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349669	15349669	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1052018084	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	15	338	0	ENST00000263377.2:c.3905C>T	p.Ala1302Val	p.A1302V	ENST00000263377	NM_058243.2	1302	gCt/gTt	19/20	1	2	FACETS	0.192	0.14	0.254	0.192	0.14	0.254	SUBCLONAL	1	TRUE	1	0.64	2		338	244	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350626	15350626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1234699192	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	134	508	0	ENST00000263377.2:c.3289C>T	p.Arg1097Cys	p.R1097C	ENST00000263377	NM_058243.2	1097	Cgt/Tgt	16/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.64	2		508	354	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355306	15355306	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	67	209	0	ENST00000263377.2:c.2317C>T	p.Gln773Ter	p.Q773*	ENST00000263377	NM_058243.2	773	Caa/Taa	13/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.64	2		209	162	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948010	17948010	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	25	753	0	ENST00000458235.1:c.1714G>T	p.Ala572Ser	p.A572S	ENST00000458235	NM_000215.3	572	Gca/Tca	13/24	1	2	FACETS	0.121	0.095	0.151	0.121	0.095	0.151	SUBCLONAL	1	TRUE	1	0.64	2		753	646	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952223	17952223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	26	484	0	ENST00000458235.1:c.1117G>A	p.Ala373Thr	p.A373T	ENST00000458235	NM_000215.3	373	Gcc/Acc	8/24	1	2	FACETS	0.214	0.169	0.266	0.214	0.169	0.266	SUBCLONAL	1	TRUE	1	0.64	2		484	379	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955159	17955159	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	157	603	1	ENST00000458235.1:c.68C>A	p.Ala23Asp	p.A23D	ENST00000458235	NM_000215.3	23	gCt/gAt	2/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.64	2		604	451	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271340	18271340	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	210	728	0	ENST00000222254.8:c.382C>A	p.Leu128Met	p.L128M	ENST00000222254	NM_005027.3	128	Ctg/Atg	3/16	1	2	FACETS	0.996	0.929	1	0.996	0.929	1	CLONAL	1	TRUE	1	0.64	2		728	659	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277075	18277075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376215289	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	205	647	0	ENST00000222254.8:c.1522C>T	p.Arg508Cys	p.R508C	ENST00000222254	NM_005027.3	508	Cgc/Tgc	12/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.64	2		647	592	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257137	19257137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	50	280	0	ENST00000162023.5:c.826G>A	p.Ala276Thr	p.A276T	ENST00000162023		276	Gcc/Acc	12/13	1	2	FACETS	0.947	0.819	1	0.947	0.819	1	CLONAL	1	TRUE	1	0.64	2		280	165	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793295	33793295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	24	351	1	ENST00000498907.2:c.26C>T	p.Ala9Val	p.A9V	ENST00000498907	NM_004364.3	9	gCg/gTg	1/1	1	2	FACETS	0.221	0.173	0.276	0.221	0.173	0.276	SUBCLONAL	1	TRUE	1	0.64	2		352	340	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748452	40748452	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs575460456	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	33	721	2	ENST00000392038.2:c.430C>T	p.Arg144Trp	p.R144W	ENST00000392038	NM_001626.4	144	Cgg/Tgg	5/14	1	2	FACETS	0.174	0.141	0.212	0.174	0.141	0.212	SUBCLONAL	1	TRUE	1	0.64	2		723	591	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763452	41763452	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	44	795	0	ENST00000301178.4:c.2251C>A	p.Pro751Thr	p.P751T	ENST00000301178	NM_021913.4	751	Ccg/Acg	19/20	1	2	FACETS	0.202	0.169	0.239	0.202	0.169	0.239	SUBCLONAL	1	TRUE	1	0.64	2		795	681	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867304	45867304	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1372639983	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	14	338	0	ENST00000391945.4:c.889G>A	p.Ala297Thr	p.A297T	ENST00000391945	NM_000400.3	297	Gcc/Acc	10/23	1	2	FACETS	0.171	0.123	0.229	0.171	0.123	0.229	SUBCLONAL	1	TRUE	1	0.64	2		338	256	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725157	47725157	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1361673951	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	28	495	3	ENST00000449228.1:c.587C>T	p.Ala196Val	p.A196V	ENST00000449228	NM_001127240.2	196	gCg/gTg	4/4	1	2	FACETS	0.183	0.146	0.226	0.183	0.146	0.226	SUBCLONAL	1	TRUE	1	0.64	2		498	478	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731581	47731581	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	21	141	0	ENST00000449228.1:c.211C>A	p.Leu71Met	p.L71M	ENST00000449228	NM_001127240.2	71	Ctg/Atg	2/4	1	2	FACETS	0.297	0.229	0.375	0.297	0.229	0.375	SUBCLONAL	1	TRUE	1	0.64	2		141	221	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919025	50919025	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	28	856	2	ENST00000440232.2:c.2762G>A	p.Arg921His	p.R921H	ENST00000440232	NM_002691.3	921	cGc/cAc	22/27	1	2	FACETS	0.159	0.127	0.197	0.159	0.127	0.197	SUBCLONAL	1	TRUE	1	0.64	2		858	549	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716012	52716012	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	187	782	0	ENST00000322088.6:c.577G>A	p.Ala193Thr	p.A193T	ENST00000322088	NM_014225.5	193	Gcc/Acc	5/15	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.64	2		782	579	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082215	16082215	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	28	724	0	ENST00000281043.3:c.29C>A	p.Pro10Gln	p.P10Q	ENST00000281043	NM_005378.4	10	cCg/cAg	2/3	1	2	FACETS	0.174	0.138	0.215	0.174	0.138	0.215	SUBCLONAL	1	TRUE	1	0.64	2		724	503	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085899	16085899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768128271	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	18	442	0	ENST00000281043.3:c.1075C>T	p.Leu359Phe	p.L359F	ENST00000281043	NM_005378.4	359	Ctc/Ttc	3/3	1	2	FACETS	0.163	0.122	0.211	0.163	0.122	0.211	SUBCLONAL	1	TRUE	1	0.64	2		442	346	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009093	27009093	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	126	225	0	ENST00000335756.4:c.29C>A	p.Pro10His	p.P10H	ENST00000335756	NM_001809.3	10	cCc/cAc	1/5	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.64	2		225	313	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47672779	47672779	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	143	555	0	ENST00000233146.2:c.1369A>C	p.Thr457Pro	p.T457P	ENST00000233146	NM_000251.2	457	Act/Cct	8/16	1	2	FACETS	0.752	0.689	0.819	0.752	0.689	0.819	SUBCLONAL	1	TRUE	1	0.64	2		555	594	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707890	47707890	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	64	520	1	ENST00000233146.2:c.2514G>T	p.Lys838Asn	p.K838N	ENST00000233146	NM_000251.2	838	aaG/aaT	15/16	1	2	FACETS	0.353	0.306	0.405	0.353	0.306	0.405	SUBCLONAL	1	TRUE	1	0.64	2		521	566	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010475	48010475	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	120	378	0	ENST00000234420.5:c.103G>A	p.Ala35Thr	p.A35T	ENST00000234420	NM_000179.2	35	Gcc/Acc	1/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.64	2		378	306	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032816	48032816	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	59	644	1	ENST00000234420.5:c.3616G>T	p.Ala1206Ser	p.A1206S	ENST00000234420	NM_000179.2	1206	Gca/Tca	7/10	1	2	FACETS	0.245	0.21	0.283	0.245	0.21	0.283	SUBCLONAL	1	TRUE	1	0.64	2		645	754	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719617	61719617	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	24	473	0	ENST00000401558.2:c.1567-1G>T		p.X523_splice	ENST00000401558	NM_003400.3	523			1	2	FACETS	0.184	0.144	0.231	0.184	0.144	0.231	SUBCLONAL	1	TRUE	1	0.64	2		473	407	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61725875	61725875	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	189	523	0	ENST00000401558.2:c.692G>T	p.Arg231Ile	p.R231I	ENST00000401558	NM_003400.3	231	aGa/aTa	9/25	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.64	2		523	585	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61749811	61749811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	158	365	0	ENST00000401558.2:c.236G>A	p.Gly79Glu	p.G79E	ENST00000401558	NM_003400.3	79	gGa/gAa	4/25	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.64	2		365	420	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881440	111881440	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	179	585	0	ENST00000393256.3:c.118C>A	p.Pro40Thr	p.P40T	ENST00000393256	NM_006538.4	40	Cca/Aca	2/4	0.161389291406258	4	FACETS	0.927	0.862	0.993	0.927	0.862	0.993	INDETERMINATE	2	TRUE	2	0.64	4		585	495	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872552	136872552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145335491	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	49	916	4	ENST00000241393.3:c.946G>A	p.Ala316Thr	p.A316T	ENST00000241393	NM_003467.2	316	Gca/Aca	2/2	1	2	FACETS	0.159	0.134	0.187	0.159	0.134	0.187	SUBCLONAL	1	TRUE	1	0.64	2		920	962	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872795	136872795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1272938495	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	279	1030	1	ENST00000241393.3:c.703C>T	p.Arg235Cys	p.R235C	ENST00000241393	NM_003467.2	235	Cgc/Tgc	2/2	1	2	FACETS	0.956	0.9	1	0.956	0.9	1	CLONAL	1	TRUE	1	0.64	2		1031	912	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873449	136873449	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	89	981	1	ENST00000241393.3:c.49G>A	p.Gly17Ser	p.G17S	ENST00000241393	NM_003467.2	17	Ggc/Agc	2/2	1	2	FACETS	0.259	0.229	0.292	0.259	0.229	0.292	SUBCLONAL	1	TRUE	1	0.64	2		982	1073	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622483	158622483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	49	931	0	ENST00000263640.3:c.1016G>A	p.Ser339Asn	p.S339N	ENST00000263640	NM_001105.4	339	aGc/aAc	8/11	1	2	FACETS	0.162	0.136	0.19	0.162	0.136	0.19	SUBCLONAL	1	TRUE	1	0.64	2		931	947	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190670403	190670403	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	245	632	0	ENST00000441310.2:c.341C>A	p.Ala114Asp	p.A114D	ENST00000441310	NM_000534.4	114	gCt/gAt	4/13	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.64	2		632	740	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719668	190719668	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	52	356	1	ENST00000441310.2:c.1670C>A	p.Ser557Tyr	p.S557Y	ENST00000441310	NM_000534.4	557	tCt/tAt	9/13	1	2	FACETS	0.445	0.38	0.516	0.445	0.38	0.516	SUBCLONAL	1	TRUE	1	0.64	2		357	365	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732673	204732673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	28	574	1	ENST00000302823.3:c.8G>A	p.Cys3Tyr	p.C3Y	ENST00000302823	NM_005214.4	3	tGc/tAc	1/4	1	2	FACETS	0.161	0.128	0.199	0.161	0.128	0.199	SUBCLONAL	1	TRUE	1	0.64	2		575	544	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248560	212248560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763559555	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	45	751	1	ENST00000342788.4:c.3707C>T	p.Ala1236Val	p.A1236V	ENST00000342788	NM_005235.2	1236	gCg/gTg	28/28	1	2	FACETS	0.158	0.132	0.187	0.158	0.132	0.187	SUBCLONAL	1	TRUE	1	0.64	2		752	889	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593543	215593543	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs76744638	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	31	475	1	ENST00000260947.4:c.2191C>T	p.Arg731Cys	p.R731C	ENST00000260947	NM_000465.2	731	Cgc/Tgc	11/11	1	2	FACETS	0.2	0.161	0.244	0.2	0.161	0.244	SUBCLONAL	1	TRUE	1	0.64	2		476	484	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660085	227660085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	97	455	1	ENST00000305123.5:c.3370G>A	p.Ala1124Thr	p.A1124T	ENST00000305123	NM_005544.2	1124	Gca/Aca	1/2	1	2	FACETS	0.826	0.743	0.913	0.826	0.743	0.913	CLONAL	1	TRUE	1	0.64	2		456	367	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793225	242793225	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	175	558	0	ENST00000334409.5:c.852C>A	p.Cys284Ter	p.C284*	ENST00000334409	NM_005018.2	284	tgC/tgA	5/5	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.64	2		558	505	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793238	242793238	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	204	542	0	ENST00000334409.5:c.839A>T	p.Glu280Val	p.E280V	ENST00000334409	NM_005018.2	280	gAg/gTg	5/5	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.64	2		542	500	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794117	242794117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773349951	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	52	682	0	ENST00000334409.5:c.611G>A	p.Arg204His	p.R204H	ENST00000334409	NM_005018.2	204	cGc/cAc	4/5	1	2	FACETS	0.247	0.209	0.288	0.247	0.209	0.288	SUBCLONAL	1	TRUE	1	0.64	2		682	659	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30956910	30956910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1296130945	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	58	739	1	ENST00000375687.4:c.236G>A	p.Ser79Asn	p.S79N	ENST00000375687	NM_015338.5	79	aGc/aAc	4/13	1	2	FACETS	0.221	0.189	0.256	0.221	0.189	0.256	SUBCLONAL	1	TRUE	1	0.64	2		740	820	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021343	31021343	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	78	395	0	ENST00000375687.4:c.1342C>A	p.Leu448Ile	p.L448I	ENST00000375687	NM_015338.5	448	Ctc/Atc	12/13	1	2	FACETS	0.702	0.622	0.788	0.702	0.622	0.788	SUBCLONAL	1	TRUE	1	0.64	2		395	347	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024170	31024170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774688930	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	32	649	1	ENST00000375687.4:c.3655C>T	p.Pro1219Ser	p.P1219S	ENST00000375687	NM_015338.5	1219	Ccc/Tcc	13/13	1	2	FACETS	0.178	0.144	0.217	0.178	0.144	0.217	SUBCLONAL	1	TRUE	1	0.64	2		650	562	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31372564	31372564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	197	542	1	ENST00000328111.2:c.205G>T	p.Asp69Tyr	p.D69Y	ENST00000328111	NM_006892.3	69	Gac/Tac	4/23	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.64	2		543	585	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374377	31374377	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	47	739	0	ENST00000328111.2:c.376G>T	p.Gly126Cys	p.G126C	ENST00000328111	NM_006892.3	126	Ggc/Tgc	5/23	1	2	FACETS	0.227	0.191	0.267	0.227	0.191	0.267	SUBCLONAL	1	TRUE	1	0.64	2		739	647	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31390277	31390277	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1468904331	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	147	515	0	ENST00000328111.2:c.2231+1G>A		p.X744_splice	ENST00000328111	NM_006892.3	744			1	2	FACETS	0.955	0.878	1	0.955	0.878	1	CLONAL	1	TRUE	1	0.64	2		515	481	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419906	41419906	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	211	651	0	ENST00000373198.4:c.415T>C	p.Ser139Pro	p.S139P	ENST00000373198	NM_133170.3	139	Tcc/Ccc	3/32	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.64	2		651	640	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514545	41514545	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	45	570	1	ENST00000373198.4:c.116G>A	p.Ser39Asn	p.S39N	ENST00000373198	NM_133170.3	39	aGc/aAc	2/32	1	2	FACETS	0.262	0.22	0.309	0.262	0.22	0.309	SUBCLONAL	1	TRUE	1	0.64	2		571	536	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46275983	46275983	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	48	1008	0	ENST00000371998.3:c.3419A>C	p.Asn1140Thr	p.N1140T	ENST00000371998		1140	aAt/aCt	18/23	1	2	FACETS	0.177	0.149	0.208	0.177	0.149	0.208	SUBCLONAL	1	TRUE	1	0.64	2		1008	848	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485052	57485052	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	229	632	0	ENST00000371085.3:c.886C>A	p.Leu296Met	p.L296M	ENST00000371085	NM_000516.4	296	Ctg/Atg	11/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.64	2		632	647	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775583	39775583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369318352	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	165	518	1	ENST00000288319.7:c.437C>T	p.Ala146Val	p.A146V	ENST00000288319	NM_182918.3	146	gCg/gTg	4/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.64	2		519	491	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839731	42839731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	40	743	0	ENST00000398585.3:c.1508C>T	p.Ala503Val	p.A503V	ENST00000398585	NM_001135099.1	503	gCc/gTc	13/14	1	2	FACETS	0.176	0.146	0.21	0.176	0.146	0.21	SUBCLONAL	1	TRUE	1	0.64	2		743	710	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42843774	42843774	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	67	621	0	ENST00000398585.3:c.1145A>G	p.Asp382Gly	p.D382G	ENST00000398585	NM_001135099.1	382	gAc/gGc	10/14	1	2	FACETS	0.315	0.273	0.36	0.315	0.273	0.36	SUBCLONAL	1	TRUE	1	0.64	2		621	665	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651216	45651216	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200793282	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	36	675	3	ENST00000407780.3:c.809C>T	p.Ala270Val	p.A270V	ENST00000407780	NM_001283052.1	270	gCg/gTg	5/7	1	2	FACETS	0.181	0.148	0.218	0.181	0.148	0.218	SUBCLONAL	1	TRUE	1	0.64	2		678	623	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24134069	24134069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	49	829	0	ENST00000263121.7:c.220C>T	p.Pro74Ser	p.P74S	ENST00000263121	NM_003073.3	74	Cct/Tct	2/9	1	2	FACETS	0.201	0.17	0.236	0.201	0.17	0.236	SUBCLONAL	1	TRUE	1	0.64	2		829	760	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054186	30054186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	48	490	0	ENST00000338641.4:c.608C>T	p.Ala203Val	p.A203V	ENST00000338641	NM_000268.3	203	gCt/gTt	7/16	1	2	FACETS	0.259	0.218	0.303	0.259	0.218	0.303	SUBCLONAL	1	TRUE	1	0.64	2		490	580	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574832	41574832	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	113	658	0	ENST00000263253.7:c.7117C>A	p.Leu2373Ile	p.L2373I	ENST00000263253	NM_001429.3	2373	Ctt/Att	31/31	1	2	FACETS	0.627	0.566	0.691	0.627	0.566	0.691	SUBCLONAL	1	TRUE	1	0.64	2		658	563	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713710	30713710	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	76	365	0	ENST00000295754.5:c.1035G>T	p.Glu345Asp	p.E345D	ENST00000295754	NM_003242.5	345	gaG/gaT	4/7	1	2	FACETS	0.651	0.574	0.732	0.651	0.574	0.732	SUBCLONAL	1	TRUE	1	0.64	2		365	365	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732911	30732911	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	157	410	0	ENST00000295754.5:c.1525-1G>T		p.X509_splice	ENST00000295754	NM_003242.5	509			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.64	2		410	455	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30733065	30733065	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	41	471	0	ENST00000295754.5:c.1678G>T	p.Asp560Tyr	p.D560Y	ENST00000295754	NM_003242.5	560	Gac/Tac	7/7	1	2	FACETS	0.254	0.211	0.301	0.254	0.211	0.301	SUBCLONAL	1	TRUE	1	0.64	2		471	505	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035132	37035132	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs2020872	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	28	329	0	ENST00000231790.2:c.94A>G	p.Ile32Val	p.I32V	ENST00000231790	NM_000249.3	32	Atc/Gtc	1/19	1	2	FACETS	0.233	0.186	0.286	0.233	0.186	0.286	SUBCLONAL	1	TRUE	1	0.64	2		329	376	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182256	38182256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750043155	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	108	552	0	ENST00000396334.3:c.692G>A	p.Arg231Gln	p.R231Q	ENST00000396334	NM_002468.4	231	cGg/cAg	4/5	1	2	FACETS	0.689	0.621	0.76	0.689	0.621	0.76	SUBCLONAL	1	TRUE	1	0.64	2		552	490	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268826	41268826	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769825609	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	35	489	0	ENST00000349496.5:c.1064C>T	p.Pro355Leu	p.P355L	ENST00000349496	NM_001904.3	355	cCg/cTg	7/15	1	2	FACETS	0.19	0.155	0.229	0.19	0.155	0.229	SUBCLONAL	1	TRUE	1	0.64	2		489	576	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163461	47163461	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	197	548	0	ENST00000409792.3:c.2665G>T	p.Gly889Ter	p.G889*	ENST00000409792	NM_014159.6	889	Gga/Tga	3/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.64	2		548	553	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165918	47165918	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs775039657	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	251	704	3	ENST00000409792.3:c.208C>T	p.Arg70Ter	p.R70*	ENST00000409792	NM_014159.6	70	Cga/Tga	3/21	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.64	2		707	780	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52677265	52677265	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs374515597	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	292	769	1	ENST00000394830.3:c.994C>T	p.Arg332Cys	p.R332C	ENST00000394830	NM_018313.4	332	Cgt/Tgt	10/30	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.64	2		770	813	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480354	89480354	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1197239588	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	41	552	1	ENST00000336596.2:c.2191G>T	p.Ala731Ser	p.A731S	ENST00000336596	NM_005233.5	731	Gca/Tca	13/17	1	2	FACETS	0.199	0.165	0.237	0.199	0.165	0.237	SUBCLONAL	1	TRUE	1	0.64	2		553	643	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498448	89498448	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	223	677	0	ENST00000336596.2:c.2420T>C	p.Val807Ala	p.V807A	ENST00000336596	NM_005233.5	807	gTa/gCa	14/17	1	2	FACETS	0.969	0.906	1	0.969	0.906	1	CLONAL	1	TRUE	1	0.64	2		677	719	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631598	119631598	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	49	678	0	ENST00000316626.5:c.668G>T	p.Arg223Met	p.R223M	ENST00000316626		223	aGg/aTg	6/12	1	2	FACETS	0.197	0.166	0.231	0.197	0.166	0.231	SUBCLONAL	1	TRUE	1	0.64	2		678	779	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204636	128204636	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	185	699	1	ENST00000341105.2:c.805G>T	p.Gly269Cys	p.G269C	ENST00000341105	NM_032638.4	269	Ggc/Tgc	3/6	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.64	2		700	539	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851635	134851635	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	40	632	0	ENST00000398015.3:c.1041G>T	p.Glu347Asp	p.E347D	ENST00000398015	NM_004441.4	347	gaG/gaT	5/16	1	2	FACETS	0.231	0.192	0.276	0.231	0.192	0.276	SUBCLONAL	1	TRUE	1	0.64	2		632	540	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851639	134851639	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	33	618	0	ENST00000398015.3:c.1045G>T	p.Gly349Cys	p.G349C	ENST00000398015	NM_004441.4	349	Ggt/Tgt	5/16	1	2	FACETS	0.196	0.159	0.238	0.196	0.159	0.238	SUBCLONAL	1	TRUE	1	0.64	2		618	526	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138375063	138375063	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	193	539	0	ENST00000289153.2:c.2996T>G	p.Leu999Arg	p.L999R	ENST00000289153	NM_006219.2	999	cTc/cGc	21/22	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.64	2		539	556	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417787	138417787	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	42	565	0	ENST00000289153.2:c.1732C>A	p.Leu578Met	p.L578M	ENST00000289153	NM_006219.2	578	Ctg/Atg	11/22	1	2	FACETS	0.19	0.158	0.226	0.19	0.158	0.226	SUBCLONAL	1	TRUE	1	0.64	2		565	690	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478109	138478109	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs760521881	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	240	654	0	ENST00000289153.2:c.77C>A	p.Ser26Tyr	p.S26Y	ENST00000289153	NM_006219.2	26	tCt/tAt	1/22	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.64	2		654	661	SUCCESS
ATR	545	MSKCC	GRCh37	3	142177877	142177877	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376735982	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	49	600	0	ENST00000350721.4:c.7426C>T	p.Arg2476Cys	p.R2476C	ENST00000350721	NM_001184.3	2476	Cgt/Tgt	44/47	1	2	FACETS	0.211	0.178	0.248	0.211	0.178	0.248	SUBCLONAL	1	TRUE	1	0.64	2		600	725	SUCCESS
ATR	545	MSKCC	GRCh37	3	142184073	142184073	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	137	377	0	ENST00000350721.4:c.6907C>A	p.Leu2303Ile	p.L2303I	ENST00000350721	NM_001184.3	2303	Ctt/Att	41/47	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.64	2		377	422	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272137	142272137	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	36	549	0	ENST00000350721.4:c.2737G>T	p.Ala913Ser	p.A913S	ENST00000350721	NM_001184.3	913	Gct/Tct	13/47	1	2	FACETS	0.183	0.15	0.22	0.183	0.15	0.22	SUBCLONAL	1	TRUE	1	0.64	2		549	615	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430654	181430654	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	128	352	0	ENST00000325404.1:c.506G>T	p.Gly169Val	p.G169V	ENST00000325404	NM_003106.3	169	gGc/gTc	1/1	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.64	2		352	337	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430936	181430936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	50	688	0	ENST00000325404.1:c.788C>T	p.Ala263Val	p.A263V	ENST00000325404	NM_003106.3	263	gCg/gTg	1/1	1	2	FACETS	0.25	0.212	0.292	0.25	0.212	0.292	SUBCLONAL	1	TRUE	1	0.64	2		688	625	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146619	185146619	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750919427	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	25	493	0	ENST00000265026.3:c.250G>A	p.Val84Ile	p.V84I	ENST00000265026	NM_004721.4	84	Gtt/Att	2/14	1	2	FACETS	0.164	0.128	0.205	0.164	0.128	0.205	SUBCLONAL	1	TRUE	1	0.64	2		493	477	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181431	185181431	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377513650	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	35	661	0	ENST00000265026.3:c.1372C>T	p.Arg458Cys	p.R458C	ENST00000265026	NM_004721.4	458	Cgc/Tgc	8/14	1	2	FACETS	0.162	0.132	0.196	0.162	0.132	0.196	SUBCLONAL	1	TRUE	1	0.64	2		661	674	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608669	189608669	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	35	499	0	ENST00000264731.3:c.1744G>T	p.Asp582Tyr	p.D582Y	ENST00000264731	NM_003722.4	582	Gat/Tat	13/14	1	2	FACETS	0.211	0.172	0.255	0.211	0.172	0.255	SUBCLONAL	1	TRUE	1	0.64	2		499	518	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612100	189612100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1455505991	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	48	589	1	ENST00000264731.3:c.1852C>T	p.Arg618Trp	p.R618W	ENST00000264731	NM_003722.4	618	Cgg/Tgg	14/14	1	2	FACETS	0.229	0.193	0.269	0.229	0.193	0.269	SUBCLONAL	1	TRUE	1	0.64	2		590	655	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803592	1803592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs949596399	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	32	535	0	ENST00000260795.2:c.770C>T	p.Ala257Val	p.A257V	ENST00000260795		257	gCg/gTg	6/17	1	2	FACETS	0.271	0.22	0.329	0.271	0.22	0.329	SUBCLONAL	1	TRUE	1	0.64	2		535	369	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806590	1806590	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	39	700	0	ENST00000260795.2:c.1306C>T	p.Pro436Ser	p.P436S	ENST00000260795		436	Cca/Tca	9/17	1	2	FACETS	0.236	0.195	0.281	0.236	0.195	0.281	SUBCLONAL	1	TRUE	1	0.64	2		700	517	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155258	55155258	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	66	560	0	ENST00000257290.5:c.2857C>A	p.Leu953Met	p.L953M	ENST00000257290	NM_006206.4	953	Ctg/Atg	21/23	1	2	FACETS	0.312	0.27	0.357	0.312	0.27	0.357	SUBCLONAL	1	TRUE	1	0.64	2		560	661	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573306	55573306	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	175	608	0	ENST00000288135.5:c.968T>C	p.Val323Ala	p.V323A	ENST00000288135	NM_000222.2	323	gTa/gCa	6/21	1	2	FACETS	0.982	0.91	1	0.982	0.91	1	CLONAL	1	TRUE	1	0.64	2		608	557	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979469	55979469	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	39	568	0	ENST00000263923.4:c.976+2T>C		p.X326_splice	ENST00000263923	NM_002253.2	326			1	2	FACETS	0.219	0.181	0.261	0.219	0.181	0.261	SUBCLONAL	1	TRUE	1	0.64	2		568	557	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535436	66535436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	15	255	1	ENST00000273854.3:c.25G>A	p.Ala9Thr	p.A9T	ENST00000273854	NM_004439.5	9	Gcg/Acg	1/18	1	2	FACETS	0.206	0.15	0.272	0.206	0.15	0.272	SUBCLONAL	1	TRUE	1	0.64	2		256	228	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383654	84383654	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	264	786	2	ENST00000321945.7:c.1198T>A	p.Phe400Ile	p.F400I	ENST00000321945	NM_139076.2	400	Ttt/Att	9/9	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.64	2		788	793	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156966	106156966	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	144	535	0	ENST00000380013.4:c.1870del	p.Thr624GlnfsTer15	p.T624Qfs*15	ENST00000380013	NM_001127208.2	623	Aaa/aa	3/11	1	2	FACETS	0.888	0.815	0.963	0.888	0.815	0.963	CLONAL	1	TRUE	1	0.64	2		535	507	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130049	143130049	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	43	582	1	ENST00000262992.4:c.967G>A	p.Gly323Arg	p.G323R	ENST00000262992	NM_001101669.1	323	Ggg/Agg	11/24	1	2	FACETS	0.206	0.171	0.244	0.206	0.171	0.244	SUBCLONAL	1	TRUE	1	0.64	2		583	653	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247335	153247335	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	222	500	0	ENST00000281708.4:c.1467G>T	p.Glu489Asp	p.E489D	ENST00000281708	NM_033632.3	489	gaG/gaT	10/12	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.64	2		500	583	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540874	187540874	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	201	537	0	ENST00000441802.2:c.6866C>A	p.Ala2289Glu	p.A2289E	ENST00000441802	NM_005245.3	2289	gCg/gAg	10/27	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.64	2		537	550	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224560	224560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759568419	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	47	465	0	ENST00000264932.6:c.236G>A	p.Gly79Asp	p.G79D	ENST00000264932	NM_004168.2	79	gGc/gAc	3/15	1	2	FACETS	0.242	0.204	0.284	0.242	0.204	0.284	SUBCLONAL	1	TRUE	1	0.64	2		465	607	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233717	233717	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	91	392	0	ENST00000264932.6:c.1021G>A	p.Asp341Asn	p.D341N	ENST00000264932	NM_004168.2	341	Gat/Aat	8/15	1	2	FACETS	0.648	0.578	0.721	0.648	0.578	0.721	SUBCLONAL	1	TRUE	1	0.64	2		392	439	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235390	235390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878854625	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	22	498	1	ENST00000264932.6:c.1196C>T	p.Pro399Leu	p.P399L	ENST00000264932	NM_004168.2	399	cCg/cTg	9/15	1	2	FACETS	0.171	0.132	0.216	0.171	0.132	0.216	SUBCLONAL	1	TRUE	1	0.64	2		499	403	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251561	251561	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367621815	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	35	525	1	ENST00000264932.6:c.1772C>T	p.Ala591Val	p.A591V	ENST00000264932	NM_004168.2	591	gCg/gTg	13/15	1	2	FACETS	0.203	0.166	0.245	0.203	0.166	0.245	SUBCLONAL	1	TRUE	1	0.64	2		526	538	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279528	1279528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1458244308	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	157	666	1	ENST00000310581.5:c.2008G>A	p.Ala670Thr	p.A670T	ENST00000310581	NM_198253.2	670	Gcg/Acg	5/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.64	2		667	444	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293574	1293574	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1338098756	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	24	573	1	ENST00000310581.5:c.1427G>A	p.Gly476Asp	p.G476D	ENST00000310581	NM_198253.2	476	gGc/gAc	2/16	1	2	FACETS	0.195	0.153	0.245	0.195	0.153	0.245	SUBCLONAL	1	TRUE	1	0.64	2		574	384	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293834	1293834	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	34	671	0	ENST00000310581.5:c.1167G>A	p.Met389Ile	p.M389I	ENST00000310581	NM_198253.2	389	atG/atA	2/16	1	2	FACETS	0.228	0.186	0.275	0.228	0.186	0.275	SUBCLONAL	1	TRUE	1	0.64	2		671	466	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38942410	38942410	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	172	492	0	ENST00000357387.3:c.5123C>A	p.Ser1708Tyr	p.S1708Y	ENST00000357387	NM_152756.3	1708	tCc/tAc	38/38	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.64	2		492	532	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56171084	56171084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202189340	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	178	465	0	ENST00000399503.3:c.1912G>A	p.Val638Ile	p.V638I	ENST00000399503	NM_005921.1	638	Gtt/Att	10/20	1	2	FACETS	0.979	0.908	1	0.979	0.908	1	CLONAL	1	TRUE	1	0.64	2		465	568	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753092	57753092	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	37	632	0	ENST00000274289.3:c.924G>T	p.Lys308Asn	p.K308N	ENST00000274289	NM_006622.3	308	aaG/aaT	7/14	1	2	FACETS	0.178	0.146	0.214	0.178	0.146	0.214	SUBCLONAL	1	TRUE	1	0.64	2		632	648	SUCCESS
APC	324	MSKCC	GRCh37	5	112176000	112176000	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs373419559	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	82	350	0	ENST00000257430.4:c.4709A>G	p.Asp1570Gly	p.D1570G	ENST00000257430	NM_000038.5	1570	gAt/gGt	16/16	1	2	FACETS	0.718	0.638	0.802	0.718	0.638	0.802	SUBCLONAL	1	TRUE	1	0.64	2		350	357	SUCCESS
APC	324	MSKCC	GRCh37	5	112176278	112176278	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758987855	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	196	601	1	ENST00000257430.4:c.4987G>A	p.Glu1663Lys	p.E1663K	ENST00000257430	NM_000038.5	1663	Gaa/Aaa	16/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.64	2		602	571	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499605	149499605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	141	750	1	ENST00000261799.4:c.2668G>A	p.Gly890Arg	p.G890R	ENST00000261799	NM_002609.3	890	Ggg/Agg	19/23	1	2	FACETS	0.682	0.623	0.744	0.682	0.623	0.744	SUBCLONAL	1	TRUE	1	0.64	2		751	646	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170817069	170817069	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	42	536	0	ENST00000296930.5:c.73G>A	p.Ala25Thr	p.A25T	ENST00000296930	NM_002520.6	25	Gcc/Acc	2/11	1	2	FACETS	0.194	0.161	0.23	0.194	0.161	0.23	SUBCLONAL	1	TRUE	1	0.64	2		536	678	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517953	176517953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	168	633	1	ENST00000292408.4:c.451C>T	p.His151Tyr	p.H151Y	ENST00000292408	NM_213647.1	151	Cac/Tac	5/18	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.64	2		634	509	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518084	176518084	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	42	631	0	ENST00000292408.4:c.582G>T	p.Glu194Asp	p.E194D	ENST00000292408	NM_213647.1	194	gaG/gaT	5/18	1	2	FACETS	0.254	0.211	0.301	0.254	0.211	0.301	SUBCLONAL	1	TRUE	1	0.64	2		631	517	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637190	176637190	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	49	531	1	ENST00000439151.2:c.1790C>T	p.Ala597Val	p.A597V	ENST00000439151	NM_022455.4	597	gCt/gTt	5/23	1	2	FACETS	0.261	0.221	0.306	0.261	0.221	0.306	SUBCLONAL	1	TRUE	1	0.64	2		532	586	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721406	176721406	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	30	658	1	ENST00000439151.2:c.7037G>T	p.Arg2346Met	p.R2346M	ENST00000439151	NM_022455.4	2346	aGg/aTg	23/23	1	2	FACETS	0.173	0.139	0.212	0.173	0.139	0.212	SUBCLONAL	1	TRUE	1	0.64	2		659	541	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048108	180048108	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	72	637	0	ENST00000261937.6:c.2165C>A	p.Ser722Tyr	p.S722Y	ENST00000261937	NM_182925.4	722	tCt/tAt	14/30	1	2	FACETS	0.522	0.458	0.591	0.522	0.458	0.591	SUBCLONAL	1	TRUE	1	0.64	2		637	431	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048722	180048722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1310636098	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	141	515	0	ENST00000261937.6:c.1840C>T	p.His614Tyr	p.H614Y	ENST00000261937	NM_182925.4	614	Cat/Tat	13/30	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.64	2		515	410	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394902	394902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767879003	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	159	448	1	ENST00000380956.4:c.298G>A	p.Ala100Thr	p.A100T	ENST00000380956	NM_001195286.1	100	Gct/Act	3/9	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.64	2		449	491	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056398	26056398	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	28	463	0	ENST00000343677.2:c.259C>A	p.Leu87Met	p.L87M	ENST00000343677	NM_005319.3	87	Ctg/Atg	1/1	1	2	FACETS	0.165	0.132	0.204	0.165	0.132	0.204	SUBCLONAL	1	TRUE	1	0.64	2		463	529	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158771	26158771	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	27	408	0	ENST00000289316.2:c.374C>T	p.Ser125Phe	p.S125F	ENST00000289316	NM_138720.2	125	tCc/tTc	1/2	1	2	FACETS	0.157	0.124	0.195	0.157	0.124	0.195	SUBCLONAL	1	TRUE	1	0.64	2		408	537	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271387	26271387	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	66	1232	1	ENST00000305910.3:c.226G>A	p.Ala76Thr	p.A76T	ENST00000305910	NM_003534.2	76	Gct/Act	1/1	1	2	FACETS	0.199	0.172	0.229	0.199	0.172	0.229	SUBCLONAL	1	TRUE	1	0.64	2		1233	1036	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839849	27839849	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	87	1249	0	ENST00000328488.2:c.245A>G	p.Asp82Gly	p.D82G	ENST00000328488	NM_003533.2	82	gAt/gGt	1/1	1	2	FACETS	0.26	0.229	0.293	0.26	0.229	0.293	SUBCLONAL	1	TRUE	1	0.64	2		1249	1046	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673467	30673467	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	56	662	0	ENST00000376406.3:c.3493G>T	p.Ala1165Ser	p.A1165S	ENST00000376406	NM_014641.2	1165	Gcc/Tcc	10/15	1	2	FACETS	0.34	0.291	0.393	0.34	0.291	0.393	SUBCLONAL	1	TRUE	1	0.64	2		662	515	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673647	30673647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	276	800	0	ENST00000376406.3:c.3313C>T	p.Pro1105Ser	p.P1105S	ENST00000376406	NM_014641.2	1105	Cct/Tct	10/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.64	2		800	793	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181952	32181952	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	44	752	2	ENST00000375023.3:c.2102C>A	p.Ala701Asp	p.A701D	ENST00000375023	NM_004557.3	701	gCc/gAc	13/30	1	2	FACETS	0.208	0.174	0.246	0.208	0.174	0.246	SUBCLONAL	1	TRUE	1	0.64	2		754	660	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289155	33289155	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	44	524	1	ENST00000374542.5:c.397G>A	p.Val133Ile	p.V133I	ENST00000374542	NM_001141970.1	133	Gtt/Att	3/8	1	2	FACETS	0.237	0.198	0.28	0.237	0.198	0.28	SUBCLONAL	1	TRUE	1	0.64	2		525	580	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652077	36652077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372390764	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	48	653	0	ENST00000244741.5:c.199C>T	p.Arg67Cys	p.R67C	ENST00000244741	NM_000389.4	67	Cgt/Tgt	2/3	1	2	FACETS	0.268	0.226	0.314	0.268	0.226	0.314	SUBCLONAL	1	TRUE	1	0.64	2		653	560	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969087	93969087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1270476760	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	72	788	0	ENST00000369303.4:c.1909C>T	p.Arg637Cys	p.R637C	ENST00000369303	NM_004440.3	637	Cgt/Tgt	10/17	1	2	FACETS	0.259	0.226	0.296	0.259	0.226	0.296	SUBCLONAL	1	TRUE	1	0.64	2		788	868	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979244	93979244	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	56	907	0	ENST00000369303.4:c.1584del	p.Arg529AspfsTer7	p.R529Dfs*7	ENST00000369303	NM_004440.3	528	ccC/cc	7/17	1	2	FACETS	0.191	0.163	0.222	0.191	0.163	0.222	SUBCLONAL	1	TRUE	1	0.64	2		907	915	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553386	106553386	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	103	355	1	ENST00000369096.4:c.1351C>A	p.Leu451Ile	p.L451I	ENST00000369096	NM_001198.3	451	Ctc/Atc	5/7	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.64	2		356	311	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554247	106554247	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	84	458	0	ENST00000369096.4:c.1775T>C	p.Val592Ala	p.V592A	ENST00000369096	NM_001198.3	592	gTc/gCc	6/7	1	2	FACETS	0.573	0.508	0.642	0.573	0.508	0.642	SUBCLONAL	1	TRUE	1	0.64	2		458	458	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554370	106554370	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	168	527	1	ENST00000369096.4:c.1898G>A	p.Cys633Tyr	p.C633Y	ENST00000369096	NM_001198.3	633	tGc/tAc	6/7	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.64	2		528	523	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554834	106554834	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	136	467	1	ENST00000369096.4:c.1951C>T	p.Arg651Ter	p.R651*	ENST00000369096	NM_001198.3	651	Cga/Tga	7/7	1	2	FACETS	0.982	0.9	1	0.982	0.9	1	CLONAL	1	TRUE	1	0.64	2		468	433	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681120	117681120	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs748436511	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	32	576	1	ENST00000368508.3:c.3500del	p.Leu1167Ter	p.L1167*	ENST00000368508	NM_002944.2	1167	tTa/ta	23/43	0.0922914893150066	0	FACETS	0.061	0.049	0.074			1	INDETERMINATE	1	TRUE	0	0.64	0		577	594	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718165	117718165	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	32	535	1	ENST00000368508.3:c.692G>T	p.Arg231Met	p.R231M	ENST00000368508	NM_002944.2	231	aGg/aTg	7/43	0.0922914893150066	0	FACETS	0.063	0.051	0.078			1	INDETERMINATE	1	TRUE	0	0.64	0		536	567	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137528135	137528135	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	37	562	2	ENST00000367739.4:c.165G>T	p.Gln55His	p.Q55H	ENST00000367739	NM_000416.2	55	caG/caT	2/7	1	2	FACETS	0.169	0.139	0.204	0.169	0.139	0.204	SUBCLONAL	1	TRUE	1	0.64	2		564	683	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138197270	138197270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140951984	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	131	579	0	ENST00000237289.4:c.772G>A	p.Val258Ile	p.V258I	ENST00000237289	NM_001270507.1	258	Gta/Ata	5/9	1	2	FACETS	0.7	0.637	0.765	0.7	0.637	0.765	SUBCLONAL	1	TRUE	1	0.64	2		579	585	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332873	152332873	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	38	602	1	ENST00000206249.3:c.1179G>A	p.Trp393Ter	p.W393*	ENST00000206249	NM_000125.3	393	tgG/tgA	5/8	1	2	FACETS	0.177	0.146	0.213	0.177	0.146	0.213	SUBCLONAL	1	TRUE	1	0.64	2		603	670	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332896	152332896	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	195	543	0	ENST00000206249.3:c.1202A>C	p.Lys401Thr	p.K401T	ENST00000206249	NM_000125.3	401	aAg/aCg	5/8	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.64	2		543	570	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332911	152332911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	164	498	0	ENST00000206249.3:c.1217C>T	p.Pro406Leu	p.P406L	ENST00000206249	NM_000125.3	406	cCt/cTt	5/8	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.64	2		498	480	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157495145	157495145	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	224	531	0	ENST00000346085.5:c.3029C>A	p.Ser1010Tyr	p.S1010Y	ENST00000346085	NM_020732.3	1010	tCt/tAt	11/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.64	2		531	656	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522269	157522269	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	37	672	0	ENST00000346085.5:c.4541C>A	p.Ser1514Tyr	p.S1514Y	ENST00000346085	NM_020732.3	1514	tCt/tAt	18/20	1	2	FACETS	0.203	0.167	0.244	0.203	0.167	0.244	SUBCLONAL	1	TRUE	1	0.64	2		672	569	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527808	157527808	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766931727	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	28	437	0	ENST00000346085.5:c.5533C>T	p.Arg1845Cys	p.R1845C	ENST00000346085	NM_020732.3	1845	Cgc/Tgc	20/20	1	2	FACETS	0.19	0.151	0.235	0.19	0.151	0.235	SUBCLONAL	1	TRUE	1	0.64	2		437	460	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528673	157528673	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1226524520	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	217	602	2	ENST00000346085.5:c.6398C>T	p.Ala2133Val	p.A2133V	ENST00000346085	NM_020732.3	2133	gCg/gTg	20/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.64	2		604	663	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528936	157528936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1390972891	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	36	472	0	ENST00000346085.5:c.6661C>T	p.Arg2221Trp	p.R2221W	ENST00000346085	NM_020732.3	2221	Cgg/Tgg	20/20	1	2	FACETS	0.199	0.163	0.239	0.199	0.163	0.239	SUBCLONAL	1	TRUE	1	0.64	2		472	566	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975354	13975354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	184	427	1	ENST00000405192.2:c.533G>A	p.Ser178Asn	p.S178N	ENST00000405192	NM_001163147.1	178	aGc/aAc	7/12	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.64	2		428	527	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273063	55273063	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	40	594	0	ENST00000275493.2:c.3386A>G	p.His1129Arg	p.H1129R	ENST00000275493	NM_005228.3	1129	cAc/cGc	28/28	1	2	FACETS	0.223	0.185	0.266	0.223	0.185	0.266	SUBCLONAL	1	TRUE	1	0.64	2		594	560	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334734	81334734	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	55	735	0	ENST00000222390.5:c.1982C>A	p.Ala661Asp	p.A661D	ENST00000222390	NM_000601.4	661	gCt/gAt	17/18	1	2	FACETS	0.209	0.178	0.243	0.209	0.178	0.243	SUBCLONAL	1	TRUE	1	0.64	2		735	821	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355256	81355256	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1258267427	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	52	712	0	ENST00000222390.5:c.1118G>A	p.Arg373Gln	p.R373Q	ENST00000222390	NM_000601.4	373	cGa/cAa	9/18	1	2	FACETS	0.206	0.175	0.241	0.206	0.175	0.241	SUBCLONAL	1	TRUE	1	0.64	2		712	789	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386569	81386569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	38	545	0	ENST00000222390.5:c.418G>A	p.Val140Ile	p.V140I	ENST00000222390	NM_000601.4	140	Gta/Ata	4/18	1	2	FACETS	0.171	0.141	0.206	0.171	0.141	0.206	SUBCLONAL	1	TRUE	1	0.64	2		545	693	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508473	106508473	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370328855	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	26	164	1	ENST00000359195.3:c.467C>T	p.Ala156Val	p.A156V	ENST00000359195	NM_002649.2	156	gCg/gTg	2/11	1	2	FACETS	0.63	0.506	0.767	0.63	0.506	0.767	SUBCLONAL	1	TRUE	1	0.64	2		165	129	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508557	106508557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	74	243	0	ENST00000359195.3:c.551G>A	p.Arg184His	p.R184H	ENST00000359195	NM_002649.2	184	cGc/cAc	2/11	1	2	FACETS	0.984	0.874	1	0.984	0.874	1	CLONAL	1	TRUE	1	0.64	2		243	235	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509520	106509520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1317978480	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	31	545	4	ENST00000359195.3:c.1514C>T	p.Ala505Val	p.A505V	ENST00000359195	NM_002649.2	505	gCa/gTa	2/11	1	2	FACETS	0.193	0.155	0.235	0.193	0.155	0.235	SUBCLONAL	1	TRUE	1	0.64	2		549	503	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509806	106509806	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	64	733	0	ENST00000359195.3:c.1800G>T	p.Gln600His	p.Q600H	ENST00000359195	NM_002649.2	600	caG/caT	2/11	1	2	FACETS	0.308	0.266	0.353	0.308	0.266	0.353	SUBCLONAL	1	TRUE	1	0.64	2		733	650	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339328	116339328	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	217	615	1	ENST00000397752.3:c.190C>A	p.Leu64Ile	p.L64I	ENST00000397752	NM_000245.2	64	Ctt/Att	2/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.64	2		616	638	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339565	116339565	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs779093896	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	84	373	0	ENST00000397752.3:c.427C>T	p.Arg143Ter	p.R143*	ENST00000397752	NM_000245.2	143	Cga/Tga	2/21	1	2	FACETS	0.673	0.598	0.752	0.673	0.598	0.752	SUBCLONAL	1	TRUE	1	0.64	2		373	390	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398625	116398625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45587940	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	233	594	0	ENST00000397752.3:c.2215C>T	p.Arg739Cys	p.R739C	ENST00000397752	NM_000245.2	739	Cgt/Tgt	9/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.64	2		594	658	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829186	128829186	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	13	291	0	ENST00000249373.3:c.194G>A	p.Gly65Asp	p.G65D	ENST00000249373	NM_005631.4	65	gGc/gAc	1/12	1	2	FACETS	0.164	0.116	0.222	0.164	0.116	0.222	SUBCLONAL	1	TRUE	1	0.64	2		291	248	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128848687	128848687	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1204546630	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	32	492	0	ENST00000249373.3:c.1352G>A	p.Arg451His	p.R451H	ENST00000249373	NM_005631.4	451	cGc/cAc	7/12	1	2	FACETS	0.236	0.191	0.286	0.236	0.191	0.286	SUBCLONAL	1	TRUE	1	0.64	2		492	424	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848603	151848603	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	130	565	0	ENST00000262189.6:c.12590G>A	p.Trp4197Ter	p.W4197*	ENST00000262189	NM_170606.2	4197	tGg/tAg	50/59	1	2	FACETS	0.591	0.537	0.648	0.591	0.537	0.648	SUBCLONAL	1	TRUE	1	0.64	2		565	687	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853071	151853071	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	151	354	0	ENST00000262189.6:c.11884C>A	p.Leu3962Ile	p.L3962I	ENST00000262189	NM_170606.2	3962	Ctt/Att	46/59	1	2	FACETS	0.967	0.891	1	0.967	0.891	1	CLONAL	1	TRUE	1	0.64	2		354	488	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345755	152345755	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	106	494	0	ENST00000359321.1:c.815T>G	p.Ile272Ser	p.I272S	ENST00000359321	NM_005431.1	272	aTt/aGt	3/3	1	2	FACETS	0.7	0.631	0.773	0.7	0.631	0.773	SUBCLONAL	1	TRUE	1	0.64	2		494	473	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271150	38271150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758677681	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	18	350	0	ENST00000425967.3:c.2558G>A	p.Arg853His	p.R853H	ENST00000425967	NM_001174067.1	853	cGc/cAc	19/19	1	2	FACETS	0.187	0.14	0.242	0.187	0.14	0.242	SUBCLONAL	1	TRUE	1	0.64	2		350	301	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271453	38271453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	36	798	4	ENST00000425967.3:c.2368G>A	p.Ala790Thr	p.A790T	ENST00000425967	NM_001174067.1	790	Gcc/Acc	18/19	1	2	FACETS	0.183	0.149	0.22	0.183	0.149	0.22	SUBCLONAL	1	TRUE	1	0.64	2		802	616	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965779	90965779	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554558440	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	30	513	0	ENST00000265433.3:c.1538C>T	p.Pro513Leu	p.P513L	ENST00000265433	NM_002485.4	513	cCt/cTt	11/16	1	2	FACETS	0.168	0.134	0.206	0.168	0.134	0.206	SUBCLONAL	1	TRUE	1	0.64	2		513	559	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983498	90983498	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	41	420	0	ENST00000265433.3:c.605A>C	p.Glu202Ala	p.E202A	ENST00000265433	NM_002485.4	202	gAa/gCa	6/16	1	2	FACETS	0.285	0.237	0.338	0.285	0.237	0.338	SUBCLONAL	1	TRUE	1	0.64	2		420	450	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90995008	90995008	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	247	550	0	ENST00000265433.3:c.113A>T	p.Asp38Val	p.D38V	ENST00000265433	NM_002485.4	38	gAt/gTt	2/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.64	2		550	733	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751254	128751254	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	54	215	0	ENST00000377970.2:c.791G>A	p.Ser264Asn	p.S264N	ENST00000377970	NM_002467.4	264	aGc/aAc	2/3	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.64	2		215	158	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753089	128753089	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	147	424	0	ENST00000377970.2:c.1250A>G	p.Tyr417Cys	p.Y417C	ENST00000377970	NM_002467.4	417	tAc/tGc	3/3	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.64	2		424	437	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741404	145741404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs531175632	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	158	920	1	ENST00000428558.2:c.1099C>T	p.Arg367Trp	p.R367W	ENST00000428558	NM_004260.3	367	Cgg/Tgg	5/22	1	2	FACETS	0.607	0.557	0.66	0.607	0.557	0.66	SUBCLONAL	1	TRUE	1	0.64	2		921	813	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340402	8340402	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	405	527	1	ENST00000356435.5:c.5194C>A	p.Leu1732Ile	p.L1732I	ENST00000356435		1732	Ctc/Atc	31/35	1	2	FACETS	0.754	0.722	0.787	1	0.996	1	SUBCLONAL	2	TRUE	1	0.64	2		528	839	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449727	8449727	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs772305581	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	42	598	0	ENST00000356435.5:c.3986C>T	p.Pro1329Leu	p.P1329L	ENST00000356435		1329	cCg/cTg	23/35	1	2	FACETS	0.159	0.132	0.19	0.159	0.132	0.19	SUBCLONAL	1	TRUE	1	0.64	2		598	824	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499772	8499772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773166856	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	42	610	0	ENST00000356435.5:c.2197C>T	p.Arg733Cys	p.R733C	ENST00000356435		733	Cgc/Tgc	14/35	1	2	FACETS	0.157	0.131	0.187	0.157	0.131	0.187	SUBCLONAL	1	TRUE	1	0.64	2		610	834	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006190	22006190	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	49	442	0	ENST00000276925.6:c.213G>T	p.Glu71Asp	p.E71D	ENST00000276925	NM_004936.3	71	gaG/gaT	2/2	1	2	FACETS	0.326	0.276	0.381	0.326	0.276	0.381	SUBCLONAL	1	TRUE	1	0.64	2		442	469	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342620	87342620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	59	598	0	ENST00000277120.3:c.905G>A	p.Cys302Tyr	p.C302Y	ENST00000277120		302	tGc/tAc	9/19	1	2	FACETS	0.285	0.245	0.329	0.285	0.245	0.329	SUBCLONAL	1	TRUE	1	0.64	2		598	647	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224197	98224197	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	154	584	0	ENST00000331920.6:c.2644C>A	p.Leu882Ile	p.L882I	ENST00000331920	NM_000264.3	882	Ctt/Att	16/24	1	2	FACETS	0.784	0.72	0.85	0.784	0.72	0.85	SUBCLONAL	1	TRUE	1	0.64	2		584	614	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760913	133760913	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs761044550	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	43	907	0	ENST00000318560.5:c.3236A>G	p.Asn1079Ser	p.N1079S	ENST00000318560	NM_005157.4	1079	aAc/aGc	11/11	1	2	FACETS	0.189	0.157	0.224	0.189	0.157	0.224	SUBCLONAL	1	TRUE	1	0.64	2		907	712	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391982	139391982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751048658	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	28	672	0	ENST00000277541.6:c.6209G>A	p.Arg2070Gln	p.R2070Q	ENST00000277541	NM_017617.3	2070	cGg/cAg	34/34	1	2	FACETS	0.162	0.129	0.2	0.162	0.129	0.2	SUBCLONAL	1	TRUE	1	0.64	2		672	541	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393440	139393440	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs932710972	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	26	556	3	ENST00000277541.6:c.6091G>A	p.Ala2031Thr	p.A2031T	ENST00000277541	NM_017617.3	2031	Gcc/Acc	33/34	1	2	FACETS	0.177	0.14	0.22	0.177	0.14	0.22	SUBCLONAL	1	TRUE	1	0.64	2		559	458	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399194	139399194	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1290640224	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	152	427	1	ENST00000277541.6:c.4949C>T	p.Ala1650Val	p.A1650V	ENST00000277541	NM_017617.3	1650	gCc/gTc	26/34	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.64	2		428	385	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400334	139400334	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	31	127	0	ENST00000277541.6:c.4015-1G>A		p.X1339_splice	ENST00000277541	NM_017617.3	1339			1	2	FACETS	0.941	0.78	1	0.941	0.78	1	CLONAL	1	TRUE	1	0.64	2		127	103	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402695	139402695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778118508	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	35	516	0	ENST00000277541.6:c.3314C>T	p.Ala1105Val	p.A1105V	ENST00000277541	NM_017617.3	1105	gCg/gTg	20/34	1	2	FACETS	0.2	0.164	0.242	0.2	0.164	0.242	SUBCLONAL	1	TRUE	1	0.64	2		516	546	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139811000	139811000	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1240286989	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	46	841	0	ENST00000247668.2:c.611A>G	p.Asp204Gly	p.D204G	ENST00000247668	NM_021138.3	204	gAc/gGc	7/11	1	2	FACETS	0.211	0.177	0.249	0.211	0.177	0.249	SUBCLONAL	1	TRUE	1	0.64	2		841	681	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317559	1317559	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	34	602	0	ENST00000400841.2:c.506A>G	p.Asn169Ser	p.N169S	ENST00000400841		169	aAc/aGc	5/6	1	1	FACETS	0.125	0.102	0.152	0.125	0.102	0.152	SUBCLONAL	1	TRUE	0	0.64	1		602	576	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732822	44732822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	216	320	0	ENST00000377967.4:c.25G>A	p.Ala9Thr	p.A9T	ENST00000377967	NM_021140.2	9	Gct/Act	1/29	1	1	FACETS	0.752	0.719	0.785	1	0.994	1	SUBCLONAL	2	TRUE	0	0.64	1		320	305	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937733	44937733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	36	320	0	ENST00000377967.4:c.2921C>T	p.Ala974Val	p.A974V	ENST00000377967	NM_021140.2	974	gCt/gTt	19/29	1	1	FACETS	0.194	0.159	0.232	0.194	0.159	0.232	SUBCLONAL	1	TRUE	0	0.64	1		320	395	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966753	44966753	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	285	391	0	ENST00000377967.4:c.3977A>G	p.Glu1326Gly	p.E1326G	ENST00000377967	NM_021140.2	1326	gAa/gGa	27/29	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.64	1		391	412	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028805	47028805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	292	454	0	ENST00000377604.3:c.109C>T	p.Arg37Trp	p.R37W	ENST00000377604	NM_001204468.1	37	Cgg/Tgg	3/24	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.64	1		454	414	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034426	47034426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	67	355	1	ENST00000377604.3:c.511C>T	p.Arg171Trp	p.R171W	ENST00000377604	NM_001204468.1	171	Cgg/Tgg	6/24	1	1	FACETS	0.377	0.329	0.428	0.377	0.329	0.428	SUBCLONAL	1	TRUE	0	0.64	1		356	378	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039348	47039348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377736520	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	41	387	1	ENST00000377604.3:c.971C>T	p.Ala324Val	p.A324V	ENST00000377604	NM_001204468.1	324	gCg/gTg	10/24	1	1	FACETS	0.237	0.197	0.28	0.237	0.197	0.28	SUBCLONAL	1	TRUE	0	0.64	1		388	368	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222196	53222196	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782154592	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	144	308	1	ENST00000375401.3:c.4636C>T	p.Arg1546Trp	p.R1546W	ENST00000375401	NM_004187.3	1546	Cgg/Tgg	26/26	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.64	1		309	229	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230872	53230872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	57	359	0	ENST00000375401.3:c.1921G>A	p.Val641Ile	p.V641I	ENST00000375401	NM_004187.3	641	Gtc/Atc	14/26	1	1	FACETS	0.323	0.278	0.372	0.323	0.278	0.372	SUBCLONAL	1	TRUE	0	0.64	1		359	375	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340886	70340886	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	278	408	0	ENST00000374080.3:c.619C>A	p.Pro207Thr	p.P207T	ENST00000374080		207	Cca/Aca	5/45	1	1	FACETS	0.79	0.76	0.818	1	0.996	1	SUBCLONAL	2	TRUE	0	0.64	1		408	374	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348502	70348502	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1317457286	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	80	418	4	ENST00000374080.3:c.3409G>A	p.Ala1137Thr	p.A1137T	ENST00000374080		1137	Gct/Act	24/45	1	1	FACETS	0.421	0.372	0.472	0.421	0.372	0.472	SUBCLONAL	1	TRUE	0	0.64	1		422	404	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349041	70349041	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	43	488	0	ENST00000374080.3:c.3553C>A	p.Leu1185Ile	p.L1185I	ENST00000374080		1185	Ctc/Atc	25/45	1	1	FACETS	0.206	0.172	0.244	0.206	0.172	0.244	SUBCLONAL	1	TRUE	0	0.64	1		488	443	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875898	76875898	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	229	394	0	ENST00000373344.5:c.5237del	p.Leu1746Ter	p.L1746*	ENST00000373344	NM_000489.3	1746	tTa/ta	20/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.64	1		394	353	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76954099	76954099	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	41	394	0	ENST00000373344.5:c.152G>T	p.Gly51Val	p.G51V	ENST00000373344	NM_000489.3	51	gGa/gTa	3/35	1	1	FACETS	0.257	0.214	0.304	0.257	0.214	0.304	SUBCLONAL	1	TRUE	0	0.64	1		394	339	SUCCESS
BTK	695	MSKCC	GRCh37	X	100604907	100604907	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555976762	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	195	355	0	ENST00000308731.7:c.1946G>A	p.Ser649Asn	p.S649N	ENST00000308731	NM_000061.2	649	aGc/aAc	19/19	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.64	1		355	301	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615630	100615630	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	19	404	0	ENST00000308731.7:c.702G>T	p.Gln234His	p.Q234H	ENST00000308731	NM_000061.2	234	caG/caT	8/19	1	1	FACETS	0.119	0.09	0.153	0.119	0.09	0.153	SUBCLONAL	1	TRUE	0	0.64	1		404	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573269	7573967	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTGTAATGGTGAGATCTCAGCTCACCGCAACCTCTGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGGTAGCTGGGATTACAGGCATGCATCACCACGCCCGGCTACTTTTGTATTTTTAGTAGAGATGGGGTTTCTCCATGTTGGTCAGGCTGGGCTCAAACTCCCGACCTCAGGTGATCCACTCGCCTTGGCCTCCCAGAGTGTGGGATTCGTGAGCCACTGCGCCCGGCCCCCTTACCCCATTTTATATATAAGGAAACTGAGTTTGACGGGGGTCACCTAGGACCTGCCGGTGCATGGCAGGGCTGAGTATATGACCTGAAACTCTGGCTGTATTCAGTATTACACAATTATTAGGCCCCTCCTTGAGACCCTCCAGCTCTGGGCTGGGAGTTGCGGAGAATGGCAAAGAAGTATCCACACTCGTCCCTGGGTTTGGATGTTCTGTGGATACACTGAGGCAAGAATGTGGTTATAGGATTCAACCGGAGGAAGACTAAAAAAATGTCTGTGCAGGGCTGGGACCCAATGAGATGGGGTCAGCTGCCTTTGACCATGAAGGCAGGATGAGAATGGAATCCTATGGCTTTCCAACCTAGGAAGGCAGGGGAGTAGGGCCAGGAAGGGGCTGAGGTCACTCACCTGGAGTGAGCCCTGCTCCCCCCTGGCTCCTTCCCAGCCTG	AGTGTAATGGTGAGATCTCAGCTCACCGCAACCTCTGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGGTAGCTGGGATTACAGGCATGCATCACCACGCCCGGCTACTTTTGTATTTTTAGTAGAGATGGGGTTTCTCCATGTTGGTCAGGCTGGGCTCAAACTCCCGACCTCAGGTGATCCACTCGCCTTGGCCTCCCAGAGTGTGGGATTCGTGAGCCACTGCGCCCGGCCCCCTTACCCCATTTTATATATAAGGAAACTGAGTTTGACGGGGGTCACCTAGGACCTGCCGGTGCATGGCAGGGCTGAGTATATGACCTGAAACTCTGGCTGTATTCAGTATTACACAATTATTAGGCCCCTCCTTGAGACCCTCCAGCTCTGGGCTGGGAGTTGCGGAGAATGGCAAAGAAGTATCCACACTCGTCCCTGGGTTTGGATGTTCTGTGGATACACTGAGGCAAGAATGTGGTTATAGGATTCAACCGGAGGAAGACTAAAAAAATGTCTGTGCAGGGCTGGGACCCAATGAGATGGGGTCAGCTGCCTTTGACCATGAAGGCAGGATGAGAATGGAATCCTATGGCTTTCCAACCTAGGAAGGCAGGGGAGTAGGGCCAGGAAGGGGCTGAGGTCACTCACCTGGAGTGAGCCCTGCTCCCCCCTGGCTCCTTCCCAGCCTG	-	novel	NA	P-0014040-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3	113	5	0	ENST00000269305.4:c.1061_1101-260del		p.X354_splice	ENST00000269305	NM_001126112.2	354		10/11	0.33184175676683	1	FACETS		NA	1	1	0.993	1	NA	5	FALSE	0	0.340226385115419	1		5	116	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1272317	1272317	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014040-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	104	536	2	ENST00000310581.5:c.2365G>A	p.Ala789Thr	p.A789T	ENST00000310581	NM_198253.2	789	Gcc/Acc	7/16	NA	2	FACETS	0.808	0.723	0.897			1	INDETERMINATE	1	FALSE	NA	0.340226385115419	2		538	757	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0014323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	37	330	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.25688403034815	1	FACETS	0.319	0.262	0.383	0.319	0.262	0.383	SUBCLONAL	1	TRUE	0	0.329476946906389	1		330	588	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0014323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	311	717	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.965	1	1	0.996	1	CLONAL	2	TRUE	1	0.329476946906389	2		721	919	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852118	63852118	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	57	647	1	ENST00000279873.7:c.2901del	p.Lys967AsnfsTer15	p.K967Nfs*15	ENST00000279873	NM_032199.2	966	Aaa/aa	10/10	1	2	FACETS	0.412	0.353	0.478	0.412	0.353	0.478	SUBCLONAL	1	TRUE	1	0.329476946906389	2		648	839	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435198	49435199	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755159728	NA	P-0014323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	100	549	0	ENST00000301067.7:c.6354dup	p.Ala2119ArgfsTer36	p.A2119Rfs*36	ENST00000301067	NM_003482.3	2118	-/C	31/54	NA	2	FACETS	0.86	0.768	0.957			1	INDETERMINATE	1	TRUE	NA	0.329476946906389	2		549	706	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570878	226570878	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1383847803	NA	P-0014323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	106	527	0	ENST00000366794.5:c.1018C>T	p.Arg340Ter	p.R340*	ENST00000366794	NM_001618.3	340	Cga/Tga	8/23	1	2	FACETS	0.998	0.896	1	0.998	0.896	1	CLONAL	1	TRUE	1	0.329476946906389	2		527	645	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647027	23647028	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	62	682	0	ENST00000261584.4:c.839dup	p.Asn280LysfsTer3	p.N280Kfs*3	ENST00000261584	NM_024675.3	280	aac/aaAc	4/13	0.297774211271683	3	FACETS	0.551	0.475	0.635	0.276	0.237	0.318	SUBCLONAL	1	TRUE	1	0.329476946906389	3		682	795	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993243	72993243	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1399	91	844	0	ENST00000268489.5:c.802A>G	p.Lys268Glu	p.K268E	ENST00000268489	NM_006885.3	268	Aaa/Gaa	2/10	0.297774211271683	3	FACETS	0.432	0.382	0.486	0.216	0.191	0.243	SUBCLONAL	1	TRUE	1	0.329476946906389	3		844	1490	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673793	37673793	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	181	695	3	ENST00000447079.4:c.2947C>T	p.Arg983Ter	p.R983*	ENST00000447079	NM_015083.1	983	Cga/Tga	10/14	1	2	FACETS	0.992	0.913	1	0.992	0.913	1	CLONAL	1	TRUE	1	0.329476946906389	2		698	1108	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584510	48584510	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	100	395	0	ENST00000342988.3:c.683T>C	p.Ile228Thr	p.I228T	ENST00000342988	NM_005359.5	228	aTa/aCa	6/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.329476946906389	2		395	502	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211693	36211693	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1420662989	NA	P-0014323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	51	512	3	ENST00000222270.7:c.1444C>T	p.Arg482Trp	p.R482W	ENST00000222270	NM_014727.1	482	Cgg/Tgg	3/37	1	2	FACETS	0.409	0.347	0.478	0.409	0.347	0.478	SUBCLONAL	1	TRUE	1	0.329476946906389	2		515	756	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379485	225379485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	38	529	0	ENST00000264414.4:c.383G>A	p.Arg128His	p.R128H	ENST00000264414	NM_003590.4	128	cGt/cAt	4/16	1	2	FACETS	0.732	0.607	0.871	0.732	0.607	0.871	SUBCLONAL	1	TRUE	1	0.329476946906389	2		529	315	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662763	227662763	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	222	677	2	ENST00000305123.5:c.692C>T	p.Thr231Met	p.T231M	ENST00000305123	NM_005544.2	231	aCg/aTg	1/2	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.329476946906389	2		679	1125	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573905	41573905	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	158	790	2	ENST00000263253.7:c.6193del	p.Leu2065CysfsTer69	p.L2065Cfs*69	ENST00000263253	NM_001429.3	2064	Ccc/cc	31/31	1	2	FACETS	0.91	0.833	0.991	0.91	0.833	0.991	CLONAL	1	TRUE	1	0.329476946906389	2		792	1054	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402605	20402605	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775788562	NA	P-0014323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	125	255	0	ENST00000346618.3:c.142G>A	p.Ala48Thr	p.A48T	ENST00000346618	NM_001949.4	48	Gcc/Acc	1/7	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.329476946906389	2		255	553	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935582	13935582	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	88	405	0	ENST00000405192.2:c.1274T>G	p.Val425Gly	p.V425G	ENST00000405192	NM_001163147.1	425	gTg/gGg	12/12	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.329476946906389	2		405	525	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372775	81372775	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	140	487	0	ENST00000222390.5:c.759G>T	p.Lys253Asn	p.K253N	ENST00000222390	NM_000601.4	253	aaG/aaT	7/18	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.329476946906389	2		487	733	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0014422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	474	596	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.468197602131338	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.468197602131338	1		596	1319	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164509	36164509	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	77	351	1	ENST00000300305.3:c.1366G>A	p.Glu456Lys	p.E456K	ENST00000300305		456	Gag/Aag	8/8	0.317238487093806	1	FACETS	0.343	0.3	0.388	0.343	0.3	0.388	SUBCLONAL	1	TRUE	0	0.468197602131338	1		352	735	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795060	45795060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374655042	NA	P-0014422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	244	460	0	ENST00000450313.1:c.1568G>A	p.Arg523His	p.R523H	ENST00000450313	NM_012222.2	523	cGc/cAc	16/16	0.217937979440152	1	FACETS	0.76	0.71	0.811	0.76	0.71	0.811	INDETERMINATE	1	TRUE	0	0.468197602131338	1		460	1051	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491414	2491414	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	124	617	0	ENST00000355716.4:c.457G>T	p.Gly153Ter	p.G153*	ENST00000355716	NM_003820.2	153	Gga/Tga	4/8	0.326295858568015	1	FACETS	0.412	0.372	0.454	0.412	0.372	0.454	SUBCLONAL	1	TRUE	0	0.468197602131338	1		617	985	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115260837	115260837	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	79	455	0	ENST00000438362.2:c.2488G>T	p.Gly830Trp	p.G830W	ENST00000438362	NM_001242891.1	830	Ggg/Tgg	20/20	0.217937979440152	1	FACETS	0.333	0.292	0.376	0.333	0.292	0.376	INDETERMINATE	1	TRUE	0	0.468197602131338	1		455	777	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464875	120464875	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	173	372	0	ENST00000256646.2:c.5197G>A	p.Asp1733Asn	p.D1733N	ENST00000256646	NM_024408.3	1733	Gat/Aat	28/34	NA	2	FACETS	0.927	0.855	1			1	INDETERMINATE	1	TRUE	NA	0.468197602131338	2		372	797	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551696	150551696	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1351372864	NA	P-0014422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	159	248	0	ENST00000369026.2:c.311G>T	p.Arg104Leu	p.R104L	ENST00000369026	NM_021960.4	104	cGc/cTc	1/3	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.468197602131338	2		248	489	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	244006428	244006428	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	188	464	0	ENST00000263826.5:c.45G>T	p.Arg15Ser	p.R15S	ENST00000263826	NM_005465.4	15	agG/agT	1/13	1	2	FACETS	0.675	0.622	0.73	0.675	0.622	0.73	SUBCLONAL	1	TRUE	1	0.468197602131338	2		464	1190	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098431	11098431	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	199	429	0	ENST00000358026.2:c.949del	p.Ala317ProfsTer9	p.A317Pfs*9	ENST00000358026	NM_001128849.1	317	Gcc/cc	6/36	0.468197602131338	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.468197602131338	1		429	607	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464463	25464463	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	445	398	0	ENST00000264709.3:c.2050G>T	p.Val684Phe	p.V684F	ENST00000264709	NM_175629.2	684	Gtc/Ttc	17/23	0.468197602131338	2	FACETS	0.997	0.956	1	0.997	0.956	1	CLONAL	2	TRUE	0	0.468197602131338	2		398	953	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980777	40980777	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	495	458	0	ENST00000373198.4:c.1709C>A	p.Thr570Lys	p.T570K	ENST00000373198	NM_133170.3	570	aCa/aAa	10/32	0.468197602131338	3	FACETS	0.951	0.911	0.992	0.951	0.911	0.992	CLONAL	2	TRUE	1	0.468197602131338	3		458	1372	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984803	55984803	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	217	430	0	ENST00000263923.4:c.326A>T	p.Asp109Val	p.D109V	ENST00000263923	NM_002253.2	109	gAc/gTc	3/30	0.468197602131338	3	FACETS	0.87	0.807	0.935	0.435	0.403	0.468	CLONAL	1	TRUE	1	0.468197602131338	3		430	1315	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254576	1254576	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1570	218	482	0	ENST00000310581.5:c.3202G>C	p.Glu1068Gln	p.E1068Q	ENST00000310581	NM_198253.2	1068	Gag/Cag	15/16	0.468197602131338	4	FACETS	0.765	0.708	0.824	0.255	0.236	0.275	SUBCLONAL	1	TRUE	1	0.468197602131338	4		482	1788	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873702	35873702	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	143	304	0	ENST00000303115.3:c.658T>C	p.Trp220Arg	p.W220R	ENST00000303115	NM_002185.3	220	Tgg/Cgg	5/8	0.468197602131338	4	FACETS	0.71	0.645	0.778	0.237	0.215	0.26	SUBCLONAL	1	TRUE	1	0.468197602131338	4		304	1264	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495462	149495462	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	441	681	0	ENST00000261799.4:c.3185G>T	p.Ser1062Ile	p.S1062I	ENST00000261799	NM_002609.3	1062	aGc/aTc	23/23	0.468197602131338	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.468197602131338	1		681	1421	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715866	117715866	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	99	334	0	ENST00000368508.3:c.892A>G	p.Lys298Glu	p.K298E	ENST00000368508	NM_002944.2	298	Aaa/Gaa	9/43	0.217937979440152	1	FACETS	0.435	0.388	0.485	0.435	0.388	0.485	INDETERMINATE	1	TRUE	0	0.468197602131338	1		334	745	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469986	157469986	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	96	349	1	ENST00000346085.5:c.2780G>T	p.Gly927Val	p.G927V	ENST00000346085	NM_020732.3	927	gGa/gTa	9/20	0.217937979440152	1	FACETS	0.431	0.384	0.481	0.431	0.384	0.481	INDETERMINATE	1	TRUE	0	0.468197602131338	1		350	729	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971366	13971366	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs568607536	NA	P-0014422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	158	297	0	ENST00000405192.2:c.563G>T	p.Arg188Leu	p.R188L	ENST00000405192	NM_001163147.1	188	cGc/cTc	8/12	0.468197602131338	1	FACETS	0.867	0.798	0.939	0.867	0.798	0.939	CLONAL	1	TRUE	0	0.468197602131338	1		297	596	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415825	49415825	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0014422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	65	219	0	ENST00000301067.7:c.16521+1G>A		p.X5507_splice	ENST00000301067	NM_003482.3	5507			1	2	FACETS	0.504	0.437	0.576	0.504	0.437	0.576	SUBCLONAL	1	TRUE	1	0.468197602131338	2		219	551	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222498	53222498	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782272528	NA	P-0014422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	122	653	0	ENST00000375401.3:c.4334G>A	p.Arg1445His	p.R1445H	ENST00000375401	NM_004187.3	1445	cGt/cAt	26/26	0.468197602131338	1	FACETS	0.406	0.366	0.448	0.406	0.366	0.448	SUBCLONAL	1	TRUE	0	0.468197602131338	1		653	984	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0014422-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	485	596	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.505430049009197	3	FACETS	0.92	0.887	0.953	0.92	0.887	0.953	CLONAL	3	TRUE	0	0.513546218168584	3		596	860	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164509	36164509	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014422-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	103	351	1	ENST00000300305.3:c.1366G>A	p.Glu456Lys	p.E456K	ENST00000300305		456	Gag/Aag	8/8	0.513546218168584	3	FACETS	0.888	0.796	0.984	0.444	0.398	0.492	CLONAL	1	TRUE	1	0.513546218168584	3		352	568	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795060	45795060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374655042	NA	P-0014422-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	347	460	0	ENST00000450313.1:c.1568G>A	p.Arg523His	p.R523H	ENST00000450313	NM_012222.2	523	cGc/cAc	16/16	0.505430049009197	3	FACETS	0.9	0.861	0.938	0.9	0.861	0.938	CLONAL	3	TRUE	0	0.513546218168584	3		460	629	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551696	150551696	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1351372864	NA	P-0014422-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	208	248	0	ENST00000369026.2:c.311G>T	p.Arg104Leu	p.R104L	ENST00000369026	NM_021960.4	104	cGc/cTc	1/3	0.241555075995256	6	FACETS	0.983	0.933	1			1	INDETERMINATE	5	TRUE	NA	0.513546218168584	6		248	334	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	244006428	244006428	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014422-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	257	464	0	ENST00000263826.5:c.45G>T	p.Arg15Ser	p.R15S	ENST00000263826	NM_005465.4	15	agG/agT	1/13	0.391602614556047	5	FACETS	0.961	0.901	1	0.641	0.601	0.682	CLONAL	2	TRUE	2	0.513546218168584	5		464	922	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098431	11098431	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014422-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	299	429	0	ENST00000358026.2:c.949del	p.Ala317ProfsTer9	p.A317Pfs*9	ENST00000358026	NM_001128849.1	317	Gcc/cc	6/36	0.470681302240101	3	FACETS	0.976	0.933	1	0.976	0.933	1	CLONAL	3	TRUE	0	0.513546218168584	3		429	500	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464463	25464463	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014422-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	408	398	0	ENST00000264709.3:c.2050G>T	p.Val684Phe	p.V684F	ENST00000264709	NM_175629.2	684	Gtc/Ttc	17/23	0.501582155470155	4	FACETS	0.96	0.927	0.994	0.96	0.927	0.994	CLONAL	4	TRUE	0	0.513546218168584	4		398	626	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980777	40980777	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014422-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	358	458	0	ENST00000373198.4:c.1709C>A	p.Thr570Lys	p.T570K	ENST00000373198	NM_133170.3	570	aCa/aAa	10/32	0.513546218168584	5	FACETS	1	0.964	1	1	0.964	1	CLONAL	3	TRUE	2	0.513546218168584	5		458	812	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984803	55984803	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014422-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	260	430	0	ENST00000263923.4:c.326A>T	p.Asp109Val	p.D109V	ENST00000263923	NM_002253.2	109	gAc/gTc	3/30	0.513546218168584	6	FACETS	0.93	0.871	0.991	0.465	0.435	0.496	CLONAL	2	TRUE	2	0.513546218168584	6		430	1103	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254576	1254576	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014422-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	160	482	0	ENST00000310581.5:c.3202G>C	p.Glu1068Gln	p.E1068Q	ENST00000310581	NM_198253.2	1068	Gag/Cag	15/16	0.513546218168584	5	FACETS	1	0.985	1	0.335	0.308	0.365	CLONAL	1	TRUE	1	0.513546218168584	5		482	822	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873702	35873702	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014422-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	173	304	0	ENST00000303115.3:c.658T>C	p.Trp220Arg	p.W220R	ENST00000303115	NM_002185.3	220	Tgg/Cgg	5/8	0.513546218168584	7	FACETS	0.946	0.872	1	0.379	0.349	0.41	CLONAL	2	TRUE	2	0.513546218168584	7		304	813	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495462	149495462	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014422-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	280	681	0	ENST00000261799.4:c.3185G>T	p.Ser1062Ile	p.S1062I	ENST00000261799	NM_002609.3	1062	aGc/aTc	23/23	0.480231810835948	2	FACETS	0.789	0.746	0.833	0.789	0.746	0.833	SUBCLONAL	2	TRUE	0	0.513546218168584	2		681	691	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715866	117715866	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014422-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	179	334	0	ENST00000368508.3:c.892A>G	p.Lys298Glu	p.K298E	ENST00000368508	NM_002944.2	298	Aaa/Gaa	9/43	0.513546218168584	3	FACETS	0.805	0.747	0.864	0.805	0.747	0.864	CLONAL	2	TRUE	1	0.513546218168584	3		334	544	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469986	157469986	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014422-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	160	349	1	ENST00000346085.5:c.2780G>T	p.Gly927Val	p.G927V	ENST00000346085	NM_020732.3	927	gGa/gTa	9/20	0.513546218168584	3	FACETS	0.837	0.774	0.901	0.837	0.774	0.901	CLONAL	2	TRUE	1	0.513546218168584	3		350	468	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971366	13971366	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs568607536	NA	P-0014422-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	228	297	0	ENST00000405192.2:c.563G>T	p.Arg188Leu	p.R188L	ENST00000405192	NM_001163147.1	188	cGc/cTc	8/12	0.513546218168584	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.513546218168584	2		297	434	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415825	49415825	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0014422-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	65	219	0	ENST00000301067.7:c.16521+1G>A		p.X5507_splice	ENST00000301067	NM_003482.3	5507			0.513546218168584	3	FACETS	0.874	0.762	0.994	0.437	0.381	0.497	CLONAL	1	TRUE	1	0.513546218168584	3		219	364	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0014422-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	872	596	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.583775242029008	3	FACETS	0.971	0.948	0.994	0.971	0.948	0.994	CLONAL	3	TRUE	0	0.583775242029008	3		596	1325	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164509	36164509	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014422-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	189	351	1	ENST00000300305.3:c.1366G>A	p.Glu456Lys	p.E456K	ENST00000300305		456	Gag/Aag	8/8	0.521947569073188	3	FACETS	1	0.961	1	0.529	0.49	0.57	CLONAL	1	TRUE	1	0.583775242029008	3		352	790	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795060	45795060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374655042	NA	P-0014422-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	416	460	0	ENST00000450313.1:c.1568G>A	p.Arg523His	p.R523H	ENST00000450313	NM_012222.2	523	cGc/cAc	16/16	0.583775242029008	3	FACETS	0.957	0.915	0.999	0.957	0.915	0.999	CLONAL	2	TRUE	1	0.583775242029008	3		460	962	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491414	2491414	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014422-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	159	617	0	ENST00000355716.4:c.457G>T	p.Gly153Ter	p.G153*	ENST00000355716	NM_003820.2	153	Gga/Tga	4/8	0.583775242029008	3	FACETS	0.825	0.757	0.896	0.413	0.378	0.448	CLONAL	1	TRUE	1	0.583775242029008	3		617	853	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115260837	115260837	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014422-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	133	455	0	ENST00000438362.2:c.2488G>T	p.Gly830Trp	p.G830W	ENST00000438362	NM_001242891.1	830	Ggg/Tgg	20/20	0.583775242029008	3	FACETS	0.812	0.738	0.889	0.406	0.369	0.445	CLONAL	1	TRUE	1	0.583775242029008	3		455	725	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464875	120464875	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014422-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	116	372	0	ENST00000256646.2:c.5197G>A	p.Asp1733Asn	p.D1733N	ENST00000256646	NM_024408.3	1733	Gat/Aat	28/34	0.583775242029008	3	FACETS	0.861	0.779	0.949	0.431	0.389	0.475	CLONAL	1	TRUE	1	0.583775242029008	3		372	596	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551696	150551696	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1351372864	NA	P-0014422-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	311	248	0	ENST00000369026.2:c.311G>T	p.Arg104Leu	p.R104L	ENST00000369026	NM_021960.4	104	cGc/cTc	1/3	0.535776150468996	3	FACETS	0.861	0.823	0.898	0.861	0.823	0.898	CLONAL	3	TRUE	0	0.583775242029008	3		248	533	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	244006428	244006428	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014422-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	264	464	0	ENST00000263826.5:c.45G>T	p.Arg15Ser	p.R15S	ENST00000263826	NM_005465.4	15	agG/agT	1/13	0.461177546963699	4	FACETS	1	0.991	1	0.653	0.612	0.695	CLONAL	1	TRUE	2	0.583775242029008	4		464	1097	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098431	11098431	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014422-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	426	429	0	ENST00000358026.2:c.949del	p.Ala317ProfsTer9	p.A317Pfs*9	ENST00000358026	NM_001128849.1	317	Gcc/cc	6/36	0.564753950897376	2	FACETS	0.93	0.893	0.966	0.93	0.893	0.966	CLONAL	2	TRUE	0	0.583775242029008	2		429	785	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464463	25464463	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014422-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	622	398	0	ENST00000264709.3:c.2050G>T	p.Val684Phe	p.V684F	ENST00000264709	NM_175629.2	684	Gtc/Ttc	17/23	0.583775242029008	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.583775242029008	3		398	903	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980777	40980777	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014422-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	761	458	0	ENST00000373198.4:c.1709C>A	p.Thr570Lys	p.T570K	ENST00000373198	NM_133170.3	570	aCa/aAa	10/32	0.583775242029008	5	FACETS	0.889	0.863	0.915	0.889	0.863	0.915	CLONAL	4	TRUE	1	0.583775242029008	5		458	1375	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984803	55984803	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014422-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	336	430	0	ENST00000263923.4:c.326A>T	p.Asp109Val	p.D109V	ENST00000263923	NM_002253.2	109	gAc/gTc	3/30	0.583775242029008	4	FACETS	1	0.994	1	0.466	0.44	0.493	CLONAL	1	TRUE	1	0.583775242029008	4		430	1303	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254576	1254576	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014422-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1317	433	482	0	ENST00000310581.5:c.3202G>C	p.Glu1068Gln	p.E1068Q	ENST00000310581	NM_198253.2	1068	Gag/Cag	15/16	0.583775242029008	5	FACETS	0.795	0.756	0.835	0.397	0.378	0.418	SUBCLONAL	2	TRUE	1	0.583775242029008	5		482	1750	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873702	35873702	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014422-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	248	304	0	ENST00000303115.3:c.658T>C	p.Trp220Arg	p.W220R	ENST00000303115	NM_002185.3	220	Tgg/Cgg	5/8	0.583775242029008	5	FACETS	1	0.992	1	0.357	0.333	0.381	CLONAL	1	TRUE	1	0.583775242029008	5		304	1116	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495462	149495462	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014422-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	605	681	0	ENST00000261799.4:c.3185G>T	p.Ser1062Ile	p.S1062I	ENST00000261799	NM_002609.3	1062	aGc/aTc	23/23	0.541254161543824	2	FACETS	0.891	0.861	0.921	0.891	0.861	0.921	CLONAL	2	TRUE	0	0.583775242029008	2		681	1163	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715866	117715866	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014422-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	254	334	0	ENST00000368508.3:c.892A>G	p.Lys298Glu	p.K298E	ENST00000368508	NM_002944.2	298	Aaa/Gaa	9/43	0.583775242029008	3	FACETS	0.932	0.88	0.985	0.932	0.88	0.985	CLONAL	2	TRUE	1	0.583775242029008	3		334	603	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469986	157469986	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014422-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	296	349	1	ENST00000346085.5:c.2780G>T	p.Gly927Val	p.G927V	ENST00000346085	NM_020732.3	927	gGa/gTa	9/20	0.583775242029008	3	FACETS	0.976	0.926	1	0.976	0.926	1	CLONAL	2	TRUE	1	0.583775242029008	3		350	671	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971366	13971366	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs568607536	NA	P-0014422-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	286	297	0	ENST00000405192.2:c.563G>T	p.Arg188Leu	p.R188L	ENST00000405192	NM_001163147.1	188	cGc/cTc	8/12	0.564753950897376	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.583775242029008	2		297	479	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003248	143003248	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs376736923	NA	P-0014422-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	80	585	0	ENST00000262992.4:c.2578A>G	p.Ile860Val	p.I860V	ENST00000262992	NM_001101669.1	860	Atc/Gtc	23/24	0.544274321315192	2	FACETS	0.51	0.45	0.575	0.255	0.225	0.288	SUBCLONAL	1	TRUE	0	0.583775242029008	2		585	537	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205846	128205846	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	149	480	0	ENST00000341105.2:c.29G>A	p.Trp10Ter	p.W10*	ENST00000341105	NM_032638.4	10	tGg/tAg	2/6	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.540720247584649	2		480	519	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965665	90965665	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	31	452	0	ENST00000265433.3:c.1652G>A	p.Arg551Lys	p.R551K	ENST00000265433	NM_002485.4	551	aGg/aAg	11/16	1	2	FACETS	0.466	0.379	0.564	0.466	0.379	0.564	SUBCLONAL	1	TRUE	1	0.540720247584649	2		452	246	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446399	70446399	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs557747751	NA	P-0014629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	325	501	0	ENST00000373644.4:c.5339G>A	p.Arg1780Gln	p.R1780Q	ENST00000373644	NM_030625.2	1780	cGa/cAa	11/12	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.752143063937893	2		501	827	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953287	17953340	+	inframe_deletion	In_Frame_Del	DEL	CGAGTGCCGGTCTGCCTGGCAGGCGGCCACGCGGCGCAGGGCTCTGCGCACCGT	CGAGTGCCGGTCTGCCTGGCAGGCGGCCACGCGGCGCAGGGCTCTGCGCACCGT	-	novel	NA	P-0014629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	357	625	0	ENST00000458235.1:c.646_699del	p.Thr216_Ser233del	p.T216_S233del	ENST00000458235	NM_000215.3	216	ACGGTGCGCAGAGCCCTGCGCCGCGTGGCCGCCTGCCAGGCAGACCGGCACTCG/-	6/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.752143063937893	2		625	928	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466722	57466857	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	AGGCCGCCCGCGCCCGCCGCCGCCGCAGCCCGGCCGCGCCCCGCCGCCGCCGCCGCCGCCATGGGCTGCCTCGGGAACAGTAAGACCGAGGACCAGCGCAACGAGGAGAAGGCGCAGCGTGAGGCCAACAAAAAGA	AGGCCGCCCGCGCCCGCCGCCGCCGCAGCCCGGCCGCGCCCCGCCGCCGCCGCCGCCGCCATGGGCTGCCTCGGGAACAGTAAGACCGAGGACCAGCGCAACGAGGAGAAGGCGCAGCGTGAGGCCAACAAAAAGA	-	novel	NA	P-0014629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	0	36	0	0	ENST00000371085.3:c.-60_76del		p.*20*	ENST00000371085	NM_000516.4	?-26/394		1/13	1	2	FACETS		NA	1	1	0.98	1	NA	3	TRUE	1	0.752143063937893	2		0	36	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685288	89685288	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	41	273	0	ENST00000371953.3:c.183T>G	p.His61Gln	p.H61Q	ENST00000371953	NM_000314.4	61	caT/caG	3/9	0.666014575708254	1	FACETS	0.325	0.274	0.38	0.325	0.274	0.38	SUBCLONAL	1	TRUE	0	0.816140186310201	1		273	183	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421912	49421912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373731411	NA	P-0014665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	161	626	0	ENST00000301067.7:c.14395G>A	p.Val4799Met	p.V4799M	ENST00000301067	NM_003482.3	4799	Gtg/Atg	46/54	0.443406777785937	1	FACETS	0.334	0.307	0.362	0.334	0.307	0.362	INDETERMINATE	1	TRUE	0	0.816140186310201	1		626	699	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0014696-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	691	563	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	0.700042965678581	5	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	2	0.700042965678581	5		563	1252	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955432	48955432	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014696-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	543	463	0	ENST00000267163.4:c.1548G>A	p.Trp516Ter	p.W516*	ENST00000267163	NM_000321.2	516	tgG/tgA	17/27	0.700042965678581	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.700042965678581	3		463	680	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778042	27778042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014696-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	424	498	0	ENST00000369163.2:c.191G>A	p.Arg64Lys	p.R64K	ENST00000369163	NM_003536.2	64	aGa/aAa	1/1	0.687242796849354	4	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	2	0.700042965678581	4		498	1020	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031815	10031815	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs397518465	NA	P-0014696-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1340	242	515	2	ENST00000330684.3:c.1007+1G>A		p.X336_splice	ENST00000330684	NM_001134407.1	336			0.700042965678581	6	FACETS	1	0.962	1	0.262	0.244	0.281	CLONAL	1	TRUE	2	0.700042965678581	6		517	1582	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29090030	29090030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs564605612	NA	P-0014696-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	23	111	7	ENST00000328354.6:c.1451C>T	p.Pro484Leu	p.P484L	ENST00000328354	NM_007194.3	484	cCg/cTg	13/15	0.700042965678581	3	FACETS	0.765	0.622	0.913	0.51	0.415	0.609	CLONAL	2	TRUE	0	0.700042965678581	3		118	58	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0014696-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	590	563	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	0.563995325563794	3	FACETS	0.988	0.951	1	0.988	0.951	1	CLONAL	2	TRUE	1	0.563995325563794	3		563	1358	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955432	48955432	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014696-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	218	463	0	ENST00000267163.4:c.1548G>A	p.Trp516Ter	p.W516*	ENST00000267163	NM_000321.2	516	tgG/tgA	17/27	0.507124849845154	2	FACETS	0.817	0.769	0.866	0.817	0.769	0.866	CLONAL	2	TRUE	0	0.563995325563794	2		463	473	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778042	27778042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014696-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	207	498	0	ENST00000369163.2:c.191G>A	p.Arg64Lys	p.R64K	ENST00000369163	NM_003536.2	64	aGa/aAa	1/1	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.563995325563794	2		498	716	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198070	185198070	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014696-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	88	434	0	ENST00000265026.3:c.2552A>G	p.Glu851Gly	p.E851G	ENST00000265026	NM_004721.4	851	gAg/gGg	13/14	0.563995325563794	3	FACETS	0.532	0.471	0.597	0.266	0.235	0.299	SUBCLONAL	1	TRUE	1	0.563995325563794	3		434	752	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233034	55233034	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	412	358	0	ENST00000275493.2:c.1784G>A	p.Cys595Tyr	p.C595Y	ENST00000275493	NM_005228.3	595	tGc/tAc	15/28	0.830161006989351	3	FACETS	0.967	0.92	1	0.484	0.46	0.508	CLONAL	1	TRUE	1	0.841097625648311	3		358	1439	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	70	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.26	2		473	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578518	7578518	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934875	NA	P-0014914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	126	1047	0	ENST00000269305.4:c.412G>C	p.Ala138Pro	p.A138P	ENST00000269305	NM_001126112.2	138	Gcc/Ccc	5/11	1	2	FACETS	0.99	0.895	1	0.99	0.895	1	CLONAL	1	TRUE	1	0.26	2		1047	979	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713675	30713676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0014914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	58	479	0	ENST00000295754.5:c.1001dup	p.Glu335GlyfsTer30	p.E335Gfs*30	ENST00000295754	NM_003242.5	334	cag/cAag	4/7	1	2	FACETS	0.901	0.775	1	0.901	0.775	1	CLONAL	1	TRUE	1	0.26	2		479	495	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270108	66270108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756653935	NA	P-0014914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	47	535	1	ENST00000273854.3:c.1774G>A	p.Val592Ile	p.V592I	ENST00000273854	NM_004439.5	592	Gtc/Atc	8/18	1	2	FACETS	0.68	0.573	0.797	0.68	0.573	0.797	SUBCLONAL	1	TRUE	1	0.26	2		536	532	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0015048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	194	717	4	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	0.26	2		721	1175	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0015048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	21	409	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.245	0.188	0.313	0.245	0.188	0.313	SUBCLONAL	1	TRUE	1	0.26	2		409	658	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1346	183	995	3	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.921	0.847	0.998	0.921	0.847	0.998	CLONAL	1	TRUE	1	0.26	2		998	1529	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0015048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	172	684	1	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	0.26	2		685	1058	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231610	5231611	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	29	185	0	ENST00000357368.4:c.1865dup	p.Gln623SerfsTer4	p.Q623Sfs*4	ENST00000357368	NM_002850.3	622	cct/ccCt	14/38	1	2	FACETS	0.701	0.564	0.857	0.701	0.564	0.857	SUBCLONAL	1	TRUE	1	0.26	2		185	318	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780068	NA	P-0015048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1301	163	776	1	ENST00000269305.4:c.472C>T	p.Arg158Cys	p.R158C	ENST00000269305	NM_001126112.2	158	Cgc/Tgc	5/11	1	2	FACETS	0.856	0.783	0.933	0.856	0.783	0.933	CLONAL	1	TRUE	1	0.26	2		777	1464	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257366	19257366	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	103	851	0	ENST00000162023.5:c.767del	p.Pro256GlnfsTer?	p.P256Qfs*?	ENST00000162023		256	cCa/ca	11/13	1	2	FACETS	0.682	0.609	0.761	0.682	0.609	0.761	SUBCLONAL	1	TRUE	1	0.26	2		851	1161	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178258	56178258	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	80	481	1	ENST00000399503.3:c.3236del	p.Asn1079IlefsTer3	p.N1079Ifs*3	ENST00000399503	NM_005921.1	1077	tcA/tc	14/20	1	2	FACETS	0.79	0.695	0.893	0.79	0.695	0.893	SUBCLONAL	1	TRUE	1	0.26	2		482	779	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398220	25398220	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	83	552	0	ENST00000311936.3:c.99T>G	p.Asp33Glu	p.D33E	ENST00000311936	NM_004985.3	33	gaT/gaG	2/5	1	2	FACETS	0.949	0.837	1	0.949	0.837	1	CLONAL	1	TRUE	1	0.26	2		552	673	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431395	121431395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs893256143	NA	P-0015048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	137	655	2	ENST00000257555.6:c.599G>A	p.Arg200Gln	p.R200Q	ENST00000257555		200	cGg/cAg	3/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.26	2		657	964	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557628	95557628	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	175	734	0	ENST00000393063.1:c.5439G>T	p.Glu1813Asp	p.E1813D	ENST00000393063	NM_030621.3	1813	gaG/gaT	26/28	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.26	2		734	1204	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228613016	228613016	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	72	288	0	ENST00000366696.1:c.11C>T	p.Thr4Ile	p.T4I	ENST00000366696	NM_003493.2	4	aCc/aTc	1/1	0.29670945623179	3	FACETS	1	0.956	1	0.604	0.529	0.685	CLONAL	1	TRUE	1	0.26	3		288	518	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948653	71948653	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147991973	NA	P-0015048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	204	730	0	ENST00000298229.2:c.3365C>T	p.Ser1122Leu	p.S1122L	ENST00000298229	NM_001567.3	1122	tCg/tTg	26/28	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.26	2		730	1158	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	422242	422248	+	frameshift_variant	Frame_Shift_Del	DEL	CGGTCCA	CGGTCCA	-	novel	NA	P-0015048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	120	773	0	ENST00000399788.2:c.3010_3016del	p.Trp1004LeufsTer42	p.W1004Lfs*42	ENST00000399788	NM_001042603.1	1004	TGGACCGct/ct	20/28	1	2	FACETS	0.811	0.731	0.897	0.811	0.731	0.897	CLONAL	1	TRUE	1	0.26	2		773	1138	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821918	72821918	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	120	353	0	ENST00000268489.5:c.10257del	p.Lys3420AsnfsTer65	p.K3420Nfs*65	ENST00000268489	NM_006885.3	3419	ccC/cc	10/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.26	2		353	617	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435692	56435692	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	51	566	1	ENST00000407977.2:c.1445G>A	p.Cys482Tyr	p.C482Y	ENST00000407977		482	tGc/tAc	9/10	1	2	FACETS	0.405	0.343	0.474	0.405	0.343	0.474	SUBCLONAL	1	TRUE	1	0.26	2		567	969	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266981	18266981	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756267462	NA	P-0015048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	98	358	0	ENST00000222254.8:c.292G>A	p.Ala98Thr	p.A98T	ENST00000222254	NM_005027.3	98	Gcc/Acc	2/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.26	2		358	602	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39725902	39725902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1349958802	NA	P-0015048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	125	555	0	ENST00000361337.2:c.773C>T	p.Thr258Met	p.T258M	ENST00000361337	NM_003286.2	258	aCg/aTg	10/21	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.26	2		555	880	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29090060	29090060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121908706	NA	P-0015048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	64	234	0	ENST00000328354.6:c.1421G>A	p.Arg474His	p.R474H	ENST00000328354	NM_007194.3	474	cGt/cAt	13/15	1	2	FACETS	0.981	0.851	1	0.981	0.851	1	CLONAL	1	TRUE	1	0.26	2		234	502	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574656	41574656	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	241	908	0	ENST00000263253.7:c.6941C>G	p.Pro2314Arg	p.P2314R	ENST00000263253	NM_001429.3	2314	cCt/cGt	31/31	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.26	2		908	1460	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462353	89462353	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	72	768	0	ENST00000336596.2:c.1825G>T	p.Val609Phe	p.V609F	ENST00000336596	NM_005233.5	609	Gtt/Ttt	10/17	1	2	FACETS	0.509	0.443	0.581	0.509	0.443	0.581	SUBCLONAL	1	TRUE	1	0.26	2		768	1088	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628614	187628614	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1179	183	844	0	ENST00000441802.2:c.2368del	p.Leu790Ter	p.L790*	ENST00000441802	NM_005245.3	790	Ctg/tg	2/27	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.26	2		844	1362	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589135	67589135	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	32	306	0	ENST00000274335.5:c.1127del	p.Gly376GlufsTer5	p.G376Efs*5	ENST00000274335		375	Ggg/gg	9/15	1	2	FACETS	0.832	0.677	1	0.832	0.677	1	CLONAL	1	TRUE	1	0.26	2		306	296	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592160	67592160	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	83	258	0	ENST00000274335.5:c.1976G>T	p.Cys659Phe	p.C659F	ENST00000274335		659	tGc/tTc	14/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.26	2		258	446	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372092	55372092	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	83	712	1	ENST00000297316.4:c.782G>C	p.Gly261Ala	p.G261A	ENST00000297316	NM_022454.3	261	gGc/gCc	2/2	1	2	FACETS	0.672	0.592	0.759	0.672	0.592	0.759	SUBCLONAL	1	TRUE	1	0.26	2		713	950	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030855	69030855	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	116	447	0	ENST00000288368.4:c.3397T>C	p.Phe1133Leu	p.F1133L	ENST00000288368	NM_024870.2	1133	Ttc/Ctc	27/40	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.26	2		447	803	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270541	98270541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1385550193	NA	P-0015048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	86	409	2	ENST00000331920.6:c.103C>T	p.Arg35Trp	p.R35W	ENST00000331920	NM_000264.3	35	Cgg/Tgg	1/24	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.26	2		411	636	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0015132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	48	403	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	1	2	FACETS	0.242	0.204	0.285	0.242	0.204	0.285	SUBCLONAL	1	TRUE	1	0.447664745515931	2		403	885	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685298	89685299	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0015132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	19	262	0	ENST00000371953.3:c.194dup	p.Tyr65Ter	p.Y65*	ENST00000371953	NM_000314.4	65	tac/tAac	3/9	1	2	FACETS	0.367	0.279	0.471	0.367	0.279	0.471	SUBCLONAL	1	TRUE	1	0.447664745515931	2		262	231	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913718	32913723	+	inframe_deletion	In_Frame_Del	DEL	CAGTAG	CAGTAG	-	novel	NA	P-0015132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	17	435	0	ENST00000380152.3:c.5228_5233del	p.Ser1743_Ser1744del	p.S1743_S1744del	ENST00000380152		1742	aaCAGTAGc/aac	11/27	0.447664745515931	1	FACETS	0.184	0.137	0.24	0.184	0.137	0.24	SUBCLONAL	1	TRUE	0	0.447664745515931	1		435	320	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194784	30194784	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	61	576	2	ENST00000331968.5:c.361A>G	p.Ser121Gly	p.S121G	ENST00000331968	NM_002742.2	121	Agt/Ggt	2/18	1	2	FACETS	0.28	0.241	0.324	0.28	0.241	0.324	SUBCLONAL	1	TRUE	1	0.447664745515931	2		578	972	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532726	187532726	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	66	381	0	ENST00000441802.2:c.9667A>C	p.Ile3223Leu	p.I3223L	ENST00000441802	NM_005245.3	3223	Ata/Cta	14/27	1	2	FACETS	0.37	0.32	0.424	0.37	0.32	0.424	SUBCLONAL	1	TRUE	1	0.447664745515931	2		381	797	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256762	16256762	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	356	500	0	ENST00000375759.3:c.4027C>T	p.Gln1343Ter	p.Q1343*	ENST00000375759	NM_015001.2	1343	Cag/Tag	11/15	NA	2	FACETS	0.925	0.884	0.966			1	INDETERMINATE	2	TRUE	NA	0.552755676379987	2		500	696	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857335	68857335	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	153	322	0	ENST00000261769.5:c.1971del	p.Leu658Ter	p.L658*	ENST00000261769	NM_004360.3	657	gCc/gc	13/16	0.552755676379987	1	FACETS	0.954	0.882	1	0.954	0.882	1	CLONAL	1	TRUE	0	0.552755676379987	1		322	420	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0015464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	86	584	2	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.535461783598349	3	FACETS	1	0.915	1	1	0.915	1	CLONAL	2	TRUE	1	0.535461783598349	3		586	201	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207153	1207155	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs587782056	NA	P-0015464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	344	1113	3	ENST00000326873.7:c.250_252del	p.Lys84del	p.K84del	ENST00000326873	NM_000455.4	81	AAG/-	1/10	0.462535481673686	4	FACETS	0.908	0.861	0.957	0.908	0.861	0.957	CLONAL	2	TRUE	2	0.535461783598349	4		1116	1086	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589552	69589552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	46	201	2	ENST00000168712.1:c.301G>A	p.Asp101Asn	p.D101N	ENST00000168712	NM_002007.2	101	Gac/Aac	1/3	0.535461783598349	3	FACETS	0.9	0.765	1	0.45	0.382	0.524	CLONAL	1	TRUE	1	0.535461783598349	3		203	242	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459334	99459335	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTACCGGCACAATTACTGCTCCAAAGG	novel	NA	P-0015464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	92	483	0	ENST00000268035.6:c.1972_1996+2dup		p.L658_G667dup	ENST00000268035	NM_000875.3	658	ctt/ctTTACCGGCACAATTACTGCTCCAAAGGt	9/21	0.535461783598349	3	FACETS	1	0.942	1	0.54	0.483	0.601	CLONAL	1	TRUE	1	0.535461783598349	3		483	403	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344714	118344714	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	30	552	0	ENST00000534358.1:c.2840del	p.Ser947LeufsTer2	p.S947Lfs*2	ENST00000534358	NM_005933.3	947	tCt/tt	3/36	0.535461783598349	1	FACETS	0.864	0.715	1	0.864	0.715	1	CLONAL	1	TRUE	0	0.535461783598349	1		552	95	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218425	36218425	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555730957	NA	P-0015464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	252	626	2	ENST00000222270.7:c.4204C>T	p.Arg1402Ter	p.R1402*	ENST00000222270	NM_014727.1	1402	Cga/Tga	16/37	0.462535481673686	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	2	0.535461783598349	4		628	709	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015464-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	20	720	1	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.742	0.567	0.947	0.742	0.567	0.947	CLONAL	1	TRUE	1	0.16	2		721	337	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0015464-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	37	584	2	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.787	0.651	0.937	1	0.955	1	CLONAL	2	TRUE	1	0.16	2		586	294	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207153	1207155	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs587782056	NA	P-0015464-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	30	1113	3	ENST00000326873.7:c.250_252del	p.Lys84del	p.K84del	ENST00000326873	NM_000455.4	81	AAG/-	1/10	1	2	FACETS	0.942	0.759	1	0.942	0.759	1	CLONAL	1	TRUE	1	0.16	2		1116	398	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589552	69589552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015464-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	10	201	2	ENST00000168712.1:c.301G>A	p.Asp101Asn	p.D101N	ENST00000168712	NM_002007.2	101	Gac/Aac	1/3	1	2	FACETS	1	0.769	1	1	0.769	1	CLONAL	1	TRUE	1	0.16	2		203	107	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459334	99459335	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTACCGGCACAATTACTGCTCCAAAGG	novel	NA	P-0015464-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	19	483	0	ENST00000268035.6:c.1972_1996+2dup		p.L658_G667dup	ENST00000268035	NM_000875.3	658	ctt/ctTTACCGGCACAATTACTGCTCCAAAGGt	9/21	1	2	FACETS	1	0.769	1	1	0.769	1	CLONAL	1	TRUE	1	0.16	2		483	235	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344714	118344714	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015464-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	19	552	0	ENST00000534358.1:c.2840del	p.Ser947LeufsTer2	p.S947Lfs*2	ENST00000534358	NM_005933.3	947	tCt/tt	3/36	1	2	FACETS	1	0.784	1	1	0.784	1	CLONAL	1	TRUE	1	0.16	2		552	230	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218425	36218425	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555730957	NA	P-0015464-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	19	626	2	ENST00000222270.7:c.4204C>T	p.Arg1402Ter	p.R1402*	ENST00000222270	NM_014727.1	1402	Cga/Tga	16/37	1	2	FACETS	0.722	0.547	0.927	0.722	0.547	0.927	CLONAL	1	TRUE	1	0.16	2		628	329	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	91	463	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.939	0.834	1	0.939	0.834	1	CLONAL	1	TRUE	1	0.266131957152549	2		463	728	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0015537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	134	705	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.266131957152549	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.266131957152549	1		705	787	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73340186	73340186	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	125	328	0	ENST00000377767.4:c.1894C>G	p.Leu632Val	p.L632V	ENST00000377767	NM_014953.3	632	Cta/Gta	15/21	0.266131957152549	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	2	TRUE	0	0.266131957152549	2		328	462	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031973	26031973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	29	379	0	ENST00000244661.2:c.316G>C	p.Glu106Gln	p.E106Q	ENST00000244661	NM_003537.3	106	Gag/Cag	1/1	0.266131957152549	1	FACETS	0.376	0.301	0.462	0.376	0.301	0.462	SUBCLONAL	1	TRUE	0	0.266131957152549	1		379	502	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001914	29001914	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	57	596	3	ENST00000282397.4:c.1251C>A	p.Asn417Lys	p.N417K	ENST00000282397	NM_002019.4	417	aaC/aaA	9/30	0.353193005871987	1	FACETS	0.485	0.416	0.56	0.485	0.416	0.56	SUBCLONAL	1	TRUE	0	0.353193005871987	1		599	548	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061228	38061228	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	279	509	0	ENST00000250448.2:c.761T>G	p.Phe254Cys	p.F254C	ENST00000250448	NM_004496.3	254	tTc/tGc	2/2	0.346469927949137	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.353193005871987	3		509	777	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754692	42754692	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	40	306	0	ENST00000222329.4:c.48C>A	p.Tyr16Ter	p.Y16*	ENST00000222329	NM_006494.2	16	taC/taA	2/4	1	2	FACETS	0.66	0.55	0.782	0.66	0.55	0.782	SUBCLONAL	1	TRUE	1	0.353193005871987	2		306	343	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0015552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	37	385	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.787	0.648	0.943	0.787	0.648	0.943	CLONAL	1	TRUE	1	0.17	2		385	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577567	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1567549651	NA	P-0015552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	58	608	0	ENST00000269305.4:c.714dup	p.Asn239Ter	p.N239*	ENST00000269305	NM_001126112.2	238	-/T	7/11	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.17	2		608	579	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726984	61726984	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	41	567	0	ENST00000401558.2:c.454G>T	p.Asp152Tyr	p.D152Y	ENST00000401558	NM_003400.3	152	Gat/Tat	7/25	1	2	FACETS	0.768	0.639	0.913	0.768	0.639	0.913	CLONAL	1	TRUE	1	0.17	2		567	628	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	204	1199	9	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	0.333843072591766	2		1208	879	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	174	717	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	TRUE	1	0.333843072591766	2		721	767	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	196	705	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.333843072591766	2		705	876	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	176	494	8	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.333843072591766	2		502	751	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752695	42752695	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1366176199	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	157	754	7	ENST00000222329.4:c.1569del	p.Leu525SerfsTer6	p.L525Sfs*6	ENST00000222329	NM_006494.2	523	ggG/gg	4/4	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.333843072591766	2		761	723	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	105	603	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.333843072591766	2		604	501	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117746743	117746743	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	111	572	0	ENST00000368508.3:c.77A>G	p.Gln26Arg	p.Q26R	ENST00000368508	NM_002944.2	26	cAg/cGg	1/43	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.333843072591766	2		572	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs864622237	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	173	680	0	ENST00000269305.4:c.700T>C	p.Tyr234His	p.Y234H	ENST00000269305	NM_001126112.2	234	Tac/Cac	7/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.333843072591766	2		680	735	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	110	403	0	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.333843072591766	2		403	539	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764347	39764347	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	193	672	3	ENST00000288319.7:c.765del	p.Arg256GlyfsTer35	p.R256Gfs*35	ENST00000288319	NM_182918.3	255	ccC/cc	7/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.333843072591766	2		675	950	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159109	24159109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1368176286	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	99	445	0	ENST00000263121.7:c.781C>T	p.Arg261Cys	p.R261C	ENST00000263121	NM_003073.3	261	Cgc/Tgc	6/9	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.333843072591766	2		445	553	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139563029	139563029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs950942092	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	236	794	1	ENST00000308874.7:c.101G>A	p.Arg34Gln	p.R34Q	ENST00000308874		34	cGg/cAg	4/10	1	2	FACETS	0.794	0.742	0.848	1	0.993	1	SUBCLONAL	2	TRUE	1	0.333843072591766	2		795	890	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424734	47424734	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	39	303	0	ENST00000377045.4:c.547del	p.Gln183ArgfsTer109	p.Q183Rfs*109	ENST00000377045	NM_001654.4	181	aCc/ac	6/16	1	1	FACETS	0.508	0.422	0.604	0.508	0.422	0.604	SUBCLONAL	1	TRUE	0	0.333843072591766	1		303	383	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015052	27015052	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs776697460	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	160	612	0	ENST00000335756.4:c.154C>T	p.Arg52Ter	p.R52*	ENST00000335756	NM_001809.3	52	Cga/Tga	2/5	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.333843072591766	2		612	739	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693003	89693003	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs786204900	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	88	502	0	ENST00000371953.3:c.491del	p.Lys164ArgfsTer3	p.K164Rfs*3	ENST00000371953	NM_000314.4	163	Aaa/aa	5/9	0.333843072591766	1	FACETS	0.813	0.731	0.899	1	0.983	1	CLONAL	2	TRUE	0	0.333843072591766	1		502	270	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063358	67063359	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	131	525	0	ENST00000412916.2:c.54dup	p.Arg19Ter	p.R19*	ENST00000412916		16	-/T	1/6	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.333843072591766	2		525	662	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907421	32907421	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359306	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	76	396	1	ENST00000380152.3:c.1813del	p.Ile605TyrfsTer9	p.I605Yfs*9	ENST00000380152		602	ggA/gg	10/27	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.333843072591766	2		397	359	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135079	11135079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770969438	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	278	941	0	ENST00000358026.2:c.3046G>A	p.Val1016Met	p.V1016M	ENST00000358026	NM_001128849.1	1016	Gtg/Atg	21/36	1	2	FACETS	0.785	0.737	0.834	1	0.994	1	SUBCLONAL	2	TRUE	1	0.333843072591766	2		941	1061	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522741	67522741	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	86	317	2	ENST00000274335.5:c.244del	p.Ile82SerfsTer32	p.I82Sfs*32	ENST00000274335		80	Aaa/aa	1/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.333843072591766	2		319	374	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99179952	99179952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1394330959	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	212	786	2	ENST00000074304.5:c.1895C>T	p.Pro632Leu	p.P632L	ENST00000074304	NM_001134224.1	632	cCg/cTg	19/26	0.333843072591766	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.333843072591766	1		788	727	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780673	9780673	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	222	826	0	ENST00000377346.4:c.1475T>C	p.Leu492Ser	p.L492S	ENST00000377346	NM_005026.3	492	tTg/tCg	12/24	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.333843072591766	2		826	896	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298651	11298651	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1235010967	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	167	696	1	ENST00000361445.4:c.1810C>T	p.Arg604Cys	p.R604C	ENST00000361445	NM_004958.3	604	Cgc/Tgc	12/58	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.333843072591766	2		697	794	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101421	27101421	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	194	678	1	ENST00000324856.7:c.4703C>T	p.Pro1568Leu	p.P1568L	ENST00000324856	NM_006015.4	1568	cCt/cTt	18/20	1	2	FACETS	0.758	0.703	0.814	1	0.991	1	SUBCLONAL	2	TRUE	1	0.333843072591766	2		679	767	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699214	117699214	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	108	461	0	ENST00000369458.3:c.427C>A	p.Leu143Ile	p.L143I	ENST00000369458	NM_024626.3	143	Ctt/Att	3/6	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.333843072591766	2		461	441	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612801	228612801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369460992	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	180	572	1	ENST00000366696.1:c.226G>A	p.Ala76Thr	p.A76T	ENST00000366696	NM_003493.2	76	Gct/Act	1/1	1	2	FACETS	0.753	0.696	0.812	1	0.99	1	SUBCLONAL	2	TRUE	1	0.333843072591766	2		573	716	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741762	17741762	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756034622	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	200	742	0	ENST00000250003.3:c.433C>T	p.Pro145Ser	p.P145S	ENST00000250003	NM_002478.4	145	Ccc/Tcc	1/3	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.333843072591766	2		742	841	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	430249	430249	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1242334605	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	109	470	1	ENST00000399788.2:c.2453G>A	p.Arg818Gln	p.R818Q	ENST00000399788	NM_001042603.1	818	cGg/cAg	18/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.333843072591766	2		471	484	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023602	1023602	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs772494823	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	118	520	0	ENST00000358495.3:c.962T>C	p.Leu321Ser	p.L321S	ENST00000358495	NM_134424.2	321	tTa/tCa	10/12	1	2	FACETS	0.75	0.681	0.823	1	0.985	1	SUBCLONAL	2	TRUE	1	0.333843072591766	2		520	471	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905496	11905496	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1007158603	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	100	298	1	ENST00000396373.4:c.146G>A	p.Arg49His	p.R49H	ENST00000396373	NM_001987.4	49	cGc/cAc	2/8	1	2	FACETS	0.776	0.699	0.857	1	0.984	1	SUBCLONAL	2	TRUE	1	0.333843072591766	2		299	386	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418457	49418460	+	frameshift_variant	Frame_Shift_Del	DEL	AATA	AATA	-	rs398123732	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	175	634	0	ENST00000301067.7:c.15953_15956del	p.Leu5318SerfsTer14	p.L5318Sfs*14	ENST00000301067	NM_003482.3	5318	tTATTc/tc	50/54	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.333843072591766	2		634	773	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427869	49427869	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	188	600	0	ENST00000301067.7:c.10721T>A	p.Ile3574Asn	p.I3574N	ENST00000301067	NM_003482.3	3574	aTc/aAc	38/54	1	2	FACETS	0.831	0.77	0.893	1	0.992	1	CLONAL	2	TRUE	1	0.333843072591766	2		600	678	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494970	56494970	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	183	615	0	ENST00000267101.3:c.3327G>T	p.Gln1109His	p.Q1109H	ENST00000267101	NM_001982.3	1109	caG/caT	27/28	1	2	FACETS	0.755	0.699	0.813	1	0.99	1	SUBCLONAL	2	TRUE	1	0.333843072591766	2		615	726	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066796	30066796	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201010570	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	161	586	0	ENST00000331968.5:c.2335G>A	p.Gly779Ser	p.G779S	ENST00000331968	NM_002742.2	779	Ggc/Agc	16/18	1	2	FACETS	0.842	0.776	0.909	1	0.991	1	CLONAL	2	TRUE	1	0.333843072591766	2		586	573	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790545	3790545	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	185	512	0	ENST00000262367.5:c.3988C>T	p.Gln1330Ter	p.Q1330*	ENST00000262367	NM_004380.2	1330	Cag/Tag	24/31	1	2	FACETS	0.768	0.711	0.826	1	0.991	1	SUBCLONAL	2	TRUE	1	0.333843072591766	2		512	722	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349313	89349313	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	295	1041	0	ENST00000301030.4:c.3637T>C	p.Ser1213Pro	p.S1213P	ENST00000301030	NM_001256183.1	1213	Tcc/Ccc	9/13	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.333843072591766	2		1041	1319	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533268	29533268	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	93	341	0	ENST00000356175.3:c.1271A>T	p.Asp424Val	p.D424V	ENST00000356175	NM_000267.3	424	gAt/gTt	12/57	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.333843072591766	2		341	382	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37680930	37680930	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	126	364	0	ENST00000447079.4:c.3103del	p.His1035ThrfsTer22	p.H1035Tfs*22	ENST00000447079	NM_015083.1	1033	ctC/ct	12/14	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.333843072591766	2		364	526	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47613709	47613709	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs878854496	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	99	435	0	ENST00000263735.4:c.904-2A>G		p.X302_splice	ENST00000263735	NM_002354.2	302			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.333843072591766	2		435	402	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881688	111881688	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	175	757	0	ENST00000393256.3:c.366G>T	p.Gln122His	p.Q122H	ENST00000393256	NM_006538.4	122	caG/caT	2/4	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.333843072591766	2		757	803	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116173	209116173	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781398075	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	112	532	0	ENST00000345146.2:c.103G>A	p.Val35Met	p.V35M	ENST00000345146	NM_005896.2	35	Gtg/Atg	3/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.333843072591766	2		532	532	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31390273	31390273	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	189	660	0	ENST00000328111.2:c.2228A>C	p.Asn743Thr	p.N743T	ENST00000328111	NM_006892.3	743	aAc/aCc	20/23	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.333843072591766	2		660	770	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39657718	39657718	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	150	464	0	ENST00000361337.2:c.11A>T	p.Asp4Val	p.D4V	ENST00000361337	NM_003286.2	4	gAc/gTc	1/21	1	2	FACETS	0.82	0.753	0.889	1	0.99	1	CLONAL	2	TRUE	1	0.333843072591766	2		464	548	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733354	40733354	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	106	409	0	ENST00000373198.4:c.3452A>G	p.Gln1151Arg	p.Q1151R	ENST00000373198	NM_133170.3	1151	cAa/cGa	26/32	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.333843072591766	2		409	458	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171739	36171739	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	122	433	0	ENST00000300305.3:c.826T>C	p.Ser276Pro	p.S276P	ENST00000300305		276	Tcc/Ccc	7/8	1	2	FACETS	0.773	0.703	0.845	1	0.986	1	SUBCLONAL	2	TRUE	1	0.333843072591766	2		433	473	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37045957	37045957	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	106	573	0	ENST00000231790.2:c.372T>A	p.Cys124Ter	p.C124*	ENST00000231790	NM_000249.3	124	tgT/tgA	4/19	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.333843072591766	2		573	474	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277966	41277966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	104	417	0	ENST00000349496.5:c.1930C>T	p.Leu644Phe	p.L644F	ENST00000349496	NM_001904.3	644	Ctt/Ttt	12/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.333843072591766	2		417	452	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205020	128205021	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	119	636	0	ENST00000341105.2:c.420_421del	p.Tyr141ProfsTer43	p.Y141Pfs*43	ENST00000341105	NM_032638.4	140	gtGTac/gtac	3/6	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.333843072591766	2		636	605	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967186	134967186	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200311306	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	160	429	0	ENST00000398015.3:c.2525G>A	p.Arg842Gln	p.R842Q	ENST00000398015	NM_004441.4	842	cGg/cAg	14/16	0.246705706520227	5	FACETS	1	0.972	1	0.748	0.688	0.81	CLONAL	2	TRUE	2	0.333843072591766	5		429	641	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981086	55981086	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	114	683	0	ENST00000263923.4:c.613A>G	p.Asn205Asp	p.N205D	ENST00000263923	NM_002253.2	205	Aat/Gat	5/30	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.333843072591766	2		683	510	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189932	66189932	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	86	313	2	ENST00000273854.3:c.3014T>C	p.Leu1005Ser	p.L1005S	ENST00000273854	NM_004439.5	1005	tTg/tCg	18/18	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.333843072591766	2		315	372	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260674	1260674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759490631	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	248	686	0	ENST00000310581.5:c.2885G>A	p.Arg962His	p.R962H	ENST00000310581	NM_198253.2	962	cGc/cAc	12/16	1	2	FACETS	0.819	0.767	0.872	1	0.994	1	CLONAL	2	TRUE	1	0.333843072591766	2		686	907	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160577	56160577	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	90	399	0	ENST00000399503.3:c.851T>A	p.Ile284Asn	p.I284N	ENST00000399503	NM_005921.1	284	aTc/aAc	4/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.333843072591766	2		399	435	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495351	149495351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373655593	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	156	665	0	ENST00000261799.4:c.3296C>T	p.Ala1099Val	p.A1099V	ENST00000261799	NM_002609.3	1099	gCg/gTg	23/23	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.333843072591766	2		665	638	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818746	32818746	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs754955681	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	174	699	1	ENST00000354258.4:c.1205C>A	p.Pro402His	p.P402H	ENST00000354258	NM_000593.5	402	cCc/cAc	4/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.333843072591766	2		700	787	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287325	38287325	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754968374	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	39	750	5	ENST00000425967.3:c.332G>A	p.Arg111His	p.R111H	ENST00000425967	NM_001174067.1	111	cGc/cAc	4/19	1	2	FACETS	0.31	0.256	0.371	0.31	0.256	0.371	SUBCLONAL	1	TRUE	1	0.333843072591766	2		755	754	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752916	128752916	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	209	427	0	ENST00000377970.2:c.1077C>G	p.Ser359Arg	p.S359R	ENST00000377970	NM_002467.4	359	agC/agG	3/3	1	2	FACETS	0.951	0.888	1	1	0.994	1	CLONAL	2	TRUE	1	0.333843072591766	2		427	658	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738639	145738639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769977498	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	223	602	4	ENST00000428558.2:c.2425G>A	p.Gly809Arg	p.G809R	ENST00000428558	NM_004260.3	809	Ggg/Agg	15/22	1	2	FACETS	0.855	0.799	0.914	1	0.993	1	CLONAL	2	TRUE	1	0.333843072591766	2		606	781	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471063	8471063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	88	511	0	ENST00000356435.5:c.3436C>T	p.Pro1146Ser	p.P1146S	ENST00000356435		1146	Cct/Tct	20/35	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.333843072591766	2		511	447	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209593	98209593	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	151	639	3	ENST00000331920.6:c.3945del	p.Tyr1316ThrfsTer56	p.Y1316Tfs*56	ENST00000331920	NM_000264.3	1315	ccC/cc	23/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.333843072591766	2		642	667	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399278	139399278	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778271353	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	254	832	2	ENST00000277541.6:c.4865G>A	p.Arg1622His	p.R1622H	ENST00000277541	NM_017617.3	1622	cGc/cAc	26/34	1	2	FACETS	0.768	0.719	0.818	1	0.993	1	SUBCLONAL	2	TRUE	1	0.333843072591766	2		834	991	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222438	53222438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	240	434	0	ENST00000375401.3:c.4394G>A	p.Arg1465Gln	p.R1465Q	ENST00000375401	NM_004187.3	1465	cGg/cAg	26/26	1	1	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	0	0.333843072591766	1		434	520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579415	7579415	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	760	655	0	ENST00000269305.4:c.272G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tGg/tAg	4/11	0.89142603556509	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.89142603556509	2		655	849	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0015644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	630	490	0	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	0.89142603556509	2	FACETS	0.96	0.942	0.977	0.96	0.942	0.977	CLONAL	2	TRUE	0	0.89142603556509	2		490	736	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47602438	47602438	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs587780767	NA	P-0015644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	526	481	1	ENST00000263735.4:c.491C>T	p.Thr164Ile	p.T164I	ENST00000263735	NM_002354.2	164	aCt/aTt	4/9	0.545768783672235	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	2	0.89142603556509	4		482	964	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945099	151945099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219495191	NA	P-0015644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	110	620	0	ENST00000262189.6:c.2420C>T	p.Ser807Phe	p.S807F	ENST00000262189	NM_170606.2	807	tCt/tTt	14/59	0.620465694386042	3	FACETS	0.627	0.565	0.692			1	SUBCLONAL	1	TRUE	NA	0.89142603556509	3		620	569	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	65	635	0				ENST00000310581	NM_198253.2	-/1132			0.375566994210162	3	FACETS	0.799	0.695	0.911	0.399	0.347	0.456	CLONAL	1	TRUE	1	0.447435428993411	3		635	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577146	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0015826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	183	796	0	ENST00000269305.4:c.792_794del	p.Leu265del	p.L265del	ENST00000269305	NM_001126112.2	264	ctACTg/ctg	8/11	0.410803661072218	1	FACETS	0.898	0.831	0.967	0.898	0.831	0.967	CLONAL	1	TRUE	0	0.447435428993411	1		796	707	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668618	52668618	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1389898698	NA	P-0015826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	82	442	0	ENST00000394830.3:c.1301G>A	p.Arg434Gln	p.R434Q	ENST00000394830	NM_018313.4	434	cGa/cAa	12/30	1	2	FACETS	0.697	0.616	0.783	0.697	0.616	0.783	SUBCLONAL	1	TRUE	1	0.447435428993411	2		442	526	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700278	117700278	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs779266768	NA	P-0015826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	98	554	0	ENST00000368508.3:c.2541G>T	p.Trp847Cys	p.W847C	ENST00000368508	NM_002944.2	847	tgG/tgT	17/43	1	2	FACETS	0.717	0.641	0.798	0.717	0.641	0.798	SUBCLONAL	1	TRUE	1	0.447435428993411	2		554	611	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250530	110250530	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	63	367	0	ENST00000374672.4:c.145T>C	p.Ser49Pro	p.S49P	ENST00000374672	NM_004235.4	49	Tcc/Ccc	3/5	1	2	FACETS	0.412	0.356	0.474	0.412	0.356	0.474	SUBCLONAL	1	TRUE	1	0.447435428993411	2		367	683	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015826-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	432	635	0				ENST00000310581	NM_198253.2	-/1132			0.708578252567046	5	FACETS	1	0.989	1	0.737	0.704	0.771	CLONAL	2	TRUE	2	0.708578252567046	5		635	1137	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577146	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0015826-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	426	796	0	ENST00000269305.4:c.792_794del	p.Leu265del	p.L265del	ENST00000269305	NM_001126112.2	264	ctACTg/ctg	8/11	0.708578252567046	2	FACETS	0.856	0.825	0.887	0.856	0.825	0.887	CLONAL	2	TRUE	0	0.708578252567046	2		796	702	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348745	118348745	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	284	438	0	ENST00000534358.1:c.3398A>C	p.Lys1133Thr	p.K1133T	ENST00000534358	NM_005933.3	1133	aAa/aCa	5/36	0.658548106141116	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.658548106141116	1		438	544	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641011	23641011	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555460323	NA	P-0016144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	202	441	0	ENST00000261584.4:c.2464C>T	p.Gln822Ter	p.Q822*	ENST00000261584	NM_024675.3	822	Cag/Tag	5/13	NA	2	FACETS	0.921	0.858	0.986			1	INDETERMINATE	1	TRUE	NA	0.658548106141116	2		441	666	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687550	29687550	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	307	493	0	ENST00000356175.3:c.8143G>C	p.Asp2715His	p.D2715H	ENST00000356175	NM_000267.3	2715	Gat/Cat	56/57	0.612992957099637	3	FACETS	0.981	0.924	1			1	CLONAL	1	TRUE	NA	0.658548106141116	3		493	1263	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42381396	42381402	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCAAG	CTCCAAG	-	novel	NA	P-0016144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	277	467	0	ENST00000221972.3:c.25_31del	p.Gln9CysfsTer32	p.Q9Cfs*32	ENST00000221972	NM_021601.3	8	CTCCAAGct/ct	1/5	1	2	FACETS	0.975	0.918	1	0.975	0.918	1	CLONAL	1	TRUE	1	0.658548106141116	2		467	863	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589646	67589852	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATACCCGCACATCCCAGGTGAGTTTTCTATGAAAATCAGATTAAAAAATAAGAGTTCTAAACTTTTAAAGACTAACATGGAAAAAAGAATTTAAAAGGTTGAGTTTTTACGAATGAGGTGGGGGTGAGAGCATTTATTTGTGAATCATTGTTGATTATTCTAGTGTAATATCTCTAAAGCTTTAAACCAAAAATTTTAAGTATCAGA	ATACCCGCACATCCCAGGTGAGTTTTCTATGAAAATCAGATTAAAAAATAAGAGTTCTAAACTTTTAAAGACTAACATGGAAAAAAGAATTTAAAAGGTTGAGTTTTTACGAATGAGGTGGGGGTGAGAGCATTTATTTGTGAATCATTGTTGATTATTCTAGTGTAATATCTCTAAAGCTTTAAACCAAAAATTTTAAGTATCAGA	-	novel	NA	P-0016144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	130	403	0	ENST00000274335.5:c.1412_1425+193del		p.X471_splice	ENST00000274335		471		10/15	0.658548106141116	1	FACETS	0.643	0.588	0.699	0.643	0.588	0.699	SUBCLONAL	1	TRUE	0	0.658548106141116	1		403	412	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520473	176520473	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	336	712	0	ENST00000292408.4:c.1318T>C	p.Ser440Pro	p.S440P	ENST00000292408	NM_213647.1	440	Tcc/Ccc	10/18	1	2	FACETS	0.993	0.94	1	0.993	0.94	1	CLONAL	1	TRUE	1	0.658548106141116	2		712	1028	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032175	26032175	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	146	238	0	ENST00000244661.2:c.114G>C	p.Lys38Asn	p.K38N	ENST00000244661	NM_003537.3	38	aaG/aaC	1/1	0.658548106141116	6	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.658548106141116	6		238	772	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815791	32815791	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	297	565	1	ENST00000354258.4:c.1825G>T	p.Ala609Ser	p.A609S	ENST00000354258	NM_000593.5	609	Gcc/Tcc	8/11	0.196446222790544	4	FACETS	0.813	0.767	0.86	0.813	0.767	0.86	INDETERMINATE	2	TRUE	2	0.658548106141116	4		566	920	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120218	94120218	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0016144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	206	265	0	ENST00000369303.4:c.832+1G>C		p.X278_splice	ENST00000369303	NM_004440.3	278			0.658548106141116	3	FACETS	1	0.953	1			1	CLONAL	1	TRUE	NA	0.658548106141116	3		265	806	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338631	70338631	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0016144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	265	474	0	ENST00000374080.3:c.27C>G	p.Tyr9Ter	p.Y9*	ENST00000374080		9	taC/taG	1/45	NA	2	FACETS	1	0.963	1			1	INDETERMINATE	1	TRUE	NA	0.658548106141116	2		474	781	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285074	15285078	+	missense_variant	Missense_Mutation	ONP	ACCAG	ACCAG	CCCAT	novel	NA	P-0016144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	319	621	0	ENST00000263388.2:c.4537_4541delinsATGGG	p.Leu1513_Val1514delinsMetGly	p.L1513_V1514delinsMG	ENST00000263388	NM_000435.2	1513	CTGGTg/ATGGGg	25/33	0.601786494448434	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.658548106141116	1		621	596	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271792	15271803	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGGGACTGCC	CCTGGGACTGCC	A	novel	NA	P-0016144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	267	624	1	ENST00000263388.2:c.6636_6647delinsT	p.Ala2213ThrfsTer25	p.A2213Tfs*25	ENST00000263388	NM_000435.2	2212	ctGGCAGTCCCAGGa/ctTa	33/33	0.601786494448434	1	FACETS	0.939	0.889	0.99	0.939	0.889	0.99	CLONAL	1	TRUE	0	0.658548106141116	1		625	579	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207065	1207065	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	373	587	0	ENST00000326873.7:c.157del	p.Asp53ThrfsTer11	p.D53Tfs*11	ENST00000326873	NM_000455.4	51	atG/at	1/10	0.379276839389332	3	FACETS	1	0.993	1	0.829	0.79	0.868	CLONAL	2	TRUE	0	0.39368387923699	3		587	912	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595951	52595951	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	94	396	0	ENST00000394830.3:c.3964A>G	p.Lys1322Glu	p.K1322E	ENST00000394830	NM_018313.4	1322	Aag/Gag	26/30	0.342783874708423	2	FACETS	0.835	0.744	0.931	0.417	0.372	0.466	CLONAL	1	TRUE	0	0.39368387923699	2		396	572	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207065	1207065	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016148-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	338	587	0	ENST00000326873.7:c.157del	p.Asp53ThrfsTer11	p.D53Tfs*11	ENST00000326873	NM_000455.4	51	atG/at	1/10	0.36690255906769	2	FACETS	0.968	0.918	1	0.968	0.918	1	CLONAL	2	TRUE	0	0.379216554339183	2		587	921	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595951	52595951	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016148-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	91	396	0	ENST00000394830.3:c.3964A>G	p.Lys1322Glu	p.K1322E	ENST00000394830	NM_018313.4	1322	Aag/Gag	26/30	0.359951662323825	1	FACETS	0.77	0.686	0.859	0.77	0.686	0.859	SUBCLONAL	1	TRUE	0	0.379216554339183	1		396	505	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465483	99465483	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016148-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	103	453	0	ENST00000268035.6:c.2308G>T	p.Glu770Ter	p.E770*	ENST00000268035	NM_000875.3	770	Gag/Tag	11/21	0.233541397520941	4	FACETS	0.881	0.788	0.981	0.441	0.394	0.491	CLONAL	1	TRUE	2	0.379216554339183	4		453	850	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853841	59853841	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016148-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1385	100	476	0	ENST00000259008.2:c.2018A>C	p.Gln673Pro	p.Q673P	ENST00000259008	NM_032043.2	673	cAa/cCa	14/20	0.379216554339183	7	FACETS	0.692	0.615	0.774	0.115	0.102	0.129	SUBCLONAL	1	TRUE	1	0.379216554339183	7		476	1485	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260152	19260152	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016148-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	109	604	0	ENST00000162023.5:c.141C>G	p.Ile47Met	p.I47M	ENST00000162023		47	atC/atG	7/13	0.198099924732881	4	FACETS	0.843	0.755	0.935	0.421	0.377	0.468	INDETERMINATE	1	TRUE	2	0.379216554339183	4		604	941	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672392	30672392	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016148-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	41	451	0	ENST00000376406.3:c.4568C>T	p.Ser1523Phe	p.S1523F	ENST00000376406	NM_014641.2	1523	tCt/tTt	10/15	0.379216554339183	5	FACETS	0.419	0.347	0.499	0.14	0.115	0.167	SUBCLONAL	1	TRUE	2	0.379216554339183	5		451	810	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038872	12038872	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	128	501	0	ENST00000396373.4:c.1165A>G	p.Met389Val	p.M389V	ENST00000396373	NM_001987.4	389	Atg/Gtg	7/8	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.267761828221127	2		501	849	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677233	29677233	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377662483	NA	P-0016220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	66	420	0	ENST00000356175.3:c.7291C>T	p.Arg2431Cys	p.R2431C	ENST00000356175	NM_000267.3	2431	Cgc/Tgc	49/57	1	2	FACETS	0.925	0.804	1	0.925	0.804	1	CLONAL	1	TRUE	1	0.267761828221127	2		420	533	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115873	8115874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0016225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	218	632	0	ENST00000346208.3:c.1220dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tCcg	6/6	0.201797164613621	3	FACETS	0.936	0.871	1	0.312	0.29	0.335	INDETERMINATE	1	TRUE	0	0.65245392810081	3		632	947	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725045	89725046	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0016225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	34	228	0	ENST00000371953.3:c.1029_1030insGG	p.Lys344GlyfsTer9	p.K344Gfs*9	ENST00000371953	NM_000314.4	343	gtg/gtGGg	9/9	0.65245392810081	1	FACETS	0.585	0.488	0.689	0.585	0.488	0.689	SUBCLONAL	1	TRUE	0	0.65245392810081	1		228	120	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	320	463	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.811	0.77	0.852	1	0.995	1	CLONAL	2	TRUE	1	0.528999864613554	2		463	746	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950283	15950283	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	271	891	1	ENST00000268712.3:c.6661G>A	p.Gly2221Arg	p.G2221R	ENST00000268712	NM_006311.3	2221	Gga/Aga	42/46	0.528999864613554	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.528999864613554	1		892	711	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610087	10610087	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	307	773	1	ENST00000171111.5:c.623A>G	p.Tyr208Cys	p.Y208C	ENST00000171111	NM_203500.1	208	tAc/tGc	2/6	1	2	FACETS	0.896	0.843	0.949	0.896	0.843	0.949	CLONAL	1	TRUE	1	0.528999864613554	2		774	1296	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858216	9858225	+	protein_altering_variant	In_Frame_Del	DEL	GAAATGTCAG	GAAATGTCAG	A	novel	NA	P-0016359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	191	485	1	ENST00000330684.3:c.3176_3185delinsT	p.Ser1059_Ser1062delinsLeu	p.S1059_S1062delinsL	ENST00000330684	NM_001134407.1	1059	tCTGACATTTCa/tTa	13/13	0.501500002288987	1	FACETS	0.924	0.86	0.989	0.924	0.86	0.989	CLONAL	1	TRUE	0	0.528999864613554	1		486	575	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478789	56478789	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	294	469	0	ENST00000267101.3:c.245A>T	p.Glu82Val	p.E82V	ENST00000267101	NM_001982.3	82	gAa/gTa	3/28	0.271647798871736	3	FACETS	1	0.993	1	0.675	0.638	0.713	INDETERMINATE	1	TRUE	1	0.718556789187095	3		469	824	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804342	46804342	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770172581	NA	P-0016564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	232	399	0	ENST00000290295.7:c.665C>T	p.Pro222Leu	p.P222L	ENST00000290295	NM_006361.5	222	cCg/cTg	2/2	1	2	FACETS	0.943	0.884	1	0.943	0.884	1	CLONAL	1	TRUE	1	0.718556789187095	2		399	685	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485822	57485822	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	282	428	0	ENST00000371085.3:c.1123G>C	p.Val375Leu	p.V375L	ENST00000371085	NM_000516.4	375	Gtg/Ctg	13/13	0.718556789187095	3	FACETS	0.973	0.914	1			1	CLONAL	1	TRUE	NA	0.718556789187095	3		428	1097	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339179	87339193	+	inframe_deletion	In_Frame_Del	DEL	ACATTTCATCCGATG	ACATTTCATCCGATG	-	novel	NA	P-0016564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	211	606	0	ENST00000277120.3:c.764_778del	p.Ile255_Asp259del	p.I255_D259del	ENST00000277120		254	aACATTTCATCCGATGac/aac	8/19	1	2	FACETS	0.793	0.738	0.848	0.793	0.738	0.848	SUBCLONAL	1	TRUE	1	0.718556789187095	2		606	741	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410600	63410600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1314447711	NA	P-0016564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	269	595	1	ENST00000330258.3:c.2567G>A	p.Ser856Asn	p.S856N	ENST00000330258	NM_152424.3	856	aGt/aAt	2/2	0.718556789187095	1	FACETS	0.959	0.912	1	0.959	0.912	1	CLONAL	1	TRUE	0	0.718556789187095	1		596	500	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380276	+	missense_variant	Missense_Mutation	DNP	TT	TT	CA	novel	NA	P-0016748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	143	425	1	ENST00000311936.3:c.182_183delinsTG	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAA/cTG	3/5	1	2	FACETS	0.79	0.718	0.865	0.79	0.718	0.865	SUBCLONAL	1	TRUE	1	0.3	2		426	1207	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	130	785	1	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.32661369830302	1	FACETS	0.925	0.84	1	0.925	0.84	1	CLONAL	1	TRUE	0	0.32661369830302	1		786	720	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380350	14380350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	42	468	0	ENST00000256196.4:c.67G>A	p.Gly23Ser	p.G23S	ENST00000256196		23	Ggc/Agc	1/6	0.131404092996436	3	FACETS	0.638	0.533	0.755	0.319	0.266	0.378	INDETERMINATE	1	TRUE	1	0.32661369830302	3		468	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577569	7577569	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519981	NA	P-0017011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	43	491	0	ENST00000269305.4:c.712T>A	p.Cys238Ser	p.C238S	ENST00000269305	NM_001126112.2	238	Tgt/Agt	7/11	1	2	FACETS	0.71	0.592	0.84	0.71	0.592	0.84	SUBCLONAL	1	TRUE	1	0.17	2		491	713	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520208	9520208	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	36	491	0	ENST00000353224.5:c.2061G>C	p.Gln687His	p.Q687H	ENST00000353224	NM_177990.2	687	caG/caC	10/10	1	2	FACETS	0.628	0.515	0.756	0.628	0.515	0.756	SUBCLONAL	1	TRUE	1	0.17	2		491	674	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961540	18961540	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	89	327	0	ENST00000262803.5:c.673G>C	p.Asp225His	p.D225H	ENST00000262803	NM_002911.3	225	Gac/Cac	5/24	1	2	FACETS	0.954	0.848	1	1	0.985	1	CLONAL	2	TRUE	1	0.17	2		327	549	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720711	89720712	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	36	122	0	ENST00000371953.3:c.867dup	p.Val290SerfsTer8	p.V290Sfs*8	ENST00000371953	NM_000314.4	288	gaa/gAaa	8/9	0.340025108725666	2	FACETS	1	0.913	1	0.582	0.484	0.689	CLONAL	1	TRUE	0	0.340025108725666	2		122	182	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577093	7577094	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0017069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	328	543	0	ENST00000269305.4:c.844dup	p.Arg282ProfsTer24	p.R282Pfs*24	ENST00000269305	NM_001126112.2	282	cgg/cCgg	8/11	0.340025108725666	2	FACETS	0.984	0.932	1	0.984	0.932	1	CLONAL	2	TRUE	0	0.340025108725666	2		543	980	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606627	29606627	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	130	442	0	ENST00000389048.3:c.1253A>G	p.Asp418Gly	p.D418G	ENST00000389048	NM_004304.4	418	gAc/gGc	5/29	0.340025108725666	2	FACETS	1	0.933	1	0.517	0.469	0.567	CLONAL	1	TRUE	0	0.340025108725666	2		442	740	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937620	32937621	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0017168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	253	819	0	ENST00000380152.3:c.8282dup	p.Pro2762SerfsTer2	p.P2762Sfs*2	ENST00000380152		2761	tct/tCct	18/27	0.72134013951157	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.72134013951157	1		819	368	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355347	15355347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767979123	NA	P-0017168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	115	359	0	ENST00000263377.2:c.2276C>T	p.Pro759Leu	p.P759L	ENST00000263377	NM_058243.2	759	cCg/cTg	13/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.72134013951157	2		359	285	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0017188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	143	652	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	1	2	FACETS	0.938	0.853	1	0.938	0.853	1	CLONAL	1	TRUE	1	0.246001271448499	2		652	1240	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428249	33428249	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555567076	NA	P-0017188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	73	412	0	ENST00000345365.6:c.874A>G	p.Met292Val	p.M292V	ENST00000345365	NM_002878.3	292	Atg/Gtg	9/10	0.196580753756677	3	FACETS	1	0.956	1			1	CLONAL	1	TRUE	NA	0.246001271448499	3		412	552	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121097	29121097	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1320819223	NA	P-0017188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	139	662	0	ENST00000328354.6:c.460A>G	p.Asn154Asp	p.N154D	ENST00000328354	NM_007194.3	154	Aac/Gac	4/15	0.246001271448499	1	FACETS	0.971	0.882	1	0.971	0.882	1	CLONAL	1	TRUE	0	0.246001271448499	1		662	1021	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293448	1293448	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1474097655	NA	P-0017188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	125	611	0	ENST00000310581.5:c.1553C>T	p.Ala518Val	p.A518V	ENST00000310581	NM_198253.2	518	gCt/gTt	2/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.246001271448499	2		611	807	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183797	10183797	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs5030807	NA	P-0017236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	242	718	0	ENST00000256474.2:c.266T>A	p.Leu89His	p.L89H	ENST00000256474	NM_000551.3	89	cTc/cAc	1/3	0.440103922316986	1	FACETS	0.946	0.885	1	0.946	0.885	1	CLONAL	1	TRUE	0	0.440103922316986	1		718	907	SUCCESS
BLM	641	MSKCC	GRCh37	15	91341450	91341450	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	35	426	1	ENST00000355112.3:c.3241G>T	p.Val1081Leu	p.V1081L	ENST00000355112	NM_000057.2	1081	Gtg/Ttg	17/22	0.158546484313694	0	FACETS	0.498	0.412	0.591			1	INDETERMINATE	1	TRUE	0	0.440103922316986	0		427	179	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266518	198266518	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	30	495	0	ENST00000335508.6:c.2318T>G	p.Leu773Arg	p.L773R	ENST00000335508	NM_012433.2	773	cTt/cGt	16/25	1	2	FACETS	0.646	0.524	0.782	0.646	0.524	0.782	SUBCLONAL	1	TRUE	1	0.440103922316986	2		495	211	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs17849781	NA	P-0017251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	118	654	0	ENST00000269305.4:c.832C>A	p.Pro278Thr	p.P278T	ENST00000269305	NM_001126112.2	278	Cct/Act	8/11	1	2	FACETS	0.919	0.827	1	0.919	0.827	1	CLONAL	1	TRUE	1	0.224196266071288	2		654	1146	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345284	73345284	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0017251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	39	435	0	ENST00000377767.4:c.1606-1G>A		p.X536_splice	ENST00000377767	NM_014953.3	536			0.215780846913678	1	FACETS	0.707	0.586	0.841	0.707	0.586	0.841	SUBCLONAL	1	TRUE	0	0.224196266071288	1		435	437	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651967	36651967	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	70	363	0	ENST00000244741.5:c.89T>G	p.Leu30Arg	p.L30R	ENST00000244741	NM_000389.4	30	cTg/cGg	2/3	0.137549486164793	3	FACETS	0.917	0.799	1	0.459	0.399	0.523	CLONAL	1	TRUE	1	0.224196266071288	3		363	757	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488718	212488718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267599191	NA	P-0017309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	527	496	1	ENST00000342788.4:c.2131C>T	p.Arg711Cys	p.R711C	ENST00000342788	NM_005235.2	711	Cgt/Tgt	18/28	1	2	FACETS	0.936	0.899	0.975	0.936	0.899	0.975	CLONAL	1	TRUE	1	0.841806948612839	2		497	1337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578376	7578376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	352	382	1	ENST00000269305.4:c.554del	p.Ser185ThrfsTer62	p.S185Tfs*62	ENST00000269305	NM_001126112.2	185	aGc/ac	5/11	0.826485810615881	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.841806948612839	1		383	475	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981315	68981315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866864487	NA	P-0017309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	401	378	1	ENST00000288368.4:c.1387C>T	p.Arg463Cys	p.R463C	ENST00000288368	NM_024870.2	463	Cgc/Tgc	12/40	0.494507940299602	3	FACETS	1	0.955	1	0.502	0.477	0.528	INDETERMINATE	1	TRUE	1	0.841806948612839	3		379	1347	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201738	102201738	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	26	292	0	ENST00000263464.3:c.1090T>C	p.Phe364Leu	p.F364L	ENST00000263464	NM_001165.4	364	Ttt/Ctt	6/9	0.387408503939915	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.841806948612839	0		292	511	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231189	46231189	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0017309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	359	287	0	ENST00000334344.6:c.1109T>G	p.Leu370Ter	p.L370*	ENST00000334344	NM_152641.2	370	tTa/tGa	9/21	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	1	TRUE	NA	0.841806948612839	2		287	613	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016647	12016648	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0017309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	340	277	0	ENST00000353533.5:c.783_784del	p.Asp263CysfsTer4	p.D263Cfs*4	ENST00000353533	NM_003010.3	261	acAAga/acga	7/11	0.826485810615881	1	FACETS	0.985	0.95	1	0.985	0.95	1	CLONAL	1	TRUE	0	0.841806948612839	1		277	475	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198269860	198269860	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1559267105	NA	P-0017309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	154	378	0	ENST00000335508.6:c.1479del	p.Glu494ArgfsTer4	p.E494Rfs*4	ENST00000335508	NM_012433.2	493	aaA/aa	11/25	1	2	FACETS	0.308	0.281	0.337	0.308	0.281	0.337	SUBCLONAL	1	TRUE	1	0.841806948612839	2		378	1186	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591312	67591312	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	104	299	0	ENST00000274335.5:c.1810G>C	p.Glu604Gln	p.E604Q	ENST00000274335		604	Gaa/Caa	13/15	1	2	FACETS	0.291	0.26	0.324	0.291	0.26	0.324	SUBCLONAL	1	TRUE	1	0.841806948612839	2		299	849	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322876	31322928	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCCCTACCTGAACTCTTCCTCCTACACATCACAGCAGCGACCACAGCTCCGA	TTCCCTACCTGAACTCTTCCTCCTACACATCACAGCAGCGACCACAGCTCCGA	-	novel	NA	P-0017309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	495	437	0	ENST00000412585.2:c.968_1012+8del		p.X323_splice	ENST00000412585	NM_005514.6	323		5/8	0.698938300868462	1	FACETS	0.959	0.93	0.987	0.959	0.93	0.987	CLONAL	1	TRUE	0	0.841806948612839	1		437	710	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974748	21974796	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCTACCCGACCCCGGGCCGCGGCCGTGGCCAGCCAGTCAGCCGAAGG	CCTCTACCCGACCCCGGGCCGCGGCCGTGGCCAGCCAGTCAGCCGAAGG	-	novel	NA	P-0017309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	178	225	0	ENST00000304494.5:c.31_79del	p.Pro11ArgfsTer26	p.P11Rfs*26	ENST00000304494	NM_000077.4	11	CCTTCGGCTGACTGGCTGGCCACGGCCGCGGCCCGGGGTCGGGTAGAGGag/ag	1/3	0.841806948612839	1	FACETS	0.9	0.852	0.947	0.9	0.852	0.947	CLONAL	1	TRUE	0	0.841806948612839	1		225	272	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0017349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	770	498	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.659012946998346	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	4	TRUE	0	0.659012946998346	4		498	953	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0017349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	312	442	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.643309544911285	2	FACETS	0.997	0.957	1	0.997	0.957	1	CLONAL	2	TRUE	0	0.659012946998346	2		442	475	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032739	30032739	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0017349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	265	176	0	ENST00000338641.4:c.115-1G>C		p.X39_splice	ENST00000338641	NM_000268.3	39			0.659012946998346	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	3	TRUE	0	0.659012946998346	3		176	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577537	7577546	+	frameshift_variant	Frame_Shift_Del	DEL	CCGGTTCATG	CCGGTTCATG	-	novel	NA	P-0017349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	272	417	0	ENST00000269305.4:c.735_744del	p.Met246GlyfsTer96	p.M246Gfs*96	ENST00000269305	NM_001126112.2	245	ggCATGAACCGG/gg	7/11	0.643325286541477	2	FACETS	0.814	0.774	0.854	0.814	0.774	0.854	CLONAL	2	TRUE	0	0.659012946998346	2		417	507	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575102	48575102	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	233	332	0	ENST00000342988.3:c.296G>A	p.Trp99Ter	p.W99*	ENST00000342988	NM_005359.5	99	tGg/tAg	3/12	0.643325286541477	2	FACETS	0.945	0.9	0.99	0.945	0.9	0.99	CLONAL	2	TRUE	0	0.659012946998346	2		332	374	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244107	5244107	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	457	475	0	ENST00000357368.4:c.1375G>A	p.Gly459Ser	p.G459S	ENST00000357368	NM_002850.3	459	Ggc/Agc	11/38	0.643309544911285	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.659012946998346	2		475	640	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574081	41574081	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	479	416	0	ENST00000263253.7:c.6370del	p.Val2124SerfsTer10	p.V2124Sfs*10	ENST00000263253	NM_001429.3	2122	caG/ca	31/31	0.659012946998346	3	FACETS	0.939	0.911	0.967	0.939	0.911	0.967	CLONAL	3	TRUE	0	0.659012946998346	3		416	686	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541964	187541964	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0017349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	205	330	0	ENST00000441802.2:c.5776A>T	p.Lys1926Ter	p.K1926*	ENST00000441802	NM_005245.3	1926	Aag/Tag	10/27	0.659012946998346	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.659012946998346	1		330	357	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172139	32172153	+	inframe_deletion	In_Frame_Del	DEL	AGTTCTGTCCATCGT	AGTTCTGTCCATCGT	-	novel	NA	P-0017349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	375	487	0	ENST00000375023.3:c.2879_2893del	p.Tyr960_Asn964del	p.Y960_N964del	ENST00000375023	NM_004557.3	960	tACGATGGACAGAACTgc/tgc	19/30	0.659012946998346	3	FACETS	0.826	0.787	0.865	0.826	0.787	0.865	CLONAL	2	TRUE	1	0.659012946998346	3		487	916	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	178	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.172290009905476	3	FACETS	1	0.981	1	0.593	0.549	0.639	INDETERMINATE	1	TRUE	1	0.593348914532238	3		473	656	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0017558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	27	494	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.353	0.281	0.434	0.353	0.281	0.434	SUBCLONAL	1	TRUE	1	0.593348914532238	2		494	258	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604785	48604785	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	126	403	0	ENST00000342988.3:c.1607T>C	p.Leu536Pro	p.L536P	ENST00000342988	NM_005359.5	536	cTa/cCa	12/12	0.593348914532238	1	FACETS	0.561	0.511	0.614	0.561	0.511	0.614	SUBCLONAL	1	TRUE	0	0.593348914532238	1		403	532	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0017558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	122	272	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	1	2	FACETS	0.805	0.731	0.882	0.805	0.731	0.882	CLONAL	1	TRUE	1	0.593348914532238	2		272	511	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486026	29486026	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0017558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	47	135	0	ENST00000356175.3:c.205-2A>G		p.X69_splice	ENST00000356175	NM_000267.3	69			1	2	FACETS	0.564	0.479	0.656	0.564	0.479	0.656	SUBCLONAL	1	TRUE	1	0.593348914532238	2		135	281	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376176	225376176	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs748814630	NA	P-0017558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	232	474	0	ENST00000264414.4:c.778A>G	p.Ile260Val	p.I260V	ENST00000264414	NM_003590.4	260	Att/Gtt	6/16	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.593348914532238	2		474	765	SUCCESS
APC	324	MSKCC	GRCh37	5	112176363	112176427	+	frameshift_variant	Frame_Shift_Del	DEL	CTACAGAAGGCAGAAGTACAGATGAGGCTCAAGGAGGAAAAACCTCATCTGTAACCATACCTGAA	CTACAGAAGGCAGAAGTACAGATGAGGCTCAAGGAGGAAAAACCTCATCTGTAACCATACCTGAA	TGG	novel	NA	P-0017558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	102	279	1	ENST00000257430.4:c.5072_5136delinsTGG	p.Pro1691LeufsTer4	p.P1691Lfs*4	ENST00000257430	NM_000038.5	1691	cCTACAGAAGGCAGAAGTACAGATGAGGCTCAAGGAGGAAAAACCTCATCTGTAACCATACCTGAA/cTGG	16/16	0.571306361439331	1	FACETS	0.737	0.667	0.81	0.737	0.667	0.81	SUBCLONAL	1	TRUE	0	0.593348914532238	1		280	328	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405931	157405932	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	rs1554294665	NA	P-0017558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	183	426	0	ENST00000346085.5:c.2176_2177dup	p.His727LeufsTer19	p.H727Lfs*19	ENST00000346085	NM_020732.3	725	tcc/tCCcc	6/20	NA	2	FACETS	0.885	0.819	0.953			1	INDETERMINATE	1	TRUE	NA	0.593348914532238	2		426	697	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574925	41574925	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	325	778	0	ENST00000263253.7:c.7210T>G	p.Ser2404Ala	p.S2404A	ENST00000263253	NM_001429.3	2404	Tca/Gca	31/31	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	1	TRUE	NA	0.740102312711016	2		778	591	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81399278	81399279	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CACC	novel	NA	P-0017700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	210	509	0	ENST00000222390.5:c.6_9dup	p.Thr4GlyfsTer39	p.T4Gfs*39	ENST00000222390	NM_000601.4	3	-/GGTG	1/18	0.158006849291269	4	FACETS	0.869	0.813	0.926	0.869	0.813	0.926	INDETERMINATE	2	TRUE	2	0.740102312711016	4		509	568	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32449563	32449563	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	90	919	0	ENST00000332351.3:c.811C>A	p.His271Asn	p.H271N	ENST00000332351	NM_024426.4	271	Cac/Aac	3/10	0.160770716899139	1	FACETS	0.922	0.816	1	0.922	0.816	1	CLONAL	1	FALSE	0	0.160770716899139	1		919	1117	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858190	9858190	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	77	565	1	ENST00000330684.3:c.3211C>A	p.His1071Asn	p.H1071N	ENST00000330684	NM_001134407.1	1071	Cac/Aac	13/13	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	FALSE	1	0.160770716899139	2		566	954	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271696	15271696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1269	130	1161	0	ENST00000263388.2:c.6743C>T	p.Ser2248Phe	p.S2248F	ENST00000263388	NM_000435.2	2248	tCc/tTc	33/33	0.160770716899139	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	0	0.160770716899139	1		1161	1399	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375541	15375541	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1350021197	NA	P-0017715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1294	86	1018	0	ENST00000263377.2:c.886A>C	p.Thr296Pro	p.T296P	ENST00000263377	NM_058243.2	296	Acc/Ccc	6/20	0.160770716899139	1	FACETS	0.713	0.628	0.804	0.713	0.628	0.804	SUBCLONAL	1	FALSE	0	0.160770716899139	1		1018	1380	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274724	198274724	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	45	326	0	ENST00000335508.6:c.674G>T	p.Gly225Val	p.G225V	ENST00000335508	NM_012433.2	225	gGg/gTg	7/25	0.160770716899139	1	FACETS	0.96	0.807	1	0.96	0.807	1	CLONAL	1	FALSE	0	0.160770716899139	1		326	536	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93657824	93657824	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	119	465	0	ENST00000375746.1:c.1850C>A	p.Pro617His	p.P617H	ENST00000375746	NM_001174167.1	617	cCc/cAc	14/14	0.160770716899139	2	FACETS	0.924	0.834	1	0.924	0.834	1	CLONAL	2	FALSE	0	0.160770716899139	2		465	801	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375541	15375541	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1350021197	NA	P-0017715-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1301	249	1018	0	ENST00000263377.2:c.886A>C	p.Thr296Pro	p.T296P	ENST00000263377	NM_058243.2	296	Acc/Ccc	6/20	1	2	FACETS	0.607	0.566	0.65	0.607	0.566	0.65	SUBCLONAL	1	TRUE	1	0.528982816903831	2		1018	1550	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	167	330	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.67	2		330	496	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	250	894	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.67	2		894	723	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	74	366	2	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.944	0.839	1	0.944	0.839	1	CLONAL	1	TRUE	1	0.67	2		368	234	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	166	285	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.67	2		285	484	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	127	293	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.3	4	FACETS	0.816	0.747	0.887			1	INDETERMINATE	2	TRUE	NA	0.67	4		293	388	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	187	528	0	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	0.67	2		528	522	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	96	603	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.874	0.787	0.964	0.874	0.787	0.964	CLONAL	1	TRUE	1	0.67	2		604	328	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	146	378	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.67	2		378	422	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	122	383	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	1	2	FACETS	0.976	0.892	1	0.976	0.892	1	CLONAL	1	TRUE	1	0.67	2		383	373	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522598	157522598	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554236040	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	206	696	0	ENST00000346085.5:c.4870C>T	p.Arg1624Ter	p.R1624*	ENST00000346085	NM_020732.3	1624	Cga/Tga	18/20	1	2	FACETS	0.828	0.77	0.887	0.828	0.77	0.887	CLONAL	1	TRUE	1	0.67	2		696	743	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	50	198	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.899	0.777	1	0.899	0.777	1	CLONAL	1	TRUE	1	0.67	2		198	166	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971114	21971114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501269	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	111	204	0	ENST00000304494.5:c.244G>A	p.Val82Met	p.V82M	ENST00000304494	NM_000077.4	82	Gtg/Atg	2/3	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.67	2		204	294	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088788	27088788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	139	417	0	ENST00000324856.7:c.2402del	p.Gly801ValfsTer32	p.G801Vfs*32	ENST00000324856	NM_006015.4	799	caG/ca	7/20	1	2	FACETS	0.926	0.85	1	0.926	0.85	1	CLONAL	1	TRUE	1	0.67	2		417	448	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157491	106157491	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777279382	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	111	328	0	ENST00000380013.4:c.2392G>A	p.Glu798Lys	p.E798K	ENST00000380013	NM_001127208.2	798	Gag/Aag	3/11	1	2	FACETS	0.983	0.894	1	0.983	0.894	1	CLONAL	1	TRUE	1	0.67	2		328	337	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405954	157405954	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	103	357	0	ENST00000346085.5:c.2201del	p.Gly734AlafsTer11	p.G734Afs*11	ENST00000346085	NM_020732.3	732	ccG/cc	6/20	1	2	FACETS	0.912	0.825	1	0.912	0.825	1	CLONAL	1	TRUE	1	0.67	2		357	337	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434595	110434595	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs555841746	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	147	396	0	ENST00000375856.3:c.3806A>C	p.Gln1269Pro	p.Q1269P	ENST00000375856	NM_003749.2	1269	cAg/cCg	1/2	1	2	FACETS	0.892	0.82	0.966	0.892	0.82	0.966	CLONAL	1	TRUE	1	0.67	2		396	492	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165283	47165283	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	116	222	0	ENST00000409792.3:c.843del	p.Glu282LysfsTer19	p.E282Kfs*19	ENST00000409792	NM_014159.6	281	aaA/aa	3/21	1	2	FACETS	0.861	0.783	0.943	0.861	0.783	0.943	CLONAL	1	TRUE	1	0.67	2		222	402	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864776	37864776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs185670819	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	62	256	0	ENST00000269571.5:c.428G>A	p.Arg143Gln	p.R143Q	ENST00000269571		143	cGa/cAa	3/27	1	2	FACETS	0.964	0.848	1	0.964	0.848	1	CLONAL	1	TRUE	1	0.67	2		256	192	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	337	684	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.99	1	1	0.997	1	CLONAL	2	TRUE	1	0.67	2		685	469	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998127	169998128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs753143066	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	260	581	8	ENST00000295797.4:c.826dup	p.Thr276AsnfsTer16	p.T276Nfs*16	ENST00000295797	NM_002740.5	273	tta/ttAa	9/18	1	2	FACETS	0.977	0.919	1	0.977	0.919	1	CLONAL	1	TRUE	1	0.67	2		589	794	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898764	134898764	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs185655852	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	101	296	0	ENST00000398015.3:c.1822C>T	p.Arg608Trp	p.R608W	ENST00000398015	NM_004441.4	608	Cgg/Tgg	10/16	1	2	FACETS	0.9	0.813	0.99	0.9	0.813	0.99	CLONAL	1	TRUE	1	0.67	2		296	335	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	147	494	3	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	1	2	FACETS	0.995	0.917	1	0.995	0.917	1	CLONAL	1	TRUE	1	0.67	2		497	441	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	178	666	2	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.904	0.838	0.972	0.904	0.838	0.972	CLONAL	1	TRUE	1	0.67	2		668	588	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	140	1158	4	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.909	0.834	0.986	0.909	0.834	0.986	CLONAL	1	TRUE	1	0.67	2		1162	460	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696462	47696462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	103	318	3	ENST00000347630.2:c.361C>T	p.Arg121Trp	p.R121W	ENST00000347630	NM_001007230.1	121	Cgg/Tgg	6/11	1	2	FACETS	0.816	0.736	0.898	0.816	0.736	0.898	CLONAL	1	TRUE	1	0.67	2		321	377	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023415	27023415	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	197	375	0	ENST00000324856.7:c.521G>A	p.Gly174Asp	p.G174D	ENST00000324856	NM_006015.4	174	gGc/gAc	1/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.67	2		375	549	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100165	27100165	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	122	361	0	ENST00000324856.7:c.3962del	p.Pro1321LeufsTer160	p.P1321Lfs*160	ENST00000324856	NM_006015.4	1321	Cct/ct	16/20	1	2	FACETS	0.969	0.885	1	0.969	0.885	1	CLONAL	1	TRUE	1	0.67	2		361	376	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740102	162740102	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	94	293	1	ENST00000367921.3:c.1304G>T	p.Arg435Met	p.R435M	ENST00000367921	NM_006182.2	435	aGg/aTg	12/18	1	2	FACETS	0.961	0.866	1	0.961	0.866	1	CLONAL	1	TRUE	1	0.67	2		294	292	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226556021	226556021	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs759524114	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	51	192	0	ENST00000366794.5:c.2156C>T	p.Ala719Val	p.A719V	ENST00000366794	NM_001618.3	719	gCg/gTg	16/23	1	2	FACETS	0.865	0.748	0.989	0.865	0.748	0.989	CLONAL	1	TRUE	1	0.67	2		192	176	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692992	89692992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	146	345	0	ENST00000371953.3:c.476G>A	p.Arg159Lys	p.R159K	ENST00000371953	NM_000314.4	159	aGg/aAg	5/9	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.67	2		345	420	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711915	89711915	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786204866	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	167	390	0	ENST00000371953.3:c.533A>G	p.Tyr178Cys	p.Y178C	ENST00000371953	NM_000314.4	178	tAt/tGt	6/9	1	2	FACETS	0.981	0.909	1	0.981	0.909	1	CLONAL	1	TRUE	1	0.67	2		390	508	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127731	64127731	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1455628289	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	157	363	1	ENST00000334205.4:c.224G>A	p.Arg75His	p.R75H	ENST00000334205	NM_003942.2	75	cGc/cAc	3/17	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.67	2		364	455	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465979	69465979	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	149	436	0	ENST00000227507.2:c.817G>T	p.Glu273Ter	p.E273*	ENST00000227507	NM_053056.2	273	Gag/Tag	5/5	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.67	2		436	398	SUCCESS
EED	8726	MSKCC	GRCh37	11	85967478	85967478	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	143	349	0	ENST00000263360.6:c.476G>A	p.Ser159Asn	p.S159N	ENST00000263360	NM_003797.3	159	aGc/aAc	5/12	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.67	2		349	396	SUCCESS
CBL	867	MSKCC	GRCh37	11	119158652	119158652	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	161	432	1	ENST00000264033.4:c.2032G>T	p.Ala678Ser	p.A678S	ENST00000264033	NM_005188.3	678	Gcc/Tcc	12/16	1	2	FACETS	0.993	0.918	1	0.993	0.918	1	CLONAL	1	TRUE	1	0.67	2		433	484	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514135	125514135	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	132	346	0	ENST00000428830.2:c.1073A>G	p.Gln358Arg	p.Q358R	ENST00000428830	NM_001114121.2	358	cAg/cGg	10/14	1	2	FACETS	0.968	0.887	1	0.968	0.887	1	CLONAL	1	TRUE	1	0.67	2		346	407	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350861	89350862	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	260	658	0	ENST00000301030.4:c.2088dup	p.Glu697ArgfsTer5	p.E697Rfs*5	ENST00000301030	NM_001256183.1	696	-/A	9/13	1	2	FACETS	0.901	0.847	0.958	0.901	0.847	0.958	CLONAL	1	TRUE	1	0.67	2		658	861	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63531828	63531828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	158	341	0	ENST00000307078.5:c.2153C>T	p.Ala718Val	p.A718V	ENST00000307078	NM_004655.3	718	gCc/gTc	9/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.67	2		341	393	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051439	13051439	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	113	299	0	ENST00000316448.5:c.791del	p.Pro264GlnfsTer2	p.P264Qfs*2	ENST00000316448	NM_004343.3	263	Ccc/cc	6/9	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.67	2		299	330	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994354	25994355	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	103	352	0	ENST00000435504.4:c.458_459del	p.Lys153SerfsTer51	p.K153Sfs*51	ENST00000435504		153	aAA/a	6/13	1	2	FACETS	0.807	0.728	0.889	0.807	0.728	0.889	CLONAL	1	TRUE	1	0.67	2		352	381	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635674	47635674	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	153	434	0	ENST00000233146.2:c.346G>T	p.Asp116Tyr	p.D116Y	ENST00000233146	NM_000251.2	116	Gat/Tat	2/16	1	2	FACETS	0.98	0.904	1	0.98	0.904	1	CLONAL	1	TRUE	1	0.67	2		434	466	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47205399	47205399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	174	321	1	ENST00000409792.3:c.16C>T	p.Pro6Ser	p.P6S	ENST00000409792	NM_014159.6	6	Ccg/Tcg	1/21	1	2	FACETS	0.999	0.927	1	0.999	0.927	1	CLONAL	1	TRUE	1	0.67	2		322	520	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524602	176524602	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	193	577	1	ENST00000292408.4:c.2334C>A	p.Ser778Arg	p.S778R	ENST00000292408	NM_213647.1	778	agC/agA	18/18	1	2	FACETS	0.981	0.914	1	0.981	0.914	1	CLONAL	1	TRUE	1	0.67	2		578	587	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509904	106509904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	98	418	0	ENST00000359195.3:c.1898G>A	p.Cys633Tyr	p.C633Y	ENST00000359195	NM_002649.2	633	tGc/tAc	2/11	1	2	FACETS	0.66	0.592	0.732	0.66	0.592	0.732	SUBCLONAL	1	TRUE	1	0.67	2		418	443	SUCCESS
RET	5979	MSKCC	GRCh37	10	43595970	43595970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	150	568	1	ENST00000355710.3:c.137C>T	p.Ala46Val	p.A46V	ENST00000355710	NM_020975.4	46	gCc/gTc	2/20	1	2	FACETS	0.734	0.672	0.799	0.734	0.672	0.799	SUBCLONAL	1	TRUE	1	0.541211695877303	2		569	755	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	271	635	0				ENST00000310581	NM_198253.2	-/1132			0.450598838235535	5	FACETS	0.98	0.927	1	0.98	0.927	1	CLONAL	3	TRUE	2	0.541211695877303	5		635	617	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	267	550	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.45974426726246	4	FACETS	1	0.987	1	0.6	0.562	0.64	CLONAL	1	TRUE	2	0.541211695877303	4		550	1267	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024001	27024002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	19	78	0	ENST00000324856.7:c.1113dup	p.Gln372AlafsTer28	p.Q372Afs*28	ENST00000324856	NM_006015.4	369	-/G	1/20	0.45974426726246	4	FACETS	0.717	0.548	0.911	0.358	0.274	0.456	CLONAL	1	TRUE	2	0.541211695877303	4		78	151	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	141	316	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	0.438353878272778	1	FACETS	0.805	0.739	0.874	0.805	0.739	0.874	CLONAL	1	TRUE	0	0.541211695877303	1		316	472	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662582	117662582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	125	337	0	ENST00000368508.3:c.4883G>A	p.Gly1628Glu	p.G1628E	ENST00000368508	NM_002944.2	1628	gGa/gAa	29/43	0.541211695877303	3	FACETS	0.87	0.788	0.955	0.435	0.394	0.478	CLONAL	1	TRUE	1	0.541211695877303	3		337	675	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444318	50444318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1427077431	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	96	253	2	ENST00000331340.3:c.248G>A	p.Arg83Gln	p.R83Q	ENST00000331340	NM_006060.4	83	cGa/cAa	4/8	0.247086205260599	5	FACETS	1	0.98	1	0.476	0.426	0.529	INDETERMINATE	1	TRUE	2	0.541211695877303	5		255	450	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046410	69046410	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868582467	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	306	437	0	ENST00000288368.4:c.3883G>A	p.Glu1295Lys	p.E1295K	ENST00000288368	NM_024870.2	1295	Gaa/Aaa	32/40	0.247086205260599	5	FACETS	1	0.982	1	0.728	0.688	0.769	INDETERMINATE	2	TRUE	2	0.541211695877303	5		437	938	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968149	68968149	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	316	556	0	ENST00000288368.4:c.1178G>A	p.Gly393Glu	p.G393E	ENST00000288368	NM_024870.2	393	gGa/gAa	10/40	0.247086205260599	5	FACETS	0.836	0.788	0.885	0.558	0.525	0.59	INDETERMINATE	2	TRUE	2	0.541211695877303	5		556	1265	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874140	155874140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	248	488	0	ENST00000368323.3:c.391C>T	p.Leu131Phe	p.L131F	ENST00000368323	NM_006912.5	131	Ctt/Ttt	5/6	0.45974426726246	4	FACETS	1	0.981	1	0.565	0.528	0.604	CLONAL	1	TRUE	2	0.541211695877303	4		488	1249	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724997	162724997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	296	385	1	ENST00000367921.3:c.469C>T	p.Pro157Ser	p.P157S	ENST00000367921	NM_006182.2	157	Ccg/Tcg	6/18	0.45974426726246	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.541211695877303	4		386	807	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572246	64572247	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	315	405	1	ENST00000312049.6:c.1392_1393delinsAA	p.Ala465Thr	p.A465T	ENST00000312049	NM_130799.2	464	gcGGcc/gcAAcc	10/10	0.485540316713803	4	FACETS	0.847	0.805	0.889	0.847	0.805	0.889	CLONAL	3	TRUE	1	0.541211695877303	4		406	706	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716310	18716310	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	208	288	0	ENST00000266497.5:c.3658-1G>A		p.X1220_splice	ENST00000266497		1220			0.509963069505294	3	FACETS	0.84	0.786	0.896	0.84	0.786	0.896	CLONAL	2	TRUE	1	0.541211695877303	3		288	581	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66735663	66735664	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	263	387	1	ENST00000307102.5:c.484_485delinsTT	p.Pro162Phe	p.P162F	ENST00000307102	NM_002755.3	162	CCt/TTt	4/11	0.247086205260599	5	FACETS	0.987	0.927	1	0.658	0.618	0.699	INDETERMINATE	2	TRUE	2	0.541211695877303	5		388	892	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23635411	23635411	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	374	480	2	ENST00000261584.4:c.2753C>T	p.Pro918Leu	p.P918L	ENST00000261584	NM_024675.3	918	cCa/cTa	8/13	0.449027732392226	4	FACETS	0.855	0.812	0.9	0.855	0.812	0.9	CLONAL	2	TRUE	2	0.541211695877303	4		482	1245	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81941312	81941312	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	382	553	0	ENST00000359376.3:c.1490C>T	p.Ala497Val	p.A497V	ENST00000359376	NM_002661.3	497	gCc/gTc	16/33	0.449027732392226	4	FACETS	0.939	0.892	0.986	0.939	0.892	0.986	CLONAL	2	TRUE	2	0.541211695877303	4		553	1159	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761073	59761073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs968860042	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	288	431	0	ENST00000259008.2:c.3334G>A	p.Asp1112Asn	p.D1112N	ENST00000259008	NM_032043.2	1112	Gat/Aat	20/20	0.509963069505294	3	FACETS	0.75	0.707	0.794	0.75	0.707	0.794	SUBCLONAL	2	TRUE	1	0.541211695877303	3		431	901	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761496	59761496	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	103	252	0	ENST00000259008.2:c.2911C>T	p.Pro971Ser	p.P971S	ENST00000259008	NM_032043.2	971	Cca/Tca	20/20	0.509963069505294	3	FACETS	0.813	0.729	0.901	0.406	0.364	0.451	CLONAL	1	TRUE	1	0.541211695877303	3		252	595	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265139	10265139	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	104	345	2	ENST00000340748.4:c.1801C>T	p.Arg601Trp	p.R601W	ENST00000340748		601	Cgg/Tgg	21/40	0.247086205260599	5	FACETS	1	0.956	1	0.373	0.334	0.414	INDETERMINATE	1	TRUE	2	0.541211695877303	5		347	622	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272132	15272132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	284	543	0	ENST00000263388.2:c.6307G>A	p.Asp2103Asn	p.D2103N	ENST00000263388	NM_000435.2	2103	Gac/Aac	33/33	0.247086205260599	5	FACETS	1	0.948	1	0.671	0.632	0.712	INDETERMINATE	2	TRUE	2	0.541211695877303	5		543	944	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211784	36211784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1251593316	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	389	652	1	ENST00000222270.7:c.1535C>T	p.Thr512Ile	p.T512I	ENST00000222270	NM_014727.1	512	aCc/aTc	3/37	0.247086205260599	5	FACETS	1	0.977	1	0.698	0.663	0.733	INDETERMINATE	2	TRUE	2	0.541211695877303	5		653	1244	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794699	42794700	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	319	589	1	ENST00000575354.2:c.1779_1780delinsAA	p.Met593_Asp594delinsIleAsn	p.M593_D594delinsIN	ENST00000575354	NM_015125.3	593	atGGat/atAAat	10/20	0.247086205260599	5	FACETS	0.965	0.911	1	0.643	0.607	0.68	INDETERMINATE	2	TRUE	2	0.541211695877303	5		590	1107	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051207	128051207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	323	517	1	ENST00000285398.2:c.116C>T	p.Pro39Leu	p.P39L	ENST00000285398	NM_000122.1	39	cCc/cTc	2/15	0.449027732392226	4	FACETS	0.924	0.875	0.975	0.924	0.875	0.975	CLONAL	2	TRUE	2	0.541211695877303	4		518	995	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790031	40790031	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	217	392	0	ENST00000373198.4:c.2700G>A	p.Met900Ile	p.M900I	ENST00000373198	NM_133170.3	900	atG/atA	18/32	0.449027732392226	4	FACETS	0.763	0.711	0.816	0.763	0.711	0.816	SUBCLONAL	2	TRUE	2	0.541211695877303	4		392	810	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326812	62326812	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1354993689	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	303	597	0	ENST00000360203.5:c.3631G>A	p.Gly1211Arg	p.G1211R	ENST00000360203	NM_001283009.1	1211	Ggg/Agg	34/35	0.449027732392226	4	FACETS	0.834	0.786	0.882	0.834	0.786	0.882	CLONAL	2	TRUE	2	0.541211695877303	4		597	1035	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405915	49405915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866298036	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	209	623	0	ENST00000418115.1:c.223C>T	p.Pro75Ser	p.P75S	ENST00000418115	NM_001664.2	75	Cca/Tca	3/5	0.541211695877303	3	FACETS	0.741	0.686	0.798	0.37	0.343	0.399	SUBCLONAL	1	TRUE	1	0.541211695877303	3		623	1325	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247350	153247350	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	178	418	3	ENST00000281708.4:c.1452G>T	p.Arg484Ser	p.R484S	ENST00000281708	NM_033632.3	484	agG/agT	10/12	0.449027687538656	3	FACETS	0.877	0.808	0.949	0.439	0.404	0.475	CLONAL	1	TRUE	1	0.541211695877303	3		421	953	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177414	56177414	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1290999800	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	322	296	0	ENST00000399503.3:c.2387C>T	p.Ser796Phe	p.S796F	ENST00000399503	NM_005921.1	796	tCc/tTc	14/20	0.450598838235535	5	FACETS	0.874	0.829	0.92	0.874	0.829	0.92	CLONAL	3	TRUE	2	0.541211695877303	5		296	822	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965718	93965718	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1327213322	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	254	336	0	ENST00000369303.4:c.2210G>A	p.Gly737Glu	p.G737E	ENST00000369303	NM_004440.3	737	gGa/gAa	13/17	0.541211695877303	3	FACETS	0.891	0.839	0.944	0.891	0.839	0.944	CLONAL	2	TRUE	1	0.541211695877303	3		336	669	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729889	41729889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs923669088	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	298	457	0	ENST00000242208.4:c.640C>T	p.Arg214Trp	p.R214W	ENST00000242208	NM_002192.2	214	Cgg/Tgg	3/3	0.247086205260599	5	FACETS	1	0.991	1	0.829	0.784	0.875	INDETERMINATE	2	TRUE	2	0.541211695877303	5		457	802	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386517	81386517	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	241	293	0	ENST00000222390.5:c.470C>T	p.Pro157Leu	p.P157L	ENST00000222390	NM_000601.4	157	cCa/cTa	4/18	0.247086205260599	5	FACETS	1	0.973	1	0.711	0.666	0.756	INDETERMINATE	2	TRUE	2	0.541211695877303	5		293	757	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403213	116403213	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1307584609	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	413	530	1	ENST00000397752.3:c.2474G>A	p.Gly825Glu	p.G825E	ENST00000397752	NM_000245.2	825	gGg/gAg	11/21	0.247086205260599	5	FACETS	1	0.992	1	0.786	0.749	0.823	INDETERMINATE	2	TRUE	2	0.541211695877303	5		531	1173	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995569	68995569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775560862	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	306	527	0	ENST00000288368.4:c.1973C>T	p.Ser658Leu	p.S658L	ENST00000288368	NM_024870.2	658	tCg/tTg	18/40	0.247086205260599	5	FACETS	0.811	0.764	0.86	0.541	0.509	0.573	INDETERMINATE	2	TRUE	2	0.541211695877303	5		527	1263	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141582931	141582931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	378	546	0	ENST00000220592.5:c.316C>T	p.Leu106Phe	p.L106F	ENST00000220592	NM_012154.3	106	Ctt/Ttt	3/19	0.247086205260599	5	FACETS	1	0.99	1	0.765	0.727	0.803	INDETERMINATE	2	TRUE	2	0.541211695877303	5		546	1103	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127916227	127916228	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	311	423	1	ENST00000373547.4:c.416_417delinsAA	p.Trp139Ter	p.W139*	ENST00000373547	NM_002721.4	139	tGG/tAA	5/7	0.454523614134358	2	FACETS	0.778	0.738	0.818	0.778	0.738	0.818	SUBCLONAL	2	TRUE	0	0.541211695877303	2		424	739	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218658	36218664	+	protein_altering_variant	In_Frame_Del	DEL	GCGCTTC	GCGCTTC	A	novel	NA	P-0018059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	273	473	0	ENST00000222270.7:c.4362_4368delinsA	p.Arg1455_Phe1456del	p.R1455_F1456del	ENST00000222270	NM_014727.1	1454	caGCGCTTC/caA	17/37	0.247086205260599	5	FACETS	0.965	0.907	1	0.643	0.605	0.683	INDETERMINATE	2	TRUE	2	0.541211695877303	5		473	947	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1023835002	NA	P-0018184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	19	416	0	ENST00000558401.1:c.1A>G	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Gtg	1/4	NA	2	FACETS	0.204	0.154	0.262			1	INDETERMINATE	1	TRUE	NA	0.605701169234526	2		416	308	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576858	7576858	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	199	642	0	ENST00000269305.4:c.988del	p.Leu330PhefsTer15	p.L330Ffs*15	ENST00000269305	NM_001126112.2	330	Ctt/tt	9/11	0.59400320453482	2	FACETS	0.99	0.936	1	0.99	0.936	1	CLONAL	2	TRUE	0	0.605701169234526	2		642	332	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039405	49039421	+	frameshift_variant	Frame_Shift_Del	DEL	TACGGATTCCTGGAGGG	TACGGATTCCTGGAGGG	-	novel	NA	P-0018184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	62	840	1	ENST00000267163.4:c.2390_2406del	p.Leu797Ter	p.L797*	ENST00000267163	NM_000321.2	797	tTACGGATTCCTGGAGGG/t	23/27	0.603084230569902	2	FACETS	1	0.954	1	0.588	0.519	0.66	CLONAL	1	TRUE	0	0.605701169234526	2		841	174	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641122	3641122	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs766929821	NA	P-0018184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	154	1081	0	ENST00000294008.3:c.2517C>G	p.His839Gln	p.H839Q	ENST00000294008	NM_032444.2	839	caC/caG	12/15	0.605701169234526	2	FACETS	0.646	0.592	0.703	0.323	0.296	0.352	SUBCLONAL	1	TRUE	0	0.605701169234526	2		1081	787	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502246	186502246	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	30	351	0	ENST00000323963.5:c.55G>C	p.Asp19His	p.D19H	ENST00000323963		19	Gac/Cac	2/11	0.605701169234526	6	FACETS	0.416	0.334	0.509	0.104	0.083	0.128	SUBCLONAL	1	TRUE	2	0.605701169234526	6		351	527	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143043396	143043396	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	102	552	0	ENST00000262992.4:c.2020G>T	p.Asp674Tyr	p.D674Y	ENST00000262992	NM_001101669.1	674	Gat/Tat	19/24	0.603084230569902	2	FACETS	0.925	0.853	0.997	0.925	0.853	0.997	CLONAL	2	TRUE	0	0.605701169234526	2		552	182	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910582	29910597	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGGGAGCCCCGCTT	GCGGGGAGCCCCGCTT	-	novel	NA	P-0018184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	199	371	0	ENST00000376809.5:c.122_137del	p.Arg41ProfsTer31	p.R41Pfs*31	ENST00000376809	NM_002116.7	41	cGCGGGGAGCCCCGCTTc/cc	2/8	0.605701169234526	3	FACETS	0.927	0.879	0.972	1	0.993	1	CLONAL	3	TRUE	1	0.605701169234526	3		371	308	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509141	106509141	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	517	699	0	ENST00000359195.3:c.1135C>A	p.Leu379Ile	p.L379I	ENST00000359195	NM_002649.2	379	Ctc/Atc	2/11	0.605701169234526	5	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	2	0.605701169234526	5		699	943	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128230361	128230361	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	87	754	0	ENST00000265960.3:c.1235A>G	p.Asp412Gly	p.D412G	ENST00000265960	NM_001006617.1	412	gAc/gGc	10/12	0.59400320453482	2	FACETS	0.59	0.524	0.66	0.295	0.262	0.33	SUBCLONAL	1	TRUE	0	0.605701169234526	2		754	487	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003778	45003790	+	stop_gained,protein_altering_variant	Nonsense_Mutation	INS	CTACTCTCTCTTT	CTACTCTCTCTTT	TGGCCTTAGCTTAGCTTAG	novel	NA	P-0018184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	26	427	0	ENST00000558401.1:c.34_46delinsTGGCCTTAGCTTAGCTTAG	p.Leu12_Ser16delinsTrpProTer	p.L12_S16delinsWP*	ENST00000558401	NM_004048.2	12	CTACTCTCTCTTTct/TGGCCTTAGCTTAGCTTAGct	1/4	NA	2	FACETS	0.228	0.18	0.283			1	INDETERMINATE	1	TRUE	NA	0.605701169234526	2		427	376	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	39	382	1	ENST00000257430.4:c.3919dup	p.Ile1307AsnfsTer8	p.I1307Nfs*8	ENST00000257430	NM_000038.5	1306	gaa/gAaa	16/16	0.251210604052222	3	FACETS	1	0.869	1	0.526	0.437	0.625	CLONAL	1	TRUE	1	0.251210604052222	3		383	332	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66523994	66523994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	31	315	0	ENST00000358598.2:c.722G>A	p.Arg241Lys	p.R241K	ENST00000358598	NM_212471.2	241	aGa/aAa	8/11	0.226559578638054	4	FACETS	0.962	0.78	1	0.481	0.39	0.584	CLONAL	1	TRUE	2	0.251210604052222	4		315	321	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16235910	16235910	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	85	758	0	ENST00000375759.3:c.976C>G	p.Leu326Val	p.L326V	ENST00000375759	NM_015001.2	326	Ctg/Gtg	4/15	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.251210604052222	2		758	610	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195575	102195575	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	95	795	0	ENST00000263464.3:c.335C>G	p.Thr112Ser	p.T112S	ENST00000263464	NM_001165.4	112	aCt/aGt	2/9	0.251210604052222	3	FACETS	0.969	0.861	1	0.484	0.43	0.542	CLONAL	1	TRUE	1	0.251210604052222	3		795	879	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112342	115112342	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	27	334	0	ENST00000257566.3:c.1398G>T	p.Lys466Asn	p.K466N	ENST00000257566	NM_016569.3	466	aaG/aaT	7/8	0.251210604052222	3	FACETS	0.773	0.616	0.952	0.387	0.308	0.476	CLONAL	1	TRUE	1	0.251210604052222	3		334	313	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435424	110435424	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	86	749	1	ENST00000375856.3:c.2977G>T	p.Ala993Ser	p.A993S	ENST00000375856	NM_003749.2	993	Gcc/Tcc	1/2	0.251210604052222	6	FACETS	1	0.894	1	0.338	0.298	0.381	CLONAL	1	TRUE	3	0.251210604052222	6		750	1014	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579698	7579698	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0018214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	155	718	0	ENST00000269305.4:c.96+2T>G		p.X32_splice	ENST00000269305	NM_001126112.2	32			0.251210604052222	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.251210604052222	2		718	553	SUCCESS
APC	324	MSKCC	GRCh37	5	112157672	112157673	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0018214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	87	525	0	ENST00000257430.4:c.1393_1394insAG	p.Ala465GlufsTer3	p.A465Efs*3	ENST00000257430	NM_000038.5	464	-/GA	11/16	0.251210604052222	3	FACETS	0.958	0.853	1	0.958	0.853	1	CLONAL	2	TRUE	1	0.251210604052222	3		525	407	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152357831	152357831	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	62	735	1	ENST00000359321.1:c.76G>T	p.Glu26Ter	p.E26*	ENST00000359321	NM_005431.1	26	Gaa/Taa	2/3	0.251210604052222	3	FACETS	0.842	0.727	0.967	0.421	0.363	0.484	CLONAL	1	TRUE	1	0.251210604052222	3		736	660	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349189	70349189	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	61	643	0	ENST00000374080.3:c.3601T>G	p.Ser1201Ala	p.S1201A	ENST00000374080		1201	Tcc/Gcc	26/45	0.251210604052222	3	FACETS	0.848	0.731	0.975	0.424	0.365	0.488	CLONAL	1	TRUE	1	0.251210604052222	3		643	645	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888817	76888817	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	88	816	0	ENST00000373344.5:c.5012G>C	p.Arg1671Thr	p.R1671T	ENST00000373344	NM_000489.3	1671	aGg/aCg	19/35	0.251210604052222	3	FACETS	1	0.94	1	0.548	0.486	0.616	CLONAL	1	TRUE	1	0.251210604052222	3		816	719	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0018237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	215	813	1	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.300841940704465	2	FACETS	1	0.962	1	1	0.992	1	CLONAL	3	TRUE	0	0.21	2		814	655	SUCCESS
APC	324	MSKCC	GRCh37	5	112170851	112170851	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	69	756	0	ENST00000257430.4:c.1947del	p.Asn649LysfsTer8	p.N649Kfs*8	ENST00000257430	NM_000038.5	649	aaT/aa	15/16	0.300841940704465	1	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	0	0.21	1		756	555	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542118	187542118	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	39	510	0	ENST00000441802.2:c.5622C>A	p.Asp1874Glu	p.D1874E	ENST00000441802	NM_005245.3	1874	gaC/gaA	10/27	1	2	FACETS	0.434	0.36	0.517	0.434	0.36	0.517	SUBCLONAL	1	TRUE	1	0.403037818247106	2		510	446	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	85	330	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	FALSE	1	0.248180160419058	2		330	580	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	95	337	0	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	FALSE	1	0.248180160419058	2		337	736	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	83	717	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.248180160419058	2		721	569	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	85	1012	5	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.937	0.828	1	0.937	0.828	1	CLONAL	1	FALSE	1	0.248180160419058	2		1017	731	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67646013	67646014	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs1470210640	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	57	194	2	ENST00000264010.4:c.950_951del	p.Thr317ArgfsTer91	p.T317Rfs*91	ENST00000264010	NM_006565.3	314	aAC/a	4/12	1	2	FACETS	0.792	0.679	0.915	0.792	0.679	0.915	CLONAL	1	FALSE	1	0.248180160419058	2		196	580	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	54	603	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.908	0.777	1	0.908	0.777	1	CLONAL	1	FALSE	1	0.248180160419058	2		604	479	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165283	47165283	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	41	222	0	ENST00000409792.3:c.843del	p.Glu282LysfsTer19	p.E282Kfs*19	ENST00000409792	NM_014159.6	281	aaA/aa	3/21	0.248180160419058	2	FACETS	0.872	0.728	1	0.436	0.364	0.516	CLONAL	1	FALSE	0	0.248180160419058	2		222	379	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	20	148	1	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.767	0.589	0.974	0.767	0.589	0.974	CLONAL	1	FALSE	1	0.248180160419058	2		149	210	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	23	53	1	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	1	FACETS	0.752	0.596	0.924	1	0.929	1	CLONAL	2	FALSE	0	0.248180160419058	1		54	108	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	106	345	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.895	0.807	0.988	1	0.987	1	CLONAL	2	FALSE	1	0.248180160419058	2		345	477	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742463	17742463	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	75	317	0	ENST00000250003.3:c.650del	p.Pro217ArgfsTer33	p.P217Rfs*33	ENST00000250003	NM_002478.4	215	ggC/gg	2/3	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	FALSE	1	0.248180160419058	2		317	544	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	94	407	2	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	1	0.248180160419058	2		409	689	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	38	196	0	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	0.248180160419058	2	FACETS	0.779	0.645	0.929	0.39	0.322	0.465	CLONAL	1	FALSE	0	0.248180160419058	2		196	393	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	23	267	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	1	2	FACETS	0.39	0.303	0.491	0.39	0.303	0.491	SUBCLONAL	1	FALSE	1	0.248180160419058	2		267	475	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744385	41744385	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	74	302	0	ENST00000301178.4:c.1010del	p.Pro337LeufsTer29	p.P337Lfs*29	ENST00000301178	NM_021913.4	335	ggC/gg	8/20	1	2	FACETS	0.976	0.855	1	0.976	0.855	1	CLONAL	1	FALSE	1	0.248180160419058	2		302	611	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564530	86564530	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	46	207	0	ENST00000274376.6:c.266del	p.Gly89GlufsTer7	p.G89Efs*7	ENST00000274376	NM_002890.2	88	Ggg/gg	1/25	1	2	FACETS	0.963	0.813	1	0.963	0.813	1	CLONAL	1	FALSE	1	0.248180160419058	2		207	385	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795269	42795269	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs34000070	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	82	267	2	ENST00000575354.2:c.2353del	p.Ala785ProfsTer139	p.A785Pfs*139	ENST00000575354	NM_015125.3	783	caG/ca	10/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.248180160419058	2		269	549	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645893	67645893	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	86	313	1	ENST00000264010.4:c.821C>T	p.Thr274Met	p.T274M	ENST00000264010	NM_006565.3	274	aCg/aTg	4/12	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	FALSE	1	0.248180160419058	2		314	686	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737579	145737579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199658221	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	86	386	2	ENST00000428558.2:c.3184C>T	p.Arg1062Trp	p.R1062W	ENST00000428558	NM_004260.3	1062	Cgg/Tgg	19/22	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	FALSE	1	0.248180160419058	2		388	690	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17125941	17125941	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367843558	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	81	343	0	ENST00000285071.4:c.653G>A	p.Arg218His	p.R218H	ENST00000285071	NM_144997.5	218	cGt/cAt	7/14	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	FALSE	1	0.248180160419058	2		343	626	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521525	46521525	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	91	361	0	ENST00000262741.5:c.883del	p.Met295Ter	p.M295*	ENST00000262741	NM_003629.3	295	Atg/tg	7/10	1	2	FACETS	0.92	0.816	1	0.92	0.816	1	CLONAL	1	FALSE	1	0.248180160419058	2		361	797	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020818	112020819	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	50	270	0	ENST00000368678.4:c.752dup	p.Gln252ThrfsTer7	p.Q252Tfs*7	ENST00000368678		251	cca/ccCa	8/13	1	2	FACETS	0.564	0.478	0.66	0.564	0.478	0.66	SUBCLONAL	1	FALSE	1	0.248180160419058	2		270	714	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546324	46546324	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	48	223	0	ENST00000262741.5:c.205del	p.Asp69IlefsTer7	p.D69Ifs*7	ENST00000262741	NM_003629.3	69	Gat/at	2/10	1	2	FACETS	0.798	0.675	0.933	0.798	0.675	0.933	CLONAL	1	FALSE	1	0.248180160419058	2		223	485	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256321	16256321	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	58	391	0	ENST00000375759.3:c.3591del	p.Asp1198MetfsTer2	p.D1198Mfs*2	ENST00000375759	NM_015001.2	1196	Aaa/aa	11/15	1	2	FACETS	0.665	0.57	0.768	0.665	0.57	0.768	SUBCLONAL	1	FALSE	1	0.248180160419058	2		391	703	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11270924	11270924	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	69	292	2	ENST00000361445.4:c.3601C>T	p.Arg1201Ter	p.R1201*	ENST00000361445	NM_004958.3	1201	Cga/Tga	24/58	1	2	FACETS	0.841	0.732	0.959	0.841	0.732	0.959	CLONAL	1	FALSE	1	0.248180160419058	2		294	661	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228997	36228997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	99	313	1	ENST00000222270.7:c.7777C>T	p.Arg2593Cys	p.R2593C	ENST00000222270	NM_014727.1	2593	Cgc/Tgc	36/37	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	FALSE	1	0.248180160419058	2		314	789	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506416	120506416	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	80	291	0	ENST00000256646.2:c.1696T>A	p.Leu566Met	p.L566M	ENST00000256646	NM_024408.3	566	Ttg/Atg	11/34	1	2	FACETS	0.922	0.812	1	0.922	0.812	1	CLONAL	1	FALSE	1	0.248180160419058	2		291	699	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746113	162746113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1364325806	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	86	172	0	ENST00000367921.3:c.2236C>T	p.Arg746Trp	p.R746W	ENST00000367921	NM_006182.2	746	Cgg/Tgg	16/18	1	2	FACETS	0.763	0.678	0.854	1	0.98	1	SUBCLONAL	2	FALSE	1	0.248180160419058	2		172	454	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572519	64572519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555164143	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	94	341	2	ENST00000312049.6:c.1337G>A	p.Arg446His	p.R446H	ENST00000312049	NM_130799.2	446	cGt/cAt	9/10	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	FALSE	1	0.248180160419058	2		343	730	SUCCESS
ATM	472	MSKCC	GRCh37	11	108126987	108126987	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	78	336	0	ENST00000278616.4:c.2170G>T	p.Gly724Cys	p.G724C	ENST00000278616	NM_000051.3	724	Ggt/Tgt	14/63	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	FALSE	1	0.248180160419058	2		336	592	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151890	108151890	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	36	189	0	ENST00000278616.4:c.3575del	p.Lys1192ArgfsTer3	p.K1192Rfs*3	ENST00000278616	NM_000051.3	1191	Aaa/aa	24/63	1	2	FACETS	0.866	0.714	1	0.866	0.714	1	CLONAL	1	FALSE	1	0.248180160419058	2		189	335	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344954	118344955	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	43	205	0	ENST00000534358.1:c.3086dup	p.Ala1030GlyfsTer9	p.A1030Gfs*9	ENST00000534358	NM_005933.3	1027	cta/ctAa	3/36	1	2	FACETS	0.779	0.652	0.919	0.779	0.652	0.919	CLONAL	1	FALSE	1	0.248180160419058	2		205	445	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169151	119169151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	45	297	0	ENST00000264033.4:c.2335C>T	p.Pro779Ser	p.P779S	ENST00000264033	NM_005188.3	779	Cca/Tca	15/16	1	2	FACETS	0.579	0.486	0.683	0.579	0.486	0.683	SUBCLONAL	1	FALSE	1	0.248180160419058	2		297	626	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435048	49435048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369501280	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	50	247	0	ENST00000301067.7:c.6505G>A	p.Ala2169Thr	p.A2169T	ENST00000301067	NM_003482.3	2169	Gcc/Acc	31/54	1	2	FACETS	0.787	0.668	0.918	0.787	0.668	0.918	CLONAL	1	FALSE	1	0.248180160419058	2		247	512	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906576	32906576	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	68	277	1	ENST00000380152.3:c.961C>A	p.Gln321Lys	p.Q321K	ENST00000380152		321	Caa/Aaa	10/27	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	1	0.248180160419058	2		278	497	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914509	32914509	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	37	345	0	ENST00000380152.3:c.6017G>A	p.Ser2006Asn	p.S2006N	ENST00000380152		2006	aGt/aAt	11/27	1	2	FACETS	0.523	0.43	0.627	0.523	0.43	0.627	SUBCLONAL	1	FALSE	1	0.248180160419058	2		345	570	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679181	88679182	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	91	312	0	ENST00000360948.2:c.855dup	p.Ala286CysfsTer29	p.A286Cfs*29	ENST00000360948	NM_001012338.2	285	-/T	8/19	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	FALSE	1	0.248180160419058	2		312	718	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835765	68835766	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs878854690	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	111	324	0	ENST00000261769.5:c.360dup	p.His121AlafsTer47	p.H121Afs*47	ENST00000261769	NM_004360.3	119	gtg/gtGg	3/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	1	0.248180160419058	2		324	783	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805059	89805059	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs767234774	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	66	317	0	ENST00000389301.3:c.4318C>T	p.Gln1440Ter	p.Q1440*	ENST00000389301	NM_000135.2	1440	Cag/Tag	43/43	1	2	FACETS	0.834	0.723	0.953	0.834	0.723	0.953	CLONAL	1	FALSE	1	0.248180160419058	2		317	638	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249172	10249172	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	84	400	1	ENST00000340748.4:c.4010G>T	p.Arg1337Leu	p.R1337L	ENST00000340748		1337	cGg/cTg	34/40	1	2	FACETS	0.927	0.819	1	0.927	0.819	1	CLONAL	1	FALSE	1	0.248180160419058	2		401	730	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290288	15290288	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	89	403	0	ENST00000263388.2:c.3347G>A	p.Gly1116Asp	p.G1116D	ENST00000263388	NM_000435.2	1116	gGt/gAt	21/33	1	2	FACETS	0.835	0.739	0.938	0.835	0.739	0.938	CLONAL	1	FALSE	1	0.248180160419058	2		403	859	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279956	18279956	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1390411006	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	123	403	0	ENST00000222254.8:c.2039C>T	p.Ala680Val	p.A680V	ENST00000222254	NM_005027.3	680	gCg/gTg	16/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.248180160419058	2		403	862	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50916690	50916690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	88	315	0	ENST00000440232.2:c.2162C>T	p.Thr721Met	p.T721M	ENST00000440232	NM_002691.3	721	aCg/aTg	18/27	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	1	0.248180160419058	2		315	649	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46583861	46583861	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	74	315	0	ENST00000263734.3:c.370-2A>G		p.X124_splice	ENST00000263734	NM_001430.4	124			1	2	FACETS	0.877	0.767	0.995	0.877	0.767	0.995	CLONAL	1	FALSE	1	0.248180160419058	2		315	680	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587225	212587225	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	77	249	0	ENST00000342788.4:c.776T>C	p.Val259Ala	p.V259A	ENST00000342788	NM_005235.2	259	gTt/gCt	7/28	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.248180160419058	2		249	483	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662623	227662623	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	66	256	0	ENST00000305123.5:c.832A>G	p.Asn278Asp	p.N278D	ENST00000305123	NM_005544.2	278	Aac/Gac	1/2	1	2	FACETS	0.978	0.85	1	0.978	0.85	1	CLONAL	1	FALSE	1	0.248180160419058	2		256	544	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306715	41306715	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	60	304	0	ENST00000373198.4:c.944T>C	p.Ile315Thr	p.I315T	ENST00000373198	NM_133170.3	315	aTc/aCc	7/32	1	2	FACETS	0.854	0.736	0.983	0.854	0.736	0.983	CLONAL	1	FALSE	1	0.248180160419058	2		304	566	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458344	12458344	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	93	352	0	ENST00000287820.6:c.961del	p.Val321CysfsTer15	p.V321Cfs*15	ENST00000287820	NM_015869.4	321	Gtg/tg	6/7	0.248180160419058	2	FACETS	0.999	0.888	1	0.5	0.444	0.559	CLONAL	1	FALSE	0	0.248180160419058	2		352	750	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436387	52436387	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	81	298	0	ENST00000460680.1:c.2107G>T	p.Gly703Trp	p.G703W	ENST00000460680	NM_004656.3	703	Ggg/Tgg	17/17	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	FALSE	1	0.248180160419058	2		298	650	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528554	89528554	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	45	154	0	ENST00000336596.2:c.2858del	p.Lys953ArgfsTer20	p.K953Rfs*20	ENST00000336596	NM_005233.5	952	Aaa/aa	17/17	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	FALSE	1	0.248180160419058	2		154	347	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1978338	1978338	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	93	322	0	ENST00000382891.5:c.3758T>G	p.Leu1253Arg	p.L1253R	ENST00000382891	NM_133335.3	1253	cTg/cGg	21/22	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	FALSE	1	0.248180160419058	2		322	709	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753127	57753127	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	40	201	0	ENST00000274289.3:c.889T>C	p.Tyr297His	p.Y297H	ENST00000274289	NM_006622.3	297	Tat/Cat	7/14	1	2	FACETS	0.8	0.665	0.949	0.8	0.665	0.949	CLONAL	1	FALSE	1	0.248180160419058	2		201	403	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064780	80064780	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	52	325	0	ENST00000265081.6:c.2216del	p.Asn739IlefsTer7	p.N739Ifs*7	ENST00000265081	NM_002439.4	737	ctA/ct	15/24	1	2	FACETS	0.88	0.75	1	0.88	0.75	1	CLONAL	1	FALSE	1	0.248180160419058	2		325	476	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839873	27839874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	40	262	0	ENST00000328488.2:c.220dup	p.Glu74GlyfsTer7	p.E74Gfs*7	ENST00000328488	NM_003533.2	74	gag/gGag	1/1	1	2	FACETS	0.612	0.508	0.728	0.612	0.508	0.728	SUBCLONAL	1	FALSE	1	0.248180160419058	2		262	527	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671194	30671194	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	77	335	0	ENST00000376406.3:c.5682+1del		p.X1894_splice	ENST00000376406	NM_014641.2	1894			1	2	FACETS	0.856	0.751	0.969	0.856	0.751	0.969	CLONAL	1	FALSE	1	0.248180160419058	2		335	725	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323352	31323352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1428341966	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	62	236	0	ENST00000412585.2:c.637G>A	p.Val213Met	p.V213M	ENST00000412585	NM_005514.6	213	Gtg/Atg	4/8	1	2	FACETS	0.91	0.787	1	0.91	0.787	1	CLONAL	1	FALSE	1	0.248180160419058	2		236	549	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552930	106552930	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	69	394	0	ENST00000369096.4:c.895T>C	p.Tyr299His	p.Y299H	ENST00000369096	NM_001198.3	299	Tac/Cac	5/7	1	2	FACETS	0.675	0.587	0.771	0.675	0.587	0.771	SUBCLONAL	1	FALSE	1	0.248180160419058	2		394	824	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388044	81388045	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1186073562	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	47	346	0	ENST00000222390.5:c.330dup	p.Glu111ArgfsTer5	p.E111Rfs*5	ENST00000222390	NM_000601.4	110	-/A	3/18	1	2	FACETS	0.716	0.604	0.84	0.716	0.604	0.84	SUBCLONAL	1	FALSE	1	0.248180160419058	2		346	529	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185545	27185545	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1564083506	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	98	434	0	ENST00000380036.4:c.1250del	p.Pro417LeufsTer10	p.P417Lfs*10	ENST00000380036	NM_000459.3	415	ctC/ct	9/23	1	2	FACETS	0.935	0.833	1	0.935	0.833	1	CLONAL	1	FALSE	1	0.248180160419058	2		434	845	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202471	123202471	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	56	149	0	ENST00000218089.9:c.2323T>C	p.Tyr775His	p.Y775H	ENST00000218089	NM_001042749.1	775	Tac/Cac	24/35	1	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	0	0.248180160419058	1		149	277	SUCCESS
AR	367	MSKCC	GRCh37	X	66943552	66943552	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137852578	NA	P-0018605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	386	211	0	ENST00000374690.3:c.2632A>G	p.Thr878Ala	p.T878A	ENST00000374690	NM_000044.3	878	Act/Gct	8/8	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.788932874116122	1		211	484	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425518	49425519	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	375	478	0	ENST00000301067.7:c.12969dup	p.Pro4324ThrfsTer10	p.P4324Tfs*10	ENST00000301067	NM_003482.3	4323	-/A	39/54	1	2	FACETS	0.927	0.882	0.972	0.927	0.882	0.972	CLONAL	1	TRUE	1	0.788932874116122	2		478	1026	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537960	212537961	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	360	466	0	ENST00000342788.4:c.1644dup	p.Gly549TrpfsTer8	p.G549Wfs*8	ENST00000342788	NM_005235.2	548	-/T	14/28	0.788932874116122	3	FACETS	0.886	0.839	0.935	0.295	0.279	0.312	CLONAL	1	TRUE	0	0.788932874116122	3		466	1436	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711877	89711892	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AGTAACTATTCCCAGT	AGTAACTATTCCCAGT	-	novel	NA	P-0018757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	84	398	0	ENST00000371953.3:c.495_510del	p.Val166ArgfsTer12	p.V166Rfs*12	ENST00000371953	NM_000314.4	165	ggAGTAACTATTCCCAGT/gg	6/9	0.658484452693801	1	FACETS	0.97	0.885	1	0.97	0.885	1	CLONAL	1	TRUE	0	0.716801967341413	1		398	155	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579310	7579310	+	splice_donor_variant	Splice_Site	SNP	A	A	T	rs1555526469	NA	P-0018757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	109	460	0	ENST00000269305.4:c.375+2T>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.658484452693801	1	FACETS	0.929	0.856	1	0.929	0.856	1	CLONAL	1	TRUE	0	0.716801967341413	1		460	210	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137644	202137644	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	73	446	0	ENST00000358485.4:c.751A>T	p.Ser251Cys	p.S251C	ENST00000358485	NM_001080125.1	251	Agt/Tgt	5/9	1	2	FACETS	0.828	0.734	0.926	0.828	0.734	0.926	CLONAL	1	TRUE	1	0.716801967341413	2		446	246	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0018759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	883	603	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.71611020992502	4	FACETS	0.971	0.946	0.995	0.971	0.946	0.995	CLONAL	3	TRUE	1	0.71611020992502	4		603	1453	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0018759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	177	311	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.936	0.869	1	0.936	0.869	1	CLONAL	1	TRUE	1	0.71611020992502	2		312	528	SUCCESS
AR	367	MSKCC	GRCh37	X	66931477	66931477	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	659	327	0	ENST00000374690.3:c.2119G>A	p.Glu707Lys	p.E707K	ENST00000374690	NM_000044.3	707	Gaa/Aaa	4/8	0.634663880698848	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.71611020992502	2		327	849	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074228	8074228	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	256	498	0	ENST00000377482.5:c.431C>T	p.Pro144Leu	p.P144L	ENST00000377482	NM_018948.3	144	cCt/cTt	4/4	1	2	FACETS	0.969	0.911	1	0.969	0.911	1	CLONAL	1	TRUE	1	0.71611020992502	2		498	738	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201519	133201519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	753	705	0	ENST00000320574.5:c.6719G>A	p.Gly2240Glu	p.G2240E	ENST00000320574	NM_006231.2	2240	gGa/gAa	48/49	0.574196773760743	4	FACETS	1	0.976	1			1	CLONAL	2	TRUE	NA	0.71611020992502	4		705	1784	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911010	32911010	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	588	667	0	ENST00000380152.3:c.2518A>G	p.Met840Val	p.M840V	ENST00000380152		840	Atg/Gtg	11/27	0.610982432626257	4	FACETS	0.946	0.91	0.982	0.946	0.91	0.982	CLONAL	2	TRUE	2	0.71611020992502	4		667	1490	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527676	103527676	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756730021	NA	P-0018759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	381	391	0	ENST00000355739.4:c.2984C>T	p.Ser995Phe	p.S995F	ENST00000355739	NM_000123.3	995	tCc/tTc	15/15	0.610982432626257	4	FACETS	0.898	0.855	0.941	0.898	0.855	0.941	CLONAL	2	TRUE	2	0.71611020992502	4		391	1017	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43738713	43738713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	644	581	1	ENST00000382044.4:c.2912C>T	p.Pro971Leu	p.P971L	ENST00000382044	NM_001141980.1	971	cCc/cTc	14/28	0.71611020992502	3	FACETS	0.934	0.903	0.966	0.934	0.903	0.966	CLONAL	2	TRUE	1	0.71611020992502	3		582	1307	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490346	29490346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	673	588	0	ENST00000356175.3:c.431C>T	p.Ser144Phe	p.S144F	ENST00000356175	NM_000267.3	144	tCt/tTt	4/57	0.71611020992502	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.71611020992502	3		588	1269	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972854	25972854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1005506744	NA	P-0018759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	260	412	0	ENST00000435504.4:c.1571C>T	p.Ser524Leu	p.S524L	ENST00000435504		524	tCg/tTg	12/13	0.71611020992502	3	FACETS	0.973	0.912	1	0.486	0.456	0.518	CLONAL	1	TRUE	1	0.71611020992502	3		412	1014	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350130	81350130	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	281	580	0	ENST00000222390.5:c.1202G>A	p.Gly401Asp	p.G401D	ENST00000222390	NM_000601.4	401	gGc/gAc	10/18	0.71611020992502	3	FACETS	0.878	0.824	0.933	0.439	0.412	0.467	CLONAL	1	TRUE	1	0.71611020992502	3		580	1214	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68993041	68993041	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	301	551	0	ENST00000288368.4:c.1846A>T	p.Ile616Leu	p.I616L	ENST00000288368	NM_024870.2	616	Ata/Tta	17/40	0.537789794898801	4	FACETS	0.987	0.927	1	0.329	0.309	0.35	CLONAL	1	TRUE	1	0.71611020992502	4		551	1462	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	117	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.781	0.703	0.864	0.781	0.703	0.864	SUBCLONAL	1	TRUE	1	0.275909835609798	2		473	1086	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226565007	226565013	+	splice_region_variant,intron_variant	Splice_Region	DEL	GCAGTGG	GCAGTGG	TT	novel	NA	P-0018762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	92	357	1	ENST00000366794.5:c.1746-9_1746-3delinsAA		p.X582_splice	ENST00000366794	NM_001618.3	582			0.275909835609798	3	FACETS	1	0.939	1	0.542	0.482	0.607	CLONAL	1	TRUE	1	0.275909835609798	3		358	700	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1255456	1255456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374968697	NA	P-0018762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	167	612	2	ENST00000310581.5:c.3103G>A	p.Val1035Ile	p.V1035I	ENST00000310581	NM_198253.2	1035	Gtc/Atc	14/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.275909835609798	2		614	1117	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	92	330	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.29	2		330	598	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	63	425	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.29	2		426	396	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	189	453	4	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.754	0.698	0.813	1	0.99	1	SUBCLONAL	2	TRUE	1	0.29	2		457	864	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	177	409	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	1	0.974	1	1	0.993	1	CLONAL	2	TRUE	1	0.29	2		409	550	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	96	704	0	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	0.29	2		704	605	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	67	500	2	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.825	0.724	0.932	1	0.978	1	CLONAL	2	TRUE	1	0.29	2		502	280	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435160	56435161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755128667	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1460	91	377	0	ENST00000407977.2:c.1976dup	p.Pro660SerfsTer87	p.P660Sfs*87	ENST00000407977		659	ggt/ggGt	9/10	1	2	FACETS	0.405	0.357	0.455	0.405	0.357	0.455	SUBCLONAL	1	TRUE	1	0.29	2		377	1551	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779218	3779218	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	72	161	0	ENST00000262367.5:c.5830G>C	p.Ala1944Pro	p.A1944P	ENST00000262367	NM_004380.2	1944	Gcc/Ccc	31/31	1	2	FACETS	0.691	0.603	0.786	0.691	0.603	0.786	SUBCLONAL	1	TRUE	1	0.29	2		161	719	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	84	330	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	NA	2	FACETS	1	0.956	1			1	INDETERMINATE	1	TRUE	NA	0.29	2		330	498	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748914	41748914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751855310	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1311	229	404	0	ENST00000301178.4:c.1439G>A	p.Arg480His	p.R480H	ENST00000301178	NM_021913.4	480	cGt/cAt	11/20	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.29	2		404	1540	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692851	89692851	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121909230	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	21	129	0	ENST00000371953.3:c.335T>C	p.Leu112Pro	p.L112P	ENST00000371953	NM_000314.4	112	cTa/cCa	5/9	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.29	2		129	105	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435128	110435129	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs772322568	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2257	379	675	3	ENST00000375856.3:c.3272dup	p.Lys1092GlufsTer233	p.K1092Efs*233	ENST00000375856	NM_003749.2	1091	ccg/ccCg	1/2	1	2	FACETS	0.992	0.936	1	0.992	0.936	1	CLONAL	1	TRUE	1	0.29	2		678	2636	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743896	41743896	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2391	451	702	1	ENST00000301178.4:c.836del	p.Pro279GlnfsTer18	p.P279Qfs*18	ENST00000301178	NM_021913.4	277	gaC/ga	7/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.29	2		703	2842	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233090	69233090	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746910913	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	54	312	0	ENST00000462284.1:c.961del	p.Leu321PhefsTer52	p.L321Ffs*52	ENST00000462284	NM_002392.5	319	Ccc/cc	11/11	1	2	FACETS	0.885	0.757	1	0.885	0.757	1	CLONAL	1	TRUE	1	0.29	2		312	421	SUCCESS
APC	324	MSKCC	GRCh37	5	112177864	112177864	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs775076289	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	72	513	0	ENST00000257430.4:c.6579del	p.Val2194PhefsTer5	p.V2194Ffs*5	ENST00000257430	NM_000038.5	2191	ggA/gg	16/16	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.29	2		513	453	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845622	68845622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1576	90	563	0	ENST00000261769.5:c.868G>A	p.Asp290Asn	p.D290N	ENST00000261769	NM_004360.3	290	Gac/Aac	7/16	1	2	FACETS	0.373	0.329	0.42	0.373	0.329	0.42	SUBCLONAL	1	TRUE	1	0.29	2		563	1666	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606313	93606313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1235073402	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1410	270	502	0	ENST00000375746.1:c.133C>T	p.Arg45Cys	p.R45C	ENST00000375746	NM_001174167.1	45	Cgc/Tgc	2/14	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.29	2		502	1680	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825519	50825519	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	29	377	0	ENST00000398568.2:c.2156del	p.Asn719MetfsTer13	p.N719Mfs*13	ENST00000398568	NM_001042412.1	717	gAa/ga	14/18	1	2	FACETS	0.431	0.345	0.529	0.431	0.345	0.529	SUBCLONAL	1	TRUE	1	0.29	2		377	464	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309036	137309036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779808577	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2115	404	642	3	ENST00000481739.1:c.643C>T	p.Arg215Trp	p.R215W	ENST00000481739	NM_002957.4	215	Cgg/Tgg	5/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.29	2		645	2519	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223175	36223175	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3053	593	852	0	ENST00000222270.7:c.5730del	p.Arg1911AspfsTer23	p.R1911Dfs*23	ENST00000222270	NM_014727.1	1909	Ccc/cc	28/37	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.29	2		852	3646	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330468	65330468	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	50	320	0	ENST00000342505.4:c.1176+2T>C		p.X392_splice	ENST00000342505	NM_002227.2	392			1	2	FACETS	0.74	0.628	0.862	0.74	0.628	0.862	SUBCLONAL	1	TRUE	1	0.29	2		320	466	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119483	193119483	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	32	386	1	ENST00000367435.3:c.878A>G	p.Tyr293Cys	p.Y293C	ENST00000367435	NM_024529.4	293	tAc/tGc	9/17	1	2	FACETS	0.397	0.321	0.483	0.397	0.321	0.483	SUBCLONAL	1	TRUE	1	0.29	2		387	556	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100354	8100355	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2285	529	676	0	ENST00000346208.3:c.333dup	p.Trp112LeufsTer191	p.W112Lfs*191	ENST00000346208		110	tcc/tCcc	3/6	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.29	2		676	2814	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948483	71948484	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2500	536	785	0	ENST00000298229.2:c.3201dup	p.Ser1068GlnfsTer17	p.S1068Qfs*17	ENST00000298229	NM_001567.3	1065	-/C	26/28	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.29	2		785	3036	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418641	49418641	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1500	303	532	0	ENST00000301067.7:c.15873G>T	p.Glu5291Asp	p.E5291D	ENST00000301067	NM_003482.3	5291	gaG/gaT	49/54	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.29	2		532	1803	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438184	49438184	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1723	358	624	1	ENST00000301067.7:c.5083+2T>C		p.X1695_splice	ENST00000301067	NM_003482.3	1695			1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.29	2		625	2081	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445094	49445095	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1407	239	466	0	ENST00000301067.7:c.2371dup	p.Gln791ProfsTer3	p.Q791Pfs*3	ENST00000301067	NM_003482.3	791	cag/cCag	10/54	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.29	2		466	1646	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857691	9857691	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	47	233	0	ENST00000330684.3:c.3710A>G	p.Asp1237Gly	p.D1237G	ENST00000330684	NM_001134407.1	1237	gAt/gGt	13/13	1	2	FACETS	0.481	0.405	0.565	0.481	0.405	0.565	SUBCLONAL	1	TRUE	1	0.29	2		233	674	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56878487	56878487	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752264053	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	162	417	2	ENST00000308159.5:c.2426C>T	p.Ala809Val	p.A809V	ENST00000308159	NM_014669.4	809	gCg/gTg	22/22	1	2	FACETS	0.972	0.89	1	0.972	0.89	1	CLONAL	1	TRUE	1	0.29	2		419	1149	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341589	89341589	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	333	309	2	ENST00000301030.4:c.7481del	p.Pro2494LeufsTer8	p.P2494Lfs*8	ENST00000301030	NM_001256183.1	2494	cCt/ct	10/13	1	2	FACETS	0.821	0.775	0.868	1	0.995	1	CLONAL	2	TRUE	1	0.29	2		311	1399	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357063	89357063	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1344	298	334	0	ENST00000301030.4:c.571G>A	p.Gly191Arg	p.G191R	ENST00000301030	NM_001256183.1	191	Ggg/Agg	6/13	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.29	2		334	1642	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845228	89845228	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	233	495	2	ENST00000389301.3:c.1807T>C	p.Phe603Leu	p.F603L	ENST00000389301	NM_000135.2	603	Ttt/Ctt	20/43	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.29	2		497	1349	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029445	16029445	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	82	511	0	ENST00000268712.3:c.1585del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	529	Gaa/aa	15/46	1	2	FACETS	0.826	0.728	0.93	0.826	0.728	0.93	CLONAL	1	TRUE	1	0.29	2		511	685	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667665	29667665	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1135402898	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	74	306	0	ENST00000356175.3:c.6999+2T>C		p.X2333_splice	ENST00000356175	NM_000267.3	2333			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.29	2		306	392	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533643	63533643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754079144	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1683	107	492	1	ENST00000307078.5:c.1511G>A	p.Gly504Asp	p.G504D	ENST00000307078	NM_004655.3	504	gGc/gAc	6/11	1	2	FACETS	0.412	0.368	0.46	0.412	0.368	0.46	SUBCLONAL	1	TRUE	1	0.29	2		493	1790	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212170	5212170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1242977508	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1524	372	589	2	ENST00000357368.4:c.4861G>A	p.Val1621Met	p.V1621M	ENST00000357368	NM_002850.3	1621	Gtg/Atg	32/38	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.29	2		591	1896	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265265	10265265	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	106	225	0	ENST00000340748.4:c.1781A>C	p.Gln594Pro	p.Q594P	ENST00000340748		594	cAg/cCg	20/40	1	2	FACETS	0.769	0.688	0.855	0.769	0.688	0.855	SUBCLONAL	1	TRUE	1	0.29	2		225	951	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285020	15285020	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1399	285	474	0	ENST00000263388.2:c.4595T>C	p.Leu1532Pro	p.L1532P	ENST00000263388	NM_000435.2	1532	cTg/cCg	25/33	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.29	2		474	1684	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905543	50905543	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373001984	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2127	277	1017	1	ENST00000440232.2:c.671G>A	p.Arg224His	p.R224H	ENST00000440232	NM_002691.3	224	cGc/cAc	6/27	1	2	FACETS	0.795	0.742	0.849	0.795	0.742	0.849	SUBCLONAL	1	TRUE	1	0.29	2		1018	2404	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905579	50905579	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2035	454	719	0	ENST00000440232.2:c.707T>C	p.Leu236Pro	p.L236P	ENST00000440232	NM_002691.3	236	cTg/cCg	6/27	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.29	2		719	2489	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910274	50910274	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555791351	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1893	131	502	0	ENST00000440232.2:c.1529T>C	p.Val510Ala	p.V510A	ENST00000440232	NM_002691.3	510	gTg/gCg	13/27	1	2	FACETS	0.446	0.403	0.493	0.446	0.403	0.493	SUBCLONAL	1	TRUE	1	0.29	2		502	2024	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52728991	52728991	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1246	230	491	0	ENST00000322088.6:c.1683G>T	p.Lys561Asn	p.K561N	ENST00000322088	NM_014225.5	561	aaG/aaT	14/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.29	2		491	1476	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033604	48033604	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	34	392	0	ENST00000234420.5:c.3815A>G	p.Glu1272Gly	p.E1272G	ENST00000234420	NM_000179.2	1272	gAa/gGa	9/10	1	2	FACETS	0.756	0.62	0.909	0.756	0.62	0.909	CLONAL	1	TRUE	1	0.29	2		392	310	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268473	198268473	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	45	393	0	ENST00000335508.6:c.1555A>T	p.Ile519Phe	p.I519F	ENST00000335508	NM_012433.2	519	Att/Ttt	12/25	1	2	FACETS	0.595	0.499	0.7	0.595	0.499	0.7	SUBCLONAL	1	TRUE	1	0.29	2		393	522	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136316	202136316	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	96	447	0	ENST00000358485.4:c.560T>C	p.Ile187Thr	p.I187T	ENST00000358485	NM_001080125.1	187	aTc/aCc	3/9	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.29	2		447	574	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248366	212248366	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	49	185	0	ENST00000342788.4:c.3901T>C	p.Tyr1301His	p.Y1301H	ENST00000342788	NM_005235.2	1301	Tac/Cac	28/28	1	2	FACETS	0.801	0.679	0.934	0.801	0.679	0.934	CLONAL	1	TRUE	1	0.29	2		185	422	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627977	37627977	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1286584041	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1881	355	587	4	ENST00000249071.6:c.283G>A	p.Ala95Thr	p.A95T	ENST00000249071	NM_002872.4	95	Gcc/Acc	4/7	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.29	2		591	2236	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096195	71096195	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1299483404	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	129	246	0	ENST00000318789.4:c.562A>G	p.Met188Val	p.M188V	ENST00000318789	NM_032682.5	188	Atg/Gtg	10/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.29	2		246	741	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202794	128202794	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1726	198	465	0	ENST00000341105.2:c.926A>G	p.Asp309Gly	p.D309G	ENST00000341105	NM_032638.4	309	gAc/gGc	4/6	1	2	FACETS	0.71	0.654	0.768	0.71	0.654	0.768	SUBCLONAL	1	TRUE	1	0.29	2		465	1924	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204987	128204987	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	136	329	0	ENST00000341105.2:c.454A>G	p.Ser152Gly	p.S152G	ENST00000341105	NM_032638.4	152	Agc/Ggc	3/6	1	2	FACETS	0.788	0.714	0.865	0.788	0.714	0.865	SUBCLONAL	1	TRUE	1	0.29	2		329	1191	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456589	138456589	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	43	546	0	ENST00000289153.2:c.761T>C	p.Val254Ala	p.V254A	ENST00000289153	NM_006219.2	254	gTa/gCa	4/22	1	2	FACETS	0.489	0.409	0.579	0.489	0.409	0.579	SUBCLONAL	1	TRUE	1	0.29	2		546	606	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807799	1807800	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1459	354	473	0	ENST00000260795.2:c.1861dup	p.Arg621ProfsTer44	p.R621Pfs*44	ENST00000260795		620	gcc/gCcc	13/17	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.29	2		473	1813	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957488	1957488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1261	100	396	1	ENST00000382891.5:c.2587C>T	p.Pro863Ser	p.P863S	ENST00000382891	NM_133335.3	863	Cct/Tct	14/22	1	2	FACETS	0.507	0.451	0.567	0.507	0.451	0.567	SUBCLONAL	1	TRUE	1	0.29	2		397	1361	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540043	187540043	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	50	357	0	ENST00000441802.2:c.7697T>C	p.Val2566Ala	p.V2566A	ENST00000441802	NM_005245.3	2566	gTc/gCc	10/27	1	2	FACETS	0.531	0.449	0.62	0.531	0.449	0.62	SUBCLONAL	1	TRUE	1	0.29	2		357	650	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628740	187628740	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	106	531	0	ENST00000441802.2:c.2242T>C	p.Phe748Leu	p.F748L	ENST00000441802	NM_005245.3	748	Ttc/Ctc	2/27	1	2	FACETS	0.921	0.825	1	0.921	0.825	1	CLONAL	1	TRUE	1	0.29	2		531	794	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589609	67589610	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	50	374	0	ENST00000274335.5:c.1378dup	p.Ser460LysfsTer5	p.S460Kfs*5	ENST00000274335		458	gaa/gAaa	10/15	1	2	FACETS	0.825	0.701	0.96	0.825	0.701	0.96	CLONAL	1	TRUE	1	0.29	2		374	418	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590371	67590371	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	28	163	0	ENST00000274335.5:c.1433A>G	p.Gln478Arg	p.Q478R	ENST00000274335		478	cAa/cGa	11/15	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.29	2		163	169	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627275	86627275	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	33	275	0	ENST00000274376.6:c.650T>C	p.Val217Ala	p.V217A	ENST00000274376	NM_002890.2	217	gTa/gCa	2/25	1	2	FACETS	0.505	0.411	0.611	0.505	0.411	0.611	SUBCLONAL	1	TRUE	1	0.29	2		275	451	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819753	170819753	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	10	142	0	ENST00000296930.5:c.392A>G	p.Glu131Gly	p.E131G	ENST00000296930	NM_002520.6	131	gAg/gGg	5/11	1	2	FACETS	0.522	0.355	0.73	0.522	0.355	0.73	SUBCLONAL	1	TRUE	1	0.29	2		142	132	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158537	26158537	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	211	438	0	ENST00000289316.2:c.140A>G	p.Lys47Arg	p.K47R	ENST00000289316	NM_138720.2	47	aAg/aGg	1/2	0.267287208896955	3	FACETS	1	0.99	1	0.476	0.442	0.512	CLONAL	1	TRUE	0	0.29	3		438	1166	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790796	89790796	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1970	413	676	0	ENST00000336032.3:c.183del	p.Gly63GlufsTer6	p.G63Efs*6	ENST00000336032	NM_006813.2	61	ctA/ct	1/2	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.29	2		676	2383	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265478	152265478	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	237	427	0	ENST00000206249.3:c.931A>G	p.Thr311Ala	p.T311A	ENST00000206249	NM_000125.3	311	Acg/Gcg	4/8	0.185641213214475	3	FACETS	1	0.991	1	0.725	0.676	0.777	CLONAL	1	TRUE	1	0.29	3		427	1290	SUCCESS
MET	4233	MSKCC	GRCh37	7	116409770	116409770	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	27	268	0	ENST00000397752.3:c.2655A>G	p.Ile885Met	p.I885M	ENST00000397752	NM_000245.2	885	atA/atG	12/21	1	2	FACETS	0.638	0.508	0.785	0.638	0.508	0.785	SUBCLONAL	1	TRUE	1	0.29	2		268	292	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38147995	38147995	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	104	505	0	ENST00000317025.8:c.3116del	p.Lys1039ArgfsTer13	p.K1039Rfs*13	ENST00000317025	NM_023034.1	1039	aAg/ag	17/24	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.29	2		505	677	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282124	38282124	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1375	367	554	0	ENST00000425967.3:c.932A>G	p.Tyr311Cys	p.Y311C	ENST00000425967	NM_001174067.1	311	tAc/tGc	8/19	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.29	2		554	1742	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971012	21971012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1430	353	428	0	ENST00000304494.5:c.346G>A	p.Asp116Asn	p.D116N	ENST00000304494	NM_000077.4	116	Gac/Aac	2/3	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.29	2		428	1783	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814741	139814741	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	267	343	2	ENST00000247668.2:c.734C>T	p.Ala245Val	p.A245V	ENST00000247668	NM_021138.3	245	gCc/gTc	8/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.29	2		345	1435	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041005	47041005	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556779527	NA	P-0018841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	58	242	1	ENST00000377604.3:c.1535C>T	p.Ala512Val	p.A512V	ENST00000377604	NM_001204468.1	512	gCc/gTc	14/24	1	1	FACETS	0.325	0.278	0.376	0.325	0.278	0.376	SUBCLONAL	1	TRUE	0	0.29	1		243	1053	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412110	63412110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852216	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	172	586	1	ENST00000330258.3:c.1057C>T	p.Arg353Ter	p.R353*	ENST00000330258	NM_152424.3	353	Cga/Tga	2/2	1	1	FACETS	0.894	0.829	0.96	1	0.992	1	CLONAL	2	TRUE	0	0.32	1		587	505	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513282	44513287	+	inframe_deletion	In_Frame_Del	DEL	CCACCG	CCACCG	-	rs745888281	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	136	1024	0	ENST00000291552.4:c.648_653del	p.Gly222_Gly223del	p.G222_G223del	ENST00000291552	NM_006758.2	216	ggCGGTGGt/ggt	8/8	1	2	FACETS	0.839	0.762	0.92	0.839	0.762	0.92	CLONAL	1	TRUE	1	0.32	2		1024	1013	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	270	1199	9	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.782	0.734	0.832	1	0.994	1	SUBCLONAL	2	TRUE	1	0.32	2		1208	1079	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058747	180058748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755445139	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	115	824	3	ENST00000261937.6:c.89dup	p.Thr31AspfsTer15	p.T31Dfs*15	ENST00000261937	NM_182925.4	30	ccg/ccCg	2/30	1	2	FACETS	0.957	0.863	1	0.957	0.863	1	CLONAL	1	TRUE	1	0.32	2		827	751	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	118	776	5	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.835	0.753	0.922	0.835	0.753	0.922	CLONAL	1	TRUE	1	0.32	2		781	883	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	208	717	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.3	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.32	2		721	602	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	99	844	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.778	0.694	0.868	0.778	0.694	0.868	SUBCLONAL	1	TRUE	1	0.32	2		844	795	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	125	1012	5	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.999	0.905	1	0.999	0.905	1	CLONAL	1	TRUE	1	0.32	2		1017	782	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	125	936	0	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.32	2		936	757	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	156	668	3	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.32	2		671	974	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220015	5220015	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866165812	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	168	847	0	ENST00000357368.4:c.3700C>T	p.Arg1234Trp	p.R1234W	ENST00000357368	NM_002850.3	1234	Cgg/Tgg	22/38	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.32	2		847	843	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135079	11135079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770969438	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	137	941	0	ENST00000358026.2:c.3046G>A	p.Val1016Met	p.V1016M	ENST00000358026	NM_001128849.1	1016	Gtg/Atg	21/36	1	2	FACETS	0.98	0.891	1	0.98	0.891	1	CLONAL	1	TRUE	1	0.32	2		941	874	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	136	684	1	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	0.32	2		685	718	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	61	500	2	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.851	0.736	0.975	0.851	0.736	0.975	CLONAL	1	TRUE	1	0.32	2		502	448	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913837	32913837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359507	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	147	800	2	ENST00000380152.3:c.5351del	p.Asn1784ThrfsTer7	p.N1784Tfs*7	ENST00000380152		1782	cAa/ca	11/27	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.32	2		802	803	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955204	17955204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145500023	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	173	1100	3	ENST00000458235.1:c.23C>T	p.Thr8Met	p.T8M	ENST00000458235	NM_000215.3	8	aCg/aTg	2/24	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.32	2		1103	1031	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467177	99467177	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149217017	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	124	632	0	ENST00000268035.6:c.2558C>T	p.Pro853Leu	p.P853L	ENST00000268035	NM_000875.3	853	cCg/cTg	12/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.32	2		632	705	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303028	15303028	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773630799	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	140	945	4	ENST00000263388.2:c.422G>A	p.Arg141His	p.R141H	ENST00000263388	NM_000435.2	141	cGc/cAc	4/33	1	2	FACETS	0.986	0.898	1	0.986	0.898	1	CLONAL	1	TRUE	1	0.32	2		949	887	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	68	328	0	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.32	2		328	374	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750818	57750818	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	104	673	2	ENST00000274289.3:c.1786C>T	p.Arg596Ter	p.R596*	ENST00000274289	NM_006622.3	596	Cga/Tga	13/14	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.32	2		675	607	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779180	135779180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200827913	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	87	540	0	ENST00000298552.3:c.2066G>A	p.Arg689His	p.R689H	ENST00000298552	NM_001162426.1	689	cGc/cAc	17/23	1	2	FACETS	0.962	0.854	1	0.962	0.854	1	CLONAL	1	TRUE	1	0.32	2		540	565	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129329	152129329	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	82	607	2	ENST00000206249.3:c.287del	p.Gly96ValfsTer13	p.G96Vfs*13	ENST00000206249	NM_000125.3	94	ctG/ct	1/8	0.291077753788409	3	FACETS	0.953	0.841	1	0.476	0.42	0.537	CLONAL	1	TRUE	1	0.32	3		609	624	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143993	11143993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568509370	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	102	658	0	ENST00000358026.2:c.3574C>T	p.Arg1192Cys	p.R1192C	ENST00000358026	NM_001128849.1	1192	Cgc/Tgc	26/36	1	2	FACETS	0.979	0.877	1	0.979	0.877	1	CLONAL	1	TRUE	1	0.32	2		658	651	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219579	133219579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542430685	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	70	442	0	ENST00000320574.5:c.4555C>T	p.Arg1519Cys	p.R1519C	ENST00000320574	NM_006231.2	1519	Cgc/Tgc	36/49	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.32	2		442	390	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	124	565	1	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.32	2		566	651	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347983	347983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760961378	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	143	890	2	ENST00000262320.3:c.1523del	p.Gly508ValfsTer197	p.G508Vfs*197	ENST00000262320	NM_003502.3	508	gGt/gt	6/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.32	2		892	801	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444659	78444659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs908264837	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	107	624	1	ENST00000370768.2:c.30del	p.Ser11LeufsTer43	p.S11Lfs*43	ENST00000370768	NM_003902.3	10	ccC/cc	1/20	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.32	2		625	639	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502187	157502187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761227259	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	74	555	2	ENST00000346085.5:c.3220G>A	p.Asp1074Asn	p.D1074N	ENST00000346085	NM_020732.3	1074	Gac/Aac	12/20	0.291077753788409	3	FACETS	0.863	0.755	0.978	0.431	0.377	0.489	CLONAL	1	TRUE	1	0.32	3		557	622	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772950	135772951	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs118203724	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	90	564	0	ENST00000298552.3:c.2672dup	p.Asn891LysfsTer13	p.N891Kfs*13	ENST00000298552	NM_001162426.1	891	aac/aaAc	21/23	1	2	FACETS	0.934	0.83	1	0.934	0.83	1	CLONAL	1	TRUE	1	0.32	2		564	602	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793502	42793502	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755293924	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	155	771	0	ENST00000575354.2:c.1304C>T	p.Thr435Met	p.T435M	ENST00000575354	NM_015125.3	435	aCg/aTg	8/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.32	2		771	847	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258683	16258683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559309170	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	114	788	0	ENST00000375759.3:c.5948C>T	p.Ser1983Leu	p.S1983L	ENST00000375759	NM_015001.2	1983	tCg/tTg	11/15	1	2	FACETS	0.994	0.896	1	0.994	0.896	1	CLONAL	1	TRUE	1	0.32	2		788	717	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163277	47163277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149265978	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	116	706	1	ENST00000409792.3:c.2849G>A	p.Arg950His	p.R950H	ENST00000409792	NM_014159.6	950	cGt/cAt	3/21	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.32	2		707	684	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551952	150551952	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	145	681	4	ENST00000369026.2:c.55del	p.Ala19ProfsTer30	p.A19Pfs*30	ENST00000369026	NM_021960.4	19	Gcc/cc	1/3	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.32	2		685	741	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187374	32187374	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759399611	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	196	601	0	ENST00000375023.3:c.1505C>T	p.Pro502Leu	p.P502L	ENST00000375023	NM_004557.3	502	cCg/cTg	8/30	0.291077753788409	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.32	3		601	613	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916824	178916824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201269904	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	164	918	0	ENST00000263967.3:c.211G>A	p.Val71Ile	p.V71I	ENST00000263967	NM_006218.2	71	Gta/Ata	2/21	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.32	2		918	907	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244020	5244020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752283871	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	130	690	2	ENST00000357368.4:c.1462G>A	p.Val488Met	p.V488M	ENST00000357368	NM_002850.3	488	Gtg/Atg	11/38	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.32	2		692	733	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231610	5231611	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	28	185	0	ENST00000357368.4:c.1865dup	p.Gln623SerfsTer4	p.Q623Sfs*4	ENST00000357368	NM_002850.3	622	cct/ccCt	14/38	1	2	FACETS	0.841	0.677	1	0.841	0.677	1	CLONAL	1	TRUE	1	0.32	2		185	208	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46740336	46740336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754074702	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	126	740	0	ENST00000371975.4:c.1816C>T	p.Arg606Trp	p.R606W	ENST00000371975	NM_003579.3	606	Cgg/Tgg	16/18	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.32	2		740	764	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	305	963	6	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	0.291077753788409	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.32	3		969	1055	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324609	62324609	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139221232	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	103	720	0	ENST00000360203.5:c.2965C>T	p.Arg989Trp	p.R989W	ENST00000360203	NM_001283009.1	989	Cgg/Tgg	30/35	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.32	2		720	606	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775614	9775614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766440014	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	82	552	1	ENST00000377346.4:c.157G>A	p.Ala53Thr	p.A53T	ENST00000377346	NM_005026.3	53	Gcc/Acc	4/24	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.32	2		553	476	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775955	9775955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	117	785	2	ENST00000377346.4:c.419G>A	p.Arg140His	p.R140H	ENST00000377346	NM_005026.3	140	cGc/cAc	5/24	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.32	2		787	673	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11292555	11292555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	134	872	0	ENST00000361445.4:c.2452G>A	p.Asp818Asn	p.D818N	ENST00000361445	NM_004958.3	818	Gat/Aat	16/58	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.32	2		872	831	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202886	16202886	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	117	647	0	ENST00000375759.3:c.598del	p.Arg200AspfsTer166	p.R200Dfs*166	ENST00000375759	NM_015001.2	198	gaC/ga	3/15	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.32	2		647	683	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259442	16259442	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	110	647	0	ENST00000375759.3:c.6707C>A	p.Pro2236His	p.P2236H	ENST00000375759	NM_015001.2	2236	cCt/cAt	11/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.32	2		647	573	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105577	27105577	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	121	598	0	ENST00000324856.7:c.5188A>G	p.Ile1730Val	p.I1730V	ENST00000324856	NM_006015.4	1730	Att/Gtt	20/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.32	2		598	717	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28595739	28595739	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1038449460	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	128	879	0	ENST00000253063.3:c.136G>A	p.Ala46Thr	p.A46T	ENST00000253063	NM_031459.4	46	Gcc/Acc	2/10	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.32	2		879	760	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246021916	246021916	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	130	782	0	ENST00000388985.4:c.958C>A	p.Leu320Ile	p.L320I	ENST00000388985		320	Ctt/Att	10/12	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.32	2		782	812	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600496	43600496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1178140696	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	92	727	1	ENST00000355710.3:c.722C>T	p.Ala241Val	p.A241V	ENST00000355710	NM_020975.4	241	gCc/gTc	4/20	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.32	2		728	553	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104375030	104375030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs79299301	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	138	677	2	ENST00000369902.3:c.1028G>A	p.Arg343His	p.R343H	ENST00000369902	NM_016169.3	343	cGc/cAc	9/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.32	2		679	691	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136996	64136996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	164	822	1	ENST00000334205.4:c.1507G>A	p.Glu503Lys	p.E503K	ENST00000334205	NM_003942.2	503	Gag/Aag	13/17	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.32	2		823	858	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940586	71940586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1255360958	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	106	745	6	ENST00000298229.2:c.737G>A	p.Arg246His	p.R246H	ENST00000298229	NM_001567.3	246	cGc/cAc	6/28	1	2	FACETS	0.889	0.797	0.987	0.889	0.797	0.987	CLONAL	1	TRUE	1	0.32	2		751	745	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945654	71945654	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375941017	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	108	631	0	ENST00000298229.2:c.2410C>T	p.Pro804Ser	p.P804S	ENST00000298229	NM_001567.3	804	Ccc/Tcc	21/28	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.32	2		631	652	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418727	49418727	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs398123731	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	77	466	0	ENST00000301067.7:c.15787G>A	p.Val5263Met	p.V5263M	ENST00000301067	NM_003482.3	5263	Gtg/Atg	49/54	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.32	2		466	469	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864423	57864423	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	116	768	0	ENST00000228682.2:c.1903del	p.Val635SerfsTer84	p.V635Sfs*84	ENST00000228682	NM_005269.2	634	Ggg/gg	12/12	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.32	2		768	636	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884833	111884833	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1174628091	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	43	390	0	ENST00000341259.2:c.922C>T	p.Arg308Ter	p.R308*	ENST00000341259	NM_005475.2	308	Cga/Tga	4/8	1	2	FACETS	0.914	0.769	1	0.914	0.769	1	CLONAL	1	TRUE	1	0.32	2		390	294	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939033	48939033	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1131690901	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	91	484	0	ENST00000267163.4:c.869del	p.Asn290MetfsTer11	p.N290Mfs*11	ENST00000267163	NM_000321.2	289	Aaa/aa	9/27	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.32	2		484	501	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129103	2129103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45517279	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	157	947	0	ENST00000219476.3:c.3037G>A	p.Asp1013Asn	p.D1013N	ENST00000219476	NM_000548.3	1013	Gat/Aat	27/42	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.32	2		947	909	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3634842	3634842	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	173	878	0	ENST00000294008.3:c.4667C>A	p.Pro1556His	p.P1556H	ENST00000294008	NM_032444.2	1556	cCc/cAc	13/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.32	2		878	983	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639273	3639273	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760286353	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	136	877	0	ENST00000294008.3:c.4366C>T	p.Arg1456Cys	p.R1456C	ENST00000294008	NM_032444.2	1456	Cgc/Tgc	12/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.32	2		877	753	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640626	3640626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746178364	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	188	1083	2	ENST00000294008.3:c.3013G>A	p.Glu1005Lys	p.E1005K	ENST00000294008	NM_032444.2	1005	Gag/Aag	12/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.32	2		1085	1060	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129436	30129436	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	52	906	0	ENST00000263025.4:c.592A>G	p.Thr198Ala	p.T198A	ENST00000263025	NM_002746.2	198	Acc/Gcc	4/9	1	2	FACETS	0.359	0.304	0.419	0.359	0.304	0.419	SUBCLONAL	1	TRUE	1	0.32	2		906	906	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782296	56782296	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760107958	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	119	656	0	ENST00000308159.5:c.137G>A	p.Arg46His	p.R46H	ENST00000308159	NM_014669.4	46	cGt/cAt	2/22	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.32	2		656	619	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108280	8108280	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779610702	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	105	749	2	ENST00000585124.1:c.944G>A	p.Arg315Gln	p.R315Q	ENST00000585124	NM_004217.3	315	cGg/cAg	9/9	1	2	FACETS	0.982	0.881	1	0.982	0.881	1	CLONAL	1	TRUE	1	0.32	2		751	668	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210565	5210565	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770322238	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	94	693	1	ENST00000357368.4:c.5402G>A	p.Arg1801His	p.R1801H	ENST00000357368	NM_002850.3	1801	cGc/cAc	35/38	1	2	FACETS	0.847	0.754	0.946	0.847	0.754	0.946	CLONAL	1	TRUE	1	0.32	2		694	694	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170793	11170793	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854233	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	148	705	0	ENST00000358026.2:c.4937G>A	p.Arg1646Gln	p.R1646Q	ENST00000358026	NM_001128849.1	1646	cGg/cAg	35/36	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.32	2		705	712	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384762	17384762	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs544132311	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	176	1022	2	ENST00000359435.4:c.394G>A	p.Val132Met	p.V132M	ENST00000359435	NM_001033549.1	132	Gtg/Atg	4/9	1	2	FACETS	0.968	0.891	1	0.968	0.891	1	CLONAL	1	TRUE	1	0.32	2		1024	1136	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797180	42797180	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	183	1087	0	ENST00000575354.2:c.3542A>G	p.Lys1181Arg	p.K1181R	ENST00000575354	NM_015125.3	1181	aAg/aGg	15/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.32	2		1087	989	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729957	47729957	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	58	314	0	ENST00000449228.1:c.432G>T	p.Gln144His	p.Q144H	ENST00000449228	NM_001127240.2	144	caG/caT	3/4	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.32	2		314	324	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920347	50920349	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs1555793593	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	130	946	1	ENST00000440232.2:c.3115_3117del	p.Lys1039del	p.K1039del	ENST00000440232	NM_002691.3	1038	cAGAag/cag	25/27	1	2	FACETS	0.928	0.841	1	0.928	0.841	1	CLONAL	1	TRUE	1	0.32	2		947	876	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989591	212989592	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1553563398	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	25	452	0	ENST00000342788.4:c.119_120del	p.Ser40Ter	p.S40*	ENST00000342788	NM_005235.2	40	tCT/t	2/28	1	2	FACETS	0.354	0.278	0.441	0.354	0.278	0.441	SUBCLONAL	1	TRUE	1	0.32	2		452	442	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645382	215645382	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs377153250	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	108	713	2	ENST00000260947.4:c.1216C>T	p.Arg406Ter	p.R406*	ENST00000260947	NM_000465.2	406	Cga/Tga	4/11	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.32	2		715	635	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279760	46279760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757419594	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	92	534	0	ENST00000371998.3:c.3686G>A	p.Arg1229His	p.R1229H	ENST00000371998		1229	cGc/cAc	20/23	1	2	FACETS	0.998	0.889	1	0.998	0.889	1	CLONAL	1	TRUE	1	0.32	2		534	576	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119585471	119585471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	108	640	1	ENST00000316626.5:c.914C>T	p.Ser305Leu	p.S305L	ENST00000316626		305	tCg/tTg	9/12	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.32	2		641	619	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176560	142176560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151162347	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	143	907	1	ENST00000350721.4:c.7541G>A	p.Arg2514His	p.R2514H	ENST00000350721	NM_001184.3	2514	cGc/cAc	45/47	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.32	2		908	894	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751198	57751198	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	72	486	2	ENST00000274289.3:c.1669C>A	p.Pro557Thr	p.P557T	ENST00000274289	NM_006622.3	557	Cca/Aca	12/14	1	2	FACETS	0.949	0.832	1	0.949	0.832	1	CLONAL	1	TRUE	1	0.32	2		488	474	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950730	79950730	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs758656822	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	36	136	0	ENST00000265081.6:c.184G>T	p.Ala62Ser	p.A62S	ENST00000265081	NM_002439.4	62	Gcg/Tcg	1/24	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.32	2		136	156	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707758	176707758	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064796690	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	141	740	1	ENST00000439151.2:c.5815C>T	p.Arg1939Cys	p.R1939C	ENST00000439151	NM_022455.4	1939	Cgc/Tgc	18/23	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.32	2		741	808	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670564	30670564	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764807291	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	90	756	0	ENST00000376406.3:c.5956G>A	p.Ala1986Thr	p.A1986T	ENST00000376406	NM_014641.2	1986	Gca/Aca	13/15	0.291077753788409	3	FACETS	0.773	0.685	0.867	0.387	0.342	0.434	SUBCLONAL	1	TRUE	1	0.32	3		756	844	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948259	31948259	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	265	877	1	ENST00000375333.2:c.847C>T	p.Arg283Ter	p.R283*	ENST00000375333	NM_032454.1	283	Cga/Tga	6/8	0.291077753788409	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.32	3		878	937	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164701	32164701	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	158	913	0	ENST00000375023.3:c.5200+1del		p.X1734_splice	ENST00000375023	NM_004557.3	1734			0.291077753788409	3	FACETS	1	0.968	1	0.558	0.511	0.608	CLONAL	1	TRUE	1	0.32	3		913	1026	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190345	32190345	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1304701623	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	80	784	0	ENST00000375023.3:c.394C>T	p.Arg132Cys	p.R132C	ENST00000375023	NM_004557.3	132	Cgc/Tgc	3/30	0.291077753788409	3	FACETS	0.789	0.694	0.891	0.395	0.347	0.446	SUBCLONAL	1	TRUE	1	0.32	3		784	735	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798457	32798457	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	191	925	2	ENST00000374899.4:c.1399del	p.Val467LeufsTer2	p.V467Lfs*2	ENST00000374899	NM_018833.2	467	Gtt/tt	8/12	0.291077753788409	3	FACETS	1	0.984	1	0.617	0.569	0.666	CLONAL	1	TRUE	1	0.32	3		927	1123	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287248	33287248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148540788	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	132	759	1	ENST00000374542.5:c.1849G>A	p.Val617Ile	p.V617I	ENST00000374542	NM_001141970.1	617	Gtc/Atc	6/8	0.291077753788409	3	FACETS	1	0.974	1	0.6	0.544	0.658	CLONAL	1	TRUE	1	0.32	3		760	798	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439694	140439694	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	101	490	3	ENST00000288602.6:c.2045G>A	p.Arg682Gln	p.R682Q	ENST00000288602	NM_004333.4	682	cGg/cAg	17/18	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.32	2		493	499	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836816	151836816	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	143	781	0	ENST00000262189.6:c.14404G>A	p.Gly4802Arg	p.G4802R	ENST00000262189	NM_170606.2	4802	Ggg/Agg	56/59	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.32	2		781	875	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874752	151874752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769916428	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	68	386	1	ENST00000262189.6:c.7786C>T	p.Arg2596Trp	p.R2596W	ENST00000262189	NM_170606.2	2596	Cgg/Tgg	38/59	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.32	2		387	376	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878079	151878079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202108375	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	57	420	0	ENST00000262189.6:c.6866G>A	p.Arg2289His	p.R2289H	ENST00000262189	NM_170606.2	2289	cGt/cAt	36/59	1	2	FACETS	0.897	0.773	1	0.897	0.773	1	CLONAL	1	TRUE	1	0.32	2		420	397	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572588	141572588	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	124	703	0	ENST00000220592.5:c.482C>T	p.Ala161Val	p.A161V	ENST00000220592	NM_012154.3	161	gCc/gTc	4/19	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.32	2		703	658	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738792	145738792	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748416710	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	174	1063	1	ENST00000428558.2:c.2273G>A	p.Arg758Gln	p.R758Q	ENST00000428558	NM_004260.3	758	cGa/cAa	14/22	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.32	2		1064	1069	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231358	98231358	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	111	625	0	ENST00000331920.6:c.1925del	p.Pro642HisfsTer51	p.P642Hfs*51	ENST00000331920	NM_000264.3	642	cCa/ca	14/24	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.32	2		625	580	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753849	133753849	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	152	771	0	ENST00000318560.5:c.1318T>C	p.Tyr440His	p.Y440H	ENST00000318560	NM_005157.4	440	Tac/Cac	8/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.32	2		771	680	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222168	53222168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556831986	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	112	294	0	ENST00000375401.3:c.4664C>T	p.Pro1555Leu	p.P1555L	ENST00000375401	NM_004187.3	1555	cCg/cTg	26/26	1	1	FACETS	1	0.964	1	1	0.99	1	CLONAL	2	TRUE	0	0.32	1		294	267	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952090	76952092	+	inframe_deletion	In_Frame_Del	DEL	ATC	ATC	-	novel	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	121	328	0	ENST00000373344.5:c.343_345del	p.Asp115del	p.D115del	ENST00000373344	NM_000489.3	115	GAT/-	5/35	1	1	FACETS	0.78	0.711	0.852	1	0.987	1	SUBCLONAL	2	TRUE	0	0.32	1		328	407	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030943	36030944	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0019076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	124	781	0	ENST00000358208.4:c.1223_1224del	p.Phe408TrpfsTer7	p.F408Wfs*7	ENST00000358208		408	TTt/t	10/12	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.32	2		781	736	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220382	1220382	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	81	736	0	ENST00000326873.7:c.475C>T	p.Gln159Ter	p.Q159*	ENST00000326873	NM_000455.4	159	Cag/Tag	4/10	0.379862502801194	1	FACETS	0.545	0.48	0.614	0.545	0.48	0.614	SUBCLONAL	1	TRUE	0	0.379862502801194	1		736	634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	29	931	2	ENST00000269305.4:c.472C>A	p.Arg158Ser	p.R158S	ENST00000269305	NM_001126112.2	158	Cgc/Agc	5/11	0.332530630483876	1	FACETS	0.146	0.116	0.18	0.146	0.116	0.18	SUBCLONAL	1	TRUE	0	0.379862502801194	1		933	846	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274284	10274284	+	splice_region_variant,5_prime_UTR_variant	Splice_Region	SNP	T	T	G	novel	NA	P-0019271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	24	317	0	ENST00000330684.3:c.-16A>C		p.X6_splice	ENST00000330684	NM_001134407.1	6		2/13	0.379862502801194	1	FACETS	0.483	0.38	0.6	0.483	0.38	0.6	SUBCLONAL	1	TRUE	0	0.379862502801194	1		317	212	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578462	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCGGGT	novel	NA	P-0019271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	186	947	0	ENST00000269305.4:c.463_468dup	p.Thr155_Arg156dup	p.T155_R156dup	ENST00000269305	NM_001126112.2	155	-/ACCCGC	5/11	0.332530630483876	1	FACETS	0.888	0.821	0.958	0.888	0.821	0.958	CLONAL	1	TRUE	0	0.379862502801194	1		947	893	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793883	89793883	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	92	649	0	ENST00000336032.3:c.952C>A	p.His318Asn	p.H318N	ENST00000336032	NM_006813.2	318	Cac/Aac	2/2	0.287419421178635	3	FACETS	0.775	0.688	0.867	0.387	0.344	0.434	SUBCLONAL	1	TRUE	1	0.379862502801194	3		649	744	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271496	38271496	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	86	883	0	ENST00000425967.3:c.2325A>C	p.Arg775Ser	p.R775S	ENST00000425967	NM_001174067.1	775	agA/agC	18/19	0.379862502801194	4	FACETS	0.522	0.46	0.589			1	SUBCLONAL	1	TRUE	NA	0.379862502801194	4		883	1196	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737371	145737371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770193726	NA	P-0019271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	207	900	0	ENST00000428558.2:c.3316C>T	p.Arg1106Cys	p.R1106C	ENST00000428558	NM_004260.3	1106	Cgc/Tgc	20/22	0.22104643952808	3	FACETS	1	0.988	1	0.66	0.612	0.709	INDETERMINATE	1	TRUE	1	0.379862502801194	3		900	983	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471039	8471039	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	52	779	0	ENST00000356435.5:c.3460T>C	p.Phe1154Leu	p.F1154L	ENST00000356435		1154	Ttt/Ctt	20/35	0.208175017900308	0	FACETS	0.251	0.213	0.293			1	INDETERMINATE	1	TRUE	0	0.379862502801194	0		779	677	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469669	NA	P-0019611-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	290	754	0	ENST00000374080.3:c.130G>A	p.Gly44Ser	p.G44S	ENST00000374080		44	Ggt/Agt	2/45	0.314549811030512	2	FACETS	0.996	0.94	1	0.996	0.94	1	CLONAL	2	TRUE	0	0.327456400419426	2		754	889	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156740	20156740	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019611-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	151	462	0	ENST00000379607.5:c.17G>A	p.Gly6Asp	p.G6D	ENST00000379607	NM_001412.3	6	gGt/gAt	2/7	0.302096229021028	3	FACETS	0.897	0.824	0.974	0.897	0.824	0.974	CLONAL	2	TRUE	1	0.327456400419426	3		462	598	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099913	157099913	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019611-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	159	755	1	ENST00000346085.5:c.850C>A	p.Gln284Lys	p.Q284K	ENST00000346085	NM_020732.3	284	Cag/Aag	1/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.327456400419426	2		756	900	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100093	157100120	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGCGGCGGCGGCAGCAGCAGGAGGCG	GCGGCGGCGGCGGCAGCAGCAGGAGGCG	-	rs1554247989	NA	P-0019631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	57	47	0	ENST00000346085.5:c.1044_1071del	p.Ala349MetfsTer11	p.A349Mfs*11	ENST00000346085	NM_020732.3	344	GCGGCGGCGGCGGCAGCAGCAGGAGGCGgc/gc	1/20	0.356918502431733	4	FACETS	0.966	0.853	1			1	INDETERMINATE	2	TRUE	NA	0.77626447335521	4		47	135	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119789	70119789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778047936	NA	P-0019631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	408	826	0	ENST00000245479.2:c.791G>A	p.Arg264Lys	p.R264K	ENST00000245479	NM_000346.3	264	aGa/aAa	3/3	0.77626447335521	3	FACETS	1	0.969	1	0.513	0.487	0.539	CLONAL	1	TRUE	1	0.77626447335521	3		826	1423	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808901	3808901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	330	743	0	ENST00000262367.5:c.3323C>T	p.Ser1108Leu	p.S1108L	ENST00000262367	NM_004380.2	1108	tCa/tTa	17/31	1	2	FACETS	0.924	0.876	0.973	0.924	0.876	0.973	CLONAL	1	TRUE	1	0.77626447335521	2		743	920	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983361	15983361	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	222	453	2	ENST00000268712.3:c.3418C>T	p.Gln1140Ter	p.Q1140*	ENST00000268712	NM_006311.3	1140	Caa/Taa	26/46	0.708765981628309	1	FACETS	0.938	0.89	0.986	0.938	0.89	0.986	CLONAL	1	TRUE	0	0.77626447335521	1		455	373	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600407	10600407	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs867398451	NA	P-0019631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1238	113	1073	1	ENST00000171111.5:c.1448G>T	p.Arg483Leu	p.R483L	ENST00000171111	NM_203500.1	483	cGc/cTc	4/6	1	2	FACETS	0.215	0.193	0.24	0.215	0.193	0.24	SUBCLONAL	1	TRUE	1	0.77626447335521	2		1074	1351	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935090	49935090	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	104	794	1	ENST00000296474.3:c.1909G>C	p.Glu637Gln	p.E637Q	ENST00000296474	NM_002447.2	637	Gag/Cag	6/20	NA	2	FACETS	0.288	0.257	0.321			1	INDETERMINATE	1	TRUE	NA	0.77626447335521	2		795	930	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119789	70119789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778047936	NA	P-0019631-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	244	826	0	ENST00000245479.2:c.791G>A	p.Arg264Lys	p.R264K	ENST00000245479	NM_000346.3	264	aGa/aAa	3/3	0.751312347243542	3	FACETS	0.991	0.927	1	0.495	0.463	0.528	CLONAL	1	TRUE	1	0.758285979744408	3		826	896	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808901	3808901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019631-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	314	743	0	ENST00000262367.5:c.3323C>T	p.Ser1108Leu	p.S1108L	ENST00000262367	NM_004380.2	1108	tCa/tTa	17/31	0.251021569729034	5	FACETS	0.934	0.883	0.985	0.622	0.588	0.657	INDETERMINATE	2	TRUE	2	0.758285979744408	5		743	948	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983361	15983361	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019631-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	217	453	2	ENST00000268712.3:c.3418C>T	p.Gln1140Ter	p.Q1140*	ENST00000268712	NM_006311.3	1140	Caa/Taa	26/46	0.758285979744408	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.758285979744408	1		455	331	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600407	10600407	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs867398451	NA	P-0019631-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	189	1073	1	ENST00000171111.5:c.1448G>T	p.Arg483Leu	p.R483L	ENST00000171111	NM_203500.1	483	cGc/cTc	4/6	1	2	FACETS	0.538	0.497	0.581	0.538	0.497	0.581	SUBCLONAL	1	TRUE	1	0.758285979744408	2		1074	926	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752916	57752916	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019631-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	39	371	0	ENST00000274289.3:c.1012T>G	p.Phe338Val	p.F338V	ENST00000274289	NM_006622.3	338	Ttc/Gtc	8/14	0.758285979744408	1	FACETS	0.215	0.179	0.255	0.215	0.179	0.255	SUBCLONAL	1	TRUE	0	0.758285979744408	1		371	297	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037861	49037867	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TACTAGA	TACTAGA	G	novel	NA	P-0019631-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	44	290	0	ENST00000267163.4:c.2107-6_2107delinsG		p.X703_splice	ENST00000267163	NM_000321.2	703		21/27	0.758285979744408	1	FACETS	0.326	0.276	0.38	0.326	0.276	0.38	SUBCLONAL	1	TRUE	0	0.758285979744408	1		290	221	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374293	138374293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	118	711	1	ENST00000289153.2:c.3151G>A	p.Glu1051Lys	p.E1051K	ENST00000289153	NM_006219.2	1051	Gaa/Aaa	22/22	0.26165444066733	2	FACETS	0.953	0.859	1	0.477	0.429	0.527	CLONAL	1	TRUE	0	0.26165444066733	2		712	946	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576091	29576091	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1131691087	NA	P-0019647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	124	739	0	ENST00000356175.3:c.4064C>G	p.Ser1355Ter	p.S1355*	ENST00000356175	NM_000267.3	1355	tCa/tGa	30/57	0.26165444066733	3	FACETS	0.945	0.853	1	0.473	0.426	0.522	CLONAL	1	TRUE	1	0.26165444066733	3		739	1134	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17125934	17125934	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	51	767	0	ENST00000285071.4:c.660G>C	p.Gln220His	p.Q220H	ENST00000285071	NM_144997.5	220	caG/caC	7/14	0.26165444066733	3	FACETS	0.455	0.385	0.532	0.227	0.192	0.266	SUBCLONAL	1	TRUE	1	0.26165444066733	3		767	969	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181898	32181898	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	126	796	0	ENST00000375023.3:c.2156C>G	p.Thr719Arg	p.T719R	ENST00000375023	NM_004557.3	719	aCa/aGa	13/30	1	2	FACETS	0.931	0.841	1	0.931	0.841	1	CLONAL	1	TRUE	1	0.26165444066733	2		796	1035	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90976716	90976716	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	116	589	0	ENST00000265433.3:c.916C>T	p.Pro306Ser	p.P306S	ENST00000265433	NM_002485.4	306	Cct/Tct	8/16	0.26165444066733	4	FACETS	1	0.935	1	0.35	0.315	0.388	CLONAL	1	TRUE	1	0.26165444066733	4		589	1064	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0019816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	245	774	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.568450365506846	2	FACETS	0.814	0.77	0.858	0.814	0.77	0.858	CLONAL	2	TRUE	0	0.601855239169336	2		774	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0019816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	210	513	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.512953968166529	1	FACETS	0.944	0.884	1	0.944	0.884	1	CLONAL	1	TRUE	0	0.601855239169336	1		513	517	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0019816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	91	556	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.708	0.632	0.788	0.708	0.632	0.788	SUBCLONAL	1	TRUE	1	0.601855239169336	2		557	427	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0019816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	100	513	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.789	0.71	0.873	0.789	0.71	0.873	SUBCLONAL	1	TRUE	1	0.601855239169336	2		513	421	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101152	41101152	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	134	778	0	ENST00000373198.4:c.1204C>A	p.Gln402Lys	p.Q402K	ENST00000373198	NM_133170.3	402	Cag/Aag	8/32	0.577178799309033	3	FACETS	0.652	0.592	0.715			1	SUBCLONAL	1	TRUE	NA	0.601855239169336	3		778	889	SUCCESS
APC	324	MSKCC	GRCh37	5	112173299	112173299	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0019816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	91	357	0	ENST00000257430.4:c.2008A>T	p.Lys670Ter	p.K670*	ENST00000257430	NM_000038.5	670	Aaa/Taa	16/16	1	2	FACETS	0.966	0.867	1	0.966	0.867	1	CLONAL	1	TRUE	1	0.601855239169336	2		357	313	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412925	63412925	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	510	472	0	ENST00000330258.3:c.242del	p.Ser81LeufsTer19	p.S81Lfs*19	ENST00000330258	NM_152424.3	81	tCt/tt	2/2	0.601855239169336	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.601855239169336	2		472	705	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038879	12038879	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	270	645	0	ENST00000396373.4:c.1172A>G	p.Tyr391Cys	p.Y391C	ENST00000396373	NM_001987.4	391	tAt/tGt	7/8	NA	2	FACETS	0.813	0.771	0.855			1	INDETERMINATE	2	TRUE	NA	0.601855239169336	2		645	552	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39283886	39283886	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	161	812	0	ENST00000402219.2:c.467A>G	p.Glu156Gly	p.E156G	ENST00000402219	NM_005633.3	156	gAa/gGa	4/23	1	2	FACETS	0.881	0.812	0.953	0.881	0.812	0.953	CLONAL	1	TRUE	1	0.601855239169336	2		812	607	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730909	40730909	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201064715	NA	P-0019816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	64	652	0	ENST00000373198.4:c.3626G>A	p.Arg1209Gln	p.R1209Q	ENST00000373198	NM_133170.3	1209	cGg/cAg	27/32	0.577178799309033	3	FACETS	0.297	0.256	0.342			1	SUBCLONAL	1	TRUE	NA	0.601855239169336	3		652	931	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561756	55561756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376469897	NA	P-0019816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	43	429	1	ENST00000288135.5:c.146G>A	p.Arg49His	p.R49H	ENST00000288135	NM_000222.2	49	cGc/cAc	2/21	1	2	FACETS	0.476	0.4	0.56	0.476	0.4	0.56	SUBCLONAL	1	TRUE	1	0.601855239169336	2		430	300	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	163	635	0				ENST00000310581	NM_198253.2	-/1132			0.465630325290899	3	FACETS	1	0.987	1	0.648	0.602	0.695	INDETERMINATE	1	TRUE	1	0.93408604712662	3		635	395	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039133	49039133	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0019850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	74	292	0	ENST00000267163.4:c.2212-1G>C		p.X738_splice	ENST00000267163	NM_000321.2	738			0.93408604712662	1	FACETS	0.971	0.915	1	0.971	0.915	1	CLONAL	1	TRUE	0	0.93408604712662	1		292	87	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	639	716	0	ENST00000269305.4:c.527G>C	p.Cys176Ser	p.C176S	ENST00000269305	NM_001126112.2	176	tGc/tCc	5/11	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	2	TRUE	NA	0.93408604712662	2		716	669	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039164	49039164	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	142	492	0	ENST00000267163.4:c.2242G>C	p.Glu748Gln	p.E748Q	ENST00000267163	NM_000321.2	748	Gag/Cag	22/27	0.93408604712662	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.93408604712662	1		492	158	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129629	47129629	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	175	665	0	ENST00000409792.3:c.5251A>G	p.Lys1751Glu	p.K1751E	ENST00000409792	NM_014159.6	1751	Aaa/Gaa	10/21	0.543588773343345	3	FACETS	0.62	0.571	0.671	0.31	0.285	0.336	INDETERMINATE	1	TRUE	1	0.93408604712662	3		665	886	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931463	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622007	NA	P-0019933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	264	398	0	ENST00000374690.3:c.2105T>A	p.Leu702His	p.L702H	ENST00000374690	NM_000044.3	702	cTc/cAc	4/8	0.173875827798153	3	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.556453204771962	3		398	826	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845890	156845890	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750477154	NA	P-0019933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	128	957	0	ENST00000524377.1:c.1520G>A	p.Arg507His	p.R507H	ENST00000524377	NM_002529.3	507	cGc/cAc	13/17	1	2	FACETS	0.377	0.34	0.415	0.377	0.34	0.415	SUBCLONAL	1	TRUE	1	0.556453204771962	2		957	1221	SUCCESS
AR	367	MSKCC	GRCh37	X	66937372	66937372	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	38	390	0	ENST00000374690.3:c.2226G>C	p.Trp742Cys	p.W742C	ENST00000374690	NM_000044.3	742	tgG/tgC	5/8	0.173875827798153	3	FACETS	0.247	0.204	0.296			1	INDETERMINATE	1	TRUE	NA	0.556453204771962	3		390	706	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373322	118373322	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1414433521	NA	P-0019933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	87	680	0	ENST00000534358.1:c.6715C>G	p.Leu2239Val	p.L2239V	ENST00000534358	NM_005933.3	2239	Ctt/Gtt	27/36	NA	2	FACETS	0.406	0.359	0.456			1	INDETERMINATE	1	TRUE	NA	0.556453204771962	2		680	771	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025771	48025771	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	44	345	0	ENST00000234420.5:c.649G>C	p.Asp217His	p.D217H	ENST00000234420	NM_000179.2	217	Gat/Cat	4/10	0.29035257289518	2	FACETS	0.31	0.26	0.366	0.155	0.13	0.183	INDETERMINATE	1	TRUE	0	0.556453204771962	2		345	510	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022311	31022311	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	229	582	0	ENST00000375687.4:c.1796C>A	p.Pro599His	p.P599H	ENST00000375687	NM_015338.5	599	cCc/cAc	13/13	1	2	FACETS	0.981	0.916	1	0.981	0.916	1	CLONAL	1	TRUE	1	0.556453204771962	2		582	839	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346583	81346602	+	frameshift_variant	Frame_Shift_Del	DEL	GGATTTCCCGTGTAGCACCA	GGATTTCCCGTGTAGCACCA	-	novel	NA	P-0019933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	172	576	0	ENST00000222390.5:c.1351_1370del	p.Trp451ThrfsTer13	p.W451Tfs*13	ENST00000222390	NM_000601.4	451	TGGTGCTACACGGGAAATCCa/a	11/18	1	2	FACETS	0.785	0.723	0.848	0.785	0.723	0.848	SUBCLONAL	1	TRUE	1	0.556453204771962	2		576	788	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509555	106509555	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	171	816	2	ENST00000359195.3:c.1549T>A	p.Ser517Thr	p.S517T	ENST00000359195	NM_002649.2	517	Tcc/Acc	2/11	NA	2	FACETS	0.557	0.512	0.605			1	INDETERMINATE	1	TRUE	NA	0.556453204771962	2		818	1103	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661129	227661131	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	novel	NA	P-0019976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	137	901	0	ENST00000305123.5:c.2324_2326del	p.Gln775del	p.Q775del	ENST00000305123	NM_005544.2	775	cAGCgc/cgc	1/2	0.575924758452329	1	FACETS	0.524	0.478	0.573	0.524	0.478	0.573	SUBCLONAL	1	TRUE	0	0.575924758452329	1		901	646	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937477	76937478	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0019976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	178	365	0	ENST00000373344.5:c.3270_3271del	p.Lys1091GlufsTer20	p.K1091Efs*20	ENST00000373344	NM_000489.3	1090	gaGAag/gaag	9/35	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.575924758452329	1		365	328	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0020129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	16	560	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		560	661	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18576930	18576930	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	50	935	0	ENST00000266497.5:c.2338C>A	p.His780Asn	p.H780N	ENST00000266497		780	Cac/Aac	16/31	1	2	FACETS	0.921	0.779	1	0.921	0.779	1	CLONAL	1	TRUE	1	0.13	2		935	835	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256362	46256362	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	43	816	1	ENST00000371998.3:c.590G>T	p.Cys197Phe	p.C197F	ENST00000371998		197	tGc/tTc	7/23	1	2	FACETS	0.921	0.769	1	0.921	0.769	1	CLONAL	1	TRUE	1	0.13	2		817	718	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247098	53247098	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	61	485	0	ENST00000375401.3:c.402G>A	p.Trp134Ter	p.W134*	ENST00000375401	NM_004187.3	134	tgG/tgA	4/26	1	1	FACETS	1	0.947	1	1	0.982	1	CLONAL	2	TRUE	0	0.13	1		485	368	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	57	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	0.758	1	0.885	0.758	1	CLONAL	1	TRUE	1	0.18	2		473	716	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038895	12038895	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	54	625	0	ENST00000396373.4:c.1188A>T	p.Arg396Ser	p.R396S	ENST00000396373	NM_001987.4	396	agA/agT	7/8	1	2	FACETS	0.863	0.736	1	0.863	0.736	1	CLONAL	1	TRUE	1	0.18	2		625	695	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634324	23634324	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203999	NA	P-0020504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	125	1427	1	ENST00000261584.4:c.2962C>T	p.Gln988Ter	p.Q988*	ENST00000261584	NM_024675.3	988	Caa/Taa	9/13	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.18	2		1428	1215	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71050124	71050128	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TGTAG	TGTAG	-	novel	NA	P-0020512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	75	470	0	ENST00000318789.4:c.1057_1061del	p.Leu353AlafsTer106	p.L353Afs*106	ENST00000318789	NM_032682.5	353	CTACAg/g	13/21	1	2	FACETS	0.645	0.566	0.731	0.645	0.566	0.731	SUBCLONAL	1	TRUE	1	0.4	2		470	581	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135780998	135780998	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	178	763	0	ENST00000298552.3:c.1967G>A	p.Gly656Glu	p.G656E	ENST00000298552	NM_001162426.1	656	gGa/gAa	15/23	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.4	2		763	869	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0020603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	167	936	0	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	0.510660523610763	3	FACETS	0.887	0.815	0.962	0.443	0.407	0.481	CLONAL	1	TRUE	1	0.510660523610763	3		936	926	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0020603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	380	905	0	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	0.510660523610763	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.510660523610763	3		905	886	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649893	88649893	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775188308	NA	P-0020603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	225	517	0	ENST00000372037.3:c.142G>A	p.Val48Ile	p.V48I	ENST00000372037	NM_004329.2	48	Gta/Ata	4/13	0.510660523610763	3	FACETS	0.937	0.88	0.996	0.937	0.88	0.996	CLONAL	2	TRUE	1	0.510660523610763	3		517	590	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713353	43713353	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	311	1219	0	ENST00000382044.4:c.4120C>G	p.Gln1374Glu	p.Q1374E	ENST00000382044	NM_001141980.1	1374	Cag/Gag	20/28	0.188255362902724	3	FACETS	1	0.994	1	0.726	0.685	0.768	INDETERMINATE	1	TRUE	1	0.510660523610763	3		1219	1053	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37637694	37637694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1461567991	NA	P-0020603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	185	812	0	ENST00000249071.6:c.40G>A	p.Val14Met	p.V14M	ENST00000249071	NM_002872.4	14	Gtg/Atg	2/7	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.510660523610763	2		812	718	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165722	47165722	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0020603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	286	690	0	ENST00000409792.3:c.404C>G	p.Ser135Ter	p.S135*	ENST00000409792	NM_014159.6	135	tCa/tGa	3/21	0.510660523610763	2	FACETS	0.977	0.929	1	0.977	0.929	1	CLONAL	2	TRUE	0	0.510660523610763	2		690	573	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249474	153249476	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	novel	NA	P-0020603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	261	753	0	ENST00000281708.4:c.1302_1304del	p.Ile435del	p.I435del	ENST00000281708	NM_033632.3	434	atCATt/att	9/12	0.508661151853989	2	FACETS	0.856	0.809	0.904	0.856	0.809	0.904	CLONAL	2	TRUE	0	0.510660523610763	2		753	597	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638112	176638113	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTGG	novel	NA	P-0020603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	333	773	0	ENST00000439151.2:c.2713_2714insGTGGT	p.Tyr905CysfsTer9	p.Y905Cfs*9	ENST00000439151	NM_022455.4	904	-/TGTGG	5/23	NA	2	FACETS	0.949	0.905	0.994			1	INDETERMINATE	2	TRUE	NA	0.510660523610763	2		773	687	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	146	463	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.956	0.873	1	0.956	0.873	1	CLONAL	1	TRUE	1	0.368320930031728	2		463	829	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0020636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	455	1124	1	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.368320930031728	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.368320930031728	3		1125	1240	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0020636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	82	424	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.284074934304161	3	FACETS	0.853	0.753	0.96	0.427	0.376	0.48	CLONAL	1	TRUE	1	0.368320930031728	3		424	618	SUCCESS
APC	324	MSKCC	GRCh37	5	112175530	112175530	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	132	372	0	ENST00000257430.4:c.4240del	p.Val1414Ter	p.V1414*	ENST00000257430	NM_000038.5	1413	atG/at	16/16	0.284074934304161	3	FACETS	1	0.986	1	0.742	0.676	0.81	CLONAL	1	TRUE	1	0.368320930031728	3		372	572	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620522	52620523	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCAAATACAGA	novel	NA	P-0020636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	167	794	0	ENST00000394830.3:c.3220_3230dup	p.Asn1078LeufsTer60	p.N1078Lfs*60	ENST00000394830	NM_018313.4	1077	gca/gcTCTGTATTTGCa	21/30	0.368320930031728	1	FACETS	0.908	0.835	0.983	0.908	0.835	0.983	CLONAL	1	TRUE	0	0.368320930031728	1		794	815	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	268	894	0	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	0.996	1	CLONAL	2	TRUE	1	0.332452033927749	2		894	726	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	202	257	1	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.775	0.72	0.832	1	0.992	1	SUBCLONAL	2	TRUE	1	0.332452033927749	2		258	784	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	147	453	4	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.332452033927749	2		457	831	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671654	67671655	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	152	636	1	ENST00000264010.4:c.2070dup	p.Glu691ArgfsTer5	p.E691Rfs*5	ENST00000264010	NM_006565.3	688	gta/gtAa	12/12	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.332452033927749	2		637	679	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	190	621	1	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	1	0.974	1	1	0.994	1	CLONAL	2	TRUE	1	0.332452033927749	2		622	524	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646867	23646867	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	161	850	0	ENST00000261584.4:c.1000T>C	p.Tyr334His	p.Y334H	ENST00000261584	NM_024675.3	334	Tac/Cac	4/13	1	2	FACETS	0.968	0.887	1	0.968	0.887	1	CLONAL	1	TRUE	1	0.332452033927749	2		850	1001	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097304	178097304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763097686	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	107	467	5	ENST00000397062.3:c.410C>T	p.Ser137Leu	p.S137L	ENST00000397062	NM_006164.4	137	tCg/tTg	4/5	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.332452033927749	2		472	468	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230691	46230691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424958105	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	102	629	2	ENST00000334344.6:c.940C>T	p.Arg314Cys	p.R314C	ENST00000334344	NM_152641.2	314	Cgt/Tgt	8/21	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.332452033927749	2		631	562	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164543	36164543	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	168	623	0	ENST00000300305.3:c.1332del	p.Ser445AlafsTer149	p.S445Afs*149	ENST00000300305		444	ccC/cc	8/8	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.332452033927749	2		623	742	SUCCESS
APC	324	MSKCC	GRCh37	5	112175273	112175273	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123121	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	86	387	0	ENST00000257430.4:c.3982C>T	p.Gln1328Ter	p.Q1328*	ENST00000257430	NM_000038.5	1328	Cag/Tag	16/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.332452033927749	2		387	381	SUCCESS
APC	324	MSKCC	GRCh37	5	112175945	112175945	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	84	336	0	ENST00000257430.4:c.4654G>T	p.Glu1552Ter	p.E1552*	ENST00000257430	NM_000038.5	1552	Gag/Tag	16/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.332452033927749	2		336	386	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456893	149456893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3829986	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	196	735	0	ENST00000286301.3:c.835G>A	p.Val279Met	p.V279M	ENST00000286301	NM_005211.3	279	Gtg/Atg	6/22	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.332452033927749	2		735	852	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149982884	149982884	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1327531500	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	109	635	1	ENST00000253339.5:c.3374G>A	p.Arg1125His	p.R1125H	ENST00000253339		1125	cGc/cAc	7/7	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.332452033927749	2		636	547	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740623	58740624	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs763475304	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	138	722	0	ENST00000305921.3:c.1535dup	p.Asn512LysfsTer16	p.N512Kfs*16	ENST00000305921	NM_003620.3	510	caa/cAaa	6/6	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.332452033927749	2		722	722	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690846	89690846	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	62	544	0	ENST00000371953.3:c.253G>T	p.Val85Phe	p.V85F	ENST00000371953	NM_000314.4	85	Gtt/Ttt	4/9	1	2	FACETS	0.94	0.815	1	0.94	0.815	1	CLONAL	1	TRUE	1	0.332452033927749	2		544	397	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962933	2962933	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs78443994	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	224	913	5	ENST00000396946.4:c.1975G>A	p.Val659Met	p.V659M	ENST00000396946	NM_032415.4	659	Gtg/Atg	16/25	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.332452033927749	2		918	976	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411576	63411576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	206	486	1	ENST00000330258.3:c.1591C>T	p.Arg531Ter	p.R531*	ENST00000330258	NM_152424.3	531	Cga/Tga	2/2	1	1	FACETS	1	0.975	1	1	0.994	1	CLONAL	2	TRUE	0	0.332452033927749	1		487	480	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782061	66782062	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	142	583	1	ENST00000307102.5:c.1034dup	p.Asn345LysfsTer21	p.N345Kfs*21	ENST00000307102	NM_002755.3	343	ata/atAa	10/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.332452033927749	2		584	605	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028049	48028049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63751113	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	89	393	0	ENST00000234420.5:c.2927G>A	p.Arg976His	p.R976H	ENST00000234420	NM_000179.2	976	cGt/cAt	4/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.332452033927749	2		393	404	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276861	15276861	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	125	782	2	ENST00000263388.2:c.5404del	p.Ala1802LeufsTer23	p.A1802Lfs*23	ENST00000263388	NM_000435.2	1802	Gct/ct	30/33	1	2	FACETS	0.931	0.842	1	0.931	0.842	1	CLONAL	1	TRUE	1	0.332452033927749	2		784	808	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779076	3779076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776500881	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	60	753	2	ENST00000262367.5:c.5972C>T	p.Pro1991Leu	p.P1991L	ENST00000262367	NM_004380.2	1991	cCg/cTg	31/31	1	2	FACETS	0.532	0.458	0.614	0.532	0.458	0.614	SUBCLONAL	1	TRUE	1	0.332452033927749	2		755	678	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885930	111885930	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs138410505	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	127	655	2	ENST00000341259.2:c.1552C>T	p.Arg518Ter	p.R518*	ENST00000341259	NM_005475.2	518	Cga/Tga	8/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.332452033927749	2		657	650	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588972	67588972	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	73	489	0	ENST00000274335.5:c.1067del	p.Leu356TrpfsTer17	p.L356Wfs*17	ENST00000274335		355	Ttt/tt	8/15	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.332452033927749	2		489	419	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519896	66519896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	97	687	2	ENST00000358598.2:c.379G>A	p.Ala127Thr	p.A127T	ENST00000358598	NM_212471.2	127	Gct/Act	4/11	1	2	FACETS	0.767	0.683	0.856	0.767	0.683	0.856	SUBCLONAL	1	TRUE	1	0.332452033927749	2		689	761	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95596408	95596408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775207591	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	24	531	0	ENST00000393063.1:c.560G>A	p.Arg187Gln	p.R187Q	ENST00000393063	NM_030621.3	187	cGa/cAa	6/28	1	2	FACETS	0.327	0.255	0.409	0.327	0.255	0.409	SUBCLONAL	1	TRUE	1	0.332452033927749	2		531	442	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354308	354308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757610038	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	157	702	2	ENST00000262320.3:c.1250G>A	p.Arg417His	p.R417H	ENST00000262320	NM_003502.3	417	cGc/cAc	5/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.332452033927749	2		704	773	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598900	28598900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753794131	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	210	800	0	ENST00000253063.3:c.460G>A	p.Glu154Lys	p.E154K	ENST00000253063	NM_031459.4	154	Gag/Aag	4/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.332452033927749	2		800	866	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159112	24159112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1341827515	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	128	578	0	ENST00000263121.7:c.784G>A	p.Val262Ile	p.V262I	ENST00000263121	NM_003073.3	262	Gtc/Atc	6/9	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.332452033927749	2		578	547	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905312	50905312	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749334182	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	135	910	0	ENST00000440232.2:c.520C>T	p.Arg174Trp	p.R174W	ENST00000440232	NM_002691.3	174	Cgg/Tgg	5/27	1	2	FACETS	0.899	0.817	0.986	0.899	0.817	0.986	CLONAL	1	TRUE	1	0.332452033927749	2		910	903	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611717	1611717	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755856969	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	204	816	0	ENST00000344749.5:c.1945G>A	p.Gly649Arg	p.G649R	ENST00000344749	NM_001136139.2	649	Ggg/Agg	19/19	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.332452033927749	2		816	889	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266570	115266570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	148	794	0	ENST00000438362.2:c.1945C>T	p.Arg649Cys	p.R649C	ENST00000438362	NM_001242891.1	649	Cgc/Tgc	16/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.332452033927749	2		794	818	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129087	30129087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	166	657	0	ENST00000263025.4:c.679G>A	p.Asp227Asn	p.D227N	ENST00000263025	NM_002746.2	227	Gac/Aac	5/9	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.332452033927749	2		657	823	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925402	114925402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748822481	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	164	795	0	ENST00000543371.1:c.1485del	p.Ser496ProfsTer5	p.S496Pfs*5	ENST00000543371	NM_001198531.1	494	Ccc/cc	14/14	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.332452033927749	2		795	853	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258440	16258440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1440008576	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	167	712	1	ENST00000375759.3:c.5705G>A	p.Arg1902Gln	p.R1902Q	ENST00000375759	NM_015001.2	1902	cGg/cAg	11/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.332452033927749	2		713	807	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739853	46739853	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1312637312	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	183	633	2	ENST00000371975.4:c.1654C>T	p.Arg552Ter	p.R552*	ENST00000371975	NM_003579.3	552	Cga/Tga	15/18	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.332452033927749	2		635	747	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957496	175957496	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1326454203	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	124	751	0	ENST00000367669.3:c.1900C>T	p.Arg634Cys	p.R634C	ENST00000367669	NM_022457.5	634	Cgt/Tgt	17/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.332452033927749	2		751	651	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984380	201984380	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs756566923	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	189	798	1	ENST00000359651.3:c.1045C>T	p.Arg349Ter	p.R349*	ENST00000359651		349	Cga/Tga	8/8	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.332452033927749	2		799	799	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711906	89711906	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	143	689	0	ENST00000371953.3:c.524T>C	p.Val175Ala	p.V175A	ENST00000371953	NM_000314.4	175	gTg/gCg	6/9	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.332452033927749	2		689	726	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941474	71941474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778197564	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	235	897	3	ENST00000298229.2:c.1159C>T	p.Arg387Trp	p.R387W	ENST00000298229	NM_001567.3	387	Cgg/Tgg	10/28	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.332452033927749	2		900	960	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121562	108121562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780097986	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	133	664	2	ENST00000278616.4:c.1370G>A	p.Arg457Gln	p.R457Q	ENST00000278616	NM_000051.3	457	cGa/cAa	10/63	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.332452033927749	2		666	682	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492783	50492783	+	stop_lost	Nonstop_Mutation	SNP	G	G	T	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	136	681	0	ENST00000394963.4:c.1548G>T	p.Ter516TyrextTer23	p.*516Yext*23	ENST00000394963	NM_003076.4	516	taG/taT	13/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.332452033927749	2		681	652	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210807	133210807	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	189	793	0	ENST00000320574.5:c.5969C>T	p.Ala1990Val	p.A1990V	ENST00000320574	NM_006231.2	1990	gCc/gTc	43/49	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.332452033927749	2		793	848	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41023251	41023251	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	58	763	0	ENST00000267868.3:c.897-2A>G		p.X299_splice	ENST00000267868	NM_002875.4	299			1	2	FACETS	0.443	0.38	0.513	0.443	0.38	0.513	SUBCLONAL	1	TRUE	1	0.332452033927749	2		763	787	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669605	88669605	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	29	401	2	ENST00000360948.2:c.1294-1G>T		p.X432_splice	ENST00000360948	NM_001012338.2	432			1	2	FACETS	0.407	0.326	0.499	0.407	0.326	0.499	SUBCLONAL	1	TRUE	1	0.332452033927749	2		403	429	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434737	99434737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1250642880	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	224	704	2	ENST00000268035.6:c.824G>A	p.Arg275His	p.R275H	ENST00000268035	NM_000875.3	275	cGc/cAc	3/21	1	2	FACETS	0.787	0.734	0.842	1	0.992	1	SUBCLONAL	2	TRUE	1	0.332452033927749	2		706	856	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223920	2223920	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	163	639	0	ENST00000326181.6:c.1136-2A>G		p.X379_splice	ENST00000326181	NM_032271.2	379			1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.332452033927749	2		639	710	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640169	3640169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769688259	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	259	1043	3	ENST00000294008.3:c.3470C>T	p.Ser1157Leu	p.S1157L	ENST00000294008	NM_032444.2	1157	tCg/tTg	12/15	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.332452033927749	2		1046	1076	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777960	3777960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1266123570	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	269	1013	1	ENST00000262367.5:c.7088C>T	p.Pro2363Leu	p.P2363L	ENST00000262367	NM_004380.2	2363	cCg/cTg	31/31	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.332452033927749	2		1014	1102	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14028124	14028124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	29	641	0	ENST00000311895.7:c.1178C>T	p.Ala393Val	p.A393V	ENST00000311895	NM_005236.2	393	gCa/gTa	7/11	1	2	FACETS	0.351	0.281	0.431	0.351	0.281	0.431	SUBCLONAL	1	TRUE	1	0.332452033927749	2		641	497	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828334	50828334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	120	513	3	ENST00000398568.2:c.2672G>A	p.Arg891Gln	p.R891Q	ENST00000398568	NM_001042412.1	891	cGg/cAg	17/18	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.332452033927749	2		516	631	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619187	37619187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763908534	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	149	669	0	ENST00000447079.4:c.863G>A	p.Ser288Asn	p.S288N	ENST00000447079	NM_015083.1	288	aGc/aAc	1/14	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.332452033927749	2		669	686	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866411	37866411	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	56	756	0	ENST00000269571.5:c.716A>G	p.Gln239Arg	p.Q239R	ENST00000269571		239	cAg/cGg	6/27	1	2	FACETS	0.401	0.342	0.465	0.401	0.342	0.465	SUBCLONAL	1	TRUE	1	0.332452033927749	2		756	840	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119989	70119990	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	TA	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	68	257	1	ENST00000245479.2:c.991_992delinsTA	p.Ala331Ter	p.A331*	ENST00000245479	NM_000346.3	331	GCg/TAg	3/3	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.332452033927749	2		258	303	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291627	15291627	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	216	886	0	ENST00000263388.2:c.3007T>C	p.Trp1003Arg	p.W1003R	ENST00000263388	NM_000435.2	1003	Tgg/Cgg	19/33	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.332452033927749	2		886	910	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384765	17384765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754532648	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	204	772	3	ENST00000359435.4:c.397C>T	p.Arg133Trp	p.R133W	ENST00000359435	NM_001033549.1	133	Cgg/Tgg	4/9	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.332452033927749	2		775	903	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214822	36214822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	166	768	0	ENST00000222270.7:c.3248G>A	p.Arg1083Gln	p.R1083Q	ENST00000222270	NM_014727.1	1083	cGa/cAa	8/37	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.332452033927749	2		768	801	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223866	36223866	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1350017018	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	222	799	1	ENST00000222270.7:c.6416C>T	p.Ala2139Val	p.A2139V	ENST00000222270	NM_014727.1	2139	gCg/gTg	28/37	1	2	FACETS	0.765	0.713	0.818	1	0.992	1	SUBCLONAL	2	TRUE	1	0.332452033927749	2		800	873	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748545	40748545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1054914884	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	210	831	1	ENST00000392038.2:c.337C>T	p.Arg113Trp	p.R113W	ENST00000392038	NM_001626.4	113	Cgg/Tgg	5/14	1	2	FACETS	0.761	0.708	0.816	1	0.992	1	SUBCLONAL	2	TRUE	1	0.332452033927749	2		832	830	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142956	30142956	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	46	931	2	ENST00000389048.3:c.570G>A	p.Met190Ile	p.M190I	ENST00000389048	NM_004304.4	190	atG/atA	1/29	1	2	FACETS	0.314	0.264	0.371	0.314	0.264	0.371	SUBCLONAL	1	TRUE	1	0.332452033927749	2		933	880	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907671	111907671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	130	540	0	ENST00000393256.3:c.445G>T	p.Ala149Ser	p.A149S	ENST00000393256	NM_006538.4	149	Gcc/Tcc	3/4	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.332452033927749	2		540	682	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159016	24159016	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	127	825	1	ENST00000263121.7:c.688C>A	p.Pro230Thr	p.P230T	ENST00000263121	NM_003073.3	230	Ccg/Acg	6/9	1	2	FACETS	0.914	0.828	1	0.914	0.828	1	CLONAL	1	TRUE	1	0.332452033927749	2		826	836	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155382	47155382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	149	663	1	ENST00000409792.3:c.4699G>A	p.Ala1567Thr	p.A1567T	ENST00000409792	NM_014159.6	1567	Gcc/Acc	5/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.332452033927749	2		664	660	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096111	71096111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	32	390	1	ENST00000318789.4:c.646C>A	p.Leu216Ile	p.L216I	ENST00000318789	NM_032682.5	216	Ctt/Att	10/21	1	2	FACETS	0.452	0.366	0.548	0.452	0.366	0.548	SUBCLONAL	1	TRUE	1	0.332452033927749	2		391	426	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114752	73114752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777442907	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	43	248	0	ENST00000356692.5:c.1133G>A	p.Arg378His	p.R378H	ENST00000356692		378	cGt/cAt	9/9	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.332452033927749	2		248	253	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205181	128205181	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	184	806	2	ENST00000341105.2:c.260C>A	p.Pro87Gln	p.P87Q	ENST00000341105	NM_032638.4	87	cCa/cAa	3/6	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.332452033927749	2		808	783	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439284	149439284	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	172	740	0	ENST00000286301.3:c.2111T>C	p.Leu704Pro	p.L704P	ENST00000286301	NM_005211.3	704	cTc/cCc	15/22	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.332452033927749	2		740	798	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499617	149499617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1301469558	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	177	741	0	ENST00000261799.4:c.2656G>A	p.Val886Met	p.V886M	ENST00000261799	NM_002609.3	886	Gtg/Atg	19/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.332452033927749	2		741	895	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041127	180041127	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	181	1220	1	ENST00000261937.6:c.3272A>G	p.Tyr1091Cys	p.Y1091C	ENST00000261937	NM_182925.4	1091	tAc/tGc	24/30	1	2	FACETS	0.91	0.838	0.986	0.91	0.838	0.986	CLONAL	1	TRUE	1	0.332452033927749	2		1221	1196	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323288	31323288	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	14	154	0	ENST00000412585.2:c.701C>A	p.Pro234His	p.P234H	ENST00000412585	NM_005514.6	234	cCt/cAt	4/8	1	2	FACETS	0.533	0.387	0.708	0.533	0.387	0.708	SUBCLONAL	1	TRUE	1	0.332452033927749	2		154	158	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948473	31948473	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142791776	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	87	458	0	ENST00000375333.2:c.956G>A	p.Arg319Gln	p.R319Q	ENST00000375333	NM_032454.1	319	cGg/cAg	7/8	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.332452033927749	2		458	439	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165280	32165280	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	218	902	1	ENST00000375023.3:c.4848G>A	p.Trp1616Ter	p.W1616*	ENST00000375023	NM_004557.3	1616	tgG/tgA	27/30	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.332452033927749	2		903	952	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170103	32170103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764352594	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	178	795	4	ENST00000375023.3:c.3505C>T	p.Arg1169Trp	p.R1169W	ENST00000375023	NM_004557.3	1169	Cgg/Tgg	21/30	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.332452033927749	2		799	777	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202232	138202232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561168863	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	108	572	1	ENST00000237289.4:c.2149G>A	p.Ala717Thr	p.A717T	ENST00000237289	NM_001270507.1	717	Gcc/Acc	9/9	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.332452033927749	2		573	628	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934320	68934320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	112	875	0	ENST00000288368.4:c.386C>T	p.Ala129Val	p.A129V	ENST00000288368	NM_024870.2	129	gCa/gTa	4/40	1	2	FACETS	0.803	0.722	0.889	0.803	0.722	0.889	CLONAL	1	TRUE	1	0.332452033927749	2		875	839	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989706	68989706	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	126	722	0	ENST00000288368.4:c.1642+2T>C		p.X548_splice	ENST00000288368	NM_024870.2	548			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.332452033927749	2		722	689	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981780	70981780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	214	893	0	ENST00000276594.2:c.316C>T	p.His106Tyr	p.H106Y	ENST00000276594	NM_024504.3	106	Cac/Tac	2/8	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.332452033927749	2		893	905	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849283	76849283	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	34	384	0	ENST00000373344.5:c.5993C>A	p.Ala1998Asp	p.A1998D	ENST00000373344	NM_000489.3	1998	gCt/gAt	26/35	1	1	FACETS	0.461	0.377	0.555	0.461	0.377	0.555	SUBCLONAL	1	TRUE	0	0.332452033927749	1		384	370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0020760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	443	743	2	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	0.731476538124222	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.731476538124222	1		745	723	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352634	118352634	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	153	571	0	ENST00000534358.1:c.3839G>T	p.Gly1280Val	p.G1280V	ENST00000534358	NM_005933.3	1280	gGg/gTg	7/36	0.731476538124222	1	FACETS	0.474	0.436	0.513	0.474	0.436	0.513	SUBCLONAL	1	TRUE	0	0.731476538124222	1		571	560	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779826	3779826	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	403	939	0	ENST00000262367.5:c.5222A>T	p.Lys1741Met	p.K1741M	ENST00000262367	NM_004380.2	1741	aAg/aTg	31/31	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.731476538124222	2		939	1091	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222932	36222932	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374674556	NA	P-0020760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	251	1084	0	ENST00000222270.7:c.5561C>T	p.Pro1854Leu	p.P1854L	ENST00000222270	NM_014727.1	1854	cCt/cTt	27/37	0.731476538124222	1	FACETS	0.463	0.433	0.493	0.463	0.433	0.493	SUBCLONAL	1	TRUE	0	0.731476538124222	1		1084	941	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415585	152415585	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	454	800	0	ENST00000206249.3:c.1435C>G	p.Leu479Val	p.L479V	ENST00000206249	NM_000125.3	479	Ctg/Gtg	7/8	0.731476538124222	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.731476538124222	1		800	728	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0020834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	74	1199	9	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.177527389209199	4	FACETS	0.807	0.707	0.915	0.538	0.471	0.61	CLONAL	2	TRUE	1	0.177527389209199	4		1208	608	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0020834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	111	717	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.824	0.741	0.912	1	0.985	1	CLONAL	2	TRUE	1	0.177527389209199	2		721	759	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0020834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	72	1012	5	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	0.177527389209199	0	FACETS	1	0.891	1			1	CLONAL	1	TRUE	0	0.177527389209199	0		1017	653	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	61	824	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	0.916	0.789	1	0.916	0.789	1	CLONAL	1	TRUE	1	0.177527389209199	2		824	750	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	76	701	5	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	0.177527389209199	2		706	718	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0020834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	111	768	3	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	0.991	1	CLONAL	3	TRUE	1	0.177527389209199	2		771	374	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0020834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	90	1158	4	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	0.177527389209199	5	FACETS	1	0.977	1	0.479	0.424	0.538	CLONAL	1	TRUE	2	0.177527389209199	5		1162	894	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0020834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	38	704	0	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.177527389209199	2		704	356	SUCCESS
APC	324	MSKCC	GRCh37	5	112177864	112177864	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs775076289	NA	P-0020834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	20	513	0	ENST00000257430.4:c.6579del	p.Val2194PhefsTer5	p.V2194Ffs*5	ENST00000257430	NM_000038.5	2191	ggA/gg	16/16	0.177527389209199	4	FACETS	1	0.864	1	0.398	0.305	0.506	CLONAL	1	TRUE	1	0.177527389209199	4		513	222	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0020834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	59	550	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.177527389209199	3	FACETS	0.986	0.852	1	0.986	0.852	1	CLONAL	2	TRUE	1	0.177527389209199	3		550	367	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101268	27101268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	62	917	3	ENST00000324856.7:c.4555del	p.Gln1519ArgfsTer8	p.Q1519Rfs*8	ENST00000324856	NM_006015.4	1517	gCc/gc	18/20	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.177527389209199	2		920	697	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497299	149497299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142762235	NA	P-0020834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	99	1080	4	ENST00000261799.4:c.3019G>A	p.Val1007Ile	p.V1007I	ENST00000261799	NM_002609.3	1007	Gtc/Atc	22/23	0.177527389209199	0	FACETS	1	0.976	1			1	CLONAL	1	TRUE	0	0.177527389209199	0		1084	689	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0020834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	106	1393	3	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	0.177509446936364	1	FACETS	0.966	0.863	1	0.966	0.863	1	CLONAL	1	TRUE	0	0.177527389209199	1		1396	1127	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36208923	36208925	+	start_lost,inframe_deletion	Translation_Start_Site	DEL	GGC	GGC	-	rs898578503	NA	P-0020834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	10	61	0	ENST00000222270.7:c.14_16del	p.Ala5?	p.A5?	ENST00000222270	NM_014727.1	1	atGGCg/atg	1/37	0.177509446936364	1	FACETS	0.63	0.427	0.883	0.63	0.427	0.883	SUBCLONAL	1	TRUE	0	0.177527389209199	1		61	163	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323362	31323363	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748204482	NA	P-0020834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	76	923	2	ENST00000412585.2:c.626dup	p.Thr211AspfsTer10	p.T211Dfs*10	ENST00000412585	NM_005514.6	209	cca/ccCa	4/8	0.177527389209199	4	FACETS	1	0.938	1	0.558	0.488	0.634	CLONAL	1	TRUE	2	0.177527389209199	4		925	903	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193205439	193205439	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	66	786	0	ENST00000367435.3:c.1370G>T	p.Trp457Leu	p.W457L	ENST00000367435	NM_024529.4	457	tGg/tTg	15/17	1	2	FACETS	0.94	0.815	1	0.94	0.815	1	CLONAL	1	TRUE	1	0.177527389209199	2		786	791	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418397	49418397	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	111	938	0	ENST00000301067.7:c.16016C>A	p.Ala5339Asp	p.A5339D	ENST00000301067	NM_003482.3	5339	gCc/gAc	50/54	0.177527389209199	5	FACETS	0.905	0.813	1	0.603	0.542	0.669	CLONAL	2	TRUE	2	0.177527389209199	5		938	875	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437711	49437713	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs886049482	NA	P-0020834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	91	1223	0	ENST00000301067.7:c.5257_5259del	p.Lys1753del	p.K1753del	ENST00000301067	NM_003482.3	1753	AAG/-	22/54	0.177527389209199	5	FACETS	1	0.976	1	0.468	0.415	0.526	CLONAL	1	TRUE	2	0.177527389209199	5		1223	924	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112910844	112910844	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs397507531	NA	P-0020834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	48	1058	0	ENST00000351677.2:c.853T>G	p.Phe285Val	p.F285V	ENST00000351677	NM_002834.3	285	Ttt/Gtt	7/16	0.144038471943041	0	FACETS	0.839	0.709	0.982			1	CLONAL	1	TRUE	0	0.177527389209199	0		1058	530	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729108	66729108	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752994941	NA	P-0020834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	58	1092	3	ENST00000307102.5:c.316G>A	p.Ala106Thr	p.A106T	ENST00000307102	NM_002755.3	106	Gca/Aca	3/11	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.177527389209199	2		1095	597	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857386	9857386	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs754686222	NA	P-0020834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	27	712	0	ENST00000330684.3:c.4015A>G	p.Lys1339Glu	p.K1339E	ENST00000330684	NM_001134407.1	1339	Aaa/Gaa	13/13	1	2	FACETS	0.991	0.79	1	0.991	0.79	1	CLONAL	1	TRUE	1	0.177527389209199	2		712	307	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508664	38508664	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	90	1253	0	ENST00000254066.5:c.712A>G	p.Lys238Glu	p.K238E	ENST00000254066	NM_000964.3	238	Aag/Gag	6/9	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.177527389209199	2		1253	919	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696345	47696345	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	49	627	1	ENST00000347630.2:c.478G>A	p.Glu160Lys	p.E160K	ENST00000347630	NM_001007230.1	160	Gag/Aag	6/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.177527389209199	2		628	402	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59878611	59878612	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	novel	NA	P-0020834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	22	500	0	ENST00000259008.2:c.1140+2_1140+3del		p.X380_splice	ENST00000259008	NM_032043.2	380			1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.177527389209199	2		500	209	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212113	36212113	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	53	833	0	ENST00000222270.7:c.1868del	p.Pro623GlnfsTer37	p.P623Qfs*37	ENST00000222270	NM_014727.1	622	Ccc/cc	3/37	0.177509446936364	1	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	0	0.177527389209199	1		833	536	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794104	42794104	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0020834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	40	570	0	ENST00000575354.2:c.1464+1G>A		p.X488_splice	ENST00000575354	NM_015125.3	488			0.177509446936364	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.177527389209199	1		570	345	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794123	242794123	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs751280778	NA	P-0020834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	75	1161	1	ENST00000334409.5:c.605C>A	p.Ala202Asp	p.A202D	ENST00000334409	NM_005018.2	202	gCc/gAc	4/5	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.177527389209199	2		1162	670	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169955	32169956	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	63	1178	0	ENST00000375023.3:c.3652dup	p.Ser1218PhefsTer17	p.S1218Ffs*17	ENST00000375023	NM_004557.3	1218	tct/tTct	21/30	0.177527389209199	4	FACETS	1	0.945	1	0.594	0.513	0.682	CLONAL	1	TRUE	2	0.177527389209199	4		1178	704	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967930	93967931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	25	891	0	ENST00000369303.4:c.1996dup	p.Thr666AsnfsTer17	p.T666Nfs*17	ENST00000369303	NM_004440.3	666	acc/aAcc	11/17	0.177527389209199	4	FACETS	0.721	0.567	0.899	0.36	0.283	0.45	SUBCLONAL	1	TRUE	2	0.177527389209199	4		891	460	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896493	151896493	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	30	756	0	ENST00000262189.6:c.4144A>G	p.Ser1382Gly	p.S1382G	ENST00000262189	NM_170606.2	1382	Agt/Ggt	27/59	0.177527389209199	4	FACETS	1	0.919	1	0.644	0.52	0.784	CLONAL	1	TRUE	2	0.177527389209199	4		756	309	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046453	69046453	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	56	939	0	ENST00000288368.4:c.3926A>G	p.Asp1309Gly	p.D1309G	ENST00000288368	NM_024870.2	1309	gAc/gGc	32/40	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.177527389209199	2		939	542	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742149	145742149	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0020834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	69	745	0	ENST00000428558.2:c.355-1G>T		p.X119_splice	ENST00000428558	NM_004260.3	119			1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.177527389209199	2		745	582	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249911	110249911	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	85	802	2	ENST00000374672.4:c.764C>A	p.Pro255His	p.P255H	ENST00000374672	NM_004235.4	255	cCt/cAt	3/5	1	2	FACETS	0.756	0.669	0.85	1	0.978	1	SUBCLONAL	2	TRUE	1	0.177527389209199	2		804	633	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300130	137300130	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140464195	NA	P-0020834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	52	1035	0	ENST00000481739.1:c.415G>A	p.Gly139Arg	p.G139R	ENST00000481739	NM_002957.4	139	Ggg/Agg	3/10	1	2	FACETS	0.778	0.661	0.907	0.778	0.661	0.907	CLONAL	1	TRUE	1	0.177527389209199	2		1035	753	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216561	108216561	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	355	646	0	ENST00000278616.4:c.8510A>G	p.Glu2837Gly	p.E2837G	ENST00000278616	NM_000051.3	2837	gAa/gGa	58/63	0.831811178378294	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.831811178378294	1		646	486	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515360	103515362	+	inframe_deletion	In_Frame_Del	DEL	CAG	CAG	-	novel	NA	P-0020902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	23	473	1	ENST00000355739.4:c.1864_1866del	p.Gln622del	p.Q622del	ENST00000355739	NM_000123.3	621	CAG/-	8/15	0.831811178378294	1	FACETS	0.076	0.059	0.096	0.076	0.059	0.096	SUBCLONAL	1	TRUE	0	0.831811178378294	1		474	426	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	28	463	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.06	2		463	849	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0020947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	35	883	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.06	2		883	1104	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0020947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	9	435	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.806	0.532	1	0.806	0.532	1	CLONAL	1	TRUE	1	0.06	2		435	372	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003252	42003253	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	109	833	0	ENST00000219905.7:c.2790dup	p.His931SerfsTer7	p.H931Sfs*7	ENST00000219905	NM_001164273.1	930	tct/tcTt	8/24	1	2	FACETS	0.704	0.635	0.775	0.704	0.635	0.775	SUBCLONAL	1	TRUE	1	0.664686112725454	2		833	466	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521196	187521197	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0020993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	339	855	0	ENST00000441802.2:c.11957_11958dup	p.Leu3987SerfsTer4	p.L3987Sfs*4	ENST00000441802	NM_005245.3	3986	-/AG	22/27	0.664686112725454	3	FACETS	0.936	0.892	0.98	0.936	0.892	0.98	CLONAL	2	TRUE	1	0.664686112725454	3		855	726	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932628	39932629	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0020993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	44	536	0	ENST00000378444.4:c.1970dup	p.Tyr657Ter	p.Y657*	ENST00000378444	NM_001123385.1	657	tac/taAc	4/15	1	1	FACETS	0.291	0.245	0.341	0.291	0.245	0.341	SUBCLONAL	1	TRUE	0	0.664686112725454	1		536	304	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0021128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	218	636	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.983	0.917	1	0.983	0.917	1	CLONAL	1	TRUE	1	0.573865793658945	2		636	773	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6442013	6442013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	45	337	0	ENST00000356142.4:c.572C>T	p.Ala191Val	p.A191V	ENST00000356142	NM_018890.3	191	gCg/gTg	7/7	1	2	FACETS	0.393	0.331	0.462	0.393	0.331	0.462	SUBCLONAL	1	TRUE	1	0.573865793658945	2		337	399	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002946	69002946	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146486437	NA	P-0021128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	54	296	0	ENST00000288368.4:c.2246C>T	p.Thr749Met	p.T749M	ENST00000288368	NM_024870.2	749	aCg/aTg	20/40	0.507678529334342	4	FACETS	0.556	0.475	0.644	0.278	0.237	0.322	SUBCLONAL	1	TRUE	2	0.573865793658945	4		296	533	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	220	635	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.79	2		635	555	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444000	49444000	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	292	852	8	ENST00000301067.7:c.3371del	p.Pro1124LeufsTer40	p.P1124Lfs*40	ENST00000301067	NM_003482.3	1124	cCt/ct	11/54	1	2	FACETS	0.971	0.919	1	0.971	0.919	1	CLONAL	1	TRUE	1	0.79	2		860	761	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0021283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	28	561	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.852	0.681	1	0.852	0.681	1	CLONAL	1	TRUE	1	0.15	2		561	438	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522598	157522598	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554236040	NA	P-0021283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	57	696	0	ENST00000346085.5:c.4870C>T	p.Arg1624Ter	p.R1624*	ENST00000346085	NM_020732.3	1624	Cga/Tga	18/20	1	2	FACETS	0.858	0.734	0.994	0.858	0.734	0.994	CLONAL	1	TRUE	1	0.15	2		696	886	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115727	108115727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747727055	NA	P-0021283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	17	267	0	ENST00000278616.4:c.875C>T	p.Pro292Leu	p.P292L	ENST00000278616	NM_000051.3	292	cCg/cTg	7/63	1	2	FACETS	1	0.833	1	1	0.833	1	CLONAL	1	TRUE	1	0.15	2		267	196	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193931	106193931	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1235228377	NA	P-0021283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	17	305	0	ENST00000380013.4:c.4393C>T	p.Arg1465Ter	p.R1465*	ENST00000380013	NM_001127208.2	1465	Cga/Tga	10/11	1	2	FACETS	0.693	0.517	0.903	0.693	0.517	0.903	SUBCLONAL	1	TRUE	1	0.15	2		305	327	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088659	27088659	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	59	1003	0	ENST00000324856.7:c.2272del	p.Gln758ArgfsTer75	p.Q758Rfs*75	ENST00000324856	NM_006015.4	756	aaC/aa	7/20	1	2	FACETS	0.825	0.708	0.954	0.825	0.708	0.954	CLONAL	1	TRUE	1	0.15	2		1003	953	SUCCESS
ATM	472	MSKCC	GRCh37	11	108099987	108099987	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs868748140	NA	P-0021283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	21	389	2	ENST00000278616.4:c.268A>G	p.Arg90Gly	p.R90G	ENST00000278616	NM_000051.3	90	Agg/Ggg	4/63	1	2	FACETS	0.776	0.597	0.985	0.776	0.597	0.985	CLONAL	1	TRUE	1	0.15	2		391	361	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210688	36210688	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	70	630	1	ENST00000222270.7:c.439C>T	p.Arg147Ter	p.R147*	ENST00000222270	NM_014727.1	147	Cga/Tga	3/37	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.15	2		631	747	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913224	39913224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769982436	NA	P-0021283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	51	668	0	ENST00000378444.4:c.4891G>A	p.Asp1631Asn	p.D1631N	ENST00000378444	NM_001123385.1	1631	Gat/Aat	14/15	1	2	FACETS	0.787	0.667	0.92	0.787	0.667	0.92	CLONAL	1	TRUE	1	0.15	2		668	864	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046674	42046674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780027483	NA	P-0021283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	39	627	0	ENST00000219905.7:c.7048G>A	p.Val2350Met	p.V2350M	ENST00000219905	NM_001164273.1	2350	Gtg/Atg	18/24	1	2	FACETS	0.78	0.645	0.931	0.78	0.645	0.931	CLONAL	1	TRUE	1	0.15	2		627	667	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639097	176639097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771467409	NA	P-0021283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	47	505	0	ENST00000439151.2:c.3697C>T	p.Arg1233Trp	p.R1233W	ENST00000439151	NM_022455.4	1233	Cgg/Tgg	5/23	1	2	FACETS	0.993	0.837	1	0.993	0.837	1	CLONAL	1	TRUE	1	0.15	2		505	631	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257980	16257980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761228108	NA	P-0021283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	32	483	1	ENST00000375759.3:c.5245G>A	p.Val1749Ile	p.V1749I	ENST00000375759	NM_015001.2	1749	Gta/Ata	11/15	1	2	FACETS	0.772	0.625	0.938	0.772	0.625	0.938	CLONAL	1	TRUE	1	0.15	2		484	553	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301849	65301849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1013552862	NA	P-0021283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	20	322	1	ENST00000342505.4:c.3190G>A	p.Val1064Ile	p.V1064I	ENST00000342505	NM_002227.2	1064	Gtc/Atc	23/25	1	2	FACETS	0.694	0.53	0.887	0.694	0.53	0.887	SUBCLONAL	1	TRUE	1	0.15	2		323	384	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488226	56488226	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	40	627	0	ENST00000267101.3:c.1745G>A	p.Gly582Glu	p.G582E	ENST00000267101	NM_001982.3	582	gGg/gAg	15/28	1	2	FACETS	0.811	0.672	0.966	0.811	0.672	0.966	CLONAL	1	TRUE	1	0.15	2		627	658	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194881	30194881	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0021283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	25	409	0	ENST00000331968.5:c.265-1G>A		p.X89_splice	ENST00000331968	NM_002742.2	89			1	2	FACETS	0.811	0.639	1	0.811	0.639	1	CLONAL	1	TRUE	1	0.15	2		409	411	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465522	99465522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	50	675	0	ENST00000268035.6:c.2347G>A	p.Asp783Asn	p.D783N	ENST00000268035	NM_000875.3	783	Gat/Aat	11/21	1	2	FACETS	0.88	0.744	1	0.88	0.744	1	CLONAL	1	TRUE	1	0.15	2		675	758	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619272	23619272	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	43	681	1	ENST00000261584.4:c.3263C>A	p.Pro1088His	p.P1088H	ENST00000261584	NM_024675.3	1088	cCt/cAt	12/13	1	2	FACETS	0.7	0.584	0.83	0.7	0.584	0.83	SUBCLONAL	1	TRUE	1	0.15	2		682	819	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655479	67655479	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs769948988	NA	P-0021283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	33	566	0	ENST00000264010.4:c.1342C>T	p.Arg448Ter	p.R448*	ENST00000264010	NM_006565.3	448	Cga/Tga	7/12	1	2	FACETS	0.876	0.713	1	0.876	0.713	1	CLONAL	1	TRUE	1	0.15	2		566	502	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170599	7170599	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556950372	NA	P-0021283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	52	724	1	ENST00000302850.5:c.1432C>T	p.Arg478Cys	p.R478C	ENST00000302850	NM_000208.2	478	Cgc/Tgc	6/22	1	2	FACETS	0.889	0.755	1	0.889	0.755	1	CLONAL	1	TRUE	1	0.15	2		725	780	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130273	11130273	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	34	497	0	ENST00000358026.2:c.2512C>A	p.Pro838Thr	p.P838T	ENST00000358026	NM_001128849.1	838	Cca/Aca	18/36	1	2	FACETS	0.815	0.665	0.985	0.815	0.665	0.985	CLONAL	1	TRUE	1	0.15	2		497	556	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905585	50905585	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs553342844	NA	P-0021283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	86	922	1	ENST00000440232.2:c.713C>T	p.Thr238Met	p.T238M	ENST00000440232	NM_002691.3	238	aCg/aTg	6/27	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.15	2		923	976	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028136	48028136	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782324	NA	P-0021283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	22	385	0	ENST00000234420.5:c.3014G>A	p.Arg1005Gln	p.R1005Q	ENST00000234420	NM_000179.2	1005	cGa/cAa	4/10	1	2	FACETS	0.876	0.679	1	0.876	0.679	1	CLONAL	1	TRUE	1	0.15	2		385	335	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163889	47163889	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	23	511	0	ENST00000409792.3:c.2237T>C	p.Phe746Ser	p.F746S	ENST00000409792	NM_014159.6	746	tTt/tCt	3/21	1	2	FACETS	0.702	0.546	0.883	0.702	0.546	0.883	SUBCLONAL	1	TRUE	1	0.15	2		511	437	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20486961	20486961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	26	459	0	ENST00000346618.3:c.926G>A	p.Gly309Asp	p.G309D	ENST00000346618	NM_001949.4	309	gGc/gAc	5/7	1	2	FACETS	0.705	0.557	0.875	0.705	0.557	0.875	SUBCLONAL	1	TRUE	1	0.15	2		459	492	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165085	32165085	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	41	585	0	ENST00000375023.3:c.5043G>T	p.Glu1681Asp	p.E1681D	ENST00000375023	NM_004557.3	1681	gaG/gaT	27/30	1	2	FACETS	0.781	0.649	0.929	0.781	0.649	0.929	CLONAL	1	TRUE	1	0.15	2		585	700	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499814	8499814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750362550	NA	P-0021283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	31	510	1	ENST00000356435.5:c.2155G>A	p.Glu719Lys	p.E719K	ENST00000356435		719	Gag/Aag	14/35	1	2	FACETS	0.685	0.553	0.836	0.685	0.553	0.836	SUBCLONAL	1	TRUE	1	0.15	2		511	603	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861493	152861493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1442543413	NA	P-0021283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	31	440	0	ENST00000406277.2:c.259C>T	p.Arg87Trp	p.R87W	ENST00000406277	NM_152274.4	87	Cgg/Tgg	4/7	1		FACETS		0.693	1				CLONAL	1	TRUE	1	0.15	2		440	482	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0021399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	60	671	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.641	0.552	0.737	0.641	0.552	0.737	SUBCLONAL	1	FALSE	1	0.322899747895285	2		671	580	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480483	57480483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	32	596	3	ENST00000371085.3:c.478C>T	p.Arg160Cys	p.R160C	ENST00000371085	NM_000516.4	160	Cgt/Tgt	6/13	1	2	FACETS	0.366	0.297	0.446	0.366	0.297	0.446	SUBCLONAL	1	FALSE	1	0.322899747895285	2		599	541	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509577	29509577	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	46	873	0	ENST00000356175.3:c.782A>G	p.Lys261Arg	p.K261R	ENST00000356175	NM_000267.3	261	aAa/aGa	8/57	1	2	FACETS	0.491	0.413	0.578	0.491	0.413	0.578	SUBCLONAL	1	FALSE	1	0.322899747895285	2		873	580	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797951	42797951	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	88	908	2	ENST00000575354.2:c.4007del	p.Pro1336ArgfsTer3	p.P1336Rfs*3	ENST00000575354	NM_015125.3	1335	Ccc/cc	16/20	1	2	FACETS	0.715	0.633	0.803	0.715	0.633	0.803	SUBCLONAL	1	FALSE	1	0.322899747895285	2		910	762	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794922	242794922	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568397742	NA	P-0021399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	54	964	4	ENST00000334409.5:c.287G>A	p.Arg96His	p.R96H	ENST00000334409	NM_005018.2	96	cGt/cAt	2/5	1	2	FACETS	0.474	0.404	0.551	0.474	0.404	0.551	SUBCLONAL	1	FALSE	1	0.322899747895285	2		968	706	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	188	671	0	ENST00000269305.4:c.596del	p.Gly199GlufsTer48	p.G199Efs*48	ENST00000269305	NM_001126112.2	199	gGa/ga	6/11	0.442758003712683	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.442758003712683	1		671	659	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36824376	36824376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748271039	NA	P-0021534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	153	744	1	ENST00000373129.3:c.160G>A	p.Ala54Thr	p.A54T	ENST00000373129	NM_032017.1	54	Gcg/Acg	4/12	0.442758003712683	1	FACETS	0.819	0.752	0.889	0.819	0.752	0.889	CLONAL	1	TRUE	0	0.442758003712683	1		745	657	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612254	1612254	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	98	706	0	ENST00000344749.5:c.1765C>A	p.Leu589Met	p.L589M	ENST00000344749	NM_001136139.2	589	Ctg/Atg	18/19	1	2	FACETS	0.889	0.796	0.987	0.889	0.796	0.987	CLONAL	1	TRUE	1	0.442758003712683	2		706	498	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604658	55604658	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778433	NA	P-0021534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	155	642	0	ENST00000288135.5:c.2866C>T	p.Arg956Trp	p.R956W	ENST00000288135	NM_000222.2	956	Cgg/Tgg	21/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.442758003712683	2		642	630	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0021830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	114	498	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.130175220948879	3	FACETS	1	0.97	1	0.6	0.54	0.663	INDETERMINATE	1	TRUE	1	0.31	3		498	708	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0021830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	75	739	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.31	2		739	466	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610128	43610128	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193922700	NA	P-0021830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	50	876	1	ENST00000355710.3:c.2080C>T	p.Arg694Trp	p.R694W	ENST00000355710	NM_020975.4	694	Cgg/Tgg	11/20	1	2	FACETS	0.6	0.509	0.7	0.6	0.509	0.7	SUBCLONAL	1	TRUE	1	0.31	2		877	538	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579366	7579367	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0021830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	76	976	0	ENST00000269305.4:c.320dup	p.Tyr107Ter	p.Y107*	ENST00000269305	NM_001126112.2	107	tac/taAc	4/11	0.3	1	FACETS	0.695	0.61	0.786	0.695	0.61	0.786	SUBCLONAL	1	TRUE	0	0.31	1		976	596	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	136	463	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.355247578981255	2		463	692	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	162	584	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.355247578981255	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.355247578981255	1		585	709	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1023835002	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	115	416	0	ENST00000558401.1:c.1A>G	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Gtg	1/4	1	2	FACETS	0.767	0.691	0.848	0.767	0.691	0.848	SUBCLONAL	1	TRUE	1	0.355247578981255	2		416	844	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807378	36807378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780818464	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	47	735	0	ENST00000373129.3:c.1286C>T	p.Ala429Val	p.A429V	ENST00000373129	NM_032017.1	429	gCg/gTg	12/12	1	2	FACETS	0.316	0.266	0.372	0.316	0.266	0.372	SUBCLONAL	1	TRUE	1	0.355247578981255	2		735	837	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39321494	39321494	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	102	670	0	ENST00000373001.3:c.527T>C	p.Phe176Ser	p.F176S	ENST00000373001	NM_022157.3	176	tTt/tCt	3/7	1	2	FACETS	0.826	0.739	0.918	0.826	0.739	0.918	CLONAL	1	TRUE	1	0.355247578981255	2		670	695	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363405	40363405	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs960529105	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	146	705	0	ENST00000397332.2:c.824A>G	p.Glu275Gly	p.E275G	ENST00000397332	NM_001033082.2	275	gAa/gGa	3/3	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.355247578981255	2		705	821	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796909	45796909	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764276907	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	124	592	2	ENST00000450313.1:c.1421G>A	p.Arg474His	p.R474H	ENST00000450313	NM_012222.2	474	cGc/cAc	14/16	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.355247578981255	2		594	669	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743550	46743550	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	60	585	0	ENST00000371975.4:c.1931G>A	p.Cys644Tyr	p.C644Y	ENST00000371975	NM_003579.3	644	tGt/tAt	17/18	1	2	FACETS	0.514	0.442	0.592	0.514	0.442	0.592	SUBCLONAL	1	TRUE	1	0.355247578981255	2		585	657	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313336	65313336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1163622258	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	96	588	0	ENST00000342505.4:c.1778C>T	p.Thr593Met	p.T593M	ENST00000342505	NM_002227.2	593	aCg/aTg	13/25	1	2	FACETS	0.772	0.688	0.861	0.772	0.688	0.861	SUBCLONAL	1	TRUE	1	0.355247578981255	2		588	700	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456728	32456728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	66	523	0	ENST00000332351.3:c.164G>A	p.Gly55Asp	p.G55D	ENST00000332351	NM_024426.4	55	gGc/gAc	1/10	1	2	FACETS	0.589	0.511	0.673	0.589	0.511	0.673	SUBCLONAL	1	TRUE	1	0.355247578981255	2		523	631	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137706	64137706	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	97	736	0	ENST00000334205.4:c.1807C>G	p.Leu603Val	p.L603V	ENST00000334205	NM_003942.2	603	Ctg/Gtg	15/17	1	2	FACETS	0.753	0.672	0.84	0.753	0.672	0.84	SUBCLONAL	1	TRUE	1	0.355247578981255	2		736	725	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574512	64574512	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1046929915	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	147	697	2	ENST00000312049.6:c.883C>T	p.Arg295Trp	p.R295W	ENST00000312049	NM_130799.2	295	Cgg/Tgg	6/10	1	2	FACETS	0.992	0.906	1	0.992	0.906	1	CLONAL	1	TRUE	1	0.355247578981255	2		699	834	SUCCESS
EED	8726	MSKCC	GRCh37	11	85956318	85956318	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	122	320	1	ENST00000263360.6:c.47C>A	p.Pro16His	p.P16H	ENST00000263360	NM_003797.3	16	cCt/cAt	1/12	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.355247578981255	2		321	608	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981731	101981731	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	120	307	1	ENST00000282441.5:c.152G>T	p.Gly51Val	p.G51V	ENST00000282441	NM_001130145.2	51	gGg/gTg	1/9	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.355247578981255	2		308	547	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373226	118373226	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150570074	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	112	469	1	ENST00000534358.1:c.6619C>T	p.Arg2207Trp	p.R2207W	ENST00000534358	NM_005933.3	2207	Cgg/Tgg	27/36	NA	2	FACETS	0.963	0.867	1			1	INDETERMINATE	1	TRUE	NA	0.355247578981255	2		470	655	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417006	417006	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	130	496	1	ENST00000399788.2:c.3544G>T	p.Asp1182Tyr	p.D1182Y	ENST00000399788	NM_001042603.1	1182	Gac/Tac	23/28	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.355247578981255	2		497	679	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	464349	464349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772720111	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	129	720	2	ENST00000399788.2:c.845G>A	p.Arg282Gln	p.R282Q	ENST00000399788	NM_001042603.1	282	cGg/cAg	7/28	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.355247578981255	2		722	655	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231404	46231404	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	75	557	0	ENST00000334344.6:c.1244T>C	p.Val415Ala	p.V415A	ENST00000334344	NM_152641.2	415	gTa/gCa	10/21	1	2	FACETS	0.75	0.658	0.849	0.75	0.658	0.849	SUBCLONAL	1	TRUE	1	0.355247578981255	2		557	563	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422933	49422933	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372296816	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	145	797	1	ENST00000301067.7:c.14162G>A	p.Arg4721His	p.R4721H	ENST00000301067	NM_003482.3	4721	cGt/cAt	44/54	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.355247578981255	2		798	774	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445976	49445976	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371421459	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	196	918	1	ENST00000301067.7:c.1490C>T	p.Pro497Leu	p.P497L	ENST00000301067	NM_003482.3	497	cCg/cTg	10/54	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.355247578981255	2		919	1097	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50483719	50483719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746898820	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	124	570	0	ENST00000394963.4:c.824C>T	p.Pro275Leu	p.P275L	ENST00000394963	NM_003076.4	275	cCg/cTg	7/13	1	2	FACETS	0.94	0.851	1	0.94	0.851	1	CLONAL	1	TRUE	1	0.355247578981255	2		570	743	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56477655	56477655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142735651	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	175	674	0	ENST00000267101.3:c.203C>T	p.Thr68Met	p.T68M	ENST00000267101	NM_001982.3	68	aCg/aTg	2/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.355247578981255	2		674	819	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679204	88679204	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs758497443	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	123	717	0	ENST00000360948.2:c.833A>G	p.Asn278Ser	p.N278S	ENST00000360948	NM_001012338.2	278	aAt/aGt	8/19	1	2	FACETS	0.857	0.775	0.944	0.857	0.775	0.944	CLONAL	1	TRUE	1	0.355247578981255	2		717	808	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094723	2094723	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs374489979	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	126	615	1	ENST00000219066.1:c.457C>T	p.Arg153Ter	p.R153*	ENST00000219066	NM_002528.5	153	Cga/Tga	3/6	1	2	FACETS	0.94	0.851	1	0.94	0.851	1	CLONAL	1	TRUE	1	0.355247578981255	2		616	755	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639203	3639203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745883026	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	164	727	2	ENST00000294008.3:c.4436G>A	p.Arg1479Gln	p.R1479Q	ENST00000294008	NM_032444.2	1479	cGa/cAa	12/15	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.355247578981255	2		729	893	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789623	3789623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	108	606	0	ENST00000262367.5:c.4236G>A	p.Met1412Ile	p.M1412I	ENST00000262367	NM_004380.2	1412	atG/atA	25/31	1	2	FACETS	0.876	0.787	0.97	0.876	0.787	0.97	CLONAL	1	TRUE	1	0.355247578981255	2		606	694	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821482	72821482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778895240	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	145	758	1	ENST00000268489.5:c.10693G>A	p.Ala3565Thr	p.A3565T	ENST00000268489	NM_006885.3	3565	Gcc/Acc	10/10	1	2	FACETS	0.855	0.779	0.934	0.855	0.779	0.934	CLONAL	1	TRUE	1	0.355247578981255	2		759	955	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627217	37627217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370304179	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	134	715	0	ENST00000447079.4:c.1132C>T	p.Arg378Cys	p.R378C	ENST00000447079	NM_015083.1	378	Cgc/Tgc	2/14	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.355247578981255	2		715	661	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913315	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	188	652	2	ENST00000326873.7:c.580G>A	p.Asp194Asn	p.D194N	ENST00000326873	NM_000455.4	194	Gac/Aac	4/10	0.355247578981255	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.355247578981255	1		654	640	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971771	18971771	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	108	558	1	ENST00000262803.5:c.2437C>A	p.Leu813Met	p.L813M	ENST00000262803	NM_002911.3	813	Ctg/Atg	17/24	0.298966287732035	1	FACETS	0.694	0.624	0.77	0.694	0.624	0.77	SUBCLONAL	1	TRUE	0	0.355247578981255	1		559	720	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221328	36221328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1308156549	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	165	852	3	ENST00000222270.7:c.5162C>T	p.Thr1721Met	p.T1721M	ENST00000222270	NM_014727.1	1721	aCg/aTg	24/37	1	2	FACETS	0.959	0.88	1	0.959	0.88	1	CLONAL	1	TRUE	1	0.355247578981255	2		855	969	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753218	42753218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144812092	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	161	809	2	ENST00000222329.4:c.1046C>T	p.Pro349Leu	p.P349L	ENST00000222329	NM_006494.2	349	cCg/cTg	4/4	1	2	FACETS	0.967	0.887	1	0.967	0.887	1	CLONAL	1	TRUE	1	0.355247578981255	2		811	937	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910259	50910259	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1043752384	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	111	632	0	ENST00000440232.2:c.1514G>A	p.Arg505His	p.R505H	ENST00000440232	NM_002691.3	505	cGc/cAc	13/27	1	2	FACETS	0.86	0.773	0.951	0.86	0.773	0.951	CLONAL	1	TRUE	1	0.355247578981255	2		632	727	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464450	25464450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369713081	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	104	538	2	ENST00000264709.3:c.2063G>A	p.Arg688His	p.R688H	ENST00000264709	NM_175629.2	688	cGc/cAc	17/23	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.355247578981255	2		540	556	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39214733	39214733	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	28	361	0	ENST00000402219.2:c.3392-1G>T		p.X1131_splice	ENST00000402219	NM_005633.3	1131			1	2	FACETS	0.325	0.259	0.4	0.325	0.259	0.4	SUBCLONAL	1	TRUE	1	0.355247578981255	2		361	485	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	rs267608078	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	61	558	0	ENST00000234420.5:c.3260_3261dup	p.Phe1088ProfsTer3	p.F1088Pfs*3	ENST00000234420	NM_000179.2	1085	acc/aCCcc	5/10	1	2	FACETS	0.504	0.434	0.58	0.504	0.434	0.58	SUBCLONAL	1	TRUE	1	0.355247578981255	2		558	682	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99169362	99169362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	106	511	0	ENST00000074304.5:c.1292G>A	p.Arg431Gln	p.R431Q	ENST00000074304	NM_001134224.1	431	cGg/cAg	15/26	1	2	FACETS	0.988	0.888	1	0.988	0.888	1	CLONAL	1	TRUE	1	0.355247578981255	2		511	604	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251659	212251659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139785964	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	124	465	0	ENST00000342788.4:c.3400G>A	p.Val1134Met	p.V1134M	ENST00000342788	NM_005235.2	1134	Gtg/Atg	27/28	1	2	FACETS	0.897	0.812	0.987	0.897	0.812	0.987	CLONAL	1	TRUE	1	0.355247578981255	2		465	778	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41818301	41818301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388377310	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	11	52	0	ENST00000373198.4:c.73G>A	p.Ala25Thr	p.A25T	ENST00000373198	NM_133170.3	25	Gct/Act	1/32	1	2	FACETS	1	0.813	1	1	0.813	1	CLONAL	1	TRUE	1	0.355247578981255	2		52	51	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573977	41573977	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201569846	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	126	518	0	ENST00000263253.7:c.6262C>T	p.Arg2088Trp	p.R2088W	ENST00000263253	NM_001429.3	2088	Cgg/Tgg	31/31	1	2	FACETS	0.952	0.863	1	0.952	0.863	1	CLONAL	1	TRUE	1	0.355247578981255	2		518	745	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188278	10188278	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	85	725	0	ENST00000256474.2:c.421A>G	p.Asn141Asp	p.N141D	ENST00000256474	NM_000551.3	141	Aat/Gat	2/3	1	2	FACETS	0.572	0.505	0.645	0.572	0.505	0.645	SUBCLONAL	1	TRUE	1	0.355247578981255	2		725	836	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715721	30715721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893816	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	36	411	0	ENST00000295754.5:c.1379G>A	p.Arg460His	p.R460H	ENST00000295754	NM_003242.5	460	cGc/cAc	5/7	1	2	FACETS	0.348	0.285	0.419	0.348	0.285	0.419	SUBCLONAL	1	TRUE	1	0.355247578981255	2		411	582	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732985	30732985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	95	434	0	ENST00000295754.5:c.1598G>A	p.Cys533Tyr	p.C533Y	ENST00000295754	NM_003242.5	533	tGt/tAt	7/7	1	2	FACETS	0.894	0.798	0.997	0.894	0.798	0.997	CLONAL	1	TRUE	1	0.355247578981255	2		434	598	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084146	47084146	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	142	600	0	ENST00000409792.3:c.7143del	p.Ser2382LeufsTer29	p.S2382Lfs*29	ENST00000409792	NM_014159.6	2381	ccC/cc	17/21	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.355247578981255	2		600	753	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162959	47162959	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776300341	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	116	492	0	ENST00000409792.3:c.3167C>T	p.Ser1056Leu	p.S1056L	ENST00000409792	NM_014159.6	1056	tCg/tTg	3/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.355247578981255	2		492	565	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427726	72427726	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	114	449	0	ENST00000477973.2:c.764T>C	p.Val255Ala	p.V255A	ENST00000477973	NM_012234.5	255	gTc/gCc	4/4	1	2	FACETS	0.944	0.851	1	0.944	0.851	1	CLONAL	1	TRUE	1	0.355247578981255	2		449	680	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665045	138665045	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	38	122	0	ENST00000330315.3:c.520G>T	p.Gly174Cys	p.G174C	ENST00000330315	NM_023067.3	174	Ggc/Tgc	1/1	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.355247578981255	2		122	158	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916646	178916646	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	35	391	0	ENST00000263967.3:c.33G>T	p.Trp11Cys	p.W11C	ENST00000263967	NM_006218.2	11	tgG/tgT	2/21	1	2	FACETS	0.411	0.336	0.494	0.411	0.336	0.494	SUBCLONAL	1	TRUE	1	0.355247578981255	2		391	480	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191158	185191158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1267105230	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	118	544	2	ENST00000265026.3:c.2039G>A	p.Arg680Gln	p.R680Q	ENST00000265026	NM_004721.4	680	cGg/cAg	11/14	1	2	FACETS	0.961	0.869	1	0.961	0.869	1	CLONAL	1	TRUE	1	0.355247578981255	2		546	691	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156639	55156639	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768291477	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	146	622	3	ENST00000257290.5:c.3040G>A	p.Ala1014Thr	p.A1014T	ENST00000257290	NM_006206.4	1014	Gct/Act	22/23	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.355247578981255	2		625	740	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31468079	31468079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	133	666	0	ENST00000344624.3:c.2333G>A	p.Arg778His	p.R778H	ENST00000344624		778	cGc/cAc	15/33	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.355247578981255	2		666	729	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593424	67593424	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764019194	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	72	272	0	ENST00000274335.5:c.2170C>T	p.Arg724Ter	p.R724*	ENST00000274335		724	Cga/Tga	15/15	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.355247578981255	2		272	382	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950706	79950706	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	24	189	1	ENST00000265081.6:c.160G>A	p.Ala54Thr	p.A54T	ENST00000265081	NM_002439.4	54	Gct/Act	1/24	1	2	FACETS	0.477	0.375	0.595	0.477	0.375	0.595	SUBCLONAL	1	TRUE	1	0.355247578981255	2		190	283	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053156	180053156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1333005497	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	109	686	2	ENST00000261937.6:c.1213G>A	p.Ala405Thr	p.A405T	ENST00000261937	NM_182925.4	405	Gct/Act	9/30	1	2	FACETS	0.872	0.783	0.965	0.872	0.783	0.965	CLONAL	1	TRUE	1	0.355247578981255	2		688	704	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286790	33286790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752093917	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	98	501	0	ENST00000374542.5:c.2147G>A	p.Arg716Gln	p.R716Q	ENST00000374542	NM_001141970.1	716	cGg/cAg	7/8	1	2	FACETS	0.828	0.74	0.923	0.828	0.74	0.923	CLONAL	1	TRUE	1	0.355247578981255	2		501	666	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729400	41729400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	146	640	0	ENST00000242208.4:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000242208	NM_002192.2	377	Cgc/Tgc	3/3	1	2	FACETS	0.945	0.862	1	0.945	0.862	1	CLONAL	1	TRUE	1	0.355247578981255	2		640	870	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444275	50444275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	65	382	1	ENST00000331340.3:c.205C>T	p.Arg69Cys	p.R69C	ENST00000331340	NM_006060.4	69	Cgt/Tgt	4/8	1	2	FACETS	0.728	0.632	0.831	0.728	0.632	0.831	SUBCLONAL	1	TRUE	1	0.355247578981255	2		383	503	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418896	116418896	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	159	534	0	ENST00000397752.3:c.3407A>G	p.His1136Arg	p.H1136R	ENST00000397752	NM_000245.2	1136	cAt/cGt	17/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.355247578981255	2		534	726	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845485	128845485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779548739	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	56	695	1	ENST00000249373.3:c.782G>A	p.Arg261His	p.R261H	ENST00000249373	NM_005631.4	261	cGc/cAc	4/12	1	2	FACETS	0.408	0.349	0.474	0.408	0.349	0.474	SUBCLONAL	1	TRUE	1	0.355247578981255	2		696	772	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151919086	151919086	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	54	372	0	ENST00000262189.6:c.3499G>T	p.Asp1167Tyr	p.D1167Y	ENST00000262189	NM_170606.2	1167	Gac/Tac	22/59	1	2	FACETS	0.727	0.623	0.841	0.727	0.623	0.841	SUBCLONAL	1	TRUE	1	0.355247578981255	2		372	418	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282214	38282214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121909645	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	130	548	0	ENST00000425967.3:c.842G>A	p.Arg281Gln	p.R281Q	ENST00000425967	NM_001174067.1	281	cGg/cAg	8/19	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.355247578981255	2		548	651	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995482	68995482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	27	578	0	ENST00000288368.4:c.1886G>A	p.Gly629Asp	p.G629D	ENST00000288368	NM_024870.2	629	gGc/gAc	18/40	1	2	FACETS	0.311	0.247	0.385	0.311	0.247	0.385	SUBCLONAL	1	TRUE	1	0.355247578981255	2		578	489	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5522559	5522559	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	80	540	1	ENST00000397747.3:c.13C>A	p.Leu5Met	p.L5M	ENST00000397747	NM_025239.3	5	Ctg/Atg	2/7	1	2	FACETS	0.851	0.751	0.959	0.851	0.751	0.959	CLONAL	1	TRUE	1	0.355247578981255	2		541	529	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360705	70360705	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1210702033	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	25	122	0	ENST00000374080.3:c.6265C>T	p.Arg2089Trp	p.R2089W	ENST00000374080		2089	Cgg/Tgg	42/45	0.355247578981255	1	FACETS	0.845	0.675	1	0.845	0.675	1	CLONAL	1	TRUE	0	0.355247578981255	1		122	137	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955126	17955126	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	53	776	0	ENST00000458235.1:c.101G>C	p.Gly34Ala	p.G34A	ENST00000458235	NM_000215.3	34	gGc/gCc	2/24	0.334691717899526	2	FACETS	0.377	0.32	0.439	0.188	0.16	0.22	SUBCLONAL	1	TRUE	0	0.355247578981255	2		776	792	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0022031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	311	560	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.318664089231341	3	FACETS	0.872	0.829	0.914	1	0.994	1	CLONAL	3	FALSE	1	0.45213025626494	3		560	645	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0022031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	124	519	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.45213025626494	2		519	504	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070608	67070608	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	89	396	0	ENST00000412916.2:c.232C>T	p.Arg78Ter	p.R78*	ENST00000412916		78	Cga/Tga	3/6	0.45213025626494	1	FACETS	0.983	0.881	1	0.983	0.881	1	CLONAL	1	FALSE	0	0.45213025626494	1		396	310	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138094	2138099	+	inframe_deletion	In_Frame_Del	DEL	ACCGCA	ACCGCA	-	novel	NA	P-0022126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	162	875	0	ENST00000219476.3:c.5117_5122del	p.Arg1706_Asn1707del	p.R1706_N1707del	ENST00000219476	NM_000548.3	1705	gACCGCAac/gac	40/42	0.57063883765488	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.57063883765488	1		875	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579546	7579547	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0022126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	235	728	0	ENST00000269305.4:c.140dup	p.Asp48GlyfsTer4	p.D48Gfs*4	ENST00000269305	NM_001126112.2	47	ccg/ccCg	4/11	0.57063883765488	2	FACETS	0.865	0.817	0.913	0.865	0.817	0.913	CLONAL	2	TRUE	0	0.57063883765488	2		728	476	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922130	39922130	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	21	855	0	ENST00000378444.4:c.4042C>T	p.Gln1348Ter	p.Q1348*	ENST00000378444	NM_001123385.1	1348	Cag/Tag	9/15	0.57063883765488	1	FACETS	0.134	0.102	0.17	0.134	0.102	0.17	SUBCLONAL	1	TRUE	0	0.57063883765488	1		855	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0022185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	348	656	4	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.748638605062417	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.748638605062417	1		660	572	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888165	112888165	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397507510	NA	P-0022185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	38	845	2	ENST00000351677.2:c.181G>T	p.Asp61Tyr	p.D61Y	ENST00000351677	NM_002834.3	61	Gat/Tat	3/16	1	2	FACETS	0.129	0.106	0.156	0.129	0.106	0.156	SUBCLONAL	1	TRUE	1	0.748638605062417	2		847	784	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191490	185191490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372313966	NA	P-0022185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	443	911	1	ENST00000265026.3:c.2371G>A	p.Gly791Ser	p.G791S	ENST00000265026	NM_004721.4	791	Ggc/Agc	11/14	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.748638605062417	2		912	1072	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099229	4099229	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs562352756	NA	P-0022185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	47	802	1	ENST00000262948.5:c.889C>T	p.Arg297Trp	p.R297W	ENST00000262948	NM_030662.3	297	Cgg/Tgg	7/11	0.748638605062417	1	FACETS	0.152	0.128	0.179	0.152	0.128	0.179	SUBCLONAL	1	TRUE	0	0.748638605062417	1		803	516	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0022246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	898	463	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.40960683767288	10	FACETS	1	0.988	1	0.898	0.874	0.922	CLONAL	7	TRUE	2	0.40960683767288	10		463	1610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0022246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	212	617	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.36857216558762	2	FACETS	0.96	0.9	1	0.96	0.9	1	CLONAL	2	TRUE	0	0.40960683767288	2		617	539	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	59	1119	9	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	1	2	FACETS	0.331	0.284	0.383	0.331	0.284	0.383	SUBCLONAL	1	TRUE	1	0.328791733332761	2		1128	1084	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	48	366	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.396	0.334	0.465	0.396	0.334	0.465	SUBCLONAL	1	TRUE	1	0.328791733332761	2		366	737	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	57	701	5	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.5	0.428	0.578	0.5	0.428	0.578	SUBCLONAL	1	TRUE	1	0.328791733332761	2		706	694	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	56	533	3	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.679	0.582	0.784	0.679	0.582	0.784	SUBCLONAL	1	TRUE	1	0.328791733332761	2		536	502	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	57	668	3	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.361	0.308	0.418	0.361	0.308	0.418	SUBCLONAL	1	TRUE	1	0.328791733332761	2		671	961	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	214	1158	4	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.328791733332761	2		1162	1161	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	143	704	0	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.328791733332761	2		704	743	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905543	50905543	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373001984	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	81	1017	1	ENST00000440232.2:c.671G>A	p.Arg224His	p.R224H	ENST00000440232	NM_002691.3	224	cGc/cAc	6/27	1	2	FACETS	0.45	0.395	0.509	0.45	0.395	0.509	SUBCLONAL	1	TRUE	1	0.328791733332761	2		1018	1096	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260837	16260837	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	87	704	1	ENST00000375759.3:c.8102C>T	p.Thr2701Met	p.T2701M	ENST00000375759	NM_015001.2	2701	aCg/aTg	11/15	1	2	FACETS	0.688	0.609	0.773	0.688	0.609	0.773	SUBCLONAL	1	TRUE	1	0.328791733332761	2		705	769	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	125	608	0	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.328791733332761	2		608	674	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935322	36935323	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs747437399	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	186	432	2	ENST00000361632.4:c.1404dup	p.Ser469GlnfsTer5	p.S469Qfs*5	ENST00000361632		468	-/C	10/16	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.328791733332761	2		434	1121	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466515	120466515	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	51	792	0	ENST00000256646.2:c.4604C>T	p.Ala1535Val	p.A1535V	ENST00000256646	NM_024408.3	1535	gCt/gTt	26/34	1	2	FACETS	0.327	0.277	0.382	0.327	0.277	0.382	SUBCLONAL	1	TRUE	1	0.328791733332761	2		792	949	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	107	797	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	1	2	FACETS	0.747	0.67	0.83	0.747	0.67	0.83	SUBCLONAL	1	TRUE	1	0.328791733332761	2		797	871	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137077	64137077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	50	651	0	ENST00000334205.4:c.1588G>A	p.Asp530Asn	p.D530N	ENST00000334205	NM_003942.2	530	Gac/Aac	13/17	1	2	FACETS	0.43	0.364	0.502	0.43	0.364	0.502	SUBCLONAL	1	TRUE	1	0.328791733332761	2		651	708	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625218	69625218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1168737490	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	194	972	1	ENST00000334134.2:c.575G>A	p.Arg192Gln	p.R192Q	ENST00000334134	NM_005247.2	192	cGg/cAg	3/3	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.328791733332761	2		973	995	SUCCESS
EED	8726	MSKCC	GRCh37	11	85963230	85963230	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	50	582	0	ENST00000263360.6:c.308G>T	p.Trp103Leu	p.W103L	ENST00000263360	NM_003797.3	103	tGg/tTg	3/12	1	2	FACETS	0.757	0.643	0.88	0.757	0.643	0.88	SUBCLONAL	1	TRUE	1	0.328791733332761	2		582	402	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922257	100922257	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	25	561	0	ENST00000325455.5:c.2255A>G	p.Gln752Arg	p.Q752R	ENST00000325455	NM_001202474.3	752	cAg/cGg	5/8	1	2	FACETS	0.333	0.262	0.416	0.333	0.262	0.416	SUBCLONAL	1	TRUE	1	0.328791733332761	2		561	456	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139269	108139269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782298	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	59	938	2	ENST00000278616.4:c.2771G>A	p.Arg924Gln	p.R924Q	ENST00000278616	NM_000051.3	924	cGg/cAg	18/63	1	2	FACETS	0.399	0.342	0.462	0.399	0.342	0.462	SUBCLONAL	1	TRUE	1	0.328791733332761	2		940	899	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343712	118343712	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782339326	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	131	614	0	ENST00000534358.1:c.1838G>A	p.Arg613Gln	p.R613Q	ENST00000534358	NM_005933.3	613	cGa/cAa	3/36	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.328791733332761	2		614	707	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369140	118369140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	37	545	0	ENST00000534358.1:c.5858G>A	p.Cys1953Tyr	p.C1953Y	ENST00000534358	NM_005933.3	1953	tGc/tAc	22/36	1	2	FACETS	0.337	0.277	0.405	0.337	0.277	0.405	SUBCLONAL	1	TRUE	1	0.328791733332761	2		545	668	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371737	118371737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	98	406	0	ENST00000534358.1:c.6194G>A	p.Arg2065His	p.R2065H	ENST00000534358	NM_005933.3	2065	cGc/cAc	25/36	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.328791733332761	2		406	504	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426973	49426973	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1565778024	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	158	730	1	ENST00000301067.7:c.11515del	p.Gln3839SerfsTer42	p.Q3839Sfs*42	ENST00000301067	NM_003482.3	3839	Cag/ag	39/54	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.328791733332761	2		731	827	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427171	49427171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	136	985	1	ENST00000301067.7:c.11317C>T	p.Pro3773Ser	p.P3773S	ENST00000301067	NM_003482.3	3773	Ccc/Tcc	39/54	1	2	FACETS	0.756	0.686	0.83	0.756	0.686	0.83	SUBCLONAL	1	TRUE	1	0.328791733332761	2		986	1094	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924315	112924315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1355732645	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	64	949	2	ENST00000351677.2:c.1261C>T	p.Arg421Trp	p.R421W	ENST00000351677	NM_002834.3	421	Cgg/Tgg	11/16	1	2	FACETS	0.391	0.337	0.449	0.391	0.337	0.449	SUBCLONAL	1	TRUE	1	0.328791733332761	2		951	996	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	161	916	21	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.955	0.875	1	0.955	0.875	1	CLONAL	1	TRUE	1	0.328791733332761	2		937	1025	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220011	133220011	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	139	738	0	ENST00000320574.5:c.4426T>C	p.Phe1476Leu	p.F1476L	ENST00000320574	NM_006231.2	1476	Ttc/Ctc	34/49	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.328791733332761	2		738	835	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562178	21562178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775892552	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	225	1435	1	ENST00000382592.4:c.1741C>T	p.Arg581Cys	p.R581C	ENST00000382592	NM_014572.2	581	Cgc/Tgc	4/8	1	2	FACETS	0.956	0.888	1	0.956	0.888	1	CLONAL	1	TRUE	1	0.328791733332761	2		1436	1432	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563296	21563296	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	82	1111	0	ENST00000382592.4:c.623C>T	p.Pro208Leu	p.P208L	ENST00000382592	NM_014572.2	208	cCg/cTg	4/8	1	2	FACETS	0.431	0.379	0.488	0.431	0.379	0.488	SUBCLONAL	1	TRUE	1	0.328791733332761	2		1111	1157	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907230	32907230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659513	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	60	602	0	ENST00000380152.3:c.1615G>A	p.Gly539Arg	p.G539R	ENST00000380152		539	Gga/Aga	10/27	1	2	FACETS	0.617	0.531	0.71	0.617	0.531	0.71	SUBCLONAL	1	TRUE	1	0.328791733332761	2		602	592	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103513869	103513869	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	65	462	0	ENST00000355739.4:c.685T>G	p.Phe229Val	p.F229V	ENST00000355739	NM_000123.3	229	Ttt/Gtt	7/15	1	2	FACETS	0.848	0.737	0.968	0.848	0.737	0.968	CLONAL	1	TRUE	1	0.328791733332761	2		462	466	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434477	110434477	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747968639	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	70	780	1	ENST00000375856.3:c.3924del	p.Pro1309ArgfsTer22	p.P1309Rfs*22	ENST00000375856	NM_003749.2	1308	ggG/gg	1/2	1	2	FACETS	0.536	0.466	0.611	0.536	0.466	0.611	SUBCLONAL	1	TRUE	1	0.328791733332761	2		781	795	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457692	67457692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs548756379	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	111	874	0	ENST00000327367.4:c.502G>A	p.Ala168Thr	p.A168T	ENST00000327367	NM_005902.3	168	Gca/Aca	3/9	1	2	FACETS	0.784	0.704	0.869	0.784	0.704	0.869	SUBCLONAL	1	TRUE	1	0.328791733332761	2		874	861	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129568	2129568	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776855601	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	64	856	0	ENST00000219476.3:c.3295G>A	p.Gly1099Arg	p.G1099R	ENST00000219476	NM_000548.3	1099	Ggg/Agg	29/42	1	2	FACETS	0.393	0.339	0.452	0.393	0.339	0.452	SUBCLONAL	1	TRUE	1	0.328791733332761	2		856	990	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777792	3777792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200566758	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	167	1268	0	ENST00000262367.5:c.7256C>T	p.Ala2419Val	p.A2419V	ENST00000262367	NM_004380.2	2419	gCg/gTg	31/31	1	2	FACETS	0.749	0.686	0.815	0.749	0.686	0.815	SUBCLONAL	1	TRUE	1	0.328791733332761	2		1268	1357	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831211	3831212	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	108	527	0	ENST00000262367.5:c.1669dup	p.Ala557GlyfsTer14	p.A557Gfs*14	ENST00000262367	NM_004380.2	557	gcc/gGcc	7/31	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.328791733332761	2		527	599	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671654	67671655	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	39	636	1	ENST00000264010.4:c.2070dup	p.Glu691ArgfsTer5	p.E691Rfs*5	ENST00000264010	NM_006565.3	688	gta/gtAa	12/12	1	2	FACETS	0.327	0.27	0.391	0.327	0.27	0.391	SUBCLONAL	1	TRUE	1	0.328791733332761	2		637	726	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822609	72822609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771122441	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	47	784	1	ENST00000268489.5:c.9566C>T	p.Ala3189Val	p.A3189V	ENST00000268489	NM_006885.3	3189	gCg/gTg	10/10	1	2	FACETS	0.319	0.268	0.376	0.319	0.268	0.376	SUBCLONAL	1	TRUE	1	0.328791733332761	2		785	896	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81941375	81941375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1031437038	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	101	539	0	ENST00000359376.3:c.1553C>T	p.Pro518Leu	p.P518L	ENST00000359376	NM_002661.3	518	cCc/cTc	16/33	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.328791733332761	2		539	600	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351682	89351682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	137	998	2	ENST00000301030.4:c.1268G>A	p.Gly423Glu	p.G423E	ENST00000301030	NM_001256183.1	423	gGa/gAa	9/13	1	2	FACETS	0.741	0.672	0.813	0.741	0.672	0.813	SUBCLONAL	1	TRUE	1	0.328791733332761	2		1000	1125	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436128	56436128	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	94	873	0	ENST00000407977.2:c.1009C>T	p.Arg337Ter	p.R337*	ENST00000407977		337	Cga/Tga	9/10	1	2	FACETS	0.651	0.579	0.729	0.651	0.579	0.729	SUBCLONAL	1	TRUE	1	0.328791733332761	2		873	878	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533517	63533517	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555577625	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	128	918	1	ENST00000307078.5:c.1637del	p.Gly546AlafsTer143	p.G546Afs*143	ENST00000307078	NM_004655.3	546	gGc/gc	6/11	1	2	FACETS	0.749	0.678	0.825	0.749	0.678	0.825	SUBCLONAL	1	TRUE	1	0.328791733332761	2		919	1039	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774681	73774684	+	frameshift_variant	Frame_Shift_Del	DEL	CTCT	CTCT	-	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	13	160	0	ENST00000254810.4:c.403_406del	p.Arg135LeufsTer3	p.R135Lfs*3	ENST00000254810	NM_005324.3	135	AGAGct/ct	4/4	1	2	FACETS	0.513	0.368	0.69	0.513	0.368	0.69	SUBCLONAL	1	TRUE	1	0.328791733332761	2		160	154	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39629562	39629562	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	118	553	0	ENST00000262039.4:c.2260del	p.Thr754GlnfsTer7	p.T754Qfs*7	ENST00000262039	NM_002647.2	752	acA/ac	21/25	0.276594192532041	3	FACETS	0.802	0.727	0.881	0.802	0.727	0.881	CLONAL	2	TRUE	1	0.328791733332761	3		553	521	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14628987	14628987	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757131921	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	57	849	0	ENST00000254322.2:c.175C>T	p.Arg59Cys	p.R59C	ENST00000254322	NM_006145.1	59	Cgc/Tgc	1/3	1	2	FACETS	0.412	0.352	0.477	0.412	0.352	0.477	SUBCLONAL	1	TRUE	1	0.328791733332761	2		849	842	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350625	15350625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35676845	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	64	1121	2	ENST00000263377.2:c.3290G>A	p.Arg1097His	p.R1097H	ENST00000263377	NM_058243.2	1097	cGt/cAt	16/20	1	2	FACETS	0.331	0.286	0.381	0.331	0.286	0.381	SUBCLONAL	1	TRUE	1	0.328791733332761	2		1123	1175	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211082	36211082	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	217	1096	1	ENST00000222270.7:c.837del	p.Arg280GlyfsTer25	p.R280Gfs*25	ENST00000222270	NM_014727.1	278	aCc/ac	3/37	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.328791733332761	2		1097	1236	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216184	36216184	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	143	749	6	ENST00000222270.7:c.3596del	p.Gly1199AlafsTer156	p.G1199Afs*156	ENST00000222270	NM_014727.1	1198	Ggg/gg	11/37	1	2	FACETS	0.999	0.91	1	0.999	0.91	1	CLONAL	1	TRUE	1	0.328791733332761	2		755	871	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867349	45867349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375415853	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	50	992	4	ENST00000391945.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000391945	NM_000400.3	282	Cgg/Tgg	10/23	1	2	FACETS	0.305	0.258	0.358	0.305	0.258	0.358	SUBCLONAL	1	TRUE	1	0.328791733332761	2		996	997	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905960	50905960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777944185	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	195	1032	1	ENST00000440232.2:c.932G>A	p.Arg311His	p.R311H	ENST00000440232	NM_002691.3	311	cGc/cAc	8/27	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.328791733332761	2		1033	1128	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660217	227660217	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1340940219	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	195	997	0	ENST00000305123.5:c.3238A>G	p.Asn1080Asp	p.N1080D	ENST00000305123	NM_005544.2	1080	Aac/Gac	1/2	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.328791733332761	2		997	1056	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475550	12475550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479145908	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	61	753	0	ENST00000287820.6:c.1424C>T	p.Thr475Met	p.T475M	ENST00000287820	NM_015869.4	475	aCg/aTg	7/7	0.328791733332761	2	FACETS	0.399	0.343	0.46	0.199	0.171	0.23	SUBCLONAL	1	TRUE	0	0.328791733332761	2		753	931	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934828	49934828	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs61734381	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	113	918	0	ENST00000296474.3:c.2068C>T	p.Gln690Ter	p.Q690*	ENST00000296474	NM_002447.2	690	Caa/Taa	7/20	1	2	FACETS	0.723	0.649	0.801	0.723	0.649	0.801	SUBCLONAL	1	TRUE	1	0.328791733332761	2		918	951	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015131	71015131	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	68	539	0	ENST00000318789.4:c.1799G>T	p.Ser600Ile	p.S600I	ENST00000318789	NM_032682.5	600	aGc/aTc	20/21	1	2	FACETS	0.731	0.636	0.833	0.731	0.636	0.833	SUBCLONAL	1	TRUE	1	0.328791733332761	2		539	566	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027094	71027094	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	86	758	0	ENST00000318789.4:c.1233del	p.Ala412ProfsTer3	p.A412Pfs*3	ENST00000318789	NM_032682.5	411	acC/ac	15/21	1	2	FACETS	0.677	0.598	0.761	0.677	0.598	0.761	SUBCLONAL	1	TRUE	1	0.328791733332761	2		758	773	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114152	73114152	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777393029	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	90	707	2	ENST00000356692.5:c.788C>T	p.Thr263Met	p.T263M	ENST00000356692		263	aCg/aTg	8/9	1	2	FACETS	0.683	0.606	0.767	0.683	0.606	0.767	SUBCLONAL	1	TRUE	1	0.328791733332761	2		709	801	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138376557	138376557	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	117	796	2	ENST00000289153.2:c.2917del	p.Thr973GlnfsTer19	p.T973Qfs*19	ENST00000289153	NM_006219.2	973	Aca/ca	20/22	1	2	FACETS	0.804	0.724	0.889	0.804	0.724	0.889	CLONAL	1	TRUE	1	0.328791733332761	2		798	885	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665342	138665342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	139	1150	2	ENST00000330315.3:c.223C>T	p.Leu75Phe	p.L75F	ENST00000330315	NM_023067.3	75	Ctc/Ttc	1/1	1	2	FACETS	0.774	0.703	0.848	0.774	0.703	0.848	SUBCLONAL	1	TRUE	1	0.328791733332761	2		1152	1093	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446297	187446297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	111	758	0	ENST00000232014.4:c.1391G>A	p.Ser464Asn	p.S464N	ENST00000232014	NM_001130845.1	464	aGc/aAc	6/10	1	2	FACETS	0.796	0.715	0.882	0.796	0.715	0.882	SUBCLONAL	1	TRUE	1	0.328791733332761	2		758	848	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455618	189455618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	95	744	1	ENST00000264731.3:c.152G>A	p.Ser51Asn	p.S51N	ENST00000264731	NM_003722.4	51	aGt/aAt	2/14	1	2	FACETS	0.737	0.656	0.824	0.737	0.656	0.824	SUBCLONAL	1	TRUE	1	0.328791733332761	2		745	784	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586470	189586470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147148566	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	125	514	3	ENST00000264731.3:c.1094C>T	p.Ser365Leu	p.S365L	ENST00000264731	NM_003722.4	365	tCg/tTg	8/14	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.328791733332761	2		517	671	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806119	1806119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931614	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	194	1205	1	ENST00000260795.2:c.1138G>A	p.Gly380Arg	p.G380R	ENST00000260795		380	Ggg/Agg	8/17	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.328791733332761	2		1206	1172	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902419	1902420	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1324457447	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	61	911	0	ENST00000382891.5:c.40_41del	p.Ser14CysfsTer42	p.S14Cfs*42	ENST00000382891	NM_133335.3	13	cAG/c	2/22	1	2	FACETS	0.37	0.318	0.427	0.37	0.318	0.427	SUBCLONAL	1	TRUE	1	0.328791733332761	2		911	1002	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976876	55976876	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	148	881	0	ENST00000263923.4:c.1036del	p.Glu346SerfsTer17	p.E346Sfs*17	ENST00000263923	NM_002253.2	346	Gag/ag	8/30	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.328791733332761	2		881	886	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80021292	80021292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144798521	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	75	671	1	ENST00000265081.6:c.1361G>A	p.Arg454Gln	p.R454Q	ENST00000265081	NM_002439.4	454	cGa/cAa	9/24	1	2	FACETS	0.718	0.63	0.814	0.718	0.63	0.814	SUBCLONAL	1	TRUE	1	0.328791733332761	2		672	635	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149506139	149506139	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	113	774	1	ENST00000261799.4:c.1618G>A	p.Ala540Thr	p.A540T	ENST00000261799	NM_002609.3	540	Gcc/Acc	11/23	1	2	FACETS	0.82	0.738	0.908	0.82	0.738	0.908	CLONAL	1	TRUE	1	0.328791733332761	2		775	838	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665280	176665280	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784107	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	112	502	1	ENST00000439151.2:c.3964C>T	p.Arg1322Ter	p.R1322*	ENST00000439151	NM_022455.4	1322	Cga/Tga	7/23	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.328791733332761	2		503	613	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694712	176694712	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	79	470	0	ENST00000439151.2:c.5296C>T	p.Arg1766Ter	p.R1766*	ENST00000439151	NM_022455.4	1766	Cga/Tga	15/23	1	2	FACETS	0.9	0.793	1	0.9	0.793	1	CLONAL	1	TRUE	1	0.328791733332761	2		470	534	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178641	32178641	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769456012	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	74	983	0	ENST00000375023.3:c.2753G>A	p.Cys918Tyr	p.C918Y	ENST00000375023	NM_004557.3	918	tGc/tAc	18/30	1	2	FACETS	0.411	0.358	0.468	0.411	0.358	0.468	SUBCLONAL	1	TRUE	1	0.328791733332761	2		983	1096	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651912	36651912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	47	742	0	ENST00000244741.5:c.34C>T	p.Pro12Ser	p.P12S	ENST00000244741	NM_000389.4	12	Cca/Tca	2/3	1	2	FACETS	0.369	0.31	0.434	0.369	0.31	0.434	SUBCLONAL	1	TRUE	1	0.328791733332761	2		742	775	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652302	36652302	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774390644	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	113	705	1	ENST00000244741.5:c.424C>T	p.Arg142Trp	p.R142W	ENST00000244741	NM_000389.4	142	Cgg/Tgg	2/3	1	2	FACETS	0.989	0.891	1	0.989	0.891	1	CLONAL	1	TRUE	1	0.328791733332761	2		706	695	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157470017	157470018	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	32	563	0	ENST00000346085.5:c.2813_2814del	p.Val938GlufsTer3	p.V938Efs*3	ENST00000346085	NM_020732.3	937	acTGtg/actg	9/20	1	2	FACETS	0.304	0.246	0.37	0.304	0.246	0.37	SUBCLONAL	1	TRUE	1	0.328791733332761	2		563	640	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431652	6431652	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	88	719	0	ENST00000356142.4:c.205C>A	p.Pro69Thr	p.P69T	ENST00000356142	NM_018890.3	69	Ccc/Acc	3/7	1	2	FACETS	0.708	0.627	0.795	0.708	0.627	0.795	SUBCLONAL	1	TRUE	1	0.328791733332761	2		719	756	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221971	98221971	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768558478	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	49	684	1	ENST00000331920.6:c.2798C>T	p.Ala933Val	p.A933V	ENST00000331920	NM_000264.3	933	gCg/gTg	17/24	1	2	FACETS	0.394	0.333	0.462	0.394	0.333	0.462	SUBCLONAL	1	TRUE	1	0.328791733332761	2		685	756	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391307	139391307	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs567455787	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	161	1122	1	ENST00000277541.6:c.6884A>T	p.Asn2295Ile	p.N2295I	ENST00000277541	NM_017617.3	2295	aAt/aTt	34/34	1	2	FACETS	0.813	0.744	0.885	0.813	0.744	0.885	CLONAL	1	TRUE	1	0.328791733332761	2		1123	1205	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399841	139399841	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243264280	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	126	1183	0	ENST00000277541.6:c.4507G>A	p.Gly1503Ser	p.G1503S	ENST00000277541	NM_017617.3	1503	Ggc/Agc	25/34	1	2	FACETS	0.7	0.632	0.771	0.7	0.632	0.771	SUBCLONAL	1	TRUE	1	0.328791733332761	2		1183	1095	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139818316	139818316	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	107	804	1	ENST00000247668.2:c.1151G>A	p.Ser384Asn	p.S384N	ENST00000247668	NM_021138.3	384	aGc/aAc	10/11	1	2	FACETS	0.712	0.638	0.791	0.712	0.638	0.791	SUBCLONAL	1	TRUE	1	0.328791733332761	2		805	914	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321396	1321396	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	70	508	0	ENST00000400841.2:c.359G>A	p.Ser120Asn	p.S120N	ENST00000400841		120	aGt/aAt	4/6	1	1	FACETS	0.522	0.455	0.595	0.522	0.455	0.595	SUBCLONAL	1	TRUE	0	0.328791733332761	1		508	681	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226008	53226009	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	121	581	0	ENST00000375401.3:c.2840dup	p.Leu947PhefsTer17	p.L947Ffs*17	ENST00000375401	NM_004187.3	947	ttg/ttTg	19/26	1	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.328791733332761	1		581	601	SUCCESS
BTK	695	MSKCC	GRCh37	X	100612503	100612503	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	101	341	0	ENST00000308731.7:c.1171G>T	p.Gly391Ter	p.G391*	ENST00000308731	NM_000061.2	391	Gga/Tga	13/19	1	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.328791733332761	1		341	385	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458336	120458336	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022533-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	52	575	0	ENST00000256646.2:c.7009C>T	p.Pro2337Ser	p.P2337S	ENST00000256646	NM_024408.3	2337	Ccc/Tcc	34/34	0.24400768074738	2	FACETS	0.795	0.677	0.925	0.398	0.338	0.463	CLONAL	1	TRUE	0	0.244955607114098	2		575	534	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31379479	31379479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145632647	NA	P-0022586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	662	627	1	ENST00000328111.2:c.886G>A	p.Val296Ile	p.V296I	ENST00000328111	NM_006892.3	296	Gtc/Atc	8/23	0.323175043324076	10	FACETS	0.955	0.925	0.985	0.955	0.925	0.985	CLONAL	8	TRUE	2	0.323175043324076	10		628	1229	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0022586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	65	498	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.882	0.767	1	0.882	0.767	1	CLONAL	1	TRUE	1	0.323175043324076	2		498	456	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0022586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	47	333	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.323175043324076	2		333	254	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0022586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	180	687	0	ENST00000269305.4:c.560-2A>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.308358436132774	2	FACETS	0.949	0.88	1	0.949	0.88	1	CLONAL	2	TRUE	0	0.323175043324076	2		687	587	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912161	114912162	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	196	716	0	ENST00000543371.1:c.1232dup	p.Met411IlefsTer12	p.M411Ifs*12	ENST00000543371	NM_001198531.1	411	atg/aTtg	11/14	0.323175043324076	3	FACETS	0.964	0.895	1	0.964	0.895	1	CLONAL	2	TRUE	1	0.323175043324076	3		716	731	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0022614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	177	774	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.530106750011888	3	FACETS	0.992	0.924	1	0.992	0.924	1	CLONAL	2	TRUE	1	0.530106750011888	3		774	426	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0022614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	74	513	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	0.530106750011888	2		513	263	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591925	48591925	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	61	585	0	ENST00000342988.3:c.1088G>T	p.Cys363Phe	p.C363F	ENST00000342988	NM_005359.5	363	tGt/tTt	9/12	1	2	FACETS	0.992	0.867	1	0.992	0.867	1	CLONAL	1	TRUE	1	0.530106750011888	2		585	232	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879903	37879903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	372	1090	2	ENST00000269571.5:c.2198C>T	p.Thr733Ile	p.T733I	ENST00000269571		733	aCa/aTa	18/27	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.530106750011888	2		1092	1223	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161807855	161807855	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1801582	NA	P-0022614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	124	752	4	ENST00000366898.1:c.1138G>A	p.Val380Ile	p.V380I	ENST00000366898	NM_004562.2	380	Gta/Ata	10/12	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.530106750011888	2		756	426	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39644726	39644726	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	54	453	0	ENST00000262039.4:c.2455T>G	p.Leu819Val	p.L819V	ENST00000262039	NM_002647.2	819	Ttg/Gtg	23/25	1	2	FACETS	0.984	0.852	1	0.984	0.852	1	CLONAL	1	TRUE	1	0.530106750011888	2		453	207	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39347488	39347488	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1303622703	NA	P-0022614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1226	139	864	0	ENST00000402219.2:c.76G>T	p.Ala26Ser	p.A26S	ENST00000402219	NM_005633.3	26	Gcg/Tcg	1/23	1	2	FACETS	0.384	0.348	0.422	0.384	0.348	0.422	SUBCLONAL	1	TRUE	1	0.530106750011888	2		864	1365	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278082	41278082	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	104	420	0	ENST00000349496.5:c.1958C>A	p.Thr653Lys	p.T653K	ENST00000349496	NM_001904.3	653	aCa/aAa	13/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.530106750011888	2		420	357	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928358	69928358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774545277	NA	P-0022614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	200	527	0	ENST00000352241.4:c.178C>T	p.Arg60Cys	p.R60C	ENST00000352241	NM_198159.2	60	Cgc/Tgc	2/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.530106750011888	2		527	696	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467644	66467644	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs202165566	NA	P-0022614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	74	576	4	ENST00000273854.3:c.625G>C	p.Gly209Arg	p.G209R	ENST00000273854	NM_004439.5	209	Gga/Cga	3/18	1	2	FACETS	0.921	0.814	1	0.921	0.814	1	CLONAL	1	TRUE	1	0.530106750011888	2		580	303	SUCCESS
APC	324	MSKCC	GRCh37	5	112151191	112151191	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0022614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	76	488	0	ENST00000257430.4:c.836del		p.X279_splice	ENST00000257430	NM_000038.5	279			NA	2	FACETS	1	0.953	1			1	INDETERMINATE	1	TRUE	NA	0.530106750011888	2		488	252	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412634	63412634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753930754	NA	P-0022614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	561	864	7	ENST00000330258.3:c.533G>A	p.Arg178His	p.R178H	ENST00000330258	NM_152424.3	178	cGt/cAt	2/2	0.530106750011888	3	FACETS	0.846	0.817	0.875	1	0.996	1	CLONAL	3	TRUE	1	0.530106750011888	3		871	1055	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0022720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	142	1046	1	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.334070433339059	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.334070433339059	1		1047	691	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577334	64577334	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	125	849	0	ENST00000312049.6:c.248del	p.Leu83ArgfsTer36	p.L83Rfs*36	ENST00000312049	NM_130799.2	83	cTg/cg	2/10	0.334070433339059	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.334070433339059	1		849	591	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	261	425	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.784901885935792	2	FACETS	0.982	0.949	1	0.982	0.949	1	CLONAL	2	TRUE	0	0.814930473685912	2		426	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691022	NA	P-0022737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	654	727	3	ENST00000269305.4:c.1024del	p.Arg342GlufsTer3	p.R342Efs*3	ENST00000269305	NM_001126112.2	342	Cga/ga	10/11	0.814930473685912	2	FACETS	0.979	0.958	0.999	0.979	0.958	0.999	CLONAL	2	TRUE	0	0.814930473685912	2		730	820	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916840	48916841	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs1566186125	NA	P-0022737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	434	376	0	ENST00000267163.4:c.371_372del	p.Ile124ArgfsTer6	p.I124Rfs*6	ENST00000267163	NM_000321.2	124	ATa/a	3/27	0.814930473685912	3	FACETS	0.945	0.921	0.967	0.945	0.921	0.967	CLONAL	3	TRUE	0	0.814930473685912	3		376	529	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575112	64575112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	193	683	1	ENST00000312049.6:c.695G>A	p.Arg232His	p.R232H	ENST00000312049	NM_130799.2	232	cGc/cAc	4/10	1	2	FACETS	0.987	0.916	1	0.987	0.916	1	CLONAL	1	TRUE	1	0.561117346017253	2		684	697	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	193	681	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.561117346017253	6	FACETS	1	0.982	1			1	CLONAL	2	TRUE	NA	0.561117346017253	6		681	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934571	NA	P-0022933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	14	822	0	ENST00000269305.4:c.747G>C	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agC	7/11	0.459407292295717	1	FACETS	0.066	0.047	0.089	0.066	0.047	0.089	SUBCLONAL	1	TRUE	0	0.561117346017253	1		822	544	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050045	13050046	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	104	461	0	ENST00000316448.5:c.192dup	p.Gly65ArgfsTer36	p.G65Rfs*36	ENST00000316448	NM_004343.3	63	-/A	2/9	1	2	FACETS	0.831	0.749	0.918	0.831	0.749	0.918	CLONAL	1	TRUE	1	0.561117346017253	2		461	446	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62309683	62309683	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	188	634	0	ENST00000360203.5:c.1021G>T	p.Val341Phe	p.V341F	ENST00000360203	NM_001283009.1	341	Gtc/Ttc	12/35	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.561117346017253	2		634	600	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133747519	133747519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	75	493	0	ENST00000318560.5:c.826G>A	p.Asp276Asn	p.D276N	ENST00000318560	NM_005157.4	276	Gac/Aac	5/11	1	2	FACETS	0.515	0.452	0.583	0.515	0.452	0.583	SUBCLONAL	1	TRUE	1	0.561117346017253	2		493	519	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575112	64575112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022933-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	83	683	1	ENST00000312049.6:c.695G>A	p.Arg232His	p.R232H	ENST00000312049	NM_130799.2	232	cGc/cAc	4/10	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.730914600150956	2		684	227	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	311	720	1	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.680536181508494	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.680536181508494	1		721	547	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246074	46246074	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	150	385	0	ENST00000334344.6:c.4168A>G	p.Ile1390Val	p.I1390V	ENST00000334344	NM_152641.2	1390	Ata/Gta	15/21	1	2	FACETS	0.934	0.86	1	0.934	0.86	1	CLONAL	1	TRUE	1	0.680536181508494	2		385	472	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646275	23646275	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	369	829	0	ENST00000261584.4:c.1592T>C	p.Leu531Ser	p.L531S	ENST00000261584	NM_024675.3	531	tTg/tCg	4/13	1	2	FACETS	0.977	0.928	1	0.977	0.928	1	CLONAL	1	TRUE	1	0.680536181508494	2		829	1110	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598037	55598037	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	84	349	1	ENST00000288135.5:c.2234G>T	p.Gly745Val	p.G745V	ENST00000288135	NM_000222.2	745	gGc/gTc	16/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.312228270774475	2		350	380	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061833	38061850	+	inframe_deletion	In_Frame_Del	DEL	GGTGTTCATGGTCATGTA	GGTGTTCATGGTCATGTA	-	novel	NA	P-0023030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	230	1376	0	ENST00000250448.2:c.139_156del	p.Tyr47_Thr52del	p.Y47_T52del	ENST00000250448	NM_004496.3	47	TACATGACCATGAACACC/-	2/2	0.205709251638725	4	FACETS	1	0.99	1	0.703	0.654	0.754	CLONAL	1	TRUE	2	0.312228270774475	4		1376	1375	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051170	13051170	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1468810845	NA	P-0023030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	129	521	0	ENST00000316448.5:c.607del	p.Leu203CysfsTer6	p.L203Cfs*6	ENST00000316448	NM_004343.3	202	ttC/tt	5/9	0.0585366804626537	4	FACETS	0.902	0.821	0.987	0.902	0.821	0.987	INDETERMINATE	2	TRUE	2	0.312228270774475	4		521	601	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032071	48032072	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCAGATGGGTTG	novel	NA	P-0023030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	102	337	0	ENST00000234420.5:c.3462_3473dup	p.Gln1155_Cys1158dup	p.Q1155_C1158dup	ENST00000234420	NM_000179.2	1155	gcc/gcCCAGATGGGTTGc	6/10	0.222310541565125	3	FACETS	1	0.981	1	0.729	0.654	0.808	CLONAL	1	TRUE	1	0.312228270774475	3		337	518	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061225	38061231	+	protein_altering_variant	In_Frame_Del	DEL	TCGAACA	TCGAACA	G	novel	NA	P-0023030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	187	882	0	ENST00000250448.2:c.758_764delinsC	p.Met253_Glu255delinsThr	p.M253_E255delinsT	ENST00000250448	NM_004496.3	253	aTGTTCGAg/aCg	2/2	0.205709251638725	4	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	2	0.312228270774475	4		882	781	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578467	7578469	+	missense_variant	Missense_Mutation	TNP	TGC	TGC	GGG	novel	NA	P-0023030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	210	979	0	ENST00000269305.4:c.461_463delinsCCC	p.Gly154_Thr155delinsAlaPro	p.G154_T155delinsAP	ENST00000269305	NM_001126112.2	154	gGCAcc/gCCCcc	5/11	0.312228270774475	2	FACETS	0.836	0.778	0.895	0.836	0.778	0.895	CLONAL	2	TRUE	0	0.312228270774475	2		979	805	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265379	46265379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	85	396	0	ENST00000371998.3:c.2249C>T	p.Ala750Val	p.A750V	ENST00000371998		750	gCa/gTa	12/23	0.728836301867674	5	FACETS	1	0.898	1	0.338	0.299	0.378	CLONAL	1	TRUE	2	0.728836301867674	5		396	482	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170827849	170827849	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	49	236	0	ENST00000296930.5:c.589C>G	p.Arg197Gly	p.R197G	ENST00000296930	NM_002520.6	197	Cga/Gga	8/11	0.717310277269419	4	FACETS	0.915	0.782	1	0.458	0.391	0.53	CLONAL	1	TRUE	2	0.728836301867674	4		236	254	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0023402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	155	941	1	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	1	2	FACETS	0.665	0.611	0.722	0.665	0.611	0.722	SUBCLONAL	1	TRUE	1	0.689410085390292	2		942	676	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100587	67100587	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	86	558	0	ENST00000412916.2:c.285del	p.Tyr96IlefsTer2	p.Y96Ifs*2	ENST00000412916		95	gtA/gt	4/6	0.476960321486159	1	FACETS	0.468	0.418	0.522	0.468	0.418	0.522	SUBCLONAL	1	TRUE	0	0.689410085390292	1		558	349	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847368	68847368	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	129	731	0	ENST00000261769.5:c.1290del	p.Asn431ThrfsTer6	p.N431Tfs*6	ENST00000261769	NM_004360.3	430	gtG/gt	9/16	0.476960321486159	1	FACETS	0.461	0.42	0.504	0.461	0.42	0.504	SUBCLONAL	1	TRUE	0	0.689410085390292	1		731	532	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879900	37879900	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	131	957	0	ENST00000269571.5:c.2195G>C	p.Gly732Ala	p.G732A	ENST00000269571		732	gGc/gCc	18/27	1	2	FACETS	0.555	0.504	0.608	0.555	0.504	0.608	SUBCLONAL	1	TRUE	1	0.689410085390292	2		957	685	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0023475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	118	463	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.842	0.762	0.925	1	0.987	1	CLONAL	2	TRUE	1	0.257283279181615	2		463	545	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	47	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.67	0.565	0.786	0.67	0.565	0.786	SUBCLONAL	1	TRUE	1	0.257283279181615	2		473	545	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0023475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	55	685	2	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.257283279181615	2		687	386	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0023475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	37	743	0	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	0.257283279181615	1	FACETS	0.811	0.671	0.966	0.811	0.671	0.966	CLONAL	1	TRUE	0	0.257283279181615	1		743	309	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858561	9858561	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	67	780	0	ENST00000330684.3:c.2840G>C	p.Arg947Thr	p.R947T	ENST00000330684	NM_001134407.1	947	aGg/aCg	13/13	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.257283279181615	2		780	470	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492685	56492685	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0023475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	25	651	0	ENST00000407977.2:c.252+2C>A		p.X84_splice	ENST00000407977		84			1	2	FACETS	0.479	0.377	0.596	0.479	0.377	0.596	SUBCLONAL	1	TRUE	1	0.257283279181615	2		651	406	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971086	21971100	+	frameshift_variant	Frame_Shift_Del	DEL	AGGAAGCCCTCCCGG	AGGAAGCCCTCCCGG	T	novel	NA	P-0023475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	29	658	2	ENST00000304494.5:c.258_272delinsA	p.Arg87GlyfsTer28	p.R87Gfs*28	ENST00000304494	NM_000077.4	86	gcCCGGGAGGGCTTCCTg/gcAg	2/3	1	2	FACETS	0.692	0.556	0.845	0.692	0.556	0.845	SUBCLONAL	1	TRUE	1	0.257283279181615	2		660	326	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0023508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	60	1124	1	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.200283053140831	4	FACETS	0.877	0.754	1	0.292	0.251	0.337	CLONAL	1	TRUE	1	0.226463956709228	4		1125	741	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692886	89692886	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	128	394	0	ENST00000371953.3:c.370T>A	p.Cys124Ser	p.C124S	ENST00000371953	NM_000314.4	124	Tgt/Agt	5/9	0.221761973661817	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	3	TRUE	0	0.226463956709228	3		394	399	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204511945	204511945	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	53	423	0	ENST00000367182.3:c.545A>G	p.Glu182Gly	p.E182G	ENST00000367182	NM_001278516.1	182	gAa/gGa	8/11	0.200283053140831	4	FACETS	1	0.853	1	0.333	0.284	0.388	CLONAL	1	TRUE	1	0.226463956709228	4		423	574	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109836	115109845	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCTGGCGG	GGGCTGGCGG	-	novel	NA	P-0023508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	176	750	0	ENST00000257566.3:c.2033_2042del	p.Ala678GlyfsTer208	p.A678Gfs*208	ENST00000257566	NM_016569.3	678	gCCGCCAGCCCg/gg	8/8	0.226463956709228	3	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	1	0.226463956709228	3		750	858	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842391	68842400	+	frameshift_variant	Frame_Shift_Del	DEL	GACAGAAGAG	GACAGAAGAG	-	novel	NA	P-0023508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	209	673	0	ENST00000261769.5:c.452_461del	p.Arg151LysfsTer61	p.R151Kfs*61	ENST00000261769	NM_004360.3	151	aGACAGAAGAGa/aa	4/16	0.210578513362217	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.226463956709228	2		673	824	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919199	178919199	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	102	342	0	ENST00000263967.3:c.684A>C	p.Lys228Asn	p.K228N	ENST00000263967	NM_006218.2	228	aaA/aaC	4/21	0.200283053140831	4	FACETS	0.966	0.866	1	0.644	0.577	0.714	CLONAL	2	TRUE	1	0.226463956709228	4		342	572	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161805	56161805	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0023508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	64	431	0	ENST00000399503.3:c.1301+1G>T		p.X434_splice	ENST00000399503	NM_005921.1	434			0.226463956709228	3	FACETS	0.882	0.763	1	0.441	0.381	0.506	CLONAL	1	TRUE	1	0.226463956709228	3		431	713	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177009	56177010	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0023508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	108	539	0	ENST00000399503.3:c.2282_2283dup	p.Asp762Ter	p.D762*	ENST00000399503	NM_005921.1	760	ctt/ctTAt	13/20	0.226463956709228	3	FACETS	0.858	0.771	0.949	0.858	0.771	0.949	CLONAL	2	TRUE	1	0.226463956709228	3		539	619	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	115	635	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.991	0.901	1	0.991	0.901	1	CLONAL	1	TRUE	1	0.599583461745878	2		635	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0023523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	244	832	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.768	0.725	0.811	1	0.994	1	SUBCLONAL	2	TRUE	1	0.599583461745878	2		834	530	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267698	198267698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	195	607	0	ENST00000335508.6:c.1781G>A	p.Arg594Gln	p.R594Q	ENST00000335508	NM_012433.2	594	cGa/cAa	13/25	1	2	FACETS	0.906	0.841	0.973	0.906	0.841	0.973	CLONAL	1	TRUE	1	0.599583461745878	2		607	718	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711908	89711910	+	inframe_deletion	In_Frame_Del	DEL	TAT	TAT	-	rs587780711	NA	P-0023523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	131	631	0	ENST00000371953.3:c.532_534del	p.Tyr178del	p.Y178del	ENST00000371953	NM_000314.4	176	TAT/-	6/9	0.599583461745878	1	FACETS	0.736	0.673	0.8	0.736	0.673	0.8	SUBCLONAL	1	TRUE	0	0.599583461745878	1		631	416	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0023589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	18	425	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.899	0.679	1	0.899	0.679	1	CLONAL	1	FALSE	1	0.19442908242111	2		426	206	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855921	68855921	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	26	584	2	ENST00000261769.5:c.1730del	p.Gly577GlufsTer7	p.G577Efs*7	ENST00000261769	NM_004360.3	577	Gga/ga	12/16	1	2	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	FALSE	1	0.19442908242111	2		586	248	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230605	46230605	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303729294	NA	P-0023589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	10	728	1	ENST00000334344.6:c.854G>A	p.Arg285Gln	p.R285Q	ENST00000334344	NM_152641.2	285	cGg/cAg	8/21	0.194521977640358	4	FACETS	0.394	0.266	0.556	0.197	0.133	0.278	SUBCLONAL	1	FALSE	2	0.19442908242111	4		729	312	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	123	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.944	0.854	1	0.944	0.854	1	CLONAL	1	TRUE	1	0.33	2		473	790	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398280	25398281	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCA	novel	NA	P-0023599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	138	904	0	ENST00000311936.3:c.36_38dup	p.Gly13dup	p.G13dup	ENST00000311936	NM_004985.3	13	ggc/ggTGGc	2/5	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.33	2		904	794	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550434	29550459	+	splice_region_variant,intron_variant	Splice_Region	DEL	AGTAACAATGAACTTTATGTTACTGC	AGTAACAATGAACTTTATGTTACTGC	-	novel	NA	P-0023599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	33	144	0	ENST00000356175.3:c.1722-26_1722-1del		p.X574_splice	ENST00000356175	NM_000267.3	574			1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.33	2		144	155	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339221	87339221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs997635600	NA	P-0023599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	128	834	0	ENST00000277120.3:c.803C>T	p.Ala268Val	p.A268V	ENST00000277120		268	gCg/gTg	8/19	1	2	FACETS	0.865	0.783	0.951	0.865	0.783	0.951	CLONAL	1	TRUE	1	0.33	2		834	897	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440443	49440443	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	133	979	1	ENST00000301067.7:c.4367G>T	p.Cys1456Phe	p.C1456F	ENST00000301067	NM_003482.3	1456	tGc/tTc	15/54	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.2	2		980	1157	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968120	55968120	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	72	688	0	ENST00000263923.4:c.2210G>T	p.Cys737Phe	p.C737F	ENST00000263923	NM_002253.2	737	tGc/tTc	15/30	1	2	FACETS	0.866	0.756	0.986	0.866	0.756	0.986	CLONAL	1	TRUE	1	0.2	2		688	831	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036038	180036038	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	181	827	1	ENST00000261937.6:c.3823A>C	p.Ser1275Arg	p.S1275R	ENST00000261937	NM_182925.4	1275	Agt/Cgt	29/30	0.3	1	FACETS	1	0.935	1	1	0.993	1	CLONAL	2	TRUE	0	0.2	1		828	804	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844109	68844110	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	59	336	0	ENST00000261769.5:c.698dup	p.His233GlnfsTer11	p.H233Qfs*11	ENST00000261769	NM_004360.3	233	cac/cAac	6/16	0.265677024695814	0	FACETS	1	0.925	1			1	CLONAL	1	TRUE	0	0.317923042987659	0		336	232	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061240	38061240	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	62	462	1	ENST00000250448.2:c.749C>A	p.Ser250Tyr	p.S250Y	ENST00000250448	NM_004496.3	250	tCc/tAc	2/2	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.317923042987659	2		463	389	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260809	16260809	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765749217	NA	P-0023845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	38	312	1	ENST00000375759.3:c.8074G>A	p.Val2692Ile	p.V2692I	ENST00000375759	NM_015001.2	2692	Gtc/Atc	11/15	1	2	FACETS	0.81	0.673	0.963	0.81	0.673	0.963	CLONAL	1	TRUE	1	0.317923042987659	2		313	295	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112540	115112932	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGACGTGGTGGTGGAGATCTTGGCCGCGTCGCAGGCCTCGGGGCCATGCTCCTCTTTGCTCTCGGCCTCGGCGTCGCTCTCACCCTCGCTGGGACATAAATCTACCACAGGCGAAGGAAAAAACCAAGGCAGAAGGGCGTTATCTCCAGTATGAGCCAACGGAACTCCAGTTCCCAAGTTGGAATCCCAGCTCGTGGCTTAGTGGCTGTGTAATCCCGGGGAAAGCCCCTTAGCCTCTCTGCACCTCAGTGTTGTCATCTGCAAAATGGGGATAATCGTGCCCAACAACATTGCTGGAAAATTCAATAAGCGATTATGAATTTAAAGTATTTACCCAGAGTTTAAACTTTCCCTTAGATGGACAATCCCCTAATCAGTAGCTCTTCTTATTTT	CGACGTGGTGGTGGAGATCTTGGCCGCGTCGCAGGCCTCGGGGCCATGCTCCTCTTTGCTCTCGGCCTCGGCGTCGCTCTCACCCTCGCTGGGACATAAATCTACCACAGGCGAAGGAAAAAACCAAGGCAGAAGGGCGTTATCTCCAGTATGAGCCAACGGAACTCCAGTTCCCAAGTTGGAATCCCAGCTCGTGGCTTAGTGGCTGTGTAATCCCGGGGAAAGCCCCTTAGCCTCTCTGCACCTCAGTGTTGTCATCTGCAAAATGGGGATAATCGTGCCCAACAACATTGCTGGAAAATTCAATAAGCGATTATGAATTTAAAGTATTTACCCAGAGTTTAAACTTTCCCTTAGATGGACAATCCCCTAATCAGTAGCTCTTCTTATTTT	-	novel	NA	P-0023845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	79	482	0	ENST00000257566.3:c.1100-292_1200del		p.X367_splice	ENST00000257566	NM_016569.3	367		7/8	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.317923042987659	2		482	425	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913558	32913559	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359479	NA	P-0023855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	30	234	0	ENST00000380152.3:c.5073dup	p.Trp1692MetfsTer3	p.W1692Mfs*3	ENST00000380152		1689	gca/gcAa	11/27	1	2	FACETS	0.8	0.654	0.96	0.8	0.654	0.96	CLONAL	1	TRUE	1	0.535745333363513	2		234	140	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0023855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	53	303	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.535745333363513	2		303	191	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313209	65313230	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTTGCCAGGGAAATATCCCTG	ACTTGCCAGGGAAATATCCCTG	CCCT	novel	NA	P-0023855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	44	287	1	ENST00000342505.4:c.1884_1899+6delinsAGGG		p.X628_splice	ENST00000342505	NM_002227.2	628		13/25	0.535745333363513	1	FACETS	0.796	0.681	0.919	0.796	0.681	0.919	CLONAL	1	TRUE	0	0.535745333363513	1		288	151	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692826	89692826	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	27	102	0	ENST00000371953.3:c.310T>G	p.Phe104Val	p.F104V	ENST00000371953	NM_000314.4	104	Ttt/Gtt	5/9	0.535745333363513	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.535745333363513	1		102	58	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40872320	40872320	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	98	436	1	ENST00000428826.2:c.635C>T	p.Thr212Ile	p.T212I	ENST00000428826		212	aCa/aTa	7/21	0.535745333363513	3	FACETS	1	0.979	1	0.68	0.613	0.75	CLONAL	1	TRUE	1	0.535745333363513	3		437	341	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71019885	71019885	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0023855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	34	153	0	ENST00000318789.4:c.1722+2T>G		p.X574_splice	ENST00000318789	NM_032682.5	574			1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.535745333363513	2		153	107	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188820	32188820	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	80	337	0	ENST00000375023.3:c.734A>T	p.Asn245Ile	p.N245I	ENST00000375023	NM_004557.3	245	aAt/aTt	4/30	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.535745333363513	2		337	264	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0023947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	429	832	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.886494065545039	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.886494065545039	1		834	513	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037952	49037953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCCTCATGCTGTTCAG	novel	NA	P-0023947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	302	617	1	ENST00000267163.4:c.2193_2208dup	p.Glu737SerfsTer19	p.E737Sfs*19	ENST00000267163	NM_000321.2	731	ctt/ctTCCTCATGCTGTTCAGt	21/27	0.886494065545039	1	FACETS	0.769	0.736	0.802	0.769	0.736	0.802	SUBCLONAL	1	TRUE	0	0.886494065545039	1		618	493	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288255	21288259	+	frameshift_variant	Frame_Shift_Del	DEL	ATGGC	ATGGC	TTGG	novel	NA	P-0023947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2236	449	871	4	ENST00000354336.3:c.500_504delinsTTGG	p.Asp167ValfsTer6	p.D167Vfs*6	ENST00000354336	NM_005207.3	167	gATGGC/gTTGG	2/3	0.813499696053445	6	FACETS	1	0.976	1			1	CLONAL	1	TRUE	NA	0.886494065545039	6		875	2685	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266753	142266753	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0023947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	167	549	0	ENST00000350721.4:c.3172-1G>C		p.X1058_splice	ENST00000350721	NM_001184.3	1058			0.886494065545039	4	FACETS	0.56	0.513	0.609	0.187	0.171	0.203	SUBCLONAL	1	TRUE	1	0.886494065545039	4		549	1269	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968538	55968538	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	147	591	0	ENST00000263923.4:c.2125G>C	p.Glu709Gln	p.E709Q	ENST00000263923	NM_002253.2	709	Gaa/Caa	14/30	1	2	FACETS	0.434	0.397	0.473	0.434	0.397	0.473	SUBCLONAL	1	TRUE	1	0.886494065545039	2		591	764	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513195	106513195	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	124	422	1	ENST00000359195.3:c.2099G>T	p.Arg700Ile	p.R700I	ENST00000359195	NM_002649.2	700	aGa/aTa	4/11	0.446144528647925	1	FACETS	0.366	0.334	0.4	0.366	0.334	0.4	INDETERMINATE	1	TRUE	0	0.886494065545039	1		423	425	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739329	145739329	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	160	730	0	ENST00000428558.2:c.2041G>T	p.Asp681Tyr	p.D681Y	ENST00000428558	NM_004260.3	681	Gac/Tac	12/22	0.881469620853551	1	FACETS	0.461	0.427	0.496	0.461	0.427	0.496	SUBCLONAL	1	TRUE	0	0.886494065545039	1		730	436	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56477666	56477666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1175477384	NA	P-0024053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	58	648	0	ENST00000267101.3:c.214G>A	p.Ala72Thr	p.A72T	ENST00000267101	NM_001982.3	72	Gcc/Acc	2/28	1	2	FACETS	0.52	0.447	0.599	0.52	0.447	0.599	SUBCLONAL	1	TRUE	1	0.411773423054048	2		648	542	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99440009	99440009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	36	441	0	ENST00000268035.6:c.977G>A	p.Gly326Asp	p.G326D	ENST00000268035	NM_000875.3	326	gGt/gAt	4/21	1	2	FACETS	0.433	0.356	0.519	0.433	0.356	0.519	SUBCLONAL	1	TRUE	1	0.411773423054048	2		441	404	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993576	72993576	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	41	660	0	ENST00000268489.5:c.469T>A	p.Cys157Ser	p.C157S	ENST00000268489	NM_006885.3	157	Tgt/Agt	2/10	1	2	FACETS	0.426	0.355	0.506	0.426	0.355	0.506	SUBCLONAL	1	TRUE	1	0.411773423054048	2		660	467	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657658	37657658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	48	610	1	ENST00000447079.4:c.2575G>A	p.Asp859Asn	p.D859N	ENST00000447079	NM_015083.1	859	Gat/Aat	6/14	1	2	FACETS	0.458	0.387	0.536	0.458	0.387	0.536	SUBCLONAL	1	TRUE	1	0.411773423054048	2		611	509	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725049	47725049	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1034388452	NA	P-0024053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	52	894	1	ENST00000449228.1:c.695C>G	p.Thr232Ser	p.T232S	ENST00000449228	NM_001127240.2	232	aCc/aGc	4/4	0.314290142674769	2	FACETS	0.348	0.296	0.406	0.174	0.148	0.203	SUBCLONAL	1	TRUE	0	0.411773423054048	2		895	725	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562659	176562659	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	59	645	0	ENST00000439151.2:c.555G>C	p.Glu185Asp	p.E185D	ENST00000439151	NM_022455.4	185	gaG/gaC	2/23	1	2	FACETS	0.466	0.401	0.537	0.466	0.401	0.537	SUBCLONAL	1	TRUE	1	0.411773423054048	2		645	615	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969369	44969369	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1318649487	NA	P-0024053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	30	627	0	ENST00000377967.4:c.4051C>T	p.Arg1351Ter	p.R1351*	ENST00000377967	NM_021140.2	1351	Cga/Tga	28/29	1	2	FACETS	0.294	0.236	0.36	0.294	0.236	0.36	SUBCLONAL	1	TRUE	1	0.411773423054048	2		627	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0024159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	259	1170	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	1	2	FACETS	0.802	0.75	0.855	1	0.993	1	CLONAL	2	TRUE	1	0.264076986474758	2		1170	1223	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729619	162729728	+	frameshift_variant	Frame_Shift_Del	DEL	TGTGTCTGGCCTGGACGATTTCACCCAGACCCATGAATACCACGTGTGGCCCGGCTATGACTATGTGGGCTGGCGGAACGAGAGTGCCACCAATGGCTACATTGAGATCA	TGTGTCTGGCCTGGACGATTTCACCCAGACCCATGAATACCACGTGTGGCCCGGCTATGACTATGTGGGCTGGCGGAACGAGAGTGCCACCAATGGCTACATTGAGATCA	-	novel	NA	P-0024159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	68	858	0	ENST00000367921.3:c.708_817del	p.Ser237Ter	p.S237*	ENST00000367921	NM_006182.2	235	ggTGTGTCTGGCCTGGACGATTTCACCCAGACCCATGAATACCACGTGTGGCCCGGCTATGACTATGTGGGCTGGCGGAACGAGAGTGCCACCAATGGCTACATTGAGATCAtg/ggtg	8/18	1	2	FACETS	0.566	0.491	0.647	0.566	0.491	0.647	SUBCLONAL	1	TRUE	1	0.264076986474758	2		858	910	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434346	49434346	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	102	1020	0	ENST00000301067.7:c.7207C>A	p.Leu2403Met	p.L2403M	ENST00000301067	NM_003482.3	2403	Ctg/Atg	31/54	1	2	FACETS	0.681	0.607	0.759	0.681	0.607	0.759	SUBCLONAL	1	TRUE	1	0.264076986474758	2		1020	1135	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437560	49437634	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCTTCCTGTGGGGCAGTCAAGGAGAAACAGTTTTCTTCATGCCCTGCAGGGCACAGACACCTCCCTCACTGCTT	GGCTTCCTGTGGGGCAGTCAAGGAGAAACAGTTTTCTTCATGCCCTGCAGGGCACAGACACCTCCCTCACTGCTT	-	novel	NA	P-0024159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	137	875	0	ENST00000301067.7:c.5319+17_5325del		p.X1773_splice	ENST00000301067	NM_003482.3	1773		23/54	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.264076986474758	2		875	904	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512459	38512459	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	142	852	0	ENST00000254066.5:c.1370C>A	p.Pro457Gln	p.P457Q	ENST00000254066	NM_000964.3	457	cCg/cAg	9/9	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.264076986474758	2		852	959	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575219	48575219	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	71	527	0	ENST00000342988.3:c.413C>A	p.Ser138Ter	p.S138*	ENST00000342988	NM_005359.5	138	tCa/tAa	3/12	0.264076986474758	1	FACETS	0.882	0.771	1	0.882	0.771	1	CLONAL	1	TRUE	0	0.264076986474758	1		527	529	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469626	25469626	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	204	914	1	ENST00000264709.3:c.1142G>T	p.Gly381Val	p.G381V	ENST00000264709	NM_175629.2	381	gGg/gTg	10/23	1	2	FACETS	0.811	0.753	0.872	1	0.992	1	CLONAL	2	TRUE	1	0.264076986474758	2		915	952	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233129	69233129	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	43	476	0	ENST00000462284.1:c.994C>G	p.Arg332Gly	p.R332G	ENST00000462284	NM_002392.5	332	Cgt/Ggt	11/11	0.150504154552944	3	FACETS	1	0.947	1	0.673	0.563	0.794	CLONAL	1	TRUE	1	0.15	3		476	458	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134857	41134857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	47	620	0	ENST00000379561.5:c.771G>A	p.Met257Ile	p.M257I	ENST00000379561	NM_002015.3	257	atG/atA	2/3	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.15	2		620	542	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288306	21288306	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	48	739	0	ENST00000354336.3:c.551C>G	p.Ser184Cys	p.S184C	ENST00000354336	NM_005207.3	184	tCc/tGc	2/3	1	2	FACETS	0.908	0.766	1	0.908	0.766	1	CLONAL	1	TRUE	1	0.15	2		739	705	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0024239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	145	385	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.261990602139578	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	FALSE	1	0.26845443052133	3		385	551	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455075	50455075	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	102	412	0	ENST00000331340.3:c.622C>T	p.Arg208Ter	p.R208*	ENST00000331340	NM_006060.4	208	Cga/Tga	6/8	0.26845443052133	6	FACETS	1	0.907	1	0.506	0.454	0.562	CLONAL	2	FALSE	2	0.26845443052133	6		412	577	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293664	1293664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111952055	NA	P-0024239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	170	767	0	ENST00000310581.5:c.1337G>A	p.Arg446His	p.R446H	ENST00000310581	NM_198253.2	446	cGt/cAt	2/16	0.202675501979816	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	FALSE	2	0.26845443052133	4		767	729	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913255	NA	P-0024239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	198	739	0	ENST00000369535.4:c.183A>T	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caT	3/7	0.261990602139578	3	FACETS	0.983	0.912	1	0.983	0.912	1	CLONAL	2	FALSE	1	0.26845443052133	3		739	851	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739824	41739824	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs779271157	NA	P-0024239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	60	544	0	ENST00000242208.4:c.149C>G	p.Ser50Cys	p.S50C	ENST00000242208	NM_002192.2	50	tCt/tGt	2/3	0.26845443052133	6	FACETS	0.941	0.81	1	0.235	0.202	0.272	CLONAL	1	FALSE	2	0.26845443052133	6		544	730	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255118	16255118	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	159	458	1	ENST00000375759.3:c.2383C>T	p.Arg795Ter	p.R795*	ENST00000375759	NM_015001.2	795	Cga/Tga	11/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.584635784669751	2		459	500	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900243	32900243	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	128	538	0	ENST00000380152.3:c.431T>C	p.Val144Ala	p.V144A	ENST00000380152		144	gTt/gCt	5/27	0.584635784669751	1	FACETS	0.906	0.832	0.982	0.906	0.832	0.982	CLONAL	1	TRUE	0	0.584635784669751	1		538	342	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778128	3778128	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	349	1110	0	ENST00000262367.5:c.6920C>G	p.Ser2307Cys	p.S2307C	ENST00000262367	NM_004380.2	2307	tCc/tGc	31/31	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.584635784669751	2		1110	1068	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533286	29533332	+	frameshift_variant	Frame_Shift_Del	DEL	ATGCTGTGTATTGTCACTCGGTTGAACTTCGAAATATGTTTGGTGAA	ATGCTGTGTATTGTCACTCGGTTGAACTTCGAAATATGTTTGGTGAA	-	novel	NA	P-0024266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	85	432	0	ENST00000356175.3:c.1290_1336del	p.Ala431ThrfsTer3	p.A431Tfs*3	ENST00000356175	NM_000267.3	430	gATGCTGTGTATTGTCACTCGGTTGAACTTCGAAATATGTTTGGTGAA/g	12/57	0.584635784669751	1	FACETS	0.759	0.68	0.842	0.759	0.68	0.842	SUBCLONAL	1	TRUE	0	0.584635784669751	1		432	271	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47710033	47710033	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	112	434	0	ENST00000233146.2:c.2750C>G	p.Ala917Gly	p.A917G	ENST00000233146	NM_000251.2	917	gCa/gGa	16/16	0.584635784669751	1	FACETS	0.955	0.873	1	0.955	0.873	1	CLONAL	1	TRUE	0	0.584635784669751	1		434	284	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339243	70339243	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	235	809	0	ENST00000374080.3:c.120T>G	p.Asn40Lys	p.N40K	ENST00000374080		40	aaT/aaG	2/45	1	2	FACETS	0.995	0.931	1	0.995	0.931	1	CLONAL	1	TRUE	1	0.584635784669751	2		809	808	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0024462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	149	463	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.3442292803334	4	FACETS	0.861	0.788	0.936	0.861	0.788	0.936	CLONAL	2	TRUE	2	0.3442292803334	4		463	676	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0024462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	132	572	2	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.197117029433424	5	FACETS	0.958	0.873	1	0.639	0.582	0.698	INDETERMINATE	2	TRUE	2	0.3442292803334	5		574	607	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256510	115256510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	48	924	1	ENST00000369535.4:c.201G>A	p.Met67Ile	p.M67I	ENST00000369535	NM_002524.4	67	atG/atA	3/7	0.3442292803334	3	FACETS	0.498	0.42	0.584	0.249	0.21	0.292	SUBCLONAL	1	TRUE	1	0.3442292803334	3		925	656	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562345	21562345	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1204055851	NA	P-0024462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	72	840	0	ENST00000382592.4:c.1574G>A	p.Arg525His	p.R525H	ENST00000382592	NM_014572.2	525	cGc/cAc	4/8	0.3442292803334	4	FACETS	0.749	0.653	0.852	0.374	0.326	0.426	SUBCLONAL	1	TRUE	2	0.3442292803334	4		840	751	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121525	108121525	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	155	659	0	ENST00000278616.4:c.1333C>T	p.Gln445Ter	p.Q445*	ENST00000278616	NM_000051.3	445	Caa/Taa	10/63	0.3442292803334	2	FACETS	0.958	0.884	1	0.958	0.884	1	CLONAL	2	TRUE	0	0.3442292803334	2		659	470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	67	857	1	ENST00000269305.4:c.166G>T	p.Glu56Ter	p.E56*	ENST00000269305	NM_001126112.2	56	Gaa/Taa	4/11	1	2	FACETS	0.26	0.225	0.299	0.26	0.225	0.299	SUBCLONAL	1	TRUE	1	0.469476078558278	2		858	1097	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428344	33428344	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	82	739	1	ENST00000345365.6:c.779T>A	p.Leu260His	p.L260H	ENST00000345365	NM_002878.3	260	cTc/cAc	9/10	1	2	FACETS	0.291	0.255	0.33	0.291	0.255	0.33	SUBCLONAL	1	TRUE	1	0.469476078558278	2		740	1200	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551243	141551371	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTTCCAAGAGGCGCCCACCTGCTGGAACTGGCCTTCAGAGACACCGTCGCGGTAGAAGATGATGCGGGTGGGCTTGAAGCGCGTGGACTTGTAGAACTGGATGAGGAGCTCGCGGACCATGGCGGCC	AGGTTCCAAGAGGCGCCCACCTGCTGGAACTGGCCTTCAGAGACACCGTCGCGGTAGAAGATGATGCGGGTGGGCTTGAAGCGCGTGGACTTGTAGAACTGGATGAGGAGCTCGCGGACCATGGCGGCC	-	novel	NA	P-0024469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	61	609	0	ENST00000220592.5:c.1926_2034+20del		p.X642_splice	ENST00000220592	NM_012154.3	642		15/19	0.278107911229067	3	FACETS	0.343	0.295	0.396	0.171	0.147	0.198	INDETERMINATE	1	TRUE	1	0.469476078558278	3		609	936	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295234	+	upstream_gene_variant	5'Flank	ONP	GGGGGCT	GGGGGCT	AGGGGCA	novel	NA	P-0024469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	43	450	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.348	0.291	0.412	0.348	0.291	0.412	SUBCLONAL	1	TRUE	1	0.469476078558278	2		450	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0024515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	227	662	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.348738483975989	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.348738483975989	2		662	579	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100451	8100451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1266983268	NA	P-0024515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	136	706	0	ENST00000346208.3:c.425C>T	p.Ser142Leu	p.S142L	ENST00000346208		142	tCg/tTg	3/6	0.348738483975989	2	FACETS	1	0.918	1	0.504	0.459	0.552	CLONAL	1	TRUE	0	0.348738483975989	2		706	773	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518103	176518103	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs866476239	NA	P-0024515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	52	513	0	ENST00000292408.4:c.601C>T	p.Arg201Trp	p.R201W	ENST00000292408	NM_213647.1	201	Cgg/Tgg	5/18	1	2	FACETS	0.537	0.457	0.625	0.537	0.457	0.625	SUBCLONAL	1	TRUE	1	0.348738483975989	2		513	555	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432651	49432651	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs727503983	NA	P-0024515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	146	807	1	ENST00000301067.7:c.8488C>T	p.Arg2830Ter	p.R2830*	ENST00000301067	NM_003482.3	2830	Cga/Tga	34/54	0.338271641609838	2	FACETS	1	0.933	1	0.512	0.468	0.559	CLONAL	1	TRUE	0	0.348738483975989	2		808	817	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385230	41385230	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	90	565	0	ENST00000373198.4:c.731A>C	p.Asn244Thr	p.N244T	ENST00000373198	NM_133170.3	244	aAc/aCc	6/32	0.106813846996391	3	FACETS	0.938	0.833	1	0.313	0.277	0.35	INDETERMINATE	1	TRUE	0	0.348738483975989	3		565	646	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262300	16262300	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	91	253	0	ENST00000375759.3:c.9565T>C	p.Tyr3189His	p.Y3189H	ENST00000375759	NM_015001.2	3189	Tat/Cat	11/15	NA	2	FACETS	1	0.954	1			1	INDETERMINATE	2	TRUE	NA	0.348738483975989	2		253	238	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716211	52716211	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	125	547	0	ENST00000322088.6:c.655T>G	p.Ser219Ala	p.S219A	ENST00000322088	NM_014225.5	219	Tcg/Gcg	6/15	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.348738483975989	2		547	508	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917829	29917829	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs764532876	NA	P-0024515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	121	765	0	ENST00000389048.3:c.839T>C	p.Leu280Pro	p.L280P	ENST00000389048	NM_004304.4	280	cTg/cCg	3/29	1	2	FACETS	0.947	0.856	1	0.947	0.856	1	CLONAL	1	TRUE	1	0.348738483975989	2		765	733	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440060	220440060	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	287	802	0	ENST00000243786.2:c.913C>A	p.Leu305Ile	p.L305I	ENST00000243786	NM_002191.3	305	Ctt/Att	2/2	0.131469255888447	3	FACETS	0.973	0.916	1			1	INDETERMINATE	2	TRUE	NA	0.348738483975989	3		802	993	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0024629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	81	463	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.749	0.661	0.844	0.749	0.661	0.844	SUBCLONAL	1	TRUE	1	0.356805327220229	2		463	606	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0024629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	88	556	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.905	0.804	1	0.905	0.804	1	CLONAL	1	TRUE	1	0.356805327220229	2		557	545	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0024629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	56	563	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	1	2	FACETS	0.568	0.486	0.657	0.568	0.486	0.657	SUBCLONAL	1	TRUE	1	0.356805327220229	2		563	553	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457270	67457270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1566991421	NA	P-0024629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	93	673	3	ENST00000327367.4:c.244G>A	p.Gly82Arg	p.G82R	ENST00000327367	NM_005902.3	82	Ggg/Agg	2/9	0.356805327220229	1	FACETS	0.925	0.826	1	0.925	0.826	1	CLONAL	1	TRUE	0	0.356805327220229	1		676	463	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593405	48593405	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519962	NA	P-0024629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	96	404	0	ENST00000342988.3:c.1156G>A	p.Gly386Ser	p.G386S	ENST00000342988	NM_005359.5	386	Ggt/Agt	10/12	0.356805327220229	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.356805327220229	1		404	371	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352593	68352593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	79	386	0	ENST00000487270.1:c.460G>A	p.Glu154Lys	p.E154K	ENST00000487270	NM_133509.3	154	Gaa/Aaa	6/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.356805327220229	2		386	395	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463193	25463193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	105	665	0	ENST00000264709.3:c.2300G>A	p.Arg767Lys	p.R767K	ENST00000264709	NM_175629.2	767	aGg/aAg	19/23	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.356805327220229	2		665	576	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805685	32805685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	97	703	4	ENST00000374899.4:c.326C>T	p.Ala109Val	p.A109V	ENST00000374899	NM_018833.2	109	gCg/gTg	2/12	0.356805327220229	1	FACETS	0.908	0.813	1	0.908	0.813	1	CLONAL	1	TRUE	0	0.356805327220229	1		707	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579463	7579463	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	251	702	1	ENST00000269305.4:c.224del	p.Pro75LeufsTer48	p.P75Lfs*48	ENST00000269305	NM_001126112.2	75	cCt/ct	4/11	0.469354310787919	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.469354310787919	2		703	489	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65323409	65323409	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	130	727	1	ENST00000342505.4:c.1388A>G	p.Tyr463Cys	p.Y463C	ENST00000342505	NM_002227.2	463	tAc/tGc	10/25	0.260638446319197	3	FACETS	1	0.971	1	0.582	0.529	0.636	INDETERMINATE	1	TRUE	1	0.469354310787919	3		728	588	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844167	68844167	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	300	667	0	ENST00000261769.5:c.755T>G	p.Val252Gly	p.V252G	ENST00000261769	NM_004360.3	252	gTa/gGa	6/16	0.469354310787919	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.469354310787919	2		667	579	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873250	136873250	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	145	391	0	ENST00000241393.3:c.248C>T	p.Ala83Val	p.A83V	ENST00000241393	NM_003467.2	83	gCc/gTc	2/2	0.377139996964265	5	FACETS	0.882	0.813	0.952	0.882	0.813	0.952	CLONAL	3	TRUE	2	0.469354310787919	5		391	398	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109321747	109321747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	157	834	0	ENST00000436639.2:c.676C>T	p.Leu226Phe	p.L226F	ENST00000436639	NM_014454.2	226	Ctt/Ttt	4/10	0.469354310787919	2	FACETS	0.982	0.902	1	0.491	0.451	0.533	CLONAL	1	TRUE	0	0.469354310787919	2		834	681	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039463	49039465	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0024897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	75	641	0	ENST00000267163.4:c.2450_2452del	p.Glu817del	p.E817del	ENST00000267163	NM_000321.2	816	tcAGAa/tca	23/27	0.194624228069365	2	FACETS	1	0.898	1	0.513	0.45	0.582	CLONAL	1	TRUE	0	0.229314403525675	2		641	637	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80083442	80083442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	79	948	4	ENST00000265081.6:c.2494G>A	p.Asp832Asn	p.D832N	ENST00000265081	NM_002439.4	832	Gac/Aac	18/24	0.229314403525675	1	FACETS	0.853	0.75	0.964	0.853	0.75	0.964	CLONAL	1	TRUE	0	0.229314403525675	1		952	715	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86668002	86668002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769775990	NA	P-0024897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	38	404	0	ENST00000274376.6:c.1766G>A	p.Arg589His	p.R589H	ENST00000274376	NM_002890.2	589	cGc/cAc	13/25	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.229314403525675	2		404	248	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0025085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	90	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.221793713470943	2		473	745	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971101	21971101	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	53	383	0	ENST00000579755.1:c.300C>A	p.Cys100Ter	p.C100*	ENST00000579755		100	tgC/tgA	2/3	0.221793713470943	1	FACETS	0.781	0.666	0.907	0.781	0.666	0.907	CLONAL	1	TRUE	0	0.221793713470943	1		383	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579349	7579349	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	100	548	0	ENST00000269305.4:c.338del	p.Phe113SerfsTer10	p.F113Sfs*10	ENST00000269305	NM_001126112.2	113	tTc/tc	4/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.221793713470943	2		548	685	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250661	26250661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293611508	NA	P-0025085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	40	498	0	ENST00000446824.2:c.173C>T	p.Ser58Leu	p.S58L	ENST00000446824	NM_021018.2	58	tCg/tTg	1/1	1	2	FACETS	0.555	0.46	0.661	0.555	0.46	0.661	SUBCLONAL	1	TRUE	1	0.221793713470943	2		498	650	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041046	47041046	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0025085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	48	265	0	ENST00000377604.3:c.1575+1G>A		p.X525_splice	ENST00000377604	NM_001204468.1	525			1	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.221793713470943	1		265	311	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508932	106508932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	218	313	0	ENST00000359195.3:c.926C>T	p.Thr309Met	p.T309M	ENST00000359195	NM_002649.2	309	aCg/aTg	2/11	1	2	FACETS	0.973	0.915	1	0.973	0.915	1	CLONAL	1	TRUE	1	0.90328078065503	2		313	496	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849866	156849866	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	395	540	0	ENST00000524377.1:c.2122A>G	p.Ser708Gly	p.S708G	ENST00000524377	NM_002529.3	708	Agc/Ggc	16/17	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.90328078065503	2		540	865	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21565432	21565432	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	497	653	0	ENST00000382592.4:c.454G>A	p.Val152Ile	p.V152I	ENST00000382592	NM_014572.2	152	Gtc/Atc	3/8	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.90328078065503	2		653	1022	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912172	32912173	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs80359395	NA	P-0025097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	450	651	1	ENST00000380152.3:c.3680_3681del	p.Leu1227GlnfsTer5	p.L1227Qfs*5	ENST00000380152		1227	cTG/c	11/27	1	2	FACETS	0.954	0.914	0.995	0.954	0.914	0.995	CLONAL	1	TRUE	1	0.90328078065503	2		652	1044	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813918	50813918	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	310	584	0	ENST00000398568.2:c.1472C>G	p.Pro491Arg	p.P491R	ENST00000398568	NM_001042412.1	491	cCa/cGa	8/18	NA	2	FACETS	0.857	0.812	0.903			1	INDETERMINATE	1	TRUE	NA	0.90328078065503	2		584	801	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024662	11024662	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	311	458	0	ENST00000327064.4:c.779G>C	p.Gly260Ala	p.G260A	ENST00000327064	NM_199141.1	260	gGc/gCc	6/16	1	2	FACETS	0.975	0.926	1	0.975	0.926	1	CLONAL	1	TRUE	1	0.90328078065503	2		458	706	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495713	72495713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778318924	NA	P-0025097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	400	552	0	ENST00000477973.2:c.359C>T	p.Thr120Ile	p.T120I	ENST00000477973	NM_012234.5	120	aCc/aTc	1/4	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.90328078065503	2		552	873	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108653	8108653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749454960	NA	P-0025253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	430	489	1	ENST00000585124.1:c.742C>T	p.Arg248Cys	p.R248C	ENST00000585124	NM_004217.3	248	Cgc/Tgc	8/9	0.480376558577366	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.511335513049974	2		490	836	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193181580	193181580	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	311	431	0	ENST00000367435.3:c.1127A>T	p.Asn376Ile	p.N376I	ENST00000367435	NM_024529.4	376	aAt/aTt	13/17	0.491800253599813	4	FACETS	1	0.989	1	0.575	0.544	0.605	CLONAL	2	TRUE	0	0.511335513049974	4		431	800	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253969	133253969	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	161	551	1	ENST00000320574.5:c.781G>A	p.Asp261Asn	p.D261N	ENST00000320574	NM_006231.2	261	Gat/Aat	8/49	0.492474838056808	2	FACETS	0.761	0.698	0.826	0.38	0.349	0.413	SUBCLONAL	1	TRUE	0	0.511335513049974	2		552	828	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578369	7578369	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0025253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	313	389	0	ENST00000269305.4:c.559+2T>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.480376558577366	2	FACETS	0.983	0.936	1	0.983	0.936	1	CLONAL	2	TRUE	0	0.511335513049974	2		389	623	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63553898	63553943	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCACCCGCCCCCGTCAAAGTCTTACCTGTATCCACTGTCAACAGT	CCCACCCGCCCCCGTCAAAGTCTTACCTGTATCCACTGTCAACAGT	TTATTATTATAATAATAATAATTAATTATTA	novel	NA	P-0025253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	47	370	2	ENST00000307078.5:c.796_815+26delinsTAATAATTAATTATTATTATTATAATAATAA		p.X266_splice	ENST00000307078	NM_004655.3	266		2/11	0.480376558577366	2	FACETS	0.375	0.316	0.44	0.188	0.158	0.22	SUBCLONAL	1	TRUE	0	0.511335513049974	2		372	490	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966669	44966669	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	104	351	0	ENST00000377967.4:c.3893G>C	p.Arg1298Thr	p.R1298T	ENST00000377967	NM_021140.2	1298	aGa/aCa	27/29	0.492474838056808	2	FACETS	1	0.91	1	0.505	0.455	0.556	CLONAL	1	TRUE	0	0.511335513049974	2		351	403	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279815	46279841	+	inframe_deletion	In_Frame_Del	DEL	GCAGCAGCAGCAGCAGCAGCAACAGCA	GCAGCAGCAGCAGCAGCAGCAACAGCA	-	rs759271230	NA	P-0025253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	76	381	0	ENST00000371998.3:c.3762_3788del	p.Gln1268_Gln1276del	p.Q1268_Q1276del	ENST00000371998		1247	atGCAGCAGCAGCAGCAGCAGCAACAGCAg/atg	20/23	0.511335513049974	4	FACETS	0.547	0.479	0.621	0.182	0.159	0.207	SUBCLONAL	1	TRUE	1	0.511335513049974	4		381	821	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0025341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	78	797	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.161274237774481	3	FACETS	1	0.952	1	1	0.982	1	CLONAL	3	FALSE	1	0.161274237774481	3		797	306	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236104	108236104	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	29	648	0	ENST00000278616.4:c.9040C>T	p.Gln3014Ter	p.Q3014*	ENST00000278616	NM_000051.3	3014	Caa/Taa	63/63	1	2	FACETS	0.86	0.695	1	1	0.95	1	CLONAL	2	FALSE	1	0.161274237774481	2		648	209	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188164	11188164	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	106	488	0	ENST00000361445.4:c.5930C>G	p.Thr1977Arg	p.T1977R	ENST00000361445	NM_004958.3	1977	aCa/aGa	43/58	0.814045769127232	1	FACETS	0.322	0.29	0.355	0.322	0.29	0.355	SUBCLONAL	1	TRUE	0	0.814045769127232	1		488	480	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324201	31324201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1071652	NA	P-0025493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	14	264	10	ENST00000412585.2:c.362G>A	p.Ser121Asn	p.S121N	ENST00000412585	NM_005514.6	121	aGc/aAc	3/8	0.814045769127232	1	FACETS	0.358	0.266	0.462	0.358	0.266	0.462	SUBCLONAL	1	TRUE	0	0.814045769127232	1		274	57	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575476	64575480	+	frameshift_variant	Frame_Shift_Del	DEL	GATCC	GATCC	-	novel	NA	P-0025493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	419	650	0	ENST00000312049.6:c.537_541del	p.Asp180CysfsTer14	p.D180Cfs*14	ENST00000312049	NM_130799.2	179	gaGGATCat/gaat	3/10	0.814045769127232	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.814045769127232	1		650	592	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41542815	41542815	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	72	488	0	ENST00000263253.7:c.2126A>G	p.Gln709Arg	p.Q709R	ENST00000263253	NM_001429.3	709	cAa/cGa	11/31	0.814045769127232	1	FACETS	0.343	0.302	0.386	0.343	0.302	0.386	SUBCLONAL	1	TRUE	0	0.814045769127232	1		488	306	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814225	76814225	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	161	474	0	ENST00000373344.5:c.6419A>G	p.Asn2140Ser	p.N2140S	ENST00000373344	NM_000489.3	2140	aAt/aGt	29/35	0.814045769127232	1	FACETS	0.927	0.874	0.979	0.927	0.874	0.979	CLONAL	1	TRUE	0	0.814045769127232	1		474	253	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255225	16255227	+	frameshift_variant	Frame_Shift_Del	DEL	CCC	CCC	A	novel	NA	P-0025493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	85	380	1	ENST00000375759.3:c.2490_2492delinsA	p.Pro831Ter	p.P831*	ENST00000375759	NM_015001.2	830	tcCCCt/tcAt	11/15	0.814045769127232	1	FACETS	0.335	0.298	0.374	0.335	0.298	0.374	SUBCLONAL	1	TRUE	0	0.814045769127232	1		381	370	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	27	635	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.585	0.467	0.718	0.585	0.467	0.718	SUBCLONAL	1	TRUE	1	0.38	2		635	243	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0025536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	85	494	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.956	0.848	1	0.956	0.848	1	CLONAL	1	TRUE	1	0.38	2		494	468	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0025536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	110	603	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	0.38	2		603	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0025645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	228	556	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.844997802611561	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.844997802611561	1		556	299	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427506	49427506	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	43	477	0	ENST00000301067.7:c.10982G>T	p.Gly3661Val	p.G3661V	ENST00000301067	NM_003482.3	3661	gGt/gTt	39/54	1	2	FACETS	0.274	0.229	0.323	0.274	0.229	0.323	SUBCLONAL	1	TRUE	1	0.844997802611561	2		477	372	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947607	48947638	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAATCTGATTTCCTATTTTAACGTAAGCCATA	AAATCTGATTTCCTATTTTAACGTAAGCCATA	TCAT	novel	NA	P-0025645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	31	493	1	ENST00000267163.4:c.1194_1215+10delinsTCAT		p.X398_splice	ENST00000267163	NM_000321.2	398		12/27	0.844997802611561	1	FACETS	0.228	0.186	0.274	0.228	0.186	0.274	SUBCLONAL	1	TRUE	0	0.844997802611561	1		494	186	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281668	49281668	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201815757	NA	P-0025645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	16	699	2	ENST00000282018.3:c.715C>T	p.Arg239Trp	p.R239W	ENST00000282018	NM_020377.2	239	Cgg/Tgg	1/1	0.844997802611561	1	FACETS	0.071	0.052	0.093	0.071	0.052	0.093	SUBCLONAL	1	TRUE	0	0.844997802611561	1		701	310	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	115	635	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.408494417306848	2		635	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0025666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	386	513	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	1	2	FACETS	1	0.97	1	1	0.997	1	CLONAL	2	TRUE	1	0.408494417306848	2		513	924	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441147	149441147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	212	512	0	ENST00000286301.3:c.1765G>A	p.Gly589Arg	p.G589R	ENST00000286301	NM_005211.3	589	Gga/Aga	13/22	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.408494417306848	2		512	913	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628185	187628185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767176687	NA	P-0025666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	122	628	0	ENST00000441802.2:c.2797C>T	p.Arg933Cys	p.R933C	ENST00000441802	NM_005245.3	933	Cgt/Tgt	2/27	0.244756740700765	1	FACETS	0.479	0.432	0.528	0.479	0.432	0.528	INDETERMINATE	1	TRUE	0	0.408494417306848	1		628	993	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120308	70120314	+	frameshift_variant	Frame_Shift_Del	DEL	GCTCACA	GCTCACA	-	novel	NA	P-0025666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1228	298	765	0	ENST00000245479.2:c.1311_1317del	p.Ser438ThrfsTer30	p.S438Tfs*30	ENST00000245479	NM_000346.3	437	cGCTCACAg/cg	3/3	1	2	FACETS	0.956	0.898	1	0.956	0.898	1	CLONAL	1	TRUE	1	0.408494417306848	2		765	1526	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674283	117674283	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	90	498	0	ENST00000368508.3:c.4191G>T	p.Trp1397Cys	p.W1397C	ENST00000368508	NM_002944.2	1397	tgG/tgT	26/43	0.244756740700765	1	FACETS	0.435	0.385	0.488	0.435	0.385	0.488	INDETERMINATE	1	TRUE	0	0.408494417306848	1		498	807	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971067	21971067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	201	226	0	ENST00000579755.1:c.334G>A	p.Ala112Thr	p.A112T	ENST00000579755		112	Gca/Aca	2/3	0.408494417306848	1	FACETS	0.768	0.718	0.818	1	0.992	1	SUBCLONAL	2	TRUE	0	0.408494417306848	1		226	510	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399350	139399350	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	101	579	0	ENST00000277541.6:c.4793G>T	p.Arg1598Leu	p.R1598L	ENST00000277541	NM_017617.3	1598	cGc/cTc	26/34	0.385517405211717	2	FACETS	0.462	0.412	0.516	0.231	0.206	0.258	SUBCLONAL	1	TRUE	0	0.408494417306848	2		579	1070	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191726	123191726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	143	321	1	ENST00000218089.9:c.1315C>T	p.Arg439Cys	p.R439C	ENST00000218089	NM_001042749.1	439	Cgt/Tgt	15/35	0.19987763058271	3	FACETS	1	0.98	1	0.626	0.572	0.683	INDETERMINATE	1	TRUE	1	0.408494417306848	3		322	673	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	178	635	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.547300534821628	2		635	648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0025827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	652	821	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.547300534821628	2	FACETS	0.969	0.938	1	0.969	0.938	1	CLONAL	2	TRUE	0	0.547300534821628	2		823	1229	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520017	NA	P-0025827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	323	1333	0	ENST00000326873.7:c.647C>T	p.Ser216Phe	p.S216F	ENST00000326873	NM_000455.4	216	tCc/tTc	5/10	0.547300534821628	1	FACETS	0.923	0.874	0.973	0.923	0.874	0.973	CLONAL	1	TRUE	0	0.547300534821628	1		1333	929	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652097	36652098	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0025827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	221	1075	0	ENST00000244741.5:c.222dup	p.Lys75GlnfsTer14	p.K75Qfs*14	ENST00000244741	NM_000389.4	73	-/C	2/3	1	2	FACETS	0.769	0.715	0.825	0.769	0.715	0.825	SUBCLONAL	1	TRUE	1	0.547300534821628	2		1075	1050	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857403	68857415	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTTAGAGGTCA	ACCTTAGAGGTCA	-	novel	NA	P-0025827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	242	772	0	ENST00000261769.5:c.2038_2050del	p.Thr680AlafsTer38	p.T680Afs*38	ENST00000261769	NM_004360.3	680	ACCTTAGAGGTCAgc/gc	13/16	0.547300534821628	1	FACETS	0.981	0.922	1	0.981	0.922	1	CLONAL	1	TRUE	0	0.547300534821628	1		772	655	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858308	59858308	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	161	627	1	ENST00000259008.2:c.1687G>C	p.Asp563His	p.D563H	ENST00000259008	NM_032043.2	563	Gat/Cat	12/20	1	2	FACETS	0.729	0.669	0.791	0.729	0.669	0.791	SUBCLONAL	1	TRUE	1	0.547300534821628	2		628	807	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873020	134873020	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	241	797	0	ENST00000398015.3:c.1324C>T	p.Gln442Ter	p.Q442*	ENST00000398015	NM_004441.4	442	Caa/Taa	6/16	1	2	FACETS	0.941	0.88	1	0.941	0.88	1	CLONAL	1	TRUE	1	0.547300534821628	2		797	936	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447681	187447681	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316769730	NA	P-0025827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	250	798	0	ENST00000232014.4:c.512G>A	p.Ser171Asn	p.S171N	ENST00000232014	NM_001130845.1	171	aGc/aAc	5/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.547300534821628	2		798	872	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36653535	36653535	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	264	637	0	ENST00000244741.5:c.454del	p.His152ThrfsTer6	p.H152Tfs*6	ENST00000244741	NM_000389.4	151	taC/ta	3/3	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.547300534821628	2		637	831	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372385	55372385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1310	253	1421	1	ENST00000297316.4:c.1075G>A	p.Asp359Asn	p.D359N	ENST00000297316	NM_022454.3	359	Gac/Aac	2/2	1	2	FACETS	0.592	0.552	0.633	0.592	0.552	0.633	SUBCLONAL	1	TRUE	1	0.547300534821628	2		1422	1563	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65312373	65312400	+	frameshift_variant	Frame_Shift_Del	DEL	TGTTTGTGGGAGACCTGTCTCATCATGC	TGTTTGTGGGAGACCTGTCTCATCATGC	-	novel	NA	P-0025851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	171	642	0	ENST00000342505.4:c.1919_1946del	p.Ser640ThrfsTer54	p.S640Tfs*54	ENST00000342505	NM_002227.2	640	aGCATGATGAGACAGGTCTCCCACAAACAc/ac	14/25	NA	2	FACETS	0.959	0.888	1			1	INDETERMINATE	2	TRUE	NA	0.328440949867553	2		642	543	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579182	7579319	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAACTATAAAAAAACACTGACAGGAAGCCAAAGGGTGAAGAGGAATCCCAAAGTTCCAAACAAAAGAAATGCAGGGGGATACGGCCAGGCATTGAAGTCTCATGGAAGCCAGCCCCTCAGGGCAACTGACCGTGCAAG	AAACTATAAAAAAACACTGACAGGAAGCCAAAGGGTGAAGAGGAATCCCAAAGTTCCAAACAAAAGAAATGCAGGGGGATACGGCCAGGCATTGAAGTCTCATGGAAGCCAGCCCCTCAGGGCAACTGACCGTGCAAG	-	novel	NA	P-0025851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	202	68	0	ENST00000269305.4:c.368_375+130del		p.X123_splice	ENST00000269305	NM_001126112.2	123		4/11	0.218593215992972	1	FACETS	1	0.992	1	1	0.996	1	CLONAL	4	TRUE	0	0.328440949867553	1		68	234	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942080	17942080	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	140	772	0	ENST00000458235.1:c.2935G>C	p.Asp979His	p.D979H	ENST00000458235	NM_000215.3	979	Gac/Cac	21/24	0.328440949867553	2	FACETS	0.831	0.756	0.91	0.415	0.378	0.455	CLONAL	1	TRUE	0	0.328440949867553	2		772	1026	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942143	17942143	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs749741343	NA	P-0025851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	146	681	0	ENST00000458235.1:c.2872G>C	p.Glu958Gln	p.E958Q	ENST00000458235	NM_000215.3	958	Gag/Cag	21/24	0.328440949867553	2	FACETS	0.882	0.804	0.964	0.441	0.402	0.482	CLONAL	1	TRUE	0	0.328440949867553	2		681	1008	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943413	17943413	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	137	759	0	ENST00000458235.1:c.2595G>C	p.Gln865His	p.Q865H	ENST00000458235	NM_000215.3	865	caG/caC	19/24	0.328440949867553	2	FACETS	0.886	0.805	0.971	0.443	0.402	0.486	CLONAL	1	TRUE	0	0.328440949867553	2		759	942	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943484	17943484	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	139	623	0	ENST00000458235.1:c.2524G>T	p.Asp842Tyr	p.D842Y	ENST00000458235	NM_000215.3	842	Gac/Tac	19/24	0.328440949867553	2	FACETS	1	0.932	1	0.514	0.467	0.562	CLONAL	1	TRUE	0	0.328440949867553	2		623	824	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945740	17945740	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	124	702	0	ENST00000458235.1:c.2120A>C	p.Asp707Ala	p.D707A	ENST00000458235	NM_000215.3	707	gAc/gCc	16/24	0.328440949867553	2	FACETS	0.814	0.735	0.896	0.407	0.367	0.448	CLONAL	1	TRUE	0	0.328440949867553	2		702	928	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212845	27212845	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	162	686	0	ENST00000380036.4:c.2827C>A	p.His943Asn	p.H943N	ENST00000380036	NM_000459.3	943	Cac/Aac	17/23	0.328440949867553	3	FACETS	1	0.974	1	0.575	0.527	0.625	CLONAL	1	TRUE	1	0.328440949867553	3		686	999	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579182	7579319	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAACTATAAAAAAACACTGACAGGAAGCCAAAGGGTGAAGAGGAATCCCAAAGTTCCAAACAAAAGAAATGCAGGGGGATACGGCCAGGCATTGAAGTCTCATGGAAGCCAGCCCCTCAGGGCAACTGACCGTGCAAG	AAACTATAAAAAAACACTGACAGGAAGCCAAAGGGTGAAGAGGAATCCCAAAGTTCCAAACAAAAGAAATGCAGGGGGATACGGCCAGGCATTGAAGTCTCATGGAAGCCAGCCCCTCAGGGCAACTGACCGTGCAAG	-	novel	NA	P-0025851-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	185	68	0	ENST00000269305.4:c.368_375+130del		p.X123_splice	ENST00000269305	NM_001126112.2	123		4/11	0.265437196846041	2	FACETS		NA	1	1	0.996	1	NA	5	TRUE	0	0.41	2		68	192	SUCCESS
EED	8726	MSKCC	GRCh37	11	85975282	85975282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025851-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	148	373	1	ENST00000263360.6:c.703C>T	p.His235Tyr	p.H235Y	ENST00000263360	NM_003797.3	235	Cac/Tac	7/12	0.303485338813305	5	FACETS	0.89	0.815	0.968	0.89	0.815	0.968	CLONAL	2	TRUE	3	0.41	5		374	655	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133300	38133300	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025851-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	186	507	0	ENST00000317025.8:c.4173G>C	p.Lys1391Asn	p.K1391N	ENST00000317025	NM_023034.1	1391	aaG/aaC	24/24	0.303485338813305	6	FACETS	1	0.967	1			1	CLONAL	2	TRUE	NA	0.41	6		507	766	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	119	480	1	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	0.959	0.867	1	0.959	0.867	1	CLONAL	1	TRUE	1	0.370813909934328	2		481	669	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	103	557	0	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	0.796	0.713	0.884	0.796	0.713	0.884	SUBCLONAL	1	TRUE	1	0.370813909934328	2		557	698	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	85	560	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.897	0.795	1	0.897	0.795	1	CLONAL	1	TRUE	1	0.370813909934328	2		560	511	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	72	269	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.897	0.787	1	0.897	0.787	1	CLONAL	1	TRUE	1	0.370813909934328	2		269	433	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	81	356	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.370813909934328	3	FACETS	0.95	0.839	1	0.475	0.419	0.535	CLONAL	1	TRUE	1	0.370813909934328	3		356	545	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822586	72822586	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	65	314	1	ENST00000268489.5:c.9589del	p.Gln3197SerfsTer44	p.Q3197Sfs*44	ENST00000268489	NM_006885.3	3197	Cag/ag	10/10	1	2	FACETS	0.918	0.8	1	0.918	0.8	1	CLONAL	1	TRUE	1	0.370813909934328	2		315	382	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	129	494	3	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	0.370813909934328	2		497	637	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	134	345	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.944	0.867	1	1	0.991	1	CLONAL	2	TRUE	1	0.370813909934328	2		345	383	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372206	55372206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	70	392	0	ENST00000297316.4:c.896C>T	p.Ala299Val	p.A299V	ENST00000297316	NM_022454.3	299	gCg/gTg	2/2	1	2	FACETS	0.949	0.831	1	0.949	0.831	1	CLONAL	1	TRUE	1	0.370813909934328	2		392	398	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	121	347	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.370813909934328	3	FACETS	1	0.981	1	0.669	0.607	0.735	CLONAL	1	TRUE	1	0.370813909934328	3		347	578	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679733	30679733	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	119	452	0	ENST00000376406.3:c.1986G>C	p.Gln662His	p.Q662H	ENST00000376406	NM_014641.2	662	caG/caC	5/15	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.370813909934328	2		452	634	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888210	112888210	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121918464	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	63	513	0	ENST00000351677.2:c.226G>C	p.Glu76Gln	p.E76Q	ENST00000351677	NM_002834.3	76	Gag/Cag	3/16	1	2	FACETS	0.644	0.557	0.737	0.644	0.557	0.737	SUBCLONAL	1	TRUE	1	0.370813909934328	2		513	528	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261554	142261555	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1043355995	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	116	539	0	ENST00000350721.4:c.3402dup	p.Asn1135Ter	p.N1135*	ENST00000350721	NM_001184.3	1134	-/T	17/47	1	2	FACETS	0.909	0.821	1	0.909	0.821	1	CLONAL	1	TRUE	1	0.370813909934328	2		539	688	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117054	193117054	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878855091	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	74	448	0	ENST00000367435.3:c.787C>T	p.Arg263Cys	p.R263C	ENST00000367435	NM_024529.4	263	Cgt/Tgt	8/17	1	2	FACETS	0.727	0.637	0.823	0.727	0.637	0.823	SUBCLONAL	1	TRUE	1	0.370813909934328	2		448	549	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361148	70361149	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAC	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	23	196	2	ENST00000374080.3:c.6338_6339insCCA	p.Gln2112_Gln2113insHis	p.Q2112_Q2113insH	ENST00000374080		2112	-/CAC	43/45	0.255939395608573	2	FACETS	0.344	0.267	0.432			1	SUBCLONAL	1	TRUE	NA	0.370813909934328	2		198	361	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554355	81554355	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747687365	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	88	404	0	ENST00000298171.2:c.379del	p.Leu127SerfsTer2	p.L127Sfs*2	ENST00000298171	NM_000369.2	125	ctC/ct	4/10	1	2	FACETS	0.94	0.835	1	0.94	0.835	1	CLONAL	1	TRUE	1	0.370813909934328	2		404	505	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270530	98270530	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs751977093	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	13	210	0	ENST00000331920.6:c.114del	p.Leu39CysfsTer41	p.L39Cfs*41	ENST00000331920	NM_000264.3	38	ggG/gg	1/24	1	2	FACETS	0.282	0.2	0.381	0.282	0.2	0.381	SUBCLONAL	1	TRUE	1	0.370813909934328	2		210	249	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505462	157505462	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	98	380	0	ENST00000346085.5:c.3443A>G	p.Tyr1148Cys	p.Y1148C	ENST00000346085	NM_020732.3	1148	tAc/tGc	13/20	1	2	FACETS	0.919	0.822	1	0.919	0.822	1	CLONAL	1	TRUE	1	0.370813909934328	2		380	575	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367288	50367288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775793261	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	72	354	0	ENST00000331340.3:c.95C>T	p.Pro32Leu	p.P32L	ENST00000331340	NM_006060.4	32	cCg/cTg	3/8	1	2	FACETS	0.758	0.664	0.86	0.758	0.664	0.86	SUBCLONAL	1	TRUE	1	0.370813909934328	2		354	512	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346158	89346158	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs878855327	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	25	154	0	ENST00000301030.4:c.6792del	p.Ala2265ProfsTer72	p.A2265Pfs*72	ENST00000301030	NM_001256183.1	2264	ccC/cc	9/13	1	2	FACETS	0.729	0.579	0.899	0.729	0.579	0.899	SUBCLONAL	1	TRUE	1	0.370813909934328	2		154	185	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1620992	1620992	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	161	685	0	ENST00000344749.5:c.1068del	p.Val357TrpfsTer37	p.V357Wfs*37	ENST00000344749	NM_001136139.2	356	ccC/cc	13/19	1	2	FACETS	0.933	0.855	1	0.933	0.855	1	CLONAL	1	TRUE	1	0.370813909934328	2		685	931	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123837	46123837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	57	265	0	ENST00000334344.6:c.109del	p.Ile37SerfsTer21	p.I37Sfs*21	ENST00000334344	NM_152641.2	35	Aaa/aa	2/21	1	2	FACETS	0.856	0.738	0.984	0.856	0.738	0.984	CLONAL	1	TRUE	1	0.370813909934328	2		265	359	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106562	27106562	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	141	518	0	ENST00000324856.7:c.6176del	p.Asn2059ThrfsTer76	p.N2059Tfs*76	ENST00000324856	NM_006015.4	2058	gAa/ga	20/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.370813909934328	2		518	680	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863319	57863319	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	114	494	0	ENST00000228682.2:c.1418del	p.Gly473AlafsTer40	p.G473Afs*40	ENST00000228682	NM_005269.2	472	Ggg/gg	11/12	1	2	FACETS	0.99	0.894	1	0.99	0.894	1	CLONAL	1	TRUE	1	0.370813909934328	2		494	621	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148504761	148504761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397515548	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	120	459	0	ENST00000320356.2:c.2233G>A	p.Glu745Lys	p.E745K	ENST00000320356	NM_004456.4	745	Gaa/Aaa	20/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.370813909934328	2		459	596	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163554	32163554	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	105	394	1	ENST00000375023.3:c.5672del	p.Gly1891AlafsTer13	p.G1891Afs*13	ENST00000375023	NM_004557.3	1891	gGc/gc	30/30	1	2	FACETS	0.828	0.75	0.909	1	0.986	1	CLONAL	2	TRUE	1	0.370813909934328	2		395	342	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186895	142186895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866304619	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	58	320	1	ENST00000350721.4:c.6568C>T	p.Arg2190Cys	p.R2190C	ENST00000350721	NM_001184.3	2190	Cgt/Tgt	39/47	1	2	FACETS	0.761	0.656	0.875	0.761	0.656	0.875	SUBCLONAL	1	TRUE	1	0.370813909934328	2		321	411	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401004	139401004	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180096756	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	115	473	0	ENST00000277541.6:c.3989G>A	p.Arg1330His	p.R1330H	ENST00000277541	NM_017617.3	1330	cGc/cAc	24/34	1	2	FACETS	0.913	0.824	1	0.913	0.824	1	CLONAL	1	TRUE	1	0.370813909934328	2		473	679	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462643	29462643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs187200776	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	123	570	0	ENST00000389048.3:c.2258G>A	p.Arg753Gln	p.R753Q	ENST00000389048	NM_004304.4	753	cGg/cAg	13/29	1	2	FACETS	0.974	0.882	1	0.974	0.882	1	CLONAL	1	TRUE	1	0.370813909934328	2		570	681	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025857	48025857	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs267608041	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	69	345	0	ENST00000234420.5:c.741del	p.Lys247AsnfsTer32	p.K247Nfs*32	ENST00000234420	NM_000179.2	245	atA/at	4/10	1	2	FACETS	0.854	0.746	0.969	0.854	0.746	0.969	CLONAL	1	TRUE	1	0.370813909934328	2		345	436	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821959	72821959	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	42	197	0	ENST00000268489.5:c.10216G>C	p.Gly3406Arg	p.G3406R	ENST00000268489	NM_006885.3	3406	Ggg/Cgg	10/10	1	2	FACETS	0.848	0.713	0.997	0.848	0.713	0.997	CLONAL	1	TRUE	1	0.370813909934328	2		197	267	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2492097	2492097	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs772088410	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	139	639	2	ENST00000355716.4:c.500del	p.Pro167ArgfsTer23	p.P167Rfs*23	ENST00000355716	NM_003820.2	165	tgC/tg	5/8	1	2	FACETS	0.926	0.843	1	0.926	0.843	1	CLONAL	1	TRUE	1	0.370813909934328	2		641	810	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873597	37873597	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	112	537	0	ENST00000269571.5:c.1762G>A	p.Ala588Thr	p.A588T	ENST00000269571		588	Gcc/Acc	15/27	1	2	FACETS	0.934	0.841	1	0.934	0.841	1	CLONAL	1	TRUE	1	0.370813909934328	2		537	647	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12043203	12043203	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	61	349	0	ENST00000353533.5:c.1086+2T>C		p.X362_splice	ENST00000353533	NM_003010.3	362			1	2	FACETS	0.778	0.673	0.891	0.778	0.673	0.891	SUBCLONAL	1	TRUE	1	0.370813909934328	2		349	423	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306544	41306544	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751487270	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	89	422	0	ENST00000373198.4:c.1115C>T	p.Pro372Leu	p.P372L	ENST00000373198	NM_133170.3	372	cCg/cTg	7/32	1	2	FACETS	0.941	0.837	1	0.941	0.837	1	CLONAL	1	TRUE	1	0.370813909934328	2		422	510	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229011	36229011	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	79	586	0	ENST00000222270.7:c.7795del	p.Glu2599ArgfsTer15	p.E2599Rfs*15	ENST00000222270	NM_014727.1	2597	gcG/gc	36/37	1	2	FACETS	0.51	0.447	0.577	0.51	0.447	0.577	SUBCLONAL	1	TRUE	1	0.370813909934328	2		586	836	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356269	70356269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	78	187	0	ENST00000374080.3:c.5164C>T	p.Arg1722Trp	p.R1722W	ENST00000374080		1722	Cgg/Tgg	37/45	0.255939395608573	2	FACETS	1	0.961	1			1	CLONAL	1	TRUE	NA	0.370813909934328	2		187	349	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435199	49435199	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	73	317	0	ENST00000301067.7:c.6354del	p.Ala2119LeufsTer25	p.A2119Lfs*25	ENST00000301067	NM_003482.3	2118	ccC/cc	31/54	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.370813909934328	2		317	355	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863054	56863054	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1266824391	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	39	471	2	ENST00000519728.1:c.327del	p.Glu110LysfsTer15	p.E110Kfs*15	ENST00000519728	NM_002350.3	107	acA/ac	5/13	1	2	FACETS	0.361	0.299	0.431	0.361	0.299	0.431	SUBCLONAL	1	TRUE	1	0.370813909934328	2		473	582	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994848	73994848	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910584858	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	25	83	0	ENST00000318443.5:c.332G>A	p.Arg111His	p.R111H	ENST00000318443	NM_001024736.1	111	cGc/cAc	3/10	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.370813909934328	2		83	106	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039143	49039143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs529366765	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	70	239	0	ENST00000267163.4:c.2221C>T	p.Arg741Cys	p.R741C	ENST00000267163	NM_000321.2	741	Cgt/Tgt	22/27	1	2	FACETS	0.991	0.869	1	0.991	0.869	1	CLONAL	1	TRUE	1	0.370813909934328	2		239	381	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993738	72993738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759648686	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	90	295	0	ENST00000268489.5:c.307C>T	p.Arg103Cys	p.R103C	ENST00000268489	NM_006885.3	103	Cgc/Tgc	2/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.370813909934328	2		295	412	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856434	111856434	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs776317487	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	72	282	0	ENST00000341259.2:c.489del	p.Thr165ProfsTer32	p.T165Pfs*32	ENST00000341259	NM_005475.2	162	gCc/gc	2/8	1	2	FACETS	0.959	0.842	1	0.959	0.842	1	CLONAL	1	TRUE	1	0.370813909934328	2		282	405	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595382	141595382	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	112	551	1	ENST00000220592.5:c.51del	p.Ile18SerfsTer121	p.I18Sfs*121	ENST00000220592	NM_012154.3	17	ccC/cc	2/19	1	2	FACETS	0.971	0.875	1	0.971	0.875	1	CLONAL	1	TRUE	1	0.370813909934328	2		552	622	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942232	71942232	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs775939148	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	68	282	0	ENST00000298229.2:c.1496C>T	p.Pro499Leu	p.P499L	ENST00000298229	NM_001567.3	499	cCg/cTg	12/28	1	2	FACETS	0.804	0.702	0.915	0.804	0.702	0.915	CLONAL	1	TRUE	1	0.370813909934328	2		282	456	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780280	9780280	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	68	421	0	ENST00000377346.4:c.1450T>C	p.Tyr484His	p.Y484H	ENST00000377346	NM_005026.3	484	Tac/Cac	11/24	1	2	FACETS	0.75	0.654	0.854	0.75	0.654	0.854	SUBCLONAL	1	TRUE	1	0.370813909934328	2		421	489	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263923	16263923	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	127	600	0	ENST00000375759.3:c.10292T>A	p.Phe3431Tyr	p.F3431Y	ENST00000375759	NM_015001.2	3431	tTc/tAc	12/15	1	2	FACETS	0.838	0.76	0.921	0.838	0.76	0.921	CLONAL	1	TRUE	1	0.370813909934328	2		600	817	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105916	27105916	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	97	348	2	ENST00000324856.7:c.5527C>T	p.His1843Tyr	p.H1843Y	ENST00000324856	NM_006015.4	1843	Cac/Tac	20/20	1	2	FACETS	0.938	0.838	1	0.938	0.838	1	CLONAL	1	TRUE	1	0.370813909934328	2		350	558	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797951	45797951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769237459	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	88	492	0	ENST00000450313.1:c.820C>T	p.Arg274Trp	p.R274W	ENST00000450313	NM_012222.2	274	Cgg/Tgg	10/16	1	2	FACETS	0.691	0.612	0.775	0.691	0.612	0.775	SUBCLONAL	1	TRUE	1	0.370813909934328	2		492	687	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261337	115261337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772339521	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	78	342	0	ENST00000438362.2:c.2384G>A	p.Arg795Gln	p.R795Q	ENST00000438362	NM_001242891.1	795	cGa/cAa	19/20	1	2	FACETS	0.948	0.836	1	0.948	0.836	1	CLONAL	1	TRUE	1	0.370813909934328	2		342	444	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100532	8100532	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	113	475	1	ENST00000346208.3:c.509del	p.Pro170GlnfsTer25	p.P170Qfs*25	ENST00000346208		169	aCc/ac	3/6	0.296202514453314	1	FACETS	0.891	0.805	0.982	0.891	0.805	0.982	CLONAL	1	TRUE	0	0.370813909934328	1		476	557	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601998	43601998	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1183365192	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	113	531	2	ENST00000355710.3:c.1042C>T	p.Arg348Trp	p.R348W	ENST00000355710	NM_020975.4	348	Cgg/Tgg	5/20	1	2	FACETS	0.82	0.738	0.907	0.82	0.738	0.907	CLONAL	1	TRUE	1	0.370813909934328	2		533	743	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202516	67202516	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	103	459	2	ENST00000312629.5:c.1325C>A	p.Pro442His	p.P442H	ENST00000312629	NM_003952.2	442	cCc/cAc	15/15	1	2	FACETS	0.857	0.768	0.952	0.857	0.768	0.952	CLONAL	1	TRUE	1	0.370813909934328	2		461	648	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307639	118307639	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	112	503	0	ENST00000534358.1:c.416del	p.Gly139GlufsTer11	p.G139Efs*11	ENST00000534358	NM_005933.3	138	Ggg/gg	1/36	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.370813909934328	2		503	507	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427545	49427545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758858726	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	92	383	1	ENST00000301067.7:c.10943C>T	p.Pro3648Leu	p.P3648L	ENST00000301067	NM_003482.3	3648	cCg/cTg	39/54	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.370813909934328	2		384	481	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563282	21563282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756335536	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	88	537	1	ENST00000382592.4:c.637G>A	p.Asp213Asn	p.D213N	ENST00000382592	NM_014572.2	213	Gac/Aac	4/8	1	2	FACETS	0.709	0.629	0.796	0.709	0.629	0.796	SUBCLONAL	1	TRUE	1	0.370813909934328	2		538	669	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975674	26975675	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	105	442	0	ENST00000381527.3:c.1189_1190dup	p.Gln397HisfsTer6	p.Q397Hfs*6	ENST00000381527	NM_001260.1	394	-/CA	12/13	1	2	FACETS	0.874	0.784	0.969	0.874	0.784	0.969	CLONAL	1	TRUE	1	0.370813909934328	2		442	648	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871732	35871732	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	95	411	0	ENST00000216797.5:c.774G>T	p.Trp258Cys	p.W258C	ENST00000216797	NM_020529.2	258	tgG/tgT	5/6	1	2	FACETS	0.844	0.753	0.941	0.844	0.753	0.941	CLONAL	1	TRUE	1	0.370813909934328	2		411	607	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396895	396895	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	147	589	0	ENST00000262320.3:c.131T>C	p.Phe44Ser	p.F44S	ENST00000262320	NM_003502.3	44	tTc/tCc	2/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.370813909934328	2		589	753	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3634797	3634797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765601038	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	152	575	4	ENST00000294008.3:c.4712C>T	p.Thr1571Met	p.T1571M	ENST00000294008	NM_032444.2	1571	aCg/aTg	13/15	1	2	FACETS	0.928	0.849	1	0.928	0.849	1	CLONAL	1	TRUE	1	0.370813909934328	2		579	883	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3842002	3842002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	92	341	0	ENST00000262367.5:c.1310G>A	p.Ser437Asn	p.S437N	ENST00000262367	NM_004380.2	437	aGt/aAt	5/31	1	2	FACETS	0.917	0.817	1	0.917	0.817	1	CLONAL	1	TRUE	1	0.370813909934328	2		341	541	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619314	23619314	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	53	439	0	ENST00000261584.4:c.3221T>C	p.Leu1074Pro	p.L1074P	ENST00000261584	NM_024675.3	1074	cTg/cCg	12/13	1	2	FACETS	0.461	0.393	0.536	0.461	0.393	0.536	SUBCLONAL	1	TRUE	1	0.370813909934328	2		439	620	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832058	72832058	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	87	440	0	ENST00000268489.5:c.4523G>A	p.Ser1508Asn	p.S1508N	ENST00000268489	NM_006885.3	1508	aGt/aAt	9/10	1	2	FACETS	0.867	0.77	0.971	0.867	0.77	0.971	CLONAL	1	TRUE	1	0.370813909934328	2		440	541	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984466	72984466	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	71	464	0	ENST00000268489.5:c.3118C>A	p.Leu1040Ile	p.L1040I	ENST00000268489	NM_006885.3	1040	Ctc/Atc	3/10	1	2	FACETS	0.604	0.527	0.687	0.604	0.527	0.687	SUBCLONAL	1	TRUE	1	0.370813909934328	2		464	634	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347173	89347173	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	60	370	1	ENST00000301030.4:c.5777del	p.Pro1926ArgfsTer37	p.P1926Rfs*37	ENST00000301030	NM_001256183.1	1926	cCg/cg	9/13	1	2	FACETS	0.689	0.594	0.791	0.689	0.594	0.791	SUBCLONAL	1	TRUE	1	0.370813909934328	2		371	470	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351124	89351124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	111	439	0	ENST00000301030.4:c.1826G>A	p.Ser609Asn	p.S609N	ENST00000301030	NM_001256183.1	609	aGc/aAc	9/13	1	2	FACETS	0.993	0.895	1	0.993	0.895	1	CLONAL	1	TRUE	1	0.370813909934328	2		439	603	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879673	37879673	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765387989	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	91	500	0	ENST00000269571.5:c.2048G>A	p.Arg683Gln	p.R683Q	ENST00000269571		683	cGg/cAg	17/27	1	2	FACETS	0.799	0.711	0.894	0.799	0.711	0.894	SUBCLONAL	1	TRUE	1	0.370813909934328	2		500	614	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117738	70117739	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	100	541	0	ENST00000245479.2:c.210dup	p.Val71ArgfsTer181	p.V71Rfs*181	ENST00000245479	NM_000346.3	69	ttc/ttCc	1/3	1	2	FACETS	0.811	0.725	0.902	0.811	0.725	0.902	CLONAL	1	TRUE	1	0.370813909934328	2		541	665	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279932	18279932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1423694208	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	155	544	2	ENST00000222254.8:c.2015G>A	p.Arg672His	p.R672H	ENST00000222254	NM_005027.3	672	cGc/cAc	16/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.370813909934328	2		546	751	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965724	18965724	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	152	640	1	ENST00000262803.5:c.1302G>T	p.Glu434Asp	p.E434D	ENST00000262803	NM_002911.3	434	gaG/gaT	10/24	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.370813909934328	2		641	804	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216188	36216188	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	131	445	0	ENST00000222270.7:c.3596G>C	p.Gly1199Ala	p.G1199A	ENST00000222270	NM_014727.1	1199	gGc/gCc	11/37	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.370813909934328	2		445	623	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229184	36229184	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	26	364	2	ENST00000222270.7:c.7874G>A	p.Gly2625Asp	p.G2625D	ENST00000222270	NM_014727.1	2625	gGc/gAc	37/37	1	2	FACETS	0.308	0.243	0.383	0.308	0.243	0.383	SUBCLONAL	1	TRUE	1	0.370813909934328	2		366	455	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140130	50140130	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1488434625	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	87	491	2	ENST00000246792.3:c.295C>T	p.Arg99Cys	p.R99C	ENST00000246792	NM_006270.3	99	Cgt/Tgt	3/6	1	2	FACETS	0.645	0.571	0.725	0.645	0.571	0.725	SUBCLONAL	1	TRUE	1	0.370813909934328	2		493	727	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469629	25469629	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750837407	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	125	484	1	ENST00000264709.3:c.1139C>T	p.Ala380Val	p.A380V	ENST00000264709	NM_175629.2	380	gCg/gTg	10/23	1	2	FACETS	0.929	0.841	1	0.929	0.841	1	CLONAL	1	TRUE	1	0.370813909934328	2		485	726	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964965	25964965	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	102	366	2	ENST00000435504.4:c.4241G>A	p.Gly1414Asp	p.G1414D	ENST00000435504		1414	gGc/gAc	13/13	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.370813909934328	2		368	490	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607487	46607487	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	130	556	2	ENST00000263734.3:c.1681del	p.Gln561SerfsTer7	p.Q561Sfs*7	ENST00000263734	NM_001430.4	559	aCc/ac	12/16	1	2	FACETS	0.92	0.835	1	0.92	0.835	1	CLONAL	1	TRUE	1	0.370813909934328	2		558	762	SUCCESS
REL	5966	MSKCC	GRCh37	2	61144018	61144018	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	45	292	0	ENST00000295025.8:c.405del	p.Lys135AsnfsTer3	p.K135Nfs*3	ENST00000295025	NM_002908.2	134	gAa/ga	5/11	1	2	FACETS	0.843	0.712	0.985	0.843	0.712	0.985	CLONAL	1	TRUE	1	0.370813909934328	2		292	288	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279815	46279820	+	inframe_deletion	In_Frame_Del	DEL	GCAGCA	GCAGCA	-	rs3830810	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	22	332	1	ENST00000371998.3:c.3756_3761del	p.Gln1275_Gln1276del	p.Q1275_Q1276del	ENST00000371998		1247	atGCAGCAg/atg	20/23	1	2	FACETS	0.293	0.226	0.371	0.293	0.226	0.371	SUBCLONAL	1	TRUE	1	0.370813909934328	2		333	405	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945542	54945542	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs200181472	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	142	678	1	ENST00000312783.6:c.1028G>A	p.Arg343Gln	p.R343Q	ENST00000312783	NM_198436.1	343	cGg/cAg	9/10	1	2	FACETS	0.88	0.802	0.962	0.88	0.802	0.962	CLONAL	1	TRUE	1	0.370813909934328	2		679	870	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397752	49397752	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	134	499	0	ENST00000418115.1:c.472G>T	p.Glu158Ter	p.E158*	ENST00000418115	NM_001664.2	158	Gag/Tag	5/5	1	2	FACETS	0.891	0.81	0.977	0.891	0.81	0.977	CLONAL	1	TRUE	1	0.370813909934328	2		499	811	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940111	49940111	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	101	428	0	ENST00000296474.3:c.932C>G	p.Ala311Gly	p.A311G	ENST00000296474	NM_002447.2	311	gCc/gGc	1/20	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.370813909934328	2		428	545	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825389	134825389	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	99	437	0	ENST00000398015.3:c.905C>A	p.Thr302Asn	p.T302N	ENST00000398015	NM_004441.4	302	aCc/aAc	4/16	1	2	FACETS	0.88	0.787	0.978	0.88	0.787	0.978	CLONAL	1	TRUE	1	0.370813909934328	2		437	607	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442853	187442853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766041104	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	79	289	1	ENST00000232014.4:c.1853G>A	p.Arg618His	p.R618H	ENST00000232014	NM_001130845.1	618	cGt/cAt	9/10	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.370813909934328	2		290	405	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196928	106196928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	20	263	1	ENST00000380013.4:c.5261G>A	p.Gly1754Asp	p.G1754D	ENST00000380013	NM_001127208.2	1754	gGt/gAt	11/11	1	2	FACETS	0.42	0.321	0.535	0.42	0.321	0.535	SUBCLONAL	1	TRUE	1	0.370813909934328	2		264	257	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176662870	176662870	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	86	454	0	ENST00000439151.2:c.3845T>C	p.Leu1282Ser	p.L1282S	ENST00000439151	NM_022455.4	1282	tTg/tCg	6/23	0.370813909934328	3	FACETS	0.937	0.83	1	0.468	0.415	0.526	CLONAL	1	TRUE	1	0.370813909934328	3		454	587	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964472	93964472	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	96	525	0	ENST00000369303.4:c.2425C>T	p.Gln809Ter	p.Q809*	ENST00000369303	NM_004440.3	809	Cag/Tag	14/17	1	2	FACETS	0.992	0.887	1	0.992	0.887	1	CLONAL	1	TRUE	1	0.370813909934328	2		525	522	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200183	138200183	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	69	351	0	ENST00000237289.4:c.1601G>A	p.Gly534Glu	p.G534E	ENST00000237289	NM_001270507.1	534	gGg/gAg	7/9	1	2	FACETS	0.78	0.681	0.887	0.78	0.681	0.887	SUBCLONAL	1	TRUE	1	0.370813909934328	2		351	477	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100434	157100445	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGCGGG	GGCGGCGGCGGG	-	rs1239601972	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	13	20	1	ENST00000346085.5:c.1383_1394del	p.Ala462_Gly465del	p.A462_G465del	ENST00000346085	NM_020732.3	457	gcGGCGGCGGCGGGg/gcg	1/20	1	2	FACETS	1	0.831	1	1	0.926	1	CLONAL	2	TRUE	1	0.370813909934328	2		21	31	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371882	55371882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	58	211	0	ENST00000297316.4:c.572G>A	p.Gly191Asp	p.G191D	ENST00000297316	NM_022454.3	191	gGc/gAc	2/2	1	2	FACETS	0.987	0.854	1	0.987	0.854	1	CLONAL	1	TRUE	1	0.370813909934328	2		211	317	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325566	87325566	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	23	350	0	ENST00000277120.3:c.443A>G	p.Asn148Ser	p.N148S	ENST00000277120		148	aAt/aGt	6/19	1	2	FACETS	0.311	0.242	0.391	0.311	0.242	0.391	SUBCLONAL	1	TRUE	1	0.370813909934328	2		350	399	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242751	98242751	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1221172962	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	99	381	0	ENST00000331920.6:c.866A>G	p.His289Arg	p.H289R	ENST00000331920	NM_000264.3	289	cAt/cGt	6/24	1	2	FACETS	0.871	0.779	0.969	0.871	0.779	0.969	CLONAL	1	TRUE	1	0.370813909934328	2		381	613	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778112	135778112	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	83	468	0	ENST00000298552.3:c.2271A>C	p.Glu757Asp	p.E757D	ENST00000298552	NM_001162426.1	757	gaA/gaC	18/23	1	2	FACETS	0.715	0.631	0.805	0.715	0.631	0.805	SUBCLONAL	1	TRUE	1	0.370813909934328	2		468	626	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135800991	135800993	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	45	370	0	ENST00000298552.3:c.344_346del	p.Ser115del	p.S115del	ENST00000298552	NM_001162426.1	115	tCTTta/tta	5/23	1	2	FACETS	0.473	0.397	0.557	0.473	0.397	0.557	SUBCLONAL	1	TRUE	1	0.370813909934328	2		370	513	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137218489	137218489	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	20	128	0	ENST00000481739.1:c.12A>T	p.Lys4Asn	p.K4N	ENST00000481739	NM_002957.4	4	aaA/aaT	1/10	1	2	FACETS	0.553	0.425	0.702	0.553	0.425	0.702	SUBCLONAL	1	TRUE	1	0.370813909934328	2		128	195	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15838418	15838418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	165	198	0	ENST00000307771.7:c.916C>T	p.Arg306Trp	p.R306W	ENST00000307771	NM_005089.3	306	Cgg/Tgg	10/11	0.255939395608573	2	FACETS	0.883	0.825	0.941			1	CLONAL	3	TRUE	NA	0.370813909934328	2		198	336	SUCCESS
AR	367	MSKCC	GRCh37	X	66766195	66766195	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	45	139	0	ENST00000374690.3:c.1207G>A	p.Ala403Thr	p.A403T	ENST00000374690	NM_000044.3	403	Gcg/Acg	1/8	0.255939395608573	2	FACETS	1	0.895	1			1	CLONAL	1	TRUE	NA	0.370813909934328	2		139	227	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347951	70347951	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	23	270	0	ENST00000374080.3:c.3190G>T	p.Gly1064Trp	p.G1064W	ENST00000374080		1064	Ggg/Tgg	22/45	0.255939395608573	2	FACETS	0.27	0.21	0.34			1	SUBCLONAL	1	TRUE	NA	0.370813909934328	2		270	459	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050384	37050387	+	frameshift_variant	Frame_Shift_Ins	INS	AAGT	AAGT	GGAAGC	novel	NA	P-0025883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	64	424	0	ENST00000231790.2:c.533_536delinsGGAAGC	p.Glu178GlyfsTer25	p.E178Gfs*25	ENST00000231790	NM_000249.3	178	gAAGTt/gGGAAGCt	6/19	0.369226770729876	1	FACETS	0.668	0.58	0.762	0.668	0.58	0.762	SUBCLONAL	1	TRUE	0	0.370813909934328	1		424	421	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0025912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	74	425	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.979	0.857	1	0.979	0.857	1	CLONAL	1	TRUE	1	0.22	2		426	687	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349350	89349350	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	222	778	0	ENST00000301030.4:c.3600A>T	p.Lys1200Asn	p.K1200N	ENST00000301030	NM_001256183.1	1200	aaA/aaT	9/13	0.217652256909678	2	FACETS	0.776	0.721	0.834	0.776	0.721	0.834	SUBCLONAL	2	TRUE	0	0.22	2		778	1300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577035	7577036	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0025912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	196	584	0	ENST00000269305.4:c.902dup	p.Gly302ArgfsTer4	p.G302Rfs*4	ENST00000269305	NM_001126112.2	301	cca/ccCa	8/11	0.217652256909678	2	FACETS	0.911	0.843	0.981	0.911	0.843	0.981	CLONAL	2	TRUE	0	0.22	2		584	978	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252941	36252943	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0025912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	63	418	0	ENST00000300305.3:c.419_421del	p.Tyr140del	p.Y140del	ENST00000300305		140	tACTcg/tcg	4/8	1	2	FACETS	0.836	0.722	0.96	0.836	0.722	0.96	CLONAL	1	TRUE	1	0.22	2		418	685	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696178	52696178	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	60	719	0	ENST00000394830.3:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000394830	NM_018313.4	167	Caa/Taa	5/30	0.183311540228213	2	FACETS	0.527	0.452	0.608	0.263	0.226	0.304	SUBCLONAL	1	TRUE	0	0.22	2		719	1036	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186826	142186826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	47	499	0	ENST00000350721.4:c.6637G>A	p.Gly2213Arg	p.G2213R	ENST00000350721	NM_001184.3	2213	Gga/Aga	39/47	0.298454169967342	3	FACETS	0.582	0.489	0.685	0.291	0.244	0.343	SUBCLONAL	1	TRUE	1	0.22	3		499	815	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526639	106526639	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	158	454	0	ENST00000359195.3:c.2932A>T	p.Ile978Phe	p.I978F	ENST00000359195	NM_002649.2	978	Att/Ttt	10/11	0.21657570353348	3	FACETS	0.874	0.801	0.951	0.874	0.801	0.951	CLONAL	2	TRUE	1	0.22	3		454	912	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27172718	27172718	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	124	553	0	ENST00000380036.4:c.733G>T	p.Gly245Trp	p.G245W	ENST00000380036	NM_000459.3	245	Ggg/Tgg	5/23	0.166581745699002	2	FACETS	1	0.977	1	0.633	0.572	0.698	CLONAL	1	TRUE	0	0.22	2		553	890	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223540	53223541	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0025912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	47	330	0	ENST00000375401.3:c.3818_3819del	p.Pro1273ArgfsTer26	p.P1273Rfs*26	ENST00000375401	NM_004187.3	1273	cCC/c	23/26	0.22259607478624	1	FACETS	0.768	0.648	0.9	0.768	0.648	0.9	SUBCLONAL	1	TRUE	0	0.22	1		330	495	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	49	186	1	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.694	0.599	0.796	0.694	0.599	0.796	SUBCLONAL	1	TRUE	1	0.84	2		187	168	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821890	72821890	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	189	322	3	ENST00000268489.5:c.10285del	p.Arg3429ValfsTer56	p.R3429Vfs*56	ENST00000268489	NM_006885.3	3429	Cgt/gt	10/10	1	2	FACETS	0.962	0.898	1	0.962	0.898	1	CLONAL	1	TRUE	1	0.84	2		325	468	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	324	995	3	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.886	0.84	0.932	0.886	0.84	0.932	CLONAL	1	TRUE	1	0.84	2		998	871	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177626	56177626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530669321	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	158	337	0	ENST00000399503.3:c.2599G>A	p.Glu867Lys	p.E867K	ENST00000399503	NM_005921.1	867	Gaa/Aaa	14/20	1	2	FACETS	0.913	0.846	0.981	0.913	0.846	0.981	CLONAL	1	TRUE	1	0.84	2		337	412	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321245	65321245	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771960711	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	232	467	0	ENST00000342505.4:c.1595G>A	p.Arg532His	p.R532H	ENST00000342505	NM_002227.2	532	cGc/cAc	11/25	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.84	2		467	532	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692791	89692791	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1114167623	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	180	292	0	ENST00000371953.3:c.275A>G	p.Asp92Gly	p.D92G	ENST00000371953	NM_000314.4	92	gAc/gGc	5/9	0.839139388540166	1	FACETS	0.96	0.912	1	0.96	0.912	1	CLONAL	1	TRUE	0	0.84	1		292	259	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469823	157469823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542660265	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	231	565	0	ENST00000346085.5:c.2617G>A	p.Gly873Ser	p.G873S	ENST00000346085	NM_020732.3	873	Ggt/Agt	9/20	1	2	FACETS	0.851	0.799	0.905	0.851	0.799	0.905	CLONAL	1	TRUE	1	0.84	2		565	646	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103828	47103828	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs976581260	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	316	335	1	ENST00000409792.3:c.6118C>T	p.Arg2040Ter	p.R2040*	ENST00000409792	NM_014159.6	2040	Cga/Tga	14/21	0.839139388540166	3	FACETS	0.882	0.841	0.922	0.882	0.841	0.922	CLONAL	2	TRUE	1	0.84	3		336	606	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022592	31022592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs373221034	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	239	502	0	ENST00000375687.4:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000375687	NM_015338.5	693	Cga/Tga	13/13	1	2	FACETS	0.944	0.888	1	0.944	0.888	1	CLONAL	1	TRUE	1	0.84	2		502	603	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932714	49932714	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748943477	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	287	703	1	ENST00000296474.3:c.3157C>T	p.Arg1053Trp	p.R1053W	ENST00000296474	NM_002447.2	1053	Cgg/Tgg	14/20	0.839139388540166	3	FACETS	0.936	0.881	0.992	0.468	0.44	0.496	CLONAL	1	TRUE	1	0.84	3		704	1037	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31372633	31372633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149520896	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	224	518	1	ENST00000328111.2:c.274C>T	p.Arg92Trp	p.R92W	ENST00000328111	NM_006892.3	92	Cgg/Tgg	4/23	1	2	FACETS	0.921	0.864	0.979	0.921	0.864	0.979	CLONAL	1	TRUE	1	0.84	2		519	579	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385183	41385183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1423243089	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	261	516	2	ENST00000373198.4:c.778C>T	p.Arg260Trp	p.R260W	ENST00000373198	NM_133170.3	260	Cgg/Tgg	6/32	1	2	FACETS	0.985	0.93	1	0.985	0.93	1	CLONAL	1	TRUE	1	0.84	2		518	631	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374251	138374251	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	247	420	0	ENST00000289153.2:c.3193C>T	p.Arg1065Trp	p.R1065W	ENST00000289153	NM_006219.2	1065	Cgg/Tgg	22/22	0.839139388540166	3	FACETS	0.994	0.932	1	0.497	0.466	0.529	CLONAL	1	TRUE	1	0.84	3		420	840	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993013	72993014	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	377	673	0	ENST00000268489.5:c.1031dup	p.Asn344LysfsTer13	p.N344Kfs*13	ENST00000268489	NM_006885.3	344	aac/aaAc	2/10	1	2	FACETS	0.95	0.905	0.995	0.95	0.905	0.995	CLONAL	1	TRUE	1	0.84	2		673	945	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561424	9561424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1234148699	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	229	382	1	ENST00000353224.5:c.358G>A	p.Ala120Thr	p.A120T	ENST00000353224	NM_177990.2	120	Gcg/Acg	4/10	1	2	FACETS	0.981	0.922	1	0.981	0.922	1	CLONAL	1	TRUE	1	0.84	2		383	556	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052626	42052626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	224	418	1	ENST00000219905.7:c.7297C>T	p.Arg2433Trp	p.R2433W	ENST00000219905	NM_001164273.1	2433	Cgg/Tgg	20/24	1	2	FACETS	0.959	0.901	1	0.959	0.901	1	CLONAL	1	TRUE	1	0.84	2		419	556	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965090	15965090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1344029820	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	184	335	1	ENST00000268712.3:c.5506G>A	p.Val1836Met	p.V1836M	ENST00000268712	NM_006311.3	1836	Gtg/Atg	37/46	1	2	FACETS	0.942	0.879	1	0.942	0.879	1	CLONAL	1	TRUE	1	0.84	2		336	465	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107231	193107231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	129	286	0	ENST00000367435.3:c.440G>A	p.Arg147His	p.R147H	ENST00000367435	NM_024529.4	147	cGc/cAc	6/17	0.839139388540166	3	FACETS	0.797	0.726	0.872	0.399	0.363	0.436	SUBCLONAL	1	TRUE	1	0.84	3		286	547	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435004	110435004	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	288	715	0	ENST00000375856.3:c.3397G>A	p.Ala1133Thr	p.A1133T	ENST00000375856	NM_003749.2	1133	Gcc/Acc	1/2	0.839139388540166	2	FACETS	0.918	0.868	0.969			1	CLONAL	1	TRUE	NA	0.84	2		715	747	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060912	38060912	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	194	371	0	ENST00000250448.2:c.1077del	p.Ile360Ter	p.I360*	ENST00000250448	NM_004496.3	359	ccC/cc	2/2	1	2	FACETS	0.987	0.923	1	0.987	0.923	1	CLONAL	1	TRUE	1	0.84	2		371	468	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939663	76939663	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1557142351	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	267	284	0	ENST00000373344.5:c.1085C>T	p.Thr362Ile	p.T362I	ENST00000373344	NM_000489.3	362	aCc/aTc	9/35	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.84	1		284	334	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943788	71943788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771815535	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	253	586	0	ENST00000298229.2:c.1831C>T	p.Arg611Cys	p.R611C	ENST00000298229	NM_001567.3	611	Cgc/Tgc	15/28	1	2	FACETS	0.947	0.893	1	0.947	0.893	1	CLONAL	1	TRUE	1	0.84	2		586	636	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240351	98240351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	194	359	0	ENST00000331920.6:c.1333G>A	p.Gly445Ser	p.G445S	ENST00000331920	NM_000264.3	445	Ggc/Agc	9/24	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.84	2		359	446	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	536	420	9	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	0.839139388540166	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	1	0.84	3		429	780	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427950	49427950	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775632051	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	238	552	1	ENST00000301067.7:c.10640G>A	p.Arg3547His	p.R3547H	ENST00000301067	NM_003482.3	3547	cGc/cAc	38/54	1	2	FACETS	0.987	0.929	1	0.987	0.929	1	CLONAL	1	TRUE	1	0.84	2		553	574	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541507	187541507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758885671	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	158	373	0	ENST00000441802.2:c.6233C>T	p.Ala2078Val	p.A2078V	ENST00000441802	NM_005245.3	2078	gCg/gTg	10/27	0.839139388540166	3	FACETS	0.823	0.757	0.892			1	CLONAL	1	TRUE	NA	0.84	3		373	649	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852212	128852212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs905977339	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	589	695	4	ENST00000249373.3:c.2284C>T	p.Arg762Cys	p.R762C	ENST00000249373	NM_005631.4	762	Cgc/Tgc	12/12	0.839139388540166	3	FACETS	0.945	0.914	0.976	0.945	0.914	0.976	CLONAL	2	TRUE	1	0.84	3		699	1054	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204515952	204515952	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	201	410	1	ENST00000367182.3:c.850C>A	p.Leu284Met	p.L284M	ENST00000367182	NM_001278516.1	284	Ctg/Atg	10/11	0.839139388540166	3	FACETS	0.945	0.879	1	0.473	0.439	0.507	CLONAL	1	TRUE	1	0.84	3		411	719	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588174	69588174	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	243	553	0	ENST00000168712.1:c.524C>T	p.Pro175Leu	p.P175L	ENST00000168712	NM_002007.2	175	cCc/cTc	3/3	1	2	FACETS	0.955	0.899	1	0.955	0.899	1	CLONAL	1	TRUE	1	0.84	2		553	606	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374788	118374789	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	204	339	0	ENST00000534358.1:c.8185_8186del	p.Ser2729Ter	p.S2729*	ENST00000534358	NM_005933.3	2727	acAGag/acag	27/36	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.84	2		339	474	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25368467	25368467	+	intron_variant	Intron	SNP	C	C	T	rs755877953	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	181	399	0	ENST00000311936.3:c.451-5622G>A		p.*151*	ENST00000311936	NM_004985.3	160/189			1	2	FACETS	0.885	0.824	0.947	0.885	0.824	0.947	CLONAL	1	TRUE	1	0.84	2		399	487	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420432	49420432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778486	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	264	521	0	ENST00000301067.7:c.15317G>A	p.Arg5106His	p.R5106H	ENST00000301067	NM_003482.3	5106	cGc/cAc	48/54	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.84	2		521	616	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437176	49437176	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371685892	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	236	568	1	ENST00000301067.7:c.5503C>T	p.Arg1835Cys	p.R1835C	ENST00000301067	NM_003482.3	1835	Cgt/Tgt	24/54	1	2	FACETS	0.949	0.893	1	0.949	0.893	1	CLONAL	1	TRUE	1	0.84	2		569	592	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249294	133249294	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	300	643	0	ENST00000320574.5:c.1605C>A	p.Asp535Glu	p.D535E	ENST00000320574	NM_006231.2	535	gaC/gaA	15/49	1	2	FACETS	0.999	0.947	1	0.999	0.947	1	CLONAL	1	TRUE	1	0.84	2		643	715	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562258	21562258	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	309	658	1	ENST00000382592.4:c.1661G>A	p.Gly554Asp	p.G554D	ENST00000382592	NM_014572.2	554	gGc/gAc	4/8	1	2	FACETS	0.974	0.924	1	0.974	0.924	1	CLONAL	1	TRUE	1	0.84	2		659	755	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975414	26975414	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867370429	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	200	382	0	ENST00000381527.3:c.1040C>T	p.Ala347Val	p.A347V	ENST00000381527	NM_001260.1	347	gCc/gTc	11/13	1	2	FACETS	0.897	0.838	0.957	0.897	0.838	0.957	CLONAL	1	TRUE	1	0.84	2		382	531	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608024	28608024	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	179	406	0	ENST00000241453.7:c.1942G>T	p.Glu648Ter	p.E648*	ENST00000241453	NM_004119.2	648	Gaa/Taa	15/24	1	2	FACETS	0.863	0.802	0.924	0.863	0.802	0.924	CLONAL	1	TRUE	1	0.84	2		406	494	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003386	42003386	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	208	414	0	ENST00000219905.7:c.2923C>T	p.Gln975Ter	p.Q975*	ENST00000219905	NM_001164273.1	975	Cag/Tag	8/24	1	2	FACETS	0.924	0.865	0.984	0.924	0.865	0.984	CLONAL	1	TRUE	1	0.84	2		414	536	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032392	42032392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754941833	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	196	403	0	ENST00000219905.7:c.4576C>T	p.Arg1526Trp	p.R1526W	ENST00000219905	NM_001164273.1	1526	Cgg/Tgg	14/24	1	2	FACETS	0.836	0.78	0.894	0.836	0.78	0.894	CLONAL	1	TRUE	1	0.84	2		403	558	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829121	72829121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs550702576	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	178	420	0	ENST00000268489.5:c.7460C>T	p.Ala2487Val	p.A2487V	ENST00000268489	NM_006885.3	2487	gCg/gTg	9/10	1	2	FACETS	0.979	0.912	1	0.979	0.912	1	CLONAL	1	TRUE	1	0.84	2		420	433	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346255	89346255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs929429805	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	96	268	0	ENST00000301030.4:c.6695G>A	p.Arg2232His	p.R2232H	ENST00000301030	NM_001256183.1	2232	cGt/cAt	9/13	1	2	FACETS	0.969	0.879	1	0.969	0.879	1	CLONAL	1	TRUE	1	0.84	2		268	236	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474422	40474422	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs886039434	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	254	554	0	ENST00000264657.5:c.1979T>C	p.Met660Thr	p.M660T	ENST00000264657	NM_139276.2	660	aTg/aCg	21/24	1	2	FACETS	0.948	0.893	1	0.948	0.893	1	CLONAL	1	TRUE	1	0.84	2		554	638	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105601	11105601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1286498410	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	301	660	2	ENST00000358026.2:c.1517C>T	p.Thr506Met	p.T506M	ENST00000358026	NM_001128849.1	506	aCg/aTg	9/36	1	2	FACETS	0.976	0.925	1	0.976	0.925	1	CLONAL	1	TRUE	1	0.84	2		662	734	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152056	11152056	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854225	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	242	503	1	ENST00000358026.2:c.4340G>A	p.Arg1447Gln	p.R1447Q	ENST00000358026	NM_001128849.1	1447	cGa/cAa	31/36	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.84	2		504	526	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212576	36212576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568272454	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	319	731	0	ENST00000222270.7:c.2327G>A	p.Arg776Gln	p.R776Q	ENST00000222270	NM_014727.1	776	cGg/cAg	3/37	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.84	2		731	758	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741911	40741911	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	254	613	0	ENST00000392038.2:c.1061A>G	p.Asp354Gly	p.D354G	ENST00000392038	NM_001626.4	354	gAc/gGc	11/14	1	2	FACETS	0.869	0.818	0.921	0.869	0.818	0.921	CLONAL	1	TRUE	1	0.84	2		613	696	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634720	158634720	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777150519	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	149	316	0	ENST00000263640.3:c.466C>T	p.Arg156Cys	p.R156C	ENST00000263640	NM_001105.4	156	Cgc/Tgc	5/11	1	2	FACETS	0.855	0.789	0.922	0.855	0.789	0.922	CLONAL	1	TRUE	1	0.84	2		316	415	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551033	41551033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	224	434	0	ENST00000263253.7:c.3177G>A	p.Met1059Ile	p.M1059I	ENST00000263253	NM_001429.3	1059	atG/atA	17/31	1	2	FACETS	0.926	0.869	0.984	0.926	0.869	0.984	CLONAL	1	TRUE	1	0.84	2		434	576	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721510	49721510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368191700	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	454	469	2	ENST00000449682.2:c.2129G>A	p.Arg710His	p.R710H	ENST00000449682	NM_020998.3	710	cGt/cAt	18/18	0.839139388540166	3	FACETS	0.995	0.959	1	0.995	0.959	1	CLONAL	2	TRUE	1	0.84	3		471	771	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582440	119582440	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	222	195	0	ENST00000316626.5:c.961C>T	p.Arg321Ter	p.R321*	ENST00000316626		321	Cga/Tga	10/12	0.839139388540166	3	FACETS	0.982	0.931	1	0.982	0.931	1	CLONAL	2	TRUE	1	0.84	3		195	382	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880977	134880977	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	341	435	0	ENST00000398015.3:c.1540T>C	p.Tyr514His	p.Y514H	ENST00000398015	NM_004441.4	514	Tac/Cac	7/16	0.839139388540166	3	FACETS	0.996	0.954	1	0.996	0.954	1	CLONAL	2	TRUE	1	0.84	3		435	579	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504426	186504427	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	232	500	0	ENST00000323963.5:c.770_771del	p.Glu257GlyfsTer9	p.E257Gfs*9	ENST00000323963		255	GAg/g	7/11	0.839139388540166	3	FACETS	0.835	0.78	0.893	0.418	0.39	0.447	CLONAL	1	TRUE	1	0.84	3		500	939	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157454196	157454196	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	224	460	0	ENST00000346085.5:c.2406G>T	p.Met802Ile	p.M802I	ENST00000346085	NM_020732.3	802	atG/atT	8/20	1	2	FACETS	0.882	0.827	0.938	0.882	0.827	0.938	CLONAL	1	TRUE	1	0.84	2		460	605	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341932	8341932	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	183	382	0	ENST00000356435.5:c.4708T>A	p.Leu1570Ile	p.L1570I	ENST00000356435		1570	Tta/Ata	29/35	1	2	FACETS	0.949	0.885	1	0.949	0.885	1	CLONAL	1	TRUE	1	0.84	2		382	459	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242736	98242736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878853859	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	191	425	1	ENST00000331920.6:c.881G>A	p.Arg294His	p.R294H	ENST00000331920	NM_000264.3	294	cGc/cAc	6/24	1	2	FACETS	0.876	0.817	0.937	0.876	0.817	0.937	CLONAL	1	TRUE	1	0.84	2		426	519	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396518	139396518	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369526652	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	239	609	0	ENST00000277541.6:c.5407G>A	p.Gly1803Ser	p.G1803S	ENST00000277541	NM_017617.3	1803	Ggt/Agt	29/34	1	2	FACETS	0.916	0.862	0.972	0.916	0.862	0.972	CLONAL	1	TRUE	1	0.84	2		609	621	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400039	139400039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780500109	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	220	560	1	ENST00000277541.6:c.4309G>A	p.Gly1437Arg	p.G1437R	ENST00000277541	NM_017617.3	1437	Ggg/Agg	25/34	1	2	FACETS	0.843	0.79	0.898	0.843	0.79	0.898	CLONAL	1	TRUE	1	0.84	2		561	621	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410637	63410637	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	300	359	0	ENST00000330258.3:c.2530G>A	p.Gly844Ser	p.G844S	ENST00000330258	NM_152424.3	844	Ggc/Agc	2/2	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.84	1		359	375	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200102	123200102	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	268	255	0	ENST00000218089.9:c.2174T>A	p.Met725Lys	p.M725K	ENST00000218089	NM_001042749.1	725	aTg/aAg	22/35	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.84	1		255	332	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0025974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	255	603	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.634451674897262	3	FACETS	0.957	0.905	1	0.957	0.905	1	CLONAL	2	TRUE	1	0.634451674897262	3		603	553	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416493	29416493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1182539285	NA	P-0025974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	255	635	0	ENST00000389048.3:c.4460C>T	p.Ser1487Leu	p.S1487L	ENST00000389048	NM_004304.4	1487	tCg/tTg	29/29	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.634451674897262	2		635	777	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534356	187534356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770029391	NA	P-0025974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	200	599	0	ENST00000441802.2:c.9370G>A	p.Glu3124Lys	p.E3124K	ENST00000441802	NM_005245.3	3124	Gaa/Aaa	13/27	0.282301322228252	2	FACETS	0.967	0.9	1	0.483	0.45	0.518	INDETERMINATE	1	TRUE	0	0.634451674897262	2		599	652	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436140	56436140	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	452	630	0	ENST00000407977.2:c.997del	p.Gln333LysfsTer86	p.Q333Kfs*86	ENST00000407977		333	Caa/aa	9/10	0.634451674897262	2	FACETS	0.964	0.93	0.998	0.964	0.93	0.998	CLONAL	2	TRUE	0	0.634451674897262	2		630	739	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274090	10274090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758117698	NA	P-0025974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	403	593	1	ENST00000330684.3:c.179C>T	p.Ala60Val	p.A60V	ENST00000330684	NM_001134407.1	60	gCg/gTg	2/13	0.634451674897262	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.634451674897262	3		594	821	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189840	11189840	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373213788	NA	P-0025974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	202	563	0	ENST00000361445.4:c.5669G>A	p.Arg1890His	p.R1890H	ENST00000361445	NM_004958.3	1890	cGt/cAt	40/58	0.634451674897262	2	FACETS	0.894	0.832	0.958	0.447	0.416	0.479	CLONAL	1	TRUE	0	0.634451674897262	2		563	712	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710688	114710688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	175	503	0	ENST00000543371.1:c.173G>A	p.Ser58Asn	p.S58N	ENST00000543371	NM_001198531.1	58	aGc/aAc	1/14	0.634451674897262	3	FACETS	1	0.961	1	0.532	0.491	0.574	CLONAL	1	TRUE	1	0.634451674897262	3		503	683	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205711	108205711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786202859	NA	P-0025974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	183	386	1	ENST00000278616.4:c.8026G>A	p.Glu2676Lys	p.E2676K	ENST00000278616	NM_000051.3	2676	Gaa/Aaa	55/63	0.557545301384696	4	FACETS	0.914	0.85	0.979	0.914	0.85	0.979	CLONAL	2	TRUE	2	0.634451674897262	4		387	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577560	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AACTGTTACAC	novel	NA	P-0025974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	394	580	1	ENST00000269305.4:c.711_721dup	p.Ser241CysfsTer10	p.S241Cfs*10	ENST00000269305	NM_001126112.2	241	tcc/tGTGTAACAGTTcc	7/11	0.634451674897262	2	FACETS	0.79	0.757	0.824	0.79	0.757	0.824	SUBCLONAL	2	TRUE	0	0.634451674897262	2		581	786	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286769	212286769	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	288	496	0	ENST00000342788.4:c.2927G>C	p.Arg976Thr	p.R976T	ENST00000342788	NM_005235.2	976	aGg/aCg	24/28	0.621151389859796	3	FACETS	0.937	0.889	0.986	0.937	0.889	0.986	CLONAL	2	TRUE	1	0.634451674897262	3		496	638	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989568	212989568	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	236	378	0	ENST00000342788.4:c.143C>A	p.Ala48Asp	p.A48D	ENST00000342788	NM_005235.2	48	gCc/gAc	2/28	0.621151389859796	3	FACETS	0.923	0.87	0.976	0.923	0.87	0.976	CLONAL	2	TRUE	1	0.634451674897262	3		378	531	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415704	152415704	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0025974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	285	456	1	ENST00000206249.3:c.1553+1G>A		p.X518_splice	ENST00000206249	NM_000125.3	518			0.621151389859796	3	FACETS	0.989	0.939	1	0.989	0.939	1	CLONAL	2	TRUE	1	0.634451674897262	3		457	598	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509567	106509567	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	218	558	0	ENST00000359195.3:c.1561G>T	p.Asp521Tyr	p.D521Y	ENST00000359195	NM_002649.2	521	Gac/Tac	2/11	0.634451674897262	3	FACETS	1	0.966	1	0.529	0.492	0.566	CLONAL	1	TRUE	1	0.634451674897262	3		558	856	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341908	8341908	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	152	532	0	ENST00000356435.5:c.4732del	p.Thr1578LeufsTer2	p.T1578Lfs*2	ENST00000356435		1578	Act/ct	29/35	0.634451674897262	1	FACETS	0.841	0.778	0.905	0.841	0.778	0.905	CLONAL	1	TRUE	0	0.634451674897262	1		532	389	SUCCESS
APC	324	MSKCC	GRCh37	5	112175324	112175324	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1211642532	NA	P-0026109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	30	311	0	ENST00000257430.4:c.4033G>T	p.Glu1345Ter	p.E1345*	ENST00000257430	NM_000038.5	1345	Gaa/Taa	16/16	1	2	FACETS	0.554	0.445	0.677	0.554	0.445	0.677	SUBCLONAL	1	TRUE	1	0.2	2		311	542	SUCCESS
APC	324	MSKCC	GRCh37	5	112128203	112128203	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554074786	NA	P-0026109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	216	550	10	ENST00000257430.4:c.706C>T	p.Gln236Ter	p.Q236*	ENST00000257430	NM_000038.5	236	Cag/Tag	7/16	1	2	FACETS	1	0.982	1	1	0.994	1	CLONAL	2	TRUE	1	0.2	2		560	934	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944608	40944608	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs752116362	NA	P-0026109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	33	384	1	ENST00000373198.4:c.1894C>T	p.Arg632Ter	p.R632*	ENST00000373198	NM_133170.3	632	Cga/Tga	12/32	1	2	FACETS	0.522	0.424	0.633	0.522	0.424	0.633	SUBCLONAL	1	TRUE	1	0.2	2		385	632	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0026117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	95	584	2	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.6478339483209	3	FACETS	0.956	0.872	1	0.956	0.872	1	CLONAL	2	TRUE	1	0.652715828500913	3		586	202	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578445	7578445	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	219	372	0	ENST00000269305.4:c.485T>A	p.Ile162Asn	p.I162N	ENST00000269305	NM_001126112.2	162	aTc/aAc	5/11	0.631470025154941	1	FACETS	0.993	0.936	1	0.993	0.936	1	CLONAL	1	TRUE	0	0.652715828500913	1		372	455	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030461	49030461	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	55	210	0	ENST00000267163.4:c.1936del	p.Ser646LeufsTer12	p.S646Lfs*12	ENST00000267163	NM_000321.2	646	Tct/ct	19/27	0.631470025154941	1	FACETS	0.962	0.851	1	0.962	0.851	1	CLONAL	1	TRUE	0	0.652715828500913	1		210	118	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0026155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	173	425	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.877	0.809	0.947	0.877	0.809	0.947	CLONAL	1	TRUE	1	0.546400402266063	2		426	722	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0026188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	23	498	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.569	0.442	0.717	0.569	0.442	0.717	SUBCLONAL	1	TRUE	1	0.13	2		498	622	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845633	72845633	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	86	483	0	ENST00000268489.5:c.3707A>T	p.Asn1236Ile	p.N1236I	ENST00000268489	NM_006885.3	1236	aAc/aTc	7/10	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.13	2		483	1171	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796856	42796856	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0026279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	68	868	0	ENST00000575354.2:c.3314C>G	p.Ser1105Ter	p.S1105*	ENST00000575354	NM_015125.3	1105	tCa/tGa	14/20	0.194021970457898	3	FACETS	1	0.871	1	0.501	0.435	0.573	CLONAL	1	TRUE	1	0.197699099270901	3		868	754	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579372	7579412	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCTGGTAGGTTTTCTGGGAAGGGACAGAAGATGACAGGG	GCCCTGGTAGGTTTTCTGGGAAGGGACAGAAGATGACAGGG	-	novel	NA	P-0026279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	188	779	0	ENST00000269305.4:c.275_315del	p.Pro92GlnfsTer43	p.P92Qfs*43	ENST00000269305	NM_001126112.2	92	cCCCTGTCATCTTCTGTCCCTTCCCAGAAAACCTACCAGGGC/c	4/11	0.197699099270901	3	FACETS	1	0.985	1	0.833	0.771	0.898	CLONAL	2	TRUE	0	0.197699099270901	3		779	836	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795001	42795001	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs373041068	NA	P-0026279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	64	733	1	ENST00000575354.2:c.2081C>G	p.Ser694Cys	p.S694C	ENST00000575354	NM_015125.3	694	tCt/tGt	10/20	0.194021970457898	3	FACETS	0.98	0.848	1	0.49	0.424	0.562	CLONAL	1	TRUE	1	0.197699099270901	3		734	726	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795752	42795752	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0026279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	67	817	1	ENST00000575354.2:c.2741C>G	p.Ser914Ter	p.S914*	ENST00000575354	NM_015125.3	914	tCa/tGa	11/20	0.194021970457898	3	FACETS	1	0.883	1	0.509	0.442	0.583	CLONAL	1	TRUE	1	0.197699099270901	3		818	731	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795970	42796255	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGTCTTTTCTCCTTCTCCATGTATCTGGTTCTCTGTCTTGCCATCTTCCGTGATGTCTCTGTGCATCCTGACTCTCTCAAGTCCTCAGTGTCTGTACCCTCCTCCTTCTCTGTGTCCCCACCTCTCACTGTCATCTTGCCCATCCTGTTCTCACCCCAAGTTCTGTGTTCCTTGCTTTTGCTTAGAGTCCCACTTGAGGTCTTGGTCTTCCCCTGCCCCAGTCTGGGGCCACAGCTCACCCTGGCCTATGGGTGCCCTTCTCCACAGATCATCCAGCTGACCCCG	CAGTCTTTTCTCCTTCTCCATGTATCTGGTTCTCTGTCTTGCCATCTTCCGTGATGTCTCTGTGCATCCTGACTCTCTCAAGTCCTCAGTGTCTGTACCCTCCTCCTTCTCTGTGTCCCCACCTCTCACTGTCATCTTGCCCATCCTGTTCTCACCCCAAGTTCTGTGTTCCTTGCTTTTGCTTAGAGTCCCACTTGAGGTCTTGGTCTTCCCCTGCCCCAGTCTGGGGCCACAGCTCACCCTGGCCTATGGGTGCCCTTCTCCACAGATCATCCAGCTGACCCCG	-	novel	NA	P-0026279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	47	280	1	ENST00000575354.2:c.2886+73_2904del		p.X962_splice	ENST00000575354	NM_015125.3	962		12/20	0.194021970457898	3	FACETS	0.775	0.657	0.905	0.775	0.657	0.905	CLONAL	2	TRUE	1	0.197699099270901	3		281	337	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796799	42796799	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	72	768	0	ENST00000575354.2:c.3257C>G	p.Ala1086Gly	p.A1086G	ENST00000575354	NM_015125.3	1086	gCc/gGc	14/20	0.194021970457898	3	FACETS	1	0.898	1	0.517	0.451	0.589	CLONAL	1	TRUE	1	0.197699099270901	3		768	774	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8501006	8501006	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747872615	NA	P-0026279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	26	517	0	ENST00000356435.5:c.1876A>G	p.Ile626Val	p.I626V	ENST00000356435		626	Att/Gtt	13/35	0.178694010602187	4	FACETS	0.691	0.546	0.857	0.23	0.182	0.286	SUBCLONAL	1	TRUE	1	0.197699099270901	4		517	456	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450243	50450243	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757521297	NA	P-0026454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	102	479	2	ENST00000331340.3:c.427C>T	p.Arg143Trp	p.R143W	ENST00000331340	NM_006060.4	143	Cgg/Tgg	5/8	0.147158591598314	3	FACETS	1	0.938	1	0.535	0.478	0.595	INDETERMINATE	1	FALSE	1	0.3	3		481	731	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691003	NA	P-0026454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	74	680	0	ENST00000269305.4:c.96+1G>T		p.X32_splice	ENST00000269305	NM_001126112.2	32			0.161846297689453	2	FACETS	0.557	0.487	0.634	0.279	0.243	0.317	INDETERMINATE	1	FALSE	0	0.3	2		680	885	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579346	7579346	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs781724995	NA	P-0026707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	625	612	2	ENST00000269305.4:c.341T>A	p.Leu114Ter	p.L114*	ENST00000269305	NM_001126112.2	114	tTg/tAg	4/11	0.886608398381658	2	FACETS	0.984	0.969	0.998	0.984	0.969	0.998	CLONAL	2	TRUE	0	0.926977974229667	2		614	685	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489788	2489788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs527252361	NA	P-0026707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	530	710	0	ENST00000355716.4:c.185G>A	p.Arg62His	p.R62H	ENST00000355716	NM_003820.2	62	cGt/cAt	3/8	1	2	FACETS	0.987	0.972	1	1	0.998	1	CLONAL	2	TRUE	1	0.926977974229667	2		710	579	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937953	36937953	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	1217	766	0	ENST00000361632.4:c.883T>C	p.Cys295Arg	p.C295R	ENST00000361632		295	Tgc/Cgc	7/16	0.926977974229667	6	FACETS	0.969	0.948	0.989	0.969	0.948	0.989	CLONAL	4	TRUE	2	0.926977974229667	6		766	1934	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650568	48650568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	666	711	1	ENST00000376670.3:c.538C>T	p.Leu180Phe	p.L180F	ENST00000376670	NM_002049.3	180	Ctc/Ttc	3/6	NA	2	FACETS	0.959	0.944	0.974			1	INDETERMINATE	2	TRUE	NA	0.926977974229667	2		712	749	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725042	89725042	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	rs1085308041	NA	P-0026733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	46	280	0	ENST00000371953.3:c.1027-2A>C		p.X343_splice	ENST00000371953	NM_000314.4	343			0.354406918521843	1	FACETS	0.949	0.808	1	0.949	0.808	1	CLONAL	1	TRUE	0	0.354406918521843	1		280	225	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27228254	27228254	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	61	724	0	ENST00000380036.4:c.3251C>A	p.Ser1084Ter	p.S1084*	ENST00000380036	NM_000459.3	1084	tCa/tAa	22/23	0.354406918521843	1	FACETS	0.271	0.232	0.312	0.271	0.232	0.312	SUBCLONAL	1	TRUE	0	0.354406918521843	1		724	1047	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201889	102201889	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1242006697	NA	P-0026733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	67	626	0	ENST00000263464.3:c.1241A>G	p.Asn414Ser	p.N414S	ENST00000263464	NM_001165.4	414	aAt/aGt	6/9	0.354406918521843	1	FACETS	0.848	0.741	0.962	0.848	0.741	0.962	CLONAL	1	TRUE	0	0.354406918521843	1		626	367	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578276	7578276	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	274	696	0	ENST00000269305.4:c.573del	p.Gln192SerfsTer55	p.Q192Sfs*55	ENST00000269305	NM_001126112.2	191	ccT/cc	6/11	0.354406918521843	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.354406918521843	1		696	942	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239983	98239983	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	176	481	1	ENST00000331920.6:c.1349T>G	p.Leu450Arg	p.L450R	ENST00000331920	NM_000264.3	450	cTc/cGc	10/24	0.354406918521843	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.354406918521843	1		482	641	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105512	27105513	+	splice_acceptor_variant	Splice_Site	INS	-	-	G	novel	NA	P-0026773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	95	226	0	ENST00000324856.7:c.5125-1dup		p.X1709_splice	ENST00000324856	NM_006015.4	1709			0.370236476723569	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.370236476723569	1		226	364	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46738191	46738191	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs561568664	NA	P-0026773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	93	345	0	ENST00000371975.4:c.1223T>C	p.Ile408Thr	p.I408T	ENST00000371975	NM_003579.3	408	aTt/aCt	11/18	1	2	FACETS	0.806	0.718	0.9	0.806	0.718	0.9	CLONAL	1	TRUE	1	0.370236476723569	2		345	623	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981502	201981513	+	frameshift_variant	Frame_Shift_Del	DEL	TCATTGAGCTGC	TCATTGAGCTGC	GCTCAGT	novel	NA	P-0026773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	115	539	3	ENST00000359651.3:c.416_427delinsGCTCAGT	p.Ile139SerfsTer20	p.I139Sfs*20	ENST00000359651		139	aTCATTGAGCTGCtg/aGCTCAGTtg	3/8	0.370236476723569	2	FACETS	0.859	0.775	0.949	0.43	0.387	0.475	CLONAL	1	TRUE	0	0.370236476723569	2		542	723	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907415	32907415	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs80358464	NA	P-0026773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	94	291	0	ENST00000380152.3:c.1800T>A	p.Tyr600Ter	p.Y600*	ENST00000380152		600	taT/taA	10/27	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.370236476723569	2		291	491	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713660	30713666	+	frameshift_variant	Frame_Shift_Del	DEL	GCCAAGG	GCCAAGG	-	novel	NA	P-0026773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	54	314	0	ENST00000295754.5:c.987_993del	p.Lys330ThrfsTer6	p.K330Tfs*6	ENST00000295754	NM_003242.5	329	GCCAAGGgc/gc	4/7	0.370236476723569	1	FACETS	0.762	0.655	0.878	0.762	0.655	0.878	SUBCLONAL	1	TRUE	0	0.370236476723569	1		314	312	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50454841	50455077	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATGAGTTCTTGGTACAATTAAAGAAACCCTTGGCCACCAACGTTTTTAAATTCAGGAATTTCACCAAGTCCGTAACAGTTTTAGCTCTCAAGGGTAGAATTTTTTTTTTAACTTTTTTGGTAATAATTGTATTGCATGCATTCCCCTTACACAGAAGGCTGGCATTTAATTGGGGTCTTGAACTCAATTGTGTTTTCTGCAGTTGGTAAACCTCACAAATGTGGATATTGTGGCCGA	ATGAGTTCTTGGTACAATTAAAGAAACCCTTGGCCACCAACGTTTTTAAATTCAGGAATTTCACCAAGTCCGTAACAGTTTTAGCTCTCAAGGGTAGAATTTTTTTTTTAACTTTTTTGGTAATAATTGTATTGCATGCATTCCCCTTACACAGAAGGCTGGCATTTAATTGGGGTCTTGAACTCAATTGTGTTTTCTGCAGTTGGTAAACCTCACAAATGTGGATATTGTGGCCGA	-	novel	NA	P-0026773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	28	3	0	ENST00000331340.3:c.590-201_625del		p.X197_splice	ENST00000331340	NM_006060.4	197		6/8	1	2	FACETS	0.917	0.827	0.986	1	0.974	1	CLONAL	5	TRUE	1	0.370236476723569	2		3	33	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0026847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	383	423	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.490440936730373	3	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.490440936730373	3		423	832	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579315	7579316	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1267047192	NA	P-0026847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	266	491	0	ENST00000269305.4:c.371dup	p.Cys124TrpfsTer25	p.C124Wfs*25	ENST00000269305	NM_001126112.2	124	tgc/tgGc	4/11	0.490440936730373	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.490440936730373	1		491	707	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0026847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	131	237	1	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	0.490440936730373	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.490440936730373	1		238	330	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591246	67591246	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0026847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	176	420	0	ENST00000274335.5:c.1746-2A>T		p.X582_splice	ENST00000274335		582			0.490440936730373	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.490440936730373	1		420	522	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891188	101891188	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	164	365	0	ENST00000374994.4:c.149C>G	p.Thr50Arg	p.T50R	ENST00000374994	NM_004612.2	50	aCa/aGa	2/9	0.490440936730373	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.490440936730373	1		365	451	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63553923	63553923	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0026847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	203	367	0	ENST00000307078.5:c.815+1G>T		p.X272_splice	ENST00000307078	NM_004655.3	272			0.490440936730373	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.490440936730373	1		367	505	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222876	5222876	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs986697718	NA	P-0026847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	93	487	0	ENST00000357368.4:c.2927G>T	p.Gly976Val	p.G976V	ENST00000357368	NM_002850.3	976	gGc/gTc	18/38	0.490440936730373	1	FACETS	0.452	0.402	0.505	0.452	0.402	0.505	SUBCLONAL	1	TRUE	0	0.490440936730373	1		487	633	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176621	56176621	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	208	350	0	ENST00000399503.3:c.2171T>C	p.Leu724Pro	p.L724P	ENST00000399503	NM_005921.1	724	cTa/cCa	12/20	0.172161698605756	6	FACETS	0.93	0.864	0.999			1	INDETERMINATE	2	TRUE	NA	0.490440936730373	6		350	903	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0026953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	140	542	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.120881325761976	3	FACETS	1	0.975	1	0.597	0.544	0.653	INDETERMINATE	1	TRUE	1	0.35795307319715	3		543	772	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0026953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	147	537	0	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	0.120881325761976	3	FACETS	1	0.982	1	0.646	0.591	0.704	INDETERMINATE	1	TRUE	1	0.35795307319715	3		537	749	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577497	64577497	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs794728615	NA	P-0026953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	92	411	1	ENST00000312049.6:c.85C>T	p.Arg29Ter	p.R29*	ENST00000312049	NM_130799.2	29	Cga/Tga	2/10	0.347831338948515	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.35795307319715	1		412	403	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100750	8100750	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11567901	NA	P-0026953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	89	543	0	ENST00000346208.3:c.724G>A	p.Gly242Ser	p.G242S	ENST00000346208		242	Ggc/Agc	3/6	0.35795307319715	1	FACETS	0.888	0.79	0.99	0.888	0.79	0.99	CLONAL	1	TRUE	0	0.35795307319715	1		543	460	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100661	8100661	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	94	610	0	ENST00000346208.3:c.635C>T	p.Ser212Phe	p.S212F	ENST00000346208		212	tCc/tTc	3/6	0.35795307319715	1	FACETS	0.914	0.817	1	0.914	0.817	1	CLONAL	1	TRUE	0	0.35795307319715	1		610	472	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100683	8100683	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	95	619	0	ENST00000346208.3:c.657C>G	p.Ile219Met	p.I219M	ENST00000346208		219	atC/atG	3/6	0.35795307319715	1	FACETS	0.952	0.851	1	0.952	0.851	1	CLONAL	1	TRUE	0	0.35795307319715	1		619	458	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493649	56493649	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	107	351	0	ENST00000267101.3:c.2965G>A	p.Gly989Arg	p.G989R	ENST00000267101	NM_001982.3	989	Ggg/Agg	25/28	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.35795307319715	2		351	485	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133238120	133238120	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0026953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	56	335	0	ENST00000320574.5:c.2857A>T	p.Lys953Ter	p.K953*	ENST00000320574	NM_006231.2	953	Aag/Tag	24/49	0.272818660855437	1	FACETS	0.681	0.586	0.785	0.681	0.586	0.785	SUBCLONAL	1	TRUE	0	0.35795307319715	1		335	377	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288528	33288684	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTGAGGTGGCAGCCAAAGTTGTAGATGAGATCGAGGTGACGTCGCTCCTGTAACCTGATGCCCACATCTCGGAAGGCATCCTGAGCCATGAGCTGGAGCTGCTGTCGGGGGAGGCCAAGGCTGTGTCGGGCAGCTGCCTTCTCTACAGCCCGAAG	CTGTGAGGTGGCAGCCAAAGTTGTAGATGAGATCGAGGTGACGTCGCTCCTGTAACCTGATGCCCACATCTCGGAAGGCATCCTGAGCCATGAGCTGGAGCTGCTGTCGGGGGAGGCCAAGGCTGTGTCGGGCAGCTGCCTTCTCTACAGCCCGAAG	-	novel	NA	P-0026953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	59	354	0	ENST00000374542.5:c.868_1024del	p.Leu290MetfsTer28	p.L290Mfs*28	ENST00000374542	NM_001141970.1	290	CTTCGGGCTGTAGAGAAGGCAGCTGCCCGACACAGCCTTGGCCTCCCCCGACAGCAGCTCCAGCTCATGGCTCAGGATGCCTTCCGAGATGTGGGCATCAGGTTACAGGAGCGACGTCACCTCGATCTCATCTACAACTTTGGCTGCCACCTCACAGat/at	3/8	0.347831338948515	1	FACETS	0.784	0.679	0.898	0.784	0.679	0.898	SUBCLONAL	1	TRUE	0	0.35795307319715	1		354	345	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336424	80336424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	51	205	0	ENST00000286548.4:c.895C>A	p.Gln299Lys	p.Q299K	ENST00000286548	NM_002072.3	299	Cag/Aag	7/7	NA	2	FACETS	0.963	0.824	1			1	INDETERMINATE	1	TRUE	NA	0.35795307319715	2		205	296	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	561	562	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	0.594942728366274	6	FACETS	1	0.992	1	0.834	0.803	0.865	CLONAL	3	TRUE	2	0.594942728366274	6		562	1238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0027007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	450	189	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	0.595012564170228	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.594942728366274	2		189	635	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	361	560	0	ENST00000322088.6:c.767C>A	p.Ser256Tyr	p.S256Y	ENST00000322088	NM_014225.5	256	tCc/tAc	6/15	0.364781373370729	3	FACETS	0.976	0.93	1			1	CLONAL	2	TRUE	NA	0.594942728366274	3		560	807	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057955	27057955	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	425	660	1	ENST00000324856.7:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000324856	NM_006015.4	555	Cag/Tag	3/20	0.515332638534277	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	2	0.594942728366274	4		661	954	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0027017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	466	385	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.616502832472205	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.616502832472205	2		385	739	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0027017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	106	207	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.927	0.839	1	0.927	0.839	1	CLONAL	1	TRUE	1	0.616502832472205	2		207	371	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338669	70338669	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	40	1086	0	ENST00000374080.3:c.65C>A	p.Pro22His	p.P22H	ENST00000374080		22	cCc/cAc	1/45	1	1	FACETS	0.229	0.19	0.272	0.229	0.19	0.272	SUBCLONAL	1	TRUE	0	0.616502832472205	1		1086	392	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0027039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	37	356	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.449	0.369	0.539	0.449	0.369	0.539	SUBCLONAL	1	TRUE	1	0.265838710726447	2		356	620	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	79	367	1	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.265838710726447	2		368	541	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138729528	NA	P-0027039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	126	553	1	ENST00000269305.4:c.523C>T	p.Arg175Cys	p.R175C	ENST00000269305	NM_001126112.2	175	Cgc/Tgc	5/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.265838710726447	2		554	701	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302307	15302307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115029695	NA	P-0027039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	65	726	1	ENST00000263388.2:c.964G>A	p.Val322Met	p.V322M	ENST00000263388	NM_000435.2	322	Gtg/Atg	6/33	1	2	FACETS	0.545	0.471	0.625	0.545	0.471	0.625	SUBCLONAL	1	TRUE	1	0.265838710726447	2		727	898	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443902	49443902	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	142	658	2	ENST00000301067.7:c.3469C>A	p.Pro1157Thr	p.P1157T	ENST00000301067	NM_003482.3	1157	Ccc/Acc	11/54	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.265838710726447	2		660	929	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71161772	71161772	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	29	365	0	ENST00000318789.4:c.197G>C	p.Arg66Thr	p.R66T	ENST00000318789	NM_032682.5	66	aGa/aCa	7/21	1	2	FACETS	0.42	0.336	0.515	0.42	0.336	0.515	SUBCLONAL	1	TRUE	1	0.265838710726447	2		365	520	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0027359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	115	346	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	0.367427903062412	3	FACETS	0.959	0.873	1	0.959	0.873	1	CLONAL	2	TRUE	1	0.404995197438695	3		346	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578234	7578234	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs786202222	NA	P-0027359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	23	706	0	ENST00000269305.4:c.615T>A	p.Tyr205Ter	p.Y205*	ENST00000269305	NM_001126112.2	205	taT/taA	6/11	0.100019772440939	3	FACETS	0.236	0.183	0.298			1	INDETERMINATE	1	TRUE	NA	0.404995197438695	3		706	578	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134079	41134079	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	23	414	0	ENST00000379561.5:c.1549A>T	p.Met517Leu	p.M517L	ENST00000379561	NM_002015.3	517	Atg/Ttg	2/3	0.135365488506565	5	FACETS	0.569	0.443	0.714	0.142	0.11	0.179	INDETERMINATE	1	TRUE	1	0.404995197438695	5		414	321	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641349	23641349	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555460485	NA	P-0027359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	80	738	0	ENST00000261584.4:c.2126A>G	p.Asn709Ser	p.N709S	ENST00000261584	NM_024675.3	709	aAt/aGt	5/13	NA	2	FACETS	0.811	0.716	0.912			1	INDETERMINATE	1	TRUE	NA	0.404995197438695	2		738	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs1202793339	NA	P-0027359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	25	550	0	ENST00000269305.4:c.560-1G>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.100019772440939	3	FACETS	0.331	0.26	0.413			1	INDETERMINATE	1	TRUE	NA	0.404995197438695	3		550	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	18	945	0	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.100019772440939	3	FACETS	0.157	0.117	0.204			1	INDETERMINATE	1	TRUE	NA	0.404995197438695	3		945	681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578556	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GAGTACT	GAGTACT	AGA	novel	NA	P-0027359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	211	903	1	ENST00000269305.4:c.376-2_380delinsTCT		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	0.100019772440939	3	FACETS	1	0.958	1			1	INDETERMINATE	2	TRUE	NA	0.404995197438695	3		904	607	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355330	15355330	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	61	398	0	ENST00000263377.2:c.2293C>A	p.Pro765Thr	p.P765T	ENST00000263377	NM_058243.2	765	Cca/Aca	13/20	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.404995197438695	2		398	284	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532603	187532603	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	29	348	0	ENST00000441802.2:c.9790G>T	p.Glu3264Ter	p.E3264*	ENST00000441802	NM_005245.3	3264	Gaa/Taa	14/27	0.354393628713533	1	FACETS	0.526	0.425	0.64	0.526	0.425	0.64	SUBCLONAL	1	TRUE	0	0.404995197438695	1		348	217	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509799	106509799	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	60	640	0	ENST00000359195.3:c.1793G>A	p.Trp598Ter	p.W598*	ENST00000359195	NM_002649.2	598	tGg/tAg	2/11	0.361242435947709	2	FACETS	0.797	0.689	0.912	0.398	0.344	0.456	CLONAL	1	TRUE	0	0.404995197438695	2		640	372	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	133	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.330861037559941	1	FACETS	0.95	0.865	1	0.95	0.865	1	CLONAL	1	FALSE	0	0.330861037559941	1		473	706	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0027590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	221	537	0	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	0.330861037559941	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	0	0.330861037559941	1		537	995	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584787	48584787	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	82	559	2	ENST00000342988.3:c.865C>T	p.Gln289Ter	p.Q289*	ENST00000342988	NM_005359.5	289	Cag/Tag	7/12	0.330861037559941	1	FACETS	0.627	0.553	0.706	0.627	0.553	0.706	SUBCLONAL	1	FALSE	0	0.330861037559941	1		561	660	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730831	40730831	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372700928	NA	P-0027590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	69	673	0	ENST00000373198.4:c.3704G>A	p.Arg1235His	p.R1235H	ENST00000373198	NM_133170.3	1235	cGc/cAc	27/32	1	2	FACETS	0.409	0.355	0.468	0.409	0.355	0.468	SUBCLONAL	1	FALSE	1	0.330861037559941	2		673	1019	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938776	76938776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1557140467	NA	P-0027590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	110	694	0	ENST00000373344.5:c.1972C>T	p.Arg658Cys	p.R658C	ENST00000373344	NM_000489.3	658	Cgt/Tgt	9/35	1	2	FACETS	0.654	0.587	0.726	0.654	0.587	0.726	SUBCLONAL	1	FALSE	1	0.330861037559941	2		694	1016	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0027597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	331	705	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.670701658046295	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.670701658046295	1		705	643	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467780	50467780	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760454379	NA	P-0027597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	380	568	2	ENST00000331340.3:c.1015G>A	p.Glu339Lys	p.E339K	ENST00000331340	NM_006060.4	339	Gag/Aag	8/8	0.485556529720117	3	FACETS	0.886	0.846	0.926	0.886	0.846	0.926	CLONAL	2	TRUE	1	0.670701658046295	3		570	854	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885928	111885928	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	272	577	0	ENST00000341259.2:c.1550G>T	p.Gly517Val	p.G517V	ENST00000341259	NM_005475.2	517	gGg/gTg	8/8	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.670701658046295	2		577	778	SUCCESS
APC	324	MSKCC	GRCh37	5	112175257	112175258	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0027597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	147	329	0	ENST00000257430.4:c.3967dup	p.Val1323GlyfsTer9	p.V1323Gfs*9	ENST00000257430	NM_000038.5	1322	-/G	16/16	0.670701658046295	1	FACETS	0.878	0.814	0.942	0.878	0.814	0.942	CLONAL	1	TRUE	0	0.670701658046295	1		329	332	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401492	401492	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752393433	NA	P-0027597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	193	461	1	ENST00000380956.4:c.814G>A	p.Glu272Lys	p.E272K	ENST00000380956	NM_001195286.1	272	Gag/Aag	7/9	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.670701658046295	2		462	560	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743932	41743933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs778012871	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	359	789	2	ENST00000301178.4:c.874dup	p.His292ProfsTer47	p.H292Pfs*47	ENST00000301178	NM_021913.4	289	-/C	7/20	1	2	FACETS	0.923	0.875	0.972	0.923	0.875	0.972	CLONAL	1	TRUE	1	0.647594345188498	2		791	1201	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	55	337	0	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.18	0.153	0.209	0.18	0.153	0.209	SUBCLONAL	1	TRUE	1	0.647594345188498	2		337	944	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	308	1199	9	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.813	0.766	0.861	0.813	0.766	0.861	CLONAL	1	TRUE	1	0.647594345188498	2		1208	1170	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	228	438	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.647594345188498	2		438	686	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	252	556	1	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	0.647594345188498	2		557	703	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572092	64572093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs767319284	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	220	575	5	ENST00000312049.6:c.1546dup	p.Arg516ProfsTer15	p.R516Pfs*15	ENST00000312049	NM_130799.2	516	cgg/cCgg	10/10	1	2	FACETS	0.803	0.749	0.859	0.803	0.749	0.859	CLONAL	1	TRUE	1	0.647594345188498	2		580	846	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070577	67070578	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	157	234	0	ENST00000412916.2:c.207dup	p.Pro70SerfsTer13	p.P70Sfs*13	ENST00000412916		67	-/T	3/6	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.647594345188498	2		234	473	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	70	557	0	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	NA	2	FACETS	0.18	0.156	0.206			1	INDETERMINATE	1	TRUE	NA	0.647594345188498	2		557	1201	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300039	137300040	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755912201	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	212	696	4	ENST00000481739.1:c.331dup	p.Leu111ProfsTer70	p.L111Pfs*70	ENST00000481739	NM_002957.4	108	-/C	3/10	1	2	FACETS	0.559	0.518	0.601	0.559	0.518	0.601	SUBCLONAL	1	TRUE	1	0.647594345188498	2		700	1172	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	140	289	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.647594345188498	2		289	322	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729163	66729163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516792	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	19	639	0	ENST00000307102.5:c.371C>T	p.Pro124Leu	p.P124L	ENST00000307102	NM_002755.3	124	cCg/cTg	3/11	1	2	FACETS	0.063	0.047	0.082	0.063	0.047	0.082	SUBCLONAL	1	TRUE	1	0.647594345188498	2		639	932	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542110	187542110	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	179	374	0	ENST00000441802.2:c.5630del	p.Pro1877LeufsTer20	p.P1877Lfs*20	ENST00000441802	NM_005245.3	1877	cCt/ct	10/27	0.647594345188498	1	FACETS	0.984	0.92	1	0.984	0.92	1	CLONAL	1	TRUE	0	0.647594345188498	1		374	380	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	233	819	0	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	1	2	FACETS	0.526	0.489	0.564	0.526	0.489	0.564	SUBCLONAL	1	TRUE	1	0.647594345188498	2		819	1368	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	114	182	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.838	0.76	0.919	0.838	0.76	0.919	CLONAL	1	TRUE	1	0.647594345188498	2		182	420	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263973	104263974	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776579	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	158	318	0	ENST00000369902.3:c.71dup	p.Ala25GlyfsTer23	p.A25Gfs*23	ENST00000369902	NM_016169.3	22	gcc/gCcc	1/12	0.210519984747438	3	FACETS	1	0.964	1	0.541	0.498	0.586	INDETERMINATE	1	TRUE	1	0.647594345188498	3		318	597	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651955	36651955	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	140	499	0	ENST00000244741.5:c.77A>G	p.Asp26Gly	p.D26G	ENST00000244741	NM_000389.4	26	gAc/gGc	2/3	1	2	FACETS	0.557	0.508	0.609	0.557	0.508	0.609	SUBCLONAL	1	TRUE	1	0.647594345188498	2		499	776	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177584	56177584	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368201444	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	62	357	0	ENST00000399503.3:c.2557C>T	p.Arg853Cys	p.R853C	ENST00000399503	NM_005921.1	853	Cgt/Tgt	14/20	1	2	FACETS	0.367	0.317	0.421	0.367	0.317	0.421	SUBCLONAL	1	TRUE	1	0.647594345188498	2		357	522	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769886672	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	56	271	0	ENST00000405192.2:c.414dup	p.Thr139HisfsTer24	p.T139Hfs*24	ENST00000405192	NM_001163147.1	138	-/C	7/12	1	2	FACETS	0.404	0.347	0.466	0.404	0.347	0.466	SUBCLONAL	1	TRUE	1	0.647594345188498	2		271	428	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	195	442	0	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	1	2	FACETS	0.774	0.718	0.832	0.774	0.718	0.832	SUBCLONAL	1	TRUE	1	0.647594345188498	2		442	778	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512383	38512383	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1188389540	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	156	477	1	ENST00000254066.5:c.1294C>T	p.Arg432Trp	p.R432W	ENST00000254066	NM_000964.3	432	Cgg/Tgg	9/9	1	2	FACETS	0.815	0.75	0.883	0.815	0.75	0.883	CLONAL	1	TRUE	1	0.647594345188498	2		478	591	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481671	56481671	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	300	642	0	ENST00000267101.3:c.706T>C	p.Ser236Pro	p.S236P	ENST00000267101	NM_001982.3	236	Tca/Cca	6/28	1	2	FACETS	0.894	0.843	0.947	0.894	0.843	0.947	CLONAL	1	TRUE	1	0.647594345188498	2		642	1036	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133242014	133242014	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500855	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	228	564	4	ENST00000320574.5:c.2342C>T	p.Ala781Val	p.A781V	ENST00000320574	NM_006231.2	781	gCg/gTg	21/49	1	2	FACETS	0.83	0.775	0.887	0.83	0.775	0.887	CLONAL	1	TRUE	1	0.647594345188498	2		568	848	SUCCESS
AR	367	MSKCC	GRCh37	X	66765242	66765243	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCA	rs753526329	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	130	176	0	ENST00000374690.3:c.271_273dup	p.Gln91dup	p.Q91dup	ENST00000374690	NM_000044.3	91	agg/agGCAg	1/8	1	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.647594345188498	1		176	255	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680489	241680489	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200007371	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	152	333	3	ENST00000366560.3:c.260G>A	p.Arg87His	p.R87H	ENST00000366560	NM_000143.3	87	cGc/cAc	2/10	1	2	FACETS	0.793	0.728	0.86	0.793	0.728	0.86	SUBCLONAL	1	TRUE	1	0.647594345188498	2		336	592	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630905	187630905	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs75367100	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	214	429	2	ENST00000441802.2:c.77G>A	p.Arg26Gln	p.R26Q	ENST00000441802	NM_005245.3	26	cGa/cAa	2/27	0.647594345188498	1	FACETS	0.982	0.924	1	0.982	0.924	1	CLONAL	1	TRUE	0	0.647594345188498	1		431	455	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	122	507	0	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	0.515	0.466	0.567	0.515	0.466	0.567	SUBCLONAL	1	TRUE	1	0.647594345188498	2		507	731	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352609	68352609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs548280411	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	133	390	0	ENST00000487270.1:c.476G>A	p.Arg159His	p.R159H	ENST00000487270	NM_133509.3	159	cGt/cAt	6/11	1	2	FACETS	0.778	0.71	0.848	0.778	0.71	0.848	SUBCLONAL	1	TRUE	1	0.647594345188498	2		390	528	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456453	29456453	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1558630501	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	172	651	0	ENST00000389048.3:c.2465del	p.Gly822ValfsTer9	p.G822Vfs*9	ENST00000389048	NM_004304.4	822	gGt/gt	14/29	1	2	FACETS	0.51	0.469	0.554	0.51	0.469	0.554	SUBCLONAL	1	TRUE	1	0.647594345188498	2		651	1041	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197505	106197506	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	147	332	0	ENST00000380013.4:c.5844dup	p.Val1949SerfsTer7	p.V1949Sfs*7	ENST00000380013	NM_001127208.2	1946	-/A	11/11	1	2	FACETS	0.91	0.836	0.986	0.91	0.836	0.986	CLONAL	1	TRUE	1	0.647594345188498	2		332	499	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934126	39934127	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	239	270	1	ENST00000378444.4:c.472dup	p.Ser158LysfsTer28	p.S158Kfs*28	ENST00000378444	NM_001123385.1	158	agt/aAgt	4/15	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.647594345188498	1		271	449	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417868	138417868	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	278	513	0	ENST00000289153.2:c.1651T>C	p.Cys551Arg	p.C551R	ENST00000289153	NM_006219.2	551	Tgt/Cgt	11/22	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.647594345188498	2		513	855	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380283	25380283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913528	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	250	462	0	ENST00000311936.3:c.175G>A	p.Ala59Thr	p.A59T	ENST00000311936	NM_004985.3	59	Gca/Aca	3/5	1	2	FACETS	0.917	0.86	0.975	0.917	0.86	0.975	CLONAL	1	TRUE	1	0.647594345188498	2		462	842	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944382	131944382	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs748536322	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	193	329	2	ENST00000265335.6:c.2801del	p.Asn934IlefsTer6	p.N934Ifs*6	ENST00000265335		932	Aaa/aa	17/25	1	2	FACETS	0.921	0.856	0.988	0.921	0.856	0.988	CLONAL	1	TRUE	1	0.647594345188498	2		331	647	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78923339	78923339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1441841406	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	208	451	0	ENST00000306801.3:c.3362C>T	p.Thr1121Met	p.T1121M	ENST00000306801	NM_020761.2	1121	aCg/aTg	28/34	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.647594345188498	2		451	630	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882050	36882050	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs780753361	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	336	754	6	ENST00000358127.4:c.963del	p.Ala322LeufsTer11	p.A322Lfs*11	ENST00000358127	NM_001280556.1	321	ccC/cc	8/10	1	2	FACETS	0.903	0.854	0.953	0.903	0.854	0.953	CLONAL	1	TRUE	1	0.647594345188498	2		760	1149	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	267	768	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.210519984747438	3	FACETS	0.774	0.73	0.819	0.774	0.73	0.819	INDETERMINATE	2	TRUE	1	0.647594345188498	3		771	705	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023267	27023267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536658556	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	195	274	0	ENST00000324856.7:c.373G>A	p.Gly125Ser	p.G125S	ENST00000324856	NM_006015.4	125	Ggt/Agt	1/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.647594345188498	2		274	526	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918759	50918759	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555793039	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	351	654	1	ENST00000440232.2:c.2629G>A	p.Asp877Asn	p.D877N	ENST00000440232	NM_002691.3	877	Gat/Aat	21/27	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.647594345188498	2		655	1036	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533535	533535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	121	640	2	ENST00000451590.1:c.368G>A	p.Arg123His	p.R123H	ENST00000451590	NM_001130442.1	123	cGc/cAc	4/5	NA	2	FACETS	0.468	0.422	0.516			1	INDETERMINATE	1	TRUE	NA	0.647594345188498	2		642	799	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73352417	73352418	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs553127065	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	137	457	0	ENST00000377767.4:c.487dup	p.Met163AsnfsTer15	p.M163Nfs*15	ENST00000377767	NM_014953.3	163	atg/aAtg	3/21	1	2	FACETS	0.542	0.494	0.594	0.542	0.494	0.594	SUBCLONAL	1	TRUE	1	0.647594345188498	2		457	780	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905055	50905055	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	194	509	2	ENST00000440232.2:c.342del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	113	Ggg/gg	4/27	1	2	FACETS	0.956	0.889	1	0.956	0.889	1	CLONAL	1	TRUE	1	0.647594345188498	2		511	627	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567647	226567647	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	157	439	1	ENST00000366794.5:c.1519del	p.Ser507AlafsTer17	p.S507Afs*17	ENST00000366794	NM_001618.3	507	Agc/gc	10/23	1	2	FACETS	0.871	0.802	0.941	0.871	0.802	0.941	CLONAL	1	TRUE	1	0.647594345188498	2		440	557	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272336	15272337	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs771517374	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	268	779	4	ENST00000263388.2:c.6102dup	p.Gly2035ArgfsTer60	p.G2035Rfs*60	ENST00000263388	NM_000435.2	2034	-/C	33/33	1	2	FACETS	0.755	0.708	0.804	0.755	0.708	0.804	SUBCLONAL	1	TRUE	1	0.647594345188498	2		783	1096	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508535	106508535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	73	211	0	ENST00000359195.3:c.529C>T	p.Arg177Cys	p.R177C	ENST00000359195	NM_002649.2	177	Cgc/Tgc	2/11	1	2	FACETS	0.808	0.714	0.907	0.808	0.714	0.907	CLONAL	1	TRUE	1	0.647594345188498	2		211	279	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154241	2154242	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755455183	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	36	584	2	ENST00000434045.2:c.686dup	p.Glu230ArgfsTer50	p.E230Rfs*50	ENST00000434045	NM_001127598.1	229	cca/ccCa	5/5	NA	2	FACETS	0.173	0.142	0.209			1	INDETERMINATE	1	TRUE	NA	0.647594345188498	2		586	641	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287386	38287386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1162148796	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	245	491	0	ENST00000425967.3:c.271C>T	p.Arg91Trp	p.R91W	ENST00000425967	NM_001174067.1	91	Cgg/Tgg	4/19	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.647594345188498	2		491	745	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736510	85736511	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs387906351	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	228	313	2	ENST00000370580.1:c.136dup	p.Ile46AsnfsTer4	p.I46Nfs*4	ENST00000370580	NM_003921.4	46	ata/aAta	2/3	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.647594345188498	2		315	499	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499363	89499363	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1317589623	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	109	357	3	ENST00000336596.2:c.2538del	p.Met847TrpfsTer10	p.M847Wfs*10	ENST00000336596	NM_005233.5	845	Ccc/cc	15/17	1	2	FACETS	0.587	0.529	0.649	0.587	0.529	0.649	SUBCLONAL	1	TRUE	1	0.647594345188498	2		360	573	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28644740	28644741	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	129	275	0	ENST00000241453.7:c.52dup	p.Ser18PhefsTer24	p.S18Ffs*24	ENST00000241453	NM_004119.2	18	tct/tTct	2/24	1	2	FACETS	0.711	0.648	0.778	0.711	0.648	0.778	SUBCLONAL	1	TRUE	1	0.647594345188498	2		275	560	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443612	29443612	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	301	674	3	ENST00000389048.3:c.3605del	p.Gly1202GlufsTer56	p.G1202Efs*56	ENST00000389048	NM_004304.4	1202	gGa/ga	23/29	1	2	FACETS	0.945	0.891	0.999	0.945	0.891	0.999	CLONAL	1	TRUE	1	0.647594345188498	2		677	984	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101117	27101117	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	320	622	0	ENST00000324856.7:c.4403del	p.Pro1468LeufsTer13	p.P1468Lfs*13	ENST00000324856	NM_006015.4	1467	Ccc/cc	18/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.647594345188498	2		622	961	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138563	37138563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775870535	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	224	551	1	ENST00000373509.5:c.97C>T	p.Pro33Ser	p.P33S	ENST00000373509	NM_002648.3	33	Ccc/Tcc	2/6	1	2	FACETS	0.934	0.873	0.996	0.934	0.873	0.996	CLONAL	1	TRUE	1	0.647594345188498	2		552	741	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728564	190728565	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	295	630	0	ENST00000441310.2:c.1958dup	p.Ile654AspfsTer21	p.I654Dfs*21	ENST00000441310	NM_000534.4	651	aga/agAa	10/13	1	2	FACETS	0.914	0.861	0.967	0.914	0.861	0.967	CLONAL	1	TRUE	1	0.647594345188498	2		630	997	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237640	133237640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	53	581	0	ENST00000320574.5:c.2975C>T	p.Ala992Val	p.A992V	ENST00000320574	NM_006231.2	992	gCc/gTc	25/49	1	2	FACETS	0.19	0.161	0.222	0.19	0.161	0.222	SUBCLONAL	1	TRUE	1	0.647594345188498	2		581	861	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259729	16259729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758740337	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	235	559	0	ENST00000375759.3:c.6994C>T	p.Arg2332Cys	p.R2332C	ENST00000375759	NM_015001.2	2332	Cgc/Tgc	11/15	1	2	FACETS	0.957	0.897	1	0.957	0.897	1	CLONAL	1	TRUE	1	0.647594345188498	2		559	758	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121535	2121535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514914	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	82	658	1	ENST00000219476.3:c.1864C>T	p.Arg622Trp	p.R622W	ENST00000219476	NM_000548.3	622	Cgg/Tgg	18/42	1	2	FACETS	0.25	0.22	0.283	0.25	0.22	0.283	SUBCLONAL	1	TRUE	1	0.647594345188498	2		659	1012	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351871	89351871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752417963	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	76	760	1	ENST00000301030.4:c.1079C>T	p.Pro360Leu	p.P360L	ENST00000301030	NM_001256183.1	360	cCg/cTg	9/13	1	2	FACETS	0.189	0.165	0.215	0.189	0.165	0.215	SUBCLONAL	1	TRUE	1	0.647594345188498	2		761	1241	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758303	41758303	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	274	601	1	ENST00000301178.4:c.1759G>A	p.Val587Ile	p.V587I	ENST00000301178	NM_021913.4	587	Gtc/Atc	15/20	1	2	FACETS	0.886	0.833	0.94	0.886	0.833	0.94	CLONAL	1	TRUE	1	0.647594345188498	2		602	955	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344748	65344748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781744573	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	167	364	1	ENST00000342505.4:c.289G>A	p.Val97Ile	p.V97I	ENST00000342505	NM_002227.2	97	Gtt/Att	4/25	1	2	FACETS	0.964	0.892	1	0.964	0.892	1	CLONAL	1	TRUE	1	0.647594345188498	2		365	535	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625348	69625348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1156753470	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	228	616	1	ENST00000334134.2:c.445G>A	p.Ala149Thr	p.A149T	ENST00000334134	NM_005247.2	149	Gcc/Acc	3/3	1	2	FACETS	0.824	0.769	0.88	0.824	0.769	0.88	CLONAL	1	TRUE	1	0.647594345188498	2		617	855	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457251	89457252	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	45	427	0	ENST00000336596.2:c.1738dup	p.Arg580LysfsTer19	p.R580Kfs*19	ENST00000336596	NM_005233.5	578	gaa/gAaa	9/17	1	2	FACETS	0.211	0.177	0.249	0.211	0.177	0.249	SUBCLONAL	1	TRUE	1	0.647594345188498	2		427	658	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856400	111856400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	27	260	0	ENST00000341259.2:c.451G>A	p.Ala151Thr	p.A151T	ENST00000341259	NM_005475.2	151	Gcc/Acc	2/8	1	2	FACETS	0.226	0.179	0.279	0.226	0.179	0.279	SUBCLONAL	1	TRUE	1	0.647594345188498	2		260	369	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745962	745963	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	59	526	0	ENST00000314574.4:c.559_560del	p.Ser187Ter	p.S187*	ENST00000314574	NM_005433.3	187	AGt/t	5/12	1	2	FACETS	0.269	0.231	0.31	0.269	0.231	0.31	SUBCLONAL	1	TRUE	1	0.647594345188498	2		526	678	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93629423	93629423	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770053469	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	32	320	0	ENST00000375746.1:c.857C>T	p.Ala286Val	p.A286V	ENST00000375746	NM_001174167.1	286	gCg/gTg	7/14	1	2	FACETS	0.167	0.135	0.204	0.167	0.135	0.204	SUBCLONAL	1	TRUE	1	0.647594345188498	2		320	591	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224141	53224141	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	200	388	0	ENST00000375401.3:c.3410C>T	p.Ala1137Val	p.A1137V	ENST00000375401	NM_004187.3	1137	gCg/gTg	22/26	1	1	FACETS	0.811	0.758	0.865	0.811	0.758	0.865	CLONAL	1	TRUE	0	0.647594345188498	1		388	515	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332152	70332153	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1196853334	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	82	248	3	ENST00000373644.4:c.65dup	p.Lys23GlufsTer37	p.K23Efs*37	ENST00000373644	NM_030625.2	19	-/A	2/12	1	2	FACETS	0.588	0.52	0.659	0.588	0.52	0.659	SUBCLONAL	1	TRUE	1	0.647594345188498	2		251	431	SUCCESS
APC	324	MSKCC	GRCh37	5	112116536	112116536	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200740020	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	42	456	0	ENST00000257430.4:c.581G>A	p.Arg194Lys	p.R194K	ENST00000257430	NM_000038.5	194	aGg/aAg	6/16	1	2	FACETS	0.223	0.185	0.264	0.223	0.185	0.264	SUBCLONAL	1	TRUE	1	0.647594345188498	2		456	582	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461563	138461563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558261053	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	190	455	0	ENST00000289153.2:c.458G>A	p.Arg153His	p.R153H	ENST00000289153	NM_006219.2	153	cGc/cAc	3/22	1	2	FACETS	0.885	0.822	0.95	0.885	0.822	0.95	CLONAL	1	TRUE	1	0.647594345188498	2		455	663	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29580009	29580010	+	intron_variant	Intron	INS	-	-	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	35	407	0	ENST00000356175.3:c.4110+3878dup		p.*1370*	ENST00000356175	NM_000267.3	1388-1389/2839			NA	2	FACETS	0.172	0.14	0.208			1	INDETERMINATE	1	TRUE	NA	0.647594345188498	2		407	628	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288785	33288785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765273333	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	161	323	0	ENST00000374542.5:c.767G>A	p.Arg256His	p.R256H	ENST00000374542	NM_001141970.1	256	cGc/cAc	3/8	1	2	FACETS	0.878	0.81	0.949	0.878	0.81	0.949	CLONAL	1	TRUE	1	0.647594345188498	2		323	566	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	411	995	3	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.952	0.905	0.998	0.952	0.905	0.998	CLONAL	1	TRUE	1	0.647594345188498	2		998	1334	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458436	120458436	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs771237928	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	118	459	0	ENST00000256646.2:c.6909del	p.Ile2304LeufsTer2	p.I2304Lfs*2	ENST00000256646	NM_024408.3	2303	ccC/cc	34/34	1	2	FACETS	0.55	0.497	0.606	0.55	0.497	0.606	SUBCLONAL	1	TRUE	1	0.647594345188498	2		459	663	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800902	120800903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs748469666	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	333	687	2	ENST00000257552.2:c.345dup	p.Leu116AlafsTer15	p.L116Afs*15	ENST00000257552	NM_002442.3	115	-/G	6/15	1	2	FACETS	0.944	0.894	0.996	0.944	0.894	0.996	CLONAL	1	TRUE	1	0.647594345188498	2		689	1089	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740438	58740439	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs758630849	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	216	499	0	ENST00000305921.3:c.1349dup	p.Leu450PhefsTer6	p.L450Ffs*6	ENST00000305921	NM_003620.3	448	aat/aaTt	6/6	1	2	FACETS	0.819	0.763	0.876	0.819	0.763	0.876	CLONAL	1	TRUE	1	0.647594345188498	2		499	815	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982134	93982134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773950345	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	108	291	0	ENST00000369303.4:c.1331C>T	p.Ser444Leu	p.S444L	ENST00000369303	NM_004440.3	444	tCg/tTg	6/17	1	2	FACETS	0.847	0.766	0.93	0.847	0.766	0.93	CLONAL	1	TRUE	1	0.647594345188498	2		291	394	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485311	8485311	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	238	415	0	ENST00000356435.5:c.3069T>A	p.Asn1023Lys	p.N1023K	ENST00000356435		1023	aaT/aaA	18/35	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.647594345188498	2		415	656	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966665	36966665	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	219	440	1	ENST00000358127.4:c.661C>T	p.Arg221Trp	p.R221W	ENST00000358127	NM_001280556.1	221	Cgg/Tgg	6/10	1	2	FACETS	0.992	0.927	1	0.992	0.927	1	CLONAL	1	TRUE	1	0.647594345188498	2		441	682	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485766	57485766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	154	322	0	ENST00000371085.3:c.1067G>A	p.Arg356His	p.R356H	ENST00000371085	NM_000516.4	356	cGt/cAt	13/13	1	2	FACETS	0.916	0.844	0.991	0.916	0.844	0.991	CLONAL	1	TRUE	1	0.647594345188498	2		322	519	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84384048	84384048	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	253	477	1	ENST00000321945.7:c.804G>T	p.Lys268Asn	p.K268N	ENST00000321945	NM_139076.2	268	aaG/aaT	9/9	1	2	FACETS	0.889	0.834	0.946	0.889	0.834	0.946	CLONAL	1	TRUE	1	0.647594345188498	2		478	879	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976922	18976922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	270	548	0	ENST00000262803.5:c.3307G>A	p.Gly1103Arg	p.G1103R	ENST00000262803	NM_002911.3	1103	Gga/Aga	23/24	1	2	FACETS	0.979	0.921	1	0.979	0.921	1	CLONAL	1	TRUE	1	0.647594345188498	2		548	852	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480570	120480571	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1553195973	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	44	449	0	ENST00000256646.2:c.3246dup	p.Ala1083SerfsTer17	p.A1083Sfs*17	ENST00000256646	NM_024408.3	1082	-/A	20/34	1	2	FACETS	0.186	0.155	0.22	0.186	0.155	0.22	SUBCLONAL	1	TRUE	1	0.647594345188498	2		449	730	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388675	31388675	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	195	544	0	ENST00000328111.2:c.1940G>A	p.Gly647Asp	p.G647D	ENST00000328111	NM_006892.3	647	gGc/gAc	18/23	1	2	FACETS	0.752	0.697	0.808	0.752	0.697	0.808	SUBCLONAL	1	TRUE	1	0.647594345188498	2		544	801	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400029	139400029	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs778742968	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	64	648	0	ENST00000277541.6:c.4319T>C	p.Ile1440Thr	p.I1440T	ENST00000277541	NM_017617.3	1440	aTc/aCc	25/34	1	2	FACETS	0.203	0.175	0.234	0.203	0.175	0.234	SUBCLONAL	1	TRUE	1	0.647594345188498	2		648	974	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350059	89350059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	237	563	0	ENST00000301030.4:c.2891G>A	p.Gly964Asp	p.G964D	ENST00000301030	NM_001256183.1	964	gGc/gAc	9/13	1	2	FACETS	0.969	0.908	1	0.969	0.908	1	CLONAL	1	TRUE	1	0.647594345188498	2		563	755	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212055	5212055	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749770933	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	185	555	0	ENST00000357368.4:c.4976G>A	p.Arg1659His	p.R1659H	ENST00000357368	NM_002850.3	1659	cGc/cAc	32/38	1	2	FACETS	0.667	0.617	0.72	0.667	0.617	0.72	SUBCLONAL	1	TRUE	1	0.647594345188498	2		555	856	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912173	29912173	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	98	193	0	ENST00000376809.5:c.894G>A	p.Trp298Ter	p.W298*	ENST00000376809	NM_002116.7	298	tgG/tgA	4/8	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.647594345188498	2		193	261	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506141	103506141	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	46	383	0	ENST00000355739.4:c.299G>A	p.Ser100Asn	p.S100N	ENST00000355739	NM_000123.3	100	aGt/aAt	3/15	1	2	FACETS	0.257	0.216	0.302	0.257	0.216	0.302	SUBCLONAL	1	TRUE	1	0.647594345188498	2		383	553	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	113	410	0	ENST00000324856.7:c.5547_5548dup	p.Asp1850GlyfsTer34	p.D1850Gfs*34	ENST00000324856	NM_006015.4	1847	-/GG	20/20	1	2	FACETS	0.496	0.446	0.548	0.496	0.446	0.548	SUBCLONAL	1	TRUE	1	0.647594345188498	2		410	704	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97888841	97888841	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777732881	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	51	578	1	ENST00000289081.3:c.866C>T	p.Ala289Val	p.A289V	ENST00000289081	NM_000136.2	289	gCc/gTc	9/15	1	2	FACETS	0.178	0.15	0.208	0.178	0.15	0.208	SUBCLONAL	1	TRUE	1	0.647594345188498	2		579	886	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924223	11924225	+	inframe_deletion	In_Frame_Del	DEL	GCG	GCG	-	rs1002526348	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	12	27	0	ENST00000353533.5:c.31_33del	p.Gly11del	p.G11del	ENST00000353533	NM_003010.3	7	aGCGgc/agc	1/11	1	2	FACETS	0.862	0.629	1	0.862	0.629	1	CLONAL	1	TRUE	1	0.647594345188498	2		27	43	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339110	65339111	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	247	449	1	ENST00000342505.4:c.425dup	p.Ile143AspfsTer9	p.I143Dfs*9	ENST00000342505	NM_002227.2	142	aag/aaAg	5/25	1	2	FACETS	0.904	0.847	0.962	0.904	0.847	0.962	CLONAL	1	TRUE	1	0.647594345188498	2		450	844	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938655	76938655	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	180	280	0	ENST00000373344.5:c.2093A>G	p.Lys698Arg	p.K698R	ENST00000373344	NM_000489.3	698	aAg/aGg	9/35	1	1	FACETS	0.919	0.859	0.98	0.919	0.859	0.98	CLONAL	1	TRUE	0	0.647594345188498	1		280	409	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967567	26967567	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	229	516	0	ENST00000381527.3:c.710G>A	p.Arg237Gln	p.R237Q	ENST00000381527	NM_001260.1	237	cGa/cAa	7/13	1	2	FACETS	0.887	0.829	0.947	0.887	0.829	0.947	CLONAL	1	TRUE	1	0.647594345188498	2		516	797	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384997	31384997	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768977355	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	51	428	0	ENST00000328111.2:c.1382G>A	p.Arg461His	p.R461H	ENST00000328111	NM_006892.3	461	cGc/cAc	14/23	1	2	FACETS	0.257	0.218	0.3	0.257	0.218	0.3	SUBCLONAL	1	TRUE	1	0.647594345188498	2		428	613	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048667	180048667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749960761	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	260	571	1	ENST00000261937.6:c.1895G>A	p.Arg632His	p.R632H	ENST00000261937	NM_182925.4	632	cGc/cAc	13/30	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.647594345188498	2		572	802	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413945	139413945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	337	710	0	ENST00000277541.6:c.815G>A	p.Cys272Tyr	p.C272Y	ENST00000277541	NM_017617.3	272	tGt/tAt	5/34	1	2	FACETS	0.942	0.892	0.993	0.942	0.892	0.993	CLONAL	1	TRUE	1	0.647594345188498	2		710	1105	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054402	42054403	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	151	363	0	ENST00000219905.7:c.7592dup	p.Lys2532GlufsTer6	p.K2532Efs*6	ENST00000219905	NM_001164273.1	2529	aga/agAa	22/24	1	2	FACETS	0.837	0.769	0.907	0.837	0.769	0.907	CLONAL	1	TRUE	1	0.647594345188498	2		363	557	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874012	151874013	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	206	429	0	ENST00000262189.6:c.8525dup	p.Asn2842LysfsTer2	p.N2842Kfs*2	ENST00000262189	NM_170606.2	2842	aat/aaAt	38/59	1	2	FACETS	0.915	0.853	0.98	0.915	0.853	0.98	CLONAL	1	TRUE	1	0.647594345188498	2		429	695	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118754	115118754	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	108	497	0	ENST00000257566.3:c.587A>G	p.Gln196Arg	p.Q196R	ENST00000257566	NM_016569.3	196	cAg/cGg	2/8	1	2	FACETS	0.41	0.368	0.455	0.41	0.368	0.455	SUBCLONAL	1	TRUE	1	0.647594345188498	2		497	813	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937983	36937983	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	216	719	0	ENST00000361632.4:c.853del	p.Leu285SerfsTer43	p.L285Sfs*43	ENST00000361632		285	Ctc/tc	7/16	1	2	FACETS	0.653	0.607	0.7	0.653	0.607	0.7	SUBCLONAL	1	TRUE	1	0.647594345188498	2		719	1022	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591092	67591092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554051268	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	64	336	0	ENST00000274335.5:c.1685G>A	p.Arg562His	p.R562H	ENST00000274335		562	cGt/cAt	12/15	1	2	FACETS	0.363	0.314	0.415	0.363	0.314	0.415	SUBCLONAL	1	TRUE	1	0.647594345188498	2		336	545	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521524	46521525	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs750652590	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	69	532	1	ENST00000262741.5:c.883dup	p.Met295AsnfsTer3	p.M295Nfs*3	ENST00000262741	NM_003629.3	295	atg/aAtg	7/10	1	2	FACETS	0.24	0.208	0.274	0.24	0.208	0.274	SUBCLONAL	1	TRUE	1	0.647594345188498	2		533	889	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104356980	104356981	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1477199832	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	260	530	0	ENST00000369902.3:c.846dup	p.Glu283ArgfsTer3	p.E283Rfs*3	ENST00000369902	NM_016169.3	280	-/C	7/12	0.210519984747438	3	FACETS	1	0.99	1	0.624	0.586	0.663	INDETERMINATE	1	TRUE	1	0.647594345188498	3		530	852	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845102	128845102	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759466401	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	336	603	0	ENST00000249373.3:c.596G>A	p.Arg199Gln	p.R199Q	ENST00000249373	NM_005631.4	199	cGg/cAg	3/12	1	2	FACETS	0.967	0.916	1	0.967	0.916	1	CLONAL	1	TRUE	1	0.647594345188498	2		603	1073	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500885	8500885	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	17	491	0	ENST00000356435.5:c.1997C>A	p.Pro666His	p.P666H	ENST00000356435		666	cCt/cAt	13/35	1	2	FACETS	0.073	0.054	0.096	0.073	0.054	0.096	SUBCLONAL	1	TRUE	1	0.647594345188498	2		491	717	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929161	32929162	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs397507899	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	267	555	0	ENST00000380152.3:c.7177dup	p.Met2393AsnfsTer19	p.M2393Nfs*19	ENST00000380152		2391	gaa/gAaa	14/27	1	2	FACETS	0.96	0.903	1	0.96	0.903	1	CLONAL	1	TRUE	1	0.647594345188498	2		555	859	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191536	185191536	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	54	500	0	ENST00000265026.3:c.2417G>T	p.Arg806Met	p.R806M	ENST00000265026	NM_004721.4	806	aGg/aTg	11/14	1	2	FACETS	0.219	0.186	0.254	0.219	0.186	0.254	SUBCLONAL	1	TRUE	1	0.647594345188498	2		500	763	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206647680	206647680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs549538401	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	177	410	0	ENST00000367120.3:c.94G>A	p.Gly32Arg	p.G32R	ENST00000367120	NM_014002.3	32	Gga/Aga	4/22	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.647594345188498	2		410	540	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879807	123879807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755330697	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	167	542	0	ENST00000330479.4:c.503G>A	p.Arg168Gln	p.R168Q	ENST00000330479	NM_020382.3	168	cGa/cAa	4/9	1	2	FACETS	0.654	0.601	0.708	0.654	0.601	0.708	SUBCLONAL	1	TRUE	1	0.647594345188498	2		542	789	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357465	89357465	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	158	575	0	ENST00000301030.4:c.353C>T	p.Ala118Val	p.A118V	ENST00000301030	NM_001256183.1	118	gCc/gTc	5/13	1	2	FACETS	0.574	0.526	0.624	0.574	0.526	0.624	SUBCLONAL	1	TRUE	1	0.647594345188498	2		575	850	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100464	2100464	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767626323	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	75	557	1	ENST00000219476.3:c.202G>A	p.Ala68Thr	p.A68T	ENST00000219476	NM_000548.3	68	Gca/Aca	3/42	1	2	FACETS	0.265	0.231	0.301	0.265	0.231	0.301	SUBCLONAL	1	TRUE	1	0.647594345188498	2		558	875	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963984	2963984	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778150	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	269	606	1	ENST00000396946.4:c.1823G>A	p.Arg608His	p.R608H	ENST00000396946	NM_032415.4	608	cGc/cAc	15/25	1	2	FACETS	0.925	0.87	0.982	0.925	0.87	0.982	CLONAL	1	TRUE	1	0.647594345188498	2		607	898	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450243	50450243	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757521297	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	170	479	2	ENST00000331340.3:c.427C>T	p.Arg143Trp	p.R143W	ENST00000331340	NM_006060.4	143	Cgg/Tgg	5/8	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.647594345188498	2		481	518	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584777	52584777	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	188	494	0	ENST00000394830.3:c.4345C>T	p.Pro1449Ser	p.P1449S	ENST00000394830	NM_018313.4	1449	Cca/Tca	28/30	1	2	FACETS	0.734	0.679	0.79	0.734	0.679	0.79	SUBCLONAL	1	TRUE	1	0.647594345188498	2		494	791	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467760	99467760	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs150221450	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	146	303	0	ENST00000268035.6:c.2629C>T	p.Arg877Ter	p.R877*	ENST00000268035	NM_000875.3	877	Cga/Tga	13/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.647594345188498	2		303	415	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187201	11187201	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	209	427	0	ENST00000361445.4:c.6217G>T	p.Ala2073Ser	p.A2073S	ENST00000361445	NM_004958.3	2073	Gcc/Tcc	45/58	1	2	FACETS	0.995	0.928	1	0.995	0.928	1	CLONAL	1	TRUE	1	0.647594345188498	2		427	649	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272941	11272942	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	182	429	0	ENST00000361445.4:c.3309dup	p.Gly1104TrpfsTer6	p.G1104Wfs*6	ENST00000361445	NM_004958.3	1103	-/T	22/58	1	2	FACETS	0.847	0.784	0.911	0.847	0.784	0.911	CLONAL	1	TRUE	1	0.647594345188498	2		429	664	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254750	16254750	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755264170	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	276	570	3	ENST00000375759.3:c.2015G>A	p.Arg672Gln	p.R672Q	ENST00000375759	NM_015001.2	672	cGa/cAa	11/15	1	2	FACETS	0.974	0.917	1	0.974	0.917	1	CLONAL	1	TRUE	1	0.647594345188498	2		573	875	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257845	16257845	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	40	420	0	ENST00000375759.3:c.5110C>A	p.Pro1704Thr	p.P1704T	ENST00000375759	NM_015001.2	1704	Cca/Aca	11/15	1	2	FACETS	0.195	0.162	0.233	0.195	0.162	0.233	SUBCLONAL	1	TRUE	1	0.647594345188498	2		420	632	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258844	16258844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	76	598	0	ENST00000375759.3:c.6109G>A	p.Ala2037Thr	p.A2037T	ENST00000375759	NM_015001.2	2037	Gca/Aca	11/15	1	2	FACETS	0.246	0.215	0.279	0.246	0.215	0.279	SUBCLONAL	1	TRUE	1	0.647594345188498	2		598	955	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260969	16260969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs529018913	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	105	324	1	ENST00000375759.3:c.8234C>T	p.Ala2745Val	p.A2745V	ENST00000375759	NM_015001.2	2745	gCg/gTg	11/15	1	2	FACETS	0.637	0.573	0.704	0.637	0.573	0.704	SUBCLONAL	1	TRUE	1	0.647594345188498	2		325	509	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263779	16263779	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	136	487	1	ENST00000375759.3:c.10148G>A	p.Ser3383Asn	p.S3383N	ENST00000375759	NM_015001.2	3383	aGc/aAc	12/15	1	2	FACETS	0.528	0.48	0.579	0.528	0.48	0.579	SUBCLONAL	1	TRUE	1	0.647594345188498	2		488	795	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17355199	17355199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752361543	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	64	450	0	ENST00000375499.3:c.319G>A	p.Gly107Arg	p.G107R	ENST00000375499	NM_003000.2	107	Gga/Aga	4/8	1	2	FACETS	0.255	0.22	0.293	0.255	0.22	0.293	SUBCLONAL	1	TRUE	1	0.647594345188498	2		450	774	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941120	36941121	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs765536522	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	196	553	0	ENST00000361632.4:c.218dup	p.Arg74GlnfsTer7	p.R74Qfs*7	ENST00000361632		73	ggc/ggGc	3/16	1	2	FACETS	0.724	0.671	0.779	0.724	0.671	0.779	SUBCLONAL	1	TRUE	1	0.647594345188498	2		553	836	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805751	43805751	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	206	709	0	ENST00000372470.3:c.807G>T	p.Trp269Cys	p.W269C	ENST00000372470	NM_005373.2	269	tgG/tgT	5/12	1	2	FACETS	0.655	0.607	0.704	0.655	0.607	0.704	SUBCLONAL	1	TRUE	1	0.647594345188498	2		709	972	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798290	45798290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	40	525	0	ENST00000450313.1:c.646G>A	p.Gly216Arg	p.G216R	ENST00000450313	NM_012222.2	216	Ggg/Agg	8/16	1	2	FACETS	0.155	0.128	0.185	0.155	0.128	0.185	SUBCLONAL	1	TRUE	1	0.647594345188498	2		525	796	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46543263	46543263	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs554826078	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	112	516	0	ENST00000262741.5:c.238C>T	p.Arg80Trp	p.R80W	ENST00000262741	NM_003629.3	80	Cgg/Tgg	3/10	1	2	FACETS	0.44	0.396	0.487	0.44	0.396	0.487	SUBCLONAL	1	TRUE	1	0.647594345188498	2		516	786	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739824	46739824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764040025	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	37	445	0	ENST00000371975.4:c.1625G>A	p.Arg542His	p.R542H	ENST00000371975	NM_003579.3	542	cGc/cAc	15/18	1	2	FACETS	0.163	0.133	0.196	0.163	0.133	0.196	SUBCLONAL	1	TRUE	1	0.647594345188498	2		445	702	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46740333	46740333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	152	541	0	ENST00000371975.4:c.1813G>A	p.Ala605Thr	p.A605T	ENST00000371975	NM_003579.3	605	Gcc/Acc	16/18	1	2	FACETS	0.58	0.53	0.631	0.58	0.53	0.631	SUBCLONAL	1	TRUE	1	0.647594345188498	2		541	810	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115251190	115251190	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	211	516	0	ENST00000369535.4:c.536A>G	p.Gln179Arg	p.Q179R	ENST00000369535	NM_002524.4	179	cAg/cGg	5/7	1	2	FACETS	0.755	0.702	0.81	0.755	0.702	0.81	SUBCLONAL	1	TRUE	1	0.647594345188498	2		516	863	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512257	120512257	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	230	484	0	ENST00000256646.2:c.985G>T	p.Gly329Cys	p.G329C	ENST00000256646	NM_024408.3	329	Ggc/Tgc	6/34	1	2	FACETS	0.896	0.837	0.956	0.896	0.837	0.956	CLONAL	1	TRUE	1	0.647594345188498	2		484	793	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880299	155880299	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	232	400	0	ENST00000368323.3:c.107-2A>G		p.X36_splice	ENST00000368323	NM_006912.5	36			1	2	FACETS	0.983	0.92	1	0.983	0.92	1	CLONAL	1	TRUE	1	0.647594345188498	2		400	729	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834187	156834187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs79678945	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	385	862	1	ENST00000524377.1:c.254G>A	p.Arg85His	p.R85H	ENST00000524377	NM_002529.3	85	cGt/cAt	2/17	1	2	FACETS	0.964	0.916	1	0.964	0.916	1	CLONAL	1	TRUE	1	0.647594345188498	2		863	1234	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841478	156841478	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	281	601	0	ENST00000524377.1:c.781A>G	p.Lys261Glu	p.K261E	ENST00000524377	NM_002529.3	261	Aag/Gag	7/17	1	2	FACETS	0.953	0.897	1	0.953	0.897	1	CLONAL	1	TRUE	1	0.647594345188498	2		601	911	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162722920	162722920	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	165	540	0	ENST00000367921.3:c.118C>A	p.Gln40Lys	p.Q40K	ENST00000367921	NM_006182.2	40	Cag/Aag	4/18	1	2	FACETS	0.609	0.559	0.66	0.609	0.559	0.66	SUBCLONAL	1	TRUE	1	0.647594345188498	2		540	837	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175996819	175996819	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	193	418	0	ENST00000367669.3:c.1618C>G	p.Leu540Val	p.L540V	ENST00000367669	NM_022457.5	540	Ctg/Gtg	15/20	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.647594345188498	2		418	588	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176104165	176104165	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	103	371	0	ENST00000367669.3:c.949G>A	p.Ala317Thr	p.A317T	ENST00000367669	NM_022457.5	317	Gct/Act	8/20	1	2	FACETS	0.618	0.555	0.684	0.618	0.555	0.684	SUBCLONAL	1	TRUE	1	0.647594345188498	2		371	515	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193121546	193121546	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	164	314	0	ENST00000367435.3:c.944A>G	p.Tyr315Cys	p.Y315C	ENST00000367435	NM_024529.4	315	tAc/tGc	10/17	1	2	FACETS	0.936	0.865	1	0.936	0.865	1	CLONAL	1	TRUE	1	0.647594345188498	2		314	541	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226551701	226551701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866456432	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	86	539	0	ENST00000366794.5:c.2729C>T	p.Thr910Met	p.T910M	ENST00000366794	NM_001618.3	910	aCg/aTg	20/23	1	2	FACETS	0.322	0.284	0.362	0.322	0.284	0.362	SUBCLONAL	1	TRUE	1	0.647594345188498	2		539	825	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680604	241680604	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	173	365	0	ENST00000366560.3:c.145T>C	p.Ser49Pro	p.S49P	ENST00000366560	NM_000143.3	49	Tcc/Ccc	2/10	1	2	FACETS	0.934	0.865	1	0.934	0.865	1	CLONAL	1	TRUE	1	0.647594345188498	2		365	572	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246091304	246091305	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	68	492	0	ENST00000388985.4:c.630dup	p.Asn211GlnfsTer37	p.N211Qfs*37	ENST00000388985		210	-/C	7/12	1	2	FACETS	0.292	0.254	0.334	0.292	0.254	0.334	SUBCLONAL	1	TRUE	1	0.647594345188498	2		492	718	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609955	43609955	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035958105	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	296	713	1	ENST00000355710.3:c.1907C>T	p.Thr636Met	p.T636M	ENST00000355710	NM_020975.4	636	aCg/aTg	11/20	1	2	FACETS	0.908	0.856	0.961	0.908	0.856	0.961	CLONAL	1	TRUE	1	0.647594345188498	2		714	1007	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615613	43615613	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587780810	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	199	460	0	ENST00000355710.3:c.2692G>T	p.Asp898Tyr	p.D898Y	ENST00000355710	NM_020975.4	898	Gat/Tat	15/20	1	2	FACETS	0.869	0.808	0.932	0.869	0.808	0.932	CLONAL	1	TRUE	1	0.647594345188498	2		460	707	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900968	114900968	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	294	456	0	ENST00000543371.1:c.578A>G	p.His193Arg	p.H193R	ENST00000543371	NM_001198531.1	193	cAc/cGc	6/14	0.210519984747438	3	FACETS	1	0.993	1	0.684	0.645	0.723	INDETERMINATE	1	TRUE	1	0.647594345188498	3		456	879	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911497	114911497	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	88	201	0	ENST00000543371.1:c.1015T>C	p.Ser339Pro	p.S339P	ENST00000543371	NM_001198531.1	339	Tcc/Ccc	10/14	0.210519984747438	3	FACETS	0.818	0.728	0.912	0.409	0.364	0.456	INDETERMINATE	1	TRUE	1	0.647594345188498	3		201	440	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156648	2156648	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	294	625	0	ENST00000434045.2:c.274del	p.Glu92SerfsTer24	p.E92Sfs*24	ENST00000434045	NM_001127598.1	92	Gag/ag	3/5	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.647594345188498	2		625	747	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741456	17741456	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	347	722	0	ENST00000250003.3:c.127T>C	p.Phe43Leu	p.F43L	ENST00000250003	NM_002478.4	43	Ttc/Ctc	1/3	1	2	FACETS	0.987	0.935	1	0.987	0.935	1	CLONAL	1	TRUE	1	0.647594345188498	2		722	1086	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202519	67202519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374535834	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	254	725	3	ENST00000312629.5:c.1328C>T	p.Thr443Met	p.T443M	ENST00000312629	NM_003952.2	443	aCg/aTg	15/15	1	2	FACETS	0.783	0.733	0.834	0.783	0.733	0.834	SUBCLONAL	1	TRUE	1	0.647594345188498	2		728	1002	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514058	69514058	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	82	580	0	ENST00000294312.3:c.623C>T	p.Ala208Val	p.A208V	ENST00000294312	NM_005117.2	208	gCc/gTc	3/3	1	2	FACETS	0.275	0.241	0.311	0.275	0.241	0.311	SUBCLONAL	1	TRUE	1	0.647594345188498	2		580	922	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589716	69589716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	76	146	0	ENST00000168712.1:c.137G>A	p.Arg46His	p.R46H	ENST00000168712	NM_002007.2	46	cGc/cAc	1/3	1	2	FACETS	0.97	0.863	1	0.97	0.863	1	CLONAL	1	TRUE	1	0.647594345188498	2		146	242	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943698	71943698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761761079	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	336	617	1	ENST00000298229.2:c.1741C>T	p.Arg581Trp	p.R581W	ENST00000298229	NM_001567.3	581	Cgg/Tgg	15/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.647594345188498	2		618	982	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948207	71948207	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	376	855	0	ENST00000298229.2:c.2920del	p.Ala974ProfsTer157	p.A974Pfs*157	ENST00000298229	NM_001567.3	973	gcG/gc	26/28	1	2	FACETS	0.869	0.824	0.914	0.869	0.824	0.914	CLONAL	1	TRUE	1	0.647594345188498	2		855	1337	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102056761	102056761	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	26	326	0	ENST00000282441.5:c.701A>G	p.Asp234Gly	p.D234G	ENST00000282441	NM_001130145.2	234	gAt/gGt	4/9	1	2	FACETS	0.158	0.124	0.196	0.158	0.124	0.196	SUBCLONAL	1	TRUE	1	0.647594345188498	2		326	509	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076768	102076768	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	330	641	0	ENST00000282441.5:c.947A>G	p.Glu316Gly	p.E316G	ENST00000282441	NM_001130145.2	316	gAg/gGg	5/9	1	2	FACETS	0.981	0.928	1	0.981	0.928	1	CLONAL	1	TRUE	1	0.647594345188498	2		641	1039	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195551	102195551	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1003047322	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	57	457	0	ENST00000263464.3:c.311A>G	p.Asn104Ser	p.N104S	ENST00000263464	NM_001165.4	104	aAc/aGc	2/9	1	2	FACETS	0.255	0.218	0.295	0.255	0.218	0.295	SUBCLONAL	1	TRUE	1	0.647594345188498	2		457	691	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142037	108142037	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	284	556	0	ENST00000278616.4:c.2981T>A	p.Val994Asp	p.V994D	ENST00000278616	NM_000051.3	994	gTc/gAc	20/63	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.647594345188498	2		556	866	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172516	108172516	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	101	231	0	ENST00000278616.4:c.5319G>T	p.Lys1773Asn	p.K1773N	ENST00000278616	NM_000051.3	1773	aaG/aaT	35/63	1	2	FACETS	0.902	0.814	0.993	0.902	0.814	0.993	CLONAL	1	TRUE	1	0.647594345188498	2		231	346	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188124	108188124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	172	327	0	ENST00000278616.4:c.6223C>T	p.His2075Tyr	p.H2075Y	ENST00000278616	NM_000051.3	2075	Cat/Tat	43/63	1	2	FACETS	0.905	0.837	0.975	0.905	0.837	0.975	CLONAL	1	TRUE	1	0.647594345188498	2		327	587	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204639	108204639	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	43	315	0	ENST00000278616.4:c.7954C>T	p.Pro2652Ser	p.P2652S	ENST00000278616	NM_000051.3	2652	Cca/Tca	54/63	1	2	FACETS	0.25	0.209	0.296	0.25	0.209	0.296	SUBCLONAL	1	TRUE	1	0.647594345188498	2		315	531	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359332	118359332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	121	254	0	ENST00000534358.1:c.4336G>A	p.Val1446Met	p.V1446M	ENST00000534358	NM_005933.3	1446	Gtg/Atg	11/36	1	2	FACETS	0.905	0.824	0.988	0.905	0.824	0.988	CLONAL	1	TRUE	1	0.647594345188498	2		254	413	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375914	118375915	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	122	452	0	ENST00000534358.1:c.9313dup	p.Ile3105AsnfsTer8	p.I3105Nfs*8	ENST00000534358	NM_005933.3	3103	caa/cAaa	27/36	1	2	FACETS	0.59	0.534	0.648	0.59	0.534	0.648	SUBCLONAL	1	TRUE	1	0.647594345188498	2		452	639	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125499316	125499316	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs867675787	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	224	507	0	ENST00000428830.2:c.385A>G	p.Arg129Gly	p.R129G	ENST00000428830	NM_001114121.2	129	Agg/Ggg	5/14	1	2	FACETS	0.862	0.804	0.92	0.862	0.804	0.92	CLONAL	1	TRUE	1	0.647594345188498	2		507	803	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416952	416953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	102	407	0	ENST00000399788.2:c.3596_3597dup	p.Gly1200LysfsTer10	p.G1200Kfs*10	ENST00000399788	NM_001042603.1	1199	-/AA	23/28	1	2	FACETS	0.479	0.428	0.532	0.479	0.428	0.532	SUBCLONAL	1	TRUE	1	0.647594345188498	2		407	658	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18648997	18648997	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	173	400	0	ENST00000266497.5:c.2672C>T	p.Ala891Val	p.A891V	ENST00000266497		891	gCa/gTa	19/31	1	2	FACETS	0.923	0.854	0.993	0.923	0.854	0.993	CLONAL	1	TRUE	1	0.647594345188498	2		400	579	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245089	46245089	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	70	465	0	ENST00000334344.6:c.3183A>T	p.Lys1061Asn	p.K1061N	ENST00000334344	NM_152641.2	1061	aaA/aaT	15/21	1	2	FACETS	0.306	0.266	0.349	0.306	0.266	0.349	SUBCLONAL	1	TRUE	1	0.647594345188498	2		465	706	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245384	46245384	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	201	396	0	ENST00000334344.6:c.3478C>A	p.Pro1160Thr	p.P1160T	ENST00000334344	NM_152641.2	1160	Cca/Aca	15/21	1	2	FACETS	0.917	0.853	0.982	0.917	0.853	0.982	CLONAL	1	TRUE	1	0.647594345188498	2		396	677	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426517	49426517	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	226	825	0	ENST00000301067.7:c.11971C>T	p.Gln3991Ter	p.Q3991*	ENST00000301067	NM_003482.3	3991	Cag/Tag	39/54	1	2	FACETS	0.559	0.52	0.6	0.559	0.52	0.6	SUBCLONAL	1	TRUE	1	0.647594345188498	2		825	1248	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427360	49427360	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757243984	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	255	563	1	ENST00000301067.7:c.11128G>A	p.Gly3710Arg	p.G3710R	ENST00000301067	NM_003482.3	3710	Gga/Aga	39/54	1	2	FACETS	0.93	0.873	0.988	0.93	0.873	0.988	CLONAL	1	TRUE	1	0.647594345188498	2		564	847	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435230	49435230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774739665	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	169	492	0	ENST00000301067.7:c.6323C>T	p.Pro2108Leu	p.P2108L	ENST00000301067	NM_003482.3	2108	cCg/cTg	31/54	1	2	FACETS	0.668	0.615	0.723	0.668	0.615	0.723	SUBCLONAL	1	TRUE	1	0.647594345188498	2		492	781	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444196	49444196	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	221	807	0	ENST00000301067.7:c.3175G>T	p.Gly1059Trp	p.G1059W	ENST00000301067	NM_003482.3	1059	Ggg/Tgg	11/54	1	2	FACETS	0.579	0.538	0.622	0.579	0.538	0.622	SUBCLONAL	1	TRUE	1	0.647594345188498	2		807	1178	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445311	49445311	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	253	908	1	ENST00000301067.7:c.2155C>T	p.Pro719Ser	p.P719S	ENST00000301067	NM_003482.3	719	Ccg/Tcg	10/54	1	2	FACETS	0.621	0.58	0.663	0.621	0.58	0.663	SUBCLONAL	1	TRUE	1	0.647594345188498	2		909	1258	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864780	57864780	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	132	594	0	ENST00000228682.2:c.2257C>A	p.Leu753Ile	p.L753I	ENST00000228682	NM_005269.2	753	Ctt/Att	12/12	1	2	FACETS	0.482	0.438	0.53	0.482	0.438	0.53	SUBCLONAL	1	TRUE	1	0.647594345188498	2		594	845	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813438	102813438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1565970471	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	134	499	3	ENST00000307046.8:c.251G>A	p.Arg84Gln	p.R84Q	ENST00000307046	NM_001111285.1	84	cGg/cAg	3/4	1	2	FACETS	0.585	0.533	0.641	0.585	0.533	0.641	SUBCLONAL	1	TRUE	1	0.647594345188498	2		502	707	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112893859	112893859	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	137	527	0	ENST00000351677.2:c.748G>A	p.Glu250Lys	p.E250K	ENST00000351677	NM_002834.3	250	Gaa/Aaa	6/16	1	2	FACETS	0.476	0.433	0.522	0.476	0.433	0.522	SUBCLONAL	1	TRUE	1	0.647594345188498	2		527	889	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120741	115120741	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	66	670	0	ENST00000257566.3:c.265C>T	p.Pro89Ser	p.P89S	ENST00000257566	NM_016569.3	89	Cct/Tct	1/8	1	2	FACETS	0.223	0.192	0.256	0.223	0.192	0.256	SUBCLONAL	1	TRUE	1	0.647594345188498	2		670	915	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536882	120536882	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	331	669	0	ENST00000229340.5:c.304T>A	p.Trp102Arg	p.W102R	ENST00000229340	NM_006861.6	102	Tgg/Agg	4/6	1	2	FACETS	0.981	0.929	1	0.981	0.929	1	CLONAL	1	TRUE	1	0.647594345188498	2		669	1042	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426829	121426829	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	195	448	0	ENST00000257555.6:c.520G>A	p.Ala174Thr	p.A174T	ENST00000257555		174	Gcg/Acg	2/10	1	2	FACETS	0.957	0.891	1	0.957	0.891	1	CLONAL	1	TRUE	1	0.647594345188498	2		448	629	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879605	123879605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	163	405	1	ENST00000330479.4:c.301G>A	p.Ala101Thr	p.A101T	ENST00000330479	NM_020382.3	101	Gct/Act	4/9	1	2	FACETS	0.888	0.819	0.958	0.888	0.819	0.958	CLONAL	1	TRUE	1	0.647594345188498	2		406	567	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219464	133219464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	285	767	1	ENST00000320574.5:c.4670C>T	p.Ala1557Val	p.A1557V	ENST00000320574	NM_006231.2	1557	gCa/gTa	36/49	1	2	FACETS	0.786	0.739	0.834	0.786	0.739	0.834	SUBCLONAL	1	TRUE	1	0.647594345188498	2		768	1120	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256104	133256104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151325267	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	183	427	1	ENST00000320574.5:c.557C>T	p.Ala186Val	p.A186V	ENST00000320574	NM_006231.2	186	gCg/gTg	6/49	1	2	FACETS	0.917	0.851	0.986	0.917	0.851	0.986	CLONAL	1	TRUE	1	0.647594345188498	2		428	616	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557745	21557745	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	56	566	0	ENST00000382592.4:c.2100del	p.Lys702ArgfsTer4	p.K702Rfs*4	ENST00000382592	NM_014572.2	700	agG/ag	5/8	1	2	FACETS	0.178	0.152	0.207	0.178	0.152	0.207	SUBCLONAL	1	TRUE	1	0.647594345188498	2		566	970	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26911748	26911748	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	191	489	1	ENST00000381527.3:c.173G>T	p.Gly58Val	p.G58V	ENST00000381527	NM_001260.1	58	gGg/gTg	2/13	1	2	FACETS	0.859	0.797	0.922	0.859	0.797	0.922	CLONAL	1	TRUE	1	0.647594345188498	2		490	687	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589381	28589381	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	190	476	0	ENST00000241453.7:c.2666A>G	p.Tyr889Cys	p.Y889C	ENST00000241453	NM_004119.2	889	tAc/tGc	22/24	1	2	FACETS	0.798	0.74	0.858	0.798	0.74	0.858	SUBCLONAL	1	TRUE	1	0.647594345188498	2		476	735	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610144	28610144	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	66	494	0	ENST00000241453.7:c.1346A>G	p.Gln449Arg	p.Q449R	ENST00000241453	NM_004119.2	449	cAg/cGg	11/24	1	2	FACETS	0.254	0.219	0.291	0.254	0.219	0.291	SUBCLONAL	1	TRUE	1	0.647594345188498	2		494	804	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964116	28964116	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	142	386	0	ENST00000282397.4:c.1786A>G	p.Asn596Asp	p.N596D	ENST00000282397	NM_002019.4	596	Aat/Gat	13/30	1	2	FACETS	0.665	0.608	0.725	0.665	0.608	0.725	SUBCLONAL	1	TRUE	1	0.647594345188498	2		386	659	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893268	32893268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201716	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	126	457	0	ENST00000380152.3:c.122C>T	p.Pro41Leu	p.P41L	ENST00000380152		41	cCc/cTc	3/27	1	2	FACETS	0.532	0.482	0.585	0.532	0.482	0.585	SUBCLONAL	1	TRUE	1	0.647594345188498	2		457	731	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907074	32907074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	145	416	0	ENST00000380152.3:c.1459G>A	p.Ala487Thr	p.A487T	ENST00000380152		487	Gca/Aca	10/27	1	2	FACETS	0.764	0.7	0.831	0.764	0.7	0.831	SUBCLONAL	1	TRUE	1	0.647594345188498	2		416	586	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910629	32910629	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886040407	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	65	457	1	ENST00000380152.3:c.2137C>T	p.Gln713Ter	p.Q713*	ENST00000380152		713	Cag/Tag	11/27	1	2	FACETS	0.293	0.253	0.335	0.293	0.253	0.335	SUBCLONAL	1	TRUE	1	0.647594345188498	2		458	686	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911037	32911037	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786202105	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	227	494	0	ENST00000380152.3:c.2545G>T	p.Val849Leu	p.V849L	ENST00000380152		849	Gta/Tta	11/27	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.647594345188498	2		494	679	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912770	32912771	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	189	414	0	ENST00000380152.3:c.4283_4284dup	p.Gln1429PhefsTer20	p.Q1429Ffs*20	ENST00000380152		1426	-/TT	11/27	1	2	FACETS	0.863	0.801	0.928	0.863	0.801	0.928	CLONAL	1	TRUE	1	0.647594345188498	2		414	676	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49051504	49051504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1566241168	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	166	393	0	ENST00000267163.4:c.2677G>A	p.Gly893Arg	p.G893R	ENST00000267163	NM_000321.2	893	Gga/Aga	26/27	1	2	FACETS	0.853	0.787	0.921	0.853	0.787	0.921	CLONAL	1	TRUE	1	0.647594345188498	2		393	601	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434802	110434802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	282	639	2	ENST00000375856.3:c.3599C>T	p.Pro1200Leu	p.P1200L	ENST00000375856	NM_003749.2	1200	cCg/cTg	1/2	1	2	FACETS	0.885	0.833	0.939	0.885	0.833	0.939	CLONAL	1	TRUE	1	0.647594345188498	2		641	984	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422035	81422035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	38	315	0	ENST00000298171.2:c.11C>T	p.Ala4Val	p.A4V	ENST00000298171	NM_000369.2	4	gCg/gTg	1/10	1	2	FACETS	0.276	0.228	0.33	0.276	0.228	0.33	SUBCLONAL	1	TRUE	1	0.647594345188498	2		315	425	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582154	95582154	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	118	233	0	ENST00000393063.1:c.1757T>C	p.Leu586Ser	p.L586S	ENST00000393063	NM_030621.3	586	tTg/tCg	12/28	1	2	FACETS	0.942	0.858	1	0.942	0.858	1	CLONAL	1	TRUE	1	0.647594345188498	2		233	387	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643795	38643795	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	321	588	0	ENST00000299084.4:c.1265C>A	p.Pro422His	p.P422H	ENST00000299084	NM_152594.2	422	cCt/cAt	7/7	1	2	FACETS	0.985	0.932	1	0.985	0.932	1	CLONAL	1	TRUE	1	0.647594345188498	2		588	1006	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042317	42042317	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	245	502	0	ENST00000219905.7:c.6512G>T	p.Arg2171Met	p.R2171M	ENST00000219905	NM_001164273.1	2171	aGg/aTg	17/24	1	2	FACETS	0.882	0.826	0.939	0.882	0.826	0.939	CLONAL	1	TRUE	1	0.647594345188498	2		502	858	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042378	42042378	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	267	584	0	ENST00000219905.7:c.6573G>T	p.Gln2191His	p.Q2191H	ENST00000219905	NM_001164273.1	2191	caG/caT	17/24	1	2	FACETS	0.87	0.817	0.924	0.87	0.817	0.924	CLONAL	1	TRUE	1	0.647594345188498	2		584	948	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058328	42058328	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs762039202	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	165	331	0	ENST00000219905.7:c.8048A>G	p.His2683Arg	p.H2683R	ENST00000219905	NM_001164273.1	2683	cAt/cGt	24/24	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.647594345188498	2		331	497	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713287	43713287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	313	732	1	ENST00000382044.4:c.4186G>A	p.Ala1396Thr	p.A1396T	ENST00000382044	NM_001141980.1	1396	Gct/Act	20/28	1	2	FACETS	0.891	0.841	0.942	0.891	0.841	0.942	CLONAL	1	TRUE	1	0.647594345188498	2		733	1085	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762070	43762070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	63	505	0	ENST00000382044.4:c.1375C>T	p.Pro459Ser	p.P459S	ENST00000382044	NM_001141980.1	459	Cct/Tct	11/28	1	2	FACETS	0.254	0.219	0.292	0.254	0.219	0.292	SUBCLONAL	1	TRUE	1	0.647594345188498	2		505	766	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472621	88472621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1429499898	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	71	353	0	ENST00000360948.2:c.1934G>A	p.Arg645His	p.R645H	ENST00000360948	NM_001012338.2	645	cGc/cAc	16/19	1	2	FACETS	0.467	0.408	0.529	0.467	0.408	0.529	SUBCLONAL	1	TRUE	1	0.647594345188498	2		353	470	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680664	88680664	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	141	597	0	ENST00000360948.2:c.593C>A	p.Pro198His	p.P198H	ENST00000360948	NM_001012338.2	198	cCt/cAt	6/19	1	2	FACETS	0.586	0.534	0.64	0.586	0.534	0.64	SUBCLONAL	1	TRUE	1	0.647594345188498	2		597	743	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304138	91304139	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	121	538	0	ENST00000355112.3:c.1543_1544dup	p.Asn515LysfsTer17	p.N515Kfs*17	ENST00000355112	NM_000057.2	512	gga/ggAAa	7/22	1	2	FACETS	0.444	0.401	0.49	0.444	0.401	0.49	SUBCLONAL	1	TRUE	1	0.647594345188498	2		538	841	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99192829	99192829	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	250	457	0	ENST00000268035.6:c.19G>A	p.Gly7Arg	p.G7R	ENST00000268035	NM_000875.3	7	Gga/Aga	1/21	1	2	FACETS	0.957	0.898	1	0.957	0.898	1	CLONAL	1	TRUE	1	0.647594345188498	2		457	807	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99491922	99491922	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1171490584	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	103	488	1	ENST00000268035.6:c.3707A>G	p.Asn1236Ser	p.N1236S	ENST00000268035	NM_000875.3	1236	aAc/aGc	20/21	1	2	FACETS	0.469	0.42	0.521	0.469	0.42	0.521	SUBCLONAL	1	TRUE	1	0.647594345188498	2		489	678	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640196	3640196	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	417	782	0	ENST00000294008.3:c.3443A>G	p.Glu1148Gly	p.E1148G	ENST00000294008	NM_032444.2	1148	gAa/gGa	12/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.647594345188498	2		782	1261	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642754	3642754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747563780	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	370	749	0	ENST00000294008.3:c.2273C>T	p.Ala758Val	p.A758V	ENST00000294008	NM_032444.2	758	gCg/gTg	11/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.647594345188498	2		749	1134	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647607	3647607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1483311055	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	380	774	3	ENST00000294008.3:c.1456C>T	p.Arg486Cys	p.R486C	ENST00000294008	NM_032444.2	486	Cgt/Tgt	7/15	1	2	FACETS	0.955	0.907	1	0.955	0.907	1	CLONAL	1	TRUE	1	0.647594345188498	2		777	1229	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647684	3647684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369994733	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	359	712	0	ENST00000294008.3:c.1379G>A	p.Arg460His	p.R460H	ENST00000294008	NM_032444.2	460	cGc/cAc	7/15	1	2	FACETS	0.938	0.889	0.988	0.938	0.889	0.988	CLONAL	1	TRUE	1	0.647594345188498	2		712	1182	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778483	3778483	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	384	938	0	ENST00000262367.5:c.6565T>C	p.Tyr2189His	p.Y2189H	ENST00000262367	NM_004380.2	2189	Tac/Cac	31/31	1	2	FACETS	0.98	0.931	1	0.98	0.931	1	CLONAL	1	TRUE	1	0.647594345188498	2		938	1210	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858027	9858027	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	192	450	0	ENST00000330684.3:c.3374A>G	p.Glu1125Gly	p.E1125G	ENST00000330684	NM_001134407.1	1125	gAg/gGg	13/13	1	2	FACETS	0.89	0.827	0.956	0.89	0.827	0.956	CLONAL	1	TRUE	1	0.647594345188498	2		450	666	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858741	9858741	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	74	245	0	ENST00000330684.3:c.2660T>C	p.Leu887Pro	p.L887P	ENST00000330684	NM_001134407.1	887	cTg/cCg	13/13	1	2	FACETS	0.555	0.488	0.626	0.555	0.488	0.626	SUBCLONAL	1	TRUE	1	0.647594345188498	2		245	412	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23625413	23625413	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	134	398	0	ENST00000261584.4:c.3114-1G>T		p.X1038_splice	ENST00000261584	NM_024675.3	1038			1	2	FACETS	0.641	0.583	0.7	0.641	0.583	0.7	SUBCLONAL	1	TRUE	1	0.647594345188498	2		398	646	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862193	68862193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779648243	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	155	563	1	ENST00000261769.5:c.2281G>A	p.Gly761Arg	p.G761R	ENST00000261769	NM_004360.3	761	Gga/Aga	14/16	1	2	FACETS	0.561	0.513	0.61	0.561	0.513	0.61	SUBCLONAL	1	TRUE	1	0.647594345188498	2		564	854	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821889	72821890	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	31	358	0	ENST00000268489.5:c.10285dup	p.Arg3429ProfsTer2	p.R3429Pfs*2	ENST00000268489	NM_006885.3	3429	cgt/cCgt	10/10	1	2	FACETS	0.187	0.15	0.228	0.187	0.15	0.228	SUBCLONAL	1	TRUE	1	0.647594345188498	2		358	513	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822540	72822540	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	186	443	0	ENST00000268489.5:c.9635del	p.Pro3212ArgfsTer29	p.P3212Rfs*29	ENST00000268489	NM_006885.3	3212	cCg/cg	10/10	1	2	FACETS	0.866	0.803	0.931	0.866	0.803	0.931	CLONAL	1	TRUE	1	0.647594345188498	2		443	663	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822657	72822657	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753839132	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	240	631	1	ENST00000268489.5:c.9518C>T	p.Pro3173Leu	p.P3173L	ENST00000268489	NM_006885.3	3173	cCg/cTg	10/10	1	2	FACETS	0.87	0.814	0.927	0.87	0.814	0.927	CLONAL	1	TRUE	1	0.647594345188498	2		632	852	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828384	72828384	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	188	425	0	ENST00000268489.5:c.8197C>A	p.Arg2733Ser	p.R2733S	ENST00000268489	NM_006885.3	2733	Cgt/Agt	9/10	1	2	FACETS	0.968	0.899	1	0.968	0.899	1	CLONAL	1	TRUE	1	0.647594345188498	2		425	600	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991643	72991643	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	140	559	0	ENST00000268489.5:c.2402A>G	p.Lys801Arg	p.K801R	ENST00000268489	NM_006885.3	801	aAa/aGa	2/10	1	2	FACETS	0.535	0.487	0.585	0.535	0.487	0.585	SUBCLONAL	1	TRUE	1	0.647594345188498	2		559	808	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942124	81942125	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	100	586	0	ENST00000359376.3:c.1667dup	p.Lys557GlnfsTer16	p.K557Qfs*16	ENST00000359376	NM_002661.3	554	acg/acGg	17/33	1	2	FACETS	0.334	0.298	0.373	0.334	0.298	0.373	SUBCLONAL	1	TRUE	1	0.647594345188498	2		586	924	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341566	89341566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1350510474	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	255	432	1	ENST00000301030.4:c.7504A>G	p.Lys2502Glu	p.K2502E	ENST00000301030	NM_001256183.1	2502	Aag/Gag	10/13	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.647594345188498	2		433	748	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89809327	89809327	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1262639465	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	223	401	0	ENST00000389301.3:c.3646G>A	p.Ala1216Thr	p.A1216T	ENST00000389301	NM_000135.2	1216	Gcc/Acc	37/43	1	2	FACETS	0.953	0.89	1	0.953	0.89	1	CLONAL	1	TRUE	1	0.647594345188498	2		401	723	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217850	7217850	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	161	560	2	ENST00000380728.2:c.161del	p.Lys54ArgfsTer9	p.K54Rfs*9	ENST00000380728		54	aAg/ag	3/11	1	2	FACETS	0.534	0.489	0.58	0.534	0.489	0.58	SUBCLONAL	1	TRUE	1	0.647594345188498	2		562	932	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983279	15983279	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	39	374	0	ENST00000268712.3:c.3500A>G	p.Gln1167Arg	p.Q1167R	ENST00000268712	NM_006311.3	1167	cAg/cGg	26/46	1	2	FACETS	0.221	0.183	0.264	0.221	0.183	0.264	SUBCLONAL	1	TRUE	1	0.647594345188498	2		374	544	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983740	15983740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	185	409	0	ENST00000268712.3:c.3382C>T	p.His1128Tyr	p.H1128Y	ENST00000268712	NM_006311.3	1128	Cat/Tat	25/46	1	2	FACETS	0.851	0.789	0.916	0.851	0.789	0.916	CLONAL	1	TRUE	1	0.647594345188498	2		409	671	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989754	15989754	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	95	196	0	ENST00000268712.3:c.3019C>A	p.Leu1007Ile	p.L1007I	ENST00000268712	NM_006311.3	1007	Ctt/Att	23/46	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.647594345188498	2		196	288	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16062141	16062141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1214744460	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	253	492	0	ENST00000268712.3:c.665C>T	p.Pro222Leu	p.P222L	ENST00000268712	NM_006311.3	222	cCc/cTc	6/46	1	2	FACETS	0.896	0.84	0.953	0.896	0.84	0.953	CLONAL	1	TRUE	1	0.647594345188498	2		492	872	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37871995	37871995	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	166	544	2	ENST00000269571.5:c.1316G>A	p.Gly439Asp	p.G439D	ENST00000269571		439	gGc/gAc	12/27	1	2	FACETS	0.719	0.662	0.778	0.719	0.662	0.778	SUBCLONAL	1	TRUE	1	0.647594345188498	2		546	713	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40865263	40865263	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	153	598	0	ENST00000428826.2:c.1168A>G	p.Arg390Gly	p.R390G	ENST00000428826		390	Agg/Ggg	11/21	1	2	FACETS	0.547	0.5	0.596	0.547	0.5	0.596	SUBCLONAL	1	TRUE	1	0.647594345188498	2		598	864	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41209151	41209151	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	157	484	0	ENST00000357654.3:c.5195A>G	p.His1732Arg	p.H1732R	ENST00000357654	NM_007294.3	1732	cAt/cGt	19/23	1	2	FACETS	0.649	0.596	0.705	0.649	0.596	0.705	SUBCLONAL	1	TRUE	1	0.647594345188498	2		484	747	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215947	41215947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41293459	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	282	560	1	ENST00000357654.3:c.5096G>A	p.Arg1699Gln	p.R1699Q	ENST00000357654	NM_007294.3	1699	cGg/cAg	17/23	1	2	FACETS	0.995	0.938	1	0.995	0.938	1	CLONAL	1	TRUE	1	0.647594345188498	2		561	875	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245300	41245300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	222	665	0	ENST00000357654.3:c.2248C>T	p.Leu750Phe	p.L750F	ENST00000357654	NM_007294.3	750	Ctc/Ttc	10/23	1	2	FACETS	0.644	0.599	0.69	0.644	0.599	0.69	SUBCLONAL	1	TRUE	1	0.647594345188498	2		665	1065	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699308	47699308	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	106	356	0	ENST00000347630.2:c.200G>A	p.Trp67Ter	p.W67*	ENST00000347630	NM_001007230.1	67	tGg/tAg	4/11	1	2	FACETS	0.535	0.48	0.593	0.535	0.48	0.593	SUBCLONAL	1	TRUE	1	0.647594345188498	2		356	612	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55674230	55674231	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	182	347	0	ENST00000284073.2:c.459dup	p.Gly154TrpfsTer6	p.G154Wfs*6	ENST00000284073	NM_138962.2	152	-/T	8/14	1	2	FACETS	0.951	0.882	1	0.951	0.882	1	CLONAL	1	TRUE	1	0.647594345188498	2		347	591	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435047	56435047	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	73	602	0	ENST00000407977.2:c.2090A>C	p.His697Pro	p.H697P	ENST00000407977		697	cAc/cCc	9/10	1	2	FACETS	0.241	0.21	0.275	0.241	0.21	0.275	SUBCLONAL	1	TRUE	1	0.647594345188498	2		602	934	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492826	56492826	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	143	473	1	ENST00000407977.2:c.113C>A	p.Ser38Tyr	p.S38Y	ENST00000407977		38	tCt/tAt	2/10	1	2	FACETS	0.677	0.619	0.738	0.677	0.619	0.738	SUBCLONAL	1	TRUE	1	0.647594345188498	2		474	652	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59878628	59878628	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1028347439	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	143	367	0	ENST00000259008.2:c.1126C>T	p.Gln376Ter	p.Q376*	ENST00000259008	NM_032043.2	376	Caa/Taa	8/20	1	2	FACETS	0.883	0.811	0.958	0.883	0.811	0.958	CLONAL	1	TRUE	1	0.647594345188498	2		367	500	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007437	62007437	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	28	315	0	ENST00000392795.3:c.430A>G	p.Met144Val	p.M144V	ENST00000392795	NM_001039933.1	144	Atg/Gtg	3/6	1	2	FACETS	0.17	0.135	0.21	0.17	0.135	0.21	SUBCLONAL	1	TRUE	1	0.647594345188498	2		315	508	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007488	62007488	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	158	519	0	ENST00000392795.3:c.379T>C	p.Cys127Arg	p.C127R	ENST00000392795	NM_001039933.1	127	Tgc/Cgc	3/6	1	2	FACETS	0.628	0.576	0.682	0.628	0.576	0.682	SUBCLONAL	1	TRUE	1	0.647594345188498	2		519	777	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39575921	39575921	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	172	394	0	ENST00000262039.4:c.854A>T	p.Asp285Val	p.D285V	ENST00000262039	NM_002647.2	285	gAt/gTt	8/25	1	2	FACETS	0.862	0.797	0.93	0.862	0.797	0.93	CLONAL	1	TRUE	1	0.647594345188498	2		394	616	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581190	48581190	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	171	354	1	ENST00000342988.3:c.494A>T	p.Asp165Val	p.D165V	ENST00000342988	NM_005359.5	165	gAc/gTc	5/12	0.210519984747438	3	FACETS	1	0.979	1	0.581	0.537	0.626	INDETERMINATE	1	TRUE	1	0.647594345188498	3		355	602	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348560	56348561	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1450997592	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	132	255	0	ENST00000348428.3:c.374dup	p.Gly126ArgfsTer40	p.G126Rfs*40	ENST00000348428	NM_006785.3	123	agc/agCc	2/17	0.210519984747438	3	FACETS	1	0.976	1	0.594	0.543	0.647	INDETERMINATE	1	TRUE	1	0.647594345188498	3		255	454	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414980	56414980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	237	441	0	ENST00000348428.3:c.2381C>T	p.Ala794Val	p.A794V	ENST00000348428	NM_006785.3	794	gCt/gTt	17/17	0.210519984747438	3	FACETS	1	0.984	1	0.578	0.541	0.617	INDETERMINATE	1	TRUE	1	0.647594345188498	3		441	838	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1620979	1620979	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1329397192	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1201	64	792	3	ENST00000344749.5:c.1081del	p.Gln361ArgfsTer33	p.Q361Rfs*33	ENST00000344749	NM_001136139.2	361	Cag/ag	13/19	1	2	FACETS	0.156	0.134	0.18	0.156	0.134	0.18	SUBCLONAL	1	TRUE	1	0.647594345188498	2		795	1265	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632361	1632361	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	182	746	0	ENST00000344749.5:c.189C>A	p.Asp63Glu	p.D63E	ENST00000344749	NM_001136139.2	63	gaC/gaA	4/19	1	2	FACETS	0.511	0.47	0.553	0.511	0.47	0.553	SUBCLONAL	1	TRUE	1	0.647594345188498	2		746	1101	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2202735	2202735	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	266	648	0	ENST00000398665.3:c.744G>T	p.Glu248Asp	p.E248D	ENST00000398665	NM_032482.2	248	gaG/gaT	9/28	1	2	FACETS	0.912	0.857	0.968	0.912	0.857	0.968	CLONAL	1	TRUE	1	0.647594345188498	2		648	901	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210634	2210634	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	246	531	0	ENST00000398665.3:c.1131G>T	p.Glu377Asp	p.E377D	ENST00000398665	NM_032482.2	377	gaG/gaT	14/28	1	2	FACETS	0.909	0.852	0.967	0.909	0.852	0.967	CLONAL	1	TRUE	1	0.647594345188498	2		531	836	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222401	2222401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	149	497	0	ENST00000398665.3:c.3233G>A	p.Ser1078Asn	p.S1078N	ENST00000398665	NM_032482.2	1078	aGc/aAc	24/28	1	2	FACETS	0.648	0.593	0.705	0.648	0.593	0.705	SUBCLONAL	1	TRUE	1	0.647594345188498	2		497	710	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5258082	5258082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	270	515	0	ENST00000357368.4:c.652G>A	p.Ala218Thr	p.A218T	ENST00000357368	NM_002850.3	218	Gcc/Acc	8/38	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.647594345188498	2		515	786	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7141702	7141702	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1568440846	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	225	542	0	ENST00000302850.5:c.2668C>T	p.Arg890Ter	p.R890*	ENST00000302850	NM_000208.2	890	Cga/Tga	13/22	1	2	FACETS	0.823	0.768	0.88	0.823	0.768	0.88	CLONAL	1	TRUE	1	0.647594345188498	2		542	844	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250398	10250398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1010743136	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	68	478	0	ENST00000340748.4:c.3854G>A	p.Arg1285His	p.R1285H	ENST00000340748		1285	cGc/cAc	33/40	1	2	FACETS	0.286	0.248	0.327	0.286	0.248	0.327	SUBCLONAL	1	TRUE	1	0.647594345188498	2		478	734	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600491	10600491	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	303	606	0	ENST00000171111.5:c.1364C>A	p.Pro455Gln	p.P455Q	ENST00000171111	NM_203500.1	455	cCa/cAa	4/6	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.647594345188498	2		606	880	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11015748	11015749	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	176	361	0	ENST00000327064.4:c.344dup	p.Asn115LysfsTer76	p.N115Kfs*76	ENST00000327064	NM_199141.1	114	-/A	2/16	1	2	FACETS	0.918	0.85	0.988	0.918	0.85	0.988	CLONAL	1	TRUE	1	0.647594345188498	2		361	592	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105656	11105656	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	242	552	0	ENST00000358026.2:c.1572G>T	p.Lys524Asn	p.K524N	ENST00000358026	NM_001128849.1	524	aaG/aaT	9/36	1	2	FACETS	0.85	0.796	0.906	0.85	0.796	0.906	CLONAL	1	TRUE	1	0.647594345188498	2		552	879	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107188	11107188	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	68	512	1	ENST00000358026.2:c.1781del	p.Gly594AspfsTer19	p.G594Dfs*19	ENST00000358026	NM_001128849.1	594	Gga/ga	11/36	1	2	FACETS	0.262	0.227	0.3	0.262	0.227	0.3	SUBCLONAL	1	TRUE	1	0.647594345188498	2		513	801	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138494	11138494	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	266	543	0	ENST00000358026.2:c.3250C>A	p.Leu1084Ile	p.L1084I	ENST00000358026	NM_001128849.1	1084	Ctt/Att	24/36	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.647594345188498	2		543	821	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272072	15272072	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	308	683	0	ENST00000263388.2:c.6367del	p.Glu2124ArgfsTer25	p.E2124Rfs*25	ENST00000263388	NM_000435.2	2123	Ctt/tt	33/33	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.647594345188498	2		683	916	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298716	15298716	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	59	704	0	ENST00000263388.2:c.1582G>T	p.Gly528Cys	p.G528C	ENST00000263388	NM_000435.2	528	Ggc/Tgc	10/33	1	2	FACETS	0.162	0.139	0.188	0.162	0.139	0.188	SUBCLONAL	1	TRUE	1	0.647594345188498	2		704	1124	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354214	15354214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	222	708	0	ENST00000263377.2:c.2666C>T	p.Ala889Val	p.A889V	ENST00000263377	NM_058243.2	889	gCc/gTc	14/20	1	2	FACETS	0.654	0.608	0.701	0.654	0.608	0.701	SUBCLONAL	1	TRUE	1	0.647594345188498	2		708	1049	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367037	15367037	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	115	254	0	ENST00000263377.2:c.1589A>G	p.Gln530Arg	p.Q530R	ENST00000263377	NM_058243.2	530	cAg/cGg	9/20	1	2	FACETS	0.848	0.769	0.929	0.848	0.769	0.929	CLONAL	1	TRUE	1	0.647594345188498	2		254	419	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943481	17943481	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	268	496	0	ENST00000458235.1:c.2527C>T	p.Pro843Ser	p.P843S	ENST00000458235	NM_000215.3	843	Ccg/Tcg	19/24	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.647594345188498	2		496	823	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955066	17955066	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	367	745	2	ENST00000458235.1:c.161G>A	p.Cys54Tyr	p.C54Y	ENST00000458235	NM_000215.3	54	tGc/tAc	2/24	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.647594345188498	2		747	1082	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965942	18965942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1309527755	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	244	587	2	ENST00000262803.5:c.1435G>A	p.Val479Met	p.V479M	ENST00000262803	NM_002911.3	479	Gtg/Atg	11/24	1	2	FACETS	0.927	0.869	0.987	0.927	0.869	0.987	CLONAL	1	TRUE	1	0.647594345188498	2		589	813	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967047	18967047	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	193	607	1	ENST00000262803.5:c.1762T>C	p.Ser588Pro	p.S588P	ENST00000262803	NM_002911.3	588	Tcg/Ccg	13/24	1	2	FACETS	0.697	0.646	0.751	0.697	0.646	0.751	SUBCLONAL	1	TRUE	1	0.647594345188498	2		608	855	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218354	36218354	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	322	706	0	ENST00000222270.7:c.4133T>C	p.Ile1378Thr	p.I1378T	ENST00000222270	NM_014727.1	1378	aTc/aCc	16/37	1	2	FACETS	0.973	0.92	1	0.973	0.92	1	CLONAL	1	TRUE	1	0.647594345188498	2		706	1022	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224099	36224099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	374	737	2	ENST00000222270.7:c.6649C>T	p.Gln2217Ter	p.Q2217*	ENST00000222270	NM_014727.1	2217	Cag/Tag	28/37	1	2	FACETS	0.954	0.905	1	0.954	0.905	1	CLONAL	1	TRUE	1	0.647594345188498	2		739	1211	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229441	36229441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	112	406	1	ENST00000222270.7:c.8131C>T	p.Arg2711Cys	p.R2711C	ENST00000222270	NM_014727.1	2711	Cgt/Tgt	37/37	1	2	FACETS	0.567	0.511	0.626	0.567	0.511	0.626	SUBCLONAL	1	TRUE	1	0.647594345188498	2		407	610	SUCCESS
AXL	558	MSKCC	GRCh37	19	41759553	41759553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	345	662	0	ENST00000301178.4:c.1976G>A	p.Gly659Asp	p.G659D	ENST00000301178	NM_021913.4	659	gGc/gAc	17/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.647594345188498	2		662	1052	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754535	42754535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745819984	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	61	764	1	ENST00000222329.4:c.205G>A	p.Val69Ile	p.V69I	ENST00000222329	NM_006494.2	69	Gtt/Att	2/4	1	2	FACETS	0.17	0.145	0.196	0.17	0.145	0.196	SUBCLONAL	1	TRUE	1	0.647594345188498	2		765	1110	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794506	42794506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1248145762	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	311	793	0	ENST00000575354.2:c.1586G>A	p.Gly529Asp	p.G529D	ENST00000575354	NM_015125.3	529	gGt/gAt	10/20	1	2	FACETS	0.868	0.819	0.918	0.868	0.819	0.918	CLONAL	1	TRUE	1	0.647594345188498	2		793	1107	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794988	42794988	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	281	638	0	ENST00000575354.2:c.2068C>T	p.Pro690Ser	p.P690S	ENST00000575354	NM_015125.3	690	Ccc/Tcc	10/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.647594345188498	2		638	853	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731593	47731593	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	83	136	0	ENST00000449228.1:c.199C>A	p.Leu67Ile	p.L67I	ENST00000449228	NM_001127240.2	67	Ctc/Atc	2/4	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.647594345188498	2		136	239	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50916691	50916691	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568634881	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	266	523	0	ENST00000440232.2:c.2166del	p.Phe723SerfsTer5	p.F723Sfs*5	ENST00000440232	NM_002691.3	721	acG/ac	18/27	1	2	FACETS	0.974	0.916	1	0.974	0.916	1	CLONAL	1	TRUE	1	0.647594345188498	2		523	843	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917074	50917074	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780138978	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	360	768	3	ENST00000440232.2:c.2326C>T	p.Arg776Trp	p.R776W	ENST00000440232	NM_002691.3	776	Cgg/Tgg	19/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.647594345188498	2		771	1048	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505333	25505333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1449714685	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	162	519	0	ENST00000264709.3:c.425G>A	p.Gly142Asp	p.G142D	ENST00000264709	NM_175629.2	142	gGc/gAc	4/23	1	2	FACETS	0.635	0.583	0.689	0.635	0.583	0.689	SUBCLONAL	1	TRUE	1	0.647594345188498	2		519	788	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973274	25973274	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	42	212	0	ENST00000435504.4:c.1151T>C	p.Leu384Pro	p.L384P	ENST00000435504		384	cTg/cCg	12/13	1	2	FACETS	0.41	0.344	0.484	0.41	0.344	0.484	SUBCLONAL	1	TRUE	1	0.647594345188498	2		212	316	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982515	25982515	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	89	186	0	ENST00000435504.4:c.776-1G>T		p.X259_splice	ENST00000435504		259			1	2	FACETS	0.859	0.769	0.952	0.859	0.769	0.952	CLONAL	1	TRUE	1	0.647594345188498	2		186	320	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022395	26022395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	169	364	0	ENST00000435504.4:c.262C>T	p.Pro88Ser	p.P88S	ENST00000435504		88	Ccg/Tcg	5/13	1	2	FACETS	0.914	0.845	0.985	0.914	0.845	0.985	CLONAL	1	TRUE	1	0.647594345188498	2		364	571	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416548	29416548	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	110	484	2	ENST00000389048.3:c.4405C>A	p.Pro1469Thr	p.P1469T	ENST00000389048	NM_004304.4	1469	Ccg/Acg	29/29	1	2	FACETS	0.49	0.441	0.543	0.49	0.441	0.543	SUBCLONAL	1	TRUE	1	0.647594345188498	2		486	693	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416719	29416719	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	89	352	0	ENST00000389048.3:c.4234C>T	p.Pro1412Ser	p.P1412S	ENST00000389048	NM_004304.4	1412	Cct/Tct	29/29	1	2	FACETS	0.493	0.437	0.551	0.493	0.437	0.551	SUBCLONAL	1	TRUE	1	0.647594345188498	2		352	558	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754800	29754800	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	113	392	0	ENST00000389048.3:c.1135C>A	p.Pro379Thr	p.P379T	ENST00000389048	NM_004304.4	379	Ccc/Acc	4/29	1	2	FACETS	0.544	0.491	0.601	0.544	0.491	0.601	SUBCLONAL	1	TRUE	1	0.647594345188498	2		392	641	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143174	30143174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	238	562	1	ENST00000389048.3:c.352G>A	p.Ala118Thr	p.A118T	ENST00000389048	NM_004304.4	118	Gca/Aca	1/29	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.647594345188498	2		563	708	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224122	39224122	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517163	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	189	569	1	ENST00000402219.2:c.3022T>C	p.Tyr1008His	p.Y1008H	ENST00000402219	NM_005633.3	1008	Tat/Cat	19/23	1	2	FACETS	0.644	0.595	0.694	0.644	0.595	0.694	SUBCLONAL	1	TRUE	1	0.647594345188498	2		570	907	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690171	47690171	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	186	399	0	ENST00000233146.2:c.1388T>C	p.Val463Ala	p.V463A	ENST00000233146	NM_000251.2	463	gTg/gCg	9/16	1	2	FACETS	0.956	0.888	1	0.956	0.888	1	CLONAL	1	TRUE	1	0.647594345188498	2		399	601	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693883	47693883	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	271	483	0	ENST00000233146.2:c.1597C>A	p.Leu533Ile	p.L533I	ENST00000233146	NM_000251.2	533	Ctt/Att	10/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.647594345188498	2		483	766	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010380	48010380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	100	650	0	ENST00000234420.5:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000234420	NM_000179.2	3	cGa/cAa	1/10	1	2	FACETS	0.315	0.281	0.352	0.315	0.281	0.352	SUBCLONAL	1	TRUE	1	0.647594345188498	2		650	979	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147754	61147754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	46	339	0	ENST00000295025.8:c.1064G>A	p.Gly355Glu	p.G355E	ENST00000295025	NM_002908.2	355	gGa/gAa	10/11	1	2	FACETS	0.265	0.223	0.312	0.265	0.223	0.312	SUBCLONAL	1	TRUE	1	0.647594345188498	2		339	536	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193581	99193581	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	186	496	0	ENST00000074304.5:c.2776A>G	p.Thr926Ala	p.T926A	ENST00000074304	NM_001134224.1	926	Acc/Gcc	25/26	1	2	FACETS	0.985	0.916	1	0.985	0.916	1	CLONAL	1	TRUE	1	0.647594345188498	2		496	583	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198272822	198272822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	188	422	0	ENST00000335508.6:c.1139C>T	p.Pro380Leu	p.P380L	ENST00000335508	NM_012433.2	380	cCt/cTt	9/25	1	2	FACETS	0.886	0.823	0.952	0.886	0.823	0.952	CLONAL	1	TRUE	1	0.647594345188498	2		422	655	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149610	202149610	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	205	436	0	ENST00000358485.4:c.1051A>T	p.Ile351Phe	p.I351F	ENST00000358485	NM_001080125.1	351	Atc/Ttc	8/9	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.647594345188498	2		436	596	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248710	212248710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	159	335	0	ENST00000342788.4:c.3557C>T	p.Pro1186Leu	p.P1186L	ENST00000342788	NM_005235.2	1186	cCc/cTc	28/28	1	2	FACETS	0.974	0.9	1	0.974	0.9	1	CLONAL	1	TRUE	1	0.647594345188498	2		335	504	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530078	212530078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	23	271	0	ENST00000342788.4:c.1841G>A	p.Cys614Tyr	p.C614Y	ENST00000342788	NM_005235.2	614	tGc/tAc	15/28	1	2	FACETS	0.172	0.133	0.216	0.172	0.133	0.216	SUBCLONAL	1	TRUE	1	0.647594345188498	2		271	414	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662842	227662842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	151	554	1	ENST00000305123.5:c.613G>A	p.Val205Met	p.V205M	ENST00000305123	NM_005544.2	205	Gtg/Atg	1/2	1	2	FACETS	0.556	0.509	0.606	0.556	0.509	0.606	SUBCLONAL	1	TRUE	1	0.647594345188498	2		555	838	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGG	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	24	197	0	ENST00000375687.4:c.1932_1934dup	p.Gly646dup	p.G646dup	ENST00000375687	NM_015338.5	646	-/GGG	13/13	1	2	FACETS	0.298	0.234	0.371	0.298	0.234	0.371	SUBCLONAL	1	TRUE	1	0.647594345188498	2		197	249	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368209	31368209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	204	670	1	ENST00000328111.2:c.80G>A	p.Cys27Tyr	p.C27Y	ENST00000328111	NM_006892.3	27	tGc/tAc	2/23	1	2	FACETS	0.667	0.618	0.717	0.667	0.618	0.717	SUBCLONAL	1	TRUE	1	0.647594345188498	2		671	945	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388081	31388081	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748988879	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	93	316	0	ENST00000328111.2:c.1882G>A	p.Val628Met	p.V628M	ENST00000328111	NM_006892.3	628	Gtg/Atg	17/23	1	2	FACETS	0.597	0.533	0.665	0.597	0.533	0.665	SUBCLONAL	1	TRUE	1	0.647594345188498	2		316	481	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39746808	39746808	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	58	540	0	ENST00000361337.2:c.1823-1G>A		p.X608_splice	ENST00000361337	NM_003286.2	608			1	2	FACETS	0.228	0.195	0.264	0.228	0.195	0.264	SUBCLONAL	1	TRUE	1	0.647594345188498	2		540	786	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420082	41420082	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	26	310	0	ENST00000373198.4:c.239C>A	p.Ser80Tyr	p.S80Y	ENST00000373198	NM_133170.3	80	tCt/tAt	3/32	1	2	FACETS	0.196	0.155	0.244	0.196	0.155	0.244	SUBCLONAL	1	TRUE	1	0.647594345188498	2		310	409	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319737	62319737	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	79	677	0	ENST00000360203.5:c.1720C>T	p.Arg574Trp	p.R574W	ENST00000360203	NM_001283009.1	574	Cgg/Tgg	20/35	1	2	FACETS	0.244	0.214	0.277	0.244	0.214	0.277	SUBCLONAL	1	TRUE	1	0.647594345188498	2		677	999	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259203	36259204	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	99	715	0	ENST00000300305.3:c.287dup	p.Asn96LysfsTer42	p.N96Kfs*42	ENST00000300305		96	aac/aaAc	3/8	1	2	FACETS	0.317	0.283	0.355	0.317	0.283	0.355	SUBCLONAL	1	TRUE	1	0.647594345188498	2		715	963	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44515615	44515615	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	102	696	1	ENST00000291552.4:c.281G>T	p.Gly94Val	p.G94V	ENST00000291552	NM_006758.2	94	gGg/gTg	5/8	1	2	FACETS	0.313	0.279	0.349	0.313	0.279	0.349	SUBCLONAL	1	TRUE	1	0.647594345188498	2		697	1008	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656994	45656994	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	199	596	0	ENST00000407780.3:c.162G>A	p.Trp54Ter	p.W54*	ENST00000407780	NM_001283052.1	54	tgG/tgA	3/7	1	2	FACETS	0.651	0.603	0.701	0.651	0.603	0.701	SUBCLONAL	1	TRUE	1	0.647594345188498	2		596	944	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37637628	37637628	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	352	770	5	ENST00000249071.6:c.106G>A	p.Val36Met	p.V36M	ENST00000249071	NM_002872.4	36	Gtg/Atg	2/7	1	2	FACETS	0.935	0.886	0.985	0.935	0.886	0.985	CLONAL	1	TRUE	1	0.647594345188498	2		775	1163	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513436	41513436	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	266	592	1	ENST00000263253.7:c.340G>T	p.Gly114Ter	p.G114*	ENST00000263253	NM_001429.3	114	Gga/Tga	2/31	1	2	FACETS	0.936	0.879	0.993	0.936	0.879	0.993	CLONAL	1	TRUE	1	0.647594345188498	2		593	878	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547846	41547846	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	191	381	1	ENST00000263253.7:c.2827C>T	p.Pro943Ser	p.P943S	ENST00000263253	NM_001429.3	943	Cca/Tca	15/31	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.647594345188498	2		382	569	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422989	12422989	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	35	433	0	ENST00000287820.6:c.479A>G	p.Lys160Arg	p.K160R	ENST00000287820	NM_015869.4	160	aAg/aGg	3/7	1	2	FACETS	0.162	0.132	0.196	0.162	0.132	0.196	SUBCLONAL	1	TRUE	1	0.647594345188498	2		433	666	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067433	37067433	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587779952	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	61	504	0	ENST00000231790.2:c.1344G>T	p.Glu448Asp	p.E448D	ENST00000231790	NM_000249.3	448	gaG/gaT	12/19	1	2	FACETS	0.238	0.204	0.274	0.238	0.204	0.274	SUBCLONAL	1	TRUE	1	0.647594345188498	2		504	792	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164477	47164477	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1445389349	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	120	335	0	ENST00000409792.3:c.1649G>A	p.Ser550Asn	p.S550N	ENST00000409792	NM_014159.6	550	aGt/aAt	3/21	1	2	FACETS	0.593	0.537	0.652	0.593	0.537	0.652	SUBCLONAL	1	TRUE	1	0.647594345188498	2		335	625	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165230	47165230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	100	325	0	ENST00000409792.3:c.896G>A	p.Ser299Asn	p.S299N	ENST00000409792	NM_014159.6	299	aGt/aAt	3/21	1	2	FACETS	0.62	0.556	0.688	0.62	0.556	0.688	SUBCLONAL	1	TRUE	1	0.647594345188498	2		325	498	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723029	49723029	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1225484117	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	184	358	0	ENST00000449682.2:c.1387G>A	p.Ala463Thr	p.A463T	ENST00000449682	NM_020998.3	463	Gct/Act	11/18	1	2	FACETS	0.957	0.888	1	0.957	0.888	1	CLONAL	1	TRUE	1	0.647594345188498	2		358	594	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932949	49932949	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	117	733	0	ENST00000296474.3:c.2995C>A	p.Leu999Met	p.L999M	ENST00000296474	NM_002447.2	999	Ctg/Atg	13/20	1	2	FACETS	0.314	0.282	0.348	0.314	0.282	0.348	SUBCLONAL	1	TRUE	1	0.647594345188498	2		733	1151	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940111	49940112	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760002850	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	230	549	0	ENST00000296474.3:c.931dup	p.Ala311GlyfsTer26	p.A311Gfs*26	ENST00000296474	NM_002447.2	311	gcc/gGcc	1/20	1	2	FACETS	0.911	0.852	0.971	0.911	0.852	0.971	CLONAL	1	TRUE	1	0.647594345188498	2		549	780	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940243	49940243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	53	616	1	ENST00000296474.3:c.800C>T	p.Ala267Val	p.A267V	ENST00000296474	NM_002447.2	267	gCc/gTc	1/20	1	2	FACETS	0.191	0.162	0.222	0.191	0.162	0.222	SUBCLONAL	1	TRUE	1	0.647594345188498	2		617	859	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713639	52713639	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	126	412	0	ENST00000394830.3:c.89G>A	p.Gly30Asp	p.G30D	ENST00000394830	NM_018313.4	30	gGc/gAc	2/30	1	2	FACETS	0.525	0.476	0.577	0.525	0.476	0.577	SUBCLONAL	1	TRUE	1	0.647594345188498	2		412	741	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72861887	72861887	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	244	551	0	ENST00000325599.8:c.995C>A	p.Pro332Gln	p.P332Q	ENST00000325599	NM_018130.2	332	cCa/cAa	9/11	1	2	FACETS	0.929	0.871	0.989	0.929	0.871	0.989	CLONAL	1	TRUE	1	0.647594345188498	2		551	811	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920478	134920478	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	254	575	1	ENST00000398015.3:c.2293C>A	p.Leu765Ile	p.L765I	ENST00000398015	NM_004441.4	765	Ctc/Atc	12/16	1	2	FACETS	0.949	0.89	1	0.949	0.89	1	CLONAL	1	TRUE	1	0.647594345188498	2		576	827	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977922	134977922	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	256	589	0	ENST00000398015.3:c.2915T>C	p.Met972Thr	p.M972T	ENST00000398015	NM_004441.4	972	aTg/aCg	16/16	1	2	FACETS	0.91	0.854	0.967	0.91	0.854	0.967	CLONAL	1	TRUE	1	0.647594345188498	2		589	869	SUCCESS
ATR	545	MSKCC	GRCh37	3	142204007	142204007	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369309229	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	181	442	0	ENST00000350721.4:c.6196C>T	p.Arg2066Trp	p.R2066W	ENST00000350721	NM_001184.3	2066	Cgg/Tgg	36/47	1	2	FACETS	0.817	0.756	0.88	0.817	0.756	0.88	CLONAL	1	TRUE	1	0.647594345188498	2		442	684	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274739	142274740	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	46	324	0	ENST00000350721.4:c.2319_2320dup	p.Ile774LysfsTer6	p.I774Kfs*6	ENST00000350721	NM_001184.3	774	ata/aAAta	10/47	1	2	FACETS	0.276	0.232	0.324	0.276	0.232	0.324	SUBCLONAL	1	TRUE	1	0.647594345188498	2		324	515	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278206	142278207	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs758475337	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	123	511	0	ENST00000350721.4:c.1618dup	p.Tyr540LeufsTer6	p.Y540Lfs*6	ENST00000350721	NM_001184.3	540	tac/tTac	7/47	1	2	FACETS	0.453	0.41	0.499	0.453	0.41	0.499	SUBCLONAL	1	TRUE	1	0.647594345188498	2		511	838	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281577	142281578	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	143	524	0	ENST00000350721.4:c.666dup	p.Arg223Ter	p.R223*	ENST00000350721	NM_001184.3	222	-/T	4/47	1	2	FACETS	0.544	0.496	0.594	0.544	0.496	0.594	SUBCLONAL	1	TRUE	1	0.647594345188498	2		524	812	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998127	169998128	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAA	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	125	681	0	ENST00000295797.4:c.824_826dup	p.Lys275dup	p.K275dup	ENST00000295797	NM_002740.5	275	tta/ttAAAa	9/18	1	2	FACETS	0.411	0.371	0.453	0.411	0.371	0.453	SUBCLONAL	1	TRUE	1	0.647594345188498	2		681	939	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185169181	185169181	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	39	451	0	ENST00000265026.3:c.1276C>T	p.Gln426Ter	p.Q426*	ENST00000265026	NM_004721.4	426	Cag/Tag	7/14	1	2	FACETS	0.179	0.147	0.214	0.179	0.147	0.214	SUBCLONAL	1	TRUE	1	0.647594345188498	2		451	674	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505039	186505039	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	128	270	0	ENST00000323963.5:c.895A>G	p.Thr299Ala	p.T299A	ENST00000323963		299	Aca/Gca	8/11	1	2	FACETS	0.996	0.911	1	0.996	0.911	1	CLONAL	1	TRUE	1	0.647594345188498	2		270	397	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444518	187444518	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	167	432	1	ENST00000232014.4:c.1708+1G>A		p.X570_splice	ENST00000232014	NM_001130845.1	570			1	2	FACETS	0.841	0.777	0.908	0.841	0.777	0.908	CLONAL	1	TRUE	1	0.647594345188498	2		433	613	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805488	1805488	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373496046	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	274	664	5	ENST00000260795.2:c.1000G>A	p.Ala334Thr	p.A334T	ENST00000260795		334	Gcc/Acc	7/17	1	2	FACETS	0.845	0.793	0.897	0.845	0.793	0.897	CLONAL	1	TRUE	1	0.647594345188498	2		669	1002	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807167	1807167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751635116	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	307	722	3	ENST00000260795.2:c.1498G>A	p.Ala500Thr	p.A500T	ENST00000260795		500	Gcc/Acc	10/17	1	2	FACETS	0.974	0.92	1	0.974	0.92	1	CLONAL	1	TRUE	1	0.647594345188498	2		725	973	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152124	55152124	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	225	629	0	ENST00000257290.5:c.2556A>C	p.Lys852Asn	p.K852N	ENST00000257290	NM_006206.4	852	aaA/aaC	18/23	1	2	FACETS	0.858	0.801	0.916	0.858	0.801	0.916	CLONAL	1	TRUE	1	0.647594345188498	2		629	810	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213920	66213920	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	116	353	0	ENST00000273854.3:c.2510G>A	p.Gly837Glu	p.G837E	ENST00000273854	NM_004439.5	837	gGa/gAa	15/18	1	2	FACETS	0.859	0.78	0.941	0.859	0.78	0.941	CLONAL	1	TRUE	1	0.647594345188498	2		353	417	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84384746	84384747	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	42	280	0	ENST00000321945.7:c.696dup	p.Val233SerfsTer5	p.V233Sfs*5	ENST00000321945	NM_139076.2	232	-/A	8/9	1	2	FACETS	0.259	0.216	0.307	0.259	0.216	0.307	SUBCLONAL	1	TRUE	1	0.647594345188498	2		280	500	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007349	143007349	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	101	330	0	ENST00000262992.4:c.2435del	p.Asn812IlefsTer10	p.N812Ifs*10	ENST00000262992	NM_001101669.1	812	aAt/at	22/24	1	2	FACETS	0.56	0.502	0.621	0.56	0.502	0.621	SUBCLONAL	1	TRUE	1	0.647594345188498	2		330	557	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067091	143067091	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	173	374	0	ENST00000262992.4:c.1622A>G	p.Lys541Arg	p.K541R	ENST00000262992	NM_001101669.1	541	aAa/aGa	16/24	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.647594345188498	2		374	531	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541534	187541534	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	115	370	0	ENST00000441802.2:c.6206T>C	p.Val2069Ala	p.V2069A	ENST00000441802	NM_005245.3	2069	gTc/gCc	10/27	0.647594345188498	1	FACETS	0.582	0.528	0.637	0.582	0.528	0.637	SUBCLONAL	1	TRUE	0	0.647594345188498	1		370	413	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226094	226094	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775827529	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	202	428	1	ENST00000264932.6:c.553C>T	p.Gln185Ter	p.Q185*	ENST00000264932	NM_004168.2	185	Cag/Tag	5/15	1	2	FACETS	0.927	0.863	0.993	0.927	0.863	0.993	CLONAL	1	TRUE	1	0.647594345188498	2		429	673	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31468155	31468155	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	208	501	0	ENST00000344624.3:c.2257C>T	p.Arg753Cys	p.R753C	ENST00000344624		753	Cgt/Tgt	15/33	1	2	FACETS	0.776	0.721	0.832	0.776	0.721	0.832	SUBCLONAL	1	TRUE	1	0.647594345188498	2		501	828	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38942976	38942976	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	180	395	0	ENST00000357387.3:c.5011A>G	p.Arg1671Gly	p.R1671G	ENST00000357387	NM_152756.3	1671	Agg/Ggg	37/38	1	2	FACETS	0.933	0.865	1	0.933	0.865	1	CLONAL	1	TRUE	1	0.647594345188498	2		395	596	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959918	38959918	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	79	293	1	ENST00000357387.3:c.2014G>T	p.Gly672Ter	p.G672*	ENST00000357387	NM_152756.3	672	Gga/Tga	21/38	1	2	FACETS	0.502	0.443	0.565	0.502	0.443	0.565	SUBCLONAL	1	TRUE	1	0.647594345188498	2		294	486	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750455	57750456	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	209	437	0	ENST00000274289.3:c.2012dup	p.Asn671LysfsTer15	p.N671Kfs*15	ENST00000274289	NM_006622.3	671	aat/aaAt	14/14	1	2	FACETS	0.941	0.877	1	0.941	0.877	1	CLONAL	1	TRUE	1	0.647594345188498	2		437	686	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79952352	79952352	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	203	483	0	ENST00000265081.6:c.358+2T>C		p.X120_splice	ENST00000265081	NM_002439.4	120			1	2	FACETS	0.827	0.769	0.887	0.827	0.769	0.887	CLONAL	1	TRUE	1	0.647594345188498	2		483	758	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80083470	80083470	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	56	661	0	ENST00000265081.6:c.2522C>A	p.Ala841Asp	p.A841D	ENST00000265081	NM_002439.4	841	gCt/gAt	18/24	1	2	FACETS	0.173	0.148	0.202	0.173	0.148	0.202	SUBCLONAL	1	TRUE	1	0.647594345188498	2		661	998	SUCCESS
APC	324	MSKCC	GRCh37	5	112102105	112102105	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	88	295	0	ENST00000257430.4:c.218A>G	p.Lys73Arg	p.K73R	ENST00000257430	NM_000038.5	73	aAa/aGa	3/16	1	2	FACETS	0.635	0.565	0.708	0.635	0.565	0.708	SUBCLONAL	1	TRUE	1	0.647594345188498	2		295	428	SUCCESS
APC	324	MSKCC	GRCh37	5	112162846	112162846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	173	406	0	ENST00000257430.4:c.1450G>A	p.Glu484Lys	p.E484K	ENST00000257430	NM_000038.5	484	Gaa/Aaa	12/16	1	2	FACETS	0.877	0.811	0.945	0.877	0.811	0.945	CLONAL	1	TRUE	1	0.647594345188498	2		406	609	SUCCESS
APC	324	MSKCC	GRCh37	5	112178280	112178280	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	179	396	0	ENST00000257430.4:c.6992del	p.Pro2331LeufsTer6	p.P2331Lfs*6	ENST00000257430	NM_000038.5	2330	tCc/tc	16/16	1	2	FACETS	0.98	0.909	1	0.98	0.909	1	CLONAL	1	TRUE	1	0.647594345188498	2		396	564	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924458	131924458	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	222	415	1	ENST00000265335.6:c.1131G>T	p.Gln377His	p.Q377H	ENST00000265335		377	caG/caT	8/25	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.647594345188498	2		416	647	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497349	149497349	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	129	549	0	ENST00000261799.4:c.2969C>T	p.Ala990Val	p.A990V	ENST00000261799	NM_002609.3	990	gCc/gTc	22/23	1	2	FACETS	0.512	0.464	0.562	0.512	0.464	0.562	SUBCLONAL	1	TRUE	1	0.647594345188498	2		549	778	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500882	149500882	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	49	448	0	ENST00000261799.4:c.2348C>A	p.Pro783His	p.P783H	ENST00000261799	NM_002609.3	783	cCt/cAt	17/23	1	2	FACETS	0.19	0.16	0.223	0.19	0.16	0.223	SUBCLONAL	1	TRUE	1	0.647594345188498	2		448	797	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562759	176562759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	253	540	1	ENST00000439151.2:c.655C>T	p.His219Tyr	p.H219Y	ENST00000439151	NM_022455.4	219	Cac/Tac	2/23	1	2	FACETS	0.912	0.855	0.97	0.912	0.855	0.97	CLONAL	1	TRUE	1	0.647594345188498	2		541	857	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480087	20480087	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	109	370	0	ENST00000346618.3:c.404G>A	p.Arg135Lys	p.R135K	ENST00000346618	NM_001949.4	135	aGg/aAg	2/7	1	2	FACETS	0.626	0.564	0.691	0.626	0.564	0.691	SUBCLONAL	1	TRUE	1	0.647594345188498	2		370	538	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20488478	20488478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	199	417	0	ENST00000346618.3:c.1134A>C	p.Lys378Asn	p.K378N	ENST00000346618	NM_001949.4	378	aaA/aaC	6/7	1	2	FACETS	0.974	0.907	1	0.974	0.907	1	CLONAL	1	TRUE	1	0.647594345188498	2		417	631	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045691	26045691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	27	251	0	ENST00000540144.1:c.53G>A	p.Arg18His	p.R18H	ENST00000540144	NM_003531.2	18	cGc/cAc	1/1	1	2	FACETS	0.262	0.209	0.323	0.262	0.209	0.323	SUBCLONAL	1	TRUE	1	0.647594345188498	2		251	318	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225480	26225480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	43	294	0	ENST00000360408.1:c.98C>T	p.Thr33Met	p.T33M	ENST00000360408	NM_003532.2	33	aCg/aTg	1/1	1	2	FACETS	0.318	0.266	0.375	0.318	0.266	0.375	SUBCLONAL	1	TRUE	1	0.647594345188498	2		294	418	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912276	29912276	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs1380293193	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	268	467	0	ENST00000376809.5:c.896-1G>T		p.X299_splice	ENST00000376809	NM_002116.7	299			1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.647594345188498	2		467	595	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672554	30672554	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	165	528	0	ENST00000376406.3:c.4406C>A	p.Pro1469His	p.P1469H	ENST00000376406	NM_014641.2	1469	cCt/cAt	10/15	1	2	FACETS	0.566	0.519	0.614	0.566	0.519	0.614	SUBCLONAL	1	TRUE	1	0.647594345188498	2		528	901	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673397	30673397	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	296	631	0	ENST00000376406.3:c.3563G>T	p.Arg1188Met	p.R1188M	ENST00000376406	NM_014641.2	1188	aGg/aTg	10/15	1	2	FACETS	0.988	0.933	1	0.988	0.933	1	CLONAL	1	TRUE	1	0.647594345188498	2		631	925	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675701	30675701	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	98	744	0	ENST00000376406.3:c.2655A>T	p.Arg885Ser	p.R885S	ENST00000376406	NM_014641.2	885	agA/agT	8/15	1	2	FACETS	0.255	0.227	0.286	0.255	0.227	0.286	SUBCLONAL	1	TRUE	1	0.647594345188498	2		744	1185	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178567	32178567	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	272	625	0	ENST00000375023.3:c.2827del	p.Ala943ProfsTer105	p.A943Pfs*105	ENST00000375023	NM_004557.3	943	Gcc/cc	18/30	1	2	FACETS	0.951	0.895	1	0.951	0.895	1	CLONAL	1	TRUE	1	0.647594345188498	2		625	883	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797830	32797830	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759127287	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	28	384	0	ENST00000374899.4:c.1672G>A	p.Gly558Ser	p.G558S	ENST00000374899	NM_018833.2	558	Ggt/Agt	10/12	1	2	FACETS	0.156	0.124	0.193	0.156	0.124	0.193	SUBCLONAL	1	TRUE	1	0.647594345188498	2		384	553	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805536	32805536	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	374	774	1	ENST00000374899.4:c.475C>A	p.Leu159Ile	p.L159I	ENST00000374899	NM_018833.2	159	Ctt/Att	2/12	1	2	FACETS	0.918	0.871	0.966	0.918	0.871	0.966	CLONAL	1	TRUE	1	0.647594345188498	2		775	1258	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818840	32818840	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	302	655	2	ENST00000354258.4:c.1111G>A	p.Val371Met	p.V371M	ENST00000354258	NM_000593.5	371	Gtg/Atg	4/11	1	2	FACETS	0.964	0.909	1	0.964	0.909	1	CLONAL	1	TRUE	1	0.647594345188498	2		657	968	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820966	32820966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	109	720	2	ENST00000354258.4:c.628G>A	p.Ala210Thr	p.A210T	ENST00000354258	NM_000593.5	210	Gca/Aca	1/11	1	2	FACETS	0.303	0.271	0.337	0.303	0.271	0.337	SUBCLONAL	1	TRUE	1	0.647594345188498	2		722	1111	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821442	32821442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1484730810	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	280	597	3	ENST00000354258.4:c.152G>A	p.Gly51Asp	p.G51D	ENST00000354258	NM_000593.5	51	gGc/gAc	1/11	1	2	FACETS	0.983	0.926	1	0.983	0.926	1	CLONAL	1	TRUE	1	0.647594345188498	2		600	880	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287212	33287213	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1268651006	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	46	460	0	ENST00000374542.5:c.1884dup	p.Cys629LeufsTer29	p.C629Lfs*29	ENST00000374542	NM_001141970.1	628	-/C	6/8	1	2	FACETS	0.199	0.167	0.235	0.199	0.167	0.235	SUBCLONAL	1	TRUE	1	0.647594345188498	2		460	714	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120846	94120846	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1300929218	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	101	469	0	ENST00000369303.4:c.205C>T	p.Arg69Ter	p.R69*	ENST00000369303	NM_004440.3	69	Cga/Tga	3/17	1	2	FACETS	0.5	0.447	0.556	0.5	0.447	0.556	SUBCLONAL	1	TRUE	1	0.647594345188498	2		469	624	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547331	106547331	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	177	431	0	ENST00000369096.4:c.568A>G	p.Ile190Val	p.I190V	ENST00000369096	NM_001198.3	190	Atc/Gtc	4/7	1	2	FACETS	0.81	0.749	0.873	0.81	0.749	0.873	CLONAL	1	TRUE	1	0.647594345188498	2		431	675	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609800	117609800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1162487585	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	229	503	0	ENST00000368508.3:c.6899G>A	p.Cys2300Tyr	p.C2300Y	ENST00000368508	NM_002944.2	2300	tGt/tAt	43/43	1	2	FACETS	0.879	0.821	0.938	0.879	0.821	0.938	CLONAL	1	TRUE	1	0.647594345188498	2		503	805	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138201285	138201285	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	57	427	0	ENST00000237289.4:c.1984T>C	p.Cys662Arg	p.C662R	ENST00000237289	NM_001270507.1	662	Tgc/Cgc	8/9	1	2	FACETS	0.238	0.204	0.276	0.238	0.204	0.276	SUBCLONAL	1	TRUE	1	0.647594345188498	2		427	739	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983071	149983071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	240	534	0	ENST00000253339.5:c.3187G>A	p.Gly1063Arg	p.G1063R	ENST00000253339		1063	Gga/Aga	7/7	1	2	FACETS	0.924	0.866	0.984	0.924	0.866	0.984	CLONAL	1	TRUE	1	0.647594345188498	2		534	802	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222590	157222591	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	229	510	0	ENST00000346085.5:c.1862dup	p.His622AlafsTer31	p.H622Afs*31	ENST00000346085	NM_020732.3	619	-/C	4/20	1	2	FACETS	0.857	0.801	0.915	0.857	0.801	0.915	CLONAL	1	TRUE	1	0.647594345188498	2		510	825	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405956	157405956	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	137	478	0	ENST00000346085.5:c.2198G>T	p.Gly733Val	p.G733V	ENST00000346085	NM_020732.3	733	gGg/gTg	6/20	1	2	FACETS	0.641	0.584	0.7	0.641	0.584	0.7	SUBCLONAL	1	TRUE	1	0.647594345188498	2		478	660	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157431687	157431687	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	157	460	0	ENST00000346085.5:c.2363A>G	p.Gln788Arg	p.Q788R	ENST00000346085	NM_020732.3	788	cAg/cGg	7/20	1	2	FACETS	0.584	0.535	0.635	0.584	0.535	0.635	SUBCLONAL	1	TRUE	1	0.647594345188498	2		460	830	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522010	157522010	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	180	416	0	ENST00000346085.5:c.4282A>G	p.Ser1428Gly	p.S1428G	ENST00000346085	NM_020732.3	1428	Agc/Ggc	18/20	1	2	FACETS	0.908	0.842	0.977	0.908	0.842	0.977	CLONAL	1	TRUE	1	0.647594345188498	2		416	612	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161970031	161970031	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1421841956	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	224	590	0	ENST00000366898.1:c.938A>G	p.Asn313Ser	p.N313S	ENST00000366898	NM_004562.2	313	aAc/aGc	9/12	1	2	FACETS	0.864	0.806	0.923	0.864	0.806	0.923	CLONAL	1	TRUE	1	0.647594345188498	2		590	801	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729828	41729828	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	32	279	0	ENST00000242208.4:c.701G>A	p.Gly234Asp	p.G234D	ENST00000242208	NM_002192.2	234	gGc/gAc	3/3	1	2	FACETS	0.266	0.215	0.322	0.266	0.215	0.322	SUBCLONAL	1	TRUE	1	0.647594345188498	2		279	372	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211156	55211156	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	227	507	0	ENST00000275493.2:c.399G>T	p.Lys133Asn	p.K133N	ENST00000275493	NM_005228.3	133	aaG/aaT	3/28	1	2	FACETS	0.971	0.908	1	0.971	0.908	1	CLONAL	1	TRUE	1	0.647594345188498	2		507	722	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336661	81336661	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	171	315	0	ENST00000222390.5:c.1561G>T	p.Gly521Ter	p.G521*	ENST00000222390	NM_000601.4	521	Gga/Tga	14/18	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.647594345188498	2		315	481	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350138	81350138	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	199	394	0	ENST00000222390.5:c.1194T>A	p.Asn398Lys	p.N398K	ENST00000222390	NM_000601.4	398	aaT/aaA	10/18	1	2	FACETS	0.991	0.923	1	0.991	0.923	1	CLONAL	1	TRUE	1	0.647594345188498	2		394	620	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81399226	81399226	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs370490787	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	307	707	0	ENST00000222390.5:c.62T>C	p.Leu21Pro	p.L21P	ENST00000222390	NM_000601.4	21	cTg/cCg	1/18	1	2	FACETS	0.911	0.859	0.963	0.911	0.859	0.963	CLONAL	1	TRUE	1	0.647594345188498	2		707	1041	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397514	116397514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	160	418	1	ENST00000397752.3:c.1886C>T	p.Ala629Val	p.A629V	ENST00000397752	NM_000245.2	629	gCc/gTc	7/21	1	2	FACETS	0.642	0.589	0.696	0.642	0.589	0.696	SUBCLONAL	1	TRUE	1	0.647594345188498	2		419	770	SUCCESS
MET	4233	MSKCC	GRCh37	7	116399505	116399505	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs748086754	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	173	396	0	ENST00000397752.3:c.2325G>T	p.Met775Ile	p.M775I	ENST00000397752	NM_000245.2	775	atG/atT	10/21	1	2	FACETS	0.882	0.815	0.95	0.882	0.815	0.95	CLONAL	1	TRUE	1	0.647594345188498	2		396	606	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829270	128829270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	200	647	0	ENST00000249373.3:c.278C>T	p.Ala93Val	p.A93V	ENST00000249373	NM_005631.4	93	gCc/gTc	1/12	1	2	FACETS	0.643	0.595	0.692	0.643	0.595	0.692	SUBCLONAL	1	TRUE	1	0.647594345188498	2		647	961	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434476	140434476	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	118	477	0	ENST00000288602.6:c.2222A>G	p.Glu741Gly	p.E741G	ENST00000288602	NM_004333.4	741	gAg/gGg	18/18	1	2	FACETS	0.58	0.525	0.639	0.58	0.525	0.639	SUBCLONAL	1	TRUE	1	0.647594345188498	2		477	628	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453195	140453195	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	42	300	0	ENST00000288602.6:c.1742-2A>G		p.X581_splice	ENST00000288602	NM_004333.4	581			1	2	FACETS	0.297	0.248	0.351	0.297	0.248	0.351	SUBCLONAL	1	TRUE	1	0.647594345188498	2		300	437	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845181	151845181	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	210	473	0	ENST00000262189.6:c.13831T>A	p.Phe4611Ile	p.F4611I	ENST00000262189	NM_170606.2	4611	Ttt/Att	52/59	1	2	FACETS	0.891	0.83	0.953	0.891	0.83	0.953	CLONAL	1	TRUE	1	0.647594345188498	2		473	728	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151868350	151868350	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	125	325	0	ENST00000262189.6:c.9452A>G	p.Gln3151Arg	p.Q3151R	ENST00000262189	NM_170606.2	3151	cAg/cGg	40/59	1	2	FACETS	0.609	0.552	0.668	0.609	0.552	0.668	SUBCLONAL	1	TRUE	1	0.647594345188498	2		325	634	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877084	151877084	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	193	428	0	ENST00000262189.6:c.7277A>G	p.Glu2426Gly	p.E2426G	ENST00000262189	NM_170606.2	2426	gAg/gGg	37/59	1	2	FACETS	0.936	0.87	1	0.936	0.87	1	CLONAL	1	TRUE	1	0.647594345188498	2		428	637	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878262	151878262	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	260	513	0	ENST00000262189.6:c.6683G>T	p.Arg2228Met	p.R2228M	ENST00000262189	NM_170606.2	2228	aGg/aTg	36/59	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.647594345188498	2		513	792	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900068	151900068	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	149	439	0	ENST00000262189.6:c.4043A>G	p.Tyr1348Cys	p.Y1348C	ENST00000262189	NM_170606.2	1348	tAc/tGc	26/59	1	2	FACETS	0.656	0.6	0.713	0.656	0.6	0.713	SUBCLONAL	1	TRUE	1	0.647594345188498	2		439	702	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151927407	151927407	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	30	47	0	ENST00000262189.6:c.2770-1G>T		p.X924_splice	ENST00000262189	NM_170606.2	924			1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.647594345188498	2		47	69	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162894	38162894	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	95	618	0	ENST00000317025.8:c.2312G>T	p.Gly771Val	p.G771V	ENST00000317025	NM_023034.1	771	gGg/gTg	13/24	1	2	FACETS	0.284	0.252	0.318	0.284	0.252	0.318	SUBCLONAL	1	TRUE	1	0.647594345188498	2		618	1033	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187126	38187126	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	248	647	0	ENST00000317025.8:c.1351A>G	p.Ser451Gly	p.S451G	ENST00000317025	NM_023034.1	451	Agc/Ggc	6/24	1	2	FACETS	0.928	0.871	0.988	0.928	0.871	0.988	CLONAL	1	TRUE	1	0.647594345188498	2		647	825	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38314891	38314891	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	32	438	0	ENST00000425967.3:c.173del	p.Pro58ArgfsTer78	p.P58Rfs*78	ENST00000425967	NM_001174067.1	58	cCg/cg	3/19	1	2	FACETS	0.16	0.129	0.195	0.16	0.129	0.195	SUBCLONAL	1	TRUE	1	0.647594345188498	2		438	617	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370864	55370864	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	141	562	0	ENST00000297316.4:c.166G>A	p.Ala56Thr	p.A56T	ENST00000297316	NM_022454.3	56	Gcc/Acc	1/2	1	2	FACETS	0.548	0.5	0.599	0.548	0.5	0.599	SUBCLONAL	1	TRUE	1	0.647594345188498	2		562	794	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372052	55372052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	41	514	1	ENST00000297316.4:c.742G>A	p.Ala248Thr	p.A248T	ENST00000297316	NM_022454.3	248	Gcc/Acc	2/2	1	2	FACETS	0.166	0.137	0.197	0.166	0.137	0.197	SUBCLONAL	1	TRUE	1	0.647594345188498	2		515	765	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56911028	56911028	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	247	551	0	ENST00000519728.1:c.1174A>T	p.Ile392Phe	p.I392F	ENST00000519728	NM_002350.3	392	Att/Ttt	11/13	1	2	FACETS	0.869	0.814	0.925	0.869	0.814	0.925	CLONAL	1	TRUE	1	0.647594345188498	2		551	878	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965417	68965417	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	341	747	0	ENST00000288368.4:c.1033del	p.Thr345HisfsTer13	p.T345Hfs*13	ENST00000288368	NM_024870.2	343	gcA/gc	9/40	1	2	FACETS	0.951	0.901	1	0.951	0.901	1	CLONAL	1	TRUE	1	0.647594345188498	2		747	1107	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967511	90967511	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	123	268	0	ENST00000265433.3:c.1397G>T	p.Arg466Met	p.R466M	ENST00000265433	NM_002485.4	466	aGg/aTg	10/16	1	2	FACETS	0.856	0.779	0.935	0.856	0.779	0.935	CLONAL	1	TRUE	1	0.647594345188498	2		268	444	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141545607	141545607	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	223	753	0	ENST00000220592.5:c.2231C>T	p.Thr744Ile	p.T744I	ENST00000220592	NM_012154.3	744	aCc/aTc	17/19	1	2	FACETS	0.597	0.555	0.64	0.597	0.555	0.64	SUBCLONAL	1	TRUE	1	0.647594345188498	2		753	1154	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738858	145738858	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771790911	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	274	706	0	ENST00000428558.2:c.2207C>T	p.Ala736Val	p.A736V	ENST00000428558	NM_004260.3	736	gCc/gTc	14/22	1	2	FACETS	0.753	0.706	0.801	0.753	0.706	0.801	SUBCLONAL	1	TRUE	1	0.647594345188498	2		706	1124	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739732	145739732	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	258	516	0	ENST00000428558.2:c.1719G>T	p.Gln573His	p.Q573H	ENST00000428558	NM_004260.3	573	caG/caT	11/22	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.647594345188498	2		516	793	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500802	8500802	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1413041664	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	185	391	0	ENST00000356435.5:c.2080G>A	p.Gly694Ser	p.G694S	ENST00000356435		694	Ggc/Agc	13/35	1	2	FACETS	0.858	0.795	0.922	0.858	0.795	0.922	CLONAL	1	TRUE	1	0.647594345188498	2		391	666	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	273	482	0	ENST00000304494.5:c.330G>T	p.Trp110Cys	p.W110C	ENST00000304494	NM_000077.4	110	tgG/tgT	2/3	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.647594345188498	2		482	736	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325592	87325592	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	84	381	0	ENST00000277120.3:c.469A>G	p.Met157Val	p.M157V	ENST00000277120		157	Atg/Gtg	6/19	1	2	FACETS	0.446	0.394	0.501	0.446	0.394	0.501	SUBCLONAL	1	TRUE	1	0.647594345188498	2		381	582	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231349	98231349	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs772841736	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	277	499	0	ENST00000331920.6:c.1934A>G	p.Tyr645Cys	p.Y645C	ENST00000331920	NM_000264.3	645	tAc/tGc	14/24	1	2	FACETS	0.968	0.911	1	0.968	0.911	1	CLONAL	1	TRUE	1	0.647594345188498	2		499	884	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128322023	128322023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	176	591	0	ENST00000265960.3:c.737C>T	p.Pro246Leu	p.P246L	ENST00000265960	NM_001006617.1	246	cCc/cTc	6/12	1	2	FACETS	0.536	0.493	0.581	0.536	0.493	0.581	SUBCLONAL	1	TRUE	1	0.647594345188498	2		591	1014	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133747526	133747526	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	40	457	0	ENST00000318560.5:c.833T>C	p.Met278Thr	p.M278T	ENST00000318560	NM_005157.4	278	aTg/aCg	5/11	1	2	FACETS	0.193	0.16	0.23	0.193	0.16	0.23	SUBCLONAL	1	TRUE	1	0.647594345188498	2		457	640	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760724	133760724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778935845	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	272	775	1	ENST00000318560.5:c.3047G>A	p.Arg1016His	p.R1016H	ENST00000318560	NM_005157.4	1016	cGc/cAc	11/11	1	2	FACETS	0.833	0.783	0.885	0.833	0.783	0.885	CLONAL	1	TRUE	1	0.647594345188498	2		776	1008	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300016	137300016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137938878	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	281	622	0	ENST00000481739.1:c.301G>A	p.Val101Ile	p.V101I	ENST00000481739	NM_002957.4	101	Gtc/Atc	3/10	1	2	FACETS	0.874	0.822	0.927	0.874	0.822	0.927	CLONAL	1	TRUE	1	0.647594345188498	2		622	993	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409082	139409082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1385662021	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	199	831	0	ENST00000277541.6:c.2087G>A	p.Gly696Asp	p.G696D	ENST00000277541	NM_017617.3	696	gGc/gAc	13/34	1	2	FACETS	0.519	0.479	0.559	0.519	0.479	0.559	SUBCLONAL	1	TRUE	1	0.647594345188498	2		831	1185	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923082	39923082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1422527923	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	285	255	1	ENST00000378444.4:c.3626G>A	p.Arg1209His	p.R1209H	ENST00000378444	NM_001123385.1	1209	cGc/cAc	8/15	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.647594345188498	1		256	482	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934192	39934192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	333	321	1	ENST00000378444.4:c.407C>T	p.Ala136Val	p.A136V	ENST00000378444	NM_001123385.1	136	gCc/gTc	4/15	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.647594345188498	1		322	524	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937676	44937676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	150	325	0	ENST00000377967.4:c.2864C>T	p.Pro955Leu	p.P955L	ENST00000377967	NM_021140.2	955	cCa/cTa	19/29	1	1	FACETS	0.77	0.711	0.83	0.77	0.711	0.83	SUBCLONAL	1	TRUE	0	0.647594345188498	1		325	407	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949968	44949968	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	15	168	2	ENST00000377967.4:c.3737C>T	p.Ala1246Val	p.A1246V	ENST00000377967	NM_021140.2	1246	gCc/gTc	26/29	1	1	FACETS	0.148	0.108	0.196	0.148	0.108	0.196	SUBCLONAL	1	TRUE	0	0.647594345188498	1		170	211	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410849	63410849	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	261	267	0	ENST00000330258.3:c.2318T>C	p.Leu773Pro	p.L773P	ENST00000330258	NM_152424.3	773	cTg/cCg	2/2	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.647594345188498	1		267	426	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411237	63411237	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	84	330	0	ENST00000330258.3:c.1930del	p.Gln644ArgfsTer9	p.Q644Rfs*9	ENST00000330258	NM_152424.3	644	Cag/ag	2/2	1	1	FACETS	0.361	0.32	0.405	0.361	0.32	0.405	SUBCLONAL	1	TRUE	0	0.647594345188498	1		330	486	SUCCESS
BTK	695	MSKCC	GRCh37	X	100604932	100604932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	197	230	0	ENST00000308731.7:c.1921C>T	p.Arg641Cys	p.R641C	ENST00000308731	NM_000061.2	641	Cgt/Tgt	19/19	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.647594345188498	1		230	343	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020147	123020147	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	340	339	0	ENST00000355640.3:c.635C>A	p.Pro212His	p.P212H	ENST00000355640		212	cCt/cAt	2/7	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.647594345188498	1		339	540	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416548	29416548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780571098	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	35	486	0	ENST00000389048.3:c.4405C>T	p.Pro1469Ser	p.P1469S	ENST00000389048	NM_004304.4	1469	Ccg/Tcg	29/29	1	2	FACETS	0.156	0.127	0.189	0.156	0.127	0.189	SUBCLONAL	1	TRUE	1	0.647594345188498	2		486	693	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211909	36211909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1225	127	869	0	ENST00000222270.7:c.1660C>A	p.Pro554Thr	p.P554T	ENST00000222270	NM_014727.1	554	Ccc/Acc	3/37	1	2	FACETS	0.29	0.262	0.32	0.29	0.262	0.32	SUBCLONAL	1	TRUE	1	0.647594345188498	2		869	1352	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973274	25973277	+	missense_variant	Missense_Mutation	ONP	AGGC	AGGC	GGGT	novel	NA	P-0027929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	17	204	0	ENST00000435504.4:c.1148_1151delinsACCC	p.Gly383_Leu384delinsAspPro	p.G383_L384delinsDP	ENST00000435504		383	gGCCTg/gACCCg	12/13	1	2	FACETS	0.177	0.131	0.231	0.177	0.131	0.231	SUBCLONAL	1	TRUE	1	0.647594345188498	2		204	297	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0027935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	82	774	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.122604088621488	3	FACETS	1	0.961	1	0.607	0.536	0.683	INDETERMINATE	1	TRUE	1	0.265142731790367	3		774	577	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610140	43610140	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	51	686	1	ENST00000355710.3:c.2092G>T	p.Asp698Tyr	p.D698Y	ENST00000355710	NM_020975.4	698	Gac/Tac	11/20	1	2	FACETS	0.475	0.402	0.555	0.475	0.402	0.555	SUBCLONAL	1	TRUE	1	0.265142731790367	2		687	810	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69456160	69456160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	79	667	1	ENST00000227507.2:c.79G>A	p.Val27Met	p.V27M	ENST00000227507	NM_053056.2	27	Gtg/Atg	1/5	1	2	FACETS	0.606	0.531	0.686	0.606	0.531	0.686	SUBCLONAL	1	TRUE	1	0.265142731790367	2		668	984	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650696	67650696	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	50	549	2	ENST00000264010.4:c.1001G>T	p.Ser334Ile	p.S334I	ENST00000264010	NM_006565.3	334	aGt/aTt	5/12	0.205312736749059	3	FACETS	0.444	0.375	0.52	0.222	0.187	0.26	SUBCLONAL	1	TRUE	1	0.265142731790367	3		551	962	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462635	29462635	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747611056	NA	P-0027935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	85	722	1	ENST00000389048.3:c.2266G>A	p.Gly756Ser	p.G756S	ENST00000389048	NM_004304.4	756	Ggc/Agc	13/29	1	2	FACETS	0.594	0.524	0.67	0.594	0.524	0.67	SUBCLONAL	1	TRUE	1	0.265142731790367	2		723	1079	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027935-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	285	635	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.839219655131057	2		635	586	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1255443	1255443	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763381198	NA	P-0027935-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	370	628	0	ENST00000310581.5:c.3116C>T	p.Thr1039Met	p.T1039M	ENST00000310581	NM_198253.2	1039	aCg/aTg	14/16	1	2	FACETS	0.894	0.851	0.938	0.894	0.851	0.938	CLONAL	1	TRUE	1	0.839219655131057	2		628	986	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017704	31017704	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027935-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	254	420	0	ENST00000375687.4:c.566G>A	p.Gly189Glu	p.G189E	ENST00000375687	NM_015338.5	189	gGg/gAg	8/13	1	2	FACETS	0.955	0.9	1	0.955	0.9	1	CLONAL	1	TRUE	1	0.839219655131057	2		420	634	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187093	11187093	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1386760919	NA	P-0028089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	134	565	0	ENST00000361445.4:c.6325C>T	p.Arg2109Ter	p.R2109*	ENST00000361445	NM_004958.3	2109	Cga/Tga	45/58	NA	2	FACETS	0.942	0.859	1			1	INDETERMINATE	1	FALSE	NA	0.487202629707455	2		565	584	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057932	27057932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	69	546	0	ENST00000324856.7:c.1640G>A	p.Ser547Asn	p.S547N	ENST00000324856	NM_006015.4	547	aGc/aAc	3/20	0.459647484468179	3	FACETS	0.435	0.378	0.497	0.218	0.189	0.249	SUBCLONAL	1	FALSE	1	0.487202629707455	3		546	809	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091426	193091426	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	642	510	1	ENST00000367435.3:c.96G>A	p.Trp32Ter	p.W32*	ENST00000367435	NM_024529.4	32	tgG/tgA	1/17	0.495862121479891	5	FACETS	0.973	0.946	0.998	0.973	0.946	0.998	CLONAL	5	FALSE	0	0.487202629707455	5		511	938	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742919	17742919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1283019508	NA	P-0028089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	65	521	0	ENST00000250003.3:c.827C>T	p.Ser276Phe	p.S276F	ENST00000250003	NM_002478.4	276	tCt/tTt	3/3	0.495862121479891	4	FACETS	0.542	0.469	0.621	0.271	0.234	0.311	SUBCLONAL	1	FALSE	2	0.487202629707455	4		521	732	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821959	72821960	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs762108866	NA	P-0028160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	42	296	3	ENST00000268489.5:c.10215dup	p.Gly3406ArgfsTer25	p.G3406Rfs*25	ENST00000268489	NM_006885.3	3405	-/C	10/10	1	2	FACETS	0.982	0.828	1	0.982	0.828	1	CLONAL	1	TRUE	1	0.380103750967888	2		299	225	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527462	29527462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs76015786	NA	P-0028160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	20	448	0	ENST00000356175.3:c.911G>A	p.Arg304Gln	p.R304Q	ENST00000356175	NM_000267.3	304	cGa/cAa	9/57	1	2	FACETS	0.322	0.246	0.411	0.322	0.246	0.411	SUBCLONAL	1	TRUE	1	0.380103750967888	2		448	327	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380683	118380683	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1450486073	NA	P-0028160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	21	453	1	ENST00000534358.1:c.10921G>A	p.Glu3641Lys	p.E3641K	ENST00000534358	NM_005933.3	3641	Gag/Aag	30/36	0.0692349940882262	3	FACETS	0.389	0.299	0.494			1	INDETERMINATE	1	TRUE	NA	0.380103750967888	3		454	338	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574369	95574369	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	18	292	0	ENST00000393063.1:c.2498A>T	p.Lys833Met	p.K833M	ENST00000393063	NM_030621.3	833	aAg/aTg	17/28	0.242496178958432	3	FACETS	0.422	0.318	0.545	0.211	0.159	0.273	SUBCLONAL	1	TRUE	1	0.380103750967888	3		292	267	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39729866	39729866	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs990347811	NA	P-0028160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	53	433	0	ENST00000361337.2:c.1181C>T	p.Ser394Phe	p.S394F	ENST00000361337	NM_003286.2	394	tCt/tTt	13/21	0.380103750967888	1	FACETS	0.807	0.693	0.929	0.807	0.693	0.929	CLONAL	1	TRUE	0	0.380103750967888	1		433	280	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87366947	87366961	+	inframe_deletion	In_Frame_Del	DEL	TGGTAATGCTGTTTC	TGGTAATGCTGTTTC	-	novel	NA	P-0028160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	48	572	0	ENST00000277120.3:c.1345_1359del	p.Val449_Leu453del	p.V449_L453del	ENST00000277120		448	tTGGTAATGCTGTTTCtg/ttg	12/19	1	2	FACETS	0.508	0.43	0.595	0.508	0.43	0.595	SUBCLONAL	1	TRUE	1	0.380103750967888	2		572	497	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0028195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	119	498	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.222483585743337	2		498	779	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305462	65305462	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	68	404	0	ENST00000342505.4:c.2666T>C	p.Val889Ala	p.V889A	ENST00000342505	NM_002227.2	889	gTt/gCt	20/25	1	2	FACETS	0.984	0.856	1	0.984	0.856	1	CLONAL	1	TRUE	1	0.222483585743337	2		404	621	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201008	108201008	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	55	456	1	ENST00000278616.4:c.7375C>A	p.Arg2459Ser	p.R2459S	ENST00000278616	NM_000051.3	2459	Cgt/Agt	50/63	1	2	FACETS	0.703	0.601	0.816	0.703	0.601	0.816	SUBCLONAL	1	TRUE	1	0.222483585743337	2		457	703	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245480	133245480	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	165	651	0	ENST00000320574.5:c.1840C>A	p.Pro614Thr	p.P614T	ENST00000320574	NM_006231.2	614	Ccc/Acc	17/49	0.218319960606208	2	FACETS	0.786	0.721	0.853	0.786	0.721	0.853	SUBCLONAL	2	TRUE	0	0.222483585743337	2		651	944	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647412	23647412	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	93	497	0	ENST00000261584.4:c.455del	p.Lys152ArgfsTer25	p.K152Rfs*25	ENST00000261584	NM_024675.3	152	aAg/ag	4/13	1	2	FACETS	0.94	0.835	1	0.94	0.835	1	CLONAL	1	TRUE	1	0.222483585743337	2		497	889	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143100	7143100	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	58	529	0	ENST00000302850.5:c.2269C>G	p.Pro757Ala	p.P757A	ENST00000302850	NM_000208.2	757	Cca/Gca	12/22	0.222483585743337	3	FACETS	0.673	0.577	0.779	0.336	0.288	0.39	SUBCLONAL	1	TRUE	1	0.222483585743337	3		529	861	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383281	42383281	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	119	675	0	ENST00000221972.3:c.301G>T	p.Gly101Trp	p.G101W	ENST00000221972	NM_021601.3	101	Ggg/Tgg	2/5	1	2	FACETS	0.953	0.858	1	0.953	0.858	1	CLONAL	1	TRUE	1	0.222483585743337	2		675	1123	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260308	149260308	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	151	879	0	ENST00000360632.3:c.585C>G	p.His195Gln	p.H195Q	ENST00000360632	NM_015472.4	195	caC/caG	4/7	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.222483585743337	2		879	1304	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958812	55958812	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	102	590	0	ENST00000263923.4:c.3041A>C	p.Lys1014Thr	p.K1014T	ENST00000263923	NM_002253.2	1014	aAg/aCg	22/30	1	2	FACETS	0.881	0.786	0.982	0.881	0.786	0.982	CLONAL	1	TRUE	1	0.222483585743337	2		590	1041	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857353	68857353	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs372182377	NA	P-0028242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	49	595	1	ENST00000261769.5:c.1988A>G	p.Tyr663Cys	p.Y663C	ENST00000261769	NM_004360.3	663	tAc/tGc	13/16	1	2	FACETS	0.571	0.483	0.667	0.571	0.483	0.667	SUBCLONAL	1	TRUE	1	0.30990823601278	2		596	554	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221990	1221990	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	138	615	0	ENST00000326873.7:c.905A>C	p.Gln302Pro	p.Q302P	ENST00000326873	NM_000455.4	302	cAg/cCg	7/10	0.244799706748741	2	FACETS	1	0.983	1	0.667	0.608	0.728	CLONAL	1	TRUE	0	0.30990823601278	2		615	668	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610222	10610222	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	210	871	0	ENST00000171111.5:c.488A>T	p.Gln163Leu	p.Q163L	ENST00000171111	NM_203500.1	163	cAg/cTg	2/6	0.244799706748741	2	FACETS	0.771	0.717	0.827	0.771	0.717	0.827	SUBCLONAL	2	TRUE	0	0.30990823601278	2		871	879	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528599	89528599	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	36	322	0	ENST00000336596.2:c.2899A>C	p.Ser967Arg	p.S967R	ENST00000336596	NM_005233.5	967	Agt/Cgt	17/17	0.114162444132442	5	FACETS	0.847	0.696	1	0.212	0.174	0.254	INDETERMINATE	1	TRUE	1	0.30990823601278	5		322	402	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020818	26020818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202236931	NA	P-0028242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	130	322	0	ENST00000357647.3:c.101G>A	p.Gly34Asp	p.G34D	ENST00000357647	NM_003529.2	34	gGc/gAc	1/1	0.252590921667636	4	FACETS	0.891	0.816	0.969	0.891	0.816	0.969	CLONAL	3	TRUE	1	0.30990823601278	4		322	411	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	72	635	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.25805861999372	2		635	462	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183797	10183797	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs5030807	NA	P-0028259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	98	718	0	ENST00000256474.2:c.266T>A	p.Leu89His	p.L89H	ENST00000256474	NM_000551.3	89	cTc/cAc	1/3	0.25805861999372	1	FACETS	0.909	0.811	1	0.909	0.811	1	CLONAL	1	TRUE	0	0.25805861999372	1		718	728	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	71	635	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.768522046442565	2		635	180	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0028338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	138	207	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.768522046442565	2		207	359	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412283	139412285	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	novel	NA	P-0028338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	61	522	0	ENST00000277541.6:c.1360_1362del	p.Asn454del	p.N454del	ENST00000277541	NM_017617.3	454	AAC/-	8/34	1	2	FACETS	0.224	0.193	0.258	0.224	0.193	0.258	SUBCLONAL	1	TRUE	1	0.768522046442565	2		522	708	SUCCESS
EED	8726	MSKCC	GRCh37	11	85966263	85966263	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0028338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	26	226	0	ENST00000263360.6:c.361-1G>A		p.X121_splice	ENST00000263360	NM_003797.3	121			1	2	FACETS	0.198	0.157	0.246	0.198	0.157	0.246	SUBCLONAL	1	TRUE	1	0.768522046442565	2		226	341	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141568	11141568	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	61	471	0	ENST00000358026.2:c.3545A>C	p.Gln1182Pro	p.Q1182P	ENST00000358026	NM_001128849.1	1182	cAg/cCg	25/36	1	2	FACETS	0.24	0.207	0.277	0.24	0.207	0.277	SUBCLONAL	1	TRUE	1	0.768522046442565	2		471	661	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412631	139412631	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	247	501	0	ENST00000277541.6:c.1213A>C	p.Thr405Pro	p.T405P	ENST00000277541	NM_017617.3	405	Acg/Ccg	7/34	1	2	FACETS	0.894	0.84	0.949	0.894	0.84	0.949	CLONAL	1	TRUE	1	0.768522046442565	2		501	719	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115269659	115269660	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0028447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	500	662	0	ENST00000438362.2:c.1546_1547del	p.Ile516CysfsTer18	p.I516Cfs*18	ENST00000438362	NM_001242891.1	516	ATt/t	13/20	0.819478368147193	1	FACETS	0.977	0.947	1	0.977	0.947	1	CLONAL	1	TRUE	0	0.819478368147193	1		662	737	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593589	55593602	+	protein_altering_variant	In_Frame_Del	DEL	TGTATGAAGTACAG	TGTATGAAGTACAG	CA	novel	NA	P-0028447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	296	507	1	ENST00000288135.5:c.1655_1668delinsCA	p.Met552_Gln556delinsThr	p.M552_Q556delinsT	ENST00000288135	NM_000222.2	552	aTGTATGAAGTACAG/aCA	11/21	0.819478368147193	1	FACETS	0.883	0.844	0.921	0.883	0.844	0.921	CLONAL	1	TRUE	0	0.819478368147193	1		508	483	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829040	128829042	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	rs570242755	NA	P-0028447-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	10	53	0	ENST00000249373.3:c.67_69del	p.Leu23del	p.L23del	ENST00000249373	NM_005631.4	16	ggGCTg/ggg	1/12	1	2	FACETS	0.159	0.108	0.224	0.159	0.108	0.224	SUBCLONAL	1	TRUE	1	0.876980551873237	2		53	143	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115269659	115269660	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0028447-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	518	662	0	ENST00000438362.2:c.1546_1547del	p.Ile516CysfsTer18	p.I516Cfs*18	ENST00000438362	NM_001242891.1	516	ATt/t	13/20	0.876980551873237	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.876980551873237	1		662	662	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593589	55593602	+	protein_altering_variant	In_Frame_Del	DEL	TGTATGAAGTACAG	TGTATGAAGTACAG	CA	novel	NA	P-0028447-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	259	507	1	ENST00000288135.5:c.1655_1668delinsCA	p.Met552_Gln556delinsThr	p.M552_Q556delinsT	ENST00000288135	NM_000222.2	552	aTGTATGAAGTACAG/aCA	11/21	0.876980551873237	1	FACETS	0.914	0.877	0.949	0.914	0.877	0.949	CLONAL	1	TRUE	0	0.876980551873237	1		508	363	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578433	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555526101	NA	P-0028449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	294	710	0	ENST00000269305.4:c.497C>G	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	166	tCa/tGa	5/11	0.247279159810899	2	FACETS	0.858	0.806	0.911	0.858	0.806	0.911	CLONAL	2	TRUE	0	0.269047014093231	2		710	1274	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675047	40675047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	111	570	0	ENST00000249776.8:c.11C>T	p.Pro4Leu	p.P4L	ENST00000249776	NM_033286.3	4	cCc/cTc	1/9	0.233088357108409	4	FACETS	0.894	0.802	0.993	0.447	0.401	0.497	CLONAL	1	TRUE	2	0.269047014093231	4		570	1171	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459227	99459227	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	148	642	1	ENST00000268035.6:c.1863del	p.Asn622ThrfsTer6	p.N622Tfs*6	ENST00000268035	NM_000875.3	621	tcG/tc	9/21	1	2	FACETS	0.888	0.809	0.971	0.888	0.809	0.971	CLONAL	1	TRUE	1	0.269047014093231	2		643	1239	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096455	178096455	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	63	284	0	ENST00000397062.3:c.876G>C	p.Glu292Asp	p.E292D	ENST00000397062	NM_006164.4	292	gaG/gaC	5/5	0.251680000553328	3	FACETS	0.952	0.824	1	0.476	0.412	0.546	CLONAL	1	TRUE	1	0.269047014093231	3		284	558	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1977030	1977030	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1242	112	583	0	ENST00000382891.5:c.3524T>A	p.Leu1175Gln	p.L1175Q	ENST00000382891	NM_133335.3	1175	cTg/cAg	20/22	0.269047014093231	5	FACETS	0.863	0.774	0.958	0.288	0.258	0.32	CLONAL	1	TRUE	2	0.269047014093231	5		583	1354	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862859	117862859	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	56	364	0	ENST00000297338.2:c.1618G>C	p.Glu540Gln	p.E540Q	ENST00000297338	NM_006265.2	540	Gag/Cag	12/14	0.269047014093231	6	FACETS	0.972	0.832	1	0.243	0.208	0.282	CLONAL	1	TRUE	2	0.269047014093231	6		364	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0028489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	555	679	2	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.886334019917003	1	FACETS	0.965	0.943	0.987	0.965	0.943	0.987	CLONAL	1	TRUE	0	0.907532466070166	1		681	692	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416378	29416380	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs755556501	NA	P-0028489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	630	645	0	ENST00000389048.3:c.4573_4575del	p.Lys1525del	p.K1525del	ENST00000389048	NM_004304.4	1525	AAG/-	29/29	1	2	FACETS	0.92	0.887	0.954	0.92	0.887	0.954	CLONAL	1	TRUE	1	0.907532466070166	2		645	1509	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2113054	2113054	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	639	708	0	ENST00000219476.3:c.1443G>T	p.Glu481Asp	p.E481D	ENST00000219476	NM_000548.3	481	gaG/gaT	14/42	0.907532466070166	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.907532466070166	1		708	751	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331979	81331979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763933267	NA	P-0028489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	214	337	0	ENST00000222390.5:c.2105G>A	p.Arg702His	p.R702H	ENST00000222390	NM_000601.4	702	cGt/cAt	18/18	1	2	FACETS	0.919	0.863	0.977	0.919	0.863	0.977	CLONAL	1	TRUE	1	0.907532466070166	2		337	513	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0028490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	313	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.251376525057984	6	FACETS	0.975	0.921	1			1	CLONAL	4	TRUE	NA	0.251376525057984	6		473	960	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0028490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	200	561	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.250249814839921	2	FACETS	0.892	0.827	0.959	0.892	0.827	0.959	CLONAL	2	TRUE	0	0.251376525057984	2		561	892	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0028490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	179	442	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.251376525057984	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.251376525057984	2		442	587	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573203	41573205	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs1569120910	NA	P-0028490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	181	571	0	ENST00000263253.7:c.5492_5494del	p.Arg1831del	p.R1831del	ENST00000263253	NM_001429.3	1830	AGG/-	31/31	0.235116385849297	4	FACETS	0.928	0.856	1	0.928	0.856	1	CLONAL	2	TRUE	2	0.251376525057984	4		571	971	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026132	71026132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751543308	NA	P-0028490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	84	435	0	ENST00000318789.4:c.1490G>A	p.Arg497Gln	p.R497Q	ENST00000318789	NM_032682.5	497	cGa/cAa	17/21	0.251376525057984	3	FACETS	0.981	0.866	1	0.49	0.433	0.552	CLONAL	1	TRUE	1	0.251376525057984	3		435	767	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820300	139820300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1019096282	NA	P-0028490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	195	613	1	ENST00000247668.2:c.1453G>A	p.Val485Met	p.V485M	ENST00000247668	NM_021138.3	485	Gtg/Atg	11/11	0.250249814839921	2	FACETS	0.842	0.78	0.907	0.842	0.78	0.907	CLONAL	2	TRUE	0	0.251376525057984	2		614	921	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32905157	32905157	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	174	578	0	ENST00000380152.3:c.783del	p.Ala262GlnfsTer15	p.A262Qfs*15	ENST00000380152		261	gcT/gc	9/27	0.20177380660716	1	FACETS	0.868	0.8	0.94	0.868	0.8	0.94	INDETERMINATE	1	TRUE	0	0.375796694294505	1		578	866	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143033724	143033740	+	frameshift_variant	Frame_Shift_Del	DEL	TCCAACATTAAAAAGTA	TCCAACATTAAAAAGTA	ACACAGCATG	novel	NA	P-0028500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	55	547	1	ENST00000262992.4:c.2231_2247delinsCATGCTGTGT	p.Val744AlafsTer57	p.V744Afs*57	ENST00000262992	NM_001101669.1	744	gTACTTTTTAATGTTGGA/gCATGCTGTGT	20/24	1	2	FACETS	0.365	0.311	0.424	0.365	0.311	0.424	SUBCLONAL	1	TRUE	1	0.375796694294505	2		548	803	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345784	152345802	+	frameshift_variant	Frame_Shift_Del	DEL	ACTTTTTAAACAACGTGAA	ACTTTTTAAACAACGTGAA	-	novel	NA	P-0028500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	65	407	0	ENST00000359321.1:c.768_786del	p.Ser257ThrfsTer3	p.S257Tfs*3	ENST00000359321	NM_005431.1	256	gtTTCACGTTGTTTAAAAAGT/gt	3/3	0.14609933707388	2	FACETS	0.493	0.427	0.565	0.247	0.213	0.283	INDETERMINATE	1	TRUE	0	0.375796694294505	2		407	701	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0028502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	129	576	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	1	2	FACETS	0.903	0.821	0.989	0.903	0.821	0.989	CLONAL	1	TRUE	1	0.45123313978744	2		576	633	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221708	22221709	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCG	rs751880548	NA	P-0028502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	14	73	1	ENST00000215832.6:c.20_22dup	p.Ala7dup	p.A7dup	ENST00000215832	NM_002745.4	7	ggc/gCGGgc	1/9	1	2	FACETS	0.496	0.362	0.657	0.496	0.362	0.657	SUBCLONAL	1	TRUE	1	0.45123313978744	2		74	125	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060937	38060937	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	93	406	3	ENST00000250448.2:c.1052C>A	p.Thr351Asn	p.T351N	ENST00000250448	NM_004496.3	351	aCt/aAt	2/2	1	2	FACETS	0.922	0.824	1	0.922	0.824	1	CLONAL	1	TRUE	1	0.45123313978744	2		409	447	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932807	39932807	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1160807200	NA	P-0028502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	174	609	1	ENST00000378444.4:c.1792G>A	p.Val598Met	p.V598M	ENST00000378444	NM_001123385.1	598	Gtg/Atg	4/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.45123313978744	2		610	726	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0028630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	107	498	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.331253772938252	3	FACETS	0.805	0.721	0.894	0.402	0.36	0.447	CLONAL	1	TRUE	1	0.331253772938252	3		498	936	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576919	7576919	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	125	629	0	ENST00000269305.4:c.927del	p.Asn310ThrfsTer35	p.N310Tfs*35	ENST00000269305	NM_001126112.2	309	ccC/cc	9/11	0.331253772938252	1	FACETS	0.836	0.757	0.919	0.836	0.757	0.919	CLONAL	1	TRUE	0	0.331253772938252	1		629	753	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591898	48591903	+	inframe_deletion	In_Frame_Del	DEL	TGGACC	TGGACC	-	novel	NA	P-0028630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	93	460	0	ENST00000342988.3:c.1061_1066del	p.Val354_Pro356delinsAla	p.V354_P356delinsA	ENST00000342988	NM_005359.5	354	gTGGACCct/gct	9/12	0.331253772938252	1	FACETS	0.829	0.739	0.925	0.829	0.739	0.925	CLONAL	1	TRUE	0	0.331253772938252	1		460	565	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0028779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	63	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.996	0.863	1	0.996	0.863	1	CLONAL	1	TRUE	1	0.261942576908326	2		473	483	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0028779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	75	312	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.261942576908326	2		312	469	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390072	89390072	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765502894	NA	P-0028779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	27	157	0	ENST00000336596.2:c.821G>A	p.Arg274Gln	p.R274Q	ENST00000336596	NM_005233.5	274	cGa/cAa	4/17	1	2	FACETS	0.744	0.594	0.915	0.744	0.594	0.915	CLONAL	1	TRUE	1	0.261942576908326	2		157	277	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520008	NA	P-0028779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	92	390	1	ENST00000269305.4:c.613T>G	p.Tyr205Asp	p.Y205D	ENST00000269305	NM_001126112.2	205	Tat/Gat	6/11	0.261942576908326	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.261942576908326	1		391	576	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030038	36030038	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	88	382	0	ENST00000358208.4:c.1073G>A	p.Gly358Asp	p.G358D	ENST00000358208		358	gGc/gAc	9/12	1	2	FACETS	0.975	0.864	1	0.975	0.864	1	CLONAL	1	TRUE	1	0.261942576908326	2		382	689	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0028791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	246	425	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.32244981875119	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.32244981875119	2		426	757	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556367	29556367	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	172	617	0	ENST00000356175.3:c.2734C>T	p.Gln912Ter	p.Q912*	ENST00000356175	NM_000267.3	912	Caa/Taa	21/57	0.32244981875119	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.32244981875119	1		617	779	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052639	42052639	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	144	607	2	ENST00000219905.7:c.7310G>T	p.Gly2437Val	p.G2437V	ENST00000219905	NM_001164273.1	2437	gGt/gTt	20/24	1	2	FACETS	0.938	0.855	1	0.938	0.855	1	CLONAL	1	TRUE	1	0.32244981875119	2		609	952	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835604	68835622	+	frameshift_variant	Frame_Shift_Del	DEL	GACAGCCTATTTTTCCCTC	GACAGCCTATTTTTCCCTC	-	novel	NA	P-0028791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	118	660	0	ENST00000261769.5:c.199_217del	p.Ala67ProfsTer10	p.A67Pfs*10	ENST00000261769	NM_004360.3	65	agGACAGCCTATTTTTCCCTC/ag	3/16	0.32244981875119	1	FACETS	0.86	0.776	0.948	0.86	0.776	0.948	CLONAL	1	TRUE	0	0.32244981875119	1		660	714	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961568	18961569	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGACC	novel	NA	P-0028791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	146	616	1	ENST00000262803.5:c.703_707dup	p.Cys237ThrfsTer86	p.C237Tfs*86	ENST00000262803	NM_002911.3	234	cag/caGGACCg	5/24	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.32244981875119	2		617	887	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936995	48936995	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778842	NA	P-0028842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	322	442	15	ENST00000267163.4:c.763C>T	p.Arg255Ter	p.R255*	ENST00000267163	NM_000321.2	255	Cga/Tga	8/27	0.584014749054985	6	FACETS	0.921	0.878	0.964	0.921	0.878	0.964	CLONAL	4	TRUE	2	0.584014749054985	6		457	649	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0028842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	32	382	1	ENST00000257430.4:c.3919dup	p.Ile1307AsnfsTer8	p.I1307Nfs*8	ENST00000257430	NM_000038.5	1306	gaa/gAaa	16/16	0.575030938420293	3	FACETS	0.944	0.777	1			1	CLONAL	1	TRUE	NA	0.584014749054985	3		383	150	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	393	593	0	ENST00000269305.4:c.799C>G	p.Arg267Gly	p.R267G	ENST00000269305	NM_001126112.2	267	Cgg/Ggg	8/11	0.575030938420293	3	FACETS	0.921	0.887	0.955			1	CLONAL	3	TRUE	NA	0.584014749054985	3		593	629	SUCCESS
APC	324	MSKCC	GRCh37	5	112173470	112174424	+	frameshift_variant	Frame_Shift_Del	DEL	AGGAATCTCATGGCAAATAGGCCTGCGAAGTACAAGGATGCCAATATTATGTCTCCTGGCTCAAGCTTGCCATCTCTTCATGTTAGGAAACAAAAAGCCCTAGAAGCAGAATTAGATGCTCAGCACTTATCAGAAACTTTTGACAATATAGACAATTTAAGTCCCAAGGCATCTCATCGTAGTAAGCAGAGACACAAGCAAAGTCTCTATGGTGATTATGTTTTTGACACCAATCGACATGATGATAATAGGTCAGACAATTTTAATACTGGCAACATGACTGTCCTTTCACCATATTTGAATACTACAGTGTTACCCAGCTCCTCTTCATCAAGAGGAAGCTTAGATAGTTCTCGTTCTGAAAAAGATAGAAGTTTGGAGAGAGAACGCGGAATTGGTCTAGGCAACTACCATCCAGCAACAGAAAATCCAGGAACTTCTTCAAAGCGAGGTTTGCAGATCTCCACCACTGCAGCCCAGATTGCCAAAGTCATGGAAGAAGTGTCAGCCATTCATACCTCTCAGGAAGACAGAAGTTCTGGGTCTACCACTGAATTACATTGTGTGACAGATGAGAGAAATGCACTTAGAAGAAGCTCTGCTGCCCATACACATTCAAACACTTACAATTTCACTAAGTCGGAAAATTCAAATAGGACATGTTCTATGCCTTATGCCAAATTAGAATACAAGAGATCTTCAAATGATAGTTTAAATAGTGTCAGTAGTAGTGATGGTTATGGTAAAAGAGGTCAAATGAAACCCTCGATTGAATCCTATTCTGAAGATGATGAAAGTAAGTTTTGCAGTTATGGTCAATACCCAGCCGACCTAGCCCATAAAATACATAGTGCAAATCATATGGATGATAATGATGGAGAACTAGATACACCAATAAATTATAGTCTTAAATATTCAGATGAGCAGTTGAACTCTGGAAGGCAAAGTCCTTCAC	AGGAATCTCATGGCAAATAGGCCTGCGAAGTACAAGGATGCCAATATTATGTCTCCTGGCTCAAGCTTGCCATCTCTTCATGTTAGGAAACAAAAAGCCCTAGAAGCAGAATTAGATGCTCAGCACTTATCAGAAACTTTTGACAATATAGACAATTTAAGTCCCAAGGCATCTCATCGTAGTAAGCAGAGACACAAGCAAAGTCTCTATGGTGATTATGTTTTTGACACCAATCGACATGATGATAATAGGTCAGACAATTTTAATACTGGCAACATGACTGTCCTTTCACCATATTTGAATACTACAGTGTTACCCAGCTCCTCTTCATCAAGAGGAAGCTTAGATAGTTCTCGTTCTGAAAAAGATAGAAGTTTGGAGAGAGAACGCGGAATTGGTCTAGGCAACTACCATCCAGCAACAGAAAATCCAGGAACTTCTTCAAAGCGAGGTTTGCAGATCTCCACCACTGCAGCCCAGATTGCCAAAGTCATGGAAGAAGTGTCAGCCATTCATACCTCTCAGGAAGACAGAAGTTCTGGGTCTACCACTGAATTACATTGTGTGACAGATGAGAGAAATGCACTTAGAAGAAGCTCTGCTGCCCATACACATTCAAACACTTACAATTTCACTAAGTCGGAAAATTCAAATAGGACATGTTCTATGCCTTATGCCAAATTAGAATACAAGAGATCTTCAAATGATAGTTTAAATAGTGTCAGTAGTAGTGATGGTTATGGTAAAAGAGGTCAAATGAAACCCTCGATTGAATCCTATTCTGAAGATGATGAAAGTAAGTTTTGCAGTTATGGTCAATACCCAGCCGACCTAGCCCATAAAATACATAGTGCAAATCATATGGATGATAATGATGGAGAACTAGATACACCAATAAATTATAGTCTTAAATATTCAGATGAGCAGTTGAACTCTGGAAGGCAAAGTCCTTCAC	-	novel	NA	P-0028842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	22	301	0	ENST00000257430.4:c.2181_3135del	p.Asn728MetfsTer10	p.N728Mfs*10	ENST00000257430	NM_000038.5	727	AGGAATCTCATGGCAAATAGGCCTGCGAAGTACAAGGATGCCAATATTATGTCTCCTGGCTCAAGCTTGCCATCTCTTCATGTTAGGAAACAAAAAGCCCTAGAAGCAGAATTAGATGCTCAGCACTTATCAGAAACTTTTGACAATATAGACAATTTAAGTCCCAAGGCATCTCATCGTAGTAAGCAGAGACACAAGCAAAGTCTCTATGGTGATTATGTTTTTGACACCAATCGACATGATGATAATAGGTCAGACAATTTTAATACTGGCAACATGACTGTCCTTTCACCATATTTGAATACTACAGTGTTACCCAGCTCCTCTTCATCAAGAGGAAGCTTAGATAGTTCTCGTTCTGAAAAAGATAGAAGTTTGGAGAGAGAACGCGGAATTGGTCTAGGCAACTACCATCCAGCAACAGAAAATCCAGGAACTTCTTCAAAGCGAGGTTTGCAGATCTCCACCACTGCAGCCCAGATTGCCAAAGTCATGGAAGAAGTGTCAGCCATTCATACCTCTCAGGAAGACAGAAGTTCTGGGTCTACCACTGAATTACATTGTGTGACAGATGAGAGAAATGCACTTAGAAGAAGCTCTGCTGCCCATACACATTCAAACACTTACAATTTCACTAAGTCGGAAAATTCAAATAGGACATGTTCTATGCCTTATGCCAAATTAGAATACAAGAGATCTTCAAATGATAGTTTAAATAGTGTCAGTAGTAGTGATGGTTATGGTAAAAGAGGTCAAATGAAACCCTCGATTGAATCCTATTCTGAAGATGATGAAAGTAAGTTTTGCAGTTATGGTCAATACCCAGCCGACCTAGCCCATAAAATACATAGTGCAAATCATATGGATGATAATGATGGAGAACTAGATACACCAATAAATTATAGTCTTAAATATTCAGATGAGCAGTTGAACTCTGGAAGGCAAAGTCCTTCACag/ag	16/16	0.575030938420293	3	FACETS	0.464	0.361	0.582			1	SUBCLONAL	1	TRUE	NA	0.584014749054985	3		301	210	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287955	33287955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	32	418	0	ENST00000374542.5:c.1298C>T	p.Ala433Val	p.A433V	ENST00000374542	NM_001141970.1	433	gCt/gTt	5/8	0.584014749054985	3	FACETS	0.303	0.245	0.368	0.101	0.081	0.123	SUBCLONAL	1	TRUE	0	0.584014749054985	3		418	468	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956557	93956557	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	158	334	0	ENST00000369303.4:c.2679G>T	p.Met893Ile	p.M893I	ENST00000369303	NM_004440.3	893	atG/atT	15/17	0.584014749054985	3	FACETS	0.841	0.789	0.893	0.841	0.789	0.893	CLONAL	3	TRUE	0	0.584014749054985	3		334	277	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0028999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	144	425	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.423904109762822	2		426	579	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345768	152345769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs759063323	NA	P-0028999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	119	307	0	ENST00000359321.1:c.801dup	p.His268ThrfsTer11	p.H268Tfs*11	ENST00000359321	NM_005431.1	267	-/A	3/3	1	2	FACETS	0.968	0.877	1	0.968	0.877	1	CLONAL	1	TRUE	1	0.423904109762822	2		307	580	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032461	12032462	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	97	389	0	ENST00000353533.5:c.899dup	p.Leu300PhefsTer13	p.L300Ffs*13	ENST00000353533	NM_003010.3	299	-/T	9/11	0.423904109762822	1	FACETS	0.972	0.874	1	0.972	0.874	1	CLONAL	1	TRUE	0	0.423904109762822	1		389	371	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212008	36212008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758647357	NA	P-0028999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	241	898	0	ENST00000222270.7:c.1759C>T	p.Pro587Ser	p.P587S	ENST00000222270	NM_014727.1	587	Cca/Tca	3/37	0.423904109762822	3	FACETS	1	0.968	1	0.531	0.495	0.568	CLONAL	1	TRUE	1	0.423904109762822	3		898	1298	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	75	463	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.229972288148852	1	FACETS	0.96	0.842	1	0.96	0.842	1	CLONAL	1	FALSE	0	0.229972288148852	1		463	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578457	+	frameshift_variant	Frame_Shift_Del	DEL	GCGC	GCGC	-	novel	NA	P-0029093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	157	687	0	ENST00000269305.4:c.473_476del	p.Arg158ProfsTer11	p.R158Pfs*11	ENST00000269305	NM_001126112.2	158	cGCGCc/cc	5/11	0.229972288148852	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	0	0.229972288148852	1		687	1065	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372205	55372205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs904970570	NA	P-0029093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	55	388	1	ENST00000297316.4:c.895G>A	p.Ala299Thr	p.A299T	ENST00000297316	NM_022454.3	299	Gcg/Acg	2/2	0.229972288148852	3	FACETS	0.751	0.641	0.872	0.376	0.32	0.436	SUBCLONAL	1	FALSE	1	0.229972288148852	3		389	710	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918675	44918692	+	inframe_deletion	In_Frame_Del	DEL	TACCTCTGCACTTGCAGC	TACCTCTGCACTTGCAGC	-	novel	NA	P-0029093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	54	502	0	ENST00000377967.4:c.1158_1175del	p.Asn386_Ala392delinsLys	p.N386_A392delinsK	ENST00000377967	NM_021140.2	386	aaTACCTCTGCACTTGCAGCa/aaa	12/29	1	2	FACETS	0.593	0.505	0.69	0.593	0.505	0.69	SUBCLONAL	1	FALSE	1	0.229972288148852	2		502	792	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	53	635	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.18404890232309	2		635	389	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0029108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	41	269	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.685	0.573	0.808	0.685	0.573	0.808	SUBCLONAL	1	TRUE	1	0.397724924380738	2		269	301	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314876	1314876	+	downstream_gene_variant	3'Flank	SNP	G	G	A	rs757104826	NA	P-0029108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	45	347	0				ENST00000400841		-/233			NA	2	FACETS	0.814	0.688	0.951			1	INDETERMINATE	1	TRUE	NA	0.397724924380738	2		347	278	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911573	114911573	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	136	557	0	ENST00000543371.1:c.1091T>G	p.Met364Arg	p.M364R	ENST00000543371	NM_001198531.1	364	aTg/aGg	10/14	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.397724924380738	2		557	574	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0029128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	427	634	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.613293328409953	2	FACETS	1	0.991	1	1	0.998	1	CLONAL	3	FALSE	0	0.613293328409953	2		635	459	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490331	56490331	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	57	359	0	ENST00000267101.3:c.2100G>C	p.Leu700Phe	p.L700F	ENST00000267101	NM_001982.3	700	ttG/ttC	18/28	0.613293328409953	3	FACETS	0.754	0.651	0.865	0.251	0.217	0.289	SUBCLONAL	1	FALSE	0	0.613293328409953	3		359	322	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909624	76909625	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGTC	novel	NA	P-0029128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	94	150	0	ENST00000373344.5:c.4277_4280dup	p.Ile1428ThrfsTer3	p.I1428Tfs*3	ENST00000373344	NM_000489.3	1427	cgt/cgGACGt	14/35	0.613293328409953	3	FACETS	1	0.971	1	0.614	0.552	0.679	CLONAL	1	FALSE	1	0.613293328409953	3		150	326	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0029166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	236	595	0				ENST00000310581	NM_198253.2	-/1132			0.262615525039729	0	FACETS	0.812	0.77	0.854			1	CLONAL	2	FALSE	0	0.405423453572849	0		595	426	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0029166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	638	909	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	0.129711336683499	4	FACETS	1	0.99	1	1	0.997	1	INDETERMINATE	3	FALSE	2	0.405423453572849	4		909	1389	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68292235	68292235	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200355697	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	143	487	1	ENST00000487270.1:c.139C>T	p.Arg47Ter	p.R47*	ENST00000487270	NM_133509.3	47	Cga/Tga	3/11	1	2	FACETS	0.91	0.833	0.99	0.91	0.833	0.99	CLONAL	1	TRUE	1	0.53	2		488	593	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420670	49420670	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs797045659	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	205	530	0	ENST00000301067.7:c.15079C>T	p.Arg5027Ter	p.R5027*	ENST00000301067	NM_003482.3	5027	Cga/Tga	48/54	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.53	2		530	716	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	152	366	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.95	0.872	1	0.95	0.872	1	CLONAL	1	TRUE	1	0.53	2		366	604	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	224	802	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	0.899	0.838	0.962	0.899	0.838	0.962	CLONAL	1	TRUE	1	0.53	2		802	940	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791758	42791758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1380826096	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	179	591	3	ENST00000575354.2:c.644G>A	p.Arg215Gln	p.R215Q	ENST00000575354	NM_015125.3	215	cGg/cAg	5/20	1	2	FACETS	0.846	0.782	0.914	0.846	0.782	0.914	CLONAL	1	TRUE	1	0.53	2		594	798	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045847	26045847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	150	464	0	ENST00000540144.1:c.209G>A	p.Arg70His	p.R70H	ENST00000540144	NM_003531.2	70	cGc/cAc	1/1	1	2	FACETS	0.896	0.821	0.973	0.896	0.821	0.973	CLONAL	1	TRUE	1	0.53	2		464	632	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459890	149459890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs535129002	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	231	672	1	ENST00000286301.3:c.317G>A	p.Arg106Gln	p.R106Q	ENST00000286301	NM_005211.3	106	cGg/cAg	4/22	1	2	FACETS	0.877	0.818	0.938	0.877	0.818	0.938	CLONAL	1	TRUE	1	0.53	2		673	994	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823760	3823760	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376314132	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	142	492	2	ENST00000262367.5:c.2455G>A	p.Val819Met	p.V819M	ENST00000262367	NM_004380.2	819	Gtg/Atg	13/31	1	2	FACETS	0.932	0.853	1	0.932	0.853	1	CLONAL	1	TRUE	1	0.53	2		494	575	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015168	71015168	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202173892	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	139	330	0	ENST00000318789.4:c.1762G>A	p.Ala588Thr	p.A588T	ENST00000318789	NM_032682.5	588	Gct/Act	20/21	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.53	2		330	504	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801726	3801726	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs587783483	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	191	502	2	ENST00000262367.5:c.3779+1G>A		p.X1260_splice	ENST00000262367	NM_004380.2	1260			1	2	FACETS	0.993	0.921	1	0.993	0.921	1	CLONAL	1	TRUE	1	0.53	2		504	726	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431760	49431760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748336297	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	176	679	1	ENST00000301067.7:c.9379C>T	p.Arg3127Cys	p.R3127C	ENST00000301067	NM_003482.3	3127	Cgc/Tgc	34/54	1	2	FACETS	0.896	0.828	0.967	0.896	0.828	0.967	CLONAL	1	TRUE	1	0.53	2		680	741	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81558901	81558901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772600260	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	158	575	3	ENST00000298171.2:c.494C>T	p.Thr165Met	p.T165M	ENST00000298171	NM_000369.2	165	aCg/aTg	6/10	1	2	FACETS	0.96	0.883	1	0.96	0.883	1	CLONAL	1	TRUE	1	0.53	2		578	621	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905566	50905566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774789534	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	263	699	0	ENST00000440232.2:c.694C>T	p.Arg232Cys	p.R232C	ENST00000440232	NM_002691.3	232	Cgt/Tgt	6/27	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.53	2		699	978	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874092	151874093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	177	571	0	ENST00000262189.6:c.8445dup	p.Ser2816IlefsTer6	p.S2816Ifs*6	ENST00000262189	NM_170606.2	2815	-/A	38/59	1	2	FACETS	0.853	0.787	0.921	0.853	0.787	0.921	CLONAL	1	TRUE	1	0.53	2		571	783	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921124	50921124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1307047144	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	199	643	1	ENST00000440232.2:c.3244C>T	p.Arg1082Cys	p.R1082C	ENST00000440232	NM_002691.3	1082	Cgc/Tgc	27/27	1	2	FACETS	0.912	0.847	0.98	0.912	0.847	0.98	CLONAL	1	TRUE	1	0.53	2		644	823	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433620	49433620	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555191740	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	296	934	3	ENST00000301067.7:c.7933C>T	p.Arg2645Ter	p.R2645*	ENST00000301067	NM_003482.3	2645	Cga/Tga	31/54	1	2	FACETS	0.916	0.861	0.971	0.916	0.861	0.971	CLONAL	1	TRUE	1	0.53	2		937	1220	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911881	94911881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1489329660	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	226	595	3	ENST00000536441.1:c.1049G>A	p.Arg350Gln	p.R350Q	ENST00000536441	NM_144665.3	350	cGa/cAa	7/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.53	2		598	761	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36823877	36823877	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373166224	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	151	497	0	ENST00000373129.3:c.305C>T	p.Thr102Met	p.T102M	ENST00000373129	NM_032017.1	102	aCg/aTg	5/12	1	2	FACETS	0.791	0.725	0.861	0.791	0.725	0.861	SUBCLONAL	1	TRUE	1	0.53	2		497	720	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193205400	193205400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	165	514	0	ENST00000367435.3:c.1331C>T	p.Ala444Val	p.A444V	ENST00000367435	NM_024529.4	444	gCc/gTc	15/17	1	2	FACETS	0.946	0.872	1	0.946	0.872	1	CLONAL	1	TRUE	1	0.53	2		514	658	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653446	206653446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	193	513	0	ENST00000367120.3:c.1330C>T	p.His444Tyr	p.H444Y	ENST00000367120	NM_014002.3	444	Cac/Tac	12/22	1	2	FACETS	0.925	0.858	0.995	0.925	0.858	0.995	CLONAL	1	TRUE	1	0.53	2		513	787	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106053	8106054	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAAATG	novel	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	182	630	0	ENST00000346208.3:c.876_881dup	p.Lys292_Met293dup	p.K292_M293dup	ENST00000346208		292	-/AAAATG	4/6	1	2	FACETS	0.844	0.78	0.91	0.844	0.78	0.91	CLONAL	1	TRUE	1	0.53	2		630	814	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373560	118373560	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	114	459	0	ENST00000534358.1:c.6953G>A	p.Ser2318Asn	p.S2318N	ENST00000534358	NM_005933.3	2318	aGc/aAc	27/36	1	2	FACETS	0.84	0.76	0.924	0.84	0.76	0.924	CLONAL	1	TRUE	1	0.53	2		459	512	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427701	49427701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532898944	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	164	645	2	ENST00000301067.7:c.10787G>A	p.Arg3596Gln	p.R3596Q	ENST00000301067	NM_003482.3	3596	cGg/cAg	39/54	1	2	FACETS	0.762	0.7	0.827	0.762	0.7	0.827	SUBCLONAL	1	TRUE	1	0.53	2		647	812	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435129	110435129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs533420684	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	204	629	0	ENST00000375856.3:c.3272C>T	p.Pro1091Leu	p.P1091L	ENST00000375856	NM_003749.2	1091	cCg/cTg	1/2	1	2	FACETS	0.871	0.808	0.935	0.871	0.808	0.935	CLONAL	1	TRUE	1	0.53	2		629	884	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779170	3779170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772270271	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	36	476	1	ENST00000262367.5:c.5878C>T	p.Arg1960Trp	p.R1960W	ENST00000262367	NM_004380.2	1960	Cgg/Tgg	31/31	1	2	FACETS	0.219	0.179	0.264	0.219	0.179	0.264	SUBCLONAL	1	TRUE	1	0.53	2		477	620	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118668	11118668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	234	814	0	ENST00000358026.2:c.2092G>A	p.Val698Ile	p.V698I	ENST00000358026	NM_001128849.1	698	Gtc/Atc	14/36	1	2	FACETS	0.863	0.805	0.923	0.863	0.805	0.923	CLONAL	1	TRUE	1	0.53	2		814	1023	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976408	18976408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550009751	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	279	734	1	ENST00000262803.5:c.3058C>T	p.Arg1020Cys	p.R1020C	ENST00000262803	NM_002911.3	1020	Cgc/Tgc	22/24	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.53	2		735	1046	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223292	36223292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749284326	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	307	889	4	ENST00000222270.7:c.5842G>A	p.Val1948Ile	p.V1948I	ENST00000222270	NM_014727.1	1948	Gtc/Atc	28/37	1	2	FACETS	0.963	0.907	1	0.963	0.907	1	CLONAL	1	TRUE	1	0.53	2		893	1203	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754476	41754476	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	126	712	0	ENST00000301178.4:c.1595A>G	p.Asp532Gly	p.D532G	ENST00000301178	NM_021913.4	532	gAc/gGc	13/20	1	2	FACETS	0.476	0.43	0.524	0.476	0.43	0.524	SUBCLONAL	1	TRUE	1	0.53	2		712	999	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906795	50906795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555790574	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	319	892	2	ENST00000440232.2:c.1183G>A	p.Gly395Ser	p.G395S	ENST00000440232	NM_002691.3	395	Ggt/Agt	10/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.53	2		894	1117	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032085	48032086	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs587782111	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	126	465	0	ENST00000234420.5:c.3476dup	p.Tyr1159Ter	p.Y1159*	ENST00000234420	NM_000179.2	1159	tac/tAac	6/10	1	2	FACETS	0.938	0.854	1	0.938	0.854	1	CLONAL	1	TRUE	1	0.53	2		465	507	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379453	225379453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	192	691	2	ENST00000264414.4:c.415G>A	p.Val139Ile	p.V139I	ENST00000264414	NM_003590.4	139	Gtc/Atc	4/16	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.53	2		693	718	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86686674	86686674	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1437757630	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	153	517	0	ENST00000274376.6:c.3118T>C	p.Tyr1040His	p.Y1040H	ENST00000274376	NM_002890.2	1040	Tat/Cat	25/25	1	2	FACETS	0.956	0.878	1	0.956	0.878	1	CLONAL	1	TRUE	1	0.53	2		517	604	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43745316	43745316	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	228	759	0	ENST00000523873.1:c.229T>G	p.Cys77Gly	p.C77G	ENST00000523873		77	Tgt/Ggt	3/8	1	2	FACETS	0.823	0.766	0.881	0.823	0.766	0.881	CLONAL	1	TRUE	1	0.53	2		759	1046	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434542	140434542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368528867	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	89	285	0	ENST00000288602.6:c.2156G>A	p.Arg719His	p.R719H	ENST00000288602	NM_004333.4	719	cGc/cAc	18/18	1	2	FACETS	0.997	0.892	1	0.997	0.892	1	CLONAL	1	TRUE	1	0.53	2		285	337	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212732	27212732	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	239	723	0	ENST00000380036.4:c.2714C>T	p.Ala905Val	p.A905V	ENST00000380036	NM_000459.3	905	gCg/gTg	17/23	1	2	FACETS	0.902	0.842	0.963	0.902	0.842	0.963	CLONAL	1	TRUE	1	0.53	2		723	1000	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426492	47426492	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765113993	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	244	371	0	ENST00000377045.4:c.835C>T	p.Arg279Cys	p.R279C	ENST00000377045	NM_001654.4	279	Cgc/Tgc	9/16	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.53	1		371	534	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858011	152858011	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	12	132	0	ENST00000406277.2:c.604G>A	p.Gly202Arg	p.G202R	ENST00000406277	NM_152274.4	202	Gga/Aga	6/7	1	1	FACETS	0.211	0.148	0.287	0.211	0.148	0.287	SUBCLONAL	1	TRUE	0	0.53	1		132	158	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	338	465	3	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.75	2		468	863	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	646	717	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.948	0.923	0.971	1	0.998	1	CLONAL	2	TRUE	1	0.75	2		721	909	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	296	483	14	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.939	0.887	0.991	0.939	0.887	0.991	CLONAL	1	TRUE	1	0.75	2		497	841	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	247	462	4	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	1	2	FACETS	0.956	0.899	1	0.956	0.899	1	CLONAL	1	TRUE	1	0.75	2		466	689	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139411726	139411726	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs377535397	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	46	474	0	ENST00000277541.6:c.1553C>T	p.Thr518Met	p.T518M	ENST00000277541	NM_017617.3	518	aCg/aTg	9/34	1	2	FACETS	0.144	0.121	0.17	0.144	0.121	0.17	SUBCLONAL	1	TRUE	1	0.75	2		474	851	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	266	494	8	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.858	0.807	0.91	0.858	0.807	0.91	CLONAL	1	TRUE	1	0.75	2		502	827	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965666	90965666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	109	322	2	ENST00000265433.3:c.1651del	p.Arg551GlyfsTer8	p.R551Gfs*8	ENST00000265433	NM_002485.4	551	Agg/gg	11/16	1	2	FACETS	0.779	0.706	0.855	0.779	0.706	0.855	SUBCLONAL	1	TRUE	1	0.75	2		324	373	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	106	186	1	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.734	0.664	0.808	0.734	0.664	0.808	SUBCLONAL	1	TRUE	1	0.75	2		187	385	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103755	47103756	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	302	413	1	ENST00000409792.3:c.6190_6191del	p.Asp2064ProfsTer8	p.D2064Pfs*8	ENST00000409792	NM_014159.6	2064	GAc/c	14/21	1	2	FACETS	0.9	0.85	0.95	0.9	0.85	0.95	CLONAL	1	TRUE	1	0.75	2		414	895	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28880860	28880860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746322044	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	371	504	1	ENST00000282397.4:c.3770G>A	p.Arg1257His	p.R1257H	ENST00000282397	NM_002019.4	1257	cGc/cAc	29/30	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.75	2		505	950	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970927	21970927	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501274	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	52	523	0	ENST00000304494.5:c.431G>A	p.Arg144His	p.R144H	ENST00000304494	NM_000077.4	144	cGc/cAc	2/3	1	2	FACETS	0.139	0.117	0.162	0.139	0.117	0.162	SUBCLONAL	1	TRUE	1	0.75	2		523	999	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821890	72821890	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	211	322	3	ENST00000268489.5:c.10285del	p.Arg3429ValfsTer56	p.R3429Vfs*56	ENST00000268489	NM_006885.3	3429	Cgt/gt	10/10	1	2	FACETS	0.97	0.908	1	0.97	0.908	1	CLONAL	1	TRUE	1	0.75	2		325	580	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539018	187539018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374444088	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	324	554	1	ENST00000441802.2:c.8722G>A	p.Val2908Ile	p.V2908I	ENST00000441802	NM_005245.3	2908	Gtc/Atc	10/27	1	2	FACETS	0.994	0.943	1	0.994	0.943	1	CLONAL	1	TRUE	1	0.75	2		555	869	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831357	72831358	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTG	rs34918837	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	113	320	2	ENST00000268489.5:c.5221_5223dup	p.Gln1741dup	p.Q1741dup	ENST00000268489	NM_006885.3	1741	-/CAA	9/10	1	2	FACETS	0.579	0.524	0.638	0.579	0.524	0.638	SUBCLONAL	1	TRUE	1	0.75	2		322	520	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793677	89793677	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	179	347	0	ENST00000336032.3:c.752del	p.Lys251SerfsTer14	p.K251Sfs*14	ENST00000336032	NM_006813.2	249	gAa/ga	2/2	1	2	FACETS	0.852	0.791	0.916	0.852	0.791	0.916	CLONAL	1	TRUE	1	0.75	2		347	560	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337684	73337684	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771690280	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	172	303	1	ENST00000377767.4:c.2032del	p.Ile678PhefsTer59	p.I678Ffs*59	ENST00000377767	NM_014953.3	678	Att/tt	16/21	1	2	FACETS	0.908	0.842	0.976	0.908	0.842	0.976	CLONAL	1	TRUE	1	0.75	2		304	505	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822586	72822586	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	239	314	1	ENST00000268489.5:c.9589del	p.Gln3197SerfsTer44	p.Q3197Sfs*44	ENST00000268489	NM_006885.3	3197	Cag/ag	10/10	1	2	FACETS	0.904	0.848	0.961	0.904	0.848	0.961	CLONAL	1	TRUE	1	0.75	2		315	705	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467747	50467747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	341	574	2	ENST00000331340.3:c.982C>T	p.Arg328Cys	p.R328C	ENST00000331340	NM_006060.4	328	Cgc/Tgc	8/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.75	2		576	877	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752695	42752695	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1366176199	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	353	754	7	ENST00000222329.4:c.1569del	p.Leu525SerfsTer6	p.L525Sfs*6	ENST00000222329	NM_006494.2	523	ggG/gg	4/4	1	2	FACETS	0.965	0.917	1	0.965	0.917	1	CLONAL	1	TRUE	1	0.75	2		761	975	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647657	3647657	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs774532876	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	438	751	3	ENST00000294008.3:c.1406del	p.Pro469HisfsTer4	p.P469Hfs*4	ENST00000294008	NM_032444.2	469	cCa/ca	7/15	1	2	FACETS	0.983	0.939	1	0.983	0.939	1	CLONAL	1	TRUE	1	0.75	2		754	1188	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790090	40790090	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	134	576	0	ENST00000373198.4:c.2641del	p.Arg881GlyfsTer20	p.R881Gfs*20	ENST00000373198	NM_133170.3	881	Cgg/gg	18/32	1	2	FACETS	0.421	0.382	0.462	0.421	0.382	0.462	SUBCLONAL	1	TRUE	1	0.75	2		576	849	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	63	668	3	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.175	0.151	0.202	0.175	0.151	0.202	SUBCLONAL	1	TRUE	1	0.75	2		671	959	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944928	31944928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	31	259	0	ENST00000340398.3:c.173C>T	p.Thr58Ile	p.T58I	ENST00000340398	NM_001013699.2	58	aCc/aTc	1/1	1	2	FACETS	0.196	0.158	0.239	0.196	0.158	0.239	SUBCLONAL	1	TRUE	1	0.75	2		259	421	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571939	64571939	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	264	780	2	ENST00000312049.6:c.1700C>T	p.Ala567Val	p.A567V	ENST00000312049	NM_130799.2	567	gCc/gTc	10/10	1	2	FACETS	0.522	0.488	0.557	0.522	0.488	0.557	SUBCLONAL	1	TRUE	1	0.75	2		782	1349	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420433	49420433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1401520080	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	371	596	0	ENST00000301067.7:c.15316C>T	p.Arg5106Cys	p.R5106C	ENST00000301067	NM_003482.3	5106	Cgc/Tgc	48/54	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.75	2		596	892	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826572	50826572	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	174	265	1	ENST00000398568.2:c.2301del	p.Pro768LeufsTer5	p.P768Lfs*5	ENST00000398568	NM_001042412.1	766	aTt/at	15/18	0.3	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.75	0		266	331	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989691	15989691	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	261	396	0	ENST00000268712.3:c.3082C>T	p.Arg1028Ter	p.R1028*	ENST00000268712	NM_006311.3	1028	Cga/Tga	23/46	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.75	2		396	684	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753002	42753002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	292	545	0	ENST00000222329.4:c.1262del	p.Pro421ArgfsTer18	p.P421Rfs*18	ENST00000222329	NM_006494.2	421	cCg/cg	4/4	1	2	FACETS	0.887	0.837	0.938	0.887	0.837	0.938	CLONAL	1	TRUE	1	0.75	2		545	878	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797251	42797251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540906276	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	79	575	0	ENST00000575354.2:c.3613C>T	p.Arg1205Trp	p.R1205W	ENST00000575354	NM_015125.3	1205	Cgg/Tgg	15/20	1	2	FACETS	0.209	0.183	0.237	0.209	0.183	0.237	SUBCLONAL	1	TRUE	1	0.75	2		575	1008	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250103	39250103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs994463655	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	248	597	0	ENST00000402219.2:c.1466G>A	p.Arg489His	p.R489H	ENST00000402219	NM_005633.3	489	cGt/cAt	10/23	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.75	2		597	660	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46602931	46602931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303549858	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	368	585	1	ENST00000263734.3:c.989G>A	p.Arg330His	p.R330H	ENST00000263734	NM_001430.4	330	cGc/cAc	8/16	1	2	FACETS	0.994	0.946	1	0.994	0.946	1	CLONAL	1	TRUE	1	0.75	2		586	987	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656803	45656803	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	53	575	0	ENST00000407780.3:c.353A>G	p.Gln118Arg	p.Q118R	ENST00000407780	NM_001283052.1	118	cAa/cGa	3/7	0.3	2	FACETS	0.16	0.136	0.187			1	INDETERMINATE	1	TRUE	NA	0.75	2		575	884	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162237	47162237	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1000273506	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	254	353	1	ENST00000409792.3:c.3889C>T	p.Arg1297Cys	p.R1297C	ENST00000409792	NM_014159.6	1297	Cgt/Tgt	3/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.75	2		354	654	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027115	71027744	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTAAGCTCTGTGGAGAAGCCTCCGATGCGGACTTGGAGAGAGTGACACTTGATACCAGATTCAACTGCAAGGAAAAAAACAACGTCTTAGAAGACCTTCAGAAAACCAGAGCAACCCAGGAACCACATCTAGCAGGAGTAACACAGAGGATGCGTGGGCACCGTTTCTTCCTCTATGTAGATGGTATGTTTACCATGAACCGAAACACACGGTGAGTCCTGCGTGAATTCACTTAGGATGCAGTGTAAGATATCTCTGGCAGCGGTCTCTTTTCCAAAGGCTGCTACATGGGTGTTTACAGGCTCAAAAAGGGGTTACCTACCTGAGGGAGTGTGAGAAACCCTGAGTCAAGACATTTATTTCATTGTGATGTCTCACCTATAGGCTTTGATCGCCCATCAGGCCTTGTCAACCTCAAAGAGGGAGAGAAGTCCTTAGCAATACCAGTGAAGCTGAGTATTTTAGGTGACACCAGTTGGGATACGCTGGTGTAGATCTGAAGAAGTGTCCAGCAGAATTTCTGCAATATGCTAGCACAACCAAAGAGCTGTTTTTACTTGATTTTTATTAAAATTAAACTTTAATAAATGTAAATGGAAAGAGCCCCATGTGGCTAGTAGCTACCATA	AGGTAAGCTCTGTGGAGAAGCCTCCGATGCGGACTTGGAGAGAGTGACACTTGATACCAGATTCAACTGCAAGGAAAAAAACAACGTCTTAGAAGACCTTCAGAAAACCAGAGCAACCCAGGAACCACATCTAGCAGGAGTAACACAGAGGATGCGTGGGCACCGTTTCTTCCTCTATGTAGATGGTATGTTTACCATGAACCGAAACACACGGTGAGTCCTGCGTGAATTCACTTAGGATGCAGTGTAAGATATCTCTGGCAGCGGTCTCTTTTCCAAAGGCTGCTACATGGGTGTTTACAGGCTCAAAAAGGGGTTACCTACCTGAGGGAGTGTGAGAAACCCTGAGTCAAGACATTTATTTCATTGTGATGTCTCACCTATAGGCTTTGATCGCCCATCAGGCCTTGTCAACCTCAAAGAGGGAGAGAAGTCCTTAGCAATACCAGTGAAGCTGAGTATTTTAGGTGACACCAGTTGGGATACGCTGGTGTAGATCTGAAGAAGTGTCCAGCAGAATTTCTGCAATATGCTAGCACAACCAAAGAGCTGTTTTTACTTGATTTTTATTAAAATTAAACTTTAATAAATGTAAATGGAAAGAGCCCCATGTGGCTAGTAGCTACCATA	-	novel	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	109	508	0	ENST00000318789.4:c.1147-564_1212del		p.X383_splice	ENST00000318789	NM_032682.5	383		15/21	1	2	FACETS	0.455	0.409	0.503	0.455	0.409	0.503	SUBCLONAL	1	TRUE	1	0.75	2		508	639	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89478316	89478316	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs575730567	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	149	379	1	ENST00000336596.2:c.2135G>A	p.Arg712His	p.R712H	ENST00000336596	NM_005233.5	712	cGt/cAt	12/17	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.75	2		380	396	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35857131	35857131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1320815333	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	125	264	0	ENST00000303115.3:c.52G>A	p.Val18Ile	p.V18I	ENST00000303115	NM_002185.3	18	Gtt/Att	1/8	1	2	FACETS	0.868	0.794	0.945	0.868	0.794	0.945	CLONAL	1	TRUE	1	0.75	2		264	384	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161180	56161180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs995383293	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	95	375	0	ENST00000399503.3:c.1049C>T	p.Ala350Val	p.A350V	ENST00000399503	NM_005921.1	350	gCa/gTa	5/20	1	2	FACETS	0.483	0.432	0.538	0.483	0.432	0.538	SUBCLONAL	1	TRUE	1	0.75	2		375	524	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69039636	69039636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	145	423	1	ENST00000288368.4:c.3748G>A	p.Ala1250Thr	p.A1250T	ENST00000288368	NM_024870.2	1250	Gct/Act	31/40	1	2	FACETS	0.875	0.805	0.946	0.875	0.805	0.946	CLONAL	1	TRUE	1	0.75	2		424	442	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044422	5044422	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	260	466	2	ENST00000381652.3:c.370T>C	p.Tyr124His	p.Y124H	ENST00000381652	NM_004972.3	124	Tat/Cat	5/25	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.75	2		468	658	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416378	29416380	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs755556501	NA	P-0029301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	22	645	0	ENST00000389048.3:c.4573_4575del	p.Lys1525del	p.K1525del	ENST00000389048	NM_004304.4	1525	AAG/-	29/29	0.232520174475254	1	FACETS	0.995	0.791	1	0.995	0.791	1	INDETERMINATE	1	TRUE	0	0.42899566631259	1		645	81	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513281	44513282	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCACCG	rs745888281	NA	P-0029301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	13	593	0	ENST00000291552.4:c.648_653dup	p.Gly222_Gly223dup	p.G222_G223dup	ENST00000291552	NM_006758.2	222	ggt/ggCGGTGGt	8/8	0.42899566631259	1	FACETS	0.491	0.354	0.653	0.491	0.354	0.653	SUBCLONAL	1	TRUE	0	0.42899566631259	1		593	97	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733279	40733279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201275244	NA	P-0029301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	20	444	1	ENST00000373198.4:c.3527G>A	p.Arg1176His	p.R1176H	ENST00000373198	NM_133170.3	1176	cGt/cAt	26/32	0.186924735113758	2	FACETS	0.951	0.741	1	0.476	0.37	0.594	INDETERMINATE	1	TRUE	0	0.42899566631259	2		445	98	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105537	27105553	+	protein_altering_variant	In_Frame_Del	DEL	TGTAGAATATTTCCGAC	TGTAGAATATTTCCGAC	GG	novel	NA	P-0029301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	17	367	2	ENST00000324856.7:c.5148_5164delinsGG	p.Val1717_Arg1722delinsGly	p.V1717_R1722delinsG	ENST00000324856	NM_006015.4	1716	ctTGTAGAATATTTCCGACga/ctGGga	20/20	0.42899566631259	2	FACETS	1	0.84	1	1	0.84	1	CLONAL	2	TRUE	0	0.42899566631259	2		369	37	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742483	17742483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs922852099	NA	P-0029301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	44	555	0	ENST00000250003.3:c.665G>A	p.Arg222Gln	p.R222Q	ENST00000250003	NM_002478.4	222	cGg/cAg	2/3	0.1884568100658	4	FACETS	0.91	0.777	1	0.91	0.777	1	INDETERMINATE	2	TRUE	2	0.42899566631259	4		555	161	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418596	49418596	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	30	449	0	ENST00000301067.7:c.15918A>T	p.Glu5306Asp	p.E5306D	ENST00000301067	NM_003482.3	5306	gaA/gaT	49/54	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.42899566631259	2		449	129	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610606	10610606	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	57	631	0	ENST00000171111.5:c.104C>G	p.Ser35Cys	p.S35C	ENST00000171111	NM_203500.1	35	tCc/tGc	2/6	0.186924735113758	2	FACETS	0.841	0.738	0.948	0.841	0.738	0.948	INDETERMINATE	2	TRUE	0	0.42899566631259	2		631	158	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144124	11144134	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGAAGTCCT	CCAGAAGTCCT	-	novel	NA	P-0029301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	18	595	0	ENST00000358026.2:c.3709_3719del	p.Lys1237ProfsTer2	p.K1237Pfs*2	ENST00000358026	NM_001128849.1	1235	gaCCAGAAGTCCTcc/gacc	26/36	0.186924735113758	2	FACETS	0.699	0.533	0.891	0.35	0.266	0.446	INDETERMINATE	1	TRUE	0	0.42899566631259	2		595	120	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366149	15366149	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	44	494	0	ENST00000263377.2:c.2006G>T	p.Arg669Leu	p.R669L	ENST00000263377	NM_058243.2	669	cGc/cTc	10/20	0.186924735113758	2	FACETS	0.977	0.846	1	0.977	0.846	1	INDETERMINATE	2	TRUE	0	0.42899566631259	2		494	105	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248342	212248342	+	stop_lost	Nonstop_Mutation	SNP	A	A	T	novel	NA	P-0029301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	10	171	0	ENST00000342788.4:c.3925T>A	p.Ter1309LysextTer33	p.*1309Kext*33	ENST00000342788	NM_005235.2	1309	Taa/Aaa	28/28	0.232520174475254	1	FACETS	0.509	0.35	0.701	0.509	0.35	0.701	INDETERMINATE	1	TRUE	0	0.42899566631259	1		171	72	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827952	40827953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	24	404	0	ENST00000373198.4:c.2475dup	p.Pro826ThrfsTer11	p.P826Tfs*11	ENST00000373198	NM_133170.3	825	-/A	17/32	0.186924735113758	2	FACETS	0.805	0.639	0.991	0.402	0.319	0.496	INDETERMINATE	1	TRUE	0	0.42899566631259	2		404	139	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968172	55968173	+	missense_variant	Missense_Mutation	DNP	GG	GG	CC	novel	NA	P-0029301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	17	343	2	ENST00000263923.4:c.2157_2158inv	p.Asn719_Arg720delinsLysGly	p.N719_R720delinsKG	ENST00000263923	NM_002253.2	719	aaCCgg/aaGGgg	15/30	0.186924735113758	2	FACETS	1	0.84	1	0.566	0.433	0.715	INDETERMINATE	1	TRUE	0	0.42899566631259	2		345	70	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340879	70340879	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0029301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	26	258	0	ENST00000374080.3:c.612C>G	p.Tyr204Ter	p.Y204*	ENST00000374080		204	taC/taG	5/45	1	1	FACETS	1	0.872	1	1	0.963	1	CLONAL	2	TRUE	0	0.42899566631259	1		258	46	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0029478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	133	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	0.792	0.961	0.874	0.792	0.961	CLONAL	1	TRUE	1	0.255765395925008	2		473	1190	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs967461896	NA	P-0029478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	153	746	0	ENST00000269305.4:c.526T>A	p.Cys176Ser	p.C176S	ENST00000269305	NM_001126112.2	176	Tgc/Agc	5/11	0.242932386497496	1	FACETS	0.972	0.888	1	0.972	0.888	1	CLONAL	1	TRUE	0	0.255765395925008	1		746	1073	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513168	106513168	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs745475345	NA	P-0029478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	85	331	0	ENST00000359195.3:c.2072T>C	p.Ile691Thr	p.I691T	ENST00000359195	NM_002649.2	691	aTt/aCt	4/11	1	2	FACETS	0.945	0.836	1	0.945	0.836	1	CLONAL	1	TRUE	1	0.255765395925008	2		331	703	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974809	21974809	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	19	149	0	ENST00000304494.5:c.18del	p.Ser7AlafsTer19	p.S7Afs*19	ENST00000304494	NM_000077.4	6	ggG/gg	1/3	0.255765395925008	1	FACETS	0.815	0.623	1	0.815	0.623	1	CLONAL	1	TRUE	0	0.255765395925008	1		149	159	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0029770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	17	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.433	0.321	0.567	0.433	0.321	0.567	SUBCLONAL	1	TRUE	1	0.11	2		473	714	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27093058	27093058	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs886042036	NA	P-0029770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	29	425	1	ENST00000324856.7:c.2988+1G>A		p.X996_splice	ENST00000324856	NM_006015.4	996			1	2	FACETS	1	0.807	1	1	0.807	1	CLONAL	1	TRUE	1	0.11	2		426	523	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46252737	46252737	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	32	416	0	ENST00000371998.3:c.166C>G	p.Leu56Val	p.L56V	ENST00000371998		56	Ctt/Gtt	4/23	1	2	FACETS	0.986	0.799	1	0.986	0.799	1	CLONAL	1	TRUE	1	0.11	2		416	590	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170016819	170016819	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	40	647	0	ENST00000295797.4:c.1624A>C	p.Asn542His	p.N542H	ENST00000295797	NM_002740.5	542	Aat/Cat	17/18	1	2	FACETS	0.996	0.826	1	0.996	0.826	1	CLONAL	1	TRUE	1	0.11	2		647	730	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155725	56155726	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0029981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	192	293	0	ENST00000399503.3:c.819_820del	p.Arg273SerfsTer27	p.R273Sfs*27	ENST00000399503	NM_005921.1	273	AGa/a	3/20	1	2	FACETS	0.89	0.829	0.953	0.89	0.829	0.953	CLONAL	1	TRUE	1	0.755687045160526	2		293	571	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881002	37881003	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCTCCCCA	rs397516982	NA	P-0029981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	1259	497	0	ENST00000269571.5:c.2332_2340dup	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	-/GGCTCCCCA	20/27	0.664793956572734	4	FACETS	1	0.997	1			1	CLONAL	3	TRUE	NA	0.755687045160526	4		497	1782	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578273	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0029981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	569	456	0	ENST00000269305.4:c.576_577delinsTT	p.Gln192_His193delinsHisTyr	p.Q192_H193delinsHY	ENST00000269305	NM_001126112.2	192	caGCat/caTTat	6/11	0.755687045160526	2	FACETS	0.979	0.954	1	0.979	0.954	1	CLONAL	2	TRUE	0	0.755687045160526	2		456	769	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435005	49435005	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1281047785	NA	P-0029981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	296	383	0	ENST00000301067.7:c.6548A>G	p.Tyr2183Cys	p.Y2183C	ENST00000301067	NM_003482.3	2183	tAt/tGt	31/54	1	2	FACETS	0.973	0.92	1	0.973	0.92	1	CLONAL	1	TRUE	1	0.755687045160526	2		383	805	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435201	110435201	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	164	318	1	ENST00000375856.3:c.3200G>T	p.Gly1067Val	p.G1067V	ENST00000375856	NM_003749.2	1067	gGg/gTg	1/2	0.755687045160526	4	FACETS	0.575	0.526	0.626			1	SUBCLONAL	1	TRUE	NA	0.755687045160526	4		319	1325	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246569	41246569	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	314	494	0	ENST00000357654.3:c.979A>T	p.Thr327Ser	p.T327S	ENST00000357654	NM_007294.3	327	Aca/Tca	10/23	0.755687045160526	2	FACETS	0.969	0.917	1	0.484	0.458	0.511	CLONAL	1	TRUE	0	0.755687045160526	2		494	858	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161268	56161278	+	frameshift_variant	Frame_Shift_Del	DEL	TTTAAAGAATT	TTTAAAGAATT	-	novel	NA	P-0029981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	159	304	0	ENST00000399503.3:c.1139_1149del	p.Leu380Ter	p.L380*	ENST00000399503	NM_005921.1	379	acTTTAAAGAATTtt/actt	5/20	1	2	FACETS	0.817	0.754	0.882	0.817	0.754	0.882	CLONAL	1	TRUE	1	0.755687045160526	2		304	515	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109322462	109322566	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAACAATTTTTCACTGAATGTTTACAAACCATTATTCCAATGTAGTGACGATAATGTAGGGGTAACGGCCCATCCATTTGCAGTAGATAGTGCTGAGTTTTTAAG	AAACAATTTTTCACTGAATGTTTACAAACCATTATTCCAATGTAGTGACGATAATGTAGGGGTAACGGCCCATCCATTTGCAGTAGATAGTGCTGAGTTTTTAAG	-	novel	NA	P-0029981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	158	266	0	ENST00000436639.2:c.471_546+29del		p.X157_splice	ENST00000436639	NM_014454.2	157		3/10	0.591222137228015	3	FACETS	0.866	0.796	0.939			1	CLONAL	1	TRUE	NA	0.755687045160526	3		266	665	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202341	138202341	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	329	435	0	ENST00000237289.4:c.2258C>A	p.Ala753Asp	p.A753D	ENST00000237289	NM_001270507.1	753	gCc/gAc	9/9	0.755687045160526	2	FACETS	0.953	0.903	1	0.476	0.451	0.502	CLONAL	1	TRUE	0	0.755687045160526	2		435	914	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0030131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	140	513	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	0.651521450049395	2		513	428	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0030131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	238	377	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.344939638495285	2	FACETS	0.771	0.729	0.813	0.771	0.729	0.813	INDETERMINATE	2	TRUE	0	0.651521450049395	2		377	474	SUCCESS
AR	367	MSKCC	GRCh37	X	66905872	66905872	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137852569	NA	P-0030131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	124	349	0	ENST00000374690.3:c.1789G>A	p.Ala597Thr	p.A597T	ENST00000374690	NM_000044.3	597	Gcc/Acc	3/8	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.651521450049395	2		349	361	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411411	63411411	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	221	590	1	ENST00000330258.3:c.1756C>T	p.Arg586Ter	p.R586*	ENST00000330258	NM_152424.3	586	Cga/Tga	2/2	1	2	FACETS	0.98	0.917	1	0.98	0.917	1	CLONAL	1	TRUE	1	0.651521450049395	2		591	692	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097629	27097629	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	211	467	0	ENST00000324856.7:c.3218G>A	p.Trp1073Ter	p.W1073*	ENST00000324856	NM_006015.4	1073	tGg/tAg	12/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.651521450049395	2		467	629	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119945	70119946	+	stop_gained,inframe_insertion	Nonsense_Mutation	INS	-	-	GTA	novel	NA	P-0030131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	292	311	0	ENST00000245479.2:c.948_949insTAG	p.Thr316_Gly317insTer	p.T316_G317ins*	ENST00000245479	NM_000346.3	316	acg/acGTAg	3/3	0.651521450049395	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.651521450049395	2		311	445	SUCCESS
APC	324	MSKCC	GRCh37	5	112173560	112173560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	131	295	0	ENST00000257430.4:c.2269C>T	p.Gln757Ter	p.Q757*	ENST00000257430	NM_000038.5	757	Caa/Taa	16/16	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.651521450049395	2		295	396	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679900	30679900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768909425	NA	P-0030131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	145	388	0	ENST00000376406.3:c.1819G>A	p.Gly607Arg	p.G607R	ENST00000376406	NM_014641.2	607	Ggg/Agg	5/15	1	2	FACETS	0.974	0.896	1	0.974	0.896	1	CLONAL	1	TRUE	1	0.651521450049395	2		388	457	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907104	101907105	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TACT	novel	NA	P-0030131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	122	430	0	ENST00000374994.4:c.1064_1065insTACT	p.Val356ThrfsTer5	p.V356Tfs*5	ENST00000374994	NM_004612.2	355	gca/gcTACTa	6/9	1	2	FACETS	0.811	0.737	0.887	0.811	0.737	0.887	CLONAL	1	TRUE	1	0.651521450049395	2		430	462	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780172	9780172	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	140	782	0	ENST00000377346.4:c.1342G>A	p.Glu448Lys	p.E448K	ENST00000377346	NM_005026.3	448	Gag/Aag	11/24	0.347003215986501	5	FACETS	0.877	0.803	0.953	0.585	0.535	0.635	INDETERMINATE	2	TRUE	2	0.590220264443073	5		782	510	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845436	156845436	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	152	925	0	ENST00000524377.1:c.1479C>A	p.Asn493Lys	p.N493K	ENST00000524377	NM_002529.3	493	aaC/aaA	12/17	0.536778865321729	3	FACETS	0.996	0.913	1	0.332	0.304	0.361	CLONAL	1	TRUE	0	0.590220264443073	3		925	670	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243675729	243675729	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0030174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	10	276	0	ENST00000263826.5:c.1252-1G>A		p.X418_splice	ENST00000263826	NM_005465.4	418			0.536778865321729	3	FACETS	1	0.846	1	0.457	0.325	0.605	CLONAL	1	TRUE	0	0.590220264443073	3		276	32	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577575	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587782289	NA	P-0030174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	168	765	0	ENST00000269305.4:c.706T>G	p.Tyr236Asp	p.Y236D	ENST00000269305	NM_001126112.2	236	Tac/Gac	7/11	0.517354202297751	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.590220264443073	2		765	250	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440659	56440659	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	128	737	0	ENST00000407977.2:c.559G>C	p.Glu187Gln	p.E187Q	ENST00000407977		187	Gag/Cag	5/10	0.590220264443073	4	FACETS	1	0.982	1	0.33	0.3	0.361	CLONAL	1	TRUE	0	0.590220264443073	4		737	523	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797743	42797743	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0030174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	68	723	0	ENST00000575354.2:c.3796-1G>T		p.X1266_splice	ENST00000575354	NM_015125.3	1266			0.407267439722156	3	FACETS	0.598	0.521	0.681	0.299	0.26	0.341	SUBCLONAL	1	TRUE	1	0.590220264443073	3		723	499	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097980	178097980	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	20	608	0	ENST00000397062.3:c.400G>C	p.Glu134Gln	p.E134Q	ENST00000397062	NM_006164.4	134	Gag/Cag	3/5	0.407267439722156	3	FACETS	0.601	0.464	0.759	0.301	0.232	0.38	SUBCLONAL	1	TRUE	1	0.590220264443073	3		608	146	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309515	30309541	+	inframe_deletion	In_Frame_Del	DEL	CCAAGCTGCGATCCGACTCACCAATAC	CCAAGCTGCGATCCGACTCACCAATAC	-	novel	NA	P-0030174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	146	804	0	ENST00000307677.4:c.481_507del	p.Val161_Trp169del	p.V161_W169del	ENST00000307677	NM_138578.1	161	GTATTGGTGAGTCGGATCGCAGCTTGG/-	2/3	0.248448006734737	4	FACETS	1	0.937	1	1	0.937	1	INDETERMINATE	2	TRUE	2	0.590220264443073	4		804	387	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016212	31016212	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	20	467	0	ENST00000375687.4:c.458G>C	p.Arg153Thr	p.R153T	ENST00000375687	NM_015338.5	153	aGa/aCa	6/13	0.248448006734737	4	FACETS	0.98	0.761	1	0.49	0.38	0.614	INDETERMINATE	1	TRUE	2	0.590220264443073	4		467	110	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665451	176665451	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	168	492	0	ENST00000439151.2:c.4135C>G	p.Pro1379Ala	p.P1379A	ENST00000439151	NM_022455.4	1379	Ccg/Gcg	7/23	0.517354202297751	2	FACETS	0.982	0.923	1	0.982	0.923	1	CLONAL	2	TRUE	0	0.590220264443073	2		492	290	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3120985	3120985	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0030174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	20	522	4	ENST00000078429.4:c.890-2A>T		p.X297_splice	ENST00000078429	NM_002067.2	297			0.536819685401182	2	FACETS	0.188	0.143	0.241	0.094	0.071	0.121	SUBCLONAL	1	TRUE	0	0.590220264443073	2		526	360	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988118	85988118	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	185	401	0	ENST00000263360.6:c.1063C>T	p.Arg355Ter	p.R355*	ENST00000263360	NM_003797.3	355	Cga/Tga	10/12	0.449387934198952	2	FACETS	0.917	0.857	0.978	0.917	0.857	0.978	CLONAL	2	TRUE	0	0.461684231610941	2		401	437	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103224	119103224	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	151	481	0	ENST00000264033.4:c.262C>A	p.Leu88Ile	p.L88I	ENST00000264033	NM_005188.3	88	Cta/Ata	2/16	0.449387934198952	2	FACETS	0.892	0.817	0.971	0.446	0.408	0.486	CLONAL	1	TRUE	0	0.461684231610941	2		481	733	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784570	43784649	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCTTTCAGGCTGAGAATCTTCAATTATCAGGCAAGGAGTATCTTGCTGAGAGAAATCTGAATCCAACTGACTTCCAGT	TGGCTTTCAGGCTGAGAATCTTCAATTATCAGGCAAGGAGTATCTTGCTGAGAGAAATCTGAATCCAACTGACTTCCAGT	-	novel	NA	P-0030301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	107	513	0	ENST00000382044.4:c.25_104del	p.Thr9GlyfsTer5	p.T9Gfs*5	ENST00000382044	NM_001141980.1	9	ACTGGAAGTCAGTTGGATTCAGATTTCTCTCAGCAAGATACTCCTTGCCTGATAATTGAAGATTCTCAGCCTGAAAGCCAg/g	2/28	0.461711362026017	1	FACETS	0.413	0.37	0.458	0.413	0.37	0.458	SUBCLONAL	1	TRUE	0	0.461684231610941	1		513	864	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988118	85988118	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030301-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	479	401	0	ENST00000263360.6:c.1063C>T	p.Arg355Ter	p.R355*	ENST00000263360	NM_003797.3	355	Cga/Tga	10/12	0.901950091179982	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.904821040435826	2		401	520	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103224	119103224	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030301-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	214	481	0	ENST00000264033.4:c.262C>A	p.Leu88Ile	p.L88I	ENST00000264033	NM_005188.3	88	Cta/Ata	2/16	0.901950091179982	2	FACETS	0.99	0.93	1	0.495	0.465	0.525	CLONAL	1	TRUE	0	0.904821040435826	2		481	478	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784570	43784649	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCTTTCAGGCTGAGAATCTTCAATTATCAGGCAAGGAGTATCTTGCTGAGAGAAATCTGAATCCAACTGACTTCCAGT	TGGCTTTCAGGCTGAGAATCTTCAATTATCAGGCAAGGAGTATCTTGCTGAGAGAAATCTGAATCCAACTGACTTCCAGT	-	novel	NA	P-0030301-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	185	513	0	ENST00000382044.4:c.25_104del	p.Thr9GlyfsTer5	p.T9Gfs*5	ENST00000382044	NM_001141980.1	9	ACTGGAAGTCAGTTGGATTCAGATTTCTCTCAGCAAGATACTCCTTGCCTGATAATTGAAGATTCTCAGCCTGAAAGCCAg/g	2/28	0.892599692148309	3	FACETS	0.665	0.614	0.718	0.222	0.204	0.24	SUBCLONAL	1	TRUE	0	0.904821040435826	3		513	893	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279597	18279597	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030301-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	70	467	1	ENST00000222254.8:c.1870G>A	p.Val624Met	p.V624M	ENST00000222254	NM_005027.3	624	Gtg/Atg	15/16	0.904821040435826	3	FACETS	0.415	0.362	0.472	0.207	0.181	0.236	SUBCLONAL	1	TRUE	1	0.904821040435826	3		468	542	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	137	435	0	ENST00000206249.3:c.1610A>G	p.Tyr537Cys	p.Y537C	ENST00000206249	NM_000125.3	537	tAt/tGt	8/8	0.578122353163314	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.584474426263109	1		435	313	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0030379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	224	941	1	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.584474426263109	3	FACETS	1	0.989	1	0.651	0.608	0.695	CLONAL	1	TRUE	1	0.584474426263109	3		942	761	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835780	68835781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0030379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	128	413	0	ENST00000261769.5:c.377dup	p.Pro127AlafsTer41	p.P127Afs*41	ENST00000261769	NM_004360.3	124	cgc/cgCc	3/16	0.578122353163314	1	FACETS	0.859	0.787	0.932	0.859	0.787	0.932	CLONAL	1	TRUE	0	0.584474426263109	1		413	361	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238944	5238944	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs946180785	NA	P-0030379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	67	428	0	ENST00000357368.4:c.1835G>A	p.Arg612His	p.R612H	ENST00000357368	NM_002850.3	612	cGc/cAc	13/38	1	2	FACETS	0.666	0.583	0.756	0.666	0.583	0.756	SUBCLONAL	1	TRUE	1	0.584474426263109	2		428	344	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101527	27101528	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCTCCATTCCTGCACTCCAT	novel	NA	P-0030379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	151	496	0	ENST00000324856.7:c.4826_4827insCATTCTCCATTCCTGCACTC	p.Gly1610IlefsTer9	p.G1610Ifs*9	ENST00000324856	NM_006015.4	1603	-/TCTCCATTCCTGCACTCCAT	18/20	1	2	FACETS	0.799	0.732	0.867	0.799	0.732	0.867	SUBCLONAL	1	TRUE	1	0.584474426263109	2		496	647	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46736349	46736349	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	32	326	0	ENST00000371975.4:c.1061A>C	p.Lys354Thr	p.K354T	ENST00000371975	NM_003579.3	354	aAg/aCg	10/18	1	2	FACETS	0.277	0.225	0.336	0.277	0.225	0.336	SUBCLONAL	1	TRUE	1	0.584474426263109	2		326	395	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115927	8115930	+	frameshift_variant	Frame_Shift_Del	DEL	CCAT	CCAT	-	novel	NA	P-0030379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	97	294	0	ENST00000346208.3:c.1276_1279del	p.Ser426AlafsTer48	p.S426Afs*48	ENST00000346208		425	CCATcc/cc	6/6	1	2	FACETS	0.9	0.809	0.994	0.9	0.809	0.994	CLONAL	1	TRUE	1	0.584474426263109	2		294	369	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740636	58740642	+	frameshift_variant	Frame_Shift_Del	DEL	AGATGTC	AGATGTC	-	novel	NA	P-0030379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	112	522	0	ENST00000305921.3:c.1542_1548del	p.Met515LeufsTer5	p.M515Lfs*5	ENST00000305921	NM_003620.3	514	aAGATGTCa/aa	6/6	0.584474426263109	3	FACETS	0.61	0.548	0.675	0.305	0.274	0.338	SUBCLONAL	1	TRUE	1	0.584474426263109	3		522	812	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137500	202137500	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0030379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	129	465	0	ENST00000358485.4:c.727+1G>T		p.X243_splice	ENST00000358485	NM_001080125.1	243			1	2	FACETS	0.846	0.771	0.924	0.846	0.771	0.924	CLONAL	1	TRUE	1	0.584474426263109	2		465	522	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382149	152382149	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	78	296	0	ENST00000206249.3:c.1259G>A	p.Gly420Asp	p.G420D	ENST00000206249	NM_000125.3	420	gGc/gAc	6/8	0.578122353163314	1	FACETS	0.855	0.764	0.948	0.855	0.764	0.948	CLONAL	1	TRUE	0	0.584474426263109	1		296	221	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0030501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	35	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.338250349805224	3	FACETS	0.997	0.849	1	1	0.959	1	CLONAL	3	FALSE	1	0.337732267811901	3		473	81	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0030501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	18	828	0	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	0.338250349805224	3	FACETS	0.789	0.607	0.992	0.789	0.607	0.992	CLONAL	2	FALSE	1	0.337732267811901	3		828	79	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089705	27089706	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1286891446	NA	P-0030658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	94	654	0	ENST00000324856.7:c.2666dup	p.Met890HisfsTer46	p.M890Hfs*46	ENST00000324856	NM_006015.4	887	-/G	8/20	1	2	FACETS	0.838	0.746	0.937	0.838	0.746	0.937	CLONAL	1	TRUE	1	0.310559046356685	2		654	722	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916726	178916726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772110575	NA	P-0030658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	50	500	0	ENST00000263967.3:c.113G>A	p.Arg38His	p.R38H	ENST00000263967	NM_006218.2	38	cGt/cAt	2/21	1	2	FACETS	0.749	0.636	0.872	0.749	0.636	0.872	SUBCLONAL	1	TRUE	1	0.310559046356685	2		500	430	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832852	3832852	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	95	521	0	ENST00000262367.5:c.1406C>A	p.Ser469Tyr	p.S469Y	ENST00000262367	NM_004380.2	469	tCt/tAt	6/31	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.310559046356685	2		521	554	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219414	133219414	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878854876	NA	P-0030658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	85	691	0	ENST00000320574.5:c.4720G>A	p.Ala1574Thr	p.A1574T	ENST00000320574	NM_006231.2	1574	Gcc/Acc	36/49	1	2	FACETS	0.781	0.69	0.878	0.781	0.69	0.878	SUBCLONAL	1	TRUE	1	0.310559046356685	2		691	701	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348283	89348283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781186923	NA	P-0030658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	119	907	1	ENST00000301030.4:c.4667C>T	p.Ala1556Val	p.A1556V	ENST00000301030	NM_001256183.1	1556	gCg/gTg	9/13	1	2	FACETS	0.937	0.845	1	0.937	0.845	1	CLONAL	1	TRUE	1	0.310559046356685	2		908	818	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55729502	55729502	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	131	627	0	ENST00000284073.2:c.770T>C	p.Val257Ala	p.V257A	ENST00000284073	NM_138962.2	257	gTg/gCg	11/14	1	2	FACETS	0.934	0.847	1	0.934	0.847	1	CLONAL	1	TRUE	1	0.310559046356685	2		627	903	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707633	176707633	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	41	573	0	ENST00000439151.2:c.5690G>C	p.Cys1897Ser	p.C1897S	ENST00000439151	NM_022455.4	1897	tGt/tCt	18/23	1	2	FACETS	0.46	0.382	0.546	0.46	0.382	0.546	SUBCLONAL	1	TRUE	1	0.310559046356685	2		573	574	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0030787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	103	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.315820022362762	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.315820022362762	1		473	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0030787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	129	599	1	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.315820022362762	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.315820022362762	1		600	633	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371691	225371691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	147	609	1	ENST00000264414.4:c.913C>T	p.Arg305Cys	p.R305C	ENST00000264414	NM_003590.4	305	Cgt/Tgt	7/16	0.312912907925608	2	FACETS	1	0.949	1	0.528	0.482	0.577	CLONAL	1	TRUE	0	0.315820022362762	2		610	881	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111688	56112072	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGACGCAGCGGGGAGTGGGACCGGCTTCCAGCCTGTGGCGGTGCCGCCGCCCCACGGAGCCGCGAGCCGCGGCGGCGCCCACCTTACCGAGTCGGTGGCGGCGCCGGACAGCGGCGCCTCGAGTCCCGCAGCGGCCGAGCCCGGGGAGAAGCGGGCGCCCGCCGCCGAGCCGTCTCCTGCAGCGGCCCCCGCCGGGTGAGCAGCACGGCCGGGGTCGCGGCGGGGACTTGGAGAGCGGGCAGAGGGCAATGAATGAACCCCGGGCACCATGCACGGCGTCCCGGGGTTCAGCGCAGCGAGGCTACGCGCCGCTCGCCGGGACCTACGCCCCTGAGCACCCCCCGACCCCTTCGGAGTCGGGCGGCGCCCCGGACCCAGCCTGGGG	GGACGCAGCGGGGAGTGGGACCGGCTTCCAGCCTGTGGCGGTGCCGCCGCCCCACGGAGCCGCGAGCCGCGGCGGCGCCCACCTTACCGAGTCGGTGGCGGCGCCGGACAGCGGCGCCTCGAGTCCCGCAGCGGCCGAGCCCGGGGAGAAGCGGGCGCCCGCCGCCGAGCCGTCTCCTGCAGCGGCCCCCGCCGGGTGAGCAGCACGGCCGGGGTCGCGGCGGGGACTTGGAGAGCGGGCAGAGGGCAATGAATGAACCCCGGGCACCATGCACGGCGTCCCGGGGTTCAGCGCAGCGAGGCTACGCGCCGCTCGCCGGGACCTACGCCCCTGAGCACCCCCCGACCCCTTCGGAGTCGGGCGGCGCCCCGGACCCAGCCTGGGG	-	novel	NA	P-0030787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	84	251	0	ENST00000399503.3:c.289_482+191del		p.X97_splice	ENST00000399503	NM_005921.1	97		1/20	0.315820022362762	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.315820022362762	1		251	343	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008973	152008997	+	frameshift_variant	Frame_Shift_Del	DEL	AAGCTGTCTGGGTGCTTACACTTAC	AAGCTGTCTGGGTGCTTACACTTAC	-	novel	NA	P-0030787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	81	447	0	ENST00000262189.6:c.625_649del	p.Val209GlnfsTer44	p.V209Qfs*44	ENST00000262189	NM_170606.2	209	GTAAGTGTAAGCACCCAGACAGCTTca/ca	5/59	1	2	FACETS	0.647	0.569	0.73	0.647	0.569	0.73	SUBCLONAL	1	TRUE	1	0.315820022362762	2		447	793	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604785	48604785	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	328	403	0	ENST00000342988.3:c.1607T>C	p.Leu536Pro	p.L536P	ENST00000342988	NM_005359.5	536	cTa/cCa	12/12	0.887881317154637	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.887881317154637	1		403	396	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11205073	11205073	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	399	543	0	ENST00000361445.4:c.4716T>A	p.Asp1572Glu	p.D1572E	ENST00000361445	NM_004958.3	1572	gaT/gaA	33/58	1	2	FACETS	0.957	0.914	1	0.957	0.914	1	CLONAL	1	TRUE	1	0.887881317154637	2		543	939	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846303	156846319	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCGCCCCCTGCTCAT	GGCCGCCCCCTGCTCAT	-	novel	NA	P-0030794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	540	684	0	ENST00000524377.1:c.1746_1762del	p.Arg583LeufsTer2	p.R583Lfs*2	ENST00000524377	NM_002529.3	582	GGCCGCCCCCTGCTCATg/g	14/17	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.887881317154637	2		684	1216	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909986	100909986	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	233	411	0	ENST00000325455.5:c.2663A>T	p.His888Leu	p.H888L	ENST00000325455	NM_001202474.3	888	cAt/cTt	8/8	0.887881317154637	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.887881317154637	1		411	290	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352452	118352452	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	166	422	0	ENST00000534358.1:c.3657G>C	p.Lys1219Asn	p.K1219N	ENST00000534358	NM_005933.3	1219	aaG/aaC	7/36	NA	2	FACETS	0.509	0.468	0.551			1	INDETERMINATE	1	TRUE	NA	0.887881317154637	2		422	735	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351470	89351470	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	772	492	0	ENST00000301030.4:c.1480G>C	p.Asp494His	p.D494H	ENST00000301030	NM_001256183.1	494	Gac/Cac	9/13	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	2	TRUE	NA	0.887881317154637	2		492	850	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212615386	212615386	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	394	524	0	ENST00000342788.4:c.600del	p.Thr201GlnfsTer8	p.T201Qfs*8	ENST00000342788	NM_005235.2	200	ccC/cc	5/28	0.887881317154637	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.887881317154637	1		524	490	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163784	47163784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1313153861	NA	P-0030794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	161	404	0	ENST00000409792.3:c.2342C>T	p.Thr781Met	p.T781M	ENST00000409792	NM_014159.6	781	aCg/aTg	3/21	0.442453399890542	1	FACETS	0.369	0.341	0.399	0.369	0.341	0.399	INDETERMINATE	1	TRUE	0	0.887881317154637	1		404	546	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700121	117700237	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGAAAATGTTTATTGAAGGAATAAATGAATTTCCATGCATTATCATTTATGACTGACAAGTTTTCTTCTCAATCAATTGCCTTTGAGGGACTCTACTTACCTCTGTCCCCGAAGAA	CAGAAAATGTTTATTGAAGGAATAAATGAATTTCCATGCATTATCATTTATGACTGACAAGTTTTCTTCTCAATCAATTGCCTTTGAGGGACTCTACTTACCTCTGTCCCCGAAGAA	-	novel	NA	P-0030794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	204	93	0	ENST00000368508.3:c.2582_2597+101del		p.X861_splice	ENST00000368508	NM_002944.2	861		17/43	1	2	FACETS	0.861	0.825	0.894	1	0.995	1	CLONAL	2	TRUE	1	0.887881317154637	2		93	267	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412059	63412059	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	403	359	0	ENST00000330258.3:c.1108del	p.Glu370ArgfsTer21	p.E370Rfs*21	ENST00000330258	NM_152424.3	370	Gag/ag	2/2	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.887881317154637	1		359	488	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412463	63412463	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	401	425	1	ENST00000330258.3:c.704C>T	p.Pro235Leu	p.P235L	ENST00000330258	NM_152424.3	235	cCt/cTt	2/2	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.887881317154637	1		426	469	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	97	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.422010750443346	1	FACETS	0.473	0.425	0.524	0.473	0.425	0.524	SUBCLONAL	1	TRUE	0	0.68320749817264	1		473	395	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936995	48936995	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778842	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	121	442	15	ENST00000267163.4:c.763C>T	p.Arg255Ter	p.R255*	ENST00000267163	NM_000321.2	255	Cga/Tga	8/27	0.132576304351444	4	FACETS	1	0.986	1	0.747	0.681	0.815	INDETERMINATE	1	TRUE	2	0.68320749817264	4		457	399	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	136	465	3	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	0.957	0.878	1	0.957	0.878	1	CLONAL	1	TRUE	1	0.68320749817264	2		468	416	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	193	717	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.68320749817264	2		721	552	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1040408	1040408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370272002	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	121	614	0	ENST00000358495.3:c.164G>A	p.Arg55His	p.R55H	ENST00000358495	NM_134424.2	55	cGc/cAc	3/12	NA	2	FACETS	0.845	0.77	0.923			1	INDETERMINATE	1	TRUE	NA	0.68320749817264	2		614	419	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	119	572	2	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.68320749817264	2		574	346	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	59	182	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.881	0.771	0.997	0.881	0.771	0.997	CLONAL	1	TRUE	1	0.68320749817264	2		182	196	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133805	55133805	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376626935	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	71	556	1	ENST00000257290.5:c.1018C>T	p.Arg340Trp	p.R340W	ENST00000257290	NM_006206.4	340	Cgg/Tgg	7/23	0.183879547422862	1	FACETS	0.568	0.502	0.636	0.568	0.502	0.636	INDETERMINATE	1	TRUE	0	0.68320749817264	1		557	241	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	70	356	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.676	0.595	0.763	0.676	0.595	0.763	SUBCLONAL	1	TRUE	1	0.68320749817264	2		356	303	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781467	135781467	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203537	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	26	612	1	ENST00000298552.3:c.1498C>T	p.Arg500Ter	p.R500*	ENST00000298552	NM_001162426.1	500	Cga/Tga	15/23	0.410530460743934	3	FACETS	0.242	0.191	0.3	0.081	0.063	0.1	SUBCLONAL	1	TRUE	0	0.68320749817264	3		613	422	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931452	131931452	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507178	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	82	464	18	ENST00000265335.6:c.2165del	p.Lys722ArgfsTer14	p.K722Rfs*14	ENST00000265335		719	ctA/ct	13/25	0.68320749817264	1	FACETS	0.841	0.759	0.924	0.841	0.759	0.924	CLONAL	1	TRUE	0	0.68320749817264	1		482	188	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027168	49027168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913305	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	129	630	1	ENST00000267163.4:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	579	Cga/Tga	18/27	0.132576304351444	4	FACETS	0.88	0.808	0.955	0.88	0.808	0.955	INDETERMINATE	2	TRUE	2	0.68320749817264	4		631	361	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41526008	41526008	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	113	545	1	ENST00000263253.7:c.1282+1G>A		p.X428_splice	ENST00000263253	NM_001429.3	428			1	2	FACETS	0.999	0.91	1	0.999	0.91	1	CLONAL	1	TRUE	1	0.68320749817264	2		546	331	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835781	68835781	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060501215	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	230	612	2	ENST00000261769.5:c.377del	p.Pro126ArgfsTer89	p.P126Rfs*89	ENST00000261769	NM_004360.3	124	cgC/cg	3/16	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.68320749817264	2		614	624	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533938	63533939	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	108	474	0	ENST00000307078.5:c.1214_1215dup	p.Gly406ArgfsTer53	p.G406Rfs*53	ENST00000307078	NM_004655.3	405	-/AG	6/11	1	2	FACETS	0.779	0.704	0.856	0.779	0.704	0.856	SUBCLONAL	1	TRUE	1	0.68320749817264	2		474	406	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413100	139413100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201236538	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	467	661	0	ENST00000277541.6:c.1042G>A	p.Ala348Thr	p.A348T	ENST00000277541	NM_017617.3	348	Gcc/Acc	6/34	0.410530460743934	3	FACETS	1	0.996	1	0.832	0.804	0.859	CLONAL	2	TRUE	0	0.68320749817264	3		661	735	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495016	56495016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776728303	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	232	653	1	ENST00000267101.3:c.3373C>T	p.Arg1125Trp	p.R1125W	ENST00000267101	NM_001982.3	1125	Cgg/Tgg	27/28	0.35251935439234	4	FACETS	0.799	0.749	0.851	0.799	0.749	0.851	INDETERMINATE	2	TRUE	2	0.68320749817264	4		654	715	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916526	39916526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265777184	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	210	719	0	ENST00000378444.4:c.4477C>T	p.Arg1493Trp	p.R1493W	ENST00000378444	NM_001123385.1	1493	Cgg/Tgg	11/15	0.422010750443346	1	FACETS	0.684	0.639	0.729	0.684	0.639	0.729	SUBCLONAL	1	TRUE	0	0.68320749817264	1		719	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	206	719	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			1	2	FACETS	0.998	0.932	1	0.998	0.932	1	CLONAL	1	TRUE	1	0.68320749817264	2		719	604	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953040	2953040	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141751925	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	167	716	0	ENST00000396946.4:c.2900G>A	p.Arg967His	p.R967H	ENST00000396946	NM_032415.4	967	cGc/cAc	22/25	1	2	FACETS	0.843	0.779	0.909	0.843	0.779	0.909	CLONAL	1	TRUE	1	0.68320749817264	2		716	580	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40497641	40497641	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1417279405	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	199	507	1	ENST00000264657.5:c.308G>A	p.Arg103Gln	p.R103Q	ENST00000264657	NM_139276.2	103	cGg/cAg	4/24	1	2	FACETS	0.876	0.815	0.939	0.876	0.815	0.939	CLONAL	1	TRUE	1	0.68320749817264	2		508	665	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863593	68863593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777078601	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	222	665	0	ENST00000261769.5:c.2332G>A	p.Ala778Thr	p.A778T	ENST00000261769	NM_004360.3	778	Gct/Act	15/16	1	2	FACETS	0.875	0.817	0.934	0.875	0.817	0.934	CLONAL	1	TRUE	1	0.68320749817264	2		665	743	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88676897	88676897	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782682	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	142	544	0	ENST00000372037.3:c.682C>T	p.Arg228Ter	p.R228*	ENST00000372037	NM_004329.2	228	Cga/Tga	9/13	0.68320749817264	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.68320749817264	1		544	233	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016182	31016182	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144437064	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	128	591	1	ENST00000375687.4:c.428G>A	p.Arg143Gln	p.R143Q	ENST00000375687	NM_015338.5	143	cGa/cAa	6/13	1	2	FACETS	0.966	0.884	1	0.966	0.884	1	CLONAL	1	TRUE	1	0.68320749817264	2		592	388	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033781	48033781	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs184131049	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	65	465	1	ENST00000234420.5:c.3992G>A	p.Arg1331Gln	p.R1331Q	ENST00000234420	NM_000179.2	1331	cGa/cAa	9/10	1	2	FACETS	0.91	0.802	1	0.91	0.802	1	CLONAL	1	TRUE	1	0.68320749817264	2		466	209	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152566	56152566	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	73	450	0	ENST00000399503.3:c.622C>T	p.Arg208Ter	p.R208*	ENST00000399503	NM_005921.1	208	Cga/Tga	2/20	1	2	FACETS	0.715	0.631	0.803	0.715	0.631	0.803	SUBCLONAL	1	TRUE	1	0.68320749817264	2		450	299	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509432	106509432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs567756361	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	120	639	1	ENST00000359195.3:c.1426C>T	p.Arg476Cys	p.R476C	ENST00000359195	NM_002649.2	476	Cgc/Tgc	2/11	1	2	FACETS	0.754	0.685	0.826	0.754	0.685	0.826	SUBCLONAL	1	TRUE	1	0.68320749817264	2		640	466	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354055	15354055	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765227557	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	86	479	0	ENST00000263377.2:c.2825C>T	p.Thr942Met	p.T942M	ENST00000263377	NM_058243.2	942	aCg/aTg	14/20	1	2	FACETS	0.856	0.766	0.95	0.856	0.766	0.95	CLONAL	1	TRUE	1	0.68320749817264	2		479	294	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815761	32815761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755212442	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	207	612	0	ENST00000354258.4:c.1855G>A	p.Gly619Arg	p.G619R	ENST00000354258	NM_000593.5	619	Ggg/Agg	8/11	0.163717507887349	5	FACETS	0.968	0.903	1	0.645	0.602	0.689	INDETERMINATE	2	TRUE	2	0.68320749817264	5		612	634	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405126	139405126	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757628476	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	380	665	1	ENST00000277541.6:c.2719G>A	p.Asp907Asn	p.D907N	ENST00000277541	NM_017617.3	907	Gac/Aac	17/34	0.410530460743934	3	FACETS	1	0.991	1	0.744	0.713	0.773	CLONAL	2	TRUE	0	0.68320749817264	3		666	669	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046617	30046617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149150061	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	104	614	0	ENST00000331968.5:c.2566G>A	p.Gly856Arg	p.G856R	ENST00000331968	NM_002742.2	856	Ggg/Agg	18/18	0.422010750443346	1	FACETS	0.6	0.543	0.659	0.6	0.543	0.659	SUBCLONAL	1	TRUE	0	0.68320749817264	1		614	334	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164101	108164101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781712	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	74	421	1	ENST00000278616.4:c.4673C>T	p.Thr1558Met	p.T1558M	ENST00000278616	NM_000051.3	1558	aCg/aTg	31/63	1	2	FACETS	0.863	0.766	0.965	0.863	0.766	0.965	CLONAL	1	TRUE	1	0.68320749817264	2		422	251	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838097	89838097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200284845	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	162	523	0	ENST00000389301.3:c.2140C>T	p.Arg714Trp	p.R714W	ENST00000389301	NM_000135.2	714	Cgg/Tgg	23/43	1	2	FACETS	0.926	0.856	0.999	0.926	0.856	0.999	CLONAL	1	TRUE	1	0.68320749817264	2		523	512	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134255	41134255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs994659376	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	97	501	0	ENST00000379561.5:c.1373C>T	p.Ala458Val	p.A458V	ENST00000379561	NM_002015.3	458	gCg/gTg	2/3	0.132576304351444	4	FACETS	0.768	0.693	0.846	0.768	0.693	0.846	INDETERMINATE	2	TRUE	2	0.68320749817264	4		501	311	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263929	16263929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	173	838	1	ENST00000375759.3:c.10298C>T	p.Ser3433Phe	p.S3433F	ENST00000375759	NM_015001.2	3433	tCc/tTc	12/15	1	2	FACETS	0.857	0.793	0.923	0.857	0.793	0.923	CLONAL	1	TRUE	1	0.68320749817264	2		839	591	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162722894	162722894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1340393535	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	118	587	0	ENST00000367921.3:c.92G>A	p.Arg31His	p.R31H	ENST00000367921	NM_006182.2	31	cGc/cAc	4/18	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.68320749817264	2		587	327	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8105994	8105994	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	157	535	0	ENST00000346208.3:c.814C>A	p.Pro272Thr	p.P272T	ENST00000346208		272	Cca/Aca	4/6	1	2	FACETS	0.919	0.848	0.992	0.919	0.848	0.992	CLONAL	1	TRUE	1	0.68320749817264	2		535	500	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14303236	14303236	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782047286	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	82	676	0	ENST00000256196.4:c.439C>T	p.Arg147Trp	p.R147W	ENST00000256196		147	Cgg/Tgg	5/6	1	2	FACETS	0.842	0.751	0.937	0.842	0.751	0.937	CLONAL	1	TRUE	1	0.68320749817264	2		676	285	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948545	71948545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138596491	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	156	682	3	ENST00000298229.2:c.3257G>A	p.Arg1086His	p.R1086H	ENST00000298229	NM_001567.3	1086	cGt/cAt	26/28	1	2	FACETS	0.94	0.867	1	0.94	0.867	1	CLONAL	1	TRUE	1	0.68320749817264	2		685	486	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106477	108106477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150661813	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	66	491	0	ENST00000278616.4:c.412G>A	p.Gly138Arg	p.G138R	ENST00000278616	NM_000051.3	138	Gga/Aga	5/63	1	2	FACETS	0.866	0.763	0.975	0.866	0.763	0.975	CLONAL	1	TRUE	1	0.68320749817264	2		491	223	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121543	108121543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201719927	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	27	582	1	ENST00000278616.4:c.1351C>T	p.Arg451Cys	p.R451C	ENST00000278616	NM_000051.3	451	Cgt/Tgt	10/63	1	2	FACETS	0.228	0.181	0.281	0.228	0.181	0.281	SUBCLONAL	1	TRUE	1	0.68320749817264	2		583	347	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699306	18699306	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	93	493	0	ENST00000266497.5:c.3407A>G	p.Tyr1136Cys	p.Y1136C	ENST00000266497		1136	tAt/tGt	24/31	0.422010750443346	1	FACETS	0.862	0.784	0.941	0.862	0.784	0.941	CLONAL	1	TRUE	0	0.68320749817264	1		493	208	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420091	49420091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770413324	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	211	602	0	ENST00000301067.7:c.15658C>T	p.Arg5220Cys	p.R5220C	ENST00000301067	NM_003482.3	5220	Cgc/Tgc	48/54	0.35251935439234	4	FACETS	0.887	0.83	0.946	0.887	0.83	0.946	INDETERMINATE	2	TRUE	2	0.68320749817264	4		602	586	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562807	21562807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777111663	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	96	364	1	ENST00000382592.4:c.1112C>T	p.Pro371Leu	p.P371L	ENST00000382592	NM_014572.2	371	cCg/cTg	4/8	0.132576304351444	4	FACETS	1	0.98	1	0.708	0.637	0.782	INDETERMINATE	1	TRUE	2	0.68320749817264	4		365	334	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336167	73336167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs541536936	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	75	410	0	ENST00000377767.4:c.2236C>T	p.Arg746Cys	p.R746C	ENST00000377767	NM_014953.3	746	Cgc/Tgc	17/21	0.132576304351444	4	FACETS	0.776	0.69	0.866	0.776	0.69	0.866	INDETERMINATE	2	TRUE	2	0.68320749817264	4		410	238	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436278	110436278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	35	143	0	ENST00000375856.3:c.2123C>T	p.Ala708Val	p.A708V	ENST00000375856	NM_003749.2	708	gCg/gTg	1/2	0.132576304351444	4	FACETS	1	0.95	1	0.707	0.592	0.83	INDETERMINATE	1	TRUE	2	0.68320749817264	4		143	122	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630705	90630705	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	164	678	0	ENST00000330062.3:c.781C>T	p.Arg261Cys	p.R261C	ENST00000330062	NM_002168.2	261	Cgt/Tgt	6/11	0.68320749817264	1	FACETS	0.847	0.789	0.906	0.847	0.789	0.906	CLONAL	1	TRUE	0	0.68320749817264	1		678	373	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993837	72993837	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1373994234	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	93	512	0	ENST00000268489.5:c.208C>G	p.Pro70Ala	p.P70A	ENST00000268489	NM_006885.3	70	Ccc/Gcc	2/10	1	2	FACETS	0.878	0.79	0.97	0.878	0.79	0.97	CLONAL	1	TRUE	1	0.68320749817264	2		512	310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577497	7577497	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	144	579	0	ENST00000269305.4:c.782+2T>C		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	0.765	0.701	0.831	0.765	0.701	0.831	SUBCLONAL	1	TRUE	1	0.68320749817264	2		579	551	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562993	29562993	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	123	624	0	ENST00000356175.3:c.3928A>G	p.Thr1310Ala	p.T1310A	ENST00000356175	NM_000267.3	1310	Aca/Gca	29/57	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.68320749817264	2		624	348	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673694	37673694	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	139	566	2	ENST00000447079.4:c.2848C>T	p.Arg950Ter	p.R950*	ENST00000447079	NM_015083.1	950	Cga/Tga	10/14	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.68320749817264	2		568	392	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532643	63532644	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	197	668	0	ENST00000307078.5:c.1935dup	p.Glu647GlyfsTer60	p.E647Gfs*60	ENST00000307078	NM_004655.3	645	-/C	8/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.68320749817264	2		668	557	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526480	66526480	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	132	522	0	ENST00000358598.2:c.1036A>G	p.Lys346Glu	p.K346E	ENST00000358598	NM_212471.2	346	Aag/Gag	11/11	1	2	FACETS	0.705	0.643	0.77	0.705	0.643	0.77	SUBCLONAL	1	TRUE	1	0.68320749817264	2		522	548	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10264977	10264977	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1486893166	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	139	350	1	ENST00000340748.4:c.1963G>A	p.Val655Ile	p.V655I	ENST00000340748		655	Gtc/Atc	21/40	1	2	FACETS	0.976	0.897	1	0.976	0.897	1	CLONAL	1	TRUE	1	0.68320749817264	2		351	417	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292520	15292520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	132	683	2	ENST00000263388.2:c.2659G>A	p.Asp887Asn	p.D887N	ENST00000263388	NM_000435.2	887	Gat/Aat	17/33	1	2	FACETS	0.793	0.725	0.865	0.793	0.725	0.865	SUBCLONAL	1	TRUE	1	0.68320749817264	2		685	487	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953941	17953941	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	147	719	0	ENST00000458235.1:c.461T>C	p.Leu154Pro	p.L154P	ENST00000458235	NM_000215.3	154	cTc/cCc	5/24	1	2	FACETS	0.849	0.78	0.92	0.849	0.78	0.92	CLONAL	1	TRUE	1	0.68320749817264	2		719	507	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228761	36228761	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	151	669	3	ENST00000222270.7:c.7660C>T	p.Arg2554Cys	p.R2554C	ENST00000222270	NM_014727.1	2554	Cgt/Tgt	35/37	1	2	FACETS	0.857	0.788	0.927	0.857	0.788	0.927	CLONAL	1	TRUE	1	0.68320749817264	2		672	516	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027730	48027730	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	79	485	0	ENST00000234420.5:c.2611del	p.Ile871LeufsTer2	p.I871Lfs*2	ENST00000234420	NM_000179.2	870	Aaa/aa	4/10	1	2	FACETS	0.918	0.819	1	0.918	0.819	1	CLONAL	1	TRUE	1	0.68320749817264	2		485	252	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440168	220440168	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757864159	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	199	705	0	ENST00000243786.2:c.1021C>T	p.Arg341Cys	p.R341C	ENST00000243786	NM_002191.3	341	Cgc/Tgc	2/2	0.183879547422862	1	FACETS	0.758	0.709	0.808	0.758	0.709	0.808	INDETERMINATE	1	TRUE	0	0.68320749817264	1		705	506	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419867	41419867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1569159161	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	187	566	2	ENST00000373198.4:c.454G>A	p.Ala152Thr	p.A152T	ENST00000373198	NM_133170.3	152	Gcc/Acc	3/32	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.68320749817264	2		568	454	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162450	47162450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	66	551	0	ENST00000409792.3:c.3676C>T	p.Pro1226Ser	p.P1226S	ENST00000409792	NM_014159.6	1226	Cca/Tca	3/21	1	2	FACETS	0.752	0.66	0.849	0.752	0.66	0.849	SUBCLONAL	1	TRUE	1	0.68320749817264	2		551	257	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928957	49928957	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	192	742	0	ENST00000296474.3:c.3409G>T	p.Gly1137Cys	p.G1137C	ENST00000296474	NM_002447.2	1137	Ggc/Tgc	16/20	1	2	FACETS	0.877	0.815	0.941	0.877	0.815	0.941	CLONAL	1	TRUE	1	0.68320749817264	2		742	641	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670226	134670226	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	97	589	0	ENST00000398015.3:c.137G>A	p.Ser46Asn	p.S46N	ENST00000398015	NM_004441.4	46	aGt/aAt	3/16	1	2	FACETS	0.956	0.863	1	0.956	0.863	1	CLONAL	1	TRUE	1	0.68320749817264	2		589	297	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948256	31948256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373414495	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	132	679	0	ENST00000375333.2:c.844G>A	p.Val282Ile	p.V282I	ENST00000375333	NM_032454.1	282	Gtc/Atc	6/8	0.163717507887349	5	FACETS	0.795	0.726	0.867	0.53	0.484	0.578	INDETERMINATE	2	TRUE	2	0.68320749817264	5		679	492	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32802939	32802939	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140532996	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	110	423	0	ENST00000374899.4:c.937C>T	p.Arg313Cys	p.R313C	ENST00000374899	NM_018833.2	313	Cgc/Tgc	5/12	0.163717507887349	5	FACETS	0.988	0.898	1	0.659	0.599	0.72	INDETERMINATE	2	TRUE	2	0.68320749817264	5		423	330	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845381	151845381	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1483473593	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	164	692	2	ENST00000262189.6:c.13631G>A	p.Arg4544Gln	p.R4544Q	ENST00000262189	NM_170606.2	4544	cGg/cAg	52/59	1	2	FACETS	0.956	0.885	1	0.956	0.885	1	CLONAL	1	TRUE	1	0.68320749817264	2		694	502	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949770	151949770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377571241	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	95	514	2	ENST00000262189.6:c.1330C>T	p.Arg444Trp	p.R444W	ENST00000262189	NM_170606.2	444	Cgg/Tgg	10/59	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.68320749817264	2		516	270	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737370	145737370	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs34236392	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	168	762	2	ENST00000428558.2:c.3317G>A	p.Arg1106His	p.R1106H	ENST00000428558	NM_004260.3	1106	cGc/cAc	20/22	1	2	FACETS	0.889	0.822	0.958	0.889	0.822	0.958	CLONAL	1	TRUE	1	0.68320749817264	2		764	553	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738378	133738378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772834697	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	323	563	0	ENST00000318560.5:c.778G>A	p.Val260Met	p.V260M	ENST00000318560	NM_005157.4	260	Gtg/Atg	4/11	0.410530460743934	3	FACETS	1	0.99	1	0.742	0.709	0.774	CLONAL	2	TRUE	0	0.68320749817264	3		563	570	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564444	139564444	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749488982	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	326	708	0	ENST00000308874.7:c.392G>A	p.Gly131Asp	p.G131D	ENST00000308874		131	gGt/gAt	6/10	0.410530460743934	3	FACETS	1	0.993	1	0.804	0.77	0.837	CLONAL	2	TRUE	0	0.68320749817264	3		708	531	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412118	63412118	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	87	832	0	ENST00000330258.3:c.1049G>A	p.Arg350Lys	p.R350K	ENST00000330258	NM_152424.3	350	aGa/aAa	2/2	0.422010750443346	1	FACETS	0.39	0.347	0.436	0.39	0.347	0.436	SUBCLONAL	1	TRUE	0	0.68320749817264	1		832	430	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0030937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	125	832	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.237802392239722	1	FACETS	0.896	0.81	0.987	0.896	0.81	0.987	CLONAL	1	TRUE	0	0.260833752529884	1		834	930	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692849	89692849	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554898097	NA	P-0030937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	40	198	1	ENST00000371953.3:c.333G>A	p.Trp111Ter	p.W111*	ENST00000371953	NM_000314.4	111	tgG/tgA	5/9	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.260833752529884	2		199	278	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65300252	65300252	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	30	387	0	ENST00000342505.4:c.3458T>C	p.Leu1153Ser	p.L1153S	ENST00000342505	NM_002227.2	1153	tTa/tCa	25/25	1	2	FACETS	0.44	0.353	0.538	0.44	0.353	0.538	SUBCLONAL	1	TRUE	1	0.260833752529884	2		387	523	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442492	52442492	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	109	577	0	ENST00000460680.1:c.253C>A	p.Gln85Lys	p.Q85K	ENST00000460680	NM_004656.3	85	Cag/Aag	4/17	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.260833752529884	2		577	773	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980324	55980324	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	103	622	0	ENST00000263923.4:c.767T>C	p.Ile256Thr	p.I256T	ENST00000263923	NM_002253.2	256	aTt/aCt	6/30	0.260833752529884	1	FACETS	0.894	0.8	0.994	0.894	0.8	0.994	CLONAL	1	TRUE	0	0.260833752529884	1		622	768	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430574	80430574	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	96	428	0	ENST00000286548.4:c.434A>G	p.Tyr145Cys	p.Y145C	ENST00000286548	NM_002072.3	145	tAt/tGt	3/7	0.147450327781974	3	FACETS	0.789	0.706	0.878	0.789	0.706	0.878	INDETERMINATE	2	TRUE	1	0.260833752529884	3		428	527	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577522	7577522	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567549129	NA	P-0031018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	76	562	0	ENST00000269305.4:c.759del	p.Ile254SerfsTer91	p.I254Sfs*91	ENST00000269305	NM_001126112.2	253	acC/ac	7/11	0.23801165027549	2	FACETS	0.968	0.861	1	0.968	0.861	1	CLONAL	2	FALSE	0	0.315438070445933	2		562	249	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254926	16254926	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	48	530	0	ENST00000375759.3:c.2191T>A	p.Leu731Met	p.L731M	ENST00000375759	NM_015001.2	731	Ttg/Atg	11/15	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	FALSE	1	0.315438070445933	2		530	286	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518171	103518171	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	32	345	0	ENST00000355739.4:c.2109C>G	p.Asp703Glu	p.D703E	ENST00000355739	NM_000123.3	703	gaC/gaG	9/15	0.315438070445933	3	FACETS	0.833	0.687	0.992	0.833	0.687	0.992	CLONAL	2	FALSE	1	0.315438070445933	3		345	141	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411030	63411030	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031129-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	66	325	0	ENST00000330258.3:c.2137G>C	p.Asp713His	p.D713H	ENST00000330258	NM_152424.3	713	Gat/Cat	2/2	0.107567756298782	2	FACETS	1	0.938	1			1	INDETERMINATE	1	TRUE	NA	0.477173925670474	2		325	249	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844177	156844177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031129-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	278	699	0	ENST00000524377.1:c.1180T>A	p.Ser394Thr	p.S394T	ENST00000524377	NM_002529.3	394	Tcc/Acc	9/17	0.383587309049387	3	FACETS	0.965	0.911	1	0.965	0.911	1	CLONAL	2	TRUE	1	0.477173925670474	3		699	748	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347911	73347911	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031129-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	27	276	0	ENST00000377767.4:c.1150C>A	p.Arg384Ser	p.R384S	ENST00000377767	NM_014953.3	384	Cgc/Agc	8/21	1	2	FACETS	0.589	0.472	0.721	0.589	0.472	0.721	SUBCLONAL	1	TRUE	1	0.477173925670474	2		276	192	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576809	212576809	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031129-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	52	486	0	ENST00000342788.4:c.1090G>C	p.Gly364Arg	p.G364R	ENST00000342788	NM_005235.2	364	Ggg/Cgg	9/28	0.477173925670474	1	FACETS	0.572	0.49	0.661	0.572	0.49	0.661	SUBCLONAL	1	TRUE	0	0.477173925670474	1		486	290	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	171	717	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.93	0.855	1	0.93	0.855	1	CLONAL	1	TRUE	1	0.403743512556302	2		721	911	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	246	801	5	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	0.403743512556302	2		806	1197	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	223	634	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.403743512556302	1	FACETS	0.949	0.884	1	0.949	0.884	1	CLONAL	1	TRUE	0	0.403743512556302	1		635	929	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455151	50455151	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446212014	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	134	413	1	ENST00000331340.3:c.698C>T	p.Pro233Leu	p.P233L	ENST00000331340	NM_006060.4	233	cCg/cTg	6/8	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.403743512556302	2		414	624	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	175	613	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.884	0.813	0.957	0.884	0.813	0.957	CLONAL	1	TRUE	1	0.403743512556302	2		613	981	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	164	701	5	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.968	0.89	1	0.968	0.89	1	CLONAL	1	TRUE	1	0.403743512556302	2		706	839	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	155	533	3	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.403743512556302	2		536	727	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	157	637	0	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	NA	2	FACETS	0.947	0.868	1			1	INDETERMINATE	1	TRUE	NA	0.403743512556302	2		637	821	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553478	29553478	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781807	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	173	599	0	ENST00000356175.3:c.2033del	p.Pro678ArgfsTer10	p.P678Rfs*10	ENST00000356175	NM_000267.3	676	aCc/ac	18/57	1	2	FACETS	0.86	0.791	0.931	0.86	0.791	0.931	CLONAL	1	TRUE	1	0.403743512556302	2		599	997	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	191	483	14	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.971	0.898	1	0.971	0.898	1	CLONAL	1	TRUE	1	0.403743512556302	2		497	974	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924551	131924551	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	219	624	0	ENST00000265335.6:c.1228del	p.Thr410LeufsTer5	p.T410Lfs*5	ENST00000265335		408	gcA/gc	8/25	0.214339065368861	1	FACETS	0.979	0.912	1	0.979	0.912	1	INDETERMINATE	1	TRUE	0	0.403743512556302	1		624	884	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974770	21974775	+	inframe_deletion	In_Frame_Del	DEL	GGCCGT	GGCCGT	-	novel	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	66	220	0	ENST00000304494.5:c.52_57del	p.Thr18_Ala19del	p.T18_A19del	ENST00000304494	NM_000077.4	18	ACGGCC/-	1/3	0.403743512556302	1	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	0	0.403743512556302	1		220	253	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759623	133759623	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	131	791	0	ENST00000318560.5:c.1950del	p.Leu651TrpfsTer43	p.L651Wfs*43	ENST00000318560	NM_005157.4	649	aCc/ac	11/11	1	2	FACETS	0.754	0.684	0.827	0.754	0.684	0.827	SUBCLONAL	1	TRUE	1	0.403743512556302	2		791	861	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458147	120458147	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1325403451	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	199	722	0	ENST00000256646.2:c.7198C>T	p.Arg2400Ter	p.R2400*	ENST00000256646	NM_024408.3	2400	Cga/Tga	34/34	1	2	FACETS	0.968	0.897	1	0.968	0.897	1	CLONAL	1	TRUE	1	0.403743512556302	2		722	1018	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021211	31021211	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs373145711	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	229	637	1	ENST00000375687.4:c.1210C>T	p.Arg404Ter	p.R404*	ENST00000375687	NM_015338.5	404	Cga/Tga	12/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.403743512556302	2		638	1074	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486050	29486050	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1438566555	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	106	526	1	ENST00000356175.3:c.233del	p.Asn78IlefsTer7	p.N78Ifs*7	ENST00000356175	NM_000267.3	76	gAa/ga	3/57	1	2	FACETS	0.902	0.811	0.998	0.902	0.811	0.998	CLONAL	1	TRUE	1	0.403743512556302	2		527	582	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66679734	66679734	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	171	559	1	ENST00000307102.5:c.49G>T	p.Gly17Cys	p.G17C	ENST00000307102	NM_002755.3	17	Ggc/Tgc	1/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.403743512556302	2		560	749	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732956	74732956	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	93	364	0	ENST00000359995.5:c.287del	p.Pro96ArgfsTer136	p.P96Rfs*136	ENST00000359995	NM_001195427.1	96	cCg/cg	1/3	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.403743512556302	2		364	452	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564569	41564569	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	231	682	1	ENST00000263253.7:c.3994del	p.Thr1332ProfsTer4	p.T1332Pfs*4	ENST00000263253	NM_001429.3	1331	Aaa/aa	24/31	1	2	FACETS	0.976	0.909	1	0.976	0.909	1	CLONAL	1	TRUE	1	0.403743512556302	2		683	1172	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421039	49421039	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398123721	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	153	578	1	ENST00000301067.7:c.14710C>T	p.Arg4904Ter	p.R4904*	ENST00000301067	NM_003482.3	4904	Cga/Tga	48/54	1	2	FACETS	0.949	0.869	1	0.949	0.869	1	CLONAL	1	TRUE	1	0.403743512556302	2		579	799	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574030	7574030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769934890	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	197	604	1	ENST00000269305.4:c.997C>T	p.Arg333Cys	p.R333C	ENST00000269305	NM_001126112.2	333	Cgt/Tgt	10/11	0.403743512556302	1	FACETS	0.97	0.9	1	0.97	0.9	1	CLONAL	1	TRUE	0	0.403743512556302	1		605	803	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657050	215657050	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781591	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	179	550	0	ENST00000260947.4:c.335G>A	p.Arg112Gln	p.R112Q	ENST00000260947	NM_000465.2	112	cGa/cAa	3/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.403743512556302	2		550	834	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1627411	1627411	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377688933	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	223	715	1	ENST00000344749.5:c.313C>T	p.Arg105Trp	p.R105W	ENST00000344749	NM_001136139.2	105	Cgg/Tgg	6/19	1	2	FACETS	0.969	0.901	1	0.969	0.901	1	CLONAL	1	TRUE	1	0.403743512556302	2		716	1140	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847252	68847252	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141864044	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	67	617	1	ENST00000261769.5:c.1174G>A	p.Val392Ile	p.V392I	ENST00000261769	NM_004360.3	392	Gta/Ata	9/16	1	2	FACETS	0.313	0.27	0.358	0.313	0.27	0.358	SUBCLONAL	1	TRUE	1	0.403743512556302	2		618	1062	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063694	67063702	+	inframe_deletion	In_Frame_Del	DEL	GCCGCGACG	GCCGCGACG	-	novel	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	113	425	0	ENST00000412916.2:c.148_156del	p.Asp50_Arg52del	p.D50_R52del	ENST00000412916		48	tGCCGCGACGgc/tgc	2/6	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.403743512556302	2		425	558	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352586	118352586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782683534	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	226	612	0	ENST00000534358.1:c.3791G>A	p.Arg1264Gln	p.R1264Q	ENST00000534358	NM_005933.3	1264	cGa/cAa	7/36	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.403743512556302	2		612	1102	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420628	49420628	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	183	653	1	ENST00000301067.7:c.15121G>A	p.Gly5041Arg	p.G5041R	ENST00000301067	NM_003482.3	5041	Ggg/Agg	48/54	1	2	FACETS	0.956	0.882	1	0.956	0.882	1	CLONAL	1	TRUE	1	0.403743512556302	2		654	948	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424113	49424114	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	222	786	0	ENST00000301067.7:c.13948dup	p.Glu4650GlyfsTer12	p.E4650Gfs*12	ENST00000301067	NM_003482.3	4650	gag/gGag	42/54	1	2	FACETS	0.993	0.923	1	0.993	0.923	1	CLONAL	1	TRUE	1	0.403743512556302	2		786	1108	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447009	49447009	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750484458	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	177	561	1	ENST00000301067.7:c.935C>T	p.Ala312Val	p.A312V	ENST00000301067	NM_003482.3	312	gCt/gTt	7/54	1	2	FACETS	0.999	0.921	1	0.999	0.921	1	CLONAL	1	TRUE	1	0.403743512556302	2		562	878	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131764	2131764	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776738338	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	226	740	0	ENST00000219476.3:c.3779C>T	p.Thr1260Met	p.T1260M	ENST00000219476	NM_000548.3	1260	aCg/aTg	31/42	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.403743512556302	2		740	1065	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16041476	16041476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1391290639	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	160	474	0	ENST00000268712.3:c.1403G>A	p.Arg468Lys	p.R468K	ENST00000268712	NM_006311.3	468	aGg/aAg	13/46	0.403743512556302	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.403743512556302	1		474	597	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127376	17127376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	232	827	0	ENST00000285071.4:c.478G>A	p.Asp160Asn	p.D160N	ENST00000285071	NM_144997.5	160	Gac/Aac	6/14	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.403743512556302	2		827	1129	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117712	70117714	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs778226772	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	199	792	0	ENST00000245479.2:c.184_186del	p.Lys62del	p.K62del	ENST00000245479	NM_000346.3	60	ctGAAg/ctg	1/3	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.403743512556302	2		792	964	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350513	15350513	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	202	708	1	ENST00000263377.2:c.3402del	p.Lys1135SerfsTer18	p.K1135Sfs*18	ENST00000263377	NM_058243.2	1134	ccC/cc	16/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.403743512556302	2		709	860	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416692	29416692	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	171	485	0	ENST00000389048.3:c.4261del	p.Val1421PhefsTer56	p.V1421Ffs*56	ENST00000389048	NM_004304.4	1421	Gtt/tt	29/29	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.403743512556302	2		485	738	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39251160	39251160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	190	566	1	ENST00000402219.2:c.1193G>A	p.Arg398Gln	p.R398Q	ENST00000402219	NM_005633.3	398	cGa/cAa	9/23	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.403743512556302	2		567	858	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209110063	209110063	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	195	649	0	ENST00000345146.2:c.500A>G	p.Tyr167Cys	p.Y167C	ENST00000345146	NM_005896.2	167	tAc/tGc	5/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.403743512556302	2		649	874	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569645	41569645	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	113	379	0	ENST00000263253.7:c.4640del	p.Asn1547MetfsTer17	p.N1547Mfs*17	ENST00000263253	NM_001429.3	1546	Aaa/aa	29/31	1	2	FACETS	0.91	0.821	1	0.91	0.821	1	CLONAL	1	TRUE	1	0.403743512556302	2		379	615	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244085	153244085	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	166	531	0	ENST00000281708.4:c.2072G>T	p.Gly691Val	p.G691V	ENST00000281708	NM_033632.3	691	gGg/gTg	12/12	1	2	FACETS	0.874	0.802	0.948	0.874	0.802	0.948	CLONAL	1	TRUE	1	0.403743512556302	2		531	941	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673346	30673346	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	308	860	2	ENST00000376406.3:c.3614C>T	p.Thr1205Ile	p.T1205I	ENST00000376406	NM_014641.2	1205	aCa/aTa	10/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.403743512556302	2		862	1330	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954958	2954958	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	248	663	1	ENST00000396946.4:c.2752C>T	p.Arg918Trp	p.R918W	ENST00000396946	NM_032415.4	918	Cgg/Tgg	21/25	0.188186890232063	5	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.403743512556302	5		664	1441	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042182	6042182	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	184	596	0	ENST00000265849.7:c.439A>G	p.Thr147Ala	p.T147A	ENST00000265849	NM_000535.5	147	Acc/Gcc	5/15	0.188186890232063	5	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.403743512556302	5		596	1155	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877018	151877018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	171	523	0	ENST00000262189.6:c.7343C>T	p.Ala2448Val	p.A2448V	ENST00000262189	NM_170606.2	2448	gCc/gTc	37/59	0.403743512556302	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.403743512556302	1		523	625	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866559	117866561	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	novel	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	99	602	0	ENST00000297338.2:c.1084_1086del	p.Met362del	p.M362del	ENST00000297338	NM_006265.2	362	ATG/-	9/14	0.327730733587213	4	FACETS	0.62	0.552	0.692	0.207	0.184	0.231	SUBCLONAL	1	TRUE	1	0.403743512556302	4		602	1111	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559293	141559293	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	175	688	0	ENST00000220592.5:c.1508C>A	p.Pro503His	p.P503H	ENST00000220592	NM_012154.3	503	cCc/cAc	12/19	0.327730733587213	4	FACETS	0.943	0.867	1	0.314	0.289	0.342	CLONAL	1	TRUE	1	0.403743512556302	4		688	1290	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336310	80336310	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1059527	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	150	582	0	ENST00000286548.4:c.1009A>G	p.Ile337Val	p.I337V	ENST00000286548	NM_002072.3	337	Atc/Gtc	7/7	1	2	FACETS	0.915	0.837	0.997	0.915	0.837	0.997	CLONAL	1	TRUE	1	0.403743512556302	2		582	812	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801074	135801074	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	152	618	0	ENST00000298552.3:c.263C>A	p.Ser88Tyr	p.S88Y	ENST00000298552	NM_001162426.1	88	tCc/tAc	5/23	1	2	FACETS	0.927	0.849	1	0.927	0.849	1	CLONAL	1	TRUE	1	0.403743512556302	2		618	812	SUCCESS
AR	367	MSKCC	GRCh37	X	66765256	66765256	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555969545	NA	P-0031173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	133	235	0	ENST00000374690.3:c.268C>T	p.Gln90Ter	p.Q90*	ENST00000374690	NM_000044.3	90	Cag/Tag	1/8	1	1	FACETS	0.865	0.799	0.932	1	0.99	1	CLONAL	2	TRUE	0	0.403743512556302	1		235	304	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871758	12871758	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0031178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	118	352	1	ENST00000228872.4:c.476-1G>T		p.X159_splice	ENST00000228872	NM_004064.3	159			1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.476673381826011	2		353	466	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541079	187541079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764035128	NA	P-0031178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	127	529	1	ENST00000441802.2:c.6661G>A	p.Gly2221Arg	p.G2221R	ENST00000441802	NM_005245.3	2221	Gga/Aga	10/27	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.476673381826011	2		530	517	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849452	68849452	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	157	797	1	ENST00000261769.5:c.1355T>C	p.Leu452Pro	p.L452P	ENST00000261769	NM_004360.3	452	cTa/cCa	10/16	0.476673381826011	1	FACETS	0.845	0.777	0.914	0.845	0.777	0.914	CLONAL	1	TRUE	0	0.476673381826011	1		798	594	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871758	12871758	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0031178-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	63	352	1	ENST00000228872.4:c.476-1G>T		p.X159_splice	ENST00000228872	NM_004064.3	159			0.642934274260412	3	FACETS	0.893	0.794	0.994	0.893	0.794	0.994	CLONAL	2	TRUE	1	0.642934274260412	3		353	145	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541079	187541079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764035128	NA	P-0031178-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	241	529	1	ENST00000441802.2:c.6661G>A	p.Gly2221Arg	p.G2221R	ENST00000441802	NM_005245.3	2221	Gga/Aga	10/27	0.596548310847532	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	2	0.642934274260412	4		530	579	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0031243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	204	425	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.367747590182152	3	FACETS	0.949	0.884	1	0.949	0.884	1	CLONAL	2	TRUE	1	0.367747590182152	3		426	692	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579386	7579386	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0031243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	178	618	0	ENST00000269305.4:c.301A>T	p.Lys101Ter	p.K101*	ENST00000269305	NM_001126112.2	101	Aaa/Taa	4/11	0.367747590182152	1	FACETS	0.932	0.86	1	0.932	0.86	1	CLONAL	1	TRUE	0	0.367747590182152	1		618	848	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0031243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	122	439	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.367747590182152	2		439	657	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0031243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	98	519	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.741	0.661	0.826	0.741	0.661	0.826	SUBCLONAL	1	TRUE	1	0.367747590182152	2		519	719	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266718	142266718	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	91	459	0	ENST00000350721.4:c.3206G>C	p.Arg1069Thr	p.R1069T	ENST00000350721	NM_001184.3	1069	aGa/aCa	16/47	0.341344094724479	1	FACETS	0.918	0.819	1	0.918	0.819	1	CLONAL	1	TRUE	0	0.367747590182152	1		459	440	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221322	1221322	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	170	596	0	ENST00000326873.7:c.845T>G	p.Leu282Arg	p.L282R	ENST00000326873	NM_000455.4	282	cTc/cGc	6/10	0.367747590182152	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.367747590182152	1		596	706	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201110	108201110	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	86	391	0	ENST00000278616.4:c.7477G>C	p.Glu2493Gln	p.E2493Q	ENST00000278616	NM_000051.3	2493	Gaa/Caa	50/63	1	2	FACETS	0.838	0.743	0.94	0.838	0.743	0.94	CLONAL	1	TRUE	1	0.367747590182152	2		391	558	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201120	108201120	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs764478418	NA	P-0031243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	86	372	0	ENST00000278616.4:c.7487G>C	p.Gly2496Ala	p.G2496A	ENST00000278616	NM_000051.3	2496	gGa/gCa	50/63	1	2	FACETS	0.884	0.784	0.991	0.884	0.784	0.991	CLONAL	1	TRUE	1	0.367747590182152	2		372	529	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21643313	21643313	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0031243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	49	459	0	ENST00000421138.2:c.215-1G>T		p.X72_splice	ENST00000421138		72			1	2	FACETS	0.467	0.395	0.546	0.467	0.395	0.546	SUBCLONAL	1	TRUE	1	0.367747590182152	2		459	571	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900813	3900813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756802946	NA	P-0031243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	115	508	1	ENST00000262367.5:c.283G>A	p.Val95Met	p.V95M	ENST00000262367	NM_004380.2	95	Gtg/Atg	2/31	0.186813540724695	3	FACETS	0.947	0.853	1	0.473	0.426	0.523	INDETERMINATE	1	TRUE	1	0.367747590182152	3		509	782	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832035	72832035	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763864463	NA	P-0031243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	115	504	0	ENST00000268489.5:c.4546G>T	p.Asp1516Tyr	p.D1516Y	ENST00000268489	NM_006885.3	1516	Gac/Tac	9/10	1	2	FACETS	0.758	0.683	0.838	0.758	0.683	0.838	SUBCLONAL	1	TRUE	1	0.367747590182152	2		504	825	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53254021	53254021	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	150	574	0	ENST00000375401.3:c.51C>G	p.Phe17Leu	p.F17L	ENST00000375401	NM_004187.3	17	ttC/ttG	1/26	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.367747590182152	2		574	778	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0031327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	66	498	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.68	0.588	0.779	0.68	0.588	0.779	SUBCLONAL	1	FALSE	1	0.23181095180586	2		498	838	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577061	7577070	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTCTTGCG	CTTTCTTGCG	-	novel	NA	P-0031327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	89	824	0	ENST00000269305.4:c.868_877del	p.Arg290GlyfsTer52	p.R290Gfs*52	ENST00000269305	NM_001126112.2	290	CGCAAGAAAGgg/gg	8/11	1	2	FACETS	0.793	0.702	0.891	0.793	0.702	0.891	SUBCLONAL	1	FALSE	1	0.23181095180586	2		824	968	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436624	52436624	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs387906848	NA	P-0031375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	544	638	0	ENST00000460680.1:c.2050C>T	p.Gln684Ter	p.Q684*	ENST00000460680	NM_004656.3	684	Cag/Tag	16/17	0.655459118145502	3	FACETS	0.972	0.936	1	0.972	0.936	1	CLONAL	2	TRUE	1	0.655459118145502	3		638	1134	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720741	89720741	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs371387815	NA	P-0031375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	32	219	0	ENST00000371953.3:c.892C>T	p.Gln298Ter	p.Q298*	ENST00000371953	NM_000314.4	298	Caa/Taa	8/9	0.643910205027366	1	FACETS	0.479	0.395	0.57	0.479	0.395	0.57	SUBCLONAL	1	TRUE	0	0.655459118145502	1		219	137	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441996	52441997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGTCC	novel	NA	P-0031375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	205	535	3	ENST00000460680.1:c.348_352dup	p.Phe118TrpfsTer71	p.F118Wfs*71	ENST00000460680	NM_004656.3	118	ttc/tGGACTtc	5/17	0.655459118145502	3	FACETS	0.919	0.853	0.987	0.459	0.426	0.494	CLONAL	1	TRUE	1	0.655459118145502	3		538	904	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106383	27106384	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0031383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	370	624	0	ENST00000324856.7:c.5997dup	p.Glu2000Ter	p.E2000*	ENST00000324856	NM_006015.4	1998	-/T	20/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.735117810221117	2		624	950	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673025	30673025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1188324930	NA	P-0031383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	502	832	0	ENST00000376406.3:c.3935G>A	p.Ser1312Asn	p.S1312N	ENST00000376406	NM_014641.2	1312	aGc/aAc	10/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.735117810221117	2		832	1291	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0031431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	69	739	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.422679217930716	1	FACETS	0.873	0.767	0.985	0.873	0.767	0.985	CLONAL	1	TRUE	0	0.422679217930716	1		739	295	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938248	36938248	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	287	630	1	ENST00000361632.4:c.713G>A	p.Ser238Asn	p.S238N	ENST00000361632		238	aGc/aAc	6/16	1	2	FACETS	0.918	0.868	0.968	1	0.995	1	CLONAL	2	TRUE	1	0.422679217930716	2		631	740	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664463	29664463	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0031431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	283	455	0	ENST00000356175.3:c.6442A>T	p.Lys2148Ter	p.K2148*	ENST00000356175	NM_000267.3	2148	Aaa/Taa	42/57	0.422679217930716	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.422679217930716	2		455	650	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006656	62006656	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	278	546	0	ENST00000392795.3:c.623A>C	p.Tyr208Ser	p.Y208S	ENST00000392795	NM_001039933.1	208	tAt/tCt	6/6	0.422679217930716	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.422679217930716	2		546	639	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817519	39817519	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	74	488	0	ENST00000288319.7:c.44A>G	p.Asp15Gly	p.D15G	ENST00000288319	NM_182918.3	15	gAc/gGc	2/10	0.241192607277246	0	FACETS	0.376	0.329	0.426			1	INDETERMINATE	1	TRUE	0	0.422679217930716	0		488	538	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271376	26271408	+	inframe_deletion	In_Frame_Del	DEL	GAAGTCCTGAGCGATTTCTCGCACCAGGCGTTG	GAAGTCCTGAGCGATTTCTCGCACCAGGCGTTG	-	novel	NA	P-0031431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	26	441	0	ENST00000305910.3:c.205_237del	p.Gln69_Phe79del	p.Q69_F79del	ENST00000305910	NM_003534.2	69	CAACGCCTGGTGCGAGAAATCGCTCAGGACTTC/-	1/1	1	2	FACETS	0.252	0.199	0.313	0.252	0.199	0.313	SUBCLONAL	1	TRUE	1	0.422679217930716	2		441	489	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974787	21974788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0031431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	51	168	0	ENST00000304494.5:c.39dup	p.Asp14Ter	p.D14*	ENST00000304494	NM_000077.4	13	-/T	1/3	0.422679217930716	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.422679217930716	1		168	150	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27168596	27168596	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0031431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	137	490	0	ENST00000380036.4:c.468C>G	p.Tyr156Ter	p.Y156*	ENST00000380036	NM_000459.3	156	taC/taG	3/23	0.422679217930716	1	FACETS	0.985	0.901	1	0.985	0.901	1	CLONAL	1	TRUE	0	0.422679217930716	1		490	519	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923199	39923199	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	83	210	0	ENST00000378444.4:c.3509G>T	p.Trp1170Leu	p.W1170L	ENST00000378444	NM_001123385.1	1170	tGg/tTg	8/15	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.422679217930716	1		210	209	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422727	47422727	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	106	269	0	ENST00000377045.4:c.199G>T	p.Gly67Ter	p.G67*	ENST00000377045	NM_001654.4	67	Gga/Tga	3/16	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.422679217930716	1		269	264	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	92	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.242020139591802	4	FACETS	0.967	0.863	1	0.967	0.863	1	CLONAL	2	TRUE	2	0.255211923179835	4		473	468	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167577	NA	P-0031482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	106	360	0	ENST00000257430.4:c.4463del	p.Leu1488TyrfsTer19	p.L1488Yfs*19	ENST00000257430	NM_000038.5	1487	acT/ac	16/16	0.255211923179835	3	FACETS	1	0.909	1	1	0.909	1	CLONAL	3	TRUE	0	0.255211923179835	3		360	312	SUCCESS
AR	367	MSKCC	GRCh37	X	66766412	66766412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200390780	NA	P-0031482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	33	128	0	ENST00000374690.3:c.1424C>T	p.Ala475Val	p.A475V	ENST00000374690	NM_000044.3	475	gCg/gTg	1/8	0.244101307284546	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	2	TRUE	0	0.255211923179835	2		128	122	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0031482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	45	366	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.974	0.821	1	0.974	0.821	1	CLONAL	1	TRUE	1	0.255211923179835	2		366	362	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717717	89717717	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	110	440	0	ENST00000371953.3:c.743del	p.Pro248LeufsTer8	p.P248Lfs*8	ENST00000371953	NM_000314.4	248	Cct/ct	7/9	0.244101307284546	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.255211923179835	2		440	401	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891120	112891120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1395524782	NA	P-0031482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	114	652	0	ENST00000351677.2:c.454C>T	p.Arg152Cys	p.R152C	ENST00000351677	NM_002834.3	152	Cgc/Tgc	4/16	0.242020139591802	4	FACETS	0.877	0.792	0.968	0.877	0.792	0.968	CLONAL	2	TRUE	2	0.255211923179835	4		652	639	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99823087	99823087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772918368	NA	P-0031482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	46	332	0	ENST00000280892.6:c.125C>T	p.Thr42Met	p.T42M	ENST00000280892	NM_001130678.1	42	aCg/aTg	2/7	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.255211923179835	2		332	287	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904941	101904941	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	87	406	0	ENST00000374994.4:c.929C>A	p.Ala310Glu	p.A310E	ENST00000374994	NM_004612.2	310	gCg/gAg	5/9	0.207345009114506	4	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	2	0.255211923179835	4		406	397	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458843	120458843	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	47	738	1	ENST00000256646.2:c.6502C>A	p.Pro2168Thr	p.P2168T	ENST00000256646	NM_024408.3	2168	Cca/Aca	34/34	1	2	FACETS	0.819	0.69	0.961	0.819	0.69	0.961	CLONAL	1	TRUE	1	0.18581360921911	2		739	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578376	7578379	+	frameshift_variant	Frame_Shift_Del	DEL	CTAT	CTAT	-	novel	NA	P-0031613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	341	517	1	ENST00000269305.4:c.551_554del	p.Asp184AlafsTer62	p.D184Afs*62	ENST00000269305	NM_001126112.2	184	gATAGc/gc	5/11	NA	2	FACETS	0.986	0.951	1			1	INDETERMINATE	2	TRUE	NA	0.728431320379999	2		518	475	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255265	16255265	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	402	520	0	ENST00000375759.3:c.2530C>T	p.Arg844Ter	p.R844*	ENST00000375759	NM_015001.2	844	Cga/Tga	11/15	0.728431320379999	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.728431320379999	3		520	738	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475229	475229	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3183	187	601	0	ENST00000399788.2:c.408G>T	p.Glu136Asp	p.E136D	ENST00000399788	NM_001042603.1	136	gaG/gaT	4/28	0.728431320379999	16	FACETS	0.929	0.853	1			1	CLONAL	1	TRUE	NA	0.728431320379999	16		601	3370	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350472	15350472	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	139	498	0	ENST00000263377.2:c.3443A>T	p.Gln1148Leu	p.Q1148L	ENST00000263377	NM_058243.2	1148	cAg/cTg	16/20	0.586776592154182	5	FACETS	0.959	0.873	1			1	CLONAL	1	TRUE	NA	0.728431320379999	5		498	833	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872243	45872243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773453200	NA	P-0031613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	217	539	0	ENST00000391945.4:c.191C>T	p.Pro64Leu	p.P64L	ENST00000391945	NM_000400.3	64	cCg/cTg	4/23	0.728431320379999	6	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.728431320379999	6		539	1292	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0031619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	374	385	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.357330450245066	4	FACETS	0.936	0.908	0.963			1	INDETERMINATE	4	TRUE	NA	0.700187604648181	4		385	485	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478161	138478161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	191	450	0	ENST00000289153.2:c.25C>T	p.Pro9Ser	p.P9S	ENST00000289153	NM_006219.2	9	Cct/Tct	1/22	0.332163619546152	4	FACETS	0.985	0.92	1	0.985	0.92	1	INDETERMINATE	2	TRUE	2	0.700187604648181	4		450	471	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428201	49428201	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	175	576	0	ENST00000301067.7:c.10499del	p.Gly3500GlufsTer2	p.G3500Efs*2	ENST00000301067	NM_003482.3	3500	gGa/ga	37/54	0.332163619546152	4	FACETS	0.84	0.78	0.901	0.84	0.78	0.901	INDETERMINATE	2	TRUE	2	0.700187604648181	4		576	506	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434310	49434328	+	frameshift_variant	Frame_Shift_Del	DEL	GACTGGCAGGCACTCGGGA	GACTGGCAGGCACTCGGGA	-	novel	NA	P-0031619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	222	706	0	ENST00000301067.7:c.7225_7243del	p.Ser2409LeufsTer11	p.S2409Lfs*11	ENST00000301067	NM_003482.3	2409	TCCCGAGTGCCTGCCAGTCct/ct	31/54	0.332163619546152	4	FACETS	0.837	0.784	0.892	0.837	0.784	0.892	INDETERMINATE	2	TRUE	2	0.700187604648181	4		706	644	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0031646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	191	425	1	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	0.548602995638317	2		426	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579575	7579575	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555526795	NA	P-0031646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	41	733	1	ENST00000269305.4:c.112del	p.Gln38LysfsTer6	p.Q38Kfs*6	ENST00000269305	NM_001126112.2	38	Caa/aa	4/11	0.548602995638317	1	FACETS	0.201	0.167	0.239	0.201	0.167	0.239	SUBCLONAL	1	TRUE	0	0.548602995638317	1		734	539	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732969	30732969	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	24	373	0	ENST00000295754.5:c.1582C>G	p.Arg528Gly	p.R528G	ENST00000295754	NM_003242.5	528	Cgt/Ggt	7/7	1	2	FACETS	0.192	0.15	0.241	0.192	0.15	0.241	SUBCLONAL	1	TRUE	1	0.548602995638317	2		373	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577157	7577157	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0031646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	150	580	0	ENST00000269305.4:c.783-2A>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.548602995638317	1	FACETS	0.789	0.726	0.854	0.789	0.726	0.854	SUBCLONAL	1	TRUE	0	0.548602995638317	1		580	503	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928945	49928945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	60	836	2	ENST00000296474.3:c.3421C>T	p.Pro1141Ser	p.P1141S	ENST00000296474	NM_002447.2	1141	Ccg/Tcg	16/20	0.548602995638317	1	FACETS	0.234	0.201	0.27	0.234	0.201	0.27	SUBCLONAL	1	TRUE	0	0.548602995638317	1		838	677	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47088081	47088081	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	231	539	0	ENST00000409792.3:c.6994C>T	p.Gln2332Ter	p.Q2332*	ENST00000409792	NM_014159.6	2332	Cag/Tag	16/21	0.548602995638317	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.548602995638317	1		539	540	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441430	52441430	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	211	604	0	ENST00000460680.1:c.422A>G	p.His141Arg	p.H141R	ENST00000460680	NM_004656.3	141	cAt/cGt	6/17	0.548602995638317	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.548602995638317	1		604	534	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577525	7577527	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0031751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	303	791	0	ENST00000269305.4:c.754_756del	p.Leu252del	p.L252del	ENST00000269305	NM_001126112.2	252	CTC/-	7/11	0.104773704731785	3	FACETS	1	0.985	1			1	INDETERMINATE	2	TRUE	NA	0.425799393070713	3		791	780	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624300	89624300	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs786204912	NA	P-0031751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	220	677	0	ENST00000371953.3:c.74T>A	p.Leu25Ter	p.L25*	ENST00000371953	NM_000314.4	25	tTg/tAg	1/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.425799393070713	NA		677	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0031938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	154	519	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.402329672057421	3	FACETS	0.85	0.786	0.916	0.567	0.524	0.611	CLONAL	2	FALSE	0	0.540077632512847	3		519	426	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0031938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	54	498	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.264337265909037	5	FACETS	0.787	0.68	0.901	0.525	0.453	0.601	INDETERMINATE	2	FALSE	2	0.540077632512847	5		498	230	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593505	48593506	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	rs730881956	NA	P-0031938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	34	376	0	ENST00000342988.3:c.1258_1259dup	p.Ala421ValfsTer16	p.A421Vfs*16	ENST00000342988	NM_005359.5	419	ggg/ggGCg	10/12	0.286590445990781	3	FACETS	1	0.953	1	0.494	0.413	0.579	INDETERMINATE	1	FALSE	0	0.540077632512847	3		376	108	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0032010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	85	542	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.21	2		543	691	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0032010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	28	705	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.539	0.43	0.664	0.539	0.43	0.664	SUBCLONAL	1	TRUE	1	0.21	2		705	495	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0032010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	60	685	2	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.21	2		687	475	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0032010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	42	313	0	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	1	2	FACETS	1	0.838	1	1	0.838	1	CLONAL	1	TRUE	1	0.21	2		313	399	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395643	45395643	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	61	395	1	ENST00000262160.6:c.491C>T	p.Pro164Leu	p.P164L	ENST00000262160	NM_005901.5	164	cCt/cTt	4/11	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.21	2		396	580	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556484	29556484	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1131691122	NA	P-0032010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	21	343	0	ENST00000356175.3:c.2850+1G>A		p.X950_splice	ENST00000356175	NM_000267.3	950			1	2	FACETS	0.477	0.367	0.607	0.477	0.367	0.607	SUBCLONAL	1	TRUE	1	0.21	2		343	419	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286229	66286229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	45	546	0	ENST00000273854.3:c.1457C>T	p.Ser486Phe	p.S486F	ENST00000273854	NM_004439.5	486	tCt/tTt	6/18	1	2	FACETS	0.739	0.62	0.87	0.739	0.62	0.87	SUBCLONAL	1	TRUE	1	0.21	2		546	580	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	85	635	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.4372032974569	2		635	346	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0032063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3448	3127	400	0	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.4372032974569	42	FACETS	1	0.991	1	0.505	0.497	0.513	CLONAL	21	TRUE	0	0.4372032974569	42		400	6575	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843410	128843410	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143083812	NA	P-0032063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	86	343	0	ENST00000249373.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000249373	NM_005631.4	173	Cgc/Tgc	2/12	0.4372032974569	3	FACETS	0.821	0.727	0.921	0.41	0.363	0.461	CLONAL	1	TRUE	1	0.4372032974569	3		343	584	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999161	100999161	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1050185598	NA	P-0032250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	160	556	2	ENST00000325455.5:c.641C>T	p.Pro214Leu	p.P214L	ENST00000325455	NM_001202474.3	214	cCg/cTg	1/8	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.780671699592961	2		558	381	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066901	30066901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	80	367	0	ENST00000331968.5:c.2230G>A	p.Val744Met	p.V744M	ENST00000331968	NM_002742.2	744	Gtg/Atg	16/18	1	2	FACETS	0.47	0.415	0.528	0.47	0.415	0.528	SUBCLONAL	1	TRUE	1	0.780671699592961	2		367	436	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061143	38061202	+	inframe_deletion	In_Frame_Del	DEL	GCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTG	GCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTG	-	novel	NA	P-0032250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	95	119	0	ENST00000250448.2:c.787_846del	p.Gln263_Ser282del	p.Q263_S282del	ENST00000250448	NM_004496.3	263	CAGAAGCGCTTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGC/-	2/2	1	2	FACETS	0.79	0.73	0.849	1	0.988	1	SUBCLONAL	2	TRUE	1	0.780671699592961	2		119	154	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138997	37138997	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	178	624	0	ENST00000373509.5:c.337C>G	p.Pro113Ala	p.P113A	ENST00000373509	NM_002648.3	113	Ccc/Gcc	4/6	1	2	FACETS	0.976	0.909	1	0.976	0.909	1	CLONAL	1	TRUE	1	0.780671699592961	2		624	467	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879525	151879526	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0032250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	124	328	0	ENST00000262189.6:c.5419_5420del	p.Gln1807GlufsTer20	p.Q1807Efs*20	ENST00000262189	NM_170606.2	1807	CAg/g	36/59	1	2	FACETS	0.943	0.864	1	0.943	0.864	1	CLONAL	1	TRUE	1	0.780671699592961	2		328	337	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061210	38061213	+	missense_variant	Missense_Mutation	ONP	AAGT	AAGT	GAGA	novel	NA	P-0032250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	105	391	0	ENST00000250448.2:c.776_779delinsTCTC	p.Tyr259_Leu260delinsPheSer	p.Y259_L260delinsFS	ENST00000250448	NM_004496.3	259	tACTTg/tTCTCg	2/2	1	2	FACETS	0.782	0.708	0.859	0.782	0.708	0.859	SUBCLONAL	1	TRUE	1	0.780671699592961	2		391	344	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0032402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	37	169	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.806	0.672	0.952	0.806	0.672	0.952	CLONAL	1	TRUE	1	0.490867794922195	2		169	187	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0032402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	139	544	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.982	0.897	1	0.982	0.897	1	CLONAL	1	TRUE	1	0.490867794922195	2		544	577	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188177	11188177	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	90	377	0	ENST00000361445.4:c.5917A>T	p.Ile1973Phe	p.I1973F	ENST00000361445	NM_004958.3	1973	Atc/Ttc	43/58	0.490867794922195	1	FACETS	0.867	0.778	0.961	0.867	0.778	0.961	CLONAL	1	TRUE	0	0.490867794922195	1		377	319	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555685	21555685	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747591469	NA	P-0032402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	131	585	0	ENST00000382592.4:c.2585G>A	p.Arg862Gln	p.R862Q	ENST00000382592	NM_014572.2	862	cGg/cAg	6/8	1	2	FACETS	0.858	0.781	0.939	0.858	0.781	0.939	CLONAL	1	TRUE	1	0.490867794922195	2		585	622	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230625	46230625	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	101	495	0	ENST00000334344.6:c.874A>G	p.Ile292Val	p.I292V	ENST00000334344	NM_152641.2	292	Att/Gtt	8/21	1	2	FACETS	0.891	0.8	0.986	0.891	0.8	0.986	CLONAL	1	TRUE	1	0.490867794922195	2		495	462	SUCCESS
APC	324	MSKCC	GRCh37	5	112174781	112174785	+	frameshift_variant	Frame_Shift_Del	DEL	ATAAA	ATAAA	-	novel	NA	P-0032402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	37	215	0	ENST00000257430.4:c.3493_3497del	p.Lys1165Ter	p.K1165*	ENST00000257430	NM_000038.5	1164	ATAAAa/a	16/16	1	2	FACETS	0.704	0.586	0.835	0.704	0.586	0.835	SUBCLONAL	1	TRUE	1	0.490867794922195	2		215	214	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0032498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	31	774	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.508	0.409	0.62	0.508	0.409	0.62	SUBCLONAL	1	TRUE	1	0.183021614449394	2		774	667	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0032498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	96	671	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.171295367209918	3	FACETS	0.773	0.688	0.863	0.773	0.688	0.863	SUBCLONAL	2	TRUE	1	0.183021614449394	3		671	741	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549345	187549345	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	58	593	0	ENST00000441802.2:c.4773A>C	p.Lys1591Asn	p.K1591N	ENST00000441802	NM_005245.3	1591	aaA/aaC	9/27	1	2	FACETS	0.787	0.675	0.91	0.787	0.675	0.91	CLONAL	1	TRUE	1	0.183021614449394	2		593	805	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922258	100922258	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	93	468	0	ENST00000325455.5:c.2254C>T	p.Gln752Ter	p.Q752*	ENST00000325455	NM_001202474.3	752	Cag/Tag	5/8	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.809728455008363	2		468	220	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593637	55593660	+	protein_altering_variant	In_Frame_Del	DEL	ATGTTTACATAGACCCAACACAAC	ATGTTTACATAGACCCAACACAAC	GTG	novel	NA	P-0032594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	181	631	3	ENST00000288135.5:c.1703_1726delinsGTG	p.Tyr568_Leu576delinsCysVal	p.Y568_L576delinsCV	ENST00000288135	NM_000222.2	568	tATGTTTACATAGACCCAACACAACtt/tGTGtt	11/21	1	2	FACETS	0.996	0.928	1	0.996	0.928	1	CLONAL	1	TRUE	1	0.809728455008363	2		634	449	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922258	100922258	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032594-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	221	468	0	ENST00000325455.5:c.2254C>T	p.Gln752Ter	p.Q752*	ENST00000325455	NM_001202474.3	752	Cag/Tag	5/8	1	2	FACETS	0.951	0.895	1	0.951	0.895	1	CLONAL	1	TRUE	1	0.938531355477804	2		468	495	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593637	55593660	+	protein_altering_variant	In_Frame_Del	DEL	ATGTTTACATAGACCCAACACAAC	ATGTTTACATAGACCCAACACAAC	GTG	novel	NA	P-0032594-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	306	631	3	ENST00000288135.5:c.1703_1726delinsGTG	p.Tyr568_Leu576delinsCysVal	p.Y568_L576delinsCV	ENST00000288135	NM_000222.2	568	tATGTTTACATAGACCCAACACAACtt/tGTGtt	11/21	NA	2	FACETS	0.933	0.885	0.981			1	INDETERMINATE	1	TRUE	NA	0.938531355477804	2		634	699	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0032658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	235	761	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	2	TRUE	NA	0.638924387755958	2		761	350	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6442009	6442009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	24	320	1	ENST00000356142.4:c.568G>A	p.Glu190Lys	p.E190K	ENST00000356142	NM_018890.3	190	Gaa/Aaa	7/7	0.221805022630717	3	FACETS	0.774	0.616	0.952	0.387	0.308	0.476	INDETERMINATE	1	TRUE	1	0.638924387755958	3		321	128	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828143	243828143	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	120	612	0	ENST00000263826.5:c.215T>A	p.Phe72Tyr	p.F72Y	ENST00000263826	NM_005465.4	72	tTt/tAt	3/13	0.630787303418289	4	FACETS	1	0.959	1			1	CLONAL	1	TRUE	NA	0.638924387755958	4		612	557	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246033	41246033	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	23	822	0	ENST00000357654.3:c.1515A>C	p.Lys505Asn	p.K505N	ENST00000357654	NM_007294.3	505	aaA/aaC	10/23	0.639987712120864	2	FACETS	0.207	0.161	0.26	0.103	0.08	0.13	SUBCLONAL	1	TRUE	0	0.638924387755958	2		822	348	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225338978	225338978	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	80	542	0	ENST00000264414.4:c.2291A>G	p.Tyr764Cys	p.Y764C	ENST00000264414	NM_003590.4	764	tAc/tGc	16/16	0.639987712120864	3	FACETS	0.908	0.805	1	0.454	0.402	0.509	CLONAL	1	TRUE	1	0.638924387755958	3		542	364	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499325	89499325	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0032658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	59	368	0	ENST00000336596.2:c.2497-2A>T		p.X833_splice	ENST00000336596	NM_005233.5	833			0.561595477761935	3	FACETS	0.745	0.645	0.853	0.248	0.215	0.285	SUBCLONAL	1	TRUE	0	0.638924387755958	3		368	327	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121242	29121242	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137853007	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	35	679	0	ENST00000328354.6:c.433C>T	p.Arg145Trp	p.R145W	ENST00000328354	NM_007194.3	145	Cgg/Tgg	3/15	1	2	FACETS	0.784	0.641	0.946	0.784	0.641	0.946	CLONAL	1	TRUE	1	0.13	2		679	687	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	29	520	4	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.92	0.737	1	0.92	0.737	1	CLONAL	1	TRUE	1	0.13	2		524	485	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482437	56482437	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	26	488	0	ENST00000267101.3:c.985A>G	p.Lys329Glu	p.K329E	ENST00000267101	NM_001982.3	329	Aaa/Gaa	8/28	1	2	FACETS	0.775	0.613	0.963	0.775	0.613	0.963	CLONAL	1	TRUE	1	0.13	2		488	516	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	24	531	0	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	1	2	FACETS	0.914	0.716	1	0.914	0.716	1	CLONAL	1	TRUE	1	0.13	2		531	404	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	51	529	0	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.13	2		529	702	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421519	32421519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	32	524	0	ENST00000332351.3:c.1073C>T	p.Thr358Met	p.T358M	ENST00000332351	NM_024426.4	358	aCg/aTg	6/10	1	2	FACETS	0.781	0.633	0.951	0.781	0.633	0.951	CLONAL	1	TRUE	1	0.13	2		524	630	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864491	56864491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746856372	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	40	547	0	ENST00000308159.5:c.979C>T	p.Arg327Cys	p.R327C	ENST00000308159	NM_014669.4	327	Cgc/Tgc	10/22	1	2	FACETS	0.954	0.791	1	0.954	0.791	1	CLONAL	1	TRUE	1	0.13	2		547	645	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2493197	2493197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762075584	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	36	579	0	ENST00000355716.4:c.637G>A	p.Val213Ile	p.V213I	ENST00000355716	NM_003820.2	213	Gtc/Atc	6/8	1	2	FACETS	0.802	0.657	0.964	0.802	0.657	0.964	CLONAL	1	TRUE	1	0.13	2		579	691	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538941	187538941	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs113224498	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	29	408	2	ENST00000441802.2:c.8799del	p.Gly2934ValfsTer3	p.G2934Vfs*3	ENST00000441802	NM_005245.3	2933	caA/ca	10/27	1	2	FACETS	0.85	0.681	1	0.85	0.681	1	CLONAL	1	TRUE	1	0.13	2		410	525	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907420	32907421	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359306	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	16	295	0	ENST00000380152.3:c.1813dup	p.Ile605AsnfsTer11	p.I605Nfs*11	ENST00000380152		602	gga/ggAa	10/27	1	2	FACETS	0.812	0.6	1	0.812	0.6	1	CLONAL	1	TRUE	1	0.13	2		295	303	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56910960	56910960	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	46	566	0	ENST00000519728.1:c.1106G>A	p.Arg369Gln	p.R369Q	ENST00000519728	NM_002350.3	369	cGa/cAa	11/13	1	2	FACETS	0.896	0.752	1	0.896	0.752	1	CLONAL	1	TRUE	1	0.13	2		566	790	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683558	29683558	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060500295	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	13	295	0	ENST00000356175.3:c.7638del	p.Met2548Ter	p.M2548*	ENST00000356175	NM_000267.3	2545	Ccc/cc	51/57	1	2	FACETS	0.8	0.57	1	0.8	0.57	1	CLONAL	1	TRUE	1	0.13	2		295	250	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272115	38272115	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	38	563	0	ENST00000425967.3:c.2103G>T	p.Glu701Asp	p.E701D	ENST00000425967	NM_001174067.1	701	gaG/gaT	16/19	1	2	FACETS	0.978	0.807	1	0.978	0.807	1	CLONAL	1	TRUE	1	0.13	2		563	598	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300039	137300040	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755912201	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	44	696	4	ENST00000481739.1:c.331dup	p.Leu111ProfsTer70	p.L111Pfs*70	ENST00000481739	NM_002957.4	108	-/C	3/10	1	2	FACETS	0.833	0.696	0.985	0.833	0.696	0.985	CLONAL	1	TRUE	1	0.13	2		700	813	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732986	74732986	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	26	339	0	ENST00000359995.5:c.257G>T	p.Arg86Leu	p.R86L	ENST00000359995	NM_001195427.1	86	cGg/cTg	1/3	1	2	FACETS	0.866	0.685	1	0.866	0.685	1	CLONAL	1	TRUE	1	0.13	2		339	462	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533595	533595	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	34	654	0	ENST00000451590.1:c.308T>C	p.Val103Ala	p.V103A	ENST00000451590	NM_001130442.1	103	gTg/gCg	4/5	1	2	FACETS	0.771	0.629	0.933	0.771	0.629	0.933	CLONAL	1	TRUE	1	0.13	2		654	678	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550901	150550901	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1485362622	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	38	430	0	ENST00000369026.2:c.755A>G	p.His252Arg	p.H252R	ENST00000369026	NM_021960.4	252	cAt/cGt	2/3	1	2	FACETS	0.888	0.733	1	0.888	0.733	1	CLONAL	1	TRUE	1	0.13	2		430	658	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420972	49420972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	25	371	1	ENST00000301067.7:c.14777C>T	p.Ala4926Val	p.A4926V	ENST00000301067	NM_003482.3	4926	gCc/gTc	48/54	1	2	FACETS	0.836	0.658	1	0.836	0.658	1	CLONAL	1	TRUE	1	0.13	2		372	460	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433136	49433136	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	40	594	0	ENST00000301067.7:c.8235G>T	p.Lys2745Asn	p.K2745N	ENST00000301067	NM_003482.3	2745	aaG/aaT	33/54	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.13	2		594	552	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110108	115110108	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	34	634	0	ENST00000257566.3:c.1771-1G>T		p.X591_splice	ENST00000257566	NM_016569.3	591			1	2	FACETS	0.782	0.637	0.946	0.782	0.637	0.946	CLONAL	1	TRUE	1	0.13	2		634	669	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123880898	123880898	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	26	329	0	ENST00000330479.4:c.516A>C	p.Gln172His	p.Q172H	ENST00000330479	NM_020382.3	172	caA/caC	5/9	1	2	FACETS	0.993	0.786	1	0.993	0.786	1	CLONAL	1	TRUE	1	0.13	2		329	403	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28611427	28611427	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	27	344	0	ENST00000241453.7:c.1206-2A>C		p.X402_splice	ENST00000241453	NM_004119.2	402			1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.13	2		344	340	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008234	29008234	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	27	500	0	ENST00000282397.4:c.637G>T	p.Gly213Trp	p.G213W	ENST00000282397	NM_002019.4	213	Ggg/Tgg	5/30	1	2	FACETS	0.799	0.634	0.988	0.799	0.634	0.988	CLONAL	1	TRUE	1	0.13	2		500	520	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066864	30066864	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	33	494	0	ENST00000331968.5:c.2267G>T	p.Arg756Met	p.R756M	ENST00000331968	NM_002742.2	756	aGg/aTg	16/18	1	2	FACETS	0.921	0.749	1	0.921	0.749	1	CLONAL	1	TRUE	1	0.13	2		494	551	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500289	99500289	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	37	512	0	ENST00000268035.6:c.3723-1G>T		p.X1241_splice	ENST00000268035	NM_000875.3	1241			1	2	FACETS	0.835	0.686	1	0.835	0.686	1	CLONAL	1	TRUE	1	0.13	2		512	682	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56870512	56870512	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	17	328	0	ENST00000308159.5:c.1783-1G>T		p.X595_splice	ENST00000308159	NM_014669.4	595			1	2	FACETS	0.788	0.587	1	0.788	0.587	1	CLONAL	1	TRUE	1	0.13	2		328	332	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37863243	37863243	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs755921683	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	60	478	0	ENST00000269571.5:c.74T>C	p.Val25Ala	p.V25A	ENST00000269571		25	gTg/gCg	2/27	1	2	FACETS	0.882	0.761	1	1	0.975	1	CLONAL	2	TRUE	1	0.13	2		478	523	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271478	15271478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	48	865	0	ENST00000263388.2:c.6961G>A	p.Ala2321Thr	p.A2321T	ENST00000263388	NM_000435.2	2321	Gcc/Acc	33/33	1	2	FACETS	0.851	0.717	0.999	0.851	0.717	0.999	CLONAL	1	TRUE	1	0.13	2		865	868	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290259	15290259	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	44	749	0	ENST00000263388.2:c.3376T>C	p.Cys1126Arg	p.C1126R	ENST00000263388	NM_000435.2	1126	Tgt/Cgt	21/33	1	2	FACETS	0.799	0.668	0.945	0.799	0.668	0.945	CLONAL	1	TRUE	1	0.13	2		749	847	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367884	15367884	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765955810	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	42	645	1	ENST00000263377.2:c.1442C>T	p.Ala481Val	p.A481V	ENST00000263377	NM_058243.2	481	gCc/gTc	8/20	1	2	FACETS	0.889	0.74	1	0.889	0.74	1	CLONAL	1	TRUE	1	0.13	2		646	727	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902121	50902121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs9282830	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	23	420	1	ENST00000440232.2:c.13C>T	p.Arg5Trp	p.R5W	ENST00000440232	NM_002691.3	5	Cgg/Tgg	2/27	1	2	FACETS	0.898	0.699	1	0.898	0.699	1	CLONAL	1	TRUE	1	0.13	2		421	394	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028154	48028154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1387534158	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	20	352	0	ENST00000234420.5:c.3032T>C	p.Ile1011Thr	p.I1011T	ENST00000234420	NM_000179.2	1011	aTt/aCt	4/10	1	2	FACETS	0.795	0.607	1	0.795	0.607	1	CLONAL	1	TRUE	1	0.13	2		352	387	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149925	202149925	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	36	591	1	ENST00000358485.4:c.1366G>T	p.Ala456Ser	p.A456S	ENST00000358485	NM_001080125.1	456	Gct/Tct	8/9	1	2	FACETS	0.835	0.685	1	0.835	0.685	1	CLONAL	1	TRUE	1	0.13	2		592	663	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911130	40911130	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	20	378	0	ENST00000373198.4:c.2175del	p.Ala726HisfsTer8	p.A726Hfs*8	ENST00000373198	NM_133170.3	725	aaA/aa	13/32	1	2	FACETS	0.832	0.635	1	0.832	0.635	1	CLONAL	1	TRUE	1	0.13	2		378	370	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324324	62324324	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	36	602	0	ENST00000360203.5:c.2819C>A	p.Ala940Asp	p.A940D	ENST00000360203	NM_001283009.1	940	gCt/gAt	29/35	1	2	FACETS	0.923	0.757	1	0.923	0.757	1	CLONAL	1	TRUE	1	0.13	2		602	600	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656816	45656816	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	28	482	0	ENST00000407780.3:c.340C>A	p.Leu114Met	p.L114M	ENST00000407780	NM_001283052.1	114	Ctg/Atg	3/7	1	2	FACETS	0.776	0.619	0.957	0.776	0.619	0.957	CLONAL	1	TRUE	1	0.13	2		482	555	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513293	41513293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	31	519	1	ENST00000263253.7:c.197C>T	p.Thr66Ile	p.T66I	ENST00000263253	NM_001429.3	66	aCa/aTa	2/31	1	2	FACETS	0.825	0.666	1	0.825	0.666	1	CLONAL	1	TRUE	1	0.13	2		520	578	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190790	185190790	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	36	547	0	ENST00000265026.3:c.1674del	p.Thr559ProfsTer48	p.T559Pfs*48	ENST00000265026	NM_004721.4	557	atC/at	11/14	1	2	FACETS	0.908	0.745	1	0.908	0.745	1	CLONAL	1	TRUE	1	0.13	2		547	610	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151555	55151555	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs757362953	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	28	494	0	ENST00000257290.5:c.2341C>A	p.Leu781Ile	p.L781I	ENST00000257290	NM_006206.4	781	Ctc/Atc	17/23	1	2	FACETS	0.892	0.712	1	0.892	0.712	1	CLONAL	1	TRUE	1	0.13	2		494	483	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158352	106158352	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	19	304	0	ENST00000380013.4:c.3253A>G	p.Thr1085Ala	p.T1085A	ENST00000380013	NM_001127208.2	1085	Aca/Gca	3/11	1	2	FACETS	0.905	0.687	1	0.905	0.687	1	CLONAL	1	TRUE	1	0.13	2		304	323	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278878	1278878	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	38	574	0	ENST00000310581.5:c.2164del	p.Gln722ArgfsTer45	p.Q722Rfs*45	ENST00000310581	NM_198253.2	722	Cag/ag	6/16	1	2	FACETS	0.882	0.727	1	0.882	0.727	1	CLONAL	1	TRUE	1	0.13	2		574	663	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754226	57754226	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	29	369	0	ENST00000274289.3:c.625G>T	p.Gly209Trp	p.G209W	ENST00000274289	NM_006622.3	209	Ggg/Tgg	4/14	1	2	FACETS	1	0.833	1	1	0.833	1	CLONAL	1	TRUE	1	0.13	2		369	428	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590490	67590490	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	15	174	0	ENST00000274335.5:c.1552G>T	p.Glu518Ter	p.E518*	ENST00000274335		518	Gag/Tag	11/15	1	2	FACETS	1	0.738	1	1	0.738	1	CLONAL	1	TRUE	1	0.13	2		174	229	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449570	149449570	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	44	587	0	ENST00000286301.3:c.1376G>T	p.Ser459Ile	p.S459I	ENST00000286301	NM_005211.3	459	aGc/aTc	10/22	1	2	FACETS	0.94	0.787	1	0.94	0.787	1	CLONAL	1	TRUE	1	0.13	2		587	720	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265394	152265394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	29	385	1	ENST00000206249.3:c.847G>A	p.Ala283Thr	p.A283T	ENST00000206249	NM_000125.3	283	Gct/Act	4/8	1	2	FACETS	0.855	0.685	1	0.855	0.685	1	CLONAL	1	TRUE	1	0.13	2		386	522	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978318	2978318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	30	506	0	ENST00000396946.4:c.1012G>A	p.Asp338Asn	p.D338N	ENST00000396946	NM_032415.4	338	Gac/Aac	7/25	1	2	FACETS	0.773	0.621	0.946	0.773	0.621	0.946	CLONAL	1	TRUE	1	0.13	2		506	597	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935668	13935668	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	35	417	0	ENST00000405192.2:c.1188A>C	p.Glu396Asp	p.E396D	ENST00000405192	NM_001163147.1	396	gaA/gaC	12/12	1	2	FACETS	0.97	0.794	1	0.97	0.794	1	CLONAL	1	TRUE	1	0.13	2		417	555	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940442	13940442	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	37	392	0	ENST00000405192.2:c.1064A>G	p.Gln355Arg	p.Q355R	ENST00000405192	NM_001163147.1	355	cAg/cGg	11/12	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.13	2		392	477	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512628	148512628	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	19	269	0	ENST00000320356.2:c.1516G>A	p.Ala506Thr	p.A506T	ENST00000320356	NM_004456.4	506	Gca/Aca	13/20	1	2	FACETS	0.905	0.687	1	0.905	0.687	1	CLONAL	1	TRUE	1	0.13	2		269	323	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180318	27180318	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	29	491	0	ENST00000380036.4:c.982G>T	p.Gly328Ter	p.G328*	ENST00000380036	NM_000459.3	328	Gga/Tga	7/23	1	2	FACETS	0.773	0.619	0.95	0.773	0.619	0.95	CLONAL	1	TRUE	1	0.13	2		491	577	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300870	137300870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1174764642	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	40	644	1	ENST00000481739.1:c.515G>A	p.Arg172His	p.R172H	ENST00000481739	NM_002957.4	172	cGc/cAc	4/10	1	2	FACETS	0.792	0.656	0.944	0.792	0.656	0.944	CLONAL	1	TRUE	1	0.13	2		645	777	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390535	139390535	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	46	671	0	ENST00000277541.6:c.7656G>T	p.Glu2552Asp	p.E2552D	ENST00000277541	NM_017617.3	2552	gaG/gaT	34/34	1	2	FACETS	0.96	0.807	1	0.96	0.807	1	CLONAL	1	TRUE	1	0.13	2		671	737	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781504	NA	P-0032797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	648	659	0	ENST00000269305.4:c.314G>T	p.Gly105Val	p.G105V	ENST00000269305	NM_001126112.2	105	gGc/gTc	4/11	0.779373542684697	3	FACETS	0.972	0.952	0.991	0.972	0.952	0.991	CLONAL	3	TRUE	0	0.785552971982888	3		659	788	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0032797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	346	485	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	0.785552971982888	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.785552971982888	3		485	605	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783285	9783285	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	402	545	0	ENST00000377346.4:c.2529C>A	p.Asn843Lys	p.N843K	ENST00000377346	NM_005026.3	843	aaC/aaA	20/24	0.773716262969676	2	FACETS	0.999	0.971	1	0.999	0.971	1	CLONAL	2	TRUE	0	0.785552971982888	2		545	512	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417850	32417850	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	130	512	0	ENST00000332351.3:c.1202G>C	p.Arg401Thr	p.R401T	ENST00000332351	NM_024426.4	401	aGa/aCa	7/10	0.785552971982888	3	FACETS	0.694	0.631	0.761	0.347	0.315	0.381	SUBCLONAL	1	TRUE	1	0.785552971982888	3		512	664	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36024649	36024649	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	215	769	0	ENST00000358208.4:c.638G>T	p.Gly213Val	p.G213V	ENST00000358208		213	gGc/gTc	6/12	0.659585209276302	4	FACETS	0.823	0.764	0.884	0.411	0.382	0.442	CLONAL	1	TRUE	2	0.785552971982888	4		769	1188	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457985	69457985	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771952150	NA	P-0032813-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	58	251	0	ENST00000227507.2:c.385G>A	p.Asp129Asn	p.D129N	ENST00000227507	NM_053056.2	129	Gac/Aac	2/5	0.725339816200689	2	FACETS	0.539	0.466	0.616	0.269	0.233	0.308	SUBCLONAL	1	TRUE	0	0.727565627304612	2		251	296	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517475	176517475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751304047	NA	P-0032813-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	75	550	1	ENST00000292408.4:c.176G>A	p.Arg59Gln	p.R59Q	ENST00000292408	NM_213647.1	59	cGg/cAg	3/18	0.467236609830207	3	FACETS	0.534	0.468	0.604	0.267	0.234	0.302	SUBCLONAL	1	TRUE	1	0.727565627304612	3		551	527	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0032813-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	231	490	0	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.727565627304612	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.727565627304612	1		490	355	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874536	155874536	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032813-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	97	503	0	ENST00000368323.3:c.223G>C	p.Asp75His	p.D75H	ENST00000368323	NM_006912.5	75	Gat/Cat	4/6	0.360957246931201	1	FACETS	0.38	0.34	0.421	0.38	0.34	0.421	INDETERMINATE	1	TRUE	0	0.727565627304612	1		503	447	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949057	71949085	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	GCTCCCCCTGACATGCCCTGTTTCCTTAG	GCTCCCCCTGACATGCCCTGTTTCCTTAG	-	novel	NA	P-0032813-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	15	416	0	ENST00000298229.2:c.3553-24_3557del		p.X1185_splice	ENST00000298229	NM_001567.3	1185			0.725339816200689	2	FACETS	0.147	0.107	0.195	0.074	0.053	0.098	SUBCLONAL	1	TRUE	0	0.727565627304612	2		416	280	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216554	7216581	+	frameshift_variant	Frame_Shift_Del	DEL	GGTTAGCATGTTCCATCTGCTTTTGCAA	GGTTAGCATGTTCCATCTGCTTTTGCAA	-	novel	NA	P-0032813-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	78	455	1	ENST00000380728.2:c.754_781del	p.Leu252SerfsTer84	p.L252Sfs*84	ENST00000380728		252	TTGCAAAAGCAGATGGAACATGCTAACCag/ag	9/11	0.727565627304612	1	FACETS	0.382	0.338	0.429	0.382	0.338	0.429	SUBCLONAL	1	TRUE	0	0.727565627304612	1		456	357	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61749764	61749766	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0032813-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	141	467	0	ENST00000401558.2:c.281_283del	p.Leu94del	p.L94del	ENST00000401558	NM_003400.3	94	cTTCca/cca	4/25	1	2	FACETS	0.834	0.765	0.904	0.834	0.765	0.904	CLONAL	1	TRUE	1	0.727565627304612	2		467	465	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288638	33288638	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032813-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	65	388	0	ENST00000374542.5:c.914C>A	p.Pro305His	p.P305H	ENST00000374542	NM_001141970.1	305	cCc/cAc	3/8	NA	2	FACETS	0.358	0.311	0.409			1	INDETERMINATE	1	TRUE	NA	0.727565627304612	2		388	499	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760279	133760279	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032813-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	82	421	1	ENST00000318560.5:c.2602G>T	p.Gly868Cys	p.G868C	ENST00000318560	NM_005157.4	868	Ggc/Tgc	11/11	0.727565627304612	1	FACETS	0.598	0.535	0.662	0.598	0.535	0.662	SUBCLONAL	1	TRUE	0	0.727565627304612	1		422	240	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222406	53222406	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032813-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	21	609	0	ENST00000375401.3:c.4426G>C	p.Glu1476Gln	p.E1476Q	ENST00000375401	NM_004187.3	1476	Gag/Cag	26/26	0.727565627304612	1	FACETS	0.122	0.093	0.155	0.122	0.093	0.155	SUBCLONAL	1	TRUE	0	0.727565627304612	1		609	302	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054212	30054212	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	56	449	0	ENST00000338641.4:c.634C>T	p.Gln212Ter	p.Q212*	ENST00000338641	NM_000268.3	212	Cag/Tag	7/16	0.235463336961844	1	FACETS	0.867	0.744	1	0.867	0.744	1	CLONAL	1	TRUE	0	0.235463336961844	1		449	484	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143035	58143035	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	47	581	0	ENST00000257904.6:c.749C>G	p.Pro250Arg	p.P250R	ENST00000257904	NM_000075.3	250	cCc/cGc	7/8	0.196857164026266	3	FACETS	0.642	0.54	0.754	0.321	0.27	0.377	SUBCLONAL	1	TRUE	1	0.235463336961844	3		581	695	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36217144	36217144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	72	589	0	ENST00000222270.7:c.3893C>T	p.Ser1298Leu	p.S1298L	ENST00000222270	NM_014727.1	1298	tCa/tTa	14/37	1	2	FACETS	0.903	0.789	1	0.903	0.789	1	CLONAL	1	TRUE	1	0.235463336961844	2		589	677	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639023	176639025	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0032853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	51	502	0	ENST00000439151.2:c.3625_3627del	p.Pro1209del	p.P1209del	ENST00000439151	NM_022455.4	1208	aCTCct/act	5/23	0.111820327181887	3	FACETS	0.888	0.755	1	0.444	0.377	0.518	INDETERMINATE	1	TRUE	1	0.235463336961844	3		502	545	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407513	407513	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	49	445	0	ENST00000380956.4:c.1271T>C	p.Phe424Ser	p.F424S	ENST00000380956	NM_001195286.1	424	tTc/tCc	9/9	NA	2	FACETS	1	0.894	1			1	INDETERMINATE	1	TRUE	NA	0.235463336961844	2		445	390	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971132	21971133	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0032853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	49	296	0	ENST00000304494.5:c.225dup	p.Ala76ArgfsTer44	p.A76Rfs*44	ENST00000304494	NM_000077.4	75	-/C	2/3	0.235463336961844	1	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	0	0.235463336961844	1		296	364	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs786203436	NA	P-0032995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	163	835	0	ENST00000269305.4:c.487T>A	p.Tyr163Asn	p.Y163N	ENST00000269305	NM_001126112.2	163	Tac/Aac	5/11	0.286419517915139	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.286419517915139	2		835	512	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667635	29667638	+	frameshift_variant	Frame_Shift_Del	DEL	TAGA	TAGA	-	novel	NA	P-0032995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	118	591	0	ENST00000356175.3:c.6974_6977del	p.Asp2325ValfsTer49	p.D2325Vfs*49	ENST00000356175	NM_000267.3	2324	tTAGAt/tt	46/57	0.286419517915139	2	FACETS	0.951	0.865	1	0.951	0.865	1	CLONAL	2	TRUE	0	0.286419517915139	2		591	433	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436986	110436986	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779042709	NA	P-0032995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	10	33	0	ENST00000375856.3:c.1415C>T	p.Pro472Leu	p.P472L	ENST00000375856	NM_003749.2	472	cCg/cTg	1/2	0.286419517915139	2	FACETS	0.776	0.542	1	0.776	0.542	1	CLONAL	2	TRUE	0	0.286419517915139	2		33	45	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246550	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	TC	TC	CG	novel	NA	P-0032995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	265	544	0	ENST00000349310.3:c.49_50delinsCG	p.Glu17Arg	p.E17R	ENST00000349310	NM_001014432.1	17	GAg/CGg	4/15	0.286419517915139	6	FACETS	1	0.983	1	1	0.983	1	CLONAL	5	TRUE	1	0.286419517915139	6		544	536	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873748	35873748	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	45	522	0	ENST00000216797.5:c.103G>T	p.Asp35Tyr	p.D35Y	ENST00000216797	NM_020529.2	35	Gac/Tac	1/6	1	2	FACETS	0.436	0.365	0.513	0.436	0.365	0.513	SUBCLONAL	1	FALSE	1	0.33064903518859	2		522	625	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842680	68842691	+	inframe_deletion	In_Frame_Del	DEL	ATTATTGAAAGA	ATTATTGAAAGA	-	novel	NA	P-0033058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	52	655	0	ENST00000261769.5:c.616_627del	p.Ile206_Arg209del	p.I206_R209del	ENST00000261769	NM_004360.3	206	ATTATTGAAAGA/-	5/16	1	2	FACETS	0.925	0.791	1	0.925	0.791	1	CLONAL	1	FALSE	1	0.33064903518859	2		655	340	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875055	151875055	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	44	216	1	ENST00000262189.6:c.7483C>T	p.Gln2495Ter	p.Q2495*	ENST00000262189	NM_170606.2	2495	Caa/Taa	38/59	0.320292911206418	3	FACETS	0.958	0.806	1	0.479	0.403	0.562	CLONAL	1	TRUE	1	0.329328697352838	3		217	325	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0033120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	149	811	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.700363347867272	3	FACETS	0.892	0.848	0.934	0.892	0.848	0.934	CLONAL	3	TRUE	0	0.787440097827515	3		811	197	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0033120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	62	303	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.744696533712644	4	FACETS	1	0.92	1	0.269	0.234	0.305	CLONAL	1	TRUE	0	0.787440097827515	4		303	262	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447842	49447842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1280814073	NA	P-0033120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	149	639	1	ENST00000301067.7:c.592G>A	p.Ala198Thr	p.A198T	ENST00000301067	NM_003482.3	198	Gcg/Acg	5/54	0.748538855033947	2	FACETS	0.98	0.933	1	0.98	0.933	1	CLONAL	2	TRUE	0	0.787440097827515	2		640	193	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056285	180056285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762045883	NA	P-0033120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	176	835	0	ENST00000261937.6:c.959G>A	p.Arg320Gln	p.R320Q	ENST00000261937	NM_182925.4	320	cGg/cAg	7/30	0.77433883646661	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	TRUE	1	0.787440097827515	4		835	258	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998629	100998630	+	missense_variant	Missense_Mutation	DNP	CT	CT	AC	novel	NA	P-0033120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	58	517	0	ENST00000325455.5:c.1172_1173delinsGT	p.Glu391Gly	p.E391G	ENST00000325455	NM_001202474.3	391	gAG/gGT	1/8	1	2	FACETS	0.814	0.712	0.92	0.814	0.712	0.92	CLONAL	1	TRUE	1	0.787440097827515	2		517	181	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30099965	30099965	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	72	537	3	ENST00000331968.5:c.1655C>A	p.Thr552Lys	p.T552K	ENST00000331968	NM_002742.2	552	aCa/aAa	10/18	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.787440097827515	2		540	170	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348982	11348982	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	78	482	1	ENST00000332029.2:c.354G>T	p.Lys118Asn	p.K118N	ENST00000332029	NM_003745.1	118	aaG/aaT	2/2	0.75069326710003	2	FACETS	1	0.969	1	0.597	0.539	0.655	CLONAL	1	TRUE	0	0.787440097827515	2		483	166	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004674	16004674	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	71	766	1	ENST00000268712.3:c.2580G>T	p.Leu860Phe	p.L860F	ENST00000268712	NM_006311.3	860	ttG/ttT	20/46	0.700363347867272	3	FACETS	0.762	0.682	0.843	0.508	0.454	0.562	SUBCLONAL	2	TRUE	0	0.787440097827515	3		767	165	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591865	48591865	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	31	657	0	ENST00000342988.3:c.1028C>A	p.Ser343Ter	p.S343*	ENST00000342988	NM_005359.5	343	tCa/tAa	9/12	0.725422490563611	1	FACETS	0.783	0.666	0.898	0.783	0.666	0.898	SUBCLONAL	1	TRUE	0	0.787440097827515	1		657	61	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793373	42793373	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	167	617	1	ENST00000575354.2:c.1175C>A	p.Ser392Tyr	p.S392Y	ENST00000575354	NM_015125.3	392	tCt/tAt	8/20	0.77433883646661	4	FACETS	0.936	0.882	0.988	0.936	0.882	0.988	CLONAL	3	TRUE	1	0.787440097827515	4		618	270	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750770	39750770	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	48	668	0	ENST00000361337.2:c.2170C>G	p.Leu724Val	p.L724V	ENST00000361337	NM_003286.2	724	Ctg/Gtg	20/21	0.787440097827515	3	FACETS	0.858	0.735	0.99	0.429	0.367	0.495	CLONAL	1	TRUE	1	0.787440097827515	3		668	198	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79965995	79965995	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	45	604	0	ENST00000265081.6:c.659C>A	p.Ser220Ter	p.S220*	ENST00000265081	NM_002439.4	220	tCa/tAa	4/24	0.104870084859766	4	FACETS	0.817	0.705	0.934	0.817	0.705	0.934	INDETERMINATE	2	TRUE	2	0.787440097827515	4		604	125	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271236	26271236	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	69	554	1	ENST00000305910.3:c.377A>T	p.Gln126Leu	p.Q126L	ENST00000305910	NM_003534.2	126	cAg/cTg	1/1	0.787440097827515	4	FACETS	0.911	0.812	1	0.455	0.406	0.506	CLONAL	2	TRUE	0	0.787440097827515	4		555	172	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2955007	2955007	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0033120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	62	581	1	ENST00000396946.4:c.2704-1G>T		p.X902_splice	ENST00000396946	NM_032415.4	902			0.787440097827515	3	FACETS	1	0.942	1	0.563	0.494	0.634	CLONAL	1	TRUE	1	0.787440097827515	3		582	195	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0033167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	288	556	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.982	0.931	1	0.982	0.931	1	CLONAL	1	TRUE	1	0.889861170930718	2		557	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0033167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	517	710	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.889861170930718	2		710	1088	SUCCESS
ATR	545	MSKCC	GRCh37	3	142243011	142243011	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	518	447	0	ENST00000350721.4:c.3976G>T	p.Glu1326Ter	p.E1326*	ENST00000350721	NM_001184.3	1326	Gaa/Taa	22/47	0.768326155925759	4	FACETS	0.946	0.909	0.983	0.946	0.909	0.983	CLONAL	2	TRUE	2	0.889861170930718	4		447	1163	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642456	117642456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759091073	NA	P-0033167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	521	752	0	ENST00000368508.3:c.5743G>A	p.Gly1915Arg	p.G1915R	ENST00000368508	NM_002944.2	1915	Gga/Aga	35/43	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.889861170930718	2		752	1157	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589607	67589612	+	inframe_deletion	In_Frame_Del	DEL	AAGAAA	AAGAAA	-	novel	NA	P-0033167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	179	220	0	ENST00000274335.5:c.1372_1377del	p.Glu458_Lys459del	p.E458_K459del	ENST00000274335		457	cAAGAAAaa/caa	10/15	0.889861170930718	2	FACETS	0.927	0.891	0.96	0.927	0.891	0.96	CLONAL	2	TRUE	0	0.889861170930718	2		220	217	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896549	78896549	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774124294	NA	P-0033167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	2180	847	1	ENST00000306801.3:c.2546G>A	p.Arg849His	p.R849H	ENST00000306801	NM_020761.2	849	cGc/cAc	22/34	0.883272085885709	4	FACETS	1	0.998	1	1	0.998	1	CLONAL	4	TRUE	0	0.889861170930718	4		848	2285	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896536	78896536	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770010373	NA	P-0033167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1253	987	828	0	ENST00000306801.3:c.2533G>A	p.Ala845Thr	p.A845T	ENST00000306801	NM_020761.2	845	Gcc/Acc	22/34	0.883272085885709	4	FACETS	0.936	0.909	0.963	0.468	0.454	0.482	CLONAL	2	TRUE	0	0.889861170930718	4		828	2240	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303260	15303260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555729604	NA	P-0033167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	576	821	1	ENST00000263388.2:c.268C>T	p.Arg90Cys	p.R90C	ENST00000263388	NM_000435.2	90	Cgt/Tgt	3/33	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.889861170930718	2		822	1253	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396278	139396278	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376689092	NA	P-0033167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1192	539	852	1	ENST00000277541.6:c.5560C>T	p.Arg1854Cys	p.R1854C	ENST00000277541	NM_017617.3	1854	Cgc/Tgc	30/34	0.860656614466528	3	FACETS	1	0.967	1	0.506	0.484	0.528	CLONAL	1	TRUE	1	0.889861170930718	3		853	1731	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913407	NA	P-0033238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	52	222	0	ENST00000349496.5:c.133T>G	p.Ser45Ala	p.S45A	ENST00000349496	NM_001904.3	45	Tct/Gct	3/15	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.49	2		222	192	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858152	40858152	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	83	536	0	ENST00000428826.2:c.1712A>G	p.Gln571Arg	p.Q571R	ENST00000428826		571	cAa/cGa	16/21	1	2	FACETS	0.911	0.809	1	0.911	0.809	1	CLONAL	1	TRUE	1	0.49	2		536	372	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	212	720	1	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.674636996877188	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.674636996877188	1		721	395	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057834	27057835	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0033444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	116	440	0	ENST00000324856.7:c.1542_1543insG	p.Gln515AlafsTer108	p.Q515Afs*108	ENST00000324856	NM_006015.4	514	-/G	3/20	0.655573784385703	1	FACETS	0.959	0.886	1	0.959	0.886	1	CLONAL	1	TRUE	0	0.701349296479179	1		440	224	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519920	NA	P-0033444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	34	215	0	ENST00000397062.3:c.85G>C	p.Asp29His	p.D29H	ENST00000397062	NM_006164.4	29	Gat/Cat	2/5	0.236507626771397	3	FACETS	0.753	0.622	0.895	0.376	0.311	0.448	INDETERMINATE	1	TRUE	1	0.701349296479179	3		215	174	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215219	142215219	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	68	264	0	ENST00000350721.4:c.5882A>C	p.Lys1961Thr	p.K1961T	ENST00000350721	NM_001184.3	1961	aAg/aCg	34/47	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.701349296479179	2		264	175	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444590	187444590	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	36	322	0	ENST00000232014.4:c.1637A>T	p.Tyr546Phe	p.Y546F	ENST00000232014	NM_001130845.1	546	tAc/tTc	7/10	0.276376653798268	4	FACETS	0.525	0.432	0.627	0.262	0.216	0.314	INDETERMINATE	1	TRUE	2	0.701349296479179	4		322	333	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176516694	176516694	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	43	262	0	ENST00000292408.4:c.91G>C	p.Glu31Gln	p.E31Q	ENST00000292408	NM_213647.1	31	Gag/Cag	2/18	1	2	FACETS	0.487	0.41	0.57	0.487	0.41	0.57	SUBCLONAL	1	TRUE	1	0.701349296479179	2		262	252	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	188	425	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.593548285330294	2		426	615	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	188	410	2	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.996	0.925	1	0.996	0.925	1	CLONAL	1	TRUE	1	0.593548285330294	2		412	636	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913559	32913559	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359479	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	189	435	2	ENST00000380152.3:c.5073del	p.Lys1691AsnfsTer15	p.K1691Nfs*15	ENST00000380152		1689	gcA/gc	11/27	1	2	FACETS	0.883	0.819	0.95	0.883	0.819	0.95	CLONAL	1	TRUE	1	0.593548285330294	2		437	721	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	282	526	1	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.593548285330294	2		527	906	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420315	88420315	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773244598	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	168	449	1	ENST00000360948.2:c.2371C>T	p.Arg791Trp	p.R791W	ENST00000360948	NM_001012338.2	791	Cgg/Tgg	19/19	1	2	FACETS	0.91	0.84	0.982	0.91	0.84	0.982	CLONAL	1	TRUE	1	0.593548285330294	2		450	622	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	139	278	2	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	0.808	0.749	0.866	1	0.99	1	CLONAL	2	TRUE	1	0.593548285330294	2		280	290	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	142	328	5	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	1	2	FACETS	0.896	0.821	0.974	0.896	0.821	0.974	CLONAL	1	TRUE	1	0.593548285330294	2		333	534	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023747	27023747	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	208	447	0	ENST00000324856.7:c.853G>T	p.Gly285Ter	p.G285*	ENST00000324856	NM_006015.4	285	Gga/Tga	1/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.593548285330294	2		447	646	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099103	27099103	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	184	448	0	ENST00000324856.7:c.3524del	p.Pro1175HisfsTer5	p.P1175Hfs*5	ENST00000324856	NM_006015.4	1173	atC/at	13/20	1	2	FACETS	0.96	0.89	1	0.96	0.89	1	CLONAL	1	TRUE	1	0.593548285330294	2		448	646	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630626	158630626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912678	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	120	239	0	ENST00000263640.3:c.617G>A	p.Arg206His	p.R206H	ENST00000263640	NM_001105.4	206	cGc/cAc	6/11	0.593548285330294	3	FACETS	0.88	0.797	0.967	0.44	0.398	0.484	CLONAL	1	TRUE	1	0.593548285330294	3		239	596	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156719	20156719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	254	580	0	ENST00000379607.5:c.38G>A	p.Arg13His	p.R13H	ENST00000379607	NM_001412.3	13	cGc/cAc	2/7	1	2	FACETS	0.917	0.86	0.976	0.917	0.86	0.976	CLONAL	1	TRUE	1	0.593548285330294	2		580	933	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522190	157522190	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	255	581	0	ENST00000346085.5:c.4466del	p.Pro1489LeufsTer5	p.P1489Lfs*5	ENST00000346085	NM_020732.3	1488	Ccc/cc	18/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.593548285330294	2		581	797	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	207	530	0	ENST00000263967.3:c.317G>A	p.Gly106Asp	p.G106D	ENST00000263967	NM_006218.2	106	gGc/gAc	2/21	1	2	FACETS	0.906	0.843	0.971	0.906	0.843	0.971	CLONAL	1	TRUE	1	0.593548285330294	2		530	770	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380346	14380346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	174	313	0	ENST00000256196.4:c.71G>A	p.Gly24Asp	p.G24D	ENST00000256196		24	gGc/gAc	1/6	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.593548285330294	2		313	497	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599234	28599234	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	307	789	2	ENST00000253063.3:c.685del	p.Gln229ArgfsTer18	p.Q229Rfs*18	ENST00000253063	NM_031459.4	227	gCc/gc	5/10	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.593548285330294	2		791	1015	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	156	740	2	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	1	2	FACETS	0.627	0.574	0.681	0.627	0.574	0.681	SUBCLONAL	1	TRUE	1	0.593548285330294	2		742	839	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436343	110436343	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	159	424	0	ENST00000375856.3:c.2058del	p.Lys687SerfsTer140	p.K687Sfs*140	ENST00000375856	NM_003749.2	686	ccC/cc	1/2	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.593548285330294	2		424	512	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042041	42042041	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	263	588	0	ENST00000219905.7:c.6240del	p.Val2081TrpfsTer21	p.V2081Wfs*21	ENST00000219905	NM_001164273.1	2079	gAa/ga	17/24	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.593548285330294	2		588	872	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258036	123258036	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	299	700	0	ENST00000358487.5:c.1645A>G	p.Asn549Asp	p.N549D	ENST00000358487	NM_000141.4	549	Aat/Gat	12/18	1	2	FACETS	0.986	0.93	1	0.986	0.93	1	CLONAL	1	TRUE	1	0.593548285330294	2		700	1022	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28601436	28601436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	313	714	0	ENST00000253063.3:c.1121C>T	p.Thr374Ile	p.T374I	ENST00000253063	NM_031459.4	374	aCc/aTc	8/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.593548285330294	2		714	1007	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670459	246670459	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	247	611	0	ENST00000388985.4:c.61G>A	p.Val21Met	p.V21M	ENST00000388985		21	Gtg/Atg	1/12	0.555296198797859	4	FACETS	0.999	0.932	1	0.333	0.31	0.356	CLONAL	1	TRUE	1	0.593548285330294	4		611	1328	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456750	32456750	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	267	610	0	ENST00000332351.3:c.142G>A	p.Ala48Thr	p.A48T	ENST00000332351	NM_024426.4	48	Gcc/Acc	1/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.593548285330294	2		610	829	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873823	35873823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	179	331	0	ENST00000216797.5:c.28G>A	p.Glu10Lys	p.E10K	ENST00000216797	NM_020529.2	10	Gag/Aag	1/6	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.593548285330294	2		331	566	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828986	72828986	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	276	778	2	ENST00000268489.5:c.7595G>A	p.Cys2532Tyr	p.C2532Y	ENST00000268489	NM_006885.3	2532	tGt/tAt	9/10	1	2	FACETS	0.904	0.849	0.96	0.904	0.849	0.96	CLONAL	1	TRUE	1	0.593548285330294	2		780	1029	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993444	72993444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370976962	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	344	878	0	ENST00000268489.5:c.601G>A	p.Ala201Thr	p.A201T	ENST00000268489	NM_006885.3	201	Gcc/Acc	2/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.593548285330294	2		878	1038	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244612	41244612	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80356985	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	338	841	1	ENST00000357654.3:c.2936G>A	p.Arg979His	p.R979H	ENST00000357654	NM_007294.3	979	cGt/cAt	10/23	1	2	FACETS	0.986	0.933	1	0.986	0.933	1	CLONAL	1	TRUE	1	0.593548285330294	2		842	1155	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621019	1621019	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	368	815	0	ENST00000344749.5:c.1041T>A	p.Asn347Lys	p.N347K	ENST00000344749	NM_001136139.2	347	aaT/aaA	13/19	0.276980660480484	1	FACETS	0.769	0.73	0.809	0.769	0.73	0.809	INDETERMINATE	1	TRUE	0	0.593548285330294	1		815	1134	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085979	16085979	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	235	509	0	ENST00000281043.3:c.1155C>A	p.Asn385Lys	p.N385K	ENST00000281043	NM_005378.4	385	aaC/aaA	3/3	0.593548285330294	3	FACETS	1	0.978	1	0.554	0.517	0.592	CLONAL	1	TRUE	1	0.593548285330294	3		509	927	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703569	47703569	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	293	688	0	ENST00000233146.2:c.2069A>G	p.Gln690Arg	p.Q690R	ENST00000233146	NM_000251.2	690	cAa/cGa	13/16	0.593548285330294	3	FACETS	1	0.96	1	0.514	0.483	0.546	CLONAL	1	TRUE	1	0.593548285330294	3		688	1246	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209110100	209110100	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	322	671	1	ENST00000345146.2:c.463A>T	p.Thr155Ser	p.T155S	ENST00000345146	NM_005896.2	155	Acc/Tcc	5/10	0.593548285330294	3	FACETS	1	0.977	1	0.533	0.503	0.565	CLONAL	1	TRUE	1	0.593548285330294	3		672	1319	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456643	138456643	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	282	540	0	ENST00000289153.2:c.707G>T	p.Gly236Val	p.G236V	ENST00000289153	NM_006219.2	236	gGg/gTg	4/22	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.593548285330294	2		540	892	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31435970	31435970	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs777416100	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	133	250	1	ENST00000344624.3:c.2944G>A	p.Val982Ile	p.V982I	ENST00000344624		982	Gtc/Atc	22/33	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.593548285330294	2		251	416	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181822	56181822	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	223	455	0	ENST00000399503.3:c.4046A>G	p.Tyr1349Cys	p.Y1349C	ENST00000399503	NM_005921.1	1349	tAc/tGc	17/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.593548285330294	2		455	717	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673261	30673262	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	270	587	0	ENST00000376406.3:c.3698dup	p.Asn1233LysfsTer2	p.N1233Kfs*2	ENST00000376406	NM_014641.2	1233	aat/aaAt	10/15	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.593548285330294	2		587	906	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880236	151880236	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	202	464	0	ENST00000262189.6:c.5088del	p.Ala1697ProfsTer20	p.A1697Pfs*20	ENST00000262189	NM_170606.2	1696	aaA/aa	35/59	1	2	FACETS	0.94	0.874	1	0.94	0.874	1	CLONAL	1	TRUE	1	0.593548285330294	2		464	724	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981360	68981360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1474820456	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	154	352	2	ENST00000288368.4:c.1432G>A	p.Val478Met	p.V478M	ENST00000288368	NM_024870.2	478	Gtg/Atg	12/40	1	2	FACETS	0.875	0.804	0.948	0.875	0.804	0.948	CLONAL	1	TRUE	1	0.593548285330294	2		354	593	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357213	70357213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773945032	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	169	586	2	ENST00000374080.3:c.5728C>T	p.Arg1910Cys	p.R1910C	ENST00000374080		1910	Cgc/Tgc	39/45	1	2	FACETS	0.83	0.766	0.897	0.83	0.766	0.897	CLONAL	1	TRUE	1	0.593548285330294	2		588	686	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418437	49418437	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	281	719	2	ENST00000301067.7:c.15976del	p.Met5327TrpfsTer6	p.M5327Wfs*6	ENST00000301067	NM_003482.3	5326	Ctt/tt	50/54	1	2	FACETS	0.937	0.881	0.994	0.937	0.881	0.994	CLONAL	1	TRUE	1	0.593548285330294	2		721	1011	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0033647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	154	207	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.119586985349672	3	FACETS	0.961	0.887	1	1	0.988	1	INDETERMINATE	3	TRUE	1	0.260213498438753	3		207	464	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663299	227663301	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs753296153	NA	P-0033647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	180	428	0	ENST00000305123.5:c.154_156del	p.Lys52del	p.K52del	ENST00000305123	NM_005544.2	52	AAG/-	1/2	0.119586985349672	3	FACETS	0.882	0.818	0.948	1	0.988	1	INDETERMINATE	3	TRUE	1	0.260213498438753	3		428	591	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932110	39932111	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555918014	NA	P-0033647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	208	333	0	ENST00000378444.4:c.2488_2489del	p.Ser830CysfsTer6	p.S830Cfs*6	ENST00000378444	NM_001123385.1	830	AGt/t	4/15	0.145041368009684	2	FACETS	0.961	0.905	1			1	INDETERMINATE	4	TRUE	NA	0.260213498438753	2		333	416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579412	7579413	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCA	novel	NA	P-0033647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	525	577	0	ENST00000269305.4:c.271_274dup	p.Pro92LeufsTer58	p.P92Lfs*58	ENST00000269305	NM_001126112.2	92	ccc/cTGGCcc	4/11	0.260213498438753	2	FACETS	0.953	0.927	0.977	1	0.998	1	CLONAL	6	TRUE	0	0.260213498438753	2		577	706	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814246	76814248	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	novel	NA	P-0033647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	212	162	0	ENST00000373344.5:c.6396_6398del	p.Ile2134del	p.I2134del	ENST00000373344	NM_000489.3	2132	gtAATt/gtt	29/35	1	1	FACETS	0.914	0.872	0.956	1	0.996	1	CLONAL	5	TRUE	0	0.260213498438753	1		162	310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579349	7579349	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	474	610	0	ENST00000269305.4:c.338T>C	p.Phe113Ser	p.F113S	ENST00000269305	NM_001126112.2	113	tTc/tCc	4/11	0.802514534368533	3	FACETS	0.955	0.932	0.976	0.955	0.932	0.976	CLONAL	3	FALSE	0	0.802514534368533	3		610	578	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436086	51436086	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	51	270	0	ENST00000262662.1:c.46G>A	p.Gly16Arg	p.G16R	ENST00000262662		16	Ggg/Agg	3/4	0.687123255202629	5	FACETS	0.639	0.544	0.744	0.213	0.181	0.248	SUBCLONAL	1	FALSE	2	0.802514534368533	5		270	438	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826520	50826520	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	104	335	0	ENST00000398568.2:c.2245C>G	p.Leu749Val	p.L749V	ENST00000398568	NM_001042412.1	749	Ctg/Gtg	15/18	0.157020611252995	6	FACETS	1	0.974	1			1	INDETERMINATE	1	FALSE	NA	0.802514534368533	6		335	537	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243801005	243801005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	130	482	0	ENST00000263826.5:c.469G>A	p.Gly157Ser	p.G157S	ENST00000263826	NM_005465.4	157	Ggc/Agc	5/13	NA	2	FACETS	0.634	0.578	0.692			1	INDETERMINATE	1	FALSE	NA	0.802514534368533	2		482	511	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749149	43749150	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0033818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	219	737	0	ENST00000382044.4:c.1656_1657del	p.Thr553GlyfsTer10	p.T553Gfs*10	ENST00000382044	NM_001141980.1	552	gaTAcg/gacg	12/28	0.802514534368533	2	FACETS	0.946	0.887	1	0.473	0.443	0.503	CLONAL	1	FALSE	0	0.802514534368533	2		737	577	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754047	42754047	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	194	611	0	ENST00000222329.4:c.305T>A	p.Phe102Tyr	p.F102Y	ENST00000222329	NM_006494.2	102	tTc/tAc	3/4	0.614074262254559	5	FACETS	0.878	0.811	0.948	0.293	0.27	0.316	CLONAL	1	FALSE	2	0.802514534368533	5		611	1213	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456523	29456523	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	170	579	0	ENST00000389048.3:c.2395A>C	p.Asn799His	p.N799H	ENST00000389048	NM_004304.4	799	Aat/Cat	14/29	0.802514534368533	2	FACETS	1	0.955	1	0.517	0.481	0.553	CLONAL	1	FALSE	0	0.802514534368533	2		579	410	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554955	106554955	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs750519043	NA	P-0033818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	79	376	0	ENST00000369096.4:c.2072A>G	p.Gln691Arg	p.Q691R	ENST00000369096	NM_001198.3	691	cAg/cGg	7/7	0.802514534368533	6	FACETS	0.822	0.723	0.928	0.205	0.18	0.232	CLONAL	1	FALSE	2	0.802514534368533	6		376	624	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	88	463	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.908	0.813	1	0.908	0.813	1	CLONAL	1	TRUE	1	0.631404961985774	2		463	307	SUCCESS
ATR	545	MSKCC	GRCh37	3	142257354	142257354	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs201150434	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	46	414	0	ENST00000350721.4:c.3695C>A	p.Ala1232Asp	p.A1232D	ENST00000350721	NM_001184.3	1232	gCt/gAt	19/47	1	2	FACETS	0.554	0.47	0.645	0.554	0.47	0.645	SUBCLONAL	1	TRUE	1	0.631404961985774	2		414	263	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	15	406	0	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	0.631404961985774	1	FACETS	0.164	0.12	0.217	0.164	0.12	0.217	SUBCLONAL	1	TRUE	0	0.631404961985774	1		406	198	SUCCESS
APC	324	MSKCC	GRCh37	5	112137081	112137081	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1554076225	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	41	192	0	ENST00000257430.4:c.834+1G>A		p.X278_splice	ENST00000257430	NM_000038.5	278			0.118919804398412	4	FACETS	0.768	0.653	0.89	0.768	0.653	0.89	INDETERMINATE	2	TRUE	2	0.631404961985774	4		192	138	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003747	45003747	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs1057519877	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	27	381	0	ENST00000558401.1:c.3G>A	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	atG/atA	1/4	1	2	FACETS	0.213	0.169	0.264	0.213	0.169	0.264	SUBCLONAL	1	TRUE	1	0.631404961985774	2		381	401	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	46	360	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	0.442	0.373	0.516	0.442	0.373	0.516	SUBCLONAL	1	TRUE	1	0.631404961985774	2		360	330	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	47	244	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.118919804398412	4	FACETS	0.832	0.717	0.953	0.832	0.717	0.953	INDETERMINATE	2	TRUE	2	0.631404961985774	4		244	146	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	95	824	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	0.734	0.658	0.814	0.734	0.658	0.814	SUBCLONAL	1	TRUE	1	0.631404961985774	2		824	410	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404348	139404348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773847667	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	36	640	0	ENST00000277541.6:c.2806G>A	p.Gly936Ser	p.G936S	ENST00000277541	NM_017617.3	936	Ggc/Agc	18/34	0.194251347279379	1	FACETS	0.166	0.136	0.2	0.166	0.136	0.2	INDETERMINATE	1	TRUE	0	0.631404961985774	1		640	470	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900984	114900984	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778855667	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	101	437	0	ENST00000543371.1:c.598del	p.Leu200SerfsTer25	p.L200Sfs*25	ENST00000543371	NM_001198531.1	198	caC/ca	6/14	1	2	FACETS	0.804	0.724	0.887	0.804	0.724	0.887	CLONAL	1	TRUE	1	0.631404961985774	2		437	398	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397700	49397700	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	72	444	2	ENST00000418115.1:c.524C>T	p.Thr175Met	p.T175M	ENST00000418115	NM_001664.2	175	aCg/aTg	5/5	0.118919804398412	4	FACETS	0.926	0.813	1	0.463	0.406	0.523	INDETERMINATE	1	TRUE	2	0.631404961985774	4		446	402	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884834	111884834	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs181079548	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	12	322	0	ENST00000341259.2:c.923G>A	p.Arg308Gln	p.R308Q	ENST00000341259	NM_005475.2	308	cGa/cAa	4/8	0.302660541967741	4	FACETS	0.277	0.194	0.378	0.138	0.097	0.189	INDETERMINATE	1	TRUE	2	0.631404961985774	4		322	224	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023957	31023957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139435094	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	49	505	1	ENST00000375687.4:c.3442C>T	p.Arg1148Cys	p.R1148C	ENST00000375687	NM_015338.5	1148	Cgc/Tgc	13/13	0.265804812667933	2	FACETS	0.478	0.406	0.555	0.239	0.203	0.278	INDETERMINATE	1	TRUE	0	0.631404961985774	2		506	325	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151290	202151290	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	137	339	0	ENST00000358485.4:c.1596del	p.Lys532AsnfsTer73	p.K532Nfs*73	ENST00000358485	NM_001080125.1	530	agA/ag	9/9	0.352838991416814	3	FACETS	1	0.981	1	0.621	0.569	0.674	INDETERMINATE	1	TRUE	1	0.631404961985774	3		339	460	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029511	16029511	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	34	369	0	ENST00000268712.3:c.1519C>T	p.Arg507Ter	p.R507*	ENST00000268712	NM_006311.3	507	Cga/Tga	15/46	1	2	FACETS	0.263	0.215	0.318	0.263	0.215	0.318	SUBCLONAL	1	TRUE	1	0.631404961985774	2		369	409	SUCCESS
AR	367	MSKCC	GRCh37	X	66943588	66943588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886041133	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	15	457	0	ENST00000374690.3:c.2668G>A	p.Val890Met	p.V890M	ENST00000374690	NM_000044.3	890	Gtg/Atg	8/8	0.515827455204518	1	FACETS	0.156	0.114	0.206	0.156	0.114	0.206	SUBCLONAL	1	TRUE	0	0.631404961985774	1		457	209	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119780	70119781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	19	528	0	ENST00000245479.2:c.788dup	p.Arg264GlnfsTer32	p.R264Qfs*32	ENST00000245479	NM_000346.3	261	gag/gaGg	3/3	1	2	FACETS	0.204	0.154	0.262	0.204	0.154	0.262	SUBCLONAL	1	TRUE	1	0.631404961985774	2		528	295	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293605	1293605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	16	650	1	ENST00000310581.5:c.1396C>T	p.Arg466Trp	p.R466W	ENST00000310581	NM_198253.2	466	Cgg/Tgg	2/16	0.528410868552737	1	FACETS	0.112	0.082	0.147	0.112	0.082	0.147	SUBCLONAL	1	TRUE	0	0.631404961985774	1		651	310	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523271	9523271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775109543	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	67	522	1	ENST00000353224.5:c.1966C>T	p.Arg656Trp	p.R656W	ENST00000353224	NM_177990.2	656	Cgg/Tgg	9/10	0.265804812667933	2	FACETS	1	0.914	1	0.52	0.46	0.583	INDETERMINATE	1	TRUE	0	0.631404961985774	2		523	204	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740749	58740749	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs779070661	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	19	426	1	ENST00000305921.3:c.1654C>T	p.Arg552Ter	p.R552*	ENST00000305921	NM_003620.3	552	Cga/Tga	6/6	1	2	FACETS	0.203	0.153	0.26	0.203	0.153	0.26	SUBCLONAL	1	TRUE	1	0.631404961985774	2		427	297	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966754	18966754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568279022	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	96	603	3	ENST00000262803.5:c.1565C>T	p.Pro522Leu	p.P522L	ENST00000262803	NM_002911.3	522	cCg/cTg	12/24	1	2	FACETS	0.71	0.637	0.788	0.71	0.637	0.788	SUBCLONAL	1	TRUE	1	0.631404961985774	2		606	428	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807319	3807319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1315374383	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	47	333	0	ENST00000262367.5:c.3668G>A	p.Arg1223His	p.R1223H	ENST00000262367	NM_004380.2	1223	cGc/cAc	19/31	1	2	FACETS	0.584	0.496	0.678	0.584	0.496	0.678	SUBCLONAL	1	TRUE	1	0.631404961985774	2		333	255	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436299	110436299	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1406456002	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	17	169	1	ENST00000375856.3:c.2102C>T	p.Ala701Val	p.A701V	ENST00000375856	NM_003749.2	701	gCc/gTc	1/2	0.605794554577814	5	FACETS	0.439	0.328	0.57	0.146	0.109	0.19	SUBCLONAL	1	TRUE	2	0.631404961985774	5		170	239	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513676	41513676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs996577997	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	19	496	0	ENST00000263253.7:c.580G>A	p.Gly194Ser	p.G194S	ENST00000263253	NM_001429.3	194	Ggt/Agt	2/31	1	2	FACETS	0.223	0.169	0.286	0.223	0.169	0.286	SUBCLONAL	1	TRUE	1	0.631404961985774	2		496	270	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981111	201981111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	125	491	0	ENST00000359651.3:c.190C>T	p.Pro64Ser	p.P64S	ENST00000359651		64	Ccc/Tcc	2/8	1	2	FACETS	0.802	0.73	0.876	0.802	0.73	0.876	CLONAL	1	TRUE	1	0.631404961985774	2		491	494	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114799795	114799795	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	83	360	0	ENST00000543371.1:c.462G>T	p.Met154Ile	p.M154I	ENST00000543371	NM_001198531.1	154	atG/atT	5/14	1	2	FACETS	0.942	0.842	1	0.942	0.842	1	CLONAL	1	TRUE	1	0.631404961985774	2		360	279	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125513702	125513702	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775245290	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	36	344	0	ENST00000428830.2:c.830G>A	p.Arg277Gln	p.R277Q	ENST00000428830	NM_001114121.2	277	cGa/cAa	9/14	1	2	FACETS	0.507	0.42	0.603	0.507	0.42	0.603	SUBCLONAL	1	TRUE	1	0.631404961985774	2		344	225	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435248	49435248	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	23	642	0	ENST00000301067.7:c.6305T>C	p.Leu2102Pro	p.L2102P	ENST00000301067	NM_003482.3	2102	cTa/cCa	31/54	0.302660541967741	4	FACETS	0.323	0.251	0.406	0.161	0.125	0.203	INDETERMINATE	1	TRUE	2	0.631404961985774	4		642	368	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440181	49440181	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762536289	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	76	494	0	ENST00000301067.7:c.4445C>T	p.Ala1482Val	p.A1482V	ENST00000301067	NM_003482.3	1482	gCt/gTt	16/54	0.302660541967741	4	FACETS	1	0.96	1	0.601	0.531	0.674	INDETERMINATE	1	TRUE	2	0.631404961985774	4		494	327	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527897	103527897	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	16	238	0	ENST00000355739.4:c.3205A>G	p.Ser1069Gly	p.S1069G	ENST00000355739	NM_000123.3	1069	Agc/Ggc	15/15	0.605794554577814	5	FACETS	0.389	0.287	0.51	0.13	0.095	0.17	SUBCLONAL	1	TRUE	2	0.631404961985774	5		238	254	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058949	42058949	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs745317244	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	56	344	0	ENST00000219905.7:c.8669T>C	p.Val2890Ala	p.V2890A	ENST00000219905	NM_001164273.1	2890	gTt/gCt	24/24	1	2	FACETS	0.758	0.657	0.866	0.758	0.657	0.866	SUBCLONAL	1	TRUE	1	0.631404961985774	2		344	234	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705316	43705316	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	22	587	1	ENST00000382044.4:c.5305+1G>A		p.X1769_splice	ENST00000382044	NM_001141980.1	1769			1	2	FACETS	0.178	0.138	0.226	0.178	0.138	0.226	SUBCLONAL	1	TRUE	1	0.631404961985774	2		588	391	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828264	72828264	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	29	498	0	ENST00000268489.5:c.8317C>A	p.Leu2773Ile	p.L2773I	ENST00000268489	NM_006885.3	2773	Cta/Ata	9/10	1	2	FACETS	0.367	0.296	0.448	0.367	0.296	0.448	SUBCLONAL	1	TRUE	1	0.631404961985774	2		498	250	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980057	7980057	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	67	466	0	ENST00000319144.4:c.1280T>A	p.Leu427His	p.L427H	ENST00000319144	NM_001139.2	427	cTc/cAc	10/15	1	2	FACETS	0.687	0.602	0.777	0.687	0.602	0.777	SUBCLONAL	1	TRUE	1	0.631404961985774	2		466	309	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604784	48604784	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	48	322	0	ENST00000342988.3:c.1606C>A	p.Leu536Ile	p.L536I	ENST00000342988	NM_005359.5	536	Cta/Ata	12/12	0.631404961985774	1	FACETS	0.65	0.56	0.746	0.65	0.56	0.746	SUBCLONAL	1	TRUE	0	0.631404961985774	1		322	160	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80037342	80037342	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	26	243	0	ENST00000265081.6:c.1628G>T	p.Arg543Met	p.R543M	ENST00000265081	NM_002439.4	543	aGg/aTg	11/24	0.118919804398412	4	FACETS	0.631	0.502	0.776	0.315	0.251	0.388	INDETERMINATE	1	TRUE	2	0.631404961985774	4		243	213	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045896	180045896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	59	373	0	ENST00000261937.6:c.2875C>T	p.Arg959Cys	p.R959C	ENST00000261937	NM_182925.4	959	Cgc/Tgc	21/30	0.631192751873882	1	FACETS	0.707	0.619	0.798	0.707	0.619	0.798	SUBCLONAL	1	TRUE	0	0.631404961985774	1		373	181	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166438	32166438	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	24	531	0	ENST00000375023.3:c.4605G>T	p.Glu1535Asp	p.E1535D	ENST00000375023	NM_004557.3	1535	gaG/gaT	25/30	0.460225909070239	3	FACETS	0.263	0.205	0.329	0.088	0.068	0.11	SUBCLONAL	1	TRUE	0	0.631404961985774	3		531	381	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964370	93964370	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	55	369	0	ENST00000369303.4:c.2527C>A	p.Gln843Lys	p.Q843K	ENST00000369303	NM_004440.3	843	Caa/Aaa	14/17	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.631404961985774	2		369	148	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644891	67644891	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	22	367	0	ENST00000264010.4:c.156G>C	p.Gln52His	p.Q52H	ENST00000264010	NM_006565.3	52	caG/caC	3/12	1	2	FACETS	0.241	0.187	0.304	0.241	0.187	0.304	SUBCLONAL	1	TRUE	1	0.631404961985774	2		367	289	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662326	227662326	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	16	445	0	ENST00000305123.5:c.1129A>G	p.Met377Val	p.M377V	ENST00000305123	NM_005544.2	377	Atg/Gtg	1/2	0.352838991416814	3	FACETS	0.213	0.157	0.28	0.107	0.078	0.14	INDETERMINATE	1	TRUE	1	0.631404961985774	3		445	313	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664567	138664567	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	19	90	0	ENST00000330315.3:c.998del	p.Pro333ArgfsTer23	p.P333Rfs*23	ENST00000330315	NM_023067.3	333	cCg/cg	1/1	0.361596955642267	0	FACETS	0.317	0.247	0.394			1	INDETERMINATE	1	TRUE	0	0.631404961985774	0		90	70	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947178	178947178	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	21	259	0	ENST00000263967.3:c.2614T>C	p.Phe872Leu	p.F872L	ENST00000263967	NM_006218.2	872	Ttc/Ctc	18/21	1	2	FACETS	0.267	0.206	0.338	0.267	0.206	0.338	SUBCLONAL	1	TRUE	1	0.631404961985774	2		259	249	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26046003	26046003	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762724811	NA	P-0033852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	26	272	0	ENST00000540144.1:c.365C>T	p.Pro122Leu	p.P122L	ENST00000540144	NM_003531.2	122	cCc/cTc	1/1	0.631404961985774	5	FACETS	0.489	0.387	0.605	0.122	0.096	0.152	SUBCLONAL	1	TRUE	1	0.631404961985774	5		272	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578234	7578234	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs786202222	NA	P-0034020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	51	706	0	ENST00000269305.4:c.615T>A	p.Tyr205Ter	p.Y205*	ENST00000269305	NM_001126112.2	205	taT/taA	6/11	1	2	FACETS	0.413	0.35	0.483	0.413	0.35	0.483	SUBCLONAL	1	FALSE	1	0.367223597288221	2		706	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138729528	NA	P-0034058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	94	250	0	ENST00000269305.4:c.523C>G	p.Arg175Gly	p.R175G	ENST00000269305	NM_001126112.2	175	Cgc/Ggc	5/11	1	2	FACETS	0.776	0.691	0.866	1	0.981	1	SUBCLONAL	2	TRUE	1	0.178728998389357	2		250	678	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782095	66782095	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	30	464	0	ENST00000307102.5:c.1062A>T	p.Gln354His	p.Q354H	ENST00000307102	NM_002755.3	354	caA/caT	10/11	1	2	FACETS	0.696	0.56	0.851	0.696	0.56	0.851	SUBCLONAL	1	TRUE	1	0.178728998389357	2		464	482	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519395	137519395	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	25	317	0	ENST00000367739.4:c.1243G>T	p.Asp415Tyr	p.D415Y	ENST00000367739	NM_000416.2	415	Gat/Tat	7/7	0.163777116719428	2	FACETS	0.687	0.541	0.856	0.344	0.27	0.428	SUBCLONAL	1	TRUE	0	0.178728998389357	2		317	407	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413559	32413559	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034197-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	41	500	0	ENST00000332351.3:c.1391A>T	p.Asp464Val	p.D464V	ENST00000332351	NM_024426.4	464	gAc/gTc	9/10	0.488152299349484	2	FACETS	0.375	0.313	0.445	0.188	0.156	0.223	SUBCLONAL	1	TRUE	0	0.498714298849582	2		500	438	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225715	26225715	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034197-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	121	524	0	ENST00000360408.1:c.333C>A	p.Cys111Ter	p.C111*	ENST00000360408	NM_003532.2	111	tgC/tgA	1/1	0.476465459964228	4	FACETS	0.938	0.848	1	0.469	0.424	0.517	CLONAL	1	TRUE	2	0.498714298849582	4		524	775	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0034217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	298	425	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.678561918079293	3	FACETS	0.893	0.848	0.938			1	CLONAL	2	TRUE	NA	0.709474993554415	3		426	637	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968633	55968633	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200338299	NA	P-0034217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	256	702	1	ENST00000263923.4:c.2030C>T	p.Thr677Met	p.T677M	ENST00000263923	NM_002253.2	677	aCg/aTg	14/30	1	2	FACETS	0.895	0.841	0.951	0.895	0.841	0.951	CLONAL	1	TRUE	1	0.709474993554415	2		703	806	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625330	69625331	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTACCACA	novel	NA	P-0034217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	227	808	0	ENST00000334134.2:c.455_462dup	p.Val155CysfsTer6	p.V155Cfs*6	ENST00000334134	NM_005247.2	154	-/TGTGGTAC	3/3	1	2	FACETS	0.818	0.765	0.873	0.818	0.765	0.873	CLONAL	1	TRUE	1	0.709474993554415	2		808	782	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220099	133220100	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs758487568	NA	P-0034217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	289	754	14	ENST00000320574.5:c.4337_4338del	p.Val1446GlyfsTer3	p.V1446Gfs*3	ENST00000320574	NM_006231.2	1446	gTG/g	34/49	1	2	FACETS	0.902	0.851	0.955	0.902	0.851	0.955	CLONAL	1	TRUE	1	0.709474993554415	2		768	903	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881435	48881435	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	18	254	0	ENST00000267163.4:c.157G>T	p.Glu53Ter	p.E53*	ENST00000267163	NM_000321.2	53	Gaa/Taa	2/27	0.709474993554415	1	FACETS	0.126	0.094	0.163	0.126	0.094	0.163	SUBCLONAL	1	TRUE	0	0.709474993554415	1		254	260	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463546	25463546	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	237	553	1	ENST00000264709.3:c.2136C>A	p.Asp712Glu	p.D712E	ENST00000264709	NM_175629.2	712	gaC/gaA	18/23	1	2	FACETS	0.981	0.921	1	0.981	0.921	1	CLONAL	1	TRUE	1	0.709474993554415	2		554	681	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	61	851	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	0.0967194974587661	0	FACETS	0.756	0.651	0.87			1	INDETERMINATE	1	TRUE	0	0.19	0		851	688	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	67	293	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	0.963	1	CLONAL	1	TRUE	1	0.19	2		293	537	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	46	384	2	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	0.0967194974587661	3	FACETS	0.843	0.709	0.992	0.421	0.354	0.496	INDETERMINATE	1	TRUE	1	0.19	3		386	629	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	28	289	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.0967194974587661	3	FACETS	1	0.853	1	0.54	0.432	0.662	INDETERMINATE	1	TRUE	1	0.19	3		289	299	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	55	679	2	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	0.0967194974587661	0	FACETS	0.806	0.689	0.933			1	INDETERMINATE	1	TRUE	0	0.19	0		681	582	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850705	63850705	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs201178069	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	28	631	1	ENST00000279873.7:c.1489del	p.Ile497Ter	p.I497*	ENST00000279873	NM_032199.2	495	Aaa/aa	10/10	0.0967194974587661	3	FACETS	1	0.841	1	0.529	0.424	0.649	INDETERMINATE	1	TRUE	1	0.19	3		632	305	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374301	138374301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1170276441	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	58	773	0	ENST00000289153.2:c.3143C>T	p.Ala1048Val	p.A1048V	ENST00000289153	NM_006219.2	1048	gCg/gTg	22/22	1	2	FACETS	0.785	0.673	0.907	0.785	0.673	0.907	CLONAL	1	TRUE	1	0.19	2		773	778	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023769	27023769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	50	427	0	ENST00000324856.7:c.879del	p.Thr294ProfsTer69	p.T294Pfs*69	ENST00000324856	NM_006015.4	292	aCc/ac	1/20	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.19	2		427	449	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319406	11319406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149221273	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	62	742	0	ENST00000361445.4:c.61G>A	p.Val21Ile	p.V21I	ENST00000361445	NM_004958.3	21	Gtc/Atc	2/58	1	2	FACETS	0.906	0.782	1	0.906	0.782	1	CLONAL	1	TRUE	1	0.19	2		742	720	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151186	202151186	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746684914	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	26	283	0	ENST00000358485.4:c.1486G>A	p.Asp496Asn	p.D496N	ENST00000358485	NM_001080125.1	496	Gat/Aat	9/9	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.19	2		283	244	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176330	24176330	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1057517825	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	68	801	0	ENST00000263121.7:c.1121G>A	p.Arg374Gln	p.R374Q	ENST00000263121	NM_003073.3	374	cGg/cAg	9/9	0.0967194974587661	0	FACETS	0.95	0.827	1			1	INDETERMINATE	1	TRUE	0	0.19	0		801	610	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105997	27105997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	33	518	0	ENST00000324856.7:c.5608C>T	p.Pro1870Ser	p.P1870S	ENST00000324856	NM_006015.4	1870	Cct/Tct	20/20	1	2	FACETS	0.849	0.692	1	0.849	0.692	1	CLONAL	1	TRUE	1	0.19	2		518	409	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514302	69514302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1255340343	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	56	691	0	ENST00000294312.3:c.379C>T	p.Arg127Cys	p.R127C	ENST00000294312	NM_005117.2	127	Cgc/Tgc	3/3	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.19	2		691	526	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812205	43812205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866559375	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	65	664	1	ENST00000372470.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000372470	NM_005373.2	357	cGa/cAa	7/12	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.19	2		665	635	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912306	29912306	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761593088	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	83	960	1	ENST00000376809.5:c.925G>A	p.Val309Met	p.V309M	ENST00000376809	NM_002116.7	309	Gtg/Atg	5/8	0.0967194974587661	3	FACETS	1	0.932	1	0.543	0.478	0.613	INDETERMINATE	1	TRUE	1	0.19	3		961	881	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346792	89346792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765013102	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	16	402	0	ENST00000301030.4:c.6158C>T	p.Ala2053Val	p.A2053V	ENST00000301030	NM_001256183.1	2053	gCg/gTg	9/13	1	2	FACETS	0.674	0.498	0.883	0.674	0.498	0.883	SUBCLONAL	1	TRUE	1	0.19	2		402	250	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	44	971	0	ENST00000222270.7:c.520_521dup	p.Lys175GlnfsTer20	p.K175Qfs*20	ENST00000222270	NM_014727.1	172	acc/aCCcc	3/37	0.0967194974587661	0	FACETS	0.438	0.366	0.518			1	INDETERMINATE	1	TRUE	0	0.19	0		971	857	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213971	36213971	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	82	971	0	ENST00000222270.7:c.2801del	p.Gly934GlufsTer52	p.G934Efs*52	ENST00000222270	NM_014727.1	933	Ggg/gg	6/37	0.0967194974587661	0	FACETS	0.851	0.749	0.96			1	INDETERMINATE	1	TRUE	0	0.19	0		971	822	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31435934	31435936	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	36	438	0	ENST00000344624.3:c.2978_2980del	p.Glu993del	p.E993del	ENST00000344624		993	gAAGga/gga	22/33	1	2	FACETS	0.82	0.674	0.984	0.82	0.674	0.984	CLONAL	1	TRUE	1	0.19	2		438	462	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106074	27106074	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	28	555	0	ENST00000324856.7:c.5688del	p.Pro1898HisfsTer25	p.P1898Hfs*25	ENST00000324856	NM_006015.4	1895	gaG/ga	20/20	1	2	FACETS	0.693	0.554	0.853	0.693	0.554	0.853	SUBCLONAL	1	TRUE	1	0.19	2		555	425	SUCCESS
FH	2271	MSKCC	GRCh37	1	241683013	241683013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	26	429	0	ENST00000366560.3:c.10G>A	p.Ala4Thr	p.A4T	ENST00000366560	NM_000143.3	4	Gca/Aca	1/10	1	2	FACETS	0.619	0.49	0.768	0.619	0.49	0.768	SUBCLONAL	1	TRUE	1	0.19	2		429	442	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115000	3115000	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	58	949	0	ENST00000078429.4:c.535G>A	p.Val179Met	p.V179M	ENST00000078429	NM_002067.2	179	Gtg/Atg	4/7	0.0967194974587661	0	FACETS	0.686	0.588	0.793			1	INDETERMINATE	1	TRUE	0	0.19	0		949	721	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344959	70344959	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	57	717	1	ENST00000374080.3:c.2189G>A	p.Arg730Gln	p.R730Q	ENST00000374080		730	cGa/cAa	15/45	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.19	2		718	584	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630861	187630861	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371144856	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	52	631	0	ENST00000441802.2:c.121G>A	p.Val41Ile	p.V41I	ENST00000441802	NM_005245.3	41	Gtc/Atc	2/27	1	2	FACETS	0.75	0.637	0.874	0.75	0.637	0.874	SUBCLONAL	1	TRUE	1	0.19	2		631	730	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814756	139814756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376884527	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	58	718	1	ENST00000247668.2:c.749C>T	p.Ser250Leu	p.S250L	ENST00000247668	NM_021138.3	250	tCg/tTg	8/11	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.19	2		719	574	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275300	142275300	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878996572	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	51	621	0	ENST00000350721.4:c.2003G>A	p.Arg668Gln	p.R668Q	ENST00000350721	NM_001184.3	668	cGg/cAg	9/47	1	2	FACETS	0.81	0.687	0.945	0.81	0.687	0.945	CLONAL	1	TRUE	1	0.19	2		621	663	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118594	17118594	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750104212	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	43	624	2	ENST00000285071.4:c.1337G>A	p.Arg446His	p.R446H	ENST00000285071	NM_144997.5	446	cGt/cAt	12/14	0.0967194974587661	0	FACETS	0.643	0.538	0.761			1	INDETERMINATE	1	TRUE	0	0.19	0		626	570	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968314	18968314	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	76	910	0	ENST00000262803.5:c.2154G>T	p.Glu718Asp	p.E718D	ENST00000262803	NM_002911.3	718	gaG/gaT	15/24	0.0967194974587661	0	FACETS	0.773	0.677	0.877			1	INDETERMINATE	1	TRUE	0	0.19	0		910	838	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637504	47637505	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs63751622	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	33	487	0	ENST00000233146.2:c.638_639del	p.Leu213GlnfsTer18	p.L213Qfs*18	ENST00000233146	NM_000251.2	213	cTG/c	3/16	1	2	FACETS	0.765	0.623	0.926	0.765	0.623	0.926	CLONAL	1	TRUE	1	0.19	2		487	454	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612184	189612184	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	46	656	0	ENST00000264731.3:c.1936C>A	p.Leu646Ile	p.L646I	ENST00000264731	NM_003722.4	646	Ctc/Atc	14/14	1	2	FACETS	0.691	0.58	0.813	0.691	0.58	0.813	SUBCLONAL	1	TRUE	1	0.19	2		656	701	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973958	55973958	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	50	568	1	ENST00000263923.4:c.1358del	p.Pro453ArgfsTer24	p.P453Rfs*24	ENST00000263923	NM_002253.2	453	cCg/cg	10/30	1	2	FACETS	0.841	0.712	0.982	0.841	0.712	0.982	CLONAL	1	TRUE	1	0.19	2		569	626	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522052	157522052	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs779375711	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	47	527	0	ENST00000346085.5:c.4324G>T	p.Gly1442Ter	p.G1442*	ENST00000346085	NM_020732.3	1442	Gga/Tga	18/20	0.0967194974587661	3	FACETS	1	0.947	1	0.648	0.548	0.758	INDETERMINATE	1	TRUE	1	0.19	3		527	418	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983932	2983932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	82	1016	4	ENST00000396946.4:c.598G>A	p.Asp200Asn	p.D200N	ENST00000396946	NM_032415.4	200	Gac/Aac	5/25	0.0967194974587661	3	FACETS	0.906	0.797	1	0.453	0.398	0.512	INDETERMINATE	1	TRUE	1	0.19	3		1020	1043	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240795	55240795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373336251	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	65	977	1	ENST00000275493.2:c.2039G>A	p.Arg680Gln	p.R680Q	ENST00000275493	NM_005228.3	680	cGg/cAg	17/28	0.0967194974587661	3	FACETS	0.979	0.848	1	0.49	0.424	0.561	INDETERMINATE	1	TRUE	1	0.19	3		978	765	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509312	106509312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376853134	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	69	662	1	ENST00000359195.3:c.1306G>A	p.Gly436Ser	p.G436S	ENST00000359195	NM_002649.2	436	Ggt/Agt	2/11	0.0967194974587661	3	FACETS	1	0.96	1	0.635	0.553	0.724	INDETERMINATE	1	TRUE	1	0.19	3		663	626	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231250	98231250	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	53	817	0	ENST00000331920.6:c.2033C>T	p.Thr678Ile	p.T678I	ENST00000331920	NM_000264.3	678	aCc/aTc	14/24	1	2	FACETS	0.692	0.589	0.806	0.692	0.589	0.806	SUBCLONAL	1	TRUE	1	0.19	2		817	806	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228160	53228160	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	53	612	0	ENST00000375401.3:c.2242C>T	p.Arg748Trp	p.R748W	ENST00000375401	NM_004187.3	748	Cgg/Tgg	15/26	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.19	2		612	533	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711906	89711906	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	150	596	1	ENST00000371953.3:c.524T>A	p.Val175Glu	p.V175E	ENST00000371953	NM_000314.4	175	gTg/gAg	6/9	1	2	FACETS	0.512	0.469	0.556	0.512	0.469	0.556	SUBCLONAL	1	TRUE	1	0.909914057115858	2		597	644	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0034400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	38	92	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.366	0.305	0.434	0.366	0.305	0.434	SUBCLONAL	1	TRUE	1	0.909914057115858	2		92	228	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645308	67645308	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	90	463	0	ENST00000264010.4:c.573G>A	p.Trp191Ter	p.W191*	ENST00000264010	NM_006565.3	191	tgG/tgA	3/12	1	2	FACETS	0.364	0.324	0.407	0.364	0.324	0.407	SUBCLONAL	1	TRUE	1	0.909914057115858	2		463	543	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0034400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	124	377	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.604	0.55	0.66	0.604	0.55	0.66	SUBCLONAL	1	TRUE	1	0.909914057115858	2		377	451	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936083	178936083	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519927	NA	P-0034400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	83	452	0	ENST00000263967.3:c.1625A>T	p.Glu542Val	p.E542V	ENST00000263967	NM_006218.2	542	gAa/gTa	10/21	1	2	FACETS	0.514	0.457	0.574	0.514	0.457	0.574	SUBCLONAL	1	TRUE	1	0.909914057115858	2		452	355	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100093	157100120	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGCGGCGGCGGCAGCAGCAGGAGGCG	GCGGCGGCGGCGGCAGCAGCAGGAGGCG	-	rs1554247989	NA	P-0034400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	20	47	0	ENST00000346085.5:c.1044_1071del	p.Ala349MetfsTer11	p.A349Mfs*11	ENST00000346085	NM_020732.3	344	GCGGCGGCGGCGGCAGCAGCAGGAGGCGgc/gc	1/20	1	2	FACETS	0.771	0.613	0.94	0.771	0.613	0.94	CLONAL	1	TRUE	1	0.909914057115858	2		47	57	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs775623976	NA	P-0034445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	210	381	0	ENST00000335508.6:c.1873C>G	p.Arg625Gly	p.R625G	ENST00000335508	NM_012433.2	625	Cgt/Ggt	14/25	0.485481250998019	4	FACETS	0.963	0.9	1	0.963	0.9	1	CLONAL	2	TRUE	2	0.565039316372428	4		381	604	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643334	52643334	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	99	339	0	ENST00000394830.3:c.2562G>A	p.Met854Ile	p.M854I	ENST00000394830	NM_018313.4	854	atG/atA	17/30	0.565039316372428	3	FACETS	0.868	0.777	0.963	0.434	0.388	0.482	CLONAL	1	TRUE	1	0.565039316372428	3		339	518	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913514	NA	P-0034445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	2349	453	0	ENST00000288135.5:c.2466T>G	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaG	17/21	0.565039316372428	19	FACETS	0.979	0.969	0.988			1	CLONAL	18	TRUE	NA	0.565039316372428	19		453	2738	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551408	141551408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1205353566	NA	P-0034445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	185	597	0	ENST00000220592.5:c.1889G>A	p.Arg630His	p.R630H	ENST00000220592	NM_012154.3	630	cGc/cAc	15/19	0.565039316372428	5	FACETS	1	0.964	1	0.358	0.33	0.388	CLONAL	1	TRUE	2	0.565039316372428	5		597	1125	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223352	53223353	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0034445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	310	552	1	ENST00000375401.3:c.4006dup	p.Leu1336ProfsTer11	p.L1336Pfs*11	ENST00000375401	NM_004187.3	1336	ctc/cCtc	23/26	0.549570618226016	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.565039316372428	2		553	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0034607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	426	385	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	0.997	0.957	1			1	INDETERMINATE	2	TRUE	NA	0.522994070589136	2		385	817	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905151	50905151	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137953986	NA	P-0034607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	497	904	1	ENST00000440232.2:c.433G>A	p.Ala145Thr	p.A145T	ENST00000440232	NM_002691.3	145	Gct/Act	4/27	0.522994070589136	2	FACETS	0.966	0.929	1	0.966	0.929	1	CLONAL	2	TRUE	0	0.522994070589136	2		905	984	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266513	198266513	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	81	404	0	ENST00000335508.6:c.2323C>T	p.Arg775Ter	p.R775*	ENST00000335508	NM_012433.2	775	Cga/Tga	16/25	0.522260064558273	3	FACETS	0.699	0.617	0.787	0.35	0.308	0.394	SUBCLONAL	1	TRUE	1	0.522994070589136	3		404	559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0034727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	269	580	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.691277152208266	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.70032617382842	1		580	476	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0034727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	33	169	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.694007918484733	1	FACETS	0.839	0.713	0.967	0.839	0.713	0.967	CLONAL	1	TRUE	0	0.70032617382842	1		169	73	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78931459	78931459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761590823	NA	P-0034727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	176	762	3	ENST00000306801.3:c.3406G>A	p.Gly1136Ser	p.G1136S	ENST00000306801	NM_020761.2	1136	Ggc/Agc	29/34	0.110056613510168	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.70032617382842	0		765	491	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95593044	95593046	+	missense_variant	Missense_Mutation	TNP	GGT	GGT	CCA	novel	NA	P-0034727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	136	677	1	ENST00000393063.1:c.774_776delinsTGG	p.Pro259Gly	p.P259G	ENST00000393063	NM_030621.3	258	ggACCa/ggTGGa	8/28	0.276510392924665	3	FACETS	1	0.975	1	0.583	0.534	0.633	INDETERMINATE	1	TRUE	1	0.70032617382842	3		678	450	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827888	72827888	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	187	852	0	ENST00000268489.5:c.8693C>T	p.Ala2898Val	p.A2898V	ENST00000268489	NM_006885.3	2898	gCc/gTc	9/10	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.70032617382842	2		852	531	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575673	48575673	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	136	763	2	ENST00000342988.3:c.433G>T	p.Gly145Ter	p.G145*	ENST00000342988	NM_005359.5	145	Gga/Tga	4/12	0.691277152208266	1	FACETS	0.994	0.925	1	0.994	0.925	1	CLONAL	1	TRUE	0	0.70032617382842	1		765	254	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047332	128047332	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	144	632	0	ENST00000285398.2:c.590G>A	p.Cys197Tyr	p.C197Y	ENST00000285398	NM_000122.1	197	tGc/tAc	5/15	1	2	FACETS	0.914	0.841	0.989	0.914	0.841	0.989	CLONAL	1	TRUE	1	0.70032617382842	2		632	450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0034730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	226	644	0	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	0.677681548889222	1	FACETS	0.94	0.889	0.99	0.94	0.889	0.99	CLONAL	1	TRUE	0	0.727111205420015	1		644	421	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692926	89692926	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	21	478	0	ENST00000371953.3:c.410C>A	p.Ala137Glu	p.A137E	ENST00000371953	NM_000314.4	137	gCa/gAa	5/9	0.727111205420015	1	FACETS	0.094	0.072	0.12	0.094	0.072	0.12	SUBCLONAL	1	TRUE	0	0.727111205420015	1		478	390	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571952	64571953	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTTCAT	novel	NA	P-0034730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	364	706	0	ENST00000312049.6:c.1681_1686dup	p.Met561_Lys562dup	p.M561_K562dup	ENST00000312049	NM_130799.2	561	-/ATGAAG	10/10	0.727111205420015	1	FACETS	0.938	0.898	0.978	0.938	0.898	0.978	CLONAL	1	TRUE	0	0.727111205420015	1		706	679	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087944	27087944	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0034811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	217	706	0	ENST00000324856.7:c.2231C>G	p.Ser744Ter	p.S744*	ENST00000324856	NM_006015.4	744	tCa/tGa	6/20	1	2	FACETS	0.928	0.866	0.991	0.928	0.866	0.991	CLONAL	1	TRUE	1	0.636378921648251	2		706	735	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519717	NA	P-0034811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	179	676	1	ENST00000206249.3:c.1607T>G	p.Leu536Arg	p.L536R	ENST00000206249	NM_000125.3	536	cTc/cGc	8/8	1	2	FACETS	0.887	0.822	0.955	0.887	0.822	0.955	CLONAL	1	TRUE	1	0.636378921648251	2		677	634	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942745	68942745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781270008	NA	P-0034811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2030	127	415	1	ENST00000288368.4:c.557G>A	p.Arg186Gln	p.R186Q	ENST00000288368	NM_024870.2	186	cGg/cAg	6/40	0.636378921648251	13	FACETS	0.833	0.75	0.92	0.069	0.062	0.077	CLONAL	1	TRUE	1	0.636378921648251	13		416	2157	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335072	65335072	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	34	563	0	ENST00000342505.4:c.569T>C	p.Leu190Pro	p.L190P	ENST00000342505	NM_002227.2	190	cTa/cCa	6/25	0.626180902329285	1	FACETS	0.151	0.123	0.183	0.151	0.123	0.183	SUBCLONAL	1	TRUE	0	0.636378921648251	1		563	481	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339208	65339208	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0034811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	138	393	0	ENST00000342505.4:c.330-2A>T		p.X110_splice	ENST00000342505	NM_002227.2	110			0.626180902329285	1	FACETS	0.85	0.784	0.917	0.85	0.784	0.917	CLONAL	1	TRUE	0	0.636378921648251	1		393	348	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795102	242795102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	42	788	0	ENST00000334409.5:c.107C>T	p.Thr36Ile	p.T36I	ENST00000334409	NM_005018.2	36	aCc/aTc	2/5	NA	2	FACETS	0.173	0.143	0.205			1	INDETERMINATE	1	TRUE	NA	0.636378921648251	2		788	765	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562505	176562505	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	242	743	0	ENST00000439151.2:c.401A>C	p.Asn134Thr	p.N134T	ENST00000439151	NM_022455.4	134	aAc/aCc	2/23	1	2	FACETS	0.935	0.876	0.996	0.935	0.876	0.996	CLONAL	1	TRUE	1	0.636378921648251	2		743	813	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674320	117674320	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	34	492	0	ENST00000368508.3:c.4154T>C	p.Leu1385Pro	p.L1385P	ENST00000368508	NM_002944.2	1385	cTt/cCt	26/43	1	2	FACETS	0.183	0.149	0.222	0.183	0.149	0.222	SUBCLONAL	1	TRUE	1	0.636378921648251	2		492	583	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087944	27087944	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0034811-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	163	706	0	ENST00000324856.7:c.2231C>G	p.Ser744Ter	p.S744*	ENST00000324856	NM_006015.4	744	tCa/tGa	6/20	1	2	FACETS	0.89	0.818	0.966	0.89	0.818	0.966	CLONAL	1	TRUE	1	0.458834481325418	2		706	798	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519717	NA	P-0034811-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	209	676	1	ENST00000206249.3:c.1607T>G	p.Leu536Arg	p.L536R	ENST00000206249	NM_000125.3	536	cTc/cGc	8/8	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.458834481325418	2		677	863	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562505	176562505	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034811-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	207	743	0	ENST00000439151.2:c.401A>C	p.Asn134Thr	p.N134T	ENST00000439151	NM_022455.4	134	aAc/aCc	2/23	1	2	FACETS	0.891	0.826	0.957	0.891	0.826	0.957	CLONAL	1	TRUE	1	0.458834481325418	2		743	1013	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65316513	65316513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755406627	NA	P-0034811-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	48	521	0	ENST00000342505.4:c.1729C>T	p.Arg577Trp	p.R577W	ENST00000342505	NM_002227.2	577	Cgg/Tgg	12/25	0.132713529290174	0	FACETS	0.247	0.209	0.289			1	INDETERMINATE	1	TRUE	0	0.458834481325418	0		521	458	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305330	65305330	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs904855653	NA	P-0034811-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	75	607	0	ENST00000342505.4:c.2798A>G	p.Tyr933Cys	p.Y933C	ENST00000342505	NM_002227.2	933	tAt/tGt	20/25	0.132713529290174	0	FACETS	0.294	0.257	0.333			1	INDETERMINATE	1	TRUE	0	0.458834481325418	0		607	602	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0034821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	216	542	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.747869545497644	1	FACETS	0.825	0.778	0.873	0.825	0.778	0.873	CLONAL	1	TRUE	0	0.753497535057542	1		543	433	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720702	89720702	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	70	86	0	ENST00000371953.3:c.853G>T	p.Glu285Ter	p.E285*	ENST00000371953	NM_000314.4	285	Gaa/Taa	8/9	0.672893834352463	2	FACETS	0.948	0.874	1	0.948	0.874	1	CLONAL	2	TRUE	0	0.753497535057542	2		86	98	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88651942	88651942	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	32	398	0	ENST00000372037.3:c.289G>C	p.Ala97Pro	p.A97P	ENST00000372037	NM_004329.2	97	Gct/Cct	5/13	0.672893834352463	2	FACETS	0.388	0.317	0.467	0.194	0.158	0.234	SUBCLONAL	1	TRUE	0	0.753497535057542	2		398	219	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202134	67202134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776604371	NA	P-0034821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	70	618	3	ENST00000312629.5:c.1237C>T	p.Arg413Cys	p.R413C	ENST00000312629	NM_003952.2	413	Cgc/Tgc	14/15	0.753497535057542	6	FACETS	0.395	0.343	0.452	0.079	0.068	0.091	SUBCLONAL	1	TRUE	1	0.753497535057542	6		621	1179	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943945	71943946	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0034821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	26	730	0	ENST00000298229.2:c.1880_1881del	p.Glu627ValfsTer2	p.E627Vfs*2	ENST00000298229	NM_001567.3	626	aaAGag/aaag	16/28	0.753497535057542	1	FACETS	0.154	0.122	0.19	0.154	0.122	0.19	SUBCLONAL	1	TRUE	0	0.753497535057542	1		730	280	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011227	12011228	+	splice_donor_variant	Splice_Site	DEL	GT	GT	-	novel	NA	P-0034821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	60	332	0	ENST00000353533.5:c.633+1_633+2del		p.X211_splice	ENST00000353533	NM_003010.3	211			0.747869545497644	1	FACETS	0.827	0.738	0.916	0.827	0.738	0.916	CLONAL	1	TRUE	0	0.753497535057542	1		332	120	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654672	29654673	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0034821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	109	365	0	ENST00000356175.3:c.5363dup	p.Leu1789AlafsTer9	p.L1789Afs*9	ENST00000356175	NM_000267.3	1787	-/C	37/57	0.747869545497644	1	FACETS	0.855	0.787	0.922	0.855	0.787	0.922	CLONAL	1	TRUE	0	0.753497535057542	1		365	211	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451932	29451932	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	49	567	0	ENST00000389048.3:c.2633G>T	p.Gly878Val	p.G878V	ENST00000389048	NM_004304.4	878	gGt/gTt	16/29	0.261424299643209	1	FACETS	0.232	0.197	0.271	0.232	0.197	0.271	INDETERMINATE	1	TRUE	0	0.753497535057542	1		567	349	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589599	67589600	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAA	novel	NA	P-0034821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	70	239	0	ENST00000274335.5:c.1364_1365insACA	p.Gln455dup	p.Q455dup	ENST00000274335		455	-/CAA	10/15	0.479826832484338	1	FACETS	0.633	0.563	0.704	0.633	0.563	0.704	SUBCLONAL	1	TRUE	0	0.753497535057542	1		239	183	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574000	7574000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	648	570	2	ENST00000269305.4:c.1027G>T	p.Glu343Ter	p.E343*	ENST00000269305	NM_001126112.2	343	Gag/Tag	10/11	0.63275263958594	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.63275263958594	2		572	991	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602797	10602797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	69	748	0	ENST00000171111.5:c.781C>T	p.Arg261Trp	p.R261W	ENST00000171111	NM_203500.1	261	Cgg/Tgg	3/6	0.63275263958594	1	FACETS	0.185	0.16	0.212	0.185	0.16	0.212	SUBCLONAL	1	TRUE	0	0.63275263958594	1		748	806	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285120	15285120	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	385	643	0	ENST00000263388.2:c.4495G>T	p.Asp1499Tyr	p.D1499Y	ENST00000263388	NM_000435.2	1499	Gat/Tat	25/33	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.63275263958594	2		643	1124	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375215	15375215	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	182	379	0	ENST00000263377.2:c.1212G>C	p.Lys404Asn	p.K404N	ENST00000263377	NM_058243.2	404	aaG/aaC	6/20	1	2	FACETS	0.99	0.919	1	0.99	0.919	1	CLONAL	1	TRUE	1	0.63275263958594	2		379	581	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993751	90993751	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	56	253	0	ENST00000265433.3:c.172A>C	p.Ser58Arg	p.S58R	ENST00000265433	NM_002485.4	58	Agt/Cgt	3/16	0.623667213496727	3	FACETS	0.675	0.581	0.777	0.338	0.29	0.389	SUBCLONAL	1	TRUE	1	0.63275263958594	3		253	345	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0035011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	79	671	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.808	0.713	0.91	0.808	0.713	0.91	CLONAL	1	TRUE	1	0.403159768132309	2		671	485	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615110	43615110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	70	645	0	ENST00000355710.3:c.2524G>A	p.Asp842Asn	p.D842N	ENST00000355710	NM_020975.4	842	Gat/Aat	14/20	1	2	FACETS	0.793	0.694	0.899	0.793	0.694	0.899	SUBCLONAL	1	TRUE	1	0.403159768132309	2		645	438	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129803	108129803	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs914092098	NA	P-0035011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	106	309	0	ENST00000278616.4:c.2466+1G>A		p.X822_splice	ENST00000278616	NM_000051.3	822			0.403159768132309	1	FACETS	0.967	0.873	1	0.967	0.873	1	CLONAL	1	TRUE	0	0.403159768132309	1		309	434	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207112	1207112	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	129	726	0	ENST00000326873.7:c.200del	p.Leu67ArgfsTer29	p.L67Rfs*29	ENST00000326873	NM_000455.4	67	cTg/cg	1/10	0.403159768132309	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.403159768132309	1		726	492	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028610	42028610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761482641	NA	P-0035107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	132	571	0	ENST00000219905.7:c.4148G>A	p.Arg1383Gln	p.R1383Q	ENST00000219905	NM_001164273.1	1383	cGg/cAg	13/24	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.27	2		571	916	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578476	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0035107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	197	750	0	ENST00000269305.4:c.454_455del	p.Pro152AlafsTer28	p.P152Afs*28	ENST00000269305	NM_001126112.2	152	CCg/g	5/11	1	2	FACETS	0.777	0.72	0.837	1	0.991	1	SUBCLONAL	2	TRUE	1	0.27	2		750	939	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578440	7578440	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0035120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	870	737	0	ENST00000269305.4:c.490A>T	p.Lys164Ter	p.K164*	ENST00000269305	NM_001126112.2	164	Aag/Tag	5/11	0.753430414870476	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.755374952981217	2		737	1113	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35857155	35857155	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	118	246	0	ENST00000303115.3:c.76C>G	p.Gln26Glu	p.Q26E	ENST00000303115	NM_002185.3	26	Caa/Gaa	1/8	0.755374952981217	6	FACETS	0.86	0.775	0.95	0.215	0.193	0.238	CLONAL	1	TRUE	2	0.755374952981217	6		246	912	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70432771	70432771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	233	513	0	ENST00000373644.4:c.4793G>A	p.Arg1598Lys	p.R1598K	ENST00000373644	NM_030625.2	1598	aGa/aAa	8/12	0.739037277148891	3	FACETS	0.987	0.923	1	0.494	0.461	0.527	CLONAL	1	TRUE	1	0.755374952981217	3		513	861	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369115	118369115	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	253	354	0	ENST00000534358.1:c.5833A>G	p.Thr1945Ala	p.T1945A	ENST00000534358	NM_005933.3	1945	Acc/Gcc	22/36	0.71289113992495	3	FACETS	1	0.97	1	0.528	0.495	0.562	CLONAL	1	TRUE	1	0.755374952981217	3		354	874	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875353	35876375	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTCCCAGAGGTATATTATTGTCATGTCTTGTTCACAGAATGGATTGATATCTGTGGTCTCTGGTCCAACCCCTCCTTGAATTGATAGGGCCCCGAGGCCCAGAGAAAGCCAGTCTCTTGACCATGGTCACCCACCTAATTGTGTTAGAGCCAAGACTAGAAATCTGTTCTTCTGATTCCAAGCTCAGAATAAGTGGGAAGACTCAGTGTGCCTGTGCCCTCTGCCATTCACTTCATCTATCAATGTTCTCTGATTTCAGGATTAAGCCTATCGTATGGCCCAGTCTCCCCGATCATAAGAAGACTCTGGAACATCTTTGTAAGAAACCAAGAAAAGTGAGTGTTTTTGGTGCTTAAAAAGTGTTGTGTTGGCAACATCCCAGTGGCCAAGAATGATATTCCAGGACAAGGAACAGTTGAACCTCACCTTTTGGTATTTGATTCATCCTGTAACTAGGGTCCCTCCTAAGACCCTAGCTGCAGTAGGGAACTGAAATAAGATACACATCTCAGAACTTCTGGGCTCCCTGGGGCTGGAGGGCACAGCCAGTGGTCACTTCAAGTCTTGAAGTGTCTCAGAAGCTCCAGAAGCAAAGAGTCCATTGAGGAACATGCTGGCAATTCTGTGACATTCCCTGTCAGAAAACTCTATAGACCTACTCCTGAACTGAACATTTGATGGTGTGTCTCTCTGGTGCCATCTTAATACCCTTTCTCCTTTTTCTGTGCAGAATTTAAATGTGAGTTTCAATCCTGAAAGTTTCCTGGACTGCCAGATTCATAGGGTGGATGACATTCAAGCTAGAGATGAAGTGGAAGGTTTTCTGCAAGATACGTTTCCTCAGCAACTAGAAGAATCTGAGAAGCAGAGGCTTGGAGGGGATGTGCAGAGCCCCAACTGCCCATCTGAGGATGTAGTCATCACTCCAGAAAGCTTTGGAAGAGATTCATCCCTCACATGCCTGGCTGGGAATGTCAGTGCATGTGACGCCCCTATTCTCTCCTCTTCCAGGTCCCTAGAC	TTTTCCCAGAGGTATATTATTGTCATGTCTTGTTCACAGAATGGATTGATATCTGTGGTCTCTGGTCCAACCCCTCCTTGAATTGATAGGGCCCCGAGGCCCAGAGAAAGCCAGTCTCTTGACCATGGTCACCCACCTAATTGTGTTAGAGCCAAGACTAGAAATCTGTTCTTCTGATTCCAAGCTCAGAATAAGTGGGAAGACTCAGTGTGCCTGTGCCCTCTGCCATTCACTTCATCTATCAATGTTCTCTGATTTCAGGATTAAGCCTATCGTATGGCCCAGTCTCCCCGATCATAAGAAGACTCTGGAACATCTTTGTAAGAAACCAAGAAAAGTGAGTGTTTTTGGTGCTTAAAAAGTGTTGTGTTGGCAACATCCCAGTGGCCAAGAATGATATTCCAGGACAAGGAACAGTTGAACCTCACCTTTTGGTATTTGATTCATCCTGTAACTAGGGTCCCTCCTAAGACCCTAGCTGCAGTAGGGAACTGAAATAAGATACACATCTCAGAACTTCTGGGCTCCCTGGGGCTGGAGGGCACAGCCAGTGGTCACTTCAAGTCTTGAAGTGTCTCAGAAGCTCCAGAAGCAAAGAGTCCATTGAGGAACATGCTGGCAATTCTGTGACATTCCCTGTCAGAAAACTCTATAGACCTACTCCTGAACTGAACATTTGATGGTGTGTCTCTCTGGTGCCATCTTAATACCCTTTCTCCTTTTTCTGTGCAGAATTTAAATGTGAGTTTCAATCCTGAAAGTTTCCTGGACTGCCAGATTCATAGGGTGGATGACATTCAAGCTAGAGATGAAGTGGAAGGTTTTCTGCAAGATACGTTTCCTCAGCAACTAGAAGAATCTGAGAAGCAGAGGCTTGGAGGGGATGTGCAGAGCCCCAACTGCCCATCTGAGGATGTAGTCATCACTCCAGAAAGCTTTGGAAGAGATTCATCCCTCACATGCCTGGCTGGGAATGTCAGTGCATGTGACGCCCCTATTCTCTCCTCTTCCAGGTCCCTAGAC	-	novel	NA	P-0035120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1852	105	16	0	ENST00000303115.3:c.801-260_1168del		p.X267_splice	ENST00000303115	NM_002185.3	267		7-8/8	0.755374952981217	6	FACETS	0.357	0.318	0.398	0.089	0.079	0.1	SUBCLONAL	1	TRUE	2	0.755374952981217	6		16	1957	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553023	106553023	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	344	615	2	ENST00000369096.4:c.988C>A	p.Pro330Thr	p.P330T	ENST00000369096	NM_001198.3	330	Cca/Aca	5/7	0.739037277148891	3	FACETS	0.935	0.884	0.987	0.468	0.442	0.494	CLONAL	1	TRUE	1	0.755374952981217	3		617	1342	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578213	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs864309495	NA	P-0035125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	61	666	0	ENST00000269305.4:c.636del	p.Arg213AspfsTer34	p.R213Dfs*34	ENST00000269305	NM_001126112.2	212	ttT/tt	6/11	0.241443307362784	1	FACETS	0.797	0.688	0.916	0.797	0.688	0.916	CLONAL	1	TRUE	0	0.23	1		666	589	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808054	1808054	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	82	947	0	ENST00000260795.2:c.2030T>C	p.Val677Ala	p.V677A	ENST00000260795		677	gTc/gCc	14/17	1	2	FACETS	0.978	0.862	1	0.978	0.862	1	CLONAL	1	TRUE	1	0.23	2		947	729	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912717	100912717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1181450031	NA	P-0035163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	122	501	0	ENST00000325455.5:c.2605C>T	p.Arg869Cys	p.R869C	ENST00000325455	NM_001202474.3	869	Cgt/Tgt	7/8	0.597778264028222	2	FACETS	0.849	0.772	0.929	0.424	0.386	0.465	CLONAL	1	TRUE	0	0.597778264028222	2		501	481	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641058	23641058	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45464991	NA	P-0035163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	388	676	0	ENST00000261584.4:c.2417C>T	p.Pro806Leu	p.P806L	ENST00000261584	NM_024675.3	806	cCg/cTg	5/13	0.554440014376543	4	FACETS	0.991	0.943	1			1	CLONAL	2	TRUE	NA	0.597778264028222	4		676	1047	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120675	115120676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	160	648	0	ENST00000257566.3:c.330dup	p.Glu111ArgfsTer27	p.E111Rfs*27	ENST00000257566	NM_016569.3	110	-/A	1/8	0.597778264028222	3	FACETS	0.857	0.787	0.931	0.429	0.393	0.466	CLONAL	1	TRUE	1	0.597778264028222	3		648	811	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115944	8115945	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0035163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	116	404	0	ENST00000346208.3:c.1292dup	p.Pro432ThrfsTer75	p.P432Tfs*75	ENST00000346208		430	-/G	6/6	0.519126013173536	5	FACETS	1	0.915	1	0.254	0.229	0.28	CLONAL	1	TRUE	1	0.597778264028222	5		404	725	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366959	15366959	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	232	697	0	ENST00000263377.2:c.1667A>G	p.Glu556Gly	p.E556G	ENST00000263377	NM_058243.2	556	gAa/gGa	9/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.597778264028222	2		697	724	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217303	123217303	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	107	559	0	ENST00000218089.9:c.2957A>G	p.Asn986Ser	p.N986S	ENST00000218089	NM_001042749.1	986	aAt/aGt	29/35	1	2	FACETS	0.674	0.607	0.745	0.674	0.607	0.745	SUBCLONAL	1	TRUE	1	0.597778264028222	2		559	531	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438532	49438532	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	204	430	3	ENST00000301067.7:c.4958del	p.Gly1653ValfsTer69	p.G1653Vfs*69	ENST00000301067	NM_003482.3	1653	gGt/gt	19/54	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.54	2		433	656	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118673	115118692	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATGAAACTTACAAATCCATG	ATGAAACTTACAAATCCATG	-	novel	NA	P-0035274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	142	325	0	ENST00000257566.3:c.649_657+11del		p.X217_splice	ENST00000257566	NM_016569.3	217		2/8	0.24696149328333	3	FACETS	1	0.924	1	0.337	0.308	0.368	INDETERMINATE	1	TRUE	0	0.54	3		325	660	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608129	28608129	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0035274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	81	378	0	ENST00000241453.7:c.1838-1G>C		p.X613_splice	ENST00000241453	NM_004119.2	613			0.301694781379747	1	FACETS	0.458	0.405	0.515	0.458	0.405	0.515	INDETERMINATE	1	TRUE	0	0.54	1		378	478	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449456	31449456	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	138	393	1	ENST00000344624.3:c.2753C>T	p.Ser918Phe	p.S918F	ENST00000344624		918	tCt/tTt	19/33	0.301694781379747	3	FACETS	1	0.947	1	0.526	0.48	0.574	INDETERMINATE	1	TRUE	1	0.54	3		394	617	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786457	135786457	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	150	350	3	ENST00000298552.3:c.1073C>A	p.Pro358His	p.P358H	ENST00000298552	NM_001162426.1	358	cCt/cAt	11/23	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.54	2		353	542	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0035470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	51	463	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		463	632	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0035470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	46	542	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		543	955	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007643	45007643	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	35	424	0	ENST00000558401.1:c.90C>A	p.Tyr30Ter	p.Y30*	ENST00000558401	NM_004048.2	30	taC/taA	2/4	1	2	FACETS	0.675	0.556	0.807	0.675	0.556	0.807	SUBCLONAL	1	TRUE	1	0.38	2		424	273	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70441157	70441157	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	rs764225020	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	20	548	1	ENST00000373644.4:c.4832del	p.Asn1611ThrfsTer13	p.N1611Tfs*13	ENST00000373644	NM_030625.2	1609	gAa/ga	9/12	1	2	FACETS	1	0.827	1	1	0.827	1	CLONAL	1	TRUE	1	0.38	2		549	98	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256769	19256769	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	39	566	1	ENST00000162023.5:c.944del	p.Pro315GlnfsTer?	p.P315Qfs*?	ENST00000162023		315	cCa/ca	13/13	0.109630127417991	3	FACETS	1	0.904	1	0.56	0.468	0.661	INDETERMINATE	1	TRUE	1	0.38	3		567	218	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	13	338	2	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	0.109630127417991	0	FACETS	0.337	0.242	0.451			1	INDETERMINATE	1	TRUE	0	0.38	0		340	126	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552152	29552152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199474738	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	11	382	0	ENST00000356175.3:c.1885G>A	p.Gly629Arg	p.G629R	ENST00000356175	NM_000267.3	629	Ggg/Agg	17/57	1	2	FACETS	0.681	0.477	0.928	0.681	0.477	0.928	SUBCLONAL	1	TRUE	1	0.38	2		382	85	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	23	577	0	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	0.142233686258794	0	FACETS	0.511	0.402	0.633			1	INDETERMINATE	1	TRUE	0	0.38	0		577	147	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729163	66729163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516792	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	24	639	0	ENST00000307102.5:c.371C>T	p.Pro124Leu	p.P124L	ENST00000307102	NM_002755.3	124	cCg/cTg	3/11	1	2	FACETS	0.478	0.376	0.596	0.478	0.376	0.596	SUBCLONAL	1	TRUE	1	0.38	2		639	264	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671655	67671655	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1400980130	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	33	625	0	ENST00000264010.4:c.2070del	p.Glu691SerfsTer30	p.E691Sfs*30	ENST00000264010	NM_006565.3	688	gtA/gt	12/12	0.109630127417991	0	FACETS	0.595	0.49	0.711			1	INDETERMINATE	1	TRUE	0	0.38	0		625	181	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149945	99149945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	42	829	0	ENST00000074304.5:c.257C>T	p.Thr86Met	p.T86M	ENST00000074304	NM_001134224.1	86	aCg/aTg	5/26	1	2	FACETS	0.689	0.577	0.811	0.689	0.577	0.811	SUBCLONAL	1	TRUE	1	0.38	2		829	321	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922097	39922097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1249334408	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	60	525	2	ENST00000378444.4:c.4075G>A	p.Gly1359Arg	p.G1359R	ENST00000378444	NM_001123385.1	1359	Ggg/Agg	9/15	1	1	FACETS	0.77	0.678	0.866	1	0.975	1	SUBCLONAL	2	TRUE	0	0.38	1		527	166	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374390	31374390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773207465	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	55	560	0	ENST00000328111.2:c.389G>A	p.Arg130His	p.R130H	ENST00000328111	NM_006892.3	130	cGc/cAc	5/23	0.142233686258794	0	FACETS	0.615	0.53	0.706			1	INDETERMINATE	1	TRUE	0	0.38	0		560	292	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	25	759	0	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	0.533	0.421	0.66	0.533	0.421	0.66	SUBCLONAL	1	TRUE	1	0.38	2		759	247	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	19	619	1	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	0.109630127417991	0	FACETS	0.35	0.267	0.447			1	INDETERMINATE	1	TRUE	0	0.38	0		620	177	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	26	269	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.889	0.712	1	0.889	0.712	1	CLONAL	1	TRUE	1	0.38	2		269	154	SUCCESS
APC	324	MSKCC	GRCh37	5	112164611	112164611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587783034	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	20	416	0	ENST00000257430.4:c.1685C>T	p.Thr562Met	p.T562M	ENST00000257430	NM_000038.5	562	aCg/aTg	14/16	1	2	FACETS	0.915	0.71	1	0.915	0.71	1	CLONAL	1	TRUE	1	0.38	2		416	115	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149917	202149917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	33	780	1	ENST00000358485.4:c.1358C>T	p.Pro453Leu	p.P453L	ENST00000358485	NM_001080125.1	453	cCg/cTg	8/9	1	2	FACETS	0.914	0.752	1	0.914	0.752	1	CLONAL	1	TRUE	1	0.38	2		781	190	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448304	56448304	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	105	745	0	ENST00000407977.2:c.343del	p.Ala115ProfsTer43	p.A115Pfs*43	ENST00000407977		115	Gcc/cc	3/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.38	2		745	465	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686901	37686901	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	62	517	3	ENST00000447079.4:c.3810del	p.Gly1271AspfsTer23	p.G1271Dfs*23	ENST00000447079	NM_015083.1	1269	Ccc/cc	14/14	1	2	FACETS	0.963	0.837	1	0.963	0.837	1	CLONAL	1	TRUE	1	0.38	2		520	339	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542110	187542110	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	13	374	0	ENST00000441802.2:c.5630del	p.Pro1877LeufsTer20	p.P1877Lfs*20	ENST00000441802	NM_005245.3	1877	cCt/ct	10/27	1	2	FACETS	0.815	0.59	1	0.815	0.59	1	CLONAL	1	TRUE	1	0.38	2		374	84	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127262	17127262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200168437	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	49	688	1	ENST00000285071.4:c.592G>A	p.Asp198Asn	p.D198N	ENST00000285071	NM_144997.5	198	Gat/Aat	6/14	1	2	FACETS	0.945	0.806	1	0.945	0.806	1	CLONAL	1	TRUE	1	0.38	2		689	273	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057911	27057911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs892173376	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	89	878	3	ENST00000324856.7:c.1619C>T	p.Thr540Met	p.T540M	ENST00000324856	NM_006015.4	540	aCg/aTg	3/20	1	2	FACETS	0.903	0.803	1	0.903	0.803	1	CLONAL	1	TRUE	1	0.38	2		881	519	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712520	52712520	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	44	638	1	ENST00000394830.3:c.232C>T	p.Arg78Ter	p.R78*	ENST00000394830	NM_018313.4	78	Cga/Tga	3/30	1	2	FACETS	0.78	0.657	0.914	0.78	0.657	0.914	CLONAL	1	TRUE	1	0.38	2		639	297	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120031	70120031	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	30	78	0	ENST00000245479.2:c.1037del	p.Pro346ArgfsTer37	p.P346Rfs*37	ENST00000245479	NM_000346.3	345	Ccc/cc	3/3	1	2	FACETS	0.752	0.62	0.894	1	0.947	1	SUBCLONAL	2	TRUE	1	0.38	2		78	105	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020769	37020769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	33	617	3	ENST00000358127.4:c.76del	p.Val26PhefsTer3	p.V26Ffs*3	ENST00000358127	NM_001280556.1	26	Gtt/tt	2/10	1	2	FACETS	0.727	0.595	0.873	0.727	0.595	0.873	SUBCLONAL	1	TRUE	1	0.38	2		620	239	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151254	202151254	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	36	582	0	ENST00000358485.4:c.1557del	p.Lys520AsnfsTer10	p.K520Nfs*10	ENST00000358485	NM_001080125.1	518	atG/at	9/9	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.38	2		582	179	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206818	36206818	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	35	653	5	ENST00000300305.3:c.694C>T	p.Arg232Trp	p.R232W	ENST00000300305		232	Cgg/Tgg	6/8	0.176881706655356	0	FACETS	0.34	0.279	0.408			1	INDETERMINATE	1	TRUE	0	0.38	0		658	336	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442788	187442788	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	56	618	0	ENST00000232014.4:c.1918C>T	p.Arg640Trp	p.R640W	ENST00000232014	NM_001130845.1	640	Cgg/Tgg	9/10	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.38	2		618	260	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336166	73336166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs566599772	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	14	283	0	ENST00000377767.4:c.2237G>A	p.Arg746His	p.R746H	ENST00000377767	NM_014953.3	746	cGc/cAc	17/21	0.142233686258794	4	FACETS	1	0.841	1	0.613	0.45	0.802	INDETERMINATE	1	TRUE	2	0.38	4		283	83	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393588	139393588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752928106	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	77	1002	1	ENST00000277541.6:c.6058G>A	p.Asp2020Asn	p.D2020N	ENST00000277541	NM_017617.3	2020	Gac/Aac	32/34	1	2	FACETS	0.981	0.866	1	0.981	0.866	1	CLONAL	1	TRUE	1	0.38	2		1003	413	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	48	1056	4	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	0.109630127417991	3	FACETS	0.8	0.678	0.933	0.4	0.339	0.467	INDETERMINATE	1	TRUE	1	0.38	3		1060	376	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	54	819	0	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	0.109630127417991	3	FACETS	0.895	0.767	1	0.447	0.383	0.517	INDETERMINATE	1	TRUE	1	0.38	3		819	378	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223620	36223620	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374062006	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	61	1132	4	ENST00000222270.7:c.6170G>A	p.Arg2057His	p.R2057H	ENST00000222270	NM_014727.1	2057	cGc/cAc	28/37	0.109630127417991	3	FACETS	0.953	0.825	1	0.476	0.412	0.545	INDETERMINATE	1	TRUE	1	0.38	3		1136	401	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540974	187540974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752611276	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	58	491	0	ENST00000441802.2:c.6766G>A	p.Ala2256Thr	p.A2256T	ENST00000441802	NM_005245.3	2256	Gca/Aca	10/27	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.38	2		491	222	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041261	29041262	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	27	600	0	ENST00000282397.4:c.166dup	p.Glu56GlyfsTer5	p.E56Gfs*5	ENST00000282397	NM_002019.4	56	gaa/gGaa	3/30	0.142233686258794	4	FACETS	0.797	0.645	0.965	0.797	0.645	0.965	INDETERMINATE	2	TRUE	2	0.38	4		600	123	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977896	131977896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367683141	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	26	556	0	ENST00000265335.6:c.3779G>A	p.Arg1260His	p.R1260H	ENST00000265335		1260	cGt/cAt	25/25	1	2	FACETS	0.925	0.741	1	0.925	0.741	1	CLONAL	1	TRUE	1	0.38	2		556	148	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023715	27023716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	53	621	0	ENST00000324856.7:c.827dup	p.Gly277ArgfsTer123	p.G277Rfs*123	ENST00000324856	NM_006015.4	274	atg/atGg	1/20	1	2	FACETS	0.553	0.472	0.642	0.553	0.472	0.642	SUBCLONAL	1	TRUE	1	0.38	2		621	504	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528284	157528284	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs749055122	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	57	892	0	ENST00000346085.5:c.6013del	p.Val2005TrpfsTer16	p.V2005Wfs*16	ENST00000346085	NM_020732.3	2003	aaG/aa	20/20	0.274230754005189	3	FACETS	1	0.876	1	0.509	0.438	0.584	CLONAL	1	TRUE	1	0.38	3		892	351	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952048	178952048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	15	511	0	ENST00000263967.3:c.3103G>A	p.Ala1035Thr	p.A1035T	ENST00000263967	NM_006218.2	1035	Gct/Act	21/21	1	2	FACETS	0.897	0.667	1	0.897	0.667	1	CLONAL	1	TRUE	1	0.38	2		511	88	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41251812	41251812	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782747	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	51	893	0	ENST00000357654.3:c.527C>T	p.Thr176Met	p.T176M	ENST00000357654	NM_007294.3	176	aCg/aTg	7/23	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.38	2		893	253	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740231	162740231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773598662	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	45	505	1	ENST00000367921.3:c.1433G>A	p.Arg478His	p.R478H	ENST00000367921	NM_006182.2	478	cGc/cAc	12/18	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.38	2		506	228	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303924	30303924	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs35886256	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	29	708	0	ENST00000262643.3:c.160A>G	p.Arg54Gly	p.R54G	ENST00000262643	NM_001238.2	54	Agg/Ggg	4/12	0.109630127417991	3	FACETS	0.509	0.408	0.623	0.254	0.204	0.312	INDETERMINATE	1	TRUE	1	0.38	3		708	357	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089647	27089647	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	64	698	0	ENST00000324856.7:c.2603del	p.Tyr868LeufsTer23	p.Y868Lfs*23	ENST00000324856	NM_006015.4	868	tAt/tt	8/20	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.38	2		698	323	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118379859	118379859	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	21	373	0	ENST00000534358.1:c.10844C>T	p.Ala3615Val	p.A3615V	ENST00000534358	NM_005933.3	3615	gCt/gTt	29/36	1	2	FACETS	0.654	0.507	0.822	0.654	0.507	0.822	SUBCLONAL	1	TRUE	1	0.38	2		373	169	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609985	81609985	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571893270	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	40	500	0	ENST00000298171.2:c.1583G>A	p.Arg528His	p.R528H	ENST00000298171	NM_000369.2	528	cGc/cAc	10/10	0.142233686258794	0	FACETS	0.742	0.625	0.868			1	INDETERMINATE	1	TRUE	0	0.38	0		500	176	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007723	45007723	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	52	528	0	ENST00000558401.1:c.170T>A	p.Val57Asp	p.V57D	ENST00000558401	NM_004048.2	57	gTt/gAt	2/4	1	2	FACETS	0.847	0.725	0.98	0.847	0.725	0.98	CLONAL	1	TRUE	1	0.38	2		528	323	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639294	3639294	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	64	1053	0	ENST00000294008.3:c.4345del	p.Leu1449Ter	p.L1449*	ENST00000294008	NM_032444.2	1449	Ctg/tg	12/15	0.109630127417991	0	FACETS	0.534	0.464	0.609			1	INDETERMINATE	1	TRUE	0	0.38	0		1053	391	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81904533	81904533	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	28	389	0	ENST00000359376.3:c.645del	p.Lys215AsnfsTer48	p.K215Nfs*48	ENST00000359376	NM_002661.3	214	cAa/ca	7/33	0.109630127417991	0	FACETS	0.662	0.537	0.8			1	INDETERMINATE	1	TRUE	0	0.38	0		389	138	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110651	8110651	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752234429	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	61	619	0	ENST00000585124.1:c.241C>T	p.Arg81Cys	p.R81C	ENST00000585124	NM_004217.3	81	Cgt/Tgt	5/9	1	2	FACETS	0.858	0.744	0.982	0.858	0.744	0.982	CLONAL	1	TRUE	1	0.38	2		619	374	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40456394	40456394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	56	711	0	ENST00000345506.4:c.1204G>A	p.Val402Met	p.V402M	ENST00000345506	NM_003152.3	402	Gtg/Atg	11/20	1	2	FACETS	0.869	0.749	1	0.869	0.749	1	CLONAL	1	TRUE	1	0.38	2		711	339	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440754	56440754	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	76	609	1	ENST00000407977.2:c.464T>C	p.Leu155Pro	p.L155P	ENST00000407977		155	cTg/cCg	5/10	1	2	FACETS	0.784	0.697	0.875	1	0.98	1	SUBCLONAL	2	TRUE	1	0.38	2		610	255	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554672	63554672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	52	606	0	ENST00000307078.5:c.67C>T	p.Arg23Trp	p.R23W	ENST00000307078	NM_004655.3	23	Cgg/Tgg	2/11	1	2	FACETS	0.886	0.759	1	0.886	0.759	1	CLONAL	1	TRUE	1	0.38	2		606	309	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78797016	78797016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771235157	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	68	640	1	ENST00000306801.3:c.1129G>A	p.Ala377Thr	p.A377T	ENST00000306801	NM_020761.2	377	Gcc/Acc	9/34	1	2	FACETS	0.908	0.794	1	0.908	0.794	1	CLONAL	1	TRUE	1	0.38	2		641	394	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896543	78896543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762927626	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	71	1069	1	ENST00000306801.3:c.2540C>T	p.Pro847Leu	p.P847L	ENST00000306801	NM_020761.2	847	cCg/cTg	22/34	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.38	2		1070	340	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584483	39584483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	41	457	0	ENST00000262039.4:c.1148G>A	p.Arg383Gln	p.R383Q	ENST00000262039	NM_002647.2	383	cGg/cAg	10/25	1	2	FACETS	0.884	0.742	1	0.884	0.742	1	CLONAL	1	TRUE	1	0.38	2		457	244	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217783	2217783	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	67	900	1	ENST00000398665.3:c.2557C>A	p.Arg853Ser	p.R853S	ENST00000398665	NM_032482.2	853	Cgc/Agc	22/28	0.227139042950412	0	FACETS	0.581	0.508	0.66			1	INDETERMINATE	1	TRUE	0	0.38	0		901	376	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17947986	17947986	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	95	961	1	ENST00000458235.1:c.1738T>C	p.Ser580Pro	p.S580P	ENST00000458235	NM_000215.3	580	Tcg/Ccg	13/24	0.109630127417991	3	FACETS	1	0.973	1	0.64	0.572	0.711	INDETERMINATE	1	TRUE	1	0.38	3		962	465	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905103	50905103	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	111	1010	0	ENST00000440232.2:c.388del	p.Val130SerfsTer39	p.V130Sfs*39	ENST00000440232	NM_002691.3	129	Ggg/gg	4/27	0.3	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.38	1		1010	432	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727177	40727177	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	35	667	0	ENST00000373198.4:c.3787G>A	p.Ala1263Thr	p.A1263T	ENST00000373198	NM_133170.3	1263	Gcc/Acc	28/32	0.142233686258794	0	FACETS	0.464	0.383	0.555			1	INDETERMINATE	1	TRUE	0	0.38	0		667	246	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30733074	30733074	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	40	413	0	ENST00000295754.5:c.1687C>A	p.Leu563Ile	p.L563I	ENST00000295754	NM_003242.5	563	Cta/Ata	7/7	1	2	FACETS	0.81	0.677	0.955	0.81	0.677	0.955	CLONAL	1	TRUE	1	0.38	2		413	260	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127764	47127764	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750518294	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	54	570	1	ENST00000409792.3:c.5318G>A	p.Arg1773His	p.R1773H	ENST00000409792	NM_014159.6	1773	cGt/cAt	11/21	1	2	FACETS	0.88	0.756	1	0.88	0.756	1	CLONAL	1	TRUE	1	0.38	2		571	323	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612112	189612112	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	44	841	0	ENST00000264731.3:c.1864A>G	p.Ser622Gly	p.S622G	ENST00000264731	NM_003722.4	622	Agt/Ggt	14/14	1	2	FACETS	0.801	0.676	0.939	0.801	0.676	0.939	CLONAL	1	TRUE	1	0.38	2		841	289	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539870	187539870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	24	560	1	ENST00000441802.2:c.7870G>A	p.Asp2624Asn	p.D2624N	ENST00000441802	NM_005245.3	2624	Gat/Aat	10/27	1	2	FACETS	0.668	0.527	0.828	0.668	0.527	0.828	SUBCLONAL	1	TRUE	1	0.38	2		561	189	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177624	56177624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	39	482	0	ENST00000399503.3:c.2597C>T	p.Ala866Val	p.A866V	ENST00000399503	NM_005921.1	866	gCc/gTc	14/20	1	2	FACETS	0.848	0.708	1	0.848	0.708	1	CLONAL	1	TRUE	1	0.38	2		482	242	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188577	32188577	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	18	917	0	ENST00000375023.3:c.878A>G	p.Asp293Gly	p.D293G	ENST00000375023	NM_004557.3	293	gAt/gGt	5/30	0.227139042950412	5	FACETS	0.529	0.398	0.684	0.176	0.132	0.228	INDETERMINATE	1	TRUE	2	0.38	5		917	281	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206847	162206847	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	23	484	0	ENST00000366898.1:c.828G>C	p.Gln276His	p.Q276H	ENST00000366898	NM_004562.2	276	caG/caC	7/12	0.274230754005189	3	FACETS	0.935	0.737	1	0.468	0.368	0.581	CLONAL	1	TRUE	1	0.38	3		484	154	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214313	55214313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs532655845	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	53	649	1	ENST00000275493.2:c.439G>A	p.Ala147Thr	p.A147T	ENST00000275493	NM_005228.3	147	Gcc/Acc	4/28	1	2	FACETS	0.771	0.66	0.891	0.771	0.66	0.891	SUBCLONAL	1	TRUE	1	0.38	2		650	362	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851527	128851527	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	55	1013	0	ENST00000249373.3:c.1852T>A	p.Trp618Arg	p.W618R	ENST00000249373	NM_005631.4	618	Tgg/Agg	11/12	1	2	FACETS	0.991	0.854	1	0.991	0.854	1	CLONAL	1	TRUE	1	0.38	2		1013	292	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485879	8485879	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	23	602	0	ENST00000356435.5:c.2938A>G	p.Thr980Ala	p.T980A	ENST00000356435		980	Aca/Gca	17/35	1	2	FACETS	0.946	0.747	1	0.946	0.747	1	CLONAL	1	TRUE	1	0.38	2		602	128	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300911	137300911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754348129	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	76	876	1	ENST00000481739.1:c.556C>T	p.Arg186Trp	p.R186W	ENST00000481739	NM_002957.4	186	Cgg/Tgg	4/10	1	2	FACETS	0.897	0.79	1	0.897	0.79	1	CLONAL	1	TRUE	1	0.38	2		877	446	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941979	44941979	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	43	307	0	ENST00000377967.4:c.3229G>T	p.Gly1077Ter	p.G1077*	ENST00000377967	NM_021140.2	1077	Gga/Tga	22/29	1	1	FACETS	0.89	0.769	1	1	0.972	1	CLONAL	2	TRUE	0	0.38	1		307	103	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814262	76814262	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	28	269	0	ENST00000373344.5:c.6382G>A	p.Ala2128Thr	p.A2128T	ENST00000373344	NM_000489.3	2128	Gct/Act	29/35	1	1	FACETS	0.796	0.659	0.939	1	0.951	1	CLONAL	2	TRUE	0	0.38	1		269	75	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0035515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	157	494	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.29289683838881	3	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	1	0.339610926360049	3		494	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0035515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	100	547	0	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	1	2	FACETS	0.851	0.761	0.947	0.851	0.761	0.947	CLONAL	1	TRUE	1	0.339610926360049	2		547	692	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0035515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	100	572	0	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	1	2	FACETS	0.887	0.793	0.986	0.887	0.793	0.986	CLONAL	1	TRUE	1	0.339610926360049	2		572	664	SUCCESS
APC	324	MSKCC	GRCh37	5	112174119	112174119	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1554084512	NA	P-0035515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	109	270	0	ENST00000257430.4:c.2828C>A	p.Ser943Ter	p.S943*	ENST00000257430	NM_000038.5	943	tCa/tAa	16/16	0.288612691188975	2	FACETS	0.872	0.791	0.957	0.872	0.791	0.957	CLONAL	2	TRUE	0	0.339610926360049	2		270	368	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480469	89480469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	29	276	0	ENST00000336596.2:c.2306G>A	p.Arg769His	p.R769H	ENST00000336596	NM_005233.5	769	cGt/cAt	13/17	0.175059151499541	2	FACETS	0.407	0.326	0.499	0.203	0.163	0.25	INDETERMINATE	1	TRUE	0	0.339610926360049	2		276	420	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396278	396278	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	207	703	0	ENST00000262320.3:c.748G>T	p.Asp250Tyr	p.D250Y	ENST00000262320	NM_003502.3	250	Gac/Tac	2/11	0.198726690820117	4	FACETS	0.805	0.747	0.866	0.805	0.747	0.866	INDETERMINATE	2	TRUE	2	0.339610926360049	4		703	1014	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	159	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.993	0.914	1	0.993	0.914	1	CLONAL	1	TRUE	1	0.490328058327422	2		473	653	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578552	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GGGGAG	GGGGAG	-	novel	NA	P-0035525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	183	813	0	ENST00000269305.4:c.378_383del	p.Ser127_Pro128del	p.S127_P128del	ENST00000269305	NM_001126112.2	126	taCTCCCCt/tat	5/11	0.490328058327422	1	FACETS	0.807	0.747	0.869	0.807	0.747	0.869	CLONAL	1	TRUE	0	0.490328058327422	1		813	698	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573530	48573530	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	95	315	0	ENST00000342988.3:c.114del	p.Ala39GlnfsTer6	p.A39Qfs*6	ENST00000342988	NM_005359.5	38	agA/ag	2/12	0.490328058327422	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.490328058327422	1		315	263	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974774	21974783	+	protein_altering_variant	In_Frame_Del	DEL	GTGGCCAGCC	GTGGCCAGCC	A	novel	NA	P-0035525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	79	156	0	ENST00000304494.5:c.44_53delinsT	p.Trp15_Thr18delinsLeu	p.W15_T18delinsL	ENST00000304494	NM_000077.4	15	tGGCTGGCCACg/tTg	1/3	0.490328058327422	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.490328058327422	1		156	210	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0035555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	734	821	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.762619783795917	2		823	927	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0035555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	177	327	0	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.762619783795917	2		327	420	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716326	52716326	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	848	614	0	ENST00000322088.6:c.770G>T	p.Trp257Leu	p.W257L	ENST00000322088	NM_014225.5	257	tGg/tTg	6/15	0.275172340292765	5	FACETS	0.917	0.894	0.939	0.734	0.715	0.751	INDETERMINATE	4	TRUE	0	0.762619783795917	5		614	1300	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29002006	29002006	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	238	464	0	ENST00000282397.4:c.1159G>A	p.Gly387Ser	p.G387S	ENST00000282397	NM_002019.4	387	Ggc/Agc	9/30	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.762619783795917	2		464	611	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152044	11152044	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886054155	NA	P-0035555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	96	489	0	ENST00000358026.2:c.4328G>A	p.Arg1443Gln	p.R1443Q	ENST00000358026	NM_001128849.1	1443	cGg/cAg	31/36	0.447177430063276	5	FACETS	0.477	0.424	0.535			1	INDETERMINATE	1	TRUE	NA	0.762619783795917	5		489	1131	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0035594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	310	385	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.623333920145942	3	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.639419528330566	3		385	521	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796014	78796014	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	215	592	0	ENST00000306801.3:c.904C>G	p.Leu302Val	p.L302V	ENST00000306801	NM_020761.2	302	Ctg/Gtg	8/34	0.639419528330566	2	FACETS	0.832	0.775	0.891	0.416	0.387	0.446	CLONAL	1	TRUE	0	0.639419528330566	2		592	808	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664925	138664925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	98	188	0	ENST00000330315.3:c.640C>T	p.Pro214Ser	p.P214S	ENST00000330315	NM_023067.3	214	Ccc/Tcc	1/1	0.639419528330566	3	FACETS	1	0.95	1	0.545	0.49	0.602	CLONAL	1	TRUE	1	0.639419528330566	3		188	371	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412366	139412366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	117	668	0	ENST00000277541.6:c.1279G>T	p.Gly427Cys	p.G427C	ENST00000277541	NM_017617.3	427	Ggc/Tgc	8/34	0.639419528330566	3	FACETS	0.652	0.588	0.719	0.217	0.196	0.24	SUBCLONAL	1	TRUE	0	0.639419528330566	3		668	741	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	239	257	1	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.941	0.885	0.998	0.941	0.885	0.998	CLONAL	1	TRUE	1	0.81	2		258	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	228	584	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.926	0.869	0.984	0.926	0.869	0.984	CLONAL	1	TRUE	1	0.81	2		585	608	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598805	28598805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763209004	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	32	600	0	ENST00000253063.3:c.365G>A	p.Arg122His	p.R122H	ENST00000253063	NM_031459.4	122	cGc/cAc	4/10	1	2	FACETS	0.15	0.121	0.183	0.15	0.121	0.183	SUBCLONAL	1	TRUE	1	0.81	2		600	527	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740237	162740237	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	165	398	0	ENST00000367921.3:c.1439A>G	p.Asp480Gly	p.D480G	ENST00000367921	NM_006182.2	480	gAc/gGc	12/18	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.81	2		398	406	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	430	482	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.985	0.959	1	1	0.998	1	CLONAL	2	TRUE	1	0.81	2		482	539	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123353298	123353298	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143978938	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	211	616	1	ENST00000358487.5:c.34G>A	p.Val12Met	p.V12M	ENST00000358487	NM_000141.4	12	Gtg/Atg	2/18	1	2	FACETS	0.996	0.934	1	0.996	0.934	1	CLONAL	1	TRUE	1	0.81	2		617	523	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939803	71939803	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1463179209	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	168	561	0	ENST00000298229.2:c.430C>T	p.Arg144Cys	p.R144C	ENST00000298229	NM_001567.3	144	Cgc/Tgc	4/28	1	2	FACETS	0.855	0.793	0.919	0.855	0.793	0.919	CLONAL	1	TRUE	1	0.81	2		561	485	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186820	108186820	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778078	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	152	455	0	ENST00000278616.4:c.6178C>T	p.Arg2060Cys	p.R2060C	ENST00000278616	NM_000051.3	2060	Cgc/Tgc	42/63	1	2	FACETS	0.734	0.676	0.795	0.734	0.676	0.795	SUBCLONAL	1	TRUE	1	0.81	2		455	511	SUCCESS
CBL	867	MSKCC	GRCh37	11	119145620	119145620	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755244263	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	199	445	0	ENST00000264033.4:c.826G>A	p.Glu276Lys	p.E276K	ENST00000264033	NM_005188.3	276	Gaa/Aaa	5/16	0.3	2	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.81	2		445	482	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420268	49420268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757664799	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	240	628	1	ENST00000301067.7:c.15481G>A	p.Glu5161Lys	p.E5161K	ENST00000301067	NM_003482.3	5161	Gag/Aag	48/54	1	2	FACETS	0.932	0.876	0.989	0.932	0.876	0.989	CLONAL	1	TRUE	1	0.81	2		629	636	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420793	49420793	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765693458	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	205	553	1	ENST00000301067.7:c.14956C>T	p.Arg4986Cys	p.R4986C	ENST00000301067	NM_003482.3	4986	Cgc/Tgc	48/54	1	2	FACETS	0.979	0.917	1	0.979	0.917	1	CLONAL	1	TRUE	1	0.81	2		554	517	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347916	73347916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139907646	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	13	324	0	ENST00000377767.4:c.1145G>A	p.Arg382Gln	p.R382Q	ENST00000377767	NM_014953.3	382	cGa/cAa	8/21	1	2	FACETS	0.073	0.051	0.099	0.073	0.051	0.099	SUBCLONAL	1	TRUE	1	0.81	2		324	440	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986616	36986616	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	76	193	0	ENST00000354822.5:c.1073C>T	p.Pro358Leu	p.P358L	ENST00000354822	NM_001079668.2	358	cCg/cTg	3/3	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.81	2		193	159	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781324	3781326	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs587783502	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	226	729	0	ENST00000262367.5:c.5039_5041del	p.Ser1680del	p.S1680del	ENST00000262367	NM_004380.2	1680	tCCTtg/ttg	30/31	1	2	FACETS	0.904	0.848	0.962	0.904	0.848	0.962	CLONAL	1	TRUE	1	0.81	2		729	617	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916124	9916124	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376029542	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	147	437	0	ENST00000330684.3:c.2165C>T	p.Thr722Met	p.T722M	ENST00000330684	NM_001134407.1	722	aCg/aTg	10/13	1	2	FACETS	0.866	0.799	0.935	0.866	0.799	0.935	CLONAL	1	TRUE	1	0.81	2		437	419	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984782	11984782	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1164096095	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	58	404	0	ENST00000353533.5:c.328C>T	p.Arg110Ter	p.R110*	ENST00000353533	NM_003010.3	110	Cga/Tga	3/11	1	2	FACETS	0.441	0.381	0.505	0.441	0.381	0.505	SUBCLONAL	1	TRUE	1	0.81	2		404	325	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853886	59853886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759142191	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	169	393	1	ENST00000259008.2:c.1973G>A	p.Arg658Gln	p.R658Q	ENST00000259008	NM_032043.2	658	cGg/cAg	14/20	1	2	FACETS	0.884	0.82	0.949	0.884	0.82	0.949	CLONAL	1	TRUE	1	0.81	2		394	472	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62009608	62009608	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748240443	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	93	490	2	ENST00000392795.3:c.14C>T	p.Ala5Val	p.A5V	ENST00000392795	NM_001039933.1	5	gCg/gTg	1/6	1	2	FACETS	0.509	0.455	0.566	0.509	0.455	0.566	SUBCLONAL	1	TRUE	1	0.81	2		492	451	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245810	5245810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	252	664	1	ENST00000357368.4:c.965C>T	p.Ala322Val	p.A322V	ENST00000357368	NM_002850.3	322	gCg/gTg	10/38	0.114431755742212	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.81	0		665	596	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262117	10262119	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	novel	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	219	678	3	ENST00000340748.4:c.2172_2174del	p.Lys725del	p.K725del	ENST00000340748		724	aaGAAa/aaa	23/40	1	2	FACETS	0.795	0.743	0.848	0.795	0.743	0.848	SUBCLONAL	1	TRUE	1	0.81	2		681	680	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281517	15281517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	166	463	0	ENST00000263388.2:c.4856G>A	p.Arg1619His	p.R1619H	ENST00000263388	NM_000435.2	1619	cGc/cAc	26/33	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.81	2		463	405	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288870	15288870	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	67	126	0	ENST00000263388.2:c.3869C>T	p.Ala1290Val	p.A1290V	ENST00000263388	NM_000435.2	1290	gCg/gTg	24/33	1	2	FACETS	0.967	0.86	1	0.967	0.86	1	CLONAL	1	TRUE	1	0.81	2		126	171	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639568	47639568	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	128	248	8	ENST00000233146.2:c.662del	p.Gly221GlufsTer3	p.G221Efs*3	ENST00000233146	NM_000251.2	221	Gga/ga	4/16	1	2	FACETS	0.964	0.886	1	0.964	0.886	1	CLONAL	1	TRUE	1	0.81	2		256	328	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656924	47656924	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750558	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	163	340	0	ENST00000233146.2:c.1120C>T	p.Gln374Ter	p.Q374*	ENST00000233146	NM_000251.2	374	Cag/Tag	7/16	1	2	FACETS	0.83	0.768	0.893	0.83	0.768	0.893	CLONAL	1	TRUE	1	0.81	2		340	485	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149221	61149221	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761644483	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	32	369	1	ENST00000295025.8:c.1411G>A	p.Gly471Arg	p.G471R	ENST00000295025	NM_002908.2	471	Gga/Aga	11/11	1	2	FACETS	0.226	0.183	0.274	0.226	0.183	0.274	SUBCLONAL	1	TRUE	1	0.81	2		370	350	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944562	40944562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868189942	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	177	411	0	ENST00000373198.4:c.1940C>T	p.Ser647Leu	p.S647L	ENST00000373198	NM_133170.3	647	tCg/tTg	12/32	1	2	FACETS	0.993	0.925	1	0.993	0.925	1	CLONAL	1	TRUE	1	0.81	2		411	440	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403527	138403527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140578043	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	297	630	0	ENST00000289153.2:c.2255G>A	p.Arg752Gln	p.R752Q	ENST00000289153	NM_006219.2	752	cGg/cAg	15/22	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.81	2		630	696	SUCCESS
ATR	545	MSKCC	GRCh37	3	142255005	142255005	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	154	305	0	ENST00000350721.4:c.3764del	p.Leu1255TyrfsTer7	p.L1255Yfs*7	ENST00000350721	NM_001184.3	1255	tTa/ta	20/47	1	2	FACETS	0.823	0.76	0.888	0.823	0.76	0.888	CLONAL	1	TRUE	1	0.81	2		305	462	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590446	67590446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765178503	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	30	214	0	ENST00000274335.5:c.1508G>A	p.Arg503Gln	p.R503Q	ENST00000274335		503	cGg/cAg	11/15	1	2	FACETS	0.21	0.169	0.256	0.21	0.169	0.256	SUBCLONAL	1	TRUE	1	0.81	2		214	353	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954952	2954952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	198	662	0	ENST00000396946.4:c.2758C>T	p.Arg920Cys	p.R920C	ENST00000396946	NM_032415.4	920	Cgc/Tgc	21/25	1	2	FACETS	0.897	0.837	0.958	0.897	0.837	0.958	CLONAL	1	TRUE	1	0.81	2		662	545	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6438350	6438350	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs560647572	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	178	377	1	ENST00000356142.4:c.282+1G>A		p.X94_splice	ENST00000356142	NM_018890.3	94			1	2	FACETS	0.893	0.831	0.957	0.893	0.831	0.957	CLONAL	1	TRUE	1	0.81	2		378	492	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104619	69104619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61753704	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	302	578	0	ENST00000288368.4:c.4463C>T	p.Ser1488Leu	p.S1488L	ENST00000288368	NM_024870.2	1488	tCg/tTg	37/40	1	2	FACETS	0.992	0.939	1	0.992	0.939	1	CLONAL	1	TRUE	1	0.81	2		578	752	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8733834	8733834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1050031711	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	38	422	0	ENST00000356435.5:c.10G>A	p.Val4Ile	p.V4I	ENST00000356435		4	Gta/Ata	1/35	1	2	FACETS	0.21	0.174	0.251	0.21	0.174	0.251	SUBCLONAL	1	TRUE	1	0.81	2		422	446	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760442	133760442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746334503	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	144	544	1	ENST00000318560.5:c.2765C>T	p.Ala922Val	p.A922V	ENST00000318560	NM_005157.4	922	gCg/gTg	11/11	1	2	FACETS	0.979	0.905	1	0.979	0.905	1	CLONAL	1	TRUE	1	0.81	2		545	363	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401375	139401375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750169914	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	190	686	0	ENST00000277541.6:c.3694G>A	p.Val1232Met	p.V1232M	ENST00000277541	NM_017617.3	1232	Gtg/Atg	23/34	1	2	FACETS	0.907	0.846	0.97	0.907	0.846	0.97	CLONAL	1	TRUE	1	0.81	2		686	517	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650559	48650559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1482381233	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	236	654	2	ENST00000376670.3:c.529G>A	p.Gly177Arg	p.G177R	ENST00000376670	NM_002049.3	177	Ggg/Agg	3/6	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.81	2		656	556	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230883	53230883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	233	642	1	ENST00000375401.3:c.1910G>A	p.Arg637Gln	p.R637Q	ENST00000375401	NM_004187.3	637	cGg/cAg	14/26	1	2	FACETS	0.975	0.917	1	0.975	0.917	1	CLONAL	1	TRUE	1	0.81	2		643	590	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	101	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.316857142718959	4	FACETS	1	0.952	1	0.554	0.496	0.615	CLONAL	1	TRUE	2	0.474243577785534	4		473	567	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0035751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	124	648	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.315650655458731	2	FACETS	0.754	0.69	0.819	0.754	0.69	0.819	SUBCLONAL	2	TRUE	0	0.474243577785534	2		648	347	SUCCESS
AR	367	MSKCC	GRCh37	X	66905930	66905930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754201976	NA	P-0035751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	55	551	0	ENST00000374690.3:c.1847G>A	p.Arg616His	p.R616H	ENST00000374690	NM_000044.3	616	cGt/cAt	3/8	0.12952671917608	0	FACETS	0.345	0.297	0.398			1	INDETERMINATE	1	TRUE	0	0.474243577785534	0		551	353	SUCCESS
APC	324	MSKCC	GRCh37	5	112175147	112175147	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	80	267	0	ENST00000257430.4:c.3856G>T	p.Glu1286Ter	p.E1286*	ENST00000257430	NM_000038.5	1286	Gaa/Taa	16/16	0.337519566046374	3	FACETS	1	0.967	1	0.782	0.705	0.859	CLONAL	2	TRUE	0	0.474243577785534	3		267	178	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120528	70120528	+	stop_lost	Nonstop_Mutation	SNP	A	A	C	novel	NA	P-0035751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	91	814	0	ENST00000245479.2:c.1530A>C	p.Ter510CysextTer49	p.*510Cext*49	ENST00000245479	NM_000346.3	510	tgA/tgC	3/3	0.217045557929486	1	FACETS	0.544	0.484	0.608	0.544	0.484	0.608	INDETERMINATE	1	TRUE	0	0.474243577785534	1		814	538	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167732	185167732	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	127	598	0	ENST00000265026.3:c.1055C>G	p.Pro352Arg	p.P352R	ENST00000265026	NM_004721.4	352	cCt/cGt	6/14	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.474243577785534	2		598	491	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525919	148525919	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	77	620	1	ENST00000320356.2:c.538C>T	p.Gln180Ter	p.Q180*	ENST00000320356	NM_004456.4	180	Caa/Taa	6/20	0.434279704413973	3	FACETS	0.893	0.787	1	0.446	0.393	0.503	CLONAL	1	TRUE	1	0.474243577785534	3		621	450	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	34	774	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.623	0.509	0.75	0.623	0.509	0.75	SUBCLONAL	1	TRUE	1	0.28	2		774	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	123	385	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.311598803101611	2	FACETS	1	0.946	1			1	CLONAL	1	TRUE	NA	0.28	2		385	822	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	112	717	4	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	0.28	2		721	771	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	102	528	0	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.914	0.817	1	0.914	0.817	1	CLONAL	1	TRUE	1	0.28	2		528	797	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	65	644	1	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.311598803101611	2	FACETS	0.652	0.565	0.747			1	SUBCLONAL	1	TRUE	NA	0.28	2		645	712	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	125	603	3	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.28	2		606	866	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913253	39913253	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	58	218	0	ENST00000378444.4:c.4862del	p.Pro1621GlnfsTer53	p.P1621Qfs*53	ENST00000378444	NM_001123385.1	1621	cCa/ca	14/15	1	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.28	1		218	247	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007824	45007825	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	24	386	0	ENST00000558401.1:c.276dup	p.Thr93HisfsTer2	p.T93Hfs*2	ENST00000558401	NM_004048.2	91	acc/aCcc	2/4	1	2	FACETS	0.56	0.44	0.699	0.56	0.44	0.699	SUBCLONAL	1	TRUE	1	0.28	2		386	306	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287446	46287446	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs774801990	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	20	359	1	ENST00000334344.6:c.5305C>T	p.Arg1769Ter	p.R1769*	ENST00000334344	NM_152641.2	1769	Cga/Tga	20/21	0.228271880405355	3	FACETS	0.768	0.59	0.975	0.384	0.295	0.488	CLONAL	1	TRUE	1	0.28	3		360	212	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528596	8528596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	19	311	0	ENST00000356435.5:c.536G>A	p.Arg179Gln	p.R179Q	ENST00000356435		179	cGa/cAa	4/35	1	2	FACETS	0.582	0.443	0.746	0.582	0.443	0.746	SUBCLONAL	1	TRUE	1	0.28	2		311	233	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652078	36652078	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45548832	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	125	721	2	ENST00000244741.5:c.200G>A	p.Arg67His	p.R67H	ENST00000244741	NM_000389.4	67	cGt/cAt	2/3	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.28	2		723	875	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532654	63532654	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	39	679	1	ENST00000307078.5:c.1925del	p.Lys642ArgfsTer47	p.K642Rfs*47	ENST00000307078	NM_004655.3	642	aAg/ag	8/11	1	2	FACETS	0.382	0.316	0.457	0.382	0.316	0.457	SUBCLONAL	1	TRUE	1	0.28	2		680	729	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845477	72845477	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1395722106	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	76	458	0	ENST00000268489.5:c.3863C>T	p.Thr1288Met	p.T1288M	ENST00000268489	NM_006885.3	1288	aCg/aTg	7/10	1	2	FACETS	0.933	0.819	1	0.933	0.819	1	CLONAL	1	TRUE	1	0.28	2		458	582	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417943	32417943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554416372	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	72	427	0	ENST00000332351.3:c.1109G>A	p.Arg370His	p.R370H	ENST00000332351	NM_024426.4	370	cGt/cAt	7/10	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.28	2		427	465	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145736828	145736828	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs748047415	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	94	505	0	ENST00000428558.2:c.3613C>T	p.Gln1205Ter	p.Q1205*	ENST00000428558	NM_004260.3	1205	Cag/Tag	22/22	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.28	2		505	662	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314993	1314993	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375729637	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	93	489	1	ENST00000400841.2:c.668C>T	p.Thr223Met	p.T223M	ENST00000400841		223	aCg/aTg	6/6	1	1	FACETS	0.891	0.793	0.995	0.891	0.793	0.995	CLONAL	1	TRUE	0	0.28	1		490	641	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456461	32456461	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	43	448	0	ENST00000332351.3:c.431C>T	p.Pro144Leu	p.P144L	ENST00000332351	NM_024426.4	144	cCg/cTg	1/10	1	2	FACETS	0.585	0.489	0.691	0.585	0.489	0.691	SUBCLONAL	1	TRUE	1	0.28	2		448	525	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420670	49420670	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs797045659	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	73	530	0	ENST00000301067.7:c.15079C>T	p.Arg5027Ter	p.R5027*	ENST00000301067	NM_003482.3	5027	Cga/Tga	48/54	0.228271880405355	3	FACETS	0.842	0.736	0.957	0.421	0.368	0.479	CLONAL	1	TRUE	1	0.28	3		530	706	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431874	49431874	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	113	672	1	ENST00000301067.7:c.9265del	p.Val3089TrpfsTer30	p.V3089Wfs*30	ENST00000301067	NM_003482.3	3089	Gtg/tg	34/54	0.228271880405355	3	FACETS	1	0.899	1	0.5	0.449	0.554	CLONAL	1	TRUE	1	0.28	3		673	920	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178067	142178067	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs200556378	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	13	245	0	ENST00000350721.4:c.7349+2T>C		p.X2450_splice	ENST00000350721	NM_001184.3	2450			1	2	FACETS	0.688	0.494	0.921	0.688	0.494	0.921	SUBCLONAL	1	TRUE	1	0.28	2		245	135	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228164	36228164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	86	587	0	ENST00000222270.7:c.7550G>A	p.Arg2517Gln	p.R2517Q	ENST00000222270	NM_014727.1	2517	cGg/cAg	33/37	1	2	FACETS	0.942	0.834	1	0.942	0.834	1	CLONAL	1	TRUE	1	0.28	2		587	652	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748962	43748962	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141222111	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	39	866	2	ENST00000382044.4:c.1844C>T	p.Thr615Met	p.T615M	ENST00000382044	NM_001141980.1	615	aCg/aTg	12/28	1	2	FACETS	0.359	0.296	0.429	0.359	0.296	0.429	SUBCLONAL	1	TRUE	1	0.28	2		868	777	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133780	2133780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397515062	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	94	612	0	ENST00000219476.3:c.3968C>T	p.Ala1323Val	p.A1323V	ENST00000219476	NM_000548.3	1323	gCg/gTg	33/42	1	2	FACETS	0.931	0.829	1	0.931	0.829	1	CLONAL	1	TRUE	1	0.28	2		612	721	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38955709	38955709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762042928	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	17	296	0	ENST00000357387.3:c.2597G>A	p.Arg866Gln	p.R866Q	ENST00000357387	NM_152756.3	866	cGg/cAg	26/38	1	2	FACETS	0.675	0.506	0.873	0.675	0.506	0.873	SUBCLONAL	1	TRUE	1	0.28	2		296	180	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861951	57861951	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564218374	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	76	373	0	ENST00000228682.2:c.1252C>T	p.Arg418Trp	p.R418W	ENST00000228682	NM_005269.2	418	Cgg/Tgg	10/12	0.228271880405355	3	FACETS	1	0.917	1	0.529	0.464	0.598	CLONAL	1	TRUE	1	0.28	3		373	585	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966157	25966157	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	105	632	1	ENST00000435504.4:c.3049C>T	p.Gln1017Ter	p.Q1017*	ENST00000435504		1017	Cag/Tag	13/13	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.28	2		633	724	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374825	149374825	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	44	385	1	ENST00000360632.3:c.269C>T	p.Ser90Leu	p.S90L	ENST00000360632	NM_015472.4	90	tCg/tTg	2/7	1	2	FACETS	0.634	0.531	0.747	0.634	0.531	0.747	SUBCLONAL	1	TRUE	1	0.28	2		386	496	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400830	72400830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	36	321	0	ENST00000357731.5:c.341G>A	p.Gly114Asp	p.G114D	ENST00000357731	NM_173808.2	114	gGc/gAc	2/7	1	2	FACETS	0.801	0.66	0.958	0.801	0.66	0.958	CLONAL	1	TRUE	1	0.28	2		321	321	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28601513	28601513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374917721	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	87	712	0	ENST00000253063.3:c.1198G>A	p.Val400Ile	p.V400I	ENST00000253063	NM_031459.4	400	Gtc/Atc	8/10	1	2	FACETS	0.795	0.703	0.893	0.795	0.703	0.893	SUBCLONAL	1	TRUE	1	0.28	2		712	782	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36940986	36940986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs923298829	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	82	509	1	ENST00000361632.4:c.353G>A	p.Arg118His	p.R118H	ENST00000361632		118	cGc/cAc	3/16	1	2	FACETS	0.859	0.757	0.968	0.859	0.757	0.968	CLONAL	1	TRUE	1	0.28	2		510	682	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612878	228612878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	94	579	0	ENST00000366696.1:c.149G>A	p.Arg50His	p.R50H	ENST00000366696	NM_003493.2	50	cGc/cAc	1/1	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.28	2		579	630	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456516	32456516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs564706633	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	31	159	0	ENST00000332351.3:c.376C>T	p.Pro126Ser	p.P126S	ENST00000332351	NM_024426.4	126	Ccg/Tcg	1/10	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.28	2		159	189	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363835	118363835	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781787241	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	67	414	0	ENST00000534358.1:c.5068G>A	p.Glu1690Lys	p.E1690K	ENST00000534358	NM_005933.3	1690	Gaa/Aaa	16/36	0.311598803101611	3	FACETS	1	0.923	1			1	CLONAL	1	TRUE	NA	0.28	3		414	503	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656304	18656304	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	22	391	1	ENST00000266497.5:c.2987del	p.Lys996SerfsTer9	p.K996Sfs*9	ENST00000266497		995	Aaa/aa	21/31	1	2	FACETS	0.724	0.563	0.909	0.724	0.563	0.909	CLONAL	1	TRUE	1	0.28	2		392	217	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244167	46244167	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	61	358	0	ENST00000334344.6:c.2262del	p.Thr755GlnfsTer3	p.T755Qfs*3	ENST00000334344	NM_152641.2	754	gTt/gt	15/21	0.228271880405355	3	FACETS	0.771	0.67	0.88	0.771	0.67	0.88	SUBCLONAL	2	TRUE	1	0.28	3		358	322	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81914521	81914521	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376192123	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	56	404	0	ENST00000359376.3:c.655G>A	p.Asp219Asn	p.D219N	ENST00000359376	NM_002661.3	219	Gat/Aat	8/33	1	2	FACETS	0.911	0.782	1	0.911	0.782	1	CLONAL	1	TRUE	1	0.28	2		404	439	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55693427	55693428	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	86	530	0	ENST00000284073.2:c.636dup	p.Gly213TrpfsTer147	p.G213Wfs*147	ENST00000284073	NM_138962.2	212	ctt/cTtt	9/14	1	2	FACETS	0.838	0.741	0.942	0.838	0.741	0.942	CLONAL	1	TRUE	1	0.28	2		530	733	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770069	56770069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	73	505	0	ENST00000337432.4:c.65C>T	p.Ala22Val	p.A22V	ENST00000337432	NM_058216.2	22	gCg/gTg	1/9	1	2	FACETS	0.862	0.754	0.978	0.862	0.754	0.978	CLONAL	1	TRUE	1	0.28	2		505	605	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10257153	10257153	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	88	441	1	ENST00000340748.4:c.2720T>A	p.Ile907Asn	p.I907N	ENST00000340748		907	aTc/aAc	27/40	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.28	2		442	605	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919657	50919657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1270149320	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	121	712	0	ENST00000440232.2:c.2825C>T	p.Pro942Leu	p.P942L	ENST00000440232	NM_002691.3	942	cCg/cTg	23/27	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.28	2		712	854	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693909	47693909	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	26	332	0	ENST00000233146.2:c.1623del	p.Val542Ter	p.V542*	ENST00000233146	NM_000251.2	541	acT/ac	10/16	1	2	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	TRUE	1	0.28	2		332	175	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52677264	52677264	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs748174546	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	54	538	2	ENST00000394830.3:c.995G>A	p.Arg332His	p.R332H	ENST00000394830	NM_018313.4	332	cGt/cAt	10/30	1	2	FACETS	0.778	0.665	0.901	0.778	0.665	0.901	CLONAL	1	TRUE	1	0.28	2		540	496	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204830	128204830	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1460001422	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	106	853	0	ENST00000341105.2:c.611G>A	p.Arg204Gln	p.R204Q	ENST00000341105	NM_032638.4	204	cGa/cAa	3/6	1	2	FACETS	0.798	0.714	0.887	0.798	0.714	0.887	SUBCLONAL	1	TRUE	1	0.28	2		853	949	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519336	176519336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs969674953	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	30	469	0	ENST00000292408.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000292408	NM_213647.1	248	Cgg/Tgg	7/18	1	2	FACETS	0.402	0.323	0.492	0.402	0.323	0.492	SUBCLONAL	1	TRUE	1	0.28	2		469	533	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288942	33288942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747846898	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	63	384	2	ENST00000374542.5:c.610C>T	p.Arg204Trp	p.R204W	ENST00000374542	NM_001141970.1	204	Cgg/Tgg	3/8	1	2	FACETS	0.896	0.777	1	0.896	0.777	1	CLONAL	1	TRUE	1	0.28	2		386	502	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953017	2953017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064795307	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	147	751	1	ENST00000396946.4:c.2923C>T	p.Arg975Trp	p.R975W	ENST00000396946	NM_032415.4	975	Cgg/Tgg	22/25	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.28	2		752	848	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900330	101900330	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	15	330	0	ENST00000374994.4:c.764G>A	p.Arg255His	p.R255H	ENST00000374994	NM_004612.2	255	cGt/cAt	4/9	1	2	FACETS	0.483	0.353	0.638	0.483	0.353	0.638	SUBCLONAL	1	TRUE	1	0.28	2		330	222	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417517	139417517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375065108	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	117	941	0	ENST00000277541.6:c.527G>A	p.Arg176Gln	p.R176Q	ENST00000277541	NM_017617.3	176	cGg/cAg	4/34	1	2	FACETS	0.784	0.705	0.867	0.784	0.705	0.867	SUBCLONAL	1	TRUE	1	0.28	2		941	1066	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426675	47426675	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	89	323	0	ENST00000377045.4:c.920C>A	p.Pro307His	p.P307H	ENST00000377045	NM_001654.4	307	cCc/cAc	10/16	1	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.28	1		323	384	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342188	70342188	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	76	238	0	ENST00000374080.3:c.1240A>G	p.Thr414Ala	p.T414A	ENST00000374080		414	Act/Gct	8/45	1	1	FACETS	0.874	0.776	0.977	1	0.982	1	CLONAL	2	TRUE	0	0.28	1		238	267	SUCCESS
BTK	695	MSKCC	GRCh37	X	100604925	100604925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	22	211	0	ENST00000308731.7:c.1928C>T	p.Thr643Ile	p.T643I	ENST00000308731	NM_000061.2	643	aCt/aTt	19/19	1	1	FACETS	0.945	0.74	1	0.945	0.74	1	CLONAL	1	TRUE	0	0.28	1		211	143	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519985	NA	P-0035829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	622	776	2	ENST00000269305.4:c.857A>T	p.Glu286Val	p.E286V	ENST00000269305	NM_001126112.2	286	gAa/gTa	8/11	0.820112759122882	2	FACETS	0.99	0.969	1	0.99	0.969	1	CLONAL	2	TRUE	0	0.820112759122882	2		778	766	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040992	42040992	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs745810304	NA	P-0035829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	201	645	1	ENST00000219905.7:c.5370G>T	p.Gln1790His	p.Q1790H	ENST00000219905	NM_001164273.1	1790	caG/caT	16/24	0.26094129425074	3	FACETS	1	0.99	1	0.453	0.423	0.483	INDETERMINATE	1	TRUE	0	0.820112759122882	3		646	509	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313180	30313180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	200	690	0	ENST00000262643.3:c.874C>T	p.Leu292Phe	p.L292F	ENST00000262643	NM_001238.2	292	Ctt/Ttt	10/12	0.820112759122882	6	FACETS	0.983	0.909	1	0.197	0.181	0.212	CLONAL	1	TRUE	1	0.820112759122882	6		690	1310	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467882	50467882	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	94	325	0	ENST00000331340.3:c.1117C>A	p.Leu373Met	p.L373M	ENST00000331340	NM_006060.4	373	Ctg/Atg	8/8	0.820112759122882	3	FACETS	1	0.959	1	0.561	0.506	0.619	CLONAL	1	TRUE	1	0.820112759122882	3		325	288	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0035864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	79	481	2	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	1	2	FACETS	0.306	0.268	0.346	0.306	0.268	0.346	SUBCLONAL	1	TRUE	1	0.654432395627674	2		483	790	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	224	542	1	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.654432395627674	2		543	683	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270162	198270162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	155	389	0	ENST00000335508.6:c.1274G>A	p.Arg425Gln	p.R425Q	ENST00000335508	NM_012433.2	425	cGa/cAa	10/25	1	2	FACETS	0.732	0.672	0.794	0.732	0.672	0.794	SUBCLONAL	1	TRUE	1	0.654432395627674	2		389	647	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845360	151845360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	274	657	1	ENST00000262189.6:c.13652G>A	p.Gly4551Asp	p.G4551D	ENST00000262189	NM_170606.2	4551	gGt/gAt	52/59	1	2	FACETS	0.95	0.894	1	0.95	0.894	1	CLONAL	1	TRUE	1	0.654432395627674	2		658	881	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849907	151849907	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	188	410	0	ENST00000262189.6:c.12409G>T	p.Glu4137Ter	p.E4137*	ENST00000262189	NM_170606.2	4137	Gag/Tag	49/59	1	2	FACETS	0.921	0.855	0.988	0.921	0.855	0.988	CLONAL	1	TRUE	1	0.654432395627674	2		410	624	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928060	178928086	+	inframe_deletion	In_Frame_Del	DEL	GCCAGTACCTCATGGATTAGAAGATTT	GCCAGTACCTCATGGATTAGAAGATTT	-	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	97	553	0	ENST00000263967.3:c.1340_1366del	p.Pro447_Leu455del	p.P447_L455del	ENST00000263967	NM_006218.2	446	tgGCCAGTACCTCATGGATTAGAAGATTTg/tgg	8/21	0.152973561738649	3	FACETS	1	0.896	1	0.334	0.298	0.372	INDETERMINATE	1	TRUE	0	0.402011585527361	3		553	578	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627685	14627685	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	66	587	0	ENST00000254322.2:c.385G>A	p.Asp129Asn	p.D129N	ENST00000254322	NM_006145.1	129	Gac/Aac	2/3	1	2	FACETS	0.395	0.342	0.453	0.395	0.342	0.453	SUBCLONAL	1	TRUE	1	0.402011585527361	2		587	831	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463275	25463275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	56	433	0	ENST00000264709.3:c.2218G>A	p.Asp740Asn	p.D740N	ENST00000264709	NM_175629.2	740	Gat/Aat	19/23	1	2	FACETS	0.487	0.417	0.564	0.487	0.417	0.564	SUBCLONAL	1	TRUE	1	0.402011585527361	2		433	572	SUCCESS
APC	324	MSKCC	GRCh37	5	112175322	112175322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	31	225	0	ENST00000257430.4:c.4031C>T	p.Ser1344Leu	p.S1344L	ENST00000257430	NM_000038.5	1344	tCa/tTa	16/16	0.402011585527361	3	FACETS	0.601	0.487	0.73	0.301	0.243	0.365	SUBCLONAL	1	TRUE	1	0.402011585527361	3		225	308	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44948987	44948987	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	37	354	0	ENST00000377967.4:c.3549-1G>C		p.X1183_splice	ENST00000377967	NM_021140.2	1183			1	2	FACETS	0.374	0.308	0.448	0.374	0.308	0.448	SUBCLONAL	1	TRUE	1	0.402011585527361	2		354	492	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023257	150023257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	61	360	0	ENST00000253339.5:c.6G>C	p.Lys2Asn	p.K2N	ENST00000253339		2	aaG/aaC	1/7	0.347957291339177	3	FACETS	0.663	0.572	0.761	0.221	0.19	0.254	SUBCLONAL	1	TRUE	0	0.402011585527361	3		360	550	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433827	49433827	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs761581210	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1371	87	884	0	ENST00000301067.7:c.7726C>G	p.Gln2576Glu	p.Q2576E	ENST00000301067	NM_003482.3	2576	Caa/Gaa	31/54	0.26572878470801	4	FACETS	0.416	0.367	0.47	0.208	0.183	0.235	SUBCLONAL	1	TRUE	2	0.402011585527361	4		884	1458	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279235	142279235	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	87	541	1	ENST00000350721.4:c.1411G>A	p.Glu471Lys	p.E471K	ENST00000350721	NM_001184.3	471	Gaa/Aaa	6/47	0.152973561738649	3	FACETS	0.672	0.595	0.756	0.224	0.198	0.252	INDETERMINATE	1	TRUE	0	0.402011585527361	3		542	773	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22408266	22408266	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	98	485	0	ENST00000344548.3:c.157C>G	p.Leu53Val	p.L53V	ENST00000344548	NM_001039802.1	53	Ctt/Gtt	4/7	0.402011585527361	1	FACETS	0.687	0.614	0.764	0.687	0.614	0.764	SUBCLONAL	1	TRUE	0	0.402011585527361	1		485	567	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261293	115261293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	85	495	0	ENST00000438362.2:c.2428G>A	p.Asp810Asn	p.D810N	ENST00000438362	NM_001242891.1	810	Gat/Aat	19/20	0.152565673095137	6	FACETS	0.86	0.759	0.969			1	INDETERMINATE	1	TRUE	NA	0.402011585527361	6		495	887	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458891	120458891	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1861	102	671	0	ENST00000256646.2:c.6454G>C	p.Asp2152His	p.D2152H	ENST00000256646	NM_024408.3	2152	Gat/Cat	34/34	0.402011585527361	8	FACETS	0.57	0.507	0.638			1	SUBCLONAL	1	TRUE	NA	0.402011585527361	8		671	1963	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512146	120512146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	56	316	0	ENST00000256646.2:c.1096G>A	p.Glu366Lys	p.E366K	ENST00000256646	NM_024408.3	366	Gag/Aag	6/34	0.402011585527361	8	FACETS	0.583	0.498	0.677			1	SUBCLONAL	1	TRUE	NA	0.402011585527361	8		316	1054	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162735812	162735812	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	71	478	0	ENST00000367921.3:c.1121C>G	p.Ser374Cys	p.S374C	ENST00000367921	NM_006182.2	374	tCt/tGt	10/18	0.402011585527361	5	FACETS	0.502	0.437	0.574	0.167	0.145	0.192	SUBCLONAL	1	TRUE	2	0.402011585527361	5		478	1127	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226549202	226549202	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	54	409	0	ENST00000366794.5:c.3004C>G	p.Leu1002Val	p.L1002V	ENST00000366794	NM_001618.3	1002	Ctg/Gtg	23/23	0.402011585527361	4	FACETS	0.459	0.391	0.534	0.153	0.13	0.178	SUBCLONAL	1	TRUE	1	0.402011585527361	4		409	820	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451221	70451221	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	102	576	0	ENST00000373644.4:c.6061G>C	p.Glu2021Gln	p.E2021Q	ENST00000373644	NM_030625.2	2021	Gag/Cag	12/12	0.152973561738649	3	FACETS	0.685	0.612	0.763	0.228	0.204	0.255	INDETERMINATE	1	TRUE	0	0.402011585527361	3		576	890	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104377147	104377147	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	140	830	0	ENST00000369902.3:c.1258G>C	p.Glu420Gln	p.E420Q	ENST00000369902	NM_016169.3	420	Gag/Cag	10/12	0.152973561738649	3	FACETS	0.729	0.663	0.8	0.243	0.221	0.267	INDETERMINATE	1	TRUE	0	0.402011585527361	3		830	1147	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601278	28601278	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	67	492	0	ENST00000241453.7:c.2154C>G	p.Phe718Leu	p.F718L	ENST00000241453	NM_004119.2	718	ttC/ttG	17/24	0.402011585527361	1	FACETS	0.545	0.474	0.621	0.545	0.474	0.621	SUBCLONAL	1	TRUE	0	0.402011585527361	1		492	489	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098653	2098653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555494586	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	48	502	0	ENST00000219476.3:c.37G>A	p.Glu13Lys	p.E13K	ENST00000219476	NM_000548.3	13	Gag/Aag	2/42	1	2	FACETS	0.303	0.255	0.356	0.303	0.255	0.356	SUBCLONAL	1	TRUE	1	0.402011585527361	2		502	788	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832810	3832810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	113	545	1	ENST00000262367.5:c.1448G>A	p.Arg483Gln	p.R483Q	ENST00000262367	NM_004380.2	483	cGa/cAa	6/31	1	2	FACETS	0.642	0.578	0.711	0.642	0.578	0.711	SUBCLONAL	1	TRUE	1	0.402011585527361	2		546	875	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805044	89805044	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769025633	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	126	669	0	ENST00000389301.3:c.4333G>A	p.Asp1445Asn	p.D1445N	ENST00000389301	NM_000135.2	1445	Gac/Aac	43/43	0.402011585527361	1	FACETS	0.616	0.558	0.677	0.616	0.558	0.677	SUBCLONAL	1	TRUE	0	0.402011585527361	1		669	813	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17116983	17116983	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	89	545	0	ENST00000285071.4:c.1726G>C	p.Glu576Gln	p.E576Q	ENST00000285071	NM_144997.5	576	Gag/Cag	14/14	1	2	FACETS	0.639	0.566	0.716	0.639	0.566	0.716	SUBCLONAL	1	TRUE	1	0.402011585527361	2		545	693	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40461480	40461480	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	116	732	0	ENST00000345506.4:c.2200C>A	p.Pro734Thr	p.P734T	ENST00000345506	NM_003152.3	734	Ccc/Acc	19/20	1	2	FACETS	0.608	0.547	0.673	0.608	0.547	0.673	SUBCLONAL	1	TRUE	1	0.402011585527361	2		732	949	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699332	47699332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	68	394	0	ENST00000347630.2:c.176C>T	p.Ser59Leu	p.S59L	ENST00000347630	NM_001007230.1	59	tCa/tTa	4/11	1	2	FACETS	0.596	0.518	0.679	0.596	0.518	0.679	SUBCLONAL	1	TRUE	1	0.402011585527361	2		394	568	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56811482	56811482	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	50	354	0	ENST00000337432.4:c.1030C>T	p.Gln344Ter	p.Q344*	ENST00000337432	NM_058216.2	344	Cag/Tag	9/9	1	2	FACETS	0.515	0.437	0.6	0.515	0.437	0.6	SUBCLONAL	1	TRUE	1	0.402011585527361	2		354	483	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78938126	78938126	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	79	506	0	ENST00000306801.3:c.4004G>A	p.Arg1335Lys	p.R1335K	ENST00000306801	NM_020761.2	1335	aGa/aAa	34/34	1	2	FACETS	0.587	0.516	0.663	0.587	0.516	0.663	SUBCLONAL	1	TRUE	1	0.402011585527361	2		506	670	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7167990	7167990	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	54	405	0	ENST00000302850.5:c.1599C>G	p.Phe533Leu	p.F533L	ENST00000302850	NM_000208.2	533	ttC/ttG	7/22	1	2	FACETS	0.424	0.362	0.493	0.424	0.362	0.493	SUBCLONAL	1	TRUE	1	0.402011585527361	2		405	633	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172378	7172378	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	71	400	0	ENST00000302850.5:c.1191C>G	p.Ile397Met	p.I397M	ENST00000302850	NM_000208.2	397	atC/atG	5/22	1	2	FACETS	0.555	0.484	0.631	0.555	0.484	0.631	SUBCLONAL	1	TRUE	1	0.402011585527361	2		400	637	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627399	14627399	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	86	779	0	ENST00000254322.2:c.671G>C	p.Gly224Ala	p.G224A	ENST00000254322	NM_006145.1	224	gGa/gCa	2/3	1	2	FACETS	0.348	0.307	0.393	0.348	0.307	0.393	SUBCLONAL	1	TRUE	1	0.402011585527361	2		779	1228	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953169	17953169	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	200	670	0	ENST00000458235.1:c.817G>A	p.Val273Met	p.V273M	ENST00000458235	NM_000215.3	273	Gtg/Atg	6/24	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.402011585527361	2		670	955	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791250	42791250	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	88	623	0	ENST00000575354.2:c.310G>C	p.Glu104Gln	p.E104Q	ENST00000575354	NM_015125.3	104	Gag/Cag	3/20	1	2	FACETS	0.47	0.415	0.528	0.47	0.415	0.528	SUBCLONAL	1	TRUE	1	0.402011585527361	2		623	932	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082537	16082537	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	71	602	0	ENST00000281043.3:c.351G>C	p.Trp117Cys	p.W117C	ENST00000281043	NM_005378.4	117	tgG/tgC	2/3	1	2	FACETS	0.473	0.412	0.539	0.473	0.412	0.539	SUBCLONAL	1	TRUE	1	0.402011585527361	2		602	747	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39214688	39214688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	55	446	1	ENST00000402219.2:c.3436G>A	p.Glu1146Lys	p.E1146K	ENST00000402219	NM_005633.3	1146	Gaa/Aaa	22/23	0.105358327283889	5	FACETS	0.553	0.472	0.642			1	INDETERMINATE	1	TRUE	NA	0.402011585527361	5		447	793	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149539	61149539	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	67	447	0	ENST00000295025.8:c.1729G>C	p.Glu577Gln	p.E577Q	ENST00000295025	NM_002908.2	577	Gag/Cag	11/11	1	2	FACETS	0.55	0.478	0.628	0.55	0.478	0.628	SUBCLONAL	1	TRUE	1	0.402011585527361	2		447	606	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215595141	215595142	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	59	395	0	ENST00000260947.4:c.1994_1995insT	p.Glu665AspfsTer9	p.E665Dfs*9	ENST00000260947	NM_000465.2	665	gaa/gaTa	10/11	1	2	FACETS	0.623	0.537	0.717	0.623	0.537	0.717	SUBCLONAL	1	TRUE	1	0.402011585527361	2		395	471	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023300	31023300	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	56	514	0	ENST00000375687.4:c.2785G>C	p.Glu929Gln	p.E929Q	ENST00000375687	NM_015338.5	929	Gag/Cag	13/13	0.26572878470801	4	FACETS	0.479	0.409	0.556	0.24	0.204	0.278	SUBCLONAL	1	TRUE	2	0.402011585527361	4		514	815	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023475	31023475	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	52	415	0	ENST00000375687.4:c.2960G>A	p.Gly987Glu	p.G987E	ENST00000375687	NM_015338.5	987	gGa/gAa	13/13	0.26572878470801	4	FACETS	0.5	0.424	0.582	0.25	0.212	0.291	SUBCLONAL	1	TRUE	2	0.402011585527361	4		415	726	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945393	54945393	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	93	544	0	ENST00000312783.6:c.1033G>C	p.Glu345Gln	p.E345Q	ENST00000312783	NM_198436.1	345	Gaa/Caa	10/10	0.3485969510867	4	FACETS	0.613	0.543	0.687	0.204	0.181	0.229	SUBCLONAL	1	TRUE	1	0.402011585527361	4		544	1059	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138423302	138423302	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	122	517	0	ENST00000289153.2:c.1564G>C	p.Asp522His	p.D522H	ENST00000289153	NM_006219.2	522	Gat/Cat	10/22	0.152973561738649	3	FACETS	1	0.936	1	0.348	0.314	0.383	INDETERMINATE	1	TRUE	0	0.402011585527361	3		517	699	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928234	178928234	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	193	422	0	ENST00000263967.3:c.1420G>C	p.Glu474Gln	p.E474Q	ENST00000263967	NM_006218.2	474	Gag/Cag	9/21	0.152973561738649	3	FACETS	0.92	0.855	0.986	0.613	0.57	0.657	INDETERMINATE	2	TRUE	0	0.402011585527361	3		422	627	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947109	178947109	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	61	392	0	ENST00000263967.3:c.2545G>T	p.Glu849Ter	p.E849*	ENST00000263967	NM_006218.2	849	Gag/Tag	18/21	0.152973561738649	3	FACETS	0.642	0.554	0.737	0.214	0.184	0.246	INDETERMINATE	1	TRUE	0	0.402011585527361	3		392	568	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157188	106157188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	56	359	0	ENST00000380013.4:c.2089C>T	p.Pro697Ser	p.P697S	ENST00000380013	NM_001127208.2	697	Cca/Tca	3/11	0.284309077971902	1	FACETS	0.47	0.403	0.542	0.47	0.403	0.542	SUBCLONAL	1	TRUE	0	0.402011585527361	1		359	474	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522532	187522532	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	67	570	0	ENST00000441802.2:c.11531T>C	p.Leu3844Pro	p.L3844P	ENST00000441802	NM_005245.3	3844	cTg/cCg	21/27	0.284309077971902	1	FACETS	0.398	0.345	0.455	0.398	0.345	0.455	SUBCLONAL	1	TRUE	0	0.402011585527361	1		570	669	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952375	38952375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542644321	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	104	287	0	ENST00000357387.3:c.3050C>T	p.Ser1017Phe	p.S1017F	ENST00000357387	NM_152756.3	1017	tCt/tTt	30/38	0.402011585527361	3	FACETS	1	0.974	1	0.63	0.567	0.697	CLONAL	1	TRUE	1	0.402011585527361	3		287	493	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589247	67589247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	23	256	0	ENST00000274335.5:c.1235C>T	p.Ser412Phe	p.S412F	ENST00000274335		412	tCt/tTt	9/15	0.402011585527361	3	FACETS	0.378	0.294	0.474	0.189	0.147	0.237	SUBCLONAL	1	TRUE	1	0.402011585527361	3		256	364	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80149995	80149995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	73	381	0	ENST00000265081.6:c.2860G>A	p.Glu954Lys	p.E954K	ENST00000265081	NM_002439.4	954	Gaa/Aaa	21/24	0.402011585527361	3	FACETS	0.823	0.721	0.933	0.411	0.36	0.467	CLONAL	1	TRUE	1	0.402011585527361	3		381	530	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694574	176694574	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	67	385	0	ENST00000439151.2:c.5158C>A	p.Leu1720Met	p.L1720M	ENST00000439151	NM_022455.4	1720	Ctg/Atg	15/23	0.284309077971902	1	FACETS	0.536	0.466	0.611	0.536	0.466	0.611	SUBCLONAL	1	TRUE	0	0.402011585527361	1		385	497	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948488	31948488	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	52	391	0	ENST00000375333.2:c.971C>G	p.Ser324Ter	p.S324*	ENST00000375333	NM_032454.1	324	tCa/tGa	7/8	0.402011585527361	3	FACETS	0.441	0.374	0.514	0.22	0.187	0.257	SUBCLONAL	1	TRUE	1	0.402011585527361	3		391	705	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286544	33286544	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	85	394	0	ENST00000374542.5:c.2199C>G	p.Ile733Met	p.I733M	ENST00000374542	NM_001141970.1	733	atC/atG	8/8	0.402011585527361	3	FACETS	0.566	0.499	0.638	0.283	0.249	0.319	SUBCLONAL	1	TRUE	1	0.402011585527361	3		394	897	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139051	37139051	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	106	557	0	ENST00000373509.5:c.391G>C	p.Asp131His	p.D131H	ENST00000373509	NM_002648.3	131	Gac/Cac	4/6	0.402011585527361	3	FACETS	0.582	0.52	0.648	0.291	0.26	0.324	SUBCLONAL	1	TRUE	1	0.402011585527361	3		557	1088	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513229	106513229	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	53	335	0	ENST00000359195.3:c.2133G>C	p.Gln711His	p.Q711H	ENST00000359195	NM_002649.2	711	caG/caC	4/11	0.158031716529245	3	FACETS	0.653	0.557	0.758	0.326	0.278	0.379	INDETERMINATE	1	TRUE	1	0.402011585527361	3		335	485	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523609	148523609	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	42	304	0	ENST00000320356.2:c.844C>T	p.His282Tyr	p.H282Y	ENST00000320356	NM_004456.4	282	Cat/Tat	8/20	0.158031716529245	3	FACETS	0.555	0.464	0.657	0.278	0.232	0.329	INDETERMINATE	1	TRUE	1	0.402011585527361	3		304	452	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879329	151879329	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	59	436	0	ENST00000262189.6:c.5616G>C	p.Gln1872His	p.Q1872H	ENST00000262189	NM_170606.2	1872	caG/caC	36/59	0.158031716529245	3	FACETS	0.552	0.474	0.636	0.276	0.237	0.318	INDETERMINATE	1	TRUE	1	0.402011585527361	3		436	639	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56859043	56859043	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	74	497	0	ENST00000519728.1:c.169C>G	p.Gln57Glu	p.Q57E	ENST00000519728	NM_002350.3	57	Caa/Gaa	3/13	0.3485969510867	4	FACETS	0.57	0.497	0.648	0.19	0.165	0.216	SUBCLONAL	1	TRUE	1	0.402011585527361	4		497	906	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864809	117864810	+	missense_variant	Missense_Mutation	DNP	GC	GC	AT	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	66	468	1	ENST00000297338.2:c.1299_1300delinsAT	p.His434Tyr	p.H434Y	ENST00000297338	NM_006265.2	433	caGCat/caATat	10/14	0.3485969510867	4	FACETS	0.486	0.42	0.557	0.162	0.14	0.186	SUBCLONAL	1	TRUE	1	0.402011585527361	4		469	948	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613379	100613379	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	71	499	0	ENST00000308731.7:c.1021C>T	p.Gln341Ter	p.Q341*	ENST00000308731	NM_000061.2	341	Cag/Tag	12/19	1	2	FACETS	0.487	0.425	0.555	0.487	0.425	0.555	SUBCLONAL	1	TRUE	1	0.402011585527361	2		499	725	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205004	123205004	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	53	294	0	ENST00000218089.9:c.2364C>A	p.Phe788Leu	p.F788L	ENST00000218089	NM_001042749.1	788	ttC/ttA	25/35	1	2	FACETS	0.692	0.592	0.801	0.692	0.592	0.801	SUBCLONAL	1	TRUE	1	0.402011585527361	2		294	381	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864809	117864809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	66	468	1	ENST00000297338.2:c.1300C>T	p.His434Tyr	p.H434Y	ENST00000297338	NM_006265.2	434	Cat/Tat	10/14	0.3485969510867	4	FACETS	0.491	0.425	0.563	0.164	0.141	0.188	SUBCLONAL	1	TRUE	1	0.402011585527361	4		469	938	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0036012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	186	385	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.54304154049906	1	FACETS	0.912	0.849	0.977	0.912	0.849	0.977	CLONAL	1	TRUE	0	0.54304154049906	1		385	547	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0036012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	108	424	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.54304154049906	2		424	375	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945033	31945033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	189	1003	1	ENST00000340398.3:c.68C>T	p.Thr23Met	p.T23M	ENST00000340398	NM_001013699.2	23	aCg/aTg	1/1	0.1417686729989	0	FACETS	0.394	0.365	0.425			1	INDETERMINATE	1	TRUE	0	0.54304154049906	0		1004	807	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929412	44929415	+	frameshift_variant	Frame_Shift_Del	DEL	ACAA	ACAA	-	rs786205676	NA	P-0036012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	155	360	0	ENST00000377967.4:c.2515_2518del	p.Asn839ValfsTer27	p.N839Vfs*27	ENST00000377967	NM_021140.2	838	ACAAac/ac	17/29	0.54304154049906	2	FACETS	1	0.963	1			1	CLONAL	1	TRUE	NA	0.54304154049906	2		360	531	SUCCESS
APC	324	MSKCC	GRCh37	5	112155032	112155032	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554080162	NA	P-0036012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	131	534	0	ENST00000257430.4:c.1307del	p.Asn436IlefsTer18	p.N436Ifs*18	ENST00000257430	NM_000038.5	435	Aaa/aa	10/16	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.54304154049906	2		534	479	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107210	11107210	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777544121	NA	P-0036012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	192	657	0	ENST00000358026.2:c.1802C>T	p.Pro601Leu	p.P601L	ENST00000358026	NM_001128849.1	601	cCg/cTg	11/36	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.54304154049906	2		657	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0036015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	267	830	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.257001127688494	3	FACETS	1	0.977	1	0.717	0.674	0.761	CLONAL	2	TRUE	0	0.330469576426502	3		830	875	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100685	8100685	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	164	800	0	ENST00000346208.3:c.659C>A	p.Thr220Asn	p.T220N	ENST00000346208		220	aCc/aAc	3/6	0.137644055211083	4	FACETS	0.769	0.706	0.834			1	INDETERMINATE	2	TRUE	NA	0.330469576426502	4		800	859	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702382	47702382	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	100	329	0	ENST00000233146.2:c.1978G>C	p.Asp660His	p.D660H	ENST00000233146	NM_000251.2	660	Gat/Cat	12/16	0.20862984625341	4	FACETS	1	0.98	1	0.473	0.424	0.526	CLONAL	1	TRUE	1	0.330469576426502	4		329	567	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703574	47703574	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	155	732	0	ENST00000233146.2:c.2076del	p.Cys693ValfsTer17	p.C693Vfs*17	ENST00000233146	NM_000251.2	692	Ggg/gg	13/16	0.20862984625341	4	FACETS	1	0.974	1	0.387	0.353	0.422	CLONAL	1	TRUE	1	0.330469576426502	4		732	1075	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719243	61719243	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	52	485	0	ENST00000401558.2:c.1814G>C	p.Gly605Ala	p.G605A	ENST00000401558	NM_003400.3	605	gGa/gCa	16/25	0.20862984625341	4	FACETS	0.608	0.516	0.708	0.203	0.172	0.236	SUBCLONAL	1	TRUE	1	0.330469576426502	4		485	689	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519980	NA	P-0036063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	217	551	0	ENST00000269305.4:c.528C>G	p.Cys176Trp	p.C176W	ENST00000269305	NM_001126112.2	176	tgC/tgG	5/11	0.82691372527382	2	FACETS	0.968	0.932	1	0.968	0.932	1	CLONAL	2	TRUE	0	0.82691372527382	2		551	271	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0036164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	84	494	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.79	0.699	0.886	0.79	0.699	0.886	SUBCLONAL	1	FALSE	1	0.396197673183486	2		494	537	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692851	89692851	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	52	194	0	ENST00000371953.3:c.335T>G	p.Leu112Arg	p.L112R	ENST00000371953	NM_000314.4	112	cTa/cGa	5/9	0.396197673183486	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	0	0.396197673183486	1		194	169	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696689	47696689	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519972	NA	P-0036170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	172	679	0	ENST00000347630.2:c.259T>A	p.Tyr87Asn	p.Y87N	ENST00000347630	NM_001007230.1	87	Tac/Aac	5/11	1	2	FACETS	0.812	0.747	0.879	0.812	0.747	0.879	CLONAL	1	TRUE	1	0.459572549507291	2		679	922	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321305	65321305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368776025	NA	P-0036170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	205	844	3	ENST00000342505.4:c.1535C>T	p.Ser512Leu	p.S512L	ENST00000342505	NM_002227.2	512	tCg/tTg	11/25	0.41487108173737	1	FACETS	0.844	0.785	0.906	0.844	0.785	0.906	CLONAL	1	TRUE	0	0.459572549507291	1		847	814	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941838	44941838	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	100	254	0	ENST00000377967.4:c.3163del	p.Ser1055ValfsTer28	p.S1055Vfs*28	ENST00000377967	NM_021140.2	1054	agA/ag	21/29	1	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.459572549507291	1		254	265	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537966	212537966	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	52	491	1	ENST00000342788.4:c.1639del	p.Glu547ArgfsTer106	p.E547Rfs*106	ENST00000342788	NM_005235.2	547	Gag/ag	14/28	1	2	FACETS	0.367	0.312	0.428	0.367	0.312	0.428	SUBCLONAL	1	TRUE	1	0.459572549507291	2		492	616	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696689	47696689	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519972	NA	P-0036170-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	123	679	0	ENST00000347630.2:c.259T>A	p.Tyr87Asn	p.Y87N	ENST00000347630	NM_001007230.1	87	Tac/Aac	5/11	1	2	FACETS	0.881	0.802	0.963	0.881	0.802	0.963	CLONAL	1	TRUE	1	0.624624205138421	2		679	447	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321305	65321305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368776025	NA	P-0036170-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	212	844	3	ENST00000342505.4:c.1535C>T	p.Ser512Leu	p.S512L	ENST00000342505	NM_002227.2	512	tCg/tTg	11/25	0.624624205138421	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.624624205138421	1		847	449	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941838	44941838	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036170-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	115	254	0	ENST00000377967.4:c.3163del	p.Ser1055ValfsTer28	p.S1055Vfs*28	ENST00000377967	NM_021140.2	1054	agA/ag	21/29	1	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.624624205138421	1		254	213	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	157	635	0	ENST00000269305.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	336	Gag/Tag	10/11	0.281565605898917	3	FACETS	0.955	0.886	1	0.955	0.886	1	CLONAL	3	TRUE	0	0.32501134764846	3		635	392	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42053981	42053981	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	34	341	0	ENST00000219905.7:c.7443G>C	p.Leu2481Phe	p.L2481F	ENST00000219905	NM_001164273.1	2481	ttG/ttC	21/24	1	2	FACETS	0.769	0.631	0.923	0.769	0.631	0.923	CLONAL	1	TRUE	1	0.32501134764846	2		341	272	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332780	65333214	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTTGTTAAATTCCTTTAGGAAATCCTTGAAAACATTATTTATCCGCATCCTGGTGAGAAGGTTCCTCTGTCTGATGGACTTATTCAATGTTTCTGGAATATATCGCTTGTAGCTAAAAGACAGTAGAAAAGTACATCTCCTTTTCATGTACAGGTTAGGAGAAAATAGTTTAGAAACAAATCTAAGTCCATGAATCCACATGTTGCCAAATGGGAAAGGGAGATCTATTCCCAGAGGACGTTAGATGGAGTTAGCACTGAAGATGACCATCATAAGGAGATGCAGGTGAATAGAAACTGGGAAAGAAAAGCAAAGCACATGCTCCACAGATTTCACTGAAATGGGAATTGCTACAAGTATTGCCCAATTTTCTGGGTCACCAAGGCAGGGCATCTACATTTTTGCTTGCTAGCTTCACCATTCTTGTGCACATTA	GTTGTTAAATTCCTTTAGGAAATCCTTGAAAACATTATTTATCCGCATCCTGGTGAGAAGGTTCCTCTGTCTGATGGACTTATTCAATGTTTCTGGAATATATCGCTTGTAGCTAAAAGACAGTAGAAAAGTACATCTCCTTTTCATGTACAGGTTAGGAGAAAATAGTTTAGAAACAAATCTAAGTCCATGAATCCACATGTTGCCAAATGGGAAAGGGAGATCTATTCCCAGAGGACGTTAGATGGAGTTAGCACTGAAGATGACCATCATAAGGAGATGCAGGTGAATAGAAACTGGGAAAGAAAAGCAAAGCACATGCTCCACAGATTTCACTGAAATGGGAATTGCTACAAGTATTGCCCAATTTTCTGGGTCACCAAGGCAGGGCATCTACATTTTTGCTTGCTAGCTTCACCATTCTTGTGCACATTA	-	novel	NA	P-0036179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	20	516	0	ENST00000342505.4:c.648-323_759del		p.X216_splice	ENST00000342505	NM_002227.2	216		7/25	0.32501134764846	2	FACETS	0.32	0.244	0.409	0.16	0.122	0.205	SUBCLONAL	1	TRUE	0	0.32501134764846	2		516	385	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431505	121431505	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	34	554	0	ENST00000257555.6:c.709A>C	p.Asn237His	p.N237H	ENST00000257555		237	Aat/Cat	3/10	0.304087030020498	2	FACETS	0.636	0.521	0.765	0.318	0.26	0.383	SUBCLONAL	1	TRUE	0	0.32501134764846	2		554	329	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119290	3119290	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	51	745	0	ENST00000078429.4:c.822C>A	p.Asn274Lys	p.N274K	ENST00000078429	NM_002067.2	274	aaC/aaA	6/7	1	2	FACETS	0.769	0.655	0.894	0.769	0.655	0.894	SUBCLONAL	1	TRUE	1	0.32501134764846	2		745	408	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716030	52716030	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	50	731	0	ENST00000322088.6:c.595G>C	p.Asp199His	p.D199H	ENST00000322088	NM_014225.5	199	Gac/Cac	5/15	0.267981497751321	3	FACETS	0.753	0.639	0.878	0.377	0.319	0.439	SUBCLONAL	1	TRUE	1	0.32501134764846	3		731	475	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693887	47693887	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587778523	NA	P-0036179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	46	412	1	ENST00000233146.2:c.1601G>T	p.Arg534Leu	p.R534L	ENST00000233146	NM_000251.2	534	cGt/cTt	10/16	0.32501134764846	5	FACETS	0.925	0.78	1	0.308	0.26	0.362	CLONAL	1	TRUE	2	0.32501134764846	5		413	455	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002831	69002831	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	37	296	0	ENST00000288368.4:c.2131G>T	p.Ala711Ser	p.A711S	ENST00000288368	NM_024870.2	711	Gct/Tct	20/40	0.32501134764846	4	FACETS	1	0.843	1	0.34	0.281	0.405	CLONAL	1	TRUE	1	0.32501134764846	4		296	296	SUCCESS
AR	367	MSKCC	GRCh37	X	66765757	66765757	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	65	894	0	ENST00000374690.3:c.769C>G	p.Leu257Val	p.L257V	ENST00000374690	NM_000044.3	257	Ctg/Gtg	1/8	0.267981497751321	3	FACETS	0.49	0.424	0.563	0.245	0.212	0.282	SUBCLONAL	1	TRUE	1	0.32501134764846	3		894	948	SUCCESS
AR	367	MSKCC	GRCh37	X	66765919	66765919	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	60	799	1	ENST00000374690.3:c.931C>A	p.Pro311Thr	p.P311T	ENST00000374690	NM_000044.3	311	Cct/Act	1/8	0.267981497751321	3	FACETS	0.545	0.468	0.628	0.272	0.234	0.314	SUBCLONAL	1	TRUE	1	0.32501134764846	3		800	788	SUCCESS
AR	367	MSKCC	GRCh37	X	66766259	66766259	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs780162524	NA	P-0036179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	44	241	0	ENST00000374690.3:c.1271C>A	p.Ser424Tyr	p.S424Y	ENST00000374690	NM_000044.3	424	tCt/tAt	1/8	0.267981497751321	3	FACETS	0.771	0.648	0.908	0.386	0.324	0.454	CLONAL	1	TRUE	1	0.32501134764846	3		241	408	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0036298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	78	425	1	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		426	501	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913396	NA	P-0036298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	29	294	0	ENST00000349496.5:c.95A>G	p.Asp32Gly	p.D32G	ENST00000349496	NM_001904.3	32	gAc/gGc	3/15	0.139822491301176	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		294	494	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094443	27094453	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTATCGCCT	CTCTATCGCCT	-	novel	NA	P-0036298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	76	577	0	ENST00000324856.7:c.3153_3163del	p.Tyr1052CysfsTer49	p.Y1052Cfs*49	ENST00000324856	NM_006015.4	1051	CTCTATCGCCTc/c	11/20	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		577	693	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0036326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	358	519	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.528989707756151	3	FACETS	0.883	0.852	0.912			1	CLONAL	3	TRUE	NA	0.741378741372085	3		519	500	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628443	187628443	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	114	817	0	ENST00000441802.2:c.2539A>G	p.Thr847Ala	p.T847A	ENST00000441802	NM_005245.3	847	Aca/Gca	2/27	0.27395641624733	3	FACETS	0.803	0.726	0.884	0.401	0.363	0.442	INDETERMINATE	1	TRUE	1	0.741378741372085	3		817	525	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023104	1023104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	154	641	0	ENST00000358495.3:c.1151G>A	p.Gly384Glu	p.G384E	ENST00000358495	NM_134424.2	384	gGa/gAa	11/12	0.741378741372085	6	FACETS	1	0.937	1	0.257	0.235	0.281	CLONAL	1	TRUE	2	0.741378741372085	6		641	1002	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774194	56774194	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	106	432	0	ENST00000337432.4:c.545T>G	p.Leu182Arg	p.L182R	ENST00000337432	NM_058216.2	182	cTt/cGt	3/9	0.719958783681526	2	FACETS	0.96	0.872	1	0.48	0.436	0.525	CLONAL	1	TRUE	0	0.741378741372085	2		432	298	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637853	39637853	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	106	372	0	ENST00000262039.4:c.2270T>A	p.Leu757His	p.L757H	ENST00000262039	NM_002647.2	757	cTc/cAc	22/25	0.719958783681526	2	FACETS	1	0.925	1	0.509	0.463	0.556	CLONAL	1	TRUE	0	0.741378741372085	2		372	281	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349705	15349705	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	151	707	1	ENST00000263377.2:c.3869G>A	p.Arg1290His	p.R1290H	ENST00000263377	NM_058243.2	1290	cGc/cAc	19/20	0.48056318737964	3	FACETS	1	0.962	1			1	CLONAL	1	TRUE	NA	0.741378741372085	3		708	519	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273288	198273288	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	58	421	0	ENST00000335508.6:c.922A>C	p.Ser308Arg	p.S308R	ENST00000335508	NM_012433.2	308	Agt/Cgt	8/25	0.719958783681526	2	FACETS	0.503	0.435	0.576	0.252	0.217	0.288	SUBCLONAL	1	TRUE	0	0.741378741372085	2		421	311	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542858	187542858	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	34	372	0	ENST00000441802.2:c.4882A>G	p.Ser1628Gly	p.S1628G	ENST00000441802	NM_005245.3	1628	Agt/Ggt	10/27	0.27395641624733	3	FACETS	0.349	0.285	0.421	0.175	0.142	0.211	INDETERMINATE	1	TRUE	1	0.741378741372085	3		372	360	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35857127	35857127	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	97	338	0	ENST00000303115.3:c.48A>C	p.Gln16His	p.Q16H	ENST00000303115	NM_002185.3	16	caA/caC	1/8	0.70115216658389	3	FACETS	0.892	0.801	0.988	0.446	0.4	0.494	CLONAL	1	TRUE	1	0.741378741372085	3		338	402	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502104	157502104	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	32	365	0	ENST00000346085.5:c.3137A>C	p.Lys1046Thr	p.K1046T	ENST00000346085	NM_020732.3	1046	aAg/aCg	12/20	0.140222646901516	3	FACETS	0.499	0.407	0.602	0.25	0.203	0.301	INDETERMINATE	1	TRUE	1	0.741378741372085	3		365	237	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751067	128751067	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	94	497	0	ENST00000377970.2:c.604G>C	p.Glu202Gln	p.E202Q	ENST00000377970	NM_002467.4	202	Gag/Cag	2/3	0.741378741372085	7	FACETS	0.598	0.53	0.67			1	SUBCLONAL	1	TRUE	NA	0.741378741372085	7		497	1211	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0036423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	62	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.978	0.845	1	0.978	0.845	1	CLONAL	1	TRUE	1	0.236619714488874	2		473	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0036423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	157	936	0	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	0.19852466815846	2	FACETS	1	0.972	1	0.573	0.524	0.625	CLONAL	1	TRUE	0	0.236619714488874	2		936	1157	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37680932	37680932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	75	489	1	ENST00000447079.4:c.3101C>T	p.Pro1034Leu	p.P1034L	ENST00000447079	NM_015083.1	1034	cCc/cTc	12/14	0.088666140457325	3	FACETS	1	0.909	1	0.523	0.458	0.593	INDETERMINATE	1	TRUE	1	0.236619714488874	3		490	678	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094856	11094857	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	148	991	0	ENST00000358026.2:c.31dup	p.Thr11AsnfsTer21	p.T11Nfs*21	ENST00000358026	NM_001128849.1	10	gga/ggAa	2/36	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.236619714488874	2		991	1242	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0036443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	76	797	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.775	0.679	0.879	0.775	0.679	0.879	SUBCLONAL	1	TRUE	1	0.254299193443672	2		797	771	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0036443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	83	630	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.254299193443672	1	FACETS	0.849	0.749	0.956	0.849	0.749	0.956	CLONAL	1	TRUE	0	0.254299193443672	1		630	671	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575209	48575209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767326	NA	P-0036443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	58	391	0	ENST00000342988.3:c.403C>T	p.Arg135Ter	p.R135*	ENST00000342988	NM_005359.5	135	Cga/Tga	3/12	0.254299193443672	1	FACETS	0.913	0.787	1	0.913	0.787	1	CLONAL	1	TRUE	0	0.254299193443672	1		391	436	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0036506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	96	434	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	0.884	0.79	0.984	0.884	0.79	0.984	CLONAL	1	TRUE	1	0.39	2		434	557	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021422	42021422	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	26	338	0	ENST00000219905.7:c.3718C>T	p.Arg1240Ter	p.R1240*	ENST00000219905	NM_001164273.1	1240	Cga/Tga	11/24	1	2	FACETS	0.281	0.222	0.349	0.281	0.222	0.349	SUBCLONAL	1	TRUE	1	0.39	2		338	475	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99136557	99136557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	104	493	1	ENST00000074304.5:c.46G>A	p.Ala16Thr	p.A16T	ENST00000074304	NM_001134224.1	16	Gca/Aca	3/26	1	2	FACETS	0.958	0.86	1	0.958	0.86	1	CLONAL	1	TRUE	1	0.39	2		494	557	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138400816	138400816	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	54	255	0	ENST00000289153.2:c.2497G>C	p.Asp833His	p.D833H	ENST00000289153	NM_006219.2	833	Gat/Cat	17/22	1	2	FACETS	0.863	0.741	0.994	0.863	0.741	0.994	CLONAL	1	TRUE	1	0.39	2		255	321	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27172676	27172676	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	116	450	1	ENST00000380036.4:c.691G>T	p.Gly231Cys	p.G231C	ENST00000380036	NM_000459.3	231	Ggt/Tgt	5/23	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.39	2		451	588	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210815	2210815	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200004531	NA	P-0036626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	26	505	0	ENST00000398665.3:c.1312G>A	p.Ala438Thr	p.A438T	ENST00000398665	NM_032482.2	438	Gct/Act	14/28	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	FALSE	1	0.285365000210325	2		505	125	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456858	32456858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	14	493	0	ENST00000332351.3:c.34C>T	p.Pro12Ser	p.P12S	ENST00000332351	NM_024426.4	12	Ccg/Tcg	1/10	1	2	FACETS	1	0.823	1	1	0.823	1	CLONAL	1	FALSE	1	0.285365000210325	2		493	84	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221968	1221974	+	frameshift_variant	Frame_Shift_Del	DEL	GCCAAGA	GCCAAGA	-	novel	NA	P-0036626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	84	572	0	ENST00000326873.7:c.884_890del	p.Ala295GlyfsTer39	p.A295Gfs*39	ENST00000326873	NM_000455.4	295	GCCAAGAgg/gg	7/10	1	2	FACETS	0.842	0.757	0.93	1	0.988	1	CLONAL	3	FALSE	1	0.285365000210325	2		572	233	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595820	52595820	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	30	682	0	ENST00000394830.3:c.4095G>C	p.Trp1365Cys	p.W1365C	ENST00000394830	NM_018313.4	1365	tgG/tgC	26/30	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.285365000210325	2		682	143	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738421	133738421	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	16	367	0	ENST00000318560.5:c.821A>T	p.Lys274Met	p.K274M	ENST00000318560	NM_005157.4	274	aAg/aTg	4/11	1	2	FACETS	1	0.799	1	1	0.799	1	CLONAL	1	FALSE	1	0.285365000210325	2		367	104	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0036678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	208	644	0	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	0.4221858847588	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.4221858847588	1		644	667	SUCCESS
APC	324	MSKCC	GRCh37	5	112174742	112174742	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	69	304	0	ENST00000257430.4:c.3451G>T	p.Glu1151Ter	p.E1151*	ENST00000257430	NM_000038.5	1151	Gaa/Taa	16/16	1	2	FACETS	0.757	0.661	0.859	0.757	0.661	0.859	SUBCLONAL	1	TRUE	1	0.4221858847588	2		304	432	SUCCESS
APC	324	MSKCC	GRCh37	5	112175411	112175411	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	105	382	1	ENST00000257430.4:c.4120G>T	p.Glu1374Ter	p.E1374*	ENST00000257430	NM_000038.5	1374	Gaa/Taa	16/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.4221858847588	2		383	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578179	7578179	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	53	567	0	ENST00000269305.4:c.670G>T	p.Glu224Ter	p.E224*	ENST00000269305	NM_001126112.2	224	Gag/Tag	6/11	0.4221858847588	1	FACETS	0.294	0.25	0.343	0.294	0.25	0.343	SUBCLONAL	1	TRUE	0	0.4221858847588	1		567	673	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247168	153247168	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1560758208	NA	P-0036678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	96	320	0	ENST00000281708.4:c.1634A>G	p.Tyr545Cys	p.Y545C	ENST00000281708	NM_033632.3	545	tAt/tGt	10/12	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.4221858847588	2		320	387	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65348972	65348972	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs761628399	NA	P-0036678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	130	331	0	ENST00000342505.4:c.193G>T	p.Ala65Ser	p.A65S	ENST00000342505	NM_002227.2	65	Gca/Tca	3/25	0.4221858847588	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.4221858847588	1		331	359	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243362	46243362	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0036678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	99	266	0	ENST00000334344.6:c.1716-1G>T		p.X572_splice	ENST00000334344	NM_152641.2	572			0.323118304724057	3	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.4221858847588	3		266	393	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670394	88670394	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	102	394	0	ENST00000360948.2:c.1292G>A	p.Gly431Glu	p.G431E	ENST00000360948	NM_001012338.2	431	gGg/gAg	11/19	0.4221858847588	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.4221858847588	1		394	342	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140778	55140778	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139219072	NA	P-0036678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	107	587	0	ENST00000257290.5:c.1639G>T	p.Val547Phe	p.V547F	ENST00000257290	NM_006206.4	547	Gtc/Ttc	11/23	0.29280935027601	1	FACETS	0.597	0.536	0.661	0.597	0.536	0.661	SUBCLONAL	1	TRUE	0	0.4221858847588	1		587	670	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs985033810	NA	P-0036717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	324	580	0	ENST00000269305.4:c.731G>T	p.Gly244Val	p.G244V	ENST00000269305	NM_001126112.2	244	gGc/gTc	7/11	0.802022674074924	1	FACETS	0.891	0.854	0.929	0.891	0.854	0.929	CLONAL	1	TRUE	0	0.802022674074924	1		580	543	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870958	12870958	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	149	273	0	ENST00000228872.4:c.185T>C	p.Phe62Ser	p.F62S	ENST00000228872	NM_004064.3	62	tTc/tCc	1/3	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		273	317	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0036854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	271	678	0	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	0.380677555014966	2	FACETS	1	0.994	1	0.733	0.692	0.775	CLONAL	1	TRUE	0	0.524950247976074	2		678	704	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256435	16256435	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199763346	NA	P-0036854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	111	550	0	ENST00000375759.3:c.3700G>A	p.Asp1234Asn	p.D1234N	ENST00000375759	NM_015001.2	1234	Gat/Aat	11/15	0.383103549295658	3	FACETS	0.782	0.703	0.864	0.261	0.234	0.288	SUBCLONAL	1	TRUE	0	0.524950247976074	3		550	683	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414884	78414884	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	84	401	0	ENST00000370768.2:c.1882C>T	p.Gln628Ter	p.Q628*	ENST00000370768	NM_003902.3	628	Cag/Tag	19/20	0.524950247976074	3	FACETS	0.653	0.577	0.734	0.218	0.192	0.245	SUBCLONAL	1	TRUE	0	0.524950247976074	3		401	619	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566457	41566457	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	161	454	0	ENST00000263253.7:c.4334A>C	p.Asp1445Ala	p.D1445A	ENST00000263253	NM_001429.3	1445	gAt/gCt	27/31	0.368948303264018	4	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.524950247976074	4		454	662	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070577	67070578	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	145	234	0	ENST00000412916.2:c.207dup	p.Pro70SerfsTer13	p.P70Sfs*13	ENST00000412916		67	-/T	3/6	0.420897009437574	2	FACETS	0.771	0.71	0.834	0.771	0.71	0.834	SUBCLONAL	2	TRUE	0	0.430210626857869	2		234	437	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991933	72991933	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	44	682	0	ENST00000268489.5:c.2112C>A	p.Cys704Ter	p.C704*	ENST00000268489	NM_006885.3	704	tgC/tgA	2/10	0.420897009437574	2	FACETS	0.253	0.211	0.3	0.127	0.105	0.15	SUBCLONAL	1	TRUE	0	0.430210626857869	2		682	808	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442896	52443586	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGAGAAGAAAAGCTGGAACTGAGGGCCAAGGATGGGACAGGGTAGGAACACAAAGTAAGACAAGAACAAAAACTCTGATGAGGAACTGAGGCACTCCTTCTCACTTGTGGGCCCCAATGCAGTCAGGAAAGCAAATGAACACCCACACCAGTCTCTTTTGTTCCAGGAAATTAAAGTAGACTTCTTGGTTCAGTCACGGTTGCTACTGTTGCTACTCTCTTACACATCTATTCTGCAGGACCACTGGGAAAAGACTCTAAGTGTGGGCACCCAGGAGGGGCCTTGTCACCCCAACCAATCAATACAGGATGACTTTGTGTCAGGATTAAAGCCAAGGACACATGGGCACACTAAAATTAATACATTACACAACTGCACAAAAGACATTGTGTGACCGGGGTCTTCCCGCTGCAAGGCCAGGAAAGCAGCTGAACCAAAGGATGCTTAGGGGTGGGGAGGGGGCTGCTACAAAAAGGGAAGCGCTAAGGAAAGTTTGGGAGAAAAGAAAGTATCAGTTTGATCAGGAGCGGGCACTCAGAGAGCAAGGCTGCTGCTTTCTGTGAGATTTTACAACGTAGGGTTCCTGGCACTGTCTTCCCTAAGGGGCCCTGTTCTCTGGGACCTTCCCCAGCACTCTGGGTGTAAGGGGCAGCCCTGGTGTACAGCCACTCACCCCTGACATTTGCTCTG	AAGAGAAGAAAAGCTGGAACTGAGGGCCAAGGATGGGACAGGGTAGGAACACAAAGTAAGACAAGAACAAAAACTCTGATGAGGAACTGAGGCACTCCTTCTCACTTGTGGGCCCCAATGCAGTCAGGAAAGCAAATGAACACCCACACCAGTCTCTTTTGTTCCAGGAAATTAAAGTAGACTTCTTGGTTCAGTCACGGTTGCTACTGTTGCTACTCTCTTACACATCTATTCTGCAGGACCACTGGGAAAAGACTCTAAGTGTGGGCACCCAGGAGGGGCCTTGTCACCCCAACCAATCAATACAGGATGACTTTGTGTCAGGATTAAAGCCAAGGACACATGGGCACACTAAAATTAATACATTACACAACTGCACAAAAGACATTGTGTGACCGGGGTCTTCCCGCTGCAAGGCCAGGAAAGCAGCTGAACCAAAGGATGCTTAGGGGTGGGGAGGGGGCTGCTACAAAAAGGGAAGCGCTAAGGAAAGTTTGGGAGAAAAGAAAGTATCAGTTTGATCAGGAGCGGGCACTCAGAGAGCAAGGCTGCTGCTTTCTGTGAGATTTTACAACGTAGGGTTCCTGGCACTGTCTTCCCTAAGGGGCCCTGTTCTCTGGGACCTTCCCCAGCACTCTGGGTGTAAGGGGCAGCCCTGGTGTACAGCCACTCACCCCTGACATTTGCTCTG	-	novel	NA	P-0036900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	13	15	0	ENST00000460680.1:c.106_123-274del		p.X36_splice	ENST00000460680	NM_004656.3	36		3/17	0.430210626857869	3	FACETS	0.094	0.066	0.128	0.047	0.033	0.064	SUBCLONAL	1	TRUE	1	0.430210626857869	3		15	781	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0036919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	24	463	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	0.17	2		463	229	SUCCESS
AR	367	MSKCC	GRCh37	X	66765082	66765082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	19	323	0	ENST00000374690.3:c.94G>A	p.Glu32Lys	p.E32K	ENST00000374690	NM_000044.3	32	Gaa/Aaa	1/8	1	2	FACETS	1	0.81	1	1	0.81	1	CLONAL	1	TRUE	1	0.17	2		323	208	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575160	48575181	+	frameshift_variant	Frame_Shift_Del	DEL	GTTTGACTTAAAATGTGATAGT	GTTTGACTTAAAATGTGATAGT	-	novel	NA	P-0036919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	23	300	0	ENST00000342988.3:c.356_377del	p.Phe119SerfsTer3	p.F119Sfs*3	ENST00000342988	NM_005359.5	118	gcGTTTGACTTAAAATGTGATAGT/gc	3/12	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.17	NA		300	162	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446911	187446911	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	31	319	0	ENST00000232014.4:c.1282C>G	p.Pro428Ala	p.P428A	ENST00000232014	NM_001130845.1	428	Cca/Gca	5/10	1	2	FACETS	0.76	0.618	0.919	1	0.944	1	CLONAL	2	TRUE	1	0.17	2		319	240	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0036920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	382	574	0	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	0.56550888629637	2	FACETS	0.971	0.931	1	0.971	0.931	1	CLONAL	2	TRUE	0	0.56550888629637	2		574	696	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167577	NA	P-0036920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	166	360	0	ENST00000257430.4:c.4463del	p.Leu1488TyrfsTer19	p.L1488Yfs*19	ENST00000257430	NM_000038.5	1487	acT/ac	16/16	0.56550888629637	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.56550888629637	1		360	401	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554919	106554919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368754839	NA	P-0036920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	142	440	0	ENST00000369096.4:c.2036G>A	p.Arg679His	p.R679H	ENST00000369096	NM_001198.3	679	cGt/cAt	7/7	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.56550888629637	2		440	488	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44921958	44921958	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	29	246	0	ENST00000377967.4:c.1492C>A	p.Leu498Met	p.L498M	ENST00000377967	NM_021140.2	498	Ctg/Atg	15/29	0.527071440367548	2	FACETS	0.259	0.207	0.318			1	SUBCLONAL	1	TRUE	NA	0.56550888629637	2		246	396	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014224	14014224	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	33	285	0	ENST00000311895.7:c.202G>A	p.Glu68Lys	p.E68K	ENST00000311895	NM_005236.2	68	Gag/Aag	1/11	1	2	FACETS	0.589	0.489	0.697	0.589	0.489	0.697	SUBCLONAL	1	TRUE	1	0.896277140705594	2		285	125	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0038012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	255	560	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.937	0.88	0.995	1	0.995	1	CLONAL	2	TRUE	1	0.340924368647476	2		560	798	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443499	49443499	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369794887	NA	P-0038012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	106	441	1	ENST00000301067.7:c.3872G>A	p.Arg1291Gln	p.R1291Q	ENST00000301067	NM_003482.3	1291	cGg/cAg	11/54	1	2	FACETS	0.949	0.852	1	0.949	0.852	1	CLONAL	1	TRUE	1	0.340924368647476	2		442	655	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647122	23647123	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	98	674	0	ENST00000261584.4:c.744dup	p.Pro249SerfsTer8	p.P249Sfs*8	ENST00000261584	NM_024675.3	248	-/T	4/13	0.320625740710972	3	FACETS	0.916	0.817	1	0.458	0.408	0.511	CLONAL	1	TRUE	1	0.340924368647476	3		674	735	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513242	41513242	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs370385350	NA	P-0038012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	79	403	0	ENST00000263253.7:c.146A>G	p.Asn49Ser	p.N49S	ENST00000263253	NM_001429.3	49	aAc/aGc	2/31	1	2	FACETS	0.958	0.845	1	0.958	0.845	1	CLONAL	1	TRUE	1	0.340924368647476	2		403	484	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	28	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.837	0.668	1	0.837	0.668	1	CLONAL	1	TRUE	1	0.14	2		473	478	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832394	72832394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774988278	NA	P-0038083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	55	533	0	ENST00000268489.5:c.4187G>A	p.Arg1396His	p.R1396H	ENST00000268489	NM_006885.3	1396	cGc/cAc	9/10	1	2	FACETS	0.942	0.804	1	0.942	0.804	1	CLONAL	1	TRUE	1	0.14	2		533	834	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044955	47044955	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1450	127	1070	0	ENST00000377604.3:c.2281T>C	p.Cys761Arg	p.C761R	ENST00000377604	NM_001204468.1	761	Tgt/Cgt	20/24	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.14	2		1070	1577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0038093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	236	596	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.716710080243773	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.716710080243773	1		596	411	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027020	71027020	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	165	422	0	ENST00000318789.4:c.1307G>A	p.Arg436His	p.R436H	ENST00000318789	NM_032682.5	436	cGc/cAc	15/21	NA	2	FACETS	1	0.939	1			1	INDETERMINATE	1	TRUE	NA	0.716710080243773	2		422	454	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0038093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	217	557	0	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	0.716710080243773	1	FACETS	0.843	0.793	0.892	0.843	0.793	0.892	CLONAL	1	TRUE	0	0.716710080243773	1		557	461	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438572	52438572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201844078	NA	P-0038093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	162	425	0	ENST00000460680.1:c.1147C>T	p.Arg383Cys	p.R383C	ENST00000460680	NM_004656.3	383	Cgc/Tgc	12/17	0.667236086476262	3	FACETS	1	0.978	1	0.579	0.535	0.625	CLONAL	1	TRUE	1	0.716710080243773	3		425	530	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942208	17942208	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	77	374	0	ENST00000458235.1:c.2807G>C	p.Gly936Ala	p.G936A	ENST00000458235	NM_000215.3	936	gGc/gCc	21/24	1	2	FACETS	0.87	0.775	0.969	0.87	0.775	0.969	CLONAL	1	TRUE	1	0.716710080243773	2		374	247	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0038167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	119	498	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.545157083226451	3	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	1	0.544821635864904	3		498	269	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0038167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	265	883	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.128728410325607	3	FACETS	1	0.987	1			1	INDETERMINATE	2	TRUE	NA	0.544821635864904	3		883	550	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795352	39795352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372598575	NA	P-0038167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	88	602	1	ENST00000288319.7:c.368G>A	p.Arg123His	p.R123H	ENST00000288319	NM_182918.3	123	cGc/cAc	3/10	0.545157083226451	3	FACETS	0.75	0.666	0.839	0.375	0.333	0.42	SUBCLONAL	1	TRUE	1	0.544821635864904	3		603	548	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156836728	156836728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	103	740	0	ENST00000524377.1:c.386C>T	p.Ser129Phe	p.S129F	ENST00000524377	NM_002529.3	129	tCt/tTt	4/17	0.26461816178402	5	FACETS	0.819	0.732	0.911	0.273	0.244	0.304	INDETERMINATE	1	TRUE	2	0.544821635864904	5		740	839	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136238	202136244	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GGGTCAT	GGGTCAT	-	novel	NA	P-0038167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	61	362	0	ENST00000358485.4:c.483_489del		p.X161_splice	ENST00000358485	NM_001080125.1	161		3/9	0.498153058437517	3	FACETS	0.828	0.719	0.946	0.414	0.359	0.473	CLONAL	1	TRUE	1	0.544821635864904	3		362	344	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0038190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	368	408	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	0.595344088425718	1		408	640	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061334	38061334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	334	696	0	ENST00000250448.2:c.655C>A	p.Arg219Ser	p.R219S	ENST00000250448	NM_004496.3	219	Cgc/Agc	2/2	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.595344088425718	2		696	1111	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99185041	99185041	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536365553	NA	P-0038190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	146	540	0	ENST00000074304.5:c.2443G>A	p.Asp815Asn	p.D815N	ENST00000074304	NM_001134224.1	815	Gat/Aat	23/26	0.199797721604896	0	FACETS	0.341	0.312	0.371			1	INDETERMINATE	1	TRUE	0	0.595344088425718	0		540	582	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852565	63852565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	233	629	0	ENST00000279873.7:c.3343C>T	p.Leu1115Phe	p.L1115F	ENST00000279873	NM_032199.2	1115	Ctc/Ttc	10/10	1	2	FACETS	0.888	0.83	0.949	0.888	0.83	0.949	CLONAL	1	TRUE	1	0.595344088425718	2		629	881	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508661	38508661	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	295	884	0	ENST00000254066.5:c.709A>G	p.Ile237Val	p.I237V	ENST00000254066	NM_000964.3	237	Att/Gtt	6/9	1	2	FACETS	0.869	0.817	0.921	0.869	0.817	0.921	CLONAL	1	TRUE	1	0.595344088425718	2		884	1141	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435814	56435832	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGGGCCTGGCCCGGCGT	AGGGGGCCTGGCCCGGCGT	-	novel	NA	P-0038190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	224	680	0	ENST00000407977.2:c.1305_1323del	p.Arg436ThrfsTer60	p.R436Tfs*60	ENST00000407977		435	ctACGCCGGGCCAGGCCCCCT/ct	9/10	0.595344088425718	1	FACETS	0.937	0.88	0.995	0.937	0.88	0.995	CLONAL	1	TRUE	0	0.595344088425718	1		680	564	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987254	2987254	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	372	684	0	ENST00000396946.4:c.175G>C	p.Glu59Gln	p.E59Q	ENST00000396946	NM_032415.4	59	Gaa/Caa	3/25	0.595344088425718	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.595344088425718	1		684	701	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056053	26056067	+	inframe_deletion	In_Frame_Del	DEL	CCTTGGGCTTAGCGG	CCTTGGGCTTAGCGG	-	rs756916945	NA	P-0038433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	118	497	0	ENST00000343677.2:c.590_604del	p.Ala197_Lys201del	p.A197_K201del	ENST00000343677	NM_005319.3	197	gCCGCTAAGCCCAAGGtt/gtt	1/1	0.143409015172499	4	FACETS	1	0.92	1	1	0.986	1	INDETERMINATE	3	TRUE	2	0.246829386971846	4		497	393	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964923	25964923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	150	594	0	ENST00000435504.4:c.4283G>A	p.Cys1428Tyr	p.C1428Y	ENST00000435504		1428	tGc/tAc	13/13	0.246829907949978	0	FACETS	0.776	0.718	0.836			1	SUBCLONAL	3	TRUE	0	0.246829386971846	0		594	393	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0038486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	162	595	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.987	0.915	1	0.987	0.915	1	CLONAL	1	TRUE	1	0.73074449078446	2		595	449	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0038486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	129	207	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.73074449078446	2		207	343	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149334	119149334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	32	522	0	ENST00000264033.4:c.1342G>A	p.Glu448Lys	p.E448K	ENST00000264033	NM_005188.3	448	Gag/Aag	9/16	1	2	FACETS	0.145	0.117	0.177	0.145	0.117	0.177	SUBCLONAL	1	TRUE	1	0.73074449078446	2		522	602	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796558	42796558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	221	793	0	ENST00000575354.2:c.3115del	p.Ala1039LeufsTer2	p.A1039Lfs*2	ENST00000575354	NM_015125.3	1039	Gct/ct	13/20	0.73074449078446	1	FACETS	0.791	0.745	0.838	0.791	0.745	0.838	SUBCLONAL	1	TRUE	0	0.73074449078446	1		793	485	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799014	42799015	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0038486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	80	889	0	ENST00000575354.2:c.4498_4499del	p.Ile1500LeufsTer13	p.I1500Lfs*13	ENST00000575354	NM_015125.3	1500	ATc/c	20/20	0.73074449078446	1	FACETS	0.231	0.203	0.261	0.231	0.203	0.261	SUBCLONAL	1	TRUE	0	0.73074449078446	1		889	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0038501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	125	634	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.228312198661325	5	FACETS	0.86	0.778	0.946	0.573	0.518	0.631	CLONAL	2	TRUE	2	0.228312198661325	5		635	855	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579408	7579430	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGGGCCAGGAGGGGGCTGGTG	CAGGGGCCAGGAGGGGGCTGGTG	-	rs886041861	NA	P-0038501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	128	682	0	ENST00000269305.4:c.257_279del	p.Ala86ValfsTer55	p.A86Vfs*55	ENST00000269305	NM_001126112.2	86	gCACCAGCCCCCTCCTGGCCCCTG/g	4/11	0.228312198661325	5	FACETS	0.943	0.855	1	0.629	0.57	0.691	CLONAL	2	TRUE	2	0.228312198661325	5		682	798	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502287	157502287	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	69	530	0	ENST00000346085.5:c.3320T>G	p.Val1107Gly	p.V1107G	ENST00000346085	NM_020732.3	1107	gTc/gGc	12/20	0.0759612466623472	4	FACETS	1	0.941	1	0.571	0.497	0.651	INDETERMINATE	1	TRUE	2	0.228312198661325	4		530	650	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	134	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.484575265936448	3	FACETS	0.87	0.798	0.943	0.87	0.798	0.943	CLONAL	2	TRUE	1	0.484575265936448	3		473	395	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955383	48955383	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	27	231	0	ENST00000267163.4:c.1499G>A	p.Arg500Lys	p.R500K	ENST00000267163	NM_000321.2	500	aGa/aAa	17/27	1	2	FACETS	0.995	0.807	1	0.995	0.807	1	CLONAL	1	TRUE	1	0.484575265936448	2		231	112	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016359	150016359	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0038539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	76	381	0	ENST00000253339.5:c.349-2A>C		p.X117_splice	ENST00000253339		117			0.484575265936448	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.484575265936448	1		381	212	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455151	50455151	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446212014	NA	P-0038539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	27	413	1	ENST00000331340.3:c.698C>T	p.Pro233Leu	p.P233L	ENST00000331340	NM_006060.4	233	cCg/cTg	6/8	0.427737108423304	1	FACETS	0.343	0.274	0.422	0.343	0.274	0.422	SUBCLONAL	1	TRUE	0	0.484575265936448	1		414	246	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135804175	135804175	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	114	482	0	ENST00000298552.3:c.85T>G	p.Phe29Val	p.F29V	ENST00000298552	NM_001162426.1	29	Ttt/Gtt	3/23	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.484575265936448	2		482	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0038540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	272	868	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.650194087113011	1	FACETS	0.915	0.866	0.965	0.915	0.866	0.965	CLONAL	1	TRUE	0	0.650194087113011	1		868	617	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0038540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	122	632	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.59	0.534	0.648	0.59	0.534	0.648	SUBCLONAL	1	TRUE	1	0.650194087113011	2		632	636	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941459	71941459	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	77	842	0	ENST00000298229.2:c.1144G>C	p.Glu382Gln	p.E382Q	ENST00000298229	NM_001567.3	382	Gag/Cag	10/28	1	2	FACETS	0.285	0.249	0.323	0.285	0.249	0.323	SUBCLONAL	1	TRUE	1	0.650194087113011	2		842	832	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436300	110436300	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	31	206	1	ENST00000375856.3:c.2101G>T	p.Ala701Ser	p.A701S	ENST00000375856	NM_003749.2	701	Gcc/Tcc	1/2	0.476834329030912	1	FACETS	0.325	0.265	0.392	0.325	0.265	0.392	SUBCLONAL	1	TRUE	0	0.650194087113011	1		207	198	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974781	15974781	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	137	394	0	ENST00000268712.3:c.4094G>T	p.Arg1365Leu	p.R1365L	ENST00000268712	NM_006311.3	1365	cGg/cTg	30/46	0.492251835028677	1	FACETS	0.672	0.617	0.729	0.672	0.617	0.729	SUBCLONAL	1	TRUE	0	0.650194087113011	1		394	423	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589571	67589603	+	inframe_deletion	In_Frame_Del	DEL	TAGGGAAAAAATTACATGAATATAACACTCAGT	TAGGGAAAAAATTACATGAATATAACACTCAGT	-	novel	NA	P-0038540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	83	197	0	ENST00000274335.5:c.1335_1367del	p.Gly446_Phe456del	p.G446_F456del	ENST00000274335		445	gTAGGGAAAAAATTACATGAATATAACACTCAGTtt/gtt	10/15	0.595760293317741	1	FACETS	0.794	0.714	0.876	0.794	0.714	0.876	SUBCLONAL	1	TRUE	0	0.650194087113011	1		197	217	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965587	93965587	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1327105282	NA	P-0038540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	138	398	0	ENST00000369303.4:c.2341C>T	p.Arg781Ter	p.R781*	ENST00000369303	NM_004440.3	781	Cga/Tga	13/17	1	2	FACETS	0.935	0.858	1	0.935	0.858	1	CLONAL	1	TRUE	1	0.650194087113011	2		398	454	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	55	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.979	0.847	1	0.979	0.847	1	CLONAL	1	TRUE	1	0.48	2		473	234	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0038557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	31	264	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.691	0.564	0.831	0.691	0.564	0.831	SUBCLONAL	1	TRUE	1	0.48	2		264	187	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0038557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	53	710	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.48	2		710	213	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971099	+	missense_variant	Missense_Mutation	ONP	CCCG	CCCG	TCCA	novel	NA	P-0038557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	27	458	0	ENST00000304494.5:c.259_262delinsTGGA	p.Arg87_Glu88delinsTrpLys	p.R87_E88delinsWK	ENST00000304494	NM_000077.4	87	CGGGag/TGGAag	2/3	1	2	FACETS	0.852	0.688	1	0.852	0.688	1	CLONAL	1	TRUE	1	0.48	2		458	132	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519886	NA	P-0038585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	17	331	0	ENST00000349496.5:c.97T>C	p.Ser33Pro	p.S33P	ENST00000349496	NM_001904.3	33	Tct/Cct	3/15	1	2	FACETS	0.154	0.114	0.201	0.154	0.114	0.201	SUBCLONAL	1	TRUE	1	0.521617731941476	2		331	424	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0038585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	65	409	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.595	0.517	0.678	0.595	0.517	0.678	SUBCLONAL	1	TRUE	1	0.521617731941476	2		409	419	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938400	44938400	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	54	151	0	ENST00000377967.4:c.2951del	p.Phe984SerfsTer15	p.F984Sfs*15	ENST00000377967	NM_021140.2	983	cTt/ct	20/29	1	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.521617731941476	1		151	139	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349257	70349258	+	missense_variant	Missense_Mutation	DNP	TC	TC	GT	novel	NA	P-0038585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	55	325	0	ENST00000374080.3:c.3669_3670delinsGT	p.Leu1224Phe	p.L1224F	ENST00000374080		1223	gtTCtc/gtGTtc	26/45	1	1	FACETS	0.333	0.285	0.385	0.333	0.285	0.385	SUBCLONAL	1	TRUE	0	0.521617731941476	1		325	468	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0038664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	86	425	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.689	0.609	0.775	0.689	0.609	0.775	SUBCLONAL	1	FALSE	1	0.3	2		426	832	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857311	68857312	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	60	396	0	ENST00000261769.5:c.1947dup	p.Ile650TyrfsTer13	p.I650Yfs*13	ENST00000261769	NM_004360.3	649	tct/tcTt	13/16	0.211371838272721	1	FACETS	0.538	0.463	0.62	0.538	0.463	0.62	SUBCLONAL	1	FALSE	0	0.3	1		396	632	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333432	70333432	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	68	745	0	ENST00000373644.4:c.1337C>T	p.Pro446Leu	p.P446L	ENST00000373644	NM_030625.2	446	cCt/cTt	2/12	1	2	FACETS	0.416	0.36	0.476	0.416	0.36	0.476	SUBCLONAL	1	FALSE	1	0.3	2		745	1090	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0038689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	41	425	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.17	2		426	400	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577507	7577507	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	36	439	1	ENST00000269305.4:c.774A>C	p.Glu258Asp	p.E258D	ENST00000269305	NM_001126112.2	258	gaA/gaC	7/11	1	2	FACETS	0.521	0.427	0.628	0.521	0.427	0.628	SUBCLONAL	1	TRUE	1	0.17	2		440	813	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845839	72845839	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	39	417	0	ENST00000268489.5:c.3628C>T	p.Arg1210Ter	p.R1210*	ENST00000268489	NM_006885.3	1210	Cga/Tga	6/10	1	2	FACETS	0.611	0.505	0.73	0.611	0.505	0.73	SUBCLONAL	1	TRUE	1	0.17	2		417	751	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026678	48026678	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1285168531	NA	P-0038689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	26	312	0	ENST00000234420.5:c.1556A>G	p.Lys519Arg	p.K519R	ENST00000234420	NM_000179.2	519	aAg/aGg	4/10	1	2	FACETS	0.615	0.486	0.764	0.615	0.486	0.764	SUBCLONAL	1	TRUE	1	0.17	2		312	497	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	70	653	0	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	1	2	FACETS	0.87	0.759	0.99	0.87	0.759	0.99	CLONAL	1	TRUE	1	0.26	2		653	619	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120000	70120001	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	20	151	0	ENST00000245479.2:c.1003dup	p.Trp335LeufsTer243	p.W335Lfs*243	ENST00000245479	NM_000346.3	334	-/T	3/3	1	2	FACETS	1	0.817	1	1	0.817	1	CLONAL	1	TRUE	1	0.26	2		151	144	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0038719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	59	494	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	0.26	2		494	423	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980384	201980385	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0038719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	90	772	0	ENST00000359651.3:c.121_122dup	p.Leu42TyrfsTer2	p.L42Yfs*2	ENST00000359651		40	-/GT	1/8	1	2	FACETS	0.832	0.737	0.933	0.832	0.737	0.933	CLONAL	1	TRUE	1	0.26	2		772	832	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532586	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0038719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	79	853	0	ENST00000307078.5:c.1993_1994del	p.Gly665GlnfsTer41	p.G665Qfs*41	ENST00000307078	NM_004655.3	665	GGc/c	8/11	1	2	FACETS	0.877	0.771	0.991	0.877	0.771	0.991	CLONAL	1	TRUE	1	0.26	2		853	693	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120225	70120226	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0038719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	59	667	0	ENST00000245479.2:c.1228dup	p.Gln410ProfsTer168	p.Q410Pfs*168	ENST00000245479	NM_000346.3	409	-/C	3/3	1	2	FACETS	0.806	0.694	0.929	0.806	0.694	0.929	CLONAL	1	TRUE	1	0.26	2		667	563	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792076	42792076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	90	694	1	ENST00000575354.2:c.880G>A	p.Glu294Lys	p.E294K	ENST00000575354	NM_015125.3	294	Gag/Aag	6/20	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.26	2		695	641	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372125	55372125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	59	371	0	ENST00000297316.4:c.815C>T	p.Pro272Leu	p.P272L	ENST00000297316	NM_022454.3	272	cCc/cTc	2/2	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.26	2		371	388	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	74	894	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.78	0.683	0.885	0.78	0.683	0.885	SUBCLONAL	1	TRUE	1	0.29	2		894	654	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115600	108115600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772821016	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	29	522	0	ENST00000278616.4:c.748C>T	p.Arg250Ter	p.R250*	ENST00000278616	NM_000051.3	250	Cga/Tga	7/63	1	2	FACETS	0.405	0.324	0.497	0.405	0.324	0.497	SUBCLONAL	1	TRUE	1	0.29	2		522	494	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	66	561	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.996	0.867	1	0.996	0.867	1	CLONAL	1	TRUE	1	0.29	2		561	457	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	37	458	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	1	2	FACETS	0.624	0.515	0.746	0.624	0.515	0.746	SUBCLONAL	1	TRUE	1	0.29	2		458	409	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208036	5208036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772956659	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	27	649	0	ENST00000357368.4:c.5675C>T	p.Thr1892Met	p.T1892M	ENST00000357368	NM_002850.3	1892	aCg/aTg	37/38	1	2	FACETS	0.375	0.297	0.463	0.375	0.297	0.463	SUBCLONAL	1	TRUE	1	0.29	2		649	497	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	14	498	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.225	0.161	0.302	0.225	0.161	0.302	SUBCLONAL	1	TRUE	1	0.29	2		498	430	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	40	523	1	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	1	2	FACETS	0.614	0.511	0.73	0.614	0.511	0.73	SUBCLONAL	1	TRUE	1	0.29	2		524	449	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	83	613	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.29	2		613	568	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095836	178095836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1328262363	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	79	555	0	ENST00000397062.3:c.1495C>T	p.Arg499Trp	p.R499W	ENST00000397062	NM_006164.4	499	Cgg/Tgg	5/5	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.29	2		555	536	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217381	123217381	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	65	463	0	ENST00000218089.9:c.3035G>A	p.Arg1012Gln	p.R1012Q	ENST00000218089	NM_001042749.1	1012	cGa/cAa	29/35	1	2	FACETS	0.948	0.824	1	0.948	0.824	1	CLONAL	1	TRUE	1	0.29	2		463	473	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216568	108216568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs767845728	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	54	352	0	ENST00000278616.4:c.8517C>A	p.Phe2839Leu	p.F2839L	ENST00000278616	NM_000051.3	2839	ttC/ttA	58/63	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.29	2		352	368	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952049	178952049	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1242945375	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	36	470	0	ENST00000263967.3:c.3104C>T	p.Ala1035Val	p.A1035V	ENST00000263967	NM_006218.2	1035	gCt/gTt	21/21	1	2	FACETS	0.577	0.475	0.693	0.577	0.475	0.693	SUBCLONAL	1	TRUE	1	0.29	2		470	430	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098800	178098800	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	110	656	0	ENST00000397062.3:c.245A>G	p.Glu82Gly	p.E82G	ENST00000397062	NM_006164.4	82	gAa/gGa	2/5	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.29	2		656	724	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220477	123220477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1372684971	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	68	681	0	ENST00000218089.9:c.3134G>A	p.Arg1045Gln	p.R1045Q	ENST00000218089	NM_001042749.1	1045	cGa/cAa	30/35	1	2	FACETS	0.79	0.687	0.9	0.79	0.687	0.9	SUBCLONAL	1	TRUE	1	0.29	2		681	594	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	69	508	0	ENST00000320574.5:c.1231G>C	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ctg	13/49	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.29	2		508	400	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796804	135796804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223799508	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	54	386	0	ENST00000298552.3:c.683G>A	p.Arg228Gln	p.R228Q	ENST00000298552	NM_001162426.1	228	cGa/cAa	8/23	1	2	FACETS	0.911	0.78	1	0.911	0.78	1	CLONAL	1	TRUE	1	0.29	2		386	409	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92404108	92404108	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	26	484	0	ENST00000265734.4:c.271G>T	p.Glu91Ter	p.E91*	ENST00000265734	NM_001259.6	91	Gaa/Taa	3/8	1	2	FACETS	0.386	0.305	0.48	0.386	0.305	0.48	SUBCLONAL	1	TRUE	1	0.29	2		484	464	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692918	89692918	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1114167676	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	62	637	0	ENST00000371953.3:c.402G>T	p.Met134Ile	p.M134I	ENST00000371953	NM_000314.4	134	atG/atT	5/9	1	2	FACETS	0.799	0.691	0.917	0.799	0.691	0.917	CLONAL	1	TRUE	1	0.29	2		637	535	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	20	238	0	ENST00000256196.4:c.68G>A	p.Gly23Asp	p.G23D	ENST00000256196		23	gGc/gAc	1/6	1	2	FACETS	0.722	0.555	0.916	0.722	0.555	0.916	CLONAL	1	TRUE	1	0.29	2		238	191	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938788	76938788	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	81	738	0	ENST00000373344.5:c.1960C>T	p.Arg654Ter	p.R654*	ENST00000373344	NM_000489.3	654	Cga/Tga	9/35	1	2	FACETS	0.947	0.835	1	0.947	0.835	1	CLONAL	1	TRUE	1	0.29	2		738	590	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845580	151845580	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1287135873	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	73	651	1	ENST00000262189.6:c.13432C>T	p.Arg4478Ter	p.R4478*	ENST00000262189	NM_170606.2	4478	Cga/Tga	52/59	1	2	FACETS	0.815	0.713	0.924	0.815	0.713	0.924	CLONAL	1	TRUE	1	0.29	2		652	618	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984079	2984079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	27	537	1	ENST00000396946.4:c.451G>A	p.Glu151Lys	p.E151K	ENST00000396946	NM_032415.4	151	Gag/Aag	5/25	1	2	FACETS	0.41	0.326	0.507	0.41	0.326	0.507	SUBCLONAL	1	TRUE	1	0.29	2		538	454	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851828	63851828	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs201944744	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	103	742	0	ENST00000279873.7:c.2606C>A	p.Ser869Tyr	p.S869Y	ENST00000279873	NM_032199.2	869	tCt/tAt	10/10	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.29	2		742	678	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416600	49416600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	86	616	1	ENST00000301067.7:c.16111G>A	p.Glu5371Lys	p.E5371K	ENST00000301067	NM_003482.3	5371	Gag/Aag	51/54	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.29	2		617	545	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467884	66467884	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	29	393	0	ENST00000273854.3:c.385G>T	p.Glu129Ter	p.E129*	ENST00000273854	NM_004439.5	129	Gaa/Taa	3/18	1	2	FACETS	0.513	0.411	0.628	0.513	0.411	0.628	SUBCLONAL	1	TRUE	1	0.29	2		393	390	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981276	201981276	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	93	744	0	ENST00000359651.3:c.355G>A	p.Asp119Asn	p.D119N	ENST00000359651		119	Gac/Aac	2/8	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.29	2		744	608	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948386	71948386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760694548	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	105	837	1	ENST00000298229.2:c.3098G>A	p.Arg1033His	p.R1033H	ENST00000298229	NM_001567.3	1033	cGt/cAt	26/28	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.29	2		838	684	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383295	4383295	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	32	626	0	ENST00000261254.3:c.89T>G	p.Leu30Arg	p.L30R	ENST00000261254	NM_001759.3	30	cTg/cGg	1/5	1	2	FACETS	0.482	0.391	0.585	0.482	0.391	0.585	SUBCLONAL	1	TRUE	1	0.29	2		626	458	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95599673	95599673	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	61	430	0	ENST00000393063.1:c.123T>G	p.Ile41Met	p.I41M	ENST00000393063	NM_030621.3	41	atT/atG	3/28	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.29	2		430	419	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784494	43784494	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	43	608	0	ENST00000382044.4:c.180A>C	p.Glu60Asp	p.E60D	ENST00000382044	NM_001141980.1	60	gaA/gaC	2/28	1	2	FACETS	0.437	0.365	0.518	0.437	0.365	0.518	SUBCLONAL	1	TRUE	1	0.29	2		608	678	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303949	91303949	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	73	566	2	ENST00000355112.3:c.1346C>A	p.Ser449Tyr	p.S449Y	ENST00000355112	NM_000057.2	449	tCt/tAt	7/22	1	2	FACETS	0.948	0.831	1	0.948	0.831	1	CLONAL	1	TRUE	1	0.29	2		568	531	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655351	67655351	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	40	452	0	ENST00000264010.4:c.1214A>C	p.Lys405Thr	p.K405T	ENST00000264010	NM_006565.3	405	aAg/aCg	7/12	1	2	FACETS	0.634	0.527	0.753	0.634	0.527	0.753	SUBCLONAL	1	TRUE	1	0.29	2		452	435	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221055	5221055	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	83	624	2	ENST00000357368.4:c.3411C>A	p.Phe1137Leu	p.F1137L	ENST00000357368	NM_002850.3	1137	ttC/ttA	20/38	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.29	2		626	548	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122923	7122923	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	34	763	0	ENST00000302850.5:c.3336G>T	p.Lys1112Asn	p.K1112N	ENST00000302850	NM_000208.2	1112	aaG/aaT	18/22	1	2	FACETS	0.442	0.36	0.534	0.442	0.36	0.534	SUBCLONAL	1	TRUE	1	0.29	2		763	531	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229440	36229440	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	59	541	0	ENST00000222270.7:c.8130C>A	p.Cys2710Ter	p.C2710*	ENST00000222270	NM_014727.1	2710	tgC/tgA	37/37	1	2	FACETS	0.976	0.842	1	0.976	0.842	1	CLONAL	1	TRUE	1	0.29	2		541	417	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281904	39281904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886041241	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	65	518	0	ENST00000402219.2:c.571G>A	p.Glu191Lys	p.E191K	ENST00000402219	NM_005633.3	191	Gaa/Aaa	5/23	1	2	FACETS	0.919	0.798	1	0.919	0.798	1	CLONAL	1	TRUE	1	0.29	2		518	488	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128028923	128028923	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1366074068	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	105	534	0	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	0.29	2		534	627	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468369	89468369	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	24	274	0	ENST00000336596.2:c.1903G>A	p.Val635Met	p.V635M	ENST00000336596	NM_005233.5	635	Gtg/Atg	11/17	1	2	FACETS	0.667	0.525	0.831	0.667	0.525	0.831	SUBCLONAL	1	TRUE	1	0.29	2		274	248	SUCCESS
ATR	545	MSKCC	GRCh37	3	142259857	142259857	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	58	516	0	ENST00000350721.4:c.3470C>A	p.Ser1157Tyr	p.S1157Y	ENST00000350721	NM_001184.3	1157	tCt/tAt	18/47	1	2	FACETS	0.966	0.833	1	0.966	0.833	1	CLONAL	1	TRUE	1	0.29	2		516	414	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393303	393303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	58	513	1	ENST00000380956.4:c.151C>T	p.Arg51Cys	p.R51C	ENST00000380956	NM_001195286.1	51	Cgc/Tgc	2/9	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.29	2		514	350	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647473	117647473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	52	534	0	ENST00000368508.3:c.5471G>A	p.Gly1824Glu	p.G1824E	ENST00000368508	NM_002944.2	1824	gGa/gAa	33/43	1	2	FACETS	0.793	0.676	0.921	0.793	0.676	0.921	CLONAL	1	TRUE	1	0.29	2		534	452	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845246	151845246	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	24	498	0	ENST00000262189.6:c.13766C>T	p.Thr4589Ile	p.T4589I	ENST00000262189	NM_170606.2	4589	aCt/aTt	52/59	1	2	FACETS	0.364	0.284	0.456	0.364	0.284	0.456	SUBCLONAL	1	TRUE	1	0.29	2		498	455	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325658	87325658	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	48	572	0	ENST00000277120.3:c.535G>T	p.Glu179Ter	p.E179*	ENST00000277120		179	Gaa/Taa	6/19	1	2	FACETS	0.683	0.577	0.798	0.683	0.577	0.798	SUBCLONAL	1	TRUE	1	0.29	2		572	485	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772939	135772939	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	50	508	0	ENST00000298552.3:c.2684T>C	p.Val895Ala	p.V895A	ENST00000298552	NM_001162426.1	895	gTt/gCt	21/23	1	2	FACETS	0.737	0.626	0.859	0.737	0.626	0.859	SUBCLONAL	1	TRUE	1	0.29	2		508	468	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15827422	15827422	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	26	543	0	ENST00000307771.7:c.538G>T	p.Ala180Ser	p.A180S	ENST00000307771	NM_005089.3	180	Gct/Tct	7/11	1	2	FACETS	0.401	0.317	0.498	0.401	0.317	0.498	SUBCLONAL	1	TRUE	1	0.29	2		543	447	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652221	48652221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501251	NA	P-0038755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	72	626	0	ENST00000376670.3:c.892C>T	p.Arg298Trp	p.R298W	ENST00000376670	NM_002049.3	298	Cgg/Tgg	6/6	1	2	FACETS	0.933	0.817	1	0.933	0.817	1	CLONAL	1	TRUE	1	0.29	2		626	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0038760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	256	821	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.282095865841548	2	FACETS	0.882	0.826	0.939	0.882	0.826	0.939	CLONAL	2	TRUE	0	0.282095865841548	2		823	1029	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14303242	14303242	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	59	619	0	ENST00000256196.4:c.433T>G	p.Leu145Val	p.L145V	ENST00000256196		145	Tta/Gta	5/6	0.235761267551458	2	FACETS	0.731	0.629	0.842	0.366	0.314	0.421	SUBCLONAL	1	TRUE	0	0.282095865841548	2		619	572	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141470	11141475	+	inframe_deletion	In_Frame_Del	DEL	CTTCAT	CTTCAT	-	novel	NA	P-0038760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	73	616	0	ENST00000358026.2:c.3451_3456del	p.Ile1151_Phe1152del	p.I1151_F1152del	ENST00000358026	NM_001128849.1	1149	taCTTCATc/tac	25/36	1	2	FACETS	0.59	0.515	0.672	0.59	0.515	0.672	SUBCLONAL	1	TRUE	1	0.282095865841548	2		616	877	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524879	187524879	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs545491861	NA	P-0038760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	211	611	0	ENST00000441802.2:c.10801G>T	p.Ala3601Ser	p.A3601S	ENST00000441802	NM_005245.3	3601	Gca/Tca	19/27	0.282095865841548	5	FACETS	0.874	0.81	0.94	0.583	0.54	0.627	CLONAL	2	TRUE	2	0.282095865841548	5		611	1218	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405249	139405269	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTCTGCCCTGCGGGGCAGG	AGGTCTGCCCTGCGGGGCAGG	-	novel	NA	P-0038760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	57	516	0	ENST00000277541.6:c.2588-12_2596del		p.X863_splice	ENST00000277541	NM_017617.3	863		17/34	1	2	FACETS	0.435	0.372	0.505	0.435	0.372	0.505	SUBCLONAL	1	TRUE	1	0.282095865841548	2		516	928	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0038813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	49	423	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.772	0.655	0.899	0.772	0.655	0.899	SUBCLONAL	1	TRUE	1	0.319058581749792	2		423	398	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520155	9520155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	56	365	0	ENST00000353224.5:c.2114C>A	p.Pro705Gln	p.P705Q	ENST00000353224	NM_177990.2	705	cCa/cAa	10/10	1	2	FACETS	0.82	0.704	0.946	0.82	0.704	0.946	CLONAL	1	TRUE	1	0.319058581749792	2		365	428	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222061	2222061	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	142	694	0	ENST00000398665.3:c.2893T>A	p.Leu965Met	p.L965M	ENST00000398665	NM_032482.2	965	Ttg/Atg	24/28	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.319058581749792	2		694	808	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953635	38953635	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0038813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	30	123	0	ENST00000357387.3:c.2718T>A	p.Cys906Ter	p.C906*	ENST00000357387	NM_152756.3	906	tgT/tgA	28/38	1	2	FACETS	0.867	0.703	1	0.867	0.703	1	CLONAL	1	TRUE	1	0.319058581749792	2		123	217	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0038967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	43	595	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.897	0.749	1	0.897	0.749	1	CLONAL	1	TRUE	1	0.15	2		595	639	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0038967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	91	729	2	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	0.15	2		731	1064	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755326	39755326	+	stop_lost	Nonstop_Mutation	SNP	T	T	A	novel	NA	P-0038967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	38	426	0	ENST00000288319.7:c.1439A>T	p.Ter480LeuextTer79	p.*480Lext*79	ENST00000288319	NM_182918.3	480	tAa/tTa	10/10	1	2	FACETS	0.727	0.599	0.87	0.727	0.599	0.87	SUBCLONAL	1	TRUE	1	0.15	2		426	697	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717757	89717758	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1554825249	NA	P-0038967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	50	352	0	ENST00000371953.3:c.783_784del	p.Asn262GlnfsTer35	p.N262Qfs*35	ENST00000371953	NM_000314.4	261	cAG/c	7/9	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.15	2		352	642	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17355107	17355107	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	50	456	0	ENST00000375499.3:c.411G>T	p.Lys137Asn	p.K137N	ENST00000375499	NM_003000.2	137	aaG/aaT	4/8	1	2	FACETS	0.773	0.654	0.905	0.773	0.654	0.905	CLONAL	1	TRUE	1	0.15	2		456	862	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624263	89624264	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs587776671	NA	P-0038967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	32	304	0	ENST00000371953.3:c.39_40del	p.Arg14GlufsTer29	p.R14Efs*29	ENST00000371953	NM_000314.4	13	AAa/a	1/9	1	2	FACETS	0.799	0.647	0.971	0.799	0.647	0.971	CLONAL	1	TRUE	1	0.15	2		304	534	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796286	42796287	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0038967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	70	687	2	ENST00000575354.2:c.2935_2936delinsTT	p.Pro979Leu	p.P979L	ENST00000575354	NM_015125.3	979	CCg/TTg	12/20	1	2	FACETS	0.859	0.747	0.982	0.859	0.747	0.982	CLONAL	1	TRUE	1	0.15	2		689	1086	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931477	131931477	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	65	410	0	ENST00000265335.6:c.2182G>T	p.Glu728Ter	p.E728*	ENST00000265335		728	Gaa/Taa	13/25	1	2	FACETS	0.956	0.826	1	0.956	0.826	1	CLONAL	1	TRUE	1	0.15	2		410	907	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499829	8499829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1220058466	NA	P-0038967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	60	413	0	ENST00000356435.5:c.2140C>T	p.Pro714Ser	p.P714S	ENST00000356435		714	Cct/Tct	14/35	1	2	FACETS	0.962	0.827	1	0.962	0.827	1	CLONAL	1	TRUE	1	0.15	2		413	832	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2969697	2969697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367917190	NA	P-0039011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	114	483	0	ENST00000396946.4:c.1582G>A	p.Glu528Lys	p.E528K	ENST00000396946	NM_032415.4	528	Gag/Aag	12/25	0.487972941570136	0	FACETS		NA	1			1	NA	1	TRUE	0	0.698056456239781	0		483	445	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922301	178922301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	38	305	0	ENST00000263967.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000263967	NM_006218.2	357	cGa/cAa	6/21	0.286555473212801	1	FACETS	0.247	0.205	0.294	0.247	0.205	0.294	INDETERMINATE	1	TRUE	0	0.698056456239781	1		305	287	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780812	9780812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765797019	NA	P-0039011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	143	498	1	ENST00000377346.4:c.1534C>T	p.Arg512Trp	p.R512W	ENST00000377346	NM_005026.3	512	Cgg/Tgg	13/24	0.698056456239781	1	FACETS	0.672	0.619	0.726	0.672	0.619	0.726	SUBCLONAL	1	TRUE	0	0.698056456239781	1		499	397	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931463	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622007	NA	P-0039234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	563	398	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	0.817235464577551	1		398	672	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	85	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.87	0.77	0.976	0.87	0.77	0.976	CLONAL	1	TRUE	1	0.325298852895117	2		473	601	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	87	776	5	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.817	0.723	0.916	0.817	0.723	0.916	CLONAL	1	TRUE	1	0.325298852895117	2		781	655	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	108	289	1	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.325298852895117	1		290	406	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161222	56161222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	92	411	1	ENST00000399503.3:c.1091G>A	p.Arg364Gln	p.R364Q	ENST00000399503	NM_005921.1	364	cGg/cAg	5/20	1	2	FACETS	0.842	0.748	0.941	0.842	0.748	0.941	CLONAL	1	TRUE	1	0.325298852895117	2		412	672	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332337	70332337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761821309	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	79	445	0	ENST00000373644.4:c.242G>A	p.Arg81His	p.R81H	ENST00000373644	NM_030625.2	81	cGc/cAc	2/12	1	2	FACETS	0.715	0.629	0.808	0.715	0.629	0.808	SUBCLONAL	1	TRUE	1	0.325298852895117	2		445	679	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	272	717	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.976	0.918	1	1	0.995	1	CLONAL	2	TRUE	1	0.325298852895117	2		721	857	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65323365	65323365	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	116	480	0	ENST00000342505.4:c.1432A>G	p.Thr478Ala	p.T478A	ENST00000342505	NM_002227.2	478	Acc/Gcc	10/25	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.325298852895117	2		480	683	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	100	561	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.325298852895117	2		561	596	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	138	851	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.942	0.857	1	0.942	0.857	1	CLONAL	1	TRUE	1	0.325298852895117	2		851	901	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201874	152201874	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753014570	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	67	381	1	ENST00000206249.3:c.728G>A	p.Arg243His	p.R243H	ENST00000206249	NM_000125.3	243	cGt/cAt	3/8	1	2	FACETS	0.821	0.714	0.935	0.821	0.714	0.935	CLONAL	1	TRUE	1	0.325298852895117	2		382	502	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	90	844	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.796	0.707	0.892	0.796	0.707	0.892	SUBCLONAL	1	TRUE	1	0.325298852895117	2		844	695	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	142	1012	5	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.325298852895117	2		1017	771	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	61	655	1	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	1	2	FACETS	0.429	0.369	0.495	0.429	0.369	0.495	SUBCLONAL	1	TRUE	1	0.325298852895117	2		656	874	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966688	36966688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137870876	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	88	437	2	ENST00000358127.4:c.638C>T	p.Ser213Leu	p.S213L	ENST00000358127	NM_001280556.1	213	tCg/tTg	6/10	1	2	FACETS	0.911	0.808	1	0.911	0.808	1	CLONAL	1	TRUE	1	0.325298852895117	2		439	594	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	40	265	0	ENST00000375687.4:c.1933_1934dup	p.Gly646ValfsTer58	p.G646Vfs*58	ENST00000375687	NM_015338.5	642	-/GG	13/13	1	2	FACETS	0.734	0.612	0.869	0.734	0.612	0.869	SUBCLONAL	1	TRUE	1	0.325298852895117	2		265	335	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211097	55211097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219568637	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	100	471	0	ENST00000275493.2:c.340G>A	p.Glu114Lys	p.E114K	ENST00000275493	NM_005228.3	114	Gaa/Aaa	3/28	1	2	FACETS	0.936	0.837	1	0.936	0.837	1	CLONAL	1	TRUE	1	0.325298852895117	2		471	657	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	125	801	5	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.847	0.766	0.933	0.847	0.766	0.933	CLONAL	1	TRUE	1	0.325298852895117	2		806	907	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141631	202141631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs17860424	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	47	391	0	ENST00000358485.4:c.919C>T	p.Arg307Trp	p.R307W	ENST00000358485	NM_001080125.1	307	Cgg/Tgg	7/9	1	2	FACETS	0.423	0.356	0.497	0.423	0.356	0.497	SUBCLONAL	1	TRUE	1	0.325298852895117	2		391	683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578245	7578245	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780072	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	139	554	0	ENST00000269305.4:c.604C>T	p.Arg202Cys	p.R202C	ENST00000269305	NM_001126112.2	202	Cgt/Tgt	6/11	1	2	FACETS	0.971	0.884	1	0.971	0.884	1	CLONAL	1	TRUE	1	0.325298852895117	2		554	880	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778603	3778603	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147448293	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	113	489	0	ENST00000262367.5:c.6445G>A	p.Val2149Met	p.V2149M	ENST00000262367	NM_004380.2	2149	Gtg/Atg	31/31	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.325298852895117	2		489	694	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822585	72822586	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs764626362	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	77	456	0	ENST00000268489.5:c.9589dup	p.Gln3197ProfsTer42	p.Q3197Pfs*42	ENST00000268489	NM_006885.3	3197	cag/cCag	10/10	1	2	FACETS	0.749	0.658	0.847	0.749	0.658	0.847	SUBCLONAL	1	TRUE	1	0.325298852895117	2		456	632	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245587	41245587	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357522	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	144	578	1	ENST00000357654.3:c.1961del	p.Lys654SerfsTer47	p.K654Sfs*47	ENST00000357654	NM_007294.3	654	aAg/ag	10/23	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.325298852895117	2		579	867	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	116	402	3	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.325298852895117	2		405	706	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	86	423	4	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	0.873	0.773	0.979	0.873	0.773	0.979	CLONAL	1	TRUE	1	0.325298852895117	2		427	606	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939673	76939674	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	26	320	0	ENST00000373344.5:c.1074dup	p.Leu359ThrfsTer3	p.L359Tfs*3	ENST00000373344	NM_000489.3	358	-/A	9/35	1	1	FACETS	0.308	0.244	0.383	0.308	0.244	0.383	SUBCLONAL	1	TRUE	0	0.325298852895117	1		320	434	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	105	449	2	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	0.325298852895117	1	FACETS	0.97	0.872	1	0.97	0.872	1	CLONAL	1	TRUE	0	0.325298852895117	1		451	557	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990331	81990331	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768299957	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	132	448	0	ENST00000359376.3:c.3602G>A	p.Arg1201His	p.R1201H	ENST00000359376	NM_002661.3	1201	cGc/cAc	32/33	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.325298852895117	2		448	657	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007901	45007901	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	59	288	0	ENST00000558401.1:c.346+2T>C		p.X116_splice	ENST00000558401	NM_004048.2	116			0.325298852895117	1	FACETS	0.666	0.574	0.766	0.666	0.574	0.766	SUBCLONAL	1	TRUE	0	0.325298852895117	1		288	456	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371942	55371942	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	93	353	1	ENST00000297316.4:c.632C>T	p.Ala211Val	p.A211V	ENST00000297316	NM_022454.3	211	gCg/gTg	2/2	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.325298852895117	2		354	493	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885467	111885467	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs918140013	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	90	507	0	ENST00000341259.2:c.1244G>A	p.Arg415His	p.R415H	ENST00000341259	NM_005475.2	415	cGc/cAc	7/8	1	2	FACETS	0.851	0.756	0.953	0.851	0.756	0.953	CLONAL	1	TRUE	1	0.325298852895117	2		507	650	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637121	176637122	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1299932363	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	112	482	0	ENST00000439151.2:c.1727dup	p.Asn576LysfsTer8	p.N576Kfs*8	ENST00000439151	NM_022455.4	574	gga/ggAa	5/23	1	2	FACETS	0.96	0.864	1	0.96	0.864	1	CLONAL	1	TRUE	1	0.325298852895117	2		482	717	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67646013	67646014	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs1470210640	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	91	194	2	ENST00000264010.4:c.950_951del	p.Thr317ArgfsTer91	p.T317Rfs*91	ENST00000264010	NM_006565.3	314	aAC/a	4/12	1	2	FACETS	0.91	0.809	1	0.91	0.809	1	CLONAL	1	TRUE	1	0.325298852895117	2		196	615	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435597	110435597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762535630	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	99	413	0	ENST00000375856.3:c.2804C>T	p.Ala935Val	p.A935V	ENST00000375856	NM_003749.2	935	gCg/gTg	1/2	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.325298852895117	2		413	546	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858279	27858279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	112	509	0	ENST00000359303.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000359303	NM_003535.2	98	Gag/Aag	1/1	1	2	FACETS	0.975	0.878	1	0.975	0.878	1	CLONAL	1	TRUE	1	0.325298852895117	2		509	706	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829454	72829454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771717307	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	103	515	0	ENST00000268489.5:c.7127C>T	p.Thr2376Met	p.T2376M	ENST00000268489	NM_006885.3	2376	aCg/aTg	9/10	1	2	FACETS	0.876	0.784	0.973	0.876	0.784	0.973	CLONAL	1	TRUE	1	0.325298852895117	2		515	723	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118954	3118954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	144	650	0	ENST00000078429.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000078429	NM_002067.2	213	cGg/cAg	5/7	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.325298852895117	2		650	853	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411416	63411416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773828754	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	123	294	0	ENST00000330258.3:c.1751G>A	p.Arg584His	p.R584H	ENST00000330258	NM_152424.3	584	cGt/cAt	2/2	1	1	FACETS	0.78	0.711	0.851	1	0.987	1	SUBCLONAL	2	TRUE	0	0.325298852895117	1		294	406	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36821030	36821030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1171838543	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	110	455	0	ENST00000373129.3:c.347G>A	p.Arg116His	p.R116H	ENST00000373129	NM_032017.1	116	cGc/cAc	6/12	1	2	FACETS	0.966	0.869	1	0.966	0.869	1	CLONAL	1	TRUE	1	0.325298852895117	2		455	700	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942125	81942125	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	125	552	0	ENST00000359376.3:c.1667del	p.Gly556AlafsTer42	p.G556Afs*42	ENST00000359376	NM_002661.3	554	acG/ac	17/33	1	2	FACETS	0.968	0.876	1	0.968	0.876	1	CLONAL	1	TRUE	1	0.325298852895117	2		552	794	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827892	40827892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs573377632	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	95	417	0	ENST00000373198.4:c.2536G>A	p.Val846Ile	p.V846I	ENST00000373198	NM_133170.3	846	Gtc/Atc	17/32	1	2	FACETS	0.89	0.794	0.993	0.89	0.794	0.993	CLONAL	1	TRUE	1	0.325298852895117	2		417	656	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	49	480	1	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	0.418	0.353	0.49	0.418	0.353	0.49	SUBCLONAL	1	TRUE	1	0.325298852895117	2		481	721	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609394	39609394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1360571803	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	79	329	0	ENST00000262039.4:c.1696C>T	p.Arg566Cys	p.R566C	ENST00000262039	NM_002647.2	566	Cgt/Tgt	15/25	1	2	FACETS	0.874	0.77	0.985	0.874	0.77	0.985	CLONAL	1	TRUE	1	0.325298852895117	2		329	556	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137075	64137075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	64	498	0	ENST00000334205.4:c.1586G>A	p.Arg529His	p.R529H	ENST00000334205	NM_003942.2	529	cGc/cAc	13/17	0.223394888516944	1	FACETS	0.531	0.46	0.609	0.531	0.46	0.609	SUBCLONAL	1	TRUE	0	0.325298852895117	1		498	620	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	120	285	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.873	0.788	0.963	0.873	0.788	0.963	CLONAL	1	TRUE	1	0.325298852895117	2		285	845	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391358	84391358	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1560574509	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	48	472	0	ENST00000321945.7:c.474del	p.Gly159AspfsTer8	p.G159Dfs*8	ENST00000321945	NM_139076.2	158	aaA/aa	5/9	0.223394888516944	1	FACETS	0.421	0.355	0.493	0.421	0.355	0.493	SUBCLONAL	1	TRUE	0	0.325298852895117	1		472	587	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353974	15353974	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	35	185	0	ENST00000263377.2:c.2906A>T	p.Gln969Leu	p.Q969L	ENST00000263377	NM_058243.2	969	cAg/cTg	14/20	1	2	FACETS	0.897	0.74	1	0.897	0.74	1	CLONAL	1	TRUE	1	0.325298852895117	2		185	240	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651306	45651307	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	100	550	0	ENST00000407780.3:c.718_719del	p.Asp240GlnfsTer81	p.D240Qfs*81	ENST00000407780	NM_001283052.1	240	GAc/c	5/7	1	2	FACETS	0.852	0.761	0.948	0.852	0.761	0.948	CLONAL	1	TRUE	1	0.325298852895117	2		550	722	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808391	1808391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17882190	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	110	765	2	ENST00000260795.2:c.2149G>A	p.Ala717Thr	p.A717T	ENST00000260795		717	Gcc/Acc	15/17	0.223394888516944	1	FACETS	0.57	0.511	0.632	0.57	0.511	0.632	SUBCLONAL	1	TRUE	0	0.325298852895117	1		767	994	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906394	50906394	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556862476	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	67	731	2	ENST00000440232.2:c.1055G>A	p.Arg352His	p.R352H	ENST00000440232	NM_002691.3	352	cGc/cAc	9/27	1	2	FACETS	0.541	0.469	0.618	0.541	0.469	0.618	SUBCLONAL	1	TRUE	1	0.325298852895117	2		733	762	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434942	56434942	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772096609	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	127	616	1	ENST00000407977.2:c.2195G>A	p.Arg732His	p.R732H	ENST00000407977		732	cGc/cAc	9/10	1	2	FACETS	0.944	0.855	1	0.944	0.855	1	CLONAL	1	TRUE	1	0.325298852895117	2		617	827	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317189	11317189	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	135	472	0	ENST00000361445.4:c.305C>T	p.Thr102Ile	p.T102I	ENST00000361445	NM_004958.3	102	aCc/aTc	4/58	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.325298852895117	2		472	712	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398043	4398043	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	121	486	0	ENST00000261254.3:c.607G>A	p.Ala203Thr	p.A203T	ENST00000261254	NM_001759.3	203	Gca/Aca	4/5	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.325298852895117	2		486	727	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527348	187527348	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs184300563	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	57	414	0	ENST00000441802.2:c.10226C>T	p.Thr3409Met	p.T3409M	ENST00000441802	NM_005245.3	3409	aCg/aTg	17/27	0.223394888516944	1	FACETS	0.458	0.392	0.529	0.458	0.392	0.529	SUBCLONAL	1	TRUE	0	0.325298852895117	1		414	641	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970916	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	117	537	0	ENST00000265081.6:c.1147_1148del	p.Lys383GlyfsTer20	p.K383Gfs*20	ENST00000265081	NM_002439.4	381	AAa/a	7/24	1	2	FACETS	0.888	0.801	0.98	0.888	0.801	0.98	CLONAL	1	TRUE	1	0.325298852895117	2		537	810	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	338208	338208	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	135	659	0	ENST00000262320.3:c.2503del	p.Val835TrpfsTer103	p.V835Wfs*103	ENST00000262320	NM_003502.3	835	Gtg/tg	11/11	1	2	FACETS	0.899	0.817	0.986	0.899	0.817	0.986	CLONAL	1	TRUE	1	0.325298852895117	2		659	923	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108330	8108330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768656332	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	106	570	0	ENST00000585124.1:c.894G>A	p.Met298Ile	p.M298I	ENST00000585124	NM_004217.3	298	atG/atA	9/9	1	2	FACETS	0.819	0.734	0.909	0.819	0.734	0.909	CLONAL	1	TRUE	1	0.325298852895117	2		570	796	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918709	50918709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501818	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	137	447	0	ENST00000440232.2:c.2579C>T	p.Ala860Val	p.A860V	ENST00000440232	NM_002691.3	860	gCg/gTg	21/27	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.325298852895117	2		447	582	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	422242	422242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769792722	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	105	465	0	ENST00000399788.2:c.3016G>A	p.Ala1006Thr	p.A1006T	ENST00000399788	NM_001042603.1	1006	Gct/Act	20/28	1	2	FACETS	0.897	0.804	0.995	0.897	0.804	0.995	CLONAL	1	TRUE	1	0.325298852895117	2		465	720	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654615	67654615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	129	410	1	ENST00000264010.4:c.1102C>T	p.Arg368Cys	p.R368C	ENST00000264010	NM_006565.3	368	Cgt/Tgt	6/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.325298852895117	2		411	676	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094450	27094450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779484265	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	113	489	0	ENST00000324856.7:c.3158G>A	p.Arg1053His	p.R1053H	ENST00000324856	NM_006015.4	1053	cGc/cAc	11/20	1	2	FACETS	0.903	0.813	0.999	0.903	0.813	0.999	CLONAL	1	TRUE	1	0.325298852895117	2		489	769	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224183	36224183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771130237	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	57	569	1	ENST00000222270.7:c.6733G>A	p.Val2245Met	p.V2245M	ENST00000222270	NM_014727.1	2245	Gtg/Atg	28/37	1	2	FACETS	0.474	0.405	0.548	0.474	0.405	0.548	SUBCLONAL	1	TRUE	1	0.325298852895117	2		570	740	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933047	39933047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	124	372	0	ENST00000378444.4:c.1552G>A	p.Glu518Lys	p.E518K	ENST00000378444	NM_001123385.1	518	Gaa/Aaa	4/15	1	1	FACETS	0.769	0.702	0.839	1	0.987	1	SUBCLONAL	2	TRUE	0	0.325298852895117	1		372	415	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533536	533536	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369106578	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	137	650	0	ENST00000451590.1:c.367C>T	p.Arg123Cys	p.R123C	ENST00000451590	NM_001130442.1	123	Cgc/Tgc	4/5	0.223394888516944	1	FACETS	0.854	0.777	0.935	0.854	0.777	0.935	CLONAL	1	TRUE	0	0.325298852895117	1		650	826	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798439	32798439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765178638	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	163	661	2	ENST00000374899.4:c.1417G>A	p.Val473Ile	p.V473I	ENST00000374899	NM_018833.2	473	Gtc/Atc	8/12	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.325298852895117	2		663	938	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335545	73335546	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	100	303	0	ENST00000377767.4:c.2625dup	p.Glu876Ter	p.E876*	ENST00000377767	NM_014953.3	875	-/T	19/21	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.325298852895117	2		303	605	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851985	128851985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778688	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	141	616	0	ENST00000249373.3:c.2057C>T	p.Ala686Val	p.A686V	ENST00000249373	NM_005631.4	686	gCg/gTg	12/12	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.325298852895117	2		616	812	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14022037	14022037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370864937	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	107	469	0	ENST00000311895.7:c.737C>T	p.Ser246Leu	p.S246L	ENST00000311895	NM_005236.2	246	tCg/tTg	4/11	1	2	FACETS	0.891	0.8	0.988	0.891	0.8	0.988	CLONAL	1	TRUE	1	0.325298852895117	2		469	738	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939788	71939788	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	67	568	0	ENST00000298229.2:c.419del	p.Pro140ArgfsTer39	p.P140Rfs*39	ENST00000298229	NM_001567.3	139	Ccc/cc	4/28	0.223394888516944	1	FACETS	0.467	0.405	0.534	0.467	0.405	0.534	SUBCLONAL	1	TRUE	0	0.325298852895117	1		568	739	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941695	48941696	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	48	263	0	ENST00000267163.4:c.1010dup	p.Leu337PhefsTer4	p.L337Ffs*4	ENST00000267163	NM_000321.2	335	-/T	10/27	1	2	FACETS	0.715	0.605	0.834	0.715	0.605	0.834	SUBCLONAL	1	TRUE	1	0.325298852895117	2		263	413	SUCCESS
APC	324	MSKCC	GRCh37	5	112137003	112137003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772806807	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	91	365	0	ENST00000257430.4:c.757G>A	p.Gly253Ser	p.G253S	ENST00000257430	NM_000038.5	253	Ggc/Agc	8/16	1	2	FACETS	0.92	0.818	1	0.92	0.818	1	CLONAL	1	TRUE	1	0.325298852895117	2		365	608	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538882	23538882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1254712780	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	107	431	0	ENST00000380871.4:c.557C>T	p.Ser186Leu	p.S186L	ENST00000380871	NM_006167.3	186	tCg/tTg	2/2	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.325298852895117	2		431	615	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254932	16254932	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138206879	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	85	457	0	ENST00000375759.3:c.2197C>T	p.Arg733Cys	p.R733C	ENST00000375759	NM_015001.2	733	Cgt/Tgt	11/15	1	2	FACETS	0.81	0.717	0.91	0.81	0.717	0.91	CLONAL	1	TRUE	1	0.325298852895117	2		457	645	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256529	16256529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749587229	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	163	547	1	ENST00000375759.3:c.3794G>A	p.Arg1265Gln	p.R1265Q	ENST00000375759	NM_015001.2	1265	cGa/cAa	11/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.325298852895117	2		548	822	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056334	27056334	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs541301347	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	97	346	0	ENST00000324856.7:c.1330G>A	p.Gly444Ser	p.G444S	ENST00000324856	NM_006015.4	444	Ggc/Agc	2/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.325298852895117	2		346	482	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100865	27100865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1433790061	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	124	481	0	ENST00000324856.7:c.4147C>T	p.Arg1383Trp	p.R1383W	ENST00000324856	NM_006015.4	1383	Cgg/Tgg	18/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.325298852895117	2		481	692	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101268	27101268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	109	548	0	ENST00000324856.7:c.4550C>T	p.Ala1517Val	p.A1517V	ENST00000324856	NM_006015.4	1517	gCc/gTc	18/20	1	2	FACETS	0.908	0.816	1	0.908	0.816	1	CLONAL	1	TRUE	1	0.325298852895117	2		548	738	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105950	27105950	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	108	463	1	ENST00000324856.7:c.5561A>T	p.His1854Leu	p.H1854L	ENST00000324856	NM_006015.4	1854	cAt/cTt	20/20	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.325298852895117	2		464	650	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797105	45797105	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782120	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	161	649	0	ENST00000450313.1:c.1310G>A	p.Arg437Gln	p.R437Q	ENST00000450313	NM_012222.2	437	cGg/cAg	13/16	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.325298852895117	2		649	929	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46740250	46740250	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	89	406	0	ENST00000371975.4:c.1730G>A	p.Gly577Asp	p.G577D	ENST00000371975	NM_003579.3	577	gGc/gAc	16/18	1	2	FACETS	0.837	0.742	0.937	0.837	0.742	0.937	CLONAL	1	TRUE	1	0.325298852895117	2		406	654	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462160	120462160	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs765121641	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	108	493	0	ENST00000256646.2:c.5556G>T	p.Glu1852Asp	p.E1852D	ENST00000256646	NM_024408.3	1852	gaG/gaT	31/34	1	2	FACETS	0.937	0.841	1	0.937	0.841	1	CLONAL	1	TRUE	1	0.325298852895117	2		493	709	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421514	32421514	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	87	468	0	ENST00000332351.3:c.1078G>T	p.Gly360Cys	p.G360C	ENST00000332351	NM_024426.4	360	Ggt/Tgt	6/10	0.223394888516944	1	FACETS	0.763	0.677	0.855	0.763	0.677	0.855	SUBCLONAL	1	TRUE	0	0.325298852895117	1		468	587	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135721	64135721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1360811119	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	98	589	1	ENST00000334205.4:c.1189G>A	p.Ala397Thr	p.A397T	ENST00000334205	NM_003942.2	397	Gct/Act	10/17	0.223394888516944	1	FACETS	0.76	0.678	0.846	0.76	0.678	0.846	SUBCLONAL	1	TRUE	0	0.325298852895117	1		590	664	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941507	71941507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	80	553	1	ENST00000298229.2:c.1192G>A	p.Ala398Thr	p.A398T	ENST00000298229	NM_001567.3	398	Gcc/Acc	10/28	0.223394888516944	1	FACETS	0.578	0.508	0.652	0.578	0.508	0.652	SUBCLONAL	1	TRUE	0	0.325298852895117	1		554	713	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151837	108151837	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	110	359	0	ENST00000278616.4:c.3518T>C	p.Leu1173Ser	p.L1173S	ENST00000278616	NM_000051.3	1173	tTg/tCg	24/63	0.223394888516944	1	FACETS	0.849	0.764	0.939	0.849	0.764	0.939	CLONAL	1	TRUE	0	0.325298852895117	1		359	667	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023695	1023695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199638457	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	87	371	1	ENST00000358495.3:c.869C>T	p.Ala290Val	p.A290V	ENST00000358495	NM_134424.2	290	gCg/gTg	10/12	1	2	FACETS	0.887	0.786	0.994	0.887	0.786	0.994	CLONAL	1	TRUE	1	0.325298852895117	2		372	603	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945076	31945076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	105	557	1	ENST00000340398.3:c.25C>T	p.Arg9Cys	p.R9C	ENST00000340398	NM_001013699.2	9	Cgt/Tgt	1/1	1	2	FACETS	0.892	0.799	0.99	0.892	0.799	0.99	CLONAL	1	TRUE	1	0.325298852895117	2		558	724	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436108	49436108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754363205	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	51	333	0	ENST00000301067.7:c.5873G>A	p.Arg1958His	p.R1958H	ENST00000301067	NM_003482.3	1958	cGc/cAc	28/54	1	2	FACETS	0.724	0.617	0.842	0.724	0.617	0.842	SUBCLONAL	1	TRUE	1	0.325298852895117	2		333	433	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445799	49445799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748450844	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	145	833	1	ENST00000301067.7:c.1667C>T	p.Pro556Leu	p.P556L	ENST00000301067	NM_003482.3	556	cCg/cTg	10/54	1	2	FACETS	0.864	0.787	0.945	0.864	0.787	0.945	CLONAL	1	TRUE	1	0.325298852895117	2		834	1032	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134359	41134359	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	122	479	0	ENST00000379561.5:c.1269del	p.Lys423AsnfsTer9	p.K423Nfs*9	ENST00000379561	NM_002015.3	423	aaA/aa	2/3	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.325298852895117	2		479	660	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435150	110435150	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	108	524	0	ENST00000375856.3:c.3251C>T	p.Pro1084Leu	p.P1084L	ENST00000375856	NM_003749.2	1084	cCg/cTg	1/2	1	2	FACETS	0.9	0.808	0.997	0.9	0.808	0.997	CLONAL	1	TRUE	1	0.325298852895117	2		524	738	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436597	110436597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1267707947	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	151	673	0	ENST00000375856.3:c.1804C>T	p.Arg602Trp	p.R602W	ENST00000375856	NM_003749.2	602	Cgg/Tgg	1/2	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.325298852895117	2		673	898	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437706	110437706	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	40	600	0	ENST00000375856.3:c.695A>G	p.Asn232Ser	p.N232S	ENST00000375856	NM_003749.2	232	aAc/aGc	1/2	1	2	FACETS	0.316	0.261	0.377	0.316	0.261	0.377	SUBCLONAL	1	TRUE	1	0.325298852895117	2		600	779	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222245	2222245	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	139	658	0	ENST00000326181.6:c.529G>A	p.Val177Met	p.V177M	ENST00000326181	NM_032271.2	177	Gtg/Atg	8/21	1	2	FACETS	0.946	0.861	1	0.946	0.861	1	CLONAL	1	TRUE	1	0.325298852895117	2		658	903	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639453	3639453	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376437029	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	125	645	1	ENST00000294008.3:c.4186G>A	p.Gly1396Arg	p.G1396R	ENST00000294008	NM_032444.2	1396	Gga/Aga	12/15	1	2	FACETS	0.94	0.85	1	0.94	0.85	1	CLONAL	1	TRUE	1	0.325298852895117	2		646	818	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832868	3832868	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	111	470	0	ENST00000262367.5:c.1390C>A	p.Gln464Lys	p.Q464K	ENST00000262367	NM_004380.2	464	Caa/Aaa	6/31	1	2	FACETS	0.993	0.894	1	0.993	0.894	1	CLONAL	1	TRUE	1	0.325298852895117	2		470	687	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041882	14041882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	86	323	0	ENST00000311895.7:c.2429C>T	p.Ala810Val	p.A810V	ENST00000311895	NM_005236.2	810	gCg/gTg	11/11	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.325298852895117	2		323	482	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984481	72984481	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147374923	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	138	602	3	ENST00000268489.5:c.3103G>A	p.Gly1035Ser	p.G1035S	ENST00000268489	NM_006885.3	1035	Ggc/Agc	3/10	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.325298852895117	2		605	816	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216160	7216161	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TG	TG	-	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	76	336	0	ENST00000380728.2:c.901-3_901-2del		p.X301_splice	ENST00000380728		301			1	2	FACETS	0.982	0.864	1	0.982	0.864	1	CLONAL	1	TRUE	1	0.325298852895117	2		336	476	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011123	12011123	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	47	299	0	ENST00000353533.5:c.530G>A	p.Cys177Tyr	p.C177Y	ENST00000353533	NM_003010.3	177	tGt/tAt	5/11	1	2	FACETS	0.631	0.533	0.739	0.631	0.533	0.739	SUBCLONAL	1	TRUE	1	0.325298852895117	2		299	458	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127393	17127393	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	126	570	0	ENST00000285071.4:c.461A>G	p.His154Arg	p.H154R	ENST00000285071	NM_144997.5	154	cAc/cGc	6/14	1	2	FACETS	0.891	0.807	0.981	0.891	0.807	0.981	CLONAL	1	TRUE	1	0.325298852895117	2		570	869	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33430295	33430295	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	147	637	0	ENST00000345365.6:c.716G>T	p.Arg239Leu	p.R239L	ENST00000345365	NM_002878.3	239	cGg/cTg	8/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.325298852895117	2		637	805	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508272	38508272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1180532434	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	134	569	0	ENST00000254066.5:c.580G>A	p.Ala194Thr	p.A194T	ENST00000254066	NM_000964.3	194	Gcg/Acg	5/9	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.325298852895117	2		569	713	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511517	38511517	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	104	423	0	ENST00000254066.5:c.1015C>A	p.Arg339Ser	p.R339S	ENST00000254066	NM_000964.3	339	Cgc/Agc	8/9	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.325298852895117	2		423	607	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492830	56492830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	110	439	0	ENST00000407977.2:c.109G>A	p.Glu37Lys	p.E37K	ENST00000407977		37	Gag/Aag	2/10	1	2	FACETS	0.973	0.875	1	0.973	0.875	1	CLONAL	1	TRUE	1	0.325298852895117	2		439	695	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2164192	2164192	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	70	320	0	ENST00000398665.3:c.9G>T	p.Glu3Asp	p.E3D	ENST00000398665	NM_032482.2	3	gaG/gaT	1/28	1	2	FACETS	0.869	0.76	0.987	0.869	0.76	0.987	CLONAL	1	TRUE	1	0.325298852895117	2		320	495	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222898	5222898	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758072738	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	113	490	0	ENST00000357368.4:c.2905G>A	p.Val969Met	p.V969M	ENST00000357368	NM_002850.3	969	Gtg/Atg	18/38	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.325298852895117	2		490	690	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243936	5243937	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	95	507	0	ENST00000357368.4:c.1545dup	p.Ile516HisfsTer111	p.I516Hfs*111	ENST00000357368	NM_002850.3	515	-/C	11/38	1	2	FACETS	0.873	0.778	0.974	0.873	0.778	0.974	CLONAL	1	TRUE	1	0.325298852895117	2		507	669	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244191	5244191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237664443	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	133	544	1	ENST00000357368.4:c.1291C>T	p.Arg431Trp	p.R431W	ENST00000357368	NM_002850.3	431	Cgg/Tgg	11/38	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.325298852895117	2		545	772	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172389	7172389	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	126	473	0	ENST00000302850.5:c.1180T>C	p.Tyr394His	p.Y394H	ENST00000302850	NM_000208.2	394	Tat/Cat	5/22	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.325298852895117	2		473	754	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098410	11098410	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555754899	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	111	440	2	ENST00000358026.2:c.928C>T	p.Arg310Cys	p.R310C	ENST00000358026	NM_001128849.1	310	Cgc/Tgc	6/36	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.325298852895117	2		442	597	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101866	11101866	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs569715577	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	132	630	1	ENST00000358026.2:c.1286C>T	p.Ala429Val	p.A429V	ENST00000358026	NM_001128849.1	429	gCg/gTg	8/36	1	2	FACETS	0.98	0.89	1	0.98	0.89	1	CLONAL	1	TRUE	1	0.325298852895117	2		631	828	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107218	11107218	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	152	601	0	ENST00000358026.2:c.1810G>A	p.Glu604Lys	p.E604K	ENST00000358026	NM_001128849.1	604	Gag/Aag	11/36	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.325298852895117	2		601	821	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288807	15288807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1332840784	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	49	181	0	ENST00000263388.2:c.3932C>T	p.Pro1311Leu	p.P1311L	ENST00000263388	NM_000435.2	1311	cCg/cTg	24/33	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.325298852895117	2		181	269	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210770	36210770	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs772189245	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	233	678	0	ENST00000222270.7:c.521C>A	p.Pro174Gln	p.P174Q	ENST00000222270	NM_014727.1	174	cCa/cAa	3/37	1	2	FACETS	0.779	0.728	0.833	1	0.993	1	SUBCLONAL	2	TRUE	1	0.325298852895117	2		678	919	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227663	36227663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	69	619	0	ENST00000222270.7:c.7232G>A	p.Gly2411Asp	p.G2411D	ENST00000222270	NM_014727.1	2411	gGc/gAc	31/37	1	2	FACETS	0.51	0.444	0.583	0.51	0.444	0.583	SUBCLONAL	1	TRUE	1	0.325298852895117	2		619	831	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229342	36229342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	179	568	0	ENST00000222270.7:c.8032C>T	p.Arg2678Cys	p.R2678C	ENST00000222270	NM_014727.1	2678	Cgc/Tgc	37/37	1	2	FACETS	0.772	0.713	0.832	1	0.99	1	SUBCLONAL	2	TRUE	1	0.325298852895117	2		568	713	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752694	42752694	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	189	620	0	ENST00000222329.4:c.1570C>G	p.Pro524Ala	p.P524A	ENST00000222329	NM_006494.2	524	Ccc/Gcc	4/4	1	2	FACETS	0.788	0.731	0.848	1	0.991	1	SUBCLONAL	2	TRUE	1	0.325298852895117	2		620	737	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464521	25464521	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	147	607	0	ENST00000264709.3:c.1992G>T	p.Glu664Asp	p.E664D	ENST00000264709	NM_175629.2	664	gaG/gaT	17/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.325298852895117	2		607	782	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657019	47657019	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs63751271	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	80	365	0	ENST00000233146.2:c.1215C>G	p.Tyr405Ter	p.Y405*	ENST00000233146	NM_000251.2	405	taC/taG	7/16	1	2	FACETS	0.932	0.822	1	0.932	0.822	1	CLONAL	1	TRUE	1	0.325298852895117	2		365	528	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170738	99170738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1476382968	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	83	328	0	ENST00000074304.5:c.1367G>A	p.Arg456Gln	p.R456Q	ENST00000074304	NM_001134224.1	456	cGg/cAg	16/26	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.325298852895117	2		328	498	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021673	31021673	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs899345535	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	148	470	2	ENST00000375687.4:c.1672G>A	p.Glu558Lys	p.E558K	ENST00000375687	NM_015338.5	558	Gaa/Aaa	12/13	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.325298852895117	2		472	721	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62317172	62317172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770158407	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	139	687	1	ENST00000360203.5:c.1295G>A	p.Arg432Gln	p.R432Q	ENST00000360203	NM_001283009.1	432	cGg/cAg	16/35	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.325298852895117	2		688	825	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656873	45656873	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs865851162	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	126	546	1	ENST00000407780.3:c.283G>A	p.Asp95Asn	p.D95N	ENST00000407780	NM_001283052.1	95	Gac/Aac	3/7	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.325298852895117	2		547	749	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553308	41553308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1203250209	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	67	512	0	ENST00000263253.7:c.3397C>T	p.Arg1133Trp	p.R1133W	ENST00000263253	NM_001429.3	1133	Cgg/Tgg	18/31	1	2	FACETS	0.524	0.454	0.6	0.524	0.454	0.6	SUBCLONAL	1	TRUE	1	0.325298852895117	2		512	786	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565553	41565553	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	98	386	0	ENST00000263253.7:c.4219A>G	p.Lys1407Glu	p.K1407E	ENST00000263253	NM_001429.3	1407	Aaa/Gaa	26/31	1	2	FACETS	0.958	0.856	1	0.958	0.856	1	CLONAL	1	TRUE	1	0.325298852895117	2		386	629	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438551	52438551	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1425178905	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	136	488	0	ENST00000460680.1:c.1168C>A	p.Pro390Thr	p.P390T	ENST00000460680	NM_004656.3	390	Cca/Aca	12/17	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.325298852895117	2		488	730	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427784	72427784	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	41	302	0	ENST00000477973.2:c.704del	p.Arg236GlyfsTer2	p.R236Gfs*2	ENST00000477973	NM_012234.5	236	Cgg/gg	4/4	1	2	FACETS	0.615	0.513	0.728	0.615	0.513	0.728	SUBCLONAL	1	TRUE	1	0.325298852895117	2		302	410	SUCCESS
ATR	545	MSKCC	GRCh37	3	142223982	142223982	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	39	432	0	ENST00000350721.4:c.5195A>G	p.Gln1732Arg	p.Q1732R	ENST00000350721	NM_001184.3	1732	cAg/cGg	29/47	1	2	FACETS	0.396	0.327	0.472	0.396	0.327	0.472	SUBCLONAL	1	TRUE	1	0.325298852895117	2		432	606	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948102	178948102	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	58	225	0	ENST00000263967.3:c.2874G>T	p.Gln958His	p.Q958H	ENST00000263967	NM_006218.2	958	caG/caT	20/21	1	2	FACETS	0.874	0.753	1	0.874	0.753	1	CLONAL	1	TRUE	1	0.325298852895117	2		225	408	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604674	55604674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334133798	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	112	420	0	ENST00000288135.5:c.2882G>A	p.Gly961Asp	p.G961D	ENST00000288135	NM_000222.2	961	gGc/gAc	21/21	0.223394888516944	1	FACETS	0.936	0.844	1	0.936	0.844	1	CLONAL	1	TRUE	0	0.325298852895117	1		420	616	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955970	55955970	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs779170295	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	96	368	0	ENST00000263923.4:c.3193-1G>A		p.X1065_splice	ENST00000263923	NM_002253.2	1065			0.223394888516944	1	FACETS	0.941	0.842	1	0.941	0.842	1	CLONAL	1	TRUE	0	0.325298852895117	1		368	525	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249412	153249412	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	91	494	0	ENST00000281708.4:c.1366A>G	p.Thr456Ala	p.T456A	ENST00000281708	NM_033632.3	456	Acc/Gcc	9/12	0.223394888516944	1	FACETS	0.656	0.582	0.735	0.656	0.582	0.735	SUBCLONAL	1	TRUE	0	0.325298852895117	1		494	714	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524677	187524677	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201075554	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	166	641	1	ENST00000441802.2:c.11003G>A	p.Arg3668Gln	p.R3668Q	ENST00000441802	NM_005245.3	3668	cGg/cAg	19/27	0.223394888516944	1	FACETS	0.95	0.872	1	0.95	0.872	1	CLONAL	1	TRUE	0	0.325298852895117	1		642	900	SUCCESS
APC	324	MSKCC	GRCh37	5	112170712	112170712	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	104	467	1	ENST00000257430.4:c.1808A>G	p.Lys603Arg	p.K603R	ENST00000257430	NM_000038.5	603	aAa/aGa	15/16	1	2	FACETS	0.887	0.794	0.985	0.887	0.794	0.985	CLONAL	1	TRUE	1	0.325298852895117	2		468	721	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721025	176721025	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587784214	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	92	508	0	ENST00000439151.2:c.6656G>A	p.Arg2219His	p.R2219H	ENST00000439151	NM_022455.4	2219	cGt/cAt	23/23	1	2	FACETS	0.844	0.751	0.944	0.844	0.751	0.944	CLONAL	1	TRUE	1	0.325298852895117	2		508	670	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120433	94120433	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	70	360	0	ENST00000369303.4:c.618G>A	p.Trp206Ter	p.W206*	ENST00000369303	NM_004440.3	206	tgG/tgA	3/17	1	2	FACETS	0.961	0.84	1	0.961	0.84	1	CLONAL	1	TRUE	1	0.325298852895117	2		360	448	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129475	152129475	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1458898787	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	24	280	0	ENST00000206249.3:c.428A>G	p.Glu143Gly	p.E143G	ENST00000206249	NM_000125.3	143	gAg/gGg	1/8	1	2	FACETS	0.418	0.327	0.522	0.418	0.327	0.522	SUBCLONAL	1	TRUE	1	0.325298852895117	2		280	353	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962304	2962304	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	147	616	0	ENST00000396946.4:c.2233G>T	p.Gly745Cys	p.G745C	ENST00000396946	NM_032415.4	745	Ggc/Tgc	17/25	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.325298852895117	2		616	871	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221845	55221845	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs751667358	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	135	626	0	ENST00000275493.2:c.889C>T	p.Arg297Cys	p.R297C	ENST00000275493	NM_005228.3	297	Cgt/Tgt	7/28	1	2	FACETS	0.974	0.885	1	0.974	0.885	1	CLONAL	1	TRUE	1	0.325298852895117	2		626	852	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878272	151878272	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	119	495	1	ENST00000262189.6:c.6673C>T	p.Pro2225Ser	p.P2225S	ENST00000262189	NM_170606.2	2225	Cca/Tca	36/59	1	2	FACETS	0.925	0.835	1	0.925	0.835	1	CLONAL	1	TRUE	1	0.325298852895117	2		496	791	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371924	55371924	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	31	336	0	ENST00000297316.4:c.614A>C	p.Asp205Ala	p.D205A	ENST00000297316	NM_022454.3	205	gAc/gCc	2/2	1	2	FACETS	0.45	0.363	0.547	0.45	0.363	0.547	SUBCLONAL	1	TRUE	1	0.325298852895117	2		336	424	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56912001	56912001	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1347486935	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	130	464	2	ENST00000519728.1:c.1229C>T	p.Thr410Met	p.T410M	ENST00000519728	NM_002350.3	410	aCg/aTg	12/13	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.325298852895117	2		466	795	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537076	80537076	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	107	372	0	ENST00000286548.4:c.321+1G>A		p.X107_splice	ENST00000286548	NM_002072.3	107			1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.325298852895117	2		372	626	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245029	53245029	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	140	294	0	ENST00000375401.3:c.911C>A	p.Pro304His	p.P304H	ENST00000375401	NM_004187.3	304	cCc/cAc	7/26	1	1	FACETS	0.896	0.825	0.97	1	0.991	1	CLONAL	2	TRUE	0	0.325298852895117	1		294	402	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191765	123191765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	73	193	0	ENST00000218089.9:c.1354G>A	p.Gly452Arg	p.G452R	ENST00000218089	NM_001042749.1	452	Gga/Aga	15/35	1	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.325298852895117	1		193	303	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	114	463	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	0.321725306311841	2		463	614	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0039356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	158	519	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.313856308880709	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.321725306311841	1		519	818	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231357	5231357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	76	642	0	ENST00000357368.4:c.2119G>A	p.Glu707Lys	p.E707K	ENST00000357368	NM_002850.3	707	Gag/Aag	14/38	1	2	FACETS	0.638	0.559	0.724	0.638	0.559	0.724	SUBCLONAL	1	TRUE	1	0.321725306311841	2		642	740	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851165	63851165	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	54	723	0	ENST00000279873.7:c.1943del	p.Val648AlafsTer15	p.V648Afs*15	ENST00000279873	NM_032199.2	648	gTc/gc	10/10	1	2	FACETS	0.454	0.387	0.528	0.454	0.387	0.528	SUBCLONAL	1	TRUE	1	0.33	2		723	721	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821563	72821564	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0039497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	27	277	0	ENST00000268489.5:c.10611_10612del	p.Cys3539TrpfsTer31	p.C3539Wfs*31	ENST00000268489	NM_006885.3	3537	gcGCtc/gctc	10/10	1	2	FACETS	0.768	0.615	0.941	0.768	0.615	0.941	CLONAL	1	TRUE	1	0.33	2		277	213	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791824	42791824	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	68	864	0	ENST00000575354.2:c.710G>A	p.Trp237Ter	p.W237*	ENST00000575354	NM_015125.3	237	tGg/tAg	5/20	1	2	FACETS	0.699	0.608	0.796	0.699	0.608	0.796	SUBCLONAL	1	TRUE	1	0.33	2		864	590	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	142	635	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.765	0.702	0.83	0.765	0.702	0.83	SUBCLONAL	1	TRUE	1	0.776741110008193	2		635	478	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913273	NA	P-0039501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	92	698	0	ENST00000263967.3:c.1624G>C	p.Glu542Gln	p.E542Q	ENST00000263967	NM_006218.2	542	Gaa/Caa	10/21	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.776741110008193	2		698	225	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348840	89348840	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	359	1239	0	ENST00000301030.4:c.4110G>T	p.Lys1370Asn	p.K1370N	ENST00000301030	NM_001256183.1	1370	aaG/aaT	9/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.776741110008193	2		1239	891	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098903	47098903	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0039501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	218	898	0	ENST00000409792.3:c.6371T>A	p.Leu2124Ter	p.L2124*	ENST00000409792	NM_014159.6	2124	tTg/tAg	15/21	1	2	FACETS	0.955	0.894	1	0.955	0.894	1	CLONAL	1	TRUE	1	0.776741110008193	2		898	588	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412110	63412110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852216	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	215	586	1	ENST00000330258.3:c.1057C>T	p.Arg353Ter	p.R353*	ENST00000330258	NM_152424.3	353	Cga/Tga	2/2	1	1	FACETS	0.889	0.83	0.949	1	0.993	1	CLONAL	2	TRUE	0	0.305486352827369	1		587	671	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	354	1199	9	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.962	1	1	0.996	1	CLONAL	2	TRUE	1	0.305486352827369	2		1208	1138	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	106	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.305486352827369	2		473	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1185	62	385	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.326	0.28	0.376	0.326	0.28	0.376	SUBCLONAL	1	TRUE	1	0.305486352827369	2		385	1247	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	98	453	4	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.75	0.669	0.838	0.75	0.669	0.838	SUBCLONAL	1	TRUE	1	0.305486352827369	2		457	855	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427579	72427579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1424267110	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	106	398	0	ENST00000477973.2:c.911C>T	p.Thr304Met	p.T304M	ENST00000477973	NM_012234.5	304	aCg/aTg	4/4	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.305486352827369	2		398	493	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	138	556	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.305486352827369	2		557	762	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007620	45007620	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs111947448	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	59	260	0	ENST00000558401.1:c.68-1G>T		p.X23_splice	ENST00000558401	NM_004048.2	23			1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.305486352827369	2		260	369	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	90	513	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.305486352827369	2		513	525	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273105	18273105	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	213	852	2	ENST00000222254.8:c.1000del	p.Asp334ThrfsTer7	p.D334Tfs*7	ENST00000222254	NM_005027.3	332	tGg/tg	8/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.305486352827369	2		854	1292	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937659	17937659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144968714	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	235	850	1	ENST00000458235.1:c.3268G>A	p.Ala1090Thr	p.A1090T	ENST00000458235	NM_000215.3	1090	Gcc/Acc	24/24	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.305486352827369	2		851	1234	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317461	1317461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781459586	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	204	827	0	ENST00000400841.2:c.604G>A	p.Asp202Asn	p.D202N	ENST00000400841		202	Gac/Aac	5/6	1	1	FACETS	0.912	0.844	0.982	0.912	0.844	0.982	CLONAL	1	TRUE	0	0.305486352827369	1		827	1241	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343006	70343006	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556334969	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	188	371	1	ENST00000374080.3:c.1547G>A	p.Arg516His	p.R516H	ENST00000374080		516	cGt/cAt	11/45	1	1	FACETS	0.928	0.863	0.994	1	0.993	1	CLONAL	2	TRUE	0	0.305486352827369	1		372	562	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138521	11138521	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	165	778	0	ENST00000358026.2:c.3277C>T	p.Arg1093Ter	p.R1093*	ENST00000358026	NM_001128849.1	1093	Cga/Tga	24/36	1	2	FACETS	0.953	0.874	1	0.953	0.874	1	CLONAL	1	TRUE	1	0.305486352827369	2		778	1133	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678509	88678509	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373935634	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	115	652	2	ENST00000360948.2:c.1027C>T	p.Arg343Trp	p.R343W	ENST00000360948	NM_001012338.2	343	Cgg/Tgg	9/19	1	2	FACETS	0.978	0.881	1	0.978	0.881	1	CLONAL	1	TRUE	1	0.305486352827369	2		654	770	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568502	41568502	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	89	416	0	ENST00000263253.7:c.4453-1G>T		p.X1485_splice	ENST00000263253	NM_001429.3	1485			1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.305486352827369	2		416	571	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	90	429	0	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.937	0.832	1	0.937	0.832	1	CLONAL	1	TRUE	1	0.305486352827369	2		429	629	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	94	379	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.305486352827369	2		379	531	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149946	202149946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1280661555	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	149	773	0	ENST00000358485.4:c.1387G>A	p.Ala463Thr	p.A463T	ENST00000358485	NM_001080125.1	463	Gcc/Acc	8/9	1	2	FACETS	0.922	0.841	1	0.922	0.841	1	CLONAL	1	TRUE	1	0.305486352827369	2		773	1058	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	69	319	0	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	1	2	FACETS	0.82	0.715	0.933	0.82	0.715	0.933	CLONAL	1	TRUE	1	0.305486352827369	2		319	551	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132552	11132552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	226	1078	1	ENST00000358026.2:c.2768C>T	p.Ala923Val	p.A923V	ENST00000358026	NM_001128849.1	923	gCg/gTg	19/36	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.305486352827369	2		1079	1240	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431010	181431010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	226	915	0	ENST00000325404.1:c.862G>A	p.Ala288Thr	p.A288T	ENST00000325404	NM_003106.3	288	Gcc/Acc	1/1	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.305486352827369	2		915	1266	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187947	32187947	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771104755	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	232	997	1	ENST00000375023.3:c.1274C>T	p.Ser425Leu	p.S425L	ENST00000375023	NM_004557.3	425	tCg/tTg	7/30	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.305486352827369	2		998	1322	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528707	8528707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs545049137	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	103	450	1	ENST00000356435.5:c.425C>T	p.Thr142Met	p.T142M	ENST00000356435		142	aCg/aTg	4/35	0.305486352827369	3	FACETS	1	0.933	1	0.528	0.472	0.587	CLONAL	1	TRUE	1	0.305486352827369	3		451	736	SUCCESS
APC	324	MSKCC	GRCh37	5	112175541	112175541	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	32	342	0	ENST00000257430.4:c.4251del	p.Ile1418Ter	p.I1418*	ENST00000257430	NM_000038.5	1417	aTt/at	16/16	1	2	FACETS	0.371	0.3	0.451	0.371	0.3	0.451	SUBCLONAL	1	TRUE	1	0.305486352827369	2		342	565	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290231	15290231	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1334	261	1183	0	ENST00000263388.2:c.3404del	p.Gly1135ValfsTer137	p.G1135Vfs*137	ENST00000263388	NM_000435.2	1135	gGt/gt	21/33	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.305486352827369	2		1183	1595	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058747	180058748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755445139	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	149	824	3	ENST00000261937.6:c.89dup	p.Thr31AspfsTer15	p.T31Dfs*15	ENST00000261937	NM_182925.4	30	ccg/ccCg	2/30	1	2	FACETS	0.849	0.774	0.928	0.849	0.774	0.928	CLONAL	1	TRUE	1	0.305486352827369	2		827	1149	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578421	7578421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779000871	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	235	922	0	ENST00000269305.4:c.509C>T	p.Thr170Met	p.T170M	ENST00000269305	NM_001126112.2	170	aCg/aTg	5/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.305486352827369	2		922	1357	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844112	68844112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854694	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	177	600	2	ENST00000261769.5:c.700G>A	p.Ala234Thr	p.A234T	ENST00000261769	NM_004360.3	234	Gct/Act	6/16	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.305486352827369	2		602	828	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271870	15271870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528151296	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	228	1101	1	ENST00000263388.2:c.6569C>T	p.Ala2190Val	p.A2190V	ENST00000263388	NM_000435.2	2190	gCg/gTg	33/33	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.305486352827369	2		1102	1300	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841307	15841307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	178	362	1	ENST00000307771.7:c.1391G>A	p.Arg464His	p.R464H	ENST00000307771	NM_005089.3	464	cGt/cAt	11/11	1	1	FACETS	0.93	0.863	0.998	1	0.993	1	CLONAL	2	TRUE	0	0.305486352827369	1		363	531	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572092	64572093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs767319284	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	172	575	5	ENST00000312049.6:c.1546dup	p.Arg516ProfsTer15	p.R516Pfs*15	ENST00000312049	NM_130799.2	516	cgg/cCgg	10/10	1	2	FACETS	0.972	0.892	1	0.972	0.892	1	CLONAL	1	TRUE	1	0.305486352827369	2		580	1159	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279324	38279324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774768179	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	216	895	0	ENST00000425967.3:c.1165G>A	p.Val389Ile	p.V389I	ENST00000425967	NM_001174067.1	389	Gtt/Att	9/19	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.305486352827369	2		895	1289	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074207	30074207	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765100922	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	117	630	0	ENST00000338641.4:c.1469C>T	p.Pro490Leu	p.P490L	ENST00000338641	NM_000268.3	490	cCg/cTg	14/16	1	2	FACETS	0.877	0.791	0.969	0.877	0.791	0.969	CLONAL	1	TRUE	1	0.305486352827369	2		630	873	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643617	52643617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199976998	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	155	590	2	ENST00000394830.3:c.2279G>A	p.Arg760His	p.R760H	ENST00000394830	NM_018313.4	760	cGc/cAc	17/30	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.305486352827369	2		592	849	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105676	27105678	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs753766136	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	104	474	3	ENST00000324856.7:c.5299_5301del	p.Glu1767del	p.E1767del	ENST00000324856	NM_006015.4	1763	GAA/-	20/20	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.305486352827369	2		477	680	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979986	7979987	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs746723399	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	167	899	2	ENST00000319144.4:c.1350dup	p.Leu451AlafsTer27	p.L451Afs*27	ENST00000319144	NM_001139.2	450	-/G	10/15	1	2	FACETS	0.893	0.818	0.97	0.893	0.818	0.97	CLONAL	1	TRUE	1	0.305486352827369	2		901	1225	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15273335	15273335	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115582213	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	272	984	0	ENST00000263388.2:c.5854G>A	p.Val1952Met	p.V1952M	ENST00000263388	NM_000435.2	1952	Gtg/Atg	32/33	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.305486352827369	2		984	1386	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905974	50905974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746087148	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	205	1109	0	ENST00000440232.2:c.946G>A	p.Asp316Asn	p.D316N	ENST00000440232	NM_002691.3	316	Gat/Aat	8/27	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.305486352827369	2		1109	1318	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748583	40748583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444440253	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	93	565	2	ENST00000373198.4:c.2933C>T	p.Ala978Val	p.A978V	ENST00000373198	NM_133170.3	978	gCg/gTg	21/32	1	2	FACETS	0.864	0.768	0.966	0.864	0.768	0.966	CLONAL	1	TRUE	1	0.305486352827369	2		567	705	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643525	38643525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779966392	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	153	675	0	ENST00000299084.4:c.995G>A	p.Arg332His	p.R332H	ENST00000299084	NM_152594.2	332	cGt/cAt	7/7	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.305486352827369	2		675	936	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	221	999	4	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.305486352827369	2		1003	1347	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	120	776	5	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	0.150266303974982	0	FACETS	0.672	0.607	0.741			1	INDETERMINATE	1	TRUE	0	0.305486352827369	0		781	812	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1299	255	1119	9	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.305486352827369	2		1128	1554	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420273	49420273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1205083140	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	233	958	1	ENST00000301067.7:c.15476G>A	p.Arg5159Gln	p.R5159Q	ENST00000301067	NM_003482.3	5159	cGg/cAg	48/54	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.305486352827369	2		959	1255	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007752	45007753	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	91	408	0	ENST00000558401.1:c.204dup	p.Val69SerfsTer21	p.V69Sfs*21	ENST00000558401	NM_004048.2	67	gaa/gAaa	2/4	1	2	FACETS	0.955	0.849	1	0.955	0.849	1	CLONAL	1	TRUE	1	0.305486352827369	2		408	624	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226684	2226684	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	190	989	0	ENST00000398665.3:c.4164G>T	p.Glu1388Asp	p.E1388D	ENST00000398665	NM_032482.2	1388	gaG/gaT	27/28	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.305486352827369	2		989	1235	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934267	81934267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774111706	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	217	910	1	ENST00000359376.3:c.1244G>A	p.Arg415His	p.R415H	ENST00000359376	NM_002661.3	415	cGt/cAt	14/33	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.305486352827369	2		911	1203	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729964	41729964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1025790050	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	126	830	0	ENST00000242208.4:c.565G>A	p.Gly189Arg	p.G189R	ENST00000242208	NM_002192.2	189	Ggg/Agg	3/3	1	2	FACETS	0.802	0.725	0.883	0.802	0.725	0.883	CLONAL	1	TRUE	1	0.305486352827369	2		830	1029	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112323	115112324	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	rs1381943852	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	56	266	1	ENST00000257566.3:c.1416_1417del	p.Leu473ProfsTer218	p.L473Pfs*218	ENST00000257566	NM_016569.3	472	gcGCtc/gctc	7/8	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.305486352827369	2		267	348	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674227	117674227	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	145	640	0	ENST00000368508.3:c.4247C>T	p.Ala1416Val	p.A1416V	ENST00000368508	NM_002944.2	1416	gCc/gTc	26/43	1	2	FACETS	0.933	0.85	1	0.933	0.85	1	CLONAL	1	TRUE	1	0.305486352827369	2		640	1018	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917736	29917736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150966028	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1157	72	898	0	ENST00000389048.3:c.932G>A	p.Arg311His	p.R311H	ENST00000389048	NM_004304.4	311	cGt/cAt	3/29	1	2	FACETS	0.384	0.334	0.438	0.384	0.334	0.438	SUBCLONAL	1	TRUE	1	0.305486352827369	2		898	1229	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845574	128845574	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1405848770	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	184	691	0	ENST00000249373.3:c.871C>T	p.Arg291Ter	p.R291*	ENST00000249373	NM_005631.4	291	Cga/Tga	4/12	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.305486352827369	2		691	1041	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794869	42794869	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	158	874	0	ENST00000575354.2:c.1953del	p.Ala652ProfsTer76	p.A652Pfs*76	ENST00000575354	NM_015125.3	650	gCc/gc	10/20	1	2	FACETS	0.976	0.893	1	0.976	0.893	1	CLONAL	1	TRUE	1	0.305486352827369	2		874	1060	SUCCESS
APC	324	MSKCC	GRCh37	5	112175211	112175211	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	46	258	1	ENST00000257430.4:c.3920del	p.Ile1307LysfsTer14	p.I1307Kfs*14	ENST00000257430	NM_000038.5	1307	aTa/aa	16/16	1	2	FACETS	0.853	0.721	0.998	0.853	0.721	0.998	CLONAL	1	TRUE	1	0.305486352827369	2		259	353	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21630862	21630862	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202110155	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	129	709	1	ENST00000421138.2:c.742G>A	p.Ala248Thr	p.A248T	ENST00000421138		248	Gca/Aca	8/16	0.150266303974982	0	FACETS	0.632	0.572	0.695			1	INDETERMINATE	1	TRUE	0	0.305486352827369	0		710	928	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411266	63411266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778813513	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	192	544	0	ENST00000330258.3:c.1901G>A	p.Arg634His	p.R634H	ENST00000330258	NM_152424.3	634	cGt/cAt	2/2	1	1	FACETS	0.876	0.815	0.939	1	0.993	1	CLONAL	2	TRUE	0	0.305486352827369	1		544	608	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGG	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1409	173	1227	0	ENST00000220592.5:c.1804_1806dup	p.Pro602dup	p.P602dup	ENST00000220592	NM_012154.3	602	-/CCC	14/19	1	2	FACETS	0.716	0.656	0.778	0.716	0.656	0.778	SUBCLONAL	1	TRUE	1	0.305486352827369	2		1227	1582	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321399	1321399	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	142	428	1	ENST00000400841.2:c.356C>A	p.Pro119His	p.P119H	ENST00000400841		119	cCc/cAc	4/6	1	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.305486352827369	1		429	681	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880926	134880926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371083718	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	164	685	0	ENST00000398015.3:c.1489C>T	p.Arg497Trp	p.R497W	ENST00000398015	NM_004441.4	497	Cgg/Tgg	7/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.305486352827369	2		685	916	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900206	101900206	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs727503470	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	101	383	0	ENST00000374994.4:c.640G>T	p.Gly214Cys	p.G214C	ENST00000374994	NM_004612.2	214	Ggt/Tgt	4/9	0.305486352827369	3	FACETS	1	0.928	1	0.524	0.468	0.583	CLONAL	1	TRUE	1	0.305486352827369	3		383	727	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222199	2222199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375005675	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1238	275	1171	0	ENST00000398665.3:c.3031C>T	p.Arg1011Trp	p.R1011W	ENST00000398665	NM_032482.2	1011	Cgg/Tgg	24/28	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.305486352827369	2		1171	1513	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375463	15375463	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747608142	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	231	1075	2	ENST00000263377.2:c.964C>T	p.Arg322Trp	p.R322W	ENST00000263377	NM_058243.2	322	Cgg/Tgg	6/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.305486352827369	2		1077	1345	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128419995	128419995	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1238730432	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	394	898	0	ENST00000265960.3:c.433C>T	p.Arg145Cys	p.R145C	ENST00000265960	NM_001006617.1	145	Cgc/Tgc	4/12	0.305486352827369	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.305486352827369	3		898	1413	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436549	110436549	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1002089942	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	231	1092	0	ENST00000375856.3:c.1852G>A	p.Ala618Thr	p.A618T	ENST00000375856	NM_003749.2	618	Gcg/Acg	1/2	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.305486352827369	2		1092	1282	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916193	9916193	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	51	626	0	ENST00000330684.3:c.2096C>A	p.Pro699His	p.P699H	ENST00000330684	NM_001134407.1	699	cCc/cAc	10/13	1	2	FACETS	0.382	0.323	0.447	0.382	0.323	0.447	SUBCLONAL	1	TRUE	1	0.305486352827369	2		626	874	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817741	3817741	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	134	573	0	ENST00000262367.5:c.3230C>A	p.Pro1077His	p.P1077H	ENST00000262367	NM_004380.2	1077	cCt/cAt	16/31	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.305486352827369	2		573	868	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494606	2494606	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	62	871	0	ENST00000355716.4:c.746A>G	p.Glu249Gly	p.E249G	ENST00000355716	NM_003820.2	249	gAa/gGa	8/8	1	2	FACETS	0.361	0.31	0.416	0.361	0.31	0.416	SUBCLONAL	1	TRUE	1	0.305486352827369	2		871	1125	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775749	9775749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150205370	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	225	1036	0	ENST00000377346.4:c.292G>A	p.Val98Ile	p.V98I	ENST00000377346	NM_005026.3	98	Gtc/Atc	4/24	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.305486352827369	2		1036	1345	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294234	11294235	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs746242022	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	186	671	1	ENST00000361445.4:c.2296dup	p.Arg766ProfsTer24	p.R766Pfs*24	ENST00000361445	NM_004958.3	766	cga/cCga	14/58	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.305486352827369	2		672	1088	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260335	16260335	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	144	612	0	ENST00000375759.3:c.7600C>A	p.Leu2534Met	p.L2534M	ENST00000375759	NM_015001.2	2534	Ctg/Atg	11/15	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.305486352827369	2		612	896	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797846	45797846	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138089183	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	190	869	0	ENST00000450313.1:c.925C>T	p.Arg309Cys	p.R309C	ENST00000450313	NM_012222.2	309	Cgc/Tgc	10/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.305486352827369	2		869	1071	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65323362	65323362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	144	610	1	ENST00000342505.4:c.1435G>A	p.Val479Ile	p.V479I	ENST00000342505	NM_002227.2	479	Gtc/Atc	10/25	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.305486352827369	2		611	829	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120502048	120502048	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1352414422	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	118	469	1	ENST00000256646.2:c.1993C>T	p.Arg665Cys	p.R665C	ENST00000256646	NM_024408.3	665	Cgc/Tgc	12/34	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.305486352827369	2		470	643	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663754	241663754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758370443	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	175	884	0	ENST00000366560.3:c.1373C>T	p.Ala458Val	p.A458V	ENST00000366560	NM_000143.3	458	gCt/gTt	9/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.305486352827369	2		884	1095	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675417	241675417	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1298815479	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	54	358	0	ENST00000366560.3:c.405T>G	p.His135Gln	p.H135Q	ENST00000366560	NM_000143.3	135	caT/caG	4/10	1	2	FACETS	0.873	0.748	1	0.873	0.748	1	CLONAL	1	TRUE	1	0.305486352827369	2		358	405	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100630	8100630	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	173	1180	0	ENST00000346208.3:c.604C>A	p.Arg202Ser	p.R202S	ENST00000346208		202	Cgt/Agt	3/6	1	2	FACETS	0.957	0.879	1	0.957	0.879	1	CLONAL	1	TRUE	1	0.305486352827369	2		1180	1184	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741571	17741571	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	93	524	0	ENST00000250003.3:c.242T>C	p.Val81Ala	p.V81A	ENST00000250003	NM_002478.4	81	gTg/gCg	1/3	1	2	FACETS	0.894	0.795	0.999	0.894	0.795	0.999	CLONAL	1	TRUE	1	0.305486352827369	2		524	681	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948208	71948208	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1415	324	1321	0	ENST00000298229.2:c.2920G>C	p.Ala974Pro	p.A974P	ENST00000298229	NM_001567.3	974	Gcc/Ccc	26/28	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.305486352827369	2		1321	1739	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143518	108143518	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	120	519	0	ENST00000278616.4:c.3223A>G	p.Thr1075Ala	p.T1075A	ENST00000278616	NM_000051.3	1075	Aca/Gca	22/63	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.305486352827369	2		519	674	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190758	108190758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	79	429	0	ENST00000278616.4:c.6425C>T	p.Thr2142Ile	p.T2142I	ENST00000278616	NM_000051.3	2142	aCa/aTa	44/63	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.305486352827369	2		429	507	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307295	118307295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	20	53	0	ENST00000534358.1:c.68G>A	p.Gly23Glu	p.G23E	ENST00000534358	NM_005933.3	23	gGg/gAg	1/36	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.305486352827369	2		53	103	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360547	118360547	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	143	544	0	ENST00000534358.1:c.4520C>T	p.Pro1507Leu	p.P1507L	ENST00000534358	NM_005933.3	1507	cCt/cTt	12/36	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.305486352827369	2		544	858	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499668	18499669	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	140	605	2	ENST00000266497.5:c.1526dup	p.Asn509LysfsTer4	p.N509Kfs*4	ENST00000266497		508	gta/gtAa	10/31	0.150266303974982	0	FACETS	0.763	0.695	0.835			1	INDETERMINATE	1	TRUE	0	0.305486352827369	0		607	834	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431180	49431180	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886049478	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	193	893	1	ENST00000301067.7:c.9959C>T	p.Ala3320Val	p.A3320V	ENST00000301067	NM_003482.3	3320	gCc/gTc	34/54	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.305486352827369	2		894	1129	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484308	50484308	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	184	696	3	ENST00000394963.4:c.1068G>T	p.Glu356Asp	p.E356D	ENST00000394963	NM_003076.4	356	gaG/gaT	9/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.305486352827369	2		699	1064	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145109	58145109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555201333	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	174	648	0	ENST00000257904.6:c.235G>A	p.Ala79Thr	p.A79T	ENST00000257904	NM_000075.3	79	Gcc/Acc	3/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.305486352827369	2		648	958	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32890665	32890665	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs81002796	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	62	307	0	ENST00000380152.3:c.67+1G>A		p.X23_splice	ENST00000380152		23			1	2	FACETS	0.822	0.711	0.942	0.822	0.711	0.942	CLONAL	1	TRUE	1	0.305486352827369	2		307	494	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557644	95557644	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	125	564	0	ENST00000393063.1:c.5423T>C	p.Met1808Thr	p.M1808T	ENST00000393063	NM_030621.3	1808	aTg/aCg	26/28	1	2	FACETS	0.932	0.843	1	0.932	0.843	1	CLONAL	1	TRUE	1	0.305486352827369	2		564	878	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054381	42054381	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	99	366	1	ENST00000219905.7:c.7565A>G	p.Gln2522Arg	p.Q2522R	ENST00000219905	NM_001164273.1	2522	cAa/cGa	22/24	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.305486352827369	2		367	560	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43767868	43767868	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1405887521	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	152	646	1	ENST00000382044.4:c.980C>T	p.Pro327Leu	p.P327L	ENST00000382044	NM_001141980.1	327	cCt/cTt	9/28	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.305486352827369	2		647	926	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996269	73996269	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	11	62	0	ENST00000318443.5:c.1003G>A	p.Glu335Lys	p.E335K	ENST00000318443	NM_001024736.1	335	Gag/Aag	5/10	1	2	FACETS	1	0.767	1	1	0.767	1	CLONAL	1	TRUE	1	0.305486352827369	2		62	65	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832684	3832684	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	118	504	0	ENST00000262367.5:c.1573+1G>A		p.X525_splice	ENST00000262367	NM_004380.2	525			1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.305486352827369	2		504	749	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662297	67662297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	114	538	1	ENST00000264010.4:c.1543C>T	p.Arg515Cys	p.R515C	ENST00000264010	NM_006565.3	515	Cgc/Tgc	9/12	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.305486352827369	2		539	727	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832571	72832571	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764024381	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	98	452	0	ENST00000268489.5:c.4010G>T	p.Ser1337Ile	p.S1337I	ENST00000268489	NM_006885.3	1337	aGc/aTc	9/10	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.305486352827369	2		452	605	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925158	81925158	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	141	658	0	ENST00000359376.3:c.949C>A	p.Pro317Thr	p.P317T	ENST00000359376	NM_002661.3	317	Ccc/Acc	11/33	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.305486352827369	2		658	880	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572962	7572963	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	123	527	0	ENST00000269305.4:c.1146dup	p.Leu383ThrfsTer9	p.L383Tfs*9	ENST00000269305	NM_001126112.2	382	-/A	11/11	1	2	FACETS	0.878	0.793	0.968	0.878	0.793	0.968	CLONAL	1	TRUE	1	0.305486352827369	2		527	917	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011114	12011114	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	37	321	0	ENST00000353533.5:c.521G>A	p.Cys174Tyr	p.C174Y	ENST00000353533	NM_003010.3	174	tGt/tAt	5/11	1	2	FACETS	0.589	0.486	0.705	0.589	0.486	0.705	SUBCLONAL	1	TRUE	1	0.305486352827369	2		321	411	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011210	12011210	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	36	303	0	ENST00000353533.5:c.617G>A	p.Gly206Asp	p.G206D	ENST00000353533	NM_003010.3	206	gGc/gAc	5/11	1	2	FACETS	0.721	0.594	0.862	0.721	0.594	0.862	SUBCLONAL	1	TRUE	1	0.305486352827369	2		303	327	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657589	37657589	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1214870582	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	152	659	0	ENST00000447079.4:c.2506A>G	p.Ile836Val	p.I836V	ENST00000447079	NM_015083.1	836	Atc/Gtc	6/14	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.305486352827369	2		659	961	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682337	37682337	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	151	750	2	ENST00000447079.4:c.3528G>T	p.Glu1176Asp	p.E1176D	ENST00000447079	NM_015083.1	1176	gaG/gaT	13/14	1	2	FACETS	0.975	0.89	1	0.975	0.89	1	CLONAL	1	TRUE	1	0.305486352827369	2		752	1014	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40461396	40461396	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	126	703	0	ENST00000345506.4:c.2116T>G	p.Phe706Val	p.F706V	ENST00000345506	NM_003152.3	706	Ttt/Gtt	19/20	1	2	FACETS	0.976	0.884	1	0.976	0.884	1	CLONAL	1	TRUE	1	0.305486352827369	2		703	845	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870634	40870634	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	144	584	0	ENST00000428826.2:c.769T>C	p.Tyr257His	p.Y257H	ENST00000428826		257	Tat/Cat	9/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.305486352827369	2		584	803	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47684666	47684666	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	176	601	0	ENST00000347630.2:c.783del	p.Lys262ArgfsTer24	p.K262Rfs*24	ENST00000347630	NM_001007230.1	261	ggG/gg	9/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.305486352827369	2		601	981	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857753	59857753	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs770750488	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	83	360	0	ENST00000259008.2:c.1804G>T	p.Asp602Tyr	p.D602Y	ENST00000259008	NM_032043.2	602	Gat/Tat	13/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.305486352827369	2		360	495	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006802	62006802	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	175	890	0	ENST00000392795.3:c.586A>G	p.Thr196Ala	p.T196A	ENST00000392795	NM_001039933.1	196	Acc/Gcc	5/6	1	2	FACETS	0.961	0.883	1	0.961	0.883	1	CLONAL	1	TRUE	1	0.305486352827369	2		890	1192	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120480	70120480	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1377	241	1182	0	ENST00000245479.2:c.1486del	p.Gln496SerfsTer27	p.Q496Sfs*27	ENST00000245479	NM_000346.3	494	agC/ag	3/3	1	2	FACETS	0.975	0.908	1	0.975	0.908	1	CLONAL	1	TRUE	1	0.305486352827369	2		1182	1618	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45377665	45377666	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	74	247	1	ENST00000262160.6:c.763dup	p.Ser255PhefsTer4	p.S255Ffs*4	ENST00000262160	NM_005901.5	255	tcc/tTcc	7/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.305486352827369	2		248	324	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60795965	60795965	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	135	647	0	ENST00000333681.4:c.613A>C	p.Ser205Arg	p.S205R	ENST00000333681		205	Agc/Cgc	3/3	1	2	FACETS	0.952	0.865	1	0.952	0.865	1	CLONAL	1	TRUE	1	0.305486352827369	2		647	928	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210517	5210517	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	158	815	0	ENST00000357368.4:c.5450A>G	p.Gln1817Arg	p.Q1817R	ENST00000357368	NM_002850.3	1817	cAg/cGg	35/38	1	2	FACETS	0.98	0.897	1	0.98	0.897	1	CLONAL	1	TRUE	1	0.305486352827369	2		815	1055	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5258070	5258070	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	138	721	0	ENST00000357368.4:c.664G>A	p.Ala222Thr	p.A222T	ENST00000357368	NM_002850.3	222	Gcc/Acc	8/38	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.305486352827369	2		721	884	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10286284	10286284	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs900075322	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	183	666	0	ENST00000340748.4:c.532C>T	p.Arg178Trp	p.R178W	ENST00000340748		178	Cgg/Tgg	6/40	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.305486352827369	2		666	1017	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11022882	11022882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1316	261	1167	1	ENST00000327064.4:c.581G>A	p.Gly194Asp	p.G194D	ENST00000327064	NM_199141.1	194	gGc/gAc	5/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.305486352827369	2		1168	1577	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121109	11121109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778049192	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	224	917	0	ENST00000358026.2:c.2176C>T	p.Arg726Cys	p.R726C	ENST00000358026	NM_001128849.1	726	Cgt/Tgt	15/36	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.305486352827369	2		917	1350	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291804	15291804	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1242	208	1156	2	ENST00000263388.2:c.2962T>C	p.Cys988Arg	p.C988R	ENST00000263388	NM_000435.2	988	Tgc/Cgc	18/33	1	2	FACETS	0.939	0.869	1	0.939	0.869	1	CLONAL	1	TRUE	1	0.305486352827369	2		1158	1450	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211930	36211930	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1409	298	1230	2	ENST00000222270.7:c.1681C>T	p.Pro561Ser	p.P561S	ENST00000222270	NM_014727.1	561	Cct/Tct	3/37	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.305486352827369	2		1232	1707	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224174	36224174	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368273689	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	200	883	0	ENST00000222270.7:c.6724G>A	p.Val2242Met	p.V2242M	ENST00000222270	NM_014727.1	2242	Gtg/Atg	28/37	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.305486352827369	2		883	1188	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723490	52723490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs947631865	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	105	514	0	ENST00000322088.6:c.1351C>T	p.Leu451Phe	p.L451F	ENST00000322088	NM_014225.5	451	Ctt/Ttt	11/15	1	2	FACETS	0.866	0.775	0.962	0.866	0.775	0.962	CLONAL	1	TRUE	1	0.305486352827369	2		514	794	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309720	30309720	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	162	731	0	ENST00000307677.4:c.302A>G	p.Tyr101Cys	p.Y101C	ENST00000307677	NM_138578.1	101	tAc/tGc	2/3	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.305486352827369	2		731	982	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31369202	31369202	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	162	670	1	ENST00000328111.2:c.186T>G	p.Ser62Arg	p.S62R	ENST00000328111	NM_006892.3	62	agT/agG	3/23	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.305486352827369	2		671	1004	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264199	46264199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761801652	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	107	438	0	ENST00000371998.3:c.1246G>A	p.Ala416Thr	p.A416T	ENST00000371998		416	Gcc/Acc	11/23	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.305486352827369	2		438	598	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513315	44513315	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	175	934	0	ENST00000291552.4:c.620G>T	p.Arg207Ile	p.R207I	ENST00000291552	NM_006758.2	207	aGa/aTa	8/8	1	2	FACETS	0.895	0.822	0.971	0.895	0.822	0.971	CLONAL	1	TRUE	1	0.305486352827369	2		934	1280	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130433	29130434	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs876661156	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	170	724	0	ENST00000328354.6:c.276dup	p.Trp93LeufsTer15	p.W93Lfs*15	ENST00000328354	NM_007194.3	92	-/C	2/15	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.305486352827369	2		724	1055	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070891	30070891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	168	901	0	ENST00000338641.4:c.1407G>T	p.Lys469Asn	p.K469N	ENST00000338641	NM_000268.3	469	aaG/aaT	13/16	1	2	FACETS	0.882	0.809	0.959	0.882	0.809	0.959	CLONAL	1	TRUE	1	0.305486352827369	2		901	1247	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458474	12458474	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	198	807	0	ENST00000287820.6:c.1091A>C	p.Lys364Thr	p.K364T	ENST00000287820	NM_015869.4	364	aAa/aCa	6/7	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.305486352827369	2		807	1151	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114684	73114684	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	112	565	0	ENST00000356692.5:c.1065G>T	p.Glu355Asp	p.E355D	ENST00000356692		355	gaG/gaT	9/9	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.305486352827369	2		565	687	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445112	89445112	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	71	367	0	ENST00000336596.2:c.1431+1G>A		p.X477_splice	ENST00000336596	NM_005233.5	477			1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.305486352827369	2		367	448	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456730	138456730	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	67	405	0	ENST00000289153.2:c.622-2A>G		p.X208_splice	ENST00000289153	NM_006219.2	208			1	2	FACETS	0.836	0.727	0.953	0.836	0.727	0.953	CLONAL	1	TRUE	1	0.305486352827369	2		405	525	SUCCESS
ATR	545	MSKCC	GRCh37	3	142212117	142212117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	93	543	1	ENST00000350721.4:c.5935G>A	p.Gly1979Ser	p.G1979S	ENST00000350721	NM_001184.3	1979	Ggt/Agt	35/47	1	2	FACETS	0.914	0.813	1	0.914	0.813	1	CLONAL	1	TRUE	1	0.305486352827369	2		544	666	SUCCESS
ATR	545	MSKCC	GRCh37	3	142232468	142232468	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	78	408	0	ENST00000350721.4:c.4516C>A	p.Leu1506Ile	p.L1506I	ENST00000350721	NM_001184.3	1506	Ctt/Att	26/47	1	2	FACETS	0.978	0.862	1	0.978	0.862	1	CLONAL	1	TRUE	1	0.305486352827369	2		408	522	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281817	142281818	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs755919155	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	104	552	0	ENST00000350721.4:c.426dup	p.Gly143TrpfsTer12	p.G143Wfs*12	ENST00000350721	NM_001184.3	142	-/T	4/47	1	2	FACETS	0.885	0.793	0.984	0.885	0.793	0.984	CLONAL	1	TRUE	1	0.305486352827369	2		552	769	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442765	187442765	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	119	645	1	ENST00000232014.4:c.1941C>A	p.Ser647Arg	p.S647R	ENST00000232014	NM_001130845.1	647	agC/agA	9/10	1	2	FACETS	0.955	0.862	1	0.955	0.862	1	CLONAL	1	TRUE	1	0.305486352827369	2		646	816	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156073	106156073	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	97	351	0	ENST00000380013.4:c.974A>G	p.Gln325Arg	p.Q325R	ENST00000380013	NM_001127208.2	325	cAa/cGa	3/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.305486352827369	2		351	527	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950345	38950345	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	122	475	0	ENST00000357387.3:c.3605G>T	p.Arg1202Met	p.R1202M	ENST00000357387	NM_152756.3	1202	aGg/aTg	31/38	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.305486352827369	2		475	712	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593379	67593379	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	89	336	0	ENST00000274335.5:c.2125T>C	p.Ser709Pro	p.S709P	ENST00000274335		709	Tcc/Ccc	15/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.305486352827369	2		336	486	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80057481	80057481	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1473854805	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	50	267	0	ENST00000265081.6:c.1880G>A	p.Ser627Asn	p.S627N	ENST00000265081	NM_002439.4	627	aGc/aAc	13/24	1	2	FACETS	0.989	0.843	1	0.989	0.843	1	CLONAL	1	TRUE	1	0.305486352827369	2		267	331	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923342	131923342	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	54	282	0	ENST00000265335.6:c.845T>C	p.Met282Thr	p.M282T	ENST00000265335		282	aTg/aCg	6/25	1	2	FACETS	0.985	0.845	1	0.985	0.845	1	CLONAL	1	TRUE	1	0.305486352827369	2		282	359	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720932	176720932	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	64	609	0	ENST00000439151.2:c.6563A>G	p.Glu2188Gly	p.E2188G	ENST00000439151	NM_022455.4	2188	gAa/gGa	23/23	1	2	FACETS	0.497	0.429	0.571	0.497	0.429	0.571	SUBCLONAL	1	TRUE	1	0.305486352827369	2		609	843	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180049785	180049785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752151539	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	225	1011	0	ENST00000261937.6:c.1603G>A	p.Val535Met	p.V535M	ENST00000261937	NM_182925.4	535	Gtg/Atg	12/30	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.305486352827369	2		1011	1329	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402744	20402744	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	87	487	0	ENST00000346618.3:c.281C>T	p.Thr94Ile	p.T94I	ENST00000346618	NM_001949.4	94	aCc/aTc	1/7	1	2	FACETS	0.851	0.754	0.955	0.851	0.754	0.955	CLONAL	1	TRUE	1	0.305486352827369	2		487	669	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839999	27839999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1469620010	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	66	579	0	ENST00000328488.2:c.95C>T	p.Ala32Val	p.A32V	ENST00000328488	NM_003533.2	32	gCc/gTc	1/1	1	2	FACETS	0.597	0.517	0.683	0.597	0.517	0.683	SUBCLONAL	1	TRUE	1	0.305486352827369	2		579	724	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679701	30679701	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	187	734	0	ENST00000376406.3:c.2018A>T	p.Glu673Val	p.E673V	ENST00000376406	NM_014641.2	673	gAg/gTg	5/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.305486352827369	2		734	1107	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287463	33287463	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	147	661	0	ENST00000374542.5:c.1634C>A	p.Ala545Asp	p.A545D	ENST00000374542	NM_001141970.1	545	gCt/gAt	6/8	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.305486352827369	2		661	941	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708997	117708997	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768882618	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	142	589	0	ENST00000368508.3:c.1960C>T	p.Pro654Ser	p.P654S	ENST00000368508	NM_002944.2	654	Cca/Tca	13/43	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.305486352827369	2		589	773	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005597	150005597	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	97	348	0	ENST00000253339.5:c.628G>T	p.Asp210Tyr	p.D210Y	ENST00000253339		210	Gat/Tat	3/7	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.305486352827369	2		348	527	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528772	157528772	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	164	710	0	ENST00000346085.5:c.6497G>T	p.Gly2166Val	p.G2166V	ENST00000346085	NM_020732.3	2166	gGg/gTg	20/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.305486352827369	2		710	923	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161807840	161807840	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	116	429	0	ENST00000366898.1:c.1153G>A	p.Gly385Arg	p.G385R	ENST00000366898	NM_004562.2	385	Gga/Aga	10/12	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.305486352827369	2		429	699	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434564	140434564	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1481562268	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	73	232	0	ENST00000288602.6:c.2134G>A	p.Ala712Thr	p.A712T	ENST00000288602	NM_004333.4	712	Gcc/Acc	18/18	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.305486352827369	2		232	332	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151833939	151833939	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs751058113	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	129	614	0	ENST00000262189.6:c.14714A>G	p.Asn4905Ser	p.N4905S	ENST00000262189	NM_170606.2	4905	aAc/aGc	59/59	1	2	FACETS	0.897	0.812	0.986	0.897	0.812	0.986	CLONAL	1	TRUE	1	0.305486352827369	2		614	942	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285890	38285890	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	131	733	0	ENST00000425967.3:c.521C>T	p.Thr174Ile	p.T174I	ENST00000425967	NM_001174067.1	174	aCa/aTa	5/19	1	2	FACETS	0.938	0.851	1	0.938	0.851	1	CLONAL	1	TRUE	1	0.305486352827369	2		733	914	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372396	55372396	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	255	1075	1	ENST00000297316.4:c.1086A>T	p.Glu362Asp	p.E362D	ENST00000297316	NM_022454.3	362	gaA/gaT	2/2	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.305486352827369	2		1076	1474	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572612	141572612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	184	824	0	ENST00000220592.5:c.458G>A	p.Ser153Asn	p.S153N	ENST00000220592	NM_012154.3	153	aGc/aAc	4/19	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.305486352827369	2		824	1050	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229404	98229404	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	64	301	2	ENST00000331920.6:c.2554C>A	p.Leu852Ile	p.L852I	ENST00000331920	NM_000264.3	852	Ctt/Att	15/24	0.305486352827369	3	FACETS	0.831	0.72	0.952	0.416	0.36	0.476	CLONAL	1	TRUE	1	0.305486352827369	3		303	581	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128268619	128268619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770427858	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1169	485	1032	1	ENST00000265960.3:c.1036G>A	p.Ala346Thr	p.A346T	ENST00000265960	NM_001006617.1	346	Gca/Aca	8/12	0.305486352827369	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.305486352827369	3		1033	1654	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341566	70341566	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	233	435	0	ENST00000374080.3:c.1001C>A	p.Pro334His	p.P334H	ENST00000374080		334	cCt/cAt	7/45	1	1	FACETS	0.967	0.907	1	1	0.994	1	CLONAL	2	TRUE	0	0.305486352827369	1		435	668	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356751	70356751	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	183	479	2	ENST00000374080.3:c.5423G>T	p.Arg1808Leu	p.R1808L	ENST00000374080		1808	cGg/cTg	38/45	1	1	FACETS	0.902	0.837	0.967	1	0.993	1	CLONAL	2	TRUE	0	0.305486352827369	1		481	563	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202655	108202655	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	35	400	1	ENST00000278616.4:c.7679T>A	p.Ile2560Lys	p.I2560K	ENST00000278616	NM_000051.3	2560	aTa/aAa	52/63	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	FALSE	1	0.41617863496404	2		401	143	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0039871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	335	894	0	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	0.590394591832537	1	FACETS	0.984	0.935	1	0.984	0.935	1	CLONAL	1	TRUE	0	0.590394591832537	1		894	813	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217326	11217336	+	protein_altering_variant	In_Frame_Del	DEL	TCATACCAGGT	TCATACCAGGT	GTAAC	novel	NA	P-0039871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	51	767	1	ENST00000361445.4:c.4342_4352delinsGTTAC	p.Thr1448_Glu1451delinsValThr	p.T1448_E1451delinsVT	ENST00000361445	NM_004958.3	1448	ACCTGGTATGAg/GTTACg	30/58	0.590394591832537	1	FACETS	0.165	0.139	0.193	0.165	0.139	0.193	SUBCLONAL	1	TRUE	0	0.590394591832537	1		768	739	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872216	45872216	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	230	823	0	ENST00000391945.4:c.218G>C	p.Cys73Ser	p.C73S	ENST00000391945	NM_000400.3	73	tGc/tCc	4/23	1	2	FACETS	0.891	0.832	0.952	0.891	0.832	0.952	CLONAL	1	TRUE	1	0.590394591832537	2		823	874	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84384716	84384716	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	166	358	1	ENST00000321945.7:c.727C>A	p.Leu243Ile	p.L243I	ENST00000321945	NM_139076.2	243	Cta/Ata	8/9	1	2	FACETS	0.872	0.804	0.942	0.872	0.804	0.942	CLONAL	1	TRUE	1	0.590394591832537	2		359	645	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860806	151860806	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778258336	NA	P-0039871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	159	443	0	ENST00000262189.6:c.9856C>T	p.Pro3286Ser	p.P3286S	ENST00000262189	NM_170606.2	3286	Ccc/Tcc	43/59	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.590394591832537	2		443	535	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911404	39911405	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0039871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	180	651	0	ENST00000378444.4:c.5225_5226del	p.Glu1742ValfsTer6	p.E1742Vfs*6	ENST00000378444	NM_001123385.1	1742	gAG/g	15/15	1	2	FACETS	0.749	0.692	0.809	0.749	0.692	0.809	SUBCLONAL	1	TRUE	1	0.590394591832537	2		651	814	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0040005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	29	463	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.217385946124324	0	FACETS	0.711	0.574	0.866			1	SUBCLONAL	1	TRUE	0	0.261691492957689	0		463	230	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0040005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	120	584	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.261691492957689	1	FACETS	0.94	0.848	1	0.94	0.848	1	CLONAL	1	TRUE	0	0.261691492957689	1		585	848	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	32	706	0	ENST00000263967.3:c.278G>C	p.Arg93Pro	p.R93P	ENST00000263967	NM_006218.2	93	cGg/cCg	2/21	1	2	FACETS	0.693	0.563	0.839	0.693	0.563	0.839	SUBCLONAL	1	TRUE	1	0.261691492957689	2		706	353	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612074	43612074	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	63	960	0	ENST00000355710.3:c.2179G>C	p.Gly727Arg	p.G727R	ENST00000355710	NM_020975.4	727	Gga/Cga	12/20	0.160625908449829	4	FACETS	0.991	0.857	1	0.496	0.428	0.569	CLONAL	1	TRUE	2	0.261691492957689	4		960	613	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411285	63411285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1313722059	NA	P-0040005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	83	1061	0	ENST00000330258.3:c.1882G>T	p.Ala628Ser	p.A628S	ENST00000330258	NM_152424.3	628	Gcc/Tcc	2/2	0.213900679442823	1	FACETS	0.486	0.427	0.549	0.486	0.427	0.549	SUBCLONAL	1	TRUE	0	0.261691492957689	1		1061	1135	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0040306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	88	208	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.2604195383447	2	FACETS	1	0.944	1	1	0.99	1	CLONAL	5	TRUE	0	0.2604195383447	2		208	132	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119932	70119932	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	96	368	0	ENST00000245479.2:c.934C>T	p.Gln312Ter	p.Q312*	ENST00000245479	NM_000346.3	312	Cag/Tag	3/3	1	2	FACETS	0.805	0.721	0.894	1	0.983	1	CLONAL	2	TRUE	1	0.2604195383447	2		368	458	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913527	NA	P-0040306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	46	270	0	ENST00000311936.3:c.436G>C	p.Ala146Pro	p.A146P	ENST00000311936	NM_004985.3	146	Gca/Cca	4/5	0.2208390766894	4	FACETS	0.819	0.694	0.954	0.819	0.694	0.954	CLONAL	2	TRUE	2	0.2604195383447	4		270	272	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0040306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	58	330	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.2208390766894	4	FACETS	1	0.886	1	1	0.886	1	CLONAL	2	TRUE	2	0.2604195383447	4		330	274	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371801	55371801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746536924	NA	P-0040306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	35	109	0	ENST00000297316.4:c.491C>T	p.Ala164Val	p.A164V	ENST00000297316	NM_022454.3	164	gCg/gTg	2/2	1	2	FACETS	0.835	0.694	0.988	1	0.959	1	CLONAL	2	TRUE	1	0.2604195383447	2		109	161	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433953	49433953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	100	594	0	ENST00000301067.7:c.7600del	p.Met2534CysfsTer9	p.M2534Cfs*9	ENST00000301067	NM_003482.3	2534	Atg/tg	31/54	0.2208390766894	4	FACETS	1	0.974	1	0.651	0.582	0.725	CLONAL	1	TRUE	2	0.2604195383447	4		594	743	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4090597	4090598	+	frameshift_variant,stop_lost	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	89	403	0	ENST00000262948.5:c.1201dup	p.Ter401LeufsTer12	p.*401Lfs*12	ENST00000262948	NM_030662.3	401	tga/tTga	11/11	0.151594035889079	3	FACETS	1	0.973	1	0.667	0.592	0.747	INDETERMINATE	1	TRUE	1	0.2604195383447	3		403	579	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987092	69987092	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	72	365	0	ENST00000394351.3:c.153G>T	p.Leu51Phe	p.L51F	ENST00000394351	NM_000248.3	51	ttG/ttT	2/9	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.2604195383447	2		365	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0040307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	146	656	4	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.386385377052367	2		660	527	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0040307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	35	894	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.386385377052367	2		894	138	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720671	89720671	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587782607	NA	P-0040307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	15	143	0	ENST00000371953.3:c.822G>A	p.Trp274Ter	p.W274*	ENST00000371953	NM_000314.4	274	tgG/tgA	8/9	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.386385377052367	2		143	52	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720681	89720681	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	15	138	0	ENST00000371953.3:c.833del	p.Phe278SerfsTer13	p.F278Sfs*13	ENST00000371953	NM_000314.4	278	Ttc/tc	8/9	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.386385377052367	2		138	61	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0040327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	338	788	0	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	0.295019653335794	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.313149538235729	2		788	1068	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922694	44922694	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397514628	NA	P-0040327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	57	340	0	ENST00000377967.4:c.1555C>T	p.Arg519Ter	p.R519*	ENST00000377967	NM_021140.2	519	Cga/Tga	16/29	1	2	FACETS	0.816	0.702	0.941	0.816	0.702	0.941	CLONAL	1	TRUE	1	0.313149538235729	2		340	446	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487610	56487610	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	106	633	0	ENST00000267101.3:c.1543G>T	p.Gly515Cys	p.G515C	ENST00000267101	NM_001982.3	515	Ggt/Tgt	13/28	0.313149538235729	4	FACETS	0.837	0.749	0.931	0.279	0.249	0.311	CLONAL	1	TRUE	1	0.313149538235729	4		633	1062	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046563	30046563	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	530	561	1	ENST00000331968.5:c.2620G>T	p.Gly874Cys	p.G874C	ENST00000331968	NM_002742.2	874	Ggc/Tgc	18/18	0.313149538235729	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	4	TRUE	0	0.313149538235729	4		562	1037	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005534	150005534	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	58	315	0	ENST00000253339.5:c.691G>T	p.Gly231Ter	p.G231*	ENST00000253339		231	Gga/Tga	3/7	1	2	FACETS	0.98	0.846	1	0.98	0.846	1	CLONAL	1	TRUE	1	0.313149538235729	2		315	378	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193205431	193205431	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	74	394	0	ENST00000367435.3:c.1362C>G	p.Phe454Leu	p.F454L	ENST00000367435	NM_024529.4	454	ttC/ttG	15/17	1	2	FACETS	0.803	0.712	0.897	0.803	0.712	0.897	CLONAL	1	TRUE	1	0.734599302784081	2		394	251	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980428	201980429	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0040329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	260	594	0	ENST00000359651.3:c.163+2dup		p.X55_splice	ENST00000359651		55			1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.734599302784081	2		594	619	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894228	NA	P-0040329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	167	636	0	ENST00000451590.1:c.37G>C	p.Gly13Arg	p.G13R	ENST00000451590	NM_001130442.1	13	Ggt/Cgt	2/5	1	2	FACETS	0.953	0.884	1	0.953	0.884	1	CLONAL	1	TRUE	1	0.734599302784081	2		636	477	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575553	64575553	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	193	522	0	ENST00000312049.6:c.464C>G	p.Ser155Cys	p.S155C	ENST00000312049	NM_130799.2	155	tCc/tGc	3/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.734599302784081	2		522	478	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572535	95572535	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852978	NA	P-0040329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	34	229	0	ENST00000393063.1:c.2830C>T	p.Arg944Ter	p.R944*	ENST00000393063	NM_030621.3	944	Cga/Tga	19/28	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.734599302784081	2		229	68	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0040329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	153	595	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.734599302784081	2		595	382	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5081802	5081802	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	37	228	0	ENST00000381652.3:c.2512G>C	p.Asp838His	p.D838H	ENST00000381652	NM_004972.3	838	Gac/Cac	19/25	0.734599302784081	2	FACETS	0.884	0.779	0.982	0.884	0.779	0.982	CLONAL	2	TRUE	0	0.734599302784081	2		228	57	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412905	49412905	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519951	NA	P-0040334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	344	699	0	ENST00000418115.1:c.118G>C	p.Glu40Gln	p.E40Q	ENST00000418115	NM_001664.2	40	Gag/Cag	2/5	0.584504430674477	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.584504430674477	1		699	739	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692830	89692830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782343	NA	P-0040334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	78	156	1	ENST00000371953.3:c.314G>A	p.Cys105Tyr	p.C105Y	ENST00000371953	NM_000314.4	105	tGt/tAt	5/9	0.584504430674477	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.584504430674477	1		157	166	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923118	48923127	+	frameshift_variant	Frame_Shift_Del	DEL	TGGTGCTAAA	TGGTGCTAAA	-	novel	NA	P-0040334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	38	202	0	ENST00000267163.4:c.566_575del	p.Leu189Ter	p.L189*	ENST00000267163	NM_000321.2	189	tTGGTGCTAAAa/ta	6/27	0.584504430674477	1	FACETS	0.545	0.456	0.64	0.545	0.456	0.64	SUBCLONAL	1	TRUE	0	0.584504430674477	1		202	169	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242114	105242142	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGATGGCGGTTGTCCACTCCTCCCTGCAG	GGATGGCGGTTGTCCACTCCTCCCTGCAG	-	novel	NA	P-0040334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	193	704	0	ENST00000349310.3:c.288-6_310del		p.X96_splice	ENST00000349310	NM_001014432.1	96		6/15	0.161442523108	4	FACETS	1	0.985	1	0.622	0.576	0.67	INDETERMINATE	1	TRUE	2	0.584504430674477	4		704	841	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577508	7577514	+	frameshift_variant	Frame_Shift_Del	DEL	TCCAGTG	TCCAGTG	-	novel	NA	P-0040334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	202	706	0	ENST00000269305.4:c.767_773del	p.Thr256LysfsTer87	p.T256Kfs*87	ENST00000269305	NM_001126112.2	256	aCACTGGAa/aa	7/11	0.584504430674477	1	FACETS	0.988	0.925	1	0.988	0.925	1	CLONAL	1	TRUE	0	0.584504430674477	1		706	495	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881440	37881440	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	199	647	0	ENST00000269571.5:c.2632C>T	p.His878Tyr	p.H878Y	ENST00000269571		878	Cat/Tat	21/27	0.335752789919993	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	FALSE	2	0.340019225080812	4		647	709	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	145	653	0	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	0.335752789919993	4	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	FALSE	2	0.340019225080812	4		653	542	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881392	37881392	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	222	793	0	ENST00000269571.5:c.2584A>G	p.Thr862Ala	p.T862A	ENST00000269571		862	Aca/Gca	21/27	0.335752789919993	4	FACETS	0.985	0.918	1	0.985	0.918	1	CLONAL	2	FALSE	2	0.340019225080812	4		793	888	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	94	425	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.497715734643191	2		426	373	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	207	257	1	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.982	0.913	1	0.982	0.913	1	CLONAL	1	TRUE	1	0.497715734643191	2		258	847	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743932	41743933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs778012871	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	239	789	2	ENST00000301178.4:c.874dup	p.His292ProfsTer47	p.H292Pfs*47	ENST00000301178	NM_021913.4	289	-/C	7/20	1	2	FACETS	0.941	0.878	1	0.941	0.878	1	CLONAL	1	TRUE	1	0.497715734643191	2		791	1021	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	112	359	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.911	0.824	1	0.911	0.824	1	CLONAL	1	TRUE	1	0.497715734643191	2		360	494	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750394	133750394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	165	395	0	ENST00000318560.5:c.1225G>A	p.Glu409Lys	p.E409K	ENST00000318560	NM_005157.4	409	Gag/Aag	7/11	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.497715734643191	2		395	663	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	189	337	0	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.959	0.888	1	0.959	0.888	1	CLONAL	1	TRUE	1	0.497715734643191	2		337	792	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412110	63412110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852216	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	173	586	1	ENST00000330258.3:c.1057C>T	p.Arg353Ter	p.R353*	ENST00000330258	NM_152424.3	353	Cga/Tga	2/2	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.497715734643191	1		587	386	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	150	366	2	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.497715734643191	2		368	569	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513282	44513287	+	inframe_deletion	In_Frame_Del	DEL	CCACCG	CCACCG	-	rs745888281	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	113	1024	0	ENST00000291552.4:c.648_653del	p.Gly222_Gly223del	p.G222_G223del	ENST00000291552	NM_006758.2	216	ggCGGTGGt/ggt	8/8	1	2	FACETS	0.641	0.578	0.709	0.641	0.578	0.709	SUBCLONAL	1	TRUE	1	0.497715734643191	2		1024	708	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	154	410	2	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.948	0.87	1	0.948	0.87	1	CLONAL	1	TRUE	1	0.497715734643191	2		412	653	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981721	101981721	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555075353	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	95	195	0	ENST00000282441.5:c.147del	p.Ala50ProfsTer24	p.A50Pfs*24	ENST00000282441	NM_001130145.2	48	Ccc/cc	1/9	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.497715734643191	2		195	329	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016266	150016266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771498477	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	110	283	0	ENST00000253339.5:c.440G>A	p.Arg147Gln	p.R147Q	ENST00000253339		147	cGa/cAa	2/7	1	2	FACETS	0.801	0.722	0.884	0.801	0.722	0.884	CLONAL	1	TRUE	1	0.497715734643191	2		283	552	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656840	45656840	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	37	465	5	ENST00000407780.3:c.316del	p.Gln106ArgfsTer11	p.Q106Rfs*11	ENST00000407780	NM_001283052.1	106	Cag/ag	3/7	1	2	FACETS	0.225	0.185	0.271	0.225	0.185	0.271	SUBCLONAL	1	TRUE	1	0.497715734643191	2		470	660	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	199	1199	9	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.945	0.877	1	0.945	0.877	1	CLONAL	1	TRUE	1	0.497715734643191	2		1208	846	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793332	139793332	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376801177	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	154	365	0	ENST00000247668.2:c.140C>T	p.Ala47Val	p.A47V	ENST00000247668	NM_021138.3	47	gCg/gTg	2/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.497715734643191	2		365	585	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316397	14316397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782457908	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	114	369	0	ENST00000256196.4:c.208G>A	p.Ala70Thr	p.A70T	ENST00000256196		70	Gca/Aca	3/6	1	2	FACETS	0.946	0.857	1	0.946	0.857	1	CLONAL	1	TRUE	1	0.497715734643191	2		369	484	SUCCESS
RET	5979	MSKCC	GRCh37	10	43595970	43595970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	169	568	1	ENST00000355710.3:c.137C>T	p.Ala46Val	p.A46V	ENST00000355710	NM_020975.4	46	gCc/gTc	2/20	1	2	FACETS	0.986	0.909	1	0.986	0.909	1	CLONAL	1	TRUE	1	0.497715734643191	2		569	689	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227679	53227679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	18	157	0	ENST00000375401.3:c.2509G>A	p.Glu837Lys	p.E837K	ENST00000375401	NM_004187.3	837	Gaa/Aaa	17/26	1	1	FACETS	0.24	0.181	0.31	0.24	0.181	0.31	SUBCLONAL	1	TRUE	0	0.497715734643191	1		157	226	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136243	202136243	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	91	290	0	ENST00000358485.4:c.487A>G	p.Met163Val	p.M163V	ENST00000358485	NM_001080125.1	163	Atg/Gtg	3/9	1	2	FACETS	0.775	0.691	0.864	0.775	0.691	0.864	SUBCLONAL	1	TRUE	1	0.497715734643191	2		290	472	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	172	536	5	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	0.896	0.826	0.969	0.896	0.826	0.969	CLONAL	1	TRUE	1	0.497715734643191	2		541	771	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434562	49434562	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	100	625	1	ENST00000301067.7:c.6991del	p.Leu2331Ter	p.L2331*	ENST00000301067	NM_003482.3	2331	Ctg/tg	31/54	0.472374280822776	3	FACETS	0.432	0.384	0.482	0.216	0.192	0.241	SUBCLONAL	1	TRUE	1	0.497715734643191	3		626	1163	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	161	657	0	ENST00000220592.5:c.1805_1806dup	p.Ala603ProfsTer93	p.A603Pfs*93	ENST00000220592	NM_012154.3	602	-/CC	14/19	0.472374280822776	3	FACETS	0.648	0.593	0.706	0.324	0.296	0.353	SUBCLONAL	1	TRUE	1	0.497715734643191	3		657	1246	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376248	15376248	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	202	666	3	ENST00000263377.2:c.766del	p.Gln256SerfsTer27	p.Q256Sfs*27	ENST00000263377	NM_058243.2	256	Cag/ag	5/20	1	2	FACETS	0.835	0.774	0.898	0.835	0.774	0.898	CLONAL	1	TRUE	1	0.497715734643191	2		669	972	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794899	242794899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	158	458	0	ENST00000334409.5:c.310C>T	p.Arg104Cys	p.R104C	ENST00000334409	NM_005018.2	104	Cgt/Tgt	2/5	1	2	FACETS	0.956	0.879	1	0.956	0.879	1	CLONAL	1	TRUE	1	0.497715734643191	2		458	664	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724362	112724362	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	164	391	1	ENST00000369452.4:c.252del	p.Lys84AsnfsTer7	p.K84Nfs*7	ENST00000369452	NM_007373.3	82	agA/ag	2/9	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.497715734643191	2		392	647	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246929	10246929	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	186	467	0	ENST00000340748.4:c.4476C>A	p.Phe1492Leu	p.F1492L	ENST00000340748		1492	ttC/ttA	37/40	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.497715734643191	2		467	741	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202936	16202936	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	119	375	0	ENST00000375759.3:c.644T>C	p.Val215Ala	p.V215A	ENST00000375759	NM_015001.2	215	gTa/gCa	3/15	1	2	FACETS	0.849	0.769	0.933	0.849	0.769	0.933	CLONAL	1	TRUE	1	0.497715734643191	2		375	563	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023611	27023611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	89	222	0	ENST00000324856.7:c.719del	p.Gly240AlafsTer123	p.G240Afs*123	ENST00000324856	NM_006015.4	239	ccG/cc	1/20	1	2	FACETS	0.936	0.836	1	0.936	0.836	1	CLONAL	1	TRUE	1	0.497715734643191	2		222	382	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809573	36809573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367878651	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	193	539	0	ENST00000373129.3:c.892C>T	p.Arg298Trp	p.R298W	ENST00000373129	NM_032017.1	298	Cgg/Tgg	10/12	1	2	FACETS	0.903	0.836	0.972	0.903	0.836	0.972	CLONAL	1	TRUE	1	0.497715734643191	2		539	859	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305346	39305346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs553068233	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	153	387	0	ENST00000373001.3:c.1079G>A	p.Arg360Gln	p.R360Q	ENST00000373001	NM_022157.3	360	cGa/cAa	7/7	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.497715734643191	2		387	599	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491184	120491184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587730290	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	102	371	0	ENST00000256646.2:c.2605C>T	p.Arg869Trp	p.R869W	ENST00000256646	NM_024408.3	869	Cgg/Tgg	17/34	1	2	FACETS	0.815	0.732	0.902	0.815	0.732	0.902	CLONAL	1	TRUE	1	0.497715734643191	2		371	503	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740287	162740287	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	70	206	0	ENST00000367921.3:c.1492del	p.Glu498ArgfsTer10	p.E498Rfs*10	ENST00000367921	NM_006182.2	497	Ggg/gg	12/18	1	2	FACETS	0.963	0.848	1	0.963	0.848	1	CLONAL	1	TRUE	1	0.497715734643191	2		206	292	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711898	89711898	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	39	331	1	ENST00000371953.3:c.516G>T	p.Arg172Ser	p.R172S	ENST00000371953	NM_000314.4	172	agG/agT	6/9	1	2	FACETS	0.269	0.222	0.322	0.269	0.222	0.322	SUBCLONAL	1	TRUE	1	0.497715734643191	2		332	582	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104377093	104377093	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	143	437	0	ENST00000369902.3:c.1204G>T	p.Gly402Cys	p.G402C	ENST00000369902	NM_016169.3	402	Ggt/Tgt	10/12	1	2	FACETS	0.918	0.84	0.999	0.918	0.84	0.999	CLONAL	1	TRUE	1	0.497715734643191	2		437	626	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577154	64577154	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	204	546	0	ENST00000312049.6:c.428T>G	p.Leu143Arg	p.L143R	ENST00000312049	NM_130799.2	143	cTc/cGc	2/10	1	2	FACETS	0.88	0.816	0.945	0.88	0.816	0.945	CLONAL	1	TRUE	1	0.497715734643191	2		546	932	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023599	1023602	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	ATTA	ATTA	-	novel	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	99	324	0	ENST00000358495.3:c.962_965del	p.Leu321SerfsTer13	p.L321Sfs*13	ENST00000358495	NM_134424.2	321	tTAATc/tc	10/12	0.472374280822776	3	FACETS	0.797	0.713	0.887	0.399	0.356	0.444	SUBCLONAL	1	TRUE	1	0.497715734643191	3		324	623	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438084	110438084	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1483570448	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	178	370	0	ENST00000375856.3:c.317A>G	p.Asp106Gly	p.D106G	ENST00000375856	NM_003749.2	106	gAc/gGc	1/2	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.497715734643191	2		370	696	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052527	42052527	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	88	215	0	ENST00000219905.7:c.7198C>T	p.Pro2400Ser	p.P2400S	ENST00000219905	NM_001164273.1	2400	Cca/Tca	20/24	1	2	FACETS	0.846	0.754	0.943	0.846	0.754	0.943	CLONAL	1	TRUE	1	0.497715734643191	2		215	418	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749349	43749349	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	148	388	0	ENST00000382044.4:c.1457A>G	p.His486Arg	p.H486R	ENST00000382044	NM_001141980.1	486	cAt/cGt	12/28	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.497715734643191	2		388	585	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646974	23646974	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs763726703	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	214	500	0	ENST00000261584.4:c.893T>C	p.Val298Ala	p.V298A	ENST00000261584	NM_024675.3	298	gTc/gCc	4/13	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.497715734643191	2		500	802	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827915	72827915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753622432	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	171	536	0	ENST00000268489.5:c.8666G>A	p.Arg2889Gln	p.R2889Q	ENST00000268489	NM_006885.3	2889	cGg/cAg	9/10	1	2	FACETS	0.937	0.864	1	0.937	0.864	1	CLONAL	1	TRUE	1	0.497715734643191	2		536	733	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573418	48573418	+	start_lost	Translation_Start_Site	SNP	T	T	C	rs1372924000	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	34	115	0	ENST00000342988.3:c.2T>C	p.Met1?	p.M1?	ENST00000342988	NM_005359.5	1	aTg/aCg	2/12	1	2	FACETS	0.854	0.707	1	0.854	0.707	1	CLONAL	1	TRUE	1	0.497715734643191	2		115	160	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762854	40762855	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1444704050	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	148	451	0	ENST00000392038.2:c.153dup	p.Asn53LysfsTer77	p.N53Kfs*77	ENST00000392038	NM_001626.4	51	-/C	3/14	1	2	FACETS	0.834	0.763	0.908	0.834	0.763	0.908	CLONAL	1	TRUE	1	0.497715734643191	2		451	713	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905492	50905492	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	124	667	0	ENST00000440232.2:c.623del	p.Pro208ArgfsTer68	p.P208Rfs*68	ENST00000440232	NM_002691.3	207	tCc/tc	6/27	1	2	FACETS	0.544	0.491	0.599	0.544	0.491	0.599	SUBCLONAL	1	TRUE	1	0.497715734643191	2		667	916	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527223	187527223	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	34	303	0	ENST00000441802.2:c.10350+1G>A		p.X3450_splice	ENST00000441802	NM_005245.3	3450			1	2	FACETS	0.272	0.221	0.328	0.272	0.221	0.328	SUBCLONAL	1	TRUE	1	0.497715734643191	2		303	503	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31495464	31495464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	135	360	0	ENST00000344624.3:c.1684C>T	p.Arg562Cys	p.R562C	ENST00000344624		562	Cgt/Tgt	9/33	1	2	FACETS	0.892	0.814	0.974	0.892	0.814	0.974	CLONAL	1	TRUE	1	0.497715734643191	2		360	608	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911154	29911155	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	43	504	0	ENST00000376809.5:c.453_454del	p.Asn151LysfsTer25	p.N151Kfs*25	ENST00000376809	NM_002116.7	151	aaCGag/aaag	3/8	0.486166386322651	2	FACETS	0.273	0.228	0.324	0.137	0.114	0.162	SUBCLONAL	1	TRUE	0	0.497715734643191	2		504	632	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468108	50468108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750934235	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	81	237	0	ENST00000331340.3:c.1343C>T	p.Ala448Val	p.A448V	ENST00000331340	NM_006060.4	448	gCg/gTg	8/8	1	2	FACETS	0.912	0.809	1	0.912	0.809	1	CLONAL	1	TRUE	1	0.497715734643191	2		237	357	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833910	44833910	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0040341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	112	145	0	ENST00000377967.4:c.335-1G>A		p.X112_splice	ENST00000377967	NM_021140.2	112			1	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.497715734643191	1		145	260	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307502	118307502	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs782112520	NA	P-0040343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	81	475	0	ENST00000534358.1:c.275C>G	p.Ser92Trp	p.S92W	ENST00000534358	NM_005933.3	92	tCg/tGg	1/36	0.205141216471909	6	FACETS	1	0.94	1	0.441	0.389	0.496	CLONAL	2	FALSE	1	0.205141216471909	6		475	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	180	526	0	ENST00000269305.4:c.526del	p.Cys176AlafsTer71	p.C176Afs*71	ENST00000269305	NM_001126112.2	176	Tgc/gc	5/11	0.205141216471909	6	FACETS	1	0.951	1			1	CLONAL	5	FALSE	NA	0.205141216471909	6		526	482	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846266	156846266	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	43	541	0	ENST00000524377.1:c.1707C>G	p.His569Gln	p.H569Q	ENST00000524377	NM_002529.3	569	caC/caG	14/17	0.205141216471909	2	FACETS	1	0.957	1	0.738	0.621	0.866	CLONAL	1	FALSE	0	0.205141216471909	2		541	284	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38064133	38064133	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	23	354	0	ENST00000250448.2:c.45G>T	p.Trp15Cys	p.W15C	ENST00000250448	NM_004496.3	15	tgG/tgT	1/2	0.205141216471909	0	FACETS	1	0.816	1			1	CLONAL	1	FALSE	0	0.205141216471909	0		354	171	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650859	37650859	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	91	564	0	ENST00000447079.4:c.2331C>G	p.Ile777Met	p.I777M	ENST00000447079	NM_015083.1	777	atC/atG	5/14	0.205141216471909	5	FACETS	0.955	0.853	1			1	CLONAL	3	FALSE	NA	0.205141216471909	5		564	405	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326776	62326776	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	95	751	0	ENST00000360203.5:c.3595G>A	p.Asp1199Asn	p.D1199N	ENST00000360203	NM_001283009.1	1199	Gat/Aat	34/35	0.205141216471909	9	FACETS	0.758	0.674	0.849			1	SUBCLONAL	2	FALSE	NA	0.205141216471909	9		751	1049	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638343	117638343	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	19	298	0	ENST00000368508.3:c.6098A>T	p.Asp2033Val	p.D2033V	ENST00000368508	NM_002944.2	2033	gAc/gTc	38/43	0.205141216471909	3	FACETS	1	0.872	1	0.619	0.473	0.788	CLONAL	1	FALSE	1	0.205141216471909	3		298	165	SUCCESS
AR	367	MSKCC	GRCh37	X	66765298	66765298	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	15	607	0	ENST00000374690.3:c.310C>A	p.Pro104Thr	p.P104T	ENST00000374690	NM_000044.3	104	Ccc/Acc	1/8	0.205141216471909	0	FACETS	0.554	0.405	0.731			1	SUBCLONAL	1	FALSE	0	0.205141216471909	0		607	210	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352179	70352256	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCCTTGCCTGGCTCCCCTGTGACCCTGTGTCCTCTGTCTGTTCTCCAGCTCTCTAGAGCGCTCTGGTGTATGGCTGGT	GCCTTGCCTGGCTCCCCTGTGACCCTGTGTCCTCTGTCTGTTCTCCAGCTCTCTAGAGCGCTCTGGTGTATGGCTGGT	-	novel	NA	P-0040343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	39	331	0	ENST00000374080.3:c.4254-47_4284del		p.X1418_splice	ENST00000374080		1418		31/45	0.195649965383364	0	FACETS	0.8	0.678	0.929			1	CLONAL	3	FALSE	0	0.205141216471909	0		331	126	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0040344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	134	729	2	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.830439480272956	2		731	296	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0040345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	57	463	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.863	0.749	0.985	0.863	0.749	0.985	CLONAL	1	TRUE	1	0.543458713048067	2		463	243	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0040345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	54	301	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.798	0.688	0.916	0.798	0.688	0.916	CLONAL	1	TRUE	1	0.543458713048067	2		301	249	SUCCESS
APC	324	MSKCC	GRCh37	5	112176018	112176018	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	38	194	0	ENST00000257430.4:c.4728del	p.Glu1577AsnfsTer73	p.E1577Nfs*73	ENST00000257430	NM_000038.5	1576	gAa/ga	16/16	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.543458713048067	2		194	119	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523494	41523494	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	65	241	1	ENST00000263253.7:c.910C>T	p.Gln304Ter	p.Q304*	ENST00000263253	NM_001429.3	304	Caa/Taa	4/31	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.543458713048067	2		242	188	SUCCESS
APC	324	MSKCC	GRCh37	5	112173679	112173679	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0040345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	42	247	0	ENST00000257430.4:c.2388T>G	p.Tyr796Ter	p.Y796*	ENST00000257430	NM_000038.5	796	taT/taG	16/16	1	2	FACETS	0.991	0.842	1	0.991	0.842	1	CLONAL	1	TRUE	1	0.543458713048067	2		247	156	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0040458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	60	408	0	ENST00000374080.3:c.3670C>T	p.Leu1224Phe	p.L1224F	ENST00000374080		1224	Ctc/Ttc	26/45	1	1	FACETS	0.782	0.674	0.899	1	0.971	1	SUBCLONAL	2	TRUE	0	0.13	1		408	552	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591122	67591130	+	inframe_deletion	In_Frame_Del	DEL	AGCTGAGAA	AGCTGAGAA	-	novel	NA	P-0040458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	24	292	0	ENST00000274335.5:c.1717_1725del	p.Leu573_Lys575del	p.L573_K575del	ENST00000274335		572	cAGCTGAGAAag/cag	12/15	1	2	FACETS	0.873	0.683	1	0.873	0.683	1	CLONAL	1	TRUE	1	0.13	2		292	423	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950930	32950930	+	splice_donor_variant	Splice_Site	SNP	T	T	G	rs397507412	NA	P-0040458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	35	375	0	ENST00000380152.3:c.8754+2T>G		p.X2918_splice	ENST00000380152		2918			1	2	FACETS	0.983	0.804	1	0.983	0.804	1	CLONAL	1	TRUE	1	0.13	2		375	548	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0040460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	307	330	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.384025628826195	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.384025628826195	2		330	677	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0040460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	14	774	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.384025628826195	2	FACETS	0.108	0.077	0.146	0.054	0.038	0.073	SUBCLONAL	1	TRUE	0	0.384025628826195	2		774	673	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0040460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	17	346	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.205	0.152	0.269	0.205	0.152	0.269	SUBCLONAL	1	TRUE	1	0.384025628826195	2		346	431	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912580	NA	P-0040460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	97	312	0	ENST00000342988.3:c.1157G>A	p.Gly386Asp	p.G386D	ENST00000342988	NM_005359.5	386	gGt/gAt	10/12	0.384025628826195	1	FACETS	0.859	0.77	0.954	0.859	0.77	0.954	CLONAL	1	TRUE	0	0.384025628826195	1		312	475	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885593	111885593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746192970	NA	P-0040460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	197	727	1	ENST00000341259.2:c.1370G>A	p.Arg457Gln	p.R457Q	ENST00000341259	NM_005475.2	457	cGg/cAg	7/8	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.384025628826195	2		728	1026	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579469	7579470	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGCGG	novel	NA	P-0040460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	151	667	0	ENST00000269305.4:c.217_218insCCGCG	p.Val73AlafsTer52	p.V73Afs*52	ENST00000269305	NM_001126112.2	73	gtg/gCCGCGtg	4/11	0.384025628826195	1	FACETS	0.846	0.775	0.921	0.846	0.775	0.921	CLONAL	1	TRUE	0	0.384025628826195	1		667	751	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663810	29663810	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	46	485	0	ENST00000356175.3:c.6242A>T	p.Tyr2081Phe	p.Y2081F	ENST00000356175	NM_000267.3	2081	tAc/tTc	41/57	1	2	FACETS	0.283	0.237	0.334	0.283	0.237	0.334	SUBCLONAL	1	TRUE	1	0.384025628826195	2		485	847	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	185	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.305651270388653	4	FACETS	0.92	0.852	0.989	0.92	0.852	0.989	CLONAL	2	TRUE	2	0.406508962796418	4		473	696	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0040462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	328	385	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.406508962796418	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.406508962796418	2		385	737	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798764	135798764	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749979841	NA	P-0040462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	86	237	0	ENST00000298552.3:c.479G>A	p.Arg160His	p.R160H	ENST00000298552	NM_001162426.1	160	cGt/cAt	6/23	0.202127530924112	4	FACETS	0.769	0.685	0.858	0.769	0.685	0.858	INDETERMINATE	2	TRUE	2	0.406508962796418	4		237	387	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	77	635	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.790775983895562	2		635	177	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0040464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	549	646	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.790775983895562	6	FACETS	0.922	0.886	0.958	0.922	0.886	0.958	CLONAL	3	FALSE	3	0.790775983895562	6		647	1296	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631175	176631175	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	133	532	0	ENST00000439151.2:c.1118C>T	p.Ser373Phe	p.S373F	ENST00000439151	NM_022455.4	373	tCt/tTt	4/23	0.790775983895562	6	FACETS	0.895	0.812	0.983			1	CLONAL	1	FALSE	NA	0.790775983895562	6		532	970	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0040464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	311	592	1	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	0.796215403717212	5	FACETS	1	0.991	1			1	CLONAL	2	FALSE	NA	0.790775983895562	5		593	720	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637199	176637199	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0040464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	58	547	0	ENST00000439151.2:c.1799C>G	p.Ser600Ter	p.S600*	ENST00000439151	NM_022455.4	600	tCa/tGa	5/23	0.790775983895562	6	FACETS	0.359	0.307	0.416			1	SUBCLONAL	1	FALSE	NA	0.790775983895562	6		547	1056	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151932982	151932982	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs772146328	NA	P-0040464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	82	55	0	ENST00000262189.6:c.2689C>T	p.Arg897Ter	p.R897*	ENST00000262189	NM_170606.2	897	Cga/Tga	16/59	0.553525548575578	4	FACETS	0.91	0.854	0.96			1	CLONAL	4	FALSE	NA	0.790775983895562	4		55	102	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426814	49426814	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	253	353	0	ENST00000301067.7:c.11674C>T	p.Gln3892Ter	p.Q3892*	ENST00000301067	NM_003482.3	3892	Cag/Tag	39/54	0.790775983895562	6	FACETS	1	0.988	1	0.796	0.749	0.843	CLONAL	2	FALSE	3	0.790775983895562	6		353	692	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427522	49427522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201283589	NA	P-0040464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	431	589	0	ENST00000301067.7:c.10966C>T	p.Arg3656Cys	p.R3656C	ENST00000301067	NM_003482.3	3656	Cgc/Tgc	39/54	0.790775983895562	6	FACETS	0.887	0.848	0.926	0.887	0.848	0.926	CLONAL	3	FALSE	3	0.790775983895562	6		589	1058	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281353	15281353	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	368	567	0	ENST00000263388.2:c.4903G>C	p.Glu1635Gln	p.E1635Q	ENST00000263388	NM_000435.2	1635	Gag/Cag	27/33	0.668608433541497	6	FACETS	0.905	0.862	0.948	0.905	0.862	0.948	CLONAL	3	FALSE	3	0.790775983895562	6		567	885	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426786	212426786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866491191	NA	P-0040464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	201	430	0	ENST00000342788.4:c.2329C>T	p.His777Tyr	p.H777Y	ENST00000342788	NM_005235.2	777	Cat/Tat	20/28	0.796215403717212	4	FACETS	0.896	0.838	0.955	0.896	0.838	0.955	CLONAL	2	FALSE	2	0.790775983895562	4		430	508	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022105	5022105	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1183427218	NA	P-0040464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	255	430	0	ENST00000381652.3:c.118C>T	p.Gln40Ter	p.Q40*	ENST00000381652	NM_004972.3	40	Cag/Tag	3/25	NA	2	FACETS	0.869	0.832	0.905			1	INDETERMINATE	2	FALSE	NA	0.790775983895562	2		430	371	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911475	39911475	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	342	664	0	ENST00000378444.4:c.5155G>T	p.Glu1719Ter	p.E1719*	ENST00000378444	NM_001123385.1	1719	Gaa/Taa	15/15	0.521827678589114	4	FACETS	1	0.994	1			1	CLONAL	2	FALSE	NA	0.790775983895562	4		664	630	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981896	101981896	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	329	728	0	ENST00000282441.5:c.317G>C	p.Arg106Pro	p.R106P	ENST00000282441	NM_001130145.2	106	cGa/cCa	1/9	0.600216009585834	4	FACETS	0.868	0.824	0.913	0.868	0.824	0.913	CLONAL	2	FALSE	2	0.790775983895562	4		728	858	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246393	46246393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	29	311	0	ENST00000334344.6:c.4487C>T	p.Ser1496Phe	p.S1496F	ENST00000334344	NM_152641.2	1496	tCt/tTt	15/21	0.796215403717212	4	FACETS	0.287	0.23	0.352			1	SUBCLONAL	1	FALSE	NA	0.790775983895562	4		311	458	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426859	49426859	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	297	418	1	ENST00000301067.7:c.11629C>T	p.Gln3877Ter	p.Q3877*	ENST00000301067	NM_003482.3	3877	Cag/Tag	39/54	0.790775983895562	6	FACETS	1	0.991	1	0.815	0.771	0.86	CLONAL	2	FALSE	3	0.790775983895562	6		419	793	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427111	49427111	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1281375289	NA	P-0040464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	395	620	0	ENST00000301067.7:c.11377C>G	p.Gln3793Glu	p.Q3793E	ENST00000301067	NM_003482.3	3793	Caa/Gaa	39/54	0.790775983895562	6	FACETS	1	0.993	1	0.82	0.781	0.859	CLONAL	2	FALSE	3	0.790775983895562	6		620	1049	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445514	49445514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356632640	NA	P-0040464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	68	658	2	ENST00000301067.7:c.1952C>T	p.Ser651Leu	p.S651L	ENST00000301067	NM_003482.3	651	tCg/tTg	10/54	0.790775983895562	6	FACETS	0.354	0.307	0.406	0.118	0.102	0.136	SUBCLONAL	1	FALSE	3	0.790775983895562	6		660	1254	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23640584	23640584	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	262	440	0	ENST00000261584.4:c.2527G>C	p.Glu843Gln	p.E843Q	ENST00000261584	NM_024675.3	843	Gag/Cag	6/13	0.545316889165349	5	FACETS	1	0.986	1			1	CLONAL	2	FALSE	NA	0.790775983895562	5		440	639	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348986	89348986	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	438	732	0	ENST00000301030.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000301030	NM_001256183.1	1322	Gag/Tag	9/13	0.796215403717212	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	FALSE	1	0.790775983895562	3		732	676	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40461414	40461414	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	341	668	0	ENST00000345506.4:c.2134G>C	p.Asp712His	p.D712H	ENST00000345506	NM_003152.3	712	Gat/Cat	19/20	0.790775983895562	6	FACETS	0.866	0.818	0.914	0.577	0.545	0.61	CLONAL	2	FALSE	3	0.790775983895562	6		668	1286	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533089	63533089	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs752917795	NA	P-0040464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	251	596	0	ENST00000307078.5:c.1805G>T	p.Gly602Val	p.G602V	ENST00000307078	NM_004655.3	602	gGa/gTa	7/11	0.396842512876868	4	FACETS	0.972	0.917	1			1	INDETERMINATE	2	FALSE	NA	0.790775983895562	4		596	585	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212495	5212495	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	269	535	0	ENST00000357368.4:c.4622C>G	p.Ser1541Cys	p.S1541C	ENST00000357368	NM_002850.3	1541	tCc/tGc	31/38	0.64552194985833	2	FACETS	0.846	0.81	0.881	0.846	0.81	0.881	CLONAL	2	FALSE	0	0.790775983895562	2		535	402	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281158	15281158	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	640	816	1	ENST00000263388.2:c.5098G>T	p.Asp1700Tyr	p.D1700Y	ENST00000263388	NM_000435.2	1700	Gac/Tac	27/33	0.668608433541497	6	FACETS	0.924	0.891	0.957	0.924	0.891	0.957	CLONAL	3	FALSE	3	0.790775983895562	6		817	1508	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180327	38180327	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	392	741	0	ENST00000396334.3:c.175G>C	p.Asp59His	p.D59H	ENST00000396334	NM_002468.4	59	Gac/Cac	1/5	0.597099298018082	6	FACETS	1	0.992	1	0.789	0.752	0.827	CLONAL	2	FALSE	3	0.790775983895562	6		741	1081	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631228	176631228	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	125	429	0	ENST00000439151.2:c.1171C>A	p.Gln391Lys	p.Q391K	ENST00000439151	NM_022455.4	391	Caa/Aaa	4/23	0.790775983895562	6	FACETS	1	0.906	1			1	CLONAL	1	FALSE	NA	0.790775983895562	6		429	815	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638770	176638770	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	134	572	0	ENST00000439151.2:c.3370G>T	p.Glu1124Ter	p.E1124*	ENST00000439151	NM_022455.4	1124	Gaa/Taa	5/23	0.790775983895562	6	FACETS	0.824	0.747	0.905			1	CLONAL	1	FALSE	NA	0.790775983895562	6		572	1062	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056088	26056088	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	45	370	0	ENST00000343677.2:c.569C>G	p.Ala190Gly	p.A190G	ENST00000343677	NM_005319.3	190	gCt/gGt	1/1	0.790775983895562	7	FACETS	0.413	0.346	0.487	0.069	0.057	0.082	SUBCLONAL	1	FALSE	1	0.790775983895562	7		370	821	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681589	30681589	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	62	503	1	ENST00000376406.3:c.508G>C	p.Glu170Gln	p.E170Q	ENST00000376406	NM_014641.2	170	Gag/Cag	3/15	0.790775983895562	7	FACETS	0.449	0.387	0.518			1	SUBCLONAL	1	FALSE	NA	0.790775983895562	7		504	1039	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750797	128750797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	44	583	0	ENST00000377970.2:c.334G>A	p.Asp112Asn	p.D112N	ENST00000377970	NM_002467.4	112	Gac/Aac	2/3	0.796215403717212	5	FACETS	0.287	0.24	0.34			1	SUBCLONAL	1	FALSE	NA	0.790775983895562	5		583	847	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202964	27202964	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	195	447	0	ENST00000380036.4:c.2056G>C	p.Asp686His	p.D686H	ENST00000380036	NM_000459.3	686	Gat/Cat	13/23	0.653854689338088	2	FACETS	0.819	0.777	0.86	0.819	0.777	0.86	CLONAL	2	FALSE	0	0.790775983895562	2		447	301	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347896	70347896	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	311	582	0	ENST00000374080.3:c.3135G>C	p.Glu1045Asp	p.E1045D	ENST00000374080		1045	gaG/gaC	22/45	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	FALSE	1	0.790775983895562	2		582	595	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690831	89690831	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs786204925	NA	P-0040466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	10	279	0	ENST00000371953.3:c.238A>T	p.Lys80Ter	p.K80*	ENST00000371953	NM_000314.4	80	Aaa/Taa	4/9	0.70993293011878	1	FACETS	0.134	0.09	0.187	0.134	0.09	0.187	SUBCLONAL	1	TRUE	0	0.70993293011878	1		279	136	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759566	133759566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148775794	NA	P-0040466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	106	788	1	ENST00000318560.5:c.1889G>A	p.Arg630His	p.R630H	ENST00000318560	NM_005157.4	630	cGc/cAc	11/11	1	2	FACETS	0.247	0.22	0.275	0.247	0.22	0.275	SUBCLONAL	1	TRUE	1	0.70993293011878	2		789	1209	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	240	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.69326116293774	3	FACETS	0.938	0.887	0.989	0.938	0.887	0.989	CLONAL	2	TRUE	1	0.720570195039152	3		473	483	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098815	178098815	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	570	607	4	ENST00000397062.3:c.230A>G	p.Asp77Gly	p.D77G	ENST00000397062	NM_006164.4	77	gAt/gGt	2/5	0.720570195039152	3	FACETS	0.938	0.914	0.961	0.938	0.914	0.961	CLONAL	3	TRUE	0	0.720570195039152	3		611	765	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153709	55153709	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0040483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	257	432	0	ENST00000257290.5:c.2674+1G>T		p.X892_splice	ENST00000257290	NM_006206.4	892			0.434893636560306	3	FACETS	0.893	0.845	0.942	0.893	0.845	0.942	CLONAL	2	TRUE	1	0.720570195039152	3		432	543	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38631947	38631947	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	146	405	1	ENST00000299084.4:c.433G>T	p.Glu145Ter	p.E145*	ENST00000299084	NM_152594.2	145	Gag/Tag	5/7	1	2	FACETS	0.969	0.894	1	0.969	0.894	1	CLONAL	1	TRUE	1	0.720570195039152	2		406	418	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29526904	29527465	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGCACTTTGGGAGGCTGAGGCAGAAGGATCACTTGAGCCCAGGGGTTCAAGACCAGCTTGGCCAACATGGTGAAATCCTGTCTCTACTAAAAATACAAAAATTAGCCAGGCATGGTGGCAGGCGCCTGTAAACCCAGCTACTCTGGAGGCTGAGGCGGGAGAATCGCTTGACCCTGGGAGGCAGAGGTTGCAATGAGCCAAGATCGTGCCTTTGTACTCCAGCCTGGGCAACAGAGGAAGACACCATCTTGGGAAAAAAAAAAAAAAGAAGTTCAGAAAACAGCTTGTTTGGGAAGGACTGTTTTTTGTATTCCTTTAATAATTCAATAAAGAAAATAGAAAAAGGATTTTTTTTAAATTTGAGAAACATTTAAATGATGACCACTACTTAAATTATGAAATTGAAAACCACAAATATAAATTATGCATTCTTTATAGTATGAGTTTTAGAGGCTGTTAATTTGCTATAATATTAGCTACATCTGGAATAGAAGAAACTTCATATATTATCTTATCGCTATATTTGAATTCTGTAGAAGTTATTTCTGGACAGTCTACGAAA	AGCACTTTGGGAGGCTGAGGCAGAAGGATCACTTGAGCCCAGGGGTTCAAGACCAGCTTGGCCAACATGGTGAAATCCTGTCTCTACTAAAAATACAAAAATTAGCCAGGCATGGTGGCAGGCGCCTGTAAACCCAGCTACTCTGGAGGCTGAGGCGGGAGAATCGCTTGACCCTGGGAGGCAGAGGTTGCAATGAGCCAAGATCGTGCCTTTGTACTCCAGCCTGGGCAACAGAGGAAGACACCATCTTGGGAAAAAAAAAAAAAAGAAGTTCAGAAAACAGCTTGTTTGGGAAGGACTGTTTTTTGTATTCCTTTAATAATTCAATAAAGAAAATAGAAAAAGGATTTTTTTTAAATTTGAGAAACATTTAAATGATGACCACTACTTAAATTATGAAATTGAAAACCACAAATATAAATTATGCATTCTTTATAGTATGAGTTTTAGAGGCTGTTAATTTGCTATAATATTAGCTACATCTGGAATAGAAGAAACTTCATATATTATCTTATCGCTATATTTGAATTCTGTAGAAGTTATTTCTGGACAGTCTACGAAA	-	novel	NA	P-0040483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1	209	0	0	ENST00000356175.3:c.889-533_917del		p.X297_splice	ENST00000356175	NM_000267.3	297		9/57	0.720570195039152	3	FACETS		NA	1	1	0.996	1	NA	4	TRUE	1	0.720570195039152	3		0	210	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220656	1220656	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	527	828	2	ENST00000326873.7:c.675del	p.Asn226ThrfsTer61	p.N226Tfs*61	ENST00000326873	NM_000455.4	225	gCc/gc	5/10	0.696342653026857	2	FACETS	0.936	0.908	0.964	0.936	0.908	0.964	CLONAL	2	TRUE	0	0.720570195039152	2		830	781	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217224	66217226	+	missense_variant	Missense_Mutation	TNP	CAC	CAC	ACA	novel	NA	P-0040483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	97	359	0	ENST00000273854.3:c.2389_2391delinsTGT	p.Val797Cys	p.V797C	ENST00000273854	NM_004439.5	797	GTG/TGT	14/18	0.434893636560306	3	FACETS	0.81	0.726	0.899	0.405	0.363	0.45	CLONAL	1	TRUE	1	0.720570195039152	3		359	452	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671313	30671313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	125	419	0	ENST00000376406.3:c.5564A>G	p.Asp1855Gly	p.D1855G	ENST00000376406	NM_014641.2	1855	gAt/gGt	11/15	1	2	FACETS	0.874	0.799	0.952	0.874	0.799	0.952	CLONAL	1	TRUE	1	0.720570195039152	2		419	397	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170145	32170145	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	281	830	2	ENST00000375023.3:c.3463C>A	p.Pro1155Thr	p.P1155T	ENST00000375023	NM_004557.3	1155	Cca/Aca	21/30	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.720570195039152	2		832	690	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738425	145738425	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	470	708	1	ENST00000428558.2:c.2560A>G	p.Thr854Ala	p.T854A	ENST00000428558	NM_004260.3	854	Acc/Gcc	16/22	0.678752789884382	5	FACETS	0.972	0.928	1	0.648	0.619	0.677	CLONAL	2	TRUE	2	0.720570195039152	5		709	1397	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	472199	472199	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000377-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	66	490	0	ENST00000399788.2:c.602C>T	p.Thr201Ile	p.T201I	ENST00000399788	NM_001042603.1	201	aCc/aTc	5/28	0.183966019096887	3	FACETS	0.553	0.478	0.634	0.276	0.239	0.317	SUBCLONAL	1	TRUE	1	0.246727647701265	3		490	1087	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18747428	18747428	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000377-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	30	216	0	ENST00000266497.5:c.3889A>G	p.Ser1297Gly	p.S1297G	ENST00000266497		1297	Agt/Ggt	28/31	0.183966019096887	3	FACETS	0.584	0.47	0.713	0.292	0.235	0.357	SUBCLONAL	1	TRUE	1	0.246727647701265	3		216	468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000377-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	156	324	0	ENST00000269305.4:c.313G>T	p.Gly105Cys	p.G105C	ENST00000269305	NM_001126112.2	105	Ggc/Tgc	4/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.246727647701265	2		324	872	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573321	41573321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000377-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	54	426	0	ENST00000263253.7:c.5606C>T	p.Pro1869Leu	p.P1869L	ENST00000263253	NM_001429.3	1869	cCc/cTc	31/31	1	2	FACETS	0.481	0.409	0.56	0.481	0.409	0.56	SUBCLONAL	1	TRUE	1	0.246727647701265	2		426	910	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944458	40944458	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000377-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	73	590	0	ENST00000373198.4:c.2044G>T	p.Gly682Cys	p.G682C	ENST00000373198	NM_133170.3	682	Ggt/Tgt	12/32	1	2	FACETS	0.547	0.477	0.624	0.547	0.477	0.624	SUBCLONAL	1	TRUE	1	0.246727647701265	2		590	1081	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829037	72829037	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000377-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	150	718	0	ENST00000268489.5:c.7544del	p.Ser2515Ter	p.S2515*	ENST00000268489	NM_006885.3	2515	tCa/ta	9/10	0.224372999464819	0	FACETS	0.805	0.734	0.879			1	CLONAL	1	TRUE	0	0.246727647701265	0		718	1138	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000377-T05-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	34	324	0	ENST00000269305.4:c.313G>T	p.Gly105Cys	p.G105C	ENST00000269305	NM_001126112.2	105	Ggc/Tgc	4/11	1	2	FACETS	1	0.815	1	1	0.973	1	CLONAL	4	TRUE	1	0.017	2		324	998	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0000423-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	125	205	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.395567624746134	3	FACETS	0.818	0.749	0.89	0.818	0.749	0.89	CLONAL	2	TRUE	1	0.521886736081441	3		205	369	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931463	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622007	NA	P-0000441-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	69	406	509	1	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	0.996	1	CLONAL	1	TRUE	0	0.842505833712408	1		510	475	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421645	49421645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000441-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	503	364	749	1	ENST00000301067.7:c.14584G>A	p.Ala4862Thr	p.A4862T	ENST00000301067	NM_003482.3	4862	Gca/Aca	47/54	1	2	FACETS	0.997	0.95	1	0.997	0.95	1	CLONAL	1	TRUE	1	0.842505833712408	2		750	867	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727821	41727821	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000441-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	465	302	1002	0	ENST00000301178.4:c.446C>A	p.Thr149Asn	p.T149N	ENST00000301178	NM_021913.4	149	aCt/aAt	4/20	1	2	FACETS	0.935	0.885	0.985	0.935	0.885	0.985	CLONAL	1	TRUE	1	0.842505833712408	2		1002	767	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256699	16256727	+	frameshift_variant	Frame_Shift_Del	DEL	GATATGGCCAAAATAAAACTATCTGTCTT	GATATGGCCAAAATAAAACTATCTGTCTT	-	novel	NA	P-0000441-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	193	85	376	0	ENST00000375759.3:c.3966_3994del	p.Asp1322GlufsTer3	p.D1322Efs*3	ENST00000375759	NM_015001.2	1322	GATATGGCCAAAATAAAACTATCTGTCTTg/g	11/15	0.842505833712408	1	FACETS	0.42	0.376	0.466	0.42	0.376	0.466	SUBCLONAL	1	TRUE	0	0.842505833712408	1		376	278	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929073	32929073	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000441-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	482	373	1093	0	ENST00000380152.3:c.7085del	p.Leu2362CysfsTer5	p.L2362Cfs*5	ENST00000380152		2361	caT/ca	14/27	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.842505833712408	2		1093	855	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396209	396234	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGCAGCTTCTGAGGGAGTCTTCCG	GGAGCAGCTTCTGAGGGAGTCTTCCG	-	novel	NA	P-0000441-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	855	75	474	0	ENST00000262320.3:c.792_817del	p.Arg266AspfsTer10	p.R266Dfs*10	ENST00000262320	NM_003502.3	264	ccCGGAAGACTCCCTCAGAAGCTGCTCCtg/cctg	2/11	0.842505833712408	3	FACETS	0.272	0.238	0.309	0.136	0.119	0.155	SUBCLONAL	1	TRUE	1	0.842505833712408	3		474	930	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931463	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622007	NA	P-0000441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	122	509	1	ENST00000374690.3:c.2105T>A	p.Leu702His	p.L702H	ENST00000374690	NM_000044.3	702	cTc/cAc	4/8	0.220004656137531	2	FACETS	0.968	0.885	1			1	CLONAL	3	TRUE	NA	0.240043291193637	2		510	350	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421645	49421645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	69	749	1	ENST00000301067.7:c.14584G>A	p.Ala4862Thr	p.A4862T	ENST00000301067	NM_003482.3	4862	Gca/Aca	47/54	0.115607278759932	4	FACETS	0.816	0.713	0.926	0.816	0.713	0.926	INDETERMINATE	2	TRUE	2	0.240043291193637	4		750	437	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727821	41727821	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	44	1002	0	ENST00000301178.4:c.446C>A	p.Thr149Asn	p.T149N	ENST00000301178	NM_021913.4	149	aCt/aAt	4/20	1	2	FACETS	0.837	0.703	0.985	0.837	0.703	0.985	CLONAL	1	TRUE	1	0.240043291193637	2		1002	438	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256699	16256727	+	frameshift_variant	Frame_Shift_Del	DEL	GATATGGCCAAAATAAAACTATCTGTCTT	GATATGGCCAAAATAAAACTATCTGTCTT	-	novel	NA	P-0000441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	39	376	0	ENST00000375759.3:c.3966_3994del	p.Asp1322GlufsTer3	p.D1322Efs*3	ENST00000375759	NM_015001.2	1322	GATATGGCCAAAATAAAACTATCTGTCTTg/g	11/15	0.222864984371768	1	FACETS	0.911	0.767	1	1	0.967	1	CLONAL	2	TRUE	0	0.240043291193637	1		376	157	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929073	32929073	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	96	1093	0	ENST00000380152.3:c.7085del	p.Leu2362CysfsTer5	p.L2362Cfs*5	ENST00000380152		2361	caT/ca	14/27	0.183550433892669	0	FACETS	0.817	0.734	0.904			1	CLONAL	2	TRUE	0	0.240043291193637	0		1093	372	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0001207-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	436	205	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.696625026138288	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	TRUE	1	0.696625026138288	4		205	698	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001207-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	214	495	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.696625026138288	2	FACETS	0.954	0.892	1	0.477	0.446	0.509	CLONAL	1	TRUE	0	0.696625026138288	2		495	644	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549724	187549724	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs570583897	NA	P-0001207-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	209	597	0	ENST00000441802.2:c.4517G>A	p.Arg1506His	p.R1506H	ENST00000441802	NM_005245.3	1506	cGt/cAt	8/27	0.688007401940209	2	FACETS	0.997	0.931	1	0.498	0.465	0.532	CLONAL	1	TRUE	0	0.696625026138288	2		597	602	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510610	38510610	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001207-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	290	621	0	ENST00000254066.5:c.864C>A	p.Asp288Glu	p.D288E	ENST00000254066	NM_000964.3	288	gaC/gaA	7/9	0.696625026138288	4	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.696625026138288	4		621	1221	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141557668	141557668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001207-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2199	480	839	0	ENST00000220592.5:c.1647G>A	p.Met549Ile	p.M549I	ENST00000220592	NM_012154.3	549	atG/atA	13/19	0.696625026138288	8	FACETS	0.795	0.756	0.834	0.265	0.252	0.278	SUBCLONAL	2	TRUE	2	0.696625026138288	8		839	2679	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341696	8341696	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001207-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	246	634	0	ENST00000356435.5:c.4944T>A	p.Phe1648Leu	p.F1648L	ENST00000356435		1648	ttT/ttA	29/35	0.696625026138288	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.696625026138288	1		634	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577595	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0001231-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	211	285	0	ENST00000269305.4:c.686_687del	p.Cys229TyrfsTer10	p.C229Yfs*10	ENST00000269305	NM_001126112.2	229	tGT/t	7/11	0.665748005864308	1	FACETS	0.94	0.884	0.996	0.94	0.884	0.996	CLONAL	1	TRUE	0	0.665748005864308	1		285	450	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629978	187629978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001231-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	267	440	0	ENST00000441802.2:c.1004C>T	p.Thr335Ile	p.T335I	ENST00000441802	NM_005245.3	335	aCa/aTa	2/27	0.665748005864308	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.665748005864308	1		440	512	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741858	17741858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001231-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	119	94	0	ENST00000250003.3:c.529G>A	p.Ala177Thr	p.A177T	ENST00000250003	NM_002478.4	177	Gcc/Acc	1/3	0.333806836328586	1	FACETS	1	0.976	1	1	0.976	1	INDETERMINATE	1	TRUE	0	0.665748005864308	1		94	211	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0001298-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	54	499	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.109371131662213	5	FACETS	1	0.947	1	0.609	0.525	0.7	INDETERMINATE	2	FALSE	1	0.214529393675462	5		501	273	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288684	198288684	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001298-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	38	363	0	ENST00000335508.6:c.43A>G	p.Ile15Val	p.I15V	ENST00000335508	NM_012433.2	15	Att/Gtt	2/25	0.214529393675462	4	FACETS	0.989	0.818	1	0.495	0.409	0.59	CLONAL	1	FALSE	2	0.214529393675462	4		363	435	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588836	69588836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001298-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	44	433	0	ENST00000168712.1:c.400C>T	p.Arg134Trp	p.R134W	ENST00000168712	NM_002007.2	134	Cgg/Tgg	2/3	0.214529393675462	3	FACETS	1	0.851	1	1	0.851	1	CLONAL	2	FALSE	1	0.214529393675462	3		433	226	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138571	2138571	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137854288	NA	P-0001298-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	79	404	0	ENST00000219476.3:c.5384G>A	p.Arg1795His	p.R1795H	ENST00000219476	NM_000548.3	1795	cGc/cAc	42/42	0.214529393675462	2	FACETS	0.906	0.807	1	1	0.975	1	CLONAL	3	FALSE	0	0.214529393675462	2		404	271	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827981	40827982	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0001298-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	10	206	0	ENST00000373198.4:c.2446_2447delinsAT	p.Glu816Met	p.E816M	ENST00000373198	NM_133170.3	816	GAg/ATg	17/32	0.214529393675462	1	FACETS	0.433	0.293	0.609	0.433	0.293	0.609	SUBCLONAL	1	FALSE	0	0.214529393675462	1		206	192	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	212	534	0	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	1	2	FACETS	0.984	0.923	1	0.984	0.923	1	CLONAL	1	TRUE	1	0.83	2		534	519	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	23	258	0	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	0.824311812454321	1	FACETS	0.122	0.095	0.154	0.122	0.095	0.154	SUBCLONAL	1	TRUE	0	0.83	1		258	265	SUCCESS
AR	367	MSKCC	GRCh37	X	66943543	66943543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852581	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	330	309	0	ENST00000374690.3:c.2623C>T	p.His875Tyr	p.H875Y	ENST00000374690	NM_000044.3	875	Cat/Tat	8/8	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.83	1		309	392	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258907	16258907	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200349060	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	299	525	2	ENST00000375759.3:c.6172G>A	p.Ala2058Thr	p.A2058T	ENST00000375759	NM_015001.2	2058	Gcc/Acc	11/15	1	2	FACETS	0.943	0.893	0.994	0.943	0.893	0.994	CLONAL	1	TRUE	1	0.83	2		527	764	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754943	29754943	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	21	350	0	ENST00000389048.3:c.992A>G	p.His331Arg	p.H331R	ENST00000389048	NM_004304.4	331	cAc/cGc	4/29	0.824311812454321	1	FACETS	0.114	0.087	0.145	0.114	0.087	0.145	SUBCLONAL	1	TRUE	0	0.83	1		350	260	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61720175	61720175	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	126	533	0	ENST00000401558.2:c.1259T>C	p.Met420Thr	p.M420T	ENST00000401558	NM_003400.3	420	aTg/aCg	13/25	1	2	FACETS	0.437	0.396	0.48	0.437	0.396	0.48	SUBCLONAL	1	TRUE	1	0.83	2		533	695	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251730	212251730	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	209	500	2	ENST00000342788.4:c.3329C>A	p.Thr1110Asn	p.T1110N	ENST00000342788	NM_005235.2	1110	aCc/aAc	27/28	1	2	FACETS	0.95	0.89	1	0.95	0.89	1	CLONAL	1	TRUE	1	0.83	2		502	530	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72873620	72873620	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772128613	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	298	638	1	ENST00000325599.8:c.682G>A	p.Ala228Thr	p.A228T	ENST00000325599	NM_018130.2	228	Gcc/Acc	6/11	1	2	FACETS	0.91	0.861	0.96	0.91	0.861	0.96	CLONAL	1	TRUE	1	0.83	2		639	789	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801158	1801158	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	182	397	0	ENST00000260795.2:c.287T>A	p.Val96Glu	p.V96E	ENST00000260795		96	gTg/gAg	2/17	0.824311812454321	2	FACETS	0.945	0.881	1			1	CLONAL	1	TRUE	NA	0.83	2		397	464	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961742	55961742	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs771193917	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	288	600	1	ENST00000263923.4:c.2817+2T>C		p.X939_splice	ENST00000263923	NM_002253.2	939			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.83	2		601	658	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278883	1278883	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	185	445	0	ENST00000310581.5:c.2159T>C	p.Ile720Thr	p.I720T	ENST00000310581	NM_198253.2	720	aTc/aCc	6/16	1	2	FACETS	0.955	0.89	1	0.955	0.89	1	CLONAL	1	TRUE	1	0.83	2		445	467	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457728	149457728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	240	453	0	ENST00000286301.3:c.676G>A	p.Ala226Thr	p.A226T	ENST00000286301	NM_005211.3	226	Gcc/Acc	5/22	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.83	2		453	569	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056427	26056427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs182693914	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	218	385	0	ENST00000343677.2:c.230A>G	p.Asn77Ser	p.N77S	ENST00000343677	NM_005319.3	77	aAc/aGc	1/1	0.202589645600478	3	FACETS	1	0.992	1	0.704	0.661	0.748	INDETERMINATE	1	TRUE	1	0.83	3		385	528	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005375	150005375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775410465	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	276	610	3	ENST00000253339.5:c.850G>A	p.Val284Ile	p.V284I	ENST00000253339		284	Gta/Ata	3/7	1	2	FACETS	0.999	0.944	1	0.999	0.944	1	CLONAL	1	TRUE	1	0.83	2		613	666	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201828	152201828	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	79	580	1	ENST00000206249.3:c.682A>G	p.Thr228Ala	p.T228A	ENST00000206249	NM_000125.3	228	Acc/Gcc	3/8	1	2	FACETS	0.274	0.241	0.31	0.274	0.241	0.31	SUBCLONAL	1	TRUE	1	0.83	2		581	694	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339647	116339647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	54	384	0	ENST00000397752.3:c.509G>A	p.Ser170Asn	p.S170N	ENST00000397752	NM_000245.2	170	aGc/aAc	2/21	1	2	FACETS	0.252	0.215	0.293	0.252	0.215	0.293	SUBCLONAL	1	TRUE	1	0.83	2		384	516	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415076	116415076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	272	550	1	ENST00000397752.3:c.3170C>T	p.Ala1057Val	p.A1057V	ENST00000397752	NM_000245.2	1057	gCt/gTt	15/21	1	2	FACETS	0.907	0.855	0.959	0.907	0.855	0.959	CLONAL	1	TRUE	1	0.83	2		551	723	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523672	148523672	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	276	431	0	ENST00000320356.2:c.781A>G	p.Thr261Ala	p.T261A	ENST00000320356	NM_004456.4	261	Acc/Gcc	8/20	1	2	FACETS	0.997	0.943	1	0.997	0.943	1	CLONAL	1	TRUE	1	0.83	2		431	667	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742886	145742886	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1416508252	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	16	210	0	ENST00000428558.2:c.125A>G	p.Tyr42Cys	p.Y42C	ENST00000428558	NM_004260.3	42	tAc/tGc	3/22	1	2	FACETS	0.149	0.11	0.196	0.149	0.11	0.196	SUBCLONAL	1	TRUE	1	0.83	2		210	258	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133756042	133756042	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	192	388	1	ENST00000318560.5:c.1669G>T	p.Gly557Ter	p.G557*	ENST00000318560	NM_005157.4	557	Gga/Tga	10/11	1	2	FACETS	0.974	0.91	1	0.974	0.91	1	CLONAL	1	TRUE	1	0.83	2		389	475	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631177	69631177	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	221	524	0	ENST00000334134.2:c.235A>G	p.Thr79Ala	p.T79A	ENST00000334134	NM_005247.2	79	Acg/Gcg	2/3	1	2	FACETS	0.938	0.879	0.996	0.938	0.879	0.996	CLONAL	1	TRUE	1	0.83	2		524	568	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124655	108124655	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	250	616	0	ENST00000278616.4:c.2013A>G	p.Ile671Met	p.I671M	ENST00000278616	NM_000051.3	671	atA/atG	13/63	1	2	FACETS	0.92	0.866	0.974	0.92	0.866	0.974	CLONAL	1	TRUE	1	0.83	2		616	655	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023201	1023201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	250	477	0	ENST00000358495.3:c.1054G>A	p.Ala352Thr	p.A352T	ENST00000358495	NM_134424.2	352	Gcc/Acc	11/12	1	2	FACETS	0.992	0.936	1	0.992	0.936	1	CLONAL	1	TRUE	1	0.83	2		477	607	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037514	12037514	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	123	232	0	ENST00000396373.4:c.1145A>G	p.Asn382Ser	p.N382S	ENST00000396373	NM_001987.4	382	aAc/aGc	6/8	0.824311812454321	3	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.83	3		232	337	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893318	32893318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507603	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	347	677	0	ENST00000380152.3:c.172G>A	p.Glu58Lys	p.E58K	ENST00000380152		58	Gaa/Aaa	3/27	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.83	2		677	830	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953620	32953620	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	219	360	0	ENST00000380152.3:c.8921T>C	p.Ile2974Thr	p.I2974T	ENST00000380152		2974	aTt/aCt	22/27	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.83	2		360	502	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335810	73335810	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs183862178	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	171	432	0	ENST00000377767.4:c.2485C>T	p.Arg829Cys	p.R829C	ENST00000377767	NM_014953.3	829	Cgt/Tgt	18/21	1	2	FACETS	0.604	0.557	0.653	0.604	0.557	0.653	SUBCLONAL	1	TRUE	1	0.83	2		432	682	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514517	103514517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	243	440	0	ENST00000355739.4:c.1018C>T	p.Pro340Ser	p.P340S	ENST00000355739	NM_000123.3	340	Cct/Tct	8/15	1	2	FACETS	0.982	0.925	1	0.982	0.925	1	CLONAL	1	TRUE	1	0.83	2		440	596	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243045	105243045	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	427	445	0	ENST00000349310.3:c.238T>C	p.Trp80Arg	p.W80R	ENST00000349310	NM_001014432.1	80	Tgg/Cgg	5/15	0.824311812454321	2	FACETS	0.958	0.932	0.983	0.958	0.932	0.983	CLONAL	2	TRUE	0	0.83	2		445	537	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250898	99250898	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757195696	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	270	511	0	ENST00000268035.6:c.202G>A	p.Glu68Lys	p.E68K	ENST00000268035	NM_000875.3	68	Gag/Aag	2/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.83	2		511	636	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646199	23646199	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	68	598	0	ENST00000261584.4:c.1668A>T	p.Leu556Phe	p.L556F	ENST00000261584	NM_024675.3	556	ttA/ttT	4/13	1	2	FACETS	0.241	0.209	0.276	0.241	0.209	0.276	SUBCLONAL	1	TRUE	1	0.83	2		598	679	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696432	47696432	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519968	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	301	539	1	ENST00000347630.2:c.391T>G	p.Trp131Gly	p.W131G	ENST00000347630	NM_001007230.1	131	Tgg/Ggg	6/11	1	2	FACETS	0.9	0.851	0.949	0.9	0.851	0.949	CLONAL	1	TRUE	1	0.83	2		540	806	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39629513	39629513	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	307	570	0	ENST00000262039.4:c.2207C>G	p.Thr736Ser	p.T736S	ENST00000262039	NM_002647.2	736	aCc/aGc	21/25	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.83	2		570	706	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3113388	3113388	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	276	587	0	ENST00000078429.4:c.382T>C	p.Tyr128His	p.Y128H	ENST00000078429	NM_002067.2	128	Tac/Cac	3/7	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.83	2		587	633	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4094474	4094474	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs945585174	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	197	432	0	ENST00000262948.5:c.1069C>T	p.Arg357Trp	p.R357W	ENST00000262948	NM_030662.3	357	Cgg/Tgg	10/11	1	2	FACETS	0.94	0.878	1	0.94	0.878	1	CLONAL	1	TRUE	1	0.83	2		432	505	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278074	18278074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	187	438	0	ENST00000222254.8:c.1694C>T	p.Pro565Leu	p.P565L	ENST00000222254	NM_005027.3	565	cCg/cTg	13/16	1	2	FACETS	0.821	0.764	0.879	0.821	0.764	0.879	CLONAL	1	TRUE	1	0.83	2		438	549	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743996	41743996	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	238	582	0	ENST00000301178.4:c.931T>C	p.Cys311Arg	p.C311R	ENST00000301178	NM_021913.4	311	Tgc/Cgc	7/20	1	2	FACETS	0.975	0.918	1	0.975	0.918	1	CLONAL	1	TRUE	1	0.83	2		582	588	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164725	36164725	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	196	459	0	ENST00000300305.3:c.1150C>A	p.Pro384Thr	p.P384T	ENST00000300305		384	Ccc/Acc	8/8	1	2	FACETS	0.921	0.86	0.982	0.921	0.86	0.982	CLONAL	1	TRUE	1	0.83	2		459	513	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513243	44513243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200044775	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	67	201	0	ENST00000291552.4:c.692C>T	p.Ser231Leu	p.S231L	ENST00000291552	NM_006758.2	231	tCg/tTg	8/8	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.83	NA		201	216	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143044482	143044482	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	67	541	0	ENST00000262992.4:c.1980del	p.Leu661Ter	p.L661*	ENST00000262992	NM_001101669.1	660	ggG/gg	18/24	1	2	FACETS	0.217	0.188	0.249	0.217	0.188	0.249	SUBCLONAL	1	TRUE	1	0.83	2		541	743	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005427	150005428	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	77	521	0	ENST00000253339.5:c.797dup	p.Ser267PhefsTer48	p.S267Ffs*48	ENST00000253339		266	cct/ccCt	3/7	1	2	FACETS	0.292	0.256	0.331	0.292	0.256	0.331	SUBCLONAL	1	TRUE	1	0.83	2		521	635	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100728	8100728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs771019738	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	182	469	1	ENST00000346208.3:c.708del	p.Ser237AlafsTer28	p.S237Afs*28	ENST00000346208		234	ttC/tt	3/6	1	2	FACETS	0.919	0.856	0.984	0.919	0.856	0.984	CLONAL	1	TRUE	1	0.83	2		470	477	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447773	49447773	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	207	332	0	ENST00000301067.7:c.661del	p.Ala221LeufsTer40	p.A221Lfs*40	ENST00000301067	NM_003482.3	221	Gct/ct	5/54	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.83	2		332	490	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355942	73355942	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	224	486	0	ENST00000377767.4:c.29del	p.Lys10ArgfsTer7	p.K10Rfs*7	ENST00000377767	NM_014953.3	10	aAg/ag	1/21	1	2	FACETS	0.926	0.869	0.984	0.926	0.869	0.984	CLONAL	1	TRUE	1	0.83	2		486	583	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777898	3777898	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	249	648	0	ENST00000262367.5:c.7150del	p.His2384ThrfsTer12	p.H2384Tfs*12	ENST00000262367	NM_004380.2	2384	Cac/ac	31/31	1	2	FACETS	0.898	0.845	0.952	0.898	0.845	0.952	CLONAL	1	TRUE	1	0.83	2		648	668	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100069	27100069	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0001933-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	23	193	0	ENST00000324856.7:c.3867-2A>T		p.X1289_splice	ENST00000324856	NM_006015.4	1289			0.264984445506583	1	FACETS	0.442	0.344	0.555	0.442	0.344	0.555	SUBCLONAL	1	TRUE	0	0.264984445506583	1		193	341	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439880	52439880	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001933-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	18	206	0	ENST00000460680.1:c.832G>T	p.Glu278Ter	p.E278*	ENST00000460680	NM_004656.3	278	Gag/Tag	10/17	0.264984445506583	1	FACETS	0.35	0.263	0.453	0.35	0.263	0.453	SUBCLONAL	1	TRUE	0	0.264984445506583	1		206	337	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226573330	226573330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781235145	NA	P-0001934-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	51	168	0	ENST00000366794.5:c.886G>A	p.Glu296Lys	p.E296K	ENST00000366794	NM_001618.3	296	Gag/Aag	7/23	0.53746051239231	4	FACETS	0.443	0.376	0.517	0.148	0.125	0.173	SUBCLONAL	1	TRUE	1	0.646450979394132	4		168	586	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61724058	61724058	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001934-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	225	252	0	ENST00000401558.2:c.844C>A	p.Gln282Lys	p.Q282K	ENST00000401558	NM_003400.3	282	Caa/Aaa	10/25	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.646450979394132	2		252	665	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032474	12032474	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001934-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	117	150	0	ENST00000353533.5:c.910C>T	p.Arg304Ter	p.R304*	ENST00000353533	NM_003010.3	304	Cga/Tga	9/11	0.543626683981647	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.646450979394132	1		150	238	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602619	10602619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001934-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	54	249	0	ENST00000171111.5:c.959G>A	p.Arg320Gln	p.R320Q	ENST00000171111	NM_203500.1	320	cGg/cAg	3/6	0.256371674392338	1	FACETS	0.268	0.229	0.31	0.268	0.229	0.31	INDETERMINATE	1	TRUE	0	0.646450979394132	1		249	422	SUCCESS
APC	324	MSKCC	GRCh37	5	112176064	112176064	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554086185	NA	P-0001934-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	166	218	0	ENST00000257430.4:c.4778del	p.Lys1593SerfsTer57	p.K1593Sfs*57	ENST00000257430	NM_000038.5	1591	gcA/gc	16/16	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.646450979394132	2		218	415	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112767348	112767348	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002612-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	132	356	0	ENST00000369452.4:c.1221G>C	p.Leu407Phe	p.L407F	ENST00000369452	NM_007373.3	407	ttG/ttC	6/9	0.365963884791791	3	FACETS	0.503	0.456	0.553			1	INDETERMINATE	1	TRUE	NA	0.715794880492106	3		356	996	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627559	14627563	+	frameshift_variant	Frame_Shift_Del	DEL	AGACT	AGACT	-	novel	NA	P-0002612-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	232	392	0	ENST00000254322.2:c.507_511del	p.Val170ProfsTer2	p.V170Pfs*2	ENST00000254322	NM_006145.1	169	cgAGTCTcc/cgcc	2/3	0.295556832399993	1	FACETS	0.52	0.486	0.555	0.52	0.486	0.555	INDETERMINATE	1	TRUE	0	0.715794880492106	1		392	800	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39690101	39690101	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002612-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	241	250	0	ENST00000361337.2:c.126G>T	p.Lys42Asn	p.K42N	ENST00000361337	NM_003286.2	42	aaG/aaT	3/21	1	2	FACETS	0.965	0.906	1	0.965	0.906	1	CLONAL	1	TRUE	1	0.715794880492106	2		250	698	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950580	79950580	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002612-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	108	282	0	ENST00000265081.6:c.34G>A	p.Ala12Thr	p.A12T	ENST00000265081	NM_002439.4	12	Gct/Act	1/24	0.374167711734664	1	FACETS	0.347	0.312	0.384	0.347	0.312	0.384	INDETERMINATE	1	TRUE	0	0.715794880492106	1		282	558	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	42	286	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.338819296091504	3	FACETS	1	0.953	1	0.462	0.39	0.541	CLONAL	1	TRUE	0	0.338819296091504	3		286	209	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0003306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	122	433	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	0.313716278246924	4	FACETS	1	0.917	1	1	0.917	1	CLONAL	2	TRUE	2	0.338819296091504	4		433	478	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39074472	39074472	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753147833	NA	P-0003306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	20	387	0	ENST00000357387.3:c.8C>T	p.Ala3Val	p.A3V	ENST00000357387	NM_152756.3	3	gCg/gTg	1/38	0.236317673442353	3	FACETS	0.438	0.335	0.559	0.219	0.167	0.28	SUBCLONAL	1	TRUE	1	0.338819296091504	3		387	315	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63760059	63760059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs963038555	NA	P-0003306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	33	235	0	ENST00000279873.7:c.712G>A	p.Glu238Lys	p.E238K	ENST00000279873	NM_032199.2	238	Gag/Aag	4/10	1	2	FACETS	0.714	0.584	0.859	0.714	0.584	0.859	SUBCLONAL	1	TRUE	1	0.338819296091504	2		235	273	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246431	41246431	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	46	423	0	ENST00000357654.3:c.1117A>T	p.Ile373Leu	p.I373L	ENST00000357654	NM_007294.3	373	Ata/Tta	10/23	NA	2	FACETS	0.505	0.425	0.593			1	INDETERMINATE	1	TRUE	NA	0.338819296091504	2		423	538	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65312368	65312368	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149968614	NA	P-0003419-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	45	298	0	ENST00000342505.4:c.1951G>A	p.Val651Met	p.V651M	ENST00000342505	NM_002227.2	651	Gtg/Atg	14/25	0.428185502717057	1	FACETS	0.234	0.196	0.276	0.234	0.196	0.276	SUBCLONAL	1	TRUE	0	0.465757658256735	1		298	633	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313336	65313336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1163622258	NA	P-0003419-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	141	299	0	ENST00000342505.4:c.1778C>T	p.Thr593Met	p.T593M	ENST00000342505	NM_002227.2	593	aCg/aTg	13/25	0.428185502717057	1	FACETS	0.779	0.713	0.849	0.779	0.713	0.849	SUBCLONAL	1	TRUE	0	0.465757658256735	1		299	596	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038893	12038893	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003419-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	113	325	1	ENST00000396373.4:c.1186A>G	p.Arg396Gly	p.R396G	ENST00000396373	NM_001987.4	396	Aga/Gga	7/8	NA	2	FACETS	0.458	0.411	0.508			1	INDETERMINATE	1	TRUE	NA	0.465757658256735	2		326	1059	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	97	294	2	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.309152029753516	2		296	549	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852118	63852118	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	25	230	0	ENST00000279873.7:c.2901del	p.Lys967AsnfsTer15	p.K967Nfs*15	ENST00000279873	NM_032199.2	966	Aaa/aa	10/10	0.296170981830596	3	FACETS	0.407	0.32	0.507			1	SUBCLONAL	1	TRUE	NA	0.309152029753516	3		230	459	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	32	247	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.866	0.707	1	0.866	0.707	1	CLONAL	1	TRUE	1	0.309152029753516	2		248	239	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	159	466	8	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.309152029753516	2		474	774	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	74	439	0	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	0.514	0.449	0.585	0.514	0.449	0.585	SUBCLONAL	1	TRUE	1	0.309152029753516	2		439	931	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	127	590	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.309152029753516	2		590	821	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	125	278	0	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	0.309152029753516	3	FACETS	1	0.913	1	1	0.913	1	CLONAL	2	TRUE	1	0.309152029753516	3		278	466	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	109	395	3	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.309152029753516	2		398	638	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217234	11217234	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1031980569	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	90	366	0	ENST00000361445.4:c.4444C>T	p.Arg1482Cys	p.R1482C	ENST00000361445	NM_004958.3	1482	Cgc/Tgc	30/58	1	2	FACETS	0.977	0.868	1	0.977	0.868	1	CLONAL	1	TRUE	1	0.309152029753516	2		366	596	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675571	86675571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1561325048	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	80	191	2	ENST00000274376.6:c.2513del	p.Asn838MetfsTer4	p.N838Mfs*4	ENST00000274376	NM_002890.2	836	gAa/ga	19/25	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.309152029753516	2		193	443	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029457	16029457	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	174	453	0	ENST00000268712.3:c.1573del	p.Thr525GlnfsTer30	p.T525Qfs*30	ENST00000268712	NM_006311.3	525	Aca/ca	15/46	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.309152029753516	2		453	822	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425038	49425038	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783690	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	120	481	0	ENST00000301067.7:c.13450C>T	p.Arg4484Ter	p.R4484*	ENST00000301067	NM_003482.3	4484	Cga/Tga	39/54	1	2	FACETS	0.95	0.858	1	0.95	0.858	1	CLONAL	1	TRUE	1	0.309152029753516	2		481	817	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129329	152129329	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	62	386	0	ENST00000206249.3:c.287del	p.Gly96ValfsTer13	p.G96Vfs*13	ENST00000206249	NM_000125.3	94	ctG/ct	1/8	NA	2	FACETS	0.727	0.628	0.834			1	INDETERMINATE	1	TRUE	NA	0.309152029753516	2		386	552	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671655	67671655	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1400980130	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	85	313	0	ENST00000264010.4:c.2070del	p.Glu691SerfsTer30	p.E691Sfs*30	ENST00000264010	NM_006565.3	688	gtA/gt	12/12	1	2	FACETS	0.978	0.867	1	0.978	0.867	1	CLONAL	1	TRUE	1	0.309152029753516	2		313	562	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	125	410	2	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.309152029753516	2		412	575	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204515939	204515939	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	113	317	2	ENST00000367182.3:c.842del	p.Asn281MetfsTer10	p.N281Mfs*10	ENST00000367182	NM_001278516.1	279	ggA/gg	10/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.309152029753516	2		319	577	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317099	11317099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201093943	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	127	475	2	ENST00000361445.4:c.395G>A	p.Arg132His	p.R132H	ENST00000361445	NM_004958.3	132	cGt/cAt	4/58	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.309152029753516	2		477	778	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023384	27023384	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1229573624	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	103	224	0	ENST00000324856.7:c.490G>A	p.Ala164Thr	p.A164T	ENST00000324856	NM_006015.4	164	Gcc/Acc	1/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.309152029753516	2		224	460	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	59	272	0	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	1	2	FACETS	0.837	0.722	0.962	0.837	0.722	0.962	CLONAL	1	TRUE	1	0.309152029753516	2		272	456	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120496279	120496279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	100	320	2	ENST00000256646.2:c.2252G>A	p.Gly751Asp	p.G751D	ENST00000256646	NM_024408.3	751	gGc/gAc	14/34	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.309152029753516	2		322	623	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010590	48010590	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	92	268	0	ENST00000234420.5:c.218A>G	p.Asn73Ser	p.N73S	ENST00000234420	NM_000179.2	73	aAc/aGc	1/10	0.309152029753516	2	FACETS	1	0.956	1	0.571	0.509	0.637	CLONAL	1	TRUE	0	0.309152029753516	2		268	521	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145601	61145601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1352140789	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	158	390	0	ENST00000295025.8:c.713G>A	p.Arg238His	p.R238H	ENST00000295025	NM_002908.2	238	cGt/cAt	7/11	0.309152029753516	2	FACETS	1	0.986	1	0.677	0.621	0.735	CLONAL	1	TRUE	0	0.309152029753516	2		390	755	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280754	41280754	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	92	328	0	ENST00000349496.5:c.2267T>C	p.Leu756Pro	p.L756P	ENST00000349496	NM_001904.3	756	cTg/cCg	15/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.309152029753516	2		328	521	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725205	49725205	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	31	122	0	ENST00000449682.2:c.220T>C	p.Cys74Arg	p.C74R	ENST00000449682	NM_020998.3	74	Tgt/Cgt	2/18	1	2	FACETS	0.912	0.742	1	0.912	0.742	1	CLONAL	1	TRUE	1	0.309152029753516	2		122	220	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55991458	55991458	+	start_lost	Translation_Start_Site	SNP	C	C	T	rs773557368	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	94	380	0	ENST00000263923.4:c.3G>A	p.Met1?	p.M1?	ENST00000263923	NM_002253.2	1	atG/atA	1/30	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.309152029753516	2		380	608	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197563	106197563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745668941	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	118	456	0	ENST00000380013.4:c.5896C>T	p.Arg1966Cys	p.R1966C	ENST00000380013	NM_001127208.2	1966	Cgt/Tgt	11/11	1	2	FACETS	0.972	0.877	1	0.972	0.877	1	CLONAL	1	TRUE	1	0.309152029753516	2		456	785	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542188	187542188	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	98	394	0	ENST00000441802.2:c.5552A>C	p.Asp1851Ala	p.D1851A	ENST00000441802	NM_005245.3	1851	gAc/gCc	10/27	1	2	FACETS	0.906	0.808	1	0.906	0.808	1	CLONAL	1	TRUE	1	0.309152029753516	2		394	700	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502729	149502729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777708927	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	47	323	0	ENST00000261799.4:c.2059G>A	p.Gly687Arg	p.G687R	ENST00000261799	NM_002609.3	687	Gga/Aga	15/23	1	2	FACETS	0.691	0.584	0.809	0.691	0.584	0.809	SUBCLONAL	1	TRUE	1	0.309152029753516	2		323	440	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43749782	43749782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369593555	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	201	579	1	ENST00000523873.1:c.635G>A	p.Arg212His	p.R212H	ENST00000523873		212	cGt/cAt	7/8	0.244256722542208	3	FACETS	1	0.988	1	0.67	0.62	0.721	CLONAL	1	TRUE	1	0.309152029753516	3		580	1121	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553578	106553578	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1020395697	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	41	219	0	ENST00000369096.4:c.1543G>A	p.Gly515Arg	p.G515R	ENST00000369096	NM_001198.3	515	Ggg/Agg	5/7	0.244256722542208	3	FACETS	0.92	0.769	1	0.46	0.384	0.543	CLONAL	1	TRUE	1	0.309152029753516	3		219	333	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200087	138200087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150513567	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	54	185	1	ENST00000237289.4:c.1505G>A	p.Arg502Gln	p.R502Q	ENST00000237289	NM_001270507.1	502	cGg/cAg	7/9	0.309152029753516	4	FACETS	1	0.891	1			1	CLONAL	1	TRUE	NA	0.309152029753516	4		186	436	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522283	157522283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1285642669	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	110	403	0	ENST00000346085.5:c.4555C>T	p.Arg1519Cys	p.R1519C	ENST00000346085	NM_020732.3	1519	Cgt/Tgt	18/20	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.309152029753516	2		403	593	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395560	116395560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753407699	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	144	231	0	ENST00000397752.3:c.1853C>T	p.Thr618Met	p.T618M	ENST00000397752	NM_000245.2	618	aCg/aTg	6/21	0.309152029753516	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.309152029753516	3		231	441	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752783	128752783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	69	224	0	ENST00000377970.2:c.944G>A	p.Cys315Tyr	p.C315Y	ENST00000377970	NM_002467.4	315	tGc/tAc	3/3	1	2	FACETS	0.905	0.79	1	0.905	0.79	1	CLONAL	1	TRUE	1	0.309152029753516	2		224	493	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145736822	145736822	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	114	337	0	ENST00000428558.2:c.3619G>A	p.Ala1207Thr	p.A1207T	ENST00000428558	NM_004260.3	1207	Gcc/Acc	22/22	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.309152029753516	2		337	605	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319901	8319901	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	112	447	0	ENST00000356435.5:c.5600A>G	p.Glu1867Gly	p.E1867G	ENST00000356435		1867	gAa/gGa	34/35	1	2	FACETS	0.993	0.893	1	0.993	0.893	1	CLONAL	1	TRUE	1	0.309152029753516	2		447	730	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376675	8376675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs571411218	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	100	296	0	ENST00000356435.5:c.4438G>A	p.Val1480Ile	p.V1480I	ENST00000356435		1480	Gtt/Att	27/35	1	2	FACETS	0.995	0.89	1	0.995	0.89	1	CLONAL	1	TRUE	1	0.309152029753516	2		296	650	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211514	98211514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200029534	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	65	361	0	ENST00000331920.6:c.3641C>T	p.Thr1214Met	p.T1214M	ENST00000331920	NM_000264.3	1214	aCg/aTg	22/24	1	2	FACETS	0.812	0.705	0.927	0.812	0.705	0.927	CLONAL	1	TRUE	1	0.309152029753516	2		361	518	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753910	133753910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149852028	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	96	354	0	ENST00000318560.5:c.1379G>A	p.Arg460His	p.R460H	ENST00000318560	NM_005157.4	460	cGc/cAc	8/11	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.309152029753516	2		354	576	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397706	139397706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	78	268	0	ENST00000277541.6:c.5095G>A	p.Val1699Met	p.V1699M	ENST00000277541	NM_017617.3	1699	Gtg/Atg	27/34	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.309152029753516	2		268	475	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404348	139404348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773847667	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	103	418	0	ENST00000277541.6:c.2806G>A	p.Gly936Ser	p.G936S	ENST00000277541	NM_017617.3	936	Ggc/Agc	18/34	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.309152029753516	2		418	618	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344476	118344476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782640926	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	63	249	0	ENST00000534358.1:c.2602G>A	p.Val868Met	p.V868M	ENST00000534358	NM_005933.3	868	Gtg/Atg	3/36	1	2	FACETS	0.854	0.741	0.978	0.854	0.741	0.978	CLONAL	1	TRUE	1	0.309152029753516	2		249	477	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398080	4398080	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	83	343	0	ENST00000261254.3:c.644A>G	p.Gln215Arg	p.Q215R	ENST00000261254	NM_001759.3	215	cAg/cGg	4/5	1	2	FACETS	0.829	0.732	0.933	0.829	0.732	0.933	CLONAL	1	TRUE	1	0.309152029753516	2		343	648	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437701	49437701	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555194045	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	154	621	0	ENST00000301067.7:c.5269C>T	p.Arg1757Ter	p.R1757*	ENST00000301067	NM_003482.3	1757	Cga/Tga	22/54	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.309152029753516	2		621	930	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446066	49446066	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	85	353	0	ENST00000301067.7:c.1400T>G	p.Leu467Arg	p.L467R	ENST00000301067	NM_003482.3	467	cTg/cGg	10/54	1	2	FACETS	0.929	0.822	1	0.929	0.822	1	CLONAL	1	TRUE	1	0.309152029753516	2		353	592	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858476	57858476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199685332	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	142	676	1	ENST00000228682.2:c.214C>T	p.Arg72Trp	p.R72W	ENST00000228682	NM_005269.2	72	Cgg/Tgg	4/12	1	2	FACETS	0.908	0.826	0.994	0.908	0.826	0.994	CLONAL	1	TRUE	1	0.309152029753516	2		677	1012	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201338	133201338	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	64	414	0	ENST00000320574.5:c.6806A>G	p.Tyr2269Cys	p.Y2269C	ENST00000320574	NM_006231.2	2269	tAc/tGc	49/49	1	2	FACETS	0.688	0.595	0.788	0.688	0.595	0.788	SUBCLONAL	1	TRUE	1	0.309152029753516	2		414	602	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219278	133219278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	92	328	0	ENST00000320574.5:c.4766C>T	p.Ser1589Phe	p.S1589F	ENST00000320574	NM_006231.2	1589	tCc/tTc	37/49	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.309152029753516	2		328	589	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219579	133219579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542430685	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	39	221	0	ENST00000320574.5:c.4555C>T	p.Arg1519Cys	p.R1519C	ENST00000320574	NM_006231.2	1519	Cgc/Tgc	36/49	1	2	FACETS	0.749	0.622	0.889	0.749	0.622	0.889	SUBCLONAL	1	TRUE	1	0.309152029753516	2		221	337	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563252	21563252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	80	410	0	ENST00000382592.4:c.667G>A	p.Gly223Arg	p.G223R	ENST00000382592	NM_014572.2	223	Ggg/Agg	4/8	1	2	FACETS	0.997	0.88	1	0.997	0.88	1	CLONAL	1	TRUE	1	0.309152029753516	2		410	519	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778603	3778603	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147448293	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	64	272	0	ENST00000262367.5:c.6445G>A	p.Val2149Met	p.V2149M	ENST00000262367	NM_004380.2	2149	Gtg/Atg	31/31	1	2	FACETS	0.991	0.861	1	0.991	0.861	1	CLONAL	1	TRUE	1	0.309152029753516	2		272	418	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781417	3781417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776549587	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	36	221	0	ENST00000262367.5:c.4948G>A	p.Val1650Ile	p.V1650I	ENST00000262367	NM_004380.2	1650	Gtc/Atc	30/31	1	2	FACETS	0.876	0.724	1	0.876	0.724	1	CLONAL	1	TRUE	1	0.309152029753516	2		221	266	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117573	70117573	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	94	362	0	ENST00000245479.2:c.41A>G	p.Gln14Arg	p.Q14R	ENST00000245479	NM_000346.3	14	cAg/cGg	1/3	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.309152029753516	2		362	556	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897438	78897438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	103	457	0	ENST00000306801.3:c.2773C>T	p.Arg925Trp	p.R925W	ENST00000306801	NM_020761.2	925	Cgg/Tgg	23/34	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.309152029753516	2		457	606	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7174633	7174633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs72549237	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	122	478	1	ENST00000302850.5:c.1084G>A	p.Val362Ile	p.V362I	ENST00000302850	NM_000208.2	362	Gtc/Atc	4/22	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.309152029753516	2		479	708	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105645	11105645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	72	323	0	ENST00000358026.2:c.1561C>T	p.Arg521Trp	p.R521W	ENST00000358026	NM_001128849.1	521	Cgg/Tgg	9/36	1	2	FACETS	0.91	0.796	1	0.91	0.796	1	CLONAL	1	TRUE	1	0.309152029753516	2		323	512	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276788	15276788	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	111	466	0	ENST00000263388.2:c.5477G>A	p.Cys1826Tyr	p.C1826Y	ENST00000263388	NM_000435.2	1826	tGc/tAc	30/33	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.309152029753516	2		466	656	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281554	15281554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	115	460	0	ENST00000263388.2:c.4819G>A	p.Ala1607Thr	p.A1607T	ENST00000263388	NM_000435.2	1607	Gcc/Acc	26/33	1	2	FACETS	0.97	0.874	1	0.97	0.874	1	CLONAL	1	TRUE	1	0.309152029753516	2		460	767	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919079	50919079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064795958	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	88	497	0	ENST00000440232.2:c.2816C>T	p.Ser939Leu	p.S939L	ENST00000440232	NM_002691.3	939	tCg/tTg	22/27	0.309152029753516	1	FACETS	0.768	0.681	0.86	0.768	0.681	0.86	SUBCLONAL	1	TRUE	0	0.309152029753516	1		497	627	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032747	30032747	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555986860	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	98	261	0	ENST00000338641.4:c.122G>A	p.Trp41Ter	p.W41*	ENST00000338641	NM_000268.3	41	tGg/tAg	2/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.309152029753516	2		261	485	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431595	431595	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	113	287	0	ENST00000399788.2:c.2414del	p.Lys805SerfsTer17	p.K805Sfs*17	ENST00000399788	NM_001042603.1	805	aAg/ag	17/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.309152029753516	2		287	560	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430775	78430775	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	97	311	0	ENST00000370768.2:c.614del	p.Gly205GlufsTer17	p.G205Efs*17	ENST00000370768	NM_003902.3	205	gGa/ga	8/20	1	2	FACETS	0.906	0.808	1	0.906	0.808	1	CLONAL	1	TRUE	1	0.309152029753516	2		311	693	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115780	8115780	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	183	563	2	ENST00000346208.3:c.1131del	p.Val378CysfsTer26	p.V378Cfs*26	ENST00000346208		376	Aaa/aa	6/6	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.309152029753516	2		565	1073	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56852600	56852600	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	150	535	1	ENST00000308159.5:c.518del	p.Pro173LeufsTer25	p.P173Lfs*25	ENST00000308159	NM_014669.4	172	Ccc/cc	6/22	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.309152029753516	2		536	869	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180979	32180981	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	60	373	0	ENST00000375023.3:c.2369_2371del	p.Ser790del	p.S790del	ENST00000375023	NM_004557.3	790	tCCTgc/tgc	15/30	NA	2	FACETS	0.734	0.633	0.844			1	INDETERMINATE	1	TRUE	NA	0.309152029753516	2		373	529	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845830	72845830	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	154	617	0	ENST00000268489.5:c.3637del	p.Thr1213GlnfsTer31	p.T1213Qfs*31	ENST00000268489	NM_006885.3	1213	Aca/ca	6/10	1	2	FACETS	0.96	0.877	1	0.96	0.877	1	CLONAL	1	TRUE	1	0.309152029753516	2		617	1038	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71019947	71019950	+	frameshift_variant	Frame_Shift_Del	DEL	GGAA	GGAA	-	novel	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	52	272	0	ENST00000318789.4:c.1659_1662del	p.Ser554LeufsTer44	p.S554Lfs*44	ENST00000318789	NM_032682.5	553	ccTTCC/cc	19/21	1	2	FACETS	0.628	0.534	0.73	0.628	0.534	0.73	SUBCLONAL	1	TRUE	1	0.309152029753516	2		272	536	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181929	32181929	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	95	475	0	ENST00000375023.3:c.2125del	p.Gln709SerfsTer22	p.Q709Sfs*22	ENST00000375023	NM_004557.3	709	Cag/ag	13/30	NA	2	FACETS	1	0.947	1			1	INDETERMINATE	1	TRUE	NA	0.309152029753516	2		475	559	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005408	150005409	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	87	345	0	ENST00000253339.5:c.816_817del	p.Gln273AsnfsTer41	p.Q273Nfs*41	ENST00000253339		272	tcTCaa/tcaa	3/7	NA	2	FACETS	0.952	0.844	1			1	INDETERMINATE	1	TRUE	NA	0.309152029753516	2		345	591	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759976	63759977	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	97	247	1	ENST00000279873.7:c.635dup	p.Ile213HisfsTer18	p.I213Hfs*18	ENST00000279873	NM_032199.2	210	ctg/ctGg	4/10	0.296170981830596	3	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.309152029753516	3		248	553	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619159	43619159	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs794728689	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	65	386	0	ENST00000355710.3:c.2846del	p.Gly949GlufsTer16	p.G949Efs*16	ENST00000355710	NM_020975.4	948	Ggg/gg	17/20	0.296170981830596	3	FACETS	0.897	0.779	1			1	CLONAL	1	TRUE	NA	0.309152029753516	3		386	541	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760264	133760264	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	44	278	0	ENST00000318560.5:c.2591del	p.Gly864AlafsTer12	p.G864Afs*12	ENST00000318560	NM_005157.4	863	Ggg/gg	11/11	1	2	FACETS	0.717	0.602	0.843	0.717	0.602	0.843	SUBCLONAL	1	TRUE	1	0.309152029753516	2		278	397	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	72	294	2	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.688	0.602	0.781	0.688	0.602	0.781	SUBCLONAL	1	TRUE	1	0.371801186288509	2		296	563	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	51	158	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.371801186288509	2		159	241	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	122	528	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.371801186288509	2		528	517	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	161	305	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.371801186288509	2		305	748	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	101	271	0	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.912	0.817	1	0.912	0.817	1	CLONAL	1	TRUE	1	0.371801186288509	2		271	596	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	170	584	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.975	0.896	1	0.975	0.896	1	CLONAL	1	TRUE	1	0.371801186288509	2		584	938	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	67	259	2	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	1	2	FACETS	0.881	0.769	1	0.881	0.769	1	CLONAL	1	TRUE	1	0.371801186288509	2		261	409	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	129	386	2	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	1	2	FACETS	0.93	0.844	1	0.93	0.844	1	CLONAL	1	TRUE	1	0.371801186288509	2		388	746	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	100	652	1	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.371801186288509	2		653	521	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445041	49445041	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	33	67	0	ENST00000301067.7:c.2425del	p.Gln809ArgfsTer121	p.Q809Rfs*121	ENST00000301067	NM_003482.3	809	Cag/ag	10/54	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.371801186288509	2		67	145	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	172	646	1	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.935	0.859	1	0.935	0.859	1	CLONAL	1	TRUE	1	0.371801186288509	2		647	990	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782135	9782135	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1336890715	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	122	377	0	ENST00000377346.4:c.2158C>T	p.Arg720Trp	p.R720W	ENST00000377346	NM_005026.3	720	Cgg/Tgg	17/24	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.371801186288509	2		377	566	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272403	11272403	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs557533784	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	83	290	0	ENST00000361445.4:c.3527C>T	p.Thr1176Met	p.T1176M	ENST00000361445	NM_004958.3	1176	aCg/aTg	23/58	1	2	FACETS	0.783	0.692	0.88	0.783	0.692	0.88	SUBCLONAL	1	TRUE	1	0.371801186288509	2		290	570	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800977	243800977	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	354	431	0	ENST00000263826.5:c.497G>A	p.Arg166Gln	p.R166Q	ENST00000263826	NM_005465.4	166	cGa/cAa	5/13	0.371801186288509	3	FACETS	0.892	0.849	0.935	0.892	0.849	0.935	CLONAL	3	TRUE	0	0.371801186288509	3		431	844	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342967	225342967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	154	514	0	ENST00000264414.4:c.2125C>T	p.Arg709Trp	p.R709W	ENST00000264414	NM_003590.4	709	Cgg/Tgg	15/16	1	2	FACETS	0.88	0.805	0.959	0.88	0.805	0.959	CLONAL	1	TRUE	1	0.371801186288509	2		514	941	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225365174	225365174	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	115	258	1	ENST00000264414.4:c.1516C>T	p.Arg506Trp	p.R506W	ENST00000264414	NM_003590.4	506	Cgg/Tgg	11/16	1	2	FACETS	0.995	0.898	1	0.995	0.898	1	CLONAL	1	TRUE	1	0.371801186288509	2		259	622	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163520	47163520	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	75	299	0	ENST00000409792.3:c.2606A>G	p.Asp869Gly	p.D869G	ENST00000409792	NM_014159.6	869	gAt/gGt	3/21	1	2	FACETS	0.791	0.695	0.894	0.791	0.695	0.894	SUBCLONAL	1	TRUE	1	0.371801186288509	2		299	510	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502377	186502377	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	178	450	0	ENST00000323963.5:c.100A>G	p.Asn34Asp	p.N34D	ENST00000323963		34	Aac/Gac	3/11	1	2	FACETS	0.911	0.839	0.986	0.911	0.839	0.986	CLONAL	1	TRUE	1	0.371801186288509	2		450	1051	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280079	66280079	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	119	346	0	ENST00000273854.3:c.1610T>C	p.Val537Ala	p.V537A	ENST00000273854	NM_004439.5	537	gTc/gCc	7/18	1	2	FACETS	0.943	0.852	1	0.943	0.852	1	CLONAL	1	TRUE	1	0.371801186288509	2		346	679	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193893	106193893	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1443872036	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	88	315	0	ENST00000380013.4:c.4355G>A	p.Arg1452Gln	p.R1452Q	ENST00000380013	NM_001127208.2	1452	cGa/cAa	10/11	1	2	FACETS	0.743	0.659	0.833	0.743	0.659	0.833	SUBCLONAL	1	TRUE	1	0.371801186288509	2		315	637	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500820	149500820	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755585100	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	116	425	0	ENST00000261799.4:c.2410G>A	p.Val804Met	p.V804M	ENST00000261799	NM_002609.3	804	Gtg/Atg	17/23	1	2	FACETS	0.911	0.822	1	0.911	0.822	1	CLONAL	1	TRUE	1	0.371801186288509	2		425	685	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522485	157522485	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777745107	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	292	542	0	ENST00000346085.5:c.4757C>T	p.Thr1586Met	p.T1586M	ENST00000346085	NM_020732.3	1586	aCg/aTg	18/20	0.359490146783423	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.371801186288509	3		542	893	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459531	50459531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	76	272	0	ENST00000331340.3:c.820C>T	p.Arg274Cys	p.R274C	ENST00000331340	NM_006060.4	274	Cgt/Tgt	7/8	1	2	FACETS	0.717	0.63	0.811	0.717	0.63	0.811	SUBCLONAL	1	TRUE	1	0.371801186288509	2		272	570	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851177	151851177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141966811	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	136	390	0	ENST00000262189.6:c.12194C>T	p.Ala4065Val	p.A4065V	ENST00000262189	NM_170606.2	4065	gCg/gTg	48/59	1	2	FACETS	0.96	0.874	1	0.96	0.874	1	CLONAL	1	TRUE	1	0.371801186288509	2		390	762	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993069	90993069	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	59	177	0	ENST00000265433.3:c.373A>G	p.Lys125Glu	p.K125E	ENST00000265433	NM_002485.4	125	Aaa/Gaa	4/16	1	2	FACETS	0.889	0.769	1	0.889	0.769	1	CLONAL	1	TRUE	1	0.371801186288509	2		177	357	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8339035	8339035	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	55	300	0	ENST00000356435.5:c.5266C>T	p.Gln1756Ter	p.Q1756*	ENST00000356435		1756	Caa/Taa	32/35	1	2	FACETS	0.682	0.584	0.788	0.682	0.584	0.788	SUBCLONAL	1	TRUE	1	0.371801186288509	2		300	434	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966608	36966608	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766774692	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	92	334	0	ENST00000358127.4:c.718G>A	p.Val240Met	p.V240M	ENST00000358127	NM_001280556.1	240	Gtg/Atg	6/10	1	2	FACETS	0.864	0.769	0.964	0.864	0.769	0.964	CLONAL	1	TRUE	1	0.371801186288509	2		334	573	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390585	139390585	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111627256	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	170	386	0	ENST00000277541.6:c.7606G>A	p.Val2536Ile	p.V2536I	ENST00000277541	NM_017617.3	2536	Gtc/Atc	34/34	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.371801186288509	2		386	821	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401026	139401026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	157	443	2	ENST00000277541.6:c.3967G>A	p.Ala1323Thr	p.A1323T	ENST00000277541	NM_017617.3	1323	Gcc/Acc	24/34	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.371801186288509	2		445	735	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600633	43600633	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	124	451	1	ENST00000355710.3:c.859C>T	p.Arg287Trp	p.R287W	ENST00000355710	NM_020975.4	287	Cgg/Tgg	4/20	1	2	FACETS	0.906	0.821	0.996	0.906	0.821	0.996	CLONAL	1	TRUE	1	0.371801186288509	2		452	736	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533853	533853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730880461	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	111	348	0	ENST00000451590.1:c.203G>A	p.Arg68Gln	p.R68Q	ENST00000451590	NM_001130442.1	68	cGg/cAg	3/5	1	2	FACETS	0.894	0.805	0.988	0.894	0.805	0.988	CLONAL	1	TRUE	1	0.371801186288509	2		348	668	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377024	118377024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781919840	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	93	315	0	ENST00000534358.1:c.10417C>T	p.Arg3473Cys	p.R3473C	ENST00000534358	NM_005933.3	3473	Cgt/Tgt	27/36	1	2	FACETS	0.897	0.799	1	0.897	0.799	1	CLONAL	1	TRUE	1	0.371801186288509	2		315	558	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416705	416705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781474100	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	96	378	0	ENST00000399788.2:c.3845G>A	p.Arg1282His	p.R1282H	ENST00000399788	NM_001042603.1	1282	cGt/cAt	23/28	NA	2	FACETS	0.703	0.626	0.784			1	INDETERMINATE	1	TRUE	NA	0.371801186288509	2		378	735	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244183	133244183	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs116360781	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	133	387	0	ENST00000320574.5:c.2225G>A	p.Arg742His	p.R742H	ENST00000320574	NM_006231.2	742	cGt/cAt	20/49	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.371801186288509	2		387	674	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436257	110436257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1316736634	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	40	136	0	ENST00000375856.3:c.2144C>T	p.Ala715Val	p.A715V	ENST00000375856	NM_003749.2	715	gCg/gTg	1/2	0.34371638076937	3	FACETS	1	0.904	1	0.557	0.467	0.656	CLONAL	1	TRUE	1	0.371801186288509	3		136	229	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436306	110436306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	10	92	0	ENST00000375856.3:c.2095G>A	p.Ala699Thr	p.A699T	ENST00000375856	NM_003749.2	699	Gcc/Acc	1/2	0.34371638076937	3	FACETS	0.459	0.312	0.642	0.229	0.156	0.321	SUBCLONAL	1	TRUE	1	0.371801186288509	3		92	139	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987100	36987100	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	88	251	0	ENST00000354822.5:c.589C>A	p.Leu197Ile	p.L197I	ENST00000354822	NM_001079668.2	197	Ctc/Atc	3/3	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.371801186288509	2		251	379	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3794921	3794921	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1252438256	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	124	412	2	ENST00000262367.5:c.3956G>A	p.Arg1319Gln	p.R1319Q	ENST00000262367	NM_004380.2	1319	cGa/cAa	23/31	1	2	FACETS	0.853	0.772	0.938	0.853	0.772	0.938	CLONAL	1	TRUE	1	0.371801186288509	2		414	782	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993903	72993903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751544438	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	147	534	0	ENST00000268489.5:c.142G>A	p.Gly48Arg	p.G48R	ENST00000268489	NM_006885.3	48	Ggg/Agg	2/10	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.371801186288509	2		534	780	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337295	89337295	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1250432793	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	112	364	0	ENST00000301030.4:c.7736G>A	p.Arg2579His	p.R2579H	ENST00000301030	NM_001256183.1	2579	cGc/cAc	12/13	1	2	FACETS	0.95	0.856	1	0.95	0.856	1	CLONAL	1	TRUE	1	0.371801186288509	2		364	634	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740810	58740810	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1179832290	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	235	669	0	ENST00000305921.3:c.1715G>A	p.Arg572Gln	p.R572Q	ENST00000305921	NM_003620.3	572	cGa/cAa	6/6	1	2	FACETS	0.992	0.924	1	0.992	0.924	1	CLONAL	1	TRUE	1	0.371801186288509	2		669	1274	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532555	63532555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881401	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	48	177	0	ENST00000307078.5:c.2024G>A	p.Arg675His	p.R675H	ENST00000307078	NM_004655.3	675	cGt/cAt	8/11	1	2	FACETS	0.782	0.664	0.911	0.782	0.664	0.911	CLONAL	1	TRUE	1	0.371801186288509	2		177	330	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796929	78796929	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	108	293	0	ENST00000306801.3:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000306801	NM_020761.2	348	Cga/Tga	9/34	1	2	FACETS	0.846	0.76	0.937	0.846	0.76	0.937	CLONAL	1	TRUE	1	0.371801186288509	2		293	687	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896551	78896551	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs183024326	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	135	436	1	ENST00000306801.3:c.2548G>A	p.Val850Ile	p.V850I	ENST00000306801	NM_020761.2	850	Gtc/Atc	22/34	1	2	FACETS	0.912	0.83	0.999	0.912	0.83	0.999	CLONAL	1	TRUE	1	0.371801186288509	2		437	796	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272140	15272140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	15	76	0	ENST00000263388.2:c.6299C>T	p.Ser2100Leu	p.S2100L	ENST00000263388	NM_000435.2	2100	tCg/tTg	33/33	1	2	FACETS	0.761	0.563	0.992	0.761	0.563	0.992	CLONAL	1	TRUE	1	0.371801186288509	2		76	106	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247025	53247025	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556852786	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	158	275	1	ENST00000375401.3:c.475C>T	p.Arg159Cys	p.R159C	ENST00000375401	NM_004187.3	159	Cgc/Tgc	4/26	1	1	FACETS	0.824	0.763	0.886	1	0.991	1	CLONAL	2	TRUE	0	0.371801186288509	1		276	420	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007813	45008028	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACACTGAATTCACCCCCACTGAAAAAGATGAGTATGCCTGCCGTGTGAACCATGTGACTTTGTCACAGCCCAAGATAGTTAAGTGGGGTAAGTCTTACATTCTTTTGTAAGCTGCTGAAAGTTGTGTATGAGTAGTCATATCATAAAGCTGCTTTGATATAAAAAAGGTCTATGGCCATACTACCCTGAATGAGTCCCATCCCATCTGATATAAAC	ACACTGAATTCACCCCCACTGAAAAAGATGAGTATGCCTGCCGTGTGAACCATGTGACTTTGTCACAGCCCAAGATAGTTAAGTGGGGTAAGTCTTACATTCTTTTGTAAGCTGCTGAAAGTTGTGTATGAGTAGTCATATCATAAAGCTGCTTTGATATAAAAAAGGTCTATGGCCATACTACCCTGAATGAGTCCCATCCCATCTGATATAAAC	-	novel	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	54	229	0	ENST00000558401.1:c.261_346+130del		p.X87_splice	ENST00000558401	NM_004048.2	87		2/4	0.371801186288509	1	FACETS	0.566	0.484	0.654	0.566	0.484	0.654	SUBCLONAL	1	TRUE	0	0.371801186288509	1		229	418	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453398	40453399	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs759027671	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	87	662	1	ENST00000345506.4:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000345506	NM_003152.3	365	-/C	10/20	1	2	FACETS	0.439	0.387	0.494	0.439	0.387	0.494	SUBCLONAL	1	TRUE	1	0.371801186288509	2		663	1067	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479736	67479739	+	frameshift_variant	Frame_Shift_Del	DEL	TCGC	TCGC	-	novel	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	143	453	0	ENST00000327367.4:c.1044_1047del	p.Phe348LeufsTer18	p.F348Lfs*18	ENST00000327367	NM_005902.3	348	tTCGCt/tt	8/9	0.371801186288509	2	FACETS	0.935	0.853	1	0.467	0.426	0.511	CLONAL	1	TRUE	0	0.371801186288509	2		453	823	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084146	47084146	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	97	230	0	ENST00000409792.3:c.7143del	p.Ser2382LeufsTer29	p.S2382Lfs*29	ENST00000409792	NM_014159.6	2381	ccC/cc	17/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.371801186288509	2		230	474	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698146	47698147	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs63750393	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	130	345	0	ENST00000233146.2:c.1705_1706del	p.Glu569IlefsTer2	p.E569Ifs*2	ENST00000233146	NM_000251.2	568	acAGaa/acaa	11/16	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.371801186288509	2		345	669	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661664	227661664	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs761880048	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	184	379	4	ENST00000305123.5:c.1791del	p.His598ThrfsTer38	p.H598Tfs*38	ENST00000305123	NM_005544.2	597	ggG/gg	1/2	1	2	FACETS	1	0.969	1	1	0.994	1	CLONAL	2	TRUE	1	0.371801186288509	2		383	464	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651438	52651438	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	146	553	0	ENST00000394830.3:c.1658del	p.Lys553ArgfsTer16	p.K553Rfs*16	ENST00000394830	NM_018313.4	553	aAg/ag	15/30	1	2	FACETS	0.857	0.782	0.936	0.857	0.782	0.936	CLONAL	1	TRUE	1	0.371801186288509	2		553	916	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843775	151843775	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	134	403	0	ENST00000262189.6:c.13940del	p.Lys4647SerfsTer12	p.K4647Sfs*12	ENST00000262189	NM_170606.2	4647	aAg/ag	53/59	1	2	FACETS	0.901	0.819	0.987	0.901	0.819	0.987	CLONAL	1	TRUE	1	0.371801186288509	2		403	800	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720712	89720712	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	21	179	0	ENST00000371953.3:c.867del	p.Val290Ter	p.V290*	ENST00000371953	NM_000314.4	288	gAa/ga	8/9	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.371801186288509	2		179	89	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479217	50479218	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	81	243	1	ENST00000394963.4:c.68dup	p.Ala24ArgfsTer107	p.A24Rfs*107	ENST00000394963	NM_003076.4	22	gcg/gcGg	1/13	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.371801186288509	2		244	408	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502404	186502405	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	250	475	0	ENST00000323963.5:c.131_132del	p.Leu44ProfsTer10	p.L44Pfs*10	ENST00000323963		43	TCt/t	3/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.371801186288509	2		475	1133	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345848	152345848	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	248	656	0	ENST00000359321.1:c.722del	p.Phe241SerfsTer15	p.F241Sfs*15	ENST00000359321	NM_005431.1	241	tTc/tc	3/3	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.371801186288509	2		656	1325	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913253	39913253	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	28	229	1	ENST00000378444.4:c.4862del	p.Pro1621GlnfsTer53	p.P1621Qfs*53	ENST00000378444	NM_001123385.1	1621	cCa/ca	14/15	1	1	FACETS	0.295	0.236	0.364	0.295	0.236	0.364	SUBCLONAL	1	TRUE	0	0.371801186288509	1		230	415	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806181	1806181	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760502257	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	122	656	1	ENST00000260795.2:c.1206del	p.Lys403ArgfsTer29	p.K403Rfs*29	ENST00000260795		400	agC/ag	8/17	1	2	FACETS	0.947	0.857	1	0.947	0.857	1	CLONAL	1	TRUE	1	0.371801186288509	2		657	693	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291083	10291084	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755889652	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	113	752	1	ENST00000340748.4:c.387dup	p.Lys130GlnfsTer19	p.K130Qfs*19	ENST00000340748		129	-/C	4/40	1	2	FACETS	0.875	0.788	0.966	0.875	0.788	0.966	CLONAL	1	TRUE	1	0.371801186288509	2		753	695	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	92	299	1	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	1	2	FACETS	0.9	0.802	1	0.9	0.802	1	CLONAL	1	TRUE	1	0.371801186288509	2		300	550	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910761	32910762	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs886040420	NA	P-0003650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	359	680	0	ENST00000380152.3:c.2271_2272del	p.Leu759PhefsTer3	p.L759Ffs*3	ENST00000380152		757	AAa/a	11/27	0.34371638076937	3	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	1	0.371801186288509	3		680	1142	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641560	47641560	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	T	rs193922376	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	18	84	0	ENST00000233146.2:c.942+3A>T		p.X314_splice	ENST00000233146	NM_000251.2	314			1	2	FACETS	0.577	0.435	0.744	0.577	0.435	0.744	SUBCLONAL	1	TRUE	1	0.27	2		84	231	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	66	305	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.833	0.723	0.952	0.833	0.723	0.952	CLONAL	1	TRUE	1	0.27	2		305	587	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	101	646	1	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.873	0.779	0.973	0.873	0.779	0.973	CLONAL	1	TRUE	1	0.27	2		647	857	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	65	298	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	1	2	FACETS	0.741	0.642	0.848	0.741	0.642	0.848	SUBCLONAL	1	TRUE	1	0.27	2		298	650	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	65	247	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.71	0.615	0.813	0.71	0.615	0.813	SUBCLONAL	1	TRUE	1	0.27	2		248	678	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135707	64135707	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	89	355	1	ENST00000334205.4:c.1175C>T	p.Ala392Val	p.A392V	ENST00000334205	NM_003942.2	392	gCg/gTg	10/17	1	2	FACETS	0.939	0.833	1	0.939	0.833	1	CLONAL	1	TRUE	1	0.27	2		356	702	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143444	30143444	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500231	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	52	212	1	ENST00000389048.3:c.82C>T	p.Arg28Cys	p.R28C	ENST00000389048	NM_004304.4	28	Cgc/Tgc	1/29	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.27	2		213	378	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	41	467	0	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	0.692	0.577	0.82	0.692	0.577	0.82	SUBCLONAL	1	TRUE	1	0.27	2		467	439	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226330	2226330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778416555	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	80	396	1	ENST00000326181.6:c.1943C>T	p.Ala648Val	p.A648V	ENST00000326181	NM_032271.2	648	gCg/gTg	20/21	1	2	FACETS	0.817	0.719	0.923	0.817	0.719	0.923	CLONAL	1	TRUE	1	0.27	2		397	725	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678560	88678560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758189455	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	33	179	0	ENST00000360948.2:c.976C>T	p.Arg326Cys	p.R326C	ENST00000360948	NM_001012338.2	326	Cgt/Tgt	9/19	1	2	FACETS	0.786	0.642	0.947	0.786	0.642	0.947	CLONAL	1	TRUE	1	0.27	2		179	311	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	73	884	1	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	0.794	0.694	0.902	0.794	0.694	0.902	CLONAL	1	TRUE	1	0.27	2		885	681	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535435	66535435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	21	161	0	ENST00000273854.3:c.26C>T	p.Ala9Val	p.A9V	ENST00000273854	NM_004439.5	9	gCg/gTg	1/18	1	2	FACETS	0.426	0.328	0.541	0.426	0.328	0.541	SUBCLONAL	1	TRUE	1	0.27	2		161	365	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244133	133244133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759398253	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	62	352	0	ENST00000320574.5:c.2275C>T	p.Arg759Cys	p.R759C	ENST00000320574	NM_006231.2	759	Cgt/Tgt	20/49	1	2	FACETS	0.668	0.577	0.768	0.668	0.577	0.768	SUBCLONAL	1	TRUE	1	0.27	2		352	687	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474041	29474041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs78723472	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	78	397	1	ENST00000389048.3:c.2134G>A	p.Val712Met	p.V712M	ENST00000389048	NM_004304.4	712	Gtg/Atg	12/29	1	2	FACETS	0.815	0.716	0.922	0.815	0.716	0.922	CLONAL	1	TRUE	1	0.27	2		398	709	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647685	2647685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	75	323	0	ENST00000342085.4:c.1588G>A	p.Gly530Arg	p.G530R	ENST00000342085	NM_002613.4	530	Ggg/Agg	14/14	1	2	FACETS	0.78	0.683	0.885	0.78	0.683	0.885	SUBCLONAL	1	TRUE	1	0.27	2		323	712	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101278	27101278	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	47	298	0	ENST00000324856.7:c.4563del	p.Ala1522ProfsTer5	p.A1522Pfs*5	ENST00000324856	NM_006015.4	1520	ggC/gg	18/20	1	2	FACETS	0.623	0.525	0.731	0.623	0.525	0.731	SUBCLONAL	1	TRUE	1	0.27	2		298	559	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	155	701	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.27	2		707	948	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814797	139814797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144427288	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	78	402	0	ENST00000247668.2:c.790G>A	p.Ala264Thr	p.A264T	ENST00000247668	NM_021138.3	264	Gcg/Acg	8/11	1	2	FACETS	0.852	0.749	0.963	0.852	0.749	0.963	CLONAL	1	TRUE	1	0.27	2		402	678	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096133	2096133	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs763525759	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	86	317	1	ENST00000219066.1:c.374del	p.Pro125GlnfsTer12	p.P125Qfs*12	ENST00000219066	NM_002528.5	125	cCa/ca	2/6	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.27	2		318	605	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319854	8319854	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	71	293	0	ENST00000356435.5:c.5647C>T	p.Arg1883Ter	p.R1883*	ENST00000356435		1883	Cga/Tga	34/35	1	2	FACETS	0.859	0.75	0.977	0.859	0.75	0.977	CLONAL	1	TRUE	1	0.27	2		293	612	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	96	922	1	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.92	0.819	1	0.92	0.819	1	CLONAL	1	TRUE	1	0.27	2		923	773	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982767	7982767	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	73	350	0	ENST00000319144.4:c.1018del	p.Leu340SerfsTer12	p.L340Sfs*12	ENST00000319144	NM_001139.2	340	Ctc/tc	8/15	1	2	FACETS	0.807	0.706	0.917	0.807	0.706	0.917	CLONAL	1	TRUE	1	0.27	2		350	670	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443617	49443617	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs727503987	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	83	320	0	ENST00000301067.7:c.3754C>T	p.Arg1252Ter	p.R1252*	ENST00000301067	NM_003482.3	1252	Cga/Tga	11/54	1	2	FACETS	0.878	0.775	0.989	0.878	0.775	0.989	CLONAL	1	TRUE	1	0.27	2		320	700	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200877	67200877	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	93	352	0	ENST00000312629.5:c.870del	p.Tyr291ThrfsTer14	p.Y291Tfs*14	ENST00000312629	NM_003952.2	289	Ccc/cc	10/15	1	2	FACETS	0.973	0.865	1	0.973	0.865	1	CLONAL	1	TRUE	1	0.27	2		352	708	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427612	49427612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766696812	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	66	278	0	ENST00000301067.7:c.10876C>T	p.Arg3626Trp	p.R3626W	ENST00000301067	NM_003482.3	3626	Cgg/Tgg	39/54	1	2	FACETS	0.947	0.824	1	0.947	0.824	1	CLONAL	1	TRUE	1	0.27	2		278	516	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274710	123274710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753437208	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	106	376	0	ENST00000358487.5:c.1208C>T	p.Thr403Met	p.T403M	ENST00000358487	NM_000141.4	403	aCg/aTg	9/18	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.27	2		376	702	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231449	5231449	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	80	359	1	ENST00000357368.4:c.2027del	p.Pro676ArgfsTer134	p.P676Rfs*134	ENST00000357368	NM_002850.3	676	cCg/cg	14/38	1	2	FACETS	0.774	0.68	0.874	0.774	0.68	0.874	SUBCLONAL	1	TRUE	1	0.27	2		360	766	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879277	151879277	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs956673837	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	76	317	0	ENST00000262189.6:c.5668C>T	p.Arg1890Ter	p.R1890*	ENST00000262189	NM_170606.2	1890	Cga/Tga	36/59	1	2	FACETS	0.943	0.828	1	0.943	0.828	1	CLONAL	1	TRUE	1	0.27	2		317	597	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300488	11300488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1452329078	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	81	349	1	ENST00000361445.4:c.1658G>A	p.Arg553His	p.R553H	ENST00000361445	NM_004958.3	553	cGc/cAc	11/58	1	2	FACETS	0.831	0.732	0.938	0.831	0.732	0.938	CLONAL	1	TRUE	1	0.27	2		350	722	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305238	39305238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs890472037	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	64	317	1	ENST00000373001.3:c.1187G>A	p.Arg396Gln	p.R396Q	ENST00000373001	NM_022157.3	396	cGa/cAa	7/7	1	2	FACETS	0.817	0.708	0.936	0.817	0.708	0.936	CLONAL	1	TRUE	1	0.27	2		318	580	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109870	115109870	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	79	274	0	ENST00000257566.3:c.2008del	p.Leu670TrpfsTer219	p.L670Wfs*219	ENST00000257566	NM_016569.3	670	Ctg/tg	8/8	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.27	2		274	491	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557539	21557539	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536277703	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	70	359	0	ENST00000382592.4:c.2306G>A	p.Arg769Gln	p.R769Q	ENST00000382592	NM_014572.2	769	cGg/cAg	5/8	1	2	FACETS	0.755	0.658	0.86	0.755	0.658	0.86	SUBCLONAL	1	TRUE	1	0.27	2		359	687	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845371	89845371	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201212806	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	99	401	1	ENST00000389301.3:c.1756G>A	p.Ala586Thr	p.A586T	ENST00000389301	NM_000135.2	586	Gcc/Acc	19/43	1	2	FACETS	0.978	0.873	1	0.978	0.873	1	CLONAL	1	TRUE	1	0.27	2		402	750	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007445	62007445	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	64	310	0	ENST00000392795.3:c.422T>C	p.Leu141Pro	p.L141P	ENST00000392795	NM_001039933.1	141	cTg/cCg	3/6	1	2	FACETS	0.908	0.787	1	0.908	0.787	1	CLONAL	1	TRUE	1	0.27	2		310	522	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123751	11123751	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	83	400	1	ENST00000358026.2:c.2401C>T	p.Arg801Cys	p.R801C	ENST00000358026	NM_001128849.1	801	Cgc/Tgc	16/36	1	2	FACETS	0.895	0.79	1	0.895	0.79	1	CLONAL	1	TRUE	1	0.27	2		401	687	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271867	15271867	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	88	307	0	ENST00000263388.2:c.6572C>A	p.Pro2191Gln	p.P2191Q	ENST00000263388	NM_000435.2	2191	cCg/cAg	33/33	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.27	2		307	639	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280069	18280069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1321931050	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	27	60	0	ENST00000222254.8:c.2152G>A	p.Ala718Thr	p.A718T	ENST00000222254	NM_005027.3	718	Gcc/Acc	16/16	1	2	FACETS	0.885	0.708	1	0.885	0.708	1	CLONAL	1	TRUE	1	0.27	2		60	226	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216643	36216643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775753450	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	91	310	0	ENST00000222270.7:c.3809G>A	p.Arg1270His	p.R1270H	ENST00000222270	NM_014727.1	1270	cGc/cAc	13/37	1	2	FACETS	0.991	0.881	1	0.991	0.881	1	CLONAL	1	TRUE	1	0.27	2		310	680	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223997	36223997	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	64	365	0	ENST00000222270.7:c.6552del	p.Lys2185AsnfsTer18	p.K2185Nfs*18	ENST00000222270	NM_014727.1	2183	Ccc/cc	28/37	1	2	FACETS	0.559	0.483	0.642	0.559	0.483	0.642	SUBCLONAL	1	TRUE	1	0.27	2		365	848	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443676	29443676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56315533	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	82	371	1	ENST00000389048.3:c.3541C>T	p.Arg1181Cys	p.R1181C	ENST00000389048	NM_004304.4	1181	Cgc/Tgc	23/29	1	2	FACETS	0.793	0.699	0.894	0.793	0.699	0.894	SUBCLONAL	1	TRUE	1	0.27	2		372	766	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149870	99149870	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	81	288	0	ENST00000074304.5:c.182A>T	p.Asp61Val	p.D61V	ENST00000074304	NM_001134224.1	61	gAt/gTt	5/26	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.27	2		288	561	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097210	178097212	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	54	319	0	ENST00000397062.3:c.502_504del	p.Ser168del	p.S168del	ENST00000397062	NM_006164.4	168	TCT/-	4/5	1	2	FACETS	0.582	0.496	0.676	0.582	0.496	0.676	SUBCLONAL	1	TRUE	1	0.27	2		319	687	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732626	190732626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139826569	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	58	390	0	ENST00000441310.2:c.2444C>T	p.Ala815Val	p.A815V	ENST00000441310	NM_000534.4	815	gCg/gTg	11/13	1	2	FACETS	0.66	0.566	0.762	0.66	0.566	0.762	SUBCLONAL	1	TRUE	1	0.27	2		390	651	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31372649	31372649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200902224	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	58	310	0	ENST00000328111.2:c.290G>A	p.Arg97His	p.R97H	ENST00000328111	NM_006892.3	97	cGt/cAt	4/23	1	2	FACETS	0.8	0.688	0.922	0.8	0.688	0.922	CLONAL	1	TRUE	1	0.27	2		310	537	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612251	189612251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758317410	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	71	274	0	ENST00000264731.3:c.2003G>A	p.Arg668His	p.R668H	ENST00000264731	NM_003722.4	668	cGc/cAc	14/14	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.27	2		274	491	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839960	27839960	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	97	302	0	ENST00000328488.2:c.134G>A	p.Gly45Asp	p.G45D	ENST00000328488	NM_003533.2	45	gGc/gAc	1/1	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.27	2		302	681	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129466	152129466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759765625	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	18	139	0	ENST00000206249.3:c.419C>T	p.Thr140Met	p.T140M	ENST00000206249	NM_000125.3	140	aCg/aTg	1/8	1	2	FACETS	0.434	0.327	0.562	0.434	0.327	0.562	SUBCLONAL	1	TRUE	1	0.27	2		139	307	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740572	145740572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751616549	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	87	314	2	ENST00000428558.2:c.1445G>A	p.Arg482His	p.R482H	ENST00000428558	NM_004260.3	482	cGc/cAc	8/22	1	2	FACETS	0.906	0.802	1	0.906	0.802	1	CLONAL	1	TRUE	1	0.27	2		316	711	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98244487	98244487	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	65	358	0	ENST00000331920.6:c.585-2A>G		p.X195_splice	ENST00000331920	NM_000264.3	195			1	2	FACETS	0.824	0.715	0.943	0.824	0.715	0.943	CLONAL	1	TRUE	1	0.27	2		358	584	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323232	31323232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148667827	NA	P-0003650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	67	277	0	ENST00000412585.2:c.757G>A	p.Glu253Lys	p.E253K	ENST00000412585	NM_005514.6	253	Gag/Aag	4/8	1	2	FACETS	0.958	0.834	1	0.958	0.834	1	CLONAL	1	TRUE	1	0.27	2		277	518	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874147	151874148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs747256476	NA	P-0003684-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	180	836	10	ENST00000262189.6:c.8390dup	p.Glu2798GlyfsTer11	p.E2798Gfs*11	ENST00000262189	NM_170606.2	2797	aag/aaAg	38/59	0.636864536031269	1	FACETS	0.786	0.731	0.842	0.786	0.731	0.842	SUBCLONAL	1	TRUE	0	0.636864536031269	1		846	490	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576138	29576138	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1555617383	NA	P-0003760-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	185	273	0	ENST00000356175.3:c.4110+1G>A		p.X1370_splice	ENST00000356175	NM_000267.3	1370			1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		273	676	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436407	52436407	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003770-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	54	336	0	ENST00000460680.1:c.2087T>C	p.Ile696Thr	p.I696T	ENST00000460680	NM_004656.3	696	aTc/aCc	17/17	0.229452506009315	1	FACETS	0.848	0.73	0.975	0.848	0.73	0.975	CLONAL	1	TRUE	0	0.36320045975154	1		336	287	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486828	56486828	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003770-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	228	592	2	ENST00000267101.3:c.1242T>A	p.Asn414Lys	p.N414K	ENST00000267101	NM_001982.3	414	aaT/aaA	11/28	0.36320045975154	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.36320045975154	3		594	709	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007443	62007443	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003770-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	64	340	2	ENST00000392795.3:c.424C>T	p.Arg142Ter	p.R142*	ENST00000392795	NM_001039933.1	142	Cga/Tga	3/6	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.36320045975154	2		342	311	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166321	7166321	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762169820	NA	P-0003770-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	86	628	0	ENST00000302850.5:c.1705G>A	p.Asp569Asn	p.D569N	ENST00000302850	NM_000208.2	569	Gac/Aac	8/22	1	2	FACETS	0.945	0.839	1	0.945	0.839	1	CLONAL	1	TRUE	1	0.36320045975154	2		628	501	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256725	19256725	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003770-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	35	273	0	ENST00000162023.5:c.988C>A	p.Pro330Thr	p.P330T	ENST00000162023		330	Ccc/Acc	13/13	1	2	FACETS	0.765	0.63	0.914	0.765	0.63	0.914	CLONAL	1	TRUE	1	0.36320045975154	2		273	252	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240130	41240130	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003770-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	14	72	0	ENST00000379561.5:c.220C>A	p.Leu74Met	p.L74M	ENST00000379561	NM_002015.3	74	Ctg/Atg	1/3	0.332283779406002	1	FACETS	0.928	0.686	1	0.928	0.686	1	CLONAL	1	TRUE	0	0.36320045975154	1		72	68	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436407	52436407	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003770-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	82	336	0	ENST00000460680.1:c.2087T>C	p.Ile696Thr	p.I696T	ENST00000460680	NM_004656.3	696	aTc/aCc	17/17	1	2	FACETS	0.963	0.853	1	0.963	0.853	1	CLONAL	1	TRUE	1	0.362182032763347	2		336	470	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486828	56486828	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003770-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	332	592	2	ENST00000267101.3:c.1242T>A	p.Asn414Lys	p.N414K	ENST00000267101	NM_001982.3	414	aaT/aaA	11/28	0.362182032763347	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.362182032763347	3		594	1042	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007443	62007443	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003770-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	95	340	2	ENST00000392795.3:c.424C>T	p.Arg142Ter	p.R142*	ENST00000392795	NM_001039933.1	142	Cga/Tga	3/6	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.362182032763347	2		342	508	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166321	7166321	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762169820	NA	P-0003770-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	142	628	0	ENST00000302850.5:c.1705G>A	p.Asp569Asn	p.D569N	ENST00000302850	NM_000208.2	569	Gac/Aac	8/22	1	2	FACETS	0.974	0.888	1	0.974	0.888	1	CLONAL	1	TRUE	1	0.362182032763347	2		628	805	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256725	19256725	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003770-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	76	273	0	ENST00000162023.5:c.988C>A	p.Pro330Thr	p.P330T	ENST00000162023		330	Ccc/Acc	13/13	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.362182032763347	2		273	406	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240130	41240130	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003770-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	14	72	0	ENST00000379561.5:c.220C>A	p.Leu74Met	p.L74M	ENST00000379561	NM_002015.3	74	Ctg/Atg	1/3	0.362182032763347	1	FACETS	0.646	0.473	0.85	0.646	0.473	0.85	SUBCLONAL	1	TRUE	0	0.362182032763347	1		72	98	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946086	13946086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003770-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	96	351	0	ENST00000405192.2:c.1010G>A	p.Gly337Asp	p.G337D	ENST00000405192	NM_001163147.1	337	gGc/gAc	10/12	1	2	FACETS	0.952	0.85	1	0.952	0.85	1	CLONAL	1	TRUE	1	0.362182032763347	2		351	557	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416894	416894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs909970288	NA	P-0003770-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	123	515	0	ENST00000399788.2:c.3656G>A	p.Arg1219Gln	p.R1219Q	ENST00000399788	NM_001042603.1	1219	cGa/cAa	23/28	0.362182032763347	3	FACETS	0.749	0.676	0.827			1	SUBCLONAL	1	TRUE	NA	0.362182032763347	3		515	1071	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436407	52436407	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003770-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	24	336	0	ENST00000460680.1:c.2087T>C	p.Ile696Thr	p.I696T	ENST00000460680	NM_004656.3	696	aTc/aCc	17/17	0.21195586666148	1	FACETS	0.481	0.376	0.602	0.481	0.376	0.602	SUBCLONAL	1	TRUE	0	0.21195586666148	1		336	421	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486828	56486828	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003770-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	153	592	2	ENST00000267101.3:c.1242T>A	p.Asn414Lys	p.N414K	ENST00000267101	NM_001982.3	414	aaT/aaA	11/28	0.148631887368591	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.21195586666148	3		594	701	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007443	62007443	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003770-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	36	340	2	ENST00000392795.3:c.424C>T	p.Arg142Ter	p.R142*	ENST00000392795	NM_001039933.1	142	Cga/Tga	3/6	1	2	FACETS	0.885	0.728	1	0.885	0.728	1	CLONAL	1	TRUE	1	0.21195586666148	2		342	384	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166321	7166321	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762169820	NA	P-0003770-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	82	628	0	ENST00000302850.5:c.1705G>A	p.Asp569Asn	p.D569N	ENST00000302850	NM_000208.2	569	Gac/Aac	8/22	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.21195586666148	2		628	623	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256725	19256725	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003770-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	36	273	0	ENST00000162023.5:c.988C>A	p.Pro330Thr	p.P330T	ENST00000162023		330	Ccc/Acc	13/13	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.21195586666148	2		273	321	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191558	10191558	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	153	275	0	ENST00000256474.2:c.551T>G	p.Leu184Arg	p.L184R	ENST00000256474	NM_000551.3	184	cTc/cGc	3/3	0.214426768193007	3	FACETS	1	0.987	1	0.47	0.432	0.509	INDETERMINATE	1	TRUE	0	0.477646852712891	3		275	563	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499101	149499101	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	45	246	0	ENST00000261799.4:c.2727G>A	p.Met909Ile	p.M909I	ENST00000261799	NM_002609.3	909	atG/atA	20/23	0.28909650298414	4	FACETS	0.564	0.474	0.663	0.282	0.237	0.332	SUBCLONAL	1	TRUE	2	0.477646852712891	4		246	494	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729989	47729989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	29	111	0	ENST00000449228.1:c.400G>A	p.Gly134Ser	p.G134S	ENST00000449228	NM_001127240.2	134	Ggc/Agc	3/4	0.199600494628724	3	FACETS	0.796	0.644	0.965	0.398	0.322	0.483	INDETERMINATE	1	TRUE	1	0.477646852712891	3		111	189	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070892	30070892	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	115	284	0	ENST00000338641.4:c.1408C>T	p.Gln470Ter	p.Q470*	ENST00000338641	NM_000268.3	470	Cag/Tag	13/16	0.161147393293881	4	FACETS	1	0.983	1	0.709	0.641	0.779	INDETERMINATE	1	TRUE	2	0.477646852712891	4		284	502	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440859	52440860	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCGATACGCTCCATGATGACCCGCCGGGCCTTGTCTGTCCACTCCTCGTCCTCCCCCCAGGGCC	novel	NA	P-0004150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	32	238	0	ENST00000460680.1:c.581_644dup	p.Leu216AlafsTer48	p.L216Afs*48	ENST00000460680	NM_004656.3	215	ggc/ggGGCCCTGGGGGGAGGACGAGGAGTGGACAGACAAGGCCCGGCGGGTCATCATGGAGCGTATCGGc	8/17	NA	2	FACETS	0.256	0.207	0.311			1	INDETERMINATE	1	TRUE	NA	0.477646852712891	2		238	524	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955928	55955928	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	174	357	2	ENST00000263923.4:c.3234del	p.Phe1078LeufsTer24	p.F1078Lfs*24	ENST00000263923	NM_002253.2	1078	ttT/tt	24/30	0.3488871038417	4	FACETS	1	0.988	1	0.704	0.649	0.76	CLONAL	1	TRUE	2	0.477646852712891	4		359	765	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245759	41245759	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs55650082	NA	P-0004290-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	52	269	1	ENST00000357654.3:c.1789G>T	p.Glu597Ter	p.E597*	ENST00000357654	NM_007294.3	597	Gaa/Taa	10/23	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		270	666	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200046	128200046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1037327872	NA	P-0004290-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	92	283	1	ENST00000341105.2:c.1259G>A	p.Cys420Tyr	p.C420Y	ENST00000341105	NM_032638.4	420	tGc/tAc	6/6	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		284	1012	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965227	25965227	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	31	1039	0	ENST00000435504.4:c.3979T>C	p.Tyr1327His	p.Y1327H	ENST00000435504		1327	Tat/Cat	13/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1039	114	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149453024	149453024	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	50	877	0	ENST00000286301.3:c.922A>G	p.Asn308Asp	p.N308D	ENST00000286301	NM_005211.3	308	Aac/Gac	7/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		877	125	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334966	81334966	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	13	827	5	ENST00000222390.5:c.1861G>T	p.Gly621Ter	p.G621*	ENST00000222390	NM_000601.4	621	Gga/Tga	16/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		832	144	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41267759	41267759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879255290	NA	P-0004593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	59	1181	1	ENST00000357654.3:c.118G>A	p.Asp40Asn	p.D40N	ENST00000357654	NM_007294.3	40	Gac/Aac	3/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1182	171	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983141	201983141	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	33	1098	0	ENST00000359651.3:c.990C>G	p.Ser330Arg	p.S330R	ENST00000359651		330	agC/agG	7/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1098	382	SUCCESS
EED	8726	MSKCC	GRCh37	11	85966318	85966318	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs776117763	NA	P-0004593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	90	605	0	ENST00000263360.6:c.415G>C	p.Val139Leu	p.V139L	ENST00000263360	NM_003797.3	139	Gtg/Ctg	4/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		605	172	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170156	32170156	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	12	980	0	ENST00000375023.3:c.3452G>A	p.Gly1151Asp	p.G1151D	ENST00000375023	NM_004557.3	1151	gGc/gAc	21/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		980	239	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965227	25965227	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004593-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	314	1039	0	ENST00000435504.4:c.3979T>C	p.Tyr1327His	p.Y1327H	ENST00000435504		1327	Tat/Cat	13/13	0.824785111913291	3	FACETS	1	0.993	1	0.643	0.609	0.677	CLONAL	1	TRUE	1	0.871603811094242	3		1039	805	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149453024	149453024	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004593-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	239	877	0	ENST00000286301.3:c.922A>G	p.Asn308Asp	p.N308D	ENST00000286301	NM_005211.3	308	Aac/Gac	7/22	0.323443623124578	6	FACETS	1	0.987	1	0.59	0.554	0.626	INDETERMINATE	2	TRUE	2	0.871603811094242	6		877	638	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334966	81334966	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004593-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	149	827	5	ENST00000222390.5:c.1861G>T	p.Gly621Ter	p.G621*	ENST00000222390	NM_000601.4	621	Gga/Tga	16/18	0.871603811094242	4	FACETS	0.958	0.878	1	0.479	0.439	0.521	CLONAL	1	TRUE	2	0.871603811094242	4		832	668	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41267759	41267759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879255290	NA	P-0004593-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	293	1181	1	ENST00000357654.3:c.118G>A	p.Asp40Asn	p.D40N	ENST00000357654	NM_007294.3	40	Gac/Aac	3/23	0.323443623124578	6	FACETS	1	0.986	1	0.566	0.534	0.598	INDETERMINATE	2	TRUE	2	0.871603811094242	6		1182	815	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983141	201983141	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004593-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1468	566	1098	0	ENST00000359651.3:c.990C>G	p.Ser330Arg	p.S330R	ENST00000359651		330	agC/agG	7/8	0.871603811094242	8	FACETS	1	0.993	1	0.462	0.442	0.482	CLONAL	2	TRUE	3	0.871603811094242	8		1098	2034	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012345	176012345	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004593-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1490	197	1002	0	ENST00000367669.3:c.1589C>G	p.Ala530Gly	p.A530G	ENST00000367669	NM_022457.5	530	gCt/gGt	14/20	0.871603811094242	8	FACETS	0.969	0.893	1	0.194	0.178	0.21	CLONAL	1	TRUE	3	0.871603811094242	8		1002	1687	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707900	47707900	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004593-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	160	1077	0	ENST00000233146.2:c.2524G>C	p.Glu842Gln	p.E842Q	ENST00000233146	NM_000251.2	842	Gag/Cag	15/16	0.871603811094242	4	FACETS	0.81	0.743	0.88	0.405	0.371	0.44	CLONAL	1	TRUE	2	0.871603811094242	4		1077	848	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67459192	67459192	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0004593-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	184	897	0	ENST00000327367.4:c.607+1G>C		p.X203_splice	ENST00000327367	NM_005902.3	203			0.871603811094242	2	FACETS	0.914	0.852	0.976	0.457	0.426	0.488	CLONAL	1	TRUE	0	0.871603811094242	2		897	462	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-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	167	591	1	ENST00000378444.4:c.3848-5_3977del		p.X1283_splice	ENST00000378444	NM_001123385.1	1283		9/15	0.867681145528299	2	FACETS	0.802	0.743	0.862			1	CLONAL	1	TRUE	NA	0.871603811094242	2		592	478	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827231	72827231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375039347	NA	P-0004593-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	52	988	3	ENST00000268489.5:c.9350C>T	p.Ala3117Val	p.A3117V	ENST00000268489	NM_006885.3	3117	gCg/gTg	9/10	0.871603811094242	1	FACETS	0.216	0.185	0.25	0.216	0.185	0.25	SUBCLONAL	1	TRUE	0	0.871603811094242	1		991	311	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432829	432829	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326148362	NA	P-0004593-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	168	1025	1	ENST00000399788.2:c.2087G>A	p.Arg696Gln	p.R696Q	ENST00000399788	NM_001042603.1	696	cGg/cAg	15/28	0.811034164108771	4	FACETS	0.796	0.732	0.864	0.265	0.244	0.288	SUBCLONAL	1	TRUE	1	0.871603811094242	4		1026	906	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427512	49427512	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004593-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	147	1084	0	ENST00000301067.7:c.10976del	p.Pro3659LeufsTer90	p.P3659Lfs*90	ENST00000301067	NM_003482.3	3659	cCt/ct	39/54	0.871603811094242	3	FACETS	0.598	0.546	0.652	0.299	0.273	0.326	SUBCLONAL	1	TRUE	1	0.871603811094242	3		1084	810	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594213	55594226	+	frameshift_variant	Frame_Shift_Del	DEL	CTGAACTCAAAGTC	CTGAACTCAAAGTC	-	novel	NA	P-0004593-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	157	769	0	ENST00000288135.5:c.1920_1933del	p.Lys642ProfsTer3	p.K642Pfs*3	ENST00000288135	NM_000222.2	639	tCTGAACTCAAAGTC/t	13/21	0.871603811094242	4	FACETS	0.852	0.782	0.926	0.426	0.391	0.463	CLONAL	1	TRUE	2	0.871603811094242	4		769	791	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650804	93650804	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004593-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	146	611	0	ENST00000375746.1:c.1730A>C	p.Lys577Thr	p.K577T	ENST00000375746	NM_001174167.1	577	aAa/aCa	13/14	0.871603811094242	6	FACETS	1	0.919	1	0.252	0.229	0.275	CLONAL	1	TRUE	2	0.871603811094242	6		611	912	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0004956-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	88	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.969	0.861	1	0.969	0.861	1	CLONAL	1	TRUE	1	0.345977172384928	2		436	525	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0004956-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	191	643	0	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	1	2	FACETS	0.919	0.849	0.993	0.919	0.849	0.993	CLONAL	1	TRUE	1	0.345977172384928	2		643	1201	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993077	72993077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004956-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1439	413	1015	2	ENST00000268489.5:c.968C>T	p.Ser323Phe	p.S323F	ENST00000268489	NM_006885.3	323	tCc/tTc	2/10	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.345977172384928	2		1017	1852	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0005070-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	86	299	1	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	0.741026300382034	3	FACETS	0.56	0.496	0.628			1	SUBCLONAL	1	TRUE	NA	0.747244769444015	3		300	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs864622237	NA	P-0005070-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	492	393	0	ENST00000269305.4:c.700T>C	p.Tyr234His	p.Y234H	ENST00000269305	NM_001126112.2	234	Tac/Cac	7/11	0.749999265153079	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.747244769444015	2		393	546	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924886	49924886	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005070-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	255	479	0	ENST00000296474.3:c.4057T>C	p.Tyr1353His	p.Y1353H	ENST00000296474	NM_002447.2	1353	Tat/Cat	20/20	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.747244769444015	2		479	529	SUCCESS
APC	324	MSKCC	GRCh37	5	112177466	112177466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005070-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	129	378	1	ENST00000257430.4:c.6175G>A	p.Asp2059Asn	p.D2059N	ENST00000257430	NM_000038.5	2059	Gat/Aat	16/16	0.749999265153079	3	FACETS	0.678	0.616	0.744	0.226	0.205	0.248	SUBCLONAL	1	TRUE	0	0.747244769444015	3		379	699	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045918	180045918	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005070-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	74	214	0	ENST00000261937.6:c.2853G>C	p.Glu951Asp	p.E951D	ENST00000261937	NM_182925.4	951	gaG/gaC	21/30	NA	2	FACETS	0.593	0.523	0.667			1	INDETERMINATE	1	TRUE	NA	0.747244769444015	2		214	334	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169981	32169981	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005070-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	99	426	0	ENST00000375023.3:c.3627C>A	p.Asp1209Glu	p.D1209E	ENST00000375023	NM_004557.3	1209	gaC/gaA	21/30	1	2	FACETS	0.509	0.455	0.565	0.509	0.455	0.565	SUBCLONAL	1	TRUE	1	0.747244769444015	2		426	521	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031919	26031919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	56	498	0	ENST00000244661.2:c.370G>A	p.Asp124Asn	p.D124N	ENST00000244661	NM_003537.3	124	Gac/Aac	1/1	0.31249467276959	4	FACETS	1	0.952	1	0.64	0.548	0.741	CLONAL	1	TRUE	2	0.17	4		498	602	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845934	72845934	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	46	412	0	ENST00000268489.5:c.3533C>A	p.Ser1178Ter	p.S1178*	ENST00000268489	NM_006885.3	1178	tCg/tAg	6/10	0.142118194524246	0	FACETS	0.689	0.583	0.805			1	SUBCLONAL	2	TRUE	0	0.17	0		412	326	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857255	78857255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765037698	NA	P-0005078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	15	321	1	ENST00000306801.3:c.1621G>A	p.Val541Met	p.V541M	ENST00000306801	NM_020761.2	541	Gtg/Atg	15/34	1	2	FACETS	0.695	0.508	0.919	0.695	0.508	0.919	SUBCLONAL	1	TRUE	1	0.17	2		322	254	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922763	44922763	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	32	218	0	ENST00000377967.4:c.1624C>T	p.Gln542Ter	p.Q542*	ENST00000377967	NM_021140.2	542	Cag/Tag	16/29	1	1	FACETS	0.82	0.671	0.986	1	0.952	1	CLONAL	2	TRUE	0	0.17	1		218	210	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359429	118359431	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	novel	NA	P-0005078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	30	352	0	ENST00000534358.1:c.4434_4436del	p.Cys1479del	p.C1479del	ENST00000534358	NM_005933.3	1478	cGTTgc/cgc	11/36	1	2	FACETS	0.986	0.795	1	0.986	0.795	1	CLONAL	1	TRUE	1	0.17	2		352	358	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428569	72428569	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	24	175	0	ENST00000477973.2:c.433del	p.Ile146SerfsTer62	p.I146Sfs*62	ENST00000477973	NM_012234.5	145	cgG/cg	2/4	0.3	2	FACETS	1	0.825	1			1	CLONAL	1	TRUE	NA	0.17	2		175	267	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031919	26031919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005078-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	64	498	0	ENST00000244661.2:c.370G>A	p.Asp124Asn	p.D124N	ENST00000244661	NM_003537.3	124	Gac/Aac	1/1	1	2	FACETS	0.58	0.5	0.667	0.58	0.5	0.667	SUBCLONAL	1	TRUE	1	0.19	2		498	1162	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845934	72845934	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005078-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	80	412	0	ENST00000268489.5:c.3533C>A	p.Ser1178Ter	p.S1178*	ENST00000268489	NM_006885.3	1178	tCg/tAg	6/10	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.19	2		412	753	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359429	118359431	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	novel	NA	P-0005078-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	59	352	0	ENST00000534358.1:c.4434_4436del	p.Cys1479del	p.C1479del	ENST00000534358	NM_005933.3	1478	cGTTgc/cgc	11/36	0.201158743050409	3	FACETS	0.775	0.665	0.896	0.388	0.332	0.448	SUBCLONAL	1	TRUE	1	0.19	3		352	877	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428569	72428569	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005078-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	36	175	0	ENST00000477973.2:c.433del	p.Ile146SerfsTer62	p.I146Sfs*62	ENST00000477973	NM_012234.5	145	cgG/cg	2/4	0.201158743050409	3	FACETS	0.906	0.745	1	0.453	0.372	0.544	CLONAL	1	TRUE	1	0.19	3		175	458	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0005153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	257	398	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.198310371653545	6	FACETS	1	0.986	1			1	INDETERMINATE	4	TRUE	NA	0.462339650053158	6		398	481	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382152	152382154	+	inframe_deletion	In_Frame_Del	DEL	TGG	TGG	-	novel	NA	P-0005153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	106	291	0	ENST00000206249.3:c.1265_1267del	p.Val422del	p.V422del	ENST00000206249	NM_000125.3	421	aTGGtg/atg	6/8	0.462339650053158	3	FACETS	1	0.969	1	0.593	0.534	0.655	CLONAL	1	TRUE	1	0.462339650053158	3		291	476	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	227	433	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	0.371419799541538	5	FACETS	1	0.982	1	0.757	0.708	0.807	CLONAL	2	TRUE	2	0.462339650053158	5		433	732	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	35	368	0	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	0.462339650053158	3	FACETS	0.344	0.281	0.415	0.172	0.14	0.208	SUBCLONAL	1	TRUE	1	0.462339650053158	3		368	542	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873020	136873020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147198552	NA	P-0005153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	222	887	1	ENST00000241393.3:c.478G>A	p.Val160Ile	p.V160I	ENST00000241393	NM_003467.2	160	Gtc/Atc	2/2	0.462339650053158	3	FACETS	1	0.939	1	0.505	0.469	0.542	CLONAL	1	TRUE	1	0.462339650053158	3		888	1170	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288883	212288883	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0005153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	86	253	0	ENST00000342788.4:c.2863A>T	p.Lys955Ter	p.K955*	ENST00000342788	NM_005235.2	955	Aaa/Taa	23/28	0.433445079461286	4	FACETS	1	0.948	1	0.56	0.497	0.627	CLONAL	1	TRUE	2	0.462339650053158	4		253	486	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	42	652	1	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.848	0.706	1	0.848	0.706	1	CLONAL	1	TRUE	1	0.12	2		653	825	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0005187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	21	289	1	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	0.0773348259389569	0	FACETS	0.957	0.737	1			1	CLONAL	1	TRUE	0	0.12	0		290	322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0005187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	38	652	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	1	2	FACETS	0.772	0.636	0.926	0.772	0.636	0.926	CLONAL	1	TRUE	1	0.12	2		652	820	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053574	37053574	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	44	751	3	ENST00000231790.2:c.661G>T	p.Gly221Ter	p.G221*	ENST00000231790	NM_000249.3	221	Gga/Tga	8/19	1	2	FACETS	0.901	0.753	1	0.901	0.753	1	CLONAL	1	TRUE	1	0.12	2		754	814	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411551	116411551	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0005187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	34	447	0	ENST00000397752.3:c.2731-1G>C		p.X911_splice	ENST00000397752	NM_000245.2	911			1	2	FACETS	0.894	0.728	1	0.894	0.728	1	CLONAL	1	TRUE	1	0.12	2		447	634	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990723	7990723	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	56	678	1	ENST00000319144.4:c.38A>T	p.Asp13Val	p.D13V	ENST00000319144	NM_001139.2	13	gAc/gTc	1/15	1	2	FACETS	0.934	0.798	1	0.934	0.798	1	CLONAL	1	TRUE	1	0.12	2		679	999	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437784	52437803	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGTCCTTCTGGGACTCTT	GAGGTCCTTCTGGGACTCTT	-	novel	NA	P-0005187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	66	977	0	ENST00000460680.1:c.1358_1377del	p.Lys453IlefsTer9	p.K453Ifs*9	ENST00000460680	NM_004656.3	453	aAAGAGTCCCAGAAGGACCTC/a	13/17	1	2	FACETS	0.961	0.831	1	0.961	0.831	1	CLONAL	1	TRUE	1	0.12	2		977	1145	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252884	36252885	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	339	224	0	ENST00000300305.3:c.477dup	p.Asp160Ter	p.D160*	ENST00000300305		159	-/T	4/8	0.386256778708718	3	FACETS	0.895	0.851	0.939	0.895	0.851	0.939	CLONAL	2	TRUE	1	0.635995349187892	3		224	785	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0005676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	351	230	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.723282729295364	1	FACETS	0.999	0.957	1	0.999	0.957	1	CLONAL	1	TRUE	0	0.723282729295364	1		231	620	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553478	29553478	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781807	NA	P-0005676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	509	749	3	ENST00000356175.3:c.2033del	p.Pro678ArgfsTer10	p.P678Rfs*10	ENST00000356175	NM_000267.3	676	aCc/ac	18/57	0.723282729295364	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.723282729295364	1		752	893	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952528	38952528	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0005676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	31	153	0	ENST00000357387.3:c.2898-1G>T		p.X966_splice	ENST00000357387	NM_152756.3	966			1	2	FACETS	0.193	0.156	0.236	0.193	0.156	0.236	SUBCLONAL	1	TRUE	1	0.723282729295364	2		153	443	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652428	48652428	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	582	570	2	ENST00000376670.3:c.1099C>A	p.Leu367Met	p.L367M	ENST00000376670	NM_002049.3	367	Ctg/Atg	6/6	0.723282729295364	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.723282729295364	1		572	972	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938230	76938230	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	61	417	0	ENST00000373344.5:c.2518del	p.Arg840GlufsTer29	p.R840Efs*29	ENST00000373344	NM_000489.3	840	Aga/ga	9/35	0.723282729295364	1	FACETS	0.127	0.109	0.146	0.127	0.109	0.146	SUBCLONAL	1	TRUE	0	0.723282729295364	1		417	850	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348566	89348568	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs753054998	NA	P-0005676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1471	203	1048	1	ENST00000301030.4:c.4382_4384del	p.Lys1461del	p.K1461del	ENST00000301030	NM_001256183.1	1461	aAGAga/aga	9/13	0.723282729295364	1	FACETS	0.214	0.197	0.232	0.214	0.197	0.232	SUBCLONAL	1	TRUE	0	0.723282729295364	1		1049	1674	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223866	53223866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	136	688	1	ENST00000375401.3:c.3493C>T	p.Arg1165Cys	p.R1165C	ENST00000375401	NM_004187.3	1165	Cgt/Tgt	23/26	NA	2	FACETS	0.678	0.616	0.743			1	INDETERMINATE	1	TRUE	NA	0.455792244803899	2		689	880	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44921916	44921916	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	90	532	0	ENST00000377967.4:c.1450A>G	p.Arg484Gly	p.R484G	ENST00000377967	NM_021140.2	484	Aga/Gga	15/29	NA	2	FACETS	0.563	0.5	0.631			1	INDETERMINATE	1	TRUE	NA	0.455792244803899	2		532	701	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111502	8111503	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	257	580	0	ENST00000346208.3:c.990dup	p.Asn331GlufsTer21	p.N331Efs*21	ENST00000346208		330	agg/aGgg	5/6	0.210157274260314	5	FACETS	1	0.975	1	0.715	0.671	0.76	INDETERMINATE	2	TRUE	2	0.455792244803899	5		580	885	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138402603	138402603	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	50	422	0	ENST00000289153.2:c.2342C>G	p.Ser781Cys	p.S781C	ENST00000289153	NM_006219.2	781	tCc/tGc	16/22	0.44766216404144	3	FACETS	0.469	0.398	0.548	0.235	0.199	0.274	SUBCLONAL	1	TRUE	1	0.455792244803899	3		422	574	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974191	2974191	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	110	719	2	ENST00000396946.4:c.1414C>G	p.Gln472Glu	p.Q472E	ENST00000396946	NM_032415.4	472	Caa/Gaa	10/25	0.315143760264647	3	FACETS	0.785	0.705	0.869	0.393	0.352	0.435	SUBCLONAL	1	TRUE	1	0.455792244803899	3		721	755	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435596	18435596	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	65	289	0	ENST00000266497.5:c.581G>C	p.Arg194Thr	p.R194T	ENST00000266497		194	aGg/aCg	1/31	0.141153865670634	5	FACETS	1	0.953	1	0.302	0.263	0.345	INDETERMINATE	1	TRUE	1	0.455792244803899	5		289	397	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626758	28626758	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	74	422	1	ENST00000241453.7:c.538G>T	p.Asp180Tyr	p.D180Y	ENST00000241453	NM_004119.2	180	Gac/Tac	5/24	0.199980414183288	3	FACETS	0.736	0.645	0.833	0.245	0.215	0.278	INDETERMINATE	1	TRUE	0	0.455792244803899	3		423	542	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893363	32893363	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398122741	NA	P-0005900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	123	353	0	ENST00000380152.3:c.217C>T	p.Gln73Ter	p.Q73*	ENST00000380152		73	Cag/Tag	3/27	0.199980414183288	3	FACETS	1	0.984	1	0.472	0.429	0.516	INDETERMINATE	1	TRUE	0	0.455792244803899	3		353	468	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89355041	89355041	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0005900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	481	1047	0	ENST00000301030.4:c.639C>G	p.Tyr213Ter	p.Y213*	ENST00000301030	NM_001256183.1	213	taC/taG	7/13	0.274590494575688	3	FACETS	0.881	0.842	0.92	0.881	0.842	0.92	CLONAL	2	TRUE	1	0.455792244803899	3		1047	1471	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273832	18273832	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	134	660	0	ENST00000222254.8:c.1165T>C	p.Phe389Leu	p.F389L	ENST00000222254	NM_005027.3	389	Ttc/Ctc	10/16	0.266077397112	3	FACETS	0.781	0.709	0.856	0.39	0.354	0.428	INDETERMINATE	1	TRUE	1	0.455792244803899	3		660	925	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100144	27100145	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGACTCGGGGATGTATTCTCCTAG	novel	NA	P-0005900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	96	507	0	ENST00000324856.7:c.3942_3966dup	p.Tyr1324LeufsTer7	p.Y1324Lfs*7	ENST00000324856	NM_006015.4	1314	cca/cCAGACTCGGGGATGTATTCTCCTAGca	16/20	0.44766216404144	3	FACETS	0.755	0.673	0.842	0.378	0.336	0.421	SUBCLONAL	1	TRUE	1	0.455792244803899	3		507	685	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266797	18266817	+	inframe_deletion	In_Frame_Del	DEL	GGCCTTGCAGGCGCTGGGCGT	GGCCTTGCAGGCGCTGGGCGT	-	novel	NA	P-0005900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	85	359	1	ENST00000222254.8:c.112_132del	p.Leu38_Ala44del	p.L38_A44del	ENST00000222254	NM_005027.3	36	gcGGCCTTGCAGGCGCTGGGCGTg/gcg	2/16	0.266077397112	3	FACETS	0.918	0.814	1	0.459	0.407	0.514	INDETERMINATE	1	TRUE	1	0.455792244803899	3		360	499	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023574	27023580	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCCTA	CGGCCTA	-	novel	NA	P-0005900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	91	654	0	ENST00000324856.7:c.682_688del	p.Ala228ArgfsTer2	p.A228Rfs*2	ENST00000324856	NM_006015.4	227	cCGGCCTAc/cc	1/20	0.44766216404144	3	FACETS	0.558	0.494	0.626	0.279	0.247	0.313	SUBCLONAL	1	TRUE	1	0.455792244803899	3		654	879	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226412	133226412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200114024	NA	P-0005900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	82	640	0	ENST00000320574.5:c.3646G>A	p.Gly1216Ser	p.G1216S	ENST00000320574	NM_006231.2	1216	Ggc/Agc	30/49	0.455792244803899	3	FACETS	0.507	0.446	0.572	0.253	0.223	0.286	SUBCLONAL	1	TRUE	1	0.455792244803899	3		640	872	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021452	31021452	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	86	411	0	ENST00000375687.4:c.1451A>G	p.Glu484Gly	p.E484G	ENST00000375687	NM_015338.5	484	gAg/gGg	12/13	0.44766216404144	3	FACETS	0.722	0.639	0.81	0.361	0.319	0.405	SUBCLONAL	1	TRUE	1	0.455792244803899	3		411	642	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030928	36030965	+	frameshift_variant	Frame_Shift_Del	DEL	TGCAAAGTGGCGGACTTTGGGCTGGCTCGGCTCATTGA	TGCAAAGTGGCGGACTTTGGGCTGGCTCGGCTCATTGA	GGG	novel	NA	P-0005900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	41	584	0	ENST00000358208.4:c.1207_1244delinsGGG	p.Cys403GlyfsTer4	p.C403Gfs*4	ENST00000358208		403	TGCAAAGTGGCGGACTTTGGGCTGGCTCGGCTCATTGAa/GGGa	10/12	0.44766216404144	3	FACETS	0.316	0.263	0.377	0.158	0.131	0.189	SUBCLONAL	1	TRUE	1	0.455792244803899	3		584	698	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223866	53223866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	264	688	1	ENST00000375401.3:c.3493C>T	p.Arg1165Cys	p.R1165C	ENST00000375401	NM_004187.3	1165	Cgt/Tgt	23/26	0.178020003745393	5	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.495230358160555	5		689	1329	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44921916	44921916	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	144	532	0	ENST00000377967.4:c.1450A>G	p.Arg484Gly	p.R484G	ENST00000377967	NM_021140.2	484	Aga/Gga	15/29	0.178020003745393	5	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.495230358160555	5		532	807	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111502	8111503	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	317	580	0	ENST00000346208.3:c.990dup	p.Asn331GlufsTer21	p.N331Efs*21	ENST00000346208		330	agg/aGgg	5/6	0.498423905686986	4	FACETS	0.796	0.751	0.842	0.796	0.751	0.842	SUBCLONAL	2	TRUE	2	0.495230358160555	4		580	1203	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138402603	138402603	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	315	422	0	ENST00000289153.2:c.2342C>G	p.Ser781Cys	p.S781C	ENST00000289153	NM_006219.2	781	tCc/tGc	16/22	0.428290592636587	4	FACETS	1	0.949	1			1	CLONAL	2	TRUE	NA	0.495230358160555	4		422	948	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974191	2974191	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	184	719	2	ENST00000396946.4:c.1414C>G	p.Gln472Glu	p.Q472E	ENST00000396946	NM_032415.4	472	Caa/Gaa	10/25	0.498423905686986	3	FACETS	0.887	0.818	0.959	0.444	0.409	0.48	CLONAL	1	TRUE	1	0.495230358160555	3		721	1045	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435596	18435596	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	85	289	0	ENST00000266497.5:c.581G>C	p.Arg194Thr	p.R194T	ENST00000266497		194	aGg/aCg	1/31	0.498423905686986	3	FACETS	0.851	0.755	0.954	0.426	0.377	0.477	CLONAL	1	TRUE	1	0.495230358160555	3		289	503	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626758	28626758	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	158	422	1	ENST00000241453.7:c.538G>T	p.Asp180Tyr	p.D180Y	ENST00000241453	NM_004119.2	180	Gac/Tac	5/24	0.396238038612434	3	FACETS	0.982	0.9	1	0.491	0.45	0.533	CLONAL	1	TRUE	1	0.495230358160555	3		423	811	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893363	32893363	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398122741	NA	P-0005900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	266	353	0	ENST00000380152.3:c.217C>T	p.Gln73Ter	p.Q73*	ENST00000380152		73	Cag/Tag	3/27	0.396238038612434	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.495230358160555	3		353	561	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89355041	89355041	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0005900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	186	1047	0	ENST00000301030.4:c.639C>G	p.Tyr213Ter	p.Y213*	ENST00000301030	NM_001256183.1	213	taC/taG	7/13	1	2	FACETS	0.942	0.872	1	0.942	0.872	1	CLONAL	1	TRUE	1	0.495230358160555	2		1047	797	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273832	18273832	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	215	660	0	ENST00000222254.8:c.1165T>C	p.Phe389Leu	p.F389L	ENST00000222254	NM_005027.3	389	Ttc/Ctc	10/16	1	2	FACETS	0.97	0.903	1	0.97	0.903	1	CLONAL	1	TRUE	1	0.495230358160555	2		660	895	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100144	27100145	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGACTCGGGGATGTATTCTCCTAG	novel	NA	P-0005900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	174	507	0	ENST00000324856.7:c.3942_3966dup	p.Tyr1324LeufsTer7	p.Y1324Lfs*7	ENST00000324856	NM_006015.4	1314	cca/cCAGACTCGGGGATGTATTCTCCTAGca	16/20	0.498423905686986	3	FACETS	0.906	0.834	0.981			1	CLONAL	1	TRUE	NA	0.495230358160555	3		507	968	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266797	18266817	+	inframe_deletion	In_Frame_Del	DEL	GGCCTTGCAGGCGCTGGGCGT	GGCCTTGCAGGCGCTGGGCGT	-	novel	NA	P-0005900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	164	359	1	ENST00000222254.8:c.112_132del	p.Leu38_Ala44del	p.L38_A44del	ENST00000222254	NM_005027.3	36	gcGGCCTTGCAGGCGCTGGGCGTg/gcg	2/16	1	2	FACETS	0.975	0.898	1	0.975	0.898	1	CLONAL	1	TRUE	1	0.495230358160555	2		360	679	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023574	27023580	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCCTA	CGGCCTA	-	novel	NA	P-0005900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	125	654	0	ENST00000324856.7:c.682_688del	p.Ala228ArgfsTer2	p.A228Rfs*2	ENST00000324856	NM_006015.4	227	cCGGCCTAc/cc	1/20	0.498423905686986	3	FACETS	0.869	0.787	0.955			1	CLONAL	1	TRUE	NA	0.495230358160555	3		654	725	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032290	42032290	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778522495	NA	P-0005900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	82	902	2	ENST00000219905.7:c.4474C>T	p.Arg1492Cys	p.R1492C	ENST00000219905	NM_001164273.1	1492	Cgt/Tgt	14/24	0.228869588732205	5	FACETS	0.589	0.518	0.666			1	INDETERMINATE	1	TRUE	NA	0.495230358160555	5		904	980	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165717	185165717	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	62	529	0	ENST00000265026.3:c.992C>A	p.Ser331Tyr	p.S331Y	ENST00000265026	NM_004721.4	331	tCt/tAt	5/14	0.33200302359541	5	FACETS	0.559	0.482	0.644	0.186	0.16	0.215	SUBCLONAL	1	TRUE	2	0.495230358160555	5		529	780	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184649	185184649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	45	642	2	ENST00000265026.3:c.1541C>T	p.Thr514Ile	p.T514I	ENST00000265026	NM_004721.4	514	aCc/aTc	10/14	0.33200302359541	5	FACETS	0.398	0.333	0.47	0.133	0.111	0.157	SUBCLONAL	1	TRUE	2	0.495230358160555	5		644	796	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249172	55249172	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0005900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	78	800	0	ENST00000275493.2:c.2469+1G>C		p.X823_splice	ENST00000275493	NM_005228.3	823			0.498423905686986	3	FACETS	0.472	0.414	0.534	0.236	0.207	0.267	SUBCLONAL	1	TRUE	1	0.495230358160555	3		800	833	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994323	21994323	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	44	635	0	ENST00000579755.1:c.8G>C	p.Arg3Pro	p.R3P	ENST00000579755		3	cGc/cCc	1/3	1		FACETS		0.31	0.436				SUBCLONAL	1	TRUE	1	0.495230358160555	2		635	481	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030928	36030964	+	protein_altering_variant	In_Frame_Del	DEL	TGCAAAGTGGCGGACTTTGGGCTGGCTCGGCTCATTG	TGCAAAGTGGCGGACTTTGGGCTGGCTCGGCTCATTG	A	novel	NA	P-0005900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	317	1067	2	ENST00000358208.4:c.1207_1243delinsA	p.Cys403_Glu415delinsLys	p.C403_E415delinsK	ENST00000358208		403	TGCAAAGTGGCGGACTTTGGGCTGGCTCGGCTCATTGaa/Aaa	10/12	0.289507080134539	5	FACETS	0.986	0.93	1	0.657	0.62	0.695	INDETERMINATE	2	TRUE	2	0.495230358160555	5		1069	1132	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471712	120471712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs75423398	NA	P-0005953-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	524	242	1	ENST00000256646.2:c.3779G>A	p.Arg1260His	p.R1260H	ENST00000256646	NM_024408.3	1260	cGt/cAt	23/34	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.938127259250155	2		243	1093	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165688	108165688	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005953-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	544	262	0	ENST00000278616.4:c.4811A>T	p.Asp1604Val	p.D1604V	ENST00000278616	NM_000051.3	1604	gAt/gTt	32/63	1	2	FACETS	0.998	0.961	1	0.998	0.961	1	CLONAL	1	TRUE	1	0.938127259250155	2		262	1162	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471712	120471712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs75423398	NA	P-0005953-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	345	242	1	ENST00000256646.2:c.3779G>A	p.Arg1260His	p.R1260H	ENST00000256646	NM_024408.3	1260	cGt/cAt	23/34	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.944754849595377	2		243	730	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165688	108165688	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005953-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	347	262	0	ENST00000278616.4:c.4811A>T	p.Asp1604Val	p.D1604V	ENST00000278616	NM_000051.3	1604	gAt/gTt	32/63	1	2	FACETS	0.985	0.939	1	0.985	0.939	1	CLONAL	1	TRUE	1	0.944754849595377	2		262	746	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471712	120471712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs75423398	NA	P-0005953-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	123	242	1	ENST00000256646.2:c.3779G>A	p.Arg1260His	p.R1260H	ENST00000256646	NM_024408.3	1260	cGt/cAt	23/34	1	2	FACETS	0.76	0.689	0.836	1	0.985	1	SUBCLONAL	2	TRUE	1	0.24	2		243	674	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165688	108165688	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005953-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	33	262	0	ENST00000278616.4:c.4811A>T	p.Asp1604Val	p.D1604V	ENST00000278616	NM_000051.3	1604	gAt/gTt	32/63	1	2	FACETS	1	0.833	1	1	0.833	1	CLONAL	1	TRUE	1	0.24	2		262	270	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243866	46243866	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005953-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	15	312	1	ENST00000334344.6:c.1960C>T	p.Pro654Ser	p.P654S	ENST00000334344	NM_152641.2	654	Cct/Tct	15/21	1	2	FACETS	0.483	0.353	0.639	0.483	0.353	0.639	SUBCLONAL	1	TRUE	1	0.24	2		313	259	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867469	35867469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs191585195	NA	P-0005953-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	15	360	1	ENST00000303115.3:c.283G>A	p.Glu95Lys	p.E95K	ENST00000303115	NM_002185.3	95	Gag/Aag	3/8	1	2	FACETS	0.576	0.422	0.761	0.576	0.422	0.761	SUBCLONAL	1	TRUE	1	0.24	2		361	217	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266596	198266596	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	28	388	4	ENST00000335508.6:c.2240T>G	p.Leu747Trp	p.L747W	ENST00000335508	NM_012433.2	747	tTg/tGg	16/25	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		392	395	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001148	150001148	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	40	640	0	ENST00000253339.5:c.2456T>G	p.Val819Gly	p.V819G	ENST00000253339		819	gTt/gGt	4/7	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		640	795	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439796	52439796	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	125	652	0	ENST00000460680.1:c.916G>T	p.Glu306Ter	p.E306*	ENST00000460680	NM_004656.3	306	Gag/Tag	10/17	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		652	753	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0006358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	188	305	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.370033217965185	2		305	956	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902290	151902290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301632462	NA	P-0006358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	27	64	0	ENST00000262189.6:c.3862C>T	p.Arg1288Trp	p.R1288W	ENST00000262189	NM_170606.2	1288	Cgg/Tgg	25/59	NA	2	FACETS	0.76	0.609	0.929			1	INDETERMINATE	1	TRUE	NA	0.370033217965185	2		64	192	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447774	187447774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536118071	NA	P-0006358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	109	234	0	ENST00000232014.4:c.419G>A	p.Arg140His	p.R140H	ENST00000232014	NM_001130845.1	140	cGt/cAt	5/10	1	2	FACETS	0.781	0.702	0.866	0.781	0.702	0.866	SUBCLONAL	1	TRUE	1	0.370033217965185	2		234	754	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513012	106513012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758968659	NA	P-0006358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	126	310	0	ENST00000359195.3:c.2026G>A	p.Ala676Thr	p.A676T	ENST00000359195	NM_002649.2	676	Gcc/Acc	3/11	0.254125707998068	3	FACETS	0.842	0.762	0.928			1	CLONAL	1	TRUE	NA	0.370033217965185	3		310	958	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495749	72495749	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006749-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	264	332	1	ENST00000477973.2:c.323C>T	p.Ala108Val	p.A108V	ENST00000477973	NM_012234.5	108	gCc/gTc	1/4	NA	2	FACETS	0.872	0.823	0.921			1	INDETERMINATE	1	TRUE	NA	0.949004787418086	2		333	638	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431508	49431508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006749-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	55	479	0	ENST00000301067.7:c.9631G>A	p.Glu3211Lys	p.E3211K	ENST00000301067	NM_003482.3	3211	Gaa/Aaa	34/54	1	2	FACETS	0.183	0.156	0.213	0.183	0.156	0.213	SUBCLONAL	1	TRUE	1	0.949004787418086	2		479	633	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32905055	32905055	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs81002831	NA	P-0006749-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	159	166	0	ENST00000380152.3:c.682-1G>C		p.X228_splice	ENST00000380152		228			0.913702038103517	1	FACETS	0.989	0.956	1	0.989	0.956	1	CLONAL	1	TRUE	0	0.949004787418086	1		166	178	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857622	9857622	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006749-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	130	338	0	ENST00000330684.3:c.3779C>A	p.Pro1260Gln	p.P1260Q	ENST00000330684	NM_001134407.1	1260	cCa/cAa	13/13	NA	2	FACETS	0.614	0.561	0.669			1	INDETERMINATE	1	TRUE	NA	0.949004787418086	2		338	446	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578231	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAGTGTTTCTGTCATCC	AAAAGTGTTTCTGTCATCC	-	novel	NA	P-0006749-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	312	521	0	ENST00000269305.4:c.618_636del	p.Leu206PhefsTer35	p.L206Ffs*35	ENST00000269305	NM_001126112.2	206	ttGGATGACAGAAACACTTTT/tt	6/11	0.949004787418086	1	FACETS	0.96	0.935	0.983	0.96	0.935	0.983	CLONAL	1	TRUE	0	0.949004787418086	1		521	360	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	186	406	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	0.393223838768677	2		406	849	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0006830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	194	364	2	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.969	0.896	1	0.969	0.896	1	CLONAL	1	TRUE	1	0.393223838768677	2		366	1018	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278049	18278049	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs372272045	NA	P-0006830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	510	375	1	ENST00000222254.8:c.1669G>T	p.Asp557Tyr	p.D557Y	ENST00000222254	NM_005027.3	557	Gac/Tac	13/16	0.393223838768677	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.393223838768677	3		376	1390	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652853	212652853	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs768943270	NA	P-0006830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	180	355	0	ENST00000342788.4:c.453G>C	p.Gln151His	p.Q151H	ENST00000342788	NM_005235.2	151	caG/caC	4/28	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.393223838768677	2		355	820	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547379	106547379	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	174	260	0	ENST00000369096.4:c.616G>A	p.Glu206Lys	p.E206K	ENST00000369096	NM_001198.3	206	Gaa/Aaa	4/7	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.393223838768677	2		260	822	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171623	36171624	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0006830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	157	221	0	ENST00000300305.3:c.941_942del	p.Ser314CysfsTer285	p.S314Cfs*285	ENST00000300305		314	tCT/t	7/8	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.393223838768677	2		221	797	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589150	67589150	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	141	250	0	ENST00000274335.5:c.1139del	p.Leu380Ter	p.L380*	ENST00000274335		380	Tta/ta	9/15	1	2	FACETS	0.945	0.862	1	0.945	0.862	1	CLONAL	1	TRUE	1	0.393223838768677	2		250	759	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0006840-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	103	280	1	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.852	0.764	0.944	0.852	0.764	0.944	CLONAL	1	FALSE	1	0.410726948168731	2		281	589	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170797	99170797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750178020	NA	P-0006840-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	236	549	0	ENST00000074304.5:c.1426G>A	p.Ala476Thr	p.A476T	ENST00000074304	NM_001134224.1	476	Gct/Act	16/26	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.410726948168731	2		549	956	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678781	52678781	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006840-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	296	376	0	ENST00000394830.3:c.838T>C	p.Phe280Leu	p.F280L	ENST00000394830	NM_018313.4	280	Ttt/Ctt	9/30	1	2	FACETS	0.99	0.938	1	1	0.996	1	CLONAL	2	FALSE	1	0.410726948168731	2		376	728	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157728	106157728	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006840-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	179	436	2	ENST00000380013.4:c.2629G>C	p.Asp877His	p.D877H	ENST00000380013	NM_001127208.2	877	Gat/Cat	3/11	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	FALSE	1	0.410726948168731	2		438	869	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944570	38944570	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006840-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1191	196	523	0	ENST00000357387.3:c.4891T>C	p.Cys1631Arg	p.C1631R	ENST00000357387	NM_152756.3	1631	Tgt/Cgt	36/38	0.410726948168731	4	FACETS	0.971	0.896	1			1	CLONAL	1	FALSE	NA	0.410726948168731	4		523	1387	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93626890	93626890	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006840-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	600	625	0	ENST00000375746.1:c.737A>C	p.Tyr246Ser	p.Y246S	ENST00000375746	NM_001174167.1	246	tAt/tCt	5/14	0.410726948168731	3	FACETS	1	0.968	1	1	0.997	1	CLONAL	3	FALSE	1	0.410726948168731	3		625	1171	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33427978	33427978	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006840-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	468	639	0	ENST00000345365.6:c.981G>C	p.Gln327His	p.Q327H	ENST00000345365	NM_002878.3	327	caG/caC	10/10	1	2	FACETS	1	0.958	1	1	0.997	1	CLONAL	2	FALSE	1	0.410726948168731	2		639	1139	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347795	347816	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTGTGTGGTTCCAGGCCCCA	GGCTGTGTGGTTCCAGGCCCCA	-	novel	NA	P-0006840-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	89	619	0	ENST00000262320.3:c.1690_1711del	p.Trp564MetfsTer134	p.W564Mfs*134	ENST00000262320	NM_003502.3	564	TGGGGCCTGGAACCACACAGCCat/at	6/11	1	2	FACETS	0.373	0.329	0.42	0.373	0.329	0.42	SUBCLONAL	1	FALSE	1	0.410726948168731	2		619	1162	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937647	44937679	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GGAAAATAAACGTGATGCTTTCTTTCCTCCATT	GGAAAATAAACGTGATGCTTTCTTTCCTCCATT	-	novel	NA	P-0006840-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	94	234	0	ENST00000377967.4:c.2835_2867del	p.Glu946_Leu956del	p.E946_L956del	ENST00000377967	NM_021140.2	945	ttGGAAAATAAACGTGATGCTTTCTTTCCTCCATTa/tta	19/29	1	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	0	0.410726948168731	1		234	332	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061249	38061249	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	217	570	0	ENST00000250448.2:c.740A>G	p.His247Arg	p.H247R	ENST00000250448	NM_004496.3	247	cAc/cGc	2/2	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.4	2		570	953	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59937172	59937172	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	91	481	0	ENST00000259008.2:c.190C>A	p.Gln64Lys	p.Q64K	ENST00000259008	NM_032043.2	64	Caa/Aaa	3/20	1	2	FACETS	0.944	0.842	1	0.944	0.842	1	CLONAL	1	TRUE	1	0.4	2		481	482	SUCCESS
APC	324	MSKCC	GRCh37	5	112178891	112178903	+	frameshift_variant	Frame_Shift_Del	DEL	GAAAGTCCTTCTA	GAAAGTCCTTCTA	-	novel	NA	P-0007005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	47	459	0	ENST00000257430.4:c.7602_7614del	p.Glu2534AspfsTer24	p.E2534Dfs*24	ENST00000257430	NM_000038.5	2534	GAAAGTCCTTCTAga/ga	16/16	1	2	FACETS	0.354	0.298	0.417	0.354	0.298	0.417	SUBCLONAL	1	TRUE	1	0.4	2		459	663	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0007113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	153	495	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.345224346867668	3	FACETS	0.786	0.721	0.853	0.786	0.721	0.853	SUBCLONAL	2	TRUE	1	0.348682735084858	3		495	656	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828161	243828161	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	43	372	0	ENST00000263826.5:c.197G>C	p.Arg66Pro	p.R66P	ENST00000263826	NM_005465.4	66	cGa/cCa	3/13	1	2	FACETS	0.512	0.428	0.604	0.512	0.428	0.604	SUBCLONAL	1	TRUE	1	0.348682735084858	2		372	482	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098416	47098416	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0007113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	127	451	1	ENST00000409792.3:c.6858C>G	p.Tyr2286Ter	p.Y2286*	ENST00000409792	NM_014159.6	2286	taC/taG	15/21	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.348682735084858	2		452	711	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467484	66467484	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	79	427	0	ENST00000273854.3:c.785G>C	p.Cys262Ser	p.C262S	ENST00000273854	NM_004439.5	262	tGt/tCt	3/18	1	2	FACETS	0.844	0.744	0.951	0.844	0.744	0.951	CLONAL	1	TRUE	1	0.348682735084858	2		427	537	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057584	180057584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	351	541	1	ENST00000261937.6:c.371C>T	p.Thr124Met	p.T124M	ENST00000261937	NM_182925.4	124	aCg/aTg	3/30	0.348682735084858	2	FACETS	0.921	0.873	0.97	0.921	0.873	0.97	CLONAL	2	TRUE	0	0.348682735084858	2		542	1093	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89806486	89806486	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	190	465	1	ENST00000389301.3:c.3850G>T	p.Ala1284Ser	p.A1284S	ENST00000389301	NM_000135.2	1284	Gct/Tct	39/43	0.345224346867668	3	FACETS	1	0.988	1	0.671	0.621	0.724	CLONAL	1	TRUE	1	0.348682735084858	3		466	953	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577530	7577530	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	235	551	0	ENST00000269305.4:c.751A>T	p.Ile251Phe	p.I251F	ENST00000269305	NM_001126112.2	251	Atc/Ttc	7/11	1	2	FACETS	0.922	0.864	0.981	1	0.994	1	CLONAL	2	TRUE	1	0.348682735084858	2		551	731	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575213	48575241	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTGTATCACCTGGAATTGGTAAGTAGACT	TTGTATCACCTGGAATTGGTAAGTAGACT	-	novel	NA	P-0007113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	52	339	0	ENST00000342988.3:c.410_424+14del		p.X137_splice	ENST00000342988	NM_005359.5	137		3/12	0.252560632926157	1	FACETS	0.573	0.488	0.665	0.573	0.488	0.665	SUBCLONAL	1	TRUE	0	0.348682735084858	1		339	430	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950031	44950031	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1461259213	NA	P-0007146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	230	664	0	ENST00000377967.4:c.3800T>G	p.Ile1267Arg	p.I1267R	ENST00000377967	NM_021140.2	1267	aTa/aGa	26/29	0.305743798141586	2	FACETS	1	0.974	1	0.547	0.509	0.587	CLONAL	1	TRUE	0	0.305743798141586	2		664	1375	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879451	151879451	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	153	531	0	ENST00000262189.6:c.5494A>G	p.Lys1832Glu	p.K1832E	ENST00000262189	NM_170606.2	1832	Aaa/Gaa	36/59	0.289515139467726	4	FACETS	0.971	0.886	1	0.485	0.443	0.531	CLONAL	1	TRUE	2	0.305743798141586	4		531	1346	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950031	44950031	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1461259213	NA	P-0007146-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	94	664	0	ENST00000377967.4:c.3800T>G	p.Ile1267Arg	p.I1267R	ENST00000377967	NM_021140.2	1267	aTa/aGa	26/29	0.571678608323247	2	FACETS	0.807	0.724	0.893	0.403	0.362	0.447	CLONAL	1	TRUE	0	0.645694277514895	2		664	361	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984107	2984107	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007146-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	67	426	0	ENST00000396946.4:c.423G>C	p.Gln141His	p.Q141H	ENST00000396946	NM_032415.4	141	caG/caC	5/25	0.556493429552422	4	FACETS	0.825	0.72	0.938	0.412	0.36	0.469	CLONAL	1	TRUE	2	0.645694277514895	4		426	414	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879451	151879451	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007146-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	82	531	0	ENST00000262189.6:c.5494A>G	p.Lys1832Glu	p.K1832E	ENST00000262189	NM_170606.2	1832	Aaa/Gaa	36/59	0.406715395170674	5	FACETS	1	0.965	1	0.409	0.363	0.459	CLONAL	1	TRUE	2	0.645694277514895	5		531	407	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0007227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	10	268	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.119	0.08	0.168	0.119	0.08	0.168	SUBCLONAL	1	TRUE	1	0.37477076489073	2		268	449	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41219650	41219650	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	120	335	1	ENST00000357654.3:c.5049G>T	p.Glu1683Asp	p.E1683D	ENST00000357654	NM_007294.3	1683	gaG/gaT	16/23	0.367965577529359	2	FACETS	1	0.959	1	0.552	0.5	0.607	CLONAL	1	TRUE	0	0.37477076489073	2		336	580	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41219650	41219650	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007227-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	83	335	1	ENST00000357654.3:c.5049G>T	p.Glu1683Asp	p.E1683D	ENST00000357654	NM_007294.3	1683	gaG/gaT	16/23	0.3	3	FACETS	0.731	0.644	0.825	0.244	0.214	0.275	SUBCLONAL	1	FALSE	0	0.3	3		336	870	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	166	205	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.857	0.79	0.926	1	0.993	1	CLONAL	3	TRUE	1	0.2	2		205	646	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729147	66729147	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730880503	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	102	654	2	ENST00000307102.5:c.355C>T	p.His119Tyr	p.H119Y	ENST00000307102	NM_002755.3	119	Cat/Tat	3/11	1	2	FACETS	0.986	0.886	1	1	0.987	1	CLONAL	2	TRUE	1	0.2	2		656	517	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	132	659	7	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	0.168552875100244	0	FACETS	1	0.918	1			1	CLONAL	2	TRUE	0	0.2	0		666	525	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	163	428	2	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.953	1	1	0.994	1	CLONAL	3	TRUE	1	0.2	2		430	521	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	100	236	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	0.212252560871464	4	FACETS	1	0.941	1			1	CLONAL	4	TRUE	NA	0.2	4		236	285	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	156	562	3	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.843	0.775	0.913	1	0.993	1	CLONAL	3	TRUE	1	0.2	2		565	617	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	81	294	2	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	0.168552875100244	0	FACETS	0.818	0.725	0.917			1	CLONAL	2	TRUE	0	0.2	0		296	396	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	117	993	1	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	1	0.973	1	1	0.992	1	CLONAL	3	TRUE	1	0.2	2		994	335	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	101	471	8	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.874	0.788	0.965	1	0.99	1	CLONAL	3	TRUE	1	0.2	2		479	385	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654820	29654820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786203416	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	89	380	1	ENST00000356175.3:c.5509G>A	p.Ala1837Thr	p.A1837T	ENST00000356175	NM_000267.3	1837	Gca/Aca	37/57	1	2	FACETS	0.929	0.827	1	1	0.985	1	CLONAL	2	TRUE	1	0.2	2		381	479	SUCCESS
APC	324	MSKCC	GRCh37	5	112173669	112173670	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	120	478	0	ENST00000257430.4:c.2379_2380del	p.Tyr796TrpfsTer2	p.Y796Wfs*2	ENST00000257430	NM_000038.5	793	cAA/c	16/16	1	2	FACETS	0.844	0.767	0.924	1	0.991	1	CLONAL	3	TRUE	1	0.2	2		478	474	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030326	180030326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150279372	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	149	689	1	ENST00000261937.6:c.3958C>T	p.Arg1320Trp	p.R1320W	ENST00000261937	NM_182925.4	1320	Cgg/Tgg	30/30	0.113202477447931	0	FACETS	0.866	0.798	0.936			1	INDETERMINATE	3	TRUE	0	0.2	0		690	459	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	187	973	3	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.994	0.923	1	1	0.994	1	CLONAL	3	TRUE	1	0.2	2		976	627	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	171	853	7	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	0.218352253574304	3	FACETS	0.905	0.835	0.977	0.905	0.835	0.977	CLONAL	3	TRUE	0	0.2	3		860	693	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852118	63852118	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	64	230	0	ENST00000279873.7:c.2901del	p.Lys967AsnfsTer15	p.K967Nfs*15	ENST00000279873	NM_032199.2	966	Aaa/aa	10/10	0.3	4	FACETS	1	0.932	1			1	CLONAL	2	TRUE	NA	0.2	4		230	346	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	187	660	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.113202477447931	0	FACETS	0.819	0.76	0.879			1	INDETERMINATE	3	TRUE	0	0.2	0		663	609	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	102	504	6	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.958	1	1	0.991	1	CLONAL	3	TRUE	1	0.2	2		510	308	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165327	47165327	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs186148199	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	134	492	0	ENST00000409792.3:c.799G>A	p.Val267Ile	p.V267I	ENST00000409792	NM_014159.6	267	Gta/Ata	3/21	1	2	FACETS	0.91	0.832	0.99	1	0.992	1	CLONAL	3	TRUE	1	0.2	2		492	491	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533838	533838	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	152	596	0	ENST00000451590.1:c.218G>A	p.Arg73His	p.R73H	ENST00000451590	NM_001130442.1	73	cGc/cAc	3/5	1	2	FACETS	1	0.966	1	1	0.994	1	CLONAL	3	TRUE	1	0.2	2		596	466	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779210	3779211	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs587783507	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	36	305	0	ENST00000262367.5:c.5837dup	p.Pro1947ThrfsTer19	p.P1947Tfs*19	ENST00000262367	NM_004380.2	1946	cca/ccCa	31/31	0.168552875100244	0	FACETS	0.878	0.732	1			1	CLONAL	2	TRUE	0	0.2	0		305	164	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	211	764	1	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	0.3	1	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	0	0.2	1		765	767	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055919	180055919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1368679940	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	81	559	1	ENST00000261937.6:c.1066G>A	p.Val356Met	p.V356M	ENST00000261937	NM_182925.4	356	Gtg/Atg	8/30	0.113202477447931	0	FACETS	0.927	0.83	1			1	INDETERMINATE	3	TRUE	0	0.2	0		560	233	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247894	59247894	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	272	888	1	ENST00000371222.2:c.849del	p.Val284Ter	p.V284*	ENST00000371222	NM_002228.3	283	aaA/aa	1/1	1	2	FACETS	0.949	0.892	1	1	0.996	1	CLONAL	3	TRUE	1	0.2	2		889	955	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783217	9783217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140820694	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	110	683	1	ENST00000377346.4:c.2461C>T	p.Arg821Cys	p.R821C	ENST00000377346	NM_005026.3	821	Cgc/Tgc	20/24	1	2	FACETS	0.905	0.82	0.994	1	0.991	1	CLONAL	3	TRUE	1	0.2	2		684	405	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272533	11272533	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	23	305	0	ENST00000361445.4:c.3399-2A>G		p.X1133_splice	ENST00000361445	NM_004958.3	1133			1	2	FACETS	0.79	0.617	0.99	0.79	0.617	0.99	CLONAL	1	TRUE	1	0.2	2		305	291	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300450	11300450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	156	531	0	ENST00000361445.4:c.1696G>A	p.Ala566Thr	p.A566T	ENST00000361445	NM_004958.3	566	Gcc/Acc	11/58	1	2	FACETS	0.944	0.874	1	1	0.994	1	CLONAL	4	TRUE	1	0.2	2		531	413	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027071	48027071	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	35	615	0	ENST00000234420.5:c.1949G>A	p.Gly650Asp	p.G650D	ENST00000234420	NM_000179.2	650	gGc/gAc	4/10	1	2	FACETS	0.707	0.579	0.851	0.707	0.579	0.851	SUBCLONAL	1	TRUE	1	0.2	2		615	495	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661129	227661129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781654199	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	163	697	4	ENST00000305123.5:c.2326C>T	p.Arg776Cys	p.R776C	ENST00000305123	NM_005544.2	776	Cgc/Tgc	1/2	1	2	FACETS	0.975	0.9	1	1	0.994	1	CLONAL	3	TRUE	1	0.2	2		701	557	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053348	37053348	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs863225383	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	130	524	0	ENST00000231790.2:c.583A>T	p.Lys195Ter	p.K195*	ENST00000231790	NM_000249.3	195	Aaa/Taa	7/19	1	2	FACETS	0.938	0.857	1	1	0.992	1	CLONAL	3	TRUE	1	0.2	2		524	462	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067170	37067170	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	87	415	0	ENST00000231790.2:c.1081A>T	p.Lys361Ter	p.K361*	ENST00000231790	NM_000249.3	361	Aaa/Taa	12/19	1	2	FACETS	0.909	0.813	1	1	0.988	1	CLONAL	3	TRUE	1	0.2	2		415	319	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067474	37067474	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	112	438	0	ENST00000231790.2:c.1385G>T	p.Arg462Ile	p.R462I	ENST00000231790	NM_000249.3	462	aGa/aTa	12/19	1	2	FACETS	1	0.949	1	1	0.991	1	CLONAL	3	TRUE	1	0.2	2		438	351	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247444	71247444	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	106	509	0	ENST00000318789.4:c.89G>T	p.Gly30Val	p.G30V	ENST00000318789	NM_032682.5	30	gGc/gTc	6/21	1	2	FACETS	1	0.933	1	1	0.988	1	CLONAL	2	TRUE	1	0.2	2		509	506	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139841	55139841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	125	550	0	ENST00000257290.5:c.1502G>A	p.Cys501Tyr	p.C501Y	ENST00000257290	NM_006206.4	501	tGc/tAc	10/23	0.281814464360605	1	FACETS	0.862	0.786	0.941	1	0.992	1	CLONAL	3	TRUE	0	0.2	1		550	435	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236591	236591	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553999731	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	42	156	0	ENST00000264932.6:c.1309G>A	p.Ala437Thr	p.A437T	ENST00000264932	NM_004168.2	437	Gcc/Acc	10/15	0.3	1	FACETS	1	0.928	1	1	0.979	1	CLONAL	3	TRUE	0	0.2	1		156	111	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627257	86627257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1458179717	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	72	550	3	ENST00000274376.6:c.632G>A	p.Arg211Gln	p.R211Q	ENST00000274376	NM_002890.2	211	cGg/cAg	2/25	0.202094318680553	4	FACETS	1	0.948	1	0.584	0.509	0.664	CLONAL	1	TRUE	2	0.2	4		553	740	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176671271	176671271	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	48	526	0	ENST00000439151.2:c.4378G>T	p.Gly1460Cys	p.G1460C	ENST00000439151	NM_022455.4	1460	Ggc/Tgc	9/23	0.113202477447931	0	FACETS	0.682	0.576	0.799			1	INDETERMINATE	1	TRUE	0	0.2	0		526	563	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910638	29910638	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	53	630	0	ENST00000376809.5:c.178T>C	p.Phe60Leu	p.F60L	ENST00000376809	NM_002116.7	60	Ttc/Ctc	2/8	0.3	4	FACETS	1	0.935	1	0.591	0.504	0.686	CLONAL	1	TRUE	2	0.2	4		630	538	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910755	29910755	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs41542015	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	62	829	0	ENST00000376809.5:c.295C>T	p.Arg99Ter	p.R99*	ENST00000376809	NM_002116.7	99	Cga/Tga	2/8	0.3	4	FACETS	1	0.874	1	0.507	0.437	0.583	CLONAL	1	TRUE	2	0.2	4		829	734	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180680	32180680	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	48	709	0	ENST00000375023.3:c.2447G>T	p.Arg816Met	p.R816M	ENST00000375023	NM_004557.3	816	aGg/aTg	16/30	1	2	FACETS	0.928	0.785	1	0.928	0.785	1	CLONAL	1	TRUE	1	0.2	2		709	517	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759976	133759976	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	48	785	0	ENST00000318560.5:c.2299G>A	p.Ala767Thr	p.A767T	ENST00000318560	NM_005157.4	767	Gca/Aca	11/11	0.218352253574304	3	FACETS	0.795	0.671	0.932	0.265	0.223	0.311	CLONAL	1	TRUE	0	0.2	3		785	664	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396942	139396942	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	34	142	0	ENST00000277541.6:c.5168-2A>G		p.X1723_splice	ENST00000277541	NM_017617.3	1723			0.218352253574304	3	FACETS	0.917	0.762	1	0.917	0.762	1	CLONAL	3	TRUE	0	0.2	3		142	136	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450964	70450964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540373976	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	110	382	1	ENST00000373644.4:c.5804C>T	p.Thr1935Met	p.T1935M	ENST00000373644	NM_030625.2	1935	aCg/aTg	12/12	NA	2	FACETS	1	0.929	1			1	INDETERMINATE	3	TRUE	NA	0.2	2		383	357	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325150	123325150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	178	523	1	ENST00000358487.5:c.178G>A	p.Val60Met	p.V60M	ENST00000358487	NM_000141.4	60	Gtg/Atg	3/18	0.113202477447931	0	FACETS	1	0.939	1			1	INDETERMINATE	3	TRUE	0	0.2	0		524	470	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138858	64138858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	78	376	2	ENST00000334205.4:c.2225G>A	p.Arg742His	p.R742H	ENST00000334205	NM_003942.2	742	cGc/cAc	17/17	1	2	FACETS	1	0.958	1	1	0.988	1	CLONAL	3	TRUE	1	0.2	2		378	226	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383301	4383301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	69	514	0	ENST00000261254.3:c.95C>T	p.Thr32Ile	p.T32I	ENST00000261254	NM_001759.3	32	aCc/aTc	1/5	1	2	FACETS	0.763	0.667	0.867	1	0.974	1	SUBCLONAL	2	TRUE	1	0.2	2		514	452	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905406	11905406	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	39	422	0	ENST00000396373.4:c.56C>A	p.Pro19His	p.P19H	ENST00000396373	NM_001987.4	19	cCt/cAt	2/8	1	2	FACETS	0.739	0.612	0.881	0.739	0.612	0.881	SUBCLONAL	1	TRUE	1	0.2	2		422	528	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244911	46244911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	131	618	0	ENST00000334344.6:c.3005C>T	p.Thr1002Ile	p.T1002I	ENST00000334344	NM_152641.2	1002	aCt/aTt	15/21	1	2	FACETS	0.985	0.896	1	1	0.99	1	CLONAL	2	TRUE	1	0.2	2		618	665	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435998	49435998	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393276376	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	91	475	1	ENST00000301067.7:c.5983G>A	p.Gly1995Arg	p.G1995R	ENST00000301067	NM_003482.3	1995	Gga/Aga	28/54	1	2	FACETS	0.936	0.84	1	1	0.989	1	CLONAL	3	TRUE	1	0.2	2		476	324	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431367	121431367	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	72	491	0	ENST00000257555.6:c.571G>T	p.Gly191Cys	p.G191C	ENST00000257555		191	Ggt/Tgt	3/10	1	2	FACETS	0.955	0.839	1	1	0.982	1	CLONAL	2	TRUE	1	0.2	2		491	377	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133315	30133315	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	63	931	0	ENST00000263025.4:c.183C>A	p.Asp61Glu	p.D61E	ENST00000263025	NM_002746.2	61	gaC/gaA	2/9	0.168552875100244	0	FACETS	0.774	0.669	0.888			1	SUBCLONAL	1	TRUE	0	0.2	0		931	651	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654610	67654610	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	140	576	0	ENST00000264010.4:c.1097T>C	p.Leu366Ser	p.L366S	ENST00000264010	NM_006565.3	366	tTa/tCa	6/12	0.168552875100244	0	FACETS	1	0.963	1			1	CLONAL	2	TRUE	0	0.2	0		576	514	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923666	72923666	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	170	765	0	ENST00000268489.5:c.3412A>T	p.Ile1138Phe	p.I1138F	ENST00000268489	NM_006885.3	1138	Atc/Ttc	4/10	0.168552875100244	0	FACETS	0.802	0.742	0.864			1	CLONAL	3	TRUE	0	0.2	0		765	565	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348493	89348493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1489486003	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	157	969	0	ENST00000301030.4:c.4457G>A	p.Arg1486Gln	p.R1486Q	ENST00000301030	NM_001256183.1	1486	cGg/cAg	9/13	0.168552875100244	0	FACETS	0.848	0.782	0.915			1	CLONAL	3	TRUE	0	0.2	0		969	494	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217629	7217629	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	125	706	0	ENST00000380728.2:c.298C>T	p.Arg100Trp	p.R100W	ENST00000380728		100	Cgg/Tgg	4/11	1	2	FACETS	0.936	0.848	1	1	0.989	1	CLONAL	2	TRUE	1	0.2	2		706	668	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577093	7577093	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882008	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	86	655	1	ENST00000269305.4:c.845G>T	p.Arg282Leu	p.R282L	ENST00000269305	NM_001126112.2	282	cGg/cTg	8/11	1	2	FACETS	1	0.897	1	1	0.985	1	CLONAL	2	TRUE	1	0.2	2		656	426	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586143	29586143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771420960	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	32	337	0	ENST00000356175.3:c.4363C>T	p.Arg1455Cys	p.R1455C	ENST00000356175	NM_000267.3	1455	Cgc/Tgc	32/57	1	2	FACETS	0.726	0.589	0.881	0.726	0.589	0.881	SUBCLONAL	1	TRUE	1	0.2	2		337	441	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2214549	2214549	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	205	789	1	ENST00000398665.3:c.1877T>C	p.Leu626Pro	p.L626P	ENST00000398665	NM_032482.2	626	cTg/cCg	19/28	0.168552875100244	0	FACETS	0.999	0.935	1			1	CLONAL	3	TRUE	0	0.2	0		790	547	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10244923	10244923	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1352663970	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	153	725	0	ENST00000340748.4:c.4786A>G	p.Met1596Val	p.M1596V	ENST00000340748		1596	Atg/Gtg	39/40	0.168552875100244	0	FACETS	0.81	0.746	0.875			1	CLONAL	3	TRUE	0	0.2	0		725	504	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260539	10260539	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	141	634	1	ENST00000340748.4:c.2323T>C	p.Tyr775His	p.Y775H	ENST00000340748		775	Tat/Cat	24/40	0.168552875100244	0	FACETS	0.788	0.723	0.855			1	SUBCLONAL	3	TRUE	0	0.2	0		635	477	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281592	15281592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1438315884	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	136	824	2	ENST00000263388.2:c.4781C>T	p.Ser1594Leu	p.S1594L	ENST00000263388	NM_000435.2	1594	tCg/tTg	26/33	0.168552875100244	0	FACETS	0.808	0.74	0.877			1	CLONAL	3	TRUE	0	0.2	0		826	449	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19261495	19261495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775651286	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	140	657	5	ENST00000162023.5:c.50G>A	p.Arg17Gln	p.R17Q	ENST00000162023		17	cGg/cAg	6/13	0.168552875100244	0	FACETS	0.822	0.755	0.892			1	CLONAL	3	TRUE	0	0.2	0		662	454	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791392	42791392	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1349864904	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	171	596	2	ENST00000575354.2:c.452C>T	p.Ala151Val	p.A151V	ENST00000575354	NM_015125.3	151	gCc/gTc	3/20	0.168552875100244	0	FACETS	0.958	0.889	1			1	CLONAL	3	TRUE	0	0.2	0		598	476	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856056	45856056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	34	502	0	ENST00000391945.4:c.1850C>T	p.Ala617Val	p.A617V	ENST00000391945	NM_000400.3	617	gCc/gTc	20/23	0.168552875100244	0	FACETS	0.677	0.553	0.815			1	SUBCLONAL	1	TRUE	0	0.2	0		502	402	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867286	45867286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	73	228	1	ENST00000391945.4:c.907G>A	p.Ala303Thr	p.A303T	ENST00000391945	NM_000400.3	303	Gcc/Acc	10/23	0.168552875100244	0	FACETS	0.881	0.783	0.982			1	CLONAL	3	TRUE	0	0.2	0		229	221	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868176	45868176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559154781	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	133	1038	3	ENST00000391945.4:c.514G>A	p.Ala172Thr	p.A172T	ENST00000391945	NM_000400.3	172	Gct/Act	7/23	0.168552875100244	0	FACETS	0.909	0.835	0.986			1	CLONAL	3	TRUE	0	0.2	0		1041	390	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868194	45868194	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1032384332	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	77	573	2	ENST00000391945.4:c.496C>T	p.Arg166Cys	p.R166C	ENST00000391945	NM_000400.3	166	Cgt/Tgt	7/23	0.168552875100244	0	FACETS	0.83	0.734	0.933			1	CLONAL	2	TRUE	0	0.2	0		575	371	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389092	31389092	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	127	441	0	ENST00000328111.2:c.2005G>T	p.Gly669Cys	p.G669C	ENST00000328111	NM_006892.3	669	Ggc/Tgc	19/23	1	2	FACETS	1	0.975	1	1	0.993	1	CLONAL	3	TRUE	1	0.2	2		441	363	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092948	29092948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201206424	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	131	501	0	ENST00000328354.6:c.1036C>T	p.Arg346Cys	p.R346C	ENST00000328354	NM_007194.3	346	Cgt/Tgt	10/15	1	2	FACETS	0.929	0.849	1	1	0.992	1	CLONAL	3	TRUE	1	0.2	2		501	470	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20150318	20150318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	173	590	0	ENST00000379607.5:c.319G>A	p.Gly107Ser	p.G107S	ENST00000379607	NM_001412.3	107	Ggc/Agc	5/7	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	2	TRUE	NA	0.2	2		590	700	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430836	47430836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	102	666	0	ENST00000377045.4:c.1801G>A	p.Ala601Thr	p.A601T	ENST00000377045	NM_001654.4	601	Gca/Aca	16/16	0.3	1	FACETS	1	0.959	1	1	0.989	1	CLONAL	2	TRUE	0	0.2	1		666	408	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019820	123019820	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749157868	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	145	449	0	ENST00000355640.3:c.308C>T	p.Thr103Met	p.T103M	ENST00000355640		103	aCg/aTg	2/7	0.168552875100244	0	FACETS	0.939	0.865	1			1	CLONAL	3	TRUE	0	0.2	0		449	412	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621851	1621852	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	35	679	0	ENST00000344749.5:c.940dup	p.Ala314GlyfsTer35	p.A314Gfs*35	ENST00000344749	NM_001136139.2	314	gcc/gGcc	11/19	0.168552875100244	0	FACETS	0.776	0.637	0.931			1	CLONAL	1	TRUE	0	0.2	0		679	361	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720665	89720666	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	53	105	0	ENST00000371953.3:c.820dup	p.Trp274LeufsTer24	p.W274Lfs*24	ENST00000371953	NM_000314.4	272	-/T	8/9	0.212252560871464	4	FACETS	0.915	0.8	1			1	CLONAL	5	TRUE	NA	0.2	4		105	139	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099889	157099890	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	201	668	0	ENST00000346085.5:c.831dup	p.Gly278ArgfsTer257	p.G278Rfs*257	ENST00000346085	NM_020732.3	276	gcc/gCcc	1/20	0.170156855579137	3	FACETS	1	0.937	1	1	0.991	1	CLONAL	3	TRUE	1	0.2	3		668	731	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	464333	464334	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	44	726	0	ENST00000399788.2:c.860_861del	p.Ser287CysfsTer2	p.S287Cfs*2	ENST00000399788	NM_001042603.1	287	tCT/t	7/28	1	2	FACETS	0.602	0.503	0.712	0.602	0.503	0.712	SUBCLONAL	1	TRUE	1	0.2	2		726	731	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394066	31394066	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	37	497	0	ENST00000328111.2:c.2357del	p.Asn786ThrfsTer8	p.N786Tfs*8	ENST00000328111	NM_006892.3	785	Aaa/aa	22/23	1	2	FACETS	0.717	0.59	0.859	0.717	0.59	0.859	SUBCLONAL	1	TRUE	1	0.2	2		497	516	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271747	15271747	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs773656789	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	90	527	1	ENST00000263388.2:c.6692del	p.Pro2231GlnfsTer15	p.P2231Qfs*15	ENST00000263388	NM_000435.2	2231	cCa/ca	33/33	0.168552875100244	0	FACETS	1	0.93	1			1	CLONAL	2	TRUE	0	0.2	0		528	343	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120031	70120031	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	10	108	0	ENST00000245479.2:c.1037del	p.Pro346ArgfsTer37	p.P346Rfs*37	ENST00000245479	NM_000346.3	345	Ccc/cc	3/3	1	2	FACETS	0.98	0.694	1	1	0.911	1	CLONAL	3	TRUE	1	0.2	2		108	34	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403181	116403182	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	147	426	0	ENST00000397752.3:c.2442_2443insA	p.Leu815ThrfsTer18	p.L815Tfs*18	ENST00000397752	NM_000245.2	814	-/A	11/21	1	2	FACETS	0.937	0.861	1	1	0.993	1	CLONAL	3	TRUE	1	0.2	2		426	523	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469772	157469772	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	163	636	0	ENST00000346085.5:c.2570del	p.Pro857GlnfsTer57	p.P857Qfs*57	ENST00000346085	NM_020732.3	856	Ccc/cc	9/20	0.170156855579137	3	FACETS	1	0.944	1	1	0.99	1	CLONAL	3	TRUE	1	0.2	3		636	581	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665446	138665446	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	15	306	0	ENST00000330315.3:c.119del	p.Gly40ValfsTer110	p.G40Vfs*110	ENST00000330315	NM_023067.3	40	gGt/gt	1/1	1	2	FACETS	0.811	0.595	1	0.811	0.595	1	CLONAL	1	TRUE	1	0.2	2		306	185	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615698	1615698	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	81	1152	1	ENST00000344749.5:c.1573del	p.Arg525GlyfsTer18	p.R525Gfs*18	ENST00000344749	NM_001136139.2	525	Cgg/gg	17/19	0.168552875100244	0	FACETS	0.709	0.627	0.796			1	SUBCLONAL	2	TRUE	0	0.2	0		1153	457	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29099524	29099525	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs772683219	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	49	561	1	ENST00000328354.6:c.876dup	p.Asp293Ter	p.D293*	ENST00000328354	NM_007194.3	292	-/T	8/15	1	2	FACETS	0.988	0.837	1	0.988	0.837	1	CLONAL	1	TRUE	1	0.2	2		562	496	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845787	151845789	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	83	541	0	ENST00000262189.6:c.13223_13225del	p.Glu4408del	p.E4408del	ENST00000262189	NM_170606.2	4408	gAAGgt/ggt	52/59	1	2	FACETS	0.817	0.723	0.917	1	0.981	1	CLONAL	2	TRUE	1	0.2	2		541	508	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138915	64138915	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	44	333	0	ENST00000334205.4:c.2287del	p.Arg763AlafsTer21	p.R763Afs*21	ENST00000334205	NM_003942.2	761	gCc/gc	17/17	1	2	FACETS	1	0.893	1	1	0.973	1	CLONAL	2	TRUE	1	0.2	2		333	206	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081568	143081569	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	132	593	0	ENST00000262992.4:c.1505dup	p.Val503SerfsTer15	p.V503Sfs*15	ENST00000262992	NM_001101669.1	502	cca/ccCa	15/24	1	2	FACETS	1	0.954	1	1	0.991	1	CLONAL	2	TRUE	1	0.2	2		593	615	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98003011	98003011	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	90	440	3	ENST00000289081.3:c.265del	p.Ile89PhefsTer2	p.I89Ffs*2	ENST00000289081	NM_000136.2	89	Att/tt	4/15	0.293595743378431	4	FACETS	0.833	0.74	0.933	0.556	0.493	0.622	CLONAL	2	TRUE	1	0.2	4		443	648	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510197	187510197	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762526769	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	185	792	0	ENST00000441802.2:c.13316del	p.Pro4439GlnfsTer48	p.P4439Qfs*48	ENST00000441802	NM_005245.3	4439	cCa/ca	27/27	1	2	FACETS	1	0.945	1	1	0.995	1	CLONAL	3	TRUE	1	0.2	2		792	604	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508725	106508725	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	128	449	0	ENST00000359195.3:c.723del	p.Gly242AlafsTer17	p.G242Afs*17	ENST00000359195	NM_002649.2	240	aCc/ac	2/11	1	2	FACETS	1	0.976	1	1	0.991	1	CLONAL	2	TRUE	1	0.2	2		449	531	SUCCESS
APC	324	MSKCC	GRCh37	5	112178033	112178033	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs773874693	NA	P-0007296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	170	639	0	ENST00000257430.4:c.6747del	p.Gly2250AlafsTer29	p.G2250Afs*29	ENST00000257430	NM_000038.5	2248	Aaa/aa	16/16	1	2	FACETS	0.934	0.863	1	1	0.994	1	CLONAL	3	TRUE	1	0.2	2		639	607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578376	7578379	+	frameshift_variant	Frame_Shift_Del	DEL	CTAT	CTAT	-	novel	NA	P-0007343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	19	259	0	ENST00000269305.4:c.551_554del	p.Asp184AlafsTer62	p.D184Afs*62	ENST00000269305	NM_001126112.2	184	gATAGc/gc	5/11	1	2	FACETS	0.756	0.573	0.972	0.756	0.573	0.972	CLONAL	1	TRUE	1	0.14	2		259	359	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217858	7217858	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	100	709	1	ENST00000380728.2:c.153del	p.Lys52ArgfsTer11	p.K52Rfs*11	ENST00000380728		51	agG/ag	3/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.14	2		710	1155	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578376	7578379	+	frameshift_variant	Frame_Shift_Del	DEL	CTAT	CTAT	-	novel	NA	P-0007343-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	525	259	0	ENST00000269305.4:c.551_554del	p.Asp184AlafsTer62	p.D184Afs*62	ENST00000269305	NM_001126112.2	184	gATAGc/gc	5/11	0.946561995670047	1	FACETS	0.995	0.978	1	0.995	0.978	1	CLONAL	1	TRUE	0	0.946561995670047	1		259	587	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303679	65303679	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0007343-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	715	579	1	ENST00000342505.4:c.3076A>T	p.Lys1026Ter	p.K1026*	ENST00000342505	NM_002227.2	1026	Aaa/Taa	22/25	0.946561995670047	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.946561995670047	1		580	785	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-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	221	341	0	ENST00000371953.3:c.1009_1026+389del		p.X337_splice	ENST00000371953	NM_000314.4	337		8/9	0.946561995670047	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.946561995670047	1		341	245	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951062	48951091	+	inframe_deletion	In_Frame_Del	DEL	AGTGAATCCAAAAGAAAGTATACTGAAAAG	AGTGAATCCAAAAGAAAGTATACTGAAAAG	-	novel	NA	P-0007343-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	281	299	0	ENST00000267163.4:c.1230_1259del	p.Asn410_Val419del	p.N410_V419del	ENST00000267163	NM_000321.2	408	acAGTGAATCCAAAAGAAAGTATACTGAAAAGa/aca	13/27	0.946561995670047	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.946561995670047	1		299	312	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430729	47430729	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007343-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	661	342	0	ENST00000377045.4:c.1694C>G	p.Ala565Gly	p.A565G	ENST00000377045	NM_001654.4	565	gCc/gGc	16/16	1	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.946561995670047	1		342	691	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	105	406	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.22076764675241	3	FACETS	0.907	0.815	1	0.907	0.815	1	CLONAL	2	TRUE	1	0.225606455492758	3		406	571	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0007604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	124	305	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	0.225606455492758	2	FACETS	0.837	0.758	0.919	0.837	0.758	0.919	CLONAL	2	TRUE	0	0.225606455492758	2		305	657	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59878702	59878702	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	126	783	0	ENST00000259008.2:c.1052C>T	p.Pro351Leu	p.P351L	ENST00000259008	NM_032043.2	351	cCa/cTa	8/20	0.225606455492758	3	FACETS	0.795	0.72	0.874	0.795	0.72	0.874	SUBCLONAL	2	TRUE	1	0.225606455492758	3		783	782	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	276	655	1	ENST00000269305.4:c.892del	p.Glu298SerfsTer47	p.E298Sfs*47	ENST00000269305	NM_001126112.2	298	Gag/ag	8/11	NA	2	FACETS	0.932	0.873	0.992			1	INDETERMINATE	2	TRUE	NA	0.225606455492758	2		656	1313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0008383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	58	642	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.908	0.777	1	0.908	0.777	1	CLONAL	1	TRUE	1	0.11	2		642	1162	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0008464-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	14	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.267490631520065	3	FACETS	0.214	0.154	0.288	0.107	0.077	0.144	SUBCLONAL	1	TRUE	1	0.267490631520065	3		436	554	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0008464-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	113	495	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.267490631520065	3	FACETS	0.865	0.781	0.953	0.865	0.781	0.953	CLONAL	2	TRUE	1	0.267490631520065	3		495	554	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274911	41274911	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs868651538	NA	P-0008464-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	23	235	0	ENST00000349496.5:c.1161T>A	p.Asn387Lys	p.N387K	ENST00000349496	NM_001904.3	387	aaT/aaA	8/15	1	2	FACETS	0.377	0.293	0.475	0.377	0.293	0.475	SUBCLONAL	1	TRUE	1	0.267490631520065	2		235	456	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061218	38061238	+	inframe_deletion	In_Frame_Del	DEL	GCCGTTCTCGAACATGTTGCC	GCCGTTCTCGAACATGTTGCC	-	novel	NA	P-0008542-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	38	304	0	ENST00000250448.2:c.751_771del	p.Gly251_Gly257del	p.G251_G257del	ENST00000250448	NM_004496.3	251	GGCAACATGTTCGAGAACGGC/-	2/2	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.15	2		304	459	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35860990	35860990	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008542-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	25	321	0	ENST00000303115.3:c.119T>G	p.Phe40Cys	p.F40C	ENST00000303115	NM_002185.3	40	tTc/tGc	2/8	1	2	FACETS	0.95	0.749	1	0.95	0.749	1	CLONAL	1	TRUE	1	0.15	2		321	351	SUCCESS
AR	367	MSKCC	GRCh37	X	66863148	66863148	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	38	361	0	ENST00000374690.3:c.1667C>A	p.Pro556His	p.P556H	ENST00000374690	NM_000044.3	556	cCc/cAc	2/8	1	1	FACETS	0.605	0.501	0.722	0.605	0.501	0.722	SUBCLONAL	1	TRUE	0	0.26	1		361	420	SUCCESS
AR	367	MSKCC	GRCh37	X	66931251	66931251	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	48	415	0	ENST00000374690.3:c.1893G>T	p.Lys631Asn	p.K631N	ENST00000374690	NM_000044.3	631	aaG/aaT	4/8	1	1	FACETS	0.531	0.448	0.622	0.531	0.448	0.622	SUBCLONAL	1	TRUE	0	0.26	1		415	605	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0008706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	69	495	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.0936548322791508	3	FACETS	1	0.925	1	0.544	0.474	0.62	INDETERMINATE	1	TRUE	1	0.235316402348295	3		495	602	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0008706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	105	545	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.159726586540495	0	FACETS	0.934	0.837	1			1	CLONAL	1	TRUE	0	0.235316402348295	0		547	731	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971170	21971170	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	24	83	0	ENST00000304494.5:c.188T>A	p.Leu63Gln	p.L63Q	ENST00000304494	NM_000077.4	63	cTg/cAg	2/3	0.235316402348295	1	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	0	0.235316402348295	1		83	145	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943745	9943745	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	36	265	0	ENST00000330684.3:c.1196G>A	p.Cys399Tyr	p.C399Y	ENST00000330684	NM_001134407.1	399	tGt/tAt	5/13	1	2	FACETS	0.636	0.522	0.764	0.636	0.522	0.764	SUBCLONAL	1	TRUE	1	0.235316402348295	2		265	481	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492895	56492896	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0008706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	22	133	0	ENST00000407977.2:c.43dup	p.Trp15LeufsTer25	p.W15Lfs*25	ENST00000407977		15	tgg/tTgg	2/10	1	2	FACETS	0.862	0.671	1	0.862	0.671	1	CLONAL	1	TRUE	1	0.235316402348295	2		133	217	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11270938	11270938	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1263804740	NA	P-0008771-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	270	456	0	ENST00000361445.4:c.3587A>G	p.Asn1196Ser	p.N1196S	ENST00000361445	NM_004958.3	1196	aAt/aGt	24/58	1	2	FACETS	0.949	0.893	1	0.949	0.893	1	CLONAL	1	TRUE	1	0.689067111917941	2		456	826	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005421	42005421	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008771-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	564	794	0	ENST00000219905.7:c.3157C>T	p.Arg1053Ter	p.R1053*	ENST00000219905	NM_001164273.1	1053	Cga/Tga	9/24	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.689067111917941	2		794	1534	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435296	56435296	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008771-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	131	263	0	ENST00000407977.2:c.1841A>G	p.Gln614Arg	p.Q614R	ENST00000407977		614	cAg/cGg	9/10	1	2	FACETS	0.901	0.825	0.98	0.901	0.825	0.98	CLONAL	1	TRUE	1	0.689067111917941	2		263	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0009044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	307	398	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.127640101768577	3	FACETS	0.82	0.776	0.865	0.82	0.776	0.865	INDETERMINATE	2	TRUE	1	0.552350677953501	3		398	865	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339505	116339505	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760106468	NA	P-0009044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	119	257	0	ENST00000397752.3:c.367G>A	p.Asp123Asn	p.D123N	ENST00000397752	NM_000245.2	123	Gac/Aac	2/21	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.552350677953501	2		257	422	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778625	3778625	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	137	244	4	ENST00000262367.5:c.6423C>A	p.Asn2141Lys	p.N2141K	ENST00000262367	NM_004380.2	2141	aaC/aaA	31/31	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.552350677953501	2		248	396	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618592	37618592	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0009044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	297	310	0	ENST00000447079.4:c.268A>T	p.Lys90Ter	p.K90*	ENST00000447079	NM_015083.1	90	Aaa/Taa	1/14	0.127640101768577	3	FACETS	0.874	0.827	0.922	0.874	0.827	0.922	INDETERMINATE	2	TRUE	1	0.552350677953501	3		310	785	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618868	37618868	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	450	426	0	ENST00000447079.4:c.544G>T	p.Glu182Ter	p.E182*	ENST00000447079	NM_015083.1	182	Gag/Tag	1/14	0.127640101768577	3	FACETS	0.869	0.831	0.908	0.869	0.831	0.908	INDETERMINATE	2	TRUE	1	0.552350677953501	3		426	1196	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0009061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	188	704	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.28228639041967	1	FACETS	0.81	0.759	0.861	1	0.993	1	CLONAL	2	TRUE	0	0.444676680710571	1		705	406	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188287	10188287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs869025650	NA	P-0009061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	51	426	1	ENST00000256474.2:c.430G>A	p.Gly144Arg	p.G144R	ENST00000256474	NM_000551.3	144	Gga/Aga	2/3	1	2	FACETS	0.274	0.232	0.321	0.274	0.232	0.321	SUBCLONAL	1	TRUE	1	0.444676680710571	2		427	837	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1268646	1268646	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	24	414	0	ENST00000310581.5:c.2571T>G	p.Ile857Met	p.I857M	ENST00000310581	NM_198253.2	857	atT/atG	9/16	NA	2	FACETS	0.299	0.234	0.374			1	INDETERMINATE	1	TRUE	NA	0.444676680710571	2		414	361	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352772	70352772	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	99	582	0	ENST00000374080.3:c.4493G>T	p.Gly1498Val	p.G1498V	ENST00000374080		1498	gGa/gTa	32/45	NA	2	FACETS	0.622	0.555	0.693			1	INDETERMINATE	1	TRUE	NA	0.444676680710571	2		582	716	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053339	37053358	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCTCAGTTAAAAAAGTAAG	TTCTCAGTTAAAAAAGTAAG	-	novel	NA	P-0009061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	61	392	0	ENST00000231790.2:c.578_588+9del		p.X193_splice	ENST00000231790	NM_000249.3	193		7/19	1	2	FACETS	0.337	0.29	0.389	0.337	0.29	0.389	SUBCLONAL	1	TRUE	1	0.444676680710571	2		392	813	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131420	17131420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	598	244	0	ENST00000285071.4:c.32G>A	p.Cys11Tyr	p.C11Y	ENST00000285071	NM_144997.5	11	tGc/tAc	4/14	0.84004089318116	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.84004089318116	2		244	645	SUCCESS
CBL	867	MSKCC	GRCh37	11	119145541	119145541	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0009076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	732	367	0	ENST00000264033.4:c.748-1G>A		p.X250_splice	ENST00000264033	NM_005188.3	250			NA	2	FACETS	0.977	0.958	0.995			1	INDETERMINATE	2	TRUE	NA	0.84004089318116	2		367	892	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511649	66511649	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs281864781	NA	P-0009076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	595	278	1	ENST00000358598.2:c.109C>T	p.Gln37Ter	p.Q37*	ENST00000358598	NM_212471.2	37	Cag/Tag	2/11	0.84004089318116	2	FACETS	0.986	0.966	1	0.986	0.966	1	CLONAL	2	TRUE	0	0.84004089318116	2		279	718	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511634	66511635	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAGATTCT	novel	NA	P-0009076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	443	264	0	ENST00000358598.2:c.96_103dup	p.Ile35LysfsTer97	p.I35Kfs*97	ENST00000358598	NM_212471.2	32	aaa/aAAGATTCTaa	2/11	0.84004089318116	2	FACETS	1	0.997	1	0.732	0.706	0.758	CLONAL	1	TRUE	0	0.84004089318116	2		264	720	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131420	17131420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009076-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	221	244	0	ENST00000285071.4:c.32G>A	p.Cys11Tyr	p.C11Y	ENST00000285071	NM_144997.5	11	tGc/tAc	4/14	0.641540144968889	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.662458276726635	2		244	323	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131420	17131420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009076-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	147	244	0	ENST00000285071.4:c.32G>A	p.Cys11Tyr	p.C11Y	ENST00000285071	NM_144997.5	11	tGc/tAc	4/14	0.554085571884506	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.575235976209594	2		244	220	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148982	119148982	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1357686410	NA	P-0009076-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	64	476	0	ENST00000264033.4:c.1202G>A	p.Cys401Tyr	p.C401Y	ENST00000264033	NM_005188.3	401	tGc/tAc	8/16	0.575235976209594	2	FACETS	1	0.917	1	0.527	0.464	0.594	CLONAL	1	TRUE	0	0.575235976209594	2		476	211	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475088	40475091	+	frameshift_variant	Frame_Shift_Del	DEL	GCAG	GCAG	-	novel	NA	P-0009076-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	26	627	0	ENST00000264657.5:c.1819_1822del	p.Leu607Ter	p.L607*	ENST00000264657	NM_139276.2	607	CTGCta/ta	20/24	0.575235976209594	2	FACETS	0.464	0.37	0.57	0.232	0.185	0.285	SUBCLONAL	1	TRUE	0	0.575235976209594	2		627	195	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820227	139820238	+	inframe_deletion	In_Frame_Del	DEL	CAACGACATGAA	CAACGACATGAA	-	novel	NA	P-0009076-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	21	690	0	ENST00000247668.2:c.1382_1393del	p.Asn461_Asn464del	p.N461_N464del	ENST00000247668	NM_021138.3	460	gtCAACGACATGAAc/gtc	11/11	0.339982488182182	4	FACETS	0.42	0.323	0.532	0.21	0.161	0.266	INDETERMINATE	1	TRUE	2	0.575235976209594	4		690	274	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0009076-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	36	205	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	0.26	2		205	213	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0009076-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	54	528	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.23599182868423	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.26	1		528	320	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0009076-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	53	993	1	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.26	2		994	353	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099397	27099397	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009076-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	26	431	0	ENST00000324856.7:c.3634C>T	p.Gln1212Ter	p.Q1212*	ENST00000324856	NM_006015.4	1212	Cag/Tag	14/20	1	2	FACETS	0.699	0.555	0.864	0.699	0.555	0.864	SUBCLONAL	1	TRUE	1	0.26	2		431	286	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209504	98209504	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766315655	NA	P-0009076-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	28	436	0	ENST00000331920.6:c.4034G>A	p.Arg1345His	p.R1345H	ENST00000331920	NM_000264.3	1345	cGt/cAt	23/24	0.23599182868423	1	FACETS	0.88	0.708	1	0.88	0.708	1	CLONAL	1	TRUE	0	0.26	1		436	213	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063670	67063670	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009076-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	15	201	0	ENST00000412916.2:c.119G>T	p.Arg40Leu	p.R40L	ENST00000412916		40	cGc/cTc	2/6	0.23599182868423	1	FACETS	0.707	0.52	0.928	0.707	0.52	0.928	CLONAL	1	TRUE	0	0.26	1		201	142	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845671	68845672	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0009076-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	48	453	0	ENST00000261769.5:c.919dup	p.Gln307ProfsTer4	p.Q307Pfs*4	ENST00000261769	NM_004360.3	306	agc/agCc	7/16	0.23599182868423	1	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	0	0.26	1		453	310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0009094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	22	230	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.358	0.277	0.454	0.358	0.277	0.454	SUBCLONAL	1	TRUE	1	0.22	2		231	558	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900288	101900288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111854391	NA	P-0009094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	132	513	1	ENST00000374994.4:c.722C>T	p.Ser241Leu	p.S241L	ENST00000374994	NM_004612.2	241	tCg/tTg	4/9	1	2	FACETS	0.969	0.878	1	0.969	0.878	1	CLONAL	1	TRUE	1	0.22	2		514	1238	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270004	198270004	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	96	356	0	ENST00000335508.6:c.1432C>A	p.Leu478Ile	p.L478I	ENST00000335508	NM_012433.2	478	Cta/Ata	10/25	1	2	FACETS	0.821	0.73	0.919	0.821	0.73	0.919	CLONAL	1	TRUE	1	0.22	2		356	1063	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411624	63411624	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1399	142	532	0	ENST00000330258.3:c.1543C>G	p.Leu515Val	p.L515V	ENST00000330258	NM_152424.3	515	Ctt/Gtt	2/2	1	2	FACETS	0.838	0.761	0.919	0.838	0.761	0.919	CLONAL	1	TRUE	1	0.22	2		532	1541	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244517	46244526	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGTAGCTA	CAGGTAGCTA	-	novel	NA	P-0009094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	89	313	0	ENST00000334344.6:c.2615_2624del	p.Val872AspfsTer17	p.V872Dfs*17	ENST00000334344	NM_152641.2	871	CAGGTAGCTAca/ca	15/21	1	2	FACETS	0.878	0.777	0.987	0.878	0.777	0.987	CLONAL	1	TRUE	1	0.22	2		313	921	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009270-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	120	406	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.926	0.836	1	0.926	0.836	1	CLONAL	1	TRUE	1	0.321917006701493	2		406	805	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577562	7577563	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGT	novel	NA	P-0009270-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	134	240	0	ENST00000269305.4:c.716_718dup	p.Asn239dup	p.N239dup	ENST00000269305	NM_001126112.2	239	agt/aACAgt	7/11	0.280634647573651	1	FACETS	0.936	0.852	1	0.936	0.852	1	CLONAL	1	TRUE	0	0.321917006701493	1		240	746	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38949907	38949907	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs750970144	NA	P-0009270-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	83	331	0	ENST00000357387.3:c.4043C>G	p.Ser1348Cys	p.S1348C	ENST00000357387	NM_152756.3	1348	tCt/tGt	31/38	1	2	FACETS	0.572	0.503	0.645	0.572	0.503	0.645	SUBCLONAL	1	TRUE	1	0.321917006701493	2		331	902	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717769	89717770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0009393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	15	227	0	ENST00000371953.3:c.800dup	p.Asp268GlyfsTer30	p.D268Gfs*30	ENST00000371953	NM_000314.4	265	cta/ctAa	7/9	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.599100943463299	2		227	36	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0009421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	99	398	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.24938926957927	1	FACETS	0.78	0.695	0.87	0.78	0.695	0.87	SUBCLONAL	1	TRUE	0	0.24938926957927	1		398	891	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0009421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	93	642	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.24938926957927	1	FACETS	0.786	0.698	0.879	0.786	0.698	0.879	SUBCLONAL	1	TRUE	0	0.24938926957927	1		642	831	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044453	128044453	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1031196303	NA	P-0009421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	38	387	0	ENST00000285398.2:c.1168T>A	p.Cys390Ser	p.C390S	ENST00000285398	NM_000122.1	390	Tgc/Agc	8/15	1	2	FACETS	0.475	0.392	0.569	0.475	0.392	0.569	SUBCLONAL	1	TRUE	1	0.24938926957927	2		387	641	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750604	128750605	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAG	rs745729043	NA	P-0009421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	46	400	0	ENST00000377970.2:c.154_156dup	p.Gln52dup	p.Q52dup	ENST00000377970	NM_002467.4	52	-/CAG	2/3	1	2	FACETS	0.52	0.437	0.613	0.52	0.437	0.613	SUBCLONAL	1	TRUE	1	0.24938926957927	2		400	709	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17355104	17355104	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	455	512	2	ENST00000375499.3:c.414T>A	p.Asp138Glu	p.D138E	ENST00000375499	NM_003000.2	138	gaT/gaA	4/8	1	2	FACETS	0.956	0.911	1	0.956	0.911	1	CLONAL	1	TRUE	1	0.575310804863166	2		514	1655	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115975	8115975	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	121	139	0	ENST00000346208.3:c.1321del	p.Ala441ProfsTer34	p.A441Pfs*34	ENST00000346208		441	Gcc/cc	6/6	0.257097241613509	3	FACETS	1	0.976	1	0.609	0.554	0.666	INDETERMINATE	1	TRUE	1	0.575310804863166	3		139	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0009585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	98	704	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.151600278847489	3	FACETS	1	0.981	1	0.69	0.624	0.758	INDETERMINATE	1	TRUE	1	0.67	3		705	283	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0009585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	86	466	8	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	NA	2	FACETS	0.787	0.703	0.876			1	INDETERMINATE	1	TRUE	NA	0.67	2		474	326	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574679	41574679	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	129	911	4	ENST00000263253.7:c.6970del	p.His2324ThrfsTer29	p.H2324Tfs*29	ENST00000263253	NM_001429.3	2322	Ccc/cc	31/31	1	2	FACETS	0.99	0.907	1	0.99	0.907	1	CLONAL	1	TRUE	1	0.67	2		915	389	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0009585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	18	376	0	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	0.159028230162092	3	FACETS	0.305	0.23	0.394	0.153	0.115	0.197	INDETERMINATE	1	TRUE	1	0.67	3		376	235	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0009585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	168	312	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.0825769477156166	3	FACETS	0.962	0.914	1			1	INDETERMINATE	3	TRUE	NA	0.67	3		312	232	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0009585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	84	475	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.3	1	FACETS		NA	1	1	0.988	1	INDETERMINATE	2	TRUE	0	0.67	1		475	109	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339111	65339111	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	85	506	4	ENST00000342505.4:c.425del	p.Lys142ArgfsTer26	p.K142Rfs*26	ENST00000342505	NM_002227.2	142	aAg/ag	5/25	NA	2	FACETS	0.748	0.667	0.834			1	INDETERMINATE	1	TRUE	NA	0.67	2		510	339	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654642	67654642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	136	425	0	ENST00000264010.4:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000264010	NM_006565.3	377	Cgt/Tgt	6/12	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.67	2		425	394	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0009585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	194	337	1	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	0.3	3	FACETS	0.892	0.847	0.935	0.892	0.847	0.935	INDETERMINATE	3	TRUE	0	0.67	3		338	289	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983228	149983228	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	78	374	0	ENST00000253339.5:c.3030del	p.Phe1010LeufsTer10	p.F1010Lfs*10	ENST00000253339		1010	ttT/tt	7/7	1	2	FACETS	0.792	0.703	0.885	0.792	0.703	0.885	SUBCLONAL	1	TRUE	1	0.67	2		374	294	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940385	49940385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771132053	NA	P-0009585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	25	709	3	ENST00000296474.3:c.658C>T	p.Arg220Cys	p.R220C	ENST00000296474	NM_002447.2	220	Cgt/Tgt	1/20	1	2	FACETS	0.192	0.151	0.24	0.192	0.151	0.24	SUBCLONAL	1	TRUE	1	0.67	2		712	388	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534263	187534263	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	44	183	0	ENST00000441802.2:c.9463G>T	p.Gly3155Ter	p.G3155*	ENST00000441802	NM_005245.3	3155	Gga/Tga	13/27	1	2	FACETS	0.988	0.847	1	0.988	0.847	1	CLONAL	1	TRUE	1	0.67	2		183	133	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593403	67593403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	56	251	0	ENST00000274335.5:c.2149C>T	p.Pro717Ser	p.P717S	ENST00000274335		717	Cca/Tca	15/15	0.3	2	FACETS	0.785	0.682	0.894	0.392	0.341	0.447	INDETERMINATE	1	TRUE	0	0.67	2		251	213	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468030	50468030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375321410	NA	P-0009585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	60	282	0	ENST00000331340.3:c.1265C>T	p.Ala422Val	p.A422V	ENST00000331340	NM_006060.4	422	gCg/gTg	8/8	1	2	FACETS	0.822	0.718	0.931	0.822	0.718	0.931	CLONAL	1	TRUE	1	0.67	2		282	218	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98241359	98241359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772903899	NA	P-0009585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	111	447	0	ENST00000331920.6:c.1138G>A	p.Glu380Lys	p.E380K	ENST00000331920	NM_000264.3	380	Gag/Aag	8/24	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.67	2		447	316	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170286	119170286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	13	366	0	ENST00000264033.4:c.2516G>A	p.Ser839Asn	p.S839N	ENST00000264033	NM_005188.3	839	aGc/aAc	16/16	1	2	FACETS	0.163	0.116	0.221	0.163	0.116	0.221	SUBCLONAL	1	TRUE	1	0.67	2		366	238	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2115590	2115590	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs751618728	NA	P-0009585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	30	473	0	ENST00000219476.3:c.1670T>C	p.Leu557Ser	p.L557S	ENST00000219476	NM_000548.3	557	tTg/tCg	16/42	0.283839229785791	3	FACETS	0.363	0.293	0.443			1	INDETERMINATE	1	TRUE	NA	0.67	3		473	329	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042073	14042073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	13	365	0	ENST00000311895.7:c.2620G>A	p.Ala874Thr	p.A874T	ENST00000311895	NM_005236.2	874	Gca/Aca	11/11	1	2	FACETS	0.182	0.13	0.246	0.182	0.13	0.246	SUBCLONAL	1	TRUE	1	0.67	2		365	213	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81973526	81973526	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	107	588	0	ENST00000359376.3:c.3343C>A	p.Pro1115Thr	p.P1115T	ENST00000359376	NM_002661.3	1115	Cca/Aca	30/33	0.267912005245408	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.67	0		588	312	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226464	2226464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	13	383	1	ENST00000398665.3:c.3944G>A	p.Gly1315Asp	p.G1315D	ENST00000398665	NM_032482.2	1315	gGc/gAc	27/28	1	2	FACETS	0.194	0.138	0.262	0.194	0.138	0.262	SUBCLONAL	1	TRUE	1	0.67	2		384	200	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602616	10602616	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	53	413	0	ENST00000171111.5:c.962C>T	p.Ala321Val	p.A321V	ENST00000171111	NM_203500.1	321	gCg/gTg	3/6	1	2	FACETS	0.604	0.519	0.695	0.604	0.519	0.695	SUBCLONAL	1	TRUE	1	0.67	2		413	262	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145675	11145675	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	14	395	1	ENST00000358026.2:c.4037G>T	p.Trp1346Leu	p.W1346L	ENST00000358026	NM_001128849.1	1346	tGg/tTg	29/36	1	2	FACETS	0.171	0.123	0.229	0.171	0.123	0.229	SUBCLONAL	1	TRUE	1	0.67	2		396	244	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797778	42797778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778127638	NA	P-0009585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	83	319	0	ENST00000575354.2:c.3830G>A	p.Arg1277His	p.R1277H	ENST00000575354	NM_015125.3	1277	cGc/cAc	16/20	0.3	1	FACETS	0.535	0.477	0.596	0.535	0.477	0.596	INDETERMINATE	1	TRUE	0	0.67	1		319	308	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223769	53223769	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376572303	NA	P-0009585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	117	567	2	ENST00000375401.3:c.3590C>T	p.Ala1197Val	p.A1197V	ENST00000375401	NM_004187.3	1197	gCg/gTg	23/26	0.267912005245408	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.67	0		569	331	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613328	100613328	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	83	493	0	ENST00000308731.7:c.1072C>G	p.Leu358Val	p.L358V	ENST00000308731	NM_000061.2	358	Ctc/Gtc	12/19	0.267912005245408	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.67	0		493	251	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589552	67589587	+	inframe_deletion	In_Frame_Del	DEL	GAAGATAATATTGAAGCTGTAGGGAAAAAATTACAT	GAAGATAATATTGAAGCTGTAGGGAAAAAATTACAT	-	novel	NA	P-0009585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	151	358	0	ENST00000274335.5:c.1318_1353del	p.Asp440_Glu451del	p.D440_E451del	ENST00000274335		439	GAAGATAATATTGAAGCTGTAGGGAAAAAATTACAT/-	10/15	0.3	2	FACETS	0.829	0.775	0.882	0.829	0.775	0.882	INDETERMINATE	2	TRUE	0	0.67	2		358	272	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400212	139400212	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	48	335	0	ENST00000277541.6:c.4136del	p.Thr1379ArgfsTer66	p.T1379Rfs*66	ENST00000277541	NM_017617.3	1379	aCg/ag	25/34	1	2	FACETS	0.682	0.584	0.788	0.682	0.584	0.788	SUBCLONAL	1	TRUE	1	0.67	2		335	210	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112322	115112323	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0009585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	15	24	0	ENST00000257566.3:c.1416_1417dup	p.Leu473ArgfsTer160	p.L473Rfs*160	ENST00000257566	NM_016569.3	473	ctc/cGCtc	7/8	1	2	FACETS	1	0.777	1	1	0.777	1	CLONAL	1	TRUE	1	0.67	2		24	44	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223445	53223445	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	77	465	0	ENST00000375401.3:c.3914del	p.Leu1305TrpfsTer53	p.L1305Wfs*53	ENST00000375401	NM_004187.3	1305	tTg/tg	23/26	0.267912005245408	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.67	0		465	255	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884924	151884924	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	15	246	0	ENST00000262189.6:c.4669del	p.Ser1557HisfsTer6	p.S1557Hfs*6	ENST00000262189	NM_170606.2	1557	Tca/ca	32/59	0.151600278847489	3	FACETS	0.427	0.314	0.56	0.213	0.157	0.28	INDETERMINATE	1	TRUE	1	0.67	3		246	140	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960150	151960151	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0009585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	119	457	0	ENST00000262189.6:c.1249dup	p.Cys417LeufsTer30	p.C417Lfs*30	ENST00000262189	NM_170606.2	417	tgt/tTgt	9/59	0.151600278847489	3	FACETS	1	0.982	1	0.655	0.598	0.714	INDETERMINATE	1	TRUE	1	0.67	3		457	362	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94153333	94153335	+	inframe_deletion	In_Frame_Del	DEL	ATC	ATC	-	rs779409748	NA	P-0009585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	51	341	1	ENST00000323929.3:c.2083_2085del	p.Asp695del	p.D695del	ENST00000323929	NM_005591.3	695	GAT/-	20/20	1	2	FACETS	0.769	0.663	0.882	0.769	0.663	0.882	SUBCLONAL	1	TRUE	1	0.67	2		342	198	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566524	41566525	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0009585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	126	458	0	ENST00000263253.7:c.4408dup	p.Met1470AsnfsTer3	p.M1470Nfs*3	ENST00000263253	NM_001429.3	1467	-/A	27/31	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.67	2		458	376	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050364	13050364	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	210	636	2	ENST00000316448.5:c.320del	p.Gly107AlafsTer4	p.G107Afs*4	ENST00000316448	NM_004343.3	106	Ggg/gg	3/9	1	2	FACETS	0.929	0.866	0.993	0.929	0.866	0.993	CLONAL	1	TRUE	1	0.67	2		638	675	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25368476	25368476	+	intron_variant	Intron	DEL	A	A	-	novel	NA	P-0009585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	25	367	0	ENST00000311936.3:c.451-5631del		p.*151*	ENST00000311936	NM_004985.3	157/189			0.159028230162092	3	FACETS	0.299	0.236	0.372	0.15	0.118	0.186	INDETERMINATE	1	TRUE	1	0.67	3		367	333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0009601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	559	499	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.721993181460739	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.721993181460739	2		501	774	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133889	55133889	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	525	459	0	ENST00000257290.5:c.1102G>T	p.Glu368Ter	p.E368*	ENST00000257290	NM_006206.4	368	Gaa/Taa	7/23	0.715290455329719	2	FACETS	0.985	0.957	1	0.985	0.957	1	CLONAL	2	TRUE	0	0.721993181460739	2		459	738	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672504	30672504	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	363	673	4	ENST00000376406.3:c.4456C>A	p.Pro1486Thr	p.P1486T	ENST00000376406	NM_014641.2	1486	Cct/Act	10/15	0.712751128046762	3	FACETS	0.995	0.943	1	0.498	0.471	0.525	CLONAL	1	TRUE	1	0.721993181460739	3		677	1375	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152357786	152357786	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	381	516	0	ENST00000359321.1:c.121G>C	p.Gly41Arg	p.G41R	ENST00000359321	NM_005431.1	41	Ggt/Cgt	2/3	NA	2	FACETS	0.986	0.938	1			1	INDETERMINATE	1	TRUE	NA	0.721993181460739	2		516	1070	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752950	128752950	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1723	305	390	0	ENST00000377970.2:c.1111A>T	p.Arg371Trp	p.R371W	ENST00000377970	NM_002467.4	371	Agg/Tgg	3/3	0.721993181460739	6	FACETS	1	0.953	1			1	CLONAL	1	TRUE	NA	0.721993181460739	6		390	2028	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	493313	493313	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1291	316	505	0	ENST00000399788.2:c.250A>T	p.Thr84Ser	p.T84S	ENST00000399788	NM_001042603.1	84	Acc/Tcc	3/28	0.70780338800518	4	FACETS	0.938	0.883	0.995			1	CLONAL	1	TRUE	NA	0.721993181460739	4		505	1607	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385178	4385178	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	319	400	0	ENST00000261254.3:c.203A>C	p.Glu68Ala	p.E68A	ENST00000261254	NM_001759.3	68	gAg/gCg	2/5	0.721993181460739	3	FACETS	1	0.986	1	0.564	0.532	0.596	CLONAL	1	TRUE	1	0.721993181460739	3		400	1067	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008017	29008017	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs767050810	NA	P-0009601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	315	475	0	ENST00000282397.4:c.752A>G	p.Asn251Ser	p.N251S	ENST00000282397	NM_002019.4	251	aAt/aGt	6/30	0.721993181460739	2	FACETS	1	0.948	1	0.5	0.474	0.528	CLONAL	1	TRUE	0	0.721993181460739	2		475	872	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916712	48916802	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGATCTTTATTTTTTGTTCCCAGGGAGGTTATATTCAAAAGAAAAAGGAACTGTGGGGAATCTGTATCTTTATTGCAGCAGTTGACCTAGA	TGATCTTTATTTTTTGTTCCCAGGGAGGTTATATTCAAAAGAAAAAGGAACTGTGGGGAATCTGTATCTTTATTGCAGCAGTTGACCTAGA	-	novel	NA	P-0009601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	219	347	0	ENST00000267163.4:c.265-20_335del		p.X89_splice	ENST00000267163	NM_000321.2	89		3/27	0.721993181460739	2	FACETS	0.766	0.725	0.807	0.766	0.725	0.807	SUBCLONAL	2	TRUE	0	0.721993181460739	2		347	396	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231121	98231127	+	frameshift_variant	Frame_Shift_Del	DEL	TGGAGGC	TGGAGGC	-	novel	NA	P-0009601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	163	352	0	ENST00000331920.6:c.2156_2162del	p.Ser719ThrfsTer25	p.S719Tfs*25	ENST00000331920	NM_000264.3	719	aGCCTCCAc/ac	14/24	0.715093623181102	4	FACETS	0.899	0.825	0.976	0.3	0.275	0.326	CLONAL	1	TRUE	1	0.721993181460739	4		352	865	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0009923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	563	435	1	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	0.564542071885667	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.566293098587789	2		436	991	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162323	47162323	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs773098323	NA	P-0009923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	133	288	0	ENST00000409792.3:c.3803C>G	p.Ser1268Cys	p.S1268C	ENST00000409792	NM_014159.6	1268	tCt/tGt	3/21	0.519519959655325	1	FACETS	0.831	0.762	0.902	0.831	0.762	0.902	CLONAL	1	TRUE	0	0.566293098587789	1		288	405	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162506	47162506	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	149	417	1	ENST00000409792.3:c.3620C>T	p.Ser1207Phe	p.S1207F	ENST00000409792	NM_014159.6	1207	tCt/tTt	3/21	0.519519959655325	1	FACETS	0.72	0.662	0.78	0.72	0.662	0.78	SUBCLONAL	1	TRUE	0	0.566293098587789	1		418	524	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11803063	11803063	+	start_lost	Translation_Start_Site	SNP	T	T	A	novel	NA	P-0009923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	178	248	0	ENST00000396373.4:c.2T>A	p.Met1?	p.M1?	ENST00000396373	NM_001987.4	1	aTg/aAg	1/8	1	2	FACETS	0.833	0.769	0.899	0.833	0.769	0.899	CLONAL	1	TRUE	1	0.566293098587789	2		248	755	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878058	48878058	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0009923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	88	144	0	ENST00000267163.4:c.10A>T	p.Lys4Ter	p.K4*	ENST00000267163	NM_000321.2	4	Aaa/Taa	1/27	0.213406777584597	1	FACETS	0.738	0.661	0.818	0.738	0.661	0.818	INDETERMINATE	1	TRUE	0	0.566293098587789	1		144	302	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371748	89371748	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	223	412	0	ENST00000301030.4:c.92A>G	p.Lys31Arg	p.K31R	ENST00000301030	NM_001256183.1	31	aAa/aGa	4/13	NA	2	FACETS	0.905	0.844	0.968			1	INDETERMINATE	1	TRUE	NA	0.566293098587789	2		412	870	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098999	178099697	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTATGTTTAAGACAAAAAAAGGAAGGAGAGAGCTCATGTTTTTTAAATGACAGATACCACATAAATTAATTCACATTATGCCACTGTTGATGGTGGGAAGTGGGGAGATTACAAATACAATCTAAATGAGAACACAGATCCAATGTTCTAGAAGAGCACAGTTAATTCCATTCAATGAATCTATTCATTAAAGACAACAAACAACCTACAAACACATAGCCATCCATTCTAATCACTTGGATCATTAATGATAGGGTGATGGTAGAGGTCACTAAAGGGCAAAGTCACAAATGGTTTGAATGAGAAGAAATCCCACCCTTGTTTAATGGAATATAGAAATTAGAGCAAGCACTCTAAGCCACTGGCTTATATAAGAGAAGTGGGGTCTGGAAAACATTACTGAATACATGGAGTTTTCTTTAAACTTTGCTCAGCAAATATCCAGTTTATAGAGGGATAACTCTCAAGTTAAAGTGTCAATCTAGCAGTTGTGAAATATCACCATTCTTTCCATCTTTCCTACACTAGATTATCTTCTCCCCATCACTGCTTGCTACTCTTATCTCTGTGGCTTACCTATATGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGTGGGTGGATCACCTGAGGTCTGGAGTTCGAGATCAGCCTGGCCAACATGGTGAAACCACGTCTCTACTAAAAATACAAAAATCA	CCTATGTTTAAGACAAAAAAAGGAAGGAGAGAGCTCATGTTTTTTAAATGACAGATACCACATAAATTAATTCACATTATGCCACTGTTGATGGTGGGAAGTGGGGAGATTACAAATACAATCTAAATGAGAACACAGATCCAATGTTCTAGAAGAGCACAGTTAATTCCATTCAATGAATCTATTCATTAAAGACAACAAACAACCTACAAACACATAGCCATCCATTCTAATCACTTGGATCATTAATGATAGGGTGATGGTAGAGGTCACTAAAGGGCAAAGTCACAAATGGTTTGAATGAGAAGAAATCCCACCCTTGTTTAATGGAATATAGAAATTAGAGCAAGCACTCTAAGCCACTGGCTTATATAAGAGAAGTGGGGTCTGGAAAACATTACTGAATACATGGAGTTTTCTTTAAACTTTGCTCAGCAAATATCCAGTTTATAGAGGGATAACTCTCAAGTTAAAGTGTCAATCTAGCAGTTGTGAAATATCACCATTCTTTCCATCTTTCCTACACTAGATTATCTTCTCCCCATCACTGCTTGCTACTCTTATCTCTGTGGCTTACCTATATGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGTGGGTGGATCACCTGAGGTCTGGAGTTCGAGATCAGCCTGGCCAACATGGTGAAACCACGTCTCTACTAAAAATACAAAAATCA	-	novel	NA	P-0009923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	46	224	0	ENST00000397062.3:c.46-698_46del		p.X16_splice	ENST00000397062	NM_006164.4	16		2/5	0.538951488340655	3	FACETS	0.39	0.328	0.458	0.195	0.164	0.229	SUBCLONAL	1	TRUE	1	0.566293098587789	3		224	535	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0010197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	164	545	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.47942234328667	1	FACETS	0.873	0.805	0.943	0.873	0.805	0.943	CLONAL	1	FALSE	0	0.47942234328667	1		547	596	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944157	81944157	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761094228	NA	P-0010197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	303	870	2	ENST00000359376.3:c.1766G>A	p.Arg589His	p.R589H	ENST00000359376	NM_002661.3	589	cGc/cAc	18/33	0.124350453346397	0	FACETS	0.591	0.557	0.626			1	INDETERMINATE	1	FALSE	0	0.47942234328667	0		872	1113	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659912	227659912	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	307	687	0	ENST00000305123.5:c.3543C>G	p.Asp1181Glu	p.D1181E	ENST00000305123	NM_005544.2	1181	gaC/gaG	1/2	1	2	FACETS	0.874	0.822	0.928	0.874	0.822	0.928	CLONAL	1	FALSE	1	0.47942234328667	2		687	1465	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434325	49434325	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	257	688	3	ENST00000301067.7:c.7228C>T	p.Arg2410Ter	p.R2410*	ENST00000301067	NM_003482.3	2410	Cga/Tga	31/54	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.47942234328667	2		691	1033	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849403	68849423	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTTTCTGCTCTCTAGGGCTTG	GTTTCTGCTCTCTAGGGCTTG	-	novel	NA	P-0010197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	121	387	0	ENST00000261769.5:c.1321-14_1327del		p.X441_splice	ENST00000261769	NM_004360.3	441		10/16	0.124350453346397	0	FACETS	0.45	0.408	0.494			1	INDETERMINATE	1	FALSE	0	0.47942234328667	0		387	584	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257321	16257322	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	197	476	0	ENST00000375759.3:c.4592dup	p.Leu1531PhefsTer7	p.L1531Ffs*7	ENST00000375759	NM_015001.2	1529	cgt/cgTt	11/15	1	2	FACETS	0.875	0.811	0.942	0.875	0.811	0.942	CLONAL	1	FALSE	1	0.47942234328667	2		476	939	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	97	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	619	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446269	29446269	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1437	104	445	0	ENST00000389048.3:c.3298G>T	p.Gly1100Cys	p.G1100C	ENST00000389048	NM_004304.4	1100	Ggc/Tgc	20/29	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		445	1541	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223599	53223599	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556834165	NA	P-0010228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	47	203	0	ENST00000375401.3:c.3760C>T	p.Arg1254Cys	p.R1254C	ENST00000375401	NM_004187.3	1254	Cgc/Tgc	23/26	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		203	629	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050384	13050385	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTTCCTAA	novel	NA	P-0010228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1841	130	562	0	ENST00000316448.5:c.338_345dup	p.Ser116PhefsTer44	p.S116Ffs*44	ENST00000316448	NM_004343.3	112	-/TTTCCTAA	3/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		562	1971	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	141	428	2	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.969	0.886	1	0.969	0.886	1	CLONAL	1	TRUE	1	0.47	2		430	619	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852118	63852118	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	68	230	0	ENST00000279873.7:c.2901del	p.Lys967AsnfsTer15	p.K967Nfs*15	ENST00000279873	NM_032199.2	966	Aaa/aa	10/10	0.3	5	FACETS	1	0.97	1			1	CLONAL	1	TRUE	NA	0.47	5		230	351	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	187	660	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.97	0.898	1	0.97	0.898	1	CLONAL	1	TRUE	1	0.47	2		663	820	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	136	764	1	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	0.838	0.763	0.915	0.838	0.763	0.915	CLONAL	1	TRUE	1	0.47	2		765	691	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	33	158	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.776	0.639	0.927	0.776	0.639	0.927	CLONAL	1	TRUE	1	0.47	2		159	181	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	186	646	1	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.47	2		647	772	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	83	247	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.47	2		248	330	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	132	639	9	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.736	0.669	0.807	0.736	0.669	0.807	SUBCLONAL	1	TRUE	1	0.47	2		648	763	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	107	466	8	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	0.807	0.726	0.893	0.807	0.726	0.893	CLONAL	1	TRUE	1	0.47	2		474	564	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916726	178916726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772110575	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	26	820	1	ENST00000263967.3:c.113G>A	p.Arg38His	p.R38H	ENST00000263967	NM_006218.2	38	cGt/cAt	2/21	1	2	FACETS	0.163	0.128	0.203	0.163	0.128	0.203	SUBCLONAL	1	TRUE	1	0.47	2		821	680	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	68	372	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.834	0.73	0.945	0.834	0.73	0.945	CLONAL	1	TRUE	1	0.47	2		373	347	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057937	27057937	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	55	132	0	ENST00000324856.7:c.1650del	p.Tyr551ThrfsTer68	p.Y551Tfs*68	ENST00000324856	NM_006015.4	549	Ccc/cc	3/20	1	2	FACETS	0.87	0.751	0.998	0.87	0.751	0.998	CLONAL	1	TRUE	1	0.47	2		132	269	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	153	972	7	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	0.717	0.656	0.781	0.717	0.656	0.781	SUBCLONAL	1	TRUE	1	0.47	2		979	908	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	32	418	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	0.278	0.225	0.339	0.278	0.225	0.339	SUBCLONAL	1	TRUE	1	0.47	2		418	489	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849663	68849663	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587780113	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	91	258	0	ENST00000261769.5:c.1565+1G>A		p.X522_splice	ENST00000261769	NM_004360.3	522			1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.47	2		258	355	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	102	355	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	1	2	FACETS	0.889	0.799	0.984	0.889	0.799	0.984	CLONAL	1	TRUE	1	0.47	2		355	488	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	112	535	0	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	0.857	0.774	0.945	0.857	0.774	0.945	CLONAL	1	TRUE	1	0.47	2		535	556	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420426	49420426	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1214099522	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	75	285	0	ENST00000301067.7:c.15323G>A	p.Arg5108His	p.R5108H	ENST00000301067	NM_003482.3	5108	cGt/cAt	48/54	1	2	FACETS	0.933	0.824	1	0.933	0.824	1	CLONAL	1	TRUE	1	0.47	2		285	342	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141498	11141498	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	82	406	0	ENST00000358026.2:c.3480del	p.Leu1161SerfsTer3	p.L1161Sfs*3	ENST00000358026	NM_001128849.1	1159	Ggg/gg	25/36	1	2	FACETS	0.759	0.671	0.851	0.759	0.671	0.851	SUBCLONAL	1	TRUE	1	0.47	2		406	460	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681708	78681708	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767783333	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	123	362	0	ENST00000306801.3:c.416G>A	p.Arg139His	p.R139H	ENST00000306801	NM_020761.2	139	cGc/cAc	4/34	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.47	2		362	518	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	56	115	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	0.47	2		115	163	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069060	5069060	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	97	388	0	ENST00000381652.3:c.1370del	p.Asn457MetfsTer22	p.N457Mfs*22	ENST00000381652	NM_004972.3	455	acA/ac	11/25	1	2	FACETS	0.976	0.875	1	0.976	0.875	1	CLONAL	1	TRUE	1	0.47	2		388	423	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561767	55561767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780349712	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	99	370	0	ENST00000288135.5:c.157G>A	p.Glu53Lys	p.E53K	ENST00000288135	NM_000222.2	53	Gag/Aag	2/21	1	2	FACETS	0.77	0.69	0.855	0.77	0.69	0.855	SUBCLONAL	1	TRUE	1	0.47	2		370	547	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781371	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	121	417	2	ENST00000269305.4:c.328C>T	p.Arg110Cys	p.R110C	ENST00000269305	NM_001126112.2	110	Cgt/Tgt	4/11	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.47	2		419	498	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048662	180048662	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1468150967	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	38	287	0	ENST00000261937.6:c.1900G>A	p.Ala634Thr	p.A634T	ENST00000261937	NM_182925.4	634	Gcc/Acc	13/30	0.177328318235823	0	FACETS	0.374	0.312	0.443			1	INDETERMINATE	1	TRUE	0	0.47	0		287	229	SUCCESS
APC	324	MSKCC	GRCh37	5	112175273	112175273	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123121	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	84	266	0	ENST00000257430.4:c.3982C>T	p.Gln1328Ter	p.Q1328*	ENST00000257430	NM_000038.5	1328	Cag/Tag	16/16	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.47	2		266	345	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980402	55980402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1357848255	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	82	397	0	ENST00000263923.4:c.689C>T	p.Pro230Leu	p.P230L	ENST00000263923	NM_002253.2	230	cCg/cTg	6/30	1	2	FACETS	0.972	0.864	1	0.972	0.864	1	CLONAL	1	TRUE	1	0.47	2		397	359	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48922000	48922000	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1566187856	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	76	372	0	ENST00000267163.4:c.539+1G>A		p.X180_splice	ENST00000267163	NM_000321.2	180			1	2	FACETS	0.766	0.675	0.864	0.766	0.675	0.864	SUBCLONAL	1	TRUE	1	0.47	2		372	422	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	135	420	2	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.47	2		422	540	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567647	226567647	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	61	332	1	ENST00000366794.5:c.1519del	p.Ser507AlafsTer17	p.S507Afs*17	ENST00000366794	NM_001618.3	507	Agc/gc	10/23	1	2	FACETS	0.671	0.581	0.767	0.671	0.581	0.767	SUBCLONAL	1	TRUE	1	0.47	2		333	387	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099579	157099579	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1562376341	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	24	88	0	ENST00000346085.5:c.521del	p.Pro174ArgfsTer6	p.P174Rfs*6	ENST00000346085	NM_020732.3	172	gaC/ga	1/20	1	2	FACETS	0.982	0.785	1	0.982	0.785	1	CLONAL	1	TRUE	1	0.47	2		88	104	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717699	89717699	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554825210	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	58	313	0	ENST00000371953.3:c.724G>T	p.Glu242Ter	p.E242*	ENST00000371953	NM_000314.4	242	Gag/Tag	7/9	1	2	FACETS	0.703	0.607	0.807	0.703	0.607	0.807	SUBCLONAL	1	TRUE	1	0.47	2		313	351	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532710	187532710	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1010116749	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	125	497	2	ENST00000441802.2:c.9683del	p.Pro3228LeufsTer42	p.P3228Lfs*42	ENST00000441802	NM_005245.3	3228	cCt/ct	14/27	1	2	FACETS	0.93	0.845	1	0.93	0.845	1	CLONAL	1	TRUE	1	0.47	2		499	572	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732957	30732957	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504421	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	110	282	0	ENST00000295754.5:c.1570G>A	p.Asp524Asn	p.D524N	ENST00000295754	NM_003242.5	524	Gac/Aac	7/7	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.47	2		282	453	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636210	87636210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs957713208	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	82	282	0	ENST00000277120.3:c.2375G>A	p.Arg792His	p.R792H	ENST00000277120		792	cGc/cAc	19/19	1	2	FACETS	0.849	0.753	0.951	0.849	0.753	0.951	CLONAL	1	TRUE	1	0.47	2		282	411	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405954	157405954	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	103	352	0	ENST00000346085.5:c.2201del	p.Gly734AlafsTer11	p.G734Afs*11	ENST00000346085	NM_020732.3	732	ccG/cc	6/20	1	2	FACETS	0.863	0.775	0.955	0.863	0.775	0.955	CLONAL	1	TRUE	1	0.47	2		352	508	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65323367	65323367	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	96	342	0	ENST00000342505.4:c.1430T>C	p.Met477Thr	p.M477T	ENST00000342505	NM_002227.2	477	aTg/aCg	10/25	1	2	FACETS	0.933	0.836	1	0.933	0.836	1	CLONAL	1	TRUE	1	0.47	2		342	438	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866581	117866581	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057524012	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	120	860	0	ENST00000297338.2:c.1064C>T	p.Pro355Leu	p.P355L	ENST00000297338	NM_006265.2	355	cCg/cTg	9/14	1	2	FACETS	0.703	0.636	0.775	0.703	0.636	0.775	SUBCLONAL	1	TRUE	1	0.47	2		860	726	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866710	37866710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1258412021	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	121	391	1	ENST00000269571.5:c.877G>A	p.Ala293Thr	p.A293T	ENST00000269571		293	Gcc/Acc	7/27	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.47	2		392	488	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783245	9783245	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756497515	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	78	285	0	ENST00000377346.4:c.2489G>A	p.Arg830His	p.R830H	ENST00000377346	NM_005026.3	830	cGt/cAt	20/24	0.3	2	FACETS	0.93	0.823	1			1	CLONAL	1	TRUE	NA	0.47	2		285	357	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248510	59248510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	65	460	0	ENST00000371222.2:c.233G>A	p.Arg78His	p.R78H	ENST00000371222	NM_002228.3	78	cGc/cAc	1/1	1	2	FACETS	0.396	0.343	0.454	0.396	0.343	0.454	SUBCLONAL	1	TRUE	1	0.47	2		460	698	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432619	78432619	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	69	270	1	ENST00000370768.2:c.364C>T	p.Gln122Ter	p.Q122*	ENST00000370768	NM_003902.3	122	Cag/Tag	6/20	1	2	FACETS	0.915	0.803	1	0.915	0.803	1	CLONAL	1	TRUE	1	0.47	2		271	321	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844407	156844407	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	83	937	0	ENST00000524377.1:c.1240A>C	p.Thr414Pro	p.T414P	ENST00000524377	NM_002529.3	414	Aca/Cca	10/17	1	2	FACETS	0.434	0.383	0.49	0.434	0.383	0.49	SUBCLONAL	1	TRUE	1	0.47	2		937	813	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523087	25523087	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746009417	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	85	304	0	ENST00000264709.3:c.98G>A	p.Arg33His	p.R33H	ENST00000264709	NM_175629.2	33	cGt/cAt	3/23	1	2	FACETS	0.878	0.78	0.981	0.878	0.78	0.981	CLONAL	1	TRUE	1	0.47	2		304	412	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281604	198281604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	43	373	0	ENST00000335508.6:c.527C>T	p.Ala176Val	p.A176V	ENST00000335508	NM_012433.2	176	gCt/gTt	6/25	1	2	FACETS	0.31	0.259	0.367	0.31	0.259	0.367	SUBCLONAL	1	TRUE	1	0.47	2		373	590	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151187	202151187	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	82	429	0	ENST00000358485.4:c.1487A>G	p.Asp496Gly	p.D496G	ENST00000358485	NM_001080125.1	496	gAt/gGt	9/9	1	2	FACETS	0.951	0.844	1	0.951	0.844	1	CLONAL	1	TRUE	1	0.47	2		429	367	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483963	212483963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	79	476	0	ENST00000342788.4:c.2240C>T	p.Pro747Leu	p.P747L	ENST00000342788	NM_005235.2	747	cCt/cTt	19/28	1	2	FACETS	0.82	0.725	0.921	0.82	0.725	0.921	CLONAL	1	TRUE	1	0.47	2		476	410	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645935	215645935	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	133	698	1	ENST00000260947.4:c.663G>T	p.Glu221Asp	p.E221D	ENST00000260947	NM_000465.2	221	gaG/gaT	4/11	1	2	FACETS	0.887	0.808	0.97	0.887	0.808	0.97	CLONAL	1	TRUE	1	0.47	2		699	638	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346714	225346714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	135	509	0	ENST00000264414.4:c.1924C>T	p.Arg642Trp	p.R642W	ENST00000264414	NM_003590.4	642	Cgg/Tgg	14/16	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.47	2		509	558	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659964	227659964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	116	364	1	ENST00000305123.5:c.3491C>T	p.Ala1164Val	p.A1164V	ENST00000305123	NM_005544.2	1164	gCc/gTc	1/2	1	2	FACETS	0.912	0.826	1	0.912	0.826	1	CLONAL	1	TRUE	1	0.47	2		365	541	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397692	49397692	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	149	414	1	ENST00000418115.1:c.532G>A	p.Ala178Thr	p.A178T	ENST00000418115	NM_001664.2	178	Gct/Act	5/5	1	2	FACETS	0.902	0.826	0.981	0.902	0.826	0.981	CLONAL	1	TRUE	1	0.47	2		415	703	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49929253	49929253	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1458622585	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	184	769	0	ENST00000296474.3:c.3290A>G	p.Tyr1097Cys	p.Y1097C	ENST00000296474	NM_002447.2	1097	tAc/tGc	15/20	0.3	1	FACETS	0.846	0.783	0.911	0.846	0.783	0.911	CLONAL	1	TRUE	0	0.47	1		769	708	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873081	134873081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	83	336	0	ENST00000398015.3:c.1385G>A	p.Gly462Asp	p.G462D	ENST00000398015	NM_004441.4	462	gGc/gAc	6/16	1	2	FACETS	0.881	0.782	0.985	0.881	0.782	0.985	CLONAL	1	TRUE	1	0.47	2		336	401	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236580	236580	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747488969	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	20	53	0	ENST00000264932.6:c.1298C>T	p.Pro433Leu	p.P433L	ENST00000264932	NM_004168.2	433	cCc/cTc	10/15	1	2	FACETS	0.978	0.765	1	0.978	0.765	1	CLONAL	1	TRUE	1	0.47	2		53	87	SUCCESS
APC	324	MSKCC	GRCh37	5	112173462	112173462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	51	419	1	ENST00000257430.4:c.2171C>T	p.Ala724Val	p.A724V	ENST00000257430	NM_000038.5	724	gCa/gTa	16/16	1	2	FACETS	0.577	0.492	0.67	0.577	0.492	0.67	SUBCLONAL	1	TRUE	1	0.47	2		420	376	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131951745	131951745	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786201136	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	112	392	2	ENST00000265335.6:c.3087G>T	p.Glu1029Asp	p.E1029D	ENST00000265335		1029	gaG/gaT	20/25	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.47	2		394	463	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839726	27839726	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs761339099	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	299	1159	0	ENST00000328488.2:c.368A>C	p.Lys123Thr	p.K123T	ENST00000328488	NM_003533.2	123	aAa/aCa	1/1	0.147855396311393	3	FACETS	1	0.986	1	0.578	0.543	0.613	INDETERMINATE	1	TRUE	1	0.47	3		1159	1360	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288323	33288323	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780262381	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	83	244	0	ENST00000374542.5:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000374542	NM_001141970.1	362	cGg/cAg	4/8	0.147855396311393	3	FACETS	1	0.911	1	0.516	0.457	0.578	INDETERMINATE	1	TRUE	1	0.47	3		244	423	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94128963	94128963	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	105	448	0	ENST00000369303.4:c.97G>T	p.Val33Leu	p.V33L	ENST00000369303	NM_004440.3	33	Gta/Tta	1/17	0.3	1	FACETS	0.601	0.54	0.665	0.601	0.54	0.665	SUBCLONAL	1	TRUE	0	0.47	1		448	569	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674321	117674321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	71	376	1	ENST00000368508.3:c.4153C>T	p.Leu1385Phe	p.L1385F	ENST00000368508	NM_002944.2	1385	Ctt/Ttt	26/43	0.177328318235823	0	FACETS	0.467	0.41	0.527			1	INDETERMINATE	1	TRUE	0	0.47	0		377	343	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099840	157099840	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	128	572	0	ENST00000346085.5:c.777A>C	p.Gln259His	p.Q259H	ENST00000346085	NM_020732.3	259	caA/caC	1/20	1	2	FACETS	0.843	0.766	0.924	0.843	0.766	0.924	CLONAL	1	TRUE	1	0.47	2		572	646	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453127	140453127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372569965	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	70	319	1	ENST00000288602.6:c.1808G>A	p.Arg603Gln	p.R603Q	ENST00000288602	NM_004333.4	603	cGa/cAa	15/18	1	2	FACETS	0.937	0.823	1	0.937	0.823	1	CLONAL	1	TRUE	1	0.47	2		320	318	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012228	152012228	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	96	586	0	ENST00000262189.6:c.585G>T	p.Gln195His	p.Q195H	ENST00000262189	NM_170606.2	195	caG/caT	4/59	1	2	FACETS	0.832	0.744	0.925	0.832	0.744	0.925	CLONAL	1	TRUE	1	0.47	2		586	491	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089853	5089853	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	26	309	0	ENST00000381652.3:c.2751C>A	p.Cys917Ter	p.C917*	ENST00000381652	NM_004972.3	917	tgC/tgA	20/25	1	2	FACETS	0.398	0.316	0.492	0.398	0.316	0.492	SUBCLONAL	1	TRUE	1	0.47	2		309	278	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229434	98229434	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	116	543	2	ENST00000331920.6:c.2524A>G	p.Lys842Glu	p.K842E	ENST00000331920	NM_000264.3	842	Aaa/Gaa	15/24	1	2	FACETS	0.801	0.724	0.883	0.801	0.724	0.883	CLONAL	1	TRUE	1	0.47	2		545	616	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249393	110249393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747114701	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	287	816	1	ENST00000374672.4:c.1180G>A	p.Ala394Thr	p.A394T	ENST00000374672	NM_004235.4	394	Gcc/Acc	4/5	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.47	2		817	1147	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63829525	63829525	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	83	314	1	ENST00000279873.7:c.1168G>A	p.Ala390Thr	p.A390T	ENST00000279873	NM_032199.2	390	Gct/Act	8/10	0.3	5	FACETS	1	0.965	1			1	CLONAL	1	TRUE	NA	0.47	5		315	487	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533854	533854	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	132	398	1	ENST00000451590.1:c.202C>T	p.Arg68Trp	p.R68W	ENST00000451590	NM_001130442.1	68	Cgg/Tgg	3/5	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.47	2		399	482	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534270	534270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	37	457	1	ENST00000451590.1:c.53C>T	p.Ala18Val	p.A18V	ENST00000451590	NM_001130442.1	18	gCg/gTg	2/5	1	2	FACETS	0.359	0.295	0.429	0.359	0.295	0.429	SUBCLONAL	1	TRUE	1	0.47	2		458	439	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456377	32456377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	72	419	0	ENST00000332351.3:c.515C>T	p.Ala172Val	p.A172V	ENST00000332351	NM_024426.4	172	gCc/gTc	1/10	1	2	FACETS	0.878	0.772	0.99	0.878	0.772	0.99	CLONAL	1	TRUE	1	0.47	2		419	349	SUCCESS
EED	8726	MSKCC	GRCh37	11	85961378	85961378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1306469162	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	33	334	1	ENST00000263360.6:c.155G>A	p.Arg52His	p.R52H	ENST00000263360	NM_003797.3	52	cGc/cAc	2/12	1	2	FACETS	0.318	0.259	0.385	0.318	0.259	0.385	SUBCLONAL	1	TRUE	1	0.47	2		335	441	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180453	94180453	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200085146	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	190	524	1	ENST00000323929.3:c.1715G>A	p.Arg572Gln	p.R572Q	ENST00000323929	NM_005591.3	572	cGa/cAa	15/20	1	2	FACETS	0.894	0.827	0.964	0.894	0.827	0.964	CLONAL	1	TRUE	1	0.47	2		525	904	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	443492	443492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	73	355	1	ENST00000399788.2:c.1405C>T	p.Pro469Ser	p.P469S	ENST00000399788	NM_001042603.1	469	Ccg/Tcg	11/28	1	2	FACETS	0.922	0.812	1	0.922	0.812	1	CLONAL	1	TRUE	1	0.47	2		356	337	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813316	102813316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1404671399	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	132	434	1	ENST00000307046.8:c.373C>T	p.Arg125Cys	p.R125C	ENST00000307046	NM_001111285.1	125	Cgc/Tgc	3/4	1	2	FACETS	0.991	0.903	1	0.991	0.903	1	CLONAL	1	TRUE	1	0.47	2		435	567	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856623	111856623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	79	193	1	ENST00000341259.2:c.674G>A	p.Arg225His	p.R225H	ENST00000341259	NM_005475.2	225	cGc/cAc	2/8	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.47	2		194	307	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241993	133241993	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500813	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	70	260	1	ENST00000320574.5:c.2363C>T	p.Ala788Val	p.A788V	ENST00000320574	NM_006231.2	788	gCg/gTg	21/49	1	2	FACETS	0.83	0.728	0.938	0.83	0.728	0.938	CLONAL	1	TRUE	1	0.47	2		261	359	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877386	28877386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	102	298	0	ENST00000282397.4:c.3935C>T	p.Ala1312Val	p.A1312V	ENST00000282397	NM_002019.4	1312	gCt/gTt	30/30	1	2	FACETS	0.937	0.843	1	0.937	0.843	1	CLONAL	1	TRUE	1	0.47	2		298	463	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936658	32936658	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs81002836	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	74	349	0	ENST00000380152.3:c.7806-2A>G		p.X2602_splice	ENST00000380152		2602			1	2	FACETS	0.882	0.777	0.993	0.882	0.777	0.993	CLONAL	1	TRUE	1	0.47	2		349	357	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434934	110434934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	150	540	0	ENST00000375856.3:c.3467C>T	p.Thr1156Met	p.T1156M	ENST00000375856	NM_003749.2	1156	aCg/aTg	1/2	1	2	FACETS	0.929	0.851	1	0.929	0.851	1	CLONAL	1	TRUE	1	0.47	2		540	687	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68292236	68292236	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780272322	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	114	527	0	ENST00000487270.1:c.140G>A	p.Arg47Gln	p.R47Q	ENST00000487270	NM_133509.3	47	cGa/cAa	3/11	1	2	FACETS	0.831	0.75	0.915	0.831	0.75	0.915	CLONAL	1	TRUE	1	0.47	2		527	584	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000388	42000388	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	156	779	1	ENST00000219905.7:c.2407T>A	p.Ser803Thr	p.S803T	ENST00000219905	NM_001164273.1	803	Tct/Act	7/24	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.47	2		780	659	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631706	90631706	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749096156	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	125	402	0	ENST00000330062.3:c.563G>A	p.Arg188Gln	p.R188Q	ENST00000330062	NM_002168.2	188	cGg/cAg	5/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.47	2		402	487	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779253	3779253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867074201	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	60	241	1	ENST00000262367.5:c.5795C>T	p.Thr1932Met	p.T1932M	ENST00000262367	NM_004380.2	1932	aCg/aTg	31/31	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.47	2		242	235	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346259	89346259	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	76	390	1	ENST00000301030.4:c.6691G>A	p.Ala2231Thr	p.A2231T	ENST00000301030	NM_001256183.1	2231	Gcc/Acc	9/13	0.147855396311393	0	FACETS	0.488	0.431	0.549			1	INDETERMINATE	1	TRUE	0	0.47	0		391	351	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016616	12016616	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	128	438	0	ENST00000353533.5:c.752G>C	p.Ser251Thr	p.S251T	ENST00000353533	NM_003010.3	251	aGt/aCt	7/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.47	2		438	509	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78820340	78820340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1284870590	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	94	365	0	ENST00000306801.3:c.1280G>A	p.Arg427Gln	p.R427Q	ENST00000306801	NM_020761.2	427	cGa/cAa	11/34	1	2	FACETS	0.983	0.88	1	0.983	0.88	1	CLONAL	1	TRUE	1	0.47	2		365	407	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223014	5223014	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	17	242	2	ENST00000357368.4:c.2789G>A	p.Gly930Asp	p.G930D	ENST00000357368	NM_002850.3	930	gGc/gAc	18/38	0.112022138184962	0	FACETS	0.168	0.125	0.219			1	INDETERMINATE	1	TRUE	0	0.47	0		244	228	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251867	10251867	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	78	465	0	ENST00000340748.4:c.3262-2A>G		p.X1088_splice	ENST00000340748		1088			0.112022138184962	0	FACETS	0.391	0.345	0.44			1	INDETERMINATE	1	TRUE	0	0.47	0		465	450	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252757	10252757	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	64	245	0	ENST00000340748.4:c.3208G>A	p.Glu1070Lys	p.E1070K	ENST00000340748		1070	Gag/Aag	29/40	0.112022138184962	0	FACETS	0.411	0.358	0.468			1	INDETERMINATE	1	TRUE	0	0.47	0		245	351	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288795	15288795	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1432396805	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	16	85	0	ENST00000263388.2:c.3944G>A	p.Cys1315Tyr	p.C1315Y	ENST00000263388	NM_000435.2	1315	tGc/tAc	24/33	1	2	FACETS	0.896	0.677	1	0.896	0.677	1	CLONAL	1	TRUE	1	0.47	2		85	76	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727812	41727812	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	181	634	0	ENST00000301178.4:c.437A>G	p.Glu146Gly	p.E146G	ENST00000301178	NM_021913.4	146	gAa/gGa	4/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.47	2		634	634	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905597	50905597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753689379	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	51	716	1	ENST00000440232.2:c.725C>T	p.Ala242Val	p.A242V	ENST00000440232	NM_002691.3	242	gCg/gTg	6/27	0.3	1	FACETS	0.23	0.195	0.269	0.23	0.195	0.269	SUBCLONAL	1	TRUE	0	0.47	1		717	722	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342602	70342602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1268612180	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	136	253	0	ENST00000374080.3:c.1363C>T	p.Arg455Trp	p.R455W	ENST00000374080		455	Cgg/Tgg	10/45	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.47	1		253	328	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345554	70345554	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	143	338	0	ENST00000374080.3:c.2413A>G	p.Thr805Ala	p.T805A	ENST00000374080		805	Aca/Gca	17/45	1	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.47	1		338	396	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526199	63526202	+	frameshift_variant	Frame_Shift_Del	DEL	GCTT	GCTT	-	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	112	361	0	ENST00000307078.5:c.2424_2427del	p.Ser809MetfsTer51	p.S809Mfs*51	ENST00000307078	NM_004655.3	808	gcAAGC/gc	11/11	1	2	FACETS	0.893	0.806	0.983	0.893	0.806	0.983	CLONAL	1	TRUE	1	0.47	2		361	534	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853400	151853400	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	62	240	0	ENST00000262189.6:c.11702del	p.Pro3901LeufsTer33	p.P3901Lfs*33	ENST00000262189	NM_170606.2	3901	cCt/ct	45/59	1	2	FACETS	0.838	0.729	0.954	0.838	0.729	0.954	CLONAL	1	TRUE	1	0.47	2		240	315	SUCCESS
APC	324	MSKCC	GRCh37	5	112177265	112177265	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1554087123	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	46	253	1	ENST00000257430.4:c.5978del	p.Pro1993LeufsTer51	p.P1993Lfs*51	ENST00000257430	NM_000038.5	1992	Ccc/cc	16/16	1	2	FACETS	0.837	0.711	0.972	0.837	0.711	0.972	CLONAL	1	TRUE	1	0.47	2		254	234	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425925	49425926	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	158	645	0	ENST00000301067.7:c.12562dup	p.Val4188GlyfsTer146	p.V4188Gfs*146	ENST00000301067	NM_003482.3	4188	gtt/gGtt	39/54	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.47	2		645	671	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763860	76763860	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	134	305	0	ENST00000373344.5:c.7448del	p.Asn2483IlefsTer17	p.N2483Ifs*17	ENST00000373344	NM_000489.3	2483	aAt/at	35/35	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.47	1		305	357	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698153	47698155	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	96	431	0	ENST00000233146.2:c.1715_1717del	p.Glu572del	p.E572del	ENST00000233146	NM_000251.2	571	GAA/-	11/16	1	2	FACETS	0.865	0.775	0.961	0.865	0.775	0.961	CLONAL	1	TRUE	1	0.47	2		431	472	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356423	66356423	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	65	275	0	ENST00000273854.3:c.1074del	p.Ser359LeufsTer63	p.S359Lfs*63	ENST00000273854	NM_004439.5	358	ccC/cc	5/18	1	2	FACETS	0.934	0.817	1	0.934	0.817	1	CLONAL	1	TRUE	1	0.47	2		275	296	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15280969	15280970	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	86	452	0	ENST00000263388.2:c.5126dup	p.Glu1711Ter	p.E1711*	ENST00000263388	NM_000435.2	1709	aag/aaAg	28/33	1	2	FACETS	0.968	0.863	1	0.968	0.863	1	CLONAL	1	TRUE	1	0.47	2		452	378	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436083	51436084	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	97	349	0	ENST00000262662.1:c.49dup	p.Asp17GlyfsTer7	p.D17Gfs*7	ENST00000262662		15	agg/aGgg	3/4	1	2	FACETS	0.663	0.591	0.738	0.663	0.591	0.738	SUBCLONAL	1	TRUE	1	0.47	2		349	623	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363417	40363418	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	101	330	0	ENST00000397332.2:c.811_812del	p.Asp271CysfsTer8	p.D271Cfs*8	ENST00000397332	NM_001033082.2	271	GAt/t	3/3	1	2	FACETS	0.914	0.821	1	0.914	0.821	1	CLONAL	1	TRUE	1	0.47	2		330	470	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023252	27023255	+	frameshift_variant	Frame_Shift_Del	DEL	CCGC	CCGC	-	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	116	260	0	ENST00000324856.7:c.361_364del	p.Pro121AlafsTer110	p.P121Afs*110	ENST00000324856	NM_006015.4	120	CCGCcc/cc	1/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.47	2		260	377	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014243	70014243	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	215	773	0	ENST00000394351.3:c.1108del	p.Met370TrpfsTer9	p.M370Wfs*9	ENST00000394351	NM_000248.3	368	acA/ac	9/9	1	2	FACETS	0.919	0.855	0.986	0.919	0.855	0.986	CLONAL	1	TRUE	1	0.47	2		773	995	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433482	138433482	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	75	402	1	ENST00000289153.2:c.1130del	p.Asn377MetfsTer35	p.N377Mfs*35	ENST00000289153	NM_006219.2	377	aAt/at	7/22	1	2	FACETS	0.81	0.714	0.913	0.81	0.714	0.913	CLONAL	1	TRUE	1	0.47	2		403	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0010690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	436	584	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.364337304551926	4	FACETS	1	0.992	1			1	CLONAL	2	FALSE	NA	0.377168334809028	4		584	1364	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939920	49939920	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1316	290	831	0	ENST00000296474.3:c.1123G>C	p.Asp375His	p.D375H	ENST00000296474	NM_002447.2	375	Gac/Cac	1/20	NA	2	FACETS	0.958	0.898	1			1	INDETERMINATE	1	FALSE	NA	0.377168334809028	2		831	1606	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010866-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	70	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.783	0.681	0.893	0.783	0.681	0.893	SUBCLONAL	1	TRUE	1	0.213482541208142	2		436	838	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183599	185183599	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs756251474	NA	P-0010866-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	87	475	0	ENST00000265026.3:c.1453G>C	p.Glu485Gln	p.E485Q	ENST00000265026	NM_004721.4	485	Gaa/Caa	9/14	1	2	FACETS	0.903	0.798	1	0.903	0.798	1	CLONAL	1	TRUE	1	0.213482541208142	2		475	903	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593326	48593390	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGAACTAAAATTTAATTTAAAATACTTATCAAGATAAAATGTAATTTCTTTTTTCTTCCTAAGGT	TGAACTAAAATTTAATTTAAAATACTTATCAAGATAAAATGTAATTTCTTTTTTCTTCCTAAGGT	-	novel	NA	P-0010866-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	45	113	0	ENST00000342988.3:c.1140-61_1143del		p.X380_splice	ENST00000342988	NM_005359.5	380		10/12	0.213482541208142	1	FACETS	1	0.94	1	1	0.977	1	CLONAL	2	TRUE	0	0.213482541208142	1		113	157	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912086	32912089	+	frameshift_variant	Frame_Shift_Del	DEL	TGAC	TGAC	-	rs886040484	NA	P-0010866-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1514	313	841	0	ENST00000380152.3:c.3596_3599del	p.Asp1199ValfsTer9	p.D1199Vfs*9	ENST00000380152		1198	aaTGAC/aa	11/27	0.213482541208142	3	FACETS	0.888	0.835	0.943	0.888	0.835	0.943	CLONAL	2	TRUE	1	0.213482541208142	3		841	1827	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	51	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.723	0.614	0.844	0.723	0.614	0.844	SUBCLONAL	1	TRUE	1	0.209864883838829	2		436	672	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183599	185183599	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs756251474	NA	P-0010866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	60	475	0	ENST00000265026.3:c.1453G>C	p.Glu485Gln	p.E485Q	ENST00000265026	NM_004721.4	485	Gaa/Caa	9/14	0.184870424065994	3	FACETS	0.856	0.736	0.987	0.428	0.368	0.494	CLONAL	1	TRUE	1	0.209864883838829	3		475	738	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593326	48593390	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGAACTAAAATTTAATTTAAAATACTTATCAAGATAAAATGTAATTTCTTTTTTCTTCCTAAGGT	TGAACTAAAATTTAATTTAAAATACTTATCAAGATAAAATGTAATTTCTTTTTTCTTCCTAAGGT	-	novel	NA	P-0010866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	48	113	0	ENST00000342988.3:c.1140-61_1143del		p.X380_splice	ENST00000342988	NM_005359.5	380		10/12	1	2	FACETS	0.908	0.781	1	1	0.979	1	CLONAL	3	TRUE	1	0.209864883838829	2		113	168	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912086	32912089	+	frameshift_variant	Frame_Shift_Del	DEL	TGAC	TGAC	-	rs886040484	NA	P-0010866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	166	841	0	ENST00000380152.3:c.3596_3599del	p.Asp1199ValfsTer9	p.D1199Vfs*9	ENST00000380152		1198	aaTGAC/aa	11/27	0.184870424065994	3	FACETS	0.988	0.907	1	0.988	0.907	1	CLONAL	2	TRUE	1	0.209864883838829	3		841	885	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	246	778	1	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.356494561527789	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.356494561527789	1		779	1107	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274911	41274911	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	175	549	1	ENST00000349496.5:c.1161T>G	p.Asn387Lys	p.N387K	ENST00000349496	NM_001904.3	387	aaT/aaG	8/15	0.356494561527789	1	FACETS	0.986	0.909	1	0.986	0.909	1	CLONAL	1	TRUE	0	0.356494561527789	1		550	818	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42790999	42790999	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	186	690	0	ENST00000575354.2:c.144G>T	p.Gln48His	p.Q48H	ENST00000575354	NM_015125.3	48	caG/caT	2/20	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.356494561527789	2		690	1012	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526059	66526059	+	splice_acceptor_variant	Splice_Site	DEL	A	A	-	novel	NA	P-0010914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	207	493	1	ENST00000358598.2:c.892-2del		p.X298_splice	ENST00000358598	NM_212471.2	298			0.356494561527789	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.356494561527789	1		494	723	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0011044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	328	406	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.516119430592157	4	FACETS	1	0.98	1	0.711	0.674	0.749	CLONAL	2	FALSE	1	0.509955557033005	4		406	910	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419986	41419986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372989163	NA	P-0011044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	71	543	1	ENST00000373198.4:c.335G>A	p.Arg112His	p.R112H	ENST00000373198	NM_133170.3	112	cGt/cAt	3/32	NA	2	FACETS	0.43	0.375	0.489			1	INDETERMINATE	1	FALSE	NA	0.509955557033005	2		544	648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0011044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	232	602	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.516119430592157	3	FACETS	0.948	0.891	1	0.948	0.891	1	CLONAL	2	FALSE	1	0.509955557033005	3		602	602	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266052	41266052	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	116	424	0	ENST00000349496.5:c.49G>T	p.Asp17Tyr	p.D17Y	ENST00000349496	NM_001904.3	17	Gac/Tac	3/15	0.460563706234686	3	FACETS	0.659	0.594	0.729	0.33	0.297	0.365	SUBCLONAL	1	FALSE	1	0.509955557033005	3		424	866	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438494	52438494	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs756443059	NA	P-0011044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	87	604	0	ENST00000460680.1:c.1225G>C	p.Val409Leu	p.V409L	ENST00000460680	NM_004656.3	409	Gtg/Ctg	12/17	NA	2	FACETS	0.685	0.608	0.767			1	INDETERMINATE	1	FALSE	NA	0.509955557033005	2		604	498	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388082	81388082	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	76	518	0	ENST00000222390.5:c.293G>T	p.Trp98Leu	p.W98L	ENST00000222390	NM_000601.4	98	tGg/tTg	3/18	0.509955557033005	6	FACETS	0.603	0.527	0.685	0.151	0.131	0.172	SUBCLONAL	1	FALSE	2	0.509955557033005	6		518	999	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226089	133226089	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	44	501	0	ENST00000320574.5:c.3808G>C	p.Val1270Leu	p.V1270L	ENST00000320574	NM_006231.2	1270	Gtc/Ctc	31/49	0.267616735708696	3	FACETS	0.532	0.447	0.626	0.266	0.223	0.313	INDETERMINATE	1	FALSE	1	0.509955557033005	3		501	407	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836617	89836617	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	71	409	0	ENST00000389301.3:c.2273T>C	p.Leu758Pro	p.L758P	ENST00000389301	NM_000135.2	758	cTc/cCc	25/43	1	2	FACETS	0.7	0.614	0.792	0.7	0.614	0.792	SUBCLONAL	1	FALSE	1	0.509955557033005	2		409	398	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556874	29556874	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	73	334	0	ENST00000356175.3:c.2872A>T	p.Thr958Ser	p.T958S	ENST00000356175	NM_000267.3	958	Act/Tct	22/57	0.516119430592157	3	FACETS	0.726	0.636	0.822	0.363	0.318	0.411	SUBCLONAL	1	FALSE	1	0.509955557033005	3		334	495	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243776	41243776	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs397509105	NA	P-0011044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	89	584	0	ENST00000357654.3:c.3772G>T	p.Glu1258Ter	p.E1258*	ENST00000357654	NM_007294.3	1258	Gag/Tag	10/23	0.341280188913905	4	FACETS	0.811	0.719	0.908	0.203	0.179	0.227	CLONAL	1	FALSE	0	0.509955557033005	4		584	650	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910466	32910503	+	frameshift_variant	Frame_Shift_Del	DEL	CTTAACTAGCTCTTTTGGGACAATTCTGAGGAAATGTT	CTTAACTAGCTCTTTTGGGACAATTCTGAGGAAATGTT	-	novel	NA	P-0011044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1295	134	713	0	ENST00000380152.3:c.1976_2013del	p.Leu659Ter	p.L659*	ENST00000380152		658	tcCTTAACTAGCTCTTTTGGGACAATTCTGAGGAAATGTTct/tcct	11/27	0.509955557033005	5	FACETS	0.649	0.588	0.714	0.162	0.147	0.179	SUBCLONAL	1	FALSE	1	0.509955557033005	5		713	1429	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240025	41240061	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCGCACAGCCCCCCGGTGGCGGCCGCGGCGGCCGC	CCCCGCACAGCCCCCCGGTGGCGGCCGCGGCGGCCGC	-	novel	NA	P-0011044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	20	21	0	ENST00000379561.5:c.289_325del	p.Ala97ThrfsTer224	p.A97Tfs*224	ENST00000379561	NM_002015.3	97	GCGGCCGCCGCGGCCGCCACCGGGGGGCTGTGCGGGGac/ac	1/3	0.509955557033005	5	FACETS	0.975	0.768	1	0.487	0.384	0.601	CLONAL	2	FALSE	1	0.509955557033005	5		21	71	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0011155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	140	280	1	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.696	0.638	0.755	0.696	0.638	0.755	SUBCLONAL	1	TRUE	1	0.869032528456899	2		281	463	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024721	14024721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1340754747	NA	P-0011155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	346	250	0	ENST00000311895.7:c.947C>T	p.Thr316Met	p.T316M	ENST00000311895	NM_005236.2	316	aCg/aTg	5/11	1	2	FACETS	0.93	0.885	0.976	0.93	0.885	0.976	CLONAL	1	TRUE	1	0.869032528456899	2		250	856	SUCCESS
AR	367	MSKCC	GRCh37	X	66943543	66943543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852581	NA	P-0011155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	721	309	0	ENST00000374690.3:c.2623C>T	p.His875Tyr	p.H875Y	ENST00000374690	NM_000044.3	875	Cat/Tat	8/8	1	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.869032528456899	1		309	814	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	465598	465598	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	510	366	1	ENST00000399788.2:c.778G>T	p.Asp260Tyr	p.D260Y	ENST00000399788	NM_001042603.1	260	Gat/Tat	6/28	1	2	FACETS	0.902	0.865	0.94	0.902	0.865	0.94	CLONAL	1	TRUE	1	0.869032528456899	2		367	1301	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626706	28626706	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	445	314	0	ENST00000241453.7:c.590T>C	p.Val197Ala	p.V197A	ENST00000241453	NM_004119.2	197	gTg/gCg	5/24	NA	2	FACETS	0.963	0.921	1			1	INDETERMINATE	1	TRUE	NA	0.869032528456899	2		314	1064	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439700	220439701	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0011155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	721	551	0	ENST00000243786.2:c.562_563dup	p.Leu189CysfsTer2	p.L189Cfs*2	ENST00000243786	NM_002191.3	185	gct/gCTct	2/2	NA	2	FACETS	0.953	0.92	0.985			1	INDETERMINATE	1	TRUE	NA	0.869032528456899	2		551	1742	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264391	16264391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145335938	NA	P-0011155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	530	449	1	ENST00000375759.3:c.10594G>A	p.Val3532Ile	p.V3532I	ENST00000375759	NM_015001.2	3532	Gtc/Atc	13/15	1	2	FACETS	0.991	0.952	1	0.991	0.952	1	CLONAL	1	TRUE	1	0.869032528456899	2		450	1231	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206667296	206667296	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	489	341	0	ENST00000367120.3:c.2089C>A	p.Leu697Ile	p.L697I	ENST00000367120	NM_014002.3	697	Ctc/Atc	21/22	1	2	FACETS	0.963	0.923	1	0.963	0.923	1	CLONAL	1	TRUE	1	0.869032528456899	2		341	1169	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586482	189586482	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs772847941	NA	P-0011155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	289	171	0	ENST00000264731.3:c.1106A>G	p.Lys369Arg	p.K369R	ENST00000264731	NM_003722.4	369	aAg/aGg	8/14	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.869032528456899	2		171	644	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112029147	112029147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	756	552	4	ENST00000368678.4:c.421G>A	p.Val141Ile	p.V141I	ENST00000368678		141	Gtt/Att	5/13	0.869032528456899	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.869032528456899	1		556	984	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98244441	98244441	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	369	273	0	ENST00000331920.6:c.629T>C	p.Ile210Thr	p.I210T	ENST00000331920	NM_000264.3	210	aTc/aCc	4/24	1	2	FACETS	0.767	0.729	0.806	0.767	0.729	0.806	SUBCLONAL	1	TRUE	1	0.869032528456899	2		273	1107	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249363	110249363	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	795	612	0	ENST00000374672.4:c.1210G>A	p.Gly404Ser	p.G404S	ENST00000374672	NM_004235.4	404	Ggc/Agc	4/5	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.869032528456899	2		612	1778	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572613	64572613	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1060499974	NA	P-0011155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	493	381	1	ENST00000312049.6:c.1243C>T	p.Arg415Ter	p.R415*	ENST00000312049	NM_130799.2	415	Cga/Tga	9/10	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.869032528456899	2		382	1013	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415591	49415591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	470	292	0	ENST00000301067.7:c.16586C>T	p.Ala5529Val	p.A5529V	ENST00000301067	NM_003482.3	5529	gCc/gTc	54/54	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.869032528456899	2		292	1049	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900724	32900724	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793699	NA	P-0011155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	516	389	0	ENST00000380152.3:c.605C>T	p.Pro202Leu	p.P202L	ENST00000380152		202	cCc/cTc	7/27	0.869032528456899	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.869032528456899	1		389	656	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957464	175957465	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0011155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	538	376	0	ENST00000367669.3:c.1931dup	p.Asn644LysfsTer17	p.N644Kfs*17	ENST00000367669	NM_022457.5	644	aac/aaAc	17/20	1	2	FACETS	0.911	0.875	0.948	0.911	0.875	0.948	CLONAL	1	TRUE	1	0.869032528456899	2		376	1359	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233089	69233090	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs746910913	NA	P-0011155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	388	270	0	ENST00000462284.1:c.961dup	p.Leu321ProfsTer13	p.L321Pfs*13	ENST00000462284	NM_002392.5	318	-/C	11/11	1	2	FACETS	0.895	0.853	0.937	0.895	0.853	0.937	CLONAL	1	TRUE	1	0.869032528456899	2		270	998	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821360	72821360	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	424	451	0	ENST00000268489.5:c.10815del	p.Ser3606ProfsTer88	p.S3606Pfs*88	ENST00000268489	NM_006885.3	3605	ccC/cc	10/10	NA	2	FACETS	0.771	0.735	0.807			1	INDETERMINATE	1	TRUE	NA	0.869032528456899	2		451	1266	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348560	89348561	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0011155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1625	632	795	1	ENST00000301030.4:c.4389_4390del	p.Lys1464ThrfsTer89	p.K1464Tfs*89	ENST00000301030	NM_001256183.1	1463	gaGAaa/gaaa	9/13	1	2	FACETS	0.644	0.619	0.671	0.644	0.619	0.671	SUBCLONAL	1	TRUE	1	0.869032528456899	2		796	2257	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878083	48878120	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCCGCCGCTGCCGCCGCGGAACCCCCGGCACCGCCG	CCGCCGCCGCTGCCGCCGCGGAACCCCCGGCACCGCCG	-	novel	NA	P-0011156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	25	151	0	ENST00000267163.4:c.43_80del	p.Ala15ProfsTer3	p.A15Pfs*3	ENST00000267163	NM_000321.2	12	aCCGCCGCCGCTGCCGCCGCGGAACCCCCGGCACCGCCG/a	1/27	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		151	329	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725044	162725044	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1630	331	452	0	ENST00000367921.3:c.516C>G	p.His172Gln	p.H172Q	ENST00000367921	NM_006182.2	172	caC/caG	6/18	0.574946697251404	5	FACETS	1	0.974	1	0.265	0.249	0.282	CLONAL	1	TRUE	1	0.608912390392675	5		452	1961	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729865	41729865	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770655825	NA	P-0011367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1352	433	663	0	ENST00000242208.4:c.664C>T	p.Pro222Ser	p.P222S	ENST00000242208	NM_002192.2	222	Cct/Tct	3/3	0.542682412632173	3	FACETS	1	0.975	1	0.52	0.494	0.546	CLONAL	1	TRUE	1	0.608912390392675	3		663	1785	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0011414-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	170	440	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.736614859092051	1	FACETS	0.848	0.793	0.902	0.848	0.793	0.902	CLONAL	1	TRUE	0	0.736614859092051	1		440	344	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639094	176639094	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011414-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	108	274	0	ENST00000439151.2:c.3694C>A	p.Pro1232Thr	p.P1232T	ENST00000439151	NM_022455.4	1232	Cca/Aca	5/23	0.723570274946604	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.736614859092051	1		274	177	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428261	49428261	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0011414-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	236	523	0	ENST00000301067.7:c.10441-2A>T		p.X3481_splice	ENST00000301067	NM_003482.3	3481			0.255463096429019	3	FACETS	1	0.989	1	0.627	0.588	0.667	INDETERMINATE	1	TRUE	1	0.736614859092051	3		523	699	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519140	103519140	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs761058720	NA	P-0011414-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	12	333	0	ENST00000355739.4:c.2478T>A	p.Phe826Leu	p.F826L	ENST00000355739	NM_000123.3	826	ttT/ttA	11/15	0.731312266526149	2	FACETS	0.171	0.12	0.234	0.086	0.06	0.117	SUBCLONAL	1	TRUE	0	0.736614859092051	2		333	190	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022478	31022478	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs776979634	NA	P-0011414-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	56	228	0	ENST00000375687.4:c.1963A>G	p.Thr655Ala	p.T655A	ENST00000375687	NM_015338.5	655	Acc/Gcc	13/13	0.368668134578455	3	FACETS	0.691	0.596	0.793	0.23	0.198	0.265	INDETERMINATE	1	TRUE	0	0.736614859092051	3		228	301	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439877	49439878	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0011414-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	329	528	0	ENST00000301067.7:c.4663_4664del	p.Ser1555LeufsTer47	p.S1555Lfs*47	ENST00000301067	NM_003482.3	1555	TCc/c	17/54	0.255463096429019	3	FACETS	1	0.993	1	0.656	0.622	0.691	INDETERMINATE	1	TRUE	1	0.736614859092051	3		528	931	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610065	81610090	+	protein_altering_variant	In_Frame_Del	DEL	CTTCCTTTGGTGGGAATAAGTAGCTA	CTTCCTTTGGTGGGAATAAGTAGCTA	TCAGTATC	novel	NA	P-0011414-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	171	460	0	ENST00000298171.2:c.1663_1688delinsTCAGTATC	p.Leu555_Tyr563delinsSerValSer	p.L555_Y563delinsSVS	ENST00000298171	NM_000369.2	555	CTTCCTTTGGTGGGAATAAGTAGCTAt/TCAGTATCt	10/10	1	2	FACETS	0.663	0.612	0.717	0.663	0.612	0.717	SUBCLONAL	1	TRUE	1	0.736614859092051	2		460	700	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482852	140482852	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1562957703	NA	P-0011465-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	83	546	0	ENST00000288602.6:c.1283C>T	p.Ser428Leu	p.S428L	ENST00000288602	NM_004333.4	428	tCa/tTa	10/18	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.22	2		546	651	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0012041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	286	419	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.610640864987477	1	FACETS	0.964	0.913	1	0.964	0.913	1	CLONAL	1	TRUE	0	0.610640864987477	1		419	675	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0012041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	545	442	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.610640864987477	3	FACETS	0.891	0.857	0.926	0.891	0.857	0.926	CLONAL	2	TRUE	1	0.610640864987477	3		442	1307	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0012041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	256	383	1	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	1	2	FACETS	0.966	0.907	1	0.966	0.907	1	CLONAL	1	TRUE	1	0.610640864987477	2		384	868	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955432	48955432	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	325	262	0	ENST00000267163.4:c.1548G>A	p.Trp516Ter	p.W516*	ENST00000267163	NM_000321.2	516	tgG/tgA	17/27	NA	2	FACETS	0.947	0.906	0.987			1	INDETERMINATE	2	TRUE	NA	0.610640864987477	2		262	562	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175996758	175996758	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	371	615	0	ENST00000367669.3:c.1679G>T	p.Cys560Phe	p.C560F	ENST00000367669	NM_022457.5	560	tGt/tTt	15/20	1	2	FACETS	0.931	0.883	0.98	0.931	0.883	0.98	CLONAL	1	TRUE	1	0.610640864987477	2		615	1305	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155201	108155201	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs200196781	NA	P-0012041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	234	386	1	ENST00000278616.4:c.3993+1G>A		p.X1331_splice	ENST00000278616	NM_000051.3	1331			1	2	FACETS	0.984	0.921	1	0.984	0.921	1	CLONAL	1	TRUE	1	0.610640864987477	2		387	779	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435452	56435452	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	288	416	0	ENST00000407977.2:c.1685del	p.Phe562SerfsTer138	p.F562Sfs*138	ENST00000407977		562	tTc/tc	9/10	0.610640864987477	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.610640864987477	1		416	624	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97873805	97873807	+	inframe_deletion	In_Frame_Del	DEL	CAG	CAG	-	novel	NA	P-0012041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	292	517	0	ENST00000289081.3:c.1267_1269del	p.Leu423del	p.L423del	ENST00000289081	NM_000136.2	423	CTG/-	13/15	1	2	FACETS	0.949	0.894	1	0.949	0.894	1	CLONAL	1	TRUE	1	0.610640864987477	2		517	1008	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	53	406	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.395453022898057	3	FACETS	1	0.94	1	0.602	0.513	0.699	CLONAL	1	TRUE	1	0.18	3		406	533	SUCCESS
EED	8726	MSKCC	GRCh37	11	85967502	85967502	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	18	444	0	ENST00000263360.6:c.500G>T	p.Gly167Val	p.G167V	ENST00000263360	NM_003797.3	167	gGa/gTa	5/12	1	2	FACETS	0.619	0.466	0.801	0.619	0.466	0.801	SUBCLONAL	1	TRUE	1	0.18	2		444	323	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591881	48591882	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	72	709	0	ENST00000342988.3:c.1045dup	p.Thr349AsnfsTer3	p.T349Nfs*3	ENST00000342988	NM_005359.5	348	-/A	9/12	1	2	FACETS	0.797	0.698	0.903	1	0.977	1	CLONAL	2	TRUE	1	0.18	2		709	502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0012272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	227	422	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.888606418504831	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.888606418504831	1		422	278	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398286	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0012272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	320	442	1	ENST00000311936.3:c.33_34delinsCT	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	11	gcTGgt/gcCTgt	2/5	0.859021515489199	3	FACETS	0.848	0.809	0.888	0.848	0.809	0.888	CLONAL	2	TRUE	1	0.888606418504831	3		443	613	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566738	212566738	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	189	531	0	ENST00000342788.4:c.1443C>G	p.Ile481Met	p.I481M	ENST00000342788	NM_005235.2	481	atC/atG	12/28	0.888606418504831	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.888606418504831	1		531	233	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446794	49446794	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	227	477	0	ENST00000301067.7:c.1016G>A	p.Trp339Ter	p.W339*	ENST00000301067	NM_003482.3	339	tGg/tAg	8/54	0.888606418504831	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.888606418504831	1		477	283	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110574	4110574	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267607230	NA	P-0012272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	228	474	1	ENST00000262948.5:c.383C>T	p.Pro128Leu	p.P128L	ENST00000262948	NM_030662.3	128	cCg/cTg	3/11	0.888606418504831	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.888606418504831	1		475	284	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231848	36231848	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	179	371	0	ENST00000300305.3:c.536T>A	p.Val179Asp	p.V179D	ENST00000300305		179	gTc/gAc	5/8	0.888606418504831	1	FACETS	0.941	0.898	0.981	0.941	0.898	0.981	CLONAL	1	TRUE	0	0.888606418504831	1		371	238	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729890	30729891	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	124	198	0	ENST00000295754.5:c.1412dup	p.Pro472AlafsTer44	p.P472Afs*44	ENST00000295754	NM_003242.5	471	gag/gAag	6/7	0.888606418504831	1	FACETS	0.918	0.866	0.967	0.918	0.866	0.967	CLONAL	1	TRUE	0	0.888606418504831	1		198	169	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0012339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	95	545	2	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	0.16	2		547	1137	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862107	68862107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501244	NA	P-0012339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	86	595	0	ENST00000261769.5:c.2195G>A	p.Arg732Gln	p.R732Q	ENST00000261769	NM_004360.3	732	cGg/cAg	14/16	1	2	FACETS	0.963	0.85	1	0.963	0.85	1	CLONAL	1	TRUE	1	0.16	2		595	1116	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847399	68847399	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs886039685	NA	P-0012339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	51	474	0	ENST00000261769.5:c.1320+1G>C		p.X440_splice	ENST00000261769	NM_004360.3	440			1	2	FACETS	0.781	0.662	0.913	0.781	0.662	0.913	CLONAL	1	TRUE	1	0.16	2		474	816	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012501-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	32	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.767	0.622	0.931	0.767	0.622	0.931	CLONAL	1	TRUE	1	0.19	2		306	439	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668668	52668668	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012501-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	35	497	0	ENST00000394830.3:c.1251C>A	p.Tyr417Ter	p.Y417*	ENST00000394830	NM_018313.4	417	taC/taA	12/30	0.20141621939694	1	FACETS	0.792	0.649	0.952	0.792	0.649	0.952	CLONAL	1	TRUE	0	0.19	1		497	421	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914382	32914382	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1555284445	NA	P-0012501-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	67	917	3	ENST00000380152.3:c.5890A>T	p.Lys1964Ter	p.K1964*	ENST00000380152		1964	Aag/Tag	11/27	1	2	FACETS	0.922	0.8	1	0.922	0.8	1	CLONAL	1	TRUE	1	0.19	2		920	765	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183756	10183756	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012501-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	40	358	0	ENST00000256474.2:c.225del	p.Phe76SerfsTer83	p.F76Sfs*83	ENST00000256474	NM_000551.3	75	atC/at	1/3	1	2	FACETS	0.995	0.828	1	0.995	0.828	1	CLONAL	1	TRUE	1	0.19	2		358	423	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	103	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.806	0.722	0.894	0.806	0.722	0.894	CLONAL	1	TRUE	1	0.400838102159548	2		306	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0012941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	219	539	0	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	0.400838102159548	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.400838102159548	1		539	728	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894916	101894916	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060502040	NA	P-0012941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	339	722	0	ENST00000374994.4:c.469C>T	p.Arg157Ter	p.R157*	ENST00000374994	NM_004612.2	157	Cga/Tga	3/9	0.400838102159548	2	FACETS	1	0.994	1	0.721	0.682	0.761	CLONAL	1	TRUE	0	0.400838102159548	2		722	1173	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622209	117622209	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	215	686	0	ENST00000368508.3:c.6661T>G	p.Phe2221Val	p.F2221V	ENST00000368508	NM_002944.2	2221	Ttt/Gtt	42/43	1	2	FACETS	0.884	0.821	0.951	0.884	0.821	0.951	CLONAL	1	TRUE	1	0.400838102159548	2		686	1213	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731614	47731614	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	157	213	0	ENST00000449228.1:c.178C>T	p.Pro60Ser	p.P60S	ENST00000449228	NM_001127240.2	60	Ccc/Tcc	2/4	1	2	FACETS	0.848	0.783	0.914	1	0.991	1	CLONAL	2	TRUE	1	0.400838102159548	2		213	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578259	7578259	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1567551903	NA	P-0013148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	899	486	0	ENST00000269305.4:c.590T>A	p.Val197Glu	p.V197E	ENST00000269305	NM_001126112.2	197	gTg/gAg	6/11	0.888029698660122	2	FACETS	0.979	0.966	0.992	0.979	0.966	0.992	CLONAL	2	TRUE	0	0.908065939748301	2		486	1011	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606146	47606146	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	273	562	0	ENST00000263735.4:c.610C>G	p.Gln204Glu	p.Q204E	ENST00000263735	NM_002354.2	204	Cag/Gag	6/9	1	2	FACETS	0.964	0.912	1	0.964	0.912	1	CLONAL	1	TRUE	1	0.908065939748301	2		562	624	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968203	134968203	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	194	632	0	ENST00000398015.3:c.2716T>A	p.Ser906Thr	p.S906T	ENST00000398015	NM_004441.4	906	Tcc/Acc	15/16	0.886491733310038	2	FACETS	0.5	0.463	0.539	0.25	0.231	0.27	SUBCLONAL	1	TRUE	0	0.908065939748301	2		632	854	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789692	3789692	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	372	620	0	ENST00000262367.5:c.4167C>A	p.Phe1389Leu	p.F1389L	ENST00000262367	NM_004380.2	1389	ttC/ttA	25/31	0.831339074263791	3	FACETS	0.972	0.922	1	0.486	0.461	0.511	CLONAL	1	TRUE	1	0.908065939748301	3		620	1226	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056256	26056257	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0013148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	154	575	0	ENST00000343677.2:c.400dup	p.Ala134GlyfsTer19	p.A134Gfs*19	ENST00000343677	NM_005319.3	134	gca/gGca	1/1	0.223947261377662	4	FACETS	0.648	0.593	0.707			1	INDETERMINATE	1	TRUE	NA	0.908065939748301	4		575	998	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106904	27106904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	348	507	3	ENST00000324856.7:c.6515C>T	p.Ala2172Val	p.A2172V	ENST00000324856	NM_006015.4	2172	gCc/gTc	20/20	0.398319042932296	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	2	0.600862713579802	4		510	773	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139873	55139873	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs866988382	NA	P-0013358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	237	426	0	ENST00000257290.5:c.1534C>T	p.Arg512Ter	p.R512*	ENST00000257290	NM_006206.4	512	Cga/Tga	10/23	0.600862713579802	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.600862713579802	4		426	609	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106904	27106904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013358-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	324	507	3	ENST00000324856.7:c.6515C>T	p.Ala2172Val	p.A2172V	ENST00000324856	NM_006015.4	2172	gCc/gTc	20/20	0.369760399452289	5	FACETS	1	0.981	1	1	0.981	1	INDETERMINATE	3	TRUE	2	0.639886934106059	5		510	629	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139873	55139873	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs866988382	NA	P-0013358-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	246	426	0	ENST00000257290.5:c.1534C>T	p.Arg512Ter	p.R512*	ENST00000257290	NM_006206.4	512	Cga/Tga	10/23	0.639886934106059	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.639886934106059	4		426	581	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752425	55752425	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756674568	NA	P-0013358-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	582	1362	1	ENST00000284073.2:c.883G>A	p.Val295Met	p.V295M	ENST00000284073	NM_138962.2	295	Gtg/Atg	12/14	0.639886934106059	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	2	0.639886934106059	4		1363	1395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0013359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	545	578	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	1	2	FACETS	0.995	0.961	1	1	0.998	1	CLONAL	2	TRUE	1	0.553238584401486	2		578	990	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220133	98220362	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTAACCATGGACCTCACCACCTCGAGTAGAATAAACATATTACGGATGATGCAAGCTATACCCTCCTCCAGAGGCCCAGACATAAACAAAACTTCCCGGCTGCAGAAAGAGCTATGCTGAAAGGAATTTGACTTCCACAAAGCCCCTTATAATACACTCACAATGATCCCGGCCGTCCAGGGGTTCAGAAGGAAGACAGCGCACACGAGGAATGTGCAGGCCAACACCA	CTTAACCATGGACCTCACCACCTCGAGTAGAATAAACATATTACGGATGATGCAAGCTATACCCTCCTCCAGAGGCCCAGACATAAACAAAACTTCCCGGCTGCAGAAAGAGCTATGCTGAAAGGAATTTGACTTCCACAAAGCCCCTTATAATACACTCACAATGATCCCGGCCGTCCAGGGGTTCAGAAGGAAGACAGCGCACACGAGGAATGTGCAGGCCAACACCA	-	novel	NA	P-0013359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	102	17	0	ENST00000331920.6:c.3101_3168+162del		p.X1034_splice	ENST00000331920	NM_000264.3	1034		18/24	0.553238584401486	1	FACETS	1	0.986	1	1	0.992	1	CLONAL	2	TRUE	0	0.553238584401486	1		17	118	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0013531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	205	521	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.189443692718481	3	FACETS	0.897	0.833	0.963	0.598	0.555	0.642	CLONAL	2	FALSE	0	0.3	3		521	876	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	73	499	0	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.3	1	FACETS	0.612	0.535	0.695	0.612	0.535	0.695	SUBCLONAL	1	FALSE	0	0.3	1		499	676	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041244	47041244	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	205	415	0	ENST00000377604.3:c.1672C>T	p.Gln558Ter	p.Q558*	ENST00000377604	NM_001204468.1	558	Cag/Tag	15/24	0.290480549959985	2	FACETS	1	0.981	1			1	CLONAL	2	FALSE	NA	0.3	2		415	601	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0013613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	115	205	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	0.28295298515116	2		205	742	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167801	56167802	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	126	453	0	ENST00000399503.3:c.1368dup	p.Thr457TyrfsTer4	p.T457Yfs*4	ENST00000399503	NM_005921.1	456	ctt/cTtt	7/20	1	2	FACETS	0.939	0.85	1	0.939	0.85	1	CLONAL	1	TRUE	1	0.28295298515116	2		453	948	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650719	67650719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1131691283	NA	P-0013613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	310	688	2	ENST00000264010.4:c.1024C>T	p.Arg342Cys	p.R342C	ENST00000264010	NM_006565.3	342	Cgt/Tgt	5/12	0.279709078981545	2	FACETS	0.956	0.902	1	0.956	0.902	1	CLONAL	2	TRUE	0	0.28295298515116	2		690	1146	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206757	36206803	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGCACGAGGGTTGGGCGTGGGGGCTGGGTGGTGTGGGCTGACCCT	GAGGCACGAGGGTTGGGCGTGGGGGCTGGGTGGTGTGGGCTGACCCT	-	novel	NA	P-0013613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	207	363	0	ENST00000300305.3:c.709_755del	p.Arg237ProfsTer8	p.R237Pfs*8	ENST00000300305		237	AGGGTCAGCCCACACCACCCAGCCCCCACGCCCAACCCTCGTGCCTCc/c	6/8	0.176857951910969	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.28295298515116	3		363	717	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161654	56161654	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0013613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	101	399	0	ENST00000399503.3:c.1153-2A>C		p.X385_splice	ENST00000399503	NM_005921.1	385			1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.28295298515116	2		399	694	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0013613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	37	579	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.21	0.172	0.253	0.21	0.172	0.253	SUBCLONAL	1	TRUE	1	0.378436254169935	2		579	932	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177068	56177068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	101	343	0	ENST00000399503.3:c.2338G>A	p.Asp780Asn	p.D780N	ENST00000399503	NM_005921.1	780	Gat/Aat	13/20	0.137274445460356	4	FACETS	0.89	0.795	0.991	0.445	0.397	0.496	INDETERMINATE	1	TRUE	2	0.378436254169935	4		343	827	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178683	56178684	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTACA	novel	NA	P-0013613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	88	221	0	ENST00000399503.3:c.3657_3658insTACAT	p.Gln1220TyrfsTer27	p.Q1220Yfs*27	ENST00000399503	NM_005921.1	1219	att/atTTACAt	14/20	0.137274445460356	4	FACETS	1	0.928	1	0.531	0.471	0.595	INDETERMINATE	1	TRUE	2	0.378436254169935	4		221	604	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120026	70120026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1258787580	NA	P-0013636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	10	17	0	ENST00000245479.2:c.1028C>T	p.Pro343Leu	p.P343L	ENST00000245479	NM_000346.3	343	cCg/cTg	3/3	1	2	FACETS	0.455	0.315	0.622	0.455	0.315	0.622	SUBCLONAL	1	TRUE	1	0.770852921885798	2		17	57	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577075	7577076	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCTCTTCC	novel	NA	P-0013636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	294	824	0	ENST00000269305.4:c.855_862dup	p.Asn288ArgfsTer60	p.N288Rfs*60	ENST00000269305	NM_001126112.2	288	aat/aGGAAGAGAat	8/11	0.770852921885798	1	FACETS	0.89	0.848	0.93	0.89	0.848	0.93	CLONAL	1	TRUE	0	0.770852921885798	1		824	527	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797330	42797330	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	103	690	0	ENST00000575354.2:c.3692C>G	p.Ala1231Gly	p.A1231G	ENST00000575354	NM_015125.3	1231	gCc/gGc	15/20	0.770852921885798	3	FACETS	0.421	0.376	0.469	0.211	0.188	0.235	SUBCLONAL	1	TRUE	1	0.770852921885798	3		690	879	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30061036	30061036	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	102	721	0	ENST00000338641.4:c.868C>G	p.Leu290Val	p.L290V	ENST00000338641	NM_000268.3	290	Ctt/Gtt	9/16	NA	2	FACETS	0.459	0.411	0.509			1	INDETERMINATE	1	TRUE	NA	0.770852921885798	2		721	577	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0013915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	345	286	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.536629245991149	6	FACETS	0.902	0.86	0.944	0.902	0.86	0.944	CLONAL	4	TRUE	2	0.536629245991149	6		286	739	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778071	27778071	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	366	1312	1	ENST00000369163.2:c.220G>A	p.Glu74Lys	p.E74K	ENST00000369163	NM_003536.2	74	Gag/Aag	1/1	0.514310407699511	2	FACETS	0.975	0.924	1	0.488	0.462	0.514	CLONAL	1	TRUE	0	0.536629245991149	2		1313	1399	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874803	151874803	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	165	394	0	ENST00000262189.6:c.7735G>C	p.Gly2579Arg	p.G2579R	ENST00000262189	NM_170606.2	2579	Ggc/Cgc	38/59	0.528560670048943	1	FACETS	0.976	0.905	1	0.976	0.905	1	CLONAL	1	TRUE	0	0.536629245991149	1		394	461	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629537	187629538	+	missense_variant	Missense_Mutation	DNP	AC	AC	CT	novel	NA	P-0013915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	185	568	0	ENST00000441802.2:c.1444_1445delinsAG	p.Val482Ser	p.V482S	ENST00000441802	NM_005245.3	482	GTc/AGc	2/27	1	2	FACETS	0.919	0.851	0.99	0.919	0.851	0.99	CLONAL	1	TRUE	1	0.536629245991149	2		568	750	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	188	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.283371859874788	4	FACETS	0.875	0.809	0.944	0.875	0.809	0.944	CLONAL	2	TRUE	2	0.30709694344102	4		436	914	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0014002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	225	563	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.248920290096339	3	FACETS	0.886	0.826	0.948	0.886	0.826	0.948	CLONAL	2	TRUE	1	0.30709694344102	3		563	954	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492611	56492611	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	198	579	1	ENST00000267101.3:c.2761C>T	p.Pro921Ser	p.P921S	ENST00000267101	NM_001982.3	921	Cca/Tca	23/28	0.283371859874788	4	FACETS	0.81	0.75	0.873	0.81	0.75	0.873	CLONAL	2	TRUE	2	0.30709694344102	4		580	1040	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027160	49027160	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	236	693	0	ENST00000267163.4:c.1727C>A	p.Ser576Ter	p.S576*	ENST00000267163	NM_000321.2	576	tCa/tAa	18/27	0.207996506695934	4	FACETS	0.974	0.909	1	0.974	0.909	1	CLONAL	2	TRUE	2	0.30709694344102	4		693	1031	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579316	7579317	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0014002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	164	476	0	ENST00000269305.4:c.369_370dup	p.Cys124PhefsTer47	p.C124Ffs*47	ENST00000269305	NM_001126112.2	124	tgc/tTTgc	4/11	0.248920290096339	3	FACETS	0.868	0.799	0.939	0.868	0.799	0.939	CLONAL	2	TRUE	1	0.30709694344102	3		476	710	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495290	212495290	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	110	486	0	ENST00000342788.4:c.1976G>T	p.Gly659Val	p.G659V	ENST00000342788	NM_005235.2	659	gGt/gTt	17/28	0.248920290096339	3	FACETS	0.943	0.847	1	0.472	0.423	0.523	CLONAL	1	TRUE	1	0.30709694344102	3		486	876	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156894	106156894	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	112	705	1	ENST00000380013.4:c.1795C>A	p.Gln599Lys	p.Q599K	ENST00000380013	NM_001127208.2	599	Caa/Aaa	3/11	0.248920290096339	3	FACETS	0.868	0.78	0.962	0.434	0.39	0.481	CLONAL	1	TRUE	1	0.30709694344102	3		706	969	SUCCESS
APC	324	MSKCC	GRCh37	5	112151197	112151197	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	190	544	0	ENST00000257430.4:c.841del	p.Thr281LeufsTer12	p.T281Lfs*12	ENST00000257430	NM_000038.5	280	tcA/tc	9/16	0.243560724588967	2	FACETS	0.836	0.775	0.899	0.836	0.775	0.899	CLONAL	2	TRUE	0	0.30709694344102	2		544	740	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014070-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	39	406	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.219504358664638	5	FACETS	0.965	0.81	1	0.643	0.54	0.755	CLONAL	2	TRUE	2	0.350394230223501	5		406	176	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0014070-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	25	612	3	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.285776599130962	1	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	0	0.350394230223501	1		615	106	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914939	32914940	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359594	NA	P-0014070-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	39	983	1	ENST00000380152.3:c.6450dup	p.Val2151SerfsTer25	p.V2151Sfs*25	ENST00000380152		2149	-/A	11/27	0.350394230223501	4	FACETS	1	0.922	1	0.835	0.718	0.955	CLONAL	3	TRUE	0	0.350394230223501	4		984	90	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248651	212248651	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014070-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	20	630	0	ENST00000342788.4:c.3616C>A	p.Pro1206Thr	p.P1206T	ENST00000342788	NM_005235.2	1206	Cca/Aca	28/28	0.350394230223501	3	FACETS	1	0.869	1	0.594	0.46	0.744	CLONAL	1	TRUE	1	0.350394230223501	3		630	113	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598172	52598172	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014070-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	28	655	0	ENST00000394830.3:c.3694del	p.Cys1232ValfsTer12	p.C1232Vfs*12	ENST00000394830	NM_018313.4	1232	Tgt/gt	24/30	0.285776599130962	1	FACETS	0.909	0.736	1	0.909	0.736	1	CLONAL	1	TRUE	0	0.350394230223501	1		655	145	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0014076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	1267	1013	2	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.841031449532097	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.841031449532097	2		1015	1482	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923137	48923137	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	307	534	1	ENST00000267163.4:c.585G>A	p.Trp195Ter	p.W195*	ENST00000267163	NM_000321.2	195	tgG/tgA	6/27	0.841031449532097	1	FACETS	0.968	0.932	1	0.968	0.932	1	CLONAL	1	TRUE	0	0.841031449532097	1		535	437	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0014076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	534	821	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	0.963	0.925	1	0.963	0.925	1	CLONAL	1	TRUE	1	0.841031449532097	2		821	1319	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957495	175957495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750125741	NA	P-0014076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1350	79	872	0	ENST00000367669.3:c.1901G>A	p.Arg634His	p.R634H	ENST00000367669	NM_022457.5	634	cGt/cAt	17/20	1	2	FACETS	0.131	0.115	0.15	0.131	0.115	0.15	SUBCLONAL	1	TRUE	1	0.841031449532097	2		872	1429	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633665	69633665	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	19	86	0	ENST00000334134.2:c.37G>C	p.Glu13Gln	p.E13Q	ENST00000334134	NM_005247.2	13	Gag/Cag	1/3	0.247629642479457	1	FACETS	0.254	0.196	0.32	0.254	0.196	0.32	INDETERMINATE	1	TRUE	0	0.841031449532097	1		86	103	SUCCESS
AR	367	MSKCC	GRCh37	X	66937379	66937379	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	104	576	0	ENST00000374690.3:c.2233C>A	p.Leu745Ile	p.L745I	ENST00000374690	NM_000044.3	745	Ctc/Atc	5/8	1	1	FACETS	0.177	0.158	0.197	0.177	0.158	0.197	SUBCLONAL	1	TRUE	0	0.841031449532097	1		576	811	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858738	9858738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149698593	NA	P-0014087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	94	500	0	ENST00000330684.3:c.2663C>T	p.Thr888Met	p.T888M	ENST00000330684	NM_001134407.1	888	aCg/aTg	13/13	1	2	FACETS	0.643	0.571	0.721	0.643	0.571	0.721	SUBCLONAL	1	TRUE	1	0.32	2		500	913	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489481	56489481	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	78	414	0	ENST00000267101.3:c.1946T>G	p.Ile649Arg	p.I649R	ENST00000267101	NM_001982.3	649	aTa/aGa	17/28	1	2	FACETS	0.578	0.507	0.654	0.578	0.507	0.654	SUBCLONAL	1	TRUE	1	0.32	2		414	844	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579718	7579718	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	214	769	2	ENST00000269305.4:c.78del	p.Pro27LeufsTer17	p.P27Lfs*17	ENST00000269305	NM_001126112.2	26	ctT/ct	3/11	0.618442109281734	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.826745130221262	1		771	276	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133193	30133193	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	95	347	1	ENST00000263025.4:c.305G>C	p.Gly102Ala	p.G102A	ENST00000263025	NM_002746.2	102	gGc/gCc	2/9	0.64488443617459	3	FACETS	1	0.951	1			1	CLONAL	1	TRUE	NA	0.826745130221262	3		348	298	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246509	41246509	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs749508254	NA	P-0014299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	205	617	0	ENST00000357654.3:c.1039del	p.Leu347CysfsTer27	p.L347Cfs*27	ENST00000357654	NM_007294.3	347	Ctg/tg	10/23	0.826745130221262	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.826745130221262	1		617	272	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538906	23538906	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	145	418	4	ENST00000380871.4:c.533A>G	p.Lys178Arg	p.K178R	ENST00000380871	NM_006167.3	178	aAg/aGg	2/2	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.826745130221262	2		422	333	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519893	NA	P-0014364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	192	863	2	ENST00000267101.3:c.310G>T	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ttg	3/28	1	2	FACETS	1	0.984	1	1	0.994	1	CLONAL	2	TRUE	1	0.430403028776366	2		865	392	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0014364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	54	617	0	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.430403028776366	2		617	211	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939399	71939399	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	69	689	0	ENST00000298229.2:c.254A>G	p.Gln85Arg	p.Q85R	ENST00000298229	NM_001567.3	85	cAg/cGg	3/28	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.430403028776366	2		689	269	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059202	42059202	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	22	368	0	ENST00000219905.7:c.8922G>C	p.Glu2974Asp	p.E2974D	ENST00000219905	NM_001164273.1	2974	gaG/gaC	24/24	1	2	FACETS	0.741	0.581	0.922	0.741	0.581	0.922	CLONAL	1	TRUE	1	0.430403028776366	2		368	138	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38184259	38184259	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	216	463	0	ENST00000317025.8:c.1697C>G	p.Ser566Cys	p.S566C	ENST00000317025	NM_023034.1	566	tCt/tGt	7/24	0.430403028776366	20	FACETS	1	0.961	1			1	CLONAL	17	TRUE	NA	0.430403028776366	20		463	287	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	31	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.145940884886272	3	FACETS	1	0.939	1	0.701	0.574	0.842	INDETERMINATE	1	TRUE	1	0.31364921515533	3		436	163	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0014383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	30	544	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.31364921515533	1	FACETS	0.858	0.698	1	0.858	0.698	1	CLONAL	1	TRUE	0	0.31364921515533	1		544	188	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581211	48581211	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0014383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	29	436	0	ENST00000342988.3:c.515T>A	p.Leu172Ter	p.L172*	ENST00000342988	NM_005359.5	172	tTg/tAg	5/12	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.31364921515533	2		436	153	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239426	105239426	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	21	486	0	ENST00000349310.3:c.961C>A	p.Leu321Met	p.L321M	ENST00000349310	NM_001014432.1	321	Ctg/Atg	12/15	0.145940884886272	3	FACETS	0.846	0.656	1	0.423	0.328	0.533	INDETERMINATE	1	TRUE	1	0.31364921515533	3		486	183	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821254	72821254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs907469490	NA	P-0014383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	12	513	1	ENST00000268489.5:c.10921G>A	p.Val3641Ile	p.V3641I	ENST00000268489	NM_006885.3	3641	Gtt/Att	10/10	1	2	FACETS	0.535	0.378	0.727	0.535	0.378	0.727	SUBCLONAL	1	TRUE	1	0.31364921515533	2		514	143	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441368	149441368	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	11	623	0	ENST00000286301.3:c.1671G>T	p.Glu557Asp	p.E557D	ENST00000286301	NM_005211.3	557	gaG/gaT	12/22	1	2	FACETS	0.394	0.272	0.545	0.394	0.272	0.545	SUBCLONAL	1	TRUE	1	0.31364921515533	2		623	178	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045884	26045884	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	14	327	0	ENST00000540144.1:c.246C>A	p.Asp82Glu	p.D82E	ENST00000540144	NM_003531.2	82	gaC/gaA	1/1	0.159572008266474	2	FACETS	0.611	0.444	0.811	0.306	0.222	0.406	INDETERMINATE	1	TRUE	0	0.31364921515533	2		327	146	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971153	21971174	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCGCCGTGGAGCAGCAGCAG	CCGCGCCGTGGAGCAGCAGCAG	-	novel	NA	P-0014383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	18	302	0	ENST00000304494.5:c.184_205del	p.Leu62SerfsTer77	p.L62Sfs*77	ENST00000304494	NM_000077.4	62	CTGCTGCTGCTCCACGGCGCGGag/ag	2/3	0.239408109450796	1	FACETS	0.949	0.726	1	0.949	0.726	1	CLONAL	1	TRUE	0	0.31364921515533	1		302	102	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	34	306	0				ENST00000310581	NM_198253.2	-/1132			0.321221828067735	1	FACETS	0.576	0.476	0.684	0.576	0.476	0.684	SUBCLONAL	1	TRUE	0	0.520247065825864	1		306	168	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0014421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	219	579	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.516349824554017	3	FACETS	0.939	0.88	0.998	0.939	0.88	0.998	CLONAL	2	TRUE	1	0.520247065825864	3		579	565	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058033	27058033	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	254	496	0	ENST00000324856.7:c.1741C>T	p.Gln581Ter	p.Q581*	ENST00000324856	NM_006015.4	581	Cag/Tag	3/20	0.147393177253793	3	FACETS	0.835	0.792	0.879	0.835	0.792	0.879	INDETERMINATE	3	TRUE	0	0.520247065825864	3		496	491	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922171	100922171	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	80	458	1	ENST00000325455.5:c.2341G>A	p.Asp781Asn	p.D781N	ENST00000325455	NM_001202474.3	781	Gat/Aat	5/8	0.476544717761033	3	FACETS	0.883	0.78	0.992	0.294	0.26	0.331	CLONAL	1	TRUE	0	0.520247065825864	3		459	439	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022871	31022878	+	frameshift_variant	Frame_Shift_Del	DEL	AGAACTGA	AGAACTGA	-	novel	NA	P-0014421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	67	513	0	ENST00000375687.4:c.2357_2364del	p.Arg786MetfsTer2	p.R786Mfs*2	ENST00000375687	NM_015338.5	786	AGAACTGAa/a	13/13	0.150829728154004	2	FACETS	0.63	0.549	0.716	0.315	0.274	0.358	INDETERMINATE	1	TRUE	0	0.520247065825864	2		513	409	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141582928	141582928	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	237	610	0	ENST00000220592.5:c.319C>G	p.Pro107Ala	p.P107A	ENST00000220592	NM_012154.3	107	Ccg/Gcg	3/19	0.306719317325926	4	FACETS	0.884	0.828	0.942			1	INDETERMINATE	2	TRUE	NA	0.520247065825864	4		610	783	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226860	2226860	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	11	169	1	ENST00000398665.3:c.4340C>T	p.Ala1447Val	p.A1447V	ENST00000398665	NM_032482.2	1447	gCg/gTg	27/28	1	2	FACETS	0.822	0.568	1	0.822	0.568	1	CLONAL	1	TRUE	1	0.13	2		170	206	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922966	44922966	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0014507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	209	586	0	ENST00000377967.4:c.1827C>G	p.Tyr609Ter	p.Y609*	ENST00000377967	NM_021140.2	609	taC/taG	16/29	0.202596280446663	0	FACETS	1	0.984	1			1	CLONAL	1	TRUE	0	0.250800595309941	0		586	1036	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339981	70339981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	264	550	0	ENST00000374080.3:c.514G>A	p.Glu172Lys	p.E172K	ENST00000374080		172	Gag/Aag	4/45	0.240092574359656	1	FACETS	0.954	0.895	1	1	0.995	1	CLONAL	2	TRUE	0	0.250800595309941	1		550	965	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101213	27101213	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	84	527	0	ENST00000324856.7:c.4495C>T	p.Gln1499Ter	p.Q1499*	ENST00000324856	NM_006015.4	1499	Cag/Tag	18/20	0.250800595309941	2	FACETS	0.656	0.578	0.74	0.328	0.289	0.37	SUBCLONAL	1	TRUE	0	0.250800595309941	2		527	1021	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40367055	40367055	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1425	166	785	0	ENST00000397332.2:c.142G>T	p.Asp48Tyr	p.D48Y	ENST00000397332	NM_001033082.2	48	Gat/Tat	2/3	0.250800595309941	2	FACETS	0.832	0.761	0.906	0.416	0.38	0.453	CLONAL	1	TRUE	0	0.250800595309941	2		785	1591	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828074	72828074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766287350	NA	P-0014507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	409	678	2	ENST00000268489.5:c.8507C>T	p.Ser2836Phe	p.S2836F	ENST00000268489	NM_006885.3	2836	tCc/tTc	9/10	0.231828077022125	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.250800595309941	2		680	1343	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572947	7572947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	117	458	0	ENST00000269305.4:c.1162G>A	p.Glu388Lys	p.E388K	ENST00000269305	NM_001126112.2	388	Gaa/Aaa	11/11	1	2	FACETS	0.937	0.843	1	0.937	0.843	1	CLONAL	1	TRUE	1	0.250800595309941	2		458	996	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259307	36259307	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	98	431	1	ENST00000300305.3:c.184G>A	p.Asp62Asn	p.D62N	ENST00000300305		62	Gac/Aac	3/8	0.250800595309941	3	FACETS	0.99	0.882	1	0.495	0.441	0.553	CLONAL	1	TRUE	1	0.250800595309941	3		432	888	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637835	176637842	+	frameshift_variant	Frame_Shift_Del	DEL	TGAAATGC	TGAAATGC	-	novel	NA	P-0014507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	74	565	0	ENST00000439151.2:c.2437_2444del	p.Lys813LeufsTer3	p.K813Lfs*3	ENST00000439151	NM_022455.4	812	tTGAAATGC/t	5/23	0.203875445323174	2	FACETS	0.494	0.431	0.562	0.247	0.215	0.281	SUBCLONAL	1	TRUE	0	0.250800595309941	2		565	1195	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938567	44938567	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	92	500	0	ENST00000377967.4:c.3115C>T	p.Gln1039Ter	p.Q1039*	ENST00000377967	NM_021140.2	1039	Cag/Tag	20/29	0.202596280446663	0	FACETS	0.679	0.602	0.76			1	SUBCLONAL	1	TRUE	0	0.250800595309941	0		500	810	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	96	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.852	0.758	0.952	0.852	0.758	0.952	CLONAL	1	TRUE	1	0.27	2		436	835	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964199	28964199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745653714	NA	P-0014512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	70	286	0	ENST00000282397.4:c.1703C>T	p.Thr568Met	p.T568M	ENST00000282397	NM_002019.4	568	aCg/aTg	13/30	1	2	FACETS	0.986	0.861	1	0.986	0.861	1	CLONAL	1	TRUE	1	0.27	2		286	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578386	7578387	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCGCT	novel	NA	P-0014512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	88	421	0	ENST00000269305.4:c.539_543dup	p.Cys182SerfsTer67	p.C182Sfs*67	ENST00000269305	NM_001126112.2	181	-/AGCGC	5/11	0.3	1	FACETS	0.832	0.737	0.933	0.832	0.737	0.933	CLONAL	1	TRUE	0	0.27	1		421	678	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984290	7984290	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	104	518	1	ENST00000319144.4:c.439C>T	p.Arg147Ter	p.R147*	ENST00000319144	NM_001139.2	147	Cga/Tga	4/15	0.3	1	FACETS	0.868	0.777	0.964	0.868	0.777	0.964	CLONAL	1	TRUE	0	0.27	1		519	768	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692849	89692849	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554898097	NA	P-0014579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	68	192	2	ENST00000371953.3:c.333G>A	p.Trp111Ter	p.W111*	ENST00000371953	NM_000314.4	111	tgG/tgA	5/9	1	2	FACETS	0.86	0.76	0.964	0.86	0.76	0.964	CLONAL	1	TRUE	1	0.732102510773906	2		194	216	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382152	152382154	+	inframe_deletion	In_Frame_Del	DEL	TGG	TGG	-	novel	NA	P-0014579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	123	291	0	ENST00000206249.3:c.1265_1267del	p.Val422del	p.V422del	ENST00000206249	NM_000125.3	421	aTGGtg/atg	6/8	1	2	FACETS	0.691	0.629	0.757	0.691	0.629	0.757	SUBCLONAL	1	TRUE	1	0.732102510773906	2		291	486	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	223	529	1	ENST00000206249.3:c.1609T>C	p.Tyr537His	p.Y537H	ENST00000206249	NM_000125.3	537	Tat/Cat	8/8	1	2	FACETS	0.816	0.762	0.871	0.816	0.762	0.871	CLONAL	1	TRUE	1	0.732102510773906	2		530	747	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056181	27056181	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	207	535	0	ENST00000324856.7:c.1177C>T	p.Gln393Ter	p.Q393*	ENST00000324856	NM_006015.4	393	Cag/Tag	2/20	1	2	FACETS	0.888	0.828	0.949	0.888	0.828	0.949	CLONAL	1	TRUE	1	0.732102510773906	2		535	637	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107089	27107099	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGCCCGCGC	GCTGCCCGCGC	-	novel	NA	P-0014579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	214	364	0	ENST00000324856.7:c.6705_6715del	p.Arg2236CysfsTer38	p.R2236Cfs*38	ENST00000324856	NM_006015.4	2234	GCTGCCCGCGCg/g	20/20	1	2	FACETS	0.898	0.839	0.958	0.898	0.839	0.958	CLONAL	1	TRUE	1	0.732102510773906	2		364	651	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692864	89692865	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0014579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	72	217	0	ENST00000371953.3:c.350dup	p.Asn117LysfsTer9	p.N117Kfs*9	ENST00000371953	NM_000314.4	116	-/A	5/9	1	2	FACETS	0.787	0.696	0.881	0.787	0.696	0.881	SUBCLONAL	1	TRUE	1	0.732102510773906	2		217	250	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274777	123274777	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs387906678	NA	P-0014579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	210	554	0	ENST00000358487.5:c.1141T>G	p.Tyr381Asp	p.Y381D	ENST00000358487	NM_000141.4	381	Tac/Gac	9/18	1	2	FACETS	0.778	0.725	0.833	0.778	0.725	0.833	SUBCLONAL	1	TRUE	1	0.732102510773906	2		554	737	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274785	123274785	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	200	523	0	ENST00000358487.5:c.1133T>G	p.Ile378Arg	p.I378R	ENST00000358487	NM_000141.4	378	aTa/aGa	9/18	1	2	FACETS	0.778	0.724	0.834	0.778	0.724	0.834	SUBCLONAL	1	TRUE	1	0.732102510773906	2		523	702	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589146	67589147	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0014579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	67	190	0	ENST00000274335.5:c.1137dup	p.Leu380IlefsTer15	p.L380Ifs*15	ENST00000274335		378	-/A	9/15	1	2	FACETS	0.772	0.68	0.869	0.772	0.68	0.869	SUBCLONAL	1	TRUE	1	0.732102510773906	2		190	237	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589663	67589663	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587777709	NA	P-0014579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	59	173	0	ENST00000274335.5:c.1425+1G>T		p.X475_splice	ENST00000274335		475			1	2	FACETS	0.597	0.518	0.681	0.597	0.518	0.681	SUBCLONAL	1	TRUE	1	0.732102510773906	2		173	270	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209457	98209457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753535745	NA	P-0014579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	243	550	1	ENST00000331920.6:c.4081G>A	p.Val1361Met	p.V1361M	ENST00000331920	NM_000264.3	1361	Gtg/Atg	23/24	1	2	FACETS	0.831	0.779	0.884	0.831	0.779	0.884	CLONAL	1	TRUE	1	0.732102510773906	2		551	799	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023769	27023769	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	160	682	0	ENST00000324856.7:c.875C>G	p.Thr292Ser	p.T292S	ENST00000324856	NM_006015.4	292	aCc/aGc	1/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.31385109828467	2		682	817	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183759	10183759	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	128	893	0	ENST00000256474.2:c.228del	p.Cys77AlafsTer82	p.C77Afs*82	ENST00000256474	NM_000551.3	76	ttC/tt	1/3	0.31385109828467	1	FACETS	0.978	0.888	1	0.978	0.888	1	CLONAL	1	TRUE	0	0.31385109828467	1		893	703	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696280	52696280	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	96	499	0	ENST00000394830.3:c.397G>T	p.Glu133Ter	p.E133*	ENST00000394830	NM_018313.4	133	Gaa/Taa	5/30	0.31385109828467	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.31385109828467	1		499	486	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825519	50825519	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	35	550	1	ENST00000398568.2:c.2156del	p.Asn719MetfsTer13	p.N719Mfs*13	ENST00000398568	NM_001042412.1	717	gAa/ga	14/18	1	2	FACETS	0.156	0.127	0.189	0.156	0.127	0.189	SUBCLONAL	1	TRUE	1	0.797527959721087	2		551	562	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845090	128845090	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs760210773	NA	P-0014756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1278	314	855	5	ENST00000249373.3:c.584T>C	p.Val195Ala	p.V195A	ENST00000249373	NM_005631.4	195	gTg/gCg	3/12	0.797527959721087	4	FACETS	0.889	0.836	0.943	0.296	0.278	0.315	CLONAL	1	TRUE	1	0.797527959721087	4		860	1592	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167562	24167562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769023941	NA	P-0014756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	275	572	8	ENST00000263121.7:c.946C>T	p.Arg316Trp	p.R316W	ENST00000263121	NM_003073.3	316	Cgg/Tgg	7/9	1	2	FACETS	0.933	0.881	0.987	0.933	0.881	0.987	CLONAL	1	TRUE	1	0.797527959721087	2		580	739	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604493	43604493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	269	574	0	ENST00000355710.3:c.1078C>T	p.Arg360Trp	p.R360W	ENST00000355710	NM_020975.4	360	Cgg/Tgg	6/20	1	2	FACETS	0.942	0.889	0.996	0.942	0.889	0.996	CLONAL	1	TRUE	1	0.797527959721087	2		574	716	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151289	202151290	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0014756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	224	620	1	ENST00000358485.4:c.1596dup	p.Leu533ThrfsTer6	p.L533Tfs*6	ENST00000358485	NM_001080125.1	530	aga/agAa	9/9	1	2	FACETS	0.858	0.803	0.913	0.858	0.803	0.913	CLONAL	1	TRUE	1	0.797527959721087	2		621	655	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144880	47144880	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	518	589	4	ENST00000409792.3:c.4873C>T	p.Arg1625Cys	p.R1625C	ENST00000409792	NM_014159.6	1625	Cgt/Tgt	7/21	0.796322215027953	4	FACETS	0.942	0.905	0.98	0.628	0.603	0.654	CLONAL	2	TRUE	1	0.797527959721087	4		593	1239	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912125	50912125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1309243644	NA	P-0014756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	374	779	5	ENST00000440232.2:c.1859C>T	p.Thr620Met	p.T620M	ENST00000440232	NM_002691.3	620	aCg/aTg	15/27	1	2	FACETS	0.996	0.948	1	0.996	0.948	1	CLONAL	1	TRUE	1	0.797527959721087	2		784	942	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	181	535	0	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	0.936	0.871	1	0.936	0.871	1	CLONAL	1	TRUE	1	0.797527959721087	2		535	485	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733513	85733513	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs387906350	NA	P-0014756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	223	512	4	ENST00000370580.1:c.499del	p.Ser167LeufsTer6	p.S167Lfs*6	ENST00000370580	NM_003921.4	167	Tct/ct	3/3	1	2	FACETS	0.941	0.883	1	0.941	0.883	1	CLONAL	1	TRUE	1	0.797527959721087	2		516	594	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416796	416796	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756725945	NA	P-0014756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	374	395	0	ENST00000399788.2:c.3754C>T	p.Arg1252Cys	p.R1252C	ENST00000399788	NM_001042603.1	1252	Cgt/Tgt	23/28	0.783834422968062	3	FACETS	0.979	0.939	1			1	CLONAL	2	TRUE	NA	0.797527959721087	3		395	670	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054541	42054541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1458609443	NA	P-0014756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	207	467	2	ENST00000219905.7:c.7731del	p.Asp2578ThrfsTer10	p.D2578Tfs*10	ENST00000219905	NM_001164273.1	2575	agA/ag	22/24	0.76550868922687	1	FACETS	0.889	0.842	0.936	0.889	0.842	0.936	CLONAL	1	TRUE	0	0.797527959721087	1		469	351	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596093	43596093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1462347303	NA	P-0014756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	270	655	9	ENST00000355710.3:c.260G>A	p.Cys87Tyr	p.C87Y	ENST00000355710	NM_020975.4	87	tGc/tAc	2/20	1	2	FACETS	0.909	0.857	0.962	0.909	0.857	0.962	CLONAL	1	TRUE	1	0.797527959721087	2		664	745	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0014756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	338	869	7	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	1	2	FACETS	0.868	0.823	0.914	0.868	0.823	0.914	CLONAL	1	TRUE	1	0.797527959721087	2		876	976	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347903	347903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376143198	NA	P-0014756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	451	947	3	ENST00000262320.3:c.1603G>A	p.Val535Ile	p.V535I	ENST00000262320	NM_003502.3	535	Gtc/Atc	6/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.797527959721087	2		950	1074	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004934	16004935	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	315	650	2	ENST00000268712.3:c.2319dup	p.Pro774ThrfsTer3	p.P774Tfs*3	ENST00000268712	NM_006311.3	773	-/A	20/46	1	2	FACETS	0.991	0.94	1	0.991	0.94	1	CLONAL	1	TRUE	1	0.797527959721087	2		652	797	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243743	41243743	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	270	616	0	ENST00000357654.3:c.3805G>A	p.Asp1269Asn	p.D1269N	ENST00000357654	NM_007294.3	1269	Gac/Aac	10/23	1	2	FACETS	0.97	0.916	1	0.97	0.916	1	CLONAL	1	TRUE	1	0.797527959721087	2		616	698	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222274	2222274	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	367	798	1	ENST00000398665.3:c.3106G>T	p.Asp1036Tyr	p.D1036Y	ENST00000398665	NM_032482.2	1036	Gat/Tat	24/28	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.797527959721087	2		799	912	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15374337	15374337	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	307	726	1	ENST00000263377.2:c.1235A>G	p.Tyr412Cys	p.Y412C	ENST00000263377	NM_058243.2	412	tAc/tGc	7/20	1	2	FACETS	0.968	0.917	1	0.968	0.917	1	CLONAL	1	TRUE	1	0.797527959721087	2		727	795	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212191	36212191	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1313945983	NA	P-0014756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	259	614	4	ENST00000222270.7:c.1942C>T	p.Arg648Trp	p.R648W	ENST00000222270	NM_014727.1	648	Cgg/Tgg	3/37	1	2	FACETS	0.921	0.868	0.976	0.921	0.868	0.976	CLONAL	1	TRUE	1	0.797527959721087	2		618	705	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754583	42754583	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	310	688	3	ENST00000222329.4:c.157G>A	p.Gly53Arg	p.G53R	ENST00000222329	NM_006494.2	53	Ggg/Agg	2/4	1	2	FACETS	0.886	0.839	0.935	0.886	0.839	0.935	CLONAL	1	TRUE	1	0.797527959721087	2		691	877	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50916737	50916737	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	266	628	1	ENST00000440232.2:c.2209T>A	p.Ser737Thr	p.S737T	ENST00000440232	NM_002691.3	737	Tct/Act	18/27	1	2	FACETS	0.923	0.87	0.976	0.923	0.87	0.976	CLONAL	1	TRUE	1	0.797527959721087	2		629	723	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095601	178095602	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	AATAAGGTTTT	novel	NA	P-0014756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	156	501	0	ENST00000397062.3:c.1719_1729dup	p.Ser577Ter	p.S577*	ENST00000397062	NM_006164.4	577	tct/tAAAACCTTATTct	5/5	0.797527959721087	3	FACETS	0.736	0.676	0.8			1	SUBCLONAL	1	TRUE	NA	0.797527959721087	3		501	743	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095619	178095620	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CATCA	novel	NA	P-0014756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	173	543	0	ENST00000397062.3:c.1707_1711dup	p.Glu571ValfsTer43	p.E571Vfs*43	ENST00000397062	NM_006164.4	571	gaa/gTGATGaa	5/5	0.797527959721087	3	FACETS	0.766	0.706	0.828			1	SUBCLONAL	1	TRUE	NA	0.797527959721087	3		543	792	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29105996	29105996	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	155	380	1	ENST00000328354.6:c.844C>A	p.His282Asn	p.H282N	ENST00000328354	NM_007194.3	282	Cat/Aat	7/15	1	2	FACETS	0.898	0.83	0.967	0.898	0.83	0.967	CLONAL	1	TRUE	1	0.797527959721087	2		381	433	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691893	30691893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1402755105	NA	P-0014756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	409	462	4	ENST00000295754.5:c.395C>T	p.Thr132Ile	p.T132I	ENST00000295754	NM_003242.5	132	aCt/aTt	3/7	0.796322215027953	4	FACETS	1	0.962	1	0.671	0.641	0.701	CLONAL	2	TRUE	1	0.797527959721087	4		466	916	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549443	187549443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1193669577	NA	P-0014756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	278	576	4	ENST00000441802.2:c.4675G>A	p.Ala1559Thr	p.A1559T	ENST00000441802	NM_005245.3	1559	Gcc/Acc	9/27	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.797527959721087	2		580	652	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680916	30680916	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	333	762	4	ENST00000376406.3:c.803G>T	p.Arg268Met	p.R268M	ENST00000376406	NM_014641.2	268	aGg/aTg	5/15	1	2	FACETS	0.986	0.936	1	0.986	0.936	1	CLONAL	1	TRUE	1	0.797527959721087	2		766	847	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165126	32165126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1213449936	NA	P-0014756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	343	613	1	ENST00000375023.3:c.5002C>T	p.Arg1668Cys	p.R1668C	ENST00000375023	NM_004557.3	1668	Cgc/Tgc	27/30	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.797527959721087	2		614	811	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753100	128753100	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	458	477	2	ENST00000377970.2:c.1261G>C	p.Val421Leu	p.V421L	ENST00000377970	NM_002467.4	421	Gtc/Ctc	3/3	0.796322215027953	4	FACETS	0.995	0.954	1	0.664	0.636	0.691	CLONAL	2	TRUE	1	0.797527959721087	4		479	1037	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361095	70361097	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	rs1212763076	NA	P-0014756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	11	198	0	ENST00000374080.3:c.6285_6287del	p.Gln2115del	p.Q2115del	ENST00000374080		2095	CAA/-	43/45	1	1	FACETS	0.081	0.055	0.112	0.081	0.055	0.112	SUBCLONAL	1	TRUE	0	0.797527959721087	1		198	205	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593466	48593466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064796102	NA	P-0014864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	249	414	2	ENST00000342988.3:c.1217C>T	p.Ala406Val	p.A406V	ENST00000342988	NM_005359.5	406	gCg/gTg	10/12	0.55133742981389	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.565142482334617	1		416	624	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741739	17741739	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	373	671	0	ENST00000250003.3:c.410C>A	p.Ser137Ter	p.S137*	ENST00000250003	NM_002478.4	137	tCg/tAg	1/3	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.565142482334617	2		671	1114	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064427	30064427	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	263	585	0	ENST00000338641.4:c.991del	p.Arg331GlufsTer15	p.R331Efs*15	ENST00000338641	NM_000268.3	331	Aga/ga	10/16	0.565142482334617	1	FACETS	0.969	0.914	1	0.969	0.914	1	CLONAL	1	TRUE	0	0.565142482334617	1		585	689	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934284	68934284	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146218789	NA	P-0014864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1653	250	594	0	ENST00000288368.4:c.350G>A	p.Arg117His	p.R117H	ENST00000288368	NM_024870.2	117	cGt/cAt	4/40	0.520080027760046	4	FACETS	0.728	0.678	0.78	0.243	0.226	0.26	SUBCLONAL	1	TRUE	1	0.565142482334617	4		594	1903	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776175	135776175	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	323	569	0	ENST00000298552.3:c.2552A>G	p.Gln851Arg	p.Q851R	ENST00000298552	NM_001162426.1	851	cAg/cGg	20/23	0.471634572003898	3	FACETS	1	0.97	1	0.522	0.492	0.553	CLONAL	1	TRUE	1	0.565142482334617	3		569	1404	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0014967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	22	495	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.093	0.072	0.118	0.093	0.072	0.118	SUBCLONAL	1	TRUE	1	0.93	2		495	508	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0015021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	130	561	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.848	0.769	0.932	0.848	0.769	0.932	CLONAL	1	TRUE	1	0.344411761667772	2		562	890	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602737	10602737	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	165	850	0	ENST00000171111.5:c.841C>A	p.Leu281Met	p.L281M	ENST00000171111	NM_203500.1	281	Ctg/Atg	3/6	0.344411761667772	1	FACETS	0.912	0.838	0.989	0.912	0.838	0.989	CLONAL	1	TRUE	0	0.344411761667772	1		850	870	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221954	1221954	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	217	867	0	ENST00000326873.7:c.869T>G	p.Leu290Arg	p.L290R	ENST00000326873	NM_000455.4	290	cTt/cGt	7/10	0.344411761667772	1	FACETS	0.927	0.861	0.995	0.927	0.861	0.995	CLONAL	1	TRUE	0	0.344411761667772	1		867	1125	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982436	10982436	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	14	55	0	ENST00000327064.4:c.58C>A	p.Pro20Thr	p.P20T	ENST00000327064	NM_199141.1	20	Ccg/Acg	1/16	0.344411761667772	1	FACETS	0.886	0.652	1	0.886	0.652	1	CLONAL	1	TRUE	0	0.344411761667772	1		55	76	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213898	66213898	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	57	454	0	ENST00000273854.3:c.2532G>T	p.Trp844Cys	p.W844C	ENST00000273854	NM_004439.5	844	tgG/tgT	15/18	1	2	FACETS	0.466	0.399	0.539	0.466	0.399	0.539	SUBCLONAL	1	TRUE	1	0.344411761667772	2		454	711	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372299	55372299	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	106	873	0	ENST00000297316.4:c.989C>A	p.Pro330His	p.P330H	ENST00000297316	NM_022454.3	330	cCc/cAc	2/2	1	2	FACETS	0.563	0.503	0.627	0.563	0.503	0.627	SUBCLONAL	1	TRUE	1	0.344411761667772	2		873	1093	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115873	8115874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0015125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	287	508	0	ENST00000346208.3:c.1220dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tCcg	6/6	0.733959966056846	3	FACETS	0.985	0.926	1	0.492	0.463	0.523	CLONAL	1	TRUE	1	0.735534376374969	3		508	1084	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620098	21620098	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	301	491	1	ENST00000382592.4:c.68G>A	p.Arg23His	p.R23H	ENST00000382592	NM_014572.2	23	cGt/cAt	2/8	0.735534376374969	2	FACETS	1	0.982	1	0.541	0.512	0.57	CLONAL	1	TRUE	0	0.735534376374969	2		492	757	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075157	16075157	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	206	310	0	ENST00000268712.3:c.395C>G	p.Pro132Arg	p.P132R	ENST00000268712	NM_006311.3	132	cCg/cGg	4/46	0.735534376374969	2	FACETS	1	0.95	1	0.509	0.476	0.543	CLONAL	1	TRUE	0	0.735534376374969	2		310	550	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609095	43609095	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	334	701	0	ENST00000355710.3:c.1851G>C	p.Lys617Asn	p.K617N	ENST00000355710	NM_020975.4	617	aaG/aaC	10/20	1	2	FACETS	0.99	0.936	1	0.99	0.936	1	CLONAL	1	TRUE	1	0.546348388889127	2		701	1235	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426801	70426801	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0015138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	130	260	1	ENST00000373644.4:c.4462-1G>T		p.X1488_splice	ENST00000373644	NM_030625.2	1488			1	2	FACETS	0.768	0.698	0.84	0.768	0.698	0.84	SUBCLONAL	1	TRUE	1	0.546348388889127	2		261	620	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431717	49431717	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	276	601	0	ENST00000301067.7:c.9422T>C	p.Val3141Ala	p.V3141A	ENST00000301067	NM_003482.3	3141	gTa/gCa	34/54	1	2	FACETS	0.938	0.881	0.997	0.938	0.881	0.997	CLONAL	1	TRUE	1	0.546348388889127	2		601	1077	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100692	67100716	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCGAGCCCAGGTAGGGTAACATCAG	GCGAGCCCAGGTAGGGTAACATCAG	-	novel	NA	P-0015138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	176	508	0	ENST00000412916.2:c.392_399+17del		p.X131_splice	ENST00000412916		131		4/6	0.546348388889127	1	FACETS	0.649	0.6	0.701	0.649	0.6	0.701	SUBCLONAL	1	TRUE	0	0.546348388889127	1		508	721	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703681	47703685	+	frameshift_variant	Frame_Shift_Del	DEL	TGAAA	TGAAA	-	novel	NA	P-0015138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	210	420	0	ENST00000233146.2:c.2183_2187del	p.Glu728ValfsTer20	p.E728Vfs*20	ENST00000233146	NM_000251.2	727	gcTGAAAtg/gctg	13/16	1	2	FACETS	0.835	0.776	0.896	0.835	0.776	0.896	CLONAL	1	TRUE	1	0.546348388889127	2		420	921	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517817	187517817	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	184	263	0	ENST00000441802.2:c.12877C>A	p.His4293Asn	p.H4293N	ENST00000441802	NM_005245.3	4293	Cac/Aac	25/27	0.54506206379643	2	FACETS	1	0.967	1	0.536	0.497	0.576	CLONAL	1	TRUE	0	0.546348388889127	2		263	628	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426883	70426883	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	182	350	0	ENST00000373644.4:c.4543A>C	p.Met1515Leu	p.M1515L	ENST00000373644	NM_030625.2	1515	Atg/Ctg	7/12	1	2	FACETS	0.838	0.774	0.904	0.838	0.774	0.904	CLONAL	1	TRUE	1	0.546348388889127	2		350	795	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	163	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	0.987	0.906	1			1	INDETERMINATE	1	TRUE	NA	0.390935827923954	2		436	845	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578541	7578541	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	251	1312	0	ENST00000269305.4:c.389T>G	p.Leu130Arg	p.L130R	ENST00000269305	NM_001126112.2	130	cTc/cGc	5/11	0.390935827923954	1	FACETS	0.976	0.914	1	0.976	0.914	1	CLONAL	1	TRUE	0	0.390935827923954	1		1312	1058	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138382788	138382788	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	130	911	0	ENST00000289153.2:c.2756A>G	p.Asp919Gly	p.D919G	ENST00000289153	NM_006219.2	919	gAc/gGc	19/22	0.390935827923954	1	FACETS	0.851	0.774	0.931	0.851	0.774	0.931	CLONAL	1	TRUE	0	0.390935827923954	1		911	629	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015255-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	42	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.793	0.66	0.941	0.793	0.66	0.941	CLONAL	1	TRUE	1	0.14	2		436	757	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578541	7578541	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015255-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1169	92	1312	0	ENST00000269305.4:c.389T>G	p.Leu130Arg	p.L130R	ENST00000269305	NM_001126112.2	130	cTc/cGc	5/11	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.14	2		1312	1261	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138382788	138382788	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015255-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	44	911	0	ENST00000289153.2:c.2756A>G	p.Asp919Gly	p.D919G	ENST00000289153	NM_006219.2	919	gAc/gGc	19/22	1	2	FACETS	0.898	0.751	1	0.898	0.751	1	CLONAL	1	TRUE	1	0.14	2		911	700	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	31	406	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.474	0.382	0.578	0.474	0.382	0.578	SUBCLONAL	1	TRUE	1	0.22	2		406	595	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519998	NA	P-0015389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	48	601	0	ENST00000269305.4:c.581T>A	p.Leu194His	p.L194H	ENST00000269305	NM_001126112.2	194	cTt/cAt	6/11	1	2	FACETS	0.662	0.559	0.776	0.662	0.559	0.776	SUBCLONAL	1	TRUE	1	0.22	2		601	659	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858336	9858336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1349281989	NA	P-0015389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	29	259	0	ENST00000330684.3:c.3065G>A	p.Arg1022His	p.R1022H	ENST00000330684	NM_001134407.1	1022	cGc/cAc	13/13	1	2	FACETS	0.959	0.772	1	0.959	0.772	1	CLONAL	1	TRUE	1	0.22	2		259	275	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965332	68965332	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	28	443	0	ENST00000288368.4:c.944C>G	p.Ala315Gly	p.A315G	ENST00000288368	NM_024870.2	315	gCt/gGt	9/40	1	2	FACETS	0.624	0.498	0.767	0.624	0.498	0.767	SUBCLONAL	1	TRUE	1	0.22	2		443	408	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430390	181430390	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	310	734	0	ENST00000325404.1:c.242T>C	p.Leu81Pro	p.L81P	ENST00000325404	NM_003106.3	81	cTt/cCt	1/1	0.857562082542096	3	FACETS	0.983	0.929	1	0.492	0.464	0.52	CLONAL	1	TRUE	1	0.93060441580906	3		734	993	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26046045	26046045	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	200	288	0	ENST00000540144.1:c.407C>G	p.Ala136Gly	p.A136G	ENST00000540144	NM_003531.2	136	gCa/gGa	1/1	0.516713693390247	6	FACETS	0.84	0.786	0.895	0.84	0.786	0.895	INDETERMINATE	3	TRUE	3	0.93060441580906	6		288	488	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	526	406	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.505383602835883	7	FACETS	0.939	0.902	0.977			1	CLONAL	4	FALSE	NA	0.505383602835883	7		406	1254	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317539	1317539	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	240	538	0	ENST00000400841.2:c.526G>C	p.Asp176His	p.D176H	ENST00000400841		176	Gat/Cat	5/6	0.346213018682547	6	FACETS	1	0.989	1			1	CLONAL	1	FALSE	NA	0.505383602835883	6		538	1460	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168751	32168751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377716761	NA	P-0015422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	433	680	0	ENST00000375023.3:c.4172G>A	p.Arg1391His	p.R1391H	ENST00000375023	NM_004557.3	1391	cGc/cAc	23/30	0.310024707152603	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	FALSE	2	0.505383602835883	4		680	1277	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041627	47041627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1404	213	675	2	ENST00000377604.3:c.1852G>A	p.Ala618Thr	p.A618T	ENST00000377604	NM_001204468.1	618	Gcc/Acc	17/24	0.317480606445623	6	FACETS	1	0.957	1			1	CLONAL	1	FALSE	NA	0.505383602835883	6		677	1617	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0015564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	136	286	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.364204597049372	3	FACETS	1	0.978	1	0.409	0.373	0.447	CLONAL	1	TRUE	0	0.439648492942012	3		286	615	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	180	306	0				ENST00000310581	NM_198253.2	-/1132			0.439648492942012	6	FACETS	1	0.942	1	0.409	0.377	0.441	CLONAL	2	TRUE	1	0.439648492942012	6		306	753	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12043881	12043881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	104	432	1	ENST00000396373.4:c.1260G>A	p.Met420Ile	p.M420I	ENST00000396373	NM_001987.4	420	atG/atA	8/8	0.262462876329727	3	FACETS	1	0.92	1	0.343	0.308	0.38	INDETERMINATE	1	TRUE	0	0.439648492942012	3		433	561	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40709551	40709551	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1263	116	638	0	ENST00000373198.4:c.4351G>C	p.Glu1451Gln	p.E1451Q	ENST00000373198	NM_133170.3	1451	Gag/Cag	32/32	0.439648492942012	7	FACETS	0.803	0.721	0.89	0.201	0.18	0.223	CLONAL	1	TRUE	3	0.439648492942012	7		638	1379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253911	NA	P-0015564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	283	472	4	ENST00000269305.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000269305	NM_001126112.2	180	Gag/Aag	5/11	1	2	FACETS	1	0.984	1	1	0.996	1	CLONAL	2	TRUE	1	0.439648492942012	2		476	592	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663346	227663346	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1024227751	NA	P-0015564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	259	379	0	ENST00000305123.5:c.109G>C	p.Glu37Gln	p.E37Q	ENST00000305123	NM_005544.2	37	Gag/Cag	1/2	0.439648492942012	3	FACETS	0.984	0.934	1	0.984	0.934	1	CLONAL	3	TRUE	0	0.439648492942012	3		379	487	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211899	36211899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2132	252	1067	5	ENST00000222270.7:c.1656del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	550	gaC/ga	3/37	0.439648492942012	7	FACETS	1	0.939	1			1	CLONAL	1	TRUE	NA	0.439648492942012	7		1072	2384	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059204	27059204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	155	545	0	ENST00000324856.7:c.1841C>T	p.Ser614Leu	p.S614L	ENST00000324856	NM_006015.4	614	tCa/tTa	4/20	0.439648492942012	3	FACETS	1	0.969	1	0.373	0.342	0.406	CLONAL	1	TRUE	0	0.439648492942012	3		545	768	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176153815	176153815	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	79	417	0	ENST00000367669.3:c.421G>C	p.Asp141His	p.D141H	ENST00000367669	NM_022457.5	141	Gat/Cat	2/20	0.439648492942012	3	FACETS	1	0.917	1	0.349	0.308	0.392	CLONAL	1	TRUE	0	0.439648492942012	3		417	419	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946925	71946925	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	193	857	0	ENST00000298229.2:c.2774C>G	p.Ser925Cys	p.S925C	ENST00000298229	NM_001567.3	925	tCc/tGc	25/28	0.439648492942012	1	FACETS	0.953	0.884	1	0.953	0.884	1	CLONAL	1	TRUE	0	0.439648492942012	1		857	719	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992203	11992203	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs776026236	NA	P-0015564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	204	488	0	ENST00000396373.4:c.293C>G	p.Thr98Ser	p.T98S	ENST00000396373	NM_001987.4	98	aCc/aGc	3/8	0.262462876329727	3	FACETS	0.847	0.789	0.907	0.565	0.526	0.605	INDETERMINATE	2	TRUE	0	0.439648492942012	3		488	668	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038881	12038881	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	129	558	0	ENST00000396373.4:c.1174G>C	p.Glu392Gln	p.E392Q	ENST00000396373	NM_001987.4	392	Gag/Cag	7/8	0.262462876329727	3	FACETS	1	0.915	1	0.336	0.305	0.369	INDETERMINATE	1	TRUE	0	0.439648492942012	3		558	710	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50481198	50481198	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0015564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	99	473	0	ENST00000394963.4:c.584C>G	p.Ser195Ter	p.S195*	ENST00000394963	NM_003076.4	195	tCa/tGa	5/13	0.262462876329727	3	FACETS	0.781	0.698	0.87	0.26	0.232	0.29	INDETERMINATE	1	TRUE	0	0.439648492942012	3		473	703	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944543	32944543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	108	518	1	ENST00000380152.3:c.8336C>T	p.Ser2779Phe	p.S2779F	ENST00000380152		2779	tCt/tTt	19/27	0.439648492942012	7	FACETS	0.953	0.853	1	0.191	0.17	0.212	CLONAL	1	TRUE	2	0.439648492942012	7		519	1082	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66777391	66777391	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	141	757	0	ENST00000307102.5:c.757C>G	p.Leu253Val	p.L253V	ENST00000307102	NM_002755.3	253	Ctg/Gtg	7/11	0.439648492942012	1	FACETS	0.84	0.768	0.914	0.84	0.768	0.914	CLONAL	1	TRUE	0	0.439648492942012	1		757	596	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916278	9916278	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555491689	NA	P-0015564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	112	495	0	ENST00000330684.3:c.2011C>T	p.Gln671Ter	p.Q671*	ENST00000330684	NM_001134407.1	671	Cag/Tag	10/13	0.439648492942012	2	FACETS	1	0.952	1	0.542	0.49	0.596	CLONAL	1	TRUE	0	0.439648492942012	2		495	470	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632700	23632700	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs778705498	NA	P-0015564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	137	659	0	ENST00000261584.4:c.3096G>C	p.Met1032Ile	p.M1032I	ENST00000261584	NM_024675.3	1032	atG/atC	10/13	0.439648492942012	2	FACETS	0.999	0.911	1	0.499	0.455	0.545	CLONAL	1	TRUE	0	0.439648492942012	2		659	624	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965075	15965075	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	99	395	0	ENST00000268712.3:c.5521G>C	p.Glu1841Gln	p.E1841Q	ENST00000268712	NM_006311.3	1841	Gag/Cag	37/46	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.439648492942012	2		395	420	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654842	29654842	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1245703067	NA	P-0015564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	71	277	0	ENST00000356175.3:c.5531C>G	p.Ser1844Cys	p.S1844C	ENST00000356175	NM_000267.3	1844	tCt/tGt	37/57	1	2	FACETS	0.895	0.786	1	0.895	0.786	1	CLONAL	1	TRUE	1	0.439648492942012	2		277	361	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617761	39617761	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	90	475	0	ENST00000262039.4:c.1945C>G	p.Gln649Glu	p.Q649E	ENST00000262039	NM_002647.2	649	Caa/Gaa	17/25	0.439648492942012	3	FACETS	0.933	0.831	1	0.467	0.415	0.522	CLONAL	1	TRUE	1	0.439648492942012	3		475	535	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615717	1615717	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	169	912	0	ENST00000344749.5:c.1554G>C	p.Lys518Asn	p.K518N	ENST00000344749	NM_001136139.2	518	aaG/aaC	17/19	0.439648492942012	1	FACETS	0.958	0.885	1	0.958	0.885	1	CLONAL	1	TRUE	0	0.439648492942012	1		912	626	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765765	41765765	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	72	421	0	ENST00000301178.4:c.2641G>C	p.Asp881His	p.D881H	ENST00000301178	NM_021913.4	881	Gat/Cat	20/20	0.439648492942012	6	FACETS	0.912	0.796	1			1	CLONAL	1	TRUE	NA	0.439648492942012	6		421	675	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607603	46607603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	194	931	1	ENST00000263734.3:c.1792G>A	p.Glu598Lys	p.E598K	ENST00000263734	NM_001430.4	598	Gag/Aag	12/16	0.439648492942012	3	FACETS	1	0.927	1	0.334	0.309	0.361	CLONAL	1	TRUE	0	0.439648492942012	3		932	1073	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309496	30309496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1432	158	667	1	ENST00000307677.4:c.526G>A	p.Asp176Asn	p.D176N	ENST00000307677	NM_138578.1	176	Gac/Aac	2/3	0.439648492942012	7	FACETS	0.949	0.866	1	0.237	0.216	0.259	CLONAL	1	TRUE	3	0.439648492942012	7		668	1590	SUCCESS
ATR	545	MSKCC	GRCh37	3	142254967	142254967	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1383288417	NA	P-0015564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	136	290	0	ENST00000350721.4:c.3802C>T	p.Leu1268Phe	p.L1268F	ENST00000350721	NM_001184.3	1268	Ctc/Ttc	20/47	0.364204597049372	3	FACETS	1	0.981	1	0.801	0.74	0.863	CLONAL	2	TRUE	0	0.439648492942012	3		290	314	SUCCESS
APC	324	MSKCC	GRCh37	5	112137046	112137046	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747759906	NA	P-0015564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	141	608	0	ENST00000257430.4:c.800G>C	p.Gly267Ala	p.G267A	ENST00000257430	NM_000038.5	267	gGa/gCa	8/16	0.439648492942012	1	FACETS	0.968	0.887	1	0.968	0.887	1	CLONAL	1	TRUE	0	0.439648492942012	1		608	517	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056500	26056500	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs372319415	NA	P-0015564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	53	197	0	ENST00000343677.2:c.157G>C	p.Glu53Gln	p.E53Q	ENST00000343677	NM_005319.3	53	Gag/Cag	1/1	0.439648492942012	2	FACETS	1	0.927	1	0.558	0.482	0.639	CLONAL	1	TRUE	0	0.439648492942012	2		197	216	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974188	2974188	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	191	702	0	ENST00000396946.4:c.1417G>C	p.Glu473Gln	p.E473Q	ENST00000396946	NM_032415.4	473	Gaa/Caa	10/25	0.403339179816449	4	FACETS	1	0.961	1	0.355	0.328	0.384	CLONAL	1	TRUE	1	0.439648492942012	4		702	1174	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426870	6426870	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	125	458	0	ENST00000356142.4:c.63C>G	p.Ile21Met	p.I21M	ENST00000356142	NM_018890.3	21	atC/atG	2/7	0.403339179816449	4	FACETS	0.972	0.88	1	0.324	0.293	0.357	CLONAL	1	TRUE	1	0.439648492942012	4		458	842	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513165	106513165	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	46	219	0	ENST00000359195.3:c.2069G>C	p.Arg690Thr	p.R690T	ENST00000359195	NM_002649.2	690	aGa/aCa	4/11	0.439648492942012	5	FACETS	0.702	0.591	0.824	0.234	0.197	0.275	SUBCLONAL	1	TRUE	2	0.439648492942012	5		219	495	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372190	55372190	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	113	411	1	ENST00000297316.4:c.880C>T	p.His294Tyr	p.H294Y	ENST00000297316	NM_022454.3	294	Cac/Tac	2/2	0.439648492942012	5	FACETS	1	0.97	1	0.398	0.358	0.44	CLONAL	1	TRUE	2	0.439648492942012	5		412	714	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	26	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.762	0.612	0.93	1	0.937	1	CLONAL	2	FALSE	1	0.243562722657323	2		306	140	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982392	201982393	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	220	1024	0	ENST00000359651.3:c.772dup	p.Trp258LeufsTer43	p.W258Lfs*43	ENST00000359651		257	-/T	6/8	0.243562722657323	5	FACETS	0.997	0.929	1	0.997	0.929	1	CLONAL	3	FALSE	2	0.243562722657323	5		1024	825	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182681689	182681689	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	121	441	0	ENST00000292782.4:c.369G>T	p.Met123Ile	p.M123I	ENST00000292782	NM_020640.2	123	atG/atT	3/7	0.243562722657323	7	FACETS	0.945	0.86	1	0.945	0.86	1	CLONAL	4	FALSE	3	0.243562722657323	7		441	423	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968615	55968615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	76	816	0	ENST00000263923.4:c.2048G>A	p.Ser683Asn	p.S683N	ENST00000263923	NM_002253.2	683	aGc/aAc	14/30	0.153054571706271	4	FACETS	0.894	0.788	1	0.894	0.788	1	CLONAL	2	FALSE	2	0.243562722657323	4		816	434	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527950	157527950	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	139	733	0	ENST00000346085.5:c.5675C>A	p.Ala1892Glu	p.A1892E	ENST00000346085	NM_020732.3	1892	gCa/gAa	20/20	0.243562722657323	6	FACETS	1	0.961	1	1	0.961	1	CLONAL	3	FALSE	3	0.243562722657323	6		733	521	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797280	135797289	+	frameshift_variant	Frame_Shift_Del	DEL	AAGGGTACAT	AAGGGTACAT	-	novel	NA	P-0015663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	52	406	0	ENST00000298552.3:c.580_589del	p.Met194AlafsTer13	p.M194Afs*13	ENST00000298552	NM_001162426.1	194	ATGTACCCTTgc/gc	7/23	0.243562722657323	1	FACETS	1	0.923	1	1	0.979	1	CLONAL	2	FALSE	0	0.243562722657323	1		406	171	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0015796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	319	501	2	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	0.280964097962919	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.280964097962919	2		503	926	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579329	7579329	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912658	NA	P-0015796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	256	648	0	ENST00000269305.4:c.358A>G	p.Lys120Glu	p.K120E	ENST00000269305	NM_001126112.2	120	Aag/Gag	4/11	0.280964097962919	2	FACETS	0.883	0.827	0.941	0.883	0.827	0.941	CLONAL	2	TRUE	0	0.280964097962919	2		648	1032	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943380	71943380	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1394942069	NA	P-0015796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	158	498	1	ENST00000298229.2:c.1712G>A	p.Arg571Gln	p.R571Q	ENST00000298229	NM_001567.3	571	cGg/cAg	14/28	0.254125247958719	3	FACETS	1	0.983	1	0.65	0.595	0.707	CLONAL	1	TRUE	1	0.280964097962919	3		499	987	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495642	72495678	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTACCTGGTGGAGGTGCCTTTCCTCACATCGCAGAT	AGTACCTGGTGGAGGTGCCTTTCCTCACATCGCAGAT	-	novel	NA	P-0015906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	83	321	0	ENST00000477973.2:c.392_423+5del		p.X131_splice	ENST00000477973	NM_012234.5	131		1/4	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		321	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579431	7579432	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	427	644	0	ENST00000269305.4:c.255_256insA	p.Ala86SerfsTer63	p.A86Sfs*63	ENST00000269305	NM_001126112.2	85	-/A	4/11	0.648390848704243	2	FACETS	0.949	0.915	0.982	0.949	0.915	0.982	CLONAL	2	TRUE	0	0.663588977881792	2		644	678	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372442	55372442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	368	974	1	ENST00000297316.4:c.1132C>T	p.Pro378Ser	p.P378S	ENST00000297316	NM_022454.3	378	Ccc/Tcc	2/2	0.652699756021941	1	FACETS	0.968	0.924	1	0.968	0.924	1	CLONAL	1	TRUE	0	0.663588977881792	1		975	766	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0016011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	89	305	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	NA	2	FACETS	1	0.959	1			1	INDETERMINATE	1	FALSE	NA	0.347124910274295	2		305	442	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	55	424	0	ENST00000342988.3:c.1067C>A	p.Pro356His	p.P356H	ENST00000342988	NM_005359.5	356	cCt/cAt	9/12	0.352669749288853	1	FACETS	0.786	0.676	0.905	0.786	0.676	0.905	CLONAL	1	FALSE	0	0.347124910274295	1		424	333	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5206802	5206802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	39	648	0	ENST00000357368.4:c.5830G>A	p.Asp1944Asn	p.D1944N	ENST00000357368	NM_002850.3	1944	Gac/Aac	38/38	0.352669749288853	0	FACETS	0.53	0.441	0.627			1	SUBCLONAL	1	FALSE	0	0.347124910274295	0		648	277	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575488	64575488	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	375	478	1	ENST00000312049.6:c.529del	p.Leu177CysfsTer8	p.L177Cfs*8	ENST00000312049	NM_130799.2	177	Ctg/tg	3/10	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.691208432140062	2		479	916	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0016125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	289	579	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.692382430353273	3	FACETS	0.92	0.873	0.966	0.92	0.873	0.966	CLONAL	2	TRUE	1	0.692382430353273	3		579	611	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0016145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	33	364	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	1	2	FACETS	0.123	0.099	0.149	0.123	0.099	0.149	SUBCLONAL	1	TRUE	1	0.622639992466238	2		364	865	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0016145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	96	372	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			1	2	FACETS	0.323	0.287	0.362	0.323	0.287	0.362	SUBCLONAL	1	TRUE	1	0.622639992466238	2		372	954	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627752	187627752	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1723	106	438	0	ENST00000441802.2:c.3230C>G	p.Ser1077Cys	p.S1077C	ENST00000441802	NM_005245.3	1077	tCt/tGt	2/27	0.622639992466238	4	FACETS	0.302	0.269	0.337			1	SUBCLONAL	1	TRUE	NA	0.622639992466238	4		438	1829	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0016164-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	95	644	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	0.53279014281998	5	FACETS	1	0.977	1	0.338	0.302	0.376	CLONAL	1	FALSE	1	0.53279014281998	5		644	474	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871692	35871692	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016164-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	98	405	0	ENST00000216797.5:c.814C>G	p.Leu272Val	p.L272V	ENST00000216797	NM_020529.2	272	Ctg/Gtg	5/6	0.53279014281998	5	FACETS	0.919	0.828	1	0.46	0.414	0.508	CLONAL	2	FALSE	1	0.53279014281998	5		405	360	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828170	50828180	+	protein_altering_variant	In_Frame_Del	DEL	ACTTCCCAAAG	ACTTCCCAAAG	TT	novel	NA	P-0016164-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	41	550	2	ENST00000398568.2:c.2508_2518delinsTT	p.Leu837_Asp840delinsTyr	p.L837_D840delinsY	ENST00000398568	NM_001042412.1	836	tcACTTCCCAAAGac/tcTTac	17/18	0.318741337178955	6	FACETS	0.916	0.765	1			1	INDETERMINATE	1	FALSE	NA	0.53279014281998	6		552	347	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161413	55161413	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016164-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	32	433	0	ENST00000257290.5:c.3244G>A	p.Asp1082Asn	p.D1082N	ENST00000257290	NM_006206.4	1082	Gac/Aac	23/23	0.53279014281998	6	FACETS	0.563	0.456	0.683			1	SUBCLONAL	1	FALSE	NA	0.53279014281998	6		433	441	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928824	44928824	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016164-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	15	282	0	ENST00000377967.4:c.1924G>A	p.Gly642Arg	p.G642R	ENST00000377967	NM_021140.2	642	Ggg/Agg	17/29	0.533138975427203	3	FACETS	0.358	0.262	0.473			1	SUBCLONAL	1	FALSE	NA	0.53279014281998	3		282	199	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164505	47164505	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	86	319	0	ENST00000409792.3:c.1621C>T	p.Arg541Ter	p.R541*	ENST00000409792	NM_014159.6	541	Cga/Tga	3/21	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.39	2		319	404	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633631	69633631	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	44	66	1	ENST00000334134.2:c.71G>T	p.Arg24Leu	p.R24L	ENST00000334134	NM_005247.2	24	cGg/cTg	1/3	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.82870390479916	2		67	79	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090572	71090572	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	37	529	0	ENST00000318789.4:c.776T>G	p.Val259Gly	p.V259G	ENST00000318789	NM_032682.5	259	gTc/gGc	11/21	1	2	FACETS	0.147	0.121	0.177	0.147	0.121	0.177	SUBCLONAL	1	TRUE	1	0.82870390479916	2		529	607	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998259	100998259	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766624974	NA	P-0016291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	182	402	1	ENST00000325455.5:c.1543C>T	p.Leu515Phe	p.L515F	ENST00000325455	NM_001202474.3	515	Ctc/Ttc	1/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.84354961382098	2		403	390	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871776	12871776	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	134	295	0	ENST00000228872.4:c.496del	p.Arg166GlufsTer59	p.R166Efs*59	ENST00000228872	NM_004064.3	165	Aaa/aa	2/3	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.84354961382098	2		295	314	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81399262	81399262	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	370	824	0	ENST00000222390.5:c.26C>A	p.Ala9Asp	p.A9D	ENST00000222390	NM_000601.4	9	gCc/gAc	1/18	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.84354961382098	2		824	849	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850626	63850637	+	inframe_deletion	In_Frame_Del	DEL	ATCAGAGCAAGA	ATCAGAGCAAGA	-	novel	NA	P-0016294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	32	483	0	ENST00000279873.7:c.1405_1416del	p.Ser469_Glu472del	p.S469_E472del	ENST00000279873	NM_032199.2	468	tcATCAGAGCAAGAa/tca	10/10	1	2	FACETS	0.765	0.62	0.929	0.765	0.62	0.929	CLONAL	1	TRUE	1	0.16	2		483	523	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625353	69625353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	198	1013	0	ENST00000334134.2:c.440C>T	p.Pro147Leu	p.P147L	ENST00000334134	NM_005247.2	147	cCc/cTc	3/3	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.328853053565898	2		1013	991	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943788	71943788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771815535	NA	P-0016295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	57	1033	0	ENST00000298229.2:c.1831C>T	p.Arg611Cys	p.R611C	ENST00000298229	NM_001567.3	611	Cgc/Tgc	15/28	1	2	FACETS	0.385	0.329	0.447	0.385	0.329	0.447	SUBCLONAL	1	TRUE	1	0.328853053565898	2		1033	900	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528489	29528489	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764079291	NA	P-0016306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	204	613	0	ENST00000356175.3:c.1246C>T	p.Arg416Ter	p.R416*	ENST00000356175	NM_000267.3	416	Cga/Tga	11/57	0.643964445420029	2	FACETS	0.866	0.817	0.913	0.866	0.817	0.913	CLONAL	2	TRUE	0	0.643964445420029	2		613	366	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	178	406	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.98	0.905	1	0.98	0.905	1	CLONAL	1	TRUE	1	0.479778334573964	2		406	757	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604790	48604790	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1568211615	NA	P-0016438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	152	411	0	ENST00000342988.3:c.1612G>T	p.Glu538Ter	p.E538*	ENST00000342988	NM_005359.5	538	Gaa/Taa	12/12	0.421742666150368	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.479778334573964	1		411	469	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634347	23634347	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	212	733	0	ENST00000261584.4:c.2939G>C	p.Ser980Thr	p.S980T	ENST00000261584	NM_024675.3	980	aGc/aCc	9/13	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.479778334573964	2		733	869	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	13	205	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.157	0.111	0.213	0.157	0.111	0.213	SUBCLONAL	1	TRUE	1	0.334712563941208	2		205	496	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	145	428	2	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	0.192396766268951	3	FACETS	1	0.958	1	1	0.958	1	INDETERMINATE	2	TRUE	1	0.334712563941208	3		430	475	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	97	305	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.974	0.87	1	0.974	0.87	1	CLONAL	1	TRUE	1	0.334712563941208	2		305	595	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	158	247	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.851	0.784	0.919	1	0.991	1	CLONAL	2	TRUE	1	0.334712563941208	2		248	555	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	166	701	6	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	0.972	1	CLONAL	1	TRUE	1	0.334712563941208	2		707	882	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	234	280	5	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	0.334712563941208	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.334712563941208	3		285	694	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346884	73346884	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	56	255	2	ENST00000377767.4:c.1333del	p.Ser445HisfsTer20	p.S445Hfs*20	ENST00000377767	NM_014953.3	445	Tca/ca	9/21	1	2	FACETS	0.818	0.703	0.943	0.818	0.703	0.943	CLONAL	1	TRUE	1	0.334712563941208	2		257	409	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100171	157100172	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	24	49	0	ENST00000346085.5:c.1114dup	p.Arg372ProfsTer163	p.R372Pfs*163	ENST00000346085	NM_020732.3	370	tcc/tCcc	1/20	1	2	FACETS	0.755	0.596	0.936	0.755	0.596	0.936	CLONAL	1	TRUE	1	0.334712563941208	2		49	190	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164856	47164856	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1278528667	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	58	186	1	ENST00000409792.3:c.1270C>T	p.Arg424Ter	p.R424*	ENST00000409792	NM_014159.6	424	Cga/Tga	3/21	1	2	FACETS	0.905	0.781	1	0.905	0.781	1	CLONAL	1	TRUE	1	0.334712563941208	2		187	383	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67459125	67459125	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	139	559	1	ENST00000327367.4:c.545del	p.Pro182LeufsTer4	p.P182Lfs*4	ENST00000327367	NM_005902.3	181	Ccc/cc	4/9	1	2	FACETS	0.967	0.88	1	0.967	0.88	1	CLONAL	1	TRUE	1	0.334712563941208	2		560	859	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290180	15290180	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371437217	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	110	407	0	ENST00000263388.2:c.3455C>T	p.Thr1152Met	p.T1152M	ENST00000263388	NM_000435.2	1152	aCg/aTg	21/33	1	2	FACETS	0.964	0.867	1	0.964	0.867	1	CLONAL	1	TRUE	1	0.334712563941208	2		407	682	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508182	38508184	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs751811710	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	101	356	2	ENST00000254066.5:c.499_501del	p.Lys167del	p.K167del	ENST00000254066	NM_000964.3	164	AAG/-	5/9	1	2	FACETS	0.924	0.827	1	0.924	0.827	1	CLONAL	1	TRUE	1	0.334712563941208	2		358	653	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714649	52714649	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776781710	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	106	651	3	ENST00000322088.6:c.407C>T	p.Ala136Val	p.A136V	ENST00000322088	NM_014225.5	136	gCg/gTg	4/15	1	2	FACETS	0.957	0.859	1	0.957	0.859	1	CLONAL	1	TRUE	1	0.334712563941208	2		654	662	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138825	64138825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1388266879	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	155	436	0	ENST00000334205.4:c.2192G>A	p.Arg731Gln	p.R731Q	ENST00000334205	NM_003942.2	731	cGg/cAg	17/17	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.334712563941208	2		436	783	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	72	680	3	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	0.192396766268951	3	FACETS	0.955	0.836	1	0.477	0.418	0.542	INDETERMINATE	1	TRUE	1	0.334712563941208	3		683	526	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100934	27100934	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	67	452	1	ENST00000324856.7:c.4220del	p.Pro1407GlnfsTer74	p.P1407Qfs*74	ENST00000324856	NM_006015.4	1406	Ccc/cc	18/20	0.192396766268951	3	FACETS	0.776	0.675	0.886	0.388	0.337	0.443	INDETERMINATE	1	TRUE	1	0.334712563941208	3		453	602	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806180	1806181	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760502257	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	81	818	4	ENST00000260795.2:c.1206dup	p.Lys403GlnfsTer93	p.K403Qfs*93	ENST00000260795		400	agc/agCc	8/17	1	2	FACETS	0.625	0.55	0.705	0.625	0.55	0.705	SUBCLONAL	1	TRUE	1	0.334712563941208	2		822	775	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202148	67202148	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1265076720	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	84	394	2	ENST00000312629.5:c.1255del	p.Arg419GlyfsTer75	p.R419Gfs*75	ENST00000312629	NM_003952.2	417	agC/ag	14/15	1	2	FACETS	0.673	0.594	0.758	0.673	0.594	0.758	SUBCLONAL	1	TRUE	1	0.334712563941208	2		396	746	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149973	202149973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1272714323	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	218	370	1	ENST00000358485.4:c.1414C>T	p.Arg472Ter	p.R472*	ENST00000358485	NM_001080125.1	472	Cga/Tga	8/9	0.334712563941208	3	FACETS	0.934	0.871	0.999	0.934	0.871	0.999	CLONAL	2	TRUE	1	0.334712563941208	3		371	814	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692929	89692929	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1554898159	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	104	493	0	ENST00000371953.3:c.413A>G	p.Tyr138Cys	p.Y138C	ENST00000371953	NM_000314.4	138	tAt/tGt	5/9	0.334712563941208	1	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	0	0.334712563941208	1		493	514	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900164	101900164	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	48	206	0	ENST00000374994.4:c.598A>G	p.Thr200Ala	p.T200A	ENST00000374994	NM_004612.2	200	Aca/Gca	4/9	1	2	FACETS	0.891	0.757	1	0.891	0.757	1	CLONAL	1	TRUE	1	0.334712563941208	2		206	322	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45649954	45649954	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs186459476	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	75	411	2	ENST00000407780.3:c.881C>T	p.Pro294Leu	p.P294L	ENST00000407780	NM_001283052.1	294	cCg/cTg	6/7	1	2	FACETS	0.699	0.613	0.792	0.699	0.613	0.792	SUBCLONAL	1	TRUE	1	0.334712563941208	2		413	641	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939478	68939478	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139157434	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	87	386	3	ENST00000288368.4:c.463C>T	p.Arg155Trp	p.R155W	ENST00000288368	NM_024870.2	155	Cgg/Tgg	5/40	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.334712563941208	2		389	445	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845090	128845090	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs760210773	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	96	855	5	ENST00000249373.3:c.584T>C	p.Val195Ala	p.V195A	ENST00000249373	NM_005631.4	195	gTg/gCg	3/12	0.272899239882581	3	FACETS	0.709	0.63	0.793	0.236	0.21	0.265	SUBCLONAL	1	TRUE	0	0.334712563941208	3		860	945	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900268	101900270	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs863223830	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	64	262	0	ENST00000374994.4:c.705_707del	p.Ser236del	p.S236del	ENST00000374994	NM_004612.2	234	ttCTCc/ttc	4/9	1	2	FACETS	0.863	0.75	0.986	0.863	0.75	0.986	CLONAL	1	TRUE	1	0.334712563941208	2		262	443	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985875	60985875	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	75	408	0	ENST00000333681.4:c.25T>C	p.Tyr9His	p.Y9H	ENST00000333681		9	Tac/Cac	2/3	0.192396766268951	3	FACETS	0.8	0.701	0.907	0.4	0.35	0.454	INDETERMINATE	1	TRUE	1	0.334712563941208	3		408	654	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446040	49446040	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064210	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	144	759	1	ENST00000301067.7:c.1426G>A	p.Ala476Thr	p.A476T	ENST00000301067	NM_003482.3	476	Gca/Aca	10/54	1	2	FACETS	0.864	0.787	0.945	0.864	0.787	0.945	CLONAL	1	TRUE	1	0.334712563941208	2		760	996	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106333	27106333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201604768	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	153	395	0	ENST00000324856.7:c.5944G>A	p.Val1982Ile	p.V1982I	ENST00000324856	NM_006015.4	1982	Gtc/Atc	20/20	0.192396766268951	3	FACETS	1	0.988	1	0.743	0.681	0.808	INDETERMINATE	1	TRUE	1	0.334712563941208	3		395	718	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363396	40363396	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	144	430	0	ENST00000397332.2:c.833A>C	p.Asp278Ala	p.D278A	ENST00000397332	NM_001033082.2	278	gAt/gCt	3/3	0.192396766268951	3	FACETS	1	0.981	1	0.636	0.58	0.694	INDETERMINATE	1	TRUE	1	0.334712563941208	3		430	790	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812550	43812550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	125	423	0	ENST00000372470.3:c.1253C>T	p.Ala418Val	p.A418V	ENST00000372470	NM_005373.2	418	gCc/gTc	8/12	0.192396766268951	3	FACETS	1	0.934	1	0.52	0.471	0.573	INDETERMINATE	1	TRUE	1	0.334712563941208	3		423	838	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834205	156834205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	124	489	0	ENST00000524377.1:c.272G>A	p.Gly91Glu	p.G91E	ENST00000524377	NM_002529.3	91	gGg/gAg	2/17	1	2	FACETS	0.916	0.829	1	0.916	0.829	1	CLONAL	1	TRUE	1	0.334712563941208	2		489	809	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446279	70446279	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763447831	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	98	470	0	ENST00000373644.4:c.5219G>A	p.Arg1740His	p.R1740H	ENST00000373644	NM_030625.2	1740	cGc/cAc	11/12	0.334712563941208	1	FACETS	0.728	0.65	0.811	0.728	0.65	0.811	SUBCLONAL	1	TRUE	0	0.334712563941208	1		470	670	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392634	118392634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555053677	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	66	246	1	ENST00000534358.1:c.11666G>A	p.Arg3889Gln	p.R3889Q	ENST00000534358	NM_005933.3	3889	cGa/cAa	36/36	0.334667615243328	1	FACETS	0.922	0.805	1	0.922	0.805	1	CLONAL	1	TRUE	0	0.334712563941208	1		247	356	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46215214	46215214	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1433103583	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	19	253	1	ENST00000334344.6:c.652del	p.Ser218ProfsTer74	p.S218Pfs*74	ENST00000334344	NM_152641.2	217	Ttt/tt	6/21	1	2	FACETS	0.328	0.248	0.422	0.328	0.248	0.422	SUBCLONAL	1	TRUE	1	0.334712563941208	2		254	346	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244967	46244967	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	104	474	0	ENST00000334344.6:c.3065del	p.Pro1022HisfsTer38	p.P1022Hfs*38	ENST00000334344	NM_152641.2	1021	Ccc/cc	15/21	1	2	FACETS	0.787	0.704	0.874	0.787	0.704	0.874	SUBCLONAL	1	TRUE	1	0.334712563941208	2		474	790	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285703	46285703	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	30	224	0	ENST00000334344.6:c.5061+2T>C		p.X1687_splice	ENST00000334344	NM_152641.2	1687			1	2	FACETS	0.43	0.346	0.525	0.43	0.346	0.525	SUBCLONAL	1	TRUE	1	0.334712563941208	2		224	417	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444236	49444238	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	129	644	0	ENST00000301067.7:c.3133_3135del	p.Pro1045del	p.P1045del	ENST00000301067	NM_003482.3	1045	CCT/-	11/54	1	2	FACETS	0.869	0.787	0.955	0.869	0.787	0.955	CLONAL	1	TRUE	1	0.334712563941208	2		644	887	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219531	133219531	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138564205	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	79	328	0	ENST00000320574.5:c.4603G>A	p.Gly1535Ser	p.G1535S	ENST00000320574	NM_006231.2	1535	Ggc/Agc	36/49	1	2	FACETS	0.877	0.773	0.989	0.877	0.773	0.989	CLONAL	1	TRUE	1	0.334712563941208	2		328	538	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569717	95569717	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	35	136	0	ENST00000393063.1:c.4016A>G	p.His1339Arg	p.H1339R	ENST00000393063	NM_030621.3	1339	cAt/cGt	22/28	1	2	FACETS	0.734	0.604	0.878	0.734	0.604	0.878	SUBCLONAL	1	TRUE	1	0.334712563941208	2		136	285	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473602	67473602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223735	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	73	392	3	ENST00000327367.4:c.682G>A	p.Glu228Lys	p.E228K	ENST00000327367	NM_005902.3	228	Gag/Aag	6/9	1	2	FACETS	0.649	0.567	0.737	0.649	0.567	0.737	SUBCLONAL	1	TRUE	1	0.334712563941208	2		395	672	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831092	72831092	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757636909	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	47	197	0	ENST00000268489.5:c.5489G>A	p.Gly1830Asp	p.G1830D	ENST00000268489	NM_006885.3	1830	gGc/gAc	9/10	1	2	FACETS	0.704	0.595	0.823	0.704	0.595	0.823	SUBCLONAL	1	TRUE	1	0.334712563941208	2		197	399	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350772	89350775	+	frameshift_variant	Frame_Shift_Del	DEL	TTTG	TTTG	-	rs886039734	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	112	567	0	ENST00000301030.4:c.2175_2178del	p.Asn725LysfsTer23	p.N725Kfs*23	ENST00000301030	NM_001256183.1	725	aaCAAA/aa	9/13	1	2	FACETS	0.907	0.816	1	0.907	0.816	1	CLONAL	1	TRUE	1	0.334712563941208	2		567	738	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256182	41256182	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80357357	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	92	494	0	ENST00000357654.3:c.398G>A	p.Arg133His	p.R133H	ENST00000357654	NM_007294.3	133	cGt/cAt	6/23	1	2	FACETS	0.769	0.683	0.86	0.769	0.683	0.86	SUBCLONAL	1	TRUE	1	0.334712563941208	2		494	715	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39618774	39618774	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	78	262	0	ENST00000262039.4:c.1998A>T	p.Lys666Asn	p.K666N	ENST00000262039	NM_002647.2	666	aaA/aaT	18/25	0.192396766268951	3	FACETS	1	0.926	1	0.536	0.472	0.604	INDETERMINATE	1	TRUE	1	0.334712563941208	3		262	508	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604769	48604769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766833269	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	113	373	2	ENST00000342988.3:c.1591C>T	p.Arg531Trp	p.R531W	ENST00000342988	NM_005359.5	531	Cgg/Tgg	12/12	0.192396766268951	3	FACETS	1	0.954	1	0.55	0.496	0.608	INDETERMINATE	1	TRUE	1	0.334712563941208	3		375	716	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765501	41765501	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1006009457	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	110	449	0	ENST00000301178.4:c.2377C>T	p.Arg793Trp	p.R793W	ENST00000301178	NM_021913.4	793	Cgg/Tgg	20/20	1	2	FACETS	0.907	0.815	1	0.907	0.815	1	CLONAL	1	TRUE	1	0.334712563941208	2		449	725	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912095	50912095	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	101	610	0	ENST00000440232.2:c.1829T>C	p.Ile610Thr	p.I610T	ENST00000440232	NM_002691.3	610	aTc/aCc	15/27	1	2	FACETS	0.695	0.621	0.775	0.695	0.621	0.775	SUBCLONAL	1	TRUE	1	0.334712563941208	2		610	868	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99181228	99181228	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	32	207	0	ENST00000074304.5:c.2167+2T>C		p.X723_splice	ENST00000074304	NM_001134224.1	723			0.334712563941208	3	FACETS	0.602	0.489	0.729	0.301	0.244	0.365	SUBCLONAL	1	TRUE	1	0.334712563941208	3		207	371	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225367761	225367761	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	72	266	0	ENST00000264414.4:c.1406A>G	p.Lys469Arg	p.K469R	ENST00000264414	NM_003590.4	469	aAa/aGa	10/16	0.334712563941208	3	FACETS	1	0.958	1	0.608	0.533	0.688	CLONAL	1	TRUE	1	0.334712563941208	3		266	413	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069387	30069387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765540111	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	73	361	0	ENST00000338641.4:c.1252C>T	p.Arg418Cys	p.R418C	ENST00000338641	NM_000268.3	418	Cgc/Tgc	12/16	1	2	FACETS	0.797	0.698	0.904	0.797	0.698	0.904	CLONAL	1	TRUE	1	0.334712563941208	2		361	547	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200113	128200113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906629	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	61	515	0	ENST00000341105.2:c.1192C>T	p.Arg398Trp	p.R398W	ENST00000341105	NM_032638.4	398	Cgg/Tgg	6/6	1	2	FACETS	0.532	0.458	0.612	0.532	0.458	0.612	SUBCLONAL	1	TRUE	1	0.334712563941208	2		515	685	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807396	1807396	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	77	387	2	ENST00000260795.2:c.1645G>A	p.Gly549Arg	p.G549R	ENST00000260795		549	Ggg/Agg	11/17	1	2	FACETS	0.806	0.708	0.91	0.806	0.708	0.91	CLONAL	1	TRUE	1	0.334712563941208	2		389	571	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535375	66535375	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	75	458	3	ENST00000273854.3:c.86C>T	p.Ala29Val	p.A29V	ENST00000273854	NM_004439.5	29	gCc/gTc	1/18	1	2	FACETS	0.64	0.561	0.726	0.64	0.561	0.726	SUBCLONAL	1	TRUE	1	0.334712563941208	2		461	700	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542581	187542581	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	89	397	0	ENST00000441802.2:c.5159T>C	p.Ile1720Thr	p.I1720T	ENST00000441802	NM_005245.3	1720	aTc/aCc	10/27	1	2	FACETS	0.915	0.813	1	0.915	0.813	1	CLONAL	1	TRUE	1	0.334712563941208	2		397	581	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590478	67590478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	81	266	1	ENST00000274335.5:c.1540C>T	p.Arg514Cys	p.R514C	ENST00000274335		514	Cgt/Tgt	11/15	1	2	FACETS	0.97	0.857	1	0.97	0.857	1	CLONAL	1	TRUE	1	0.334712563941208	2		267	499	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449492	149449492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	68	356	0	ENST00000286301.3:c.1454G>A	p.Cys485Tyr	p.C485Y	ENST00000286301	NM_005211.3	485	tGc/tAc	10/22	1	2	FACETS	0.647	0.563	0.738	0.647	0.563	0.738	SUBCLONAL	1	TRUE	1	0.334712563941208	2		356	628	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397186	397186	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774593906	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	45	330	0	ENST00000380956.4:c.571C>T	p.Pro191Ser	p.P191S	ENST00000380956	NM_001195286.1	191	Ccg/Tcg	5/9	NA	2	FACETS	0.464	0.39	0.547			1	INDETERMINATE	1	TRUE	NA	0.334712563941208	2		330	579	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709122	117709122	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	83	399	0	ENST00000368508.3:c.1835T>C	p.Val612Ala	p.V612A	ENST00000368508	NM_002944.2	612	gTg/gCg	13/43	1	2	FACETS	0.873	0.772	0.981	0.873	0.772	0.981	CLONAL	1	TRUE	1	0.334712563941208	2		399	568	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528735	157528735	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	72	334	0	ENST00000346085.5:c.6460G>A	p.Gly2154Arg	p.G2154R	ENST00000346085	NM_020732.3	2154	Gga/Aga	20/20	1	2	FACETS	0.752	0.658	0.854	0.752	0.658	0.854	SUBCLONAL	1	TRUE	1	0.334712563941208	2		334	572	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983910	2983910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	86	497	0	ENST00000396946.4:c.620G>A	p.Arg207His	p.R207H	ENST00000396946	NM_032415.4	207	cGc/cAc	5/25	NA	2	FACETS	0.584	0.516	0.657			1	INDETERMINATE	1	TRUE	NA	0.334712563941208	2		497	880	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162868	38162868	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201879366	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	183	539	1	ENST00000317025.8:c.2338C>T	p.Arg780Cys	p.R780C	ENST00000317025	NM_023034.1	780	Cgc/Tgc	13/24	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.334712563941208	2		540	984	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862878	117862878	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	113	452	0	ENST00000297338.2:c.1599del	p.Glu534LysfsTer78	p.E534Kfs*78	ENST00000297338	NM_006265.2	533	aaA/aa	12/14	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.334712563941208	2		452	630	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197438	27197439	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	99	737	1	ENST00000380036.4:c.1756dup	p.Ser586LysfsTer2	p.S586Kfs*2	ENST00000380036	NM_000459.3	584	caa/cAaa	12/23	1	2	FACETS	0.735	0.656	0.819	0.735	0.656	0.819	SUBCLONAL	1	TRUE	1	0.334712563941208	2		738	805	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127916227	127916227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	76	425	1	ENST00000373547.4:c.417G>A	p.Trp139Ter	p.W139*	ENST00000373547	NM_002721.4	139	tgG/tgA	5/7	1	2	FACETS	0.872	0.766	0.985	0.872	0.766	0.985	CLONAL	1	TRUE	1	0.334712563941208	2		426	521	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759890	133759890	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	70	479	0	ENST00000318560.5:c.2213G>T	p.Arg738Leu	p.R738L	ENST00000318560	NM_005157.4	738	cGg/cTg	11/11	1	2	FACETS	0.579	0.504	0.659	0.579	0.504	0.659	SUBCLONAL	1	TRUE	1	0.334712563941208	2		479	723	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937722	44937722	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	47	434	0	ENST00000377967.4:c.2910A>G	p.Ile970Met	p.I970M	ENST00000377967	NM_021140.2	970	atA/atG	19/29	0.334712563941208	1	FACETS	0.517	0.437	0.606	0.517	0.437	0.606	SUBCLONAL	1	TRUE	0	0.334712563941208	1		434	452	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006864	47006864	+	5_prime_UTR_variant	5'UTR	SNP	G	G	A	novel	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	147	473	0	ENST00000377604.3:c.-17G>A		p.*6*	ENST00000377604	NM_001204468.1	-/852		2/24	0.334712563941208	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.334712563941208	1		473	664	SUCCESS
AR	367	MSKCC	GRCh37	X	66765613	66765613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775392428	NA	P-0016616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	112	608	2	ENST00000374690.3:c.625G>A	p.Gly209Arg	p.G209R	ENST00000374690	NM_000044.3	209	Ggg/Agg	1/8	0.219173999640734	1	FACETS	0.614	0.552	0.681	0.614	0.552	0.681	SUBCLONAL	1	TRUE	0	0.334712563941208	1		610	907	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	77	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.811	0.711	0.92	0.811	0.711	0.92	CLONAL	1	TRUE	1	0.21789256362199	2		436	871	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0016685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	99	737	1	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	0.21789256362199	1	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	0	0.21789256362199	1		738	806	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155027	108155027	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1453429915	NA	P-0016685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	47	612	0	ENST00000278616.4:c.3820C>T	p.Gln1274Ter	p.Q1274*	ENST00000278616	NM_000051.3	1274	Cag/Tag	26/63	1	2	FACETS	0.673	0.567	0.79	0.673	0.567	0.79	SUBCLONAL	1	TRUE	1	0.21789256362199	2		612	641	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597486	28597486	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0016685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	77	696	0	ENST00000241453.7:c.2418+1G>T		p.X806_splice	ENST00000241453	NM_004119.2	806			0.21789256362199	1	FACETS	0.846	0.742	0.959	0.846	0.742	0.959	CLONAL	1	TRUE	0	0.21789256362199	1		696	744	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356361	66356361	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772108237	NA	P-0016685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	63	586	0	ENST00000273854.3:c.1136C>T	p.Pro379Leu	p.P379L	ENST00000273854	NM_004439.5	379	cCg/cTg	5/18	0.21789256362199	1	FACETS	0.856	0.74	0.982	0.856	0.74	0.982	CLONAL	1	TRUE	0	0.21789256362199	1		586	602	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139873	55139873	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs866988382	NA	P-0016697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	173	426	0	ENST00000257290.5:c.1534C>T	p.Arg512Ter	p.R512*	ENST00000257290	NM_006206.4	512	Cga/Tga	10/23	1	2	FACETS	0.958	0.887	1	0.958	0.887	1	CLONAL	1	TRUE	1	0.657891362682268	2		426	549	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1040408	1040408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370272002	NA	P-0016731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	185	1111	1	ENST00000358495.3:c.164G>A	p.Arg55His	p.R55H	ENST00000358495	NM_134424.2	55	cGc/cAc	3/12	NA	2	FACETS	0.757	0.703	0.813			1	INDETERMINATE	1	TRUE	NA	0.791813610233517	2		1112	617	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980849	40980849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs548511212	NA	P-0016731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	218	998	4	ENST00000373198.4:c.1637G>A	p.Arg546Gln	p.R546Q	ENST00000373198	NM_133170.3	546	cGg/cAg	10/32	1	2	FACETS	0.987	0.925	1	0.987	0.925	1	CLONAL	1	TRUE	1	0.791813610233517	2		1002	558	SUCCESS
APC	324	MSKCC	GRCh37	5	112175651	112175651	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	202	908	0	ENST00000257430.4:c.4364del	p.Asn1455IlefsTer18	p.N1455Ifs*18	ENST00000257430	NM_000038.5	1454	Aaa/aa	16/16	0.791813610233517	1	FACETS	0.915	0.866	0.963	0.915	0.866	0.963	CLONAL	1	TRUE	0	0.791813610233517	1		908	337	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430823	78430830	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTGAAC	TCTTGAAC	-	novel	NA	P-0016731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	216	1294	0	ENST00000370768.2:c.559_566del	p.Val187AsnfsTer6	p.V187Nfs*6	ENST00000370768	NM_003902.3	187	GTTCAAGAa/a	8/20	1	2	FACETS	0.723	0.674	0.773	0.723	0.674	0.773	SUBCLONAL	1	TRUE	1	0.791813610233517	2		1294	755	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223947	36223955	+	inframe_deletion	In_Frame_Del	DEL	TCCCAGGGG	TCCCAGGGG	-	novel	NA	P-0016731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	75	1838	0	ENST00000222270.7:c.6497_6505del	p.Leu2166_Ala2169delinsPro	p.L2166_A2169delinsP	ENST00000222270	NM_014727.1	2166	cTCCCAGGGGcc/ccc	28/37	1	2	FACETS	0.201	0.175	0.229	0.201	0.175	0.229	SUBCLONAL	1	TRUE	1	0.791813610233517	2		1838	942	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409211	31409211	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	228	1210	0	ENST00000344624.3:c.3806G>C	p.Cys1269Ser	p.C1269S	ENST00000344624		1269	tGc/tCc	30/33	1	2	FACETS	0.976	0.916	1	0.976	0.916	1	CLONAL	1	TRUE	1	0.791813610233517	2		1210	590	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151947017	151947017	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	161	840	0	ENST00000262189.6:c.1757A>G	p.Glu586Gly	p.E586G	ENST00000262189	NM_170606.2	586	gAg/gGg	13/59	0.791813610233517	3	FACETS	0.916	0.843	0.99	0.458	0.421	0.495	CLONAL	1	TRUE	1	0.791813610233517	3		840	620	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685281	89685281	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1060500116	NA	P-0016768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	116	395	0	ENST00000371953.3:c.176C>G	p.Ser59Ter	p.S59*	ENST00000371953	NM_000314.4	59	tCa/tGa	3/9	0.52815761361541	6	FACETS	0.857	0.786	0.93	0.857	0.786	0.93	INDETERMINATE	3	FALSE	3	0.943665728701553	6		395	276	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061212	38061235	+	inframe_deletion	In_Frame_Del	DEL	GTAGCAGCCGTTCTCGAACATGTT	GTAGCAGCCGTTCTCGAACATGTT	-	novel	NA	P-0016768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	178	487	1	ENST00000250448.2:c.754_777del	p.Asn252_Tyr259del	p.N252_Y259del	ENST00000250448	NM_004496.3	252	AACATGTTCGAGAACGGCTGCTAC/-	2/2	0.70133854451686	6	FACETS	0.926	0.866	0.987	0.926	0.866	0.987	CLONAL	3	FALSE	3	0.943665728701553	6		488	392	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830184	72830184	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	32	289	0	ENST00000268489.5:c.6397C>T	p.Gln2133Ter	p.Q2133*	ENST00000268489	NM_006885.3	2133	Cag/Tag	9/10	0.906367792754651	2	FACETS	0.827	0.695	0.964	0.414	0.347	0.482	CLONAL	1	FALSE	0	0.943665728701553	2		289	82	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877127	89877127	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	49	604	0	ENST00000389301.3:c.510A>T	p.Leu170Phe	p.L170F	ENST00000389301	NM_000135.2	170	ttA/ttT	5/43	0.906367792754651	2	FACETS	0.895	0.782	1	0.448	0.391	0.506	CLONAL	1	FALSE	0	0.943665728701553	2		604	116	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57567446	57567446	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	81	451	0	ENST00000316660.6:c.37A>T	p.Ser13Cys	p.S13C	ENST00000316660	NM_021127.2	13	Agc/Tgc	1/2	0.70133854451686	6	FACETS	1	0.97	1	0.431	0.382	0.483	CLONAL	1	FALSE	3	0.943665728701553	6		451	383	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038130	128038130	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	88	488	0	ENST00000285398.2:c.1420G>C	p.Asp474His	p.D474H	ENST00000285398	NM_000122.1	474	Gat/Cat	9/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.943665728701553	2		488	168	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670646	134670646	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	104	733	0	ENST00000398015.3:c.557T>C	p.Leu186Pro	p.L186P	ENST00000398015	NM_004441.4	186	cTt/cCt	3/16	0.943665728701553	7	FACETS	0.921	0.831	1	0.46	0.415	0.508	CLONAL	2	FALSE	3	0.943665728701553	7		733	402	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803755	1803755	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	novel	NA	P-0016768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	138	531	1	ENST00000260795.2:c.930+3G>A		p.X310_splice	ENST00000260795		310			0.921335177270766	4	FACETS	1	0.962	1			1	CLONAL	2	FALSE	NA	0.943665728701553	4		532	270	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393371	139393374	+	missense_variant	Missense_Mutation	ONP	TGTT	TGTT	CAGG	novel	NA	P-0016768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	54	676	1	ENST00000277541.6:c.6157_6160delinsCCTG	p.Asn2053_Lys2054delinsProGlu	p.N2053_K2054delinsPE	ENST00000277541	NM_017617.3	2053	AACAaa/CCTGaa	33/34	0.449403680164788	6	FACETS	1	0.93	1	0.379	0.325	0.436	INDETERMINATE	1	FALSE	3	0.943665728701553	6		677	291	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417454	139417454	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	150	836	0	ENST00000277541.6:c.590A>T	p.Asn197Ile	p.N197I	ENST00000277541	NM_017617.3	197	aAc/aTc	4/34	0.449403680164788	6	FACETS	0.859	0.797	0.923	0.859	0.797	0.923	INDETERMINATE	3	FALSE	3	0.943665728701553	6		836	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0016812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	253	610	2	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.482698512521681	1	FACETS	0.97	0.915	1	0.97	0.915	1	CLONAL	1	TRUE	0	0.602339328496162	1		612	605	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795016	42795016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150818299	NA	P-0016812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	355	847	1	ENST00000575354.2:c.2096C>T	p.Ala699Val	p.A699V	ENST00000575354	NM_015125.3	699	gCg/gTg	10/20	1	2	FACETS	0.951	0.901	1	0.951	0.901	1	CLONAL	1	TRUE	1	0.602339328496162	2		848	1239	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48921970	48921971	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0016812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	259	524	0	ENST00000267163.4:c.511_512dup	p.Ile172LeufsTer4	p.I172Lfs*4	ENST00000267163	NM_000321.2	170	-/CT	5/27	0.585967247851998	1	FACETS	0.988	0.933	1	0.988	0.933	1	CLONAL	1	TRUE	0	0.602339328496162	1		524	608	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921798	111921798	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	193	396	0	ENST00000393256.3:c.587G>A	p.Arg196Lys	p.R196K	ENST00000393256	NM_006538.4	196	aGa/aAa	4/4	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.602339328496162	2		396	586	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0017052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	37	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.348989431594648	2	FACETS	0.26	0.213	0.313	0.13	0.106	0.157	SUBCLONAL	1	FALSE	0	0.348989431594648	2		436	815	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0017052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	48	704	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.314284121411759	2	FACETS	0.395	0.333	0.464	0.198	0.166	0.232	SUBCLONAL	1	FALSE	0	0.348989431594648	2		705	696	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551301	141551301	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	58	684	0	ENST00000220592.5:c.1996T>A	p.Phe666Ile	p.F666I	ENST00000220592	NM_012154.3	666	Ttc/Atc	15/19	0.319035527501481	2	FACETS	0.327	0.279	0.378	0.163	0.139	0.189	SUBCLONAL	1	FALSE	0	0.348989431594648	2		684	1018	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	155	671	0	ENST00000206249.3:c.1610A>G	p.Tyr537Cys	p.Y537C	ENST00000206249	NM_000125.3	537	tAt/tGt	8/8	0.286889389796456	3	FACETS	0.87	0.798	0.945	0.58	0.532	0.63	CLONAL	2	TRUE	0	0.286889389796456	3		671	710	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680556	241680562	+	frameshift_variant	Frame_Shift_Del	DEL	CATTTGG	CATTTGG	-	novel	NA	P-0017116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	74	748	0	ENST00000366560.3:c.187_193del	p.Pro63IlefsTer9	p.P63Ifs*9	ENST00000366560	NM_000143.3	63	CCAAATGat/at	2/10	0.286889389796456	4	FACETS	0.625	0.545	0.712	0.208	0.181	0.238	SUBCLONAL	1	TRUE	1	0.286889389796456	4		748	1062	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104264050	104264050	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	111	880	0	ENST00000369902.3:c.141C>G	p.Asp47Glu	p.D47E	ENST00000369902	NM_016169.3	47	gaC/gaG	1/12	0.27204929327317	3	FACETS	0.837	0.751	0.929	0.419	0.375	0.465	CLONAL	1	TRUE	1	0.286889389796456	3		880	1057	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871000	12871078	+	frameshift_variant	Frame_Shift_Del	DEL	GGCAAGAGGTGGAGAAGGGCAGCTTGCCCGAGTTCTACTACAGACCCCCGCGGCCCCCCAAAGGTGCCTGCAAGGTGCC	GGCAAGAGGTGGAGAAGGGCAGCTTGCCCGAGTTCTACTACAGACCCCCGCGGCCCCCCAAAGGTGCCTGCAAGGTGCC	-	novel	NA	P-0017116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	35	463	0	ENST00000228872.4:c.230_308del	p.Gln77ArgfsTer16	p.Q77Rfs*16	ENST00000228872	NM_004064.3	76	tGGCAAGAGGTGGAGAAGGGCAGCTTGCCCGAGTTCTACTACAGACCCCCGCGGCCCCCCAAAGGTGCCTGCAAGGTGCCg/tg	1/3	0.280076522207723	2	FACETS	0.58	0.475	0.697	0.29	0.237	0.349	SUBCLONAL	1	TRUE	0	0.286889389796456	2		463	421	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245525	133245525	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	48	469	0	ENST00000320574.5:c.1795G>C	p.Val599Leu	p.V599L	ENST00000320574	NM_006231.2	599	Gtg/Ctg	17/49	0.20139150603912	5	FACETS	0.796	0.672	0.933	0.265	0.224	0.311	CLONAL	1	TRUE	2	0.286889389796456	5		469	601	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740675	58740675	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1690	128	1049	0	ENST00000305921.3:c.1580A>G	p.Glu527Gly	p.E527G	ENST00000305921	NM_003620.3	527	gAa/gGa	6/6	0.286889389796456	8	FACETS	0.913	0.824	1			1	CLONAL	1	TRUE	NA	0.286889389796456	8		1049	1818	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265616	152265616	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	70	509	0	ENST00000206249.3:c.1069A>G	p.Met357Val	p.M357V	ENST00000206249	NM_000125.3	357	Atg/Gtg	4/8	0.286889389796456	3	FACETS	1	0.881	1	0.336	0.293	0.383	CLONAL	1	TRUE	0	0.286889389796456	3		509	553	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397765	116397765	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	116	937	0	ENST00000397752.3:c.2039A>G	p.Asn680Ser	p.N680S	ENST00000397752	NM_000245.2	680	aAt/aGt	8/21	0.20139150603912	5	FACETS	1	0.917	1	0.341	0.306	0.378	CLONAL	1	TRUE	2	0.286889389796456	5		937	1131	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229456	98229456	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	46	440	0	ENST00000331920.6:c.2502G>C	p.Leu834Phe	p.L834F	ENST00000331920	NM_000264.3	834	ttG/ttC	15/24	0.262021770961739	4	FACETS	0.674	0.567	0.793	0.337	0.283	0.397	SUBCLONAL	1	TRUE	2	0.286889389796456	4		440	612	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411197	63411197	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	76	714	0	ENST00000330258.3:c.1970G>T	p.Arg657Met	p.R657M	ENST00000330258	NM_152424.3	657	aGg/aTg	2/2	0.18050043976749	3	FACETS	0.826	0.724	0.937			1	CLONAL	1	TRUE	NA	0.286889389796456	3		714	733	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864942	57864942	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	207	582	0	ENST00000228682.2:c.2419G>C	p.Glu807Gln	p.E807Q	ENST00000228682	NM_005269.2	807	Gaa/Caa	12/12	0.288902871034671	3	FACETS	0.966	0.9	1	0.966	0.9	1	CLONAL	2	TRUE	1	0.343994059984613	3		582	730	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546074	41546074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1375233087	NA	P-0017240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	185	658	0	ENST00000263253.7:c.2689G>A	p.Val897Met	p.V897M	ENST00000263253	NM_001429.3	897	Gtg/Atg	14/31	1	2	FACETS	0.974	0.898	1	0.974	0.898	1	CLONAL	1	TRUE	1	0.343994059984613	2		658	1104	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945208	44945208	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	80	283	0	ENST00000377967.4:c.3533del	p.Asn1178MetfsTer9	p.N1178Mfs*9	ENST00000377967	NM_021140.2	1178	Aat/at	24/29	1	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.343994059984613	1		283	290	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0017476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	34	495	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.951	0.781	1	0.951	0.781	1	CLONAL	1	TRUE	1	0.26	2		495	275	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100999	41100999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1371429276	NA	P-0017476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	43	285	2	ENST00000373198.4:c.1357C>T	p.Arg453Cys	p.R453C	ENST00000373198	NM_133170.3	453	Cgc/Tgc	8/32	0.161087907752156	3	FACETS	1	0.918	1	0.577	0.484	0.678	CLONAL	1	TRUE	1	0.26	3		287	324	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587781702	NA	P-0017476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	45	344	0	ENST00000269305.4:c.920-1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.3	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.26	1		344	229	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950061	38950061	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	151	309	0	ENST00000357387.3:c.3889C>T	p.Pro1297Ser	p.P1297S	ENST00000357387	NM_152756.3	1297	Cct/Tct	31/38	0.193370870181806	2	FACETS	0.605	0.553	0.66	0.303	0.276	0.33	INDETERMINATE	1	TRUE	0	0.5617007481768	2		309	888	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs11575997	NA	P-0017599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	478	345	0	ENST00000269305.4:c.993+1G>T		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.5617007481768	2	FACETS	0.98	0.944	1	0.98	0.944	1	CLONAL	2	TRUE	0	0.5617007481768	2		345	868	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022291	31022291	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	649	608	0	ENST00000375687.4:c.1776G>T	p.Gln592His	p.Q592H	ENST00000375687	NM_015338.5	592	caG/caT	13/13	0.433407453443797	3	FACETS	0.891	0.858	0.924	0.891	0.858	0.924	CLONAL	2	TRUE	1	0.5617007481768	3		608	1661	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022736	31022736	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	340	284	0	ENST00000375687.4:c.2221G>A	p.Asp741Asn	p.D741N	ENST00000375687	NM_015338.5	741	Gat/Aat	13/13	0.433407453443797	3	FACETS	0.906	0.861	0.951	0.906	0.861	0.951	CLONAL	2	TRUE	1	0.5617007481768	3		284	856	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023354	31023354	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	360	292	0	ENST00000375687.4:c.2839G>C	p.Glu947Gln	p.E947Q	ENST00000375687	NM_015338.5	947	Gag/Cag	13/13	0.433407453443797	3	FACETS	0.896	0.853	0.94	0.896	0.853	0.94	CLONAL	2	TRUE	1	0.5617007481768	3		292	916	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942833	44942833	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	529	418	0	ENST00000377967.4:c.3414del	p.Pro1139GlnfsTer19	p.P1139Qfs*19	ENST00000377967	NM_021140.2	1138	gTt/gt	23/29	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.5617007481768	1		418	945	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121531	108121531	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779815	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	22	364	2	ENST00000278616.4:c.1339C>T	p.Arg447Ter	p.R447*	ENST00000278616	NM_000051.3	447	Cga/Tga	10/63	1	2	FACETS	0.156	0.12	0.197	0.156	0.12	0.197	SUBCLONAL	1	TRUE	1	0.76	2		366	371	SUCCESS
BLM	641	MSKCC	GRCh37	15	91328183	91328183	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779884	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	125	395	0	ENST00000355112.3:c.2695C>T	p.Arg899Ter	p.R899*	ENST00000355112	NM_000057.2	899	Cga/Tga	14/22	0.11703264212386	1	FACETS	0.535	0.489	0.583	0.535	0.489	0.583	INDETERMINATE	1	TRUE	0	0.76	1		395	381	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041117	42041117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747757361	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	343	1290	1	ENST00000219905.7:c.5495G>A	p.Arg1832Gln	p.R1832Q	ENST00000219905	NM_001164273.1	1832	cGg/cAg	16/24	0.11703264212386	1	FACETS	0.548	0.519	0.577	0.548	0.519	0.577	INDETERMINATE	1	TRUE	0	0.76	1		1291	1021	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442579	52442579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1312611941	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	14	257	0	ENST00000460680.1:c.166C>T	p.Arg56Cys	p.R56C	ENST00000460680	NM_004656.3	56	Cgc/Tgc	4/17	1	2	FACETS	0.159	0.114	0.212	0.159	0.114	0.212	SUBCLONAL	1	TRUE	1	0.76	2		257	232	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	314	642	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.76	2		642	800	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806180	1806181	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760502257	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	233	818	4	ENST00000260795.2:c.1206dup	p.Lys403GlnfsTer93	p.K403Qfs*93	ENST00000260795		400	agc/agCc	8/17	1	2	FACETS	0.908	0.852	0.966	0.908	0.852	0.966	CLONAL	1	TRUE	1	0.76	2		822	675	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073928	8073928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746056102	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	70	1375	0	ENST00000377482.5:c.731G>A	p.Arg244Gln	p.R244Q	ENST00000377482	NM_018948.3	244	cGa/cAa	4/4	1	2	FACETS	0.152	0.132	0.174	0.152	0.132	0.174	SUBCLONAL	1	TRUE	1	0.76	2		1375	1210	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775787	9775787	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	120	407	0	ENST00000377346.4:c.330G>T	p.Lys110Asn	p.K110N	ENST00000377346	NM_005026.3	110	aaG/aaT	4/24	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.76	2		407	315	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781832	9781832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756589761	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	179	619	0	ENST00000377346.4:c.1969G>A	p.Val657Met	p.V657M	ENST00000377346	NM_005026.3	657	Gtg/Atg	16/24	1	2	FACETS	0.874	0.811	0.938	0.874	0.811	0.938	CLONAL	1	TRUE	1	0.76	2		619	539	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784899	9784899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768257375	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	265	745	3	ENST00000377346.4:c.2902C>T	p.Arg968Trp	p.R968W	ENST00000377346	NM_005026.3	968	Cgg/Tgg	23/24	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.76	2		748	598	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190747	11190747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759603938	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	162	415	2	ENST00000361445.4:c.5452C>T	p.Arg1818Cys	p.R1818C	ENST00000361445	NM_004958.3	1818	Cgt/Tgt	39/58	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.76	2		417	418	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294267	11294267	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1187856229	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	131	460	2	ENST00000361445.4:c.2264G>A	p.Arg755His	p.R755H	ENST00000361445	NM_004958.3	755	cGc/cAc	14/58	1	2	FACETS	0.858	0.786	0.931	0.858	0.786	0.931	CLONAL	1	TRUE	1	0.76	2		462	402	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298591	11298591	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	128	463	1	ENST00000361445.4:c.1870C>A	p.Arg624Ser	p.R624S	ENST00000361445	NM_004958.3	624	Cgc/Agc	12/58	1	2	FACETS	0.903	0.827	0.981	0.903	0.827	0.981	CLONAL	1	TRUE	1	0.76	2		464	373	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242646	16242646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	133	416	0	ENST00000375759.3:c.1267C>T	p.Arg423Cys	p.R423C	ENST00000375759	NM_015001.2	423	Cgc/Tgc	6/15	1	2	FACETS	0.914	0.839	0.991	0.914	0.839	0.991	CLONAL	1	TRUE	1	0.76	2		416	383	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254593	16254593	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	156	487	0	ENST00000375759.3:c.1858C>T	p.Arg620Ter	p.R620*	ENST00000375759	NM_015001.2	620	Cga/Tga	11/15	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.76	2		487	401	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256492	16256492	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343994383	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	145	469	0	ENST00000375759.3:c.3757G>A	p.Glu1253Lys	p.E1253K	ENST00000375759	NM_015001.2	1253	Gaa/Aaa	11/15	1	2	FACETS	0.971	0.896	1	0.971	0.896	1	CLONAL	1	TRUE	1	0.76	2		469	393	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257520	16257521	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	124	393	0	ENST00000375759.3:c.4788dup	p.Glu1597ArgfsTer12	p.E1597Rfs*12	ENST00000375759	NM_015001.2	1595	-/A	11/15	1	2	FACETS	0.837	0.764	0.911	0.837	0.764	0.911	CLONAL	1	TRUE	1	0.76	2		393	390	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258862	16258862	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs566082553	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	175	539	0	ENST00000375759.3:c.6127C>T	p.Arg2043Cys	p.R2043C	ENST00000375759	NM_015001.2	2043	Cgt/Tgt	11/15	1	2	FACETS	0.919	0.853	0.986	0.919	0.853	0.986	CLONAL	1	TRUE	1	0.76	2		539	501	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263839	16263839	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs549789481	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	301	929	0	ENST00000375759.3:c.10208G>A	p.Arg3403His	p.R3403H	ENST00000375759	NM_015001.2	3403	cGc/cAc	12/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.76	2		929	746	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796925	45796925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779701238	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	154	534	3	ENST00000450313.1:c.1405G>A	p.Val469Ile	p.V469I	ENST00000450313	NM_012222.2	469	Gta/Ata	14/16	1	2	FACETS	0.907	0.837	0.978	0.907	0.837	0.978	CLONAL	1	TRUE	1	0.76	2		537	447	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743836	46743836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1287557291	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	191	623	1	ENST00000371975.4:c.2126G>A	p.Cys709Tyr	p.C709Y	ENST00000371975	NM_003579.3	709	tGc/tAc	18/18	1	2	FACETS	0.959	0.894	1	0.959	0.894	1	CLONAL	1	TRUE	1	0.76	2		624	524	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439848	51439848	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	54	211	0	ENST00000262662.1:c.413A>G	p.Asp138Gly	p.D138G	ENST00000262662		138	gAc/gGc	4/4	1	2	FACETS	0.866	0.755	0.983	0.866	0.755	0.983	CLONAL	1	TRUE	1	0.76	2		211	164	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165713	118165713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1278971822	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	16	297	1	ENST00000369448.3:c.223G>A	p.Ala75Thr	p.A75T	ENST00000369448	NM_017709.3	75	Gca/Aca	2/2	1	2	FACETS	0.159	0.117	0.209	0.159	0.117	0.209	SUBCLONAL	1	TRUE	1	0.76	2		298	265	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166127	118166127	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	143	473	0	ENST00000369448.3:c.637G>A	p.Glu213Lys	p.E213K	ENST00000369448	NM_017709.3	213	Gag/Aag	2/2	1	2	FACETS	0.907	0.835	0.98	0.907	0.835	0.98	CLONAL	1	TRUE	1	0.76	2		473	415	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471739	120471739	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138832326	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	198	640	1	ENST00000256646.2:c.3752G>A	p.Arg1251His	p.R1251H	ENST00000256646	NM_024408.3	1251	cGc/cAc	23/34	1	2	FACETS	0.916	0.854	0.979	0.916	0.854	0.979	CLONAL	1	TRUE	1	0.76	2		641	569	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161332147	161332147	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	123	449	0	ENST00000367975.2:c.434T>G	p.Ile145Ser	p.I145S	ENST00000367975	NM_003001.3	145	aTt/aGt	6/6	1	2	FACETS	0.88	0.804	0.957	0.88	0.804	0.957	CLONAL	1	TRUE	1	0.76	2		449	368	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746018	162746018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	132	339	1	ENST00000367921.3:c.2141G>A	p.Arg714Gln	p.R714Q	ENST00000367921	NM_006182.2	714	cGa/cAa	16/18	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.76	2		340	343	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176085764	176085764	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	96	371	0	ENST00000367669.3:c.1022C>T	p.Ser341Phe	p.S341F	ENST00000367669	NM_022457.5	341	tCt/tTt	9/20	1	2	FACETS	0.754	0.679	0.833	0.754	0.679	0.833	SUBCLONAL	1	TRUE	1	0.76	2		371	335	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193181600	193181600	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	123	313	0	ENST00000367435.3:c.1147G>A	p.Asp383Asn	p.D383N	ENST00000367435	NM_024529.4	383	Gac/Aac	13/17	1	2	FACETS	0.996	0.913	1	0.996	0.913	1	CLONAL	1	TRUE	1	0.76	2		313	325	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652446	206652446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	192	517	0	ENST00000367120.3:c.1153G>A	p.Ala385Thr	p.A385T	ENST00000367120	NM_014002.3	385	Gcc/Acc	10/22	1	2	FACETS	0.983	0.917	1	0.983	0.917	1	CLONAL	1	TRUE	1	0.76	2		517	514	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945762	206945762	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772299982	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	102	293	0	ENST00000423557.1:c.19C>T	p.Leu7Phe	p.L7F	ENST00000423557	NM_000572.2	7	Ctc/Ttc	1/5	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.76	2		293	255	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851617	63851617	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	83	253	0	ENST00000279873.7:c.2395T>C	p.Ser799Pro	p.S799P	ENST00000279873	NM_032199.2	799	Tcc/Ccc	10/10	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.76	2		253	212	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852752	63852752	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	49	149	0	ENST00000279873.7:c.3530C>A	p.Ser1177Tyr	p.S1177Y	ENST00000279873	NM_032199.2	1177	tCc/tAc	10/10	1	2	FACETS	0.97	0.842	1	0.97	0.842	1	CLONAL	1	TRUE	1	0.76	2		149	133	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333531	70333531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	70	563	0	ENST00000373644.4:c.1436C>T	p.Ser479Leu	p.S479L	ENST00000373644	NM_030625.2	479	tCa/tTa	2/12	1	2	FACETS	0.386	0.337	0.439	0.386	0.337	0.439	SUBCLONAL	1	TRUE	1	0.76	2		563	477	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88635834	88635834	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759014147	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	87	409	0	ENST00000372037.3:c.59G>A	p.Arg20His	p.R20H	ENST00000372037	NM_004329.2	20	cGt/cAt	3/13	1	2	FACETS	0.694	0.62	0.771	0.694	0.62	0.771	SUBCLONAL	1	TRUE	1	0.76	2		409	330	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911638	114911638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1427214163	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	278	783	2	ENST00000543371.1:c.1156C>T	p.Arg386Trp	p.R386W	ENST00000543371	NM_001198531.1	386	Cgg/Tgg	10/14	1	2	FACETS	0.999	0.944	1	0.999	0.944	1	CLONAL	1	TRUE	1	0.76	2		785	732	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123353244	123353244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	183	577	0	ENST00000358487.5:c.88G>A	p.Asp30Asn	p.D30N	ENST00000358487	NM_000141.4	30	Gat/Aat	2/18	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.76	2		577	461	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533490	533490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554884772	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	191	599	0	ENST00000451590.1:c.413G>A	p.Gly138Asp	p.G138D	ENST00000451590	NM_001130442.1	138	gGc/gAc	4/5	1	2	FACETS	0.965	0.899	1	0.965	0.899	1	CLONAL	1	TRUE	1	0.76	2		599	521	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533881	533881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs727503093	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	182	559	0	ENST00000451590.1:c.175G>A	p.Ala59Thr	p.A59T	ENST00000451590	NM_001130442.1	59	Gcc/Acc	3/5	1	2	FACETS	0.904	0.84	0.969	0.904	0.84	0.969	CLONAL	1	TRUE	1	0.76	2		559	530	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154241	2154242	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755455183	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	134	711	1	ENST00000434045.2:c.686dup	p.Glu230ArgfsTer50	p.E230Rfs*50	ENST00000434045	NM_001127598.1	229	cca/ccCa	5/5	1	2	FACETS	0.763	0.699	0.83	0.763	0.699	0.83	SUBCLONAL	1	TRUE	1	0.76	2		712	462	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61213499	61213499	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	30	372	0	ENST00000301761.2:c.457C>A	p.Leu153Met	p.L153M	ENST00000301761	NM_017841.2	153	Ctg/Atg	4/4	1	2	FACETS	0.215	0.173	0.262	0.215	0.173	0.262	SUBCLONAL	1	TRUE	1	0.76	2		372	368	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138092	64138092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	146	388	2	ENST00000334205.4:c.2015C>T	p.Ser672Leu	p.S672L	ENST00000334205	NM_003942.2	672	tCg/tTg	16/17	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.76	2		390	358	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138899	64138899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200411554	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	131	389	2	ENST00000334205.4:c.2266G>A	p.Val756Ile	p.V756I	ENST00000334205	NM_003942.2	756	Gtc/Atc	17/17	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.76	2		391	327	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571820	64571820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770686655	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	525	1704	3	ENST00000312049.6:c.1819C>T	p.Arg607Cys	p.R607C	ENST00000312049	NM_130799.2	607	Cgc/Tgc	10/10	1	2	FACETS	0.946	0.906	0.985	0.946	0.906	0.985	CLONAL	1	TRUE	1	0.76	2		1707	1461	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572198	64572198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	303	640	2	ENST00000312049.6:c.1441C>T	p.Arg481Trp	p.R481W	ENST00000312049	NM_130799.2	481	Cgg/Tgg	10/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.76	2		642	671	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198887	67198887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113335412	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	189	638	1	ENST00000312629.5:c.358C>T	p.Arg120Trp	p.R120W	ENST00000312629	NM_003952.2	120	Cgg/Tgg	5/15	1	2	FACETS	0.88	0.819	0.943	0.88	0.819	0.943	CLONAL	1	TRUE	1	0.76	2		639	565	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201702	67201702	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373702089	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	187	676	0	ENST00000312629.5:c.1003G>A	p.Asp335Asn	p.D335N	ENST00000312629	NM_003952.2	335	Gac/Aac	12/15	1	2	FACETS	0.95	0.885	1	0.95	0.885	1	CLONAL	1	TRUE	1	0.76	2		676	518	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69456136	69456136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	253	816	3	ENST00000227507.2:c.55G>A	p.Asp19Asn	p.D19N	ENST00000227507	NM_053056.2	19	Gat/Aat	1/5	1	2	FACETS	0.921	0.866	0.977	0.921	0.866	0.977	CLONAL	1	TRUE	1	0.76	2		819	723	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999533	100999533	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	533	1648	1	ENST00000325455.5:c.269C>T	p.Ala90Val	p.A90V	ENST00000325455	NM_001202474.3	90	gCt/gTt	1/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.76	2		1649	1344	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141998	108141998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755896387	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	19	220	0	ENST00000278616.4:c.2942G>A	p.Arg981His	p.R981H	ENST00000278616	NM_000051.3	981	cGt/cAt	20/63	1	2	FACETS	0.198	0.15	0.254	0.198	0.15	0.254	SUBCLONAL	1	TRUE	1	0.76	2		220	253	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180958	108180958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1356309376	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	77	248	0	ENST00000278616.4:c.5834C>T	p.Ala1945Val	p.A1945V	ENST00000278616	NM_000051.3	1945	gCt/gTt	39/63	1	2	FACETS	0.921	0.823	1	0.921	0.823	1	CLONAL	1	TRUE	1	0.76	2		248	220	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186757	108186757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs864622251	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	149	463	0	ENST00000278616.4:c.6115G>A	p.Glu2039Lys	p.E2039K	ENST00000278616	NM_000051.3	2039	Gaa/Aaa	42/63	1	2	FACETS	0.836	0.77	0.904	0.836	0.77	0.904	CLONAL	1	TRUE	1	0.76	2		463	469	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216611	108216611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201958469	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	67	267	0	ENST00000278616.4:c.8560C>T	p.Arg2854Cys	p.R2854C	ENST00000278616	NM_000051.3	2854	Cgc/Tgc	58/63	1	2	FACETS	0.816	0.721	0.916	0.816	0.721	0.916	CLONAL	1	TRUE	1	0.76	2		267	216	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420184	420184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs546854883	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	20	435	0	ENST00000399788.2:c.3083C>T	p.Ala1028Val	p.A1028V	ENST00000399788	NM_001042603.1	1028	gCg/gTg	21/28	0.3	2	FACETS	0.136	0.104	0.175			1	INDETERMINATE	1	TRUE	NA	0.76	2		435	386	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023246	1023246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs184776294	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	81	268	0	ENST00000358495.3:c.1009G>A	p.Asp337Asn	p.D337N	ENST00000358495	NM_134424.2	337	Gat/Aat	11/12	0.3	2	FACETS	0.899	0.805	0.997			1	INDETERMINATE	1	TRUE	NA	0.76	2		268	237	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4388007	4388007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775067994	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	141	362	0	ENST00000261254.3:c.493C>T	p.Arg165Cys	p.R165C	ENST00000261254	NM_001759.3	165	Cgc/Tgc	3/5	0.3	2	FACETS	1	0.955	1			1	INDETERMINATE	1	TRUE	NA	0.76	2		362	354	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800946	18800946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1308410556	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	103	289	0	ENST00000266497.5:c.4322G>A	p.Gly1441Glu	p.G1441E	ENST00000266497		1441	gGa/gAa	31/31	1	2	FACETS	0.961	0.873	1	0.961	0.873	1	CLONAL	1	TRUE	1	0.76	2		289	282	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123836	46123837	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	84	200	0	ENST00000334344.6:c.109dup	p.Ile37AsnfsTer29	p.I37Nfs*29	ENST00000334344	NM_152641.2	34	-/A	2/21	1	2	FACETS	0.97	0.872	1	0.97	0.872	1	CLONAL	1	TRUE	1	0.76	2		200	228	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484292	50484292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746406610	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	248	696	0	ENST00000394963.4:c.1052G>A	p.Arg351His	p.R351H	ENST00000394963	NM_003076.4	351	cGt/cAt	9/13	1	2	FACETS	0.931	0.875	0.988	0.931	0.875	0.988	CLONAL	1	TRUE	1	0.76	2		696	701	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489544	56489544	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761002408	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	122	399	0	ENST00000267101.3:c.2009G>A	p.Arg670Gln	p.R670Q	ENST00000267101	NM_001982.3	670	cGg/cAg	17/28	1	2	FACETS	0.939	0.859	1	0.939	0.859	1	CLONAL	1	TRUE	1	0.76	2		399	342	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492542	56492542	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	187	595	1	ENST00000267101.3:c.2693-1G>A		p.X898_splice	ENST00000267101	NM_001982.3	898			1	2	FACETS	0.95	0.885	1	0.95	0.885	1	CLONAL	1	TRUE	1	0.76	2		596	518	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864217	57864218	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1469076238	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	262	1174	0	ENST00000228682.2:c.1700dup	p.Gly568TrpfsTer74	p.G568Wfs*74	ENST00000228682	NM_005269.2	565	ttc/ttCc	12/12	1	2	FACETS	0.736	0.69	0.782	0.736	0.69	0.782	SUBCLONAL	1	TRUE	1	0.76	2		1174	937	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143245	58143245	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	123	287	0	ENST00000257904.6:c.675A>C	p.Lys225Asn	p.K225N	ENST00000257904	NM_000075.3	225	aaA/aaC	6/8	1	2	FACETS	0.978	0.896	1	0.978	0.896	1	CLONAL	1	TRUE	1	0.76	2		287	331	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813450	102813450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	15	266	0	ENST00000307046.8:c.239G>A	p.Gly80Asp	p.G80D	ENST00000307046	NM_001111285.1	80	gGc/gAc	3/4	1	2	FACETS	0.151	0.11	0.201	0.151	0.11	0.201	SUBCLONAL	1	TRUE	1	0.76	2		266	261	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856377	111856377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	67	169	1	ENST00000341259.2:c.428G>A	p.Arg143His	p.R143H	ENST00000341259	NM_005475.2	143	cGc/cAc	2/8	1	2	FACETS	0.791	0.697	0.888	0.791	0.697	0.888	SUBCLONAL	1	TRUE	1	0.76	2		170	223	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856661	111856661	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1479990832	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	193	547	0	ENST00000341259.2:c.712G>T	p.Glu238Ter	p.E238*	ENST00000341259	NM_005475.2	238	Gag/Tag	2/8	1	2	FACETS	0.958	0.894	1	0.958	0.894	1	CLONAL	1	TRUE	1	0.76	2		547	530	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926872	112926872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507541	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	116	542	0	ENST00000351677.2:c.1492C>T	p.Arg498Trp	p.R498W	ENST00000351677	NM_002834.3	498	Cgg/Tgg	13/16	1	2	FACETS	0.734	0.667	0.804	0.734	0.667	0.804	SUBCLONAL	1	TRUE	1	0.76	2		542	416	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926960	112926960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770363146	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	54	212	0	ENST00000351677.2:c.1580G>A	p.Arg527His	p.R527H	ENST00000351677	NM_002834.3	527	cGc/cAc	13/16	1	2	FACETS	0.703	0.609	0.803	0.703	0.609	0.803	SUBCLONAL	1	TRUE	1	0.76	2		212	202	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426764	121426764	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	262	902	0	ENST00000257555.6:c.455C>A	p.Thr152Asn	p.T152N	ENST00000257555		152	aCt/aAt	2/10	1	2	FACETS	0.904	0.85	0.958	0.904	0.85	0.958	CLONAL	1	TRUE	1	0.76	2		902	763	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215840	133215840	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	178	516	0	ENST00000320574.5:c.5423A>C	p.Gln1808Pro	p.Q1808P	ENST00000320574	NM_006231.2	1808	cAg/cCg	40/49	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.76	2		516	402	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225540	133225540	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766168647	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	199	656	2	ENST00000320574.5:c.4124C>T	p.Ala1375Val	p.A1375V	ENST00000320574	NM_006231.2	1375	gCg/gTg	32/49	1	2	FACETS	0.945	0.882	1	0.945	0.882	1	CLONAL	1	TRUE	1	0.76	2		658	554	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244231	133244231	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	16	286	0	ENST00000320574.5:c.2177A>G	p.Tyr726Cys	p.Y726C	ENST00000320574	NM_006231.2	726	tAc/tGc	20/49	1	2	FACETS	0.152	0.112	0.2	0.152	0.112	0.2	SUBCLONAL	1	TRUE	1	0.76	2		286	277	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249846	133249848	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	98	369	0	ENST00000320574.5:c.1375_1377del	p.Ser459del	p.S459del	ENST00000320574	NM_006231.2	459	TCT/-	14/49	1	2	FACETS	0.868	0.785	0.955	0.868	0.785	0.955	CLONAL	1	TRUE	1	0.76	2		369	297	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254166	133254166	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs371882716	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	91	630	3	ENST00000320574.5:c.718G>A	p.Val240Met	p.V240M	ENST00000320574	NM_006231.2	240	Gtg/Atg	7/49	1	2	FACETS	0.47	0.418	0.524	0.47	0.418	0.524	SUBCLONAL	1	TRUE	1	0.76	2		633	510	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964202	28964202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374335323	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	49	322	1	ENST00000282397.4:c.1700C>T	p.Pro567Leu	p.P567L	ENST00000282397	NM_002019.4	567	cCg/cTg	13/30	0.11703264212386	1	FACETS	0.307	0.262	0.356	0.307	0.262	0.356	INDETERMINATE	1	TRUE	0	0.76	1		323	260	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911040	32911040	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886038075	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	420	1406	1	ENST00000380152.3:c.2548C>T	p.Gln850Ter	p.Q850*	ENST00000380152		850	Caa/Taa	11/27	0.11703264212386	1	FACETS	0.593	0.565	0.621	0.593	0.565	0.621	INDETERMINATE	1	TRUE	0	0.76	1		1407	1156	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913899	32913899	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	382	1378	0	ENST00000380152.3:c.5407A>C	p.Thr1803Pro	p.T1803P	ENST00000380152		1803	Act/Cct	11/27	0.11703264212386	1	FACETS	0.626	0.596	0.657	0.626	0.596	0.657	INDETERMINATE	1	TRUE	0	0.76	1		1378	995	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914464	32914464	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80358829	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	176	1383	0	ENST00000380152.3:c.5972C>T	p.Ala1991Val	p.A1991V	ENST00000380152		1991	gCt/gTt	11/27	0.11703264212386	1	FACETS	0.255	0.234	0.277	0.255	0.234	0.277	INDETERMINATE	1	TRUE	0	0.76	1		1383	1126	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929057	32929057	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	359	1256	0	ENST00000380152.3:c.7067T>G	p.Phe2356Cys	p.F2356C	ENST00000380152		2356	tTt/tGt	14/27	0.11703264212386	1	FACETS	0.58	0.551	0.61	0.58	0.551	0.61	INDETERMINATE	1	TRUE	0	0.76	1		1256	1010	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936715	32936715	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	88	314	0	ENST00000380152.3:c.7861T>C	p.Tyr2621His	p.Y2621H	ENST00000380152		2621	Tat/Cat	17/27	0.11703264212386	1	FACETS	0.532	0.478	0.588	0.532	0.478	0.588	INDETERMINATE	1	TRUE	0	0.76	1		314	270	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73350114	73350114	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	105	354	0	ENST00000377767.4:c.771T>A	p.Asn257Lys	p.N257K	ENST00000377767	NM_014953.3	257	aaT/aaA	5/21	0.11703264212386	1	FACETS	0.565	0.513	0.619	0.565	0.513	0.619	INDETERMINATE	1	TRUE	0	0.76	1		354	303	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73352354	73352354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	152	540	0	ENST00000377767.4:c.551C>T	p.Ala184Val	p.A184V	ENST00000377767	NM_014953.3	184	gCc/gTc	3/21	0.11703264212386	1	FACETS	0.529	0.487	0.571	0.529	0.487	0.571	INDETERMINATE	1	TRUE	0	0.76	1		540	469	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524616	103524616	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs758320695	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	142	477	0	ENST00000355739.4:c.2747A>C	p.Lys916Thr	p.K916T	ENST00000355739	NM_000123.3	916	aAa/aCa	13/15	0.11703264212386	1	FACETS	0.607	0.559	0.655	0.607	0.559	0.655	INDETERMINATE	1	TRUE	0	0.76	1		477	382	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81558901	81558901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772600260	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	145	434	0	ENST00000298171.2:c.494C>T	p.Thr165Met	p.T165M	ENST00000298171	NM_000369.2	165	aCg/aTg	6/10	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.76	2		434	375	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961688	41961688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	341	1252	1	ENST00000219905.7:c.596G>A	p.Arg199His	p.R199H	ENST00000219905	NM_001164273.1	199	cGt/cAt	2/24	0.11703264212386	1	FACETS	0.501	0.474	0.528	0.501	0.474	0.528	INDETERMINATE	1	TRUE	0	0.76	1		1253	1111	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988701	41988701	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	338	1006	0	ENST00000219905.7:c.1493A>C	p.Lys498Thr	p.K498T	ENST00000219905	NM_001164273.1	498	aAa/aCa	3/24	0.11703264212386	1	FACETS	0.699	0.665	0.733	0.699	0.665	0.733	INDETERMINATE	1	TRUE	0	0.76	1		1006	789	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032354	42032354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201349807	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	345	1410	4	ENST00000219905.7:c.4538G>A	p.Arg1513His	p.R1513H	ENST00000219905	NM_001164273.1	1513	cGc/cAc	14/24	0.11703264212386	1	FACETS	0.52	0.493	0.548	0.52	0.493	0.548	INDETERMINATE	1	TRUE	0	0.76	1		1414	1082	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041414	42041414	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	283	1072	1	ENST00000219905.7:c.5609C>A	p.Ala1870Asp	p.A1870D	ENST00000219905	NM_001164273.1	1870	gCt/gAt	17/24	0.11703264212386	1	FACETS	0.497	0.468	0.527	0.497	0.468	0.527	INDETERMINATE	1	TRUE	0	0.76	1		1073	929	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473716	67473716	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	165	576	0	ENST00000327367.4:c.796T>G	p.Ser266Ala	p.S266A	ENST00000327367	NM_005902.3	266	Tcg/Gcg	6/9	0.11703264212386	1	FACETS	0.652	0.605	0.699	0.652	0.605	0.699	INDETERMINATE	1	TRUE	0	0.76	1		576	413	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423566	88423566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1361200565	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	217	678	0	ENST00000360948.2:c.2269G>A	p.Gly757Arg	p.G757R	ENST00000360948	NM_001012338.2	757	Ggg/Agg	18/19	0.11703264212386	1	FACETS	0.682	0.64	0.724	0.682	0.64	0.724	INDETERMINATE	1	TRUE	0	0.76	1		678	519	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628548	90628548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767061831	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	238	1040	2	ENST00000330062.3:c.1039G>A	p.Ala347Thr	p.A347T	ENST00000330062	NM_002168.2	347	Gct/Act	8/11	0.11703264212386	1	FACETS	0.5	0.468	0.532	0.5	0.468	0.532	INDETERMINATE	1	TRUE	0	0.76	1		1042	777	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467191	99467191	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773555066	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	133	509	0	ENST00000268035.6:c.2572C>T	p.Pro858Ser	p.P858S	ENST00000268035	NM_000875.3	858	Ccc/Tcc	12/21	0.11703264212386	1	FACETS	0.514	0.471	0.559	0.514	0.471	0.559	INDETERMINATE	1	TRUE	0	0.76	1		509	422	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341218	341218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1016858677	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	53	937	0	ENST00000262320.3:c.2266G>A	p.Val756Met	p.V756M	ENST00000262320	NM_003502.3	756	Gtg/Atg	9/11	1	2	FACETS	0.184	0.157	0.215	0.184	0.157	0.215	SUBCLONAL	1	TRUE	1	0.76	2		937	756	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129134	2129134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555510327	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	196	552	2	ENST00000219476.3:c.3068C>T	p.Thr1023Met	p.T1023M	ENST00000219476	NM_000548.3	1023	aCg/aTg	27/42	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.76	2		554	477	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136841	2136841	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45517383	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	180	604	0	ENST00000219476.3:c.4958C>T	p.Ser1653Phe	p.S1653F	ENST00000219476	NM_000548.3	1653	tCc/tTc	38/42	1	2	FACETS	0.995	0.926	1	0.995	0.926	1	CLONAL	1	TRUE	1	0.76	2		604	476	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138267	2138267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751990617	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	292	995	0	ENST00000219476.3:c.5200G>A	p.Asp1734Asn	p.D1734N	ENST00000219476	NM_000548.3	1734	Gat/Aat	41/42	1	2	FACETS	0.997	0.942	1	0.997	0.942	1	CLONAL	1	TRUE	1	0.76	2		995	771	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138312	2138312	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1193817827	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	211	732	1	ENST00000219476.3:c.5245C>T	p.Arg1749Trp	p.R1749W	ENST00000219476	NM_000548.3	1749	Cgg/Tgg	41/42	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.76	2		733	534	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778116	3778116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761751428	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	184	599	1	ENST00000262367.5:c.6932C>T	p.Pro2311Leu	p.P2311L	ENST00000262367	NM_004380.2	2311	cCg/cTg	31/31	1	2	FACETS	0.938	0.873	1	0.938	0.873	1	CLONAL	1	TRUE	1	0.76	2		600	516	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857745	9857745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs909465034	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	206	604	0	ENST00000330684.3:c.3656C>T	p.Ser1219Phe	p.S1219F	ENST00000330684	NM_001134407.1	1219	tCc/tTc	13/13	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.76	2		604	508	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858195	9858195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777249842	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	191	565	0	ENST00000330684.3:c.3206C>T	p.Thr1069Met	p.T1069M	ENST00000330684	NM_001134407.1	1069	aCg/aTg	13/13	1	2	FACETS	0.922	0.859	0.987	0.922	0.859	0.987	CLONAL	1	TRUE	1	0.76	2		565	545	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274123	10274123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774442834	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	190	486	0	ENST00000330684.3:c.146G>A	p.Arg49His	p.R49H	ENST00000330684	NM_001134407.1	49	cGc/cAc	2/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.76	2		486	485	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865783	56865783	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148421556	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	446	1376	3	ENST00000308159.5:c.1115G>A	p.Arg372Gln	p.R372Q	ENST00000308159	NM_014669.4	372	cGg/cAg	11/22	1	2	FACETS	0.972	0.929	1	0.972	0.929	1	CLONAL	1	TRUE	1	0.76	2		1379	1207	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650737	67650737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	212	623	1	ENST00000264010.4:c.1042G>A	p.Glu348Lys	p.E348K	ENST00000264010	NM_006565.3	348	Gag/Aag	5/12	1	2	FACETS	0.912	0.852	0.972	0.912	0.852	0.972	CLONAL	1	TRUE	1	0.76	2		624	612	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671770	67671770	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1192224462	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	93	320	0	ENST00000264010.4:c.2179C>T	p.Arg727Trp	p.R727W	ENST00000264010	NM_006565.3	727	Cgg/Tgg	12/12	1	2	FACETS	0.991	0.896	1	0.991	0.896	1	CLONAL	1	TRUE	1	0.76	2		320	247	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849514	68849514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs36087757	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	200	647	0	ENST00000261769.5:c.1417G>A	p.Val473Ile	p.V473I	ENST00000261769	NM_004360.3	473	Gtc/Atc	10/16	1	2	FACETS	0.831	0.774	0.89	0.831	0.774	0.89	CLONAL	1	TRUE	1	0.76	2		647	633	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862116	68862116	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782464	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	178	477	1	ENST00000261769.5:c.2204C>T	p.Ala735Val	p.A735V	ENST00000261769	NM_004360.3	735	gCg/gTg	14/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.76	2		478	441	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827948	72827948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746367905	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	512	1741	4	ENST00000268489.5:c.8633C>T	p.Ala2878Val	p.A2878V	ENST00000268489	NM_006885.3	2878	gCg/gTg	9/10	1	2	FACETS	0.971	0.931	1	0.971	0.931	1	CLONAL	1	TRUE	1	0.76	2		1745	1387	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830196	72830196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	239	912	3	ENST00000268489.5:c.6385G>A	p.Ala2129Thr	p.A2129T	ENST00000268489	NM_006885.3	2129	Gcc/Acc	9/10	1	2	FACETS	0.943	0.885	1	0.943	0.885	1	CLONAL	1	TRUE	1	0.76	2		915	667	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72833967	72833967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	217	767	1	ENST00000268489.5:c.3926G>A	p.Arg1309Gln	p.R1309Q	ENST00000268489	NM_006885.3	1309	cGa/cAa	8/10	1	2	FACETS	0.904	0.845	0.963	0.904	0.845	0.963	CLONAL	1	TRUE	1	0.76	2		768	632	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991508	72991508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755878058	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	535	1507	5	ENST00000268489.5:c.2537G>A	p.Arg846His	p.R846H	ENST00000268489	NM_006885.3	846	cGc/cAc	2/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.76	2		1512	1314	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992930	72992930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1398839726	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	444	1554	3	ENST00000268489.5:c.1115G>A	p.Arg372Gln	p.R372Q	ENST00000268489	NM_006885.3	372	cGa/cAa	2/10	1	2	FACETS	0.903	0.862	0.945	0.903	0.862	0.945	CLONAL	1	TRUE	1	0.76	2		1557	1294	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341329	89341329	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	150	421	0	ENST00000301030.4:c.7606C>T	p.Arg2536Trp	p.R2536W	ENST00000301030	NM_001256183.1	2536	Cgg/Tgg	11/13	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.76	2		421	378	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346220	89346220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200852197	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	193	553	1	ENST00000301030.4:c.6730G>A	p.Val2244Ile	p.V2244I	ENST00000301030	NM_001256183.1	2244	Gtt/Att	9/13	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.76	2		554	500	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346577	89346577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764665666	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	38	806	1	ENST00000301030.4:c.6373G>A	p.Ala2125Thr	p.A2125T	ENST00000301030	NM_001256183.1	2125	Gcc/Acc	9/13	1	2	FACETS	0.14	0.115	0.168	0.14	0.115	0.168	SUBCLONAL	1	TRUE	1	0.76	2		807	716	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371710	89371710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764805663	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	312	1057	3	ENST00000301030.4:c.130C>T	p.Arg44Cys	p.R44C	ENST00000301030	NM_001256183.1	44	Cgt/Tgt	4/13	1	2	FACETS	0.927	0.877	0.977	0.927	0.877	0.977	CLONAL	1	TRUE	1	0.76	2		1060	886	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813075	89813075	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143671872	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	159	395	0	ENST00000389301.3:c.3430C>T	p.Arg1144Trp	p.R1144W	ENST00000389301	NM_000135.2	1144	Cgg/Tgg	35/43	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.76	2		395	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576865	7576865	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	rs879254077	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	107	367	0	ENST00000269305.4:c.981T>G	p.Tyr327Ter	p.Y327*	ENST00000269305	NM_001126112.2	327	taT/taG	9/11	1	2	FACETS	0.974	0.887	1	0.974	0.887	1	CLONAL	1	TRUE	1	0.76	2		367	289	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973838	15973838	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	76	211	0	ENST00000268712.3:c.4154G>T	p.Gly1385Val	p.G1385V	ENST00000268712	NM_006311.3	1385	gGc/gTc	31/46	1	2	FACETS	0.976	0.872	1	0.976	0.872	1	CLONAL	1	TRUE	1	0.76	2		211	205	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004765	16004765	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	213	667	0	ENST00000268712.3:c.2489A>C	p.Glu830Ala	p.E830A	ENST00000268712	NM_006311.3	830	gAa/gCa	20/46	1	2	FACETS	0.877	0.82	0.936	0.877	0.82	0.936	CLONAL	1	TRUE	1	0.76	2		667	639	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553540	29553540	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	136	397	0	ENST00000356175.3:c.2089A>G	p.Asn697Asp	p.N697D	ENST00000356175	NM_000267.3	697	Aac/Gac	18/57	1	2	FACETS	0.96	0.883	1	0.96	0.883	1	CLONAL	1	TRUE	1	0.76	2		397	373	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	173	663	1	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	1	2	FACETS	0.81	0.75	0.872	0.81	0.75	0.872	CLONAL	1	TRUE	1	0.76	2		664	562	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653191	29653191	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	77	227	0	ENST00000356175.3:c.5126C>T	p.Thr1709Ile	p.T1709I	ENST00000356175	NM_000267.3	1709	aCc/aTc	36/57	1	2	FACETS	0.893	0.797	0.992	0.893	0.797	0.992	CLONAL	1	TRUE	1	0.76	2		227	227	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667643	29667643	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	171	547	0	ENST00000356175.3:c.6979C>T	p.Leu2327Phe	p.L2327F	ENST00000356175	NM_000267.3	2327	Ctc/Ttc	46/57	1	2	FACETS	0.926	0.859	0.994	0.926	0.859	0.994	CLONAL	1	TRUE	1	0.76	2		547	486	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676254	29676254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659856	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	13	254	0	ENST00000356175.3:c.7243G>A	p.Val2415Met	p.V2415M	ENST00000356175	NM_000267.3	2415	Gtg/Atg	48/57	1	2	FACETS	0.159	0.113	0.215	0.159	0.113	0.215	SUBCLONAL	1	TRUE	1	0.76	2		254	215	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879672	37879672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	52	292	0	ENST00000269571.5:c.2047C>T	p.Arg683Trp	p.R683W	ENST00000269571		683	Cgg/Tgg	17/27	1	2	FACETS	0.507	0.435	0.584	0.507	0.435	0.584	SUBCLONAL	1	TRUE	1	0.76	2		292	270	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362506	40362506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561888537	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	174	898	1	ENST00000293328.3:c.1690C>T	p.Pro564Ser	p.P564S	ENST00000293328	NM_012448.3	564	Cca/Tca	14/19	1	2	FACETS	0.541	0.499	0.586	0.541	0.499	0.586	SUBCLONAL	1	TRUE	1	0.76	2		899	846	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453468	40453468	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866679330	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	78	1602	0	ENST00000345506.4:c.1165C>T	p.Arg389Cys	p.R389C	ENST00000345506	NM_003152.3	389	Cgc/Tgc	10/20	1	2	FACETS	0.172	0.15	0.196	0.172	0.15	0.196	SUBCLONAL	1	TRUE	1	0.76	2		1602	1193	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245012	41245012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786203523	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	25	538	0	ENST00000357654.3:c.2536G>T	p.Glu846Ter	p.E846*	ENST00000357654	NM_007294.3	846	Gaa/Taa	10/23	1	2	FACETS	0.133	0.104	0.166	0.133	0.104	0.166	SUBCLONAL	1	TRUE	1	0.76	2		538	495	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245724	41245725	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	150	409	0	ENST00000357654.3:c.1823dup	p.Asn609GlufsTer2	p.N609Efs*2	ENST00000357654	NM_007294.3	608	aag/aaAg	10/23	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.76	2		409	369	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41251831	41251831	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357325	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	237	602	0	ENST00000357654.3:c.508C>T	p.Arg170Trp	p.R170W	ENST00000357654	NM_007294.3	170	Cgg/Tgg	7/23	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.76	2		602	599	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805413	46805413	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	514	1728	0	ENST00000290295.7:c.543G>T	p.Gln181His	p.Q181H	ENST00000290295	NM_006361.5	181	caG/caT	1/2	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.76	2		1728	1339	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56787287	56787287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267606997	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	37	460	1	ENST00000337432.4:c.773G>A	p.Arg258His	p.R258H	ENST00000337432	NM_058216.2	258	cGt/cAt	5/9	1	2	FACETS	0.226	0.186	0.271	0.226	0.186	0.271	SUBCLONAL	1	TRUE	1	0.76	2		461	431	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58711261	58711261	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571290585	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	384	1140	2	ENST00000305921.3:c.749G>A	p.Arg250Gln	p.R250Q	ENST00000305921	NM_003620.3	250	cGa/cAa	3/6	1	2	FACETS	0.954	0.908	1	0.954	0.908	1	CLONAL	1	TRUE	1	0.76	2		1142	1059	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821817	59821817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780235	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	147	472	0	ENST00000259008.2:c.2233G>A	p.Ala745Thr	p.A745T	ENST00000259008	NM_032043.2	745	Gca/Aca	15/20	1	2	FACETS	0.902	0.831	0.974	0.902	0.831	0.974	CLONAL	1	TRUE	1	0.76	2		472	429	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59934481	59934481	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143615668	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	139	460	0	ENST00000259008.2:c.317G>A	p.Arg106His	p.R106H	ENST00000259008	NM_032043.2	106	cGt/cAt	4/20	1	2	FACETS	0.905	0.833	0.98	0.905	0.833	0.98	CLONAL	1	TRUE	1	0.76	2		460	404	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554354	63554354	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	85	574	0	ENST00000307078.5:c.385C>T	p.Arg129Ter	p.R129*	ENST00000307078	NM_004655.3	129	Cga/Tga	2/11	1	2	FACETS	0.482	0.428	0.54	0.482	0.428	0.54	SUBCLONAL	1	TRUE	1	0.76	2		574	464	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66522024	66522024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	78	198	0	ENST00000358598.2:c.679G>A	p.Asp227Asn	p.D227N	ENST00000358598	NM_212471.2	227	Gac/Aac	7/11	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.76	2		198	205	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899231	78899231	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200514795	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	25	311	1	ENST00000306801.3:c.2870C>T	p.Thr957Met	p.T957M	ENST00000306801	NM_020761.2	957	aCg/aTg	24/34	1	2	FACETS	0.207	0.163	0.257	0.207	0.163	0.257	SUBCLONAL	1	TRUE	1	0.76	2		312	318	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936774	78936774	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	253	780	0	ENST00000306801.3:c.3856C>A	p.Leu1286Ile	p.L1286I	ENST00000306801	NM_020761.2	1286	Ctc/Atc	33/34	1	2	FACETS	0.95	0.894	1	0.95	0.894	1	CLONAL	1	TRUE	1	0.76	2		780	701	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390280	56390280	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs768976640	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	181	587	4	ENST00000348428.3:c.1019C>T	p.Ala340Val	p.A340V	ENST00000348428	NM_006785.3	340	gCg/gTg	10/17	1	2	FACETS	0.911	0.847	0.976	0.911	0.847	0.976	CLONAL	1	TRUE	1	0.76	2		591	523	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985539	60985539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	154	518	0	ENST00000333681.4:c.361C>A	p.Leu121Met	p.L121M	ENST00000333681		121	Ctg/Atg	2/3	1	2	FACETS	0.862	0.796	0.931	0.862	0.796	0.931	CLONAL	1	TRUE	1	0.76	2		518	470	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218441	1218441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782115	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	160	475	2	ENST00000326873.7:c.316C>T	p.Arg106Trp	p.R106W	ENST00000326873	NM_000455.4	106	Cgg/Tgg	2/10	1	2	FACETS	0.938	0.868	1	0.938	0.868	1	CLONAL	1	TRUE	1	0.76	2		477	449	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2220158	2220158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	344	1094	2	ENST00000398665.3:c.2743G>A	p.Glu915Lys	p.E915K	ENST00000398665	NM_032482.2	915	Gaa/Aaa	23/28	1	2	FACETS	0.943	0.895	0.992	0.943	0.895	0.992	CLONAL	1	TRUE	1	0.76	2		1096	960	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222388	2222388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	94	300	0	ENST00000398665.3:c.3220G>A	p.Asp1074Asn	p.D1074N	ENST00000398665	NM_032482.2	1074	Gac/Aac	24/28	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.76	2		300	223	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101030	4101030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730880511	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	11	299	0	ENST00000262948.5:c.692G>A	p.Arg231His	p.R231H	ENST00000262948	NM_030662.3	231	cGc/cAc	6/11	1	2	FACETS	0.133	0.091	0.184	0.133	0.091	0.184	SUBCLONAL	1	TRUE	1	0.76	2		299	218	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210506	5210506	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	208	602	0	ENST00000357368.4:c.5461C>T	p.Arg1821Ter	p.R1821*	ENST00000357368	NM_002850.3	1821	Cga/Tga	35/38	1	2	FACETS	0.974	0.911	1	0.974	0.911	1	CLONAL	1	TRUE	1	0.76	2		602	562	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215543	5215543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	193	611	0	ENST00000357368.4:c.4160C>T	p.Ala1387Val	p.A1387V	ENST00000357368	NM_002850.3	1387	gCc/gTc	27/38	1	2	FACETS	0.994	0.928	1	0.994	0.928	1	CLONAL	1	TRUE	1	0.76	2		611	511	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218488	5218488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1361339357	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	33	727	2	ENST00000357368.4:c.3991G>A	p.Ala1331Thr	p.A1331T	ENST00000357368	NM_002850.3	1331	Gcc/Acc	25/38	1	2	FACETS	0.134	0.108	0.163	0.134	0.108	0.163	SUBCLONAL	1	TRUE	1	0.76	2		729	649	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220000	5220000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369971329	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	117	384	0	ENST00000357368.4:c.3715G>A	p.Gly1239Ser	p.G1239S	ENST00000357368	NM_002850.3	1239	Ggc/Agc	22/38	1	2	FACETS	0.936	0.855	1	0.936	0.855	1	CLONAL	1	TRUE	1	0.76	2		384	329	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273534	5273534	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1397380294	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	237	659	1	ENST00000357368.4:c.298C>T	p.Arg100Trp	p.R100W	ENST00000357368	NM_002850.3	100	Cgg/Tgg	4/38	1	2	FACETS	0.975	0.915	1	0.975	0.915	1	CLONAL	1	TRUE	1	0.76	2		660	640	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7132313	7132313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144029037	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	85	284	2	ENST00000302850.5:c.2698G>A	p.Val900Ile	p.V900I	ENST00000302850	NM_000208.2	900	Gtc/Atc	14/22	1	2	FACETS	0.909	0.816	1	0.909	0.816	1	CLONAL	1	TRUE	1	0.76	2		286	246	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247925	10247925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1187348790	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	114	374	1	ENST00000340748.4:c.4277G>A	p.Arg1426Gln	p.R1426Q	ENST00000340748		1426	cGg/cAg	36/40	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.76	2		375	294	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170457	11170457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057523990	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	138	460	1	ENST00000358026.2:c.4760C>T	p.Ser1587Leu	p.S1587L	ENST00000358026	NM_001128849.1	1587	tCg/tTg	34/36	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.76	2		461	363	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626892	14626892	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	445	1334	1	ENST00000254322.2:c.883C>T	p.Arg295Ter	p.R295*	ENST00000254322	NM_006145.1	295	Cga/Tga	3/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.76	2		1335	1125	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272347	15272347	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779314594	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	18	410	0	ENST00000263388.2:c.6092G>A	p.Arg2031His	p.R2031H	ENST00000263388	NM_000435.2	2031	cGc/cAc	33/33	1	2	FACETS	0.156	0.117	0.202	0.156	0.117	0.202	SUBCLONAL	1	TRUE	1	0.76	2		410	303	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349886	15349886	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759358078	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	89	229	1	ENST00000263377.2:c.3766C>T	p.Arg1256Trp	p.R1256W	ENST00000263377	NM_058243.2	1256	Cgg/Tgg	18/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.76	2		230	196	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350023	15350023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1489035830	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	195	606	1	ENST00000263377.2:c.3629C>T	p.Pro1210Leu	p.P1210L	ENST00000263377	NM_058243.2	1210	cCg/cTg	18/20	1	2	FACETS	0.885	0.824	0.947	0.885	0.824	0.947	CLONAL	1	TRUE	1	0.76	2		607	580	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279681	18279681	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369900410	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	100	304	0	ENST00000222254.8:c.1954C>T	p.Arg652Trp	p.R652W	ENST00000222254	NM_005027.3	652	Cgg/Tgg	15/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.76	2		304	232	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258640	19258640	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs533071900	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	194	612	0	ENST00000162023.5:c.260C>T	p.Thr87Met	p.T87M	ENST00000162023		87	aCg/aTg	8/13	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.76	2		612	506	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260064	19260064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774866350	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	186	535	0	ENST00000162023.5:c.229G>A	p.Glu77Lys	p.E77K	ENST00000162023		77	Gag/Aag	7/13	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.76	2		535	469	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303597	30303597	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	166	569	0	ENST00000262643.3:c.25G>A	p.Asp9Asn	p.D9N	ENST00000262643	NM_001238.2	9	Gat/Aat	3/12	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.76	2		569	411	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741981	40741981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	262	828	4	ENST00000392038.2:c.991G>A	p.Val331Met	p.V331M	ENST00000392038	NM_001626.4	331	Gtg/Atg	11/14	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.76	2		832	674	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762445	41762445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1159339376	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	209	652	2	ENST00000301178.4:c.2125G>A	p.Ala709Thr	p.A709T	ENST00000301178	NM_021913.4	709	Gcc/Acc	18/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.76	2		654	529	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763489	41763489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201238916	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	193	729	0	ENST00000301178.4:c.2288G>A	p.Arg763His	p.R763H	ENST00000301178	NM_021913.4	763	cGc/cAc	19/20	1	2	FACETS	0.92	0.857	0.984	0.92	0.857	0.984	CLONAL	1	TRUE	1	0.76	2		729	552	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795478	42795478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	134	477	0	ENST00000575354.2:c.2558C>T	p.Pro853Leu	p.P853L	ENST00000575354	NM_015125.3	853	cCc/cTc	10/20	1	2	FACETS	0.991	0.911	1	0.991	0.911	1	CLONAL	1	TRUE	1	0.76	2		477	356	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797885	42797885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773220927	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	88	538	3	ENST00000575354.2:c.3937C>T	p.Arg1313Trp	p.R1313W	ENST00000575354	NM_015125.3	1313	Cgg/Tgg	16/20	1	2	FACETS	0.544	0.484	0.607	0.544	0.484	0.607	SUBCLONAL	1	TRUE	1	0.76	2		541	426	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798336	42798336	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	167	563	0	ENST00000575354.2:c.4207G>A	p.Ala1403Thr	p.A1403T	ENST00000575354	NM_015125.3	1403	Gca/Aca	18/20	1	2	FACETS	0.929	0.861	0.998	0.929	0.861	0.998	CLONAL	1	TRUE	1	0.76	2		563	473	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798364	42798364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	193	589	0	ENST00000575354.2:c.4235G>A	p.Arg1412His	p.R1412H	ENST00000575354	NM_015125.3	1412	cGc/cAc	18/20	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.76	2		589	499	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860770	45860770	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141457460	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	132	504	0	ENST00000391945.4:c.1339G>A	p.Val447Ile	p.V447I	ENST00000391945	NM_000400.3	447	Gta/Ata	14/23	1	2	FACETS	0.919	0.844	0.996	0.919	0.844	0.996	CLONAL	1	TRUE	1	0.76	2		504	378	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52725434	52725434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	206	696	0	ENST00000322088.6:c.1601C>T	p.Ala534Val	p.A534V	ENST00000322088	NM_014225.5	534	gCc/gTc	13/15	1	2	FACETS	0.965	0.902	1	0.965	0.902	1	CLONAL	1	TRUE	1	0.76	2		696	562	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085954	16085954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1558536330	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	112	395	0	ENST00000281043.3:c.1130C>T	p.Ser377Leu	p.S377L	ENST00000281043	NM_005378.4	377	tCg/tTg	3/3	1	2	FACETS	0.833	0.757	0.911	0.833	0.757	0.911	CLONAL	1	TRUE	1	0.76	2		395	354	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464451	25464451	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1484795800	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	189	518	0	ENST00000264709.3:c.2062C>T	p.Arg688Cys	p.R688C	ENST00000264709	NM_175629.2	688	Cgc/Tgc	17/23	1	2	FACETS	0.964	0.898	1	0.964	0.898	1	CLONAL	1	TRUE	1	0.76	2		518	516	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470491	25470491	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	32	623	0	ENST00000264709.3:c.983T>C	p.Val328Ala	p.V328A	ENST00000264709	NM_175629.2	328	gTc/gCc	8/23	1	2	FACETS	0.155	0.125	0.188	0.155	0.125	0.188	SUBCLONAL	1	TRUE	1	0.76	2		623	545	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505350	25505350	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	196	561	0	ENST00000264709.3:c.408C>A	p.Cys136Ter	p.C136*	ENST00000264709	NM_175629.2	136	tgC/tgA	4/23	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.76	2		561	473	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965023	25965023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	174	498	0	ENST00000435504.4:c.4183G>A	p.Gly1395Ser	p.G1395S	ENST00000435504		1395	Ggc/Agc	13/13	1	2	FACETS	0.923	0.857	0.991	0.923	0.857	0.991	CLONAL	1	TRUE	1	0.76	2		498	496	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47601144	47601144	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1048436074	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	85	282	0	ENST00000263735.4:c.382G>T	p.Asp128Tyr	p.D128Y	ENST00000263735	NM_002354.2	128	Gac/Tac	3/9	1	2	FACETS	0.94	0.845	1	0.94	0.845	1	CLONAL	1	TRUE	1	0.76	2		282	238	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025864	48025864	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63749980	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	82	431	0	ENST00000234420.5:c.742C>T	p.Arg248Ter	p.R248*	ENST00000234420	NM_000179.2	248	Cga/Tga	4/10	1	2	FACETS	0.552	0.489	0.618	0.552	0.489	0.618	SUBCLONAL	1	TRUE	1	0.76	2		431	391	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719886	61719886	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	G	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	86	296	0	ENST00000401558.2:c.1385-3T>C		p.X462_splice	ENST00000401558	NM_003400.3	462			1	2	FACETS	0.877	0.787	0.97	0.877	0.787	0.97	CLONAL	1	TRUE	1	0.76	2		296	258	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919751	96919751	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	23	448	0	ENST00000258439.3:c.512T>C	p.Val171Ala	p.V171A	ENST00000258439	NM_001193304.2	171	gTc/gCc	4/4	1	2	FACETS	0.169	0.131	0.212	0.169	0.131	0.212	SUBCLONAL	1	TRUE	1	0.76	2		448	359	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044340	128044340	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	33	703	2	ENST00000285398.2:c.1281G>T	p.Met427Ile	p.M427I	ENST00000285398	NM_000122.1	427	atG/atT	8/15	1	2	FACETS	0.141	0.114	0.171	0.141	0.114	0.171	SUBCLONAL	1	TRUE	1	0.76	2		705	616	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050416	128050416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1453017999	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	70	233	0	ENST00000285398.2:c.241G>A	p.Asp81Asn	p.D81N	ENST00000285398	NM_000122.1	81	Gat/Aat	3/15	1	2	FACETS	0.912	0.81	1	0.912	0.81	1	CLONAL	1	TRUE	1	0.76	2		233	202	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617503	158617503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1034717563	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	60	1335	4	ENST00000263640.3:c.1153G>A	p.Glu385Lys	p.E385K	ENST00000263640	NM_001105.4	385	Gaa/Aaa	9/11	1	2	FACETS	0.134	0.114	0.155	0.134	0.114	0.155	SUBCLONAL	1	TRUE	1	0.76	2		1339	1181	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095713	178095713	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	156	513	0	ENST00000397062.3:c.1618C>A	p.Leu540Ile	p.L540I	ENST00000397062	NM_006164.4	540	Ctc/Atc	5/5	1	2	FACETS	0.929	0.859	1	0.929	0.859	1	CLONAL	1	TRUE	1	0.76	2		513	442	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265046	198265046	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	67	337	0	ENST00000335508.6:c.2831C>T	p.Ser944Phe	p.S944F	ENST00000335508	NM_012433.2	944	tCt/tTt	19/25	1	2	FACETS	0.46	0.402	0.523	0.46	0.402	0.523	SUBCLONAL	1	TRUE	1	0.76	2		337	383	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265468	198265468	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	119	394	1	ENST00000335508.6:c.2689C>A	p.Leu897Ile	p.L897I	ENST00000335508	NM_012433.2	897	Ctt/Att	18/25	1	2	FACETS	0.858	0.783	0.936	0.858	0.783	0.936	CLONAL	1	TRUE	1	0.76	2		395	365	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483913	212483913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	165	573	0	ENST00000342788.4:c.2290G>A	p.Glu764Lys	p.E764K	ENST00000342788	NM_005235.2	764	Gag/Aag	19/28	1	2	FACETS	0.905	0.838	0.973	0.905	0.838	0.973	CLONAL	1	TRUE	1	0.76	2		573	480	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543825	212543825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770003740	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	19	418	1	ENST00000342788.4:c.1574G>A	p.Arg525His	p.R525H	ENST00000342788	NM_005235.2	525	cGc/cAc	13/28	1	2	FACETS	0.145	0.109	0.187	0.145	0.109	0.187	SUBCLONAL	1	TRUE	1	0.76	2		419	345	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576902	212576902	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	65	249	0	ENST00000342788.4:c.998-1G>T		p.X333_splice	ENST00000342788	NM_005235.2	333			1	2	FACETS	0.915	0.808	1	0.915	0.808	1	CLONAL	1	TRUE	1	0.76	2		249	187	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437266	220437266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753111199	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	418	1485	3	ENST00000243786.2:c.170G>A	p.Arg57Gln	p.R57Q	ENST00000243786	NM_002191.3	57	cGg/cAg	1/2	1	2	FACETS	0.949	0.905	0.994	0.949	0.905	0.994	CLONAL	1	TRUE	1	0.76	2		1488	1159	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440178	220440178	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1025309043	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	463	1615	2	ENST00000243786.2:c.1031C>T	p.Ser344Leu	p.S344L	ENST00000243786	NM_002191.3	344	tCg/tTg	2/2	1	2	FACETS	0.985	0.942	1	0.985	0.942	1	CLONAL	1	TRUE	1	0.76	2		1617	1237	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368172	31368172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375171362	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	31	755	2	ENST00000328111.2:c.43G>A	p.Gly15Ser	p.G15S	ENST00000328111	NM_006892.3	15	Ggc/Agc	2/23	1	2	FACETS	0.132	0.106	0.162	0.132	0.106	0.162	SUBCLONAL	1	TRUE	1	0.76	2		757	616	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383233	31383233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771192296	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	225	705	0	ENST00000328111.2:c.1145G>A	p.Arg382His	p.R382H	ENST00000328111	NM_006892.3	382	cGc/cAc	11/23	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.76	2		705	591	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389203	31389203	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs996239307	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	93	331	0	ENST00000328111.2:c.2116G>A	p.Asp706Asn	p.D706N	ENST00000328111	NM_006892.3	706	Gac/Aac	19/23	1	2	FACETS	0.856	0.771	0.943	0.856	0.771	0.943	CLONAL	1	TRUE	1	0.76	2		331	286	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54956535	54956535	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	44	502	0	ENST00000312783.6:c.659G>T	p.Arg220Ile	p.R220I	ENST00000312783	NM_198436.1	220	aGa/aTa	7/10	1	2	FACETS	0.218	0.182	0.258	0.218	0.182	0.258	SUBCLONAL	1	TRUE	1	0.76	2		502	531	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795352	39795352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372598575	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	171	640	0	ENST00000288319.7:c.368G>A	p.Arg123His	p.R123H	ENST00000288319	NM_182918.3	123	cGc/cAc	3/10	1	2	FACETS	0.924	0.857	0.992	0.924	0.857	0.992	CLONAL	1	TRUE	1	0.76	2		640	487	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29115414	29115414	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	160	514	0	ENST00000328354.6:c.652G>T	p.Asp218Tyr	p.D218Y	ENST00000328354	NM_007194.3	218	Gat/Tat	5/15	1	2	FACETS	0.802	0.74	0.866	0.802	0.74	0.866	CLONAL	1	TRUE	1	0.76	2		514	525	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191620	10191620	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199926195	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	136	392	0	ENST00000256474.2:c.613C>T	p.Arg205Cys	p.R205C	ENST00000256474	NM_000551.3	205	Cgc/Tgc	3/3	1	2	FACETS	0.965	0.888	1	0.965	0.888	1	CLONAL	1	TRUE	1	0.76	2		392	371	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180273	38180273	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs779805093	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	183	712	1	ENST00000396334.3:c.121C>T	p.Arg41Ter	p.R41*	ENST00000396334	NM_002468.4	41	Cga/Tga	1/5	1	2	FACETS	0.872	0.811	0.936	0.872	0.811	0.936	CLONAL	1	TRUE	1	0.76	2		713	552	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182001	38182001	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853064	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	157	427	0	ENST00000396334.3:c.625C>T	p.Arg209Cys	p.R209C	ENST00000396334	NM_002468.4	209	Cgc/Tgc	3/5	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.76	2		427	382	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182002	38182002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772678256	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	118	434	0	ENST00000396334.3:c.626G>A	p.Arg209His	p.R209H	ENST00000396334	NM_002468.4	209	cGc/cAc	3/5	1	2	FACETS	0.804	0.733	0.879	0.804	0.733	0.879	CLONAL	1	TRUE	1	0.76	2		434	386	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165219	47165219	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	123	264	0	ENST00000409792.3:c.907A>C	p.Lys303Gln	p.K303Q	ENST00000409792	NM_014159.6	303	Aaa/Caa	3/21	1	2	FACETS	0.902	0.825	0.981	0.902	0.825	0.981	CLONAL	1	TRUE	1	0.76	2		264	359	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936519	49936519	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757151241	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	457	1498	1	ENST00000296474.3:c.1408C>T	p.Arg470Cys	p.R470C	ENST00000296474	NM_002447.2	470	Cgt/Tgt	2/20	1	2	FACETS	0.937	0.895	0.979	0.937	0.895	0.979	CLONAL	1	TRUE	1	0.76	2		1499	1284	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70005639	70005639	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763119975	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	81	340	0	ENST00000394351.3:c.668G>A	p.Arg223His	p.R223H	ENST00000394351	NM_000248.3	223	cGc/cAc	7/9	1	2	FACETS	0.72	0.641	0.803	0.72	0.641	0.803	SUBCLONAL	1	TRUE	1	0.76	2		340	296	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427691	72427691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759180086	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	113	371	0	ENST00000477973.2:c.799C>T	p.Arg267Cys	p.R267C	ENST00000477973	NM_012234.5	267	Cgc/Tgc	4/4	1	2	FACETS	0.962	0.878	1	0.962	0.878	1	CLONAL	1	TRUE	1	0.76	2		371	309	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200056	128200056	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	198	693	0	ENST00000341105.2:c.1249C>A	p.Leu417Met	p.L417M	ENST00000341105	NM_032638.4	417	Ctg/Atg	6/6	1	2	FACETS	0.965	0.901	1	0.965	0.901	1	CLONAL	1	TRUE	1	0.76	2		693	540	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898791	134898791	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	167	514	0	ENST00000398015.3:c.1849T>A	p.Ser617Thr	p.S617T	ENST00000398015	NM_004441.4	617	Tct/Act	10/16	1	2	FACETS	0.96	0.89	1	0.96	0.89	1	CLONAL	1	TRUE	1	0.76	2		514	458	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138382797	138382797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	159	429	0	ENST00000289153.2:c.2747G>A	p.Gly916Glu	p.G916E	ENST00000289153	NM_006219.2	916	gGg/gAg	19/22	1	2	FACETS	0.994	0.921	1	0.994	0.921	1	CLONAL	1	TRUE	1	0.76	2		429	421	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176462	142176462	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1254296505	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	114	388	0	ENST00000350721.4:c.7639C>T	p.Arg2547Ter	p.R2547*	ENST00000350721	NM_001184.3	2547	Cga/Tga	45/47	1	2	FACETS	0.968	0.884	1	0.968	0.884	1	CLONAL	1	TRUE	1	0.76	2		388	310	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178157	142178157	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1211640581	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	64	278	0	ENST00000350721.4:c.7261C>T	p.Leu2421Phe	p.L2421F	ENST00000350721	NM_001184.3	2421	Ctc/Ttc	43/47	1	2	FACETS	0.818	0.72	0.92	0.818	0.72	0.92	CLONAL	1	TRUE	1	0.76	2		278	206	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279257	142279257	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	115	387	0	ENST00000350721.4:c.1389G>A	p.Trp463Ter	p.W463*	ENST00000350721	NM_001184.3	463	tgG/tgA	6/47	1	2	FACETS	0.914	0.834	0.997	0.914	0.834	0.997	CLONAL	1	TRUE	1	0.76	2		387	331	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917498	178917498	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	58	226	0	ENST00000263967.3:c.373G>T	p.Val125Leu	p.V125L	ENST00000263967	NM_006218.2	125	Gtg/Ttg	3/21	1	2	FACETS	0.909	0.797	1	0.909	0.797	1	CLONAL	1	TRUE	1	0.76	2		226	168	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917522	178917522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	89	271	0	ENST00000263967.3:c.397G>A	p.Asp133Asn	p.D133N	ENST00000263967	NM_006218.2	133	Gat/Aat	3/21	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.76	2		271	227	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922378	178922378	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	15	275	0	ENST00000263967.3:c.1145+2T>C		p.X382_splice	ENST00000263967	NM_006218.2	382			1	2	FACETS	0.132	0.096	0.175	0.132	0.096	0.175	SUBCLONAL	1	TRUE	1	0.76	2		275	300	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665344	182665344	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	94	337	0	ENST00000292782.4:c.597T>A	p.Phe199Leu	p.F199L	ENST00000292782	NM_020640.2	199	ttT/ttA	5/7	1	2	FACETS	0.822	0.74	0.907	0.822	0.74	0.907	CLONAL	1	TRUE	1	0.76	2		337	301	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165600	185165600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763026193	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	81	295	0	ENST00000265026.3:c.875C>T	p.Ala292Val	p.A292V	ENST00000265026	NM_004721.4	292	gCg/gTg	5/14	1	2	FACETS	0.82	0.732	0.911	0.82	0.732	0.911	CLONAL	1	TRUE	1	0.76	2		295	260	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505332	186505332	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	301	826	2	ENST00000323963.5:c.958C>T	p.Arg320Trp	p.R320W	ENST00000323963		320	Cgg/Tgg	9/11	1	2	FACETS	0.932	0.881	0.984	0.932	0.881	0.984	CLONAL	1	TRUE	1	0.76	2		828	850	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443402	187443402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1262719853	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	139	348	0	ENST00000232014.4:c.1724G>A	p.Arg575His	p.R575H	ENST00000232014	NM_001130845.1	575	cGt/cAt	8/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.76	2		348	344	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447552	187447552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs911074942	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	16	329	0	ENST00000232014.4:c.641G>A	p.Arg214Gln	p.R214Q	ENST00000232014	NM_001130845.1	214	cGg/cAg	5/10	1	2	FACETS	0.159	0.117	0.21	0.159	0.117	0.21	SUBCLONAL	1	TRUE	1	0.76	2		329	264	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451319	187451319	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	110	331	0	ENST00000232014.4:c.161+2T>C		p.X54_splice	ENST00000232014	NM_001130845.1	54			1	2	FACETS	0.888	0.808	0.971	0.888	0.808	0.971	CLONAL	1	TRUE	1	0.76	2		331	326	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803565	1803565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	112	346	2	ENST00000260795.2:c.743G>A	p.Arg248His	p.R248H	ENST00000260795		248	cGc/cAc	6/17	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.76	2		348	290	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808967	1808967	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	27	637	0	ENST00000260795.2:c.2399G>T	p.Ser800Ile	p.S800I	ENST00000260795		800	aGc/aTc	17/17	1	2	FACETS	0.15	0.119	0.186	0.15	0.119	0.186	SUBCLONAL	1	TRUE	1	0.76	2		637	473	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133779	55133779	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	206	579	0	ENST00000257290.5:c.992A>C	p.Glu331Ala	p.E331A	ENST00000257290	NM_006206.4	331	gAa/gCa	7/23	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.76	2		579	542	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133827	55133827	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	137	490	0	ENST00000257290.5:c.1040T>C	p.Ile347Thr	p.I347T	ENST00000257290	NM_006206.4	347	aTa/aCa	7/23	1	2	FACETS	0.884	0.812	0.958	0.884	0.812	0.958	CLONAL	1	TRUE	1	0.76	2		490	408	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156523	55156523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	121	400	1	ENST00000257290.5:c.2924C>T	p.Pro975Leu	p.P975L	ENST00000257290	NM_006206.4	975	cCt/cTt	22/23	1	2	FACETS	0.845	0.771	0.921	0.845	0.771	0.921	CLONAL	1	TRUE	1	0.76	2		401	377	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155317	106155317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760280015	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	116	383	0	ENST00000380013.4:c.218G>A	p.Arg73His	p.R73H	ENST00000380013	NM_001127208.2	73	cGt/cAt	3/11	1	2	FACETS	0.867	0.79	0.946	0.867	0.79	0.946	CLONAL	1	TRUE	1	0.76	2		383	352	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143043296	143043296	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	125	483	0	ENST00000262992.4:c.2120T>C	p.Val707Ala	p.V707A	ENST00000262992	NM_001101669.1	707	gTt/gCt	19/24	1	2	FACETS	0.761	0.695	0.831	0.761	0.695	0.831	SUBCLONAL	1	TRUE	1	0.76	2		483	432	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143181674	143181674	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	201	555	0	ENST00000262992.4:c.659G>A	p.Gly220Glu	p.G220E	ENST00000262992	NM_001101669.1	220	gGa/gAa	9/24	1	2	FACETS	0.928	0.866	0.991	0.928	0.866	0.991	CLONAL	1	TRUE	1	0.76	2		555	570	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510248	187510248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1409256573	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	134	394	1	ENST00000441802.2:c.13265C>T	p.Thr4422Met	p.T4422M	ENST00000441802	NM_005245.3	4422	aCg/aTg	27/27	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.76	2		395	340	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518260	187518260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	59	169	1	ENST00000441802.2:c.12434C>T	p.Thr4145Met	p.T4145M	ENST00000441802	NM_005245.3	4145	aCg/aTg	25/27	1	2	FACETS	0.835	0.731	0.943	0.835	0.731	0.943	CLONAL	1	TRUE	1	0.76	2		170	186	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539401	187539401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	123	466	0	ENST00000441802.2:c.8339C>T	p.Ala2780Val	p.A2780V	ENST00000441802	NM_005245.3	2780	gCc/gTc	10/27	1	2	FACETS	0.854	0.78	0.93	0.854	0.78	0.93	CLONAL	1	TRUE	1	0.76	2		466	379	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541580	187541580	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	129	336	0	ENST00000441802.2:c.6160A>G	p.Thr2054Ala	p.T2054A	ENST00000441802	NM_005245.3	2054	Aca/Gca	10/27	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.76	2		336	322	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542455	187542455	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376944386	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	96	668	0	ENST00000441802.2:c.5285C>T	p.Ala1762Val	p.A1762V	ENST00000441802	NM_005245.3	1762	gCg/gTg	10/27	1	2	FACETS	0.398	0.355	0.444	0.398	0.355	0.444	SUBCLONAL	1	TRUE	1	0.76	2		668	634	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228306	228306	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775143272	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	58	142	0	ENST00000264932.6:c.628C>T	p.Arg210Ter	p.R210*	ENST00000264932	NM_004168.2	210	Cga/Tga	6/15	0.11703264212386	1	FACETS	0.671	0.592	0.752	0.671	0.592	0.752	INDETERMINATE	1	TRUE	0	0.76	1		142	141	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282598	1282598	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	180	526	0	ENST00000310581.5:c.1715G>A	p.Arg572Lys	p.R572K	ENST00000310581	NM_198253.2	572	aGg/aAg	3/16	0.11703264212386	1	FACETS	0.617	0.574	0.661	0.617	0.574	0.661	INDETERMINATE	1	TRUE	0	0.76	1		526	476	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873664	35873664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	124	432	0	ENST00000303115.3:c.620C>T	p.Ser207Phe	p.S207F	ENST00000303115	NM_002185.3	207	tCc/tTc	5/8	1	2	FACETS	0.901	0.825	0.98	0.901	0.825	0.98	CLONAL	1	TRUE	1	0.76	2		432	362	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38942462	38942462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	144	376	0	ENST00000357387.3:c.5071G>A	p.Ala1691Thr	p.A1691T	ENST00000357387	NM_152756.3	1691	Gct/Act	38/38	1	2	FACETS	0.913	0.841	0.987	0.913	0.841	0.987	CLONAL	1	TRUE	1	0.76	2		376	415	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56171079	56171079	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	83	238	0	ENST00000399503.3:c.1907G>A	p.Cys636Tyr	p.C636Y	ENST00000399503	NM_005921.1	636	tGc/tAc	10/20	1	2	FACETS	0.958	0.86	1	0.958	0.86	1	CLONAL	1	TRUE	1	0.76	2		238	228	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522723	67522723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755953968	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	92	303	0	ENST00000274335.5:c.220G>A	p.Val74Ile	p.V74I	ENST00000274335		74	Gta/Ata	1/15	1	2	FACETS	0.968	0.875	1	0.968	0.875	1	CLONAL	1	TRUE	1	0.76	2		303	250	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522819	67522819	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	88	223	0	ENST00000274335.5:c.316G>T	p.Ala106Ser	p.A106S	ENST00000274335		106	Gca/Tca	1/15	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.76	2		223	224	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645075	86645075	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	93	301	0	ENST00000274376.6:c.1147C>A	p.Pro383Thr	p.P383T	ENST00000274376	NM_002890.2	383	Cct/Act	8/25	1	2	FACETS	0.941	0.85	1	0.941	0.85	1	CLONAL	1	TRUE	1	0.76	2		301	260	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685250	86685250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773025020	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	67	380	0	ENST00000274376.6:c.2966C>T	p.Thr989Met	p.T989M	ENST00000274376	NM_002890.2	989	aCg/aTg	24/25	1	2	FACETS	0.464	0.405	0.527	0.464	0.405	0.527	SUBCLONAL	1	TRUE	1	0.76	2		380	380	SUCCESS
APC	324	MSKCC	GRCh37	5	112102898	112102898	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs562833260	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	105	337	0	ENST00000257430.4:c.233A>C	p.Asp78Ala	p.D78A	ENST00000257430	NM_000038.5	78	gAt/gCt	4/16	1	2	FACETS	0.861	0.781	0.944	0.861	0.781	0.944	CLONAL	1	TRUE	1	0.76	2		337	321	SUCCESS
APC	324	MSKCC	GRCh37	5	112128185	112128185	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779805	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	150	330	0	ENST00000257430.4:c.688C>T	p.Arg230Cys	p.R230C	ENST00000257430	NM_000038.5	230	Cgt/Tgt	7/16	1	2	FACETS	0.944	0.872	1	0.944	0.872	1	CLONAL	1	TRUE	1	0.76	2		330	418	SUCCESS
APC	324	MSKCC	GRCh37	5	112174747	112174747	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	19	329	0	ENST00000257430.4:c.3456G>T	p.Gln1152His	p.Q1152H	ENST00000257430	NM_000038.5	1152	caG/caT	16/16	1	2	FACETS	0.175	0.132	0.225	0.175	0.132	0.225	SUBCLONAL	1	TRUE	1	0.76	2		329	286	SUCCESS
APC	324	MSKCC	GRCh37	5	112176555	112176555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771967537	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	77	229	0	ENST00000257430.4:c.5264C>T	p.Ala1755Val	p.A1755V	ENST00000257430	NM_000038.5	1755	gCg/gTg	16/16	1	2	FACETS	0.776	0.69	0.866	0.776	0.69	0.866	SUBCLONAL	1	TRUE	1	0.76	2		229	261	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915576	131915576	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	47	185	0	ENST00000265335.6:c.574C>A	p.Leu192Ile	p.L192I	ENST00000265335		192	Ctt/Att	5/25	1	2	FACETS	0.803	0.691	0.921	0.803	0.691	0.921	CLONAL	1	TRUE	1	0.76	2		185	154	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924403	131924403	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1184353235	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	88	249	0	ENST00000265335.6:c.1076G>A	p.Arg359His	p.R359H	ENST00000265335		359	cGc/cAc	8/25	1	2	FACETS	0.969	0.873	1	0.969	0.873	1	CLONAL	1	TRUE	1	0.76	2		249	239	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131926953	131926953	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1351416655	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	15	301	0	ENST00000265335.6:c.1490T>C	p.Val497Ala	p.V497A	ENST00000265335		497	gTa/gCa	10/25	1	2	FACETS	0.159	0.116	0.21	0.159	0.116	0.21	SUBCLONAL	1	TRUE	1	0.76	2		301	249	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433980	149433980	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	29	482	0	ENST00000286301.3:c.2668C>T	p.Gln890Ter	p.Q890*	ENST00000286301	NM_005211.3	890	Cag/Tag	21/22	1	2	FACETS	0.18	0.144	0.221	0.18	0.144	0.221	SUBCLONAL	1	TRUE	1	0.76	2		482	424	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459795	149459795	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755093010	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	126	420	0	ENST00000286301.3:c.412G>A	p.Val138Ile	p.V138I	ENST00000286301	NM_005211.3	138	Gtc/Atc	4/22	1	2	FACETS	0.947	0.868	1	0.947	0.868	1	CLONAL	1	TRUE	1	0.76	2		420	350	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497358	149497358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35731372	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	127	481	1	ENST00000261799.4:c.2960G>A	p.Arg987Gln	p.R987Q	ENST00000261799	NM_002609.3	987	cGg/cAg	22/23	1	2	FACETS	0.918	0.841	0.997	0.918	0.841	0.997	CLONAL	1	TRUE	1	0.76	2		482	364	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515409	149515409	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	82	323	0	ENST00000261799.4:c.73C>A	p.Leu25Met	p.L25M	ENST00000261799	NM_002609.3	25	Ctg/Atg	3/23	1	2	FACETS	0.968	0.869	1	0.968	0.869	1	CLONAL	1	TRUE	1	0.76	2		323	223	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519418	176519418	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	214	685	1	ENST00000292408.4:c.824G>T	p.Ser275Ile	p.S275I	ENST00000292408	NM_213647.1	275	aGc/aTc	7/18	1	2	FACETS	0.976	0.914	1	0.976	0.914	1	CLONAL	1	TRUE	1	0.76	2		686	577	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673711	176673711	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs570278338	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	127	388	2	ENST00000439151.2:c.4411C>T	p.Arg1471Ter	p.R1471*	ENST00000439151	NM_022455.4	1471	Cga/Tga	10/23	1	2	FACETS	0.877	0.803	0.954	0.877	0.803	0.954	CLONAL	1	TRUE	1	0.76	2		390	381	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405027	405027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568315642	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	160	485	0	ENST00000380956.4:c.1109C>T	p.Ala370Val	p.A370V	ENST00000380956	NM_001195286.1	370	gCg/gTg	8/9	1	2	FACETS	0.986	0.914	1	0.986	0.914	1	CLONAL	1	TRUE	1	0.76	2		485	427	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407527	407527	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs908661692	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	161	484	1	ENST00000380956.4:c.1285G>A	p.Asp429Asn	p.D429N	ENST00000380956	NM_001195286.1	429	Gat/Aat	9/9	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.76	2		485	420	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032161	26032161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866029344	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	352	1065	0	ENST00000244661.2:c.128G>A	p.Arg43His	p.R43H	ENST00000244661	NM_003537.3	43	cGc/cAc	1/1	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.76	2		1065	919	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910615	29910615	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	29	474	0	ENST00000376809.5:c.155T>C	p.Val52Ala	p.V52A	ENST00000376809	NM_002116.7	52	gTg/gCg	2/8	1	2	FACETS	0.221	0.177	0.271	0.221	0.177	0.271	SUBCLONAL	1	TRUE	1	0.76	2		474	345	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286540	33286540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	62	200	1	ENST00000374542.5:c.2203G>A	p.Val735Met	p.V735M	ENST00000374542	NM_001141970.1	735	Gtg/Atg	8/8	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.76	2		201	146	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287491	33287491	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	85	356	0	ENST00000374542.5:c.1606G>T	p.Glu536Ter	p.E536*	ENST00000374542	NM_001141970.1	536	Gaa/Taa	6/8	1	2	FACETS	0.748	0.669	0.831	0.748	0.669	0.831	SUBCLONAL	1	TRUE	1	0.76	2		356	299	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289539	33289539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	155	545	0	ENST00000374542.5:c.164G>A	p.Gly55Asp	p.G55D	ENST00000374542	NM_001141970.1	55	gGc/gAc	2/8	1	2	FACETS	0.893	0.824	0.962	0.893	0.824	0.962	CLONAL	1	TRUE	1	0.76	2		545	457	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140832	37140832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	141	413	0	ENST00000373509.5:c.668C>T	p.Ala223Val	p.A223V	ENST00000373509	NM_002648.3	223	gCg/gTg	5/6	1	2	FACETS	0.93	0.856	1	0.93	0.856	1	CLONAL	1	TRUE	1	0.76	2		413	399	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793686	89793686	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	119	317	0	ENST00000336032.3:c.755C>A	p.Pro252His	p.P252H	ENST00000336032	NM_006813.2	252	cCt/cAt	2/2	1	2	FACETS	0.89	0.812	0.969	0.89	0.812	0.969	CLONAL	1	TRUE	1	0.76	2		317	352	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553312	106553312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1245478888	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	52	351	0	ENST00000369096.4:c.1277G>A	p.Ser426Asn	p.S426N	ENST00000369096	NM_001198.3	426	aGc/aAc	5/7	1	2	FACETS	0.416	0.356	0.481	0.416	0.356	0.481	SUBCLONAL	1	TRUE	1	0.76	2		351	329	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554339	106554339	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	145	543	1	ENST00000369096.4:c.1867C>A	p.Leu623Met	p.L623M	ENST00000369096	NM_001198.3	623	Ctg/Atg	6/7	1	2	FACETS	0.798	0.734	0.865	0.798	0.734	0.865	SUBCLONAL	1	TRUE	1	0.76	2		544	478	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200482	138200482	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	62	164	0	ENST00000237289.4:c.1900A>C	p.Asn634His	p.N634H	ENST00000237289	NM_001270507.1	634	Aac/Cac	7/9	1	2	FACETS	0.863	0.759	0.972	0.863	0.759	0.972	CLONAL	1	TRUE	1	0.76	2		164	189	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983290	149983290	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs761840476	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	34	277	0	ENST00000253339.5:c.2968C>T	p.Arg990Ter	p.R990*	ENST00000253339		990	Cga/Tga	7/7	1	2	FACETS	0.302	0.248	0.363	0.302	0.248	0.363	SUBCLONAL	1	TRUE	1	0.76	2		277	296	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997756	149997756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754664378	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	23	465	0	ENST00000253339.5:c.2711G>A	p.Arg904Gln	p.R904Q	ENST00000253339		904	cGa/cAa	5/7	1	2	FACETS	0.166	0.129	0.209	0.166	0.129	0.209	SUBCLONAL	1	TRUE	1	0.76	2		465	365	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005366	150005366	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	191	716	0	ENST00000253339.5:c.859C>T	p.Arg287Ter	p.R287*	ENST00000253339		287	Cga/Tga	3/7	1	2	FACETS	0.902	0.84	0.966	0.902	0.84	0.966	CLONAL	1	TRUE	1	0.76	2		716	557	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469884	157469884	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	30	548	0	ENST00000346085.5:c.2678C>A	p.Ala893Asp	p.A893D	ENST00000346085	NM_020732.3	893	gCt/gAt	9/20	1	2	FACETS	0.15	0.12	0.184	0.15	0.12	0.184	SUBCLONAL	1	TRUE	1	0.76	2		548	527	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522130	157522130	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758892744	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	85	314	1	ENST00000346085.5:c.4402C>T	p.Arg1468Cys	p.R1468C	ENST00000346085	NM_020732.3	1468	Cgc/Tgc	18/20	1	2	FACETS	0.948	0.852	1	0.948	0.852	1	CLONAL	1	TRUE	1	0.76	2		315	236	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522353	157522353	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs570186838	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	36	554	0	ENST00000346085.5:c.4625C>T	p.Thr1542Met	p.T1542M	ENST00000346085	NM_020732.3	1542	aCg/aTg	18/20	1	2	FACETS	0.175	0.143	0.21	0.175	0.143	0.21	SUBCLONAL	1	TRUE	1	0.76	2		554	542	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953062	2953062	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	166	446	0	ENST00000396946.4:c.2878C>A	p.Leu960Ile	p.L960I	ENST00000396946	NM_032415.4	960	Ctc/Atc	22/25	1	2	FACETS	0.982	0.911	1	0.982	0.911	1	CLONAL	1	TRUE	1	0.76	2		446	445	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026756	6026757	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs863224498	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	26	154	0	ENST00000265849.7:c.1639dup	p.Ser547PhefsTer15	p.S547Ffs*15	ENST00000265849	NM_000535.5	547	tca/tTca	11/15	1	2	FACETS	0.664	0.537	0.803	0.664	0.537	0.803	SUBCLONAL	1	TRUE	1	0.76	2		154	103	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042262	6042262	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1060503139	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	173	524	0	ENST00000265849.7:c.359T>C	p.Val120Ala	p.V120A	ENST00000265849	NM_000535.5	120	gTc/gCc	5/15	1	2	FACETS	0.84	0.778	0.903	0.84	0.778	0.903	CLONAL	1	TRUE	1	0.76	2		524	542	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392134	81392134	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	124	399	1	ENST00000222390.5:c.143C>T	p.Thr48Ile	p.T48I	ENST00000222390	NM_000601.4	48	aCt/aTt	2/18	1	2	FACETS	0.856	0.783	0.932	0.856	0.783	0.932	CLONAL	1	TRUE	1	0.76	2		400	381	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339163	116339163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	73	458	1	ENST00000397752.3:c.25C>T	p.Pro9Ser	p.P9S	ENST00000397752	NM_000245.2	9	Cct/Tct	2/21	1	2	FACETS	0.503	0.442	0.568	0.503	0.442	0.568	SUBCLONAL	1	TRUE	1	0.76	2		459	382	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140487381	140487381	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	426	1140	0	ENST00000288602.6:c.1144T>G	p.Leu382Val	p.L382V	ENST00000288602	NM_004333.4	382	Ttg/Gtg	9/18	1	2	FACETS	0.991	0.946	1	0.991	0.946	1	CLONAL	1	TRUE	1	0.76	2		1140	1131	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151168490	151168490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1015240074	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	216	877	1	ENST00000262187.5:c.370C>T	p.His124Tyr	p.H124Y	ENST00000262187	NM_005614.3	124	Cat/Tat	6/8	1	2	FACETS	0.809	0.755	0.864	0.809	0.755	0.864	CLONAL	1	TRUE	1	0.76	2		878	703	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188085	151188085	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867628277	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	55	976	1	ENST00000262187.5:c.68C>T	p.Thr23Met	p.T23M	ENST00000262187	NM_005614.3	23	aCg/aTg	2/8	1	2	FACETS	0.16	0.136	0.187	0.16	0.136	0.187	SUBCLONAL	1	TRUE	1	0.76	2		977	903	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346380	152346380	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs151110146	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	374	1162	0	ENST00000359321.1:c.190C>T	p.Arg64Ter	p.R64*	ENST00000359321	NM_005431.1	64	Cga/Tga	3/3	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.76	2		1162	979	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372116	55372116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	47	101	0	ENST00000297316.4:c.806C>T	p.Pro269Leu	p.P269L	ENST00000297316	NM_022454.3	269	cCc/cTc	2/2	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.76	2		101	107	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90995052	90995052	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	54	248	0	ENST00000265433.3:c.69G>T	p.Glu23Asp	p.E23D	ENST00000265433	NM_002485.4	23	gaG/gaT	2/16	1	2	FACETS	0.634	0.548	0.726	0.634	0.548	0.726	SUBCLONAL	1	TRUE	1	0.76	2		248	224	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90995074	90995074	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	42	203	1	ENST00000265433.3:c.47A>G	p.Tyr16Cys	p.Y16C	ENST00000265433	NM_002485.4	16	tAc/tGc	2/16	1	2	FACETS	0.594	0.502	0.693	0.594	0.502	0.693	SUBCLONAL	1	TRUE	1	0.76	2		204	186	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859872	117859872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	319	885	1	ENST00000297338.2:c.1763C>T	p.Thr588Met	p.T588M	ENST00000297338	NM_006265.2	588	aCg/aTg	14/14	1	2	FACETS	0.96	0.91	1	0.96	0.91	1	CLONAL	1	TRUE	1	0.76	2		886	874	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341147	8341147	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs724159865	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	111	401	0	ENST00000356435.5:c.5069C>T	p.Pro1690Leu	p.P1690L	ENST00000356435		1690	cCt/cTt	30/35	1	2	FACETS	0.936	0.853	1	0.936	0.853	1	CLONAL	1	TRUE	1	0.76	2		401	312	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499756	8499756	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs113573567	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	156	517	0	ENST00000356435.5:c.2213A>G	p.Asn738Ser	p.N738S	ENST00000356435		738	aAt/aGt	14/35	1	2	FACETS	0.91	0.841	0.981	0.91	0.841	0.981	CLONAL	1	TRUE	1	0.76	2		517	451	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020751	37020751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	165	674	0	ENST00000358127.4:c.94C>T	p.Pro32Ser	p.P32S	ENST00000358127	NM_001280556.1	32	Cca/Tca	2/10	1	2	FACETS	0.841	0.778	0.906	0.841	0.778	0.906	CLONAL	1	TRUE	1	0.76	2		674	516	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359954	87359954	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	176	468	0	ENST00000277120.3:c.1262A>C	p.Asp421Ala	p.D421A	ENST00000277120		421	gAc/gCc	11/19	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.76	2		468	448	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563419	87563419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	121	371	1	ENST00000277120.3:c.1807C>T	p.Arg603Cys	p.R603C	ENST00000277120		603	Cgt/Tgt	16/19	1	2	FACETS	0.965	0.883	1	0.965	0.883	1	CLONAL	1	TRUE	1	0.76	2		372	330	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127911974	127911974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144776498	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	379	1275	0	ENST00000373547.4:c.896C>T	p.Thr299Met	p.T299M	ENST00000373547	NM_002721.4	299	aCg/aTg	7/7	1	2	FACETS	0.885	0.841	0.929	0.885	0.841	0.929	CLONAL	1	TRUE	1	0.76	2		1275	1127	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401765	139401765	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	40	690	0	ENST00000277541.6:c.3635G>T	p.Gly1212Val	p.G1212V	ENST00000277541	NM_017617.3	1212	gGc/gTc	22/34	1	2	FACETS	0.172	0.142	0.206	0.172	0.142	0.206	SUBCLONAL	1	TRUE	1	0.76	2		690	611	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402695	139402695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778118508	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	22	431	0	ENST00000277541.6:c.3314C>T	p.Ala1105Val	p.A1105V	ENST00000277541	NM_017617.3	1105	gCg/gTg	20/34	1	2	FACETS	0.159	0.122	0.201	0.159	0.122	0.201	SUBCLONAL	1	TRUE	1	0.76	2		431	365	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405724	139405724	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	141	411	0	ENST00000277541.6:c.2468-1G>T		p.X823_splice	ENST00000277541	NM_017617.3	823			1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.76	2		411	355	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407979	139407979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200816814	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	138	399	1	ENST00000277541.6:c.2218G>A	p.Asp740Asn	p.D740N	ENST00000277541	NM_017617.3	740	Gac/Aac	14/34	1	2	FACETS	0.956	0.88	1	0.956	0.88	1	CLONAL	1	TRUE	1	0.76	2		400	380	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793317	139793317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755436517	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	409	1215	8	ENST00000247668.2:c.125G>A	p.Arg42His	p.R42H	ENST00000247668	NM_021138.3	42	cGc/cAc	2/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.76	2		1223	985	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841276	15841276	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756515856	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	225	321	1	ENST00000307771.7:c.1360C>T	p.Arg454Trp	p.R454W	ENST00000307771	NM_005089.3	454	Cgg/Tgg	11/11	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.76	1		322	304	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914723	39914723	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	301	459	1	ENST00000378444.4:c.4639C>T	p.Arg1547Ter	p.R1547*	ENST00000378444	NM_001123385.1	1547	Cga/Tga	12/15	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.76	1		460	414	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732864	44732864	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	23	215	0	ENST00000377967.4:c.67A>C	p.Lys23Gln	p.K23Q	ENST00000377967	NM_021140.2	23	Aag/Cag	1/29	1	1	FACETS	0.186	0.145	0.232	0.186	0.145	0.232	SUBCLONAL	1	TRUE	0	0.76	1		215	202	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411147	63411147	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	251	446	0	ENST00000330258.3:c.2020T>C	p.Ser674Pro	p.S674P	ENST00000330258	NM_152424.3	674	Tct/Cct	2/2	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.76	1		446	344	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344629	70344629	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	255	434	0	ENST00000374080.3:c.1990G>T	p.Glu664Ter	p.E664*	ENST00000374080		664	Gaa/Taa	14/45	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.76	1		434	360	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344839	70344839	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	257	484	0	ENST00000374080.3:c.2069C>T	p.Thr690Ile	p.T690I	ENST00000374080		690	aCt/aTt	15/45	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.76	1		484	364	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875930	76875930	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	244	370	0	ENST00000373344.5:c.5205G>A	p.Met1735Ile	p.M1735I	ENST00000373344	NM_000489.3	1735	atG/atA	20/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.76	1		370	315	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907611	76907611	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	25	422	0	ENST00000373344.5:c.4550T>C	p.Leu1517Ser	p.L1517S	ENST00000373344	NM_000489.3	1517	tTg/tCg	15/35	1	1	FACETS	0.099	0.078	0.124	0.099	0.078	0.124	SUBCLONAL	1	TRUE	0	0.76	1		422	410	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123040852	123040852	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	94	265	0	ENST00000355640.3:c.1315G>T	p.Glu439Ter	p.E439*	ENST00000355640		439	Gag/Tag	7/7	1	1	FACETS	0.54	0.487	0.595	0.54	0.487	0.595	SUBCLONAL	1	TRUE	0	0.76	1		265	284	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184056	123184056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	27	242	0	ENST00000218089.9:c.914G>A	p.Arg305Gln	p.R305Q	ENST00000218089	NM_001042749.1	305	cGa/cAa	11/35	1	1	FACETS	0.21	0.168	0.257	0.21	0.168	0.257	SUBCLONAL	1	TRUE	0	0.76	1		242	210	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10267124	10267124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751093624	NA	P-0017739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	8	538	0	ENST00000340748.4:c.1294G>A	p.Glu432Lys	p.E432K	ENST00000340748		432	Gaa/Aaa	17/40	1	2	FACETS	0.054	0.034	0.08	0.054	0.034	0.08	SUBCLONAL	1	TRUE	1	0.777530089168773	2		538	379	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705471	43705471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	98	500	0	ENST00000382044.4:c.5151del	p.Ser1718LeufsTer92	p.S1718Lfs*92	ENST00000382044	NM_001141980.1	1717	ccC/cc	24/28	1	2	FACETS	0.599	0.534	0.669	0.599	0.534	0.669	SUBCLONAL	1	TRUE	1	0.388081243673589	2		500	843	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181892	56181892	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0017754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	44	241	0	ENST00000399503.3:c.4114+2T>G		p.X1372_splice	ENST00000399503	NM_005921.1	1372			1	2	FACETS	0.427	0.358	0.504	0.427	0.358	0.504	SUBCLONAL	1	TRUE	1	0.388081243673589	2		241	531	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246445	105246445	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	59	753	0	ENST00000349310.3:c.155T>G	p.Leu52Arg	p.L52R	ENST00000349310	NM_001014432.1	52	cTc/cGc	4/15	1	2	FACETS	0.349	0.3	0.404	0.349	0.3	0.404	SUBCLONAL	1	TRUE	1	0.388081243673589	2		753	870	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052636	42052638	+	inframe_deletion	In_Frame_Del	DEL	GTG	GTG	-	novel	NA	P-0017754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	70	434	1	ENST00000219905.7:c.7310_7312del	p.Gly2437del	p.G2437del	ENST00000219905	NM_001164273.1	2436	cGTGgt/cgt	20/24	1	2	FACETS	0.407	0.354	0.464	0.407	0.354	0.464	SUBCLONAL	1	TRUE	1	0.388081243673589	2		435	887	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402576	139402576	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777684045	NA	P-0017754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	126	673	0	ENST00000277541.6:c.3341G>A	p.Arg1114His	p.R1114H	ENST00000277541	NM_017617.3	1114	cGc/cAc	21/34	1	2	FACETS	0.813	0.739	0.891	0.813	0.739	0.891	CLONAL	1	TRUE	1	0.524355278871726	2		673	591	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705471	43705471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	111	500	0	ENST00000382044.4:c.5151del	p.Ser1718LeufsTer92	p.S1718Lfs*92	ENST00000382044	NM_001141980.1	1717	ccC/cc	24/28	1	2	FACETS	0.773	0.697	0.852	0.773	0.697	0.852	SUBCLONAL	1	TRUE	1	0.524355278871726	2		500	548	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181892	56181892	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0017754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	81	241	0	ENST00000399503.3:c.4114+2T>G		p.X1372_splice	ENST00000399503	NM_005921.1	1372			1	2	FACETS	0.978	0.87	1	0.978	0.87	1	CLONAL	1	TRUE	1	0.524355278871726	2		241	316	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720712	89720712	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	154	179	0	ENST00000371953.3:c.867del	p.Val290Ter	p.V290*	ENST00000371953	NM_000314.4	288	gAa/ga	8/9	0.771511199352892	2	FACETS	0.891	0.842	0.938	0.891	0.842	0.938	CLONAL	2	TRUE	0	0.771511199352892	2		179	224	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589575	67589576	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	173	443	0	ENST00000274335.5:c.1344dup	p.Leu449IlefsTer3	p.L449Ifs*3	ENST00000274335		446	-/A	10/15	0.771511199352892	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.771511199352892	1		443	272	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0017800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	230	480	1	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.771511199352892	2		481	573	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0017800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	130	275	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	0.771511199352892	2		275	336	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36826894	36826894	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1468	336	681	0	ENST00000373129.3:c.40T>C	p.Ser14Pro	p.S14P	ENST00000373129	NM_032017.1	14	Tcg/Ccg	3/12	0.748439073055398	5	FACETS	1	0.969	1			1	CLONAL	1	TRUE	NA	0.771511199352892	5		681	1804	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813396	102813396	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316717107	NA	P-0017800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	215	456	0	ENST00000307046.8:c.293G>A	p.Arg98Gln	p.R98Q	ENST00000307046	NM_001111285.1	98	cGg/cAg	3/4	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.771511199352892	2		456	542	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921536	178921537	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTGCAACCTACGTGAATGTAAATATGC	novel	NA	P-0017800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	131	505	0	ENST00000263967.3:c.1043_1044insGCGTGCAACCTACGTGAATGTAAATAT	p.Asn347_Ile348insMetArgAlaThrTyrValAsnValAsn	p.N347_I348insMRATYVNVN	ENST00000263967	NM_006218.2	340	tgt/tGTGCAACCTACGTGAATGTAAATATGCgt	5/21	1	2	FACETS	0.62	0.565	0.677	0.62	0.565	0.677	SUBCLONAL	1	TRUE	1	0.771511199352892	2		505	548	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183755	10183757	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs5030648	NA	P-0017835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	239	420	0	ENST00000256474.2:c.227_229del	p.Phe76del	p.F76del	ENST00000256474	NM_000551.3	75	aTCTtc/atc	1/3	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	2	TRUE	NA	0.386846863389983	2		420	569	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121619	108121619	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	93	367	0	ENST00000278616.4:c.1430del	p.Lys477SerfsTer5	p.K477Sfs*5	ENST00000278616	NM_000051.3	476	cAa/ca	10/63	0.386846863389983	1	FACETS	0.721	0.643	0.804	0.721	0.643	0.804	SUBCLONAL	1	TRUE	0	0.386846863389983	1		367	538	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220396	123220396	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0017835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	56	122	0	ENST00000218089.9:c.3054del		p.X1018_splice	ENST00000218089	NM_001042749.1	1018			1	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.386846863389983	1		122	188	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889133	76889137	+	frameshift_variant	Frame_Shift_Del	DEL	CAAAC	CAAAC	-	novel	NA	P-0017852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	76	387	0	ENST00000373344.5:c.4873_4877del	p.Val1625SerfsTer3	p.V1625Sfs*3	ENST00000373344	NM_000489.3	1625	GTTTGt/t	18/35	1	1	FACETS	0.871	0.771	0.976	1	0.981	1	CLONAL	2	TRUE	0	0.248936397240725	1		387	307	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0017919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	451	1047	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.43322678165238	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	0	0.43322678165238	3		1049	800	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0017919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	230	869	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.300670259736194	5	FACETS	1	0.985	1	0.778	0.727	0.829	CLONAL	2	TRUE	2	0.43322678165238	5		869	751	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0017919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	138	275	0	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	0.43322678165238	3	FACETS	0.953	0.886	1	0.953	0.886	1	CLONAL	3	TRUE	0	0.43322678165238	3		275	271	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933232	100933232	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	79	567	0	ENST00000325455.5:c.2158C>A	p.Gln720Lys	p.Q720K	ENST00000325455	NM_001202474.3	720	Caa/Aaa	4/8	0.400963365290632	3	FACETS	0.772	0.68	0.87	0.386	0.34	0.435	SUBCLONAL	1	TRUE	1	0.43322678165238	3		567	575	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017816	31017816	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	79	637	0	ENST00000375687.4:c.678C>A	p.Asp226Glu	p.D226E	ENST00000375687	NM_015338.5	226	gaC/gaA	8/13	0.43322678165238	6	FACETS	0.691	0.606	0.783			1	SUBCLONAL	1	TRUE	NA	0.43322678165238	6		637	985	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130427	29130427	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587781269	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	108	848	3	ENST00000328354.6:c.283C>T	p.Arg95Ter	p.R95*	ENST00000328354	NM_007194.3	95	Cga/Tga	2/15	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.27	2		851	735	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	85	406	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.889	0.786	1	0.889	0.786	1	CLONAL	1	TRUE	1	0.27	2		406	708	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	134	646	1	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.963	0.873	1	0.963	0.873	1	CLONAL	1	TRUE	1	0.27	2		647	1031	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	87	639	9	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.873	0.773	0.981	0.873	0.773	0.981	CLONAL	1	TRUE	1	0.27	2		648	738	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	81	398	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.27	2		398	565	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	70	706	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	0.212500514601687	3	FACETS	0.872	0.76	0.993	0.436	0.38	0.497	CLONAL	1	TRUE	1	0.27	3		706	675	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	106	698	2	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.965	0.864	1	0.965	0.864	1	CLONAL	1	TRUE	1	0.27	2		700	814	SUCCESS
APC	324	MSKCC	GRCh37	5	112163677	112163677	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	65	530	0	ENST00000257430.4:c.1600A>T	p.Lys534Ter	p.K534*	ENST00000257430	NM_000038.5	534	Aaa/Taa	13/16	1	2	FACETS	0.872	0.757	0.997	0.872	0.757	0.997	CLONAL	1	TRUE	1	0.27	2		530	552	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	69	695	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	0.968	0.844	1	0.968	0.844	1	CLONAL	1	TRUE	1	0.27	2		695	528	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486232	8486232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142397137	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	51	438	1	ENST00000356435.5:c.2585G>A	p.Arg862His	p.R862H	ENST00000356435		862	cGc/cAc	17/35	1	2	FACETS	0.832	0.708	0.968	0.832	0.708	0.968	CLONAL	1	TRUE	1	0.27	2		439	454	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007824	45007825	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	103	635	0	ENST00000558401.1:c.276dup	p.Thr93HisfsTer2	p.T93Hfs*2	ENST00000558401	NM_004048.2	91	acc/aCcc	2/4	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.27	2		635	642	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144446	58144446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140644696	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	48	536	1	ENST00000257904.6:c.625C>T	p.Arg209Cys	p.R209C	ENST00000257904	NM_000075.3	209	Cgt/Tgt	5/8	1	2	FACETS	0.744	0.629	0.87	0.744	0.629	0.87	SUBCLONAL	1	TRUE	1	0.27	2		537	478	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280142	66280142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1327931544	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	28	346	0	ENST00000273854.3:c.1547C>T	p.Thr516Met	p.T516M	ENST00000273854	NM_004439.5	516	aCg/aTg	7/18	1	2	FACETS	0.708	0.567	0.868	0.708	0.567	0.868	SUBCLONAL	1	TRUE	1	0.27	2		346	293	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630407	47630407	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	66	698	0	ENST00000233146.2:c.77T>C	p.Met26Thr	p.M26T	ENST00000233146	NM_000251.2	26	aTg/aCg	1/16	1	2	FACETS	0.742	0.644	0.848	0.742	0.644	0.848	SUBCLONAL	1	TRUE	1	0.27	2		698	659	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915939	127915939	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	97	726	2	ENST00000373547.4:c.542G>A	p.Arg181Gln	p.R181Q	ENST00000373547	NM_002721.4	181	cGg/cAg	6/7	1	2	FACETS	0.902	0.803	1	0.902	0.803	1	CLONAL	1	TRUE	1	0.27	2		728	797	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100462	8100462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752779081	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	94	1041	4	ENST00000346208.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000346208		146	Gcc/Acc	3/6	1	2	FACETS	0.825	0.733	0.923	0.825	0.733	0.923	CLONAL	1	TRUE	1	0.27	2		1045	844	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151290	202151290	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	85	795	0	ENST00000358485.4:c.1596del	p.Lys532AsnfsTer73	p.K532Nfs*73	ENST00000358485	NM_001080125.1	530	agA/ag	9/9	1	2	FACETS	0.771	0.68	0.868	0.771	0.68	0.868	SUBCLONAL	1	TRUE	1	0.27	2		795	817	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759752	133759752	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1332380683	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	62	566	0	ENST00000318560.5:c.2075C>T	p.Thr692Met	p.T692M	ENST00000318560	NM_005157.4	692	aCg/aTg	11/11	1	2	FACETS	0.939	0.813	1	0.939	0.813	1	CLONAL	1	TRUE	1	0.27	2		566	489	SUCCESS
APC	324	MSKCC	GRCh37	5	112176021	112176021	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	67	521	0	ENST00000257430.4:c.4731del	p.Glu1577AspfsTer73	p.E1577Dfs*73	ENST00000257430	NM_000038.5	1577	gAa/ga	16/16	1	2	FACETS	0.891	0.775	1	0.891	0.775	1	CLONAL	1	TRUE	1	0.27	2		521	557	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88676912	88676912	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554890743	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	101	711	0	ENST00000372037.3:c.697C>T	p.Gln233Ter	p.Q233*	ENST00000372037	NM_004329.2	233	Cag/Tag	9/13	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.27	2		711	746	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104359295	104359295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369910221	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	95	693	1	ENST00000369902.3:c.1016G>A	p.Arg339Gln	p.R339Q	ENST00000369902	NM_016169.3	339	cGg/cAg	8/12	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.27	2		694	700	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66777380	66777380	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	99	671	1	ENST00000307102.5:c.746T>C	p.Met249Thr	p.M249T	ENST00000307102	NM_002755.3	249	aTg/aCg	7/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.27	2		672	604	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	360011	360011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759808424	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	98	932	1	ENST00000262320.3:c.1078G>A	p.Val360Met	p.V360M	ENST00000262320	NM_003502.3	360	Gtg/Atg	4/11	1	2	FACETS	0.91	0.811	1	0.91	0.811	1	CLONAL	1	TRUE	1	0.27	2		933	798	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106646	2106646	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	92	774	0	ENST00000219476.3:c.650T>C	p.Val217Ala	p.V217A	ENST00000219476	NM_000548.3	217	gTc/gCc	8/42	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.27	2		774	621	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862845	9862845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764289741	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	84	852	1	ENST00000330684.3:c.2458G>A	p.Val820Ile	p.V820I	ENST00000330684	NM_001134407.1	820	Gta/Ata	12/13	1	2	FACETS	0.91	0.804	1	0.91	0.804	1	CLONAL	1	TRUE	1	0.27	2		853	684	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828193	50828193	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	78	679	3	ENST00000398568.2:c.2531G>A	p.Trp844Ter	p.W844*	ENST00000398568	NM_001042412.1	844	tGg/tAg	17/18	1	2	FACETS	0.92	0.809	1	0.92	0.809	1	CLONAL	1	TRUE	1	0.27	2		682	628	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349003	89349003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	105	871	0	ENST00000301030.4:c.3947G>A	p.Gly1316Glu	p.G1316E	ENST00000301030	NM_001256183.1	1316	gGg/gAg	9/13	1	2	FACETS	0.971	0.87	1	0.971	0.87	1	CLONAL	1	TRUE	1	0.27	2		871	801	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349211	89349211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755642596	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1259	197	1470	2	ENST00000301030.4:c.3739G>A	p.Ala1247Thr	p.A1247T	ENST00000301030	NM_001256183.1	1247	Gct/Act	9/13	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.27	2		1472	1456	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676214	29676214	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	79	704	0	ENST00000356175.3:c.7203A>C	p.Lys2401Asn	p.K2401N	ENST00000356175	NM_000267.3	2401	aaA/aaC	48/57	1	2	FACETS	0.823	0.724	0.93	0.823	0.724	0.93	CLONAL	1	TRUE	1	0.27	2		704	711	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681121	37681121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	67	559	0	ENST00000447079.4:c.3290G>A	p.Gly1097Glu	p.G1097E	ENST00000447079	NM_015083.1	1097	gGg/gAg	12/14	1	2	FACETS	0.834	0.725	0.952	0.834	0.725	0.952	CLONAL	1	TRUE	1	0.27	2		559	595	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243940	41243940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55930959	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	101	849	0	ENST00000357654.3:c.3608G>A	p.Arg1203Gln	p.R1203Q	ENST00000357654	NM_007294.3	1203	cGa/cAa	10/23	1	2	FACETS	0.923	0.824	1	0.923	0.824	1	CLONAL	1	TRUE	1	0.27	2		849	811	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752473	55752473	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145329279	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	131	1089	2	ENST00000284073.2:c.931G>A	p.Gly311Ser	p.G311S	ENST00000284073	NM_138962.2	311	Ggc/Agc	12/14	1	2	FACETS	0.967	0.877	1	0.967	0.877	1	CLONAL	1	TRUE	1	0.27	2		1091	1003	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604668	48604668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	56	449	1	ENST00000342988.3:c.1490G>A	p.Arg497His	p.R497H	ENST00000342988	NM_005359.5	497	cGc/cAc	12/12	1	2	FACETS	0.871	0.748	1	0.871	0.748	1	CLONAL	1	TRUE	1	0.27	2		450	476	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7120676	7120676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1295645322	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	116	1009	3	ENST00000302850.5:c.3614C>T	p.Pro1205Leu	p.P1205L	ENST00000302850	NM_000208.2	1205	cCg/cTg	20/22	1	2	FACETS	0.858	0.772	0.95	0.858	0.772	0.95	CLONAL	1	TRUE	1	0.27	2		1012	1001	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383645	15383645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	64	452	0	ENST00000263377.2:c.266C>T	p.Ala89Val	p.A89V	ENST00000263377	NM_058243.2	89	gCc/gTc	2/20	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.27	2		452	463	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266904	18266904	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	49	449	0	ENST00000222254.8:c.215G>T	p.Gly72Val	p.G72V	ENST00000222254	NM_005027.3	72	gGc/gTc	2/16	1	2	FACETS	0.846	0.718	0.987	0.846	0.718	0.987	CLONAL	1	TRUE	1	0.27	2		449	429	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965458	18965458	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	66	599	0	ENST00000262803.5:c.1205C>A	p.Pro402His	p.P402H	ENST00000262803	NM_002911.3	402	cCt/cAt	9/24	1	2	FACETS	0.884	0.768	1	0.884	0.768	1	CLONAL	1	TRUE	1	0.27	2		599	553	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211138	36211138	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	312	1321	2	ENST00000222270.7:c.889C>T	p.Arg297Ter	p.R297*	ENST00000222270	NM_014727.1	297	Cga/Tga	3/37	0.212500514601687	3	FACETS	0.937	0.882	0.993	0.937	0.882	0.993	CLONAL	2	TRUE	1	0.27	3		1323	1400	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36014498	36014498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	92	730	1	ENST00000358208.4:c.271G>A	p.Ala91Thr	p.A91T	ENST00000358208		91	Gcc/Acc	3/12	1	2	FACETS	0.964	0.857	1	0.964	0.857	1	CLONAL	1	TRUE	1	0.27	2		731	707	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164799	36164799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	111	887	2	ENST00000300305.3:c.1076C>T	p.Pro359Leu	p.P359L	ENST00000300305		359	cCg/cTg	8/8	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.27	2		889	730	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817529	39817529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	99	835	0	ENST00000288319.7:c.34G>A	p.Val12Met	p.V12M	ENST00000288319	NM_182918.3	12	Gtg/Atg	2/10	1	2	FACETS	0.913	0.815	1	0.913	0.815	1	CLONAL	1	TRUE	1	0.27	2		835	803	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44520605	44520605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	63	568	0	ENST00000291552.4:c.157C>T	p.Arg53Cys	p.R53C	ENST00000291552	NM_006758.2	53	Cgt/Tgt	3/8	1	2	FACETS	0.829	0.717	0.95	0.829	0.717	0.95	CLONAL	1	TRUE	1	0.27	2		568	563	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873058	134873058	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	131	809	0	ENST00000398015.3:c.1362G>A	p.Trp454Ter	p.W454*	ENST00000398015	NM_004441.4	454	tgG/tgA	6/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.27	2		809	809	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193793	106193793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	45	394	1	ENST00000380013.4:c.4255C>T	p.Pro1419Ser	p.P1419S	ENST00000380013	NM_001127208.2	1419	Cct/Tct	10/11	1	2	FACETS	0.744	0.626	0.874	0.744	0.626	0.874	SUBCLONAL	1	TRUE	1	0.27	2		395	448	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1272314	1272314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371413388	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	84	724	2	ENST00000310581.5:c.2368G>A	p.Val790Ile	p.V790I	ENST00000310581	NM_198253.2	790	Gtc/Atc	7/16	1	2	FACETS	0.957	0.846	1	0.957	0.846	1	CLONAL	1	TRUE	1	0.27	2		726	650	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38148047	38148047	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	133	1030	1	ENST00000317025.8:c.3064G>T	p.Gly1022Ter	p.G1022*	ENST00000317025	NM_023034.1	1022	Gga/Tga	17/24	1	2	FACETS	0.976	0.886	1	0.976	0.886	1	CLONAL	1	TRUE	1	0.27	2		1031	1009	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741466	145741466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746740293	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	123	1022	1	ENST00000428558.2:c.1037C>T	p.Ala346Val	p.A346V	ENST00000428558	NM_004260.3	346	gCc/gTc	5/22	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.27	2		1023	829	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397681	139397681	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	93	857	0	ENST00000277541.6:c.5120C>T	p.Ala1707Val	p.A1707V	ENST00000277541	NM_017617.3	1707	gCc/gTc	27/34	1	2	FACETS	0.944	0.839	1	0.944	0.839	1	CLONAL	1	TRUE	1	0.27	2		857	730	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227954	53227954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1192107564	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	100	954	0	ENST00000375401.3:c.2360G>A	p.Arg787Gln	p.R787Q	ENST00000375401	NM_004187.3	787	cGg/cAg	16/26	1	2	FACETS	0.806	0.719	0.899	0.806	0.719	0.899	CLONAL	1	TRUE	1	0.27	2		954	919	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247133	53247133	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	80	675	1	ENST00000375401.3:c.367G>T	p.Gly123Cys	p.G123C	ENST00000375401	NM_004187.3	123	Ggt/Tgt	4/26	1	2	FACETS	0.93	0.819	1	0.93	0.819	1	CLONAL	1	TRUE	1	0.27	2		676	637	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411231	63411231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775711054	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	92	907	0	ENST00000330258.3:c.1936C>T	p.Arg646Trp	p.R646W	ENST00000330258	NM_152424.3	646	Cgg/Tgg	2/2	1	2	FACETS	0.846	0.751	0.947	0.846	0.751	0.947	CLONAL	1	TRUE	1	0.27	2		907	806	SUCCESS
AR	367	MSKCC	GRCh37	X	66765746	66765746	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769445750	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	159	1435	2	ENST00000374690.3:c.758C>T	p.Ala253Val	p.A253V	ENST00000374690	NM_000044.3	253	gCg/gTg	1/8	1	2	FACETS	0.937	0.857	1	0.937	0.857	1	CLONAL	1	TRUE	1	0.27	2		1437	1257	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339711	70339711	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775072642	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	112	981	0	ENST00000374080.3:c.380C>T	p.Thr127Met	p.T127M	ENST00000374080		127	aCg/aTg	3/45	1	2	FACETS	0.914	0.821	1	0.914	0.821	1	CLONAL	1	TRUE	1	0.27	2		981	908	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347196	70347196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	75	673	0	ENST00000374080.3:c.2860G>A	p.Val954Ile	p.V954I	ENST00000374080		954	Gtc/Atc	21/45	1	2	FACETS	0.96	0.842	1	0.96	0.842	1	CLONAL	1	TRUE	1	0.27	2		673	579	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508752	38508754	+	missense_variant	Missense_Mutation	TNP	ACA	ACA	TCT	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	70	701	0	ENST00000254066.5:c.800_802delinsTCT	p.Asp267_Ile268delinsValPhe	p.D267_I268delinsVF	ENST00000254066	NM_000964.3	267	gACAtc/gTCTtc	6/9	1	2	FACETS	0.87	0.759	0.99	0.87	0.759	0.99	CLONAL	1	TRUE	1	0.27	2		701	596	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	43	566	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	1	2	FACETS	0.579	0.484	0.685	0.579	0.484	0.685	SUBCLONAL	1	TRUE	1	0.27	2		566	550	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798845	45798845	+	splice_region_variant,intron_variant	Splice_Region	DEL	G	G	-	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	72	730	0	ENST00000450313.1:c.389-3del		p.X130_splice	ENST00000450313	NM_012222.2	130			1	2	FACETS	0.964	0.844	1	0.964	0.844	1	CLONAL	1	TRUE	1	0.27	2		730	553	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175747	176175747	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	88	1060	0	ENST00000367669.3:c.368T>C	p.Leu123Pro	p.L123P	ENST00000367669	NM_022457.5	123	cTc/cCc	1/20	1	2	FACETS	0.616	0.544	0.693	0.616	0.544	0.693	SUBCLONAL	1	TRUE	1	0.27	2		1060	1059	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925616	114925616	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	80	1022	2	ENST00000543371.1:c.1694C>A	p.Pro565His	p.P565H	ENST00000543371	NM_001198531.1	565	cCt/cAt	14/14	1	2	FACETS	0.671	0.59	0.759	0.671	0.59	0.759	SUBCLONAL	1	TRUE	1	0.27	2		1024	883	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424710	49424710	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	65	778	1	ENST00000301067.7:c.13637G>T	p.Arg4546Met	p.R4546M	ENST00000301067	NM_003482.3	4546	aGg/aTg	40/54	1	2	FACETS	0.648	0.561	0.743	0.648	0.561	0.743	SUBCLONAL	1	TRUE	1	0.27	2		779	743	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43730536	43730536	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	53	610	5	ENST00000382044.4:c.3177del	p.Thr1060ProfsTer36	p.T1060Pfs*36	ENST00000382044	NM_001141980.1	1059	ccC/cc	16/28	1	2	FACETS	0.523	0.445	0.609	0.523	0.445	0.609	SUBCLONAL	1	TRUE	1	0.27	2		615	751	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991826	72991826	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	69	826	0	ENST00000268489.5:c.2219A>G	p.Asn740Ser	p.N740S	ENST00000268489	NM_006885.3	740	aAc/aGc	2/10	1	2	FACETS	0.693	0.602	0.79	0.693	0.602	0.79	SUBCLONAL	1	TRUE	1	0.27	2		826	738	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52693362	52693362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	55	764	1	ENST00000322088.6:c.13G>A	p.Asp5Asn	p.D5N	ENST00000322088	NM_014225.5	5	Gac/Aac	1/15	0.212500514601687	3	FACETS	0.576	0.491	0.669	0.288	0.245	0.335	SUBCLONAL	1	TRUE	1	0.27	3		765	803	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260608	1260608	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	69	859	1	ENST00000310581.5:c.2951G>T	p.Ser984Ile	p.S984I	ENST00000310581	NM_198253.2	984	aGc/aTc	12/16	1	2	FACETS	0.567	0.493	0.648	0.567	0.493	0.648	SUBCLONAL	1	TRUE	1	0.27	2		860	901	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672975	30672975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446862496	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	94	790	0	ENST00000376406.3:c.3985G>A	p.Ala1329Thr	p.A1329T	ENST00000376406	NM_014641.2	1329	Gcc/Acc	10/15	1	2	FACETS	0.964	0.858	1	0.964	0.858	1	CLONAL	1	TRUE	1	0.27	2		790	722	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286827	33286827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	25	588	0	ENST00000374542.5:c.2110G>A	p.Ala704Thr	p.A704T	ENST00000374542	NM_001141970.1	704	Gcc/Acc	7/8	1	2	FACETS	0.383	0.301	0.477	0.383	0.301	0.477	SUBCLONAL	1	TRUE	1	0.27	2		588	484	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419976	152419976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754403698	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	106	658	1	ENST00000206249.3:c.1663C>T	p.Arg555Cys	p.R555C	ENST00000206249	NM_000125.3	555	Cgt/Tgt	8/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.27	2		659	647	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946152	13946152	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	74	837	0	ENST00000405192.2:c.944G>T	p.Trp315Leu	p.W315L	ENST00000405192	NM_001163147.1	315	tGg/tTg	10/12	0.212500514601687	3	FACETS	0.673	0.588	0.766	0.337	0.294	0.383	SUBCLONAL	1	TRUE	1	0.27	3		837	924	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539096	23539096	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	34	597	0	ENST00000380871.4:c.343A>G	p.Arg115Gly	p.R115G	ENST00000380871	NM_006167.3	115	Agg/Ggg	2/2	1	2	FACETS	0.438	0.357	0.53	0.438	0.357	0.53	SUBCLONAL	1	TRUE	1	0.27	2		597	575	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250454	110250454	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	28	487	0	ENST00000374672.4:c.221T>C	p.Leu74Pro	p.L74P	ENST00000374672	NM_004235.4	74	cTg/cCg	3/5	1	2	FACETS	0.438	0.349	0.539	0.438	0.349	0.539	SUBCLONAL	1	TRUE	1	0.27	2		487	474	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130427	29130427	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587781269	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	254	848	3	ENST00000328354.6:c.283C>T	p.Arg95Ter	p.R95*	ENST00000328354	NM_007194.3	95	Cga/Tga	2/15	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.529732041396132	2		851	956	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	167	406	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	0.873	0.804	0.945			1	INDETERMINATE	1	TRUE	NA	0.529732041396132	2		406	722	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	207	660	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.961	0.894	1	0.961	0.894	1	CLONAL	1	TRUE	1	0.529732041396132	2		663	813	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	667	646	1	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	0.529732041396132	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.529732041396132	3		647	1488	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	205	639	9	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.901	0.837	0.967	0.901	0.837	0.967	CLONAL	1	TRUE	1	0.529732041396132	2		648	859	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	611	398	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.19014601240464	5	FACETS	1	0.994	1			1	INDETERMINATE	3	TRUE	NA	0.529732041396132	5		398	1220	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	240	706	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.976	0.913	1	0.976	0.913	1	CLONAL	1	TRUE	1	0.529732041396132	2		706	928	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	262	698	2	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.963	0.903	1	0.963	0.903	1	CLONAL	1	TRUE	1	0.529732041396132	2		700	1027	SUCCESS
APC	324	MSKCC	GRCh37	5	112163677	112163677	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	168	530	0	ENST00000257430.4:c.1600A>T	p.Lys534Ter	p.K534*	ENST00000257430	NM_000038.5	534	Aaa/Taa	13/16	0.529732041396132	3	FACETS	0.934	0.859	1	0.467	0.429	0.506	CLONAL	1	TRUE	1	0.529732041396132	3		530	859	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	314	695	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.529732041396132	3	FACETS	0.851	0.806	0.897	0.851	0.806	0.897	CLONAL	2	TRUE	1	0.529732041396132	3		695	881	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486232	8486232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142397137	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	169	438	1	ENST00000356435.5:c.2585G>A	p.Arg862His	p.R862H	ENST00000356435		862	cGc/cAc	17/35	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.529732041396132	2		439	593	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007824	45007825	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	375	635	0	ENST00000558401.1:c.276dup	p.Thr93HisfsTer2	p.T93Hfs*2	ENST00000558401	NM_004048.2	91	acc/aCcc	2/4	0.529732041396132	2	FACETS	0.846	0.807	0.885	0.846	0.807	0.885	CLONAL	2	TRUE	0	0.529732041396132	2		635	837	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144446	58144446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140644696	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	165	536	1	ENST00000257904.6:c.625C>T	p.Arg209Cys	p.R209C	ENST00000257904	NM_000075.3	209	Cgt/Tgt	5/8	0.529732041396132	3	FACETS	1	0.927	1	0.504	0.464	0.547	CLONAL	1	TRUE	1	0.529732041396132	3		537	781	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280142	66280142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1327931544	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	89	346	0	ENST00000273854.3:c.1547C>T	p.Thr516Met	p.T516M	ENST00000273854	NM_004439.5	516	aCg/aTg	7/18	1	2	FACETS	0.765	0.682	0.854	0.765	0.682	0.854	SUBCLONAL	1	TRUE	1	0.529732041396132	2		346	439	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630407	47630407	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	287	698	0	ENST00000233146.2:c.77T>C	p.Met26Thr	p.M26T	ENST00000233146	NM_000251.2	26	aTg/aCg	1/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.529732041396132	2		698	1046	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915939	127915939	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	264	726	2	ENST00000373547.4:c.542G>A	p.Arg181Gln	p.R181Q	ENST00000373547	NM_002721.4	181	cGg/cAg	6/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.529732041396132	2		728	924	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100462	8100462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752779081	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	286	1041	4	ENST00000346208.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000346208		146	Gcc/Acc	3/6	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.529732041396132	2		1045	1020	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151290	202151290	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	228	795	0	ENST00000358485.4:c.1596del	p.Lys532AsnfsTer73	p.K532Nfs*73	ENST00000358485	NM_001080125.1	530	agA/ag	9/9	1	2	FACETS	0.968	0.904	1	0.968	0.904	1	CLONAL	1	TRUE	1	0.529732041396132	2		795	889	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759752	133759752	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1332380683	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	212	566	0	ENST00000318560.5:c.2075C>T	p.Thr692Met	p.T692M	ENST00000318560	NM_005157.4	692	aCg/aTg	11/11	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.529732041396132	2		566	784	SUCCESS
APC	324	MSKCC	GRCh37	5	112176021	112176021	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	306	521	0	ENST00000257430.4:c.4731del	p.Glu1577AspfsTer73	p.E1577Dfs*73	ENST00000257430	NM_000038.5	1577	gAa/ga	16/16	0.529732041396132	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.529732041396132	3		521	691	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948523	31948523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756991872	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	15	119	0	ENST00000375333.2:c.1006C>T	p.Arg336Trp	p.R336W	ENST00000375333	NM_032454.1	336	Cgg/Tgg	7/8	0.529732041396132	2	FACETS	0.584	0.433	0.76	0.292	0.216	0.38	SUBCLONAL	1	TRUE	0	0.529732041396132	2		119	97	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88676912	88676912	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554890743	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	197	711	0	ENST00000372037.3:c.697C>T	p.Gln233Ter	p.Q233*	ENST00000372037	NM_004329.2	233	Cag/Tag	9/13	1	2	FACETS	0.944	0.876	1	0.944	0.876	1	CLONAL	1	TRUE	1	0.529732041396132	2		711	788	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104359295	104359295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369910221	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	179	693	1	ENST00000369902.3:c.1016G>A	p.Arg339Gln	p.R339Q	ENST00000369902	NM_016169.3	339	cGg/cAg	8/12	1	2	FACETS	0.899	0.83	0.969	0.899	0.83	0.969	CLONAL	1	TRUE	1	0.529732041396132	2		694	752	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66777380	66777380	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	511	671	1	ENST00000307102.5:c.746T>C	p.Met249Thr	p.M249T	ENST00000307102	NM_002755.3	249	aTg/aCg	7/11	0.529732041396132	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.529732041396132	2		672	956	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	360011	360011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759808424	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	297	932	1	ENST00000262320.3:c.1078G>A	p.Val360Met	p.V360M	ENST00000262320	NM_003502.3	360	Gtg/Atg	4/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.529732041396132	2		933	1116	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106646	2106646	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	248	774	0	ENST00000219476.3:c.650T>C	p.Val217Ala	p.V217A	ENST00000219476	NM_000548.3	217	gTc/gCc	8/42	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.529732041396132	2		774	922	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862845	9862845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764289741	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	289	852	1	ENST00000330684.3:c.2458G>A	p.Val820Ile	p.V820I	ENST00000330684	NM_001134407.1	820	Gta/Ata	12/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.529732041396132	2		853	986	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828193	50828193	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	171	679	3	ENST00000398568.2:c.2531G>A	p.Trp844Ter	p.W844*	ENST00000398568	NM_001042412.1	844	tGg/tAg	17/18	1	2	FACETS	0.829	0.764	0.896	0.829	0.764	0.896	CLONAL	1	TRUE	1	0.529732041396132	2		682	779	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349003	89349003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	304	871	0	ENST00000301030.4:c.3947G>A	p.Gly1316Glu	p.G1316E	ENST00000301030	NM_001256183.1	1316	gGg/gAg	9/13	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.529732041396132	2		871	1018	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349211	89349211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755642596	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	351	1470	2	ENST00000301030.4:c.3739G>A	p.Ala1247Thr	p.A1247T	ENST00000301030	NM_001256183.1	1247	Gct/Act	9/13	1	2	FACETS	0.927	0.876	0.978	0.927	0.876	0.978	CLONAL	1	TRUE	1	0.529732041396132	2		1472	1430	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676214	29676214	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	194	704	0	ENST00000356175.3:c.7203A>C	p.Lys2401Asn	p.K2401N	ENST00000356175	NM_000267.3	2401	aaA/aaC	48/57	1	2	FACETS	0.982	0.911	1	0.982	0.911	1	CLONAL	1	TRUE	1	0.529732041396132	2		704	746	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681121	37681121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	209	559	0	ENST00000447079.4:c.3290G>A	p.Gly1097Glu	p.G1097E	ENST00000447079	NM_015083.1	1097	gGg/gAg	12/14	1	2	FACETS	0.972	0.904	1	0.972	0.904	1	CLONAL	1	TRUE	1	0.529732041396132	2		559	812	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243940	41243940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55930959	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	271	849	0	ENST00000357654.3:c.3608G>A	p.Arg1203Gln	p.R1203Q	ENST00000357654	NM_007294.3	1203	cGa/cAa	10/23	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.529732041396132	2		849	1005	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752473	55752473	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145329279	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	305	1089	2	ENST00000284073.2:c.931G>A	p.Gly311Ser	p.G311S	ENST00000284073	NM_138962.2	311	Ggc/Agc	12/14	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.529732041396132	2		1091	1100	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604668	48604668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	163	449	1	ENST00000342988.3:c.1490G>A	p.Arg497His	p.R497H	ENST00000342988	NM_005359.5	497	cGc/cAc	12/12	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.529732041396132	2		450	583	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7120676	7120676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1295645322	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	319	1009	3	ENST00000302850.5:c.3614C>T	p.Pro1205Leu	p.P1205L	ENST00000302850	NM_000208.2	1205	cCg/cTg	20/22	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.529732041396132	2		1012	1128	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383645	15383645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	176	452	0	ENST00000263377.2:c.266C>T	p.Ala89Val	p.A89V	ENST00000263377	NM_058243.2	89	gCc/gTc	2/20	1	2	FACETS	0.986	0.911	1	0.986	0.911	1	CLONAL	1	TRUE	1	0.529732041396132	2		452	674	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266904	18266904	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	184	449	0	ENST00000222254.8:c.215G>T	p.Gly72Val	p.G72V	ENST00000222254	NM_005027.3	72	gGc/gTc	2/16	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.529732041396132	2		449	670	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965458	18965458	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	214	599	0	ENST00000262803.5:c.1205C>A	p.Pro402His	p.P402H	ENST00000262803	NM_002911.3	402	cCt/cAt	9/24	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.529732041396132	2		599	792	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211138	36211138	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	361	1321	2	ENST00000222270.7:c.889C>T	p.Arg297Ter	p.R297*	ENST00000222270	NM_014727.1	297	Cga/Tga	3/37	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.529732041396132	2		1323	1305	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36014498	36014498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	519	730	1	ENST00000358208.4:c.271G>A	p.Ala91Thr	p.A91T	ENST00000358208		91	Gcc/Acc	3/12	0.529732041396132	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.529732041396132	3		731	1170	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164799	36164799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	312	887	2	ENST00000300305.3:c.1076C>T	p.Pro359Leu	p.P359L	ENST00000300305		359	cCg/cTg	8/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.529732041396132	2		889	1123	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817529	39817529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	205	835	0	ENST00000288319.7:c.34G>A	p.Val12Met	p.V12M	ENST00000288319	NM_182918.3	12	Gtg/Atg	2/10	1	2	FACETS	0.864	0.802	0.928	0.864	0.802	0.928	CLONAL	1	TRUE	1	0.529732041396132	2		835	896	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44520605	44520605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	174	568	0	ENST00000291552.4:c.157C>T	p.Arg53Cys	p.R53C	ENST00000291552	NM_006758.2	53	Cgt/Tgt	3/8	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.529732041396132	2		568	639	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873058	134873058	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	266	809	0	ENST00000398015.3:c.1362G>A	p.Trp454Ter	p.W454*	ENST00000398015	NM_004441.4	454	tgG/tgA	6/16	1	2	FACETS	0.958	0.899	1	0.958	0.899	1	CLONAL	1	TRUE	1	0.529732041396132	2		809	1048	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193793	106193793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	154	394	1	ENST00000380013.4:c.4255C>T	p.Pro1419Ser	p.P1419S	ENST00000380013	NM_001127208.2	1419	Cct/Tct	10/11	1	2	FACETS	0.979	0.9	1	0.979	0.9	1	CLONAL	1	TRUE	1	0.529732041396132	2		395	594	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1272314	1272314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371413388	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	986	724	2	ENST00000310581.5:c.2368G>A	p.Val790Ile	p.V790I	ENST00000310581	NM_198253.2	790	Gtc/Atc	7/16	0.529732041396132	5	FACETS	1	0.983	1	1	0.983	1	CLONAL	4	TRUE	1	0.529732041396132	5		726	1655	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38148047	38148047	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	305	1030	1	ENST00000317025.8:c.3064G>T	p.Gly1022Ter	p.G1022*	ENST00000317025	NM_023034.1	1022	Gga/Tga	17/24	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.529732041396132	2		1031	1087	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741466	145741466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746740293	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	322	1022	1	ENST00000428558.2:c.1037C>T	p.Ala346Val	p.A346V	ENST00000428558	NM_004260.3	346	gCc/gTc	5/22	1	2	FACETS	0.981	0.926	1	0.981	0.926	1	CLONAL	1	TRUE	1	0.529732041396132	2		1023	1239	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397681	139397681	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	236	857	0	ENST00000277541.6:c.5120C>T	p.Ala1707Val	p.A1707V	ENST00000277541	NM_017617.3	1707	gCc/gTc	27/34	1	2	FACETS	0.919	0.858	0.981	0.919	0.858	0.981	CLONAL	1	TRUE	1	0.529732041396132	2		857	970	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227954	53227954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1192107564	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	272	954	0	ENST00000375401.3:c.2360G>A	p.Arg787Gln	p.R787Q	ENST00000375401	NM_004187.3	787	cGg/cAg	16/26	1	2	FACETS	0.904	0.848	0.962	0.904	0.848	0.962	CLONAL	1	TRUE	1	0.529732041396132	2		954	1136	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247133	53247133	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	161	675	1	ENST00000375401.3:c.367G>T	p.Gly123Cys	p.G123C	ENST00000375401	NM_004187.3	123	Ggt/Tgt	4/26	1	2	FACETS	0.928	0.854	1	0.928	0.854	1	CLONAL	1	TRUE	1	0.529732041396132	2		676	655	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411231	63411231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775711054	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	246	907	0	ENST00000330258.3:c.1936C>T	p.Arg646Trp	p.R646W	ENST00000330258	NM_152424.3	646	Cgg/Tgg	2/2	1	2	FACETS	0.976	0.913	1	0.976	0.913	1	CLONAL	1	TRUE	1	0.529732041396132	2		907	952	SUCCESS
AR	367	MSKCC	GRCh37	X	66765746	66765746	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769445750	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	338	1435	2	ENST00000374690.3:c.758C>T	p.Ala253Val	p.A253V	ENST00000374690	NM_000044.3	253	gCg/gTg	1/8	1	2	FACETS	0.993	0.939	1	0.993	0.939	1	CLONAL	1	TRUE	1	0.529732041396132	2		1437	1285	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339711	70339711	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775072642	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	270	981	0	ENST00000374080.3:c.380C>T	p.Thr127Met	p.T127M	ENST00000374080		127	aCg/aTg	3/45	1	2	FACETS	0.974	0.914	1	0.974	0.914	1	CLONAL	1	TRUE	1	0.529732041396132	2		981	1047	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347196	70347196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	214	673	0	ENST00000374080.3:c.2860G>A	p.Val954Ile	p.V954I	ENST00000374080		954	Gtc/Atc	21/45	1	2	FACETS	0.871	0.81	0.934	0.871	0.81	0.934	CLONAL	1	TRUE	1	0.529732041396132	2		673	928	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508752	38508754	+	missense_variant	Missense_Mutation	TNP	ACA	ACA	TCT	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	175	701	0	ENST00000254066.5:c.800_802delinsTCT	p.Asp267_Ile268delinsValPhe	p.D267_I268delinsVF	ENST00000254066	NM_000964.3	267	gACAtc/gTCTtc	6/9	1	2	FACETS	0.886	0.817	0.956	0.886	0.817	0.956	CLONAL	1	TRUE	1	0.529732041396132	2		701	746	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856254	111856254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	67	98	0	ENST00000341259.2:c.305C>T	p.Ala102Val	p.A102V	ENST00000341259	NM_005475.2	102	gCg/gTg	2/8	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.529732041396132	2		98	194	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199534	16199534	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	188	501	0	ENST00000375759.3:c.307G>T	p.Glu103Ter	p.E103*	ENST00000375759	NM_015001.2	103	Gag/Tag	2/15	1	2	FACETS	0.914	0.846	0.983	0.914	0.846	0.983	CLONAL	1	TRUE	1	0.529732041396132	2		501	777	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39311694	39311694	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	326	826	0	ENST00000373001.3:c.965A>G	p.Asn322Ser	p.N322S	ENST00000373001	NM_022157.3	322	aAt/aGt	6/7	1	2	FACETS	0.982	0.927	1	0.982	0.927	1	CLONAL	1	TRUE	1	0.529732041396132	2		826	1254	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100519	8100519	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	64	721	1	ENST00000346208.3:c.493C>A	p.Pro165Thr	p.P165T	ENST00000346208		165	Cca/Aca	3/6	1	2	FACETS	0.23	0.198	0.265	0.23	0.198	0.265	SUBCLONAL	1	TRUE	1	0.529732041396132	2		722	1050	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457950	69457950	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	269	615	2	ENST00000227507.2:c.350T>C	p.Ile117Thr	p.I117T	ENST00000227507	NM_053056.2	117	aTc/aCc	2/5	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.529732041396132	2		617	942	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981797	101981797	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	242	665	0	ENST00000282441.5:c.218T>C	p.Met73Thr	p.M73T	ENST00000282441	NM_001130145.2	73	aTg/aCg	1/9	1	2	FACETS	0.896	0.837	0.956	0.896	0.837	0.956	CLONAL	1	TRUE	1	0.529732041396132	2		665	1020	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420931	49420931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	448	620	0	ENST00000301067.7:c.14818C>T	p.Pro4940Ser	p.P4940S	ENST00000301067	NM_003482.3	4940	Ccc/Tcc	48/54	0.529732041396132	3	FACETS	0.93	0.889	0.971	0.93	0.889	0.971	CLONAL	2	TRUE	1	0.529732041396132	3		620	1150	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435114	49435114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886531057	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	523	612	0	ENST00000301067.7:c.6439G>A	p.Ala2147Thr	p.A2147T	ENST00000301067	NM_003482.3	2147	Gcg/Acg	31/54	0.529732041396132	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.529732041396132	3		612	1165	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007896	45007897	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	200	418	0	ENST00000558401.1:c.346+1dup		p.W115fs	ENST00000558401	NM_004048.2	115	tgg/tGgg	2/4	0.529732041396132	2	FACETS	1	0.968	1	0.536	0.498	0.574	CLONAL	1	TRUE	0	0.529732041396132	2		418	705	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40384054	40384054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	236	580	0	ENST00000293328.3:c.92G>A	p.Arg31Gln	p.R31Q	ENST00000293328	NM_012448.3	31	cGg/cAg	2/19	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.529732041396132	2		580	880	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158636932	158636932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	204	517	0	ENST00000263640.3:c.248C>T	p.Thr83Ile	p.T83I	ENST00000263640	NM_001105.4	83	aCc/aTc	4/11	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.529732041396132	2		517	767	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264298	46264298	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	158	430	0	ENST00000371998.3:c.1345C>T	p.Gln449Ter	p.Q449*	ENST00000371998		449	Caa/Taa	11/23	0.529732041396132	3	FACETS	0.934	0.857	1	0.467	0.428	0.507	CLONAL	1	TRUE	1	0.529732041396132	3		430	808	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114721	73114721	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	160	405	0	ENST00000356692.5:c.1102G>T	p.Gly368Cys	p.G368C	ENST00000356692		368	Ggc/Tgc	9/9	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.529732041396132	2		405	578	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981196	55981196	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	153	502	0	ENST00000263923.4:c.503A>C	p.Lys168Thr	p.K168T	ENST00000263923	NM_002253.2	168	aAg/aCg	5/30	1	2	FACETS	0.981	0.901	1	0.981	0.901	1	CLONAL	1	TRUE	1	0.529732041396132	2		502	589	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224769	123224769	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	249	798	1	ENST00000218089.9:c.3533C>T	p.Ala1178Val	p.A1178V	ENST00000218089	NM_001042749.1	1178	gCa/gTa	32/35	1	2	FACETS	0.962	0.901	1	0.962	0.901	1	CLONAL	1	TRUE	1	0.529732041396132	2		799	977	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0017987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	23	376	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	0.143	0.111	0.18	0.143	0.111	0.18	SUBCLONAL	1	TRUE	1	0.646187344478324	2		376	499	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246445	105246445	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	52	753	0	ENST00000349310.3:c.155T>G	p.Leu52Arg	p.L52R	ENST00000349310	NM_001014432.1	52	cTc/cGc	4/15	1	2	FACETS	0.231	0.196	0.27	0.231	0.196	0.27	SUBCLONAL	1	TRUE	1	0.646187344478324	2		753	696	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150549852	150549853	+	frameshift_variant,stop_lost	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0017987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	387	639	0	ENST00000369026.2:c.1051_1052del	p.Ter351AlafsTer4	p.*351Afs*4	ENST00000369026	NM_021960.4	351	TAg/g	3/3	0.518187849484365	3	FACETS	0.815	0.777	0.854	0.815	0.777	0.854	CLONAL	2	TRUE	1	0.646187344478324	3		639	972	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	71	406	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.949	0.83	1	0.949	0.83	1	CLONAL	1	TRUE	1	0.29	2		406	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578525	7578525	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	134	1200	6	ENST00000269305.4:c.405C>A	p.Cys135Ter	p.C135*	ENST00000269305	NM_001126112.2	135	tgC/tgA	5/11	0.296009779912632	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.29	1		1206	776	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971069	21971069	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	46	336	0	ENST00000304494.5:c.289C>G	p.Leu97Val	p.L97V	ENST00000304494	NM_000077.4	97	Ctg/Gtg	2/3	0.296009779912632	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.29	1		336	228	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931463	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622007	NA	P-0018315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	133	509	1	ENST00000374690.3:c.2105T>A	p.Leu702His	p.L702H	ENST00000374690	NM_000044.3	702	cTc/cAc	4/8	0.389921534505328	2	FACETS	1	0.937	1			1	CLONAL	1	FALSE	NA	0.389921534505328	2		510	658	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0018315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	125	312	3	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	0.389921534505328	3	FACETS	0.785	0.715	0.858			1	SUBCLONAL	2	FALSE	NA	0.389921534505328	3		315	488	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274090	10274090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758117698	NA	P-0018315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	121	598	2	ENST00000330684.3:c.179C>T	p.Ala60Val	p.A60V	ENST00000330684	NM_001134407.1	60	gCg/gTg	2/13	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	FALSE	1	0.389921534505328	2		600	612	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40468851	40468851	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	248	568	0	ENST00000264657.5:c.2213G>C	p.Gly738Ala	p.G738A	ENST00000264657	NM_139276.2	738	gGa/gCa	23/24	0.331686174404371	4	FACETS	0.971	0.91	1			1	CLONAL	2	FALSE	NA	0.389921534505328	4		568	910	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0018413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	58	471	8	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	0.726538348203147	3	FACETS	0.775	0.671	0.885	0.258	0.223	0.295	SUBCLONAL	1	TRUE	0	0.726538348203147	3		479	281	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588810	69588810	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	136	509	0	ENST00000168712.1:c.426G>T	p.Lys142Asn	p.K142N	ENST00000168712	NM_002007.2	142	aaG/aaT	2/3	0.726538348203147	3	FACETS	0.764	0.696	0.835	0.382	0.348	0.418	SUBCLONAL	1	TRUE	1	0.726538348203147	3		509	668	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811605	102811605	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1565968684	NA	P-0018413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	63	606	1	ENST00000307046.8:c.579del	p.Gly194GlufsTer8	p.G194Efs*8	ENST00000307046	NM_001111285.1	193	aaA/aa	4/4	0.532695692261092	5	FACETS	0.911	0.791	1	0.304	0.263	0.347	CLONAL	1	TRUE	2	0.726538348203147	5		607	398	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32905116	32905116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55854959	NA	P-0018413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	64	393	0	ENST00000380152.3:c.742G>A	p.Ala248Thr	p.A248T	ENST00000380152		248	Gct/Act	9/27	0.726538348203147	5	FACETS	0.673	0.583	0.77	0.224	0.194	0.257	SUBCLONAL	1	TRUE	2	0.726538348203147	5		393	547	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355831	73355831	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1208729394	NA	P-0018413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	28	387	1	ENST00000377767.4:c.140C>T	p.Ala47Val	p.A47V	ENST00000377767	NM_014953.3	47	gCc/gTc	1/21	0.726538348203147	4	FACETS	0.355	0.283	0.436	0.089	0.07	0.109	SUBCLONAL	1	TRUE	0	0.726538348203147	4		388	375	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437755	110437755	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	48	544	0	ENST00000375856.3:c.646del	p.Val216CysfsTer14	p.V216Cfs*14	ENST00000375856	NM_003749.2	216	Gtg/tg	1/2	0.726538348203147	4	FACETS	0.279	0.235	0.328	0.07	0.058	0.082	SUBCLONAL	1	TRUE	0	0.726538348203147	4		544	818	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2105497	2105497	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	160	453	0	ENST00000219476.3:c.576C>G	p.Asp192Glu	p.D192E	ENST00000219476	NM_000548.3	192	gaC/gaG	6/42	0.726538348203147	3	FACETS	1	0.986	1	0.651	0.602	0.701	CLONAL	1	TRUE	1	0.726538348203147	3		453	461	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788609	3788609	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs945398646	NA	P-0018413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	119	525	1	ENST00000262367.5:c.4345G>A	p.Val1449Ile	p.V1449I	ENST00000262367	NM_004380.2	1449	Gtt/Att	26/31	0.726538348203147	3	FACETS	1	0.953	1	0.537	0.488	0.587	CLONAL	1	TRUE	1	0.726538348203147	3		526	416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0018413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	837	528	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.488431543334856	6	FACETS	1	0.993	1	1	0.999	1	CLONAL	6	TRUE	3	0.726538348203147	6		528	930	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211154	2211154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	122	557	1	ENST00000398665.3:c.1408C>T	p.His470Tyr	p.H470Y	ENST00000398665	NM_032482.2	470	Cac/Tac	15/28	0.726538348203147	5	FACETS	0.636	0.573	0.702			1	SUBCLONAL	1	TRUE	NA	0.726538348203147	5		558	1104	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710578	40710578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs943054949	NA	P-0018413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	43	477	1	ENST00000373198.4:c.4273G>A	p.Val1425Met	p.V1425M	ENST00000373198	NM_133170.3	1425	Gtg/Atg	31/32	0.726538348203147	6	FACETS	0.368	0.307	0.437	0.092	0.076	0.11	SUBCLONAL	1	TRUE	2	0.726538348203147	6		478	788	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184621	185184621	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	76	303	2	ENST00000265026.3:c.1513C>T	p.Gln505Ter	p.Q505*	ENST00000265026	NM_004721.4	505	Caa/Taa	10/14	0.726538348203147	7	FACETS	1	0.962	1	0.206	0.181	0.233	CLONAL	1	TRUE	1	0.726538348203147	7		305	477	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526976	31526976	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1485879154	NA	P-0018413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	72	484	2	ENST00000344624.3:c.64C>T	p.Arg22Ter	p.R22*	ENST00000344624		22	Cga/Tga	2/33	0.726538348203147	2	FACETS	0.487	0.427	0.551	0.243	0.213	0.276	SUBCLONAL	1	TRUE	0	0.726538348203147	2		486	407	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876454	35876454	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	18	527	0	ENST00000303115.3:c.1250del	p.Pro417LeufsTer10	p.P417Lfs*10	ENST00000303115	NM_002185.3	416	Ccc/cc	8/8	0.726538348203147	2	FACETS	0.141	0.105	0.183	0.07	0.052	0.092	SUBCLONAL	1	TRUE	0	0.726538348203147	2		527	352	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005549	150005549	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773529417	NA	P-0018413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	29	272	0	ENST00000253339.5:c.676G>A	p.Ala226Thr	p.A226T	ENST00000253339		226	Gct/Act	3/7	0.726538348203147	2	FACETS	0.554	0.451	0.668	0.277	0.225	0.334	SUBCLONAL	1	TRUE	0	0.726538348203147	2		272	144	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978321	2978321	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs138920531	NA	P-0018413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	120	381	0	ENST00000396946.4:c.1009C>T	p.Arg337Ter	p.R337*	ENST00000396946	NM_032415.4	337	Cga/Tga	7/25	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.726538348203147	2		381	308	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339859	116339859	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs746216803	NA	P-0018413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	87	408	0	ENST00000397752.3:c.721T>C	p.Phe241Leu	p.F241L	ENST00000397752	NM_000245.2	241	Ttc/Ctc	2/21	0.726538348203147	8	FACETS	0.994	0.88	1	0.199	0.176	0.224	CLONAL	1	TRUE	3	0.726538348203147	8		408	766	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879429	151879429	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140631041	NA	P-0018413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	32	352	2	ENST00000262189.6:c.5516C>T	p.Thr1839Met	p.T1839M	ENST00000262189	NM_170606.2	1839	aCg/aTg	36/59	0.726538348203147	8	FACETS	0.48	0.389	0.584	0.096	0.077	0.117	SUBCLONAL	1	TRUE	3	0.726538348203147	8		354	583	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611219	100611219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781792640	NA	P-0018413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	45	371	2	ENST00000308731.7:c.1387G>A	p.Val463Ile	p.V463I	ENST00000308731	NM_000061.2	463	Gtc/Atc	15/19	0.370274629918951	1	FACETS	0.311	0.263	0.362	0.311	0.263	0.362	INDETERMINATE	1	TRUE	0	0.726538348203147	1		373	254	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916929	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519931	NA	P-0018454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	207	619	0	ENST00000263967.3:c.316G>C	p.Gly106Arg	p.G106R	ENST00000263967	NM_006218.2	106	Ggc/Cgc	2/21	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.367964871588613	2		619	888	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0018454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	147	554	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.367964871588613	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.367964871588613	1		554	636	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	167	576	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.367964871588613	2		576	651	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9786966	9786966	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0018454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	86	423	0	ENST00000377346.4:c.2998-1G>T		p.X1000_splice	ENST00000377346	NM_005026.3	1000			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.367964871588613	NA		423	510	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145424	61145424	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	75	314	0	ENST00000295025.8:c.634C>T	p.Gln212Ter	p.Q212*	ENST00000295025	NM_002908.2	212	Cag/Tag	6/11	1	2	FACETS	0.769	0.675	0.87	0.769	0.675	0.87	SUBCLONAL	1	TRUE	1	0.367964871588613	2		314	530	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	127	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.802	0.732	0.875	0.802	0.732	0.875	CLONAL	1	TRUE	1	0.700499429654585	2		306	452	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0018466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	231	511	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	0.954	0.894	1	0.954	0.894	1	CLONAL	1	TRUE	1	0.700499429654585	2		511	691	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170021	32170021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	321	593	0	ENST00000375023.3:c.3587G>A	p.Gly1196Glu	p.G1196E	ENST00000375023	NM_004557.3	1196	gGa/gAa	21/30	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.700499429654585	2		593	883	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55154995	55154995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	192	451	0	ENST00000257290.5:c.2704G>A	p.Asp902Asn	p.D902N	ENST00000257290	NM_006206.4	902	Gat/Aat	20/23	1	2	FACETS	0.957	0.891	1	0.957	0.891	1	CLONAL	1	TRUE	1	0.700499429654585	2		451	573	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155016	108155016	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	152	428	0	ENST00000278616.4:c.3809C>T	p.Ser1270Phe	p.S1270F	ENST00000278616	NM_000051.3	1270	tCc/tTc	26/63	0.700499429654585	1	FACETS	0.921	0.859	0.984	0.921	0.859	0.984	CLONAL	1	TRUE	0	0.700499429654585	1		428	306	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576647	7576980	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGGTCTGGTCCTTTAAAATATATATTATGGTATAAGTTGGTGTTCTGAAGTTAGTTAGCTACAACCAGGAGCCATTGTCTTTGAGGCATCACTGCCCCCTGATGGCAAATGCCCCAATTGCAGGTAAAACAGTCAAGAAGAAAACGGCATTTTGAGTGTTAGACTGGAAACTTTCCACTTGATAAGAGGTCCCAAGACTTAGTACCTGAAGGGTGAAATATTCTCCATCCAGTGGTTTCTTCTTTGGCTGGGGAGAGGAGCTGGTGTTGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAAAGTGAATCTGAGGCATAACTGCACC	CTGGTCTGGTCCTTTAAAATATATATTATGGTATAAGTTGGTGTTCTGAAGTTAGTTAGCTACAACCAGGAGCCATTGTCTTTGAGGCATCACTGCCCCCTGATGGCAAATGCCCCAATTGCAGGTAAAACAGTCAAGAAGAAAACGGCATTTTGAGTGTTAGACTGGAAACTTTCCACTTGATAAGAGGTCCCAAGACTTAGTACCTGAAGGGTGAAATATTCTCCATCCAGTGGTTTCTTCTTTGGCTGGGGAGAGGAGCTGGTGTTGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAAAGTGAATCTGAGGCATAACTGCACC	-	novel	NA	P-0018466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	246	426	0	ENST00000269305.4:c.919+39_993+206del		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	0.700499429654585	1	FACETS	0.99	0.939	1	0.99	0.939	1	CLONAL	1	TRUE	0	0.700499429654585	1		426	461	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483928	212483928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	172	485	0	ENST00000342788.4:c.2275C>T	p.Pro759Ser	p.P759S	ENST00000342788	NM_005235.2	759	Ccc/Tcc	19/28	1	2	FACETS	0.886	0.821	0.954	0.886	0.821	0.954	CLONAL	1	TRUE	1	0.700499429654585	2		485	554	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422845	12422845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	221	441	2	ENST00000287820.6:c.335C>T	p.Ser112Phe	p.S112F	ENST00000287820	NM_015869.4	112	tCt/tTt	3/7	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.700499429654585	2		443	592	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141119	55141119	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	130	284	0	ENST00000257290.5:c.1765C>T	p.Pro589Ser	p.P589S	ENST00000257290	NM_006206.4	589	Cca/Tca	12/23	1	2	FACETS	0.834	0.762	0.908	0.834	0.762	0.908	CLONAL	1	TRUE	1	0.700499429654585	2		284	445	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510811	157510811	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554232934	NA	P-0018466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	224	455	0	ENST00000346085.5:c.3586C>T	p.Gln1196Ter	p.Q1196*	ENST00000346085	NM_020732.3	1196	Cag/Tag	14/20	0.700499429654585	1	FACETS	0.982	0.929	1	0.982	0.929	1	CLONAL	1	TRUE	0	0.700499429654585	1		455	423	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	140	406	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.99	0.903	1	0.99	0.903	1	CLONAL	1	TRUE	1	0.37198856805686	2		406	760	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0018514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	107	480	1	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.763	0.684	0.846	0.763	0.684	0.846	SUBCLONAL	1	TRUE	1	0.37198856805686	2		481	754	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0018514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	113	269	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.37198856805686	2		269	503	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982096	93982096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1484017296	NA	P-0018514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	73	387	0	ENST00000369303.4:c.1369C>T	p.Arg457Trp	p.R457W	ENST00000369303	NM_004440.3	457	Cgg/Tgg	6/17	0.165586495801135	2	FACETS	0.523	0.457	0.595	0.262	0.228	0.298	INDETERMINATE	1	TRUE	0	0.37198856805686	2		387	750	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88676897	88676897	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782682	NA	P-0018514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	224	530	0	ENST00000372037.3:c.682C>T	p.Arg228Ter	p.R228*	ENST00000372037	NM_004329.2	228	Cga/Tga	9/13	0.37198856805686	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.37198856805686	1		530	897	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	213	437	0	ENST00000269305.4:c.775del	p.Asp259ThrfsTer86	p.D259Tfs*86	ENST00000269305	NM_001126112.2	259	Gac/ac	7/11	0.37198856805686	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.37198856805686	1		437	729	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098948	47098948	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	73	459	2	ENST00000409792.3:c.6326G>T	p.Arg2109Leu	p.R2109L	ENST00000409792	NM_014159.6	2109	cGa/cTa	15/21	1	2	FACETS	0.49	0.428	0.557	0.49	0.428	0.557	SUBCLONAL	1	TRUE	1	0.37198856805686	2		461	801	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0018565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	99	230	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	0.215657000361385	2		231	849	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	138	406	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.149823839275904	3	FACETS	1	0.913	1	1	0.913	1	CLONAL	2	TRUE	1	0.215657000361385	3		406	708	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650101	206650129	+	protein_altering_variant	In_Frame_Del	DEL	TGGAGTGACCTTGTACCATGCAGCCACTG	TGGAGTGACCTTGTACCATGCAGCCACTG	GTCGGGAT	novel	NA	P-0018565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	57	577	2	ENST00000367120.3:c.621_649delinsGTCGGGAT	p.Ile207_Gly217delinsMetSerGlyCys	p.I207_G217delinsMSGC	ENST00000367120	NM_014002.3	207	atTGGAGTGACCTTGTACCATGCAGCCACTGgc/atGTCGGGATgc	7/22	1	2	FACETS	0.596	0.51	0.691	0.596	0.51	0.691	SUBCLONAL	1	TRUE	1	0.215657000361385	2		579	887	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56477555	56477555	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	69	342	0	ENST00000267101.3:c.103G>T	p.Gly35Cys	p.G35C	ENST00000267101	NM_001982.3	35	Ggc/Tgc	2/28	0.215657000361385	1	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	0	0.215657000361385	1		342	558	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99491858	99491858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	67	439	1	ENST00000268035.6:c.3643G>A	p.Gly1215Ser	p.G1215S	ENST00000268035	NM_000875.3	1215	Ggc/Agc	20/21	1	2	FACETS	0.753	0.653	0.862	0.753	0.653	0.862	SUBCLONAL	1	TRUE	1	0.215657000361385	2		440	825	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190318	32190318	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	59	414	0	ENST00000375023.3:c.421C>A	p.Pro141Thr	p.P141T	ENST00000375023	NM_004557.3	141	Cca/Aca	3/30	0.149823839275904	3	FACETS	0.944	0.812	1	0.472	0.406	0.545	CLONAL	1	TRUE	1	0.215657000361385	3		414	642	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236616	236616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1296066077	NA	P-0018677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	198	329	0	ENST00000264932.6:c.1334C>T	p.Ser445Leu	p.S445L	ENST00000264932	NM_004168.2	445	tCg/tTg	10/15	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.7	2		329	555	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942685	48942685	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913301	NA	P-0018834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	761	405	2	ENST00000267163.4:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000267163	NM_000321.2	358	Cga/Tga	11/27	0.87820705431149	2	FACETS	0.988	0.972	1	0.988	0.972	1	CLONAL	2	TRUE	0	0.87820705431149	2		407	877	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579495	7579495	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	1088	532	1	ENST00000269305.4:c.192del	p.Arg65GlufsTer58	p.R65Efs*58	ENST00000269305	NM_001126112.2	64	ccC/cc	4/11	0.865259295649704	2	FACETS	0.99	0.977	1	0.99	0.977	1	CLONAL	2	TRUE	0	0.87820705431149	2		533	1251	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293799	1293799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs539667998	NA	P-0018922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	76	565	0	ENST00000310581.5:c.1202C>T	p.Ala401Val	p.A401V	ENST00000310581	NM_198253.2	401	gCg/gTg	2/16	0.381172298435275	4	FACETS	0.705	0.618	0.799	0.352	0.309	0.4	SUBCLONAL	1	TRUE	2	0.436138777893041	4		565	710	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878109	151878109	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	119	347	0	ENST00000262189.6:c.6836del	p.Pro2279LeufsTer26	p.P2279Lfs*26	ENST00000262189	NM_170606.2	2279	cCt/ct	36/59	0.339533443260051	5	FACETS	0.975	0.886	1	0.65	0.59	0.712	CLONAL	2	TRUE	2	0.436138777893041	5		347	463	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106528	27106528	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	273	712	1	ENST00000324856.7:c.6139G>T	p.Glu2047Ter	p.E2047*	ENST00000324856	NM_006015.4	2047	Gag/Tag	20/20	0.389708209307324	2	FACETS	0.934	0.883	0.986	0.934	0.883	0.986	CLONAL	2	TRUE	0	0.436138777893041	2		713	670	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32918787	32918787	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	101	483	0	ENST00000380152.3:c.6934G>C	p.Asp2312His	p.D2312H	ENST00000380152		2312	Gat/Cat	12/27	1	2	FACETS	0.847	0.759	0.939	0.847	0.759	0.939	CLONAL	1	TRUE	1	0.436138777893041	2		483	547	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795352	39795352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372598575	NA	P-0019107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	175	640	0	ENST00000288319.7:c.368G>A	p.Arg123His	p.R123H	ENST00000288319	NM_182918.3	123	cGc/cAc	3/10	1	2	FACETS	0.646	0.595	0.699	0.646	0.595	0.699	SUBCLONAL	1	TRUE	1	0.62	2		640	874	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921566	178921566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793349	NA	P-0019107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	133	468	0	ENST00000263967.3:c.1048G>A	p.Asp350Asn	p.D350N	ENST00000263967	NM_006218.2	350	Gac/Aac	5/21	1	2	FACETS	0.816	0.745	0.889	0.816	0.745	0.889	CLONAL	1	TRUE	1	0.62	2		468	526	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519934	NA	P-0019107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	23	642	0	ENST00000263967.3:c.333G>C	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaC	2/21	1	2	FACETS	0.103	0.079	0.13	0.103	0.079	0.13	SUBCLONAL	1	TRUE	1	0.62	2		642	723	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488249	56488249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	671	715	0	ENST00000267101.3:c.1768C>T	p.Pro590Ser	p.P590S	ENST00000267101	NM_001982.3	590	Ccc/Tcc	15/28	0.3	6	FACETS	0.887	0.858	0.917			1	INDETERMINATE	4	TRUE	NA	0.62	6		715	1366	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060645	38060645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	277	914	0	ENST00000250448.2:c.1344C>A	p.Ser448Arg	p.S448R	ENST00000250448	NM_004496.3	448	agC/agA	2/2	1	2	FACETS	0.746	0.7	0.794	0.746	0.7	0.794	SUBCLONAL	1	TRUE	1	0.62	2		914	1197	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0019321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	379	1113	1	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.521409843041032	1	FACETS	0.998	0.951	1	0.998	0.951	1	CLONAL	1	TRUE	0	0.574901178839041	1		1114	941	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130354	2130354	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1555511585	NA	P-0019321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	267	703	1	ENST00000219476.3:c.3586G>T	p.Glu1196Ter	p.E1196*	ENST00000219476	NM_000548.3	1196	Gag/Tag	30/42	0.574901178839041	1	FACETS	0.931	0.878	0.985	0.931	0.878	0.985	CLONAL	1	TRUE	0	0.574901178839041	1		704	711	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0019321-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	245	1113	1	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.452837162163369	1	FACETS	0.912	0.855	0.97	0.912	0.855	0.97	CLONAL	1	TRUE	0	0.50993508547132	1		1114	785	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156719	20156719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019321-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	14	195	0	ENST00000379607.5:c.38G>A	p.Arg13His	p.R13H	ENST00000379607	NM_001412.3	13	cGc/cAc	2/7	1	1	FACETS	0.147	0.105	0.196	0.147	0.105	0.196	SUBCLONAL	1	TRUE	0	0.50993508547132	1		195	279	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134965	2134965	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019321-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	234	560	0	ENST00000219476.3:c.4507C>A	p.Gln1503Lys	p.Q1503K	ENST00000219476	NM_000548.3	1503	Cag/Aag	35/42	0.497711228995444	1	FACETS	0.903	0.846	0.962	0.903	0.846	0.962	CLONAL	1	TRUE	0	0.50993508547132	1		560	757	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0019618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	182	495	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.956	0.884	1	0.956	0.884	1	CLONAL	1	TRUE	1	0.461859545460165	2		495	824	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981505	201981505	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	156	939	0	ENST00000359651.3:c.419T>C	p.Ile140Thr	p.I140T	ENST00000359651		140	aTt/aCt	3/8	0.461859545460165	3	FACETS	0.754	0.689	0.822	0.377	0.344	0.411	SUBCLONAL	1	TRUE	1	0.461859545460165	3		939	1103	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909944	100909944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	176	777	0	ENST00000325455.5:c.2705G>A	p.Ser902Asn	p.S902N	ENST00000325455	NM_001202474.3	902	aGt/aAt	8/8	0.461859545460165	1	FACETS	0.857	0.792	0.924	0.857	0.792	0.924	CLONAL	1	TRUE	0	0.461859545460165	1		777	684	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914531	32914562	+	frameshift_variant	Frame_Shift_Del	DEL	AGTATTGTTTAAAAGTAACGAACATTCAGACC	AGTATTGTTTAAAAGTAACGAACATTCAGACC	-	novel	NA	P-0019618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	180	932	0	ENST00000380152.3:c.6041_6072del	p.Val2014AlafsTer24	p.V2014Afs*24	ENST00000380152		2013	aaAGTATTGTTTAAAAGTAACGAACATTCAGACCag/aaag	11/27	1	2	FACETS	0.808	0.745	0.873	0.808	0.745	0.873	CLONAL	1	TRUE	1	0.461859545460165	2		932	965	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575206	48575206	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	112	419	0	ENST00000342988.3:c.400G>T	p.Glu134Ter	p.E134*	ENST00000342988	NM_005359.5	134	Gaa/Taa	3/12	0.461859545460165	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.461859545460165	1		419	368	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395024	139395024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1414380652	NA	P-0019618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	166	633	0	ENST00000277541.6:c.5914G>A	p.Asp1972Asn	p.D1972N	ENST00000277541	NM_017617.3	1972	Gac/Aac	31/34	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.461859545460165	2		633	648	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0019667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	227	758	1	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.518724415143997	3	FACETS	0.993	0.924	1	0.496	0.462	0.532	CLONAL	1	TRUE	1	0.518724415143997	3		759	1110	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43772095	43772095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	345	1110	0	ENST00000382044.4:c.620C>T	p.Ser207Phe	p.S207F	ENST00000382044	NM_001141980.1	207	tCt/tTt	6/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.518724415143997	2		1110	1283	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1650182	1650182	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	319	1132	0	ENST00000344749.5:c.66C>G	p.Phe22Leu	p.F22L	ENST00000344749	NM_001136139.2	22	ttC/ttG	2/19	1	2	FACETS	0.935	0.881	0.989	0.935	0.881	0.989	CLONAL	1	TRUE	1	0.518724415143997	2		1132	1316	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610601	10610601	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	258	829	0	ENST00000171111.5:c.109G>C	p.Glu37Gln	p.E37Q	ENST00000171111	NM_203500.1	37	Gag/Cag	2/6	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.518724415143997	2		829	957	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526199	189526199	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	582	1013	0	ENST00000264731.3:c.463A>C	p.Thr155Pro	p.T155P	ENST00000264731	NM_003722.4	155	Acc/Ccc	4/14	0.518724415143997	3	FACETS	0.989	0.951	1	0.989	0.951	1	CLONAL	2	TRUE	1	0.518724415143997	3		1013	1429	SUCCESS
APC	324	MSKCC	GRCh37	5	112162930	112162930	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	160	647	0	ENST00000257430.4:c.1534G>C	p.Asp512His	p.D512H	ENST00000257430	NM_000038.5	512	Gat/Cat	12/16	0.518724415143997	1	FACETS	0.995	0.921	1	0.995	0.921	1	CLONAL	1	TRUE	0	0.518724415143997	1		647	459	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946288	2946288	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	538	1038	0	ENST00000396946.4:c.3449A>C	p.Asp1150Ala	p.D1150A	ENST00000396946	NM_032415.4	1150	gAc/gCc	25/25	0.518724415143997	3	FACETS	0.973	0.935	1	0.973	0.935	1	CLONAL	2	TRUE	1	0.518724415143997	3		1038	1342	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967634	90967634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060503478	NA	P-0019667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	171	569	0	ENST00000265433.3:c.1274G>A	p.Arg425Lys	p.R425K	ENST00000265433	NM_002485.4	425	aGa/aAa	10/16	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.518724415143997	2		569	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0019668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	602	1041	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.887795965016146	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.887795965016146	1		1041	659	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266570	115266570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	110	967	0	ENST00000438362.2:c.1945C>T	p.Arg649Cys	p.R649C	ENST00000438362	NM_001242891.1	649	Cgc/Tgc	16/20	0.441008503576917	3	FACETS	0.505	0.454	0.559	0.253	0.227	0.28	INDETERMINATE	1	TRUE	1	0.887795965016146	3		967	708	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535421	66535494	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	GCCGCCGGCGTCCCGCACCCCGGGGCCCCGAGCCCCGCATCTTCTCCGAGCCTCCTCCGGTGCCGCTGTCCCGA	GCCGCCGGCGTCCCGCACCCCGGGGCCCCGAGCCCCGCATCTTCTCCGAGCCTCCTCCGGTGCCGCTGTCCCGA	-	novel	NA	P-0019668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	118	399	0	ENST00000273854.3:c.-34_40del		p.*12*	ENST00000273854	NM_004439.5	?-14/1037		1/18	0.516452679926544	3	FACETS	1	0.986	1	0.719	0.66	0.778	INDETERMINATE	1	TRUE	1	0.887795965016146	3		399	267	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	217	205	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.475070800832618	9	FACETS	1	0.968	1	0.842	0.789	0.896	CLONAL	4	TRUE	4	0.475070800832618	9		205	578	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	58	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.342658459132106	4	FACETS	0.958	0.827	1	0.479	0.413	0.55	CLONAL	1	TRUE	2	0.475070800832618	4		436	376	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932020	36932020	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	71	754	0	ENST00000361632.4:c.2449C>G	p.Leu817Val	p.L817V	ENST00000361632		817	Ctc/Gtc	16/16	0.471738377579207	2	FACETS	0.806	0.707	0.911	0.403	0.353	0.456	CLONAL	1	TRUE	0	0.475070800832618	2		754	371	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641768	23641768	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1060502759	NA	P-0019678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	91	571	1	ENST00000261584.4:c.1707del	p.Glu570ArgfsTer29	p.E570Rfs*29	ENST00000261584	NM_024675.3	569	aaA/aa	5/13	NA	2	FACETS	0.921	0.836	1			1	INDETERMINATE	2	TRUE	NA	0.475070800832618	2		572	208	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627932	187627932	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs187106653	NA	P-0019678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	169	807	0	ENST00000441802.2:c.3050A>G	p.Tyr1017Cys	p.Y1017C	ENST00000441802	NM_005245.3	1017	tAt/tGt	2/27	0.475070800832618	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	0	0.475070800832618	2		807	354	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0019898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	58	286	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.792	0.68	0.914	0.792	0.68	0.914	CLONAL	1	TRUE	1	0.24	2		286	610	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0019898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	32	358	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	0.747	0.607	0.905	0.747	0.607	0.905	CLONAL	1	TRUE	1	0.24	2		358	357	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0019898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	103	684	4	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.24	2		688	636	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39216452	39216452	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs754314057	NA	P-0019898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	48	675	0	ENST00000402219.2:c.3350A>G	p.Asn1117Ser	p.N1117S	ENST00000402219	NM_005633.3	1117	aAt/aGt	21/23	1	2	FACETS	0.585	0.493	0.686	0.585	0.493	0.686	SUBCLONAL	1	TRUE	1	0.24	2		675	684	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631362	117631362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150262256	NA	P-0019898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	39	529	4	ENST00000368508.3:c.6316G>A	p.Ala2106Thr	p.A2106T	ENST00000368508	NM_002944.2	2106	Gcc/Acc	40/43	1	2	FACETS	0.653	0.54	0.778	0.653	0.54	0.778	SUBCLONAL	1	TRUE	1	0.24	2		533	498	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120031	70120031	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	21	108	0	ENST00000245479.2:c.1037del	p.Pro346ArgfsTer37	p.P346Rfs*37	ENST00000245479	NM_000346.3	345	Ccc/cc	3/3	1	2	FACETS	0.922	0.715	1	0.922	0.715	1	CLONAL	1	TRUE	1	0.268084863998163	2		108	170	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	203	701	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	0.268084863998163	2		707	1224	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	148	922	1	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.268084863998163	2		923	901	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	118	610	2	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.268084863998163	2		612	708	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028638	12028638	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	114	627	0	ENST00000353533.5:c.841C>T	p.Arg281Ter	p.R281*	ENST00000353533	NM_003010.3	281	Cga/Tga	8/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.268084863998163	2		627	711	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120115	70120115	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	38	156	0	ENST00000245479.2:c.1121del	p.Pro374ArgfsTer9	p.P374Rfs*9	ENST00000245479	NM_000346.3	373	Ccc/cc	3/3	1	2	FACETS	0.829	0.695	0.974	1	0.961	1	CLONAL	2	TRUE	1	0.268084863998163	2		156	171	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	120	632	10	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	0.268084863998163	2		642	705	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	121	695	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.268084863998163	2		695	836	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	145	652	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	0.268084863998163	2		652	802	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46740279	46740279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150315374	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	104	610	0	ENST00000371975.4:c.1759C>T	p.Arg587Trp	p.R587W	ENST00000371975	NM_003579.3	587	Cgg/Tgg	16/18	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.268084863998163	2		610	653	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	112	683	3	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.268084863998163	2		686	810	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	109	688	3	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.268084863998163	2		691	670	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144146	11144146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	132	789	1	ENST00000358026.2:c.3727C>T	p.Arg1243Trp	p.R1243W	ENST00000358026	NM_001128849.1	1243	Cgg/Tgg	26/36	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.268084863998163	2		790	818	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553478	29553478	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781807	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	127	749	3	ENST00000356175.3:c.2033del	p.Pro678ArgfsTer10	p.P678Rfs*10	ENST00000356175	NM_000267.3	676	aCc/ac	18/57	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.268084863998163	2		752	839	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521114	187521114	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760053140	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	115	571	1	ENST00000441802.2:c.12041C>T	p.Thr4014Met	p.T4014M	ENST00000441802	NM_005245.3	4014	aCg/aTg	22/27	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.268084863998163	2		572	676	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730075	41730075	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748897120	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	95	696	0	ENST00000242208.4:c.454C>T	p.Arg152Cys	p.R152C	ENST00000242208	NM_002192.2	152	Cgt/Tgt	3/3	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.268084863998163	2		696	698	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399387	139399387	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1418474023	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	160	810	2	ENST00000277541.6:c.4756C>T	p.Arg1586Cys	p.R1586C	ENST00000277541	NM_017617.3	1586	Cgc/Tgc	26/34	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.268084863998163	2		812	814	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	119	562	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.268084863998163	2		562	734	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	129	888	2	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.268084863998163	2		890	957	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	124	418	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.268084863998163	2		418	817	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064780	80064780	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	125	734	0	ENST00000265081.6:c.2216del	p.Asn739IlefsTer7	p.N739Ifs*7	ENST00000265081	NM_002439.4	737	ctA/ct	15/24	1	2	FACETS	0.992	0.897	1	0.992	0.897	1	CLONAL	1	TRUE	1	0.268084863998163	2		734	940	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229256	36229256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	140	825	2	ENST00000222270.7:c.7946G>A	p.Arg2649His	p.R2649H	ENST00000222270	NM_014727.1	2649	cGc/cAc	37/37	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.268084863998163	2		827	797	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355047	73355047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	101	684	1	ENST00000377767.4:c.323G>A	p.Arg108His	p.R108H	ENST00000377767	NM_014953.3	108	cGc/cAc	2/21	1	2	FACETS	0.862	0.77	0.961	0.862	0.77	0.961	CLONAL	1	TRUE	1	0.268084863998163	2		685	874	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17116976	17116976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1048214486	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	100	596	2	ENST00000285071.4:c.1733G>A	p.Arg578Gln	p.R578Q	ENST00000285071	NM_144997.5	578	cGg/cAg	14/14	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.268084863998163	2		598	588	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654765	29654765	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	87	623	4	ENST00000356175.3:c.5458del	p.Gln1820AsnfsTer22	p.Q1820Nfs*22	ENST00000356175	NM_000267.3	1818	atC/at	37/57	1	2	FACETS	0.997	0.883	1	0.997	0.883	1	CLONAL	1	TRUE	1	0.268084863998163	2		627	651	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244440	41244440	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80357841	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	138	761	1	ENST00000357654.3:c.3108del	p.Phe1036LeufsTer12	p.F1036Lfs*12	ENST00000357654	NM_007294.3	1036	ttT/tt	10/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.268084863998163	2		762	879	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760703	59760703	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	56	828	0	ENST00000259008.2:c.3704A>C	p.Lys1235Thr	p.K1235T	ENST00000259008	NM_032043.2	1235	aAa/aCa	20/20	1	2	FACETS	0.374	0.319	0.435	0.374	0.319	0.435	SUBCLONAL	1	TRUE	1	0.268084863998163	2		828	1117	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602781	10602781	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	151	832	1	ENST00000171111.5:c.797C>T	p.Ala266Val	p.A266V	ENST00000171111	NM_203500.1	266	gCg/gTg	3/6	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.268084863998163	2		833	908	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955122	17955122	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	114	911	0	ENST00000458235.1:c.105del	p.Gln39SerfsTer108	p.Q39Sfs*108	ENST00000458235	NM_000215.3	35	ccC/cc	2/24	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.268084863998163	2		911	790	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47600946	47600946	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	45	643	0	ENST00000263735.4:c.185-1G>C		p.X62_splice	ENST00000263735	NM_002354.2	62			1	2	FACETS	0.41	0.343	0.484	0.41	0.343	0.484	SUBCLONAL	1	TRUE	1	0.268084863998163	2		643	819	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145736	61145736	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	90	493	0	ENST00000295025.8:c.852del	p.Asp285IlefsTer24	p.D285Ifs*24	ENST00000295025	NM_002908.2	283	gAa/ga	7/11	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.268084863998163	2		493	632	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046961	128046961	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	137	775	0	ENST00000285398.2:c.774T>A	p.Asp258Glu	p.D258E	ENST00000285398	NM_000122.1	258	gaT/gaA	6/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.268084863998163	2		775	875	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589875	212589875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758827443	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	126	791	1	ENST00000342788.4:c.667G>A	p.Gly223Arg	p.G223R	ENST00000342788	NM_005235.2	223	Gga/Aga	6/28	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.268084863998163	2		792	893	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262906	46262906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	138	720	2	ENST00000371998.3:c.1079G>A	p.Arg360Gln	p.R360Q	ENST00000371998		360	cGa/cAa	10/23	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.268084863998163	2		722	943	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321719	62321719	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	122	789	0	ENST00000360203.5:c.2338C>A	p.Pro780Thr	p.P780T	ENST00000360203	NM_001283009.1	780	Cct/Act	26/35	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.268084863998163	2		789	794	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980497	1980497	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773117985	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	173	891	1	ENST00000382891.5:c.3959G>A	p.Arg1320Gln	p.R1320Q	ENST00000382891	NM_133335.3	1320	cGg/cAg	22/22	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.268084863998163	2		892	881	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201750	66201750	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	96	729	0	ENST00000273854.3:c.2752G>A	p.Glu918Lys	p.E918K	ENST00000273854	NM_004439.5	918	Gag/Aag	16/18	1	2	FACETS	0.896	0.798	1	0.896	0.798	1	CLONAL	1	TRUE	1	0.268084863998163	2		729	799	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481637	20481637	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	84	521	0	ENST00000346618.3:c.710del	p.Asn237ThrfsTer27	p.N237Tfs*27	ENST00000346618	NM_001949.4	236	Aaa/aa	3/7	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.268084863998163	2		521	626	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553432	106553432	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	73	441	0	ENST00000369096.4:c.1397T>C	p.Leu466Pro	p.L466P	ENST00000369096	NM_001198.3	466	cTc/cCc	5/7	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.268084863998163	2		441	446	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201882	152201882	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs956399300	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	84	722	0	ENST00000206249.3:c.736T>C	p.Tyr246His	p.Y246H	ENST00000206249	NM_000125.3	246	Tac/Cac	3/8	1	2	FACETS	0.884	0.78	0.995	0.884	0.78	0.995	CLONAL	1	TRUE	1	0.268084863998163	2		722	709	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395478	116395478	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45602940	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	130	685	0	ENST00000397752.3:c.1771C>T	p.Arg591Trp	p.R591W	ENST00000397752	NM_000245.2	591	Cgg/Tgg	6/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.268084863998163	2		685	830	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342764	87342764	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	82	711	0	ENST00000277120.3:c.1049A>C	p.Asn350Thr	p.N350T	ENST00000277120		350	aAt/aCt	9/19	1	2	FACETS	0.837	0.738	0.944	0.837	0.738	0.944	CLONAL	1	TRUE	1	0.268084863998163	2		711	731	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932356	39932356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771287230	NA	P-0019949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	188	463	0	ENST00000378444.4:c.2243G>A	p.Arg748Gln	p.R748Q	ENST00000378444	NM_001123385.1	748	cGg/cAg	4/15	1	1	FACETS	1	0.967	1	1	0.994	1	CLONAL	2	TRUE	0	0.268084863998163	1		463	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574030	7574030	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	281	742	0	ENST00000269305.4:c.997del	p.Arg333ValfsTer12	p.R333Vfs*12	ENST00000269305	NM_001126112.2	333	Cgt/gt	10/11	0.63694459119217	1	FACETS	0.986	0.936	1	0.986	0.936	1	CLONAL	1	TRUE	0	0.650556252293084	1		742	591	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0020161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	321	614	1	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.650556252293084	NA		615	1032	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636326	87636326	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	266	838	1	ENST00000277120.3:c.2491C>A	p.Pro831Thr	p.P831T	ENST00000277120		831	Ccg/Acg	19/19	1	2	FACETS	0.843	0.791	0.896	0.843	0.791	0.896	CLONAL	1	TRUE	1	0.650556252293084	2		839	970	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342373	70342373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368913305	NA	P-0020161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	261	599	5	ENST00000374080.3:c.1264C>T	p.Arg422Trp	p.R422W	ENST00000374080		422	Cgg/Tgg	9/45	1	2	FACETS	0.917	0.861	0.974	0.917	0.861	0.974	CLONAL	1	TRUE	1	0.650556252293084	2		604	875	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0020188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	9	579	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.194	0.127	0.279	0.194	0.127	0.279	SUBCLONAL	1	TRUE	1	0.22	2		579	422	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0020188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	15	545	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.266	0.194	0.354	0.266	0.194	0.354	SUBCLONAL	1	TRUE	1	0.22	2		545	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0020229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	674	1221	1	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			NA	2	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.844650224648994	2		1222	794	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845391	76845391	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	190	653	0	ENST00000373344.5:c.6130C>G	p.Leu2044Val	p.L2044V	ENST00000373344	NM_000489.3	2044	Ctc/Gtc	27/35	0.807245792438712	4	FACETS	0.78	0.727	0.834	0.39	0.363	0.417	SUBCLONAL	2	TRUE	0	0.844650224648994	4		653	532	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	333	660	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.989	1	1	0.997	1	CLONAL	2	FALSE	1	0.537460668126037	2		663	565	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783217	9783217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140820694	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	220	683	1	ENST00000377346.4:c.2461C>T	p.Arg821Cys	p.R821C	ENST00000377346	NM_005026.3	821	Cgc/Tgc	20/24	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.537460668126037	2		684	774	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120031	70120031	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	36	108	0	ENST00000245479.2:c.1037del	p.Pro346ArgfsTer37	p.P346Rfs*37	ENST00000245479	NM_000346.3	345	Ccc/cc	3/3	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	FALSE	1	0.537460668126037	2		108	120	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	255	884	1	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.537460668126037	2		885	892	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	144	701	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.811	0.741	0.883	0.811	0.741	0.883	CLONAL	1	FALSE	1	0.537460668126037	2		707	661	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	99	399	1	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	0.998	0.899	1	0.998	0.899	1	CLONAL	1	FALSE	1	0.537460668126037	2		400	369	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	46	280	1	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.751	0.638	0.872	0.751	0.638	0.872	SUBCLONAL	1	FALSE	1	0.537460668126037	2		281	228	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	77	425	1	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.537460668126037	2		426	261	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	226	898	5	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.846	0.788	0.906	0.846	0.788	0.906	CLONAL	1	FALSE	1	0.537460668126037	2		903	994	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346220	152346220	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	171	622	8	ENST00000359321.1:c.350del	p.Leu117TrpfsTer17	p.L117Wfs*17	ENST00000359321	NM_005431.1	117	tTg/tg	3/3	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	1	0.537460668126037	2		630	623	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268793	98268793	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1554708751	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	217	659	1	ENST00000331920.6:c.290del	p.Asn97ThrfsTer20	p.N97Tfs*20	ENST00000331920	NM_000264.3	97	aAc/ac	2/24	1	2	FACETS	0.927	0.863	0.993	0.927	0.863	0.993	CLONAL	1	FALSE	1	0.537460668126037	2		660	871	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	243	566	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	1	2	FACETS	1	0.983	1	1	0.996	1	CLONAL	2	FALSE	1	0.537460668126037	2		566	419	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	68	389	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	FALSE	1	0.537460668126037	2		389	237	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	88	433	1	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	1	2	FACETS	0.803	0.715	0.895	0.803	0.715	0.895	CLONAL	1	FALSE	1	0.537460668126037	2		434	408	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641389	18641389	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1229278001	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	59	202	2	ENST00000266497.5:c.2393del	p.Asn798MetfsTer16	p.N798Mfs*16	ENST00000266497		796	ctA/ct	17/31	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.537460668126037	2		204	164	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395776	45395776	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	118	437	0	ENST00000262160.6:c.358C>T	p.Arg120Ter	p.R120*	ENST00000262160	NM_005901.5	120	Cga/Tga	4/11	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	FALSE	1	0.537460668126037	2		437	421	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	305	767	0	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	FALSE	1	0.537460668126037	2		767	986	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	99	437	4	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	FALSE	1	0.537460668126037	2		441	356	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951156	48951156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060503078	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	76	453	0	ENST00000267163.4:c.1318G>A	p.Glu440Lys	p.E440K	ENST00000267163	NM_000321.2	440	Gaa/Aaa	13/27	1	2	FACETS	0.906	0.802	1	0.906	0.802	1	CLONAL	1	FALSE	1	0.537460668126037	2		453	312	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16022738	16022738	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	116	655	0	ENST00000268712.3:c.1914del	p.Gly639ValfsTer2	p.G639Vfs*2	ENST00000268712	NM_006311.3	638	aaA/aa	17/46	1	2	FACETS	0.89	0.807	0.977	0.89	0.807	0.977	CLONAL	1	FALSE	1	0.537460668126037	2		655	485	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030692	48030692	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs267608092	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	119	461	4	ENST00000234420.5:c.3312del	p.Phe1104LeufsTer11	p.F1104Lfs*11	ENST00000234420	NM_000179.2	1102	acT/ac	5/10	1	2	FACETS	0.913	0.829	1	0.913	0.829	1	CLONAL	1	FALSE	1	0.537460668126037	2		465	485	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347484	91347484	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	192	726	6	ENST00000355112.3:c.3651del	p.Lys1217AsnfsTer62	p.K1217Nfs*62	ENST00000355112	NM_000057.2	1216	Aaa/aa	19/22	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.537460668126037	2		732	686	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120326	94120326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370195460	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	96	324	1	ENST00000369303.4:c.725C>T	p.Ala242Val	p.A242V	ENST00000369303	NM_004440.3	242	gCg/gTg	3/17	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	FALSE	1	0.537460668126037	2		325	344	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645694	12645694	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs3730271	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	105	356	0	ENST00000251849.4:c.775T>C	p.Ser259Pro	p.S259P	ENST00000251849	NM_002880.3	259	Tcc/Ccc	7/17	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	1	0.537460668126037	2		356	363	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513282	44513287	+	inframe_deletion	In_Frame_Del	DEL	CCACCG	CCACCG	-	rs745888281	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	207	856	1	ENST00000291552.4:c.648_653del	p.Gly222_Gly223del	p.G222_G223del	ENST00000291552	NM_006758.2	216	ggCGGTGGt/ggt	8/8	1	2	FACETS	0.751	0.696	0.807	0.751	0.696	0.807	SUBCLONAL	1	FALSE	1	0.537460668126037	2		857	1026	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344134	70344134	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	499	792	0	ENST00000374080.3:c.1870C>T	p.Leu624Phe	p.L624F	ENST00000374080		624	Ctt/Ttt	13/45	0.537460668126037	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	FALSE	1	0.537460668126037	3		792	1157	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855029	76855029	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1557085898	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	130	618	1	ENST00000373344.5:c.5807A>G	p.Lys1936Arg	p.K1936R	ENST00000373344	NM_000489.3	1936	aAg/aGg	25/35	0.537460668126037	3	FACETS	1	0.971	1	0.577	0.526	0.63	CLONAL	1	FALSE	1	0.537460668126037	3		619	532	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043349	6043349	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781716	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	85	281	1	ENST00000265849.7:c.325del	p.Glu109LysfsTer3	p.E109Kfs*3	ENST00000265849	NM_000535.5	109	Gaa/aa	4/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.537460668126037	2		282	262	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384651	31384651	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	226	767	3	ENST00000328111.2:c.1359del	p.Leu454SerfsTer136	p.L454Sfs*136	ENST00000328111	NM_006892.3	451	gaG/ga	13/23	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.537460668126037	2		770	818	SUCCESS
APC	324	MSKCC	GRCh37	5	112116587	112116587	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	82	486	0	ENST00000257430.4:c.636del	p.Lys212AsnfsTer7	p.K212Nfs*7	ENST00000257430	NM_000038.5	211	gAa/ga	6/16	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	FALSE	1	0.537460668126037	2		486	285	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992076	72992076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772258894	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	229	670	0	ENST00000268489.5:c.1969G>A	p.Gly657Ser	p.G657S	ENST00000268489	NM_006885.3	657	Ggc/Agc	2/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.537460668126037	2		670	707	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868072	56868072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771065608	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	185	519	0	ENST00000308159.5:c.1570C>T	p.Arg524Trp	p.R524W	ENST00000308159	NM_014669.4	524	Cgg/Tgg	14/22	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.537460668126037	2		519	608	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240767	55240767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770193776	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	298	869	4	ENST00000275493.2:c.2011C>T	p.Arg671Cys	p.R671C	ENST00000275493	NM_005228.3	671	Cgc/Tgc	17/28	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.537460668126037	2		873	965	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78858811	78858811	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1440436634	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	225	636	1	ENST00000306801.3:c.1846C>T	p.Arg616Cys	p.R616C	ENST00000306801	NM_020761.2	616	Cgc/Tgc	17/34	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.537460668126037	2		637	818	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435894	149435894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs690016548	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	210	636	0	ENST00000286301.3:c.2330G>A	p.Arg777Gln	p.R777Q	ENST00000286301	NM_005211.3	777	cGg/cAg	18/22	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.537460668126037	2		636	763	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223175	36223175	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	120	1107	6	ENST00000222270.7:c.5730del	p.Arg1911AspfsTer23	p.R1911Dfs*23	ENST00000222270	NM_014727.1	1909	Ccc/cc	28/37	1	2	FACETS	0.354	0.318	0.391	0.354	0.318	0.391	SUBCLONAL	1	FALSE	1	0.537460668126037	2		1113	1263	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256430	16256430	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760748544	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	184	655	0	ENST00000375759.3:c.3695A>G	p.His1232Arg	p.H1232R	ENST00000375759	NM_015001.2	1232	cAt/cGt	11/15	1	2	FACETS	0.951	0.88	1	0.951	0.88	1	CLONAL	1	FALSE	1	0.537460668126037	2		655	720	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023708	27023708	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	178	685	0	ENST00000324856.7:c.817del	p.Ala273ProfsTer90	p.A273Pfs*90	ENST00000324856	NM_006015.4	272	Ggg/gg	1/20	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	FALSE	1	0.537460668126037	2		685	661	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40367000	40367000	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	232	874	1	ENST00000397332.2:c.197T>C	p.Val66Ala	p.V66A	ENST00000397332	NM_001033082.2	66	gTg/gCg	2/3	1	2	FACETS	0.974	0.91	1	0.974	0.91	1	CLONAL	1	FALSE	1	0.537460668126037	2		875	886	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532635	46532635	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	106	491	0	ENST00000262741.5:c.443A>G	p.Tyr148Cys	p.Y148C	ENST00000262741	NM_003629.3	148	tAc/tGc	4/10	1	2	FACETS	0.999	0.903	1	0.999	0.903	1	CLONAL	1	FALSE	1	0.537460668126037	2		491	395	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400951	72400951	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	131	506	1	ENST00000357731.5:c.220C>T	p.Arg74Trp	p.R74W	ENST00000357731	NM_173808.2	74	Cgg/Tgg	2/7	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	1	0.537460668126037	2		507	465	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428478	78428478	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	104	632	2	ENST00000370768.2:c.1321C>T	p.Gln441Ter	p.Q441*	ENST00000370768	NM_003902.3	441	Caa/Taa	14/20	1	2	FACETS	0.949	0.856	1	0.949	0.856	1	CLONAL	1	FALSE	1	0.537460668126037	2		634	408	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162688861	162688861	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	176	675	0	ENST00000367921.3:c.8T>C	p.Leu3Pro	p.L3P	ENST00000367921	NM_006182.2	3	cTg/cCg	3/18	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.537460668126037	2		675	593	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175819	176175819	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	116	584	0	ENST00000367669.3:c.296T>C	p.Val99Ala	p.V99A	ENST00000367669	NM_022457.5	99	gTa/gCa	1/20	1	2	FACETS	0.827	0.749	0.909	0.827	0.749	0.909	CLONAL	1	FALSE	1	0.537460668126037	2		584	522	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658600	206658600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781867739	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	222	573	0	ENST00000367120.3:c.1573C>T	p.Arg525Trp	p.R525W	ENST00000367120	NM_014002.3	525	Cgg/Tgg	15/22	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.537460668126037	2		573	692	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570820	226570820	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	201	717	1	ENST00000366794.5:c.1076del	p.Pro359GlnfsTer22	p.P359Qfs*22	ENST00000366794	NM_001618.3	359	cCa/ca	8/23	1	2	FACETS	0.883	0.82	0.949	0.883	0.82	0.949	CLONAL	1	FALSE	1	0.537460668126037	2		718	847	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100750	8100750	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11567901	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	214	766	1	ENST00000346208.3:c.724G>A	p.Gly242Ser	p.G242S	ENST00000346208		242	Ggc/Agc	3/6	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.537460668126037	2		767	733	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608300	43608300	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	259	919	0	ENST00000355710.3:c.1649-1G>T		p.X550_splice	ENST00000355710	NM_020975.4	550			1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.537460668126037	2		919	925	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138166	64138166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1017388898	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	311	849	3	ENST00000334205.4:c.2089G>A	p.Ala697Thr	p.A697T	ENST00000334205	NM_003942.2	697	Gca/Aca	16/17	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.537460668126037	2		852	1027	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197281	94197282	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs774440500	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	97	580	0	ENST00000323929.3:c.1222dup	p.Thr408AsnfsTer49	p.T408Nfs*49	ENST00000323929	NM_005591.3	408	aca/aAca	11/20	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	FALSE	1	0.537460668126037	2		580	352	SUCCESS
ATM	472	MSKCC	GRCh37	11	108159759	108159759	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	112	617	0	ENST00000278616.4:c.4165A>G	p.Thr1389Ala	p.T1389A	ENST00000278616	NM_000051.3	1389	Aca/Gca	28/63	1	2	FACETS	0.992	0.899	1	0.992	0.899	1	CLONAL	1	FALSE	1	0.537460668126037	2		617	420	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658349	18658350	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	152	520	0	ENST00000266497.5:c.3155_3156del	p.Phe1052TrpfsTer52	p.F1052Wfs*52	ENST00000266497		1052	TTt/t	22/31	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.537460668126037	2		520	445	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434683	49434683	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	296	912	0	ENST00000301067.7:c.6870A>C	p.Glu2290Asp	p.E2290D	ENST00000301067	NM_003482.3	2290	gaA/gaC	31/54	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.537460668126037	2		912	993	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493782	56493782	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	182	499	0	ENST00000267101.3:c.3098T>C	p.Leu1033Pro	p.L1033P	ENST00000267101	NM_001982.3	1033	cTa/cCa	25/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.537460668126037	2		499	589	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495453	56495453	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	270	782	0	ENST00000267101.3:c.3643A>C	p.Ser1215Arg	p.S1215R	ENST00000267101	NM_001982.3	1215	Agt/Cgt	28/28	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	1	0.537460668126037	2		782	792	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858929	57858929	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	252	880	1	ENST00000228682.2:c.429del	p.Ser146ArgfsTer19	p.S146Rfs*19	ENST00000228682	NM_005269.2	142	cAa/ca	5/12	1	2	FACETS	0.977	0.915	1	0.977	0.915	1	CLONAL	1	FALSE	1	0.537460668126037	2		881	960	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437363	121437363	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	285	910	1	ENST00000257555.6:c.1704del	p.Ser569AlafsTer91	p.S569Afs*91	ENST00000257555		567	gtC/gt	9/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.537460668126037	2		911	1029	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29068932	29068932	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	54	467	0	ENST00000282397.4:c.49T>C	p.Cys17Arg	p.C17R	ENST00000282397	NM_002019.4	17	Tgt/Cgt	1/30	1	2	FACETS	0.378	0.322	0.438	0.378	0.322	0.438	SUBCLONAL	1	FALSE	1	0.537460668126037	2		467	532	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873826	35873826	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	110	363	0	ENST00000216797.5:c.25del	p.Gln9ArgfsTer12	p.Q9Rfs*12	ENST00000216797	NM_020529.2	9	Cag/ag	1/6	1	2	FACETS	0.996	0.902	1	0.996	0.902	1	CLONAL	1	FALSE	1	0.537460668126037	2		363	411	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100412	2100412	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	106	675	0	ENST00000219476.3:c.150G>T	p.Met50Ile	p.M50I	ENST00000219476	NM_000548.3	50	atG/atT	3/42	1	2	FACETS	0.521	0.467	0.578	0.521	0.467	0.578	SUBCLONAL	1	FALSE	1	0.537460668126037	2		675	757	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245873	41245873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	138	670	0	ENST00000357654.3:c.1675G>T	p.Gly559Cys	p.G559C	ENST00000357654	NM_007294.3	559	Ggt/Tgt	10/23	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.537460668126037	2		670	460	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2164212	2164212	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	41	601	0	ENST00000398665.3:c.29A>C	p.Lys10Thr	p.K10T	ENST00000398665	NM_032482.2	10	aAg/aCg	1/28	1	2	FACETS	0.19	0.158	0.227	0.19	0.158	0.227	SUBCLONAL	1	FALSE	1	0.537460668126037	2		601	801	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099222	4099222	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	189	726	2	ENST00000262948.5:c.896G>T	p.Arg299Met	p.R299M	ENST00000262948	NM_030662.3	299	aGg/aTg	7/11	1	2	FACETS	0.958	0.888	1	0.958	0.888	1	CLONAL	1	FALSE	1	0.537460668126037	2		728	734	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170698	7170699	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	277	1007	1	ENST00000302850.5:c.1332_1333del	p.His444GlnfsTer14	p.H444Qfs*14	ENST00000302850	NM_000208.2	444	caCAac/caac	6/22	1	2	FACETS	0.958	0.9	1	0.958	0.9	1	CLONAL	1	FALSE	1	0.537460668126037	2		1008	1076	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031119	11031119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765573504	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	285	838	1	ENST00000327064.4:c.1204G>A	p.Val402Met	p.V402M	ENST00000327064	NM_199141.1	402	Gtg/Atg	11/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.537460668126037	2		839	965	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101895	11101895	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	59	887	1	ENST00000358026.2:c.1315T>C	p.Tyr439His	p.Y439H	ENST00000358026	NM_001128849.1	439	Tac/Cac	8/36	1	2	FACETS	0.218	0.187	0.253	0.218	0.187	0.253	SUBCLONAL	1	FALSE	1	0.537460668126037	2		888	1005	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276713	15276713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238520484	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	268	808	1	ENST00000263388.2:c.5552G>A	p.Arg1851His	p.R1851H	ENST00000263388	NM_000435.2	1851	cGt/cAt	30/33	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.537460668126037	2		809	901	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754077	42754077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1381343253	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	234	696	0	ENST00000222329.4:c.275G>A	p.Arg92His	p.R92H	ENST00000222329	NM_006494.2	92	cGc/cAc	3/4	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.537460668126037	2		696	790	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798427	42798428	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	286	868	0	ENST00000575354.2:c.4303dup	p.Asp1435GlyfsTer6	p.D1435Gfs*6	ENST00000575354	NM_015125.3	1433	gag/gaGg	18/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.537460668126037	2		868	1013	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799129	42799129	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs139613152	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	274	915	0	ENST00000575354.2:c.4613C>A	p.Pro1538Gln	p.P1538Q	ENST00000575354	NM_015125.3	1538	cCg/cAg	20/20	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	1	0.537460668126037	2		915	1009	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902109	50902109	+	start_lost,splice_region_variant	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	62	463	0	ENST00000440232.2:c.1A>G	p.Met1?	p.M1?	ENST00000440232	NM_002691.3	1	Atg/Gtg	2/27	1	2	FACETS	0.395	0.341	0.454	0.395	0.341	0.454	SUBCLONAL	1	FALSE	1	0.537460668126037	2		463	584	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39234251	39234251	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	39	769	0	ENST00000402219.2:c.2594T>C	p.Leu865Ser	p.L865S	ENST00000402219	NM_005633.3	865	tTg/tCg	16/23	1	2	FACETS	0.241	0.199	0.289	0.241	0.199	0.289	SUBCLONAL	1	FALSE	1	0.537460668126037	2		769	601	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662562	227662562	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	44	555	0	ENST00000305123.5:c.893G>T	p.Gly298Val	p.G298V	ENST00000305123	NM_005544.2	298	gGg/gTg	1/2	1	2	FACETS	0.293	0.246	0.347	0.293	0.246	0.347	SUBCLONAL	1	FALSE	1	0.537460668126037	2		555	558	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662776	227662776	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	252	766	2	ENST00000305123.5:c.679C>T	p.Arg227Cys	p.R227C	ENST00000305123	NM_005544.2	227	Cgt/Tgt	1/2	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	FALSE	1	0.537460668126037	2		768	926	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090420	37090421	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	181	683	0	ENST00000231790.2:c.2018_2019dup	p.Glu674LeufsTer110	p.E674Lfs*110	ENST00000231790	NM_000249.3	672	tgt/tgTTt	18/19	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.537460668126037	2		683	611	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383908	84383908	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	134	750	0	ENST00000321945.7:c.944A>G	p.His315Arg	p.H315R	ENST00000321945	NM_139076.2	315	cAc/cGc	9/9	1	2	FACETS	0.943	0.861	1	0.943	0.861	1	CLONAL	1	FALSE	1	0.537460668126037	2		750	529	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84393376	84393376	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	90	473	0	ENST00000321945.7:c.281del	p.Lys94ArgfsTer4	p.K94Rfs*4	ENST00000321945	NM_139076.2	94	aAg/ag	4/9	1	2	FACETS	0.903	0.807	1	0.903	0.807	1	CLONAL	1	FALSE	1	0.537460668126037	2		473	371	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159123	143159123	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	81	563	0	ENST00000262992.4:c.730T>C	p.Ser244Pro	p.S244P	ENST00000262992	NM_001101669.1	244	Tct/Cct	10/24	1	2	FACETS	0.835	0.741	0.934	0.835	0.741	0.934	CLONAL	1	FALSE	1	0.537460668126037	2		563	361	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152566	56152566	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	71	322	0	ENST00000399503.3:c.622C>T	p.Arg208Ter	p.R208*	ENST00000399503	NM_005921.1	208	Cga/Tga	2/20	1	2	FACETS	0.803	0.706	0.906	0.803	0.706	0.906	CLONAL	1	FALSE	1	0.537460668126037	2		322	329	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161183	56161183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765046318	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	90	565	0	ENST00000399503.3:c.1052G>A	p.Arg351His	p.R351H	ENST00000399503	NM_005921.1	351	cGt/cAt	5/20	1	2	FACETS	0.938	0.839	1	0.938	0.839	1	CLONAL	1	FALSE	1	0.537460668126037	2		565	357	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80074558	80074558	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	162	661	0	ENST00000265081.6:c.2338T>C	p.Phe780Leu	p.F780L	ENST00000265081	NM_002439.4	780	Ttt/Ctt	17/24	1	2	FACETS	0.988	0.911	1	0.988	0.911	1	CLONAL	1	FALSE	1	0.537460668126037	2		661	610	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645168	86645168	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	66	297	0	ENST00000274376.6:c.1240C>T	p.Arg414Trp	p.R414W	ENST00000274376	NM_002890.2	414	Cgg/Tgg	8/25	1	2	FACETS	0.956	0.839	1	0.956	0.839	1	CLONAL	1	FALSE	1	0.537460668126037	2		297	257	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057561	180057561	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1374141592	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	233	752	1	ENST00000261937.6:c.394G>A	p.Val132Met	p.V132M	ENST00000261937	NM_182925.4	132	Gtg/Atg	3/30	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.537460668126037	2		753	773	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524316	148524316	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	24	544	0	ENST00000320356.2:c.668T>A	p.Ile223Asn	p.I223N	ENST00000320356	NM_004456.4	223	aTt/aAt	7/20	1	2	FACETS	0.203	0.159	0.255	0.203	0.159	0.255	SUBCLONAL	1	FALSE	1	0.537460668126037	2		544	439	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878944	151878944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	58	591	0	ENST00000262189.6:c.6001G>A	p.Ala2001Thr	p.A2001T	ENST00000262189	NM_170606.2	2001	Gct/Act	36/59	1	2	FACETS	0.344	0.295	0.397	0.344	0.295	0.397	SUBCLONAL	1	FALSE	1	0.537460668126037	2		591	628	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104748	69104748	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762825228	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	167	583	1	ENST00000288368.4:c.4592G>A	p.Ser1531Asn	p.S1531N	ENST00000288368	NM_024870.2	1531	aGc/aAc	37/40	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.537460668126037	2		584	597	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90949263	90949263	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	19	372	0	ENST00000265433.3:c.2225A>G	p.Asp742Gly	p.D742G	ENST00000265433	NM_002485.4	742	gAt/gGt	15/16	1	2	FACETS	0.263	0.199	0.337	0.263	0.199	0.337	SUBCLONAL	1	FALSE	1	0.537460668126037	2		372	269	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958369	90958369	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	71	424	0	ENST00000265433.3:c.2069del	p.Lys690ArgfsTer19	p.K690Rfs*19	ENST00000265433	NM_002485.4	690	aAg/ag	13/16	1	2	FACETS	0.902	0.795	1	0.902	0.795	1	CLONAL	1	FALSE	1	0.537460668126037	2		424	293	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606343	93606343	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200078199	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	203	724	0	ENST00000375746.1:c.163G>A	p.Val55Met	p.V55M	ENST00000375746	NM_001174167.1	55	Gtg/Atg	2/14	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.537460668126037	2		724	736	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936025	44936025	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	305	813	1	ENST00000377967.4:c.2786C>A	p.Pro929His	p.P929H	ENST00000377967	NM_021140.2	929	cCt/cAt	18/29	0.537460668126037	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	FALSE	1	0.537460668126037	3		814	709	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813089	76813089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057517707	NA	P-0020242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	113	774	2	ENST00000373344.5:c.6532C>T	p.Arg2178Trp	p.R2178W	ENST00000373344	NM_000489.3	2178	Cgg/Tgg	30/35	0.537460668126037	3	FACETS	0.854	0.77	0.942	0.427	0.385	0.471	CLONAL	1	FALSE	1	0.537460668126037	3		776	625	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374347	118374348	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	100	815	0	ENST00000534358.1:c.7741dup	p.Thr2581AsnfsTer9	p.T2581Nfs*9	ENST00000534358	NM_005933.3	2580	-/A	27/36	0.443501996230109	3	FACETS	0.438	0.391	0.488	0.146	0.13	0.163	INDETERMINATE	1	TRUE	0	0.91738616704882	3		815	726	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716208	52716208	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	74	758	0	ENST00000322088.6:c.652G>A	p.Asp218Asn	p.D218N	ENST00000322088	NM_014225.5	218	Gac/Aac	6/15	1	2	FACETS	0.394	0.344	0.449	0.394	0.344	0.449	SUBCLONAL	1	TRUE	1	0.414559763756283	2		758	905	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0020528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	53	450	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.238966629091838	2		451	323	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195650	123195650	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	194	477	0	ENST00000218089.9:c.1564A>T	p.Ile522Phe	p.I522F	ENST00000218089	NM_001042749.1	522	Att/Ttt	17/35	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.529163448717213	2		477	723	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969458	44969459	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	C	novel	NA	P-0020647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	258	692	0	ENST00000377967.4:c.4140_4141delinsC	p.Met1380IlefsTer4	p.M1380Ifs*4	ENST00000377967	NM_021140.2	1380	atGGag/atCag	28/29	1	2	FACETS	0.881	0.825	0.939	0.881	0.825	0.939	CLONAL	1	TRUE	1	0.529163448717213	2		692	1107	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592045	67592133	+	frameshift_variant	Frame_Shift_Del	DEL	GAGAAGACATGGAATGTTGGAAGCAGCAACCGAAACAAAGCTGAAAACCTGTTGCGAGGGAAGCGAGATGGCACTTTTCTTGTCCGGGA	GAGAAGACATGGAATGTTGGAAGCAGCAACCGAAACAAAGCTGAAAACCTGTTGCGAGGGAAGCGAGATGGCACTTTTCTTGTCCGGGA	-	novel	NA	P-0020647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	25	324	0	ENST00000274335.5:c.1864_1952del	p.Lys622GlnfsTer2	p.K622Qfs*2	ENST00000274335		621	GAGAAGACATGGAATGTTGGAAGCAGCAACCGAAACAAAGCTGAAAACCTGTTGCGAGGGAAGCGAGATGGCACTTTTCTTGTCCGGGAg/g	14/15	0.529163448717213	1	FACETS	0.19	0.15	0.237	0.19	0.15	0.237	SUBCLONAL	1	TRUE	0	0.529163448717213	1		324	365	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195650	123195650	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020647-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	50	477	0	ENST00000218089.9:c.1564A>T	p.Ile522Phe	p.I522F	ENST00000218089	NM_001042749.1	522	Att/Ttt	17/35	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.221948388791275	2		477	413	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969458	44969459	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	C	novel	NA	P-0020647-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	74	692	0	ENST00000377967.4:c.4140_4141delinsC	p.Met1380IlefsTer4	p.M1380Ifs*4	ENST00000377967	NM_021140.2	1380	atGGag/atCag	28/29	1	2	FACETS	0.873	0.763	0.991	0.873	0.763	0.991	CLONAL	1	TRUE	1	0.221948388791275	2		692	764	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	120	1047	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.862	0.776	0.953	0.862	0.776	0.953	CLONAL	1	TRUE	1	0.22	2		1049	1266	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	88	158	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.768	0.682	0.859	1	0.98	1	SUBCLONAL	2	TRUE	1	0.22	2		159	521	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1174	111	646	1	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.785	0.704	0.872	0.785	0.704	0.872	SUBCLONAL	1	TRUE	1	0.22	2		647	1285	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	91	247	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.984	0.872	1	0.984	0.872	1	CLONAL	1	TRUE	1	0.22	2		248	841	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150022	202150022	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	80	840	2	ENST00000358485.4:c.1463T>C	p.Leu488Pro	p.L488P	ENST00000358485	NM_001080125.1	488	cTg/cCg	8/9	1	2	FACETS	0.75	0.658	0.848	0.75	0.658	0.848	SUBCLONAL	1	TRUE	1	0.22	2		842	970	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	106	976	4	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.936	0.838	1	0.936	0.838	1	CLONAL	1	TRUE	1	0.22	2		980	1029	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	100	1064	3	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.897	0.799	1	0.897	0.799	1	CLONAL	1	TRUE	1	0.22	2		1067	1014	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	93	1044	2	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.837	0.743	0.938	0.837	0.743	0.938	CLONAL	1	TRUE	1	0.22	2		1046	1010	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7152776	7152776	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	110	947	2	ENST00000302850.5:c.2192C>T	p.Thr731Met	p.T731M	ENST00000302850	NM_000208.2	731	aCg/aTg	10/22	1	2	FACETS	0.883	0.791	0.98	0.883	0.791	0.98	CLONAL	1	TRUE	1	0.22	2		949	1133	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057937	27057937	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	196	132	0	ENST00000324856.7:c.1650del	p.Tyr551ThrfsTer68	p.Y551Tfs*68	ENST00000324856	NM_006015.4	549	Ccc/cc	3/20	0.181280102235278	3	FACETS	0.898	0.831	0.969	0.898	0.831	0.969	CLONAL	2	TRUE	1	0.22	3		132	1101	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	55	434	1	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.22	2		435	491	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	83	680	3	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	0.181280102235278	3	FACETS	1	0.913	1	0.522	0.459	0.588	CLONAL	1	TRUE	1	0.22	3		683	803	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	96	1178	0	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	0.181280102235278	3	FACETS	0.773	0.686	0.865	0.386	0.343	0.433	SUBCLONAL	1	TRUE	1	0.22	3		1178	1254	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1284	232	1257	2	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	0.181280102235278	3	FACETS	0.772	0.718	0.829	0.772	0.718	0.829	SUBCLONAL	2	TRUE	1	0.22	3		1259	1516	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371810	55371831	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGCCCCGAGGGCGGCCGCGT	TGGGCCCCGAGGGCGGCCGCGT	-	novel	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	26	116	0	ENST00000297316.4:c.500_521del	p.Leu167ArgfsTer213	p.L167Rfs*213	ENST00000297316	NM_022454.3	167	cTGGGCCCCGAGGGCGGCCGCGTg/cg	2/2	1	2	FACETS	0.916	0.737	1	1	0.95	1	CLONAL	2	TRUE	1	0.22	2		116	129	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	56	614	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	1	2	FACETS	0.966	0.828	1	0.966	0.828	1	CLONAL	1	TRUE	1	0.22	2		614	527	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	61	656	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	0.811	0.699	0.933	0.811	0.699	0.933	CLONAL	1	TRUE	1	0.22	2		656	684	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675571	86675571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1561325048	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	44	191	2	ENST00000274376.6:c.2513del	p.Asn838MetfsTer4	p.N838Mfs*4	ENST00000274376	NM_002890.2	836	gAa/ga	19/25	1	2	FACETS	0.78	0.654	0.919	0.78	0.654	0.919	CLONAL	1	TRUE	1	0.22	2		193	513	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644679	134644679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773064927	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	83	759	1	ENST00000398015.3:c.80C>T	p.Thr27Met	p.T27M	ENST00000398015	NM_004441.4	27	aCg/aTg	2/16	1	2	FACETS	0.844	0.743	0.952	0.844	0.743	0.952	CLONAL	1	TRUE	1	0.22	2		760	894	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885956	59885956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28997569	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	76	804	1	ENST00000259008.2:c.790C>T	p.Arg264Trp	p.R264W	ENST00000259008	NM_032043.2	264	Cgg/Tgg	7/20	1	2	FACETS	0.762	0.667	0.865	0.762	0.667	0.865	SUBCLONAL	1	TRUE	1	0.22	2		805	907	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578217	7578217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	136	1049	0	ENST00000269305.4:c.632C>T	p.Thr211Ile	p.T211I	ENST00000269305	NM_001126112.2	211	aCt/aTt	6/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.22	2		1049	1158	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549883	187549883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs186220887	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	74	734	2	ENST00000441802.2:c.4358G>A	p.Arg1453His	p.R1453H	ENST00000441802	NM_005245.3	1453	cGt/cAt	8/27	1	2	FACETS	0.925	0.809	1	0.925	0.809	1	CLONAL	1	TRUE	1	0.22	2		736	727	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444659	78444659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs908264837	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	127	673	0	ENST00000370768.2:c.30del	p.Ser11LeufsTer43	p.S11Lfs*43	ENST00000370768	NM_003902.3	10	ccC/cc	1/20	0.181280102235278	3	FACETS	0.781	0.708	0.859	0.781	0.708	0.859	SUBCLONAL	2	TRUE	1	0.22	3		673	820	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314671	30314671	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147896943	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	77	838	3	ENST00000262643.3:c.1220C>T	p.Pro407Leu	p.P407L	ENST00000262643	NM_001238.2	407	cCg/cTg	12/12	0.181280102235278	3	FACETS	0.827	0.725	0.939	0.414	0.362	0.47	CLONAL	1	TRUE	1	0.22	3		841	939	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21553861	21553861	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	85	866	1	ENST00000382592.4:c.2741del	p.Leu914TrpfsTer10	p.L914Wfs*10	ENST00000382592	NM_014572.2	914	tTg/tg	7/8	1	2	FACETS	0.853	0.752	0.961	0.853	0.752	0.961	CLONAL	1	TRUE	1	0.22	2		867	906	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662450	67662450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	143	982	0	ENST00000264010.4:c.1696C>T	p.Arg566Cys	p.R566C	ENST00000264010	NM_006565.3	566	Cgt/Tgt	9/12	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.22	2		982	1207	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211389	98211389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150850039	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	114	1101	0	ENST00000331920.6:c.3766G>A	p.Val1256Met	p.V1256M	ENST00000331920	NM_000264.3	1256	Gtg/Atg	22/24	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.22	2		1101	981	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039484	49039484	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	72	755	2	ENST00000267163.4:c.2473del	p.Met825Ter	p.M825*	ENST00000267163	NM_000321.2	823	acA/ac	23/27	1	2	FACETS	0.784	0.684	0.893	0.784	0.684	0.893	SUBCLONAL	1	TRUE	1	0.22	2		757	835	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240271	5240271	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	143	1167	3	ENST00000357368.4:c.1643del	p.Pro548ArgfsTer37	p.P548Rfs*37	ENST00000357368	NM_002850.3	548	cCg/cg	12/38	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.22	2		1170	1144	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119007	3119007	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769503200	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	121	1094	3	ENST00000078429.4:c.691G>A	p.Ala231Thr	p.A231T	ENST00000078429	NM_002067.2	231	Gcc/Acc	5/7	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.22	2		1097	1055	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100172	157100172	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1235492881	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	27	145	0	ENST00000346085.5:c.1114del	p.Arg372GlyfsTer7	p.R372Gfs*7	ENST00000346085	NM_020732.3	370	tCc/tc	1/20	0.181280102235278	3	FACETS	0.851	0.685	1	0.851	0.685	1	CLONAL	2	TRUE	1	0.22	3		145	160	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790908	89790910	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs746966684	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	45	701	0	ENST00000336032.3:c.301_303del	p.Lys101del	p.K101del	ENST00000336032	NM_006813.2	99	AAG/-	1/2	0.181280102235278	3	FACETS	0.637	0.534	0.751	0.318	0.267	0.376	SUBCLONAL	1	TRUE	1	0.22	3		701	713	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104375030	104375030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs79299301	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	65	706	2	ENST00000369902.3:c.1028G>A	p.Arg343His	p.R343H	ENST00000369902	NM_016169.3	343	cGc/cAc	9/12	1	2	FACETS	0.739	0.639	0.847	0.739	0.639	0.847	SUBCLONAL	1	TRUE	1	0.22	2		708	800	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599271	28599271	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs770146088	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1188	131	1193	0	ENST00000253063.3:c.722del	p.Pro241GlnfsTer6	p.P241Qfs*6	ENST00000253063	NM_031459.4	239	agC/ag	5/10	0.181280102235278	3	FACETS	1	0.907	1	0.501	0.453	0.552	CLONAL	1	TRUE	1	0.22	3		1193	1319	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465600	8465600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1427192894	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	67	852	4	ENST00000356435.5:c.3580G>A	p.Ala1194Thr	p.A1194T	ENST00000356435		1194	Gct/Act	21/35	0.154775062542694	1	FACETS	0.734	0.637	0.839	0.734	0.637	0.839	SUBCLONAL	1	TRUE	0	0.22	1		856	739	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106726	27106727	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	174	834	0	ENST00000324856.7:c.6341dup	p.Gln2115AlafsTer35	p.Q2115Afs*35	ENST00000324856	NM_006015.4	2113	tcc/tCcc	20/20	0.181280102235278	3	FACETS	0.867	0.798	0.94	0.867	0.798	0.94	CLONAL	2	TRUE	1	0.22	3		834	1012	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166260	118166260	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	51	496	0	ENST00000369448.3:c.770C>A	p.Pro257His	p.P257H	ENST00000369448	NM_017709.3	257	cCc/cAc	2/2	1	2	FACETS	0.904	0.768	1	0.904	0.768	1	CLONAL	1	TRUE	1	0.22	2		496	513	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196696	67196696	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	71	623	1	ENST00000312629.5:c.230del	p.Gly77AlafsTer22	p.G77Afs*22	ENST00000312629	NM_003952.2	75	aaG/aa	3/15	1	2	FACETS	0.919	0.802	1	0.919	0.802	1	CLONAL	1	TRUE	1	0.22	2		624	702	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342935	118342935	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	55	463	1	ENST00000534358.1:c.1061G>T	p.Arg354Met	p.R354M	ENST00000534358	NM_005933.3	354	aGg/aTg	3/36	1	2	FACETS	0.926	0.792	1	0.926	0.792	1	CLONAL	1	TRUE	1	0.22	2		464	540	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	440993	440993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	73	525	1	ENST00000399788.2:c.1765G>A	p.Ala589Thr	p.A589T	ENST00000399788	NM_001042603.1	589	Gct/Act	13/28	1	2	FACETS	0.985	0.861	1	0.985	0.861	1	CLONAL	1	TRUE	1	0.22	2		526	674	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446927	18446927	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	45	659	0	ENST00000266497.5:c.1012G>T	p.Gly338Cys	p.G338C	ENST00000266497		338	Ggc/Tgc	4/31	1	2	FACETS	0.685	0.575	0.807	0.685	0.575	0.807	SUBCLONAL	1	TRUE	1	0.22	2		659	597	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433960	49433960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	94	1017	0	ENST00000301067.7:c.7593del	p.Ser2532LeufsTer11	p.S2532Lfs*11	ENST00000301067	NM_003482.3	2531	ccC/cc	31/54	1	2	FACETS	0.89	0.791	0.997	0.89	0.791	0.997	CLONAL	1	TRUE	1	0.22	2		1017	960	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784110	120784110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs538550275	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	115	1187	3	ENST00000257552.2:c.875C>T	p.Thr292Met	p.T292M	ENST00000257552	NM_002442.3	292	aCg/aTg	13/15	1	2	FACETS	0.956	0.859	1	0.956	0.859	1	CLONAL	1	TRUE	1	0.22	2		1190	1094	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436318	110436318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	36	278	2	ENST00000375856.3:c.2083G>A	p.Ala695Thr	p.A695T	ENST00000375856	NM_003749.2	695	Gcc/Acc	1/2	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.22	2		280	265	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633467	3633467	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	145	1289	0	ENST00000294008.3:c.4784T>C	p.Leu1595Pro	p.L1595P	ENST00000294008	NM_032444.2	1595	cTg/cCg	14/15	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.22	2		1289	1290	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639416	3639416	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	91	975	0	ENST00000294008.3:c.4223A>G	p.Gln1408Arg	p.Q1408R	ENST00000294008	NM_032444.2	1408	cAg/cGg	12/15	1	2	FACETS	0.808	0.716	0.907	0.808	0.716	0.907	CLONAL	1	TRUE	1	0.22	2		975	1024	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849457	68849457	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780112	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	107	959	2	ENST00000261769.5:c.1360G>A	p.Val454Ile	p.V454I	ENST00000261769	NM_004360.3	454	Gta/Ata	10/16	1	2	FACETS	0.917	0.821	1	0.917	0.821	1	CLONAL	1	TRUE	1	0.22	2		961	1061	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821301	72821301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs578203724	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	64	640	1	ENST00000268489.5:c.10874C>T	p.Ser3625Leu	p.S3625L	ENST00000268489	NM_006885.3	3625	tCg/tTg	10/10	1	2	FACETS	0.965	0.836	1	0.965	0.836	1	CLONAL	1	TRUE	1	0.22	2		641	603	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290030	15290030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752282553	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	110	1098	4	ENST00000263388.2:c.3524G>A	p.Arg1175Gln	p.R1175Q	ENST00000263388	NM_000435.2	1175	cGg/cAg	22/33	1	2	FACETS	0.947	0.849	1	0.947	0.849	1	CLONAL	1	TRUE	1	0.22	2		1102	1056	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280012	18280012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1438495093	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	79	661	1	ENST00000222254.8:c.2095G>A	p.Ala699Thr	p.A699T	ENST00000222254	NM_005027.3	699	Gcc/Acc	16/16	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.22	2		662	715	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383356	42383356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782043875	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	56	628	1	ENST00000221972.3:c.376C>T	p.Arg126Cys	p.R126C	ENST00000221972	NM_021601.3	126	Cgc/Tgc	2/5	0.181280102235278	3	FACETS	0.742	0.634	0.86	0.371	0.317	0.43	SUBCLONAL	1	TRUE	1	0.22	3		629	762	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152653	99152653	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	64	782	1	ENST00000074304.5:c.449G>T	p.Arg150Met	p.R150M	ENST00000074304	NM_001134224.1	150	aGg/aTg	7/26	1	2	FACETS	0.749	0.647	0.859	0.749	0.647	0.859	SUBCLONAL	1	TRUE	1	0.22	2		783	777	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050272	128050272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145762413	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	89	772	1	ENST00000285398.2:c.385G>A	p.Val129Ile	p.V129I	ENST00000285398	NM_000122.1	129	Gtt/Att	3/15	1	2	FACETS	0.941	0.833	1	0.941	0.833	1	CLONAL	1	TRUE	1	0.22	2		773	860	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139611	202139611	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	94	520	0	ENST00000358485.4:c.775del		p.X259_splice	ENST00000358485	NM_001080125.1	259			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.22	2		520	624	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422524	225422524	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	60	627	1	ENST00000264414.4:c.116del	p.Asn39MetfsTer39	p.N39Mfs*39	ENST00000264414	NM_003590.4	39	aAt/at	2/16	1	2	FACETS	0.735	0.632	0.847	0.735	0.632	0.847	SUBCLONAL	1	TRUE	1	0.22	2		628	742	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660720	227660720	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761390879	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	119	1035	2	ENST00000305123.5:c.2735C>T	p.Pro912Leu	p.P912L	ENST00000305123	NM_005544.2	912	cCg/cTg	1/2	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.22	2		1037	996	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523682	41523683	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	117	1062	0	ENST00000263253.7:c.1102dup	p.His368ProfsTer43	p.H368Pfs*43	ENST00000263253	NM_001429.3	366	-/C	4/31	1	2	FACETS	0.874	0.786	0.968	0.874	0.786	0.968	CLONAL	1	TRUE	1	0.22	2		1062	1217	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467869	66467869	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	33	581	0	ENST00000273854.3:c.400C>A	p.Leu134Met	p.L134M	ENST00000273854	NM_004439.5	134	Ctg/Atg	3/18	1	2	FACETS	0.587	0.477	0.711	0.587	0.477	0.711	SUBCLONAL	1	TRUE	1	0.22	2		581	511	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674240	86674240	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	51	608	0	ENST00000274376.6:c.2372C>T	p.Thr791Ile	p.T791I	ENST00000274376	NM_002890.2	791	aCa/aTa	18/25	1	2	FACETS	0.745	0.633	0.869	0.745	0.633	0.869	SUBCLONAL	1	TRUE	1	0.22	2		608	622	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047893	180047893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	107	1152	0	ENST00000261937.6:c.2282C>T	p.Ala761Val	p.A761V	ENST00000261937	NM_182925.4	761	gCc/gTc	15/30	1	2	FACETS	0.932	0.834	1	0.932	0.834	1	CLONAL	1	TRUE	1	0.22	2		1152	1044	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777927	27777927	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	136	575	1	ENST00000369163.2:c.76G>A	p.Ala26Thr	p.A26T	ENST00000369163	NM_003536.2	26	Gct/Act	1/1	0.181280102235278	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.22	3		576	617	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187428	32187428	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	128	1014	0	ENST00000375023.3:c.1451G>A	p.Cys484Tyr	p.C484Y	ENST00000375023	NM_004557.3	484	tGc/tAc	8/30	0.181280102235278	3	FACETS	1	0.956	1	0.549	0.496	0.605	CLONAL	1	TRUE	1	0.22	3		1014	1177	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798106	32798106	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	125	1046	0	ENST00000374899.4:c.1573G>A	p.Gly525Arg	p.G525R	ENST00000374899	NM_018833.2	525	Gga/Aga	9/12	0.181280102235278	3	FACETS	1	0.94	1	0.528	0.477	0.583	CLONAL	1	TRUE	1	0.22	3		1046	1194	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64289966	64289966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	127	574	1	ENST00000370651.3:c.409C>T	p.Arg137Trp	p.R137W	ENST00000370651	NM_003463.4	137	Cgg/Tgg	6/6	0.181280102235278	3	FACETS	0.918	0.833	1	0.918	0.833	1	CLONAL	2	TRUE	1	0.22	3		575	698	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522102	157522102	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587779746	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	146	791	0	ENST00000346085.5:c.4377del	p.Pro1460LeufsTer34	p.P1460Lfs*34	ENST00000346085	NM_020732.3	1458	gaG/ga	18/20	0.181280102235278	3	FACETS	0.931	0.851	1	0.931	0.851	1	CLONAL	2	TRUE	1	0.22	3		791	791	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738360	133738360	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	85	723	0	ENST00000318560.5:c.763del	p.Glu255ArgfsTer12	p.E255Rfs*12	ENST00000318560	NM_005157.4	254	Ggg/gg	4/11	1	2	FACETS	0.962	0.85	1	0.962	0.85	1	CLONAL	1	TRUE	1	0.22	2		723	803	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495396	149495396	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1160163328	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	89	1159	0	ENST00000261799.4:c.3251C>T	p.Pro1084Leu	p.P1084L	ENST00000261799	NM_002609.3	1084	cCa/cTa	23/23	1	2	FACETS	0.739	0.653	0.831	0.739	0.653	0.831	SUBCLONAL	1	TRUE	1	0.22	2		1159	1095	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656956	47656957	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	T	novel	NA	P-0020757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	40	594	0	ENST00000233146.2:c.1152_1153delinsT	p.Pro385GlnfsTer27	p.P385Qfs*27	ENST00000233146	NM_000251.2	384	ttCCca/ttTca	7/16	1	2	FACETS	0.491	0.407	0.586	0.491	0.407	0.586	SUBCLONAL	1	TRUE	1	0.22	2		594	740	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	116	956	1	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.665	0.598	0.735	0.665	0.598	0.735	SUBCLONAL	1	TRUE	1	0.383549885815182	2		957	910	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0020969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	311	1016	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	0.373981344710361	3	FACETS	0.948	0.896	1	0.948	0.896	1	CLONAL	2	TRUE	1	0.383549885815182	3		1016	1019	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720670	89720670	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786204875	NA	P-0020969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	140	341	0	ENST00000371953.3:c.821G>A	p.Trp274Ter	p.W274*	ENST00000371953	NM_000314.4	274	tGg/tAg	8/9	0.373981344710361	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.383549885815182	3		341	407	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591115	67591116	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1561299903	NA	P-0020969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	80	486	0	ENST00000274335.5:c.1710dup	p.Ile571TyrfsTer31	p.I571Yfs*31	ENST00000274335		570	ctt/cTtt	12/15	1	2	FACETS	0.931	0.823	1	0.931	0.823	1	CLONAL	1	TRUE	1	0.383549885815182	2		486	448	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371810	55371831	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGCCCCGAGGGCGGCCGCGT	TGGGCCCCGAGGGCGGCCGCGT	-	novel	NA	P-0020969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	82	116	0	ENST00000297316.4:c.500_521del	p.Leu167ArgfsTer213	p.L167Rfs*213	ENST00000297316	NM_022454.3	167	cTGGGCCCCGAGGGCGGCCGCGTg/cg	2/2	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.383549885815182	2		116	357	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023867	27023868	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	68	498	0	ENST00000324856.7:c.975dup	p.Gly326ArgfsTer74	p.G326Rfs*74	ENST00000324856	NM_006015.4	325	gcc/gCcc	1/20	1	2	FACETS	0.974	0.852	1	0.974	0.852	1	CLONAL	1	TRUE	1	0.383549885815182	2		498	364	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717617	89717617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	84	753	0	ENST00000371953.3:c.642del	p.Gln214HisfsTer7	p.Q214Hfs*7	ENST00000371953	NM_000314.4	214	caG/ca	7/9	0.373981344710361	3	FACETS	0.736	0.65	0.829	0.368	0.325	0.415	SUBCLONAL	1	TRUE	1	0.383549885815182	3		753	709	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589283	67589283	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0020969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	92	596	0	ENST00000274335.5:c.1271T>G	p.Leu424Ter	p.L424*	ENST00000274335		424	tTa/tGa	9/15	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.383549885815182	2		596	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064794618	NA	P-0020992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	40	702	0	ENST00000269305.4:c.159G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgG/tgA	4/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		702	771	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552957	106552957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	53	733	1	ENST00000369096.4:c.922G>A	p.Asp308Asn	p.D308N	ENST00000369096	NM_001198.3	308	Gac/Aac	5/7	0.196434788894734	4	FACETS		NA	1			1	NA	NA	FALSE	2	NA	4		734	794	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0021023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	452	1013	2	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.791864834164832	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.791864834164832	2		1015	550	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691802	30691802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	182	807	0	ENST00000295754.5:c.304C>T	p.His102Tyr	p.H102Y	ENST00000295754	NM_003242.5	102	Cat/Tat	3/7	0.791864834164832	4	FACETS	0.903	0.834	0.976	0.452	0.417	0.488	CLONAL	1	TRUE	2	0.791864834164832	4		807	912	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291801	15291801	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	298	1124	1	ENST00000263388.2:c.2965C>A	p.Leu989Ile	p.L989I	ENST00000263388	NM_000435.2	989	Ctc/Atc	18/33	0.435979055674194	4	FACETS	0.955	0.901	1	0.955	0.901	1	CLONAL	2	TRUE	2	0.45735286686454	4		1125	994	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0021156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	50	286	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.95	0.804	1	0.95	0.804	1	CLONAL	1	TRUE	1	0.15	2		286	702	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427783	72427783	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750741044	NA	P-0021156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	24	285	0	ENST00000477973.2:c.707G>A	p.Arg236Gln	p.R236Q	ENST00000477973	NM_012234.5	236	cGg/cAg	4/4	1	2	FACETS	1	0.806	1	1	0.806	1	CLONAL	1	TRUE	1	0.15	2		285	311	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0021156-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	33	495	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.151222206730733	1	FACETS	0.513	0.416	0.622	0.513	0.416	0.622	SUBCLONAL	1	TRUE	0	0.191185146471963	1		495	609	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064794618	NA	P-0021156-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	63	702	0	ENST00000269305.4:c.159G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgG/tgA	4/11	0.191185146471963	1	FACETS	0.945	0.817	1	0.945	0.817	1	CLONAL	1	TRUE	0	0.191185146471963	1		702	631	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591933	48591933	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060500733	NA	P-0021156-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	32	506	0	ENST00000342988.3:c.1096C>T	p.Gln366Ter	p.Q366*	ENST00000342988	NM_005359.5	366	Caa/Taa	9/12	1	2	FACETS	0.854	0.693	1	0.854	0.693	1	CLONAL	1	TRUE	1	0.191185146471963	2		506	392	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794777	42794789	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTCCCAGCGGA	CCCTCCCAGCGGA	TG	novel	NA	P-0021156-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	31	528	3	ENST00000575354.2:c.1857_1869delinsTG	p.Pro620GlyfsTer66	p.P620Gfs*66	ENST00000575354	NM_015125.3	619	gcCCCTCCCAGCGGA/gcTG	10/20	1	2	FACETS	0.635	0.512	0.774	0.635	0.512	0.774	SUBCLONAL	1	TRUE	1	0.191185146471963	2		531	511	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478763	57478763	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555889031	NA	P-0021156-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	46	407	0	ENST00000371085.3:c.349G>A	p.Val117Met	p.V117M	ENST00000371085	NM_000516.4	117	Gtg/Atg	5/13	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.191185146471963	2		407	460	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0021156-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	79	495	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	NA	2	FACETS	0.92	0.814	1			1	INDETERMINATE	1	TRUE	NA	0.440555708601628	2		495	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064794618	NA	P-0021156-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	323	702	0	ENST00000269305.4:c.159G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgG/tgA	4/11	0.411861526283973	2	FACETS	0.962	0.914	1	0.962	0.914	1	CLONAL	2	TRUE	0	0.440555708601628	2		702	762	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591933	48591933	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060500733	NA	P-0021156-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	83	506	0	ENST00000342988.3:c.1096C>T	p.Gln366Ter	p.Q366*	ENST00000342988	NM_005359.5	366	Caa/Taa	9/12	0.440555708601628	1	FACETS	0.91	0.81	1	0.91	0.81	1	CLONAL	1	TRUE	0	0.440555708601628	1		506	323	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794777	42794789	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTCCCAGCGGA	CCCTCCCAGCGGA	TG	novel	NA	P-0021156-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	126	528	3	ENST00000575354.2:c.1857_1869delinsTG	p.Pro620GlyfsTer66	p.P620Gfs*66	ENST00000575354	NM_015125.3	619	gcCCCTCCCAGCGGA/gcTG	10/20	1	2	FACETS	0.831	0.754	0.913	0.831	0.754	0.913	CLONAL	1	TRUE	1	0.440555708601628	2		531	688	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478763	57478763	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555889031	NA	P-0021156-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	76	407	0	ENST00000371085.3:c.349G>A	p.Val117Met	p.V117M	ENST00000371085	NM_000516.4	117	Gtg/Atg	5/13	1	2	FACETS	0.869	0.766	0.978	0.869	0.766	0.978	CLONAL	1	TRUE	1	0.440555708601628	2		407	397	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794788	42794788	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs891723299	NA	P-0021156-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	126	547	1	ENST00000575354.2:c.1868G>T	p.Gly623Val	p.G623V	ENST00000575354	NM_015125.3	623	gGa/gTa	10/20	1	2	FACETS	0.855	0.776	0.938	0.855	0.776	0.938	CLONAL	1	TRUE	1	0.440555708601628	2		548	669	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726243	46726243	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021156-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	86	412	0	ENST00000371975.4:c.437A>G	p.Asp146Gly	p.D146G	ENST00000371975	NM_003579.3	146	gAc/gGc	6/18	0.442691590488108	3	FACETS	0.705	0.624	0.792	0.352	0.312	0.396	SUBCLONAL	1	TRUE	1	0.440555708601628	3		412	676	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244690	41244691	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021156-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	117	557	1	ENST00000357654.3:c.2857dup	p.Cys953LeufsTer18	p.C953Lfs*18	ENST00000357654	NM_007294.3	953	tgt/tTgt	10/23	0.429298290227454	1	FACETS	0.783	0.709	0.86	0.783	0.709	0.86	SUBCLONAL	1	TRUE	0	0.440555708601628	1		558	529	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0021174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	437	954	2	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.637141325528474	2	FACETS	0.963	0.929	0.997	0.963	0.929	0.997	CLONAL	2	TRUE	0	0.637141325528474	2		956	712	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325158	123325158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56226109	NA	P-0021174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	352	747	0	ENST00000358487.5:c.170C>T	p.Ser57Leu	p.S57L	ENST00000358487	NM_000141.4	57	tCg/tTg	3/18	0.637141325528474	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.637141325528474	2		747	533	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306677	41306677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs724159835	NA	P-0021174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	384	900	0	ENST00000373198.4:c.982C>T	p.Arg328Cys	p.R328C	ENST00000373198	NM_133170.3	328	Cgc/Tgc	7/32	0.500342662033139	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.637141325528474	4		900	933	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936024	44936024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	215	921	0	ENST00000377967.4:c.2785C>T	p.Pro929Ser	p.P929S	ENST00000377967	NM_021140.2	929	Cct/Tct	18/29	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.637141325528474	2		921	663	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0021174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	116	593	2				ENST00000310581	NM_198253.2	-/1132			0.637141325528474	3	FACETS	1	0.945	1	0.53	0.481	0.581	CLONAL	1	TRUE	1	0.637141325528474	3		595	453	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233249	46233249	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs865903558	NA	P-0021174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	316	599	0	ENST00000334344.6:c.1468C>T	p.Gln490Ter	p.Q490*	ENST00000334344	NM_152641.2	490	Caa/Taa	11/21	0.637141325528474	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.637141325528474	2		599	487	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195335	102195335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	125	636	0	ENST00000263464.3:c.95G>A	p.Arg32Gln	p.R32Q	ENST00000263464	NM_001165.4	32	cGa/cAa	2/9	0.637141325528474	2	FACETS	0.896	0.817	0.977	0.448	0.408	0.489	CLONAL	1	TRUE	0	0.637141325528474	2		636	438	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69230522	69230522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	340	612	0	ENST00000462284.1:c.911C>T	p.Ser304Phe	p.S304F	ENST00000462284	NM_002392.5	304	tCc/tTc	10/11	0.637141325528474	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.637141325528474	2		612	505	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597543	28597543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	295	954	0	ENST00000241453.7:c.2362C>T	p.Leu788Phe	p.L788F	ENST00000241453	NM_004119.2	788	Ctt/Ttt	19/24	0.637141325528474	3	FACETS	1	0.944	1	0.502	0.472	0.532	CLONAL	1	TRUE	1	0.637141325528474	3		954	1217	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911912	32911912	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	374	796	0	ENST00000380152.3:c.3420T>A	p.Ser1140Arg	p.S1140R	ENST00000380152		1140	agT/agA	11/27	0.637141325528474	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.637141325528474	3		796	761	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858313	9858313	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	214	478	0	ENST00000330684.3:c.3088C>T	p.Pro1030Ser	p.P1030S	ENST00000330684	NM_001134407.1	1030	Cca/Tca	13/13	0.637141325528474	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.637141325528474	3		478	408	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221763	36221763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761123223	NA	P-0021174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	220	1118	0	ENST00000222270.7:c.5432C>T	p.Ser1811Phe	p.S1811F	ENST00000222270	NM_014727.1	1811	tCc/tTc	26/37	1	2	FACETS	0.884	0.825	0.945	0.884	0.825	0.945	CLONAL	1	TRUE	1	0.637141325528474	2		1118	781	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964962	55964962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	230	405	0	ENST00000263923.4:c.2275G>A	p.Glu759Lys	p.E759K	ENST00000263923	NM_002253.2	759	Gaa/Aaa	16/30	0.524775000713674	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.637141325528474	4		405	573	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628185	187628185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767176687	NA	P-0021174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	418	937	0	ENST00000441802.2:c.2797C>T	p.Arg933Cys	p.R933C	ENST00000441802	NM_005245.3	933	Cgt/Tgt	2/27	0.637141325528474	3	FACETS	0.912	0.872	0.951	0.912	0.872	0.951	CLONAL	2	TRUE	1	0.637141325528474	3		937	949	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031699	69031699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	393	820	0	ENST00000288368.4:c.3454C>T	p.His1152Tyr	p.H1152Y	ENST00000288368	NM_024870.2	1152	Cat/Tat	28/40	0.524775000713674	4	FACETS	0.978	0.932	1	0.978	0.932	1	CLONAL	2	TRUE	2	0.637141325528474	4		820	1033	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923406	36923406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1393968437	NA	P-0021174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	229	1010	1	ENST00000358127.4:c.856C>T	p.Pro286Ser	p.P286S	ENST00000358127	NM_001280556.1	286	Cct/Tct	7/10	0.637141325528474	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.637141325528474	1		1011	441	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624594	93624594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	146	690	0	ENST00000375746.1:c.685C>T	p.Pro229Ser	p.P229S	ENST00000375746	NM_001174167.1	229	Ccc/Tcc	4/14	0.637141325528474	2	FACETS	1	0.923	1	0.501	0.461	0.543	CLONAL	1	TRUE	0	0.637141325528474	2		690	457	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	84	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.824	0.731	0.922	0.824	0.731	0.922	CLONAL	1	TRUE	1	0.481044149908111	2		306	424	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0021205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	16	278	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.476161170426151	1	FACETS	0.335	0.249	0.436	0.335	0.249	0.436	SUBCLONAL	1	TRUE	0	0.481044149908111	1		278	151	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804224	43804224	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148276667	NA	P-0021205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	83	627	1	ENST00000372470.3:c.224G>A	p.Arg75His	p.R75H	ENST00000372470	NM_005373.2	75	cGt/cAt	3/12	1	2	FACETS	0.73	0.646	0.818	0.73	0.646	0.818	SUBCLONAL	1	TRUE	1	0.481044149908111	2		628	473	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0021350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	274	406	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.498578086094626	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.498578086094626	1		406	631	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581272	48581273	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0021350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	54	730	1	ENST00000342988.3:c.579_580del	p.Glu193AspfsTer12	p.E193Dfs*12	ENST00000342988	NM_005359.5	192	acAGag/acag	5/12	0.458458776921606	1	FACETS	0.191	0.163	0.223	0.191	0.163	0.223	SUBCLONAL	1	TRUE	0	0.498578086094626	1		731	850	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944592	40944592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371723954	NA	P-0021350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	187	592	0	ENST00000373198.4:c.1910G>A	p.Arg637Gln	p.R637Q	ENST00000373198	NM_133170.3	637	cGg/cAg	12/32	0.119616555015979	4	FACETS	0.754	0.699	0.812	0.754	0.699	0.812	INDETERMINATE	2	TRUE	2	0.498578086094626	4		592	745	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448157	49448157	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	191	835	0	ENST00000301067.7:c.443G>T	p.Gly148Val	p.G148V	ENST00000301067	NM_003482.3	148	gGc/gTc	4/54	1	2	FACETS	0.726	0.671	0.784	0.726	0.671	0.784	SUBCLONAL	1	TRUE	1	0.498578086094626	2		835	1055	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577608	7577609	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	CC	CC	-	novel	NA	P-0021350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	192	693	0	ENST00000269305.4:c.673-1_673del		p.X225_splice	ENST00000269305	NM_001126112.2	225		7/11	0.458458776921606	1	FACETS	0.779	0.723	0.838	0.779	0.723	0.838	SUBCLONAL	1	TRUE	0	0.498578086094626	1		693	742	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127702	47127702	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	142	667	0	ENST00000409792.3:c.5380C>T	p.Gln1794Ter	p.Q1794*	ENST00000409792	NM_014159.6	1794	Cag/Tag	11/21	1	2	FACETS	0.673	0.614	0.736	0.673	0.614	0.736	SUBCLONAL	1	TRUE	1	0.498578086094626	2		667	846	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	72	610	2	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.351581695578184	2		612	360	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	72	879	0	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	0.727	0.636	0.826	0.727	0.636	0.826	SUBCLONAL	1	TRUE	1	0.351581695578184	2		879	563	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	80	869	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.916	0.808	1	0.916	0.808	1	CLONAL	1	TRUE	1	0.351581695578184	2		869	497	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151290	202151290	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	100	795	0	ENST00000358485.4:c.1596del	p.Lys532AsnfsTer73	p.K532Nfs*73	ENST00000358485	NM_001080125.1	530	agA/ag	9/9	1	2	FACETS	0.89	0.796	0.99	0.89	0.796	0.99	CLONAL	1	TRUE	1	0.351581695578184	2		795	639	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	112	278	0	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	0.351581695578184	3	FACETS	0.972	0.874	1	0.486	0.437	0.538	CLONAL	1	TRUE	1	0.351581695578184	3		278	771	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	103	833	2	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	0.351581695578184	3	FACETS	0.966	0.865	1	0.483	0.432	0.537	CLONAL	1	TRUE	1	0.351581695578184	3		835	713	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661663	227661664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	38	649	1	ENST00000305123.5:c.1790_1791dup	p.His598GlyfsTer39	p.H598Gfs*39	ENST00000305123	NM_005544.2	597	-/GG	1/2	1	2	FACETS	0.538	0.445	0.641	0.538	0.445	0.641	SUBCLONAL	1	TRUE	1	0.351581695578184	2		650	402	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	74	728	5	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			0.349060883141791	4	FACETS	0.813	0.711	0.922	0.271	0.237	0.308	CLONAL	1	TRUE	1	0.351581695578184	4		733	700	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216189	36216189	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	48	858	1	ENST00000222270.7:c.3602del	p.Pro1201ArgfsTer154	p.P1201Rfs*154	ENST00000222270	NM_014727.1	1199	ggC/gg	11/37	0.349060883141791	4	FACETS	0.398	0.335	0.468	0.133	0.111	0.156	SUBCLONAL	1	TRUE	1	0.351581695578184	4		859	927	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	165	725	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.351581695578184	2	FACETS	0.761	0.701	0.822	0.761	0.701	0.822	SUBCLONAL	2	TRUE	0	0.351581695578184	2		725	617	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572252	41572254	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	95	759	0	ENST00000263253.7:c.4785_4787del	p.Phe1596del	p.F1596del	ENST00000263253	NM_001429.3	1594	gTCTtc/gtc	30/31	1	2	FACETS	0.895	0.798	0.997	0.895	0.798	0.997	CLONAL	1	TRUE	1	0.351581695578184	2		759	604	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149798	202149799	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	71	817	0	ENST00000358485.4:c.1245dup	p.Ile416TyrfsTer8	p.I416Yfs*8	ENST00000358485	NM_001080125.1	413	-/T	8/9	1	2	FACETS	0.699	0.61	0.794	0.699	0.61	0.794	SUBCLONAL	1	TRUE	1	0.351581695578184	2		817	578	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244091	153244091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	116	684	0	ENST00000281708.4:c.2066G>A	p.Arg689Gln	p.R689Q	ENST00000281708	NM_033632.3	689	cGg/cAg	12/12	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.351581695578184	2		684	583	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973851	131973851	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747603489	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	79	616	0	ENST00000265335.6:c.3554G>A	p.Arg1185Gln	p.R1185Q	ENST00000265335		1185	cGa/cAa	23/25	1	2	FACETS	0.848	0.747	0.955	0.848	0.747	0.955	CLONAL	1	TRUE	1	0.351581695578184	2		616	530	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217234	11217234	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1031980569	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	99	366	0	ENST00000361445.4:c.4444C>T	p.Arg1482Cys	p.R1482C	ENST00000361445	NM_004958.3	1482	Cgc/Tgc	30/58	1	2	FACETS	0.866	0.774	0.964	0.866	0.774	0.964	CLONAL	1	TRUE	1	0.351581695578184	2		366	650	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882049	36882050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs780753361	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	90	847	4	ENST00000358127.4:c.963dup	p.Ala322ArgfsTer19	p.A322Rfs*19	ENST00000358127	NM_001280556.1	321	-/C	8/10	1	2	FACETS	0.69	0.612	0.773	0.69	0.612	0.773	SUBCLONAL	1	TRUE	1	0.351581695578184	2		851	742	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162932	47162932	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745925708	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	71	729	1	ENST00000409792.3:c.3194G>A	p.Arg1065His	p.R1065H	ENST00000409792	NM_014159.6	1065	cGt/cAt	3/21	1	2	FACETS	0.937	0.821	1	0.937	0.821	1	CLONAL	1	TRUE	1	0.351581695578184	2		730	431	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435312	56435312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139405076	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	122	831	6	ENST00000407977.2:c.1825C>T	p.Arg609Trp	p.R609W	ENST00000407977		609	Cgg/Tgg	9/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.351581695578184	2		837	640	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103754	47103755	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	rs749901643	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	73	858	2	ENST00000409792.3:c.6190_6191dup	p.Asp2064GlufsTer84	p.D2064Efs*84	ENST00000409792	NM_014159.6	2064	gac/gaGAc	14/21	1	2	FACETS	0.647	0.566	0.734	0.647	0.566	0.734	SUBCLONAL	1	TRUE	1	0.351581695578184	2		860	642	SUCCESS
APC	324	MSKCC	GRCh37	5	112128198	112128198	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	65	799	0	ENST00000257430.4:c.704del	p.Leu235TyrfsTer58	p.L235Yfs*58	ENST00000257430	NM_000038.5	234	cTt/ct	7/16	1	2	FACETS	0.862	0.75	0.983	0.862	0.75	0.983	CLONAL	1	TRUE	1	0.351581695578184	2		799	429	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652257	36652257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1463561308	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	53	753	2	ENST00000244741.5:c.379G>A	p.Ala127Thr	p.A127T	ENST00000244741	NM_000389.4	127	Gct/Act	2/3	1	2	FACETS	0.508	0.433	0.591	0.508	0.433	0.591	SUBCLONAL	1	TRUE	1	0.351581695578184	2		755	593	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800902	120800903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs748469666	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	68	803	4	ENST00000257552.2:c.345dup	p.Leu116AlafsTer15	p.L116Afs*15	ENST00000257552	NM_002442.3	115	-/G	6/15	1	2	FACETS	0.451	0.392	0.516	0.451	0.392	0.516	SUBCLONAL	1	TRUE	1	0.351581695578184	2		807	857	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18960950	18960950	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	129	901	1	ENST00000262803.5:c.532del	p.Glu178ArgfsTer55	p.E178Rfs*55	ENST00000262803	NM_002911.3	176	ctG/ct	4/24	1	2	FACETS	0.967	0.877	1	0.967	0.877	1	CLONAL	1	TRUE	1	0.351581695578184	2		902	759	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38616977	38616977	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	68	622	0	ENST00000299084.4:c.395del	p.Asn132MetfsTer20	p.N132Mfs*20	ENST00000299084	NM_152594.2	130	tcA/tc	4/7	0.351581695578184	2	FACETS	0.977	0.854	1	0.488	0.427	0.555	CLONAL	1	TRUE	0	0.351581695578184	2		622	396	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991697	25991697	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	105	712	1	ENST00000435504.4:c.545G>A	p.Cys182Tyr	p.C182Y	ENST00000435504		182	tGc/tAc	7/13	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.351581695578184	2		713	595	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912895	32912895	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555283769	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	63	662	0	ENST00000380152.3:c.4403C>G	p.Ser1468Cys	p.S1468C	ENST00000380152		1468	tCt/tGt	11/27	0.351581695578184	3	FACETS	0.883	0.766	1	0.442	0.383	0.506	CLONAL	1	TRUE	1	0.351581695578184	3		662	477	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222519	39222520	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	65	711	2	ENST00000402219.2:c.3090dup	p.Tyr1031IlefsTer2	p.Y1031Ifs*2	ENST00000402219	NM_005633.3	1030	-/A	20/23	1	2	FACETS	0.756	0.657	0.863	0.756	0.657	0.863	SUBCLONAL	1	TRUE	1	0.351581695578184	2		713	489	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838380	156838380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202030811	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	153	978	3	ENST00000524377.1:c.658C>T	p.Arg220Trp	p.R220W	ENST00000524377	NM_002529.3	220	Cgg/Tgg	6/17	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.351581695578184	2		981	744	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325855	65325855	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	102	672	2	ENST00000342505.4:c.1267C>A	p.Leu423Ile	p.L423I	ENST00000342505	NM_002227.2	423	Ctc/Atc	9/25	1	2	FACETS	0.947	0.848	1	0.947	0.848	1	CLONAL	1	TRUE	1	0.351581695578184	2		674	613	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123324036	123324036	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	87	872	2	ENST00000358487.5:c.434G>A	p.Ser145Asn	p.S145N	ENST00000358487	NM_000141.4	145	aGt/aAt	4/18	1	2	FACETS	0.761	0.674	0.854	0.761	0.674	0.854	SUBCLONAL	1	TRUE	1	0.351581695578184	2		874	650	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465896	69465896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565073727	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	102	829	2	ENST00000227507.2:c.734G>A	p.Arg245Gln	p.R245Q	ENST00000227507	NM_053056.2	245	cGg/cAg	5/5	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.351581695578184	2		831	562	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998742	100998742	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	28	824	3	ENST00000325455.5:c.1060G>A	p.Ala354Thr	p.A354T	ENST00000325455	NM_001202474.3	354	Gct/Act	1/8	1	2	FACETS	0.307	0.244	0.378	0.307	0.244	0.378	SUBCLONAL	1	TRUE	1	0.351581695578184	2		827	519	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117706	108117707	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	27	488	0	ENST00000278616.4:c.921dup	p.Trp308MetfsTer10	p.W308Mfs*10	ENST00000278616	NM_000051.3	306	aca/acAa	8/63	1	2	FACETS	0.635	0.507	0.779	0.635	0.507	0.779	SUBCLONAL	1	TRUE	1	0.351581695578184	2		488	242	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344518	118344518	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	46	525	1	ENST00000534358.1:c.2644A>G	p.Lys882Glu	p.K882E	ENST00000534358	NM_005933.3	882	Aag/Gag	3/36	1	2	FACETS	0.702	0.592	0.821	0.702	0.592	0.821	SUBCLONAL	1	TRUE	1	0.351581695578184	2		526	373	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373487	118373487	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	53	535	0	ENST00000534358.1:c.6880T>C	p.Ser2294Pro	p.S2294P	ENST00000534358	NM_005933.3	2294	Tcc/Ccc	27/36	1	2	FACETS	0.992	0.851	1	0.992	0.851	1	CLONAL	1	TRUE	1	0.351581695578184	2		535	304	SUCCESS
CBL	867	MSKCC	GRCh37	11	119077131	119077131	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	45	479	0	ENST00000264033.4:c.4G>A	p.Ala2Thr	p.A2T	ENST00000264033	NM_005188.3	2	Gcc/Acc	1/16	1	2	FACETS	0.582	0.489	0.684	0.582	0.489	0.684	SUBCLONAL	1	TRUE	1	0.351581695578184	2		479	440	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431880	49431880	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs538335897	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	124	880	1	ENST00000301067.7:c.9259C>T	p.Arg3087Trp	p.R3087W	ENST00000301067	NM_003482.3	3087	Cgg/Tgg	34/54	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.351581695578184	2		881	650	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249278	133249278	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555228286	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	128	955	1	ENST00000320574.5:c.1621G>A	p.Gly541Arg	p.G541R	ENST00000320574	NM_006231.2	541	Ggg/Agg	15/49	1	2	FACETS	0.879	0.797	0.966	0.879	0.797	0.966	CLONAL	1	TRUE	1	0.351581695578184	2		956	828	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28885870	28885870	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	49	582	1	ENST00000282397.4:c.3493-1G>T		p.X1165_splice	ENST00000282397	NM_002019.4	1165			0.351581695578184	3	FACETS	0.981	0.835	1	0.491	0.417	0.571	CLONAL	1	TRUE	1	0.351581695578184	3		583	334	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105258971	105258971	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754031503	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	88	876	1	ENST00000349310.3:c.10G>A	p.Val4Met	p.V4M	ENST00000349310	NM_001014432.1	4	Gtg/Atg	3/15	1	2	FACETS	0.768	0.681	0.861	0.768	0.681	0.861	SUBCLONAL	1	TRUE	1	0.351581695578184	2		877	652	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647530	23647530	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	54	863	2	ENST00000261584.4:c.337C>A	p.Pro113Thr	p.P113T	ENST00000261584	NM_024675.3	113	Cca/Aca	4/13	1	2	FACETS	0.538	0.459	0.624	0.538	0.459	0.624	SUBCLONAL	1	TRUE	1	0.351581695578184	2		865	571	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998988	11998988	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	39	576	0	ENST00000353533.5:c.493del	p.Tyr165MetfsTer32	p.Y165Mfs*32	ENST00000353533	NM_003010.3	164	Ttt/tt	4/11	1	2	FACETS	0.853	0.712	1	0.853	0.712	1	CLONAL	1	TRUE	1	0.351581695578184	2		576	260	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974829	15974829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	52	670	0	ENST00000268712.3:c.4046G>A	p.Arg1349His	p.R1349H	ENST00000268712	NM_006311.3	1349	cGt/cAt	30/46	1	2	FACETS	0.653	0.557	0.758	0.653	0.557	0.758	SUBCLONAL	1	TRUE	1	0.351581695578184	2		670	453	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119683	70119683	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	98	690	0	ENST00000245479.2:c.686-1G>T		p.X229_splice	ENST00000245479	NM_000346.3	229			1	2	FACETS	0.958	0.857	1	0.958	0.857	1	CLONAL	1	TRUE	1	0.351581695578184	2		690	582	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226512	1226512	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374078532	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	127	919	2	ENST00000326873.7:c.1168G>A	p.Val390Met	p.V390M	ENST00000326873	NM_000455.4	390	Gtg/Atg	9/10	1	2	FACETS	0.984	0.893	1	0.984	0.893	1	CLONAL	1	TRUE	1	0.351581695578184	2		921	734	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211748	5211748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377152398	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	134	873	1	ENST00000357368.4:c.5087G>A	p.Arg1696His	p.R1696H	ENST00000357368	NM_002850.3	1696	cGc/cAc	33/38	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.351581695578184	2		874	759	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054418	13054418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	114	751	0	ENST00000316448.5:c.1028G>A	p.Gly343Asp	p.G343D	ENST00000316448	NM_004343.3	343	gGc/gAc	8/9	1	2	FACETS	0.92	0.829	1	0.92	0.829	1	CLONAL	1	TRUE	1	0.351581695578184	2		751	705	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276274	15276274	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	133	901	0	ENST00000263388.2:c.5720C>T	p.Ser1907Leu	p.S1907L	ENST00000263388	NM_000435.2	1907	tCa/tTa	31/33	1	2	FACETS	0.939	0.853	1	0.939	0.853	1	CLONAL	1	TRUE	1	0.351581695578184	2		901	806	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354055	15354055	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765227557	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	69	700	1	ENST00000263377.2:c.2825C>T	p.Thr942Met	p.T942M	ENST00000263377	NM_058243.2	942	aCg/aTg	14/20	1	2	FACETS	0.767	0.669	0.872	0.767	0.669	0.872	SUBCLONAL	1	TRUE	1	0.351581695578184	2		701	512	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762431	41762431	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748730668	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	111	758	2	ENST00000301178.4:c.2111G>A	p.Arg704His	p.R704H	ENST00000301178	NM_021913.4	704	cGc/cAc	18/20	0.349060883141791	4	FACETS	0.991	0.89	1	0.33	0.296	0.366	CLONAL	1	TRUE	1	0.351581695578184	4		760	861	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753452	42753452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	124	929	3	ENST00000222329.4:c.812C>T	p.Thr271Met	p.T271M	ENST00000222329	NM_006494.2	271	aCg/aTg	4/4	0.349060883141791	4	FACETS	0.998	0.902	1	0.333	0.3	0.367	CLONAL	1	TRUE	1	0.351581695578184	4		932	955	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637357	47637357	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786204082	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	96	995	1	ENST00000233146.2:c.491G>A	p.Gly164Glu	p.G164E	ENST00000233146	NM_000251.2	164	gGg/gAg	3/16	1	2	FACETS	0.904	0.807	1	0.904	0.807	1	CLONAL	1	TRUE	1	0.351581695578184	2		996	604	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098831	178098831	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1135118	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	121	951	2	ENST00000397062.3:c.214G>A	p.Ala72Thr	p.A72T	ENST00000397062	NM_006164.4	72	Gct/Act	2/5	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.351581695578184	2		953	621	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274670	198274670	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	97	770	0	ENST00000335508.6:c.728A>G	p.Glu243Gly	p.E243G	ENST00000335508	NM_012433.2	243	gAg/gGg	7/25	1	2	FACETS	0.891	0.796	0.993	0.891	0.796	0.993	CLONAL	1	TRUE	1	0.351581695578184	2		770	619	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661277	227661278	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	111	897	0	ENST00000305123.5:c.2177dup	p.Leu726PhefsTer6	p.L726Ffs*6	ENST00000305123	NM_005544.2	726	tta/ttTa	1/2	1	2	FACETS	0.985	0.887	1	0.985	0.887	1	CLONAL	1	TRUE	1	0.351581695578184	2		897	641	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662850	227662850	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	133	802	6	ENST00000305123.5:c.605C>T	p.Ala202Val	p.A202V	ENST00000305123	NM_005544.2	202	gCg/gTg	1/2	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.351581695578184	2		808	687	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264413	46264413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375958201	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	82	664	0	ENST00000371998.3:c.1460G>A	p.Arg487His	p.R487H	ENST00000371998		487	cGt/cAt	11/23	0.335466765025128	3	FACETS	0.93	0.821	1	0.465	0.41	0.523	CLONAL	1	TRUE	1	0.351581695578184	3		664	590	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42851110	42851110	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	77	695	0	ENST00000398585.3:c.783del	p.Lys261AsnfsTer19	p.K261Nfs*19	ENST00000398585	NM_001135099.1	261	aaA/aa	7/14	1	2	FACETS	0.856	0.753	0.965	0.856	0.753	0.965	CLONAL	1	TRUE	1	0.351581695578184	2		695	512	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574430	41574430	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1263446940	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	30	780	0	ENST00000263253.7:c.6715A>G	p.Met2239Val	p.M2239V	ENST00000263253	NM_001429.3	2239	Atg/Gtg	31/31	1	2	FACETS	0.286	0.229	0.35	0.286	0.229	0.35	SUBCLONAL	1	TRUE	1	0.351581695578184	2		780	597	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645724	12645724	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	27	510	0	ENST00000251849.4:c.745G>T	p.Gly249Cys	p.G249C	ENST00000251849	NM_002880.3	249	Ggt/Tgt	7/17	1	2	FACETS	0.39	0.31	0.481	0.39	0.31	0.481	SUBCLONAL	1	TRUE	1	0.351581695578184	2		510	394	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181893	38181893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769446050	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	67	471	0	ENST00000396334.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000396334	NM_002468.4	173	Cgt/Tgt	3/5	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.351581695578184	2		471	380	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927391	49927391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777901325	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	105	838	2	ENST00000296474.3:c.3913C>T	p.Arg1305Cys	p.R1305C	ENST00000296474	NM_002447.2	1305	Cgc/Tgc	19/20	1	2	FACETS	0.981	0.881	1	0.981	0.881	1	CLONAL	1	TRUE	1	0.351581695578184	2		840	609	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437527	52437527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs71651687	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	134	859	0	ENST00000460680.1:c.1634G>A	p.Arg545His	p.R545H	ENST00000460680	NM_004656.3	545	cGc/cAc	13/17	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.351581695578184	2		859	706	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480468	89480468	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	52	501	2	ENST00000336596.2:c.2305C>T	p.Arg769Cys	p.R769C	ENST00000336596	NM_005233.5	769	Cgt/Tgt	13/17	1	2	FACETS	0.732	0.625	0.849	0.732	0.625	0.849	SUBCLONAL	1	TRUE	1	0.351581695578184	2		503	404	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808391	1808391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17882190	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	141	1369	5	ENST00000260795.2:c.2149G>A	p.Ala717Thr	p.A717T	ENST00000260795		717	Gcc/Acc	15/17	NA	2	FACETS	0.894	0.814	0.978			1	INDETERMINATE	1	TRUE	NA	0.351581695578184	2		1374	897	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55963865	55963865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	74	837	1	ENST00000263923.4:c.2578G>A	p.Ala860Thr	p.A860T	ENST00000263923	NM_002253.2	860	Gca/Aca	18/30	1	2	FACETS	0.832	0.73	0.941	0.832	0.73	0.941	CLONAL	1	TRUE	1	0.351581695578184	2		838	506	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509831	187509831	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	51	432	0	ENST00000441802.2:c.13682T>C	p.Met4561Thr	p.M4561T	ENST00000441802	NM_005245.3	4561	aTg/aCg	27/27	1	2	FACETS	0.895	0.765	1	0.895	0.765	1	CLONAL	1	TRUE	1	0.351581695578184	2		432	324	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294385	1294385	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	102	758	0	ENST00000310581.5:c.616A>G	p.Ser206Gly	p.S206G	ENST00000310581	NM_198253.2	206	Agc/Ggc	2/16	1	2	FACETS	0.873	0.781	0.969	0.873	0.781	0.969	CLONAL	1	TRUE	1	0.351581695578184	2		758	665	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526438	31526438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	163	1200	1	ENST00000344624.3:c.602G>A	p.Ser201Asn	p.S201N	ENST00000344624		201	aGt/aAt	2/33	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.351581695578184	2		1201	839	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512491	149512491	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759481106	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	52	582	0	ENST00000261799.4:c.949C>T	p.Arg317Trp	p.R317W	ENST00000261799	NM_002609.3	317	Cgg/Tgg	7/23	1	2	FACETS	0.768	0.656	0.89	0.768	0.656	0.89	SUBCLONAL	1	TRUE	1	0.351581695578184	2		582	385	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225717	26225717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	147	879	0	ENST00000360408.1:c.335C>T	p.Ala112Val	p.A112V	ENST00000360408	NM_003532.2	112	gCt/gTt	1/1	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.351581695578184	2		879	828	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250695	26250695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	89	755	0	ENST00000446824.2:c.139G>A	p.Val47Ile	p.V47I	ENST00000446824	NM_021018.2	47	Gtc/Atc	1/1	1	2	FACETS	0.861	0.765	0.964	0.861	0.765	0.964	CLONAL	1	TRUE	1	0.351581695578184	2		755	588	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323315	31323315	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	38	488	0	ENST00000412585.2:c.674T>G	p.Leu225Arg	p.L225R	ENST00000412585	NM_005514.6	225	cTg/cGg	4/8	1	2	FACETS	0.57	0.472	0.68	0.57	0.472	0.68	SUBCLONAL	1	TRUE	1	0.351581695578184	2		488	379	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553264	106553264	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	113	691	0	ENST00000369096.4:c.1229A>G	p.Tyr410Cys	p.Y410C	ENST00000369096	NM_001198.3	410	tAc/tGc	5/7	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.351581695578184	2		691	576	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109321836	109321836	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs375028635	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	84	837	0	ENST00000436639.2:c.587A>G	p.His196Arg	p.H196R	ENST00000436639	NM_014454.2	196	cAt/cGt	4/10	1	2	FACETS	0.882	0.78	0.99	0.882	0.78	0.99	CLONAL	1	TRUE	1	0.351581695578184	2		837	542	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200098	138200098	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780969004	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	80	603	0	ENST00000237289.4:c.1516G>A	p.Ala506Thr	p.A506T	ENST00000237289	NM_001270507.1	506	Gcc/Acc	7/9	1	2	FACETS	0.908	0.802	1	0.908	0.802	1	CLONAL	1	TRUE	1	0.351581695578184	2		603	501	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100592	157100592	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	103	806	0	ENST00000346085.5:c.1529T>C	p.Met510Thr	p.M510T	ENST00000346085	NM_020732.3	510	aTg/aCg	1/20	1	2	FACETS	0.972	0.871	1	0.972	0.871	1	CLONAL	1	TRUE	1	0.351581695578184	2		806	603	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397800	116397800	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	72	887	0	ENST00000397752.3:c.2074A>G	p.Ile692Val	p.I692V	ENST00000397752	NM_000245.2	692	Att/Gtt	8/21	0.351581695578184	3	FACETS	0.833	0.729	0.946	0.417	0.364	0.473	CLONAL	1	TRUE	1	0.351581695578184	3		887	578	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850221	128850221	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	96	759	0	ENST00000249373.3:c.1484C>T	p.Thr495Ile	p.T495I	ENST00000249373	NM_005631.4	495	aCc/aTc	9/12	0.351581695578184	3	FACETS	0.886	0.789	0.988	0.443	0.394	0.494	CLONAL	1	TRUE	1	0.351581695578184	3		759	725	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534444	140534444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1258111302	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	153	732	0	ENST00000288602.6:c.469G>A	p.Val157Ile	p.V157I	ENST00000288602	NM_004333.4	157	Gtt/Att	3/18	0.351581695578184	3	FACETS	0.925	0.851	1	0.925	0.851	1	CLONAL	2	TRUE	1	0.351581695578184	3		732	553	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141568653	141568653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	101	864	1	ENST00000220592.5:c.809C>T	p.Thr270Met	p.T270M	ENST00000220592	NM_012154.3	270	aCg/aTg	7/19	1	2	FACETS	0.867	0.775	0.963	0.867	0.775	0.963	CLONAL	1	TRUE	1	0.351581695578184	2		865	663	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741379	145741379	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398124115	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	164	970	1	ENST00000428558.2:c.1124G>A	p.Arg375His	p.R375H	ENST00000428558	NM_004260.3	375	cGc/cAc	5/22	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.351581695578184	2		971	810	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772716	135772716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751362258	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	94	654	1	ENST00000298552.3:c.2830G>A	p.Ala944Thr	p.A944T	ENST00000298552	NM_001162426.1	944	Gca/Aca	22/23	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.351581695578184	2		655	464	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300039	137300040	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755912201	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	101	912	4	ENST00000481739.1:c.331dup	p.Leu111ProfsTer70	p.L111Pfs*70	ENST00000481739	NM_002957.4	108	-/C	3/10	1	2	FACETS	0.753	0.673	0.838	0.753	0.673	0.838	SUBCLONAL	1	TRUE	1	0.351581695578184	2		916	763	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426667	47426667	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	61	432	0	ENST00000377045.4:c.912G>T	p.Glu304Asp	p.E304D	ENST00000377045	NM_001654.4	304	gaG/gaT	10/16	1	1	FACETS	0.829	0.719	0.947	0.829	0.719	0.947	CLONAL	1	TRUE	0	0.351581695578184	1		432	345	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0021484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	103	631	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.629	0.565	0.696	0.629	0.565	0.696	SUBCLONAL	1	TRUE	1	0.670147427830887	2		631	489	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0021484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	297	1164	0				ENST00000310581	NM_198253.2	-/1132			0.33919714634594	1	FACETS	0.73	0.69	0.771	0.73	0.69	0.771	INDETERMINATE	1	TRUE	0	0.670147427830887	1		1164	807	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872219	45872219	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	430	1303	0	ENST00000391945.4:c.215A>G	p.Tyr72Cys	p.Y72C	ENST00000391945	NM_000400.3	72	tAc/tGc	4/23	0.33919714634594	1	FACETS	0.811	0.775	0.847	0.811	0.775	0.847	INDETERMINATE	1	TRUE	0	0.670147427830887	1		1303	1052	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	489	1309	0	ENST00000269305.4:c.772G>C	p.Glu258Gln	p.E258Q	ENST00000269305	NM_001126112.2	258	Gaa/Caa	7/11	0.670147427830887	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.670147427830887	1		1309	904	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942737	44942737	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	338	553	0	ENST00000377967.4:c.3317T>G	p.Leu1106Arg	p.L1106R	ENST00000377967	NM_021140.2	1106	cTt/cGt	23/29	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.670147427830887	1		553	506	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434122	12434122	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1170672782	NA	P-0021484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	151	720	1	ENST00000287820.6:c.490C>T	p.Arg164Trp	p.R164W	ENST00000287820	NM_015869.4	164	Cgg/Tgg	4/7	0.670147427830887	1	FACETS	0.916	0.852	0.981	0.916	0.852	0.981	CLONAL	1	TRUE	0	0.670147427830887	1		721	327	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs199469669	NA	P-0021484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	416	590	0	ENST00000374080.3:c.130G>C	p.Gly44Arg	p.G44R	ENST00000374080		44	Ggt/Cgt	2/45	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.670147427830887	1		590	648	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087891	27087909	+	frameshift_variant	Frame_Shift_Del	DEL	TCGGCCACCCAGTGGCCAG	TCGGCCACCCAGTGGCCAG	-	novel	NA	P-0021484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	250	1162	0	ENST00000324856.7:c.2182_2200del	p.Pro728ThrfsTer8	p.P728Tfs*8	ENST00000324856	NM_006015.4	726	ccTCGGCCACCCAGTGGCCAG/cc	6/20	0.324268267381638	1	FACETS	0.486	0.454	0.518	0.486	0.454	0.518	INDETERMINATE	1	TRUE	0	0.670147427830887	1		1162	1021	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494858	56494858	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	281	923	0	ENST00000267101.3:c.3215C>A	p.Ser1072Tyr	p.S1072Y	ENST00000267101	NM_001982.3	1072	tCt/tAt	27/28	0.33919714634594	1	FACETS	0.746	0.705	0.789	0.746	0.705	0.789	INDETERMINATE	1	TRUE	0	0.670147427830887	1		923	747	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495511	56495511	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	291	976	0	ENST00000267101.3:c.3701C>G	p.Ser1234Cys	p.S1234C	ENST00000267101	NM_001982.3	1234	tCt/tGt	28/28	0.33919714634594	1	FACETS	0.724	0.684	0.764	0.724	0.684	0.764	INDETERMINATE	1	TRUE	0	0.670147427830887	1		976	798	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352665	68352665	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471706907	NA	P-0021484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	143	813	0	ENST00000487270.1:c.532C>T	p.His178Tyr	p.H178Y	ENST00000487270	NM_133509.3	178	Cat/Tat	6/11	1	2	FACETS	0.889	0.816	0.964	0.889	0.816	0.964	CLONAL	1	TRUE	1	0.670147427830887	2		813	480	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439430	220439430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	216	635	1	ENST00000243786.2:c.283G>A	p.Asp95Asn	p.D95N	ENST00000243786	NM_002191.3	95	Gac/Aac	2/2	0.551688135782878	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.670147427830887	1		636	419	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170016856	170016856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	285	1132	0	ENST00000295797.4:c.1661C>T	p.Ser554Phe	p.S554F	ENST00000295797	NM_002740.5	554	tCt/tTt	17/18	0.232614064857264	3	FACETS	0.935	0.878	0.993	0.312	0.292	0.331	INDETERMINATE	1	TRUE	0	0.670147427830887	3		1132	1215	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803150	1803150	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	788	1406	1	ENST00000260795.2:c.502G>T	p.Ala168Ser	p.A168S	ENST00000260795		168	Gcc/Tcc	4/17	0.38031494150014	4	FACETS	1	0.976	1			1	INDETERMINATE	2	TRUE	NA	0.670147427830887	4		1407	1944	SUCCESS
APC	324	MSKCC	GRCh37	5	112174365	112174365	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	85	449	0	ENST00000257430.4:c.3074T>A	p.Ile1025Lys	p.I1025K	ENST00000257430	NM_000038.5	1025	aTa/aAa	16/16	0.670147427830887	1	FACETS	0.902	0.817	0.988	0.902	0.817	0.988	CLONAL	1	TRUE	0	0.670147427830887	1		449	187	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	188	993	1	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	0.2943629320055	3	FACETS	0.846	0.787	0.907	0.846	0.787	0.907	CLONAL	2	TRUE	1	0.480774570604578	3		994	573	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	311	1164	0				ENST00000310581	NM_198253.2	-/1132			0.340190127769545	6	FACETS	1	0.975	1			1	CLONAL	5	TRUE	NA	0.480774570604578	6		1164	496	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023702	31023702	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1311033207	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	241	937	1	ENST00000375687.4:c.3187C>T	p.Gln1063Ter	p.Q1063*	ENST00000375687	NM_015338.5	1063	Cag/Tag	13/13	0.368032946050655	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	2	0.480774570604578	4		938	719	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	246	830	0	ENST00000335508.6:c.2704G>A	p.Glu902Lys	p.E902K	ENST00000335508	NM_012433.2	902	Gaa/Aaa	18/25	0.480774570604578	3	FACETS	0.931	0.875	0.987	0.931	0.875	0.987	CLONAL	2	TRUE	1	0.480774570604578	3		830	682	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	264	318	1	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	0.480774570604578	3	FACETS	0.911	0.874	0.946			1	CLONAL	4	TRUE	NA	0.480774570604578	3		319	374	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350198	89350198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	115	1073	0	ENST00000301030.4:c.2752G>A	p.Glu918Lys	p.E918K	ENST00000301030	NM_001256183.1	918	Gag/Aag	9/13	0.480774570604578	4	FACETS	0.878	0.791	0.97	0.293	0.263	0.324	CLONAL	1	TRUE	1	0.480774570604578	4		1073	807	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646021	215646021	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	221	815	0	ENST00000260947.4:c.577G>C	p.Glu193Gln	p.E193Q	ENST00000260947	NM_000465.2	193	Gag/Cag	4/11	0.480774570604578	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.480774570604578	2		815	454	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348883	89348883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	148	1169	0	ENST00000301030.4:c.4067C>T	p.Ser1356Leu	p.S1356L	ENST00000301030	NM_001256183.1	1356	tCa/tTa	9/13	0.480774570604578	4	FACETS	1	0.979	1	0.406	0.371	0.443	CLONAL	1	TRUE	1	0.480774570604578	4		1169	748	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651902	36651902	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	355	823	0	ENST00000244741.5:c.25del	p.Arg9ValfsTer22	p.R9Vfs*22	ENST00000244741	NM_000389.4	8	gtC/gt	2/3	0.466784654411008	4	FACETS	0.994	0.956	1	0.994	0.956	1	CLONAL	4	TRUE	0	0.480774570604578	4		823	550	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665162	138665162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	80	833	0	ENST00000330315.3:c.403G>A	p.Glu135Lys	p.E135K	ENST00000330315	NM_023067.3	135	Gaa/Aaa	1/1	0.402996238405945	5	FACETS	0.915	0.806	1	0.305	0.268	0.344	CLONAL	1	TRUE	2	0.480774570604578	5		833	626	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351512	89351512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	82	959	1	ENST00000301030.4:c.1438G>A	p.Glu480Lys	p.E480K	ENST00000301030	NM_001256183.1	480	Gag/Aag	9/13	0.480774570604578	4	FACETS	0.79	0.697	0.89	0.263	0.232	0.297	SUBCLONAL	1	TRUE	1	0.480774570604578	4		960	639	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518539	204518539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	91	489	1	ENST00000367182.3:c.1202C>T	p.Ser401Phe	p.S401F	ENST00000367182	NM_001278516.1	401	tCt/tTt	11/11	0.419076718911755	4	FACETS	1	0.952	1	0.563	0.501	0.628	CLONAL	1	TRUE	2	0.480774570604578	4		490	498	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222667	69222667	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	177	871	1	ENST00000462284.1:c.640G>C	p.Glu214Gln	p.E214Q	ENST00000462284	NM_002392.5	214	Gaa/Caa	8/11	0.480774570604578	4	FACETS	1	0.968	1	0.548	0.504	0.593	CLONAL	1	TRUE	2	0.480774570604578	4		872	995	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95592997	95592997	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	145	867	0	ENST00000393063.1:c.823G>C	p.Glu275Gln	p.E275Q	ENST00000393063	NM_030621.3	275	Gaa/Caa	8/28	0.480774570604578	2	FACETS	0.956	0.875	1	0.478	0.437	0.52	CLONAL	1	TRUE	0	0.480774570604578	2		867	631	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347999	89347999	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	150	1161	0	ENST00000301030.4:c.4951G>T	p.Asp1651Tyr	p.D1651Y	ENST00000301030	NM_001256183.1	1651	Gac/Tac	9/13	0.480774570604578	4	FACETS	1	0.97	1	0.378	0.346	0.412	CLONAL	1	TRUE	1	0.480774570604578	4		1161	814	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348726	89348726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	143	1186	0	ENST00000301030.4:c.4224G>A	p.Met1408Ile	p.M1408I	ENST00000301030	NM_001256183.1	1408	atG/atA	9/13	0.480774570604578	4	FACETS	0.978	0.891	1	0.326	0.297	0.357	CLONAL	1	TRUE	1	0.480774570604578	4		1186	901	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349149	89349149	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	203	1316	0	ENST00000301030.4:c.3801G>C	p.Glu1267Asp	p.E1267D	ENST00000301030	NM_001256183.1	1267	gaG/gaC	9/13	0.480774570604578	4	FACETS	1	0.986	1	0.419	0.388	0.451	CLONAL	1	TRUE	1	0.480774570604578	4		1316	995	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349727	89349727	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	127	1201	0	ENST00000301030.4:c.3223G>C	p.Glu1075Gln	p.E1075Q	ENST00000301030	NM_001256183.1	1075	Gaa/Caa	9/13	0.480774570604578	4	FACETS	0.872	0.79	0.959	0.291	0.263	0.32	CLONAL	1	TRUE	1	0.480774570604578	4		1201	897	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350006	89350006	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779463117	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	115	1066	2	ENST00000301030.4:c.2944G>A	p.Glu982Lys	p.E982K	ENST00000301030	NM_001256183.1	982	Gag/Aag	9/13	0.480774570604578	4	FACETS	1	0.915	1	0.339	0.305	0.374	CLONAL	1	TRUE	1	0.480774570604578	4		1068	697	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350072	89350073	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	104	1044	1	ENST00000301030.4:c.2877_2878delinsAA	p.Glu960Lys	p.E960K	ENST00000301030	NM_001256183.1	959	aaGGag/aaAAag	9/13	0.480774570604578	4	FACETS	1	0.917	1	0.342	0.306	0.379	CLONAL	1	TRUE	1	0.480774570604578	4		1045	625	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350190	89350190	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs769880695	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	114	1071	1	ENST00000301030.4:c.2760G>T	p.Arg920Ser	p.R920S	ENST00000301030	NM_001256183.1	920	agG/agT	9/13	0.480774570604578	4	FACETS	0.864	0.777	0.955	0.288	0.259	0.319	CLONAL	1	TRUE	1	0.480774570604578	4		1072	813	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350537	89350537	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	138	903	2	ENST00000301030.4:c.2413G>T	p.Glu805Ter	p.E805*	ENST00000301030	NM_001256183.1	805	Gaa/Taa	9/13	0.480774570604578	4	FACETS	1	0.959	1	0.364	0.331	0.399	CLONAL	1	TRUE	1	0.480774570604578	4		905	778	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350648	89350649	+	stop_gained	Nonsense_Mutation	DNP	TC	TC	AT	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	181	1516	3	ENST00000301030.4:c.2301_2302delinsAT	p.Lys768Ter	p.K768*	ENST00000301030	NM_001256183.1	767	aaGAaa/aaATaa	9/13	0.480774570604578	4	FACETS	0.947	0.872	1	0.316	0.29	0.342	CLONAL	1	TRUE	1	0.480774570604578	4		1519	1177	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350791	89350791	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	163	1353	1	ENST00000301030.4:c.2159G>A	p.Arg720Lys	p.R720K	ENST00000301030	NM_001256183.1	720	aGa/aAa	9/13	0.480774570604578	4	FACETS	1	0.952	1	0.351	0.322	0.382	CLONAL	1	TRUE	1	0.480774570604578	4		1354	953	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350800	89350800	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	166	1338	0	ENST00000301030.4:c.2150C>T	p.Ser717Leu	p.S717L	ENST00000301030	NM_001256183.1	717	tCa/tTa	9/13	0.480774570604578	4	FACETS	1	0.963	1	0.361	0.331	0.392	CLONAL	1	TRUE	1	0.480774570604578	4		1338	944	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350909	89350909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	168	1206	1	ENST00000301030.4:c.2041G>A	p.Glu681Lys	p.E681K	ENST00000301030	NM_001256183.1	681	Gaa/Aaa	9/13	0.480774570604578	4	FACETS	0.982	0.901	1	0.327	0.3	0.356	CLONAL	1	TRUE	1	0.480774570604578	4		1207	1054	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351104	89351104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	118	970	0	ENST00000301030.4:c.1846G>A	p.Glu616Lys	p.E616K	ENST00000301030	NM_001256183.1	616	Gag/Aag	9/13	0.480774570604578	4	FACETS	1	0.966	1	0.383	0.346	0.422	CLONAL	1	TRUE	1	0.480774570604578	4		970	633	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351148	89351148	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371119186	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	86	878	2	ENST00000301030.4:c.1802G>A	p.Arg601Gln	p.R601Q	ENST00000301030	NM_001256183.1	601	cGa/cAa	9/13	0.480774570604578	4	FACETS	0.96	0.851	1	0.32	0.283	0.359	CLONAL	1	TRUE	1	0.480774570604578	4		880	552	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351476	89351476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	60	860	0	ENST00000301030.4:c.1474G>A	p.Asp492Asn	p.D492N	ENST00000301030	NM_001256183.1	492	Gac/Aac	9/13	0.480774570604578	4	FACETS	0.709	0.612	0.816	0.236	0.204	0.272	SUBCLONAL	1	TRUE	1	0.480774570604578	4		860	521	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351533	89351534	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	95	1020	0	ENST00000301030.4:c.1416_1417delinsAT	p.Ser473Cys	p.S473C	ENST00000301030	NM_001256183.1	472	cgGAgc/cgATgc	9/13	0.480774570604578	4	FACETS	0.805	0.717	0.899	0.268	0.239	0.3	CLONAL	1	TRUE	1	0.480774570604578	4		1020	727	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351920	89352942	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGACGGGGGCCGTGGCCTTCTGTGGCTCTGGGTTCTTGGCCTTGTGCTTGAGGCCTTTTTCGAACTCGGAGTCCGTGTTGTTGCCGTCGACTGAACTGGAAGGTGCGAAGGATGGTGCGTCTTCCTCTTCTGAGCTCTCTGTTGGAGGTAGGAAGCGAGAGGTCACAGGCAGGCTCAAAACAGCTCTCCCCAGAATGGCAGAGGAGGGAGGCTCTGCAGATGTGTCTGCGGGAAGGTTCCCACCCTGCCTCTGCAGAGACACTTTGCTCGACTCATGGAAACCAGCCACAGGCAGGAGGAAACCAGACAGAGCTCAGCTGACAGACAGGGCTGGCATCTTAGAATGAAGACTGCAGGCTTCTCGGCAGTGACACACCTGGGCGGGGTCTCCCGCAGTCCAGAAGCTCCTGTAAGCCCCCAGCATCCGAGGAGGAGCTGATCAGAGGGGCAACACTGTGCAAACACCACAGGGCAGCTCCTACCATCCCTGCATAAAAGAACAGGCAGCTCAGGTGGCCGTGACTTACCCGTCGAGCTCTCCTCGCTGGAAGTGTAAGTGCCTTTGCCTAACAGGAGGTTCACCATCGTGGGGGAGTTGGCCACTTTCAGCGGCGTCTCGCCTTTCCTGTTGCTCTGCTGCGGGTTCCCTCCGTACCGCAGCAGCAGCTTCACCACCTACAAGACAGTAACACCCGCGTCAGGGACTGCTGGAGAAGCACAACTCCTCTACCGTTCCGCATAACACGGCAGCCCCTTCCGAGAACCCTGGGGTTCGACCCGAGAGCAGCCCCTCACGGTCTGAGGGTGTGGGAGCCGAGCGCCCAGGGACTGCCTGGCGAGGCTCTGGGTGTGGTGGGCGAGGCTGTGGCTCCTCTGTGGGAAGGGCTGCAGCCGCGGGGGCTCCCGCACCCCTCCTGTGCTCTCCTTCAGAAGGGCTCTGCCTCCTTTGGATTTTTTTCCACCATTTCTCCGTTGCCGCAAGTAGACGACTTCCCAGGAATCTTCTCACGAAGGCTCTCCCCT	TGACGGGGGCCGTGGCCTTCTGTGGCTCTGGGTTCTTGGCCTTGTGCTTGAGGCCTTTTTCGAACTCGGAGTCCGTGTTGTTGCCGTCGACTGAACTGGAAGGTGCGAAGGATGGTGCGTCTTCCTCTTCTGAGCTCTCTGTTGGAGGTAGGAAGCGAGAGGTCACAGGCAGGCTCAAAACAGCTCTCCCCAGAATGGCAGAGGAGGGAGGCTCTGCAGATGTGTCTGCGGGAAGGTTCCCACCCTGCCTCTGCAGAGACACTTTGCTCGACTCATGGAAACCAGCCACAGGCAGGAGGAAACCAGACAGAGCTCAGCTGACAGACAGGGCTGGCATCTTAGAATGAAGACTGCAGGCTTCTCGGCAGTGACACACCTGGGCGGGGTCTCCCGCAGTCCAGAAGCTCCTGTAAGCCCCCAGCATCCGAGGAGGAGCTGATCAGAGGGGCAACACTGTGCAAACACCACAGGGCAGCTCCTACCATCCCTGCATAAAAGAACAGGCAGCTCAGGTGGCCGTGACTTACCCGTCGAGCTCTCCTCGCTGGAAGTGTAAGTGCCTTTGCCTAACAGGAGGTTCACCATCGTGGGGGAGTTGGCCACTTTCAGCGGCGTCTCGCCTTTCCTGTTGCTCTGCTGCGGGTTCCCTCCGTACCGCAGCAGCAGCTTCACCACCTACAAGACAGTAACACCCGCGTCAGGGACTGCTGGAGAAGCACAACTCCTCTACCGTTCCGCATAACACGGCAGCCCCTTCCGAGAACCCTGGGGTTCGACCCGAGAGCAGCCCCTCACGGTCTGAGGGTGTGGGAGCCGAGCGCCCAGGGACTGCCTGGCGAGGCTCTGGGTGTGGTGGGCGAGGCTGTGGCTCCTCTGTGGGAAGGGCTGCAGCCGCGGGGGCTCCCGCACCCCTCCTGTGCTCTCCTTCAGAAGGGCTCTGCCTCCTTTGGATTTTTTTCCACCATTTCTCCGTTGCCGCAAGTAGACGACTTCCCAGGAATCTTCTCACGAAGGCTCTCCCCT	-	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	95	1230	1	ENST00000301030.4:c.745-345_1033del		p.X249_splice	ENST00000301030	NM_001256183.1	249		8-9/13	0.480774570604578	4	FACETS	0.663	0.589	0.741	0.221	0.196	0.247	SUBCLONAL	1	TRUE	1	0.480774570604578	4		1231	883	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573991	7573991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	98	1104	2	ENST00000269305.4:c.1036G>A	p.Glu346Lys	p.E346K	ENST00000269305	NM_001126112.2	346	Gag/Aag	10/11	0.368032946050655	4	FACETS	0.83	0.741	0.926	0.415	0.37	0.463	CLONAL	1	TRUE	2	0.480774570604578	4		1106	727	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39623696	39623696	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs201615084	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	72	510	2	ENST00000262039.4:c.2104-1G>A		p.X702_splice	ENST00000262039	NM_002647.2	702			0.480774570604578	2	FACETS	0.856	0.753	0.965	0.428	0.376	0.483	CLONAL	1	TRUE	0	0.480774570604578	2		512	350	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030568	11030568	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	78	922	0	ENST00000327064.4:c.1122C>G	p.Phe374Leu	p.F374L	ENST00000327064	NM_199141.1	374	ttC/ttG	10/16	0.285364267498471	4	FACETS	0.833	0.733	0.94	0.416	0.366	0.47	INDETERMINATE	1	TRUE	2	0.480774570604578	4		922	577	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095722	178095722	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	153	698	0	ENST00000397062.3:c.1609G>C	p.Glu537Gln	p.E537Q	ENST00000397062	NM_006164.4	537	Gaa/Caa	5/5	0.480774570604578	3	FACETS	1	0.981	1	0.614	0.563	0.666	CLONAL	1	TRUE	1	0.480774570604578	3		698	643	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475573	12475573	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2817	450	694	0	ENST00000287820.6:c.1447G>T	p.Val483Leu	p.V483L	ENST00000287820	NM_015869.4	483	Gtg/Ttg	7/7	0.480774570604578	29	FACETS	1	0.982	1			1	CLONAL	4	TRUE	NA	0.480774570604578	29		694	3267	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475599	12475599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	2920	693	1	ENST00000287820.6:c.1473G>A	p.Met491Ile	p.M491I	ENST00000287820	NM_015869.4	491	atG/atA	7/7	0.480774570604578	29	FACETS	0.985	0.977	0.993			1	CLONAL	28	TRUE	NA	0.480774570604578	29		694	3298	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713864	30713864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223845	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	120	849	1	ENST00000295754.5:c.1189G>A	p.Asp397Asn	p.D397N	ENST00000295754	NM_003242.5	397	Gac/Aac	4/7	0.2943629320055	3	FACETS	1	0.952	1	0.539	0.489	0.593	CLONAL	1	TRUE	1	0.480774570604578	3		850	574	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046343	180046343	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1489676984	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	72	896	1	ENST00000261937.6:c.2671C>T	p.Arg891Cys	p.R891C	ENST00000261937	NM_182925.4	891	Cgc/Tgc	19/30	0.480774570604578	3	FACETS	0.92	0.807	1	0.307	0.269	0.347	CLONAL	1	TRUE	0	0.480774570604578	3		897	404	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90995015	90995015	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	122	832	0	ENST00000265433.3:c.106G>C	p.Glu36Gln	p.E36Q	ENST00000265433	NM_002485.4	36	Gaa/Caa	2/16	0.480774570604578	6	FACETS	0.84	0.757	0.928	0.21	0.189	0.232	CLONAL	1	TRUE	2	0.480774570604578	6		832	1185	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019685	123019685	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	108	451	0	ENST00000355640.3:c.173G>T	p.Gly58Val	p.G58V	ENST00000355640		58	gGa/gTa	2/7	0.480774570604578	3	FACETS	1	0.944	1			1	CLONAL	1	TRUE	NA	0.480774570604578	3		451	521	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350072	89350072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	102	1043	0	ENST00000301030.4:c.2878G>A	p.Glu960Lys	p.E960K	ENST00000301030	NM_001256183.1	960	Gag/Aag	9/13	0.480774570604578	4	FACETS	1	0.906	1	0.337	0.302	0.375	CLONAL	1	TRUE	1	0.480774570604578	4		1043	621	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351533	89351533	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	94	1009	0	ENST00000301030.4:c.1417A>T	p.Ser473Cys	p.S473C	ENST00000301030	NM_001256183.1	473	Agc/Tgc	9/13	0.480774570604578	4	FACETS	0.813	0.724	0.909	0.271	0.241	0.303	CLONAL	1	TRUE	1	0.480774570604578	4		1009	712	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350648	89350648	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	181	1519	0	ENST00000301030.4:c.2302A>T	p.Lys768Ter	p.K768*	ENST00000301030	NM_001256183.1	768	Aaa/Taa	9/13	0.480774570604578	4	FACETS	0.947	0.872	1	0.316	0.29	0.342	CLONAL	1	TRUE	1	0.480774570604578	4		1519	1177	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023212	27023226	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGGGCCCTAGGCC	CGCGGGCCCTAGGCC	A	novel	NA	P-0021549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	121	521	0	ENST00000324856.7:c.318_332delinsA	p.Asn106LysfsTer6	p.N106Kfs*6	ENST00000324856	NM_006015.4	106	aaCGCGGGCCCTAGGCCc/aaAc	1/20	0.421569119953319	3	FACETS	0.997	0.914	1			1	CLONAL	2	TRUE	NA	0.480774570604578	3		521	313	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115872	8115894	+	frameshift_variant	Frame_Shift_Del	DEL	CTCGCCCTTCAGCCACTCCAGCC	CTCGCCCTTCAGCCACTCCAGCC	-	novel	NA	P-0021712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	93	623	2	ENST00000346208.3:c.1218_1240del	p.Ser407HisfsTer92	p.S407Hfs*92	ENST00000346208		406	atCTCGCCCTTCAGCCACTCCAGCCac/atac	6/6	0.262249624592923	5	FACETS	1	0.965	1	0.4	0.357	0.446	INDETERMINATE	1	TRUE	2	0.590884521738341	5		625	495	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427974	49427974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	232	687	0	ENST00000301067.7:c.10616G>A	p.Arg3539Gln	p.R3539Q	ENST00000301067	NM_003482.3	3539	cGg/cAg	38/54	1	2	FACETS	0.903	0.843	0.964	0.903	0.843	0.964	CLONAL	1	TRUE	1	0.564868046361668	2		687	910	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509444	106509444	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	227	732	0	ENST00000359195.3:c.1438T>C	p.Tyr480His	p.Y480H	ENST00000359195	NM_002649.2	480	Tac/Cac	2/11	1	2	FACETS	0.939	0.876	1	0.939	0.876	1	CLONAL	1	TRUE	1	0.564868046361668	2		732	856	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0021762-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	296	545	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.729525005058427	2	FACETS	0.974	0.937	1	0.974	0.937	1	CLONAL	2	TRUE	0	0.733973196650224	2		547	414	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0021762-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	100	954	2	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.714084494287063	4	FACETS	0.976	0.876	1	0.488	0.438	0.541	CLONAL	1	TRUE	2	0.733973196650224	4		956	484	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282460	115282460	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs766864451	NA	P-0021762-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	47	882	0	ENST00000438362.2:c.190A>G	p.Asn64Asp	p.N64D	ENST00000438362	NM_001242891.1	64	Aat/Gat	3/20	0.714084494287063	4	FACETS	0.527	0.446	0.617	0.264	0.223	0.309	SUBCLONAL	1	TRUE	2	0.733973196650224	4		882	421	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041093	42041108	+	frameshift_variant	Frame_Shift_Del	DEL	CCAACTTACAGCCTGT	CCAACTTACAGCCTGT	-	novel	NA	P-0021762-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	76	971	0	ENST00000219905.7:c.5472_5487del	p.Asn1825CysfsTer8	p.N1825Cfs*8	ENST00000219905	NM_001164273.1	1824	cCCAACTTACAGCCTGTc/cc	16/24	0.725351330737646	2	FACETS	0.633	0.56	0.711	0.317	0.28	0.356	SUBCLONAL	1	TRUE	0	0.733973196650224	2		971	327	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788462	3788680	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AACGCATAAAACTTAAAATACCCATTATTTCACGGAATAAACATACAGTAAAAAATAAAGGGTTCTTACTAGTTCCAAATAATTTAATCCAAACTCACCCTAATTTCTTCACATACTCTAAATATCCAATAAGGATCTCATGGTAAACGGCTGTGCGGAGGCAACGTGGCCGGAAGAAATGAATACTATCCAGATAAGAAATGTACACACGCCTGTGGG	AACGCATAAAACTTAAAATACCCATTATTTCACGGAATAAACATACAGTAAAAAATAAAGGGTTCTTACTAGTTCCAAATAATTTAATCCAAACTCACCCTAATTTCTTCACATACTCTAAATATCCAATAAGGATCTCATGGTAAACGGCTGTGCGGAGGCAACGTGGCCGGAAGAAATGAATACTATCCAGATAAGAAATGTACACACGCCTGTGGG	-	novel	NA	P-0021762-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	10	131	0	ENST00000262367.5:c.4281-7_4394+98del		p.X1427_splice	ENST00000262367	NM_004380.2	1427		26/31	0.734302557027381	3	FACETS	0.81	0.565	1	0.405	0.282	0.548	CLONAL	1	TRUE	1	0.733973196650224	3		131	46	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47601113	47601113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs994384264	NA	P-0021762-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	42	758	0	ENST00000263735.4:c.351G>C	p.Trp117Cys	p.W117C	ENST00000263735	NM_002354.2	117	tgG/tgC	3/9	0.716306061188364	3	FACETS	0.283	0.236	0.335	0.094	0.078	0.112	SUBCLONAL	1	TRUE	0	0.733973196650224	3		758	553	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682394	52682394	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021762-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	105	726	0	ENST00000394830.3:c.779A>G	p.Lys260Arg	p.K260R	ENST00000394830	NM_018313.4	260	aAa/aGa	8/30	0.734302557027381	3	FACETS	1	0.953	1	0.543	0.491	0.597	CLONAL	1	TRUE	1	0.733973196650224	3		726	360	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	151	294	2	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.945	0.87	1	0.945	0.87	1	CLONAL	1	TRUE	1	0.613309435139173	2		296	521	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	192	504	6	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	0.613309435139173	2		510	607	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	114	416	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.76	0.688	0.836	0.76	0.688	0.836	SUBCLONAL	1	TRUE	1	0.613309435139173	2		417	489	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	119	516	1	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	1	2	FACETS	0.635	0.575	0.699	0.635	0.575	0.699	SUBCLONAL	1	TRUE	1	0.613309435139173	2		517	611	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	310	898	5	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	NA	2	FACETS	0.981	0.926	1			1	INDETERMINATE	1	TRUE	NA	0.613309435139173	2		903	1031	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574679	41574679	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	288	911	4	ENST00000263253.7:c.6970del	p.His2324ThrfsTer29	p.H2324Tfs*29	ENST00000263253	NM_001429.3	2322	Ccc/cc	31/31	1	2	FACETS	0.84	0.79	0.891	0.84	0.79	0.891	CLONAL	1	TRUE	1	0.613309435139173	2		915	1118	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	56	698	2	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.603886753381071	2	FACETS	0.176	0.15	0.204	0.088	0.075	0.102	SUBCLONAL	1	TRUE	0	0.613309435139173	2		700	1039	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161907	47161907	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	147	512	0	ENST00000409792.3:c.4219del	p.Arg1407GlyfsTer5	p.R1407Gfs*5	ENST00000409792	NM_014159.6	1407	Agg/gg	3/21	1	2	FACETS	0.787	0.721	0.855	0.787	0.721	0.855	SUBCLONAL	1	TRUE	1	0.613309435139173	2		512	609	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714649	52714649	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776781710	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	274	651	3	ENST00000322088.6:c.407C>T	p.Ala136Val	p.A136V	ENST00000322088	NM_014225.5	136	gCg/gTg	4/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.613309435139173	2		654	858	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197438	27197439	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	247	737	1	ENST00000380036.4:c.1756dup	p.Ser586LysfsTer2	p.S586Kfs*2	ENST00000380036	NM_000459.3	584	caa/cAaa	12/23	1	2	FACETS	0.902	0.845	0.961	0.902	0.845	0.961	CLONAL	1	TRUE	1	0.613309435139173	2		738	893	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553478	29553478	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781807	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	456	749	3	ENST00000356175.3:c.2033del	p.Pro678ArgfsTer10	p.P678Rfs*10	ENST00000356175	NM_000267.3	676	aCc/ac	18/57	0.603886753381071	2	FACETS	0.844	0.811	0.877	0.844	0.811	0.877	CLONAL	2	TRUE	0	0.613309435139173	2		752	881	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	263	728	5	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.613309435139173	2		733	822	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099424	157099426	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	rs754060642	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	70	444	0	ENST00000346085.5:c.363_365del	p.Gln131del	p.Q131del	ENST00000346085	NM_020732.3	121	CAA/-	1/20	1	2	FACETS	0.49	0.428	0.556	0.49	0.428	0.556	SUBCLONAL	1	TRUE	1	0.613309435139173	2		444	466	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101402	27101402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	209	542	1	ENST00000324856.7:c.4689del	p.Met1564Ter	p.M1564*	ENST00000324856	NM_006015.4	1562	Ccc/cc	18/20	1	2	FACETS	0.908	0.845	0.972	0.908	0.845	0.972	CLONAL	1	TRUE	1	0.613309435139173	2		543	751	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799299	42799300	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1158987717	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	84	373	0	ENST00000575354.2:c.4790dup	p.Pro1598ThrfsTer16	p.P1598Tfs*16	ENST00000575354	NM_015125.3	1595	tcc/tCcc	20/20	1	2	FACETS	0.584	0.518	0.655	0.584	0.518	0.655	SUBCLONAL	1	TRUE	1	0.613309435139173	2		373	469	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572612	64572612	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446518998	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	284	830	0	ENST00000312049.6:c.1244G>A	p.Arg415Gln	p.R415Q	ENST00000312049	NM_130799.2	415	cGa/cAa	9/10	1	2	FACETS	0.828	0.778	0.879	0.828	0.778	0.879	CLONAL	1	TRUE	1	0.613309435139173	2		830	1119	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353819	15353819	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	168	775	4	ENST00000263377.2:c.3061del	p.His1021IlefsTer47	p.H1021Ifs*47	ENST00000263377	NM_058243.2	1021	Cat/at	14/20	1	2	FACETS	0.641	0.589	0.694	0.641	0.589	0.694	SUBCLONAL	1	TRUE	1	0.613309435139173	2		779	855	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754890	29754890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370848188	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	140	453	0	ENST00000389048.3:c.1045G>A	p.Val349Ile	p.V349I	ENST00000389048	NM_004304.4	349	Gtc/Atc	4/29	0.613309435139173	2	FACETS	0.815	0.746	0.887	0.408	0.373	0.444	CLONAL	1	TRUE	0	0.613309435139173	2		453	560	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101751	71101751	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	95	354	0	ENST00000318789.4:c.447del	p.Lys149AsnfsTer57	p.K149Nfs*57	ENST00000318789	NM_032682.5	149	aaA/aa	9/21	1	2	FACETS	0.805	0.722	0.891	0.805	0.722	0.891	CLONAL	1	TRUE	1	0.613309435139173	2		354	385	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	367	584	4	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	0.603886753381071	2	FACETS	0.898	0.861	0.936	0.898	0.861	0.936	CLONAL	2	TRUE	0	0.613309435139173	2		588	666	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	184	367	2	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.613309435139173	2		369	569	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607597	43607597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs545625150	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	102	809	1	ENST00000355710.3:c.1573C>T	p.Arg525Trp	p.R525W	ENST00000355710	NM_020975.4	525	Cgg/Tgg	8/20	1	2	FACETS	0.332	0.296	0.37	0.332	0.296	0.37	SUBCLONAL	1	TRUE	1	0.613309435139173	2		810	1003	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138083	64138083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777650305	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	303	757	1	ENST00000334205.4:c.2006G>A	p.Arg669Gln	p.R669Q	ENST00000334205	NM_003942.2	669	cGg/cAg	16/17	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.613309435139173	2		758	954	SUCCESS
APC	324	MSKCC	GRCh37	5	112175952	112175952	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587783031	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	50	266	0	ENST00000257430.4:c.4666del	p.Thr1556LeufsTer9	p.T1556Lfs*9	ENST00000257430	NM_000038.5	1554	gAa/ga	16/16	1	2	FACETS	0.84	0.723	0.965	0.84	0.723	0.965	CLONAL	1	TRUE	1	0.613309435139173	2		266	194	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482607	56482607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs993665271	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	310	800	1	ENST00000267101.3:c.1064C>T	p.Thr355Ile	p.T355I	ENST00000267101	NM_001982.3	355	aCc/aTc	9/28	1	2	FACETS	0.992	0.937	1	0.992	0.937	1	CLONAL	1	TRUE	1	0.613309435139173	2		801	1019	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748850	41748850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138698106	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	288	878	5	ENST00000301178.4:c.1375G>A	p.Val459Met	p.V459M	ENST00000301178	NM_021913.4	459	Gtg/Atg	11/20	1	2	FACETS	0.913	0.859	0.968	0.913	0.859	0.968	CLONAL	1	TRUE	1	0.613309435139173	2		883	1029	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117512	4117512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457644550	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	98	312	0	ENST00000262948.5:c.208G>A	p.Asp70Asn	p.D70N	ENST00000262948	NM_030662.3	70	Gat/Aat	2/11	1	2	FACETS	0.957	0.863	1	0.957	0.863	1	CLONAL	1	TRUE	1	0.613309435139173	2		312	334	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681787	30681787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	498	690	0	ENST00000376406.3:c.310C>T	p.Pro104Ser	p.P104S	ENST00000376406	NM_014641.2	104	Cct/Tct	3/15	0.599988066550614	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.613309435139173	2		690	806	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18964077	18964077	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	137	574	0	ENST00000262803.5:c.1078del	p.Asp360MetfsTer46	p.D360Mfs*46	ENST00000262803	NM_002911.3	358	caG/ca	8/24	1	2	FACETS	0.655	0.597	0.716	0.655	0.597	0.716	SUBCLONAL	1	TRUE	1	0.613309435139173	2		574	682	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712851	43712851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750560493	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	267	739	1	ENST00000382044.4:c.4333G>A	p.Val1445Met	p.V1445M	ENST00000382044	NM_001141980.1	1445	Gtg/Atg	21/28	1	2	FACETS	0.851	0.799	0.905	0.851	0.799	0.905	CLONAL	1	TRUE	1	0.613309435139173	2		740	1023	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845397	42845397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762854045	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	245	660	0	ENST00000398585.3:c.865C>T	p.Arg289Cys	p.R289C	ENST00000398585	NM_001135099.1	289	Cgc/Tgc	9/14	1	2	FACETS	0.845	0.791	0.901	0.845	0.791	0.901	CLONAL	1	TRUE	1	0.613309435139173	2		660	945	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098012	178098012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	146	480	2	ENST00000397062.3:c.368del	p.Leu123TrpfsTer8	p.L123Wfs*8	ENST00000397062	NM_006164.4	123	tTg/tg	3/5	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.613309435139173	2		482	466	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101068	27101068	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	214	789	0	ENST00000324856.7:c.4354del	p.Gln1452ArgfsTer29	p.Q1452Rfs*29	ENST00000324856	NM_006015.4	1450	ggC/gg	18/20	1	2	FACETS	0.746	0.693	0.8	0.746	0.693	0.8	SUBCLONAL	1	TRUE	1	0.613309435139173	2		789	936	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251724	212251724	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770460785	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	135	409	1	ENST00000342788.4:c.3335G>A	p.Arg1112His	p.R1112H	ENST00000342788	NM_005235.2	1112	cGc/cAc	27/28	1	2	FACETS	0.935	0.856	1	0.935	0.856	1	CLONAL	1	TRUE	1	0.613309435139173	2		410	471	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185545	27185545	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1564083506	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	237	821	3	ENST00000380036.4:c.1250del	p.Pro417LeufsTer10	p.P417Lfs*10	ENST00000380036	NM_000459.3	415	ctC/ct	9/23	1	2	FACETS	0.883	0.826	0.942	0.883	0.826	0.942	CLONAL	1	TRUE	1	0.613309435139173	2		824	875	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022747	12022747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376242225	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	188	528	1	ENST00000396373.4:c.853G>A	p.Val285Met	p.V285M	ENST00000396373	NM_001987.4	285	Gtg/Atg	5/8	1	2	FACETS	0.997	0.926	1	0.997	0.926	1	CLONAL	1	TRUE	1	0.613309435139173	2		529	615	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430942	181430942	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	236	764	3	ENST00000325404.1:c.794G>A	p.Cys265Tyr	p.C265Y	ENST00000325404	NM_003106.3	265	tGc/tAc	1/1	1	2	FACETS	0.997	0.934	1	0.997	0.934	1	CLONAL	1	TRUE	1	0.613309435139173	2		767	772	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780039	9780039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	262	752	0	ENST00000377346.4:c.1303G>A	p.Gly435Arg	p.G435R	ENST00000377346	NM_005026.3	435	Ggg/Agg	10/24	1	2	FACETS	0.952	0.894	1	0.952	0.894	1	CLONAL	1	TRUE	1	0.613309435139173	2		752	897	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106846	27106846	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781033223	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	37	560	1	ENST00000324856.7:c.6457C>T	p.Arg2153Cys	p.R2153C	ENST00000324856	NM_006015.4	2153	Cgc/Tgc	20/20	1	2	FACETS	0.168	0.138	0.202	0.168	0.138	0.202	SUBCLONAL	1	TRUE	1	0.613309435139173	2		561	719	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797418	45797418	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs768130289	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	59	747	0	ENST00000450313.1:c.1101del	p.Arg368GlyfsTer40	p.R368Gfs*40	ENST00000450313	NM_012222.2	367	ccC/cc	12/16	1	2	FACETS	0.3	0.257	0.346	0.3	0.257	0.346	SUBCLONAL	1	TRUE	1	0.613309435139173	2		747	642	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78425912	78425913	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	100	448	0	ENST00000370768.2:c.1532dup	p.Asn512LysfsTer13	p.N512Kfs*13	ENST00000370768	NM_003902.3	511	gga/ggGa	16/20	1	2	FACETS	0.731	0.657	0.809	0.731	0.657	0.809	SUBCLONAL	1	TRUE	1	0.613309435139173	2		448	446	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597924	43597924	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	204	874	0	ENST00000355710.3:c.472A>G	p.Ser158Gly	p.S158G	ENST00000355710	NM_020975.4	158	Agc/Ggc	3/20	1	2	FACETS	0.747	0.693	0.802	0.747	0.693	0.802	SUBCLONAL	1	TRUE	1	0.613309435139173	2		874	891	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447410	49447410	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758710579	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	243	715	0	ENST00000301067.7:c.688G>A	p.Ala230Thr	p.A230T	ENST00000301067	NM_003482.3	230	Gca/Aca	6/54	1	2	FACETS	0.828	0.774	0.883	0.828	0.774	0.883	CLONAL	1	TRUE	1	0.613309435139173	2		715	957	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514622	103514622	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1566468572	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	150	390	0	ENST00000355739.4:c.1123C>T	p.Pro375Ser	p.P375S	ENST00000355739	NM_000123.3	375	Cct/Tct	8/15	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.613309435139173	2		390	469	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591705	38591705	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	172	587	1	ENST00000299084.4:c.164G>A	p.Cys55Tyr	p.C55Y	ENST00000299084	NM_152594.2	55	tGt/tAt	2/7	1	2	FACETS	0.855	0.79	0.923	0.855	0.79	0.923	CLONAL	1	TRUE	1	0.613309435139173	2		588	656	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041458	42041458	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	39	561	0	ENST00000219905.7:c.5653T>C	p.Ser1885Pro	p.S1885P	ENST00000219905	NM_001164273.1	1885	Tca/Cca	17/24	1	2	FACETS	0.197	0.162	0.235	0.197	0.162	0.235	SUBCLONAL	1	TRUE	1	0.613309435139173	2		561	646	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293063	91293063	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1180631656	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	101	479	0	ENST00000355112.3:c.565G>T	p.Gly189Cys	p.G189C	ENST00000355112	NM_000057.2	189	Ggt/Tgt	3/22	1	2	FACETS	0.578	0.518	0.641	0.578	0.518	0.641	SUBCLONAL	1	TRUE	1	0.613309435139173	2		479	570	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500661	99500661	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370843278	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	132	333	0	ENST00000268035.6:c.4094C>T	p.Ser1365Leu	p.S1365L	ENST00000268035	NM_000875.3	1365	tCg/tTg	21/21	1	2	FACETS	0.856	0.781	0.933	0.856	0.781	0.933	CLONAL	1	TRUE	1	0.613309435139173	2		333	503	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127614	2127615	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs796053504	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	292	800	2	ENST00000219476.3:c.2859dup	p.Lys954GlnfsTer6	p.K954Qfs*6	ENST00000219476	NM_000548.3	951	-/C	26/42	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.613309435139173	2		802	934	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778899	3778899	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	132	560	1	ENST00000262367.5:c.6149G>T	p.Gly2050Val	p.G2050V	ENST00000262367	NM_004380.2	2050	gGg/gTg	31/31	1	2	FACETS	0.806	0.735	0.88	0.806	0.735	0.88	CLONAL	1	TRUE	1	0.613309435139173	2		561	534	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50788288	50788288	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	246	811	3	ENST00000398568.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000398568	NM_001042412.1	289	gCg/gTg	5/18	1	2	FACETS	0.932	0.873	0.992	0.932	0.873	0.992	CLONAL	1	TRUE	1	0.613309435139173	2		814	861	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830139	72830139	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs745488121	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	187	588	0	ENST00000268489.5:c.6442C>A	p.Pro2148Thr	p.P2148T	ENST00000268489	NM_006885.3	2148	Cct/Act	9/10	1	2	FACETS	0.845	0.783	0.909	0.845	0.783	0.909	CLONAL	1	TRUE	1	0.613309435139173	2		588	722	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475595	40475595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	436	527	0	ENST00000264657.5:c.1649G>A	p.Cys550Tyr	p.C550Y	ENST00000264657	NM_139276.2	550	tGc/tAc	18/24	0.603886753381071	2	FACETS	0.914	0.879	0.948	0.914	0.879	0.948	CLONAL	2	TRUE	0	0.613309435139173	2		527	778	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619460	1619463	+	frameshift_variant	Frame_Shift_Del	DEL	TCTA	TCTA	-	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	271	801	0	ENST00000344749.5:c.1178_1181del	p.Ile393LysfsTer92	p.I393Kfs*92	ENST00000344749	NM_001136139.2	393	aTAGAa/aa	15/19	1	2	FACETS	0.891	0.837	0.946	0.891	0.837	0.946	CLONAL	1	TRUE	1	0.613309435139173	2		801	992	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272237	15272238	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	197	655	0	ENST00000263388.2:c.6201dup	p.Gly2068ArgfsTer27	p.G2068Rfs*27	ENST00000263388	NM_000435.2	2067	-/C	33/33	1	2	FACETS	0.89	0.827	0.955	0.89	0.827	0.955	CLONAL	1	TRUE	1	0.613309435139173	2		655	722	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284984	15284984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	273	784	1	ENST00000263388.2:c.4631G>A	p.Arg1544His	p.R1544H	ENST00000263388	NM_000435.2	1544	cGc/cAc	25/33	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.613309435139173	2		785	875	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221002	36221003	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	275	700	0	ENST00000222270.7:c.5056_5057del	p.Thr1686Ter	p.T1686*	ENST00000222270	NM_014727.1	1684	aaACac/aaac	23/37	1	2	FACETS	0.933	0.877	0.99	0.933	0.877	0.99	CLONAL	1	TRUE	1	0.613309435139173	2		700	961	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221770	36221770	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	306	784	0	ENST00000222270.7:c.5437+2T>C		p.X1813_splice	ENST00000222270	NM_014727.1	1813			1	2	FACETS	0.94	0.886	0.994	0.94	0.886	0.994	CLONAL	1	TRUE	1	0.613309435139173	2		784	1062	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754460	41754460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374709166	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	314	775	0	ENST00000301178.4:c.1579C>T	p.Arg527Trp	p.R527W	ENST00000301178	NM_021913.4	527	Cgg/Tgg	13/20	1	2	FACETS	0.959	0.905	1	0.959	0.905	1	CLONAL	1	TRUE	1	0.613309435139173	2		775	1068	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31390258	31390258	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	192	617	0	ENST00000328111.2:c.2213A>G	p.Asn738Ser	p.N738S	ENST00000328111	NM_006892.3	738	aAc/aGc	20/23	1	2	FACETS	0.894	0.83	0.961	0.894	0.83	0.961	CLONAL	1	TRUE	1	0.613309435139173	2		617	700	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319499	62319499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1367858373	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	263	843	1	ENST00000360203.5:c.1603G>A	p.Glu535Lys	p.E535K	ENST00000360203	NM_001283009.1	535	Gag/Aag	19/35	1	2	FACETS	0.827	0.775	0.88	0.827	0.775	0.88	CLONAL	1	TRUE	1	0.613309435139173	2		844	1037	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164608	36164608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	217	577	1	ENST00000300305.3:c.1267C>T	p.Arg423Cys	p.R423C	ENST00000300305		423	Cgc/Tgc	8/8	1	2	FACETS	0.935	0.872	0.999	0.935	0.872	0.999	CLONAL	1	TRUE	1	0.613309435139173	2		578	757	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764321	39764321	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866293609	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	257	762	3	ENST00000288319.7:c.791G>A	p.Gly264Asp	p.G264D	ENST00000288319	NM_182918.3	264	gGc/gAc	7/10	1	2	FACETS	0.807	0.756	0.86	0.807	0.756	0.86	CLONAL	1	TRUE	1	0.613309435139173	2		765	1038	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574191	41574303	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGGATGAGCCCCCAGGCTCAGCAGATGAACATGAACCACAACACCATGCCTTCACAATTCCGAGACATCTTGAGACGACAGCAAATGATGCAACAGCAGCAGCAACAGGGA	GAGGGATGAGCCCCCAGGCTCAGCAGATGAACATGAACCACAACACCATGCCTTCACAATTCCGAGACATCTTGAGACGACAGCAAATGATGCAACAGCAGCAGCAACAGGGA	-	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	161	556	0	ENST00000263253.7:c.6477_6589del	p.Gly2160ArgfsTer12	p.G2160Rfs*12	ENST00000263253	NM_001429.3	2159	gGAGGGATGAGCCCCCAGGCTCAGCAGATGAACATGAACCACAACACCATGCCTTCACAATTCCGAGACATCTTGAGACGACAGCAAATGATGCAACAGCAGCAGCAACAGGGA/g	31/31	1	2	FACETS	0.827	0.761	0.895	0.827	0.761	0.895	CLONAL	1	TRUE	1	0.613309435139173	2		556	635	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266155	41266155	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	150	404	0	ENST00000349496.5:c.152A>C	p.Asn51Thr	p.N51T	ENST00000349496	NM_001904.3	51	aAt/aCt	3/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.613309435139173	2		404	445	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468397	89468398	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1467832547	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	67	300	2	ENST00000336596.2:c.1938dup	p.Glu647ArgfsTer7	p.E647Rfs*7	ENST00000336596	NM_005233.5	644	tca/tcAa	11/17	1	2	FACETS	0.85	0.747	0.958	0.85	0.747	0.958	CLONAL	1	TRUE	1	0.613309435139173	2		302	257	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444681	187444681	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373425354	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	115	302	0	ENST00000232014.4:c.1546G>A	p.Gly516Arg	p.G516R	ENST00000232014	NM_001130845.1	516	Ggg/Agg	7/10	1	2	FACETS	0.848	0.77	0.931	0.848	0.77	0.931	CLONAL	1	TRUE	1	0.613309435139173	2		302	442	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561792	55561792	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs557317141	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	177	439	1	ENST00000288135.5:c.182C>T	p.Pro61Leu	p.P61L	ENST00000288135	NM_000222.2	61	cCg/cTg	2/21	1	2	FACETS	0.988	0.916	1	0.988	0.916	1	CLONAL	1	TRUE	1	0.613309435139173	2		440	584	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193843	106193843	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	97	397	0	ENST00000380013.4:c.4305G>T	p.Gln1435His	p.Q1435H	ENST00000380013	NM_001127208.2	1435	caG/caT	10/11	1	2	FACETS	0.595	0.532	0.661	0.595	0.532	0.661	SUBCLONAL	1	TRUE	1	0.613309435139173	2		397	532	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80057379	80057379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764832633	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	120	464	0	ENST00000265081.6:c.1778G>A	p.Arg593Gln	p.R593Q	ENST00000265081	NM_002439.4	593	cGg/cAg	13/24	1	2	FACETS	0.849	0.771	0.929	0.849	0.771	0.929	CLONAL	1	TRUE	1	0.613309435139173	2		464	461	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672317	86672317	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	139	535	2	ENST00000274376.6:c.2119C>T	p.Arg707Cys	p.R707C	ENST00000274376	NM_002890.2	707	Cgt/Tgt	16/25	1	2	FACETS	0.907	0.831	0.985	0.907	0.831	0.985	CLONAL	1	TRUE	1	0.613309435139173	2		537	500	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675668	86675668	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs983011713	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	90	387	0	ENST00000274376.6:c.2603+1G>A		p.X868_splice	ENST00000274376	NM_002890.2	868			1	2	FACETS	0.914	0.82	1	0.914	0.82	1	CLONAL	1	TRUE	1	0.613309435139173	2		387	321	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520497	176520497	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145635664	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	360	793	0	ENST00000292408.4:c.1342G>A	p.Gly448Ser	p.G448S	ENST00000292408	NM_213647.1	448	Ggc/Agc	10/18	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.613309435139173	2		793	1113	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048156	180048156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747033940	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	340	853	0	ENST00000261937.6:c.2117C>T	p.Ala706Val	p.A706V	ENST00000261937	NM_182925.4	706	gCg/gTg	14/30	1	2	FACETS	0.996	0.943	1	0.996	0.943	1	CLONAL	1	TRUE	1	0.613309435139173	2		853	1113	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129222	152129222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	319	775	1	ENST00000206249.3:c.175G>A	p.Ala59Thr	p.A59T	ENST00000206249	NM_000125.3	59	Gcc/Acc	1/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.613309435139173	2		776	927	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522410	157522410	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1235911089	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	262	700	1	ENST00000346085.5:c.4682G>A	p.Arg1561His	p.R1561H	ENST00000346085	NM_020732.3	1561	cGc/cAc	18/20	1	2	FACETS	0.972	0.913	1	0.972	0.913	1	CLONAL	1	TRUE	1	0.613309435139173	2		701	879	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148513780	148513781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	201	657	0	ENST00000320356.2:c.1500dup	p.His501ThrfsTer20	p.H501Tfs*20	ENST00000320356	NM_004456.4	500	-/A	12/20	1	2	FACETS	0.932	0.867	0.999	0.932	0.867	0.999	CLONAL	1	TRUE	1	0.613309435139173	2		657	703	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271255	38271255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555706876	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	212	917	0	ENST00000425967.3:c.2453C>T	p.Thr818Met	p.T818M	ENST00000425967	NM_001174067.1	818	aCg/aTg	19/19	1	2	FACETS	0.681	0.633	0.731	0.681	0.633	0.731	SUBCLONAL	1	TRUE	1	0.613309435139173	2		917	1015	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740573	145740573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573164516	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	631	762	0	ENST00000428558.2:c.1444C>T	p.Arg482Cys	p.R482C	ENST00000428558	NM_004260.3	482	Cgc/Tgc	8/22	1	2	FACETS	1	0.971	1	1	0.998	1	CLONAL	2	TRUE	1	0.613309435139173	2		762	1028	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340369	8340369	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771603044	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	204	601	2	ENST00000356435.5:c.5227C>T	p.Leu1743Phe	p.L1743F	ENST00000356435		1743	Ctc/Ttc	31/35	1	2	FACETS	0.97	0.903	1	0.97	0.903	1	CLONAL	1	TRUE	1	0.613309435139173	2		603	686	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249833	110249833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1310912820	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	254	692	2	ENST00000374672.4:c.842C>T	p.Ala281Val	p.A281V	ENST00000374672	NM_004235.4	281	gCg/gTg	3/5	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.613309435139173	2		694	801	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738315	133738315	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	194	565	1	ENST00000318560.5:c.715C>T	p.Arg239Cys	p.R239C	ENST00000318560	NM_005157.4	239	Cgc/Tgc	4/11	1	2	FACETS	0.887	0.824	0.953	0.887	0.824	0.953	CLONAL	1	TRUE	1	0.613309435139173	2		566	713	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417631	139417631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	230	849	0	ENST00000277541.6:c.413G>A	p.Cys138Tyr	p.C138Y	ENST00000277541	NM_017617.3	138	tGc/tAc	4/34	1	2	FACETS	0.705	0.657	0.755	0.705	0.657	0.755	SUBCLONAL	1	TRUE	1	0.613309435139173	2		849	1064	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418328	139418328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs571831870	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	241	851	1	ENST00000277541.6:c.244G>A	p.Val82Met	p.V82M	ENST00000277541	NM_017617.3	82	Gtg/Atg	3/34	1	2	FACETS	0.71	0.663	0.759	0.71	0.663	0.759	SUBCLONAL	1	TRUE	1	0.613309435139173	2		852	1107	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426180	47426180	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	174	369	0	ENST00000377045.4:c.699+1G>A		p.X233_splice	ENST00000377045	NM_001654.4	233			1	1	FACETS	0.964	0.899	1	0.964	0.899	1	CLONAL	1	TRUE	0	0.613309435139173	1		369	408	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426743	47426743	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	315	403	0	ENST00000377045.4:c.988C>T	p.His330Tyr	p.H330Y	ENST00000377045	NM_001654.4	330	Cat/Tat	10/16	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.613309435139173	1		403	516	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410693	63410693	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	23	420	0	ENST00000330258.3:c.2474A>T	p.Asn825Ile	p.N825I	ENST00000330258	NM_152424.3	825	aAt/aTt	2/2	1	1	FACETS	0.12	0.093	0.151	0.12	0.093	0.151	SUBCLONAL	1	TRUE	0	0.613309435139173	1		420	435	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829788	76829788	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	215	408	0	ENST00000373344.5:c.6253C>T	p.Arg2085Cys	p.R2085C	ENST00000373344	NM_000489.3	2085	Cgt/Tgt	28/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.613309435139173	1		408	340	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426729	49426730	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs576788910	NA	P-0021796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	74	300	1	ENST00000301067.7:c.11756_11758dup	p.Gln3919dup	p.Q3919dup	ENST00000301067	NM_003482.3	3919	cta/cAGCta	39/54	1	2	FACETS	0.527	0.463	0.596	0.527	0.463	0.596	SUBCLONAL	1	TRUE	1	0.613309435139173	2		301	458	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0021854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	47	421	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	0.949	0.801	1	0.949	0.801	1	CLONAL	1	TRUE	1	0.2	2		421	495	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753152	42753152	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs767470579	NA	P-0021854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	48	638	0	ENST00000222329.4:c.1112C>G	p.Ser371Cys	p.S371C	ENST00000222329	NM_006494.2	371	tCt/tGt	4/4	1	2	FACETS	0.575	0.484	0.675	0.575	0.484	0.675	SUBCLONAL	1	TRUE	1	0.2	2		638	835	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106194000	106194000	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	177	351	0	ENST00000380013.4:c.4462A>G	p.Lys1488Glu	p.K1488E	ENST00000380013	NM_001127208.2	1488	Aaa/Gaa	10/11	0.787550654694719	4	FACETS	0.887	0.826	0.949	0.887	0.826	0.949	CLONAL	2	TRUE	2	0.787550654694719	4		351	453	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0021935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	213	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.380743301707375	2		436	1097	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115710	108115714	+	frameshift_variant	Frame_Shift_Del	DEL	AATTT	AATTT	-	novel	NA	P-0021935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	87	347	0	ENST00000278616.4:c.859_863del	p.Ile287TyrfsTer16	p.I287Yfs*16	ENST00000278616	NM_000051.3	286	caAATTTat/caat	7/63	1	2	FACETS	0.813	0.721	0.911	0.813	0.721	0.911	CLONAL	1	TRUE	1	0.380743301707375	2		347	562	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39214687	39214688	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0021935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	193	586	0	ENST00000402219.2:c.3436dup	p.Glu1146GlyfsTer25	p.E1146Gfs*25	ENST00000402219	NM_005633.3	1146	gaa/gGaa	22/23	1	2	FACETS	0.917	0.847	0.989	0.917	0.847	0.989	CLONAL	1	TRUE	1	0.380743301707375	2		586	1106	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971174	21971175	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0021935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	259	452	0	ENST00000304494.5:c.183_184del	p.Glu61AspfsTer58	p.E61Dfs*58	ENST00000304494	NM_000077.4	61	gaGCtg/gatg	2/3	0.361527831379787	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.380743301707375	2		452	678	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945181	44945181	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	232	720	1	ENST00000377967.4:c.3505G>T	p.Val1169Phe	p.V1169F	ENST00000377967	NM_021140.2	1169	Gtt/Ttt	24/29	0.380743301707375	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.380743301707375	1		721	945	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258625	19258625	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	343	804	1	ENST00000162023.5:c.275G>T	p.Gly92Val	p.G92V	ENST00000162023		92	gGc/gTc	8/13	0.428471022549045	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.482219463637331	4		805	985	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818435	43818435	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	131	681	0	ENST00000372470.3:c.1900C>G	p.Gln634Glu	p.Q634E	ENST00000372470	NM_005373.2	634	Cag/Gag	12/12	0.483675438642714	2	FACETS	0.947	0.862	1	0.473	0.431	0.517	CLONAL	1	TRUE	0	0.482219463637331	2		681	574	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333886	70333886	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	116	477	0	ENST00000373644.4:c.1791C>A	p.Cys597Ter	p.C597*	ENST00000373644	NM_030625.2	597	tgC/tgA	2/12	0.483675438642714	4	FACETS	1	0.962	1	0.565	0.51	0.623	CLONAL	1	TRUE	2	0.482219463637331	4		477	631	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61197650	61197650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148425779	NA	P-0021942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	281	609	0	ENST00000301761.2:c.32C>T	p.Ser11Leu	p.S11L	ENST00000301761	NM_017841.2	11	tCg/tTg	1/4	0.483675438642714	4	FACETS	0.996	0.939	1	0.996	0.939	1	CLONAL	2	TRUE	2	0.482219463637331	4		609	867	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129189	64129189	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	221	935	0	ENST00000334205.4:c.727G>C	p.Glu243Gln	p.E243Q	ENST00000334205	NM_003942.2	243	Gag/Cag	7/17	0.483675438642714	4	FACETS	1	0.982	1	0.582	0.54	0.624	CLONAL	1	TRUE	2	0.482219463637331	4		935	1168	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082930	16082930	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	96	332	0	ENST00000281043.3:c.744C>A	p.Asp248Glu	p.D248E	ENST00000281043	NM_005378.4	248	gaC/gaA	2/3	0.476548988764245	5	FACETS	1	0.956	1	0.379	0.338	0.422	CLONAL	1	TRUE	2	0.482219463637331	5		332	604	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131315	202131315	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	133	610	0	ENST00000358485.4:c.283G>C	p.Glu95Gln	p.E95Q	ENST00000358485	NM_001080125.1	95	Gaa/Caa	2/9	0.483675438642714	4	FACETS	0.969	0.88	1	0.484	0.44	0.531	CLONAL	1	TRUE	2	0.482219463637331	4		610	844	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54963243	54963243	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	120	548	2	ENST00000312783.6:c.11C>A	p.Ser4Tyr	p.S4Y	ENST00000312783	NM_198436.1	4	tCt/tAt	3/10	0.482219463637331	9	FACETS	1	0.976	1	0.255	0.229	0.282	CLONAL	1	TRUE	4	0.482219463637331	9		550	1050	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971098	55971098	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	133	681	0	ENST00000263923.4:c.1699del	p.Val567CysfsTer46	p.V567Cfs*46	ENST00000263923	NM_002253.2	567	Gtg/tg	13/30	0.483675438642714	3	FACETS	0.919	0.835	1	0.459	0.417	0.504	CLONAL	1	TRUE	1	0.482219463637331	3		681	745	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721690	176721690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1249673539	NA	P-0021942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	129	608	0	ENST00000439151.2:c.7321C>T	p.Pro2441Ser	p.P2441S	ENST00000439151	NM_022455.4	2441	Cct/Tct	23/23	0.483675438642714	3	FACETS	1	0.946	1	0.529	0.48	0.579	CLONAL	1	TRUE	1	0.482219463637331	3		608	628	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979403	2979403	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	143	746	0	ENST00000396946.4:c.844G>C	p.Glu282Gln	p.E282Q	ENST00000396946	NM_032415.4	282	Gag/Cag	6/25	0.482219463637331	6	FACETS	0.965	0.878	1	0.241	0.219	0.265	CLONAL	1	TRUE	2	0.482219463637331	6		746	1207	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854931	76854931	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	239	914	0	ENST00000373344.5:c.5905A>C	p.Asn1969His	p.N1969H	ENST00000373344	NM_000489.3	1969	Aat/Cat	25/35	0.483675438642714	3	FACETS	1	0.971	1	0.536	0.5	0.574	CLONAL	1	TRUE	1	0.482219463637331	3		914	1147	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76856009	76856009	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	160	794	0	ENST00000373344.5:c.5591G>A	p.Gly1864Glu	p.G1864E	ENST00000373344	NM_000489.3	1864	gGa/gAa	23/35	0.483675438642714	3	FACETS	1	0.926	1	0.505	0.463	0.548	CLONAL	1	TRUE	1	0.482219463637331	3		794	816	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	46	428	2	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.283	0.238	0.333	0.283	0.238	0.333	SUBCLONAL	1	TRUE	1	0.548199364230757	2		430	593	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	37	294	2	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.273	0.225	0.328	0.273	0.225	0.328	SUBCLONAL	1	TRUE	1	0.548199364230757	2		296	494	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	285	993	1	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.548199364230757	2		994	990	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	253	853	7	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.548199364230757	2		860	901	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720712	89720712	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	53	179	0	ENST00000371953.3:c.867del	p.Val290Ter	p.V290*	ENST00000371953	NM_000314.4	288	gAa/ga	8/9	0.548199364230757	2	FACETS	0.786	0.691	0.883	0.786	0.691	0.883	SUBCLONAL	2	TRUE	0	0.548199364230757	2		179	123	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	438	866	4	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	0.548199364230757	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.548199364230757	2		870	787	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	124	372	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.548199364230757	2		373	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	125	545	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.43	0.388	0.474	0.43	0.388	0.474	SUBCLONAL	1	TRUE	1	0.548199364230757	2		547	1060	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	280	475	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.548199364230757	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.548199364230757	2		475	498	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	217	844	0	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.548199364230757	2		844	788	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973911	55973911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs941528100	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	179	708	1	ENST00000263923.4:c.1405G>A	p.Glu469Lys	p.E469K	ENST00000263923	NM_002253.2	469	Gag/Aag	10/30	1	2	FACETS	0.969	0.897	1	0.969	0.897	1	CLONAL	1	TRUE	1	0.548199364230757	2		709	674	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656951	47656951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63749849	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	98	659	4	ENST00000233146.2:c.1147C>T	p.Arg383Ter	p.R383*	ENST00000233146	NM_000251.2	383	Cga/Tga	7/16	1	2	FACETS	0.866	0.777	0.958	0.866	0.777	0.958	CLONAL	1	TRUE	1	0.548199364230757	2		663	413	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	307	355	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	1	2	FACETS	0.983	0.927	1	0.983	0.927	1	CLONAL	1	TRUE	1	0.548199364230757	2		355	1139	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982440	25982440	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	49	646	3	ENST00000435504.4:c.850C>T	p.Arg284Ter	p.R284*	ENST00000435504		284	Cga/Tga	9/13	1	2	FACETS	0.294	0.248	0.344	0.294	0.248	0.344	SUBCLONAL	1	TRUE	1	0.548199364230757	2		649	608	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	57	395	3	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.454	0.39	0.524	0.454	0.39	0.524	SUBCLONAL	1	TRUE	1	0.548199364230757	2		398	458	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101416	27101417	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	163	695	3	ENST00000324856.7:c.4703dup	p.Pro1569SerfsTer3	p.P1569Sfs*3	ENST00000324856	NM_006015.4	1566	-/C	18/20	1	2	FACETS	0.877	0.807	0.949	0.877	0.807	0.949	CLONAL	1	TRUE	1	0.548199364230757	2		698	678	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602973	55602973	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774405431	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	149	623	1	ENST00000288135.5:c.2683G>A	p.Ala895Thr	p.A895T	ENST00000288135	NM_000222.2	895	Gca/Aca	19/21	1	2	FACETS	0.971	0.891	1	0.971	0.891	1	CLONAL	1	TRUE	1	0.548199364230757	2		624	560	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628637	187628637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199928348	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	218	1050	1	ENST00000441802.2:c.2345G>A	p.Arg782His	p.R782H	ENST00000441802	NM_005245.3	782	cGt/cAt	2/27	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.548199364230757	2		1051	761	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405652	70405652	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	34	774	0	ENST00000373644.4:c.3171del	p.Lys1057AsnfsTer25	p.K1057Nfs*25	ENST00000373644	NM_030625.2	1056	Aaa/aa	4/12	0.548199364230757	2	FACETS	0.326	0.266	0.392	0.163	0.133	0.196	SUBCLONAL	1	TRUE	0	0.548199364230757	2		774	381	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8733794	8733794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs949202374	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	207	760	1	ENST00000356435.5:c.50G>A	p.Arg17His	p.R17H	ENST00000356435		17	cGc/cAc	1/35	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.548199364230757	2		761	740	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727174	40727174	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200157212	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	111	791	1	ENST00000373198.4:c.3790G>A	p.Ala1264Thr	p.A1264T	ENST00000373198	NM_133170.3	1264	Gcc/Acc	28/32	1	2	FACETS	0.446	0.401	0.495	0.446	0.401	0.495	SUBCLONAL	1	TRUE	1	0.548199364230757	2		792	907	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508473	106508473	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370328855	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	62	271	1	ENST00000359195.3:c.467C>T	p.Ala156Val	p.A156V	ENST00000359195	NM_002649.2	156	gCg/gTg	2/11	1	2	FACETS	0.919	0.804	1	0.919	0.804	1	CLONAL	1	TRUE	1	0.548199364230757	2		272	246	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118632	11118632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555771625	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	238	947	0	ENST00000358026.2:c.2056G>A	p.Glu686Lys	p.E686K	ENST00000358026	NM_001128849.1	686	Gag/Aag	14/36	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.548199364230757	2		947	862	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157335	106157335	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs777797154	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	45	638	0	ENST00000380013.4:c.2236C>T	p.Gln746Ter	p.Q746*	ENST00000380013	NM_001127208.2	746	Caa/Taa	3/11	1	2	FACETS	0.384	0.323	0.452	0.384	0.323	0.452	SUBCLONAL	1	TRUE	1	0.548199364230757	2		638	427	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032072	26032072	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	47	602	1	ENST00000244661.2:c.217C>T	p.Arg73Ter	p.R73*	ENST00000244661	NM_003537.3	73	Cga/Tga	1/1	1	2	FACETS	0.308	0.259	0.361	0.308	0.259	0.361	SUBCLONAL	1	TRUE	1	0.548199364230757	2		603	557	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996755	100996757	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	216	682	0	ENST00000325455.5:c.1770_1772del	p.Phe591del	p.F591del	ENST00000325455	NM_001202474.3	590	ttCTTt/ttt	2/8	0.548199364230757	2	FACETS	0.904	0.852	0.956	0.904	0.852	0.956	CLONAL	2	TRUE	0	0.548199364230757	2		682	436	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743987	41743987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1306116384	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	310	1085	0	ENST00000301178.4:c.922C>T	p.Arg308Cys	p.R308C	ENST00000301178	NM_021913.4	308	Cgc/Tgc	7/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.548199364230757	2		1085	1059	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	198	728	5	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.548199364230757	2		733	673	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216189	36216189	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	78	858	1	ENST00000222270.7:c.3602del	p.Pro1201ArgfsTer154	p.P1201Rfs*154	ENST00000222270	NM_014727.1	1199	ggC/gg	11/37	1	2	FACETS	0.296	0.26	0.336	0.296	0.26	0.336	SUBCLONAL	1	TRUE	1	0.548199364230757	2		859	960	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061726	38061726	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	56	463	1	ENST00000250448.2:c.263del	p.Gly88AlafsTer6	p.G88Afs*6	ENST00000250448	NM_004496.3	88	gGc/gc	2/2	1	2	FACETS	0.385	0.33	0.445	0.385	0.33	0.445	SUBCLONAL	1	TRUE	1	0.548199364230757	2		464	531	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243675683	243675683	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	44	638	0	ENST00000263826.5:c.1297A>G	p.Arg433Gly	p.R433G	ENST00000263826	NM_005465.4	433	Aga/Gga	12/13	1	2	FACETS	0.363	0.305	0.428	0.363	0.305	0.428	SUBCLONAL	1	TRUE	1	0.548199364230757	2		638	442	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246021879	246021879	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	287	927	0	ENST00000388985.4:c.995A>G	p.Asp332Gly	p.D332G	ENST00000388985		332	gAc/gGc	10/12	1	2	FACETS	0.977	0.919	1	0.977	0.919	1	CLONAL	1	TRUE	1	0.548199364230757	2		927	1072	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022790	12022790	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	56	719	0	ENST00000396373.4:c.896G>T	p.Arg299Met	p.R299M	ENST00000396373	NM_001987.4	299	aGg/aTg	5/8	1	2	FACETS	0.304	0.26	0.353	0.304	0.26	0.353	SUBCLONAL	1	TRUE	1	0.548199364230757	2		719	671	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434235	49434235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375114492	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	420	1276	0	ENST00000301067.7:c.7318G>A	p.Val2440Ile	p.V2440I	ENST00000301067	NM_003482.3	2440	Gtt/Att	31/54	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.548199364230757	2		1276	1350	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652150	3652150	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	288	984	0	ENST00000294008.3:c.919A>G	p.Asn307Asp	p.N307D	ENST00000294008	NM_032444.2	307	Aac/Gac	4/15	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.548199364230757	2		984	1042	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779424	3779424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1032604340	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	336	1013	2	ENST00000262367.5:c.5624G>A	p.Arg1875His	p.R1875H	ENST00000262367	NM_004380.2	1875	cGc/cAc	31/31	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.548199364230757	2		1015	1006	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56857697	56857697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765711298	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	283	784	1	ENST00000308159.5:c.733C>T	p.Arg245Cys	p.R245C	ENST00000308159	NM_014669.4	245	Cgc/Tgc	8/22	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.548199364230757	2		785	902	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670707	67670707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs890921910	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	312	791	0	ENST00000264010.4:c.1952G>A	p.Arg651Gln	p.R651Q	ENST00000264010	NM_006565.3	651	cGg/cAg	11/12	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.548199364230757	2		791	1004	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828578	72828578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1199271359	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	58	937	0	ENST00000268489.5:c.8003G>A	p.Arg2668Gln	p.R2668Q	ENST00000268489	NM_006885.3	2668	cGa/cAa	9/10	1	2	FACETS	0.233	0.199	0.27	0.233	0.199	0.27	SUBCLONAL	1	TRUE	1	0.548199364230757	2		937	908	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347191	89347191	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	165	712	1	ENST00000301030.4:c.5759C>T	p.Thr1920Met	p.T1920M	ENST00000301030	NM_001256183.1	1920	aCg/aTg	9/13	1	2	FACETS	0.905	0.834	0.979	0.905	0.834	0.979	CLONAL	1	TRUE	1	0.548199364230757	2		713	665	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678182	58678182	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	166	917	0	ENST00000305921.3:c.407C>T	p.Ala136Val	p.A136V	ENST00000305921	NM_003620.3	136	gCt/gTt	1/6	1	2	FACETS	0.597	0.547	0.648	0.597	0.547	0.648	SUBCLONAL	1	TRUE	1	0.548199364230757	2		917	1015	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534358	63534358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368502813	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	310	988	0	ENST00000307078.5:c.1163G>A	p.Arg388His	p.R388H	ENST00000307078	NM_004655.3	388	cGc/cAc	5/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.548199364230757	2		988	1073	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120257	70120257	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	114	1094	0	ENST00000245479.2:c.1259A>G	p.Tyr420Cys	p.Y420C	ENST00000245479	NM_000346.3	420	tAc/tGc	3/3	1	2	FACETS	0.344	0.309	0.382	0.344	0.309	0.382	SUBCLONAL	1	TRUE	1	0.548199364230757	2		1094	1209	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226905	2226905	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	30	354	1	ENST00000398665.3:c.4385G>T	p.Arg1462Leu	p.R1462L	ENST00000398665	NM_032482.2	1462	cGg/cTg	27/28	1	2	FACETS	0.282	0.227	0.345	0.282	0.227	0.345	SUBCLONAL	1	TRUE	1	0.548199364230757	2		355	388	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229306	36229306	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	272	908	1	ENST00000222270.7:c.7996G>A	p.Val2666Met	p.V2666M	ENST00000222270	NM_014727.1	2666	Gtg/Atg	37/37	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.548199364230757	2		909	970	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383357	42383357	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs782709381	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	158	641	0	ENST00000221972.3:c.377G>A	p.Arg126His	p.R126H	ENST00000221972	NM_021601.3	126	cGc/cAc	2/5	1	2	FACETS	0.953	0.877	1	0.953	0.877	1	CLONAL	1	TRUE	1	0.548199364230757	2		641	605	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867700	45867700	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1340806384	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	260	911	3	ENST00000391945.4:c.700G>A	p.Asp234Asn	p.D234N	ENST00000391945	NM_000400.3	234	Gac/Aac	8/23	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.548199364230757	2		914	868	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707986	47707986	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	112	609	0	ENST00000233146.2:c.2612del	p.Lys871ArgfsTer21	p.K871Rfs*21	ENST00000233146	NM_000251.2	870	gcA/gc	15/16	1	2	FACETS	0.955	0.865	1	0.955	0.865	1	CLONAL	1	TRUE	1	0.548199364230757	2		609	428	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661167	227661168	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	248	974	0	ENST00000305123.5:c.2287_2288del	p.Ser763LeufsTer9	p.S763Lfs*9	ENST00000305123	NM_005544.2	763	TCc/c	1/2	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.548199364230757	2		974	876	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069277	30069277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	64	729	2	ENST00000338641.4:c.1142C>T	p.Ala381Val	p.A381V	ENST00000338641	NM_000268.3	381	gCt/gTt	12/16	1	2	FACETS	0.298	0.257	0.343	0.298	0.257	0.343	SUBCLONAL	1	TRUE	1	0.548199364230757	2		731	783	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49726048	49726048	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	15	177	0	ENST00000449682.2:c.77A>G	p.Gln26Arg	p.Q26R	ENST00000449682	NM_020998.3	26	cAa/cGa	1/18	1	2	FACETS	0.358	0.263	0.47	0.358	0.263	0.47	SUBCLONAL	1	TRUE	1	0.548199364230757	2		177	153	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867524	35867525	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs1561421608	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	65	564	0	ENST00000303115.3:c.340_341del	p.Lys114GlufsTer14	p.K114Efs*14	ENST00000303115	NM_002185.3	113	gAA/g	3/8	1	2	FACETS	0.763	0.666	0.865	0.763	0.666	0.865	SUBCLONAL	1	TRUE	1	0.548199364230757	2		564	311	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181834	56181835	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACTCC	novel	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	54	672	0	ENST00000399503.3:c.4059_4063dup	p.Arg1355HisfsTer24	p.R1355Hfs*24	ENST00000399503	NM_005921.1	1353	tta/ttACTCCa	17/20	1	2	FACETS	0.407	0.348	0.472	0.407	0.348	0.472	SUBCLONAL	1	TRUE	1	0.548199364230757	2		672	484	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048589	180048589	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540963025	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	111	939	1	ENST00000261937.6:c.1973G>A	p.Arg658Gln	p.R658Q	ENST00000261937	NM_182925.4	658	cGg/cAg	13/30	1	2	FACETS	0.427	0.383	0.473	0.427	0.383	0.473	SUBCLONAL	1	TRUE	1	0.548199364230757	2		940	949	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672362	30672362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	93	767	0	ENST00000376406.3:c.4598C>T	p.Ala1533Val	p.A1533V	ENST00000376406	NM_014641.2	1533	gCa/gTa	10/15	1	2	FACETS	0.5	0.444	0.559	0.5	0.444	0.559	SUBCLONAL	1	TRUE	1	0.548199364230757	2		767	679	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187059	38187059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1460044917	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	180	983	0	ENST00000317025.8:c.1418C>T	p.Ala473Val	p.A473V	ENST00000317025	NM_023034.1	473	gCg/gTg	6/24	1	2	FACETS	0.73	0.673	0.789	0.73	0.673	0.789	SUBCLONAL	1	TRUE	1	0.548199364230757	2		983	900	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371714	55371714	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	167	741	1	ENST00000297316.4:c.404A>T	p.Tyr135Phe	p.Y135F	ENST00000297316	NM_022454.3	135	tAc/tTc	2/2	1	2	FACETS	0.9	0.83	0.973	0.9	0.83	0.973	CLONAL	1	TRUE	1	0.548199364230757	2		742	677	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69032431	69032431	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	48	826	0	ENST00000288368.4:c.3505G>A	p.Val1169Met	p.V1169M	ENST00000288368	NM_024870.2	1169	Gtg/Atg	29/40	1	2	FACETS	0.307	0.259	0.36	0.307	0.259	0.36	SUBCLONAL	1	TRUE	1	0.548199364230757	2		826	570	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090802	5090802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	93	490	0	ENST00000381652.3:c.2950G>A	p.Val984Met	p.V984M	ENST00000381652	NM_004972.3	984	Gtg/Atg	22/25	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.548199364230757	2		490	325	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908874	101908874	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1389908628	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	123	794	0	ENST00000374994.4:c.1238G>A	p.Arg413Gln	p.R413Q	ENST00000374994	NM_004612.2	413	cGa/cAa	7/9	1	2	FACETS	0.836	0.759	0.916	0.836	0.759	0.916	CLONAL	1	TRUE	1	0.548199364230757	2		794	537	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249404	110249404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762644117	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	381	1158	0	ENST00000374672.4:c.1169G>A	p.Arg390Gln	p.R390Q	ENST00000374672	NM_004235.4	390	cGg/cAg	4/5	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.548199364230757	2		1158	1321	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128230352	128230352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530682321	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	222	949	2	ENST00000265960.3:c.1244C>T	p.Thr415Met	p.T415M	ENST00000265960	NM_001006617.1	415	aCg/aTg	10/12	1	2	FACETS	0.965	0.9	1	0.965	0.9	1	CLONAL	1	TRUE	1	0.548199364230757	2		951	839	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759635	133759635	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1231116230	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	253	967	0	ENST00000318560.5:c.1958C>T	p.Thr653Ile	p.T653I	ENST00000318560	NM_005157.4	653	aCa/aTa	11/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.548199364230757	2		967	839	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405140	139405140	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373075482	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	298	991	3	ENST00000277541.6:c.2705G>A	p.Arg902His	p.R902H	ENST00000277541	NM_017617.3	902	cGc/cAc	17/34	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.548199364230757	2		994	956	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815623	139815623	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775158129	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	269	831	4	ENST00000247668.2:c.1094G>A	p.Arg365His	p.R365H	ENST00000247668	NM_021138.3	365	cGc/cAc	9/11	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.548199364230757	2		835	969	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914693	39914693	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1276484212	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	72	854	0	ENST00000378444.4:c.4669A>G	p.Thr1557Ala	p.T1557A	ENST00000378444	NM_001123385.1	1557	Acc/Gcc	12/15	1	2	FACETS	0.347	0.303	0.396	0.347	0.303	0.396	SUBCLONAL	1	TRUE	1	0.548199364230757	2		854	756	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650777	48650777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387907207	NA	P-0022010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	289	943	1	ENST00000376670.3:c.646C>T	p.Arg216Trp	p.R216W	ENST00000376670	NM_002049.3	216	Cgg/Tgg	4/6	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.548199364230757	2		944	969	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0022030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	71	387	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.531	0.467	0.599	0.531	0.467	0.599	SUBCLONAL	1	TRUE	1	0.859854565018575	2		387	311	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100699	67100699	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	153	594	0	ENST00000412916.2:c.397C>T	p.Gln133Ter	p.Q133*	ENST00000412916		133	Cag/Tag	4/6	0.557604295971428	1	FACETS	0.497	0.46	0.536	0.497	0.46	0.536	SUBCLONAL	1	TRUE	0	0.859854565018575	1		594	408	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115700	8115702	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGA	AGA	-	novel	NA	P-0022030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	28	358	0	ENST00000346208.3:c.1048-2_1048del		p.X350_splice	ENST00000346208		350		6/6	1	2	FACETS	0.238	0.19	0.291	0.238	0.19	0.291	SUBCLONAL	1	TRUE	1	0.859854565018575	2		358	274	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056154	27056154	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs999411101	NA	P-0022030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	46	272	0	ENST00000324856.7:c.1150A>G	p.Met384Val	p.M384V	ENST00000324856	NM_006015.4	384	Atg/Gtg	2/20	1	2	FACETS	0.579	0.489	0.679	0.579	0.489	0.679	SUBCLONAL	1	TRUE	1	0.404021774026574	2		272	393	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871007	12871007	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	39	243	0	ENST00000228872.4:c.235del	p.Val79TrpfsTer40	p.V79Wfs*40	ENST00000228872	NM_004064.3	78	gaG/ga	1/3	1	2	FACETS	0.55	0.457	0.653	0.55	0.457	0.653	SUBCLONAL	1	TRUE	1	0.404021774026574	2		243	351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs864622237	NA	P-0022070-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	614	393	0	ENST00000269305.4:c.700T>C	p.Tyr234His	p.Y234H	ENST00000269305	NM_001126112.2	234	Tac/Cac	7/11	0.832949153931022	4	FACETS	0.942	0.907	0.976	0.942	0.907	0.976	CLONAL	2	TRUE	2	0.832949153931022	4		393	1435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577523	7577523	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1555525465	NA	P-0022070-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	652	549	0	ENST00000269305.4:c.758C>A	p.Thr253Asn	p.T253N	ENST00000269305	NM_001126112.2	253	aCc/aAc	7/11	0.832949153931022	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.832949153931022	4		549	1386	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256418	16256438	+	inframe_deletion	In_Frame_Del	DEL	AAAGGATGGATCATGTCGATT	AAAGGATGGATCATGTCGATT	-	novel	NA	P-0022070-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	604	653	0	ENST00000375759.3:c.3683_3703del	p.Lys1228_Phe1235delinsIle	p.K1228_F1235delinsI	ENST00000375759	NM_015001.2	1228	aAAAGGATGGATCATGTCGATTtt/att	11/15	0.832949153931022	3	FACETS	0.969	0.938	1	0.969	0.938	1	CLONAL	2	TRUE	1	0.832949153931022	3		653	1060	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003494	42003495	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0022070-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	618	551	2	ENST00000219905.7:c.3032dup	p.Tyr1011Ter	p.Y1011*	ENST00000219905	NM_001164273.1	1011	tac/tAac	8/24	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	2	TRUE	NA	0.832949153931022	2		553	737	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445457	29445457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757580052	NA	P-0022070-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	290	514	0	ENST00000389048.3:c.3376G>A	p.Ala1126Thr	p.A1126T	ENST00000389048	NM_004304.4	1126	Gcc/Acc	21/29	0.806297125212599	3	FACETS	1	0.978	1	0.536	0.505	0.568	CLONAL	1	TRUE	1	0.832949153931022	3		514	920	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962379	2962379	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022070-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	243	539	0	ENST00000396946.4:c.2158C>T	p.Arg720Ter	p.R720*	ENST00000396946	NM_032415.4	720	Cga/Tga	17/25	0.832949153931022	3	FACETS	0.899	0.841	0.959	0.45	0.42	0.48	CLONAL	1	TRUE	1	0.832949153931022	3		539	919	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	49	294	2	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.516	0.436	0.604	0.516	0.436	0.604	SUBCLONAL	1	TRUE	1	0.26	2		296	731	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	65	528	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.156946598154394	3	FACETS	0.826	0.716	0.946	0.413	0.358	0.473	CLONAL	1	TRUE	1	0.26	3		528	684	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	47	364	2	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.456	0.384	0.537	0.456	0.384	0.537	SUBCLONAL	1	TRUE	1	0.26	2		366	792	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	41	479	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.534	0.444	0.634	0.534	0.444	0.634	SUBCLONAL	1	TRUE	1	0.26	2		480	591	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435160	56435161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755128667	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	56	668	2	ENST00000407977.2:c.1976dup	p.Pro660SerfsTer87	p.P660Sfs*87	ENST00000407977		659	ggt/ggGt	9/10	1	2	FACETS	0.42	0.359	0.488	0.42	0.359	0.488	SUBCLONAL	1	TRUE	1	0.26	2		670	1025	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	34	352	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.514	0.419	0.621	0.514	0.419	0.621	SUBCLONAL	1	TRUE	1	0.26	2		352	509	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197255	106197255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1222260506	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	45	310	0	ENST00000380013.4:c.5588C>T	p.Ala1863Val	p.A1863V	ENST00000380013	NM_001127208.2	1863	gCc/gTc	11/11	1	2	FACETS	0.683	0.574	0.803	0.683	0.574	0.803	SUBCLONAL	1	TRUE	1	0.26	2		310	507	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	78	576	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.61	0.534	0.691	0.61	0.534	0.691	SUBCLONAL	1	TRUE	1	0.26	2		576	984	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99154326	99154326	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs749286893	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	58	364	0	ENST00000074304.5:c.468G>T	p.Arg156Ser	p.R156S	ENST00000074304	NM_001134224.1	156	agG/agT	8/26	1	2	FACETS	0.713	0.612	0.823	0.713	0.612	0.823	SUBCLONAL	1	TRUE	1	0.26	2		364	626	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931788	39931788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	84	338	0	ENST00000378444.4:c.2811del	p.Thr938ProfsTer18	p.T938Pfs*18	ENST00000378444	NM_001123385.1	937	ccC/cc	4/15	1	1	FACETS	0.94	0.831	1	0.94	0.831	1	CLONAL	1	TRUE	0	0.26	1		338	598	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	29	339	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	0.494	0.395	0.605	0.494	0.395	0.605	SUBCLONAL	1	TRUE	1	0.26	2		339	452	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905546	50905546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144979965	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	106	738	3	ENST00000440232.2:c.674G>A	p.Arg225His	p.R225H	ENST00000440232	NM_002691.3	225	cGt/cAt	6/27	1	2	FACETS	0.65	0.58	0.724	0.65	0.58	0.724	SUBCLONAL	1	TRUE	1	0.26	2		741	1255	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743988	41743988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776310618	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	86	918	3	ENST00000301178.4:c.923G>A	p.Arg308His	p.R308H	ENST00000301178	NM_021913.4	308	cGc/cAc	7/20	1	2	FACETS	0.557	0.491	0.628	0.557	0.491	0.628	SUBCLONAL	1	TRUE	1	0.26	2		921	1188	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108653	8108653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749454960	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	61	620	1	ENST00000585124.1:c.742C>T	p.Arg248Cys	p.R248C	ENST00000585124	NM_004217.3	248	Cgc/Tgc	8/9	1	2	FACETS	0.421	0.362	0.486	0.421	0.362	0.486	SUBCLONAL	1	TRUE	1	0.26	2		621	1114	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200961	108200961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782310	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	52	390	0	ENST00000278616.4:c.7328G>A	p.Arg2443Gln	p.R2443Q	ENST00000278616	NM_000051.3	2443	cGa/cAa	50/63	1	2	FACETS	0.635	0.54	0.739	0.635	0.54	0.739	SUBCLONAL	1	TRUE	1	0.26	2		390	630	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026204	48026204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750440	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	42	420	0	ENST00000234420.5:c.1082G>A	p.Arg361His	p.R361H	ENST00000234420	NM_000179.2	361	cGc/cAc	4/10	1	2	FACETS	0.528	0.44	0.626	0.528	0.44	0.626	SUBCLONAL	1	TRUE	1	0.26	2		420	612	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715678	30715678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039551	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	49	380	2	ENST00000295754.5:c.1336G>A	p.Asp446Asn	p.D446N	ENST00000295754	NM_003242.5	446	Gat/Aat	5/7	1	2	FACETS	0.583	0.493	0.683	0.583	0.493	0.683	SUBCLONAL	1	TRUE	1	0.26	2		382	646	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076826	72076826	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	36	364	1	ENST00000357731.5:c.671C>T	p.Ala224Val	p.A224V	ENST00000357731	NM_173808.2	224	gCt/gTt	5/7	1	2	FACETS	0.472	0.387	0.567	0.472	0.387	0.567	SUBCLONAL	1	TRUE	1	0.26	2		365	587	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779158	3779158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1278592398	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	49	558	2	ENST00000262367.5:c.5890C>T	p.Arg1964Cys	p.R1964C	ENST00000262367	NM_004380.2	1964	Cgt/Tgt	31/31	1	2	FACETS	0.429	0.362	0.503	0.429	0.362	0.503	SUBCLONAL	1	TRUE	1	0.26	2		560	879	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480469	89480469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	39	342	0	ENST00000336596.2:c.2306G>A	p.Arg769His	p.R769H	ENST00000336596	NM_005233.5	769	cGt/cAt	13/17	0.3	2	FACETS	0.532	0.44	0.635			1	SUBCLONAL	1	TRUE	NA	0.26	2		342	564	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105892	27105892	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	54	446	0	ENST00000324856.7:c.5503C>T	p.Gln1835Ter	p.Q1835*	ENST00000324856	NM_006015.4	1835	Cag/Tag	20/20	1	2	FACETS	0.552	0.471	0.642	0.552	0.471	0.642	SUBCLONAL	1	TRUE	1	0.26	2		446	752	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946355	2946355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372251654	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	89	808	3	ENST00000396946.4:c.3382G>A	p.Val1128Ile	p.V1128I	ENST00000396946	NM_032415.4	1128	Gta/Ata	25/25	1	2	FACETS	0.546	0.482	0.615	0.546	0.482	0.615	SUBCLONAL	1	TRUE	1	0.26	2		811	1254	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281256	15281256	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752437137	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	77	810	0	ENST00000263388.2:c.5000G>A	p.Arg1667His	p.R1667H	ENST00000263388	NM_000435.2	1667	cGc/cAc	27/33	1	2	FACETS	0.536	0.469	0.609	0.536	0.469	0.609	SUBCLONAL	1	TRUE	1	0.26	2		810	1105	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264985	46264985	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	47	431	2	ENST00000371998.3:c.1860del	p.Lys620AsnfsTer18	p.K620Nfs*18	ENST00000371998		619	Aaa/aa	12/23	1	2	FACETS	0.462	0.389	0.544	0.462	0.389	0.544	SUBCLONAL	1	TRUE	1	0.26	2		433	782	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128009	30128009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372149021	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	77	724	1	ENST00000263025.4:c.1120G>A	p.Gly374Arg	p.G374R	ENST00000263025	NM_002746.2	374	Gga/Aga	8/9	1	2	FACETS	0.553	0.483	0.627	0.553	0.483	0.627	SUBCLONAL	1	TRUE	1	0.26	2		725	1072	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495016	56495016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776728303	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	161	617	2	ENST00000267101.3:c.3373C>T	p.Arg1125Trp	p.R1125W	ENST00000267101	NM_001982.3	1125	Cgg/Tgg	27/28	0.156946598154394	3	FACETS	1	0.985	1	0.678	0.621	0.738	CLONAL	1	TRUE	1	0.26	3		619	1032	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450876	70450876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757931991	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	49	475	0	ENST00000373644.4:c.5716G>A	p.Glu1906Lys	p.E1906K	ENST00000373644	NM_030625.2	1906	Gaa/Aaa	12/12	1	2	FACETS	0.51	0.431	0.598	0.51	0.431	0.598	SUBCLONAL	1	TRUE	1	0.26	2		475	739	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592353	29592353	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500316	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	57	469	0	ENST00000356175.3:c.4768C>T	p.Arg1590Trp	p.R1590W	ENST00000356175	NM_000267.3	1590	Cgg/Tgg	35/57	1	2	FACETS	0.608	0.521	0.704	0.608	0.521	0.704	SUBCLONAL	1	TRUE	1	0.26	2		469	721	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034522	123034522	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	47	246	0	ENST00000355640.3:c.1279A>G	p.Ser427Gly	p.S427G	ENST00000355640		427	Agt/Ggt	6/7	0.3	2	FACETS	0.847	0.716	0.991	0.423	0.358	0.496	CLONAL	1	TRUE	0	0.26	2		246	427	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958789	55958789	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	76	547	0	ENST00000263923.4:c.3064C>T	p.Arg1022Ter	p.R1022*	ENST00000263923	NM_002253.2	1022	Cga/Tga	22/30	1	2	FACETS	0.597	0.522	0.677	0.597	0.522	0.677	SUBCLONAL	1	TRUE	1	0.26	2		547	980	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27192600	27192600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs539332352	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	61	452	0	ENST00000380036.4:c.1603C>T	p.Arg535Cys	p.R535C	ENST00000380036	NM_000459.3	535	Cgc/Tgc	11/23	1	2	FACETS	0.553	0.475	0.637	0.553	0.475	0.637	SUBCLONAL	1	TRUE	1	0.26	2		452	849	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993832	72993832	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	32	473	1	ENST00000268489.5:c.213del	p.Ser72ProfsTer37	p.S72Pfs*37	ENST00000268489	NM_006885.3	71	ccC/cc	2/10	1	2	FACETS	0.417	0.337	0.507	0.417	0.337	0.507	SUBCLONAL	1	TRUE	1	0.26	2		474	591	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031919	10031919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs901717931	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	60	669	1	ENST00000330684.3:c.904G>A	p.Ala302Thr	p.A302T	ENST00000330684	NM_001134407.1	302	Gct/Act	3/13	1	2	FACETS	0.516	0.443	0.596	0.516	0.443	0.596	SUBCLONAL	1	TRUE	1	0.26	2		670	894	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007752	45007753	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	116	450	0	ENST00000558401.1:c.204dup	p.Val69SerfsTer21	p.V69Sfs*21	ENST00000558401	NM_004048.2	67	gaa/gAaa	2/4	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.26	2		450	765	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419949	152419949	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	59	591	0	ENST00000206249.3:c.1636G>A	p.Ala546Thr	p.A546T	ENST00000206249	NM_000125.3	546	Gcc/Acc	8/8	1	2	FACETS	0.531	0.456	0.614	0.531	0.456	0.614	SUBCLONAL	1	TRUE	1	0.26	2		591	854	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046674	42046674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780027483	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	75	552	1	ENST00000219905.7:c.7048G>A	p.Val2350Met	p.V2350M	ENST00000219905	NM_001164273.1	2350	Gtg/Atg	18/24	1	2	FACETS	0.631	0.552	0.717	0.631	0.552	0.717	SUBCLONAL	1	TRUE	1	0.26	2		553	914	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431649	6431649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	74	515	5	ENST00000356142.4:c.202C>T	p.Arg68Cys	p.R68C	ENST00000356142	NM_018890.3	68	Cgc/Tgc	3/7	1	2	FACETS	0.602	0.525	0.684	0.602	0.525	0.684	SUBCLONAL	1	TRUE	1	0.26	2		520	946	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073398	8073398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201286989	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	63	586	0	ENST00000377482.5:c.1261G>A	p.Ala421Thr	p.A421T	ENST00000377482	NM_018948.3	421	Gcc/Acc	4/4	1	2	FACETS	0.486	0.419	0.559	0.486	0.419	0.559	SUBCLONAL	1	TRUE	1	0.26	2		586	997	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186766	11186766	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs370987224	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	53	617	0	ENST00000361445.4:c.6439A>G	p.Asn2147Asp	p.N2147D	ENST00000361445	NM_004958.3	2147	Aac/Gac	46/58	1	2	FACETS	0.426	0.362	0.497	0.426	0.362	0.497	SUBCLONAL	1	TRUE	1	0.26	2		617	957	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254995	16254995	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	50	306	0	ENST00000375759.3:c.2260A>G	p.Arg754Gly	p.R754G	ENST00000375759	NM_015001.2	754	Agg/Ggg	11/15	1	2	FACETS	0.643	0.545	0.751	0.643	0.545	0.751	SUBCLONAL	1	TRUE	1	0.26	2		306	598	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521524	46521525	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs750652590	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	87	702	0	ENST00000262741.5:c.883dup	p.Met295AsnfsTer3	p.M295Nfs*3	ENST00000262741	NM_003629.3	295	atg/aAtg	7/10	1	2	FACETS	0.549	0.484	0.618	0.549	0.484	0.618	SUBCLONAL	1	TRUE	1	0.26	2		702	1220	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46714238	46714238	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1447153423	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	57	598	0	ENST00000371975.4:c.58T>C	p.Cys20Arg	p.C20R	ENST00000371975	NM_003579.3	20	Tgt/Cgt	2/18	1	2	FACETS	0.492	0.421	0.57	0.492	0.421	0.57	SUBCLONAL	1	TRUE	1	0.26	2		598	891	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46738164	46738164	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	59	555	0	ENST00000371975.4:c.1196T>A	p.Ile399Asn	p.I399N	ENST00000371975	NM_003579.3	399	aTc/aAc	11/18	1	2	FACETS	0.549	0.471	0.635	0.549	0.471	0.635	SUBCLONAL	1	TRUE	1	0.26	2		555	826	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161326466	161326466	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1226	84	818	0	ENST00000367975.2:c.244del		p.X82_splice	ENST00000367975	NM_003001.3	82			1	2	FACETS	0.493	0.434	0.557	0.493	0.434	0.557	SUBCLONAL	1	TRUE	1	0.26	2		818	1310	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318766	163318766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	40	505	0	ENST00000271452.3:c.1156G>A	p.Ala386Thr	p.A386T	ENST00000271452	NM_145697.2	386	Gct/Act	13/14	1	2	FACETS	0.523	0.434	0.623	0.523	0.434	0.623	SUBCLONAL	1	TRUE	1	0.26	2		505	588	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920442	114920442	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	48	521	0	ENST00000543371.1:c.1383A>C	p.Lys461Asn	p.K461N	ENST00000543371	NM_001198531.1	461	aaA/aaC	13/14	1	2	FACETS	0.446	0.376	0.524	0.446	0.376	0.524	SUBCLONAL	1	TRUE	1	0.26	2		521	828	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948388	71948388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1257	126	893	1	ENST00000298229.2:c.3100G>A	p.Val1034Met	p.V1034M	ENST00000298229	NM_001567.3	1034	Gtg/Atg	26/28	1	2	FACETS	0.701	0.632	0.773	0.701	0.632	0.773	SUBCLONAL	1	TRUE	1	0.26	2		894	1383	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352712	118352712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555039426	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	65	557	0	ENST00000534358.1:c.3917C>T	p.Pro1306Leu	p.P1306L	ENST00000534358	NM_005933.3	1306	cCg/cTg	7/36	1	2	FACETS	0.52	0.45	0.597	0.52	0.45	0.597	SUBCLONAL	1	TRUE	1	0.26	2		557	961	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380738	118380738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782142171	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	49	472	1	ENST00000534358.1:c.10976G>A	p.Arg3659Gln	p.R3659Q	ENST00000534358	NM_005933.3	3659	cGg/cAg	30/36	1	2	FACETS	0.488	0.412	0.572	0.488	0.412	0.572	SUBCLONAL	1	TRUE	1	0.26	2		473	772	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497570	125497570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	50	303	0	ENST00000428830.2:c.134C>T	p.Ala45Val	p.A45V	ENST00000428830	NM_001114121.2	45	gCc/gTc	3/14	1	2	FACETS	0.702	0.595	0.819	0.702	0.595	0.819	SUBCLONAL	1	TRUE	1	0.26	2		303	548	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436538	49436538	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	65	630	0	ENST00000301067.7:c.5768G>T	p.Arg1923Met	p.R1923M	ENST00000301067	NM_003482.3	1923	aGg/aTg	26/54	0.156946598154394	3	FACETS	0.495	0.428	0.569	0.248	0.214	0.285	SUBCLONAL	1	TRUE	1	0.26	3		630	1141	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445415	49445415	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1466	121	980	1	ENST00000301067.7:c.2051C>A	p.Pro684His	p.P684H	ENST00000301067	NM_003482.3	684	cCt/cAt	10/54	0.156946598154394	3	FACETS	0.663	0.596	0.734	0.331	0.298	0.367	SUBCLONAL	1	TRUE	1	0.26	3		981	1587	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493456	56493456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781502670	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	47	511	0	ENST00000267101.3:c.2864G>A	p.Arg955His	p.R955H	ENST00000267101	NM_001982.3	955	cGc/cAc	24/28	0.156946598154394	3	FACETS	0.472	0.397	0.555	0.236	0.198	0.278	SUBCLONAL	1	TRUE	1	0.26	3		511	866	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26956958	26956958	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	39	331	0	ENST00000381527.3:c.464C>T	p.Ala155Val	p.A155V	ENST00000381527	NM_001260.1	155	gCt/gTt	5/13	1	2	FACETS	0.517	0.428	0.617	0.517	0.428	0.617	SUBCLONAL	1	TRUE	1	0.26	2		331	580	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133887	41133887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755827604	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	40	285	2	ENST00000379561.5:c.1741G>A	p.Val581Met	p.V581M	ENST00000379561	NM_002015.3	581	Gtg/Atg	2/3	1	2	FACETS	0.607	0.504	0.722	0.607	0.504	0.722	SUBCLONAL	1	TRUE	1	0.26	2		287	507	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436207	110436207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	64	570	2	ENST00000375856.3:c.2194C>T	p.Pro732Ser	p.P732S	ENST00000375856	NM_003749.2	732	Ccc/Tcc	1/2	1	2	FACETS	0.553	0.478	0.636	0.553	0.478	0.636	SUBCLONAL	1	TRUE	1	0.26	2		572	890	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543291	65543291	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	81	460	1	ENST00000358664.4:c.386G>A	p.Ser129Asn	p.S129N	ENST00000358664	NM_002382.4	129	aGc/aAc	5/5	1	2	FACETS	0.726	0.639	0.82	0.726	0.639	0.82	SUBCLONAL	1	TRUE	1	0.26	2		461	858	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479817	67479817	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1232656160	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	133	574	0	ENST00000327367.4:c.1124G>A	p.Ser375Asn	p.S375N	ENST00000327367	NM_005902.3	375	aGc/aAc	8/9	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.26	2		574	954	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679730	88679730	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	59	551	0	ENST00000360948.2:c.733G>T	p.Val245Phe	p.V245F	ENST00000360948	NM_001012338.2	245	Gtc/Ttc	7/19	1	2	FACETS	0.468	0.401	0.542	0.468	0.401	0.542	SUBCLONAL	1	TRUE	1	0.26	2		551	969	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131727	2131727	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	85	782	1	ENST00000219476.3:c.3742G>A	p.Ala1248Thr	p.A1248T	ENST00000219476	NM_000548.3	1248	Gcc/Acc	31/42	1	2	FACETS	0.552	0.486	0.623	0.552	0.486	0.623	SUBCLONAL	1	TRUE	1	0.26	2		783	1185	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778990	3778990	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1213926680	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	53	503	1	ENST00000262367.5:c.6058C>T	p.Gln2020Ter	p.Q2020*	ENST00000262367	NM_004380.2	2020	Cag/Tag	31/31	1	2	FACETS	0.556	0.473	0.647	0.556	0.473	0.647	SUBCLONAL	1	TRUE	1	0.26	2		504	733	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129463	30129463	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780719391	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	76	636	0	ENST00000263025.4:c.565C>T	p.Arg189Trp	p.R189W	ENST00000263025	NM_002746.2	189	Cgg/Tgg	4/9	1	2	FACETS	0.548	0.479	0.623	0.548	0.479	0.623	SUBCLONAL	1	TRUE	1	0.26	2		636	1066	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070660	67070660	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	19	148	0	ENST00000412916.2:c.282+2T>C		p.X94_splice	ENST00000412916		94			1	2	FACETS	0.487	0.37	0.625	0.487	0.37	0.625	SUBCLONAL	1	TRUE	1	0.26	2		148	300	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644729	67644729	+	splice_region_variant,5_prime_UTR_variant	Splice_Region	SNP	A	A	G	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	52	436	0	ENST00000264010.4:c.-7A>G		p.X3_splice	ENST00000264010	NM_006565.3	3		3/12	1	2	FACETS	0.535	0.454	0.624	0.535	0.454	0.624	SUBCLONAL	1	TRUE	1	0.26	2		436	748	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867355	68867355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs864622630	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	54	460	0	ENST00000261769.5:c.2602C>T	p.Arg868Cys	p.R868C	ENST00000261769	NM_004360.3	868	Cgc/Tgc	16/16	1	2	FACETS	0.538	0.458	0.626	0.538	0.458	0.626	SUBCLONAL	1	TRUE	1	0.26	2		460	772	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8111056	8111056	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs548042738	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	81	719	1	ENST00000585124.1:c.151G>T	p.Ala51Ser	p.A51S	ENST00000585124	NM_004217.3	51	Gct/Tct	3/9	1	2	FACETS	0.563	0.495	0.638	0.563	0.495	0.638	SUBCLONAL	1	TRUE	1	0.26	2		720	1106	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127438	17127438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1207311795	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	71	589	0	ENST00000285071.4:c.416G>A	p.Gly139Asp	p.G139D	ENST00000285071	NM_144997.5	139	gGc/gAc	6/14	1	2	FACETS	0.577	0.502	0.659	0.577	0.502	0.659	SUBCLONAL	1	TRUE	1	0.26	2		589	946	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441905	40441905	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	76	763	0	ENST00000345506.4:c.150T>A	p.Asn50Lys	p.N50K	ENST00000345506	NM_003152.3	50	aaT/aaA	4/20	1	2	FACETS	0.485	0.423	0.551	0.485	0.423	0.551	SUBCLONAL	1	TRUE	1	0.26	2		763	1206	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459688	40459688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780900178	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	75	645	0	ENST00000345506.4:c.1853G>A	p.Arg618His	p.R618H	ENST00000345506	NM_003152.3	618	cGc/cAc	16/20	1	2	FACETS	0.579	0.506	0.658	0.579	0.506	0.658	SUBCLONAL	1	TRUE	1	0.26	2		645	997	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212379	5212379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237948621	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	93	808	3	ENST00000357368.4:c.4738C>T	p.Pro1580Ser	p.P1580S	ENST00000357368	NM_002850.3	1580	Cca/Tca	31/38	1	2	FACETS	0.563	0.499	0.632	0.563	0.499	0.632	SUBCLONAL	1	TRUE	1	0.26	2		811	1270	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222747	5222747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	81	738	3	ENST00000357368.4:c.3056G>A	p.Gly1019Asp	p.G1019D	ENST00000357368	NM_002850.3	1019	gGc/gAc	18/38	1	2	FACETS	0.601	0.528	0.68	0.601	0.528	0.68	SUBCLONAL	1	TRUE	1	0.26	2		741	1037	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5258034	5258034	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	52	431	0	ENST00000357368.4:c.700G>T	p.Val234Leu	p.V234L	ENST00000357368	NM_002850.3	234	Gtg/Ttg	8/38	1	2	FACETS	0.648	0.551	0.755	0.648	0.551	0.755	SUBCLONAL	1	TRUE	1	0.26	2		431	617	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976962	18976962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	43	446	0	ENST00000262803.5:c.3347C>T	p.Ser1116Phe	p.S1116F	ENST00000262803	NM_002911.3	1116	tCc/tTc	23/24	1	2	FACETS	0.424	0.353	0.502	0.424	0.353	0.502	SUBCLONAL	1	TRUE	1	0.26	2		446	781	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905891	50905891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755550936	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	101	771	1	ENST00000440232.2:c.863C>T	p.Ala288Val	p.A288V	ENST00000440232	NM_002691.3	288	gCg/gTg	8/27	1	2	FACETS	0.673	0.599	0.751	0.673	0.599	0.751	SUBCLONAL	1	TRUE	1	0.26	2		772	1155	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241009	39241009	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	43	487	0	ENST00000402219.2:c.2062C>T	p.Arg688Ter	p.R688*	ENST00000402219	NM_005633.3	688	Cga/Tga	12/23	1	2	FACETS	0.578	0.483	0.684	0.578	0.483	0.684	SUBCLONAL	1	TRUE	1	0.26	2		487	572	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250344	39250344	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	60	761	0	ENST00000402219.2:c.1225A>G	p.Ser409Gly	p.S409G	ENST00000402219	NM_005633.3	409	Agt/Ggt	10/23	1	2	FACETS	0.433	0.371	0.5	0.433	0.371	0.5	SUBCLONAL	1	TRUE	1	0.26	2		761	1067	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182598	99182598	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253335546	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	40	420	0	ENST00000074304.5:c.2401G>A	p.Val801Met	p.V801M	ENST00000074304	NM_001134224.1	801	Gtg/Atg	22/26	1	2	FACETS	0.444	0.368	0.529	0.444	0.368	0.529	SUBCLONAL	1	TRUE	1	0.26	2		420	693	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038162	128038162	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	57	596	0	ENST00000285398.2:c.1388A>T	p.Lys463Met	p.K463M	ENST00000285398	NM_000122.1	463	aAg/aTg	9/15	1	2	FACETS	0.529	0.452	0.613	0.529	0.452	0.613	SUBCLONAL	1	TRUE	1	0.26	2		596	829	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266794	198266794	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	75	503	0	ENST00000335508.6:c.2138C>A	p.Ala713Asp	p.A713D	ENST00000335508	NM_012433.2	713	gCt/gAt	15/25	1	2	FACETS	0.662	0.578	0.751	0.662	0.578	0.751	SUBCLONAL	1	TRUE	1	0.26	2		503	872	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441997	52441997	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	80	458	0	ENST00000460680.1:c.352T>G	p.Phe118Val	p.F118V	ENST00000460680	NM_004656.3	118	Ttc/Gtc	5/17	1	2	FACETS	0.757	0.665	0.856	0.757	0.665	0.856	SUBCLONAL	1	TRUE	1	0.26	2		458	813	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205805	128205805	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	56	669	0	ENST00000341105.2:c.70T>G	p.Ser24Ala	p.S24A	ENST00000341105	NM_032638.4	24	Tca/Gca	2/6	1	2	FACETS	0.475	0.405	0.551	0.475	0.405	0.551	SUBCLONAL	1	TRUE	1	0.26	2		669	907	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808883	1808883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756484252	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	91	749	0	ENST00000260795.2:c.2315C>T	p.Pro772Leu	p.P772L	ENST00000260795		772	cCg/cTg	17/17	1	2	FACETS	0.552	0.488	0.621	0.552	0.488	0.621	SUBCLONAL	1	TRUE	1	0.26	2		749	1268	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197713	66197713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238493512	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	49	515	0	ENST00000273854.3:c.2986G>A	p.Ala996Thr	p.A996T	ENST00000273854	NM_004439.5	996	Gct/Act	17/18	1	2	FACETS	0.464	0.391	0.544	0.464	0.391	0.544	SUBCLONAL	1	TRUE	1	0.26	2		515	813	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251980	153251980	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	48	623	0	ENST00000281708.4:c.1026A>G	p.Ile342Met	p.I342M	ENST00000281708	NM_033632.3	342	atA/atG	7/12	1	2	FACETS	0.427	0.359	0.502	0.427	0.359	0.502	SUBCLONAL	1	TRUE	1	0.26	2		623	865	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158525	26158525	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1222808686	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	67	549	0	ENST00000289316.2:c.128A>G	p.Tyr43Cys	p.Y43C	ENST00000289316	NM_138720.2	43	tAc/tGc	1/2	1	2	FACETS	0.601	0.521	0.688	0.601	0.521	0.688	SUBCLONAL	1	TRUE	1	0.26	2		549	858	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31939960	31939960	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	65	547	0	ENST00000375333.2:c.187C>T	p.Arg63Trp	p.R63W	ENST00000375333	NM_032454.1	63	Cgg/Tgg	1/8	1	2	FACETS	0.591	0.511	0.678	0.591	0.511	0.678	SUBCLONAL	1	TRUE	1	0.26	2		547	846	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288885	33288885	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	48	392	0	ENST00000374542.5:c.667C>A	p.Leu223Met	p.L223M	ENST00000374542	NM_001141970.1	223	Ctg/Atg	3/8	1	2	FACETS	0.588	0.496	0.689	0.588	0.496	0.689	SUBCLONAL	1	TRUE	1	0.26	2		392	628	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983091	111983091	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	53	610	1	ENST00000368678.4:c.1456C>T	p.Gln486Ter	p.Q486*	ENST00000368678		486	Cag/Tag	13/13	1	2	FACETS	0.446	0.379	0.519	0.446	0.379	0.519	SUBCLONAL	1	TRUE	1	0.26	2		611	915	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956939	2956939	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	47	529	0	ENST00000396946.4:c.2688del	p.Phe896LeufsTer18	p.F896Lfs*18	ENST00000396946	NM_032415.4	896	ttT/tt	20/25	1	2	FACETS	0.416	0.35	0.49	0.416	0.35	0.49	SUBCLONAL	1	TRUE	1	0.26	2		529	869	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468113	50468113	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	66	395	0	ENST00000331340.3:c.1348C>T	p.Arg450Cys	p.R450C	ENST00000331340	NM_006060.4	450	Cgc/Tgc	8/8	1	2	FACETS	0.742	0.644	0.849	0.742	0.644	0.849	SUBCLONAL	1	TRUE	1	0.26	2		395	684	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55229195	55229195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	31	260	0	ENST00000275493.2:c.1502C>T	p.Ala501Val	p.A501V	ENST00000275493	NM_005228.3	501	gCc/gTc	13/28	1	2	FACETS	0.648	0.524	0.788	0.648	0.524	0.788	SUBCLONAL	1	TRUE	1	0.26	2		260	368	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879276	151879276	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146455116	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	63	420	0	ENST00000262189.6:c.5669G>A	p.Arg1890Gln	p.R1890Q	ENST00000262189	NM_170606.2	1890	cGa/cAa	36/59	1	2	FACETS	0.609	0.525	0.7	0.609	0.525	0.7	SUBCLONAL	1	TRUE	1	0.26	2		420	796	SUCCESS
AR	367	MSKCC	GRCh37	X	66765308	66765308	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	83	363	0	ENST00000374690.3:c.320A>G	p.Tyr107Cys	p.Y107C	ENST00000374690	NM_000044.3	107	tAc/tGc	1/8	1	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.26	1		363	518	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361197	70361197	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	80	359	0	ENST00000374080.3:c.6385C>T	p.Pro2129Ser	p.P2129S	ENST00000374080		2129	Ccc/Tcc	43/45	0.3	2	FACETS	0.87	0.766	0.983	0.435	0.383	0.492	CLONAL	1	TRUE	0	0.26	2		359	707	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797337	135797337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs118203395	NA	P-0022179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	199	440	1	ENST00000298552.3:c.532G>A	p.Val178Ile	p.V178I	ENST00000298552	NM_001162426.1	178	Gtc/Atc	7/23	0.312005000532212	3	FACETS	0.768	0.717	0.82	0.768	0.717	0.82	INDETERMINATE	2	TRUE	1	0.645342725596957	3		441	531	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196424	106196424	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	178	635	1	ENST00000380013.4:c.4757C>A	p.Ser1586Ter	p.S1586*	ENST00000380013	NM_001127208.2	1586	tCa/tAa	11/11	1	2	FACETS	0.859	0.795	0.925	0.859	0.795	0.925	CLONAL	1	TRUE	1	0.645342725596957	2		636	642	SUCCESS
AR	367	MSKCC	GRCh37	X	66943606	66943606	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	288	378	0	ENST00000374690.3:c.2686A>G	p.Met896Val	p.M896V	ENST00000374690	NM_000044.3	896	Atg/Gtg	8/8	0.525108908697115	2	FACETS	0.788	0.75	0.827			1	SUBCLONAL	2	TRUE	NA	0.645342725596957	2		378	566	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763873	76763873	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs200478641	NA	P-0022179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	91	389	0	ENST00000373344.5:c.7435A>G	p.Met2479Val	p.M2479V	ENST00000373344	NM_000489.3	2479	Atg/Gtg	35/35	0.645342725596957	2	FACETS	0.499	0.444	0.558			1	SUBCLONAL	1	TRUE	NA	0.645342725596957	2		389	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0022423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	208	960	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.319800012988133	3	FACETS	0.995	0.927	1	0.664	0.618	0.711	CLONAL	2	FALSE	0	0.319800012988133	3		960	758	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060745	38060745	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	77	1227	0	ENST00000250448.2:c.1244T>G	p.Leu415Arg	p.L415R	ENST00000250448	NM_004496.3	415	cTg/cGg	2/2	1	2	FACETS	0.64	0.561	0.724	0.64	0.561	0.724	SUBCLONAL	1	FALSE	1	0.319800012988133	2		1227	753	SUCCESS
REL	5966	MSKCC	GRCh37	2	61148949	61148949	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	116	594	0	ENST00000295025.8:c.1139T>A	p.Val380Asp	p.V380D	ENST00000295025	NM_002908.2	380	gTt/gAt	11/11	0.319800012988133	4	FACETS	0.853	0.772	0.939	0.853	0.772	0.939	CLONAL	2	FALSE	2	0.319800012988133	4		594	561	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	121	406	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	0.421937822872215	2		406	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0022472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	217	539	0	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	0.421937822872215	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.421937822872215	1		539	751	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0022536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	324	1047	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.961	0.909	1	0.961	0.909	1	CLONAL	1	TRUE	1	0.621793990232151	2		1049	1084	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	223	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.621793990232151	2		306	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0022536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	317	545	2	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	0.621793990232151	2		547	1009	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641350	23641350	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1286704342	NA	P-0022536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	326	699	0	ENST00000261584.4:c.2125A>T	p.Asn709Tyr	p.N709Y	ENST00000261584	NM_024675.3	709	Aat/Tat	5/13	1	2	FACETS	0.943	0.891	0.996	0.943	0.891	0.996	CLONAL	1	TRUE	1	0.621793990232151	2		699	1112	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215379	123215379	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0022536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	180	322	0	ENST00000218089.9:c.2924+1G>C		p.X975_splice	ENST00000218089	NM_001042749.1	975			1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.621793990232151	2		322	573	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0022637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	34	646	1	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.368	0.299	0.446	0.368	0.299	0.446	SUBCLONAL	1	TRUE	1	0.203964541550675	2		647	906	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476307	88476307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772244244	NA	P-0022637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	110	985	1	ENST00000360948.2:c.1825G>A	p.Asp609Asn	p.D609N	ENST00000360948	NM_001012338.2	609	Gat/Aat	15/19	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.203964541550675	2		986	880	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0022669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	116	545	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.28864175392294	1	FACETS	0.803	0.724	0.886	0.803	0.724	0.886	CLONAL	1	TRUE	0	0.320568916041397	1		547	757	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849663	68849663	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587780113	NA	P-0022669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	77	258	0	ENST00000261769.5:c.1565+1G>A		p.X522_splice	ENST00000261769	NM_004360.3	522			1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.320568916041397	2		258	429	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217348	11217348	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	88	643	0	ENST00000361445.4:c.4330del	p.Glu1444ArgfsTer33	p.E1444Rfs*33	ENST00000361445	NM_004958.3	1444	Gag/ag	30/58	1	2	FACETS	0.758	0.672	0.851	0.758	0.672	0.851	SUBCLONAL	1	TRUE	1	0.320568916041397	2		643	724	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509394	46509394	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	122	833	0	ENST00000262741.5:c.1337del	p.Val446AlafsTer45	p.V446Afs*45	ENST00000262741	NM_003629.3	446	gTc/gc	10/10	1	2	FACETS	0.981	0.891	1	0.981	0.891	1	CLONAL	1	TRUE	1	0.454642092100426	2		833	547	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965069	15965071	+	inframe_deletion	In_Frame_Del	DEL	TAC	TAC	-	novel	NA	P-0022780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	105	692	1	ENST00000268712.3:c.5525_5527del	p.Ser1842del	p.S1842del	ENST00000268712	NM_006311.3	1842	aGTAag/aag	37/46	1	2	FACETS	0.991	0.893	1	0.991	0.893	1	CLONAL	1	TRUE	1	0.454642092100426	2		693	466	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	99	205	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	0.29	2		205	632	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118942	115118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	45	365	0	ENST00000257566.3:c.399T>A	p.Phe133Leu	p.F133L	ENST00000257566	NM_016569.3	133	ttT/ttA	2/8	1	2	FACETS	0.712	0.599	0.836	0.712	0.599	0.836	SUBCLONAL	1	TRUE	1	0.29	2		365	436	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098615	47098615	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	46	822	0	ENST00000409792.3:c.6659del	p.Pro2220LeufsTer28	p.P2220Lfs*28	ENST00000409792	NM_014159.6	2220	cCt/ct	15/21	1	2	FACETS	0.655	0.55	0.77	0.655	0.55	0.77	SUBCLONAL	1	TRUE	1	0.23	2		822	611	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442507	52442508	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0022888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	75	872	0	ENST00000460680.1:c.237_238del	p.Met80ValfsTer45	p.M80Vfs*45	ENST00000460680	NM_004656.3	79	aaCAtg/aatg	4/17	1	2	FACETS	0.878	0.768	0.996	0.878	0.768	0.996	CLONAL	1	TRUE	1	0.23	2		872	743	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2488144	2488144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1458	228	837	2	ENST00000355716.4:c.41C>T	p.Ser14Phe	p.S14F	ENST00000355716	NM_003820.2	14	tCc/tTc	1/8	0.446232599469409	5	FACETS	1	0.939	1			1	CLONAL	1	TRUE	NA	0.446232599469409	5		839	1686	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953545	32953545	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	137	806	0	ENST00000380152.3:c.8847del	p.Lys2950ArgfsTer26	p.K2950Rfs*26	ENST00000380152		2949	aGg/ag	22/27	1	2	FACETS	0.965	0.881	1	0.965	0.881	1	CLONAL	1	TRUE	1	0.446232599469409	2		806	636	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991563	72991563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	628	1129	0	ENST00000268489.5:c.2482C>T	p.His828Tyr	p.H828Y	ENST00000268489	NM_006885.3	828	Cac/Tac	2/10	0.446232599469409	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.446232599469409	2		1129	1334	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219331	1219333	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0022995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	239	964	1	ENST00000326873.7:c.385_387del	p.Met129del	p.M129del	ENST00000326873	NM_000455.4	128	gTGAtg/gtg	3/10	0.446232599469409	1	FACETS	0.931	0.871	0.993	0.931	0.871	0.993	CLONAL	1	TRUE	0	0.446232599469409	1		965	894	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227067	2227067	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	309	904	0	ENST00000398665.3:c.4547G>C	p.Arg1516Thr	p.R1516T	ENST00000398665	NM_032482.2	1516	aGa/aCa	27/28	0.446232599469409	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.446232599469409	1		904	1014	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001085	150001085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	115	767	0	ENST00000253339.5:c.2519G>A	p.Gly840Asp	p.G840D	ENST00000253339		840	gGt/gAt	4/7	0.446232599469409	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.446232599469409	1		767	397	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0023061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	23	389	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.128000481556239	3	FACETS	1	0.907	1	0.675	0.527	0.846	CLONAL	1	TRUE	1	0.12	3		389	301	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589594	67589596	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	novel	NA	P-0023061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	79	349	1	ENST00000274335.5:c.1358_1360del	p.Asn453del	p.N453del	ENST00000274335		453	AAC/-	10/15	1	2	FACETS	0.839	0.74	0.945	1	0.986	1	CLONAL	3	TRUE	1	0.12	2		350	523	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101300	27101300	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	124	924	0	ENST00000324856.7:c.4582C>T	p.Arg1528Ter	p.R1528*	ENST00000324856	NM_006015.4	1528	Cga/Tga	18/20	1	2	FACETS	0.957	0.869	1	1	0.992	1	CLONAL	4	TRUE	1	0.12	2		924	540	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662446	67662447	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	72	1025	1	ENST00000264010.4:c.1693dup	p.Thr565AsnfsTer11	p.T565Nfs*11	ENST00000264010	NM_006565.3	564	-/A	9/12	1	2	FACETS	0.839	0.735	0.95	1	0.985	1	CLONAL	3	TRUE	1	0.12	2		1026	477	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0023084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	340	704	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.306951721154989	4	FACETS	0.926	0.883	0.969	0.926	0.883	0.969	CLONAL	4	TRUE	0	0.347483056749555	4		705	712	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846080	68846080	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555515726	NA	P-0023084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	125	855	0	ENST00000261769.5:c.1051C>T	p.Gln351Ter	p.Q351*	ENST00000261769	NM_004360.3	351	Caa/Taa	8/16	0.347483056749555	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.347483056749555	1		855	491	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729940	30729940	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752444160	NA	P-0023084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	60	502	1	ENST00000295754.5:c.1461G>A	p.Met487Ile	p.M487I	ENST00000295754	NM_003242.5	487	atG/atA	6/7	0.347483056749555	3	FACETS	0.696	0.6	0.801	0.348	0.3	0.401	SUBCLONAL	1	TRUE	1	0.347483056749555	3		503	582	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856617	111856617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1364785726	NA	P-0023084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	26	262	1	ENST00000341259.2:c.668C>T	p.Ala223Val	p.A223V	ENST00000341259	NM_005475.2	223	gCg/gTg	2/8	0.265205534404006	2	FACETS	0.648	0.515	0.798	0.324	0.257	0.399	SUBCLONAL	1	TRUE	0	0.347483056749555	2		263	231	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88671966	88671966	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0023084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	11	381	1	ENST00000360948.2:c.1205-1G>A		p.X402_splice	ENST00000360948	NM_001012338.2	402			0.347483056749555	0	FACETS	0.193	0.133	0.268			1	SUBCLONAL	1	TRUE	0	0.347483056749555	0		382	214	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317120	11317120	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	97	746	0	ENST00000361445.4:c.374T>C	p.Met125Thr	p.M125T	ENST00000361445	NM_004958.3	125	aTg/aCg	4/58	NA	2	FACETS	1	0.953	1			1	INDETERMINATE	1	TRUE	NA	0.347483056749555	2		746	500	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194116	94194116	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	118	652	1	ENST00000323929.3:c.1312C>A	p.Gln438Lys	p.Q438K	ENST00000323929	NM_005591.3	438	Caa/Aaa	12/20	0.286991805100515	3	FACETS	1	0.977	1	0.422	0.382	0.465	CLONAL	1	TRUE	0	0.347483056749555	3		653	629	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426373	49426373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	63	839	2	ENST00000301067.7:c.12115G>A	p.Glu4039Lys	p.E4039K	ENST00000301067	NM_003482.3	4039	Gag/Aag	39/54	0.347483056749555	3	FACETS	0.528	0.456	0.607	0.264	0.228	0.304	SUBCLONAL	1	TRUE	1	0.347483056749555	3		841	806	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865434	57865434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	73	843	0	ENST00000228682.2:c.2911C>T	p.His971Tyr	p.H971Y	ENST00000228682	NM_005269.2	971	Cat/Tat	12/12	0.347483056749555	3	FACETS	0.79	0.691	0.897	0.395	0.345	0.449	SUBCLONAL	1	TRUE	1	0.347483056749555	3		843	624	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577073	7577073	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555525154	NA	P-0023084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	110	718	0	ENST00000269305.4:c.865C>G	p.Leu289Val	p.L289V	ENST00000269305	NM_001126112.2	289	Ctc/Gtc	8/11	0.306951721154989	4	FACETS	1	0.972	1	0.306	0.275	0.339	CLONAL	1	TRUE	0	0.347483056749555	4		718	697	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053581	37053581	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs756045117	NA	P-0023084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	52	547	0	ENST00000231790.2:c.668C>G	p.Ala223Gly	p.A223G	ENST00000231790	NM_000249.3	223	gCt/gGt	8/19	0.347483056749555	3	FACETS	0.533	0.453	0.621	0.267	0.226	0.311	SUBCLONAL	1	TRUE	1	0.347483056749555	3		547	659	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217497	142217497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	67	607	0	ENST00000350721.4:c.5500C>T	p.Leu1834Phe	p.L1834F	ENST00000350721	NM_001184.3	1834	Ctt/Ttt	32/47	0.347483056749555	5	FACETS	0.757	0.657	0.866	0.252	0.219	0.289	SUBCLONAL	1	TRUE	2	0.347483056749555	5		607	775	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84403334	84403334	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	107	616	0	ENST00000321945.7:c.151G>T	p.Asp51Tyr	p.D51Y	ENST00000321945	NM_139076.2	51	Gat/Tat	2/9	0.228669409400377	3	FACETS	1	0.91	1	0.338	0.303	0.375	CLONAL	1	TRUE	0	0.347483056749555	3		616	712	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944863	131944863	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	113	369	0	ENST00000265335.6:c.2884G>C	p.Glu962Gln	p.E962Q	ENST00000265335		962	Gag/Cag	18/25	0.225766906029965	5	FACETS	1	0.915	1	0.674	0.61	0.742	CLONAL	2	TRUE	2	0.347483056749555	5		369	489	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465576	8465576	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780829320	NA	P-0023084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	62	664	0	ENST00000356435.5:c.3604G>A	p.Glu1202Lys	p.E1202K	ENST00000356435		1202	Gag/Aag	21/35	1	2	FACETS	0.616	0.532	0.708	0.616	0.532	0.708	SUBCLONAL	1	TRUE	1	0.347483056749555	2		664	579	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518024	8518024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	70	570	2	ENST00000356435.5:c.1367C>T	p.Thr456Ile	p.T456I	ENST00000356435		456	aCa/aTa	10/35	1	2	FACETS	0.937	0.82	1	0.937	0.82	1	CLONAL	1	TRUE	1	0.347483056749555	2		572	430	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939430	76939430	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	88	765	1	ENST00000373344.5:c.1318G>A	p.Glu440Lys	p.E440K	ENST00000373344	NM_000489.3	440	Gaa/Aaa	9/35	0.122533097094826	3	FACETS	0.685	0.606	0.77			1	INDETERMINATE	1	TRUE	NA	0.347483056749555	3		766	868	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630396	47630399	+	protein_altering_variant	In_Frame_Del	DEL	CTTT	CTTT	G	novel	NA	P-0023084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	125	631	0	ENST00000233146.2:c.66_69delinsG	p.Phe22_Phe23delinsLeu	p.F22_F23delinsL	ENST00000233146	NM_000251.2	22	ttCTTT/ttG	1/16	0.319888984318518	3	FACETS	0.775	0.704	0.848	0.516	0.469	0.566	SUBCLONAL	2	TRUE	0	0.347483056749555	3		631	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579704	7579705	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0023086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	147	812	0	ENST00000269305.4:c.91_92del	p.Val31SerfsTer11	p.V31Sfs*11	ENST00000269305	NM_001126112.2	31	GTt/t	3/11	0.379753341359713	1	FACETS	0.953	0.873	1	0.953	0.873	1	CLONAL	1	TRUE	0	0.379753341359713	1		812	658	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575068	48575068	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0023086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	135	515	0	ENST00000342988.3:c.262A>T	p.Lys88Ter	p.K88*	ENST00000342988	NM_005359.5	88	Aaa/Taa	3/12	0.379753341359713	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.379753341359713	1		515	520	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971106	21971107	+	missense_variant	Missense_Mutation	DNP	GT	GT	AG	novel	NA	P-0023086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	92	629	2	ENST00000304494.5:c.251_252delinsCT	p.Asp84Ala	p.D84A	ENST00000304494	NM_000077.4	84	gAC/gCT	2/3	0.379753341359713	1	FACETS	0.882	0.788	0.982	0.882	0.788	0.982	CLONAL	1	TRUE	0	0.379753341359713	1		631	445	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0023299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	135	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.346747575818156	2		436	775	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs371769427	NA	P-0023299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	99	394	0	ENST00000291552.4:c.101C>A	p.Ser34Tyr	p.S34Y	ENST00000291552	NM_006758.2	34	tCt/tAt	2/8	1	2	FACETS	0.998	0.893	1	0.998	0.893	1	CLONAL	1	TRUE	1	0.346747575818156	2		394	572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579410	7579410	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567556123	NA	P-0023299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	126	803	0	ENST00000269305.4:c.277del	p.Leu93CysfsTer30	p.L93Cfs*30	ENST00000269305	NM_001126112.2	93	Ctg/tg	4/11	0.323261765475482	1	FACETS	0.813	0.737	0.893	0.813	0.737	0.893	CLONAL	1	TRUE	0	0.346747575818156	1		803	739	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0023454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	205	398	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.362075785733864	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.372010298356579	4		398	726	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0023454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	229	699	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.372010298356579	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.372010298356579	2		699	567	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092833	27092833	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	109	754	0	ENST00000324856.7:c.2854G>A	p.Gly952Arg	p.G952R	ENST00000324856	NM_006015.4	952	Gga/Aga	9/20	1	2	FACETS	0.897	0.807	0.993	0.897	0.807	0.993	CLONAL	1	TRUE	1	0.372010298356579	2		754	653	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445635	49445635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1304802509	NA	P-0023454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1363	312	1239	0	ENST00000301067.7:c.1831C>T	p.Pro611Ser	p.P611S	ENST00000301067	NM_003482.3	611	Cca/Tca	10/54	0.372010298356579	6	FACETS	0.873	0.821	0.927	0.437	0.41	0.464	CLONAL	2	TRUE	2	0.372010298356579	6		1239	1675	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061261	38061261	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	239	797	1	ENST00000250448.2:c.728A>G	p.Tyr243Cys	p.Y243C	ENST00000250448	NM_004496.3	243	tAc/tGc	2/2	0.362075785733864	4	FACETS	0.985	0.921	1	0.985	0.921	1	CLONAL	2	TRUE	2	0.372010298356579	4		798	895	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367845	15367845	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265135334	NA	P-0023454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	141	888	0	ENST00000263377.2:c.1481C>T	p.Ser494Leu	p.S494L	ENST00000263377	NM_058243.2	494	tCg/tTg	8/20	0.372010298356579	3	FACETS	1	0.949	1	0.53	0.483	0.58	CLONAL	1	TRUE	1	0.372010298356579	3		888	848	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151195	202151195	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	90	445	0	ENST00000358485.4:c.1495C>A	p.Leu499Ile	p.L499I	ENST00000358485	NM_001080125.1	499	Ctc/Atc	9/9	0.372010298356579	3	FACETS	1	0.968	1	0.616	0.549	0.687	CLONAL	1	TRUE	1	0.372010298356579	3		445	466	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030884	36030887	+	frameshift_variant	Frame_Shift_Del	DEL	GGGA	GGGA	-	novel	NA	P-0023454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	244	799	0	ENST00000358208.4:c.1163_1166del	p.Arg388ProfsTer67	p.R388Pfs*67	ENST00000358208		388	cGGGAc/cc	10/12	0.362075785733864	4	FACETS	0.913	0.853	0.974	0.913	0.853	0.974	CLONAL	2	TRUE	2	0.372010298356579	4		799	986	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131972816	131972816	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	136	492	0	ENST00000265335.6:c.3399G>T	p.Met1133Ile	p.M1133I	ENST00000265335		1133	atG/atT	22/25	0.317217732492339	4	FACETS	0.889	0.812	0.97	0.889	0.812	0.97	CLONAL	2	TRUE	2	0.372010298356579	4		492	564	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268078	55268078	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	212	866	0	ENST00000275493.2:c.2918G>C	p.Arg973Pro	p.R973P	ENST00000275493	NM_005228.3	973	cGa/cCa	24/28	0.372010298356579	3	FACETS	1	0.991	1	0.721	0.67	0.773	CLONAL	1	TRUE	1	0.372010298356579	3		866	938	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864214	57864214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	33	639	0	ENST00000228682.2:c.1691C>T	p.Pro564Leu	p.P564L	ENST00000228682	NM_005269.2	564	cCt/cTt	12/12	1	2	FACETS	0.324	0.263	0.393	0.324	0.263	0.393	SUBCLONAL	1	TRUE	1	0.329400177702608	2		639	619	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836769	151836769	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0023509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	65	567	1	ENST00000262189.6:c.14451T>A	p.Tyr4817Ter	p.Y4817*	ENST00000262189	NM_170606.2	4817	taT/taA	56/59	1	2	FACETS	0.563	0.487	0.645	0.563	0.487	0.645	SUBCLONAL	1	TRUE	1	0.329400177702608	2		568	701	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0023509-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	12	389	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		389	494	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588751	29588751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760703505	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	30	415	0	ENST00000356175.3:c.4537C>T	p.Arg1513Ter	p.R1513*	ENST00000356175	NM_000267.3	1513	Cga/Tga	34/57	1	2	FACETS	0.369	0.297	0.449	0.369	0.297	0.449	SUBCLONAL	1	TRUE	1	0.55	2		415	296	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	9	205	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.125	0.082	0.18	0.125	0.082	0.18	SUBCLONAL	1	TRUE	1	0.55	2		205	261	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868176	45868176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559154781	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	69	1038	3	ENST00000391945.4:c.514G>A	p.Ala172Thr	p.A172T	ENST00000391945	NM_000400.3	172	Gct/Act	7/23	1	2	FACETS	0.369	0.321	0.421	0.369	0.321	0.421	SUBCLONAL	1	TRUE	1	0.55	2		1041	680	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	66	158	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.909	0.798	1	0.909	0.798	1	CLONAL	1	TRUE	1	0.55	2		159	264	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	83	661	10	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.72	0.639	0.807	0.72	0.639	0.807	SUBCLONAL	1	TRUE	1	0.55	2		671	419	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	30	718	0	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.228	0.183	0.279	0.228	0.183	0.279	SUBCLONAL	1	TRUE	1	0.55	2		718	478	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	79	556	3	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.762	0.674	0.855	0.762	0.674	0.855	SUBCLONAL	1	TRUE	1	0.55	2		559	377	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	19	684	4	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	0.209	0.158	0.269	0.209	0.158	0.269	SUBCLONAL	1	TRUE	1	0.55	2		688	330	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	140	758	1	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.55	2		759	413	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	162	833	2	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.985	0.908	1	0.985	0.908	1	CLONAL	1	TRUE	1	0.55	2		835	598	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	133	268	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.79	0.72	0.864	0.79	0.72	0.864	SUBCLONAL	1	TRUE	1	0.55	2		268	612	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101268	27101268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	52	730	3	ENST00000324856.7:c.4555del	p.Gln1519ArgfsTer8	p.Q1519Rfs*8	ENST00000324856	NM_006015.4	1517	gCc/gc	18/20	1	2	FACETS	0.368	0.313	0.428	0.368	0.313	0.428	SUBCLONAL	1	TRUE	1	0.55	2		733	514	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65312353	65312353	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375353661	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	153	688	0	ENST00000342505.4:c.1966G>A	p.Val656Ile	p.V656I	ENST00000342505	NM_002227.2	656	Gtc/Atc	14/25	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.55	2		688	517	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556463	29556463	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1567849208	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	34	606	1	ENST00000356175.3:c.2835del	p.Phe945LeufsTer9	p.F945Lfs*9	ENST00000356175	NM_000267.3	944	Ttt/tt	21/57	1	2	FACETS	0.325	0.265	0.391	0.325	0.265	0.391	SUBCLONAL	1	TRUE	1	0.55	2		607	381	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954272	32954273	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359752	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	76	589	2	ENST00000380152.3:c.9253dup	p.Thr3085AsnfsTer26	p.T3085Nfs*26	ENST00000380152		3082	-/A	24/27	1	2	FACETS	0.794	0.702	0.892	0.794	0.702	0.892	SUBCLONAL	1	TRUE	1	0.55	2		591	348	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799060	42799060	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	95	1008	2	ENST00000575354.2:c.4544G>A	p.Arg1515His	p.R1515H	ENST00000575354	NM_015125.3	1515	cGc/cAc	20/20	1	2	FACETS	0.457	0.407	0.511	0.457	0.407	0.511	SUBCLONAL	1	TRUE	1	0.55	2		1010	756	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	39	712	0	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	0.277	0.229	0.33	0.277	0.229	0.33	SUBCLONAL	1	TRUE	1	0.55	2		712	512	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921567	178921567	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553821144	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	19	381	0	ENST00000263967.3:c.1049A>G	p.Asp350Gly	p.D350G	ENST00000263967	NM_006218.2	350	gAc/gGc	5/21	1	2	FACETS	0.317	0.241	0.406	0.317	0.241	0.406	SUBCLONAL	1	TRUE	1	0.55	2		381	218	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685308	89685308	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876660634	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	85	552	0	ENST00000371953.3:c.203A>G	p.Tyr68Cys	p.Y68C	ENST00000371953	NM_000314.4	68	tAc/tGc	3/9	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.55	2		552	286	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180040101	180040101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909652	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	52	763	2	ENST00000261937.6:c.3341C>T	p.Pro1114Leu	p.P1114L	ENST00000261937	NM_182925.4	1114	cCg/cTg	25/30	1	2	FACETS	0.376	0.32	0.437	0.376	0.32	0.437	SUBCLONAL	1	TRUE	1	0.55	2		765	503	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713601	30713601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202168735	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	22	462	1	ENST00000295754.5:c.926C>T	p.Thr309Met	p.T309M	ENST00000295754	NM_003242.5	309	aCg/aTg	4/7	1	2	FACETS	0.208	0.16	0.263	0.208	0.16	0.263	SUBCLONAL	1	TRUE	1	0.55	2		463	385	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928036	49928036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199869962	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	55	872	3	ENST00000296474.3:c.3692G>A	p.Arg1231His	p.R1231H	ENST00000296474	NM_002447.2	1231	cGc/cAc	18/20	1	2	FACETS	0.289	0.247	0.336	0.289	0.247	0.336	SUBCLONAL	1	TRUE	1	0.55	2		875	692	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224583	108224583	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881329	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	24	446	0	ENST00000278616.4:c.8762C>T	p.Thr2921Met	p.T2921M	ENST00000278616	NM_000051.3	2921	aCg/aTg	60/63	1	2	FACETS	0.311	0.244	0.387	0.311	0.244	0.387	SUBCLONAL	1	TRUE	1	0.55	2		446	281	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215357	5215357	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1440179947	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	148	767	0	ENST00000357368.4:c.4261C>T	p.Arg1421Cys	p.R1421C	ENST00000357368	NM_002850.3	1421	Cgc/Tgc	28/38	1	2	FACETS	0.968	0.889	1	0.968	0.889	1	CLONAL	1	TRUE	1	0.55	2		767	556	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671654	67671655	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	40	654	0	ENST00000264010.4:c.2070dup	p.Glu691ArgfsTer5	p.E691Rfs*5	ENST00000264010	NM_006565.3	688	gta/gtAa	12/12	1	2	FACETS	0.309	0.257	0.368	0.309	0.257	0.368	SUBCLONAL	1	TRUE	1	0.55	2		654	470	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515176	148515176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1390180981	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	120	451	1	ENST00000320356.2:c.1033G>A	p.Ala345Thr	p.A345T	ENST00000320356	NM_004456.4	345	Gct/Act	10/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.55	2		452	372	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610522	81610522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368452281	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	39	459	1	ENST00000298171.2:c.2120G>A	p.Arg707Gln	p.R707Q	ENST00000298171	NM_000369.2	707	cGg/cAg	10/10	1	2	FACETS	0.385	0.32	0.458	0.385	0.32	0.458	SUBCLONAL	1	TRUE	1	0.55	2		460	368	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023717	31023717	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764651405	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	34	832	0	ENST00000375687.4:c.3202C>T	p.Arg1068Ter	p.R1068*	ENST00000375687	NM_015338.5	1068	Cga/Tga	13/13	1	2	FACETS	0.205	0.167	0.248	0.205	0.167	0.248	SUBCLONAL	1	TRUE	1	0.55	2		832	603	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226860	2226860	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	26	169	1	ENST00000398665.3:c.4340C>T	p.Ala1447Val	p.A1447V	ENST00000398665	NM_032482.2	1447	gCg/gTg	27/28	1	2	FACETS	0.188	0.148	0.234	0.188	0.148	0.234	SUBCLONAL	1	TRUE	1	0.55	2		170	502	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167562	24167562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769023941	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	52	572	8	ENST00000263121.7:c.946C>T	p.Arg316Trp	p.R316W	ENST00000263121	NM_003073.3	316	Cgg/Tgg	7/9	1	2	FACETS	0.316	0.268	0.368	0.316	0.268	0.368	SUBCLONAL	1	TRUE	1	0.55	2		580	599	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056421	180056421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	110	570	0	ENST00000261937.6:c.823C>T	p.Arg275Trp	p.R275W	ENST00000261937	NM_182925.4	275	Cgg/Tgg	7/30	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.55	2		570	390	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262483	16262488	+	inframe_deletion	In_Frame_Del	DEL	GTCCCT	GTCCCT	-	rs752807690	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	15	263	0	ENST00000375759.3:c.9759_9764del	p.Val3254_Pro3255del	p.V3254_P3255del	ENST00000375759	NM_015001.2	3250	GTCCCT/-	11/15	1	2	FACETS	0.312	0.229	0.411	0.312	0.229	0.411	SUBCLONAL	1	TRUE	1	0.55	2		263	175	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258350	16258350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756861745	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	60	748	0	ENST00000375759.3:c.5615C>T	p.Ala1872Val	p.A1872V	ENST00000375759	NM_015001.2	1872	gCa/gTa	11/15	1	2	FACETS	0.379	0.326	0.436	0.379	0.326	0.436	SUBCLONAL	1	TRUE	1	0.55	2		748	576	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417386	139417386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754236791	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	218	1125	1	ENST00000277541.6:c.658G>A	p.Val220Met	p.V220M	ENST00000277541	NM_017617.3	220	Gtg/Atg	4/34	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.55	2		1126	709	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307747	11307747	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	176	768	0	ENST00000361445.4:c.1160T>C	p.Leu387Pro	p.L387P	ENST00000361445	NM_004958.3	387	cTg/cCg	8/58	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.55	2		768	584	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106421	27106421	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	154	603	0	ENST00000324856.7:c.6032T>C	p.Leu2011Pro	p.L2011P	ENST00000324856	NM_006015.4	2011	cTg/cCg	20/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.55	2		603	511	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849914	156849914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763122825	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	198	910	1	ENST00000524377.1:c.2170G>A	p.Gly724Ser	p.G724S	ENST00000524377	NM_002529.3	724	Ggc/Agc	16/17	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.55	2		911	717	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94908685	94908685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764427282	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	152	849	0	ENST00000536441.1:c.1369C>T	p.Arg457Trp	p.R457W	ENST00000536441	NM_144665.3	457	Cgg/Tgg	9/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.55	2		849	514	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999308	100999308	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	42	911	0	ENST00000325455.5:c.494T>C	p.Met165Thr	p.M165T	ENST00000325455	NM_001202474.3	165	aTg/aCg	1/8	1	2	FACETS	0.216	0.18	0.257	0.216	0.18	0.257	SUBCLONAL	1	TRUE	1	0.55	2		911	706	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633396	3633396	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567166561	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	81	1086	1	ENST00000294008.3:c.4855C>T	p.Pro1619Ser	p.P1619S	ENST00000294008	NM_032444.2	1619	Ccg/Tcg	14/15	1	2	FACETS	0.355	0.312	0.401	0.355	0.312	0.401	SUBCLONAL	1	TRUE	1	0.55	2		1087	830	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647909	3647909	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs941244697	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	58	1154	4	ENST00000294008.3:c.1255G>A	p.Glu419Lys	p.E419K	ENST00000294008	NM_032444.2	419	Gag/Aag	6/15	1	2	FACETS	0.296	0.254	0.343	0.296	0.254	0.343	SUBCLONAL	1	TRUE	1	0.55	2		1158	712	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831629	72831629	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs117283459	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	162	794	0	ENST00000268489.5:c.4952C>T	p.Thr1651Met	p.T1651M	ENST00000268489	NM_006885.3	1651	aCg/aTg	9/10	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.55	2		794	575	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559741	29559741	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	18	343	0	ENST00000356175.3:c.3338T>C	p.Leu1113Pro	p.L1113P	ENST00000356175	NM_000267.3	1113	cTt/cCt	26/57	1	2	FACETS	0.21	0.158	0.272	0.21	0.158	0.272	SUBCLONAL	1	TRUE	1	0.55	2		343	311	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867626	78867626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781190662	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	148	976	1	ENST00000306801.3:c.2362C>T	p.Arg788Cys	p.R788C	ENST00000306801	NM_020761.2	788	Cgc/Tgc	20/34	1	2	FACETS	0.724	0.662	0.789	0.724	0.662	0.789	SUBCLONAL	1	TRUE	1	0.55	2		977	743	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593508	48593508	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793725	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	109	347	0	ENST00000342988.3:c.1259G>A	p.Arg420His	p.R420H	ENST00000342988	NM_005359.5	420	cGt/cAt	10/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.55	2		347	344	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099211	4099211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770521279	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	128	626	1	ENST00000262948.5:c.907C>T	p.Arg303Cys	p.R303C	ENST00000262948	NM_030662.3	303	Cgc/Tgc	7/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.55	2		627	441	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966009	18966009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766944357	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	65	780	1	ENST00000262803.5:c.1502C>T	p.Thr501Met	p.T501M	ENST00000262803	NM_002911.3	501	aCg/aTg	11/24	1	2	FACETS	0.424	0.368	0.485	0.424	0.368	0.485	SUBCLONAL	1	TRUE	1	0.55	2		781	557	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798773	42798773	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	55	718	0	ENST00000575354.2:c.4345del	p.Val1449CysfsTer5	p.V1449Cfs*5	ENST00000575354	NM_015125.3	1449	Gtg/tg	19/20	1	2	FACETS	0.387	0.331	0.448	0.387	0.331	0.448	SUBCLONAL	1	TRUE	1	0.55	2		718	517	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250176	39250176	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	47	997	0	ENST00000402219.2:c.1393G>A	p.Asp465Asn	p.D465N	ENST00000402219	NM_005633.3	465	Gat/Aat	10/23	1	2	FACETS	0.363	0.306	0.425	0.363	0.306	0.425	SUBCLONAL	1	TRUE	1	0.55	2		997	471	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656894	47656894	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	77	410	1	ENST00000233146.2:c.1090G>T	p.Glu364Ter	p.E364*	ENST00000233146	NM_000251.2	364	Gaa/Taa	7/16	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.55	2		411	271	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017758	31017758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	57	693	2	ENST00000375687.4:c.620G>A	p.Ser207Asn	p.S207N	ENST00000375687	NM_015338.5	207	aGc/aAc	8/13	1	2	FACETS	0.485	0.417	0.559	0.485	0.417	0.559	SUBCLONAL	1	TRUE	1	0.55	2		695	427	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551019	41551019	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886041830	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	128	598	0	ENST00000263253.7:c.3163C>T	p.Arg1055Ter	p.R1055*	ENST00000263253	NM_001429.3	1055	Cga/Tga	17/31	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.55	2		598	448	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52663037	52663037	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	12	373	0	ENST00000394830.3:c.1316A>C	p.Asn439Thr	p.N439T	ENST00000394830	NM_018313.4	439	aAt/aCt	13/30	1	2	FACETS	0.182	0.127	0.249	0.182	0.127	0.249	SUBCLONAL	1	TRUE	1	0.55	2		373	240	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31423021	31423021	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	152	880	0	ENST00000344624.3:c.3292A>G	p.Ile1098Val	p.I1098V	ENST00000344624		1098	Att/Gtt	26/33	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.55	2		880	509	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322901	31322901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1178323640	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	78	834	1	ENST00000412585.2:c.995G>A	p.Cys332Tyr	p.C332Y	ENST00000412585	NM_005514.6	332	tGt/tAt	5/8	1	2	FACETS	0.488	0.429	0.551	0.488	0.429	0.551	SUBCLONAL	1	TRUE	1	0.55	2		835	581	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652128	36652128	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs781404776	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	47	756	0	ENST00000244741.5:c.250C>T	p.Arg84Ter	p.R84*	ENST00000244741	NM_000389.4	84	Cga/Tga	2/3	1	2	FACETS	0.32	0.27	0.376	0.32	0.27	0.376	SUBCLONAL	1	TRUE	1	0.55	2		756	534	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793797	89793799	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	32	674	0	ENST00000336032.3:c.868_870del	p.Pro290del	p.P290del	ENST00000336032	NM_006813.2	289	tCTCct/tct	2/2	1	2	FACETS	0.261	0.212	0.318	0.261	0.212	0.318	SUBCLONAL	1	TRUE	1	0.55	2		674	445	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946226	13946226	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	50	522	0	ENST00000405192.2:c.872-2A>G		p.X291_splice	ENST00000405192	NM_001163147.1	291			1	2	FACETS	0.498	0.424	0.579	0.498	0.424	0.579	SUBCLONAL	1	TRUE	1	0.55	2		522	365	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137313588	137313588	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	74	1012	1	ENST00000481739.1:c.847G>A	p.Ala283Thr	p.A283T	ENST00000481739	NM_002957.4	283	Gcc/Acc	6/10	1	2	FACETS	0.371	0.324	0.422	0.371	0.324	0.422	SUBCLONAL	1	TRUE	1	0.55	2		1013	725	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15818068	15818069	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	40	468	0	ENST00000307771.7:c.202_203dup	p.Gln69GlyfsTer10	p.Q69Gfs*10	ENST00000307771	NM_005089.3	65	-/AG	3/11	1	2	FACETS	0.452	0.376	0.535	0.452	0.376	0.535	SUBCLONAL	1	TRUE	1	0.55	2		468	322	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617593	100617593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	40	963	0	ENST00000308731.7:c.476C>T	p.Ala159Val	p.A159V	ENST00000308731	NM_000061.2	159	gCc/gTc	6/19	1	2	FACETS	0.233	0.193	0.278	0.233	0.193	0.278	SUBCLONAL	1	TRUE	1	0.55	2		963	623	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0023674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	133	286	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.994	0.904	1	0.994	0.904	1	CLONAL	1	TRUE	1	0.38018855800077	2		286	704	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0023674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	101	484	1	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.38018855800077	2		485	505	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059230	27059230	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs267598525	NA	P-0023674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	173	799	3	ENST00000324856.7:c.1867G>T	p.Gly623Ter	p.G623*	ENST00000324856	NM_006015.4	623	Gga/Tga	4/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.38018855800077	2		802	834	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390878	139390878	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199777870	NA	P-0023674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	200	1096	0	ENST00000277541.6:c.7313C>T	p.Pro2438Leu	p.P2438L	ENST00000277541	NM_017617.3	2438	cCg/cTg	34/34	1	2	FACETS	0.999	0.925	1	0.999	0.925	1	CLONAL	1	TRUE	1	0.38018855800077	2		1096	1053	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692892	89692892	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	197	538	0	ENST00000371953.3:c.376G>C	p.Ala126Pro	p.A126P	ENST00000371953	NM_000314.4	126	Gct/Cct	5/9	0.38018855800077	2	FACETS	0.924	0.861	0.987	0.924	0.861	0.987	CLONAL	2	TRUE	0	0.38018855800077	2		538	561	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670645	67670645	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	230	687	0	ENST00000264010.4:c.1890del	p.Glu631LysfsTer11	p.E631Kfs*11	ENST00000264010	NM_006565.3	630	gtA/gt	11/12	0.38018855800077	2	FACETS	0.856	0.801	0.911	0.856	0.801	0.911	CLONAL	2	TRUE	0	0.38018855800077	2		687	707	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352358	70352358	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	155	722	2	ENST00000374080.3:c.4385G>A	p.Arg1462His	p.R1462H	ENST00000374080		1462	cGc/cAc	31/45	1	2	FACETS	0.929	0.85	1	0.929	0.85	1	CLONAL	1	TRUE	1	0.38018855800077	2		724	878	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518215	187518215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781295226	NA	P-0023707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	74	369	0	ENST00000441802.2:c.12479G>A	p.Arg4160His	p.R4160H	ENST00000441802	NM_005245.3	4160	cGt/cAt	25/27	1	2	FACETS	0.925	0.816	1	0.925	0.816	1	CLONAL	1	TRUE	1	0.492470334482873	2		369	325	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0023789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	138	407	1	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.610292936024676	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.612406434226069	1		408	309	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626716	28626716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146030737	NA	P-0023789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	32	341	1	ENST00000241453.7:c.580G>A	p.Val194Met	p.V194M	ENST00000241453	NM_004119.2	194	Gtg/Atg	5/24	0.575858143979092	3	FACETS	0.289	0.234	0.351	0.145	0.117	0.176	SUBCLONAL	1	TRUE	1	0.612406434226069	3		342	472	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169953127	169953127	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	85	299	0	ENST00000295797.4:c.211A>C	p.Ile71Leu	p.I71L	ENST00000295797	NM_002740.5	71	Ata/Cta	2/18	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.612406434226069	2		299	248	SUCCESS
APC	324	MSKCC	GRCh37	5	112175189	112175189	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	39	160	0	ENST00000257430.4:c.3899del	p.Asn1300IlefsTer5	p.N1300Ifs*5	ENST00000257430	NM_000038.5	1300	Aat/at	16/16	0.612406434226069	1	FACETS	0.803	0.684	0.928	0.803	0.684	0.928	CLONAL	1	TRUE	0	0.612406434226069	1		160	110	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129156	152129156	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	103	400	0	ENST00000206249.3:c.109C>T	p.Arg37Trp	p.R37W	ENST00000206249	NM_000125.3	37	Cgg/Tgg	1/8	0.368220406022046	1	FACETS	0.831	0.754	0.909	0.831	0.754	0.909	CLONAL	1	TRUE	0	0.612406434226069	1		400	281	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055678	152055679	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0023789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	106	429	0	ENST00000262189.6:c.242_243dup	p.Glu82TrpfsTer24	p.E82Wfs*24	ENST00000262189	NM_170606.2	81	-/TG	2/59	0.612406434226069	3	FACETS	0.921	0.829	1	0.46	0.414	0.509	CLONAL	1	TRUE	1	0.612406434226069	3		429	491	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624612	93624612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	152	272	0	ENST00000375746.1:c.703G>A	p.Asp235Asn	p.D235N	ENST00000375746	NM_001174167.1	235	Gac/Aac	4/14	0.575858143979092	3	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	1	0.612406434226069	3		272	324	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0023817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	45	383	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.284531157880356	1	FACETS	0.939	0.794	1	0.939	0.794	1	CLONAL	1	TRUE	0	0.284531157880356	1		383	289	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678783	52678784	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	24	275	0	ENST00000394830.3:c.835dup	p.Ile279AsnfsTer8	p.I279Nfs*8	ENST00000394830	NM_018313.4	279	ata/aAta	9/30	0.2546093329495	1	FACETS	0.832	0.657	1	0.832	0.657	1	CLONAL	1	TRUE	0	0.284531157880356	1		275	174	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578247	7578247	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	119	444	0	ENST00000269305.4:c.602del	p.Leu201CysfsTer46	p.L201Cfs*46	ENST00000269305	NM_001126112.2	201	tTg/tg	6/11	1	2	FACETS	1	0.962	1	1	0.99	1	CLONAL	2	TRUE	1	0.284531157880356	2		444	379	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710974	117710974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	19	159	0	ENST00000368508.3:c.1298G>A	p.Arg433Lys	p.R433K	ENST00000368508	NM_002944.2	433	aGa/aAa	12/43	1	2	FACETS	0.909	0.696	1	0.909	0.696	1	CLONAL	1	TRUE	1	0.284531157880356	2		159	147	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434384	49434384	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866926540	NA	P-0023817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	25	480	0	ENST00000301067.7:c.7169C>T	p.Pro2390Leu	p.P2390L	ENST00000301067	NM_003482.3	2390	cCg/cTg	31/54	1	2	FACETS	0.472	0.372	0.588	0.472	0.372	0.588	SUBCLONAL	1	TRUE	1	0.284531157880356	2		480	372	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0023851-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	208	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.902	0.839	0.966	0.902	0.839	0.966	CLONAL	1	TRUE	1	0.612705354679787	2		436	753	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023831	27023831	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1415214478	NA	P-0023851-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	117	394	0	ENST00000324856.7:c.941del	p.Gly314AlafsTer49	p.G314Afs*49	ENST00000324856	NM_006015.4	313	Ggg/gg	1/20	0.583959134306204	1	FACETS	0.8	0.731	0.872	0.8	0.731	0.872	SUBCLONAL	1	TRUE	0	0.612705354679787	1		394	331	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446175	49446175	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023851-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	228	588	0	ENST00000301067.7:c.1291G>T	p.Glu431Ter	p.E431*	ENST00000301067	NM_003482.3	431	Gag/Tag	10/54	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.612705354679787	2		588	716	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524889	187524889	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023851-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	194	507	0	ENST00000441802.2:c.10791del	p.Lys3598SerfsTer2	p.K3598Sfs*2	ENST00000441802	NM_005245.3	3597	ggC/gg	19/27	0.612705354679787	1	FACETS	0.898	0.839	0.958	0.898	0.839	0.958	CLONAL	1	TRUE	0	0.612705354679787	1		507	489	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879658	151879658	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023851-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	70	199	0	ENST00000262189.6:c.5287C>T	p.Gln1763Ter	p.Q1763*	ENST00000262189	NM_170606.2	1763	Cag/Tag	36/59	1	2	FACETS	0.828	0.73	0.932	0.828	0.73	0.932	CLONAL	1	TRUE	1	0.612705354679787	2		199	276	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412313	139412315	+	inframe_deletion	In_Frame_Del	DEL	GTA	GTA	-	novel	NA	P-0023870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	10	738	0	ENST00000277541.6:c.1330_1332del	p.Tyr444del	p.Y444del	ENST00000277541	NM_017617.3	444	TAC/-	8/34	0.221863774363986	4	FACETS	0.558	0.381	0.776	0.279	0.19	0.388	INDETERMINATE	1	TRUE	2	0.5669420182053	4		738	99	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	25	406	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.714	0.561	0.89	0.714	0.561	0.89	SUBCLONAL	1	TRUE	1	0.13	2		406	539	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578551	7578551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	39	607	0	ENST00000269305.4:c.379T>C	p.Ser127Pro	p.S127P	ENST00000269305	NM_001126112.2	127	Tcc/Ccc	5/11	1	2	FACETS	0.942	0.779	1	0.942	0.779	1	CLONAL	1	TRUE	1	0.13	2		607	637	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577575	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782289	NA	P-0023916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	153	394	0	ENST00000269305.4:c.706T>C	p.Tyr236His	p.Y236H	ENST00000269305	NM_001126112.2	236	Tac/Cac	7/11	0.248177966403805	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.259768131518914	2		394	531	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0023916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	85	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.230409235136885	3	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	1	0.259768131518914	3		436	341	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172029	99172029	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	51	308	0	ENST00000074304.5:c.1595T>C	p.Leu532Pro	p.L532P	ENST00000074304	NM_001134224.1	532	cTg/cCg	17/26	0.230409235136885	3	FACETS	0.861	0.732	1	0.431	0.366	0.502	CLONAL	1	TRUE	1	0.259768131518914	3		308	515	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974676	21974677	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	75	369	0	ENST00000304494.5:c.150_150+1insT	p.Val51CysfsTer69	p.V51Cfs*69	ENST00000304494	NM_000077.4	50	-/T		0.259768131518914	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.259768131518914	1		369	473	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	56	306	0				ENST00000310581	NM_198253.2	-/1132			0.61836314421409	6	FACETS	0.993	0.887	1	0.993	0.887	1	CLONAL	4	TRUE	2	0.61836314421409	6		306	102	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0023918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	57	409	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.499752303246803	3	FACETS	0.997	0.885	1			1	CLONAL	2	TRUE	NA	0.61836314421409	3		409	121	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599251	28599271	+	inframe_deletion	In_Frame_Del	DEL	CCCCCTAGTGAACAGAGCAGC	CCCCCTAGTGAACAGAGCAGC	-	novel	NA	P-0023918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	61	607	0	ENST00000253063.3:c.702_722del	p.Glu236_Ser242del	p.E236_S242del	ENST00000253063	NM_031459.4	233	CCCCCTAGTGAACAGAGCAGC/-	5/10	0.61836314421409	3	FACETS	1	0.969	1	0.687	0.603	0.774	CLONAL	1	TRUE	1	0.61836314421409	3		607	188	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44896922	44896932	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	ATATGAAACCC	ATATGAAACCC	-	novel	NA	P-0023918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	84	511	0	ENST00000377967.4:c.643_653del	p.Tyr215GlufsTer11	p.Y215Efs*11	ENST00000377967	NM_021140.2	214	ttATATGAAACCCag/ttag	8/29	0.61836314421409	3	FACETS	0.907	0.82	0.997	0.907	0.82	0.997	CLONAL	2	TRUE	1	0.61836314421409	3		511	196	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	61	406	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.991	0.854	1	0.991	0.854	1	CLONAL	1	TRUE	1	0.17	2		406	724	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0023965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	32	771	0	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	1	2	FACETS	0.835	0.677	1	0.835	0.677	1	CLONAL	1	TRUE	1	0.17	2		771	451	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492700	56492700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	38	703	0	ENST00000407977.2:c.239G>A	p.Gly80Glu	p.G80E	ENST00000407977		80	gGa/gAa	2/10	1	2	FACETS	0.845	0.698	1	0.845	0.698	1	CLONAL	1	TRUE	1	0.17	2		703	529	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575152	48575152	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	32	562	0	ENST00000342988.3:c.346C>A	p.Gln116Lys	p.Q116K	ENST00000342988	NM_005359.5	116	Cag/Aag	3/12	1	2	FACETS	0.808	0.655	0.981	0.808	0.655	0.981	CLONAL	1	TRUE	1	0.17	2		562	466	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188404	32188404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763926116	NA	P-0023965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	18	619	0	ENST00000375023.3:c.937G>A	p.Glu313Lys	p.E313K	ENST00000375023	NM_004557.3	313	Gaa/Aaa	6/30	1	2	FACETS	0.6	0.451	0.777	0.6	0.451	0.777	SUBCLONAL	1	TRUE	1	0.17	2		619	353	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974711	21974721	+	frameshift_variant	Frame_Shift_Del	DEL	TTGGGCAGCGC	TTGGGCAGCGC	-	novel	NA	P-0023965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	21	544	0	ENST00000304494.5:c.106_116del	p.Ala36ArgfsTer4	p.A36Rfs*4	ENST00000304494	NM_000077.4	36	GCGCTGCCCAAc/c	1/3	1	2	FACETS	1	0.781	1	1	0.781	1	CLONAL	1	TRUE	1	0.17	2		544	244	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0023968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	81	294	2	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.79	0.7	0.886	0.79	0.7	0.886	SUBCLONAL	1	TRUE	1	0.512606264283735	2		296	400	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0023968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	62	364	2	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.674	0.585	0.769	0.674	0.585	0.769	SUBCLONAL	1	TRUE	1	0.512606264283735	2		366	359	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874147	151874148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs747256476	NA	P-0023968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	146	836	10	ENST00000262189.6:c.8390dup	p.Glu2798GlyfsTer11	p.E2798Gfs*11	ENST00000262189	NM_170606.2	2797	aag/aaAg	38/59	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.512606264283735	2		846	457	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154241	2154242	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755455183	NA	P-0023968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	69	711	1	ENST00000434045.2:c.686dup	p.Glu230ArgfsTer50	p.E230Rfs*50	ENST00000434045	NM_001127598.1	229	cca/ccCa	5/5	1	2	FACETS	0.758	0.665	0.858	0.758	0.665	0.858	SUBCLONAL	1	TRUE	1	0.512606264283735	2		712	355	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0023968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	85	599	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.759	0.674	0.849	0.759	0.674	0.849	SUBCLONAL	1	TRUE	1	0.512606264283735	2		599	437	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089705	27089706	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1286891446	NA	P-0023968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	119	701	2	ENST00000324856.7:c.2666dup	p.Met890HisfsTer46	p.M890Hfs*46	ENST00000324856	NM_006015.4	887	-/G	8/20	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.512606264283735	2		703	452	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959351	26959351	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	34	423	0	ENST00000381527.3:c.518A>G	p.Asp173Gly	p.D173G	ENST00000381527	NM_001260.1	173	gAc/gGc	6/13	1	2	FACETS	0.484	0.397	0.581	0.484	0.397	0.581	SUBCLONAL	1	TRUE	1	0.512606264283735	2		423	274	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967511	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	rs1349928568	NA	P-0023968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	173	449	0	ENST00000265433.3:c.1396dup	p.Arg466LysfsTer5	p.R466Kfs*5	ENST00000265433	NM_002485.4	466	agg/aAgg	10/16	0.512606264283735	3	FACETS	0.794	0.736	0.854	0.794	0.736	0.854	SUBCLONAL	2	TRUE	1	0.512606264283735	3		449	534	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213242	39213243	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1558454973	NA	P-0023968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	116	800	1	ENST00000402219.2:c.3724dup	p.Ser1242LysfsTer2	p.S1242Kfs*2	ENST00000402219	NM_005633.3	1242	agt/aAgt	23/23	NA	2	FACETS	0.736	0.665	0.811			1	INDETERMINATE	1	TRUE	NA	0.512606264283735	2		801	615	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263192	115263192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	112	710	0	ENST00000438362.2:c.2158C>T	p.Arg720Cys	p.R720C	ENST00000438362	NM_001242891.1	720	Cgc/Tgc	17/20	1	2	FACETS	0.914	0.827	1	0.914	0.827	1	CLONAL	1	TRUE	1	0.512606264283735	2		710	478	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15378304	15378305	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	76	704	0	ENST00000263377.2:c.481dup	p.Ile161AsnfsTer3	p.I161Nfs*3	ENST00000263377	NM_058243.2	161	ata/aAta	4/20	1	2	FACETS	0.686	0.604	0.774	0.686	0.604	0.774	SUBCLONAL	1	TRUE	1	0.512606264283735	2		704	432	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836816	151836816	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	125	692	0	ENST00000262189.6:c.14404G>A	p.Gly4802Arg	p.G4802R	ENST00000262189	NM_170606.2	4802	Ggg/Agg	56/59	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.512606264283735	2		692	459	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0023968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	194	1257	2	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.512606264283735	2		1259	525	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428410	49428411	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1284500089	NA	P-0023968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	132	774	0	ENST00000301067.7:c.10394dup	p.Pro3466ThrfsTer2	p.P3466Tfs*2	ENST00000301067	NM_003482.3	3465	gga/ggGa	36/54	1	2	FACETS	0.866	0.789	0.946	0.866	0.789	0.946	CLONAL	1	TRUE	1	0.512606264283735	2		774	595	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339776	116339776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367722737	NA	P-0023968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	78	564	1	ENST00000397752.3:c.638C>T	p.Ser213Leu	p.S213L	ENST00000397752	NM_000245.2	213	tCg/tTg	2/21	1	2	FACETS	0.633	0.558	0.713	0.633	0.558	0.713	SUBCLONAL	1	TRUE	1	0.512606264283735	2		565	481	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661663	227661664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0023968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	54	649	1	ENST00000305123.5:c.1790_1791dup	p.His598GlyfsTer39	p.H598Gfs*39	ENST00000305123	NM_005544.2	597	-/GG	1/2	1	2	FACETS	0.717	0.616	0.825	0.717	0.616	0.825	SUBCLONAL	1	TRUE	1	0.512606264283735	2		650	294	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551934	150551934	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	96	568	0	ENST00000369026.2:c.73A>G	p.Ser25Gly	p.S25G	ENST00000369026	NM_021960.4	25	Agc/Ggc	1/3	1	2	FACETS	0.92	0.826	1	0.92	0.826	1	CLONAL	1	TRUE	1	0.512606264283735	2		568	407	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981252	201981252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761284995	NA	P-0023968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	159	798	1	ENST00000359651.3:c.331C>T	p.Arg111Cys	p.R111C	ENST00000359651		111	Cgt/Tgt	2/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.512606264283735	2		799	554	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871259	35871259	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs750102278	NA	P-0023968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	136	584	0	ENST00000216797.5:c.914A>G	p.Tyr305Cys	p.Y305C	ENST00000216797	NM_020529.2	305	tAt/tGt	6/6	1	2	FACETS	0.992	0.907	1	0.992	0.907	1	CLONAL	1	TRUE	1	0.512606264283735	2		584	535	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610685	10610685	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs187892356	NA	P-0023968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	87	619	1	ENST00000171111.5:c.25G>A	p.Gly9Arg	p.G9R	ENST00000171111	NM_203500.1	9	Ggg/Agg	2/6	1	2	FACETS	0.84	0.748	0.937	0.84	0.748	0.937	CLONAL	1	TRUE	1	0.512606264283735	2		620	404	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299961	15299961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	131	729	1	ENST00000263388.2:c.1217G>A	p.Gly406Asp	p.G406D	ENST00000263388	NM_000435.2	406	gGc/gAc	8/33	1	2	FACETS	0.985	0.898	1	0.985	0.898	1	CLONAL	1	TRUE	1	0.512606264283735	2		730	519	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228608	36228608	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	128	868	0	ENST00000222270.7:c.7622A>G	p.Asp2541Gly	p.D2541G	ENST00000222270	NM_014727.1	2541	gAt/gGt	34/37	1	2	FACETS	0.959	0.873	1	0.959	0.873	1	CLONAL	1	TRUE	1	0.512606264283735	2		868	521	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142950047	142950047	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	40	638	0	ENST00000262992.4:c.2663A>G	p.Asn888Ser	p.N888S	ENST00000262992	NM_001101669.1	888	aAt/aGt	24/24	1	2	FACETS	0.382	0.317	0.453	0.382	0.317	0.453	SUBCLONAL	1	TRUE	1	0.512606264283735	2		638	409	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035240	6035240	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs757324104	NA	P-0023968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	108	628	0	ENST00000265849.7:c.828C>A	p.Cys276Ter	p.C276*	ENST00000265849	NM_000535.5	276	tgC/tgA	8/15	1	2	FACETS	0.943	0.851	1	0.943	0.851	1	CLONAL	1	TRUE	1	0.512606264283735	2		628	447	SUCCESS
AR	367	MSKCC	GRCh37	X	66943675	66943675	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	125	647	0	ENST00000374690.3:c.2755A>G	p.Thr919Ala	p.T919A	ENST00000374690	NM_000044.3	919	Acc/Gcc	8/8	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.512606264283735	2		647	450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0024139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	121	590	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.312620780227119	2		590	643	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0024139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	51	432	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.312620780227119	2		432	268	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685315	89685315	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1554897280	NA	P-0024139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	54	494	0	ENST00000371953.3:c.209+1G>A		p.X70_splice	ENST00000371953	NM_000314.4	70			1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.312620780227119	2		494	291	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626708	28626708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	79	561	0	ENST00000241453.7:c.588G>A	p.Trp196Ter	p.W196*	ENST00000241453	NM_004119.2	196	tgG/tgA	5/24	1	2	FACETS	0.852	0.75	0.962	0.852	0.75	0.962	CLONAL	1	TRUE	1	0.312620780227119	2		561	593	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437365	110437365	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	15	136	0	ENST00000375856.3:c.1036A>T	p.Ser346Cys	p.S346C	ENST00000375856	NM_003749.2	346	Agc/Tgc	1/2	1	2	FACETS	0.842	0.622	1	0.842	0.622	1	CLONAL	1	TRUE	1	0.312620780227119	2		136	114	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645820	215645820	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	71	603	0	ENST00000260947.4:c.778T>A	p.Leu260Ile	p.L260I	ENST00000260947	NM_000465.2	260	Tta/Ata	4/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.312620780227119	2		603	380	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	94	584	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.197566997223837	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	0	0.197566997223837	1		584	636	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	21	280	1	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	0.154316114310814	0	FACETS	0.958	0.754	1			1	CLONAL	2	FALSE	0	0.197566997223837	0		281	89	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177584	56177584	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368201444	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	84	470	2	ENST00000399503.3:c.2557C>T	p.Arg853Cys	p.R853C	ENST00000399503	NM_005921.1	853	Cgt/Tgt	14/20	1	2	FACETS	0.939	0.833	1	1	0.984	1	CLONAL	2	FALSE	1	0.197566997223837	2		472	453	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636794	8636794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	132	678	0	ENST00000356435.5:c.115G>A	p.Gly39Arg	p.G39R	ENST00000356435		39	Gga/Aga	2/35	1	2	FACETS	0.854	0.776	0.937	1	0.988	1	CLONAL	2	FALSE	1	0.197566997223837	2		678	782	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791757	42791757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568504941	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	19	782	0	ENST00000575354.2:c.643C>T	p.Arg215Trp	p.R215W	ENST00000575354	NM_015125.3	215	Cgg/Tgg	5/20	0.154316114310814	0	FACETS	0.308	0.233	0.397			1	SUBCLONAL	1	FALSE	0	0.197566997223837	0		782	501	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116263	209116263	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	20	421	0	ENST00000345146.2:c.13del	p.Ile5SerfsTer7	p.I5Sfs*7	ENST00000345146	NM_005896.2	5	Atc/tc	3/10	1	2	FACETS	0.637	0.487	0.812	0.637	0.487	0.812	SUBCLONAL	1	FALSE	1	0.197566997223837	2		421	318	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905873	50905873	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756829126	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	46	797	1	ENST00000440232.2:c.845C>T	p.Thr282Met	p.T282M	ENST00000440232	NM_002691.3	282	aCg/aTg	8/27	0.154316114310814	0	FACETS	1	0.871	1			1	CLONAL	1	FALSE	0	0.197566997223837	0		798	361	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421519	32421519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	68	630	0	ENST00000332351.3:c.1073C>T	p.Thr358Met	p.T358M	ENST00000332351	NM_024426.4	358	aCg/aTg	6/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.197566997223837	2		630	574	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458147	120458147	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1325403451	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	56	691	1	ENST00000256646.2:c.7198C>T	p.Arg2400Ter	p.R2400*	ENST00000256646	NM_024408.3	2400	Cga/Tga	34/34	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.197566997223837	2		692	411	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925441	114925441	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138649767	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	47	676	3	ENST00000543371.1:c.1519G>A	p.Ala507Thr	p.A507T	ENST00000543371	NM_001198531.1	507	Gcc/Acc	14/14	1	2	FACETS	0.891	0.752	1	0.891	0.752	1	CLONAL	1	FALSE	1	0.197566997223837	2		679	534	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725019	47725019	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs762488821	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	37	924	2	ENST00000449228.1:c.725del	p.Gly242AlafsTer48	p.G242Afs*48	ENST00000449228	NM_001127240.2	242	gGc/gc	4/4	0.154316114310814	0	FACETS	0.616	0.507	0.738			1	SUBCLONAL	1	FALSE	0	0.197566997223837	0		926	488	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965779	18965779	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1395016855	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	46	902	2	ENST00000262803.5:c.1357G>A	p.Val453Ile	p.V453I	ENST00000262803	NM_002911.3	453	Gta/Ata	10/24	0.154316114310814	0	FACETS	0.666	0.56	0.783			1	SUBCLONAL	1	FALSE	0	0.197566997223837	0		904	561	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830807	72830807	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	83	733	1	ENST00000268489.5:c.5774del	p.Gly1925ValfsTer72	p.G1925Vfs*72	ENST00000268489	NM_006885.3	1925	gGt/gt	9/10	0.197566997223837	1	FACETS	0.802	0.71	0.9	1	0.98	1	CLONAL	2	FALSE	0	0.197566997223837	1		734	472	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288965	33288965	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774538403	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	88	501	0	ENST00000374542.5:c.587C>T	p.Ala196Val	p.A196V	ENST00000374542	NM_001141970.1	196	gCg/gTg	3/8	1	2	FACETS	0.994	0.885	1	1	0.985	1	CLONAL	2	FALSE	1	0.197566997223837	2		501	448	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446160	49446160	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776768333	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	29	838	0	ENST00000301067.7:c.1306G>A	p.Glu436Lys	p.E436K	ENST00000301067	NM_003482.3	436	Gag/Aag	10/54	0.107915888195682	4	FACETS	0.821	0.659	1	0.411	0.329	0.504	INDETERMINATE	1	FALSE	2	0.197566997223837	4		838	428	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222293	2222293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763973302	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	65	856	5	ENST00000326181.6:c.577C>T	p.Arg193Trp	p.R193W	ENST00000326181	NM_032271.2	193	Cgg/Tgg	8/21	0.197566997223837	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	0	0.197566997223837	1		861	416	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11291110	11291110	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	45	648	0	ENST00000361445.4:c.2651C>T	p.Ala884Val	p.A884V	ENST00000361445	NM_004958.3	884	gCc/gTc	18/58	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	FALSE	1	0.197566997223837	2		648	419	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428598	78428598	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	44	587	3	ENST00000370768.2:c.1201del	p.Ser401AlafsTer2	p.S401Afs*2	ENST00000370768	NM_003902.3	401	Agc/gc	14/20	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	FALSE	1	0.197566997223837	2		590	349	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608364	43608364	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	91	914	1	ENST00000355710.3:c.1712A>T	p.Asp571Val	p.D571V	ENST00000355710	NM_020975.4	571	gAt/gTt	9/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.197566997223837	2		915	669	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134521	2134521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45517335	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	96	849	1	ENST00000219476.3:c.4298C>T	p.Ser1433Leu	p.S1433L	ENST00000219476	NM_000548.3	1433	tCg/tTg	34/42	0.197566997223837	1	FACETS	0.885	0.791	0.983	1	0.985	1	CLONAL	2	FALSE	0	0.197566997223837	1		850	495	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639839	3639839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775711964	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	59	779	2	ENST00000294008.3:c.3800G>A	p.Arg1267His	p.R1267H	ENST00000294008	NM_032444.2	1267	cGt/cAt	12/15	0.197566997223837	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	0	0.197566997223837	1		781	402	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781860	3781860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375557093	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	86	962	0	ENST00000262367.5:c.4807G>A	p.Ala1603Thr	p.A1603T	ENST00000262367	NM_004380.2	1603	Gcc/Acc	29/31	0.197566997223837	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	0	0.197566997223837	1		962	625	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808001	3808001	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	52	656	1	ENST00000262367.5:c.3418C>T	p.Arg1140Trp	p.R1140W	ENST00000262367	NM_004380.2	1140	Cgg/Tgg	18/31	0.197566997223837	1	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	FALSE	0	0.197566997223837	1		657	440	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485713	40485713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	86	647	3	ENST00000264657.5:c.1027G>A	p.Val343Ile	p.V343I	ENST00000264657	NM_139276.2	343	Gtc/Atc	10/24	0.197566997223837	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	0	0.197566997223837	1		650	579	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40497608	40497608	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1344978308	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	107	880	2	ENST00000264657.5:c.341G>A	p.Arg114His	p.R114H	ENST00000264657	NM_139276.2	114	cGc/cAc	4/24	0.197566997223837	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	0	0.197566997223837	1		882	774	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554621	63554621	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	23	689	0	ENST00000307078.5:c.118G>C	p.Val40Leu	p.V40L	ENST00000307078	NM_004655.3	40	Gtg/Ctg	2/11	0.197566997223837	1	FACETS	0.467	0.363	0.588	0.467	0.363	0.588	SUBCLONAL	1	FALSE	0	0.197566997223837	1		689	449	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220134	5220134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115469963	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	32	624	2	ENST00000357368.4:c.3581G>A	p.Arg1194His	p.R1194H	ENST00000357368	NM_002850.3	1194	cGc/cAc	22/38	0.154316114310814	0	FACETS	0.852	0.694	1			1	CLONAL	1	FALSE	0	0.197566997223837	0		626	305	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11172483	11172483	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1060504456	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	92	783	0	ENST00000358026.2:c.5031A>C	p.Glu1677Asp	p.E1677D	ENST00000358026	NM_001128849.1	1677	gaA/gaC	36/36	0.154316114310814	0	FACETS	1	0.967	1			1	CLONAL	1	FALSE	0	0.197566997223837	0		783	606	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210791	36210791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368286257	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	41	969	3	ENST00000222270.7:c.542G>A	p.Arg181Gln	p.R181Q	ENST00000222270	NM_014727.1	181	cGg/cAg	3/37	0.154316114310814	0	FACETS	0.657	0.547	0.779			1	SUBCLONAL	1	FALSE	0	0.197566997223837	0		972	507	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212401	36212401	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555495072	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	79	876	2	ENST00000222270.7:c.2152G>A	p.Glu718Lys	p.E718K	ENST00000222270	NM_014727.1	718	Gag/Aag	3/37	0.154316114310814	0	FACETS	1	0.965	1			1	CLONAL	1	FALSE	0	0.197566997223837	0		878	508	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607469	46607469	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201311893	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	114	921	2	ENST00000263734.3:c.1658C>T	p.Ala553Val	p.A553V	ENST00000263734	NM_001430.4	553	gCg/gTg	12/16	0.19761882169776	0	FACETS	0.786	0.71	0.866			1	SUBCLONAL	2	FALSE	0	0.197566997223837	0		923	589	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023600	31023600	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	28	673	0	ENST00000375687.4:c.3085G>A	p.Val1029Met	p.V1029M	ENST00000375687	NM_015338.5	1029	Gtg/Atg	13/13	0.154316114310814	0	FACETS	0.571	0.456	0.703			1	SUBCLONAL	1	FALSE	0	0.197566997223837	0		673	398	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747831	41747831	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	48	427	0	ENST00000226382.2:c.938T>C	p.Met313Thr	p.M313T	ENST00000226382	NM_003924.3	313	aTg/aCg	3/3	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.197566997223837	2		427	357	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131972843	131972843	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	48	469	0	ENST00000265335.6:c.3426A>T	p.Glu1142Asp	p.E1142D	ENST00000265335		1142	gaA/gaT	22/25	1	2	FACETS	0.791	0.673	0.921	1	0.966	1	CLONAL	2	FALSE	1	0.197566997223837	2		469	307	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433981	149433981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	46	911	3	ENST00000286301.3:c.2667G>A	p.Met889Ile	p.M889I	ENST00000286301	NM_005211.3	889	atG/atA	21/22	1	2	FACETS	0.807	0.679	0.949	0.807	0.679	0.949	CLONAL	1	FALSE	1	0.197566997223837	2		914	577	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683650	162683650	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	81	630	0	ENST00000366898.1:c.319C>A	p.Leu107Ile	p.L107I	ENST00000366898	NM_004562.2	107	Ctc/Atc	3/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.197566997223837	2		630	598	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884448	151884448	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773744238	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	79	467	0	ENST00000262189.6:c.4907C>T	p.Thr1636Met	p.T1636M	ENST00000262189	NM_170606.2	1636	aCg/aTg	33/59	1	2	FACETS	1	0.884	1	1	0.984	1	CLONAL	2	FALSE	1	0.197566997223837	2		467	400	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900065	151900065	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	86	617	0	ENST00000262189.6:c.4046G>A	p.Arg1349Gln	p.R1349Q	ENST00000262189	NM_170606.2	1349	cGa/cAa	26/59	1	2	FACETS	0.84	0.745	0.941	1	0.982	1	CLONAL	2	FALSE	1	0.197566997223837	2		617	518	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030503	47030503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs933666676	NA	P-0024219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	75	471	1	ENST00000377604.3:c.278C>T	p.Pro93Leu	p.P93L	ENST00000377604	NM_001204468.1	93	cCg/cTg	4/24	1	1	FACETS	0.992	0.883	1	1	0.987	1	CLONAL	3	FALSE	0	0.197566997223837	1		472	230	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	79	286	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.968	0.851	1	0.968	0.851	1	CLONAL	1	TRUE	1	0.221522237399378	2		286	737	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936103	178936103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519699	NA	P-0024420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	98	609	0	ENST00000263967.3:c.1645G>A	p.Asp549Asn	p.D549N	ENST00000263967	NM_006218.2	549	Gat/Aat	10/21	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.221522237399378	2		609	867	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948044	178948044	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	34	286	0	ENST00000263967.3:c.2816A>G	p.Asp939Gly	p.D939G	ENST00000263967	NM_006218.2	939	gAt/gGt	20/21	1	2	FACETS	0.699	0.571	0.843	0.699	0.571	0.843	SUBCLONAL	1	TRUE	1	0.221522237399378	2		286	439	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252955	36252955	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	66	424	0	ENST00000300305.3:c.407A>G	p.Asn136Ser	p.N136S	ENST00000300305		136	aAt/aGt	4/8	0.221522237399378	1	FACETS	0.906	0.787	1	0.906	0.787	1	CLONAL	1	TRUE	0	0.221522237399378	1		424	585	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0024579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	71	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.877	0.763	1	0.877	0.763	1	CLONAL	1	TRUE	1	0.16	2		436	1012	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520006	NA	P-0024579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	78	669	0	ENST00000269305.4:c.821T>G	p.Val274Gly	p.V274G	ENST00000269305	NM_001126112.2	274	gTt/gGt	8/11	1	2	FACETS	0.913	0.8	1	0.913	0.8	1	CLONAL	1	TRUE	1	0.16	2		669	1068	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0024579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	24	305	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	0.166867018869023	1	FACETS	0.721	0.564	0.901	0.721	0.564	0.901	CLONAL	1	TRUE	0	0.16	1		305	383	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591809	48591809	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0024579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	72	480	0	ENST00000342988.3:c.972T>A	p.Cys324Ter	p.C324*	ENST00000342988	NM_005359.5	324	tgT/tgA	9/12	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.16	2		480	776	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410151	139410151	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	59	574	1	ENST00000277541.6:c.1687T>A	p.Cys563Ser	p.C563S	ENST00000277541	NM_017617.3	563	Tgc/Agc	11/34	1	2	FACETS	0.862	0.739	0.995	0.862	0.739	0.995	CLONAL	1	TRUE	1	0.16	2		575	856	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0024749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	72	499	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.503	0.438	0.572	0.503	0.438	0.572	SUBCLONAL	1	TRUE	1	0.36	2		501	796	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0024749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	115	561	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.142151502462039	4	FACETS	0.811	0.729	0.898	0.405	0.364	0.449	INDETERMINATE	1	TRUE	2	0.36	4		562	1072	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881401	37881401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	40	597	0	ENST00000269571.5:c.2593G>A	p.Gly865Arg	p.G865R	ENST00000269571		865	Ggg/Agg	21/27	1	2	FACETS	0.287	0.238	0.343	0.287	0.238	0.343	SUBCLONAL	1	TRUE	1	0.36	2		597	774	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971048	21971062	+	inframe_deletion	In_Frame_Del	DEL	GCCGCGCCCCGGCCC	GCCGCGCCCCGGCCC	-	novel	NA	P-0024749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	49	148	0	ENST00000304494.5:c.296_310del	p.Arg99_Arg103del	p.R99_R103del	ENST00000304494	NM_000077.4	99	cGGGCCGGGGCGCGGCtg/ctg	2/3	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.36	2		148	251	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0024777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	196	537	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.776	0.717	0.836	1	0.991	1	SUBCLONAL	2	TRUE	1	0.228928473353174	2		537	1104	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641295	23641295	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	76	530	1	ENST00000261584.4:c.2180C>A	p.Ala727Asp	p.A727D	ENST00000261584	NM_024675.3	727	gCt/gAt	5/13	1	2	FACETS	0.583	0.509	0.663	0.583	0.509	0.663	SUBCLONAL	1	TRUE	1	0.228928473353174	2		531	1139	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157809	106157809	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	40	270	0	ENST00000380013.4:c.2710C>A	p.Gln904Lys	p.Q904K	ENST00000380013	NM_001127208.2	904	Caa/Aaa	3/11	1	2	FACETS	0.644	0.534	0.766	0.644	0.534	0.766	SUBCLONAL	1	TRUE	1	0.228928473353174	2		270	543	SUCCESS
APC	324	MSKCC	GRCh37	5	112176390	112176390	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	37	227	0	ENST00000257430.4:c.5099C>A	p.Ala1700Asp	p.A1700D	ENST00000257430	NM_000038.5	1700	gCt/gAt	16/16	1	2	FACETS	0.698	0.575	0.836	0.698	0.575	0.836	SUBCLONAL	1	TRUE	1	0.228928473353174	2		227	463	SUCCESS
APC	324	MSKCC	GRCh37	5	112179129	112179129	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	35	272	2	ENST00000257430.4:c.7838G>T	p.Arg2613Ile	p.R2613I	ENST00000257430	NM_000038.5	2613	aGa/aTa	16/16	1	2	FACETS	0.612	0.501	0.736	0.612	0.501	0.736	SUBCLONAL	1	TRUE	1	0.228928473353174	2		274	500	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266481	41266481	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	190	400	0	ENST00000349496.5:c.278G>A	p.Arg93Lys	p.R93K	ENST00000349496	NM_001904.3	93	aGg/aAg	4/15	0.228928473353174	63	FACETS	0.964	0.891	1			1	CLONAL	13	TRUE	NA	0.228928473353174	63		400	1057	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0024782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	66	579	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.314915065609908	5	FACETS	1	0.957	1	0.794	0.701	0.891	CLONAL	2	TRUE	2	0.470089834709428	5		579	201	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0024782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	228	1164	0				ENST00000310581	NM_198253.2	-/1132			0.321026629136136	6	FACETS	0.923	0.88	0.964	0.923	0.88	0.964	CLONAL	6	TRUE	0	0.470089834709428	6		1164	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253911	NA	P-0024782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	174	472	4	ENST00000269305.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000269305	NM_001126112.2	180	Gag/Aag	5/11	0.372910084170062	3	FACETS	0.974	0.915	1	0.974	0.915	1	CLONAL	3	TRUE	0	0.470089834709428	3		476	313	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0024782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	139	565	8	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	0.470089834709428	3	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	1	0.470089834709428	3		573	357	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132428	11132428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	204	571	1	ENST00000358026.2:c.2644G>A	p.Glu882Lys	p.E882K	ENST00000358026	NM_001128849.1	882	Gaa/Aaa	19/36	0.438811698863119	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	0	0.470089834709428	3		572	342	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280062	66280062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	48	382	1	ENST00000273854.3:c.1627C>T	p.Arg543Cys	p.R543C	ENST00000273854	NM_004439.5	543	Cgt/Tgt	7/18	0.171176961314471	3	FACETS	0.846	0.731	0.968	0.564	0.487	0.645	INDETERMINATE	2	TRUE	0	0.470089834709428	3		383	149	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955394	48955394	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886043247	NA	P-0024782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	66	269	1	ENST00000267163.4:c.1510C>T	p.Gln504Ter	p.Q504*	ENST00000267163	NM_000321.2	504	Cag/Tag	17/27	0.372910084170062	3	FACETS	1	0.968	1	0.826	0.739	0.913	CLONAL	2	TRUE	0	0.470089834709428	3		270	140	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120787	115120787	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	42	433	0	ENST00000257566.3:c.219G>C	p.Glu73Asp	p.E73D	ENST00000257566	NM_016569.3	73	gaG/gaC	1/8	0.470089834709428	3	FACETS	0.647	0.542	0.763	0.324	0.271	0.382	SUBCLONAL	1	TRUE	1	0.470089834709428	3		433	341	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530475	187530475	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0024782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	43	278	4	ENST00000441802.2:c.10069-1G>A		p.X3357_splice	ENST00000441802	NM_005245.3	3357			0.171176961314471	3	FACETS	0.807	0.689	0.931	0.538	0.459	0.621	INDETERMINATE	2	TRUE	0	0.470089834709428	3		282	140	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256342	16256342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	122	446	2	ENST00000375759.3:c.3607G>A	p.Glu1203Lys	p.E1203K	ENST00000375759	NM_015001.2	1203	Gaa/Aaa	11/15	0.438811698863119	3	FACETS	0.963	0.893	1	0.963	0.893	1	CLONAL	3	TRUE	0	0.470089834709428	3		448	222	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428461	78428461	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	84	409	7	ENST00000370768.2:c.1338G>C	p.Lys446Asn	p.K446N	ENST00000370768	NM_003902.3	446	aaG/aaC	14/20	0.438811698863119	3	FACETS	0.836	0.758	0.914	0.836	0.758	0.914	CLONAL	3	TRUE	0	0.470089834709428	3		416	176	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344572	118344572	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	80	483	5	ENST00000534358.1:c.2698C>T	p.Gln900Ter	p.Q900*	ENST00000534358	NM_005933.3	900	Cag/Tag	3/36	0.204733566648022	5	FACETS	0.918	0.816	1	0.612	0.544	0.684	INDETERMINATE	2	TRUE	2	0.470089834709428	5		488	316	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390773	118390773	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	90	341	4	ENST00000534358.1:c.11423C>T	p.Ser3808Leu	p.S3808L	ENST00000534358	NM_005933.3	3808	tCa/tTa	33/36	0.204733566648022	5	FACETS	0.857	0.772	0.944	0.857	0.772	0.944	INDETERMINATE	3	TRUE	2	0.470089834709428	5		345	254	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495457	56495457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1281265231	NA	P-0024782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	91	585	11	ENST00000267101.3:c.3647C>T	p.Ser1216Phe	p.S1216F	ENST00000267101	NM_001982.3	1216	tCc/tTc	28/28	0.470089834709428	3	FACETS	1	0.98	1	0.714	0.64	0.791	CLONAL	1	TRUE	1	0.470089834709428	3		596	335	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518112	103518112	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	58	314	9	ENST00000355739.4:c.2050G>A	p.Glu684Lys	p.E684K	ENST00000355739	NM_000123.3	684	Gaa/Aaa	9/15	0.372910084170062	3	FACETS	0.781	0.682	0.886	0.521	0.455	0.591	SUBCLONAL	2	TRUE	0	0.470089834709428	3		323	195	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653160	29653160	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	62	308	1	ENST00000356175.3:c.5095G>C	p.Glu1699Gln	p.E1699Q	ENST00000356175	NM_000267.3	1699	Gag/Cag	36/57	0.337434209595785	3	FACETS	1	0.971	1	0.714	0.625	0.808	CLONAL	1	TRUE	1	0.470089834709428	3		309	228	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264387	30264387	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	43	241	1	ENST00000322652.5:c.122C>G	p.Ser41Cys	p.S41C	ENST00000322652	NM_015355.2	41	tCc/tGc	1/16	0.337434209595785	3	FACETS	1	0.942	1	0.624	0.529	0.726	CLONAL	1	TRUE	1	0.470089834709428	3		242	181	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026974	48026974	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1411268654	NA	P-0024782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	57	374	1	ENST00000234420.5:c.1852C>G	p.Gln618Glu	p.Q618E	ENST00000234420	NM_000179.2	618	Cag/Gag	4/10	0.230151186509535	4	FACETS	1	0.922	1	1	0.922	1	INDETERMINATE	2	TRUE	2	0.470089834709428	4		375	166	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280134	142280134	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	104	554	5	ENST00000350721.4:c.1300C>G	p.Leu434Val	p.L434V	ENST00000350721	NM_001184.3	434	Ctc/Gtc	5/47	0.314915065609908	5	FACETS	0.889	0.808	0.972	0.889	0.808	0.972	CLONAL	3	TRUE	2	0.470089834709428	5		559	283	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32802989	32802989	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	121	527	0	ENST00000374899.4:c.887C>T	p.Ser296Phe	p.S296F	ENST00000374899	NM_018833.2	296	tCt/tTt	5/12	0.433979207040351	5	FACETS	0.956	0.87	1	0.637	0.58	0.698	CLONAL	2	TRUE	2	0.470089834709428	5		527	459	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891308	101891308	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0024782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	67	592	7	ENST00000374994.4:c.269C>G	p.Ser90Ter	p.S90*	ENST00000374994	NM_004612.2	90	tCa/tGa	2/9	0.171176961314471	3	FACETS	0.834	0.737	0.936	0.556	0.491	0.624	INDETERMINATE	2	TRUE	0	0.470089834709428	3		599	211	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468319	50468319	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	69	431	0	ENST00000331340.3:c.1554G>A	p.Met518Ile	p.M518I	ENST00000331340	NM_006060.4	518	atG/atA	8/8	0.179276738759953	5	FACETS	0.752	0.659	0.85	0.501	0.439	0.567	INDETERMINATE	2	TRUE	2	0.470089834709428	5		431	333	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0024782-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	102	579	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.318151003030127	4	FACETS	0.955	0.863	1	0.955	0.863	1	CLONAL	2	TRUE	2	0.439211386119618	4		579	350	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0024782-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	345	1164	0				ENST00000310581	NM_198253.2	-/1132			0.439211386119618	8	FACETS	1	0.987	1	1	0.987	1	CLONAL	7	TRUE	1	0.439211386119618	8		1164	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253911	NA	P-0024782-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	94	472	4	ENST00000269305.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000269305	NM_001126112.2	180	Gag/Aag	5/11	0.439211386119618	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.439211386119618	1		476	309	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0024782-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	227	565	8	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	0.331249856065097	3	FACETS	1	0.988	1	0.802	0.755	0.85	CLONAL	2	TRUE	0	0.439211386119618	3		573	524	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132428	11132428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024782-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	206	571	1	ENST00000358026.2:c.2644G>A	p.Glu882Lys	p.E882K	ENST00000358026	NM_001128849.1	882	Gaa/Aaa	19/36	0.331249856065097	3	FACETS	1	0.977	1	0.728	0.681	0.775	CLONAL	2	TRUE	0	0.439211386119618	3		572	524	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280062	66280062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024782-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	96	382	1	ENST00000273854.3:c.1627C>T	p.Arg543Cys	p.R543C	ENST00000273854	NM_004439.5	543	Cgt/Tgt	7/18	0.336242501138161	2	FACETS	0.854	0.773	0.936	0.854	0.773	0.936	CLONAL	2	TRUE	0	0.439211386119618	2		383	256	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955394	48955394	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886043247	NA	P-0024782-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	70	269	1	ENST00000267163.4:c.1510C>T	p.Gln504Ter	p.Q504*	ENST00000267163	NM_000321.2	504	Cag/Tag	17/27	0.331249856065097	3	FACETS	1	0.956	1	0.762	0.681	0.846	CLONAL	2	TRUE	0	0.439211386119618	3		270	170	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120787	115120787	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024782-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	57	433	0	ENST00000257566.3:c.219G>C	p.Glu73Asp	p.E73D	ENST00000257566	NM_016569.3	73	gaG/gaC	1/8	0.439211386119618	3	FACETS	0.808	0.695	0.929	0.404	0.347	0.465	CLONAL	1	TRUE	1	0.439211386119618	3		433	392	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530475	187530475	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0024782-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	70	278	4	ENST00000441802.2:c.10069-1G>A		p.X3357_splice	ENST00000441802	NM_005245.3	3357			0.336242501138161	2	FACETS	1	0.975	1	0.721	0.639	0.807	CLONAL	1	TRUE	0	0.439211386119618	2		282	221	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256342	16256342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024782-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	170	446	2	ENST00000375759.3:c.3607G>A	p.Glu1203Lys	p.E1203K	ENST00000375759	NM_015001.2	1203	Gaa/Aaa	11/15	0.331249856065097	3	FACETS	1	0.986	1	0.815	0.76	0.871	CLONAL	2	TRUE	0	0.439211386119618	3		448	386	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428461	78428461	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024782-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	119	409	7	ENST00000370768.2:c.1338G>C	p.Lys446Asn	p.K446N	ENST00000370768	NM_003902.3	446	aaG/aaC	14/20	0.331249856065097	3	FACETS	1	0.978	1	0.798	0.733	0.864	CLONAL	2	TRUE	0	0.439211386119618	3		416	276	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344572	118344572	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024782-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	72	483	5	ENST00000534358.1:c.2698C>T	p.Gln900Ter	p.Q900*	ENST00000534358	NM_005933.3	900	Cag/Tag	3/36	0.334415284279592	3	FACETS	0.959	0.841	1	0.479	0.42	0.542	CLONAL	1	TRUE	1	0.439211386119618	3		488	417	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390773	118390773	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024782-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	54	341	4	ENST00000534358.1:c.11423C>T	p.Ser3808Leu	p.S3808L	ENST00000534358	NM_005933.3	3808	tCa/tTa	33/36	0.334415284279592	3	FACETS	0.845	0.725	0.975	0.422	0.362	0.488	CLONAL	1	TRUE	1	0.439211386119618	3		345	355	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495457	56495457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1281265231	NA	P-0024782-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	144	585	11	ENST00000267101.3:c.3647C>T	p.Ser1216Phe	p.S1216F	ENST00000267101	NM_001982.3	1216	tCc/tTc	28/28	0.331249856065097	3	FACETS	0.769	0.705	0.835	0.513	0.47	0.557	SUBCLONAL	2	TRUE	0	0.439211386119618	3		596	520	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518112	103518112	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024782-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	113	314	9	ENST00000355739.4:c.2050G>A	p.Glu684Lys	p.E684K	ENST00000355739	NM_000123.3	684	Gaa/Aaa	9/15	0.331249856065097	3	FACETS	0.821	0.746	0.9	0.548	0.497	0.6	CLONAL	2	TRUE	0	0.439211386119618	3		323	382	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653160	29653160	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024782-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	121	308	1	ENST00000356175.3:c.5095G>C	p.Glu1699Gln	p.E1699Q	ENST00000356175	NM_000267.3	1699	Gag/Cag	36/57	0.20496894465827	5	FACETS	0.873	0.798	0.95			1	INDETERMINATE	3	TRUE	NA	0.439211386119618	5		309	349	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264387	30264387	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024782-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	32	241	1	ENST00000322652.5:c.122C>G	p.Ser41Cys	p.S41C	ENST00000322652	NM_015355.2	41	tCc/tGc	1/16	0.20496894465827	5	FACETS	0.983	0.802	1			1	INDETERMINATE	1	TRUE	NA	0.439211386119618	5		242	246	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026974	48026974	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1411268654	NA	P-0024782-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	42	374	1	ENST00000234420.5:c.1852C>G	p.Gln618Glu	p.Q618E	ENST00000234420	NM_000179.2	618	Cag/Gag	4/10	0.334415284279592	3	FACETS	0.785	0.659	0.924	0.393	0.329	0.462	CLONAL	1	TRUE	1	0.439211386119618	3		375	297	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280134	142280134	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024782-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	84	554	5	ENST00000350721.4:c.1300C>G	p.Leu434Val	p.L434V	ENST00000350721	NM_001184.3	434	Ctc/Gtc	5/47	0.318151003030127	4	FACETS	1	0.973	1	0.665	0.59	0.744	CLONAL	1	TRUE	2	0.439211386119618	4		559	414	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32802989	32802989	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024782-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	144	527	0	ENST00000374899.4:c.887C>T	p.Ser296Phe	p.S296F	ENST00000374899	NM_018833.2	296	tCt/tTt	5/12	0.318151003030127	4	FACETS	0.874	0.801	0.949	0.874	0.801	0.949	CLONAL	2	TRUE	2	0.439211386119618	4		527	540	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891308	101891308	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0024782-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	133	592	7	ENST00000374994.4:c.269C>G	p.Ser90Ter	p.S90*	ENST00000374994	NM_004612.2	90	tCa/tGa	2/9	0.334415284279592	3	FACETS	0.907	0.832	0.985	0.907	0.832	0.985	CLONAL	2	TRUE	1	0.439211386119618	3		599	407	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0024959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	61	495	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.256666683974671	3	FACETS	1	0.901	1	0.527	0.455	0.605	CLONAL	1	TRUE	1	0.256666683974671	3		495	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578259	7578259	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1567551903	NA	P-0024959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	128	486	0	ENST00000269305.4:c.590T>A	p.Val197Glu	p.V197E	ENST00000269305	NM_001126112.2	197	gTg/gAg	6/11	0.240809508416359	2	FACETS	0.907	0.825	0.992	0.907	0.825	0.992	CLONAL	2	TRUE	0	0.256666683974671	2		486	550	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851687	134851687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	39	347	0	ENST00000398015.3:c.1093G>A	p.Ala365Thr	p.A365T	ENST00000398015	NM_004441.4	365	Gca/Aca	5/16	0.256666683974671	4	FACETS	0.807	0.669	0.962	0.269	0.223	0.321	CLONAL	1	TRUE	1	0.256666683974671	4		347	473	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374379	81374379	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	54	401	0	ENST00000222390.5:c.683C>A	p.Ser228Ter	p.S228*	ENST00000222390	NM_000601.4	228	tCa/tAa	6/18	0.256666683974671	4	FACETS	1	0.936	1	0.392	0.335	0.454	CLONAL	1	TRUE	1	0.256666683974671	4		401	450	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447081	49447088	+	frameshift_variant	Frame_Shift_Del	DEL	ATCTTAGA	ATCTTAGA	T	novel	NA	P-0024959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	31	485	0	ENST00000301067.7:c.856_863delinsA	p.Lys287TrpfsTer15	p.K287Wfs*15	ENST00000301067	NM_003482.3	286	TCTAAGATg/Ag	7/54	0.256666683974671	3	FACETS	0.492	0.397	0.6	0.246	0.198	0.3	SUBCLONAL	1	TRUE	1	0.256666683974671	3		485	554	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348903	118349105	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGCAGTGCTGCAAGTAAGTGGGTGTTTCACTCTGAGATGTTGACCTCTCAACCATAAAGGTTGCTTATTTATCCCTAGTTTGTTGCAGAGATACATCAGGAAACTGAATGTGGTTGTAATTGAGTTGCAAGACTTGTTACAGTTAGATTTTGTGGTGTGGGCTGTGCTTAAATAAGAAATACTCTGGGGCCATGCTGTCATT	AAGCAGTGCTGCAAGTAAGTGGGTGTTTCACTCTGAGATGTTGACCTCTCAACCATAAAGGTTGCTTATTTATCCCTAGTTTGTTGCAGAGATACATCAGGAAACTGAATGTGGTTGTAATTGAGTTGCAAGACTTGTTACAGTTAGATTTTGTGGTGTGGGCTGTGCTTAAATAAGAAATACTCTGGGGCCATGCTGTCATT	-	novel	NA	P-0025176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	35	209	0	ENST00000534358.1:c.3558_3569+191del		p.X1186_splice	ENST00000534358	NM_005933.3	1186		5/36	0.326141806085661	5	FACETS	0.63	0.517	0.758			1	SUBCLONAL	1	TRUE	NA	0.46761601896973	5		209	404	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432085	121432085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1344788314	NA	P-0025176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	136	564	0	ENST00000257555.6:c.832C>T	p.Arg278Trp	p.R278W	ENST00000257555		278	Cgg/Tgg	4/10	0.471187898877739	1	FACETS	0.844	0.772	0.919	0.844	0.772	0.919	CLONAL	1	TRUE	0	0.46761601896973	1		564	528	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281905	49281905	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	172	658	0	ENST00000282018.3:c.952T>C	p.Ser318Pro	p.S318P	ENST00000282018	NM_020377.2	318	Tct/Cct	1/1	0.471187898877739	5	FACETS	1	0.975	1	0.288	0.264	0.312	CLONAL	1	TRUE	1	0.46761601896973	5		658	1088	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0025176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	416	549	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.27884313451151	3	FACETS	0.993	0.954	1	0.993	0.954	1	INDETERMINATE	3	TRUE	0	0.46761601896973	3		549	737	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627640	37627640	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	33	486	0	ENST00000447079.4:c.1555G>C	p.Glu519Gln	p.E519Q	ENST00000447079	NM_015083.1	519	Gaa/Caa	2/14	0.471187898877739	3	FACETS	0.267	0.216	0.324	0.089	0.072	0.108	SUBCLONAL	1	TRUE	0	0.46761601896973	3		486	653	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42788890	42789627	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCAGCGCGGCCTCCCGTGGCCTCGGCATGTTCGGTCAGTAGCGCCTGGGCCCTGGGACTGCAGGGGTCAAGGTGTCGGGGTGCTAAGTGCGGAGTAACGGTGGTGGGGGTATAGTAGGGGAGAGAACAGTAGAGGCAGAGTAAAGGGATGACGGGGAAAGTTACGGAGCTCGGCCGGGCCGAGTGGTTAGTGATGGCAGGTGGGAGTGTAGCGGAGTGGGGCGTATCTGGGGACAGCTGTGATGTTAAAGTGATGGGATGGCACAGGTCCGCTGTAATAGAAAGGTGAGGGGTGCAGAGTAACTGGCTCTGGAGCATGGGGTAGAATAGGAACAGCACGAGACCTGCTGGTCCTAGGGGAGGAGGCTTGGATTGGGTAGTGGGGCTAAGGACAGGGCTCAGGAAGCGAGTGAGGCACTGTTAGCTGAGATCAGAGTGACAGGCTGCAGTGTGTGGTGTAGTTTGCAGAGAGCGCGACACCTAAGAACCTGGAGGGTTGTGCACTGGGGAGGGGTTCAGGAGGGAGCAGGACCAAAGGACTGCCCTCCATTGTCTGCTGGGTCCCTTTTCCCCACCCCCCAGAAAAGAGGAGGCCTTGATGGGAAAGATCTTTGCAAAGAGAGGCACAGGTCTAAGTCCCTGGAGGCTTTTATATGGGGTTGGAGGGCCCAGCGGGTTTTCAGGGGTAAGGGACAGGGTCATCGTAGTCTTGAGTGCTCTTCAGTGCTGTCTTCGTGA	TCCAGCGCGGCCTCCCGTGGCCTCGGCATGTTCGGTCAGTAGCGCCTGGGCCCTGGGACTGCAGGGGTCAAGGTGTCGGGGTGCTAAGTGCGGAGTAACGGTGGTGGGGGTATAGTAGGGGAGAGAACAGTAGAGGCAGAGTAAAGGGATGACGGGGAAAGTTACGGAGCTCGGCCGGGCCGAGTGGTTAGTGATGGCAGGTGGGAGTGTAGCGGAGTGGGGCGTATCTGGGGACAGCTGTGATGTTAAAGTGATGGGATGGCACAGGTCCGCTGTAATAGAAAGGTGAGGGGTGCAGAGTAACTGGCTCTGGAGCATGGGGTAGAATAGGAACAGCACGAGACCTGCTGGTCCTAGGGGAGGAGGCTTGGATTGGGTAGTGGGGCTAAGGACAGGGCTCAGGAAGCGAGTGAGGCACTGTTAGCTGAGATCAGAGTGACAGGCTGCAGTGTGTGGTGTAGTTTGCAGAGAGCGCGACACCTAAGAACCTGGAGGGTTGTGCACTGGGGAGGGGTTCAGGAGGGAGCAGGACCAAAGGACTGCCCTCCATTGTCTGCTGGGTCCCTTTTCCCCACCCCCCAGAAAAGAGGAGGCCTTGATGGGAAAGATCTTTGCAAAGAGAGGCACAGGTCTAAGTCCCTGGAGGCTTTTATATGGGGTTGGAGGGCCCAGCGGGTTTTCAGGGGTAAGGGACAGGGTCATCGTAGTCTTGAGTGCTCTTCAGTGCTGTCTTCGTGA	-	novel	NA	P-0025176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	72	427	0	ENST00000575354.2:c.37_67+707del		p.X13_splice	ENST00000575354	NM_015125.3	13		1/20	0.416792873891553	3	FACETS	0.607	0.53	0.69			1	SUBCLONAL	1	TRUE	NA	0.46761601896973	3		427	626	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965173	25965173	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	96	550	0	ENST00000435504.4:c.4033G>C	p.Val1345Leu	p.V1345L	ENST00000435504		1345	Gta/Cta	13/13	0.471187898877739	5	FACETS	0.658	0.585	0.736	0.219	0.195	0.246	SUBCLONAL	1	TRUE	2	0.46761601896973	5		550	1062	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61724034	61724055	+	frameshift_variant	Frame_Shift_Del	DEL	TCAGAGTAAATAGTGTTACAAA	TCAGAGTAAATAGTGTTACAAA	-	novel	NA	P-0025176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	72	507	0	ENST00000401558.2:c.847_868del	p.Phe283GlnfsTer2	p.F283Qfs*2	ENST00000401558	NM_003400.3	283	TTTGTAACACTATTTACTCTGAca/ca	10/25	0.253911200468199	3	FACETS	0.593	0.518	0.674			1	INDETERMINATE	1	TRUE	NA	0.46761601896973	3		507	641	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467845	66467845	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	154	402	0	ENST00000273854.3:c.424G>C	p.Gly142Arg	p.G142R	ENST00000273854	NM_004439.5	142	Gga/Cga	3/18	0.471187898877739	3	FACETS	1	0.987	1	0.463	0.426	0.502	CLONAL	1	TRUE	0	0.46761601896973	3		402	585	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797286	32797286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	179	652	0	ENST00000374899.4:c.1823C>T	p.Ala608Val	p.A608V	ENST00000374899	NM_018833.2	608	gCt/gTt	11/12	0.471187898877739	4	FACETS	1	0.969	1	0.366	0.337	0.396	CLONAL	1	TRUE	1	0.46761601896973	4		652	1023	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015721	112015764	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTGCAGCCACCTGTGGAAACCCAGGGAACAGGACATGTTACAC	CCTGCAGCCACCTGTGGAAACCCAGGGAACAGGACATGTTACAC	-	novel	NA	P-0025176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	77	478	0	ENST00000368678.4:c.1111-33_1121del		p.X371_splice	ENST00000368678		371		11/13	0.240287455997227	3	FACETS	0.676	0.594	0.764	0.225	0.198	0.255	INDETERMINATE	1	TRUE	0	0.46761601896973	3		478	601	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	84	306	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.963	1			1	INDETERMINATE	1	TRUE	NA	0.814977940179897	2		306	182	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718671	190718671	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768246348	NA	P-0025221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	156	410	3	ENST00000441310.2:c.829C>T	p.Arg277Ter	p.R277*	ENST00000441310	NM_000534.4	277	Cga/Tga	8/13	1	2	FACETS	0.909	0.842	0.978	0.909	0.842	0.978	CLONAL	1	TRUE	1	0.814977940179897	2		413	421	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385053	31385053	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339280595	NA	P-0025221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	225	513	0	ENST00000328111.2:c.1438G>A	p.Val480Met	p.V480M	ENST00000328111	NM_006892.3	480	Gtg/Atg	14/23	0.796410602050164	3	FACETS	1	0.937	1	0.501	0.468	0.535	CLONAL	1	TRUE	1	0.814977940179897	3		513	775	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947841	178947841	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	155	420	0	ENST00000263967.3:c.2716G>T	p.Val906Leu	p.V906L	ENST00000263967	NM_006218.2	906	Gta/Tta	19/21	1	2	FACETS	0.961	0.89	1	0.961	0.89	1	CLONAL	1	TRUE	1	0.814977940179897	2		420	396	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	629	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.446569609230626	5	FACETS	0.976	0.941	1			1	CLONAL	3	TRUE	NA	0.488711974781708	5		436	1523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0025400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	366	534	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.488711974781708	2		534	701	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155052	55155052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	91	515	3	ENST00000257290.5:c.2761G>A	p.Ala921Thr	p.A921T	ENST00000257290	NM_006206.4	921	Gct/Act	20/23	0.341774876852852	4	FACETS	0.63	0.558	0.707	0.315	0.279	0.354	SUBCLONAL	1	TRUE	2	0.488711974781708	4		518	880	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953926	131953926	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	137	517	0	ENST00000265335.6:c.3329T>A	p.Val1110Asp	p.V1110D	ENST00000265335		1110	gTt/gAt	21/25	0.488711974781708	3	FACETS	0.818	0.744	0.896	0.409	0.372	0.448	CLONAL	1	TRUE	1	0.488711974781708	3		517	853	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922668	44922669	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0025400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	249	195	0	ENST00000377967.4:c.1529_1530insTC	p.Met510IlefsTer39	p.M510Ifs*39	ENST00000377967	NM_021140.2	510	atg/atTCg	16/29	0.472399868384863	2	FACETS	0.845	0.805	0.884			1	CLONAL	3	TRUE	NA	0.488711974781708	2		195	402	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0025403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	615	406	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.31682792917653	3	FACETS	0.927	0.894	0.959	0.927	0.894	0.959	CLONAL	3	TRUE	0	0.413183206508476	3		406	1292	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0025403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	292	704	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.413183206508476	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.413183206508476	1		705	823	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0025403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	139	321	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.413183206508476	2		321	583	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0025403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	186	511	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.413183206508476	1	FACETS	0.959	0.888	1	0.959	0.888	1	CLONAL	1	TRUE	0	0.413183206508476	1		511	745	SUCCESS
APC	324	MSKCC	GRCh37	5	112137018	112137018	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	225	503	0	ENST00000257430.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000257430	NM_000038.5	258	Gag/Tag	8/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.413183206508476	2		503	982	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428194	72428194	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0025403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	239	544	0	ENST00000477973.2:c.698C>G	p.Ser233Ter	p.S233*	ENST00000477973	NM_012234.5	233	tCa/tGa	3/4	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.413183206508476	2		544	1046	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178379	56178379	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	182	353	0	ENST00000399503.3:c.3352G>A	p.Glu1118Lys	p.E1118K	ENST00000399503	NM_005921.1	1118	Gag/Aag	14/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.413183206508476	2		353	654	SUCCESS
APC	324	MSKCC	GRCh37	5	112176396	112176396	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	103	270	0	ENST00000257430.4:c.5105G>C	p.Gly1702Ala	p.G1702A	ENST00000257430	NM_000038.5	1702	gGa/gCa	16/16	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.413183206508476	2		270	449	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970962	21970971	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGCGCAGG	CGCGCGCAGG	-	novel	NA	P-0025403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	537	588	0	ENST00000304494.5:c.387_396del	p.Tyr129Ter	p.Y129*	ENST00000304494	NM_000077.4	129	taCCTGCGCGCG/ta	2/3	0.413183206508476	2	FACETS	0.92	0.889	0.951	1	0.997	1	CLONAL	3	TRUE	0	0.413183206508476	2		588	942	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118379850	118379850	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0025469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	58	236	0	ENST00000534358.1:c.10836-1G>C		p.X3612_splice	ENST00000534358	NM_005933.3	3612			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		236	252	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0025471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	196	545	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.228749771315692	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.330454356708928	1		547	925	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724361	52724361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	97	390	1	ENST00000322088.6:c.1493G>A	p.Arg498His	p.R498H	ENST00000322088	NM_014225.5	498	cGc/cAc	12/15	0.330454356708928	2	FACETS	0.861	0.768	0.96	0.43	0.384	0.48	CLONAL	1	TRUE	0	0.330454356708928	2		391	682	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104264013	104264013	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	117	405	0	ENST00000369902.3:c.104A>G	p.His35Arg	p.H35R	ENST00000369902	NM_016169.3	35	cAc/cGc	1/12	0.330454356708928	1	FACETS	0.984	0.889	1	0.984	0.889	1	CLONAL	1	TRUE	0	0.330454356708928	1		405	601	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920487	50920487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762090110	NA	P-0025471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	308	484	1	ENST00000440232.2:c.3179G>A	p.Arg1060His	p.R1060H	ENST00000440232	NM_002691.3	1060	cGc/cAc	26/27	0.330454356708928	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.330454356708928	2		485	861	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	213	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.322223487520354	3	FACETS	1	0.989	1	0.646	0.605	0.688	INDETERMINATE	1	TRUE	1	0.807921456714678	3		436	573	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0025486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	200	543	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	0.807921456714678	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.807921456714678	1		543	293	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0025486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	382	579	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.771609014374014	3	FACETS	0.966	0.941	0.99	0.966	0.941	0.99	CLONAL	3	TRUE	0	0.807921456714678	3		579	458	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0025486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	255	484	1	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	0.807921456714678	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.807921456714678	1		485	326	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727916	41727916	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200904022	NA	P-0025486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	360	635	0	ENST00000301178.4:c.541G>T	p.Ala181Ser	p.A181S	ENST00000301178	NM_021913.4	181	Gcc/Tcc	4/20	0.246068480684385	2	FACETS	1	0.995	1	0.65	0.622	0.679	INDETERMINATE	1	TRUE	0	0.807921456714678	2		635	685	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057879	27057879	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	179	849	0	ENST00000324856.7:c.1587G>T	p.Gln529His	p.Q529H	ENST00000324856	NM_006015.4	529	caG/caT	3/20	0.807921456714678	1	FACETS	0.48	0.445	0.516	0.48	0.445	0.516	SUBCLONAL	1	TRUE	0	0.807921456714678	1		849	550	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107147	27107148	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0025486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	336	512	0	ENST00000324856.7:c.6759_6760del	p.Tyr2254ArgfsTer23	p.Y2254Rfs*23	ENST00000324856	NM_006015.4	2253	cTG/c	20/20	0.807921456714678	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.807921456714678	1		512	438	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042634	42042634	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	219	477	0	ENST00000219905.7:c.6830del	p.Pro2277LeufsTer58	p.P2277Lfs*58	ENST00000219905	NM_001164273.1	2277	Cct/ct	17/24	0.807921456714678	1	FACETS	0.948	0.901	0.993	0.948	0.901	0.993	CLONAL	1	TRUE	0	0.807921456714678	1		477	341	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023008	27023010	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs587779737	NA	P-0025606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	10	43	0	ENST00000324856.7:c.126_128del	p.Ala45del	p.A45del	ENST00000324856	NM_006015.4	38	gaGGCg/gag	1/20	1	2	FACETS	0.174	0.118	0.245	0.174	0.118	0.245	SUBCLONAL	1	TRUE	1	0.785029756791889	2		43	146	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641280	3641284	+	frameshift_variant	Frame_Shift_Del	DEL	CGCAC	CGCAC	T	novel	NA	P-0025606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	386	887	0	ENST00000294008.3:c.2355_2359delinsA	p.Cys786AsnfsTer33	p.C786Nfs*33	ENST00000294008	NM_032444.2	785	ctGTGCGaa/ctAaa	12/15	0.628322966132178	4	FACETS	1	0.989	1			1	CLONAL	1	TRUE	NA	0.785029756791889	4		887	1532	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451032	70451032	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	73	365	0	ENST00000373644.4:c.5872G>A	p.Glu1958Lys	p.E1958K	ENST00000373644	NM_030625.2	1958	Gaa/Aaa	12/12	1	2	FACETS	0.972	0.853	1	0.972	0.853	1	CLONAL	1	TRUE	1	0.335971106284434	2		365	447	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938029	76938029	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	99	474	1	ENST00000373344.5:c.2719C>T	p.Arg907Ter	p.R907*	ENST00000373344	NM_000489.3	907	Cga/Tga	9/35	1	2	FACETS	0.907	0.81	1	0.907	0.81	1	CLONAL	1	TRUE	1	0.335971106284434	2		475	650	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517994	8517994	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	75	308	0	ENST00000356435.5:c.1397G>A	p.Trp466Ter	p.W466*	ENST00000356435		466	tGg/tAg	10/35	0.335971106284434	1	FACETS	0.835	0.734	0.942	0.835	0.734	0.942	CLONAL	1	TRUE	0	0.335971106284434	1		308	445	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273929	10273929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	84	483	0	ENST00000330684.3:c.340G>A	p.Asp114Asn	p.D114N	ENST00000330684	NM_001134407.1	114	Gat/Aat	2/13	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.335971106284434	NA		483	414	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098441	11098441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060502062	NA	P-0025707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	39	166	0	ENST00000358026.2:c.959C>T	p.Pro320Leu	p.P320L	ENST00000358026	NM_001128849.1	320	cCc/cTc	6/36	1	2	FACETS	0.992	0.829	1	0.992	0.829	1	CLONAL	1	TRUE	1	0.335971106284434	2		166	234	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464433	120464433	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0025707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	74	298	0	ENST00000256646.2:c.5214-1G>A		p.X1738_splice	ENST00000256646	NM_024408.3	1738			1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.335971106284434	2		298	428	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924766	94924766	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1218922129	NA	P-0025707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	101	407	0	ENST00000536441.1:c.145-1G>A		p.X49_splice	ENST00000536441	NM_144665.3	49			1	2	FACETS	0.793	0.709	0.883	0.793	0.709	0.883	SUBCLONAL	1	TRUE	1	0.335971106284434	2		407	758	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999632	100999632	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	61	525	0	ENST00000325455.5:c.170G>T	p.Gly57Val	p.G57V	ENST00000325455	NM_001202474.3	57	gGg/gTg	1/8	1	2	FACETS	0.784	0.678	0.899	0.784	0.678	0.899	SUBCLONAL	1	TRUE	1	0.335971106284434	2		525	463	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426367	49426367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	109	532	1	ENST00000301067.7:c.12121C>T	p.Pro4041Ser	p.P4041S	ENST00000301067	NM_003482.3	4041	Ccc/Tcc	39/54	1	2	FACETS	0.983	0.884	1	0.983	0.884	1	CLONAL	1	TRUE	1	0.335971106284434	2		533	660	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639764	3639764	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779981907	NA	P-0025707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	75	427	0	ENST00000294008.3:c.3875C>T	p.Pro1292Leu	p.P1292L	ENST00000294008	NM_032444.2	1292	cCc/cTc	12/15	1	2	FACETS	0.95	0.835	1	0.95	0.835	1	CLONAL	1	TRUE	1	0.335971106284434	2		427	470	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474384	40474384	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	41	432	0	ENST00000264657.5:c.2017C>T	p.Leu673Phe	p.L673F	ENST00000264657	NM_139276.2	673	Ctc/Ttc	21/24	1	2	FACETS	0.438	0.364	0.52	0.438	0.364	0.52	SUBCLONAL	1	TRUE	1	0.335971106284434	2		432	557	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257576	19257576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	59	373	0	ENST00000162023.5:c.650G>A	p.Gly217Glu	p.G217E	ENST00000162023		217	gGg/gAg	10/13	1	2	FACETS	0.779	0.672	0.895	0.779	0.672	0.895	SUBCLONAL	1	TRUE	1	0.335971106284434	2		373	451	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031771	36031771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	50	289	2	ENST00000358208.4:c.1600G>A	p.Glu534Lys	p.E534K	ENST00000358208		534	Gag/Aag	12/12	1	2	FACETS	0.948	0.809	1	0.948	0.809	1	CLONAL	1	TRUE	1	0.335971106284434	2		291	314	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103730	47103730	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	113	387	0	ENST00000409792.3:c.6216A>C	p.Lys2072Asn	p.K2072N	ENST00000409792	NM_014159.6	2072	aaA/aaC	14/21	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.335971106284434	2		387	612	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165273	47165273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	111	365	0	ENST00000409792.3:c.853C>T	p.His285Tyr	p.H285Y	ENST00000409792	NM_014159.6	285	Cat/Tat	3/21	1	2	FACETS	0.982	0.884	1	0.982	0.884	1	CLONAL	1	TRUE	1	0.335971106284434	2		365	673	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672710	30672710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1429946970	NA	P-0025707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	95	510	1	ENST00000376406.3:c.4250C>T	p.Ser1417Phe	p.S1417F	ENST00000376406	NM_014641.2	1417	tCc/tTc	10/15	1	2	FACETS	0.85	0.758	0.949	0.85	0.758	0.949	CLONAL	1	TRUE	1	0.335971106284434	2		511	665	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372316	55372316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	41	302	2	ENST00000297316.4:c.1006C>T	p.Pro336Ser	p.P336S	ENST00000297316	NM_022454.3	336	Cct/Tct	2/2	1	2	FACETS	0.85	0.712	1	0.85	0.712	1	CLONAL	1	TRUE	1	0.335971106284434	2		304	287	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793224	139793224	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	49	348	0	ENST00000247668.2:c.32C>T	p.Ser11Phe	p.S11F	ENST00000247668	NM_021138.3	11	tCc/tTc	2/11	0.335971106284434	1	FACETS	0.602	0.511	0.702	0.602	0.511	0.702	SUBCLONAL	1	TRUE	0	0.335971106284434	1		348	403	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929079	44929080	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCC	novel	NA	P-0025707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	59	293	0	ENST00000377967.4:c.2182_2185dup	p.Glu729AlafsTer2	p.E729Afs*2	ENST00000377967	NM_021140.2	727	gtg/gTGCCtg	17/29	1	2	FACETS	0.852	0.736	0.979	0.852	0.736	0.979	CLONAL	1	TRUE	1	0.335971106284434	2		293	412	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411957	63411957	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	52	446	1	ENST00000330258.3:c.1210G>A	p.Asp404Asn	p.D404N	ENST00000330258	NM_152424.3	404	Gat/Aat	2/2	1	2	FACETS	0.713	0.608	0.828	0.713	0.608	0.828	SUBCLONAL	1	TRUE	1	0.335971106284434	2		447	434	SUCCESS
AR	367	MSKCC	GRCh37	X	66941694	66941694	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	59	424	0	ENST00000374690.3:c.2338C>T	p.Arg780Trp	p.R780W	ENST00000374690	NM_000044.3	780	Cgg/Tgg	6/8	1	2	FACETS	0.782	0.675	0.899	0.782	0.675	0.899	SUBCLONAL	1	TRUE	1	0.335971106284434	2		424	449	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	161	205	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.180239791628803	2	FACETS	1	0.986	1	0.641	0.594	0.688	INDETERMINATE	1	TRUE	0	0.59	2		205	426	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	49	993	1	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.180239791628803	3	FACETS	0.333	0.281	0.39	0.166	0.14	0.195	INDETERMINATE	1	TRUE	1	0.59	3		994	646	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	139	660	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.929	0.851	1	0.929	0.851	1	CLONAL	1	TRUE	1	0.59	2		663	507	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	180	528	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.59	2		528	511	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	189	247	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.59	2		248	566	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	271	701	6	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	0.59	2		707	860	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	105	611	9	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	1	2	FACETS	0.543	0.487	0.603	0.543	0.487	0.603	SUBCLONAL	1	TRUE	1	0.59	2		620	655	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798769	135798769	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	72	382	2	ENST00000298552.3:c.474del	p.Phe158LeufsTer9	p.F158Lfs*9	ENST00000298552	NM_001162426.1	158	ttT/tt	6/23	0.180239791628803	2	FACETS	0.517	0.453	0.586	0.259	0.226	0.293	INDETERMINATE	1	TRUE	0	0.59	2		384	472	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	142	278	0	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.872	0.799	0.948	0.872	0.799	0.948	CLONAL	1	TRUE	1	0.59	2		278	552	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641389	18641389	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1229278001	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	26	202	2	ENST00000266497.5:c.2393del	p.Asn798MetfsTer16	p.N798Mfs*16	ENST00000266497		796	ctA/ct	17/31	1	2	FACETS	0.343	0.272	0.423	0.343	0.272	0.423	SUBCLONAL	1	TRUE	1	0.59	2		204	257	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947865	178947865	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776932	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	84	424	3	ENST00000263967.3:c.2740G>A	p.Gly914Arg	p.G914R	ENST00000263967	NM_006218.2	914	Gga/Aga	19/21	0.180239791628803	2	FACETS	0.684	0.608	0.766	0.342	0.304	0.383	INDETERMINATE	1	TRUE	0	0.59	2		427	416	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112154	115112154	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	37	393	2	ENST00000257566.3:c.1586del	p.Gly529AlafsTer103	p.G529Afs*103	ENST00000257566	NM_016569.3	529	gGc/gc	7/8	0.180239791628803	3	FACETS	0.261	0.214	0.314	0.131	0.107	0.157	INDETERMINATE	1	TRUE	1	0.59	3		395	622	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738411	145738416	+	inframe_deletion	In_Frame_Del	DEL	GGTGCA	GGTGCA	-	rs548804317	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	35	484	0	ENST00000428558.2:c.2569_2574del	p.Cys857_Thr858del	p.C857_T858del	ENST00000428558	NM_004260.3	857	TGCACC/-	16/22	1	2	FACETS	0.2	0.164	0.242	0.2	0.164	0.242	SUBCLONAL	1	TRUE	1	0.59	2		484	592	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	32	455	2	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	1	2	FACETS	0.192	0.155	0.234	0.192	0.155	0.234	SUBCLONAL	1	TRUE	1	0.59	2		457	564	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	126	599	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.861	0.784	0.941	0.861	0.784	0.941	CLONAL	1	TRUE	1	0.59	2		599	496	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789591	3789591	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	46	356	0	ENST00000262367.5:c.4268del	p.Pro1423LeufsTer36	p.P1423Lfs*36	ENST00000262367	NM_004380.2	1423	cCt/ct	25/31	1	2	FACETS	0.268	0.225	0.316	0.268	0.225	0.316	SUBCLONAL	1	TRUE	1	0.59	2		356	581	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149728	202149728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	190	527	0	ENST00000358485.4:c.1173del	p.Ile392SerfsTer4	p.I392Sfs*4	ENST00000358485	NM_001080125.1	390	gCc/gc	8/9	1	2	FACETS	0.949	0.88	1	0.949	0.88	1	CLONAL	1	TRUE	1	0.59	2		527	679	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199469669	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	61	317	0	ENST00000374080.3:c.130G>T	p.Gly44Cys	p.G44C	ENST00000374080		44	Ggt/Tgt	2/45	1	1	FACETS	0.316	0.273	0.363	0.316	0.273	0.363	SUBCLONAL	1	TRUE	0	0.59	1		317	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	104	576	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	1	2	FACETS	0.382	0.341	0.425	0.382	0.341	0.425	SUBCLONAL	1	TRUE	1	0.59	2		576	923	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845901	156845901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769486223	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	214	626	1	ENST00000524377.1:c.1531G>A	p.Val511Met	p.V511M	ENST00000524377	NM_002529.3	511	Gtg/Atg	13/17	1	2	FACETS	0.918	0.856	0.983	0.918	0.856	0.983	CLONAL	1	TRUE	1	0.59	2		627	790	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244454	46244454	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs751704736	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	43	437	0	ENST00000334344.6:c.2552del	p.Pro851HisfsTer4	p.P851Hfs*4	ENST00000334344	NM_152641.2	850	Ccc/cc	15/21	0.180239791628803	3	FACETS	0.298	0.248	0.353	0.149	0.124	0.177	INDETERMINATE	1	TRUE	1	0.59	3		437	634	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696410	47696410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	58	604	1	ENST00000347630.2:c.413G>A	p.Arg138His	p.R138H	ENST00000347630	NM_001007230.1	138	cGt/cAt	6/11	1	2	FACETS	0.268	0.23	0.31	0.268	0.23	0.31	SUBCLONAL	1	TRUE	1	0.59	2		605	733	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	63	457	2	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	1	2	FACETS	0.375	0.324	0.43	0.375	0.324	0.43	SUBCLONAL	1	TRUE	1	0.59	2		459	570	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249887	110249887	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	28	324	1	ENST00000374672.4:c.788T>C	p.Val263Ala	p.V263A	ENST00000374672	NM_004235.4	263	gTg/gCg	3/5	0.180239791628803	2	FACETS	0.224	0.178	0.276	0.112	0.089	0.138	INDETERMINATE	1	TRUE	0	0.59	2		325	424	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142446	119142446	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs267602720	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	117	425	1	ENST00000264033.4:c.445C>T	p.Arg149Ter	p.R149*	ENST00000264033	NM_005188.3	149	Cga/Tga	3/16	1	2	FACETS	0.91	0.826	0.996	0.91	0.826	0.996	CLONAL	1	TRUE	1	0.59	2		426	436	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004238	150004239	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	139	405	0	ENST00000253339.5:c.1986dup	p.Gln663ThrfsTer5	p.Q663Tfs*5	ENST00000253339		662	-/A	3/7	0.180239791628803	3	FACETS	1	0.962	1	0.546	0.499	0.594	INDETERMINATE	1	TRUE	1	0.59	3		405	559	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	219	575	0	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	0.97	0.906	1	0.97	0.906	1	CLONAL	1	TRUE	1	0.59	2		575	765	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306553	41306553	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	44	449	1	ENST00000373198.4:c.1106del	p.Gly369ValfsTer28	p.G369Vfs*28	ENST00000373198	NM_133170.3	369	gGt/gt	7/32	0.3	1	FACETS	0.232	0.194	0.274	0.232	0.194	0.274	INDETERMINATE	1	TRUE	0	0.59	1		450	453	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911132	29911132	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	35	477	2	ENST00000376809.5:c.431G>A	p.Gly144Asp	p.G144D	ENST00000376809	NM_002116.7	144	gGc/gAc	3/8	0.180239791628803	3	FACETS	0.252	0.206	0.304	0.126	0.103	0.152	INDETERMINATE	1	TRUE	1	0.59	3		479	609	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263369	123263369	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	49	356	0	ENST00000358487.5:c.1374del	p.Met459CysfsTer23	p.M459Cfs*23	ENST00000358487	NM_000141.4	458	ccC/cc	10/18	1	2	FACETS	0.313	0.265	0.367	0.313	0.265	0.367	SUBCLONAL	1	TRUE	1	0.59	2		356	530	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	120	1178	0	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.554	0.501	0.611	0.554	0.501	0.611	SUBCLONAL	1	TRUE	1	0.59	2		1178	734	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572272	64572272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372468697	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	140	340	1	ENST00000312049.6:c.1367G>A	p.Arg456His	p.R456H	ENST00000312049	NM_130799.2	456	cGc/cAc	10/10	1	2	FACETS	0.895	0.82	0.974	0.895	0.82	0.974	CLONAL	1	TRUE	1	0.59	2		341	530	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910804	29910804	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	43	414	0	ENST00000376809.5:c.343+1G>A		p.X115_splice	ENST00000376809	NM_002116.7	115			0.180239791628803	3	FACETS	0.397	0.332	0.469	0.199	0.166	0.235	INDETERMINATE	1	TRUE	1	0.59	3		414	475	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212248	5212248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776677741	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	113	395	2	ENST00000357368.4:c.4783C>T	p.Arg1595Cys	p.R1595C	ENST00000357368	NM_002850.3	1595	Cgc/Tgc	32/38	1	2	FACETS	0.879	0.796	0.964	0.879	0.796	0.964	CLONAL	1	TRUE	1	0.59	2		397	436	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599271	28599272	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	64	694	0	ENST00000253063.3:c.721_722del	p.Pro241LysfsTer12	p.P241Kfs*12	ENST00000253063	NM_031459.4	239	agCCcc/agcc	5/10	1	2	FACETS	0.265	0.229	0.305	0.265	0.229	0.305	SUBCLONAL	1	TRUE	1	0.59	2		694	818	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138911	64138911	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1185256919	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	99	302	0	ENST00000334205.4:c.2281del	p.Ala761ProfsTer23	p.A761Pfs*23	ENST00000334205	NM_003942.2	760	Ggg/gg	17/17	1	2	FACETS	0.888	0.799	0.98	0.888	0.799	0.98	CLONAL	1	TRUE	1	0.59	2		302	378	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420063	49420063	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201628357	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	197	474	1	ENST00000301067.7:c.15686G>A	p.Arg5229His	p.R5229H	ENST00000301067	NM_003482.3	5229	cGc/cAc	48/54	0.180239791628803	3	FACETS	1	0.978	1	0.564	0.523	0.606	INDETERMINATE	1	TRUE	1	0.59	3		475	767	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109941	115109941	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	54	402	0	ENST00000257566.3:c.1937C>A	p.Pro646Gln	p.P646Q	ENST00000257566	NM_016569.3	646	cCg/cAg	8/8	0.180239791628803	3	FACETS	0.416	0.355	0.483	0.208	0.177	0.242	INDETERMINATE	1	TRUE	1	0.59	3		402	570	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724485	724485	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	126	444	0	ENST00000314574.4:c.1571C>A	p.Ser524Tyr	p.S524Y	ENST00000314574	NM_005433.3	524	tCc/tAc	12/12	0.180239791628803	3	FACETS	0.944	0.858	1	0.472	0.429	0.517	INDETERMINATE	1	TRUE	1	0.59	3		444	586	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366255	15366255	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	156	476	1	ENST00000263377.2:c.1900G>A	p.Val634Met	p.V634M	ENST00000263377	NM_058243.2	634	Gtg/Atg	10/20	1	2	FACETS	0.849	0.78	0.92	0.849	0.78	0.92	CLONAL	1	TRUE	1	0.59	2		477	623	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17389832	17389832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	228	665	3	ENST00000359435.4:c.965C>T	p.Ala322Val	p.A322V	ENST00000359435	NM_001033549.1	322	gCc/gTc	9/9	1	2	FACETS	0.945	0.883	1	0.945	0.883	1	CLONAL	1	TRUE	1	0.59	2		668	818	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803721	1803721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780313125	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	194	503	0	ENST00000260795.2:c.899C>T	p.Pro300Leu	p.P300L	ENST00000260795		300	cCg/cTg	6/17	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.59	2		503	651	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976689	55976689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747477930	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	166	478	0	ENST00000263923.4:c.1136C>T	p.Ala379Val	p.A379V	ENST00000263923	NM_002253.2	379	gCg/gTg	9/30	0.3	1	FACETS	0.735	0.679	0.792	0.735	0.679	0.792	INDETERMINATE	1	TRUE	0	0.59	1		478	540	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790905	89790905	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	161	372	0	ENST00000336032.3:c.292C>T	p.Arg98Ter	p.R98*	ENST00000336032	NM_006813.2	98	Cga/Tga	1/2	0.180239791628803	3	FACETS	1	0.984	1	0.632	0.583	0.683	INDETERMINATE	1	TRUE	1	0.59	3		372	559	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522202	157522202	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	222	483	1	ENST00000346085.5:c.4474G>T	p.Gly1492Cys	p.G1492C	ENST00000346085	NM_020732.3	1492	Ggc/Tgc	18/20	0.180239791628803	3	FACETS	0.792	0.742	0.843	0.792	0.742	0.843	INDETERMINATE	2	TRUE	1	0.59	3		484	615	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739431	145739431	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775127620	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	111	400	0	ENST00000428558.2:c.1939C>T	p.Arg647Cys	p.R647C	ENST00000428558	NM_004260.3	647	Cgc/Tgc	12/22	1	2	FACETS	0.765	0.691	0.842	0.765	0.691	0.842	SUBCLONAL	1	TRUE	1	0.59	2		400	492	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248100	59248100	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	29	125	0	ENST00000371222.2:c.643A>G	p.Met215Val	p.M215V	ENST00000371222	NM_002228.3	215	Atg/Gtg	1/1	1	2	FACETS	0.534	0.432	0.648	0.534	0.432	0.648	SUBCLONAL	1	TRUE	1	0.59	2		125	184	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198878	67198878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753540467	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	81	483	1	ENST00000312629.5:c.349C>T	p.Arg117Trp	p.R117W	ENST00000312629	NM_003952.2	117	Cgg/Tgg	5/15	1	2	FACETS	0.39	0.343	0.44	0.39	0.343	0.44	SUBCLONAL	1	TRUE	1	0.59	2		484	704	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244292	46244292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1035031192	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	51	388	1	ENST00000334344.6:c.2386G>A	p.Val796Ile	p.V796I	ENST00000334344	NM_152641.2	796	Gtc/Atc	15/21	0.180239791628803	3	FACETS	0.451	0.384	0.526	0.226	0.192	0.263	INDETERMINATE	1	TRUE	1	0.59	3		389	496	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257810	133257810	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	70	504	0	ENST00000320574.5:c.118T>A	p.Trp40Arg	p.W40R	ENST00000320574	NM_006231.2	40	Tgg/Agg	2/49	0.180239791628803	3	FACETS	0.41	0.357	0.468	0.205	0.178	0.234	INDETERMINATE	1	TRUE	1	0.59	3		504	749	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041478	14041478	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	107	321	0	ENST00000311895.7:c.2025G>T	p.Gln675His	p.Q675H	ENST00000311895	NM_005236.2	675	caG/caT	11/11	1	2	FACETS	0.928	0.839	1	0.928	0.839	1	CLONAL	1	TRUE	1	0.59	2		321	391	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29563005	29563005	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	79	517	0	ENST00000356175.3:c.3940T>G	p.Trp1314Gly	p.W1314G	ENST00000356175	NM_000267.3	1314	Tgg/Ggg	29/57	1	2	FACETS	0.501	0.442	0.565	0.501	0.442	0.565	SUBCLONAL	1	TRUE	1	0.59	2		517	534	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487619	38487619	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	50	552	0	ENST00000254066.5:c.149T>A	p.Val50Asp	p.V50D	ENST00000254066	NM_000964.3	50	gTt/gAt	2/9	1	2	FACETS	0.224	0.189	0.262	0.224	0.189	0.262	SUBCLONAL	1	TRUE	1	0.59	2		552	758	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211110	2211110	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	60	570	0	ENST00000398665.3:c.1367del	p.Pro456LeufsTer33	p.P456Lfs*33	ENST00000398665	NM_032482.2	455	tCc/tc	15/28	1	2	FACETS	0.286	0.245	0.33	0.286	0.245	0.33	SUBCLONAL	1	TRUE	1	0.59	2		570	712	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244163	5244163	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373884789	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	43	443	1	ENST00000357368.4:c.1319C>T	p.Ala440Val	p.A440V	ENST00000357368	NM_002850.3	440	gCg/gTg	11/38	1	2	FACETS	0.312	0.261	0.369	0.312	0.261	0.369	SUBCLONAL	1	TRUE	1	0.59	2		444	467	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250352	10250352	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	23	266	0	ENST00000340748.4:c.3900G>T	p.Gln1300His	p.Q1300H	ENST00000340748		1300	caG/caT	33/40	1	2	FACETS	0.252	0.196	0.316	0.252	0.196	0.316	SUBCLONAL	1	TRUE	1	0.59	2		266	310	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214870	36214870	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs200663900	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	77	644	2	ENST00000222270.7:c.3296G>C	p.Gly1099Ala	p.G1099A	ENST00000222270	NM_014727.1	1099	gGc/gCc	8/37	1	2	FACETS	0.333	0.292	0.377	0.333	0.292	0.377	SUBCLONAL	1	TRUE	1	0.59	2		646	784	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794869	42794869	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	108	371	0	ENST00000575354.2:c.1953del	p.Ala652ProfsTer76	p.A652Pfs*76	ENST00000575354	NM_015125.3	650	gCc/gc	10/20	1	2	FACETS	0.749	0.675	0.826	0.749	0.675	0.826	SUBCLONAL	1	TRUE	1	0.59	2		371	489	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798172	42798172	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	62	551	0	ENST00000575354.2:c.4126C>A	p.Leu1376Met	p.L1376M	ENST00000575354	NM_015125.3	1376	Ctg/Atg	17/20	1	2	FACETS	0.31	0.267	0.357	0.31	0.267	0.357	SUBCLONAL	1	TRUE	1	0.59	2		551	678	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212522479	212522479	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs978290380	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	73	401	0	ENST00000342788.4:c.1946G>T	p.Arg649Ile	p.R649I	ENST00000342788	NM_005235.2	649	aGa/aTa	16/28	1	2	FACETS	0.591	0.519	0.667	0.591	0.519	0.667	SUBCLONAL	1	TRUE	1	0.59	2		401	419	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610572	52610573	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	96	460	0	ENST00000394830.3:c.3600dup	p.Met1201HisfsTer23	p.M1201Hfs*23	ENST00000394830	NM_018313.4	1200	-/C	23/30	0.590495416373876	2	FACETS	0.597	0.533	0.665	0.299	0.266	0.333	SUBCLONAL	1	TRUE	0	0.59	2		460	545	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52677263	52677263	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	73	486	2	ENST00000394830.3:c.995+1G>A		p.X332_splice	ENST00000394830	NM_018313.4	332			0.590495416373876	2	FACETS	0.355	0.31	0.404	0.178	0.155	0.202	SUBCLONAL	1	TRUE	0	0.59	2		488	697	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444666	187444666	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	169	295	0	ENST00000232014.4:c.1561A>G	p.Asn521Asp	p.N521D	ENST00000232014	NM_001130845.1	521	Aat/Gat	7/10	0.180239791628803	2	FACETS	1	0.989	1	0.677	0.63	0.726	INDETERMINATE	1	TRUE	0	0.59	2		295	423	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753180	57753180	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	87	261	0	ENST00000274289.3:c.836del	p.Pro279HisfsTer14	p.P279Hfs*14	ENST00000274289	NM_006622.3	279	cCa/ca	7/14	1	2	FACETS	0.835	0.746	0.93	0.835	0.746	0.93	CLONAL	1	TRUE	1	0.59	2		261	353	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80074634	80074634	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	59	432	0	ENST00000265081.6:c.2414C>A	p.Ala805Asp	p.A805D	ENST00000265081	NM_002439.4	805	gCt/gAt	17/24	1	2	FACETS	0.336	0.288	0.387	0.336	0.288	0.387	SUBCLONAL	1	TRUE	1	0.59	2		432	596	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912176	29912176	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	15	135	0	ENST00000376809.5:c.895+2T>C		p.X299_splice	ENST00000376809	NM_002116.7	299			0.180239791628803	3	FACETS	0.364	0.267	0.48	0.182	0.133	0.24	INDETERMINATE	1	TRUE	1	0.59	3		135	181	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741415	145741415	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	81	633	0	ENST00000428558.2:c.1088A>G	p.Tyr363Cys	p.Y363C	ENST00000428558	NM_004260.3	363	tAc/tGc	5/22	1	2	FACETS	0.332	0.291	0.375	0.332	0.291	0.375	SUBCLONAL	1	TRUE	1	0.59	2		633	828	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520328	176520328	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200070761	NA	P-0025864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1202	205	540	0	ENST00000292408.4:c.1247G>A	p.Arg416Gln	p.R416Q	ENST00000292408	NM_213647.1	416	cGa/cAa	9/18	0.830851124539498	3	FACETS	0.497	0.459	0.536	0.248	0.229	0.268	SUBCLONAL	1	TRUE	1	0.830128766130451	3		540	1407	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264306	16264306	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0025864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	472	389	0	ENST00000375759.3:c.10510-1G>T		p.X3504_splice	ENST00000375759	NM_015001.2	3504			0.797452189282257	2	FACETS	0.969	0.944	0.992	0.969	0.944	0.992	CLONAL	2	TRUE	0	0.830128766130451	2		389	587	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858884	89858884	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375895456	NA	P-0025864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	192	608	1	ENST00000389301.3:c.1078C>T	p.Arg360Cys	p.R360C	ENST00000389301	NM_000135.2	360	Cgc/Tgc	12/43	0.830851124539498	1	FACETS	0.451	0.419	0.483	0.451	0.419	0.483	SUBCLONAL	1	TRUE	0	0.830128766130451	1		609	600	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984389	72984389	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	60	533	0	ENST00000268489.5:c.3195G>C	p.Glu1065Asp	p.E1065D	ENST00000268489	NM_006885.3	1065	gaG/gaC	3/10	0.175347865673255	3	FACETS	0.922	0.794	1	0.461	0.397	0.53	CLONAL	1	TRUE	1	0.25	3		533	586	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517903	187517903	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	45	506	0	ENST00000441802.2:c.12791C>T	p.Ser4264Leu	p.S4264L	ENST00000441802	NM_005245.3	4264	tCa/tTa	25/27	0.175347865673255	3	FACETS	0.74	0.622	0.872	0.37	0.311	0.436	SUBCLONAL	1	TRUE	1	0.25	3		506	547	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873999	151873999	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	29	527	0	ENST00000262189.6:c.8539G>A	p.Asp2847Asn	p.D2847N	ENST00000262189	NM_170606.2	2847	Gat/Aat	38/59	1	2	FACETS	0.532	0.427	0.652	0.532	0.427	0.652	SUBCLONAL	1	TRUE	1	0.25	2		527	436	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563396	87563396	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	43	599	0	ENST00000277120.3:c.1784A>G	p.Asp595Gly	p.D595G	ENST00000277120		595	gAc/gGc	16/19	0.232484859476718	0	FACETS	0.462	0.386	0.547			1	SUBCLONAL	1	TRUE	0	0.25	0		599	558	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744048	41744048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376355256	NA	P-0026162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	162	598	1	ENST00000301178.4:c.983C>T	p.Thr328Met	p.T328M	ENST00000301178	NM_021913.4	328	aCg/aTg	7/20	1	2	FACETS	0.948	0.874	1	0.948	0.874	1	CLONAL	1	TRUE	1	0.560371364567911	2		599	610	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278061	18278061	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519801	NA	P-0026162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	220	720	0	ENST00000222254.8:c.1681A>G	p.Asn561Asp	p.N561D	ENST00000222254	NM_005027.3	561	Aac/Gac	13/16	1	2	FACETS	0.983	0.917	1	0.983	0.917	1	CLONAL	1	TRUE	1	0.560371364567911	2		720	799	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457251	89457252	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	127	419	0	ENST00000336596.2:c.1738dup	p.Arg580LysfsTer19	p.R580Kfs*19	ENST00000336596	NM_005233.5	578	gaa/gAaa	9/17	NA	2	FACETS	0.83	0.755	0.908			1	INDETERMINATE	1	TRUE	NA	0.560371364567911	2		419	546	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900823	114900953	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGCATCTTAGAAAATCCAGGTGAGAGGCTGTGGCCAAGGGAACCCACGGGCCCGGTGCTCTGAAGCCCTGGGCTGCTGGAACCGGCTTGACGGTGTCTTTCTCTGTTCTCCTCCCCACAGTCTAACAAAGT	TGCATCTTAGAAAATCCAGGTGAGAGGCTGTGGCCAAGGGAACCCACGGGCCCGGTGCTCTGAAGCCCTGGGCTGCTGGAACCGGCTTGACGGTGTCTTTCTCTGTTCTCCTCCCCACAGTCTAACAAAGT	-	novel	NA	P-0026162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	124	68	0	ENST00000543371.1:c.553-120_563del		p.X185_splice	ENST00000543371	NM_001198531.1	185		6/14	1	2	FACETS	1	0.984	1	1	0.993	1	CLONAL	2	TRUE	1	0.560371364567911	2		68	187	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934603	9934603	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	139	509	0	ENST00000330684.3:c.1552C>A	p.Arg518Ser	p.R518S	ENST00000330684	NM_001134407.1	518	Cgt/Agt	7/13	1	2	FACETS	0.902	0.825	0.982	0.902	0.825	0.982	CLONAL	1	TRUE	1	0.560371364567911	2		509	550	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976402	25976402	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0026162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	169	456	0	ENST00000435504.4:c.1142+1G>C		p.X381_splice	ENST00000435504		381			0.286038522539441	3	FACETS	0.938	0.864	1	0.469	0.432	0.508	INDETERMINATE	1	TRUE	1	0.560371364567911	3		456	823	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022332	31022332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778061	NA	P-0026213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	100	341	1	ENST00000375687.4:c.1817G>A	p.Arg606Gln	p.R606Q	ENST00000375687	NM_015338.5	606	cGg/cAg	13/13	1	2	FACETS	0.969	0.872	1	0.969	0.872	1	CLONAL	1	TRUE	1	0.522438456006413	2		342	395	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896552	78896552	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	141	509	0	ENST00000306801.3:c.2549T>A	p.Val850Asp	p.V850D	ENST00000306801	NM_020761.2	850	gTc/gAc	22/34	1	2	FACETS	0.823	0.752	0.897	0.823	0.752	0.897	CLONAL	1	TRUE	1	0.522438456006413	2		509	656	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412381	63412381	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs977145718	NA	P-0026213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	130	635	0	ENST00000330258.3:c.786G>A	p.Met262Ile	p.M262I	ENST00000330258	NM_152424.3	262	atG/atA	2/2	1	2	FACETS	0.834	0.759	0.912	0.834	0.759	0.912	CLONAL	1	TRUE	1	0.522438456006413	2		635	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0026217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	228	1047	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.318670706234926	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.333060712084847	1		1049	819	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338671	70338671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	135	515	1	ENST00000374080.3:c.67G>T	p.Asp23Tyr	p.D23Y	ENST00000374080		23	Gat/Tat	1/45	0.281919364248762	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.333060712084847	1		516	624	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416979	416979	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	35	454	0	ENST00000399788.2:c.3571C>A	p.Leu1191Ile	p.L1191I	ENST00000399788	NM_001042603.1	1191	Ctt/Att	23/28	1	2	FACETS	0.437	0.358	0.526	0.437	0.358	0.526	SUBCLONAL	1	TRUE	1	0.333060712084847	2		454	481	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988382	41988382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774833703	NA	P-0026217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	41	611	2	ENST00000219905.7:c.1174G>A	p.Glu392Lys	p.E392K	ENST00000219905	NM_001164273.1	392	Gaa/Aaa	3/24	0.281919364248762	1	FACETS	0.369	0.307	0.438	0.369	0.307	0.438	SUBCLONAL	1	TRUE	0	0.333060712084847	1		613	556	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988800	41988800	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	41	603	0	ENST00000219905.7:c.1592G>T	p.Arg531Ile	p.R531I	ENST00000219905	NM_001164273.1	531	aGa/aTa	3/24	0.281919364248762	1	FACETS	0.384	0.32	0.456	0.384	0.32	0.456	SUBCLONAL	1	TRUE	0	0.333060712084847	1		603	534	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858349	9858349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775756583	NA	P-0026217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	40	360	0	ENST00000330684.3:c.3052G>A	p.Val1018Met	p.V1018M	ENST00000330684	NM_001134407.1	1018	Gtg/Atg	13/13	1	2	FACETS	0.509	0.423	0.605	0.509	0.423	0.605	SUBCLONAL	1	TRUE	1	0.333060712084847	2		360	472	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122996	7122996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377722635	NA	P-0026217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	125	639	1	ENST00000302850.5:c.3263G>A	p.Arg1088His	p.R1088H	ENST00000302850	NM_000208.2	1088	cGc/cAc	18/22	0.333060712084847	1	FACETS	0.971	0.881	1	0.971	0.881	1	CLONAL	1	TRUE	0	0.333060712084847	1		640	644	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469996	25469996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	54	525	2	ENST00000264709.3:c.1046C>T	p.Ser349Leu	p.S349L	ENST00000264709	NM_175629.2	349	tCg/tTg	9/23	0.281919364248762	1	FACETS	0.437	0.373	0.508	0.437	0.373	0.508	SUBCLONAL	1	TRUE	0	0.333060712084847	1		527	618	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121031	29121031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876661085	NA	P-0026217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	59	639	1	ENST00000328354.6:c.526G>A	p.Gly176Arg	p.G176R	ENST00000328354	NM_007194.3	176	Ggg/Agg	4/15	0.281919364248762	1	FACETS	0.47	0.404	0.542	0.47	0.404	0.542	SUBCLONAL	1	TRUE	0	0.333060712084847	1		640	628	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0026217-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	121	1047	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.23778421501983	2	FACETS	0.868	0.79	0.948	0.868	0.79	0.948	CLONAL	2	TRUE	0	0.323533134803238	2		1049	431	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338671	70338671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026217-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	66	515	1	ENST00000374080.3:c.67G>T	p.Asp23Tyr	p.D23Y	ENST00000374080		23	Gat/Tat	1/45	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.323533134803238	2		516	296	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122996	7122996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377722635	NA	P-0026217-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	82	639	1	ENST00000302850.5:c.3263G>A	p.Arg1088His	p.R1088H	ENST00000302850	NM_000208.2	1088	cGc/cAc	18/22	0.259031218989493	2	FACETS	1	0.977	1	0.718	0.638	0.802	CLONAL	1	TRUE	0	0.323533134803238	2		640	353	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469996	25469996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026217-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	46	525	2	ENST00000264709.3:c.1046C>T	p.Ser349Leu	p.S349L	ENST00000264709	NM_175629.2	349	tCg/tTg	9/23	0.284732564886088	3	FACETS	0.925	0.782	1	0.463	0.391	0.542	CLONAL	1	TRUE	1	0.323533134803238	3		527	357	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121031	29121031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876661085	NA	P-0026217-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	109	639	1	ENST00000328354.6:c.526G>A	p.Gly176Arg	p.G176R	ENST00000328354	NM_007194.3	176	Ggg/Agg	4/15	0.265270648968438	4	FACETS	0.818	0.737	0.903	0.818	0.737	0.903	CLONAL	2	TRUE	2	0.323533134803238	4		640	545	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807294	3807294	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026217-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	25	488	0	ENST00000262367.5:c.3693del	p.Asn1232IlefsTer18	p.N1232Ifs*18	ENST00000262367	NM_004380.2	1231	caG/ca	19/31	1	2	FACETS	0.365	0.287	0.455	0.365	0.287	0.455	SUBCLONAL	1	TRUE	1	0.323533134803238	2		488	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576870	7576870	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs876659384	NA	P-0026247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	247	334	0	ENST00000269305.4:c.976G>T	p.Glu326Ter	p.E326*	ENST00000269305	NM_001126112.2	326	Gaa/Taa	9/11	0.49271414874866	3	FACETS	0.925	0.88	0.97	0.925	0.88	0.97	CLONAL	3	TRUE	0	0.526494182867016	3		334	427	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554166	63554166	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	243	349	0	ENST00000307078.5:c.573G>C	p.Leu191Phe	p.L191F	ENST00000307078	NM_004655.3	191	ttG/ttC	2/11	0.49271414874866	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	3	TRUE	0	0.526494182867016	3		349	384	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979518	55979518	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	72	234	0	ENST00000263923.4:c.929C>G	p.Ser310Cys	p.S310C	ENST00000263923	NM_002253.2	310	tCc/tGc	7/30	0.358121380273554	4	FACETS	1	0.934	1	0.548	0.481	0.619	CLONAL	1	TRUE	2	0.526494182867016	4		234	381	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151833985	151833985	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	82	283	0	ENST00000262189.6:c.14668T>C	p.Phe4890Leu	p.F4890L	ENST00000262189	NM_170606.2	4890	Ttt/Ctt	59/59	0.403425459775775	5	FACETS	1	0.946	1	0.374	0.33	0.42	CLONAL	1	TRUE	2	0.526494182867016	5		283	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576870	7576870	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs876659384	NA	P-0026247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	398	334	0	ENST00000269305.4:c.976G>T	p.Glu326Ter	p.E326*	ENST00000269305	NM_001126112.2	326	Gaa/Taa	9/11	0.307650748742446	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	0	0.307650748742446	3		334	921	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554166	63554166	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	484	349	0	ENST00000307078.5:c.573G>C	p.Leu191Phe	p.L191F	ENST00000307078	NM_004655.3	191	ttG/ttC	2/11	0.307650748742446	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	4	TRUE	0	0.307650748742446	4		349	1015	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979518	55979518	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	107	234	0	ENST00000263923.4:c.929C>G	p.Ser310Cys	p.S310C	ENST00000263923	NM_002253.2	310	tCc/tGc	7/30	0.307650748742446	3	FACETS	0.933	0.836	1	0.467	0.418	0.518	CLONAL	1	TRUE	1	0.307650748742446	3		234	860	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151833985	151833985	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	86	283	0	ENST00000262189.6:c.14668T>C	p.Phe4890Leu	p.F4890L	ENST00000262189	NM_170606.2	4890	Ttt/Ctt	59/59	0.307650748742446	6	FACETS	0.716	0.631	0.808	0.143	0.126	0.162	SUBCLONAL	1	TRUE	1	0.307650748742446	6		283	1261	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	166	406	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.444248561056431	1	FACETS	0.998	0.926	1	0.998	0.926	1	CLONAL	1	TRUE	0	0.525919364755662	1		406	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577595	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0026503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	202	285	0	ENST00000269305.4:c.686_687del	p.Cys229TyrfsTer10	p.C229Yfs*10	ENST00000269305	NM_001126112.2	229	tGT/t	7/11	0.365463751728823	2	FACETS	1	0.991	1	0.707	0.661	0.755	CLONAL	1	TRUE	0	0.525919364755662	2		285	543	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203563	108203563	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	36	469	0	ENST00000278616.4:c.7863G>C	p.Glu2621Asp	p.E2621D	ENST00000278616	NM_000051.3	2621	gaG/gaC	53/63	0.401039442177082	4	FACETS	0.382	0.313	0.459	0.191	0.156	0.23	SUBCLONAL	1	TRUE	2	0.525919364755662	4		469	547	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961005	18961005	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	62	671	1	ENST00000262803.5:c.583G>T	p.Gly195Cys	p.G195C	ENST00000262803	NM_002911.3	195	Ggc/Tgc	4/24	0.365463751728823	2	FACETS	0.365	0.315	0.42	0.182	0.157	0.21	SUBCLONAL	1	TRUE	0	0.525919364755662	2		672	646	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750939	128750941	+	inframe_deletion	In_Frame_Del	DEL	TCG	TCG	-	novel	NA	P-0026503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	169	412	0	ENST00000377970.2:c.478_480del	p.Val160del	p.V160del	ENST00000377970	NM_002467.4	159	cTCGtc/ctc	2/3	0.383656649426267	4	FACETS	0.771	0.712	0.832	0.771	0.712	0.832	SUBCLONAL	2	TRUE	2	0.525919364755662	4		412	636	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519886	NA	P-0026537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	123	306	0	ENST00000349496.5:c.97T>C	p.Ser33Pro	p.S33P	ENST00000349496	NM_001904.3	33	Tct/Cct	3/15	0.408993739227294	4	FACETS	0.939	0.856	1	0.939	0.856	1	CLONAL	2	TRUE	2	0.451477625675127	4		306	421	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699369	47699369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	175	469	0	ENST00000347630.2:c.139G>A	p.Glu47Lys	p.E47K	ENST00000347630	NM_001007230.1	47	Gaa/Aaa	4/11	0.451477625675127	3	FACETS	0.982	0.912	1	0.982	0.912	1	CLONAL	2	TRUE	1	0.451477625675127	3		469	484	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696444	47696444	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	88	490	0	ENST00000347630.2:c.379C>T	p.Gln127Ter	p.Q127*	ENST00000347630	NM_001007230.1	127	Caa/Taa	6/11	0.451477625675127	3	FACETS	0.969	0.862	1	0.485	0.431	0.542	CLONAL	1	TRUE	1	0.451477625675127	3		490	493	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675190	30675190	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	96	606	1	ENST00000376406.3:c.3055A>T	p.Arg1019Trp	p.R1019W	ENST00000376406	NM_014641.2	1019	Agg/Tgg	9/15	1	2	FACETS	0.905	0.81	1	0.905	0.81	1	CLONAL	1	TRUE	1	0.451477625675127	2		607	470	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913396	NA	P-0026673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	115	224	0	ENST00000349496.5:c.95A>C	p.Asp32Ala	p.D32A	ENST00000349496	NM_001904.3	32	gAc/gCc	3/15	0.827412513667398	4	FACETS	0.811	0.733	0.894			1	CLONAL	1	TRUE	NA	0.827412513667398	4		224	626	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519325	176519325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	195	333	1	ENST00000292408.4:c.731G>A	p.Arg244Gln	p.R244Q	ENST00000292408	NM_213647.1	244	cGg/cAg	7/18	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.827412513667398	2		334	439	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703538	47703538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63749932	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	84	335	0	ENST00000233146.2:c.2038C>T	p.Arg680Ter	p.R680*	ENST00000233146	NM_000251.2	680	Cga/Tga	13/16	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.35003761877016	2		335	448	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	72	158	1	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	0.35003761877016	2		159	279	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	70	276	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.35003761877016	2		276	376	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	79	466	8	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	NA	2	FACETS	1	0.961	1			1	INDETERMINATE	1	TRUE	NA	0.35003761877016	2		474	375	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	55	372	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.776	0.666	0.896	0.776	0.666	0.896	SUBCLONAL	1	TRUE	1	0.35003761877016	2		373	405	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	113	1064	3	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.35003761877016	2		1067	533	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	76	869	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.35003761877016	2		869	408	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161907	47161907	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	73	512	0	ENST00000409792.3:c.4219del	p.Arg1407GlyfsTer5	p.R1407Gfs*5	ENST00000409792	NM_014159.6	1407	Agg/gg	3/21	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.35003761877016	2		512	394	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479811	67479811	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500766	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	114	315	0	ENST00000327367.4:c.1118G>A	p.Arg373His	p.R373H	ENST00000327367	NM_005902.3	373	cGc/cAc	8/9	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.35003761877016	2		315	537	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951838	2951838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199916182	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	87	425	0	ENST00000396946.4:c.3112G>A	p.Ala1038Thr	p.A1038T	ENST00000396946	NM_032415.4	1038	Gcc/Acc	23/25	1	2	FACETS	0.945	0.839	1	0.945	0.839	1	CLONAL	1	TRUE	1	0.35003761877016	2		425	526	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749415085	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	50	238	0	ENST00000263967.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000263967	NM_006218.2	38	Cgt/Tgt	2/21	1	2	FACETS	0.882	0.752	1	0.882	0.752	1	CLONAL	1	TRUE	1	0.35003761877016	2		238	324	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	65	279	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.35003761877016	2		279	328	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346884	73346884	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	51	255	2	ENST00000377767.4:c.1333del	p.Ser445HisfsTer20	p.S445Hfs*20	ENST00000377767	NM_014953.3	445	Tca/ca	9/21	1	2	FACETS	0.984	0.842	1	0.984	0.842	1	CLONAL	1	TRUE	1	0.35003761877016	2		257	296	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	82	278	0	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.903	0.798	1	0.903	0.798	1	CLONAL	1	TRUE	1	0.35003761877016	2		278	519	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739031	40739031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1358914349	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	79	314	2	ENST00000373198.4:c.3253G>A	p.Val1085Ile	p.V1085I	ENST00000373198	NM_133170.3	1085	Gtc/Atc	24/32	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.35003761877016	2		316	433	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	62	252	1	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	0.987	0.857	1	0.987	0.857	1	CLONAL	1	TRUE	1	0.35003761877016	2		253	359	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225603	2225603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	96	407	1	ENST00000326181.6:c.1606G>A	p.Gly536Ser	p.G536S	ENST00000326181	NM_032271.2	536	Ggc/Agc	17/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.35003761877016	2		408	491	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	125	972	7	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.35003761877016	2		979	655	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	27	262	2	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.478	0.38	0.589	0.478	0.38	0.589	SUBCLONAL	1	TRUE	1	0.35003761877016	2		264	323	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821959	72821960	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs762108866	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	44	188	0	ENST00000268489.5:c.10215dup	p.Gly3406ArgfsTer25	p.G3406Rfs*25	ENST00000268489	NM_006885.3	3405	-/C	10/10	1	2	FACETS	0.844	0.711	0.989	0.844	0.711	0.989	CLONAL	1	TRUE	1	0.35003761877016	2		188	298	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268793	98268793	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1554708751	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	83	659	1	ENST00000331920.6:c.290del	p.Asn97ThrfsTer20	p.N97Tfs*20	ENST00000331920	NM_000264.3	97	aAc/ac	2/24	1	2	FACETS	0.829	0.733	0.932	0.829	0.733	0.932	CLONAL	1	TRUE	1	0.35003761877016	2		660	572	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434413	140434413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775889922	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	66	268	0	ENST00000288602.6:c.2285C>T	p.Ala762Val	p.A762V	ENST00000288602	NM_004333.4	762	gCg/gTg	18/18	1	2	FACETS	0.84	0.731	0.957	0.84	0.731	0.957	CLONAL	1	TRUE	1	0.35003761877016	2		268	449	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543829	212543829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771154734	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	53	269	1	ENST00000342788.4:c.1570C>T	p.Arg524Cys	p.R524C	ENST00000342788	NM_005235.2	524	Cgc/Tgc	13/28	1	2	FACETS	0.708	0.605	0.82	0.708	0.605	0.82	SUBCLONAL	1	TRUE	1	0.35003761877016	2		270	428	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618715	37618716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	56	355	2	ENST00000447079.4:c.397dup	p.Ser133LysfsTer24	p.S133Kfs*24	ENST00000447079	NM_015083.1	131	gaa/gAaa	1/14	1	2	FACETS	0.598	0.512	0.691	0.598	0.512	0.691	SUBCLONAL	1	TRUE	1	0.35003761877016	2		357	535	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15967432	15967432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1013043730	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	87	351	0	ENST00000268712.3:c.5171G>A	p.Arg1724Gln	p.R1724Q	ENST00000268712	NM_006311.3	1724	cGg/cAg	35/46	1	2	FACETS	0.877	0.778	0.982	0.877	0.778	0.982	CLONAL	1	TRUE	1	0.35003761877016	2		351	567	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806569	1806569	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs182935140	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	103	377	0	ENST00000260795.2:c.1285G>A	p.Ala429Thr	p.A429T	ENST00000260795		429	Gcg/Acg	9/17	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.35003761877016	2		377	507	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459777	149459777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1214590308	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	96	431	1	ENST00000286301.3:c.430C>T	p.Arg144Cys	p.R144C	ENST00000286301	NM_005211.3	144	Cgt/Tgt	4/22	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.35003761877016	2		432	517	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546324	46546324	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	71	239	2	ENST00000262741.5:c.205del	p.Asp69IlefsTer7	p.D69Ifs*7	ENST00000262741	NM_003629.3	69	Gat/at	2/10	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.35003761877016	2		241	363	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538941	187538941	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs113224498	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	60	273	1	ENST00000441802.2:c.8799del	p.Gly2934ValfsTer3	p.G2934Vfs*3	ENST00000441802	NM_005245.3	2933	caA/ca	10/27	1	2	FACETS	0.861	0.745	0.987	0.861	0.745	0.987	CLONAL	1	TRUE	1	0.35003761877016	2		274	398	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992721	68992721	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs764112302	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	83	395	2	ENST00000288368.4:c.1693del	p.Ser565ArgfsTer10	p.S565Rfs*10	ENST00000288368	NM_024870.2	562	cgT/cg	16/40	1	2	FACETS	0.974	0.862	1	0.974	0.862	1	CLONAL	1	TRUE	1	0.35003761877016	2		397	487	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494881	56494881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373840207	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	114	294	1	ENST00000267101.3:c.3238C>T	p.Arg1080Cys	p.R1080C	ENST00000267101	NM_001982.3	1080	Cgt/Tgt	27/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.35003761877016	2		295	471	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32814948	32814948	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	156	326	0	ENST00000354258.4:c.2117del	p.Gly706ValfsTer12	p.G706Vfs*12	ENST00000354258	NM_000593.5	706	gGt/gt	10/11	0.35003761877016	2	FACETS	0.942	0.87	1	0.942	0.87	1	CLONAL	2	TRUE	0	0.35003761877016	2		326	473	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144027	11144027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770680174	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	104	385	0	ENST00000358026.2:c.3608G>A	p.Arg1203His	p.R1203H	ENST00000358026	NM_001128849.1	1203	cGc/cAc	26/36	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.35003761877016	2		385	572	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589609	67589610	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	59	190	0	ENST00000274335.5:c.1378dup	p.Ser460LysfsTer5	p.S460Kfs*5	ENST00000274335		458	gaa/gAaa	10/15	1	2	FACETS	0.806	0.696	0.926	0.806	0.696	0.926	CLONAL	1	TRUE	1	0.35003761877016	2		190	418	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15938117	15938117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769360451	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	60	188	0	ENST00000268712.3:c.7097C>T	p.Thr2366Met	p.T2366M	ENST00000268712	NM_006311.3	2366	aCg/aTg	45/46	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.35003761877016	2		188	295	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621185	1621185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1159477032	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	96	410	1	ENST00000344749.5:c.961C>T	p.Arg321Ter	p.R321*	ENST00000344749	NM_001136139.2	321	Cga/Tga	12/19	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.35003761877016	2		411	469	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021277	31021277	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	33	311	0	ENST00000375687.4:c.1281del	p.Lys427AsnfsTer35	p.K427Nfs*35	ENST00000375687	NM_015338.5	426	Aaa/aa	12/13	1	2	FACETS	0.39	0.317	0.473	0.39	0.317	0.473	SUBCLONAL	1	TRUE	1	0.35003761877016	2		311	483	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228164	36228164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	87	355	0	ENST00000222270.7:c.7550G>A	p.Arg2517Gln	p.R2517Q	ENST00000222270	NM_014727.1	2517	cGg/cAg	33/37	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.35003761877016	2		355	475	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2115581	2115581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45471596	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	130	415	1	ENST00000219476.3:c.1661C>T	p.Ser554Leu	p.S554L	ENST00000219476	NM_000548.3	554	tCg/tTg	16/42	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.35003761877016	2		416	599	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437711	49437713	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs886049482	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	103	377	0	ENST00000301067.7:c.5257_5259del	p.Lys1753del	p.K1753del	ENST00000301067	NM_003482.3	1753	AAG/-	22/54	1	2	FACETS	0.89	0.798	0.988	0.89	0.798	0.988	CLONAL	1	TRUE	1	0.35003761877016	2		377	661	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146944	38146945	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	101	524	0	ENST00000317025.8:c.3197dup	p.Asn1066LysfsTer14	p.N1066Kfs*14	ENST00000317025	NM_023034.1	1066	aac/aaAc	18/24	1	2	FACETS	0.923	0.827	1	0.923	0.827	1	CLONAL	1	TRUE	1	0.35003761877016	2		524	625	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047947	180047947	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	74	383	2	ENST00000261937.6:c.2228C>T	p.Ala743Val	p.A743V	ENST00000261937	NM_182925.4	743	gCg/gTg	15/30	1	2	FACETS	0.826	0.724	0.934	0.826	0.724	0.934	CLONAL	1	TRUE	1	0.35003761877016	2		385	512	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685289	89685289	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554897267	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	54	195	1	ENST00000371953.3:c.188del	p.Asn63ThrfsTer36	p.N63Tfs*36	ENST00000371953	NM_000314.4	62	Aaa/aa	3/9	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.35003761877016	2		196	296	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635191	87635191	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367769334	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	32	320	0	ENST00000277120.3:c.2243C>T	p.Thr748Met	p.T748M	ENST00000277120		748	aCg/aTg	18/19	1	2	FACETS	0.387	0.314	0.471	0.387	0.314	0.471	SUBCLONAL	1	TRUE	1	0.35003761877016	2		320	472	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912140	114912140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	83	360	0	ENST00000543371.1:c.1210C>T	p.Arg404Trp	p.R404W	ENST00000543371	NM_001198531.1	404	Cgg/Tgg	11/14	1	2	FACETS	0.91	0.805	1	0.91	0.805	1	CLONAL	1	TRUE	1	0.35003761877016	2		360	521	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11227537	11227537	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	85	349	0	ENST00000361445.4:c.4291G>A	p.Gly1431Arg	p.G1431R	ENST00000361445	NM_004958.3	1431	Gga/Aga	29/58	1	2	FACETS	0.96	0.851	1	0.96	0.851	1	CLONAL	1	TRUE	1	0.35003761877016	2		349	506	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260906	16260906	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	63	252	0	ENST00000375759.3:c.8171C>T	p.Thr2724Ile	p.T2724I	ENST00000375759	NM_015001.2	2724	aCa/aTa	11/15	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.35003761877016	2		252	304	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094435	27094436	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	97	343	0	ENST00000324856.7:c.3145_3146del	p.Leu1049GlyfsTer55	p.L1049Gfs*55	ENST00000324856	NM_006015.4	1048	cCT/c	11/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.35003761877016	2		343	516	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332760	70332760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749194238	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	66	304	0	ENST00000373644.4:c.665G>A	p.Arg222His	p.R222H	ENST00000373644	NM_030625.2	222	cGc/cAc	2/12	1	2	FACETS	0.94	0.82	1	0.94	0.82	1	CLONAL	1	TRUE	1	0.35003761877016	2		304	401	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	532724	532724	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748729430	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	118	401	0	ENST00000451590.1:c.482G>A	p.Arg161His	p.R161H	ENST00000451590	NM_001130442.1	161	cGt/cAt	5/5	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.35003761877016	2		401	599	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533532	533532	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	51	460	1	ENST00000451590.1:c.371C>T	p.Thr124Ile	p.T124I	ENST00000451590	NM_001130442.1	124	aCt/aTt	4/5	1	2	FACETS	0.467	0.396	0.545	0.467	0.396	0.545	SUBCLONAL	1	TRUE	1	0.35003761877016	2		461	624	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200270	67200270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201348433	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	99	371	0	ENST00000312629.5:c.578G>A	p.Arg193Gln	p.R193Q	ENST00000312629	NM_003952.2	193	cGg/cAg	7/15	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.35003761877016	2		371	536	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156112	119156112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776999573	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	83	361	0	ENST00000264033.4:c.1777C>T	p.Arg593Trp	p.R593W	ENST00000264033	NM_005188.3	593	Cgg/Tgg	11/16	1	2	FACETS	0.801	0.708	0.901	0.801	0.708	0.901	CLONAL	1	TRUE	1	0.35003761877016	2		361	592	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426543	49426543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760983900	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	153	431	1	ENST00000301067.7:c.11945G>A	p.Arg3982Gln	p.R3982Q	ENST00000301067	NM_003482.3	3982	cGa/cAa	39/54	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.35003761877016	2		432	785	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133234521	133234521	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs531705054	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	69	300	1	ENST00000320574.5:c.3311C>T	p.Thr1104Met	p.T1104M	ENST00000320574	NM_006231.2	1104	aCg/aTg	27/49	1	2	FACETS	0.75	0.654	0.853	0.75	0.654	0.853	SUBCLONAL	1	TRUE	1	0.35003761877016	2		301	526	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241894	133241894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757051826	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	77	338	0	ENST00000320574.5:c.2462G>A	p.Arg821His	p.R821H	ENST00000320574	NM_006231.2	821	cGc/cAc	21/49	1	2	FACETS	0.92	0.811	1	0.92	0.811	1	CLONAL	1	TRUE	1	0.35003761877016	2		338	478	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100025	30100025	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	41	384	0	ENST00000331968.5:c.1595G>A	p.Trp532Ter	p.W532*	ENST00000331968	NM_002742.2	532	tGg/tAg	10/18	1	2	FACETS	0.516	0.43	0.612	0.516	0.43	0.612	SUBCLONAL	1	TRUE	1	0.35003761877016	2		384	454	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135376	30135376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1249972372	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	82	271	0	ENST00000331968.5:c.442G>A	p.Ala148Thr	p.A148T	ENST00000331968	NM_002742.2	148	Gct/Act	3/18	1	2	FACETS	0.945	0.835	1	0.945	0.835	1	CLONAL	1	TRUE	1	0.35003761877016	2		271	496	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570368	95570368	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	47	195	0	ENST00000393063.1:c.3365G>A	p.Cys1122Tyr	p.C1122Y	ENST00000393063	NM_030621.3	1122	tGt/tAt	22/28	1	2	FACETS	0.959	0.815	1	0.959	0.815	1	CLONAL	1	TRUE	1	0.35003761877016	2		195	280	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250880	99250880	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	47	286	0	ENST00000268035.6:c.184C>A	p.Leu62Met	p.L62M	ENST00000268035	NM_000875.3	62	Ctg/Atg	2/21	1	2	FACETS	0.636	0.538	0.745	0.636	0.538	0.745	SUBCLONAL	1	TRUE	1	0.35003761877016	2		286	422	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348076	348076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781377815	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	30	419	0	ENST00000262320.3:c.1430G>A	p.Arg477His	p.R477H	ENST00000262320	NM_003502.3	477	cGt/cAt	6/11	1	2	FACETS	0.299	0.24	0.366	0.299	0.24	0.366	SUBCLONAL	1	TRUE	1	0.35003761877016	2		419	573	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106730	2106730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397515011	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	126	396	0	ENST00000219476.3:c.734G>A	p.Arg245His	p.R245H	ENST00000219476	NM_000548.3	245	cGc/cAc	8/42	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.35003761877016	2		396	609	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129423	30129423	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1321995174	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	103	352	1	ENST00000263025.4:c.605C>T	p.Thr202Met	p.T202M	ENST00000263025	NM_002746.2	202	aCg/aTg	4/9	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.35003761877016	2		353	564	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822307	72822307	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	52	448	0	ENST00000268489.5:c.9868G>T	p.Ala3290Ser	p.A3290S	ENST00000268489	NM_006885.3	3290	Gcc/Tcc	10/10	1	2	FACETS	0.562	0.478	0.653	0.562	0.478	0.653	SUBCLONAL	1	TRUE	1	0.35003761877016	2		448	529	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649131	37649131	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	73	277	0	ENST00000447079.4:c.2236G>T	p.Asp746Tyr	p.D746Y	ENST00000447079	NM_015083.1	746	Gac/Tac	4/14	1	2	FACETS	0.873	0.765	0.988	0.873	0.765	0.988	CLONAL	1	TRUE	1	0.35003761877016	2		277	478	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866709	37866710	+	missense_variant	Missense_Mutation	DNP	CG	CG	TA	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	114	380	2	ENST00000269571.5:c.876_877delinsTA	p.Ala293Thr	p.A293T	ENST00000269571		292	ggCGcc/ggTAcc	7/27	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.35003761877016	2		382	638	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879801	37879801	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	78	254	0	ENST00000269571.5:c.2096C>T	p.Pro699Leu	p.P699L	ENST00000269571		699	cCg/cTg	18/27	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.35003761877016	2		254	314	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858194	40858194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs905112048	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	80	390	0	ENST00000428826.2:c.1670G>A	p.Arg557His	p.R557H	ENST00000428826		557	cGt/cAt	16/21	1	2	FACETS	0.816	0.72	0.92	0.816	0.72	0.92	CLONAL	1	TRUE	1	0.35003761877016	2		390	560	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439903	56439903	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	167	345	0	ENST00000407977.2:c.687+2T>C		p.X229_splice	ENST00000407977		229			0.35003761877016	2	FACETS	0.994	0.921	1	0.994	0.921	1	CLONAL	2	TRUE	0	0.35003761877016	2		345	480	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554231	63554232	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	GATGGAATCAATC	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	155	335	0	ENST00000307078.5:c.495_507dup	p.Met170AspfsTer2	p.M170Dfs*2	ENST00000307078	NM_004655.3	169	-/GATTGATTCCATC	2/11	0.35003761877016	2	FACETS	0.863	0.796	0.933	0.863	0.796	0.933	CLONAL	2	TRUE	0	0.35003761877016	2		335	513	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244243	5244243	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1390768500	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	74	336	1	ENST00000357368.4:c.1239del	p.Ser414AlafsTer30	p.S414Afs*30	ENST00000357368	NM_002850.3	413	ccC/cc	11/38	1	2	FACETS	0.881	0.773	0.996	0.881	0.773	0.996	CLONAL	1	TRUE	1	0.35003761877016	2		337	480	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250363	10250363	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767041788	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	80	209	0	ENST00000340748.4:c.3889G>A	p.Gly1297Ser	p.G1297S	ENST00000340748		1297	Ggc/Agc	33/40	1	2	FACETS	0.813	0.724	0.906	1	0.981	1	CLONAL	2	TRUE	1	0.35003761877016	2		209	281	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272852	18272852	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	89	412	0	ENST00000222254.8:c.892G>A	p.Ala298Thr	p.A298T	ENST00000222254	NM_005027.3	298	Gcg/Acg	7/16	1	2	FACETS	0.959	0.853	1	0.959	0.853	1	CLONAL	1	TRUE	1	0.35003761877016	2		412	530	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210913	36210913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1462444181	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	45	381	1	ENST00000222270.7:c.664C>T	p.Arg222Trp	p.R222W	ENST00000222270	NM_014727.1	222	Cgg/Tgg	3/37	1	2	FACETS	0.52	0.437	0.612	0.52	0.437	0.612	SUBCLONAL	1	TRUE	1	0.35003761877016	2		382	494	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212307	36212308	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	85	411	0	ENST00000222270.7:c.2061_2062del	p.Pro688SerfsTer2	p.P688Sfs*2	ENST00000222270	NM_014727.1	686	gaCTct/gact	3/37	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.35003761877016	2		411	484	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702368	47702369	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATACTTTG	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	73	236	0	ENST00000233146.2:c.1966_1973dup	p.Glu658AspfsTer30	p.E658Dfs*30	ENST00000233146	NM_000251.2	655	gta/gtATACTTTGa	12/16	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.35003761877016	2		236	395	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264407	46264407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529456958	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	100	289	0	ENST00000371998.3:c.1454G>A	p.Arg485His	p.R485H	ENST00000371998		485	cGt/cAt	11/23	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.35003761877016	2		289	484	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092957	29092957	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	86	302	0	ENST00000328354.6:c.1027A>T	p.Ile343Phe	p.I343F	ENST00000328354	NM_007194.3	343	Att/Ttt	10/15	0.35003761877016	2	FACETS	0.949	0.842	1	0.474	0.421	0.531	CLONAL	1	TRUE	0	0.35003761877016	2		302	518	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069366	30069366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773296925	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	174	400	1	ENST00000338641.4:c.1231C>T	p.Arg411Cys	p.R411C	ENST00000338641	NM_000268.3	411	Cgc/Tgc	12/16	0.35003761877016	2	FACETS	0.943	0.875	1	0.943	0.875	1	CLONAL	2	TRUE	0	0.35003761877016	2		401	527	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628572	187628572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	130	425	0	ENST00000441802.2:c.2410G>A	p.Ala804Thr	p.A804T	ENST00000441802	NM_005245.3	804	Gcg/Acg	2/27	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.35003761877016	2		425	602	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235329	235329	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749309213	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	61	338	0	ENST00000264932.6:c.1135C>T	p.Arg379Cys	p.R379C	ENST00000264932	NM_004168.2	379	Cgc/Tgc	9/15	1	2	FACETS	0.783	0.677	0.898	0.783	0.677	0.898	SUBCLONAL	1	TRUE	1	0.35003761877016	2		338	445	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948505	31948505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1226536047	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	87	176	0	ENST00000375333.2:c.988C>T	p.Arg330Trp	p.R330W	ENST00000375333	NM_032454.1	330	Cgg/Tgg	7/8	0.35003761877016	2	FACETS	0.941	0.845	1	0.941	0.845	1	CLONAL	2	TRUE	0	0.35003761877016	2		176	264	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129146	152129146	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	94	412	1	ENST00000206249.3:c.103del	p.Leu35TrpfsTer74	p.L35Wfs*74	ENST00000206249	NM_000125.3	33	atC/at	1/8	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.35003761877016	2		413	497	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845479	128845479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	102	400	0	ENST00000249373.3:c.776C>T	p.Ser259Leu	p.S259L	ENST00000249373	NM_005631.4	259	tCg/tTg	4/12	1	2	FACETS	0.991	0.889	1	0.991	0.889	1	CLONAL	1	TRUE	1	0.35003761877016	2		400	588	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162915	38162915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199766344	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	133	395	0	ENST00000317025.8:c.2291G>A	p.Arg764His	p.R764H	ENST00000317025	NM_023034.1	764	cGt/cAt	13/24	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.35003761877016	2		395	623	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864663	68864663	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773560075	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	29	164	0	ENST00000288368.4:c.34G>A	p.Glu12Lys	p.E12K	ENST00000288368	NM_024870.2	12	Gag/Aag	1/40	1	2	FACETS	0.696	0.562	0.848	0.696	0.562	0.848	SUBCLONAL	1	TRUE	1	0.35003761877016	2		164	238	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956778	68956778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746227590	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	41	388	0	ENST00000288368.4:c.896G>A	p.Arg299Gln	p.R299Q	ENST00000288368	NM_024870.2	299	cGg/cAg	8/40	1	2	FACETS	0.363	0.302	0.432	0.363	0.302	0.432	SUBCLONAL	1	TRUE	1	0.35003761877016	2		388	645	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028127	69028127	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	88	426	0	ENST00000288368.4:c.3286G>A	p.Asp1096Asn	p.D1096N	ENST00000288368	NM_024870.2	1096	Gat/Aat	26/40	1	2	FACETS	0.831	0.737	0.931	0.831	0.737	0.931	CLONAL	1	TRUE	1	0.35003761877016	2		426	605	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737945	145737945	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	36	355	0	ENST00000428558.2:c.2886-1G>T		p.X962_splice	ENST00000428558	NM_004260.3	962			1	2	FACETS	0.415	0.34	0.498	0.415	0.34	0.498	SUBCLONAL	1	TRUE	1	0.35003761877016	2		355	496	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914694	39914694	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	108	358	0	ENST00000378444.4:c.4668del	p.Thr1557ProfsTer11	p.T1557Pfs*11	ENST00000378444	NM_001123385.1	1556	ccC/cc	12/15	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.35003761877016	2		358	579	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410971	63410971	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	78	382	0	ENST00000330258.3:c.2196G>A	p.Met732Ile	p.M732I	ENST00000330258	NM_152424.3	732	atG/atA	2/2	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.35003761877016	2		382	415	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391808	139391808	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770713134	NA	P-0026754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	410	577	1	ENST00000277541.6:c.6383C>T	p.Pro2128Leu	p.P2128L	ENST00000277541	NM_017617.3	2128	cCg/cTg	34/34	1	2	FACETS	0.998	0.953	1	0.998	0.953	1	CLONAL	1	TRUE	1	0.795811995311086	2		578	1032	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60795958	60795958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369294037	NA	P-0026754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	409	634	0	ENST00000333681.4:c.620G>A	p.Arg207Gln	p.R207Q	ENST00000333681		207	cGg/cAg	3/3	1	2	FACETS	0.923	0.88	0.966	0.923	0.88	0.966	CLONAL	1	TRUE	1	0.795811995311086	2		634	1114	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0026767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	12	205	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.605	0.429	0.818	0.605	0.429	0.818	SUBCLONAL	1	TRUE	1	0.357227870969191	2		205	111	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	12	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.779	1	1	0.779	1	CLONAL	1	TRUE	1	0.357227870969191	2		306	61	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572986	7572986	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555524156	NA	P-0026767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	25	363	0	ENST00000269305.4:c.1123C>T	p.Gln375Ter	p.Q375*	ENST00000269305	NM_001126112.2	375	Cag/Tag	11/11	0.357227870969191	2	FACETS	0.804	0.651	0.971	0.804	0.651	0.971	CLONAL	2	TRUE	0	0.357227870969191	2		363	87	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0026770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	169	230	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.230475712477787	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.232008841871632	2		231	688	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0026770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	152	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.232008841871632	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	1	0.232008841871632	3		436	698	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219187	94219187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1023372148	NA	P-0026770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	92	486	2	ENST00000323929.3:c.217C>T	p.His73Tyr	p.H73Y	ENST00000323929	NM_005591.3	73	Cat/Tat	4/20	0.232008841871632	5	FACETS	1	0.947	1	0.28	0.248	0.314	CLONAL	1	TRUE	1	0.232008841871632	5		488	956	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292415	15292415	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1379963173	NA	P-0026770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	89	521	0	ENST00000263388.2:c.2764G>C	p.Glu922Gln	p.E922Q	ENST00000263388	NM_000435.2	922	Gaa/Caa	17/33	0.194173397608029	4	FACETS	0.97	0.859	1	0.485	0.429	0.546	CLONAL	1	TRUE	2	0.232008841871632	4		521	974	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726325	41727089	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GACGGGATGGACGCTAGATCCCAGTCCCTTGGGAGGGCTCCCGTCCTCCTCTCAGAGCCTCCGCCCTCCACCCCACTCTGAGGTCACTCTGCAACTATGTCGGCCTAAGGGCCTGGCGGGGTCCTGGCCGCCGGTGGGCAGGCAAGGACAGGGTGGAACTGAGGGCCGGAAGGAGCTGGGGGGTTCCTAAGCTAACTCTTCCCATCTCCCCTCCAGGCACGCAGGCTGAAGAAAGTCCCTTCGTGGGCAACCCAGGGAATATCACAGGTGCCCGGGGACTCACGGGCACCCTTCGGTGTCAGCTCCAGGTTCAGGGAGAGCCCCCCGAGGTACATTGGCTTCGGGATGGACAGATCCTGGAGCTCGCGGACAGCACCCAGACCCAGGTGCCCCTGGGTGAGGATGAACAGGATGACTGGATAGTGGTCAGCCAGCTCAGGTGTGTGGCCACATCCCCGAATCCCACTCCCACCTCCGTCACACAGAGGGCAGAAAGCCCACCTGGGTGGGAACCCCAGTTTGACCACTTGTCAGCCGTGCGGCTTTGAGCATGTGATGGAACCTCTAGGTTTCGTTTTCCTCTTCTGCAAAATGAGTTAATAATAGGACATACTTCGTGGTTGTCATGAGCTTCCAGACTGGACACCCTCTTTCCGTTCTGACAGACCCCCTCCCAGTGTCCAGCTCTGACCCTGAACCTCTCTGTCTCTCCTCTTGCCCTGTCAGAATCACCTCCCTGCAGCTTTCCGACACGGGACAGTACCA	GACGGGATGGACGCTAGATCCCAGTCCCTTGGGAGGGCTCCCGTCCTCCTCTCAGAGCCTCCGCCCTCCACCCCACTCTGAGGTCACTCTGCAACTATGTCGGCCTAAGGGCCTGGCGGGGTCCTGGCCGCCGGTGGGCAGGCAAGGACAGGGTGGAACTGAGGGCCGGAAGGAGCTGGGGGGTTCCTAAGCTAACTCTTCCCATCTCCCCTCCAGGCACGCAGGCTGAAGAAAGTCCCTTCGTGGGCAACCCAGGGAATATCACAGGTGCCCGGGGACTCACGGGCACCCTTCGGTGTCAGCTCCAGGTTCAGGGAGAGCCCCCCGAGGTACATTGGCTTCGGGATGGACAGATCCTGGAGCTCGCGGACAGCACCCAGACCCAGGTGCCCCTGGGTGAGGATGAACAGGATGACTGGATAGTGGTCAGCCAGCTCAGGTGTGTGGCCACATCCCCGAATCCCACTCCCACCTCCGTCACACAGAGGGCAGAAAGCCCACCTGGGTGGGAACCCCAGTTTGACCACTTGTCAGCCGTGCGGCTTTGAGCATGTGATGGAACCTCTAGGTTTCGTTTTCCTCTTCTGCAAAATGAGTTAATAATAGGACATACTTCGTGGTTGTCATGAGCTTCCAGACTGGACACCCTCTTTCCGTTCTGACAGACCCCCTCCCAGTGTCCAGCTCTGACCCTGAACCTCTCTGTCTCTCCTCTTGCCCTGTCAGAATCACCTCCCTGCAGCTTTCCGACACGGGACAGTACCA	-	novel	NA	P-0026770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	76	10	0	ENST00000301178.4:c.86-215_348del		p.X29_splice	ENST00000301178	NM_021913.4	29		2-3/20	0.194173397608029	4	FACETS	0.986	0.927	1	1	0.99	1	CLONAL	9	TRUE	2	0.232008841871632	4		10	91	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858983	57858983	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	48	742	1	ENST00000228682.2:c.479C>T	p.Ala160Val	p.A160V	ENST00000228682	NM_005269.2	160	gCc/gTc	5/12	1	2	FACETS	0.856	0.722	1	0.856	0.722	1	CLONAL	1	TRUE	1	0.14	2		743	801	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877847	151877868	+	frameshift_variant	Frame_Shift_Del	DEL	ATCAGTTACTCCTGAAGTTGGC	ATCAGTTACTCCTGAAGTTGGC	-	novel	NA	P-0026866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	45	396	0	ENST00000262189.6:c.7077_7098del	p.Pro2360HisfsTer5	p.P2360Hfs*5	ENST00000262189	NM_170606.2	2359	gtGCCAACTTCAGGAGTAACTGAT/gt	36/59	1	2	FACETS	0.987	0.828	1	0.987	0.828	1	CLONAL	1	TRUE	1	0.14	2		396	651	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0026947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	360	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.663289598083194	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	1	0.663289598083194	4		436	569	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114901057	114901057	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776719680	NA	P-0026947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	173	562	0	ENST00000543371.1:c.667G>A	p.Asp223Asn	p.D223N	ENST00000543371	NM_001198531.1	223	Gac/Aac	6/14	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.663289598083194	2		562	519	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127916013	127916016	+	frameshift_variant	Frame_Shift_Del	DEL	ATCT	ATCT	-	novel	NA	P-0026947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	64	297	0	ENST00000373547.4:c.465_468del	p.Ile155MetfsTer75	p.I155Mfs*75	ENST00000373547	NM_002721.4	155	atAGAT/at	6/7	1	2	FACETS	0.869	0.764	0.98	0.869	0.764	0.98	CLONAL	1	TRUE	1	0.663289598083194	2		297	222	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	49	583	0	ENST00000269305.4:c.528C>A	p.Cys176Ter	p.C176*	ENST00000269305	NM_001126112.2	176	tgC/tgA	5/11	1	2	FACETS	0.353	0.298	0.414	0.353	0.298	0.414	SUBCLONAL	1	TRUE	1	0.31	2		583	895	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934251	48934251	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0026949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	54	447	0	ENST00000267163.4:c.706A>T	p.Lys236Ter	p.K236*	ENST00000267163	NM_000321.2	236	Aaa/Taa	7/27	1	2	FACETS	0.577	0.492	0.67	0.577	0.492	0.67	SUBCLONAL	1	TRUE	1	0.31	2		447	604	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219378	1219378	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	57	586	0	ENST00000326873.7:c.431del	p.Pro144ArgfsTer17	p.P144Rfs*17	ENST00000326873	NM_000455.4	144	Ccg/cg	3/10	1	2	FACETS	0.404	0.345	0.469	0.404	0.345	0.469	SUBCLONAL	1	TRUE	1	0.31	2		586	910	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	65	406	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	0.19	2		406	682	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0026963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	40	340	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.791	0.657	0.941	0.791	0.657	0.941	CLONAL	1	TRUE	1	0.19	2		341	532	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73340190	73340190	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	139	258	0	ENST00000377767.4:c.1890G>C	p.Leu630Phe	p.L630F	ENST00000377767	NM_014953.3	630	ttG/ttC	15/21	1	2	FACETS	0.957	0.876	1	0.957	0.876	1	CLONAL	1	TRUE	1	0.542059102401413	2		258	536	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	226	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.988	0.925	1	0.988	0.925	1	CLONAL	1	TRUE	1	0.687237451338457	2		306	666	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579709	7579710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	348	529	0	ENST00000269305.4:c.86dup	p.Asn29LysfsTer14	p.N29Kfs*14	ENST00000269305	NM_001126112.2	29	aac/aaAc	3/11	0.577686044625807	1	FACETS	0.942	0.899	0.984	0.942	0.899	0.984	CLONAL	1	TRUE	0	0.687237451338457	1		529	706	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444456	49444456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530585519	NA	P-0027026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	57	548	0	ENST00000301067.7:c.2915C>T	p.Pro972Leu	p.P972L	ENST00000301067	NM_003482.3	972	cCg/cTg	11/54	0.21751351567967	1	FACETS	0.118	0.101	0.137	0.118	0.101	0.137	INDETERMINATE	1	TRUE	0	0.687237451338457	1		548	921	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574030	7574030	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	310	742	0	ENST00000269305.4:c.997del	p.Arg333ValfsTer12	p.R333Vfs*12	ENST00000269305	NM_001126112.2	333	Cgt/gt	10/11	0.449180509917846	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.449180509917846	2		742	655	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993842	72993842	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	70	362	0	ENST00000268489.5:c.203C>G	p.Ala68Gly	p.A68G	ENST00000268489	NM_006885.3	68	gCc/gGc	2/10	0.449180509917846	2	FACETS	0.74	0.648	0.839	0.37	0.324	0.42	SUBCLONAL	1	TRUE	0	0.449180509917846	2		362	421	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857655	59857655	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	86	329	0	ENST00000259008.2:c.1902G>T	p.Gln634His	p.Q634H	ENST00000259008	NM_032043.2	634	caG/caT	13/20	0.449180509917846	2	FACETS	1	0.955	1	0.566	0.505	0.63	CLONAL	1	TRUE	0	0.449180509917846	2		329	338	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430166	181430166	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	20	144	0	ENST00000325404.1:c.18G>C	p.Glu6Asp	p.E6D	ENST00000325404	NM_003106.3	6	gaG/gaC	1/1	0.449180509917846	3	FACETS	0.551	0.423	0.699	0.275	0.211	0.35	SUBCLONAL	1	TRUE	1	0.449180509917846	3		144	198	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961436	1961436	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	121	550	0	ENST00000382891.5:c.3224G>T	p.Trp1075Leu	p.W1075L	ENST00000382891	NM_133335.3	1075	tGg/tTg	17/22	0.449180509917846	2	FACETS	0.818	0.74	0.899	0.409	0.37	0.45	CLONAL	1	TRUE	0	0.449180509917846	2		550	659	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524687	187524687	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs928653182	NA	P-0027072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	126	663	0	ENST00000441802.2:c.10993C>T	p.Arg3665Ter	p.R3665*	ENST00000441802	NM_005245.3	3665	Cga/Tga	19/27	0.449180509917846	2	FACETS	0.733	0.664	0.806	0.367	0.332	0.403	SUBCLONAL	1	TRUE	0	0.449180509917846	2		663	765	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771849	135771849	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs776694051	NA	P-0027072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	144	568	0	ENST00000298552.3:c.3268A>G	p.Met1090Val	p.M1090V	ENST00000298552	NM_001162426.1	1090	Atg/Gtg	23/23	0.449180509917846	2	FACETS	1	0.964	1	0.547	0.501	0.595	CLONAL	1	TRUE	0	0.449180509917846	2		568	586	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061221	38061232	+	inframe_deletion	In_Frame_Del	DEL	GTTCTCGAACAT	GTTCTCGAACAT	-	novel	NA	P-0027219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	134	638	0	ENST00000250448.2:c.757_768del	p.Met253_Asn256del	p.M253_N256del	ENST00000250448	NM_004496.3	253	ATGTTCGAGAAC/-	2/2	1	2	FACETS	0.847	0.776	0.92	1	0.992	1	CLONAL	3	TRUE	1	0.240873503083553	2		638	438	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180333	32180333	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	31	742	1	ENST00000375023.3:c.2598C>A	p.Phe866Leu	p.F866L	ENST00000375023	NM_004557.3	866	ttC/ttA	17/30	0.124141560076393	4	FACETS	1	0.856	1	1	0.856	1	INDETERMINATE	2	TRUE	2	0.240873503083553	4		743	152	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559213	141559213	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	11	678	0	ENST00000220592.5:c.1588G>A	p.Ala530Thr	p.A530T	ENST00000220592	NM_012154.3	530	Gcc/Acc	12/19	0.240873503083553	8	FACETS	0.739	0.51	1	0.123	0.085	0.171	CLONAL	1	TRUE	2	0.240873503083553	8		678	213	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0027226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	36	398	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.572065172266154	2	FACETS	0.141	0.115	0.17	0.07	0.057	0.085	SUBCLONAL	1	TRUE	0	0.577268108255781	2		398	885	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750439	57750439	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	92	457	0	ENST00000274289.3:c.2029C>G	p.Leu677Val	p.L677V	ENST00000274289	NM_006622.3	677	Ctg/Gtg	14/14	1	2	FACETS	0.465	0.413	0.521	0.465	0.413	0.521	SUBCLONAL	1	TRUE	1	0.577268108255781	2		457	685	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240681	55240681	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	157	680	0	ENST00000275493.2:c.1925A>C	p.Lys642Thr	p.K642T	ENST00000275493	NM_005228.3	642	aAg/aCg	17/28	0.409639032283128	1	FACETS	0.396	0.363	0.432	0.396	0.363	0.432	SUBCLONAL	1	TRUE	0	0.577268108255781	1		680	976	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760700	59760700	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265133595	NA	P-0027264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	66	577	0	ENST00000259008.2:c.3707C>T	p.Pro1236Leu	p.P1236L	ENST00000259008	NM_032043.2	1236	cCa/cTa	20/20	1	2	FACETS	0.23	0.199	0.263	0.23	0.199	0.263	SUBCLONAL	1	TRUE	1	0.728703360720235	2		577	789	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940087	76940087	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0027264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	186	438	0	ENST00000373344.5:c.663-2A>G		p.X221_splice	ENST00000373344	NM_000489.3	221			1	2	FACETS	0.825	0.766	0.886	0.825	0.766	0.886	CLONAL	1	TRUE	1	0.728703360720235	2		438	619	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15365009	15365009	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs543066899	NA	P-0027314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	222	429	0	ENST00000263377.2:c.2112G>C	p.Glu704Asp	p.E704D	ENST00000263377	NM_058243.2	704	gaG/gaC	11/20	0.263029082702274	2	FACETS	0.96	0.895	1	0.96	0.895	1	CLONAL	2	TRUE	0	0.263029082702274	2		429	879	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944366	131944367	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0027314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	58	188	0	ENST00000265335.6:c.2779_2780del	p.Glu927ArgfsTer16	p.E927Rfs*16	ENST00000265335		926	aaAGaa/aaaa	17/25	1	2	FACETS	0.821	0.706	0.947	0.821	0.706	0.947	CLONAL	1	TRUE	1	0.263029082702274	2		188	537	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	296	406	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.409718352473849	3	FACETS	0.858	0.809	0.907	0.858	0.809	0.907	CLONAL	2	TRUE	1	0.46432267220161	3		406	916	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991727	72991727	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755455411	NA	P-0027348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	139	379	0	ENST00000268489.5:c.2318C>T	p.Ala773Val	p.A773V	ENST00000268489	NM_006885.3	773	gCg/gTg	2/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.46432267220161	2		379	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578496	7578496	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	495	644	0	ENST00000269305.4:c.434T>G	p.Leu145Arg	p.L145R	ENST00000269305	NM_001126112.2	145	cTg/cGg	5/11	0.191126788515883	3	FACETS	0.991	0.953	1			1	INDETERMINATE	3	TRUE	NA	0.388500202138184	3		644	1024	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090496	5090496	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs750978665	NA	P-0027466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	92	381	0	ENST00000381652.3:c.2812C>T	p.Arg938Ter	p.R938*	ENST00000381652	NM_004972.3	938	Cga/Tga	21/25	1	2	FACETS	0.961	0.857	1	0.961	0.857	1	CLONAL	1	TRUE	1	0.388500202138184	2		381	493	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114846	108114846	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0027466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	84	377	0	ENST00000278616.4:c.662+1G>T		p.X221_splice	ENST00000278616	NM_000051.3	221			0.387735137557913	3	FACETS	0.848	0.75	0.953	0.424	0.375	0.477	CLONAL	1	TRUE	1	0.388500202138184	3		377	609	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842360	68842363	+	frameshift_variant	Frame_Shift_Del	DEL	ACAT	ACAT	-	novel	NA	P-0027466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	90	475	0	ENST00000261769.5:c.421_424del	p.Thr141PhefsTer73	p.T141Ffs*73	ENST00000261769	NM_004360.3	141	ACATtt/tt	4/16	0.388500202138184	1	FACETS	0.776	0.691	0.866	0.776	0.691	0.866	SUBCLONAL	1	TRUE	0	0.388500202138184	1		475	481	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80088610	80088610	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	118	504	0	ENST00000265081.6:c.2602G>C	p.Asp868His	p.D868H	ENST00000265081	NM_002439.4	868	Gat/Cat	19/24	0.388500202138184	3	FACETS	0.881	0.795	0.973	0.441	0.397	0.487	CLONAL	1	TRUE	1	0.388500202138184	3		504	823	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0027526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	113	579	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.984	0.891	1	0.984	0.891	1	CLONAL	1	TRUE	1	0.530647599131134	2		579	433	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645676	215645676	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1407053508	NA	P-0027526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	155	368	0	ENST00000260947.4:c.922C>G	p.Leu308Val	p.L308V	ENST00000260947	NM_000465.2	308	Ctt/Gtt	4/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.530647599131134	2		368	561	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120574	94120574	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	106	361	1	ENST00000369303.4:c.477C>A	p.Asp159Glu	p.D159E	ENST00000369303	NM_004440.3	159	gaC/gaA	3/17	0.214921487263776	1	FACETS	0.635	0.573	0.701	0.635	0.573	0.701	INDETERMINATE	1	TRUE	0	0.530647599131134	1		362	462	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133323	38133323	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	197	458	0	ENST00000317025.8:c.4150T>G	p.Ser1384Ala	p.S1384A	ENST00000317025	NM_023034.1	1384	Tca/Gca	24/24	1	2	FACETS	0.88	0.816	0.946	0.88	0.816	0.946	CLONAL	1	TRUE	1	0.530647599131134	2		458	844	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0027542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	135	513	0	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	1	2	FACETS	1	0.977	1	1	0.993	1	CLONAL	2	TRUE	1	0.556597474731916	2		513	221	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188989	11188989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	31	385	0	ENST00000361445.4:c.5734G>A	p.Asp1912Asn	p.D1912N	ENST00000361445	NM_004958.3	1912	Gat/Aat	41/58	0.249125170617081	3	FACETS	0.982	0.806	1	0.491	0.403	0.588	INDETERMINATE	1	TRUE	1	0.556597474731916	3		385	145	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842748	68842748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	121	366	0	ENST00000261769.5:c.684del	p.Tyr228Ter	p.Y228*	ENST00000261769	NM_004360.3	228	taC/ta	5/16	0.556597474731916	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.556597474731916	2		366	179	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029406	16029406	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	98	419	0	ENST00000268712.3:c.1624G>T	p.Glu542Ter	p.E542*	ENST00000268712	NM_006311.3	542	Gaa/Taa	15/46	1	2	FACETS	1	0.974	1	1	0.99	1	CLONAL	2	TRUE	1	0.556597474731916	2		419	156	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39542576	39542576	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	78	415	1	ENST00000262039.4:c.380T>A	p.Val127Asp	p.V127D	ENST00000262039	NM_002647.2	127	gTt/gAt	3/25	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.556597474731916	2		416	228	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467710	66467710	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	32	304	0	ENST00000273854.3:c.559G>T	p.Asp187Tyr	p.D187Y	ENST00000273854	NM_004439.5	187	Gat/Tat	3/18	0.420979952918636	4	FACETS	0.904	0.74	1	0.452	0.37	0.543	CLONAL	1	TRUE	2	0.556597474731916	4		304	198	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797274	32797274	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	45	610	0	ENST00000374899.4:c.1835A>C	p.Lys612Thr	p.K612T	ENST00000374899	NM_018833.2	612	aAa/aCa	11/12	0.503898521014778	3	FACETS	1	0.921	1	0.376	0.321	0.436	CLONAL	1	TRUE	0	0.556597474731916	3		610	183	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974126	2974126	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	73	421	0	ENST00000396946.4:c.1479C>A	p.Tyr493Ter	p.Y493*	ENST00000396946	NM_032415.4	493	taC/taA	10/25	0.314114014765365	5	FACETS	1	0.945	1	0.736	0.654	0.821	INDETERMINATE	2	TRUE	2	0.556597474731916	5		421	218	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396731	139396731	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	94	527	0	ENST00000277541.6:c.5377G>C	p.Gly1793Arg	p.G1793R	ENST00000277541	NM_017617.3	1793	Ggc/Cgc	28/34	0.556597474731916	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.556597474731916	2		527	159	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0027641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	106	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	890	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038929	12038929	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	57	385	0	ENST00000396373.4:c.1222A>T	p.Arg408Trp	p.R408W	ENST00000396373	NM_001987.4	408	Agg/Tgg	7/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		385	860	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482861	67482861	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	71	268	0	ENST00000327367.4:c.1265C>T	p.Ser422Phe	p.S422F	ENST00000327367	NM_005902.3	422	tCc/tTc	9/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		268	738	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211490	46211490	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	24	232	0	ENST00000334344.6:c.456T>G	p.Phe152Leu	p.F152L	ENST00000334344	NM_152641.2	152	ttT/ttG	5/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		232	479	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492694	56492694	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	38	317	0	ENST00000407977.2:c.245T>C	p.Leu82Ser	p.L82S	ENST00000407977		82	tTa/tCa	2/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		317	758	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0027820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	309	612	3	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.801324605350464	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.801324605350464	1		615	455	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0027820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	493	579	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.758854465947776	3	FACETS	0.948	0.913	0.982			1	CLONAL	2	TRUE	NA	0.801324605350464	3		579	909	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41560094	41560094	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	361	600	0	ENST00000263253.7:c.3766C>T	p.Gln1256Ter	p.Q1256*	ENST00000263253	NM_001429.3	1256	Cag/Tag	22/31	0.801324605350464	1	FACETS	0.985	0.949	1	0.985	0.949	1	CLONAL	1	TRUE	0	0.801324605350464	1		600	548	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760779	59760779	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	437	665	1	ENST00000259008.2:c.3628G>T	p.Asp1210Tyr	p.D1210Y	ENST00000259008	NM_032043.2	1210	Gat/Tat	20/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.801324605350464	2		666	1057	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	130	561	2	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.587835353166008	3	FACETS	0.89	0.809	0.974	0.445	0.404	0.487	CLONAL	1	TRUE	1	0.587835353166008	3		563	643	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936984	48936984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772678500	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	108	384	0	ENST00000267163.4:c.752G>A	p.Arg251Gln	p.R251Q	ENST00000267163	NM_000321.2	251	cGa/cAa	8/27	0.587835353166008	4	FACETS	0.994	0.894	1	0.497	0.447	0.55	CLONAL	1	TRUE	2	0.587835353166008	4		384	587	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	344	674	1	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	2	TRUE	NA	0.587835353166008	2		675	548	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252856	36252857	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	160	323	0	ENST00000300305.3:c.505dup	p.Arg169LysfsTer44	p.R169Kfs*44	ENST00000300305		169	aga/aAga	4/8	0.587835353166008	3	FACETS	0.831	0.77	0.893	0.831	0.77	0.893	CLONAL	2	TRUE	1	0.587835353166008	3		323	424	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051636	128051636	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756810937	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	124	525	0	ENST00000285398.2:c.22G>A	p.Asp8Asn	p.D8N	ENST00000285398	NM_000122.1	8	Gac/Aac	1/15	0.193533402704747	5	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.587835353166008	5		525	584	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840069	27840069	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	91	302	0	ENST00000328488.2:c.25C>T	p.Arg9Cys	p.R9C	ENST00000328488	NM_003533.2	9	Cgc/Tgc	1/1	0.587835353166008	5	FACETS	1	0.953	1			1	CLONAL	1	TRUE	NA	0.587835353166008	5		302	516	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605127	46605127	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs760600266	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	134	594	0	ENST00000263734.3:c.1344G>C	p.Gln448His	p.Q448H	ENST00000263734	NM_001430.4	448	caG/caC	10/16	0.587835353166008	4	FACETS	0.978	0.89	1	0.489	0.445	0.536	CLONAL	1	TRUE	2	0.587835353166008	4		594	740	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644597	21644597	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	95	399	0	ENST00000421138.2:c.70C>G	p.Gln24Glu	p.Q24E	ENST00000421138		24	Caa/Gaa	4/16	0.293573164746573	3	FACETS	1	0.933	1			1	INDETERMINATE	1	TRUE	NA	0.587835353166008	3		399	397	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020224	123020224	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs111978474	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	108	548	1	ENST00000355640.3:c.712C>T	p.Arg238Ter	p.R238*	ENST00000355640		238	Cga/Tga	2/7	0.587835353166008	3	FACETS	0.929	0.837	1	0.464	0.418	0.513	CLONAL	1	TRUE	1	0.587835353166008	3		549	512	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546389	46546389	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	105	376	0	ENST00000262741.5:c.140C>G	p.Ser47Ter	p.S47*	ENST00000262741	NM_003629.3	47	tCa/tGa	2/10	0.587835353166008	4	FACETS	0.963	0.865	1			1	CLONAL	1	TRUE	NA	0.587835353166008	4		376	589	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546420	46546420	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	84	293	0	ENST00000262741.5:c.109C>G	p.Leu37Val	p.L37V	ENST00000262741	NM_003629.3	37	Ctt/Gtt	2/10	0.587835353166008	4	FACETS	0.953	0.845	1			1	CLONAL	1	TRUE	NA	0.587835353166008	4		293	476	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282436	115282436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1314208666	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	107	517	0	ENST00000438362.2:c.214G>A	p.Glu72Lys	p.E72K	ENST00000438362	NM_001242891.1	72	Gaa/Aaa	3/20	0.587835353166008	2	FACETS	0.894	0.808	0.984	0.447	0.404	0.492	CLONAL	1	TRUE	0	0.587835353166008	2		517	407	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465306	120465306	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	79	398	0	ENST00000256646.2:c.4955C>T	p.Ser1652Phe	p.S1652F	ENST00000256646	NM_024408.3	1652	tCt/tTt	27/34	0.587835353166008	2	FACETS	0.74	0.656	0.83	0.37	0.328	0.415	SUBCLONAL	1	TRUE	0	0.587835353166008	2		398	363	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999539	100999539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	151	809	2	ENST00000325455.5:c.263C>A	p.Ser88Tyr	p.S88Y	ENST00000325455	NM_001202474.3	88	tCc/tAc	1/8	0.587835353166008	3	FACETS	0.969	0.888	1	0.485	0.444	0.527	CLONAL	1	TRUE	1	0.587835353166008	3		811	686	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111959722	111959722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1165258369	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	129	601	0	ENST00000375549.3:c.301C>T	p.Leu101Phe	p.L101F	ENST00000375549	NM_003002.3	101	Ctt/Ttt	3/4	0.272846306212817	5	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.587835353166008	5		601	603	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118339541	118339541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	107	462	0	ENST00000534358.1:c.484C>T	p.Pro162Ser	p.P162S	ENST00000534358	NM_005933.3	162	Ccc/Tcc	2/36	0.272846306212817	5	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.587835353166008	5		462	531	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906804	32906804	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	122	614	0	ENST00000380152.3:c.1189C>A	p.Gln397Lys	p.Q397K	ENST00000380152		397	Caa/Aaa	10/27	0.587835353166008	4	FACETS	0.91	0.824	1	0.455	0.412	0.501	CLONAL	1	TRUE	2	0.587835353166008	4		614	724	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519066	103519066	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	103	454	2	ENST00000355739.4:c.2404C>T	p.Gln802Ter	p.Q802*	ENST00000355739	NM_000123.3	802	Cag/Tag	11/15	0.330648297156039	5	FACETS	1	0.967	1	0.396	0.355	0.439	INDETERMINATE	1	TRUE	2	0.587835353166008	5		456	555	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632800	23632800	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs754465466	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	178	401	0	ENST00000261584.4:c.2997-1G>A		p.X999_splice	ENST00000261584	NM_024675.3	999			0.564375849615073	5	FACETS	1	0.943	1	0.68	0.63	0.73	CLONAL	2	TRUE	2	0.587835353166008	5		401	559	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559770	29559770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	84	315	0	ENST00000356175.3:c.3367G>A	p.Glu1123Lys	p.E1123K	ENST00000356175	NM_000267.3	1123	Gaa/Aaa	26/57	0.587835353166008	3	FACETS	0.953	0.847	1	0.477	0.423	0.533	CLONAL	1	TRUE	1	0.587835353166008	3		315	388	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59793381	59793381	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	96	459	0	ENST00000259008.2:c.2423G>A	p.Arg808Lys	p.R808K	ENST00000259008	NM_032043.2	808	aGa/aAa	17/20	0.587835353166008	3	FACETS	1	0.908	1	0.507	0.454	0.562	CLONAL	1	TRUE	1	0.587835353166008	3		459	417	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78935258	78935258	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779966402	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	136	662	0	ENST00000306801.3:c.3670G>A	p.Asp1224Asn	p.D1224N	ENST00000306801	NM_020761.2	1224	Gac/Aac	31/34	0.587835353166008	3	FACETS	0.986	0.9	1	0.493	0.45	0.538	CLONAL	1	TRUE	1	0.587835353166008	3		662	607	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139896	50139896	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	184	774	0	ENST00000246792.3:c.433G>T	p.Asp145Tyr	p.D145Y	ENST00000246792	NM_006270.3	145	Gat/Tat	4/6	0.587835353166008	3	FACETS	0.964	0.891	1	0.482	0.445	0.52	CLONAL	1	TRUE	1	0.587835353166008	3		774	840	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009111	27009111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	70	230	0	ENST00000335756.4:c.47G>T	p.Arg16Leu	p.R16L	ENST00000335756	NM_001809.3	16	cGc/cTc	1/5	0.178427157862497	5	FACETS	1	0.932	1			1	INDETERMINATE	2	TRUE	NA	0.587835353166008	5		230	209	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051641	128051641	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs893323064	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	114	539	0	ENST00000285398.2:c.17G>C	p.Arg6Pro	p.R6P	ENST00000285398	NM_000122.1	6	cGa/cCa	1/15	0.193533402704747	5	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.587835353166008	5		539	573	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279712	46279727	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCTTGGGTATTAGCA	TTCTTGGGTATTAGCA	-	novel	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	49	373	0	ENST00000371998.3:c.3652-14_3653del		p.X1218_splice	ENST00000371998		1218		20/23	0.587835353166008	4	FACETS	0.581	0.492	0.678	0.29	0.246	0.339	SUBCLONAL	1	TRUE	2	0.587835353166008	4		373	456	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184164	56184164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	61	323	0	ENST00000399503.3:c.4369C>T	p.His1457Tyr	p.H1457Y	ENST00000399503	NM_005921.1	1457	Cat/Tat	19/20	0.330648297156039	5	FACETS	1	0.954	1	0.409	0.355	0.467	INDETERMINATE	1	TRUE	2	0.587835353166008	5		323	318	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131893029	131893029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756334508	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	75	331	0	ENST00000265335.6:c.13G>A	p.Glu5Lys	p.E5K	ENST00000265335		5	Gaa/Aaa	1/25	0.587835353166008	3	FACETS	0.888	0.783	0.999	0.444	0.391	0.5	CLONAL	1	TRUE	1	0.587835353166008	3		331	372	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911614	131911614	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	54	290	0	ENST00000265335.6:c.359G>C	p.Arg120Thr	p.R120T	ENST00000265335		120	aGa/aCa	3/25	0.587835353166008	3	FACETS	0.823	0.708	0.946	0.411	0.354	0.473	CLONAL	1	TRUE	1	0.587835353166008	3		290	289	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435670	149435670	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	94	643	1	ENST00000286301.3:c.2473G>A	p.Glu825Lys	p.E825K	ENST00000286301	NM_005211.3	825	Gag/Aag	19/22	0.587835353166008	3	FACETS	0.816	0.729	0.909	0.408	0.364	0.455	CLONAL	1	TRUE	1	0.587835353166008	3		644	507	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165096	32165096	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	147	576	0	ENST00000375023.3:c.5032G>C	p.Asp1678His	p.D1678H	ENST00000375023	NM_004557.3	1678	Gat/Cat	27/30	0.587835353166008	4	FACETS	0.951	0.869	1	0.476	0.434	0.519	CLONAL	1	TRUE	2	0.587835353166008	4		576	835	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965728	93965728	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	41	263	0	ENST00000369303.4:c.2200C>T	p.Gln734Ter	p.Q734*	ENST00000369303	NM_004440.3	734	Cag/Tag	13/17	0.193533402704747	5	FACETS	1	0.861	1			1	INDETERMINATE	1	TRUE	NA	0.587835353166008	5		263	255	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268887	55268887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	136	720	0	ENST00000275493.2:c.2953G>A	p.Glu985Lys	p.E985K	ENST00000275493	NM_005228.3	985	Gaa/Aaa	25/28	0.580799009770922	3	FACETS	0.955	0.871	1	0.477	0.435	0.522	CLONAL	1	TRUE	1	0.587835353166008	3		720	627	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842252	151842252	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	68	320	0	ENST00000262189.6:c.14160G>C	p.Lys4720Asn	p.K4720N	ENST00000262189	NM_170606.2	4720	aaG/aaC	54/59	0.237609891924738	5	FACETS	1	0.887	1			1	INDETERMINATE	1	TRUE	NA	0.587835353166008	5		320	428	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542540	141542540	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	86	439	0	ENST00000220592.5:c.2446C>T	p.His816Tyr	p.H816Y	ENST00000220592	NM_012154.3	816	Cac/Tac	18/19	0.587835353166008	3	FACETS	0.91	0.81	1	0.455	0.405	0.508	CLONAL	1	TRUE	1	0.587835353166008	3		439	416	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882030	36882030	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	109	647	1	ENST00000358127.4:c.983C>G	p.Ser328Ter	p.S328*	ENST00000358127	NM_001280556.1	328	tCa/tGa	8/10	0.363902788913068	4	FACETS	0.924	0.832	1	0.462	0.416	0.511	CLONAL	1	TRUE	2	0.587835353166008	4		648	637	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139565433	139565433	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	127	802	0	ENST00000308874.7:c.603G>C	p.Gln201His	p.Q201H	ENST00000308874		201	caG/caC	8/10	0.330648297156039	5	FACETS	0.886	0.802	0.974	0.295	0.267	0.325	INDETERMINATE	1	TRUE	2	0.587835353166008	5		802	918	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411333	63411333	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	92	603	0	ENST00000330258.3:c.1834G>A	p.Glu612Lys	p.E612K	ENST00000330258	NM_152424.3	612	Gag/Aag	2/2	0.587835353166008	3	FACETS	0.853	0.761	0.95	0.426	0.38	0.475	CLONAL	1	TRUE	1	0.587835353166008	3		603	475	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918995	76918995	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	43	389	0	ENST00000373344.5:c.3996G>C	p.Lys1332Asn	p.K1332N	ENST00000373344	NM_000489.3	1332	aaG/aaC	12/35	0.587835353166008	3	FACETS	0.557	0.467	0.655	0.278	0.233	0.328	SUBCLONAL	1	TRUE	1	0.587835353166008	3		389	340	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906732	32906732	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	118	536	1	ENST00000380152.3:c.1117C>G	p.Gln373Glu	p.Q373E	ENST00000380152		373	Cag/Gag	10/27	0.587835353166008	4	FACETS	0.96	0.868	1	0.48	0.434	0.529	CLONAL	1	TRUE	2	0.587835353166008	4		537	664	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0028040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	126	427	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.176967495993305	3	FACETS	0.903	0.819	0.991	0.903	0.819	0.991	CLONAL	2	TRUE	1	0.22	3		427	704	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870386	155870387	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0028040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	96	435	0	ENST00000368323.3:c.452_453delinsTT	p.Ala151Val	p.A151V	ENST00000368323	NM_006912.5	151	gCC/gTT	6/6	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.22	2		435	705	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310941	123310941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	58	363	0	ENST00000358487.5:c.487G>A	p.Glu163Lys	p.E163K	ENST00000358487	NM_000141.4	163	Gaa/Aaa	5/18	1	2	FACETS	0.993	0.854	1	0.993	0.854	1	CLONAL	1	TRUE	1	0.22	2		363	531	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349354	73349354	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	50	318	0	ENST00000377767.4:c.982C>T	p.Arg328Ter	p.R328*	ENST00000377767	NM_014953.3	328	Cga/Tga	6/21	1	2	FACETS	0.92	0.781	1	0.92	0.781	1	CLONAL	1	TRUE	1	0.22	2		318	494	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042236	42042236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	92	494	0	ENST00000219905.7:c.6431G>A	p.Gly2144Glu	p.G2144E	ENST00000219905	NM_001164273.1	2144	gGa/gAa	17/24	1	2	FACETS	0.969	0.86	1	0.969	0.86	1	CLONAL	1	TRUE	1	0.22	2		494	863	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678437	88678437	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0028040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	129	703	1	ENST00000360948.2:c.1099A>T	p.Lys367Ter	p.K367*	ENST00000360948	NM_001012338.2	367	Aag/Tag	9/19	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.22	2		704	974	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024885	31024885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	98	495	1	ENST00000375687.4:c.4370C>T	p.Ser1457Phe	p.S1457F	ENST00000375687	NM_015338.5	1457	tCc/tTc	13/13	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.22	2		496	813	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36028521	36028521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	80	619	0	ENST00000358208.4:c.863C>T	p.Thr288Ile	p.T288I	ENST00000358208		288	aCc/aTc	8/12	1	2	FACETS	0.911	0.801	1	0.911	0.801	1	CLONAL	1	TRUE	1	0.22	2		619	798	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670486	134670487	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0028040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	81	532	2	ENST00000398015.3:c.397_398delinsTT	p.Pro133Phe	p.P133F	ENST00000398015	NM_004441.4	133	CCc/TTc	3/16	1	2	FACETS	0.955	0.841	1	0.955	0.841	1	CLONAL	1	TRUE	1	0.22	2		534	771	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808247	99808247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	89	570	1	ENST00000280892.6:c.442C>T	p.Arg148Cys	p.R148C	ENST00000280892	NM_001130678.1	148	Cgc/Tgc	5/7	1	2	FACETS	0.968	0.857	1	0.968	0.857	1	CLONAL	1	TRUE	1	0.22	2		571	836	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0028040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	51	1164	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.22	2		1164	431	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962983	38962983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1292288715	NA	P-0028040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	49	207	0	ENST00000357387.3:c.1561C>T	p.Leu521Phe	p.L521F	ENST00000357387	NM_152756.3	521	Ctt/Ttt	17/38	1	2	FACETS	0.779	0.664	0.903	1	0.966	1	CLONAL	2	TRUE	1	0.22	2		207	286	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180679	32180680	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0028040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	98	671	2	ENST00000375023.3:c.2447_2448delinsAA	p.Arg816Lys	p.R816K	ENST00000375023	NM_004557.3	816	aGG/aAA	16/30	1	2	FACETS	0.87	0.774	0.972	0.87	0.774	0.972	CLONAL	1	TRUE	1	0.22	2		673	1024	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933653	39933653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200052076	NA	P-0028040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	85	234	0	ENST00000378444.4:c.946C>T	p.Pro316Ser	p.P316S	ENST00000378444	NM_001123385.1	316	Ccc/Tcc	4/15	1	1	FACETS	0.937	0.834	1	1	0.984	1	CLONAL	2	TRUE	0	0.22	1		234	367	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652395	48652395	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1557020608	NA	P-0028040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	95	365	0	ENST00000376670.3:c.1066G>C	p.Gly356Arg	p.G356R	ENST00000376670	NM_002049.3	356	Ggc/Cgc	6/6	1	1	FACETS	0.807	0.722	0.897	1	0.983	1	CLONAL	2	TRUE	0	0.22	1		365	476	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245372	53245372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	67	226	1	ENST00000375401.3:c.665C>T	p.Pro222Leu	p.P222L	ENST00000375401	NM_004187.3	222	cCc/cTc	6/26	1	1	FACETS	0.77	0.673	0.873	1	0.975	1	SUBCLONAL	2	TRUE	0	0.22	1		227	352	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0028202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	75	398	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.811	0.71	0.921	0.811	0.71	0.921	CLONAL	1	TRUE	1	0.23	2		398	804	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0028202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	88	340	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.23	2		341	664	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs730881677	NA	P-0028202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	40	397	0	ENST00000304494.5:c.151-1G>T		p.X51_splice	ENST00000304494	NM_000077.4	51			0.169485948747845	1	FACETS	0.704	0.586	0.837	0.704	0.586	0.837	SUBCLONAL	1	TRUE	0	0.23	1		397	437	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161862	47161862	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	48	347	0	ENST00000409792.3:c.4264C>T	p.Gln1422Ter	p.Q1422*	ENST00000409792	NM_014159.6	1422	Cag/Tag	3/21	1	2	FACETS	0.737	0.623	0.864	0.737	0.623	0.864	SUBCLONAL	1	TRUE	1	0.23	2		347	566	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830615	72830615	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	89	570	0	ENST00000268489.5:c.5966G>C	p.Gly1989Ala	p.G1989A	ENST00000268489	NM_006885.3	1989	gGc/gCc	9/10	1	2	FACETS	0.897	0.794	1	0.897	0.794	1	CLONAL	1	TRUE	1	0.23	2		570	863	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510309	187510309	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	133	290	0	ENST00000441802.2:c.13204A>T	p.Asn4402Tyr	p.N4402Y	ENST00000441802	NM_005245.3	4402	Aac/Tac	27/27	1	2	FACETS	0.887	0.814	0.961	0.887	0.814	0.961	CLONAL	1	TRUE	1	0.783268301982799	2		290	383	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0028453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	235	610	2	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.284872881223593	2	FACETS	0.918	0.861	0.977	0.918	0.861	0.977	CLONAL	2	TRUE	0	0.36400388909644	2		612	703	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56857713	56857713	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	186	574	0	ENST00000308159.5:c.749T>A	p.Val250Glu	p.V250E	ENST00000308159	NM_014669.4	250	gTg/gAg	8/22	0.269101405376011	3	FACETS	0.795	0.736	0.856	0.795	0.736	0.856	SUBCLONAL	2	TRUE	1	0.36400388909644	3		574	760	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103696	47103696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	180	489	0	ENST00000409792.3:c.6250C>T	p.Pro2084Ser	p.P2084S	ENST00000409792	NM_014159.6	2084	Ccc/Tcc	14/21	0.277832219940537	5	FACETS	0.801	0.739	0.866	0.534	0.492	0.578	CLONAL	2	TRUE	2	0.36400388909644	5		489	954	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125295	47125295	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	79	556	0	ENST00000409792.3:c.5975G>A	p.Ser1992Asn	p.S1992N	ENST00000409792	NM_014159.6	1992	aGt/aAt	12/21	0.277832219940537	5	FACETS	0.718	0.63	0.814	0.239	0.21	0.272	SUBCLONAL	1	TRUE	2	0.36400388909644	5		556	934	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189585660	189585660	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	44	620	0	ENST00000264731.3:c.921G>A	p.Met307Ile	p.M307I	ENST00000264731	NM_003722.4	307	atG/atA	7/14	0.269101405376011	3	FACETS	0.327	0.273	0.387	0.163	0.136	0.194	SUBCLONAL	1	TRUE	1	0.36400388909644	3		620	874	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139804384	139804384	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1564414790	NA	P-0028453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	254	894	0	ENST00000247668.2:c.541G>T	p.Val181Phe	p.V181F	ENST00000247668	NM_021138.3	181	Gtc/Ttc	6/11	0.303588641910136	4	FACETS	0.834	0.78	0.89	0.417	0.39	0.445	CLONAL	2	TRUE	0	0.36400388909644	4		894	1141	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0028483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	250	406	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	0.633612672509063	2		406	534	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0028483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	253	312	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.160504517136329	4	FACETS	0.838	0.793	0.883	0.838	0.793	0.883	INDETERMINATE	3	TRUE	1	0.633612672509063	4		312	519	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557642	95557642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	146	450	1	ENST00000393063.1:c.5425G>A	p.Gly1809Arg	p.G1809R	ENST00000393063	NM_030621.3	1809	Ggg/Agg	26/28	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.633612672509063	2		451	444	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160451	108160451	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	153	421	0	ENST00000278616.4:c.4363del	p.Ser1455ValfsTer3	p.S1455Vfs*3	ENST00000278616	NM_000051.3	1453	atA/at	29/63	0.402909048772618	1	FACETS	0.736	0.68	0.795	0.736	0.68	0.795	SUBCLONAL	1	TRUE	0	0.633612672509063	1		421	448	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711993	89711993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	116	275	0	ENST00000371953.3:c.611C>T	p.Pro204Leu	p.P204L	ENST00000371953	NM_000314.4	204	cCa/cTa	6/9	0.160504517136329	4	FACETS	0.862	0.786	0.94	0.575	0.524	0.627	INDETERMINATE	2	TRUE	1	0.633612672509063	4		275	347	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574406	95574406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	120	202	0	ENST00000393063.1:c.2461C>T	p.Arg821Cys	p.R821C	ENST00000393063	NM_030621.3	821	Cgc/Tgc	17/28	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.633612672509063	2		202	256	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100943	27100943	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	322	506	1	ENST00000324856.7:c.4225C>T	p.Gln1409Ter	p.Q1409*	ENST00000324856	NM_006015.4	1409	Cag/Tag	18/20	0.633612672509063	2	FACETS	0.851	0.826	0.875	1	0.996	1	CLONAL	3	TRUE	0	0.633612672509063	2		507	398	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653861	89653862	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0028483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	141	364	0	ENST00000371953.3:c.160dup	p.Val54GlyfsTer9	p.V54Gfs*9	ENST00000371953	NM_000314.4	53	-/G	2/9	0.160504517136329	4	FACETS	0.817	0.751	0.885	0.545	0.5	0.59	INDETERMINATE	2	TRUE	1	0.633612672509063	4		364	445	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137051	64137051	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	159	609	0	ENST00000334205.4:c.1562A>T	p.His521Leu	p.H521L	ENST00000334205	NM_003942.2	521	cAc/cTc	13/17	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.633612672509063	2		609	455	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644964	67644965	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0028483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	137	473	0	ENST00000264010.4:c.229_230del	p.Val77AsnfsTer62	p.V77Nfs*62	ENST00000264010	NM_006565.3	77	GTa/a	3/12	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.633612672509063	2		473	407	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928070	178928087	+	inframe_deletion	In_Frame_Del	DEL	CATGGATTAGAAGATTTG	CATGGATTAGAAGATTTG	-	novel	NA	P-0028483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	120	459	0	ENST00000263967.3:c.1349_1366del	p.His450_Leu455del	p.H450_L455del	ENST00000263967	NM_006218.2	450	CATGGATTAGAAGATTTG/-	8/21	1	2	FACETS	0.808	0.734	0.884	0.808	0.734	0.884	CLONAL	1	TRUE	1	0.633612672509063	2		459	469	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481412	140481412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913353	NA	P-0028549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	200	544	0	ENST00000288602.6:c.1396G>A	p.Gly466Arg	p.G466R	ENST00000288602	NM_004333.4	466	Gga/Aga	11/18	0.484721675865174	3	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	1	0.484721675865174	3		544	508	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16198985	16199354	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCCAGAGGTGGAGCTTGCAGTGAGCTGAGATTGTGCCACTGCACTCCAGCCTGGGCAACAGAGCGAGACTCCATCTCAAAAAAAAAAAAAAAAGAAATGAGAGTAATGTAATAATGCGATACAGATATTTTCCCCAGAGAGAAAAACGTTAAGTGTAAAAGAGAGCCATTTAAAAAGTCATTTTGCAGGTCGTCCCTCCTACATACATAACGCAAATTGTCCAAAAAAAATCTAAAAACTCATTTTGGAAAATTATTGATATGCAGCAATAACGTTGACTTTATTTTTTCCAGATATGGCCGCGTGGAAAGTGTCAAAATTCTTCCCAAGAGGGGAT	CTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCCAGAGGTGGAGCTTGCAGTGAGCTGAGATTGTGCCACTGCACTCCAGCCTGGGCAACAGAGCGAGACTCCATCTCAAAAAAAAAAAAAAAAGAAATGAGAGTAATGTAATAATGCGATACAGATATTTTCCCCAGAGAGAAAAACGTTAAGTGTAAAAGAGAGCCATTTAAAAAGTCATTTTGCAGGTCGTCCCTCCTACATACATAACGCAAATTGTCCAAAAAAAATCTAAAAACTCATTTTGGAAAATTATTGATATGCAGCAATAACGTTGACTTTATTTTTTCCAGATATGGCCGCGTGGAAAGTGTCAAAATTCTTCCCAAGAGGGGAT	-	novel	NA	P-0028567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2	254	0	0	ENST00000375759.3:c.84-324_129del		p.X28_splice	ENST00000375759	NM_015001.2	28		2/15	0.848077955919667	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.860419768639223	1		0	256	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612813	228612813	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	227	665	0	ENST00000366696.1:c.214A>C	p.Met72Leu	p.M72L	ENST00000366696	NM_003493.2	72	Atg/Ctg	1/1	1	2	FACETS	0.472	0.44	0.506	0.472	0.44	0.506	SUBCLONAL	1	TRUE	1	0.860419768639223	2		665	1117	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046765	42046765	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs768068238	NA	P-0028567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	48	599	0	ENST00000219905.7:c.7139C>T	p.Pro2380Leu	p.P2380L	ENST00000219905	NM_001164273.1	2380	cCg/cTg	18/24	0.841442065582606	2	FACETS	0.132	0.111	0.155	0.066	0.055	0.078	SUBCLONAL	1	TRUE	0	0.860419768639223	2		599	847	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645284	215645284	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	115	435	0	ENST00000260947.4:c.1314G>C	p.Lys438Asn	p.K438N	ENST00000260947	NM_000465.2	438	aaG/aaC	4/11	0.442170379318928	1	FACETS	0.298	0.269	0.328	0.298	0.269	0.328	INDETERMINATE	1	TRUE	0	0.860419768639223	1		435	511	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200748	128200748	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	638	689	0	ENST00000341105.2:c.1057C>A	p.Gln353Lys	p.Q353K	ENST00000341105	NM_032638.4	353	Cag/Aag	5/6	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.860419768639223	2		689	1418	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185016	32185016	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	562	738	0	ENST00000375023.3:c.1652A>G	p.Asp551Gly	p.D551G	ENST00000375023	NM_004557.3	551	gAt/gGt	10/30	1	2	FACETS	0.995	0.957	1	0.995	0.957	1	CLONAL	1	TRUE	1	0.860419768639223	2		738	1313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577579	7577581	+	inframe_deletion	In_Frame_Del	DEL	GTA	GTA	-	novel	NA	P-0028599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	513	718	0	ENST00000269305.4:c.700_702del	p.Tyr234del	p.Y234del	ENST00000269305	NM_001126112.2	234	TAC/-	7/11	0.564918463841146	2	FACETS	0.941	0.908	0.974	0.941	0.908	0.974	CLONAL	2	TRUE	0	0.584328051831483	2		718	933	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660196	12660196	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	257	605	0	ENST00000251849.4:c.25A>G	p.Lys9Glu	p.K9E	ENST00000251849	NM_002880.3	9	Aag/Gag	2/17	0.584328051831483	1	FACETS	0.973	0.917	1	0.973	0.917	1	CLONAL	1	TRUE	0	0.584328051831483	1		605	640	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916831	48916831	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	110	485	0	ENST00000267163.4:c.361C>T	p.Gln121Ter	p.Q121*	ENST00000267163	NM_000321.2	121	Cag/Tag	3/27	0.584328051831483	1	FACETS	0.698	0.632	0.765	0.698	0.632	0.765	SUBCLONAL	1	TRUE	0	0.584328051831483	1		485	382	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104356917	104356917	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs749533220	NA	P-0028599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	179	594	0	ENST00000369902.3:c.777C>G	p.Ile259Met	p.I259M	ENST00000369902	NM_016169.3	259	atC/atG	7/12	0.584328051831483	1	FACETS	0.642	0.594	0.692	0.642	0.594	0.692	SUBCLONAL	1	TRUE	0	0.584328051831483	1		594	675	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965451	25965451	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1438565703	NA	P-0028599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	110	705	0	ENST00000435504.4:c.3755G>C	p.Arg1252Thr	p.R1252T	ENST00000435504		1252	aGa/aCa	13/13	1	2	FACETS	0.369	0.331	0.41	0.369	0.331	0.41	SUBCLONAL	1	TRUE	1	0.584328051831483	2		705	1019	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204686	128204686	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	234	896	0	ENST00000341105.2:c.755A>T	p.Tyr252Phe	p.Y252F	ENST00000341105	NM_032638.4	252	tAt/tTt	3/6	1	2	FACETS	0.689	0.642	0.738	0.689	0.642	0.738	SUBCLONAL	1	TRUE	1	0.584328051831483	2		896	1162	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577579	7577581	+	inframe_deletion	In_Frame_Del	DEL	GTA	GTA	-	novel	NA	P-0028599-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	61	718	0	ENST00000269305.4:c.700_702del	p.Tyr234del	p.Y234del	ENST00000269305	NM_001126112.2	234	TAC/-	7/11	0.605645978645547	5	FACETS	0.973	0.899	1	1	0.984	1	CLONAL	5	TRUE	2	0.605645978645547	5		718	79	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660196	12660196	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028599-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	38	605	0	ENST00000251849.4:c.25A>G	p.Lys9Glu	p.K9E	ENST00000251849	NM_002880.3	9	Aag/Gag	2/17	0.539117178510089	3	FACETS	1	0.938	1	1	0.938	1	CLONAL	3	TRUE	0	0.605645978645547	3		605	51	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916831	48916831	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028599-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	36	485	0	ENST00000267163.4:c.361C>T	p.Gln121Ter	p.Q121*	ENST00000267163	NM_000321.2	121	Cag/Tag	3/27	0.42552914265184	5	FACETS	0.915	0.797	1			1	CLONAL	4	TRUE	NA	0.605645978645547	5		485	62	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104356917	104356917	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs749533220	NA	P-0028599-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	27	594	0	ENST00000369902.3:c.777C>G	p.Ile259Met	p.I259M	ENST00000369902	NM_016169.3	259	atC/atG	7/12	0.560793880953869	2	FACETS	0.929	0.788	1	0.929	0.788	1	CLONAL	2	TRUE	0	0.605645978645547	2		594	48	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204686	128204686	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028599-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	25	896	0	ENST00000341105.2:c.755A>T	p.Tyr252Phe	p.Y252F	ENST00000341105	NM_032638.4	252	tAt/tTt	3/6	0.605645978645547	5	FACETS	1	0.911	1	1	0.911	1	CLONAL	3	TRUE	2	0.605645978645547	5		896	46	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0028633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	144	584	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.697527437133163	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.719786454676496	2		584	185	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361160	70361160	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs79912241	NA	P-0028633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	19	252	0	ENST00000374080.3:c.6348C>A	p.His2116Gln	p.H2116Q	ENST00000374080		2116	caC/caA	43/45	0.573676031385858	2	FACETS	0.302	0.23	0.385			1	SUBCLONAL	1	TRUE	NA	0.719786454676496	2		252	175	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971077	21971077	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	84	257	0	ENST00000304494.5:c.281T>A	p.Leu94Gln	p.L94Q	ENST00000304494	NM_000077.4	94	cTg/cAg	2/3	0.719786454676496	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.719786454676496	2		257	106	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104642	69104642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	69	513	0	ENST00000288368.4:c.4486G>A	p.Ala1496Thr	p.A1496T	ENST00000288368	NM_024870.2	1496	Gct/Act	37/40	0.379633713453921	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.719786454676496	0		513	172	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466326	120466326	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	102	401	2	ENST00000256646.2:c.4793C>T	p.Ala1598Val	p.A1598V	ENST00000256646	NM_024408.3	1598	gCt/gTt	26/34	0.435653922195095	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.719786454676496	3		403	180	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786134	3786134	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	56	561	0	ENST00000262367.5:c.4631T>G	p.Phe1544Cys	p.F1544C	ENST00000262367	NM_004380.2	1544	tTc/tGc	28/31	0.719786454676496	3	FACETS	0.932	0.808	1	0.466	0.404	0.532	CLONAL	1	TRUE	1	0.719786454676496	3		561	227	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795423	42795423	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	51	439	0	ENST00000575354.2:c.2503C>A	p.Gln835Lys	p.Q835K	ENST00000575354	NM_015125.3	835	Cag/Aag	10/20	0.691183237836653	3	FACETS	1	0.879	1	0.51	0.44	0.584	CLONAL	1	TRUE	1	0.719786454676496	3		439	189	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902158	50902158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373637566	NA	P-0028633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	55	497	0	ENST00000440232.2:c.50G>A	p.Arg17Gln	p.R17Q	ENST00000440232	NM_002691.3	17	cGg/cAg	2/27	0.691183237836653	3	FACETS	1	0.948	1	0.59	0.514	0.67	CLONAL	1	TRUE	1	0.719786454676496	3		497	176	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569662	41569662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	47	254	0	ENST00000263253.7:c.4653G>T	p.Lys1551Asn	p.K1551N	ENST00000263253	NM_001429.3	1551	aaG/aaT	29/31	0.719786454676496	3	FACETS	0.875	0.747	1	0.437	0.373	0.506	CLONAL	1	TRUE	1	0.719786454676496	3		254	203	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670622	134670622	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	46	526	2	ENST00000398015.3:c.533A>G	p.Gln178Arg	p.Q178R	ENST00000398015	NM_004441.4	178	cAg/cGg	3/16	0.719786454676496	3	FACETS	0.836	0.712	0.969	0.418	0.356	0.485	CLONAL	1	TRUE	1	0.719786454676496	3		528	208	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005134	150005134	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	131	373	1	ENST00000253339.5:c.1091del	p.Pro364LeufsTer5	p.P364Lfs*5	ENST00000253339		364	cCt/ct	3/7	0.479522818619881	3	FACETS	1	0.98	1			1	CLONAL	2	TRUE	NA	0.719786454676496	3		374	218	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381519	81381519	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	89	338	0	ENST00000222390.5:c.542G>C	p.Arg181Pro	p.R181P	ENST00000222390	NM_000601.4	181	cGa/cCa	5/18	0.356953972438	5	FACETS	1	0.967	1	0.776	0.701	0.852	INDETERMINATE	2	TRUE	2	0.719786454676496	5		338	221	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139411787	139411787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	128	575	1	ENST00000277541.6:c.1492C>T	p.Pro498Ser	p.P498S	ENST00000277541	NM_017617.3	498	Ccc/Tcc	9/34	0.719786454676496	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.719786454676496	2		576	171	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652291	206652291	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	314	554	0	ENST00000367120.3:c.998C>G	p.Ala333Gly	p.A333G	ENST00000367120	NM_014002.3	333	gCc/gGc	10/22	0.322730098496426	4	FACETS	0.882	0.833	0.933	0.882	0.833	0.933	CLONAL	2	TRUE	2	0.49626527054532	4		554	1073	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213485	36213485	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1284	523	1032	0	ENST00000222270.7:c.2587G>T	p.Val863Leu	p.V863L	ENST00000222270	NM_014727.1	863	Gtg/Ttg	5/37	0.410792101767396	4	FACETS	0.873	0.835	0.911	0.873	0.835	0.911	CLONAL	2	TRUE	2	0.49626527054532	4		1032	1807	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437441	52437441	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	59	413	0	ENST00000460680.1:c.1720G>T	p.Ala574Ser	p.A574S	ENST00000460680	NM_004656.3	574	Gcg/Tcg	13/17	0.467225710535105	2	FACETS	0.433	0.373	0.499	0.217	0.186	0.25	SUBCLONAL	1	TRUE	0	0.49626527054532	2		413	549	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0028906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	98	561	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.306843219537953	1	FACETS	0.956	0.858	1	0.956	0.858	1	CLONAL	1	TRUE	0	0.388569907417651	1		562	425	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220691	1220691	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs878853247	NA	P-0028906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	155	653	0	ENST00000326873.7:c.709G>T	p.Asp237Tyr	p.D237Y	ENST00000326873	NM_000455.4	237	Gac/Tac	5/10	0.388569907417651	1	FACETS	0.824	0.755	0.896	0.824	0.755	0.896	CLONAL	1	TRUE	0	0.388569907417651	1		653	780	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156848967	156848967	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	156	567	0	ENST00000524377.1:c.1859G>T	p.Gly620Val	p.G620V	ENST00000524377	NM_002529.3	620	gGc/gTc	15/17	1	2	FACETS	0.895	0.82	0.974	0.895	0.82	0.974	CLONAL	1	TRUE	1	0.388569907417651	2		567	897	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200943	108200943	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	74	272	0	ENST00000278616.4:c.7310A>C	p.Tyr2437Ser	p.Y2437S	ENST00000278616	NM_000051.3	2437	tAc/tCc	50/63	0.388569907417651	1	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	0	0.388569907417651	1		272	304	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197707	66197707	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	117	369	0	ENST00000273854.3:c.2992G>T	p.Ala998Ser	p.A998S	ENST00000273854	NM_004439.5	998	Gct/Tct	17/18	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.388569907417651	2		369	592	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1266635	1266635	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	118	488	0	ENST00000310581.5:c.2598G>C	p.Leu866Phe	p.L866F	ENST00000310581	NM_198253.2	866	ttG/ttC	10/16	NA	2	FACETS	0.823	0.743	0.907			1	INDETERMINATE	1	TRUE	NA	0.388569907417651	2		488	738	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372708	81372708	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	95	343	0	ENST00000222390.5:c.826C>A	p.Pro276Thr	p.P276T	ENST00000222390	NM_000601.4	276	Cct/Act	7/18	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.388569907417651	2		343	483	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0028925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	55	286	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.220792535225544	5	FACETS	1	0.955	1	0.796	0.701	0.894	INDETERMINATE	2	TRUE	2	0.743831381274532	5		286	131	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836985	89836985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs539161141	NA	P-0028925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	11	529	0	ENST00000389301.3:c.2209G>A	p.Ala737Thr	p.A737T	ENST00000389301	NM_000135.2	737	Gct/Act	24/43	0.743831381274532	1	FACETS	0.094	0.065	0.131	0.094	0.065	0.131	SUBCLONAL	1	TRUE	0	0.743831381274532	1		529	197	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578421	7578421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779000871	NA	P-0028925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	10	548	0	ENST00000269305.4:c.509C>T	p.Thr170Met	p.T170M	ENST00000269305	NM_001126112.2	170	aCg/aTg	5/11	0.38462288734408	4	FACETS	0.156	0.105	0.221	0.078	0.052	0.111	INDETERMINATE	1	TRUE	2	0.743831381274532	4		548	300	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0028925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	100	720	0	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	0.201353047180817	4	FACETS	0.953	0.867	1	0.953	0.867	1	INDETERMINATE	2	TRUE	2	0.743831381274532	4		720	246	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536873	120536873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	15	628	1	ENST00000229340.5:c.313G>A	p.Glu105Lys	p.E105K	ENST00000229340	NM_006861.6	105	Gaa/Aaa	4/6	0.152010091894986	4	FACETS	0.236	0.172	0.313	0.118	0.086	0.157	INDETERMINATE	1	TRUE	2	0.743831381274532	4		629	298	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115940	8115940	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	145	404	0	ENST00000346208.3:c.1287del	p.Phe430LeufsTer45	p.F430Lfs*45	ENST00000346208		429	tCc/tc	6/6	0.201353047180817	4	FACETS	0.968	0.896	1	0.968	0.896	1	INDETERMINATE	2	TRUE	2	0.743831381274532	4		404	351	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352538	118352538	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	109	599	0	ENST00000534358.1:c.3743del	p.Ala1248GlufsTer108	p.A1248Efs*108	ENST00000534358	NM_005933.3	1248	gCa/ga	7/36	0.201353047180817	4	FACETS	1	0.92	1	1	0.92	1	INDETERMINATE	2	TRUE	2	0.743831381274532	4		599	254	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351844	89351844	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1041612791	NA	P-0028925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	10	743	1	ENST00000301030.4:c.1106A>G	p.Lys369Arg	p.K369R	ENST00000301030	NM_001256183.1	369	aAg/aGg	9/13	0.743831381274532	1	FACETS	0.12	0.081	0.168	0.12	0.081	0.168	SUBCLONAL	1	TRUE	0	0.743831381274532	1		744	141	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177762	56177763	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0028925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	47	382	0	ENST00000399503.3:c.2739dup	p.Gly914ArgfsTer16	p.G914Rfs*16	ENST00000399503	NM_005921.1	912	gga/ggAa	14/20	0.743831381274532	4	FACETS	1	0.965	1	0.74	0.637	0.848	CLONAL	1	TRUE	2	0.743831381274532	4		382	149	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777996	27777996	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	125	533	0	ENST00000369163.2:c.145C>G	p.Leu49Val	p.L49V	ENST00000369163	NM_003536.2	49	Ctc/Gtc	1/1	0.743831381274532	8	FACETS	0.877	0.8	0.955	0.657	0.6	0.717	CLONAL	3	TRUE	4	0.743831381274532	8		533	413	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841834	151841834	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	57	314	0	ENST00000262189.6:c.14307G>A	p.Trp4769Ter	p.W4769*	ENST00000262189	NM_170606.2	4769	tgG/tgA	55/59	0.201353047180817	4	FACETS	0.903	0.794	1	0.903	0.794	1	INDETERMINATE	2	TRUE	2	0.743831381274532	4		314	148	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012175	16012175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184177098	NA	P-0028978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	142	502	0	ENST00000268712.3:c.2107G>A	p.Ala703Thr	p.A703T	ENST00000268712	NM_006311.3	703	Gct/Act	19/46	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.341765614598086	2		502	774	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795390	39795392	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0028978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	136	666	0	ENST00000288319.7:c.328_330del	p.Glu110del	p.E110del	ENST00000288319	NM_182918.3	110	GAG/-	3/10	1	2	FACETS	0.942	0.856	1	0.942	0.856	1	CLONAL	1	TRUE	1	0.341765614598086	2		666	845	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0029065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	32	340	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.437	0.354	0.53	0.437	0.354	0.53	SUBCLONAL	1	TRUE	1	0.316555089464578	2		341	463	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331979	81331979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763933267	NA	P-0029065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	20	272	1	ENST00000222390.5:c.2105G>A	p.Arg702His	p.R702H	ENST00000222390	NM_000601.4	702	cGt/cAt	18/18	1	2	FACETS	0.466	0.357	0.594	0.466	0.357	0.594	SUBCLONAL	1	TRUE	1	0.316555089464578	2		273	271	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66524024	66524025	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TAAA	novel	NA	P-0029065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	18	205	0	ENST00000358598.2:c.753_756dup	p.Val253Ter	p.V253*	ENST00000358598	NM_212471.2	251	agt/agTAAAt	8/11	1	2	FACETS	0.552	0.417	0.711	0.552	0.417	0.711	SUBCLONAL	1	TRUE	1	0.316555089464578	2		205	206	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	176	205	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.263921799704457	3	FACETS	0.848	0.787	0.909	0.848	0.787	0.909	INDETERMINATE	2	TRUE	1	0.532144215867236	3		205	494	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	408	660	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.986	1	1	0.997	1	CLONAL	2	TRUE	1	0.532144215867236	2		663	725	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	330	584	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.532144215867236	2		584	1143	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	161	639	9	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.877	0.807	0.95	0.877	0.807	0.95	CLONAL	1	TRUE	1	0.532144215867236	2		648	690	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176338	24176338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	297	695	0	ENST00000263121.7:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000263121	NM_003073.3	377	Cgt/Tgt	9/9	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.532144215867236	2		695	1113	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118934	70118934	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	302	815	0	ENST00000245479.2:c.506A>G	p.His169Arg	p.H169R	ENST00000245479	NM_000346.3	169	cAc/cGc	2/3	1	2	FACETS	0.973	0.916	1	0.973	0.916	1	CLONAL	1	TRUE	1	0.532144215867236	2		815	1167	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	110	869	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.303741854453563	1	FACETS	0.731	0.662	0.803	0.731	0.662	0.803	INDETERMINATE	1	TRUE	0	0.532144215867236	1		869	415	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	111	339	2	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	1	2	FACETS	0.948	0.858	1	0.948	0.858	1	CLONAL	1	TRUE	1	0.532144215867236	2		341	440	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	47	156	0	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	1	FACETS	0.888	0.765	1	0.888	0.765	1	CLONAL	1	TRUE	0	0.532144215867236	1		156	146	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659675	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	304	627	1	ENST00000269305.4:c.764T>C	p.Ile255Thr	p.I255T	ENST00000269305	NM_001126112.2	255	aTc/aCc	7/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.532144215867236	2		628	974	SUCCESS
APC	324	MSKCC	GRCh37	5	112174096	112174096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs137854575	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	139	385	0	ENST00000257430.4:c.2805C>A	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	taC/taA	16/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.532144215867236	2		385	443	SUCCESS
APC	324	MSKCC	GRCh37	5	112175675	112175676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	124	403	0	ENST00000257430.4:c.4393_4394dup	p.Ser1465ArgfsTer9	p.S1465Rfs*9	ENST00000257430	NM_000038.5	1462	aag/aAGag	16/16	1	2	FACETS	0.896	0.815	0.981	0.896	0.815	0.981	CLONAL	1	TRUE	1	0.532144215867236	2		403	520	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	400	258	0	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	0.532144215867236	3	FACETS	0.942	0.899	0.986	0.942	0.899	0.986	CLONAL	2	TRUE	1	0.532144215867236	3		258	1010	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239082	98239082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781101191	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	203	459	1	ENST00000331920.6:c.1561G>A	p.Ala521Thr	p.A521T	ENST00000331920	NM_000264.3	521	Gcc/Acc	11/24	1	2	FACETS	0.966	0.898	1	0.966	0.898	1	CLONAL	1	TRUE	1	0.532144215867236	2		460	790	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	54	314	1	ENST00000375687.4:c.1933_1934dup	p.Gly646ValfsTer58	p.G646Vfs*58	ENST00000375687	NM_015338.5	642	-/GG	13/13	1	2	FACETS	0.628	0.54	0.724	0.628	0.54	0.724	SUBCLONAL	1	TRUE	1	0.532144215867236	2		315	323	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687471	37687472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs760014508	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	116	343	2	ENST00000447079.4:c.4382dup	p.Thr1463AsnfsTer50	p.T1463Nfs*50	ENST00000447079	NM_015083.1	1459	tgg/tGgg	14/14	1	2	FACETS	0.791	0.716	0.87	0.791	0.716	0.87	SUBCLONAL	1	TRUE	1	0.532144215867236	2		345	551	SUCCESS
AR	367	MSKCC	GRCh37	X	66765164	66765164	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs867801558	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	34	142	0	ENST00000374690.3:c.176A>T	p.Gln59Leu	p.Q59L	ENST00000374690	NM_000044.3	59	cAg/cTg	1/8	1	1	FACETS	0.665	0.553	0.787	0.665	0.553	0.787	SUBCLONAL	1	TRUE	0	0.532144215867236	1		142	141	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939260	71939260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	287	697	0	ENST00000298229.2:c.209G>A	p.Arg70His	p.R70H	ENST00000298229	NM_001567.3	70	cGc/cAc	2/28	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.532144215867236	2		697	1041	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948208	71948209	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs749079348	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	372	934	7	ENST00000298229.2:c.2927dup	p.Pro977ThrfsTer7	p.P977Tfs*7	ENST00000298229	NM_001567.3	974	gcc/gCcc	26/28	1	2	FACETS	0.934	0.885	0.984	0.934	0.885	0.984	CLONAL	1	TRUE	1	0.532144215867236	2		941	1497	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089688	27089688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	308	615	1	ENST00000324856.7:c.2644G>A	p.Gly882Arg	p.G882R	ENST00000324856	NM_006015.4	882	Ggg/Agg	8/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.532144215867236	2		616	962	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101687	27101687	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	68	870	0	ENST00000324856.7:c.4969del	p.Arg1657GlyfsTer5	p.R1657Gfs*5	ENST00000324856	NM_006015.4	1657	Agg/gg	18/20	1	2	FACETS	0.216	0.187	0.248	0.216	0.187	0.248	SUBCLONAL	1	TRUE	1	0.532144215867236	2		870	1182	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981777	201981778	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	322	711	0	ENST00000359651.3:c.492dup	p.Phe165LeufsTer31	p.F165Lfs*31	ENST00000359651		163	agc/agCc	4/8	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.532144215867236	2		711	1058	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421542	32421542	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	216	514	0	ENST00000332351.3:c.1050C>A	p.Cys350Ter	p.C350*	ENST00000332351	NM_024426.4	350	tgC/tgA	6/10	1	2	FACETS	0.918	0.855	0.984	0.918	0.855	0.984	CLONAL	1	TRUE	1	0.532144215867236	2		514	884	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456500	32456502	+	inframe_deletion	In_Frame_Del	DEL	GGT	GGT	-	novel	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	17	123	0	ENST00000332351.3:c.390_392del	p.Pro136del	p.P136del	ENST00000332351	NM_024426.4	130	ccACCc/ccc	1/10	1	2	FACETS	0.307	0.23	0.399	0.307	0.23	0.399	SUBCLONAL	1	TRUE	1	0.532144215867236	2		123	208	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562379	21562379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760674320	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	250	586	0	ENST00000382592.4:c.1540C>T	p.Pro514Ser	p.P514S	ENST00000382592	NM_014572.2	514	Ccg/Tcg	4/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.532144215867236	2		586	885	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819299	3819299	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	259	646	1	ENST00000262367.5:c.2936C>T	p.Ala979Val	p.A979V	ENST00000262367	NM_004380.2	979	gCc/gTc	15/31	1	2	FACETS	0.96	0.9	1	0.96	0.9	1	CLONAL	1	TRUE	1	0.532144215867236	2		647	1014	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67646012	67646013	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	185	447	3	ENST00000264010.4:c.950_951dup	p.Gly318GlnfsTer16	p.G318Qfs*16	ENST00000264010	NM_006565.3	314	aac/aACac	4/12	1	2	FACETS	0.977	0.905	1	0.977	0.905	1	CLONAL	1	TRUE	1	0.532144215867236	2		450	712	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044533	12044533	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	186	475	0	ENST00000353533.5:c.1156G>T	p.Asp386Tyr	p.D386Y	ENST00000353533	NM_003010.3	386	Gat/Tat	11/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.532144215867236	2		475	652	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40364060	40364060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	138	236	0	ENST00000293328.3:c.1622G>A	p.Ser541Asn	p.S541N	ENST00000293328	NM_012448.3	541	aGc/aAc	13/19	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.532144215867236	2		236	414	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40498603	40498603	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	37	399	0	ENST00000264657.5:c.257T>C	p.Ile86Thr	p.I86T	ENST00000264657	NM_139276.2	86	aTc/aCc	3/24	1	2	FACETS	0.224	0.184	0.269	0.224	0.184	0.269	SUBCLONAL	1	TRUE	1	0.532144215867236	2		399	621	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609310	39609310	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	119	285	0	ENST00000262039.4:c.1612A>G	p.Met538Val	p.M538V	ENST00000262039	NM_002647.2	538	Atg/Gtg	15/25	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.532144215867236	2		285	422	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551222	29551222	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	233	572	0	ENST00000389048.3:c.1408A>G	p.Met470Val	p.M470V	ENST00000389048	NM_004304.4	470	Atg/Gtg	6/29	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.532144215867236	2		572	755	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389170	31389170	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	230	576	0	ENST00000328111.2:c.2083A>G	p.Met695Val	p.M695V	ENST00000328111	NM_006892.3	695	Atg/Gtg	19/23	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.532144215867236	2		576	858	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934211	49934211	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1250580860	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	316	766	0	ENST00000296474.3:c.2296T>C	p.Tyr766His	p.Y766H	ENST00000296474	NM_002447.2	766	Tac/Cac	8/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.532144215867236	2		766	1081	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231299	142231299	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	176	391	0	ENST00000350721.4:c.4655T>A	p.Ile1552Asn	p.I1552N	ENST00000350721	NM_001184.3	1552	aTt/aAt	27/47	0.263921799704457	3	FACETS	0.777	0.721	0.835	0.777	0.721	0.835	INDETERMINATE	2	TRUE	1	0.532144215867236	3		391	539	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245352	153245352	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	176	541	1	ENST00000281708.4:c.1839T>A	p.Cys613Ter	p.C613*	ENST00000281708	NM_033632.3	613	tgT/tgA	11/12	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.532144215867236	2		542	580	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109322563	109322563	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	242	664	1	ENST00000436639.2:c.474A>T	p.Leu158Phe	p.L158F	ENST00000436639	NM_014454.2	158	ttA/ttT	3/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.532144215867236	2		665	741	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710800	117710800	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	144	420	0	ENST00000368508.3:c.1472T>C	p.Leu491Pro	p.L491P	ENST00000368508	NM_002944.2	491	cTa/cCa	12/43	1	2	FACETS	0.997	0.914	1	0.997	0.914	1	CLONAL	1	TRUE	1	0.532144215867236	2		420	543	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026709	6026709	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587778618	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	279	817	0	ENST00000265849.7:c.1687C>T	p.Arg563Ter	p.R563*	ENST00000265849	NM_000535.5	563	Cga/Tga	11/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.532144215867236	2		817	1017	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845958	151845959	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	193	581	0	ENST00000262189.6:c.13053dup	p.Trp4352MetfsTer17	p.W4352Mfs*17	ENST00000262189	NM_170606.2	4351	-/A	52/59	1	2	FACETS	0.923	0.856	0.992	0.923	0.856	0.992	CLONAL	1	TRUE	1	0.532144215867236	2		581	786	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964514	70964514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762086448	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	220	618	0	ENST00000276594.2:c.1514G>A	p.Arg505His	p.R505H	ENST00000276594	NM_024504.3	505	cGc/cAc	8/8	0.532144215867236	3	FACETS	0.913	0.848	0.979	0.456	0.424	0.49	CLONAL	1	TRUE	1	0.532144215867236	3		618	1147	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412261	63412262	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	289	423	0	ENST00000330258.3:c.905dup	p.Asn302LysfsTer22	p.N302Kfs*22	ENST00000330258	NM_152424.3	302	aat/aaAt	2/2	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.532144215867236	1		423	572	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268766	41268766	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	236	532	0	ENST00000349496.5:c.1004A>C	p.Lys335Thr	p.K335T	ENST00000349496	NM_001904.3	335	aAa/aCa	7/15	0.504473496258577	5	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	2	0.519657197671547	5		532	504	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163325254	163325338	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	ACCTGATTAACAAAATTACATGTCTTTTTGTAAATGGCTTGCCATCTTTTAATTTTCTATTTAGAAAGAAAAGTTGAAGCGAATG	ACCTGATTAACAAAATTACATGTCTTTTTGTAAATGGCTTGCCATCTTTTAATTTTCTATTTAGAAAGAAAAGTTGAAGCGAATG	CA	novel	NA	P-0029243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	34	359	2	ENST00000271452.3:c.1390_*79delinsCA		p.*464*	ENST00000271452	NM_145697.2	464		14/14	0.352887165045584	5	FACETS	1	0.938	1	0.446	0.369	0.531	CLONAL	1	TRUE	2	0.519657197671547	5		361	174	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112242	115112242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	106	190	1	ENST00000257566.3:c.1498G>A	p.Gly500Ser	p.G500S	ENST00000257566	NM_016569.3	500	Ggc/Agc	7/8	0.484141816218339	3	FACETS	1	0.961	1	0.726	0.664	0.788	CLONAL	2	TRUE	0	0.519657197671547	3		191	236	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339029	225339029	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	65	572	0	ENST00000264414.4:c.2240G>A	p.Gly747Glu	p.G747E	ENST00000264414	NM_003590.4	747	gGa/gAa	16/16	0.519657197671547	3	FACETS	0.911	0.795	1	0.455	0.397	0.518	CLONAL	1	TRUE	1	0.519657197671547	3		572	346	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268721	98268722	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCTC	novel	NA	P-0029243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	130	454	0	ENST00000331920.6:c.361_362insGAGC	p.Leu121ArgfsTer20	p.L121Rfs*20	ENST00000331920	NM_000264.3	121	ctc/cGAGCtc	2/24	0.493062451235156	5	FACETS	0.998	0.905	1	0.333	0.301	0.366	CLONAL	1	TRUE	2	0.519657197671547	5		454	892	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911462	101911462	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	82	273	0	ENST00000374994.4:c.1387G>A	p.Ala463Thr	p.A463T	ENST00000374994	NM_004612.2	463	Gcc/Acc	9/9	0.493062451235156	5	FACETS	1	0.943	1	0.723	0.646	0.802	CLONAL	2	TRUE	2	0.519657197671547	5		273	259	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0029254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	171	875	1	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.154660208523218	2	FACETS	1	0.987	1	0.683	0.629	0.741	INDETERMINATE	1	TRUE	0	0.274960587806602	2		876	910	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0029254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	107	631	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.0709229161574414	4	FACETS	1	0.976	1	0.651	0.584	0.722	INDETERMINATE	1	TRUE	2	0.274960587806602	4		631	762	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841514	156841514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151334385	NA	P-0029254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	149	887	3	ENST00000524377.1:c.817C>T	p.Arg273Trp	p.R273W	ENST00000524377	NM_002529.3	273	Cgg/Tgg	7/17	0.0903718237804145	3	FACETS	1	0.969	1	0.569	0.518	0.621	INDETERMINATE	1	TRUE	1	0.274960587806602	3		890	1084	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523018	25523018	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	90	777	0	ENST00000264709.3:c.167A>G	p.Lys56Arg	p.K56R	ENST00000264709	NM_175629.2	56	aAg/aGg	3/23	1	2	FACETS	0.659	0.584	0.741	0.659	0.584	0.741	SUBCLONAL	1	TRUE	1	0.274960587806602	2		777	993	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0029260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	13	531	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.826	0.589	1	0.826	0.589	1	CLONAL	1	TRUE	1	0.13	2		531	242	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10267124	10267124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751093624	NA	P-0029260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	10	538	0	ENST00000340748.4:c.1294G>A	p.Glu432Lys	p.E432K	ENST00000340748		432	Gaa/Aaa	17/40	1	2	FACETS	0.367	0.247	0.519	0.367	0.247	0.519	SUBCLONAL	1	TRUE	1	0.13	2		538	419	SUCCESS
APC	324	MSKCC	GRCh37	5	112179566	112179566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755366812	NA	P-0029260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	10	455	3	ENST00000257430.4:c.8275C>T	p.Arg2759Cys	p.R2759C	ENST00000257430	NM_000038.5	2759	Cgt/Tgt	16/16	1	2	FACETS	0.921	0.625	1	0.921	0.625	1	CLONAL	1	TRUE	1	0.13	2		458	167	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0029292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	987	398	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.911775464536531	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.911775464536531	2		398	1035	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050884	49050884	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	369	488	0	ENST00000267163.4:c.2569del	p.Arg857ValfsTer16	p.R857Vfs*16	ENST00000267163	NM_000321.2	856	gaC/ga	25/27	0.42139363869747	3	FACETS	0.865	0.829	0.901	0.865	0.829	0.901	INDETERMINATE	2	TRUE	1	0.911775464536531	3		488	681	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0029322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	138	427	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.846100498603805	3	FACETS	0.953	0.873	1	0.477	0.436	0.518	CLONAL	1	TRUE	1	0.846100498603805	3		427	487	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	147	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.893	0.825	0.963	0.893	0.825	0.963	CLONAL	1	TRUE	1	0.846100498603805	2		306	389	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885731	23885731	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	277	541	0	ENST00000374561.5:c.187C>T	p.Gln63Ter	p.Q63*	ENST00000374561	NM_002167.4	63	Cag/Tag	1/3	1	2	FACETS	0.982	0.928	1	0.982	0.928	1	CLONAL	1	TRUE	1	0.846100498603805	2		541	667	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100463	8100463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	348	640	0	ENST00000346208.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000346208		146	gCc/gTc	3/6	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.846100498603805	2		640	765	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121064	3121064	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	271	654	0	ENST00000078429.4:c.967A>G	p.Ile323Val	p.I323V	ENST00000078429	NM_002067.2	323	Atc/Gtc	7/7	1	2	FACETS	0.881	0.831	0.932	0.881	0.831	0.932	CLONAL	1	TRUE	1	0.846100498603805	2		654	727	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0029378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	186	286	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.349997457654894	3	FACETS	0.845	0.782	0.91	0.845	0.782	0.91	CLONAL	2	TRUE	1	0.349997457654894	3		286	739	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88677065	88677065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765530074	NA	P-0029378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	116	552	0	ENST00000372037.3:c.850C>T	p.Arg284Cys	p.R284C	ENST00000372037	NM_004329.2	284	Cgc/Tgc	9/13	1	2	FACETS	0.831	0.749	0.917	0.831	0.749	0.917	CLONAL	1	TRUE	1	0.349997457654894	2		552	798	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115394	115115394	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	112	516	0	ENST00000257566.3:c.932G>C	p.Arg311Thr	p.R311T	ENST00000257566	NM_016569.3	311	aGa/aCa	5/8	1	2	FACETS	0.816	0.734	0.903	0.816	0.734	0.903	CLONAL	1	TRUE	1	0.349997457654894	2		516	784	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484436	57484436	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	83	399	0	ENST00000371085.3:c.617G>A	p.Gly206Glu	p.G206E	ENST00000371085	NM_000516.4	206	gGa/gAa	8/13	0.305190629124318	3	FACETS	0.868	0.766	0.977	0.434	0.383	0.489	CLONAL	1	TRUE	1	0.349997457654894	3		399	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0029391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	241	551	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.591087369930266	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.607820265190341	1		551	508	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056314	26056314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1355795147	NA	P-0029391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	143	327	0	ENST00000343677.2:c.343G>A	p.Glu115Lys	p.E115K	ENST00000343677	NM_005319.3	115	Gaa/Aaa	1/1	1	2	FACETS	0.966	0.887	1	0.966	0.887	1	CLONAL	1	TRUE	1	0.607820265190341	2		327	487	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852737	63852737	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	171	418	0	ENST00000279873.7:c.3515C>T	p.Ala1172Val	p.A1172V	ENST00000279873	NM_032199.2	1172	gCt/gTt	10/10	1	2	FACETS	0.863	0.797	0.931	0.863	0.797	0.931	CLONAL	1	TRUE	1	0.607820265190341	2		418	652	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752376	55752376	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	304	777	0	ENST00000284073.2:c.834C>G	p.Ser278Arg	p.S278R	ENST00000284073	NM_138962.2	278	agC/agG	12/14	0.607793670009462	2	FACETS	0.968	0.914	1	0.484	0.457	0.512	CLONAL	1	TRUE	0	0.607820265190341	2		777	1033	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15280910	15280910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761061422	NA	P-0029391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2821	325	720	0	ENST00000263388.2:c.5186C>T	p.Ala1729Val	p.A1729V	ENST00000263388	NM_000435.2	1729	gCc/gTc	28/33	0.607820265190341	8	FACETS	0.96	0.901	1			1	CLONAL	1	TRUE	NA	0.607820265190341	8		720	3146	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504977	186504977	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	165	353	0	ENST00000323963.5:c.837del	p.Leu280SerfsTer10	p.L280Sfs*10	ENST00000323963		278	aTt/at	8/11	NA	2	FACETS	0.948	0.875	1			1	INDETERMINATE	1	TRUE	NA	0.607820265190341	2		353	573	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742490	145742490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776385170	NA	P-0029391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1602	296	604	1	ENST00000428558.2:c.298G>A	p.Gly100Ser	p.G100S	ENST00000428558	NM_004260.3	100	Ggc/Agc	4/22	0.535444120084434	5	FACETS	0.981	0.92	1			1	CLONAL	1	TRUE	NA	0.607820265190341	5		605	1898	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	92	532	1	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	0.313	0.277	0.351	0.313	0.277	0.351	SUBCLONAL	1	TRUE	1	0.680634147894121	2		533	864	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661664	227661664	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs761880048	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	141	379	4	ENST00000305123.5:c.1791del	p.His598ThrfsTer38	p.H598Tfs*38	ENST00000305123	NM_005544.2	597	ggG/gg	1/2	1	2	FACETS	0.863	0.792	0.937	0.863	0.792	0.937	CLONAL	1	TRUE	1	0.680634147894121	2		383	480	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806181	1806181	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760502257	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	302	656	1	ENST00000260795.2:c.1206del	p.Lys403ArgfsTer29	p.K403Rfs*29	ENST00000260795		400	agC/ag	8/17	1	2	FACETS	0.957	0.904	1	0.957	0.904	1	CLONAL	1	TRUE	1	0.680634147894121	2		657	927	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	62	866	4	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.249	0.215	0.287	0.249	0.215	0.287	SUBCLONAL	1	TRUE	1	0.680634147894121	2		870	731	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31379479	31379479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145632647	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	80	472	2	ENST00000328111.2:c.886G>A	p.Val296Ile	p.V296I	ENST00000328111	NM_006892.3	296	Gtc/Atc	8/23	1	2	FACETS	0.328	0.289	0.371	0.328	0.289	0.371	SUBCLONAL	1	TRUE	1	0.680634147894121	2		474	716	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	217	526	2	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.858	0.801	0.917	0.858	0.801	0.917	CLONAL	1	TRUE	1	0.680634147894121	2		528	743	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	217	632	10	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.956	0.893	1	0.956	0.893	1	CLONAL	1	TRUE	1	0.680634147894121	2		642	667	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769886672	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	104	268	1	ENST00000405192.2:c.414dup	p.Thr139HisfsTer24	p.T139Hfs*24	ENST00000405192	NM_001163147.1	138	-/C	7/12	1	2	FACETS	0.782	0.705	0.861	0.782	0.705	0.861	SUBCLONAL	1	TRUE	1	0.680634147894121	2		269	391	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	137	484	1	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.956	0.878	1	0.956	0.878	1	CLONAL	1	TRUE	1	0.680634147894121	2		485	421	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103755	47103756	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	53	484	1	ENST00000409792.3:c.6190_6191del	p.Asp2064ProfsTer8	p.D2064Pfs*8	ENST00000409792	NM_014159.6	2064	GAc/c	14/21	1	2	FACETS	0.235	0.2	0.274	0.235	0.2	0.274	SUBCLONAL	1	TRUE	1	0.680634147894121	2		485	663	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533905	63533905	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	47	380	0	ENST00000307078.5:c.1249del	p.Ala417ArgfsTer41	p.A417Rfs*41	ENST00000307078	NM_004655.3	417	Gcg/cg	6/11	1	2	FACETS	0.227	0.191	0.267	0.227	0.191	0.267	SUBCLONAL	1	TRUE	1	0.680634147894121	2		380	609	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	226	280	5	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	0.942	0.881	1	0.942	0.881	1	CLONAL	1	TRUE	1	0.680634147894121	2		285	705	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121266	29121266	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730881701	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	203	568	0	ENST00000328354.6:c.409C>T	p.Arg137Ter	p.R137*	ENST00000328354	NM_007194.3	137	Cga/Tga	3/15	1	2	FACETS	0.89	0.829	0.953	0.89	0.829	0.953	CLONAL	1	TRUE	1	0.680634147894121	2		568	670	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611131	100611131	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782338603	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	234	558	1	ENST00000308731.7:c.1475G>A	p.Arg492His	p.R492H	ENST00000308731	NM_000061.2	492	cGc/cAc	15/19	1	2	FACETS	0.911	0.853	0.97	0.911	0.853	0.97	CLONAL	1	TRUE	1	0.680634147894121	2		559	755	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912075	50912077	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs398122386	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	267	635	1	ENST00000440232.2:c.1812_1814del	p.Ser605del	p.S605del	ENST00000440232	NM_002691.3	603	ttCTCc/ttc	15/27	1	2	FACETS	0.871	0.818	0.924	0.871	0.818	0.924	CLONAL	1	TRUE	1	0.680634147894121	2		636	901	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	89	376	0	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.336	0.298	0.377	0.336	0.298	0.377	SUBCLONAL	1	TRUE	1	0.680634147894121	2		376	778	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135247	2135247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769834772	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	147	616	0	ENST00000219476.3:c.4586G>A	p.Arg1529Gln	p.R1529Q	ENST00000219476	NM_000548.3	1529	cGg/cAg	36/42	1	2	FACETS	0.439	0.4	0.48	0.439	0.4	0.48	SUBCLONAL	1	TRUE	1	0.680634147894121	2		616	984	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	273	650	0	ENST00000227507.2:c.859C>A	p.Pro287Thr	p.P287T	ENST00000227507	NM_053056.2	287	Ccc/Acc	5/5	1	2	FACETS	0.994	0.936	1	0.994	0.936	1	CLONAL	1	TRUE	1	0.680634147894121	2		650	807	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726567	41726567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781049505	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	243	528	0	ENST00000301178.4:c.112G>A	p.Val38Met	p.V38M	ENST00000301178	NM_021913.4	38	Gtg/Atg	2/20	1	2	FACETS	0.93	0.872	0.989	0.93	0.872	0.989	CLONAL	1	TRUE	1	0.680634147894121	2		528	768	SUCCESS
AR	367	MSKCC	GRCh37	X	66766198	66766198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	144	321	0	ENST00000374690.3:c.1210G>A	p.Ala404Thr	p.A404T	ENST00000374690	NM_000044.3	404	Gcg/Acg	1/8	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.680634147894121	2		321	417	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092758	27092758	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	199	469	2	ENST00000324856.7:c.2780del	p.Gly927AspfsTer14	p.G927Dfs*14	ENST00000324856	NM_006015.4	927	Gga/ga	9/20	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.680634147894121	2		471	583	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100452	8100452	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	175	569	1	ENST00000346208.3:c.431del	p.Gly144AlafsTer51	p.G144Afs*51	ENST00000346208		142	tcG/tc	3/6	1	2	FACETS	0.563	0.519	0.61	0.563	0.519	0.61	SUBCLONAL	1	TRUE	1	0.680634147894121	2		570	913	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685287	89685287	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	159	286	0	ENST00000371953.3:c.182A>C	p.His61Pro	p.H61P	ENST00000371953	NM_000314.4	61	cAt/cCt	3/9	0.677618885274133	2	FACETS	0.831	0.779	0.883	0.831	0.779	0.883	CLONAL	2	TRUE	0	0.680634147894121	2		286	281	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137231	64137231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1410769083	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	131	615	1	ENST00000334205.4:c.1663G>A	p.Ala555Thr	p.A555T	ENST00000334205	NM_003942.2	555	Gcg/Acg	14/17	1	2	FACETS	0.362	0.328	0.398	0.362	0.328	0.398	SUBCLONAL	1	TRUE	1	0.680634147894121	2		616	1063	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245309	46245309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	159	444	0	ENST00000334344.6:c.3403C>T	p.Pro1135Ser	p.P1135S	ENST00000334344	NM_152641.2	1135	Cca/Tca	15/21	1	2	FACETS	0.824	0.759	0.891	0.824	0.759	0.891	CLONAL	1	TRUE	1	0.680634147894121	2		444	567	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563285	21563285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1207863433	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	299	656	1	ENST00000382592.4:c.634G>A	p.Val212Met	p.V212M	ENST00000382592	NM_014572.2	212	Gtg/Atg	4/8	1	2	FACETS	0.956	0.903	1	0.956	0.903	1	CLONAL	1	TRUE	1	0.680634147894121	2		657	919	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975436	26975436	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	152	481	0	ENST00000381527.3:c.1065del	p.Lys355AsnfsTer5	p.K355Nfs*5	ENST00000381527	NM_001260.1	354	ccA/cc	11/13	1	2	FACETS	0.954	0.88	1	0.954	0.88	1	CLONAL	1	TRUE	1	0.680634147894121	2		481	468	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953563	32953563	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	169	613	2	ENST00000380152.3:c.8864C>T	p.Ala2955Val	p.A2955V	ENST00000380152		2955	gCt/gTt	22/27	1	2	FACETS	0.826	0.763	0.891	0.826	0.763	0.891	CLONAL	1	TRUE	1	0.680634147894121	2		615	601	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900569	3900569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	99	626	0	ENST00000262367.5:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000262367	NM_004380.2	176	tGc/tAc	2/31	1	2	FACETS	0.341	0.304	0.381	0.341	0.304	0.381	SUBCLONAL	1	TRUE	1	0.680634147894121	2		626	852	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029321	14029321	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs761759726	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	131	354	1	ENST00000311895.7:c.1532A>G	p.Glu511Gly	p.E511G	ENST00000311895	NM_005236.2	511	gAg/gGg	8/11	1	2	FACETS	0.761	0.694	0.83	0.761	0.694	0.83	SUBCLONAL	1	TRUE	1	0.680634147894121	2		355	506	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637666	23637666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	60	551	0	ENST00000261584.4:c.2639C>T	p.Ala880Val	p.A880V	ENST00000261584	NM_024675.3	880	gCc/gTc	7/13	1	2	FACETS	0.227	0.194	0.262	0.227	0.194	0.262	SUBCLONAL	1	TRUE	1	0.680634147894121	2		551	778	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645155	67645156	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	247	594	0	ENST00000264010.4:c.421dup	p.Glu141GlyfsTer4	p.E141Gfs*4	ENST00000264010	NM_006565.3	140	-/G	3/12	1	2	FACETS	0.986	0.926	1	0.986	0.926	1	CLONAL	1	TRUE	1	0.680634147894121	2		594	736	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110173	3110173	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	250	458	0	ENST00000078429.4:c.163T>A	p.Phe55Ile	p.F55I	ENST00000078429	NM_002067.2	55	Ttc/Atc	2/7	1	2	FACETS	0.972	0.913	1	0.972	0.913	1	CLONAL	1	TRUE	1	0.680634147894121	2		458	756	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18960928	18960928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	291	608	1	ENST00000262803.5:c.506C>T	p.Thr169Ile	p.T169I	ENST00000262803	NM_002911.3	169	aCc/aTc	4/24	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.680634147894121	2		609	828	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662789	227662791	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs755451703	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	283	580	0	ENST00000305123.5:c.664_666del	p.Phe222del	p.F222del	ENST00000305123	NM_005544.2	222	TTC/-	1/2	1	2	FACETS	0.891	0.839	0.944	0.891	0.839	0.944	CLONAL	1	TRUE	1	0.680634147894121	2		580	933	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589175	67589237	+	inframe_deletion	In_Frame_Del	DEL	GGAAATATGGCTTCTCTGACCCATTAACCTTCAGTTCTGTGGTTGAATTAATAAACCACTACC	GGAAATATGGCTTCTCTGACCCATTAACCTTCAGTTCTGTGGTTGAATTAATAAACCACTACC	-	novel	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	36	344	0	ENST00000274335.5:c.1167_1229del	p.Lys389_Arg409del	p.K389_R409del	ENST00000274335		388	gGGAAATATGGCTTCTCTGACCCATTAACCTTCAGTTCTGTGGTTGAATTAATAAACCACTACCgg/ggg	9/15	1	2	FACETS	0.346	0.285	0.413	0.346	0.285	0.413	SUBCLONAL	1	TRUE	1	0.680634147894121	2		344	306	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969445	44969445	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	226	558	0	ENST00000377967.4:c.4128del	p.Glu1376AspfsTer8	p.E1376Dfs*8	ENST00000377967	NM_021140.2	1376	gAa/ga	28/29	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.680634147894121	2		558	593	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183755	10183757	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs5030648	NA	P-0029642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	126	420	0	ENST00000256474.2:c.227_229del	p.Phe76del	p.F76del	ENST00000256474	NM_000551.3	75	aTCTtc/atc	1/3	1	2	FACETS	0.812	0.733	0.895	0.812	0.733	0.895	CLONAL	1	TRUE	1	0.282198527046014	2		420	1100	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439564	51439564	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0029642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	37	341	0	ENST00000262662.1:c.130-1G>T		p.X44_splice	ENST00000262662		44			1	2	FACETS	0.716	0.592	0.856	0.716	0.592	0.856	SUBCLONAL	1	TRUE	1	0.282198527046014	2		341	366	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374653	118374658	+	inframe_deletion	In_Frame_Del	DEL	ATACTA	ATACTA	-	novel	NA	P-0029642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	58	545	0	ENST00000534358.1:c.8046_8051del	p.Leu2682_Tyr2684delinsPhe	p.L2682_Y2684delinsF	ENST00000534358	NM_005933.3	2682	ttATACTAt/ttt	27/36	1	2	FACETS	0.739	0.635	0.853	0.739	0.635	0.853	SUBCLONAL	1	TRUE	1	0.282198527046014	2		545	556	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487930	56487930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370634710	NA	P-0029642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	101	799	0	ENST00000267101.3:c.1661C>T	p.Pro554Leu	p.P554L	ENST00000267101	NM_001982.3	554	cCg/cTg	14/28	1	2	FACETS	0.676	0.603	0.754	0.676	0.603	0.754	SUBCLONAL	1	TRUE	1	0.282198527046014	2		799	1059	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878068	48878069	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	42	286	1	ENST00000267163.4:c.25dup	p.Thr9AsnfsTer22	p.T9Nfs*22	ENST00000267163	NM_000321.2	7	cga/cgAa	1/27	1	2	FACETS	0.669	0.559	0.791	0.669	0.559	0.791	SUBCLONAL	1	TRUE	1	0.282198527046014	2		287	445	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632769	23632770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0029642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	70	691	0	ENST00000261584.4:c.3026dup	p.Glu1010Ter	p.E1010*	ENST00000261584	NM_024675.3	1009	cct/ccCt	10/13	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.282198527046014	2		691	482	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39542579	39542579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200002230	NA	P-0029642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	76	620	0	ENST00000262039.4:c.383C>T	p.Ser128Leu	p.S128L	ENST00000262039	NM_002647.2	128	tCg/tTg	3/25	1	2	FACETS	0.777	0.681	0.88	0.777	0.681	0.88	SUBCLONAL	1	TRUE	1	0.282198527046014	2		620	693	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262128	10262128	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	101	869	0	ENST00000340748.4:c.2163del	p.Lys722ArgfsTer55	p.K722Rfs*55	ENST00000340748		721	ggG/gg	23/40	1	2	FACETS	0.637	0.568	0.712	0.637	0.568	0.712	SUBCLONAL	1	TRUE	1	0.282198527046014	2		869	1123	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210908	36210908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369563501	NA	P-0029642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	121	989	3	ENST00000222270.7:c.659G>A	p.Arg220Gln	p.R220Q	ENST00000222270	NM_014727.1	220	cGg/cAg	3/37	1	2	FACETS	0.742	0.668	0.82	0.742	0.668	0.82	SUBCLONAL	1	TRUE	1	0.282198527046014	2		992	1156	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229086	36229110	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGGAAGGTGGGCTCCCAGTGGCTG	TGGGAAGGTGGGCTCCCAGTGGCTG	-	novel	NA	P-0029642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	85	818	1	ENST00000222270.7:c.7872+1_7872+25del		p.X2624_splice	ENST00000222270	NM_014727.1	2624		36/37	1	2	FACETS	0.575	0.507	0.648	0.575	0.507	0.648	SUBCLONAL	1	TRUE	1	0.282198527046014	2		819	1048	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162078	47162078	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	38	390	1	ENST00000409792.3:c.4048del	p.Ser1350GlnfsTer23	p.S1350Qfs*23	ENST00000409792	NM_014159.6	1350	Tca/ca	3/21	1	2	FACETS	0.748	0.62	0.891	0.748	0.62	0.891	SUBCLONAL	1	TRUE	1	0.282198527046014	2		391	360	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637540	52637540	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	37	539	0	ENST00000394830.3:c.2776del	p.Arg926GlufsTer82	p.R926Efs*82	ENST00000394830	NM_018313.4	926	Aga/ga	18/30	1	2	FACETS	0.947	0.784	1	0.947	0.784	1	CLONAL	1	TRUE	1	0.282198527046014	2		539	277	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672218	86672218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370631681	NA	P-0029642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	32	397	2	ENST00000274376.6:c.2020C>T	p.Arg674Cys	p.R674C	ENST00000274376	NM_002890.2	674	Cgc/Tgc	16/25	1	2	FACETS	0.52	0.422	0.631	0.52	0.422	0.631	SUBCLONAL	1	TRUE	1	0.282198527046014	2		399	436	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562686	176562686	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	74	806	0	ENST00000439151.2:c.582T>G	p.Asn194Lys	p.N194K	ENST00000439151	NM_022455.4	194	aaT/aaG	2/23	1	2	FACETS	0.633	0.553	0.719	0.633	0.553	0.719	SUBCLONAL	1	TRUE	1	0.282198527046014	2		806	829	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048554	180048554	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	97	723	2	ENST00000261937.6:c.2008C>A	p.Leu670Met	p.L670M	ENST00000261937	NM_182925.4	670	Ctg/Atg	13/30	1	2	FACETS	0.727	0.647	0.813	0.727	0.647	0.813	SUBCLONAL	1	TRUE	1	0.282198527046014	2		725	945	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0029768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	714	573	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.537463678956923	3	FACETS	0.939	0.921	0.956			1	CLONAL	3	TRUE	NA	0.845679519965231	3		573	853	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446209	29446209	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs774951734	NA	P-0029768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	161	361	0	ENST00000389048.3:c.3358C>T	p.Arg1120Trp	p.R1120W	ENST00000389048	NM_004304.4	1120	Cgg/Tgg	20/29	0.568213251383236	4	FACETS	0.997	0.917	1	0.498	0.458	0.54	CLONAL	1	TRUE	2	0.845679519965231	4		361	705	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	135	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.705433159078693	2		306	352	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0029776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	115	434	1	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	0.596396984234872	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.705433159078693	1		435	206	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0029776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	259	419	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.526252865515965	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.705433159078693	1		419	447	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980435	7980435	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760428119	NA	P-0029776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	310	601	0	ENST00000319144.4:c.1148C>T	p.Thr383Met	p.T383M	ENST00000319144	NM_001139.2	383	aCg/aTg	9/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.705433159078693	2		601	811	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692785	89692786	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGAAGACCATAACCCACCACAGCTAGAAC	novel	NA	P-0029776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	90	287	0	ENST00000371953.3:c.271_299dup	p.Ile101LysfsTer8	p.I101Kfs*8	ENST00000371953	NM_000314.4	90	ttt/ttTGAAGACCATAACCCACCACAGCTAGAACt	5/9	0.705433159078693	1	FACETS	0.616	0.555	0.68	0.616	0.555	0.68	SUBCLONAL	1	TRUE	0	0.705433159078693	1		287	268	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751550	57751550	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	122	267	0	ENST00000274289.3:c.1441G>T	p.Gly481Ter	p.G481*	ENST00000274289	NM_006622.3	481	Gga/Tga	11/14	1	2	FACETS	0.878	0.801	0.957	0.878	0.801	0.957	CLONAL	1	TRUE	1	0.705433159078693	2		267	394	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339422	116339422	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	104	310	0	ENST00000397752.3:c.284G>T	p.Cys95Phe	p.C95F	ENST00000397752	NM_000245.2	95	tGt/tTt	2/21	0.705433159078693	4	FACETS	0.651	0.583	0.724	0.326	0.291	0.362	SUBCLONAL	1	TRUE	2	0.705433159078693	4		310	772	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0029998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	36	416	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.225713478643649	1	FACETS	0.724	0.596	0.867	0.724	0.596	0.867	SUBCLONAL	1	TRUE	0	0.225713478643649	1		417	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0029998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	265	584	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.225713478643649	1	FACETS	0.959	0.904	1	1	0.996	1	CLONAL	3	TRUE	0	0.225713478643649	1		584	724	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0029998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	102	286	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	0.989	1	CLONAL	2	TRUE	1	0.225713478643649	2		286	390	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936983	48936983	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690863	NA	P-0029998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	229	404	1	ENST00000267163.4:c.751C>T	p.Arg251Ter	p.R251*	ENST00000267163	NM_000321.2	251	Cga/Tga	8/27	0.192184233882315	3	FACETS	0.982	0.927	1			1	CLONAL	5	TRUE	NA	0.225713478643649	3		405	460	SUCCESS
APC	324	MSKCC	GRCh37	5	112175982	112175982	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0029998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	78	281	0	ENST00000257430.4:c.4691T>G	p.Leu1564Ter	p.L1564*	ENST00000257430	NM_000038.5	1564	tTa/tGa	16/16	0.225713478643649	1	FACETS	1	0.955	1	1	0.986	1	CLONAL	2	TRUE	0	0.225713478643649	1		281	267	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908873	101908873	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200595614	NA	P-0029998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	140	517	1	ENST00000374994.4:c.1237C>T	p.Arg413Ter	p.R413*	ENST00000374994	NM_004612.2	413	Cga/Tga	7/9	0.210406444973787	3	FACETS	0.887	0.812	0.964	1	0.984	1	CLONAL	3	TRUE	1	0.225713478643649	3		518	519	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380276	+	missense_variant	Missense_Mutation	DNP	TT	TT	CA	novel	NA	P-0029998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	351	516	0	ENST00000311936.3:c.182_183delinsTG	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAA/cTG	3/5	0.225713478643649	4	FACETS	1	0.988	1	1	0.995	1	CLONAL	5	TRUE	0	0.225713478643649	4		516	697	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451807	29451807	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	257	749	0	ENST00000389048.3:c.2758G>T	p.Gly920Cys	p.G920C	ENST00000389048	NM_004304.4	920	Ggt/Tgt	16/29	0.225713478643649	1	FACETS	1	0.948	1	1	0.996	1	CLONAL	3	TRUE	0	0.225713478643649	1		749	669	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467476	66467476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766222138	NA	P-0029998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	42	306	0	ENST00000273854.3:c.793C>T	p.His265Tyr	p.H265Y	ENST00000273854	NM_004439.5	265	Cat/Tat	3/18	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.225713478643649	2		306	324	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979240	93979240	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	115	333	0	ENST00000369303.4:c.1588C>A	p.Leu530Ile	p.L530I	ENST00000369303	NM_004440.3	530	Ctt/Att	7/17	1	2	FACETS	0.923	0.84	1	1	0.991	1	CLONAL	3	TRUE	1	0.225713478643649	2		333	368	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900168	101900168	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	74	279	0	ENST00000374994.4:c.602T>C	p.Ile201Thr	p.I201T	ENST00000374994	NM_004612.2	201	aTt/aCt	4/9	0.210406444973787	3	FACETS	1	0.899	1	1	0.899	1	CLONAL	2	TRUE	1	0.225713478643649	3		279	357	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760742	133760742	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	177	796	0	ENST00000318560.5:c.3065T>G	p.Ile1022Ser	p.I1022S	ENST00000318560	NM_005157.4	1022	aTc/aGc	11/11	0.210406444973787	3	FACETS	0.991	0.913	1	0.991	0.913	1	CLONAL	2	TRUE	1	0.225713478643649	3		796	881	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224792	123224792	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs777611309	NA	P-0029998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	137	474	0	ENST00000218089.9:c.3556C>T	p.Arg1186Ter	p.R1186*	ENST00000218089	NM_001042749.1	1186	Cga/Tga	32/35	0.21346876644822	4	FACETS	1	0.949	1			1	CLONAL	2	TRUE	NA	0.225713478643649	4		474	703	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	22	495	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.166317213457164	2	FACETS	0.298	0.229	0.378	0.149	0.114	0.189	SUBCLONAL	1	FALSE	0	0.166317213457164	2		495	888	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155411	185155411	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140970208	NA	P-0030251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	33	306	1	ENST00000265026.3:c.652G>A	p.Ala218Thr	p.A218T	ENST00000265026	NM_004721.4	218	Gca/Aca	3/14	0.166317213457164	3	FACETS	0.675	0.548	0.818	0.337	0.274	0.409	SUBCLONAL	1	FALSE	1	0.166317213457164	3		307	637	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097761	8097761	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	129	517	1	ENST00000346208.3:c.143A>T	p.Asp48Val	p.D48V	ENST00000346208		48	gAt/gTt	2/6	1	2	FACETS	0.78	0.706	0.858	1	0.986	1	SUBCLONAL	2	FALSE	1	0.166317213457164	2		518	994	SUCCESS
AR	367	MSKCC	GRCh37	X	66937404	66937404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057523747	NA	P-0030251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	66	552	1	ENST00000374690.3:c.2258G>A	p.Arg753Gln	p.R753Q	ENST00000374690	NM_000044.3	753	cGa/cAa	5/8	1	2	FACETS	0.843	0.729	0.966	0.843	0.729	0.966	CLONAL	1	FALSE	1	0.166317213457164	2		553	942	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	147	428	2	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.882	0.811	0.956	0.882	0.811	0.956	CLONAL	1	TRUE	1	0.68	2		430	490	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	184	531	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.917	0.852	0.985	0.917	0.852	0.985	CLONAL	1	TRUE	1	0.68	2		531	590	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346158	89346158	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs878855327	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	46	216	0	ENST00000301030.4:c.6792del	p.Ala2265ProfsTer72	p.A2265Pfs*72	ENST00000301030	NM_001256183.1	2264	ccC/cc	9/13	1	2	FACETS	0.564	0.479	0.656	0.564	0.479	0.656	SUBCLONAL	1	TRUE	1	0.68	2		216	240	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258894	16258894	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	329	611	8	ENST00000375759.3:c.6164del	p.Pro2055LeufsTer9	p.P2055Lfs*9	ENST00000375759	NM_015001.2	2053	aaC/aa	11/15	1	2	FACETS	0.925	0.875	0.976	0.925	0.875	0.976	CLONAL	1	TRUE	1	0.68	2		619	1046	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262680	16262680	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	151	303	3	ENST00000375759.3:c.9950del	p.Pro3317ArgfsTer83	p.P3317Rfs*83	ENST00000375759	NM_015001.2	3315	caC/ca	11/15	1	2	FACETS	0.885	0.814	0.957	0.885	0.814	0.957	CLONAL	1	TRUE	1	0.68	2		306	502	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28607255	28607255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs988053889	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	60	406	0	ENST00000253063.3:c.1385C>T	p.Ala462Val	p.A462V	ENST00000253063	NM_031459.4	462	gCg/gTg	10/10	1	2	FACETS	0.326	0.281	0.375	0.326	0.281	0.375	SUBCLONAL	1	TRUE	1	0.68	2		406	541	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70442623	70442623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867702783	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	240	436	0	ENST00000373644.4:c.4945C>T	p.Arg1649Trp	p.R1649W	ENST00000373644	NM_030625.2	1649	Cgg/Tgg	10/12	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.68	2		436	699	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	203	684	4	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	0.86	0.801	0.921	0.86	0.801	0.921	CLONAL	1	TRUE	1	0.68	2		688	694	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912186	114912186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	87	442	0	ENST00000543371.1:c.1256C>T	p.Ala419Val	p.A419V	ENST00000543371	NM_001198531.1	419	gCg/gTg	11/14	1	2	FACETS	0.371	0.328	0.417	0.371	0.328	0.417	SUBCLONAL	1	TRUE	1	0.68	2		442	690	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098609	108098609	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	97	227	1	ENST00000278616.4:c.183del	p.Phe61LeufsTer15	p.F61Lfs*15	ENST00000278616	NM_000051.3	60	gTt/gt	3/63	1	2	FACETS	0.897	0.809	0.989	0.897	0.809	0.989	CLONAL	1	TRUE	1	0.68	2		228	318	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376527	118376528	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	182	343	0	ENST00000534358.1:c.9922_9923del	p.Ser3308CysfsTer19	p.S3308Cfs*19	ENST00000534358	NM_005933.3	3307	cAG/c	27/36	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.68	2		343	486	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233483	69233483	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	77	434	0	ENST00000462284.1:c.1348C>T	p.Arg450Ter	p.R450*	ENST00000462284	NM_002392.5	450	Cga/Tga	11/11	1	2	FACETS	0.423	0.372	0.478	0.423	0.372	0.478	SUBCLONAL	1	TRUE	1	0.68	2		434	535	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120546245	120546245	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	262	506	0	ENST00000229340.5:c.79C>G	p.Arg27Gly	p.R27G	ENST00000229340	NM_006861.6	27	Cgt/Ggt	2/6	1	2	FACETS	0.969	0.912	1	0.969	0.912	1	CLONAL	1	TRUE	1	0.68	2		506	795	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557569	21557569	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	248	568	1	ENST00000382592.4:c.2276G>T	p.Arg759Leu	p.R759L	ENST00000382592	NM_014572.2	759	cGg/cTg	5/8	1	2	FACETS	0.942	0.884	1	0.942	0.884	1	CLONAL	1	TRUE	1	0.68	2		569	774	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435831	110435831	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	161	355	1	ENST00000375856.3:c.2570G>A	p.Gly857Asp	p.G857D	ENST00000375856	NM_003749.2	857	gGc/gAc	1/2	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.68	2		356	435	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347168	347168	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375543956	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	245	524	0	ENST00000262320.3:c.1843G>A	p.Ala615Thr	p.A615T	ENST00000262320	NM_003502.3	615	Gcc/Acc	7/11	1	2	FACETS	0.931	0.873	0.99	0.931	0.873	0.99	CLONAL	1	TRUE	1	0.68	2		524	774	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821875	72821875	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	29	354	0	ENST00000268489.5:c.10300del	p.Leu3434SerfsTer51	p.L3434Sfs*51	ENST00000268489	NM_006885.3	3434	Ctc/tc	10/10	1	2	FACETS	0.172	0.138	0.212	0.172	0.138	0.212	SUBCLONAL	1	TRUE	1	0.68	2		354	495	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828579	72828579	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	285	568	1	ENST00000268489.5:c.8002C>T	p.Arg2668Ter	p.R2668*	ENST00000268489	NM_006885.3	2668	Cga/Tga	9/10	1	2	FACETS	0.983	0.927	1	0.983	0.927	1	CLONAL	1	TRUE	1	0.68	2		569	853	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341328	89341328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	145	320	0	ENST00000301030.4:c.7607G>A	p.Arg2536Gln	p.R2536Q	ENST00000301030	NM_001256183.1	2536	cGg/cAg	11/13	1	2	FACETS	0.983	0.905	1	0.983	0.905	1	CLONAL	1	TRUE	1	0.68	2		320	434	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347792	89347792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1394966920	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	186	430	0	ENST00000301030.4:c.5158C>T	p.His1720Tyr	p.H1720Y	ENST00000301030	NM_001256183.1	1720	Cac/Tac	9/13	1	2	FACETS	0.932	0.866	1	0.932	0.866	1	CLONAL	1	TRUE	1	0.68	2		430	587	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352560	89352560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768058427	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	206	382	0	ENST00000301030.4:c.779C>T	p.Pro260Leu	p.P260L	ENST00000301030	NM_001256183.1	260	cCg/cTg	8/13	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.68	2		382	536	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866696	37866696	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760205387	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	303	579	1	ENST00000269571.5:c.863G>A	p.Arg288Gln	p.R288Q	ENST00000269571		288	cGg/cAg	7/27	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.68	2		580	860	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120313	70120313	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	351	755	0	ENST00000245479.2:c.1315C>T	p.Gln439Ter	p.Q439*	ENST00000245479	NM_000346.3	439	Cag/Tag	3/3	0.679428205357256	1	FACETS	0.92	0.877	0.962	0.92	0.877	0.962	CLONAL	1	TRUE	0	0.68	1		755	741	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78829285	78829285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	245	486	1	ENST00000306801.3:c.1336C>T	p.Arg446Trp	p.R446W	ENST00000306801	NM_020761.2	446	Cgg/Tgg	12/34	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.68	2		487	708	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7174642	7174642	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	267	550	2	ENST00000302850.5:c.1075G>T	p.Gly359Ter	p.G359*	ENST00000302850	NM_000208.2	359	Gga/Tga	4/22	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.68	2		552	763	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272337	15272337	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs771517374	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	274	697	2	ENST00000263388.2:c.6102del	p.Gly2035ValfsTer50	p.G2035Vfs*50	ENST00000263388	NM_000435.2	2034	ccC/cc	33/33	1	2	FACETS	0.963	0.907	1	0.963	0.907	1	CLONAL	1	TRUE	1	0.68	2		699	837	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212113	36212113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757405245	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	202	463	0	ENST00000222270.7:c.1864C>T	p.Pro622Ser	p.P622S	ENST00000222270	NM_014727.1	622	Ccc/Tcc	3/37	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.68	2		463	593	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224216	36224216	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	271	553	0	ENST00000222270.7:c.6766C>T	p.Pro2256Ser	p.P2256S	ENST00000222270	NM_014727.1	2256	Cca/Tca	28/37	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.68	2		553	739	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752843	42752844	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	301	676	0	ENST00000222329.4:c.1419_1420dup	p.Ala474GlyfsTer58	p.A474Gfs*58	ENST00000222329	NM_006494.2	474	gca/gGGca	4/4	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.68	2		676	883	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	297	719	0	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.889	0.838	0.94	0.889	0.838	0.94	CLONAL	1	TRUE	1	0.68	2		719	983	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753645	42753645	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555750795	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	311	627	1	ENST00000222329.4:c.619C>T	p.Arg207Ter	p.R207*	ENST00000222329	NM_006494.2	207	Cga/Tga	4/4	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.68	2		628	848	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248518	212248518	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753616912	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	206	408	1	ENST00000342788.4:c.3749G>A	p.Arg1250Gln	p.R1250Q	ENST00000342788	NM_005235.2	1250	cGg/cAg	28/28	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.68	2		409	595	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661663	227661664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761880048	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	140	450	6	ENST00000305123.5:c.1791dup	p.His598AlafsTer13	p.H598Afs*13	ENST00000305123	NM_005544.2	597	-/G	1/2	1	2	FACETS	0.787	0.721	0.856	0.787	0.721	0.856	SUBCLONAL	1	TRUE	1	0.68	2		456	523	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651304	52651304	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	212	360	0	ENST00000394830.3:c.1792A>G	p.Arg598Gly	p.R598G	ENST00000394830	NM_018313.4	598	Agg/Ggg	15/30	1	2	FACETS	0.985	0.92	1	0.985	0.92	1	CLONAL	1	TRUE	1	0.68	2		360	633	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803172	1803172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775241791	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	130	659	2	ENST00000260795.2:c.524G>A	p.Arg175His	p.R175H	ENST00000260795		175	cGc/cAc	4/17	1	2	FACETS	0.437	0.396	0.48	0.437	0.396	0.48	SUBCLONAL	1	TRUE	1	0.68	2		661	875	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535436	66535436	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	178	362	0	ENST00000273854.3:c.25G>C	p.Ala9Pro	p.A9P	ENST00000273854	NM_004439.5	9	Gcg/Ccg	1/18	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.68	2		362	485	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541886	187541886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762168387	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	234	467	0	ENST00000441802.2:c.5854G>A	p.Val1952Ile	p.V1952I	ENST00000441802	NM_005245.3	1952	Gtt/Att	10/27	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.68	2		467	630	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152429	56152429	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs747333403	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	76	173	0	ENST00000399503.3:c.485G>A	p.Arg162His	p.R162H	ENST00000399503	NM_005921.1	162	cGt/cAt	2/20	1	2	FACETS	0.816	0.724	0.912	0.816	0.724	0.912	CLONAL	1	TRUE	1	0.68	2		173	274	SUCCESS
APC	324	MSKCC	GRCh37	5	112175761	112175761	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	45	305	0	ENST00000257430.4:c.4473del	p.Phe1491LeufsTer16	p.F1491Lfs*16	ENST00000257430	NM_000038.5	1490	caT/ca	16/16	1	2	FACETS	0.347	0.292	0.408	0.347	0.292	0.408	SUBCLONAL	1	TRUE	1	0.68	2		305	381	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520087	106520087	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774448553	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	109	242	0	ENST00000359195.3:c.2515C>T	p.Arg839Cys	p.R839C	ENST00000359195	NM_002649.2	839	Cgc/Tgc	6/11	1	2	FACETS	0.911	0.826	0.998	0.911	0.826	0.998	CLONAL	1	TRUE	1	0.68	2		242	352	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836322	151836322	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064796342	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	193	387	1	ENST00000262189.6:c.14483G>A	p.Arg4828His	p.R4828H	ENST00000262189	NM_170606.2	4828	cGc/cAc	57/59	1	2	FACETS	0.854	0.793	0.916	0.854	0.793	0.916	CLONAL	1	TRUE	1	0.68	2		388	665	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117861247	117861247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	40	364	0	ENST00000297338.2:c.1642G>A	p.Asp548Asn	p.D548N	ENST00000297338	NM_006265.2	548	Gat/Aat	13/14	1	2	FACETS	0.215	0.178	0.257	0.215	0.178	0.257	SUBCLONAL	1	TRUE	1	0.68	2		364	546	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970951	21970951	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	267	587	0	ENST00000304494.5:c.407del	p.Gly136AlafsTer10	p.G136Afs*10	ENST00000304494	NM_000077.4	136	gGc/gc	2/3	1	2	FACETS	0.937	0.881	0.994	0.937	0.881	0.994	CLONAL	1	TRUE	1	0.68	2		587	838	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87366925	87366925	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	322	648	0	ENST00000277120.3:c.1321T>A	p.Ser441Thr	p.S441T	ENST00000277120		441	Tct/Act	12/19	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.68	2		648	892	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0030383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	45	156	0	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	1	FACETS	0.91	0.794	1	0.91	0.794	1	CLONAL	1	TRUE	0	0.68	1		156	96	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0030513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	182	701	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.0949343751081433	4	FACETS	0.954	0.88	1	0.954	0.88	1	INDETERMINATE	2	TRUE	2	0.242200458442553	4		707	978	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0030513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	105	276	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	0.230898572854908	2	FACETS	0.938	0.845	1	0.938	0.845	1	CLONAL	2	TRUE	0	0.242200458442553	2		276	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578277	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs1555525902	NA	P-0030513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	170	596	3	ENST00000269305.4:c.572_574del	p.Pro191del	p.P191del	ENST00000269305	NM_001126112.2	191	cCTCag/cag	6/11	0.230898572854908	2	FACETS	0.829	0.763	0.897	0.829	0.763	0.897	CLONAL	2	TRUE	0	0.242200458442553	2		599	847	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951087	48951088	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs1131690889	NA	P-0030513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	64	275	0	ENST00000267163.4:c.1251_1252del	p.Arg418SerfsTer9	p.R418Sfs*9	ENST00000267163	NM_000321.2	417	AAa/a	13/27	0.242200458442553	2	FACETS	0.775	0.675	0.882	0.775	0.675	0.882	SUBCLONAL	2	TRUE	0	0.242200458442553	2		275	341	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350213	15350213	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368540009	NA	P-0030513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	289	659	0	ENST00000263377.2:c.3566C>T	p.Ala1189Val	p.A1189V	ENST00000263377	NM_058243.2	1189	gCg/gTg	17/20	0.0949343751081433	4	FACETS	1	0.986	1	1	0.986	1	INDETERMINATE	2	TRUE	2	0.242200458442553	4		659	1285	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451406	187451406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779268890	NA	P-0030513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	181	393	1	ENST00000232014.4:c.76C>T	p.Arg26Trp	p.R26W	ENST00000232014	NM_001130845.1	26	Cgg/Tgg	3/10	0.230898572854908	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	0	0.242200458442553	2		394	723	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384650	31384651	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs756395138	NA	P-0030513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	90	613	1	ENST00000328111.2:c.1359dup	p.Leu454AlafsTer11	p.L454Afs*11	ENST00000328111	NM_006892.3	451	gag/gaGg	13/23	0.153764716021104	4	FACETS	0.777	0.687	0.874	0.389	0.343	0.437	SUBCLONAL	1	TRUE	2	0.242200458442553	4		614	1188	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134999	2134999	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs74363455	NA	P-0030513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	275	706	0	ENST00000219476.3:c.4541C>A	p.Ser1514Ter	p.S1514*	ENST00000219476	NM_000548.3	1514	tCa/tAa	35/42	0.242165457624188	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.242200458442553	2		706	1107	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985395	60985395	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	130	638	0	ENST00000333681.4:c.505C>A	p.Leu169Met	p.L169M	ENST00000333681		169	Ctg/Atg	2/3	0.230898572854908	2	FACETS	0.928	0.84	1	0.464	0.42	0.511	CLONAL	1	TRUE	0	0.242200458442553	2		638	1157	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11027167	11027167	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	163	634	0	ENST00000327064.4:c.932A>T	p.Asn311Ile	p.N311I	ENST00000327064	NM_199141.1	311	aAc/aTc	7/16	0.0949343751081433	4	FACETS	1	0.984	1	0.655	0.599	0.713	INDETERMINATE	1	TRUE	2	0.242200458442553	4		634	1277	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287787	33287787	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0030513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	320	655	0	ENST00000374542.5:c.1465+1G>A		p.X489_splice	ENST00000374542	NM_001141970.1	489			0.230898572854908	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.242200458442553	2		655	1268	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0030672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	52	347	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.187656499180582	2		347	438	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0030672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	8	412	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	0.305	0.195	0.447	0.305	0.195	0.447	SUBCLONAL	1	TRUE	1	0.187656499180582	2		412	280	SUCCESS
APC	324	MSKCC	GRCh37	5	112173830	112173831	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	17	357	0	ENST00000257430.4:c.2544dup	p.Asp849ArgfsTer2	p.D849Rfs*2	ENST00000257430	NM_000038.5	847	gaa/gAaa	16/16	1	2	FACETS	0.634	0.473	0.825	0.634	0.473	0.825	SUBCLONAL	1	TRUE	1	0.187656499180582	2		357	286	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333991	70333993	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	rs903550402	NA	P-0030672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	18	303	0	ENST00000373644.4:c.1902_1904del	p.Val635del	p.V635del	ENST00000373644	NM_030625.2	632	tcTGTt/tct	2/12	1	2	FACETS	0.648	0.488	0.838	0.648	0.488	0.838	SUBCLONAL	1	TRUE	1	0.187656499180582	2		303	296	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508284	106508284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	25	302	0	ENST00000359195.3:c.278C>T	p.Pro93Leu	p.P93L	ENST00000359195	NM_002649.2	93	cCg/cTg	2/11	1	2	FACETS	0.613	0.482	0.763	0.613	0.482	0.763	SUBCLONAL	1	TRUE	1	0.187656499180582	2		302	435	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604763	48604763	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	99	407	0	ENST00000342988.3:c.1586del	p.Leu529TyrfsTer8	p.L529Yfs*8	ENST00000342988	NM_005359.5	529	Tta/ta	12/12	0.17354887413103	1	FACETS	0.84	0.752	0.934	1	0.984	1	CLONAL	2	TRUE	0	0.187656499180582	1		407	569	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398283	25398284	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCAGCT	novel	NA	P-0030672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	84	431	0	ENST00000311936.3:c.30_35dup	p.Ala11_Gly12dup	p.A11_G12dup	ENST00000311936	NM_004985.3	11	ggt/ggAGCTGGt	2/5	0.187656499180582	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.187656499180582	3		431	420	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670721	134670721	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	45	474	1	ENST00000398015.3:c.632C>A	p.Thr211Lys	p.T211K	ENST00000398015	NM_004441.4	211	aCa/aAa	3/16	1	2	FACETS	0.864	0.726	1	0.864	0.726	1	CLONAL	1	TRUE	1	0.187656499180582	2		475	555	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30946636	30946636	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0030672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	44	129	1	ENST00000375687.4:c.57+1G>A		p.X19_splice	ENST00000375687	NM_015338.5	19			0.17354887413103	1	FACETS	0.897	0.752	1	0.897	0.752	1	CLONAL	1	TRUE	0	0.187656499180582	1		130	474	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939081	131939081	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	33	505	0	ENST00000265335.6:c.2297A>T	p.Asn766Ile	p.N766I	ENST00000265335		766	aAc/aTc	14/25	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.187656499180582	2		505	275	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	442	993	1	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	0.733023581295001	2		994	1132	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	248	660	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.733023581295001	2		663	661	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	500	504	6	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.975	1	1	0.998	1	CLONAL	2	TRUE	1	0.733023581295001	2		510	680	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	325	247	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.733023581295001	2		248	827	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	418	701	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.955	0.924	0.985	1	0.997	1	CLONAL	2	TRUE	1	0.733023581295001	2		707	597	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	161	299	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.935	0.865	1	0.935	0.865	1	CLONAL	1	TRUE	1	0.733023581295001	2		299	470	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411411	63411411	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	359	254	0	ENST00000330258.3:c.1756C>T	p.Arg586Ter	p.R586*	ENST00000330258	NM_152424.3	586	Cga/Tga	2/2	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.733023581295001	1		254	480	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173696	108173696	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	89	288	0	ENST00000278616.4:c.5441del	p.Leu1814TrpfsTer14	p.L1814Wfs*14	ENST00000278616	NM_000051.3	1812	gcT/gc	36/63	1	2	FACETS	0.818	0.734	0.905	0.818	0.734	0.905	CLONAL	1	TRUE	1	0.733023581295001	2		288	297	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753011	57753012	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	105	298	3	ENST00000274289.3:c.1004dup	p.Leu335PhefsTer12	p.L335Ffs*12	ENST00000274289	NM_006622.3	335	ttg/ttTg	7/14	1	2	FACETS	0.768	0.694	0.845	0.768	0.694	0.845	SUBCLONAL	1	TRUE	1	0.733023581295001	2		301	373	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736166	204736166	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	200	283	0	ENST00000302823.3:c.529del	p.Tyr177IlefsTer10	p.Y177Ifs*10	ENST00000302823	NM_005214.4	175	Ttt/tt	3/4	1	2	FACETS	0.956	0.892	1	0.956	0.892	1	CLONAL	1	TRUE	1	0.733023581295001	2		283	571	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	156	276	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	0.733023581295001	2	FACETS	0.938	0.866	1	0.469	0.433	0.505	CLONAL	1	TRUE	0	0.733023581295001	2		276	454	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100425	8100425	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	358	533	0	ENST00000346208.3:c.404del	p.Pro135ArgfsTer60	p.P135Rfs*60	ENST00000346208		133	taC/ta	3/6	1	2	FACETS	0.879	0.834	0.925	0.879	0.834	0.925	CLONAL	1	TRUE	1	0.733023581295001	2		533	1111	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255500	16255500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140341054	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	210	401	0	ENST00000375759.3:c.2765C>T	p.Thr922Met	p.T922M	ENST00000375759	NM_015001.2	922	aCg/aTg	11/15	1	2	FACETS	0.844	0.787	0.902	0.844	0.787	0.902	CLONAL	1	TRUE	1	0.733023581295001	2		401	679	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	525	534	0	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	1	2	FACETS	0.963	0.923	1	0.963	0.923	1	CLONAL	1	TRUE	1	0.733023581295001	2		534	1488	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	339	898	5	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.836	0.792	0.882	0.836	0.792	0.882	CLONAL	1	TRUE	1	0.733023581295001	2		903	1106	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293457	1293457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	372	478	0	ENST00000310581.5:c.1544G>A	p.Arg515Gln	p.R515Q	ENST00000310581	NM_198253.2	515	cGg/cAg	2/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.733023581295001	2		478	989	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176338	24176338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	467	695	0	ENST00000263121.7:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000263121	NM_003073.3	377	Cgt/Tgt	9/9	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.733023581295001	2		695	1196	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279825	46279836	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAA	CAGCAGCAGCAA	-	rs769295684	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	59	287	3	ENST00000371998.3:c.3762_3773del	p.Gln1273_Gln1276del	p.Q1273_Q1276del	ENST00000371998		1251	CAGCAGCAGCAA/-	20/23	1	2	FACETS	0.287	0.247	0.331	0.287	0.247	0.331	SUBCLONAL	1	TRUE	1	0.733023581295001	2		290	560	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255883	16255883	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	213	305	0	ENST00000375759.3:c.3154del	p.Ile1052SerfsTer40	p.I1052Sfs*40	ENST00000375759	NM_015001.2	1050	Aaa/aa	11/15	1	2	FACETS	0.992	0.928	1	0.992	0.928	1	CLONAL	1	TRUE	1	0.733023581295001	2		305	586	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	194	466	8	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	0.902	0.84	0.965	0.902	0.84	0.965	CLONAL	1	TRUE	1	0.733023581295001	2		474	587	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281250	15281250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184522923	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	502	648	0	ENST00000263388.2:c.5006G>A	p.Arg1669His	p.R1669H	ENST00000263388	NM_000435.2	1669	cGc/cAc	27/33	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.733023581295001	2		648	1303	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276722	15276722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446718967	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	402	525	2	ENST00000263388.2:c.5543G>A	p.Arg1848His	p.R1848H	ENST00000263388	NM_000435.2	1848	cGt/cAt	30/33	1	2	FACETS	0.99	0.943	1	0.99	0.943	1	CLONAL	1	TRUE	1	0.733023581295001	2		527	1108	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	151	661	10	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.733023581295001	2		671	404	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924382	131924382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757836195	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	83	200	0	ENST00000265335.6:c.1055G>A	p.Arg352His	p.R352H	ENST00000265335		352	cGt/cAt	8/25	1	2	FACETS	0.858	0.767	0.952	0.858	0.767	0.952	CLONAL	1	TRUE	1	0.733023581295001	2		200	264	SUCCESS
APC	324	MSKCC	GRCh37	5	112137039	112137039	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	199	358	0	ENST00000257430.4:c.793G>T	p.Gly265Ter	p.G265*	ENST00000257430	NM_000038.5	265	Gga/Tga	8/16	1	2	FACETS	0.894	0.834	0.957	0.894	0.834	0.957	CLONAL	1	TRUE	1	0.733023581295001	2		358	607	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510723	38510723	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752501819	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	250	309	0	ENST00000254066.5:c.977C>T	p.Thr326Met	p.T326M	ENST00000254066	NM_000964.3	326	aCg/aTg	7/9	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.733023581295001	2		309	676	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564530	86564530	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	78	390	0	ENST00000274376.6:c.266del	p.Gly89GlufsTer7	p.G89Efs*7	ENST00000274376	NM_002890.2	88	Ggg/gg	1/25	1	2	FACETS	0.299	0.263	0.339	0.299	0.263	0.339	SUBCLONAL	1	TRUE	1	0.733023581295001	2		390	711	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244155	153244156	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	282	388	0	ENST00000281708.4:c.2001dup	p.Ser668GlufsTer26	p.S668Efs*26	ENST00000281708	NM_033632.3	667	-/G	12/12	1	2	FACETS	0.831	0.782	0.881	0.831	0.782	0.881	CLONAL	1	TRUE	1	0.733023581295001	2		388	926	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916726	178916726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772110575	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	213	820	1	ENST00000263967.3:c.113G>A	p.Arg38His	p.R38H	ENST00000263967	NM_006218.2	38	cGt/cAt	2/21	0.733023581295001	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.733023581295001	2		821	278	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070361	37070361	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	206	311	0	ENST00000231790.2:c.1496G>T	p.Arg499Met	p.R499M	ENST00000231790	NM_000249.3	499	aGg/aTg	13/19	0.733023581295001	2	FACETS	0.951	0.888	1	0.476	0.444	0.508	CLONAL	1	TRUE	0	0.733023581295001	2		311	591	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574679	41574679	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	473	911	4	ENST00000263253.7:c.6970del	p.His2324ThrfsTer29	p.H2324Tfs*29	ENST00000263253	NM_001429.3	2322	Ccc/cc	31/31	1	2	FACETS	0.97	0.928	1	0.97	0.928	1	CLONAL	1	TRUE	1	0.733023581295001	2		915	1330	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780181	9780181	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	366	442	0	ENST00000377346.4:c.1351G>A	p.Glu451Lys	p.E451K	ENST00000377346	NM_005026.3	451	Gag/Aag	11/24	1	2	FACETS	0.985	0.936	1	0.985	0.936	1	CLONAL	1	TRUE	1	0.733023581295001	2		442	1014	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348561	56348561	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	112	198	0	ENST00000348428.3:c.374del	p.Pro125GlnfsTer3	p.P125Qfs*3	ENST00000348428	NM_006785.3	123	agC/ag	2/17	1	2	FACETS	0.983	0.896	1	0.983	0.896	1	CLONAL	1	TRUE	1	0.733023581295001	2		198	311	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940112	49940112	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760002850	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	301	540	2	ENST00000296474.3:c.931del	p.Ala311ProfsTer27	p.A311Pfs*27	ENST00000296474	NM_002447.2	311	Gcc/cc	1/20	1	2	FACETS	0.941	0.889	0.993	0.941	0.889	0.993	CLONAL	1	TRUE	1	0.733023581295001	2		542	873	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	341	866	4	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.733023581295001	2		870	909	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396886	139396886	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752754662	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	175	419	1	ENST00000277541.6:c.5222C>T	p.Ala1741Val	p.A1741V	ENST00000277541	NM_017617.3	1741	gCg/gTg	28/34	1	2	FACETS	0.46	0.423	0.499	0.46	0.423	0.499	SUBCLONAL	1	TRUE	1	0.733023581295001	2		420	1037	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825519	50825519	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	107	550	1	ENST00000398568.2:c.2156del	p.Asn719MetfsTer13	p.N719Mfs*13	ENST00000398568	NM_001042412.1	717	gAa/ga	14/18	1	2	FACETS	0.896	0.813	0.981	0.896	0.813	0.981	CLONAL	1	TRUE	1	0.733023581295001	2		551	326	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339280	116339280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374050750	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	52	249	0	ENST00000397752.3:c.142G>A	p.Ala48Thr	p.A48T	ENST00000397752	NM_000245.2	48	Gcg/Acg	2/21	1	2	FACETS	0.275	0.234	0.32	0.275	0.234	0.32	SUBCLONAL	1	TRUE	1	0.733023581295001	2		249	516	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728847	39728847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	149	257	0	ENST00000361337.2:c.1127G>A	p.Arg376Gln	p.R376Q	ENST00000361337	NM_003286.2	376	cGa/cAa	12/21	1	2	FACETS	0.654	0.599	0.71	0.654	0.599	0.71	SUBCLONAL	1	TRUE	1	0.733023581295001	2		257	622	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779743	3779743	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	292	452	0	ENST00000262367.5:c.5305C>T	p.Arg1769Trp	p.R1769W	ENST00000262367	NM_004380.2	1769	Cgg/Tgg	31/31	1	2	FACETS	0.992	0.938	1	0.992	0.938	1	CLONAL	1	TRUE	1	0.733023581295001	2		452	803	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	282	641	1	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	1	2	FACETS	0.631	0.592	0.671	0.631	0.592	0.671	SUBCLONAL	1	TRUE	1	0.733023581295001	2		642	1219	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226576366	226576366	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	199	383	0	ENST00000366794.5:c.708del	p.Ala237ProfsTer2	p.A237Pfs*2	ENST00000366794	NM_001618.3	236	aaA/aa	5/23	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.733023581295001	2		383	530	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597883	43597883	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs551142665	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	438	603	1	ENST00000355710.3:c.431G>A	p.Arg144His	p.R144H	ENST00000355710	NM_020975.4	144	cGc/cAc	3/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.733023581295001	2		604	1181	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048787	180048787	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	312	632	2	ENST00000261937.6:c.1775G>A	p.Arg592His	p.R592H	ENST00000261937	NM_182925.4	592	cGc/cAc	13/30	1	2	FACETS	0.682	0.642	0.722	0.682	0.642	0.722	SUBCLONAL	1	TRUE	1	0.733023581295001	2		634	1249	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214866	36214866	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568372429	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	519	625	3	ENST00000222270.7:c.3296del	p.Gly1099AlafsTer83	p.G1099Afs*83	ENST00000222270	NM_014727.1	1098	Ggg/gg	8/37	1	2	FACETS	0.976	0.935	1	0.976	0.935	1	CLONAL	1	TRUE	1	0.733023581295001	2		628	1451	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184610	7184610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1228919172	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	225	241	0	ENST00000302850.5:c.691G>A	p.Glu231Lys	p.E231K	ENST00000302850	NM_000208.2	231	Gaa/Aaa	3/22	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.733023581295001	2		241	567	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361086	70361091	+	inframe_deletion	In_Frame_Del	DEL	CAGCAA	CAGCAA	-	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	106	143	0	ENST00000374080.3:c.6285_6290del	p.Gln2114_Gln2115del	p.Q2114_Q2115del	ENST00000374080		2092	CAGCAA/-	43/45	1	1	FACETS	0.739	0.675	0.804	0.739	0.675	0.804	SUBCLONAL	1	TRUE	0	0.733023581295001	1		143	248	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136268	202136268	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	206	397	0	ENST00000358485.4:c.512T>C	p.Val171Ala	p.V171A	ENST00000358485	NM_001080125.1	171	gTg/gCg	3/9	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.733023581295001	2		397	516	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361092	70361100	+	inframe_deletion	In_Frame_Del	DEL	CAGCAACAG	CAGCAACAG	-	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	21	152	0	ENST00000374080.3:c.6285_6293del	p.Gln2113_Gln2115del	p.Q2113_Q2115del	ENST00000374080		2094	CAGCAACAG/-	43/45	1	1	FACETS	0.132	0.101	0.168	0.132	0.101	0.168	SUBCLONAL	1	TRUE	0	0.733023581295001	1		152	275	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267849	46267849	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	226	439	1	ENST00000371998.3:c.2615del	p.Asn872IlefsTer20	p.N872Ifs*20	ENST00000371998		870	gtA/gt	14/23	1	2	FACETS	0.982	0.92	1	0.982	0.92	1	CLONAL	1	TRUE	1	0.733023581295001	2		440	628	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969978	81969978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755551138	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	203	273	0	ENST00000359376.3:c.3047C>T	p.Thr1016Met	p.T1016M	ENST00000359376	NM_002661.3	1016	aCg/aTg	27/33	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.733023581295001	2		273	511	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102033228	102033228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	416	425	0	ENST00000282441.5:c.614C>T	p.Ala205Val	p.A205V	ENST00000282441	NM_001130145.2	205	gCc/gTc	3/9	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.733023581295001	2		425	1001	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145678	61145678	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773764180	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	158	375	0	ENST00000295025.8:c.790C>T	p.Arg264Trp	p.R264W	ENST00000295025	NM_002908.2	264	Cgg/Tgg	7/11	1	2	FACETS	0.847	0.782	0.914	0.847	0.782	0.914	CLONAL	1	TRUE	1	0.733023581295001	2		375	509	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190344	32190344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146490163	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	318	459	1	ENST00000375023.3:c.395G>A	p.Arg132His	p.R132H	ENST00000375023	NM_004557.3	132	cGc/cAc	3/30	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.733023581295001	2		460	849	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89355061	89355061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	330	424	0	ENST00000301030.4:c.619G>A	p.Glu207Lys	p.E207K	ENST00000301030	NM_001256183.1	207	Gag/Aag	7/13	1	2	FACETS	0.977	0.926	1	0.977	0.926	1	CLONAL	1	TRUE	1	0.733023581295001	2		424	922	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227816	36227816	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190286476	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	469	578	0	ENST00000222270.7:c.7301C>T	p.Ala2434Val	p.A2434V	ENST00000222270	NM_014727.1	2434	gCg/gTg	32/37	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.733023581295001	2		578	1249	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159144	143159144	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	81	222	0	ENST00000262992.4:c.709A>G	p.Lys237Glu	p.K237E	ENST00000262992	NM_001101669.1	237	Aaa/Gaa	10/24	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.733023581295001	2		222	217	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123260445	123260445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	275	392	0	ENST00000358487.5:c.1456C>T	p.Pro486Ser	p.P486S	ENST00000358487	NM_000141.4	486	Ccc/Tcc	11/18	1	2	FACETS	0.964	0.909	1	0.964	0.909	1	CLONAL	1	TRUE	1	0.733023581295001	2		392	778	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780881	9780881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768558857	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	420	596	0	ENST00000377346.4:c.1603C>T	p.Arg535Trp	p.R535W	ENST00000377346	NM_005026.3	535	Cgg/Tgg	13/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.733023581295001	2		596	1070	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781541	9781541	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	284	388	0	ENST00000377346.4:c.1851G>T	p.Gln617His	p.Q617H	ENST00000377346	NM_005026.3	617	caG/caT	15/24	1	2	FACETS	0.96	0.906	1	0.96	0.906	1	CLONAL	1	TRUE	1	0.733023581295001	2		388	807	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466341	120466341	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587743026	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	97	382	0	ENST00000256646.2:c.4778A>G	p.Tyr1593Cys	p.Y1593C	ENST00000256646	NM_024408.3	1593	tAt/tGt	26/34	1	2	FACETS	0.433	0.387	0.483	0.433	0.387	0.483	SUBCLONAL	1	TRUE	1	0.733023581295001	2		382	611	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104359302	104359302	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776578	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	286	328	0	ENST00000369902.3:c.1022+1G>A		p.X341_splice	ENST00000369902	NM_016169.3	341			1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.733023581295001	2		328	776	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21629872	21629872	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	134	379	0	ENST00000421138.2:c.922A>G	p.Ile308Val	p.I308V	ENST00000421138		308	Att/Gtt	9/16	1	2	FACETS	0.928	0.852	1	0.928	0.852	1	CLONAL	1	TRUE	1	0.733023581295001	2		379	394	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944698	31944701	+	frameshift_variant	Frame_Shift_Del	DEL	CTCT	CTCT	-	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	17	40	0	ENST00000340398.3:c.400_403del	p.Arg134LeufsTer3	p.R134Lfs*3	ENST00000340398	NM_001013699.2	134	AGAGct/ct	1/1	1	2	FACETS	1	0.82	1	1	0.82	1	CLONAL	1	TRUE	1	0.733023581295001	2		40	44	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562394	21562394	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	380	406	0	ENST00000382592.4:c.1525C>A	p.Pro509Thr	p.P509T	ENST00000382592	NM_014572.2	509	Cca/Aca	4/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.733023581295001	2		406	979	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358330	91358331	+	splice_acceptor_variant	Splice_Site	INS	-	-	G	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	140	244	0	ENST00000355112.3:c.4080dup		p.X1360_splice	ENST00000355112	NM_000057.2	1360			1	2	FACETS	0.927	0.853	1	0.927	0.853	1	CLONAL	1	TRUE	1	0.733023581295001	2		244	412	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250907	99250907	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	301	371	0	ENST00000268035.6:c.211C>A	p.Arg71Ser	p.R71S	ENST00000268035	NM_000875.3	71	Cgc/Agc	2/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.733023581295001	2		371	792	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99482454	99482454	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	271	355	0	ENST00000268035.6:c.3322A>C	p.Ser1108Arg	p.S1108R	ENST00000268035	NM_000875.3	1108	Agc/Cgc	18/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.733023581295001	2		355	681	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124201	2124201	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs767252128	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	299	383	0	ENST00000219476.3:c.2356C>T	p.Arg786Cys	p.R786C	ENST00000219476	NM_000548.3	786	Cgc/Tgc	22/42	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.733023581295001	2		383	764	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133731	2133731	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs62642481	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	115	605	0	ENST00000219476.3:c.3919G>A	p.Glu1307Lys	p.E1307K	ENST00000219476	NM_000548.3	1307	Gag/Aag	33/42	1	2	FACETS	0.254	0.227	0.282	0.254	0.227	0.282	SUBCLONAL	1	TRUE	1	0.733023581295001	2		605	1237	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779749	3779749	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	315	464	0	ENST00000262367.5:c.5299T>A	p.Ser1767Thr	p.S1767T	ENST00000262367	NM_004380.2	1767	Tca/Aca	31/31	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.733023581295001	2		464	820	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3929878	3929878	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	284	399	1	ENST00000262367.5:c.40del	p.Arg14GlufsTer31	p.R14Efs*31	ENST00000262367	NM_004380.2	14	Aga/ga	1/31	1	2	FACETS	0.996	0.94	1	0.996	0.94	1	CLONAL	1	TRUE	1	0.733023581295001	2		400	778	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984391	72984391	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760112688	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	278	342	0	ENST00000268489.5:c.3193G>A	p.Glu1065Lys	p.E1065K	ENST00000268489	NM_006885.3	1065	Gag/Aag	3/10	1	2	FACETS	0.999	0.943	1	0.999	0.943	1	CLONAL	1	TRUE	1	0.733023581295001	2		342	759	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16062081	16062083	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	201	262	0	ENST00000268712.3:c.723_725del	p.Asp241del	p.D241del	ENST00000268712	NM_006311.3	241	gaTGAg/gag	6/46	1	2	FACETS	0.931	0.869	0.995	0.931	0.869	0.995	CLONAL	1	TRUE	1	0.733023581295001	2		262	589	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16097774	16097774	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	271	397	0	ENST00000268712.3:c.108+2T>C		p.X36_splice	ENST00000268712	NM_006311.3	36			1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.733023581295001	2		397	663	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321667	30321667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1213455983	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	196	463	1	ENST00000322652.5:c.1522C>T	p.Arg508Cys	p.R508C	ENST00000322652	NM_015355.2	508	Cgc/Tgc	13/16	1	2	FACETS	0.932	0.868	0.996	0.932	0.868	0.996	CLONAL	1	TRUE	1	0.733023581295001	2		464	574	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646884	37646884	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	355	505	2	ENST00000447079.4:c.2006T>C	p.Leu669Pro	p.L669P	ENST00000447079	NM_015083.1	669	cTt/cCt	3/14	1	2	FACETS	0.952	0.904	1	0.952	0.904	1	CLONAL	1	TRUE	1	0.733023581295001	2		507	1017	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604770	48604770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	244	278	0	ENST00000342988.3:c.1592G>A	p.Arg531Gln	p.R531Q	ENST00000342988	NM_005359.5	531	cGg/cAg	12/12	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.733023581295001	2		278	654	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1627406	1627407	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	470	574	1	ENST00000344749.5:c.317dup	p.Ala107ArgfsTer85	p.A107Rfs*85	ENST00000344749	NM_001136139.2	106	ggc/ggGc	6/19	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.733023581295001	2		575	1165	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5239011	5239011	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	421	579	1	ENST00000357368.4:c.1768T>C	p.Tyr590His	p.Y590H	ENST00000357368	NM_002850.3	590	Tac/Cac	13/38	1	2	FACETS	0.99	0.945	1	0.99	0.945	1	CLONAL	1	TRUE	1	0.733023581295001	2		580	1160	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281364	15281364	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1487491390	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	300	505	0	ENST00000263388.2:c.4892G>A	p.Gly1631Glu	p.G1631E	ENST00000263388	NM_000435.2	1631	gGg/gAg	27/33	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.733023581295001	2		505	811	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210892	36210893	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs764234724	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	351	627	0	ENST00000222270.7:c.649dup	p.Arg217ProfsTer35	p.R217Pfs*35	ENST00000222270	NM_014727.1	215	acc/aCcc	3/37	1	2	FACETS	0.864	0.819	0.91	0.864	0.819	0.91	CLONAL	1	TRUE	1	0.733023581295001	2		627	1108	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40761168	40761168	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	324	390	0	ENST00000392038.2:c.184C>A	p.Leu62Met	p.L62M	ENST00000392038	NM_001626.4	62	Ctg/Atg	4/14	1	2	FACETS	0.986	0.934	1	0.986	0.934	1	CLONAL	1	TRUE	1	0.733023581295001	2		390	897	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467502	25467502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	370	489	1	ENST00000264709.3:c.1574C>T	p.Ala525Val	p.A525V	ENST00000264709	NM_175629.2	525	gCg/gTg	14/23	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.733023581295001	2		490	1002	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189344	99189344	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs758176960	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	382	415	0	ENST00000074304.5:c.2600A>G	p.His867Arg	p.H867R	ENST00000074304	NM_001134224.1	867	cAt/cGt	24/26	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.733023581295001	2		415	1006	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137425	202137425	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	203	334	0	ENST00000358485.4:c.653T>C	p.Ile218Thr	p.I218T	ENST00000358485	NM_001080125.1	218	aTc/aCc	4/9	1	2	FACETS	0.998	0.932	1	0.998	0.932	1	CLONAL	1	TRUE	1	0.733023581295001	2		334	555	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660772	227660772	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	280	428	0	ENST00000305123.5:c.2683del	p.Glu895AsnfsTer48	p.E895Nfs*48	ENST00000305123	NM_005544.2	895	Gaa/aa	1/2	1	2	FACETS	0.966	0.911	1	0.966	0.911	1	CLONAL	1	TRUE	1	0.733023581295001	2		428	791	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958233	54958233	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	145	254	0	ENST00000312783.6:c.375-1G>A		p.X125_splice	ENST00000312783	NM_198436.1	125			1	2	FACETS	0.97	0.894	1	0.97	0.894	1	CLONAL	1	TRUE	1	0.733023581295001	2		254	408	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484242	57484242	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	244	302	0	ENST00000371085.3:c.556A>G	p.Lys186Glu	p.K186E	ENST00000371085	NM_000516.4	186	Aag/Gag	7/13	1	2	FACETS	0.973	0.915	1	0.973	0.915	1	CLONAL	1	TRUE	1	0.733023581295001	2		302	684	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321659	62321660	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	355	484	0	ENST00000360203.5:c.2284dup	p.Arg762ProfsTer29	p.R762Pfs*29	ENST00000360203	NM_001283009.1	760	gcc/gCcc	26/35	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.733023581295001	2		484	948	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574269	41574269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1413325383	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	376	516	0	ENST00000263253.7:c.6554G>A	p.Arg2185Gln	p.R2185Q	ENST00000263253	NM_001429.3	2185	cGa/cAa	31/31	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.733023581295001	2		516	952	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439909	52439909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	77	346	0	ENST00000460680.1:c.803C>T	p.Pro268Leu	p.P268L	ENST00000460680	NM_004656.3	268	cCa/cTa	10/17	1	2	FACETS	0.331	0.291	0.375	0.331	0.291	0.375	SUBCLONAL	1	TRUE	1	0.733023581295001	2		346	634	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440867	52440867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	402	462	0	ENST00000460680.1:c.637C>T	p.Arg213Cys	p.R213C	ENST00000460680	NM_004656.3	213	Cgt/Tgt	8/17	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.733023581295001	2		462	1052	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749379	41749379	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	163	223	0	ENST00000226382.2:c.416A>C	p.Glu139Ala	p.E139A	ENST00000226382	NM_003924.3	139	gAg/gCg	2/3	1	2	FACETS	0.999	0.926	1	0.999	0.926	1	CLONAL	1	TRUE	1	0.733023581295001	2		223	445	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564559	55564559	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	301	429	0	ENST00000288135.5:c.450del	p.Cys151AlafsTer10	p.C151Afs*10	ENST00000288135	NM_000222.2	149	aaG/aa	3/21	1	2	FACETS	0.889	0.839	0.939	0.889	0.839	0.939	CLONAL	1	TRUE	1	0.733023581295001	2		429	924	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293760	1293760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1471089239	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	442	602	0	ENST00000310581.5:c.1241C>T	p.Pro414Leu	p.P414L	ENST00000310581	NM_198253.2	414	cCg/cTg	2/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.733023581295001	2		602	1137	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518050	176518050	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149737957	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	454	524	3	ENST00000292408.4:c.548G>A	p.Arg183His	p.R183H	ENST00000292408	NM_213647.1	183	cGc/cAc	5/18	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.733023581295001	2		527	1146	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910704	29910704	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs199474415	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	353	704	0	ENST00000376809.5:c.244G>T	p.Glu82Ter	p.E82*	ENST00000376809	NM_002116.7	82	Gag/Tag	2/8	1	2	FACETS	0.782	0.74	0.824	0.782	0.74	0.824	SUBCLONAL	1	TRUE	1	0.733023581295001	2		704	1232	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163553	32163554	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	112	406	0	ENST00000375023.3:c.5671_5672dup	p.Gly1892AlafsTer13	p.G1892Afs*13	ENST00000375023	NM_004557.3	1891	ggc/ggGGc	30/30	1	2	FACETS	0.504	0.454	0.557	0.504	0.454	0.557	SUBCLONAL	1	TRUE	1	0.733023581295001	2		406	606	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815832	32815832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370875392	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	383	465	0	ENST00000354258.4:c.1784C>T	p.Ala595Val	p.A595V	ENST00000354258	NM_000593.5	595	gCg/gTg	8/11	1	2	FACETS	0.985	0.937	1	0.985	0.937	1	CLONAL	1	TRUE	1	0.733023581295001	2		465	1061	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748504	43748504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775464274	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	318	358	1	ENST00000523873.1:c.458G>A	p.Arg153Gln	p.R153Q	ENST00000523873		153	cGa/cAa	6/8	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.733023581295001	2		359	777	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2952951	2952951	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	433	452	0	ENST00000396946.4:c.2989G>T	p.Gly997Cys	p.G997C	ENST00000396946	NM_032415.4	997	Ggt/Tgt	22/25	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.733023581295001	2		452	1155	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959181	2959181	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	395	486	0	ENST00000396946.4:c.2335C>T	p.Arg779Trp	p.R779W	ENST00000396946	NM_032415.4	779	Cgg/Tgg	18/25	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.733023581295001	2		486	1048	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968238	2968238	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	461	507	0	ENST00000396946.4:c.1748A>G	p.His583Arg	p.H583R	ENST00000396946	NM_032415.4	583	cAt/cGt	13/25	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.733023581295001	2		507	1190	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5064973	5064973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	98	288	0	ENST00000381652.3:c.1147C>T	p.Leu383Phe	p.L383F	ENST00000381652	NM_004972.3	383	Ctc/Ttc	9/25	1	2	FACETS	0.99	0.897	1	0.99	0.897	1	CLONAL	1	TRUE	1	0.733023581295001	2		288	270	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606412	93606412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773659676	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	348	481	1	ENST00000375746.1:c.232G>A	p.Gly78Ser	p.G78S	ENST00000375746	NM_001174167.1	78	Ggt/Agt	2/14	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.733023581295001	2		482	875	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209582	98209582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs572658914	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	330	474	1	ENST00000331920.6:c.3956G>A	p.Arg1319His	p.R1319H	ENST00000331920	NM_000264.3	1319	cGc/cAc	23/24	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.733023581295001	2		475	772	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403510	139403510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868369610	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	387	513	0	ENST00000277541.6:c.2983G>A	p.Gly995Ser	p.G995S	ENST00000277541	NM_017617.3	995	Ggt/Agt	19/34	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.733023581295001	2		513	1027	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139563106	139563106	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755489905	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	331	443	1	ENST00000308874.7:c.178C>T	p.Arg60Trp	p.R60W	ENST00000308874		60	Cgg/Tgg	4/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.733023581295001	2		444	900	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411302	63411302	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs987506209	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	368	271	0	ENST00000330258.3:c.1865A>G	p.Glu622Gly	p.E622G	ENST00000330258	NM_152424.3	622	gAg/gGg	2/2	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.733023581295001	1		271	475	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360645	70360647	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	rs1312048351	NA	P-0030774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	10	150	0	ENST00000374080.3:c.6207_6209del	p.Gln2076del	p.Q2076del	ENST00000374080		2069	CAA/-	42/45	1	1	FACETS	0.092	0.062	0.13	0.092	0.062	0.13	SUBCLONAL	1	TRUE	0	0.733023581295001	1		150	187	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913078	32913078	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	129	596	0	ENST00000380152.3:c.4586G>A	p.Gly1529Glu	p.G1529E	ENST00000380152		1529	gGg/gAg	11/27	1	2	FACETS	0.609	0.553	0.668	0.609	0.553	0.668	SUBCLONAL	1	TRUE	1	0.636746964931828	2		596	665	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862177	68862177	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	209	523	0	ENST00000261769.5:c.2265del	p.Tyr755Ter	p.Y755*	ENST00000261769	NM_004360.3	755	taT/ta	14/16	0.335701648410604	2	FACETS	1	0.947	1	0.508	0.474	0.543	INDETERMINATE	1	TRUE	0	0.636746964931828	2		523	646	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576882	7576883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTTC	novel	NA	P-0030989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	236	674	0	ENST00000269305.4:c.960_963dup	p.Pro322GlufsTer16	p.P322Efs*16	ENST00000269305	NM_001126112.2	321	-/GAAA	9/11	0.335701648410604	2	FACETS	1	0.967	1	0.523	0.491	0.557	INDETERMINATE	1	TRUE	0	0.636746964931828	2		674	708	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40744837	40744837	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	128	761	0	ENST00000392038.2:c.683T>C	p.Val228Ala	p.V228A	ENST00000392038	NM_001626.4	228	gTg/gCg	8/14	0.636764928848357	4	FACETS	0.517	0.467	0.57			1	SUBCLONAL	1	TRUE	NA	0.636746964931828	4		761	1273	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807368	1807368	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	108	616	0	ENST00000260795.2:c.1617C>G	p.Ile539Met	p.I539M	ENST00000260795		539	atC/atG	11/17	NA	2	FACETS	0.425	0.381	0.472			1	INDETERMINATE	1	TRUE	NA	0.636746964931828	2		616	798	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953012	2953012	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	209	797	0	ENST00000396946.4:c.2928del	p.Val977CysfsTer88	p.V977Cfs*88	ENST00000396946	NM_032415.4	976	ccC/cc	22/25	0.375527944778447	5	FACETS	1	0.973	1	0.366	0.339	0.394	INDETERMINATE	1	TRUE	2	0.636746964931828	5		797	1168	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8733778	8733778	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0030989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	86	605	0	ENST00000356435.5:c.64+2T>C		p.X22_splice	ENST00000356435		22			0.350494064287771	3	FACETS	0.518	0.458	0.582	0.259	0.229	0.291	INDETERMINATE	1	TRUE	1	0.636746964931828	3		605	688	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879628	37880645	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGTGGTCTTTGGGATCCTCATCAAGCGACGGCAGCAGAAGATCCGGAAGTACACGATGCGGAGACTGCTGCAGGAAACGGAGGTGAGGCGGGGTGAAGTCCTCCCAGCCCGCGTGGGGTCTGCACCGGCCCCCGGCACTGACCCACCACCCCCTCACCCCAGCTGGTGGAGCCGCTGACACCTAGCGGAGCGATGCCCAACCAGGCGCAGATGCGGATCCTGAAAGAGACGGAGCTGAGGAAGGTGAAGGTGCTTGGATCTGGCGCTTTTGGCACAGTCTACAAGGTCAGGGCCAGGTCCTGGGGTGGGCGGCCCCAGAGGATGGGGGCGGTGCCTGGAGGGGTGTGGTCGGCAGTTCTGATGGGAGGGGCAAGAGCTGGAGGCAGTGTTTGGGGGAGGGCAGTTACAGCGGAGAAGGGAGCGGGGCCAAGCCCTAGGGTGGTGAAGGATGTTTGGAGGACAAGTAATGATCTCCTGGAAGGCAGGTAGGATCCAGCCCACGCTCTTCTCACTCATATCCTCCTCTTTCTGCCCAGGGCATCTGGATCCCTGATGGGGAGAATGTGAAAATTCCAGTGGCCATCAAAGTGTTGAGGGAAAACACATCCCCCAAAGCCAACAAAGAAATCTTAGACGTAAGCCCCTCCACCCTCTCCTGCTAGGAGGACAGGAAGGACCCCATGGCTGCAGGTCTGGGCTCTGGTCTCTCTTCATTGGGGTTTGGGGAGATATGACTCCCGCAAACCTAGACTATTTTTTTGGAGACGGAGTCTTGCTCTGTCACCCAGGCTGGAGTGCAGTGGCGTTATCTCGGCTCACTGCAACCTCCACCTCCTGGACTCAAGCGATTTTCATGCCTCAGGCTCCTGAGTAGCTGGGATTACAAGCGCCCGCTAATTTTTTTTTTTTTTTTGAGACAGAGTCTCGCTCTGTCACCCAGGCTAGAGTGAAATGGTGCGGTCTCAGCTCAGCCTCCCAGGTTAAAGCGATTCTTCTCCCTCAGTCTCCTGAGTAGCT	GGGTGGTCTTTGGGATCCTCATCAAGCGACGGCAGCAGAAGATCCGGAAGTACACGATGCGGAGACTGCTGCAGGAAACGGAGGTGAGGCGGGGTGAAGTCCTCCCAGCCCGCGTGGGGTCTGCACCGGCCCCCGGCACTGACCCACCACCCCCTCACCCCAGCTGGTGGAGCCGCTGACACCTAGCGGAGCGATGCCCAACCAGGCGCAGATGCGGATCCTGAAAGAGACGGAGCTGAGGAAGGTGAAGGTGCTTGGATCTGGCGCTTTTGGCACAGTCTACAAGGTCAGGGCCAGGTCCTGGGGTGGGCGGCCCCAGAGGATGGGGGCGGTGCCTGGAGGGGTGTGGTCGGCAGTTCTGATGGGAGGGGCAAGAGCTGGAGGCAGTGTTTGGGGGAGGGCAGTTACAGCGGAGAAGGGAGCGGGGCCAAGCCCTAGGGTGGTGAAGGATGTTTGGAGGACAAGTAATGATCTCCTGGAAGGCAGGTAGGATCCAGCCCACGCTCTTCTCACTCATATCCTCCTCTTTCTGCCCAGGGCATCTGGATCCCTGATGGGGAGAATGTGAAAATTCCAGTGGCCATCAAAGTGTTGAGGGAAAACACATCCCCCAAAGCCAACAAAGAAATCTTAGACGTAAGCCCCTCCACCCTCTCCTGCTAGGAGGACAGGAAGGACCCCATGGCTGCAGGTCTGGGCTCTGGTCTCTCTTCATTGGGGTTTGGGGAGATATGACTCCCGCAAACCTAGACTATTTTTTTGGAGACGGAGTCTTGCTCTGTCACCCAGGCTGGAGTGCAGTGGCGTTATCTCGGCTCACTGCAACCTCCACCTCCTGGACTCAAGCGATTTTCATGCCTCAGGCTCCTGAGTAGCTGGGATTACAAGCGCCCGCTAATTTTTTTTTTTTTTTTGAGACAGAGTCTCGCTCTGTCACCCAGGCTAGAGTGAAATGGTGCGGTCTCAGCTCAGCCTCCCAGGTTAAAGCGATTCTTCTCCCTCAGTCTCCTGAGTAGCT	-	novel	NA	P-0030989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10980	600	692	0	ENST00000269571.5:c.2006_2308-331del		p.X669_splice	ENST00000269571		669		17-19/27	0.636746964931828	32	FACETS	0.859	0.818	0.9			1	CLONAL	2	TRUE	NA	0.636746964931828	32		692	11580	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0031061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	372	704	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.447709899751172	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.447709899751172	2		705	809	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	272	306	0				ENST00000310581	NM_198253.2	-/1132			0.447709899751172	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.447709899751172	3		306	691	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39575891	39575891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	192	384	0	ENST00000262039.4:c.824G>A	p.Arg275Gln	p.R275Q	ENST00000262039	NM_002647.2	275	cGg/cAg	8/25	0.441832928037703	4	FACETS	0.832	0.772	0.895	0.832	0.772	0.895	CLONAL	2	TRUE	2	0.447709899751172	4		384	746	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070862	30070862	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	318	488	0	ENST00000338641.4:c.1378G>T	p.Glu460Ter	p.E460*	ENST00000338641	NM_000268.3	460	Gaa/Taa	13/16	0.447709899751172	2	FACETS	0.974	0.926	1	0.974	0.926	1	CLONAL	2	TRUE	0	0.447709899751172	2		488	729	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403120	116403120	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371939364	NA	P-0031061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	202	354	0	ENST00000397752.3:c.2381C>G	p.Ser794Cys	p.S794C	ENST00000397752	NM_000245.2	794	tCt/tGt	11/21	0.447709899751172	3	FACETS	0.863	0.804	0.923	0.863	0.804	0.923	CLONAL	2	TRUE	1	0.447709899751172	3		354	640	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	69	406	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.613	0.534	0.699	0.613	0.534	0.699	SUBCLONAL	1	TRUE	1	0.329018914512985	2		406	684	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0031131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	161	1221	1	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.329018914512985	1	FACETS	0.799	0.732	0.869	0.799	0.732	0.869	SUBCLONAL	1	TRUE	0	0.329018914512985	1		1222	1023	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047205	77047205	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	93	506	0	ENST00000356341.3:c.1339A>G	p.Ile447Val	p.I447V	ENST00000356341	NM_002576.4	447	Atc/Gtc	13/15	0.329018914512985	1	FACETS	0.629	0.559	0.704	0.629	0.559	0.704	SUBCLONAL	1	TRUE	0	0.329018914512985	1		506	751	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0031265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	1353	457	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.854819963687978	6	FACETS	1	0.997	1			1	CLONAL	5	TRUE	NA	0.854819963687978	6		457	1654	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39713203	39713203	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	173	407	0	ENST00000361337.2:c.609G>A	p.Trp203Ter	p.W203*	ENST00000361337	NM_003286.2	203	tgG/tgA	8/21	0.821404236542766	3	FACETS	1	0.943	1	0.51	0.472	0.549	CLONAL	1	TRUE	1	0.854819963687978	3		407	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578415	7578415	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	163	661	0	ENST00000269305.4:c.515T>A	p.Val172Asp	p.V172D	ENST00000269305	NM_001126112.2	172	gTt/gAt	5/11	0.359500766463065	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.359500766463065	1		661	600	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836299	151836299	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	126	523	0	ENST00000262189.6:c.14506G>T	p.Asp4836Tyr	p.D4836Y	ENST00000262189	NM_170606.2	4836	Gac/Tac	57/59	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.359500766463065	2		523	696	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0031402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	458	617	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.562726992330762	3	FACETS	0.92	0.889	0.951	0.92	0.889	0.951	CLONAL	3	TRUE	0	0.602949806390511	3		617	716	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479187	50479187	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	256	445	0	ENST00000394963.4:c.35C>A	p.Pro12Gln	p.P12Q	ENST00000394963	NM_003076.4	12	cCa/cAa	1/13	0.466286271274499	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.602949806390511	4		445	608	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832585	72832585	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	76	254	0	ENST00000268489.5:c.3996C>G	p.Ile1332Met	p.I1332M	ENST00000268489	NM_006885.3	1332	atC/atG	9/10	0.531475527776332	3	FACETS	1	0.957	1	0.584	0.518	0.653	CLONAL	1	TRUE	1	0.602949806390511	3		254	281	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794841	242794841	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	242	542	0	ENST00000334409.5:c.368G>C	p.Cys123Ser	p.C123S	ENST00000334409	NM_005018.2	123	tGt/tCt	2/5	0.466286271274499	4	FACETS	0.994	0.935	1	0.994	0.935	1	CLONAL	2	TRUE	2	0.602949806390511	4		542	647	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420021	41420049	+	frameshift_variant	Frame_Shift_Del	DEL	GGTGTCATTCTCCTTCAGGGTTGGCAGGA	GGTGTCATTCTCCTTCAGGGTTGGCAGGA	-	novel	NA	P-0031402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	105	405	0	ENST00000373198.4:c.272_300del	p.Leu91ProfsTer13	p.L91Pfs*13	ENST00000373198	NM_133170.3	91	cTCCTGCCAACCCTGAAGGAGAATGACACC/c	3/32	0.249016828181316	5	FACETS	1	0.955	1	0.372	0.333	0.412	INDETERMINATE	1	TRUE	2	0.602949806390511	5		405	595	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921354	178921354	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	549	559	0	ENST00000263967.3:c.836T>A	p.Leu279His	p.L279H	ENST00000263967	NM_006218.2	279	cTt/cAt	5/21	0.566041493505475	5	FACETS	0.945	0.92	0.969	0.945	0.92	0.969	CLONAL	5	TRUE	0	0.602949806390511	5		559	734	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55130026	55130026	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	170	604	0	ENST00000257290.5:c.560A>G	p.Tyr187Cys	p.Y187C	ENST00000257290	NM_006206.4	187	tAt/tGt	4/23	0.466286271274499	4	FACETS	1	0.923	1	0.502	0.461	0.544	CLONAL	1	TRUE	2	0.602949806390511	4		604	901	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249278	10249278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	20	423	0	ENST00000340748.4:c.3904G>A	p.Gly1302Ser	p.G1302S	ENST00000340748		1302	Ggt/Agt	34/40	0.26811826776827	1	FACETS	0.395	0.302	0.504	0.395	0.302	0.504	SUBCLONAL	1	TRUE	0	0.26811826776827	1		423	327	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755493	39755494	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGGGCGTGATAGGAGCCCATGTACGGGAGGTCTGAGGGGTA	novel	NA	P-0031536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	40	495	0	ENST00000288319.7:c.1231_1271dup	p.Pro425ThrfsTer18	p.P425Tfs*18	ENST00000288319	NM_182918.3	424	cac/caTACCCCTCAGACCTCCCGTACATGGGCTCCTATCACGCCCAc	10/10	0.26811826776827	1	FACETS	0.582	0.484	0.691	0.582	0.484	0.691	SUBCLONAL	1	TRUE	0	0.26811826776827	1		495	444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578369	7578369	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0031648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	367	606	0	ENST00000269305.4:c.559+2T>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.831336202913666	3	FACETS	0.96	0.936	0.981	0.96	0.936	0.981	CLONAL	3	TRUE	0	0.851255649182483	3		606	427	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204737485	204737485	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	125	581	0	ENST00000302823.3:c.622G>A	p.Glu208Lys	p.E208K	ENST00000302823	NM_005214.4	208	Gag/Aag	4/4	1	2	FACETS	0.877	0.804	0.951	0.877	0.804	0.951	CLONAL	1	TRUE	1	0.851255649182483	2		581	335	SUCCESS
APC	324	MSKCC	GRCh37	5	112178706	112178706	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs200399245	NA	P-0031648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	279	556	0	ENST00000257430.4:c.7415C>G	p.Ala2472Gly	p.A2472G	ENST00000257430	NM_000038.5	2472	gCt/gGt	16/16	0.851255649182483	3	FACETS	1	0.961	1			1	CLONAL	2	TRUE	NA	0.851255649182483	3		556	464	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820986	32820986	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	153	912	2	ENST00000354258.4:c.608G>T	p.Ser203Ile	p.S203I	ENST00000354258	NM_000593.5	203	aGt/aTt	1/11	0.279040869831732	2	FACETS	0.687	0.633	0.744	0.344	0.316	0.372	INDETERMINATE	1	TRUE	0	0.851255649182483	2		914	523	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150000934	150001106	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TACCATCTTATATTTTACTACATCAATAAATTACATTATTATGAACAAACTAAAATAAATTTTATGAGTTTACTTACCACTCTGATAGTACTTAGAATCGTGTGTCCATCTGAAGCCAGTGCAGAGGCCAAAGTCAGTCAATTTAATATGACCATCACGATCAATCAAAATAT	TACCATCTTATATTTTACTACATCAATAAATTACATTATTATGAACAAACTAAAATAAATTTTATGAGTTTACTTACCACTCTGATAGTACTTAGAATCGTGTGTCCATCTGAAGCCAGTGCAGAGGCCAAAGTCAGTCAATTTAATATGACCATCACGATCAATCAAAATAT	-	novel	NA	P-0031648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	148	120	0	ENST00000253339.5:c.2498_2593+77del		p.X833_splice	ENST00000253339		833		4/7	0.843505466602926	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.851255649182483	2		120	158	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0031650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	626	584	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.45721906966029	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.460114005929423	2		584	1230	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0031650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	214	339	2	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	0.45721906966029	2	FACETS	0.942	0.875	1	0.471	0.437	0.505	CLONAL	1	TRUE	0	0.460114005929423	2		341	988	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814713	139814713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753016580	NA	P-0031650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	52	597	0	ENST00000247668.2:c.706G>A	p.Glu236Lys	p.E236K	ENST00000247668	NM_021138.3	236	Gag/Aag	8/11	0.182114698719675	3	FACETS	0.289	0.245	0.338	0.145	0.122	0.169	INDETERMINATE	1	TRUE	1	0.460114005929423	3		597	961	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961349	41961349	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1417576296	NA	P-0031650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	227	542	0	ENST00000219905.7:c.257A>G	p.Asn86Ser	p.N86S	ENST00000219905	NM_001164273.1	86	aAt/aGt	2/24	0.266610102721588	1	FACETS	1	0.938	1	1	0.938	1	INDETERMINATE	1	TRUE	0	0.460114005929423	1		542	757	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244672	41244672	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	326	792	0	ENST00000357654.3:c.2876G>C	p.Arg959Thr	p.R959T	ENST00000357654	NM_007294.3	959	aGa/aCa	10/23	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.460114005929423	2		792	1365	SUCCESS
MET	4233	MSKCC	GRCh37	7	116413850	116413851	+	intron_variant	Intron	INS	-	-	T	novel	NA	P-0031650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	398	903	0	ENST00000397752.3:c.3029-1083dup		p.*1010*	ENST00000397752	NM_000245.2	-/1390			0.460114005929423	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.460114005929423	1		903	1242	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0031650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	433	440	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	NA	2	FACETS	0.957	0.922	0.992			1	INDETERMINATE	2	TRUE	NA	0.629998813350784	2		440	718	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267448	7267448	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1412618950	NA	P-0031650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	694	592	0	ENST00000302850.5:c.560C>T	p.Pro187Leu	p.P187L	ENST00000302850	NM_000208.2	187	cCg/cTg	2/22	0.61993042295109	4	FACETS	0.95	0.927	0.972	0.95	0.927	0.972	CLONAL	4	TRUE	0	0.629998813350784	4		592	945	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878147	48878147	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	123	129	0	ENST00000267163.4:c.99del	p.Glu34SerfsTer31	p.E34Sfs*31	ENST00000267163	NM_000321.2	33	ccA/cc	1/27	0.586107869668298	3	FACETS	0.989	0.931	1	0.989	0.931	1	CLONAL	3	TRUE	0	0.629998813350784	3		129	173	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050652	30050652	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	126	440	0	ENST00000338641.4:c.454G>A	p.Asp152Asn	p.D152N	ENST00000338641	NM_000268.3	152	Gac/Aac	5/16	0.62788415705807	3	FACETS	0.893	0.811	0.978	0.447	0.405	0.489	CLONAL	1	TRUE	1	0.629998813350784	3		440	589	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111502	8111503	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0031684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	94	580	0	ENST00000346208.3:c.990dup	p.Asn331GlufsTer21	p.N331Efs*21	ENST00000346208		330	agg/aGgg	5/6	1	2	FACETS	0.857	0.761	0.959	0.857	0.761	0.959	CLONAL	1	TRUE	1	0.238764043087913	2		580	919	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0031684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	191	398	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.238764043087913	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.238764043087913	2		398	729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0031684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	106	537	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.238764043087913	1	FACETS	0.982	0.88	1	0.982	0.88	1	CLONAL	1	TRUE	0	0.238764043087913	1		537	796	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111502	8111503	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0031684-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	250	580	0	ENST00000346208.3:c.990dup	p.Asn331GlufsTer21	p.N331Efs*21	ENST00000346208		330	agg/aGgg	5/6	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.649693591692272	2		580	682	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0031684-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	162	398	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.948	0.876	1	0.948	0.876	1	CLONAL	1	TRUE	1	0.649693591692272	2		398	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0031684-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	235	537	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.649693591692272	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.649693591692272	1		537	481	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910549	29910549	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45585732	NA	P-0032031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	24	591	0	ENST00000376809.5:c.89G>A	p.Arg30Lys	p.R30K	ENST00000376809	NM_002116.7	30	aGg/aAg	2/8	0.595411698128973	2	FACETS	0.319	0.251	0.398	0.16	0.125	0.199	SUBCLONAL	1	TRUE	0	0.613319578493766	2		591	245	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907798	76907798	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	100	397	0	ENST00000373344.5:c.4363G>T	p.Glu1455Ter	p.E1455*	ENST00000373344	NM_000489.3	1455	Gag/Tag	15/35	0.613319578493766	1	FACETS	0.709	0.64	0.78	0.709	0.64	0.78	SUBCLONAL	1	TRUE	0	0.613319578493766	1		397	319	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618667	37618667	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	73	409	0	ENST00000447079.4:c.343C>T	p.Gln115Ter	p.Q115*	ENST00000447079	NM_015083.1	115	Cag/Tag	1/14	0.212973262344032	3	FACETS	0.763	0.671	0.861	0.763	0.671	0.861	SUBCLONAL	2	TRUE	1	0.287138924132472	3		409	381	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	188	633	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.287643230126419	3	FACETS	0.912	0.844	0.982	0.912	0.844	0.982	CLONAL	2	FALSE	1	0.287643230126419	3		633	820	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	97	706	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.914	0.815	1	0.914	0.815	1	CLONAL	1	FALSE	1	0.287643230126419	2		706	738	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514495	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	116	545	0	ENST00000269305.4:c.542G>A	p.Arg181His	p.R181H	ENST00000269305	NM_001126112.2	181	cGc/cAc	5/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.287643230126419	2		545	722	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164805	36164805	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	98	718	1	ENST00000300305.3:c.1070del	p.Pro357ArgfsTer237	p.P357Rfs*237	ENST00000300305		357	cCg/cg	8/8	1	2	FACETS	0.806	0.719	0.9	0.806	0.719	0.9	CLONAL	1	FALSE	1	0.287643230126419	2		719	845	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106732	27106732	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	90	600	1	ENST00000324856.7:c.6343C>T	p.Gln2115Ter	p.Q2115*	ENST00000324856	NM_006015.4	2115	Cag/Tag	20/20	1	2	FACETS	0.848	0.752	0.95	0.848	0.752	0.95	CLONAL	1	FALSE	1	0.287643230126419	2		601	738	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057937	27057937	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	114	132	0	ENST00000324856.7:c.1650del	p.Tyr551ThrfsTer68	p.Y551Tfs*68	ENST00000324856	NM_006015.4	549	Ccc/cc	3/20	1	2	FACETS	0.971	0.874	1	0.971	0.874	1	CLONAL	1	FALSE	1	0.287643230126419	2		132	816	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690846	89690846	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	63	349	0	ENST00000371953.3:c.253G>T	p.Val85Phe	p.V85F	ENST00000371953	NM_000314.4	85	Gtt/Ttt	4/9	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	FALSE	1	0.287643230126419	2		349	427	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220339	98220339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772406487	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	71	373	0	ENST00000331920.6:c.3124G>A	p.Val1042Met	p.V1042M	ENST00000331920	NM_000264.3	1042	Gtg/Atg	18/24	1	2	FACETS	0.891	0.779	1	0.891	0.779	1	CLONAL	1	FALSE	1	0.287643230126419	2		373	554	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692792	89692792	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs779530981	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	70	380	1	ENST00000371953.3:c.276C>A	p.Asp92Glu	p.D92E	ENST00000371953	NM_000314.4	92	gaC/gaA	5/9	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	FALSE	1	0.287643230126419	2		381	446	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	58	556	3	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.78	0.671	0.899	0.78	0.671	0.899	SUBCLONAL	1	FALSE	1	0.287643230126419	2		559	517	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860345	42860345	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1385130606	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	104	527	1	ENST00000398585.3:c.532G>A	p.Gly178Ser	p.G178S	ENST00000398585	NM_001135099.1	178	Ggc/Agc	5/14	1	2	FACETS	0.811	0.725	0.902	0.811	0.725	0.902	CLONAL	1	FALSE	1	0.287643230126419	2		528	892	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs371769427	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	59	394	0	ENST00000291552.4:c.101C>A	p.Ser34Tyr	p.S34Y	ENST00000291552	NM_006758.2	34	tCt/tAt	2/8	1	2	FACETS	0.842	0.726	0.969	0.842	0.726	0.969	CLONAL	1	FALSE	1	0.287643230126419	2		394	487	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003812	45003812	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	57	490	0	ENST00000558401.1:c.67+1G>A		p.X23_splice	ENST00000558401	NM_004048.2	23			1	2	FACETS	0.708	0.607	0.817	0.708	0.607	0.817	SUBCLONAL	1	FALSE	1	0.287643230126419	2		490	560	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88676946	88676946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147971049	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	45	219	1	ENST00000372037.3:c.731G>A	p.Arg244Gln	p.R244Q	ENST00000372037	NM_004329.2	244	cGa/cAa	9/13	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	FALSE	1	0.287643230126419	2		220	284	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11206806	11206806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760642166	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	104	577	1	ENST00000361445.4:c.4613G>A	p.Arg1538Gln	p.R1538Q	ENST00000361445	NM_004958.3	1538	cGg/cAg	32/58	1	2	FACETS	0.894	0.8	0.994	0.894	0.8	0.994	CLONAL	1	FALSE	1	0.287643230126419	2		578	809	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359648	40359648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1339796170	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	108	625	2	ENST00000293328.3:c.2005G>A	p.Val669Met	p.V669M	ENST00000293328	NM_012448.3	669	Gtg/Atg	16/19	1	2	FACETS	0.849	0.761	0.942	0.849	0.761	0.942	CLONAL	1	FALSE	1	0.287643230126419	2		627	885	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533914	63533914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751229839	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	65	414	0	ENST00000307078.5:c.1240C>T	p.Arg414Trp	p.R414W	ENST00000307078	NM_004655.3	414	Cgg/Tgg	6/11	1	2	FACETS	0.798	0.693	0.913	0.798	0.693	0.913	CLONAL	1	FALSE	1	0.287643230126419	2		414	566	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104304	2104304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764529584	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	59	526	0	ENST00000219476.3:c.344G>A	p.Arg115His	p.R115H	ENST00000219476	NM_000548.3	115	cGt/cAt	5/42	1	2	FACETS	0.585	0.503	0.675	0.585	0.503	0.675	SUBCLONAL	1	FALSE	1	0.287643230126419	2		526	701	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194905	29194905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375453930	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	104	621	1	ENST00000240100.2:c.823C>T	p.Arg275Cys	p.R275C	ENST00000240100	NM_001394.6	275	Cgc/Tgc	4/4	1	2	FACETS	0.813	0.727	0.905	0.813	0.727	0.905	CLONAL	1	FALSE	1	0.287643230126419	2		622	889	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111855990	111855990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201886863	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	103	498	1	ENST00000341259.2:c.41C>T	p.Ala14Val	p.A14V	ENST00000341259	NM_005475.2	14	gCg/gTg	2/8	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	FALSE	1	0.287643230126419	2		499	713	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209367	98209367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45535032	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	74	478	0	ENST00000331920.6:c.4171C>T	p.Arg1391Trp	p.R1391W	ENST00000331920	NM_000264.3	1391	Cgg/Tgg	23/24	1	2	FACETS	0.89	0.78	1	0.89	0.78	1	CLONAL	1	FALSE	1	0.287643230126419	2		478	578	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135304	30135304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	83	389	1	ENST00000331968.5:c.514C>T	p.Arg172Cys	p.R172C	ENST00000331968	NM_002742.2	172	Cgt/Tgt	3/18	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	FALSE	1	0.287643230126419	2		390	560	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022454	12022454	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753079378	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	117	757	0	ENST00000396373.4:c.560C>T	p.Thr187Met	p.T187M	ENST00000396373	NM_001987.4	187	aCg/aTg	5/8	1	2	FACETS	0.875	0.788	0.967	0.875	0.788	0.967	CLONAL	1	FALSE	1	0.287643230126419	2		757	930	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714075	43714075	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs773155828	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	92	599	0	ENST00000382044.4:c.4078C>T	p.Arg1360Ter	p.R1360*	ENST00000382044	NM_001141980.1	1360	Cga/Tga	19/28	1	2	FACETS	0.768	0.682	0.86	0.768	0.682	0.86	SUBCLONAL	1	FALSE	1	0.287643230126419	2		599	833	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385105	31385105	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs777301633	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	112	494	0	ENST00000328111.2:c.1490G>A	p.Arg497Gln	p.R497Q	ENST00000328111	NM_006892.3	497	cGg/cAg	14/23	1	2	FACETS	0.987	0.888	1	0.987	0.888	1	CLONAL	1	FALSE	1	0.287643230126419	2		494	789	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074223	8074223	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	74	391	0	ENST00000377482.5:c.436del	p.Cys146ValfsTer29	p.C146Vfs*29	ENST00000377482	NM_018948.3	146	Tgt/gt	4/4	1	2	FACETS	0.903	0.791	1	0.903	0.791	1	CLONAL	1	FALSE	1	0.287643230126419	2		391	570	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176153781	176153781	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	69	468	0	ENST00000367669.3:c.455G>A	p.Gly152Asp	p.G152D	ENST00000367669	NM_022457.5	152	gGc/gAc	2/20	1	2	FACETS	0.897	0.782	1	0.897	0.782	1	CLONAL	1	FALSE	1	0.287643230126419	2		468	535	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111958641	111958641	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199901239	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	81	432	2	ENST00000375549.3:c.113G>A	p.Arg38Gln	p.R38Q	ENST00000375549	NM_003002.3	38	cGa/cAa	2/4	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	FALSE	1	0.287643230126419	2		434	561	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73342974	73342974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143183542	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	79	475	0	ENST00000377767.4:c.1832G>A	p.Arg611His	p.R611H	ENST00000377767	NM_014953.3	611	cGt/cAt	14/21	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	FALSE	1	0.287643230126419	2		475	532	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093358	30093358	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	94	507	0	ENST00000331968.5:c.1905G>T	p.Gln635His	p.Q635H	ENST00000331968	NM_002742.2	635	caG/caT	13/18	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.287643230126419	2		507	566	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779704	3779704	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567263529	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	95	614	0	ENST00000262367.5:c.5344G>A	p.Ala1782Thr	p.A1782T	ENST00000262367	NM_004380.2	1782	Gcg/Acg	31/31	1	2	FACETS	0.904	0.805	1	0.904	0.805	1	CLONAL	1	FALSE	1	0.287643230126419	2		614	731	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351106	89351106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs115797011	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	120	625	0	ENST00000301030.4:c.1844C>T	p.Ala615Val	p.A615V	ENST00000301030	NM_001256183.1	615	gCg/gTg	9/13	1	2	FACETS	0.968	0.874	1	0.968	0.874	1	CLONAL	1	FALSE	1	0.287643230126419	2		625	862	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974898	15974898	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1219026707	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	80	582	0	ENST00000268712.3:c.3977G>A	p.Arg1326Gln	p.R1326Q	ENST00000268712	NM_006311.3	1326	cGa/cAa	30/46	1	2	FACETS	0.872	0.768	0.983	0.872	0.768	0.983	CLONAL	1	FALSE	1	0.287643230126419	2		582	638	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47685282	47685282	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767942932	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	64	350	0	ENST00000347630.2:c.668C>T	p.Pro223Leu	p.P223L	ENST00000347630	NM_001007230.1	223	cCg/cTg	8/11	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	FALSE	1	0.287643230126419	2		350	441	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435278	56435278	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	84	616	0	ENST00000407977.2:c.1859C>A	p.Pro620His	p.P620H	ENST00000407977		620	cCt/cAt	9/10	1	2	FACETS	0.836	0.738	0.94	0.836	0.738	0.94	CLONAL	1	FALSE	1	0.287643230126419	2		616	699	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119045	70119045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	81	430	0	ENST00000245479.2:c.617C>T	p.Ala206Val	p.A206V	ENST00000245479	NM_000346.3	206	gCg/gTg	2/3	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	FALSE	1	0.287643230126419	2		430	529	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143063	7143063	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	90	533	0	ENST00000302850.5:c.2306A>G	p.Asn769Ser	p.N769S	ENST00000302850	NM_000208.2	769	aAt/aGt	12/22	1	2	FACETS	0.945	0.839	1	0.945	0.839	1	CLONAL	1	FALSE	1	0.287643230126419	2		533	662	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271692	15271692	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	124	722	1	ENST00000263388.2:c.6747del	p.Glu2250AsnfsTer79	p.E2250Nfs*79	ENST00000263388	NM_000435.2	2249	ccC/cc	33/33	1	2	FACETS	0.965	0.873	1	0.965	0.873	1	CLONAL	1	FALSE	1	0.287643230126419	2		723	893	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266720	18266720	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751392338	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	114	609	0	ENST00000222254.8:c.31G>A	p.Ala11Thr	p.A11T	ENST00000222254	NM_005027.3	11	Gct/Act	2/16	1	2	FACETS	0.95	0.855	1	0.95	0.855	1	CLONAL	1	FALSE	1	0.287643230126419	2		609	834	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61706044	61706044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	103	647	0	ENST00000401558.2:c.3127C>T	p.Arg1043Trp	p.R1043W	ENST00000401558	NM_003400.3	1043	Cgg/Tgg	25/25	1	2	FACETS	0.912	0.816	1	0.912	0.816	1	CLONAL	1	FALSE	1	0.287643230126419	2		647	785	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137374	202137374	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	56	367	0	ENST00000358485.4:c.602T>G	p.Ile201Ser	p.I201S	ENST00000358485	NM_001080125.1	201	aTt/aGt	4/9	1	2	FACETS	0.903	0.776	1	0.903	0.776	1	CLONAL	1	FALSE	1	0.287643230126419	2		367	431	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54948503	54948503	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	75	466	0	ENST00000312783.6:c.815T>A	p.Ile272Asn	p.I272N	ENST00000312783	NM_198436.1	272	aTt/aAt	8/10	1	2	FACETS	0.891	0.782	1	0.891	0.782	1	CLONAL	1	FALSE	1	0.287643230126419	2		466	585	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474810	138474810	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	49	409	0	ENST00000289153.2:c.183G>C	p.Lys61Asn	p.K61N	ENST00000289153	NM_006219.2	61	aaG/aaC	2/22	1	2	FACETS	0.755	0.641	0.881	0.755	0.641	0.881	SUBCLONAL	1	FALSE	1	0.287643230126419	2		409	451	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951888	178951888	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	120	457	0	ENST00000263967.3:c.2943G>T	p.Gln981His	p.Q981H	ENST00000263967	NM_006218.2	981	caG/caT	21/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.287643230126419	2		457	579	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56171073	56171073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	73	351	0	ENST00000399503.3:c.1901C>T	p.Ala634Val	p.A634V	ENST00000399503	NM_005921.1	634	gCa/gTa	10/20	1	2	FACETS	0.928	0.813	1	0.928	0.813	1	CLONAL	1	FALSE	1	0.287643230126419	2		351	547	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057582	180057582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	116	661	0	ENST00000261937.6:c.373G>A	p.Ala125Thr	p.A125T	ENST00000261937	NM_182925.4	125	Gcc/Acc	3/30	1	2	FACETS	0.897	0.808	0.992	0.897	0.808	0.992	CLONAL	1	FALSE	1	0.287643230126419	2		661	899	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287293	33287293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	92	540	0	ENST00000374542.5:c.1804G>A	p.Glu602Lys	p.E602K	ENST00000374542	NM_001141970.1	602	Gag/Aag	6/8	1	2	FACETS	0.992	0.882	1	0.992	0.882	1	CLONAL	1	FALSE	1	0.287643230126419	2		540	645	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199637	138199637	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1163634415	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	71	485	0	ENST00000237289.4:c.1055A>G	p.Glu352Gly	p.E352G	ENST00000237289	NM_001270507.1	352	gAg/gGg	7/9	1	2	FACETS	0.913	0.798	1	0.913	0.798	1	CLONAL	1	FALSE	1	0.287643230126419	2		485	541	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287337	38287337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143241978	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	81	596	1	ENST00000425967.3:c.320C>T	p.Ala107Val	p.A107V	ENST00000425967	NM_001174067.1	107	gCg/gTg	4/19	1	2	FACETS	0.816	0.719	0.921	0.816	0.719	0.921	CLONAL	1	FALSE	1	0.287643230126419	2		597	690	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37034000	37034000	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	112	428	0	ENST00000358127.4:c.29C>A	p.Pro10His	p.P10H	ENST00000358127	NM_001280556.1	10	cCt/cAt	1/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.287643230126419	2		428	672	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786872	135786872	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057520994	NA	P-0032113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	90	435	0	ENST00000298552.3:c.997C>T	p.Pro333Ser	p.P333S	ENST00000298552	NM_001162426.1	333	Cca/Tca	10/23	1	2	FACETS	0.876	0.778	0.982	0.876	0.778	0.982	CLONAL	1	FALSE	1	0.287643230126419	2		435	714	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0032130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	102	1040	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.4572725046469	2	FACETS	0.824	0.752	0.898	0.824	0.752	0.898	CLONAL	2	TRUE	0	0.526523115296188	2		1040	235	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129355	64129355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	46	838	1	ENST00000334205.4:c.787C>T	p.Pro263Ser	p.P263S	ENST00000334205	NM_003942.2	263	Cct/Tct	8/17	0.409740424771587	3	FACETS	0.649	0.549	0.759	0.325	0.274	0.38	SUBCLONAL	1	TRUE	1	0.526523115296188	3		839	340	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244008	46244008	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	23	590	0	ENST00000334344.6:c.2102C>T	p.Thr701Ile	p.T701I	ENST00000334344	NM_152641.2	701	aCt/aTt	15/21	0.443210319728919	3	FACETS	1	0.847	1	0.361	0.286	0.443	CLONAL	1	TRUE	0	0.526523115296188	3		590	102	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355153	15355494	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGAAGTGGCCGATGGGGTCAAAGACGCTGCCTGGGAGCTGGGGCTCCAGGACGGGCACCTGGGTGGCAATGAAGGGTGGGGGCGAGGACTTCATCGCCGGGGCTGCCTGCTGCGGCATGGAGGGTGGGGGAGGCGGGGGTGGCGGCTGCTGTTGCTGCTGCGGAGGTGGAGGCGGTGGGGGCTGCTGGGGAGGCGGGGGCGGCTGCTGGGGCACAGGAGCCGGGGCCTGCTGCATCTGCTGATGGTGGTGATGATGGTGCTGCAGACAGAGAGACAGACAGACAGACAGGCTGATGTCAGGCAGGCAGAACTGGCCCGGGCCAGACCCAACGTCCCACCTAA	TGAAGTGGCCGATGGGGTCAAAGACGCTGCCTGGGAGCTGGGGCTCCAGGACGGGCACCTGGGTGGCAATGAAGGGTGGGGGCGAGGACTTCATCGCCGGGGCTGCCTGCTGCGGCATGGAGGGTGGGGGAGGCGGGGGTGGCGGCTGCTGTTGCTGCTGCGGAGGTGGAGGCGGTGGGGGCTGCTGGGGAGGCGGGGGCGGCTGCTGGGGCACAGGAGCCGGGGCCTGCTGCATCTGCTGATGGTGGTGATGATGGTGCTGCAGACAGAGAGACAGACAGACAGACAGGCTGATGTCAGGCAGGCAGAACTGGCCCGGGCCAGACCCAACGTCCCACCTAA	-	novel	NA	P-0032130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	67	850	0	ENST00000263377.2:c.2211+27_2470del		p.X737_splice	ENST00000263377	NM_058243.2	737		13/20	0.100824913625889	4	FACETS	1	0.968	1	0.67	0.587	0.757	INDETERMINATE	1	TRUE	2	0.526523115296188	4		850	290	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213846	66213846	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	38	553	1	ENST00000273854.3:c.2584T>C	p.Trp862Arg	p.W862R	ENST00000273854	NM_004439.5	862	Tgg/Cgg	15/18	0.256019618602252	4	FACETS	0.911	0.77	1	0.607	0.513	0.706	INDETERMINATE	2	TRUE	1	0.526523115296188	4		554	121	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342621	87342644	+	inframe_deletion	In_Frame_Del	DEL	CATTCCATTCACTGTGAAAGGCAA	CATTCCATTCACTGTGAAAGGCAA	-	novel	NA	P-0032130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	22	548	0	ENST00000277120.3:c.907_930del	p.Ile303_Asn310del	p.I303_N310del	ENST00000277120		302	tgCATTCCATTCACTGTGAAAGGCAAc/tgc	9/19	0.348817171475256	4	FACETS	0.599	0.466	0.752	0.299	0.233	0.376	SUBCLONAL	1	TRUE	2	0.526523115296188	4		548	213	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	191	247	1	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	0.52	2		248	691	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	56	398	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.383	0.328	0.443	0.383	0.328	0.443	SUBCLONAL	1	TRUE	1	0.52	2		398	562	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	157	706	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.996	0.917	1	0.996	0.917	1	CLONAL	1	TRUE	1	0.52	2		706	606	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	227	549	1	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	0.52	2		550	858	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	227	454	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.52	2		454	774	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs79184941	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	120	247	0	ENST00000358487.5:c.755C>T	p.Ser252Leu	p.S252L	ENST00000358487	NM_000141.4	252	tCg/tTg	7/18	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.52	2		247	386	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	172	364	2	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.944	0.871	1	0.944	0.871	1	CLONAL	1	TRUE	1	0.52	2		366	701	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466019	69466019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	184	474	0	ENST00000227507.2:c.857C>T	p.Thr286Ile	p.T286I	ENST00000227507	NM_053056.2	286	aCa/aTa	5/5	1	2	FACETS	0.962	0.89	1	0.962	0.89	1	CLONAL	1	TRUE	1	0.52	2		474	736	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	37	358	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	0.314	0.259	0.376	0.314	0.259	0.376	SUBCLONAL	1	TRUE	1	0.52	2		358	453	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412110	63412110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852216	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	190	617	1	ENST00000330258.3:c.1057C>T	p.Arg353Ter	p.R353*	ENST00000330258	NM_152424.3	353	Cga/Tga	2/2	1	2	FACETS	0.768	0.71	0.829	0.768	0.71	0.829	SUBCLONAL	1	TRUE	1	0.52	2		618	951	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341448	70341448	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	107	570	0	ENST00000374080.3:c.883C>T	p.Arg295Cys	p.R295C	ENST00000374080		295	Cgc/Tgc	7/45	1	2	FACETS	0.52	0.466	0.577	0.52	0.466	0.577	SUBCLONAL	1	TRUE	1	0.52	2		570	792	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674233	86674233	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1463885690	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	136	326	0	ENST00000274376.6:c.2365C>T	p.Arg789Ter	p.R789*	ENST00000274376	NM_002890.2	789	Cga/Tga	18/25	1	2	FACETS	0.974	0.89	1	0.974	0.89	1	CLONAL	1	TRUE	1	0.52	2		326	537	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497901	25497901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1447483341	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	134	415	0	ENST00000264709.3:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000264709	NM_175629.2	183	cGg/cAg	6/23	1	2	FACETS	0.917	0.837	1	0.917	0.837	1	CLONAL	1	TRUE	1	0.52	2		415	562	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610125	81610125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757875222	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	123	336	0	ENST00000298171.2:c.1723G>A	p.Glu575Lys	p.E575K	ENST00000298171	NM_000369.2	575	Gag/Aag	10/10	1	2	FACETS	0.83	0.753	0.91	0.83	0.753	0.91	CLONAL	1	TRUE	1	0.52	2		336	570	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451546	70451546	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768089885	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	178	483	0	ENST00000373644.4:c.6386C>T	p.Ala2129Val	p.A2129V	ENST00000373644	NM_030625.2	2129	gCg/gTg	12/12	1	2	FACETS	0.875	0.808	0.945	0.875	0.808	0.945	CLONAL	1	TRUE	1	0.52	2		483	782	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508257	106508257	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766854286	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	102	213	0	ENST00000359195.3:c.251C>T	p.Ala84Val	p.A84V	ENST00000359195	NM_002649.2	84	gCg/gTg	2/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.52	2		213	358	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964199	28964199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745653714	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	123	286	0	ENST00000282397.4:c.1703C>T	p.Thr568Met	p.T568M	ENST00000282397	NM_002019.4	568	aCg/aTg	13/30	1	2	FACETS	0.977	0.889	1	0.977	0.889	1	CLONAL	1	TRUE	1	0.52	2		286	484	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856607	111856607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs982851788	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	80	170	0	ENST00000341259.2:c.658G>A	p.Gly220Arg	p.G220R	ENST00000341259	NM_005475.2	220	Ggg/Agg	2/8	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.52	2		170	297	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447080	49447080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	84	401	0	ENST00000301067.7:c.864G>A	p.Met288Ile	p.M288I	ENST00000301067	NM_003482.3	288	atG/atA	7/54	1	2	FACETS	0.511	0.452	0.575	0.511	0.452	0.575	SUBCLONAL	1	TRUE	1	0.52	2		401	632	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103398	2103398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200045926	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	63	522	2	ENST00000219476.3:c.281C>T	p.Pro94Leu	p.P94L	ENST00000219476	NM_000548.3	94	cCg/cTg	4/42	1	2	FACETS	0.313	0.27	0.36	0.313	0.27	0.36	SUBCLONAL	1	TRUE	1	0.52	2		524	775	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023715	27023716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	116	351	0	ENST00000324856.7:c.827dup	p.Gly277ArgfsTer123	p.G277Rfs*123	ENST00000324856	NM_006015.4	274	atg/atGg	1/20	1	2	FACETS	0.788	0.713	0.867	0.788	0.713	0.867	SUBCLONAL	1	TRUE	1	0.52	2		351	566	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772614	135772615	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	82	466	0	ENST00000298552.3:c.2931dup	p.Leu978ThrfsTer2	p.L978Tfs*2	ENST00000298552	NM_001162426.1	977	-/A	22/23	1	2	FACETS	0.42	0.37	0.474	0.42	0.37	0.474	SUBCLONAL	1	TRUE	1	0.52	2		466	751	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527703	157527703	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554237318	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	79	416	0	ENST00000346085.5:c.5428C>T	p.Gln1810Ter	p.Q1810*	ENST00000346085	NM_020732.3	1810	Cag/Tag	20/20	1	2	FACETS	0.454	0.399	0.513	0.454	0.399	0.513	SUBCLONAL	1	TRUE	1	0.52	2		416	669	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481915	56481915	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	208	527	2	ENST00000267101.3:c.843G>T	p.Gln281His	p.Q281H	ENST00000267101	NM_001982.3	281	caG/caT	7/28	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.52	2		529	755	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78435635	78435635	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	106	429	1	ENST00000370768.2:c.185del	p.Gly62AspfsTer6	p.G62Dfs*6	ENST00000370768	NM_003902.3	62	gGa/ga	2/20	1	2	FACETS	0.533	0.478	0.592	0.533	0.478	0.592	SUBCLONAL	1	TRUE	1	0.52	2		430	765	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625363	69625363	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1242191483	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	53	463	2	ENST00000334134.2:c.430C>T	p.Arg144Cys	p.R144C	ENST00000334134	NM_005247.2	144	Cgc/Tgc	3/3	1	2	FACETS	0.328	0.279	0.382	0.328	0.279	0.382	SUBCLONAL	1	TRUE	1	0.52	2		465	621	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518224	103518224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376753356	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	96	203	0	ENST00000355739.4:c.2162C>T	p.Ala721Val	p.A721V	ENST00000355739	NM_000123.3	721	gCg/gTg	9/15	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.52	2		203	369	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456473	99456473	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	98	353	0	ENST00000268035.6:c.1790C>G	p.Ala597Gly	p.A597G	ENST00000268035	NM_000875.3	597	gCc/gGc	8/21	1	2	FACETS	0.76	0.681	0.844	0.76	0.681	0.844	SUBCLONAL	1	TRUE	1	0.52	2		353	496	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964780	15964780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1001018811	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	48	511	1	ENST00000268712.3:c.5816G>A	p.Arg1939Gln	p.R1939Q	ENST00000268712	NM_006311.3	1939	cGg/cAg	37/46	1	2	FACETS	0.227	0.191	0.267	0.227	0.191	0.267	SUBCLONAL	1	TRUE	1	0.52	2		512	812	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868298	37868298	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs532077147	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	141	354	0	ENST00000269571.5:c.1019G>A	p.Arg340Gln	p.R340Q	ENST00000269571		340	cGa/cAa	8/27	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.52	2		354	538	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40460264	40460264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1331759850	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	78	445	1	ENST00000345506.4:c.1975C>T	p.Arg659Trp	p.R659W	ENST00000345506	NM_003152.3	659	Cgg/Tgg	17/20	1	2	FACETS	0.481	0.422	0.543	0.481	0.422	0.543	SUBCLONAL	1	TRUE	1	0.52	2		446	624	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260114	19260114	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757104393	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	120	628	0	ENST00000162023.5:c.179C>T	p.Thr60Met	p.T60M	ENST00000162023		60	aCg/aTg	7/13	1	2	FACETS	0.59	0.533	0.651	0.59	0.533	0.651	SUBCLONAL	1	TRUE	1	0.52	2		628	782	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227687	36227687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	84	455	0	ENST00000222270.7:c.7256G>A	p.Ser2419Asn	p.S2419N	ENST00000222270	NM_014727.1	2419	aGc/aAc	31/37	1	2	FACETS	0.531	0.469	0.596	0.531	0.469	0.596	SUBCLONAL	1	TRUE	1	0.52	2		455	609	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872227	45872227	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	134	519	0	ENST00000391945.4:c.207A>T	p.Lys69Asn	p.K69N	ENST00000391945	NM_000400.3	69	aaA/aaT	4/23	1	2	FACETS	0.669	0.608	0.733	0.669	0.608	0.733	SUBCLONAL	1	TRUE	1	0.52	2		519	770	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46611668	46611668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749690854	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	200	563	1	ENST00000263734.3:c.2482G>A	p.Gly828Arg	p.G828R	ENST00000263734	NM_001430.4	828	Ggg/Agg	16/16	1	2	FACETS	0.888	0.824	0.955	0.888	0.824	0.955	CLONAL	1	TRUE	1	0.52	2		564	866	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033653	48033654	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	128	341	0	ENST00000234420.5:c.3864_3865del	p.Lys1288AsnfsTer3	p.K1288Nfs*3	ENST00000234420	NM_000179.2	1288	aaATtc/aatc	9/10	1	2	FACETS	0.908	0.827	0.993	0.908	0.827	0.993	CLONAL	1	TRUE	1	0.52	2		341	542	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189365	99189365	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	84	474	0	ENST00000074304.5:c.2621T>G	p.Val874Gly	p.V874G	ENST00000074304	NM_001134224.1	874	gTc/gGc	24/26	1	2	FACETS	0.497	0.439	0.559	0.497	0.439	0.559	SUBCLONAL	1	TRUE	1	0.52	2		474	650	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439914	220439914	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373504529	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	186	577	0	ENST00000243786.2:c.767C>T	p.Pro256Leu	p.P256L	ENST00000243786	NM_002191.3	256	cCg/cTg	2/2	1	2	FACETS	0.899	0.832	0.968	0.899	0.832	0.968	CLONAL	1	TRUE	1	0.52	2		577	796	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309882	30309882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	168	418	1	ENST00000307677.4:c.140C>T	p.Thr47Ile	p.T47I	ENST00000307677	NM_138578.1	47	aCc/aTc	2/3	1	2	FACETS	0.889	0.819	0.961	0.889	0.819	0.961	CLONAL	1	TRUE	1	0.52	2		419	727	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913413	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	16	250	0	ENST00000349496.5:c.122C>A	p.Thr41Asn	p.T41N	ENST00000349496	NM_001904.3	41	aCc/aAc	3/15	1	2	FACETS	0.136	0.1	0.18	0.136	0.1	0.18	SUBCLONAL	1	TRUE	1	0.52	2		250	451	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84384700	84384700	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	197	356	0	ENST00000321945.7:c.743A>G	p.Asn248Ser	p.N248S	ENST00000321945	NM_139076.2	248	aAc/aGc	8/9	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.52	2		356	709	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628413	187628413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1425439780	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	247	613	1	ENST00000441802.2:c.2569G>A	p.Val857Met	p.V857M	ENST00000441802	NM_005245.3	857	Gtg/Atg	2/27	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.52	2		614	880	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499064	149499064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143067190	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	178	520	2	ENST00000261799.4:c.2764C>T	p.Arg922Cys	p.R922C	ENST00000261799	NM_002609.3	922	Cgc/Tgc	20/23	1	2	FACETS	0.893	0.824	0.963	0.893	0.824	0.963	CLONAL	1	TRUE	1	0.52	2		522	767	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047686	180047686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	88	460	0	ENST00000261937.6:c.2329G>A	p.Val777Met	p.V777M	ENST00000261937	NM_182925.4	777	Gtg/Atg	16/30	1	2	FACETS	0.501	0.444	0.562	0.501	0.444	0.562	SUBCLONAL	1	TRUE	1	0.52	2		460	676	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542515	141542515	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	69	326	0	ENST00000220592.5:c.2471G>T	p.Ser824Ile	p.S824I	ENST00000220592	NM_012154.3	824	aGt/aTt	18/19	1	2	FACETS	0.562	0.491	0.639	0.562	0.491	0.639	SUBCLONAL	1	TRUE	1	0.52	2		326	472	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141570599	141570599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	124	304	0	ENST00000220592.5:c.529G>A	p.Val177Met	p.V177M	ENST00000220592	NM_012154.3	177	Gtg/Atg	5/19	1	2	FACETS	0.965	0.878	1	0.965	0.878	1	CLONAL	1	TRUE	1	0.52	2		304	494	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141582935	141582935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760795850	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	110	505	1	ENST00000220592.5:c.312G>A	p.Met104Ile	p.M104I	ENST00000220592	NM_012154.3	104	atG/atA	3/19	1	2	FACETS	0.539	0.484	0.597	0.539	0.484	0.597	SUBCLONAL	1	TRUE	1	0.52	2		506	785	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841046	15841046	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	170	452	0	ENST00000307771.7:c.1130T>G	p.Leu377Arg	p.L377R	ENST00000307771	NM_005089.3	377	cTg/cGg	11/11	1	2	FACETS	0.962	0.887	1	0.962	0.887	1	CLONAL	1	TRUE	1	0.52	2		452	680	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440386	52440386	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	117	503	0	ENST00000460680.1:c.666del	p.Tyr223ThrfsTer8	p.Y223Tfs*8	ENST00000460680	NM_004656.3	222	ccC/cc	9/17	0.631654699491748	1	FACETS	0.909	0.834	0.985	0.909	0.834	0.985	CLONAL	1	TRUE	0	0.636216294248467	1		503	276	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0032246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	1513	561	2	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.390502004864768	12	FACETS	1	0.995	1			1	CLONAL	10	TRUE	NA	0.390502004864768	12		563	2222	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577575	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782289	NA	P-0032246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	43	394	0	ENST00000269305.4:c.706T>C	p.Tyr236His	p.Y236H	ENST00000269305	NM_001126112.2	236	Tac/Cac	7/11	1	2	FACETS	0.325	0.271	0.385	0.325	0.271	0.385	SUBCLONAL	1	TRUE	1	0.390502004864768	2		394	678	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266219	198266219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	30	380	0	ENST00000335508.6:c.2401G>A	p.Val801Ile	p.V801I	ENST00000335508	NM_012433.2	801	Gta/Ata	17/25	1	2	FACETS	0.275	0.221	0.337	0.275	0.221	0.337	SUBCLONAL	1	TRUE	1	0.390502004864768	2		380	558	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424178	49424178	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs886040960	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	57	403	1	ENST00000301067.7:c.13884del	p.Thr4629ProfsTer11	p.T4629Pfs*11	ENST00000301067	NM_003482.3	4628	ccC/cc	42/54	1	2	FACETS	0.469	0.404	0.54	0.469	0.404	0.54	SUBCLONAL	1	TRUE	1	0.618338912276417	2		404	393	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023559	27023560	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	73	489	0	ENST00000324856.7:c.671dup	p.Pro225AlafsTer175	p.P225Afs*175	ENST00000324856	NM_006015.4	222	tac/taCc	1/20	1	2	FACETS	0.472	0.414	0.535	0.472	0.414	0.535	SUBCLONAL	1	TRUE	1	0.618338912276417	2		489	500	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213909	66213909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	37	362	1	ENST00000273854.3:c.2521C>T	p.Pro841Ser	p.P841S	ENST00000273854	NM_004439.5	841	Cca/Tca	15/18	1	2	FACETS	0.381	0.315	0.455	0.381	0.315	0.455	SUBCLONAL	1	TRUE	1	0.618338912276417	2		363	314	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030479	49030479	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	19	270	0	ENST00000267163.4:c.1959del	p.Val654CysfsTer4	p.V654Cfs*4	ENST00000267163	NM_000321.2	652	Aaa/aa	19/27	1	2	FACETS	0.172	0.13	0.221	0.172	0.13	0.221	SUBCLONAL	1	TRUE	1	0.618338912276417	2		270	358	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799098	42799098	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	106	795	1	ENST00000575354.2:c.4586del	p.Pro1529LeufsTer91	p.P1529Lfs*91	ENST00000575354	NM_015125.3	1528	Ccc/cc	20/20	1	2	FACETS	0.5	0.448	0.554	0.5	0.448	0.554	SUBCLONAL	1	TRUE	1	0.618338912276417	2		796	686	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	69	355	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	1	2	FACETS	0.552	0.483	0.627	0.552	0.483	0.627	SUBCLONAL	1	TRUE	1	0.618338912276417	2		355	404	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521525	46521525	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	164	607	0	ENST00000262741.5:c.883del	p.Met295Ter	p.M295*	ENST00000262741	NM_003629.3	295	Atg/tg	7/10	1	2	FACETS	0.628	0.577	0.682	0.628	0.577	0.682	SUBCLONAL	1	TRUE	1	0.618338912276417	2		607	844	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346220	152346220	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	108	622	8	ENST00000359321.1:c.350del	p.Leu117TrpfsTer17	p.L117Wfs*17	ENST00000359321	NM_005431.1	117	tTg/tg	3/3	1	2	FACETS	0.555	0.499	0.615	0.555	0.499	0.615	SUBCLONAL	1	TRUE	1	0.618338912276417	2		630	629	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346204	89346204	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201043388	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	28	261	0	ENST00000301030.4:c.6746G>A	p.Arg2249His	p.R2249H	ENST00000301030	NM_001256183.1	2249	cGc/cAc	9/13	1	2	FACETS	0.539	0.435	0.655	0.539	0.435	0.655	SUBCLONAL	1	TRUE	1	0.618338912276417	2		261	168	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830868	72830868	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	109	656	0	ENST00000268489.5:c.5713C>T	p.Pro1905Ser	p.P1905S	ENST00000268489	NM_006885.3	1905	Ccg/Tcg	9/10	1	2	FACETS	0.578	0.52	0.639	0.578	0.52	0.639	SUBCLONAL	1	TRUE	1	0.618338912276417	2		656	610	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	46	360	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.568	0.482	0.662	0.568	0.482	0.662	SUBCLONAL	1	TRUE	1	0.618338912276417	2		360	262	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856545	111856545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1157707616	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	58	182	0	ENST00000341259.2:c.596C>T	p.Ala199Val	p.A199V	ENST00000341259	NM_005475.2	199	gCg/gTg	2/8	1	2	FACETS	0.623	0.539	0.713	0.623	0.539	0.713	SUBCLONAL	1	TRUE	1	0.618338912276417	2		182	301	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427950	49427950	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775632051	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	121	588	0	ENST00000301067.7:c.10640G>A	p.Arg3547His	p.R3547H	ENST00000301067	NM_003482.3	3547	cGc/cAc	38/54	1	2	FACETS	0.599	0.542	0.659	0.599	0.542	0.659	SUBCLONAL	1	TRUE	1	0.618338912276417	2		588	653	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945645	71945645	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	82	464	0	ENST00000298229.2:c.2401del	p.Arg801AlafsTer44	p.R801Afs*44	ENST00000298229	NM_001567.3	801	Cgc/gc	21/28	1	2	FACETS	0.585	0.518	0.657	0.585	0.518	0.657	SUBCLONAL	1	TRUE	1	0.618338912276417	2		464	453	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775948	9775948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	95	616	0	ENST00000377346.4:c.412G>A	p.Asp138Asn	p.D138N	ENST00000377346	NM_005026.3	138	Gac/Aac	5/24	1	2	FACETS	0.62	0.554	0.689	0.62	0.554	0.689	SUBCLONAL	1	TRUE	1	0.618338912276417	2		616	496	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948755	71948755	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1565399032	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	113	686	1	ENST00000298229.2:c.3470del	p.Gly1157AspfsTer45	p.G1157Dfs*45	ENST00000298229	NM_001567.3	1156	cGg/cg	26/28	1	2	FACETS	0.704	0.636	0.775	0.704	0.636	0.775	SUBCLONAL	1	TRUE	1	0.618338912276417	2		687	519	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784073	9784073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	95	618	0	ENST00000377346.4:c.2641G>A	p.Gly881Ser	p.G881S	ENST00000377346	NM_005026.3	881	Ggc/Agc	21/24	1	2	FACETS	0.542	0.483	0.604	0.542	0.483	0.604	SUBCLONAL	1	TRUE	1	0.618338912276417	2		618	567	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246093208	246093208	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs181459217	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	54	418	0	ENST00000388985.4:c.563C>T	p.Ala188Val	p.A188V	ENST00000388985		188	gCg/gTg	6/12	0.618338912276417	3	FACETS	0.365	0.311	0.424	0.182	0.155	0.212	SUBCLONAL	1	TRUE	1	0.618338912276417	3		418	627	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720855	89720856	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	158	346	0	ENST00000371953.3:c.1007dup	p.Tyr336Ter	p.Y336*	ENST00000371953	NM_000314.4	336	tac/tAac	8/9	0.348171857610879	2	FACETS	1	0.98	1	0.585	0.541	0.629	INDETERMINATE	1	TRUE	0	0.618338912276417	2		346	437	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257818	133257818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377002290	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	63	423	0	ENST00000320574.5:c.110G>A	p.Arg37Gln	p.R37Q	ENST00000320574	NM_006231.2	37	cGg/cAg	2/49	1	2	FACETS	0.455	0.394	0.52	0.455	0.394	0.52	SUBCLONAL	1	TRUE	1	0.618338912276417	2		423	448	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355792	73355792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	81	459	0	ENST00000377767.4:c.179G>A	p.Cys60Tyr	p.C60Y	ENST00000377767	NM_014953.3	60	tGc/tAc	1/21	1	2	FACETS	0.616	0.546	0.692	0.616	0.546	0.692	SUBCLONAL	1	TRUE	1	0.618338912276417	2		459	425	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645310	67645310	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	65	404	0	ENST00000264010.4:c.579del	p.Asp194ThrfsTer28	p.D194Tfs*28	ENST00000264010	NM_006565.3	192	cAa/ca	3/12	1	2	FACETS	0.514	0.447	0.586	0.514	0.447	0.586	SUBCLONAL	1	TRUE	1	0.618338912276417	2		404	409	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688801	47688801	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	80	355	0	ENST00000347630.2:c.499T>G	p.Ser167Ala	p.S167A	ENST00000347630	NM_001007230.1	167	Tct/Gct	7/11	1	2	FACETS	0.652	0.577	0.731	0.652	0.577	0.731	SUBCLONAL	1	TRUE	1	0.618338912276417	2		355	397	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554537	63554537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	80	454	1	ENST00000307078.5:c.202C>T	p.Arg68Trp	p.R68W	ENST00000307078	NM_004655.3	68	Cgg/Tgg	2/11	1	2	FACETS	0.583	0.515	0.655	0.583	0.515	0.655	SUBCLONAL	1	TRUE	1	0.618338912276417	2		455	444	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210868	36210868	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376781845	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	117	692	0	ENST00000222270.7:c.619C>T	p.Arg207Trp	p.R207W	ENST00000222270	NM_014727.1	207	Cgg/Tgg	3/37	1	2	FACETS	0.589	0.532	0.648	0.589	0.532	0.648	SUBCLONAL	1	TRUE	1	0.618338912276417	2		692	643	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212653	36212726	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGCTATTCAAGATCGATCAGCAGCAGCAGCAGAAGGTGGCAGCTTCCATGCCGGTGAGTGTGGTCCCTGGGCC	CAGCTATTCAAGATCGATCAGCAGCAGCAGCAGAAGGTGGCAGCTTCCATGCCGGTGAGTGTGGTCCCTGGGCC	-	novel	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	58	729	0	ENST00000222270.7:c.2408_2457+24del		p.X803_splice	ENST00000222270	NM_014727.1	803		3/37	1	2	FACETS	0.262	0.224	0.303	0.262	0.224	0.303	SUBCLONAL	1	TRUE	1	0.618338912276417	2		729	717	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221463	36221463	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	115	817	0	ENST00000222270.7:c.5222G>T	p.Gly1741Val	p.G1741V	ENST00000222270	NM_014727.1	1741	gGt/gTt	25/37	1	2	FACETS	0.474	0.427	0.524	0.474	0.427	0.524	SUBCLONAL	1	TRUE	1	0.618338912276417	2		817	784	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543743	29543743	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	21	422	0	ENST00000389048.3:c.1420C>A	p.Leu474Met	p.L474M	ENST00000389048	NM_004304.4	474	Ctg/Atg	7/29	1	2	FACETS	0.172	0.132	0.219	0.172	0.132	0.219	SUBCLONAL	1	TRUE	1	0.618338912276417	2		422	395	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637469	47637469	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	29	431	1	ENST00000233146.2:c.603A>T	p.Leu201Phe	p.L201F	ENST00000233146	NM_000251.2	201	ttA/ttT	3/16	1	2	FACETS	0.198	0.158	0.243	0.198	0.158	0.243	SUBCLONAL	1	TRUE	1	0.618338912276417	2		432	474	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265429	46265429	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	16	193	0	ENST00000371998.3:c.2299A>C	p.Ser767Arg	p.S767R	ENST00000371998		767	Agt/Cgt	12/23	1	2	FACETS	0.185	0.137	0.244	0.185	0.137	0.244	SUBCLONAL	1	TRUE	1	0.618338912276417	2		193	279	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444678	187444678	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	17	306	0	ENST00000232014.4:c.1549del	p.Ala517ProfsTer73	p.A517Pfs*73	ENST00000232014	NM_001130845.1	517	Gcc/cc	7/10	1	2	FACETS	0.18	0.134	0.234	0.18	0.134	0.234	SUBCLONAL	1	TRUE	1	0.618338912276417	2		306	306	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233723	233723	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	112	651	0	ENST00000264932.6:c.1027G>T	p.Val343Leu	p.V343L	ENST00000264932	NM_004168.2	343	Gtg/Ttg	8/15	1	2	FACETS	0.52	0.468	0.575	0.52	0.468	0.575	SUBCLONAL	1	TRUE	1	0.618338912276417	2		651	696	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589569	67589574	+	inframe_deletion	In_Frame_Del	DEL	TGTAGG	TGTAGG	-	novel	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	30	193	0	ENST00000274335.5:c.1332_1337del	p.Val445_Gly446del	p.V445_G446del	ENST00000274335		444	gcTGTAGGg/gcg	10/15	1	2	FACETS	0.48	0.39	0.581	0.48	0.39	0.581	SUBCLONAL	1	TRUE	1	0.618338912276417	2		193	202	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041136	180041136	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	39	754	0	ENST00000261937.6:c.3263A>G	p.Asp1088Gly	p.D1088G	ENST00000261937	NM_182925.4	1088	gAc/gGc	24/30	1	2	FACETS	0.167	0.137	0.2	0.167	0.137	0.2	SUBCLONAL	1	TRUE	1	0.618338912276417	2		754	756	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324464	31324464	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	18	285	0	ENST00000412585.2:c.343+1G>T		p.X115_splice	ENST00000412585	NM_005514.6	115			1	2	FACETS	0.31	0.234	0.398	0.31	0.234	0.398	SUBCLONAL	1	TRUE	1	0.618338912276417	2		285	188	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520036	106520036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	43	269	0	ENST00000359195.3:c.2464G>A	p.Ala822Thr	p.A822T	ENST00000359195	NM_002649.2	822	Gcc/Acc	6/11	1	2	FACETS	0.381	0.319	0.449	0.381	0.319	0.449	SUBCLONAL	1	TRUE	1	0.618338912276417	2		269	365	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857196	9857196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs74935155	NA	P-0032454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	32	531	0	ENST00000330684.3:c.4205G>A	p.Arg1402Gln	p.R1402Q	ENST00000330684	NM_001134407.1	1402	cGg/cAg	13/13	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		531	626	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190351	32190351	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs780145569	NA	P-0032454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	124	712	3	ENST00000375023.3:c.388A>G	p.Arg130Gly	p.R130G	ENST00000375023	NM_004557.3	130	Agg/Ggg	3/30	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		715	853	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0032503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	22	698	2	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.133	0.102	0.169	0.133	0.102	0.169	SUBCLONAL	1	TRUE	1	0.409939306981541	2		700	809	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880256	155880256	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	249	348	0	ENST00000368323.3:c.148C>A	p.His50Asn	p.H50N	ENST00000368323	NM_006912.5	50	Cat/Aat	3/6	0.409939306981541	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.409939306981541	3		348	710	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223520	2223520	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	127	658	0	ENST00000326181.6:c.1051C>G	p.Leu351Val	p.L351V	ENST00000326181	NM_032271.2	351	Ctc/Gtc	11/21	1	2	FACETS	0.838	0.76	0.921	0.838	0.76	0.921	CLONAL	1	TRUE	1	0.409939306981541	2		658	739	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286812	212286812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	77	329	0	ENST00000342788.4:c.2884G>A	p.Asp962Asn	p.D962N	ENST00000342788	NM_005235.2	962	Gac/Aac	24/28	1	2	FACETS	0.958	0.846	1	0.958	0.846	1	CLONAL	1	TRUE	1	0.409939306981541	2		329	392	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879337	151879337	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	75	365	0	ENST00000262189.6:c.5608C>G	p.Gln1870Glu	p.Q1870E	ENST00000262189	NM_170606.2	1870	Cag/Gag	36/59	1	2	FACETS	0.795	0.699	0.898	0.795	0.699	0.898	SUBCLONAL	1	TRUE	1	0.409939306981541	2		365	460	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207472	29207472	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0032503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	68	408	0	ENST00000240100.2:c.324C>G	p.Tyr108Ter	p.Y108*	ENST00000240100	NM_001394.6	108	taC/taG	1/4	1	2	FACETS	0.821	0.718	0.932	0.821	0.718	0.932	CLONAL	1	TRUE	1	0.409939306981541	2		408	404	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057682	27057682	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520585	NA	P-0032571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	171	720	0	ENST00000324856.7:c.1390C>T	p.Gln464Ter	p.Q464*	ENST00000324856	NM_006015.4	464	Caa/Taa	3/20	1	2	FACETS	0.924	0.849	1	0.924	0.849	1	CLONAL	1	TRUE	1	0.34	2		720	1089	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577113	7577113	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555525279	NA	P-0032571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	174	725	0	ENST00000269305.4:c.825T>G	p.Cys275Trp	p.C275W	ENST00000269305	NM_001126112.2	275	tgT/tgG	8/11	0.302124207532307	1	FACETS	0.798	0.734	0.866	0.798	0.734	0.866	SUBCLONAL	1	TRUE	0	0.34	1		725	1064	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967203	134967203	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	232	455	0	ENST00000398015.3:c.2542G>T	p.Asp848Tyr	p.D848Y	ENST00000398015	NM_004441.4	848	Gac/Tac	14/16	0.262171177372595	4	FACETS	0.808	0.753	0.866			1	CLONAL	2	TRUE	NA	0.34	4		455	1131	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967301	134967301	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	228	477	2	ENST00000398015.3:c.2640G>C	p.Lys880Asn	p.K880N	ENST00000398015	NM_004441.4	880	aaG/aaC	14/16	0.262171177372595	4	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.34	4		479	1228	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057682	27057682	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520585	NA	P-0032571-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	70	720	0	ENST00000324856.7:c.1390C>T	p.Gln464Ter	p.Q464*	ENST00000324856	NM_006015.4	464	Caa/Taa	3/20	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.224302779308684	2		720	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577113	7577113	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555525279	NA	P-0032571-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	54	725	0	ENST00000269305.4:c.825T>G	p.Cys275Trp	p.C275W	ENST00000269305	NM_001126112.2	275	tgT/tgG	8/11	0.177046612454107	1	FACETS	0.896	0.766	1	0.896	0.766	1	CLONAL	1	TRUE	0	0.224302779308684	1		725	477	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967203	134967203	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032571-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	105	455	0	ENST00000398015.3:c.2542G>T	p.Asp848Tyr	p.D848Y	ENST00000398015	NM_004441.4	848	Gac/Tac	14/16	0.175127997251381	3	FACETS	0.93	0.835	1	0.93	0.835	1	CLONAL	2	TRUE	1	0.224302779308684	3		455	560	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967301	134967301	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032571-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	93	477	2	ENST00000398015.3:c.2640G>C	p.Lys880Asn	p.K880N	ENST00000398015	NM_004441.4	880	aaG/aaC	14/16	0.175127997251381	3	FACETS	1	0.977	1	0.701	0.624	0.783	CLONAL	1	TRUE	1	0.224302779308684	3		479	658	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578496	7578496	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587782197	NA	P-0032590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	93	754	0	ENST00000269305.4:c.434T>A	p.Leu145Gln	p.L145Q	ENST00000269305	NM_001126112.2	145	cTg/cAg	5/11	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.16	2		754	1141	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874287	155874287	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs869025194	NA	P-0032590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	44	502	0	ENST00000368323.3:c.244T>G	p.Phe82Val	p.F82V	ENST00000368323	NM_006912.5	82	Ttt/Gtt	5/6	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.16	2		502	534	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488280	56488280	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	52	532	0	ENST00000267101.3:c.1799T>C	p.Ile600Thr	p.I600T	ENST00000267101	NM_001982.3	600	aTc/aCc	15/28	1	2	FACETS	0.908	0.771	1	0.908	0.771	1	CLONAL	1	TRUE	1	0.16	2		532	716	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41554424	41554444	+	inframe_deletion	In_Frame_Del	DEL	CTCTCCACAGACACTGTGTTG	CTCTCCACAGACACTGTGTTG	-	novel	NA	P-0032590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	37	436	2	ENST00000263253.7:c.3512_3532del	p.Ser1171_Cys1177del	p.S1171_C1177del	ENST00000263253	NM_001429.3	1170	ttCTCTCCACAGACACTGTGTTGc/ttc	19/31	1	2	FACETS	0.864	0.712	1	0.864	0.712	1	CLONAL	1	TRUE	1	0.16	2		438	535	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	215	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.962323973271069	2		306	435	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17349180	17349180	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	356	562	0	ENST00000375499.3:c.688C>G	p.Arg230Gly	p.R230G	ENST00000375499	NM_003000.2	230	Cgc/Ggc	7/8	1	2	FACETS	0.943	0.899	0.987	0.943	0.899	0.987	CLONAL	1	TRUE	1	0.962323973271069	2		562	785	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36217200	36217200	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751755267	NA	P-0032636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	71	772	3	ENST00000222270.7:c.3949G>A	p.Glu1317Lys	p.E1317K	ENST00000222270	NM_014727.1	1317	Gag/Aag	14/37	1	2	FACETS	0.128	0.111	0.147	0.128	0.111	0.147	SUBCLONAL	1	TRUE	1	0.962323973271069	2		775	1150	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061223	38061228	+	inframe_deletion	In_Frame_Del	DEL	TCTCGA	TCTCGA	-	novel	NA	P-0032651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	100	535	1	ENST00000250448.2:c.761_766del	p.Phe254_Asn256delinsTyr	p.F254_N256delinsY	ENST00000250448	NM_004496.3	254	tTCGAGAac/tac	2/2	1	2	FACETS	0.886	0.795	0.983	0.886	0.795	0.983	CLONAL	1	FALSE	1	0.444267085788435	2		536	508	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94211984	94211984	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	90	597	0	ENST00000323929.3:c.461G>T	p.Gly154Val	p.G154V	ENST00000323929	NM_005591.3	154	gGa/gTa	6/20	1	2	FACETS	0.896	0.811	0.984	1	0.986	1	CLONAL	2	FALSE	1	0.444267085788435	2		597	226	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968199	134968199	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1232280655	NA	P-0032651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	128	641	0	ENST00000398015.3:c.2712C>A	p.Asp904Glu	p.D904E	ENST00000398015	NM_004441.4	904	gaC/gaA	15/16	1	2	FACETS	0.796	0.73	0.864	1	0.988	1	SUBCLONAL	2	FALSE	1	0.444267085788435	2		641	362	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600042	10600042	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs148641376	NA	P-0032701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	24	677	0	ENST00000171111.5:c.1534G>A	p.Val512Ile	p.V512I	ENST00000171111	NM_203500.1	512	Gtc/Atc	5/6	0.0988845905072111	0	FACETS	0.867	0.68	1			1	CLONAL	1	TRUE	0	0.14	0		677	340	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0032701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	12	562	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	0.539	0.378	0.739	0.539	0.378	0.739	SUBCLONAL	1	TRUE	1	0.14	2		562	318	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727483	66727483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504317	NA	P-0032701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	11	496	0	ENST00000307102.5:c.199G>A	p.Asp67Asn	p.D67N	ENST00000307102	NM_002755.3	67	Gac/Aac	2/11	1	2	FACETS	0.634	0.437	0.879	0.634	0.437	0.879	SUBCLONAL	1	TRUE	1	0.14	2		496	248	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754535	42754535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745819984	NA	P-0032701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	29	869	1	ENST00000222329.4:c.205G>A	p.Val69Ile	p.V69I	ENST00000222329	NM_006494.2	69	Gtt/Att	2/4	0.0988845905072111	0	FACETS	0.656	0.525	0.806			1	SUBCLONAL	1	TRUE	0	0.14	0		870	543	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050932	49050933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	15	284	0	ENST00000267163.4:c.2622dup	p.Leu875ThrfsTer4	p.L875Tfs*4	ENST00000267163	NM_000321.2	872	-/A	25/27	1	2	FACETS	0.824	0.603	1	0.824	0.603	1	CLONAL	1	TRUE	1	0.14	2		284	260	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245318	46245318	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	19	466	0	ENST00000334344.6:c.3416del	p.Gly1139GlufsTer17	p.G1139Efs*17	ENST00000334344	NM_152641.2	1138	Ggg/gg	15/21	0.0988845905072111	3	FACETS	0.896	0.68	1	0.448	0.34	0.576	CLONAL	1	TRUE	1	0.14	3		466	324	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913831	32913831	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	18	444	0	ENST00000380152.3:c.5339A>G	p.Glu1780Gly	p.E1780G	ENST00000380152		1780	gAa/gGa	11/27	1	2	FACETS	0.872	0.656	1	0.872	0.656	1	CLONAL	1	TRUE	1	0.14	2		444	295	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630338	47630355	+	frameshift_variant	Frame_Shift_Del	DEL	TGCAGCCGAAGGAGACGC	TGCAGCCGAAGGAGACGC	ACGG	novel	NA	P-0032701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	19	609	2	ENST00000233146.2:c.8_25delinsACGG	p.Val3AspfsTer74	p.V3Dfs*74	ENST00000233146	NM_000251.2	3	gTGCAGCCGAAGGAGACGCtg/gACGGtg	1/16	0.0988845905072111	0	FACETS	0.687	0.521	0.882			1	SUBCLONAL	1	TRUE	0	0.14	0		611	340	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807542	1807542	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	22	665	3	ENST00000260795.2:c.1711C>T	p.Arg571Trp	p.R571W	ENST00000260795		571	Cgg/Tgg	12/17	1	2	FACETS	1	0.791	1	1	0.791	1	CLONAL	1	TRUE	1	0.14	2		668	308	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526993	31526993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769152940	NA	P-0032701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	21	700	0	ENST00000344624.3:c.47G>A	p.Arg16Gln	p.R16Q	ENST00000344624		16	cGa/cAa	2/33	1	2	FACETS	0.746	0.574	0.948	0.746	0.574	0.948	CLONAL	1	TRUE	1	0.14	2		700	402	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094954	11094954	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs375812959	NA	P-0032701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	24	767	0	ENST00000358026.2:c.127A>T	p.Met43Leu	p.M43L	ENST00000358026	NM_001128849.1	43	Atg/Ttg	2/36	0.0988845905072111	0	FACETS	1	0.822	1			1	CLONAL	1	TRUE	0	0.14	0		767	280	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0032701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	134	532	1	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	0.703	0.639	0.771	0.703	0.639	0.771	SUBCLONAL	1	TRUE	1	0.487153510690209	2		533	782	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753011	57753012	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	98	298	3	ENST00000274289.3:c.1004dup	p.Leu335PhefsTer12	p.L335Ffs*12	ENST00000274289	NM_006622.3	335	ttg/ttTg	7/14	1	2	FACETS	0.816	0.731	0.906	0.816	0.731	0.906	CLONAL	1	TRUE	1	0.487153510690209	2		301	493	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442579	52442579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1312611941	NA	P-0032701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	122	257	0	ENST00000460680.1:c.166C>T	p.Arg56Cys	p.R56C	ENST00000460680	NM_004656.3	56	Cgc/Tgc	4/17	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.487153510690209	2		257	482	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600042	10600042	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs148641376	NA	P-0032701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	208	677	0	ENST00000171111.5:c.1534G>A	p.Val512Ile	p.V512I	ENST00000171111	NM_203500.1	512	Gtc/Atc	5/6	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.487153510690209	2		677	809	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0032701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	151	562	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	0.86	0.788	0.935	0.86	0.788	0.935	CLONAL	1	TRUE	1	0.487153510690209	2		562	721	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727483	66727483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504317	NA	P-0032701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	127	496	0	ENST00000307102.5:c.199G>A	p.Asp67Asn	p.D67N	ENST00000307102	NM_002755.3	67	Gac/Aac	2/11	1	2	FACETS	0.897	0.816	0.983	0.897	0.816	0.983	CLONAL	1	TRUE	1	0.487153510690209	2		496	581	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346158	89346158	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs878855327	NA	P-0032701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	19	216	0	ENST00000301030.4:c.6792del	p.Ala2265ProfsTer72	p.A2265Pfs*72	ENST00000301030	NM_001256183.1	2264	ccC/cc	9/13	0.487153510690209	1	FACETS	0.292	0.222	0.373	0.292	0.222	0.373	SUBCLONAL	1	TRUE	0	0.487153510690209	1		216	202	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835781	68835781	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060501215	NA	P-0032701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	165	478	0	ENST00000261769.5:c.377del	p.Pro126ArgfsTer89	p.P126Rfs*89	ENST00000261769	NM_004360.3	124	cgC/cg	3/16	0.487153510690209	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.487153510690209	1		478	467	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0032701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	188	1044	2	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.855	0.79	0.922	0.855	0.79	0.922	CLONAL	1	TRUE	1	0.487153510690209	2		1046	903	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954248	17954248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776850935	NA	P-0032701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	162	449	1	ENST00000458235.1:c.361C>T	p.Arg121Cys	p.R121C	ENST00000458235	NM_000215.3	121	Cgc/Tgc	4/24	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.487153510690209	2		450	658	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410918	31410918	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	212	664	0	ENST00000344624.3:c.3602T>C	p.Ile1201Thr	p.I1201T	ENST00000344624		1201	aTa/aCa	28/33	1	2	FACETS	0.876	0.813	0.94	0.876	0.813	0.94	CLONAL	1	TRUE	1	0.487153510690209	2		664	994	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797157	45797157	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs144079536	NA	P-0032701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	199	692	0	ENST00000450313.1:c.1258C>A	p.Leu420Met	p.L420M	ENST00000450313	NM_012222.2	420	Ctg/Atg	13/16	1	2	FACETS	0.962	0.893	1	0.962	0.893	1	CLONAL	1	TRUE	1	0.487153510690209	2		692	849	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754535	42754535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745819984	NA	P-0032701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	225	869	1	ENST00000222329.4:c.205G>A	p.Val69Ile	p.V69I	ENST00000222329	NM_006494.2	69	Gtt/Att	2/4	1	2	FACETS	0.939	0.875	1	0.939	0.875	1	CLONAL	1	TRUE	1	0.487153510690209	2		870	984	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050932	49050933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	103	284	0	ENST00000267163.4:c.2622dup	p.Leu875ThrfsTer4	p.L875Tfs*4	ENST00000267163	NM_000321.2	872	-/A	25/27	1	2	FACETS	0.919	0.827	1	0.919	0.827	1	CLONAL	1	TRUE	1	0.487153510690209	2		284	460	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245318	46245318	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	138	466	0	ENST00000334344.6:c.3416del	p.Gly1139GlufsTer17	p.G1139Efs*17	ENST00000334344	NM_152641.2	1138	Ggg/gg	15/21	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.487153510690209	2		466	552	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913831	32913831	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	145	444	0	ENST00000380152.3:c.5339A>G	p.Glu1780Gly	p.E1780G	ENST00000380152		1780	gAa/gGa	11/27	1	2	FACETS	0.916	0.838	0.997	0.916	0.838	0.997	CLONAL	1	TRUE	1	0.487153510690209	2		444	650	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630338	47630355	+	frameshift_variant	Frame_Shift_Del	DEL	TGCAGCCGAAGGAGACGC	TGCAGCCGAAGGAGACGC	ACGG	novel	NA	P-0032701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	135	609	2	ENST00000233146.2:c.8_25delinsACGG	p.Val3AspfsTer74	p.V3Dfs*74	ENST00000233146	NM_000251.2	3	gTGCAGCCGAAGGAGACGCtg/gACGGtg	1/16	0.487153510690209	1	FACETS	0.883	0.808	0.96	0.883	0.808	0.96	CLONAL	1	TRUE	0	0.487153510690209	1		611	475	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630355	47630355	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	135	504	0	ENST00000233146.2:c.25C>G	p.Leu9Val	p.L9V	ENST00000233146	NM_000251.2	9	Ctg/Gtg	1/16	0.487153510690209	1	FACETS	0.888	0.813	0.966	0.888	0.813	0.966	CLONAL	1	TRUE	0	0.487153510690209	1		504	472	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807542	1807542	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	183	665	3	ENST00000260795.2:c.1711C>T	p.Arg571Trp	p.R571W	ENST00000260795		571	Cgg/Tgg	12/17	0.215099397624453	1	FACETS	0.738	0.682	0.796	0.738	0.682	0.796	INDETERMINATE	1	TRUE	0	0.487153510690209	1		668	770	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526993	31526993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769152940	NA	P-0032701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	194	700	0	ENST00000344624.3:c.47G>A	p.Arg16Gln	p.R16Q	ENST00000344624		16	cGa/cAa	2/33	1	2	FACETS	0.971	0.9	1	0.971	0.9	1	CLONAL	1	TRUE	1	0.487153510690209	2		700	820	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836624	89836624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556748657	NA	P-0032701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	193	641	2	ENST00000389301.3:c.2266C>T	p.Arg756Cys	p.R756C	ENST00000389301	NM_000135.2	756	Cgt/Tgt	25/43	0.487153510690209	1	FACETS	0.942	0.876	1	0.942	0.876	1	CLONAL	1	TRUE	0	0.487153510690209	1		643	636	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37882053	37882053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	166	563	1	ENST00000269571.5:c.2819G>A	p.Arg940Gln	p.R940Q	ENST00000269571		940	cGg/cAg	23/27	1	2	FACETS	0.844	0.777	0.915	0.844	0.777	0.915	CLONAL	1	TRUE	1	0.487153510690209	2		564	807	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279646	18279646	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141407533	NA	P-0032701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	160	510	0	ENST00000222254.8:c.1919G>A	p.Arg640Gln	p.R640Q	ENST00000222254	NM_005027.3	640	cGg/cAg	15/16	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.487153510690209	2		510	648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579476	7579477	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	151	615	0	ENST00000269305.4:c.210dup	p.Pro71SerfsTer78	p.P71Sfs*78	ENST00000269305	NM_001126112.2	70	-/T	4/11	0.655816167766139	2	FACETS	0.837	0.783	0.891	0.837	0.783	0.891	CLONAL	2	TRUE	0	0.655816167766139	2		615	275	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	66	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.402	0.349	0.46	0.402	0.349	0.46	SUBCLONAL	1	TRUE	1	0.552764927473357	2		436	594	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0032851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	115	286	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.683	0.617	0.753	0.683	0.617	0.753	SUBCLONAL	1	TRUE	1	0.552764927473357	2		286	609	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0032851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	96	372	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.515	0.459	0.574	0.515	0.459	0.574	SUBCLONAL	1	TRUE	1	0.552764927473357	2		373	675	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028638	12028638	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	69	627	0	ENST00000353533.5:c.841C>T	p.Arg281Ter	p.R281*	ENST00000353533	NM_003010.3	281	Cga/Tga	8/11	1	2	FACETS	0.436	0.38	0.497	0.436	0.38	0.497	SUBCLONAL	1	TRUE	1	0.552764927473357	2		627	572	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120639	115120639	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	120	677	0	ENST00000257566.3:c.367A>G	p.Met123Val	p.M123V	ENST00000257566	NM_016569.3	123	Atg/Gtg	1/8	1	2	FACETS	0.449	0.405	0.496	0.449	0.405	0.496	SUBCLONAL	1	TRUE	1	0.552764927473357	2		677	966	SUCCESS
APC	324	MSKCC	GRCh37	5	112173672	112173690	+	frameshift_variant	Frame_Shift_Del	DEL	GTCTCTATGGTGATTATGT	GTCTCTATGGTGATTATGT	-	novel	NA	P-0032851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	42	363	0	ENST00000257430.4:c.2381_2399del	p.Ser794IlefsTer20	p.S794Ifs*20	ENST00000257430	NM_000038.5	794	aGTCTCTATGGTGATTATGTt/at	16/16	1	2	FACETS	0.286	0.238	0.339	0.286	0.238	0.339	SUBCLONAL	1	TRUE	1	0.552764927473357	2		363	532	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877381	40877381	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	47	561	3	ENST00000373198.4:c.2315G>A	p.Gly772Asp	p.G772D	ENST00000373198	NM_133170.3	772	gGc/gAc	15/32	1	2	FACETS	0.981	0.827	1	0.981	0.827	1	CLONAL	1	FALSE	1	0.172688801729117	2		564	555	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0033035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	66	606	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			1	2	FACETS	1	0.9	1	1	0.981	1	CLONAL	2	FALSE	1	0.172688801729117	2		606	369	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145807	11145814	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTACAT	AGGTACAT	-	novel	NA	P-0033035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	28	384	0	ENST00000358026.2:c.4169_4170+6del		p.X1390_splice	ENST00000358026	NM_001128849.1	1390		29/36	1	2	FACETS	0.893	0.714	1	0.893	0.714	1	CLONAL	1	FALSE	1	0.172688801729117	2		384	363	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0033138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	561	588	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.906733365453186	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.906733365453186	2		588	611	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346576	89346576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753162681	NA	P-0033138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	85	444	0	ENST00000301030.4:c.6374C>T	p.Ala2125Val	p.A2125V	ENST00000301030	NM_001256183.1	2125	gCc/gTc	9/13	0.641112280620165	1	FACETS	0.307	0.273	0.342	0.307	0.273	0.342	SUBCLONAL	1	TRUE	0	0.906733365453186	1		444	334	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562669	29562669	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs199474765	NA	P-0033138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	120	559	0	ENST00000356175.3:c.3749G>C	p.Arg1250Pro	p.R1250P	ENST00000356175	NM_000267.3	1250	cGg/cCg	28/57	1	2	FACETS	0.388	0.35	0.427	0.388	0.35	0.427	SUBCLONAL	1	TRUE	1	0.906733365453186	2		559	683	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627316	37627316	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	135	499	0	ENST00000447079.4:c.1231G>C	p.Ala411Pro	p.A411P	ENST00000447079	NM_015083.1	411	Gct/Cct	2/14	1	2	FACETS	0.446	0.406	0.488	0.446	0.406	0.488	SUBCLONAL	1	TRUE	1	0.906733365453186	2		499	668	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943620	17943620	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	203	750	0	ENST00000458235.1:c.2469del	p.Lys823AsnfsTer22	p.K823Nfs*22	ENST00000458235	NM_000215.3	823	aaG/aa	18/24	0.42180492875688	5	FACETS	0.754	0.697	0.813	0.251	0.232	0.271	INDETERMINATE	1	TRUE	2	0.906733365453186	5		750	1402	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463533	25463533	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	128	495	0	ENST00000264709.3:c.2149A>C	p.Asn717His	p.N717H	ENST00000264709	NM_175629.2	717	Aac/Cac	18/23	0.906733365453186	1	FACETS	0.337	0.307	0.368	0.337	0.307	0.368	SUBCLONAL	1	TRUE	0	0.906733365453186	1		495	458	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399942	139399942	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	93	782	0	ENST00000277541.6:c.4406A>G	p.Asn1469Ser	p.N1469S	ENST00000277541	NM_017617.3	1469	aAc/aGc	25/34	0.906733365453186	1	FACETS	0.169	0.15	0.189	0.169	0.15	0.189	SUBCLONAL	1	TRUE	0	0.906733365453186	1		782	663	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578469	+	frameshift_variant	Frame_Shift_Del	DEL	CGGACGCGGGTGC	CGGACGCGGGTGC	-	novel	NA	P-0033219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	196	412	0	ENST00000269305.4:c.461_473del	p.Gly154AlafsTer12	p.G154Afs*12	ENST00000269305	NM_001126112.2	154	gGCACCCGCGTCCGc/gc	5/11	0.345784675367357	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.345784675367357	1		412	785	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874012	151874012	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	140	404	0	ENST00000262189.6:c.8526T>G	p.Asn2842Lys	p.N2842K	ENST00000262189	NM_170606.2	2842	aaT/aaG	38/59	0.345784675367357	3	FACETS	1	0.967	1	0.565	0.514	0.618	CLONAL	1	TRUE	1	0.345784675367357	3		404	841	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	451	973	3	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.933	0.891	0.975	0.933	0.891	0.975	CLONAL	1	TRUE	1	0.743821222895337	2		976	1300	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	405	247	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.998	0.952	1	0.998	0.952	1	CLONAL	1	TRUE	1	0.743821222895337	2		248	1091	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	110	467	0	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	0.58	0.523	0.639	0.58	0.523	0.639	SUBCLONAL	1	TRUE	1	0.743821222895337	2		467	510	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	276	612	3	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.705745869226455	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.743821222895337	1		615	466	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690584	88690584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368222977	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	197	409	1	ENST00000360948.2:c.446C>T	p.Thr149Met	p.T149M	ENST00000360948	NM_001012338.2	149	aCg/aTg	5/19	1	2	FACETS	0.899	0.838	0.962	0.899	0.838	0.962	CLONAL	1	TRUE	1	0.743821222895337	2		410	589	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	350	720	0	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	1	2	FACETS	0.881	0.836	0.928	0.881	0.836	0.928	CLONAL	1	TRUE	1	0.743821222895337	2		720	1068	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	293	869	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.955	0.902	1	0.955	0.902	1	CLONAL	1	TRUE	1	0.743821222895337	2		869	825	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778759	9778759	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	299	693	0	ENST00000377346.4:c.1028T>C	p.Val343Ala	p.V343A	ENST00000377346	NM_005026.3	343	gTg/gCg	9/24	1	2	FACETS	0.955	0.903	1	0.955	0.903	1	CLONAL	1	TRUE	1	0.743821222895337	2		693	842	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11313919	11313919	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	428	825	0	ENST00000361445.4:c.817C>T	p.Arg273Ter	p.R273*	ENST00000361445	NM_004958.3	273	Cga/Tga	6/58	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.743821222895337	2		825	1149	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106078	27106078	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	266	510	0	ENST00000324856.7:c.5693del	p.Pro1898HisfsTer25	p.P1898Hfs*25	ENST00000324856	NM_006015.4	1897	Ccc/cc	20/20	1	2	FACETS	0.967	0.911	1	0.967	0.911	1	CLONAL	1	TRUE	1	0.743821222895337	2		510	740	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938276	36938276	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751578398	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	457	976	1	ENST00000361632.4:c.685C>T	p.Pro229Ser	p.P229S	ENST00000361632		229	Ccc/Tcc	6/16	1	2	FACETS	0.963	0.92	1	0.963	0.92	1	CLONAL	1	TRUE	1	0.743821222895337	2		977	1276	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313339	65313339	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	351	543	0	ENST00000342505.4:c.1775G>A	p.Gly592Asp	p.G592D	ENST00000342505	NM_002227.2	592	gGc/gAc	13/25	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.743821222895337	2		543	858	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325846	65325846	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747767226	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	272	450	0	ENST00000342505.4:c.1276G>A	p.Asp426Asn	p.D426N	ENST00000342505	NM_002227.2	426	Gac/Aac	9/25	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.743821222895337	2		450	723	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617398	43617398	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs78347871	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	251	522	0	ENST00000355710.3:c.2735G>A	p.Arg912Gln	p.R912Q	ENST00000355710	NM_020975.4	912	cGg/cAg	16/20	1	2	FACETS	0.88	0.826	0.935	0.88	0.826	0.935	CLONAL	1	TRUE	1	0.743821222895337	2		522	767	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332820	70332820	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	367	684	1	ENST00000373644.4:c.725T>A	p.Met242Lys	p.M242K	ENST00000373644	NM_030625.2	242	aTg/aAg	2/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.743821222895337	2		685	941	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138055	64138055	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	514	1173	0	ENST00000334205.4:c.1978G>A	p.Ala660Thr	p.A660T	ENST00000334205	NM_003942.2	660	Gcc/Acc	16/17	1	2	FACETS	0.952	0.912	0.992	0.952	0.912	0.992	CLONAL	1	TRUE	1	0.743821222895337	2		1173	1452	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186743	108186743	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3218670	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	213	409	1	ENST00000278616.4:c.6101G>A	p.Arg2034Gln	p.R2034Q	ENST00000278616	NM_000051.3	2034	cGa/cAa	42/63	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.743821222895337	2		410	571	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498139	498139	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1307567536	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	319	498	0	ENST00000399788.2:c.119G>A	p.Arg40Gln	p.R40Q	ENST00000399788	NM_001042603.1	40	cGg/cAg	1/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.743821222895337	2		498	816	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18473957	18473957	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	125	374	0	ENST00000266497.5:c.1199A>C	p.Lys400Thr	p.K400T	ENST00000266497		400	aAa/aCa	6/31	1	2	FACETS	0.52	0.472	0.571	0.52	0.472	0.571	SUBCLONAL	1	TRUE	1	0.743821222895337	2		374	646	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230571	46230571	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	257	489	1	ENST00000334344.6:c.820C>T	p.Arg274Ter	p.R274*	ENST00000334344	NM_152641.2	274	Cga/Tga	8/21	1	2	FACETS	0.957	0.901	1	0.957	0.901	1	CLONAL	1	TRUE	1	0.743821222895337	2		490	722	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446710	49446710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs547979245	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	272	537	0	ENST00000301067.7:c.1100C>T	p.Pro367Leu	p.P367L	ENST00000301067	NM_003482.3	367	cCg/cTg	8/54	1	2	FACETS	0.97	0.915	1	0.97	0.915	1	CLONAL	1	TRUE	1	0.743821222895337	2		537	754	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489534	56489534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775164134	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	311	616	1	ENST00000267101.3:c.1999C>T	p.Arg667Cys	p.R667C	ENST00000267101	NM_001982.3	667	Cgt/Tgt	17/28	1	2	FACETS	0.955	0.903	1	0.955	0.903	1	CLONAL	1	TRUE	1	0.743821222895337	2		617	876	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120805863	120805863	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	586	1205	3	ENST00000257552.2:c.215C>T	p.Ala72Val	p.A72V	ENST00000257552	NM_002442.3	72	gCg/gTg	4/15	1	2	FACETS	0.94	0.902	0.977	0.94	0.902	0.977	CLONAL	1	TRUE	1	0.743821222895337	2		1208	1677	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432064	121432064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886039386	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	586	1096	2	ENST00000257555.6:c.811C>T	p.Arg271Trp	p.R271W	ENST00000257555		271	Cgg/Tgg	4/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.743821222895337	2		1098	1496	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244145	133244145	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1222472060	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	366	685	0	ENST00000320574.5:c.2263G>A	p.Val755Met	p.V755M	ENST00000320574	NM_006231.2	755	Gtg/Atg	20/49	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.743821222895337	2		685	931	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562607	21562607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750798997	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	215	456	1	ENST00000382592.4:c.1312G>A	p.Ala438Thr	p.A438T	ENST00000382592	NM_014572.2	438	Gcg/Acg	4/8	1	2	FACETS	0.981	0.919	1	0.981	0.919	1	CLONAL	1	TRUE	1	0.743821222895337	2		457	589	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48921986	48921986	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	199	351	0	ENST00000267163.4:c.526C>T	p.Gln176Ter	p.Q176*	ENST00000267163	NM_000321.2	176	Caa/Taa	5/27	1	2	FACETS	0.961	0.897	1	0.961	0.897	1	CLONAL	1	TRUE	1	0.743821222895337	2		351	557	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337651	73337651	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs745945890	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	168	280	0	ENST00000377767.4:c.2065C>T	p.Arg689Ter	p.R689*	ENST00000377767	NM_014953.3	689	Cga/Tga	16/21	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.743821222895337	2		280	446	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	172	272	7	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.743821222895337	2		279	450	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566251	95566251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1185001854	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	277	493	0	ENST00000393063.1:c.4072C>T	p.Arg1358Cys	p.R1358C	ENST00000393063	NM_030621.3	1358	Cgc/Tgc	23/28	1	2	FACETS	0.949	0.895	1	0.949	0.895	1	CLONAL	1	TRUE	1	0.743821222895337	2		493	785	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028430	42028430	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	25	416	0	ENST00000219905.7:c.3968A>G	p.Tyr1323Cys	p.Y1323C	ENST00000219905	NM_001164273.1	1323	tAt/tGt	13/24	0.409073320151374	1	FACETS	0.085	0.066	0.107	0.085	0.066	0.107	INDETERMINATE	1	TRUE	0	0.743821222895337	1		416	496	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032393	42032393	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373262820	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	291	457	0	ENST00000219905.7:c.4577G>A	p.Arg1526Gln	p.R1526Q	ENST00000219905	NM_001164273.1	1526	cGg/cAg	14/24	0.409073320151374	1	FACETS	0.902	0.859	0.945	0.902	0.859	0.945	INDETERMINATE	1	TRUE	0	0.743821222895337	1		457	545	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250908	99250908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780055504	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	346	608	0	ENST00000268035.6:c.212G>A	p.Arg71His	p.R71H	ENST00000268035	NM_000875.3	71	cGc/cAc	2/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.743821222895337	2		608	875	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652269	3652269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752160984	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	403	835	0	ENST00000294008.3:c.800C>T	p.Ala267Val	p.A267V	ENST00000294008	NM_032444.2	267	gCg/gTg	4/15	1	2	FACETS	0.992	0.946	1	0.992	0.946	1	CLONAL	1	TRUE	1	0.743821222895337	2		835	1092	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779810	3779810	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	513	1165	0	ENST00000262367.5:c.5238del	p.Leu1747TrpfsTer24	p.L1747Wfs*24	ENST00000262367	NM_004380.2	1746	ggG/gg	31/31	1	2	FACETS	0.915	0.876	0.954	0.915	0.876	0.954	CLONAL	1	TRUE	1	0.743821222895337	2		1165	1508	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274101	10274102	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	377	911	0	ENST00000330684.3:c.167dup	p.Glu58ArgfsTer80	p.E58Rfs*80	ENST00000330684	NM_001134407.1	56	ggc/ggGc	2/13	1	2	FACETS	0.923	0.878	0.969	0.923	0.878	0.969	CLONAL	1	TRUE	1	0.743821222895337	2		911	1098	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024573	14024573	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373570729	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	222	392	0	ENST00000311895.7:c.799C>T	p.Arg267Cys	p.R267C	ENST00000311895	NM_005236.2	267	Cgc/Tgc	5/11	1	2	FACETS	0.952	0.892	1	0.952	0.892	1	CLONAL	1	TRUE	1	0.743821222895337	2		392	627	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128084	30128084	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	519	957	2	ENST00000263025.4:c.1045G>A	p.Ala349Thr	p.A349T	ENST00000263025	NM_002746.2	349	Gcc/Acc	8/9	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.743821222895337	2		959	1360	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829974	72829974	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	447	933	2	ENST00000268489.5:c.6607C>T	p.Arg2203Cys	p.R2203C	ENST00000268489	NM_006885.3	2203	Cgt/Tgt	9/10	1	2	FACETS	0.96	0.917	1	0.96	0.917	1	CLONAL	1	TRUE	1	0.743821222895337	2		935	1252	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992274	72992274	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767435394	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	579	1277	2	ENST00000268489.5:c.1771G>A	p.Ala591Thr	p.A591T	ENST00000268489	NM_006885.3	591	Gct/Act	2/10	1	2	FACETS	0.983	0.944	1	0.983	0.944	1	CLONAL	1	TRUE	1	0.743821222895337	2		1279	1584	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993509	72993509	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	351	850	5	ENST00000268489.5:c.536del	p.Gly179AlafsTer22	p.G179Afs*22	ENST00000268489	NM_006885.3	179	gGc/gc	2/10	1	2	FACETS	0.863	0.818	0.908	0.863	0.818	0.908	CLONAL	1	TRUE	1	0.743821222895337	2		855	1094	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341353	89341353	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1417276333	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	464	947	2	ENST00000301030.4:c.7582G>A	p.Val2528Ile	p.V2528I	ENST00000301030	NM_001256183.1	2528	Gta/Ata	11/13	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.743821222895337	2		949	1176	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349526	89349526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373193679	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	546	1109	0	ENST00000301030.4:c.3424G>A	p.Asp1142Asn	p.D1142N	ENST00000301030	NM_001256183.1	1142	Gac/Aac	9/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.743821222895337	2		1109	1405	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108238	8108238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573707475	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	372	799	0	ENST00000585124.1:c.986C>T	p.Ala329Val	p.A329V	ENST00000585124	NM_004217.3	329	gCc/gTc	9/9	1	2	FACETS	0.915	0.87	0.961	0.915	0.87	0.961	CLONAL	1	TRUE	1	0.743821222895337	2		799	1093	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	231	683	3	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	1	2	FACETS	0.669	0.624	0.715	0.669	0.624	0.715	SUBCLONAL	1	TRUE	1	0.743821222895337	2		686	929	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131402	17131402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398124537	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	437	825	2	ENST00000285071.4:c.50G>A	p.Arg17His	p.R17H	ENST00000285071	NM_144997.5	17	cGc/cAc	4/14	1	2	FACETS	0.965	0.921	1	0.965	0.921	1	CLONAL	1	TRUE	1	0.743821222895337	2		827	1218	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654671	29654671	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760649828	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	187	309	0	ENST00000356175.3:c.5360C>T	p.Thr1787Met	p.T1787M	ENST00000356175	NM_000267.3	1787	aCg/aTg	37/57	1	2	FACETS	0.998	0.93	1	0.998	0.93	1	CLONAL	1	TRUE	1	0.743821222895337	2		309	504	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37665977	37665977	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	248	455	0	ENST00000447079.4:c.2629G>T	p.Asp877Tyr	p.D877Y	ENST00000447079	NM_015083.1	877	Gat/Tat	7/14	1	2	FACETS	0.862	0.809	0.916	0.862	0.809	0.916	CLONAL	1	TRUE	1	0.743821222895337	2		455	774	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489585	40489585	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764674735	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	362	675	0	ENST00000264657.5:c.665C>T	p.Ala222Val	p.A222V	ENST00000264657	NM_139276.2	222	gCg/gTg	8/24	1	2	FACETS	0.969	0.92	1	0.969	0.92	1	CLONAL	1	TRUE	1	0.743821222895337	2		675	1005	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244679	41244679	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs80356973	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	308	1020	0	ENST00000357654.3:c.2869C>T	p.Gln957Ter	p.Q957*	ENST00000357654	NM_007294.3	957	Cag/Tag	10/23	1	2	FACETS	0.586	0.551	0.621	0.586	0.551	0.621	SUBCLONAL	1	TRUE	1	0.743821222895337	2		1020	1414	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492686	56492686	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	281	495	1	ENST00000407977.2:c.252+1G>A		p.X84_splice	ENST00000407977		84			1	2	FACETS	0.937	0.884	0.992	0.937	0.884	0.992	CLONAL	1	TRUE	1	0.743821222895337	2		496	806	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609313	39609313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760479037	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	207	359	0	ENST00000262039.4:c.1615C>T	p.Arg539Cys	p.R539C	ENST00000262039	NM_002647.2	539	Cgt/Tgt	15/25	0.705745869226455	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.743821222895337	1		359	336	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985569	60985569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	277	470	0	ENST00000333681.4:c.331G>A	p.Asp111Asn	p.D111N	ENST00000333681		111	Gac/Aac	2/3	0.705745869226455	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.743821222895337	1		470	460	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099265	4099265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150369301	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	561	1167	1	ENST00000262948.5:c.853G>A	p.Asp285Asn	p.D285N	ENST00000262948	NM_030662.3	285	Gac/Aac	7/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.743821222895337	2		1168	1449	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215345	5215345	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768182732	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	328	748	0	ENST00000357368.4:c.4273G>A	p.Val1425Ile	p.V1425I	ENST00000357368	NM_002850.3	1425	Gtc/Atc	28/38	1	2	FACETS	0.881	0.834	0.929	0.881	0.834	0.929	CLONAL	1	TRUE	1	0.743821222895337	2		748	1001	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7152776	7152776	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	485	947	2	ENST00000302850.5:c.2192C>T	p.Thr731Met	p.T731M	ENST00000302850	NM_000208.2	731	aCg/aTg	10/22	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.743821222895337	2		949	1142	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10259611	10259611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303994790	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	479	871	2	ENST00000340748.4:c.2621C>T	p.Ala874Val	p.A874V	ENST00000340748		874	gCg/gTg	26/40	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.743821222895337	2		873	1266	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276696	15276696	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752169336	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	478	1070	3	ENST00000263388.2:c.5569C>T	p.Arg1857Trp	p.R1857W	ENST00000263388	NM_000435.2	1857	Cgg/Tgg	30/33	1	2	FACETS	0.935	0.895	0.977	0.935	0.895	0.977	CLONAL	1	TRUE	1	0.743821222895337	2		1073	1374	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350825	15350825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768141679	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	325	684	1	ENST00000263377.2:c.3178C>T	p.Arg1060Cys	p.R1060C	ENST00000263377	NM_058243.2	1060	Cgc/Tgc	15/20	1	2	FACETS	0.921	0.872	0.97	0.921	0.872	0.97	CLONAL	1	TRUE	1	0.743821222895337	2		685	949	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18962999	18962999	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	641	1166	0	ENST00000262803.5:c.866C>T	p.Pro289Leu	p.P289L	ENST00000262803	NM_002911.3	289	cCg/cTg	6/24	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.743821222895337	2		1166	1613	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209081	36209081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs923041517	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	59	123	0	ENST00000222270.7:c.161C>T	p.Thr54Met	p.T54M	ENST00000222270	NM_014727.1	54	aCg/aTg	1/37	1	2	FACETS	0.778	0.679	0.881	0.778	0.679	0.881	SUBCLONAL	1	TRUE	1	0.743821222895337	2		123	204	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725076	47725076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs571014601	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	685	1317	0	ENST00000449228.1:c.668G>A	p.Arg223Gln	p.R223Q	ENST00000449228	NM_001127240.2	223	cGa/cAa	4/4	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.743821222895337	2		1317	1753	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467488	25467488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	392	835	0	ENST00000264709.3:c.1588G>A	p.Asp530Asn	p.D530N	ENST00000264709	NM_175629.2	530	Gac/Aac	14/23	1	2	FACETS	0.956	0.911	1	0.956	0.911	1	CLONAL	1	TRUE	1	0.743821222895337	2		835	1102	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607487	46607487	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	484	1181	4	ENST00000263734.3:c.1681del	p.Gln561SerfsTer7	p.Q561Sfs*7	ENST00000263734	NM_001430.4	559	aCc/ac	12/16	1	2	FACETS	0.843	0.805	0.881	0.843	0.805	0.881	CLONAL	1	TRUE	1	0.743821222895337	2		1185	1544	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702257	47702258	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	356	597	0	ENST00000233146.2:c.1854dup	p.Tyr619IlefsTer25	p.Y619Ifs*25	ENST00000233146	NM_000251.2	618	cca/ccAa	12/16	1	2	FACETS	0.999	0.95	1	0.999	0.95	1	CLONAL	1	TRUE	1	0.743821222895337	2		597	958	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721053	61721053	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	253	452	0	ENST00000401558.2:c.1221G>T	p.Gln407His	p.Q407H	ENST00000401558	NM_003400.3	407	caG/caT	12/25	1	2	FACETS	0.873	0.82	0.927	0.873	0.82	0.927	CLONAL	1	TRUE	1	0.743821222895337	2		452	779	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265140	198265140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	251	391	0	ENST00000335508.6:c.2737G>A	p.Gly913Ser	p.G913S	ENST00000335508	NM_012433.2	913	Ggc/Agc	19/25	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.743821222895337	2		391	659	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023718	31023718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752058283	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	413	869	2	ENST00000375687.4:c.3203G>A	p.Arg1068Gln	p.R1068Q	ENST00000375687	NM_015338.5	1068	cGa/cAa	13/13	1	2	FACETS	0.963	0.918	1	0.963	0.918	1	CLONAL	1	TRUE	1	0.743821222895337	2		871	1153	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256365	46256365	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773838233	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	242	430	0	ENST00000371998.3:c.593G>A	p.Arg198His	p.R198H	ENST00000371998		198	cGt/cAt	7/23	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.743821222895337	2		430	643	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441235	52441235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910211860	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	275	524	0	ENST00000460680.1:c.535C>T	p.Arg179Trp	p.R179W	ENST00000460680	NM_004656.3	179	Cgg/Tgg	7/17	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.743821222895337	2		524	733	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643348	52643348	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	247	489	0	ENST00000394830.3:c.2548C>T	p.Arg850Ter	p.R850*	ENST00000394830	NM_018313.4	850	Cga/Tga	17/30	1	2	FACETS	0.937	0.88	0.994	0.937	0.88	0.994	CLONAL	1	TRUE	1	0.743821222895337	2		489	709	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390945	89390945	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	185	444	0	ENST00000336596.2:c.1011C>G	p.Asn337Lys	p.N337K	ENST00000336596	NM_005233.5	337	aaC/aaG	5/17	1	2	FACETS	0.835	0.775	0.896	0.835	0.775	0.896	CLONAL	1	TRUE	1	0.743821222895337	2		444	596	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480396	89480396	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs369276620	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	227	357	0	ENST00000336596.2:c.2233C>T	p.Arg745Ter	p.R745*	ENST00000336596	NM_005233.5	745	Cga/Tga	13/17	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.743821222895337	2		357	510	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202786	128202786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	438	983	2	ENST00000341105.2:c.934G>A	p.Gly312Ser	p.G312S	ENST00000341105	NM_032638.4	312	Ggc/Agc	4/6	1	2	FACETS	0.987	0.943	1	0.987	0.943	1	CLONAL	1	TRUE	1	0.743821222895337	2		985	1193	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013719	170013719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388201066	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	292	509	0	ENST00000295797.4:c.1438C>T	p.Arg480Cys	p.R480C	ENST00000295797	NM_002740.5	480	Cgc/Tgc	15/18	1	2	FACETS	0.927	0.875	0.98	0.927	0.875	0.98	CLONAL	1	TRUE	1	0.743821222895337	2		509	847	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807543	1807543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	612	1244	1	ENST00000260795.2:c.1712G>A	p.Arg571Gln	p.R571Q	ENST00000260795		571	cGg/cAg	12/17	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.743821222895337	2		1245	1547	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	123	346	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	0.75	0.683	0.819	0.75	0.683	0.819	SUBCLONAL	1	TRUE	1	0.743821222895337	2		346	441	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540295	187540296	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	260	483	0	ENST00000441802.2:c.7444_7445del	p.Val2482AsnfsTer16	p.V2482Nfs*16	ENST00000441802	NM_005245.3	2482	GTa/a	10/27	1	2	FACETS	0.943	0.888	1	0.943	0.888	1	CLONAL	1	TRUE	1	0.743821222895337	2		483	741	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542779	187542779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369592206	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	293	534	2	ENST00000441802.2:c.4961G>A	p.Arg1654His	p.R1654H	ENST00000441802	NM_005245.3	1654	cGt/cAt	10/27	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.743821222895337	2		536	788	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526754	31526754	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	272	714	0	ENST00000344624.3:c.286del	p.Cys96AlafsTer12	p.C96Afs*12	ENST00000344624		96	Tgc/gc	2/33	1	2	FACETS	0.741	0.696	0.787	0.741	0.696	0.787	SUBCLONAL	1	TRUE	1	0.743821222895337	2		714	987	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590452	67590452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	92	177	0	ENST00000274335.5:c.1514G>A	p.Ser505Asn	p.S505N	ENST00000274335		505	aGc/aAc	11/15	1	2	FACETS	0.944	0.852	1	0.944	0.852	1	CLONAL	1	TRUE	1	0.743821222895337	2		177	262	SUCCESS
APC	324	MSKCC	GRCh37	5	112116593	112116593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1235428754	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	152	261	0	ENST00000257430.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000257430	NM_000038.5	213	cGa/cAa	6/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.743821222895337	2		261	387	SUCCESS
APC	324	MSKCC	GRCh37	5	112176192	112176192	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370433763	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	162	445	0	ENST00000257430.4:c.4901C>T	p.Pro1634Leu	p.P1634L	ENST00000257430	NM_000038.5	1634	cCg/cTg	16/16	1	2	FACETS	0.662	0.609	0.717	0.662	0.609	0.717	SUBCLONAL	1	TRUE	1	0.743821222895337	2		445	658	SUCCESS
APC	324	MSKCC	GRCh37	5	112178001	112178001	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1299714632	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	43	384	1	ENST00000257430.4:c.6710G>A	p.Arg2237Gln	p.R2237Q	ENST00000257430	NM_000038.5	2237	cGa/cAa	16/16	1	2	FACETS	0.19	0.158	0.225	0.19	0.158	0.225	SUBCLONAL	1	TRUE	1	0.743821222895337	2		385	608	SUCCESS
APC	324	MSKCC	GRCh37	5	112179333	112179333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182456139	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	218	387	0	ENST00000257430.4:c.8042C>T	p.Pro2681Leu	p.P2681L	ENST00000257430	NM_000038.5	2681	cCg/cTg	16/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.743821222895337	2		387	578	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149440505	149440505	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	369	793	0	ENST00000286301.3:c.1889T>C	p.Leu630Pro	p.L630P	ENST00000286301	NM_005211.3	630	cTc/cCc	14/22	1	2	FACETS	0.97	0.922	1	0.97	0.922	1	CLONAL	1	TRUE	1	0.743821222895337	2		793	1023	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522601	176522601	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	556	1118	4	ENST00000292408.4:c.1703del	p.Pro568GlnfsTer53	p.P568Qfs*53	ENST00000292408	NM_213647.1	566	cgC/cg	13/18	1	2	FACETS	0.952	0.913	0.991	0.952	0.913	0.991	CLONAL	1	TRUE	1	0.743821222895337	2		1122	1571	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053022	180053023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750808726	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	470	1347	5	ENST00000261937.6:c.1267dup	p.Gln423ProfsTer4	p.Q423Pfs*4	ENST00000261937	NM_182925.4	423	cag/cCag	10/30	NA	2	FACETS	0.799	0.762	0.836			1	INDETERMINATE	1	TRUE	NA	0.743821222895337	2		1352	1582	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394981	394981	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	223	439	0	ENST00000380956.4:c.377G>T	p.Arg126Met	p.R126M	ENST00000380956	NM_001195286.1	126	aGg/aTg	3/9	1	2	FACETS	0.941	0.882	1	0.941	0.882	1	CLONAL	1	TRUE	1	0.743821222895337	2		439	637	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225402	26225402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1294167641	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	102	206	0	ENST00000360408.1:c.20C>T	p.Thr7Met	p.T7M	ENST00000360408	NM_003532.2	7	aCg/aTg	1/1	1	2	FACETS	0.936	0.849	1	0.936	0.849	1	CLONAL	1	TRUE	1	0.743821222895337	2		206	293	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271224	26271224	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	40	483	3	ENST00000305910.3:c.389G>A	p.Arg130His	p.R130H	ENST00000305910	NM_003534.2	130	cGc/cAc	1/1	1	2	FACETS	0.171	0.141	0.204	0.171	0.141	0.204	SUBCLONAL	1	TRUE	1	0.743821222895337	2		486	630	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552984	106552984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	369	747	0	ENST00000369096.4:c.949G>A	p.Gly317Arg	p.G317R	ENST00000369096	NM_001198.3	317	Ggg/Agg	5/7	1	2	FACETS	0.94	0.894	0.988	0.94	0.894	0.988	CLONAL	1	TRUE	1	0.743821222895337	2		747	1055	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004798	150004798	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	284	521	0	ENST00000253339.5:c.1427C>T	p.Ser476Phe	p.S476F	ENST00000253339		476	tCt/tTt	3/7	1	2	FACETS	0.888	0.837	0.94	0.888	0.837	0.94	CLONAL	1	TRUE	1	0.743821222895337	2		521	860	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099835	157099835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	476	907	0	ENST00000346085.5:c.772C>T	p.Gln258Ter	p.Q258*	ENST00000346085	NM_020732.3	258	Caa/Taa	1/20	1	2	FACETS	0.999	0.956	1	0.999	0.956	1	CLONAL	1	TRUE	1	0.743821222895337	2		907	1281	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214367	55214367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778252	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	362	779	2	ENST00000275493.2:c.493C>T	p.Arg165Trp	p.R165W	ENST00000275493	NM_005228.3	165	Cgg/Tgg	4/28	1	2	FACETS	0.923	0.877	0.971	0.923	0.877	0.971	CLONAL	1	TRUE	1	0.743821222895337	2		781	1054	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878749	151878749	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1211949081	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	214	484	0	ENST00000262189.6:c.6196C>T	p.Arg2066Ter	p.R2066*	ENST00000262189	NM_170606.2	2066	Cga/Tga	36/59	1	2	FACETS	0.893	0.835	0.953	0.893	0.835	0.953	CLONAL	1	TRUE	1	0.743821222895337	2		484	644	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275752	38275752	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747333248	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	336	594	1	ENST00000425967.3:c.1517G>A	p.Arg506Gln	p.R506Q	ENST00000425967	NM_001174067.1	506	cGg/cAg	11/19	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.743821222895337	2		595	798	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287325	38287325	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754968374	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	305	968	4	ENST00000425967.3:c.332G>A	p.Arg111His	p.R111H	ENST00000425967	NM_001174067.1	111	cGc/cAc	4/19	1	2	FACETS	0.625	0.588	0.663	0.625	0.588	0.663	SUBCLONAL	1	TRUE	1	0.743821222895337	2		972	1312	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371918	55371918	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	168	619	0	ENST00000297316.4:c.608A>T	p.Tyr203Phe	p.Y203F	ENST00000297316	NM_022454.3	203	tAc/tTc	2/2	1	2	FACETS	0.598	0.55	0.647	0.598	0.55	0.647	SUBCLONAL	1	TRUE	1	0.743821222895337	2		619	756	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931890	68931890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	295	645	0	ENST00000288368.4:c.320C>T	p.Thr107Ile	p.T107I	ENST00000288368	NM_024870.2	107	aCc/aTc	3/40	1	2	FACETS	0.831	0.784	0.88	0.831	0.784	0.88	CLONAL	1	TRUE	1	0.743821222895337	2		645	954	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738861	145738861	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773155492	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	574	1248	0	ENST00000428558.2:c.2204G>A	p.Arg735His	p.R735H	ENST00000428558	NM_004260.3	735	cGt/cAt	14/22	1	2	FACETS	0.975	0.936	1	0.975	0.936	1	CLONAL	1	TRUE	1	0.743821222895337	2		1248	1583	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126343	5126343	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41316003	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	179	297	0	ENST00000381652.3:c.3188G>A	p.Arg1063His	p.R1063H	ENST00000381652	NM_004972.3	1063	cGt/cAt	24/25	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.743821222895337	2		297	467	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636793	8636793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	249	568	0	ENST00000356435.5:c.116G>A	p.Gly39Glu	p.G39E	ENST00000356435		39	gGa/gAa	2/35	1	2	FACETS	0.895	0.841	0.951	0.895	0.841	0.951	CLONAL	1	TRUE	1	0.743821222895337	2		568	748	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169538	27169538	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	401	780	0	ENST00000380036.4:c.539A>G	p.His180Arg	p.H180R	ENST00000380036	NM_000459.3	180	cAt/cGt	4/23	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.743821222895337	2		780	1058	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97873744	97873744	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1554829441	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	41	549	0	ENST00000289081.3:c.1329+1G>T		p.X443_splice	ENST00000289081	NM_000136.2	443			1	2	FACETS	0.142	0.118	0.17	0.142	0.118	0.17	SUBCLONAL	1	TRUE	1	0.743821222895337	2		549	774	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760702	133760702	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	646	1356	0	ENST00000318560.5:c.3025C>T	p.Arg1009Ter	p.R1009*	ENST00000318560	NM_005157.4	1009	Cga/Tga	11/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.743821222895337	2		1356	1699	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205089	123205089	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	366	638	0	ENST00000218089.9:c.2449C>A	p.Pro817Thr	p.P817T	ENST00000218089	NM_001042749.1	817	Cct/Act	25/35	0.705745869226455	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.743821222895337	1		638	605	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8497249	8497249	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	34	231	0	ENST00000356435.5:c.2342C>A	p.Thr781Asn	p.T781N	ENST00000356435		781	aCt/aAt	15/35	1	2	FACETS	0.244	0.2	0.295	0.244	0.2	0.295	SUBCLONAL	1	TRUE	1	0.743821222895337	2		231	374	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0033400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	93	539	1	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.467630703298162	2		540	378	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346763	91346763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751765688	NA	P-0033400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	42	351	0	ENST00000355112.3:c.3371C>T	p.Ala1124Val	p.A1124V	ENST00000355112	NM_000057.2	1124	gCa/gTa	18/22	1	2	FACETS	0.68	0.572	0.799	0.68	0.572	0.799	SUBCLONAL	1	TRUE	1	0.467630703298162	2		351	264	SUCCESS
APC	324	MSKCC	GRCh37	5	112176182	112176182	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	67	367	0	ENST00000257430.4:c.4891del	p.Ser1631ValfsTer19	p.S1631Vfs*19	ENST00000257430	NM_000038.5	1631	Agt/gt	16/16	0.467630703298162	1	FACETS	0.934	0.823	1	0.934	0.823	1	CLONAL	1	TRUE	0	0.467630703298162	1		367	235	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152009033	152009033	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0033400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	47	255	0	ENST00000262189.6:c.591-2A>C		p.X197_splice	ENST00000262189	NM_170606.2	197			1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.467630703298162	2		255	192	SUCCESS
BLM	641	MSKCC	GRCh37	15	91328183	91328183	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779884	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	62	395	0	ENST00000355112.3:c.2695C>T	p.Arg899Ter	p.R899*	ENST00000355112	NM_000057.2	899	Cga/Tga	14/22	1	2	FACETS	0.649	0.56	0.746	0.649	0.56	0.746	SUBCLONAL	1	FALSE	1	0.261022676419105	2		395	732	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	92	406	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.109670442535258	3	FACETS	1	0.958	1	0.583	0.518	0.652	INDETERMINATE	1	FALSE	1	0.261022676419105	3		406	684	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	37	718	0	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.424	0.349	0.509	0.424	0.349	0.509	SUBCLONAL	1	FALSE	1	0.261022676419105	2		718	668	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024001	27024002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	10	67	0	ENST00000324856.7:c.1113dup	p.Gln372AlafsTer28	p.Q372Afs*28	ENST00000324856	NM_006015.4	369	-/G	1/20	1	2	FACETS	0.891	0.61	1	0.891	0.61	1	CLONAL	1	FALSE	1	0.261022676419105	2		67	86	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238958	5238958	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	36	492	0	ENST00000357368.4:c.1821del	p.Val608TrpfsTer30	p.V608Wfs*30	ENST00000357368	NM_002850.3	607	ccC/cc	13/38	1	2	FACETS	0.465	0.381	0.559	0.465	0.381	0.559	SUBCLONAL	1	FALSE	1	0.261022676419105	2		492	593	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	82	646	3	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	1	2	FACETS	0.759	0.668	0.856	0.759	0.668	0.856	SUBCLONAL	1	FALSE	1	0.261022676419105	2		649	828	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139794922	139794922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs551577118	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	69	522	1	ENST00000247668.2:c.316G>A	p.Val106Ile	p.V106I	ENST00000247668	NM_021138.3	106	Gtc/Atc	4/11	1	2	FACETS	0.829	0.722	0.944	0.829	0.722	0.944	CLONAL	1	FALSE	1	0.261022676419105	2		523	638	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123499636	123499636	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs111033623	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	61	356	2	ENST00000371139.4:c.163C>T	p.Arg55Ter	p.R55*	ENST00000371139	NM_001114937.2	55	Cga/Tga	2/4	1	1	FACETS	0.989	0.856	1	0.989	0.856	1	CLONAL	1	FALSE	0	0.261022676419105	1		358	411	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905055	50905055	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	77	629	4	ENST00000440232.2:c.342del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	113	Ggg/gg	4/27	1	2	FACETS	0.728	0.638	0.825	0.728	0.638	0.825	SUBCLONAL	1	FALSE	1	0.261022676419105	2		633	810	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101031	4101031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375843855	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	77	537	0	ENST00000262948.5:c.691C>T	p.Arg231Cys	p.R231C	ENST00000262948	NM_030662.3	231	Cgc/Tgc	6/11	1	2	FACETS	0.814	0.714	0.921	0.814	0.714	0.921	CLONAL	1	FALSE	1	0.261022676419105	2		537	725	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462032	120462032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201996575	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	68	559	0	ENST00000256646.2:c.5684G>A	p.Arg1895His	p.R1895H	ENST00000256646	NM_024408.3	1895	cGt/cAt	31/34	1	2	FACETS	0.648	0.563	0.741	0.648	0.563	0.741	SUBCLONAL	1	FALSE	1	0.261022676419105	2		559	804	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435079	56435079	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	64	685	0	ENST00000407977.2:c.2058del	p.Ser687ValfsTer13	p.S687Vfs*13	ENST00000407977		686	ccC/cc	9/10	1	2	FACETS	0.559	0.483	0.642	0.559	0.483	0.642	SUBCLONAL	1	FALSE	1	0.261022676419105	2		685	877	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501544	149501544	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs537725629	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	83	659	1	ENST00000261799.4:c.2243C>T	p.Ser748Leu	p.S748L	ENST00000261799	NM_002609.3	748	tCg/tTg	16/23	1	2	FACETS	0.659	0.58	0.744	0.659	0.58	0.744	SUBCLONAL	1	FALSE	1	0.261022676419105	2		660	965	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426973	49426973	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1565778024	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	91	563	7	ENST00000301067.7:c.11515del	p.Gln3839SerfsTer42	p.Q3839Sfs*42	ENST00000301067	NM_003482.3	3839	Cag/ag	39/54	0.109670442535258	3	FACETS	0.993	0.881	1	0.496	0.44	0.556	INDETERMINATE	1	FALSE	1	0.261022676419105	3		570	794	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80150077	80150077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761465174	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	46	610	1	ENST00000265081.6:c.2942C>T	p.Thr981Met	p.T981M	ENST00000265081	NM_002439.4	981	aCg/aTg	21/24	1	2	FACETS	0.451	0.378	0.531	0.451	0.378	0.531	SUBCLONAL	1	FALSE	1	0.261022676419105	2		611	782	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971088	21971089	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	45	394	0	ENST00000304494.5:c.269dup	p.Leu91ProfsTer29	p.L91Pfs*29	ENST00000304494	NM_000077.4	90	ttc/ttTc	2/3	0.261022676419105	1	FACETS	0.611	0.513	0.718	0.611	0.513	0.718	SUBCLONAL	1	FALSE	0	0.261022676419105	1		394	491	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896624	78896624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1310325848	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	60	558	0	ENST00000306801.3:c.2621C>T	p.Ala874Val	p.A874V	ENST00000306801	NM_020761.2	874	gCg/gTg	22/34	1	2	FACETS	0.677	0.583	0.78	0.677	0.583	0.78	SUBCLONAL	1	FALSE	1	0.261022676419105	2		558	679	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066913	30066913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	43	417	0	ENST00000331968.5:c.2218C>T	p.Arg740Trp	p.R740W	ENST00000331968	NM_002742.2	740	Cgg/Tgg	16/18	1	2	FACETS	0.543	0.453	0.642	0.543	0.453	0.642	SUBCLONAL	1	FALSE	1	0.261022676419105	2		417	607	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660509	67660509	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1259626314	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	86	536	0	ENST00000264010.4:c.1409G>A	p.Arg470His	p.R470H	ENST00000264010	NM_006565.3	470	cGt/cAt	8/12	1	2	FACETS	0.821	0.725	0.923	0.821	0.725	0.923	CLONAL	1	FALSE	1	0.261022676419105	2		536	803	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732955	74732956	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs754601892	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	33	318	2	ENST00000359995.5:c.287dup	p.Asp97GlyfsTer27	p.D97Gfs*27	ENST00000359995	NM_001195427.1	96	ccg/ccCg	1/3	1	2	FACETS	0.606	0.494	0.733	0.606	0.494	0.733	SUBCLONAL	1	FALSE	1	0.261022676419105	2		320	417	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123875192	123875192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745678227	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	105	518	0	ENST00000330479.4:c.148G>A	p.Gly50Arg	p.G50R	ENST00000330479	NM_020382.3	50	Ggg/Agg	3/9	0.109670442535258	3	FACETS	1	0.969	1	0.607	0.544	0.674	INDETERMINATE	1	FALSE	1	0.261022676419105	3		518	749	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494872	56494872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112651994	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	90	606	1	ENST00000267101.3:c.3229C>T	p.Arg1077Trp	p.R1077W	ENST00000267101	NM_001982.3	1077	Cgg/Tgg	27/28	0.109670442535258	3	FACETS	0.997	0.884	1	0.498	0.442	0.559	INDETERMINATE	1	FALSE	1	0.261022676419105	3		607	782	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2193766	2193766	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	69	627	0	ENST00000398665.3:c.572C>T	p.Pro191Leu	p.P191L	ENST00000398665	NM_032482.2	191	cCg/cTg	6/28	1	2	FACETS	0.611	0.531	0.698	0.611	0.531	0.698	SUBCLONAL	1	FALSE	1	0.261022676419105	2		627	865	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444809	49444809	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	75	829	1	ENST00000301067.7:c.2657del	p.Pro886LeufsTer44	p.P886Lfs*44	ENST00000301067	NM_003482.3	886	cCt/ct	10/54	0.109670442535258	3	FACETS	0.561	0.49	0.638	0.281	0.245	0.319	INDETERMINATE	1	FALSE	1	0.261022676419105	3		830	1158	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851906	63851906	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	54	506	0	ENST00000279873.7:c.2684C>T	p.Ala895Val	p.A895V	ENST00000279873	NM_032199.2	895	gCg/gTg	10/10	1	2	FACETS	0.569	0.485	0.662	0.569	0.485	0.662	SUBCLONAL	1	FALSE	1	0.261022676419105	2		506	727	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14300947	14300947	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	50	518	0	ENST00000256196.4:c.551C>A	p.Pro184His	p.P184H	ENST00000256196		184	cCt/cAt	6/6	1	2	FACETS	0.578	0.489	0.675	0.578	0.489	0.675	SUBCLONAL	1	FALSE	1	0.261022676419105	2		518	663	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418394	49418394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1565756106	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	97	533	1	ENST00000301067.7:c.16019G>A	p.Arg5340Gln	p.R5340Q	ENST00000301067	NM_003482.3	5340	cGa/cAa	50/54	0.109670442535258	3	FACETS	0.997	0.888	1	0.498	0.444	0.557	INDETERMINATE	1	FALSE	1	0.261022676419105	3		534	843	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425776	49425776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123714	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	80	609	0	ENST00000301067.7:c.12712C>T	p.Arg4238Cys	p.R4238C	ENST00000301067	NM_003482.3	4238	Cgc/Tgc	39/54	0.109670442535258	3	FACETS	0.827	0.727	0.935	0.413	0.363	0.468	INDETERMINATE	1	FALSE	1	0.261022676419105	3		609	838	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434073	49434074	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1555192051	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	61	612	0	ENST00000301067.7:c.7479dup	p.Phe2494ValfsTer12	p.F2494Vfs*12	ENST00000301067	NM_003482.3	2493	-/G	31/54	0.109670442535258	3	FACETS	0.65	0.559	0.749	0.325	0.279	0.375	INDETERMINATE	1	FALSE	1	0.261022676419105	3		612	813	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495750	56495750	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1183624765	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	111	487	0	ENST00000267101.3:c.3940C>T	p.Arg1314Cys	p.R1314C	ENST00000267101	NM_001982.3	1314	Cgt/Tgt	28/28	0.109670442535258	3	FACETS	1	0.974	1	0.628	0.564	0.695	INDETERMINATE	1	FALSE	1	0.261022676419105	3		487	766	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865564	57865564	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	148	787	0	ENST00000228682.2:c.3041C>A	p.Pro1014His	p.P1014H	ENST00000228682	NM_005269.2	1014	cCt/cAt	12/12	0.109670442535258	3	FACETS	1	0.974	1	0.588	0.536	0.643	INDETERMINATE	1	FALSE	1	0.261022676419105	3		787	1090	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003137	42003137	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	72	721	0	ENST00000219905.7:c.2678del	p.Pro893LeufsTer40	p.P893Lfs*40	ENST00000219905	NM_001164273.1	892	Ccc/cc	8/24	1	2	FACETS	0.578	0.504	0.659	0.578	0.504	0.659	SUBCLONAL	1	FALSE	1	0.261022676419105	2		721	954	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790413	3790413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747582040	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	58	376	2	ENST00000262367.5:c.4120G>A	p.Gly1374Arg	p.G1374R	ENST00000262367	NM_004380.2	1374	Ggg/Agg	24/31	1	2	FACETS	0.702	0.603	0.811	0.702	0.603	0.811	SUBCLONAL	1	FALSE	1	0.261022676419105	2		378	633	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846147	68846147	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782359	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	88	638	0	ENST00000261769.5:c.1118C>T	p.Pro373Leu	p.P373L	ENST00000261769	NM_004360.3	373	cCg/cTg	8/16	1	2	FACETS	0.687	0.607	0.773	0.687	0.607	0.773	SUBCLONAL	1	FALSE	1	0.261022676419105	2		638	981	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813056	89813056	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	40	620	0	ENST00000389301.3:c.3449T>C	p.Leu1150Pro	p.L1150P	ENST00000389301	NM_000135.2	1150	cTg/cCg	35/43	1	2	FACETS	0.399	0.33	0.476	0.399	0.33	0.476	SUBCLONAL	1	FALSE	1	0.261022676419105	2		620	768	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872108	37872108	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755121772	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	93	803	2	ENST00000269571.5:c.1429G>A	p.Val477Met	p.V477M	ENST00000269571		477	Gtg/Atg	12/27	1	2	FACETS	0.604	0.535	0.678	0.604	0.535	0.678	SUBCLONAL	1	FALSE	1	0.261022676419105	2		805	1180	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121013	3121013	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1317335037	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	58	550	1	ENST00000078429.4:c.916C>T	p.Arg306Trp	p.R306W	ENST00000078429	NM_002067.2	306	Cgg/Tgg	7/7	1	2	FACETS	0.597	0.511	0.69	0.597	0.511	0.69	SUBCLONAL	1	FALSE	1	0.261022676419105	2		551	745	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5258061	5258061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773920614	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	76	617	1	ENST00000357368.4:c.673C>T	p.Arg225Cys	p.R225C	ENST00000357368	NM_002850.3	225	Cgc/Tgc	8/38	1	2	FACETS	0.782	0.685	0.886	0.782	0.685	0.886	SUBCLONAL	1	FALSE	1	0.261022676419105	2		618	745	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214792	36214792	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	65	658	0	ENST00000222270.7:c.3218G>A	p.Arg1073His	p.R1073H	ENST00000222270	NM_014727.1	1073	cGc/cAc	8/37	1	2	FACETS	0.597	0.517	0.685	0.597	0.517	0.685	SUBCLONAL	1	FALSE	1	0.261022676419105	2		658	834	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705646	47705646	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63749917	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	44	348	0	ENST00000233146.2:c.2446C>T	p.Gln816Ter	p.Q816*	ENST00000233146	NM_000251.2	816	Cag/Tag	14/16	1	2	FACETS	0.66	0.553	0.778	0.66	0.553	0.778	SUBCLONAL	1	FALSE	1	0.261022676419105	2		348	511	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634732	158634732	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771363719	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	48	352	0	ENST00000263640.3:c.454C>T	p.Arg152Cys	p.R152C	ENST00000263640	NM_001105.4	152	Cgc/Tgc	5/11	1	2	FACETS	0.627	0.529	0.734	0.627	0.529	0.734	SUBCLONAL	1	FALSE	1	0.261022676419105	2		352	587	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449526	31449526	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	30	316	0	ENST00000344624.3:c.2683C>A	p.Leu895Met	p.L895M	ENST00000344624		895	Ctg/Atg	19/33	1	2	FACETS	0.618	0.498	0.754	0.618	0.498	0.754	SUBCLONAL	1	FALSE	1	0.261022676419105	2		316	372	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288765	33288765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761608312	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	54	495	0	ENST00000374542.5:c.787C>T	p.Arg263Cys	p.R263C	ENST00000374542	NM_001141970.1	263	Cgc/Tgc	3/8	1	2	FACETS	0.629	0.536	0.73	0.629	0.536	0.73	SUBCLONAL	1	FALSE	1	0.261022676419105	2		495	658	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100309	157100310	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	36	185	0	ENST00000346085.5:c.1250dup	p.Thr418AspfsTer117	p.T418Dfs*117	ENST00000346085	NM_020732.3	416	acc/aCcc	1/20	1	2	FACETS	0.7	0.576	0.839	0.7	0.576	0.839	SUBCLONAL	1	FALSE	1	0.261022676419105	2		185	394	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859612	151859615	+	frameshift_variant	Frame_Shift_Del	DEL	GTTT	GTTT	-	novel	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	49	522	0	ENST00000262189.6:c.11047_11050del	p.Lys3683CysfsTer21	p.K3683Cfs*21	ENST00000262189	NM_170606.2	3683	AAACtg/tg	43/59	1	2	FACETS	0.526	0.444	0.616	0.526	0.444	0.616	SUBCLONAL	1	FALSE	1	0.261022676419105	2		522	714	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566339	141566339	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	74	564	0	ENST00000220592.5:c.1073A>G	p.Asp358Gly	p.D358G	ENST00000220592	NM_012154.3	358	gAc/gGc	9/19	1	2	FACETS	0.683	0.597	0.776	0.683	0.597	0.776	SUBCLONAL	1	FALSE	1	0.261022676419105	2		564	830	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038781	47038781	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556777817	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	91	362	0	ENST00000377604.3:c.788G>A	p.Arg263Gln	p.R263Q	ENST00000377604	NM_001204468.1	263	cGg/cAg	9/24	1	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	0	0.261022676419105	1		362	534	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041717	47041717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556780313	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	43	228	0	ENST00000377604.3:c.1942G>A	p.Ala648Thr	p.A648T	ENST00000377604	NM_001204468.1	648	Gct/Act	17/24	1	1	FACETS	0.868	0.729	1	0.868	0.729	1	CLONAL	1	FALSE	0	0.261022676419105	1		228	330	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890110	76890110	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	52	283	1	ENST00000373344.5:c.4784G>A	p.Cys1595Tyr	p.C1595Y	ENST00000373344	NM_000489.3	1595	tGt/tAt	17/35	1	1	FACETS	0.939	0.802	1	0.939	0.802	1	CLONAL	1	FALSE	0	0.261022676419105	1		284	369	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436021	116436021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1453842331	NA	P-0033410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	75	704	0	ENST00000397752.3:c.4016C>T	p.Ala1339Val	p.A1339V	ENST00000397752	NM_000245.2	1339	gCg/gTg	21/21	1	2	FACETS	0.562	0.491	0.639	0.562	0.491	0.639	SUBCLONAL	1	FALSE	1	0.261022676419105	2		704	1022	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	549	887	0	ENST00000269305.4:c.859G>T	p.Glu287Ter	p.E287*	ENST00000269305	NM_001126112.2	287	Gag/Tag	8/11	0.210794316012211	3	FACETS	0.973	0.94	1	1	0.998	1	CLONAL	6	FALSE	0	0.210794316012211	3		887	986	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728676	190728678	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs777263508	NA	P-0033464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	31	470	0	ENST00000441310.2:c.2067_2069del	p.Arg690del	p.R690del	ENST00000441310	NM_000534.4	688	aaAAGa/aaa	10/13	0.194126250221127	3	FACETS	0.869	0.704	1	0.435	0.352	0.529	CLONAL	1	FALSE	1	0.210794316012211	3		470	374	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424178	49424178	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs886040960	NA	P-0033464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	64	403	1	ENST00000301067.7:c.13884del	p.Thr4629ProfsTer11	p.T4629Pfs*11	ENST00000301067	NM_003482.3	4628	ccC/cc	42/54	0.210794316012211	5	FACETS	0.779	0.675	0.891	0.389	0.337	0.446	SUBCLONAL	2	FALSE	1	0.210794316012211	5		404	513	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930727	32930727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80358987	NA	P-0033464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	177	598	1	ENST00000380152.3:c.7598C>T	p.Ser2533Phe	p.S2533F	ENST00000380152		2533	tCt/tTt	15/27	0.210794316012211	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	FALSE	1	0.210794316012211	3		599	743	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068451	16068451	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs775887208	NA	P-0033464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	15	147	0	ENST00000268712.3:c.460G>T	p.Glu154Ter	p.E154*	ENST00000268712	NM_006311.3	154	Gaa/Taa	5/46	0.210794316012211	3	FACETS	1	0.781	1	0.357	0.262	0.469	CLONAL	1	FALSE	0	0.210794316012211	3		147	147	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061392	38061392	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	179	738	1	ENST00000250448.2:c.597G>A	p.Trp199Ter	p.W199*	ENST00000250448	NM_004496.3	199	tgG/tgA	2/2	0.13932041077249	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	FALSE	1	0.210794316012211	3		739	765	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849482	68849482	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782622	NA	P-0033464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	98	690	0	ENST00000261769.5:c.1385T>C	p.Phe462Ser	p.F462S	ENST00000261769	NM_004360.3	462	tTt/tCt	10/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.210794316012211	2		690	702	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821914	72821914	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs8044440	NA	P-0033464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	40	394	0	ENST00000268489.5:c.10261C>G	p.Pro3421Ala	p.P3421A	ENST00000268489	NM_006885.3	3421	Cca/Gca	10/10	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	FALSE	1	0.210794316012211	2		394	344	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459510	40459510	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	216	613	0	ENST00000345506.4:c.1771G>T	p.Asp591Tyr	p.D591Y	ENST00000345506	NM_003152.3	591	Gat/Tat	15/20	0.210794316012211	5	FACETS	0.979	0.914	1	1	0.989	1	CLONAL	4	FALSE	2	0.210794316012211	5		613	689	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622144	1622144	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	142	755	0	ENST00000344749.5:c.731C>A	p.Ser244Ter	p.S244*	ENST00000344749	NM_001136139.2	244	tCa/tAa	10/19	1	2	FACETS	1	0.973	1	1	0.992	1	CLONAL	2	FALSE	1	0.210794316012211	2		755	586	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285021	15285021	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1012770337	NA	P-0033464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	165	882	0	ENST00000263388.2:c.4594C>G	p.Leu1532Val	p.L1532V	ENST00000263388	NM_000435.2	1532	Ctg/Gtg	25/33	1	2	FACETS	1	0.971	1	1	0.993	1	CLONAL	2	FALSE	1	0.210794316012211	2		882	702	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169999038	169999038	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	133	429	0	ENST00000295797.4:c.967C>T	p.Gln323Ter	p.Q323*	ENST00000295797	NM_002740.5	323	Cag/Tag	10/18	0.210794316012211	5	FACETS	0.876	0.801	0.954	1	0.974	1	CLONAL	4	FALSE	2	0.210794316012211	5		429	474	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64289191	64289191	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	49	491	0	ENST00000370651.3:c.359T>C	p.Ile120Thr	p.I120T	ENST00000370651	NM_003463.4	120	aTt/aCt	5/6	0.210794316012211	7	FACETS	1	0.859	1	0.203	0.172	0.239	CLONAL	1	FALSE	2	0.210794316012211	7		491	698	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14027772	14027772	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	42	574	0	ENST00000405192.2:c.72G>C	p.Glu24Asp	p.E24D	ENST00000405192	NM_001163147.1	24	gaG/gaC	3/12	0.13932041077249	3	FACETS	0.709	0.591	0.841	0.355	0.295	0.421	SUBCLONAL	1	FALSE	1	0.210794316012211	3		574	621	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139440202	139440202	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	91	88	0	ENST00000277541.6:c.37C>A	p.Leu13Met	p.L13M	ENST00000277541	NM_017617.3	13	Ctg/Atg	1/34	0.210794316012211	3	FACETS	0.925	0.846	1	1	0.988	1	CLONAL	6	FALSE	0	0.210794316012211	3		88	172	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972693	76972693	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	37	280	0	ENST00000373344.5:c.48G>T	p.Gln16His	p.Q16H	ENST00000373344	NM_000489.3	16	caG/caT	2/35	0.210794316012211	4	FACETS	0.942	0.777	1			1	CLONAL	1	FALSE	NA	0.210794316012211	4		280	451	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711892	89711892	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	148	492	0	ENST00000371953.3:c.510del	p.Gln171ArgfsTer12	p.Q171Rfs*12	ENST00000371953	NM_000314.4	170	agT/ag	6/9	1	2	FACETS	0.893	0.828	0.958	1	0.993	1	CLONAL	3	TRUE	1	0.33	2		492	335	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548948	29548948	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1131691096	NA	P-0033580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	67	269	0	ENST00000356175.3:c.1721+1G>A		p.X574_splice	ENST00000356175	NM_000267.3	574			1	2	FACETS	0.681	0.594	0.773	0.681	0.594	0.773	SUBCLONAL	1	TRUE	1	0.499713432934546	2		269	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0033643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	272	584	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.649071524311539	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.649134968497226	1		584	536	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0033643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	166	869	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.982	0.908	1	0.982	0.908	1	CLONAL	1	TRUE	1	0.649134968497226	2		869	521	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0033643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	302	579	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.649134968497226	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.649134968497226	2		579	423	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0033643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	131	278	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.959	0.878	1	0.959	0.878	1	CLONAL	1	TRUE	1	0.649134968497226	2		278	421	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742473	17742473	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1288774741	NA	P-0033643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	96	405	0	ENST00000250003.3:c.655G>A	p.Gly219Ser	p.G219S	ENST00000250003	NM_002478.4	219	Ggc/Agc	2/3	0.2175384997235	1	FACETS	0.314	0.28	0.35	0.314	0.28	0.35	INDETERMINATE	1	TRUE	0	0.649134968497226	1		405	636	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276256	15276256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759704420	NA	P-0033643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	128	543	0	ENST00000263388.2:c.5738C>T	p.Ala1913Val	p.A1913V	ENST00000263388	NM_000435.2	1913	gCg/gTg	31/33	0.348925382969463	1	FACETS	0.391	0.355	0.429	0.391	0.355	0.429	INDETERMINATE	1	TRUE	0	0.649134968497226	1		543	681	SUCCESS
APC	324	MSKCC	GRCh37	5	112175551	112175552	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0033643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	126	267	0	ENST00000257430.4:c.4260_4261del	p.Ser1421Ter	p.S1421*	ENST00000257430	NM_000038.5	1420	ccCAgt/ccgt	16/16	1	2	FACETS	0.985	0.901	1	0.985	0.901	1	CLONAL	1	TRUE	1	0.649134968497226	2		267	394	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226802	2226803	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0033643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	116	453	0	ENST00000398665.3:c.4286_4287dup	p.Ala1430LeufsTer89	p.A1430Lfs*89	ENST00000398665	NM_032482.2	1428	atc/aTCtc	27/28	0.348925382969463	1	FACETS	0.427	0.386	0.47	0.427	0.386	0.47	INDETERMINATE	1	TRUE	0	0.649134968497226	1		453	565	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916640	178916669	+	inframe_deletion	In_Frame_Del	DEL	ACTGTGGGGCATCCACTTGATGCCCCCAAG	ACTGTGGGGCATCCACTTGATGCCCCCAAG	-	novel	NA	P-0033643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	226	238	0	ENST00000263967.3:c.28_57del	p.Leu10_Arg19del	p.L10_R19del	ENST00000263967	NM_006218.2	9	gaACTGTGGGGCATCCACTTGATGCCCCCAAGa/gaa	2/21	0.649134968497226	2	FACETS	0.886	0.84	0.931	0.886	0.84	0.931	CLONAL	2	TRUE	0	0.649134968497226	2		238	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0033853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	331	642	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.472187237961491	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.472187237961491	2		642	648	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0033853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	22	450	0	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	0.472187237961491	2	FACETS	0.157	0.121	0.2	0.079	0.06	0.1	SUBCLONAL	1	TRUE	0	0.472187237961491	2		450	592	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029437	16029439	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	rs774778469	NA	P-0033853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	308	485	0	ENST00000268712.3:c.1591_1593del	p.Glu531del	p.E531del	ENST00000268712	NM_006311.3	531	GAA/-	15/46	0.472187237961491	2	FACETS	0.911	0.865	0.958	0.911	0.865	0.958	CLONAL	2	TRUE	0	0.472187237961491	2		485	716	SUCCESS
APC	324	MSKCC	GRCh37	5	112176863	112176863	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1270783041	NA	P-0033853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	217	342	0	ENST00000257430.4:c.5572C>T	p.Arg1858Ter	p.R1858*	ENST00000257430	NM_000038.5	1858	Cga/Tga	16/16	0.472187237961491	2	FACETS	0.984	0.926	1	0.984	0.926	1	CLONAL	2	TRUE	0	0.472187237961491	2		342	467	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670324	134670324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775406650	NA	P-0033853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	182	315	0	ENST00000398015.3:c.235C>T	p.Arg79Trp	p.R79W	ENST00000398015	NM_004441.4	79	Cgg/Tgg	3/16	0.424212181358428	3	FACETS	0.949	0.883	1	0.949	0.883	1	CLONAL	2	TRUE	1	0.472187237961491	3		315	502	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610417	81610417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908875	NA	P-0033853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	115	356	1	ENST00000298171.2:c.2015G>A	p.Cys672Tyr	p.C672Y	ENST00000298171	NM_000369.2	672	tGt/tAt	10/10	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.472187237961491	2		357	464	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519712	137519712	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs560014238	NA	P-0033903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	170	402	0	ENST00000367739.4:c.926C>T	p.Thr309Met	p.T309M	ENST00000367739	NM_000416.2	309	aCg/aTg	7/7	1	2	FACETS	0.96	0.895	1	0.96	0.895	1	CLONAL	1	TRUE	1	0.90829013590499	2		402	390	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97933362	97933362	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs781542763	NA	P-0033934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	38	364	0	ENST00000289081.3:c.520C>T	p.Arg174Ter	p.R174*	ENST00000289081	NM_000136.2	174	Cga/Tga	6/15	1	2	FACETS	0.606	0.502	0.723	0.606	0.502	0.723	SUBCLONAL	1	TRUE	1	0.331552543945624	2		364	378	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237740	16237740	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	106	505	0	ENST00000375759.3:c.1187C>A	p.Ser396Ter	p.S396*	ENST00000375759	NM_015001.2	396	tCa/tAa	5/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.331552543945624	2		505	564	SUCCESS
APC	324	MSKCC	GRCh37	5	112173517	112173518	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	21	364	0	ENST00000257430.4:c.2227dup	p.Met743AsnfsTer13	p.M743Nfs*13	ENST00000257430	NM_000038.5	742	-/A	16/16	1	2	FACETS	0.322	0.247	0.409	0.322	0.247	0.409	SUBCLONAL	1	TRUE	1	0.331552543945624	2		364	394	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0033969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	13	205	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.781	0.557	1	0.781	0.557	1	CLONAL	1	TRUE	1	0.13	2		205	256	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976745	2976745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748839211	NA	P-0033969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	18	768	2	ENST00000396946.4:c.1267C>T	p.Arg423Trp	p.R423W	ENST00000396946	NM_032415.4	423	Cgg/Tgg	9/25	0.3	2	FACETS	0.874	0.657	1			1	CLONAL	1	TRUE	NA	0.13	2		770	317	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422419	225422419	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	28	635	0	ENST00000264414.4:c.221A>G	p.Tyr74Cys	p.Y74C	ENST00000264414	NM_003590.4	74	tAc/tGc	2/16	1	2	FACETS	0.951	0.759	1	0.951	0.759	1	CLONAL	1	TRUE	1	0.13	2		635	453	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0034078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	290	205	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.75105066488828	9	FACETS	1	0.989	1			1	CLONAL	7	TRUE	NA	0.75105066488828	9		205	376	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0034078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	247	444	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	0.411923174204638	5	FACETS	0.914	0.883	0.944			1	INDETERMINATE	5	TRUE	NA	0.75105066488828	5		444	306	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576101	88576101	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs759925027	NA	P-0034078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1351	147	838	0	ENST00000360948.2:c.1572C>G	p.His524Gln	p.H524Q	ENST00000360948	NM_001012338.2	524	caC/caG	13/19	0.75105066488828	5	FACETS	0.556	0.505	0.609	0.139	0.126	0.153	SUBCLONAL	1	TRUE	1	0.75105066488828	5		838	1498	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101709	27101751	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTGGTAAGGAGATCTTCCTCATTCGGTTGCCTAATCTGCCCCT	TTGGTAAGGAGATCTTCCTCATTCGGTTGCCTAATCTGCCCCT	-	novel	NA	P-0034078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	208	900	0	ENST00000324856.7:c.4993_4993+42del		p.X1665_splice	ENST00000324856	NM_006015.4	1665		18/20	0.593024609810604	3	FACETS	1	0.986	1	0.61	0.569	0.651	CLONAL	1	TRUE	1	0.75105066488828	3		900	625	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	465703	465703	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	83	518	1	ENST00000399788.2:c.673T>A	p.Ser225Thr	p.S225T	ENST00000399788	NM_001042603.1	225	Tca/Aca	6/28	NA	2	FACETS	0.87	0.779	0.965			1	INDETERMINATE	1	TRUE	NA	0.75105066488828	2		519	254	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574004	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAACATCTCGAAGCT	novel	NA	P-0034078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	422	851	0	ENST00000269305.4:c.1023_1024insAGCTTCGAGATGTTC	p.Phe341_Arg342insSerPheGluMetPhe	p.F341_R342insSFEMF	ENST00000269305	NM_001126112.2	341	-/AGCTTCGAGATGTTC	10/11	0.75105066488828	2	FACETS	1	0.996	1	0.708	0.679	0.736	CLONAL	1	TRUE	0	0.75105066488828	2		851	794	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099277	4099277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759998177	NA	P-0034078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	33	893	0	ENST00000262948.5:c.841C>T	p.Arg281Trp	p.R281W	ENST00000262948	NM_030662.3	281	Cgg/Tgg	7/11	1	2	FACETS	0.138	0.111	0.167	0.138	0.111	0.167	SUBCLONAL	1	TRUE	1	0.75105066488828	2		893	638	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867107	45867107	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	226	656	0	ENST00000391945.4:c.1012G>A	p.Glu338Lys	p.E338K	ENST00000391945	NM_000400.3	338	Gag/Aag	11/23	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.75105066488828	2		656	592	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545825	106545825	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	50	475	0	ENST00000359195.3:c.3302C>T	p.Ser1101Leu	p.S1101L	ENST00000359195	NM_002649.2	1101	tCa/tTa	11/11	0.75105066488828	3	FACETS	1	0.968	1	0.715	0.624	0.81	CLONAL	1	TRUE	1	0.75105066488828	3		475	128	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881103	37881103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775752713	NA	P-0034078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3009	212	881	1	ENST00000269571.5:c.2432G>A	p.Arg811Gln	p.R811Q	ENST00000269571		811	cGg/cAg	20/27	0.75105066488828	12	FACETS	0.833	0.769	0.901			1	CLONAL	1	TRUE	NA	0.75105066488828	12		882	3221	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0034142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	62	286	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.118058670347361	3	FACETS	1	0.903	1	0.527	0.456	0.605	INDETERMINATE	1	TRUE	1	0.25	3		286	529	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0034142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	49	459	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.69	0.584	0.807	0.69	0.584	0.807	SUBCLONAL	1	TRUE	1	0.25	2		459	568	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856020	68856020	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	59	477	0	ENST00000261769.5:c.1828C>T	p.Gln610Ter	p.Q610*	ENST00000261769	NM_004360.3	610	Cag/Tag	12/16	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.25	2		477	450	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184588	7184588	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	42	370	0	ENST00000302850.5:c.713A>G	p.Glu238Gly	p.E238G	ENST00000302850	NM_000208.2	238	gAg/gGg	3/22	1	2	FACETS	0.667	0.556	0.789	0.667	0.556	0.789	SUBCLONAL	1	TRUE	1	0.25	2		370	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0034239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	202	499	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.248250483182806	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	3	TRUE	0	0.3522397340909	3		501	441	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258775	115258775	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	51	437	0	ENST00000369535.4:c.7G>T	p.Glu3Ter	p.E3*	ENST00000369535	NM_002524.4	3	Gag/Tag	2/7	0.245503075413296	3	FACETS	0.864	0.737	1	0.288	0.245	0.335	CLONAL	1	TRUE	0	0.3522397340909	3		437	394	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097796	8097796	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	65	741	0	ENST00000346208.3:c.178G>T	p.Val60Phe	p.V60F	ENST00000346208		60	Gtc/Ttc	2/6	0.3522397340909	4	FACETS	1	0.894	1	0.344	0.299	0.393	CLONAL	1	TRUE	1	0.3522397340909	4		741	483	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38616996	38616996	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1282540245	NA	P-0034239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	40	471	0	ENST00000299084.4:c.409G>T	p.Ala137Ser	p.A137S	ENST00000299084	NM_152594.2	137	Gca/Tca	4/7	0.245503075413296	3	FACETS	0.752	0.627	0.892	0.251	0.209	0.298	SUBCLONAL	1	TRUE	0	0.3522397340909	3		471	355	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883092	37883092	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238729193	NA	P-0034239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	86	792	1	ENST00000269571.5:c.2995C>T	p.Pro999Ser	p.P999S	ENST00000269571		999	Ccc/Tcc	25/27	0.248250483182806	3	FACETS	0.828	0.738	0.921	0.552	0.492	0.614	CLONAL	2	TRUE	0	0.3522397340909	3		793	347	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659835	227659835	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	45	509	0	ENST00000305123.5:c.3620C>A	p.Pro1207His	p.P1207H	ENST00000305123	NM_005544.2	1207	cCt/cAt	1/2	0.3522397340909	3	FACETS	0.722	0.608	0.848			1	SUBCLONAL	1	TRUE	NA	0.3522397340909	3		509	416	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845370	42845370	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	76	695	0	ENST00000398585.3:c.892A>G	p.Ser298Gly	p.S298G	ENST00000398585	NM_001135099.1	298	Agc/Ggc	9/14	0.157038218985732	3	FACETS	1	0.964	1	0.628	0.554	0.707	INDETERMINATE	1	TRUE	1	0.3522397340909	3		695	404	SUCCESS
ATR	545	MSKCC	GRCh37	3	142257465	142257465	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1389009165	NA	P-0034239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	39	358	0	ENST00000350721.4:c.3584C>T	p.Ala1195Val	p.A1195V	ENST00000350721	NM_001184.3	1195	gCt/gTt	19/47	0.342182885756717	3	FACETS	0.889	0.74	1	0.444	0.37	0.527	CLONAL	1	TRUE	1	0.3522397340909	3		358	293	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189585671	189585671	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	69	703	0	ENST00000264731.3:c.932G>C	p.Ser311Thr	p.S311T	ENST00000264731	NM_003722.4	311	aGt/aCt	7/14	0.3522397340909	7	FACETS	0.897	0.78	1	0.224	0.195	0.257	CLONAL	1	TRUE	3	0.3522397340909	7		703	821	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681074	117681074	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1228020371	NA	P-0034239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	78	627	0	ENST00000368508.3:c.3546A>T	p.Arg1182Ser	p.R1182S	ENST00000368508	NM_002944.2	1182	agA/agT	23/43	0.11385542032194	5	FACETS	1	0.974	1	0.476	0.419	0.536	INDETERMINATE	1	TRUE	2	0.3522397340909	5		627	474	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309080	137309080	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	106	1066	0	ENST00000481739.1:c.687C>A	p.Asp229Glu	p.D229E	ENST00000481739	NM_002957.4	229	gaC/gaA	5/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.3522397340909	2		1066	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0034301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	435	704	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.588471907742351	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.653393443162814	1		705	768	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589618	67589619	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAGAATATGATA	novel	NA	P-0034301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	84	222	0	ENST00000274335.5:c.1384_1395dup	p.Glu462_Arg465dup	p.E462_R465dup	ENST00000274335		462	cga/cGAGAATATGATAga	10/15	0.329914247433999	3	FACETS	0.958	0.853	1	0.479	0.426	0.535	INDETERMINATE	1	TRUE	1	0.653393443162814	3		222	356	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933162	36933162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	252	745	0	ENST00000361632.4:c.1955C>T	p.Pro652Leu	p.P652L	ENST00000361632		652	cCc/cTc	14/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.653393443162814	2		745	742	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161268	56161269	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0034301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	50	560	0	ENST00000399503.3:c.1138_1139del	p.Leu380LysfsTer4	p.L380Kfs*4	ENST00000399503	NM_005921.1	379	acTTta/acta	5/20	0.329914247433999	3	FACETS	0.302	0.256	0.353	0.151	0.128	0.177	INDETERMINATE	1	TRUE	1	0.653393443162814	3		560	672	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925428	131925428	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	144	271	0	ENST00000265335.6:c.1351A>G	p.Ser451Gly	p.S451G	ENST00000265335		451	Agt/Ggt	9/25	0.329914247433999	3	FACETS	0.786	0.726	0.847	0.786	0.726	0.847	INDETERMINATE	2	TRUE	1	0.653393443162814	3		271	372	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845367	151845367	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	139	875	0	ENST00000262189.6:c.13645del	p.Arg4549AlafsTer77	p.R4549Afs*77	ENST00000262189	NM_170606.2	4549	Cgc/gc	52/59	1	2	FACETS	0.476	0.433	0.521	0.476	0.433	0.521	SUBCLONAL	1	TRUE	1	0.653393443162814	2		875	894	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0034416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	22	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.1639603099976	0	FACETS	0.121	0.093	0.152			1	INDETERMINATE	1	TRUE	0	0.606398481051445	0		436	237	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574002	7574002	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs375338359	NA	P-0034416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	344	617	0	ENST00000269305.4:c.1025G>C	p.Arg342Pro	p.R342P	ENST00000269305	NM_001126112.2	342	cGa/cCa	10/11	0.571665386636888	2	FACETS	0.845	0.807	0.883	0.845	0.807	0.883	CLONAL	2	TRUE	0	0.606398481051445	2		617	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0034418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	174	534	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.483417552052144	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.483417552052144	1		534	518	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243789	41243792	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	rs80357868	NA	P-0034444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	22	562	0	ENST00000357654.3:c.3756_3759del	p.Ser1253ArgfsTer10	p.S1253Rfs*10	ENST00000357654	NM_007294.3	1252	ctGTCT/ct	10/23	0.813828764290433	2	FACETS	0.138	0.106	0.174	0.069	0.053	0.087	SUBCLONAL	1	TRUE	0	0.810797896894181	2		562	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0034444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	604	590	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.785909401587491	3	FACETS	1	0.998	1			1	CLONAL	3	TRUE	NA	0.810797896894181	3		590	639	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117712753	117712753	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	343	344	0	ENST00000369458.3:c.73C>G	p.Leu25Val	p.L25V	ENST00000369458	NM_024626.3	25	Ctc/Gtc	2/6	0.813828764290433	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	1	0.810797896894181	4		344	480	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749903	162749910	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CTTACCTC	CTTACCTC	-	novel	NA	P-0034444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	133	391	0	ENST00000367921.3:c.2436_2443del	p.Tyr813SerfsTer7	p.Y813Sfs*7	ENST00000367921	NM_006182.2	812	aCTTACCTC/a	18/18	0.813828764290433	5	FACETS	1	0.92	1	0.338	0.307	0.37	CLONAL	1	TRUE	2	0.810797896894181	5		391	718	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654641	29654641	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	204	274	1	ENST00000356175.3:c.5330A>T	p.Gln1777Leu	p.Q1777L	ENST00000356175	NM_000267.3	1777	cAg/cTg	37/57	0.813828764290433	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.810797896894181	2		275	233	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243811	41243844	+	frameshift_variant	Frame_Shift_Del	DEL	GTGCTATGCCTAGTAGACTGAGAAGGTATATTGT	GTGCTATGCCTAGTAGACTGAGAAGGTATATTGT	-	novel	NA	P-0034444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	69	594	0	ENST00000357654.3:c.3704_3737del	p.Asn1235ThrfsTer18	p.N1235Tfs*18	ENST00000357654	NM_007294.3	1235	aACAATATACCTTCTCAGTCTACTAGGCATAGCACc/ac	10/23	0.813828764290433	2	FACETS	0.43	0.376	0.488	0.215	0.188	0.244	SUBCLONAL	1	TRUE	0	0.810797896894181	2		594	396	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621115	1621144	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CATGCCCCACGCCTCACCGAGGCCAGTGCT	CATGCCCCACGCCTCACCGAGGCCAGTGCT	-	novel	NA	P-0034444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	360	757	0	ENST00000344749.5:c.1002_1014+17del		p.X334_splice	ENST00000344749	NM_001136139.2	334		12/19	0.813828764290433	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.810797896894181	2		757	406	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280059	18280069	+	frameshift_variant	Frame_Shift_Del	DEL	CCCAGTGCGCG	CCCAGTGCGCG	-	novel	NA	P-0034444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	64	240	0	ENST00000222254.8:c.2145_2155del	p.Val716GlyfsTer91	p.V716Gfs*91	ENST00000222254	NM_005027.3	714	caCCCAGTGCGCGcc/cacc	16/16	0.414175270687456	6	FACETS	1	0.957	1	0.413	0.36	0.47	INDETERMINATE	1	TRUE	3	0.810797896894181	6		240	334	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728507	190728507	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	165	281	0	ENST00000441310.2:c.1895A>C	p.Asn632Thr	p.N632T	ENST00000441310	NM_000534.4	632	aAt/aCt	10/13	0.64579915971825	3	FACETS	0.953	0.894	1			1	CLONAL	2	TRUE	NA	0.810797896894181	3		281	300	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41558785	41558785	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0034444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	276	426	0	ENST00000263253.7:c.3728+2T>G		p.X1243_splice	ENST00000263253	NM_001429.3	1243			0.785909401587491	3	FACETS	1	0.984	1			1	CLONAL	2	TRUE	NA	0.810797896894181	3		426	449	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638460	176638460	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	619	676	0	ENST00000439151.2:c.3060C>A	p.Asn1020Lys	p.N1020K	ENST00000439151	NM_022455.4	1020	aaC/aaA	5/23	0.813828764290433	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.810797896894181	3		676	679	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752691	128752691	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs756770497	NA	P-0034444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	73	264	0	ENST00000377970.2:c.852G>C	p.Lys284Asn	p.K284N	ENST00000377970	NM_002467.4	284	aaG/aaC	3/3	0.810797896894181	6	FACETS	0.992	0.87	1			1	CLONAL	1	TRUE	NA	0.810797896894181	6		264	476	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521427	8521437	+	frameshift_variant	Frame_Shift_Del	DEL	ACATCCACTTT	ACATCCACTTT	-	novel	NA	P-0034444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	192	681	0	ENST00000356435.5:c.801_811del	p.Lys268GlyfsTer8	p.K268Gfs*8	ENST00000356435		267	gtAAAGTGGATGTtg/gttg	9/35	0.813828764290433	2	FACETS	0.981	0.916	1	0.49	0.458	0.523	CLONAL	1	TRUE	0	0.810797896894181	2		681	483	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752673	128752675	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0034514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	34	168	0	ENST00000377970.2:c.838_840del	p.Val280del	p.V280del	ENST00000377970	NM_002467.4	278	gaTGTt/gat	3/3	0.655275071506556	5	FACETS	0.399	0.325	0.482	0.1	0.081	0.121	SUBCLONAL	1	TRUE	1	0.655275071506556	5		168	516	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865356	57865356	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1439280977	NA	P-0034514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	485	582	1	ENST00000228682.2:c.2833G>A	p.Val945Met	p.V945M	ENST00000228682	NM_005269.2	945	Gtg/Atg	12/12	0.655275071506556	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.655275071506556	3		583	960	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42381403	42381403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555843091	NA	P-0034514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	257	497	0	ENST00000221972.3:c.29C>T	p.Ala10Val	p.A10V	ENST00000221972	NM_021601.3	10	gCt/gTt	1/5	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.655275071506556	2		497	715	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0034664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	158	376	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.377243853251208	3	FACETS	1	0.985	1	0.814	0.759	0.869	CLONAL	2	TRUE	0	0.502947591142857	3		376	322	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781371	3781371	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	828	714	0	ENST00000262367.5:c.4994A>C	p.Asp1665Ala	p.D1665A	ENST00000262367	NM_004380.2	1665	gAc/gCc	30/31	0.502947591142857	10	FACETS	1	0.989	1			1	CLONAL	6	TRUE	NA	0.502947591142857	10		714	1596	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349934	70349934	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	213	715	0	ENST00000374080.3:c.3917A>G	p.Asp1306Gly	p.D1306G	ENST00000374080		1306	gAc/gGc	28/45	0.140037773208369	6	FACETS	0.988	0.919	1	0.659	0.613	0.706	INDETERMINATE	2	TRUE	3	0.502947591142857	6		715	860	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0034761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	102	847	2	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.204405936364384	2		849	720	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248399	59248399	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	36	428	0	ENST00000371222.2:c.344T>G	p.Val115Gly	p.V115G	ENST00000371222	NM_002228.3	115	gTg/gGg	1/1	1	2	FACETS	0.837	0.688	1	0.837	0.688	1	CLONAL	1	TRUE	1	0.204405936364384	2		428	421	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714494	40714494	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1397520284	NA	P-0034761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	36	449	0	ENST00000373198.4:c.3904-1G>T		p.X1302_splice	ENST00000373198	NM_133170.3	1302			1	2	FACETS	0.825	0.678	0.989	0.825	0.678	0.989	CLONAL	1	TRUE	1	0.204405936364384	2		449	427	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191567	10191586	+	frameshift_variant	Frame_Shift_Del	DEL	ATCTGGAAGACCACCCAAAT	ATCTGGAAGACCACCCAAAT	-	novel	NA	P-0034761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	87	584	0	ENST00000256474.2:c.560_579del	p.Asp187GlyfsTer62	p.D187Gfs*62	ENST00000256474	NM_000551.3	187	gATCTGGAAGACCACCCAAAT/g	3/3	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.204405936364384	2		584	614	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441263	52441263	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	67	589	0	ENST00000460680.1:c.507C>A	p.His169Gln	p.H169Q	ENST00000460680	NM_004656.3	169	caC/caA	7/17	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.204405936364384	2		589	494	SUCCESS
AR	367	MSKCC	GRCh37	X	66905880	66905880	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	66	561	0	ENST00000374690.3:c.1799del	p.Asn600MetfsTer26	p.N600Mfs*26	ENST00000374690	NM_000044.3	599	agA/ag	3/8	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.204405936364384	2		561	509	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163309173	163309173	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs1300597624	NA	P-0034778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	73	525	0	ENST00000271452.3:c.512C>G	p.Ser171Cys	p.S171C	ENST00000271452	NM_145697.2	171	tCt/tGt	8/14	0.547443091519344	3	FACETS	0.562	0.492	0.638	0.187	0.164	0.213	SUBCLONAL	1	TRUE	0	0.547443091519344	3		525	604	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245075	53245075	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs782081983	NA	P-0034778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	217	411	0	ENST00000375401.3:c.865A>G	p.Lys289Glu	p.K289E	ENST00000375401	NM_004187.3	289	Aag/Gag	7/26	1	1	FACETS	0.784	0.744	0.825	1	0.994	1	SUBCLONAL	2	TRUE	0	0.547443091519344	1		411	367	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0034796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	141	230	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.3	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.25	1		231	690	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	107	406	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.25	2		406	626	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223251	5223251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199604489	NA	P-0034796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	95	539	1	ENST00000357368.4:c.2552G>A	p.Arg851His	p.R851H	ENST00000357368	NM_002850.3	851	cGc/cAc	18/38	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.25	2		540	711	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023919	27023937	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCAGCTGCGGCGGCGGC	CGGCAGCTGCGGCGGCGGC	-	novel	NA	P-0034796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	31	77	0	ENST00000324856.7:c.1027_1045del	p.Ala343ProfsTer14	p.A343Pfs*14	ENST00000324856	NM_006015.4	342	gCGGCAGCTGCGGCGGCGGCc/gc	1/20	1	2	FACETS	0.954	0.785	1	1	0.96	1	CLONAL	2	TRUE	1	0.25	2		77	130	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426093	49426094	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0034796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	142	571	0	ENST00000301067.7:c.12394dup	p.His4132ProfsTer36	p.H4132Pfs*36	ENST00000301067	NM_003482.3	4132	cac/cCac	39/54	1	2	FACETS	0.768	0.7	0.838	1	0.987	1	SUBCLONAL	2	TRUE	1	0.25	2		571	740	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667566	29667566	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	130	535	0	ENST00000356175.3:c.6902T>C	p.Val2301Ala	p.V2301A	ENST00000356175	NM_000267.3	2301	gTg/gCg	46/57	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.25	2		535	927	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020739	26020739	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	27	239	0	ENST00000357647.3:c.22G>A	p.Ala8Thr	p.A8T	ENST00000357647	NM_003529.2	8	Gct/Act	1/1	1	2	FACETS	0.677	0.539	0.834	0.677	0.539	0.834	SUBCLONAL	1	TRUE	1	0.25	2		239	319	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588873	29588873	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	262	273	0	ENST00000356175.3:c.4659del	p.Arg1554GlyfsTer13	p.R1554Gfs*13	ENST00000356175	NM_000267.3	1553	acT/ac	34/57	0.694613494572987	3	FACETS	0.92	0.889	0.95	0.92	0.889	0.95	CLONAL	3	TRUE	0	0.813995560142194	3		273	328	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23640963	23640963	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	337	515	0	ENST00000261584.4:c.2512C>A	p.Gln838Lys	p.Q838K	ENST00000261584	NM_024675.3	838	Cag/Aag	5/13	NA	2	FACETS	0.979	0.941	1			1	INDETERMINATE	2	TRUE	NA	0.66057793968653	2		515	521	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115723	8115723	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0034852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	135	378	0	ENST00000346208.3:c.1069A>T	p.Lys357Ter	p.K357*	ENST00000346208		357	Aag/Tag	6/6	0.336087245803138	4	FACETS	0.996	0.91	1	0.996	0.91	1	CLONAL	2	TRUE	2	0.336087245803138	4		378	539	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112276	115112277	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCGTCCGTCTGCACCGTGA	novel	NA	P-0034852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	27	123	0	ENST00000257566.3:c.1445_1463dup	p.Ala489HisfsTer209	p.A489Hfs*209	ENST00000257566	NM_016569.3	488	gcg/gcTCACGGTGCAGACGGACGCg	7/8	0.336087245803138	4	FACETS	1	0.932	1	0.711	0.572	0.865	CLONAL	1	TRUE	2	0.336087245803138	4		123	151	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100633	67100633	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0034852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	293	691	0	ENST00000412916.2:c.331A>T	p.Lys111Ter	p.K111*	ENST00000412916		111	Aaa/Taa	4/6	0.336087245803138	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.336087245803138	2		691	733	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786494	135786494	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	109	461	0	ENST00000298552.3:c.1036C>G	p.Leu346Val	p.L346V	ENST00000298552	NM_001162426.1	346	Ctt/Gtt	11/23	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.336087245803138	2		461	497	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115723	8115723	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0034852-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	159	378	0	ENST00000346208.3:c.1069A>T	p.Lys357Ter	p.K357*	ENST00000346208		357	Aag/Tag	6/6	1	2	FACETS	1	0.972	1	1	0.994	1	CLONAL	3	FALSE	1	0.181032994091358	2		378	526	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112276	115112277	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCGTCCGTCTGCACCGTGA	novel	NA	P-0034852-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	13	123	0	ENST00000257566.3:c.1445_1463dup	p.Ala489HisfsTer209	p.A489Hfs*209	ENST00000257566	NM_016569.3	488	gcg/gcTCACGGTGCAGACGGACGCg	7/8	1	2	FACETS	0.977	0.7	1	0.977	0.7	1	CLONAL	1	FALSE	1	0.181032994091358	2		123	147	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100633	67100633	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0034852-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	271	691	0	ENST00000412916.2:c.331A>T	p.Lys111Ter	p.K111*	ENST00000412916		111	Aaa/Taa	4/6	0.181558820700249	0	FACETS	0.883	0.834	0.933			1	CLONAL	4	FALSE	0	0.181032994091358	0		691	694	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786494	135786494	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034852-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	92	461	0	ENST00000298552.3:c.1036C>G	p.Leu346Val	p.L346V	ENST00000298552	NM_001162426.1	346	Ctt/Gtt	11/23	0.181558820700249	0	FACETS	0.925	0.826	1			1	CLONAL	2	FALSE	0	0.181032994091358	0		461	450	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0034875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	105	416	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.924	0.835	1	0.924	0.835	1	CLONAL	1	TRUE	1	0.628157607567334	2		417	362	SUCCESS
APC	324	MSKCC	GRCh37	5	112175548	112175548	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	91	295	0	ENST00000257430.4:c.4260del	p.Ser1421ValfsTer52	p.S1421Vfs*52	ENST00000257430	NM_000038.5	1419	agC/ag	16/16	1	2	FACETS	0.862	0.773	0.956	0.862	0.773	0.956	CLONAL	1	TRUE	1	0.628157607567334	2		295	336	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119096	70119096	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	108	295	0	ENST00000245479.2:c.672del	p.Gly225AlafsTer28	p.G225Afs*28	ENST00000245479	NM_000346.3	223	tCc/tc	2/3	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.628157607567334	2		295	312	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570101	95570101	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	209	492	0	ENST00000393063.1:c.3632T>C	p.Val1211Ala	p.V1211A	ENST00000393063	NM_030621.3	1211	gTg/gCg	22/28	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.628157607567334	2		492	646	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965388	68965388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	245	665	0	ENST00000288368.4:c.1000G>A	p.Ala334Thr	p.A334T	ENST00000288368	NM_024870.2	334	Gca/Aca	9/40	1	2	FACETS	0.978	0.917	1	0.978	0.917	1	CLONAL	1	TRUE	1	0.628157607567334	2		665	798	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0034877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	459	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.771802357235248	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.804159282948575	3		436	797	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0034877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	738	704	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.797351786420307	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.804159282948575	2		705	911	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0034877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	196	387	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.804159282948575	3	FACETS	1	0.987	1	0.625	0.583	0.668	CLONAL	1	TRUE	1	0.804159282948575	3		387	547	SUCCESS
APC	324	MSKCC	GRCh37	5	112174112	112174112	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	133	371	0	ENST00000257430.4:c.2821G>T	p.Glu941Ter	p.E941*	ENST00000257430	NM_000038.5	941	Gaa/Taa	16/16	0.396613919669501	3	FACETS	1	0.947	1	0.523	0.479	0.569	INDETERMINATE	1	TRUE	1	0.804159282948575	3		371	443	SUCCESS
APC	324	MSKCC	GRCh37	5	112175360	112175360	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	190	314	2	ENST00000257430.4:c.4069G>T	p.Gly1357Ter	p.G1357*	ENST00000257430	NM_000038.5	1357	Gga/Tga	16/16	0.396613919669501	3	FACETS	0.888	0.834	0.942	0.888	0.834	0.942	INDETERMINATE	2	TRUE	1	0.804159282948575	3		316	373	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143044	30143044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	414	895	4	ENST00000389048.3:c.482C>T	p.Ala161Val	p.A161V	ENST00000389048	NM_004304.4	161	gCg/gTg	1/29	0.396613919669501	3	FACETS	1	0.991	1	0.584	0.556	0.612	INDETERMINATE	1	TRUE	1	0.804159282948575	3		899	1237	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757428	40757428	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763638227	NA	P-0034877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	1207	754	0	ENST00000373198.4:c.2870C>T	p.Pro957Leu	p.P957L	ENST00000373198	NM_133170.3	957	cCg/cTg	20/32	0.751654170933298	6	FACETS	0.989	0.968	1	0.989	0.968	1	CLONAL	4	TRUE	2	0.804159282948575	6		754	1979	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533755	63533760	+	inframe_deletion	In_Frame_Del	DEL	GGGAGC	GGGAGC	-	novel	NA	P-0034877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	583	631	5	ENST00000307078.5:c.1394_1399del	p.Arg465_Ser466del	p.R465_S466del	ENST00000307078	NM_004655.3	465	cGCTCCCcg/ccg	6/11	0.797351786420307	2	FACETS	0.922	0.899	0.945	0.922	0.899	0.945	CLONAL	2	TRUE	0	0.804159282948575	2		636	786	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215661836	215661836	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	260	403	0	ENST00000260947.4:c.164A>T	p.Asn55Ile	p.N55I	ENST00000260947	NM_000465.2	55	aAc/aTc	2/11	0.324954059575762	2	FACETS	1	0.994	1	0.697	0.662	0.731	INDETERMINATE	1	TRUE	0	0.804159282948575	2		403	464	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162397	47162397	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	488	499	1	ENST00000409792.3:c.3729A>G	p.Ile1243Met	p.I1243M	ENST00000409792	NM_014159.6	1243	atA/atG	3/21	0.367262694470715	3	FACETS	1	0.995	1	0.78	0.756	0.804	INDETERMINATE	2	TRUE	0	0.804159282948575	3		500	727	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515173	31515173	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	416	1036	0	ENST00000344624.3:c.1212A>T	p.Glu404Asp	p.E404D	ENST00000344624		404	gaA/gaT	5/33	0.396613919669501	3	FACETS	1	0.989	1	0.559	0.532	0.586	INDETERMINATE	1	TRUE	1	0.804159282948575	3		1036	1298	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372215	55372215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1056128511	NA	P-0034877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	212	292	0	ENST00000297316.4:c.905C>T	p.Ser302Leu	p.S302L	ENST00000297316	NM_022454.3	302	tCg/tTg	2/2	0.804159282948575	3	FACETS	1	0.985	1	0.394	0.368	0.42	CLONAL	1	TRUE	0	0.804159282948575	3		292	626	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061334	38061334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	119	698	0	ENST00000250448.2:c.655C>A	p.Arg219Ser	p.R219S	ENST00000250448	NM_004496.3	219	Cgc/Agc	2/2	1	2	FACETS	0.998	0.899	1	0.998	0.899	1	CLONAL	1	TRUE	1	0.24	2		698	994	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307243	118307243	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555138451	NA	P-0034921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	28	222	2	ENST00000534358.1:c.16C>T	p.Arg6Trp	p.R6W	ENST00000534358	NM_005933.3	6	Cgg/Tgg	1/36	0.183684045207717	1	FACETS	0.671	0.537	0.823	0.671	0.537	0.823	SUBCLONAL	1	TRUE	0	0.24	1		224	306	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051240	13051240	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs938433963	NA	P-0034921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	49	398	0	ENST00000316448.5:c.676G>C	p.Asp226His	p.D226H	ENST00000316448	NM_004343.3	226	Gat/Cat	5/9	1	2	FACETS	0.825	0.699	0.963	0.825	0.699	0.963	CLONAL	1	TRUE	1	0.24	2		398	495	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610650	52610650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	225	634	0	ENST00000394830.3:c.3523G>A	p.Glu1175Lys	p.E1175K	ENST00000394830	NM_018313.4	1175	Gaa/Aaa	23/30	0.560012786848753	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.579382759591233	1		634	530	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271962	18271962	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	117	476	0	ENST00000222254.8:c.565G>T	p.Glu189Ter	p.E189*	ENST00000222254	NM_005027.3	189	Gag/Tag	5/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.579382759591233	2		476	308	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152243	99152243	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs367674308	NA	P-0034941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	231	498	0	ENST00000074304.5:c.322C>G	p.Leu108Val	p.L108V	ENST00000074304	NM_001134224.1	108	Ctt/Gtt	6/26	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.579382759591233	2		498	770	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056435	26056435	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs769566015	NA	P-0034941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	61	487	0	ENST00000343677.2:c.222G>C	p.Glu74Asp	p.E74D	ENST00000343677	NM_005319.3	74	gaG/gaC	1/1	0.246028402320839	3	FACETS	0.512	0.442	0.589	0.256	0.221	0.295	INDETERMINATE	1	TRUE	1	0.579382759591233	3		487	530	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610650	52610650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	124	634	0	ENST00000394830.3:c.3523G>A	p.Glu1175Lys	p.E1175K	ENST00000394830	NM_018313.4	1175	Gaa/Aaa	23/30	0.313826724350153	2	FACETS	0.913	0.834	0.995	0.913	0.834	0.995	CLONAL	2	TRUE	0	0.340348975716544	2		634	399	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271962	18271962	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	152	476	0	ENST00000222254.8:c.565G>T	p.Glu189Ter	p.E189*	ENST00000222254	NM_005027.3	189	Gag/Tag	5/16	0.296548221873125	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	2	0.340348975716544	4		476	558	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152243	99152243	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs367674308	NA	P-0034941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	105	498	0	ENST00000074304.5:c.322C>G	p.Leu108Val	p.L108V	ENST00000074304	NM_001134224.1	108	Ctt/Gtt	6/26	0.268894783287212	4	FACETS	0.819	0.737	0.905	0.819	0.737	0.905	CLONAL	2	TRUE	2	0.340348975716544	4		498	505	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056435	26056435	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs769566015	NA	P-0034941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	112	487	0	ENST00000343677.2:c.222G>C	p.Glu74Asp	p.E74D	ENST00000343677	NM_005319.3	74	gaG/gaC	1/1	0.340348975716544	6	FACETS	0.955	0.862	1			1	CLONAL	2	TRUE	NA	0.340348975716544	6		487	579	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138409963	138409963	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	31	487	0	ENST00000289153.2:c.1915C>G	p.Leu639Val	p.L639V	ENST00000289153	NM_006219.2	639	Ctt/Gtt	13/22	0.340348975716544	6	FACETS	0.539	0.435	0.658	0.18	0.145	0.22	SUBCLONAL	1	TRUE	3	0.340348975716544	6		487	568	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568569	41568569	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	43	781	1	ENST00000263253.7:c.4519G>A	p.Asp1507Asn	p.D1507N	ENST00000263253	NM_001429.3	1507	Gat/Aat	28/31	0.296548221873125	4	FACETS	0.443	0.37	0.525	0.222	0.185	0.263	SUBCLONAL	1	TRUE	2	0.340348975716544	4		782	764	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39657738	39657738	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	24	397	0	ENST00000361337.2:c.31C>A	p.Gln11Lys	p.Q11K	ENST00000361337	NM_003286.2	11	Cag/Aag	1/21	0.296548221873125	4	FACETS	0.414	0.323	0.518	0.207	0.161	0.259	SUBCLONAL	1	TRUE	2	0.340348975716544	4		397	457	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933048	39933048	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	31	560	0	ENST00000378444.4:c.1551C>G	p.Asn517Lys	p.N517K	ENST00000378444	NM_001123385.1	517	aaC/aaG	4/15	0.340348975716544	2	FACETS	0.393	0.318	0.479			1	SUBCLONAL	1	TRUE	NA	0.340348975716544	2		560	463	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	102	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.509470989182066	2		306	396	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0034972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	92	450	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.903	0.808	1	0.903	0.808	1	CLONAL	1	TRUE	1	0.509470989182066	2		451	400	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654653	67654653	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	136	443	0	ENST00000264010.4:c.1140G>T	p.Gln380His	p.Q380H	ENST00000264010	NM_006565.3	380	caG/caT	6/12	1	2	FACETS	0.716	0.651	0.783	0.716	0.651	0.783	SUBCLONAL	1	TRUE	1	0.509470989182066	2		443	746	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820601	44820601	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	101	286	0	ENST00000377967.4:c.298G>C	p.Gly100Arg	p.G100R	ENST00000377967	NM_021140.2	100	Ggt/Cgt	3/29	1	1	FACETS	0.78	0.703	0.86	0.78	0.703	0.86	SUBCLONAL	1	TRUE	0	0.509470989182066	1		286	379	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	35	415	0	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	1	2	FACETS	0.982	0.807	1	0.982	0.807	1	CLONAL	1	TRUE	1	0.23	2		415	310	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	34	444	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.989	0.811	1	0.989	0.811	1	CLONAL	1	TRUE	1	0.23	2		444	299	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	55	633	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.812	0.694	0.941	0.812	0.694	0.941	CLONAL	1	TRUE	1	0.23	2		633	589	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	58	565	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.23	2		565	462	SUCCESS
APC	324	MSKCC	GRCh37	5	112179431	112179431	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs864622205	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	46	587	1	ENST00000257430.4:c.8140C>T	p.Arg2714Cys	p.R2714C	ENST00000257430	NM_000038.5	2714	Cgt/Tgt	16/16	1	2	FACETS	0.851	0.717	0.999	0.851	0.717	0.999	CLONAL	1	TRUE	1	0.23	2		588	470	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952006	178952006	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	49	558	0	ENST00000263967.3:c.3061T>C	p.Tyr1021His	p.Y1021H	ENST00000263967	NM_006218.2	1021	Tac/Cac	21/21	1	2	FACETS	0.955	0.81	1	0.955	0.81	1	CLONAL	1	TRUE	1	0.23	2		558	446	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	23	290	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.735	0.574	0.921	0.735	0.574	0.921	CLONAL	1	TRUE	1	0.23	2		290	272	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	48	531	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	TRUE	1	0.23	2		531	395	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	43	1064	3	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.719	0.601	0.85	0.719	0.601	0.85	SUBCLONAL	1	TRUE	1	0.23	2		1067	520	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	66	571	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	0.971	0.843	1	0.971	0.843	1	CLONAL	1	TRUE	1	0.23	2		571	591	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941657	48941657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1060503077	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	25	366	0	ENST00000267163.4:c.967G>T	p.Glu323Ter	p.E323*	ENST00000267163	NM_000321.2	323	Gaa/Taa	10/27	1	2	FACETS	0.717	0.566	0.891	0.717	0.566	0.891	SUBCLONAL	1	TRUE	1	0.23	2		366	303	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337650	73337650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	27	357	0	ENST00000377767.4:c.2066G>A	p.Arg689Gln	p.R689Q	ENST00000377767	NM_014953.3	689	cGa/cAa	16/21	1	2	FACETS	0.917	0.733	1	0.917	0.733	1	CLONAL	1	TRUE	1	0.23	2		357	256	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491273	2491273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771419721	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	59	637	0	ENST00000355716.4:c.316C>T	p.Arg106Cys	p.R106C	ENST00000355716	NM_003820.2	106	Cgc/Tgc	4/8	1	2	FACETS	0.938	0.807	1	0.938	0.807	1	CLONAL	1	TRUE	1	0.23	2		637	547	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	25	543	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	0.599	0.472	0.745	0.599	0.472	0.745	SUBCLONAL	1	TRUE	1	0.23	2		543	363	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380283	25380283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913528	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	67	586	0	ENST00000311936.3:c.175G>A	p.Ala59Thr	p.A59T	ENST00000311936	NM_004985.3	59	Gca/Aca	3/5	1	2	FACETS	0.971	0.844	1	0.971	0.844	1	CLONAL	1	TRUE	1	0.23	2		586	600	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546620	9546620	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764351685	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	60	712	0	ENST00000353224.5:c.1402G>A	p.Glu468Lys	p.E468K	ENST00000353224	NM_177990.2	468	Gag/Aag	5/10	1	2	FACETS	0.919	0.792	1	0.919	0.792	1	CLONAL	1	TRUE	1	0.23	2		712	568	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12647784	12647784	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	27	354	0	ENST00000251849.4:c.596C>T	p.Ser199Phe	p.S199F	ENST00000251849	NM_002880.3	199	tCc/tTc	6/17	1	2	FACETS	0.824	0.657	1	0.824	0.657	1	CLONAL	1	TRUE	1	0.23	2		354	285	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793712	89793712	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	43	453	0	ENST00000336032.3:c.781A>C	p.Asn261His	p.N261H	ENST00000336032	NM_006813.2	261	Aat/Cat	2/2	1	2	FACETS	0.979	0.821	1	0.979	0.821	1	CLONAL	1	TRUE	1	0.23	2		453	382	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131412	202131412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339962485	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	48	550	0	ENST00000358485.4:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000358485	NM_001080125.1	127	cGa/cAa	2/9	1	2	FACETS	0.827	0.699	0.967	0.827	0.699	0.967	CLONAL	1	TRUE	1	0.23	2		550	505	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178199	142178199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746049210	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	34	394	0	ENST00000350721.4:c.7219C>T	p.Arg2407Cys	p.R2407C	ENST00000350721	NM_001184.3	2407	Cgc/Tgc	43/47	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.23	2		394	272	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881438	48881438	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	17	342	0	ENST00000267163.4:c.160G>A	p.Glu54Lys	p.E54K	ENST00000267163	NM_000321.2	54	Gaa/Aaa	2/27	1	2	FACETS	0.624	0.466	0.81	0.624	0.466	0.81	SUBCLONAL	1	TRUE	1	0.23	2		342	237	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29107974	29107974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121908702	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	37	668	0	ENST00000328354.6:c.715G>A	p.Glu239Lys	p.E239K	ENST00000328354	NM_007194.3	239	Gag/Aag	6/15	1	2	FACETS	0.606	0.499	0.726	0.606	0.499	0.726	SUBCLONAL	1	TRUE	1	0.23	2		668	531	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148504761	148504761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397515548	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	36	523	0	ENST00000320356.2:c.2233G>A	p.Glu745Lys	p.E745K	ENST00000320356	NM_004456.4	745	Gaa/Aaa	20/20	1	2	FACETS	0.619	0.508	0.743	0.619	0.508	0.743	SUBCLONAL	1	TRUE	1	0.23	2		523	506	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87322770	87322770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781137734	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	41	609	0	ENST00000277120.3:c.371G>A	p.Arg124Gln	p.R124Q	ENST00000277120		124	cGa/cAa	5/19	1	2	FACETS	0.823	0.686	0.975	0.823	0.686	0.975	CLONAL	1	TRUE	1	0.23	2		609	433	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437275	220437275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370513243	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	31	836	0	ENST00000243786.2:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000243786	NM_002191.3	60	cGa/cAa	1/2	1	2	FACETS	0.445	0.359	0.543	0.445	0.359	0.543	SUBCLONAL	1	TRUE	1	0.23	2		836	606	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005419	29005419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55687105	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	36	489	0	ENST00000282397.4:c.842G>A	p.Arg281Gln	p.R281Q	ENST00000282397	NM_002019.4	281	cGa/cAa	7/30	1	2	FACETS	0.773	0.636	0.926	0.773	0.636	0.926	CLONAL	1	TRUE	1	0.23	2		489	405	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97897654	97897654	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143181565	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	45	504	0	ENST00000289081.3:c.817G>A	p.Glu273Lys	p.E273K	ENST00000289081	NM_000136.2	273	Gaa/Aaa	8/15	1	2	FACETS	0.814	0.684	0.957	0.814	0.684	0.957	CLONAL	1	TRUE	1	0.23	2		504	481	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624245	89624245	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554890335	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	19	240	0	ENST00000371953.3:c.19G>T	p.Glu7Ter	p.E7*	ENST00000371953	NM_000314.4	7	Gag/Tag	1/9	1	2	FACETS	0.81	0.617	1	0.81	0.617	1	CLONAL	1	TRUE	1	0.23	2		240	204	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098519	108098519	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs876658520	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	16	432	0	ENST00000278616.4:c.89T>G	p.Phe30Cys	p.F30C	ENST00000278616	NM_000051.3	30	tTt/tGt	3/63	1	2	FACETS	0.449	0.331	0.59	0.449	0.331	0.59	SUBCLONAL	1	TRUE	1	0.23	2		432	310	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029072	14029072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763619616	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	37	311	0	ENST00000311895.7:c.1283C>T	p.Ala428Val	p.A428V	ENST00000311895	NM_005236.2	428	gCg/gTg	8/11	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.23	2		311	276	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105736	27105736	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	36	409	0	ENST00000324856.7:c.5347G>T	p.Glu1783Ter	p.E1783*	ENST00000324856	NM_006015.4	1783	Gaa/Taa	20/20	1	2	FACETS	0.824	0.678	0.987	0.824	0.678	0.987	CLONAL	1	TRUE	1	0.23	2		409	380	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453531	138453531	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372119491	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	40	543	0	ENST00000289153.2:c.917G>A	p.Arg306Gln	p.R306Q	ENST00000289153	NM_006219.2	306	cGa/cAa	5/22	1	2	FACETS	0.874	0.727	1	0.874	0.727	1	CLONAL	1	TRUE	1	0.23	2		543	398	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830958	72830958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393698686	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	63	584	0	ENST00000268489.5:c.5623G>A	p.Glu1875Lys	p.E1875K	ENST00000268489	NM_006885.3	1875	Gaa/Aaa	9/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.23	2		584	452	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278079	41278079	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1031583127	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	48	463	0	ENST00000349496.5:c.1955C>T	p.Ala652Val	p.A652V	ENST00000349496	NM_001904.3	652	gCg/gTg	13/15	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.23	2		463	406	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99163066	99163066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769868588	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	44	501	1	ENST00000074304.5:c.1072G>A	p.Val358Ile	p.V358I	ENST00000074304	NM_001134224.1	358	Gtc/Atc	13/26	1	2	FACETS	0.959	0.806	1	0.959	0.806	1	CLONAL	1	TRUE	1	0.23	2		502	399	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94923091	94923091	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	51	582	0	ENST00000536441.1:c.377A>G	p.Asn126Ser	p.N126S	ENST00000536441	NM_144665.3	126	aAc/aGc	4/10	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.23	2		582	378	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39708808	39708808	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs183058581	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	15	384	0	ENST00000361337.2:c.419G>A	p.Arg140Gln	p.R140Q	ENST00000361337	NM_003286.2	140	cGa/cAa	6/21	1	2	FACETS	0.593	0.434	0.783	0.593	0.434	0.783	SUBCLONAL	1	TRUE	1	0.23	2		384	220	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165078	47165078	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	42	478	0	ENST00000409792.3:c.1048G>T	p.Asp350Tyr	p.D350Y	ENST00000409792	NM_014159.6	350	Gat/Tat	3/21	1	2	FACETS	0.941	0.787	1	0.941	0.787	1	CLONAL	1	TRUE	1	0.23	2		478	388	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611203	100611203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555977836	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	73	554	0	ENST00000308731.7:c.1403G>A	p.Arg468His	p.R468H	ENST00000308731	NM_000061.2	468	cGc/cAc	15/19	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.23	2		554	527	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521857	157521857	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	45	445	0	ENST00000346085.5:c.4129G>T	p.Asp1377Tyr	p.D1377Y	ENST00000346085	NM_020732.3	1377	Gac/Tac	18/20	1	2	FACETS	0.95	0.8	1	0.95	0.8	1	CLONAL	1	TRUE	1	0.23	2		445	412	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609759	117609759	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs771164515	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	66	662	0	ENST00000368508.3:c.6940G>T	p.Asp2314Tyr	p.D2314Y	ENST00000368508	NM_002944.2	2314	Gat/Tat	43/43	1	2	FACETS	0.859	0.745	0.983	0.859	0.745	0.983	CLONAL	1	TRUE	1	0.23	2		662	668	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098638	2098638	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	28	525	0	ENST00000219476.3:c.22G>T	p.Asp8Tyr	p.D8Y	ENST00000219476	NM_000548.3	8	Gat/Tat	2/42	1	2	FACETS	0.512	0.408	0.63	0.512	0.408	0.63	SUBCLONAL	1	TRUE	1	0.23	2		525	476	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1255446	1255446	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	45	682	0	ENST00000310581.5:c.3113A>G	p.Asp1038Gly	p.D1038G	ENST00000310581	NM_198253.2	1038	gAc/gGc	14/16	1	2	FACETS	0.711	0.597	0.838	0.711	0.597	0.838	SUBCLONAL	1	TRUE	1	0.23	2		682	550	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090886	5090886	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	13	194	0	ENST00000381652.3:c.3034G>T	p.Glu1012Ter	p.E1012*	ENST00000381652	NM_004972.3	1012	Gaa/Taa	22/25	1	2	FACETS	0.897	0.645	1	0.897	0.645	1	CLONAL	1	TRUE	1	0.23	2		194	126	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020559	14020559	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1567243770	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	42	659	0	ENST00000311895.7:c.530A>G	p.His177Arg	p.H177R	ENST00000311895	NM_005236.2	177	cAt/cGt	3/11	1	2	FACETS	0.739	0.617	0.875	0.739	0.617	0.875	SUBCLONAL	1	TRUE	1	0.23	2		659	494	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180254	32180254	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs751888857	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	35	581	0	ENST00000375023.3:c.2677C>A	p.Gln893Lys	p.Q893K	ENST00000375023	NM_004557.3	893	Caa/Aaa	17/30	1	2	FACETS	0.705	0.577	0.847	0.705	0.577	0.847	SUBCLONAL	1	TRUE	1	0.23	2		581	432	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164817	106164817	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	47	564	0	ENST00000380013.4:c.3685C>A	p.Leu1229Ile	p.L1229I	ENST00000380013	NM_001127208.2	1229	Ctc/Atc	6/11	1	2	FACETS	0.777	0.655	0.911	0.777	0.655	0.911	CLONAL	1	TRUE	1	0.23	2		564	526	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152510	56152510	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs387906788	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	28	285	0	ENST00000399503.3:c.566T>G	p.Leu189Arg	p.L189R	ENST00000399503	NM_005921.1	189	cTg/cGg	2/20	1	2	FACETS	0.842	0.675	1	0.842	0.675	1	CLONAL	1	TRUE	1	0.23	2		285	289	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914274	32914274	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs56253082	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	40	565	0	ENST00000380152.3:c.5782G>T	p.Glu1928Ter	p.E1928*	ENST00000380152		1928	Gaa/Taa	11/27	1	2	FACETS	0.983	0.819	1	0.983	0.819	1	CLONAL	1	TRUE	1	0.23	2		565	354	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163610	47163610	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	45	530	0	ENST00000409792.3:c.2516G>T	p.Arg839Ile	p.R839I	ENST00000409792	NM_014159.6	839	aGa/aTa	3/21	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.23	2		530	387	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416445	49416445	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	72	696	0	ENST00000301067.7:c.16266G>A	p.Met5422Ile	p.M5422I	ENST00000301067	NM_003482.3	5422	atG/atA	51/54	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.23	2		696	613	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073433	8073433	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs147996134	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	45	602	0	ENST00000377482.5:c.1226A>C	p.Lys409Thr	p.K409T	ENST00000377482	NM_018948.3	409	aAa/aCa	4/4	1	2	FACETS	0.714	0.6	0.841	0.714	0.6	0.841	SUBCLONAL	1	TRUE	1	0.23	2		602	548	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780857	9780857	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749871179	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	47	754	1	ENST00000377346.4:c.1579G>A	p.Glu527Lys	p.E527K	ENST00000377346	NM_005026.3	527	Gag/Aag	13/24	1	2	FACETS	0.757	0.638	0.888	0.757	0.638	0.888	SUBCLONAL	1	TRUE	1	0.23	2		755	540	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256661	16256661	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs371456542	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	41	526	0	ENST00000375759.3:c.3926T>G	p.Phe1309Cys	p.F1309C	ENST00000375759	NM_015001.2	1309	tTt/tGt	11/15	1	2	FACETS	0.843	0.703	0.998	0.843	0.703	0.998	CLONAL	1	TRUE	1	0.23	2		526	423	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39317412	39317412	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	63	653	0	ENST00000373001.3:c.774A>C	p.Lys258Asn	p.K258N	ENST00000373001	NM_022157.3	258	aaA/aaC	5/7	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.23	2		653	518	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812149	43812149	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	50	390	0	ENST00000372470.3:c.1014G>T	p.Glu338Asp	p.E338D	ENST00000372470	NM_005373.2	338	gaG/gaT	7/12	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.23	2		390	412	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798775	45798775	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	52	763	0	ENST00000450313.1:c.456G>T	p.Trp152Cys	p.W152C	ENST00000450313	NM_012222.2	152	tgG/tgT	5/16	1	2	FACETS	0.772	0.656	0.898	0.772	0.656	0.898	SUBCLONAL	1	TRUE	1	0.23	2		763	586	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45805924	45805924	+	start_lost	Translation_Start_Site	SNP	C	C	A	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	45	492	0	ENST00000450313.1:c.3G>T	p.Met1?	p.M1?	ENST00000450313	NM_012222.2	1	atG/atT	1/16	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.23	2		492	377	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076802	72076802	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	38	438	0	ENST00000357731.5:c.695C>A	p.Ser232Tyr	p.S232Y	ENST00000357731	NM_173808.2	232	tCt/tAt	5/7	1	2	FACETS	0.739	0.611	0.882	0.739	0.611	0.882	SUBCLONAL	1	TRUE	1	0.23	2		438	447	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165692	118165692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771057074	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	43	430	0	ENST00000369448.3:c.202G>A	p.Asp68Asn	p.D68N	ENST00000369448	NM_017709.3	68	Gac/Aac	2/2	1	2	FACETS	0.91	0.762	1	0.91	0.762	1	CLONAL	1	TRUE	1	0.23	2		430	411	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737061	162737061	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	47	606	0	ENST00000367921.3:c.1205T>G	p.Ile402Ser	p.I402S	ENST00000367921	NM_006182.2	402	aTt/aGt	11/18	1	2	FACETS	0.583	0.491	0.685	0.583	0.491	0.685	SUBCLONAL	1	TRUE	1	0.23	2		606	701	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743286	162743286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	26	315	0	ENST00000367921.3:c.1756G>A	p.Glu586Lys	p.E586K	ENST00000367921	NM_006182.2	586	Gaa/Aaa	14/18	1	2	FACETS	0.774	0.614	0.957	0.774	0.614	0.957	CLONAL	1	TRUE	1	0.23	2		315	292	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956176	175956176	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	37	528	0	ENST00000367669.3:c.2036A>C	p.Lys679Thr	p.K679T	ENST00000367669	NM_022457.5	679	aAg/aCg	18/20	1	2	FACETS	0.773	0.638	0.925	0.773	0.638	0.925	CLONAL	1	TRUE	1	0.23	2		528	416	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623695	43623695	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	54	559	0	ENST00000355710.3:c.3323T>G	p.Leu1108Ter	p.L1108*	ENST00000355710	NM_020975.4	1108	tTa/tGa	20/20	1	2	FACETS	0.814	0.695	0.944	0.814	0.695	0.944	CLONAL	1	TRUE	1	0.23	2		559	577	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653782	89653782	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	rs886041877	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	21	439	0	ENST00000371953.3:c.80A>C	p.Tyr27Ser	p.Y27S	ENST00000371953	NM_000314.4	27	tAt/tCt	2/9	1	2	FACETS	0.613	0.472	0.777	0.613	0.472	0.777	SUBCLONAL	1	TRUE	1	0.23	2		439	298	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690833	89690833	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	32	475	0	ENST00000371953.3:c.240A>C	p.Lys80Asn	p.K80N	ENST00000371953	NM_000314.4	80	aaA/aaC	4/9	1	2	FACETS	0.881	0.716	1	0.881	0.716	1	CLONAL	1	TRUE	1	0.23	2		475	316	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692947	89692947	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	59	659	0	ENST00000371953.3:c.431A>C	p.Lys144Thr	p.K144T	ENST00000371953	NM_000314.4	144	aAa/aCa	5/9	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.23	2		659	452	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911514	114911514	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	20	308	0	ENST00000543371.1:c.1032A>C	p.Glu344Asp	p.E344D	ENST00000543371	NM_001198531.1	344	gaA/gaC	10/14	1	2	FACETS	0.737	0.565	0.937	0.737	0.565	0.937	CLONAL	1	TRUE	1	0.23	2		308	236	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920777	100920777	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	39	512	0	ENST00000325455.5:c.2371G>T	p.Glu791Ter	p.E791*	ENST00000325455	NM_001202474.3	791	Gaa/Taa	6/8	1	2	FACETS	0.986	0.819	1	0.986	0.819	1	CLONAL	1	TRUE	1	0.23	2		512	344	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115575	108115575	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	43	611	0	ENST00000278616.4:c.723G>T	p.Lys241Asn	p.K241N	ENST00000278616	NM_000051.3	241	aaG/aaT	7/63	1	2	FACETS	0.856	0.717	1	0.856	0.717	1	CLONAL	1	TRUE	1	0.23	2		611	437	SUCCESS
ATM	472	MSKCC	GRCh37	11	108138012	108138012	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	29	499	0	ENST00000278616.4:c.2581T>G	p.Tyr861Asp	p.Y861D	ENST00000278616	NM_000051.3	861	Tac/Gac	17/63	1	2	FACETS	0.648	0.52	0.794	0.648	0.52	0.794	SUBCLONAL	1	TRUE	1	0.23	2		499	389	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164158	108164158	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	26	364	0	ENST00000278616.4:c.4730C>A	p.Thr1577Asn	p.T1577N	ENST00000278616	NM_000051.3	1577	aCt/aAt	31/63	1	2	FACETS	0.711	0.564	0.879	0.711	0.564	0.879	SUBCLONAL	1	TRUE	1	0.23	2		364	318	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165730	108165730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765759912	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	43	450	0	ENST00000278616.4:c.4853G>A	p.Arg1618Gln	p.R1618Q	ENST00000278616	NM_000051.3	1618	cGa/cAa	32/63	1	2	FACETS	0.916	0.768	1	0.916	0.768	1	CLONAL	1	TRUE	1	0.23	2		450	408	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1034629	1034629	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	59	662	0	ENST00000358495.3:c.530A>C	p.Lys177Thr	p.K177T	ENST00000358495	NM_134424.2	177	aAg/aCg	7/12	0.3	2	FACETS	0.975	0.84	1			1	CLONAL	1	TRUE	NA	0.23	2		662	526	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245252	46245252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	27	510	0	ENST00000334344.6:c.3346C>T	p.Pro1116Ser	p.P1116S	ENST00000334344	NM_152641.2	1116	Cca/Tca	15/21	1	2	FACETS	0.518	0.412	0.641	0.518	0.412	0.641	SUBCLONAL	1	TRUE	1	0.23	2		510	453	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495832	56495832	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	40	363	0	ENST00000267101.3:c.4022G>T	p.Arg1341Ile	p.R1341I	ENST00000267101	NM_001982.3	1341	aGa/aTa	28/28	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.23	2		363	340	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256218	133256218	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs12315832	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	56	641	0	ENST00000320574.5:c.443T>A	p.Leu148Ter	p.L148*	ENST00000320574	NM_006231.2	148	tTg/tAg	6/49	1	2	FACETS	0.914	0.783	1	0.914	0.783	1	CLONAL	1	TRUE	1	0.23	2		641	533	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906993	32906993	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1270441968	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	26	547	0	ENST00000380152.3:c.1378A>C	p.Asn460His	p.N460H	ENST00000380152		460	Aat/Cat	10/27	1	2	FACETS	0.621	0.492	0.769	0.621	0.492	0.769	SUBCLONAL	1	TRUE	1	0.23	2		547	364	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911360	32911360	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	34	532	0	ENST00000380152.3:c.2868A>C	p.Lys956Asn	p.K956N	ENST00000380152		956	aaA/aaC	11/27	1	2	FACETS	0.88	0.721	1	0.88	0.721	1	CLONAL	1	TRUE	1	0.23	2		532	336	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972633	32972633	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs770826575	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	21	499	0	ENST00000380152.3:c.9983T>G	p.Phe3328Cys	p.F3328C	ENST00000380152		3328	tTc/tGc	27/27	1	2	FACETS	0.465	0.357	0.59	0.465	0.357	0.59	SUBCLONAL	1	TRUE	1	0.23	2		499	393	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872009	35872009	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	43	457	0	ENST00000216797.5:c.604T>G	p.Leu202Val	p.L202V	ENST00000216797	NM_020529.2	202	Ttg/Gtg	4/6	1	2	FACETS	0.831	0.696	0.981	0.831	0.696	0.981	CLONAL	1	TRUE	1	0.23	2		457	450	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422098	81422098	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	55	510	0	ENST00000298171.2:c.74C>T	p.Ser25Leu	p.S25L	ENST00000298171	NM_000369.2	25	tCg/tTg	1/10	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.23	2		510	451	SUCCESS
BLM	641	MSKCC	GRCh37	15	91337519	91337519	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	50	572	0	ENST00000355112.3:c.3142A>C	p.Asn1048His	p.N1048H	ENST00000355112	NM_000057.2	1048	Aat/Cat	16/22	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.23	2		572	407	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3799671	3799671	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs976949877	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	45	507	0	ENST00000262367.5:c.3793G>A	p.Asp1265Asn	p.D1265N	ENST00000262367	NM_004380.2	1265	Gat/Aat	21/31	1	2	FACETS	0.833	0.7	0.979	0.833	0.7	0.979	CLONAL	1	TRUE	1	0.23	2		507	470	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858594	9858594	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	52	646	0	ENST00000330684.3:c.2807C>A	p.Ser936Ter	p.S936*	ENST00000330684	NM_001134407.1	936	tCa/tAa	13/13	1	2	FACETS	0.836	0.712	0.972	0.836	0.712	0.972	CLONAL	1	TRUE	1	0.23	2		646	541	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029402	14029402	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	53	464	1	ENST00000311895.7:c.1613T>A	p.Leu538Ter	p.L538*	ENST00000311895	NM_005236.2	538	tTg/tAg	8/11	1	2	FACETS	0.974	0.832	1	0.974	0.832	1	CLONAL	1	TRUE	1	0.23	2		465	473	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993029	72993029	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	87	857	0	ENST00000268489.5:c.1016T>A	p.Phe339Tyr	p.F339Y	ENST00000268489	NM_006885.3	339	tTt/tAt	2/10	1	2	FACETS	0.826	0.73	0.929	0.826	0.73	0.929	CLONAL	1	TRUE	1	0.23	2		857	916	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554580	29554580	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	14	291	0	ENST00000356175.3:c.2365A>C	p.Lys789Gln	p.K789Q	ENST00000356175	NM_000267.3	789	Aag/Cag	20/57	1	2	FACETS	0.516	0.373	0.689	0.516	0.373	0.689	SUBCLONAL	1	TRUE	1	0.23	2		291	236	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59770859	59770859	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	34	418	0	ENST00000259008.2:c.2507G>A	p.Arg836Lys	p.R836K	ENST00000259008	NM_032043.2	836	aGa/aAa	18/20	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.23	2		418	266	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375463	15375463	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747608142	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	89	727	2	ENST00000263377.2:c.964C>T	p.Arg322Trp	p.R322W	ENST00000263377	NM_058243.2	322	Cgg/Tgg	6/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.23	2		729	640	SUCCESS
AXL	558	MSKCC	GRCh37	19	41736878	41736878	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	47	635	0	ENST00000301178.4:c.593A>G	p.Asn198Ser	p.N198S	ENST00000301178	NM_021913.4	198	aAc/aGc	5/20	1	2	FACETS	0.716	0.603	0.84	0.716	0.603	0.84	SUBCLONAL	1	TRUE	1	0.23	2		635	571	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026615	48026615	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	42	502	0	ENST00000234420.5:c.1493A>C	p.Lys498Thr	p.K498T	ENST00000234420	NM_000179.2	498	aAg/aCg	4/10	1	2	FACETS	0.838	0.7	0.99	0.838	0.7	0.99	CLONAL	1	TRUE	1	0.23	2		502	436	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149170	61149170	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	31	446	0	ENST00000295025.8:c.1360G>T	p.Asp454Tyr	p.D454Y	ENST00000295025	NM_002908.2	454	Gat/Tat	11/11	1	2	FACETS	0.688	0.556	0.836	0.688	0.556	0.836	SUBCLONAL	1	TRUE	1	0.23	2		446	392	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128030455	128030455	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	62	606	0	ENST00000285398.2:c.1813A>C	p.Ile605Leu	p.I605L	ENST00000285398	NM_000122.1	605	Atc/Ctc	11/15	1	2	FACETS	0.872	0.753	1	0.872	0.753	1	CLONAL	1	TRUE	1	0.23	2		606	618	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251716	212251716	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs773165657	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	32	458	1	ENST00000342788.4:c.3343G>T	p.Val1115Leu	p.V1115L	ENST00000342788	NM_005235.2	1115	Gtg/Ttg	27/28	1	2	FACETS	0.643	0.521	0.78	0.643	0.521	0.78	SUBCLONAL	1	TRUE	1	0.23	2		459	433	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285282	212285282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	33	513	0	ENST00000342788.4:c.3019C>T	p.Leu1007Phe	p.L1007F	ENST00000342788	NM_005235.2	1007	Ctc/Ttc	25/28	1	2	FACETS	0.678	0.552	0.82	0.678	0.552	0.82	SUBCLONAL	1	TRUE	1	0.23	2		513	423	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286796	212286796	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1157390905	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	22	503	0	ENST00000342788.4:c.2900T>G	p.Phe967Cys	p.F967C	ENST00000342788	NM_005235.2	967	tTt/tGt	24/28	1	2	FACETS	0.512	0.396	0.646	0.512	0.396	0.646	SUBCLONAL	1	TRUE	1	0.23	2		503	374	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624881	9624881	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	45	627	0	ENST00000353224.5:c.96T>G	p.Phe32Leu	p.F32L	ENST00000353224	NM_177990.2	32	ttT/ttG	3/10	1	2	FACETS	0.704	0.591	0.829	0.704	0.591	0.829	SUBCLONAL	1	TRUE	1	0.23	2		627	556	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309577	30309577	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	63	636	0	ENST00000307677.4:c.445G>T	p.Ala149Ser	p.A149S	ENST00000307677	NM_138578.1	149	Gca/Tca	2/3	1	2	FACETS	0.807	0.697	0.926	0.807	0.697	0.926	CLONAL	1	TRUE	1	0.23	2		636	679	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742794	39742794	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	51	386	0	ENST00000361337.2:c.1637G>A	p.Arg546Gln	p.R546Q	ENST00000361337	NM_003286.2	546	cGa/cAa	15/21	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.23	2		386	392	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748586	40748586	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	37	410	0	ENST00000373198.4:c.2930T>G	p.Ile977Ser	p.I977S	ENST00000373198	NM_133170.3	977	aTt/aGt	21/32	1	2	FACETS	0.867	0.716	1	0.867	0.716	1	CLONAL	1	TRUE	1	0.23	2		410	371	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553286	41553286	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	64	655	0	ENST00000263253.7:c.3375C>A	p.Phe1125Leu	p.F1125L	ENST00000263253	NM_001429.3	1125	ttC/ttA	18/31	1	2	FACETS	0.934	0.809	1	0.934	0.809	1	CLONAL	1	TRUE	1	0.23	2		655	596	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12653459	12653459	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	38	500	0	ENST00000251849.4:c.310G>T	p.Glu104Ter	p.E104*	ENST00000251849	NM_002880.3	104	Gaa/Taa	3/17	1	2	FACETS	0.703	0.581	0.839	0.703	0.581	0.839	SUBCLONAL	1	TRUE	1	0.23	2		500	470	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643911	52643911	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	50	629	0	ENST00000394830.3:c.1985T>G	p.Leu662Arg	p.L662R	ENST00000394830	NM_018313.4	662	cTa/cGa	17/30	1	2	FACETS	0.97	0.825	1	0.97	0.825	1	CLONAL	1	TRUE	1	0.23	2		629	448	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278209	142278209	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	45	660	0	ENST00000350721.4:c.1616T>G	p.Phe539Cys	p.F539C	ENST00000350721	NM_001184.3	539	tTt/tGt	7/47	1	2	FACETS	0.834	0.702	0.981	0.834	0.702	0.981	CLONAL	1	TRUE	1	0.23	2		660	469	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156490	55156490	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	27	445	0	ENST00000257290.5:c.2891A>C	p.Lys964Thr	p.K964T	ENST00000257290	NM_006206.4	964	aAa/aCa	22/23	1	2	FACETS	0.566	0.45	0.699	0.566	0.45	0.699	SUBCLONAL	1	TRUE	1	0.23	2		445	415	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158262	106158262	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	48	402	0	ENST00000380013.4:c.3163A>C	p.Lys1055Gln	p.K1055Q	ENST00000380013	NM_001127208.2	1055	Aaa/Caa	3/11	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.23	2		402	415	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524715	187524715	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	85	801	0	ENST00000441802.2:c.10965C>A	p.Phe3655Leu	p.F3655L	ENST00000441802	NM_005245.3	3655	ttC/ttA	19/27	0.128070233418613	3	FACETS	0.952	0.84	1	0.476	0.42	0.536	INDETERMINATE	1	TRUE	1	0.23	3		801	866	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160633	56160633	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs76076026	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	49	364	0	ENST00000399503.3:c.907G>A	p.Glu303Lys	p.E303K	ENST00000399503	NM_005921.1	303	Gaa/Aaa	4/20	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.23	2		364	365	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177491	56177491	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	44	550	0	ENST00000399503.3:c.2464A>C	p.Ser822Arg	p.S822R	ENST00000399503	NM_005921.1	822	Agt/Cgt	14/20	1	2	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	TRUE	1	0.23	2		550	380	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751234	57751234	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	27	440	0	ENST00000274289.3:c.1633C>A	p.His545Asn	p.H545N	ENST00000274289	NM_006622.3	545	Cac/Aac	12/14	1	2	FACETS	0.677	0.539	0.834	0.677	0.539	0.834	SUBCLONAL	1	TRUE	1	0.23	2		440	347	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80071530	80071530	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	53	459	0	ENST00000265081.6:c.2271G>T	p.Lys757Asn	p.K757N	ENST00000265081	NM_002439.4	757	aaG/aaT	16/24	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.23	2		459	406	SUCCESS
APC	324	MSKCC	GRCh37	5	112174365	112174365	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	23	314	0	ENST00000257430.4:c.3074T>G	p.Ile1025Arg	p.I1025R	ENST00000257430	NM_000038.5	1025	aTa/aGa	16/16	1	2	FACETS	0.93	0.729	1	0.93	0.729	1	CLONAL	1	TRUE	1	0.23	2		314	215	SUCCESS
APC	324	MSKCC	GRCh37	5	112176881	112176881	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	33	486	0	ENST00000257430.4:c.5590T>G	p.Ser1864Ala	p.S1864A	ENST00000257430	NM_000038.5	1864	Tct/Gct	16/16	1	2	FACETS	0.738	0.601	0.891	0.738	0.601	0.891	SUBCLONAL	1	TRUE	1	0.23	2		486	389	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722414	176722414	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	28	416	0	ENST00000439151.2:c.8045A>G	p.Asn2682Ser	p.N2682S	ENST00000439151	NM_022455.4	2682	aAc/aGc	23/23	1	2	FACETS	0.649	0.519	0.798	0.649	0.519	0.798	SUBCLONAL	1	TRUE	1	0.23	2		416	375	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672744	30672744	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	66	796	0	ENST00000376406.3:c.4216A>G	p.Thr1406Ala	p.T1406A	ENST00000376406	NM_014641.2	1406	Aca/Gca	10/15	1	2	FACETS	0.809	0.702	0.926	0.809	0.702	0.926	CLONAL	1	TRUE	1	0.23	2		796	709	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184750	32184750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	28	600	0	ENST00000375023.3:c.1833C>A	p.Phe611Leu	p.F611L	ENST00000375023	NM_004557.3	611	ttC/ttA	11/30	1	2	FACETS	0.444	0.354	0.548	0.444	0.354	0.548	SUBCLONAL	1	TRUE	1	0.23	2		600	548	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109322568	109322568	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	64	721	0	ENST00000436639.2:c.469T>G	p.Phe157Val	p.F157V	ENST00000436639	NM_014454.2	157	Ttc/Gtc	3/10	1	2	FACETS	0.92	0.797	1	0.92	0.797	1	CLONAL	1	TRUE	1	0.23	2		721	605	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112025283	112025283	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	51	539	2	ENST00000368678.4:c.466C>T	p.Arg156Ter	p.R156*	ENST00000368678		156	Cga/Tga	6/13	1	2	FACETS	0.786	0.668	0.916	0.786	0.668	0.916	CLONAL	1	TRUE	1	0.23	2		541	564	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631430	117631430	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	43	393	0	ENST00000368508.3:c.6248G>T	p.Arg2083Ile	p.R2083I	ENST00000368508	NM_002944.2	2083	aGa/aTa	40/43	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.23	2		393	331	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662568	117662568	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	33	495	1	ENST00000368508.3:c.4897T>A	p.Leu1633Ile	p.L1633I	ENST00000368508	NM_002944.2	1633	Tta/Ata	29/43	1	2	FACETS	0.813	0.663	0.981	0.813	0.663	0.981	CLONAL	1	TRUE	1	0.23	2		496	353	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026525	6026525	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	88	792	1	ENST00000265849.7:c.1871C>A	p.Ser624Tyr	p.S624Y	ENST00000265849	NM_000535.5	624	tCt/tAt	11/15	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.23	2		793	684	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520104	106520104	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	21	305	0	ENST00000359195.3:c.2532T>G	p.Ile844Met	p.I844M	ENST00000359195	NM_002649.2	844	atT/atG	6/11	1	2	FACETS	0.808	0.624	1	0.808	0.624	1	CLONAL	1	TRUE	1	0.23	2		305	226	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412192	116412192	+	intron_variant	Intron	SNP	T	T	C	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	80	774	0	ENST00000397752.3:c.3028+149T>C		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.23	2		774	570	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850267	128850267	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	34	803	0	ENST00000249373.3:c.1530G>T	p.Lys510Asn	p.K510N	ENST00000249373	NM_005631.4	510	aaG/aaT	9/12	1	2	FACETS	0.454	0.37	0.549	0.454	0.37	0.549	SUBCLONAL	1	TRUE	1	0.23	2		803	651	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891323	151891323	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	44	481	0	ENST00000262189.6:c.4531A>C	p.Lys1511Gln	p.K1511Q	ENST00000262189	NM_170606.2	1511	Aaa/Caa	30/59	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.23	2		481	367	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942834	68942834	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	76	605	1	ENST00000288368.4:c.646A>G	p.Arg216Gly	p.R216G	ENST00000288368	NM_024870.2	216	Aga/Gga	6/40	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.23	2		606	593	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978485	70978485	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs112783392	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	40	445	0	ENST00000276594.2:c.1168T>C	p.Ser390Pro	p.S390P	ENST00000276594	NM_024504.3	390	Tct/Cct	5/8	1	2	FACETS	1	0.84	1	1	0.84	1	CLONAL	1	TRUE	1	0.23	2		445	345	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862899	117862899	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	41	633	0	ENST00000297338.2:c.1578G>T	p.Glu526Asp	p.E526D	ENST00000297338	NM_006265.2	526	gaG/gaT	12/14	1	2	FACETS	0.785	0.654	0.931	0.785	0.654	0.931	CLONAL	1	TRUE	1	0.23	2		633	454	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141582991	141582991	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	77	672	0	ENST00000220592.5:c.256A>C	p.Ile86Leu	p.I86L	ENST00000220592	NM_012154.3	86	Atc/Ctc	3/19	1	2	FACETS	0.983	0.863	1	0.983	0.863	1	CLONAL	1	TRUE	1	0.23	2		672	681	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5064889	5064889	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	26	398	0	ENST00000381652.3:c.1063G>T	p.Glu355Ter	p.E355*	ENST00000381652	NM_004972.3	355	Gaa/Taa	9/25	1	2	FACETS	0.785	0.623	0.97	0.785	0.623	0.97	CLONAL	1	TRUE	1	0.23	2		398	288	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080593	5080593	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	38	550	0	ENST00000381652.3:c.2344A>C	p.Asn782His	p.N782H	ENST00000381652	NM_004972.3	782	Aac/Cac	18/25	1	2	FACETS	0.91	0.754	1	0.91	0.754	1	CLONAL	1	TRUE	1	0.23	2		550	363	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319913	8319913	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	42	446	1	ENST00000356435.5:c.5588G>T	p.Arg1863Ile	p.R1863I	ENST00000356435		1863	aGa/aTa	34/35	1	2	FACETS	0.849	0.71	1	0.849	0.71	1	CLONAL	1	TRUE	1	0.23	2		447	430	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465575	8465575	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	54	709	0	ENST00000356435.5:c.3605A>C	p.Glu1202Ala	p.E1202A	ENST00000356435		1202	gAg/gCg	21/35	1	2	FACETS	0.852	0.728	0.988	0.852	0.728	0.988	CLONAL	1	TRUE	1	0.23	2		709	551	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471012	8471012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	27	527	0	ENST00000356435.5:c.3487G>T	p.Glu1163Ter	p.E1163*	ENST00000356435		1163	Gaa/Taa	20/35	1	2	FACETS	0.541	0.43	0.668	0.541	0.43	0.668	SUBCLONAL	1	TRUE	1	0.23	2		527	434	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484366	8484366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	29	464	1	ENST00000356435.5:c.3166G>T	p.Asp1056Tyr	p.D1056Y	ENST00000356435		1056	Gat/Tat	19/35	1	2	FACETS	0.766	0.616	0.937	0.766	0.616	0.937	CLONAL	1	TRUE	1	0.23	2		465	329	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202956	27202956	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	69	615	0	ENST00000380036.4:c.2048A>C	p.Gln683Pro	p.Q683P	ENST00000380036	NM_000459.3	683	cAg/cCg	13/23	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.23	2		615	537	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229599	98229599	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	47	508	0	ENST00000331920.6:c.2359G>T	p.Glu787Ter	p.E787*	ENST00000331920	NM_000264.3	787	Gaa/Taa	15/24	1	2	FACETS	0.896	0.757	1	0.896	0.757	1	CLONAL	1	TRUE	1	0.23	2		508	456	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849193	76849193	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557082310	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	28	466	1	ENST00000373344.5:c.6083G>A	p.Arg2028Gln	p.R2028Q	ENST00000373344	NM_000489.3	2028	cGa/cAa	26/35	1	2	FACETS	0.791	0.633	0.969	0.791	0.633	0.969	CLONAL	1	TRUE	1	0.23	2		467	308	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855047	76855047	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	35	476	0	ENST00000373344.5:c.5789A>C	p.Lys1930Thr	p.K1930T	ENST00000373344	NM_000489.3	1930	aAg/aCg	25/35	1	2	FACETS	0.991	0.815	1	0.991	0.815	1	CLONAL	1	TRUE	1	0.23	2		476	307	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872174	76872174	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	49	554	0	ENST00000373344.5:c.5473A>C	p.Lys1825Gln	p.K1825Q	ENST00000373344	NM_000489.3	1825	Aaa/Caa	22/35	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.23	2		554	398	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611778	100611778	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	60	573	0	ENST00000308731.7:c.1343T>C	p.Val448Ala	p.V448A	ENST00000308731	NM_000061.2	448	gTc/gCc	14/19	1	2	FACETS	0.906	0.781	1	0.906	0.781	1	CLONAL	1	TRUE	1	0.23	2		573	576	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626652	100626652	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1569295678	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	40	542	1	ENST00000308731.7:c.278C>A	p.Ser93Ter	p.S93*	ENST00000308731	NM_000061.2	93	tCa/tAa	4/19	1	2	FACETS	0.809	0.673	0.96	0.809	0.673	0.96	CLONAL	1	TRUE	1	0.23	2		543	430	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182891	123182891	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	39	450	0	ENST00000218089.9:c.856A>C	p.Asn286His	p.N286H	ENST00000218089	NM_001042749.1	286	Aat/Cat	10/35	1	2	FACETS	0.815	0.676	0.97	0.815	0.676	0.97	CLONAL	1	TRUE	1	0.23	2		450	416	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185164	123185164	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	41	552	0	ENST00000218089.9:c.1117-1G>T		p.X373_splice	ENST00000218089	NM_001042749.1	373			1	2	FACETS	0.896	0.747	1	0.896	0.747	1	CLONAL	1	TRUE	1	0.23	2		552	398	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197029	123197029	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	32	632	0	ENST00000218089.9:c.1795A>G	p.Ile599Val	p.I599V	ENST00000218089	NM_001042749.1	599	Ata/Gta	19/35	1	2	FACETS	0.674	0.547	0.817	0.674	0.547	0.817	SUBCLONAL	1	TRUE	1	0.23	2		632	413	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205096	123205096	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	43	736	0	ENST00000218089.9:c.2456C>A	p.Ser819Tyr	p.S819Y	ENST00000218089	NM_001042749.1	819	tCt/tAt	25/35	1	2	FACETS	0.84	0.704	0.991	0.84	0.704	0.991	CLONAL	1	TRUE	1	0.23	2		736	445	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861584	152861584	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	62	712	1	ENST00000406277.2:c.168C>A	p.Phe56Leu	p.F56L	ENST00000406277	NM_152274.4	56	ttC/ttA	4/7	1		FACETS		0.781	1				CLONAL	1	TRUE	1	0.23	2		713	596	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221995	1221995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201090	NA	P-0035197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	77	521	0	ENST00000326873.7:c.910C>T	p.Arg304Trp	p.R304W	ENST00000326873	NM_000455.4	304	Cgg/Tgg	7/10	NA	2	FACETS	1	0.963	1			1	INDETERMINATE	1	TRUE	NA	0.17	2		521	721	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390793	139390793	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	83	684	0	ENST00000277541.6:c.7398del	p.Ser2467ArgfsTer10	p.S2467Rfs*10	ENST00000277541	NM_017617.3	2466	acG/ac	34/34	1	2	FACETS	0.88	0.774	0.994	0.88	0.774	0.994	CLONAL	1	TRUE	1	0.17	2		684	1110	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399474	139399474	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	122	672	0	ENST00000277541.6:c.4669G>T	p.Asp1557Tyr	p.D1557Y	ENST00000277541	NM_017617.3	1557	Gac/Tac	26/34	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.17	2		672	1235	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0035227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	351	551	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.590567785951253	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.595793284571083	2		551	576	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020768	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs926053251	NA	P-0035227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	152	345	0	ENST00000358127.4:c.77T>G	p.Val26Gly	p.V26G	ENST00000358127	NM_001280556.1	26	gTt/gGt	2/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.595793284571083	2		345	477	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087503	27087503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	237	566	0	ENST00000324856.7:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000324856	NM_006015.4	693	Cga/Tga	5/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.595793284571083	2		566	763	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445001	49445027	+	inframe_deletion	In_Frame_Del	DEL	GGCTCCTCAGGCACAGGAGACAGGTGC	GGCTCCTCAGGCACAGGAGACAGGTGC	-	rs1451648935	NA	P-0035227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	104	415	0	ENST00000301067.7:c.2439_2465del	p.His814_Pro822del	p.H814_P822del	ENST00000301067	NM_003482.3	813	ccGCACCTGTCTCCTGTGCCTGAGGAGCCa/cca	10/54	1	2	FACETS	0.657	0.591	0.728	0.657	0.591	0.728	SUBCLONAL	1	TRUE	1	0.595793284571083	2		415	531	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376076	225376076	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	165	397	0	ENST00000264414.4:c.878C>G	p.Thr293Arg	p.T293R	ENST00000264414	NM_003590.4	293	aCa/aGa	6/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.595793284571083	2		397	470	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111498	8111502	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGA	GAGGA	-	novel	NA	P-0035277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	254	513	0	ENST00000346208.3:c.985_989del	p.Arg329GlufsTer21	p.R329Efs*21	ENST00000346208		328	tgGAGGAgg/tggg	5/6	0.173037902220542	1	FACETS	0.978	0.92	1	0.978	0.92	1	INDETERMINATE	1	TRUE	0	0.513275193841152	1		513	752	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441259	52441259	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	54	459	0	ENST00000460680.1:c.511G>T	p.Val171Phe	p.V171F	ENST00000460680	NM_004656.3	171	Gtc/Ttc	7/17	0.466057917222975	1	FACETS	0.418	0.358	0.483	0.418	0.358	0.483	SUBCLONAL	1	TRUE	0	0.513275193841152	1		459	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0035288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	162	230	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.22286918533727	2	FACETS	0.833	0.768	0.9	0.833	0.768	0.9	CLONAL	2	FALSE	0	0.332316402355399	2		231	585	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14303198	14303198	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	40	536	0	ENST00000256196.4:c.477G>T	p.Lys159Asn	p.K159N	ENST00000256196		159	aaG/aaT	5/6	0.327006271440522	3	FACETS	0.622	0.517	0.739	0.207	0.172	0.247	SUBCLONAL	1	FALSE	0	0.332316402355399	3		536	451	SUCCESS
APC	324	MSKCC	GRCh37	5	112175483	112175483	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	38	279	0	ENST00000257430.4:c.4192del	p.Ser1398ValfsTer17	p.S1398Vfs*17	ENST00000257430	NM_000038.5	1398	Agt/gt	16/16	0.066079434369408	4	FACETS	1	0.837	1	0.504	0.419	0.6	INDETERMINATE	1	FALSE	2	0.332316402355399	4		279	302	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075673	8075673	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	34	326	0	ENST00000377482.5:c.7A>T	p.Ile3Leu	p.I3L	ENST00000377482	NM_018948.3	3	Ata/Tta	2/4	0.22286918533727	2	FACETS	0.544	0.445	0.656	0.272	0.222	0.328	SUBCLONAL	1	FALSE	0	0.332316402355399	2		326	376	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508443	29508443	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	19	236	0	ENST00000356175.3:c.590C>T	p.Thr197Ile	p.T197I	ENST00000356175	NM_000267.3	197	aCa/aTa	6/57	0.066079434369408	4	FACETS	0.729	0.555	0.932	0.364	0.277	0.466	INDETERMINATE	1	FALSE	2	0.332316402355399	4		236	209	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533458	63533458	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	283	543	0	ENST00000307078.5:c.1696C>T	p.Pro566Ser	p.P566S	ENST00000307078	NM_004655.3	566	Ccc/Tcc	6/11	0.066079434369408	4	FACETS	0.888	0.837	0.94	1	0.992	1	INDETERMINATE	3	FALSE	2	0.332316402355399	4		543	852	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542897	187542898	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	AGGATCA	novel	NA	P-0035288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	14	262	0	ENST00000441802.2:c.4836_4842dup	p.Val1615Ter	p.V1615*	ENST00000441802	NM_005245.3	1614	-/TGATCCT	10/27	0.152206747915301	3	FACETS	0.387	0.279	0.517	0.193	0.139	0.259	INDETERMINATE	1	FALSE	1	0.332316402355399	3		262	254	SUCCESS
APC	324	MSKCC	GRCh37	5	112116598	112116598	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs137854577	NA	P-0035288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	20	234	0	ENST00000257430.4:c.643C>T	p.Gln215Ter	p.Q215*	ENST00000257430	NM_000038.5	215	Cag/Tag	6/16	0.066079434369408	4	FACETS	1	0.849	1	0.569	0.439	0.717	INDETERMINATE	1	FALSE	2	0.332316402355399	4		234	141	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0035473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	251	230	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.541063860441187	1	FACETS	0.98	0.923	1	0.98	0.923	1	CLONAL	1	TRUE	0	0.569559414399248	1		231	643	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118784	115118784	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	493	679	0	ENST00000257566.3:c.557T>G	p.Ile186Ser	p.I186S	ENST00000257566	NM_016569.3	186	aTt/aGt	2/8	0.558090373743575	2	FACETS	0.931	0.896	0.965	0.931	0.896	0.965	CLONAL	2	TRUE	0	0.569559414399248	2		679	930	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857632	78857632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753964006	NA	P-0035473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1231	368	862	0	ENST00000306801.3:c.1702G>A	p.Asp568Asn	p.D568N	ENST00000306801	NM_020761.2	568	Gac/Aac	16/34	0.569559414399248	3	FACETS	1	0.971	1	0.519	0.491	0.548	CLONAL	1	TRUE	1	0.569559414399248	3		862	1599	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484634	57484634	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	188	598	0	ENST00000371085.3:c.718G>A	p.Asp240Asn	p.D240N	ENST00000371085	NM_000516.4	240	Gat/Aat	9/13	1	2	FACETS	0.83	0.769	0.894	0.83	0.769	0.894	CLONAL	1	TRUE	1	0.569559414399248	2		598	795	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188202	10188202	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	330	678	0	ENST00000256474.2:c.346del	p.Leu116PhefsTer43	p.L116Ffs*43	ENST00000256474	NM_000551.3	115	caC/ca	2/3	0.569559414399248	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.569559414399248	1		678	753	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643962	52643962	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	132	397	0	ENST00000394830.3:c.1934G>T	p.Ser645Ile	p.S645I	ENST00000394830	NM_018313.4	645	aGt/aTt	17/30	0.569559414399248	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.569559414399248	1		397	297	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294111	1294111	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	277	1100	0	ENST00000310581.5:c.890C>G	p.Pro297Arg	p.P297R	ENST00000310581	NM_198253.2	297	cCa/cGa	2/16	1	2	FACETS	0.707	0.662	0.753	0.707	0.662	0.753	SUBCLONAL	1	TRUE	1	0.569559414399248	2		1100	1376	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591102	67591113	+	inframe_deletion	In_Frame_Del	DEL	CATTAAACCAGA	CATTAAACCAGA	-	novel	NA	P-0035473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	61	232	0	ENST00000274335.5:c.1696_1707del	p.Ile566_Asp569del	p.I566_D569del	ENST00000274335		565	agCATTAAACCAGAc/agc	12/15	0.528053776769242	1	FACETS	0.774	0.679	0.873	0.774	0.679	0.873	SUBCLONAL	1	TRUE	0	0.569559414399248	1		232	198	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637615	176637615	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	111	616	0	ENST00000439151.2:c.2215G>T	p.Val739Phe	p.V739F	ENST00000439151	NM_022455.4	739	Gtt/Ttt	5/23	0.124766434117131	4	FACETS	0.671	0.602	0.744	0.335	0.301	0.372	INDETERMINATE	1	TRUE	2	0.569559414399248	4		616	912	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782201	135782201	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	98	453	0	ENST00000298552.3:c.1355del	p.Gly452ValfsTer5	p.G452Vfs*5	ENST00000298552	NM_001162426.1	452	gGt/gt	14/23	0.541063860441187	1	FACETS	0.912	0.826	1	0.912	0.826	1	CLONAL	1	TRUE	0	0.569559414399248	1		453	270	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0035518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	353	398	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.183956490962577	3	FACETS	1	0.991	1	1	0.991	1	INDETERMINATE	2	TRUE	1	0.56736759733886	3		398	701	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115712	8115712	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	62	253	0	ENST00000346208.3:c.1058C>A	p.Pro353His	p.P353H	ENST00000346208		353	cCc/cAc	6/6	1	2	FACETS	0.881	0.77	0.999	0.881	0.77	0.999	CLONAL	1	TRUE	1	0.56736759733886	2		253	248	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953965	32953965	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	51	342	1	ENST00000380152.3:c.9032T>G	p.Leu3011Arg	p.L3011R	ENST00000380152		3011	cTt/cGt	23/27	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.56736759733886	2		343	154	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603622	48604644	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTAAAATTGAACTGTGTGCCAGGTTTCACACTGATGGGGAATTTTTTACTGCAGAGTTAAACTCCTGACTATAGACTTTTATGATGGAAACACGTGGCACCCATCTTCCACGTCTGAAGGCATAACTAGTGATTCATTCAACCCCTGTTCTTAACCTCTTCAGTGTGGTAAGCAAATCACACTGGCTAAGAAAACTGCAGTGGCCCTGCAGGTTTCTCTACAGTACATGCAAATTCCTCCCATTAGTTTCATTGTAATATTGATGAATGCAGATGGACTATATGACTGTATGTTCTGACTGGAAAATTAGATGCAGTCTCCATTGTGACTTATGTTCAGGAGTTTACAATTTAGAGGTAGATTAGGCATATTCATTGAGAGAATTTGATTTTTTAAAATTTGGGGTGATACCATTAATTTGCTGGTTTCAGTGTTATAAACATGCTTTTACTGAAGAATCCAGAACTATTATTAAGTTTCATATTCTCATCAGTTGCCACCACTGAGTAATAGTGTATTACTCTGTTACACTTTGAAATTGAGAGAGAGACTTCATCTCGGTCATCTAAGAGGTCTTAGTGGAACTAAGAATATTAACTGCTTCATTATTAGTTATGTCTTATTCTGAACTAGGCTGTTTAGACAGTAAGGTTTTTAGAAGCAACCTGTGGACACGCACTACCTCTTAAAAACAAGTTGTTTCTTATCCCTTCACCTCCACTTCTAAAGAAAAAAATAGGTGAGGTGTTGGTGGATTGTGGTAATTTACTTTATAATTGGTTGTAGCTAGAAGACACATGTGAAATGTAAAGTTCCTTAACCAAAAGTGTGCAGCTTGTTGATAAAGTTTAGATCTACTGTTACTTCTTGGCACTTTAGCAGAGAAGTTATATGCTGAGGAGAATGAAATACAGAAAGCTGGTCACTTGATTAATTTAGAATGTAGGGAGGATGGGAAGAGATCACCCTGTCCCTCTGATGTCTTCCAAATCTTTTCTGTTAGGTCTGTCAGCTGCTGCTGG	GGTAAAATTGAACTGTGTGCCAGGTTTCACACTGATGGGGAATTTTTTACTGCAGAGTTAAACTCCTGACTATAGACTTTTATGATGGAAACACGTGGCACCCATCTTCCACGTCTGAAGGCATAACTAGTGATTCATTCAACCCCTGTTCTTAACCTCTTCAGTGTGGTAAGCAAATCACACTGGCTAAGAAAACTGCAGTGGCCCTGCAGGTTTCTCTACAGTACATGCAAATTCCTCCCATTAGTTTCATTGTAATATTGATGAATGCAGATGGACTATATGACTGTATGTTCTGACTGGAAAATTAGATGCAGTCTCCATTGTGACTTATGTTCAGGAGTTTACAATTTAGAGGTAGATTAGGCATATTCATTGAGAGAATTTGATTTTTTAAAATTTGGGGTGATACCATTAATTTGCTGGTTTCAGTGTTATAAACATGCTTTTACTGAAGAATCCAGAACTATTATTAAGTTTCATATTCTCATCAGTTGCCACCACTGAGTAATAGTGTATTACTCTGTTACACTTTGAAATTGAGAGAGAGACTTCATCTCGGTCATCTAAGAGGTCTTAGTGGAACTAAGAATATTAACTGCTTCATTATTAGTTATGTCTTATTCTGAACTAGGCTGTTTAGACAGTAAGGTTTTTAGAAGCAACCTGTGGACACGCACTACCTCTTAAAAACAAGTTGTTTCTTATCCCTTCACCTCCACTTCTAAAGAAAAAAATAGGTGAGGTGTTGGTGGATTGTGGTAATTTACTTTATAATTGGTTGTAGCTAGAAGACACATGTGAAATGTAAAGTTCCTTAACCAAAAGTGTGCAGCTTGTTGATAAAGTTTAGATCTACTGTTACTTCTTGGCACTTTAGCAGAGAAGTTATATGCTGAGGAGAATGAAATACAGAAAGCTGGTCACTTGATTAATTTAGAATGTAGGGAGGATGGGAAGAGATCACCCTGTCCCTCTGATGTCTTCCAAATCTTTTCTGTTAGGTCTGTCAGCTGCTGCTGG	-	novel	NA	P-0035518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2	81	0	0	ENST00000342988.3:c.1447+476_1466del		p.X483_splice	ENST00000342988	NM_005359.5	483		12/12	0.56736759733886	1	FACETS	1	0.99	1	1	0.991	1	CLONAL	2	TRUE	0	0.56736759733886	1		0	83	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260186	149260186	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1319845181	NA	P-0035518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	272	496	1	ENST00000360632.3:c.707G>A	p.Arg236Gln	p.R236Q	ENST00000360632	NM_015472.4	236	cGg/cAg	4/7	0.46793189924347	3	FACETS	1	0.993	1	0.727	0.685	0.771	CLONAL	1	TRUE	1	0.56736759733886	3		497	846	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821404	32821404	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	268	595	0	ENST00000354258.4:c.190T>G	p.Ser64Ala	p.S64A	ENST00000354258	NM_000593.5	64	Tct/Gct	1/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.56736759733886	2		595	919	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39935769	39935769	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	194	508	0	ENST00000378444.4:c.103G>C	p.Asp35His	p.D35H	ENST00000378444	NM_001123385.1	35	Gat/Cat	3/15	NA	2	FACETS	1	0.948	1			1	INDETERMINATE	1	TRUE	NA	0.56736759733886	2		508	668	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045946	47045946	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	252	567	0	ENST00000377604.3:c.2741A>C	p.Tyr914Ser	p.Y914S	ENST00000377604	NM_001204468.1	914	tAc/tCc	24/24	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.56736759733886	2		567	820	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057520000	NA	P-0035556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	332	823	0	ENST00000269305.4:c.452C>A	p.Pro151His	p.P151H	ENST00000269305	NM_001126112.2	151	cCc/cAc	5/11	0.546703136178232	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.546703136178232	1		823	772	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031999	26031999	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1411351920	NA	P-0035556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	43	423	0	ENST00000244661.2:c.290G>C	p.Cys97Ser	p.C97S	ENST00000244661	NM_003537.3	97	tGt/tCt	1/1	1	2	FACETS	0.358	0.3	0.423	0.358	0.3	0.423	SUBCLONAL	1	TRUE	1	0.546703136178232	2		423	439	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168617	32168618	+	missense_variant	Missense_Mutation	DNP	CA	CA	AC	novel	NA	P-0035556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	148	536	1	ENST00000375023.3:c.4305_4306delinsGT	p.His1435_Ala1436delinsGlnSer	p.H1435_A1436delinsQS	ENST00000375023	NM_004557.3	1435	caTGca/caGTca	23/30	1	2	FACETS	0.849	0.778	0.922	0.849	0.778	0.922	CLONAL	1	TRUE	1	0.546703136178232	2		537	638	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243903	53243903	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	271	772	0	ENST00000375401.3:c.1090G>T	p.Gly364Cys	p.G364C	ENST00000375401	NM_004187.3	364	Ggt/Tgt	8/26	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.546703136178232	2		772	915	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	373	406	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	1	TRUE	NA	0.647851863750696	2		406	872	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0035577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	578	835	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.647851863750696	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.647851863750696	1		835	1175	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625652	1625652	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs533848977	NA	P-0035577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	261	850	1	ENST00000344749.5:c.422C>T	p.Ser141Leu	p.S141L	ENST00000344749	NM_001136139.2	141	tCg/tTg	7/19	0.387658330050404	1	FACETS	0.4	0.373	0.427	0.4	0.373	0.427	INDETERMINATE	1	TRUE	0	0.647851863750696	1		851	1363	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535316	66535316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	340	624	4	ENST00000273854.3:c.145G>A	p.Ala49Thr	p.A49T	ENST00000273854	NM_004439.5	49	Gca/Aca	1/18	0.647851863750696	1	FACETS	0.891	0.848	0.935	0.891	0.848	0.935	CLONAL	1	TRUE	0	0.647851863750696	1		628	796	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076813	72076813	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	396	367	1	ENST00000357731.5:c.684G>T	p.Gln228His	p.Q228H	ENST00000357731	NM_173808.2	228	caG/caT	5/7	0.647851863750696	2	FACETS	0.958	0.922	0.993	0.958	0.922	0.993	CLONAL	2	TRUE	0	0.647851863750696	2		368	638	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610010	81610010	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	196	340	0	ENST00000298171.2:c.1608G>C	p.Arg536Ser	p.R536S	ENST00000298171	NM_000369.2	536	agG/agC	10/10	0.387658330050404	1	FACETS	0.773	0.722	0.826	0.773	0.722	0.826	INDETERMINATE	1	TRUE	0	0.647851863750696	1		340	529	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972491	81972491	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	153	463	0	ENST00000359376.3:c.3284A>C	p.Asp1095Ala	p.D1095A	ENST00000359376	NM_002661.3	1095	gAc/gCc	29/33	1	2	FACETS	0.479	0.438	0.522	0.479	0.438	0.522	SUBCLONAL	1	TRUE	1	0.647851863750696	2		463	986	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663777	29663777	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555534696	NA	P-0035577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	395	677	0	ENST00000356175.3:c.6209A>G	p.Asn2070Ser	p.N2070S	ENST00000356175	NM_000267.3	2070	aAc/aGc	41/57	0.647851863750696	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.647851863750696	1		677	780	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851709	134851709	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373296912	NA	P-0035577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	265	509	0	ENST00000398015.3:c.1115G>A	p.Arg372His	p.R372H	ENST00000398015	NM_004441.4	372	cGc/cAc	5/16	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.647851863750696	2		509	677	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001287	150001287	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	281	611	0	ENST00000253339.5:c.2317C>T	p.Gln773Ter	p.Q773*	ENST00000253339		773	Caa/Taa	4/7	0.647851863750696	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.647851863750696	1		611	550	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0035619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	135	230	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.353166786021263	1	FACETS	0.916	0.835	1	0.916	0.835	1	CLONAL	1	TRUE	0	0.353166786021263	1		231	687	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0035619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	47	407	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	1	2	FACETS	0.557	0.47	0.653	0.557	0.47	0.653	SUBCLONAL	1	TRUE	1	0.353166786021263	2		407	478	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446313	187446313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137878288	NA	P-0035619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	75	594	0	ENST00000232014.4:c.1375C>T	p.Arg459Cys	p.R459C	ENST00000232014	NM_001130845.1	459	Cgc/Tgc	6/10	1	2	FACETS	0.676	0.593	0.766	0.676	0.593	0.766	SUBCLONAL	1	TRUE	1	0.353166786021263	2		594	628	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391881	139391881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1307220376	NA	P-0035619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	84	568	0	ENST00000277541.6:c.6310C>T	p.Arg2104Cys	p.R2104C	ENST00000277541	NM_017617.3	2104	Cgc/Tgc	34/34	0.353166786021263	1	FACETS	0.624	0.551	0.701	0.624	0.551	0.701	SUBCLONAL	1	TRUE	0	0.353166786021263	1		568	628	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0035619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	35	387	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	0.463	0.379	0.557	0.463	0.379	0.557	SUBCLONAL	1	TRUE	1	0.353166786021263	2		387	428	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086076	16086076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760647298	NA	P-0035619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	70	540	0	ENST00000281043.3:c.1252G>A	p.Ala418Thr	p.A418T	ENST00000281043	NM_005378.4	418	Gcc/Acc	3/3	NA	2	FACETS	0.824	0.72	0.936			1	INDETERMINATE	1	TRUE	NA	0.353166786021263	2		540	481	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907654	111907654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141962978	NA	P-0035619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	100	447	0	ENST00000393256.3:c.428G>A	p.Arg143His	p.R143H	ENST00000393256	NM_006538.4	143	cGc/cAc	3/4	1	2	FACETS	0.903	0.808	1	0.903	0.808	1	CLONAL	1	TRUE	1	0.353166786021263	2		447	627	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685515	29685516	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1555536882	NA	P-0035619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	62	339	0	ENST00000356175.3:c.7926dup	p.Lys2643Ter	p.K2643*	ENST00000356175	NM_000267.3	2642	tct/tcTt	54/57	0.353166786021263	1	FACETS	0.831	0.722	0.948	0.831	0.722	0.948	CLONAL	1	TRUE	0	0.353166786021263	1		339	348	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65349020	65349020	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754991396	NA	P-0035619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	97	462	0	ENST00000342505.4:c.145C>T	p.Arg49Trp	p.R49W	ENST00000342505	NM_002227.2	49	Cgg/Tgg	3/25	1	2	FACETS	0.836	0.746	0.932	0.836	0.746	0.932	CLONAL	1	TRUE	1	0.353166786021263	2		462	657	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851903	63851903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776160603	NA	P-0035619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	63	482	4	ENST00000279873.7:c.2681C>T	p.Ser894Leu	p.S894L	ENST00000279873	NM_032199.2	894	tCg/tTg	10/10	0.353166786021263	5	FACETS	0.728	0.628	0.836			1	SUBCLONAL	1	TRUE	NA	0.353166786021263	5		486	750	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641054	3641054	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143558209	NA	P-0035619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	129	813	0	ENST00000294008.3:c.2585G>A	p.Arg862Gln	p.R862Q	ENST00000294008	NM_032444.2	862	cGa/cAa	12/15	1	2	FACETS	0.839	0.76	0.922	0.839	0.76	0.922	CLONAL	1	TRUE	1	0.353166786021263	2		813	871	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853277	68853277	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	112	540	0	ENST00000261769.5:c.1660G>T	p.Glu554Ter	p.E554*	ENST00000261769	NM_004360.3	554	Gag/Tag	11/16	0.353166786021263	1	FACETS	0.985	0.89	1	0.985	0.89	1	CLONAL	1	TRUE	0	0.353166786021263	1		540	530	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81957192	81957192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1216454496	NA	P-0035619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	55	524	0	ENST00000359376.3:c.2410G>A	p.Gly804Arg	p.G804R	ENST00000359376	NM_002661.3	804	Ggg/Agg	22/33	0.353166786021263	1	FACETS	0.521	0.446	0.603	0.521	0.446	0.603	SUBCLONAL	1	TRUE	0	0.353166786021263	1		524	492	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419875	152419875	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	47	495	0	ENST00000206249.3:c.1562G>T	p.Gly521Val	p.G521V	ENST00000206249	NM_000125.3	521	gGc/gTc	8/8	1	2	FACETS	0.452	0.381	0.531	0.452	0.381	0.531	SUBCLONAL	1	TRUE	1	0.353166786021263	2		495	589	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443583	52443584	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTGA	novel	NA	P-0035719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	89	423	0	ENST00000460680.1:c.105_108dup	p.Lys38GlufsTer32	p.K38Efs*32	ENST00000460680	NM_004656.3	36	-/TCAG	3/17	0.296481591804095	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.26	1		423	557	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374302	138374302	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs992990404	NA	P-0035719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	200	556	0	ENST00000289153.2:c.3142G>T	p.Ala1048Ser	p.A1048S	ENST00000289153	NM_006219.2	1048	Gcg/Tcg	22/22	0.232103057914899	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.26	4		556	917	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547349	106547349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	100	396	0	ENST00000369096.4:c.586C>T	p.Leu196Phe	p.L196F	ENST00000369096	NM_001198.3	196	Ctt/Ttt	4/7	0.296481591804095	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.26	1		396	587	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508490	106508490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	110	220	0	ENST00000359195.3:c.484G>A	p.Val162Ile	p.V162I	ENST00000359195	NM_002649.2	162	Gtc/Atc	2/11	1	2	FACETS	0.876	0.8	0.952	0.876	0.8	0.952	CLONAL	1	TRUE	1	0.930463759547088	2		220	270	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864513	57864513	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	102	680	0	ENST00000228682.2:c.1990C>A	p.His664Asn	p.H664N	ENST00000228682	NM_005269.2	664	Cat/Aat	12/12	1	2	FACETS	0.311	0.278	0.346	0.311	0.278	0.346	SUBCLONAL	1	TRUE	1	0.930463759547088	2		680	706	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593717	215593717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	163	345	0	ENST00000260947.4:c.2017G>A	p.Asp673Asn	p.D673N	ENST00000260947	NM_000465.2	673	Gat/Aat	11/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.930463759547088	2		345	326	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131951761	131951761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	80	244	0	ENST00000265335.6:c.3103G>A	p.Glu1035Lys	p.E1035K	ENST00000265335		1035	Gaa/Aaa	20/25	0.342879870727784	1	FACETS	0.442	0.397	0.489	0.442	0.397	0.489	INDETERMINATE	1	TRUE	0	0.930463759547088	1		244	208	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510102	149510102	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	259	713	0	ENST00000261799.4:c.1367G>A	p.Arg456Lys	p.R456K	ENST00000261799	NM_002609.3	456	aGg/aAg	9/23	0.342879870727784	1	FACETS	0.578	0.548	0.608	0.578	0.548	0.608	INDETERMINATE	1	TRUE	0	0.930463759547088	1		713	515	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465637	99465637	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	115	473	0	ENST00000268035.6:c.2462T>A	p.Val821Asp	p.V821D	ENST00000268035	NM_000875.3	821	gTc/gAc	11/21	1	2	FACETS	0.958	0.868	1	0.958	0.868	1	CLONAL	1	TRUE	1	0.503476525506294	2		473	477	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161259	185161259	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	197	669	0	ENST00000265026.3:c.686A>C	p.Tyr229Ser	p.Y229S	ENST00000265026	NM_004721.4	229	tAt/tCt	4/14	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.503476525506294	2		669	747	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0035841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	353	546	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	1	2	FACETS	1	0.991	1	1	0.997	1	CLONAL	2	FALSE	1	0.336183587838977	2		546	890	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0035963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	97	784	1	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	0.528986099105419	2	FACETS	1	0.972	1	0.601	0.544	0.661	CLONAL	1	FALSE	0	0.584429634905575	2		785	276	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223614	36223614	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	56	1055	0	ENST00000222270.7:c.6169del	p.Arg2057AlafsTer34	p.R2057Afs*34	ENST00000222270	NM_014727.1	2055	gCc/gc	28/37	1	2	FACETS	0.608	0.524	0.699	0.608	0.524	0.699	SUBCLONAL	1	FALSE	1	0.584429634905575	2		1055	315	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654725	29654725	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs878853902	NA	P-0035963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	48	415	0	ENST00000356175.3:c.5414A>G	p.His1805Arg	p.H1805R	ENST00000356175	NM_000267.3	1805	cAt/cGt	37/57	0.528986099105419	2	FACETS	0.505	0.429	0.589	0.253	0.214	0.295	SUBCLONAL	1	FALSE	0	0.584429634905575	2		415	325	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638534	176638534	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1359539320	NA	P-0035963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	177	797	2	ENST00000439151.2:c.3134G>A	p.Arg1045His	p.R1045H	ENST00000439151	NM_022455.4	1045	cGt/cAt	5/23	0.466189173035975	2	FACETS	1	0.99	1	0.698	0.65	0.746	CLONAL	1	FALSE	0	0.584429634905575	2		799	434	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28931822	28931822	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	88	421	0	ENST00000282397.4:c.2117del	p.Gly706GlufsTer4	p.G706Efs*4	ENST00000282397	NM_002019.4	706	gGa/ga	15/30	0.771198293693912	4	FACETS	0.783	0.696	0.876			1	SUBCLONAL	1	TRUE	NA	0.771198293693912	4		421	516	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988430	41988430	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	140	601	0	ENST00000219905.7:c.1222G>C	p.Asp408His	p.D408H	ENST00000219905	NM_001164273.1	408	Gat/Cat	3/24	0.232110212329452	4	FACETS	0.851	0.784	0.919	0.851	0.784	0.919	INDETERMINATE	2	TRUE	2	0.771198293693912	4		601	378	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853197	68853197	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	112	564	0	ENST00000261769.5:c.1580G>A	p.Arg527Lys	p.R527K	ENST00000261769	NM_004360.3	527	aGa/aAa	11/16	0.771198293693912	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.771198293693912	1		564	174	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828513	72828513	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	37	867	0	ENST00000268489.5:c.8068C>T	p.Gln2690Ter	p.Q2690*	ENST00000268489	NM_006885.3	2690	Cag/Tag	9/10	0.771198293693912	1	FACETS	0.264	0.219	0.314	0.264	0.219	0.314	SUBCLONAL	1	TRUE	0	0.771198293693912	1		867	223	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0036018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	32	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.532	0.431	0.648	0.532	0.431	0.648	SUBCLONAL	1	TRUE	1	0.17	2		436	707	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194859	29194859	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	58	931	1	ENST00000240100.2:c.869T>A	p.Ile290Asn	p.I290N	ENST00000240100	NM_001394.6	290	aTc/aAc	4/4	1	2	FACETS	0.92	0.789	1	0.92	0.789	1	CLONAL	1	TRUE	1	0.17	2		932	742	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0036026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	434	537	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.218514753982395	4	FACETS	0.951	0.921	0.981			1	INDETERMINATE	4	TRUE	NA	0.571758743083327	4		537	627	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0036026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	90	403	1	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	0.577679341617991	2	FACETS	0.828	0.754	0.904	0.828	0.754	0.904	CLONAL	2	TRUE	0	0.571758743083327	2		404	190	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331723	8331723	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367558329	NA	P-0036026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	84	563	0	ENST00000356435.5:c.5393G>A	p.Arg1798Gln	p.R1798Q	ENST00000356435		1798	cGa/cAa	33/35	0.578180368622999	1	FACETS	0.739	0.66	0.821	0.739	0.66	0.821	SUBCLONAL	1	TRUE	0	0.571758743083327	1		563	284	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38173513	38173513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	92	711	0	ENST00000317025.8:c.1903C>T	p.Arg635Cys	p.R635C	ENST00000317025	NM_023034.1	635	Cgc/Tgc	10/24	NA	2	FACETS	0.694	0.619	0.772			1	INDETERMINATE	1	TRUE	NA	0.571758743083327	2		711	464	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851612	128851612	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs757625155	NA	P-0036026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	47	839	1	ENST00000249373.3:c.1936+1G>A		p.X646_splice	ENST00000249373	NM_005631.4	646			0.568806160931034	3	FACETS	0.531	0.449	0.621	0.266	0.224	0.311	SUBCLONAL	1	TRUE	1	0.571758743083327	3		840	398	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532681	46532681	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201330473	NA	P-0036026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	70	561	1	ENST00000262741.5:c.397G>A	p.Val133Met	p.V133M	ENST00000262741	NM_003629.3	133	Gtg/Atg	4/10	NA	2	FACETS	0.71	0.623	0.802			1	INDETERMINATE	1	TRUE	NA	0.571758743083327	2		562	345	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998441	100998441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	30	473	0	ENST00000325455.5:c.1361C>T	p.Ser454Leu	p.S454L	ENST00000325455	NM_001202474.3	454	tCg/tTg	1/8	0.510489172654678	0	FACETS	0.314	0.257	0.378			1	SUBCLONAL	1	TRUE	0	0.571758743083327	0		473	143	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375779	118375779	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	777	645	0	ENST00000534358.1:c.9172G>A	p.Gly3058Ser	p.G3058S	ENST00000534358	NM_005933.3	3058	Ggc/Agc	27/36	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	2	TRUE	NA	0.571758743083327	2		645	1195	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955049	93955049	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs374288532	NA	P-0036026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	76	425	0	ENST00000369303.4:c.2849A>G	p.Asn950Ser	p.N950S	ENST00000369303	NM_004440.3	950	aAt/aGt	16/17	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.571758743083327	2		425	220	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591104	67591115	+	inframe_deletion	In_Frame_Del	DEL	TTAAACCAGACC	TTAAACCAGACC	-	novel	NA	P-0036178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	263	350	0	ENST00000274335.5:c.1700_1711del	p.Lys567_Leu570del	p.K567_L570del	ENST00000274335		566	aTTAAACCAGACCtt/att	12/15	0.735118621015226	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	2	0.735118621015226	4		350	614	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023168	27023184	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGGCCCGGCGCGGA	GGCGGGCCCGGCGCGGA	-	novel	NA	P-0036178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	213	66	0	ENST00000324856.7:c.275_291del	p.Gly92AlafsTer13	p.G92Afs*13	ENST00000324856	NM_006015.4	92	GGCGGGCCCGGCGCGGAg/g	1/20	0.313712594273237	3	FACETS	1	0.994	1	1	0.994	1	INDETERMINATE	3	TRUE	0	0.735118621015226	3		66	234	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653830	206653830	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	269	655	0	ENST00000367120.3:c.1381G>T	p.Ala461Ser	p.A461S	ENST00000367120	NM_014002.3	461	Gca/Tca	13/22	0.735118621015226	4	FACETS	1	0.945	1	0.252	0.236	0.269	CLONAL	1	TRUE	0	0.735118621015226	4		655	1258	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444665	187444665	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs560242782	NA	P-0036178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	259	441	0	ENST00000232014.4:c.1562A>G	p.Asn521Ser	p.N521S	ENST00000232014	NM_001130845.1	521	aAt/aGt	7/10	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.735118621015226	2		441	500	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0036283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	133	406	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.47515262449947	3	FACETS	0.747	0.677	0.819	0.373	0.338	0.41	SUBCLONAL	1	TRUE	1	0.47515262449947	3		406	928	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0036283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	133	305	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	NA	2	FACETS	0.818	0.745	0.896			1	INDETERMINATE	1	TRUE	NA	0.47515262449947	2		305	684	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876545	59876545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748105919	NA	P-0036283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	109	555	0	ENST00000259008.2:c.1256G>A	p.Arg419Gln	p.R419Q	ENST00000259008	NM_032043.2	419	cGg/cAg	9/20	1	2	FACETS	0.772	0.695	0.854	0.772	0.695	0.854	SUBCLONAL	1	TRUE	1	0.47515262449947	2		555	594	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410598	63410598	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1394000391	NA	P-0036283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	179	785	0	ENST00000330258.3:c.2569C>T	p.Arg857Ter	p.R857*	ENST00000330258	NM_152424.3	857	Cga/Tga	2/2	0.47515262449947	1	FACETS	0.803	0.743	0.866	0.803	0.743	0.866	CLONAL	1	TRUE	0	0.47515262449947	1		785	715	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941900	71941900	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	150	685	0	ENST00000298229.2:c.1258G>T	p.Glu420Ter	p.E420*	ENST00000298229	NM_001567.3	420	Gag/Tag	11/28	NA	2	FACETS	0.893	0.818	0.971			1	INDETERMINATE	1	TRUE	NA	0.47515262449947	2		685	707	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368212	45368212	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	180	411	0	ENST00000262160.6:c.1390del	p.Ser464GlnfsTer16	p.S464Qfs*16	ENST00000262160	NM_005901.5	464	Tca/ca	11/11	0.364001789636325	2	FACETS	0.811	0.755	0.868	0.811	0.755	0.868	CLONAL	2	TRUE	0	0.47515262449947	2		411	467	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391539	84391539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	78	379	0	ENST00000321945.7:c.293G>A	p.Gly98Asp	p.G98D	ENST00000321945	NM_139076.2	98	gGt/gAt	5/9	1	2	FACETS	0.739	0.652	0.832	0.739	0.652	0.832	SUBCLONAL	1	TRUE	1	0.47515262449947	2		379	444	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894994	101894994	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	62	302	1	ENST00000374994.4:c.547G>T	p.Asp183Tyr	p.D183Y	ENST00000374994	NM_004612.2	183	Gat/Tat	3/9	1	2	FACETS	0.667	0.579	0.763	0.667	0.579	0.763	SUBCLONAL	1	TRUE	1	0.47515262449947	2		303	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0036315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	348	230	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.517168848434674	3	FACETS	0.933	0.894	0.972	0.933	0.894	0.972	CLONAL	3	FALSE	0	0.517168848434674	3		231	605	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434142	49434142	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057518571	NA	P-0036315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	99	748	0	ENST00000301067.7:c.7411C>T	p.Arg2471Ter	p.R2471*	ENST00000301067	NM_003482.3	2471	Cga/Tga	31/54	0.517168848434674	6	FACETS	0.936	0.835	1	0.312	0.278	0.348	CLONAL	1	FALSE	3	0.517168848434674	6		748	832	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499487	89499487	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	70	504	0	ENST00000336596.2:c.2657G>T	p.Gly886Val	p.G886V	ENST00000336596	NM_005233.5	886	gGc/gTc	15/17	0.413617609523931	5	FACETS	0.811	0.707	0.922	0.27	0.235	0.308	CLONAL	1	FALSE	2	0.517168848434674	5		504	593	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297952	15297952	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	210	856	0	ENST00000263388.2:c.1804G>T	p.Asp602Tyr	p.D602Y	ENST00000263388	NM_000435.2	602	Gac/Tac	11/33	0.476325800499054	4	FACETS	1	0.991	1	0.494	0.46	0.53	CLONAL	1	FALSE	1	0.517168848434674	4		856	831	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289106	33289106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776829106	NA	P-0036315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	493	757	1	ENST00000374542.5:c.446C>T	p.Ala149Val	p.A149V	ENST00000374542	NM_001141970.1	149	gCc/gTc	3/8	0.517168848434674	6	FACETS	0.923	0.886	0.959	0.923	0.886	0.959	CLONAL	4	FALSE	2	0.517168848434674	6		758	1051	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465553	8465553	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	78	659	0	ENST00000356435.5:c.3627G>C	p.Lys1209Asn	p.K1209N	ENST00000356435		1209	aaG/aaC	21/35	0.436866672041385	5	FACETS	0.675	0.592	0.764	0.169	0.148	0.191	SUBCLONAL	1	FALSE	1	0.517168848434674	5		659	794	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298117	15298117	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	176	749	0	ENST00000263388.2:c.1639G>C	p.Asp547His	p.D547H	ENST00000263388	NM_000435.2	547	Gac/Cac	11/33	0.476325800499054	4	FACETS	1	0.989	1	0.471	0.435	0.508	CLONAL	1	FALSE	1	0.517168848434674	4		749	731	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448686	49448686	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	84	480	0	ENST00000301067.7:c.173G>T	p.Cys58Phe	p.C58F	ENST00000301067	NM_003482.3	58	tGc/tTc	2/54	0.517168848434674	6	FACETS	0.961	0.848	1	0.32	0.282	0.361	CLONAL	1	FALSE	3	0.517168848434674	6		480	688	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0036378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	175	584	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.213808477649579	2	FACETS	1	0.985	1	0.636	0.587	0.686	INDETERMINATE	1	TRUE	0	0.392161965931517	2		584	702	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs104886003	NA	P-0036378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	190	514	0	ENST00000263967.3:c.1633G>C	p.Glu545Gln	p.E545Q	ENST00000263967	NM_006218.2	545	Gag/Cag	10/21	0.111802726623283	4	FACETS	0.857	0.794	0.922	0.857	0.794	0.922	INDETERMINATE	2	TRUE	2	0.392161965931517	4		514	787	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838389	156838389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1357016517	NA	P-0036378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	55	753	0	ENST00000524377.1:c.667G>A	p.Glu223Lys	p.E223K	ENST00000524377	NM_002529.3	223	Gag/Aag	6/17	1	2	FACETS	0.316	0.269	0.367	0.316	0.269	0.367	SUBCLONAL	1	TRUE	1	0.392161965931517	2		753	888	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227019	2227019	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	118	643	0	ENST00000398665.3:c.4499C>G	p.Ser1500Cys	p.S1500C	ENST00000398665	NM_032482.2	1500	tCt/tGt	27/28	0.392161965931517	1	FACETS	0.643	0.581	0.71	0.643	0.581	0.71	SUBCLONAL	1	TRUE	0	0.392161965931517	1		643	752	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675071	40675071	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	63	621	0	ENST00000249776.8:c.35T>G	p.Val12Gly	p.V12G	ENST00000249776	NM_033286.3	12	gTt/gGt	1/9	0.392161965931517	1	FACETS	0.399	0.344	0.458	0.399	0.344	0.458	SUBCLONAL	1	TRUE	0	0.392161965931517	1		621	648	SUCCESS
APC	324	MSKCC	GRCh37	5	112177488	112177488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	19	286	0	ENST00000257430.4:c.6197G>A	p.Arg2066Lys	p.R2066K	ENST00000257430	NM_000038.5	2066	aGa/aAa	16/16	1	2	FACETS	0.33	0.25	0.423	0.33	0.25	0.423	SUBCLONAL	1	TRUE	1	0.392161965931517	2		286	294	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028623	12028623	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	26	314	0	ENST00000353533.5:c.826G>T	p.Asp276Tyr	p.D276Y	ENST00000353533	NM_003010.3	276	Gac/Tac	8/11	0.213808477649579	2	FACETS	0.369	0.292	0.458	0.185	0.146	0.229	INDETERMINATE	1	TRUE	0	0.392161965931517	2		314	359	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120929	115120939	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGCCCGGTG	GGCGCCCGGTG	-	novel	NA	P-0036378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	135	457	0	ENST00000257566.3:c.67_77del	p.His23GlyfsTer84	p.H23Gfs*84	ENST00000257566	NM_016569.3	23	CACCGGGCGCCg/g	1/8	0.321120024847948	2	FACETS	1	0.986	1	0.704	0.644	0.766	CLONAL	1	TRUE	0	0.392161965931517	2		457	489	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226024	133226024	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	62	703	0	ENST00000320574.5:c.3873G>C	p.Lys1291Asn	p.K1291N	ENST00000320574	NM_006231.2	1291	aaG/aaC	31/49	0.321120024847948	2	FACETS	0.464	0.4	0.533	0.232	0.2	0.267	SUBCLONAL	1	TRUE	0	0.392161965931517	2		703	682	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061385	38061385	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	95	592	0	ENST00000250448.2:c.604G>T	p.Asp202Tyr	p.D202Y	ENST00000250448	NM_004496.3	202	Gac/Tac	2/2	0.273693605937552	3	FACETS	0.766	0.681	0.855	0.255	0.227	0.285	SUBCLONAL	1	TRUE	0	0.392161965931517	3		592	757	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134383	30134383	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	141	658	1	ENST00000263025.4:c.148G>A	p.Glu50Lys	p.E50K	ENST00000263025	NM_002746.2	50	Gag/Aag	1/9	0.292633118723252	1	FACETS	0.62	0.565	0.679	0.62	0.565	0.679	SUBCLONAL	1	TRUE	0	0.392161965931517	1		659	932	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950277	15950277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1325864679	NA	P-0036378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	62	613	2	ENST00000268712.3:c.6667G>A	p.Asp2223Asn	p.D2223N	ENST00000268712	NM_006311.3	2223	Gac/Aac	42/46	0.213808477649579	2	FACETS	0.473	0.408	0.543	0.236	0.204	0.272	INDETERMINATE	1	TRUE	0	0.392161965931517	2		615	669	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325702	30325702	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	32	191	0	ENST00000322652.5:c.1900C>G	p.His634Asp	p.H634D	ENST00000322652	NM_015355.2	634	Cat/Gat	16/16	0.381564673363168	2	FACETS	0.533	0.434	0.645	0.267	0.217	0.323	SUBCLONAL	1	TRUE	0	0.392161965931517	2		191	306	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589249	67589249	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	14	198	0	ENST00000274335.5:c.1237del	p.Leu413Ter	p.L413*	ENST00000274335		413	Cta/ta	9/15	1	2	FACETS	0.268	0.194	0.359	0.268	0.194	0.359	SUBCLONAL	1	TRUE	1	0.392161965931517	2		198	266	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020880	26020880	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	37	279	0	ENST00000357647.3:c.163T>C	p.Tyr55His	p.Y55H	ENST00000357647	NM_003529.2	55	Tat/Cat	1/1	1	2	FACETS	0.581	0.48	0.692	0.581	0.48	0.692	SUBCLONAL	1	TRUE	1	0.392161965931517	2		279	325	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900251	101900251	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	100	314	0	ENST00000374994.4:c.685G>T	p.Val229Phe	p.V229F	ENST00000374994	NM_004612.2	229	Gtt/Ttt	4/9	0.28264518049547	2	FACETS	1	0.979	1	0.68	0.612	0.75	CLONAL	1	TRUE	0	0.392161965931517	2		314	375	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	355	993	1	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.419949330708502	3	FACETS	0.941	0.893	0.991	0.941	0.893	0.991	CLONAL	2	TRUE	1	0.421576052871232	3		994	1083	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	119	660	3	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	0.421576052871232	2		663	476	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	69	299	0	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	0.421576052871232	2		299	310	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	65	425	1	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	0.382769070205025	3	FACETS	1	0.958	1	0.618	0.54	0.701	CLONAL	1	TRUE	1	0.421576052871232	3		426	302	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429978	78429978	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	62	372	0	ENST00000370768.2:c.901del	p.Ile301TyrfsTer22	p.I301Yfs*22	ENST00000370768	NM_003902.3	301	Ata/ta	11/20	1	2	FACETS	0.853	0.741	0.973	0.853	0.741	0.973	CLONAL	1	TRUE	1	0.421576052871232	2		372	345	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	107	507	2	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.421576052871232	2		509	428	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	42	321	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.421576052871232	2		321	190	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777838	3777838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863223334	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	303	989	1	ENST00000262367.5:c.7210G>A	p.Glu2404Lys	p.E2404K	ENST00000262367	NM_004380.2	2404	Gaa/Aaa	31/31	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.421576052871232	2		990	1285	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480483	57480483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	110	302	0	ENST00000371085.3:c.478C>T	p.Arg160Cys	p.R160C	ENST00000371085	NM_000516.4	160	Cgt/Tgt	6/13	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.421576052871232	2		302	457	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534473	187534473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	83	314	0	ENST00000441802.2:c.9253del	p.Asp3086IlefsTer30	p.D3086Ifs*30	ENST00000441802	NM_005245.3	3085	Ctt/tt	13/27	1	2	FACETS	0.972	0.863	1	0.972	0.863	1	CLONAL	1	TRUE	1	0.421576052871232	2		314	405	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424734	47424734	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	166	244	1	ENST00000377045.4:c.547del	p.Gln183ArgfsTer109	p.Q183Rfs*109	ENST00000377045	NM_001654.4	181	aCc/ac	6/16	1	1	FACETS	0.863	0.805	0.922	1	0.992	1	CLONAL	2	TRUE	0	0.421576052871232	1		245	360	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120115	70120115	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	41	156	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	0.421576052871232	2		156	161	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201816	66201816	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556854839	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	117	429	0	ENST00000273854.3:c.2686C>T	p.Arg896Cys	p.R896C	ENST00000273854	NM_004439.5	896	Cgt/Tgt	16/18	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.421576052871232	2		429	521	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058747	180058748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755445139	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	130	604	3	ENST00000261937.6:c.89dup	p.Thr31AspfsTer15	p.T31Dfs*15	ENST00000261937	NM_182925.4	30	ccg/ccCg	2/30	1	2	FACETS	0.829	0.753	0.909	0.829	0.753	0.909	CLONAL	1	TRUE	1	0.421576052871232	2		607	744	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416952	416953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs771545848	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	199	454	6	ENST00000399788.2:c.3597dup	p.Gly1200ArgfsTer7	p.G1200Rfs*7	ENST00000399788	NM_001042603.1	1199	-/A	23/28	NA	2	FACETS	0.769	0.716	0.823			1	INDETERMINATE	2	TRUE	NA	0.421576052871232	2		460	614	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032120	10032120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	165	618	0	ENST00000330684.3:c.703G>A	p.Glu235Lys	p.E235K	ENST00000330684	NM_001134407.1	235	Gag/Aag	3/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.421576052871232	2		618	631	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	105	976	4	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	NA	2	FACETS	0.811	0.728	0.899			1	INDETERMINATE	1	TRUE	NA	0.421576052871232	2		980	614	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118934	70118934	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	217	815	0	ENST00000245479.2:c.506A>G	p.His169Arg	p.H169R	ENST00000245479	NM_000346.3	169	cAc/cGc	2/3	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.421576052871232	2		815	991	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228998	36228998	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	206	790	3	ENST00000222270.7:c.7778G>A	p.Arg2593His	p.R2593H	ENST00000222270	NM_014727.1	2593	cGc/cAc	36/37	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.421576052871232	2		793	930	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639398	3639398	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748691881	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	203	680	1	ENST00000294008.3:c.4241del	p.Pro1414HisfsTer36	p.P1414Hfs*36	ENST00000294008	NM_032444.2	1414	cCa/ca	12/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.421576052871232	2		681	796	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026137	36026137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1464185975	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	272	824	1	ENST00000358208.4:c.739G>A	p.Val247Met	p.V247M	ENST00000358208		247	Gtg/Atg	7/12	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.421576052871232	2		825	1093	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746101	162746101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374058699	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	110	316	1	ENST00000367921.3:c.2224C>T	p.Arg742Trp	p.R742W	ENST00000367921	NM_006182.2	742	Cgg/Tgg	16/18	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.421576052871232	2		317	386	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651576	206651576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339859715	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	267	712	0	ENST00000367120.3:c.886G>A	p.Asp296Asn	p.D296N	ENST00000367120	NM_014002.3	296	Gac/Aac	9/22	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.421576052871232	2		712	1048	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076801	102076801	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781457667	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	227	636	0	ENST00000282441.5:c.980G>A	p.Arg327Gln	p.R327Q	ENST00000282441	NM_001130145.2	327	cGg/cAg	5/9	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.421576052871232	2		636	864	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435499	18435499	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs762601548	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	59	208	0	ENST00000266497.5:c.484A>G	p.Asn162Asp	p.N162D	ENST00000266497		162	Aat/Gat	1/31	NA	2	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.421576052871232	2		208	202	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515143	103515143	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	71	290	0	ENST00000355739.4:c.1644A>T	p.Glu548Asp	p.E548D	ENST00000355739	NM_000123.3	548	gaA/gaT	8/15	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.421576052871232	2		290	292	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89851374	89851374	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	112	380	0	ENST00000389301.3:c.1360-2A>G		p.X454_splice	ENST00000389301	NM_000135.2	454			1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.421576052871232	2		380	501	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562776	29562776	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	106	428	0	ENST00000356175.3:c.3856A>G	p.Thr1286Ala	p.T1286A	ENST00000356175	NM_000267.3	1286	Aca/Gca	28/57	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.421576052871232	2		428	388	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533767	63533767	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	169	560	0	ENST00000307078.5:c.1387del	p.Arg463AlafsTer44	p.R463Afs*44	ENST00000307078	NM_004655.3	463	Cgc/gc	6/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.421576052871232	2		560	642	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144104	11144104	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	215	688	0	ENST00000358026.2:c.3685A>G	p.Ile1229Val	p.I1229V	ENST00000358026	NM_001128849.1	1229	Atc/Gtc	26/36	1	2	FACETS	0.988	0.918	1	0.988	0.918	1	CLONAL	1	TRUE	1	0.421576052871232	2		688	1032	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169029	11169029	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1400097305	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	180	567	0	ENST00000358026.2:c.4619A>G	p.Lys1540Arg	p.K1540R	ENST00000358026	NM_001128849.1	1540	aAg/aGg	32/36	1	2	FACETS	0.996	0.92	1	0.996	0.92	1	CLONAL	1	TRUE	1	0.421576052871232	2		567	857	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735326	204735326	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	70	229	0	ENST00000302823.3:c.127C>T	p.Pro43Ser	p.P43S	ENST00000302823	NM_005214.4	43	Cct/Tct	2/4	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.421576052871232	2		229	272	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456493	89456493	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	90	429	0	ENST00000336596.2:c.1669A>G	p.Thr557Ala	p.T557A	ENST00000336596	NM_005233.5	557	Act/Gct	8/17	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.421576052871232	2		429	400	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751463	57751463	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	97	378	0	ENST00000274289.3:c.1528T>C	p.Tyr510His	p.Y510H	ENST00000274289	NM_006622.3	510	Tac/Cac	11/14	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.421576052871232	2		378	424	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80063861	80063861	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372048303	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	94	489	1	ENST00000265081.6:c.2006G>A	p.Arg669Gln	p.R669Q	ENST00000265081	NM_002439.4	669	cGg/cAg	14/24	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.421576052871232	2		490	364	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813388	32813388	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs780766118	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	322	909	0	ENST00000354258.4:c.2395A>G	p.Met799Val	p.M799V	ENST00000354258	NM_000593.5	799	Atg/Gtg	11/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.421576052871232	2		909	1350	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821466	32821466	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	168	646	0	ENST00000354258.4:c.128G>T	p.Arg43Leu	p.R43L	ENST00000354258	NM_000593.5	43	cGg/cTg	1/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.421576052871232	2		646	747	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715449	117715449	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780553416	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	64	350	0	ENST00000368508.3:c.1040C>T	p.Ala347Val	p.A347V	ENST00000368508	NM_002944.2	347	gCg/gTg	10/43	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.421576052871232	2		350	268	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543573	148543573	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388815758	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	100	407	1	ENST00000320356.2:c.235G>A	p.Gly79Arg	p.G79R	ENST00000320356	NM_004456.4	79	Ggg/Agg	3/20	1	2	FACETS	0.976	0.876	1	0.976	0.876	1	CLONAL	1	TRUE	1	0.421576052871232	2		408	486	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981725	70981725	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	411	905	2	ENST00000276594.2:c.371C>T	p.Ala124Val	p.A124V	ENST00000276594	NM_024504.3	124	gCc/gTc	2/8	0.382769070205025	3	FACETS	0.956	0.91	1	0.956	0.91	1	CLONAL	2	TRUE	1	0.421576052871232	3		907	1235	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376086	8376086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	130	269	0	ENST00000356435.5:c.4511G>A	p.Gly1504Asp	p.G1504D	ENST00000356435		1504	gGt/gAt	28/35	0.421576052871232	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.421576052871232	2		269	268	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411963	63411963	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	190	437	0	ENST00000330258.3:c.1204G>T	p.Glu402Ter	p.E402*	ENST00000330258	NM_152424.3	402	Gaa/Taa	2/2	1	1	FACETS	0.887	0.832	0.943	1	0.993	1	CLONAL	2	TRUE	0	0.421576052871232	1		437	401	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	291	439	0	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.705282959575088	2		439	822	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227982	53227982	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1556840029	NA	P-0036383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	819	475	0	ENST00000375401.3:c.2332C>T	p.Arg778Ter	p.R778*	ENST00000375401	NM_004187.3	778	Cga/Tga	16/26	0.633228564462033	2	FACETS	1	0.998	1			1	CLONAL	2	TRUE	NA	0.705282959575088	2		475	1016	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857925	9857925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs534440095	NA	P-0036383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	625	676	1	ENST00000330684.3:c.3476G>A	p.Arg1159His	p.R1159H	ENST00000330684	NM_001134407.1	1159	cGc/cAc	13/13	0.651706371205689	3	FACETS	1	0.978	1			1	CLONAL	2	TRUE	NA	0.705282959575088	3		677	1182	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094981	11094981	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502103	NA	P-0036383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	416	1051	1	ENST00000358026.2:c.154G>A	p.Ala52Thr	p.A52T	ENST00000358026	NM_001128849.1	52	Gca/Aca	2/36	1	2	FACETS	0.914	0.871	0.959	0.914	0.871	0.959	CLONAL	1	TRUE	1	0.705282959575088	2		1052	1290	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443761	52443761	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0036383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	364	758	0	ENST00000460680.1:c.38-2A>T		p.X13_splice	ENST00000460680	NM_004656.3	13			0.700936196844302	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.705282959575088	1		758	665	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447423	187447423	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	334	787	0	ENST00000232014.4:c.770A>G	p.Asn257Ser	p.N257S	ENST00000232014	NM_001130845.1	257	aAt/aGt	5/10	1	2	FACETS	0.957	0.906	1	0.957	0.906	1	CLONAL	1	TRUE	1	0.705282959575088	2		787	990	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196491	106196491	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0036383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	194	388	0	ENST00000380013.4:c.4824T>A	p.Tyr1608Ter	p.Y1608*	ENST00000380013	NM_001127208.2	1608	taT/taA	11/11	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.705282959575088	2		388	545	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0036614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	37	450	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.336327656946466	1	FACETS	1	0.834	1	1	0.834	1	CLONAL	1	FALSE	0	0.336327656946466	1		451	183	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0036614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	368	1221	1	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.336327656946466	2	FACETS	0.975	0.932	1	1	0.996	1	CLONAL	3	FALSE	0	0.336327656946466	2		1222	748	SUCCESS
AR	367	MSKCC	GRCh37	X	66766348	66766348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	11	200	0	ENST00000374690.3:c.1360G>A	p.Gly454Arg	p.G454R	ENST00000374690	NM_000044.3	454	Ggg/Agg	1/8	1	2	FACETS	0.411	0.285	0.568	0.411	0.285	0.568	SUBCLONAL	1	FALSE	1	0.336327656946466	2		200	159	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94923018	94923018	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	86	486	0	ENST00000536441.1:c.450A>C	p.Gln150His	p.Q150H	ENST00000536441	NM_144665.3	150	caA/caC	4/10	1	2	FACETS	0.828	0.733	0.929	0.828	0.733	0.929	CLONAL	1	FALSE	1	0.336327656946466	2		486	618	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814153	76814153	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	63	217	0	ENST00000373344.5:c.6491G>T	p.Arg2164Met	p.R2164M	ENST00000373344	NM_000489.3	2164	aGg/aTg	29/35	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.336327656946466	2		217	278	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0036705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	290	559	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.684703652586876	1	FACETS	0.977	0.929	1	0.977	0.929	1	CLONAL	1	TRUE	0	0.684703652586876	1		559	570	SUCCESS
BLM	641	MSKCC	GRCh37	15	91306198	91306198	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0036705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	73	341	0	ENST00000355112.3:c.1885A>T	p.Lys629Ter	p.K629*	ENST00000355112	NM_000057.2	629	Aag/Tag	8/22	0.605243983469146	3	FACETS	0.542	0.475	0.614	0.181	0.158	0.205	SUBCLONAL	1	TRUE	0	0.684703652586876	3		341	528	SUCCESS
BLM	641	MSKCC	GRCh37	15	91306207	91306207	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	76	363	0	ENST00000355112.3:c.1894C>G	p.Gln632Glu	p.Q632E	ENST00000355112	NM_000057.2	632	Caa/Gaa	8/22	0.605243983469146	3	FACETS	0.526	0.461	0.594	0.175	0.153	0.198	SUBCLONAL	1	TRUE	0	0.684703652586876	3		363	567	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626101	12626101	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	172	410	0	ENST00000251849.4:c.1859C>T	p.Ala620Val	p.A620V	ENST00000251849	NM_002880.3	620	gCt/gTt	17/17	1	2	FACETS	0.95	0.88	1	0.95	0.88	1	CLONAL	1	TRUE	1	0.684703652586876	2		410	529	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534285	534285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894226	NA	P-0036788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	84	586	0	ENST00000451590.1:c.38G>T	p.Gly13Val	p.G13V	ENST00000451590	NM_001130442.1	13	gGt/gTt	2/5	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.844785357879346	2		586	176	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0036788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	79	330	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.117571702468646	4	FACETS	0.958	0.864	1	0.958	0.864	1	INDETERMINATE	2	TRUE	2	0.844785357879346	4		330	180	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652020	36652020	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1407742055	NA	P-0036788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	14	731	0	ENST00000244741.5:c.142C>T	p.Arg48Ter	p.R48*	ENST00000244741	NM_000389.4	48	Cga/Tga	2/3	1	2	FACETS	0.119	0.086	0.16	0.119	0.086	0.16	SUBCLONAL	1	TRUE	1	0.844785357879346	2		731	278	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652005	36652005	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	26	691	0	ENST00000244741.5:c.127C>T	p.Gln43Ter	p.Q43*	ENST00000244741	NM_000389.4	43	Cag/Tag	2/3	1	2	FACETS	0.249	0.198	0.308	0.249	0.198	0.308	SUBCLONAL	1	TRUE	1	0.844785357879346	2		691	247	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646865	37646865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749022057	NA	P-0036788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	47	532	0	ENST00000447079.4:c.1987C>T	p.Arg663Cys	p.R663C	ENST00000447079	NM_015083.1	663	Cgt/Tgt	3/14	1	2	FACETS	0.433	0.368	0.503	0.433	0.368	0.503	SUBCLONAL	1	TRUE	1	0.844785357879346	2		532	257	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44733219	44733219	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	33	320	0	ENST00000377967.4:c.211G>T	p.Ala71Ser	p.A71S	ENST00000377967	NM_021140.2	71	Gcc/Tcc	2/29	1	2	FACETS	0.488	0.403	0.582	0.488	0.403	0.582	SUBCLONAL	1	TRUE	1	0.844785357879346	2		320	160	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481649	56481649	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	69	703	0	ENST00000267101.3:c.684T>G	p.His228Gln	p.H228Q	ENST00000267101	NM_001982.3	228	caT/caG	6/28	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		703	616	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18964144	18964144	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	18	449	0	ENST00000262803.5:c.1141A>G	p.Ile381Val	p.I381V	ENST00000262803	NM_002911.3	381	Atc/Gtc	8/24	0.176671071636699	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		449	357	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39746905	39746905	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	29	349	0	ENST00000361337.2:c.1919T>C	p.Phe640Ser	p.F640S	ENST00000361337	NM_003286.2	640	tTt/tCt	18/21	0.22153563883262	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		349	252	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725043	89725043	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1057517809	NA	P-0037899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	92	149	0	ENST00000371953.3:c.1027-1G>A		p.X343_splice	ENST00000371953	NM_000314.4	343			0.730104670051914	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.730104670051914	1		149	147	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058536	69058536	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61753703	NA	P-0037899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	202	369	0	ENST00000288368.4:c.4180C>T	p.Arg1394Trp	p.R1394W	ENST00000288368	NM_024870.2	1394	Cgg/Tgg	34/40	1	2	FACETS	0.888	0.828	0.95	0.888	0.828	0.95	CLONAL	1	TRUE	1	0.730104670051914	2		369	623	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128648	64128648	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	274	435	0	ENST00000334205.4:c.505C>A	p.Leu169Met	p.L169M	ENST00000334205	NM_003942.2	169	Ctg/Atg	5/17	1	2	FACETS	0.903	0.851	0.957	0.903	0.851	0.957	CLONAL	1	TRUE	1	0.730104670051914	2		435	831	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579584	7579585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0037988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	400	695	1	ENST00000269305.4:c.102dup	p.Pro36AlafsTer7	p.P36Afs*7	ENST00000269305	NM_001126112.2	34	-/C	4/11	0.464137668140665	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.464137668140665	3		696	672	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620539	52620539	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143085435	NA	P-0037988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	141	537	0	ENST00000394830.3:c.3214G>A	p.Val1072Met	p.V1072M	ENST00000394830	NM_018313.4	1072	Gtg/Atg	21/30	0.464137668140665	3	FACETS	1	0.952	1	0.532	0.486	0.581	CLONAL	1	TRUE	1	0.464137668140665	3		537	703	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0038090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	139	499	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.387555687214565	1	FACETS	0.918	0.838	1	0.918	0.838	1	CLONAL	1	TRUE	0	0.387555687214565	1		501	630	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	72	406	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.87	0.763	0.984	0.87	0.763	0.984	CLONAL	1	TRUE	1	0.387555687214565	2		406	427	SUCCESS
ALK	238	MSKCC	GRCh37	2	29473987	29473987	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	99	682	0	ENST00000389048.3:c.2188G>T	p.Ala730Ser	p.A730S	ENST00000389048	NM_004304.4	730	Gcc/Tcc	12/29	1	2	FACETS	0.817	0.731	0.909	0.817	0.731	0.909	CLONAL	1	TRUE	1	0.387555687214565	2		682	625	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782188	135782189	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554816245	NA	P-0038090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	82	429	0	ENST00000298552.3:c.1367dup	p.Ser457LysfsTer2	p.S457Kfs*2	ENST00000298552	NM_001162426.1	456	cta/ctTa	14/23	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.387555687214565	2		429	406	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696431	47696431	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	85	544	0	ENST00000347630.2:c.392G>T	p.Trp131Leu	p.W131L	ENST00000347630	NM_001007230.1	131	tGg/tTg	6/11	1	2	FACETS	0.943	0.834	1	0.943	0.834	1	CLONAL	1	TRUE	1	0.283595717168797	2		544	636	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371857	45371857	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0038160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	53	348	1	ENST00000262160.6:c.1136-2A>G		p.X379_splice	ENST00000262160	NM_005901.5	379			1	2	FACETS	0.971	0.831	1	0.971	0.831	1	CLONAL	1	TRUE	1	0.283595717168797	2		349	385	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498459	89498459	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	116	410	0	ENST00000336596.2:c.2431G>T	p.Gly811Trp	p.G811W	ENST00000336596	NM_005233.5	811	Ggg/Tgg	14/17	1	2	FACETS	0.946	0.857	1	0.946	0.857	1	CLONAL	1	TRUE	1	0.51198687984564	2		410	479	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217302	11217302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	44	574	0	ENST00000361445.4:c.4376C>A	p.Ala1459Asp	p.A1459D	ENST00000361445	NM_004958.3	1459	gCc/gAc	30/58	1	2	FACETS	0.694	0.581	0.819	0.694	0.581	0.819	SUBCLONAL	1	TRUE	1	0.23182219433074	2		574	547	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311619	15311621	+	inframe_deletion	In_Frame_Del	DEL	AGC	AGC	-	rs746497955	NA	P-0038275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	10	107	1	ENST00000263388.2:c.96_98del	p.Leu33del	p.L33del	ENST00000263388	NM_000435.2	32	ctGCTa/cta	1/33	1	2	FACETS	0.731	0.498	1	0.731	0.498	1	CLONAL	1	TRUE	1	0.23182219433074	2		108	118	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637546	52637546	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	21	238	0	ENST00000394830.3:c.2770G>T	p.Glu924Ter	p.E924*	ENST00000394830	NM_018313.4	924	Gaa/Taa	18/30	1	2	FACETS	0.959	0.742	1	0.959	0.742	1	CLONAL	1	TRUE	1	0.23182219433074	2		238	189	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466024	69466024	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	38	676	0	ENST00000227507.2:c.862A>C	p.Thr288Pro	p.T288P	ENST00000227507	NM_053056.2	288	Acc/Ccc	5/5	1	2	FACETS	0.563	0.465	0.674	0.563	0.465	0.674	SUBCLONAL	1	TRUE	1	0.23182219433074	2		676	582	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188250	10188250	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	52	504	0	ENST00000256474.2:c.394del	p.Gln132LysfsTer27	p.Q132Kfs*27	ENST00000256474	NM_000551.3	131	aaC/aa	2/3	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.23182219433074	2		504	437	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202635	67202635	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs202063609	NA	P-0038467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	204	439	0	ENST00000312629.5:c.1444C>A	p.Arg482Ser	p.R482S	ENST00000312629	NM_003952.2	482	Cgc/Agc	15/15	1	2	FACETS	0.892	0.828	0.957	0.892	0.828	0.957	CLONAL	1	TRUE	1	0.535190052641725	2		439	855	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41251864	41251864	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs886037976	NA	P-0038467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	283	370	0	ENST00000357654.3:c.475del	p.Gly160GlufsTer3	p.G160Efs*3	ENST00000357654	NM_007294.3	159	Ctt/tt	7/23	0.347517387410125	3	FACETS	0.963	0.911	1	0.963	0.911	1	CLONAL	2	TRUE	1	0.535190052641725	3		370	696	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043975	180043975	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	211	491	0	ENST00000261937.6:c.3021C>A	p.Ser1007Arg	p.S1007R	ENST00000261937	NM_182925.4	1007	agC/agA	22/30	1	2	FACETS	0.931	0.866	0.998	0.931	0.866	0.998	CLONAL	1	TRUE	1	0.535190052641725	2		491	847	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0038534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	274	422	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.778293162322144	3	FACETS	1	0.987	1			1	CLONAL	3	TRUE	NA	0.778293162322144	3		422	317	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983131	149983131	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1470913808	NA	P-0038534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	20	554	0	ENST00000253339.5:c.3127G>A	p.Asp1043Asn	p.D1043N	ENST00000253339		1043	Gat/Aat	7/7	0.717364085601789	1	FACETS	0.436	0.343	0.538	0.436	0.343	0.538	SUBCLONAL	1	TRUE	0	0.778293162322144	1		554	72	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729204	66729204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730880504	NA	P-0038534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	53	610	0	ENST00000307102.5:c.412G>A	p.Glu138Lys	p.E138K	ENST00000307102	NM_002755.3	138	Gag/Aag	3/11	1	2	FACETS	0.547	0.471	0.629	0.547	0.471	0.629	SUBCLONAL	1	TRUE	1	0.778293162322144	2		610	249	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258067	16258067	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	23	504	0	ENST00000375759.3:c.5332G>C	p.Asp1778His	p.D1778H	ENST00000375759	NM_015001.2	1778	Gac/Cac	11/15	0.778293162322144	3	FACETS	0.446	0.35	0.556	0.223	0.175	0.278	SUBCLONAL	1	TRUE	1	0.778293162322144	3		504	184	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001099	150001099	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	21	463	0	ENST00000253339.5:c.2505G>C	p.Leu835Phe	p.L835F	ENST00000253339		835	ttG/ttC	4/7	0.717364085601789	1	FACETS	0.485	0.385	0.592	0.485	0.385	0.592	SUBCLONAL	1	TRUE	0	0.778293162322144	1		463	68	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201891	102201891	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	34	348	0	ENST00000263464.3:c.1243G>C	p.Asp415His	p.D415H	ENST00000263464	NM_001165.4	415	Gat/Cat	6/9	0.778293162322144	3	FACETS	0.626	0.516	0.746	0.313	0.258	0.373	SUBCLONAL	1	TRUE	1	0.778293162322144	3		348	194	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574003	95574003	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	25	262	0	ENST00000393063.1:c.2746A>G	p.Lys916Glu	p.K916E	ENST00000393063	NM_030621.3	916	Aaa/Gaa	18/28	0.348265644291062	2	FACETS	0.564	0.452	0.687	0.282	0.226	0.344	INDETERMINATE	1	TRUE	0	0.778293162322144	2		262	114	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224237	53224237	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	12	807	0	ENST00000375401.3:c.3314G>T	p.Cys1105Phe	p.C1105F	ENST00000375401	NM_004187.3	1105	tGt/tTt	22/26	0.346196324031369	1	FACETS	0.111	0.078	0.151	0.111	0.078	0.151	INDETERMINATE	1	TRUE	0	0.778293162322144	1		807	170	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	54	428	2	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.679	0.58	0.787	0.679	0.58	0.787	SUBCLONAL	1	TRUE	1	0.3	2		430	530	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	93	993	1	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.551	0.488	0.618	0.551	0.488	0.618	SUBCLONAL	1	TRUE	1	0.3	2		994	1126	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291083	10291084	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755889652	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	81	752	1	ENST00000340748.4:c.387dup	p.Lys130GlnfsTer19	p.K130Qfs*19	ENST00000340748		129	-/C	4/40	1	2	FACETS	0.541	0.475	0.612	0.541	0.475	0.612	SUBCLONAL	1	TRUE	1	0.3	2		753	998	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	165	701	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	0.3	2		707	841	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	136	922	1	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.765	0.694	0.84	0.765	0.694	0.84	SUBCLONAL	1	TRUE	1	0.3	2		923	1185	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491355	2491355	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	97	853	0	ENST00000355716.4:c.398A>G	p.Asp133Gly	p.D133G	ENST00000355716	NM_003820.2	133	gAc/gGc	4/8	1	2	FACETS	0.576	0.512	0.645	0.576	0.512	0.645	SUBCLONAL	1	TRUE	1	0.3	2		853	1122	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199670	11199670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766533620	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	111	558	1	ENST00000361445.4:c.4918C>T	p.Arg1640Trp	p.R1640W	ENST00000361445	NM_004958.3	1640	Cgg/Tgg	35/58	1	2	FACETS	0.908	0.816	1	0.908	0.816	1	CLONAL	1	TRUE	1	0.3	2		559	815	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254717	16254717	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	84	624	0	ENST00000375759.3:c.1982G>T	p.Trp661Leu	p.W661L	ENST00000375759	NM_015001.2	661	tGg/tTg	11/15	1	2	FACETS	0.635	0.56	0.716	0.635	0.56	0.716	SUBCLONAL	1	TRUE	1	0.3	2		624	882	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	24	84	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	1	2	FACETS	0.964	0.763	1	0.964	0.763	1	CLONAL	1	TRUE	1	0.3	2		84	166	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087372	27087373	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	86	550	0	ENST00000324856.7:c.1950dup	p.Met651HisfsTer25	p.M651Hfs*25	ENST00000324856	NM_006015.4	649	ctc/ctCc	5/20	1	2	FACETS	0.722	0.638	0.812	0.722	0.638	0.812	SUBCLONAL	1	TRUE	1	0.3	2		550	794	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100862	27100862	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	89	527	0	ENST00000324856.7:c.4144A>G	p.Lys1382Glu	p.K1382E	ENST00000324856	NM_006015.4	1382	Aag/Gag	18/20	1	2	FACETS	0.801	0.71	0.898	0.801	0.71	0.898	CLONAL	1	TRUE	1	0.3	2		527	741	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46715736	46715736	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	138	586	1	ENST00000371975.4:c.155G>A	p.Arg52Gln	p.R52Q	ENST00000371975	NM_003579.3	52	cGg/cAg	3/18	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.3	2		587	729	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321194	65321194	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1409622807	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	51	331	0	ENST00000342505.4:c.1646G>A	p.Arg549Gln	p.R549Q	ENST00000342505	NM_002227.2	549	cGa/cAa	11/25	1	2	FACETS	0.612	0.519	0.713	0.612	0.519	0.713	SUBCLONAL	1	TRUE	1	0.3	2		331	556	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	32	516	1	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	1	2	FACETS	0.427	0.346	0.518	0.427	0.346	0.518	SUBCLONAL	1	TRUE	1	0.3	2		517	500	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115251216	115251216	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	68	500	0	ENST00000369535.4:c.510del	p.Lys170AsnfsTer19	p.K170Nfs*19	ENST00000369535	NM_002524.4	170	aaA/aa	5/7	1	2	FACETS	0.725	0.631	0.827	0.725	0.631	0.827	SUBCLONAL	1	TRUE	1	0.3	2		500	625	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491682	120491683	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	55	339	0	ENST00000256646.2:c.2546_2547del	p.Lys849ArgfsTer6	p.K849Rfs*6	ENST00000256646	NM_024408.3	849	aAA/a	16/34	0.187411459965699	1	FACETS	0.797	0.684	0.92	0.797	0.684	0.92	CLONAL	1	TRUE	0	0.3	1		339	391	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551757	150551757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs966392600	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	46	157	0	ENST00000369026.2:c.250G>A	p.Ala84Thr	p.A84T	ENST00000369026	NM_021960.4	84	Gcc/Acc	1/3	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.3	2		157	301	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648211	206648211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202128741	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	47	383	0	ENST00000367120.3:c.232G>A	p.Gly78Arg	p.G78R	ENST00000367120	NM_014002.3	78	Gga/Aga	5/22	1	2	FACETS	0.582	0.491	0.683	0.582	0.491	0.683	SUBCLONAL	1	TRUE	1	0.3	2		383	538	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333597	70333597	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	61	471	0	ENST00000373644.4:c.1502A>G	p.Lys501Arg	p.K501R	ENST00000373644	NM_030625.2	501	aAg/aGg	2/12	1	2	FACETS	0.618	0.533	0.711	0.618	0.533	0.711	SUBCLONAL	1	TRUE	1	0.3	2		471	658	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446447	70446447	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	85	436	0	ENST00000373644.4:c.5387C>T	p.Ser1796Leu	p.S1796L	ENST00000373644	NM_030625.2	1796	tCg/tTg	11/12	1	2	FACETS	0.914	0.809	1	0.914	0.809	1	CLONAL	1	TRUE	1	0.3	2		436	620	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88672029	88672029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749780872	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	107	421	1	ENST00000372037.3:c.563G>A	p.Arg188His	p.R188H	ENST00000372037	NM_004329.2	188	cGt/cAt	8/13	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.3	2		422	593	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741343	17741343	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	75	656	2	ENST00000250003.3:c.14C>T	p.Ser5Leu	p.S5L	ENST00000250003	NM_002478.4	5	tCg/tTg	1/3	1	2	FACETS	0.609	0.533	0.692	0.609	0.533	0.692	SUBCLONAL	1	TRUE	1	0.3	2		658	821	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741526	17741526	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	67	513	1	ENST00000250003.3:c.197C>A	p.Pro66His	p.P66H	ENST00000250003	NM_002478.4	66	cCc/cAc	1/3	1	2	FACETS	0.639	0.555	0.73	0.639	0.555	0.73	SUBCLONAL	1	TRUE	1	0.3	2		514	699	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138840	64138840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761347218	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	117	643	1	ENST00000334205.4:c.2207G>A	p.Arg736Gln	p.R736Q	ENST00000334205	NM_003942.2	736	cGg/cAg	17/17	1	2	FACETS	0.859	0.774	0.949	0.859	0.774	0.949	CLONAL	1	TRUE	1	0.3	2		644	908	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577330	64577333	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	rs587776841	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	105	749	0	ENST00000312049.6:c.249_252del	p.Ile85SerfsTer33	p.I85Sfs*33	ENST00000312049	NM_130799.2	83	ctGTCT/ct	2/10	1	2	FACETS	0.688	0.615	0.766	0.688	0.615	0.766	SUBCLONAL	1	TRUE	1	0.3	2		749	1017	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201947	67201947	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201713248	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	168	669	1	ENST00000312629.5:c.1147G>A	p.Ala383Thr	p.A383T	ENST00000312629	NM_003952.2	383	Gcc/Acc	13/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.3	2		670	990	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94201032	94201032	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs570102851	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	27	346	0	ENST00000323929.3:c.1045C>T	p.Arg349Trp	p.R349W	ENST00000323929	NM_005591.3	349	Cgg/Tgg	10/20	1	2	FACETS	0.409	0.325	0.506	0.409	0.325	0.506	SUBCLONAL	1	TRUE	1	0.3	2		346	440	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94963966	94963966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	56	297	0	ENST00000536441.1:c.59G>A	p.Cys20Tyr	p.C20Y	ENST00000536441	NM_144665.3	20	tGc/tAc	1/10	1	2	FACETS	0.644	0.551	0.745	0.644	0.551	0.745	SUBCLONAL	1	TRUE	1	0.3	2		297	580	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920786	100920786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752995251	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	30	308	2	ENST00000325455.5:c.2362C>T	p.Arg788Trp	p.R788W	ENST00000325455	NM_001202474.3	788	Cgg/Tgg	6/8	1	2	FACETS	0.548	0.442	0.668	0.548	0.442	0.668	SUBCLONAL	1	TRUE	1	0.3	2		310	365	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142096	108142096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782163	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	55	513	0	ENST00000278616.4:c.3040G>A	p.Ala1014Thr	p.A1014T	ENST00000278616	NM_000051.3	1014	Gct/Act	20/63	1	2	FACETS	0.564	0.482	0.654	0.564	0.482	0.654	SUBCLONAL	1	TRUE	1	0.3	2		513	650	SUCCESS
ATM	472	MSKCC	GRCh37	11	108168020	108168020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752459491	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	45	286	0	ENST00000278616.4:c.4916C>T	p.Pro1639Leu	p.P1639L	ENST00000278616	NM_000051.3	1639	cCg/cTg	33/63	1	2	FACETS	0.906	0.765	1	0.906	0.765	1	CLONAL	1	TRUE	1	0.3	2		286	331	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173696	108173696	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	28	288	0	ENST00000278616.4:c.5441del	p.Leu1814TrpfsTer14	p.L1814Wfs*14	ENST00000278616	NM_000051.3	1812	gcT/gc	36/63	1	2	FACETS	0.441	0.352	0.543	0.441	0.352	0.543	SUBCLONAL	1	TRUE	1	0.3	2		288	423	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409089	4409089	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	59	412	0	ENST00000261254.3:c.784C>A	p.Arg262Ser	p.R262S	ENST00000261254	NM_001759.3	262	Cgt/Agt	5/5	1	2	FACETS	0.614	0.527	0.708	0.614	0.527	0.708	SUBCLONAL	1	TRUE	1	0.3	2		412	641	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398279	25398279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894365	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	95	372	0	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	0.3	2		372	544	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426990	49426990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1320906608	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	83	639	0	ENST00000301067.7:c.11498G>A	p.Arg3833Gln	p.R3833Q	ENST00000301067	NM_003482.3	3833	cGg/cAg	39/54	1	2	FACETS	0.615	0.542	0.695	0.615	0.542	0.695	SUBCLONAL	1	TRUE	1	0.3	2		639	899	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446488	49446488	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	85	440	0	ENST00000301067.7:c.1117del	p.Ser373HisfsTer29	p.S373Hfs*29	ENST00000301067	NM_003482.3	373	Tca/ca	9/54	1	2	FACETS	0.865	0.765	0.972	0.865	0.765	0.972	CLONAL	1	TRUE	1	0.3	2		440	655	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967543	26967543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	61	348	0	ENST00000381527.3:c.686C>T	p.Thr229Met	p.T229M	ENST00000381527	NM_001260.1	229	aCg/aTg	7/13	1	2	FACETS	0.82	0.708	0.941	0.82	0.708	0.941	CLONAL	1	TRUE	1	0.3	2		348	496	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877353	28877353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536239359	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	154	453	0	ENST00000282397.4:c.3968C>T	p.Pro1323Leu	p.P1323L	ENST00000282397	NM_002019.4	1323	cCg/cTg	30/30	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.3	2		453	772	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435300	110435302	+	inframe_deletion	In_Frame_Del	DEL	GGT	GGT	-	rs765493638	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	53	163	6	ENST00000375856.3:c.3099_3101del	p.Pro1036del	p.P1036del	ENST00000375856	NM_003749.2	1033	ccACCg/ccg	1/2	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.3	2		169	276	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987138	36987138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415981843	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	73	690	1	ENST00000354822.5:c.551C>T	p.Ala184Val	p.A184V	ENST00000354822	NM_001079668.2	184	gCc/gTc	3/3	1	2	FACETS	0.517	0.451	0.588	0.517	0.451	0.588	SUBCLONAL	1	TRUE	1	0.3	2		691	942	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81534643	81534645	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	27	367	0	ENST00000298171.2:c.290_292del	p.Phe97del	p.F97del	ENST00000298171	NM_000369.2	96	tcCTTc/tcc	3/10	1	2	FACETS	0.382	0.303	0.473	0.382	0.303	0.473	SUBCLONAL	1	TRUE	1	0.3	2		367	471	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000020	42000020	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	77	640	1	ENST00000219905.7:c.2287del	p.Trp763GlyfsTer54	p.W763Gfs*54	ENST00000219905	NM_001164273.1	761	ccT/cc	6/24	1	2	FACETS	0.603	0.528	0.683	0.603	0.528	0.683	SUBCLONAL	1	TRUE	1	0.3	2		641	852	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690584	88690584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368222977	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	53	409	1	ENST00000360948.2:c.446C>T	p.Thr149Met	p.T149M	ENST00000360948	NM_001012338.2	149	aCg/aTg	5/19	0.3	1	FACETS	0.481	0.41	0.56	0.481	0.41	0.56	SUBCLONAL	1	TRUE	0	0.3	1		410	624	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130288	2130288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs529298825	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	100	748	0	ENST00000219476.3:c.3520C>T	p.Arg1174Trp	p.R1174W	ENST00000219476	NM_000548.3	1174	Cgg/Tgg	30/42	1	2	FACETS	0.637	0.567	0.711	0.637	0.567	0.711	SUBCLONAL	1	TRUE	1	0.3	2		748	1047	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220703	2220703	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	70	448	0	ENST00000326181.6:c.320T>G	p.Phe107Cys	p.F107C	ENST00000326181	NM_032271.2	107	tTc/tGc	5/21	1	2	FACETS	0.755	0.658	0.86	0.755	0.658	0.86	SUBCLONAL	1	TRUE	1	0.3	2		448	618	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857680	9857680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303700994	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	98	449	1	ENST00000330684.3:c.3721C>T	p.Arg1241Trp	p.R1241W	ENST00000330684	NM_001134407.1	1241	Cgg/Tgg	13/13	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.3	2		450	604	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646308	23646308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	72	586	1	ENST00000261584.4:c.1559G>A	p.Cys520Tyr	p.C520Y	ENST00000261584	NM_024675.3	520	tGc/tAc	4/13	1	2	FACETS	0.55	0.479	0.626	0.55	0.479	0.626	SUBCLONAL	1	TRUE	1	0.3	2		587	873	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50810143	50810143	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	53	535	0	ENST00000398568.2:c.967G>C	p.Val323Leu	p.V323L	ENST00000398568	NM_001042412.1	323	Gtt/Ctt	6/18	1	2	FACETS	0.528	0.45	0.614	0.528	0.45	0.614	SUBCLONAL	1	TRUE	1	0.3	2		535	669	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813627	50813627	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370428449	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	126	632	0	ENST00000398568.2:c.1181G>A	p.Arg394His	p.R394H	ENST00000398568	NM_001042412.1	394	cGt/cAt	8/18	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.3	2		632	825	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56872937	56872937	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	53	327	0	ENST00000308159.5:c.2097del	p.Phe699LeufsTer19	p.F699Lfs*19	ENST00000308159	NM_014669.4	698	Ttt/tt	19/22	1	2	FACETS	0.79	0.675	0.916	0.79	0.675	0.916	CLONAL	1	TRUE	1	0.3	2		327	447	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863643	68863643	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	90	655	0	ENST00000261769.5:c.2386del	p.Arg796GlyfsTer20	p.R796Gfs*20	ENST00000261769	NM_004360.3	794	gtC/gt	15/16	1	2	FACETS	0.659	0.584	0.74	0.659	0.584	0.74	SUBCLONAL	1	TRUE	1	0.3	2		655	910	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829463	72829471	+	inframe_deletion	In_Frame_Del	DEL	TCCATGGCA	TCCATGGCA	-	rs746065760	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	64	567	0	ENST00000268489.5:c.7110_7118del	p.Asp2370_Met2372del	p.D2370_M2372del	ENST00000268489	NM_006885.3	2370	gaTGCCATGGAa/gaa	9/10	1	2	FACETS	0.506	0.437	0.581	0.506	0.437	0.581	SUBCLONAL	1	TRUE	1	0.3	2		567	844	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845896	72845896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	39	462	0	ENST00000268489.5:c.3571G>A	p.Ala1191Thr	p.A1191T	ENST00000268489	NM_006885.3	1191	Gca/Aca	6/10	1	2	FACETS	0.364	0.3	0.435	0.364	0.3	0.435	SUBCLONAL	1	TRUE	1	0.3	2		462	715	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348658	89348658	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	174	827	0	ENST00000301030.4:c.4292del	p.Asn1431MetfsTer11	p.N1431Mfs*11	ENST00000301030	NM_001256183.1	1431	aAt/at	9/13	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.3	2		827	1140	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562668	29562668	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1452005208	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	55	495	1	ENST00000356175.3:c.3748C>T	p.Arg1250Trp	p.R1250W	ENST00000356175	NM_000267.3	1250	Cgg/Tgg	28/57	1	2	FACETS	0.516	0.44	0.599	0.516	0.44	0.599	SUBCLONAL	1	TRUE	1	0.3	2		496	711	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264325	30264326	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	18	70	0	ENST00000322652.5:c.65dup	p.Gly23ArgfsTer60	p.G23Rfs*60	ENST00000322652	NM_015355.2	20	-/G	1/16	1	2	FACETS	1	0.781	1	1	0.781	1	CLONAL	1	TRUE	1	0.3	2		70	117	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487554	38487554	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	111	676	0	ENST00000254066.5:c.89del	p.Pro30LeufsTer12	p.P30Lfs*12	ENST00000254066	NM_000964.3	28	ttC/tt	2/9	1	2	FACETS	0.855	0.768	0.948	0.855	0.768	0.948	CLONAL	1	TRUE	1	0.3	2		676	865	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512270	38512270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866777491	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	169	756	0	ENST00000254066.5:c.1181G>A	p.Arg394Gln	p.R394Q	ENST00000254066	NM_000964.3	394	cGg/cAg	9/9	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.3	2		756	1010	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	139	738	3	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	1	2	FACETS	0.922	0.838	1	0.922	0.838	1	CLONAL	1	TRUE	1	0.3	2		741	1005	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492694	56492694	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	118	456	0	ENST00000407977.2:c.245del	p.Leu82Ter	p.L82*	ENST00000407977		82	tTa/ta	2/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.3	2		456	571	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533938	63533939	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	54	452	0	ENST00000307078.5:c.1214_1215dup	p.Gly406ArgfsTer53	p.G406Rfs*53	ENST00000307078	NM_004655.3	405	-/AG	6/11	1	2	FACETS	0.613	0.523	0.712	0.613	0.523	0.712	SUBCLONAL	1	TRUE	1	0.3	2		452	587	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63537586	63537587	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	126	484	0	ENST00000307078.5:c.1045_1046del	p.Leu349ThrfsTer24	p.L349Tfs*24	ENST00000307078	NM_004655.3	349	CTa/a	4/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.3	2		484	724	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63553975	63553976	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	107	532	0	ENST00000307078.5:c.763_764del	p.Leu255GlufsTer13	p.L255Efs*13	ENST00000307078	NM_004655.3	255	CTg/g	2/11	1	2	FACETS	0.999	0.897	1	0.999	0.897	1	CLONAL	1	TRUE	1	0.3	2		532	714	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66518957	66518957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	64	455	0	ENST00000358598.2:c.238G>A	p.Asp80Asn	p.D80N	ENST00000358598	NM_212471.2	80	Gat/Aat	3/11	1	2	FACETS	0.673	0.582	0.771	0.673	0.582	0.771	SUBCLONAL	1	TRUE	1	0.3	2		455	634	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191069	2191069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746714270	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	89	593	0	ENST00000398665.3:c.323G>A	p.Arg108His	p.R108H	ENST00000398665	NM_032482.2	108	cGc/cAc	5/28	1	2	FACETS	0.74	0.655	0.83	0.74	0.655	0.83	SUBCLONAL	1	TRUE	1	0.3	2		593	802	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110242	3110242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	114	778	0	ENST00000078429.4:c.232C>T	p.Leu78Phe	p.L78F	ENST00000078429	NM_002067.2	78	Ctc/Ttc	2/7	1	2	FACETS	0.667	0.599	0.739	0.667	0.599	0.739	SUBCLONAL	1	TRUE	1	0.3	2		778	1140	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210500	5210500	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	60	610	0	ENST00000357368.4:c.5467T>C	p.Phe1823Leu	p.F1823L	ENST00000357368	NM_002850.3	1823	Ttc/Ctc	35/38	1	2	FACETS	0.498	0.428	0.575	0.498	0.428	0.575	SUBCLONAL	1	TRUE	1	0.3	2		610	803	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	147	289	1	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.3	2		290	882	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610610	10610610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372654184	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	84	712	1	ENST00000171111.5:c.100G>A	p.Ala34Thr	p.A34T	ENST00000171111	NM_203500.1	34	Gcc/Acc	2/6	1	2	FACETS	0.573	0.505	0.647	0.573	0.505	0.647	SUBCLONAL	1	TRUE	1	0.3	2		713	977	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144149	11144149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	98	674	0	ENST00000358026.2:c.3730C>T	p.Arg1244Cys	p.R1244C	ENST00000358026	NM_001128849.1	1244	Cgc/Tgc	26/36	1	2	FACETS	0.678	0.603	0.757	0.678	0.603	0.757	SUBCLONAL	1	TRUE	1	0.3	2		674	964	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210689	36210689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754616271	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	89	594	0	ENST00000222270.7:c.440G>A	p.Arg147Gln	p.R147Q	ENST00000222270	NM_014727.1	147	cGa/cAa	3/37	1	2	FACETS	0.617	0.546	0.693	0.617	0.546	0.693	SUBCLONAL	1	TRUE	1	0.3	2		594	962	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918231	50918231	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760898812	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	96	661	0	ENST00000440232.2:c.2548C>T	p.Arg850Cys	p.R850C	ENST00000440232	NM_002691.3	850	Cgc/Tgc	20/27	1	2	FACETS	0.675	0.6	0.755	0.675	0.6	0.755	SUBCLONAL	1	TRUE	1	0.3	2		661	948	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	97	639	9	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.3	2		648	633	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170773	99170773	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1433594545	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	65	458	0	ENST00000074304.5:c.1402G>A	p.Ala468Thr	p.A468T	ENST00000074304	NM_001134224.1	468	Gcc/Acc	16/26	1	2	FACETS	0.644	0.558	0.737	0.644	0.558	0.737	SUBCLONAL	1	TRUE	1	0.3	2		458	673	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046441	128046441	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	73	355	0	ENST00000285398.2:c.823-1G>A		p.X275_splice	ENST00000285398	NM_000122.1	275			1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.3	2		355	474	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645975	215645975	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs587780033	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	50	475	0	ENST00000260947.4:c.623del	p.Lys208ArgfsTer4	p.K208Rfs*4	ENST00000260947	NM_000465.2	208	aAg/ag	4/11	1	2	FACETS	0.533	0.452	0.623	0.533	0.452	0.623	SUBCLONAL	1	TRUE	1	0.3	2		475	625	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023445	31023445	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	61	588	0	ENST00000375687.4:c.2930A>C	p.Gln977Pro	p.Q977P	ENST00000375687	NM_015338.5	977	cAg/cCg	13/13	1	2	FACETS	0.642	0.554	0.739	0.642	0.554	0.739	SUBCLONAL	1	TRUE	1	0.3	2		588	633	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730910	40730910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370873414	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	115	578	1	ENST00000373198.4:c.3625C>T	p.Arg1209Trp	p.R1209W	ENST00000373198	NM_133170.3	1209	Cgg/Tgg	27/32	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.3	2		579	731	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12647737	12647737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773051648	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	49	355	2	ENST00000251849.4:c.643C>T	p.Arg215Cys	p.R215C	ENST00000251849	NM_002880.3	215	Cgt/Tgt	6/17	1	2	FACETS	0.642	0.544	0.75	0.642	0.544	0.75	SUBCLONAL	1	TRUE	1	0.3	2		357	509	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468398	89468398	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1467832547	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	36	254	0	ENST00000336596.2:c.1938del	p.Glu647ArgfsTer9	p.E647Rfs*9	ENST00000336596	NM_005233.5	644	tcA/tc	11/17	1	2	FACETS	0.647	0.532	0.775	0.647	0.532	0.775	SUBCLONAL	1	TRUE	1	0.3	2		254	371	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204842	128204842	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs768767517	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1169	82	908	2	ENST00000341105.2:c.599del	p.Gly200ValfsTer18	p.G200Vfs*18	ENST00000341105	NM_032638.4	200	gGt/gt	3/6	1	2	FACETS	0.437	0.384	0.495	0.437	0.384	0.495	SUBCLONAL	1	TRUE	1	0.3	2		910	1251	SUCCESS
ATR	545	MSKCC	GRCh37	3	142172007	142172007	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762196224	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	55	541	0	ENST00000350721.4:c.7724C>T	p.Ala2575Val	p.A2575V	ENST00000350721	NM_001184.3	2575	gCg/gTg	46/47	1	2	FACETS	0.497	0.424	0.577	0.497	0.424	0.577	SUBCLONAL	1	TRUE	1	0.3	2		541	738	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998128	169998128	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs753143066	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	86	666	5	ENST00000295797.4:c.826del	p.Thr276GlnfsTer7	p.T276Qfs*7	ENST00000295797	NM_002740.5	273	ttA/tt	9/18	1	2	FACETS	0.572	0.505	0.645	0.572	0.505	0.645	SUBCLONAL	1	TRUE	1	0.3	2		671	1002	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803450	1803450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759641808	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	146	696	0	ENST00000260795.2:c.719C>T	p.Thr240Met	p.T240M	ENST00000260795		240	aCg/aTg	5/17	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.3	2		696	926	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920288	1920288	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	108	683	1	ENST00000382891.5:c.1348C>T	p.Arg450Ter	p.R450*	ENST00000382891	NM_133335.3	450	Cga/Tga	5/22	1	2	FACETS	0.773	0.693	0.859	0.773	0.693	0.859	SUBCLONAL	1	TRUE	1	0.3	2		684	931	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1976593	1976593	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	85	642	0	ENST00000382891.5:c.3376C>T	p.Arg1126Cys	p.R1126C	ENST00000382891	NM_133335.3	1126	Cgt/Tgt	19/22	1	2	FACETS	0.675	0.595	0.76	0.675	0.595	0.76	SUBCLONAL	1	TRUE	1	0.3	2		642	840	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201815	66201815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764665078	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	92	425	0	ENST00000273854.3:c.2687G>A	p.Arg896His	p.R896H	ENST00000273854	NM_004439.5	896	cGt/cAt	16/18	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.3	2		425	573	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286238	66286238	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	35	339	0	ENST00000273854.3:c.1448del	p.Asn483ThrfsTer18	p.N483Tfs*18	ENST00000273854	NM_004439.5	483	aAc/ac	6/18	1	2	FACETS	0.627	0.515	0.753	0.627	0.515	0.753	SUBCLONAL	1	TRUE	1	0.3	2		339	372	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250856	153250858	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	49	343	0	ENST00000281708.4:c.1202_1204del	p.Asn401del	p.N401del	ENST00000281708	NM_033632.3	401	aACAct/act	8/12	1	2	FACETS	0.831	0.706	0.968	0.831	0.706	0.968	CLONAL	1	TRUE	1	0.3	2		343	393	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1268636	1268636	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1554039721	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	94	684	0	ENST00000310581.5:c.2581G>A	p.Gly861Arg	p.G861R	ENST00000310581	NM_198253.2	861	Ggg/Agg	9/16	1	2	FACETS	0.652	0.579	0.73	0.652	0.579	0.73	SUBCLONAL	1	TRUE	1	0.3	2		684	961	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279527	1279527	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767382450	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	202	880	0	ENST00000310581.5:c.2009C>T	p.Ala670Val	p.A670V	ENST00000310581	NM_198253.2	670	gCg/gTg	5/16	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.3	2		880	1092	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963112	38963112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750569880	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	38	255	0	ENST00000357387.3:c.1432C>T	p.Arg478Cys	p.R478C	ENST00000357387	NM_152756.3	478	Cgc/Tgc	17/38	1	2	FACETS	0.799	0.663	0.95	0.799	0.663	0.95	CLONAL	1	TRUE	1	0.3	2		255	317	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161690	56161690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	44	395	0	ENST00000399503.3:c.1187G>A	p.Arg396His	p.R396H	ENST00000399503	NM_005921.1	396	cGt/cAt	6/20	1	2	FACETS	0.512	0.429	0.604	0.512	0.429	0.604	SUBCLONAL	1	TRUE	1	0.3	2		395	573	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753011	57753012	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	64	298	3	ENST00000274289.3:c.1004dup	p.Leu335PhefsTer12	p.L335Ffs*12	ENST00000274289	NM_006622.3	335	ttg/ttTg	7/14	1	2	FACETS	0.871	0.755	0.995	0.871	0.755	0.995	CLONAL	1	TRUE	1	0.3	2		301	490	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753950	57753950	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	34	369	0	ENST00000274289.3:c.674G>A	p.Gly225Asp	p.G225D	ENST00000274289	NM_006622.3	225	gGt/gAt	5/14	1	2	FACETS	0.424	0.346	0.513	0.424	0.346	0.513	SUBCLONAL	1	TRUE	1	0.3	2		369	534	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564366	86564366	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	67	535	0	ENST00000274376.6:c.98T>C	p.Val33Ala	p.V33A	ENST00000274376	NM_002890.2	33	gTg/gCg	1/25	1	2	FACETS	0.636	0.552	0.727	0.636	0.552	0.727	SUBCLONAL	1	TRUE	1	0.3	2		535	702	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931451	131931452	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	46	433	0	ENST00000265335.6:c.2164_2165dup	p.Glu723ArgfsTer14	p.E723Rfs*14	ENST00000265335		719	cta/ctAAa	13/25	1	2	FACETS	0.534	0.449	0.628	0.534	0.449	0.628	SUBCLONAL	1	TRUE	1	0.3	2		433	574	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562442	176562442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	77	736	0	ENST00000439151.2:c.338G>A	p.Cys113Tyr	p.C113Y	ENST00000439151	NM_022455.4	113	tGc/tAc	2/23	1	2	FACETS	0.511	0.447	0.58	0.511	0.447	0.58	SUBCLONAL	1	TRUE	1	0.3	2		736	1004	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020979	26020979	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	61	442	0	ENST00000357647.3:c.262T>C	p.Ser88Pro	p.S88P	ENST00000357647	NM_003529.2	88	Tcc/Ccc	1/1	1	2	FACETS	0.634	0.547	0.73	0.634	0.547	0.73	SUBCLONAL	1	TRUE	1	0.3	2		442	641	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672177	30672177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762832250	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	114	776	0	ENST00000376406.3:c.4783C>T	p.Arg1595Trp	p.R1595W	ENST00000376406	NM_014641.2	1595	Cgg/Tgg	10/15	1	2	FACETS	0.704	0.633	0.781	0.704	0.633	0.781	SUBCLONAL	1	TRUE	1	0.3	2		776	1079	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178537	32178537	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	48	547	0	ENST00000375023.3:c.2857C>A	p.Leu953Ile	p.L953I	ENST00000375023	NM_004557.3	953	Ctc/Atc	18/30	1	2	FACETS	0.462	0.389	0.542	0.462	0.389	0.542	SUBCLONAL	1	TRUE	1	0.3	2		547	693	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288240	33288240	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs573854582	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	63	504	0	ENST00000374542.5:c.1168G>A	p.Glu390Lys	p.E390K	ENST00000374542	NM_001141970.1	390	Gag/Aag	4/8	1	2	FACETS	0.553	0.478	0.636	0.553	0.478	0.636	SUBCLONAL	1	TRUE	1	0.3	2		504	759	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202351	138202351	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	84	586	1	ENST00000237289.4:c.2274del	p.Lys759SerfsTer57	p.K759Sfs*57	ENST00000237289	NM_001270507.1	756	gaC/ga	9/9	1	2	FACETS	0.653	0.575	0.736	0.653	0.575	0.736	SUBCLONAL	1	TRUE	1	0.3	2		587	858	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157488275	157488275	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377351099	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	62	395	3	ENST00000346085.5:c.2981C>T	p.Ala994Val	p.A994V	ENST00000346085	NM_020732.3	994	gCg/gTg	10/20	1	2	FACETS	0.67	0.578	0.769	0.67	0.578	0.769	SUBCLONAL	1	TRUE	1	0.3	2		398	617	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771166	161771166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1490851246	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	84	691	0	ENST00000366898.1:c.1363C>T	p.Arg455Cys	p.R455C	ENST00000366898	NM_004562.2	455	Cgc/Tgc	12/12	1	2	FACETS	0.633	0.558	0.713	0.633	0.558	0.713	SUBCLONAL	1	TRUE	1	0.3	2		691	885	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864403	162864403	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148990138	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	87	461	1	ENST00000366898.1:c.110C>T	p.Pro37Leu	p.P37L	ENST00000366898	NM_004562.2	37	cCg/cTg	2/12	1	2	FACETS	0.901	0.798	1	0.901	0.798	1	CLONAL	1	TRUE	1	0.3	2		462	644	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958168	2958168	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs928782717	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	78	767	1	ENST00000396946.4:c.2564G>A	p.Arg855Gln	p.R855Q	ENST00000396946	NM_032415.4	855	cGg/cAg	19/25	1	2	FACETS	0.562	0.492	0.636	0.562	0.492	0.636	SUBCLONAL	1	TRUE	1	0.3	2		768	926	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508673	106508673	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs554272230	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	158	540	0	ENST00000359195.3:c.667G>A	p.Val223Ile	p.V223I	ENST00000359195	NM_002649.2	223	Gtc/Atc	2/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.3	2		540	833	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411880	116411883	+	intron_variant	Intron	DEL	TCTT	TCTT	-	rs747887276	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	141	914	0	ENST00000397752.3:c.2888-16_2888-13del		p.*963*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.723	0.656	0.793	0.723	0.656	0.793	SUBCLONAL	1	TRUE	1	0.3	2		914	1301	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843748	151843748	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778512	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	58	399	1	ENST00000262189.6:c.13967C>T	p.Ala4656Val	p.A4656V	ENST00000262189	NM_170606.2	4656	gCg/gTg	53/59	1	2	FACETS	0.655	0.563	0.756	0.655	0.563	0.756	SUBCLONAL	1	TRUE	1	0.3	2		400	590	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	66	425	1	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.3	2		426	426	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022033	5022033	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1422678517	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	54	431	0	ENST00000381652.3:c.46A>G	p.Thr16Ala	p.T16A	ENST00000381652	NM_004972.3	16	Acc/Gcc	3/25	1	2	FACETS	0.628	0.536	0.729	0.628	0.536	0.729	SUBCLONAL	1	TRUE	1	0.3	2		431	573	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209593	98209593	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	130	614	3	ENST00000331920.6:c.3945del	p.Tyr1316ThrfsTer56	p.Y1316Tfs*56	ENST00000331920	NM_000264.3	1315	ccC/cc	23/24	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.3	2		617	766	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231105	98231105	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	114	568	0	ENST00000331920.6:c.2178del	p.Cys727ValfsTer19	p.C727Vfs*19	ENST00000331920	NM_000264.3	726	ccC/cc	14/24	1	2	FACETS	0.891	0.802	0.986	0.891	0.802	0.986	CLONAL	1	TRUE	1	0.3	2		568	853	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760231	133760232	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	83	582	0	ENST00000318560.5:c.2559dup	p.Thr854HisfsTer30	p.T854Hfs*30	ENST00000318560	NM_005157.4	852	acc/aCcc	11/11	1	2	FACETS	0.735	0.648	0.828	0.735	0.648	0.828	SUBCLONAL	1	TRUE	1	0.3	2		582	753	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300040	137300040	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	83	769	3	ENST00000481739.1:c.331del	p.Leu111TrpfsTer57	p.L111Wfs*57	ENST00000481739	NM_002957.4	109	Ccc/cc	3/10	1	2	FACETS	0.526	0.463	0.594	0.526	0.463	0.594	SUBCLONAL	1	TRUE	1	0.3	2		772	1052	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197044	123197044	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	37	206	0	ENST00000218089.9:c.1810C>T	p.Arg604Ter	p.R604*	ENST00000218089	NM_001042749.1	604	Cga/Tga	19/35	1	1	FACETS	0.924	0.767	1	0.924	0.767	1	CLONAL	1	TRUE	0	0.3	1		206	227	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803386	1803386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	90	768	0	ENST00000260795.2:c.655G>A	p.Val219Met	p.V219M	ENST00000260795		219	Gtg/Atg	5/17	1	2	FACETS	0.606	0.536	0.681	0.606	0.536	0.681	SUBCLONAL	1	TRUE	1	0.3	2		768	990	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0038963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	414	230	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.517264450558299	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.528982539646147	2		231	715	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	153	406	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.528982539646147	3	FACETS	0.883	0.817	0.951	0.883	0.817	0.951	CLONAL	2	TRUE	1	0.528982539646147	3		406	414	SUCCESS
APC	324	MSKCC	GRCh37	5	112175766	112175766	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	104	238	0	ENST00000257430.4:c.4476del	p.Thr1493ArgfsTer14	p.T1493Rfs*14	ENST00000257430	NM_000038.5	1492	gCc/gc	16/16	0.528982539646147	3	FACETS	0.837	0.76	0.916	0.837	0.76	0.916	CLONAL	2	TRUE	1	0.528982539646147	3		238	297	SUCCESS
APC	324	MSKCC	GRCh37	5	112174494	112174494	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1554084848	NA	P-0038963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	95	270	0	ENST00000257430.4:c.3203C>G	p.Ser1068Ter	p.S1068*	ENST00000257430	NM_000038.5	1068	tCa/tGa	16/16	0.528982539646147	3	FACETS	1	0.98	1	0.707	0.637	0.781	CLONAL	1	TRUE	1	0.528982539646147	3		270	321	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589618	67589619	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAGAATATGATA	novel	NA	P-0039233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	16	222	0	ENST00000274335.5:c.1384_1395dup	p.Glu462_Arg465dup	p.E462_R465dup	ENST00000274335		462	cga/cGAGAATATGATAga	10/15	1	2	FACETS	0.336	0.248	0.441	0.336	0.248	0.441	SUBCLONAL	1	TRUE	1	0.338081257437726	2		222	282	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0039233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	34	286	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.4	0.326	0.483	0.4	0.326	0.483	SUBCLONAL	1	TRUE	1	0.338081257437726	2		286	503	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0039233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	133	565	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.806	0.731	0.885	0.806	0.731	0.885	CLONAL	1	TRUE	1	0.338081257437726	2		565	976	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0039233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	185	415	0	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	0.338081257437726	1	FACETS	0.755	0.701	0.811	1	0.991	1	SUBCLONAL	2	TRUE	0	0.338081257437726	1		415	602	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099958	27099958	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0039233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	210	511	0	ENST00000324856.7:c.3837T>A	p.Tyr1279Ter	p.Y1279*	ENST00000324856	NM_006015.4	1279	taT/taA	15/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.338081257437726	2		511	1063	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720857	89720858	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	157	307	0	ENST00000371953.3:c.1012dup	p.Ser338PhefsTer5	p.S338Ffs*5	ENST00000371953	NM_000314.4	336	-/T	8/9	0.338081257437726	1	FACETS	0.91	0.842	0.979	1	0.992	1	CLONAL	2	TRUE	0	0.338081257437726	1		307	424	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0039266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	11	427	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.339838393380045	3	FACETS	0.14	0.096	0.196	0.07	0.048	0.098	SUBCLONAL	1	TRUE	1	0.339838393380045	3		427	540	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	60	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.973	0.842	1	0.973	0.842	1	CLONAL	1	TRUE	1	0.339838393380045	2		306	363	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692826	89692826	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	55	154	0	ENST00000371953.3:c.313del	p.Cys105ValfsTer8	p.C105Vfs*8	ENST00000371953	NM_000314.4	104	Ttt/tt	5/9	0.339838393380045	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.339838393380045	1		154	212	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579331	7579331	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	232	621	0	ENST00000269305.4:c.356C>G	p.Ala119Gly	p.A119G	ENST00000269305	NM_001126112.2	119	gCc/gGc	4/11	0.489017401505184	2	FACETS	1	0.991	1	0.678	0.637	0.72	CLONAL	1	TRUE	0	0.562582447041448	2		621	608	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253388	226253388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	68	234	0	ENST00000366813.1:c.160C>T	p.Arg54Cys	p.R54C	ENST00000366813		54	Cgt/Tgt	2/3	0.562582447041448	3	FACETS	0.774	0.677	0.879	0.387	0.338	0.44	SUBCLONAL	1	TRUE	1	0.562582447041448	3		234	400	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456502	29456502	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	113	671	0	ENST00000389048.3:c.2416C>G	p.Arg806Gly	p.R806G	ENST00000389048	NM_004304.4	806	Cgt/Ggt	14/29	0.562582447041448	3	FACETS	0.51	0.458	0.565	0.17	0.152	0.189	SUBCLONAL	1	TRUE	0	0.562582447041448	3		671	1010	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641116	117641116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	105	636	0	ENST00000368508.3:c.5855G>A	p.Gly1952Glu	p.G1952E	ENST00000368508	NM_002944.2	1952	gGa/gAa	36/43	0.562582447041448	3	FACETS	0.589	0.527	0.655	0.295	0.263	0.328	SUBCLONAL	1	TRUE	1	0.562582447041448	3		636	812	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457953	69457953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	125	503	0	ENST00000227507.2:c.353C>T	p.Pro118Leu	p.P118L	ENST00000227507	NM_053056.2	118	cCc/cTc	2/5	0.484507472294624	3	FACETS	0.854	0.774	0.937	0.285	0.258	0.313	CLONAL	1	TRUE	0	0.562582447041448	3		503	667	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69210673	69210673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	108	425	0	ENST00000462284.1:c.256G>A	p.Asp86Asn	p.D86N	ENST00000462284	NM_002392.5	86	Gat/Aat	4/11	0.497621980319641	3	FACETS	0.786	0.707	0.87	0.262	0.235	0.29	SUBCLONAL	1	TRUE	0	0.562582447041448	3		425	626	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112371	115112371	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs755898047	NA	P-0039363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	139	529	1	ENST00000257566.3:c.1369C>A	p.Pro457Thr	p.P457T	ENST00000257566	NM_016569.3	457	Ccg/Acg	7/8	0.497621980319641	3	FACETS	1	0.93	1	0.34	0.311	0.371	CLONAL	1	TRUE	0	0.562582447041448	3		530	620	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126069	2126069	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	43	616	0	ENST00000219476.3:c.2640G>C	p.Lys880Asn	p.K880N	ENST00000219476	NM_000548.3	880	aaG/aaC	24/42	0.497621980319641	3	FACETS	0.236	0.196	0.28	0.079	0.065	0.094	SUBCLONAL	1	TRUE	0	0.562582447041448	3		616	831	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533449	63533449	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	73	592	0	ENST00000307078.5:c.1705C>T	p.Gln569Ter	p.Q569*	ENST00000307078	NM_004655.3	569	Cag/Tag	6/11	0.489017401505184	2	FACETS	0.413	0.361	0.469	0.207	0.18	0.235	SUBCLONAL	1	TRUE	0	0.562582447041448	2		592	628	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52709288	52709288	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	129	575	0	ENST00000322088.6:c.242G>A	p.Gly81Glu	p.G81E	ENST00000322088	NM_014225.5	81	gGa/gAa	3/15	0.489017401505184	2	FACETS	0.837	0.762	0.915	0.418	0.381	0.458	CLONAL	1	TRUE	0	0.562582447041448	2		575	548	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267916	46267916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	79	519	0	ENST00000371998.3:c.2677G>A	p.Asp893Asn	p.D893N	ENST00000371998		893	Gat/Aat	14/23	0.360822835990656	5	FACETS	0.597	0.524	0.675	0.199	0.174	0.225	SUBCLONAL	1	TRUE	2	0.562582447041448	5		519	868	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162783	47162783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	53	436	1	ENST00000409792.3:c.3343G>A	p.Glu1115Lys	p.E1115K	ENST00000409792	NM_014159.6	1115	Gaa/Aaa	3/21	0.512271548301646	3	FACETS	0.389	0.331	0.452			1	SUBCLONAL	1	TRUE	NA	0.562582447041448	3		437	621	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169988213	169988213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	170	296	0	ENST00000295797.4:c.455C>T	p.Ala152Val	p.A152V	ENST00000295797	NM_002740.5	152	gCt/gTt	6/18	0.557503549491479	5	FACETS	0.877	0.81	0.947	0.351	0.324	0.379	CLONAL	2	TRUE	0	0.562582447041448	5		296	635	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231313	98231313	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	209	758	0	ENST00000331920.6:c.1970C>T	p.Thr657Ile	p.T657I	ENST00000331920	NM_000264.3	657	aCc/aTc	14/24	0.459503212355622	1	FACETS	0.959	0.897	1	0.959	0.897	1	CLONAL	1	TRUE	0	0.562582447041448	1		758	557	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	77	406	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.768	0.675	0.868	0.768	0.675	0.868	SUBCLONAL	1	FALSE	1	0.362542607995626	2		406	553	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	67	236	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.899	0.785	1	0.899	0.785	1	CLONAL	1	FALSE	1	0.362542607995626	2		236	411	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	136	294	2	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.925	0.842	1	0.925	0.842	1	CLONAL	1	FALSE	1	0.362542607995626	2		296	811	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	115	660	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	FALSE	1	0.362542607995626	2		663	592	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	354	247	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.973	0.923	1	1	0.996	1	CLONAL	2	FALSE	1	0.362542607995626	2		248	1004	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427721	72427721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1382885623	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	114	433	1	ENST00000477973.2:c.769G>A	p.Val257Ile	p.V257I	ENST00000477973	NM_012234.5	257	Gtc/Atc	4/4	1	2	FACETS	0.956	0.862	1	0.956	0.862	1	CLONAL	1	FALSE	1	0.362542607995626	2		434	658	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	62	399	1	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	0.868	0.753	0.992	0.868	0.753	0.992	CLONAL	1	FALSE	1	0.362542607995626	2		400	394	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	60	280	1	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.935	0.81	1	0.935	0.81	1	CLONAL	1	FALSE	1	0.362542607995626	2		281	354	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	66	610	2	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.884	0.77	1	0.884	0.77	1	CLONAL	1	FALSE	1	0.362542607995626	2		612	412	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129374	64129374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142374327	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	197	887	2	ENST00000334205.4:c.806C>T	p.Ala269Val	p.A269V	ENST00000334205	NM_003942.2	269	gCg/gTg	8/17	1	2	FACETS	0.947	0.875	1	0.947	0.875	1	CLONAL	1	FALSE	1	0.362542607995626	2		889	1148	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808647	1808647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373425119	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	202	1058	0	ENST00000260795.2:c.2260G>A	p.Val754Met	p.V754M	ENST00000260795		754	Gtg/Atg	16/17	1	2	FACETS	0.989	0.916	1	0.989	0.916	1	CLONAL	1	FALSE	1	0.362542607995626	2		1058	1127	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	92	389	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.987	0.88	1	0.987	0.88	1	CLONAL	1	FALSE	1	0.362542607995626	2		389	514	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	208	611	9	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	0.362140048502638	2	FACETS	0.885	0.82	0.953	0.443	0.41	0.477	CLONAL	1	FALSE	0	0.362542607995626	2		620	1296	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	103	633	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.701	0.627	0.78	0.701	0.627	0.78	SUBCLONAL	1	FALSE	1	0.362542607995626	2		633	810	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	129	499	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	0.938	0.851	1	0.938	0.851	1	CLONAL	1	FALSE	1	0.362542607995626	2		499	759	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	127	879	0	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	0.85	0.77	0.935	0.85	0.77	0.935	CLONAL	1	FALSE	1	0.362542607995626	2		879	824	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195289	102195289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs186307109	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	78	364	0	ENST00000263464.3:c.49G>A	p.Ala17Thr	p.A17T	ENST00000263464	NM_001165.4	17	Gcc/Acc	2/9	1	2	FACETS	0.827	0.729	0.933	0.827	0.729	0.933	CLONAL	1	FALSE	1	0.362542607995626	2		364	520	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150022	202150022	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	77	840	2	ENST00000358485.4:c.1463T>C	p.Leu488Pro	p.L488P	ENST00000358485	NM_001080125.1	488	cTg/cCg	8/9	1	2	FACETS	0.474	0.415	0.537	0.474	0.415	0.537	SUBCLONAL	1	FALSE	1	0.362542607995626	2		842	897	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404693	70404693	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756914683	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	143	477	0	ENST00000373644.4:c.2207C>T	p.Ser736Leu	p.S736L	ENST00000373644	NM_030625.2	736	tCg/tTg	4/12	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	FALSE	1	0.362542607995626	2		477	787	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966159	25966159	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747070149	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	160	746	0	ENST00000435504.4:c.3047C>T	p.Thr1016Met	p.T1016M	ENST00000435504		1016	aCg/aTg	13/13	0.362140048502638	2	FACETS	0.991	0.908	1	0.495	0.454	0.538	CLONAL	1	FALSE	0	0.362542607995626	2		746	891	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041117	42041117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747757361	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	155	1290	1	ENST00000219905.7:c.5495G>A	p.Arg1832Gln	p.R1832Q	ENST00000219905	NM_001164273.1	1832	cGg/cAg	16/24	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	FALSE	1	0.362542607995626	2		1291	833	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711908	89711910	+	inframe_deletion	In_Frame_Del	DEL	TAT	TAT	-	rs587780711	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	55	423	0	ENST00000371953.3:c.532_534del	p.Tyr178del	p.Y178del	ENST00000371953	NM_000314.4	176	TAT/-	6/9	1	2	FACETS	0.498	0.426	0.578	0.498	0.426	0.578	SUBCLONAL	1	FALSE	1	0.362542607995626	2		423	609	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981721	101981721	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555075353	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	70	329	1	ENST00000282441.5:c.147del	p.Ala50ProfsTer24	p.A50Pfs*24	ENST00000282441	NM_001130145.2	48	Ccc/cc	1/9	1	2	FACETS	0.928	0.813	1	0.928	0.813	1	CLONAL	1	FALSE	1	0.362542607995626	2		330	416	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965736	93965736	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	53	257	0	ENST00000369303.4:c.2192C>T	p.Thr731Ile	p.T731I	ENST00000369303	NM_004440.3	731	aCa/aTa	13/17	1	2	FACETS	0.81	0.693	0.936	0.81	0.693	0.936	CLONAL	1	FALSE	1	0.362542607995626	2		257	361	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246447	53246447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782726212	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	131	695	0	ENST00000375401.3:c.535C>T	p.Arg179Cys	p.R179C	ENST00000375401	NM_004187.3	179	Cgt/Tgt	5/26	1	2	FACETS	0.934	0.848	1	0.934	0.848	1	CLONAL	1	FALSE	1	0.362542607995626	2		695	774	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836386	89836386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746098172	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	162	743	1	ENST00000389301.3:c.2363C>T	p.Ala788Val	p.A788V	ENST00000389301	NM_000135.2	788	gCc/gTc	26/43	1	2	FACETS	0.963	0.883	1	0.963	0.883	1	CLONAL	1	FALSE	1	0.362542607995626	2		744	928	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250399	10250399	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755492225	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	81	627	0	ENST00000340748.4:c.3853C>T	p.Arg1285Cys	p.R1285C	ENST00000340748		1285	Cgc/Tgc	33/40	1	2	FACETS	0.592	0.521	0.668	0.592	0.521	0.668	SUBCLONAL	1	FALSE	1	0.362542607995626	2		627	755	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40376852	40376852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs892570954	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	161	722	0	ENST00000293328.3:c.320G>A	p.Arg107His	p.R107H	ENST00000293328	NM_012448.3	107	cGc/cAc	4/19	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.362542607995626	2		722	843	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099427	157099432	+	inframe_deletion	In_Frame_Del	DEL	CAGCAG	CAGCAG	-	rs587779744	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	37	296	2	ENST00000346085.5:c.381_386del	p.Gln130_Gln131del	p.Q130_Q131del	ENST00000346085	NM_020732.3	122	CAGCAG/-	1/20	1	2	FACETS	0.517	0.426	0.618	0.517	0.426	0.618	SUBCLONAL	1	FALSE	1	0.362542607995626	2		298	395	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816544	32816544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376553490	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	213	966	2	ENST00000354258.4:c.1631G>A	p.Arg544His	p.R544H	ENST00000354258	NM_000593.5	544	cGc/cAc	7/11	1	2	FACETS	0.921	0.854	0.99	0.921	0.854	0.99	CLONAL	1	FALSE	1	0.362542607995626	2		968	1276	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468426	120468426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	91	661	0	ENST00000256646.2:c.4013C>T	p.Ser1338Phe	p.S1338F	ENST00000256646	NM_024408.3	1338	tCc/tTc	25/34	1	2	FACETS	0.619	0.549	0.694	0.619	0.549	0.694	SUBCLONAL	1	FALSE	1	0.362542607995626	2		661	811	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350882	89350882	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751750670	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	224	761	0	ENST00000301030.4:c.2068G>A	p.Asp690Asn	p.D690N	ENST00000301030	NM_001256183.1	690	Gat/Aat	9/13	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.362542607995626	2		761	1150	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595382	141595382	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	223	851	1	ENST00000220592.5:c.51del	p.Ile18SerfsTer121	p.I18Sfs*121	ENST00000220592	NM_012154.3	17	ccC/cc	2/19	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.362542607995626	2		852	1063	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458824	120458824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	191	787	0	ENST00000256646.2:c.6521G>A	p.Gly2174Glu	p.G2174E	ENST00000256646	NM_024408.3	2174	gGg/gAg	34/34	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.362542607995626	2		787	918	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798769	135798769	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	63	382	2	ENST00000298552.3:c.474del	p.Phe158LeufsTer9	p.F158Lfs*9	ENST00000298552	NM_001162426.1	158	ttT/tt	6/23	1	2	FACETS	0.772	0.67	0.883	0.772	0.67	0.883	SUBCLONAL	1	FALSE	1	0.362542607995626	2		384	450	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120094	70120094	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	16	73	0	ENST00000245479.2:c.1100del	p.Pro367HisfsTer16	p.P367Hfs*16	ENST00000245479	NM_000346.3	366	Ccc/cc	3/3	1	2	FACETS	0.992	0.746	1	0.992	0.746	1	CLONAL	1	FALSE	1	0.362542607995626	2		73	89	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647142	2647142	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	108	492	0	ENST00000342085.4:c.1420C>T	p.Arg474Ter	p.R474*	ENST00000342085	NM_002613.4	474	Cga/Tga	13/14	1	2	FACETS	0.952	0.856	1	0.952	0.856	1	CLONAL	1	FALSE	1	0.362542607995626	2		492	626	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255775	16255775	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199847404	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	103	492	0	ENST00000375759.3:c.3040G>A	p.Val1014Met	p.V1014M	ENST00000375759	NM_015001.2	1014	Gtg/Atg	11/15	1	2	FACETS	0.896	0.803	0.995	0.896	0.803	0.995	CLONAL	1	FALSE	1	0.362542607995626	2		492	634	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301191	65301192	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TA	TA	-	novel	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	45	211	0	ENST00000342505.4:c.3259-3_3259-2del		p.X1087_splice	ENST00000342505	NM_002227.2	1087			1	2	FACETS	0.89	0.753	1	0.89	0.753	1	CLONAL	1	FALSE	1	0.362542607995626	2		211	279	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552736	226552736	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	179	648	1	ENST00000366794.5:c.2625G>T	p.Gln875His	p.Q875H	ENST00000366794	NM_001618.3	875	caG/caT	19/23	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.362542607995626	2		649	804	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724708	112724708	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	70	442	0	ENST00000369452.4:c.592T>C	p.Tyr198His	p.Y198H	ENST00000369452	NM_007373.3	198	Tac/Cac	2/9	1	2	FACETS	0.53	0.462	0.605	0.53	0.462	0.605	SUBCLONAL	1	FALSE	1	0.362542607995626	2		442	728	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445229	49445229	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371911838	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	218	1058	0	ENST00000301067.7:c.2237G>A	p.Arg746Gln	p.R746Q	ENST00000301067	NM_003482.3	746	cGg/cAg	10/54	1	2	FACETS	0.981	0.911	1	0.981	0.911	1	CLONAL	1	FALSE	1	0.362542607995626	2		1058	1226	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046610	30046610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559828373	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	155	645	0	ENST00000331968.5:c.2573G>A	p.Arg858His	p.R858H	ENST00000331968	NM_002742.2	858	cGc/cAc	18/18	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.362542607995626	2		645	806	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81528547	81528547	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	44	110	0	ENST00000298171.2:c.226C>T	p.Pro76Ser	p.P76S	ENST00000298171	NM_000369.2	76	Ccc/Tcc	2/10	1	2	FACETS	0.913	0.771	1	0.913	0.771	1	CLONAL	1	FALSE	1	0.362542607995626	2		110	266	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2097758	2097758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	170	821	0	ENST00000219066.1:c.91G>A	p.Gly31Arg	p.G31R	ENST00000219066	NM_002528.5	31	Ggg/Agg	1/6	1	2	FACETS	0.955	0.878	1	0.955	0.878	1	CLONAL	1	FALSE	1	0.362542607995626	2		821	982	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821200	72821200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1374726770	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	177	845	0	ENST00000268489.5:c.10975G>A	p.Asp3659Asn	p.D3659N	ENST00000268489	NM_006885.3	3659	Gac/Aac	10/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.362542607995626	2		845	949	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984678	72984678	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1355742857	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	218	824	4	ENST00000268489.5:c.2906G>A	p.Arg969His	p.R969H	ENST00000268489	NM_006885.3	969	cGc/cAc	3/10	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	FALSE	1	0.362542607995626	2		828	1175	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89811380	89811380	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1313006784	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	109	1025	2	ENST00000389301.3:c.3613C>T	p.Gln1205Ter	p.Q1205*	ENST00000389301	NM_000135.2	1205	Cag/Tag	36/43	1	2	FACETS	0.453	0.405	0.504	0.453	0.405	0.504	SUBCLONAL	1	FALSE	1	0.362542607995626	2		1027	1328	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120439	70120439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1348267601	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1212	239	1147	0	ENST00000245479.2:c.1441G>A	p.Ala481Thr	p.A481T	ENST00000245479	NM_000346.3	481	Gcc/Acc	3/3	1	2	FACETS	0.909	0.846	0.974	0.909	0.846	0.974	CLONAL	1	FALSE	1	0.362542607995626	2		1147	1451	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210687	2210687	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745691240	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	222	1034	3	ENST00000398665.3:c.1184G>A	p.Arg395His	p.R395H	ENST00000398665	NM_032482.2	395	cGc/cAc	14/28	1	2	FACETS	0.975	0.906	1	0.975	0.906	1	CLONAL	1	FALSE	1	0.362542607995626	2		1037	1256	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273315	18273315	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	89	443	1	ENST00000222254.8:c.1108A>G	p.Arg370Gly	p.R370G	ENST00000222254	NM_005027.3	370	Agg/Ggg	9/16	1	2	FACETS	0.986	0.877	1	0.986	0.877	1	CLONAL	1	FALSE	1	0.362542607995626	2		444	498	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229355	36229355	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	148	716	1	ENST00000222270.7:c.8045G>A	p.Arg2682His	p.R2682H	ENST00000222270	NM_014727.1	2682	cGt/cAt	37/37	1	2	FACETS	0.996	0.91	1	0.996	0.91	1	CLONAL	1	FALSE	1	0.362542607995626	2		717	820	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856030	45856030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139002770	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	221	904	2	ENST00000391945.4:c.1876G>A	p.Val626Ile	p.V626I	ENST00000391945	NM_000400.3	626	Gtc/Atc	20/23	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.362542607995626	2		906	1113	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082483	16082483	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	174	843	3	ENST00000281043.3:c.302del	p.Gly101AspfsTer30	p.G101Dfs*30	ENST00000281043	NM_005378.4	99	ctG/ct	2/3	0.362140048502638	2	FACETS	0.908	0.835	0.984	0.454	0.417	0.492	CLONAL	1	FALSE	0	0.362542607995626	2		846	1057	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573881	41573881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752770043	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	181	963	2	ENST00000263253.7:c.6166C>T	p.Arg2056Trp	p.R2056W	ENST00000263253	NM_001429.3	2056	Cgg/Tgg	31/31	1	2	FACETS	0.856	0.788	0.926	0.856	0.788	0.926	CLONAL	1	FALSE	1	0.362542607995626	2		965	1167	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80149965	80149966	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	50	342	0	ENST00000265081.6:c.2838_2839dup	p.Lys947IlefsTer11	p.K947Ifs*11	ENST00000265081	NM_002439.4	944	aat/aATat	21/24	1	2	FACETS	0.665	0.565	0.774	0.665	0.565	0.774	SUBCLONAL	1	FALSE	1	0.362542607995626	2		342	415	SUCCESS
APC	324	MSKCC	GRCh37	5	112102982	112102982	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201764637	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	109	534	0	ENST00000257430.4:c.317G>A	p.Arg106His	p.R106H	ENST00000257430	NM_000038.5	106	cGt/cAt	4/16	1	2	FACETS	0.951	0.856	1	0.951	0.856	1	CLONAL	1	FALSE	1	0.362542607995626	2		534	632	SUCCESS
APC	324	MSKCC	GRCh37	5	112176661	112176661	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	59	213	0	ENST00000257430.4:c.5375del	p.Asn1792MetfsTer8	p.N1792Mfs*8	ENST00000257430	NM_000038.5	1790	agA/ag	16/16	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	1	0.362542607995626	2		213	282	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131926920	131926920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776949511	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	35	165	0	ENST00000265335.6:c.1457G>A	p.Arg486His	p.R486H	ENST00000265335		486	cGt/cAt	10/25	1	2	FACETS	0.882	0.728	1	0.882	0.728	1	CLONAL	1	FALSE	1	0.362542607995626	2		165	219	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858420	27858420	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	121	578	0	ENST00000359303.2:c.151G>T	p.Glu51Ter	p.E51*	ENST00000359303	NM_003535.2	51	Gag/Tag	1/1	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.362542607995626	2		578	569	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680619	30680619	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768028369	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	144	606	2	ENST00000376406.3:c.1100C>T	p.Ala367Val	p.A367V	ENST00000376406	NM_014641.2	367	gCc/gTc	5/15	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	1	0.362542607995626	2		608	757	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800444	32800444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758423176	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	264	1169	2	ENST00000374899.4:c.1103G>A	p.Arg368Gln	p.R368Q	ENST00000374899	NM_018833.2	368	cGg/cAg	6/12	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.362542607995626	2		1171	1428	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748539	43748539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367571103	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	139	538	0	ENST00000523873.1:c.493G>A	p.Val165Met	p.V165M	ENST00000523873		165	Gtg/Atg	6/8	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.362542607995626	2		538	707	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100411	157100411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752684703	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	23	84	0	ENST00000346085.5:c.1348C>T	p.Pro450Ser	p.P450S	ENST00000346085	NM_020732.3	450	Ccg/Tcg	1/20	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	1	0.362542607995626	2		84	91	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508868	106508868	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	39	630	1	ENST00000359195.3:c.866del	p.Asn289ThrfsTer5	p.N289Tfs*5	ENST00000359195	NM_002649.2	288	Aaa/aa	2/11	1	2	FACETS	0.325	0.269	0.389	0.325	0.269	0.389	SUBCLONAL	1	FALSE	1	0.362542607995626	2		631	661	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127951922	127951922	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	206	796	1	ENST00000373547.4:c.75+1G>A		p.X25_splice	ENST00000373547	NM_002721.4	25			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.362542607995626	2		797	994	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300801	137300801	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	49	796	0	ENST00000481739.1:c.446T>C	p.Val149Ala	p.V149A	ENST00000481739	NM_002957.4	149	gTg/gCg	4/10	1	2	FACETS	0.277	0.233	0.325	0.277	0.233	0.325	SUBCLONAL	1	FALSE	1	0.362542607995626	2		796	977	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006837	47006837	+	5_prime_UTR_variant	5'UTR	SNP	G	G	A	rs782058256	NA	P-0039443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	224	919	0	ENST00000377604.3:c.-44G>A		p.*15*	ENST00000377604	NM_001204468.1	-/852		2/24	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.362542607995626	2		919	1133	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0039443-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	14	205	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.445	0.32	0.598	0.445	0.32	0.598	SUBCLONAL	1	TRUE	1	0.12	2		205	524	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007878	45007878	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039443-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	32	268	0	ENST00000558401.1:c.325C>T	p.Gln109Ter	p.Q109*	ENST00000558401	NM_004048.2	109	Cag/Tag	2/4	1	2	FACETS	0.946	0.766	1	0.946	0.766	1	CLONAL	1	TRUE	1	0.12	2		268	564	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233453	69233453	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039443-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	32	353	0	ENST00000462284.1:c.1318G>A	p.Ala440Thr	p.A440T	ENST00000462284	NM_002392.5	440	Gcc/Acc	11/11	1	2	FACETS	0.833	0.675	1	0.833	0.675	1	CLONAL	1	TRUE	1	0.12	2		353	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578200	7578200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35163653	NA	P-0039443-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	35	537	0	ENST00000269305.4:c.649G>A	p.Val217Met	p.V217M	ENST00000269305	NM_001126112.2	217	Gtg/Atg	6/11	1	2	FACETS	0.513	0.418	0.62	0.513	0.418	0.62	SUBCLONAL	1	TRUE	1	0.12	2		537	1138	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661200	227661200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039443-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	61	638	0	ENST00000305123.5:c.2255G>A	p.Gly752Asp	p.G752D	ENST00000305123	NM_005544.2	752	gGc/gAc	1/2	0.3	2	FACETS	0.867	0.745	1			1	CLONAL	1	TRUE	NA	0.12	2		638	1173	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	261	644	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	0.485940318227103	1	FACETS	0.684	0.647	0.72	0.684	0.647	0.72	INDETERMINATE	1	FALSE	0	0.809997418013945	1		644	561	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581272	48581273	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0039580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	124	730	1	ENST00000342988.3:c.579_580del	p.Glu193AspfsTer12	p.E193Dfs*12	ENST00000342988	NM_005359.5	192	acAGag/acag	5/12	0.809997418013945	1	FACETS	0.979	0.918	1	0.979	0.918	1	CLONAL	1	FALSE	0	0.809997418013945	1		731	186	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118708	115118711	+	frameshift_variant	Frame_Shift_Del	DEL	GTTG	GTTG	-	novel	NA	P-0039580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	192	536	0	ENST00000257566.3:c.630_633del	p.Asn211ThrfsTer31	p.N211Tfs*31	ENST00000257566	NM_016569.3	210	acCAAC/ac	2/8	0.13898178894947	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.809997418013945	0		536	442	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936072	44936072	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1135401809	NA	P-0039585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	136	535	0	ENST00000377967.4:c.2832+1G>A		p.X944_splice	ENST00000377967	NM_021140.2	944			0.604088533315778	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.604088533315778	2		535	206	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988376	36988376	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs751469975	NA	P-0039585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	141	455	0	ENST00000354822.5:c.277G>T	p.Ala93Ser	p.A93S	ENST00000354822	NM_001079668.2	93	Gcc/Tcc	2/3	0.469272643173975	3	FACETS	0.783	0.722	0.846	0.783	0.722	0.846	SUBCLONAL	2	TRUE	1	0.604088533315778	3		455	388	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051383	13051383	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	25	511	0	ENST00000316448.5:c.731A>C	p.Asp244Ala	p.D244A	ENST00000316448	NM_004343.3	244	gAc/gCc	6/9	1	2	FACETS	0.286	0.226	0.356	0.286	0.226	0.356	SUBCLONAL	1	TRUE	1	0.604088533315778	2		511	289	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433654	149433654	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	268	952	0	ENST00000286301.3:c.2897C>T	p.Pro966Leu	p.P966L	ENST00000286301	NM_005211.3	966	cCc/cTc	22/22	0.226704400207699	5	FACETS	1	0.984	1	0.745	0.702	0.789	INDETERMINATE	2	TRUE	2	0.604088533315778	5		952	757	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057321	180057321	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	238	1028	0	ENST00000261937.6:c.417C>A	p.Phe139Leu	p.F139L	ENST00000261937	NM_182925.4	139	ttC/ttA	4/30	0.226704400207699	5	FACETS	1	0.963	1	0.692	0.649	0.737	INDETERMINATE	2	TRUE	2	0.604088533315778	5		1028	723	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054612	5054612	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	50	314	0	ENST00000381652.3:c.664C>G	p.His222Asp	p.H222D	ENST00000381652	NM_004972.3	222	Cat/Gat	7/25	0.226704400207699	5	FACETS	1	0.903	1	0.701	0.608	0.799	INDETERMINATE	2	TRUE	2	0.604088533315778	5		314	150	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856002	111856002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	55	533	0	ENST00000341259.2:c.53C>T	p.Ser18Phe	p.S18F	ENST00000341259	NM_005475.2	18	tCc/tTc	2/8	1	2	FACETS	0.323	0.275	0.376	0.323	0.275	0.376	SUBCLONAL	1	TRUE	1	0.330575885409602	2		533	1031	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112497	115112497	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	194	714	0	ENST00000257566.3:c.1243C>A	p.His415Asn	p.H415N	ENST00000257566	NM_016569.3	415	Cac/Aac	7/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.330575885409602	2		714	1055	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023851	27023871	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCCAGGACGGGGGCGCCGG	GCCCCAGGACGGGGGCGCCGG	A	novel	NA	P-0039705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	110	268	0	ENST00000324856.7:c.957_977delinsA	p.Pro320GlnfsTer73	p.P320Qfs*73	ENST00000324856	NM_006015.4	319	ggGCCCCAGGACGGGGGCGCCGGc/ggAc	1/20	0.306912926799351	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.330575885409602	1		268	546	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0039835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	246	299	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.520405981797818	3	FACETS	0.905	0.859	0.95	0.905	0.859	0.95	CLONAL	3	TRUE	0	0.520405981797818	3		299	439	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934874	NA	P-0039835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	455	965	1	ENST00000269305.4:c.451C>A	p.Pro151Thr	p.P151T	ENST00000269305	NM_001126112.2	151	Ccc/Acc	5/11	0.471215518316133	2	FACETS	0.873	0.837	0.91	0.873	0.837	0.91	CLONAL	2	TRUE	0	0.520405981797818	2		966	1001	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913527	NA	P-0039835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	301	420	0	ENST00000311936.3:c.436G>C	p.Ala146Pro	p.A146P	ENST00000311936	NM_004985.3	146	Gca/Cca	4/5	0.49927729876752	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.520405981797818	3		420	673	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411411	63411411	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	296	254	0	ENST00000330258.3:c.1756C>T	p.Arg586Ter	p.R586*	ENST00000330258	NM_152424.3	586	Cga/Tga	2/2	0.520405981797818	2	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.520405981797818	2		254	515	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604785	48604785	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	92	406	2	ENST00000342988.3:c.1607T>C	p.Leu536Pro	p.L536P	ENST00000342988	NM_005359.5	536	cTa/cCa	12/12	0.485318260878184	1	FACETS	0.745	0.668	0.826	0.745	0.668	0.826	SUBCLONAL	1	TRUE	0	0.520405981797818	1		408	351	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212639	36212639	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1477968559	NA	P-0039835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1318	152	998	0	ENST00000222270.7:c.2390A>G	p.Lys797Arg	p.K797R	ENST00000222270	NM_014727.1	797	aAg/aGg	3/37	0.165251517248511	6	FACETS	0.811	0.739	0.887	0.27	0.246	0.296	INDETERMINATE	1	TRUE	3	0.520405981797818	6		998	1470	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702248	47702248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765493709	NA	P-0039835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	207	518	1	ENST00000233146.2:c.1844C>T	p.Ala615Val	p.A615V	ENST00000233146	NM_000251.2	615	gCa/gTa	12/16	0.496834432912592	3	FACETS	0.774	0.721	0.827	0.774	0.721	0.827	SUBCLONAL	2	TRUE	1	0.520405981797818	3		519	648	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593724	215593724	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	49	231	0	ENST00000260947.4:c.2010G>T	p.Lys670Asn	p.K670N	ENST00000260947	NM_000465.2	670	aaG/aaT	11/11	0.165251517248511	6	FACETS	0.978	0.83	1	0.326	0.276	0.38	INDETERMINATE	1	TRUE	3	0.520405981797818	6		231	393	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582100	189582100	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	278	416	0	ENST00000264731.3:c.659C>G	p.Pro220Arg	p.P220R	ENST00000264731	NM_003722.4	220	cCt/cGt	5/14	0.127782836475258	6	FACETS	0.918	0.865	0.971	0.918	0.865	0.971	INDETERMINATE	3	TRUE	3	0.520405981797818	6		416	792	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44894231	44894232	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0039835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	176	199	0	ENST00000377967.4:c.619+2dup		p.X207_splice	ENST00000377967	NM_021140.2	207			0.427847448413834	2	FACETS	0.851	0.806	0.894			1	CLONAL	3	TRUE	NA	0.520405981797818	2		199	265	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577983	7578262	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGGAGGCCCTTAGCCTCTGTAAGCTTCAGTTTTTTCAACTGTGCAATAGTTAAACCCATTTACTTTGCACATCTCATGGGGTTATAGGGAGGTCAAATAAGCAGCAGGAGAAAGCCCCCCTACTGCTCACCTGGAGGGCCACTGACAACCACCCTTAACCCCTCCTCCCAGAGACCCCAGTTGCAAACCAGACCTCAGGCGGCTCATAGGGCACCACCACACTATGTCGAAAAGTGTTTCTGTCATCCAAATACTCCACACGCAAATTTCCTTCCACTC	GGGGAGGCCCTTAGCCTCTGTAAGCTTCAGTTTTTTCAACTGTGCAATAGTTAAACCCATTTACTTTGCACATCTCATGGGGTTATAGGGAGGTCAAATAAGCAGCAGGAGAAAGCCCCCCTACTGCTCACCTGGAGGGCCACTGACAACCACCCTTAACCCCTCCTCCCAGAGACCCCAGTTGCAAACCAGACCTCAGGCGGCTCATAGGGCACCACCACACTATGTCGAAAAGTGTTTCTGTCATCCAAATACTCCACACGCAAATTTCCTTCCACTC	-	novel	NA	P-0039927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	200	97	0	ENST00000269305.4:c.587_672+194del		p.X196_splice	ENST00000269305	NM_001126112.2	196		6/11	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.71303275788683	2		97	233	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556250	29556250	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs199474739	NA	P-0039927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	245	376	0	ENST00000356175.3:c.2617C>G	p.Arg873Gly	p.R873G	ENST00000356175	NM_000267.3	873	Cgt/Ggt	21/57	0.71303275788683	1	FACETS	0.97	0.92	1	0.97	0.92	1	CLONAL	1	TRUE	0	0.71303275788683	1		376	456	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721810	176721810	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1297747587	NA	P-0039927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	59	452	0	ENST00000439151.2:c.7441G>A	p.Glu2481Lys	p.E2481K	ENST00000439151	NM_022455.4	2481	Gag/Aag	23/23	0.48956421885438	3	FACETS	0.243	0.209	0.282	0.122	0.104	0.141	SUBCLONAL	1	TRUE	1	0.71303275788683	3		452	922	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729978	41729978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	323	562	1	ENST00000242208.4:c.551G>A	p.Gly184Asp	p.G184D	ENST00000242208	NM_002192.2	184	gGc/gAc	3/3	1	2	FACETS	0.93	0.88	0.981	0.93	0.88	0.981	CLONAL	1	TRUE	1	0.71303275788683	2		563	974	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	107	668	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.27	2		668	703	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573229	64573229	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863224807	NA	P-0039985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	85	631	1	ENST00000312049.6:c.1063C>T	p.Arg355Trp	p.R355W	ENST00000312049	NM_130799.2	355	Cgg/Tgg	8/10	0.269328878205628	3	FACETS	0.914	0.807	1			1	CLONAL	1	TRUE	NA	0.27	3		632	782	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	214	406	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.395136159391622	3	FACETS	0.995	0.929	1	0.995	0.929	1	CLONAL	2	TRUE	1	0.395136159391622	3		406	652	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0040202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	180	779	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.392399235208608	1	FACETS	0.97	0.896	1	0.97	0.896	1	CLONAL	1	TRUE	0	0.395136159391622	1		779	754	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839736	27839745	+	frameshift_variant	Frame_Shift_Del	DEL	TAGTGACGCG	TAGTGACGCG	CAC	novel	NA	P-0040202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	118	627	0	ENST00000328488.2:c.349_358delinsGTG	p.Arg117ValfsTer?	p.R117Vfs*?	ENST00000328488	NM_003533.2	117	CGCGTCACTAtt/GTGtt	1/1	0.209852020804028	3	FACETS	0.946	0.854	1	0.473	0.427	0.522	INDETERMINATE	1	TRUE	1	0.395136159391622	3		627	756	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552891	106552891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771056895	NA	P-0000158-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	244	902	0	ENST00000369096.4:c.856C>T	p.Arg286Cys	p.R286C	ENST00000369096	NM_001198.3	286	Cgt/Tgt	5/7	0.199347113582115	2	FACETS	0.789	0.735	0.844	0.789	0.735	0.844	SUBCLONAL	2	FALSE	0	0.220618771398121	2		902	1402	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436912	49436912	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000158-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	54	465	0	ENST00000301067.7:c.5591del	p.Gly1864AlafsTer12	p.G1864Afs*12	ENST00000301067	NM_003482.3	1864	gGc/gc	25/54	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.220618771398121	NA		465	864	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0000449-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	180	247	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.527089817481392	1	FACETS	0.979	0.91	1	0.979	0.91	1	CLONAL	1	TRUE	0	0.526807150845727	1		247	514	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0000449-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	178	247	1	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	0.494387722552276	1	FACETS	0.943	0.875	1	0.943	0.875	1	CLONAL	1	TRUE	0	0.526807150845727	1		248	528	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126418	5126418	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000449-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	108	241	0	ENST00000381652.3:c.3263T>C	p.Leu1088Ser	p.L1088S	ENST00000381652	NM_004972.3	1088	tTa/tCa	24/25	0.284144106279065	2	FACETS	0.55	0.494	0.61	0.275	0.247	0.305	INDETERMINATE	1	TRUE	0	0.526807150845727	2		241	745	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404290	139404290	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs557049479	NA	P-0000449-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	396	338	0	ENST00000277541.6:c.2864G>A	p.Arg955His	p.R955H	ENST00000277541	NM_017617.3	955	cGc/cAc	18/34	0.284144106279065	2	FACETS	0.855	0.817	0.893	0.855	0.817	0.893	INDETERMINATE	2	TRUE	0	0.526807150845727	2		338	879	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596002	43596002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876658284	NA	P-0000449-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	133	362	0	ENST00000355710.3:c.169C>T	p.Arg57Trp	p.R57W	ENST00000355710	NM_020975.4	57	Cgg/Tgg	2/20	0.117066452582824	5	FACETS	0.904	0.82	0.993	0.226	0.205	0.249	INDETERMINATE	1	TRUE	1	0.526807150845727	5		362	1000	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156760	2156760	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0000449-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	79	376	0	ENST00000434045.2:c.163-1G>T		p.X55_splice	ENST00000434045	NM_001127598.1	55			1		FACETS		0.315	0.407				SUBCLONAL	1	TRUE	1	0.526807150845727	2		376	835	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395738	45395738	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000449-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	303	352	0	ENST00000262160.6:c.396G>A	p.Trp132Ter	p.W132*	ENST00000262160	NM_005901.5	132	tgG/tgA	4/11	0.527089817481392	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.526807150845727	1		352	731	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950437	17950437	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000449-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	41	309	0	ENST00000458235.1:c.1290C>G	p.Ile430Met	p.I430M	ENST00000458235	NM_000215.3	430	atC/atG	10/24	0.527089817481392	1	FACETS	0.189	0.157	0.225	0.189	0.157	0.225	SUBCLONAL	1	TRUE	0	0.526807150845727	1		309	606	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819743	170819745	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0000449-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	83	169	0	ENST00000296930.5:c.384_386del	p.Glu131del	p.E131del	ENST00000296930	NM_002520.6	128	GAA/-	5/11	1	2	FACETS	0.618	0.547	0.694	0.618	0.547	0.694	SUBCLONAL	1	TRUE	1	0.526807150845727	2		169	510	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423453	116423454	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000449-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	173	371	0	ENST00000397752.3:c.3731dup	p.Leu1245AlafsTer42	p.L1245Afs*42	ENST00000397752	NM_000245.2	1243	gca/gcAa	19/21	0.526807150845727	2	FACETS	0.681	0.626	0.737	0.34	0.313	0.369	SUBCLONAL	1	TRUE	0	0.526807150845727	2		371	965	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332272	70332273	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1446158817	NA	P-0000449-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	139	516	1	ENST00000373644.4:c.184dup	p.Thr62AsnfsTer4	p.T62Nfs*4	ENST00000373644	NM_030625.2	59	-/A	2/12	0.117066452582824	5	FACETS	0.753	0.684	0.827	0.188	0.171	0.207	INDETERMINATE	1	TRUE	1	0.526807150845727	5		517	1254	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717769	89717770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000449-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	100	154	0	ENST00000371953.3:c.800dup	p.Asp268GlyfsTer30	p.D268Gfs*30	ENST00000371953	NM_000314.4	265	cta/ctAa	7/9	0.527089817481392	1	FACETS	0.82	0.74	0.903	0.82	0.74	0.903	CLONAL	1	TRUE	0	0.526807150845727	1		154	341	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944900	31944901	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000449-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	65	118	0	ENST00000340398.3:c.200dup	p.Gln68ProfsTer14	p.Q68Pfs*14	ENST00000340398	NM_001013699.2	67	ttc/ttTc	1/1	1	2	FACETS	0.628	0.547	0.715	0.628	0.547	0.715	SUBCLONAL	1	TRUE	1	0.526807150845727	2		118	393	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488208	56488208	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748808887	NA	P-0000449-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	62	262	0	ENST00000267101.3:c.1727G>A	p.Cys576Tyr	p.C576Y	ENST00000267101	NM_001982.3	576	tGt/tAt	15/28	1	2	FACETS	0.273	0.235	0.315	0.273	0.235	0.315	SUBCLONAL	1	TRUE	1	0.526807150845727	2		262	862	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657460	29657460	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000449-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	64	347	0	ENST00000356175.3:c.5693A>G	p.Glu1898Gly	p.E1898G	ENST00000356175	NM_000267.3	1898	gAg/gGg	38/57	1	2	FACETS	0.235	0.202	0.27	0.235	0.202	0.27	SUBCLONAL	1	TRUE	1	0.526807150845727	2		347	1035	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339248	87339249	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0000449-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	133	287	0	ENST00000277120.3:c.832dup	p.Ser278PhefsTer43	p.S278Ffs*43	ENST00000277120		277	gat/gaTt	8/19	0.284144106279065	2	FACETS	0.55	0.499	0.604	0.275	0.249	0.302	INDETERMINATE	1	TRUE	0	0.526807150845727	2		287	918	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029445	16029446	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0000449-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	550	520	6	ENST00000268712.3:c.1584dup	p.Glu529ArgfsTer7	p.E529Rfs*7	ENST00000268712	NM_006311.3	528	-/A	15/46	1	2	FACETS	0.835	0.801	0.87	0.835	0.801	0.87	CLONAL	1	TRUE	1	0.815303325395036	2		526	1616	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0000449-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	326	247	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.815303325395036	1	FACETS	0.995	0.958	1	0.995	0.958	1	CLONAL	1	TRUE	0	0.815303325395036	1		247	476	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0000449-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	263	247	1	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	0.748152044613127	1	FACETS	0.934	0.893	0.975	0.934	0.893	0.975	CLONAL	1	TRUE	0	0.815303325395036	1		248	409	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126418	5126418	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000449-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	50	241	0	ENST00000381652.3:c.3263T>C	p.Leu1088Ser	p.L1088S	ENST00000381652	NM_004972.3	1088	tTa/tCa	24/25	0.524483931996897	1	FACETS	0.137	0.116	0.161	0.137	0.116	0.161	SUBCLONAL	1	TRUE	0	0.815303325395036	1		241	529	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404290	139404290	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs557049479	NA	P-0000449-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	369	338	0	ENST00000277541.6:c.2864G>A	p.Arg955His	p.R955H	ENST00000277541	NM_017617.3	955	cGc/cAc	18/34	0.815303325395036	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.815303325395036	1		338	524	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596002	43596002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876658284	NA	P-0000449-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	172	362	0	ENST00000355710.3:c.169C>T	p.Arg57Trp	p.R57W	ENST00000355710	NM_020975.4	57	Cgg/Tgg	2/20	0.421484369976413	2	FACETS	0.587	0.541	0.634	0.293	0.27	0.317	INDETERMINATE	1	TRUE	0	0.815303325395036	2		362	719	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156760	2156760	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0000449-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	171	376	0	ENST00000434045.2:c.163-1G>T		p.X55_splice	ENST00000434045	NM_001127598.1	55			1		FACETS		0.493	0.58				SUBCLONAL	1	TRUE	1	0.815303325395036	2		376	783	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395738	45395738	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000449-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	389	352	0	ENST00000262160.6:c.396G>A	p.Trp132Ter	p.W132*	ENST00000262160	NM_005901.5	132	tgG/tgA	4/11	0.815303325395036	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.815303325395036	1		352	521	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950437	17950437	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000449-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	154	309	0	ENST00000458235.1:c.1290C>G	p.Ile430Met	p.I430M	ENST00000458235	NM_000215.3	430	atC/atG	10/24	0.400713474336527	1	FACETS	0.43	0.396	0.466	0.43	0.396	0.466	INDETERMINATE	1	TRUE	0	0.815303325395036	1		309	520	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819743	170819745	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0000449-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	114	169	0	ENST00000296930.5:c.384_386del	p.Glu131del	p.E131del	ENST00000296930	NM_002520.6	128	GAA/-	5/11	1	2	FACETS	0.447	0.403	0.494	0.447	0.403	0.494	SUBCLONAL	1	TRUE	1	0.815303325395036	2		169	625	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423453	116423454	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000449-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	182	371	0	ENST00000397752.3:c.3731dup	p.Leu1245AlafsTer42	p.L1245Afs*42	ENST00000397752	NM_000245.2	1243	gca/gcAa	19/21	0.792477300733559	2	FACETS	0.535	0.494	0.578	0.268	0.247	0.289	SUBCLONAL	1	TRUE	0	0.815303325395036	2		371	834	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332272	70332273	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1446158817	NA	P-0000449-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	249	516	1	ENST00000373644.4:c.184dup	p.Thr62AsnfsTer4	p.T62Nfs*4	ENST00000373644	NM_030625.2	59	-/A	2/12	NA	2	FACETS	0.484	0.451	0.517			1	INDETERMINATE	1	TRUE	NA	0.815303325395036	2		517	1263	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717769	89717770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000449-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	75	154	0	ENST00000371953.3:c.800dup	p.Asp268GlyfsTer30	p.D268Gfs*30	ENST00000371953	NM_000314.4	265	cta/ctAa	7/9	0.815303325395036	1	FACETS	0.752	0.68	0.823	0.752	0.68	0.823	SUBCLONAL	1	TRUE	0	0.815303325395036	1		154	145	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944900	31944901	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000449-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	101	118	0	ENST00000340398.3:c.200dup	p.Gln68ProfsTer14	p.Q68Pfs*14	ENST00000340398	NM_001013699.2	67	ttc/ttTc	1/1	NA	2	FACETS	0.486	0.436	0.539			1	INDETERMINATE	1	TRUE	NA	0.815303325395036	2		118	510	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99162489	99162489	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000449-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	158	556	0	ENST00000074304.5:c.1007C>A	p.Thr336Lys	p.T336K	ENST00000074304	NM_001134224.1	336	aCa/aAa	12/26	1	2	FACETS	0.467	0.428	0.508	0.467	0.428	0.508	SUBCLONAL	1	TRUE	1	0.815303325395036	2		556	830	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890293	72890293	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000449-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	67	503	0	ENST00000325599.8:c.389A>G	p.Glu130Gly	p.E130G	ENST00000325599	NM_018130.2	130	gAg/gGg	4/11	NA	2	FACETS	0.168	0.146	0.193			1	INDETERMINATE	1	TRUE	NA	0.815303325395036	2		503	976	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456547	138456547	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0000449-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	70	451	0	ENST00000289153.2:c.801+2T>C		p.X267_splice	ENST00000289153	NM_006219.2	267			0.527971825240146	3	FACETS	0.235	0.204	0.269	0.118	0.102	0.135	SUBCLONAL	1	TRUE	1	0.815303325395036	3		451	1028	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288333	33288333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200104639	NA	P-0000449-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	43	300	0	ENST00000374542.5:c.1075C>T	p.Arg359Trp	p.R359W	ENST00000374542	NM_001141970.1	359	Cgg/Tgg	4/8	0.400713474336527	1	FACETS	0.102	0.085	0.122	0.102	0.085	0.122	INDETERMINATE	1	TRUE	0	0.815303325395036	1		300	610	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552711	106552711	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000449-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	75	541	0	ENST00000369096.4:c.676A>C	p.Ser226Arg	p.S226R	ENST00000369096	NM_001198.3	226	Agc/Cgc	5/7	0.400713474336527	1	FACETS	0.118	0.103	0.135	0.118	0.103	0.135	INDETERMINATE	1	TRUE	0	0.815303325395036	1		541	922	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38506100	38506100	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000449-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	74	475	0	ENST00000254066.5:c.392T>C	p.Ile131Thr	p.I131T	ENST00000254066	NM_000964.3	131	aTc/aCc	4/9	1	2	FACETS	0.179	0.156	0.204	0.179	0.156	0.204	SUBCLONAL	1	TRUE	1	0.815303325395036	2		475	1016	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40462634	40462634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774831875	NA	P-0000449-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1243	98	913	1	ENST00000345506.4:c.2332C>T	p.Arg778Cys	p.R778C	ENST00000345506	NM_003152.3	778	Cgc/Tgc	20/20	NA	2	FACETS	0.179	0.159	0.201			1	INDETERMINATE	1	TRUE	NA	0.815303325395036	2		914	1341	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799164	42799164	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000449-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	26	245	0	ENST00000575354.2:c.4648A>G	p.Thr1550Ala	p.T1550A	ENST00000575354	NM_015125.3	1550	Act/Gct	20/20	NA	2	FACETS	0.175	0.138	0.217			1	INDETERMINATE	1	TRUE	NA	0.815303325395036	2		245	364	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626859	14626860	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0000449-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1340	247	886	0	ENST00000254322.2:c.915dup	p.Lys306GlnfsTer12	p.K306Qfs*12	ENST00000254322	NM_006145.1	305	-/C	3/3	0.400713474336527	1	FACETS	0.226	0.21	0.243	0.226	0.21	0.243	INDETERMINATE	1	TRUE	0	0.815303325395036	1		886	1587	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812165	212812165	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000541-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	133	668	0	ENST00000342788.4:c.411G>C	p.Lys137Asn	p.K137N	ENST00000342788	NM_005235.2	137	aaG/aaC	3/28	0.168426908602233	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.168426908602233	2		668	682	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486143	8486143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370631792	NA	P-0000541-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	161	837	0	ENST00000356435.5:c.2674G>A	p.Val892Ile	p.V892I	ENST00000356435		892	Gtc/Atc	17/35	0.168426908602233	2	FACETS	1	0.967	1	1	0.99	1	CLONAL	3	TRUE	0	0.168426908602233	2		837	585	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987002	36987002	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000541-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	25	499	0	ENST00000354822.5:c.687C>G	p.His229Gln	p.H229Q	ENST00000354822	NM_001079668.2	229	caC/caG	3/3	0.168426908602233	6	FACETS	0.959	0.76	1	0.639	0.506	0.79	CLONAL	2	TRUE	3	0.168426908602233	6		499	207	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812165	212812165	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	72	668	0	ENST00000342788.4:c.411G>C	p.Lys137Asn	p.K137N	ENST00000342788	NM_005235.2	137	aaG/aaC	3/28	0.130166889868921	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	0	0.130166889868921	1		668	717	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486143	8486143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370631792	NA	P-0000541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	96	837	0	ENST00000356435.5:c.2674G>A	p.Val892Ile	p.V892I	ENST00000356435		892	Gtc/Atc	17/35	1	2	FACETS	0.953	0.849	1	1	0.985	1	CLONAL	2	FALSE	1	0.130166889868921	2		837	774	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41228535	41228535	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	104	881	0	ENST00000357654.3:c.4454C>G	p.Thr1485Ser	p.T1485S	ENST00000357654	NM_007294.3	1485	aCc/aGc	13/23	0.130166889868921	1	FACETS	0.818	0.732	0.91	1	0.984	1	CLONAL	2	FALSE	0	0.130166889868921	1		881	913	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061133	38061191	+	frameshift_variant	Frame_Shift_Del	DEL	CGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTG	CGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTG	-	novel	NA	P-0000541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	63	70	0	ENST00000250448.2:c.798_856del	p.Phe266LeufsTer7	p.F266Lfs*7	ENST00000250448	NM_004496.3	266	ttCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGCGgc/ttgc	2/2	0.130166889868921	1	FACETS	0.965	0.861	1	1	0.988	1	CLONAL	7	FALSE	0	0.130166889868921	1		70	134	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812165	212812165	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000541-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	202	668	0	ENST00000342788.4:c.411G>C	p.Lys137Asn	p.K137N	ENST00000342788	NM_005235.2	137	aaG/aaC	3/28	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.728441204657692	2		668	528	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486143	8486143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370631792	NA	P-0000541-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	225	837	0	ENST00000356435.5:c.2674G>A	p.Val892Ile	p.V892I	ENST00000356435		892	Gtc/Atc	17/35	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.728441204657692	2		837	581	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41228535	41228535	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000541-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	325	881	0	ENST00000357654.3:c.4454C>G	p.Thr1485Ser	p.T1485S	ENST00000357654	NM_007294.3	1485	aCc/aGc	13/23	1	2	FACETS	0.952	0.902	1	0.952	0.902	1	CLONAL	1	TRUE	1	0.728441204657692	2		881	937	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061133	38061191	+	frameshift_variant	Frame_Shift_Del	DEL	CGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTG	CGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTG	-	novel	NA	P-0000541-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	217	70	0	ENST00000250448.2:c.798_856del	p.Phe266LeufsTer7	p.F266Lfs*7	ENST00000250448	NM_004496.3	266	ttCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGCGgc/ttgc	2/2	0.728441204657692	3	FACETS	0.838	0.788	0.888	0.838	0.788	0.888	CLONAL	2	TRUE	1	0.728441204657692	3		70	485	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692660	89692804	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTTTTAAATACCTGTTAAGTTTGTATGCAACATTTCTAAAGTTACCTACTTGTTAATTAAAAATTCAAGAGTTTTTTTTTCTTATTCTGAGGTTATCTTTTTACCACAGTTGCACAATATCCTTTTGAAGACCATAACCCACCA	TCTTTTAAATACCTGTTAAGTTTGTATGCAACATTTCTAAAGTTACCTACTTGTTAATTAAAAATTCAAGAGTTTTTTTTTCTTATTCTGAGGTTATCTTTTTACCACAGTTGCACAATATCCTTTTGAAGACCATAACCCACCA	-	novel	NA	P-0000541-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	49	116	0	ENST00000371953.3:c.254-110_288del		p.X85_splice	ENST00000371953	NM_000314.4	85		5/9	0.728441204657692	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.728441204657692	1		116	77	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724286	112724286	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000541-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	336	985	0	ENST00000369452.4:c.170C>G	p.Ser57Cys	p.S57C	ENST00000369452	NM_007373.3	57	tCc/tGc	2/9	0.728441204657692	1	FACETS	0.931	0.89	0.972	0.931	0.89	0.972	CLONAL	1	TRUE	0	0.728441204657692	1		985	630	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571767	64572614	+	splice_acceptor_variant,splice_donor_variant,stop_lost,3_prime_UTR_variant,intron_variant	Splice_Site	DEL	AGCCTGGGTCCCCACAAGCGGTCCGAAGTCCCCAGTAGTTCAGAGGCCTTTGCGCTGCCGCTTGAGGAAAGACAGAGTGTAGTCACTAGGGGTGGACACTTTCTGCTTCTTCATCTGCACTTGCGACTGTGCCGTGAGTTGCAGCTTGATGGCGCTCGAGTTGATCTTGGTGGCCACCAGCAGCTCCTTCATGCCCTTCATCTTCTCACTCTGGAAAGTGAGCACTGGACCCTCCGGCGGTGGTGATGCTGTGGGTGCTGGCACCTGAGCCGTGCTGCCACCTTCAGGGCCTCGGGCTGTGCCAGCGACAGTCCCAGGAGGCTTCCGGGGGGGTCCTGACACTGCACCCTGGCCGGTGCCCAGGCCCTTGTCCAGTGCTGGCTTCTTGGGCGGCGGGGGCTCCTCTGGCTTGGACTCCCGCCGTGGGCCCCGCCGCCGGCCTTCCCGGGCTTCCTCGCCCCACGGCTCCTCGGCCTCGGCCGCCTCGGCCTCTCGGCTCACTATGCGCACCTTCTGCCGCACCTGGGCCAGTGGGGAGAGCAAGGTGAGAGCAAGGTTGCCGGCCAGTGGCTGGAACTCCAGGACCCTGCTCTGGCCATCCCATCCCACCCAGGGGGTCTCAGTCCCATCGGCACCCAAGGGGATGGGCAGATGCTGCCCCTGGGCCAGAAAAGTCTGACAAGCCCGTGGCTGCTGTCACCACCTGTAGTGCCCAGACCTCTGTGCAGCTGTCCCTCACCTGTCCCTCAAAACGGCCTAGGGACTGCACAAGAAAGGTGGCCCAGCCCACATGCAGCACAGGCGTGGGACTGCCCTCCTCCCATTTGCAGATGCCGTCGTAGAATCGC	AGCCTGGGTCCCCACAAGCGGTCCGAAGTCCCCAGTAGTTCAGAGGCCTTTGCGCTGCCGCTTGAGGAAAGACAGAGTGTAGTCACTAGGGGTGGACACTTTCTGCTTCTTCATCTGCACTTGCGACTGTGCCGTGAGTTGCAGCTTGATGGCGCTCGAGTTGATCTTGGTGGCCACCAGCAGCTCCTTCATGCCCTTCATCTTCTCACTCTGGAAAGTGAGCACTGGACCCTCCGGCGGTGGTGATGCTGTGGGTGCTGGCACCTGAGCCGTGCTGCCACCTTCAGGGCCTCGGGCTGTGCCAGCGACAGTCCCAGGAGGCTTCCGGGGGGGTCCTGACACTGCACCCTGGCCGGTGCCCAGGCCCTTGTCCAGTGCTGGCTTCTTGGGCGGCGGGGGCTCCTCTGGCTTGGACTCCCGCCGTGGGCCCCGCCGCCGGCCTTCCCGGGCTTCCTCGCCCCACGGCTCCTCGGCCTCGGCCGCCTCGGCCTCTCGGCTCACTATGCGCACCTTCTGCCGCACCTGGGCCAGTGGGGAGAGCAAGGTGAGAGCAAGGTTGCCGGCCAGTGGCTGGAACTCCAGGACCCTGCTCTGGCCATCCCATCCCACCCAGGGGGTCTCAGTCCCATCGGCACCCAAGGGGATGGGCAGATGCTGCCCCTGGGCCAGAAAAGTCTGACAAGCCCGTGGCTGCTGTCACCACCTGTAGTGCCCAGACCTCTGTGCAGCTGTCCCTCACCTGTCCCTCAAAACGGCCTAGGGACTGCACAAGAAAGGTGGCCCAGCCCACATGCAGCACAGGCGTGGGACTGCCCTCCTCCCATTTGCAGATGCCGTCGTAGAATCGC	-	novel	NA	P-0000541-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	147	563	0	ENST00000312049.6:c.1242_*39del		p.X414_splice	ENST00000312049	NM_130799.2	414		9-10/10	1	2	FACETS	0.769	0.706	0.834	0.769	0.706	0.834	SUBCLONAL	1	TRUE	1	0.728441204657692	2		563	525	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639975	3639975	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000541-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	318	875	0	ENST00000294008.3:c.3664C>G	p.Leu1222Val	p.L1222V	ENST00000294008	NM_032444.2	1222	Ctg/Gtg	12/15	0.728441204657692	3	FACETS	0.972	0.917	1	0.324	0.305	0.343	CLONAL	1	TRUE	0	0.728441204657692	3		875	1225	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630177	47630419	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	GACTCCCACCCACCGAAACGCAGCCCTGGAAGCTGATTGGGTGTGGTCGCCGTGGCCGGACGCCGCTCGGGGGACGTGGGAGGGGAGGCGGGAAACAGCTTAGTGGGTGTGGGGTCGCGCATTTTCTTCAACCAGGAGGTGAGGAGGTTTCGACATGGCGGTGCAGCCGAAGGAGACGCTGCAGTTGGAGAGCGCGGCCGAGGTCGGCTTCGTGCGCTTCTTTCAGGGCATGCCGGAGAAGCC	GACTCCCACCCACCGAAACGCAGCCCTGGAAGCTGATTGGGTGTGGTCGCCGTGGCCGGACGCCGCTCGGGGGACGTGGGAGGGGAGGCGGGAAACAGCTTAGTGGGTGTGGGGTCGCGCATTTTCTTCAACCAGGAGGTGAGGAGGTTTCGACATGGCGGTGCAGCCGAAGGAGACGCTGCAGTTGGAGAGCGCGGCCGAGGTCGGCTTCGTGCGCTTCTTTCAGGGCATGCCGGAGAAGCC	-	novel	NA	P-0000541-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	154	47	0	ENST00000233146.2:c.-151_92del		p.*51*	ENST00000233146	NM_000251.2	?-30/934		1/16	1	2	FACETS	1	0.99	1	1	0.994	1	CLONAL	2	TRUE	1	0.728441204657692	2		47	186	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467633	50467633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000707-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	21	126	0	ENST00000331340.3:c.868G>A	p.Asp290Asn	p.D290N	ENST00000331340	NM_006060.4	290	Gac/Aac	8/8	0.242492414378934	4	FACETS	0.44	0.338	0.559	0.22	0.169	0.28	SUBCLONAL	1	TRUE	2	0.395156224458681	4		126	337	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360551	118360551	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1349887077	NA	P-0000707-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	85	401	0	ENST00000534358.1:c.4524G>C	p.Glu1508Asp	p.E1508D	ENST00000534358	NM_005933.3	1508	gaG/gaC	12/36	0.293994309850932	2	FACETS	0.76	0.673	0.853	0.38	0.336	0.427	SUBCLONAL	1	TRUE	0	0.395156224458681	2		401	566	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679576	86679576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	21	416	0	ENST00000274376.6:c.2737C>T	p.Arg913Trp	p.R913W	ENST00000274376	NM_002890.2	913	Cgg/Tgg	21/25	1	2	FACETS	0.356	0.275	0.45	0.356	0.275	0.45	SUBCLONAL	1	TRUE	1	0.5	2		416	236	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577098	7577098	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001157-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	473	626	0	ENST00000269305.4:c.840A>T	p.Arg280Ser	p.R280S	ENST00000269305	NM_001126112.2	280	agA/agT	8/11	1	2	FACETS	0.864	0.826	0.902	1	0.997	1	CLONAL	2	TRUE	1	0.406294283888243	2		626	1348	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061137	38061167	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCCCGCTTCCGCTCCCGCCCCCGCCGCCG	GCCCCCGCTTCCGCTCCCGCCCCCGCCGCCG	-	novel	NA	P-0001221-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	122	93	1	ENST00000250448.2:c.822_852del	p.Gly275AlafsTer36	p.G275Afs*36	ENST00000250448	NM_004496.3	274	gcCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGC/gc	2/2	1	2	FACETS	1	0.941	1	1	0.992	1	CLONAL	2	TRUE	1	0.667347389048817	2		94	182	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0001326-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	618	283	303	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.497061964115846	4	FACETS	0.896	0.844	0.949	0.896	0.844	0.949	CLONAL	2	TRUE	2	0.539604473764625	4		303	901	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0001326-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	252	303	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.714357702762369	4	FACETS	0.99	0.933	1	0.99	0.933	1	CLONAL	2	TRUE	2	0.714357702762369	4		303	611	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118354966	118354966	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001326-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	71	540	0	ENST00000534358.1:c.4155T>G	p.Asn1385Lys	p.N1385K	ENST00000534358	NM_005933.3	1385	aaT/aaG	9/36	0.714357702762369	3	FACETS	0.423	0.369	0.481	0.211	0.184	0.241	SUBCLONAL	1	TRUE	1	0.714357702762369	3		540	638	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032332	10032332	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001326-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	31	460	1	ENST00000330684.3:c.491A>G	p.Asp164Gly	p.D164G	ENST00000330684	NM_001134407.1	164	gAt/gGt	3/13	0.714357702762369	3	FACETS	0.239	0.193	0.291	0.119	0.096	0.146	SUBCLONAL	1	TRUE	1	0.714357702762369	3		461	493	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37871740	37871740	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769778398	NA	P-0001326-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	95	701	0	ENST00000269571.5:c.1264C>T	p.Leu422Phe	p.L422F	ENST00000269571		422	Ctc/Ttc	11/27	0.324654839098218	6	FACETS	0.618	0.549	0.692	0.206	0.183	0.231	INDETERMINATE	1	TRUE	3	0.714357702762369	6		701	1045	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271637	15271637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs996150018	NA	P-0001326-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	53	851	1	ENST00000263388.2:c.6802G>A	p.Glu2268Lys	p.E2268K	ENST00000263388	NM_000435.2	2268	Gaa/Aaa	33/33	0.714357702762369	3	FACETS	0.202	0.172	0.236	0.101	0.086	0.118	SUBCLONAL	1	TRUE	1	0.714357702762369	3		852	995	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257028	198257034	+	frameshift_variant,stop_lost	Frame_Shift_Del	DEL	TATAAGA	TATAAGA	-	novel	NA	P-0001326-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	29	317	0	ENST00000335508.6:c.3908_3914del	p.Ile1303AsnfsTer20	p.I1303Nfs*20	ENST00000335508	NM_012433.2	1303	aTCTTATAa/aa	25/25	0.714357702762369	4	FACETS	0.311	0.249	0.381	0.155	0.124	0.191	SUBCLONAL	1	TRUE	2	0.714357702762369	4		317	448	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349012	70349012	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001326-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	80	580	0	ENST00000374080.3:c.3524del	p.Ile1175ThrfsTer23	p.I1175Tfs*23	ENST00000374080		1175	aTc/ac	25/45	1	2	FACETS	0.424	0.374	0.478	0.424	0.374	0.478	SUBCLONAL	1	TRUE	1	0.714357702762369	2		580	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0002897-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	38	380	1	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	1	2	FACETS	0.999	0.836	1	0.999	0.836	1	CLONAL	1	TRUE	1	0.43	2		381	177	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004651	16004651	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1284332015	NA	P-0002897-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	41	443	0	ENST00000268712.3:c.2603C>T	p.Ala868Val	p.A868V	ENST00000268712	NM_006311.3	868	gCc/gTc	20/46	1	2	FACETS	0.953	0.803	1	0.953	0.803	1	CLONAL	1	TRUE	1	0.43	2		443	200	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0002897-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	44	495	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	1	2	FACETS	0.984	0.834	1	0.984	0.834	1	CLONAL	1	TRUE	1	0.43	2		495	208	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003777-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	201	188	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.932	0.872	0.992	0.932	0.872	0.992	CLONAL	1	TRUE	1	0.878806747709012	2		188	491	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0003777-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	1784	949	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.878806747709012	6	FACETS	0.974	0.961	0.988	0.974	0.961	0.988	CLONAL	5	TRUE	1	0.878806747709012	6		949	2298	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692799	89692799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003777-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	372	560	0	ENST00000371953.3:c.283C>T	p.Pro95Ser	p.P95S	ENST00000371953	NM_000314.4	95	Cca/Tca	5/9	0.878806747709012	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.878806747709012	2		560	417	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619180	37619180	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003777-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	306	728	0	ENST00000447079.4:c.856C>T	p.Gln286Ter	p.Q286*	ENST00000447079	NM_015083.1	286	Cag/Tag	1/14	1	2	FACETS	0.982	0.932	1	0.982	0.932	1	CLONAL	1	TRUE	1	0.878806747709012	2		728	709	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578287	212578287	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	160	499	0	ENST00000342788.4:c.970A>C	p.Lys324Gln	p.K324Q	ENST00000342788	NM_005235.2	324	Aaa/Caa	8/28	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.312496562878185	2		499	943	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770006	56770006	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0003843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	70	213	0	ENST00000337432.4:c.2T>C	p.Met1?	p.M1?	ENST00000337432	NM_058216.2	1	aTg/aCg	1/9	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.312496562878185	2		213	415	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240632	53240724	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGCCTAAGCTCACACAGCTGACACGTAACCATGAATCATCCACTCACCTCCTCTTCGGGGGTTAGGTGCCGTTTACTGTCACTGACAGGGAAA	TGCCTAAGCTCACACAGCTGACACGTAACCATGAATCATCCACTCACCTCCTCTTCGGGGGTTAGGTGCCGTTTACTGTCACTGACAGGGAAA	-	novel	NA	P-0003843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	103	196	0	ENST00000375401.3:c.1356_1401+47del		p.X452_splice	ENST00000375401	NM_004187.3	452		10/26	1	1	FACETS	0.866	0.785	0.951	1	0.987	1	CLONAL	2	TRUE	0	0.312496562878185	1		196	321	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191470	10191470	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0003843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	85	217	0	ENST00000256474.2:c.464-1del		p.X155_splice	ENST00000256474	NM_000551.3	155			0.312496562878185	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.312496562878185	1		217	417	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591118	67591132	+	inframe_deletion	In_Frame_Del	DEL	ATCCAGCTGAGAAAG	ATCCAGCTGAGAAAG	-	novel	NA	P-0003843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	47	183	0	ENST00000274335.5:c.1712_1726del	p.Ile571_Lys575del	p.I571_K575del	ENST00000274335		571	ATCCAGCTGAGAAAG/-	12/15	0.296324093071634	2	FACETS	0.69	0.583	0.808	0.345	0.291	0.404	SUBCLONAL	1	TRUE	0	0.312496562878185	2		183	436	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911088	29911099	+	inframe_deletion	In_Frame_Del	DEL	GGACGGGCGCTT	GGACGGGCGCTT	-	novel	NA	P-0003843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	24	254	0	ENST00000376809.5:c.387_398del	p.Asp130_Phe133del	p.D130_F133del	ENST00000376809	NM_002116.7	129	tcGGACGGGCGCTTc/tcc	3/8	0.312496562878185	1	FACETS	0.373	0.293	0.467	0.373	0.293	0.467	SUBCLONAL	1	TRUE	0	0.312496562878185	1		254	347	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578287	212578287	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003843-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	39	499	0	ENST00000342788.4:c.970A>C	p.Lys324Gln	p.K324Q	ENST00000342788	NM_005235.2	324	Aaa/Caa	8/28	0.30298402806736	5	FACETS	0.845	0.703	1	0.282	0.234	0.334	INDETERMINATE	1	FALSE	2	0.531651816634294	5		499	312	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240632	53240724	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGCCTAAGCTCACACAGCTGACACGTAACCATGAATCATCCACTCACCTCCTCTTCGGGGGTTAGGTGCCGTTTACTGTCACTGACAGGGAAA	TGCCTAAGCTCACACAGCTGACACGTAACCATGAATCATCCACTCACCTCCTCTTCGGGGGTTAGGTGCCGTTTACTGTCACTGACAGGGAAA	-	novel	NA	P-0003843-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	43	196	0	ENST00000375401.3:c.1356_1401+47del		p.X452_splice	ENST00000375401	NM_004187.3	452		10/26	0.482510984436164	2	FACETS	1	0.965	1			1	CLONAL	1	FALSE	NA	0.531651816634294	2		196	108	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191470	10191470	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0003843-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	42	217	0	ENST00000256474.2:c.464-1del		p.X155_splice	ENST00000256474	NM_000551.3	155			0.532925971616404	4	FACETS	1	0.944	1	0.427	0.361	0.498	CLONAL	1	FALSE	1	0.531651816634294	4		217	189	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444301	50444301	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003843-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	22	152	0	ENST00000331340.3:c.231A>T	p.Glu77Asp	p.E77D	ENST00000331340	NM_006060.4	77	gaA/gaT	4/8	0.532925971616404	5	FACETS	0.579	0.449	0.728	0.145	0.112	0.182	SUBCLONAL	1	FALSE	1	0.531651816634294	5		152	257	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845635	151845635	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003843-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	32	276	0	ENST00000262189.6:c.13377A>T	p.Gln4459His	p.Q4459H	ENST00000262189	NM_170606.2	4459	caA/caT	52/59	0.41601807763583	4	FACETS	0.68	0.554	0.821			1	SUBCLONAL	1	FALSE	NA	0.531651816634294	4		276	271	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162035	47162035	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003843-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	47	295	0	ENST00000409792.3:c.4091del	p.Lys1364ArgfsTer9	p.K1364Rfs*9	ENST00000409792	NM_014159.6	1364	aAg/ag	3/21	0.14786284074115	3	FACETS	1	0.87	1			1	INDETERMINATE	1	FALSE	NA	0.531651816634294	3		295	219	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	26	188	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.834	1	1	0.834	1	CLONAL	1	TRUE	1	0.45601445848453	2		188	110	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288934	212288934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	114	467	1	ENST00000342788.4:c.2812C>T	p.Arg938Cys	p.R938C	ENST00000342788	NM_005235.2	938	Cgt/Tgt	23/28	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.45601445848453	2		468	487	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222261	2222261	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	75	571	1	ENST00000326181.6:c.545G>A	p.Gly182Glu	p.G182E	ENST00000326181	NM_032271.2	182	gGg/gAg	8/21	1	2	FACETS	0.734	0.646	0.829	0.734	0.646	0.829	SUBCLONAL	1	TRUE	1	0.45601445848453	2		572	448	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646608	23646608	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1391272505	NA	P-0003853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	30	307	0	ENST00000261584.4:c.1259A>G	p.Gln420Arg	p.Q420R	ENST00000261584	NM_024675.3	420	cAg/cGg	4/13	1	2	FACETS	0.47	0.38	0.572	0.47	0.38	0.572	SUBCLONAL	1	TRUE	1	0.45601445848453	2		307	280	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664894	29664894	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1567617727	NA	P-0003853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	106	405	0	ENST00000356175.3:c.6637C>T	p.Gln2213Ter	p.Q2213*	ENST00000356175	NM_000267.3	2213	Caa/Taa	43/57	0.45601445848453	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.45601445848453	1		405	341	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589594	67589608	+	inframe_deletion	In_Frame_Del	DEL	AACACTCAGTTTCAA	AACACTCAGTTTCAA	-	novel	NA	P-0003853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	70	379	0	ENST00000274335.5:c.1357_1371del	p.Asn453_Gln457del	p.N453_Q457del	ENST00000274335		453	AACACTCAGTTTCAA/-	10/15	1	2	FACETS	0.679	0.594	0.771	0.679	0.594	0.771	SUBCLONAL	1	TRUE	1	0.45601445848453	2		379	452	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	59	510	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.415480021998861	1	FACETS	0.889	0.773	1	0.889	0.773	1	CLONAL	1	TRUE	0	0.415480021998861	1		510	253	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260749	16260749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769855469	NA	P-0004289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	72	436	0	ENST00000375759.3:c.8014G>A	p.Val2672Met	p.V2672M	ENST00000375759	NM_015001.2	2672	Gtg/Atg	11/15	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.415480021998861	2		436	343	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956952	2956952	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	58	379	1	ENST00000396946.4:c.2675C>A	p.Ala892Glu	p.A892E	ENST00000396946	NM_032415.4	892	gCa/gAa	20/25	0.415480021998861	5	FACETS	0.973	0.837	1	0.324	0.279	0.373	CLONAL	1	TRUE	2	0.415480021998861	5		380	466	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115745	8115745	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	111	620	0	ENST00000346208.3:c.1091G>C	p.Arg364Thr	p.R364T	ENST00000346208		364	aGa/aCa	6/6	0.262150390103925	4	FACETS	0.769	0.694	0.846	0.512	0.463	0.564	SUBCLONAL	2	TRUE	1	0.415480021998861	4		620	492	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115980	8115980	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	63	242	0	ENST00000346208.3:c.1328del	p.Gly443ValfsTer32	p.G443Vfs*32	ENST00000346208		442	atG/at	6/6	0.262150390103925	4	FACETS	0.898	0.786	1	0.599	0.524	0.677	CLONAL	2	TRUE	1	0.415480021998861	4		242	239	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	232	510	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.648044526016079	2	FACETS	0.95	0.889	1	0.475	0.444	0.506	CLONAL	1	TRUE	0	0.648044526016079	2		510	754	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260749	16260749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769855469	NA	P-0004289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	209	436	0	ENST00000375759.3:c.8014G>A	p.Val2672Met	p.V2672M	ENST00000375759	NM_015001.2	2672	Gtg/Atg	11/15	1	2	FACETS	0.938	0.874	1	0.938	0.874	1	CLONAL	1	TRUE	1	0.648044526016079	2		436	688	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115980	8115980	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	206	242	0	ENST00000346208.3:c.1328del	p.Gly443ValfsTer32	p.G443Vfs*32	ENST00000346208		442	atG/at	6/6	0.432383903296986	6	FACETS	0.888	0.83	0.946			1	CLONAL	3	TRUE	NA	0.648044526016079	6		242	548	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101688	27101688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	92	794	1	ENST00000324856.7:c.4970G>A	p.Arg1657Lys	p.R1657K	ENST00000324856	NM_006015.4	1657	aGg/aAg	18/20	1	2	FACETS	0.228	0.202	0.256	0.228	0.202	0.256	SUBCLONAL	1	TRUE	1	0.648044526016079	2		795	1245	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36823865	36823865	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	154	294	0	ENST00000373129.3:c.317T>C	p.Val106Ala	p.V106A	ENST00000373129	NM_032017.1	106	gTg/gCg	5/12	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.648044526016079	2		294	468	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521609	46521609	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	213	380	0	ENST00000262741.5:c.799C>A	p.Leu267Met	p.L267M	ENST00000262741	NM_003629.3	267	Ctg/Atg	7/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.648044526016079	2		380	607	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264922	46264922	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	177	458	0	ENST00000371998.3:c.1792A>C	p.Ser598Arg	p.S598R	ENST00000371998		598	Agt/Cgt	12/23	0.648044526016079	5	FACETS	0.851	0.782	0.923	0.284	0.26	0.308	CLONAL	1	TRUE	2	0.648044526016079	5		458	1266	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035057	37035057	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	157	324	0	ENST00000231790.2:c.19G>A	p.Val7Ile	p.V7I	ENST00000231790	NM_000249.3	7	Gtt/Att	1/19	1	2	FACETS	0.926	0.854	1	0.926	0.854	1	CLONAL	1	TRUE	1	0.648044526016079	2		324	523	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931463	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622007	NA	P-0004489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	127	686	1	ENST00000374690.3:c.2105T>A	p.Leu702His	p.L702H	ENST00000374690	NM_000044.3	702	cTc/cAc	4/8	0.221771060967697	2	FACETS	1	0.955	1			1	CLONAL	3	TRUE	NA	0.221771060967697	2		687	359	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212187	98212187	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	89	838	0	ENST00000331920.6:c.3485T>G	p.Leu1162Arg	p.L1162R	ENST00000331920	NM_000264.3	1162	cTc/cGc	21/24	0.221771060967697	9	FACETS	1	0.944	1	0.368	0.326	0.412	CLONAL	2	TRUE	3	0.221771060967697	9		838	646	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417173	417173	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0004489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	113	588	0	ENST00000399788.2:c.3379-2A>C		p.X1127_splice	ENST00000399788	NM_001042603.1	1127			0.221771060967697	7	FACETS	0.966	0.876	1			1	CLONAL	4	TRUE	NA	0.221771060967697	7		588	410	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212403	5212403	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs558410776	NA	P-0004489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	149	864	0	ENST00000357368.4:c.4714C>G	p.Arg1572Gly	p.R1572G	ENST00000357368	NM_002850.3	1572	Cgg/Ggg	31/38	0.221771060967697	2	FACETS	0.896	0.829	0.964	1	0.991	1	CLONAL	4	TRUE	0	0.221771060967697	2		864	375	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221024	5221024	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	56	607	0	ENST00000357368.4:c.3442C>G	p.Pro1148Ala	p.P1148A	ENST00000357368	NM_002850.3	1148	Ccc/Gcc	20/38	0.221771060967697	2	FACETS	0.975	0.843	1	0.975	0.843	1	CLONAL	2	TRUE	0	0.221771060967697	2		607	259	SUCCESS
ATM	472	MSKCC	GRCh37	11	108225556	108225556	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004644-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	188	344	0	ENST00000278616.4:c.8805G>T	p.Met2935Ile	p.M2935I	ENST00000278616	NM_000051.3	2935	atG/atT	61/63	1	2	FACETS	0.854	0.79	0.92	0.854	0.79	0.92	CLONAL	1	TRUE	1	0.534176361547865	2		344	824	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47088079	47088092	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGATATACTGAA	CTGGATATACTGAA	-	novel	NA	P-0004644-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	126	297	0	ENST00000409792.3:c.6983_6996del	p.Leu2328ArgfsTer36	p.L2328Rfs*36	ENST00000409792	NM_014159.6	2328	cTTCAGTATATCCAG/c	16/21	0.495996659856309	1	FACETS	0.703	0.64	0.768	0.703	0.64	0.768	SUBCLONAL	1	TRUE	0	0.534176361547865	1		297	492	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	123	570	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.304534451584477	4	FACETS	1	0.983	1	0.701	0.636	0.769	CLONAL	1	TRUE	2	0.437305719081931	4		570	577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0005035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	54	353	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.417361759076585	1	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	0	0.437305719081931	1		353	189	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023988	27023988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	52	194	0	ENST00000324856.7:c.1094G>A	p.Gly365Glu	p.G365E	ENST00000324856	NM_006015.4	365	gGg/gAg	1/20	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.437305719081931	2		194	198	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736334	243736334	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771134997	NA	P-0005035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	113	627	0	ENST00000263826.5:c.713C>T	p.Ser238Leu	p.S238L	ENST00000263826	NM_005465.4	238	tCg/tTg	8/13	NA	2	FACETS	0.915	0.826	1			1	INDETERMINATE	1	TRUE	NA	0.437305719081931	2		627	565	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637727	176637727	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	82	541	0	ENST00000439151.2:c.2327C>G	p.Ala776Gly	p.A776G	ENST00000439151	NM_022455.4	776	gCt/gGt	5/23	0.396637716768864	0	FACETS	0.762	0.68	0.847			1	SUBCLONAL	1	TRUE	0	0.437305719081931	0		541	277	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5029783	5029783	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	89	409	0	ENST00000381652.3:c.227G>C	p.Gly76Ala	p.G76A	ENST00000381652	NM_004972.3	76	gGt/gCt	4/25	0.437305719081931	1	FACETS	0.833	0.743	0.926	0.833	0.743	0.926	CLONAL	1	TRUE	0	0.437305719081931	1		409	382	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584708	48584708	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0005035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	126	539	0	ENST00000342988.3:c.788-2A>T		p.X263_splice	ENST00000342988	NM_005359.5	263			0.300682259312148	2	FACETS	1	0.979	1	0.622	0.567	0.679	CLONAL	1	TRUE	0	0.437305719081931	2		539	463	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570009	95570009	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	132	658	0	ENST00000393063.1:c.3724T>C	p.Tyr1242His	p.Y1242H	ENST00000393063	NM_030621.3	1242	Tac/Cac	22/28	0.505541036964	4	FACETS	0.851	0.785	0.918	1	0.984	1	CLONAL	3	FALSE	2	0.505541036964	4		658	308	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075298	16075298	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005084-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	208	404	0	ENST00000268712.3:c.254G>C	p.Arg85Thr	p.R85T	ENST00000268712	NM_006311.3	85	aGg/aCg	4/46	0.385935759576953	1	FACETS	0.991	0.921	1	0.991	0.921	1	CLONAL	1	TRUE	0	0.385935759576953	1		404	878	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39607450	39607450	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005084-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	207	530	0	ENST00000262039.4:c.1528G>C	p.Asp510His	p.D510H	ENST00000262039	NM_002647.2	510	Gat/Cat	14/25	1	2	FACETS	0.883	0.818	0.95	0.883	0.818	0.95	CLONAL	1	TRUE	1	0.385935759576953	2		530	1215	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483087	29483095	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CAAGTTTTC	CAAGTTTTC	TTGA	novel	NA	P-0005084-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	114	558	0	ENST00000356175.3:c.147_155delinsTTGA	p.Lys50Ter	p.K50*	ENST00000356175	NM_000267.3	49	taCAAGTTTTCt/taTTGAt	2/57	1	2	FACETS	0.498	0.447	0.552	0.498	0.447	0.552	SUBCLONAL	1	TRUE	1	0.385935759576953	2		558	1186	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189847	11189847	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	142	467	0	ENST00000361445.4:c.5662T>A	p.Phe1888Ile	p.F1888I	ENST00000361445	NM_004958.3	1888	Ttc/Atc	40/58	0.280655153446624	0	FACETS	1	0.967	1			1	CLONAL	1	TRUE	0	0.29	0		467	624	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620464	52620464	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	170	419	0	ENST00000394830.3:c.3289G>T	p.Glu1097Ter	p.E1097*	ENST00000394830	NM_018313.4	1097	Gaa/Taa	21/30	0.29845581222474	1	FACETS	0.758	0.7	0.819	1	0.99	1	SUBCLONAL	2	TRUE	0	0.29	1		419	661	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163474	108163474	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	56	494	0	ENST00000278616.4:c.4565G>C	p.Gly1522Ala	p.G1522A	ENST00000278616	NM_000051.3	1522	gGt/gCt	30/63	1	2	FACETS	0.426	0.364	0.495	0.426	0.364	0.495	SUBCLONAL	1	TRUE	1	0.29	2		494	906	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201106	108201106	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	42	332	0	ENST00000278616.4:c.7473G>C	p.Trp2491Cys	p.W2491C	ENST00000278616	NM_000051.3	2491	tgG/tgC	50/63	1	2	FACETS	0.41	0.341	0.487	0.41	0.341	0.487	SUBCLONAL	1	TRUE	1	0.29	2		332	706	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239420	105239420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	34	291	0	ENST00000349310.3:c.967G>A	p.Asp323Asn	p.D323N	ENST00000349310	NM_001014432.1	323	Gac/Aac	12/15	0.260802072926953	1	FACETS	0.583	0.477	0.701	0.583	0.477	0.701	SUBCLONAL	1	TRUE	0	0.29	1		291	344	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0005391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	135	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.200172488224927	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	2	0.316355888431362	4		436	505	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519893	NA	P-0005391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	177	551	1	ENST00000267101.3:c.310G>T	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ttg	3/28	0.252038696934848	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.316355888431362	4		552	685	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101034	26101034	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0005391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	461	551	0	ENST00000435504.4:c.57+1G>C		p.X19_splice	ENST00000435504		19			0.316355888431362	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	4	TRUE	0	0.316355888431362	4		551	899	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937426	32937426	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs80359050	NA	P-0005391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	106	366	0	ENST00000380152.3:c.8087T>A	p.Leu2696Ter	p.L2696*	ENST00000380152		2696	tTg/tAg	18/27	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.316355888431362	2		366	482	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482864	67482864	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	193	325	0	ENST00000327367.4:c.1268G>T	p.Ser423Ile	p.S423I	ENST00000327367	NM_005902.3	423	aGt/aTt	9/9	0.261746417851833	3	FACETS	1	0.98	1			1	CLONAL	3	TRUE	NA	0.316355888431362	3		325	424	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425755	49425755	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	126	435	0	ENST00000301067.7:c.12733del	p.Glu4245SerfsTer33	p.E4245Sfs*33	ENST00000301067	NM_003482.3	4245	Gag/ag	39/54	0.245698549165033	1	FACETS	0.862	0.788	0.938	1	0.989	1	CLONAL	2	TRUE	0	0.316355888431362	1		435	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0005636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	155	492	1	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.146855621558793	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.236363524351081	1		493	911	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117626	70117626	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1377	111	418	0	ENST00000245479.2:c.94G>T	p.Gly32Cys	p.G32C	ENST00000245479	NM_000346.3	32	Ggc/Tgc	1/3	0.236363524351081	5	FACETS	0.855	0.766	0.95	0.285	0.255	0.317	CLONAL	1	TRUE	2	0.236363524351081	5		418	1488	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291040	15291040	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368146879	NA	P-0005636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	58	466	0	ENST00000263388.2:c.3170C>T	p.Ala1057Val	p.A1057V	ENST00000263388	NM_000435.2	1057	gCg/gTg	20/33	0.129062489984685	1	FACETS	0.421	0.361	0.488	0.421	0.361	0.488	INDETERMINATE	1	TRUE	0	0.236363524351081	1		466	1027	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195630	123195630	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	48	131	0	ENST00000218089.9:c.1544A>T	p.Asp515Val	p.D515V	ENST00000218089	NM_001042749.1	515	gAt/gTt	17/35	1	1	FACETS	0.82	0.694	0.958	0.82	0.694	0.958	CLONAL	1	TRUE	0	0.236363524351081	1		131	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0005636-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	258	492	1	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.388799657215139	2	FACETS	1	0.991	1	0.663	0.623	0.704	CLONAL	1	TRUE	0	0.469458833354025	2		493	829	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117626	70117626	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005636-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	118	418	0	ENST00000245479.2:c.94G>T	p.Gly32Cys	p.G32C	ENST00000245479	NM_000346.3	32	Ggc/Tgc	1/3	0.469458833354025	5	FACETS	0.655	0.589	0.725	0.218	0.196	0.242	SUBCLONAL	1	TRUE	2	0.469458833354025	5		418	1308	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291040	15291040	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368146879	NA	P-0005636-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1227	348	466	0	ENST00000263388.2:c.3170C>T	p.Ala1057Val	p.A1057V	ENST00000263388	NM_000435.2	1057	gCg/gTg	20/33	0.353419325086868	4	FACETS	1	0.994	1	0.461	0.435	0.488	CLONAL	1	TRUE	1	0.469458833354025	4		466	1575	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195630	123195630	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005636-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	39	131	0	ENST00000218089.9:c.1544A>T	p.Asp515Val	p.D515V	ENST00000218089	NM_001042749.1	515	gAt/gTt	17/35	0.123657914230037	2	FACETS	1	0.874	1			1	INDETERMINATE	1	TRUE	NA	0.469458833354025	2		131	159	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632201	3632347	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	TCACAGCGCAGAGCTGATGTGGTCCCCAGGCCCAGAAATGCCTGTGGAGGCCTGACCCACGCTGGGTGTCCCAGGTCCTCCCTGCAAATGGCGGGGGTGGGGGCTGCTGATGGCAGGTTGGGGTGGGGTCGGGATGGCCCCATCAGT	TCACAGCGCAGAGCTGATGTGGTCCCCAGGCCCAGAAATGCCTGTGGAGGCCTGACCCACGCTGGGTGTCCCAGGTCCTCCCTGCAAATGGCGGGGGTGGGGGCTGCTGATGGCAGGTTGGGGTGGGGTCGGGATGGCCCCATCAGT	-	novel	NA	P-0005636-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	31	98	0	ENST00000294008.3:c.5501_*142del		p.*1834*	ENST00000294008	NM_032444.2	1834		15/15	0.443359755687209	5	FACETS	0.824	0.669	0.998	0.275	0.223	0.333	CLONAL	1	TRUE	2	0.469458833354025	5		98	273	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725077	47725077	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs748900635	NA	P-0005636-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1290	123	875	1	ENST00000449228.1:c.667C>T	p.Arg223Ter	p.R223*	ENST00000449228	NM_001127240.2	223	Cga/Tga	4/4	0.186561512252232	5	FACETS	0.632	0.569	0.699			1	INDETERMINATE	1	TRUE	NA	0.469458833354025	5		876	1413	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0005688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	190	478	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.605851578602468	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	FALSE	2	0.599164853852354	4		478	410	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0005688-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	117	478	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.974	0.885	1	0.974	0.885	1	CLONAL	1	TRUE	1	0.548271999542275	2		478	438	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005688-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	185	596	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	0.917	0.849	0.987	0.917	0.849	0.987	CLONAL	1	TRUE	1	0.548271999542275	2		596	736	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553441	106553441	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005688-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	108	338	0	ENST00000369096.4:c.1406C>A	p.Ser469Ter	p.S469*	ENST00000369096	NM_001198.3	469	tCg/tAg	5/7	1	2	FACETS	0.904	0.816	0.995	0.904	0.816	0.995	CLONAL	1	TRUE	1	0.548271999542275	2		338	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578462	7578463	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0005787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	166	406	0	ENST00000269305.4:c.467dup	p.Val157ArgfsTer24	p.V157Rfs*24	ENST00000269305	NM_001126112.2	156	cgc/cgGc	5/11	0.50436991238159	1	FACETS	0.882	0.815	0.951	0.882	0.815	0.951	CLONAL	1	TRUE	0	0.50436991238159	1		406	558	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258683	16258683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559309170	NA	P-0005787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	69	720	2	ENST00000375759.3:c.5948C>T	p.Ser1983Leu	p.S1983L	ENST00000375759	NM_015001.2	1983	tCg/tTg	11/15	0.267458127743288	3	FACETS	0.443	0.385	0.506	0.222	0.192	0.253	INDETERMINATE	1	TRUE	1	0.50436991238159	3		722	773	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804273	46804274	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0005787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	148	1045	1	ENST00000290295.7:c.733_734del	p.Lys245GlufsTer76	p.K245Efs*76	ENST00000290295	NM_006361.5	245	AAg/g	2/2	0.267458127743288	3	FACETS	0.619	0.564	0.677	0.31	0.282	0.339	INDETERMINATE	1	TRUE	1	0.50436991238159	3		1046	1187	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578462	7578463	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0005787-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	95	406	0	ENST00000269305.4:c.467dup	p.Val157ArgfsTer24	p.V157Rfs*24	ENST00000269305	NM_001126112.2	156	cgc/cgGc	5/11	0.264564548291768	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.264564548291768	1		406	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578462	7578463	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0005787-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	316	406	0	ENST00000269305.4:c.467dup	p.Val157ArgfsTer24	p.V157Rfs*24	ENST00000269305	NM_001126112.2	156	cgc/cgGc	5/11	0.193928845462906	1	FACETS	0.818	0.775	0.862	1	0.995	1	INDETERMINATE	2	TRUE	0	0.36462525975217	1		406	866	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578462	7578463	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0005787-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	256	406	0	ENST00000269305.4:c.467dup	p.Val157ArgfsTer24	p.V157Rfs*24	ENST00000269305	NM_001126112.2	156	cgc/cgGc	5/11	0.83853094980979	1	FACETS	0.946	0.906	0.985	0.946	0.906	0.985	CLONAL	1	TRUE	0	0.843519213527138	1		406	371	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0005836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	61	455	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.998	0.871	1	0.998	0.871	1	CLONAL	1	TRUE	1	0.502969899417934	2		455	243	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0005915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	952	469	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.847371770486198	2	FACETS	0.972	0.957	0.987	0.972	0.957	0.987	CLONAL	2	TRUE	0	0.868671984583791	2		469	1127	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527391	157527391	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1375206963	NA	P-0005915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	382	462	0	ENST00000346085.5:c.5116C>G	p.Pro1706Ala	p.P1706A	ENST00000346085	NM_020732.3	1706	Ccc/Gcc	20/20	1	2	FACETS	0.917	0.874	0.961	0.917	0.874	0.961	CLONAL	1	TRUE	1	0.868671984583791	2		462	959	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359363	118359363	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1131691433	NA	P-0005915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	362	397	0	ENST00000534358.1:c.4367A>G	p.His1456Arg	p.H1456R	ENST00000534358	NM_005933.3	1456	cAc/cGc	11/36	0.708089499993474	4	FACETS	0.993	0.939	1	0.496	0.469	0.524	CLONAL	1	TRUE	2	0.868671984583791	4		397	1569	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422454	47422454	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1953	804	329	1	ENST00000377045.4:c.88C>T	p.Arg30Cys	p.R30C	ENST00000377045	NM_001654.4	30	Cgc/Tgc	2/16	0.868671984583791	4	FACETS	1	0.996	1			1	CLONAL	1	TRUE	NA	0.868671984583791	4		330	2757	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430720	47430720	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0005915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1981	180	276	0	ENST00000377045.4:c.1687-2A>T		p.X563_splice	ENST00000377045	NM_001654.4	563			0.868671984583791	4	FACETS	0.358	0.329	0.39			1	SUBCLONAL	1	TRUE	NA	0.868671984583791	4		276	2161	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0005947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	222	607	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.762008085162208	1	FACETS	0.607	0.569	0.646	0.607	0.569	0.646	SUBCLONAL	1	TRUE	0	0.762008085162208	1		613	594	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	227	466	2	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.974	0.913	1	0.974	0.913	1	CLONAL	1	TRUE	1	0.762008085162208	2		468	612	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0005947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	145	468	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.818	0.753	0.886	0.818	0.753	0.886	CLONAL	1	TRUE	1	0.762008085162208	2		472	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0005947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	92	663	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.277	0.246	0.311	0.277	0.246	0.311	SUBCLONAL	1	TRUE	1	0.762008085162208	2		664	871	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	228	256	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.953	0.894	1	0.953	0.894	1	CLONAL	1	TRUE	1	0.762008085162208	2		257	628	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430563	80430563	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	97	194	0	ENST00000286548.4:c.445C>T	p.Arg149Ter	p.R149*	ENST00000286548	NM_002072.3	149	Cga/Tga	3/7	1	2	FACETS	0.762	0.687	0.841	0.762	0.687	0.841	SUBCLONAL	1	TRUE	1	0.762008085162208	2		194	334	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0005947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	83	152	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	0.762008085162208	1	FACETS	0.864	0.787	0.941	0.864	0.787	0.941	CLONAL	1	TRUE	0	0.762008085162208	1		152	156	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448122	49448122	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	265	512	0	ENST00000301067.7:c.478G>A	p.Val160Met	p.V160M	ENST00000301067	NM_003482.3	160	Gtg/Atg	4/54	1	2	FACETS	0.953	0.898	1	0.953	0.898	1	CLONAL	1	TRUE	1	0.762008085162208	2		512	730	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084146	47084146	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	209	444	0	ENST00000409792.3:c.7143del	p.Ser2382LeufsTer29	p.S2382Lfs*29	ENST00000409792	NM_014159.6	2381	ccC/cc	17/21	0.762008085162208	1	FACETS	0.954	0.903	1	0.954	0.903	1	CLONAL	1	TRUE	0	0.762008085162208	1		444	356	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46252809	46252809	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	401	742	0	ENST00000371998.3:c.238C>T	p.Arg80Cys	p.R80C	ENST00000371998		80	Cgt/Tgt	4/23	1	2	FACETS	0.957	0.912	1	0.957	0.912	1	CLONAL	1	TRUE	1	0.762008085162208	2		742	1100	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444659	78444659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs908264837	NA	P-0005947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	194	292	2	ENST00000370768.2:c.30del	p.Ser11LeufsTer43	p.S11Lfs*43	ENST00000370768	NM_003902.3	10	ccC/cc	1/20	0.646809571848557	1	FACETS	0.919	0.867	0.97	0.919	0.867	0.97	CLONAL	1	TRUE	0	0.762008085162208	1		294	343	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874013	151874013	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1248944002	NA	P-0005947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	300	530	0	ENST00000262189.6:c.8525del	p.Asn2842MetfsTer21	p.N2842Mfs*21	ENST00000262189	NM_170606.2	2842	aAt/at	38/59	NA	2	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.762008085162208	2		530	762	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120502056	120502056	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	261	430	0	ENST00000256646.2:c.1985G>C	p.Gly662Ala	p.G662A	ENST00000256646	NM_024408.3	662	gGc/gCc	12/34	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.762008085162208	2		430	614	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225432	26225432	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1490	94	808	0	ENST00000360408.1:c.50C>T	p.Pro17Leu	p.P17L	ENST00000360408	NM_003532.2	17	cCg/cTg	1/1	0.158797458828699	4	FACETS	0.274	0.243	0.308	0.137	0.121	0.154	INDETERMINATE	1	TRUE	2	0.762008085162208	4		808	1584	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144639	119144639	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	318	476	0	ENST00000264033.4:c.652G>A	p.Gly218Arg	p.G218R	ENST00000264033	NM_005188.3	218	Ggg/Agg	4/16	0.762008085162208	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.762008085162208	1		476	479	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111886075	111886075	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148791142	NA	P-0005947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	373	630	2	ENST00000341259.2:c.1697G>A	p.Arg566Gln	p.R566Q	ENST00000341259	NM_005475.2	566	cGg/cAg	8/8	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.762008085162208	2		632	978	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215865	133215865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199777048	NA	P-0005947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	175	388	1	ENST00000320574.5:c.5398G>A	p.Val1800Met	p.V1800M	ENST00000320574	NM_006231.2	1800	Gtg/Atg	40/49	0.19195003404493	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.762008085162208	0		389	458	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103498626	103498626	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	298	519	0	ENST00000355739.4:c.10C>T	p.Gln4Ter	p.Q4*	ENST00000355739	NM_000123.3	4	Cag/Tag	1/15	1	2	FACETS	0.945	0.893	0.997	0.945	0.893	0.997	CLONAL	1	TRUE	1	0.762008085162208	2		519	828	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435258	110435258	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	82	136	0	ENST00000375856.3:c.3143C>T	p.Ser1048Leu	p.S1048L	ENST00000375856	NM_003749.2	1048	tCg/tTg	1/2	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.762008085162208	2		136	191	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857881	89857881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772567344	NA	P-0005947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	248	534	0	ENST00000389301.3:c.1289C>T	p.Ala430Val	p.A430V	ENST00000389301	NM_000135.2	430	gCg/gTg	14/43	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.762008085162208	2		534	639	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367812	15367812	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	184	485	0	ENST00000263377.2:c.1514A>C	p.Glu505Ala	p.E505A	ENST00000263377	NM_058243.2	505	gAg/gCg	8/20	0.114239025070118	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.762008085162208	0		485	517	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100998	41100998	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772057709	NA	P-0005947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	180	489	3	ENST00000373198.4:c.1358G>A	p.Arg453His	p.R453H	ENST00000373198	NM_133170.3	453	cGc/cAc	8/32	1	2	FACETS	0.789	0.731	0.848	0.789	0.731	0.848	SUBCLONAL	1	TRUE	1	0.762008085162208	2		492	599	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257102	19257102	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	75	284	1	ENST00000162023.5:c.861del	p.Ala288ProfsTer?	p.A288Pfs*?	ENST00000162023		287	ccC/cc	12/13	0.114239025070118	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.762008085162208	0		285	334	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463298	25463300	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs761103716	NA	P-0005947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	193	447	0	ENST00000264709.3:c.2193_2195del	p.Phe732del	p.F732del	ENST00000264709	NM_175629.2	731	ttCTTt/ttt	19/23	1	2	FACETS	0.887	0.826	0.949	0.887	0.826	0.949	CLONAL	1	TRUE	1	0.762008085162208	2		447	571	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187558039	187558039	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	146	237	1	ENST00000441802.2:c.3672del	p.Lys1225AsnfsTer9	p.K1225Nfs*9	ENST00000441802	NM_005245.3	1224	ccC/cc	5/27	1	2	FACETS	0.902	0.831	0.974	0.902	0.831	0.974	CLONAL	1	TRUE	1	0.762008085162208	2		238	425	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434822	49434822	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	286	622	0	ENST00000301067.7:c.6731del	p.Phe2244SerfsTer20	p.F2244Sfs*20	ENST00000301067	NM_003482.3	2244	tTc/tc	31/54	1	2	FACETS	0.955	0.902	1	0.955	0.902	1	CLONAL	1	TRUE	1	0.762008085162208	2		622	786	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106562	27106562	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	357	579	0	ENST00000324856.7:c.6176del	p.Asn2059ThrfsTer76	p.N2059Tfs*76	ENST00000324856	NM_006015.4	2058	gAa/ga	20/20	1	2	FACETS	0.997	0.948	1	0.997	0.948	1	CLONAL	1	TRUE	1	0.762008085162208	2		579	940	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691807	30691807	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	253	489	1	ENST00000295754.5:c.312del	p.Lys105SerfsTer19	p.K105Sfs*19	ENST00000295754	NM_003242.5	103	gaC/ga	3/7	0.762008085162208	1	FACETS	0.882	0.837	0.927	0.882	0.837	0.927	CLONAL	1	TRUE	0	0.762008085162208	1		490	466	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061459	38061459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1349901575	NA	P-0006212-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	44	971	1	ENST00000250448.2:c.530C>T	p.Ser177Leu	p.S177L	ENST00000250448	NM_004496.3	177	tCg/tTg	2/2	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		972	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0006414-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	333	663	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.147972503693289	3	FACETS	0.856	0.81	0.903	0.571	0.54	0.602	INDETERMINATE	2	TRUE	0	0.424433980528043	3		664	1111	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864388	162864388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368134308	NA	P-0006414-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	99	675	0	ENST00000366898.1:c.125G>A	p.Arg42His	p.R42H	ENST00000366898	NM_004562.2	42	cGt/cAt	2/12	NA	2	FACETS	0.492	0.438	0.55			1	INDETERMINATE	1	TRUE	NA	0.424433980528043	2		675	948	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578376	7578379	+	frameshift_variant	Frame_Shift_Del	DEL	CTAT	CTAT	-	novel	NA	P-0006414-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	67	393	0	ENST00000269305.4:c.551_554del	p.Asp184AlafsTer62	p.D184Afs*62	ENST00000269305	NM_001126112.2	184	gATAGc/gc	5/11	0.147972503693289	3	FACETS	0.618	0.537	0.706	0.206	0.179	0.236	INDETERMINATE	1	TRUE	0	0.424433980528043	3		393	619	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264353	16264353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006414-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	108	653	0	ENST00000375759.3:c.10556C>T	p.Thr3519Ile	p.T3519I	ENST00000375759	NM_015001.2	3519	aCa/aTa	13/15	0.214201139862812	2	FACETS	0.481	0.431	0.535	0.241	0.215	0.268	INDETERMINATE	1	TRUE	0	0.424433980528043	2		653	1058	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157810	106157810	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006414-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	168	509	0	ENST00000380013.4:c.2711A>C	p.Gln904Pro	p.Q904P	ENST00000380013	NM_001127208.2	904	cAa/cCa	3/11	0.424433980528043	2	FACETS	1	0.982	1	0.611	0.563	0.66	CLONAL	1	TRUE	0	0.424433980528043	2		509	648	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711894	89711894	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786204865	NA	P-0006414-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	33	463	0	ENST00000371953.3:c.512A>G	p.Gln171Arg	p.Q171R	ENST00000371953	NM_000314.4	171	cAg/cGg	6/9	0.379832682348595	1	FACETS	0.21	0.17	0.255	0.21	0.17	0.255	SUBCLONAL	1	TRUE	0	0.424433980528043	1		463	583	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157816	106157906	+	frameshift_variant	Frame_Shift_Del	DEL	TGTCTGGTCAACAAGCTGCGCAACTTGCTCAGCAAAGGTACTTGATACATAACCATGCAAATGTTTTTCCTGTGCCTGACCAGGGAGGAAG	TGTCTGGTCAACAAGCTGCGCAACTTGCTCAGCAAAGGTACTTGATACATAACCATGCAAATGTTTTTCCTGTGCCTGACCAGGGAGGAAG	-	novel	NA	P-0006414-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	147	504	0	ENST00000380013.4:c.2718_2808del	p.Met906IlefsTer17	p.M906Ifs*17	ENST00000380013	NM_001127208.2	906	aTGTCTGGTCAACAAGCTGCGCAACTTGCTCAGCAAAGGTACTTGATACATAACCATGCAAATGTTTTTCCTGTGCCTGACCAGGGAGGAAGt/at	3/11	0.424433980528043	2	FACETS	1	0.965	1	0.551	0.504	0.599	CLONAL	1	TRUE	0	0.424433980528043	2		504	629	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0006526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	161	378	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.501153014946146	9	FACETS	1	0.976	1			1	CLONAL	5	TRUE	NA	0.501153014946146	9		378	323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579529	7579529	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658483	NA	P-0006526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	45	377	0	ENST00000269305.4:c.158G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tGg/tAg	4/11	0.479578633045647	3	FACETS	0.851	0.746	0.955			1	CLONAL	3	TRUE	NA	0.501153014946146	3		377	88	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945129	32945129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80359104	NA	P-0006526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	20	472	0	ENST00000380152.3:c.8524C>T	p.Arg2842Cys	p.R2842C	ENST00000380152		2842	Cgc/Tgc	20/27	0.501153014946146	4	FACETS	0.81	0.625	1	0.27	0.208	0.341	CLONAL	1	TRUE	1	0.501153014946146	4		472	148	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741559	145741559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376493359	NA	P-0006526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	72	532	0	ENST00000428558.2:c.944C>T	p.Ser315Leu	p.S315L	ENST00000428558	NM_004260.3	315	tCg/tTg	5/22	0.501153014946146	6	FACETS	1	0.904	1	0.514	0.453	0.577	CLONAL	2	TRUE	2	0.501153014946146	6		532	280	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276833	123276833	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	23	437	0	ENST00000358487.5:c.1084G>T	p.Ala362Ser	p.A362S	ENST00000358487	NM_000141.4	362	Gcg/Tcg	8/18	NA	2	FACETS	0.771	0.611	0.951			1	INDETERMINATE	1	TRUE	NA	0.501153014946146	2		437	119	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36028691	36028691	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	35	399	0	ENST00000358208.4:c.1033A>T	p.Ser345Cys	p.S345C	ENST00000358208		345	Agc/Tgc	8/12	0.383165007774208	3	FACETS	0.809	0.68	0.945	0.809	0.68	0.945	CLONAL	2	TRUE	1	0.501153014946146	3		399	108	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288345	21288345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	42	533	0	ENST00000354336.3:c.590G>A	p.Ser197Asn	p.S197N	ENST00000354336	NM_005207.3	197	aGt/aAt	2/3	0.34300325390252	2	FACETS	0.896	0.758	1	0.448	0.379	0.523	CLONAL	1	TRUE	0	0.501153014946146	2		533	187	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0006602-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	97	375	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.362715065942212	3	FACETS	1	0.91	1	1	0.91	1	CLONAL	2	TRUE	1	0.369794976269457	3		375	308	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845529	63845529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771981107	NA	P-0006602-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	94	401	0	ENST00000279873.7:c.1268G>A	p.Arg423Gln	p.R423Q	ENST00000279873	NM_032199.2	423	cGg/cAg	9/10	0.362715065942212	3	FACETS	1	0.925	1	1	0.925	1	CLONAL	2	TRUE	1	0.369794976269457	3		401	292	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906663	32906663	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006602-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	12	358	0	ENST00000380152.3:c.1048G>C	p.Glu350Gln	p.E350Q	ENST00000380152		350	Gaa/Caa	10/27	0.362715065942212	3	FACETS	0.394	0.277	0.538	0.197	0.138	0.269	SUBCLONAL	1	TRUE	1	0.369794976269457	3		358	195	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489543	40489544	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGAGAGTTTTC	novel	NA	P-0006602-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	33	507	1	ENST00000264657.5:c.696_706dup	p.Thr236ArgfsTer29	p.T236Rfs*29	ENST00000264657	NM_139276.2	236	acg/aGAAAACTCTCAcg	8/24	0.348082981869333	0	FACETS	0.67	0.552	0.799			1	SUBCLONAL	1	TRUE	0	0.369794976269457	0		508	168	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0006602-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	236	375	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.561589858918715	3	FACETS	0.849	0.805	0.893	0.849	0.805	0.893	INDETERMINATE	2	TRUE	1	0.948602261274004	3		375	432	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845529	63845529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771981107	NA	P-0006602-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	262	401	0	ENST00000279873.7:c.1268G>A	p.Arg423Gln	p.R423Q	ENST00000279873	NM_032199.2	423	cGg/cAg	9/10	0.510327570751942	3	FACETS	0.797	0.756	0.838	0.797	0.756	0.838	INDETERMINATE	2	TRUE	1	0.948602261274004	3		401	511	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906663	32906663	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006602-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	156	358	0	ENST00000380152.3:c.1048G>C	p.Glu350Gln	p.E350Q	ENST00000380152		350	Gaa/Caa	10/27	0.500860305169429	4	FACETS	0.741	0.679	0.806	0.37	0.339	0.403	INDETERMINATE	1	TRUE	2	0.948602261274004	4		358	865	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489543	40489544	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGAGAGTTTTC	novel	NA	P-0006602-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	248	507	1	ENST00000264657.5:c.696_706dup	p.Thr236ArgfsTer29	p.T236Rfs*29	ENST00000264657	NM_139276.2	236	acg/aGAAAACTCTCAcg	8/24	0.948916386167528	1	FACETS	0.757	0.724	0.789	0.757	0.724	0.789	SUBCLONAL	1	TRUE	0	0.948602261274004	1		508	363	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39239300	39239300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006602-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	297	604	0	ENST00000402219.2:c.2357G>A	p.Arg786Gln	p.R786Q	ENST00000402219	NM_005633.3	786	cGa/cAa	14/23	1	2	FACETS	0.949	0.9	0.997	0.949	0.9	0.997	CLONAL	1	TRUE	1	0.948602261274004	2		604	660	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951053	48951053	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs587778831	NA	P-0006670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	178	306	0	ENST00000267163.4:c.1216-1G>A		p.X406_splice	ENST00000267163	NM_000321.2	406			0.676334304429347	3	FACETS	0.93	0.887	0.97	0.93	0.887	0.97	CLONAL	3	TRUE	0	0.737004539940072	3		306	237	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39762932	39762932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1401427882	NA	P-0006918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	106	256	1	ENST00000288319.7:c.904C>T	p.Arg302Cys	p.R302C	ENST00000288319	NM_182918.3	302	Cgc/Tgc	9/10	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		257	1038	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39762932	39762932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1401427882	NA	P-0006918-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	62	256	1	ENST00000288319.7:c.904C>T	p.Arg302Cys	p.R302C	ENST00000288319	NM_182918.3	302	Cgc/Tgc	9/10	1	2	FACETS	0.781	0.673	0.899	0.781	0.673	0.899	SUBCLONAL	1	TRUE	1	0.17	2		257	934	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280308	1280308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151121796	NA	P-0006918-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1236	117	444	0	ENST00000310581.5:c.1915G>A	p.Val639Ile	p.V639I	ENST00000310581	NM_198253.2	639	Gtc/Atc	4/16	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.17	2		444	1353	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060730	38060730	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs771991531	NA	P-0006918-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1841	122	766	0	ENST00000250448.2:c.1259A>G	p.Tyr420Cys	p.Y420C	ENST00000250448	NM_004496.3	420	tAc/tGc	2/2	1	2	FACETS	0.731	0.658	0.81	0.731	0.658	0.81	SUBCLONAL	1	TRUE	1	0.17	2		766	1963	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0007174-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	33	455	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.3	3	FACETS	0.613	0.498	0.744	0.307	0.249	0.372	SUBCLONAL	1	TRUE	1	0.19	3		455	620	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953587	32953587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886040798	NA	P-0007174-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	26	679	0	ENST00000380152.3:c.8888C>T	p.Ser2963Leu	p.S2963L	ENST00000380152		2963	tCa/tTa	22/27	0.155399628546725	4	FACETS	0.658	0.52	0.817	0.329	0.26	0.409	SUBCLONAL	1	TRUE	2	0.19	4		679	495	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784481	9784481	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0007174-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	25	429	0	ENST00000377346.4:c.2864+2T>C		p.X955_splice	ENST00000377346	NM_005026.3	955			0.292003861910569	1	FACETS	1	0.805	1	1	0.805	1	CLONAL	1	TRUE	0	0.19	1		429	234	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538198	187538198	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007174-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	45	777	0	ENST00000441802.2:c.9036A>C	p.Lys3012Asn	p.K3012N	ENST00000441802	NM_005245.3	3012	aaA/aaC	11/27	1	2	FACETS	0.907	0.762	1	0.907	0.762	1	CLONAL	1	TRUE	1	0.19	2		777	522	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880108	151880108	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1554505381	NA	P-0007174-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	39	656	0	ENST00000262189.6:c.5216del	p.Pro1739LeufsTer2	p.P1739Lfs*2	ENST00000262189	NM_170606.2	1739	cCt/ct	35/59	1	2	FACETS	0.918	0.761	1	0.918	0.761	1	CLONAL	1	TRUE	1	0.19	2		656	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0007175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	292	663	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.426342259234522	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.426342259234522	1		664	940	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99204054	99204054	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs76257041	NA	P-0007175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	96	434	0	ENST00000074304.5:c.2917G>A	p.Gly973Arg	p.G973R	ENST00000074304	NM_001134224.1	973	Gga/Aga	26/26	1	2	FACETS	0.58	0.517	0.648	0.58	0.517	0.648	SUBCLONAL	1	TRUE	1	0.426342259234522	2		434	776	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573556	48573556	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	132	548	1	ENST00000342988.3:c.140T>A	p.Leu47Gln	p.L47Q	ENST00000342988	NM_005359.5	47	cTg/cAg	2/12	0.311239633934452	0	FACETS	0.483	0.438	0.529			1	SUBCLONAL	1	TRUE	0	0.426342259234522	0		549	736	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288868	15288868	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	60	195	0	ENST00000263388.2:c.3871C>T	p.Arg1291Cys	p.R1291C	ENST00000263388	NM_000435.2	1291	Cgc/Tgc	24/33	0.243615154778978	1	FACETS	0.651	0.564	0.745	0.651	0.564	0.745	INDETERMINATE	1	TRUE	0	0.426342259234522	1		195	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0007175-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	345	663	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.625879085019475	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	FALSE	0	0.625879085019475	2		664	507	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99204054	99204054	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs76257041	NA	P-0007175-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	89	434	0	ENST00000074304.5:c.2917G>A	p.Gly973Arg	p.G973R	ENST00000074304	NM_001134224.1	973	Gga/Aga	26/26	0.447624576969598	4	FACETS	1	0.973	1	0.431	0.385	0.479	CLONAL	1	FALSE	1	0.625879085019475	4		434	358	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573556	48573556	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007175-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	89	548	1	ENST00000342988.3:c.140T>A	p.Leu47Gln	p.L47Q	ENST00000342988	NM_005359.5	47	cTg/cAg	2/12	0.625879085019475	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	0	0.625879085019475	1		549	171	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288868	15288868	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007175-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	54	195	0	ENST00000263388.2:c.3871C>T	p.Arg1291Cys	p.R1291C	ENST00000263388	NM_000435.2	1291	Cgc/Tgc	24/33	0.625879085019475	3	FACETS	0.888	0.766	1	0.444	0.383	0.51	CLONAL	1	FALSE	1	0.625879085019475	3		195	255	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444975	49444975	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1377099051	NA	P-0007175-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	113	770	0	ENST00000301067.7:c.2491T>C	p.Ser831Pro	p.S831P	ENST00000301067	NM_003482.3	831	Tca/Cca	10/54	0.21632341205821	4	FACETS	1	0.981	1	0.678	0.614	0.744	INDETERMINATE	1	FALSE	2	0.625879085019475	4		770	433	SUCCESS
APC	324	MSKCC	GRCh37	5	112174760	112174760	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007175-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	65	418	0	ENST00000257430.4:c.3469G>T	p.Glu1157Ter	p.E1157*	ENST00000257430	NM_000038.5	1157	Gag/Tag	16/16	0.447624576969598	4	FACETS	0.999	0.872	1	0.333	0.29	0.379	CLONAL	1	FALSE	1	0.625879085019475	4		418	338	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259324	11259324	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	255	421	0	ENST00000361445.4:c.4244C>G	p.Ser1415Cys	p.S1415C	ENST00000361445	NM_004958.3	1415	tCt/tGt	28/58	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.781357489701373	2		421	624	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375474	118375474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	90	365	0	ENST00000534358.1:c.8867C>T	p.Ser2956Leu	p.S2956L	ENST00000534358	NM_005933.3	2956	tCa/tTa	27/36	0.782067492264151	3	FACETS	0.424	0.376	0.475	0.212	0.188	0.238	SUBCLONAL	1	TRUE	1	0.781357489701373	3		365	756	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993640	72993640	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0007515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	650	424	0	ENST00000268489.5:c.405C>G	p.Tyr135Ter	p.Y135*	ENST00000268489	NM_006885.3	135	taC/taG	2/10	0.782067492264151	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	1	0.781357489701373	3		424	1064	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696432	47696432	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519968	NA	P-0007529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	150	496	0	ENST00000347630.2:c.391T>G	p.Trp131Gly	p.W131G	ENST00000347630	NM_001007230.1	131	Tgg/Ggg	6/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.323142072800155	2		496	763	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512269	38512269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	113	383	0	ENST00000254066.5:c.1180C>T	p.Arg394Trp	p.R394W	ENST00000254066	NM_000964.3	394	Cgg/Tgg	9/9	1	2	FACETS	0.949	0.854	1	0.949	0.854	1	CLONAL	1	TRUE	1	0.323142072800155	2		383	737	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415891	49415891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	181	433	0	ENST00000301067.7:c.16456G>A	p.Val5486Met	p.V5486M	ENST00000301067	NM_003482.3	5486	Gtg/Atg	53/54	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.323142072800155	2		433	939	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508173	38508173	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	154	414	0	ENST00000254066.5:c.481G>A	p.Asp161Asn	p.D161N	ENST00000254066	NM_000964.3	161	Gac/Aac	5/9	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.323142072800155	2		414	930	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0007679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	249	562	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.612690970180445	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.638528815954561	1		562	529	SUCCESS
APC	324	MSKCC	GRCh37	5	112175513	112175513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	205	417	1	ENST00000257430.4:c.4222G>T	p.Glu1408Ter	p.E1408*	ENST00000257430	NM_000038.5	1408	Gaa/Taa	16/16	0.469255689748627	3	FACETS	1	0.939	1			1	CLONAL	1	TRUE	NA	0.638528815954561	3		418	837	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0007679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	488	523	2	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	0.469255689748627	3	FACETS	1	0.976	1			1	CLONAL	2	TRUE	NA	0.638528815954561	3		525	989	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930579	39930910	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGAGTATCTATATATAAGTAGTCACACATTCTTTATTCATAAAGTCATGTGTATATAGATATATATGCGATGTGTATGTATATCCACACATACACTATTGCATACAGACAGACATTCTCTTTTGAAGGTAAATAAAACAAAACGAAAACACAACGCAAAGAAAACAAAACAAAAACACAACAGAAAAGAAACAAAATACACAATGAATAAAGACGACCATGGCCCACAAACTTCCCTTTGTATATTTGGAAATGAAATTTAACTCAAAAGGTTTATGTAAGATTCTAGTAATAAAAATTTGAAGAACTGACCTCACAGTAAGCAGCGGGTAG	AGAGTATCTATATATAAGTAGTCACACATTCTTTATTCATAAAGTCATGTGTATATAGATATATATGCGATGTGTATGTATATCCACACATACACTATTGCATACAGACAGACATTCTCTTTTGAAGGTAAATAAAACAAAACGAAAACACAACGCAAAGAAAACAAAACAAAAACACAACAGAAAAGAAACAAAATACACAATGAATAAAGACGACCATGGCCCACAAACTTCCCTTTGTATATTTGGAAATGAAATTTAACTCAAAAGGTTTATGTAAGATTCTAGTAATAAAAATTTGAAGAACTGACCTCACAGTAAGCAGCGGGTAG	-	novel	NA	P-0007679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3	155	6	0	ENST00000378444.4:c.3031_3052-167del		p.X1011_splice	ENST00000378444	NM_001123385.1	1011		5/15	1	1	FACETS	1	0.993	1	1	0.995	1	CLONAL	2	TRUE	0	0.638528815954561	1		6	158	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007780-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	67	188	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.894	1			1	INDETERMINATE	1	TRUE	NA	0.53793266228602	2		188	245	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692896	89692896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123322	NA	P-0007780-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	145	300	0	ENST00000371953.3:c.380G>A	p.Gly127Glu	p.G127E	ENST00000371953	NM_000314.4	127	gGa/gAa	5/9	0.53793266228602	1	FACETS	0.993	0.916	1	0.993	0.916	1	CLONAL	1	TRUE	0	0.53793266228602	1		300	397	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199956	128199956	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007780-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	117	376	1	ENST00000341105.2:c.1349G>A	p.Gly450Glu	p.G450E	ENST00000341105	NM_032638.4	450	gGa/gAa	6/6	1	2	FACETS	0.784	0.709	0.862	0.784	0.709	0.862	SUBCLONAL	1	TRUE	1	0.53793266228602	2		377	555	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925480	131925480	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007780-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	234	387	0	ENST00000265335.6:c.1403A>G	p.Glu468Gly	p.E468G	ENST00000265335		468	gAa/gGa	9/25	1	2	FACETS	0.921	0.86	0.983	0.921	0.86	0.983	CLONAL	1	TRUE	1	0.53793266228602	2		387	945	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577524	7577524	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	182	540	0	ENST00000269305.4:c.757A>G	p.Thr253Ala	p.T253A	ENST00000269305	NM_001126112.2	253	Acc/Gcc	7/11	0.502108201197923	1	FACETS	0.73	0.676	0.785	0.73	0.676	0.785	SUBCLONAL	1	TRUE	0	0.561556133434581	1		540	639	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945595	38945595	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0007856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	97	312	0	ENST00000357387.3:c.4631C>G	p.Ser1544Ter	p.S1544*	ENST00000357387	NM_152756.3	1544	tCa/tGa	34/38	0.398627538287278	3	FACETS	0.888	0.795	0.987			1	CLONAL	1	TRUE	NA	0.561556133434581	3		312	498	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061185	38061202	+	inframe_deletion	In_Frame_Del	DEL	GCACTTGAAGCGCTTCTG	GCACTTGAAGCGCTTCTG	-	novel	NA	P-0007856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	84	255	0	ENST00000250448.2:c.787_804del	p.Gln263_Cys268del	p.Q263_C268del	ENST00000250448	NM_004496.3	263	CAGAAGCGCTTCAAGTGC/-	2/2	1	2	FACETS	0.855	0.761	0.953	0.855	0.761	0.953	CLONAL	1	TRUE	1	0.561556133434581	2		255	350	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23652445	23652445	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	181	422	0	ENST00000261584.4:c.34G>T	p.Glu12Ter	p.E12*	ENST00000261584	NM_024675.3	12	Gag/Tag	1/13	1	2	FACETS	0.852	0.787	0.92	0.852	0.787	0.92	CLONAL	1	TRUE	1	0.511060145073888	2		422	831	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829081	128829081	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	11	25	0	ENST00000249373.3:c.89C>T	p.Ala30Val	p.A30V	ENST00000249373	NM_005631.4	30	gCg/gTg	1/12	1	2	FACETS	0.285	0.197	0.393	0.285	0.197	0.393	SUBCLONAL	1	TRUE	1	0.511060145073888	2		25	151	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23652445	23652445	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007875-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	229	422	0	ENST00000261584.4:c.34G>T	p.Glu12Ter	p.E12*	ENST00000261584	NM_024675.3	12	Gag/Tag	1/13	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.584802938997477	2		422	748	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256972	16256972	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs763419267	NA	P-0007875-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	216	692	0	ENST00000375759.3:c.4237G>C	p.Asp1413His	p.D1413H	ENST00000375759	NM_015001.2	1413	Gac/Cac	11/15	1	2	FACETS	0.936	0.873	1	0.936	0.873	1	CLONAL	1	TRUE	1	0.584802938997477	2		692	789	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980323	201980323	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007875-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	558	808	0	ENST00000359651.3:c.59G>C	p.Ser20Thr	p.S20T	ENST00000359651		20	aGc/aCc	1/8	0.58483242169032	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.584802938997477	3		808	1142	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849464	68849464	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007875-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	197	619	0	ENST00000261769.5:c.1367T>C	p.Val456Ala	p.V456A	ENST00000261769	NM_004360.3	456	gTg/gCg	10/16	0.584802938997477	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.584802938997477	1		619	431	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391198	89391198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007875-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	151	435	1	ENST00000336596.2:c.1264C>T	p.Pro422Ser	p.P422S	ENST00000336596	NM_005233.5	422	Cca/Tca	5/17	NA	2	FACETS	0.986	0.907	1			1	INDETERMINATE	1	TRUE	NA	0.584802938997477	2		436	524	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197505	27197505	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007875-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	454	766	0	ENST00000380036.4:c.1817A>C	p.His606Pro	p.H606P	ENST00000380036	NM_000459.3	606	cAt/cCt	12/23	0.578886349282774	3	FACETS	0.93	0.89	0.97	0.93	0.89	0.97	CLONAL	2	TRUE	1	0.584802938997477	3		766	1079	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578505	7578505	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	121	415	0	ENST00000269305.4:c.425del	p.Pro142LeufsTer28	p.P142Lfs*28	ENST00000269305	NM_001126112.2	142	cCt/ct	5/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.323993589417215	2		415	678	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086032	16086032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777508469	NA	P-0008127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	31	407	1	ENST00000281043.3:c.1208C>T	p.Thr403Met	p.T403M	ENST00000281043	NM_005378.4	403	aCg/aTg	3/3	0.234724182300172	1	FACETS	0.266	0.215	0.325	0.266	0.215	0.325	SUBCLONAL	1	TRUE	0	0.323993589417215	1		408	602	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442530	52442530	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	105	322	0	ENST00000460680.1:c.215T>G	p.Ile72Ser	p.I72S	ENST00000460680	NM_004656.3	72	aTt/aGt	4/17	1	2	FACETS	0.966	0.866	1	0.966	0.866	1	CLONAL	1	TRUE	1	0.323993589417215	2		322	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578464	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCGGACGCG	GCGCGGACGCG	ACGC	novel	NA	P-0008127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	106	242	0	ENST00000269305.4:c.466_476delinsGCGT	p.Arg156AlafsTer12	p.R156Afs*12	ENST00000269305	NM_001126112.2	156	CGCGTCCGCGCc/GCGTc	5/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.323993589417215	2		242	609	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578505	7578505	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	93	415	0	ENST00000269305.4:c.425del	p.Pro142LeufsTer28	p.P142Lfs*28	ENST00000269305	NM_001126112.2	142	cCt/ct	5/11	1	2	FACETS	0.786	0.699	0.879	0.786	0.699	0.879	SUBCLONAL	1	TRUE	1	0.349974377223253	2		415	676	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086032	16086032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777508469	NA	P-0008127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	105	407	1	ENST00000281043.3:c.1208C>T	p.Thr403Met	p.T403M	ENST00000281043	NM_005378.4	403	aCg/aTg	3/3	0.184783463788966	2	FACETS	0.745	0.667	0.828	0.373	0.333	0.414	INDETERMINATE	1	TRUE	0	0.349974377223253	2		408	805	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442530	52442530	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	98	322	0	ENST00000460680.1:c.215T>G	p.Ile72Ser	p.I72S	ENST00000460680	NM_004656.3	72	aTt/aGt	4/17	0.349974377223253	3	FACETS	1	0.939	1	0.537	0.479	0.597	CLONAL	1	TRUE	1	0.349974377223253	3		322	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578464	+	frameshift_variant	Frame_Shift_Del	DEL	GGACGCG	GGACGCG	-	novel	NA	P-0008127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	149	351	0	ENST00000269305.4:c.466_472del	p.Arg156AlafsTer12	p.R156Afs*12	ENST00000269305	NM_001126112.2	156	CGCGTCCgc/gc	5/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.349974377223253	2		351	612	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750778	57750778	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008162-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	53	793	0	ENST00000274289.3:c.1826A>G	p.Asp609Gly	p.D609G	ENST00000274289	NM_006622.3	609	gAt/gGt	13/14	1	2	FACETS	0.29	0.247	0.339	0.29	0.247	0.339	SUBCLONAL	1	TRUE	1	0.402427958373908	2		793	907	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0008173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	320	525	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.557103708481568	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.557103708481568	1		525	693	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0008173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	139	232	1	ENST00000257430.4:c.3919dup	p.Ile1307AsnfsTer8	p.I1307Nfs*8	ENST00000257430	NM_000038.5	1306	gaa/gAaa	16/16	0.277359556698499	1	FACETS	0.905	0.832	0.979	0.905	0.832	0.979	INDETERMINATE	1	TRUE	0	0.557103708481568	1		233	398	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259357	89259357	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	75	596	0	ENST00000336596.2:c.501G>T	p.Glu167Asp	p.E167D	ENST00000336596	NM_005233.5	167	gaG/gaT	3/17	1	2	FACETS	0.211	0.184	0.24	0.211	0.184	0.24	SUBCLONAL	1	TRUE	1	0.557103708481568	2		596	1278	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431777	49431777	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	191	317	0	ENST00000301067.7:c.9362A>G	p.Lys3121Arg	p.K3121R	ENST00000301067	NM_003482.3	3121	aAg/aGg	34/54	0.178373338848965	3	FACETS	1	0.989	1	0.679	0.63	0.728	INDETERMINATE	1	TRUE	1	0.557103708481568	3		317	646	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400938	72400938	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	131	1003	0	ENST00000357731.5:c.233T>G	p.Ile78Ser	p.I78S	ENST00000357731	NM_173808.2	78	aTt/aGt	2/7	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	1	0.280471510106343	2		1003	916	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251967	8251967	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	118	484	0	ENST00000335790.3:c.110T>C	p.Leu37Pro	p.L37P	ENST00000335790	NM_002315.2	37	cTg/cCg	2/4	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	FALSE	1	0.280471510106343	2		484	817	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0008371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	66	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.227027348770322	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.227027348770322	1		436	371	SUCCESS
APC	324	MSKCC	GRCh37	5	112175921	112175921	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	55	436	0	ENST00000257430.4:c.4630G>T	p.Glu1544Ter	p.E1544*	ENST00000257430	NM_000038.5	1544	Gaa/Taa	16/16	0.227027348770322	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	0	0.227027348770322	1		436	399	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156089	119156089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504640	NA	P-0008371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	124	543	1	ENST00000264033.4:c.1754G>A	p.Arg585His	p.R585H	ENST00000264033	NM_005188.3	585	cGc/cAc	11/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.227027348770322	2		544	911	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581211	48581211	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0008371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	80	488	0	ENST00000342988.3:c.515T>A	p.Leu172Ter	p.L172*	ENST00000342988	NM_005359.5	172	tTg/tAg	5/12	0.227027348770322	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.227027348770322	1		488	489	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17940947	17940947	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	26	374	0	ENST00000458235.1:c.3177G>T	p.Arg1059Ser	p.R1059S	ENST00000458235	NM_000215.3	1059	agG/agT	23/24	1	2	FACETS	0.446	0.352	0.554	0.446	0.352	0.554	SUBCLONAL	1	TRUE	1	0.227027348770322	2		374	514	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	175	690	12	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.678	0.626	0.732	0.678	0.626	0.732	SUBCLONAL	1	TRUE	1	0.705438617983811	2		702	732	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	145	478	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.680162476889878	3	FACETS	1	0.941	1	0.516	0.473	0.56	CLONAL	1	TRUE	1	0.705438617983811	3		478	539	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	313	758	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.705438617983811	1	FACETS	0.957	0.913	1	0.957	0.913	1	CLONAL	1	TRUE	0	0.705438617983811	1		759	600	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928518	69928518	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758694666	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	293	816	2	ENST00000352241.4:c.338C>T	p.Pro113Leu	p.P113L	ENST00000352241	NM_198159.2	113	cCg/cTg	2/10	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.705438617983811	2		818	816	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339111	65339111	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	243	767	1	ENST00000342505.4:c.425del	p.Lys142ArgfsTer26	p.K142Rfs*26	ENST00000342505	NM_002227.2	142	aAg/ag	5/25	0.705438617983811	1	FACETS	0.976	0.925	1	0.976	0.925	1	CLONAL	1	TRUE	0	0.705438617983811	1		768	457	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259551	55259551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	199	754	0	ENST00000275493.2:c.2609A>G	p.His870Arg	p.H870R	ENST00000275493	NM_005228.3	870	cAt/cGt	21/28	0.680162476889878	3	FACETS	0.798	0.74	0.859	0.399	0.37	0.43	SUBCLONAL	1	TRUE	1	0.705438617983811	3		754	956	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945696	17945696	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3213409	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	310	847	3	ENST00000458235.1:c.2164G>A	p.Val722Ile	p.V722I	ENST00000458235	NM_000215.3	722	Gtc/Atc	16/24	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.705438617983811	2		850	875	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152491	56152491	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561183082	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	138	390	0	ENST00000399503.3:c.547C>T	p.Arg183Ter	p.R183*	ENST00000399503	NM_005921.1	183	Cga/Tga	2/20	1	2	FACETS	0.998	0.918	1	0.998	0.918	1	CLONAL	1	TRUE	1	0.705438617983811	2		390	392	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661664	227661664	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs761880048	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	185	603	16	ENST00000305123.5:c.1791del	p.His598ThrfsTer38	p.H598Tfs*38	ENST00000305123	NM_005544.2	597	ggG/gg	1/2	1	2	FACETS	0.937	0.871	1	0.937	0.871	1	CLONAL	1	TRUE	1	0.705438617983811	2		619	560	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	227	607	6	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	0.705438617983811	2		613	607	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347874	73347874	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369590515	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	100	593	0	ENST00000377767.4:c.1187G>A	p.Arg396Gln	p.R396Q	ENST00000377767	NM_014953.3	396	cGg/cAg	8/21	0.705438617983811	6	FACETS	0.761	0.679	0.849	0.19	0.169	0.213	SUBCLONAL	1	TRUE	2	0.705438617983811	6		593	898	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31379488	31379488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	212	610	1	ENST00000328111.2:c.895C>T	p.Arg299Ter	p.R299*	ENST00000328111	NM_006892.3	299	Cga/Tga	8/23	0.64667266807511	3	FACETS	0.961	0.894	1	0.481	0.447	0.515	CLONAL	1	TRUE	1	0.705438617983811	3		611	846	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371654	55371654	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	262	749	1	ENST00000297316.4:c.344G>A	p.Arg115Gln	p.R115Q	ENST00000297316	NM_022454.3	115	cGg/cAg	2/2	0.667437666420919	3	FACETS	0.92	0.862	0.98	0.46	0.431	0.49	CLONAL	1	TRUE	1	0.705438617983811	3		750	1092	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217623	7217623	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	171	614	1	ENST00000380728.2:c.304C>T	p.Arg102Ter	p.R102*	ENST00000380728		102	Cga/Tga	4/11	0.705438617983811	1	FACETS	0.926	0.867	0.985	0.926	0.867	0.985	CLONAL	1	TRUE	0	0.705438617983811	1		615	339	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987000	36987000	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	398	540	2	ENST00000354822.5:c.689T>C	p.Leu230Pro	p.L230P	ENST00000354822	NM_001079668.2	230	cTg/cCg	3/3	0.676294719159052	3	FACETS	0.989	0.947	1	0.659	0.631	0.687	CLONAL	2	TRUE	0	0.705438617983811	3		542	772	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713544	30713546	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	179	575	0	ENST00000295754.5:c.871_873del	p.Lys291del	p.K291del	ENST00000295754	NM_003242.5	290	gAGAag/gag	4/7	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.705438617983811	2		575	499	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	201	530	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.746	0.693	0.8	0.746	0.693	0.8	SUBCLONAL	1	TRUE	1	0.705438617983811	2		534	764	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964199	28964199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745653714	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	99	478	2	ENST00000282397.4:c.1703C>T	p.Thr568Met	p.T568M	ENST00000282397	NM_002019.4	568	aCg/aTg	13/30	0.705438617983811	6	FACETS	0.792	0.707	0.884	0.198	0.176	0.221	SUBCLONAL	1	TRUE	2	0.705438617983811	6		480	854	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259934	16259934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs988832507	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	274	826	0	ENST00000375759.3:c.7199C>T	p.Ser2400Phe	p.S2400F	ENST00000375759	NM_015001.2	2400	tCt/tTt	11/15	0.705438617983811	2	FACETS	1	0.983	1	0.549	0.518	0.58	CLONAL	1	TRUE	0	0.705438617983811	2		826	708	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937910	36937910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	44	844	1	ENST00000361632.4:c.926G>A	p.Cys309Tyr	p.C309Y	ENST00000361632		309	tGc/tAc	7/16	0.705438617983811	2	FACETS	0.146	0.122	0.173	0.073	0.061	0.087	SUBCLONAL	1	TRUE	0	0.705438617983811	2		845	853	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805744	43805744	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	92	833	2	ENST00000372470.3:c.800G>T	p.Gly267Val	p.G267V	ENST00000372470	NM_005373.2	267	gGc/gTc	5/12	0.705438617983811	2	FACETS	0.311	0.275	0.348	0.155	0.137	0.174	SUBCLONAL	1	TRUE	0	0.705438617983811	2		835	840	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663805	241663805	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1357584529	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	87	316	0	ENST00000366560.3:c.1322A>G	p.Asn441Ser	p.N441S	ENST00000366560	NM_000143.3	441	aAt/aGt	9/10	0.705438617983811	2	FACETS	1	0.957	1	0.556	0.501	0.611	CLONAL	1	TRUE	0	0.705438617983811	2		316	222	SUCCESS
ATM	472	MSKCC	GRCh37	11	108183140	108183140	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	22	602	0	ENST00000278616.4:c.5921G>C	p.Ser1974Thr	p.S1974T	ENST00000278616	NM_000051.3	1974	aGt/aCt	40/63	1	2	FACETS	0.165	0.127	0.209	0.165	0.127	0.209	SUBCLONAL	1	TRUE	1	0.705438617983811	2		602	378	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376020	118376020	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	241	728	0	ENST00000534358.1:c.9413T>C	p.Leu3138Pro	p.L3138P	ENST00000534358	NM_005933.3	3138	cTa/cCa	27/36	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.705438617983811	2		728	647	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431466	121431466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193922600	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	68	750	1	ENST00000257555.6:c.670C>T	p.Pro224Ser	p.P224S	ENST00000257555		224	Cct/Tct	3/10	NA	2	FACETS	0.245	0.212	0.28			1	INDETERMINATE	1	TRUE	NA	0.705438617983811	2		751	788	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434583	110434583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	230	582	0	ENST00000375856.3:c.3818C>T	p.Pro1273Leu	p.P1273L	ENST00000375856	NM_003749.2	1273	cCg/cTg	1/2	0.53928962780436	5	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.705438617983811	5		582	1189	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986680	36986680	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	13	47	0	ENST00000354822.5:c.1009G>T	p.Gly337Cys	p.G337C	ENST00000354822	NM_001079668.2	337	Ggc/Tgc	3/3	0.676294719159052	3	FACETS	0.466	0.335	0.621	0.155	0.111	0.207	SUBCLONAL	1	TRUE	0	0.705438617983811	3		47	107	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632465	3632465	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762619200	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	482	866	1	ENST00000294008.3:c.5383C>T	p.Arg1795Cys	p.R1795C	ENST00000294008	NM_032444.2	1795	Cgc/Tgc	15/15	0.680162476889878	3	FACETS	0.89	0.854	0.925	0.89	0.854	0.925	CLONAL	2	TRUE	1	0.705438617983811	3		867	1039	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777751	3777751	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	380	1024	0	ENST00000262367.5:c.7297del	p.Asp2433ThrfsTer3	p.D2433Tfs*3	ENST00000262367	NM_004380.2	2433	Gac/ac	31/31	0.680162476889878	3	FACETS	1	0.984	1	0.544	0.516	0.572	CLONAL	1	TRUE	1	0.705438617983811	3		1024	1340	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953211	81953211	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	40	482	0	ENST00000359376.3:c.2177A>G	p.Tyr726Cys	p.Y726C	ENST00000359376	NM_002661.3	726	tAc/tGc	20/33	1	2	FACETS	0.199	0.164	0.237	0.199	0.164	0.237	SUBCLONAL	1	TRUE	1	0.705438617983811	2		482	571	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40860063	40860063	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	155	853	0	ENST00000428826.2:c.1573G>A	p.Asp525Asn	p.D525N	ENST00000428826		525	Gac/Aac	15/21	0.705438617983811	1	FACETS	0.503	0.462	0.544	0.503	0.462	0.544	SUBCLONAL	1	TRUE	0	0.705438617983811	1		853	566	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59878645	59878645	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs777511615	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	131	608	0	ENST00000259008.2:c.1109A>G	p.Asn370Ser	p.N370S	ENST00000259008	NM_032043.2	370	aAc/aGc	8/20	1	2	FACETS	0.811	0.741	0.883	0.811	0.741	0.883	CLONAL	1	TRUE	1	0.705438617983811	2		608	458	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303885	30303885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1225643119	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	52	834	0	ENST00000262643.3:c.121G>A	p.Asp41Asn	p.D41N	ENST00000262643	NM_001238.2	41	Gat/Aat	4/12	1	2	FACETS	0.186	0.157	0.217	0.186	0.157	0.217	SUBCLONAL	1	TRUE	1	0.705438617983811	2		834	793	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209106811	209106811	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201394139	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	46	705	1	ENST00000345146.2:c.757G>A	p.Asp253Asn	p.D253N	ENST00000345146	NM_005896.2	253	Gac/Aac	7/10	1	2	FACETS	0.176	0.147	0.207	0.176	0.147	0.207	SUBCLONAL	1	TRUE	1	0.705438617983811	2		706	742	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655356	45655356	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	359	972	0	ENST00000407780.3:c.496A>G	p.Arg166Gly	p.R166G	ENST00000407780	NM_001283052.1	166	Agg/Ggg	4/7	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.705438617983811	2		972	991	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069444	30069444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	33	606	0	ENST00000338641.4:c.1309G>A	p.Ala437Thr	p.A437T	ENST00000338641	NM_000268.3	437	Gca/Aca	12/16	0.705438617983811	2	FACETS	0.149	0.121	0.181	0.075	0.06	0.091	SUBCLONAL	1	TRUE	0	0.705438617983811	2		606	627	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191223	185191223	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	125	485	1	ENST00000265026.3:c.2104G>T	p.Ala702Ser	p.A702S	ENST00000265026	NM_004721.4	702	Gcc/Tcc	11/14	0.680162476889878	3	FACETS	0.886	0.806	0.97	0.443	0.403	0.485	CLONAL	1	TRUE	1	0.705438617983811	3		486	541	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672315	86672315	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	177	659	2	ENST00000274376.6:c.2117T>C	p.Leu706Pro	p.L706P	ENST00000274376	NM_002890.2	706	cTg/cCg	16/25	0.705438617983811	1	FACETS	0.892	0.835	0.949	0.892	0.835	0.949	CLONAL	1	TRUE	0	0.705438617983811	1		661	364	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056325	26056325	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776025497	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	186	546	0	ENST00000343677.2:c.332C>T	p.Ala111Val	p.A111V	ENST00000343677	NM_005319.3	111	gCa/gTa	1/1	0.680162476889878	3	FACETS	0.98	0.908	1	0.49	0.454	0.528	CLONAL	1	TRUE	1	0.705438617983811	3		546	728	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157488275	157488275	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377351099	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	176	652	1	ENST00000346085.5:c.2981C>T	p.Ala994Val	p.A994V	ENST00000346085	NM_020732.3	994	gCg/gTg	10/20	0.680162476889878	3	FACETS	0.824	0.76	0.891	0.412	0.38	0.446	CLONAL	1	TRUE	1	0.705438617983811	3		653	819	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395569	116395569	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs375951814	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	180	561	2	ENST00000397752.3:c.1862C>T	p.Thr621Ile	p.T621I	ENST00000397752	NM_000245.2	621	aCa/aTa	6/21	0.705438617983811	2	FACETS	1	0.968	1	0.535	0.498	0.573	CLONAL	1	TRUE	0	0.705438617983811	2		563	477	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128321939	128321939	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774697813	NA	P-0008417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	209	713	0	ENST00000265960.3:c.821C>T	p.Thr274Ile	p.T274I	ENST00000265960	NM_001006617.1	274	aCa/aTa	6/12	1	2	FACETS	0.869	0.81	0.929	0.869	0.81	0.929	CLONAL	1	TRUE	1	0.705438617983811	2		713	682	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729864	47729943	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTGGGCCCCGATCTCCCGGGCCCACTGTTCCTCCTCCCCGCGGACTCCCGGGGCCGCCTGGGTGGGACCGCCCGCCAG	AGCTGGGCCCCGATCTCCCGGGCCCACTGTTCCTCCTCCCCGCGGACTCCCGGGGCCGCCTGGGTGGGACCGCCCGCCAG	-	novel	NA	P-0121555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	173	625	0	ENST00000449228.1:c.446_525del	p.Ser149CysfsTer74	p.S149Cfs*74	ENST00000449228	NM_001127240.2	149	tCTGGCGGGCGGTCCCACCCAGGCGGCCCCGGGAGTCCGCGGGGAGGAGGAACAGTGGGCCCGGGAGATCGGGGCCCAGCT/t	3/4	0.496757738699132	1	FACETS	0.7	0.645	0.756	0.7	0.645	0.756	SUBCLONAL	1	NA	0	0.496757738699132	1		625	748	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879687	37879687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0121555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	104	280	3	ENST00000269571.5:c.2062C>T	p.Arg688Trp	p.R688W	ENST00000269571		688	Cgg/Tgg	17/27	0.480329039014641	2	FACETS	0.737	0.662	0.817	0.369	0.331	0.409	SUBCLONAL	1	NA	0	0.496757738699132	2		283	568	SUCCESS
APC	324	MSKCC	GRCh37	5	112090721	112090727	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTATC	AGGTATC	-	novel	NA	P-0121555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	136	391	0	ENST00000257430.4:c.135_135+6del		p.X45_splice	ENST00000257430	NM_000038.5	45		2/16	1	2	FACETS	0.762	0.693	0.833	0.762	0.693	0.833	SUBCLONAL	1	NA	1	0.496757738699132	2		391	719	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729864	47729943	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTGGGCCCCGATCTCCCGGGCCCACTGTTCCTCCTCCCCGCGGACTCCCGGGGCCGCCTGGGTGGGACCGCCCGCCAG	AGCTGGGCCCCGATCTCCCGGGCCCACTGTTCCTCCTCCCCGCGGACTCCCGGGGCCGCCTGGGTGGGACCGCCCGCCAG	-	novel	NA	P-0121555-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	142	625	0	ENST00000449228.1:c.446_525del	p.Ser149CysfsTer74	p.S149Cfs*74	ENST00000449228	NM_001127240.2	149	tCTGGCGGGCGGTCCCACCCAGGCGGCCCCGGGAGTCCGCGGGGAGGAGGAACAGTGGGCCCGGGAGATCGGGGCCCAGCT/t	3/4	0.588146208202227	1	FACETS	0.733	0.673	0.795	0.733	0.673	0.795	SUBCLONAL	1	NA	0	0.588146208202227	1		625	465	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740287	162740287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771800247	NA	P-0121555-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	202	412	0	ENST00000367921.3:c.1489G>A	p.Gly497Arg	p.G497R	ENST00000367921	NM_006182.2	497	Ggg/Agg	12/18	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	NA	1	0.588146208202227	2		412	666	SUCCESS
APC	324	MSKCC	GRCh37	5	112175873	112175873	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121555-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	136	363	0	ENST00000257430.4:c.4582G>T	p.Val1528Phe	p.V1528F	ENST00000257430	NM_000038.5	1528	Gtt/Ttt	16/16	0.494011713695284	3	FACETS	0.846	0.771	0.926	0.423	0.385	0.463	CLONAL	1	NA	1	0.588146208202227	3		363	707	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343021	118343021	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0121555-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	161	304	0	ENST00000534358.1:c.1147G>A	p.Ala383Thr	p.A383T	ENST00000534358	NM_005933.3	383	Gct/Act	3/36	0.179712451441504	1	FACETS	0.819	0.757	0.882	0.819	0.757	0.882	INDETERMINATE	1	NA	0	0.588146208202227	1		304	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578518	7578518	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934875	NA	P-0008551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	247	340	0	ENST00000269305.4:c.412G>C	p.Ala138Pro	p.A138P	ENST00000269305	NM_001126112.2	138	Gcc/Ccc	5/11	0.436209418748011	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.436209418748011	1		340	777	SUCCESS
APC	324	MSKCC	GRCh37	5	112175536	112175536	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	146	316	0	ENST00000257430.4:c.4245del	p.Ser1415ArgfsTer4	p.S1415Rfs*4	ENST00000257430	NM_000038.5	1415	agT/ag	16/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.436209418748011	2		316	625	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001303	29001303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201407326	NA	P-0008551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	133	328	0	ENST00000282397.4:c.1429G>A	p.Glu477Lys	p.E477K	ENST00000282397	NM_002019.4	477	Gaa/Aaa	10/30	0.436209418748011	3	FACETS	0.783	0.71	0.859	0.391	0.355	0.43	SUBCLONAL	1	TRUE	1	0.436209418748011	3		328	949	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933744	49933744	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs750582514	NA	P-0008551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	75	605	2	ENST00000296474.3:c.2533C>T	p.Arg845Ter	p.R845*	ENST00000296474	NM_002447.2	845	Cga/Tga	10/20	1	2	FACETS	0.304	0.265	0.346	0.304	0.265	0.346	SUBCLONAL	1	TRUE	1	0.436209418748011	2		607	1131	SUCCESS
APC	324	MSKCC	GRCh37	5	112173599	112173599	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	118	379	0	ENST00000257430.4:c.2308del	p.Ser770GlnfsTer7	p.S770Qfs*7	ENST00000257430	NM_000038.5	770	Tca/ca	16/16	1	2	FACETS	0.809	0.731	0.891	0.809	0.731	0.891	CLONAL	1	TRUE	1	0.436209418748011	2		379	669	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	356	188	0				ENST00000310581	NM_198253.2	-/1132			0.370503036613861	4	FACETS	0.993	0.945	1			1	CLONAL	3	TRUE	NA	0.370503036613861	4		188	884	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0008718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	46	294	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	0.370503036613861	2		294	213	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572971	7572971	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1496	128	697	0	ENST00000269305.4:c.1138del	p.His380IlefsTer42	p.H380Ifs*42	ENST00000269305	NM_001126112.2	380	Cat/at	11/11	1	2	FACETS	0.425	0.384	0.47	0.425	0.384	0.47	SUBCLONAL	1	TRUE	1	0.370503036613861	2		697	1624	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356216	66356216	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	54	410	0	ENST00000273854.3:c.1281G>A	p.Met427Ile	p.M427I	ENST00000273854	NM_004439.5	427	atG/atA	5/18	1	2	FACETS	0.316	0.269	0.368	0.316	0.269	0.368	SUBCLONAL	1	TRUE	1	0.370503036613861	2		410	923	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629238	187629238	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	63	433	2	ENST00000441802.2:c.1744C>A	p.Leu582Ile	p.L582I	ENST00000441802	NM_005245.3	582	Cta/Ata	2/27	1	2	FACETS	0.421	0.363	0.484	0.421	0.363	0.484	SUBCLONAL	1	TRUE	1	0.370503036613861	2		435	808	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375945	8375945	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1564384162	NA	P-0008718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	70	416	0	ENST00000356435.5:c.4652T>C	p.Val1551Ala	p.V1551A	ENST00000356435		1551	gTg/gCg	28/35	1	2	FACETS	0.475	0.413	0.542	0.475	0.413	0.542	SUBCLONAL	1	TRUE	1	0.370503036613861	2		416	796	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620418	43620418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1007307889	NA	P-0008718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	131	256	0	ENST00000355710.3:c.3027G>A	p.Met1009Ile	p.M1009I	ENST00000355710	NM_020975.4	1009	atG/atA	18/20	1	2	FACETS	0.783	0.71	0.86	0.783	0.71	0.86	SUBCLONAL	1	TRUE	1	0.370503036613861	2		256	903	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856106	68856106	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	154	462	1	ENST00000261769.5:c.1914G>A	p.Trp638Ter	p.W638*	ENST00000261769	NM_004360.3	638	tgG/tgA	12/16	0.312474818639616	1	FACETS	0.827	0.757	0.9	0.827	0.757	0.9	CLONAL	1	TRUE	0	0.370503036613861	1		463	819	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050034	13050034	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1365	203	770	2	ENST00000316448.5:c.178G>A	p.Glu60Lys	p.E60K	ENST00000316448	NM_004343.3	60	Gag/Aag	2/9	1	2	FACETS	0.699	0.646	0.754	0.699	0.646	0.754	SUBCLONAL	1	TRUE	1	0.370503036613861	2		772	1568	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054182	30054182	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	72	416	0	ENST00000338641.4:c.604G>T	p.Glu202Ter	p.E202*	ENST00000338641	NM_000268.3	202	Gaa/Taa	7/16	0.312474818639616	1	FACETS	0.447	0.39	0.508	0.447	0.39	0.508	SUBCLONAL	1	TRUE	0	0.370503036613861	1		416	709	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699366	117699367	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0008718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	61	422	0	ENST00000369458.3:c.274dup	p.Glu92GlyfsTer4	p.E92Gfs*4	ENST00000369458	NM_024626.3	92	gag/gGag	3/6	1	2	FACETS	0.327	0.281	0.378	0.327	0.281	0.378	SUBCLONAL	1	TRUE	1	0.370503036613861	2		422	1006	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36653529	36653529	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	221	433	0	ENST00000244741.5:c.449del	p.Phe150SerfsTer8	p.F150Sfs*8	ENST00000244741	NM_000389.4	149	gaT/ga	3/3	0.201164266939358	2	FACETS	1	0.986	1	0.611	0.568	0.654	INDETERMINATE	1	TRUE	0	0.370503036613861	2		433	977	SUCCESS
APC	324	MSKCC	GRCh37	5	112177500	112177500	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	279	282	2	ENST00000257430.4:c.6209G>T	p.Gly2070Val	p.G2070V	ENST00000257430	NM_000038.5	2070	gGc/gTc	16/16	0.399132683159021	1	FACETS	0.89	0.845	0.935	0.89	0.845	0.935	INDETERMINATE	1	TRUE	0	0.723614414250051	1		284	553	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570235	87570235	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	89	154	0	ENST00000277120.3:c.1975A>C	p.Asn659His	p.N659H	ENST00000277120		659	Aac/Cac	17/19	0.405226057918736	1	FACETS	0.46	0.412	0.511	0.46	0.412	0.511	INDETERMINATE	1	TRUE	0	0.723614414250051	1		154	341	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604245	189604245	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756980788	NA	P-0009195-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	118	536	2	ENST00000264731.3:c.1412G>A	p.Ser471Asn	p.S471N	ENST00000264731	NM_003722.4	471	aGc/aAc	11/14	1	2	FACETS	0.44	0.397	0.485	0.44	0.397	0.485	SUBCLONAL	1	TRUE	1	0.773687681902535	2		538	693	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0009261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	1397	403	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.253125971839575	18	FACETS	0.978	0.96	0.997			1	CLONAL	16	TRUE	NA	0.253125971839575	18		403	2133	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	141	275	0	ENST00000269305.4:c.380C>A	p.Ser127Tyr	p.S127Y	ENST00000269305	NM_001126112.2	127	tCc/tAc	5/11	0.253125971839575	2	FACETS	0.974	0.891	1	0.974	0.891	1	CLONAL	2	TRUE	0	0.253125971839575	2		275	572	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	1412	404	0	ENST00000269571.5:c.829G>T	p.Asp277Tyr	p.D277Y	ENST00000269571		277	Gac/Tac	7/27	0.253125971839575	18	FACETS	1	0.988	1			1	CLONAL	16	TRUE	NA	0.253125971839575	18		404	2092	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224496	224496	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	28	102	0	ENST00000264932.6:c.172G>C	p.Val58Leu	p.V58L	ENST00000264932	NM_004168.2	58	Gtg/Ctg	3/15	0.253125971839575	3	FACETS	1	0.886	1	0.577	0.464	0.704	CLONAL	1	TRUE	1	0.253125971839575	3		102	216	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864368	162864368	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	152	326	0	ENST00000366898.1:c.145G>A	p.Glu49Lys	p.E49K	ENST00000366898	NM_004562.2	49	Gag/Aag	2/12	0.253125971839575	3	FACETS	0.839	0.768	0.914	0.839	0.768	0.914	CLONAL	2	TRUE	1	0.253125971839575	3		326	806	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534564	140534564	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	91	356	0	ENST00000288602.6:c.349A>T	p.Met117Leu	p.M117L	ENST00000288602	NM_004333.4	117	Atg/Ttg	3/18	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.253125971839575	2		356	694	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953228	81953228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369760877	NA	P-0009261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	145	531	3	ENST00000359376.3:c.2194C>T	p.Arg732Cys	p.R732C	ENST00000359376	NM_002661.3	732	Cgc/Tgc	20/33	0.151187836605839	2	FACETS	0.897	0.816	0.982	0.449	0.408	0.491	INDETERMINATE	1	TRUE	0	0.253125971839575	2		534	1277	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967262	38967262	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0009261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	70	362	0	ENST00000357387.3:c.1218+1G>T		p.X406_splice	ENST00000357387	NM_152756.3	406			0.253125971839575	3	FACETS	0.92	0.802	1	0.46	0.401	0.524	CLONAL	1	TRUE	1	0.253125971839575	3		362	677	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0009261-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	708	403	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.487097604493109	7	FACETS	0.941	0.912	0.971			1	CLONAL	5	TRUE	NA	0.487097604493109	7		403	1370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009261-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	419	275	0	ENST00000269305.4:c.380C>A	p.Ser127Tyr	p.S127Y	ENST00000269305	NM_001126112.2	127	tCc/tAc	5/11	0.354785476328577	2	FACETS	0.818	0.781	0.855	0.818	0.781	0.855	CLONAL	2	TRUE	0	0.487097604493109	2		275	1052	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009261-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	777	404	0	ENST00000269571.5:c.829G>T	p.Asp277Tyr	p.D277Y	ENST00000269571		277	Gac/Tac	7/27	0.487097604493109	7	FACETS	0.988	0.959	1			1	CLONAL	5	TRUE	NA	0.487097604493109	7		404	1432	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224496	224496	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009261-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	38	102	0	ENST00000264932.6:c.172G>C	p.Val58Leu	p.V58L	ENST00000264932	NM_004168.2	58	Gtg/Ctg	3/15	0.353524425815439	3	FACETS	0.933	0.779	1	0.466	0.389	0.551	CLONAL	1	TRUE	1	0.487097604493109	3		102	208	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864368	162864368	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009261-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	169	326	0	ENST00000366898.1:c.145G>A	p.Glu49Lys	p.E49K	ENST00000366898	NM_004562.2	49	Gag/Aag	2/12	0.353524425815439	3	FACETS	0.839	0.777	0.903	0.839	0.777	0.903	CLONAL	2	TRUE	1	0.487097604493109	3		326	514	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534564	140534564	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009261-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	82	356	0	ENST00000288602.6:c.349A>T	p.Met117Leu	p.M117L	ENST00000288602	NM_004333.4	117	Atg/Ttg	3/18	1	2	FACETS	0.787	0.697	0.882	0.787	0.697	0.882	SUBCLONAL	1	TRUE	1	0.487097604493109	2		356	428	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953228	81953228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369760877	NA	P-0009261-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	69	531	3	ENST00000359376.3:c.2194C>T	p.Arg732Cys	p.R732C	ENST00000359376	NM_002661.3	732	Cgc/Tgc	20/33	0.265435911031648	2	FACETS	0.732	0.641	0.83	0.366	0.32	0.415	INDETERMINATE	1	TRUE	0	0.487097604493109	2		534	387	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-0009261-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	29	261	0	ENST00000371085.3:c.1038+1_1039-1del		p.X346_splice	ENST00000371085	NM_000516.4	346		12/13	0.382813615646532	2	FACETS	0.276	0.221	0.338	0.138	0.11	0.169	SUBCLONAL	1	TRUE	0	0.487097604493109	2		261	432	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967262	38967262	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0009261-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	63	362	0	ENST00000357387.3:c.1218+1G>T		p.X406_splice	ENST00000357387	NM_152756.3	406			0.353524425815439	3	FACETS	0.672	0.582	0.768	0.336	0.291	0.384	SUBCLONAL	1	TRUE	1	0.487097604493109	3		362	479	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370879	55370879	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009543-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	151	213	0	ENST00000297316.4:c.181C>T	p.Arg61Ter	p.R61*	ENST00000297316	NM_022454.3	61	Cga/Tga	1/2	0.763802582117536	6	FACETS	1	0.962	1	0.274	0.25	0.299	CLONAL	1	TRUE	2	0.763802582117536	6		213	913	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154288	2154288	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748459239	NA	P-0009543-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	600	462	0	ENST00000434045.2:c.640del	p.Leu214Ter	p.L214*	ENST00000434045	NM_001127598.1	214	Ctg/tg	5/5	0.763802582117536	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.763802582117536	3		462	1059	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0009943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	134	523	2	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	NA	2	FACETS	1	0.961	1			1	INDETERMINATE	1	TRUE	NA	0.280085180886338	2		525	866	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0009943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	63	611	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.270455678174137	3	FACETS	1	0.971	1			1	CLONAL	1	TRUE	NA	0.280085180886338	3		611	346	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971206	13971206	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs749510540	NA	P-0009943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	124	471	0	ENST00000405192.2:c.723G>C	p.Met241Ile	p.M241I	ENST00000405192	NM_001163147.1	241	atG/atC	8/12	0.280085180886338	3	FACETS	1	0.982	1	0.693	0.628	0.762	CLONAL	1	TRUE	1	0.280085180886338	3		471	728	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196137	108196137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555119121	NA	P-0009943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	36	515	2	ENST00000278616.4:c.6673G>A	p.Ala2225Thr	p.A2225T	ENST00000278616	NM_000051.3	2225	Gct/Act	46/63	0.280085180886338	1	FACETS	0.906	0.75	1	0.906	0.75	1	CLONAL	1	TRUE	0	0.280085180886338	1		517	244	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276723	15276723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1031506714	NA	P-0009943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	158	559	0	ENST00000263388.2:c.5542C>T	p.Arg1848Cys	p.R1848C	ENST00000263388	NM_000435.2	1848	Cgt/Tgt	30/33	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.280085180886338	2		559	988	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0009943-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	750	523	2	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	0.861452314120743	2	FACETS	0.952	0.934	0.968	0.952	0.934	0.968	CLONAL	2	TRUE	0	0.873799649071021	2		525	902	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0009943-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	1321	611	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.708938642644714	6	FACETS	0.999	0.978	1	0.999	0.978	1	CLONAL	4	TRUE	2	0.873799649071021	6		611	2080	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971206	13971206	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs749510540	NA	P-0009943-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	524	471	0	ENST00000405192.2:c.723G>C	p.Met241Ile	p.M241I	ENST00000405192	NM_001163147.1	241	atG/atC	8/12	0.87380264357846	4	FACETS	0.751	0.72	0.783	0.501	0.48	0.522	SUBCLONAL	2	TRUE	1	0.873799649071021	4		471	1496	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196137	108196137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555119121	NA	P-0009943-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	328	515	2	ENST00000278616.4:c.6673G>A	p.Ala2225Thr	p.A2225T	ENST00000278616	NM_000051.3	2225	Gct/Act	46/63	0.873799649071021	1	FACETS	0.983	0.951	1	0.983	0.951	1	CLONAL	1	TRUE	0	0.873799649071021	1		517	430	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276723	15276723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1031506714	NA	P-0009943-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	706	559	0	ENST00000263388.2:c.5542C>T	p.Arg1848Cys	p.R1848C	ENST00000263388	NM_000435.2	1848	Cgt/Tgt	30/33	0.87380264357846	3	FACETS	0.997	0.969	1	0.997	0.969	1	CLONAL	2	TRUE	1	0.873799649071021	3		559	1164	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94906477	94906477	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009943-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	282	674	0	ENST00000536441.1:c.1421C>G	p.Ala474Gly	p.A474G	ENST00000536441	NM_144665.3	474	gCa/gGa	10/10	0.873799649071021	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.873799649071021	1		674	363	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410987	31410987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1236254462	NA	P-0009943-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1623	141	803	0	ENST00000344624.3:c.3533G>A	p.Arg1178Gln	p.R1178Q	ENST00000344624		1178	cGa/cAa	28/33	0.752753552615852	4	FACETS	0.343	0.311	0.377	0.114	0.103	0.126	SUBCLONAL	1	TRUE	1	0.873799649071021	4		803	1764	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0009965-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	90	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.118092754380936	3	FACETS	0.999	0.885	1	0.5	0.442	0.561	INDETERMINATE	1	TRUE	1	0.21	3		436	948	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0009965-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	53	141	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.220492697174431	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.21	1		141	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0009965-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	101	389	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.157466199764818	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.21	1		389	810	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0010176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	148	570	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	0.226154569183443	2		570	891	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199953	108199953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	63	373	0	ENST00000278616.4:c.7296del	p.Gln2433ArgfsTer7	p.Q2433Rfs*7	ENST00000278616	NM_000051.3	2432	aTt/at	49/63	1	2	FACETS	0.635	0.548	0.731	0.635	0.548	0.731	SUBCLONAL	1	TRUE	1	0.226154569183443	2		373	877	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0010237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	270	727	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	0.162034926789879	3	FACETS	1	0.99	1	0.637	0.598	0.676	INDETERMINATE	1	TRUE	1	0.563960089803513	3		727	964	SUCCESS
APC	324	MSKCC	GRCh37	5	112174901	112174901	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	201	589	0	ENST00000257430.4:c.3610C>T	p.Gln1204Ter	p.Q1204*	ENST00000257430	NM_000038.5	1204	Caa/Taa	16/16	0.328437200868723	1	FACETS	0.998	0.933	1	0.998	0.933	1	INDETERMINATE	1	TRUE	0	0.563960089803513	1		589	513	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911575	32911575	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs730881519	NA	P-0010237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1348	461	908	0	ENST00000380152.3:c.3083A>G	p.Lys1028Arg	p.K1028R	ENST00000380152		1028	aAa/aGa	11/27	0.563960089803513	5	FACETS	0.834	0.795	0.875	0.556	0.53	0.583	CLONAL	2	TRUE	2	0.563960089803513	5		908	1809	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670412	88670412	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	282	637	0	ENST00000360948.2:c.1274C>T	p.Pro425Leu	p.P425L	ENST00000360948	NM_001012338.2	425	cCa/cTa	11/19	0.162034926789879	3	FACETS	1	0.994	1	0.742	0.699	0.786	INDETERMINATE	1	TRUE	1	0.563960089803513	3		637	864	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760143	133760145	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0010237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	207	579	0	ENST00000318560.5:c.2467_2469del	p.Thr823del	p.T823del	ENST00000318560	NM_005157.4	822	gtCACc/gtc	11/11	0.161881171177233	2	FACETS	1	0.989	1	0.646	0.604	0.689	INDETERMINATE	1	TRUE	0	0.563960089803513	2		579	568	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	304	294	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.522758127499705	3	FACETS	0.874	0.827	0.922	0.874	0.827	0.922	CLONAL	2	TRUE	1	0.522758127499705	3		294	839	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	168	466	2	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	0.522758127499705	3	FACETS	0.81	0.744	0.879	0.405	0.372	0.44	CLONAL	1	TRUE	1	0.522758127499705	3		468	1001	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	336	885	0	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	0.903	0.853	0.955	0.903	0.853	0.955	CLONAL	1	TRUE	1	0.522758127499705	2		885	1423	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347484	91347484	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1481	326	805	1	ENST00000355112.3:c.3651del	p.Lys1217AsnfsTer62	p.K1217Nfs*62	ENST00000355112	NM_000057.2	1216	Aaa/aa	19/22	0.522758127499705	3	FACETS	0.871	0.82	0.923	0.435	0.41	0.462	CLONAL	1	TRUE	1	0.522758127499705	3		806	1807	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1157	346	920	8	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	NA	2	FACETS	0.881	0.832	0.931			1	INDETERMINATE	1	TRUE	NA	0.522758127499705	2		928	1503	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	198	506	2	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	0.522758127499705	3	FACETS	0.822	0.76	0.886	0.411	0.38	0.443	CLONAL	1	TRUE	1	0.522758127499705	3		508	1163	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435287	18435287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	73	615	0	ENST00000266497.5:c.272C>T	p.Ser91Phe	p.S91F	ENST00000266497		91	tCt/tTt	1/31	NA	2	FACETS	0.233	0.202	0.266			1	INDETERMINATE	1	TRUE	NA	0.522758127499705	2		615	1200	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004651	16004651	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1284332015	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	285	443	0	ENST00000268712.3:c.2603C>T	p.Ala868Val	p.A868V	ENST00000268712	NM_006311.3	868	gCc/gTc	20/46	1	2	FACETS	0.898	0.844	0.954	0.898	0.844	0.954	CLONAL	1	TRUE	1	0.522758127499705	2		443	1214	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435199	49435199	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	32	259	1	ENST00000301067.7:c.6354del	p.Ala2119LeufsTer25	p.A2119Lfs*25	ENST00000301067	NM_003482.3	2118	ccC/cc	31/54	0.522758127499705	3	FACETS	0.32	0.259	0.389	0.16	0.129	0.195	SUBCLONAL	1	TRUE	1	0.522758127499705	3		260	482	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646981	23646981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	303	659	0	ENST00000261584.4:c.886del	p.Met296Ter	p.M296*	ENST00000261584	NM_024675.3	296	Atg/tg	4/13	1	2	FACETS	0.888	0.835	0.941	0.888	0.835	0.941	CLONAL	1	TRUE	1	0.522758127499705	2		659	1306	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894916	101894916	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060502040	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	275	663	0	ENST00000374994.4:c.469C>T	p.Arg157Ter	p.R157*	ENST00000374994	NM_004612.2	157	Cga/Tga	3/9	0.522758127499705	3	FACETS	0.929	0.871	0.99	0.465	0.435	0.495	CLONAL	1	TRUE	1	0.522758127499705	3		663	1428	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022535	12022535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159947	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1355	280	436	0	ENST00000396373.4:c.641C>T	p.Pro214Leu	p.P214L	ENST00000396373	NM_001987.4	214	cCg/cTg	5/8	0.522758127499705	4	FACETS	0.998	0.934	1	0.499	0.467	0.532	CLONAL	1	TRUE	2	0.522758127499705	4		436	1635	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120493	2120493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370324876	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	259	551	1	ENST00000219476.3:c.1753C>T	p.Arg585Cys	p.R585C	ENST00000219476	NM_000548.3	585	Cgt/Tgt	17/42	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.522758127499705	2		552	980	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	226	698	4	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	0.504332646510536	1	FACETS	0.835	0.78	0.891	0.835	0.78	0.891	CLONAL	1	TRUE	0	0.522758127499705	1		702	765	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679538	86679538	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	164	385	0	ENST00000274376.6:c.2703del	p.Leu902PhefsTer9	p.L902Ffs*9	ENST00000274376	NM_002890.2	900	gTt/gt	21/25	0.513297548967478	1	FACETS	0.822	0.759	0.887	0.822	0.759	0.887	CLONAL	1	TRUE	0	0.522758127499705	1		385	564	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107171	27107171	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	170	353	0	ENST00000324856.7:c.6782T>C	p.Ile2261Thr	p.I2261T	ENST00000324856	NM_006015.4	2261	aTc/aCc	20/20	1	2	FACETS	0.915	0.844	0.989	0.915	0.844	0.989	CLONAL	1	TRUE	1	0.522758127499705	2		353	711	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307182	65307182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	244	552	0	ENST00000342505.4:c.2506C>T	p.Pro836Ser	p.P836S	ENST00000342505	NM_002227.2	836	Cct/Tct	18/25	1	2	FACETS	0.851	0.795	0.909	0.851	0.795	0.909	CLONAL	1	TRUE	1	0.522758127499705	2		552	1097	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841522	156841522	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	209	530	0	ENST00000524377.1:c.825G>T	p.Glu275Asp	p.E275D	ENST00000524377	NM_002529.3	275	gaG/gaT	7/17	0.522758127499705	3	FACETS	0.989	0.918	1	0.494	0.459	0.531	CLONAL	1	TRUE	1	0.522758127499705	3		530	1020	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846004	156846004	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	136	470	0	ENST00000524377.1:c.1632+2T>C		p.X544_splice	ENST00000524377	NM_002529.3	544			0.522758127499705	3	FACETS	0.791	0.719	0.866	0.395	0.359	0.433	SUBCLONAL	1	TRUE	1	0.522758127499705	3		470	830	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149930	99149930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766419021	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	448	435	0	ENST00000074304.5:c.242C>T	p.Thr81Met	p.T81M	ENST00000074304	NM_001134224.1	81	aCg/aTg	5/26	0.486662385918479	2	FACETS	0.934	0.896	0.971	0.934	0.896	0.971	CLONAL	2	TRUE	0	0.522758127499705	2		435	918	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907653	111907653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	583	547	0	ENST00000393256.3:c.427C>T	p.Arg143Cys	p.R143C	ENST00000393256	NM_006538.4	143	Cgc/Tgc	3/4	0.486662385918479	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.522758127499705	2		547	1018	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096384	178096384	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	259	533	0	ENST00000397062.3:c.947C>A	p.Pro316His	p.P316H	ENST00000397062	NM_006164.4	316	cCc/cAc	5/5	0.522758127499705	2	FACETS	0.919	0.861	0.979	0.46	0.43	0.49	CLONAL	1	TRUE	0	0.522758127499705	2		533	1078	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748321	41748321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	123	439	1	ENST00000226382.2:c.448C>T	p.Arg150Cys	p.R150C	ENST00000226382	NM_003924.3	150	Cgc/Tgc	3/3	0.456928412558141	1	FACETS	0.593	0.538	0.651	0.593	0.538	0.651	SUBCLONAL	1	TRUE	0	0.522758127499705	1		440	586	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565871	55565871	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767174569	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	301	657	1	ENST00000288135.5:c.695C>T	p.Thr232Met	p.T232M	ENST00000288135	NM_000222.2	232	aCg/aTg	4/21	1	2	FACETS	0.898	0.845	0.952	0.898	0.845	0.952	CLONAL	1	TRUE	1	0.522758127499705	2		658	1283	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630438	187630438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1425607166	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	331	778	0	ENST00000441802.2:c.544G>A	p.Gly182Arg	p.G182R	ENST00000441802	NM_005245.3	182	Ggg/Agg	2/27	1	2	FACETS	0.906	0.855	0.959	0.906	0.855	0.959	CLONAL	1	TRUE	1	0.522758127499705	2		778	1397	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056475	26056475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756498899	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	109	210	0	ENST00000343677.2:c.182C>T	p.Ala61Val	p.A61V	ENST00000343677	NM_005319.3	61	gCt/gTt	1/1	1	2	FACETS	0.972	0.879	1	0.972	0.879	1	CLONAL	1	TRUE	1	0.522758127499705	2		210	429	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225667	26225667	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1553	455	1283	0	ENST00000360408.1:c.285G>T	p.Glu95Asp	p.E95D	ENST00000360408	NM_003532.2	95	gaG/gaT	1/1	1	2	FACETS	0.867	0.825	0.91	0.867	0.825	0.91	CLONAL	1	TRUE	1	0.522758127499705	2		1283	2008	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168784	32168784	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	256	654	0	ENST00000375023.3:c.4140-1G>T		p.X1380_splice	ENST00000375023	NM_004557.3	1380			1	2	FACETS	0.992	0.93	1	0.992	0.93	1	CLONAL	1	TRUE	1	0.522758127499705	2		654	987	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729480	41729480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1618	392	926	1	ENST00000242208.4:c.1049G>A	p.Cys350Tyr	p.C350Y	ENST00000242208	NM_002192.2	350	tGc/tAc	3/3	0.522758127499705	3	FACETS	0.941	0.891	0.993	0.471	0.445	0.497	CLONAL	1	TRUE	1	0.522758127499705	3		927	2010	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268880	55268880	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	90	581	0	ENST00000275493.2:c.2947-1G>T		p.X983_splice	ENST00000275493	NM_005228.3	983			0.522758127499705	3	FACETS	0.332	0.293	0.373	0.166	0.146	0.187	SUBCLONAL	1	TRUE	1	0.522758127499705	3		581	1310	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508578	106508578	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1445337101	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	39	242	0	ENST00000359195.3:c.572G>A	p.Arg191His	p.R191H	ENST00000359195	NM_002649.2	191	cGc/cAc	2/11	0.522758127499705	3	FACETS	0.287	0.237	0.343	0.144	0.118	0.172	SUBCLONAL	1	TRUE	1	0.522758127499705	3		242	655	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836275	151836275	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1469176725	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	84	331	3	ENST00000262189.6:c.14530G>A	p.Ala4844Thr	p.A4844T	ENST00000262189	NM_170606.2	4844	Gca/Aca	57/59	0.522758127499705	3	FACETS	0.543	0.479	0.612	0.272	0.239	0.306	SUBCLONAL	1	TRUE	1	0.522758127499705	3		334	746	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022127	5022127	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1378	151	683	0	ENST00000381652.3:c.140T>C	p.Leu47Pro	p.L47P	ENST00000381652	NM_004972.3	47	cTt/cCt	3/25	0.522758127499705	3	FACETS	0.477	0.434	0.522	0.238	0.217	0.261	SUBCLONAL	1	TRUE	1	0.522758127499705	3		683	1529	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5078373	5078373	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1266	95	558	0	ENST00000381652.3:c.2060G>T	p.Arg687Met	p.R687M	ENST00000381652	NM_004972.3	687	aGg/aTg	16/25	0.522758127499705	3	FACETS	0.337	0.299	0.378	0.168	0.149	0.189	SUBCLONAL	1	TRUE	1	0.522758127499705	3		558	1361	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221953	98221953	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	233	538	1	ENST00000331920.6:c.2816C>T	p.Ala939Val	p.A939V	ENST00000331920	NM_000264.3	939	gCc/gTc	17/24	0.522758127499705	3	FACETS	0.992	0.924	1	0.496	0.462	0.531	CLONAL	1	TRUE	1	0.522758127499705	3		539	1134	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779056	135779056	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	158	377	0	ENST00000298552.3:c.2190G>T	p.Glu730Asp	p.E730D	ENST00000298552	NM_001162426.1	730	gaG/gaT	17/23	0.522758127499705	3	FACETS	0.939	0.861	1	0.47	0.43	0.51	CLONAL	1	TRUE	1	0.522758127499705	3		377	812	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390711	139390711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	295	717	4	ENST00000277541.6:c.7480G>A	p.Val2494Met	p.V2494M	ENST00000277541	NM_017617.3	2494	Gtg/Atg	34/34	0.522758127499705	3	FACETS	1	0.981	1	0.549	0.516	0.583	CLONAL	1	TRUE	1	0.522758127499705	3		721	1297	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793196	139793196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1169	308	670	0	ENST00000247668.2:c.4G>A	p.Ala2Thr	p.A2T	ENST00000247668	NM_021138.3	2	Gct/Act	2/11	0.522758127499705	3	FACETS	1	0.946	1	0.503	0.473	0.534	CLONAL	1	TRUE	1	0.522758127499705	3		670	1477	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742888	17742888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749457890	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	263	352	0	ENST00000250003.3:c.796G>A	p.Ala266Thr	p.A266T	ENST00000250003	NM_002478.4	266	Gcg/Acg	3/3	0.522758127499705	3	FACETS	0.877	0.826	0.928	0.877	0.826	0.928	CLONAL	2	TRUE	1	0.522758127499705	3		352	724	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138839	64138839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1321401996	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	162	377	1	ENST00000334205.4:c.2206C>T	p.Arg736Trp	p.R736W	ENST00000334205	NM_003942.2	736	Cgg/Tgg	17/17	0.504332646510536	1	FACETS	0.862	0.796	0.93	0.862	0.796	0.93	CLONAL	1	TRUE	0	0.522758127499705	1		378	531	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421106	49421106	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	178	410	2	ENST00000301067.7:c.14644-1G>T		p.X4882_splice	ENST00000301067	NM_003482.3	4882			0.522758127499705	3	FACETS	1	0.97	1	0.55	0.508	0.594	CLONAL	1	TRUE	1	0.522758127499705	3		412	781	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885578	111885578	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs751470371	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	333	813	0	ENST00000341259.2:c.1355C>G	p.Ala452Gly	p.A452G	ENST00000341259	NM_005475.2	452	gCc/gGc	7/8	1	2	FACETS	0.932	0.88	0.985	0.932	0.88	0.985	CLONAL	1	TRUE	1	0.522758127499705	2		813	1367	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202701	133202701	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	175	459	0	ENST00000320574.5:c.6531+2T>C		p.X2177_splice	ENST00000320574	NM_006231.2	2177			1	2	FACETS	0.889	0.821	0.96	0.889	0.821	0.96	CLONAL	1	TRUE	1	0.522758127499705	2		459	753	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237742	133237742	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1383071724	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	214	460	0	ENST00000320574.5:c.2873T>C	p.Val958Ala	p.V958A	ENST00000320574	NM_006231.2	958	gTg/gCg	25/49	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.522758127499705	2		460	808	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472462	88472462	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	251	593	0	ENST00000360948.2:c.2093T>C	p.Phe698Ser	p.F698S	ENST00000360948	NM_001012338.2	698	tTc/tCc	16/19	0.522758127499705	3	FACETS	0.944	0.882	1	0.472	0.441	0.505	CLONAL	1	TRUE	1	0.522758127499705	3		593	1283	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782284	56782284	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781513723	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	316	784	0	ENST00000308159.5:c.125G>A	p.Arg42His	p.R42H	ENST00000308159	NM_014669.4	42	cGc/cAc	2/22	1	2	FACETS	0.985	0.929	1	0.985	0.929	1	CLONAL	1	TRUE	1	0.522758127499705	2		784	1228	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822603	72822603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1157	97	825	2	ENST00000268489.5:c.9572G>A	p.Gly3191Asp	p.G3191D	ENST00000268489	NM_006885.3	3191	gGc/gAc	10/10	1	2	FACETS	0.296	0.263	0.332	0.296	0.263	0.332	SUBCLONAL	1	TRUE	1	0.522758127499705	2		827	1254	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676254	29676254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659856	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	267	487	0	ENST00000356175.3:c.7243G>A	p.Val2415Met	p.V2415M	ENST00000356175	NM_000267.3	2415	Gtg/Atg	48/57	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.522758127499705	2		487	981	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804360	46804360	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	72	713	1	ENST00000290295.7:c.647G>T	p.Gly216Val	p.G216V	ENST00000290295	NM_006361.5	216	gGc/gTc	2/2	1	2	FACETS	0.245	0.213	0.28	0.245	0.213	0.28	SUBCLONAL	1	TRUE	1	0.522758127499705	2		714	1124	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66518966	66518966	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	241	588	0	ENST00000358598.2:c.247T>C	p.Ser83Pro	p.S83P	ENST00000358598	NM_212471.2	83	Tct/Cct	3/11	1	2	FACETS	0.93	0.869	0.993	0.93	0.869	0.993	CLONAL	1	TRUE	1	0.522758127499705	2		588	991	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271961	15271961	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	124	252	0	ENST00000263388.2:c.6478C>A	p.Leu2160Met	p.L2160M	ENST00000263388	NM_000435.2	2160	Ctg/Atg	33/33	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.522758127499705	2		252	426	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279337	18279337	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	180	438	0	ENST00000222254.8:c.1789A>C	p.Ile597Leu	p.I597L	ENST00000222254	NM_005027.3	597	Att/Ctt	14/16	1	2	FACETS	0.907	0.839	0.979	0.907	0.839	0.979	CLONAL	1	TRUE	1	0.522758127499705	2		438	759	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796361	42796361	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	253	587	0	ENST00000575354.2:c.3008+2T>C		p.X1003_splice	ENST00000575354	NM_015125.3	1003			1	2	FACETS	0.966	0.905	1	0.966	0.905	1	CLONAL	1	TRUE	1	0.522758127499705	2		587	1002	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797203	42797203	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202242046	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	213	508	1	ENST00000575354.2:c.3565G>A	p.Val1189Met	p.V1189M	ENST00000575354	NM_015125.3	1189	Gtg/Atg	15/20	1	2	FACETS	0.923	0.859	0.989	0.923	0.859	0.989	CLONAL	1	TRUE	1	0.522758127499705	2		509	883	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022716	31022716	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	56	385	1	ENST00000375687.4:c.2201G>A	p.Arg734Lys	p.R734K	ENST00000375687	NM_015338.5	734	aGg/aAg	13/13	1	2	FACETS	0.329	0.281	0.381	0.329	0.281	0.381	SUBCLONAL	1	TRUE	1	0.522758127499705	2		386	651	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36022656	36022656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143889833	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	276	669	1	ENST00000358208.4:c.529G>A	p.Val177Met	p.V177M	ENST00000358208		177	Gtg/Atg	5/12	1	2	FACETS	0.905	0.849	0.962	0.905	0.849	0.962	CLONAL	1	TRUE	1	0.522758127499705	2		670	1167	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29083898	29083898	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1569101970	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	31	210	0	ENST00000328354.6:c.1619C>T	p.Ala540Val	p.A540V	ENST00000328354	NM_007194.3	540	gCt/gTt	15/15	1	2	FACETS	0.398	0.323	0.483	0.398	0.323	0.483	SUBCLONAL	1	TRUE	1	0.522758127499705	2		210	298	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911618	39911618	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs766235061	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1226	113	634	0	ENST00000378444.4:c.5012A>G	p.Lys1671Arg	p.K1671R	ENST00000378444	NM_001123385.1	1671	aAg/aGg	15/15	1	2	FACETS	0.323	0.289	0.359	0.323	0.289	0.359	SUBCLONAL	1	TRUE	1	0.522758127499705	2		634	1339	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922716	44922716	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	353	722	0	ENST00000377967.4:c.1577G>A	p.Gly526Glu	p.G526E	ENST00000377967	NM_021140.2	526	gGg/gAg	16/29	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.522758127499705	2		722	1313	SUCCESS
AR	367	MSKCC	GRCh37	X	66766417	66766417	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	80	175	0	ENST00000374690.3:c.1429G>C	p.Ala477Pro	p.A477P	ENST00000374690	NM_000044.3	477	Gct/Cct	1/8	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.522758127499705	2		175	278	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940011	76940011	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	308	685	2	ENST00000373344.5:c.737G>A	p.Arg246His	p.R246H	ENST00000373344	NM_000489.3	246	cGc/cAc	9/35	1	2	FACETS	0.895	0.842	0.948	0.895	0.842	0.948	CLONAL	1	TRUE	1	0.522758127499705	2		687	1317	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811605	102811605	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1565968684	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1174	378	960	1	ENST00000307046.8:c.579del	p.Gly194GlufsTer8	p.G194Efs*8	ENST00000307046	NM_001111285.1	193	aaA/aa	4/4	1	2	FACETS	0.932	0.883	0.982	0.932	0.883	0.982	CLONAL	1	TRUE	1	0.522758127499705	2		961	1552	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551952	150551952	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1154	224	566	1	ENST00000369026.2:c.55del	p.Ala19ProfsTer30	p.A19Pfs*30	ENST00000369026	NM_021960.4	19	Gcc/cc	1/3	0.522758127499705	3	FACETS	0.784	0.729	0.843	0.392	0.364	0.422	SUBCLONAL	1	TRUE	1	0.522758127499705	3		567	1378	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099214	4099215	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	144	503	0	ENST00000262948.5:c.903dup	p.Gly302ArgfsTer11	p.G302Rfs*11	ENST00000262948	NM_030662.3	301	-/C	7/11	1	2	FACETS	0.749	0.684	0.816	0.749	0.684	0.816	SUBCLONAL	1	TRUE	1	0.522758127499705	2		503	736	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28908171	28908171	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	263	586	0	ENST00000282397.4:c.2584del	p.Met862CysfsTer2	p.M862Cfs*2	ENST00000282397	NM_002019.4	862	Atg/tg	18/30	1	2	FACETS	0.901	0.844	0.959	0.901	0.844	0.959	CLONAL	1	TRUE	1	0.522758127499705	2		586	1117	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713413	40713414	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	105	475	0	ENST00000373198.4:c.4101dup	p.Ser1368LeufsTer20	p.S1368Lfs*20	ENST00000373198	NM_133170.3	1367	-/C	30/32	1	2	FACETS	0.485	0.434	0.539	0.485	0.434	0.539	SUBCLONAL	1	TRUE	1	0.522758127499705	2		475	829	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457251	89457252	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	249	527	0	ENST00000336596.2:c.1738dup	p.Arg580LysfsTer19	p.R580Kfs*19	ENST00000336596	NM_005233.5	578	gaa/gAaa	9/17	0.504332646510536	1	FACETS	0.847	0.794	0.901	0.847	0.794	0.901	CLONAL	1	TRUE	0	0.522758127499705	1		527	831	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611137	100611137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010254-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	39	846	0	ENST00000308731.7:c.1469G>A	p.Arg490His	p.R490H	ENST00000308731	NM_000061.2	490	cGc/cAc	15/19	0.501751168701749	2	FACETS	0.182	0.15	0.217	0.091	0.075	0.109	SUBCLONAL	1	TRUE	0	0.691043488202119	2		846	621	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191506	10191506	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs5030820	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	216	433	1	ENST00000256474.2:c.499C>T	p.Arg167Trp	p.R167W	ENST00000256474	NM_000551.3	167	Cgg/Tgg	3/3	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	2	FALSE	NA	0.430698343983114	2		434	470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	101	663	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.430698343983114	1	FACETS	0.976	0.88	1	0.976	0.88	1	CLONAL	1	FALSE	0	0.430698343983114	1		664	377	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	69	191	1	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.430698343983114	2		192	225	SUCCESS
AR	367	MSKCC	GRCh37	X	66943552	66943552	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137852578	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	364	387	0	ENST00000374690.3:c.2632A>G	p.Thr878Ala	p.T878A	ENST00000374690	NM_000044.3	878	Act/Gct	8/8	0.205889005557738	0	FACETS		NA	1			1	INDETERMINATE	3	FALSE	NA	0.430698343983114	0		387	395	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	87	618	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	0.431031936047224	1	FACETS	0.828	0.738	0.922	0.828	0.738	0.922	CLONAL	1	FALSE	0	0.430698343983114	1		618	383	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	172	254	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.243679160676107	3	FACETS	1	0.983	1	1	0.983	1	INDETERMINATE	2	FALSE	1	0.430698343983114	3		254	412	SUCCESS
AR	367	MSKCC	GRCh37	X	66937372	66937372	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	385	379	0	ENST00000374690.3:c.2226G>T	p.Trp742Cys	p.W742C	ENST00000374690	NM_000044.3	742	tgG/tgT	5/8	0.205889005557738	0	FACETS		NA	1			1	INDETERMINATE	3	FALSE	NA	0.430698343983114	0		379	439	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156742	20156742	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	57	247	0	ENST00000379607.5:c.17-2A>G		p.X6_splice	ENST00000379607	NM_001412.3	6			0.205889005557738	0	FACETS	0.427	0.368	0.491			1	INDETERMINATE	1	FALSE	NA	0.430698343983114	0		247	353	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	34	172	2	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	0.431031936047224	0	FACETS	0.702	0.585	0.828			1	SUBCLONAL	1	FALSE	0	0.430698343983114	0		174	128	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827732	72827732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241554729	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	143	825	1	ENST00000268489.5:c.8849G>A	p.Arg2950His	p.R2950H	ENST00000268489	NM_006885.3	2950	cGc/cAc	9/10	0.193022115739284	0	FACETS	0.493	0.45	0.538			1	INDETERMINATE	1	FALSE	0	0.430698343983114	0		826	767	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245024	133245024	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs752846614	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	97	402	4	ENST00000320574.5:c.2091del	p.Leu698CysfsTer94	p.L698Cfs*94	ENST00000320574	NM_006231.2	697	ccC/cc	19/49	0.193022115739284	0	FACETS	0.939	0.85	1			1	INDETERMINATE	1	FALSE	0	0.430698343983114	0		406	273	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526226	189526226	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765564666	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	105	315	1	ENST00000264731.3:c.490G>A	p.Ala164Thr	p.A164T	ENST00000264731	NM_003722.4	164	Gcc/Acc	4/14	0.243679160676107	3	FACETS	1	0.921	1	0.514	0.462	0.57	INDETERMINATE	1	FALSE	1	0.430698343983114	3		316	576	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968633	55968633	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200338299	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	104	551	0	ENST00000263923.4:c.2030C>T	p.Thr677Met	p.T677M	ENST00000263923	NM_002253.2	677	aCg/aTg	14/30	1	2	FACETS	0.827	0.742	0.916	0.827	0.742	0.916	CLONAL	1	FALSE	1	0.430698343983114	2		551	584	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696438	47696438	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	256	530	0	ENST00000347630.2:c.385A>G	p.Lys129Glu	p.K129E	ENST00000347630	NM_001007230.1	129	Aaa/Gaa	6/11	0.313854846991267	0	FACETS	0.815	0.777	0.853			1	CLONAL	2	FALSE	0	0.430698343983114	0		530	415	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65348960	65348960	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs762318572	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	111	186	0	ENST00000342505.4:c.205C>T	p.Arg69Cys	p.R69C	ENST00000342505	NM_002227.2	69	Cgt/Tgt	3/25	1	2	FACETS	1	0.956	1	1	0.99	1	CLONAL	2	FALSE	1	0.430698343983114	2		186	242	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651106	206651106	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148172544	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	114	596	1	ENST00000367120.3:c.716C>T	p.Thr239Met	p.T239M	ENST00000367120	NM_014002.3	239	aCg/aTg	8/22	1	2	FACETS	0.95	0.859	1	0.95	0.859	1	CLONAL	1	FALSE	1	0.430698343983114	2		597	557	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651612	206651612	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1410830322	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	221	647	0	ENST00000367120.3:c.922C>T	p.Arg308Ter	p.R308*	ENST00000367120	NM_014002.3	308	Cga/Tga	9/22	1	2	FACETS	0.977	0.918	1	1	0.994	1	CLONAL	2	FALSE	1	0.430698343983114	2		647	525	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653377	206653377	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376382831	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	161	292	0	ENST00000367120.3:c.1261G>A	p.Ala421Thr	p.A421T	ENST00000367120	NM_014002.3	421	Gcc/Acc	12/22	1	2	FACETS	0.966	0.897	1	1	0.993	1	CLONAL	2	FALSE	1	0.430698343983114	2		292	387	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716094	243716094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	145	534	0	ENST00000263826.5:c.1100G>A	p.Arg367Gln	p.R367Q	ENST00000263826	NM_005465.4	367	cGa/cAa	10/13	1	2	FACETS	0.914	0.835	0.996	0.914	0.835	0.996	CLONAL	1	FALSE	1	0.430698343983114	2		534	737	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736242	243736242	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	192	317	2	ENST00000263826.5:c.805T>C	p.Tyr269His	p.Y269H	ENST00000263826	NM_005465.4	269	Tac/Cac	8/13	1	2	FACETS	1	0.971	1	1	0.994	1	CLONAL	2	FALSE	1	0.430698343983114	2		319	420	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225362495	225362495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	101	380	0	ENST00000264414.4:c.1682C>T	p.Ala561Val	p.A561V	ENST00000264414	NM_003590.4	561	gCc/gTc	12/16	NA	2	FACETS	0.841	0.753	0.933			1	INDETERMINATE	1	FALSE	NA	0.430698343983114	2		380	558	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934279	49934279	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757719557	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	235	1008	2	ENST00000296474.3:c.2228C>T	p.Thr743Met	p.T743M	ENST00000296474	NM_002447.2	743	aCg/aTg	8/20	0.384361269818887	0	FACETS	0.58	0.546	0.614			1	SUBCLONAL	2	FALSE	0	0.430698343983114	0		1010	536	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119666143	119666143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769576748	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	257	416	0	ENST00000316626.5:c.338G>A	p.Arg113His	p.R113H	ENST00000316626		113	cGt/cAt	3/12	0.205663201679524	4	FACETS	1	0.961	1	1	0.994	1	INDETERMINATE	3	FALSE	2	0.430698343983114	4		416	558	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981044	55981044	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	180	319	1	ENST00000263923.4:c.655G>T	p.Val219Leu	p.V219L	ENST00000263923	NM_002253.2	219	Gta/Tta	5/30	1	2	FACETS	0.907	0.845	0.97	1	0.993	1	CLONAL	2	FALSE	1	0.430698343983114	2		320	461	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519192	187519192	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	90	470	0	ENST00000441802.2:c.12191G>T	p.Gly4064Val	p.G4064V	ENST00000441802	NM_005245.3	4064	gGg/gTg	23/27	1	2	FACETS	0.799	0.711	0.892	0.799	0.711	0.892	SUBCLONAL	1	FALSE	1	0.430698343983114	2		470	523	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539572	187539572	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	203	408	0	ENST00000441802.2:c.8168A>T	p.Asp2723Val	p.D2723V	ENST00000441802	NM_005245.3	2723	gAt/gTt	10/27	1	2	FACETS	1	0.966	1	1	0.994	1	CLONAL	2	FALSE	1	0.430698343983114	2		408	452	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177792	56177792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	241	387	0	ENST00000399503.3:c.2765C>T	p.Ala922Val	p.A922V	ENST00000399503	NM_005921.1	922	gCc/gTc	14/20	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	FALSE	1	0.430698343983114	2		387	495	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750748	57750748	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	137	433	0	ENST00000274289.3:c.1856G>A	p.Gly619Asp	p.G619D	ENST00000274289	NM_006622.3	619	gGc/gAc	13/14	1	2	FACETS	0.965	0.88	1	0.965	0.88	1	CLONAL	1	FALSE	1	0.430698343983114	2		433	659	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925462	131925462	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs781307208	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	273	380	0	ENST00000265335.6:c.1385A>G	p.Tyr462Cys	p.Y462C	ENST00000265335		462	tAt/tGt	9/25	0.431031936047224	1	FACETS	1	0.961	1	1	0.996	1	CLONAL	2	FALSE	0	0.430698343983114	1		380	492	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166737	32166737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1416850963	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	197	396	0	ENST00000375023.3:c.4501C>T	p.Arg1501Trp	p.R1501W	ENST00000375023	NM_004557.3	1501	Cgg/Tgg	24/30	1	2	FACETS	1	0.939	1	1	0.994	1	CLONAL	2	FALSE	1	0.430698343983114	2		396	456	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553755	106553755	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	100	361	0	ENST00000369096.4:c.1720A>G	p.Lys574Glu	p.K574E	ENST00000369096	NM_001198.3	574	Aag/Gag	5/7	0.431031936047224	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	0	0.430698343983114	1		361	301	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866581	117866581	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057524012	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	229	1130	2	ENST00000297338.2:c.1064C>T	p.Pro355Leu	p.P355L	ENST00000297338	NM_006265.2	355	cCg/cTg	9/14	NA	2	FACETS	1	0.969	1			1	INDETERMINATE	1	FALSE	NA	0.430698343983114	2		1132	997	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427951	49427951	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	209	600	2	ENST00000301067.7:c.10639C>T	p.Arg3547Cys	p.R3547C	ENST00000301067	NM_003482.3	3547	Cgc/Tgc	38/54	1	2	FACETS	1	0.945	1	1	0.994	1	CLONAL	2	FALSE	1	0.430698343983114	2		602	482	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867329	68867329	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	230	463	0	ENST00000261769.5:c.2576A>G	p.Tyr859Cys	p.Y859C	ENST00000261769	NM_004360.3	859	tAt/tGt	16/16	0.193022115739284	0	FACETS	0.561	0.528	0.595			1	INDETERMINATE	2	FALSE	0	0.430698343983114	0		463	542	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579365	7579365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782461	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	172	449	0	ENST00000269305.4:c.322G>A	p.Gly108Ser	p.G108S	ENST00000269305	NM_001126112.2	108	Ggt/Agt	4/11	0.430698343983114	1	FACETS	1	0.946	1	1	0.994	1	CLONAL	2	FALSE	0	0.430698343983114	1		449	311	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119796	17119796	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148257120	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	147	411	4	ENST00000285071.4:c.1198G>A	p.Val400Ile	p.V400I	ENST00000285071	NM_144997.5	400	Gtc/Atc	11/14	0.430698343983114	1	FACETS	0.936	0.872	1	1	0.992	1	CLONAL	2	FALSE	0	0.430698343983114	1		415	286	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533304	29533304	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755190083	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	292	595	1	ENST00000356175.3:c.1307C>T	p.Ser436Leu	p.S436L	ENST00000356175	NM_000267.3	436	tCg/tTg	12/57	0.348767177291274	0	FACETS	0.689	0.656	0.723			1	SUBCLONAL	2	FALSE	0	0.430698343983114	0		596	560	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56411726	56411726	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	198	789	0	ENST00000348428.3:c.1910T>G	p.Leu637Arg	p.L637R	ENST00000348428	NM_006785.3	637	cTt/cGt	15/17	0.430698343983114	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	0	0.430698343983114	1		789	693	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097165	11097165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371832808	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	55	215	0	ENST00000358026.2:c.656C>T	p.Thr219Met	p.T219M	ENST00000358026	NM_001128849.1	219	aCg/aTg	4/36	0.431031936047224	1	FACETS	0.903	0.801	1	1	0.979	1	CLONAL	2	FALSE	0	0.430698343983114	1		215	111	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867712	45867712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1244316049	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	103	555	1	ENST00000391945.4:c.688G>A	p.Val230Ile	p.V230I	ENST00000391945	NM_000400.3	230	Gtc/Atc	8/23	0.33181981343673	1	FACETS	0.995	0.899	1	0.995	0.899	1	CLONAL	1	FALSE	0	0.430698343983114	1		556	377	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021232	31021232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148964601	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	175	411	0	ENST00000375687.4:c.1231C>T	p.Arg411Cys	p.R411C	ENST00000375687	NM_015338.5	411	Cgc/Tgc	12/13	1	2	FACETS	0.967	0.902	1	1	0.993	1	CLONAL	2	FALSE	1	0.430698343983114	2		411	420	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345884	70345884	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	124	293	0	ENST00000374080.3:c.2423-2A>G		p.X808_splice	ENST00000374080		808			0.205889005557738	0	FACETS	1	0.932	1			1	INDETERMINATE	1	FALSE	NA	0.430698343983114	0		293	322	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822586	72822586	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	312	989	1	ENST00000268489.5:c.9589del	p.Gln3197SerfsTer44	p.Q3197Sfs*44	ENST00000268489	NM_006885.3	3197	Cag/ag	10/10	0.193022115739284	0	FACETS	1	0.978	1			1	INDETERMINATE	1	FALSE	0	0.430698343983114	0		990	781	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972820	25972820	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	319	628	2	ENST00000435504.4:c.1605del	p.Lys535AsnfsTer3	p.K535Nfs*3	ENST00000435504		535	aaA/aa	12/13	1	2	FACETS	0.992	0.942	1	1	0.996	1	CLONAL	2	FALSE	1	0.430698343983114	2		630	747	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860383	151860390	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGCAAA	GCTGCAAA	AAAC	novel	NA	P-0010382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	537	262	0	ENST00000262189.6:c.10272_10279delinsGTTT	p.Leu3425PhefsTer16	p.L3425Ffs*16	ENST00000262189	NM_170606.2	3424	gcTTTGCAGCag/gcGTTTag	43/59	0.179581179273587	1	FACETS	1	0.993	1	1	0.998	1	INDETERMINATE	2	FALSE	0	0.430698343983114	1		262	895	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631839	90631839	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519906	NA	P-0010392-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1594	209	493	0	ENST00000330062.3:c.514A>T	p.Arg172Trp	p.R172W	ENST00000330062	NM_002168.2	172	Agg/Tgg	4/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.178478346818979	2		493	1803	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500637	99500637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200539075	NA	P-0010392-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	84	213	0	ENST00000268035.6:c.4070G>A	p.Arg1357Gln	p.R1357Q	ENST00000268035	NM_000875.3	1357	cGg/cAg	21/21	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.178478346818979	2		213	896	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853008	151853008	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010392-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	99	219	0	ENST00000262189.6:c.11947C>T	p.Gln3983Ter	p.Q3983*	ENST00000262189	NM_170606.2	3983	Cag/Tag	46/59	1	2	FACETS	0.898	0.803	0.998	1	0.985	1	CLONAL	2	TRUE	1	0.178478346818979	2		219	618	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441236	52441239	+	frameshift_variant	Frame_Shift_Del	DEL	GCCT	GCCT	-	novel	NA	P-0010392-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	117	326	0	ENST00000460680.1:c.531_534del	p.Arg179SerfsTer7	p.R179Sfs*7	ENST00000460680	NM_004656.3	177	acAGGC/ac	7/17	0.178478346818979	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.178478346818979	1		326	1136	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	23	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.682	0.53	0.858	0.682	0.53	0.858	SUBCLONAL	1	TRUE	1	0.14	2		436	482	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0010432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	11	254	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.476	0.328	0.662	0.476	0.328	0.662	SUBCLONAL	1	TRUE	1	0.14	2		254	330	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022535	12022535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159947	NA	P-0010432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	63	436	0	ENST00000396373.4:c.641C>T	p.Pro214Leu	p.P214L	ENST00000396373	NM_001987.4	214	cCg/cTg	5/8	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.14	2		436	878	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0010432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	37	617	1	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.557	0.457	0.67	0.557	0.457	0.67	SUBCLONAL	1	TRUE	1	0.14	2		618	949	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942757	44942758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	47	406	0	ENST00000377967.4:c.3338dup	p.Ser1114IlefsTer37	p.S1114Ifs*37	ENST00000377967	NM_021140.2	1113	gta/gTta	23/29	1	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.14	1		406	533	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492686	56492686	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0010432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	62	452	1	ENST00000407977.2:c.252+1G>A		p.X84_splice	ENST00000407977		84			1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.14	2		453	842	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0010598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	242	380	1	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.260426767992691	4	FACETS	1	0.951	1	0.759	0.714	0.805	CLONAL	3	TRUE	0	0.34	4		381	628	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945406	17945406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1251299279	NA	P-0010598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	166	631	2	ENST00000458235.1:c.2324G>A	p.Arg775His	p.R775H	ENST00000458235	NM_000215.3	775	cGt/cAt	17/24	0.300678088657496	5	FACETS	0.99	0.911	1	0.66	0.607	0.714	CLONAL	2	TRUE	2	0.34	5		633	745	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	282	570	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.795	0.748	0.843	1	0.994	1	SUBCLONAL	2	TRUE	1	0.37651327996888	2		570	942	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	413	607	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.784	0.746	0.823	1	0.996	1	SUBCLONAL	2	TRUE	1	0.37651327996888	2		613	1399	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	317	468	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.955	0.911	0.998	1	0.997	1	CLONAL	3	TRUE	1	0.37651327996888	2		472	588	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029445	16029446	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	311	520	6	ENST00000268712.3:c.1584dup	p.Glu529ArgfsTer7	p.E529Rfs*7	ENST00000268712	NM_006311.3	528	-/A	15/46	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.37651327996888	2		526	1406	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	283	447	1	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.818	0.77	0.866	1	0.994	1	CLONAL	2	TRUE	1	0.37651327996888	2		448	919	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	104	256	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	0.352544017488466	1	FACETS	0.579	0.518	0.643	0.579	0.518	0.643	SUBCLONAL	1	TRUE	0	0.37651327996888	1		257	775	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	280	525	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.37651327996888	2		525	1149	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	193	744	4	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	0.352544017488466	1	FACETS	0.722	0.667	0.78	0.722	0.667	0.78	SUBCLONAL	1	TRUE	0	0.37651327996888	1		748	1152	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	222	424	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.85	0.794	0.906	1	0.993	1	CLONAL	2	TRUE	1	0.37651327996888	2		424	694	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	67	232	3	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	0.37651327996888	1	FACETS	0.983	0.862	1	0.983	0.862	1	CLONAL	1	TRUE	0	0.37651327996888	1		235	294	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	302	488	7	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.37651327996888	2		495	1118	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084146	47084146	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	145	444	0	ENST00000409792.3:c.7143del	p.Ser2382LeufsTer29	p.S2382Lfs*29	ENST00000409792	NM_014159.6	2381	ccC/cc	17/21	0.37651327996888	1	FACETS	0.677	0.618	0.74	0.677	0.618	0.74	SUBCLONAL	1	TRUE	0	0.37651327996888	1		444	923	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	276	506	2	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.802	0.755	0.851	1	0.994	1	CLONAL	2	TRUE	1	0.37651327996888	2		508	914	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431874	49431874	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	184	371	0	ENST00000301067.7:c.9265del	p.Val3089TrpfsTer30	p.V3089Wfs*30	ENST00000301067	NM_003482.3	3089	Gtg/tg	34/54	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.37651327996888	2		371	762	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206647788	206647788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781937364	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	296	461	0	ENST00000367120.3:c.202G>A	p.Val68Ile	p.V68I	ENST00000367120	NM_014002.3	68	Gtc/Atc	4/22	1	2	FACETS	0.843	0.795	0.891	1	0.995	1	CLONAL	2	TRUE	1	0.37651327996888	2		461	933	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020768	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs926053251	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	363	552	0	ENST00000358127.4:c.77T>G	p.Val26Gly	p.V26G	ENST00000358127	NM_001280556.1	26	gTt/gGt	2/10	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.37651327996888	2		552	1358	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	134	335	1	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	0.352544017488466	1	FACETS	0.829	0.754	0.907	0.829	0.754	0.907	CLONAL	1	TRUE	0	0.37651327996888	1		336	697	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965666	90965666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	451	561	0	ENST00000265433.3:c.1651del	p.Arg551GlyfsTer8	p.R551Gfs*8	ENST00000265433	NM_002485.4	551	Agg/gg	11/16	0.138628854051158	3	FACETS	0.909	0.867	0.953	0.909	0.867	0.953	INDETERMINATE	2	TRUE	1	0.37651327996888	3		561	1565	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438316	110438317	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	rs532810290	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	40	96	0	ENST00000375856.3:c.82_84dup	p.Asn28dup	p.N28dup	ENST00000375856	NM_003749.2	28	-/AAC	1/2	1	2	FACETS	0.808	0.675	0.953	0.808	0.675	0.953	CLONAL	1	TRUE	1	0.37651327996888	2		96	263	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	157	319	6	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	0.962	0.9	1	1	0.994	1	CLONAL	3	TRUE	1	0.37651327996888	2		325	289	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256424	46256424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs6094752	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	489	788	0	ENST00000371998.3:c.652C>T	p.Arg218Cys	p.R218C	ENST00000371998		218	Cgc/Tgc	7/23	1	2	FACETS	0.768	0.733	0.803	1	0.996	1	SUBCLONAL	2	TRUE	1	0.37651327996888	2		788	1692	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	373	426	6	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	1	2	FACETS	0.825	0.783	0.868	1	0.996	1	CLONAL	2	TRUE	1	0.37651327996888	2		432	1201	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245587	41245587	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357522	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	371	568	3	ENST00000357654.3:c.1961del	p.Lys654SerfsTer47	p.K654Sfs*47	ENST00000357654	NM_007294.3	654	aAg/ag	10/23	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.37651327996888	2		571	1364	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45391501	45391501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	204	332	1	ENST00000262160.6:c.659C>T	p.Thr220Met	p.T220M	ENST00000262160	NM_005901.5	220	aCg/aTg	6/11	0.37651327996888	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.37651327996888	1		333	687	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993849	72993849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758323451	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	329	599	1	ENST00000268489.5:c.196G>A	p.Ala66Thr	p.A66T	ENST00000268489	NM_006885.3	66	Gcg/Acg	2/10	1	2	FACETS	0.789	0.746	0.833	1	0.995	1	SUBCLONAL	2	TRUE	1	0.37651327996888	2		600	1107	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796882	42796883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761345552	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1308	255	608	2	ENST00000575354.2:c.3347dup	p.Ser1117LysfsTer34	p.S1117Kfs*34	ENST00000575354	NM_015125.3	1114	gcc/gCcc	14/20	0.37651327996888	3	FACETS	1	0.955	1	0.515	0.48	0.551	CLONAL	1	TRUE	1	0.37651327996888	3		610	1563	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542110	187542110	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	128	393	0	ENST00000441802.2:c.5630del	p.Pro1877LeufsTer20	p.P1877Lfs*20	ENST00000441802	NM_005245.3	1877	cCt/ct	10/27	0.352544017488466	1	FACETS	0.742	0.673	0.814	0.742	0.673	0.814	SUBCLONAL	1	TRUE	0	0.37651327996888	1		393	744	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141507	11141507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	326	489	0	ENST00000358026.2:c.3484G>A	p.Gly1162Ser	p.G1162S	ENST00000358026	NM_001128849.1	1162	Ggc/Agc	25/36	0.352242975855546	0	FACETS	0.756	0.719	0.793			1	SUBCLONAL	2	TRUE	0	0.37651327996888	0		489	714	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233090	69233090	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746910913	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	292	374	1	ENST00000462284.1:c.961del	p.Leu321PhefsTer52	p.L321Ffs*52	ENST00000462284	NM_002392.5	319	Ccc/cc	11/11	1	2	FACETS	0.871	0.822	0.922	1	0.995	1	CLONAL	2	TRUE	1	0.37651327996888	2		375	890	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518306	187518306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs935510544	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	53	130	0	ENST00000441802.2:c.12388G>A	p.Glu4130Lys	p.E4130K	ENST00000441802	NM_005245.3	4130	Gag/Aag	25/27	0.352544017488466	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.37651327996888	1		130	158	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713742	30713742	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs727504292	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	182	307	1	ENST00000295754.5:c.1067G>C	p.Arg356Pro	p.R356P	ENST00000295754	NM_003242.5	356	cGg/cCg	4/7	0.37651327996888	1	FACETS	0.796	0.741	0.852	1	0.992	1	SUBCLONAL	2	TRUE	0	0.37651327996888	1		308	493	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169116	32169116	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1263727065	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	211	454	2	ENST00000375023.3:c.3917del	p.Pro1306GlnfsTer3	p.P1306Qfs*3	ENST00000375023	NM_004557.3	1306	cCa/ca	22/30	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.37651327996888	2		456	802	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969882	81969882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	513	633	2	ENST00000359376.3:c.2951G>A	p.Arg984His	p.R984H	ENST00000359376	NM_002661.3	984	cGc/cAc	27/33	1	2	FACETS	0.821	0.786	0.858	1	0.997	1	CLONAL	2	TRUE	1	0.37651327996888	2		635	1659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578530	7578530	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs267605077	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	346	425	0	ENST00000269305.4:c.400T>C	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	Ttt/Ctt	5/11	1	2	FACETS	0.895	0.849	0.942	1	0.996	1	CLONAL	2	TRUE	1	0.37651327996888	2		425	1027	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209652	98209652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372828014	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	123	278	0	ENST00000331920.6:c.3886G>A	p.Gly1296Arg	p.G1296R	ENST00000331920	NM_000264.3	1296	Gga/Aga	23/24	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.37651327996888	2		278	524	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138915	64138915	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	41	422	0	ENST00000334205.4:c.2287del	p.Arg763AlafsTer21	p.R763Afs*21	ENST00000334205	NM_003942.2	761	gCc/gc	17/17	0.352544017488466	1	FACETS	0.285	0.237	0.339	0.285	0.237	0.339	SUBCLONAL	1	TRUE	0	0.37651327996888	1		422	620	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799131	42799131	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	224	363	0	ENST00000575354.2:c.4620del	p.Thr1541LeufsTer79	p.T1541Lfs*79	ENST00000575354	NM_015125.3	1539	Ccc/cc	20/20	0.37651327996888	3	FACETS	0.772	0.719	0.826	0.772	0.719	0.826	SUBCLONAL	2	TRUE	1	0.37651327996888	3		363	916	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256846	16256846	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	145	354	0	ENST00000375759.3:c.4111C>T	p.Arg1371Ter	p.R1371*	ENST00000375759	NM_015001.2	1371	Cga/Tga	11/15	0.352544017488466	1	FACETS	0.729	0.665	0.796	0.729	0.665	0.796	SUBCLONAL	1	TRUE	0	0.37651327996888	1		354	858	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166214	118166214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	266	447	2	ENST00000369448.3:c.724G>A	p.Gly242Arg	p.G242R	ENST00000369448	NM_017709.3	242	Ggg/Agg	2/2	0.352544017488466	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.37651327996888	1		449	849	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851394	156851394	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	260	459	0	ENST00000524377.1:c.2351T>C	p.Leu784Pro	p.L784P	ENST00000524377	NM_002529.3	784	cTg/cCg	17/17	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.37651327996888	2		459	1011	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612869	228612869	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201904037	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1225	391	797	1	ENST00000366696.1:c.158G>A	p.Arg53His	p.R53H	ENST00000366696	NM_003493.2	53	cGc/cAc	1/1	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.37651327996888	2		798	1616	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098598	47098598	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	315	456	1	ENST00000409792.3:c.6676G>T	p.Val2226Leu	p.V2226L	ENST00000409792	NM_014159.6	2226	Gtg/Ttg	15/21	0.37651327996888	1	FACETS	0.815	0.772	0.859	1	0.995	1	CLONAL	2	TRUE	0	0.37651327996888	1		457	833	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045875	143045875	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	246	494	0	ENST00000262992.4:c.1759C>A	p.Leu587Met	p.L587M	ENST00000262992	NM_001101669.1	587	Ctg/Atg	17/24	0.352544017488466	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.37651327996888	1		494	860	SUCCESS
APC	324	MSKCC	GRCh37	5	112177540	112177540	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs374625279	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	122	271	0	ENST00000257430.4:c.6249A>G	p.Ile2083Met	p.I2083M	ENST00000257430	NM_000038.5	2083	atA/atG	16/16	0.352544017488466	1	FACETS	0.951	0.863	1	0.951	0.863	1	CLONAL	1	TRUE	0	0.37651327996888	1		271	553	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504392	149504392	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs541926152	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	125	387	0	ENST00000261799.4:c.1810C>T	p.Arg604Cys	p.R604C	ENST00000261799	NM_002609.3	604	Cgc/Tgc	13/23	0.352544017488466	1	FACETS	0.837	0.759	0.918	0.837	0.759	0.918	CLONAL	1	TRUE	0	0.37651327996888	1		387	644	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522591	176522591	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139461102	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	307	532	0	ENST00000292408.4:c.1688G>A	p.Arg563Gln	p.R563Q	ENST00000292408	NM_213647.1	563	cGg/cAg	13/18	1	2	FACETS	0.898	0.849	0.948	1	0.995	1	CLONAL	2	TRUE	1	0.37651327996888	2		532	908	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522695	176522695	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs767126447	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	321	462	1	ENST00000292408.4:c.1792C>T	p.Arg598Ter	p.R598*	ENST00000292408	NM_213647.1	598	Cga/Tga	13/18	1	2	FACETS	0.87	0.823	0.918	1	0.995	1	CLONAL	2	TRUE	1	0.37651327996888	2		463	980	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523068	176523068	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1387211815	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	84	335	0	ENST00000292408.4:c.1832G>A	p.Arg611Gln	p.R611Q	ENST00000292408	NM_213647.1	611	cGg/cAg	14/18	1	2	FACETS	0.63	0.556	0.709	0.63	0.556	0.709	SUBCLONAL	1	TRUE	1	0.37651327996888	2		335	708	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163737	32163737	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	210	367	0	ENST00000375023.3:c.5489A>G	p.Lys1830Arg	p.K1830R	ENST00000375023	NM_004557.3	1830	aAa/aGa	30/30	1	2	FACETS	0.835	0.779	0.892	1	0.993	1	CLONAL	2	TRUE	1	0.37651327996888	2		367	668	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117632201	117632201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779401784	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	241	438	1	ENST00000368508.3:c.6215G>A	p.Arg2072Gln	p.R2072Q	ENST00000368508	NM_002944.2	2072	cGg/cAg	39/43	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.37651327996888	2		439	1016	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441974	6441974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	263	346	0	ENST00000356142.4:c.533C>T	p.Ala178Val	p.A178V	ENST00000356142	NM_018890.3	178	gCg/gTg	7/7	1	2	FACETS	0.891	0.838	0.945	1	0.995	1	CLONAL	2	TRUE	1	0.37651327996888	2		346	784	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399128	139399128	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372830543	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	280	420	0	ENST00000277541.6:c.5015G>A	p.Arg1672His	p.R1672H	ENST00000277541	NM_017617.3	1672	cGc/cAc	26/34	1	2	FACETS	0.838	0.79	0.888	1	0.995	1	CLONAL	2	TRUE	1	0.37651327996888	2		420	887	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412350	139412350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200562991	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	235	400	0	ENST00000277541.6:c.1295C>T	p.Thr432Met	p.T432M	ENST00000277541	NM_017617.3	432	aCg/aTg	8/34	1	2	FACETS	0.828	0.775	0.882	1	0.993	1	CLONAL	2	TRUE	1	0.37651327996888	2		400	754	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066883	77066883	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	145	333	0	ENST00000356341.3:c.602A>G	p.Tyr201Cys	p.Y201C	ENST00000356341	NM_002576.4	201	tAc/tGc	7/15	0.352544017488466	1	FACETS	0.926	0.847	1	0.926	0.847	1	CLONAL	1	TRUE	0	0.37651327996888	1		333	675	SUCCESS
EED	8726	MSKCC	GRCh37	11	85956323	85956323	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	148	316	0	ENST00000263360.6:c.52G>A	p.Ala18Thr	p.A18T	ENST00000263360	NM_003797.3	18	Gcc/Acc	1/12	0.352544017488466	1	FACETS	0.95	0.87	1	0.95	0.87	1	CLONAL	1	TRUE	0	0.37651327996888	1		316	672	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025831	1025831	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	314	487	0	ENST00000358495.3:c.699A>G	p.Ile233Met	p.I233M	ENST00000358495	NM_134424.2	233	atA/atG	8/12	1	2	FACETS	0.832	0.786	0.879	1	0.995	1	CLONAL	2	TRUE	1	0.37651327996888	2		487	1002	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424724	49424724	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	396	526	0	ENST00000301067.7:c.13623G>T	p.Lys4541Asn	p.K4541N	ENST00000301067	NM_003482.3	4541	aaG/aaT	40/54	1	2	FACETS	0.762	0.723	0.801	1	0.995	1	SUBCLONAL	2	TRUE	1	0.37651327996888	2		526	1381	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431543	49431543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1232234078	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	254	453	0	ENST00000301067.7:c.9596G>A	p.Ser3199Asn	p.S3199N	ENST00000301067	NM_003482.3	3199	aGc/aAc	34/54	1	2	FACETS	0.885	0.832	0.94	1	0.994	1	CLONAL	2	TRUE	1	0.37651327996888	2		453	762	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442932	49442932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886049484	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	265	409	1	ENST00000301067.7:c.3976C>T	p.Arg1326Trp	p.R1326W	ENST00000301067	NM_003482.3	1326	Cgg/Tgg	12/54	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.37651327996888	2		410	1016	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112400	115112400	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770040454	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	182	311	0	ENST00000257566.3:c.1340G>A	p.Arg447His	p.R447H	ENST00000257566	NM_016569.3	447	cGc/cAc	7/8	0.290843569526192	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.37651327996888	1		311	530	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435345	110435345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	188	237	0	ENST00000375856.3:c.3056C>T	p.Pro1019Leu	p.P1019L	ENST00000375856	NM_003749.2	1019	cCg/cTg	1/2	1	2	FACETS	0.916	0.853	0.981	1	0.993	1	CLONAL	2	TRUE	1	0.37651327996888	2		237	545	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019539	42019539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	534	663	0	ENST00000219905.7:c.3592G>A	p.Val1198Met	p.V1198M	ENST00000219905	NM_001164273.1	1198	Gtg/Atg	10/24	0.290843569526192	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.37651327996888	1		663	1711	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779279	3779279	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	212	418	2	ENST00000262367.5:c.5769C>A	p.Ser1923Arg	p.S1923R	ENST00000262367	NM_004380.2	1923	agC/agA	31/31	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.37651327996888	2		420	794	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788618	3788618	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	336	471	0	ENST00000262367.5:c.4336C>A	p.Arg1446Ser	p.R1446S	ENST00000262367	NM_004380.2	1446	Cgc/Agc	26/31	1	2	FACETS	0.818	0.774	0.863	1	0.995	1	CLONAL	2	TRUE	1	0.37651327996888	2		471	1091	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923711	72923711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs537344910	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	356	744	3	ENST00000268489.5:c.3367C>T	p.Arg1123Trp	p.R1123W	ENST00000268489	NM_006885.3	1123	Cgg/Tgg	4/10	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.37651327996888	2		747	1450	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982776	7982776	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	79	523	0	ENST00000319144.4:c.1009T>C	p.Cys337Arg	p.C337R	ENST00000319144	NM_001139.2	337	Tgc/Cgc	8/15	1	2	FACETS	0.386	0.338	0.438	0.386	0.338	0.438	SUBCLONAL	1	TRUE	1	0.37651327996888	2		523	1087	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38504636	38504636	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316046808	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	333	518	0	ENST00000254066.5:c.247C>T	p.Arg83Cys	p.R83C	ENST00000254066	NM_000964.3	83	Cgc/Tgc	3/9	1	2	FACETS	0.753	0.712	0.795	1	0.995	1	SUBCLONAL	2	TRUE	1	0.37651327996888	2		518	1174	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2220218	2220218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376474660	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	51	426	2	ENST00000398665.3:c.2803G>A	p.Ala935Thr	p.A935T	ENST00000398665	NM_032482.2	935	Gca/Aca	23/28	0.352242975855546	0	FACETS	0.272	0.231	0.318			1	SUBCLONAL	1	TRUE	0	0.37651327996888	0		428	620	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170801	11170801	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	25	353	0	ENST00000358026.2:c.4945A>G	p.Ser1649Gly	p.S1649G	ENST00000358026	NM_001128849.1	1649	Agc/Ggc	35/36	0.352242975855546	0	FACETS	0.184	0.144	0.229			1	SUBCLONAL	1	TRUE	0	0.37651327996888	0		353	451	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15838419	15838419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1326273832	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	144	579	0	ENST00000307771.7:c.917G>A	p.Arg306Gln	p.R306Q	ENST00000307771	NM_005089.3	306	cGg/cAg	10/11	0.37651327996888	1	FACETS	0.545	0.496	0.597	0.545	0.496	0.597	SUBCLONAL	1	TRUE	0	0.37651327996888	1		579	1139	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159746	20159746	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	39	511	0	ENST00000379607.5:c.13A>G	p.Lys5Glu	p.K5E	ENST00000379607	NM_001412.3	5	Aaa/Gaa	1/7	0.37651327996888	1	FACETS	0.216	0.178	0.259	0.216	0.178	0.259	SUBCLONAL	1	TRUE	0	0.37651327996888	1		511	777	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923001	44923001	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369284316	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	163	590	1	ENST00000377967.4:c.1862G>A	p.Arg621His	p.R621H	ENST00000377967	NM_021140.2	621	cGc/cAc	16/29	0.37651327996888	1	FACETS	0.55	0.503	0.599	0.55	0.503	0.599	SUBCLONAL	1	TRUE	0	0.37651327996888	1		591	1279	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274086	18274088	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	272	454	0	ENST00000222254.8:c.1308_1310del	p.Glu436del	p.E436del	ENST00000222254	NM_005027.3	435	aAGGag/aag	11/16	0.352242975855546	0	FACETS	0.725	0.686	0.765			1	SUBCLONAL	2	TRUE	0	0.37651327996888	0		454	621	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441983	40441984	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	565	838	0	ENST00000345506.4:c.228_229insT	p.Gly77TrpfsTer23	p.G77Wfs*23	ENST00000345506	NM_003152.3	76	-/T	4/20	1	2	FACETS	0.9	0.864	0.937	1	0.997	1	CLONAL	2	TRUE	1	0.37651327996888	2		838	1667	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817777	3817778	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1366	517	741	1	ENST00000262367.5:c.3193_3194del	p.Ser1065Ter	p.S1065*	ENST00000262367	NM_004380.2	1065	AGt/t	16/31	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.37651327996888	2		742	1883	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65311293	65311293	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	346	480	0	ENST00000342505.4:c.2018del	p.Gly673ValfsTer30	p.G673Vfs*30	ENST00000342505	NM_002227.2	673	gGt/gt	15/25	0.352544017488466	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.37651327996888	1		480	1055	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867543	+	inframe_deletion	In_Frame_Del	DEL	GGCGGC	GGCGGC	-	rs11466445	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	12	26	0	ENST00000374994.4:c.73_78del	p.Ala25_Ala26del	p.A25_A26del	ENST00000374994	NM_004612.2	17	ctGGCGGCg/ctg	1/9	1	2	FACETS	0.55	0.389	0.743	0.55	0.389	0.743	SUBCLONAL	1	TRUE	1	0.37651327996888	2		26	116	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198265	138198265	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	215	306	0	ENST00000237289.4:c.861del	p.Val288PhefsTer4	p.V288Ffs*4	ENST00000237289	NM_001270507.1	286	ttA/tt	6/9	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.37651327996888	2		306	850	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288188	21288188	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	77	554	1	ENST00000354336.3:c.437del	p.Lys146ArgfsTer5	p.K146Rfs*5	ENST00000354336	NM_005207.3	145	Aaa/aa	2/3	1	2	FACETS	0.331	0.289	0.376	0.331	0.289	0.376	SUBCLONAL	1	TRUE	1	0.37651327996888	2		555	1237	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726645	41726645	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1222	289	547	1	ENST00000301178.4:c.195del	p.Glu66ArgfsTer32	p.E66Rfs*32	ENST00000301178	NM_021913.4	64	Ccc/cc	2/20	0.37651327996888	3	FACETS	1	0.988	1	0.604	0.566	0.642	CLONAL	1	TRUE	1	0.37651327996888	3		548	1511	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	195	559	0	ENST00000263967.3:c.3012G>A	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atA	21/21	0.372696872826901	4	FACETS	1	0.931	1	0.504	0.466	0.545	CLONAL	1	TRUE	2	0.423675144205308	4		559	1299	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050364	176050364	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1335	117	553	0	ENST00000367669.3:c.1201C>G	p.Arg401Gly	p.R401G	ENST00000367669	NM_022457.5	401	Cga/Gga	11/20	0.423675144205308	6	FACETS	0.703	0.631	0.779			1	SUBCLONAL	1	TRUE	NA	0.423675144205308	6		553	1452	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793386	242793386	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs756100729	NA	P-0010895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	256	529	0	ENST00000334409.5:c.691C>T	p.Arg231Ter	p.R231*	ENST00000334409	NM_005018.2	231	Cga/Tga	5/5	0.423675144205308	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.423675144205308	1		529	755	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287283	38287283	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1762	216	633	0	ENST00000425967.3:c.374T>A	p.Val125Glu	p.V125E	ENST00000425967	NM_001174067.1	125	gTg/gAg	4/19	0.423675144205308	7	FACETS	1	0.962	1			1	CLONAL	1	TRUE	NA	0.423675144205308	7		633	1978	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641094	93641094	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	362	497	0	ENST00000375746.1:c.1440G>C	p.Met480Ile	p.M480I	ENST00000375746	NM_001174167.1	480	atG/atC	11/14	0.423675144205308	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.423675144205308	3		497	1014	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760322	133760322	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	126	443	0	ENST00000318560.5:c.2645C>G	p.Ser882Cys	p.S882C	ENST00000318560	NM_005157.4	882	tCt/tGt	11/11	0.351971168398176	5	FACETS	0.876	0.791	0.965	0.292	0.263	0.322	CLONAL	1	TRUE	2	0.423675144205308	5		443	1111	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914464	32914464	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1477	266	1025	0	ENST00000380152.3:c.5972C>G	p.Ala1991Gly	p.A1991G	ENST00000380152		1991	gCt/gGt	11/27	0.423675144205308	3	FACETS	0.873	0.816	0.933	0.437	0.408	0.467	CLONAL	1	TRUE	1	0.423675144205308	3		1025	1743	SUCCESS
YES1	7525	MSKCC	GRCh37	18	751762	751762	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	29	402	0	ENST00000314574.4:c.314G>C	p.Arg105Thr	p.R105T	ENST00000314574	NM_005433.3	105	aGa/aCa	3/12	0.423675144205308	1	FACETS	0.198	0.158	0.244	0.198	0.158	0.244	SUBCLONAL	1	TRUE	0	0.423675144205308	1		402	544	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410556	63410556	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1505	81	886	3	ENST00000330258.3:c.2611C>T	p.Arg871Ter	p.R871*	ENST00000330258	NM_152424.3	871	Cga/Tga	2/2	0.423675144205308	3	FACETS	0.292	0.256	0.331	0.146	0.128	0.166	SUBCLONAL	1	TRUE	1	0.423675144205308	3		889	1586	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099326	193099334	+	inframe_deletion	In_Frame_Del	DEL	GAAGACCTG	GAAGACCTG	-	novel	NA	P-0010895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	115	433	0	ENST00000367435.3:c.260_268del	p.Arg87_Asp90delinsAsn	p.R87_D90delinsN	ENST00000367435	NM_024529.4	87	aGAAGACCTGat/aat	3/17	0.168869670827491	6	FACETS	1	0.958	1			1	INDETERMINATE	1	TRUE	NA	0.423675144205308	6		433	894	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0010899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	347	451	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.945	0.897	0.993	0.945	0.897	0.993	CLONAL	1	TRUE	1	0.775413275772608	2		451	947	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0010899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	357	500	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.977	0.929	1	0.977	0.929	1	CLONAL	1	TRUE	1	0.775413275772608	2		501	942	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508260	106508260	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	171	232	1	ENST00000359195.3:c.254C>T	p.Ala85Val	p.A85V	ENST00000359195	NM_002649.2	85	gCg/gTg	2/11	0.774200369050149	3	FACETS	1	0.961	1	0.529	0.49	0.571	CLONAL	1	TRUE	1	0.775413275772608	3		233	578	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0010899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	414	551	4	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	1	2	FACETS	0.972	0.927	1	0.972	0.927	1	CLONAL	1	TRUE	1	0.775413275772608	2		555	1099	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0010899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	359	430	2	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	1	2	FACETS	0.973	0.925	1	0.973	0.925	1	CLONAL	1	TRUE	1	0.775413275772608	2		432	952	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158539	26158539	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	207	355	0	ENST00000289316.2:c.142C>T	p.Gln48Ter	p.Q48*	ENST00000289316	NM_138720.2	48	Cag/Tag	1/2	1	2	FACETS	0.924	0.863	0.985	0.924	0.863	0.985	CLONAL	1	TRUE	1	0.775413275772608	2		355	578	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642443	117642443	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	568	799	0	ENST00000368508.3:c.5756C>A	p.Ala1919Asp	p.A1919D	ENST00000368508	NM_002944.2	1919	gCt/gAt	35/43	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.775413275772608	2		799	1416	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431142	49431142	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	427	653	0	ENST00000301067.7:c.9997C>T	p.Gln3333Ter	p.Q3333*	ENST00000301067	NM_003482.3	3333	Cag/Tag	34/54	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.775413275772608	2		653	1096	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47679370	47679370	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0010899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	238	374	0	ENST00000347630.2:c.838-1G>A		p.X280_splice	ENST00000347630	NM_001007230.1	280			1	2	FACETS	0.977	0.919	1	0.977	0.919	1	CLONAL	1	TRUE	1	0.775413275772608	2		374	628	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681777	78681777	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	433	555	0	ENST00000306801.3:c.485G>A	p.Gly162Glu	p.G162E	ENST00000306801	NM_020761.2	162	gGg/gAg	4/34	1	2	FACETS	0.948	0.905	0.991	0.948	0.905	0.991	CLONAL	1	TRUE	1	0.775413275772608	2		555	1178	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101949	11101949	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	309	447	1	ENST00000358026.2:c.1369G>A	p.Glu457Lys	p.E457K	ENST00000358026	NM_001128849.1	457	Gag/Aag	8/36	1	2	FACETS	0.947	0.896	0.998	0.947	0.896	0.998	CLONAL	1	TRUE	1	0.775413275772608	2		448	842	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022953	31022953	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1386086869	NA	P-0010899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	437	599	0	ENST00000375687.4:c.2438C>T	p.Pro813Leu	p.P813L	ENST00000375687	NM_015338.5	813	cCc/cTc	13/13	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.775413275772608	2		599	1126	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874284	76874284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	488	337	0	ENST00000373344.5:c.5438G>A	p.Gly1813Glu	p.G1813E	ENST00000373344	NM_000489.3	1813	gGa/gAa	21/35	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.775413275772608	1		337	634	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549237	21549237	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1362	107	1023	0	ENST00000382592.4:c.3039T>A	p.Asp1013Glu	p.D1013E	ENST00000382592	NM_014572.2	1013	gaT/gaA	8/8	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		1023	1469	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627625	37627625	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	57	625	0	ENST00000447079.4:c.1540del	p.Thr514LeufsTer96	p.T514Lfs*96	ENST00000447079	NM_015083.1	514	Act/ct	2/14	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		625	719	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156719	20156719	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	141	298	0	ENST00000379607.5:c.38G>T	p.Arg13Leu	p.R13L	ENST00000379607	NM_001412.3	13	cGc/cTc	2/7	1	1	FACETS	0.861	0.8	0.923	1	0.991	1	CLONAL	2	TRUE	0	0.442598406272123	1		298	288	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061231	38061231	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	169	501	1	ENST00000250448.2:c.758T>A	p.Met253Lys	p.M253K	ENST00000250448	NM_004496.3	253	aTg/aAg	2/2	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.442598406272123	2		502	746	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746132	162746132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1374086542	NA	P-0011046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	127	460	0	ENST00000367921.3:c.2255G>A	p.Arg752His	p.R752H	ENST00000367921	NM_006182.2	752	cGc/cAc	16/18	1	2	FACETS	0.984	0.895	1	0.984	0.895	1	CLONAL	1	TRUE	1	0.442598406272123	2		460	583	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231257	142231257	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	140	609	1	ENST00000350721.4:c.4697C>A	p.Thr1566Asn	p.T1566N	ENST00000350721	NM_001184.3	1566	aCc/aAc	27/47	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.442598406272123	2		610	528	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829606	72829612	+	frameshift_variant	Frame_Shift_Del	DEL	GTTGCTT	GTTGCTT	-	novel	NA	P-0011046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	55	886	0	ENST00000268489.5:c.6969_6975del	p.Ser2324Ter	p.S2324*	ENST00000268489	NM_006885.3	2323	acAAGCAAC/ac	9/10	0.422941580615949	0	FACETS	0.234	0.2	0.272			1	SUBCLONAL	1	TRUE	0	0.442598406272123	0		886	591	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287448	38287448	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	157	499	0	ENST00000425967.3:c.209C>A	p.Pro70His	p.P70H	ENST00000425967	NM_001174067.1	70	cCt/cAt	4/19	0.683579242887192	3	FACETS	0.94	0.864	1			1	CLONAL	1	TRUE	NA	0.71398186533424	3		499	635	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796937	42796937	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	555	1016	0	ENST00000575354.2:c.3395C>G	p.Thr1132Ser	p.T1132S	ENST00000575354	NM_015125.3	1132	aCc/aGc	14/20	0.627304239037974	4	FACETS	0.897	0.861	0.933	0.897	0.861	0.933	CLONAL	2	TRUE	2	0.71398186533424	4		1016	1485	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864192	117864205	+	frameshift_variant	Frame_Shift_Del	DEL	TCACAGGCTCTGGG	TCACAGGCTCTGGG	-	novel	NA	P-0011048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	233	534	0	ENST00000297338.2:c.1452_1465del	p.Pro485AlafsTer47	p.P485Afs*47	ENST00000297338	NM_006265.2	484	gaCCCAGAGCCTGTGAtg/gatg	11/14	0.71398186533424	8	FACETS	0.763	0.71	0.818			1	SUBCLONAL	2	TRUE	NA	0.71398186533424	8		534	1343	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343160	118343160	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	133	384	0	ENST00000534358.1:c.1286T>C	p.Ile429Thr	p.I429T	ENST00000534358	NM_005933.3	429	aTa/aCa	3/36	0.70665251159432	2	FACETS	0.965	0.886	1	0.483	0.443	0.523	CLONAL	1	TRUE	0	0.71398186533424	2		384	386	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118354931	118354934	+	frameshift_variant	Frame_Shift_Del	DEL	GCAG	GCAG	-	novel	NA	P-0011048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	407	694	0	ENST00000534358.1:c.4123_4126del	p.Gly1375LeufsTer2	p.G1375Lfs*2	ENST00000534358	NM_005933.3	1374	GCAGgc/gc	9/36	0.70665251159432	2	FACETS	0.963	0.931	0.994	0.963	0.931	0.994	CLONAL	2	TRUE	0	0.71398186533424	2		694	592	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848649	151848649	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	204	335	0	ENST00000262189.6:c.12544G>T	p.Asp4182Tyr	p.D4182Y	ENST00000262189	NM_170606.2	4182	Gat/Tat	50/59	0.682489385422627	4	FACETS	0.889	0.831	0.948	0.889	0.831	0.948	CLONAL	2	TRUE	2	0.71398186533424	4		335	551	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0011208-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	443	570	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.388534158099953	3	FACETS	0.933	0.892	0.976			1	CLONAL	2	TRUE	NA	0.482448206304235	3		570	1221	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578224	7578224	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1429743956	NA	P-0011208-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	370	742	1	ENST00000269305.4:c.625A>T	p.Arg209Ter	p.R209*	ENST00000269305	NM_001126112.2	209	Aga/Tga	6/11	0.480463495115858	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.482448206304235	1		743	1048	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799141	45799141	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011208-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	217	799	0	ENST00000450313.1:c.292G>T	p.Gly98Trp	p.G98W	ENST00000450313	NM_012222.2	98	Ggg/Tgg	3/16	0.453791713272222	1	FACETS	0.651	0.605	0.698	0.651	0.605	0.698	SUBCLONAL	1	TRUE	0	0.482448206304235	1		799	1049	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180274	38180274	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011208-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	509	635	0	ENST00000396334.3:c.122G>C	p.Arg41Pro	p.R41P	ENST00000396334	NM_002468.4	41	cGa/cCa	1/5	0.440645127868933	3	FACETS	0.837	0.801	0.873	0.837	0.801	0.873	CLONAL	2	TRUE	1	0.482448206304235	3		635	1565	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468495	89468495	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011208-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	58	470	0	ENST00000336596.2:c.2029T>A	p.Phe677Ile	p.F677I	ENST00000336596	NM_005233.5	677	Ttt/Att	11/17	1	2	FACETS	0.231	0.197	0.267	0.231	0.197	0.267	SUBCLONAL	1	TRUE	1	0.482448206304235	2		470	1043	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911541	134911541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011208-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	219	620	1	ENST00000398015.3:c.2006C>T	p.Ala669Val	p.A669V	ENST00000398015	NM_004441.4	669	gCg/gTg	11/16	1	2	FACETS	0.824	0.766	0.884	0.824	0.766	0.884	CLONAL	1	TRUE	1	0.482448206304235	2		621	1102	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900300	101900300	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011208-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	313	693	0	ENST00000374994.4:c.734A>T	p.Glu245Val	p.E245V	ENST00000374994	NM_004612.2	245	gAg/gTg	4/9	1	2	FACETS	0.907	0.854	0.961	0.907	0.854	0.961	CLONAL	1	TRUE	1	0.482448206304235	2		693	1431	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256608	19256608	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	novel	NA	P-0011208-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	83	309	0	ENST00000162023.5:c.1105T>C	p.Ter369GlnextTer?	p.*369Qext*?	ENST00000162023		369	Tag/Cag	13/13	1	2	FACETS	0.72	0.637	0.807	0.72	0.637	0.807	SUBCLONAL	1	TRUE	1	0.482448206304235	2		309	478	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573618	48573701	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTAGTAAATGTGTTACCATACAGAGAACATTGGATGGGAGGCTTCAGGTTAGTCTTATAAGAGTTTTTCTATACCCTCTATGG	CCTAGTAAATGTGTTACCATACAGAGAACATTGGATGGGAGGCTTCAGGTTAGTCTTATAAGAGTTTTTCTATACCCTCTATGG	-	novel	NA	P-0011208-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	85	301	0	ENST00000342988.3:c.202_249+36del		p.X68_splice	ENST00000342988	NM_005359.5	68		2/12	0.480463495115858	1	FACETS	0.601	0.533	0.672	0.601	0.533	0.672	SUBCLONAL	1	TRUE	0	0.482448206304235	1		301	445	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0011222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	326	422	2	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.498341401659815	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	0	0.498341401659815	3		424	534	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0011222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	168	466	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.498341401659815	2		466	630	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438316	110438317	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	rs532810290	NA	P-0011222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	13	96	0	ENST00000375856.3:c.82_84dup	p.Asn28dup	p.N28dup	ENST00000375856	NM_003749.2	28	-/AAC	1/2	1	2	FACETS	0.454	0.326	0.606	0.454	0.326	0.606	SUBCLONAL	1	TRUE	1	0.498341401659815	2		96	115	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0011222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	83	308	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.498341401659815	2		308	293	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0011222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	201	693	1	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.498341401659815	2		694	777	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983228	149983228	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0011222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	191	505	0	ENST00000253339.5:c.3030del	p.Phe1010LeufsTer10	p.F1010Lfs*10	ENST00000253339		1010	ttT/tt	7/7	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.498341401659815	2		505	648	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958479	90958480	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs780235686	NA	P-0011222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	137	383	0	ENST00000265433.3:c.1958dup	p.Leu654AlafsTer5	p.L654Afs*5	ENST00000265433	NM_002485.4	653	aag/aaAg	13/16	1	2	FACETS	0.898	0.82	0.98	0.898	0.82	0.98	CLONAL	1	TRUE	1	0.498341401659815	2		383	612	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374914	45374914	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	482	546	0	ENST00000262160.6:c.929G>C	p.Arg310Thr	p.R310T	ENST00000262160	NM_005901.5	310	aGg/aCg	8/11	1	2	FACETS	1	0.995	1	1	0.998	1	CLONAL	2	TRUE	1	0.498341401659815	2		546	829	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	253	704	0	ENST00000397062.3:c.246A>C	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaC	2/5	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.498341401659815	2		704	876	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119562194	119562194	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0011222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	186	553	0	ENST00000316626.5:c.1142C>G	p.Ser381Ter	p.S381*	ENST00000316626		381	tCa/tGa	11/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.498341401659815	2		553	650	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200694	128200694	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	128	627	0	ENST00000341105.2:c.1111A>G	p.Asn371Asp	p.N371D	ENST00000341105	NM_032638.4	371	Aac/Gac	5/6	1	2	FACETS	0.793	0.72	0.869	0.793	0.72	0.869	SUBCLONAL	1	TRUE	1	0.498341401659815	2		627	648	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803435	1803435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	214	625	1	ENST00000260795.2:c.704G>A	p.Gly235Asp	p.G235D	ENST00000260795		235	gGc/gAc	5/17	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.498341401659815	2		626	763	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935556	13935556	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	131	379	0	ENST00000405192.2:c.1300A>G	p.Met434Val	p.M434V	ENST00000405192	NM_001163147.1	434	Atg/Gtg	12/12	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.498341401659815	2		379	493	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891188	101891188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	184	535	0	ENST00000374994.4:c.149C>T	p.Thr50Ile	p.T50I	ENST00000374994	NM_004612.2	50	aCa/aTa	2/9	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.498341401659815	2		535	676	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409974	139409974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367873715	NA	P-0011222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	206	541	1	ENST00000277541.6:c.1864G>A	p.Asp622Asn	p.D622N	ENST00000277541	NM_017617.3	622	Gac/Aac	11/34	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.498341401659815	2		542	693	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77064580	77064580	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs199690644	NA	P-0011222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	236	726	0	ENST00000356341.3:c.836+1G>T		p.X279_splice	ENST00000356341	NM_002576.4	279			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.498341401659815	2		726	861	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211461	46211461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	133	387	1	ENST00000334344.6:c.427C>T	p.Arg143Cys	p.R143C	ENST00000334344	NM_152641.2	143	Cgt/Tgt	5/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.498341401659815	2		388	452	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433934	49433934	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	150	444	0	ENST00000301067.7:c.7619A>G	p.Gln2540Arg	p.Q2540R	ENST00000301067	NM_003482.3	2540	cAg/cGg	31/54	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.498341401659815	2		444	542	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563354	21563354	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	137	753	0	ENST00000382592.4:c.565A>G	p.Thr189Ala	p.T189A	ENST00000382592	NM_014572.2	189	Acc/Gcc	4/8	1	2	FACETS	0.663	0.603	0.726	0.663	0.603	0.726	SUBCLONAL	1	TRUE	1	0.498341401659815	2		753	829	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037892	49037892	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	116	561	0	ENST00000267163.4:c.2132T>C	p.Ile711Thr	p.I711T	ENST00000267163	NM_000321.2	711	aTa/aCa	21/27	1	2	FACETS	0.769	0.695	0.847	0.769	0.695	0.847	SUBCLONAL	1	TRUE	1	0.498341401659815	2		561	605	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473732	67473732	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	199	607	0	ENST00000327367.4:c.812T>C	p.Leu271Pro	p.L271P	ENST00000327367	NM_005902.3	271	cTa/cCa	6/9	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.498341401659815	2		607	705	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644994	67644994	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	195	458	1	ENST00000264010.4:c.259G>T	p.Glu87Ter	p.E87*	ENST00000264010	NM_006565.3	87	Gag/Tag	3/12	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.498341401659815	2		459	702	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050447	13050447	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0011222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	217	723	0	ENST00000316448.5:c.397+2T>C		p.X133_splice	ENST00000316448	NM_004343.3	133			1	2	FACETS	0.888	0.826	0.952	0.888	0.826	0.952	CLONAL	1	TRUE	1	0.498341401659815	2		723	981	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217275	11217304	+	inframe_deletion	In_Frame_Del	DEL	TCCATTTTCTTGTCATAGGCCACAAGGGCA	TCCATTTTCTTGTCATAGGCCACAAGGGCA	-	novel	NA	P-0011222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	166	699	1	ENST00000361445.4:c.4374_4403del	p.Ala1459_Asp1468del	p.A1459_D1468del	ENST00000361445	NM_004958.3	1458	gaTGCCCTTGTGGCCTATGACAAGAAAATGGAc/gac	30/58	1	2	FACETS	0.929	0.856	1	0.929	0.856	1	CLONAL	1	TRUE	1	0.498341401659815	2		700	717	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589220	67589267	+	inframe_deletion	In_Frame_Del	DEL	AATTAATAAACCACTACCGGAATGAATCTCTAGCTCAGTATAATCCCA	AATTAATAAACCACTACCGGAATGAATCTCTAGCTCAGTATAATCCCA	-	novel	NA	P-0011222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	145	597	0	ENST00000274335.5:c.1212_1259del	p.Ile405_Leu420del	p.I405_L420del	ENST00000274335		403	gAATTAATAAACCACTACCGGAATGAATCTCTAGCTCAGTATAATCCCAaa/gaa	9/15	1	2	FACETS	0.911	0.834	0.991	0.911	0.834	0.991	CLONAL	1	TRUE	1	0.498341401659815	2		597	639	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435187	49435187	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	99	235	0	ENST00000301067.7:c.6366del	p.Thr2123ProfsTer21	p.T2123Pfs*21	ENST00000301067	NM_003482.3	2122	ccC/cc	31/54	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.498341401659815	2		235	345	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303227	11303228	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0011222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	232	591	0	ENST00000361445.4:c.1355dup	p.Leu452PhefsTer20	p.L452Ffs*20	ENST00000361445	NM_004958.3	452	ttg/ttTg	9/58	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.498341401659815	2		591	803	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881488	48881489	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0011222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	119	495	0	ENST00000267163.4:c.219_220dup	p.Ala74GlufsTer4	p.A74Efs*4	ENST00000267163	NM_000321.2	70	-/AG	2/27	1	2	FACETS	0.78	0.706	0.858	0.78	0.706	0.858	SUBCLONAL	1	TRUE	1	0.498341401659815	2		495	612	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432071	121432073	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs1288094664	NA	P-0011222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	226	642	0	ENST00000257555.6:c.824_826del	p.Glu275del	p.E275del	ENST00000257555		273	aAAGaa/aaa	4/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.498341401659815	2		642	845	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	20	580	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.055	0.041	0.071	0.055	0.041	0.071	SUBCLONAL	1	TRUE	1	0.85	2		580	857	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874749	151874749	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	253	424	0	ENST00000262189.6:c.7789C>G	p.Pro2597Ala	p.P2597A	ENST00000262189	NM_170606.2	2597	Cca/Gca	38/59	1	2	FACETS	0.991	0.935	1	0.991	0.935	1	CLONAL	1	TRUE	1	0.85	2		424	601	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	352	403	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.999	0.951	1	0.999	0.951	1	CLONAL	1	TRUE	1	0.85	2		403	829	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	259	424	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.985	0.929	1	0.985	0.929	1	CLONAL	1	TRUE	1	0.85	2		424	619	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177626	56177626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530669321	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	310	453	0	ENST00000399503.3:c.2599G>A	p.Glu867Lys	p.E867K	ENST00000399503	NM_005921.1	867	Gaa/Aaa	14/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.85	2		453	702	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054983	176054983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs991566021	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	55	658	0	ENST00000367669.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000367669	NM_022457.5	357	cGa/cAa	10/20	1	2	FACETS	0.134	0.113	0.156	0.134	0.113	0.156	SUBCLONAL	1	TRUE	1	0.85	2		658	969	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	317	535	0	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	0.898	0.851	0.945	0.898	0.851	0.945	CLONAL	1	TRUE	1	0.85	2		535	831	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133701	2133701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45517319	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	273	513	0	ENST00000219476.3:c.3889G>A	p.Ala1297Thr	p.A1297T	ENST00000219476	NM_000548.3	1297	Gcc/Acc	33/42	1	2	FACETS	0.869	0.82	0.919	0.869	0.82	0.919	CLONAL	1	TRUE	1	0.85	2		513	739	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	220	311	0	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.85	2		311	494	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039356	47039358	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	345	335	0	ENST00000377604.3:c.985_987del	p.Ser329del	p.S329del	ENST00000377604	NM_001204468.1	327	TCC/-	10/24	1	1	FACETS	0.999	0.966	1	0.999	0.966	1	CLONAL	1	TRUE	0	0.85	1		335	467	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874314	76874314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	410	402	3	ENST00000373344.5:c.5408G>A	p.Arg1803His	p.R1803H	ENST00000373344	NM_000489.3	1803	cGt/cAt	21/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.85	1		405	477	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426544	49426544	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555188379	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	448	666	2	ENST00000301067.7:c.11944C>T	p.Arg3982Ter	p.R3982*	ENST00000301067	NM_003482.3	3982	Cga/Tga	39/54	1	2	FACETS	0.925	0.885	0.966	0.925	0.885	0.966	CLONAL	1	TRUE	1	0.85	2		668	1139	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821890	72821890	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	443	755	0	ENST00000268489.5:c.10285del	p.Arg3429ValfsTer56	p.R3429Vfs*56	ENST00000268489	NM_006885.3	3429	Cgt/gt	10/10	1	2	FACETS	0.892	0.853	0.932	0.892	0.853	0.932	CLONAL	1	TRUE	1	0.85	2		755	1168	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352585	118352585	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555039343	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	378	676	1	ENST00000534358.1:c.3790C>T	p.Arg1264Ter	p.R1264*	ENST00000534358	NM_005933.3	1264	Cga/Tga	7/36	1	2	FACETS	0.957	0.912	1	0.957	0.912	1	CLONAL	1	TRUE	1	0.85	2		677	929	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627774	187627774	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1183516785	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	447	640	2	ENST00000441802.2:c.3208C>T	p.Arg1070Ter	p.R1070*	ENST00000441802	NM_005245.3	1070	Cga/Tga	2/27	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.85	2		642	1016	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351422	70351422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	455	365	1	ENST00000374080.3:c.4070G>A	p.Arg1357His	p.R1357H	ENST00000374080		1357	cGc/cAc	29/45	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.85	1		366	543	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917610	151917610	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	152	287	0	ENST00000262189.6:c.3710G>A	p.Arg1237Gln	p.R1237Q	ENST00000262189	NM_170606.2	1237	cGa/cAa	23/59	1	2	FACETS	0.864	0.799	0.931	0.864	0.799	0.931	CLONAL	1	TRUE	1	0.85	2		287	414	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099103	27099103	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	110	430	1	ENST00000324856.7:c.3524del	p.Pro1175HisfsTer5	p.P1175Hfs*5	ENST00000324856	NM_006015.4	1173	atC/at	13/20	1	2	FACETS	0.34	0.305	0.377	0.34	0.305	0.377	SUBCLONAL	1	TRUE	1	0.85	2		431	761	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807902	3807902	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	346	488	1	ENST00000262367.5:c.3517C>T	p.Arg1173Ter	p.R1173*	ENST00000262367	NM_004380.2	1173	Cga/Tga	18/31	1	2	FACETS	0.961	0.914	1	0.961	0.914	1	CLONAL	1	TRUE	1	0.85	2		489	847	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518900	187518900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745695748	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	376	565	1	ENST00000441802.2:c.12304G>A	p.Gly4102Arg	p.G4102R	ENST00000441802	NM_005245.3	4102	Gga/Aga	24/27	1	2	FACETS	0.879	0.837	0.922	0.879	0.837	0.922	CLONAL	1	TRUE	1	0.85	2		566	1006	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643392	52643392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200522912	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	364	601	2	ENST00000394830.3:c.2504G>A	p.Arg835His	p.R835H	ENST00000394830	NM_018313.4	835	cGt/cAt	17/30	1	2	FACETS	0.832	0.79	0.874	0.832	0.79	0.874	CLONAL	1	TRUE	1	0.85	2		603	1030	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247358	71247358	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	229	365	0	ENST00000318789.4:c.175C>T	p.Gln59Ter	p.Q59*	ENST00000318789	NM_032682.5	59	Caa/Taa	6/21	1	2	FACETS	0.809	0.758	0.861	0.809	0.758	0.861	CLONAL	1	TRUE	1	0.85	2		365	666	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808396	1808396	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	272	463	0	ENST00000260795.2:c.2154C>A	p.Asn718Lys	p.N718K	ENST00000260795		718	aaC/aaA	15/17	1	2	FACETS	0.974	0.921	1	0.974	0.921	1	CLONAL	1	TRUE	1	0.85	2		463	657	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958788	55958788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780764266	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	456	636	2	ENST00000263923.4:c.3065G>A	p.Arg1022Gln	p.R1022Q	ENST00000263923	NM_002253.2	1022	cGa/cAa	22/30	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.85	2		638	1059	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915055	131915055	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786203485	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	258	423	0	ENST00000265335.6:c.412C>T	p.Arg138Ter	p.R138*	ENST00000265335		138	Cga/Tga	4/25	1	2	FACETS	0.808	0.76	0.857	0.808	0.76	0.857	CLONAL	1	TRUE	1	0.85	2		423	751	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790672	89790672	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	405	629	0	ENST00000336032.3:c.59C>A	p.Pro20Gln	p.P20Q	ENST00000336032	NM_006813.2	20	cCg/cAg	1/2	1	2	FACETS	0.996	0.951	1	0.996	0.951	1	CLONAL	1	TRUE	1	0.85	2		629	957	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836816	151836816	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	401	524	0	ENST00000262189.6:c.14404G>T	p.Gly4802Trp	p.G4802W	ENST00000262189	NM_170606.2	4802	Ggg/Tgg	56/59	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.85	2		524	926	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856070	151856070	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	379	692	2	ENST00000262189.6:c.11548C>T	p.Arg3850Ter	p.R3850*	ENST00000262189	NM_170606.2	3850	Cga/Tga	44/59	1	2	FACETS	0.943	0.898	0.988	0.943	0.898	0.988	CLONAL	1	TRUE	1	0.85	2		694	946	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275753	38275753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	298	427	1	ENST00000425967.3:c.1516C>T	p.Arg506Trp	p.R506W	ENST00000425967	NM_001174067.1	506	Cgg/Tgg	11/19	1	2	FACETS	0.897	0.848	0.946	0.897	0.848	0.946	CLONAL	1	TRUE	1	0.85	2		428	782	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738280	145738280	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372205013	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	246	383	1	ENST00000428558.2:c.2705G>A	p.Arg902Gln	p.R902Q	ENST00000428558	NM_004260.3	902	cGg/cAg	16/22	1	2	FACETS	0.988	0.931	1	0.988	0.931	1	CLONAL	1	TRUE	1	0.85	2		384	586	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430659	80430659	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	173	303	0	ENST00000286548.4:c.349G>T	p.Asp117Tyr	p.D117Y	ENST00000286548	NM_002072.3	117	Gat/Tat	3/7	1	2	FACETS	0.915	0.851	0.98	0.915	0.851	0.98	CLONAL	1	TRUE	1	0.85	2		303	445	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221971	98221971	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768558478	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	90	415	0	ENST00000331920.6:c.2798C>T	p.Ala933Val	p.A933V	ENST00000331920	NM_000264.3	933	gCg/gTg	17/24	1	2	FACETS	0.328	0.291	0.367	0.328	0.291	0.367	SUBCLONAL	1	TRUE	1	0.85	2		415	646	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400282	139400282	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778567	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	132	177	0	ENST00000277541.6:c.4066C>T	p.Arg1356Cys	p.R1356C	ENST00000277541	NM_017617.3	1356	Cgc/Tgc	25/34	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.85	2		177	272	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534304	534304	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	178	334	0	ENST00000451590.1:c.19G>C	p.Val7Leu	p.V7L	ENST00000451590	NM_001130442.1	7	Gtg/Ctg	2/5	1	2	FACETS	0.804	0.747	0.863	0.804	0.747	0.863	CLONAL	1	TRUE	1	0.85	2		334	521	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573828	64573828	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	40	340	0	ENST00000312049.6:c.925G>C	p.Ala309Pro	p.A309P	ENST00000312049	NM_130799.2	309	Gcc/Ccc	7/10	1	2	FACETS	0.173	0.143	0.207	0.173	0.143	0.207	SUBCLONAL	1	TRUE	1	0.85	2		340	543	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625318	69625318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138021053	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	399	567	0	ENST00000334134.2:c.475G>A	p.Gly159Ser	p.G159S	ENST00000334134	NM_005247.2	159	Ggc/Agc	3/3	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.85	2		567	894	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111956053	111956053	+	upstream_gene_variant	5'Flank	SNP	C	C	T	rs766033074	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	116	170	0				ENST00000375549	NM_003002.3	88/98			1	2	FACETS	0.958	0.877	1	0.958	0.877	1	CLONAL	1	TRUE	1	0.85	2		170	285	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374168	118374168	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540886080	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	50	524	0	ENST00000534358.1:c.7561C>T	p.Arg2521Cys	p.R2521C	ENST00000534358	NM_005933.3	2521	Cgc/Tgc	27/36	1	2	FACETS	0.146	0.123	0.171	0.146	0.123	0.171	SUBCLONAL	1	TRUE	1	0.85	2		524	806	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022523	12022523	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201298740	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	393	504	0	ENST00000396373.4:c.629G>A	p.Arg210His	p.R210H	ENST00000396373	NM_001987.4	210	cGc/cAc	5/8	0.0827882686146928	3	FACETS	0.76	0.726	0.794	0.76	0.726	0.794	INDETERMINATE	2	TRUE	1	0.85	3		504	867	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562286	21562286	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755582869	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	288	416	0	ENST00000382592.4:c.1633C>T	p.Arg545Cys	p.R545C	ENST00000382592	NM_014572.2	545	Cgt/Tgt	4/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.85	2		416	652	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914518	32914518	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1285547765	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	496	907	0	ENST00000380152.3:c.6026A>G	p.Gln2009Arg	p.Q2009R	ENST00000380152		2009	cAa/cGa	11/27	1	2	FACETS	0.931	0.892	0.97	0.931	0.892	0.97	CLONAL	1	TRUE	1	0.85	2		907	1254	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435342	110435342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	122	149	0	ENST00000375856.3:c.3059G>A	p.Arg1020His	p.R1020H	ENST00000375856	NM_003749.2	1020	cGt/cAt	1/2	1	2	FACETS	0.923	0.847	1	0.923	0.847	1	CLONAL	1	TRUE	1	0.85	2		149	311	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436204	110436204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	229	362	0	ENST00000375856.3:c.2197G>A	p.Ala733Thr	p.A733T	ENST00000375856	NM_003749.2	733	Gcc/Acc	1/2	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.85	2		362	519	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021441	42021441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	504	836	0	ENST00000219905.7:c.3737G>A	p.Arg1246Gln	p.R1246Q	ENST00000219905	NM_001164273.1	1246	cGa/cAa	11/24	0.3	1	FACETS	0.581	0.557	0.604	0.581	0.557	0.604	INDETERMINATE	1	TRUE	0	0.85	1		836	1174	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727501	88727501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147992979	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	104	507	3	ENST00000360948.2:c.278C>T	p.Thr93Met	p.T93M	ENST00000360948	NM_001012338.2	93	aCg/aTg	3/19	1	2	FACETS	0.328	0.293	0.364	0.328	0.293	0.364	SUBCLONAL	1	TRUE	1	0.85	2		510	747	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134359	2134359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137854065	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	369	533	0	ENST00000219476.3:c.4136C>T	p.Ser1379Leu	p.S1379L	ENST00000219476	NM_000548.3	1379	tCg/tTg	34/42	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.85	2		533	852	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588752	29588752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867955218	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	334	565	1	ENST00000356175.3:c.4538G>A	p.Arg1513Gln	p.R1513Q	ENST00000356175	NM_000267.3	1513	cGa/cAa	34/57	1	2	FACETS	0.882	0.837	0.928	0.882	0.837	0.928	CLONAL	1	TRUE	1	0.85	2		566	891	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763274	59763274	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	392	569	0	ENST00000259008.2:c.2828T>A	p.Val943Asp	p.V943D	ENST00000259008	NM_032043.2	943	gTc/gAc	19/20	1	2	FACETS	0.949	0.905	0.993	0.949	0.905	0.993	CLONAL	1	TRUE	1	0.85	2		569	972	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619203	1619203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201830800	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	48	560	1	ENST00000344749.5:c.1357G>A	p.Ala453Thr	p.A453T	ENST00000344749	NM_001136139.2	453	Gca/Aca	16/19	1	2	FACETS	0.127	0.107	0.15	0.127	0.107	0.15	SUBCLONAL	1	TRUE	1	0.85	2		561	888	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141427	11141427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	328	468	0	ENST00000358026.2:c.3404G>A	p.Arg1135Gln	p.R1135Q	ENST00000358026	NM_001128849.1	1135	cGg/cAg	25/36	1	2	FACETS	0.928	0.88	0.975	0.928	0.88	0.975	CLONAL	1	TRUE	1	0.85	2		468	832	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906411	50906411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751775497	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	394	548	2	ENST00000440232.2:c.1072C>T	p.Arg358Trp	p.R358W	ENST00000440232	NM_002691.3	358	Cgg/Tgg	9/27	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.85	2		550	916	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910273	50910273	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555791349	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	452	738	1	ENST00000440232.2:c.1528G>A	p.Val510Met	p.V510M	ENST00000440232	NM_002691.3	510	Gtg/Atg	13/27	1	2	FACETS	0.972	0.931	1	0.972	0.931	1	CLONAL	1	TRUE	1	0.85	2		739	1094	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46252810	46252810	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751452957	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	488	679	0	ENST00000371998.3:c.239G>A	p.Arg80His	p.R80H	ENST00000371998		80	cGt/cAt	4/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.85	2		679	1134	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566556	41566556	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756061989	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	318	519	2	ENST00000263253.7:c.4433G>A	p.Arg1478His	p.R1478H	ENST00000263253	NM_001429.3	1478	cGt/cAt	27/31	1	2	FACETS	0.906	0.859	0.954	0.906	0.859	0.954	CLONAL	1	TRUE	1	0.85	2		521	826	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933164	39933164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763751220	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	383	363	1	ENST00000378444.4:c.1435G>A	p.Gly479Arg	p.G479R	ENST00000378444	NM_001123385.1	479	Gga/Aga	4/15	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.85	1		364	473	SUCCESS
AR	367	MSKCC	GRCh37	X	66943588	66943588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886041133	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	461	332	0	ENST00000374690.3:c.2668G>A	p.Val890Met	p.V890M	ENST00000374690	NM_000044.3	890	Gtg/Atg	8/8	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.85	1		332	557	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188297	32188297	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs753855314	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	369	617	1	ENST00000375023.3:c.1044del	p.Gly349AlafsTer49	p.G349Afs*49	ENST00000375023	NM_004557.3	348	ggC/gg	6/30	1	2	FACETS	0.894	0.851	0.938	0.894	0.851	0.938	CLONAL	1	TRUE	1	0.85	2		618	971	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418317	139418318	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	281	488	0	ENST00000277541.6:c.254_255del	p.Tyr85CysfsTer57	p.Y85Cfs*57	ENST00000277541	NM_017617.3	85	tAT/t	3/34	1	2	FACETS	0.886	0.837	0.936	0.886	0.837	0.936	CLONAL	1	TRUE	1	0.85	2		488	746	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	242	490	0	ENST00000264010.4:c.609_610dup	p.Thr204LysfsTer19	p.T204Kfs*19	ENST00000264010	NM_006565.3	201	-/AA	3/12	1	2	FACETS	0.727	0.682	0.774	0.727	0.682	0.774	SUBCLONAL	1	TRUE	1	0.85	2		490	783	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630490	47630490	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660480	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	248	436	0	ENST00000233146.2:c.160del	p.Ala54ProfsTer10	p.A54Pfs*10	ENST00000233146	NM_000251.2	54	Gcc/cc	1/16	1	2	FACETS	0.912	0.858	0.966	0.912	0.858	0.966	CLONAL	1	TRUE	1	0.85	2		436	640	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721114	176721114	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	174	254	0	ENST00000439151.2:c.6748del	p.Met2250CysfsTer44	p.M2250Cfs*44	ENST00000439151	NM_022455.4	2249	Aaa/aa	23/23	1	2	FACETS	0.97	0.904	1	0.97	0.904	1	CLONAL	1	TRUE	1	0.85	2		254	422	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082313	16082314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs780080562	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	36	498	0	ENST00000281043.3:c.134dup	p.Glu47GlyfsTer8	p.E47Gfs*8	ENST00000281043	NM_005378.4	43	acc/aCcc	2/3	1	2	FACETS	0.121	0.099	0.146	0.121	0.099	0.146	SUBCLONAL	1	TRUE	1	0.85	2		498	700	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16056694	16056696	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	311	524	1	ENST00000268712.3:c.746_748del	p.Glu249del	p.E249del	ENST00000268712	NM_006311.3	249	gAAGct/gct	7/46	1	2	FACETS	0.805	0.761	0.849	0.805	0.761	0.849	CLONAL	1	TRUE	1	0.85	2		525	909	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164515	36164517	+	inframe_deletion	In_Frame_Del	DEL	CCA	CCA	-	novel	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	180	290	0	ENST00000300305.3:c.1358_1360del	p.Val453del	p.V453del	ENST00000300305		453	gTGGag/gag	8/8	1	2	FACETS	0.923	0.86	0.987	0.923	0.86	0.987	CLONAL	1	TRUE	1	0.85	2		290	459	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424178	49424178	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs886040960	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	247	335	0	ENST00000301067.7:c.13884del	p.Thr4629ProfsTer11	p.T4629Pfs*11	ENST00000301067	NM_003482.3	4628	ccC/cc	42/54	1	2	FACETS	0.945	0.89	1	0.945	0.89	1	CLONAL	1	TRUE	1	0.85	2		335	615	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132635	11132635	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	118	427	0	ENST00000358026.2:c.2854del	p.Glu952LysfsTer5	p.E952Kfs*5	ENST00000358026	NM_001128849.1	951	Ggg/gg	19/36	1	2	FACETS	0.333	0.3	0.368	0.333	0.3	0.368	SUBCLONAL	1	TRUE	1	0.85	2		427	834	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713860	30713860	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	272	474	0	ENST00000295754.5:c.1185del	p.Cys396ValfsTer35	p.C396Vfs*35	ENST00000295754	NM_003242.5	395	ctG/ct	4/7	1	2	FACETS	0.859	0.81	0.909	0.859	0.81	0.909	CLONAL	1	TRUE	1	0.85	2		474	745	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940362	13940362	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0011363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	101	308	0	ENST00000405192.2:c.1143+1G>A		p.X381_splice	ENST00000405192	NM_001163147.1	381			0.408525192684042	3	FACETS	0.841	0.752	0.936	0.421	0.376	0.468	CLONAL	1	TRUE	1	0.408525192684042	3		308	708	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907240	32907241	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0011363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	71	384	0	ENST00000380152.3:c.1626dup	p.His543ThrfsTer17	p.H543Tfs*17	ENST00000380152		542	ata/atAa	10/27	1	2	FACETS	0.562	0.49	0.639	0.562	0.49	0.639	SUBCLONAL	1	TRUE	1	0.408525192684042	2		384	619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	301	689	1	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	0.377455202219652	1	FACETS	0.971	0.913	1	0.971	0.913	1	CLONAL	1	TRUE	0	0.393791567413805	1		690	1265	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0011455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	93	385	1	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.819	0.729	0.913	0.819	0.729	0.913	CLONAL	1	TRUE	1	0.393791567413805	2		386	577	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955109	17955109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140784576	NA	P-0011455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	173	528	0	ENST00000458235.1:c.118C>T	p.Arg40Cys	p.R40C	ENST00000458235	NM_000215.3	40	Cgc/Tgc	2/24	1	2	FACETS	0.963	0.887	1	0.963	0.887	1	CLONAL	1	TRUE	1	0.393791567413805	2		528	912	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591915	48591915	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	86	558	0	ENST00000342988.3:c.1078G>T	p.Asp360Tyr	p.D360Y	ENST00000342988	NM_005359.5	360	Gat/Tat	9/12	0.393791567413805	1	FACETS	0.362	0.319	0.408	0.362	0.319	0.408	SUBCLONAL	1	TRUE	0	0.393791567413805	1		558	970	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325359	1325359	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	107	529	2	ENST00000400841.2:c.316G>A	p.Val106Ile	p.V106I	ENST00000400841		106	Gtt/Att	3/6	1	2	FACETS	0.423	0.378	0.471	0.423	0.378	0.471	SUBCLONAL	1	TRUE	1	0.393791567413805	2		531	1284	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998926	11998927	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	T	novel	NA	P-0011455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	44	458	0	ENST00000353533.5:c.428_429delinsT	p.Lys143IlefsTer9	p.K143Ifs*9	ENST00000353533	NM_003010.3	143	aAA/aT	4/11	0.377455202219652	1	FACETS	0.338	0.283	0.399	0.338	0.283	0.399	SUBCLONAL	1	TRUE	0	0.393791567413805	1		458	531	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0011513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	47	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.16689437691138	4	FACETS		NA	1			1	NA	NA	FALSE	2	NA	4		436	1026	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0011513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	38	534	0	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		534	457	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593477	48593477	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	74	893	3	ENST00000342988.3:c.1228C>T	p.Gln410Ter	p.Q410*	ENST00000342988	NM_005359.5	410	Cag/Tag	10/12	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		896	809	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222657	69222657	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1321816960	NA	P-0011513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	65	1074	0	ENST00000462284.1:c.630G>T	p.Glu210Asp	p.E210D	ENST00000462284	NM_002392.5	210	gaG/gaT	8/11	0.16689437691138	4	FACETS		NA	1			1	NA	NA	FALSE	2	NA	4		1074	1189	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183843	10183860	+	inframe_deletion	In_Frame_Del	DEL	CACGGGCCGCCGCATCCA	CACGGGCCGCCGCATCCA	-	novel	NA	P-0012231-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	18	268	0	ENST00000256474.2:c.314_331del	p.Thr105_His110del	p.T105_H110del	ENST00000256474	NM_000551.3	104	ggCACGGGCCGCCGCATCCAc/ggc	1/3	0.551840510904392	1	FACETS	0.265	0.2	0.341	0.265	0.2	0.341	SUBCLONAL	1	TRUE	0	0.551840510904392	1		268	178	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188265	10188275	+	frameshift_variant	Frame_Shift_Del	DEL	TGTGCCATCTC	TGTGCCATCTC	G	novel	NA	P-0012231-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	122	722	0	ENST00000256474.2:c.408_418delinsG	p.Phe136LeufsTer20	p.F136Lfs*20	ENST00000256474	NM_000551.3	136	ttTGTGCCATCTCtc/ttGtc	2/3	0.551840510904392	1	FACETS	0.455	0.411	0.5	0.455	0.411	0.5	SUBCLONAL	1	TRUE	0	0.551840510904392	1		722	704	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0012288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	236	422	2	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.92	0.86	0.98	0.92	0.86	0.98	CLONAL	1	TRUE	1	0.626757160313716	2		424	819	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790788	89790788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1375885569	NA	P-0012334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	141	649	0	ENST00000336032.3:c.175C>T	p.His59Tyr	p.H59Y	ENST00000336032	NM_006813.2	59	Cat/Tat	1/2	0.483227177019792	2	FACETS	0.963	0.893	1	0.963	0.893	1	CLONAL	2	TRUE	0	0.483227177019792	2		649	303	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499661	8499661	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs142331255	NA	P-0012334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	77	420	0	ENST00000356435.5:c.2308C>G	p.Leu770Val	p.L770V	ENST00000356435		770	Ctg/Gtg	14/35	0.483227177019792	2	FACETS	1	0.937	1	0.542	0.481	0.606	CLONAL	1	TRUE	0	0.483227177019792	2		420	294	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307243	118307243	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555138451	NA	P-0012334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	26	52	0	ENST00000534358.1:c.16C>T	p.Arg6Trp	p.R6W	ENST00000534358	NM_005933.3	6	Cgg/Tgg	1/36	0.483227177019792	2	FACETS	0.944	0.785	1	0.944	0.785	1	CLONAL	2	TRUE	0	0.483227177019792	2		52	57	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678536	88678536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	102	364	0	ENST00000360948.2:c.1000C>T	p.His334Tyr	p.H334Y	ENST00000360948	NM_001012338.2	334	Cac/Tac	9/19	0.483227177019792	6	FACETS	0.878	0.789	0.971	0.439	0.394	0.486	CLONAL	2	TRUE	2	0.483227177019792	6		364	473	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56811524	56811524	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	134	605	0	ENST00000337432.4:c.1072C>A	p.Gln358Lys	p.Q358K	ENST00000337432	NM_058216.2	358	Caa/Aaa	9/9	0.483227177019792	6	FACETS	0.913	0.833	0.997			1	CLONAL	2	TRUE	NA	0.483227177019792	6		605	597	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117530	4117530	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730880518	NA	P-0012334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	66	209	0	ENST00000262948.5:c.190G>T	p.Val64Phe	p.V64F	ENST00000262948	NM_030662.3	64	Gtc/Ttc	2/11	0.242610793235004	5	FACETS	0.892	0.791	0.996	0.892	0.791	0.996	INDETERMINATE	3	TRUE	2	0.483227177019792	5		209	176	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309837	30309837	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	133	461	0	ENST00000307677.4:c.185G>A	p.Ser62Asn	p.S62N	ENST00000307677	NM_138578.1	62	aGc/aAc	2/3	0.453007365955697	4	FACETS	1	0.917	1	1	0.917	1	CLONAL	2	TRUE	2	0.483227177019792	4		461	408	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106483	27106861	+	frameshift_variant	Frame_Shift_Del	DEL	GAAAAGGAGGAGGAACAGGACCAAGGGGTGAGCTGCAACAAAGTGGAGTGGTGGTGGGACTGCTTGGAGATGCTCCGGGAAAACACCTTGGTTACACTCGCCAACATCTCGGGGCAGTTGGACCTATCTCCATACCCCGAGAGCATTTGCCTGCCTGTCCTGGACGGACTCCTACACTGGGCAGTTTGCCCTTCAGCTGAAGCCCAGGACCCCTTTTCCACCCTGGGCCCCAATGCCGTCCTTTCCCCGCAGAGACTGGTCTTGGAAACCCTCAGCAAACTCAGCATCCAGGACAACAATGTGGACCTGATTCTGGCCACACCCCCCTTCAGCCGCCTGGAGAAGTTGTATAGCACTATGGTGCGCTTCCTCAGTGACC	GAAAAGGAGGAGGAACAGGACCAAGGGGTGAGCTGCAACAAAGTGGAGTGGTGGTGGGACTGCTTGGAGATGCTCCGGGAAAACACCTTGGTTACACTCGCCAACATCTCGGGGCAGTTGGACCTATCTCCATACCCCGAGAGCATTTGCCTGCCTGTCCTGGACGGACTCCTACACTGGGCAGTTTGCCCTTCAGCTGAAGCCCAGGACCCCTTTTCCACCCTGGGCCCCAATGCCGTCCTTTCCCCGCAGAGACTGGTCTTGGAAACCCTCAGCAAACTCAGCATCCAGGACAACAATGTGGACCTGATTCTGGCCACACCCCCCTTCAGCCGCCTGGAGAAGTTGTATAGCACTATGGTGCGCTTCCTCAGTGACC	-	novel	NA	P-0012334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	90	618	0	ENST00000324856.7:c.6098_6476del	p.Lys2033ArgfsTer41	p.K2033Rfs*41	ENST00000324856	NM_006015.4	2032	GAAAAGGAGGAGGAACAGGACCAAGGGGTGAGCTGCAACAAAGTGGAGTGGTGGTGGGACTGCTTGGAGATGCTCCGGGAAAACACCTTGGTTACACTCGCCAACATCTCGGGGCAGTTGGACCTATCTCCATACCCCGAGAGCATTTGCCTGCCTGTCCTGGACGGACTCCTACACTGGGCAGTTTGCCCTTCAGCTGAAGCCCAGGACCCCTTTTCCACCCTGGGCCCCAATGCCGTCCTTTCCCCGCAGAGACTGGTCTTGGAAACCCTCAGCAAACTCAGCATCCAGGACAACAATGTGGACCTGATTCTGGCCACACCCCCCTTCAGCCGCCTGGAGAAGTTGTATAGCACTATGGTGCGCTTCCTCAGTGACCga/ga	20/20	0.483227177019792	2	FACETS	0.817	0.739	0.897	0.817	0.739	0.897	CLONAL	2	TRUE	0	0.483227177019792	2		618	228	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424830	49425109	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCCCATTGAAGGCTGCTACCCTCCTCCTCAGAGCCCTCATCTCTTCTGTCTGACCCAGGCTCACTCATTCTGCCCCCCGCTGGCTCTAGGACCCACTCTACCTGCTCCACTCTACTCAGAGTACTCACCTCCTTGTTGCTGGGGGTACCCTGTAGTTTCTGCTCCAGCCCAGCCAGCTTGCTGTCAATGTGCCCGTTGATCTCAGCTCGCAGCCCCTCGGACCCCCGCCCAGTGCTGAGTTGCACATTCTTTGCCCGGAGTAGCTTCTGCAAGAGCAGAT	GCCCATTGAAGGCTGCTACCCTCCTCCTCAGAGCCCTCATCTCTTCTGTCTGACCCAGGCTCACTCATTCTGCCCCCCGCTGGCTCTAGGACCCACTCTACCTGCTCCACTCTACTCAGAGTACTCACCTCCTTGTTGCTGGGGGTACCCTGTAGTTTCTGCTCCAGCCCAGCCAGCTTGCTGTCAATGTGCCCGTTGATCTCAGCTCGCAGCCCCTCGGACCCCCGCCCAGTGCTGAGTTGCACATTCTTTGCCCGGAGTAGCTTCTGCAAGAGCAGAT	-	novel	NA	P-0012334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	178	503	0	ENST00000301067.7:c.13379_13531-14del		p.X4460_splice	ENST00000301067	NM_003482.3	4460		39/54	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.483227177019792	NA		503	424	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425321	49425440	+	inframe_deletion	In_Frame_Del	DEL	TGGCTTCTGGGTTTCTGCTAGGTTGTCTGGGGGATCCCAAGGTCCCAGACCCTTGCTAAACAAGGTATCTGCAAGCTGGGCAGCAGCAGGTGAGACCCTCCCAGGAGGCGGCTCCAAGGT	TGGCTTCTGGGTTTCTGCTAGGTTGTCTGGGGGATCCCAAGGTCCCAGACCCTTGCTAAACAAGGTATCTGCAAGCTGGGCAGCAGCAGGTGAGACCCTCCCAGGAGGCGGCTCCAAGGT	-	novel	NA	P-0012334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	113	693	1	ENST00000301067.7:c.13048_13167del	p.Thr4350_Pro4389del	p.T4350_P4389del	ENST00000301067	NM_003482.3	4350	ACCTTGGAGCCGCCTCCTGGGAGGGTCTCACCTGCTGCTGCCCAGCTTGCAGATACCTTGTTTAGCAAGGGTCTGGGACCTTGGGATCCCCCAGACAACCTAGCAGAAACCCAGAAGCCA/-	39/54	0.25902574579268	4	FACETS	0.903	0.82	0.989	0.602	0.547	0.66	INDETERMINATE	2	TRUE	1	0.483227177019792	4		694	384	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673751	37673751	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	116	571	1	ENST00000447079.4:c.2906del	p.Phe969SerfsTer4	p.F969Sfs*4	ENST00000447079	NM_015083.1	969	Ttc/tc	10/14	0.37501972414312	4	FACETS	0.807	0.733	0.885			1	CLONAL	2	TRUE	NA	0.483227177019792	4		572	441	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035202	30035202	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0012379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	481	595	2	ENST00000338641.4:c.363+1G>T		p.X121_splice	ENST00000338641	NM_000268.3	121			0.878519317304742	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.878519317304742	1		597	583	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0012409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	221	455	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.941	0.877	1	0.941	0.877	1	CLONAL	1	TRUE	1	0.552061884311678	2		455	851	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577571	7577572	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGTAGT	novel	NA	P-0012409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	179	506	0	ENST00000269305.4:c.704_709dup	p.Asn235_Tyr236dup	p.N235_Y236dup	ENST00000269305	NM_001126112.2	235	atg/aACTACAtg	7/11	0.498475814332221	1	FACETS	0.683	0.632	0.736	0.683	0.632	0.736	SUBCLONAL	1	TRUE	0	0.552061884311678	1		506	687	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0012415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	879	582	2	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.66475352309079	3	FACETS	0.98	0.953	1	0.98	0.953	1	CLONAL	2	TRUE	1	0.724918528315888	3		584	1685	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0012415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	192	185	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	1	2	FACETS	0.996	0.928	1	0.996	0.928	1	CLONAL	1	TRUE	1	0.724918528315888	2		185	532	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0012415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	299	378	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	NA	2	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.724918528315888	2		378	802	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0012415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	379	454	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.724918528315888	2		454	997	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805834	46805834	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199799743	NA	P-0012415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1471	556	723	1	ENST00000290295.7:c.122C>T	p.Thr41Met	p.T41M	ENST00000290295	NM_006361.5	41	aCg/aTg	1/2	0.66475352309079	3	FACETS	1	0.977	1	0.516	0.493	0.538	CLONAL	1	TRUE	1	0.724918528315888	3		724	2027	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793211	139793212	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs748531430	NA	P-0012415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	392	670	2	ENST00000247668.2:c.26dup	p.Gly10TrpfsTer70	p.G10Wfs*70	ENST00000247668	NM_021138.3	7	acc/aCcc	2/11	1	2	FACETS	0.833	0.791	0.875	0.833	0.791	0.875	CLONAL	1	TRUE	1	0.724918528315888	2		672	1299	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119759	70119778	+	frameshift_variant	Frame_Shift_Del	DEL	GAGAGGGGCGCCCCTTGCCA	GAGAGGGGCGCCCCTTGCCA	-	novel	NA	P-0012415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	726	536	1	ENST00000245479.2:c.764_783del	p.Glu255GlyfsTer34	p.E255Gfs*34	ENST00000245479	NM_000346.3	254	cGAGAGGGGCGCCCCTTGCCA/c	3/3	0.66475352309079	3	FACETS	0.971	0.941	1	0.971	0.941	1	CLONAL	2	TRUE	1	0.724918528315888	3		537	1405	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692839	89692839	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	90	115	0	ENST00000371953.3:c.323T>A	p.Leu108His	p.L108H	ENST00000371953	NM_000314.4	108	cTt/cAt	5/9	0.691282924258015	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.724918528315888	1		115	139	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049691	16049691	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	470	589	1	ENST00000268712.3:c.1081C>T	p.Arg361Ter	p.R361*	ENST00000268712	NM_006311.3	361	Cga/Tga	10/46	0.724918528315888	1	FACETS	0.987	0.95	1	0.987	0.95	1	CLONAL	1	TRUE	0	0.724918528315888	1		590	838	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845360	42845360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775494034	NA	P-0012415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	199	392	1	ENST00000398585.3:c.902C>T	p.Pro301Leu	p.P301L	ENST00000398585	NM_001135099.1	301	cCg/cTg	9/14	1	2	FACETS	0.679	0.63	0.729	0.679	0.63	0.729	SUBCLONAL	1	TRUE	1	0.724918528315888	2		393	809	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575183	48575184	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0012415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	289	362	0	ENST00000342988.3:c.378_379del	p.Val128GlufsTer14	p.V128Efs*14	ENST00000342988	NM_005359.5	126	gTC/g	3/12	0.724918528315888	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.724918528315888	1		362	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0012572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	144	758	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.427172667099407	1	FACETS	0.937	0.86	1	0.937	0.86	1	CLONAL	1	TRUE	0	0.458374647114456	1		759	517	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623672	43623687	+	frameshift_variant	Frame_Shift_Del	DEL	GCTTTCACCCTCAGCG	GCTTTCACCCTCAGCG	-	novel	NA	P-0012572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	54	877	1	ENST00000355710.3:c.3302_3317del	p.Leu1101GlnfsTer3	p.L1101Qfs*3	ENST00000355710	NM_020975.4	1100	atGCTTTCACCCTCAGCG/at	20/20	1	2	FACETS	0.457	0.39	0.529	0.457	0.39	0.529	SUBCLONAL	1	TRUE	1	0.458374647114456	2		878	516	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88428958	88428958	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1439739326	NA	P-0012572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	71	709	0	ENST00000360948.2:c.2142T>A	p.Asn714Lys	p.N714K	ENST00000360948	NM_001012338.2	714	aaT/aaA	17/19	0.372245530127313	3	FACETS	1	0.959	1	0.404	0.356	0.456	CLONAL	1	TRUE	0	0.458374647114456	3		709	314	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699394	47699394	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	62	801	0	ENST00000347630.2:c.114C>G	p.Ile38Met	p.I38M	ENST00000347630	NM_001007230.1	38	atC/atG	4/11	0.330750313950293	3	FACETS	0.602	0.521	0.691			1	SUBCLONAL	1	TRUE	NA	0.458374647114456	3		801	552	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012705-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	102	188	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.93	0.843	1	0.93	0.843	1	CLONAL	1	TRUE	1	0.716564351198031	2		188	306	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0012705-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	112	246	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.854	0.776	0.935	0.854	0.776	0.935	CLONAL	1	TRUE	1	0.716564351198031	2		247	366	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs11554290	NA	P-0012705-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	85	507	0	ENST00000369535.4:c.182A>C	p.Gln61Pro	p.Q61P	ENST00000369535	NM_002524.4	61	cAa/cCa	3/7	0.716564351198031	1	FACETS	0.3	0.265	0.336	0.3	0.265	0.336	SUBCLONAL	1	TRUE	0	0.716564351198031	1		507	508	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141426	11141426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012705-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	30	581	3	ENST00000358026.2:c.3403C>T	p.Arg1135Trp	p.R1135W	ENST00000358026	NM_001128849.1	1135	Cgg/Tgg	25/36	1	2	FACETS	0.141	0.113	0.173	0.141	0.113	0.173	SUBCLONAL	1	TRUE	1	0.716564351198031	2		584	594	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645683	12645683	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs397516829	NA	P-0012705-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	104	202	1	ENST00000251849.4:c.786T>A	p.Asn262Lys	p.N262K	ENST00000251849	NM_002880.3	262	aaT/aaA	7/17	1	2	FACETS	0.998	0.906	1	0.998	0.906	1	CLONAL	1	TRUE	1	0.716564351198031	2		203	291	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923394	36923394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759191217	NA	P-0012705-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	63	542	1	ENST00000358127.4:c.868G>A	p.Gly290Arg	p.G290R	ENST00000358127	NM_001280556.1	290	Ggg/Agg	7/10	1	2	FACETS	0.285	0.246	0.327	0.285	0.246	0.327	SUBCLONAL	1	TRUE	1	0.716564351198031	2		543	618	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037402	12037402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765031845	NA	P-0012705-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	323	584	0	ENST00000396373.4:c.1033G>A	p.Val345Ile	p.V345I	ENST00000396373	NM_001987.4	345	Gtc/Atc	6/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.716564351198031	2		584	841	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430361	78430361	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012705-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	288	413	0	ENST00000370768.2:c.807del	p.Ser270GlnfsTer3	p.S270Qfs*3	ENST00000370768	NM_003902.3	269	ggG/gg	10/20	0.716564351198031	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.716564351198031	1		413	487	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165774	118165774	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1371399685	NA	P-0012705-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	13	311	0	ENST00000369448.3:c.284T>C	p.Phe95Ser	p.F95S	ENST00000369448	NM_017709.3	95	tTc/tCc	2/2	0.716564351198031	1	FACETS	0.09	0.063	0.121	0.09	0.063	0.121	SUBCLONAL	1	TRUE	0	0.716564351198031	1		311	260	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14021973	14021974	+	inframe_insertion	In_Frame_Ins	INS	-	-	TACAGACTG	novel	NA	P-0012705-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	124	417	0	ENST00000311895.7:c.674_682dup	p.Thr227_Ala228insValGlnThr	p.T227_A228insVQT	ENST00000311895	NM_005236.2	225	ata/aTACAGACTGta	4/11	1	2	FACETS	0.428	0.387	0.472	0.428	0.387	0.472	SUBCLONAL	1	TRUE	1	0.716564351198031	2		417	808	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899176	78899176	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1390339463	NA	P-0012705-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	27	308	0	ENST00000306801.3:c.2815G>A	p.Asp939Asn	p.D939N	ENST00000306801	NM_020761.2	939	Gac/Aac	24/34	1	2	FACETS	0.173	0.137	0.214	0.173	0.137	0.214	SUBCLONAL	1	TRUE	1	0.716564351198031	2		308	435	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791730	42791731	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0012705-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	48	450	1	ENST00000575354.2:c.616_617delinsTT	p.Ala206Phe	p.A206F	ENST00000575354	NM_015125.3	206	GCc/TTc	5/20	0.716564351198031	1	FACETS	0.274	0.232	0.319	0.274	0.232	0.319	SUBCLONAL	1	TRUE	0	0.716564351198031	1		451	314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0012777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	166	520	2	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.299672481668482	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.347023731963795	1		522	694	SUCCESS
H3C13	653604	MSKCC	GRCh37	1	149785223	149785223	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs781806302	NA	P-0012777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	11	28	0	ENST00000331491.1:c.14A>G	p.Lys5Arg	p.K5R	ENST00000331491	NM_001123375.2	5	aAg/aGg	1/1	0.347023731963795	3	FACETS	0.767	0.535	1	0.383	0.267	0.524	CLONAL	1	TRUE	1	0.347023731963795	3		28	97	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026431	48026431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	94	563	0	ENST00000234420.5:c.1309C>T	p.His437Tyr	p.H437Y	ENST00000234420	NM_000179.2	437	Cac/Tac	4/10	0.21579830030452	3	FACETS	0.588	0.521	0.659	0.196	0.173	0.22	SUBCLONAL	1	TRUE	0	0.347023731963795	3		563	1082	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426687	212426687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	130	623	0	ENST00000342788.4:c.2428G>A	p.Glu810Lys	p.E810K	ENST00000342788	NM_005235.2	810	Gag/Aag	20/28	1	2	FACETS	0.863	0.783	0.948	0.863	0.783	0.948	CLONAL	1	TRUE	1	0.347023731963795	2		623	868	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282638	1282638	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	65	532	0	ENST00000310581.5:c.1675T>A	p.Ser559Thr	p.S559T	ENST00000310581	NM_198253.2	559	Tct/Act	3/16	0.307899856201708	5	FACETS	0.453	0.391	0.521	0.151	0.13	0.174	SUBCLONAL	1	TRUE	2	0.347023731963795	5		532	1258	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436797	110436797	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	63	427	0	ENST00000375856.3:c.1604G>T	p.Gly535Val	p.G535V	ENST00000375856	NM_003749.2	535	gGc/gTc	1/2	0.334516334856721	2	FACETS	0.473	0.408	0.543	0.236	0.204	0.272	SUBCLONAL	1	TRUE	0	0.347023731963795	2		427	768	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618629	37618629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1296	148	439	0	ENST00000447079.4:c.305C>T	p.Ser102Leu	p.S102L	ENST00000447079	NM_015083.1	102	tCa/tTa	1/14	0.347023731963795	5	FACETS	0.898	0.818	0.983			1	CLONAL	1	TRUE	NA	0.347023731963795	5		439	1444	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618851	37618851	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1365	137	493	0	ENST00000447079.4:c.527C>T	p.Ser176Leu	p.S176L	ENST00000447079	NM_015083.1	176	tCa/tTa	1/14	0.347023731963795	5	FACETS	0.799	0.724	0.879			1	SUBCLONAL	1	TRUE	NA	0.347023731963795	5		493	1502	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222776	5222776	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	31	244	0	ENST00000357368.4:c.3027A>T	p.Gln1009His	p.Q1009H	ENST00000357368	NM_002850.3	1009	caA/caT	18/38	0.347023731963795	2	FACETS	0.451	0.365	0.549	0.226	0.182	0.275	SUBCLONAL	1	TRUE	0	0.347023731963795	2		244	396	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796328	42796328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	123	691	0	ENST00000575354.2:c.2977C>T	p.Pro993Ser	p.P993S	ENST00000575354	NM_015125.3	993	Cct/Tct	12/20	0.347023731963795	2	FACETS	0.636	0.573	0.702	0.318	0.286	0.351	SUBCLONAL	1	TRUE	0	0.347023731963795	2		691	1115	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797808	42797808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	70	479	0	ENST00000575354.2:c.3860G>A	p.Gly1287Glu	p.G1287E	ENST00000575354	NM_015125.3	1287	gGg/gAg	16/20	0.347023731963795	2	FACETS	0.558	0.486	0.636	0.279	0.243	0.318	SUBCLONAL	1	TRUE	0	0.347023731963795	2		479	723	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164781	36164781	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	55	509	0	ENST00000300305.3:c.1094G>A	p.Gly365Asp	p.G365D	ENST00000300305		365	gGc/gAc	8/8	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.347023731963795	NA		509	795	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937115	76937115	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	99	380	1	ENST00000373344.5:c.3633T>A	p.Asp1211Glu	p.D1211E	ENST00000373344	NM_000489.3	1211	gaT/gaA	9/35	0.300464810553158	2	FACETS	0.72	0.643	0.803			1	SUBCLONAL	1	TRUE	NA	0.347023731963795	2		381	792	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0012892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	450	777	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	0.945923947420739	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.945923947420739	1		777	478	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0012892-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	299	777	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	0.833996577410639	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.833996577410639	1		777	377	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0012892-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	446	777	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	0.796415833922447	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.796415833922447	1		777	658	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0012920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	188	758	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.308395430901646	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.308395430901646	2		758	533	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477837	140477851	+	inframe_deletion	In_Frame_Del	DEL	TAGGTGCTGTCACAT	TAGGTGCTGTCACAT	-	novel	NA	P-0012920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	159	716	0	ENST00000288602.6:c.1457_1471del	p.Asn486_Pro490del	p.N486_P490del	ENST00000288602	NM_004333.4	486	aATGTGACAGCACCTAca/aca	12/18	0.308395430901646	5	FACETS	0.994	0.912	1	0.662	0.608	0.719	CLONAL	2	TRUE	2	0.308395430901646	5		716	759	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178669	32178669	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766521222	NA	P-0012920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	69	676	0	ENST00000375023.3:c.2725G>A	p.Asp909Asn	p.D909N	ENST00000375023	NM_004557.3	909	Gac/Aac	18/30	0.308395430901646	3	FACETS	0.936	0.816	1	0.468	0.408	0.533	CLONAL	1	TRUE	1	0.308395430901646	3		676	552	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427465	427465	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769625142	NA	P-0012920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	97	682	3	ENST00000399788.2:c.2704C>T	p.Arg902Trp	p.R902W	ENST00000399788	NM_001042603.1	902	Cgg/Tgg	19/28	0.308395430901646	4	FACETS	1	0.953	1	0.562	0.501	0.627	CLONAL	1	TRUE	2	0.308395430901646	4		685	732	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858477	57858477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760192848	NA	P-0012920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	136	942	0	ENST00000228682.2:c.215G>A	p.Arg72Gln	p.R72Q	ENST00000228682	NM_005269.2	72	cGg/cAg	4/12	0.308395430901646	4	FACETS	1	0.977	1	0.616	0.559	0.675	CLONAL	1	TRUE	2	0.308395430901646	4		942	937	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271828	15271828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371738874	NA	P-0012920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	43	349	1	ENST00000263388.2:c.6611C>T	p.Pro2204Leu	p.P2204L	ENST00000263388	NM_000435.2	2204	cCg/cTg	33/33	0.308395430901646	4	FACETS	0.901	0.755	1	0.45	0.377	0.531	CLONAL	1	TRUE	2	0.308395430901646	4		350	405	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245152	53245152	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	47	744	2	ENST00000375401.3:c.788A>G	p.Glu263Gly	p.E263G	ENST00000375401	NM_004187.3	263	gAg/gGg	7/26	0.308395430901646	1	FACETS	0.496	0.418	0.581	0.496	0.418	0.581	SUBCLONAL	1	TRUE	0	0.308395430901646	1		746	520	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	17	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.192870659540732	3	FACETS	1	0.802	1	0.541	0.406	0.701	CLONAL	1	TRUE	1	0.19	3		436	181	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0013021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	21	611	1	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	1	2	FACETS	0.822	0.634	1	0.822	0.634	1	CLONAL	1	TRUE	1	0.19	2		612	269	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445944	49445944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	37	745	0	ENST00000301067.7:c.1522G>A	p.Glu508Lys	p.E508K	ENST00000301067	NM_003482.3	508	Gaa/Aaa	10/54	0.192870659540732	3	FACETS	1	0.887	1	0.551	0.455	0.658	CLONAL	1	TRUE	1	0.19	3		745	387	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259087	36259150	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCGGCCTCGCCGGCCTCCGCCTGTCCTCCCACCACCCTCTCCGGGCCAGTACCTTGAAAGCGA	CCCGGCCTCGCCGGCCTCCGCCTGTCCTCCCACCACCCTCTCCGGGCCAGTACCTTGAAAGCGA	-	novel	NA	P-0013021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	15	377	0	ENST00000300305.3:c.341_351+53del		p.X114_splice	ENST00000300305		114		3/8	1	2	FACETS	0.81	0.594	1	0.81	0.594	1	CLONAL	1	TRUE	1	0.19	2		377	195	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971031	21971037	+	protein_altering_variant	In_Frame_Del	DEL	GGCATCG	GGCATCG	C	novel	NA	P-0013021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	28	384	0	ENST00000304494.5:c.321_327delinsG	p.Asp108_Ala109del	p.D108_A109del	ENST00000304494	NM_000077.4	107	cgCGATGCC/cgG	2/3	1	2	FACETS	0.784	0.632	0.954	1	0.942	1	CLONAL	2	TRUE	1	0.19	2		384	188	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0013037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	175	346	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.289927110005482	3	FACETS	0.841	0.783	0.899	0.841	0.783	0.899	INDETERMINATE	2	TRUE	1	0.631076478119365	3		346	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0013037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	185	534	0	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	0.289927110005482	3	FACETS	0.773	0.72	0.827	0.773	0.72	0.827	INDETERMINATE	2	TRUE	1	0.631076478119365	3		534	499	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0013037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	240	727	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	0.339184344307754	4	FACETS	0.792	0.742	0.843			1	INDETERMINATE	2	TRUE	NA	0.631076478119365	4		727	783	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143033806	143033806	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	234	448	0	ENST00000262992.4:c.2165C>G	p.Pro722Arg	p.P722R	ENST00000262992	NM_001101669.1	722	cCa/cGa	20/24	0.194956648733551	4	FACETS	0.968	0.909	1	0.968	0.909	1	INDETERMINATE	2	TRUE	2	0.631076478119365	4		448	625	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521300	187521300	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	313	866	1	ENST00000441802.2:c.11855T>C	p.Phe3952Ser	p.F3952S	ENST00000441802	NM_005245.3	3952	tTt/tCt	22/27	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.631076478119365	2		867	936	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89791122	89791122	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	35	72	1	ENST00000336032.3:c.509C>T	p.Ala170Val	p.A170V	ENST00000336032	NM_006813.2	170	gCg/gTg	1/2	0.631076478119365	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.631076478119365	1		73	67	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120247	70120247	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886043831	NA	P-0013037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	499	919	1	ENST00000245479.2:c.1249C>T	p.Gln417Ter	p.Q417*	ENST00000245479	NM_000346.3	417	Cag/Tag	3/3	0.339184344307754	4	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.631076478119365	4		920	1197	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798975	42798975	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0013037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	263	722	0	ENST00000575354.2:c.4460-1G>T		p.X1487_splice	ENST00000575354	NM_015125.3	1487			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.631076478119365	NA		722	758	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630235	100630235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868924845	NA	P-0013037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	49	414	0	ENST00000308731.7:c.38G>A	p.Arg13Gln	p.R13Q	ENST00000308731	NM_000061.2	13	cGa/cAa	2/19	1	1	FACETS	0.262	0.222	0.305	0.262	0.222	0.305	SUBCLONAL	1	TRUE	0	0.631076478119365	1		414	406	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163277	32163277	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	340	983	1	ENST00000375023.3:c.5949del	p.Asp1984ThrfsTer12	p.D1984Tfs*12	ENST00000375023	NM_004557.3	1983	ctT/ct	30/30	0.194956648733551	4	FACETS	0.753	0.712	0.794	0.753	0.712	0.794	INDETERMINATE	2	TRUE	2	0.631076478119365	4		984	1167	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0013037-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	27	346	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.293	0.232	0.364	0.293	0.232	0.364	SUBCLONAL	1	TRUE	1	0.19	2		346	969	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429345	78429345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013089-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	191	755	0	ENST00000370768.2:c.1097G>A	p.Gly366Asp	p.G366D	ENST00000370768	NM_003902.3	366	gGc/gAc	13/20	1	2	FACETS	0.784	0.724	0.845	0.784	0.724	0.845	SUBCLONAL	1	TRUE	1	0.487921846578935	2		755	999	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808555	1808555	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0013089-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	96	736	0	ENST00000260795.2:c.2169-1G>A		p.X723_splice	ENST00000260795		723			1	2	FACETS	0.924	0.828	1	0.924	0.828	1	CLONAL	1	TRUE	1	0.487921846578935	2		736	426	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874907	151874907	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs752687658	NA	P-0013089-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	153	583	0	ENST00000262189.6:c.7631A>G	p.Gln2544Arg	p.Q2544R	ENST00000262189	NM_170606.2	2544	cAg/cGg	38/59	1	2	FACETS	0.891	0.817	0.968	0.891	0.817	0.968	CLONAL	1	TRUE	1	0.487921846578935	2		583	704	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52705248	52705248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746459436	NA	P-0013089-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	180	859	0	ENST00000322088.6:c.130G>A	p.Val44Ile	p.V44I	ENST00000322088	NM_014225.5	44	Gtt/Att	2/15	1	2	FACETS	0.939	0.867	1	0.939	0.867	1	CLONAL	1	TRUE	1	0.487921846578935	2		859	786	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508023	106508025	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	ATA	ATA	-	novel	NA	P-0013089-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	60	272	0	ENST00000359195.3:c.18_20del	p.Tyr6_Lys7delinsTer	p.Y6_K7delins*	ENST00000359195	NM_002649.2	6	tATAaa/taa	2/11	1	2	FACETS	0.683	0.591	0.782	0.683	0.591	0.782	SUBCLONAL	1	TRUE	1	0.487921846578935	2		272	360	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188296	10188297	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs869025653	NA	P-0013089-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	182	863	2	ENST00000256474.2:c.444dup	p.Ala149CysfsTer25	p.A149Cfs*25	ENST00000256474	NM_000551.3	147	att/aTtt	2/3	0.487921846578935	1	FACETS	0.831	0.769	0.894	0.831	0.769	0.894	CLONAL	1	TRUE	0	0.487921846578935	1		865	679	SUCCESS
APC	324	MSKCC	GRCh37	5	112175696	112175696	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060503288	NA	P-0013287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	33	498	1	ENST00000257430.4:c.4405C>T	p.Gln1469Ter	p.Q1469*	ENST00000257430	NM_000038.5	1469	Caa/Taa	16/16	1	2	FACETS	0.471	0.382	0.57	0.471	0.382	0.57	SUBCLONAL	1	TRUE	1	0.2509267835107	2		499	559	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781005	135781006	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs118203603	NA	P-0013287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	164	1244	0	ENST00000298552.3:c.1959dup	p.Gln654ThrfsTer34	p.Q654Tfs*34	ENST00000298552	NM_001162426.1	653	-/A	15/23	0.241172104781538	1	FACETS	0.985	0.902	1	0.985	0.902	1	CLONAL	1	TRUE	0	0.2509267835107	1		1244	1161	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0013303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	112	533	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.24715788034321	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.346267044073745	1		533	488	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518208	8518208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775600962	NA	P-0013303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	72	525	1	ENST00000356435.5:c.1183G>A	p.Ala395Thr	p.A395T	ENST00000356435		395	Gct/Act	10/35	0.346267044073745	1	FACETS	0.819	0.718	0.926	0.819	0.718	0.926	CLONAL	1	TRUE	0	0.346267044073745	1		526	420	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39744043	39744043	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	79	359	0	ENST00000361337.2:c.1671C>A	p.Asn557Lys	p.N557K	ENST00000361337	NM_003286.2	557	aaC/aaA	16/21	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.346267044073745	2		359	414	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345240	73345240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013336-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	264	557	0	ENST00000377767.4:c.1649C>T	p.Ser550Phe	p.S550F	ENST00000377767	NM_014953.3	550	tCc/tTc	12/21	0.0731929275342504	3	FACETS	0.89	0.836	0.944			1	INDETERMINATE	3	FALSE	NA	0.263720932291925	3		557	849	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061148	38061212	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTGGCGGCGCAAG	CGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTGGCGGCGCAAG	-	novel	NA	P-0013336-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	51	106	0	ENST00000250448.2:c.777_841del	p.Tyr259Ter	p.Y259*	ENST00000250448	NM_004496.3	259	taCTTGCGCCGCCAGAAGCGCTTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGga/taga	2/2	0.263720932291925	15	FACETS	0.896	0.766	1			1	CLONAL	4	FALSE	NA	0.263720932291925	15		106	293	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	204	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.352182223460838	3	FACETS	0.941	0.876	1	0.941	0.876	1	CLONAL	2	TRUE	1	0.352182223460838	3		436	724	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99160392	99160392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377398401	NA	P-0013346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	169	705	1	ENST00000074304.5:c.871C>T	p.Arg291Trp	p.R291W	ENST00000074304	NM_001134224.1	291	Cgg/Tgg	11/26	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.352182223460838	2		706	715	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742054	145742054	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	102	539	0	ENST00000428558.2:c.449C>A	p.Ser150Tyr	p.S150Y	ENST00000428558	NM_004260.3	150	tCc/tAc	5/22	0.352182223460838	3	FACETS	1	0.918	1	0.515	0.46	0.572	CLONAL	1	TRUE	1	0.352182223460838	3		539	662	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664443	29664443	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	74	698	0	ENST00000356175.3:c.6422A>G	p.Tyr2141Cys	p.Y2141C	ENST00000356175	NM_000267.3	2141	tAc/tGc	42/57	0.352182223460838	2	FACETS	0.544	0.476	0.618	0.272	0.238	0.309	SUBCLONAL	1	TRUE	0	0.352182223460838	2		698	772	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	187	578	0	ENST00000269305.4:c.406del	p.Gln136AsnfsTer34	p.Q136Nfs*34	ENST00000269305	NM_001126112.2	136	Caa/aa	5/11	NA	2	FACETS	0.94	0.874	1			1	INDETERMINATE	2	TRUE	NA	0.352182223460838	2		578	565	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099879	27099881	+	frameshift_variant	Frame_Shift_Del	DEL	ACG	ACG	C	novel	NA	P-0013346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	109	548	0	ENST00000324856.7:c.3758_3760delinsC	p.Asn1253ThrfsTer5	p.N1253Tfs*5	ENST00000324856	NM_006015.4	1253	aACGgc/aCgc	15/20	1	2	FACETS	0.997	0.897	1	0.997	0.897	1	CLONAL	1	TRUE	1	0.352182223460838	2		548	621	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0013371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	269	536	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.248111657202301	3	FACETS	0.781	0.732	0.831	0.781	0.732	0.831	SUBCLONAL	2	TRUE	1	0.348984681891534	3		536	1159	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952006	178952006	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	30	639	0	ENST00000263967.3:c.3061T>C	p.Tyr1021His	p.Y1021H	ENST00000263967	NM_006218.2	1021	Tac/Cac	21/21	1	2	FACETS	0.679	0.548	0.827	0.679	0.548	0.827	SUBCLONAL	1	TRUE	1	0.274578726169165	2		639	322	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508728	148508728	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs267601395	NA	P-0013562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	11	721	0	ENST00000320356.2:c.1936T>C	p.Tyr646His	p.Y646H	ENST00000320356	NM_004456.4	646	Tac/Cac	16/20	0.226678019993459	3	FACETS	0.248	0.171	0.346	0.124	0.085	0.173	SUBCLONAL	1	TRUE	1	0.274578726169165	3		721	367	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0013562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	34	956	2	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	0.175403727988287	0	FACETS	0.515	0.421	0.62			1	SUBCLONAL	1	TRUE	0	0.274578726169165	0		958	349	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226171	53226171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	29	607	0	ENST00000375401.3:c.2678C>T	p.Ser893Leu	p.S893L	ENST00000375401	NM_004187.3	893	tCa/tTa	19/26	0.24443828924143	0	FACETS	0.681	0.55	0.828			1	SUBCLONAL	1	TRUE	0	0.274578726169165	0		607	225	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966955	25966955	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs773343381	NA	P-0013695-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	260	637	0	ENST00000435504.4:c.2251C>G	p.Gln751Glu	p.Q751E	ENST00000435504		751	Cag/Gag	13/13	0.260620084419591	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.320581505288184	4		637	979	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032069	26032069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013695-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1277	155	1099	1	ENST00000244661.2:c.220G>A	p.Glu74Lys	p.E74K	ENST00000244661	NM_003537.3	74	Gaa/Aaa	1/1	0.0923380841486372	4	FACETS	0.892	0.814	0.974			1	INDETERMINATE	1	TRUE	NA	0.320581505288184	4		1100	1432	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032185	26032185	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013695-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	107	748	1	ENST00000244661.2:c.104G>T	p.Gly35Val	p.G35V	ENST00000244661	NM_003537.3	35	gGc/gTc	1/1	0.0923380841486372	4	FACETS	0.849	0.76	0.944			1	INDETERMINATE	1	TRUE	NA	0.320581505288184	4		749	1038	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502208	157502208	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013695-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	159	427	0	ENST00000346085.5:c.3241G>C	p.Glu1081Gln	p.E1081Q	ENST00000346085	NM_020732.3	1081	Gaa/Caa	12/20	0.320581505288184	2	FACETS	0.956	0.882	1	0.956	0.882	1	CLONAL	2	TRUE	0	0.320581505288184	2		427	519	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106379	27106381	+	frameshift_variant	Frame_Shift_Del	DEL	ATG	ATG	T	novel	NA	P-0013695-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	145	403	0	ENST00000324856.7:c.5990_5992delinsT	p.Asn1997IlefsTer3	p.N1997Ifs*3	ENST00000324856	NM_006015.4	1997	aATGac/aTac	20/20	0.303083138248506	4	FACETS	1	0.977	1	0.784	0.72	0.85	CLONAL	2	TRUE	1	0.320581505288184	4		403	508	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201787	102201787	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	GT	novel	NA	P-0013695-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	114	829	0	ENST00000263464.3:c.1139delinsGT	p.Pro380ArgfsTer4	p.P380Rfs*4	ENST00000263464	NM_001165.4	380	cCt/cGTt	6/9	0.320581505288184	2	FACETS	0.988	0.89	1	0.494	0.445	0.546	CLONAL	1	TRUE	0	0.320581505288184	2		829	720	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0013754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	86	618	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.677	0.598	0.762	0.677	0.598	0.762	SUBCLONAL	1	TRUE	1	0.29	2		618	876	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	96	548	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.871	0.776	0.973	0.871	0.776	0.973	CLONAL	1	TRUE	1	0.29	2		549	760	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0013754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	38	401	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.429	0.354	0.513	0.429	0.354	0.513	SUBCLONAL	1	TRUE	1	0.29	2		402	611	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918921	76918921	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1317	74	1166	3	ENST00000373344.5:c.4070del	p.Lys1357ArgfsTer18	p.K1357Rfs*18	ENST00000373344	NM_000489.3	1357	aAg/ag	12/35	1	2	FACETS	0.367	0.32	0.418	0.367	0.32	0.418	SUBCLONAL	1	TRUE	1	0.29	2		1169	1391	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057727	27057727	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1217	183	1021	0	ENST00000324856.7:c.1435C>T	p.Gln479Ter	p.Q479*	ENST00000324856	NM_006015.4	479	Cag/Tag	3/20	1	2	FACETS	0.901	0.83	0.977	0.901	0.83	0.977	CLONAL	1	TRUE	1	0.29	2		1021	1400	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750639	128750639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775522201	NA	P-0013754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	114	670	1	ENST00000377970.2:c.176C>T	p.Ala59Val	p.A59V	ENST00000377970	NM_002467.4	59	gCg/gTg	2/3	1	2	FACETS	0.916	0.824	1	0.916	0.824	1	CLONAL	1	TRUE	1	0.29	2		671	858	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647028	23647028	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1555461597	NA	P-0013754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	49	723	0	ENST00000261584.4:c.839del	p.Asn280ThrfsTer8	p.N280Tfs*8	ENST00000261584	NM_024675.3	280	aAc/ac	4/13	1	2	FACETS	0.351	0.296	0.411	0.351	0.296	0.411	SUBCLONAL	1	TRUE	1	0.29	2		723	964	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158465	26158467	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs766586530	NA	P-0013754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	62	527	0	ENST00000289316.2:c.73_75del	p.Lys25del	p.K25del	ENST00000289316	NM_138720.2	23	cAGAag/cag	1/2	1	2	FACETS	0.66	0.57	0.758	0.66	0.57	0.758	SUBCLONAL	1	TRUE	1	0.29	2		527	648	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997825	149997826	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0013754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	53	648	0	ENST00000253339.5:c.2641dup	p.Asp881GlyfsTer40	p.D881Gfs*40	ENST00000253339		881	gat/gGat	5/7	1	2	FACETS	0.455	0.386	0.53	0.455	0.386	0.53	SUBCLONAL	1	TRUE	1	0.29	2		648	804	SUCCESS
ATM	472	MSKCC	GRCh37	11	108126993	108126994	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	84	804	0	ENST00000278616.4:c.2178dup	p.Gly727TrpfsTer11	p.G727Wfs*11	ENST00000278616	NM_000051.3	726	ctt/cTtt	14/63	1	2	FACETS	0.559	0.492	0.631	0.559	0.492	0.631	SUBCLONAL	1	TRUE	1	0.29	2		804	1036	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421042	49421042	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757465818	NA	P-0013754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	115	616	0	ENST00000301067.7:c.14707G>A	p.Val4903Met	p.V4903M	ENST00000301067	NM_003482.3	4903	Gtg/Atg	48/54	1	2	FACETS	0.934	0.841	1	0.934	0.841	1	CLONAL	1	TRUE	1	0.29	2		616	849	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991949	72991949	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs753977275	NA	P-0013754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	139	940	0	ENST00000268489.5:c.2096del	p.Gly699AlafsTer125	p.G699Afs*125	ENST00000268489	NM_006885.3	699	gGc/gc	2/10	1	2	FACETS	0.85	0.772	0.932	0.85	0.772	0.932	CLONAL	1	TRUE	1	0.29	2		940	1128	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075224	16075224	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	71	600	1	ENST00000268712.3:c.328C>T	p.Arg110Cys	p.R110C	ENST00000268712	NM_006311.3	110	Cgt/Tgt	4/46	1	2	FACETS	0.568	0.495	0.648	0.568	0.495	0.648	SUBCLONAL	1	TRUE	1	0.29	2		601	862	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298020	15298020	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	97	607	0	ENST00000263388.2:c.1736G>A	p.Cys579Tyr	p.C579Y	ENST00000263388	NM_000435.2	579	tGc/tAc	11/33	1	2	FACETS	0.776	0.691	0.867	0.776	0.691	0.867	SUBCLONAL	1	TRUE	1	0.29	2		607	862	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928220	178928220	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	74	463	0	ENST00000263967.3:c.1406A>G	p.Glu469Gly	p.E469G	ENST00000263967	NM_006218.2	469	gAa/gGa	9/21	1	2	FACETS	0.916	0.803	1	0.916	0.803	1	CLONAL	1	TRUE	1	0.29	2		463	557	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056464	26056465	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	26	324	0	ENST00000343677.2:c.192dup	p.Ala65SerfsTer8	p.A65Sfs*8	ENST00000343677	NM_005319.3	64	-/A	1/1	1	2	FACETS	0.463	0.367	0.574	0.463	0.367	0.574	SUBCLONAL	1	TRUE	1	0.29	2		324	387	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673776	30673776	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	51	583	4	ENST00000376406.3:c.3184G>T	p.Ala1062Ser	p.A1062S	ENST00000376406	NM_014641.2	1062	Gca/Tca	10/15	1	2	FACETS	0.396	0.335	0.463	0.396	0.335	0.463	SUBCLONAL	1	TRUE	1	0.29	2		587	889	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180951	32180951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs978741176	NA	P-0013754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	99	559	0	ENST00000375023.3:c.2399C>T	p.Pro800Leu	p.P800L	ENST00000375023	NM_004557.3	800	cCg/cTg	15/30	1	2	FACETS	0.802	0.715	0.895	0.802	0.715	0.895	CLONAL	1	TRUE	1	0.29	2		559	851	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528099	157528099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	46	407	0	ENST00000346085.5:c.5824G>A	p.Ala1942Thr	p.A1942T	ENST00000346085	NM_020732.3	1942	Gct/Act	20/20	1	2	FACETS	0.581	0.489	0.683	0.581	0.489	0.683	SUBCLONAL	1	TRUE	1	0.29	2		407	546	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	103	570	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.152821012231501	3	FACETS	0.881	0.789	0.979	0.881	0.789	0.979	CLONAL	2	TRUE	1	0.18	3		570	708	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0013824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	68	758	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.18	2		758	748	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974727	21974744	+	inframe_deletion	In_Frame_Del	DEL	CCTCCAGCAGCGCCCGCA	CCTCCAGCAGCGCCCGCA	-	novel	NA	P-0013824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	34	441	0	ENST00000304494.5:c.83_100del	p.Val28_Glu33del	p.V28_E33del	ENST00000304494	NM_000077.4	28	gTGCGGGCGCTGCTGGAGGcg/gcg	1/3	0.159667108609311	1	FACETS	0.673	0.549	0.812	0.673	0.549	0.812	SUBCLONAL	1	TRUE	0	0.18	1		441	511	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120457964	120457964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	40	567	0	ENST00000256646.2:c.7381G>A	p.Glu2461Lys	p.E2461K	ENST00000256646	NM_024408.3	2461	Gag/Aag	34/34	1	2	FACETS	0.78	0.647	0.928	0.78	0.647	0.928	CLONAL	1	TRUE	1	0.18	2		567	570	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434502	49434502	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	280	436	0	ENST00000301067.7:c.7051G>T	p.Glu2351Ter	p.E2351*	ENST00000301067	NM_003482.3	2351	Gag/Tag	31/54	1	2	FACETS	0.982	0.928	1	0.982	0.928	1	CLONAL	1	TRUE	1	0.788390661804299	2		436	723	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930723	32930723	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	306	462	0	ENST00000380152.3:c.7596del	p.Ser2533LeufsTer18	p.S2533Lfs*18	ENST00000380152		2532	Ccc/cc	15/27	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.788390661804299	2		462	770	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740820	145740820	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	411	930	0	ENST00000428558.2:c.1280C>T	p.Ala427Val	p.A427V	ENST00000428558	NM_004260.3	427	gCt/gTt	7/22	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.825425102924903	2		930	990	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051618	30051618	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	329	858	1	ENST00000338641.4:c.552G>A	p.Trp184Ter	p.W184*	ENST00000338641	NM_000268.3	184	tgG/tgA	6/16	0.825425102924903	1	FACETS	0.971	0.935	1	0.971	0.935	1	CLONAL	1	TRUE	0	0.825425102924903	1		859	482	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163813	47163825	+	frameshift_variant	Frame_Shift_Del	DEL	GGAATAATCCACA	GGAATAATCCACA	-	novel	NA	P-0013842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	307	853	0	ENST00000409792.3:c.2301_2313del	p.Val768LysfsTer3	p.V768Kfs*3	ENST00000409792	NM_014159.6	767	acTGTGGATTATTCC/ac	3/21	0.825425102924903	1	FACETS	0.95	0.912	0.986	0.95	0.912	0.986	CLONAL	1	TRUE	0	0.825425102924903	1		853	460	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909601	76909601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	363	710	0	ENST00000373344.5:c.4304C>T	p.Ser1435Phe	p.S1435F	ENST00000373344	NM_000489.3	1435	tCc/tTc	14/35	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.825425102924903	1		710	444	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	55	294	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.829	0.712	0.954	0.829	0.712	0.954	CLONAL	1	TRUE	1	0.389331159188883	2		294	341	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	128	468	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.389331159188883	2		472	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	270	663	1	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	0.389331159188883	2		664	1001	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	427	665	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	1	0.983	1	1	0.998	1	CLONAL	3	TRUE	1	0.389331159188883	2		665	706	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820970	36820970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	243	870	0	ENST00000373129.3:c.407G>A	p.Arg136His	p.R136H	ENST00000373129	NM_032017.1	136	cGc/cAc	6/12	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.389331159188883	2		870	886	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	75	600	1	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	1	2	FACETS	0.657	0.577	0.744	0.657	0.577	0.744	SUBCLONAL	1	TRUE	1	0.389331159188883	2		601	586	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	132	319	6	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	0.966	0.9	1	1	0.993	1	CLONAL	3	TRUE	1	0.389331159188883	2		325	234	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487554	38487554	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	277	973	1	ENST00000254066.5:c.89del	p.Pro30LeufsTer12	p.P30Lfs*12	ENST00000254066	NM_000964.3	28	ttC/tt	2/9	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.389331159188883	2		974	990	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	186	621	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.389331159188883	2		621	655	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604533	43604533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs546866208	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	207	846	2	ENST00000355710.3:c.1118C>T	p.Ala373Val	p.A373V	ENST00000355710	NM_020975.4	373	gCg/gTg	6/20	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.389331159188883	2		848	748	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	108	574	4	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.389331159188883	2		578	548	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477184	67477184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1320208623	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	41	455	1	ENST00000327367.4:c.991G>A	p.Val331Ile	p.V331I	ENST00000327367	NM_005902.3	331	Gtc/Atc	7/9	1	2	FACETS	0.377	0.313	0.448	0.377	0.313	0.448	SUBCLONAL	1	TRUE	1	0.389331159188883	2		456	559	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	38	722	1	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.282	0.232	0.338	0.282	0.232	0.338	SUBCLONAL	1	TRUE	1	0.389331159188883	2		723	693	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	19	164	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	1	2	FACETS	0.458	0.349	0.586	0.458	0.349	0.586	SUBCLONAL	1	TRUE	1	0.389331159188883	2		164	213	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586102	29586102	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370852681	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	98	511	0	ENST00000356175.3:c.4322G>A	p.Arg1441Gln	p.R1441Q	ENST00000356175	NM_000267.3	1441	cGg/cAg	32/57	1	2	FACETS	0.819	0.731	0.911	0.819	0.731	0.911	CLONAL	1	TRUE	1	0.389331159188883	2		511	615	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051011	180051011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146167161	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	47	815	3	ENST00000261937.6:c.1472C>T	p.Ala491Val	p.A491V	ENST00000261937	NM_182925.4	491	gCg/gTg	11/30	1	2	FACETS	0.328	0.275	0.385	0.328	0.275	0.385	SUBCLONAL	1	TRUE	1	0.389331159188883	2		818	737	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405652	70405652	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	118	623	1	ENST00000373644.4:c.3171del	p.Lys1057AsnfsTer25	p.K1057Nfs*25	ENST00000373644	NM_030625.2	1056	Aaa/aa	4/12	1	2	FACETS	0.955	0.863	1	0.955	0.863	1	CLONAL	1	TRUE	1	0.389331159188883	2		624	635	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519896	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	228	695	0	ENST00000281708.4:c.1514G>T	p.Arg505Leu	p.R505L	ENST00000281708	NM_033632.3	505	cGc/cTc	10/12	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.389331159188883	2		695	804	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606273	93606273	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	140	803	0	ENST00000375746.1:c.98del	p.Gly33AlafsTer2	p.G33Afs*2	ENST00000375746	NM_001174167.1	31	caG/ca	2/14	1	2	FACETS	0.936	0.854	1	0.936	0.854	1	CLONAL	1	TRUE	1	0.389331159188883	2		803	768	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202738	133202738	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs759795841	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	228	691	0	ENST00000320574.5:c.6496G>T	p.Asp2166Tyr	p.D2166Y	ENST00000320574	NM_006231.2	2166	Gac/Tac	46/49	1	2	FACETS	0.77	0.719	0.821	1	0.993	1	SUBCLONAL	2	TRUE	1	0.389331159188883	2		691	761	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248325	59248325	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	30	169	0	ENST00000371222.2:c.418del	p.Ala140GlnfsTer8	p.A140Qfs*8	ENST00000371222	NM_002228.3	140	Gca/ca	1/1	1	2	FACETS	0.94	0.766	1	0.94	0.766	1	CLONAL	1	TRUE	1	0.389331159188883	2		169	164	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470551	25470551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	244	720	2	ENST00000264709.3:c.923G>A	p.Gly308Asp	p.G308D	ENST00000264709	NM_175629.2	308	gGc/gAc	8/23	1	2	FACETS	0.757	0.709	0.806	1	0.993	1	SUBCLONAL	2	TRUE	1	0.389331159188883	2		722	828	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288785	33288785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765273333	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	76	385	1	ENST00000374542.5:c.767G>A	p.Arg256His	p.R256H	ENST00000374542	NM_001141970.1	256	cGc/cAc	3/8	1	2	FACETS	0.832	0.732	0.939	0.832	0.732	0.939	CLONAL	1	TRUE	1	0.389331159188883	2		386	469	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925318	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	236	1059	0	ENST00000543371.1:c.1402_1403del	p.Lys468ValfsTer8	p.K468Vfs*8	ENST00000543371	NM_001198531.1	465	agAAaa/agaa	14/14	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.389331159188883	2		1059	1097	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256321	16256321	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	142	513	0	ENST00000375759.3:c.3591del	p.Asp1198MetfsTer2	p.D1198Mfs*2	ENST00000375759	NM_015001.2	1196	Aaa/aa	11/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.389331159188883	2		513	567	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094322	193094322	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	230	551	0	ENST00000367435.3:c.212A>G	p.His71Arg	p.H71R	ENST00000367435	NM_024529.4	71	cAt/cGt	2/17	1	2	FACETS	0.867	0.813	0.923	1	0.994	1	CLONAL	2	TRUE	1	0.389331159188883	2		551	681	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404897	70404897	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1328525221	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	151	539	1	ENST00000373644.4:c.2411T>C	p.Met804Thr	p.M804T	ENST00000373644	NM_030625.2	804	aTg/aCg	4/12	1	2	FACETS	0.77	0.708	0.833	1	0.989	1	SUBCLONAL	2	TRUE	1	0.389331159188883	2		540	504	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683175	88683175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1418504897	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	104	281	0	ENST00000372037.3:c.1385C>T	p.Pro462Leu	p.P462L	ENST00000372037	NM_004329.2	462	cCg/cTg	12/13	1	2	FACETS	0.77	0.696	0.846	1	0.984	1	SUBCLONAL	2	TRUE	1	0.389331159188883	2		281	347	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138902	64138902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1192515568	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	50	595	1	ENST00000334205.4:c.2269G>A	p.Ala757Thr	p.A757T	ENST00000334205	NM_003942.2	757	Gcc/Acc	17/17	1	2	FACETS	0.48	0.407	0.56	0.48	0.407	0.56	SUBCLONAL	1	TRUE	1	0.389331159188883	2		596	535	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999601	100999601	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	321	1300	0	ENST00000325455.5:c.201G>T	p.Gln67His	p.Q67H	ENST00000325455	NM_001202474.3	67	caG/caT	1/8	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.389331159188883	2		1300	1115	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432461	49432461	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs945205127	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	163	1003	0	ENST00000301067.7:c.8678C>T	p.Thr2893Ile	p.T2893I	ENST00000301067	NM_003482.3	2893	aCt/aTt	34/54	1	2	FACETS	0.906	0.832	0.984	0.906	0.832	0.984	CLONAL	1	TRUE	1	0.389331159188883	2		1003	924	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482642	56482642	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758130617	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	201	676	1	ENST00000267101.3:c.1099G>A	p.Gly367Ser	p.G367S	ENST00000267101	NM_001982.3	367	Ggc/Agc	9/28	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.389331159188883	2		677	748	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134600	41134600	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	361	1406	0	ENST00000379561.5:c.1028T>C	p.Val343Ala	p.V343A	ENST00000379561	NM_002015.3	343	gTg/gCg	2/3	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.389331159188883	2		1406	1333	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95579427	95579429	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ACA	ACA	-	novel	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	126	413	0	ENST00000393063.1:c.2040_2040+2del		p.X680_splice	ENST00000393063	NM_030621.3	680		13/28	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.389331159188883	2		413	443	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857428	9857428	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	188	764	0	ENST00000330684.3:c.3973del	p.Tyr1325ThrfsTer72	p.Y1325Tfs*72	ENST00000330684	NM_001134407.1	1325	Tac/ac	13/13	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.389331159188883	2		764	696	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646215	23646215	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	282	916	0	ENST00000261584.4:c.1652A>G	p.Tyr551Cys	p.Y551C	ENST00000261584	NM_024675.3	551	tAt/tGt	4/13	1	2	FACETS	0.762	0.717	0.807	1	0.994	1	SUBCLONAL	2	TRUE	1	0.389331159188883	2		916	951	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89839751	89839751	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	53	952	2	ENST00000389301.3:c.1942G>A	p.Glu648Lys	p.E648K	ENST00000389301	NM_000135.2	648	Gag/Aag	22/43	1	2	FACETS	0.293	0.249	0.342	0.293	0.249	0.342	SUBCLONAL	1	TRUE	1	0.389331159188883	2		954	930	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974830	15974830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	212	724	0	ENST00000268712.3:c.4045C>T	p.Arg1349Cys	p.R1349C	ENST00000268712	NM_006311.3	1349	Cgt/Tgt	30/46	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.389331159188883	2		724	747	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37865618	37865618	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	302	932	1	ENST00000269571.5:c.487T>C	p.Tyr163His	p.Y163H	ENST00000269571		163	Tac/Cac	4/27	1	2	FACETS	0.826	0.78	0.873	1	0.995	1	CLONAL	2	TRUE	1	0.389331159188883	2		933	939	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512370	38512370	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567767560	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	109	600	2	ENST00000254066.5:c.1286del	p.Gly429ValfsTer214	p.G429Vfs*214	ENST00000254066	NM_000964.3	427	ccG/cc	9/9	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.389331159188883	2		602	523	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732956	74732956	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	209	648	2	ENST00000359995.5:c.287del	p.Pro96ArgfsTer136	p.P96Rfs*136	ENST00000359995	NM_001195427.1	96	cCg/cg	1/3	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.389331159188883	2		650	751	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985776	60985776	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1184260603	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	143	415	3	ENST00000333681.4:c.124del	p.Ala42ProfsTer54	p.A42Pfs*54	ENST00000333681		42	Gcc/cc	2/3	1	2	FACETS	0.833	0.766	0.902	1	0.99	1	CLONAL	2	TRUE	1	0.389331159188883	2		418	441	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281155	15281155	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	191	866	0	ENST00000263388.2:c.5101G>A	p.Ala1701Thr	p.A1701T	ENST00000263388	NM_000435.2	1701	Gcg/Acg	27/33	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.389331159188883	2		866	839	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355128	15355128	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	113	634	0	ENST00000263377.2:c.2495A>C	p.Gln832Pro	p.Q832P	ENST00000263377	NM_058243.2	832	cAg/cCg	13/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.389331159188883	2		634	549	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792016	42792016	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1199661448	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	213	808	0	ENST00000575354.2:c.820C>T	p.Arg274Ter	p.R274*	ENST00000575354	NM_015125.3	274	Cga/Tga	6/20	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.389331159188883	2		808	745	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732667	204732667	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	36	557	0	ENST00000302823.3:c.2T>C	p.Met1?	p.M1?	ENST00000302823	NM_005214.4	1	aTg/aCg	1/4	1	2	FACETS	0.312	0.256	0.375	0.312	0.256	0.375	SUBCLONAL	1	TRUE	1	0.389331159188883	2		557	593	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251713	212251713	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	54	630	0	ENST00000342788.4:c.3346G>T	p.Ala1116Ser	p.A1116S	ENST00000342788	NM_005235.2	1116	Gca/Tca	27/28	1	2	FACETS	0.453	0.387	0.526	0.453	0.387	0.526	SUBCLONAL	1	TRUE	1	0.389331159188883	2		630	612	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523692	41523692	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	268	883	0	ENST00000263253.7:c.1108C>T	p.Arg370Cys	p.R370C	ENST00000263253	NM_001429.3	370	Cgc/Tgc	4/31	1	2	FACETS	0.767	0.721	0.815	1	0.994	1	SUBCLONAL	2	TRUE	1	0.389331159188883	2		883	897	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564766	41564766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303184977	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	64	864	2	ENST00000263253.7:c.4067G>A	p.Arg1356Gln	p.R1356Q	ENST00000263253	NM_001429.3	1356	cGa/cAa	25/31	1	2	FACETS	0.351	0.302	0.403	0.351	0.302	0.403	SUBCLONAL	1	TRUE	1	0.389331159188883	2		866	938	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259635	89259635	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	26	282	0	ENST00000336596.2:c.779A>G	p.Asn260Ser	p.N260S	ENST00000336596	NM_005233.5	260	aAt/aGt	3/17	1	2	FACETS	0.586	0.466	0.722	0.586	0.466	0.722	SUBCLONAL	1	TRUE	1	0.389331159188883	2		282	228	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403527	138403527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140578043	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	267	911	1	ENST00000289153.2:c.2255G>A	p.Arg752Gln	p.R752Q	ENST00000289153	NM_006219.2	752	cGg/cAg	15/22	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.389331159188883	2		912	967	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582134	189582135	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	209	684	0	ENST00000264731.3:c.699dup	p.Ala234SerfsTer2	p.A234Sfs*2	ENST00000264731	NM_003722.4	231	-/A	5/14	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.389331159188883	2		684	775	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561861	55561861	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201872586	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	126	676	0	ENST00000288135.5:c.251C>T	p.Thr84Met	p.T84M	ENST00000288135	NM_000222.2	84	aCg/aTg	2/21	1	2	FACETS	0.946	0.858	1	0.946	0.858	1	CLONAL	1	TRUE	1	0.389331159188883	2		676	684	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156217	106156218	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	34	570	0	ENST00000380013.4:c.1120_1121del	p.Asn374Ter	p.N374*	ENST00000380013	NM_001127208.2	373	cAA/c	3/11	1	2	FACETS	0.293	0.239	0.355	0.293	0.239	0.355	SUBCLONAL	1	TRUE	1	0.389331159188883	2		570	596	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157059	106157060	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	225	963	0	ENST00000380013.4:c.1965dup	p.Pro656ThrfsTer25	p.P656Tfs*25	ENST00000380013	NM_001127208.2	654	caa/cAaa	3/11	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.389331159188883	2		963	1150	SUCCESS
APC	324	MSKCC	GRCh37	5	112176909	112176909	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	44	599	0	ENST00000257430.4:c.5618A>G	p.Asp1873Gly	p.D1873G	ENST00000257430	NM_000038.5	1873	gAc/gGc	16/16	1	2	FACETS	0.332	0.277	0.392	0.332	0.277	0.392	SUBCLONAL	1	TRUE	1	0.389331159188883	2		599	681	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524541	176524541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759861753	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	250	1009	3	ENST00000292408.4:c.2273G>A	p.Arg758His	p.R758H	ENST00000292408	NM_213647.1	758	cGc/cAc	18/18	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.389331159188883	2		1012	947	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015676	112015676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	315	1098	2	ENST00000368678.4:c.1166G>A	p.Arg389Gln	p.R389Q	ENST00000368678		389	cGa/cAa	11/13	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.389331159188883	2		1100	1107	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878928	151878928	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	100	613	0	ENST00000262189.6:c.6017A>G	p.His2006Arg	p.H2006R	ENST00000262189	NM_170606.2	2006	cAc/cGc	36/59	1	2	FACETS	0.975	0.874	1	0.975	0.874	1	CLONAL	1	TRUE	1	0.389331159188883	2		613	527	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211575	98211575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	35	582	0	ENST00000331920.6:c.3580C>T	p.Pro1194Ser	p.P1194S	ENST00000331920	NM_000264.3	1194	Ccc/Tcc	22/24	1	2	FACETS	0.29	0.237	0.35	0.29	0.237	0.35	SUBCLONAL	1	TRUE	1	0.389331159188883	2		582	620	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98241381	98241381	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	151	638	0	ENST00000331920.6:c.1116G>A	p.Met372Ile	p.M372I	ENST00000331920	NM_000264.3	372	atG/atA	8/24	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.389331159188883	2		638	680	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900204	101900204	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	303	808	0	ENST00000374994.4:c.638A>G	p.Lys213Arg	p.K213R	ENST00000374994	NM_004612.2	213	aAa/aGa	4/9	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.389331159188883	2		808	1100	SUCCESS
AR	367	MSKCC	GRCh37	X	66943552	66943552	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137852578	NA	P-0014009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4344	192	387	0	ENST00000374690.3:c.2632A>G	p.Thr878Ala	p.T878A	ENST00000374690	NM_000044.3	878	Act/Gct	8/8	0.632494821297232	10	FACETS	0.472	0.434	0.513			1	SUBCLONAL	1	TRUE	NA	0.632494821297232	10		387	4536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0014009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	312	597	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.632494821297232	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.632494821297232	1		597	623	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843694	151843717	+	inframe_deletion	In_Frame_Del	DEL	ATGCGTGCCACTGCAGAGACGGTC	ATGCGTGCCACTGCAGAGACGGTC	-	novel	NA	P-0014009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	233	438	0	ENST00000262189.6:c.13998_14021del	p.Thr4667_Ile4674del	p.T4667_I4674del	ENST00000262189	NM_170606.2	4666	ctGACCGTCTCTGCAGTGGCACGCATa/cta	53/59	0.316877251176164	3	FACETS	0.753	0.706	0.8	0.753	0.706	0.8	INDETERMINATE	2	TRUE	1	0.632494821297232	3		438	644	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900164	101900164	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	267	514	0	ENST00000374994.4:c.598A>G	p.Thr200Ala	p.T200A	ENST00000374994	NM_004612.2	200	Aca/Gca	4/9	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.632494821297232	2		514	832	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798764	135798764	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749979841	NA	P-0014009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	81	393	1	ENST00000298552.3:c.479G>A	p.Arg160His	p.R160H	ENST00000298552	NM_001162426.1	160	cGt/cAt	6/23	1	2	FACETS	0.414	0.365	0.466	0.414	0.365	0.466	SUBCLONAL	1	TRUE	1	0.632494821297232	2		394	619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0014015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	86	626	17	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	NA	2	FACETS	0.733	0.652	0.82			1	INDETERMINATE	1	TRUE	NA	0.522310821903186	2		643	449	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104359276	104359276	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	237	622	0	ENST00000369902.3:c.998del	p.Asn333MetfsTer28	p.N333Mfs*28	ENST00000369902	NM_016169.3	333	Aat/at	8/12	NA	2	FACETS	1	0.958	1			1	INDETERMINATE	2	TRUE	NA	0.522310821903186	2		622	448	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427974	49427974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	82	727	0	ENST00000301067.7:c.10616G>A	p.Arg3539Gln	p.R3539Q	ENST00000301067	NM_003482.3	3539	cGg/cAg	38/54	NA	2	FACETS	0.599	0.53	0.674			1	INDETERMINATE	1	TRUE	NA	0.522310821903186	2		727	524	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481882	56481882	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	308	874	0	ENST00000267101.3:c.810C>G	p.Phe270Leu	p.F270L	ENST00000267101	NM_001982.3	270	ttC/ttG	7/28	NA	2	FACETS	0.888	0.844	0.932			1	INDETERMINATE	2	TRUE	NA	0.522310821903186	2		874	664	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041800	14041800	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	164	637	0	ENST00000311895.7:c.2347G>T	p.Asp783Tyr	p.D783Y	ENST00000311895	NM_005236.2	783	Gac/Tac	11/11	NA	2	FACETS	0.77	0.715	0.825			1	INDETERMINATE	2	TRUE	NA	0.522310821903186	2		637	408	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125800	47125800	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	129	392	0	ENST00000409792.3:c.5470A>G	p.Ile1824Val	p.I1824V	ENST00000409792	NM_014159.6	1824	Att/Gtt	12/21	0.533308374080358	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.522310821903186	1		392	272	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799968	72799968	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	120	368	0	ENST00000325599.8:c.1201C>T	p.Leu401Phe	p.L401F	ENST00000325599	NM_018130.2	401	Ctt/Ttt	11/11	0.533308374080358	1	FACETS	0.812	0.754	0.869	1	0.99	1	CLONAL	2	TRUE	0	0.522310821903186	1		368	209	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272715	142272715	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	186	893	0	ENST00000350721.4:c.2484C>G	p.Ile828Met	p.I828M	ENST00000350721	NM_001184.3	828	atC/atG	11/47	0.533308374080358	3	FACETS	1	0.986	1	0.638	0.591	0.686	CLONAL	1	TRUE	1	0.522310821903186	3		893	704	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6038854	6038854	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	105	753	0	ENST00000265849.7:c.590G>C	p.Gly197Ala	p.G197A	ENST00000265849	NM_000535.5	197	gGc/gCc	6/15	0.388129256057184	5	FACETS	1	0.912	1			1	CLONAL	1	TRUE	NA	0.522310821903186	5		753	704	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763954	76763954	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	126	534	0	ENST00000373344.5:c.7354C>G	p.Gln2452Glu	p.Q2452E	ENST00000373344	NM_000489.3	2452	Cag/Gag	35/35	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.522310821903186	1		534	247	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	379	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.561477899390141	3	FACETS	1	0.981	1			1	CLONAL	2	TRUE	NA	0.663272584584928	3		436	729	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809299	243809299	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	249	640	0	ENST00000263826.5:c.325C>A	p.Leu109Met	p.L109M	ENST00000263826	NM_005465.4	109	Ctg/Atg	4/13	0.660707078448761	4	FACETS	0.956	0.893	1	0.319	0.297	0.341	CLONAL	1	TRUE	1	0.663272584584928	4		640	1306	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662366	67662366	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	304	644	0	ENST00000264010.4:c.1612C>G	p.Leu538Val	p.L538V	ENST00000264010	NM_006565.3	538	Ctc/Gtc	9/12	1	2	FACETS	0.95	0.897	1	0.95	0.897	1	CLONAL	1	TRUE	1	0.663272584584928	2		644	965	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732950	30732950	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1553631968	NA	P-0014144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	179	423	0	ENST00000295754.5:c.1563G>A	p.Trp521Ter	p.W521*	ENST00000295754	NM_003242.5	521	tgG/tgA	7/7	0.663272584584928	1	FACETS	0.911	0.851	0.971	0.911	0.851	0.971	CLONAL	1	TRUE	0	0.663272584584928	1		423	396	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682409	52682409	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	287	660	0	ENST00000394830.3:c.764T>C	p.Leu255Pro	p.L255P	ENST00000394830	NM_018313.4	255	cTc/cCc	8/30	0.663272584584928	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.663272584584928	1		660	496	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592079	55592079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200518498	NA	P-0014144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	273	668	1	ENST00000288135.5:c.1403C>T	p.Pro468Leu	p.P468L	ENST00000288135	NM_000222.2	468	cCg/cTg	9/21	1	2	FACETS	0.977	0.919	1	0.977	0.919	1	CLONAL	1	TRUE	1	0.663272584584928	2		669	843	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528478	157528478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	171	416	0	ENST00000346085.5:c.6203C>T	p.Pro2068Leu	p.P2068L	ENST00000346085	NM_020732.3	2068	cCa/cTa	20/20	0.663272584584928	1	FACETS	0.834	0.777	0.893	0.834	0.777	0.893	CLONAL	1	TRUE	0	0.663272584584928	1		416	413	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0014147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	115	874	1	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	1	2	FACETS	0.848	0.762	0.94	0.848	0.762	0.94	CLONAL	1	TRUE	1	0.23510525375991	2		875	1153	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191488	10191488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs5030818	NA	P-0014147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	92	482	0	ENST00000256474.2:c.481C>T	p.Arg161Ter	p.R161*	ENST00000256474	NM_000551.3	161	Cga/Tga	3/3	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.23510525375991	2		482	644	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509603	29509603	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	39	596	1	ENST00000356175.3:c.808C>T	p.Gln270Ter	p.Q270*	ENST00000356175	NM_000267.3	270	Caa/Taa	8/57	1	2	FACETS	0.645	0.534	0.769	0.645	0.534	0.769	SUBCLONAL	1	TRUE	1	0.23510525375991	2		597	514	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610656	52610657	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0014147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	75	587	0	ENST00000394830.3:c.3516dup	p.His1173SerfsTer8	p.H1173Sfs*8	ENST00000394830	NM_018313.4	1172	-/T	23/30	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.23510525375991	2		587	564	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565803	55565803	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	38	701	0	ENST00000288135.5:c.627A>T	p.Lys209Asn	p.K209N	ENST00000288135	NM_000222.2	209	aaA/aaT	4/21	1	2	FACETS	0.465	0.383	0.557	0.465	0.383	0.557	SUBCLONAL	1	TRUE	1	0.23510525375991	2		701	695	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246393	53246393	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	159	508	0	ENST00000375401.3:c.589del	p.Leu197TyrfsTer37	p.L197Yfs*37	ENST00000375401	NM_004187.3	197	Cta/ta	5/26	1	1	FACETS	0.754	0.691	0.818	1	0.988	1	SUBCLONAL	2	TRUE	0	0.23510525375991	1		508	792	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161720	47161730	+	frameshift_variant	Frame_Shift_Del	DEL	ATTTTCCCTTG	ATTTTCCCTTG	T	novel	NA	P-0014147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	111	683	0	ENST00000409792.3:c.4396_4406delinsA	p.Gln1466SerfsTer14	p.Q1466Sfs*14	ENST00000409792	NM_014159.6	1466	CAAGGGAAAATg/Ag	3/21	1	2	FACETS	0.97	0.871	1	0.97	0.871	1	CLONAL	1	TRUE	1	0.23510525375991	2		683	973	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955064	93955064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151105732	NA	P-0014193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	133	333	1	ENST00000369303.4:c.2834C>T	p.Thr945Met	p.T945M	ENST00000369303	NM_004440.3	945	aCg/aTg	16/17	0.416677016440668	2	FACETS	1	0.988	1	0.731	0.672	0.79	CLONAL	1	TRUE	0	0.52466282290134	2		334	347	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954968	2954968	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	90	822	0	ENST00000396946.4:c.2742C>A	p.Asn914Lys	p.N914K	ENST00000396946	NM_032415.4	914	aaC/aaA	21/25	0.124230375164337	4	FACETS	0.428	0.379	0.482	0.214	0.189	0.241	INDETERMINATE	1	TRUE	2	0.52466282290134	4		822	1221	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	112	570	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.845	0.763	0.93	0.845	0.763	0.93	CLONAL	1	TRUE	1	0.51	2		570	520	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0014388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	106	530	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.524	0.47	0.582	0.524	0.47	0.582	SUBCLONAL	1	TRUE	1	0.51	2		534	793	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	156	499	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	0.92	0.845	0.998	0.92	0.845	0.998	CLONAL	1	TRUE	1	0.51	2		499	665	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0014388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	132	468	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.728	0.662	0.797	0.728	0.662	0.797	SUBCLONAL	1	TRUE	1	0.51	2		472	711	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0014388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	137	464	1	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.898	0.82	0.98	0.898	0.82	0.98	CLONAL	1	TRUE	1	0.51	2		465	598	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0014388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	35	499	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.195	0.159	0.236	0.195	0.159	0.236	SUBCLONAL	1	TRUE	1	0.51	2		500	704	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	241	879	1	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.813	0.758	0.869	0.813	0.758	0.869	CLONAL	1	TRUE	1	0.51	2		880	1163	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0014388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	226	536	1	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	0.51	2		537	740	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27213538	27213538	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	137	469	0	ENST00000380036.4:c.2938del	p.Ile980Ter	p.I980*	ENST00000380036	NM_000459.3	978	gcA/gc	18/23	1	2	FACETS	0.851	0.777	0.929	0.851	0.777	0.929	CLONAL	1	TRUE	1	0.51	2		469	631	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0014388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	124	408	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.899	0.817	0.985	0.899	0.817	0.985	CLONAL	1	TRUE	1	0.51	2		408	541	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101268	27101268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	168	506	1	ENST00000324856.7:c.4555del	p.Gln1519ArgfsTer8	p.Q1519Rfs*8	ENST00000324856	NM_006015.4	1517	gCc/gc	18/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.51	2		507	612	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	107	256	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.902	0.814	0.995	0.902	0.814	0.995	CLONAL	1	TRUE	1	0.51	2		257	465	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0014388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	45	247	1	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	1	2	FACETS	0.299	0.25	0.352	0.299	0.25	0.352	SUBCLONAL	1	TRUE	1	0.51	2		248	591	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310208	91310208	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs747341586	NA	P-0014388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	129	304	1	ENST00000355112.3:c.2268del	p.Asp757ThrfsTer4	p.D757Tfs*4	ENST00000355112	NM_000057.2	754	tcA/tc	10/22	1	2	FACETS	0.958	0.873	1	0.958	0.873	1	CLONAL	1	TRUE	1	0.51	2		305	528	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131402	17131402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398124537	NA	P-0014388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	188	450	3	ENST00000285071.4:c.50G>A	p.Arg17His	p.R17H	ENST00000285071	NM_144997.5	17	cGc/cAc	4/14	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.51	2		453	690	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991961	72991961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1262542686	NA	P-0014388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	41	358	0	ENST00000268489.5:c.2084C>T	p.Pro695Leu	p.P695L	ENST00000268489	NM_006885.3	695	cCg/cTg	2/10	1	2	FACETS	0.296	0.246	0.352	0.296	0.246	0.352	SUBCLONAL	1	TRUE	1	0.51	2		358	543	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658404	206658404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781938435	NA	P-0014388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	33	397	1	ENST00000367120.3:c.1498C>T	p.Arg500Trp	p.R500W	ENST00000367120	NM_014002.3	500	Cgg/Tgg	14/22	1	2	FACETS	0.206	0.167	0.25	0.206	0.167	0.25	SUBCLONAL	1	TRUE	1	0.51	2		398	629	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264500	16264500	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1023242507	NA	P-0014388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	159	489	0	ENST00000375759.3:c.10703C>T	p.Thr3568Met	p.T3568M	ENST00000375759	NM_015001.2	3568	aCg/aTg	13/15	1	2	FACETS	0.977	0.899	1	0.977	0.899	1	CLONAL	1	TRUE	1	0.51	2		489	638	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932275	36932275	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	171	594	0	ENST00000361632.4:c.2194del	p.Asp732ThrfsTer70	p.D732Tfs*70	ENST00000361632		732	Gac/ac	16/16	1	2	FACETS	0.958	0.884	1	0.958	0.884	1	CLONAL	1	TRUE	1	0.51	2		594	700	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307276	65307277	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0014388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	87	294	0	ENST00000342505.4:c.2411_2412del	p.Arg804IlefsTer3	p.R804Ifs*3	ENST00000342505	NM_002227.2	804	aGA/a	18/25	1	2	FACETS	0.726	0.645	0.812	0.726	0.645	0.812	SUBCLONAL	1	TRUE	1	0.51	2		294	470	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400932	72400932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	99	335	0	ENST00000357731.5:c.239C>T	p.Ala80Val	p.A80V	ENST00000357731	NM_173808.2	80	gCg/gTg	2/7	1	2	FACETS	0.794	0.712	0.88	0.794	0.712	0.88	SUBCLONAL	1	TRUE	1	0.51	2		335	489	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446321	70446321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	173	429	0	ENST00000373644.4:c.5261C>T	p.Ser1754Phe	p.S1754F	ENST00000373644	NM_030625.2	1754	tCt/tTt	11/12	1	2	FACETS	0.889	0.82	0.961	0.889	0.82	0.961	CLONAL	1	TRUE	1	0.51	2		429	763	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466040	69466040	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	205	600	0	ENST00000227507.2:c.878T>A	p.Val293Glu	p.V293E	ENST00000227507	NM_053056.2	293	gTg/gAg	5/5	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.51	2		600	697	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518529	69518529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	145	335	0	ENST00000294312.3:c.116G>A	p.Gly39Asp	p.G39D	ENST00000294312	NM_005117.2	39	gGc/gAc	1/3	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.51	2		335	516	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437380	121437380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	103	598	0	ENST00000257555.6:c.1718C>T	p.Ala573Val	p.A573V	ENST00000257555		573	gCc/gTc	9/10	1	2	FACETS	0.49	0.438	0.545	0.49	0.438	0.545	SUBCLONAL	1	TRUE	1	0.51	2		598	825	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7132271	7132271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	34	426	2	ENST00000302850.5:c.2740C>T	p.Arg914Cys	p.R914C	ENST00000302850	NM_000208.2	914	Cgt/Tgt	14/22	1	2	FACETS	0.204	0.165	0.247	0.204	0.165	0.247	SUBCLONAL	1	TRUE	1	0.51	2		428	655	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250215	39250215	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	172	667	0	ENST00000402219.2:c.1354C>A	p.Arg452Ser	p.R452S	ENST00000402219	NM_005633.3	452	Cgt/Agt	10/23	1	2	FACETS	0.925	0.853	1	0.925	0.853	1	CLONAL	1	TRUE	1	0.51	2		667	729	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248638	212248638	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	107	390	0	ENST00000342788.4:c.3629A>G	p.Asn1210Ser	p.N1210S	ENST00000342788	NM_005235.2	1210	aAc/aGc	28/28	1	2	FACETS	0.908	0.819	1	0.908	0.819	1	CLONAL	1	TRUE	1	0.51	2		390	462	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119562149	119562149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149631706	NA	P-0014388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	33	287	0	ENST00000316626.5:c.1187G>A	p.Arg396Gln	p.R396Q	ENST00000316626		396	cGg/cAg	11/12	1	2	FACETS	0.267	0.217	0.324	0.267	0.217	0.324	SUBCLONAL	1	TRUE	1	0.51	2		287	484	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948313	31948313	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1426360881	NA	P-0014388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	117	440	0	ENST00000375333.2:c.901T>A	p.Tyr301Asn	p.Y301N	ENST00000375333	NM_032454.1	301	Tac/Aac	6/8	1	2	FACETS	0.786	0.711	0.864	0.786	0.711	0.864	SUBCLONAL	1	TRUE	1	0.51	2		440	584	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6031676	6031676	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780063	NA	P-0014388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	128	490	0	ENST00000265849.7:c.916G>A	p.Val306Met	p.V306M	ENST00000265849	NM_000535.5	306	Gtg/Atg	9/15	1	2	FACETS	0.832	0.757	0.912	0.832	0.757	0.912	CLONAL	1	TRUE	1	0.51	2		490	603	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382152	152382154	+	inframe_deletion	In_Frame_Del	DEL	TGG	TGG	-	novel	NA	P-0014435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	205	363	0	ENST00000206249.3:c.1265_1267del	p.Val422del	p.V422del	ENST00000206249	NM_000125.3	421	aTGGtg/atg	6/8	NA	2	FACETS	0.866	0.817	0.914			1	INDETERMINATE	2	TRUE	NA	0.634720735013666	2		363	373	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675423	241675427	+	frameshift_variant	Frame_Shift_Del	DEL	ATTTA	ATTTA	-	rs863223995	NA	P-0014547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	120	261	0	ENST00000366560.3:c.395_399del	p.Leu132Ter	p.L132*	ENST00000366560	NM_000143.3	132	tTAAAT/t	4/10	1	2	FACETS	0.965	0.88	1	0.965	0.88	1	CLONAL	1	TRUE	1	0.650756837678439	2		261	382	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050707	30050708	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0014547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	27	315	0	ENST00000338641.4:c.514dup	p.Arg172LysfsTer31	p.R172Kfs*31	ENST00000338641	NM_000268.3	170	cca/ccAa	5/16	0.650756837678439	1	FACETS	0.174	0.139	0.215	0.174	0.139	0.215	SUBCLONAL	1	TRUE	0	0.650756837678439	1		315	321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0014710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1309	43	758	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.197630475034015	3	FACETS	0.354	0.294	0.42	0.177	0.147	0.21	SUBCLONAL	1	FALSE	1	0.197630475034015	3		759	1352	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0014710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	11	308	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.197630475034015	3	FACETS	0.232	0.159	0.324	0.116	0.079	0.162	SUBCLONAL	1	FALSE	1	0.197630475034015	3		308	527	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0014710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	11	423	1	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	1	0.762	1	1	0.762	1	CLONAL	1	FALSE	1	0.197630475034015	2		424	100	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0014710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1195	55	753	1	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.197630475034015	3	FACETS	0.489	0.417	0.569	0.245	0.208	0.285	SUBCLONAL	1	FALSE	1	0.197630475034015	3		754	1250	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107089	27107099	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGCCCGCGC	GCTGCCCGCGC	CGG	novel	NA	P-0014710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	125	468	2	ENST00000324856.7:c.6700_6710delinsCGG	p.Ala2234ArgfsTer41	p.A2234Rfs*41	ENST00000324856	NM_006015.4	2234	GCTGCCCGCGCg/CGGg	20/20	0.197630475034015	3	FACETS	1	0.982	1	0.69	0.624	0.761	CLONAL	1	FALSE	1	0.197630475034015	3		470	1007	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578177	7578187	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CTCAGGCGGCT	CTCAGGCGGCT	-	novel	NA	P-0014710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	71	867	0	ENST00000269305.4:c.662_672del	p.Glu221GlyfsTer4	p.E221Gfs*4	ENST00000269305	NM_001126112.2	221	gAGCCGCCTGAG/g	6/11	0.197630475034015	3	FACETS	0.633	0.55	0.723	0.316	0.275	0.362	SUBCLONAL	1	FALSE	1	0.197630475034015	3		867	1248	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372699	81372699	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	41	425	0	ENST00000222390.5:c.835C>G	p.Arg279Gly	p.R279G	ENST00000222390	NM_000601.4	279	Cgc/Ggc	7/18	1	2	FACETS	0.733	0.61	0.87	0.733	0.61	0.87	SUBCLONAL	1	FALSE	1	0.197630475034015	2		425	566	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	104	455	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.2	2		455	862	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	17	478	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.214	0.159	0.281	0.214	0.159	0.281	SUBCLONAL	1	TRUE	1	0.2	2		478	794	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1485978447	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	82	440	0	ENST00000324856.7:c.5164C>T	p.Arg1722Ter	p.R1722*	ENST00000324856	NM_006015.4	1722	Cga/Tga	20/20	1	2	FACETS	0.937	0.825	1	0.937	0.825	1	CLONAL	1	TRUE	1	0.2	2		440	875	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1289	103	499	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.74	0.66	0.826	0.74	0.66	0.826	SUBCLONAL	1	TRUE	1	0.2	2		500	1392	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	73	408	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.772	0.674	0.879	0.772	0.674	0.879	SUBCLONAL	1	TRUE	1	0.2	2		408	945	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421039	49421039	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398123721	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	74	477	0	ENST00000301067.7:c.14710C>T	p.Arg4904Ter	p.R4904*	ENST00000301067	NM_003482.3	4904	Cga/Tga	48/54	1	2	FACETS	0.902	0.789	1	0.902	0.789	1	CLONAL	1	TRUE	1	0.2	2		477	820	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	27	483	2	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.276	0.218	0.342	0.276	0.218	0.342	SUBCLONAL	1	TRUE	1	0.2	2		485	980	SUCCESS
AR	367	MSKCC	GRCh37	X	66931247	66931247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868669253	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	79	316	0	ENST00000374690.3:c.1889G>A	p.Arg630Gln	p.R630Q	ENST00000374690	NM_000044.3	630	cGg/cAg	4/8	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.2	2		316	706	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971292	13971292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772105404	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	73	479	1	ENST00000405192.2:c.637C>T	p.Arg213Cys	p.R213C	ENST00000405192	NM_001163147.1	213	Cgc/Tgc	8/12	1	2	FACETS	0.76	0.663	0.865	0.76	0.663	0.865	SUBCLONAL	1	TRUE	1	0.2	2		480	961	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222281	2222281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1268399486	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	126	686	0	ENST00000326181.6:c.565C>T	p.Arg189Trp	p.R189W	ENST00000326181	NM_032271.2	189	Cgg/Tgg	8/21	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.2	2		686	1203	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717629	89717629	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1554825165	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	81	448	0	ENST00000371953.3:c.654C>A	p.Cys218Ter	p.C218*	ENST00000371953	NM_000314.4	218	tgC/tgA	7/9	1	2	FACETS	0.96	0.844	1	0.96	0.844	1	CLONAL	1	TRUE	1	0.2	2		448	844	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131719	2131719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746588726	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1317	120	720	3	ENST00000219476.3:c.3734G>A	p.Arg1245Gln	p.R1245Q	ENST00000219476	NM_000548.3	1245	cGg/cAg	31/42	1	2	FACETS	0.835	0.751	0.924	0.835	0.751	0.924	CLONAL	1	TRUE	1	0.2	2		723	1437	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720711	89720712	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	33	185	1	ENST00000371953.3:c.867dup	p.Val290SerfsTer8	p.V290Sfs*8	ENST00000371953	NM_000314.4	288	gaa/gAaa	8/9	1	2	FACETS	0.789	0.643	0.955	0.789	0.643	0.955	CLONAL	1	TRUE	1	0.2	2		186	418	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877407	28877407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759739030	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	71	439	1	ENST00000282397.4:c.3914G>A	p.Arg1305His	p.R1305H	ENST00000282397	NM_002019.4	1305	cGc/cAc	30/30	1	2	FACETS	0.745	0.648	0.85	0.745	0.648	0.85	SUBCLONAL	1	TRUE	1	0.2	2		440	953	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542861	187542861	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1340793072	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	75	379	0	ENST00000441802.2:c.4879C>T	p.Arg1627Ter	p.R1627*	ENST00000441802	NM_005245.3	1627	Cga/Tga	10/27	1	2	FACETS	0.921	0.806	1	0.921	0.806	1	CLONAL	1	TRUE	1	0.2	2		379	814	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746131	162746131	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121964863	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	47	274	0	ENST00000367921.3:c.2254C>T	p.Arg752Cys	p.R752C	ENST00000367921	NM_006182.2	752	Cgc/Tgc	16/18	1	2	FACETS	0.707	0.595	0.83	0.707	0.595	0.83	SUBCLONAL	1	TRUE	1	0.2	2		274	665	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947119	178947119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199943173	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	109	379	1	ENST00000263967.3:c.2555G>A	p.Arg852Gln	p.R852Q	ENST00000263967	NM_006218.2	852	cGa/cAa	18/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.2	2		380	908	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599359	55599359	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	80	407	0	ENST00000288135.5:c.2484+1G>A		p.X828_splice	ENST00000288135	NM_000222.2	828			1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.2	2		407	772	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247103	53247103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782434611	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	114	565	2	ENST00000375401.3:c.397C>T	p.Arg133Trp	p.R133W	ENST00000375401	NM_004187.3	133	Cgg/Tgg	4/26	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.2	2		567	1125	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518175	8518175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1354824749	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	78	385	1	ENST00000356435.5:c.1216G>A	p.Glu406Lys	p.E406K	ENST00000356435		406	Gaa/Aaa	10/35	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.2	2		386	779	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225657	26225657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202067024	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	80	366	1	ENST00000360408.1:c.275C>T	p.Ala92Val	p.A92V	ENST00000360408	NM_003532.2	92	gCg/gTg	1/1	1	2	FACETS	0.99	0.87	1	0.99	0.87	1	CLONAL	1	TRUE	1	0.2	2		367	808	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099056	27099056	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	108	612	2	ENST00000324856.7:c.3472G>T	p.Gly1158Ter	p.G1158*	ENST00000324856	NM_006015.4	1158	Gga/Tga	13/20	1	2	FACETS	0.874	0.782	0.972	0.874	0.782	0.972	CLONAL	1	TRUE	1	0.2	2		614	1236	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246078900	246078900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1367184255	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	102	501	0	ENST00000388985.4:c.745C>T	p.Arg249Cys	p.R249C	ENST00000388985		249	Cgc/Tgc	8/12	1	2	FACETS	0.958	0.855	1	0.958	0.855	1	CLONAL	1	TRUE	1	0.2	2		501	1065	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742864	17742864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	94	669	0	ENST00000250003.3:c.772C>T	p.Arg258Cys	p.R258C	ENST00000250003	NM_002478.4	258	Cgc/Tgc	3/3	1	2	FACETS	0.964	0.856	1	0.964	0.856	1	CLONAL	1	TRUE	1	0.2	2		669	975	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466022	69466022	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	112	718	1	ENST00000227507.2:c.860C>A	p.Pro287His	p.P287H	ENST00000227507	NM_053056.2	287	cCc/cAc	5/5	1	2	FACETS	0.999	0.896	1	0.999	0.896	1	CLONAL	1	TRUE	1	0.2	2		719	1121	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203579	108203579	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	76	338	0	ENST00000278616.4:c.7879T>C	p.Tyr2627His	p.Y2627H	ENST00000278616	NM_000051.3	2627	Tat/Cat	53/63	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.2	2		338	657	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206648	108206648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881321	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	98	464	0	ENST00000278616.4:c.8228C>T	p.Thr2743Met	p.T2743M	ENST00000278616	NM_000051.3	2743	aCg/aTg	56/63	1	2	FACETS	0.914	0.814	1	0.914	0.814	1	CLONAL	1	TRUE	1	0.2	2		464	1072	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360531	118360531	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs150800017	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	124	535	1	ENST00000534358.1:c.4504C>T	p.Arg1502Ter	p.R1502*	ENST00000534358	NM_005933.3	1502	Cga/Tga	12/36	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.2	2		536	1123	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445862	49445862	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1560	164	1039	1	ENST00000301067.7:c.1604C>A	p.Pro535His	p.P535H	ENST00000301067	NM_003482.3	535	cCt/cAt	10/54	1	2	FACETS	0.951	0.87	1	0.951	0.87	1	CLONAL	1	TRUE	1	0.2	2		1040	1724	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108338	8108338	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1454860641	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	101	749	1	ENST00000585124.1:c.886G>A	p.Val296Met	p.V296M	ENST00000585124	NM_004217.3	296	Gtg/Atg	9/9	1	2	FACETS	0.839	0.747	0.937	0.839	0.747	0.937	CLONAL	1	TRUE	1	0.2	2		750	1204	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110941	8110941	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	97	580	0	ENST00000585124.1:c.154G>A	p.Ala52Thr	p.A52T	ENST00000585124	NM_004217.3	52	Gcc/Acc	4/9	1	2	FACETS	0.886	0.788	0.991	0.886	0.788	0.991	CLONAL	1	TRUE	1	0.2	2		580	1095	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226881	2226881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1303690024	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	56	278	1	ENST00000398665.3:c.4361C>T	p.Ala1454Val	p.A1454V	ENST00000398665	NM_032482.2	1454	gCg/gTg	27/28	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.2	2		279	508	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110171	3110171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1335558363	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	87	490	0	ENST00000078429.4:c.161C>T	p.Thr54Met	p.T54M	ENST00000078429	NM_002067.2	54	aCg/aTg	2/7	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.2	2		490	856	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211899	36211899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1381	132	892	4	ENST00000222270.7:c.1656del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	550	gaC/ga	3/37	1	2	FACETS	0.872	0.789	0.961	0.872	0.789	0.961	CLONAL	1	TRUE	1	0.2	2		896	1513	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794925	42794925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768549918	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	112	544	2	ENST00000575354.2:c.2005G>A	p.Ala669Thr	p.A669T	ENST00000575354	NM_015125.3	669	Gcc/Acc	10/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.2	2		546	982	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858977	45858977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199738290	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	112	593	0	ENST00000391945.4:c.1489C>T	p.Arg497Cys	p.R497C	ENST00000391945	NM_000400.3	497	Cgt/Tgt	16/23	1	2	FACETS	0.937	0.841	1	0.937	0.841	1	CLONAL	1	TRUE	1	0.2	2		593	1195	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497884	25497884	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	88	515	0	ENST00000264709.3:c.565A>G	p.Thr189Ala	p.T189A	ENST00000264709	NM_175629.2	189	Acc/Gcc	6/23	1	2	FACETS	0.865	0.765	0.973	0.865	0.765	0.973	CLONAL	1	TRUE	1	0.2	2		515	1017	SUCCESS
ALK	238	MSKCC	GRCh37	2	29420414	29420414	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	112	493	0	ENST00000389048.3:c.4067G>T	p.Gly1356Val	p.G1356V	ENST00000389048	NM_004304.4	1356	gGg/gTg	27/29	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.2	2		493	1040	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622517	158622517	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs387906588	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	104	528	0	ENST00000263640.3:c.982G>T	p.Gly328Trp	p.G328W	ENST00000263640	NM_001105.4	328	Ggg/Tgg	8/11	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.2	2		528	1018	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400185	41400185	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	78	551	0	ENST00000373198.4:c.574G>A	p.Ala192Thr	p.A192T	ENST00000373198	NM_133170.3	192	Gca/Aca	5/32	1	2	FACETS	0.746	0.653	0.846	0.746	0.653	0.846	SUBCLONAL	1	TRUE	1	0.2	2		551	1046	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573810	41573810	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1397675543	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1331	155	769	0	ENST00000263253.7:c.6095G>A	p.Gly2032Glu	p.G2032E	ENST00000263253	NM_001429.3	2032	gGa/gAa	31/31	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.2	2		769	1486	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478130	138478130	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148660928	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	91	571	0	ENST00000289153.2:c.56C>T	p.Ala19Val	p.A19V	ENST00000289153	NM_006219.2	19	gCg/gTg	1/22	1	2	FACETS	0.92	0.815	1	0.92	0.815	1	CLONAL	1	TRUE	1	0.2	2		571	989	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519941	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	72	364	0	ENST00000263967.3:c.1031T>C	p.Val344Ala	p.V344A	ENST00000263967	NM_006218.2	344	gTg/gCg	5/21	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.2	2		364	719	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502852	186502853	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	78	549	0	ENST00000323963.5:c.311dup	p.Leu105ThrfsTer40	p.L105Tfs*40	ENST00000323963		104	gca/gCca	4/11	1	2	FACETS	0.732	0.642	0.831	0.732	0.642	0.831	SUBCLONAL	1	TRUE	1	0.2	2		549	1065	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629420	187629420	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376472322	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1223	124	665	2	ENST00000441802.2:c.1562C>T	p.Thr521Met	p.T521M	ENST00000441802	NM_005245.3	521	aCg/aTg	2/27	1	2	FACETS	0.921	0.83	1	0.921	0.83	1	CLONAL	1	TRUE	1	0.2	2		667	1347	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1253890	1253890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756628621	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	72	612	3	ENST00000310581.5:c.3352G>A	p.Ala1118Thr	p.A1118T	ENST00000310581	NM_198253.2	1118	Gca/Aca	16/16	1	2	FACETS	0.662	0.576	0.755	0.662	0.576	0.755	SUBCLONAL	1	TRUE	1	0.2	2		615	1088	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410919	31410919	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1314	152	656	0	ENST00000344624.3:c.3601A>G	p.Ile1201Val	p.I1201V	ENST00000344624		1201	Ata/Gta	28/33	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.2	2		656	1466	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803483	32803483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536291251	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1399	132	852	0	ENST00000374899.4:c.676C>T	p.Arg226Trp	p.R226W	ENST00000374899	NM_018833.2	226	Cgg/Tgg	4/12	1	2	FACETS	0.862	0.78	0.95	0.862	0.78	0.95	CLONAL	1	TRUE	1	0.2	2		852	1531	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453127	140453127	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	98	497	0	ENST00000288602.6:c.1808G>T	p.Arg603Leu	p.R603L	ENST00000288602	NM_004333.4	603	cGa/cTa	15/18	1	2	FACETS	0.966	0.86	1	0.966	0.86	1	CLONAL	1	TRUE	1	0.2	2		497	1014	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336306	80336306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	91	391	1	ENST00000286548.4:c.1013G>A	p.Arg338His	p.R338H	ENST00000286548	NM_002072.3	338	cGc/cAc	7/7	0.264277061966881	1	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	0	0.2	1		392	803	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402714	139402714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1274	99	699	1	ENST00000277541.6:c.3295G>A	p.Val1099Met	p.V1099M	ENST00000277541	NM_017617.3	1099	Gtg/Atg	20/34	1	2	FACETS	0.721	0.641	0.807	0.721	0.641	0.807	SUBCLONAL	1	TRUE	1	0.2	2		700	1373	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	140	570	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.907	0.831	0.986	0.907	0.831	0.986	CLONAL	1	TRUE	1	0.601455801800727	2		570	513	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577017	7577017	+	splice_donor_variant	Splice_Site	SNP	A	A	C	rs1131691016	NA	P-0014977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	135	599	0	ENST00000269305.4:c.919+2T>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.601455801800727	1	FACETS	0.94	0.867	1	0.94	0.867	1	CLONAL	1	TRUE	0	0.601455801800727	1		599	334	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603085	48603098	+	frameshift_variant	Frame_Shift_Del	DEL	AGCAGCCGTGGCAG	AGCAGCCGTGGCAG	-	novel	NA	P-0014977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	136	514	0	ENST00000342988.3:c.1386_1399del	p.Ala463LysfsTer26	p.A463Kfs*26	ENST00000342988	NM_005359.5	462	gcAGCAGCCGTGGCAGga/gcga	11/12	0.601455801800727	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.601455801800727	1		514	309	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242470	+	missense_variant	Missense_Mutation	DNP	TT	TT	CC	rs397517096	NA	P-0014996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	122	642	0	ENST00000275493.2:c.2239_2240delinsCC	p.Leu747Pro	p.L747P	ENST00000275493	NM_005228.3	747	TTa/CCa	19/28	0.368847448523943	5	FACETS	1	0.97	1	1	0.97	1	CLONAL	4	FALSE	1	0.368847448523943	5		642	234	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510202	120510202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1296386834	NA	P-0014996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	17	509	2	ENST00000256646.2:c.1307C>T	p.Thr436Met	p.T436M	ENST00000256646	NM_024408.3	436	aCg/aTg	8/34	0.374016391326092	3	FACETS	0.437	0.326	0.568	0.218	0.163	0.284	SUBCLONAL	1	FALSE	1	0.368847448523943	3		511	250	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344813	65344813	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014996-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	21	260	0	ENST00000342505.4:c.224A>G	p.His75Arg	p.H75R	ENST00000342505	NM_002227.2	75	cAc/cGc	4/25	1	2	FACETS	0.976	0.752	1	0.976	0.752	1	CLONAL	1	TRUE	1	0.15	2		260	287	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388055	81388055	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1475727560	NA	P-0014996-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	56	489	0	ENST00000222390.5:c.320G>C	p.Gly107Ala	p.G107A	ENST00000222390	NM_000601.4	107	gGa/gCa	3/18	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.15	2		489	528	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6439807	6439807	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014996-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	23	415	0	ENST00000356142.4:c.333T>A	p.Asn111Lys	p.N111K	ENST00000356142	NM_018890.3	111	aaT/aaA	5/7	1	2	FACETS	0.815	0.635	1	0.815	0.635	1	CLONAL	1	TRUE	1	0.14	2		415	403	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161434	55161434	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014996-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	34	544	1	ENST00000257290.5:c.3265C>A	p.Leu1089Met	p.L1089M	ENST00000257290	NM_006206.4	1089	Ctg/Atg	23/23	1	2	FACETS	0.783	0.639	0.947	0.783	0.639	0.947	CLONAL	1	TRUE	1	0.14	2		545	620	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106429	108106429	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014996-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	14	242	0	ENST00000278616.4:c.364A>C	p.Asn122His	p.N122H	ENST00000278616	NM_000051.3	122	Aat/Cat	5/63	1	2	FACETS	0.741	0.535	0.99	0.741	0.535	0.99	CLONAL	1	TRUE	1	0.14	2		242	270	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934874	NA	P-0015178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	214	935	0	ENST00000269305.4:c.451C>G	p.Pro151Ala	p.P151A	ENST00000269305	NM_001126112.2	151	Ccc/Gcc	5/11	0.649225941065905	1	FACETS	0.888	0.833	0.942	0.888	0.833	0.942	CLONAL	1	TRUE	0	0.649816514215579	1		935	501	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500901	8500901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	264	508	2	ENST00000356435.5:c.1981G>A	p.Glu661Lys	p.E661K	ENST00000356435		661	Gag/Aag	13/35	0.237841007191973	2	FACETS	1	0.986	1	0.575	0.541	0.608	INDETERMINATE	1	TRUE	0	0.649816514215579	2		510	707	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845598	68845618	+	inframe_deletion	In_Frame_Del	DEL	ATGGAGGTCACAGCCACAGAC	ATGGAGGTCACAGCCACAGAC	-	novel	NA	P-0015178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	232	529	0	ENST00000261769.5:c.844_864del	p.Met282_Asp288del	p.M282_D288del	ENST00000261769	NM_004360.3	282	ATGGAGGTCACAGCCACAGAC/-	7/16	0.649816514215579	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.649816514215579	1		529	399	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934874	NA	P-0015178-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	374	935	0	ENST00000269305.4:c.451C>G	p.Pro151Ala	p.P151A	ENST00000269305	NM_001126112.2	151	Ccc/Gcc	5/11	0.624856882127506	1	FACETS	0.891	0.85	0.932	0.891	0.85	0.932	CLONAL	1	TRUE	0	0.671836701767398	1		935	830	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500901	8500901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015178-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	215	508	2	ENST00000356435.5:c.1981G>A	p.Glu661Lys	p.E661K	ENST00000356435		661	Gag/Aag	13/35	1	2	FACETS	0.799	0.744	0.855	0.799	0.744	0.855	SUBCLONAL	1	TRUE	1	0.671836701767398	2		510	801	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845598	68845618	+	inframe_deletion	In_Frame_Del	DEL	ATGGAGGTCACAGCCACAGAC	ATGGAGGTCACAGCCACAGAC	-	novel	NA	P-0015178-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	259	529	0	ENST00000261769.5:c.844_864del	p.Met282_Asp288del	p.M282_D288del	ENST00000261769	NM_004360.3	282	ATGGAGGTCACAGCCACAGAC/-	7/16	0.649746581323265	1	FACETS	0.878	0.83	0.927	0.878	0.83	0.927	CLONAL	1	TRUE	0	0.671836701767398	1		529	583	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	140	694	7	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	0.487342910004756	2		701	502	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	146	607	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.994	0.911	1	0.994	0.911	1	CLONAL	1	TRUE	1	0.487342910004756	2		613	603	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099579	157099579	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1562376341	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	11	167	0	ENST00000346085.5:c.521del	p.Pro174ArgfsTer6	p.P174Rfs*6	ENST00000346085	NM_020732.3	172	gaC/ga	1/20	1	2	FACETS	0.23	0.159	0.319	0.23	0.159	0.319	SUBCLONAL	1	TRUE	1	0.487342910004756	2		167	196	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	223	375	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.487342910004756	5	FACETS	0.989	0.929	1	0.742	0.697	0.787	CLONAL	3	TRUE	1	0.487342910004756	5		375	534	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	219	247	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.854	0.802	0.907	1	0.994	1	CLONAL	2	TRUE	1	0.487342910004756	2		247	526	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	72	600	1	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	1	2	FACETS	0.325	0.283	0.371	0.325	0.283	0.371	SUBCLONAL	1	TRUE	1	0.487342910004756	2		601	908	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097621	27097622	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	59	870	0	ENST00000324856.7:c.3216dup	p.Trp1073MetfsTer32	p.W1073Mfs*32	ENST00000324856	NM_006015.4	1070	-/A	12/20	1	2	FACETS	0.275	0.236	0.318	0.275	0.236	0.318	SUBCLONAL	1	TRUE	1	0.487342910004756	2		870	880	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405953	49405953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	206	1063	0	ENST00000418115.1:c.185G>A	p.Gly62Glu	p.G62E	ENST00000418115	NM_001664.2	62	gGg/gAg	3/5	0.487342910004756	5	FACETS	0.849	0.789	0.911	0.424	0.394	0.456	CLONAL	2	TRUE	1	0.487342910004756	5		1063	862	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs767894241	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	144	984	1	ENST00000358127.4:c.76dup	p.Val26GlyfsTer49	p.V26Gfs*49	ENST00000358127	NM_001280556.1	26	gtt/gGtt	2/10	1	2	FACETS	0.629	0.573	0.687	0.629	0.573	0.687	SUBCLONAL	1	TRUE	1	0.487342910004756	2		985	940	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139411768	139411768	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201768800	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	47	1203	1	ENST00000277541.6:c.1511G>A	p.Arg504His	p.R504H	ENST00000277541	NM_017617.3	504	cGc/cAc	9/34	1	2	FACETS	0.226	0.189	0.266	0.226	0.189	0.266	SUBCLONAL	1	TRUE	1	0.487342910004756	2		1204	855	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	73	830	1	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	NA	2	FACETS	0.565	0.495	0.641			1	INDETERMINATE	1	TRUE	NA	0.487342910004756	2		831	530	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37038192	37038192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750206	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	215	492	0	ENST00000231790.2:c.199G>A	p.Gly67Arg	p.G67R	ENST00000231790	NM_000249.3	67	Ggg/Agg	2/19	0.487342910004756	5	FACETS	1	0.982	1	0.83	0.781	0.879	CLONAL	3	TRUE	1	0.487342910004756	5		492	460	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354008	15354008	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	32	403	3	ENST00000263377.2:c.2872del	p.Leu958CysfsTer110	p.L958Cfs*110	ENST00000263377	NM_058243.2	958	Ctg/tg	14/20	1	2	FACETS	0.677	0.554	0.813	0.677	0.554	0.813	SUBCLONAL	1	TRUE	1	0.487342910004756	2		406	194	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914478	32914478	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358833	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	49	931	0	ENST00000380152.3:c.5986G>A	p.Ala1996Thr	p.A1996T	ENST00000380152		1996	Gca/Aca	11/27	1	2	FACETS	0.234	0.197	0.274	0.234	0.197	0.274	SUBCLONAL	1	TRUE	1	0.487342910004756	2		931	861	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687306	37687306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1172789499	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	90	828	0	ENST00000447079.4:c.4210C>T	p.Arg1404Cys	p.R1404C	ENST00000447079	NM_015083.1	1404	Cgt/Tgt	14/14	1	2	FACETS	0.485	0.43	0.544	0.485	0.43	0.544	SUBCLONAL	1	TRUE	1	0.487342910004756	2		828	761	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835781	68835781	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060501215	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	41	829	0	ENST00000261769.5:c.377del	p.Pro126ArgfsTer89	p.P126Rfs*89	ENST00000261769	NM_004360.3	124	cgC/cg	3/16	1	2	FACETS	0.209	0.173	0.249	0.209	0.173	0.249	SUBCLONAL	1	TRUE	1	0.487342910004756	2		829	806	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209298	133209298	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060500809	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	111	916	0	ENST00000320574.5:c.6088del	p.Ala2030ProfsTer18	p.A2030Pfs*18	ENST00000320574	NM_006231.2	2030	Gcc/cc	44/49	1	2	FACETS	0.683	0.615	0.755	0.683	0.615	0.755	SUBCLONAL	1	TRUE	1	0.487342910004756	2		916	667	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440882	52440882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	50	869	3	ENST00000460680.1:c.622C>T	p.Arg208Trp	p.R208W	ENST00000460680	NM_004656.3	208	Cgg/Tgg	8/17	1	2	FACETS	0.265	0.224	0.311	0.265	0.224	0.311	SUBCLONAL	1	TRUE	1	0.487342910004756	2		872	773	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954342	48954342	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780248969	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	56	525	0	ENST00000267163.4:c.1463C>T	p.Ala488Val	p.A488V	ENST00000267163	NM_000321.2	488	gCg/gTg	16/27	1	2	FACETS	0.354	0.303	0.41	0.354	0.303	0.41	SUBCLONAL	1	TRUE	1	0.487342910004756	2		525	649	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609934	81609934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369995834	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	26	419	0	ENST00000298171.2:c.1532C>T	p.Thr511Met	p.T511M	ENST00000298171	NM_000369.2	511	aCg/aTg	10/10	1	2	FACETS	0.317	0.251	0.392	0.317	0.251	0.392	SUBCLONAL	1	TRUE	1	0.487342910004756	2		419	337	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856389	111856389	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	65	232	0	ENST00000341259.2:c.440G>A	p.Arg147His	p.R147H	ENST00000341259	NM_005475.2	147	cGc/cAc	2/8	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.487342910004756	2		232	259	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794767	120794767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs555207756	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	108	1164	0	ENST00000257552.2:c.590G>A	p.Arg197Gln	p.R197Q	ENST00000257552	NM_002442.3	197	cGg/cAg	9/15	1	2	FACETS	0.445	0.399	0.495	0.445	0.399	0.495	SUBCLONAL	1	TRUE	1	0.487342910004756	2		1164	995	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26970441	26970441	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	36	525	0	ENST00000381527.3:c.815del	p.Lys272ArgfsTer8	p.K272Rfs*8	ENST00000381527	NM_001260.1	270	atA/at	8/13	1	2	FACETS	0.28	0.229	0.336	0.28	0.229	0.336	SUBCLONAL	1	TRUE	1	0.487342910004756	2		525	528	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348011	348011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769972546	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	174	1088	2	ENST00000262320.3:c.1495G>A	p.Val499Met	p.V499M	ENST00000262320	NM_003502.3	499	Gtg/Atg	6/11	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.487342910004756	2		1090	701	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2221351	2221351	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	56	877	0	ENST00000326181.6:c.435del	p.Cys146ValfsTer11	p.C146Vfs*11	ENST00000326181	NM_032271.2	145	acG/ac	6/21	1	2	FACETS	0.387	0.331	0.448	0.387	0.331	0.448	SUBCLONAL	1	TRUE	1	0.487342910004756	2		877	594	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346839	89346847	+	inframe_deletion	In_Frame_Del	DEL	GACGTCCTC	GACGTCCTC	-	rs756624276	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	12	393	0	ENST00000301030.4:c.6103_6111del	p.Glu2035_Val2037del	p.E2035_V2037del	ENST00000301030	NM_001256183.1	2035	GAGGACGTC/-	9/13	1	2	FACETS	0.22	0.154	0.301	0.22	0.154	0.301	SUBCLONAL	1	TRUE	1	0.487342910004756	2		393	224	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877363	89877363	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	83	717	1	ENST00000389301.3:c.400C>A	p.Pro134Thr	p.P134T	ENST00000389301	NM_000135.2	134	Cct/Act	4/43	1	2	FACETS	0.477	0.421	0.538	0.477	0.421	0.538	SUBCLONAL	1	TRUE	1	0.487342910004756	2		718	714	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130337	11130337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs281875226	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	89	1008	1	ENST00000358026.2:c.2576C>T	p.Thr859Met	p.T859M	ENST00000358026	NM_001128849.1	859	aCg/aTg	18/36	1	2	FACETS	0.457	0.405	0.513	0.457	0.405	0.513	SUBCLONAL	1	TRUE	1	0.487342910004756	2		1009	799	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291861	15291861	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1485768768	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	80	1072	1	ENST00000263388.2:c.2905C>T	p.Arg969Trp	p.R969W	ENST00000263388	NM_000435.2	969	Cgg/Tgg	18/33	1	2	FACETS	0.489	0.431	0.552	0.489	0.431	0.552	SUBCLONAL	1	TRUE	1	0.487342910004756	2		1073	671	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302669	15302669	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	40	1101	0	ENST00000263388.2:c.689del	p.Gly230ValfsTer6	p.G230Vfs*6	ENST00000263388	NM_000435.2	230	gGt/gt	5/33	1	2	FACETS	0.21	0.174	0.251	0.21	0.174	0.251	SUBCLONAL	1	TRUE	1	0.487342910004756	2		1101	781	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216189	36216189	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	38	943	2	ENST00000222270.7:c.3602del	p.Pro1201ArgfsTer154	p.P1201Rfs*154	ENST00000222270	NM_014727.1	1199	ggC/gg	11/37	1	2	FACETS	0.226	0.186	0.271	0.226	0.186	0.271	SUBCLONAL	1	TRUE	1	0.487342910004756	2		945	691	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909674	50909674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199700312	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	71	978	0	ENST00000440232.2:c.1394G>A	p.Arg465Gln	p.R465Q	ENST00000440232	NM_002691.3	465	cGg/cAg	12/27	1	2	FACETS	0.377	0.328	0.43	0.377	0.328	0.43	SUBCLONAL	1	TRUE	1	0.487342910004756	2		978	773	SUCCESS
ALK	238	MSKCC	GRCh37	2	29419708	29419708	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	34	744	0	ENST00000389048.3:c.4092G>T	p.Gln1364His	p.Q1364H	ENST00000389048	NM_004304.4	1364	caG/caT	28/29	1	2	FACETS	0.209	0.17	0.253	0.209	0.17	0.253	SUBCLONAL	1	TRUE	1	0.487342910004756	2		744	667	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022809	31022809	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	44	769	0	ENST00000375687.4:c.2294T>G	p.Leu765Arg	p.L765R	ENST00000375687	NM_015338.5	765	cTg/cGg	13/13	1	2	FACETS	0.305	0.255	0.36	0.305	0.255	0.36	SUBCLONAL	1	TRUE	1	0.487342910004756	2		769	593	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643390	52643390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1438592568	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	80	816	0	ENST00000394830.3:c.2506C>T	p.Arg836Trp	p.R836W	ENST00000394830	NM_018313.4	836	Cgg/Tgg	17/30	1	2	FACETS	0.377	0.331	0.427	0.377	0.331	0.427	SUBCLONAL	1	TRUE	1	0.487342910004756	2		816	870	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530381	187530381	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753202486	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	135	576	2	ENST00000441802.2:c.10162G>A	p.Val3388Ile	p.V3388I	ENST00000441802	NM_005245.3	3388	Gtc/Atc	16/27	1	2	FACETS	0.974	0.889	1	0.974	0.889	1	CLONAL	1	TRUE	1	0.487342910004756	2		578	569	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31468080	31468080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1458058411	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	185	993	8	ENST00000344624.3:c.2332C>T	p.Arg778Cys	p.R778C	ENST00000344624		778	Cgc/Tgc	15/33	1	2	FACETS	0.823	0.76	0.888	0.823	0.76	0.888	CLONAL	1	TRUE	1	0.487342910004756	2		1001	923	SUCCESS
APC	324	MSKCC	GRCh37	5	112178831	112178831	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs545125246	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	30	620	0	ENST00000257430.4:c.7540A>G	p.Thr2514Ala	p.T2514A	ENST00000257430	NM_000038.5	2514	Act/Gct	16/16	1	2	FACETS	0.228	0.183	0.279	0.228	0.183	0.279	SUBCLONAL	1	TRUE	1	0.487342910004756	2		620	541	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395000	395001	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	123	721	0	ENST00000380956.4:c.402dup	p.Gly135ArgfsTer77	p.G135Rfs*77	ENST00000380956	NM_001195286.1	132	-/A	3/9	1	2	FACETS	0.853	0.774	0.936	0.853	0.774	0.936	CLONAL	1	TRUE	1	0.487342910004756	2		721	592	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32814930	32814930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1458831913	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	227	969	2	ENST00000354258.4:c.2135C>T	p.Ala712Val	p.A712V	ENST00000354258	NM_000593.5	712	gCg/gTg	10/11	1	2	FACETS	0.984	0.917	1	0.984	0.917	1	CLONAL	1	TRUE	1	0.487342910004756	2		971	947	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89791059	89791059	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2231272	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	10	78	0	ENST00000336032.3:c.446C>T	p.Pro149Leu	p.P149L	ENST00000336032	NM_006813.2	149	cCg/cTg	1/2	1	2	FACETS	0.423	0.289	0.588	0.423	0.289	0.588	SUBCLONAL	1	TRUE	1	0.487342910004756	2		78	97	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982087	93982087	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1448138791	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	41	729	1	ENST00000369303.4:c.1378G>A	p.Glu460Lys	p.E460K	ENST00000369303	NM_004440.3	460	Gag/Aag	6/17	1	2	FACETS	0.244	0.202	0.29	0.244	0.202	0.29	SUBCLONAL	1	TRUE	1	0.487342910004756	2		730	691	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129277	152129277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	79	910	5	ENST00000206249.3:c.230G>A	p.Gly77Asp	p.G77D	ENST00000206249	NM_000125.3	77	gGc/gAc	1/8	1	2	FACETS	0.536	0.472	0.605	0.536	0.472	0.605	SUBCLONAL	1	TRUE	1	0.487342910004756	2		915	605	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026910	6026910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	13	213	0	ENST00000265849.7:c.1486C>T	p.His496Tyr	p.H496Y	ENST00000265849	NM_000535.5	496	Cac/Tac	11/15	1	2	FACETS	0.329	0.235	0.443	0.329	0.235	0.443	SUBCLONAL	1	TRUE	1	0.487342910004756	2		213	162	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194905	29194905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375453930	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	178	995	1	ENST00000240100.2:c.823C>T	p.Arg275Cys	p.R275C	ENST00000240100	NM_001394.6	275	Cgc/Tgc	4/4	1	2	FACETS	0.89	0.821	0.961	0.89	0.821	0.961	CLONAL	1	TRUE	1	0.487342910004756	2		996	821	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139811005	139811005	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369480645	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	106	1036	0	ENST00000247668.2:c.616G>A	p.Val206Ile	p.V206I	ENST00000247668	NM_021138.3	206	Gtc/Atc	7/11	1	2	FACETS	0.492	0.44	0.546	0.492	0.44	0.546	SUBCLONAL	1	TRUE	1	0.487342910004756	2		1036	885	SUCCESS
AR	367	MSKCC	GRCh37	X	66765712	66765712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	51	646	1	ENST00000374690.3:c.724G>A	p.Ala242Thr	p.A242T	ENST00000374690	NM_000044.3	242	Gca/Aca	1/8	1	1	FACETS	0.282	0.239	0.329	0.282	0.239	0.329	SUBCLONAL	1	TRUE	0	0.487342910004756	1		647	561	SUCCESS
BTK	695	MSKCC	GRCh37	X	100625010	100625010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	165	388	0	ENST00000308731.7:c.367C>T	p.Arg123Trp	p.R123W	ENST00000308731	NM_000061.2	123	Cgg/Tgg	5/19	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.487342910004756	1		388	410	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	115	302	0				ENST00000310581	NM_198253.2	-/1132			0.248453437347699	0	FACETS	0.369	0.336	0.402			1	INDETERMINATE	1	TRUE	0	0.663832951952823	0		302	316	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	177	225	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.982	0.911	1	0.982	0.911	1	CLONAL	1	TRUE	1	0.663832951952823	2		225	543	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226845	2226845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	161	501	2	ENST00000398665.3:c.4325C>T	p.Pro1442Leu	p.P1442L	ENST00000398665	NM_032482.2	1442	cCc/cTc	27/28	0.520230043066174	1	FACETS	0.787	0.73	0.844	0.787	0.73	0.844	SUBCLONAL	1	TRUE	0	0.663832951952823	1		503	412	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562628	29562628	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1555615431	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	125	560	0	ENST00000356175.3:c.3709-1G>A		p.X1237_splice	ENST00000356175	NM_000267.3	1237			1	2	FACETS	0.978	0.894	1	0.978	0.894	1	CLONAL	1	TRUE	1	0.663832951952823	2		560	385	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211050	55211050	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17289589	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	182	832	3	ENST00000275493.2:c.293G>A	p.Arg98Gln	p.R98Q	ENST00000275493	NM_005228.3	98	cGa/cAa	3/28	1	2	FACETS	0.869	0.805	0.934	0.869	0.805	0.934	CLONAL	1	TRUE	1	0.663832951952823	2		835	631	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434090	49434090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779629382	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	163	863	0	ENST00000301067.7:c.7463C>T	p.Ser2488Leu	p.S2488L	ENST00000301067	NM_003482.3	2488	tCg/tTg	31/54	1	2	FACETS	0.965	0.892	1	0.965	0.892	1	CLONAL	1	TRUE	1	0.663832951952823	2		863	509	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679366	29679366	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs866445127	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	194	730	0	ENST00000356175.3:c.7486C>T	p.Arg2496Ter	p.R2496*	ENST00000356175	NM_000267.3	2496	Cga/Tga	50/57	1	2	FACETS	0.991	0.922	1	0.991	0.922	1	CLONAL	1	TRUE	1	0.663832951952823	2		730	590	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713470	40713470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318044562	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	165	918	2	ENST00000373198.4:c.4045C>T	p.Arg1349Cys	p.R1349C	ENST00000373198	NM_133170.3	1349	Cgt/Tgt	30/32	1	2	FACETS	0.892	0.824	0.963	0.892	0.824	0.963	CLONAL	1	TRUE	1	0.663832951952823	2		920	557	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257278	16257278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	213	963	0	ENST00000375759.3:c.4543C>T	p.His1515Tyr	p.H1515Y	ENST00000375759	NM_015001.2	1515	Cat/Tat	11/15	1	2	FACETS	0.874	0.815	0.935	0.874	0.815	0.935	CLONAL	1	TRUE	1	0.663832951952823	2		963	734	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100109	27100109	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	201	839	2	ENST00000324856.7:c.3905C>T	p.Thr1302Ile	p.T1302I	ENST00000324856	NM_006015.4	1302	aCt/aTt	16/20	1	2	FACETS	0.942	0.877	1	0.942	0.877	1	CLONAL	1	TRUE	1	0.663832951952823	2		841	643	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94923091	94923091	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	198	787	0	ENST00000536441.1:c.377A>G	p.Asn126Ser	p.N126S	ENST00000536441	NM_144665.3	126	aAc/aGc	4/10	1	2	FACETS	0.889	0.827	0.953	0.889	0.827	0.953	CLONAL	1	TRUE	1	0.663832951952823	2		787	671	SUCCESS
ATM	472	MSKCC	GRCh37	11	108128304	108128304	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	183	675	0	ENST00000278616.4:c.2347T>A	p.Cys783Ser	p.C783S	ENST00000278616	NM_000051.3	783	Tgt/Agt	15/63	1	2	FACETS	0.891	0.826	0.957	0.891	0.826	0.957	CLONAL	1	TRUE	1	0.663832951952823	2		675	619	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691191	18691191	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	122	596	0	ENST00000266497.5:c.3302G>C	p.Arg1101Pro	p.R1101P	ENST00000266497		1101	cGt/cCt	23/31	1	2	FACETS	0.792	0.721	0.867	0.792	0.721	0.867	SUBCLONAL	1	TRUE	1	0.663832951952823	2		596	464	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800939	18800939	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	123	621	1	ENST00000266497.5:c.4315C>T	p.Pro1439Ser	p.P1439S	ENST00000266497		1439	Cca/Tca	31/31	1	2	FACETS	0.88	0.803	0.961	0.88	0.803	0.961	CLONAL	1	TRUE	1	0.663832951952823	2		622	421	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231122	46231122	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	112	593	0	ENST00000334344.6:c.1042G>A	p.Asp348Asn	p.D348N	ENST00000334344	NM_152641.2	348	Gat/Aat	9/21	1	2	FACETS	0.716	0.648	0.788	0.716	0.648	0.788	SUBCLONAL	1	TRUE	1	0.663832951952823	2		593	471	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244652	46244652	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	214	846	1	ENST00000334344.6:c.2746C>T	p.Gln916Ter	p.Q916*	ENST00000334344	NM_152641.2	916	Caa/Taa	15/21	1	2	FACETS	0.902	0.841	0.964	0.902	0.841	0.964	CLONAL	1	TRUE	1	0.663832951952823	2		847	715	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445909	49445910	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	315	1301	5	ENST00000301067.7:c.1556_1557delinsTT	p.Pro519Leu	p.P519L	ENST00000301067	NM_003482.3	519	cCC/cTT	10/54	1	2	FACETS	0.942	0.89	0.994	0.942	0.89	0.994	CLONAL	1	TRUE	1	0.663832951952823	2		1306	1008	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910653	32910653	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867089743	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	149	693	0	ENST00000380152.3:c.2161C>T	p.Pro721Ser	p.P721S	ENST00000380152		721	Cca/Tca	11/27	1	2	FACETS	0.833	0.765	0.903	0.833	0.765	0.903	CLONAL	1	TRUE	1	0.663832951952823	2		693	539	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093464	30093465	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	98	448	4	ENST00000331968.5:c.1799-1_1799delinsAA		p.X600_splice	ENST00000331968	NM_002742.2	600		13/18	1	2	FACETS	0.853	0.769	0.941	0.853	0.769	0.941	CLONAL	1	TRUE	1	0.663832951952823	2		452	346	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986625	36986625	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	88	312	0	ENST00000354822.5:c.1064G>A	p.Gly355Asp	p.G355D	ENST00000354822	NM_001079668.2	355	gGc/gAc	3/3	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.663832951952823	2		312	250	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43771663	43771663	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	220	1014	0	ENST00000382044.4:c.720C>A	p.Asp240Glu	p.D240E	ENST00000382044	NM_001141980.1	240	gaC/gaA	7/28	0.663832951952823	1	FACETS	0.942	0.887	0.997	0.942	0.887	0.997	CLONAL	1	TRUE	0	0.663832951952823	1		1014	470	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639055	3639056	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	137	828	2	ENST00000294008.3:c.4583_4584delinsTT	p.Ala1528Val	p.A1528V	ENST00000294008	NM_032444.2	1528	gCC/gTT	12/15	1	2	FACETS	0.905	0.83	0.983	0.905	0.83	0.983	CLONAL	1	TRUE	1	0.663832951952823	2		830	456	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858687	9858687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	134	594	0	ENST00000330684.3:c.2714C>T	p.Ser905Phe	p.S905F	ENST00000330684	NM_001134407.1	905	tCc/tTc	13/13	1	2	FACETS	0.978	0.897	1	0.978	0.897	1	CLONAL	1	TRUE	1	0.663832951952823	2		594	413	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858772	9858772	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	72	326	0	ENST00000330684.3:c.2629G>A	p.Glu877Lys	p.E877K	ENST00000330684	NM_001134407.1	877	Gaa/Aaa	13/13	1	2	FACETS	0.973	0.864	1	0.973	0.864	1	CLONAL	1	TRUE	1	0.663832951952823	2		326	223	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862946	9862946	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	138	668	0	ENST00000330684.3:c.2357G>A	p.Gly786Asp	p.G786D	ENST00000330684	NM_001134407.1	786	gGt/gAt	12/13	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.663832951952823	2		668	395	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864462	56864462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	207	839	0	ENST00000308159.5:c.950C>T	p.Pro317Leu	p.P317L	ENST00000308159	NM_014669.4	317	cCt/cTt	10/22	1	2	FACETS	0.957	0.892	1	0.957	0.892	1	CLONAL	1	TRUE	1	0.663832951952823	2		839	652	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990468	81990468	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	139	798	0	ENST00000359376.3:c.3739G>A	p.Glu1247Lys	p.E1247K	ENST00000359376	NM_002661.3	1247	Gag/Aag	32/33	0.520230043066174	1	FACETS	0.554	0.507	0.602	0.554	0.507	0.602	SUBCLONAL	1	TRUE	0	0.663832951952823	1		798	505	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984445	7984445	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	256	875	1	ENST00000319144.4:c.413G>A	p.Arg138Lys	p.R138K	ENST00000319144	NM_001139.2	138	aGa/aAa	3/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.663832951952823	2		876	672	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17125816	17125816	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	194	821	0	ENST00000285071.4:c.778T>C	p.Trp260Arg	p.W260R	ENST00000285071	NM_144997.5	260	Tgg/Cgg	7/14	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.663832951952823	2		821	584	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244231	41244231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	169	788	1	ENST00000357654.3:c.3317C>T	p.Pro1106Leu	p.P1106L	ENST00000357654	NM_007294.3	1106	cCt/cTt	10/23	1	2	FACETS	0.9	0.832	0.969	0.9	0.832	0.969	CLONAL	1	TRUE	1	0.663832951952823	2		789	566	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244528	41244528	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	153	834	0	ENST00000357654.3:c.3020C>T	p.Ser1007Leu	p.S1007L	ENST00000357654	NM_007294.3	1007	tCa/tTa	10/23	1	2	FACETS	0.82	0.754	0.888	0.82	0.754	0.888	CLONAL	1	TRUE	1	0.663832951952823	2		834	562	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191141	2191141	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	200	1023	2	ENST00000398665.3:c.395C>T	p.Ser132Phe	p.S132F	ENST00000398665	NM_032482.2	132	tCc/tTc	5/28	0.520230043066174	1	FACETS	0.595	0.553	0.637	0.595	0.553	0.637	SUBCLONAL	1	TRUE	0	0.663832951952823	1		1025	677	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2193765	2193765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	216	872	0	ENST00000398665.3:c.571C>T	p.Pro191Ser	p.P191S	ENST00000398665	NM_032482.2	191	Ccg/Tcg	6/28	0.520230043066174	1	FACETS	0.692	0.647	0.738	0.692	0.647	0.738	SUBCLONAL	1	TRUE	0	0.663832951952823	1		872	628	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172370	7172370	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	154	792	0	ENST00000302850.5:c.1199C>T	p.Ser400Phe	p.S400F	ENST00000302850	NM_000208.2	400	tCc/tTc	5/22	0.520230043066174	1	FACETS	0.642	0.592	0.693	0.642	0.592	0.693	SUBCLONAL	1	TRUE	0	0.663832951952823	1		792	483	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113819	11113819	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	164	812	0	ENST00000358026.2:c.1927C>T	p.Leu643Phe	p.L643F	ENST00000358026	NM_001128849.1	643	Ctc/Ttc	12/36	0.520230043066174	1	FACETS	0.666	0.616	0.717	0.666	0.616	0.717	SUBCLONAL	1	TRUE	0	0.663832951952823	1		812	496	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221642	36221642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471498012	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	232	1028	2	ENST00000222270.7:c.5311C>T	p.Arg1771Trp	p.R1771W	ENST00000222270	NM_014727.1	1771	Cgg/Tgg	26/37	0.520230043066174	1	FACETS	0.654	0.612	0.696	0.654	0.612	0.696	SUBCLONAL	1	TRUE	0	0.663832951952823	1		1030	714	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754929	29754929	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	198	754	0	ENST00000389048.3:c.1006C>T	p.Pro336Ser	p.P336S	ENST00000389048	NM_004304.4	336	Ccg/Tcg	4/29	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.663832951952823	2		754	563	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607618	46607618	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1019548129	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	243	1053	0	ENST00000263734.3:c.1807C>T	p.Pro603Ser	p.P603S	ENST00000263734	NM_001430.4	603	Ccc/Tcc	12/16	1	2	FACETS	0.961	0.901	1	0.961	0.901	1	CLONAL	1	TRUE	1	0.663832951952823	2		1053	762	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190670463	190670463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776398978	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	139	536	0	ENST00000441310.2:c.401C>T	p.Pro134Leu	p.P134L	ENST00000441310	NM_000534.4	134	cCt/cTt	4/13	1	2	FACETS	0.908	0.833	0.986	0.908	0.833	0.986	CLONAL	1	TRUE	1	0.663832951952823	2		536	461	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46275847	46275847	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	197	838	0	ENST00000371998.3:c.3283T>G	p.Phe1095Val	p.F1095V	ENST00000371998		1095	Ttc/Gtc	18/23	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.663832951952823	2		838	592	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169999008	169999008	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	120	536	0	ENST00000295797.4:c.937C>T	p.Pro313Ser	p.P313S	ENST00000295797	NM_002740.5	313	Cct/Tct	10/18	1	2	FACETS	0.833	0.758	0.911	0.833	0.758	0.911	CLONAL	1	TRUE	1	0.663832951952823	2		536	434	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920067	1920068	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	207	894	0	ENST00000382891.5:c.1127_1128delinsTT	p.Ser376Phe	p.S376F	ENST00000382891	NM_133335.3	376	tCC/tTT	5/22	1	2	FACETS	0.949	0.885	1	0.949	0.885	1	CLONAL	1	TRUE	1	0.663832951952823	2		894	657	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750596	41750596	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	177	741	1	ENST00000226382.2:c.32C>T	p.Ser11Phe	p.S11F	ENST00000226382	NM_003924.3	11	tCc/tTc	1/3	1	2	FACETS	0.986	0.915	1	0.986	0.915	1	CLONAL	1	TRUE	1	0.663832951952823	2		742	541	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961097	55961097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	271	993	0	ENST00000263923.4:c.2843G>A	p.Gly948Glu	p.G948E	ENST00000263923	NM_002253.2	948	gGg/gAg	21/30	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.663832951952823	2		993	786	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970967	55970967	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	170	851	1	ENST00000263923.4:c.1830G>A	p.Trp610Ter	p.W610*	ENST00000263923	NM_002253.2	610	tgG/tgA	13/30	1	2	FACETS	0.903	0.836	0.973	0.903	0.836	0.973	CLONAL	1	TRUE	1	0.663832951952823	2		852	567	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268098	153268098	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	102	425	0	ENST00000281708.4:c.710G>A	p.Trp237Ter	p.W237*	ENST00000281708	NM_033632.3	237	tGg/tAg	4/12	1	2	FACETS	0.634	0.569	0.701	0.634	0.569	0.701	SUBCLONAL	1	TRUE	1	0.663832951952823	2		425	485	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1253896	1253896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1196160200	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	139	929	1	ENST00000310581.5:c.3346G>A	p.Glu1116Lys	p.E1116K	ENST00000310581	NM_198253.2	1116	Gag/Aag	16/16	0.248453437347699	0	FACETS	0.301	0.276	0.328			1	INDETERMINATE	1	TRUE	0	0.663832951952823	0		930	467	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876454	35876454	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	209	787	1	ENST00000303115.3:c.1246C>A	p.Pro416Thr	p.P416T	ENST00000303115	NM_002185.3	416	Ccc/Acc	8/8	1	2	FACETS	0.99	0.924	1	0.99	0.924	1	CLONAL	1	TRUE	1	0.663832951952823	2		788	636	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80057472	80057472	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	122	554	0	ENST00000265081.6:c.1871G>T	p.Gly624Val	p.G624V	ENST00000265081	NM_002439.4	624	gGa/gTa	13/24	1	2	FACETS	0.875	0.798	0.956	0.875	0.798	0.956	CLONAL	1	TRUE	1	0.663832951952823	2		554	420	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449471	149449471	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	164	753	0	ENST00000286301.3:c.1475G>A	p.Gly492Glu	p.G492E	ENST00000286301	NM_005211.3	492	gGg/gAg	10/22	1	2	FACETS	0.99	0.916	1	0.99	0.916	1	CLONAL	1	TRUE	1	0.663832951952823	2		753	499	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180037013	180037013	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	145	773	1	ENST00000261937.6:c.3699G>A	p.Trp1233Ter	p.W1233*	ENST00000261937	NM_182925.4	1233	tgG/tgA	28/30	0.388420439284266	0	FACETS	0.347	0.32	0.376			1	INDETERMINATE	1	TRUE	0	0.663832951952823	0		774	423	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671253	30671253	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	226	826	0	ENST00000376406.3:c.5624G>A	p.Arg1875Lys	p.R1875K	ENST00000376406	NM_014641.2	1875	aGa/aAa	11/15	0.658520079164393	3	FACETS	0.92	0.857	0.985	0.46	0.428	0.493	CLONAL	1	TRUE	1	0.663832951952823	3		826	986	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178698	32178698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	254	1012	0	ENST00000375023.3:c.2696C>T	p.Ser899Phe	p.S899F	ENST00000375023	NM_004557.3	899	tCc/tTc	18/30	0.658520079164393	3	FACETS	0.979	0.917	1	0.49	0.458	0.522	CLONAL	1	TRUE	1	0.663832951952823	3		1012	1041	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188980	32188980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	195	944	0	ENST00000375023.3:c.574G>A	p.Glu192Lys	p.E192K	ENST00000375023	NM_004557.3	192	Gaa/Aaa	4/30	0.658520079164393	3	FACETS	0.981	0.909	1	0.49	0.454	0.527	CLONAL	1	TRUE	1	0.663832951952823	3		944	798	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798435	32798435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	503	1018	1	ENST00000374899.4:c.1421C>T	p.Ser474Phe	p.S474F	ENST00000374899	NM_018833.2	474	tCc/tTc	8/12	0.658520079164393	3	FACETS	0.943	0.907	0.98	0.943	0.907	0.98	CLONAL	2	TRUE	1	0.663832951952823	3		1019	1070	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120731	94120731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	103	616	0	ENST00000369303.4:c.320G>A	p.Arg107Lys	p.R107K	ENST00000369303	NM_004440.3	107	aGg/aAg	3/17	1	2	FACETS	0.73	0.658	0.806	0.73	0.658	0.806	SUBCLONAL	1	TRUE	1	0.663832951952823	2		616	425	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395517	116395517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	152	691	0	ENST00000397752.3:c.1810C>T	p.Leu604Phe	p.L604F	ENST00000397752	NM_000245.2	604	Ctc/Ttc	6/21	1	2	FACETS	0.876	0.806	0.948	0.876	0.806	0.948	CLONAL	1	TRUE	1	0.663832951952823	2		691	523	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538946	23538946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	212	804	0	ENST00000380871.4:c.493G>A	p.Glu165Lys	p.E165K	ENST00000380871	NM_006167.3	165	Gag/Aag	2/2	1	2	FACETS	0.95	0.887	1	0.95	0.887	1	CLONAL	1	TRUE	1	0.663832951952823	2		804	672	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521505	8521505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	189	869	0	ENST00000356435.5:c.733C>T	p.His245Tyr	p.H245Y	ENST00000356435		245	Cat/Tat	9/35	1	2	FACETS	0.877	0.815	0.942	0.877	0.815	0.942	CLONAL	1	TRUE	1	0.663832951952823	2		869	649	SUCCESS
AR	367	MSKCC	GRCh37	X	66765632	66765632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	179	1139	2	ENST00000374690.3:c.644C>T	p.Ser215Leu	p.S215L	ENST00000374690	NM_000044.3	215	tCg/tTg	1/8	0.520230043066174	1	FACETS	0.53	0.49	0.571	0.53	0.49	0.571	SUBCLONAL	1	TRUE	0	0.663832951952823	1		1141	680	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778811	76778812	+	missense_variant	Missense_Mutation	DNP	AG	AG	CA	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	207	899	2	ENST00000373344.5:c.6767_6768delinsTG	p.Ser2256Leu	p.S2256L	ENST00000373344	NM_000489.3	2256	tCT/tTG	31/35	0.520230043066174	1	FACETS	0.673	0.628	0.719	0.673	0.628	0.719	SUBCLONAL	1	TRUE	0	0.663832951952823	1		901	619	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849248	76849248	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	177	767	2	ENST00000373344.5:c.6028G>A	p.Asp2010Asn	p.D2010N	ENST00000373344	NM_000489.3	2010	Gat/Aat	26/35	0.520230043066174	1	FACETS	0.659	0.611	0.707	0.659	0.611	0.707	SUBCLONAL	1	TRUE	0	0.663832951952823	1		769	541	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937518	76937518	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	156	741	0	ENST00000373344.5:c.3230C>T	p.Ser1077Leu	p.S1077L	ENST00000373344	NM_000489.3	1077	tCa/tTa	9/35	0.520230043066174	1	FACETS	0.65	0.6	0.702	0.65	0.6	0.702	SUBCLONAL	1	TRUE	0	0.663832951952823	1		741	483	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191766	123191766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	178	807	0	ENST00000218089.9:c.1355G>A	p.Gly452Glu	p.G452E	ENST00000218089	NM_001042749.1	452	gGa/gAa	15/35	0.520230043066174	1	FACETS	0.573	0.531	0.617	0.573	0.531	0.617	SUBCLONAL	1	TRUE	0	0.663832951952823	1		807	625	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200039	123200039	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	115	414	2	ENST00000218089.9:c.2111C>T	p.Ser704Leu	p.S704L	ENST00000218089	NM_001042749.1	704	tCa/tTa	22/35	0.520230043066174	1	FACETS	0.679	0.619	0.741	0.679	0.619	0.741	SUBCLONAL	1	TRUE	0	0.663832951952823	1		416	341	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217393	123217393	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1569520230	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	127	628	1	ENST00000218089.9:c.3047G>A	p.Arg1016Lys	p.R1016K	ENST00000218089	NM_001042749.1	1016	aGa/aAa	29/35	0.520230043066174	1	FACETS	0.581	0.53	0.634	0.581	0.53	0.634	SUBCLONAL	1	TRUE	0	0.663832951952823	1		629	440	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504102	123504102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	148	684	0	ENST00000371139.4:c.278G>A	p.Gly93Asp	p.G93D	ENST00000371139	NM_001114937.2	93	gGc/gAc	3/4	0.520230043066174	1	FACETS	0.595	0.547	0.644	0.595	0.547	0.644	SUBCLONAL	1	TRUE	0	0.663832951952823	1		684	501	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858079	152858105	+	inframe_deletion	In_Frame_Del	DEL	GCCCCATGGTAGCTGTCCCGCAGCAGG	GCCCCATGGTAGCTGTCCCGCAGCAGG	-	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	136	786	0	ENST00000406277.2:c.510_536del	p.Leu172_Leu180del	p.L172_L180del	ENST00000406277	NM_152274.4	170	gcCCTGCTGCGGGACAGCTACCATGGGGCg/gcg	6/7	0.520230043066174	1	FACETS	0.663	0.608	0.719	0.663	0.608	0.719	SUBCLONAL	1	TRUE	0	0.663832951952823	1		786	413	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245621	46245623	+	frameshift_variant	Frame_Shift_Del	DEL	GGT	GGT	A	novel	NA	P-0015257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	122	590	0	ENST00000334344.6:c.3715_3717delinsA	p.Gly1239ArgfsTer2	p.G1239Rfs*2	ENST00000334344	NM_152641.2	1239	GGT/A	15/21	1	2	FACETS	0.822	0.749	0.899	0.822	0.749	0.899	CLONAL	1	TRUE	1	0.663832951952823	2		590	447	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0015280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	91	375	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.601	0.533	0.673	0.601	0.533	0.673	SUBCLONAL	1	TRUE	1	0.4	2		375	757	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	137	690	12	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.464	0.421	0.508	0.464	0.421	0.508	SUBCLONAL	1	TRUE	1	0.68419064607355	2		702	864	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	211	478	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.935	0.872	0.998	0.935	0.872	0.998	CLONAL	1	TRUE	1	0.68419064607355	2		478	660	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	271	530	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.577	0.54	0.615	0.577	0.54	0.615	SUBCLONAL	1	TRUE	1	0.68419064607355	2		534	1373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	296	562	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.68419064607355	2		562	790	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	235	408	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.907	0.85	0.966	0.907	0.85	0.966	CLONAL	1	TRUE	1	0.68419064607355	2		408	757	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795103	242795104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs768249210	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	59	997	0	ENST00000334409.5:c.105dup	p.Thr36HisfsTer70	p.T36Hfs*70	ENST00000334409	NM_005018.2	35	-/C	2/5	1	2	FACETS	0.215	0.184	0.249	0.215	0.184	0.249	SUBCLONAL	1	TRUE	1	0.68419064607355	2		997	801	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	70	191	1	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.68419064607355	2		192	169	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	153	694	2	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	0.483	0.441	0.526	0.483	0.441	0.526	SUBCLONAL	1	TRUE	1	0.68419064607355	2		696	926	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653796	89653798	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs1554893765	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	68	518	0	ENST00000371953.3:c.97_99del	p.Ile33del	p.I33del	ENST00000371953	NM_000314.4	32	ATT/-	2/9	1	2	FACETS	0.273	0.237	0.313	0.273	0.237	0.313	SUBCLONAL	1	TRUE	1	0.68419064607355	2		518	727	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	91	409	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.489	0.435	0.546	0.489	0.435	0.546	SUBCLONAL	1	TRUE	1	0.68419064607355	2		410	544	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039225	49039225	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	148	726	0	ENST00000267163.4:c.2306del	p.Leu769CysfsTer41	p.L769Cfs*41	ENST00000267163	NM_000321.2	768	aTt/at	22/27	1	2	FACETS	0.42	0.383	0.46	0.42	0.383	0.46	SUBCLONAL	1	TRUE	1	0.68419064607355	2		726	1029	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420670	49420670	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs797045659	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	72	659	0	ENST00000301067.7:c.15079C>T	p.Arg5027Ter	p.R5027*	ENST00000301067	NM_003482.3	5027	Cga/Tga	48/54	NA	2	FACETS	0.296	0.258	0.337			1	INDETERMINATE	1	TRUE	NA	0.68419064607355	2		659	710	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030478	49030479	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1566234123	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	179	507	1	ENST00000267163.4:c.1959dup	p.Val654SerfsTer14	p.V654Sfs*14	ENST00000267163	NM_000321.2	651	-/A	19/27	1	2	FACETS	0.832	0.77	0.895	0.832	0.77	0.895	CLONAL	1	TRUE	1	0.68419064607355	2		508	629	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107096	27107096	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	162	574	0	ENST00000324856.7:c.6707G>C	p.Arg2236Pro	p.R2236P	ENST00000324856	NM_006015.4	2236	cGc/cCc	20/20	1	2	FACETS	0.795	0.732	0.859	0.795	0.732	0.859	SUBCLONAL	1	TRUE	1	0.68419064607355	2		574	596	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	55	613	0	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	0.273	0.233	0.317	0.273	0.233	0.317	SUBCLONAL	1	TRUE	1	0.68419064607355	2		613	588	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559173	29559173	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	275	572	1	ENST00000356175.3:c.3280G>T	p.Glu1094Ter	p.E1094*	ENST00000356175	NM_000267.3	1094	Gaa/Taa	25/57	1	2	FACETS	0.938	0.883	0.994	0.938	0.883	0.994	CLONAL	1	TRUE	1	0.68419064607355	2		573	857	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412898	49412898	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519954	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	20	843	0	ENST00000418115.1:c.125A>G	p.Tyr42Cys	p.Y42C	ENST00000418115	NM_001664.2	42	tAt/tGt	2/5	1	2	FACETS	0.061	0.046	0.079	0.061	0.046	0.079	SUBCLONAL	1	TRUE	1	0.68419064607355	2		843	959	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106803	27106804	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	77	804	0	ENST00000324856.7:c.6420dup	p.Phe2141LeufsTer9	p.F2141Lfs*9	ENST00000324856	NM_006015.4	2138	-/C	20/20	1	2	FACETS	0.273	0.239	0.31	0.273	0.239	0.31	SUBCLONAL	1	TRUE	1	0.68419064607355	2		804	823	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508239	106508239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	37	405	0	ENST00000359195.3:c.233C>T	p.Ala78Val	p.A78V	ENST00000359195	NM_002649.2	78	gCg/gTg	2/11	0.665049662494719	3	FACETS	0.315	0.259	0.377	0.157	0.129	0.189	SUBCLONAL	1	TRUE	1	0.68419064607355	3		405	461	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966872	25966873	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	147	542	0	ENST00000435504.4:c.2333dup	p.Val779SerfsTer25	p.V779Sfs*25	ENST00000435504		778	cca/ccCa	13/13	1	2	FACETS	0.654	0.599	0.712	0.654	0.599	0.712	SUBCLONAL	1	TRUE	1	0.68419064607355	2		542	657	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28908194	28908194	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767930948	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	269	778	1	ENST00000282397.4:c.2561C>T	p.Thr854Met	p.T854M	ENST00000282397	NM_002019.4	854	aCg/aTg	18/30	1	2	FACETS	0.932	0.877	0.988	0.932	0.877	0.988	CLONAL	1	TRUE	1	0.68419064607355	2		779	844	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724542	162724542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1041487062	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	66	584	1	ENST00000367921.3:c.314G>A	p.Arg105His	p.R105H	ENST00000367921	NM_006182.2	105	cGc/cAc	5/18	1	2	FACETS	0.306	0.265	0.35	0.306	0.265	0.35	SUBCLONAL	1	TRUE	1	0.68419064607355	2		585	631	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736254	243736254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772090769	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	85	651	1	ENST00000263826.5:c.793G>A	p.Gly265Arg	p.G265R	ENST00000263826	NM_005465.4	265	Gga/Aga	8/13	NA	2	FACETS	0.312	0.275	0.351			1	INDETERMINATE	1	TRUE	NA	0.68419064607355	2		652	797	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717718	89717719	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	93	598	0	ENST00000371953.3:c.750_751dup	p.Gly251ValfsTer6	p.G251Vfs*6	ENST00000371953	NM_000314.4	248	cct/ccTGt	7/9	1	2	FACETS	0.335	0.297	0.375	0.335	0.297	0.375	SUBCLONAL	1	TRUE	1	0.68419064607355	2		598	812	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129350	64129351	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1166600152	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	125	777	0	ENST00000334205.4:c.788dup	p.Arg264SerfsTer16	p.R264Sfs*16	ENST00000334205	NM_003942.2	261	ttc/ttCc	8/17	1	2	FACETS	0.562	0.51	0.617	0.562	0.51	0.617	SUBCLONAL	1	TRUE	1	0.68419064607355	2		777	650	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138112	64138112	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	207	727	1	ENST00000334205.4:c.2035G>A	p.Ala679Thr	p.A679T	ENST00000334205	NM_003942.2	679	Gcg/Acg	16/17	1	2	FACETS	0.973	0.908	1	0.973	0.908	1	CLONAL	1	TRUE	1	0.68419064607355	2		728	622	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948433	71948433	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	107	1046	1	ENST00000298229.2:c.3149del	p.Pro1050LeufsTer81	p.P1050Lfs*81	ENST00000298229	NM_001567.3	1049	Ccc/cc	26/28	1	2	FACETS	0.349	0.312	0.388	0.349	0.312	0.388	SUBCLONAL	1	TRUE	1	0.68419064607355	2		1047	896	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163444	108163444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	136	709	0	ENST00000278616.4:c.4535C>T	p.Ala1512Val	p.A1512V	ENST00000278616	NM_000051.3	1512	gCt/gTt	30/63	1	2	FACETS	0.405	0.367	0.444	0.405	0.367	0.444	SUBCLONAL	1	TRUE	1	0.68419064607355	2		709	982	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856283	111856283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1420086510	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	19	76	1	ENST00000341259.2:c.334G>A	p.Ala112Thr	p.A112T	ENST00000341259	NM_005475.2	112	Gcc/Acc	2/8	1	2	FACETS	0.712	0.554	0.888	0.712	0.554	0.888	SUBCLONAL	1	TRUE	1	0.68419064607355	2		77	78	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941668	48941669	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	34	411	0	ENST00000267163.4:c.983dup	p.Asn328LysfsTer2	p.N328Kfs*2	ENST00000267163	NM_000321.2	326	-/A	10/27	1	2	FACETS	0.191	0.156	0.232	0.191	0.156	0.232	SUBCLONAL	1	TRUE	1	0.68419064607355	2		411	519	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434972	110434973	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	137	988	2	ENST00000375856.3:c.3428dup	p.Arg1144ProfsTer181	p.R1144Pfs*181	ENST00000375856	NM_003749.2	1143	ggc/ggGc	1/2	1	2	FACETS	0.34	0.308	0.373	0.34	0.308	0.373	SUBCLONAL	1	TRUE	1	0.68419064607355	2		990	1178	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060596	38060596	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	403	1075	0	ENST00000250448.2:c.1393T>C	p.Ser465Pro	p.S465P	ENST00000250448	NM_004496.3	465	Tcc/Ccc	2/2	1	2	FACETS	0.929	0.884	0.975	0.929	0.884	0.975	CLONAL	1	TRUE	1	0.68419064607355	2		1075	1268	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061649	38061649	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	35	249	0	ENST00000250448.2:c.340G>T	p.Gly114Cys	p.G114C	ENST00000250448	NM_004496.3	114	Ggc/Tgc	2/2	1	2	FACETS	0.371	0.305	0.444	0.371	0.305	0.444	SUBCLONAL	1	TRUE	1	0.68419064607355	2		249	276	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331723	68331723	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	33	212	0	ENST00000487270.1:c.319A>T	p.Thr107Ser	p.T107S	ENST00000487270	NM_133509.3	107	Aca/Tca	5/11	1	2	FACETS	0.392	0.321	0.471	0.392	0.321	0.471	SUBCLONAL	1	TRUE	1	0.68419064607355	2		212	246	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566115	95566115	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	105	393	0	ENST00000393063.1:c.4206+2T>C		p.X1402_splice	ENST00000393063	NM_030621.3	1402			1	2	FACETS	0.704	0.635	0.777	0.704	0.635	0.777	SUBCLONAL	1	TRUE	1	0.68419064607355	2		393	436	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2107148	2107148	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1357428836	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	115	895	0	ENST00000219476.3:c.817A>G	p.Ile273Val	p.I273V	ENST00000219476	NM_000548.3	273	Atc/Gtc	9/42	1	2	FACETS	0.382	0.343	0.422	0.382	0.343	0.422	SUBCLONAL	1	TRUE	1	0.68419064607355	2		895	881	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858094	9858094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748879665	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	95	694	0	ENST00000330684.3:c.3307C>T	p.Arg1103Cys	p.R1103C	ENST00000330684	NM_001134407.1	1103	Cgc/Tgc	13/13	1	2	FACETS	0.333	0.296	0.373	0.333	0.296	0.373	SUBCLONAL	1	TRUE	1	0.68419064607355	2		694	834	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821959	72821959	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	55	370	0	ENST00000268489.5:c.10216G>C	p.Gly3406Arg	p.G3406R	ENST00000268489	NM_006885.3	3406	Ggg/Cgg	10/10	1	2	FACETS	0.395	0.339	0.456	0.395	0.339	0.456	SUBCLONAL	1	TRUE	1	0.68419064607355	2		370	407	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81960686	81960686	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	97	715	0	ENST00000359376.3:c.2418-1G>A		p.X806_splice	ENST00000359376	NM_002661.3	806			1	2	FACETS	0.379	0.337	0.423	0.379	0.337	0.423	SUBCLONAL	1	TRUE	1	0.68419064607355	2		715	749	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435428	56435428	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	40	786	0	ENST00000407977.2:c.1709G>T	p.Gly570Val	p.G570V	ENST00000407977		570	gGc/gTc	9/10	1	2	FACETS	0.155	0.128	0.185	0.155	0.128	0.185	SUBCLONAL	1	TRUE	1	0.68419064607355	2		786	754	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371787	45371787	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	285	726	0	ENST00000262160.6:c.1204T>C	p.Phe402Leu	p.F402L	ENST00000262160	NM_005901.5	402	Ttt/Ctt	10/11	1	2	FACETS	0.976	0.92	1	0.976	0.92	1	CLONAL	1	TRUE	1	0.68419064607355	2		726	854	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575670	48575670	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	108	628	0	ENST00000342988.3:c.430T>C	p.Ser144Pro	p.S144P	ENST00000342988	NM_005359.5	144	Tca/Cca	4/12	1	2	FACETS	0.374	0.336	0.416	0.374	0.336	0.416	SUBCLONAL	1	TRUE	1	0.68419064607355	2		628	843	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220018	5220018	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	80	961	0	ENST00000357368.4:c.3697A>G	p.Asn1233Asp	p.N1233D	ENST00000357368	NM_002850.3	1233	Aac/Gac	22/38	1	2	FACETS	0.282	0.248	0.32	0.282	0.248	0.32	SUBCLONAL	1	TRUE	1	0.68419064607355	2		961	828	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122672	7122672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	71	808	0	ENST00000302850.5:c.3482C>T	p.Ala1161Val	p.A1161V	ENST00000302850	NM_000208.2	1161	gCa/gTa	19/22	1	2	FACETS	0.258	0.225	0.294	0.258	0.225	0.294	SUBCLONAL	1	TRUE	1	0.68419064607355	2		808	804	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251596	212251596	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1170963831	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	60	546	0	ENST00000342788.4:c.3463C>T	p.Arg1155Ter	p.R1155*	ENST00000342788	NM_005235.2	1155	Cga/Tga	27/28	1	2	FACETS	0.225	0.193	0.26	0.225	0.193	0.26	SUBCLONAL	1	TRUE	1	0.68419064607355	2		546	779	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755553	39755554	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	34	538	2	ENST00000288319.7:c.1211dup	p.Glu405GlyfsTer61	p.E405Gfs*61	ENST00000288319	NM_182918.3	404	ccg/ccCg	10/10	1	2	FACETS	0.165	0.134	0.2	0.165	0.134	0.2	SUBCLONAL	1	TRUE	1	0.68419064607355	2		540	602	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41554488	41554488	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	59	646	0	ENST00000263253.7:c.3574T>C	p.Tyr1192His	p.Y1192H	ENST00000263253	NM_001429.3	1192	Tac/Cac	19/31	1	2	FACETS	0.247	0.212	0.285	0.247	0.212	0.285	SUBCLONAL	1	TRUE	1	0.68419064607355	2		646	698	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434182	12434182	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776687	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	109	697	0	ENST00000287820.6:c.556del	p.Ser186ValfsTer47	p.S186Vfs*47	ENST00000287820	NM_015869.4	184	Aaa/aa	4/7	1	2	FACETS	0.373	0.334	0.414	0.373	0.334	0.414	SUBCLONAL	1	TRUE	1	0.68419064607355	2		697	854	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119642308	119642308	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	308	635	0	ENST00000316626.5:c.389T>G	p.Leu130Arg	p.L130R	ENST00000316626		130	cTg/cGg	4/12	1	2	FACETS	0.962	0.909	1	0.962	0.909	1	CLONAL	1	TRUE	1	0.68419064607355	2		635	936	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146518	55146518	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	185	479	0	ENST00000257290.5:c.2192A>G	p.Tyr731Cys	p.Y731C	ENST00000257290	NM_006206.4	731	tAc/tGc	16/23	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.68419064607355	2		479	511	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981461	55981461	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	75	667	0	ENST00000263923.4:c.476T>C	p.Val159Ala	p.V159A	ENST00000263923	NM_002253.2	159	gTg/gCg	4/30	1	2	FACETS	0.278	0.243	0.315	0.278	0.243	0.315	SUBCLONAL	1	TRUE	1	0.68419064607355	2		667	790	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861050	35861050	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	79	561	2	ENST00000303115.3:c.179A>G	p.Glu60Gly	p.E60G	ENST00000303115	NM_002185.3	60	gAg/gGg	2/8	1	2	FACETS	0.29	0.254	0.328	0.29	0.254	0.328	SUBCLONAL	1	TRUE	1	0.68419064607355	2		563	797	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950696	38950696	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	34	473	0	ENST00000357387.3:c.3254T>C	p.Phe1085Ser	p.F1085S	ENST00000357387	NM_152756.3	1085	tTc/tCc	31/38	1	2	FACETS	0.164	0.134	0.199	0.164	0.134	0.199	SUBCLONAL	1	TRUE	1	0.68419064607355	2		473	605	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952519	38952519	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	162	341	0	ENST00000357387.3:c.2906T>C	p.Val969Ala	p.V969A	ENST00000357387	NM_152756.3	969	gTa/gCa	30/38	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.68419064607355	2		341	458	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564809	86564809	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	339	836	0	ENST00000274376.6:c.539+2T>C		p.X180_splice	ENST00000274376	NM_002890.2	180			1	2	FACETS	0.902	0.854	0.951	0.902	0.854	0.951	CLONAL	1	TRUE	1	0.68419064607355	2		836	1099	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679557	86679557	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	275	546	0	ENST00000274376.6:c.2718T>G	p.Cys906Trp	p.C906W	ENST00000274376	NM_002890.2	906	tgT/tgG	21/25	1	2	FACETS	0.907	0.854	0.962	0.907	0.854	0.962	CLONAL	1	TRUE	1	0.68419064607355	2		546	886	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205370	38205370	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	205	951	0	ENST00000317025.8:c.320G>A	p.Ser107Asn	p.S107N	ENST00000317025	NM_023034.1	107	aGc/aAc	2/24	1	2	FACETS	0.473	0.438	0.51	0.473	0.438	0.51	SUBCLONAL	1	TRUE	1	0.68419064607355	2		951	1267	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776978	76776978	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	33	579	0	ENST00000373344.5:c.6976-2A>G		p.X2326_splice	ENST00000373344	NM_000489.3	2326			1	2	FACETS	0.148	0.12	0.18	0.148	0.12	0.18	SUBCLONAL	1	TRUE	1	0.68419064607355	2		579	650	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220559	123220560	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	83	802	0	ENST00000218089.9:c.3222dup	p.Ser1075IlefsTer12	p.S1075Ifs*12	ENST00000218089	NM_001042749.1	1072	-/A	30/35	1	2	FACETS	0.253	0.222	0.286	0.253	0.222	0.286	SUBCLONAL	1	TRUE	1	0.68419064607355	2		802	960	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10283798	10283798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201749864	NA	P-0015476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	122	658	0	ENST00000340748.4:c.688C>T	p.Arg230Cys	p.R230C	ENST00000340748		230	Cgc/Tgc	8/40	0.298524825101444	0	FACETS	0.608	0.548	0.67			1	SUBCLONAL	1	TRUE	0	0.305732140272326	0		658	912	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758774	41758774	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs758985963	NA	P-0015476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	203	649	1	ENST00000301178.4:c.1828C>T	p.Arg610Ter	p.R610*	ENST00000301178	NM_021913.4	610	Cga/Tga	16/20	0.305732140272326	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.305732140272326	1		650	755	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574091	46574091	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	100	665	0	ENST00000263734.3:c.106G>C	p.Glu36Gln	p.E36Q	ENST00000263734	NM_001430.4	36	Gag/Cag	2/16	0.258838453785425	2	FACETS	0.566	0.504	0.633	0.283	0.252	0.317	SUBCLONAL	1	TRUE	0	0.305732140272326	2		665	1155	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478013	138478055	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ACCTGCTTAATATAAGAAATGGTAGCTTCCCGAGGTACCTCCA	ACCTGCTTAATATAAGAAATGGTAGCTTCCCGAGGTACCTCCA	-	novel	NA	P-0015476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	120	402	0	ENST00000289153.2:c.131_171+2del		p.X44_splice	ENST00000289153	NM_006219.2	44		1/22	0.227058085082438	4	FACETS	1	0.976	1			1	CLONAL	1	TRUE	NA	0.305732140272326	4		402	818	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74868188	74868211	+	inframe_deletion	In_Frame_Del	DEL	CATGTTCTCTTTTTACAATAAATT	CATGTTCTCTTTTTACAATAAATT	-	novel	NA	P-0015476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	47	97	0	ENST00000284811.8:c.83_106del	p.Glu28_His35del	p.E28_H35del	ENST00000284811		28	gAATTTATTGTAAAAAGAGAACATGca/gca	3/4	0.227058085082438	4	FACETS	0.858	0.731	0.995			1	CLONAL	2	TRUE	NA	0.305732140272326	4		97	234	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90976685	90976685	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2034	188	553	2	ENST00000265433.3:c.947del	p.Phe316SerfsTer2	p.F316Sfs*2	ENST00000265433	NM_002485.4	316	tTc/tc	8/16	0.305732140272326	8	FACETS	1	0.957	1	0.212	0.195	0.231	CLONAL	1	TRUE	3	0.305732140272326	8		555	2222	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0015480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	103	528	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	0.533	0.476	0.594	0.533	0.476	0.594	SUBCLONAL	1	TRUE	1	0.42	2		528	920	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426646	49426714	+	inframe_deletion	In_Frame_Del	DEL	GCTGTTGCTGCTGCTGTTGTTGAAGCTGCTGCTGCTGTTGCTGCTGTTGAAGCTGTTGCTGCTGAAGTT	GCTGTTGCTGCTGCTGTTGTTGAAGCTGCTGCTGCTGTTGCTGCTGTTGAAGCTGTTGCTGCTGAAGTT	-	novel	NA	P-0015480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	22	172	0	ENST00000301067.7:c.11774_11842del	p.Gln3925_Gln3947del	p.Q3925_Q3947del	ENST00000301067	NM_003482.3	3925	cAACTTCAGCAGCAACAGCTTCAACAGCAGCAACAGCAGCAGCAGCTTCAACAACAGCAGCAGCAACAGCtt/ctt	39/54	1	2	FACETS	0.308	0.238	0.389	0.308	0.238	0.389	SUBCLONAL	1	TRUE	1	0.42	2		172	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578192	7578192	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	49	818	0	ENST00000269305.4:c.657del	p.Tyr220MetfsTer27	p.Y220Mfs*27	ENST00000269305	NM_001126112.2	219	ccC/cc	6/11	0.376213499904187	1	FACETS	0.283	0.239	0.332	0.283	0.239	0.332	SUBCLONAL	1	TRUE	0	0.376213499904187	1		818	747	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061198	38061199	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0015572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	181	395	0	ENST00000250448.2:c.789_790dup	p.Lys264ArgfsTer58	p.K264Rfs*58	ENST00000250448	NM_004496.3	264	aag/aGAag	2/2	1	2	FACETS	0.934	0.869	1	1	0.993	1	CLONAL	2	TRUE	1	0.376213499904187	2		395	515	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916926	178916937	+	inframe_deletion	In_Frame_Del	DEL	GTAGGCAACCGT	GTAGGCAACCGT	-	novel	NA	P-0015572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	179	514	0	ENST00000263967.3:c.314_325del	p.Val105_Arg108del	p.V105_R108del	ENST00000263967	NM_006218.2	105	GTAGGCAACCGT/-	2/21	1	2	FACETS	0.842	0.781	0.905	1	0.992	1	CLONAL	2	TRUE	1	0.376213499904187	2		514	565	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557322	187557322	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1318017548	NA	P-0015866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	247	718	0	ENST00000441802.2:c.4040C>G	p.Ser1347Cys	p.S1347C	ENST00000441802	NM_005245.3	1347	tCc/tGc	6/27	1	2	FACETS	0.901	0.845	0.959	0.901	0.845	0.959	CLONAL	1	TRUE	1	0.662237090794072	2		718	828	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251536	251536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	132	498	0	ENST00000264932.6:c.1747G>A	p.Glu583Lys	p.E583K	ENST00000264932	NM_004168.2	583	Gag/Aag	13/15	1	2	FACETS	0.686	0.625	0.75	0.686	0.625	0.75	SUBCLONAL	1	TRUE	1	0.662237090794072	2		498	581	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254507	1254507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	412	858	0	ENST00000310581.5:c.3271C>T	p.Pro1091Ser	p.P1091S	ENST00000310581	NM_198253.2	1091	Cca/Tca	15/16	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.662237090794072	2		858	945	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482877	140482877	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	327	666	1	ENST00000288602.6:c.1258C>A	p.Pro420Thr	p.P420T	ENST00000288602	NM_004333.4	420	Cca/Aca	10/18	0.200819729579763	3	FACETS	0.792	0.752	0.833	0.792	0.752	0.833	INDETERMINATE	2	TRUE	1	0.662237090794072	3		667	830	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339535	70339535	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0015887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	112	313	0	ENST00000374080.3:c.205-1G>C		p.X69_splice	ENST00000374080		69			1	1	FACETS	0.741	0.673	0.811	0.741	0.673	0.811	SUBCLONAL	1	TRUE	0	0.583455197168818	1		313	367	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441300	52441300	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	236	578	0	ENST00000460680.1:c.470del	p.Asn157MetfsTer30	p.N157Mfs*30	ENST00000460680	NM_004656.3	157	aAt/at	7/17	0.583455197168818	1	FACETS	0.993	0.934	1	0.993	0.934	1	CLONAL	1	TRUE	0	0.583455197168818	1		578	577	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	114	188	0				ENST00000310581	NM_198253.2	-/1132			0.272147527088986	4	FACETS	0.979	0.902	1			1	INDETERMINATE	3	TRUE	NA	0.502761753024632	4		188	232	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737107	145737109	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs780986647	NA	P-0016006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	207	492	0	ENST00000428558.2:c.3457_3459del	p.Glu1153del	p.E1153del	ENST00000428558	NM_004260.3	1153	GAG/-	21/22	0.324808691331956	6	FACETS	0.976	0.913	1	0.976	0.913	1	CLONAL	3	TRUE	3	0.502761753024632	6		492	564	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2115528	2115529	+	frameshift_variant	Frame_Shift_Ins	INS	CC	CC	GGT	novel	NA	P-0016090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	101	627	0	ENST00000219476.3:c.1608_1609delinsGGT	p.Arg537ValfsTer52	p.R537Vfs*52	ENST00000219476	NM_000548.3	536	gcCCgc/gcGGTgc	16/42	0.278212334803427	2	FACETS	1	0.981	1	0.712	0.64	0.787	CLONAL	1	TRUE	0	0.332261104536357	2		627	427	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	372	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.648200791960169	2		436	1058	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755773	39755773	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	38	291	0	ENST00000288319.7:c.992C>G	p.Thr331Ser	p.T331S	ENST00000288319	NM_182918.3	331	aCc/aGc	10/10	0.648200791960169	1	FACETS	0.294	0.244	0.349	0.294	0.244	0.349	SUBCLONAL	1	TRUE	0	0.648200791960169	1		291	270	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196294	106196294	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	138	199	0	ENST00000380013.4:c.4627A>G	p.Arg1543Gly	p.R1543G	ENST00000380013	NM_001127208.2	1543	Aga/Gga	11/11	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.648200791960169	2		199	415	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356309	70356309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1304949884	NA	P-0016201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	240	606	0	ENST00000374080.3:c.5204G>A	p.Arg1735His	p.R1735H	ENST00000374080		1735	cGc/cAc	37/45	NA	2	FACETS	0.879	0.823	0.937			1	INDETERMINATE	1	TRUE	NA	0.648200791960169	2		606	842	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259440	11259440	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs975577894	NA	P-0016248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	39	302	0	ENST00000361445.4:c.4128T>A	p.Asp1376Glu	p.D1376E	ENST00000361445	NM_004958.3	1376	gaT/gaA	28/58	1	2	FACETS	0.741	0.615	0.882	0.741	0.615	0.882	SUBCLONAL	1	TRUE	1	0.254796366348952	2		302	413	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626974	14626974	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0016248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	73	489	0	ENST00000254322.2:c.801T>A	p.Cys267Ter	p.C267*	ENST00000254322	NM_006145.1	267	tgT/tgA	3/3	1	2	FACETS	0.774	0.676	0.88	0.774	0.676	0.88	SUBCLONAL	1	TRUE	1	0.254796366348952	2		489	740	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	267	570	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.297500121328433	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.32	3		570	931	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0016579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	297	1108	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.297500121328433	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	0	0.32	2		1109	923	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028632	12028632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753665559	NA	P-0016579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	166	335	0	ENST00000353533.5:c.835G>A	p.Ala279Thr	p.A279T	ENST00000353533	NM_003010.3	279	Gca/Aca	8/11	0.297500121328433	2	FACETS	0.867	0.801	0.936	0.867	0.801	0.936	CLONAL	2	TRUE	0	0.32	2		335	598	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806657	1806657	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	134	439	0	ENST00000260795.2:c.1373A>T	p.Glu458Val	p.E458V	ENST00000260795		458	gAg/gTg	9/17	0.297500121328433	3	FACETS	0.93	0.843	1	0.465	0.421	0.511	CLONAL	1	TRUE	1	0.32	3		439	1045	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974713	21974714	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0016579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	193	257	0	ENST00000304494.5:c.113_114insG	p.Asn39GlnfsTer5	p.N39Qfs*5	ENST00000304494	NM_000077.4	38	ccc/ccGc	1/3	0.297500121328433	2	FACETS	0.962	0.895	1	0.962	0.895	1	CLONAL	2	TRUE	0	0.32	2		257	627	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209504	98209504	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766315655	NA	P-0016625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	93	353	1	ENST00000331920.6:c.4034G>A	p.Arg1345His	p.R1345H	ENST00000331920	NM_000264.3	1345	cGt/cAt	23/24	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.24	2		354	684	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692830	89692830	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	58	227	0	ENST00000371953.3:c.314G>T	p.Cys105Phe	p.C105F	ENST00000371953	NM_000314.4	105	tGt/tTt	5/9	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.24	2		227	404	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096052	11096052	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763471007	NA	P-0016625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1239	115	925	1	ENST00000358026.2:c.326C>T	p.Pro109Leu	p.P109L	ENST00000358026	NM_001128849.1	109	cCg/cTg	3/36	1	2	FACETS	0.708	0.635	0.785	0.708	0.635	0.785	SUBCLONAL	1	TRUE	1	0.24	2		926	1354	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42861337	42861455	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCCTCCAGAGGTCTCAATAGCCCAGAGAGCAGGGTCTGGCTCAGAGCACTGGGGACTGCAGGAGCACATGGTGGGATCGAGGCTCCCTGCACTTACTGAACTTCCAGAGTAGGCCAGC	GGCCTCCAGAGGTCTCAATAGCCCAGAGAGCAGGGTCTGGCTCAGAGCACTGGGGACTGCAGGAGCACATGGTGGGATCGAGGCTCCCTGCACTTACTGAACTTCCAGAGTAGGCCAGC	-	novel	NA	P-0016625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	12	72	0	ENST00000398585.3:c.415_436+97del		p.X139_splice	ENST00000398585	NM_001135099.1	139		4/14	1	2	FACETS	0.794	0.561	1	0.794	0.561	1	CLONAL	1	TRUE	1	0.24	2		72	126	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271490	26271492	+	missense_variant	Missense_Mutation	TNP	GCG	GCG	CGA	novel	NA	P-0016625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	40	227	0	ENST00000305910.3:c.121_123delinsTCG	p.Arg41Ser	p.R41S	ENST00000305910	NM_003534.2	41	CGC/TCG	1/1	0.249823396246	4	FACETS	0.83	0.689	0.987	0.415	0.344	0.494	CLONAL	1	TRUE	2	0.24	4		227	498	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0016712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	72	461	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	0.344313103907588	1	FACETS	0.807	0.708	0.913	0.807	0.708	0.913	CLONAL	1	TRUE	0	0.344313103907588	1		461	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0016712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	165	964	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	1	2	FACETS	0.994	0.913	1	0.994	0.913	1	CLONAL	1	TRUE	1	0.344313103907588	2		964	964	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10267096	10267096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	115	619	0	ENST00000340748.4:c.1322C>T	p.Pro441Leu	p.P441L	ENST00000340748		441	cCa/cTa	17/40	1	2	FACETS	0.925	0.834	1	0.925	0.834	1	CLONAL	1	TRUE	1	0.344313103907588	2		619	722	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753938	57753938	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	37	507	0	ENST00000274289.3:c.686G>A	p.Arg229Lys	p.R229K	ENST00000274289	NM_006622.3	229	aGg/aAg	5/14	1	2	FACETS	0.417	0.343	0.5	0.417	0.343	0.5	SUBCLONAL	1	TRUE	1	0.344313103907588	2		507	515	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	173	188	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.982	0.912	1	0.982	0.912	1	CLONAL	1	TRUE	1	0.731302095221669	2		188	482	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481857	56481857	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519817	NA	P-0016915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	361	547	0	ENST00000267101.3:c.785C>A	p.Pro262His	p.P262H	ENST00000267101	NM_001982.3	262	cCt/cAt	7/28	1	2	FACETS	0.922	0.875	0.969	0.922	0.875	0.969	CLONAL	1	TRUE	1	0.731302095221669	2		547	1071	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894229	NA	P-0016915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	302	446	1	ENST00000451590.1:c.34G>T	p.Gly12Cys	p.G12C	ENST00000451590	NM_001130442.1	12	Ggc/Tgc	2/5	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.731302095221669	2		447	824	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874261	155874261	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs483352822	NA	P-0016915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	342	471	0	ENST00000368323.3:c.270G>C	p.Met90Ile	p.M90I	ENST00000368323	NM_006912.5	90	atG/atC	5/6	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.731302095221669	2		471	924	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105693	27105694	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0016915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	156	201	0	ENST00000324856.7:c.5305_5306del	p.Leu1769ArgfsTer3	p.L1769Rfs*3	ENST00000324856	NM_006015.4	1768	ctTCta/ctta	20/20	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.731302095221669	2		201	424	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874221	155874221	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	386	573	0	ENST00000368323.3:c.310G>A	p.Asp104Asn	p.D104N	ENST00000368323	NM_006912.5	104	Gat/Aat	5/6	1	2	FACETS	0.954	0.907	1	0.954	0.907	1	CLONAL	1	TRUE	1	0.731302095221669	2		573	1107	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427899	49427899	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	348	473	0	ENST00000301067.7:c.10691T>G	p.Leu3564Arg	p.L3564R	ENST00000301067	NM_003482.3	3564	cTc/cGc	38/54	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.731302095221669	2		473	925	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432346	49432347	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0016915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	294	513	0	ENST00000301067.7:c.8792dup	p.Gln2932ThrfsTer10	p.Q2932Tfs*10	ENST00000301067	NM_003482.3	2931	cca/ccCa	34/54	1	2	FACETS	0.914	0.862	0.966	0.914	0.862	0.966	CLONAL	1	TRUE	1	0.731302095221669	2		513	880	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37882832	37882832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs767813285	NA	P-0016915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	292	439	0	ENST00000269571.5:c.2890G>C	p.Glu964Gln	p.E964Q	ENST00000269571		964	Gaa/Caa	24/27	0.731302095221669	3	FACETS	1	0.97	1			1	CLONAL	1	TRUE	NA	0.731302095221669	3		439	1043	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359093	81359093	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	187	292	0	ENST00000222390.5:c.868G>A	p.Asp290Asn	p.D290N	ENST00000222390	NM_000601.4	290	Gac/Aac	8/18	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.731302095221669	2		292	483	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023664	27023664	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	277	425	0	ENST00000324856.7:c.771del	p.Ser258ProfsTer105	p.S258Pfs*105	ENST00000324856	NM_006015.4	257	gCc/gc	1/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.731302095221669	2		425	750	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056588	26056590	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs751086925	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	39	227	0	ENST00000343677.2:c.67_69del	p.Lys23del	p.K23del	ENST00000343677	NM_005319.3	23	AAG/-	1/1	1	2	FACETS	0.646	0.537	0.768	0.646	0.537	0.768	SUBCLONAL	1	TRUE	1	0.32351887197939	2		227	373	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489582	56489582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56387488	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	84	362	0	ENST00000267101.3:c.2047C>T	p.Arg683Trp	p.R683W	ENST00000267101	NM_001982.3	683	Cgg/Tgg	17/28	1	2	FACETS	0.794	0.702	0.893	0.794	0.702	0.893	SUBCLONAL	1	TRUE	1	0.32351887197939	2		362	654	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	108	463	0	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS	0.857	0.769	0.95	0.857	0.769	0.95	CLONAL	1	TRUE	1	0.32351887197939	2		463	779	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	94	396	3	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	0.32351887197939	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	0	0.32351887197939	1		399	478	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	162	599	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	1	2	FACETS	0.942	0.863	1	0.942	0.863	1	CLONAL	1	TRUE	1	0.32351887197939	2		599	1063	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219487	133219487	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	79	571	2	ENST00000320574.5:c.4647del	p.Lys1550AsnfsTer12	p.K1550Nfs*12	ENST00000320574	NM_006231.2	1549	ccC/cc	36/49	1	2	FACETS	0.518	0.454	0.587	0.518	0.454	0.587	SUBCLONAL	1	TRUE	1	0.32351887197939	2		573	943	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430563	80430563	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	127	194	0	ENST00000286548.4:c.445C>T	p.Arg149Ter	p.R149*	ENST00000286548	NM_002072.3	149	Cga/Tga	3/7	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.32351887197939	2		194	733	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625456	69625456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781938977	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	160	591	0	ENST00000334134.2:c.337G>A	p.Ala113Thr	p.A113T	ENST00000334134	NM_005247.2	113	Gcc/Acc	3/3	1	2	FACETS	0.979	0.897	1	0.979	0.897	1	CLONAL	1	TRUE	1	0.32351887197939	2		591	1010	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610314	81610314	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	119	432	1	ENST00000298171.2:c.1912G>A	p.Ala638Thr	p.A638T	ENST00000298171	NM_000369.2	638	Gcc/Acc	10/10	1	2	FACETS	0.855	0.772	0.944	0.855	0.772	0.944	CLONAL	1	TRUE	1	0.32351887197939	2		433	860	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502665	149502665	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200519248	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	108	338	1	ENST00000261799.4:c.2123G>A	p.Arg708His	p.R708H	ENST00000261799	NM_002609.3	708	cGc/cAc	15/23	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.32351887197939	2		339	595	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438067	49438067	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886043414	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	160	613	3	ENST00000301067.7:c.5104C>T	p.Arg1702Ter	p.R1702*	ENST00000301067	NM_003482.3	1702	Cga/Tga	21/54	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.32351887197939	2		616	930	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254593	16254593	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	116	479	0	ENST00000375759.3:c.1858C>T	p.Arg620Ter	p.R620*	ENST00000375759	NM_015001.2	620	Cga/Tga	11/15	0.32351887197939	1	FACETS	0.854	0.77	0.942	0.854	0.77	0.942	CLONAL	1	TRUE	0	0.32351887197939	1		479	704	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36821016	36821016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142405214	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	77	572	0	ENST00000373129.3:c.361G>A	p.Val121Ile	p.V121I	ENST00000373129	NM_032017.1	121	Gtt/Att	6/12	1	2	FACETS	0.542	0.474	0.614	0.542	0.474	0.614	SUBCLONAL	1	TRUE	1	0.32351887197939	2		572	879	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512177	120512177	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	96	418	0	ENST00000256646.2:c.1065C>G	p.Asp355Glu	p.D355E	ENST00000256646	NM_024408.3	355	gaC/gaG	6/34	1	2	FACETS	0.957	0.854	1	0.957	0.854	1	CLONAL	1	TRUE	1	0.32351887197939	2		418	620	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874176	155874176	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	168	651	0	ENST00000368323.3:c.355T>C	p.Tyr119His	p.Y119H	ENST00000368323	NM_006912.5	119	Tat/Cat	5/6	1	2	FACETS	0.836	0.766	0.908	0.836	0.766	0.908	CLONAL	1	TRUE	1	0.32351887197939	2		651	1243	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885497	111885497	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761530554	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	133	500	1	ENST00000341259.2:c.1274G>A	p.Arg425His	p.R425H	ENST00000341259	NM_005475.2	425	cGt/cAt	7/8	1	2	FACETS	0.906	0.822	0.994	0.906	0.822	0.994	CLONAL	1	TRUE	1	0.32351887197939	2		501	908	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28980012	28980012	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	74	487	0	ENST00000282397.4:c.1456A>G	p.Asn486Asp	p.N486D	ENST00000282397	NM_002019.4	486	Aat/Gat	11/30	1	2	FACETS	0.468	0.409	0.533	0.468	0.409	0.533	SUBCLONAL	1	TRUE	1	0.32351887197939	2		487	977	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050943	49050943	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767232453	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	173	516	0	ENST00000267163.4:c.2627G>A	p.Arg876His	p.R876H	ENST00000267163	NM_000321.2	876	cGc/cAc	25/27	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.32351887197939	2		516	1013	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098392	11098392	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	116	541	0	ENST00000358026.2:c.914del	p.Pro305ArgfsTer21	p.P305Rfs*21	ENST00000358026	NM_001128849.1	304	Ccc/cc	6/36	1	2	FACETS	0.819	0.737	0.905	0.819	0.737	0.905	CLONAL	1	TRUE	1	0.32351887197939	2		541	876	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349876	15349876	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1422529717	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	56	329	0	ENST00000263377.2:c.3776G>A	p.Arg1259His	p.R1259H	ENST00000263377	NM_058243.2	1259	cGc/cAc	18/20	1	2	FACETS	0.663	0.568	0.767	0.663	0.568	0.767	SUBCLONAL	1	TRUE	1	0.32351887197939	2		329	522	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951064	17951064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	160	537	2	ENST00000458235.1:c.1229G>A	p.Ser410Asn	p.S410N	ENST00000458235	NM_000215.3	410	aGc/aAc	9/24	1	2	FACETS	0.971	0.889	1	0.971	0.889	1	CLONAL	1	TRUE	1	0.32351887197939	2		539	1019	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219035	36219035	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1456547984	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	165	588	1	ENST00000222270.7:c.4534G>A	p.Asp1512Asn	p.D1512N	ENST00000222270	NM_014727.1	1512	Gac/Aac	19/37	0.261586509874401	3	FACETS	0.987	0.904	1	0.493	0.452	0.537	CLONAL	1	TRUE	1	0.32351887197939	3		589	1201	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910307	50910307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143076166	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	141	604	0	ENST00000440232.2:c.1562G>A	p.Arg521Gln	p.R521Q	ENST00000440232	NM_002691.3	521	cGg/cAg	13/27	0.261586509874401	3	FACETS	0.988	0.899	1	0.494	0.449	0.541	CLONAL	1	TRUE	1	0.32351887197939	3		604	1025	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641478	47641478	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587779189	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	165	674	0	ENST00000233146.2:c.863del	p.Gln288ArgfsTer4	p.Q288Rfs*4	ENST00000233146	NM_000251.2	288	cAg/cg	5/16	1	2	FACETS	0.851	0.78	0.925	0.851	0.78	0.925	CLONAL	1	TRUE	1	0.32351887197939	2		674	1199	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881633	111881633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	106	663	1	ENST00000393256.3:c.311G>A	p.Ser104Asn	p.S104N	ENST00000393256	NM_006538.4	104	aGc/aAc	2/4	1	2	FACETS	0.528	0.472	0.589	0.528	0.472	0.589	SUBCLONAL	1	TRUE	1	0.32351887197939	2		664	1240	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634827	158634827	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	84	327	0	ENST00000263640.3:c.359T>C	p.Phe120Ser	p.F120S	ENST00000263640	NM_001105.4	120	tTc/tCc	5/11	1	2	FACETS	0.815	0.72	0.917	0.815	0.72	0.917	CLONAL	1	TRUE	1	0.32351887197939	2		327	637	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572335	41572335	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745809259	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	55	562	3	ENST00000263253.7:c.4864G>A	p.Asp1622Asn	p.D1622N	ENST00000263253	NM_001429.3	1622	Gat/Aat	30/31	1	2	FACETS	0.392	0.334	0.456	0.392	0.334	0.456	SUBCLONAL	1	TRUE	1	0.32351887197939	2		565	867	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925426	131925429	+	frameshift_variant	Frame_Shift_Del	DEL	TAAG	TAAG	-	rs1272811865	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	80	337	0	ENST00000265335.6:c.1353_1356del	p.Ser451ArgfsTer6	p.S451Rfs*6	ENST00000265335		450	cTAAGt/ct	9/25	1	2	FACETS	0.731	0.643	0.825	0.731	0.643	0.825	SUBCLONAL	1	TRUE	1	0.32351887197939	2		337	677	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469889	157469889	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	62	547	0	ENST00000346085.5:c.2686del	p.Leu896TrpfsTer18	p.L896Wfs*18	ENST00000346085	NM_020732.3	895	Ccc/cc	9/20	1	2	FACETS	0.46	0.396	0.529	0.46	0.396	0.529	SUBCLONAL	1	TRUE	1	0.32351887197939	2		547	834	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55231514	55231514	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs760471492	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	113	436	0	ENST00000275493.2:c.1720C>T	p.Arg574Trp	p.R574W	ENST00000275493	NM_005228.3	574	Cgg/Tgg	14/28	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.32351887197939	2		436	683	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194775	29194775	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	190	717	1	ENST00000240100.2:c.953C>T	p.Ser318Leu	p.S318L	ENST00000240100	NM_001394.6	318	tCg/tTg	4/4	1	2	FACETS	0.931	0.859	1	0.931	0.859	1	CLONAL	1	TRUE	1	0.32351887197939	2		718	1261	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572709	141572709	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	115	430	0	ENST00000220592.5:c.361G>T	p.Gly121Ter	p.G121*	ENST00000220592	NM_012154.3	121	Gga/Tga	4/19	1	2	FACETS	0.95	0.857	1	0.95	0.857	1	CLONAL	1	TRUE	1	0.32351887197939	2		430	748	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737323	145737323	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369843844	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	135	581	1	ENST00000428558.2:c.3364G>A	p.Ala1122Thr	p.A1122T	ENST00000428558	NM_004260.3	1122	Gca/Aca	20/22	1	2	FACETS	0.955	0.868	1	0.955	0.868	1	CLONAL	1	TRUE	1	0.32351887197939	2		582	874	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739827	145739827	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	80	622	0	ENST00000428558.2:c.1703A>C	p.Lys568Thr	p.K568T	ENST00000428558	NM_004260.3	568	aAg/aCg	10/22	1	2	FACETS	0.498	0.437	0.563	0.498	0.437	0.563	SUBCLONAL	1	TRUE	1	0.32351887197939	2		622	994	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971053	21971053	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	69	134	0	ENST00000304494.5:c.305del	p.Ala102GlyfsTer44	p.A102Gfs*44	ENST00000304494	NM_000077.4	102	gCg/gg	2/3	0.32351887197939	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.32351887197939	1		134	245	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250163	110250163	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	100	374	0	ENST00000374672.4:c.512T>C	p.Leu171Pro	p.L171P	ENST00000374672	NM_004235.4	171	cTc/cCc	3/5	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.32351887197939	2		374	525	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401813	139401813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	159	665	0	ENST00000277541.6:c.3587G>A	p.Gly1196Asp	p.G1196D	ENST00000277541	NM_017617.3	1196	gGc/gAc	22/34	1	2	FACETS	0.924	0.846	1	0.924	0.846	1	CLONAL	1	TRUE	1	0.32351887197939	2		665	1064	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913514	NA	P-0017486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	325	433	0	ENST00000288135.5:c.2466T>G	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaG	17/21	0.463639086181997	2	FACETS	0.992	0.939	1	0.496	0.469	0.523	CLONAL	1	TRUE	0	0.682604681287044	2		433	960	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797217	135797217	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	245	437	0	ENST00000298552.3:c.652G>T	p.Glu218Ter	p.E218*	ENST00000298552	NM_001162426.1	218	Gaa/Taa	7/23	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.682604681287044	2		437	669	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573871	18573876	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTAGTT	TTAGTT	-	novel	NA	P-0017486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	152	474	0	ENST00000266497.5:c.2193-2_2196del		p.X731_splice	ENST00000266497		731		15/31	1	2	FACETS	0.43	0.392	0.469	0.43	0.392	0.469	SUBCLONAL	1	TRUE	1	0.682604681287044	2		474	1036	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544634	65544634	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	56	386	0	ENST00000358664.4:c.292C>T	p.Gln98Ter	p.Q98*	ENST00000358664	NM_002382.4	98	Caa/Taa	4/5	0.682604681287044	1	FACETS	0.219	0.188	0.254	0.219	0.188	0.254	SUBCLONAL	1	TRUE	0	0.682604681287044	1		386	493	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843483	3843483	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	302	395	1	ENST00000262367.5:c.1120A>T	p.Asn374Tyr	p.N374Y	ENST00000262367	NM_004380.2	374	Aac/Tac	4/31	0.682604681287044	1	FACETS	0.983	0.936	1	0.983	0.936	1	CLONAL	1	TRUE	0	0.682604681287044	1		396	593	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593624	+	inframe_deletion	In_Frame_Del	DEL	TTGTTGAGGAGATAA	TTGTTGAGGAGATAA	-	novel	NA	P-0017486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	499	393	0	ENST00000288135.5:c.1676_1690del	p.Val559_Asn564delinsAsp	p.V559_N564delinsD	ENST00000288135	NM_000222.2	559	gTTGTTGAGGAGATAAat/gat	11/21	0.463639086181997	2	FACETS	0.818	0.788	0.847	0.818	0.788	0.847	CLONAL	2	TRUE	0	0.682604681287044	2		393	894	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599342	+	missense_variant	Missense_Mutation	TNP	TTA	TTA	ATT	novel	NA	P-0017486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	226	433	0	ENST00000288135.5:c.2466_2468delinsATT	p.Asn822_Tyr823delinsLysPhe	p.N822_Y823delinsKF	ENST00000288135	NM_000222.2	822	aaTTAt/aaATTt	17/21	0.463639086181997	2	FACETS	0.69	0.643	0.738	0.345	0.321	0.369	SUBCLONAL	1	TRUE	0	0.682604681287044	2		433	960	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0017486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	540	1231	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.760411927592211	2	FACETS	0.963	0.937	0.988	0.963	0.937	0.988	CLONAL	2	TRUE	0	0.764272934888537	2		1231	734	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0017486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	103	247	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.764272934888537	1	FACETS	0.963	0.89	1	0.963	0.89	1	CLONAL	1	TRUE	0	0.764272934888537	1		247	173	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0017486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	317	291	0	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	0.755948423537443	3	FACETS	0.934	0.904	0.963	0.934	0.904	0.963	CLONAL	3	TRUE	0	0.764272934888537	3		291	409	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838096	89838096	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1054636249	NA	P-0017486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	210	457	2	ENST00000389301.3:c.2141G>A	p.Arg714Gln	p.R714Q	ENST00000389301	NM_000135.2	714	cGg/cAg	23/43	0.760411927592211	2	FACETS	1	0.963	1	0.519	0.486	0.553	CLONAL	1	TRUE	0	0.764272934888537	2		459	529	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460351	149460351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1318254419	NA	P-0017486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	134	378	2	ENST00000286301.3:c.286G>A	p.Ala96Thr	p.A96T	ENST00000286301	NM_005211.3	96	Gcc/Acc	3/22	0.764272934888537	1	FACETS	0.959	0.895	1	0.959	0.895	1	CLONAL	1	TRUE	0	0.764272934888537	1		380	226	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737400	145737400	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765087683	NA	P-0017486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	444	646	0	ENST00000428558.2:c.3287G>A	p.Arg1096His	p.R1096H	ENST00000428558	NM_004260.3	1096	cGc/cAc	20/22	0.764272934888537	3	FACETS	0.99	0.952	1	0.99	0.952	1	CLONAL	2	TRUE	1	0.764272934888537	3		646	811	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579717	7579717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs922736614	NA	P-0017491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	478	695	0	ENST00000269305.4:c.79C>T	p.Pro27Ser	p.P27S	ENST00000269305	NM_001126112.2	27	Cct/Tct	3/11	0.296879545142469	1	FACETS	1	0.988	1	1	0.998	1	CLONAL	3	TRUE	0	0.26	1		695	1000	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550464	29550464	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs915463951	NA	P-0017491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	77	249	0	ENST00000356175.3:c.1724C>T	p.Ser575Leu	p.S575L	ENST00000356175	NM_000267.3	575	tCa/tTa	16/57	0.251288643794597	1	FACETS	0.865	0.767	0.967	1	0.982	1	CLONAL	2	TRUE	0	0.26	1		249	298	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006021	22006021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747908376	NA	P-0017491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	53	642	0	ENST00000276925.6:c.382G>A	p.Val128Ile	p.V128I	ENST00000276925	NM_004936.3	128	Gtt/Att	2/2	1	2	FACETS	0.391	0.332	0.456	0.391	0.332	0.456	SUBCLONAL	1	TRUE	1	0.26	2		642	1042	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017552-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	407	570	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.328275220241239	3	FACETS	0.912	0.874	0.95	0.912	0.874	0.95	INDETERMINATE	2	TRUE	1	0.752854881190354	3		570	816	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882019	NA	P-0017552-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	289	468	0	ENST00000269305.4:c.455del	p.Pro152ArgfsTer18	p.P152Rfs*18	ENST00000269305	NM_001126112.2	152	cCg/cg	5/11	0.72844676364872	1	FACETS	0.944	0.901	0.987	0.944	0.901	0.987	CLONAL	1	TRUE	0	0.752854881190354	1		468	507	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974760	21974760	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017552-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	185	306	0	ENST00000304494.5:c.67G>C	p.Gly23Arg	p.G23R	ENST00000304494	NM_000077.4	23	Ggt/Cgt	1/3	0.752854881190354	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.752854881190354	1		306	305	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231813	36231813	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017631-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	184	579	0	ENST00000300305.3:c.571A>G	p.Arg191Gly	p.R191G	ENST00000300305		191	Aga/Gga	5/8	1	2	FACETS	0.914	0.845	0.987	0.914	0.845	0.987	CLONAL	1	TRUE	1	0.454191181012825	2		579	886	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	128	570	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	0.87	0.789	0.956			1	INDETERMINATE	1	TRUE	NA	0.353625352497057	2		570	832	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0017660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	201	786	0	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	0.353625352497057	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.353625352497057	1		786	880	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023855	27023855	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	109	314	0	ENST00000324856.7:c.961C>T	p.Gln321Ter	p.Q321*	ENST00000324856	NM_006015.4	321	Cag/Tag	1/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.353625352497057	2		314	550	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971104	21971105	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0017660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	61	263	0	ENST00000304494.5:c.253_254del	p.Ala85CysfsTer34	p.A85Cfs*34	ENST00000304494	NM_000077.4	85	GCt/t	2/3	0.353625352497057	1	FACETS	0.848	0.736	0.968	0.848	0.736	0.968	CLONAL	1	TRUE	0	0.353625352497057	1		263	335	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105793	27105793	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	81	382	1	ENST00000324856.7:c.5404G>T	p.Glu1802Ter	p.E1802*	ENST00000324856	NM_006015.4	1802	Gag/Tag	20/20	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.362771206380482	2		383	440	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144110	55144110	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	94	408	0	ENST00000257290.5:c.1939A>G	p.Ile647Val	p.I647V	ENST00000257290	NM_006206.4	647	Ata/Gta	14/23	1	2	FACETS	0.976	0.871	1	0.976	0.871	1	CLONAL	1	TRUE	1	0.362771206380482	2		408	531	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370856	55370856	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	87	245	0	ENST00000297316.4:c.158G>C	p.Gly53Ala	p.G53A	ENST00000297316	NM_022454.3	53	gGa/gCa	1/2	0.348297957180959	3	FACETS	0.926	0.829	1	0.926	0.829	1	CLONAL	2	TRUE	1	0.362771206380482	3		245	306	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105793	27105793	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017666-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	181	382	1	ENST00000324856.7:c.5404G>T	p.Glu1802Ter	p.E1802*	ENST00000324856	NM_006015.4	1802	Gag/Tag	20/20	1	2	FACETS	0.966	0.892	1	0.966	0.892	1	CLONAL	1	TRUE	1	0.443971515028075	2		383	844	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144110	55144110	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017666-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	165	408	0	ENST00000257290.5:c.1939A>G	p.Ile647Val	p.I647V	ENST00000257290	NM_006206.4	647	Ata/Gta	14/23	1	2	FACETS	0.911	0.837	0.987	0.911	0.837	0.987	CLONAL	1	TRUE	1	0.443971515028075	2		408	816	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370856	55370856	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017666-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	267	245	0	ENST00000297316.4:c.158G>C	p.Gly53Ala	p.G53A	ENST00000297316	NM_022454.3	53	gGa/gCa	1/2	0.283277680092258	3	FACETS	0.82	0.771	0.871	0.82	0.771	0.871	CLONAL	2	TRUE	1	0.443971515028075	3		245	896	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194143	94194143	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017666-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	168	582	0	ENST00000323929.3:c.1285G>T	p.Val429Leu	p.V429L	ENST00000323929	NM_005591.3	429	Gta/Tta	12/20	0.671495540284125	1	FACETS	0.992	0.928	1	0.992	0.928	1	CLONAL	1	TRUE	0	0.671495540284125	1		582	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0017686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	265	664	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.480038296449132	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.480038296449132	1		665	782	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0017686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	110	455	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.81	0.73	0.894	0.81	0.73	0.894	CLONAL	1	TRUE	1	0.480038296449132	2		455	566	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881049	37881049	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766958268	NA	P-0017686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	263	629	1	ENST00000269571.5:c.2378C>T	p.Thr793Met	p.T793M	ENST00000269571		793	aCg/aTg	20/27	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.480038296449132	2		630	930	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63537616	63537616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	46	723	0	ENST00000307078.5:c.1016G>A	p.Arg339His	p.R339H	ENST00000307078	NM_004655.3	339	cGc/cAc	4/11	0.312786683018198	2	FACETS	0.693	0.587	0.808	0.346	0.293	0.404	SUBCLONAL	1	TRUE	0	0.456525832315295	2		723	291	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577138	7577138	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587780075	NA	P-0017795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	126	719	0	ENST00000269305.4:c.800G>C	p.Arg267Pro	p.R267P	ENST00000269305	NM_001126112.2	267	cGg/cCg	8/11	0.294321365227163	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.456525832315295	2		719	261	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416552	49416552	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	74	478	1	ENST00000301067.7:c.16159C>T	p.Gln5387Ter	p.Q5387*	ENST00000301067	NM_003482.3	5387	Cag/Tag	51/54	0.456525832315295	4	FACETS	0.868	0.769	0.972	0.579	0.512	0.648	CLONAL	2	TRUE	1	0.456525832315295	4		479	272	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265075	5265075	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	13	701	1	ENST00000357368.4:c.512A>T	p.Asp171Val	p.D171V	ENST00000357368	NM_002850.3	171	gAc/gTc	5/38	0.362942809003257	3	FACETS	0.315	0.225	0.425	0.158	0.112	0.213	SUBCLONAL	1	TRUE	1	0.456525832315295	3		702	222	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932768	49932768	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	31	877	0	ENST00000296474.3:c.3103G>T	p.Val1035Phe	p.V1035F	ENST00000296474	NM_002447.2	1035	Gtc/Ttc	14/20	0.456525832315295	4	FACETS	0.612	0.496	0.743	0.204	0.165	0.248	SUBCLONAL	1	TRUE	1	0.456525832315295	4		877	323	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413042	63413042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	24	434	0	ENST00000330258.3:c.125C>T	p.Ser42Leu	p.S42L	ENST00000330258	NM_152424.3	42	tCa/tTa	2/2	0.456525832315295	2	FACETS	0.74	0.587	0.912			1	CLONAL	1	TRUE	NA	0.456525832315295	2		434	142	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0017798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	373	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.401089673767527	3	FACETS	1	0.959	1	1	0.996	1	CLONAL	3	FALSE	1	0.401089673767527	3		436	742	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936092	+	missense_variant	Missense_Mutation	DNP	GA	GA	AC	novel	NA	P-0017798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	35	776	2	ENST00000263967.3:c.1633_1634delinsAC	p.Glu545Thr	p.E545T	ENST00000263967	NM_006218.2	545	GAg/ACg	10/21	0.401089673767527	5	FACETS	0.734	0.602	0.881	0.183	0.15	0.221	SUBCLONAL	1	FALSE	1	0.401089673767527	5		778	381	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0017799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	174	401	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.545076338082989	2		401	637	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0017846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	140	626	17	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	NA	2	FACETS	1	0.959	1			1	INDETERMINATE	2	TRUE	NA	0.191631344847272	2		643	674	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0017846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	90	323	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.182958670365422	3	FACETS	0.88	0.782	0.984	0.586	0.521	0.656	CLONAL	2	TRUE	0	0.191631344847272	3		323	585	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39620705	39620705	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	30	212	0	ENST00000262039.4:c.2103G>C	p.Gln701His	p.Q701H	ENST00000262039	NM_002647.2	701	caG/caC	19/25	0.191631344847272	2	FACETS	0.867	0.699	1	0.434	0.349	0.529	CLONAL	1	TRUE	0	0.191631344847272	2		212	361	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970901	21970901	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	55	1092	0	ENST00000304494.5:c.457G>C	p.Asp153His	p.D153H	ENST00000304494	NM_000077.4	153	Gac/Cac	2/3	0.249890387593444	1	FACETS	0.83	0.709	0.963	0.83	0.709	0.963	CLONAL	1	TRUE	0	0.17	1		1092	713	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	129	570	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	0.99	1	CLONAL	2	TRUE	1	0.17	2		570	722	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0017893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	40	663	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.807	0.67	0.961	0.807	0.67	0.961	CLONAL	1	TRUE	1	0.17	2		664	583	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102199	27102199	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0017893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	33	529	0	ENST00000324856.7:c.5124+1G>A		p.X1708_splice	ENST00000324856	NM_006015.4	1708			1	2	FACETS	0.993	0.809	1	0.993	0.809	1	CLONAL	1	TRUE	1	0.17	2		529	391	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625143	69625143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	52	967	0	ENST00000334134.2:c.650C>T	p.Pro217Leu	p.P217L	ENST00000334134	NM_005247.2	217	cCg/cTg	3/3	1	2	FACETS	0.837	0.711	0.975	0.837	0.711	0.975	CLONAL	1	TRUE	1	0.17	2		967	731	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0017923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	408	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.275098015735987	4	FACETS	0.96	0.914	1	0.96	0.914	1	CLONAL	3	TRUE	1	0.275098015735987	4		436	1313	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433917	149433917	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1187766051	NA	P-0017923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	132	717	0	ENST00000286301.3:c.2731C>T	p.Gln911Ter	p.Q911*	ENST00000286301	NM_005211.3	911	Cag/Tag	21/22	0.275098015735987	3	FACETS	0.939	0.85	1	0.469	0.425	0.516	CLONAL	1	TRUE	1	0.275098015735987	3		717	1163	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579579	7579580	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCAAGGG	novel	NA	P-0017923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	176	606	0	ENST00000269305.4:c.100_107dup	p.Ser37ProfsTer10	p.S37Pfs*10	ENST00000269305	NM_001126112.2	36	ccg/ccCCCTTGCCg	4/11	0.274574278305011	2	FACETS	0.751	0.692	0.812	0.751	0.692	0.812	SUBCLONAL	2	TRUE	0	0.275098015735987	2		606	852	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922145	39922145	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	149	311	0	ENST00000378444.4:c.4027G>C	p.Ala1343Pro	p.A1343P	ENST00000378444	NM_001123385.1	1343	Gct/Cct	9/15	1	1	FACETS	0.942	0.867	1	1	0.991	1	CLONAL	2	TRUE	0	0.275098015735987	1		311	496	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0018015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	136	482	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.277338023211851	3	FACETS	1	0.951	1	0.536	0.487	0.589	CLONAL	1	TRUE	1	0.277338023211851	3		482	1041	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882025	NA	P-0018015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	380	672	1	ENST00000269305.4:c.646G>T	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ttg	6/11	0.272352799094474	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.277338023211851	2		673	1314	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212392	36212392	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	156	605	0	ENST00000222270.7:c.2143G>T	p.Val715Phe	p.V715F	ENST00000222270	NM_014727.1	715	Gtt/Ttt	3/37	0.277338023211851	3	FACETS	1	0.933	1	0.512	0.468	0.559	CLONAL	1	TRUE	1	0.277338023211851	3		605	1250	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266072	41266131	+	inframe_deletion	In_Frame_Del	DEL	TCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGC	TCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGC	-	novel	NA	P-0018015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	185	326	0	ENST00000349496.5:c.71_130del	p.His24_Ala43del	p.H24_A43del	ENST00000349496	NM_001904.3	23	agTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCt/agt	3/15	0.277338023211851	3	FACETS	1	0.985	1	0.829	0.769	0.89	CLONAL	2	TRUE	0	0.277338023211851	3		326	611	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884875	134884875	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368240835	NA	P-0018015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	110	429	0	ENST00000398015.3:c.1651G>A	p.Val551Met	p.V551M	ENST00000398015	NM_004441.4	551	Gtg/Atg	8/16	0.277338023211851	3	FACETS	0.973	0.873	1	0.487	0.436	0.54	CLONAL	1	TRUE	1	0.277338023211851	3		429	928	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0018061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	264	455	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.95	0.89	1	1	0.996	1	CLONAL	3	TRUE	1	0.16	2		455	1158	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2215878	2215878	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0018061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1162	103	666	0	ENST00000326181.6:c.82-2A>G		p.X28_splice	ENST00000326181	NM_032271.2	28			1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.16	2		666	1265	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2215884	2215884	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1202	105	682	0	ENST00000326181.6:c.86G>C	p.Arg29Thr	p.R29T	ENST00000326181	NM_032271.2	29	aGa/aCa	3/21	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.16	2		682	1307	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578274	7578288	+	protein_altering_variant,splice_region_variant	In_Frame_Del	DEL	TGAGGAGGGGCCAGA	TGAGGAGGGGCCAGA	CCCTCG	novel	NA	P-0018061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	72	582	4	ENST00000269305.4:c.561_575delinsCGAGGG	p.Leu188_Gln192delinsGluGly	p.L188_Q192delinsEG	ENST00000269305	NM_001126112.2	187	ggTCTGGCCCCTCCTCAg/ggCGAGGGg	6/11	1	2	FACETS	0.937	0.816	1	0.937	0.816	1	CLONAL	1	TRUE	1	0.16	2		586	961	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974762	21974762	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	32	174	0	ENST00000304494.5:c.65G>C	p.Arg22Pro	p.R22P	ENST00000304494	NM_000077.4	22	cGg/cCg	1/3	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.16	2		174	294	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061212	38061232	+	inframe_deletion	In_Frame_Del	DEL	GTAGCAGCCGTTCTCGAACAT	GTAGCAGCCGTTCTCGAACAT	-	novel	NA	P-0018086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	203	348	0	ENST00000250448.2:c.757_777del	p.Met253_Tyr259del	p.M253_Y259del	ENST00000250448	NM_004496.3	253	ATGTTCGAGAACGGCTGCTAC/-	2/2	1	2	FACETS	1	0.95	1	1	0.994	1	CLONAL	2	FALSE	1	0.272003863040839	2		348	727	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376215	15376215	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	99	311	0	ENST00000263377.2:c.799C>G	p.Pro267Ala	p.P267A	ENST00000263377	NM_058243.2	267	Ccc/Gcc	5/20	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	FALSE	1	0.272003863040839	2		311	713	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47613741	47613741	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	250	428	0	ENST00000263735.4:c.934C>T	p.Leu312Phe	p.L312F	ENST00000263735	NM_002354.2	312	Ctc/Ttc	9/9	1	2	FACETS	0.948	0.887	1	1	0.994	1	CLONAL	2	FALSE	1	0.272003863040839	2		428	970	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972859	55972859	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	115	430	0	ENST00000263923.4:c.1531A>T	p.Asn511Tyr	p.N511Y	ENST00000263923	NM_002253.2	511	Aac/Tac	11/30	1	2	FACETS	0.811	0.729	0.898	0.811	0.729	0.898	CLONAL	1	FALSE	1	0.272003863040839	2		430	1043	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163668	32163668	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	63	244	0	ENST00000375023.3:c.5558A>C	p.His1853Pro	p.H1853P	ENST00000375023	NM_004557.3	1853	cAt/cCt	30/30	1	2	FACETS	0.945	0.819	1	0.945	0.819	1	CLONAL	1	FALSE	1	0.272003863040839	2		244	490	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92247415	92247415	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	193	317	0	ENST00000265734.4:c.805A>G	p.Ile269Val	p.I269V	ENST00000265734	NM_001259.6	269	Atc/Gtc	7/8	0.203806875851291	3	FACETS	1	0.97	1			1	CLONAL	2	FALSE	NA	0.272003863040839	3		317	742	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257731	16257732	+	frameshift_variant	Frame_Shift_Ins	INS	CC	CC	TTTGTTTCTG	novel	NA	P-0018086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	204	450	0	ENST00000375759.3:c.4996_4997delinsTTTGTTTCTG	p.Pro1666PhefsTer6	p.P1666Ffs*6	ENST00000375759	NM_015001.2	1666	CCt/TTTGTTTCTGt	11/15	0.272003863040839	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	0	0.272003863040839	1		450	882	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	155	765	7	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	NA	2	FACETS	0.9	0.824	0.98			1	INDETERMINATE	1	TRUE	NA	0.37	2		772	931	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	131	529	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.37	2		529	676	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117799	108117799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202160435	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	93	353	0	ENST00000278616.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000278616	NM_000051.3	337	cGt/cAt	8/63	0.124458364626336	4	FACETS	0.755	0.675	0.84	0.755	0.675	0.84	INDETERMINATE	2	TRUE	2	0.37	4		353	456	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168695	32168695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143103753	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	105	617	0	ENST00000375023.3:c.4228C>T	p.Arg1410Cys	p.R1410C	ENST00000375023	NM_004557.3	1410	Cgc/Tgc	23/30	1	2	FACETS	0.861	0.773	0.955	0.861	0.773	0.955	CLONAL	1	TRUE	1	0.37	2		617	659	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913396	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	54	484	0	ENST00000349496.5:c.95A>G	p.Asp32Gly	p.D32G	ENST00000349496	NM_001904.3	32	gAc/gGc	3/15	1	2	FACETS	0.866	0.744	0.999	0.866	0.744	0.999	CLONAL	1	TRUE	1	0.37	2		484	337	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39647380	39647380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1306170227	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	108	333	1	ENST00000262039.4:c.2552C>T	p.Ser851Leu	p.S851L	ENST00000262039	NM_002647.2	851	tCg/tTg	24/25	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.37	2		334	406	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104375092	104375092	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1305395503	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	125	523	0	ENST00000369902.3:c.1090C>T	p.Arg364Trp	p.R364W	ENST00000369902	NM_016169.3	364	Cgg/Tgg	9/12	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.37	2		523	626	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118821	61118821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146326268	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	45	164	0	ENST00000295025.8:c.14C>T	p.Ala5Val	p.A5V	ENST00000295025	NM_002908.2	5	gCg/gTg	2/11	NA	2	FACETS	0.894	0.757	1			1	INDETERMINATE	1	TRUE	NA	0.37	2		164	272	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399976	139399976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200495793	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	87	648	1	ENST00000277541.6:c.4372G>A	p.Ala1458Thr	p.A1458T	ENST00000277541	NM_017617.3	1458	Gcg/Acg	25/34	1	2	FACETS	0.63	0.557	0.707	0.63	0.557	0.707	SUBCLONAL	1	TRUE	1	0.37	2		649	747	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401080	139401080	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775602958	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	48	528	0	ENST00000277541.6:c.3913G>A	p.Glu1305Lys	p.E1305K	ENST00000277541	NM_017617.3	1305	Gag/Aag	24/34	1	2	FACETS	0.472	0.398	0.553	0.472	0.398	0.553	SUBCLONAL	1	TRUE	1	0.37	2		528	550	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197518	106197518	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1043057789	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	63	351	1	ENST00000380013.4:c.5851C>T	p.Arg1951Trp	p.R1951W	ENST00000380013	NM_001127208.2	1951	Cgg/Tgg	11/11	1	2	FACETS	0.767	0.665	0.877	0.767	0.665	0.877	SUBCLONAL	1	TRUE	1	0.37	2		352	444	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087408	27087408	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	60	630	0	ENST00000324856.7:c.1982T>C	p.Val661Ala	p.V661A	ENST00000324856	NM_006015.4	661	gTg/gCg	5/20	1	2	FACETS	0.453	0.389	0.522	0.453	0.389	0.522	SUBCLONAL	1	TRUE	1	0.37	2		630	716	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439772	51439772	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	74	210	0	ENST00000262662.1:c.337G>C	p.Glu113Gln	p.E113Q	ENST00000262662		113	Gaa/Caa	4/4	1	2	FACETS	0.763	0.677	0.854	1	0.978	1	SUBCLONAL	2	TRUE	1	0.37	2		210	262	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615108	43615108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149891333	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	58	627	1	ENST00000355710.3:c.2522C>T	p.Pro841Leu	p.P841L	ENST00000355710	NM_020975.4	841	cCg/cTg	14/20	0.200771885732113	1	FACETS	0.411	0.353	0.475	0.411	0.353	0.475	INDETERMINATE	1	TRUE	0	0.37	1		628	621	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451416	70451439	+	inframe_deletion	In_Frame_Del	DEL	CAGGCAGCTAATGAAGGTCCAGAA	CAGGCAGCTAATGAAGGTCCAGAA	-	novel	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	102	600	0	ENST00000373644.4:c.6259_6282del	p.Ala2087_Gln2094del	p.A2087_Q2094del	ENST00000373644	NM_030625.2	2086	CAGGCAGCTAATGAAGGTCCAGAA/-	12/12	1	2	FACETS	0.837	0.749	0.929	0.837	0.749	0.929	CLONAL	1	TRUE	1	0.37	2		600	659	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373313	118373313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1335499500	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	144	487	0	ENST00000534358.1:c.6706G>A	p.Ala2236Thr	p.A2236T	ENST00000534358	NM_005933.3	2236	Gct/Act	27/36	0.124458364626336	4	FACETS	0.898	0.822	0.976	0.898	0.822	0.976	INDETERMINATE	2	TRUE	2	0.37	4		487	594	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245709	46245709	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	84	472	0	ENST00000334344.6:c.3803A>G	p.Asn1268Ser	p.N1268S	ENST00000334344	NM_152641.2	1268	aAc/aGc	15/21	1	2	FACETS	0.885	0.784	0.993	0.885	0.784	0.993	CLONAL	1	TRUE	1	0.37	2		472	513	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557762	21557762	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1172808550	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	95	580	3	ENST00000382592.4:c.2083G>A	p.Ala695Thr	p.A695T	ENST00000382592	NM_014572.2	695	Gcc/Acc	5/8	1	2	FACETS	0.854	0.762	0.952	0.854	0.762	0.952	CLONAL	1	TRUE	1	0.37	2		583	601	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896484	28896484	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	66	556	0	ENST00000282397.4:c.2966del	p.Phe989SerfsTer11	p.F989Sfs*11	ENST00000282397	NM_002019.4	989	tTc/tc	22/30	1	2	FACETS	0.646	0.561	0.738	0.646	0.561	0.738	SUBCLONAL	1	TRUE	1	0.37	2		556	552	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643524	38643524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758102077	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	42	588	2	ENST00000299084.4:c.994C>T	p.Arg332Cys	p.R332C	ENST00000299084	NM_152594.2	332	Cgt/Tgt	7/7	1	2	FACETS	0.343	0.286	0.408	0.343	0.286	0.408	SUBCLONAL	1	TRUE	1	0.37	2		590	661	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650720	67650720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	116	563	2	ENST00000264010.4:c.1025G>A	p.Arg342His	p.R342H	ENST00000264010	NM_006565.3	342	cGt/cAt	5/12	1	2	FACETS	0.875	0.789	0.965	0.875	0.789	0.965	CLONAL	1	TRUE	1	0.37	2		565	717	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866342	37866342	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770976272	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	76	303	0	ENST00000269571.5:c.647C>T	p.Thr216Met	p.T216M	ENST00000269571		216	aCg/aTg	6/27	1	2	FACETS	0.927	0.817	1	0.927	0.817	1	CLONAL	1	TRUE	1	0.37	2		303	443	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534428	63534428	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761901627	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	114	638	0	ENST00000307078.5:c.1093G>A	p.Val365Met	p.V365M	ENST00000307078	NM_004655.3	365	Gtg/Atg	5/11	1	2	FACETS	0.936	0.845	1	0.936	0.845	1	CLONAL	1	TRUE	1	0.37	2		638	658	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125341	7125341	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	126	574	0	ENST00000302850.5:c.3211T>C	p.Phe1071Leu	p.F1071L	ENST00000302850	NM_000208.2	1071	Ttc/Ctc	17/22	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.37	2		574	639	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610156	10610156	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	109	632	0	ENST00000171111.5:c.554T>C	p.Ile185Thr	p.I185T	ENST00000171111	NM_203500.1	185	aTc/aCc	2/6	1	2	FACETS	0.938	0.844	1	0.938	0.844	1	CLONAL	1	TRUE	1	0.37	2		632	628	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144509	11144509	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778685	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	76	594	1	ENST00000358026.2:c.3841G>A	p.Val1281Ile	p.V1281I	ENST00000358026	NM_001128849.1	1281	Gtc/Atc	27/36	1	2	FACETS	0.666	0.584	0.754	0.666	0.584	0.754	SUBCLONAL	1	TRUE	1	0.37	2		595	617	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281482	15281482	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	96	352	0	ENST00000263388.2:c.4891G>T	p.Gly1631Trp	p.G1631W	ENST00000263388	NM_000435.2	1631	Ggg/Tgg	26/33	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.37	2		352	471	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945810	17945810	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	36	525	0	ENST00000458235.1:c.2050C>T	p.Leu684Phe	p.L684F	ENST00000458235	NM_000215.3	684	Ctc/Ttc	16/24	1	2	FACETS	0.374	0.306	0.449	0.374	0.306	0.449	SUBCLONAL	1	TRUE	1	0.37	2		525	521	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213980	36213980	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	172	667	0	ENST00000222270.7:c.2806T>C	p.Ser936Pro	p.S936P	ENST00000222270	NM_014727.1	936	Tca/Cca	6/37	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.37	2		667	802	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714640	52714640	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	50	503	0	ENST00000322088.6:c.398A>G	p.Lys133Arg	p.K133R	ENST00000322088	NM_014225.5	133	aAg/aGg	4/15	1	2	FACETS	0.504	0.428	0.588	0.504	0.428	0.588	SUBCLONAL	1	TRUE	1	0.37	2		503	536	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251724	212251724	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770460785	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	58	274	0	ENST00000342788.4:c.3335G>A	p.Arg1112His	p.R1112H	ENST00000342788	NM_005235.2	1112	cGc/cAc	27/28	0.200771885732113	1	FACETS	0.95	0.824	1	0.95	0.824	1	INDETERMINATE	1	TRUE	0	0.37	1		274	269	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058590	47058590	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	40	506	0	ENST00000409792.3:c.7688T>C	p.Leu2563Ser	p.L2563S	ENST00000409792	NM_014159.6	2563	tTa/tCa	21/21	1	2	FACETS	0.371	0.307	0.442	0.371	0.307	0.442	SUBCLONAL	1	TRUE	1	0.37	2		506	583	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383988	84383988	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs35378950	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	88	539	3	ENST00000321945.7:c.864del	p.Pro289GlnfsTer13	p.P289Qfs*13	ENST00000321945	NM_139076.2	288	ttT/tt	9/9	1	2	FACETS	0.714	0.633	0.801	0.714	0.633	0.801	SUBCLONAL	1	TRUE	1	0.37	2		542	666	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540904	187540904	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	20	313	0	ENST00000441802.2:c.6836A>G	p.Asn2279Ser	p.N2279S	ENST00000441802	NM_005245.3	2279	aAc/aGc	10/27	1	2	FACETS	0.288	0.22	0.369	0.288	0.22	0.369	SUBCLONAL	1	TRUE	1	0.37	2		313	375	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499653	149499653	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	89	502	0	ENST00000261799.4:c.2620A>C	p.Ser874Arg	p.S874R	ENST00000261799	NM_002609.3	874	Agc/Cgc	19/23	1	2	FACETS	0.87	0.773	0.973	0.87	0.773	0.973	CLONAL	1	TRUE	1	0.37	2		502	553	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908131	41908131	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762395134	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	71	499	2	ENST00000372991.4:c.391G>A	p.Ala131Thr	p.A131T	ENST00000372991	NM_001760.3	131	Gct/Act	2/5	1	2	FACETS	0.633	0.553	0.72	0.633	0.553	0.72	SUBCLONAL	1	TRUE	1	0.37	2		501	606	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864310	151864310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773186070	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	63	408	1	ENST00000262189.6:c.9671G>A	p.Arg3224His	p.R3224H	ENST00000262189	NM_170606.2	3224	cGt/cAt	42/59	1	2	FACETS	0.645	0.558	0.739	0.645	0.558	0.739	SUBCLONAL	1	TRUE	1	0.37	2		409	528	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538751	23538751	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	23	249	0	ENST00000380871.4:c.688A>G	p.Ser230Gly	p.S230G	ENST00000380871	NM_006167.3	230	Agc/Ggc	2/2	1	2	FACETS	0.372	0.29	0.467	0.372	0.29	0.467	SUBCLONAL	1	TRUE	1	0.37	2		249	334	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572580	141572580	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1232302381	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	111	442	2	ENST00000220592.5:c.490G>A	p.Val164Met	p.V164M	ENST00000220592	NM_012154.3	164	Gtg/Atg	4/19	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.37	2		444	530	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359969	87359969	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	63	350	0	ENST00000277120.3:c.1277C>A	p.Thr426Asn	p.T426N	ENST00000277120		426	aCc/aAc	11/19	1	2	FACETS	0.785	0.681	0.897	0.785	0.681	0.897	SUBCLONAL	1	TRUE	1	0.37	2		350	434	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309037	137309037	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs537231520	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	169	699	0	ENST00000481739.1:c.644G>A	p.Arg215Gln	p.R215Q	ENST00000481739	NM_002957.4	215	cGg/cAg	5/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.37	2		699	834	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53254069	53254069	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0018147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	40	199	0	ENST00000375401.3:c.3G>A	p.Met1?	p.M1?	ENST00000375401	NM_004187.3	1	atG/atA	1/26	0.3	2	FACETS	0.851	0.712	1			1	CLONAL	1	TRUE	NA	0.37	2		199	254	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631102	69631102	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121917704	NA	P-0018149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	41	588	1	ENST00000334134.2:c.310C>T	p.Arg104Ter	p.R104*	ENST00000334134	NM_005247.2	104	Cga/Tga	2/3	1	2	FACETS	0.771	0.644	0.911	0.771	0.644	0.911	CLONAL	1	TRUE	1	0.312681623984183	2		589	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0018322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	24	652	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.185925886713429	2	FACETS	1	0.874	1	0.571	0.455	0.701	INDETERMINATE	1	TRUE	0	0.350271286097107	2		652	120	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218912	133218912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1011938171	NA	P-0018322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	16	526	2	ENST00000320574.5:c.5024G>A	p.Arg1675His	p.R1675H	ENST00000320574	NM_006231.2	1675	cGc/cAc	38/49	0.167996734455123	3	FACETS	0.405	0.299	0.532	0.135	0.099	0.178	INDETERMINATE	1	TRUE	0	0.350271286097107	3		528	265	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044886	47044889	+	frameshift_variant	Frame_Shift_Del	DEL	AGTG	AGTG	-	rs1131691421	NA	P-0018322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	94	286	0	ENST00000377604.3:c.2214_2217del	p.Ser738ArgfsTer63	p.S738Rfs*63	ENST00000377604	NM_001204468.1	738	AGTGag/ag	20/24	0.318215558475172	2	FACETS	0.998	0.901	1			1	CLONAL	2	TRUE	NA	0.350271286097107	2		286	269	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053258	180053258	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	36	569	0	ENST00000261937.6:c.1111G>C	p.Asp371His	p.D371H	ENST00000261937	NM_182925.4	371	Gat/Cat	9/30	0.36919323983459	3	FACETS	0.579	0.476	0.695	0.29	0.238	0.348	SUBCLONAL	1	TRUE	1	0.350271286097107	3		569	417	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978583	70978583	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	18	540	0	ENST00000276594.2:c.1070A>G	p.His357Arg	p.H357R	ENST00000276594	NM_024504.3	357	cAt/cGt	5/8	0.36919323983459	3	FACETS	0.598	0.452	0.769	0.299	0.226	0.385	SUBCLONAL	1	TRUE	1	0.350271286097107	3		540	202	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851285	156851285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778520978	NA	P-0018439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	49	419	2	ENST00000524377.1:c.2242C>T	p.Arg748Trp	p.R748W	ENST00000524377	NM_002529.3	748	Cgg/Tgg	17/17	0.607326041460072	2	FACETS	0.232	0.196	0.272	0.116	0.098	0.136	SUBCLONAL	1	TRUE	0	0.633367557058933	2		421	667	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877330	40877330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750253646	NA	P-0018439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	101	252	0	ENST00000373198.4:c.2366G>A	p.Arg789Lys	p.R789K	ENST00000373198	NM_133170.3	789	aGg/aAg	15/32	1	2	FACETS	0.709	0.637	0.784	0.709	0.637	0.784	SUBCLONAL	1	TRUE	1	0.633367557058933	2		252	450	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120509018	120509018	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	50	445	1	ENST00000256646.2:c.1548C>A	p.Phe516Leu	p.F516L	ENST00000256646	NM_024408.3	516	ttC/ttA	9/34	0.633367557058933	1	FACETS	0.158	0.134	0.185	0.158	0.134	0.185	SUBCLONAL	1	TRUE	0	0.633367557058933	1		446	682	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479828	67479828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	216	361	0	ENST00000327367.4:c.1135G>A	p.Gly379Ser	p.G379S	ENST00000327367	NM_005902.3	379	Ggc/Agc	8/9	0.633367557058933	1	FACETS	0.967	0.909	1	0.967	0.909	1	CLONAL	1	TRUE	0	0.633367557058933	1		361	482	SUCCESS
BLM	641	MSKCC	GRCh37	15	91298016	91298049	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCTTAACATTTTTTTTATTTGCAGTACGTTAAA	GGCTTAACATTTTTTTTATTTGCAGTACGTTAAA	-	novel	NA	P-0018439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	38	182	0	ENST00000355112.3:c.960-23_970del		p.X320_splice	ENST00000355112	NM_000057.2	320		5/22	0.633367557058933	1	FACETS	0.201	0.166	0.241	0.201	0.166	0.241	SUBCLONAL	1	TRUE	0	0.633367557058933	1		182	407	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40869996	40869996	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	173	371	1	ENST00000428826.2:c.1021C>A	p.Leu341Met	p.L341M	ENST00000428826		341	Ctg/Atg	10/21	0.633367557058933	1	FACETS	0.508	0.468	0.549	0.508	0.468	0.549	SUBCLONAL	1	TRUE	0	0.633367557058933	1		372	735	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526171	63526171	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	59	520	0	ENST00000307078.5:c.2455G>T	p.Glu819Ter	p.E819*	ENST00000307078	NM_004655.3	819	Gag/Tag	11/11	0.633367557058933	1	FACETS	0.152	0.13	0.176	0.152	0.13	0.176	SUBCLONAL	1	TRUE	0	0.633367557058933	1		520	837	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273627	18273816	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGGTGGAGGTTGCAGTGAGCCGAAATCGCACCACTGCACTGCAGCCTGGACAACAGAGCAGCAAGACTCTGTCTCAAAAAAAAAGGGGACAGGGATTGAGGGTCAGGTGCGGGGTCCCACTGGGTGCCGACACCCCTCTCCTCCCCCAGGAAAGGCGGGAACAATAAGCTGATCAAGGTCTTCCACCGA	GAGGTGGAGGTTGCAGTGAGCCGAAATCGCACCACTGCACTGCAGCCTGGACAACAGAGCAGCAAGACTCTGTCTCAAAAAAAAAGGGGACAGGGATTGAGGGTCAGGTGCGGGGTCCCACTGGGTGCCGACACCCCTCTCCTCCCCCAGGAAAGGCGGGAACAATAAGCTGATCAAGGTCTTCCACCGA	-	novel	NA	P-0018439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	24	26	0	ENST00000222254.8:c.1110-148_1151del		p.X370_splice	ENST00000222254	NM_005027.3	370		10/16	0.633367557058933	1	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	0	0.633367557058933	1		26	50	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156004	106156004	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	234	319	0	ENST00000380013.4:c.905A>G	p.Asp302Gly	p.D302G	ENST00000380013	NM_001127208.2	302	gAt/gGt	3/11	0.633367557058933	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.633367557058933	1		319	453	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853298	151853298	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	82	278	0	ENST00000262189.6:c.11804G>T	p.Ser3935Ile	p.S3935I	ENST00000262189	NM_170606.2	3935	aGc/aTc	45/59	0.633367557058933	1	FACETS	0.457	0.405	0.512	0.457	0.405	0.512	SUBCLONAL	1	TRUE	0	0.633367557058933	1		278	387	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018441-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	46	188	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.535826948341959	2		188	156	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813023	89813023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142833057	NA	P-0018441-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	150	486	0	ENST00000389301.3:c.3482C>T	p.Thr1161Met	p.T1161M	ENST00000389301	NM_000135.2	1161	aCg/aTg	35/43	1	2	FACETS	0.93	0.854	1	0.93	0.854	1	CLONAL	1	TRUE	1	0.535826948341959	2		486	602	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508260	106508260	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018441-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	37	232	1	ENST00000359195.3:c.254C>T	p.Ala85Val	p.A85V	ENST00000359195	NM_002649.2	85	gCg/gTg	2/11	0.475559766961068	3	FACETS	0.736	0.611	0.873	0.368	0.305	0.437	SUBCLONAL	1	TRUE	1	0.535826948341959	3		233	238	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39239348	39239348	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018441-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	175	464	0	ENST00000402219.2:c.2309A>G	p.His770Arg	p.H770R	ENST00000402219	NM_005633.3	770	cAc/cGc	14/23	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.535826948341959	2		464	605	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	226	570	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.270693056829817	3	FACETS	0.926	0.863	0.992	0.926	0.863	0.992	CLONAL	2	TRUE	1	0.28169070624837	3		570	988	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0018540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	121	346	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.864	0.78	0.954	0.864	0.78	0.954	CLONAL	1	TRUE	1	0.28169070624837	2		346	994	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243480	41243483	+	frameshift_variant	Frame_Shift_Del	DEL	TTGA	TTGA	-	rs80357508	NA	P-0018550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	210	680	1	ENST00000357654.3:c.4065_4068del	p.Asn1355LysfsTer10	p.N1355Kfs*10	ENST00000357654	NM_007294.3	1355	aaTCAA/aa	10/23	0.539275670139557	2	FACETS	0.809	0.76	0.859	0.809	0.76	0.859	CLONAL	2	TRUE	0	0.546432640593725	2		681	475	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577144	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs879253942	NA	P-0018550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	170	637	0	ENST00000269305.4:c.794T>C	p.Leu265Pro	p.L265P	ENST00000269305	NM_001126112.2	265	cTg/cCg	8/11	0.546432640593725	1	FACETS	0.912	0.845	0.98	0.912	0.845	0.98	CLONAL	1	TRUE	0	0.546432640593725	1		637	496	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023366	27023366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	97	433	0	ENST00000324856.7:c.472C>A	p.Pro158Thr	p.P158T	ENST00000324856	NM_006015.4	158	Ccg/Acg	1/20	0.532951210711269	2	FACETS	1	0.91	1	0.506	0.455	0.559	CLONAL	1	TRUE	0	0.546432640593725	2		433	351	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595795	52595795	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	112	455	0	ENST00000394830.3:c.4120G>A	p.Ala1374Thr	p.A1374T	ENST00000394830	NM_018313.4	1374	Gca/Aca	26/30	1	2	FACETS	0.893	0.808	0.982	0.893	0.808	0.982	CLONAL	1	TRUE	1	0.546432640593725	2		455	459	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795103	242795104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs768249210	NA	P-0018865-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	264	997	0	ENST00000334409.5:c.105dup	p.Thr36HisfsTer70	p.T36Hfs*70	ENST00000334409	NM_005018.2	35	-/C	2/5	0.370664915163746	3	FACETS	0.876	0.822	0.931	0.876	0.822	0.931	CLONAL	2	TRUE	1	0.374214264923415	3		997	956	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0018865-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	294	1075	0	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	0.128916700045371	3	FACETS	1	0.99	1	0.798	0.755	0.842	INDETERMINATE	2	TRUE	0	0.374214264923415	3		1075	779	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944755	71944755	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018865-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	351	1197	0	ENST00000298229.2:c.2179G>T	p.Val727Phe	p.V727F	ENST00000298229	NM_001567.3	727	Gtt/Ttt	19/28	0.284585341753812	4	FACETS	0.913	0.863	0.964	0.913	0.863	0.964	CLONAL	2	TRUE	2	0.374214264923415	4		1197	1412	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715624	30715624	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397516838	NA	P-0018865-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	81	399	0	ENST00000295754.5:c.1282G>C	p.Glu428Gln	p.E428Q	ENST00000295754	NM_003242.5	428	Gaa/Caa	5/7	0.153562170736476	4	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.374214264923415	4		399	518	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73113284	73113284	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs944326202	NA	P-0018865-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	47	422	0	ENST00000356692.5:c.625G>A	p.Glu209Lys	p.E209K	ENST00000356692		209	Gag/Aag	7/9	0.232031935584749	3	FACETS	0.994	0.844	1			1	CLONAL	1	TRUE	NA	0.374214264923415	3		422	300	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664876	138664876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018865-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	47	170	0	ENST00000330315.3:c.689C>T	p.Ala230Val	p.A230V	ENST00000330315	NM_023067.3	230	gCg/gTg	1/1	0.374214264923415	5	FACETS	0.961	0.821	1	0.641	0.547	0.741	CLONAL	2	TRUE	2	0.374214264923415	5		170	204	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913658	32913662	+	frameshift_variant	Frame_Shift_Del	DEL	TACTA	TACTA	-	novel	NA	P-0018865-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	62	392	0	ENST00000380152.3:c.5168_5172del	p.Thr1723SerfsTer2	p.T1723Sfs*2	ENST00000380152		1722	agTACTAta/agta	11/27	0.37151892153989	2	FACETS	0.947	0.822	1	0.473	0.411	0.54	CLONAL	1	TRUE	0	0.374214264923415	2		392	350	SUCCESS
APC	324	MSKCC	GRCh37	5	112177531	112177531	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018865-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	135	403	0	ENST00000257430.4:c.6240G>C	p.Leu2080Phe	p.L2080F	ENST00000257430	NM_000038.5	2080	ttG/ttC	16/16	0.359735708248777	3	FACETS	0.969	0.888	1	0.969	0.888	1	CLONAL	2	TRUE	1	0.374214264923415	3		403	442	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139818405	139818405	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018865-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	135	644	0	ENST00000247668.2:c.1240A>C	p.Met414Leu	p.M414L	ENST00000247668	NM_021138.3	414	Atg/Ctg	10/11	0.359735708248777	3	FACETS	0.877	0.796	0.962	0.438	0.398	0.481	CLONAL	1	TRUE	1	0.374214264923415	3		644	977	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864328	57864328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201538749	NA	P-0018870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	353	796	0	ENST00000228682.2:c.1805C>T	p.Ser602Leu	p.S602L	ENST00000228682	NM_005269.2	602	tCg/tTg	12/12	0.542676672329349	4	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	2	0.583390475548575	4		796	957	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662633	227662633	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	106	597	0	ENST00000305123.5:c.822del	p.Asn275ThrfsTer25	p.N275Tfs*25	ENST00000305123	NM_005544.2	274	tcC/tc	1/2	0.583390475548575	3	FACETS	0.825	0.742	0.913	0.412	0.371	0.457	CLONAL	1	TRUE	1	0.583390475548575	3		597	569	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097282	178097282	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	67	592	0	ENST00000397062.3:c.432del	p.Pro145LeufsTer28	p.P145Lfs*28	ENST00000397062	NM_006164.4	144	gtT/gt	4/5	0.231131868026615	3	FACETS	0.791	0.687	0.905	0.396	0.343	0.453	CLONAL	1	TRUE	1	0.272939786860416	3		592	705	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458150	120458150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752104735	NA	P-0018927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	57	554	0	ENST00000256646.2:c.7195G>A	p.Glu2399Lys	p.E2399K	ENST00000256646	NM_024408.3	2399	Gag/Aag	34/34	0.154673755179162	4	FACETS	0.955	0.819	1	0.477	0.409	0.551	INDETERMINATE	1	TRUE	2	0.272939786860416	4		554	557	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112559	115112559	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs769533777	NA	P-0018927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	67	754	0	ENST00000257566.3:c.1181A>C	p.Lys394Thr	p.K394T	ENST00000257566	NM_016569.3	394	aAg/aCg	7/8	0.192840414867703	4	FACETS	0.783	0.679	0.896	0.392	0.339	0.448	SUBCLONAL	1	TRUE	2	0.272939786860416	4		754	798	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90634844	90634844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201999104	NA	P-0018927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	165	785	0	ENST00000330062.3:c.148G>A	p.Val50Met	p.V50M	ENST00000330062	NM_002168.2	50	Gtg/Atg	2/11	1	2	FACETS	0.853	0.785	0.923	1	0.991	1	CLONAL	2	TRUE	1	0.272939786860416	2		785	709	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732617	190732617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375020232	NA	P-0018927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	69	721	0	ENST00000441310.2:c.2435G>A	p.Arg812His	p.R812H	ENST00000441310	NM_000534.4	812	cGt/cAt	11/13	0.231131868026615	3	FACETS	0.839	0.73	0.957	0.419	0.365	0.479	CLONAL	1	TRUE	1	0.272939786860416	3		721	685	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274568	198274568	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	69	551	0	ENST00000335508.6:c.830C>G	p.Ala277Gly	p.A277G	ENST00000335508	NM_012433.2	277	gCg/gGg	7/25	0.231131868026615	3	FACETS	0.951	0.829	1	0.476	0.414	0.542	CLONAL	1	TRUE	1	0.272939786860416	3		551	604	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143044500	143044500	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	48	609	0	ENST00000262992.4:c.1962G>C	p.Gln654His	p.Q654H	ENST00000262992	NM_001101669.1	654	caG/caC	18/24	0.181178406186154	2	FACETS	0.597	0.504	0.7	0.299	0.252	0.35	SUBCLONAL	1	TRUE	0	0.272939786860416	2		609	589	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334980	81334980	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	140	769	0	ENST00000222390.5:c.1847G>T	p.Gly616Val	p.G616V	ENST00000222390	NM_000601.4	616	gGc/gTc	16/18	0.154673755179162	4	FACETS	0.885	0.807	0.966	0.885	0.807	0.966	INDETERMINATE	2	TRUE	2	0.272939786860416	4		769	738	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745588	162745588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754868982	NA	P-0018927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	102	458	0	ENST00000367921.3:c.2003G>A	p.Arg668His	p.R668H	ENST00000367921	NM_006182.2	668	cGc/cAc	15/18	0.401201503363053	3	FACETS	0.579	0.517	0.645	0.289	0.258	0.323	SUBCLONAL	1	TRUE	1	0.489911666960047	3		458	896	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097282	178097282	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	155	592	0	ENST00000397062.3:c.432del	p.Pro145LeufsTer28	p.P145Lfs*28	ENST00000397062	NM_006164.4	144	gtT/gt	4/5	0.297955243811638	1	FACETS	0.684	0.627	0.742	0.684	0.627	0.742	SUBCLONAL	1	TRUE	0	0.489911666960047	1		592	699	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435463	18435463	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	16	195	0	ENST00000266497.5:c.448A>G	p.Ser150Gly	p.S150G	ENST00000266497		150	Agt/Ggt	1/31	0.152609438973482	1	FACETS	0.19	0.14	0.249	0.19	0.14	0.249	INDETERMINATE	1	TRUE	0	0.489911666960047	1		195	260	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346505	89346505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024078594	NA	P-0018927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	117	619	0	ENST00000301030.4:c.6445G>A	p.Ala2149Thr	p.A2149T	ENST00000301030	NM_001256183.1	2149	Gca/Aca	9/13	0.300134381351918	2	FACETS	0.484	0.436	0.536	0.242	0.218	0.268	SUBCLONAL	1	TRUE	0	0.489911666960047	2		619	986	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79966104	79966104	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0018927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	121	435	0	ENST00000265081.6:c.768T>A	p.Tyr256Ter	p.Y256*	ENST00000265081	NM_002439.4	256	taT/taA	4/24	0.296159910511074	2	FACETS	0.566	0.511	0.624	0.283	0.255	0.312	SUBCLONAL	1	TRUE	0	0.489911666960047	2		435	873	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	83	478	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.325570102837088	2		478	498	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863559	68863560	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	122	792	0	ENST00000261769.5:c.2301dup	p.Asp768Ter	p.D768*	ENST00000261769	NM_004360.3	766	-/T	15/16	0.325570102837088	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.325570102837088	1		792	536	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155737	56155738	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	82	478	0	ENST00000399503.3:c.830dup	p.Pro278AlafsTer23	p.P278Afs*23	ENST00000399503	NM_005921.1	277	gtg/gTtg	3/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.325570102837088	2		478	380	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180518	56180518	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	44	509	0	ENST00000399503.3:c.3847del	p.Glu1283SerfsTer5	p.E1283Sfs*5	ENST00000399503	NM_005921.1	1283	Gag/ag	16/20	1	2	FACETS	0.711	0.598	0.836	0.711	0.598	0.836	SUBCLONAL	1	TRUE	1	0.325570102837088	2		509	380	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845415	151845415	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	107	822	1	ENST00000262189.6:c.13597C>T	p.Arg4533Ter	p.R4533*	ENST00000262189	NM_170606.2	4533	Cga/Tga	52/59	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.325570102837088	2		823	651	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019167-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	82	478	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.828	0.73	0.933	0.828	0.73	0.933	CLONAL	1	TRUE	1	0.287929942902759	2		478	688	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863559	68863560	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019167-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	116	792	0	ENST00000261769.5:c.2301dup	p.Asp768Ter	p.D768*	ENST00000261769	NM_004360.3	766	-/T	15/16	0.287929942902759	1	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	0	0.287929942902759	1		792	684	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155737	56155738	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019167-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	120	478	0	ENST00000399503.3:c.830dup	p.Pro278AlafsTer23	p.P278Afs*23	ENST00000399503	NM_005921.1	277	gtg/gTtg	3/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.287929942902759	2		478	729	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180518	56180518	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019167-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	101	509	0	ENST00000399503.3:c.3847del	p.Glu1283SerfsTer5	p.E1283Sfs*5	ENST00000399503	NM_005921.1	1283	Gag/ag	16/20	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.287929942902759	2		509	646	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845415	151845415	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019167-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	121	822	1	ENST00000262189.6:c.13597C>T	p.Arg4533Ter	p.R4533*	ENST00000262189	NM_170606.2	4533	Cga/Tga	52/59	1	2	FACETS	0.983	0.888	1	0.983	0.888	1	CLONAL	1	TRUE	1	0.287929942902759	2		823	855	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100919	27100919	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019167-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	55	505	0	ENST00000324856.7:c.4201C>T	p.Gln1401Ter	p.Q1401*	ENST00000324856	NM_006015.4	1401	Cag/Tag	18/20	1	2	FACETS	0.524	0.447	0.608	0.524	0.447	0.608	SUBCLONAL	1	TRUE	1	0.287929942902759	2		505	729	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	246	478	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.495292748564705	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.495292748564705	3		478	608	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673738	37673738	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	155	762	0	ENST00000447079.4:c.2892C>G	p.Ile964Met	p.I964M	ENST00000447079	NM_015083.1	964	atC/atG	10/14	0.13836424052195	6	FACETS	1	0.953	1			1	INDETERMINATE	1	TRUE	NA	0.495292748564705	6		762	1171	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646254	23646256	+	missense_variant	Missense_Mutation	TNP	ATC	ATC	TTG	novel	NA	P-0019349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	128	785	0	ENST00000261584.4:c.1611_1613delinsCAA	p.Ile538Asn	p.I538N	ENST00000261584	NM_024675.3	537	tcGATt/tcCAAt	4/13	1	2	FACETS	0.609	0.551	0.669	0.609	0.551	0.669	SUBCLONAL	1	TRUE	1	0.495292748564705	2		785	849	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	72	570	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.191322874242323	3	FACETS	0.916	0.799	1	0.458	0.399	0.522	CLONAL	1	FALSE	1	0.205619693232718	3		570	843	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422700	49422700	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	85	634	0	ENST00000301067.7:c.14293G>T	p.Val4765Phe	p.V4765F	ENST00000301067	NM_003482.3	4765	Gtc/Ttc	45/54	1	2	FACETS	0.914	0.806	1	0.914	0.806	1	CLONAL	1	FALSE	1	0.205619693232718	2		634	905	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68292215	68292219	+	frameshift_variant	Frame_Shift_Del	DEL	AGGTG	AGGTG	GTTA	novel	NA	P-0019384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	43	404	0	ENST00000487270.1:c.119_123delinsGTTA	p.Lys40SerfsTer2	p.K40Sfs*2	ENST00000487270	NM_133509.3	40	aAGGTG/aGTTA	3/11	1	2	FACETS	0.676	0.564	0.799	0.676	0.564	0.799	SUBCLONAL	1	FALSE	1	0.205619693232718	2		404	619	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120341	70120341	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1636	177	1320	0	ENST00000245479.2:c.1343C>A	p.Ser448Tyr	p.S448Y	ENST00000245479	NM_000346.3	448	tCc/tAc	3/3	0.205619693232718	3	FACETS	1	0.949	1	0.524	0.48	0.569	CLONAL	1	FALSE	1	0.205619693232718	3		1320	1813	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17389754	17389754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs999462407	NA	P-0019384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1179	128	914	3	ENST00000359435.4:c.887C>T	p.Ala296Val	p.A296V	ENST00000359435	NM_001033549.1	296	gCg/gTg	9/9	1	2	FACETS	0.953	0.861	1	0.953	0.861	1	CLONAL	1	FALSE	1	0.205619693232718	2		917	1307	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981858	70981858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	104	848	2	ENST00000276594.2:c.238C>T	p.Pro80Ser	p.P80S	ENST00000276594	NM_024504.3	80	Ccg/Tcg	2/8	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.205619693232718	NA		850	1084	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044278	47044778	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGAAAGGTGGTCAGGAGCCGTAGCCCAGAGGCCAGATGAAGCCTTCTGCAGTGGTTCGGACTAGGGATAGTGGCTGGCCCGTGTTTGAGGATGCAGGGCAGTGGGTCAGCAGATAGAGTTAGTAGCCCCAGGGTCATGAGGGTTCTGGGAACCTCACCTCCACCCTCACCCCCAGATTGCCAAGGACATGGAACGCTGGGCCCGCAGTCTCAACAAACAAAAAGAAAACTTCAAAAATAGCTTCCAGCCTATCAGCTCCCTGCGAGATGACGAGAGGCGGGAGTCAGCCACTGCAGATGCTGGCTATGCCATCCTCGAGAAGAAGGTGTGTTGGGGCCACCCCCCTGCACCCTGCCCCACAATCTTGTCCTTCCTTTGGGCCCTCTGTGGAGTCCCTGAATTTCTGTGTCCCTCCACCCCAGGGAGCACTAGCCGAGAGACAGCACACCAGCATGGATCTCCCGAAATTGGCCAGTGACGACCGCCCAGTGAGTGCCCAA	GGGAAAGGTGGTCAGGAGCCGTAGCCCAGAGGCCAGATGAAGCCTTCTGCAGTGGTTCGGACTAGGGATAGTGGCTGGCCCGTGTTTGAGGATGCAGGGCAGTGGGTCAGCAGATAGAGTTAGTAGCCCCAGGGTCATGAGGGTTCTGGGAACCTCACCTCCACCCTCACCCCCAGATTGCCAAGGACATGGAACGCTGGGCCCGCAGTCTCAACAAACAAAAAGAAAACTTCAAAAATAGCTTCCAGCCTATCAGCTCCCTGCGAGATGACGAGAGGCGGGAGTCAGCCACTGCAGATGCTGGCTATGCCATCCTCGAGAAGAAGGTGTGTTGGGGCCACCCCCCTGCACCCTGCCCCACAATCTTGTCCTTCCTTTGGGCCCTCTGTGGAGTCCCTGAATTTCTGTGTCCCTCCACCCCAGGGAGCACTAGCCGAGAGACAGCACACCAGCATGGATCTCCCGAAATTGGCCAGTGACGACCGCCCAGTGAGTGCCCAA	-	novel	NA	P-0019384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	37	63	0	ENST00000377604.3:c.1951-174_2166+14del		p.X651_splice	ENST00000377604	NM_001204468.1	651		18-19/24	0.205619693232718	1	FACETS	0.997	0.844	1	1	0.975	1	CLONAL	3	FALSE	0	0.205619693232718	1		63	108	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	86	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.2	2		436	735	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0019427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	68	880	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.738	0.64	0.844	0.738	0.64	0.844	SUBCLONAL	1	TRUE	1	0.2	2		880	922	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699447	117699454	+	frameshift_variant	Frame_Shift_Del	DEL	GAAAGTTT	GAAAGTTT	-	novel	NA	P-0019427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	48	570	0	ENST00000369458.3:c.187_194del	p.Lys63Ter	p.K63*	ENST00000369458	NM_024626.3	63	AAACTTTCt/t	3/6	1	2	FACETS	0.665	0.561	0.78	0.665	0.561	0.78	SUBCLONAL	1	TRUE	1	0.2	2		570	722	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497572	125497572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768467449	NA	P-0019427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	51	493	0	ENST00000428830.2:c.136G>A	p.Val46Ile	p.V46I	ENST00000428830	NM_001114121.2	46	Gta/Ata	3/14	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.2	2		493	495	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750560	128750560	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	92	768	1	ENST00000377970.2:c.97T>A	p.Ser33Thr	p.S33T	ENST00000377970	NM_002467.4	33	Tcg/Acg	2/3	1	2	FACETS	0.969	0.86	1	0.969	0.86	1	CLONAL	1	TRUE	1	0.2	2		769	949	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858351	9858351	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	118	538	0	ENST00000330684.3:c.3050C>A	p.Ser1017Tyr	p.S1017Y	ENST00000330684	NM_001134407.1	1017	tCc/tAc	13/13	NA	2	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.519039912246912	2		538	425	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78765275	78765276	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTG	novel	NA	P-0019462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	117	595	0	ENST00000306801.3:c.857_858insTGT	p.Val287dup	p.V287dup	ENST00000306801	NM_020761.2	287	ctg/cTTGtg	7/34	0.518249048238954	3	FACETS	0.976	0.883	1	0.488	0.441	0.537	CLONAL	1	TRUE	1	0.519039912246912	3		595	582	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280088	18280088	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1239460949	NA	P-0019462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	87	236	0	ENST00000222254.8:c.2171C>T	p.Pro724Leu	p.P724L	ENST00000222254	NM_005027.3	724	cCg/cTg	16/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.519039912246912	2		236	251	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573003	41573003	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	263	1027	1	ENST00000263253.7:c.5288G>A	p.Arg1763Gln	p.R1763Q	ENST00000263253	NM_001429.3	1763	cGg/cAg	31/31	0.519039912246912	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.519039912246912	1		1028	643	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170816861	170817121	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTATAGTCTTTTATGGGTGTCTGTAGAGGTTTCTGTTCAAGAAATCTAGGAATTGATCATTCTGCTTTGCCCTCTGGTAGCTAAAATAGTGAAAAACTAGTTCAAAAGTTAGACCTGACCTTTTTGGTTACCCACACTTAAGTTTCAGTGTTATTTTTCTCCTTGTTAGAGTTGCTTTTTTCTTCATTTACAGGTTGTGAACTAAAGGCCGACAAAGATTATCACTTTAAGGTGGATAATGATGAAAATGAGCACCAGTT	ATTATAGTCTTTTATGGGTGTCTGTAGAGGTTTCTGTTCAAGAAATCTAGGAATTGATCATTCTGCTTTGCCCTCTGGTAGCTAAAATAGTGAAAAACTAGTTCAAAAGTTAGACCTGACCTTTTTGGTTACCCACACTTAAGTTTCAGTGTTATTTTTCTCCTTGTTAGAGTTGCTTTTTTCTTCATTTACAGGTTGTGAACTAAAGGCCGACAAAGATTATCACTTTAAGGTGGATAATGATGAAAATGAGCACCAGTT	-	novel	NA	P-0019462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	66	34	0	ENST00000296930.5:c.59-192_127del		p.X20_splice	ENST00000296930	NM_002520.6	20		2/11	1	2	FACETS	1	0.954	1	1	0.988	1	CLONAL	3	TRUE	1	0.519039912246912	2		34	82	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045712	26045712	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	100	260	0	ENST00000540144.1:c.74C>T	p.Ala25Val	p.A25V	ENST00000540144	NM_003531.2	25	gCa/gTa	1/1	0.211276864976467	3	FACETS	1	0.983	1	0.747	0.674	0.822	INDETERMINATE	1	TRUE	1	0.519039912246912	3		260	325	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710637	40710637	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	55	841	1	ENST00000373198.4:c.4214G>T	p.Gly1405Val	p.G1405V	ENST00000373198	NM_133170.3	1405	gGa/gTa	31/32	0.289219536349633	1	FACETS	0.309	0.263	0.359	0.309	0.263	0.359	SUBCLONAL	1	TRUE	0	0.390120410153331	1		842	735	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569748	41569781	+	frameshift_variant	Frame_Shift_Del	DEL	TCTCACAGAAACTATATGCCACCATGGAGAAGCA	TCTCACAGAAACTATATGCCACCATGGAGAAGCA	-	novel	NA	P-0019476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	85	824	0	ENST00000263253.7:c.4740_4773del	p.Ser1581LysfsTer6	p.S1581Kfs*6	ENST00000263253	NM_001429.3	1580	cTCTCACAGAAACTATATGCCACCATGGAGAAGCAt/ct	29/31	0.390120410153331	1	FACETS	0.608	0.538	0.682	0.608	0.538	0.682	SUBCLONAL	1	TRUE	0	0.390120410153331	1		824	577	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542252	187542252	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	50	658	0	ENST00000441802.2:c.5488del	p.His1830IlefsTer4	p.H1830Ifs*4	ENST00000441802	NM_005245.3	1830	Cat/at	10/27	0.390120410153331	1	FACETS	0.437	0.371	0.51	0.437	0.371	0.51	SUBCLONAL	1	TRUE	0	0.390120410153331	1		658	472	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	23	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.415	0.322	0.524	0.415	0.322	0.524	SUBCLONAL	1	TRUE	1	0.14	2		436	791	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089689	27089698	+	frameshift_variant	Frame_Shift_Del	DEL	GGATGTGTCC	GGATGTGTCC	-	novel	NA	P-0019575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	80	814	0	ENST00000324856.7:c.2645_2654del	p.Gly882AlafsTer6	p.G882Afs*6	ENST00000324856	NM_006015.4	882	gGGATGTGTCCc/gc	8/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.14	2		814	853	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660507	67660507	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	42	628	1	ENST00000264010.4:c.1407C>A	p.Cys469Ter	p.C469*	ENST00000264010	NM_006565.3	469	tgC/tgA	8/12	1	2	FACETS	0.726	0.604	0.863	0.726	0.604	0.863	SUBCLONAL	1	TRUE	1	0.14	2		629	826	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048772	180048772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758587669	NA	P-0019575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	71	930	1	ENST00000261937.6:c.1790C>T	p.Thr597Met	p.T597M	ENST00000261937	NM_182925.4	597	aCg/aTg	13/30	1	2	FACETS	0.937	0.816	1	0.937	0.816	1	CLONAL	1	TRUE	1	0.14	2		931	1082	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	774	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.860603920032143	3	FACETS	0.964	0.937	0.99	0.964	0.937	0.99	CLONAL	2	TRUE	1	0.860603920032143	3		436	1335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0019641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	487	1108	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.860603920032143	1	FACETS	0.992	0.964	1	0.992	0.964	1	CLONAL	1	TRUE	0	0.860603920032143	1		1109	650	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955573	48955573	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	245	604	0	ENST00000267163.4:c.1689G>A	p.Trp563Ter	p.W563*	ENST00000267163	NM_000321.2	563	tgG/tgA	17/27	0.860603920032143	1	FACETS	0.963	0.923	1	0.963	0.923	1	CLONAL	1	TRUE	0	0.860603920032143	1		604	337	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	58	188	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.999	0.858	1	0.999	0.858	1	CLONAL	1	TRUE	1	0.19	2		188	611	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0019718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	22	346	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.333	0.257	0.423	0.333	0.257	0.423	SUBCLONAL	1	TRUE	1	0.19	2		346	695	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857228	78857228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	473	752	1	ENST00000306801.3:c.1594C>T	p.Arg532Trp	p.R532W	ENST00000306801	NM_020761.2	532	Cgg/Tgg	15/34	1	2	FACETS	0.971	0.931	1	0.971	0.931	1	CLONAL	1	TRUE	1	0.909521679922187	2		753	1071	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250188	39250188	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1175506046	NA	P-0019757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	573	824	0	ENST00000402219.2:c.1381A>G	p.Ile461Val	p.I461V	ENST00000402219	NM_005633.3	461	Ata/Gta	10/23	1	2	FACETS	0.979	0.943	1	0.979	0.943	1	CLONAL	1	TRUE	1	0.909521679922187	2		824	1287	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0019807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	524	582	2	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.3	6	FACETS	1	0.982	1			1	CLONAL	10	TRUE	NA	0.08	6		584	1458	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0019807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	21	580	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.579	0.444	0.739	0.579	0.444	0.739	SUBCLONAL	1	TRUE	1	0.08	2		580	906	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0019807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	35	469	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	1	2	FACETS	0.722	0.589	0.873	0.722	0.589	0.873	SUBCLONAL	1	TRUE	1	0.08	2		469	1212	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019807-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	202	188	0				ENST00000310581	NM_198253.2	-/1132			0.236579199631808	3	FACETS	0.954	0.892	1	1	0.991	1	CLONAL	3	FALSE	1	0.3	3		188	541	SUCCESS
APC	324	MSKCC	GRCh37	5	112170814	112170815	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GATATTACGGAATGTGTCCAGCTTGATA	novel	NA	P-0019807-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	164	649	0	ENST00000257430.4:c.1912_1939dup	p.Ala647AspfsTer13	p.A647Dfs*13	ENST00000257430	NM_000038.5	637	ggg/ggGATATTACGGAATGTGTCCAGCTTGATAg	15/16	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.3	2		649	753	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	6130	582	2	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.535196137539554	15	FACETS	1	0.999	1			1	CLONAL	15	TRUE	NA	0.535196137539554	15		584	6629	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	105	580	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.725	0.652	0.803	0.725	0.652	0.803	SUBCLONAL	1	TRUE	1	0.535196137539554	2		580	541	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	237	707	28	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.817	0.762	0.874	0.817	0.762	0.874	CLONAL	1	TRUE	1	0.535196137539554	2		735	1084	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	215	819	1	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	0.918	0.855	0.984	0.918	0.855	0.984	CLONAL	1	TRUE	1	0.535196137539554	2		820	875	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214871	36214871	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	367	814	3	ENST00000222270.7:c.3302del	p.Pro1101LeufsTer81	p.P1101Lfs*81	ENST00000222270	NM_014727.1	1099	ggC/gg	8/37	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.535196137539554	2		817	1337	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959120	28959120	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753133916	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	151	433	0	ENST00000282397.4:c.2018C>T	p.Ala673Val	p.A673V	ENST00000282397	NM_002019.4	673	gCc/gTc	14/30	1	2	FACETS	0.864	0.792	0.939	0.864	0.792	0.939	CLONAL	1	TRUE	1	0.535196137539554	2		433	653	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	329	469	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.535196137539554	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.535196137539554	1		469	872	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	95	364	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.768	0.687	0.854	0.768	0.687	0.854	SUBCLONAL	1	TRUE	1	0.535196137539554	2		364	462	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	82	268	4	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	1	2	FACETS	0.878	0.78	0.981	0.878	0.78	0.981	CLONAL	1	TRUE	1	0.535196137539554	2		272	349	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286237	66286238	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	86	553	0	ENST00000273854.3:c.1448dup	p.Asn483LysfsTer21	p.N483Kfs*21	ENST00000273854	NM_004439.5	483	aac/aaAc	6/18	1	2	FACETS	0.588	0.521	0.659	0.588	0.521	0.659	SUBCLONAL	1	TRUE	1	0.535196137539554	2		553	547	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67646013	67646014	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs1470210640	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	188	526	1	ENST00000264010.4:c.950_951del	p.Thr317ArgfsTer91	p.T317Rfs*91	ENST00000264010	NM_006565.3	314	aAC/a	4/12	1	2	FACETS	0.823	0.761	0.887	0.823	0.761	0.887	CLONAL	1	TRUE	1	0.535196137539554	2		527	854	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459858	149459858	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs566891025	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	279	821	1	ENST00000286301.3:c.349G>A	p.Val117Met	p.V117M	ENST00000286301	NM_005211.3	117	Gtg/Atg	4/22	1	2	FACETS	0.928	0.871	0.986	0.928	0.871	0.986	CLONAL	1	TRUE	1	0.535196137539554	2		822	1124	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273944	10273944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	348	972	7	ENST00000330684.3:c.325G>A	p.Val109Ile	p.V109I	ENST00000330684	NM_001134407.1	109	Gta/Ata	2/13	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.535196137539554	2		979	1254	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131127	55131127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1248275606	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	207	618	1	ENST00000257290.5:c.670G>A	p.Val224Met	p.V224M	ENST00000257290	NM_006206.4	224	Gtg/Atg	5/23	1	2	FACETS	0.884	0.821	0.949	0.884	0.821	0.949	CLONAL	1	TRUE	1	0.535196137539554	2		619	875	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825519	50825519	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	129	572	1	ENST00000398568.2:c.2156del	p.Asn719MetfsTer13	p.N719Mfs*13	ENST00000398568	NM_001042412.1	717	gAa/ga	14/18	1	2	FACETS	0.785	0.714	0.86	0.785	0.714	0.86	SUBCLONAL	1	TRUE	1	0.535196137539554	2		573	614	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	472178	472178	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372866054	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	234	753	0	ENST00000399788.2:c.623G>A	p.Gly208Asp	p.G208D	ENST00000399788	NM_001042603.1	208	gGc/gAc	5/28	1	2	FACETS	0.67	0.624	0.718	0.67	0.624	0.718	SUBCLONAL	1	TRUE	1	0.535196137539554	2		753	1305	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948747	71948748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760925109	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	238	735	9	ENST00000298229.2:c.3466dup	p.Arg1156ProfsTer59	p.R1156Pfs*59	ENST00000298229	NM_001567.3	1153	-/C	26/28	1	2	FACETS	0.905	0.845	0.966	0.905	0.845	0.966	CLONAL	1	TRUE	1	0.535196137539554	2		744	983	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195679	102195679	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	133	583	0	ENST00000263464.3:c.439A>C	p.Asn147His	p.N147H	ENST00000263464	NM_001165.4	147	Aac/Cac	2/9	1	2	FACETS	0.763	0.695	0.835	0.763	0.695	0.835	SUBCLONAL	1	TRUE	1	0.535196137539554	2		583	651	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570309	95570309	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	127	411	0	ENST00000393063.1:c.3424T>G	p.Ser1142Ala	p.S1142A	ENST00000393063	NM_030621.3	1142	Tct/Gct	22/28	1	2	FACETS	0.907	0.826	0.992	0.907	0.826	0.992	CLONAL	1	TRUE	1	0.535196137539554	2		411	523	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420314	88420314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767941638	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	186	496	0	ENST00000360948.2:c.2372G>A	p.Arg791Gln	p.R791Q	ENST00000360948	NM_001012338.2	791	cGg/cAg	19/19	1	2	FACETS	0.975	0.903	1	0.975	0.903	1	CLONAL	1	TRUE	1	0.535196137539554	2		496	713	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134451	30134452	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	243	809	0	ENST00000263025.4:c.79dup	p.Glu27GlyfsTer35	p.E27Gfs*35	ENST00000263025	NM_002746.2	27	gag/gGag	1/9	1	2	FACETS	0.814	0.76	0.87	0.814	0.76	0.87	CLONAL	1	TRUE	1	0.535196137539554	2		809	1115	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684014	29684014	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	200	710	0	ENST00000356175.3:c.7712A>C	p.His2571Pro	p.H2571P	ENST00000356175	NM_000267.3	2571	cAt/cCt	52/57	1	2	FACETS	0.933	0.866	1	0.933	0.866	1	CLONAL	1	TRUE	1	0.535196137539554	2		710	801	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216509	2216509	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	329	753	1	ENST00000398665.3:c.2153C>T	p.Ala718Val	p.A718V	ENST00000398665	NM_032482.2	718	gCt/gTt	20/28	1	2	FACETS	0.963	0.909	1	0.963	0.909	1	CLONAL	1	TRUE	1	0.535196137539554	2		754	1277	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292407	15292408	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCC	novel	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	257	780	0	ENST00000263388.2:c.2769_2771dup	p.Gln923_Asp924insGlu	p.Q923_D924insE	ENST00000263388	NM_000435.2	924	gac/gaGGAc	17/33	1	2	FACETS	0.948	0.888	1	0.948	0.888	1	CLONAL	1	TRUE	1	0.535196137539554	2		780	1013	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143425	30143425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	249	634	0	ENST00000389048.3:c.101C>T	p.Ala34Val	p.A34V	ENST00000389048	NM_004304.4	34	gCg/gTg	1/29	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.535196137539554	2		634	735	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249728	39249728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	128	647	0	ENST00000402219.2:c.1841C>T	p.Thr614Met	p.T614M	ENST00000402219	NM_005633.3	614	aCg/aTg	10/23	1	2	FACETS	0.845	0.769	0.925	0.845	0.769	0.925	CLONAL	1	TRUE	1	0.535196137539554	2		647	566	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651306	45651307	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	258	625	1	ENST00000407780.3:c.718_719del	p.Asp240GlnfsTer81	p.D240Qfs*81	ENST00000407780	NM_001283052.1	240	GAc/c	5/7	1	2	FACETS	0.879	0.823	0.937	0.879	0.823	0.937	CLONAL	1	TRUE	1	0.535196137539554	2		626	1097	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573720	41573720	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	265	829	0	ENST00000263253.7:c.6005A>G	p.Gln2002Arg	p.Q2002R	ENST00000263253	NM_001429.3	2002	cAg/cGg	31/31	1	2	FACETS	0.981	0.921	1	0.981	0.921	1	CLONAL	1	TRUE	1	0.535196137539554	2		829	1009	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37045920	37045920	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs775914775	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	168	657	0	ENST00000231790.2:c.335A>G	p.His112Arg	p.H112R	ENST00000231790	NM_000249.3	112	cAt/cGt	4/19	1	2	FACETS	0.853	0.786	0.923	0.853	0.786	0.923	CLONAL	1	TRUE	1	0.535196137539554	2		657	736	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712614	52712614	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	146	437	0	ENST00000394830.3:c.139-1G>T		p.X47_splice	ENST00000394830	NM_018313.4	47			1	2	FACETS	0.994	0.912	1	0.994	0.912	1	CLONAL	1	TRUE	1	0.535196137539554	2		437	549	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957847	1957847	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200311175	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	290	733	0	ENST00000382891.5:c.2813C>T	p.Pro938Leu	p.P938L	ENST00000382891	NM_133335.3	938	cCg/cTg	15/22	1	2	FACETS	0.959	0.902	1	0.959	0.902	1	CLONAL	1	TRUE	1	0.535196137539554	2		733	1130	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528282	157528282	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	247	748	0	ENST00000346085.5:c.6008del	p.Lys2003ArgfsTer18	p.K2003Rfs*18	ENST00000346085	NM_020732.3	2003	Aag/ag	20/20	1	2	FACETS	0.945	0.884	1	0.945	0.884	1	CLONAL	1	TRUE	1	0.535196137539554	2		748	977	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954948	2954948	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	359	742	0	ENST00000396946.4:c.2762T>A	p.Ile921Asn	p.I921N	ENST00000396946	NM_032415.4	921	aTc/aAc	21/25	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.535196137539554	2		742	1245	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467904	50467904	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	151	474	0	ENST00000331340.3:c.1139A>C	p.Lys380Thr	p.K380T	ENST00000331340	NM_006060.4	380	aAg/aCg	8/8	1	2	FACETS	0.909	0.834	0.986	0.909	0.834	0.986	CLONAL	1	TRUE	1	0.535196137539554	2		474	621	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850922	128850922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs114406835	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	243	672	1	ENST00000249373.3:c.1769G>A	p.Ser590Asn	p.S590N	ENST00000249373	NM_005631.4	590	aGc/aAc	10/12	1	2	FACETS	0.959	0.897	1	0.959	0.897	1	CLONAL	1	TRUE	1	0.535196137539554	2		673	947	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738650	145738650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765894032	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	327	626	2	ENST00000428558.2:c.2414C>T	p.Ala805Val	p.A805V	ENST00000428558	NM_004260.3	805	gCc/gTc	15/22	0.535196137539554	3	FACETS	1	0.989	1	0.587	0.554	0.621	CLONAL	1	TRUE	1	0.535196137539554	3		628	1320	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418408	139418408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1286892980	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	341	720	0	ENST00000277541.6:c.164C>T	p.Pro55Leu	p.P55L	ENST00000277541	NM_017617.3	55	cCg/cTg	3/34	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.535196137539554	2		720	1216	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006774	47006774	+	5_prime_UTR_variant	5'UTR	SNP	C	C	T	novel	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	209	626	0	ENST00000377604.3:c.-107C>T		p.*36*	ENST00000377604	NM_001204468.1	-/852		2/24	1	2	FACETS	0.799	0.742	0.859	0.799	0.742	0.859	SUBCLONAL	1	TRUE	1	0.535196137539554	2		626	977	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944515	71944515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878853123	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	189	692	1	ENST00000298229.2:c.2071C>T	p.Arg691Trp	p.R691W	ENST00000298229	NM_001567.3	691	Cgg/Tgg	18/28	1	2	FACETS	0.614	0.567	0.664	0.614	0.567	0.664	SUBCLONAL	1	TRUE	1	0.535196137539554	2		693	1150	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137524653	137524653	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	85	578	0	ENST00000367739.4:c.716del	p.Phe239SerfsTer5	p.F239Sfs*5	ENST00000367739	NM_000416.2	239	tTc/tc	5/7	1	2	FACETS	0.533	0.472	0.599	0.533	0.472	0.599	SUBCLONAL	1	TRUE	1	0.535196137539554	2		578	596	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099678	157099678	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	21	37	0	ENST00000346085.5:c.617del	p.Gly206AlafsTer60	p.G206Afs*60	ENST00000346085	NM_020732.3	205	ttG/tt	1/20	1	2	FACETS	0.809	0.635	1	0.809	0.635	1	CLONAL	1	TRUE	1	0.535196137539554	2		37	97	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	5965	582	2	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.562600003898696	22	FACETS	1	0.996	1			1	CLONAL	22	TRUE	NA	0.562600003898696	22		584	6381	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	190	580	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.999	0.927	1	0.999	0.927	1	CLONAL	1	TRUE	1	0.562600003898696	2		580	676	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	228	707	28	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.903	0.842	0.965	0.903	0.842	0.965	CLONAL	1	TRUE	1	0.562600003898696	2		735	898	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	228	819	1	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.562600003898696	2		820	790	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	31	290	2	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	0.183	0.147	0.224	0.183	0.147	0.224	SUBCLONAL	1	TRUE	1	0.562600003898696	2		292	602	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214871	36214871	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	306	814	3	ENST00000222270.7:c.3302del	p.Pro1101LeufsTer81	p.P1101Lfs*81	ENST00000222270	NM_014727.1	1099	ggC/gg	8/37	1	2	FACETS	0.97	0.914	1	0.97	0.914	1	CLONAL	1	TRUE	1	0.562600003898696	2		817	1122	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959120	28959120	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753133916	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	153	433	0	ENST00000282397.4:c.2018C>T	p.Ala673Val	p.A673V	ENST00000282397	NM_002019.4	673	gCc/gTc	14/30	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.562600003898696	2		433	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	294	469	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.561762658807965	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.562600003898696	1		469	722	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	128	364	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.966	0.881	1	0.966	0.881	1	CLONAL	1	TRUE	1	0.562600003898696	2		364	471	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	133	268	4	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.562600003898696	2		272	449	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286237	66286238	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	131	553	0	ENST00000273854.3:c.1448dup	p.Asn483LysfsTer21	p.N483Kfs*21	ENST00000273854	NM_004439.5	483	aac/aaAc	6/18	1	2	FACETS	0.956	0.873	1	0.956	0.873	1	CLONAL	1	TRUE	1	0.562600003898696	2		553	487	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954273	32954273	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359752	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	44	277	2	ENST00000380152.3:c.9253del	p.Thr3085GlnfsTer19	p.T3085Qfs*19	ENST00000380152		3083	Aaa/aa	24/27	1	2	FACETS	0.297	0.249	0.351	0.297	0.249	0.351	SUBCLONAL	1	TRUE	1	0.562600003898696	2		279	526	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67646013	67646014	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs1470210640	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	170	526	1	ENST00000264010.4:c.950_951del	p.Thr317ArgfsTer91	p.T317Rfs*91	ENST00000264010	NM_006565.3	314	aAC/a	4/12	1	2	FACETS	0.886	0.818	0.957	0.886	0.818	0.957	CLONAL	1	TRUE	1	0.562600003898696	2		527	682	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459858	149459858	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs566891025	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	345	821	1	ENST00000286301.3:c.349G>A	p.Val117Met	p.V117M	ENST00000286301	NM_005211.3	117	Gtg/Atg	4/22	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.562600003898696	2		822	1039	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273944	10273944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	306	972	7	ENST00000330684.3:c.325G>A	p.Val109Ile	p.V109I	ENST00000330684	NM_001134407.1	109	Gta/Ata	2/13	1	2	FACETS	0.983	0.927	1	0.983	0.927	1	CLONAL	1	TRUE	1	0.562600003898696	2		979	1107	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131127	55131127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1248275606	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	225	618	1	ENST00000257290.5:c.670G>A	p.Val224Met	p.V224M	ENST00000257290	NM_006206.4	224	Gtg/Atg	5/23	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.562600003898696	2		619	765	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825519	50825519	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	138	572	1	ENST00000398568.2:c.2156del	p.Asn719MetfsTer13	p.N719Mfs*13	ENST00000398568	NM_001042412.1	717	gAa/ga	14/18	1	2	FACETS	0.905	0.828	0.985	0.905	0.828	0.985	CLONAL	1	TRUE	1	0.562600003898696	2		573	542	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	472178	472178	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372866054	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	214	753	0	ENST00000399788.2:c.623G>A	p.Gly208Asp	p.G208D	ENST00000399788	NM_001042603.1	208	gGc/gAc	5/28	0.519271239445128	3	FACETS	0.986	0.916	1	0.493	0.458	0.529	CLONAL	1	TRUE	1	0.562600003898696	3		753	989	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948747	71948748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760925109	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	251	735	9	ENST00000298229.2:c.3466dup	p.Arg1156ProfsTer59	p.R1156Pfs*59	ENST00000298229	NM_001567.3	1153	-/C	26/28	1	2	FACETS	0.927	0.868	0.987	0.927	0.868	0.987	CLONAL	1	TRUE	1	0.562600003898696	2		744	963	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195679	102195679	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	162	583	0	ENST00000263464.3:c.439A>C	p.Asn147His	p.N147H	ENST00000263464	NM_001165.4	147	Aac/Cac	2/9	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.562600003898696	2		583	568	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570309	95570309	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	134	411	0	ENST00000393063.1:c.3424T>G	p.Ser1142Ala	p.S1142A	ENST00000393063	NM_030621.3	1142	Tct/Gct	22/28	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.562600003898696	2		411	449	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420314	88420314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767941638	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	175	496	0	ENST00000360948.2:c.2372G>A	p.Arg791Gln	p.R791Q	ENST00000360948	NM_001012338.2	791	cGg/cAg	19/19	1	2	FACETS	0.927	0.857	1	0.927	0.857	1	CLONAL	1	TRUE	1	0.562600003898696	2		496	671	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134451	30134452	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	261	809	0	ENST00000263025.4:c.79dup	p.Glu27GlyfsTer35	p.E27Gfs*35	ENST00000263025	NM_002746.2	27	gag/gGag	1/9	1	2	FACETS	0.891	0.835	0.949	0.891	0.835	0.949	CLONAL	1	TRUE	1	0.562600003898696	2		809	1041	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684014	29684014	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	207	710	0	ENST00000356175.3:c.7712A>C	p.His2571Pro	p.H2571P	ENST00000356175	NM_000267.3	2571	cAt/cCt	52/57	1	2	FACETS	0.943	0.878	1	0.943	0.878	1	CLONAL	1	TRUE	1	0.562600003898696	2		710	780	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216509	2216509	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	322	753	1	ENST00000398665.3:c.2153C>T	p.Ala718Val	p.A718V	ENST00000398665	NM_032482.2	718	gCt/gTt	20/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.562600003898696	2		754	1060	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292407	15292408	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCC	novel	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	269	780	0	ENST00000263388.2:c.2769_2771dup	p.Gln923_Asp924insGlu	p.Q923_D924insE	ENST00000263388	NM_000435.2	924	gac/gaGGAc	17/33	1	2	FACETS	0.942	0.884	1	0.942	0.884	1	CLONAL	1	TRUE	1	0.562600003898696	2		780	1015	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143425	30143425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	231	634	0	ENST00000389048.3:c.101C>T	p.Ala34Val	p.A34V	ENST00000389048	NM_004304.4	34	gCg/gTg	1/29	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.562600003898696	2		634	555	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249728	39249728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	167	647	0	ENST00000402219.2:c.1841C>T	p.Thr614Met	p.T614M	ENST00000402219	NM_005633.3	614	aCg/aTg	10/23	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.562600003898696	2		647	559	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651306	45651307	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	214	625	1	ENST00000407780.3:c.718_719del	p.Asp240GlnfsTer81	p.D240Qfs*81	ENST00000407780	NM_001283052.1	240	GAc/c	5/7	1	2	FACETS	0.915	0.852	0.98	0.915	0.852	0.98	CLONAL	1	TRUE	1	0.562600003898696	2		626	831	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573720	41573720	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	287	829	0	ENST00000263253.7:c.6005A>G	p.Gln2002Arg	p.Q2002R	ENST00000263253	NM_001429.3	2002	cAg/cGg	31/31	1	2	FACETS	0.963	0.906	1	0.963	0.906	1	CLONAL	1	TRUE	1	0.562600003898696	2		829	1060	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37045920	37045920	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs775914775	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	208	657	0	ENST00000231790.2:c.335A>G	p.His112Arg	p.H112R	ENST00000231790	NM_000249.3	112	cAt/cGt	4/19	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.562600003898696	2		657	723	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712614	52712614	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	116	437	0	ENST00000394830.3:c.139-1G>T		p.X47_splice	ENST00000394830	NM_018313.4	47			1	2	FACETS	0.908	0.824	0.996	0.908	0.824	0.996	CLONAL	1	TRUE	1	0.562600003898696	2		437	454	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957847	1957847	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200311175	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	231	733	0	ENST00000382891.5:c.2813C>T	p.Pro938Leu	p.P938L	ENST00000382891	NM_133335.3	938	cCg/cTg	15/22	NA	2	FACETS	0.975	0.911	1			1	INDETERMINATE	1	TRUE	NA	0.562600003898696	2		733	842	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528282	157528282	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	258	748	0	ENST00000346085.5:c.6008del	p.Lys2003ArgfsTer18	p.K2003Rfs*18	ENST00000346085	NM_020732.3	2003	Aag/ag	20/20	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.562600003898696	2		748	910	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954948	2954948	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	281	742	0	ENST00000396946.4:c.2762T>A	p.Ile921Asn	p.I921N	ENST00000396946	NM_032415.4	921	aTc/aAc	21/25	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.562600003898696	2		742	975	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467904	50467904	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	169	474	0	ENST00000331340.3:c.1139A>C	p.Lys380Thr	p.K380T	ENST00000331340	NM_006060.4	380	aAg/aCg	8/8	1	2	FACETS	0.946	0.873	1	0.946	0.873	1	CLONAL	1	TRUE	1	0.562600003898696	2		474	635	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850922	128850922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs114406835	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	255	672	1	ENST00000249373.3:c.1769G>A	p.Ser590Asn	p.S590N	ENST00000249373	NM_005631.4	590	aGc/aAc	10/12	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.562600003898696	2		673	836	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738650	145738650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765894032	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	250	626	2	ENST00000428558.2:c.2414C>T	p.Ala805Val	p.A805V	ENST00000428558	NM_004260.3	805	gCc/gTc	15/22	0.562600003898696	3	FACETS	0.895	0.836	0.956	0.448	0.418	0.478	CLONAL	1	TRUE	1	0.562600003898696	3		628	1272	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418408	139418408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1286892980	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	348	720	0	ENST00000277541.6:c.164C>T	p.Pro55Leu	p.P55L	ENST00000277541	NM_017617.3	55	cCg/cTg	3/34	0.193363189402713	4	FACETS	0.916	0.869	0.964	0.916	0.869	0.964	INDETERMINATE	2	TRUE	2	0.562600003898696	4		720	1055	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006774	47006774	+	5_prime_UTR_variant	5'UTR	SNP	C	C	T	novel	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	187	626	0	ENST00000377604.3:c.-107C>T		p.*36*	ENST00000377604	NM_001204468.1	-/852		2/24	0.562600003898696	3	FACETS	0.753	0.695	0.814	0.377	0.347	0.407	SUBCLONAL	1	TRUE	1	0.562600003898696	3		626	1131	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11210268	11210268	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	229	411	2	ENST00000361445.4:c.4485G>T	p.Gln1495His	p.Q1495H	ENST00000361445	NM_004958.3	1495	caG/caT	31/58	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.562600003898696	2		413	749	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56477561	56477561	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	150	366	0	ENST00000267101.3:c.109A>G	p.Ser37Gly	p.S37G	ENST00000267101	NM_001982.3	37	Agt/Ggt	2/28	1	2	FACETS	0.732	0.671	0.797	0.732	0.671	0.797	SUBCLONAL	1	TRUE	1	0.562600003898696	2		366	728	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50830340	50830340	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	70	322	0	ENST00000398568.2:c.2783T>C	p.Ile928Thr	p.I928T	ENST00000398568	NM_001042412.1	928	aTc/aCc	18/18	1	2	FACETS	0.368	0.32	0.419	0.368	0.32	0.419	SUBCLONAL	1	TRUE	1	0.562600003898696	2		322	677	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245996	5245996	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	195	459	0	ENST00000357368.4:c.779del	p.Gly260AlafsTer3	p.G260Afs*3	ENST00000357368	NM_002850.3	260	gGc/gc	10/38	1	2	FACETS	0.737	0.682	0.793	0.737	0.682	0.793	SUBCLONAL	1	TRUE	1	0.562600003898696	2		459	941	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027272	48027272	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	26	219	0	ENST00000234420.5:c.2150T>C	p.Val717Ala	p.V717A	ENST00000234420	NM_000179.2	717	gTc/gCc	4/10	1	2	FACETS	0.227	0.179	0.282	0.227	0.179	0.282	SUBCLONAL	1	TRUE	1	0.562600003898696	2		219	407	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803513	32803513	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	305	613	0	ENST00000374899.4:c.646T>C	p.Tyr216His	p.Y216H	ENST00000374899	NM_018833.2	216	Tac/Cac	4/12	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.562600003898696	2		613	1067	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129112	152129112	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	184	669	0	ENST00000206249.3:c.65del	p.Glu22GlyfsTer5	p.E22Gfs*5	ENST00000206249	NM_000125.3	22	gAg/gg	1/8	1	2	FACETS	0.65	0.6	0.703	0.65	0.6	0.703	SUBCLONAL	1	TRUE	1	0.562600003898696	2		669	1006	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843251	128843251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1412787004	NA	P-0019807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	346	635	1	ENST00000249373.3:c.358G>A	p.Ala120Thr	p.A120T	ENST00000249373	NM_005631.4	120	Gca/Aca	2/12	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.562600003898696	2		636	1131	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0019820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	157	751	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	0.926	0.851	1	0.926	0.851	1	CLONAL	1	TRUE	1	0.54626305581256	2		751	621	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482752	67482752	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0019820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	23	571	0	ENST00000327367.4:c.1156A>T	p.Arg386Ter	p.R386*	ENST00000327367	NM_005902.3	386	Aga/Tga	9/9	0.54626305581256	1	FACETS	0.198	0.154	0.249	0.198	0.154	0.249	SUBCLONAL	1	TRUE	0	0.54626305581256	1		571	309	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589570	67589570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	104	542	0	ENST00000274335.5:c.1333G>A	p.Val445Ile	p.V445I	ENST00000274335		445	Gta/Ata	10/15	0.415757971668955	1	FACETS	0.673	0.607	0.743	0.673	0.607	0.743	SUBCLONAL	1	TRUE	0	0.54626305581256	1		542	411	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639170	176639170	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	44	626	0	ENST00000439151.2:c.3770C>A	p.Thr1257Lys	p.T1257K	ENST00000439151	NM_022455.4	1257	aCa/aAa	5/23	1	2	FACETS	0.334	0.279	0.393	0.334	0.279	0.393	SUBCLONAL	1	TRUE	1	0.54626305581256	2		626	483	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198896	67198896	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	139	688	0	ENST00000312629.5:c.367C>G	p.Leu123Val	p.L123V	ENST00000312629	NM_003952.2	123	Cta/Gta	5/15	0.123187366221364	5	FACETS	0.919	0.835	1			1	INDETERMINATE	1	TRUE	NA	0.387532672639622	5		688	1234	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177785	56177789	+	frameshift_variant	Frame_Shift_Del	DEL	TTGAG	TTGAG	-	novel	NA	P-0019838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	76	454	0	ENST00000399503.3:c.2759_2763del	p.Leu920CysfsTer8	p.L920Cfs*8	ENST00000399503	NM_005921.1	920	TTGAGt/t	14/20	1	2	FACETS	0.822	0.723	0.928	0.822	0.723	0.928	CLONAL	1	TRUE	1	0.387532672639622	2		454	477	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111500	8111500	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	CA	novel	NA	P-0019838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	198	919	0	ENST00000346208.3:c.986delinsCA	p.Arg329ThrfsTer23	p.R329Tfs*23	ENST00000346208		329	aGg/aCAg	5/6	1	2	FACETS	0.931	0.862	1	0.931	0.862	1	CLONAL	1	TRUE	1	0.387532672639622	2		919	1097	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913351	NA	P-0019840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	235	560	2	ENST00000288602.6:c.1397G>T	p.Gly466Val	p.G466V	ENST00000288602	NM_004333.4	466	gGa/gTa	11/18	1	2	FACETS	0.964	0.904	1	0.964	0.904	1	CLONAL	1	TRUE	1	0.704447777939887	2		562	692	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039193	49039193	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	223	672	0	ENST00000267163.4:c.2271C>G	p.Asn757Lys	p.N757K	ENST00000267163	NM_000321.2	757	aaC/aaG	22/27	0.704447777939887	1	FACETS	0.834	0.785	0.883	0.834	0.785	0.883	CLONAL	1	TRUE	0	0.704447777939887	1		672	492	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943673	9943673	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	329	700	0	ENST00000330684.3:c.1268A>G	p.Asp423Gly	p.D423G	ENST00000330684	NM_001134407.1	423	gAc/gGc	5/13	0.641616370451985	3	FACETS	0.875	0.826	0.926	0.438	0.413	0.463	CLONAL	1	TRUE	1	0.704447777939887	3		700	1443	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934746	49934746	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	435	804	1	ENST00000296474.3:c.2150T>C	p.Val717Ala	p.V717A	ENST00000296474	NM_002447.2	717	gTg/gCg	7/20	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.704447777939887	2		805	1207	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561741	55561741	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	188	429	0	ENST00000288135.5:c.131C>T	p.Ser44Leu	p.S44L	ENST00000288135	NM_000222.2	44	tCa/tTa	2/21	1	2	FACETS	0.927	0.862	0.993	0.927	0.862	0.993	CLONAL	1	TRUE	1	0.704447777939887	2		429	576	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435719	116435719	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	197	403	0	ENST00000397752.3:c.3809G>A	p.Gly1270Asp	p.G1270D	ENST00000397752	NM_000245.2	1270	gGc/gAc	20/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.704447777939887	2		403	506	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738431	145738431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1565	241	738	0	ENST00000428558.2:c.2554G>A	p.Ala852Thr	p.A852T	ENST00000428558	NM_004260.3	852	Gcc/Acc	16/22	0.671264957457934	4	FACETS	0.646	0.601	0.693	0.215	0.2	0.231	SUBCLONAL	1	TRUE	1	0.704447777939887	4		738	1806	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	216	188	0				ENST00000310581	NM_198253.2	-/1132			0.273878664184946	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	2	0.403938557409752	4		188	684	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0020047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	320	688	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.403938557409752	2	FACETS	0.96	0.911	1	0.96	0.911	1	CLONAL	2	TRUE	0	0.403938557409752	2		688	825	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217236	7217236	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs775804583	NA	P-0020047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	305	597	0	ENST00000380728.2:c.469del	p.Gln157LysfsTer188	p.Q157Kfs*188	ENST00000380728		157	Caa/aa	6/11	0.403938557409752	2	FACETS	0.926	0.877	0.977	0.926	0.877	0.977	CLONAL	2	TRUE	0	0.403938557409752	2		597	815	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371717	225371717	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	181	565	0	ENST00000264414.4:c.887T>G	p.Leu296Arg	p.L296R	ENST00000264414	NM_003590.4	296	cTt/cGt	7/16	0.182885238637349	2	FACETS	0.813	0.755	0.873	0.813	0.755	0.873	INDETERMINATE	2	TRUE	0	0.403938557409752	2		565	551	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131146	55131146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752886996	NA	P-0020047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	67	597	0	ENST00000257290.5:c.689C>T	p.Thr230Met	p.T230M	ENST00000257290	NM_006206.4	230	aCg/aTg	5/23	1	2	FACETS	0.452	0.392	0.517	0.452	0.392	0.517	SUBCLONAL	1	TRUE	1	0.403938557409752	2		597	734	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800593	32800607	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGCACTTCCTGGAA	AAGCACTTCCTGGAA	-	novel	NA	P-0020047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	53	637	0	ENST00000374899.4:c.946-6_954del		p.X316_splice	ENST00000374899	NM_018833.2	316		6/12	0.233650038758856	3	FACETS	0.344	0.292	0.402	0.115	0.097	0.134	INDETERMINATE	1	TRUE	0	0.403938557409752	3		637	916	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358920	81358920	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0020047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	154	439	0	ENST00000222390.5:c.1040+1G>C		p.X347_splice	ENST00000222390	NM_000601.4	347			0.269695775238081	4	FACETS	0.752	0.689	0.817	0.752	0.689	0.817	SUBCLONAL	2	TRUE	2	0.403938557409752	4		439	712	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928929	44928929	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	256	475	0	ENST00000377967.4:c.2029C>G	p.Gln677Glu	p.Q677E	ENST00000377967	NM_021140.2	677	Cag/Gag	17/29	0.234916591257302	5	FACETS	1	0.961	1			1	INDETERMINATE	2	TRUE	NA	0.403938557409752	5		475	983	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929161	44929182	+	frameshift_variant	Frame_Shift_Del	DEL	TGACGGCAGATGCTGTTTGCAG	TGACGGCAGATGCTGTTTGCAG	-	novel	NA	P-0020047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	291	552	0	ENST00000377967.4:c.2262_2283del	p.Met754IlefsTer13	p.M754Ifs*13	ENST00000377967	NM_021140.2	754	aTGACGGCAGATGCTGTTTGCAGt/at	17/29	0.234916591257302	5	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.403938557409752	5		552	991	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945142	44945157	+	frameshift_variant	Frame_Shift_Del	DEL	AACATAAATATTGGCC	AACATAAATATTGGCC	GTTATTCA	novel	NA	P-0020047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	158	615	3	ENST00000377967.4:c.3466_3481delinsGTTATTCA	p.Asn1156ValfsTer5	p.N1156Vfs*5	ENST00000377967	NM_021140.2	1156	AACATAAATATTGGCCca/GTTATTCAca	24/29	0.234916591257302	5	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.403938557409752	5		618	855	SUCCESS
AR	367	MSKCC	GRCh37	X	66766544	66766544	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	338	796	1	ENST00000374690.3:c.1556G>T	p.Cys519Phe	p.C519F	ENST00000374690	NM_000044.3	519	tGt/tTt	1/8	0.257310116496791	3	FACETS	0.857	0.81	0.904	0.857	0.81	0.904	CLONAL	2	TRUE	1	0.403938557409752	3		797	1174	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0020067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	213	649	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.271113581285643	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.318099765271882	1		649	1005	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974746	21974746	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1060504184	NA	P-0020067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	37	282	0	ENST00000304494.5:c.81G>C	p.Glu27Asp	p.E27D	ENST00000304494	NM_000077.4	27	gaG/gaC	1/3	1	2	FACETS	0.727	0.601	0.867	0.727	0.601	0.867	SUBCLONAL	1	TRUE	1	0.318099765271882	2		282	320	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46738436	46738436	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	97	714	0	ENST00000371975.4:c.1337C>A	p.Ser446Tyr	p.S446Y	ENST00000371975	NM_003579.3	446	tCc/tAc	12/18	0.276513447687871	3	FACETS	0.57	0.506	0.638	0.285	0.253	0.319	SUBCLONAL	1	TRUE	1	0.318099765271882	3		714	1241	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348787	118348787	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	120	414	0	ENST00000534358.1:c.3440A>T	p.Lys1147Met	p.K1147M	ENST00000534358	NM_005933.3	1147	aAg/aTg	5/36	0.244010665514788	3	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.318099765271882	3		414	619	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562600	21562600	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	40	324	1	ENST00000382592.4:c.1319T>A	p.Ile440Asn	p.I440N	ENST00000382592	NM_014572.2	440	aTc/aAc	4/8	1	2	FACETS	0.505	0.419	0.601	0.505	0.419	0.601	SUBCLONAL	1	TRUE	1	0.318099765271882	2		325	498	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061312	38061313	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0020067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	85	763	4	ENST00000250448.2:c.676_677delinsTT	p.Asp226Phe	p.D226F	ENST00000250448	NM_004496.3	226	GAc/TTc	2/2	1	2	FACETS	0.57	0.503	0.643	0.57	0.503	0.643	SUBCLONAL	1	TRUE	1	0.318099765271882	2		767	937	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347374	89347374	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767688937	NA	P-0020067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	118	772	0	ENST00000301030.4:c.5576C>T	p.Ser1859Leu	p.S1859L	ENST00000301030	NM_001256183.1	1859	tCg/tTg	9/13	1	2	FACETS	0.712	0.641	0.787	0.712	0.641	0.787	SUBCLONAL	1	TRUE	1	0.318099765271882	2		772	1042	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984731	11984731	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	10	262	0	ENST00000353533.5:c.277C>T	p.Gln93Ter	p.Q93*	ENST00000353533	NM_003010.3	93	Caa/Taa	3/11	0.271113581285643	1	FACETS	0.328	0.223	0.461	0.328	0.223	0.461	SUBCLONAL	1	TRUE	0	0.318099765271882	1		262	161	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748805	41748805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	253	856	0	ENST00000301178.4:c.1330C>T	p.Pro444Ser	p.P444S	ENST00000301178	NM_021913.4	444	Cct/Tct	11/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.318099765271882	2		856	1301	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456502	29456502	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	224	682	0	ENST00000389048.3:c.2416C>G	p.Arg806Gly	p.R806G	ENST00000389048	NM_004304.4	806	Cgt/Ggt	14/29	0.318099765271882	3	FACETS	1	0.988	1	0.645	0.6	0.693	CLONAL	1	TRUE	1	0.318099765271882	3		682	1265	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46266457	46266457	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	45	741	0	ENST00000371998.3:c.2442T>G	p.Asn814Lys	p.N814K	ENST00000371998		814	aaT/aaG	13/23	1	2	FACETS	0.499	0.419	0.588	0.499	0.419	0.588	SUBCLONAL	1	TRUE	1	0.318099765271882	2		741	567	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595862	52595862	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	113	630	2	ENST00000394830.3:c.4053C>A	p.Asp1351Glu	p.D1351E	ENST00000394830	NM_018313.4	1351	gaC/gaA	26/30	0.218502395468043	2	FACETS	0.723	0.65	0.802	0.362	0.325	0.401	SUBCLONAL	1	TRUE	0	0.318099765271882	2		632	982	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295384	1295384	+	upstream_gene_variant	5'Flank	SNP	C	C	G	novel	NA	P-0020067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	43	302	0				ENST00000310581	NM_198253.2	-/1132			0.244010665514788	3	FACETS	0.795	0.667	0.937			1	CLONAL	1	TRUE	NA	0.318099765271882	3		302	394	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815311	32815328	+	inframe_deletion	In_Frame_Del	DEL	GTCCAGAGATGAAACTAT	GTCCAGAGATGAAACTAT	-	novel	NA	P-0020067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	99	914	0	ENST00000354258.4:c.2045_2062del	p.His682_Gly687del	p.H682_G687del	ENST00000354258	NM_000593.5	682	cATAGTTTCATCTCTGGACtc/ctc	9/11	0.221314234619241	2	FACETS	0.614	0.547	0.686	0.307	0.273	0.343	SUBCLONAL	1	TRUE	0	0.318099765271882	2		914	1014	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389276	8389276	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	53	764	0	ENST00000356435.5:c.4342A>G	p.Ser1448Gly	p.S1448G	ENST00000356435		1448	Agt/Ggt	26/35	1	2	FACETS	0.535	0.456	0.622	0.535	0.456	0.622	SUBCLONAL	1	TRUE	1	0.318099765271882	2		764	623	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	85	188	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.340396788174043	2		188	467	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0020121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	88	684	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.987	0.877	1	0.987	0.877	1	CLONAL	1	TRUE	1	0.340396788174043	2		684	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0020121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	139	346	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.340396788174043	2		346	742	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0020121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	116	1017	1	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	1	2	FACETS	0.844	0.76	0.932	0.844	0.76	0.932	CLONAL	1	TRUE	1	0.340396788174043	2		1018	808	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023471	27023471	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	326	747	0	ENST00000324856.7:c.577G>T	p.Glu193Ter	p.E193*	ENST00000324856	NM_006015.4	193	Gag/Tag	1/20	0.311950303113003	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	3	TRUE	0	0.340396788174043	3		747	745	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198371	108198371	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0020121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	130	619	0	ENST00000278616.4:c.6976-1G>A		p.X2326_splice	ENST00000278616	NM_000051.3	2326			0.313425307726702	3	FACETS	1	0.944	1	0.694	0.635	0.756	CLONAL	2	TRUE	0	0.340396788174043	3		619	429	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243882	46243882	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	153	638	0	ENST00000334344.6:c.1976C>G	p.Ser659Cys	p.S659C	ENST00000334344	NM_152641.2	659	tCt/tGt	15/21	0.229541195127354	2	FACETS	0.897	0.827	0.97	0.897	0.827	0.97	CLONAL	2	TRUE	0	0.340396788174043	2		638	501	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441822	49441822	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	57	910	0	ENST00000301067.7:c.4162del	p.Arg1388GlyfsTer29	p.R1388Gfs*29	ENST00000301067	NM_003482.3	1388	Cgg/gg	14/54	0.229541195127354	2	FACETS	0.398	0.341	0.461	0.199	0.17	0.231	SUBCLONAL	1	TRUE	0	0.340396788174043	2		910	841	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444360	49444360	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	204	986	0	ENST00000301067.7:c.3011C>G	p.Ser1004Cys	p.S1004C	ENST00000301067	NM_003482.3	1004	tCt/tGt	11/54	0.229541195127354	2	FACETS	0.764	0.711	0.82	0.764	0.711	0.82	SUBCLONAL	2	TRUE	0	0.340396788174043	2		986	784	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444482	49444482	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	231	991	1	ENST00000301067.7:c.2889del	p.Asp966ThrfsTer34	p.D966Tfs*34	ENST00000301067	NM_003482.3	963	gcC/gc	11/54	0.229541195127354	2	FACETS	0.899	0.841	0.958	0.899	0.841	0.958	CLONAL	2	TRUE	0	0.340396788174043	2		992	755	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845403	89845403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	209	848	0	ENST00000389301.3:c.1724G>A	p.Arg575Lys	p.R575K	ENST00000389301	NM_000135.2	575	aGg/aAg	19/43	0.339355702302927	3	FACETS	0.854	0.794	0.916	0.854	0.794	0.916	CLONAL	2	TRUE	1	0.340396788174043	3		848	841	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579906	7579906	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	111	852	1	ENST00000269305.4:c.7G>T	p.Glu3Ter	p.E3*	ENST00000269305	NM_001126112.2	3	Gag/Tag	2/11	1	2	FACETS	0.919	0.826	1	0.919	0.826	1	CLONAL	1	TRUE	1	0.340396788174043	2		853	710	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950320	15950320	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	101	992	0	ENST00000268712.3:c.6624G>C	p.Lys2208Asn	p.K2208N	ENST00000268712	NM_006311.3	2208	aaG/aaC	42/46	1	2	FACETS	0.821	0.734	0.913	0.821	0.734	0.913	CLONAL	1	TRUE	1	0.340396788174043	2		992	723	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395803	45395803	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	127	488	0	ENST00000262160.6:c.331C>G	p.Leu111Val	p.L111V	ENST00000262160	NM_005901.5	111	Ctt/Gtt	4/11	0.330490140649071	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.340396788174043	2		488	338	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213502	36213502	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1568370990	NA	P-0020121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	154	1288	0	ENST00000222270.7:c.2604C>G	p.Ile868Met	p.I868M	ENST00000222270	NM_014727.1	868	atC/atG	5/37	0.339355702302927	3	FACETS	0.901	0.823	0.983	0.451	0.411	0.492	CLONAL	1	TRUE	1	0.340396788174043	3		1288	1175	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39234174	39234174	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1553353452	NA	P-0020121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	54	894	0	ENST00000402219.2:c.2671G>A	p.Glu891Lys	p.E891K	ENST00000402219	NM_005633.3	891	Gag/Aag	16/23	1	2	FACETS	0.733	0.627	0.848	0.733	0.627	0.848	SUBCLONAL	1	TRUE	1	0.340396788174043	2		894	433	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374864	149374864	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	118	534	0	ENST00000360632.3:c.230G>C	p.Arg77Pro	p.R77P	ENST00000360632	NM_015472.4	77	cGa/cCa	2/7	0.323106504622256	5	FACETS	0.856	0.774	0.941	0.57	0.516	0.628	CLONAL	2	TRUE	2	0.340396788174043	5		534	612	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808924	1808924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs548817695	NA	P-0020121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	137	932	1	ENST00000260795.2:c.2356G>A	p.Asp786Asn	p.D786N	ENST00000260795		786	Gac/Aac	17/17	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.340396788174043	2		933	711	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526322	31526322	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs970742651	NA	P-0020121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	56	1197	1	ENST00000344624.3:c.718C>T	p.Arg240Ter	p.R240*	ENST00000344624		240	Cga/Tga	2/33	1	2	FACETS	0.306	0.261	0.355	0.306	0.261	0.355	SUBCLONAL	1	TRUE	1	0.340396788174043	2		1198	1076	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0020145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	336	943	0	ENST00000269305.4:c.920-2A>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.472180891832509	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.472180891832509	2		943	677	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793686	89793686	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	92	608	0	ENST00000336032.3:c.755C>A	p.Pro252His	p.P252H	ENST00000336032	NM_006813.2	252	cCt/cAt	2/2	0.472180891832509	3	FACETS	0.839	0.747	0.937	0.42	0.373	0.469	CLONAL	1	TRUE	1	0.472180891832509	3		608	574	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317004	11317004	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	95	601	1	ENST00000361445.4:c.490C>T	p.Arg164Trp	p.R164W	ENST00000361445	NM_004958.3	164	Cgg/Tgg	4/58	0.329022922875706	5	FACETS	0.939	0.836	1			1	CLONAL	1	TRUE	NA	0.472180891832509	5		602	732	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087560	27087560	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	137	940	0	ENST00000324856.7:c.2134G>C	p.Gly712Arg	p.G712R	ENST00000324856	NM_006015.4	712	Gga/Cga	5/20	0.451026397579502	4	FACETS	0.895	0.813	0.98	0.298	0.271	0.327	CLONAL	1	TRUE	1	0.472180891832509	4		940	955	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578390	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0020145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	153	765	0	ENST00000269305.4:c.539_540dup	p.Arg181SerfsTer67	p.R181Sfs*67	ENST00000269305	NM_001126112.2	180	-/AG	5/11	0.472180891832509	2	FACETS	1	0.927	1	0.506	0.464	0.549	CLONAL	1	TRUE	0	0.472180891832509	2		765	641	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214838	36214888	+	inframe_deletion	In_Frame_Del	DEL	CTTCGAGGATTCGGATGACTCGGAGCCCGGGGGCCCCCCTGCTCCTCGGCG	CTTCGAGGATTCGGATGACTCGGAGCCCGGGGGCCCCCCTGCTCCTCGGCG	-	novel	NA	P-0020145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	677	1066	0	ENST00000222270.7:c.3264_3314del	p.Phe1089_Arg1105del	p.F1089_R1105del	ENST00000222270	NM_014727.1	1088	atCTTCGAGGATTCGGATGACTCGGAGCCCGGGGGCCCCCCTGCTCCTCGGCGt/att	8/37	0.472180891832509	6	FACETS	1	0.995	1			1	CLONAL	4	TRUE	NA	0.472180891832509	6		1066	1247	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0020245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	381	525	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.176194028354451	2	FACETS	0.959	0.915	1	1	0.997	1	CLONAL	5	FALSE	0	0.176194028354451	2		525	902	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0020245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	253	949	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.176194028354451	5	FACETS	1	0.982	1	1	0.982	1	CLONAL	4	FALSE	1	0.176194028354451	5		949	815	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486247	8486247	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139171396	NA	P-0020245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	77	470	0	ENST00000356435.5:c.2570G>A	p.Arg857His	p.R857H	ENST00000356435		857	cGt/cAt	17/35	0.176194028354451	4	FACETS	1	0.948	1	0.76	0.67	0.856	CLONAL	2	FALSE	1	0.176194028354451	4		470	451	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520761	176520761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141530067	NA	P-0020245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	118	645	3	ENST00000292408.4:c.1504G>A	p.Val502Ile	p.V502I	ENST00000292408	NM_213647.1	502	Gtc/Atc	11/18	0.176194028354451	3	FACETS	1	0.963	1	0.753	0.681	0.829	CLONAL	2	FALSE	0	0.176194028354451	3		648	645	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026606	48026606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1358771617	NA	P-0020245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	26	525	1	ENST00000234420.5:c.1484G>A	p.Arg495Gln	p.R495Q	ENST00000234420	NM_000179.2	495	cGa/cAa	4/10	0.176194028354451	5	FACETS	0.74	0.585	0.919	0.185	0.146	0.23	CLONAL	1	FALSE	1	0.176194028354451	5		526	504	SUCCESS
APC	324	MSKCC	GRCh37	5	112175608	112175608	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	182	450	0	ENST00000257430.4:c.4317del	p.Pro1440HisfsTer33	p.P1440Hfs*33	ENST00000257430	NM_000038.5	1439	ccT/cc	16/16	0.176194028354451	3	FACETS	0.966	0.904	1	1	0.994	1	CLONAL	6	FALSE	0	0.176194028354451	3		450	388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	59	663	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.173	0.148	0.2	0.173	0.148	0.2	SUBCLONAL	1	TRUE	1	0.747102061051973	2		664	914	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	154	188	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.888	0.82	0.959	0.888	0.82	0.959	CLONAL	1	TRUE	1	0.747102061051973	2		188	464	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	313	663	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.865	0.817	0.913	0.865	0.817	0.913	CLONAL	1	TRUE	1	0.747102061051973	2		664	969	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939506	68939506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1309816810	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	168	793	0	ENST00000288368.4:c.491G>A	p.Gly164Glu	p.G164E	ENST00000288368	NM_024870.2	164	gGa/gAa	5/40	1	2	FACETS	0.931	0.863	1	0.931	0.863	1	CLONAL	1	TRUE	1	0.747102061051973	2		793	483	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	190	500	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.721	0.669	0.775	0.721	0.669	0.775	SUBCLONAL	1	TRUE	1	0.747102061051973	2		501	705	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	270	757	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.747102061051973	2		757	670	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913403	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	212	488	0	ENST00000349496.5:c.110C>A	p.Ser37Tyr	p.S37Y	ENST00000349496	NM_001904.3	37	tCt/tAt	3/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.747102061051973	2		488	542	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	74	232	3	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.747102061051973	1		235	120	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727111	40727111	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779663880	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	282	779	2	ENST00000373198.4:c.3853G>A	p.Asp1285Asn	p.D1285N	ENST00000373198	NM_133170.3	1285	Gat/Aat	28/32	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.747102061051973	2		781	737	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606652	29606652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764207516	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	276	759	0	ENST00000389048.3:c.1228G>A	p.Gly410Arg	p.G410R	ENST00000389048	NM_004304.4	410	Gga/Aga	5/29	1	2	FACETS	0.944	0.89	0.998	0.944	0.89	0.998	CLONAL	1	TRUE	1	0.747102061051973	2		759	783	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363463	40363463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751858236	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	271	784	0	ENST00000397332.2:c.766G>A	p.Glu256Lys	p.E256K	ENST00000397332	NM_001033082.2	256	Gaa/Aaa	3/3	1	2	FACETS	0.834	0.784	0.884	0.834	0.784	0.884	CLONAL	1	TRUE	1	0.747102061051973	2		784	870	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	200	736	3	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.747102061051973	2		739	519	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	235	688	1	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	1	2	FACETS	0.917	0.86	0.975	0.917	0.86	0.975	CLONAL	1	TRUE	1	0.747102061051973	2		689	686	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735422	204735422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	235	433	0	ENST00000302823.3:c.223C>T	p.Arg75Trp	p.R75W	ENST00000302823	NM_005214.4	75	Cgg/Tgg	2/4	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.747102061051973	2		433	555	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134988	41134988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	126	385	0	ENST00000379561.5:c.640C>T	p.Arg214Cys	p.R214C	ENST00000379561	NM_002015.3	214	Cgt/Tgt	2/3	1	2	FACETS	0.932	0.853	1	0.932	0.853	1	CLONAL	1	TRUE	1	0.747102061051973	2		385	362	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915952	127915952	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs865855853	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	217	778	5	ENST00000373547.4:c.529C>T	p.Arg177Ter	p.R177*	ENST00000373547	NM_002721.4	177	Cga/Tga	6/7	1	2	FACETS	0.973	0.911	1	0.973	0.911	1	CLONAL	1	TRUE	1	0.747102061051973	2		783	597	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288993	212288993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867944951	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	174	859	0	ENST00000342788.4:c.2753G>A	p.Gly918Glu	p.G918E	ENST00000342788	NM_005235.2	918	gGa/gAa	23/28	1	2	FACETS	0.956	0.888	1	0.956	0.888	1	CLONAL	1	TRUE	1	0.747102061051973	2		859	487	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265591	198265591	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	212	881	1	ENST00000335508.6:c.2566G>A	p.Asp856Asn	p.D856N	ENST00000335508	NM_012433.2	856	Gat/Aat	18/25	1	2	FACETS	0.978	0.916	1	0.978	0.916	1	CLONAL	1	TRUE	1	0.747102061051973	2		882	580	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971178	13971178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs904139873	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	203	483	0	ENST00000405192.2:c.751C>T	p.Pro251Ser	p.P251S	ENST00000405192	NM_001163147.1	251	Ccc/Tcc	8/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.747102061051973	2		483	515	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984919	9984919	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	266	800	0	ENST00000330684.3:c.1046C>T	p.Ser349Phe	p.S349F	ENST00000330684	NM_001134407.1	349	tCc/tTc	4/13	1	2	FACETS	0.979	0.923	1	0.979	0.923	1	CLONAL	1	TRUE	1	0.747102061051973	2		800	727	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979242	93979242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	152	627	3	ENST00000369303.4:c.1586G>A	p.Arg529Lys	p.R529K	ENST00000369303	NM_004440.3	529	aGa/aAa	7/17	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.747102061051973	2		630	404	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217310	66217310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	114	316	0	ENST00000273854.3:c.2305G>A	p.Asp769Asn	p.D769N	ENST00000273854	NM_004439.5	769	Gat/Aat	14/18	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.747102061051973	2		316	293	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699196	117699196	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	144	534	0	ENST00000369458.3:c.445G>A	p.Ala149Thr	p.A149T	ENST00000369458	NM_024626.3	149	Gcc/Acc	3/6	1	2	FACETS	0.903	0.831	0.976	0.903	0.831	0.976	CLONAL	1	TRUE	1	0.747102061051973	2		534	427	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874163	155874163	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	333	902	0	ENST00000368323.3:c.368G>C	p.Arg123Pro	p.R123P	ENST00000368323	NM_006912.5	123	cGt/cCt	5/6	1	2	FACETS	0.963	0.913	1	0.963	0.913	1	CLONAL	1	TRUE	1	0.747102061051973	2		902	926	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858979	243858979	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	145	812	1	ENST00000263826.5:c.86T>C	p.Leu29Ser	p.L29S	ENST00000263826	NM_005465.4	29	tTg/tCg	2/13	1	2	FACETS	0.903	0.831	0.976	0.903	0.831	0.976	CLONAL	1	TRUE	1	0.747102061051973	2		813	430	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720864	89720864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	139	436	0	ENST00000371953.3:c.1015C>T	p.Pro339Ser	p.P339S	ENST00000371953	NM_000314.4	339	Cca/Tca	8/9	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.747102061051973	2		436	328	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195348	102195348	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	221	627	0	ENST00000263464.3:c.108T>A	p.Tyr36Ter	p.Y36*	ENST00000263464	NM_001165.4	36	taT/taA	2/9	1	2	FACETS	0.976	0.915	1	0.976	0.915	1	CLONAL	1	TRUE	1	0.747102061051973	2		627	606	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343421	118343421	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	157	595	0	ENST00000534358.1:c.1547C>T	p.Ser516Phe	p.S516F	ENST00000534358	NM_005933.3	516	tCc/tTc	3/36	1	2	FACETS	0.792	0.73	0.855	0.792	0.73	0.855	SUBCLONAL	1	TRUE	1	0.747102061051973	2		595	531	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390431	118390431	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782366377	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	302	787	2	ENST00000534358.1:c.11245C>T	p.Arg3749Cys	p.R3749C	ENST00000534358	NM_005933.3	3749	Cgt/Tgt	32/36	1	2	FACETS	0.981	0.928	1	0.981	0.928	1	CLONAL	1	TRUE	1	0.747102061051973	2		789	824	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156073	119156073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763754559	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	285	831	0	ENST00000264033.4:c.1738C>T	p.Pro580Ser	p.P580S	ENST00000264033	NM_005188.3	580	Cct/Tct	11/16	1	2	FACETS	0.954	0.9	1	0.954	0.9	1	CLONAL	1	TRUE	1	0.747102061051973	2		831	800	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431274	49431274	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	270	501	2	ENST00000301067.7:c.9865C>T	p.Pro3289Ser	p.P3289S	ENST00000301067	NM_003482.3	3289	Cca/Tca	34/54	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.747102061051973	2		503	599	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442950	49442950	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	346	779	2	ENST00000301067.7:c.3958G>A	p.Gly1320Arg	p.G1320R	ENST00000301067	NM_003482.3	1320	Gga/Aga	12/54	1	2	FACETS	0.983	0.934	1	0.983	0.934	1	CLONAL	1	TRUE	1	0.747102061051973	2		781	942	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26970466	26970466	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	111	514	0	ENST00000381527.3:c.835T>A	p.Leu279Ile	p.L279I	ENST00000381527	NM_001260.1	279	Tta/Ata	8/13	1	2	FACETS	0.997	0.91	1	0.997	0.91	1	CLONAL	1	TRUE	1	0.747102061051973	2		514	298	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434895	110434896	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	327	1044	2	ENST00000375856.3:c.3505_3506delinsTT	p.Pro1169Phe	p.P1169F	ENST00000375856	NM_003749.2	1169	CCc/TTc	1/2	1	2	FACETS	0.917	0.868	0.966	0.917	0.868	0.966	CLONAL	1	TRUE	1	0.747102061051973	2		1046	955	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422133	81422133	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	334	727	2	ENST00000298171.2:c.109T>C	p.Phe37Leu	p.F37L	ENST00000298171	NM_000369.2	37	Ttc/Ctc	1/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.747102061051973	2		729	872	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358509	67358509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863223749	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	157	316	1	ENST00000327367.4:c.17C>T	p.Pro6Leu	p.P6L	ENST00000327367	NM_005902.3	6	cCt/cTt	1/9	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.747102061051973	2		317	380	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934917	9934917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	228	720	1	ENST00000330684.3:c.1373G>A	p.Gly458Glu	p.G458E	ENST00000330684	NM_001134407.1	458	gGg/gAg	6/13	1	2	FACETS	0.978	0.917	1	0.978	0.917	1	CLONAL	1	TRUE	1	0.747102061051973	2		721	624	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50820792	50820792	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	203	728	0	ENST00000398568.2:c.1967T>A	p.Ile656Asn	p.I656N	ENST00000398568	NM_001042412.1	656	aTt/aAt	12/18	NA	2	FACETS	0.962	0.898	1			1	INDETERMINATE	1	TRUE	NA	0.747102061051973	2		728	565	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50830258	50830258	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	211	594	3	ENST00000398568.2:c.2701C>T	p.Pro901Ser	p.P901S	ENST00000398568	NM_001042412.1	901	Cct/Tct	18/18	NA	2	FACETS	1	0.954	1			1	INDETERMINATE	1	TRUE	NA	0.747102061051973	2		597	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579563	7579563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756847009	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	317	845	1	ENST00000269305.4:c.124G>A	p.Asp42Asn	p.D42N	ENST00000269305	NM_001126112.2	42	Gat/Aat	4/11	1	2	FACETS	0.942	0.892	0.993	0.942	0.892	0.993	CLONAL	1	TRUE	1	0.747102061051973	2		846	901	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552227	29552227	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765281937	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	203	810	2	ENST00000356175.3:c.1960C>T	p.Pro654Ser	p.P654S	ENST00000356175	NM_000267.3	654	Cct/Tct	17/57	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.747102061051973	2		812	510	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687246	37687246	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	292	740	1	ENST00000447079.4:c.4150G>A	p.Gly1384Arg	p.G1384R	ENST00000447079	NM_015083.1	1384	Ggg/Agg	14/14	1	2	FACETS	0.964	0.911	1	0.964	0.911	1	CLONAL	1	TRUE	1	0.747102061051973	2		741	811	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872120	37872120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	370	881	2	ENST00000269571.5:c.1441C>T	p.Pro481Ser	p.P481S	ENST00000269571		481	Ccc/Tcc	12/27	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.747102061051973	2		883	989	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743082	743082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	248	889	0	ENST00000314574.4:c.896C>T	p.Thr299Ile	p.T299I	ENST00000314574	NM_005433.3	299	aCc/aTc	8/12	1	2	FACETS	0.904	0.85	0.961	0.904	0.85	0.961	CLONAL	1	TRUE	1	0.747102061051973	2		889	734	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213470	36213471	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	345	994	3	ENST00000222270.7:c.2572_2573delinsAA	p.Gly858Asn	p.G858N	ENST00000222270	NM_014727.1	858	GGt/AAt	5/37	1	2	FACETS	0.941	0.893	0.99	0.941	0.893	0.99	CLONAL	1	TRUE	1	0.747102061051973	2		997	981	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855574	45855574	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	359	757	0	ENST00000391945.4:c.2083C>G	p.Arg695Gly	p.R695G	ENST00000391945	NM_000400.3	695	Cgc/Ggc	22/23	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.747102061051973	2		757	885	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867691	45867691	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	391	797	1	ENST00000391945.4:c.709C>A	p.His237Asn	p.H237N	ENST00000391945	NM_000400.3	237	Cac/Aac	8/23	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.747102061051973	2		798	989	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725053	47725053	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	383	918	3	ENST00000449228.1:c.691T>C	p.Cys231Arg	p.C231R	ENST00000449228	NM_001127240.2	231	Tgc/Cgc	4/4	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.747102061051973	2		921	1003	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545096	41545096	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	332	891	1	ENST00000263253.7:c.2296C>T	p.Pro766Ser	p.P766S	ENST00000263253	NM_001429.3	766	Cct/Tct	13/31	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.747102061051973	2		892	880	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070326	37070327	+	missense_variant	Missense_Mutation	DNP	AA	AA	GC	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	192	658	0	ENST00000231790.2:c.1461_1462delinsGC	p.Lys488Gln	p.K488Q	ENST00000231790	NM_000249.3	487	cgAAag/cgGCag	13/19	1	2	FACETS	0.972	0.906	1	0.972	0.906	1	CLONAL	1	TRUE	1	0.747102061051973	2		658	529	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125841	47125841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	175	472	0	ENST00000409792.3:c.5429C>T	p.Pro1810Leu	p.P1810L	ENST00000409792	NM_014159.6	1810	cCt/cTt	12/21	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.747102061051973	2		472	432	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643329	52643330	+	inframe_insertion,splice_region_variant	In_Frame_Ins	INS	-	-	GAT	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	196	644	0	ENST00000394830.3:c.2564_2566dup	p.Asn855_Arg856insHis	p.N855_R856insH	ENST00000394830	NM_018313.4	856	cgg/cATCgg	17/30	1	2	FACETS	0.963	0.898	1	0.963	0.898	1	CLONAL	1	TRUE	1	0.747102061051973	2		644	545	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52677358	52677358	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	257	634	0	ENST00000394830.3:c.901A>G	p.Thr301Ala	p.T301A	ENST00000394830	NM_018313.4	301	Act/Gct	10/30	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.747102061051973	2		634	659	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430845	181430845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1177158004	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	331	946	3	ENST00000325404.1:c.697C>T	p.Pro233Ser	p.P233S	ENST00000325404	NM_003106.3	233	Cct/Tct	1/1	1	2	FACETS	0.906	0.858	0.955	0.906	0.858	0.955	CLONAL	1	TRUE	1	0.747102061051973	2		949	978	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184669	185184669	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202042288	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	207	638	1	ENST00000265026.3:c.1561C>T	p.Arg521Cys	p.R521C	ENST00000265026	NM_004721.4	521	Cgt/Tgt	10/14	1	2	FACETS	0.867	0.809	0.927	0.867	0.809	0.927	CLONAL	1	TRUE	1	0.747102061051973	2		639	639	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526751	31526751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	198	663	0	ENST00000344624.3:c.289C>T	p.Pro97Ser	p.P97S	ENST00000344624		97	Cca/Tca	2/33	1	2	FACETS	0.817	0.76	0.875	0.817	0.76	0.875	CLONAL	1	TRUE	1	0.747102061051973	2		663	649	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177590	56177590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747288100	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	214	538	2	ENST00000399503.3:c.2563C>T	p.Arg855Cys	p.R855C	ENST00000399503	NM_005921.1	855	Cgt/Tgt	14/20	1	2	FACETS	0.971	0.909	1	0.971	0.909	1	CLONAL	1	TRUE	1	0.747102061051973	2		540	590	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633791	86633791	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	113	417	0	ENST00000274376.6:c.900T>A	p.Ser300Arg	p.S300R	ENST00000274376	NM_002890.2	300	agT/agA	5/25	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.747102061051973	2		417	274	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915149	131915149	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1561635954	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	274	931	0	ENST00000265335.6:c.506G>A	p.Gly169Glu	p.G169E	ENST00000265335		169	gGa/gAa	4/25	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.747102061051973	2		931	635	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460463	149460463	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	333	782	4	ENST00000286301.3:c.174G>A	p.Trp58Ter	p.W58*	ENST00000286301	NM_005211.3	58	tgG/tgA	3/22	1	2	FACETS	0.939	0.89	0.989	0.939	0.89	0.989	CLONAL	1	TRUE	1	0.747102061051973	2		786	949	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176662909	176662909	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs985459596	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	187	677	0	ENST00000439151.2:c.3884A>G	p.Lys1295Arg	p.K1295R	ENST00000439151	NM_022455.4	1295	aAg/aGg	6/23	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.747102061051973	2		677	483	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670413	30670413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	301	746	3	ENST00000376406.3:c.6019G>A	p.Val2007Ile	p.V2007I	ENST00000376406	NM_014641.2	2007	Gtc/Atc	14/15	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.747102061051973	2		749	804	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671828	30671828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	382	888	0	ENST00000376406.3:c.5132C>T	p.Ser1711Phe	p.S1711F	ENST00000376406	NM_014641.2	1711	tCc/tTc	10/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.747102061051973	2		888	959	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818172	32818173	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	306	980	2	ENST00000354258.4:c.1352_1353delinsAA	p.Arg451Lys	p.R451K	ENST00000354258	NM_000593.5	451	aGG/aAA	5/11	1	2	FACETS	0.871	0.822	0.92	0.871	0.822	0.92	CLONAL	1	TRUE	1	0.747102061051973	2		982	941	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964502	93964502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	190	633	1	ENST00000369303.4:c.2395C>T	p.Pro799Ser	p.P799S	ENST00000369303	NM_004440.3	799	Cca/Tca	14/17	1	2	FACETS	0.988	0.921	1	0.988	0.921	1	CLONAL	1	TRUE	1	0.747102061051973	2		634	515	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965694	93965694	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	169	696	1	ENST00000369303.4:c.2234G>A	p.Gly745Glu	p.G745E	ENST00000369303	NM_004440.3	745	gGa/gAa	13/17	1	2	FACETS	0.979	0.909	1	0.979	0.909	1	CLONAL	1	TRUE	1	0.747102061051973	2		697	462	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6027053	6027053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060503118	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	254	616	3	ENST00000265849.7:c.1343G>A	p.Gly448Glu	p.G448E	ENST00000265849	NM_000535.5	448	gGa/gAa	11/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.747102061051973	2		619	632	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29195996	29195996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	351	808	1	ENST00000240100.2:c.602C>T	p.Pro201Leu	p.P201L	ENST00000240100	NM_001394.6	201	cCc/cTc	3/4	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.747102061051973	2		809	940	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923405	36923405	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778590	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	322	928	2	ENST00000358127.4:c.857C>T	p.Pro286Leu	p.P286L	ENST00000358127	NM_001280556.1	286	cCt/cTt	7/10	0.747102061051973	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.747102061051973	1		930	529	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229623	98229623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1323606391	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	226	650	2	ENST00000331920.6:c.2335G>A	p.Asp779Asn	p.D779N	ENST00000331920	NM_000264.3	779	Gac/Aac	15/24	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.747102061051973	2		652	602	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395288	139395288	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	322	695	0	ENST00000277541.6:c.5650C>T	p.Pro1884Ser	p.P1884S	ENST00000277541	NM_017617.3	1884	Ccg/Tcg	31/34	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.747102061051973	2		695	808	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15826386	15826386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769746691	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	250	384	2	ENST00000307771.7:c.430G>A	p.Glu144Lys	p.E144K	ENST00000307771	NM_005089.3	144	Gaa/Aaa	6/11	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.747102061051973	1		386	325	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913167	44913167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	239	414	0	ENST00000377967.4:c.842C>T	p.Pro281Leu	p.P281L	ENST00000377967	NM_021140.2	281	cCt/cTt	10/29	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.747102061051973	1		414	312	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0020378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	355	422	2	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.589463138374272	2	FACETS	0.858	0.82	0.896	0.858	0.82	0.896	CLONAL	2	TRUE	0	0.596969893259197	2		424	693	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0020378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	32	375	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.271	0.219	0.329	0.271	0.219	0.329	SUBCLONAL	1	TRUE	1	0.596969893259197	2		375	396	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0020378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	139	600	1	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	1	2	FACETS	0.628	0.572	0.686	0.628	0.572	0.686	SUBCLONAL	1	TRUE	1	0.596969893259197	2		601	742	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100175	27100176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	119	621	2	ENST00000324856.7:c.3977dup	p.Gln1327AlafsTer11	p.Q1327Afs*11	ENST00000324856	NM_006015.4	1324	tac/taCc	16/20	1	2	FACETS	0.713	0.646	0.784	0.713	0.646	0.784	SUBCLONAL	1	TRUE	1	0.596969893259197	2		623	559	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913396	NA	P-0020378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	21	484	0	ENST00000349496.5:c.95A>G	p.Asp32Gly	p.D32G	ENST00000349496	NM_001904.3	32	gAc/gGc	3/15	1	2	FACETS	0.176	0.135	0.224	0.176	0.135	0.224	SUBCLONAL	1	TRUE	1	0.596969893259197	2		484	399	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435160	56435161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755128667	NA	P-0020378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	152	796	1	ENST00000407977.2:c.1976dup	p.Pro660SerfsTer87	p.P660Sfs*87	ENST00000407977		659	ggt/ggGt	9/10	1	2	FACETS	0.684	0.627	0.744	0.684	0.627	0.744	SUBCLONAL	1	TRUE	1	0.596969893259197	2		797	744	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519886	NA	P-0020378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	12	482	0	ENST00000349496.5:c.97T>C	p.Ser33Pro	p.S33P	ENST00000349496	NM_001904.3	33	Tct/Cct	3/15	1	2	FACETS	0.1	0.069	0.137	0.1	0.069	0.137	SUBCLONAL	1	TRUE	1	0.596969893259197	2		482	403	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0020378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	114	669	8	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	1	2	FACETS	0.653	0.589	0.72	0.653	0.589	0.72	SUBCLONAL	1	TRUE	1	0.596969893259197	2		677	585	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217234	11217234	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1031980569	NA	P-0020378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	178	839	0	ENST00000361445.4:c.4444C>T	p.Arg1482Cys	p.R1482C	ENST00000361445	NM_004958.3	1482	Cgc/Tgc	30/58	1	2	FACETS	0.778	0.718	0.839	0.778	0.718	0.839	SUBCLONAL	1	TRUE	1	0.596969893259197	2		839	767	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598940	28598940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886369318	NA	P-0020378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	239	892	1	ENST00000253063.3:c.500C>T	p.Ala167Val	p.A167V	ENST00000253063	NM_031459.4	167	gCg/gTg	4/10	1	2	FACETS	0.926	0.866	0.987	0.926	0.866	0.987	CLONAL	1	TRUE	1	0.596969893259197	2		893	865	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885746	23885746	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	209	896	1	ENST00000374561.5:c.172G>A	p.Val58Ile	p.V58I	ENST00000374561	NM_002167.4	58	Gtc/Atc	1/3	1	2	FACETS	0.883	0.822	0.946	0.883	0.822	0.946	CLONAL	1	TRUE	1	0.596969893259197	2		897	793	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101611	27101612	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	251	1085	0	ENST00000324856.7:c.4899dup	p.Met1634HisfsTer14	p.M1634Hfs*14	ENST00000324856	NM_006015.4	1631	-/C	18/20	1	2	FACETS	0.889	0.833	0.947	0.889	0.833	0.947	CLONAL	1	TRUE	1	0.596969893259197	2		1085	946	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346871	91346871	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	29	707	0	ENST00000355112.3:c.3479A>G	p.Tyr1160Cys	p.Y1160C	ENST00000355112	NM_000057.2	1160	tAt/tGt	18/22	1	2	FACETS	0.189	0.151	0.232	0.189	0.151	0.232	SUBCLONAL	1	TRUE	1	0.596969893259197	2		707	514	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3645616	3645616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	85	919	0	ENST00000294008.3:c.2003G>A	p.Gly668Asp	p.G668D	ENST00000294008	NM_032444.2	668	gGc/gAc	9/15	1	2	FACETS	0.296	0.26	0.334	0.296	0.26	0.334	SUBCLONAL	1	TRUE	1	0.596969893259197	2		919	963	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660472	67660472	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0020378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	32	598	0	ENST00000264010.4:c.1372A>T	p.Lys458Ter	p.K458*	ENST00000264010	NM_006565.3	458	Aag/Tag	8/12	1	2	FACETS	0.178	0.144	0.217	0.178	0.144	0.217	SUBCLONAL	1	TRUE	1	0.596969893259197	2		598	602	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211357	36211358	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	208	936	1	ENST00000222270.7:c.1110dup	p.Glu371ArgfsTer18	p.E371Rfs*18	ENST00000222270	NM_014727.1	370	gaa/gAaa	3/37	1	2	FACETS	0.882	0.821	0.945	0.882	0.821	0.945	CLONAL	1	TRUE	1	0.596969893259197	2		937	790	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152518	56152518	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	83	390	0	ENST00000399503.3:c.574A>G	p.Thr192Ala	p.T192A	ENST00000399503	NM_005921.1	192	Acc/Gcc	2/20	1	2	FACETS	0.903	0.805	1	0.903	0.805	1	CLONAL	1	TRUE	1	0.596969893259197	2		390	308	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86686625	86686626	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	83	444	0	ENST00000274376.6:c.3074dup	p.Leu1026AlafsTer20	p.L1026Afs*20	ENST00000274376	NM_002890.2	1023	-/A	25/25	1	2	FACETS	0.843	0.75	0.94	0.843	0.75	0.94	CLONAL	1	TRUE	1	0.596969893259197	2		444	330	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874012	151874013	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	186	714	0	ENST00000262189.6:c.8525dup	p.Asn2842LysfsTer2	p.N2842Kfs*2	ENST00000262189	NM_170606.2	2842	aat/aaAt	38/59	0.598399844051794	3	FACETS	0.872	0.805	0.941	0.436	0.402	0.471	CLONAL	1	TRUE	1	0.596969893259197	3		714	928	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028034	69028034	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	176	882	0	ENST00000288368.4:c.3193del	p.Ser1065GlnfsTer4	p.S1065Qfs*4	ENST00000288368	NM_024870.2	1065	Tca/ca	26/40	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.596969893259197	2		882	550	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424061	49424061	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0020439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	490	1249	0	ENST00000301067.7:c.13999+2T>A		p.X4667_splice	ENST00000301067	NM_003482.3	4667			NA	2	FACETS	0.955	0.931	0.979			1	INDETERMINATE	2	TRUE	NA	0.821874169799332	2		1249	624	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578192	7578200	+	inframe_deletion	In_Frame_Del	DEL	GGGCACCAC	GGGCACCAC	-	novel	NA	P-0020439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	422	1018	0	ENST00000269305.4:c.649_657del	p.Val217_Pro219del	p.V217_P219del	ENST00000269305	NM_001126112.2	217	GTGGTGCCC/-	6/11	0.821874169799332	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.821874169799332	2		1018	511	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588131	67588131	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	60	579	0	ENST00000274335.5:c.961G>T	p.Gly321Cys	p.G321C	ENST00000274335		321	Ggt/Tgt	7/15	0.821874169799332	2	FACETS	0.83	0.729	0.934	0.415	0.364	0.467	CLONAL	1	TRUE	0	0.821874169799332	2		579	176	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860146	151860146	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	82	672	1	ENST00000262189.6:c.10516G>T	p.Glu3506Ter	p.E3506*	ENST00000262189	NM_170606.2	3506	Gag/Tag	43/59	0.431609634865345	4	FACETS	1	0.961	1			1	INDETERMINATE	1	TRUE	NA	0.821874169799332	4		673	309	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929603	44929603	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0020439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	112	433	0	ENST00000377967.4:c.2702+1G>T		p.X901_splice	ENST00000377967	NM_021140.2	901			0.821874169799332	5	FACETS	0.886	0.815	0.957	0.886	0.815	0.957	CLONAL	3	TRUE	2	0.821874169799332	5		433	229	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1272	90	1231	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.881	0.779	0.991	0.881	0.779	0.991	CLONAL	1	TRUE	1	0.15	2		1231	1362	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	51	570	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.73	0.619	0.854	0.73	0.619	0.854	SUBCLONAL	1	TRUE	1	0.15	2		570	931	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	62	499	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.794	0.684	0.915	0.794	0.684	0.915	CLONAL	1	TRUE	1	0.15	2		500	1041	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437701	49437701	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555194045	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1266	67	1202	4	ENST00000301067.7:c.5269C>T	p.Arg1757Ter	p.R1757*	ENST00000301067	NM_003482.3	1757	Cga/Tga	22/54	1	2	FACETS	0.67	0.58	0.769	0.67	0.58	0.769	SUBCLONAL	1	TRUE	1	0.15	2		1206	1333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578552	7578552	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1314	70	1247	0	ENST00000269305.4:c.378C>A	p.Tyr126Ter	p.Y126*	ENST00000269305	NM_001126112.2	126	taC/taA	5/11	1	2	FACETS	0.674	0.585	0.771	0.674	0.585	0.771	SUBCLONAL	1	TRUE	1	0.15	2		1247	1384	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797217	135797217	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	24	437	0	ENST00000298552.3:c.652G>T	p.Glu218Ter	p.E218*	ENST00000298552	NM_001162426.1	218	Gaa/Taa	7/23	1	2	FACETS	0.814	0.638	1	0.814	0.638	1	CLONAL	1	TRUE	1	0.15	2		437	393	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527931	103527931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs4150388	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	109	532	0	ENST00000355739.4:c.3239G>A	p.Gly1080Glu	p.G1080E	ENST00000355739	NM_000123.3	1080	gGa/gAa	15/15	0.20223714783538	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.15	3		532	651	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	46	637	1	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.15	2		638	577	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118950	115118950	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	22	363	0	ENST00000257566.3:c.391C>T	p.Arg131Ter	p.R131*	ENST00000257566	NM_016569.3	131	Cga/Tga	2/8	1	2	FACETS	0.739	0.572	0.934	0.739	0.572	0.934	CLONAL	1	TRUE	1	0.15	2		363	397	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572534	95572534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555370340	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	29	444	0	ENST00000393063.1:c.2831G>A	p.Arg944Gln	p.R944Q	ENST00000393063	NM_030621.3	944	cGa/cAa	19/28	1	2	FACETS	0.792	0.635	0.972	0.792	0.635	0.972	CLONAL	1	TRUE	1	0.15	2		444	488	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164577	47164577	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	30	538	0	ENST00000409792.3:c.1549G>T	p.Glu517Ter	p.E517*	ENST00000409792	NM_014159.6	517	Gaa/Taa	3/21	1	2	FACETS	0.772	0.621	0.944	0.772	0.621	0.944	CLONAL	1	TRUE	1	0.15	2		538	518	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	54	812	1	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.761	0.648	0.886	0.761	0.648	0.886	SUBCLONAL	1	TRUE	1	0.15	2		813	946	SUCCESS
APC	324	MSKCC	GRCh37	5	112175930	112175930	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	22	359	0	ENST00000257430.4:c.4639G>T	p.Glu1547Ter	p.E1547*	ENST00000257430	NM_000038.5	1547	Gaa/Taa	16/16	1	2	FACETS	0.709	0.548	0.895	0.709	0.548	0.895	SUBCLONAL	1	TRUE	1	0.15	2		359	414	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098419	108098419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587779858	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	39	606	1	ENST00000278616.4:c.68G>A	p.Arg23Gln	p.R23Q	ENST00000278616	NM_000051.3	23	cGa/cAa	2/63	1	2	FACETS	0.798	0.66	0.952	0.798	0.66	0.952	CLONAL	1	TRUE	1	0.15	2		607	652	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508127	106508127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226250464	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	27	365	0	ENST00000359195.3:c.121G>A	p.Glu41Lys	p.E41K	ENST00000359195	NM_002649.2	41	Gag/Aag	2/11	1	2	FACETS	0.898	0.714	1	0.898	0.714	1	CLONAL	1	TRUE	1	0.15	2		365	401	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662211	227662211	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	63	1015	0	ENST00000305123.5:c.1244C>T	p.Ser415Leu	p.S415L	ENST00000305123	NM_005544.2	415	tCg/tTg	1/2	1	2	FACETS	0.778	0.67	0.895	0.778	0.67	0.895	SUBCLONAL	1	TRUE	1	0.15	2		1015	1080	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026984	71026984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763413735	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	55	706	0	ENST00000318789.4:c.1343C>T	p.Ser448Leu	p.S448L	ENST00000318789	NM_032682.5	448	tCg/tTg	15/21	1	2	FACETS	0.922	0.787	1	0.922	0.787	1	CLONAL	1	TRUE	1	0.15	2		706	795	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920785	100920785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371165895	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	38	755	0	ENST00000325455.5:c.2363G>A	p.Arg788Gln	p.R788Q	ENST00000325455	NM_001202474.3	788	cGg/cAg	6/8	1	2	FACETS	0.944	0.779	1	0.944	0.779	1	CLONAL	1	TRUE	1	0.15	2		755	537	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702266	47702266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759263820	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	52	892	3	ENST00000233146.2:c.1862G>A	p.Arg621Gln	p.R621Q	ENST00000233146	NM_000251.2	621	cGa/cAa	12/16	1	2	FACETS	0.682	0.578	0.796	0.682	0.578	0.796	SUBCLONAL	1	TRUE	1	0.15	2		895	1017	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	55	731	2	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	1	2	FACETS	0.979	0.836	1	0.979	0.836	1	CLONAL	1	TRUE	1	0.15	2		733	749	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861838	57861838	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381253752	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	71	1024	2	ENST00000228682.2:c.1139G>A	p.Arg380Gln	p.R380Q	ENST00000228682	NM_005269.2	380	cGa/cAa	10/12	1	2	FACETS	0.86	0.748	0.981	0.86	0.748	0.981	CLONAL	1	TRUE	1	0.15	2		1026	1101	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	45	738	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.926	0.777	1	0.926	0.777	1	CLONAL	1	TRUE	1	0.15	2		738	648	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156829	106156829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	51	744	0	ENST00000380013.4:c.1730C>T	p.Ser577Phe	p.S577F	ENST00000380013	NM_001127208.2	577	tCc/tTc	3/11	1	2	FACETS	0.88	0.746	1	0.88	0.746	1	CLONAL	1	TRUE	1	0.15	2		744	773	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216091	7216091	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1332522267	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	52	528	0	ENST00000380728.2:c.968G>A	p.Arg323Gln	p.R323Q	ENST00000380728		323	cGa/cAa	11/11	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.15	2		528	644	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	31	550	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	0.827	0.668	1	0.827	0.668	1	CLONAL	1	TRUE	1	0.15	2		550	500	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509045	106509045	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752896730	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	63	816	0	ENST00000359195.3:c.1039G>A	p.Glu347Lys	p.E347K	ENST00000359195	NM_002649.2	347	Gag/Aag	2/11	1	2	FACETS	0.866	0.747	0.996	0.866	0.747	0.996	CLONAL	1	TRUE	1	0.15	2		816	970	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201008	108201008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881383	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	54	635	0	ENST00000278616.4:c.7375C>T	p.Arg2459Cys	p.R2459C	ENST00000278616	NM_000051.3	2459	Cgt/Tgt	50/63	1	2	FACETS	0.984	0.839	1	0.984	0.839	1	CLONAL	1	TRUE	1	0.15	2		635	732	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944947	31944947	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868835690	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	49	642	0	ENST00000340398.3:c.154C>T	p.Arg52Cys	p.R52C	ENST00000340398	NM_001013699.2	52	Cgt/Tgt	1/1	1	2	FACETS	0.906	0.766	1	0.906	0.766	1	CLONAL	1	TRUE	1	0.15	2		642	721	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225362541	225362541	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs767240461	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	55	769	0	ENST00000264414.4:c.1636C>T	p.Arg546Ter	p.R546*	ENST00000264414	NM_003590.4	546	Cga/Tga	12/16	1	2	FACETS	0.955	0.815	1	0.955	0.815	1	CLONAL	1	TRUE	1	0.15	2		769	768	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612879	228612879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767647652	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	64	927	0	ENST00000366696.1:c.148C>T	p.Arg50Cys	p.R50C	ENST00000366696	NM_003493.2	50	Cgc/Tgc	1/1	1	2	FACETS	0.917	0.792	1	0.917	0.792	1	CLONAL	1	TRUE	1	0.15	2		927	931	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73333960	73333960	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	60	979	1	ENST00000377767.4:c.2850G>T	p.Lys950Asn	p.K950N	ENST00000377767	NM_014953.3	950	aaG/aaT	21/21	0.20223714783538	3	FACETS	0.871	0.748	1	0.436	0.374	0.503	CLONAL	1	TRUE	1	0.15	3		980	987	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591086	67591086	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	24	429	1	ENST00000274335.5:c.1679A>G	p.Asp560Gly	p.D560G	ENST00000274335		560	gAc/gGc	12/15	1	2	FACETS	0.677	0.529	0.847	0.677	0.529	0.847	SUBCLONAL	1	TRUE	1	0.15	2		430	473	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457192	25457192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771922296	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	60	927	2	ENST00000264709.3:c.2695C>T	p.Arg899Cys	p.R899C	ENST00000264709	NM_175629.2	899	Cgc/Tgc	23/23	1	2	FACETS	0.797	0.684	0.92	0.797	0.684	0.92	CLONAL	1	TRUE	1	0.15	2		929	1004	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350062	81350062	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs759145490	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	44	631	1	ENST00000222390.5:c.1270C>T	p.Arg424Cys	p.R424C	ENST00000222390	NM_000601.4	424	Cgt/Tgt	10/18	1	2	FACETS	0.931	0.78	1	0.931	0.78	1	CLONAL	1	TRUE	1	0.15	2		632	630	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518106	103518106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759972289	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	79	474	0	ENST00000355739.4:c.2044G>A	p.Glu682Lys	p.E682K	ENST00000355739	NM_000123.3	682	Gaa/Aaa	9/15	0.20223714783538	3	FACETS	1	0.918	1	1	0.918	1	CLONAL	2	TRUE	1	0.15	3		474	538	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992667	72992667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2073852	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	41	680	0	ENST00000268489.5:c.1378G>A	p.Glu460Lys	p.E460K	ENST00000268489	NM_006885.3	460	Gaa/Aaa	2/10	1	2	FACETS	0.761	0.632	0.905	0.761	0.632	0.905	CLONAL	1	TRUE	1	0.15	2		680	718	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178943780	178943780	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	49	711	0	ENST00000263967.3:c.2447T>G	p.Ile816Ser	p.I816S	ENST00000263967	NM_006218.2	816	aTt/aGt	17/21	1	2	FACETS	0.901	0.762	1	0.901	0.762	1	CLONAL	1	TRUE	1	0.15	2		711	725	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905514	11905514	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	34	411	0	ENST00000396373.4:c.163+1G>A		p.X55_splice	ENST00000396373	NM_001987.4	55			1	2	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	1	0.15	2		411	434	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159157	143159157	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	28	541	0	ENST00000262992.4:c.696G>T	p.Lys232Asn	p.K232N	ENST00000262992	NM_001101669.1	232	aaG/aaT	10/24	1	2	FACETS	0.977	0.781	1	0.977	0.781	1	CLONAL	1	TRUE	1	0.15	2		541	382	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159098	143159098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1321044670	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	42	830	1	ENST00000262992.4:c.755G>A	p.Arg252Gln	p.R252Q	ENST00000262992	NM_001101669.1	252	cGa/cAa	10/24	1	2	FACETS	0.871	0.726	1	0.871	0.726	1	CLONAL	1	TRUE	1	0.15	2		831	643	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509138	106509138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753981231	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	75	814	4	ENST00000359195.3:c.1132G>A	p.Asp378Asn	p.D378N	ENST00000359195	NM_002649.2	378	Gac/Aac	2/11	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.15	2		818	990	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176999	56176999	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765970866	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	53	726	2	ENST00000399503.3:c.2269C>T	p.Arg757Cys	p.R757C	ENST00000399503	NM_005921.1	757	Cgc/Tgc	13/20	1	2	FACETS	0.977	0.832	1	0.977	0.832	1	CLONAL	1	TRUE	1	0.15	2		728	723	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260151	149260151	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1307297959	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	48	744	1	ENST00000360632.3:c.742C>T	p.Arg248Ter	p.R248*	ENST00000360632	NM_015472.4	248	Cga/Tga	4/7	1	2	FACETS	0.841	0.709	0.987	0.841	0.709	0.987	CLONAL	1	TRUE	1	0.15	2		745	761	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085971	16085971	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	49	783	2	ENST00000281043.3:c.1147C>T	p.Arg383Cys	p.R383C	ENST00000281043	NM_005378.4	383	Cgc/Tgc	3/3	1	2	FACETS	0.799	0.675	0.936	0.799	0.675	0.936	CLONAL	1	TRUE	1	0.15	2		785	818	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776674	9776674	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	73	1055	1	ENST00000377346.4:c.777C>A	p.Phe259Leu	p.F259L	ENST00000377346	NM_005026.3	259	ttC/ttA	6/24	1	2	FACETS	0.862	0.751	0.982	0.862	0.751	0.982	CLONAL	1	TRUE	1	0.15	2		1056	1129	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257495	16257495	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	49	593	0	ENST00000375759.3:c.4760T>G	p.Phe1587Cys	p.F1587C	ENST00000375759	NM_015001.2	1587	tTt/tGt	11/15	1	2	FACETS	0.866	0.732	1	0.866	0.732	1	CLONAL	1	TRUE	1	0.15	2		593	754	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933246	36933246	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144754091	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	59	959	4	ENST00000361632.4:c.1871C>T	p.Ser624Leu	p.S624L	ENST00000361632		624	tCg/tTg	14/16	1	2	FACETS	0.78	0.669	0.902	0.78	0.669	0.902	CLONAL	1	TRUE	1	0.15	2		963	1009	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795028	45795028	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144616312	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	59	965	2	ENST00000450313.1:c.1600C>T	p.Arg534Trp	p.R534W	ENST00000450313	NM_012222.2	534	Cgg/Tgg	16/16	1	2	FACETS	0.78	0.669	0.902	0.78	0.669	0.902	CLONAL	1	TRUE	1	0.15	2		967	1009	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46725722	46725722	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	55	811	0	ENST00000371975.4:c.358C>A	p.Leu120Met	p.L120M	ENST00000371975	NM_003579.3	120	Ctg/Atg	5/18	1	2	FACETS	0.88	0.751	1	0.88	0.751	1	CLONAL	1	TRUE	1	0.15	2		811	833	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439711	51439711	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	44	482	0	ENST00000262662.1:c.276T>G	p.Phe92Leu	p.F92L	ENST00000262662		92	ttT/ttG	4/4	1	2	FACETS	0.993	0.832	1	0.993	0.832	1	CLONAL	1	TRUE	1	0.15	2		482	591	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263336	115263336	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs562518461	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	60	903	0	ENST00000438362.2:c.2014G>A	p.Asp672Asn	p.D672N	ENST00000438362	NM_001242891.1	672	Gat/Aat	17/20	1	2	FACETS	0.819	0.703	0.945	0.819	0.703	0.945	CLONAL	1	TRUE	1	0.15	2		903	977	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406000	70406000	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	65	918	2	ENST00000373644.4:c.3514G>T	p.Asp1172Tyr	p.D1172Y	ENST00000373644	NM_030625.2	1172	Gat/Tat	4/12	1	2	FACETS	0.838	0.724	0.962	0.838	0.724	0.962	CLONAL	1	TRUE	1	0.15	2		920	1034	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251854	8251854	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs753080445	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	51	864	0	ENST00000335790.3:c.223C>T	p.Arg75Ter	p.R75*	ENST00000335790	NM_002315.2	75	Cga/Tga	2/4	1	2	FACETS	0.763	0.647	0.892	0.763	0.647	0.892	SUBCLONAL	1	TRUE	1	0.15	2		864	891	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129419	64129419	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	102	1122	2	ENST00000334205.4:c.851G>A	p.Arg284Gln	p.R284Q	ENST00000334205	NM_003942.2	284	cGa/cAa	8/17	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.15	2		1124	1250	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918560	94918560	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	51	996	0	ENST00000536441.1:c.622T>G	p.Phe208Val	p.F208V	ENST00000536441	NM_144665.3	208	Ttt/Gtt	5/10	1	2	FACETS	0.692	0.586	0.81	0.692	0.586	0.81	SUBCLONAL	1	TRUE	1	0.15	2		996	982	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912699	100912699	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs750565074	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	47	771	0	ENST00000325455.5:c.2623A>C	p.Lys875Gln	p.K875Q	ENST00000325455	NM_001202474.3	875	Aaa/Caa	7/8	1	2	FACETS	0.897	0.755	1	0.897	0.755	1	CLONAL	1	TRUE	1	0.15	2		771	699	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203577	108203577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555125394	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	37	676	0	ENST00000278616.4:c.7877C>T	p.Ala2626Val	p.A2626V	ENST00000278616	NM_000051.3	2626	gCt/gTt	53/63	1	2	FACETS	0.699	0.574	0.839	0.699	0.574	0.839	SUBCLONAL	1	TRUE	1	0.15	2		676	706	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352474	118352474	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	32	639	0	ENST00000534358.1:c.3679G>T	p.Asp1227Tyr	p.D1227Y	ENST00000534358	NM_005933.3	1227	Gac/Tac	7/36	1	2	FACETS	0.688	0.557	0.837	0.688	0.557	0.837	SUBCLONAL	1	TRUE	1	0.15	2		639	620	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374150	118374150	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	38	617	0	ENST00000534358.1:c.7543T>G	p.Leu2515Val	p.L2515V	ENST00000534358	NM_005933.3	2515	Tta/Gta	27/36	1	2	FACETS	0.76	0.626	0.909	0.76	0.626	0.909	CLONAL	1	TRUE	1	0.15	2		617	667	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514077	125514077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	64	954	0	ENST00000428830.2:c.1015G>A	p.Val339Ile	p.V339I	ENST00000428830	NM_001114121.2	339	Gta/Ata	10/14	1	2	FACETS	0.827	0.714	0.95	0.827	0.714	0.95	CLONAL	1	TRUE	1	0.15	2		954	1032	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438161	438161	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	51	699	1	ENST00000399788.2:c.1808G>A	p.Arg603Gln	p.R603Q	ENST00000399788	NM_001042603.1	603	cGa/cAa	14/28	1	2	FACETS	0.892	0.757	1	0.892	0.757	1	CLONAL	1	TRUE	1	0.15	2		700	762	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475203	475203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754666448	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	66	1140	1	ENST00000399788.2:c.434G>A	p.Arg145His	p.R145H	ENST00000399788	NM_001042603.1	145	cGc/cAc	4/28	1	2	FACETS	0.712	0.616	0.817	0.712	0.616	0.817	SUBCLONAL	1	TRUE	1	0.15	2		1141	1236	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	495135	495135	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	42	643	0	ENST00000399788.2:c.171G>A	p.Trp57Ter	p.W57*	ENST00000399788	NM_001042603.1	57	tgG/tgA	2/28	1	2	FACETS	0.826	0.688	0.98	0.826	0.688	0.98	CLONAL	1	TRUE	1	0.15	2		643	678	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385180	4385180	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	40	675	0	ENST00000261254.3:c.205G>A	p.Glu69Lys	p.E69K	ENST00000261254	NM_001759.3	69	Gaa/Aaa	2/5	1	2	FACETS	0.757	0.627	0.902	0.757	0.627	0.902	CLONAL	1	TRUE	1	0.15	2		675	705	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715741	18715741	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	38	585	0	ENST00000266497.5:c.3572C>T	p.Thr1191Ile	p.T1191I	ENST00000266497		1191	aCt/aTt	25/31	0.3	2	FACETS	0.809	0.668	0.968			1	CLONAL	1	TRUE	NA	0.15	2		585	626	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46215235	46215235	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	26	532	0	ENST00000334344.6:c.670G>T	p.Glu224Ter	p.E224*	ENST00000334344	NM_152641.2	224	Gaa/Taa	6/21	1	2	FACETS	0.731	0.578	0.908	0.731	0.578	0.908	CLONAL	1	TRUE	1	0.15	2		532	474	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865213	57865213	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1228	76	1120	0	ENST00000228682.2:c.2690T>G	p.Leu897Arg	p.L897R	ENST00000228682	NM_005269.2	897	cTt/cGt	12/12	1	2	FACETS	0.777	0.679	0.884	0.777	0.679	0.884	SUBCLONAL	1	TRUE	1	0.15	2		1120	1304	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620051	21620051	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750829854	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	78	1026	6	ENST00000382592.4:c.115G>A	p.Ala39Thr	p.A39T	ENST00000382592	NM_014572.2	39	Gca/Aca	2/8	0.20223714783538	3	FACETS	0.892	0.781	1	0.446	0.39	0.507	CLONAL	1	TRUE	1	0.15	3		1032	1253	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959447	26959447	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	147	775	0	ENST00000381527.3:c.614T>G	p.Leu205Arg	p.L205R	ENST00000381527	NM_001260.1	205	cTt/cGt	6/13	0.20223714783538	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.15	3		775	908	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134681	41134681	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	107	661	0	ENST00000379561.5:c.947G>A	p.Arg316Gln	p.R316Q	ENST00000379561	NM_002015.3	316	cGa/cAa	2/3	0.20223714783538	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.15	3		661	682	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093357	30093357	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	40	850	2	ENST00000331968.5:c.1905+1G>A		p.X635_splice	ENST00000331968	NM_002742.2	635			1	2	FACETS	0.803	0.666	0.957	0.803	0.666	0.957	CLONAL	1	TRUE	1	0.15	2		852	664	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986833	36986833	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	50	565	0	ENST00000354822.5:c.856C>T	p.Arg286Ter	p.R286*	ENST00000354822	NM_001079668.2	286	Cga/Tga	3/3	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.15	2		565	519	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641221	3641221	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1650	134	1552	1	ENST00000294008.3:c.2418G>T	p.Glu806Asp	p.E806D	ENST00000294008	NM_032444.2	806	gaG/gaT	12/15	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.15	2		1553	1784	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273878	10273878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	82	1157	2	ENST00000330684.3:c.391G>A	p.Ala131Thr	p.A131T	ENST00000330684	NM_001134407.1	131	Gca/Aca	2/13	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.15	2		1159	1073	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647343	23647343	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	70	982	1	ENST00000261584.4:c.524G>T	p.Arg175Ile	p.R175I	ENST00000261584	NM_024675.3	175	aGa/aTa	4/13	1	2	FACETS	0.887	0.771	1	0.887	0.771	1	CLONAL	1	TRUE	1	0.15	2		983	1052	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56852631	56852631	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	60	814	0	ENST00000308159.5:c.545A>G	p.Glu182Gly	p.E182G	ENST00000308159	NM_014669.4	182	gAg/gGg	6/22	1	2	FACETS	0.945	0.812	1	0.945	0.812	1	CLONAL	1	TRUE	1	0.15	2		814	847	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655373	67655373	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	79	923	0	ENST00000264010.4:c.1236T>A	p.Cys412Ter	p.C412*	ENST00000264010	NM_006565.3	412	tgT/tgA	7/12	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.15	2		923	1053	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827421	72827421	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	60	1111	0	ENST00000268489.5:c.9160G>T	p.Asp3054Tyr	p.D3054Y	ENST00000268489	NM_006885.3	3054	Gac/Tac	9/10	1	2	FACETS	0.741	0.636	0.857	0.741	0.636	0.857	SUBCLONAL	1	TRUE	1	0.15	2		1111	1079	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944267	81944267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	75	1032	1	ENST00000359376.3:c.1876G>A	p.Glu626Lys	p.E626K	ENST00000359376	NM_002661.3	626	Gag/Aag	18/33	1	2	FACETS	0.919	0.803	1	0.919	0.803	1	CLONAL	1	TRUE	1	0.15	2		1033	1088	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81973552	81973552	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	67	958	0	ENST00000359376.3:c.3369A>C	p.Glu1123Asp	p.E1123D	ENST00000359376	NM_002661.3	1123	gaA/gaC	30/33	1	2	FACETS	0.857	0.742	0.981	0.857	0.742	0.981	CLONAL	1	TRUE	1	0.15	2		958	1043	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346073	89346073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	13	108	0	ENST00000301030.4:c.6877G>A	p.Asp2293Asn	p.D2293N	ENST00000301030	NM_001256183.1	2293	Gac/Aac	9/13	1	2	FACETS	0.795	0.573	1	1	0.885	1	CLONAL	2	TRUE	1	0.15	2		108	109	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347486	89347486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373805397	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	44	803	1	ENST00000301030.4:c.5464G>A	p.Asp1822Asn	p.D1822N	ENST00000301030	NM_001256183.1	1822	Gac/Aac	9/13	1	2	FACETS	0.689	0.575	0.815	0.689	0.575	0.815	SUBCLONAL	1	TRUE	1	0.15	2		804	852	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349877	89349877	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1337062402	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1492	110	1562	0	ENST00000301030.4:c.3073C>A	p.Pro1025Thr	p.P1025T	ENST00000301030	NM_001256183.1	1025	Cca/Aca	9/13	1	2	FACETS	0.916	0.819	1	0.916	0.819	1	CLONAL	1	TRUE	1	0.15	2		1562	1602	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351718	89351718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1414996600	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1224	76	1155	0	ENST00000301030.4:c.1232C>T	p.Ser411Leu	p.S411L	ENST00000301030	NM_001256183.1	411	tCg/tTg	9/13	1	2	FACETS	0.779	0.681	0.886	0.779	0.681	0.886	SUBCLONAL	1	TRUE	1	0.15	2		1155	1300	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971357	15971357	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151311067	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	67	921	0	ENST00000268712.3:c.4592C>T	p.Ala1531Val	p.A1531V	ENST00000268712	NM_006311.3	1531	gCg/gTg	32/46	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.15	2		921	890	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131373	17131373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779449668	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	88	956	2	ENST00000285071.4:c.79G>A	p.Ala27Thr	p.A27T	ENST00000285071	NM_144997.5	27	Gcc/Acc	4/14	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.15	2		958	1089	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435098	56435098	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	84	973	0	ENST00000407977.2:c.2039T>G	p.Ile680Ser	p.I680S	ENST00000407977		680	aTt/aGt	9/10	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.15	2		973	975	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740723	58740723	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	51	848	1	ENST00000305921.3:c.1628C>A	p.Ser543Tyr	p.S543Y	ENST00000305921	NM_003620.3	543	tCt/tAt	6/6	1	2	FACETS	0.718	0.608	0.84	0.718	0.608	0.84	SUBCLONAL	1	TRUE	1	0.15	2		849	947	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796881	78796881	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	43	639	0	ENST00000306801.3:c.994C>A	p.Leu332Ile	p.L332I	ENST00000306801	NM_020761.2	332	Ctc/Atc	9/34	1	2	FACETS	0.792	0.661	0.938	0.792	0.661	0.938	CLONAL	1	TRUE	1	0.15	2		639	724	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122984	7122984	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	75	1269	0	ENST00000302850.5:c.3275T>G	p.Val1092Gly	p.V1092G	ENST00000302850	NM_000208.2	1092	gTg/gGg	18/22	1	2	FACETS	0.799	0.698	0.91	0.799	0.698	0.91	CLONAL	1	TRUE	1	0.15	2		1269	1251	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7168072	7168072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751178759	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	69	878	0	ENST00000302850.5:c.1517G>A	p.Arg506Gln	p.R506Q	ENST00000302850	NM_000208.2	506	cGg/cAg	7/22	1	2	FACETS	0.947	0.823	1	0.947	0.823	1	CLONAL	1	TRUE	1	0.15	2		878	971	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246843	10246843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1225	82	1202	1	ENST00000340748.4:c.4562G>A	p.Gly1521Asp	p.G1521D	ENST00000340748		1521	gGc/gAc	37/40	1	2	FACETS	0.837	0.735	0.946	0.837	0.735	0.946	CLONAL	1	TRUE	1	0.15	2		1203	1307	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246861	10246861	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1271	75	1208	0	ENST00000340748.4:c.4544G>A	p.Gly1515Glu	p.G1515E	ENST00000340748		1515	gGa/gAa	37/40	1	2	FACETS	0.743	0.648	0.846	0.743	0.648	0.846	SUBCLONAL	1	TRUE	1	0.15	2		1208	1346	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265385	10265385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397509392	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	66	1133	2	ENST00000340748.4:c.1661C>T	p.Ala554Val	p.A554V	ENST00000340748		554	gCg/gTg	20/40	1	2	FACETS	0.82	0.709	0.941	0.82	0.709	0.941	CLONAL	1	TRUE	1	0.15	2		1135	1073	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602769	10602769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1304	107	1194	3	ENST00000171111.5:c.809C>T	p.Ala270Val	p.A270V	ENST00000171111	NM_203500.1	270	gCc/gTc	3/6	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.15	2		1197	1411	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349232	15349232	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	62	892	0	ENST00000263377.2:c.4045T>G	p.Phe1349Val	p.F1349V	ENST00000263377	NM_058243.2	1349	Ttc/Gtc	20/20	1	2	FACETS	0.852	0.734	0.982	0.852	0.734	0.982	CLONAL	1	TRUE	1	0.15	2		892	970	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375309	15375309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	66	1061	1	ENST00000263377.2:c.1118C>T	p.Ala373Val	p.A373V	ENST00000263377	NM_058243.2	373	gCc/gTc	6/20	1	2	FACETS	0.728	0.63	0.836	0.728	0.63	0.836	SUBCLONAL	1	TRUE	1	0.15	2		1062	1208	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17949196	17949196	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	81	814	0	ENST00000458235.1:c.1445A>C	p.Lys482Thr	p.K482T	ENST00000458235	NM_000215.3	482	aAg/aCg	11/24	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.15	2		814	1068	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128036895	128036895	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	89	1020	0	ENST00000285398.2:c.1584G>T	p.Lys528Asn	p.K528N	ENST00000285398	NM_000122.1	528	aaG/aaT	10/15	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.15	2		1020	1149	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095813	178095813	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	58	705	0	ENST00000397062.3:c.1518G>T	p.Lys506Asn	p.K506N	ENST00000397062	NM_006164.4	506	aaG/aaT	5/5	1	2	FACETS	0.942	0.807	1	0.942	0.807	1	CLONAL	1	TRUE	1	0.15	2		705	821	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663425	227663425	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	44	526	0	ENST00000305123.5:c.30C>A	p.Phe10Leu	p.F10L	ENST00000305123	NM_005544.2	10	ttC/ttA	1/2	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.15	2		526	532	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839671	42839671	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs572530227	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	84	1076	3	ENST00000398585.3:c.1568G>A	p.Arg523Gln	p.R523Q	ENST00000398585	NM_001135099.1	523	cGa/cAa	13/14	1	2	FACETS	0.977	0.861	1	0.977	0.861	1	CLONAL	1	TRUE	1	0.15	2		1079	1146	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035134	30035134	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	63	870	0	ENST00000338641.4:c.296A>C	p.Lys99Thr	p.K99T	ENST00000338641	NM_000268.3	99	aAa/aCa	3/16	1	2	FACETS	0.873	0.753	1	0.873	0.753	1	CLONAL	1	TRUE	1	0.15	2		870	962	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523693	41523693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs983340187	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	70	1193	2	ENST00000263253.7:c.1109G>A	p.Arg370His	p.R370H	ENST00000263253	NM_001429.3	370	cGc/cAc	4/31	1	2	FACETS	0.724	0.629	0.828	0.724	0.629	0.828	SUBCLONAL	1	TRUE	1	0.15	2		1195	1289	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551082	41551082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750235600	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	64	1063	2	ENST00000263253.7:c.3226C>T	p.Arg1076Cys	p.R1076C	ENST00000263253	NM_001429.3	1076	Cgt/Tgt	17/31	1	2	FACETS	0.73	0.63	0.84	0.73	0.63	0.84	SUBCLONAL	1	TRUE	1	0.15	2		1065	1169	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641287	12641287	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	50	758	0	ENST00000251849.4:c.1011T>G	p.Asp337Glu	p.D337E	ENST00000251849	NM_002880.3	337	gaT/gaG	10/17	1	2	FACETS	0.846	0.716	0.99	0.846	0.716	0.99	CLONAL	1	TRUE	1	0.15	2		758	788	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163387	47163387	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	42	529	0	ENST00000409792.3:c.2739G>T	p.Lys913Asn	p.K913N	ENST00000409792	NM_014159.6	913	aaG/aaT	3/21	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.15	2		529	537	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723053	49723053	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	25	337	3	ENST00000449682.2:c.1363G>A	p.Asp455Asn	p.D455N	ENST00000449682	NM_020998.3	455	Gac/Aac	11/18	1	2	FACETS	0.903	0.712	1	0.903	0.712	1	CLONAL	1	TRUE	1	0.15	2		340	369	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442051	52442051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	74	891	1	ENST00000460680.1:c.298C>T	p.Leu100Phe	p.L100F	ENST00000460680	NM_004656.3	100	Ctc/Ttc	5/17	1	2	FACETS	0.954	0.833	1	0.954	0.833	1	CLONAL	1	TRUE	1	0.15	2		892	1034	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643618	52643618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1328407334	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	62	772	1	ENST00000394830.3:c.2278C>T	p.Arg760Cys	p.R760C	ENST00000394830	NM_018313.4	760	Cgc/Tgc	17/30	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.15	2		773	795	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52649387	52649387	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	68	1180	2	ENST00000394830.3:c.1904C>T	p.Ala635Val	p.A635V	ENST00000394830	NM_018313.4	635	gCt/gTt	16/30	1	2	FACETS	0.754	0.653	0.863	0.754	0.653	0.863	SUBCLONAL	1	TRUE	1	0.15	2		1182	1203	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651531	52651531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	45	727	0	ENST00000394830.3:c.1565G>A	p.Arg522Gln	p.R522Q	ENST00000394830	NM_018313.4	522	cGa/cAa	15/30	1	2	FACETS	0.71	0.595	0.838	0.71	0.595	0.838	SUBCLONAL	1	TRUE	1	0.15	2		727	845	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498444	89498444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	35	530	0	ENST00000336596.2:c.2416G>A	p.Asp806Asn	p.D806N	ENST00000336596	NM_005233.5	806	Gat/Aat	14/17	1	2	FACETS	0.792	0.648	0.955	0.792	0.648	0.955	CLONAL	1	TRUE	1	0.15	2		530	589	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720900	119720900	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	39	599	0	ENST00000316626.5:c.275G>T	p.Arg92Ile	p.R92I	ENST00000316626		92	aGa/aTa	2/12	1	2	FACETS	0.768	0.635	0.917	0.768	0.635	0.917	CLONAL	1	TRUE	1	0.15	2		599	677	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279197	142279197	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs200968047	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	63	962	3	ENST00000350721.4:c.1449G>T	p.Lys483Asn	p.K483N	ENST00000350721	NM_001184.3	483	aaG/aaT	6/47	1	2	FACETS	0.94	0.811	1	0.94	0.811	1	CLONAL	1	TRUE	1	0.15	2		965	894	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185195171	185195171	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	42	579	1	ENST00000265026.3:c.2488C>T	p.Pro830Ser	p.P830S	ENST00000265026	NM_004721.4	830	Cca/Tca	12/14	1	2	FACETS	0.991	0.827	1	0.991	0.827	1	CLONAL	1	TRUE	1	0.15	2		580	565	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920289	1920289	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	79	976	3	ENST00000382891.5:c.1349G>T	p.Arg450Leu	p.R450L	ENST00000382891	NM_133335.3	450	cGa/cTa	5/22	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.15	2		979	1043	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251901	153251901	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	43	838	0	ENST00000281708.4:c.1105G>T	p.Glu369Ter	p.E369*	ENST00000281708	NM_033632.3	369	Gaa/Taa	7/12	1	2	FACETS	0.781	0.652	0.925	0.781	0.652	0.925	CLONAL	1	TRUE	1	0.15	2		838	734	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517775	187517775	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	32	332	0	ENST00000441802.2:c.12919A>C	p.Asn4307His	p.N4307H	ENST00000441802	NM_005245.3	4307	Aac/Cac	25/27	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.15	2		332	379	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524651	187524651	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754963553	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	72	1110	0	ENST00000441802.2:c.11029G>A	p.Asp3677Asn	p.D3677N	ENST00000441802	NM_005245.3	3677	Gac/Aac	19/27	1	2	FACETS	0.878	0.764	1	0.878	0.764	1	CLONAL	1	TRUE	1	0.15	2		1110	1094	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534462	187534462	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	41	585	0	ENST00000441802.2:c.9264G>T	p.Glu3088Asp	p.E3088D	ENST00000441802	NM_005245.3	3088	gaG/gaT	13/27	1	2	FACETS	0.931	0.775	1	0.931	0.775	1	CLONAL	1	TRUE	1	0.15	2		585	587	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	218531	218531	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1553996375	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	23	179	2	ENST00000264932.6:c.61G>A	p.Ala21Thr	p.A21T	ENST00000264932	NM_004168.2	21	Gcg/Acg	1/15	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.15	2		181	233	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962629	38962629	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	35	784	1	ENST00000357387.3:c.1626G>T	p.Glu542Asp	p.E542D	ENST00000357387	NM_152756.3	542	gaG/gaT	18/38	1	2	FACETS	0.718	0.587	0.866	0.718	0.587	0.866	SUBCLONAL	1	TRUE	1	0.15	2		785	650	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589552	67589552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	18	407	0	ENST00000274335.5:c.1315G>A	p.Glu439Lys	p.E439K	ENST00000274335		439	Gaa/Aaa	10/15	1	2	FACETS	0.706	0.531	0.913	0.706	0.531	0.913	CLONAL	1	TRUE	1	0.15	2		407	340	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80160683	80160684	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	73	1297	0	ENST00000265081.6:c.3059dup	p.Asn1020LysfsTer17	p.N1020Kfs*17	ENST00000265081	NM_002439.4	1018	gaa/gAaa	22/24	1	2	FACETS	0.847	0.738	0.965	0.847	0.738	0.965	CLONAL	1	TRUE	1	0.15	2		1297	1149	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80169100	80169100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs545543643	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	33	561	2	ENST00000265081.6:c.3296C>T	p.Thr1099Met	p.T1099M	ENST00000265081	NM_002439.4	1099	aCg/aTg	23/24	1	2	FACETS	0.818	0.665	0.991	0.818	0.665	0.991	CLONAL	1	TRUE	1	0.15	2		563	538	SUCCESS
APC	324	MSKCC	GRCh37	5	112173632	112173632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060503302	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	37	504	1	ENST00000257430.4:c.2341C>T	p.Pro781Ser	p.P781S	ENST00000257430	NM_000038.5	781	Ccc/Tcc	16/16	1	2	FACETS	0.859	0.707	1	0.859	0.707	1	CLONAL	1	TRUE	1	0.15	2		505	574	SUCCESS
APC	324	MSKCC	GRCh37	5	112177223	112177223	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	39	394	1	ENST00000257430.4:c.5932G>T	p.Glu1978Ter	p.E1978*	ENST00000257430	NM_000038.5	1978	Gaa/Taa	16/16	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.15	2		395	447	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631256	176631256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	35	502	0	ENST00000439151.2:c.1199G>A	p.Arg400Lys	p.R400K	ENST00000439151	NM_022455.4	400	aGa/aAa	4/23	0.3	2	FACETS	0.787	0.644	0.949			1	CLONAL	1	TRUE	NA	0.15	2		502	593	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180050958	180050958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781305649	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1265	78	1302	4	ENST00000261937.6:c.1525G>A	p.Glu509Lys	p.E509K	ENST00000261937	NM_182925.4	509	Gag/Aag	11/30	0.3	2	FACETS	0.774	0.678	0.879			1	SUBCLONAL	1	TRUE	NA	0.15	2		1306	1343	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166821	32166821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1041758474	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	82	1013	1	ENST00000375023.3:c.4417C>T	p.Arg1473Cys	p.R1473C	ENST00000375023	NM_004557.3	1473	Cgt/Tgt	24/30	1	2	FACETS	0.853	0.75	0.966	0.853	0.75	0.966	CLONAL	1	TRUE	1	0.15	2		1014	1281	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797788	32797788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370090254	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	54	985	2	ENST00000374899.4:c.1714G>A	p.Glu572Lys	p.E572K	ENST00000374899	NM_018833.2	572	Gaa/Aaa	10/12	1	2	FACETS	0.691	0.588	0.805	0.691	0.588	0.805	SUBCLONAL	1	TRUE	1	0.15	2		987	1042	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979253	93979253	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	37	661	0	ENST00000369303.4:c.1575T>G	p.Asn525Lys	p.N525K	ENST00000369303	NM_004440.3	525	aaT/aaG	7/17	1	2	FACETS	0.89	0.733	1	0.89	0.733	1	CLONAL	1	TRUE	1	0.15	2		661	554	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106534430	106534430	+	start_lost	Translation_Start_Site	SNP	T	T	G	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	35	591	0	ENST00000369096.4:c.2T>G	p.Met1?	p.M1?	ENST00000369096	NM_001198.3	1	aTg/aGg	1/7	1	2	FACETS	0.678	0.554	0.818	0.678	0.554	0.818	SUBCLONAL	1	TRUE	1	0.15	2		591	688	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109314090	109314090	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	47	870	0	ENST00000436639.2:c.1133T>G	p.Val378Gly	p.V378G	ENST00000436639	NM_014454.2	378	gTt/gGt	7/10	1	2	FACETS	0.707	0.595	0.832	0.707	0.595	0.832	SUBCLONAL	1	TRUE	1	0.15	2		870	886	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729631	41729631	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	42	760	0	ENST00000242208.4:c.898T>G	p.Ser300Ala	p.S300A	ENST00000242208	NM_002192.2	300	Tct/Gct	3/3	1	2	FACETS	0.672	0.559	0.798	0.672	0.559	0.798	SUBCLONAL	1	TRUE	1	0.15	2		760	833	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210116	55210116	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs778638117	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	44	850	0	ENST00000275493.2:c.226C>A	p.Leu76Ile	p.L76I	ENST00000275493	NM_005228.3	76	Ctt/Att	2/28	1	2	FACETS	0.73	0.61	0.863	0.73	0.61	0.863	SUBCLONAL	1	TRUE	1	0.15	2		850	804	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339776	116339776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367722737	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	37	587	0	ENST00000397752.3:c.638C>T	p.Ser213Leu	p.S213L	ENST00000397752	NM_000245.2	213	tCg/tTg	2/21	1	2	FACETS	0.758	0.623	0.909	0.758	0.623	0.909	CLONAL	1	TRUE	1	0.15	2		587	651	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845367	151845367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	59	882	0	ENST00000262189.6:c.13645C>T	p.Arg4549Cys	p.R4549C	ENST00000262189	NM_170606.2	4549	Cgc/Tgc	52/59	1	2	FACETS	0.824	0.707	0.952	0.824	0.707	0.952	CLONAL	1	TRUE	1	0.15	2		882	955	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878749	151878749	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1211949081	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	37	589	1	ENST00000262189.6:c.6196C>T	p.Arg2066Ter	p.R2066*	ENST00000262189	NM_170606.2	2066	Cga/Tga	36/59	1	2	FACETS	0.712	0.585	0.854	0.712	0.585	0.854	SUBCLONAL	1	TRUE	1	0.15	2		590	693	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279438	38279438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1563475734	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	68	876	1	ENST00000425967.3:c.1051G>A	p.Asp351Asn	p.D351N	ENST00000425967	NM_001174067.1	351	Gac/Aac	9/19	1	2	FACETS	0.919	0.797	1	0.919	0.797	1	CLONAL	1	TRUE	1	0.15	2		877	987	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117874125	117874125	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	56	865	0	ENST00000297338.2:c.329T>C	p.Leu110Ser	p.L110S	ENST00000297338	NM_006265.2	110	tTa/tCa	4/14	1	2	FACETS	0.951	0.813	1	0.951	0.813	1	CLONAL	1	TRUE	1	0.15	2		865	785	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485846	8485846	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146684382	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	32	557	1	ENST00000356435.5:c.2971G>A	p.Asp991Asn	p.D991N	ENST00000356435		991	Gat/Aat	17/35	1	2	FACETS	0.724	0.587	0.881	0.724	0.587	0.881	SUBCLONAL	1	TRUE	1	0.15	2		558	589	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157936	27157936	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	47	868	1	ENST00000380036.4:c.160C>A	p.Pro54Thr	p.P54T	ENST00000380036	NM_000459.3	54	Ccc/Acc	2/23	1	2	FACETS	0.67	0.563	0.788	0.67	0.563	0.788	SUBCLONAL	1	TRUE	1	0.15	2		869	936	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37034011	37034011	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	52	641	0	ENST00000358127.4:c.18T>A	p.Asn6Lys	p.N6K	ENST00000358127	NM_001280556.1	6	aaT/aaA	1/10	1	2	FACETS	0.921	0.782	1	0.921	0.782	1	CLONAL	1	TRUE	1	0.15	2		641	753	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650169	93650169	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	51	713	0	ENST00000375746.1:c.1720C>T	p.Arg574Ter	p.R574*	ENST00000375746	NM_001174167.1	574	Cga/Tga	12/14	1	2	FACETS	0.916	0.777	1	0.916	0.777	1	CLONAL	1	TRUE	1	0.15	2		713	742	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238441	98238441	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	34	542	0	ENST00000331920.6:c.1603G>A	p.Asp535Asn	p.D535N	ENST00000331920	NM_000264.3	535	Gac/Aac	12/24	1	2	FACETS	0.865	0.706	1	0.865	0.706	1	CLONAL	1	TRUE	1	0.15	2		542	524	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128347994	128347994	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1415224147	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	72	1157	1	ENST00000265960.3:c.511A>G	p.Thr171Ala	p.T171A	ENST00000265960	NM_001006617.1	171	Aca/Gca	5/12	1	2	FACETS	0.832	0.724	0.949	0.832	0.724	0.949	CLONAL	1	TRUE	1	0.15	2		1158	1154	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760166	133760166	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	46	784	1	ENST00000318560.5:c.2489T>A	p.Leu830His	p.L830H	ENST00000318560	NM_005157.4	830	cTc/cAc	11/11	1	2	FACETS	0.752	0.631	0.886	0.752	0.631	0.886	SUBCLONAL	1	TRUE	1	0.15	2		785	816	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577514	7577515	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCA	novel	NA	P-0020568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	242	793	0	ENST00000269305.4:c.766_767insTGA	p.Ile255_Thr256insMet	p.I255_T256insM	ENST00000269305	NM_001126112.2	256	aca/aTGAca	7/11	0.423149410609946	2	FACETS	0.927	0.872	0.982	0.927	0.872	0.982	CLONAL	2	TRUE	0	0.423149410609946	2		793	617	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55130003	55130003	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	81	714	0	ENST00000257290.5:c.537T>A	p.Asn179Lys	p.N179K	ENST00000257290	NM_006206.4	179	aaT/aaA	4/23	0.423149410609946	2	FACETS	0.884	0.783	0.992	0.442	0.391	0.496	CLONAL	1	TRUE	0	0.423149410609946	2		714	433	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50811826	50811826	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs886040872	NA	P-0020587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	431	810	1	ENST00000398568.2:c.1103C>A	p.Ser368Ter	p.S368*	ENST00000398568	NM_001042412.1	368	tCa/tAa	7/18	0.9272816339233	1	FACETS	0.917	0.896	0.938	0.917	0.896	0.938	CLONAL	1	TRUE	0	0.958037796306188	1		811	511	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131894981	131894983	+	frameshift_variant	Frame_Shift_Del	DEL	CAT	CAT	A	novel	NA	P-0020587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	158	482	0	ENST00000265335.6:c.135_137delinsA	p.Ile46Ter	p.I46*	ENST00000265335		45	atCATt/atAt	2/25	1	2	FACETS	0.82	0.761	0.881	0.82	0.761	0.881	CLONAL	1	TRUE	1	0.958037796306188	2		482	402	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243712	41243712	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	166	789	1	ENST00000357654.3:c.3836C>A	p.Ala1279Glu	p.A1279E	ENST00000357654	NM_007294.3	1279	gCa/gAa	10/23	1	2	FACETS	0.418	0.384	0.453	0.418	0.384	0.453	SUBCLONAL	1	TRUE	1	0.958037796306188	2		790	830	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50811826	50811826	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs886040872	NA	P-0020587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	268	810	1	ENST00000398568.2:c.1103C>A	p.Ser368Ter	p.S368*	ENST00000398568	NM_001042412.1	368	tCa/tAa	7/18	0.634903641096445	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.634903641096445	1		811	575	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131894981	131894983	+	frameshift_variant	Frame_Shift_Del	DEL	CAT	CAT	A	novel	NA	P-0020587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	161	482	0	ENST00000265335.6:c.135_137delinsA	p.Ile46Ter	p.I46*	ENST00000265335		45	atCATt/atAt	2/25	1	2	FACETS	0.934	0.862	1	0.934	0.862	1	CLONAL	1	TRUE	1	0.634903641096445	2		482	543	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	1028	570	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.414234827669182	7	FACETS	1	0.995	1			1	CLONAL	5	TRUE	NA	0.414234827669182	7		570	1879	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913385	NA	P-0020763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	310	557	0	ENST00000304494.5:c.247C>G	p.His83Asp	p.H83D	ENST00000304494	NM_000077.4	83	Cac/Gac	2/3	0.414234827669182	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.414234827669182	2		557	655	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0020763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	264	614	0	ENST00000269305.4:c.559+1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.336126275531509	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.414234827669182	2		614	589	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977591	2977591	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	359	841	0	ENST00000396946.4:c.1093A>G	p.Met365Val	p.M365V	ENST00000396946	NM_032415.4	365	Atg/Gtg	8/25	0.40082714699192	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.414234827669182	4		841	1209	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0020903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	341	346	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.376236546731034	2	FACETS	0.938	0.891	0.987	0.938	0.891	0.987	CLONAL	2	TRUE	0	0.397165377541741	2		346	915	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396740	396740	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	130	840	0	ENST00000262320.3:c.286C>T	p.Gln96Ter	p.Q96*	ENST00000262320	NM_003502.3	96	Caa/Taa	2/11	0.397165377541741	1	FACETS	0.784	0.713	0.859	0.784	0.713	0.859	SUBCLONAL	1	TRUE	0	0.397165377541741	1		840	669	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931471	131931471	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753002904	NA	P-0020903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	117	505	0	ENST00000265335.6:c.2176C>T	p.Arg726Cys	p.R726C	ENST00000265335		726	Cgt/Tgt	13/25	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.397165377541741	2		505	550	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862838	9862838	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	296	889	0	ENST00000330684.3:c.2465A>T	p.Tyr822Phe	p.Y822F	ENST00000330684	NM_001134407.1	822	tAc/tTc	12/13	0.37886755961464	3	FACETS	0.826	0.778	0.875			1	CLONAL	2	TRUE	NA	0.397165377541741	3		889	1082	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531033	187531033	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	164	763	0	ENST00000441802.2:c.9990T>G	p.Asp3330Glu	p.D3330E	ENST00000441802	NM_005245.3	3330	gaT/gaG	15/27	0.397165377541741	1	FACETS	0.989	0.911	1	0.989	0.911	1	CLONAL	1	TRUE	0	0.397165377541741	1		763	669	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974726	21974733	+	frameshift_variant	Frame_Shift_Del	DEL	GCCTCCAG	GCCTCCAG	-	novel	NA	P-0020903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	188	536	0	ENST00000304494.5:c.94_101del	p.Leu32GlyfsTer9	p.L32Gfs*9	ENST00000304494	NM_000077.4	32	CTGGAGGCg/g	1/3	0.397165377541741	2	FACETS	0.858	0.798	0.918	0.858	0.798	0.918	CLONAL	2	TRUE	0	0.397165377541741	2		536	552	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726683	41726815	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGAGCTCGCGGACAGCACCCAGACCCAGGTGCCCCTGGGTGAGGATGAACAGGATGACTGGATAGTGGTCAGCCAGCTCAGGTGTGTGGCCACATCCCCGAATCCCACTCCCACCTCCGTCACACAGAGGGCA	GGAGCTCGCGGACAGCACCCAGACCCAGGTGCCCCTGGGTGAGGATGAACAGGATGACTGGATAGTGGTCAGCCAGCTCAGGTGTGTGGCCACATCCCCGAATCCCACTCCCACCTCCGTCACACAGAGGGCA	-	novel	NA	P-0021028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	110	895	0	ENST00000301178.4:c.229_308+53del		p.X77_splice	ENST00000301178	NM_021913.4	77		2/20	1	2	FACETS	0.634	0.571	0.7	0.634	0.571	0.7	SUBCLONAL	1	TRUE	1	0.599430547518438	2		895	579	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557909	29557909	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs866069972	NA	P-0021050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	28	130	0	ENST00000356175.3:c.3163C>T	p.Gln1055Ter	p.Q1055*	ENST00000356175	NM_000267.3	1055	Caa/Taa	24/57	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.6545366961343	2		130	70	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637062	93637062	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369986984	NA	P-0021050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	32	750	0	ENST00000375746.1:c.1112C>T	p.Thr371Met	p.T371M	ENST00000375746	NM_001174167.1	371	aCg/aTg	9/14	1	2	FACETS	0.153	0.123	0.187	0.153	0.123	0.187	SUBCLONAL	1	TRUE	1	0.6545366961343	2		750	639	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440741	56440741	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	191	627	0	ENST00000407977.2:c.477G>A	p.Trp159Ter	p.W159*	ENST00000407977		159	tgG/tgA	5/10	0.427252823525329	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.427252823525329	2		627	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0021063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	224	650	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.427252823525329	2	FACETS	0.98	0.921	1	0.98	0.921	1	CLONAL	2	TRUE	0	0.427252823525329	2		650	535	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22412959	22412959	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	49	230	0	ENST00000344548.3:c.206C>T	p.Pro69Leu	p.P69L	ENST00000344548	NM_001039802.1	69	cCg/cTg	5/7	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.427252823525329	2		230	229	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405956	49405956	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	266	750	2	ENST00000418115.1:c.182C>T	p.Ala61Val	p.A61V	ENST00000418115	NM_001664.2	61	gCt/gTt	3/5	0.369392638534555	3	FACETS	0.845	0.799	0.891	0.845	0.799	0.891	CLONAL	3	TRUE	0	0.427252823525329	3		752	596	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411202	63411202	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	251	878	0	ENST00000330258.3:c.1965G>T	p.Gln655His	p.Q655H	ENST00000330258	NM_152424.3	655	caG/caT	2/2	0.568339528080136	1	FACETS	0.775	0.732	0.817	0.775	0.732	0.817	SUBCLONAL	1	TRUE	0	0.749096436633323	1		878	541	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0021193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	286	756	0	ENST00000269305.4:c.673-1G>C		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.749096436633323	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.749096436633323	1		756	467	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422058	81422059	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1318223887	NA	P-0021193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	218	623	0	ENST00000298171.2:c.35dup	p.Leu13AlafsTer49	p.L13Afs*49	ENST00000298171	NM_000369.2	12	ctg/cTtg	1/10	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.749096436633323	2		623	567	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0021397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	336	880	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.553596161744252	2	FACETS	0.898	0.857	0.939	0.898	0.857	0.939	CLONAL	2	TRUE	0	0.569616718098858	2		880	657	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0021397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	74	398	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.569616718098858	2		398	238	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0021397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	53	185	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	1	2	FACETS	0.651	0.559	0.75	0.651	0.559	0.75	SUBCLONAL	1	TRUE	1	0.569616718098858	2		185	286	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588981	67588981	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	23	500	1	ENST00000274335.5:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000274335		358	Cga/Tga	8/15	1	2	FACETS	0.353	0.276	0.441	0.353	0.276	0.441	SUBCLONAL	1	TRUE	1	0.569616718098858	2		501	229	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726267	46726267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371935755	NA	P-0021397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	110	645	0	ENST00000371975.4:c.461G>A	p.Arg154Gln	p.R154Q	ENST00000371975	NM_003579.3	154	cGg/cAg	6/18	1	2	FACETS	0.701	0.632	0.774	0.701	0.632	0.774	SUBCLONAL	1	TRUE	1	0.569616718098858	2		645	551	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414940	56414940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1459153703	NA	P-0021397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	116	680	1	ENST00000348428.3:c.2341C>T	p.Arg781Trp	p.R781W	ENST00000348428	NM_006785.3	781	Cgg/Tgg	17/17	0.569616718098858	1	FACETS	0.937	0.856	1	0.937	0.856	1	CLONAL	1	TRUE	0	0.569616718098858	1		681	311	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220578	1220578	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1131690934	NA	P-0021442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	521	769	0	ENST00000326873.7:c.598-2A>G		p.X200_splice	ENST00000326873	NM_000455.4	200			0.511111774191768	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.511111774191768	2		769	967	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874286	155874286	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs868208063	NA	P-0021442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	808	593	0	ENST00000368323.3:c.245T>G	p.Phe82Cys	p.F82C	ENST00000368323	NM_006912.5	82	tTt/tGt	5/6	0.511111774191768	6	FACETS	0.94	0.911	0.968			1	CLONAL	4	TRUE	NA	0.511111774191768	6		593	1701	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243668583	243668583	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	369	641	0	ENST00000263826.5:c.1408C>T	p.Gln470Ter	p.Q470*	ENST00000263826	NM_005465.4	470	Caa/Taa	13/13	0.511111774191768	5	FACETS	0.971	0.921	1	0.486	0.46	0.512	CLONAL	2	TRUE	1	0.511111774191768	5		641	1313	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624268	89624268	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	330	497	1	ENST00000371953.3:c.42G>T	p.Arg14Ser	p.R14S	ENST00000371953	NM_000314.4	14	agG/agT	1/9	0.308206594867468	5	FACETS	0.872	0.827	0.917	0.872	0.827	0.917	CLONAL	3	TRUE	2	0.511111774191768	5		498	872	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119752	108119752	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	125	335	0	ENST00000278616.4:c.1158G>T	p.Arg386Ser	p.R386S	ENST00000278616	NM_000051.3	386	agG/agT	9/63	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.511111774191768	2		335	410	SUCCESS
CBL	867	MSKCC	GRCh37	11	119077161	119077161	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs866162034	NA	P-0021442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	250	641	0	ENST00000264033.4:c.34G>T	p.Gly12Trp	p.G12W	ENST00000264033	NM_005188.3	12	Ggg/Tgg	1/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.511111774191768	2		641	866	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610523	10610523	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	605	884	0	ENST00000171111.5:c.187del	p.Ala63ProfsTer5	p.A63Pfs*5	ENST00000171111	NM_203500.1	63	Gcc/cc	2/6	0.511111774191768	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.511111774191768	2		884	1143	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513326	41513326	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	238	723	1	ENST00000263253.7:c.230A>T	p.Lys77Ile	p.K77I	ENST00000263253	NM_001429.3	77	aAa/aTa	2/31	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.511111774191768	2		724	853	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47061306	47061306	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	346	591	1	ENST00000409792.3:c.7375G>T	p.Glu2459Ter	p.E2459*	ENST00000409792	NM_014159.6	2459	Gaa/Taa	19/21	0.511111774191768	3	FACETS	0.978	0.93	1	0.978	0.93	1	CLONAL	2	TRUE	1	0.511111774191768	3		592	869	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519270	187519270	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	198	606	1	ENST00000441802.2:c.12113G>T	p.Cys4038Phe	p.C4038F	ENST00000441802	NM_005245.3	4038	tGc/tTc	23/27	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.511111774191768	2		607	753	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513565	149513565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	227	639	0	ENST00000261799.4:c.638C>T	p.Ser213Phe	p.S213F	ENST00000261799	NM_002609.3	213	tCc/tTc	5/23	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.511111774191768	2		639	865	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412937	63412937	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	343	974	0	ENST00000330258.3:c.230G>C	p.Arg77Pro	p.R77P	ENST00000330258	NM_152424.3	77	cGg/cCg	2/2	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.511111774191768	2		974	1311	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0021496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	196	611	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.320573201069593	3	FACETS	1	0.989	1	0.702	0.649	0.756	CLONAL	1	TRUE	1	0.320573201069593	3		611	1011	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954210	48954210	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1354030520	NA	P-0021496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	341	444	0	ENST00000267163.4:c.1411C>T	p.Gln471Ter	p.Q471*	ENST00000267163	NM_000321.2	471	Caa/Taa	15/27	0.320573201069593	5	FACETS	1	0.974	1	0.827	0.787	0.867	CLONAL	4	TRUE	0	0.320573201069593	5		444	762	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	250	1140	0	ENST00000269305.4:c.403del	p.Cys135AlafsTer35	p.C135Afs*35	ENST00000269305	NM_001126112.2	135	Tgc/gc	5/11	NA	2	FACETS	0.797	0.746	0.849			1	INDETERMINATE	2	TRUE	NA	0.320573201069593	2		1140	979	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371776	118371776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555045451	NA	P-0021496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	150	650	1	ENST00000534358.1:c.6233G>A	p.Arg2078His	p.R2078H	ENST00000534358	NM_005933.3	2078	cGt/cAt	25/36	0.176124349527444	5	FACETS	0.945	0.866	1	0.63	0.577	0.686	INDETERMINATE	2	TRUE	2	0.320573201069593	5		651	733	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	160	468	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.763	0.7	0.829	1	0.989	1	SUBCLONAL	2	TRUE	1	0.25	2		472	839	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	122	879	1	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.859	0.775	0.949	0.859	0.775	0.949	CLONAL	1	TRUE	1	0.25	2		880	1136	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31405819	31405819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	41	450	1	ENST00000344624.3:c.3959C>T	p.Ala1320Val	p.A1320V	ENST00000344624		1320	gCg/gTg	32/33	1	2	FACETS	0.863	0.72	1	0.863	0.72	1	CLONAL	1	TRUE	1	0.25	2		451	380	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850704	63850705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	32	422	0	ENST00000279873.7:c.1489dup	p.Ile497AsnfsTer31	p.I497Nfs*31	ENST00000279873	NM_032199.2	494	-/A	10/10	1	2	FACETS	0.566	0.459	0.688	0.566	0.459	0.688	SUBCLONAL	1	TRUE	1	0.25	2		422	452	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	73	409	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.807	0.71	0.909	1	0.978	1	CLONAL	2	TRUE	1	0.25	2		410	362	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073616	8073616	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	66	460	0	ENST00000377482.5:c.1043del	p.Pro348ArgfsTer104	p.P348Rfs*104	ENST00000377482	NM_018948.3	348	cCg/cg	4/4	1	2	FACETS	0.996	0.866	1	0.996	0.866	1	CLONAL	1	TRUE	1	0.25	2		460	530	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775779	9775779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1205317546	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	91	792	0	ENST00000377346.4:c.322C>T	p.Arg108Cys	p.R108C	ENST00000377346	NM_005026.3	108	Cgc/Tgc	4/24	1	2	FACETS	0.718	0.636	0.806	0.718	0.636	0.806	SUBCLONAL	1	TRUE	1	0.25	2		792	1014	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333117	70333117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140752046	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	108	696	0	ENST00000373644.4:c.1022C>T	p.Ala341Val	p.A341V	ENST00000373644	NM_030625.2	341	gCt/gTt	2/12	1	2	FACETS	0.971	0.87	1	0.971	0.87	1	CLONAL	1	TRUE	1	0.25	2		696	890	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720818	89720818	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	33	329	0	ENST00000371953.3:c.969del	p.Asn323LysfsTer21	p.N323Kfs*21	ENST00000371953	NM_000314.4	323	aaT/aa	8/9	1	2	FACETS	0.967	0.791	1	0.967	0.791	1	CLONAL	1	TRUE	1	0.25	2		329	273	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944152	71944152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757172795	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	75	724	2	ENST00000298229.2:c.1985G>A	p.Arg662His	p.R662H	ENST00000298229	NM_001567.3	662	cGc/cAc	17/28	1	2	FACETS	0.688	0.602	0.782	0.688	0.602	0.782	SUBCLONAL	1	TRUE	1	0.25	2		726	872	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424206	49424206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	36	298	1	ENST00000301067.7:c.13856C>T	p.Pro4619Leu	p.P4619L	ENST00000301067	NM_003482.3	4619	cCg/cTg	42/54	1	2	FACETS	0.713	0.586	0.854	0.713	0.586	0.854	SUBCLONAL	1	TRUE	1	0.25	2		299	404	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434228	49434228	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555192192	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	150	1066	0	ENST00000301067.7:c.7325del	p.Pro2442LeufsTer43	p.P2442Lfs*43	ENST00000301067	NM_003482.3	2442	cCt/ct	31/54	1	2	FACETS	0.916	0.835	1	0.916	0.835	1	CLONAL	1	TRUE	1	0.25	2		1066	1310	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145358	58145360	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-	rs1555201374	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	73	689	0	ENST00000257904.6:c.141_143del	p.Gly48del	p.G48del	ENST00000257904	NM_000075.3	47	ggAGGc/ggc	2/8	1	2	FACETS	0.739	0.646	0.841	0.739	0.646	0.841	SUBCLONAL	1	TRUE	1	0.25	2		689	790	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562577	21562577	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1395329857	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	24	247	1	ENST00000382592.4:c.1342C>T	p.Arg448Cys	p.R448C	ENST00000382592	NM_014572.2	448	Cgt/Tgt	4/8	1	2	FACETS	0.632	0.496	0.788	0.632	0.496	0.788	SUBCLONAL	1	TRUE	1	0.25	2		248	304	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941631	48941631	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs780006952	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	49	334	0	ENST00000267163.4:c.941T>C	p.Val314Ala	p.V314A	ENST00000267163	NM_000321.2	314	gTt/gCt	10/27	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.25	2		334	277	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614463	38614463	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	46	619	2	ENST00000299084.4:c.234del	p.Asp79ThrfsTer42	p.D79Tfs*42	ENST00000299084	NM_152594.2	77	Aaa/aa	3/7	1	2	FACETS	0.818	0.689	0.959	0.818	0.689	0.959	CLONAL	1	TRUE	1	0.25	2		621	450	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989136	41989136	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	66	628	0	ENST00000219905.7:c.1928C>A	p.Pro643His	p.P643H	ENST00000219905	NM_001164273.1	643	cCt/cAt	3/24	1	2	FACETS	0.811	0.704	0.927	0.811	0.704	0.927	CLONAL	1	TRUE	1	0.25	2		628	651	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779205	3779205	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	55	435	0	ENST00000262367.5:c.5843del	p.Pro1948ArgfsTer28	p.P1948Rfs*28	ENST00000262367	NM_004380.2	1948	cCg/cg	31/31	1	2	FACETS	0.94	0.806	1	0.94	0.806	1	CLONAL	1	TRUE	1	0.25	2		435	468	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864585	56864585	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1260970116	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	51	457	0	ENST00000308159.5:c.1073G>A	p.Ser358Asn	p.S358N	ENST00000308159	NM_014669.4	358	aGc/aAc	10/22	1	2	FACETS	0.77	0.654	0.897	0.77	0.654	0.897	SUBCLONAL	1	TRUE	1	0.25	2		457	530	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	68	333	1	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	0.25	2		334	459	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969806	81969806	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	66	569	2	ENST00000359376.3:c.2875G>A	p.Val959Met	p.V959M	ENST00000359376	NM_002661.3	959	Gtg/Atg	27/33	1	2	FACETS	0.723	0.627	0.828	0.723	0.627	0.828	SUBCLONAL	1	TRUE	1	0.25	2		571	730	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346613	89346613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370535812	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	58	478	0	ENST00000301030.4:c.6337G>A	p.Gly2113Ser	p.G2113S	ENST00000301030	NM_001256183.1	2113	Ggc/Agc	9/13	1	2	FACETS	0.922	0.794	1	0.922	0.794	1	CLONAL	1	TRUE	1	0.25	2		478	503	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982745	7982745	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	65	665	0	ENST00000319144.4:c.1040C>A	p.Pro347His	p.P347H	ENST00000319144	NM_001139.2	347	cCc/cAc	8/15	1	2	FACETS	0.755	0.654	0.864	0.755	0.654	0.864	SUBCLONAL	1	TRUE	1	0.25	2		665	689	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552250	29552250	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	44	613	1	ENST00000356175.3:c.1986del	p.Asn664ThrfsTer24	p.N664Tfs*24	ENST00000356175	NM_000267.3	661	ggA/gg	17/57	1	2	FACETS	0.73	0.612	0.861	0.73	0.612	0.861	SUBCLONAL	1	TRUE	1	0.25	2		614	482	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657479	29657480	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	32	528	0	ENST00000356175.3:c.5717dup	p.Leu1906PhefsTer9	p.L1906Ffs*9	ENST00000356175	NM_000267.3	1904	-/T	38/57	1	2	FACETS	0.612	0.497	0.743	0.612	0.497	0.743	SUBCLONAL	1	TRUE	1	0.25	2		528	418	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40490752	40490752	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	61	548	0	ENST00000264657.5:c.547G>T	p.Gly183Ter	p.G183*	ENST00000264657	NM_139276.2	183	Gga/Tga	6/24	1	2	FACETS	0.776	0.669	0.892	0.776	0.669	0.892	SUBCLONAL	1	TRUE	1	0.25	2		548	629	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226521	2226521	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	106	975	0	ENST00000398665.3:c.4001G>A	p.Gly1334Asp	p.G1334D	ENST00000398665	NM_032482.2	1334	gGt/gAt	27/28	1	2	FACETS	0.752	0.673	0.838	0.752	0.673	0.838	SUBCLONAL	1	TRUE	1	0.25	2		975	1127	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097624	11097625	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1165714406	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	109	975	0	ENST00000358026.2:c.810dup	p.Gly271ArgfsTer16	p.G271Rfs*16	ENST00000358026	NM_001128849.1	268	-/C	5/36	1	2	FACETS	0.804	0.72	0.893	0.804	0.72	0.893	CLONAL	1	TRUE	1	0.25	2		975	1085	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130331	11130331	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	89	697	0	ENST00000358026.2:c.2570T>C	p.Leu857Pro	p.L857P	ENST00000358026	NM_001128849.1	857	cTg/cCg	18/36	1	2	FACETS	0.768	0.68	0.863	0.768	0.68	0.863	SUBCLONAL	1	TRUE	1	0.25	2		697	927	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349964	15349964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1411701353	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	72	734	0	ENST00000263377.2:c.3688G>A	p.Ala1230Thr	p.A1230T	ENST00000263377	NM_058243.2	1230	Gcc/Acc	18/20	1	2	FACETS	0.627	0.547	0.715	0.627	0.547	0.715	SUBCLONAL	1	TRUE	1	0.25	2		734	918	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375215	15375216	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	70	565	0	ENST00000263377.2:c.1211dup	p.Ser405ValfsTer2	p.S405Vfs*2	ENST00000263377	NM_058243.2	404	aag/aaAg	6/20	1	2	FACETS	0.923	0.805	1	0.923	0.805	1	CLONAL	1	TRUE	1	0.25	2		565	607	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257615	19257615	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139889780	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	99	892	1	ENST00000162023.5:c.611C>T	p.Thr204Met	p.T204M	ENST00000162023		204	aCg/aTg	10/13	1	2	FACETS	0.773	0.688	0.863	0.773	0.688	0.863	SUBCLONAL	1	TRUE	1	0.25	2		893	1025	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212149	36212149	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	52	489	0	ENST00000222270.7:c.1904del	p.Pro635LeufsTer25	p.P635Lfs*25	ENST00000222270	NM_014727.1	634	Ccc/cc	3/37	1	2	FACETS	0.802	0.683	0.932	0.802	0.683	0.932	CLONAL	1	TRUE	1	0.25	2		489	519	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	101	899	5	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.73	0.651	0.815	0.73	0.651	0.815	SUBCLONAL	1	TRUE	1	0.25	2		904	1107	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906394	50906394	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556862476	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	88	806	2	ENST00000440232.2:c.1055G>A	p.Arg352His	p.R352H	ENST00000440232	NM_002691.3	352	cGc/cAc	9/27	1	2	FACETS	0.774	0.685	0.871	0.774	0.685	0.871	SUBCLONAL	1	TRUE	1	0.25	2		808	909	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082321	16082321	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	86	926	1	ENST00000281043.3:c.139del	p.Glu47ArgfsTer84	p.E47Rfs*84	ENST00000281043	NM_005378.4	45	ccG/cc	2/3	1	2	FACETS	0.622	0.549	0.701	0.622	0.549	0.701	SUBCLONAL	1	TRUE	1	0.25	2		927	1106	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456453	29456453	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1558630501	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	102	832	0	ENST00000389048.3:c.2465del	p.Gly822ValfsTer9	p.G822Vfs*9	ENST00000389048	NM_004304.4	822	gGt/gt	14/29	1	2	FACETS	0.821	0.733	0.915	0.821	0.733	0.915	CLONAL	1	TRUE	1	0.25	2		832	994	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519818	29519818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772496459	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	138	731	1	ENST00000389048.3:c.1753G>A	p.Ala585Thr	p.A585T	ENST00000389048	NM_004304.4	585	Gcc/Acc	9/29	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.25	2		732	953	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919721	96919721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	73	539	0	ENST00000258439.3:c.542C>T	p.Ala181Val	p.A181V	ENST00000258439	NM_001193304.2	181	gCa/gTa	4/4	1	2	FACETS	0.843	0.737	0.957	0.843	0.737	0.957	CLONAL	1	TRUE	1	0.25	2		539	693	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178129298	178129298	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	67	565	0	ENST00000397062.3:c.7G>A	p.Asp3Asn	p.D3N	ENST00000397062	NM_006164.4	3	Gac/Aac	1/5	1	2	FACETS	0.74	0.643	0.846	0.74	0.643	0.846	SUBCLONAL	1	TRUE	1	0.25	2		565	724	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384650	31384651	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs756395138	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	75	728	5	ENST00000328111.2:c.1359dup	p.Leu454AlafsTer11	p.L454Afs*11	ENST00000328111	NM_006892.3	451	gag/gaGg	13/23	1	2	FACETS	0.689	0.602	0.782	0.689	0.602	0.782	SUBCLONAL	1	TRUE	1	0.25	2		733	871	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39726906	39726906	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	15	370	0	ENST00000361337.2:c.904T>G	p.Phe302Val	p.F302V	ENST00000361337	NM_003286.2	302	Ttt/Gtt	11/21	1	2	FACETS	0.412	0.301	0.546	0.412	0.301	0.546	SUBCLONAL	1	TRUE	1	0.25	2		370	291	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042540	37042540	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs267607727	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	49	552	0	ENST00000231790.2:c.302G>T	p.Gly101Val	p.G101V	ENST00000231790	NM_000249.3	101	gGt/gTt	3/19	1	2	FACETS	0.812	0.688	0.948	0.812	0.688	0.948	CLONAL	1	TRUE	1	0.25	2		552	483	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799979	72799979	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	47	379	0	ENST00000325599.8:c.1190del	p.Lys397SerfsTer9	p.K397Sfs*9	ENST00000325599	NM_018130.2	397	aAg/ag	11/11	1	2	FACETS	0.915	0.773	1	0.915	0.773	1	CLONAL	1	TRUE	1	0.25	2		379	411	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155325	185155325	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746379057	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	69	546	1	ENST00000265026.3:c.566C>T	p.Ala189Val	p.A189V	ENST00000265026	NM_004721.4	189	gCg/gTg	3/14	1	2	FACETS	0.766	0.666	0.873	0.766	0.666	0.873	SUBCLONAL	1	TRUE	1	0.25	2		547	721	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467437	66467437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749830045	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	43	314	0	ENST00000273854.3:c.832G>A	p.Ala278Thr	p.A278T	ENST00000273854	NM_004439.5	278	Gcc/Acc	3/18	1	2	FACETS	0.92	0.772	1	0.92	0.772	1	CLONAL	1	TRUE	1	0.25	2		314	374	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467697	66467697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779449792	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	61	448	0	ENST00000273854.3:c.572G>A	p.Arg191His	p.R191H	ENST00000273854	NM_004439.5	191	cGt/cAt	3/18	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.25	2		448	454	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106182962	106182962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	47	476	0	ENST00000380013.4:c.4001C>T	p.Ala1334Val	p.A1334V	ENST00000380013	NM_001127208.2	1334	gCa/gTa	8/11	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.25	2		476	334	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542552	187542552	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	70	707	0	ENST00000441802.2:c.5188T>A	p.Leu1730Met	p.L1730M	ENST00000441802	NM_005245.3	1730	Ttg/Atg	10/27	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.25	2		707	485	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86668013	86668013	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	32	320	0	ENST00000274376.6:c.1776+1G>A		p.X592_splice	ENST00000274376	NM_002890.2	592			1	2	FACETS	0.871	0.709	1	0.871	0.709	1	CLONAL	1	TRUE	1	0.25	2		320	294	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460564	149460564	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	84	731	1	ENST00000286301.3:c.73C>T	p.Pro25Ser	p.P25S	ENST00000286301	NM_005211.3	25	Ccc/Tcc	3/22	1	2	FACETS	0.784	0.691	0.884	0.784	0.691	0.884	SUBCLONAL	1	TRUE	1	0.25	2		732	857	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324132	31324132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41561215	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	43	285	0	ENST00000412585.2:c.431G>A	p.Gly144Asp	p.G144D	ENST00000412585	NM_005514.6	144	gGc/gAc	3/8	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.25	2		285	289	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517326	157517326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371538726	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	80	469	0	ENST00000346085.5:c.3890C>T	p.Thr1297Met	p.T1297M	ENST00000346085	NM_020732.3	1297	aCg/aTg	16/20	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.25	2		469	604	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946443	2946445	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	86	809	0	ENST00000396946.4:c.3292_3294del	p.Glu1098del	p.E1098del	ENST00000396946	NM_032415.4	1098	GAG/-	25/25	1	2	FACETS	0.667	0.589	0.752	0.667	0.589	0.752	SUBCLONAL	1	TRUE	1	0.25	2		809	1031	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965389	68965390	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1202177107	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	72	808	0	ENST00000288368.4:c.1007dup	p.Asn336LysfsTer2	p.N336Kfs*2	ENST00000288368	NM_024870.2	334	gca/gcAa	9/40	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.25	2		808	575	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868492	117868492	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760261220	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	74	520	0	ENST00000297338.2:c.850G>A	p.Val284Ile	p.V284I	ENST00000297338	NM_006265.2	284	Gtt/Att	8/14	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.25	2		520	538	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250077	110250077	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	83	663	0	ENST00000374672.4:c.598G>A	p.Val200Met	p.V200M	ENST00000374672	NM_004235.4	200	Gtg/Atg	3/5	1	2	FACETS	0.964	0.851	1	0.964	0.851	1	CLONAL	1	TRUE	1	0.25	2		663	689	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044919	47044919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	55	889	0	ENST00000377604.3:c.2245C>T	p.Arg749Trp	p.R749W	ENST00000377604	NM_001204468.1	749	Cgg/Tgg	20/24	1	2	FACETS	0.403	0.343	0.469	0.403	0.343	0.469	SUBCLONAL	1	TRUE	1	0.25	2		889	1091	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412070	63412070	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	103	1014	0	ENST00000330258.3:c.1097A>G	p.Gln366Arg	p.Q366R	ENST00000330258	NM_152424.3	366	cAa/cGa	2/2	1	2	FACETS	0.73	0.651	0.814	0.73	0.651	0.814	SUBCLONAL	1	TRUE	1	0.25	2		1014	1129	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720818	89720818	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	16	328	1	ENST00000371953.3:c.969T>A	p.Asn323Lys	p.N323K	ENST00000371953	NM_000314.4	323	aaT/aaA	8/9	1	2	FACETS	0.469	0.346	0.615	0.469	0.346	0.615	SUBCLONAL	1	TRUE	1	0.25	2		329	273	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037972	49037972	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0021624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	100	674	1	ENST00000267163.4:c.2211+1G>A		p.X737_splice	ENST00000267163	NM_000321.2	737			0.533863874612922	1	FACETS	0.925	0.837	1	0.925	0.837	1	CLONAL	1	TRUE	0	0.533863874612922	1		675	297	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156660	2156660	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	155	996	1	ENST00000434045.2:c.262C>A	p.Leu88Met	p.L88M	ENST00000434045	NM_001127598.1	88	Ctg/Atg	3/5	1	2	FACETS	0.885	0.813	0.96	0.885	0.813	0.96	CLONAL	1	TRUE	1	0.533863874612922	2		997	656	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046546	30046546	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	117	931	0	ENST00000331968.5:c.2637G>C	p.Gln879His	p.Q879H	ENST00000331968	NM_002742.2	879	caG/caC	18/18	1	2	FACETS	0.706	0.638	0.777	0.706	0.638	0.777	SUBCLONAL	1	TRUE	1	0.533863874612922	2		931	621	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724583	43724583	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs771197371	NA	P-0021624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	44	1366	0	ENST00000382044.4:c.3484A>G	p.Met1162Val	p.M1162V	ENST00000382044	NM_001141980.1	1162	Atg/Gtg	17/28	0.3445810661204	1	FACETS	0.144	0.12	0.171	0.144	0.12	0.171	SUBCLONAL	1	TRUE	0	0.533863874612922	1		1366	840	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56832451	56832451	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0021624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	96	462	1	ENST00000308159.5:c.360+1G>T		p.X120_splice	ENST00000308159	NM_014669.4	120			1	2	FACETS	0.967	0.869	1	0.967	0.869	1	CLONAL	1	TRUE	1	0.533863874612922	2		463	372	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939507	68939515	+	inframe_deletion	In_Frame_Del	DEL	ATATTTAGT	ATATTTAGT	-	novel	NA	P-0021624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	326	812	0	ENST00000288368.4:c.493_501del	p.Tyr165_Val167del	p.Y165_V167del	ENST00000288368	NM_024870.2	164	ggATATTTAGTa/gga	5/40	0.533863874612922	6	FACETS	0.971	0.921	1	0.728	0.69	0.766	CLONAL	3	TRUE	2	0.533863874612922	6		812	867	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	64	188	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.369100112516592	2		188	264	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851754	134851754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56396912	NA	P-0021715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	53	815	2	ENST00000398015.3:c.1160C>T	p.Thr387Met	p.T387M	ENST00000398015	NM_004441.4	387	aCg/aTg	5/16	0.369100112516592	3	FACETS	0.81	0.692	0.938	0.405	0.346	0.469	CLONAL	1	TRUE	1	0.369100112516592	3		817	420	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798098	42798098	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0021715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	181	711	0	ENST00000575354.2:c.4052C>G	p.Ser1351Ter	p.S1351*	ENST00000575354	NM_015125.3	1351	tCa/tGa	17/20	0.349591064944239	5	FACETS	1	0.963	1	1	0.963	1	CLONAL	3	TRUE	2	0.369100112516592	5		711	483	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11292568	11292568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	144	553	0	ENST00000361445.4:c.2439G>A	p.Met813Ile	p.M813I	ENST00000361445	NM_004958.3	813	atG/atA	16/58	0.369100112516592	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.369100112516592	3		553	424	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366776	40366776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1219869007	NA	P-0021715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	70	723	1	ENST00000397332.2:c.421G>A	p.Asp141Asn	p.D141N	ENST00000397332	NM_001033082.2	141	Gac/Aac	2/3	0.369100112516592	3	FACETS	1	0.952	1	0.59	0.517	0.668	CLONAL	1	TRUE	1	0.369100112516592	3		724	381	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46733239	46733239	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	222	870	0	ENST00000371975.4:c.1000G>C	p.Glu334Gln	p.E334Q	ENST00000371975	NM_003579.3	334	Gag/Cag	9/18	0.369100112516592	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.369100112516592	3		870	633	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263335	123263335	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	59	632	0	ENST00000358487.5:c.1408G>A	p.Glu470Lys	p.E470K	ENST00000358487	NM_000141.4	470	Gag/Aag	10/18	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.369100112516592	2		632	306	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436344	49436344	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	149	828	2	ENST00000301067.7:c.5867G>A	p.Arg1956Lys	p.R1956K	ENST00000301067	NM_003482.3	1956	aGg/aAg	27/54	0.168434275657755	6	FACETS	1	0.98	1	0.815	0.748	0.884	INDETERMINATE	2	TRUE	3	0.369100112516592	6		830	574	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489566	56489566	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	183	694	0	ENST00000267101.3:c.2031G>C	p.Met677Ile	p.M677I	ENST00000267101	NM_001982.3	677	atG/atC	17/28	0.168434275657755	6	FACETS	0.911	0.844	0.979	0.911	0.844	0.979	INDETERMINATE	3	TRUE	3	0.369100112516592	6		694	631	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109735	115109735	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	215	1020	0	ENST00000257566.3:c.2143G>C	p.Glu715Gln	p.E715Q	ENST00000257566	NM_016569.3	715	Gag/Cag	8/8	0.144030669112437	4	FACETS	1	0.975	1	1	0.975	1	INDETERMINATE	2	TRUE	2	0.369100112516592	4		1020	732	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434137	121434137	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	186	924	0	ENST00000257555.6:c.1028C>A	p.Thr343Lys	p.T343K	ENST00000257555		343	aCa/aAa	5/10	0.144030669112437	4	FACETS	1	0.962	1	1	0.962	1	INDETERMINATE	2	TRUE	2	0.369100112516592	4		924	653	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906503	32906513	+	frameshift_variant	Frame_Shift_Del	DEL	TGAAACAGTTG	TGAAACAGTTG	-	novel	NA	P-0021715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	105	658	0	ENST00000380152.3:c.889_899del	p.Glu297ArgfsTer4	p.E297Rfs*4	ENST00000380152		296	taTGAAACAGTTGta/tata	10/27	0.369100112516592	3	FACETS	1	0.981	1	0.701	0.631	0.774	CLONAL	1	TRUE	1	0.369100112516592	3		658	481	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103525622	103525622	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	65	580	1	ENST00000355739.4:c.2893T>C	p.Tyr965His	p.Y965H	ENST00000355739	NM_000123.3	965	Tat/Cat	14/15	0.369100112516592	3	FACETS	0.973	0.846	1	0.486	0.423	0.555	CLONAL	1	TRUE	1	0.369100112516592	3		581	429	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987039	36987039	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1447379564	NA	P-0021715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	69	710	1	ENST00000354822.5:c.650C>T	p.Ser217Leu	p.S217L	ENST00000354822	NM_001079668.2	217	tCg/tTg	3/3	0.102099560377151	6	FACETS	1	0.973	1	0.495	0.432	0.562	INDETERMINATE	1	TRUE	3	0.369100112516592	6		711	438	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670412	88670412	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	30	655	0	ENST00000360948.2:c.1274C>A	p.Pro425Gln	p.P425Q	ENST00000360948	NM_001012338.2	425	cCa/cAa	11/19	0.369100112516592	3	FACETS	0.431	0.347	0.526	0.215	0.173	0.263	SUBCLONAL	1	TRUE	1	0.369100112516592	3		655	447	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3645643	3645643	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs372150541	NA	P-0021715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	202	930	0	ENST00000294008.3:c.1976C>G	p.Ser659Trp	p.S659W	ENST00000294008	NM_032444.2	659	tCg/tGg	9/15	0.369100112516592	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.369100112516592	3		930	580	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586049	29586049	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0021715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	30	566	0	ENST00000356175.3:c.4270-1G>C		p.X1424_splice	ENST00000356175	NM_000267.3	1424			0.369100112516592	2	FACETS	0.664	0.537	0.805	0.332	0.268	0.403	SUBCLONAL	1	TRUE	0	0.369100112516592	2		566	245	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248658	10248658	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	104	716	0	ENST00000340748.4:c.4095C>G	p.Ile1365Met	p.I1365M	ENST00000340748		1365	atC/atG	35/40	0.0497941020322963	3	FACETS	1	0.982	1	0.721	0.649	0.796	INDETERMINATE	1	TRUE	1	0.369100112516592	3		716	463	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262364	39262364	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	294	802	0	ENST00000402219.2:c.1063G>C	p.Glu355Gln	p.E355Q	ENST00000402219	NM_005633.3	355	Gaa/Caa	8/23	0.369100112516592	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	0	0.369100112516592	3		802	593	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262430	39262430	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	277	753	0	ENST00000402219.2:c.997G>C	p.Glu333Gln	p.E333Q	ENST00000402219	NM_005633.3	333	Gaa/Caa	8/23	0.369100112516592	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	0	0.369100112516592	3		753	571	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376224	225376224	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	270	803	1	ENST00000264414.4:c.730G>A	p.Glu244Lys	p.E244K	ENST00000264414	NM_003590.4	244	Gaa/Aaa	6/16	0.334344229796389	4	FACETS	0.952	0.899	1	0.952	0.899	1	CLONAL	3	TRUE	1	0.369100112516592	4		804	701	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021335	31021336	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0021715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	115	719	0	ENST00000375687.4:c.1336_1337dup	p.Pro447PhefsTer16	p.P447Ffs*16	ENST00000375687	NM_015338.5	445	gat/gaTGt	12/13	0.144030669112437	4	FACETS	0.944	0.856	1	0.944	0.856	1	INDETERMINATE	2	TRUE	2	0.369100112516592	4		719	452	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091777	29091777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780169	NA	P-0021715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	62	707	1	ENST00000328354.6:c.1180G>A	p.Glu394Lys	p.E394K	ENST00000328354	NM_007194.3	394	Gaa/Aaa	11/15	0.189017141884298	2	FACETS	0.719	0.623	0.824	0.36	0.311	0.412	INDETERMINATE	1	TRUE	0	0.369100112516592	2		708	467	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29107905	29107905	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0021715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	156	752	0	ENST00000328354.6:c.784A>T	p.Arg262Ter	p.R262*	ENST00000328354	NM_007194.3	262	Aga/Tga	6/15	0.189017141884298	2	FACETS	0.818	0.754	0.883	0.818	0.754	0.883	INDETERMINATE	2	TRUE	0	0.369100112516592	2		752	517	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584639	52584639	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	60	760	0	ENST00000394830.3:c.4374del	p.Pro1459LeufsTer30	p.P1459Lfs*30	ENST00000394830	NM_018313.4	1458	ggG/gg	29/30	0.369100112516592	3	FACETS	0.915	0.791	1	0.457	0.395	0.525	CLONAL	1	TRUE	1	0.369100112516592	3		760	421	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52675999	52675999	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0021715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	252	862	0	ENST00000394830.3:c.1058C>G	p.Ser353Ter	p.S353*	ENST00000394830	NM_018313.4	353	tCa/tGa	11/30	0.369100112516592	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.369100112516592	3		862	702	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748514	43748514	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	62	670	0	ENST00000523873.1:c.468G>C	p.Lys156Asn	p.K156N	ENST00000523873		156	aaG/aaC	6/8	0.369100112516592	3	FACETS	0.852	0.738	0.976	0.426	0.369	0.488	CLONAL	1	TRUE	1	0.369100112516592	3		670	467	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100253	157100253	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	18	213	0	ENST00000346085.5:c.1190C>G	p.Ser397Trp	p.S397W	ENST00000346085	NM_020732.3	397	tCg/tGg	1/20	0.369100112516592	3	FACETS	0.955	0.727	1	0.477	0.363	0.609	CLONAL	1	TRUE	1	0.369100112516592	3		213	121	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509636	106509636	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	104	715	0	ENST00000359195.3:c.1630C>G	p.Arg544Gly	p.R544G	ENST00000359195	NM_002649.2	544	Cga/Gga	2/11	0.196303814362353	3	FACETS	0.837	0.755	0.922	0.558	0.503	0.615	INDETERMINATE	2	TRUE	0	0.369100112516592	3		715	399	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534578	140534578	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	146	721	0	ENST00000288602.6:c.335C>G	p.Ser112Cys	p.S112C	ENST00000288602	NM_004333.4	112	tCt/tGt	3/18	0.196303814362353	3	FACETS	0.989	0.909	1	0.659	0.606	0.714	INDETERMINATE	2	TRUE	0	0.369100112516592	3		721	474	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969378	44969381	+	frameshift_variant	Frame_Shift_Del	DEL	TACA	TACA	-	novel	NA	P-0021715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	182	422	0	ENST00000377967.4:c.4062_4065del	p.Tyr1354Ter	p.Y1354*	ENST00000377967	NM_021140.2	1354	TACAta/ta	28/29	0.21303104618142	2	FACETS	0.964	0.906	1			1	INDETERMINATE	3	TRUE	NA	0.369100112516592	2		422	341	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938961	76938961	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	231	459	0	ENST00000373344.5:c.1787C>G	p.Ser596Cys	p.S596C	ENST00000373344	NM_000489.3	596	tCt/tGt	9/35	0.21303104618142	2	FACETS	0.968	0.916	1			1	INDETERMINATE	3	TRUE	NA	0.369100112516592	2		459	431	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922318	39922318	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	128	230	0	ENST00000378444.4:c.3854del	p.Pro1285LeufsTer9	p.P1285Lfs*9	ENST00000378444	NM_001123385.1	1285	cCt/ct	9/15	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.685894010220381	1		230	196	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	160	580	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.45311711767994	3	FACETS	1	0.977	1	0.584	0.537	0.634	CLONAL	1	TRUE	1	0.45311711767994	3		580	741	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316397	14316397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782457908	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	310	767	0	ENST00000256196.4:c.208G>A	p.Ala70Thr	p.A70T	ENST00000256196		70	Gca/Aca	3/6	0.441299277450213	3	FACETS	1	0.992	1	0.814	0.774	0.855	CLONAL	2	TRUE	0	0.45311711767994	3		767	687	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	381	256	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	0.201751255127818	3	FACETS	1	0.993	1	1	0.993	1	INDETERMINATE	3	TRUE	0	0.45311711767994	3		257	597	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	188	672	2	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.18313761048987	5	FACETS	1	0.932	1	0.67	0.622	0.721	INDETERMINATE	2	TRUE	2	0.45311711767994	5		674	693	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	266	908	1	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	0.159338947248602	5	FACETS	1	0.99	1	0.819	0.77	0.868	INDETERMINATE	2	TRUE	2	0.45311711767994	5		909	803	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	72	423	1	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	0.441299277450213	3	FACETS	0.582	0.508	0.661	0.194	0.169	0.221	SUBCLONAL	1	TRUE	0	0.45311711767994	3		424	670	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478786	56478786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324972550	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	273	749	0	ENST00000267101.3:c.242G>A	p.Arg81Gln	p.R81Q	ENST00000267101	NM_001982.3	81	cGa/cAa	3/28	0.314472176033069	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	2	0.45311711767994	4		749	833	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134252	11134252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	96	805	2	ENST00000358026.2:c.2918G>A	p.Arg973Gln	p.R973Q	ENST00000358026	NM_001128849.1	973	cGg/cAg	20/36	0.225662567263041	3	FACETS	0.764	0.681	0.853	0.255	0.227	0.285	INDETERMINATE	1	TRUE	0	0.45311711767994	3		807	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203436	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	669	1031	2	ENST00000269305.4:c.487T>C	p.Tyr163His	p.Y163H	ENST00000269305	NM_001126112.2	163	Tac/Cac	5/11	0.321324089071124	3	FACETS	0.943	0.919	0.967	1	0.998	1	CLONAL	4	TRUE	1	0.45311711767994	3		1033	960	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563021	21563021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	33	673	1	ENST00000382592.4:c.898G>A	p.Ala300Thr	p.A300T	ENST00000382592	NM_014572.2	300	Gcc/Acc	4/8	0.11376013625884	3	FACETS	0.345	0.28	0.418	0.115	0.093	0.14	INDETERMINATE	1	TRUE	0	0.45311711767994	3		674	518	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692961	89692961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060500122	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	295	666	0	ENST00000371953.3:c.445C>T	p.Gln149Ter	p.Q149*	ENST00000371953	NM_000314.4	149	Caa/Taa	5/9	0.18313761048987	5	FACETS	0.988	0.935	1	0.988	0.935	1	INDETERMINATE	3	TRUE	2	0.45311711767994	5		666	738	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467855	99467856	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	56	527	0	ENST00000268035.6:c.2732_2733dup	p.Gly912LeufsTer26	p.G912Lfs*26	ENST00000268035	NM_000875.3	908	-/TC	13/21	1	2	FACETS	0.525	0.45	0.606	0.525	0.45	0.606	SUBCLONAL	1	TRUE	1	0.45311711767994	2		527	471	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189906	66189906	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149835568	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	261	569	0	ENST00000273854.3:c.3040G>A	p.Gly1014Ser	p.G1014S	ENST00000273854	NM_004439.5	1014	Ggt/Agt	18/18	0.45311711767994	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.45311711767994	3		569	634	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813361	102813361	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1280732914	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	276	799	4	ENST00000307046.8:c.328G>A	p.Ala110Thr	p.A110T	ENST00000307046	NM_001111285.1	110	Gca/Aca	3/4	0.314472176033069	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.45311711767994	4		803	779	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891277	101891277	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	385	787	2	ENST00000374994.4:c.238C>T	p.Arg80Ter	p.R80*	ENST00000374994	NM_004612.2	80	Cga/Tga	2/9	0.45311711767994	3	FACETS	0.933	0.893	0.972	0.933	0.893	0.972	CLONAL	3	TRUE	0	0.45311711767994	3		789	745	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482242	87482242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	441	975	0	ENST00000277120.3:c.1529C>T	p.Ser510Leu	p.S510L	ENST00000277120		510	tCg/tTg	14/19	0.45311711767994	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.45311711767994	3		975	745	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119007	3119007	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769503200	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	93	1073	1	ENST00000078429.4:c.691G>A	p.Ala231Thr	p.A231T	ENST00000078429	NM_002067.2	231	Gcc/Acc	5/7	0.225662567263041	3	FACETS	0.655	0.582	0.733	0.218	0.194	0.245	INDETERMINATE	1	TRUE	0	0.45311711767994	3		1074	769	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820970	36820970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	427	870	0	ENST00000373129.3:c.407G>A	p.Arg136His	p.R136H	ENST00000373129	NM_032017.1	136	cGc/cAc	6/12	0.201751255127818	3	FACETS	0.863	0.827	0.899	0.863	0.827	0.899	INDETERMINATE	3	TRUE	0	0.45311711767994	3		870	893	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	51	789	8	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	1	2	FACETS	0.244	0.207	0.286	0.244	0.207	0.286	SUBCLONAL	1	TRUE	1	0.45311711767994	2		797	921	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909518	50909518	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376711125	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	364	1013	0	ENST00000440232.2:c.1322C>T	p.Thr441Met	p.T441M	ENST00000440232	NM_002691.3	441	aCg/aTg	11/27	0.159338947248602	5	FACETS	0.839	0.797	0.882	0.839	0.797	0.882	INDETERMINATE	3	TRUE	2	0.45311711767994	5		1013	1072	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128989	64128989	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	433	953	0	ENST00000334205.4:c.619G>A	p.Glu207Lys	p.E207K	ENST00000334205	NM_003942.2	207	Gaa/Aaa	6/17	0.329467472827374	3	FACETS	0.992	0.953	1	0.992	0.953	1	CLONAL	3	TRUE	0	0.45311711767994	3		953	788	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432651	49432651	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs727503983	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	416	1090	3	ENST00000301067.7:c.8488C>T	p.Arg2830Ter	p.R2830*	ENST00000301067	NM_003482.3	2830	Cga/Tga	34/54	0.314472176033069	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	2	0.45311711767994	4		1093	1146	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696462	47696462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	225	666	1	ENST00000347630.2:c.361C>T	p.Arg121Trp	p.R121W	ENST00000347630	NM_001007230.1	121	Cgg/Tgg	6/11	0.321324089071124	3	FACETS	0.926	0.867	0.986	0.926	0.867	0.986	CLONAL	2	TRUE	1	0.45311711767994	3		667	658	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878530	151878530	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1396109953	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	376	872	2	ENST00000262189.6:c.6415C>T	p.Arg2139Ter	p.R2139*	ENST00000262189	NM_170606.2	2139	Cga/Tga	36/59	0.45311711767994	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.45311711767994	3		874	864	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856595	111856595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1454335466	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	47	101	0	ENST00000341259.2:c.646C>T	p.Arg216Cys	p.R216C	ENST00000341259	NM_005475.2	216	Cgc/Tgc	2/8	0.314472176033069	4	FACETS	0.913	0.796	1	1	0.964	1	CLONAL	3	TRUE	2	0.45311711767994	4		101	110	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783197	9783197	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	44	693	0	ENST00000377346.4:c.2441G>T	p.Gly814Val	p.G814V	ENST00000377346	NM_005026.3	814	gGc/gTc	20/24	0.201751255127818	3	FACETS	0.373	0.312	0.441	0.124	0.104	0.147	INDETERMINATE	1	TRUE	0	0.45311711767994	3		693	639	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599917	28599917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	352	861	0	ENST00000253063.3:c.799C>T	p.Gln267Ter	p.Q267*	ENST00000253063	NM_031459.4	267	Cag/Tag	6/10	0.201751255127818	3	FACETS	0.874	0.834	0.914	0.874	0.834	0.914	INDETERMINATE	3	TRUE	0	0.45311711767994	3		861	727	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748153	72748153	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	148	609	0	ENST00000357731.5:c.25G>T	p.Gly9Cys	p.G9C	ENST00000357731	NM_173808.2	9	Ggt/Tgt	1/7	0.201751255127818	3	FACETS	1	0.986	1	0.455	0.417	0.494	INDETERMINATE	1	TRUE	0	0.45311711767994	3		609	587	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166017	118166017	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	146	613	0	ENST00000369448.3:c.527A>G	p.Gln176Arg	p.Q176R	ENST00000369448	NM_017709.3	176	cAg/cGg	2/2	0.45311711767994	3	FACETS	1	0.965	1	0.553	0.505	0.602	CLONAL	1	TRUE	1	0.45311711767994	3		613	715	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983080	201983080	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	412	1026	0	ENST00000359651.3:c.929C>G	p.Ala310Gly	p.A310G	ENST00000359651		310	gCt/gGt	7/8	0.45311711767994	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	1	0.45311711767994	3		1026	893	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226568810	226568810	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757100394	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	75	1015	0	ENST00000366794.5:c.1259C>T	p.Thr420Met	p.T420M	ENST00000366794	NM_001618.3	420	aCg/aTg	9/23	0.45311711767994	3	FACETS	0.359	0.313	0.408	0.179	0.156	0.204	SUBCLONAL	1	TRUE	1	0.45311711767994	3		1015	1132	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137306	64137306	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	50	908	0	ENST00000334205.4:c.1738C>G	p.Leu580Val	p.L580V	ENST00000334205	NM_003942.2	580	Ctg/Gtg	14/17	0.329467472827374	3	FACETS	0.37	0.313	0.433	0.123	0.104	0.145	SUBCLONAL	1	TRUE	0	0.45311711767994	3		908	732	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943355	71943355	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	116	933	0	ENST00000298229.2:c.1687A>G	p.Thr563Ala	p.T563A	ENST00000298229	NM_001567.3	563	Acc/Gcc	14/28	0.329467472827374	3	FACETS	0.718	0.646	0.793	0.239	0.215	0.265	SUBCLONAL	1	TRUE	0	0.45311711767994	3		933	875	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392770	118392770	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	405	815	0	ENST00000534358.1:c.11802G>T	p.Met3934Ile	p.M3934I	ENST00000534358	NM_005933.3	3934	atG/atT	36/36	0.441299277450213	3	FACETS	0.973	0.934	1	0.973	0.934	1	CLONAL	3	TRUE	0	0.45311711767994	3		815	751	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498173	498173	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	116	621	0	ENST00000399788.2:c.85T>C	p.Phe29Leu	p.F29L	ENST00000399788	NM_001042603.1	29	Ttc/Ctc	1/28	0.207305873188851	5	FACETS	1	0.934	1			1	INDETERMINATE	1	TRUE	NA	0.45311711767994	5		621	821	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4388016	4388016	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	257	609	1	ENST00000261254.3:c.502C>T	p.Pro168Ser	p.P168S	ENST00000261254	NM_001759.3	168	Ccc/Tcc	3/5	0.207305873188851	5	FACETS	0.922	0.868	0.976			1	INDETERMINATE	3	TRUE	NA	0.45311711767994	5		610	689	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420229	49420229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	388	944	1	ENST00000301067.7:c.15520C>T	p.Arg5174Trp	p.R5174W	ENST00000301067	NM_003482.3	5174	Cgg/Tgg	48/54	0.314472176033069	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	2	0.45311711767994	4		945	1027	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426033	49426033	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	369	862	0	ENST00000301067.7:c.12455T>G	p.Leu4152Arg	p.L4152R	ENST00000301067	NM_003482.3	4152	cTt/cGt	39/54	0.314472176033069	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	2	0.45311711767994	4		862	982	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69203008	69203008	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	180	716	0	ENST00000462284.1:c.35T>C	p.Met12Thr	p.M12T	ENST00000462284	NM_002392.5	12	aTg/aCg	2/11	0.314472176033069	4	FACETS	1	0.975	1	0.569	0.524	0.616	CLONAL	1	TRUE	2	0.45311711767994	4		716	1014	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620053	21620053	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	68	944	1	ENST00000382592.4:c.113C>A	p.Pro38His	p.P38H	ENST00000382592	NM_014572.2	38	cCc/cAc	2/8	0.11376013625884	3	FACETS	0.426	0.369	0.487	0.142	0.123	0.163	INDETERMINATE	1	TRUE	0	0.45311711767994	3		945	865	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73348128	73348128	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	140	753	0	ENST00000377767.4:c.1057T>C	p.Trp353Arg	p.W353R	ENST00000377767	NM_014953.3	353	Tgg/Cgg	7/21	0.11376013625884	3	FACETS	1	0.963	1	0.368	0.335	0.402	INDETERMINATE	1	TRUE	0	0.45311711767994	3		753	687	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514819	103514819	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	133	489	0	ENST00000355739.4:c.1320A>G	p.Ile440Met	p.I440M	ENST00000355739	NM_000123.3	440	atA/atG	8/15	0.11376013625884	3	FACETS	1	0.985	1	0.471	0.43	0.513	INDETERMINATE	1	TRUE	0	0.45311711767994	3		489	510	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81557426	81557426	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	147	709	0	ENST00000298171.2:c.406A>G	p.Thr136Ala	p.T136A	ENST00000298171	NM_000369.2	136	Act/Gct	5/10	0.201751255127818	3	FACETS	1	0.941	1	0.346	0.316	0.377	INDETERMINATE	1	TRUE	0	0.45311711767994	3		709	767	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570213	95570213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	24	515	2	ENST00000393063.1:c.3520G>A	p.Ala1174Thr	p.A1174T	ENST00000393063	NM_030621.3	1174	Gca/Aca	22/28	0.201751255127818	3	FACETS	0.276	0.216	0.346	0.092	0.072	0.116	INDETERMINATE	1	TRUE	0	0.45311711767994	3		517	470	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040979	42040979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781312897	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	290	990	0	ENST00000219905.7:c.5357G>A	p.Arg1786Gln	p.R1786Q	ENST00000219905	NM_001164273.1	1786	cGg/cAg	16/24	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.45311711767994	2		990	859	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354312	354312	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1432410713	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	331	898	0	ENST00000262320.3:c.1246G>A	p.Val416Met	p.V416M	ENST00000262320	NM_003502.3	416	Gtg/Atg	5/11	0.18313761048987	5	FACETS	0.867	0.821	0.913	0.867	0.821	0.913	INDETERMINATE	3	TRUE	2	0.45311711767994	5		898	944	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354354	354354	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	395	962	0	ENST00000262320.3:c.1204A>G	p.Thr402Ala	p.T402A	ENST00000262320	NM_003502.3	402	Acg/Gcg	5/11	0.18313761048987	5	FACETS	0.879	0.837	0.922	0.879	0.837	0.922	INDETERMINATE	3	TRUE	2	0.45311711767994	5		962	1110	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129279	2129279	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	146	928	0	ENST00000219476.3:c.3134del	p.Ser1045PhefsTer8	p.S1045Ffs*8	ENST00000219476	NM_000548.3	1045	tCt/tt	28/42	0.18313761048987	5	FACETS	1	0.98	1	0.417	0.38	0.456	INDETERMINATE	1	TRUE	2	0.45311711767994	5		928	865	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823784	3823784	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	123	664	0	ENST00000262367.5:c.2431G>T	p.Gly811Trp	p.G811W	ENST00000262367	NM_004380.2	811	Ggg/Tgg	13/31	0.18313761048987	5	FACETS	1	0.977	1	0.42	0.38	0.463	INDETERMINATE	1	TRUE	2	0.45311711767994	5		664	723	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900812	3900812	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	124	730	0	ENST00000262367.5:c.284T>C	p.Val95Ala	p.V95A	ENST00000262367	NM_004380.2	95	gTg/gCg	2/31	0.18313761048987	5	FACETS	1	0.977	1	0.419	0.379	0.461	INDETERMINATE	1	TRUE	2	0.45311711767994	5		730	731	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647347	23647347	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	155	924	0	ENST00000261584.4:c.520A>G	p.Lys174Glu	p.K174E	ENST00000261584	NM_024675.3	174	Aaa/Gaa	4/13	0.314472176033069	4	FACETS	1	0.962	1	0.544	0.498	0.593	CLONAL	1	TRUE	2	0.45311711767994	4		924	913	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993738	72993738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759648686	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	233	586	0	ENST00000268489.5:c.307C>T	p.Arg103Cys	p.R103C	ENST00000268489	NM_006885.3	103	Cgc/Tgc	2/10	0.314472176033069	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.45311711767994	4		586	660	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346972	89346972	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1251064433	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	161	453	0	ENST00000301030.4:c.5978G>A	p.Arg1993His	p.R1993H	ENST00000301030	NM_001256183.1	1993	cGt/cAt	9/13	0.18313761048987	5	FACETS	1	0.983	1	0.82	0.758	0.884	INDETERMINATE	2	TRUE	2	0.45311711767994	5		453	485	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562996	29562996	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	244	690	0	ENST00000356175.3:c.3931T>C	p.Ser1311Pro	p.S1311P	ENST00000356175	NM_000267.3	1311	Tcc/Ccc	29/57	0.207305873188851	5	FACETS	1	0.966	1			1	INDETERMINATE	2	TRUE	NA	0.45311711767994	5		690	864	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38506045	38506045	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779120079	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	220	747	0	ENST00000254066.5:c.337C>T	p.Arg113Cys	p.R113C	ENST00000254066	NM_000964.3	113	Cgc/Tgc	4/9	0.321324089071124	3	FACETS	0.777	0.726	0.831	0.777	0.726	0.831	SUBCLONAL	2	TRUE	1	0.45311711767994	3		747	766	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492688	56492688	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	191	590	0	ENST00000407977.2:c.251A>G	p.Gln84Arg	p.Q84R	ENST00000407977		84	cAg/cGg	2/10	0.321324089071124	3	FACETS	1	0.99	1	0.721	0.669	0.775	CLONAL	1	TRUE	1	0.45311711767994	3		590	717	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581330	48581330	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863224732	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	279	683	1	ENST00000342988.3:c.634G>A	p.Ala212Thr	p.A212T	ENST00000342988	NM_005359.5	212	Gcc/Acc	5/12	0.314472176033069	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.45311711767994	4		684	861	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626897	14626897	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	262	936	0	ENST00000254322.2:c.878T>C	p.Met293Thr	p.M293T	ENST00000254322	NM_006145.1	293	aTg/aCg	3/3	0.225662567263041	3	FACETS	1	0.991	1	0.446	0.418	0.475	INDETERMINATE	1	TRUE	0	0.45311711767994	3		936	1060	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942086	17942086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	429	1190	1	ENST00000458235.1:c.2929G>A	p.Asp977Asn	p.D977N	ENST00000458235	NM_000215.3	977	Gac/Aac	21/24	0.225662567263041	3	FACETS	0.853	0.817	0.888	0.853	0.817	0.888	INDETERMINATE	3	TRUE	0	0.45311711767994	3		1191	908	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209215	36209215	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	18	211	0	ENST00000222270.7:c.295C>T	p.Arg99Trp	p.R99W	ENST00000222270	NM_014727.1	99	Cgg/Tgg	1/37	0.159338947248602	5	FACETS	0.473	0.356	0.611	0.158	0.118	0.204	INDETERMINATE	1	TRUE	2	0.45311711767994	5		211	282	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455272	29455272	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	320	783	1	ENST00000389048.3:c.2530G>T	p.Gly844Cys	p.G844C	ENST00000389048	NM_004304.4	844	Ggt/Tgt	15/29	0.413499324245788	4	FACETS	0.932	0.886	0.979	0.932	0.886	0.979	CLONAL	3	TRUE	1	0.45311711767994	4		784	734	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032847	48032848	+	splice_donor_variant	Splice_Site	INS	-	-	T	rs1269788253	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	294	607	0	ENST00000234420.5:c.3646+2dup		p.X1216_splice	ENST00000234420	NM_000179.2	1216			0.413499324245788	4	FACETS	0.889	0.842	0.936	0.889	0.842	0.936	CLONAL	3	TRUE	1	0.45311711767994	4		607	707	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919670	96919670	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	217	673	0	ENST00000258439.3:c.593A>G	p.His198Arg	p.H198R	ENST00000258439	NM_001193304.2	198	cAc/cGc	4/4	0.45311711767994	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.45311711767994	3		673	542	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136268	202136268	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	174	862	0	ENST00000358485.4:c.512T>C	p.Val171Ala	p.V171A	ENST00000358485	NM_001080125.1	171	gTg/gCg	3/9	0.45311711767994	3	FACETS	1	0.967	1	0.546	0.503	0.591	CLONAL	1	TRUE	1	0.45311711767994	3		862	863	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62323150	62323150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144002969	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	341	735	4	ENST00000360203.5:c.2612C>T	p.Pro871Leu	p.P871L	ENST00000360203	NM_001283009.1	871	cCg/cTg	28/35	0.122479441672141	5	FACETS	1	0.969	1			1	INDETERMINATE	4	TRUE	NA	0.45311711767994	5		739	622	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852449	42852449	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	116	860	0	ENST00000398585.3:c.637T>C	p.Trp213Arg	p.W213R	ENST00000398585	NM_001135099.1	213	Tgg/Cgg	6/14	0.11376013625884	3	FACETS	0.866	0.781	0.956	0.289	0.26	0.319	INDETERMINATE	1	TRUE	0	0.45311711767994	3		860	725	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514900	44514900	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	55	479	0	ENST00000291552.4:c.349-2A>T		p.X117_splice	ENST00000291552	NM_006758.2	117			0.11376013625884	3	FACETS	0.566	0.484	0.655	0.189	0.161	0.219	INDETERMINATE	1	TRUE	0	0.45311711767994	3		479	526	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069472	30069472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	31	678	0	ENST00000338641.4:c.1337G>A	p.Arg446Lys	p.R446K	ENST00000338641	NM_000268.3	446	aGg/aAg	12/16	0.45311711767994	3	FACETS	0.298	0.24	0.363	0.149	0.12	0.182	SUBCLONAL	1	TRUE	1	0.45311711767994	3		678	564	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641885	12641885	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	256	411	0	ENST00000251849.4:c.862+2T>C		p.X288_splice	ENST00000251849	NM_002880.3	288			0.413499324245788	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	1	0.45311711767994	4		411	505	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540104	187540104	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	80	618	0	ENST00000441802.2:c.7636G>T	p.Gly2546Ter	p.G2546*	ENST00000441802	NM_005245.3	2546	Gga/Tga	10/27	0.0692590484545801	3	FACETS	0.764	0.673	0.861			1	INDETERMINATE	1	TRUE	NA	0.45311711767994	3		618	567	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629925	187629925	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	180	935	1	ENST00000441802.2:c.1057A>G	p.Ile353Val	p.I353V	ENST00000441802	NM_005245.3	353	Att/Gtt	2/27	0.0692590484545801	3	FACETS	1	0.963	1			1	INDETERMINATE	1	TRUE	NA	0.45311711767994	3		936	908	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952381	38952381	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	279	460	0	ENST00000357387.3:c.3044T>C	p.Leu1015Pro	p.L1015P	ENST00000357387	NM_152756.3	1015	cTt/cCt	30/38	0.26063780117952	5	FACETS	1	0.98	1	1	0.98	1	INDETERMINATE	3	TRUE	2	0.45311711767994	5		460	643	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456856	149456856	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	347	871	0	ENST00000286301.3:c.872T>C	p.Met291Thr	p.M291T	ENST00000286301	NM_005211.3	291	aTg/aCg	6/22	0.163033514497023	3	FACETS	1	0.991	1	0.781	0.743	0.819	INDETERMINATE	2	TRUE	0	0.45311711767994	3		871	802	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490583	20490583	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	157	719	0	ENST00000346618.3:c.1320G>T	p.Glu440Asp	p.E440D	ENST00000346618	NM_001949.4	440	gaG/gaT	7/7	0.45311711767994	5	FACETS	0.803	0.737	0.871	0.535	0.491	0.581	CLONAL	2	TRUE	2	0.45311711767994	5		719	725	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185837	32185837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	197	1051	2	ENST00000375023.3:c.1559C>T	p.Ala520Val	p.A520V	ENST00000375023	NM_004557.3	520	gCt/gTt	9/30	0.45311711767994	3	FACETS	1	0.986	1	0.633	0.586	0.68	CLONAL	1	TRUE	1	0.45311711767994	3		1053	843	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983090	111983090	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	164	877	0	ENST00000368678.4:c.1457A>G	p.Gln486Arg	p.Q486R	ENST00000368678		486	cAg/cGg	13/13	0.45311711767994	3	FACETS	1	0.97	1	0.557	0.512	0.604	CLONAL	1	TRUE	1	0.45311711767994	3		877	797	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431649	6431649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	342	790	2	ENST00000356142.4:c.202C>T	p.Arg68Cys	p.R68C	ENST00000356142	NM_018890.3	68	Cgc/Tgc	3/7	0.201751255127818	3	FACETS	0.887	0.846	0.928	0.887	0.846	0.928	INDETERMINATE	3	TRUE	0	0.45311711767994	3		792	696	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845209	128845209	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762783453	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	310	691	5	ENST00000249373.3:c.703G>A	p.Ala235Thr	p.A235T	ENST00000249373	NM_005631.4	235	Gcg/Acg	3/12	0.45311711767994	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.45311711767994	3		696	698	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868470	117868470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	359	775	0	ENST00000297338.2:c.872C>T	p.Thr291Ile	p.T291I	ENST00000297338	NM_006265.2	291	aCt/aTt	8/14	0.45311711767994	5	FACETS	1	0.948	1	0.667	0.632	0.703	CLONAL	2	TRUE	2	0.45311711767994	5		775	1330	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637008	93637008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201479078	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	269	562	1	ENST00000375746.1:c.1058C>T	p.Ala353Val	p.A353V	ENST00000375746	NM_001174167.1	353	gCg/gTg	9/14	0.45311711767994	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	0	0.45311711767994	3		563	459	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787720	135787720	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770653972	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	124	789	1	ENST00000298552.3:c.862C>T	p.Arg288Cys	p.R288C	ENST00000298552	NM_001162426.1	288	Cgt/Tgt	9/23	0.45311711767994	2	FACETS	0.727	0.658	0.799	0.363	0.329	0.4	SUBCLONAL	1	TRUE	0	0.45311711767994	2		790	753	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401269	139401269	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	532	1140	0	ENST00000277541.6:c.3800A>G	p.Asp1267Gly	p.D1267G	ENST00000277541	NM_017617.3	1267	gAt/gGt	23/34	0.45311711767994	2	FACETS	0.922	0.892	0.951	1	0.997	1	CLONAL	3	TRUE	0	0.45311711767994	2		1140	849	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0022235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	499	422	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	0.693178127229186	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.693178127229186	3		422	627	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713341	40713341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1305277749	NA	P-0022235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	286	621	1	ENST00000373198.4:c.4174C>T	p.Arg1392Cys	p.R1392C	ENST00000373198	NM_133170.3	1392	Cgt/Tgt	30/32	0.559795319406123	4	FACETS	0.992	0.93	1	0.496	0.465	0.528	CLONAL	1	TRUE	2	0.693178127229186	4		622	1409	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23640533	23640533	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	335	693	0	ENST00000261584.4:c.2578G>C	p.Glu860Gln	p.E860Q	ENST00000261584	NM_024675.3	860	Gag/Cag	6/13	NA	2	FACETS	0.937	0.89	0.986			1	INDETERMINATE	1	TRUE	NA	0.800347974452697	2		693	893	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673810	37673810	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0022252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	652	572	0	ENST00000447079.4:c.2963+1G>C		p.X988_splice	ENST00000447079	NM_015083.1	988			1	2	FACETS	1	0.988	1	1	0.998	1	CLONAL	2	TRUE	1	0.800347974452697	2		572	804	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839681	42839682	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTCC	novel	NA	P-0022252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	375	712	0	ENST00000398585.3:c.1554_1557dup	p.Trp520GlyfsTer40	p.W520Gfs*40	ENST00000398585	NM_001135099.1	519	-/GGAC	13/14	1	2	FACETS	0.914	0.87	0.959	0.914	0.87	0.959	CLONAL	1	TRUE	1	0.800347974452697	2		712	1025	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93626922	93626922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	68	638	0	ENST00000375746.1:c.769G>A	p.Val257Ile	p.V257I	ENST00000375746	NM_001174167.1	257	Gtc/Atc	5/14	0.800347974452697	3	FACETS	0.193	0.167	0.221	0.096	0.083	0.111	SUBCLONAL	1	TRUE	1	0.800347974452697	3		638	1235	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398282	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0022389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	120	781	1	ENST00000311936.3:c.37_38delinsTA	p.Gly13Tyr	p.G13Y	ENST00000311936	NM_004985.3	13	GGc/TAc	2/5	1	2	FACETS	0.95	0.859	1	0.95	0.859	1	CLONAL	1	TRUE	1	0.340399735954516	2		782	742	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0022478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	233	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.290492464119689	2		436	1098	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669553	88669553	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs200206241	NA	P-0022478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	126	493	0	ENST00000360948.2:c.1345C>G	p.Leu449Val	p.L449V	ENST00000360948	NM_001012338.2	449	Ctc/Gtc	12/19	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.290492464119689	2		493	763	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830823	156830823	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	173	481	4	ENST00000524377.1:c.97G>A	p.Ala33Thr	p.A33T	ENST00000524377	NM_002529.3	33	Gcc/Acc	1/17	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.290492464119689	2		485	946	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646825	23646858	+	frameshift_variant	Frame_Shift_Del	DEL	GTTCTTTTAAGTTTTGGTTTTCATTTGCTGGTAA	GTTCTTTTAAGTTTTGGTTTTCATTTGCTGGTAA	-	novel	NA	P-0022478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	132	624	1	ENST00000261584.4:c.1009_1042del	p.Leu337LysfsTer8	p.L337Kfs*8	ENST00000261584	NM_024675.3	337	TTACCAGCAAATGAAAACCAAAACTTAAAAGAACaa/aa	4/13	1	2	FACETS	0.837	0.758	0.92	0.837	0.758	0.92	CLONAL	1	TRUE	1	0.290492464119689	2		625	1086	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845652	68845652	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1167723442	NA	P-0022478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	103	681	0	ENST00000261769.5:c.898A>G	p.Ile300Val	p.I300V	ENST00000261769	NM_004360.3	300	Atc/Gtc	7/16	1	2	FACETS	0.555	0.495	0.619	0.555	0.495	0.619	SUBCLONAL	1	TRUE	1	0.290492464119689	2		681	1278	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543834	212543834	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761773013	NA	P-0022478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	131	415	2	ENST00000342788.4:c.1565C>T	p.Ser522Leu	p.S522L	ENST00000342788	NM_005235.2	522	tCg/tTg	13/28	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.290492464119689	2		417	808	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513356	44513356	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1234	71	710	0	ENST00000291552.4:c.579T>G	p.His193Gln	p.H193Q	ENST00000291552	NM_006758.2	193	caT/caG	8/8	0.230330996445028	3	FACETS	0.429	0.373	0.49	0.143	0.124	0.164	SUBCLONAL	1	TRUE	0	0.290492464119689	3		710	1305	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596009	43596014	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCTG	CCCCTG	T	novel	NA	P-0022478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	214	711	0	ENST00000355710.3:c.176_181delinsT	p.Ala59ValfsTer22	p.A59Vfs*22	ENST00000355710	NM_020975.4	59	gCCCCTGag/gTag	2/20	0.104584055748629	4	FACETS	0.752	0.698	0.809	0.752	0.698	0.809	INDETERMINATE	2	TRUE	2	0.290492464119689	4		711	1264	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579855	7579855	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1131691018	NA	P-0022495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	555	843	0	ENST00000269305.4:c.58del	p.Ser20GlnfsTer24	p.S20Qfs*24	ENST00000269305	NM_001126112.2	20	Tca/ca	2/11	0.621133844899231	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	FALSE	0	0.621133844899231	2		843	829	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443618	49443691	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTGGACTAACATCCGTAGAGACCCCCAACTCCATGGACAGGGAGCCACCCCCCTCCGGGTCTGGAGAGCCCA	GGCTGGACTAACATCCGTAGAGACCCCCAACTCCATGGACAGGGAGCCACCCCCCTCCGGGTCTGGAGAGCCCA	-	novel	NA	P-0022495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	498	761	2	ENST00000301067.7:c.3680_3753del	p.Leu1227ProfsTer3	p.L1227Pfs*3	ENST00000301067	NM_003482.3	1227	cTGGGCTCTCCAGACCCGGAGGGGGGTGGCTCCCTGTCCATGGAGTTGGGGGTCTCTACGGATGTTAGTCCAGCC/c	11/54	0.621133844899231	2	FACETS	0.992	0.959	1	0.992	0.959	1	CLONAL	2	FALSE	0	0.621133844899231	2		763	808	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174876	56174876	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	180	490	0	ENST00000399503.3:c.2035C>A	p.Leu679Ile	p.L679I	ENST00000399503	NM_005921.1	679	Ctt/Att	11/20	0.621133844899231	2	FACETS	1	0.966	1	0.533	0.494	0.572	CLONAL	1	FALSE	0	0.621133844899231	2		490	544	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849935	156849935	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	83	778	1	ENST00000524377.1:c.2191C>A	p.Leu731Ile	p.L731I	ENST00000524377	NM_002529.3	731	Ctc/Atc	16/17	NA	2	FACETS	0.849	0.755	0.948			1	INDETERMINATE	2	TRUE	NA	0.275424535666086	2		779	355	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844244	68844245	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	TT	novel	NA	P-0022576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	80	511	0	ENST00000261769.5:c.832_832+1delinsTT		p.X278_splice	ENST00000261769	NM_004360.3	278		6/16	0.275424535666086	1	FACETS	1	0.971	1	1	0.987	1	CLONAL	2	TRUE	0	0.275424535666086	1		511	202	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578066	7578429	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TATAGGGAGGTCAAATAAGCAGCAGGAGAAAGCCCCCCTACTGCTCACCTGGAGGGCCACTGACAACCACCCTTAACCCCTCCTCCCAGAGACCCCAGTTGCAAACCAGACCTCAGGCGGCTCATAGGGCACCACCACACTATGTCGAAAAGTGTTTCTGTCATCCAAATACTCCACACGCAAATTTCCTTCCACTCGGATAAGATGCTGAGGAGGGGCCAGACCTAAGAGCAATCAGTGAGGAATCAGAGGCCTGGGGACCCTGGGCAACCAGCCCTGTCGTCTCTCCAGCCCCAGCTGCTCACCATCGCTATCTGAGCAGCGCTCATGGTGGGGGCAGCGCCTCACAACCTCCGTCATGTGC	TATAGGGAGGTCAAATAAGCAGCAGGAGAAAGCCCCCCTACTGCTCACCTGGAGGGCCACTGACAACCACCCTTAACCCCTCCTCCCAGAGACCCCAGTTGCAAACCAGACCTCAGGCGGCTCATAGGGCACCACCACACTATGTCGAAAAGTGTTTCTGTCATCCAAATACTCCACACGCAAATTTCCTTCCACTCGGATAAGATGCTGAGGAGGGGCCAGACCTAAGAGCAATCAGTGAGGAATCAGAGGCCTGGGGACCCTGGGCAACCAGCCCTGTCGTCTCTCCAGCCCCAGCTGCTCACCATCGCTATCTGAGCAGCGCTCATGGTGGGGGCAGCGCCTCACAACCTCCGTCATGTGC	-	novel	NA	P-0022576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	11	254	0	ENST00000269305.4:c.501_672+111del		p.X167_splice	ENST00000269305	NM_001126112.2	167		5-6/11	NA	2	FACETS	0.94	0.658	1			1	INDETERMINATE	1	TRUE	NA	0.275424535666086	2		254	85	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873975	151873975	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	138	642	1	ENST00000262189.6:c.8563C>T	p.Gln2855Ter	p.Q2855*	ENST00000262189	NM_170606.2	2855	Cag/Tag	38/59	0.275424535666086	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	2	0.275424535666086	4		643	543	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0022896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	146	979	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.336413538080532	1	FACETS	0.982	0.898	1	0.982	0.898	1	CLONAL	1	TRUE	0	0.336413538080532	1		979	735	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015054	37015054	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374738065	NA	P-0022896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	174	898	1	ENST00000358127.4:c.350G>A	p.Arg117Gln	p.R117Q	ENST00000358127	NM_001280556.1	117	cGg/cAg	3/10	0.336413538080532	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.336413538080532	1		899	789	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039570	180039570	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1185976621	NA	P-0022896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	221	1437	4	ENST00000261937.6:c.3473C>T	p.Ala1158Val	p.A1158V	ENST00000261937	NM_182925.4	1158	gCg/gTg	26/30	0.205682642981847	1	FACETS	0.929	0.864	0.997	0.929	0.864	0.997	CLONAL	1	TRUE	0	0.336413538080532	1		1441	1176	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11301667	11301667	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	55	985	0	ENST00000361445.4:c.1484C>G	p.Pro495Arg	p.P495R	ENST00000361445	NM_004958.3	495	cCa/cGa	10/58	1	2	FACETS	0.313	0.267	0.364	0.313	0.267	0.364	SUBCLONAL	1	TRUE	1	0.336413538080532	2		985	1044	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101146	27101200	+	frameshift_variant	Frame_Shift_Del	DEL	GCCACCACAAATGATGGGCGGCCCCATACAGGCATCAGCTGAGGTTGCTCAGCAA	GCCACCACAAATGATGGGCGGCCCCATACAGGCATCAGCTGAGGTTGCTCAGCAA	-	novel	NA	P-0022896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	173	1068	0	ENST00000324856.7:c.4429_4483del	p.Pro1477AlafsTer10	p.P1477Afs*10	ENST00000324856	NM_006015.4	1476	atGCCACCACAAATGATGGGCGGCCCCATACAGGCATCAGCTGAGGTTGCTCAGCAA/at	18/20	0.336413538080532	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.336413538080532	1		1068	839	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795483	42795483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751769419	NA	P-0022896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	164	1102	0	ENST00000575354.2:c.2563G>A	p.Gly855Ser	p.G855S	ENST00000575354	NM_015125.3	855	Ggc/Agc	10/20	0.205682642981847	1	FACETS	0.885	0.813	0.961	0.885	0.813	0.961	CLONAL	1	TRUE	0	0.336413538080532	1		1102	916	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916824	178916824	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	260	1027	0	ENST00000263967.3:c.211G>C	p.Val71Leu	p.V71L	ENST00000263967	NM_006218.2	71	Gta/Cta	2/21	0.190391087504035	3	FACETS	0.769	0.72	0.82	0.769	0.72	0.82	INDETERMINATE	2	TRUE	1	0.336413538080532	3		1027	1174	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577375	64577375	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1057517902	NA	P-0022955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	333	809	1	ENST00000312049.6:c.207del	p.Asp70ThrfsTer49	p.D70Tfs*49	ENST00000312049	NM_130799.2	69	ccC/cc	2/10	0.709546275271221	2	FACETS	0.933	0.898	0.967	0.933	0.898	0.967	CLONAL	2	TRUE	0	0.728126284124838	2		810	490	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366353	15366353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200484332	NA	P-0022955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	42	665	3	ENST00000263377.2:c.1802C>T	p.Ser601Leu	p.S601L	ENST00000263377	NM_058243.2	601	tCg/tTg	10/20	0.292382550906845	5	FACETS	0.433	0.361	0.513	0.144	0.12	0.171	INDETERMINATE	1	TRUE	2	0.728126284124838	5		668	558	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937024	76937025	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0022955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	224	512	0	ENST00000373344.5:c.3723_3724del	p.Phe1241LeufsTer7	p.F1241Lfs*7	ENST00000373344	NM_000489.3	1241	ttTTgc/ttgc	9/35	0.709546275271221	2	FACETS	0.944	0.901	0.985	0.944	0.901	0.985	CLONAL	2	TRUE	0	0.728126284124838	2		512	326	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958622	38958622	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0022955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	19	272	0	ENST00000357387.3:c.2344-1G>A		p.X782_splice	ENST00000357387	NM_152756.3	782			0.673339711608129	4	FACETS	0.316	0.24	0.406	0.158	0.12	0.203	SUBCLONAL	1	TRUE	2	0.728126284124838	4		272	285	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78938101	78938101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1044306323	NA	P-0022955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	172	450	0	ENST00000306801.3:c.3979G>A	p.Val1327Met	p.V1327M	ENST00000306801	NM_020761.2	1327	Gtg/Atg	34/34	0.758244309335176	3	FACETS	0.932	0.861	1	0.466	0.43	0.503	CLONAL	1	TRUE	1	0.758244309335176	3		450	671	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577375	64577375	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1057517902	NA	P-0022955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	426	809	1	ENST00000312049.6:c.207del	p.Asp70ThrfsTer49	p.D70Tfs*49	ENST00000312049	NM_130799.2	69	ccC/cc	2/10	0.754004193166863	2	FACETS	0.998	0.969	1	0.998	0.969	1	CLONAL	2	TRUE	0	0.758244309335176	2		810	563	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366353	15366353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200484332	NA	P-0022955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	103	665	3	ENST00000263377.2:c.1802C>T	p.Ser601Leu	p.S601L	ENST00000263377	NM_058243.2	601	tCg/tTg	10/20	0.758244309335176	3	FACETS	0.792	0.712	0.876	0.396	0.356	0.438	SUBCLONAL	1	TRUE	1	0.758244309335176	3		668	473	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937024	76937025	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0022955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	154	512	0	ENST00000373344.5:c.3723_3724del	p.Phe1241LeufsTer7	p.F1241Lfs*7	ENST00000373344	NM_000489.3	1241	ttTTgc/ttgc	9/35	0.754344056389333	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.758244309335176	2		512	189	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845705	151845705	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	99	768	1	ENST00000262189.6:c.13307C>T	p.Ser4436Phe	p.S4436F	ENST00000262189	NM_170606.2	4436	tCc/tTc	52/59	1	2	FACETS	0.755	0.674	0.84	0.755	0.674	0.84	SUBCLONAL	1	TRUE	1	0.390922832876921	2		769	671	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572102	64572102	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	43	912	0	ENST00000312049.6:c.1537G>T	p.Gly513Ter	p.G513*	ENST00000312049	NM_130799.2	513	Gga/Tga	10/10	0.0997698897203765	4	FACETS	0.403	0.336	0.477	0.201	0.168	0.239	INDETERMINATE	1	TRUE	2	0.390922832876921	4		912	760	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845557	151845557	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	122	880	0	ENST00000262189.6:c.13455C>A	p.Phe4485Leu	p.F4485L	ENST00000262189	NM_170606.2	4485	ttC/ttA	52/59	1	2	FACETS	0.732	0.661	0.806	0.732	0.661	0.806	SUBCLONAL	1	TRUE	1	0.390922832876921	2		880	853	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	248	690	12	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.826	0.775	0.878	1	0.994	1	CLONAL	2	TRUE	1	0.38	2		702	790	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115594	108115594	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730881336	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	326	739	3	ENST00000278616.4:c.742C>T	p.Arg248Ter	p.R248*	ENST00000278616	NM_000051.3	248	Cga/Tga	7/63	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.38	2		742	763	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	280	536	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.946	0.901	0.992	1	0.996	1	CLONAL	3	TRUE	1	0.38	2		537	519	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	263	590	2	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	0.96	0.904	1	1	0.995	1	CLONAL	2	TRUE	1	0.38	2		592	721	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	299	751	3	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	0.937	0.885	0.989	1	0.995	1	CLONAL	2	TRUE	1	0.38	2		754	840	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	97	191	1	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	0.3	4	FACETS	0.936	0.849	1	0.936	0.849	1	CLONAL	3	TRUE	1	0.38	4		192	251	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	240	940	1	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.93	0.873	0.988	1	0.994	1	CLONAL	2	TRUE	1	0.38	2		941	679	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	425	798	29	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	1	2	FACETS	0.842	0.806	0.877	1	0.997	1	CLONAL	3	TRUE	1	0.38	2		827	886	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	88	848	2	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	1	2	FACETS	0.479	0.423	0.539	0.479	0.423	0.539	SUBCLONAL	1	TRUE	1	0.38	2		850	967	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624293	89624293	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs876661244	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	270	654	0	ENST00000371953.3:c.67T>G	p.Leu23Val	p.L23V	ENST00000371953	NM_000314.4	23	Tta/Gta	1/9	1	2	FACETS	1	0.974	1	1	0.996	1	CLONAL	2	TRUE	1	0.38	2		654	674	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	23	618	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	1	2	FACETS	0.24	0.186	0.303	0.24	0.186	0.303	SUBCLONAL	1	TRUE	1	0.38	2		618	504	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	91	239	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.783	0.703	0.866	1	0.983	1	SUBCLONAL	2	TRUE	1	0.38	2		239	306	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	17	671	0	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	1	2	FACETS	0.142	0.105	0.187	0.142	0.105	0.187	SUBCLONAL	1	TRUE	1	0.38	2		671	628	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755554	39755554	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	171	553	7	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	0.993	1	CLONAL	2	TRUE	1	0.38	2		560	435	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254749	16254749	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	548	737	2	ENST00000375759.3:c.2014C>T	p.Arg672Ter	p.R672*	ENST00000375759	NM_015001.2	672	Cga/Tga	11/15	1	2	FACETS	1	0.987	1	1	0.998	1	CLONAL	4	TRUE	1	0.38	2		739	708	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032388	42032388	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	185	551	0	ENST00000219905.7:c.4575del	p.Lys1525AsnfsTer18	p.K1525Nfs*18	ENST00000219905	NM_001164273.1	1524	gcA/gc	14/24	1	2	FACETS	0.857	0.796	0.919	1	0.992	1	CLONAL	2	TRUE	1	0.38	2		551	568	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	196	586	1	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	0.141283393559619	3	FACETS	0.915	0.85	0.981	0.915	0.85	0.981	INDETERMINATE	2	TRUE	1	0.38	3		587	671	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411530	63411530	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	185	470	1	ENST00000330258.3:c.1637del	p.Leu546CysfsTer16	p.L546Cfs*16	ENST00000330258	NM_152424.3	546	tTg/tg	2/2	1	1	FACETS	0.894	0.846	0.941	1	0.995	1	CLONAL	3	TRUE	0	0.38	1		471	294	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588848	69588848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs979866825	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	199	721	0	ENST00000168712.1:c.388G>A	p.Gly130Ser	p.G130S	ENST00000168712	NM_002007.2	130	Ggc/Agc	2/3	1	2	FACETS	1	0.979	1	1	0.994	1	CLONAL	2	TRUE	1	0.38	2		721	473	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857178	9857178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763219483	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	163	569	2	ENST00000330684.3:c.4223C>T	p.Thr1408Met	p.T1408M	ENST00000330684	NM_001134407.1	1408	aCg/aTg	13/13	1	2	FACETS	1	0.976	1	1	0.993	1	CLONAL	2	TRUE	1	0.38	2		571	386	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655272	45655272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764295138	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	109	903	0	ENST00000407780.3:c.580C>T	p.Arg194Trp	p.R194W	ENST00000407780	NM_001283052.1	194	Cgg/Tgg	4/7	1	2	FACETS	0.859	0.772	0.95	0.859	0.772	0.95	CLONAL	1	TRUE	1	0.38	2		903	668	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055897	180055897	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768687155	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	165	694	0	ENST00000261937.6:c.1088C>T	p.Pro363Leu	p.P363L	ENST00000261937	NM_182925.4	363	cCg/cTg	8/30	0.205728654511138	0	FACETS	0.632	0.587	0.678			1	INDETERMINATE	2	TRUE	0	0.38	0		694	426	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103410	2103410	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1478204355	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	188	913	1	ENST00000219476.3:c.293G>A	p.Arg98Gln	p.R98Q	ENST00000219476	NM_000548.3	98	cGg/cAg	4/42	1	2	FACETS	0.891	0.829	0.955	1	0.993	1	CLONAL	2	TRUE	1	0.38	2		914	555	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286540	33286540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	237	636	2	ENST00000374542.5:c.2203G>A	p.Val735Met	p.V735M	ENST00000374542	NM_001141970.1	735	Gtg/Atg	8/8	1	2	FACETS	0.992	0.932	1	1	0.995	1	CLONAL	2	TRUE	1	0.38	2		638	629	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427983	49427983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866777837	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	64	741	0	ENST00000301067.7:c.10607G>A	p.Arg3536His	p.R3536H	ENST00000301067	NM_003482.3	3536	cGc/cAc	38/54	1	2	FACETS	0.536	0.464	0.615	0.536	0.464	0.615	SUBCLONAL	1	TRUE	1	0.38	2		741	628	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816544	32816544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376553490	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	349	907	4	ENST00000354258.4:c.1631G>A	p.Arg544His	p.R544H	ENST00000354258	NM_000593.5	544	cGc/cAc	7/11	1	2	FACETS	1	0.973	1	1	0.996	1	CLONAL	2	TRUE	1	0.38	2		911	887	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180040015	180040015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564369853	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	251	825	0	ENST00000261937.6:c.3427G>A	p.Ala1143Thr	p.A1143T	ENST00000261937	NM_182925.4	1143	Gcc/Acc	25/30	0.205728654511138	0	FACETS	0.664	0.625	0.702			1	INDETERMINATE	2	TRUE	0	0.38	0		825	617	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16203059	16203060	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	241	579	0	ENST00000375759.3:c.770_771del	p.Arg257ThrfsTer3	p.R257Tfs*3	ENST00000375759	NM_015001.2	256	cAG/c	3/15	1	2	FACETS	0.971	0.913	1	1	0.995	1	CLONAL	2	TRUE	1	0.38	2		579	653	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799087	45799087	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs373766973	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	249	909	0	ENST00000450313.1:c.346C>T	p.Arg116Trp	p.R116W	ENST00000450313	NM_012222.2	116	Cgg/Tgg	3/16	1	2	FACETS	0.971	0.913	1	1	0.995	1	CLONAL	2	TRUE	1	0.38	2		909	675	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439754	51439754	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs199638281	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	145	454	0	ENST00000262662.1:c.319T>G	p.Leu107Val	p.L107V	ENST00000262662		107	Ttg/Gtg	4/4	1	2	FACETS	0.981	0.905	1	1	0.992	1	CLONAL	2	TRUE	1	0.38	2		454	389	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377048	118377048	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	34	483	0	ENST00000534358.1:c.10441C>T	p.Pro3481Ser	p.P3481S	ENST00000534358	NM_005933.3	3481	Ccc/Tcc	27/36	1	2	FACETS	0.34	0.277	0.41	0.34	0.277	0.41	SUBCLONAL	1	TRUE	1	0.38	2		483	527	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856254	111856254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	51	149	0	ENST00000341259.2:c.305C>T	p.Ala102Val	p.A102V	ENST00000341259	NM_005475.2	102	gCg/gTg	2/8	1	2	FACETS	1	0.88	1	1	0.978	1	CLONAL	2	TRUE	1	0.38	2		149	133	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879808	123879808	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	195	583	0	ENST00000330479.4:c.509del	p.Ala171LeufsTer36	p.A171Lfs*36	ENST00000330479	NM_020382.3	168	cgA/cg	4/9	1	2	FACETS	0.873	0.813	0.934	1	0.993	1	CLONAL	2	TRUE	1	0.38	2		583	588	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26970424	26970425	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	128	377	0	ENST00000381527.3:c.794_795del	p.Lys265ArgfsTer10	p.K265Rfs*10	ENST00000381527	NM_001260.1	265	AAa/a	8/13	1	2	FACETS	0.884	0.81	0.961	1	0.99	1	CLONAL	2	TRUE	1	0.38	2		377	381	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041668	14041668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765235917	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	220	577	0	ENST00000311895.7:c.2215G>A	p.Gly739Ser	p.G739S	ENST00000311895	NM_005236.2	739	Ggc/Agc	11/11	1	2	FACETS	1	0.942	1	1	0.994	1	CLONAL	2	TRUE	1	0.38	2		577	576	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670715	67670715	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	265	734	1	ENST00000264010.4:c.1960C>T	p.Arg654Ter	p.R654*	ENST00000264010	NM_006565.3	654	Cga/Tga	11/12	1	2	FACETS	0.991	0.934	1	1	0.995	1	CLONAL	2	TRUE	1	0.38	2		735	704	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830906	+	frameshift_variant	Frame_Shift_Del	DEL	CTCT	CTCT	-	novel	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	233	660	0	ENST00000268489.5:c.5675_5678del	p.Glu1892GlyfsTer21	p.E1892Gfs*21	ENST00000268489	NM_006885.3	1892	gAGAGg/gg	9/10	0.3	0	FACETS	0.663	0.631	0.696			1	SUBCLONAL	3	TRUE	0	0.38	0		660	382	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350165	89350166	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	269	973	0	ENST00000301030.4:c.2784_2785del	p.Ser929CysfsTer88	p.S929Cfs*88	ENST00000301030	NM_001256183.1	928	aaAAgt/aagt	9/13	0.149554228675938	0	FACETS	0.576	0.543	0.61			1	INDETERMINATE	2	TRUE	0	0.38	0		973	762	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127273	17127273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756807584	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	205	715	0	ENST00000285071.4:c.581G>A	p.Arg194Gln	p.R194Q	ENST00000285071	NM_144997.5	194	cGg/cAg	6/14	1	2	FACETS	0.967	0.904	1	1	0.994	1	CLONAL	2	TRUE	1	0.38	2		715	558	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17129521	17129521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	263	785	5	ENST00000285071.4:c.365G>A	p.Arg122His	p.R122H	ENST00000285071	NM_144997.5	122	cGc/cAc	5/14	1	2	FACETS	1	0.976	1	1	0.995	1	CLONAL	2	TRUE	1	0.38	2		790	653	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158636999	158636999	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772534199	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	278	759	1	ENST00000263640.3:c.181G>A	p.Asp61Asn	p.D61N	ENST00000263640	NM_001105.4	61	Gat/Aat	4/11	1	2	FACETS	1	0.976	1	1	0.996	1	CLONAL	2	TRUE	1	0.38	2		760	693	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755381	39755381	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	276	809	1	ENST00000288319.7:c.1384C>A	p.Pro462Thr	p.P462T	ENST00000288319	NM_182918.3	462	Ccc/Acc	10/10	1	2	FACETS	1	0.954	1	1	0.995	1	CLONAL	2	TRUE	1	0.38	2		810	718	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928933	49928933	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	285	835	1	ENST00000296474.3:c.3433G>T	p.Ala1145Ser	p.A1145S	ENST00000296474	NM_002447.2	1145	Gct/Tct	16/20	0.141283393559619	3	FACETS	1	0.989	1	1	0.989	1	INDETERMINATE	2	TRUE	1	0.38	3		836	753	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911435	134911435	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	231	704	0	ENST00000398015.3:c.1900T>C	p.Tyr634His	p.Y634H	ENST00000398015	NM_004441.4	634	Tac/Cac	11/16	0.3	1	FACETS	0.886	0.833	0.939	1	0.994	1	CLONAL	2	TRUE	0	0.38	1		704	556	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594183	55594183	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	156	555	0	ENST00000288135.5:c.1886C>G	p.Ala629Gly	p.A629G	ENST00000288135	NM_000222.2	629	gCc/gGc	13/21	1	2	FACETS	0.944	0.873	1	1	0.992	1	CLONAL	2	TRUE	1	0.38	2		555	435	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224507	224507	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	20	239	0	ENST00000264932.6:c.183A>T	p.Glu61Asp	p.E61D	ENST00000264932	NM_004168.2	61	gaA/gaT	3/15	0.149554228675938	0	FACETS	0.274	0.21	0.349			1	INDETERMINATE	1	TRUE	0	0.38	0		239	238	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141567294	141567294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	203	646	5	ENST00000220592.5:c.920C>T	p.Thr307Met	p.T307M	ENST00000220592	NM_012154.3	307	aCg/aTg	8/19	1	2	FACETS	0.942	0.88	1	1	0.994	1	CLONAL	2	TRUE	1	0.38	2		651	567	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572717	141572717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1015925954	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	212	585	1	ENST00000220592.5:c.353C>T	p.Thr118Met	p.T118M	ENST00000220592	NM_012154.3	118	aCg/aTg	4/19	1	2	FACETS	1	0.98	1	1	0.995	1	CLONAL	2	TRUE	1	0.38	2		586	504	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738726	145738726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372741479	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	268	966	0	ENST00000428558.2:c.2338C>T	p.Arg780Trp	p.R780W	ENST00000428558	NM_004260.3	780	Cgg/Tgg	15/22	1	2	FACETS	1	0.982	1	1	0.996	1	CLONAL	2	TRUE	1	0.38	2		966	646	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231428	98231428	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060502266	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	203	611	1	ENST00000331920.6:c.1855G>A	p.Val619Ile	p.V619I	ENST00000331920	NM_000264.3	619	Gtc/Atc	14/24	1	2	FACETS	0.949	0.886	1	1	0.994	1	CLONAL	2	TRUE	1	0.38	2		612	563	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399429	139399429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	211	810	0	ENST00000277541.6:c.4714G>A	p.Gly1572Ser	p.G1572S	ENST00000277541	NM_017617.3	1572	Ggc/Agc	26/34	1	2	FACETS	0.861	0.804	0.919	1	0.993	1	CLONAL	2	TRUE	1	0.38	2		810	645	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566487	139566487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1050441878	NA	P-0023307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	254	832	3	ENST00000308874.7:c.746G>A	p.Arg249His	p.R249H	ENST00000308874		249	cGc/cAc	9/10	1	2	FACETS	1	0.985	1	1	0.996	1	CLONAL	2	TRUE	1	0.38	2		835	596	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0023372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	151	562	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.59688502799675	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.606294837121427	1		562	335	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99160439	99160439	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	126	469	0	ENST00000074304.5:c.918G>C	p.Gln306His	p.Q306H	ENST00000074304	NM_001134224.1	306	caG/caC	11/26	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.606294837121427	2		469	333	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112412	115112412	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	140	659	0	ENST00000257566.3:c.1328C>T	p.Ser443Leu	p.S443L	ENST00000257566	NM_016569.3	443	tCg/tTg	7/8	1	2	FACETS	0.414	0.377	0.452	0.414	0.377	0.452	SUBCLONAL	1	TRUE	1	0.880108968360906	2		659	769	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115952	8115953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0023452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	204	526	0	ENST00000346208.3:c.1300dup	p.His434ProfsTer73	p.H434Pfs*73	ENST00000346208		433	cac/caCc	6/6	1	2	FACETS	0.813	0.76	0.868	0.813	0.76	0.868	CLONAL	1	TRUE	1	0.880108968360906	2		526	570	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204507407	204507407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762382380	NA	P-0023452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	664	177	0	ENST00000367182.3:c.482C>T	p.Ser161Leu	p.S161L	ENST00000367182	NM_001278516.1	161	tCa/tTa	7/11	0.507115525105445	4	FACETS	0.8	0.771	0.83	0.533	0.514	0.553	INDETERMINATE	2	TRUE	1	0.880108968360906	4		177	1773	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919762	50919762	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	210	698	2	ENST00000440232.2:c.2930G>T	p.Gly977Val	p.G977V	ENST00000440232	NM_002691.3	977	gGc/gTc	23/27	0.348274486014803	2	FACETS	0.612	0.569	0.655	0.306	0.284	0.328	INDETERMINATE	1	TRUE	0	0.880108968360906	2		700	780	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46583407	46583407	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0023452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	159	596	0	ENST00000263734.3:c.335C>G	p.Ser112Ter	p.S112*	ENST00000263734	NM_001430.4	112	tCa/tGa	3/16	1	2	FACETS	0.449	0.412	0.488	0.449	0.412	0.488	SUBCLONAL	1	TRUE	1	0.880108968360906	2		596	804	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729796	41729796	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1365746909	NA	P-0023452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	22	473	0	ENST00000242208.4:c.733G>C	p.Glu245Gln	p.E245Q	ENST00000242208	NM_002192.2	245	Gag/Cag	3/3	0.444754576372487	1	FACETS	0.066	0.051	0.084	0.066	0.051	0.084	INDETERMINATE	1	TRUE	0	0.880108968360906	1		473	422	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737811	145737811	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1342565479	NA	P-0023452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1157	273	778	0	ENST00000428558.2:c.3019C>T	p.Leu1007Phe	p.L1007F	ENST00000428558	NM_004260.3	1007	Ctc/Ttc	18/22	0.681422495912072	4	FACETS	0.816	0.764	0.869			1	CLONAL	1	TRUE	NA	0.880108968360906	4		778	1430	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518531	69518531	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	164	748	2	ENST00000294312.3:c.114G>T	p.Trp38Cys	p.W38C	ENST00000294312	NM_005117.2	38	tgG/tgT	1/3	1	2	FACETS	0.973	0.895	1	0.973	0.895	1	CLONAL	1	TRUE	1	0.434338963260638	2		750	776	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233062	69233062	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	109	417	0	ENST00000462284.1:c.927G>A	p.Trp309Ter	p.W309*	ENST00000462284	NM_002392.5	309	tgG/tgA	11/11	0.434338963260638	1	FACETS	0.931	0.842	1	0.931	0.842	1	CLONAL	1	TRUE	0	0.434338963260638	1		417	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578369	7578369	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0023453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	323	648	0	ENST00000269305.4:c.559+2T>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.43365984820581	2	FACETS	0.973	0.925	1	0.973	0.925	1	CLONAL	2	TRUE	0	0.434338963260638	2		648	764	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26021044	26021044	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs73387434	NA	P-0023453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	143	638	1	ENST00000357647.3:c.327C>A	p.Asn109Lys	p.N109K	ENST00000357647	NM_003529.2	109	aaC/aaA	1/1	0.434338963260638	3	FACETS	0.864	0.787	0.944	0.432	0.393	0.472	CLONAL	1	TRUE	1	0.434338963260638	3		639	928	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032057	26032057	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561919033	NA	P-0023453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	147	500	1	ENST00000244661.2:c.232G>A	p.Asp78Asn	p.D78N	ENST00000244661	NM_003537.3	78	Gac/Aac	1/1	0.434338963260638	3	FACETS	0.999	0.912	1	0.499	0.456	0.545	CLONAL	1	TRUE	1	0.434338963260638	3		501	825	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288345	33288345	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	77	583	0	ENST00000374542.5:c.1063C>G	p.Pro355Ala	p.P355A	ENST00000374542	NM_001141970.1	355	Cct/Gct	4/8	0.307257801438037	3	FACETS	0.53	0.464	0.6	0.265	0.232	0.3	SUBCLONAL	1	TRUE	1	0.434338963260638	3		583	815	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651925	36651925	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	174	754	0	ENST00000244741.5:c.47A>T	p.Lys16Met	p.K16M	ENST00000244741	NM_000389.4	16	aAg/aTg	2/3	0.307257801438037	3	FACETS	0.951	0.875	1	0.476	0.437	0.516	CLONAL	1	TRUE	1	0.434338963260638	3		754	1025	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0023472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	73	517	1	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.521042575599817	1	FACETS	0.46	0.404	0.52	0.46	0.404	0.52	SUBCLONAL	1	TRUE	0	0.544920078632811	1		518	424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0023472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	436	758	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.447318110417837	2	FACETS	0.849	0.814	0.885	0.849	0.814	0.885	CLONAL	2	TRUE	0	0.544920078632811	2		759	942	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345632	70346654	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTACATATTCCTTTAAGGTCCACATAGTCTGTGGTCCTCTAAACCTTTGCTTCACTGTCCCCTTCCCTTCATTCCTCCCCCATCCCTTCCTTGACCCTCCCTTCCCTGTTTCCCTCTTCCTTCCTTCCCTCCCTCCCTCCTTCCATCTCTCCCTCCCTCCCTCCCATAGCCTTCTCTCCATACCCCACTCCCCACCCCTAGTCAACTAGTTATCTTCCCTGTCTTGACTGGTCCCTTTCAACTGTCCCCTCAGGTGGGGAGGATGGGCAGAAGCGGCGACGCAACCGGCCTGAAGCCTTCCCCACTGCTGAAGATATCTTTGCTAAGTTCCAGCACCTTTCACATTATGACCAACACCAGGTCACGGCTCAGGTGTGGGCCTAAGCCCAGCCCCTTTCCCACATTCTGGCCTCCTGTTCTGTTTTCCTTTTCTTCCCTATCTTCTCCCTGCTAGGCAGGCTAAGCCTCCTGGTCTCATCCCCTTCCAGTGTCATCCTTTCCTCCTTCCCTGGTTCTTTCCTCTCTCCACTCCCATCTCACTCCCACTGCCCTTATCAGGTCTCCCGGAATGTTCTGGAGCAGATCACGAGCTTTGCCCTTGGCATGTCATACCACTTGCCTCTGGTGCAGCATGTGCAGTTCATCTTCGACCTCATGGAATATTCACTCAGCATCAGTGGCCTCATCGACTTTGCCATTCAGGTGGGGAAGTTGGGGAGATGAGGGTGGAGGCAGGAGTTCATGCCATATAGCGGCTACGGAGGGTCATAAGGACAGGCGTAGAGGCTCCAGCCAGTTTCCCAAGCTATTTGAAGGGGCAGAAAGACTAGCATGGGGGGAGTGGAACATGAGCTAAGACTGCAGGAATAGAGACTTAAGTGCTCCCTGGGGAGGCCAAGAGGCAGATTAGAGCATTGGGCACAGACCATCCTCCCACTGTGGAGTTCATAGAACTGTATCCTGGACACTGGTTAGAGGTGTTGTTGATAGAATAAACTATCAACAATAAACTATCAATAGAG	TGTACATATTCCTTTAAGGTCCACATAGTCTGTGGTCCTCTAAACCTTTGCTTCACTGTCCCCTTCCCTTCATTCCTCCCCCATCCCTTCCTTGACCCTCCCTTCCCTGTTTCCCTCTTCCTTCCTTCCCTCCCTCCCTCCTTCCATCTCTCCCTCCCTCCCTCCCATAGCCTTCTCTCCATACCCCACTCCCCACCCCTAGTCAACTAGTTATCTTCCCTGTCTTGACTGGTCCCTTTCAACTGTCCCCTCAGGTGGGGAGGATGGGCAGAAGCGGCGACGCAACCGGCCTGAAGCCTTCCCCACTGCTGAAGATATCTTTGCTAAGTTCCAGCACCTTTCACATTATGACCAACACCAGGTCACGGCTCAGGTGTGGGCCTAAGCCCAGCCCCTTTCCCACATTCTGGCCTCCTGTTCTGTTTTCCTTTTCTTCCCTATCTTCTCCCTGCTAGGCAGGCTAAGCCTCCTGGTCTCATCCCCTTCCAGTGTCATCCTTTCCTCCTTCCCTGGTTCTTTCCTCTCTCCACTCCCATCTCACTCCCACTGCCCTTATCAGGTCTCCCGGAATGTTCTGGAGCAGATCACGAGCTTTGCCCTTGGCATGTCATACCACTTGCCTCTGGTGCAGCATGTGCAGTTCATCTTCGACCTCATGGAATATTCACTCAGCATCAGTGGCCTCATCGACTTTGCCATTCAGGTGGGGAAGTTGGGGAGATGAGGGTGGAGGCAGGAGTTCATGCCATATAGCGGCTACGGAGGGTCATAAGGACAGGCGTAGAGGCTCCAGCCAGTTTCCCAAGCTATTTGAAGGGGCAGAAAGACTAGCATGGGGGGAGTGGAACATGAGCTAAGACTGCAGGAATAGAGACTTAAGTGCTCCCTGGGGAGGCCAAGAGGCAGATTAGAGCATTGGGCACAGACCATCCTCCCACTGTGGAGTTCATAGAACTGTATCCTGGACACTGGTTAGAGGTGTTGTTGATAGAATAAACTATCAACAATAAACTATCAATAGAG	-	novel	NA	P-0023472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	98	531	0	ENST00000374080.3:c.2422+69_2686-165del		p.X808_splice	ENST00000374080		808		18-19/45	0.447318110417837	2	FACETS	0.737	0.66	0.818	0.369	0.33	0.409	SUBCLONAL	1	TRUE	0	0.544920078632811	2		531	488	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346839	70346840	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	novel	NA	P-0023472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	110	864	0	ENST00000374080.3:c.2708_2710dup	p.Val903dup	p.V903dup	ENST00000374080		903	-/GTT	20/45	0.447318110417837	2	FACETS	0.52	0.467	0.576	0.26	0.233	0.288	SUBCLONAL	1	TRUE	0	0.544920078632811	2		864	776	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0023472-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	57	478	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.888	0.769	1	0.888	0.769	1	CLONAL	1	TRUE	1	0.505525179529685	2		478	254	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877872	151877872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023472-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	97	387	1	ENST00000262189.6:c.7073C>T	p.Pro2358Leu	p.P2358L	ENST00000262189	NM_170606.2	2358	cCt/cTt	36/59	1	2	FACETS	0.948	0.851	1	0.948	0.851	1	CLONAL	1	TRUE	1	0.505525179529685	2		388	405	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058582	42058582	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749386304	NA	P-0023472-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	46	306	0	ENST00000219905.7:c.8302G>A	p.Val2768Met	p.V2768M	ENST00000219905	NM_001164273.1	2768	Gtg/Atg	24/24	1	2	FACETS	0.664	0.563	0.774	0.664	0.563	0.774	SUBCLONAL	1	TRUE	1	0.505525179529685	2		306	274	SUCCESS
AR	367	MSKCC	GRCh37	X	66765109	66765117	+	frameshift_variant	Frame_Shift_Del	DEL	CACCCAGAG	CACCCAGAG	T	novel	NA	P-0023472-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	57	422	0	ENST00000374690.3:c.121_129delinsT	p.His41CysfsTer40	p.H41Cfs*40	ENST00000374690	NM_000044.3	41	CACCCAGAG/T	1/8	1	2	FACETS	0.493	0.424	0.569	0.493	0.424	0.569	SUBCLONAL	1	TRUE	1	0.505525179529685	2		422	457	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023472-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	197	188	0				ENST00000310581	NM_198253.2	-/1132			0.487776331952988	1	FACETS	0.628	0.589	0.668	0.628	0.589	0.668	INDETERMINATE	1	TRUE	0	0.849051735856362	1		188	425	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71064719	71064719	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023472-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	395	439	0	ENST00000318789.4:c.955G>C	p.Asp319His	p.D319H	ENST00000318789	NM_032682.5	319	Gat/Cat	12/21	0.849051735856362	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.849051735856362	1		439	490	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307502	118307502	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023472-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	279	470	2	ENST00000534358.1:c.275C>A	p.Ser92Ter	p.S92*	ENST00000534358	NM_005933.3	92	tCg/tAg	1/36	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.849051735856362	2		472	652	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989121	41989121	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023472-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	319	442	0	ENST00000219905.7:c.1913C>G	p.Ser638Cys	p.S638C	ENST00000219905	NM_001164273.1	638	tCt/tGt	3/24	1	2	FACETS	0.989	0.939	1	0.989	0.939	1	CLONAL	1	TRUE	1	0.849051735856362	2		442	760	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781932	3781932	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023472-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	261	259	0	ENST00000262367.5:c.4735C>T	p.Gln1579Ter	p.Q1579*	ENST00000262367	NM_004380.2	1579	Cag/Tag	29/31	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.849051735856362	2		259	599	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033759	48033759	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs540890590	NA	P-0023472-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	142	258	0	ENST00000234420.5:c.3970G>C	p.Glu1324Gln	p.E1324Q	ENST00000234420	NM_000179.2	1324	Gag/Cag	9/10	1	2	FACETS	0.832	0.766	0.899	0.832	0.766	0.899	CLONAL	1	TRUE	1	0.849051735856362	2		258	402	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166804	32166804	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023472-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	418	544	1	ENST00000375023.3:c.4434T>G	p.His1478Gln	p.H1478Q	ENST00000375023	NM_004557.3	1478	caT/caG	24/30	0.334491787074808	1	FACETS	0.7	0.672	0.729	0.7	0.672	0.729	INDETERMINATE	1	TRUE	0	0.849051735856362	1		545	809	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001398	150001398	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023472-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	314	521	0	ENST00000253339.5:c.2206C>T	p.Leu736Phe	p.L736F	ENST00000253339		736	Ctt/Ttt	4/7	0.446721626794233	1	FACETS	0.796	0.761	0.83	0.796	0.761	0.83	INDETERMINATE	1	TRUE	0	0.849051735856362	1		521	535	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860356	151860356	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747866175	NA	P-0023472-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	356	387	0	ENST00000262189.6:c.10306A>G	p.Met3436Val	p.M3436V	ENST00000262189	NM_170606.2	3436	Atg/Gtg	43/59	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.849051735856362	2		387	779	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796799	135796799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023472-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	274	334	0	ENST00000298552.3:c.688C>T	p.His230Tyr	p.H230Y	ENST00000298552	NM_001162426.1	230	Cat/Tat	8/23	0.849051735856362	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.849051735856362	1		334	346	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797267	135797267	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023472-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	219	248	0	ENST00000298552.3:c.602C>A	p.Ser201Tyr	p.S201Y	ENST00000298552	NM_001162426.1	201	tCc/tAc	7/23	0.849051735856362	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.849051735856362	1		248	280	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798792	135798792	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023472-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	245	297	0	ENST00000298552.3:c.451C>T	p.Leu151Phe	p.L151F	ENST00000298552	NM_001162426.1	151	Ctt/Ttt	6/23	0.849051735856362	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.849051735856362	1		297	318	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942030	44942030	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0023472-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	241	285	0	ENST00000377967.4:c.3280A>T	p.Lys1094Ter	p.K1094*	ENST00000377967	NM_021140.2	1094	Aaa/Taa	22/29	0.849051735856362	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.849051735856362	1		285	314	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842368	151842368	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	28	267	1	ENST00000262189.6:c.14044G>T	p.Glu4682Ter	p.E4682*	ENST00000262189	NM_170606.2	4682	Gag/Tag	54/59	1	2	FACETS	0.429	0.346	0.522	0.429	0.346	0.522	SUBCLONAL	1	TRUE	1	0.741480558355859	2		268	176	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11301653	11301653	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746964824	NA	P-0023661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	115	717	0	ENST00000361445.4:c.1498G>A	p.Asp500Asn	p.D500N	ENST00000361445	NM_004958.3	500	Gat/Aat	10/58	0.425584950789009	4	FACETS	1	0.975	1			1	INDETERMINATE	1	TRUE	NA	0.741480558355859	4		717	444	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406354	406354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	136	575	0	ENST00000399788.2:c.4087G>A	p.Val1363Met	p.V1363M	ENST00000399788	NM_001042603.1	1363	Gtg/Atg	25/28	0.652678236296844	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.741480558355859	1		575	222	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679129	88679129	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0023661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	58	365	0	ENST00000360948.2:c.907+1G>C		p.X303_splice	ENST00000360948	NM_001012338.2	303			0.346176944121908	1	FACETS	0.684	0.603	0.767	0.684	0.603	0.767	INDETERMINATE	1	TRUE	0	0.741480558355859	1		365	144	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923294	9923294	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	94	626	0	ENST00000330684.3:c.1993C>G	p.Leu665Val	p.L665V	ENST00000330684	NM_001134407.1	665	Ctc/Gtc	9/13	NA	2	FACETS	1	0.931	1			1	INDETERMINATE	1	TRUE	NA	0.741480558355859	2		626	245	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576922	7576923	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGTG	novel	NA	P-0023661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	116	703	0	ENST00000269305.4:c.920_923dup	p.Pro309ThrfsTer29	p.P309Tfs*29	ENST00000269305	NM_001126112.2	308	ctg/ctCACTg	9/11	0.741480558355859	1	FACETS	0.875	0.808	0.942	0.875	0.808	0.942	CLONAL	1	TRUE	0	0.741480558355859	1		703	225	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132786	152132786	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	128	615	0	ENST00000262189.6:c.86C>T	p.Pro29Leu	p.P29L	ENST00000262189	NM_170606.2	29	cCc/cTc	1/59	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.741480558355859	2		615	313	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	141	530	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.115268896392302	3	FACETS	1	0.976	1	0.593	0.542	0.646	INDETERMINATE	1	TRUE	1	0.51	3		534	585	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	28	466	2	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.362	0.29	0.445	0.362	0.29	0.445	SUBCLONAL	1	TRUE	1	0.51	2		468	303	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	118	468	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.51	2		472	394	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	120	542	6	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	0.3	2	FACETS	0.953	0.865	1			1	INDETERMINATE	1	TRUE	NA	0.51	2		548	494	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	43	563	6	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	0.384	0.321	0.453	0.384	0.321	0.453	SUBCLONAL	1	TRUE	1	0.51	2		569	439	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	99	423	1	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	0.3	2	FACETS	0.945	0.849	1			1	INDETERMINATE	1	TRUE	NA	0.51	2		424	411	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	68	461	2	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.773	0.677	0.875	0.773	0.677	0.875	SUBCLONAL	1	TRUE	1	0.51	2		463	345	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120115	70120115	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	21	151	0	ENST00000245479.2:c.1121del	p.Pro374ArgfsTer9	p.P374Rfs*9	ENST00000245479	NM_000346.3	373	Ccc/cc	3/3	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.51	2		151	62	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10283798	10283798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201749864	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	102	658	0	ENST00000340748.4:c.688C>T	p.Arg230Cys	p.R230C	ENST00000340748		230	Cgc/Tgc	8/40	0.3	1	FACETS	0.696	0.627	0.769	0.696	0.627	0.769	INDETERMINATE	1	TRUE	0	0.51	1		658	428	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	76	396	3	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.937	0.829	1	0.937	0.829	1	CLONAL	1	TRUE	1	0.51	2		399	318	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	87	466	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.51	2		466	336	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932352	36932352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776535279	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	88	662	1	ENST00000361632.4:c.2117C>T	p.Pro706Leu	p.P706L	ENST00000361632		706	cCg/cTg	16/16	1	2	FACETS	0.918	0.819	1	0.918	0.819	1	CLONAL	1	TRUE	1	0.51	2		663	376	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65312353	65312353	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375353661	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	103	493	0	ENST00000342505.4:c.1966G>A	p.Val656Ile	p.V656I	ENST00000342505	NM_002227.2	656	Gtc/Atc	14/25	1	2	FACETS	0.983	0.886	1	0.983	0.886	1	CLONAL	1	TRUE	1	0.51	2		493	411	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458579	120458579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147522485	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	82	540	0	ENST00000256646.2:c.6766C>T	p.Arg2256Cys	p.R2256C	ENST00000256646	NM_024408.3	2256	Cgc/Tgc	34/34	1	2	FACETS	0.972	0.864	1	0.972	0.864	1	CLONAL	1	TRUE	1	0.51	2		540	331	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464961	120464961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764895571	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	118	454	0	ENST00000256646.2:c.5111G>A	p.Arg1704His	p.R1704H	ENST00000256646	NM_024408.3	1704	cGt/cAt	28/34	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.51	2		454	411	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740170	162740170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1193186486	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	44	518	1	ENST00000367921.3:c.1372C>T	p.Arg458Cys	p.R458C	ENST00000367921	NM_006182.2	458	Cgc/Tgc	12/18	1	2	FACETS	0.39	0.327	0.459	0.39	0.327	0.459	SUBCLONAL	1	TRUE	1	0.51	2		519	443	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609084	43609086	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs377767399	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	31	592	1	ENST00000355710.3:c.1846_1848del	p.Glu616del	p.E616del	ENST00000355710	NM_020975.4	614	GAG/-	10/20	0.115268896392302	0	FACETS	0.243	0.197	0.294			1	INDETERMINATE	1	TRUE	0	0.51	0		593	245	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446395	70446395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	46	537	0	ENST00000373644.4:c.5335C>T	p.Pro1779Ser	p.P1779S	ENST00000373644	NM_030625.2	1779	Ccc/Tcc	11/12	1	2	FACETS	0.437	0.368	0.512	0.437	0.368	0.512	SUBCLONAL	1	TRUE	1	0.51	2		537	413	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88677066	88677066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	100	490	0	ENST00000372037.3:c.851G>A	p.Arg284His	p.R284H	ENST00000372037	NM_004329.2	284	cGc/cAc	9/13	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.51	2		490	392	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533907	533907	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1448375861	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	37	580	0	ENST00000451590.1:c.149C>T	p.Thr50Met	p.T50M	ENST00000451590	NM_001130442.1	50	aCg/aTg	3/5	1	2	FACETS	0.451	0.372	0.537	0.451	0.372	0.537	SUBCLONAL	1	TRUE	1	0.51	2		580	322	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136214	64136214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371615792	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	68	586	0	ENST00000334205.4:c.1373G>A	p.Arg458His	p.R458H	ENST00000334205	NM_003942.2	458	cGc/cAc	12/17	1	2	FACETS	0.895	0.786	1	0.895	0.786	1	CLONAL	1	TRUE	1	0.51	2		586	298	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945658	71945658	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs148568665	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	64	443	0	ENST00000298229.2:c.2414C>T	p.Thr805Met	p.T805M	ENST00000298229	NM_001567.3	805	aCg/aTg	21/28	1	2	FACETS	0.834	0.728	0.947	0.834	0.728	0.947	CLONAL	1	TRUE	1	0.51	2		443	301	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372453	118372453	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	82	665	0	ENST00000534358.1:c.6386C>A	p.Pro2129His	p.P2129H	ENST00000534358	NM_005933.3	2129	cCt/cAt	26/36	1	2	FACETS	0.604	0.534	0.68	0.604	0.534	0.68	SUBCLONAL	1	TRUE	1	0.51	2		665	532	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	80	488	7	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	0.8	0.709	0.897	0.8	0.709	0.897	SUBCLONAL	1	TRUE	1	0.51	2		495	392	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444534	49444534	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770488222	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	57	581	0	ENST00000301067.7:c.2837C>T	p.Ala946Val	p.A946V	ENST00000301067	NM_003482.3	946	gCg/gTg	11/54	0.192192865034744	3	FACETS	0.679	0.584	0.782	0.34	0.292	0.391	INDETERMINATE	1	TRUE	1	0.51	3		581	413	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445095	49445095	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	110	540	0	ENST00000301067.7:c.2371del	p.Gln791ArgfsTer139	p.Q791Rfs*139	ENST00000301067	NM_003482.3	791	Cag/ag	10/54	0.192192865034744	3	FACETS	0.83	0.755	0.908	0.83	0.755	0.908	INDETERMINATE	2	TRUE	1	0.51	3		540	326	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111855990	111855990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201886863	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	72	462	0	ENST00000341259.2:c.41C>T	p.Ala14Val	p.A14V	ENST00000341259	NM_005475.2	14	gCg/gTg	2/8	1	2	FACETS	0.977	0.862	1	0.977	0.862	1	CLONAL	1	TRUE	1	0.51	2		462	289	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885336	111885336	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	36	334	1	ENST00000341259.2:c.1224G>T	p.Gln408His	p.Q408H	ENST00000341259	NM_005475.2	408	caG/caT	6/8	1	2	FACETS	0.871	0.727	1	0.871	0.727	1	CLONAL	1	TRUE	1	0.51	2		335	162	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214646	133214646	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199979862	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	47	449	1	ENST00000320574.5:c.5632C>T	p.Arg1878Cys	p.R1878C	ENST00000320574	NM_006231.2	1878	Cgc/Tgc	41/49	1	2	FACETS	0.712	0.605	0.827	0.712	0.605	0.827	SUBCLONAL	1	TRUE	1	0.51	2		450	259	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562747	21562747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747638434	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	63	478	0	ENST00000382592.4:c.1172G>A	p.Arg391His	p.R391H	ENST00000382592	NM_014572.2	391	cGc/cAc	4/8	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.51	2		478	246	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907421	32907421	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359306	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	84	407	3	ENST00000380152.3:c.1813del	p.Ile605TyrfsTer9	p.I605Yfs*9	ENST00000380152		602	ggA/gg	10/27	0.115268896392302	3	FACETS	1	0.957	1	0.577	0.514	0.644	INDETERMINATE	1	TRUE	1	0.51	3		410	358	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435129	110435129	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	90	608	2	ENST00000375856.3:c.3272del	p.Pro1091ArgfsTer15	p.P1091Rfs*15	ENST00000375856	NM_003749.2	1091	cCg/cg	1/2	1	2	FACETS	0.941	0.841	1	0.941	0.841	1	CLONAL	1	TRUE	1	0.51	2		610	375	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986877	36986877	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	55	331	0	ENST00000354822.5:c.812del	p.Gly271AlafsTer24	p.G271Afs*24	ENST00000354822	NM_001079668.2	271	gGc/gc	3/3	0.192192865034744	3	FACETS	1	0.953	1	0.618	0.535	0.706	INDETERMINATE	1	TRUE	1	0.51	3		331	219	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81563048	81563048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760702366	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	66	399	1	ENST00000298171.2:c.611C>T	p.Ala204Val	p.A204V	ENST00000298171	NM_000369.2	204	gCt/gTt	7/10	1	2	FACETS	0.78	0.681	0.884	0.78	0.681	0.884	SUBCLONAL	1	TRUE	1	0.51	2		400	332	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609856	81609856	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1396470006	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	60	378	0	ENST00000298171.2:c.1454C>A	p.Ala485Asp	p.A485D	ENST00000298171	NM_000369.2	485	gCc/gAc	10/10	1	2	FACETS	0.895	0.779	1	0.895	0.779	1	CLONAL	1	TRUE	1	0.51	2		378	263	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40683721	40683721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757403176	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	27	577	0	ENST00000249776.8:c.713G>A	p.Arg238Gln	p.R238Q	ENST00000249776	NM_033286.3	238	cGa/cAa	7/9	1	2	FACETS	0.213	0.169	0.264	0.213	0.169	0.264	SUBCLONAL	1	TRUE	1	0.51	2		577	497	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473723	67473723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223740	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	102	544	0	ENST00000327367.4:c.803G>A	p.Arg268His	p.R268H	ENST00000327367	NM_005902.3	268	cGc/cAc	6/9	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.51	2		544	338	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292960	91292960	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	115	627	1	ENST00000355112.3:c.462G>A	p.Trp154Ter	p.W154*	ENST00000355112	NM_000057.2	154	tgG/tgA	3/22	0.3	2	FACETS	0.909	0.823	0.999			1	INDETERMINATE	1	TRUE	NA	0.51	2		628	496	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348158	348158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374481133	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	42	606	0	ENST00000262320.3:c.1348C>T	p.Arg450Cys	p.R450C	ENST00000262320	NM_003502.3	450	Cgc/Tgc	6/11	1	2	FACETS	0.599	0.503	0.704	0.599	0.503	0.704	SUBCLONAL	1	TRUE	1	0.51	2		606	275	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778887	3778887	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	60	522	1	ENST00000262367.5:c.6161C>A	p.Pro2054His	p.P2054H	ENST00000262367	NM_004380.2	2054	cCc/cAc	31/31	1	2	FACETS	0.941	0.82	1	0.941	0.82	1	CLONAL	1	TRUE	1	0.51	2		523	250	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857379	9857380	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	62	447	0	ENST00000330684.3:c.4021dup	p.Ser1341LysfsTer25	p.S1341Kfs*25	ENST00000330684	NM_001134407.1	1341	agc/aAgc	13/13	1	2	FACETS	0.907	0.792	1	0.907	0.792	1	CLONAL	1	TRUE	1	0.51	2		447	268	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821959	72821960	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs762108866	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	24	280	0	ENST00000268489.5:c.10215dup	p.Gly3406ArgfsTer25	p.G3406Rfs*25	ENST00000268489	NM_006885.3	3405	-/C	10/10	1	2	FACETS	0.495	0.391	0.614	0.495	0.391	0.614	SUBCLONAL	1	TRUE	1	0.51	2		280	190	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831677	72831677	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	42	506	0	ENST00000268489.5:c.4904G>A	p.Ser1635Asn	p.S1635N	ENST00000268489	NM_006885.3	1635	aGc/aAc	9/10	1	2	FACETS	0.487	0.408	0.575	0.487	0.408	0.575	SUBCLONAL	1	TRUE	1	0.51	2		506	338	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346960	89346960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370272709	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	43	281	1	ENST00000301030.4:c.5990C>T	p.Ala1997Val	p.A1997V	ENST00000301030	NM_001256183.1	1997	gCg/gTg	9/13	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.51	2		282	152	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983298	15983298	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	106	493	0	ENST00000268712.3:c.3481C>A	p.Leu1161Ile	p.L1161I	ENST00000268712	NM_006311.3	1161	Cta/Ata	26/46	1	2	FACETS	0.956	0.862	1	0.956	0.862	1	CLONAL	1	TRUE	1	0.51	2		493	435	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131363	17131363	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	78	651	0	ENST00000285071.4:c.89C>A	p.Pro30His	p.P30H	ENST00000285071	NM_144997.5	30	cCt/cAt	4/14	1	2	FACETS	0.98	0.87	1	0.98	0.87	1	CLONAL	1	TRUE	1	0.51	2		651	312	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37871716	37871716	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	123	645	1	ENST00000269571.5:c.1240G>A	p.Ala414Thr	p.A414T	ENST00000269571		414	Gca/Aca	11/27	1	2	FACETS	0.997	0.907	1	0.997	0.907	1	CLONAL	1	TRUE	1	0.51	2		646	484	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879656	37879658	+	missense_variant	Missense_Mutation	TNP	ACG	ACG	GCA	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	77	588	1	ENST00000269571.5:c.2031_2033delinsGCA	p.Arg678Gln	p.R678Q	ENST00000269571		677	cgACGg/cgGCAg	17/27	1	2	FACETS	0.944	0.836	1	0.944	0.836	1	CLONAL	1	TRUE	1	0.51	2		589	320	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245486	41245486	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	53	831	0	ENST00000357654.3:c.2062A>G	p.Thr688Ala	p.T688A	ENST00000357654	NM_007294.3	688	Aca/Gca	10/23	1	2	FACETS	0.306	0.26	0.356	0.306	0.26	0.356	SUBCLONAL	1	TRUE	1	0.51	2		831	680	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55478789	55478789	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	104	496	0	ENST00000284073.2:c.362C>A	p.Thr121Lys	p.T121K	ENST00000284073	NM_138962.2	121	aCa/aAa	6/14	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.51	2		496	367	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435311	56435311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759694077	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	84	554	0	ENST00000407977.2:c.1826G>A	p.Arg609Gln	p.R609Q	ENST00000407977		609	cGg/cAg	9/10	1	2	FACETS	0.895	0.796	0.999	0.895	0.796	0.999	CLONAL	1	TRUE	1	0.51	2		554	368	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732334	74732334	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1468393685	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	56	347	0	ENST00000359995.5:c.575C>T	p.Pro192Leu	p.P192L	ENST00000359995	NM_001195427.1	192	cCt/cTt	2/3	1	2	FACETS	0.823	0.711	0.942	0.823	0.711	0.942	CLONAL	1	TRUE	1	0.51	2		347	267	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919556	78919556	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368881284	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	52	457	0	ENST00000306801.3:c.3115G>A	p.Ala1039Thr	p.A1039T	ENST00000306801	NM_020761.2	1039	Gcc/Acc	26/34	1	2	FACETS	0.85	0.731	0.977	0.85	0.731	0.977	CLONAL	1	TRUE	1	0.51	2		457	240	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222433	2222433	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs930481759	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	69	502	0	ENST00000398665.3:c.3265C>T	p.Arg1089Trp	p.R1089W	ENST00000398665	NM_032482.2	1089	Cgg/Tgg	24/28	1	2	FACETS	0.988	0.869	1	0.988	0.869	1	CLONAL	1	TRUE	1	0.51	2		502	274	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11022948	11022948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	89	596	1	ENST00000327064.4:c.647G>A	p.Ser216Asn	p.S216N	ENST00000327064	NM_199141.1	216	aGc/aAc	5/16	0.3	2	FACETS	0.997	0.892	1			1	INDETERMINATE	1	TRUE	NA	0.51	2		597	350	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141498	11141498	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	94	550	1	ENST00000358026.2:c.3480del	p.Leu1161SerfsTer3	p.L1161Sfs*3	ENST00000358026	NM_001128849.1	1159	Ggg/gg	25/36	0.3	2	FACETS	1	0.949	1			1	INDETERMINATE	1	TRUE	NA	0.51	2		551	338	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272165	15272165	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	47	514	0	ENST00000263388.2:c.6274del	p.Leu2092TrpfsTer57	p.L2092Wfs*57	ENST00000263388	NM_000435.2	2092	Ctg/tg	33/33	0.115268896392302	0	FACETS	0.466	0.398	0.538			1	INDETERMINATE	1	TRUE	0	0.51	0		514	194	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288858	15288858	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1200376884	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	27	232	2	ENST00000263388.2:c.3881G>A	p.Arg1294Gln	p.R1294Q	ENST00000263388	NM_000435.2	1294	cGg/cAg	24/33	0.115268896392302	0	FACETS	0.529	0.431	0.636			1	INDETERMINATE	1	TRUE	0	0.51	0		234	98	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297981	15297981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763115768	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	78	617	2	ENST00000263388.2:c.1775G>A	p.Arg592His	p.R592H	ENST00000263388	NM_000435.2	592	cGc/cAc	11/33	0.115268896392302	0	FACETS	0.493	0.437	0.552			1	INDETERMINATE	1	TRUE	0	0.51	0		619	304	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308383	15308383	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	56	545	0	ENST00000263388.2:c.125del	p.Pro42LeufsTer194	p.P42Lfs*194	ENST00000263388	NM_000435.2	42	cCt/ct	2/33	0.115268896392302	0	FACETS	0.434	0.375	0.496			1	INDETERMINATE	1	TRUE	0	0.51	0		545	248	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968240	18968240	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866753538	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	61	541	1	ENST00000262803.5:c.2080C>T	p.Arg694Trp	p.R694W	ENST00000262803	NM_002911.3	694	Cgg/Tgg	15/24	0.115268896392302	0	FACETS	0.429	0.374	0.489			1	INDETERMINATE	1	TRUE	0	0.51	0		542	273	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223857	36223858	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs754806477	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	50	618	1	ENST00000222270.7:c.6413dup	p.Ala2139GlyfsTer6	p.A2139Gfs*6	ENST00000222270	NM_014727.1	2136	ctc/ctCc	28/37	0.115268896392302	0	FACETS	0.327	0.279	0.379			1	INDETERMINATE	1	TRUE	0	0.51	0		619	294	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223965	36223965	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1351153058	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	83	547	0	ENST00000222270.7:c.6515T>C	p.Val2172Ala	p.V2172A	ENST00000222270	NM_014727.1	2172	gTc/gCc	28/37	0.115268896392302	0	FACETS	0.476	0.424	0.531			1	INDETERMINATE	1	TRUE	0	0.51	0		547	335	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383351	42383351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144367487	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	53	491	0	ENST00000221972.3:c.371G>A	p.Arg124His	p.R124H	ENST00000221972	NM_021601.3	124	cGc/cAc	2/5	1	2	FACETS	0.815	0.702	0.937	0.815	0.702	0.937	CLONAL	1	TRUE	1	0.51	2		491	255	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919079	50919079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064795958	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	41	496	0	ENST00000440232.2:c.2816C>T	p.Ser939Leu	p.S939L	ENST00000440232	NM_002691.3	939	tCg/tTg	22/27	0.3	0	FACETS	0.426	0.359	0.498			1	INDETERMINATE	1	TRUE	0	0.51	0		496	185	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716301	52716301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	82	483	1	ENST00000322088.6:c.745C>T	p.Arg249Cys	p.R249C	ENST00000322088	NM_014225.5	249	Cgc/Tgc	6/15	0.3	0	FACETS	0.62	0.555	0.688			1	INDETERMINATE	1	TRUE	0	0.51	0		484	254	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703538	47703538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63749932	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	106	546	0	ENST00000233146.2:c.2038C>T	p.Arg680Ter	p.R680*	ENST00000233146	NM_000251.2	680	Cga/Tga	13/16	1	2	FACETS	0.994	0.898	1	0.994	0.898	1	CLONAL	1	TRUE	1	0.51	2		546	418	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018197	48018197	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	137	616	0	ENST00000234420.5:c.392T>C	p.Val131Ala	p.V131A	ENST00000234420	NM_000179.2	131	gTa/gCa	2/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.51	2		616	506	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721106	61721106	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	136	587	0	ENST00000401558.2:c.1168G>A	p.Ala390Thr	p.A390T	ENST00000401558	NM_003400.3	390	Gcc/Acc	12/25	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.51	2		587	513	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182508	99182508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	92	531	1	ENST00000074304.5:c.2311C>T	p.Arg771Trp	p.R771W	ENST00000074304	NM_001134224.1	771	Cgg/Tgg	22/26	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.51	2		532	353	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189310	99189310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	65	475	0	ENST00000074304.5:c.2566C>T	p.Pro856Ser	p.P856S	ENST00000074304	NM_001134224.1	856	Cca/Tca	24/26	1	2	FACETS	0.937	0.821	1	0.937	0.821	1	CLONAL	1	TRUE	1	0.51	2		475	272	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128036803	128036804	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	122	600	0	ENST00000285398.2:c.1675_1676del	p.Ile559CysfsTer4	p.I559Cfs*4	ENST00000285398	NM_000122.1	559	ATt/t	10/15	1	2	FACETS	0.972	0.884	1	0.972	0.884	1	CLONAL	1	TRUE	1	0.51	2		600	492	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225365164	225365164	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	97	401	1	ENST00000264414.4:c.1526C>T	p.Thr509Met	p.T509M	ENST00000264414	NM_003590.4	509	aCg/aTg	11/16	1	2	FACETS	0.866	0.777	0.961	0.866	0.777	0.961	CLONAL	1	TRUE	1	0.51	2		402	439	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958129	54958129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	84	447	0	ENST00000312783.6:c.478G>A	p.Ala160Thr	p.A160T	ENST00000312783	NM_198436.1	160	Gct/Act	6/10	0.115268896392302	0	FACETS	0.42	0.373	0.47			1	INDETERMINATE	1	TRUE	0	0.51	0		447	384	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42842584	42842584	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147233451	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	80	575	0	ENST00000398585.3:c.1273G>A	p.Glu425Lys	p.E425K	ENST00000398585	NM_001135099.1	425	Gag/Aag	11/14	1	2	FACETS	0.907	0.804	1	0.907	0.804	1	CLONAL	1	TRUE	1	0.51	2		575	346	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12393134	12393134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs943725719	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	120	576	2	ENST00000287820.6:c.43G>A	p.Asp15Asn	p.D15N	ENST00000287820	NM_015869.4	15	Gat/Aat	1/7	1	2	FACETS	0.945	0.858	1	0.945	0.858	1	CLONAL	1	TRUE	1	0.51	2		578	498	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163425	47163425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757476376	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	66	341	0	ENST00000409792.3:c.2701G>A	p.Gly901Arg	p.G901R	ENST00000409792	NM_014159.6	901	Gga/Aga	3/21	1	2	FACETS	0.911	0.799	1	0.911	0.799	1	CLONAL	1	TRUE	1	0.51	2		341	284	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668781	52668781	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	90	476	0	ENST00000394830.3:c.1138A>G	p.Met380Val	p.M380V	ENST00000394830	NM_018313.4	380	Atg/Gtg	12/30	1	2	FACETS	0.926	0.828	1	0.926	0.828	1	CLONAL	1	TRUE	1	0.51	2		476	381	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890221	72890221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752101890	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	120	471	0	ENST00000325599.8:c.461G>A	p.Arg154Gln	p.R154Q	ENST00000325599	NM_018130.2	154	cGa/cAa	4/11	1	2	FACETS	0.917	0.832	1	0.917	0.832	1	CLONAL	1	TRUE	1	0.51	2		471	513	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916929	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	129	485	0	ENST00000263967.3:c.316G>T	p.Gly106Cys	p.G106C	ENST00000263967	NM_006218.2	106	Ggc/Tgc	2/21	0.115268896392302	3	FACETS	1	0.976	1	0.602	0.549	0.658	INDETERMINATE	1	TRUE	1	0.51	3		485	527	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902658	1902658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761663126	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	100	611	2	ENST00000382891.5:c.277G>A	p.Ala93Thr	p.A93T	ENST00000382891	NM_133335.3	93	Gca/Aca	2/22	1	2	FACETS	0.929	0.836	1	0.929	0.836	1	CLONAL	1	TRUE	1	0.51	2		613	422	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1953916	1953916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763969166	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	40	599	2	ENST00000382891.5:c.2095C>T	p.Arg699Trp	p.R699W	ENST00000382891	NM_133335.3	699	Cgg/Tgg	11/22	1	2	FACETS	0.49	0.409	0.58	0.49	0.409	0.58	SUBCLONAL	1	TRUE	1	0.51	2		601	320	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979551	55979551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375035755	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	118	513	0	ENST00000263923.4:c.896G>A	p.Arg299Gln	p.R299Q	ENST00000263923	NM_002253.2	299	cGg/cAg	7/30	1	2	FACETS	0.978	0.888	1	0.978	0.888	1	CLONAL	1	TRUE	1	0.51	2		513	473	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286254	66286255	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	77	458	0	ENST00000273854.3:c.1431dup	p.Gly478ArgfsTer26	p.G478Rfs*26	ENST00000273854	NM_004439.5	477	-/A	6/18	1	2	FACETS	0.814	0.719	0.914	0.814	0.719	0.914	CLONAL	1	TRUE	1	0.51	2		458	371	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143033804	143033804	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	65	456	0	ENST00000262992.4:c.2167G>T	p.Ala723Ser	p.A723S	ENST00000262992	NM_001101669.1	723	Gcc/Tcc	20/24	0.3	2	FACETS	0.614	0.534	0.7			1	INDETERMINATE	1	TRUE	NA	0.51	2		456	415	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249360	153249361	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	46	423	0	ENST00000281708.4:c.1417dup	p.Arg473LysfsTer4	p.R473Kfs*4	ENST00000281708	NM_033632.3	473	aga/aAga	9/12	0.3	2	FACETS	0.505	0.427	0.591			1	INDETERMINATE	1	TRUE	NA	0.51	2		423	357	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254543	1254543	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	60	598	0	ENST00000310581.5:c.3235C>A	p.Leu1079Met	p.L1079M	ENST00000310581	NM_198253.2	1079	Ctg/Atg	15/16	1	2	FACETS	0.968	0.844	1	0.968	0.844	1	CLONAL	1	TRUE	1	0.51	2		598	243	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526271	31526271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs545917535	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	115	750	2	ENST00000344624.3:c.769G>A	p.Asp257Asn	p.D257N	ENST00000344624		257	Gac/Aac	2/33	1	2	FACETS	0.909	0.823	0.999	0.909	0.823	0.999	CLONAL	1	TRUE	1	0.51	2		752	496	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944624	38944624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1377027840	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	89	481	0	ENST00000357387.3:c.4837C>T	p.Arg1613Cys	p.R1613C	ENST00000357387	NM_152756.3	1613	Cgc/Tgc	36/38	0.115268896392302	3	FACETS	1	0.941	1	0.542	0.483	0.604	INDETERMINATE	1	TRUE	1	0.51	3		481	404	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628386	86628386	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	35	421	0	ENST00000274376.6:c.755T>C	p.Leu252Pro	p.L252P	ENST00000274376	NM_002890.2	252	cTa/cCa	3/25	0.115268896392302	3	FACETS	0.398	0.326	0.479	0.199	0.163	0.24	INDETERMINATE	1	TRUE	1	0.51	3		421	433	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675571	86675571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1561325048	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	28	333	0	ENST00000274376.6:c.2513del	p.Asn838MetfsTer4	p.N838Mfs*4	ENST00000274376	NM_002890.2	836	gAa/ga	19/25	0.115268896392302	3	FACETS	0.389	0.311	0.478	0.195	0.155	0.239	INDETERMINATE	1	TRUE	1	0.51	3		333	354	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524297	176524297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371591154	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	35	545	0	ENST00000292408.4:c.2158G>A	p.Gly720Arg	p.G720R	ENST00000292408	NM_213647.1	720	Ggg/Agg	17/18	1	2	FACETS	0.432	0.355	0.518	0.432	0.355	0.518	SUBCLONAL	1	TRUE	1	0.51	2		545	318	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32182003	32182003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780829867	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	87	601	0	ENST00000375023.3:c.2051C>T	p.Thr684Met	p.T684M	ENST00000375023	NM_004557.3	684	aCg/aTg	13/30	1	2	FACETS	0.917	0.818	1	0.917	0.818	1	CLONAL	1	TRUE	1	0.51	2		601	372	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420093	152420093	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1199517689	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	35	338	0	ENST00000206249.3:c.1780A>G	p.Thr594Ala	p.T594A	ENST00000206249	NM_000125.3	594	Acg/Gcg	8/8	1	2	FACETS	0.663	0.548	0.79	0.663	0.548	0.79	SUBCLONAL	1	TRUE	1	0.51	2		338	207	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739731	41739731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	115	669	1	ENST00000242208.4:c.242C>T	p.Ala81Val	p.A81V	ENST00000242208	NM_002192.2	81	gCg/gTg	2/3	1	2	FACETS	0.978	0.887	1	0.978	0.887	1	CLONAL	1	TRUE	1	0.51	2		670	461	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220310	55220310	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	111	601	0	ENST00000275493.2:c.700A>G	p.Asn234Asp	p.N234D	ENST00000275493	NM_005228.3	234	Aac/Gac	6/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.51	2		601	368	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884858	151884858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	85	503	0	ENST00000262189.6:c.4735C>T	p.Pro1579Ser	p.P1579S	ENST00000262189	NM_170606.2	1579	Cct/Tct	32/59	1	2	FACETS	0.797	0.709	0.891	0.797	0.709	0.891	SUBCLONAL	1	TRUE	1	0.51	2		503	418	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194635	29194635	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147027609	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	111	626	0	ENST00000240100.2:c.1093G>A	p.Val365Ile	p.V365I	ENST00000240100	NM_001394.6	365	Gtc/Atc	4/4	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.51	2		626	435	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38148122	38148122	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	132	614	0	ENST00000317025.8:c.2989del	p.Asp997ThrfsTer55	p.D997Tfs*55	ENST00000317025	NM_023034.1	997	Gac/ac	17/24	1	2	FACETS	0.919	0.838	1	0.919	0.838	1	CLONAL	1	TRUE	1	0.51	2		614	563	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992720	68992721	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs764112302	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	114	684	10	ENST00000288368.4:c.1693dup	p.Ser565PhefsTer3	p.S565Ffs*3	ENST00000288368	NM_024870.2	562	cgt/cgTt	16/40	1	2	FACETS	0.924	0.836	1	0.924	0.836	1	CLONAL	1	TRUE	1	0.51	2		694	484	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738660	145738660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs897118164	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	70	552	0	ENST00000428558.2:c.2404G>A	p.Val802Met	p.V802M	ENST00000428558	NM_004260.3	802	Gtg/Atg	15/22	1	2	FACETS	0.973	0.858	1	0.973	0.858	1	CLONAL	1	TRUE	1	0.51	2		552	282	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202926	27202926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772637203	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	83	539	0	ENST00000380036.4:c.2018G>A	p.Arg673His	p.R673H	ENST00000380036	NM_000459.3	673	cGt/cAt	13/23	1	2	FACETS	0.81	0.719	0.906	0.81	0.719	0.906	CLONAL	1	TRUE	1	0.51	2		539	402	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249371	110249371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1564293888	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	76	715	1	ENST00000374672.4:c.1202C>T	p.Ala401Val	p.A401V	ENST00000374672	NM_004235.4	401	gCg/gTg	4/5	0.3	2	FACETS	0.517	0.453	0.584			1	INDETERMINATE	1	TRUE	NA	0.51	2		716	577	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779205	135779205	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	74	395	0	ENST00000298552.3:c.2042-1G>A		p.X681_splice	ENST00000298552	NM_001162426.1	681			0.115268896392302	0	FACETS	0.583	0.517	0.651			1	INDETERMINATE	1	TRUE	0	0.51	0		395	244	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300040	137300040	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	47	604	0	ENST00000481739.1:c.331del	p.Leu111TrpfsTer57	p.L111Wfs*57	ENST00000481739	NM_002957.4	109	Ccc/cc	3/10	0.115268896392302	0	FACETS	0.35	0.297	0.407			1	INDETERMINATE	1	TRUE	0	0.51	0		604	258	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030467	47030469	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs781998738	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	65	337	6	ENST00000377604.3:c.254_256del	p.Arg85del	p.R85del	ENST00000377604	NM_001204468.1	81	aGGCgg/agg	4/24	1	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.51	1		343	155	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347793	70347793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	44	244	0	ENST00000374080.3:c.3032C>T	p.Ser1011Leu	p.S1011L	ENST00000374080		1011	tCg/tTg	22/45	1	1	FACETS	0.691	0.587	0.802	0.691	0.587	0.802	SUBCLONAL	1	TRUE	0	0.51	1		244	186	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0023743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	9	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.469	0.31	0.671	0.469	0.31	0.671	SUBCLONAL	1	TRUE	1	0.2	2		436	192	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs863224451	NA	P-0023743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	27	732	0	ENST00000269305.4:c.824G>C	p.Cys275Ser	p.C275S	ENST00000269305	NM_001126112.2	275	tGt/tCt	8/11	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.2	2		732	250	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591878	48591883	+	inframe_deletion	In_Frame_Del	DEL	TGTTAC	TGTTAC	-	novel	NA	P-0023743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	17	618	1	ENST00000342988.3:c.1045_1050del	p.Thr349_Val350del	p.T349_V350del	ENST00000342988	NM_005359.5	347	atTGTTACt/att	9/12	1	2	FACETS	1	0.75	1	1	0.75	1	CLONAL	1	TRUE	1	0.2	2		619	170	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0024110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	74	302	0				ENST00000310581	NM_198253.2	-/1132			0.256050676611594	2	FACETS	1	0.921	1	1	0.98	1	CLONAL	3	TRUE	0	0.256050676611594	2		302	186	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0024110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	148	303	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.250888164516131	4	FACETS	0.872	0.801	0.946	0.872	0.801	0.946	CLONAL	3	TRUE	1	0.256050676611594	4		303	555	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692911	89692911	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	121	907	0	ENST00000371953.3:c.395G>C	p.Gly132Ala	p.G132A	ENST00000371953	NM_000314.4	132	gGt/gCt	5/9	0.256050676611594	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.256050676611594	2		907	429	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601986	43601986	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs749883001	NA	P-0024110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	170	1135	0	ENST00000355710.3:c.1030G>C	p.Gly344Arg	p.G344R	ENST00000355710	NM_020975.4	344	Ggc/Cgc	5/20	0.256050676611594	2	FACETS	0.915	0.843	0.989	0.915	0.843	0.989	CLONAL	2	TRUE	0	0.256050676611594	2		1135	726	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804401	46804402	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0024110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	49	662	2	ENST00000290295.7:c.605_606delinsTT	p.Ser202Phe	p.S202F	ENST00000290295	NM_006361.5	202	tCC/tTT	2/2	1	2	FACETS	0.971	0.825	1	0.971	0.825	1	CLONAL	1	TRUE	1	0.256050676611594	2		664	394	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482209	87482209	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	88	1217	0	ENST00000277120.3:c.1496A>T	p.His499Leu	p.H499L	ENST00000277120		499	cAc/cTc	14/19	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.256050676611594	2		1217	682	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149250	119149250	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200341293	NA	P-0024307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	9	463	0	ENST00000264033.4:c.1258C>T	p.Arg420Ter	p.R420*	ENST00000264033	NM_005188.3	420	Cga/Tga	9/16	1	2	FACETS	0.129	0.085	0.186	0.129	0.085	0.186	SUBCLONAL	1	TRUE	1	0.434534132242951	2		463	321	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1206927	1206927	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	34	365	0	ENST00000326873.7:c.15C>A	p.Asp5Glu	p.D5E	ENST00000326873	NM_000455.4	5	gaC/gaA	1/10	1	2	FACETS	0.549	0.45	0.659	0.549	0.45	0.659	SUBCLONAL	1	TRUE	1	0.434534132242951	2		365	285	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579361	7579361	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1064796722	NA	P-0024390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	231	699	0	ENST00000269305.4:c.326T>C	p.Phe109Ser	p.F109S	ENST00000269305	NM_001126112.2	109	tTc/tCc	4/11	0.533251111131598	2	FACETS	0.791	0.746	0.836	0.791	0.746	0.836	SUBCLONAL	2	TRUE	0	0.598558509250508	2		699	488	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212248	5212248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776677741	NA	P-0024390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	226	569	0	ENST00000357368.4:c.4783C>T	p.Arg1595Cys	p.R1595C	ENST00000357368	NM_002850.3	1595	Cgc/Tgc	32/38	0.324578344976246	3	FACETS	0.966	0.909	1	0.966	0.909	1	INDETERMINATE	2	TRUE	1	0.598558509250508	3		569	508	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259068	16259068	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1172519195	NA	P-0024390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	100	537	0	ENST00000375759.3:c.6333G>C	p.Glu2111Asp	p.E2111D	ENST00000375759	NM_015001.2	2111	gaG/gaC	11/15	0.492471175020981	3	FACETS	0.897	0.805	0.994	0.448	0.402	0.497	CLONAL	1	TRUE	1	0.598558509250508	3		537	484	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965041	15965041	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	85	515	0	ENST00000268712.3:c.5555A>C	p.Asn1852Thr	p.N1852T	ENST00000268712	NM_006311.3	1852	aAt/aCt	37/46	0.533251111131598	2	FACETS	0.671	0.597	0.751	0.336	0.298	0.376	SUBCLONAL	1	TRUE	0	0.598558509250508	2		515	423	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934283	68934283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773476490	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	527	486	0	ENST00000288368.4:c.349C>T	p.Arg117Cys	p.R117C	ENST00000288368	NM_024870.2	117	Cgt/Tgt	4/40	0.755631028909093	3	FACETS	0.934	0.9	0.968	0.934	0.9	0.968	CLONAL	2	TRUE	1	0.755631028909093	3		486	1029	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256144	16256144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138355680	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	271	499	0	ENST00000375759.3:c.3409C>T	p.Arg1137Cys	p.R1137C	ENST00000375759	NM_015001.2	1137	Cgt/Tgt	11/15	1	2	FACETS	0.901	0.849	0.954	0.901	0.849	0.954	CLONAL	1	TRUE	1	0.755631028909093	2		499	796	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256750	16256750	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760134992	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	297	542	0	ENST00000375759.3:c.4015C>T	p.Arg1339Cys	p.R1339C	ENST00000375759	NM_015001.2	1339	Cgt/Tgt	11/15	1	2	FACETS	0.968	0.915	1	0.968	0.915	1	CLONAL	1	TRUE	1	0.755631028909093	2		542	812	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804212	43804212	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs867404262	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	225	384	0	ENST00000372470.3:c.213-1G>A		p.X71_splice	ENST00000372470	NM_005373.2	71			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.755631028909093	2		384	536	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462900	120462900	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1557804111	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	234	327	0	ENST00000256646.2:c.5431C>T	p.Gln1811Ter	p.Q1811*	ENST00000256646	NM_024408.3	1811	Cag/Tag	30/34	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.755631028909093	2		327	593	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465380	120465380	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	285	549	0	ENST00000256646.2:c.4881T>G	p.Ile1627Met	p.I1627M	ENST00000256646	NM_024408.3	1627	atT/atG	27/34	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.755631028909093	2		549	714	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468219	120468219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1395144495	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	337	608	0	ENST00000256646.2:c.4220C>T	p.Ser1407Leu	p.S1407L	ENST00000256646	NM_024408.3	1407	tCg/tTg	25/34	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.755631028909093	2		608	889	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851432	156851432	+	stop_lost	Nonstop_Mutation	SNP	T	T	C	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	350	760	0	ENST00000524377.1:c.2389T>C	p.Ter797GlnextTer?	p.*797Qext*?	ENST00000524377	NM_002529.3	797	Tag/Cag	17/17	1	2	FACETS	0.907	0.861	0.954	0.907	0.861	0.954	CLONAL	1	TRUE	1	0.755631028909093	2		760	1021	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163297332	163297332	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1292835761	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	247	537	1	ENST00000271452.3:c.178C>T	p.Arg60Ter	p.R60*	ENST00000271452	NM_145697.2	60	Cga/Tga	3/14	1	2	FACETS	0.913	0.858	0.969	0.913	0.858	0.969	CLONAL	1	TRUE	1	0.755631028909093	2		538	716	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982096	201982096	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	346	647	1	ENST00000359651.3:c.620C>T	p.Ser207Phe	p.S207F	ENST00000359651		207	tCc/tTc	5/8	1	2	FACETS	0.981	0.931	1	0.981	0.931	1	CLONAL	1	TRUE	1	0.755631028909093	2		648	934	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578147	226578147	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	248	497	1	ENST00000366794.5:c.581C>T	p.Ala194Val	p.A194V	ENST00000366794	NM_001618.3	194	gCc/gTc	4/23	1	2	FACETS	0.949	0.892	1	0.949	0.892	1	CLONAL	1	TRUE	1	0.755631028909093	2		498	692	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604617	43604617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1564493414	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	328	590	2	ENST00000355710.3:c.1202G>A	p.Ser401Asn	p.S401N	ENST00000355710	NM_020975.4	401	aGc/aAc	6/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.755631028909093	2		592	847	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609939	43609939	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767406	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	432	763	1	ENST00000355710.3:c.1891G>A	p.Asp631Asn	p.D631N	ENST00000355710	NM_020975.4	631	Gac/Aac	11/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.755631028909093	2		764	1129	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333432	70333432	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	380	645	1	ENST00000373644.4:c.1337C>T	p.Pro446Leu	p.P446L	ENST00000373644	NM_030625.2	446	cCt/cTt	2/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.755631028909093	2		646	948	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426809	70426809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	201	392	0	ENST00000373644.4:c.4469G>A	p.Arg1490Lys	p.R1490K	ENST00000373644	NM_030625.2	1490	aGa/aAa	7/12	1	2	FACETS	0.906	0.845	0.968	0.906	0.845	0.968	CLONAL	1	TRUE	1	0.755631028909093	2		392	587	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625228	69625228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868995912	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	285	693	0	ENST00000334134.2:c.565G>A	p.Glu189Lys	p.E189K	ENST00000334134	NM_005247.2	189	Gag/Aag	3/3	1	2	FACETS	0.82	0.772	0.868	0.82	0.772	0.868	CLONAL	1	TRUE	1	0.755631028909093	2		693	920	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111959680	111959680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1279566824	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	279	295	0	ENST00000375549.3:c.259C>T	p.Pro87Ser	p.P87S	ENST00000375549	NM_003002.3	87	Cct/Tct	3/4	0.6345246111923	4	FACETS	0.909	0.859	0.96			1	CLONAL	2	TRUE	NA	0.755631028909093	4		295	713	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307456	118307456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555138644	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	365	330	0	ENST00000534358.1:c.229G>A	p.Gly77Arg	p.G77R	ENST00000534358	NM_005933.3	77	Gga/Aga	1/36	0.6345246111923	4	FACETS	1	0.962	1			1	CLONAL	2	TRUE	NA	0.755631028909093	4		330	840	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344458	118344458	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	190	232	0	ENST00000534358.1:c.2584C>T	p.Arg862Ter	p.R862*	ENST00000534358	NM_005933.3	862	Cga/Tga	3/36	0.6345246111923	4	FACETS	0.817	0.761	0.875			1	CLONAL	2	TRUE	NA	0.755631028909093	4		232	540	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372393	118372393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	273	433	0	ENST00000534358.1:c.6326C>T	p.Ser2109Leu	p.S2109L	ENST00000534358	NM_005933.3	2109	tCa/tTa	26/36	0.6345246111923	4	FACETS	1	0.959	1			1	CLONAL	1	TRUE	NA	0.755631028909093	4		433	1232	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149244	119149244	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs745896960	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	470	540	0	ENST00000264033.4:c.1252T>G	p.Phe418Val	p.F418V	ENST00000264033	NM_005188.3	418	Ttc/Gtc	9/16	0.6345246111923	4	FACETS	0.865	0.827	0.903			1	CLONAL	2	TRUE	NA	0.755631028909093	4		540	1263	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149290	119149290	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140627020	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	316	561	0	ENST00000264033.4:c.1298C>T	p.Pro433Leu	p.P433L	ENST00000264033	NM_005188.3	433	cCg/cTg	9/16	0.6345246111923	4	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.755631028909093	4		561	1307	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149298	119149298	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	273	536	0	ENST00000264033.4:c.1306C>T	p.Pro436Ser	p.P436S	ENST00000264033	NM_005188.3	436	Cct/Tct	9/16	0.6345246111923	4	FACETS	1	0.959	1			1	CLONAL	1	TRUE	NA	0.755631028909093	4		536	1232	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435490	18435490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760928254	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	145	240	0	ENST00000266497.5:c.475G>A	p.Glu159Lys	p.E159K	ENST00000266497		159	Gaa/Aaa	1/31	0.755631028909093	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.755631028909093	1		240	232	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716344	18716344	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778895247	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	212	426	0	ENST00000266497.5:c.3691G>A	p.Glu1231Lys	p.E1231K	ENST00000266497		1231	Gaa/Aaa	26/31	0.755631028909093	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.755631028909093	1		426	349	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21643307	21643307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	275	436	0	ENST00000421138.2:c.220C>T	p.Pro74Ser	p.P74S	ENST00000421138		74	Cca/Tca	5/16	0.755631028909093	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.755631028909093	1		436	441	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425522	49425522	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	430	754	0	ENST00000301067.7:c.12966A>T	p.Gln4322His	p.Q4322H	ENST00000301067	NM_003482.3	4322	caA/caT	39/54	NA	2	FACETS	0.956	0.913	1			1	INDETERMINATE	1	TRUE	NA	0.755631028909093	2		754	1190	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432458	49432458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771221036	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	305	661	0	ENST00000301067.7:c.8681C>T	p.Pro2894Leu	p.P2894L	ENST00000301067	NM_003482.3	2894	cCg/cTg	34/54	NA	2	FACETS	0.952	0.901	1			1	INDETERMINATE	1	TRUE	NA	0.755631028909093	2		661	848	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444974	49444974	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	280	546	1	ENST00000301067.7:c.2492C>T	p.Ser831Leu	p.S831L	ENST00000301067	NM_003482.3	831	tCa/tTa	10/54	NA	2	FACETS	0.97	0.916	1			1	INDETERMINATE	1	TRUE	NA	0.755631028909093	2		547	764	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858984	57858985	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	341	724	3	ENST00000228682.2:c.480_481delinsTT	p.Arg161Trp	p.R161W	ENST00000228682	NM_005269.2	160	gcCCgg/gcTTgg	5/12	1	2	FACETS	0.964	0.915	1	0.964	0.915	1	CLONAL	1	TRUE	1	0.755631028909093	2		727	936	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434362	121434362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1225119708	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	326	575	1	ENST00000257555.6:c.1126C>T	p.Pro376Ser	p.P376S	ENST00000257555		376	Ccc/Tcc	6/10	1	2	FACETS	0.994	0.943	1	0.994	0.943	1	CLONAL	1	TRUE	1	0.755631028909093	2		576	868	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562271	21562271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	378	719	2	ENST00000382592.4:c.1648G>A	p.Glu550Lys	p.E550K	ENST00000382592	NM_014572.2	550	Gag/Aag	4/8	1	2	FACETS	0.988	0.94	1	0.988	0.94	1	CLONAL	1	TRUE	1	0.755631028909093	2		721	1013	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911082	32911082	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060502414	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	209	361	0	ENST00000380152.3:c.2590C>T	p.Gln864Ter	p.Q864*	ENST00000380152		864	Caa/Taa	11/27	1	2	FACETS	0.991	0.928	1	0.991	0.928	1	CLONAL	1	TRUE	1	0.755631028909093	2		361	558	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913305	32913305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786201175	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	55	525	0	ENST00000380152.3:c.4813G>A	p.Val1605Ile	p.V1605I	ENST00000380152		1605	Gtt/Att	11/27	1	2	FACETS	0.189	0.161	0.22	0.189	0.161	0.22	SUBCLONAL	1	TRUE	1	0.755631028909093	2		525	769	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913531	32913531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	255	441	0	ENST00000380152.3:c.5039C>T	p.Ser1680Phe	p.S1680F	ENST00000380152		1680	tCt/tTt	11/27	1	2	FACETS	0.912	0.858	0.968	0.912	0.858	0.968	CLONAL	1	TRUE	1	0.755631028909093	2		441	740	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039413	49039413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	386	642	1	ENST00000267163.4:c.2398C>T	p.Pro800Ser	p.P800S	ENST00000267163	NM_000321.2	800	Cct/Tct	23/27	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.755631028909093	2		643	980	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479757	67479757	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	564	533	1	ENST00000327367.4:c.1064C>G	p.Ser355Trp	p.S355W	ENST00000327367	NM_005902.3	355	tCg/tGg	8/9	0.755631028909093	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.755631028909093	2		534	724	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343572	343572	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	365	684	0	ENST00000262320.3:c.2102C>T	p.Pro701Leu	p.P701L	ENST00000262320	NM_003502.3	701	cCc/cTc	8/11	1	2	FACETS	0.944	0.898	0.992	0.944	0.898	0.992	CLONAL	1	TRUE	1	0.755631028909093	2		684	1023	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778347	3778348	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	306	606	0	ENST00000262367.5:c.6700_6701delinsTT	p.Pro2234Phe	p.P2234F	ENST00000262367	NM_004380.2	2234	CCt/TTt	31/31	1	2	FACETS	0.941	0.89	0.992	0.941	0.89	0.992	CLONAL	1	TRUE	1	0.755631028909093	2		606	861	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858260	9858261	+	missense_variant	Missense_Mutation	DNP	CT	CT	TA	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	181	393	2	ENST00000330684.3:c.3140_3141delinsTA	p.Lys1047Ile	p.K1047I	ENST00000330684	NM_001134407.1	1047	aAG/aTA	13/13	1	2	FACETS	0.892	0.829	0.957	0.892	0.829	0.957	CLONAL	1	TRUE	1	0.755631028909093	2		395	537	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031999	10032000	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	253	657	1	ENST00000330684.3:c.823_824delinsAA	p.Gly275Lys	p.G275K	ENST00000330684	NM_001134407.1	275	GGa/AAa	3/13	1	2	FACETS	0.846	0.794	0.898	0.846	0.794	0.898	CLONAL	1	TRUE	1	0.755631028909093	2		658	792	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273902	10273902	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	400	749	0	ENST00000330684.3:c.367C>T	p.Pro123Ser	p.P123S	ENST00000330684	NM_001134407.1	123	Ccc/Tcc	2/13	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.755631028909093	2		749	979	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274175	10274175	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1463948759	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	210	395	0	ENST00000330684.3:c.94C>T	p.Pro32Ser	p.P32S	ENST00000330684	NM_001134407.1	32	Ccc/Tcc	2/13	1	2	FACETS	0.994	0.931	1	0.994	0.931	1	CLONAL	1	TRUE	1	0.755631028909093	2		395	559	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847288	68847288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1334047600	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	268	587	0	ENST00000261769.5:c.1210C>T	p.Pro404Ser	p.P404S	ENST00000261769	NM_004360.3	404	Ccc/Tcc	9/16	1	2	FACETS	0.895	0.842	0.948	0.895	0.842	0.948	CLONAL	1	TRUE	1	0.755631028909093	2		587	793	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216407	7216407	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	360	680	0	ENST00000380728.2:c.841C>G	p.Pro281Ala	p.P281A	ENST00000380728		281	Cca/Gca	10/11	NA	2	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.755631028909093	2		680	920	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579536	7579536	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567556930	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	408	758	0	ENST00000269305.4:c.151G>T	p.Glu51Ter	p.E51*	ENST00000269305	NM_001126112.2	51	Gaa/Taa	4/11	0.734226178429263	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.755631028909093	1		758	633	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980036	7980036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1312902509	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	327	603	1	ENST00000319144.4:c.1301C>T	p.Thr434Ile	p.T434I	ENST00000319144	NM_001139.2	434	aCc/aTc	10/15	NA	2	FACETS	0.979	0.928	1			1	INDETERMINATE	1	TRUE	NA	0.755631028909093	2		604	884	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509649	29509649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	291	509	1	ENST00000356175.3:c.854C>T	p.Ser285Phe	p.S285F	ENST00000356175	NM_000267.3	285	tCc/tTc	8/57	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.755631028909093	2		510	752	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541550	29541550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	266	455	0	ENST00000356175.3:c.1474C>T	p.Leu492Phe	p.L492F	ENST00000356175	NM_000267.3	492	Ctt/Ttt	13/57	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.755631028909093	2		455	704	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654784	29654784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769843989	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	229	337	2	ENST00000356175.3:c.5473C>T	p.Arg1825Trp	p.R1825W	ENST00000356175	NM_000267.3	1825	Cgg/Tgg	37/57	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.755631028909093	2		339	559	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627785	37627785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	370	660	0	ENST00000447079.4:c.1700C>T	p.Pro567Leu	p.P567L	ENST00000447079	NM_015083.1	567	cCt/cTt	2/14	1	2	FACETS	0.915	0.87	0.961	0.915	0.87	0.961	CLONAL	1	TRUE	1	0.755631028909093	2		660	1070	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858195	40858195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777686988	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	325	629	1	ENST00000428826.2:c.1669C>T	p.Arg557Cys	p.R557C	ENST00000428826		557	Cgt/Tgt	16/21	1	2	FACETS	0.923	0.874	0.972	0.923	0.874	0.972	CLONAL	1	TRUE	1	0.755631028909093	2		630	932	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696399	47696399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	323	574	1	ENST00000347630.2:c.424C>T	p.Leu142Phe	p.L142F	ENST00000347630	NM_001007230.1	142	Ctt/Ttt	6/11	1	2	FACETS	0.993	0.941	1	0.993	0.941	1	CLONAL	1	TRUE	1	0.755631028909093	2		575	861	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55335704	55335704	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	386	688	0	ENST00000284073.2:c.259G>A	p.Asp87Asn	p.D87N	ENST00000284073	NM_138962.2	87	Gat/Aat	4/14	1	2	FACETS	0.99	0.943	1	0.99	0.943	1	CLONAL	1	TRUE	1	0.755631028909093	2		688	1032	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59861739	59861740	+	missense_variant	Missense_Mutation	DNP	AT	AT	GG	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	287	575	1	ENST00000259008.2:c.1519_1520delinsCC	p.Ile507Pro	p.I507P	ENST00000259008	NM_032043.2	507	ATt/CCt	11/20	1	2	FACETS	0.966	0.913	1	0.966	0.913	1	CLONAL	1	TRUE	1	0.755631028909093	2		576	786	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39576618	39576618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	228	408	0	ENST00000262039.4:c.908C>T	p.Pro303Leu	p.P303L	ENST00000262039	NM_002647.2	303	cCa/cTa	9/25	1	2	FACETS	0.941	0.883	1	0.941	0.883	1	CLONAL	1	TRUE	1	0.755631028909093	2		408	641	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45391457	45391458	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	219	499	0	ENST00000262160.6:c.702_703delinsTT	p.Gln235Ter	p.Q235*	ENST00000262160	NM_005901.5	234	gaCCaa/gaTTaa	6/11	1	2	FACETS	0.857	0.802	0.915	0.857	0.802	0.915	CLONAL	1	TRUE	1	0.755631028909093	2		499	676	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223006	1223006	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202431	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	343	594	0	ENST00000326873.7:c.943C>T	p.Pro315Ser	p.P315S	ENST00000326873	NM_000455.4	315	Ccg/Tcg	8/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.755631028909093	2		594	841	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216617	2216617	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	415	769	1	ENST00000398665.3:c.2261A>T	p.His754Leu	p.H754L	ENST00000398665	NM_032482.2	754	cAc/cTc	20/28	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.755631028909093	2		770	1023	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115011	3115012	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	495	919	2	ENST00000078429.4:c.546_547delinsTT	p.Arg183Cys	p.R183C	ENST00000078429	NM_002067.2	182	gtCCgc/gtTTgc	4/7	1	2	FACETS	0.966	0.925	1	0.966	0.925	1	CLONAL	1	TRUE	1	0.755631028909093	2		921	1356	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115069	3115069	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	385	818	0	ENST00000078429.4:c.604C>T	p.Arg202Trp	p.R202W	ENST00000078429	NM_002067.2	202	Cgg/Tgg	4/7	1	2	FACETS	0.888	0.844	0.932	0.888	0.844	0.932	CLONAL	1	TRUE	1	0.755631028909093	2		818	1148	SUCCESS
CALR	811	MSKCC	GRCh37	19	13049960	13049960	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	282	497	0	ENST00000316448.5:c.104C>T	p.Ser35Phe	p.S35F	ENST00000316448	NM_004343.3	35	tCc/tTc	2/9	1	2	FACETS	0.991	0.936	1	0.991	0.936	1	CLONAL	1	TRUE	1	0.755631028909093	2		497	753	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291845	15291845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1302833098	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	399	682	1	ENST00000263388.2:c.2921G>A	p.Gly974Glu	p.G974E	ENST00000263388	NM_000435.2	974	gGg/gAg	18/33	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.755631028909093	2		683	1055	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219681	36219682	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	354	661	2	ENST00000222270.7:c.4578_4579delinsTT	p.Leu1527Phe	p.L1527F	ENST00000222270	NM_014727.1	1526	gtCCtt/gtTTtt	20/37	1	2	FACETS	0.985	0.936	1	0.985	0.936	1	CLONAL	1	TRUE	1	0.755631028909093	2		663	951	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727910	41727910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	392	648	1	ENST00000301178.4:c.535C>T	p.Pro179Ser	p.P179S	ENST00000301178	NM_021913.4	179	Ccc/Tcc	4/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.755631028909093	2		649	955	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919752	50919752	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	348	725	0	ENST00000440232.2:c.2920C>A	p.Leu974Met	p.L974M	ENST00000440232	NM_002691.3	974	Ctg/Atg	23/27	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.755631028909093	2		725	919	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143120	30143120	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1386626390	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	413	716	1	ENST00000389048.3:c.406C>T	p.Arg136Trp	p.R136W	ENST00000389048	NM_004304.4	136	Cgg/Tgg	1/29	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.755631028909093	2		717	991	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702257	47702257	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1486519909	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	273	543	1	ENST00000233146.2:c.1853C>T	p.Pro618Leu	p.P618L	ENST00000233146	NM_000251.2	618	cCa/cTa	12/16	1	2	FACETS	0.925	0.872	0.979	0.925	0.872	0.979	CLONAL	1	TRUE	1	0.755631028909093	2		544	781	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719307	190719307	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	182	336	1	ENST00000441310.2:c.1309C>T	p.Gln437Ter	p.Q437*	ENST00000441310	NM_000534.4	437	Cag/Tag	9/13	0.755631028909093	3	FACETS	1	0.947	1	0.514	0.476	0.553	CLONAL	1	TRUE	1	0.755631028909093	3		337	646	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248410	212248410	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1213182678	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	126	315	0	ENST00000342788.4:c.3857C>T	p.Ser1286Phe	p.S1286F	ENST00000342788	NM_005235.2	1286	tCt/tTt	28/28	0.755631028909093	3	FACETS	0.825	0.75	0.903	0.412	0.375	0.452	CLONAL	1	TRUE	1	0.755631028909093	3		315	557	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248684	212248684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	395	393	0	ENST00000342788.4:c.3583C>T	p.Pro1195Ser	p.P1195S	ENST00000342788	NM_005235.2	1195	Cca/Tca	28/28	0.755631028909093	3	FACETS	0.948	0.908	0.987	0.948	0.908	0.987	CLONAL	2	TRUE	1	0.755631028909093	3		393	760	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714426	40714426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	268	535	2	ENST00000373198.4:c.3971C>T	p.Ser1324Phe	p.S1324F	ENST00000373198	NM_133170.3	1324	tCc/tTc	29/32	1	2	FACETS	0.952	0.897	1	0.952	0.897	1	CLONAL	1	TRUE	1	0.755631028909093	2		537	745	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980870	40980870	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780013814	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	274	526	0	ENST00000373198.4:c.1616G>A	p.Arg539Lys	p.R539K	ENST00000373198	NM_133170.3	539	aGg/aAg	10/32	1	2	FACETS	0.998	0.941	1	0.998	0.941	1	CLONAL	1	TRUE	1	0.755631028909093	2		526	727	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321665	62321665	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750251447	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	321	617	1	ENST00000360203.5:c.2284C>T	p.Arg762Trp	p.R762W	ENST00000360203	NM_001283009.1	762	Cgg/Tgg	26/35	1	2	FACETS	0.942	0.892	0.992	0.942	0.892	0.992	CLONAL	1	TRUE	1	0.755631028909093	2		618	902	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164123	47164125	+	stop_gained	Nonsense_Mutation	TNP	GGA	GGA	AGT	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	209	369	0	ENST00000409792.3:c.2001_2003delinsACT	p.Cys667_Pro668delinsTer	p.C667_P668delins*	ENST00000409792	NM_014159.6	667	tgTCCc/tgACTc	3/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.755631028909093	2		369	528	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940619	49940619	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370955872	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	282	463	1	ENST00000296474.3:c.424C>T	p.Arg142Cys	p.R142C	ENST00000296474	NM_002447.2	142	Cgc/Tgc	1/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.755631028909093	2		464	691	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70001029	70001029	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	258	427	0	ENST00000394351.3:c.626A>C	p.His209Pro	p.H209P	ENST00000394351	NM_000248.3	209	cAc/cCc	6/9	1	2	FACETS	0.983	0.925	1	0.983	0.925	1	CLONAL	1	TRUE	1	0.755631028909093	2		427	695	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799598	72799598	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	286	503	0	ENST00000325599.8:c.1571A>T	p.Lys524Met	p.K524M	ENST00000325599	NM_018130.2	524	aAg/aTg	11/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.755631028909093	2		503	717	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498473	89498473	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	196	429	0	ENST00000336596.2:c.2445G>A	p.Trp815Ter	p.W815*	ENST00000336596	NM_005233.5	815	tgG/tgA	14/17	1	2	FACETS	0.93	0.867	0.994	0.93	0.867	0.994	CLONAL	1	TRUE	1	0.755631028909093	2		429	558	SUCCESS
ATR	545	MSKCC	GRCh37	3	142172047	142172047	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	279	569	1	ENST00000350721.4:c.7684C>T	p.Leu2562Phe	p.L2562F	ENST00000350721	NM_001184.3	2562	Ctt/Ttt	46/47	1	2	FACETS	0.999	0.944	1	0.999	0.944	1	CLONAL	1	TRUE	1	0.755631028909093	2		570	739	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189349307	189349307	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	189	332	0	ENST00000264731.3:c.3G>A	p.Met1?	p.M1?	ENST00000264731	NM_003722.4	1	atG/atA	1/14	0.755631028909093	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.755631028909093	1		332	298	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129983	55129983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763718380	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	344	640	0	ENST00000257290.5:c.517G>A	p.Asp173Asn	p.D173N	ENST00000257290	NM_006206.4	173	Gac/Aac	4/23	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.755631028909093	2		640	903	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948209	55948209	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	241	453	0	ENST00000263923.4:c.3763-1G>A		p.X1255_splice	ENST00000263923	NM_002253.2	1255			1	2	FACETS	0.876	0.822	0.932	0.876	0.822	0.932	CLONAL	1	TRUE	1	0.755631028909093	2		453	728	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956163	55956163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190064889	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	341	617	3	ENST00000263923.4:c.3152G>A	p.Arg1051Gln	p.R1051Q	ENST00000263923	NM_002253.2	1051	cGg/cAg	23/30	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.755631028909093	2		620	881	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958805	55958805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	302	544	0	ENST00000263923.4:c.3048G>A	p.Met1016Ile	p.M1016I	ENST00000263923	NM_002253.2	1016	atG/atA	22/30	1	2	FACETS	0.926	0.876	0.978	0.926	0.876	0.978	CLONAL	1	TRUE	1	0.755631028909093	2		544	863	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55960969	55960969	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	183	409	0	ENST00000263923.4:c.2971G>A	p.Ala991Thr	p.A991T	ENST00000263923	NM_002253.2	991	Gct/Act	21/30	1	2	FACETS	0.959	0.893	1	0.959	0.893	1	CLONAL	1	TRUE	1	0.755631028909093	2		409	505	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968063	55968063	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	147	348	0	ENST00000263923.4:c.2266+1G>A		p.X756_splice	ENST00000263923	NM_002253.2	756			1	2	FACETS	0.899	0.828	0.971	0.899	0.828	0.971	CLONAL	1	TRUE	1	0.755631028909093	2		348	433	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155526	106155526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749618735	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	143	390	1	ENST00000380013.4:c.427G>A	p.Asp143Asn	p.D143N	ENST00000380013	NM_001127208.2	143	Gat/Aat	3/11	1	2	FACETS	0.772	0.709	0.838	0.772	0.709	0.838	SUBCLONAL	1	TRUE	1	0.755631028909093	2		391	490	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224476	224476	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	34	45	0	ENST00000264932.6:c.152T>A	p.Ile51Asn	p.I51N	ENST00000264932	NM_004168.2	51	aTt/aAt	3/15	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.755631028909093	2		45	64	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254606	1254606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	304	479	0	ENST00000310581.5:c.3172G>A	p.Ala1058Thr	p.A1058T	ENST00000310581	NM_198253.2	1058	Gcc/Acc	15/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.755631028909093	2		479	778	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294108	1294108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	400	834	0	ENST00000310581.5:c.893C>T	p.Ser298Phe	p.S298F	ENST00000310581	NM_198253.2	298	tCc/tTc	2/16	1	2	FACETS	0.939	0.895	0.985	0.939	0.895	0.985	CLONAL	1	TRUE	1	0.755631028909093	2		834	1127	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31429584	31429584	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1354342796	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	176	495	0	ENST00000344624.3:c.3214C>T	p.Pro1072Ser	p.P1072S	ENST00000344624		1072	Ccg/Tcg	24/33	1	2	FACETS	0.8	0.741	0.861	0.8	0.741	0.861	SUBCLONAL	1	TRUE	1	0.755631028909093	2		495	582	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526688	31526688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	416	761	0	ENST00000344624.3:c.352C>T	p.Pro118Ser	p.P118S	ENST00000344624		118	Cct/Tct	2/33	1	2	FACETS	0.972	0.927	1	0.972	0.927	1	CLONAL	1	TRUE	1	0.755631028909093	2		761	1133	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874562	35874562	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	268	443	1	ENST00000303115.3:c.718C>T	p.Pro240Ser	p.P240S	ENST00000303115	NM_002185.3	240	Cct/Tct	6/8	1	2	FACETS	0.936	0.882	0.991	0.936	0.882	0.991	CLONAL	1	TRUE	1	0.755631028909093	2		444	758	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456932	149456932	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148357861	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	318	628	1	ENST00000286301.3:c.796G>A	p.Asp266Asn	p.D266N	ENST00000286301	NM_005211.3	266	Gat/Aat	6/22	1	2	FACETS	0.943	0.893	0.993	0.943	0.893	0.993	CLONAL	1	TRUE	1	0.755631028909093	2		629	893	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460515	149460515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777239066	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	396	684	0	ENST00000286301.3:c.122G>A	p.Arg41Gln	p.R41Q	ENST00000286301	NM_005211.3	41	cGa/cAa	3/22	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.755631028909093	2		684	1025	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497215	149497215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748918501	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	271	510	2	ENST00000261799.4:c.3103G>A	p.Glu1035Lys	p.E1035K	ENST00000261799	NM_002609.3	1035	Gag/Aag	22/23	1	2	FACETS	0.897	0.844	0.95	0.897	0.844	0.95	CLONAL	1	TRUE	1	0.755631028909093	2		512	800	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515352	149515352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239434481	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	299	563	0	ENST00000261799.4:c.130C>T	p.Leu44Phe	p.L44F	ENST00000261799	NM_002609.3	44	Ctc/Ttc	3/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.755631028909093	2		563	749	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041106	180041106	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	495	1089	2	ENST00000261937.6:c.3293G>A	p.Trp1098Ter	p.W1098*	ENST00000261937	NM_182925.4	1098	tGg/tAg	24/30	1	2	FACETS	0.869	0.831	0.908	0.869	0.831	0.908	CLONAL	1	TRUE	1	0.755631028909093	2		1091	1507	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052969	180052970	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	385	896	0	ENST00000261937.6:c.1320_1321delinsTT	p.Gln441Ter	p.Q441*	ENST00000261937	NM_182925.4	440	cgCCag/cgTTag	10/30	1	2	FACETS	0.937	0.892	0.983	0.937	0.892	0.983	CLONAL	1	TRUE	1	0.755631028909093	2		896	1087	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324472	31324472	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs151341208	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	799	787	0	ENST00000412585.2:c.336C>G	p.Ser112Arg	p.S112R	ENST00000412585	NM_005514.6	112	agC/agG	2/8	0.741396083951606	4	FACETS	0.98	0.949	1	0.653	0.632	0.675	CLONAL	2	TRUE	1	0.755631028909093	4		787	1894	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163318	32163318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs969543760	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	428	874	1	ENST00000375023.3:c.5908C>T	p.Pro1970Ser	p.P1970S	ENST00000375023	NM_004557.3	1970	Cct/Tct	30/30	1	2	FACETS	0.968	0.924	1	0.968	0.924	1	CLONAL	1	TRUE	1	0.755631028909093	2		875	1170	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169975	32169975	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	408	702	0	ENST00000375023.3:c.3633G>A	p.Trp1211Ter	p.W1211*	ENST00000375023	NM_004557.3	1211	tgG/tgA	21/30	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.755631028909093	2		702	1014	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188789	32188789	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	349	728	0	ENST00000375023.3:c.765A>T	p.Lys255Asn	p.K255N	ENST00000375023	NM_004557.3	255	aaA/aaT	4/30	1	2	FACETS	0.96	0.912	1	0.96	0.912	1	CLONAL	1	TRUE	1	0.755631028909093	2		728	962	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286913	33286913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	317	634	0	ENST00000374542.5:c.2024C>T	p.Ser675Phe	p.S675F	ENST00000374542	NM_001141970.1	675	tCc/tTc	7/8	1	2	FACETS	0.93	0.881	0.981	0.93	0.881	0.981	CLONAL	1	TRUE	1	0.755631028909093	2		634	902	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024155	112024155	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	342	549	0	ENST00000368678.4:c.630T>G	p.Asn210Lys	p.N210K	ENST00000368678		210	aaT/aaG	7/13	0.755631028909093	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.755631028909093	1		549	537	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631443	117631443	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	181	301	0	ENST00000368508.3:c.6235G>A	p.Asp2079Asn	p.D2079N	ENST00000368508	NM_002944.2	2079	Gat/Aat	40/43	0.755631028909093	1	FACETS	0.962	0.906	1	0.962	0.906	1	CLONAL	1	TRUE	0	0.755631028909093	1		301	310	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662655	117662655	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408672277	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	250	480	0	ENST00000368508.3:c.4810C>T	p.Pro1604Ser	p.P1604S	ENST00000368508	NM_002944.2	1604	Cct/Tct	29/43	0.755631028909093	1	FACETS	0.976	0.928	1	0.976	0.928	1	CLONAL	1	TRUE	0	0.755631028909093	1		480	422	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117730798	117730798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150941257	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	267	522	1	ENST00000368508.3:c.236C>T	p.Ser79Leu	p.S79L	ENST00000368508	NM_002944.2	79	tCg/tTg	4/43	0.755631028909093	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.755631028909093	1		523	434	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954874	2954875	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	223	553	2	ENST00000396946.4:c.2835_2836delinsAA	p.Glu946Lys	p.E946K	ENST00000396946	NM_032415.4	945	caGGaa/caAAaa	21/25	1	2	FACETS	0.84	0.785	0.895	0.84	0.785	0.895	CLONAL	1	TRUE	1	0.755631028909093	2		555	703	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450325	50450325	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	262	595	0	ENST00000331340.3:c.509A>C	p.Glu170Ala	p.E170A	ENST00000331340	NM_006060.4	170	gAg/gCg	5/8	1	2	FACETS	0.954	0.898	1	0.954	0.898	1	CLONAL	1	TRUE	1	0.755631028909093	2		595	727	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859600	151859600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	239	504	0	ENST00000262189.6:c.11062G>A	p.Asp3688Asn	p.D3688N	ENST00000262189	NM_170606.2	3688	Gat/Aat	43/59	1	2	FACETS	0.91	0.854	0.967	0.91	0.854	0.967	CLONAL	1	TRUE	1	0.755631028909093	2		504	695	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876926	151876926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	134	260	0	ENST00000262189.6:c.7435G>A	p.Gly2479Arg	p.G2479R	ENST00000262189	NM_170606.2	2479	Gga/Aga	37/59	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.755631028909093	2		260	353	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539056	23539056	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	240	467	1	ENST00000380871.4:c.383G>A	p.Arg128Gln	p.R128Q	ENST00000380871	NM_006167.3	128	cGa/cAa	2/2	1	2	FACETS	0.999	0.939	1	0.999	0.939	1	CLONAL	1	TRUE	1	0.755631028909093	2		468	636	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950461	68950461	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	576	551	1	ENST00000288368.4:c.773G>A	p.Gly258Glu	p.G258E	ENST00000288368	NM_024870.2	258	gGa/gAa	7/40	0.755631028909093	3	FACETS	0.977	0.944	1	0.977	0.944	1	CLONAL	2	TRUE	1	0.755631028909093	3		552	1075	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981516	70981516	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	927	912	0	ENST00000276594.2:c.580C>T	p.Arg194Trp	p.R194W	ENST00000276594	NM_024504.3	194	Cgg/Tgg	2/8	0.755631028909093	3	FACETS	0.995	0.969	1	0.995	0.969	1	CLONAL	2	TRUE	1	0.755631028909093	3		912	1698	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981798	70981798	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	800	775	0	ENST00000276594.2:c.298C>T	p.Pro100Ser	p.P100S	ENST00000276594	NM_024504.3	100	Ccg/Tcg	2/8	0.755631028909093	3	FACETS	0.998	0.97	1	0.998	0.97	1	CLONAL	2	TRUE	1	0.755631028909093	3		775	1461	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460413	8460413	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	135	273	0	ENST00000356435.5:c.3873A>T	p.Lys1291Asn	p.K1291N	ENST00000356435		1291	aaA/aaT	22/35	0.755631028909093	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.755631028909093	1		273	196	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517993	8517993	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	224	420	0	ENST00000356435.5:c.1398G>A	p.Trp466Ter	p.W466*	ENST00000356435		466	tgG/tgA	10/35	0.755631028909093	1	FACETS	0.963	0.914	1	0.963	0.914	1	CLONAL	1	TRUE	0	0.755631028909093	1		420	383	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231254	98231254	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	303	582	0	ENST00000331920.6:c.2029A>G	p.Thr677Ala	p.T677A	ENST00000331920	NM_000264.3	677	Acc/Gcc	14/24	1	2	FACETS	0.902	0.853	0.953	0.902	0.853	0.953	CLONAL	1	TRUE	1	0.755631028909093	2		582	889	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759662	133759662	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781395627	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	319	605	0	ENST00000318560.5:c.1985C>T	p.Pro662Leu	p.P662L	ENST00000318560	NM_005157.4	662	cCc/cTc	11/11	1	2	FACETS	0.951	0.901	1	0.951	0.901	1	CLONAL	1	TRUE	1	0.755631028909093	2		605	888	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139804400	139804400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	401	665	0	ENST00000247668.2:c.557C>T	p.Pro186Leu	p.P186L	ENST00000247668	NM_021138.3	186	cCc/cTc	6/11	0.755631028909093	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.755631028909093	1		665	625	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813059	76813059	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	312	334	1	ENST00000373344.5:c.6562C>T	p.Arg2188Ter	p.R2188*	ENST00000373344	NM_000489.3	2188	Cga/Tga	30/35	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.755631028909093	1		335	414	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938967	76938967	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782774889	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	357	310	1	ENST00000373344.5:c.1781C>T	p.Ser594Phe	p.S594F	ENST00000373344	NM_000489.3	594	tCc/tTc	9/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.755631028909093	1		311	473	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527931	103527931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs4150388	NA	P-0024395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	177	532	0	ENST00000355739.4:c.3239G>A	p.Gly1080Glu	p.G1080E	ENST00000355739	NM_000123.3	1080	gGa/gAa	15/15	0.755631028909093	1	FACETS	0.975	0.919	1	0.975	0.919	1	CLONAL	1	TRUE	0	0.755631028909093	1		532	299	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0024476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	570	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.3	4	FACETS	1	0.981	1			1	CLONAL	4	TRUE	NA	0.3	4		436	1203	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0024476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	183	524	1	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	0.3	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.3	2		525	550	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371409680	NA	P-0024476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	252	703	0	ENST00000269305.4:c.848G>C	p.Arg283Pro	p.R283P	ENST00000269305	NM_001126112.2	283	cGc/cCc	8/11	0.278839044378394	2	FACETS	0.996	0.935	1	0.996	0.935	1	CLONAL	2	TRUE	0	0.3	2		703	843	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509480	149509482	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0024476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	216	715	0	ENST00000261799.4:c.1417_1419del	p.Glu473del	p.E473del	ENST00000261799	NM_002609.3	473	GAG/-	10/23	0.3	3	FACETS	0.873	0.812	0.936	0.873	0.812	0.936	CLONAL	2	TRUE	1	0.3	3		715	948	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945595	151945595	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	147	328	0	ENST00000262189.6:c.1924C>T	p.Gln642Ter	p.Q642*	ENST00000262189	NM_170606.2	642	Caa/Taa	14/59	0.269251413344906	4	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	2	0.3	4		328	585	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32439192	32439192	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	35	634	0	ENST00000332351.3:c.881T>C	p.Leu294Ser	p.L294S	ENST00000332351	NM_024426.4	294	tTa/tCa	4/10	0.528776020809361	4	FACETS	1	0.937	1	0.647	0.539	0.764	CLONAL	1	TRUE	2	0.575954507610805	4		634	148	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469134	25469134	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1205125035	NA	P-0024518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	64	822	0	ENST00000264709.3:c.1324G>C	p.Glu442Gln	p.E442Q	ENST00000264709	NM_175629.2	442	Gaa/Caa	11/23	0.528776020809361	4	FACETS	0.593	0.513	0.679	0.296	0.256	0.34	SUBCLONAL	1	TRUE	2	0.575954507610805	4		822	591	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509432	106509432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs567756361	NA	P-0024539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	48	647	0	ENST00000359195.3:c.1426C>T	p.Arg476Cys	p.R476C	ENST00000359195	NM_002649.2	476	Cgc/Tgc	2/11	0.220629500512933	2	FACETS	0.427	0.361	0.5	0.214	0.18	0.25	INDETERMINATE	1	TRUE	0	0.426486663182058	2		647	527	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656338	18656338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	71	479	0	ENST00000266497.5:c.3017C>T	p.Ala1006Val	p.A1006V	ENST00000266497		1006	gCa/gTa	21/31	0.365842397512875	3	FACETS	0.672	0.587	0.764	0.336	0.293	0.382	SUBCLONAL	1	TRUE	1	0.426486663182058	3		479	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577023	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CCTCGC	CCTCGC	-	novel	NA	P-0024539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	271	739	0	ENST00000269305.4:c.915_919+1del		p.X305_splice	ENST00000269305	NM_001126112.2	305		8/11	0.389071407060039	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.426486663182058	2		739	580	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772345	56772345	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1567785872	NA	P-0024539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	98	524	0	ENST00000337432.4:c.199G>T	p.Glu67Ter	p.E67*	ENST00000337432	NM_058216.2	67	Gaa/Taa	2/9	0.389071407060039	2	FACETS	0.938	0.84	1	0.469	0.42	0.521	CLONAL	1	TRUE	0	0.426486663182058	2		524	490	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551409	141551409	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs912917128	NA	P-0024539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	52	629	3	ENST00000220592.5:c.1888C>T	p.Arg630Cys	p.R630C	ENST00000220592	NM_012154.3	630	Cgc/Tgc	15/19	0.344946988801794	4	FACETS	0.446	0.379	0.52	0.111	0.094	0.13	SUBCLONAL	1	TRUE	0	0.426486663182058	4		632	780	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	461	570	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.447418806765578	4	FACETS	1	0.979	1			1	CLONAL	3	TRUE	NA	0.627755002259661	4		570	780	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0024569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	261	520	2	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.628152886020871	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.627755002259661	1		522	508	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427479	49427479	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs910376967	NA	P-0024569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	261	830	2	ENST00000301067.7:c.11009G>T	p.Gly3670Val	p.G3670V	ENST00000301067	NM_003482.3	3670	gGc/gTc	39/54	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.627755002259661	2		832	724	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244590	41244590	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	178	910	0	ENST00000357654.3:c.2958C>G	p.Ile986Met	p.I986M	ENST00000357654	NM_007294.3	986	atC/atG	10/23	0.628152886020871	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.627755002259661	1		910	352	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505092	149505092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	304	877	2	ENST00000261799.4:c.1723G>A	p.Asp575Asn	p.D575N	ENST00000261799	NM_002609.3	575	Gac/Aac	12/23	0.628152886020871	3	FACETS	1	0.985	1	0.564	0.531	0.597	CLONAL	1	TRUE	1	0.627755002259661	3		879	1129	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0024651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	51	478	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.721	0.613	0.839	0.721	0.613	0.839	SUBCLONAL	1	TRUE	1	0.29	2		478	488	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0024651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	129	303	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.134965875291785	3	FACETS	0.913	0.831	0.998	0.913	0.831	0.998	INDETERMINATE	2	TRUE	1	0.29	3		303	558	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0024651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	86	500	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	0.3	1	FACETS	0.893	0.8	0.99	1	0.985	1	CLONAL	2	TRUE	0	0.29	1		500	284	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593504	48593504	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	57	504	0	ENST00000342988.3:c.1255G>T	p.Gly419Trp	p.G419W	ENST00000342988	NM_005359.5	419	Ggg/Tgg	10/12	0.226953535247621	1	FACETS	0.81	0.697	0.932	0.81	0.697	0.932	CLONAL	1	TRUE	0	0.29	1		504	415	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112329	115112329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1295791270	NA	P-0024651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	50	484	0	ENST00000257566.3:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000257566	NM_016569.3	471	Cgc/Tgc	7/8	1	2	FACETS	0.92	0.783	1	0.92	0.783	1	CLONAL	1	TRUE	1	0.29	2		484	375	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358572	67358572	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	107	869	0	ENST00000327367.4:c.80A>T	p.Glu27Val	p.E27V	ENST00000327367	NM_005902.3	27	gAg/gTg	1/9	0.134965875291785	3	FACETS	1	0.915	1	0.511	0.458	0.568	INDETERMINATE	1	TRUE	1	0.29	3		869	826	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395745	45395745	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	95	646	0	ENST00000262160.6:c.389G>C	p.Arg130Pro	p.R130P	ENST00000262160	NM_005901.5	130	cGa/cCa	4/11	0.226953535247621	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.29	1		646	528	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851843	134851843	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1305200941	NA	P-0024651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	46	1109	0	ENST00000398015.3:c.1249C>A	p.Pro417Thr	p.P417T	ENST00000398015	NM_004441.4	417	Ccc/Acc	5/16	0.3	0	FACETS	0.398	0.335	0.468			1	SUBCLONAL	1	TRUE	0	0.29	0		1109	566	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277474	142277474	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	111	548	0	ENST00000350721.4:c.1877del	p.Asp626ValfsTer15	p.D626Vfs*15	ENST00000350721	NM_001184.3	626	gAt/gt	8/47	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.29	2		548	612	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0024657-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	154	517	1	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.951	0.879	1	0.951	0.879	1	CLONAL	1	TRUE	1	0.762109232731989	2		518	425	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0024657-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	140	504	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	0.762109232731989	3	FACETS	0.607	0.553	0.664	0.303	0.276	0.332	SUBCLONAL	1	TRUE	1	0.762109232731989	3		504	836	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319836	8319836	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024657-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	215	403	0	ENST00000356435.5:c.5665A>G	p.Thr1889Ala	p.T1889A	ENST00000356435		1889	Aca/Gca	34/35	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.762109232731989	2		403	562	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455056	50455056	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	42	442	0	ENST00000331340.3:c.603C>G	p.His201Gln	p.H201Q	ENST00000331340	NM_006060.4	201	caC/caG	6/8	1	2	FACETS	0.238	0.197	0.283	0.238	0.197	0.283	SUBCLONAL	1	TRUE	1	0.43089796079929	2		442	820	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0025132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	369	804	0	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	0.240067853851002	2	FACETS	0.982	0.955	1	1	0.997	1	INDETERMINATE	3	TRUE	0	0.561825373662666	2		804	446	SUCCESS
APC	324	MSKCC	GRCh37	5	112175513	112175513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	21	417	1	ENST00000257430.4:c.4222G>T	p.Glu1408Ter	p.E1408*	ENST00000257430	NM_000038.5	1408	Gaa/Taa	16/16	0.561825373662666	1	FACETS	0.995	0.801	1	0.995	0.801	1	CLONAL	1	TRUE	0	0.561825373662666	1		418	54	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030585	47030585	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs377667483	NA	P-0025132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	25	357	1	ENST00000377604.3:c.360T>G	p.Asp120Glu	p.D120E	ENST00000377604	NM_001204468.1	120	gaT/gaG	4/24	0.444814723845479	2	FACETS	0.237	0.187	0.296			1	SUBCLONAL	1	TRUE	NA	0.561825373662666	2		358	375	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984811	11984811	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	38	494	0	ENST00000353533.5:c.358del	p.Val120SerfsTer8	p.V120Sfs*8	ENST00000353533	NM_003010.3	119	atG/at	3/11	0.240067853851002	2	FACETS	1	0.93	1	1	0.93	1	INDETERMINATE	2	TRUE	0	0.561825373662666	2		494	62	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42840369	42840369	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	45	594	1	ENST00000398585.3:c.1379C>T	p.Ala460Val	p.A460V	ENST00000398585	NM_001135099.1	460	gCc/gTc	12/14	1	2	FACETS	0.67	0.568	0.781	0.67	0.568	0.781	SUBCLONAL	1	TRUE	1	0.561825373662666	2		595	239	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931898	68931898	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	23	651	0	ENST00000288368.4:c.328C>A	p.Leu110Ile	p.L110I	ENST00000288368	NM_024870.2	110	Ctt/Att	3/40	0.561825373662666	5	FACETS	0.517	0.403	0.648	0.129	0.1	0.162	SUBCLONAL	1	TRUE	1	0.561825373662666	5		651	292	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514606	44514606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	88	369	0	ENST00000291552.4:c.550G>A	p.Glu184Lys	p.E184K	ENST00000291552	NM_006758.2	184	Gag/Aag	7/8	0.468598550273458	1	FACETS	0.535	0.475	0.598	0.535	0.475	0.598	SUBCLONAL	1	TRUE	0	0.468598550273458	1		369	538	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465904	69465904	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	64	476	0	ENST00000227507.2:c.742C>A	p.Gln248Lys	p.Q248K	ENST00000227507	NM_053056.2	248	Cag/Aag	5/5	0.457997038044381	4	FACETS	0.321	0.276	0.37	0.107	0.092	0.124	SUBCLONAL	1	TRUE	1	0.468598550273458	4		476	1250	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0025198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	286	451	0	ENST00000269305.4:c.920-1del		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.28872138338349	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.468598550273458	1		451	729	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101119	41101119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755381090	NA	P-0025198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	209	467	0	ENST00000373198.4:c.1237G>A	p.Ala413Thr	p.A413T	ENST00000373198	NM_133170.3	413	Gcg/Acg	8/32	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.468598550273458	2		467	827	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790650	89790650	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs147772027	NA	P-0025198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	111	458	4	ENST00000336032.3:c.37G>T	p.Val13Phe	p.V13F	ENST00000336032	NM_006813.2	13	Gtc/Ttc	1/2	0.468598550273458	3	FACETS	0.49	0.439	0.544			1	SUBCLONAL	1	TRUE	NA	0.468598550273458	3		462	1194	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413070	63413070	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	46	206	0	ENST00000330258.3:c.97G>A	p.Ala33Thr	p.A33T	ENST00000330258	NM_152424.3	33	Gca/Aca	2/2	1	1	FACETS	0.632	0.532	0.742	0.632	0.532	0.742	SUBCLONAL	1	TRUE	0	0.26	1		206	487	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061223	38061228	+	inframe_deletion	In_Frame_Del	DEL	TCTCGA	TCTCGA	-	novel	NA	P-0025228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	106	274	1	ENST00000250448.2:c.761_766del	p.Phe254_Asn256delinsTyr	p.F254_N256delinsY	ENST00000250448	NM_004496.3	254	tTCGAGAac/tac	2/2	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.26	2		275	741	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0025228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	22	401	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.182	0.14	0.232	0.182	0.14	0.232	SUBCLONAL	1	TRUE	1	0.26	2		401	928	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162916	38162916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1030084373	NA	P-0025228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	85	346	1	ENST00000317025.8:c.2290C>T	p.Arg764Cys	p.R764C	ENST00000317025	NM_023034.1	764	Cgt/Tgt	13/24	1	2	FACETS	0.74	0.653	0.833	0.74	0.653	0.833	SUBCLONAL	1	TRUE	1	0.26	2		347	884	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0025348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	360	570	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.939	0.89	0.989	0.939	0.89	0.989	CLONAL	1	TRUE	1	0.612462626699767	2		570	1252	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0025348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	230	478	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.317387885448069	1	FACETS	0.815	0.765	0.867	0.815	0.765	0.867	INDETERMINATE	1	TRUE	0	0.612462626699767	1		478	639	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665144	29665144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs562367786	NA	P-0025348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	402	658	1	ENST00000356175.3:c.6743G>A	p.Arg2248His	p.R2248H	ENST00000356175	NM_000267.3	2248	cGt/cAt	44/57	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.612462626699767	2		659	1040	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928067	178928067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	347	664	0	ENST00000263967.3:c.1345C>T	p.Pro449Ser	p.P449S	ENST00000263967	NM_006218.2	449	Cct/Tct	8/21	0.317387885448069	1	FACETS	0.859	0.816	0.903	0.859	0.816	0.903	INDETERMINATE	1	TRUE	0	0.612462626699767	1		664	915	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248014	59248015	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GACA	novel	NA	P-0025348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	284	580	0	ENST00000371222.2:c.725_728dup	p.Pro244ValfsTer67	p.P244Vfs*67	ENST00000371222	NM_002228.3	243	tcc/tcTGTCc	1/1	0.612462626699767	1	FACETS	0.858	0.81	0.906	0.858	0.81	0.906	CLONAL	1	TRUE	0	0.612462626699767	1		580	750	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166148	118166148	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	123	473	0	ENST00000369448.3:c.658G>A	p.Glu220Lys	p.E220K	ENST00000369448	NM_017709.3	220	Gag/Aag	2/2	0.612462626699767	1	FACETS	0.492	0.447	0.54	0.492	0.447	0.54	SUBCLONAL	1	TRUE	0	0.612462626699767	1		473	566	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988400	41988400	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	179	609	0	ENST00000219905.7:c.1192G>C	p.Glu398Gln	p.E398Q	ENST00000219905	NM_001164273.1	398	Gaa/Caa	3/24	1	2	FACETS	0.522	0.481	0.566	0.522	0.481	0.566	SUBCLONAL	1	TRUE	1	0.612462626699767	2		609	1119	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265915	41266316	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATA	TATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATA	-	novel	NA	P-0025348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	38	57	0	ENST00000349496.5:c.14-102_241+72del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.573365358449725	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	2	TRUE	0	0.612462626699767	2		57	62	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545721	106545721	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	354	685	1	ENST00000359195.3:c.3198G>T	p.Lys1066Asn	p.K1066N	ENST00000359195	NM_002649.2	1066	aaG/aaT	11/11	1	2	FACETS	0.955	0.904	1	0.955	0.904	1	CLONAL	1	TRUE	1	0.612462626699767	2		686	1211	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868953	117868953	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs770374138	NA	P-0025348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	73	574	0	ENST00000297338.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000297338	NM_006265.2	249	tCt/tGt	7/14	1	2	FACETS	0.264	0.23	0.3	0.264	0.23	0.3	SUBCLONAL	1	TRUE	1	0.612462626699767	2		574	904	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654643	67654643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs968244943	NA	P-0025604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	37	473	1	ENST00000264010.4:c.1130G>A	p.Arg377His	p.R377H	ENST00000264010	NM_006565.3	377	cGt/cAt	6/12	1	2	FACETS	0.156	0.128	0.188	0.156	0.128	0.188	SUBCLONAL	1	TRUE	1	0.540191825023823	2		474	877	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645192	67645196	+	frameshift_variant	Frame_Shift_Del	DEL	ATGAT	ATGAT	-	novel	NA	P-0025604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	133	496	0	ENST00000264010.4:c.460_464del	p.Ile154ProfsTer7	p.I154Pfs*7	ENST00000264010	NM_006565.3	153	ATGATa/a	3/12	1	2	FACETS	0.64	0.582	0.702	0.64	0.582	0.702	SUBCLONAL	1	TRUE	1	0.540191825023823	2		496	769	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0025609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	123	451	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.309632893438528	3	FACETS	1	0.908	1			1	CLONAL	1	TRUE	NA	0.346607854234101	3		451	829	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0025609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	723	688	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.336730462141366	4	FACETS	1	0.99	1			1	CLONAL	4	TRUE	NA	0.346607854234101	4		688	1343	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398043	4398043	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	349	732	2	ENST00000261254.3:c.607G>A	p.Ala203Thr	p.A203T	ENST00000261254	NM_001759.3	203	Gca/Aca	4/5	0.346607854234101	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.346607854234101	2		734	1005	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350339	89350339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201607978	NA	P-0025609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	224	923	0	ENST00000301030.4:c.2611G>A	p.Asp871Asn	p.D871N	ENST00000301030	NM_001256183.1	871	Gac/Aac	9/13	0.346607854234101	2	FACETS	0.981	0.912	1	0.491	0.456	0.527	CLONAL	1	TRUE	0	0.346607854234101	2		923	1317	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0025856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	68	570	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	0.225826703939226	2		570	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057520005	NA	P-0025856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	108	764	0	ENST00000269305.4:c.820G>C	p.Val274Leu	p.V274L	ENST00000269305	NM_001126112.2	274	Gtt/Ctt	8/11	0.225826703939226	1	FACETS	0.92	0.825	1	0.92	0.825	1	CLONAL	1	TRUE	0	0.225826703939226	1		764	922	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281257	49281291	+	frameshift_variant	Frame_Shift_Del	DEL	TCCAATTGGATATTTGGAGACCTGGCCTGCAGGAT	TCCAATTGGATATTTGGAGACCTGGCCTGCAGGAT	-	novel	NA	P-0025856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	178	695	2	ENST00000282018.3:c.305_339del	p.Ser102TyrfsTer66	p.S102Yfs*66	ENST00000282018	NM_020377.2	102	TCCAATTGGATATTTGGAGACCTGGCCTGCAGGATt/t	1/1	0.225826703939226	1	FACETS	0.86	0.794	0.929	1	0.991	1	CLONAL	2	TRUE	0	0.225826703939226	1		697	813	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010533	48010544	+	inframe_deletion	In_Frame_Del	DEL	GGCCTGGGCCCA	GGCCTGGGCCCA	-	novel	NA	P-0025856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	51	282	0	ENST00000234420.5:c.165_176del	p.Gly56_Pro59del	p.G56_P59del	ENST00000234420	NM_000179.2	54	gGGCCTGGGCCCAgg/ggg	1/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.225826703939226	2		282	329	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36028530	36028530	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1207881818	NA	P-0025856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	84	726	1	ENST00000358208.4:c.872G>A	p.Gly291Asp	p.G291D	ENST00000358208		291	gGt/gAt	8/12	1	2	FACETS	0.814	0.717	0.918	0.814	0.717	0.918	CLONAL	1	TRUE	1	0.225826703939226	2		727	914	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0025919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	35	570	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.124	0.101	0.15	0.124	0.101	0.15	SUBCLONAL	1	TRUE	1	1.02	2		570	553	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	41	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.17498725389344	1	FACETS	0.689	0.574	0.817	0.689	0.574	0.817	SUBCLONAL	1	TRUE	0	0.23	1		436	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0025921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	47	880	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.67	0.565	0.787	0.67	0.565	0.787	SUBCLONAL	1	TRUE	1	0.23	2		880	610	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981535	201981536	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0025921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	65	946	0	ENST00000359651.3:c.451dup	p.Gln151ProfsTer10	p.Q151Pfs*10	ENST00000359651		150	ttc/ttCc	3/8	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.23	2		946	490	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650325	48650325	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs184815507	NA	P-0025921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	48	418	0	ENST00000376670.3:c.295G>A	p.Gly99Ser	p.G99S	ENST00000376670	NM_002049.3	99	Ggc/Agc	3/6	1	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.23	1		418	272	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692956	89692971	+	frameshift_variant	Frame_Shift_Del	DEL	AGGCACAAGAGGCCCT	AGGCACAAGAGGCCCT	-	novel	NA	P-0025991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	20	534	2	ENST00000371953.3:c.442_457del	p.Ala148IlefsTer6	p.A148Ifs*6	ENST00000371953	NM_000314.4	147	aAGGCACAAGAGGCCCTa/aa	5/9	0.180035773797342	3	FACETS	0.783	0.599	0.999	0.392	0.299	0.5	CLONAL	1	FALSE	1	0.186066752781094	3		536	300	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344077	118344087	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAGGAAAAG	AAAAGGAAAAG	-	novel	NA	P-0025991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	26	382	0	ENST00000534358.1:c.2208_2218del	p.Arg736SerfsTer3	p.R736Sfs*3	ENST00000534358	NM_005933.3	735	AAAAGGAAAAGa/a	3/36	0.180035773797342	3	FACETS	1	0.894	1	0.606	0.482	0.748	CLONAL	1	FALSE	1	0.186066752781094	3		382	252	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190656552	190656590	+	inframe_deletion	In_Frame_Del	DEL	CGGCAACAGTTCGACTCCTTTCAAGTTCTCAGATCATCA	CGGCAACAGTTCGACTCCTTTCAAGTTCTCAGATCATCA	-	novel	NA	P-0026251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	13	139	0	ENST00000441310.2:c.18_56del	p.Ala7_Thr19del	p.A7_T19del	ENST00000441310	NM_000534.4	6	gCGGCAACAGTTCGACTCCTTTCAAGTTCTCAGATCATCAct/gct	2/13	1	2	FACETS	0.954	0.681	1	0.954	0.681	1	CLONAL	1	TRUE	1	0.12	2		139	227	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437561	49437561	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	208	358	0	ENST00000301067.7:c.5324C>G	p.Ala1775Gly	p.A1775G	ENST00000301067	NM_003482.3	1775	gCc/gGc	23/54	1	2	FACETS	0.991	0.925	1	0.991	0.925	1	CLONAL	1	TRUE	1	0.652533360767846	2		358	643	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680641	88680641	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	150	335	0	ENST00000360948.2:c.616C>G	p.Gln206Glu	p.Q206E	ENST00000360948	NM_001012338.2	206	Cag/Gag	6/19	0.652533360767846	2	FACETS	0.844	0.775	0.914	0.422	0.387	0.457	CLONAL	1	TRUE	0	0.652533360767846	2		335	545	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953653	32953653	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0026290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	76	329	0	ENST00000380152.3:c.8953+1G>C		p.X2985_splice	ENST00000380152		2985			1	2	FACETS	0.77	0.683	0.862	0.77	0.683	0.862	SUBCLONAL	1	TRUE	1	0.707233787200379	2		329	279	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016652	12016671	+	frameshift_variant	Frame_Shift_Del	DEL	ATGCTGGCTGTAGGCCATAC	ATGCTGGCTGTAGGCCATAC	-	novel	NA	P-0026290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	83	343	0	ENST00000353533.5:c.791_810del	p.Ala264GlyfsTer3	p.A264Gfs*3	ENST00000353533	NM_003010.3	263	gATGCTGGCTGTAGGCCATAC/g	7/11	NA	2	FACETS	0.866	0.774	0.962			1	INDETERMINATE	1	TRUE	NA	0.707233787200379	2		343	271	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030906	36030906	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	134	611	0	ENST00000358208.4:c.1185C>G	p.Ile395Met	p.I395M	ENST00000358208		395	atC/atG	10/12	1	2	FACETS	0.94	0.863	1	0.94	0.863	1	CLONAL	1	TRUE	1	0.707233787200379	2		611	403	SUCCESS
APC	324	MSKCC	GRCh37	5	112178567	112178567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060503353	NA	P-0026290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	105	303	0	ENST00000257430.4:c.7276G>A	p.Gly2426Arg	p.G2426R	ENST00000257430	NM_000038.5	2426	Gga/Aga	16/16	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.707233787200379	2		303	274	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411173	63411173	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	96	549	1	ENST00000330258.3:c.1994G>T	p.Gly665Val	p.G665V	ENST00000330258	NM_152424.3	665	gGc/gTc	2/2	1	2	FACETS	0.83	0.748	0.916	0.83	0.748	0.916	CLONAL	1	TRUE	1	0.707233787200379	2		550	327	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	70	455	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.384167103999559	2		455	337	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	110	468	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.88	0.792	0.973	0.88	0.792	0.973	CLONAL	1	TRUE	1	0.384167103999559	2		472	651	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	81	525	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.601	0.529	0.678	0.601	0.529	0.678	SUBCLONAL	1	TRUE	1	0.384167103999559	2		525	702	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806119	1806119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931614	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	112	898	5	ENST00000260795.2:c.1138G>A	p.Gly380Arg	p.G380R	ENST00000260795		380	Ggg/Agg	8/17	1	2	FACETS	0.668	0.6	0.74	0.668	0.6	0.74	SUBCLONAL	1	TRUE	1	0.384167103999559	2		903	873	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127164	22127164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057519911	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	70	418	0	ENST00000215832.6:c.964G>A	p.Glu322Lys	p.E322K	ENST00000215832	NM_002745.4	322	Gag/Aag	7/9	1	2	FACETS	0.882	0.773	1	0.882	0.773	1	CLONAL	1	TRUE	1	0.384167103999559	2		418	413	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	48	936	0	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	1	2	FACETS	0.27	0.227	0.317	0.27	0.227	0.317	SUBCLONAL	1	TRUE	1	0.384167103999559	2		936	927	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074255	8074255	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	88	486	0	ENST00000377482.5:c.404del	p.Asn135ThrfsTer40	p.N135Tfs*40	ENST00000377482	NM_018948.3	135	aAc/ac	4/4	1	2	FACETS	0.798	0.708	0.894	0.798	0.708	0.894	SUBCLONAL	1	TRUE	1	0.384167103999559	2		486	574	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190732	11190732	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	101	631	0	ENST00000361445.4:c.5467G>T	p.Ala1823Ser	p.A1823S	ENST00000361445	NM_004958.3	1823	Gcc/Tcc	39/58	1	2	FACETS	0.671	0.599	0.747	0.671	0.599	0.747	SUBCLONAL	1	TRUE	1	0.384167103999559	2		631	784	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937710	36937710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369185176	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	89	693	0	ENST00000361632.4:c.1028G>A	p.Arg343Gln	p.R343Q	ENST00000361632		343	cGg/cAg	8/16	1	2	FACETS	0.662	0.587	0.742	0.662	0.587	0.742	SUBCLONAL	1	TRUE	1	0.384167103999559	2		693	700	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339155	65339155	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	71	504	0	ENST00000342505.4:c.381G>A	p.Trp127Ter	p.W127*	ENST00000342505	NM_002227.2	127	tgG/tgA	5/25	1	2	FACETS	0.812	0.711	0.921	0.812	0.711	0.921	CLONAL	1	TRUE	1	0.384167103999559	2		504	455	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512257	120512257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	80	554	0	ENST00000256646.2:c.985G>A	p.Gly329Ser	p.G329S	ENST00000256646	NM_024408.3	329	Ggc/Agc	6/34	1	2	FACETS	0.565	0.497	0.638	0.565	0.497	0.638	SUBCLONAL	1	TRUE	1	0.384167103999559	2		554	737	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653395	206653395	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374485120	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	135	739	3	ENST00000367120.3:c.1279C>T	p.Arg427Trp	p.R427W	ENST00000367120	NM_014002.3	427	Cgg/Tgg	12/22	1	2	FACETS	0.88	0.8	0.963	0.88	0.8	0.963	CLONAL	1	TRUE	1	0.384167103999559	2		742	799	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247528	123247528	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	69	616	0	ENST00000358487.5:c.1963G>T	p.Asp655Tyr	p.D655Y	ENST00000358487	NM_000141.4	655	Gac/Tac	14/18	1	2	FACETS	0.678	0.591	0.771	0.678	0.591	0.771	SUBCLONAL	1	TRUE	1	0.384167103999559	2		616	530	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123260390	123260390	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	114	641	0	ENST00000358487.5:c.1511A>G	p.Asp504Gly	p.D504G	ENST00000358487	NM_000141.4	504	gAc/gGc	11/18	1	2	FACETS	0.735	0.662	0.813	0.735	0.662	0.813	SUBCLONAL	1	TRUE	1	0.384167103999559	2		641	807	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572204	64572204	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	79	487	1	ENST00000312049.6:c.1435C>T	p.Arg479Trp	p.R479W	ENST00000312049	NM_130799.2	479	Cgg/Tgg	10/10	1	2	FACETS	0.836	0.737	0.941	0.836	0.737	0.941	CLONAL	1	TRUE	1	0.384167103999559	2		488	492	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416114	49416114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	75	488	2	ENST00000301067.7:c.16361G>A	p.Arg5454Gln	p.R5454Q	ENST00000301067	NM_003482.3	5454	cGa/cAa	52/54	1	2	FACETS	0.724	0.636	0.819	0.724	0.636	0.819	SUBCLONAL	1	TRUE	1	0.384167103999559	2		490	539	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426784	49426784	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	15	289	1	ENST00000301067.7:c.11704C>T	p.Gln3902Ter	p.Q3902*	ENST00000301067	NM_003482.3	3902	Cag/Tag	39/54	1	2	FACETS	0.279	0.203	0.37	0.279	0.203	0.37	SUBCLONAL	1	TRUE	1	0.384167103999559	2		290	280	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	104	424	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.777	0.696	0.862	0.777	0.696	0.862	SUBCLONAL	1	TRUE	1	0.384167103999559	2		424	697	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441853	49441853	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	108	512	0	ENST00000301067.7:c.4132-1G>T		p.X1378_splice	ENST00000301067	NM_003482.3	1378			1	2	FACETS	0.81	0.728	0.897	0.81	0.728	0.897	CLONAL	1	TRUE	1	0.384167103999559	2		512	694	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445976	49445976	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371421459	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	64	928	1	ENST00000301067.7:c.1490C>T	p.Pro497Leu	p.P497L	ENST00000301067	NM_003482.3	497	cCg/cTg	10/54	1	2	FACETS	0.278	0.239	0.32	0.278	0.239	0.32	SUBCLONAL	1	TRUE	1	0.384167103999559	2		929	1200	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245227	133245227	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779458859	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	104	750	1	ENST00000320574.5:c.2020G>A	p.Glu674Lys	p.E674K	ENST00000320574	NM_006231.2	674	Gag/Aag	18/49	1	2	FACETS	0.684	0.612	0.76	0.684	0.612	0.76	SUBCLONAL	1	TRUE	1	0.384167103999559	2		751	792	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562552	21562552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	24	102	0	ENST00000382592.4:c.1367C>T	p.Thr456Met	p.T456M	ENST00000382592	NM_014572.2	456	aCg/aTg	4/8	1	2	FACETS	0.969	0.77	1	0.969	0.77	1	CLONAL	1	TRUE	1	0.384167103999559	2		102	129	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609724	28609724	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	96	719	0	ENST00000241453.7:c.1505A>G	p.Asn502Ser	p.N502S	ENST00000241453	NM_004119.2	502	aAc/aGc	12/24	1	2	FACETS	0.863	0.771	0.961	0.863	0.771	0.961	CLONAL	1	TRUE	1	0.384167103999559	2		719	579	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907066	32907066	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	30	437	0	ENST00000380152.3:c.1451T>C	p.Val484Ala	p.V484A	ENST00000380152		484	gTa/gCa	10/27	1	2	FACETS	0.507	0.409	0.617	0.507	0.409	0.617	SUBCLONAL	1	TRUE	1	0.384167103999559	2		437	308	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518150	103518150	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	57	348	0	ENST00000355739.4:c.2088G>T	p.Glu696Asp	p.E696D	ENST00000355739	NM_000123.3	696	gaG/gaT	9/15	1	2	FACETS	0.661	0.568	0.762	0.661	0.568	0.762	SUBCLONAL	1	TRUE	1	0.384167103999559	2		348	449	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435432	110435432	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	146	830	0	ENST00000375856.3:c.2969A>C	p.Lys990Thr	p.K990T	ENST00000375856	NM_003749.2	990	aAg/aCg	1/2	1	2	FACETS	0.879	0.802	0.959	0.879	0.802	0.959	CLONAL	1	TRUE	1	0.384167103999559	2		830	865	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987139	36987139	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1460931537	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	138	786	0	ENST00000354822.5:c.550G>A	p.Ala184Thr	p.A184T	ENST00000354822	NM_001079668.2	184	Gcc/Acc	3/3	1	2	FACETS	0.984	0.897	1	0.984	0.897	1	CLONAL	1	TRUE	1	0.384167103999559	2		786	730	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749199	43749199	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	25	751	0	ENST00000382044.4:c.1607T>C	p.Leu536Ser	p.L536S	ENST00000382044	NM_001141980.1	536	tTg/tCg	12/28	1	2	FACETS	0.282	0.221	0.351	0.282	0.221	0.351	SUBCLONAL	1	TRUE	1	0.384167103999559	2		751	462	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420276	88420276	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	54	573	1	ENST00000360948.2:c.2410C>A	p.Leu804Met	p.L804M	ENST00000360948	NM_001012338.2	804	Ctg/Atg	19/19	1	2	FACETS	0.526	0.45	0.611	0.526	0.45	0.611	SUBCLONAL	1	TRUE	1	0.384167103999559	2		574	534	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354324	354324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200716081	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	111	687	1	ENST00000262320.3:c.1234C>T	p.Arg412Trp	p.R412W	ENST00000262320	NM_003502.3	412	Cgg/Tgg	5/11	1	2	FACETS	0.768	0.691	0.85	0.768	0.691	0.85	SUBCLONAL	1	TRUE	1	0.384167103999559	2		688	752	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	63	442	2	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	0.765	0.663	0.874	0.765	0.663	0.874	SUBCLONAL	1	TRUE	1	0.384167103999559	2		444	429	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829283	72829283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773115759	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	112	717	0	ENST00000268489.5:c.7298C>T	p.Ala2433Val	p.A2433V	ENST00000268489	NM_006885.3	2433	gCg/gTg	9/10	1	2	FACETS	0.735	0.661	0.814	0.735	0.661	0.814	SUBCLONAL	1	TRUE	1	0.384167103999559	2		717	793	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992138	72992138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764598603	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	91	623	0	ENST00000268489.5:c.1907C>T	p.Ser636Leu	p.S636L	ENST00000268489	NM_006885.3	636	tCg/tTg	2/10	1	2	FACETS	0.727	0.646	0.813	0.727	0.646	0.813	SUBCLONAL	1	TRUE	1	0.384167103999559	2		623	652	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371409680	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	115	698	1	ENST00000269305.4:c.848G>A	p.Arg283His	p.R283H	ENST00000269305	NM_001126112.2	283	cGc/cAc	8/11	1	2	FACETS	0.624	0.561	0.691	0.624	0.561	0.691	SUBCLONAL	1	TRUE	1	0.384167103999559	2		699	959	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687472	37687472	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	51	325	1	ENST00000447079.4:c.4382del	p.Gly1461AlafsTer38	p.G1461Afs*38	ENST00000447079	NM_015083.1	1459	tGg/tg	14/14	1	2	FACETS	0.659	0.561	0.765	0.659	0.561	0.765	SUBCLONAL	1	TRUE	1	0.384167103999559	2		326	403	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492890	56492890	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	59	252	0	ENST00000407977.2:c.49C>A	p.Leu17Met	p.L17M	ENST00000407977		17	Ctg/Atg	2/10	1	2	FACETS	0.966	0.837	1	0.966	0.837	1	CLONAL	1	TRUE	1	0.384167103999559	2		252	318	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678186	58678186	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	127	759	1	ENST00000305921.3:c.411G>T	p.Lys137Asn	p.K137N	ENST00000305921	NM_003620.3	137	aaG/aaT	1/6	1	2	FACETS	0.678	0.613	0.747	0.678	0.613	0.747	SUBCLONAL	1	TRUE	1	0.384167103999559	2		760	975	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	102	425	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.341558780644423	2	FACETS	1	0.978	1	0.667	0.601	0.736	CLONAL	1	TRUE	0	0.384167103999559	2		425	398	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612385	1612385	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771217540	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	114	812	0	ENST00000344749.5:c.1634G>A	p.Arg545Gln	p.R545Q	ENST00000344749	NM_001136139.2	545	cGg/cAg	18/19	0.333756611310916	2	FACETS	0.659	0.592	0.729	0.329	0.296	0.365	SUBCLONAL	1	TRUE	0	0.384167103999559	2		812	901	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207672	2207672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	157	580	1	ENST00000398665.3:c.956G>A	p.Arg319His	p.R319H	ENST00000398665	NM_032482.2	319	cGc/cAc	11/28	0.333756611310916	2	FACETS	1	0.986	1	0.67	0.616	0.726	CLONAL	1	TRUE	0	0.384167103999559	2		581	610	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7141719	7141719	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	121	777	0	ENST00000302850.5:c.2651A>G	p.Tyr884Cys	p.Y884C	ENST00000302850	NM_000208.2	884	tAt/tGt	13/22	1	2	FACETS	0.751	0.678	0.828	0.751	0.678	0.828	SUBCLONAL	1	TRUE	1	0.384167103999559	2		777	839	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098411	11098411	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766422429	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	84	548	2	ENST00000358026.2:c.929G>A	p.Arg310His	p.R310H	ENST00000358026	NM_001128849.1	310	cGc/cAc	6/36	1	2	FACETS	0.694	0.613	0.78	0.694	0.613	0.78	SUBCLONAL	1	TRUE	1	0.384167103999559	2		550	630	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106974	11106974	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	106	773	0	ENST00000358026.2:c.1679A>G	p.Tyr560Cys	p.Y560C	ENST00000358026	NM_001128849.1	560	tAc/tGc	10/36	1	2	FACETS	0.701	0.628	0.779	0.701	0.628	0.779	SUBCLONAL	1	TRUE	1	0.384167103999559	2		773	787	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054430	13054430	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	107	626	0	ENST00000316448.5:c.1043del	p.Gly348AlafsTer2	p.G348Afs*2	ENST00000316448	NM_004343.3	347	tGg/tg	8/9	1	2	FACETS	0.697	0.625	0.774	0.697	0.625	0.774	SUBCLONAL	1	TRUE	1	0.384167103999559	2		626	799	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272337	15272337	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs771517374	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	121	920	5	ENST00000263388.2:c.6102del	p.Gly2035ValfsTer50	p.G2035Vfs*50	ENST00000263388	NM_000435.2	2034	ccC/cc	33/33	1	2	FACETS	0.832	0.752	0.916	0.832	0.752	0.916	CLONAL	1	TRUE	1	0.384167103999559	2		925	757	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	98	586	0	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	1	2	FACETS	0.718	0.64	0.8	0.718	0.64	0.8	SUBCLONAL	1	TRUE	1	0.384167103999559	2		586	711	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256769	19256769	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	81	564	1	ENST00000162023.5:c.944del	p.Pro315GlnfsTer?	p.P315Qfs*?	ENST00000162023		315	cCa/ca	13/13	1	2	FACETS	0.756	0.667	0.851	0.756	0.667	0.851	SUBCLONAL	1	TRUE	1	0.384167103999559	2		565	558	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30311669	30311669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	55	516	3	ENST00000262643.3:c.523C>T	p.Arg175Trp	p.R175W	ENST00000262643	NM_001238.2	175	Cgg/Tgg	7/12	1	2	FACETS	0.784	0.674	0.904	0.784	0.674	0.904	CLONAL	1	TRUE	1	0.384167103999559	2		519	365	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	34	389	3	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	1	2	FACETS	0.545	0.446	0.655	0.545	0.446	0.655	SUBCLONAL	1	TRUE	1	0.384167103999559	2		392	325	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905288	50905288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376236497	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	111	936	0	ENST00000440232.2:c.496C>T	p.Arg166Trp	p.R166W	ENST00000440232	NM_002691.3	166	Cgg/Tgg	5/27	1	2	FACETS	0.634	0.569	0.703	0.634	0.569	0.703	SUBCLONAL	1	TRUE	1	0.384167103999559	2		936	911	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47643462	47643462	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750502	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	63	564	0	ENST00000233146.2:c.970C>T	p.Gln324Ter	p.Q324*	ENST00000233146	NM_000251.2	324	Cag/Tag	6/16	1	2	FACETS	0.808	0.701	0.923	0.808	0.701	0.923	CLONAL	1	TRUE	1	0.384167103999559	2		564	406	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030613	48030613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779617676	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	78	480	0	ENST00000234420.5:c.3227G>A	p.Arg1076His	p.R1076H	ENST00000234420	NM_000179.2	1076	cGc/cAc	5/10	1	2	FACETS	0.689	0.606	0.779	0.689	0.606	0.779	SUBCLONAL	1	TRUE	1	0.384167103999559	2		480	589	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736166	204736166	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	70	429	2	ENST00000302823.3:c.529del	p.Tyr177IlefsTer10	p.Y177Ifs*10	ENST00000302823	NM_005214.4	175	Ttt/tt	3/4	1	2	FACETS	0.733	0.641	0.833	0.733	0.641	0.833	SUBCLONAL	1	TRUE	1	0.384167103999559	2		431	497	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021701	31021701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	36	617	0	ENST00000375687.4:c.1700C>T	p.Pro567Leu	p.P567L	ENST00000375687	NM_015338.5	567	cCc/cTc	12/13	1	2	FACETS	0.265	0.217	0.32	0.265	0.217	0.32	SUBCLONAL	1	TRUE	1	0.384167103999559	2		617	706	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39746915	39746916	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	72	488	0	ENST00000361337.2:c.1930_1931del	p.Met644AspfsTer6	p.M644Dfs*6	ENST00000361337	NM_003286.2	643	tcTAtg/tctg	18/21	1	2	FACETS	0.949	0.833	1	0.949	0.833	1	CLONAL	1	TRUE	1	0.384167103999559	2		488	395	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770587	40770587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776338672	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	65	545	0	ENST00000373198.4:c.2795G>A	p.Arg932His	p.R932H	ENST00000373198	NM_133170.3	932	cGc/cAc	19/32	1	2	FACETS	0.728	0.632	0.83	0.728	0.632	0.83	SUBCLONAL	1	TRUE	1	0.384167103999559	2		545	465	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980756	40980756	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	73	455	0	ENST00000373198.4:c.1730del	p.Pro577LeufsTer24	p.P577Lfs*24	ENST00000373198	NM_133170.3	577	cCt/ct	10/32	1	2	FACETS	0.846	0.743	0.957	0.846	0.743	0.957	CLONAL	1	TRUE	1	0.384167103999559	2		455	449	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	74	500	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.785	0.689	0.887	0.785	0.689	0.887	SUBCLONAL	1	TRUE	1	0.384167103999559	2		501	491	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292807	62292807	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	52	380	0	ENST00000360203.5:c.259T>G	p.Ser87Ala	p.S87A	ENST00000360203	NM_001283009.1	87	Tca/Gca	3/35	1	2	FACETS	0.7	0.597	0.811	0.7	0.597	0.811	SUBCLONAL	1	TRUE	1	0.384167103999559	2		380	387	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755606	39755606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	78	491	1	ENST00000288319.7:c.1159G>A	p.Ala387Thr	p.A387T	ENST00000288319	NM_182918.3	387	Gcc/Acc	10/10	1	2	FACETS	0.76	0.669	0.858	0.76	0.669	0.858	SUBCLONAL	1	TRUE	1	0.384167103999559	2		492	534	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221610	22221610	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	29	273	0	ENST00000215832.6:c.119+2T>C		p.X40_splice	ENST00000215832	NM_002745.4	40			1	2	FACETS	0.376	0.301	0.46	0.376	0.301	0.46	SUBCLONAL	1	TRUE	1	0.384167103999559	2		273	402	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	45	318	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	1	2	FACETS	0.761	0.642	0.89	0.761	0.642	0.89	SUBCLONAL	1	TRUE	1	0.384167103999559	2		318	308	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058663	47058664	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	68	650	0	ENST00000409792.3:c.7614_7615del	p.His2538GlnfsTer7	p.H2538Qfs*7	ENST00000409792	NM_014159.6	2538	caCAaa/caaa	21/21	1	2	FACETS	0.577	0.501	0.658	0.577	0.501	0.658	SUBCLONAL	1	TRUE	1	0.384167103999559	2		650	614	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643688	52643688	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	56	534	0	ENST00000394830.3:c.2208T>A	p.Cys736Ter	p.C736*	ENST00000394830	NM_018313.4	736	tgT/tgA	17/30	1	2	FACETS	0.824	0.709	0.948	0.824	0.709	0.948	CLONAL	1	TRUE	1	0.384167103999559	2		534	354	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651438	52651438	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	63	675	0	ENST00000394830.3:c.1658del	p.Lys553ArgfsTer16	p.K553Rfs*16	ENST00000394830	NM_018313.4	553	aAg/ag	15/30	1	2	FACETS	0.779	0.676	0.89	0.779	0.676	0.89	SUBCLONAL	1	TRUE	1	0.384167103999559	2		675	421	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851645	134851645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1395878132	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	76	501	4	ENST00000398015.3:c.1051C>T	p.Arg351Trp	p.R351W	ENST00000398015	NM_004441.4	351	Cgg/Tgg	5/16	1	2	FACETS	0.817	0.719	0.923	0.817	0.719	0.923	CLONAL	1	TRUE	1	0.384167103999559	2		505	484	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1962801	1962801	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772470710	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	102	536	2	ENST00000382891.5:c.3295G>A	p.Glu1099Lys	p.E1099K	ENST00000382891	NM_133335.3	1099	Gag/Aag	18/22	1	2	FACETS	0.839	0.751	0.932	0.839	0.751	0.932	CLONAL	1	TRUE	1	0.384167103999559	2		538	633	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156721	55156721	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	65	340	0	ENST00000257290.5:c.3122G>T	p.Ser1041Ile	p.S1041I	ENST00000257290	NM_006206.4	1041	aGc/aTc	22/23	1	2	FACETS	0.987	0.861	1	0.987	0.861	1	CLONAL	1	TRUE	1	0.384167103999559	2		340	343	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961080	55961080	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757083292	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	106	724	0	ENST00000263923.4:c.2860G>A	p.Ala954Thr	p.A954T	ENST00000263923	NM_002253.2	954	Gca/Aca	21/30	1	2	FACETS	0.615	0.551	0.684	0.615	0.551	0.684	SUBCLONAL	1	TRUE	1	0.384167103999559	2		724	897	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981047	55981047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145458680	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	34	476	2	ENST00000263923.4:c.652G>A	p.Val218Ile	p.V218I	ENST00000263923	NM_002253.2	218	Gtt/Att	5/30	1	2	FACETS	0.705	0.579	0.845	0.705	0.579	0.845	SUBCLONAL	1	TRUE	1	0.384167103999559	2		478	251	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391473	84391473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	35	328	0	ENST00000321945.7:c.359del	p.Asn120ThrfsTer16	p.N120Tfs*16	ENST00000321945	NM_139076.2	120	aAc/ac	5/9	1	2	FACETS	1	0.83	1	1	0.83	1	CLONAL	1	TRUE	1	0.384167103999559	2		328	182	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249361	153249361	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	27	441	2	ENST00000281708.4:c.1417del	p.Arg473GlufsTer25	p.R473Efs*25	ENST00000281708	NM_033632.3	473	Aga/ga	9/12	1	2	FACETS	0.521	0.415	0.64	0.521	0.415	0.64	SUBCLONAL	1	TRUE	1	0.384167103999559	2		443	270	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970916	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	70	734	0	ENST00000265081.6:c.1147_1148del	p.Lys383GlyfsTer20	p.K383Gfs*20	ENST00000265081	NM_002439.4	381	AAa/a	7/24	1	2	FACETS	0.642	0.56	0.73	0.642	0.56	0.73	SUBCLONAL	1	TRUE	1	0.384167103999559	2		734	568	SUCCESS
APC	324	MSKCC	GRCh37	5	112176206	112176206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	34	464	0	ENST00000257430.4:c.4915C>T	p.Pro1639Ser	p.P1639S	ENST00000257430	NM_000038.5	1639	Cca/Tca	16/16	1	2	FACETS	0.41	0.335	0.494	0.41	0.335	0.494	SUBCLONAL	1	TRUE	1	0.384167103999559	2		464	432	SUCCESS
APC	324	MSKCC	GRCh37	5	112179428	112179428	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	32	563	0	ENST00000257430.4:c.8137A>G	p.Met2713Val	p.M2713V	ENST00000257430	NM_000038.5	2713	Atg/Gtg	16/16	1	2	FACETS	0.353	0.286	0.429	0.353	0.286	0.429	SUBCLONAL	1	TRUE	1	0.384167103999559	2		563	472	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673799	176673799	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	55	528	0	ENST00000439151.2:c.4497+2T>C		p.X1499_splice	ENST00000439151	NM_022455.4	1499			1	2	FACETS	0.648	0.555	0.749	0.648	0.555	0.749	SUBCLONAL	1	TRUE	1	0.384167103999559	2		528	442	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480087	20480087	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	46	427	0	ENST00000346618.3:c.404G>T	p.Arg135Met	p.R135M	ENST00000346618	NM_001949.4	135	aGg/aTg	2/7	1	2	FACETS	0.584	0.493	0.685	0.584	0.493	0.685	SUBCLONAL	1	TRUE	1	0.384167103999559	2		427	410	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225389	26225389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs545285022	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	27	151	0	ENST00000360408.1:c.7C>T	p.Arg3Cys	p.R3C	ENST00000360408	NM_003532.2	3	Cgt/Tgt	1/1	1	2	FACETS	0.633	0.506	0.776	0.633	0.506	0.776	SUBCLONAL	1	TRUE	1	0.384167103999559	2		151	222	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250491	26250491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	47	596	2	ENST00000446824.2:c.343G>A	p.Ala115Thr	p.A115T	ENST00000446824	NM_021018.2	115	Gcc/Acc	1/1	1	2	FACETS	0.371	0.312	0.436	0.371	0.312	0.436	SUBCLONAL	1	TRUE	1	0.384167103999559	2		598	659	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911053	29911053	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	30	411	0	ENST00000376809.5:c.352A>C	p.Thr118Pro	p.T118P	ENST00000376809	NM_002116.7	118	Acc/Ccc	3/8	1	2	FACETS	0.481	0.388	0.585	0.481	0.388	0.585	SUBCLONAL	1	TRUE	1	0.384167103999559	2		411	325	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671018	30671018	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	125	665	4	ENST00000376406.3:c.5728C>A	p.Leu1910Met	p.L1910M	ENST00000376406	NM_014641.2	1910	Ctg/Atg	12/15	1	2	FACETS	0.734	0.664	0.808	0.734	0.664	0.808	SUBCLONAL	1	TRUE	1	0.384167103999559	2		669	887	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681432	30681432	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	18	406	0	ENST00000376406.3:c.580C>A	p.Pro194Thr	p.P194T	ENST00000376406	NM_014641.2	194	Cca/Aca	4/15	1	2	FACETS	0.287	0.216	0.372	0.287	0.216	0.372	SUBCLONAL	1	TRUE	1	0.384167103999559	2		406	326	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800238	32800238	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	62	336	0	ENST00000374899.4:c.1144del	p.Val382CysfsTer9	p.V382Cfs*9	ENST00000374899	NM_018833.2	382	Gtg/tg	7/12	1	2	FACETS	0.902	0.783	1	0.902	0.783	1	CLONAL	1	TRUE	1	0.384167103999559	2		336	358	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805787	32805788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1174402903	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	106	796	0	ENST00000374899.4:c.223dup	p.Leu75ProfsTer92	p.L75Pfs*92	ENST00000374899	NM_018833.2	75	ctg/cCtg	2/12	1	2	FACETS	0.696	0.624	0.773	0.696	0.624	0.773	SUBCLONAL	1	TRUE	1	0.384167103999559	2		796	793	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820957	32820957	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	150	888	4	ENST00000354258.4:c.637C>A	p.Leu213Met	p.L213M	ENST00000354258	NM_000593.5	213	Ctg/Atg	1/11	1	2	FACETS	0.887	0.811	0.967	0.887	0.811	0.967	CLONAL	1	TRUE	1	0.384167103999559	2		892	880	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793893	89793893	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	23	387	0	ENST00000336032.3:c.962C>T	p.Thr321Met	p.T321M	ENST00000336032	NM_006813.2	321	aCg/aTg	2/2	1	2	FACETS	0.434	0.339	0.544	0.434	0.339	0.544	SUBCLONAL	1	TRUE	1	0.384167103999559	2		387	276	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265629	152265629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	48	443	0	ENST00000206249.3:c.1082C>T	p.Ala361Val	p.A361V	ENST00000206249	NM_000125.3	361	gCg/gTg	4/8	1	2	FACETS	0.567	0.48	0.662	0.567	0.48	0.662	SUBCLONAL	1	TRUE	1	0.384167103999559	2		443	441	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450267	50450267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	80	580	1	ENST00000331340.3:c.451G>A	p.Gly151Arg	p.G151R	ENST00000331340	NM_006060.4	151	Ggg/Agg	5/8	1	2	FACETS	0.675	0.595	0.761	0.675	0.595	0.761	SUBCLONAL	1	TRUE	1	0.384167103999559	2		581	617	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380910	116380910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371124109	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	68	504	1	ENST00000397752.3:c.1532C>T	p.Thr511Met	p.T511M	ENST00000397752	NM_000245.2	511	aCg/aTg	5/21	1	2	FACETS	0.715	0.623	0.814	0.715	0.623	0.814	SUBCLONAL	1	TRUE	1	0.384167103999559	2		505	495	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279438	38279438	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	82	565	0	ENST00000425967.3:c.1051G>T	p.Asp351Tyr	p.D351Y	ENST00000425967	NM_001174067.1	351	Gac/Tac	9/19	1	2	FACETS	0.744	0.657	0.837	0.744	0.657	0.837	SUBCLONAL	1	TRUE	1	0.384167103999559	2		565	574	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141567313	141567313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs905630231	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	88	554	0	ENST00000220592.5:c.901G>A	p.Gly301Arg	p.G301R	ENST00000220592	NM_012154.3	301	Ggg/Agg	8/19	1	2	FACETS	0.797	0.707	0.892	0.797	0.707	0.892	SUBCLONAL	1	TRUE	1	0.384167103999559	2		554	575	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141568673	141568673	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	98	498	0	ENST00000220592.5:c.791-2A>G		p.X264_splice	ENST00000220592	NM_012154.3	264			1	2	FACETS	0.921	0.824	1	0.921	0.824	1	CLONAL	1	TRUE	1	0.384167103999559	2		498	554	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	109	141	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	0.949	0.854	1	0.949	0.854	1	CLONAL	1	TRUE	1	0.384167103999559	2		141	598	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882050	36882050	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs780753361	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	140	782	14	ENST00000358127.4:c.963del	p.Ala322LeufsTer11	p.A322Lfs*11	ENST00000358127	NM_001280556.1	321	ccC/cc	8/10	1	2	FACETS	0.824	0.75	0.901	0.824	0.75	0.901	CLONAL	1	TRUE	1	0.384167103999559	2		796	885	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922863	39922863	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	82	453	0	ENST00000378444.4:c.3845A>G	p.Gln1282Arg	p.Q1282R	ENST00000378444	NM_001123385.1	1282	cAa/cGa	8/15	1	2	FACETS	0.859	0.76	0.965	0.859	0.76	0.965	CLONAL	1	TRUE	1	0.384167103999559	2		453	497	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422455	47422455	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398289359	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	93	745	1	ENST00000377045.4:c.89G>A	p.Arg30His	p.R30H	ENST00000377045	NM_001654.4	30	cGc/cAc	2/16	1	2	FACETS	0.609	0.541	0.682	0.609	0.541	0.682	SUBCLONAL	1	TRUE	1	0.384167103999559	2		746	795	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424734	47424734	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	108	685	2	ENST00000377045.4:c.547del	p.Gln183ArgfsTer109	p.Q183Rfs*109	ENST00000377045	NM_001654.4	181	aCc/ac	6/16	1	2	FACETS	0.789	0.708	0.874	0.789	0.708	0.874	SUBCLONAL	1	TRUE	1	0.384167103999559	2		687	713	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223589	53223589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	68	489	0	ENST00000375401.3:c.3770C>T	p.Thr1257Ile	p.T1257I	ENST00000375401	NM_004187.3	1257	aCc/aTc	23/26	1	2	FACETS	0.747	0.651	0.85	0.747	0.651	0.85	SUBCLONAL	1	TRUE	1	0.384167103999559	2		489	474	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250046	53250047	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs782600511	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	94	610	0	ENST00000375401.3:c.202dup	p.Arg68ProfsTer7	p.R68Pfs*7	ENST00000375401	NM_004187.3	68	cga/cCga	2/26	1	2	FACETS	0.737	0.656	0.823	0.737	0.656	0.823	SUBCLONAL	1	TRUE	1	0.384167103999559	2		610	664	SUCCESS
AR	367	MSKCC	GRCh37	X	66941727	66941727	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	91	637	0	ENST00000374690.3:c.2371C>A	p.Leu791Ile	p.L791I	ENST00000374690	NM_000044.3	791	Ctc/Atc	6/8	1	2	FACETS	0.686	0.609	0.768	0.686	0.609	0.768	SUBCLONAL	1	TRUE	1	0.384167103999559	2		637	691	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871027	12871027	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	53	343	0	ENST00000228872.4:c.254C>T	p.Pro85Leu	p.P85L	ENST00000228872	NM_004064.3	85	cCc/cTc	1/3	0.626539532479912	6	FACETS	0.632	0.539	0.735	0.158	0.134	0.184	SUBCLONAL	1	TRUE	2	0.626539532479912	6		343	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0026514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	247	758	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.53964991079678	3	FACETS	0.908	0.867	0.949	0.908	0.867	0.949	CLONAL	3	TRUE	0	0.626539532479912	3		758	380	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727880	41727880	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756018335	NA	P-0026514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	68	738	1	ENST00000301178.4:c.505G>A	p.Val169Met	p.V169M	ENST00000301178	NM_021913.4	169	Gtg/Atg	4/20	0.35989266271517	5	FACETS	0.555	0.482	0.634	0.185	0.16	0.212	INDETERMINATE	1	TRUE	2	0.626539532479912	5		739	759	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662482	227662482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	104	429	0	ENST00000305123.5:c.973C>T	p.Arg325Cys	p.R325C	ENST00000305123	NM_005544.2	325	Cgt/Tgt	1/2	0.399942034487972	4	FACETS	1	0.977	1	0.649	0.585	0.716	CLONAL	1	TRUE	2	0.626539532479912	4		429	416	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31405812	31405812	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs761417383	NA	P-0026514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	31	380	0	ENST00000344624.3:c.3966G>T	p.Met1322Ile	p.M1322I	ENST00000344624		1322	atG/atT	32/33	0.319714363557142	5	FACETS	0.487	0.394	0.593	0.162	0.131	0.198	INDETERMINATE	1	TRUE	2	0.626539532479912	5		380	394	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057627	180057627	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs756234174	NA	P-0026514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	106	824	0	ENST00000261937.6:c.328G>T	p.Val110Phe	p.V110F	ENST00000261937	NM_182925.4	110	Gtc/Ttc	3/30	0.200970755250204	1	FACETS	0.547	0.493	0.603	0.547	0.493	0.603	INDETERMINATE	1	TRUE	0	0.626539532479912	1		824	425	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411142	63411142	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	66	554	0	ENST00000330258.3:c.2025G>C	p.Gln675His	p.Q675H	ENST00000330258	NM_152424.3	675	caG/caC	2/2	0.626539532479912	2	FACETS	0.675	0.591	0.765	0.338	0.295	0.383	SUBCLONAL	1	TRUE	0	0.626539532479912	2		554	312	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061223	38061228	+	inframe_deletion	In_Frame_Del	DEL	TCTCGA	TCTCGA	-	novel	NA	P-0026716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	231	274	1	ENST00000250448.2:c.761_766del	p.Phe254_Asn256delinsTyr	p.F254_N256delinsY	ENST00000250448	NM_004496.3	254	tTCGAGAac/tac	2/2	0.206850499313532	3	FACETS	1	0.988	1	0.625	0.585	0.667	INDETERMINATE	1	TRUE	1	0.620499220554983	3		275	780	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870969	12870969	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	212	421	0	ENST00000228872.4:c.197del	p.Asn66IlefsTer5	p.N66Ifs*5	ENST00000228872	NM_004064.3	66	Aat/at	1/3	0.620499220554983	1	FACETS	0.937	0.879	0.995	0.937	0.879	0.995	CLONAL	1	TRUE	0	0.620499220554983	1		421	503	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0026765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	283	303	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.421020019353474	4	FACETS	0.992	0.94	1	0.992	0.94	1	CLONAL	3	TRUE	1	0.421020019353474	4		303	642	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551361	150551361	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	372	662	0	ENST00000369026.2:c.646G>T	p.Val216Phe	p.V216F	ENST00000369026	NM_021960.4	216	Gtt/Ttt	1/3	0.421020019353474	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.421020019353474	3		662	1034	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811653	102811653	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	259	463	0	ENST00000307046.8:c.531G>T	p.Glu177Asp	p.E177D	ENST00000307046	NM_001111285.1	177	gaG/gaT	4/4	0.201160250593607	5	FACETS	1	0.987	1	0.784	0.736	0.832	INDETERMINATE	2	TRUE	2	0.421020019353474	5		463	854	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315369	30315369	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	276	359	0	ENST00000322652.5:c.1054G>A	p.Gly352Arg	p.G352R	ENST00000322652	NM_015355.2	352	Gga/Aga	10/16	0.421020019353474	2	FACETS	0.836	0.794	0.877	1	0.992	1	CLONAL	3	TRUE	0	0.421020019353474	2		359	523	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437613	56437614	+	splice_acceptor_variant	Splice_Site	DNP	CT	CT	AC	novel	NA	P-0026765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	243	316	2	ENST00000407977.2:c.850-2_850-1delinsGT		p.X284_splice	ENST00000407977		284			0.421020019353474	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	0	0.421020019353474	3		318	439	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727089	41727089	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	263	580	1	ENST00000301178.4:c.347A>T	p.Gln116Leu	p.Q116L	ENST00000301178	NM_021913.4	116	cAg/cTg	3/20	0.33427345386103	3	FACETS	0.768	0.72	0.817	0.768	0.72	0.817	SUBCLONAL	2	TRUE	1	0.421020019353474	3		581	985	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50138844	50138844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748655822	NA	P-0026765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	413	616	1	ENST00000246792.3:c.646G>A	p.Val216Ile	p.V216I	ENST00000246792	NM_006270.3	216	Gtc/Atc	6/6	0.33427345386103	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.421020019353474	3		617	1096	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165290	32165290	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	278	617	0	ENST00000375023.3:c.4838C>T	p.Pro1613Leu	p.P1613L	ENST00000375023	NM_004557.3	1613	cCt/cTt	27/30	0.366514196852868	4	FACETS	0.952	0.895	1	0.952	0.895	1	CLONAL	2	TRUE	2	0.421020019353474	4		617	986	SUCCESS
AR	367	MSKCC	GRCh37	X	66766334	66766334	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	76	151	0	ENST00000374690.3:c.1346C>T	p.Pro449Leu	p.P449L	ENST00000374690	NM_000044.3	449	cCg/cTg	1/8	0.254157638164116	4	FACETS	0.943	0.837	1	0.943	0.837	1	CLONAL	2	TRUE	2	0.421020019353474	4		151	272	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577049	7577051	+	frameshift_variant	Frame_Shift_Del	DEL	GGT	GGT	A	novel	NA	P-0026765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	327	511	0	ENST00000269305.4:c.887_889delinsT	p.His296LeufsTer9	p.H296Lfs*9	ENST00000269305	NM_001126112.2	296	cACCac/cTac	8/11	0.421020019353474	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.421020019353474	2		511	684	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0026774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	102	478	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.869	0.78	0.963	0.869	0.78	0.963	CLONAL	1	TRUE	1	0.43	2		478	546	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508629	106508629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751048583	NA	P-0026774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	115	385	0	ENST00000359195.3:c.623C>T	p.Pro208Leu	p.P208L	ENST00000359195	NM_002649.2	208	cCg/cTg	2/11	1	2	FACETS	0.896	0.809	0.987	0.896	0.809	0.987	CLONAL	1	TRUE	1	0.43	2		385	597	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574693	41574693	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	75	668	0	ENST00000263253.7:c.6978del	p.Pro2327LeufsTer26	p.P2327Lfs*26	ENST00000263253	NM_001429.3	2326	agT/ag	31/31	0.443556446324586	1	FACETS	0.329	0.287	0.374	0.329	0.287	0.374	SUBCLONAL	1	TRUE	0	0.43	1		668	833	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183866	10183866	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs869025633	NA	P-0026775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	365	337	0	ENST00000256474.2:c.335A>G	p.Tyr112Cys	p.Y112C	ENST00000256474	NM_000551.3	112	tAc/tGc	1/3	0.829234801247269	1	FACETS	0.997	0.962	1	0.997	0.962	1	CLONAL	1	TRUE	0	0.829234801247269	1		337	517	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575026	64575026	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs1057520733	NA	P-0026775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	352	253	1	ENST00000312049.6:c.781C>T	p.Gln261Ter	p.Q261*	ENST00000312049	NM_130799.2	261	Cag/Tag	4/10	0.829234801247269	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.829234801247269	1		254	472	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123159736	123159736	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1251136516	NA	P-0026775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	373	192	1	ENST00000218089.9:c.91G>A	p.Glu31Lys	p.E31K	ENST00000218089	NM_001042749.1	31	Gaa/Aaa	4/35	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.829234801247269	1		193	422	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807289	3807289	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057518844	NA	P-0026775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	296	325	0	ENST00000262367.5:c.3698G>A	p.Arg1233Lys	p.R1233K	ENST00000262367	NM_004380.2	1233	aGg/aAg	19/31	0.829234801247269	1	FACETS	0.988	0.95	1	0.988	0.95	1	CLONAL	1	TRUE	0	0.829234801247269	1		325	423	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288540	33288540	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	263	316	0	ENST00000374542.5:c.1012T>C	p.Cys338Arg	p.C338R	ENST00000374542	NM_001141970.1	338	Tgc/Cgc	3/8	0.829234801247269	1	FACETS	0.942	0.902	0.982	0.942	0.902	0.982	CLONAL	1	TRUE	0	0.829234801247269	1		316	394	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974769	21974770	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCCGT	rs1563892769	NA	P-0026992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	16	221	0	ENST00000304494.5:c.52_57dup	p.Thr18_Ala19dup	p.T18_A19dup	ENST00000304494	NM_000077.4	18	-/ACGGCC	1/3	1	2	FACETS	0.98	0.727	1	0.98	0.727	1	CLONAL	1	TRUE	1	0.16	2		221	204	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846063	68846063	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	87	644	0	ENST00000261769.5:c.1034T>A	p.Val345Asp	p.V345D	ENST00000261769	NM_004360.3	345	gTt/gAt	8/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.16	2		644	821	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691943	30691943	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	31	325	0	ENST00000295754.5:c.445T>G	p.Phe149Val	p.F149V	ENST00000295754	NM_003242.5	149	Ttc/Gtc	3/7	1	2	FACETS	0.889	0.718	1	0.889	0.718	1	CLONAL	1	TRUE	1	0.16	2		325	436	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281058	49281058	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	115	631	1	ENST00000282018.3:c.105C>A	p.Asn35Lys	p.N35K	ENST00000282018	NM_020377.2	35	aaC/aaA	1/1	0.906121940341185	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.906121940341185	1		632	137	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281377	49281377	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	528	699	0	ENST00000282018.3:c.424C>G	p.His142Asp	p.H142D	ENST00000282018	NM_020377.2	142	Cac/Gac	1/1	0.906121940341185	1	FACETS	0.999	0.977	1	0.999	0.977	1	CLONAL	1	TRUE	0	0.906121940341185	1		699	638	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945952	17945953	+	missense_variant	Missense_Mutation	DNP	TC	TC	CA	novel	NA	P-0027015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1327	453	736	0	ENST00000458235.1:c.1986_1987delinsTG	p.Ser663Gly	p.S663G	ENST00000458235	NM_000215.3	662	ggGAgc/ggTGgc	15/24	0.172095470124024	4	FACETS	1	0.984	1	0.535	0.51	0.562	INDETERMINATE	1	TRUE	2	0.906121940341185	4		736	1780	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61709536	61709536	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	132	357	0	ENST00000401558.2:c.2951C>G	p.Ser984Trp	p.S984W	ENST00000401558	NM_003400.3	984	tCg/tGg	23/25	0.299082775415509	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.906121940341185	0		357	315	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945952	17945952	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1320	453	730	0	ENST00000458235.1:c.1987A>G	p.Ser663Gly	p.S663G	ENST00000458235	NM_000215.3	663	Agc/Ggc	15/24	0.172095470124024	4	FACETS	1	0.984	1	0.537	0.512	0.564	INDETERMINATE	1	TRUE	2	0.906121940341185	4		730	1773	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	169	487	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	1	2	FACETS	0.89	0.82	0.963	0.89	0.82	0.963	CLONAL	1	TRUE	1	0.502817818300237	2		487	755	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442570	52442570	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1404823823	NA	P-0027115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	212	413	0	ENST00000460680.1:c.175C>T	p.Arg59Trp	p.R59W	ENST00000460680	NM_004656.3	59	Cgg/Tgg	4/17	0.486431121408049	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.502817818300237	1		413	547	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115723	8115724	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGAAGGAAGGCATCC	novel	NA	P-0027115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	49	365	0	ENST00000346208.3:c.1073_1087dup	p.Lys358_Gln362dup	p.K358_Q362dup	ENST00000346208		358	aag/aAGAAGGAAGGCATCCag	6/6	1	2	FACETS	0.33	0.279	0.386	0.33	0.279	0.386	SUBCLONAL	1	TRUE	1	0.502817818300237	2		365	591	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0027129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	77	225	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.236303709276321	2		225	600	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847306	68847306	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	131	657	0	ENST00000261769.5:c.1228G>T	p.Glu410Ter	p.E410*	ENST00000261769	NM_004360.3	410	Gag/Tag	9/16	0.236303709276321	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.236303709276321	1		657	966	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341536	89341536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	116	549	1	ENST00000301030.4:c.7534C>T	p.Arg2512Trp	p.R2512W	ENST00000301030	NM_001256183.1	2512	Cgg/Tgg	10/13	0.236303709276321	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.236303709276321	1		550	786	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348439	56348439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	67	355	0	ENST00000348428.3:c.247G>A	p.Glu83Lys	p.E83K	ENST00000348428	NM_006785.3	83	Gag/Aag	2/17	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.236303709276321	2		355	539	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575366	64575367	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0027194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	481	489	0	ENST00000312049.6:c.650_651del	p.Glu217AlafsTer14	p.E217Afs*14	ENST00000312049	NM_130799.2	217	gAG/g	3/10	0.777660117333717	1	FACETS	0.999	0.966	1	0.999	0.966	1	CLONAL	1	TRUE	0	0.777660117333717	1		489	757	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131625	2131625	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	429	619	0	ENST00000219476.3:c.3640A>T	p.Asn1214Tyr	p.N1214Y	ENST00000219476	NM_000548.3	1214	Aac/Tac	31/42	0.771045154555093	1	FACETS	0.85	0.817	0.883	0.85	0.817	0.883	CLONAL	1	TRUE	0	0.777660117333717	1		619	793	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875863	76875863	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	129	220	0	ENST00000373344.5:c.5272T>C	p.Tyr1758His	p.Y1758H	ENST00000373344	NM_000489.3	1758	Tat/Cat	20/35	0.45393361317397	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	NA	0.777660117333717	0		220	172	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578259	7578269	+	frameshift_variant	Frame_Shift_Del	DEL	ACTCGGATAAG	ACTCGGATAAG	-	novel	NA	P-0027239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	287	541	0	ENST00000269305.4:c.580_590del	p.Leu194GlyfsTer11	p.L194Gfs*11	ENST00000269305	NM_001126112.2	194	CTTATCCGAGTg/g	6/11	0.519077041845901	2	FACETS	0.923	0.876	0.97	0.923	0.876	0.97	CLONAL	2	TRUE	0	0.519077041845901	2		541	599	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207630	2207630	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	54	704	0	ENST00000398665.3:c.914G>A	p.Trp305Ter	p.W305*	ENST00000398665	NM_032482.2	305	tGg/tAg	11/28	0.514774876873501	2	FACETS	0.287	0.245	0.334	0.144	0.122	0.167	SUBCLONAL	1	TRUE	0	0.519077041845901	2		704	724	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374732	149374732	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766632650	NA	P-0027239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	145	489	0	ENST00000360632.3:c.362C>T	p.Thr121Ile	p.T121I	ENST00000360632	NM_015472.4	121	aCc/aTc	2/7	0.519077041845901	4	FACETS	0.88	0.803	0.962	0.293	0.267	0.321	CLONAL	1	TRUE	1	0.519077041845901	4		489	964	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503846	149503846	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs770122404	NA	P-0027239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	164	607	0	ENST00000261799.4:c.1990G>C	p.Val664Leu	p.V664L	ENST00000261799	NM_002609.3	664	Gtg/Ctg	14/23	0.514774876873501	2	FACETS	1	0.949	1	0.519	0.478	0.561	CLONAL	1	TRUE	0	0.519077041845901	2		607	609	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197414	26197431	+	inframe_deletion	In_Frame_Del	DEL	GCCAGCTGCTTGCGTGGC	GCCAGCTGCTTGCGTGGC	-	novel	NA	P-0027239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	126	283	0	ENST00000356476.2:c.48_65del	p.Pro17_Ala22del	p.P17_A22del	ENST00000356476		16	gcGCCACGCAAGCAGCTGGCc/gcc	1/1	0.459092938078515	4	FACETS	0.965	0.883	1	0.644	0.589	0.7	CLONAL	2	TRUE	1	0.519077041845901	4		283	382	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0027256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	138	373	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.839	0.766	0.914	0.839	0.766	0.914	CLONAL	1	TRUE	1	0.558669162283277	2		373	589	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061194	38061555	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCTTCTGGCGGCGCAAGTAGCAGCCGTTCTCGAACATGTTGCCGGAGTCCGGGTGCAGCGTCCAGTAGGAGCCCTTGCCCGGCTTGTCCGGGGAGCGTGCCACCTTGACGAAGCAGTCATTGAAGGACAGCGAGTGGCGGATGGAGTTCTGCCAGCGCTGCTGGTTCTGCCGGTAATAGGGGAAGAGGTCCATGATCCACTGGTAGATCTCGCTCAGCGTGAGCATCTTGCTGGGCGCCTGCTGGATGGCCATGGTGATGAGCGAGATGTACGAGTAGGGCGGCTTGGCGTGCGGGTAGCTGCGCTTGAACGTCTTGGCGTCGCCGCCGCCGCCCGCGCGGCTGCGGCCCAGGTTGGACG	GCGCTTCTGGCGGCGCAAGTAGCAGCCGTTCTCGAACATGTTGCCGGAGTCCGGGTGCAGCGTCCAGTAGGAGCCCTTGCCCGGCTTGTCCGGGGAGCGTGCCACCTTGACGAAGCAGTCATTGAAGGACAGCGAGTGGCGGATGGAGTTCTGCCAGCGCTGCTGGTTCTGCCGGTAATAGGGGAAGAGGTCCATGATCCACTGGTAGATCTCGCTCAGCGTGAGCATCTTGCTGGGCGCCTGCTGGATGGCCATGGTGATGAGCGAGATGTACGAGTAGGGCGGCTTGGCGTGCGGGTAGCTGCGCTTGAACGTCTTGGCGTCGCCGCCGCCGCCCGCGCGGCTGCGGCCCAGGTTGGACG	-	novel	NA	P-0027256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	76	502	0	ENST00000250448.2:c.434_795del	p.Pro145LeufsTer27	p.P145Lfs*27	ENST00000250448	NM_004496.3	145	cCGTCCAACCTGGGCCGCAGCCGCGCGGGCGGCGGCGGCGACGCCAAGACGTTCAAGCGCAGCTACCCGCACGCCAAGCCGCCCTACTCGTACATCTCGCTCATCACCATGGCCATCCAGCAGGCGCCCAGCAAGATGCTCACGCTGAGCGAGATCTACCAGTGGATCATGGACCTCTTCCCCTATTACCGGCAGAACCAGCAGCGCTGGCAGAACTCCATCCGCCACTCGCTGTCCTTCAATGACTGCTTCGTCAAGGTGGCACGCTCCCCGGACAAGCCGGGCAAGGGCTCCTACTGGACGCTGCACCCGGACTCCGGCAACATGTTCGAGAACGGCTGCTACTTGCGCCGCCAGAAGCGC/c	2/2	1	2	FACETS	0.566	0.497	0.639	0.566	0.497	0.639	SUBCLONAL	1	TRUE	1	0.558669162283277	2		502	481	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780690	56780690	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs755849719	NA	P-0027256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	265	457	0	ENST00000337432.4:c.705G>T	p.Lys235Asn	p.K235N	ENST00000337432	NM_058216.2	235	aaG/aaT	4/9	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.558669162283277	2		457	943	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128305355	128305355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1204536063	NA	P-0027256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	295	610	1	ENST00000265960.3:c.941G>A	p.Gly314Glu	p.G314E	ENST00000265960	NM_001006617.1	314	gGa/gAa	7/12	1	2	FACETS	0.921	0.867	0.976	0.921	0.867	0.976	CLONAL	1	TRUE	1	0.558669162283277	2		611	1147	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692859	89692859	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	19	164	0	ENST00000371953.3:c.343del	p.Asp115MetfsTer19	p.D115Mfs*19	ENST00000371953	NM_000314.4	115	Gat/at	5/9	1	2	FACETS	0.785	0.596	1	0.785	0.596	1	CLONAL	1	TRUE	1	0.18	2		164	269	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061192	38061192	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs879940115	NA	P-0027272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	32	367	0	ENST00000250448.2:c.797T>A	p.Phe266Tyr	p.F266Y	ENST00000250448	NM_004496.3	266	tTc/tAc	2/2	1	2	FACETS	0.61	0.494	0.742	0.61	0.494	0.742	SUBCLONAL	1	TRUE	1	0.18	2		367	583	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821594	72821596	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	rs374416547	NA	P-0027276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	11	93	0	ENST00000268489.5:c.10579_10581del	p.Gly3527del	p.G3527del	ENST00000268489	NM_006885.3	3527	GGC/-	10/10	0.480754596922042	2	FACETS	0.358	0.248	0.492	0.179	0.124	0.246	SUBCLONAL	1	TRUE	0	0.480754596922042	2		93	128	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829040	128829042	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	rs570242755	NA	P-0027276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	10	40	0	ENST00000249373.3:c.67_69del	p.Leu23del	p.L23del	ENST00000249373	NM_005631.4	16	ggGCTg/ggg	1/12	0.311405716357423	4	FACETS	0.56	0.382	0.78	0.28	0.191	0.39	SUBCLONAL	1	TRUE	2	0.480754596922042	4		40	110	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188322	10188322	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0027339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	58	465	0	ENST00000256474.2:c.463+2T>A		p.X155_splice	ENST00000256474	NM_000551.3	155			0.275528782523107	1	FACETS	0.637	0.547	0.735	0.637	0.547	0.735	SUBCLONAL	1	TRUE	0	0.275528782523107	1		465	570	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436430	52436431	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	102	519	0	ENST00000460680.1:c.2063dup	p.Ala689GlyfsTer28	p.A689Gfs*28	ENST00000460680	NM_004656.3	688	ctg/ctTg	17/17	0.275528782523107	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.275528782523107	1		519	600	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0027394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	53	1231	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.904	0.768	1	0.904	0.768	1	CLONAL	1	TRUE	1	0.12	2		1231	977	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0027394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	39	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.0893913841056879	3	FACETS	1	0.933	1	0.638	0.528	0.761	CLONAL	1	TRUE	1	0.12	3		436	540	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40993283	40993283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1428987216	NA	P-0027394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	27	570	1	ENST00000267868.3:c.109G>A	p.Asp37Asn	p.D37N	ENST00000267868	NM_002875.4	37	Gat/Aat	3/10	1	2	FACETS	0.957	0.761	1	0.957	0.761	1	CLONAL	1	TRUE	1	0.12	2		571	470	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440652	56440652	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	59	727	0	ENST00000407977.2:c.566del	p.Lys189ArgfsTer14	p.K189Rfs*14	ENST00000407977		189	aAg/ag	5/10	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.12	2		727	835	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0027548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	314	663	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.961456017615976	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.961456017615976	2		664	321	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948100	178948100	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	174	197	0	ENST00000263967.3:c.2872C>A	p.Gln958Lys	p.Q958K	ENST00000263967	NM_006218.2	958	Cag/Aag	20/21	0.813228617889024	4	FACETS	1	0.99	1			1	CLONAL	1	TRUE	NA	0.961456017615976	4		197	498	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275358	115275358	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	160	474	1	ENST00000438362.2:c.1055C>T	p.Ser352Phe	p.S352F	ENST00000438362	NM_001242891.1	352	tCc/tTc	10/20	0.471820616680862	1	FACETS	0.309	0.285	0.334	0.309	0.285	0.334	INDETERMINATE	1	TRUE	0	0.961456017615976	1		475	559	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626681	28626681	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0027548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	88	299	0	ENST00000241453.7:c.614+1G>T		p.X205_splice	ENST00000241453	NM_004119.2	205			0.552700335771487	6	FACETS	0.591	0.522	0.664			1	INDETERMINATE	1	TRUE	NA	0.961456017615976	6		299	906	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292393	15292393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	14	519	0	ENST00000263388.2:c.2786G>A	p.Ser929Asn	p.S929N	ENST00000263388	NM_000435.2	929	aGc/aAc	17/33	0.506388539483422	1	FACETS	0.059	0.042	0.08	0.059	0.042	0.08	INDETERMINATE	1	TRUE	0	0.961456017615976	1		519	255	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441075	149441075	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	220	594	2	ENST00000286301.3:c.1837G>T	p.Val613Leu	p.V613L	ENST00000286301	NM_005211.3	613	Gtg/Ttg	13/22	1	2	FACETS	0.98	0.923	1	0.98	0.923	1	CLONAL	1	TRUE	1	0.961456017615976	2		596	467	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851931	128851931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749061719	NA	P-0027548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	293	536	0	ENST00000249373.3:c.2003G>A	p.Arg668His	p.R668H	ENST00000249373	NM_005631.4	668	cGc/cAc	12/12	0.665459210034867	3	FACETS	0.88	0.839	0.92	0.88	0.839	0.92	CLONAL	2	TRUE	1	0.961456017615976	3		536	513	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0027632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	220	294	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.354934264184281	3	FACETS	0.98	0.915	1	0.98	0.915	1	CLONAL	2	TRUE	1	0.354934264184281	3		294	745	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0027632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	190	979	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.354934264184281	1	FACETS	0.926	0.856	0.999	0.926	0.856	0.999	CLONAL	1	TRUE	0	0.354934264184281	1		979	951	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0027632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	166	734	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	NA	2	FACETS	0.888	0.815	0.965			1	INDETERMINATE	1	TRUE	NA	0.354934264184281	2		734	1053	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115850	8115850	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1268	186	827	0	ENST00000346208.3:c.1196A>T	p.His399Leu	p.H399L	ENST00000346208		399	cAc/cTc	6/6	0.341038611749364	3	FACETS	0.849	0.781	0.919	0.424	0.39	0.46	CLONAL	1	TRUE	1	0.354934264184281	3		827	1454	SUCCESS
RET	5979	MSKCC	GRCh37	10	43614990	43614990	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	156	651	0	ENST00000355710.3:c.2404C>G	p.Leu802Val	p.L802V	ENST00000355710	NM_020975.4	802	Ctc/Gtc	14/20	NA	2	FACETS	0.829	0.758	0.904			1	INDETERMINATE	1	TRUE	NA	0.354934264184281	2		651	1060	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729947	30729948	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0027632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	346	549	0	ENST00000295754.5:c.1468_1469insC	p.Asn490ThrfsTer26	p.N490Tfs*26	ENST00000295754	NM_003242.5	490	aac/aCac	6/7	NA	2	FACETS	0.958	0.908	1			1	INDETERMINATE	2	TRUE	NA	0.354934264184281	2		549	1018	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842705	68842705	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	169	708	1	ENST00000261769.5:c.641T>A	p.Leu214Gln	p.L214Q	ENST00000261769	NM_004360.3	214	cTg/cAg	5/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.3	2		709	926	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578369	7578369	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0027809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	74	611	0	ENST00000269305.4:c.559+2T>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			1	2	FACETS	0.803	0.704	0.911	0.803	0.704	0.911	CLONAL	1	TRUE	1	0.3	2		611	614	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	80	570	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	0.236850716582546	2		570	622	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0027830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	88	525	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.236850716582546	1	FACETS	0.952	0.844	1	0.952	0.844	1	CLONAL	1	TRUE	0	0.236850716582546	1		525	688	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765567	41765567	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	94	507	1	ENST00000301178.4:c.2443G>A	p.Glu815Lys	p.E815K	ENST00000301178	NM_021913.4	815	Gag/Aag	20/20	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.236850716582546	2		508	759	SUCCESS
ATM	472	MSKCC	GRCh37	11	108214065	108214074	+	frameshift_variant	Frame_Shift_Del	DEL	TTTCAGTGCC	TTTCAGTGCC	-	rs786202800	NA	P-0027831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	240	241	0	ENST00000278616.4:c.8395_8404del	p.Phe2799LysfsTer4	p.F2799Kfs*4	ENST00000278616	NM_000051.3	2795	gaTTTCAGTGCC/ga	57/63	0.887888066273923	2	FACETS	0.866	0.833	0.898	0.866	0.833	0.898	CLONAL	2	TRUE	0	0.887888066273923	2		241	312	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29497003	29497003	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397514641	NA	P-0027831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	256	217	0	ENST00000356175.3:c.574C>T	p.Arg192Ter	p.R192*	ENST00000356175	NM_000267.3	192	Cga/Tga	5/57	0.887888066273923	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.887888066273923	2		217	283	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061227	38061235	+	inframe_deletion	In_Frame_Del	DEL	GAACATGTT	GAACATGTT	-	novel	NA	P-0028000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	39	562	0	ENST00000250448.2:c.754_762del	p.Asn252_Phe254del	p.N252_F254del	ENST00000250448	NM_004496.3	252	AACATGTTC/-	2/2	1	2	FACETS	0.623	0.516	0.743	0.623	0.516	0.743	SUBCLONAL	1	TRUE	1	0.22	2		562	569	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527485	157527485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569199026	NA	P-0028000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	57	644	0	ENST00000346085.5:c.5210G>A	p.Cys1737Tyr	p.C1737Y	ENST00000346085	NM_020732.3	1737	tGt/tAt	20/20	1	2	FACETS	0.89	0.764	1	0.89	0.764	1	CLONAL	1	TRUE	1	0.22	2		644	582	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0028032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	40	525	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.3	2	FACETS	0.557	0.461	0.665			1	SUBCLONAL	1	TRUE	NA	0.16	2		525	897	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680730	88680730	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	44	598	0	ENST00000360948.2:c.527A>T	p.Glu176Val	p.E176V	ENST00000360948	NM_001012338.2	176	gAg/gTg	6/19	1	2	FACETS	0.667	0.558	0.79	0.667	0.558	0.79	SUBCLONAL	1	TRUE	1	0.16	2		598	824	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553366	41553366	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	47	500	0	ENST00000263253.7:c.3455A>T	p.Glu1152Val	p.E1152V	ENST00000263253	NM_001429.3	1152	gAa/gTa	18/31	1	2	FACETS	0.746	0.627	0.877	0.746	0.627	0.877	SUBCLONAL	1	TRUE	1	0.16	2		500	788	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574002	7574002	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	366	659	0	ENST00000269305.4:c.1025del	p.Arg342GlnfsTer3	p.R342Qfs*3	ENST00000269305	NM_001126112.2	342	cGa/ca	10/11	0.684923016203437	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.684923016203437	1		659	657	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919244	48919245	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs869041987	NA	P-0028250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	86	188	0	ENST00000267163.4:c.412dup	p.Ile138AsnfsTer2	p.I138Nfs*2	ENST00000267163	NM_000321.2	137	gaa/gAaa	4/27	0.684923016203437	3	FACETS	0.824	0.733	0.92			1	CLONAL	1	TRUE	NA	0.684923016203437	3		188	409	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319047	62319047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369940581	NA	P-0028250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1331	333	696	0	ENST00000360203.5:c.1405C>T	p.Arg469Cys	p.R469C	ENST00000360203	NM_001283009.1	469	Cgc/Tgc	17/35	0.684923016203437	4	FACETS	0.985	0.928	1	0.492	0.464	0.522	CLONAL	1	TRUE	2	0.684923016203437	4		696	1664	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940531	31940531	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	266	452	0	ENST00000375333.2:c.564G>C	p.Gln188His	p.Q188H	ENST00000375333	NM_032454.1	188	caG/caC	3/8	0.673483939841819	3	FACETS	1	0.967	1	0.523	0.491	0.556	CLONAL	1	TRUE	1	0.684923016203437	3		452	997	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969918	161969918	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1554274861	NA	P-0028250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	599	499	0	ENST00000366898.1:c.1051A>C	p.Thr351Pro	p.T351P	ENST00000366898	NM_004562.2	351	Acc/Ccc	9/12	0.670231380477011	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	0	0.684923016203437	3		499	781	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	255	607	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.942	0.887	0.997	1	0.995	1	CLONAL	2	TRUE	1	0.405952245708046	2		613	667	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	257	530	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.405952245708046	2		534	1159	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	147	466	2	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.927	0.848	1	0.927	0.848	1	CLONAL	1	TRUE	1	0.405952245708046	2		468	781	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	203	643	4	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.405952245708046	2		647	904	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210893	36210893	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	190	810	4	ENST00000222270.7:c.649del	p.Arg217GlyfsTer22	p.R217Gfs*22	ENST00000222270	NM_014727.1	215	aCc/ac	3/37	1	2	FACETS	0.93	0.86	1	0.93	0.86	1	CLONAL	1	TRUE	1	0.405952245708046	2		814	1006	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	86	383	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.747	0.662	0.838	0.747	0.662	0.838	SUBCLONAL	1	TRUE	1	0.405952245708046	2		383	567	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261555	142261555	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	153	490	3	ENST00000350721.4:c.3402del	p.Phe1134LeufsTer6	p.F1134Lfs*6	ENST00000350721	NM_001184.3	1134	ttT/tt	17/47	1	2	FACETS	0.974	0.892	1	0.974	0.892	1	CLONAL	1	TRUE	1	0.405952245708046	2		493	774	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	198	757	0	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.962	0.891	1	0.962	0.891	1	CLONAL	1	TRUE	1	0.405952245708046	2		757	1014	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	119	634	0	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	0.582	0.524	0.643	0.582	0.524	0.643	SUBCLONAL	1	TRUE	1	0.405952245708046	2		634	1008	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300383	11300383	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	148	424	0	ENST00000361445.4:c.1763C>T	p.Thr588Met	p.T588M	ENST00000361445	NM_004958.3	588	aCg/aTg	11/58	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.405952245708046	2		424	713	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300386	11300386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767105252	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	153	416	0	ENST00000361445.4:c.1760G>A	p.Arg587Gln	p.R587Q	ENST00000361445	NM_004958.3	587	cGa/cAa	11/58	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.405952245708046	2		416	705	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261683	16261683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149575630	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	203	639	0	ENST00000375759.3:c.8948C>T	p.Thr2983Met	p.T2983M	ENST00000375759	NM_015001.2	2983	aCg/aTg	11/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.405952245708046	2		639	857	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106930	27106930	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	161	551	0	ENST00000324856.7:c.6541G>T	p.Ala2181Ser	p.A2181S	ENST00000324856	NM_006015.4	2181	Gca/Tca	20/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.405952245708046	2		551	706	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739353	46739353	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	144	485	0	ENST00000371975.4:c.1544A>G	p.Lys515Arg	p.K515R	ENST00000371975	NM_003579.3	515	aAa/aGa	14/18	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.405952245708046	2		485	694	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	145	247	1	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	1	2	FACETS	0.969	0.886	1	0.969	0.886	1	CLONAL	1	TRUE	1	0.405952245708046	2		248	737	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058499	72058499	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	132	343	2	ENST00000357731.5:c.940+1G>A		p.X314_splice	ENST00000357731	NM_173808.2	314			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.405952245708046	2		345	561	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166515	118166515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376774297	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	118	444	0	ENST00000369448.3:c.1025C>T	p.Ala342Val	p.A342V	ENST00000369448	NM_017709.3	342	gCg/gTg	2/2	1	2	FACETS	0.936	0.847	1	0.936	0.847	1	CLONAL	1	TRUE	1	0.405952245708046	2		444	621	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653456	206653456	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	110	465	0	ENST00000367120.3:c.1340T>G	p.Met447Arg	p.M447R	ENST00000367120	NM_014002.3	447	aTg/aGg	12/22	1	2	FACETS	0.877	0.79	0.969	0.877	0.79	0.969	CLONAL	1	TRUE	1	0.405952245708046	2		465	618	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567661	226567661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs183533639	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	158	453	2	ENST00000366794.5:c.1505C>T	p.Ala502Val	p.A502V	ENST00000366794	NM_001618.3	502	gCg/gTg	10/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.405952245708046	2		455	687	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724631	112724631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1333953583	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	194	560	1	ENST00000369452.4:c.515G>A	p.Arg172Gln	p.R172Q	ENST00000369452	NM_007373.3	172	cGg/cAg	2/9	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.405952245708046	2		561	902	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114917780	114917780	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	130	370	0	ENST00000543371.1:c.1270G>A	p.Gly424Arg	p.G424R	ENST00000543371	NM_001198531.1	424	Gga/Aga	12/14	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.405952245708046	2		370	555	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942195	71942195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372927367	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	224	725	0	ENST00000298229.2:c.1459G>A	p.Gly487Arg	p.G487R	ENST00000298229	NM_001567.3	487	Ggg/Agg	12/28	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.405952245708046	2		725	1014	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981861	101981863	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	192	722	0	ENST00000282441.5:c.286_288del	p.Phe96del	p.F96del	ENST00000282441	NM_001130145.2	94	tcCTTc/tcc	1/9	1	2	FACETS	0.981	0.908	1	0.981	0.908	1	CLONAL	1	TRUE	1	0.405952245708046	2		722	964	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235944	108235944	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	145	442	0	ENST00000278616.4:c.8986A>G	p.Ser2996Gly	p.S2996G	ENST00000278616	NM_000051.3	2996	Agt/Ggt	62/63	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.405952245708046	2		442	707	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435202	18435202	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	120	387	0	ENST00000266497.5:c.192del	p.Phe64LeufsTer15	p.F64Lfs*15	ENST00000266497		63	Ttt/tt	1/31	1	2	FACETS	0.938	0.849	1	0.938	0.849	1	CLONAL	1	TRUE	1	0.405952245708046	2		387	630	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434384	49434384	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866926540	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	209	758	1	ENST00000301067.7:c.7169C>T	p.Pro2390Leu	p.P2390L	ENST00000301067	NM_003482.3	2390	cCg/cTg	31/54	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.405952245708046	2		759	936	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438529	49438529	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1020821794	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	46	645	0	ENST00000301067.7:c.4961A>G	p.Glu1654Gly	p.E1654G	ENST00000301067	NM_003482.3	1654	gAa/gGa	19/54	1	2	FACETS	0.27	0.227	0.319	0.27	0.227	0.319	SUBCLONAL	1	TRUE	1	0.405952245708046	2		645	838	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443787	49443787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1267389918	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	235	829	1	ENST00000301067.7:c.3584C>T	p.Thr1195Ile	p.T1195I	ENST00000301067	NM_003482.3	1195	aCa/aTa	11/54	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.405952245708046	2		830	1126	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481899	56481899	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	199	694	0	ENST00000267101.3:c.827C>A	p.Pro276His	p.P276H	ENST00000267101	NM_001982.3	276	cCc/cAc	7/28	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.405952245708046	2		694	974	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489582	56489582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56387488	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	138	362	0	ENST00000267101.3:c.2047C>T	p.Arg683Trp	p.R683W	ENST00000267101	NM_001982.3	683	Cgg/Tgg	17/28	1	2	FACETS	0.993	0.905	1	0.993	0.905	1	CLONAL	1	TRUE	1	0.405952245708046	2		362	685	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	228	828	0	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.405952245708046	2		828	1067	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	206	704	10	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	0.405952245708046	2		714	954	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959121	28959121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137937570	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	235	383	0	ENST00000282397.4:c.2017G>A	p.Ala673Thr	p.A673T	ENST00000282397	NM_002019.4	673	Gcc/Acc	14/30	0.405952245708046	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.405952245708046	3		383	660	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911359	32911359	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs761350030	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	359	553	0	ENST00000380152.3:c.2867A>G	p.Lys956Arg	p.K956R	ENST00000380152		956	aAa/aGa	11/27	0.405952245708046	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.405952245708046	3		553	1043	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913965	32913965	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	352	621	0	ENST00000380152.3:c.5473G>A	p.Ala1825Thr	p.A1825T	ENST00000380152		1825	Gca/Aca	11/27	0.405952245708046	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.405952245708046	3		621	992	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240069	41240069	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1482440466	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	12	30	0	ENST00000379561.5:c.281T>C	p.Val94Ala	p.V94A	ENST00000379561	NM_002015.3	94	gTg/gCg	1/3	0.405952245708046	3	FACETS	1	0.859	1	0.684	0.495	0.901	CLONAL	1	TRUE	1	0.405952245708046	3		30	52	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436506	110436506	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1225	75	782	1	ENST00000375856.3:c.1895A>G	p.Tyr632Cys	p.Y632C	ENST00000375856	NM_003749.2	632	tAc/tGc	1/2	0.405952245708046	3	FACETS	0.342	0.298	0.389	0.171	0.149	0.195	SUBCLONAL	1	TRUE	1	0.405952245708046	3		783	1300	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30102151	30102151	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1439477100	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	104	475	0	ENST00000331968.5:c.1316G>A	p.Arg439Gln	p.R439Q	ENST00000331968	NM_002742.2	439	cGg/cAg	9/18	1	2	FACETS	0.753	0.675	0.836	0.753	0.675	0.836	SUBCLONAL	1	TRUE	1	0.405952245708046	2		475	680	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41962080	41962080	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	143	462	0	ENST00000219905.7:c.988C>T	p.Arg330Ter	p.R330*	ENST00000219905	NM_001164273.1	330	Cga/Tga	2/24	1	2	FACETS	0.968	0.884	1	0.968	0.884	1	CLONAL	1	TRUE	1	0.405952245708046	2		462	728	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	214	920	8	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.405952245708046	2		928	843	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707837	43707837	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775609565	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	224	810	1	ENST00000382044.4:c.5044C>T	p.Arg1682Trp	p.R1682W	ENST00000382044	NM_001141980.1	1682	Cgg/Tgg	23/28	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.405952245708046	2		811	1017	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749148	43749148	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758857922	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	244	791	0	ENST00000382044.4:c.1658C>T	p.Thr553Met	p.T553M	ENST00000382044	NM_001141980.1	553	aCg/aTg	12/28	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.405952245708046	2		791	1165	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690572	88690572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs546426782	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	147	509	0	ENST00000360948.2:c.458G>A	p.Arg153Gln	p.R153Q	ENST00000360948	NM_001012338.2	153	cGg/cAg	5/19	1	2	FACETS	0.945	0.864	1	0.945	0.864	1	CLONAL	1	TRUE	1	0.405952245708046	2		509	766	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310208	91310208	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs747341586	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	154	304	1	ENST00000355112.3:c.2268del	p.Asp757ThrfsTer4	p.D757Tfs*4	ENST00000355112	NM_000057.2	754	tcA/tc	10/22	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.405952245708046	2		305	727	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223325	2223325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	205	798	1	ENST00000326181.6:c.937G>A	p.Ala313Thr	p.A313T	ENST00000326181	NM_032271.2	313	Gcc/Acc	10/21	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.405952245708046	2		799	1002	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632774	23632774	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	131	524	1	ENST00000261584.4:c.3022C>T	p.Pro1008Ser	p.P1008S	ENST00000261584	NM_024675.3	1008	Ccc/Tcc	10/13	1	2	FACETS	0.877	0.797	0.961	0.877	0.797	0.961	CLONAL	1	TRUE	1	0.405952245708046	2		525	736	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783665	50783665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374624194	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	185	620	0	ENST00000398568.2:c.56G>A	p.Arg19Gln	p.R19Q	ENST00000398568	NM_001042412.1	19	cGg/cAg	3/18	1	2	FACETS	0.993	0.917	1	0.993	0.917	1	CLONAL	1	TRUE	1	0.405952245708046	2		620	918	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56855488	56855488	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567027753	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	101	373	0	ENST00000308159.5:c.637G>A	p.Ala213Thr	p.A213T	ENST00000308159	NM_014669.4	213	Gca/Aca	7/22	1	2	FACETS	0.803	0.719	0.892	0.803	0.719	0.892	CLONAL	1	TRUE	1	0.405952245708046	2		373	620	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821875	72821875	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	106	399	1	ENST00000268489.5:c.10300del	p.Leu3434SerfsTer51	p.L3434Sfs*51	ENST00000268489	NM_006885.3	3434	Ctc/tc	10/10	1	2	FACETS	0.946	0.851	1	0.946	0.851	1	CLONAL	1	TRUE	1	0.405952245708046	2		400	552	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822480	72822480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs963874989	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	209	816	4	ENST00000268489.5:c.9695G>A	p.Arg3232His	p.R3232H	ENST00000268489	NM_006885.3	3232	cGc/cAc	10/10	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.405952245708046	2		820	1008	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923807	72923807	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766702555	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	148	582	0	ENST00000268489.5:c.3271G>A	p.Val1091Ile	p.V1091I	ENST00000268489	NM_006885.3	1091	Gtt/Att	4/10	1	2	FACETS	0.875	0.8	0.954	0.875	0.8	0.954	CLONAL	1	TRUE	1	0.405952245708046	2		582	833	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350121	89350122	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	214	740	0	ENST00000301030.4:c.2828_2829del	p.Glu943ValfsTer74	p.E943Vfs*74	ENST00000301030	NM_001256183.1	943	gAG/g	9/13	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.405952245708046	2		740	1046	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831345	89831346	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs878853663	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	195	646	5	ENST00000389301.3:c.2730_2731del	p.Trp911AspfsTer31	p.W911Dfs*31	ENST00000389301	NM_000135.2	910	ctCTgg/ctgg	28/43	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.405952245708046	2		651	870	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217286	7217286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	182	611	0	ENST00000380728.2:c.419G>A	p.Arg140His	p.R140H	ENST00000380728		140	cGc/cAc	6/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.405952245708046	2		611	827	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352697	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	244	724	0	ENST00000269305.4:c.587G>A	p.Arg196Gln	p.R196Q	ENST00000269305	NM_001126112.2	196	cGa/cAa	6/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.405952245708046	2		724	1017	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982817	7982817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	212	773	3	ENST00000319144.4:c.968G>A	p.Gly323Asp	p.G323D	ENST00000319144	NM_001139.2	323	gGc/gAc	8/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.405952245708046	2		776	928	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968279	15968279	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	97	353	0	ENST00000268712.3:c.5006del	p.Gly1669GlufsTer93	p.G1669Efs*93	ENST00000268712	NM_006311.3	1669	gGa/ga	34/46	1	2	FACETS	0.847	0.757	0.943	0.847	0.757	0.943	CLONAL	1	TRUE	1	0.405952245708046	2		353	564	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618380	37618380	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293588243	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	110	442	0	ENST00000447079.4:c.56G>A	p.Gly19Glu	p.G19E	ENST00000447079	NM_015083.1	19	gGa/gAa	1/14	1	2	FACETS	0.971	0.876	1	0.971	0.876	1	CLONAL	1	TRUE	1	0.405952245708046	2		442	558	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881426	37881426	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	219	689	0	ENST00000269571.5:c.2618A>G	p.Asp873Gly	p.D873G	ENST00000269571		873	gAc/gGc	21/27	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.405952245708046	2		689	1020	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884218	37884218	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	180	606	0	ENST00000269571.5:c.3694del	p.Ala1232LeufsTer70	p.A1232Lfs*70	ENST00000269571		1230	cGg/cg	27/27	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.405952245708046	2		606	871	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510589	38510589	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	181	634	0	ENST00000254066.5:c.843G>T	p.Gln281His	p.Q281H	ENST00000254066	NM_000964.3	281	caG/caT	7/9	1	2	FACETS	0.96	0.886	1	0.96	0.886	1	CLONAL	1	TRUE	1	0.405952245708046	2		634	929	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55693388	55693388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	138	702	0	ENST00000284073.2:c.595C>T	p.Arg199Trp	p.R199W	ENST00000284073	NM_138962.2	199	Cgg/Tgg	9/14	1	2	FACETS	0.596	0.541	0.654	0.596	0.541	0.654	SUBCLONAL	1	TRUE	1	0.405952245708046	2		702	1140	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439912	56439912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753641688	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	203	639	0	ENST00000407977.2:c.680G>A	p.Ser227Asn	p.S227N	ENST00000407977		227	aGc/aAc	6/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.405952245708046	2		639	930	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448280	56448280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	42	584	1	ENST00000407977.2:c.367G>A	p.Ala123Thr	p.A123T	ENST00000407977		123	Gct/Act	3/10	1	2	FACETS	0.248	0.206	0.294	0.248	0.206	0.294	SUBCLONAL	1	TRUE	1	0.405952245708046	2		585	836	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770008	56770008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758029117	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	108	388	0	ENST00000337432.4:c.4C>T	p.Arg2Cys	p.R2C	ENST00000337432	NM_058216.2	2	Cgc/Tgc	1/9	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.405952245708046	2		388	496	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007656	62007656	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs912718113	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	165	533	1	ENST00000392795.3:c.211G>A	p.Ala71Thr	p.A71T	ENST00000392795	NM_001039933.1	71	Gcc/Acc	3/6	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.405952245708046	2		534	753	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985400	60985400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	194	632	3	ENST00000333681.4:c.500C>T	p.Ser167Leu	p.S167L	ENST00000333681		167	tCg/tTg	2/3	NA	2	FACETS	1	0.948	1			1	INDETERMINATE	1	TRUE	NA	0.405952245708046	2		635	928	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615691	1615691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141432924	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	186	750	1	ENST00000344749.5:c.1580G>A	p.Arg527Gln	p.R527Q	ENST00000344749	NM_001136139.2	527	cGg/cAg	17/19	1	2	FACETS	0.95	0.877	1	0.95	0.877	1	CLONAL	1	TRUE	1	0.405952245708046	2		751	965	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226767	2226767	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	163	546	0	ENST00000398665.3:c.4247G>A	p.Arg1416His	p.R1416H	ENST00000398665	NM_032482.2	1416	cGc/cAc	27/28	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.405952245708046	2		546	760	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214592	5214592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369295620	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	187	676	0	ENST00000357368.4:c.4474C>T	p.Arg1492Trp	p.R1492W	ENST00000357368	NM_002850.3	1492	Cgg/Tgg	29/38	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.405952245708046	2		676	895	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134269	11134269	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	205	645	0	ENST00000358026.2:c.2935C>T	p.Arg979Ter	p.R979*	ENST00000358026	NM_001128849.1	979	Cga/Tga	20/36	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.405952245708046	2		645	914	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626865	14626865	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	243	718	0	ENST00000254322.2:c.910del	p.Leu304SerfsTer17	p.L304Sfs*17	ENST00000254322	NM_006145.1	304	Ctc/tc	3/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.405952245708046	2		718	1072	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311604	15311605	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	11	128	0	ENST00000263388.2:c.112dup	p.Ala38GlyfsTer37	p.A38Gfs*37	ENST00000263388	NM_000435.2	38	gct/gGct	1/33	1	2	FACETS	0.288	0.199	0.399	0.288	0.199	0.399	SUBCLONAL	1	TRUE	1	0.405952245708046	2		128	188	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965830	18965830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	166	575	0	ENST00000262803.5:c.1408G>A	p.Asp470Asn	p.D470N	ENST00000262803	NM_002911.3	470	Gac/Aac	10/24	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.405952245708046	2		575	806	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257366	19257366	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	229	721	2	ENST00000162023.5:c.767del	p.Pro256GlnfsTer?	p.P256Qfs*?	ENST00000162023		256	cCa/ca	11/13	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.405952245708046	2		723	1055	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213516	36213516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770865375	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	231	933	2	ENST00000222270.7:c.2618G>A	p.Arg873His	p.R873H	ENST00000222270	NM_014727.1	873	cGt/cAt	5/37	1	2	FACETS	0.979	0.912	1	0.979	0.912	1	CLONAL	1	TRUE	1	0.405952245708046	2		935	1162	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752723	42752723	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1410725157	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	198	741	1	ENST00000222329.4:c.1541G>A	p.Arg514His	p.R514H	ENST00000222329	NM_006494.2	514	cGt/cAt	4/4	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.405952245708046	2		742	957	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798840	42798840	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	255	772	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	0.405952245708046	2		773	1072	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	78	658	4	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	0.452	0.396	0.512	0.452	0.396	0.512	SUBCLONAL	1	TRUE	1	0.405952245708046	2		662	850	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919882	50919882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771789997	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	195	663	0	ENST00000440232.2:c.2969G>A	p.Arg990His	p.R990H	ENST00000440232	NM_002691.3	990	cGc/cAc	24/27	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.405952245708046	2		663	877	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719794	52719794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	175	607	0	ENST00000322088.6:c.1006G>A	p.Asp336Asn	p.D336N	ENST00000322088	NM_014225.5	336	Gat/Aat	9/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.405952245708046	2		607	797	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085894	16085894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398902296	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	177	601	0	ENST00000281043.3:c.1070G>A	p.Arg357His	p.R357H	ENST00000281043	NM_005378.4	357	cGt/cAt	3/3	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.405952245708046	2		601	798	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46596970	46596970	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	40	431	0	ENST00000263734.3:c.784A>G	p.Thr262Ala	p.T262A	ENST00000263734	NM_001430.4	262	Aca/Gca	7/16	1	2	FACETS	0.317	0.262	0.378	0.317	0.262	0.378	SUBCLONAL	1	TRUE	1	0.405952245708046	2		431	622	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702384	47702385	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs63751055	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	118	367	0	ENST00000233146.2:c.1983dup	p.Gln662ThrfsTer14	p.Q662Tfs*14	ENST00000233146	NM_000251.2	660	-/A	12/16	1	2	FACETS	0.989	0.895	1	0.989	0.895	1	CLONAL	1	TRUE	1	0.405952245708046	2		367	588	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920573	96920573	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs759138897	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	130	386	0	ENST00000258439.3:c.407C>T	p.Thr136Met	p.T136M	ENST00000258439	NM_001193304.2	136	aCg/aTg	3/4	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.405952245708046	2		386	555	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376085	225376085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	141	495	1	ENST00000264414.4:c.869del	p.Asn290MetfsTer21	p.N290Mfs*21	ENST00000264414	NM_003590.4	290	aAt/at	6/16	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.405952245708046	2		496	655	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661338	227661338	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	58	689	0	ENST00000305123.5:c.2117A>G	p.His706Arg	p.H706R	ENST00000305123	NM_005544.2	706	cAc/cGc	1/2	1	2	FACETS	0.3	0.257	0.348	0.3	0.257	0.348	SUBCLONAL	1	TRUE	1	0.405952245708046	2		689	952	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661604	227661605	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	190	635	0	ENST00000305123.5:c.1850dup	p.Gly618ArgfsTer57	p.G618Rfs*57	ENST00000305123	NM_005544.2	617	cca/ccCa	1/2	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.405952245708046	2		635	877	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024381	31024381	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755522655	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	259	632	1	ENST00000375687.4:c.3866G>A	p.Arg1289Gln	p.R1289Q	ENST00000375687	NM_015338.5	1289	cGg/cAg	13/13	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.405952245708046	2		633	1030	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945543	54945543	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs774552788	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	245	834	1	ENST00000312783.6:c.1027C>T	p.Arg343Trp	p.R343W	ENST00000312783	NM_198436.1	343	Cgg/Tgg	9/10	1	2	FACETS	0.917	0.855	0.98	0.917	0.855	0.98	CLONAL	1	TRUE	1	0.405952245708046	2		835	1317	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	17	486	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.106	0.079	0.14	0.106	0.079	0.14	SUBCLONAL	1	TRUE	1	0.405952245708046	2		486	787	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12629093	12629093	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	124	375	0	ENST00000251849.4:c.1414A>C	p.Asn472His	p.N472H	ENST00000251849	NM_002880.3	472	Aac/Cac	13/17	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.405952245708046	2		375	602	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165283	47165283	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	37	422	0	ENST00000409792.3:c.843del	p.Glu282LysfsTer19	p.E282Kfs*19	ENST00000409792	NM_014159.6	281	aaA/aa	3/21	1	2	FACETS	0.267	0.219	0.32	0.267	0.219	0.32	SUBCLONAL	1	TRUE	1	0.405952245708046	2		422	684	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723510	49723510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748083669	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	30	72	0	ENST00000449682.2:c.1132G>A	p.Asp378Asn	p.D378N	ENST00000449682	NM_020998.3	378	Gac/Aac	9/18	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.405952245708046	2		72	106	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437456	52437456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	54	610	0	ENST00000460680.1:c.1705G>A	p.Val569Met	p.V569M	ENST00000460680	NM_004656.3	569	Gtg/Atg	13/17	1	2	FACETS	0.331	0.282	0.385	0.331	0.282	0.385	SUBCLONAL	1	TRUE	1	0.405952245708046	2		610	804	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442054	52442054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	181	627	0	ENST00000460680.1:c.295G>A	p.Val99Met	p.V99M	ENST00000460680	NM_004656.3	99	Gtg/Atg	5/17	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.405952245708046	2		627	858	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204842	128204842	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs768767517	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	77	797	1	ENST00000341105.2:c.599del	p.Gly200ValfsTer18	p.G200Vfs*18	ENST00000341105	NM_032638.4	200	gGt/gt	3/6	1	2	FACETS	0.345	0.302	0.392	0.345	0.302	0.392	SUBCLONAL	1	TRUE	1	0.405952245708046	2		798	1100	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880957	134880957	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770406411	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	161	539	0	ENST00000398015.3:c.1520G>A	p.Arg507His	p.R507H	ENST00000398015	NM_004441.4	507	cGt/cAt	7/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.405952245708046	2		539	752	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413709	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs199713806	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	184	513	0	ENST00000289153.2:c.1811G>C	p.Arg604Pro	p.R604P	ENST00000289153	NM_006219.2	604	cGg/cCg	12/22	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.405952245708046	2		513	822	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	136	466	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.931	0.847	1	0.931	0.847	1	CLONAL	1	TRUE	1	0.405952245708046	2		466	720	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183614	185183614	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	145	442	0	ENST00000265026.3:c.1468A>G	p.Met490Val	p.M490V	ENST00000265026	NM_004721.4	490	Atg/Gtg	9/14	1	2	FACETS	0.976	0.892	1	0.976	0.892	1	CLONAL	1	TRUE	1	0.405952245708046	2		442	732	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806180	1806181	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760502257	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	64	785	1	ENST00000260795.2:c.1206dup	p.Lys403GlnfsTer93	p.K403Qfs*93	ENST00000260795		400	agc/agCc	8/17	1	2	FACETS	0.321	0.277	0.37	0.321	0.277	0.37	SUBCLONAL	1	TRUE	1	0.405952245708046	2		786	981	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535427	66535427	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1472517358	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	129	346	0	ENST00000273854.3:c.34C>T	p.Arg12Trp	p.R12W	ENST00000273854	NM_004439.5	12	Cgg/Tgg	1/18	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.405952245708046	2		346	492	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156204	106156204	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150072691	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	126	403	0	ENST00000380013.4:c.1105C>T	p.Arg369Trp	p.R369W	ENST00000380013	NM_001127208.2	369	Cgg/Tgg	3/11	1	2	FACETS	0.948	0.86	1	0.948	0.86	1	CLONAL	1	TRUE	1	0.405952245708046	2		403	655	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293440	1293440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1448835821	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	171	592	0	ENST00000310581.5:c.1561C>T	p.Arg521Cys	p.R521C	ENST00000310581	NM_198253.2	521	Cgc/Tgc	2/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.405952245708046	2		592	788	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38960057	38960057	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	25	277	0	ENST00000357387.3:c.1875T>A	p.Asp625Glu	p.D625E	ENST00000357387	NM_152756.3	625	gaT/gaA	21/38	1	2	FACETS	0.284	0.224	0.355	0.284	0.224	0.355	SUBCLONAL	1	TRUE	1	0.405952245708046	2		277	433	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155540	56155540	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	123	401	0	ENST00000399503.3:c.634-2A>G		p.X212_splice	ENST00000399503	NM_005921.1	212			1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.405952245708046	2		401	584	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753013	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	128	428	0	ENST00000274289.3:c.1003_1004del	p.Leu335AlafsTer11	p.L335Afs*11	ENST00000274289	NM_006622.3	335	TTg/g	7/14	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.405952245708046	2		428	623	SUCCESS
APC	324	MSKCC	GRCh37	5	112170747	112170747	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1561568632	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	181	558	2	ENST00000257430.4:c.1847del	p.Leu616TrpfsTer14	p.L616Wfs*14	ENST00000257430	NM_000038.5	615	Ttt/tt	15/16	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.405952245708046	2		560	888	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977896	131977896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367683141	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	164	428	1	ENST00000265335.6:c.3779G>A	p.Arg1260His	p.R1260H	ENST00000265335		1260	cGt/cAt	25/25	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.405952245708046	2		429	689	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520184	176520184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770529969	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	74	814	1	ENST00000292408.4:c.1103C>T	p.Thr368Met	p.T368M	ENST00000292408	NM_213647.1	368	aCg/aTg	9/18	1	2	FACETS	0.332	0.289	0.378	0.332	0.289	0.378	SUBCLONAL	1	TRUE	1	0.405952245708046	2		815	1099	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	46	339	0	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.42	0.354	0.494	0.42	0.354	0.494	SUBCLONAL	1	TRUE	1	0.405952245708046	2		339	539	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	199	649	4	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.405952245708046	2		653	926	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056503	26056503	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs141424312	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	75	259	0	ENST00000343677.2:c.154A>G	p.Lys52Glu	p.K52E	ENST00000343677	NM_005319.3	52	Aaa/Gaa	1/1	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.405952245708046	2		259	335	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163246	32163246	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1179	81	957	0	ENST00000375023.3:c.5980C>T	p.Pro1994Ser	p.P1994S	ENST00000375023	NM_004557.3	1994	Ccc/Tcc	30/30	1	2	FACETS	0.317	0.278	0.359	0.317	0.278	0.359	SUBCLONAL	1	TRUE	1	0.405952245708046	2		957	1260	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32191695	32191695	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	150	682	0	ENST00000375023.3:c.11del	p.Pro4LeufsTer39	p.P4Lfs*39	ENST00000375023	NM_004557.3	4	cCt/ct	1/30	1	2	FACETS	0.777	0.71	0.848	0.777	0.71	0.848	SUBCLONAL	1	TRUE	1	0.405952245708046	2		682	951	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679148	117679148	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1459800881	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	42	386	0	ENST00000368508.3:c.3673G>A	p.Asp1225Asn	p.D1225N	ENST00000368508	NM_002944.2	1225	Gat/Aat	24/43	1	2	FACETS	0.3	0.249	0.356	0.3	0.249	0.356	SUBCLONAL	1	TRUE	1	0.405952245708046	2		386	690	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714467	117714468	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	37	364	0	ENST00000368508.3:c.1181dup	p.Leu394PhefsTer16	p.L394Ffs*16	ENST00000368508	NM_002944.2	394	tta/ttTa	11/43	1	2	FACETS	0.299	0.246	0.359	0.299	0.246	0.359	SUBCLONAL	1	TRUE	1	0.405952245708046	2		364	609	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997780	149997780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148506316	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	191	520	0	ENST00000253339.5:c.2687G>A	p.Arg896Gln	p.R896Q	ENST00000253339		896	cGg/cAg	5/7	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.405952245708046	2		520	841	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129241	152129241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	210	678	1	ENST00000206249.3:c.194C>T	p.Ala65Val	p.A65V	ENST00000206249	NM_000125.3	65	gCg/gTg	1/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.405952245708046	2		679	875	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962930	2962930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1349831751	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	474	885	1	ENST00000396946.4:c.1978C>T	p.Arg660Trp	p.R660W	ENST00000396946	NM_032415.4	660	Cgg/Tgg	16/25	0.405952245708046	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.405952245708046	3		886	1315	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978405	2978405	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370704955	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	460	723	2	ENST00000396946.4:c.925C>T	p.Arg309Cys	p.R309C	ENST00000396946	NM_032415.4	309	Cgc/Tgc	7/25	0.405952245708046	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.405952245708046	3		725	1251	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13949275	13949275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	27	373	0	ENST00000405192.2:c.853G>A	p.Val285Ile	p.V285I	ENST00000405192	NM_001163147.1	285	Gtc/Atc	9/12	0.405952245708046	3	FACETS	0.311	0.246	0.385	0.155	0.123	0.193	SUBCLONAL	1	TRUE	1	0.405952245708046	3		373	515	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	203	334	1	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	0.405952245708046	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	1	0.405952245708046	3		335	586	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214316	55214316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1562756942	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	217	609	0	ENST00000275493.2:c.442G>A	p.Val148Met	p.V148M	ENST00000275493	NM_005228.3	148	Gtg/Atg	4/28	0.405952245708046	3	FACETS	1	0.988	1	0.641	0.596	0.688	CLONAL	1	TRUE	1	0.405952245708046	3		609	1003	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917611	151917611	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs938655561	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	318	629	0	ENST00000262189.6:c.3709C>T	p.Arg1237Ter	p.R1237*	ENST00000262189	NM_170606.2	1237	Cga/Tga	23/59	0.405952245708046	3	FACETS	0.927	0.876	0.978	0.927	0.876	0.978	CLONAL	2	TRUE	1	0.405952245708046	3		629	1017	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859878	117859878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780692465	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	119	316	0	ENST00000297338.2:c.1757G>A	p.Arg586Gln	p.R586Q	ENST00000297338	NM_006265.2	586	cGa/cAa	14/14	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.405952245708046	2		316	515	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740573	145740573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573164516	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	157	720	0	ENST00000428558.2:c.1444C>T	p.Arg482Cys	p.R482C	ENST00000428558	NM_004260.3	482	Cgc/Tgc	8/22	1	2	FACETS	0.776	0.71	0.845	0.776	0.71	0.845	SUBCLONAL	1	TRUE	1	0.405952245708046	2		720	997	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549526	5549526	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	250	833	1	ENST00000397747.3:c.557del	p.Pro186LeufsTer14	p.P186Lfs*14	ENST00000397747	NM_025239.3	185	Ccc/cc	4/7	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.405952245708046	2		834	1208	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158026	27158026	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	203	673	1	ENST00000380036.4:c.255del	p.Val86LeufsTer31	p.V86Lfs*31	ENST00000380036	NM_000459.3	84	Aaa/aa	2/23	1	2	FACETS	0.986	0.914	1	0.986	0.914	1	CLONAL	1	TRUE	1	0.405952245708046	2		674	1014	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169625	27169625	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs775884054	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	174	609	0	ENST00000380036.4:c.626G>A	p.Arg209Gln	p.R209Q	ENST00000380036	NM_000459.3	209	cGg/cAg	4/23	1	2	FACETS	0.883	0.812	0.956	0.883	0.812	0.956	CLONAL	1	TRUE	1	0.405952245708046	2		609	971	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215833	98215833	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147025073	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	183	616	1	ENST00000331920.6:c.3376G>A	p.Val1126Ile	p.V1126I	ENST00000331920	NM_000264.3	1126	Gtc/Atc	20/24	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.405952245708046	2		617	890	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900239	101900239	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564161544	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	140	388	0	ENST00000374994.4:c.673C>T	p.Arg225Trp	p.R225W	ENST00000374994	NM_004612.2	225	Cgg/Tgg	4/9	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.405952245708046	2		388	629	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412735	139412735	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564199987	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	46	641	0	ENST00000277541.6:c.1109G>A	p.Cys370Tyr	p.C370Y	ENST00000277541	NM_017617.3	370	tGc/tAc	7/34	1	2	FACETS	0.297	0.249	0.35	0.297	0.249	0.35	SUBCLONAL	1	TRUE	1	0.405952245708046	2		641	763	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039312	47039312	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	95	388	0	ENST00000377604.3:c.935C>A	p.Thr312Asn	p.T312N	ENST00000377604	NM_001204468.1	312	aCc/aAc	10/24	1	1	FACETS	0.746	0.667	0.83	0.746	0.667	0.83	SUBCLONAL	1	TRUE	0	0.405952245708046	1		388	500	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410960	63410960	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	193	345	0	ENST00000330258.3:c.2207del	p.Asn736IlefsTer32	p.N736Ifs*32	ENST00000330258	NM_152424.3	736	aAt/at	2/2	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.405952245708046	1		345	526	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413070	63413070	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	249	206	0	ENST00000330258.3:c.97G>A	p.Ala33Thr	p.A33T	ENST00000330258	NM_152424.3	33	Gca/Aca	2/2	1	1	FACETS	0.864	0.815	0.913	1	0.995	1	CLONAL	2	TRUE	0	0.405952245708046	1		206	566	SUCCESS
AR	367	MSKCC	GRCh37	X	66765820	66765820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1250886649	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	295	426	0	ENST00000374690.3:c.832G>A	p.Ala278Thr	p.A278T	ENST00000374690	NM_000044.3	278	Gct/Act	1/8	1	1	FACETS	0.882	0.836	0.927	1	0.995	1	CLONAL	2	TRUE	0	0.405952245708046	1		426	657	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279861	46279866	+	inframe_deletion	In_Frame_Del	DEL	CAGCAA	CAGCAA	-	rs748517056	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	67	596	0	ENST00000371998.3:c.3810_3815del	p.Gln1275_Gln1276del	p.Q1275_Q1276del	ENST00000371998		1263	CAGCAA/-	20/23	1	2	FACETS	0.43	0.373	0.492	0.43	0.373	0.492	SUBCLONAL	1	TRUE	1	0.405952245708046	2		596	767	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570840	226570841	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	C	novel	NA	P-0028266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	156	543	0	ENST00000366794.5:c.1055_1056delinsG	p.Lys352SerfsTer29	p.K352Sfs*29	ENST00000366794	NM_001618.3	352	aAA/aG	8/23	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.405952245708046	2		543	754	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0028312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	74	796	1	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	1	2	FACETS	0.807	0.705	0.917	0.807	0.705	0.917	CLONAL	1	TRUE	1	0.22	2		797	834	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0028312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	11	451	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.211	0.145	0.294	0.211	0.145	0.294	SUBCLONAL	1	TRUE	1	0.22	2		451	474	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913283	NA	P-0028312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	64	481	0	ENST00000263967.3:c.3129G>T	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atT	21/21	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.22	2		481	429	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	55	644	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	1	2	FACETS	0.683	0.583	0.793	0.683	0.583	0.793	SUBCLONAL	1	TRUE	1	0.22	2		644	732	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0028331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	530	742	1	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	2	TRUE	NA	0.700531251514503	2		743	744	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426106	47426106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	188	699	2	ENST00000377045.4:c.626G>A	p.Arg209His	p.R209H	ENST00000377045	NM_001654.4	209	cGc/cAc	7/16	0.615316482386337	4	FACETS	0.876	0.809	0.946	0.438	0.404	0.473	CLONAL	1	TRUE	2	0.700531251514503	4		701	1042	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282703	1282703	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1272053273	NA	P-0028331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	166	597	0	ENST00000310581.5:c.1610G>A	p.Arg537His	p.R537H	ENST00000310581	NM_198253.2	537	cGt/cAt	3/16	0.686534897856761	3	FACETS	0.844	0.777	0.914	0.422	0.388	0.457	CLONAL	1	TRUE	1	0.700531251514503	3		597	758	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916834	48916834	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	175	448	0	ENST00000267163.4:c.368del	p.Asn123ThrfsTer2	p.N123Tfs*2	ENST00000267163	NM_000321.2	122	Aaa/aa	3/27	0.698703042393788	2	FACETS	0.976	0.926	1	0.976	0.926	1	CLONAL	2	TRUE	0	0.700531251514503	2		448	256	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938156	76938190	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTTGATTATCCATTCCTTTTTTGCTGTGTTTCT	CCCTTGATTATCCATTCCTTTTTTGCTGTGTTTCT	-	novel	NA	P-0028331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	212	627	0	ENST00000373344.5:c.2558_2592del	p.Glu853AlafsTer13	p.E853Afs*13	ENST00000373344	NM_000489.3	853	gAGAAACACAGCAAAAAAGGAATGGATAATCAAGGG/g	9/35	0.649164584646527	3	FACETS	0.764	0.716	0.813			1	SUBCLONAL	2	TRUE	NA	0.700531251514503	3		627	535	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944273	81944273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	85	528	1	ENST00000359376.3:c.1882G>A	p.Glu628Lys	p.E628K	ENST00000359376	NM_002661.3	628	Gag/Aag	18/33	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.226796868305101	2		529	715	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796189	45796189	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	127	518	0	ENST00000450313.1:c.1517T>A	p.Met506Lys	p.M506K	ENST00000450313	NM_012222.2	506	aTg/aAg	15/16	0.226796868305101	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.226796868305101	1		518	799	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577119	7577119	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	125	540	0	ENST00000269305.4:c.819del	p.Val274PhefsTer71	p.V274Ffs*71	ENST00000269305	NM_001126112.2	273	cgT/cg	8/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.226796868305101	2		540	846	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251471	10251471	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	37	478	0	ENST00000340748.4:c.3461G>T	p.Gly1154Val	p.G1154V	ENST00000340748		1154	gGa/gTa	31/40	1	2	FACETS	0.525	0.431	0.629	0.525	0.431	0.629	SUBCLONAL	1	TRUE	1	0.226796868305101	2		478	622	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054397	13054397	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	51	491	0	ENST00000316448.5:c.1007A>C	p.Glu336Ala	p.E336A	ENST00000316448	NM_004343.3	336	gAg/gCg	8/9	1	2	FACETS	0.56	0.475	0.654	0.56	0.475	0.654	SUBCLONAL	1	TRUE	1	0.226796868305101	2		491	803	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579328	7579328	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	132	487	0	ENST00000269305.4:c.359A>G	p.Lys120Arg	p.K120R	ENST00000269305	NM_001126112.2	120	aAg/aGg	4/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.316583123241621	2		487	602	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200088	123200088	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	33	172	0	ENST00000218089.9:c.2160C>G	p.Ile720Met	p.I720M	ENST00000218089	NM_001042749.1	720	atC/atG	22/35	1	1	FACETS	0.591	0.483	0.712	0.591	0.483	0.712	SUBCLONAL	1	FALSE	0	0.316583123241621	1		172	297	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	232	302	0				ENST00000310581	NM_198253.2	-/1132			0.585129566581304	4	FACETS	0.988	0.927	1	0.988	0.927	1	CLONAL	2	TRUE	2	0.584226220540285	4		302	637	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805762	43805762	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	350	663	0	ENST00000372470.3:c.818C>T	p.Ser273Phe	p.S273F	ENST00000372470	NM_005373.2	273	tCc/tTc	5/12	0.585129566581304	4	FACETS	0.997	0.947	1	0.997	0.947	1	CLONAL	2	TRUE	2	0.584226220540285	4		663	952	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798597	45798597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780087	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	321	634	1	ENST00000450313.1:c.497C>T	p.Ser166Phe	p.S166F	ENST00000450313	NM_012222.2	166	tCc/tTc	6/16	0.585129566581304	4	FACETS	0.917	0.868	0.967	0.917	0.868	0.967	CLONAL	2	TRUE	2	0.584226220540285	4		635	949	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699486	117699486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	205	410	1	ENST00000369458.3:c.155G>A	p.Gly52Glu	p.G52E	ENST00000369458	NM_024626.3	52	gGa/gAa	3/6	0.585129566581304	4	FACETS	0.904	0.843	0.966	0.904	0.843	0.966	CLONAL	2	TRUE	2	0.584226220540285	4		411	615	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510119	120510120	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	202	360	2	ENST00000256646.2:c.1389_1390delinsTT	p.Pro464Ser	p.P464S	ENST00000256646	NM_024408.3	463	gaCCcc/gaTTcc	8/34	0.585129566581304	4	FACETS	0.861	0.803	0.921	0.861	0.803	0.921	CLONAL	2	TRUE	2	0.584226220540285	4		362	636	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163325242	163325242	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	209	340	1	ENST00000271452.3:c.1378T>C	p.Phe460Leu	p.F460L	ENST00000271452	NM_145697.2	460	Ttc/Ctc	14/14	0.585129566581304	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.584226220540285	4		341	516	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612711	228612711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	315	667	0	ENST00000366696.1:c.316G>A	p.Glu106Lys	p.E106K	ENST00000366696	NM_003493.2	106	Gag/Aag	1/1	0.585129566581304	4	FACETS	0.886	0.838	0.935	0.886	0.838	0.935	CLONAL	2	TRUE	2	0.584226220540285	4		667	964	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845508	63845508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	74	363	0	ENST00000279873.7:c.1247C>T	p.Pro416Leu	p.P416L	ENST00000279873	NM_032199.2	416	cCc/cTc	9/10	1	2	FACETS	0.839	0.741	0.942	0.839	0.741	0.942	CLONAL	1	TRUE	1	0.584226220540285	2		363	302	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274777	123274777	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs387906678	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	118	535	0	ENST00000358487.5:c.1141T>C	p.Tyr381His	p.Y381H	ENST00000358487	NM_000141.4	381	Tac/Cac	9/18	0.585129566581304	3	FACETS	0.952	0.863	1	0.476	0.431	0.523	CLONAL	1	TRUE	1	0.584226220540285	3		535	548	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946912	71946912	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	447	782	1	ENST00000298229.2:c.2761T>G	p.Phe921Val	p.F921V	ENST00000298229	NM_001567.3	921	Ttc/Gtc	25/28	0.584226220540285	6	FACETS	1	0.989	1	0.559	0.532	0.585	CLONAL	2	TRUE	2	0.584226220540285	6		783	1485	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435338	18435338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	213	440	1	ENST00000266497.5:c.323G>A	p.Gly108Asp	p.G108D	ENST00000266497		108	gGt/gAt	1/31	0.585129566581304	4	FACETS	0.955	0.893	1	0.955	0.893	1	CLONAL	2	TRUE	2	0.584226220540285	4		441	605	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573945	18573945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	169	346	0	ENST00000266497.5:c.2263G>A	p.Glu755Lys	p.E755K	ENST00000266497		755	Gaa/Aaa	15/31	0.585129566581304	4	FACETS	0.939	0.871	1	0.939	0.871	1	CLONAL	2	TRUE	2	0.584226220540285	4		346	488	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246655	46246656	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	96	192	0	ENST00000334344.6:c.4751_4752del	p.Tyr1584CysfsTer24	p.Y1584Cfs*24	ENST00000334344	NM_152641.2	1583	acATat/acat	15/21	0.585129566581304	4	FACETS	0.801	0.721	0.884	0.801	0.721	0.884	CLONAL	2	TRUE	2	0.584226220540285	4		192	325	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26927943	26927943	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	188	386	1	ENST00000381527.3:c.382G>A	p.Val128Met	p.V128M	ENST00000381527	NM_001260.1	128	Gtg/Atg	4/13	0.585129566581304	4	FACETS	0.874	0.813	0.937	0.874	0.813	0.937	CLONAL	2	TRUE	2	0.584226220540285	4		387	583	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589835	28589835	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs959896930	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	216	446	1	ENST00000241453.7:c.2545C>T	p.Arg849Cys	p.R849C	ENST00000241453	NM_004119.2	849	Cgt/Tgt	21/24	0.585129566581304	4	FACETS	0.949	0.888	1	0.949	0.888	1	CLONAL	2	TRUE	2	0.584226220540285	4		447	617	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609671	28609671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	276	544	0	ENST00000241453.7:c.1558C>T	p.Leu520Phe	p.L520F	ENST00000241453	NM_004119.2	520	Ctt/Ttt	12/24	0.585129566581304	4	FACETS	0.958	0.904	1	0.958	0.904	1	CLONAL	2	TRUE	2	0.584226220540285	4		544	781	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134217	41134217	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750423870	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	193	328	0	ENST00000379561.5:c.1411C>T	p.Pro471Ser	p.P471S	ENST00000379561	NM_002015.3	471	Cct/Tct	2/3	0.585129566581304	4	FACETS	0.969	0.904	1	0.969	0.904	1	CLONAL	2	TRUE	2	0.584226220540285	4		328	540	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434574	110434575	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	299	701	2	ENST00000375856.3:c.3826_3827delinsTT	p.Pro1276Phe	p.P1276F	ENST00000375856	NM_003749.2	1276	CCt/TTt	1/2	0.585129566581304	5	FACETS	0.905	0.853	0.958			1	CLONAL	2	TRUE	NA	0.584226220540285	5		703	1061	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435435	110435436	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	266	646	1	ENST00000375856.3:c.2965_2966delinsTT	p.Pro989Phe	p.P989F	ENST00000375856	NM_003749.2	989	CCt/TTt	1/2	0.585129566581304	5	FACETS	0.884	0.83	0.94			1	CLONAL	2	TRUE	NA	0.584226220540285	5		647	966	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435447	110435447	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	305	632	1	ENST00000375856.3:c.2954C>A	p.Ser985Tyr	p.S985Y	ENST00000375856	NM_003749.2	985	tCc/tAc	1/2	0.585129566581304	5	FACETS	0.98	0.925	1			1	CLONAL	2	TRUE	NA	0.584226220540285	5		633	1000	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422091	81422091	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	233	454	0	ENST00000298171.2:c.67G>A	p.Gly23Arg	p.G23R	ENST00000298171	NM_000369.2	23	Ggg/Agg	1/10	0.585129566581304	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.584226220540285	3		454	484	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	208	771	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	0.585129566581304	3	FACETS	0.986	0.916	1	0.493	0.458	0.53	CLONAL	1	TRUE	1	0.584226220540285	3		771	933	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021428	42021428	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	116	465	0	ENST00000219905.7:c.3724C>T	p.Arg1242Ter	p.R1242*	ENST00000219905	NM_001164273.1	1242	Cga/Tga	11/24	0.585129566581304	3	FACETS	0.809	0.731	0.892	0.405	0.365	0.446	CLONAL	1	TRUE	1	0.584226220540285	3		465	634	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729142	66729142	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	149	608	0	ENST00000307102.5:c.350T>C	p.Val117Ala	p.V117A	ENST00000307102	NM_002755.3	117	gTt/gCt	3/11	0.585129566581304	3	FACETS	0.942	0.862	1	0.471	0.431	0.512	CLONAL	1	TRUE	1	0.584226220540285	3		608	700	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639573	3639573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	415	794	0	ENST00000294008.3:c.4066C>T	p.Pro1356Ser	p.P1356S	ENST00000294008	NM_032444.2	1356	Ccg/Tcg	12/15	0.585129566581304	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.584226220540285	3		794	917	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647643	3647643	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	233	827	2	ENST00000294008.3:c.1420C>T	p.Gln474Ter	p.Q474*	ENST00000294008	NM_032444.2	474	Cag/Tag	7/15	0.585129566581304	3	FACETS	1	0.966	1	0.527	0.492	0.564	CLONAL	1	TRUE	1	0.584226220540285	3		829	977	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832915	3832915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	159	336	0	ENST00000262367.5:c.1343C>T	p.Ser448Phe	p.S448F	ENST00000262367	NM_004380.2	448	tCt/tTt	6/31	0.585129566581304	3	FACETS	0.94	0.874	1	0.94	0.874	1	CLONAL	2	TRUE	1	0.584226220540285	3		336	374	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923318	9923318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867335598	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	245	522	0	ENST00000330684.3:c.1969G>A	p.Glu657Lys	p.E657K	ENST00000330684	NM_001134407.1	657	Gaa/Aaa	9/13	0.585129566581304	3	FACETS	0.987	0.931	1	0.987	0.931	1	CLONAL	2	TRUE	1	0.584226220540285	3		522	549	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934623	9934623	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267604688	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	108	377	3	ENST00000330684.3:c.1532C>T	p.Ser511Leu	p.S511L	ENST00000330684	NM_001134407.1	511	tCg/tTg	7/13	0.585129566581304	3	FACETS	1	0.914	1	0.507	0.457	0.559	CLONAL	1	TRUE	1	0.584226220540285	3		380	471	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031841	10031841	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	280	632	1	ENST00000330684.3:c.982G>A	p.Glu328Lys	p.E328K	ENST00000330684	NM_001134407.1	328	Gag/Aag	3/13	0.585129566581304	3	FACETS	0.933	0.882	0.983	0.933	0.882	0.983	CLONAL	2	TRUE	1	0.584226220540285	3		633	664	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029422	14029422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773007457	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	85	363	1	ENST00000311895.7:c.1633G>A	p.Gly545Arg	p.G545R	ENST00000311895	NM_005236.2	545	Gga/Aga	8/11	0.585129566581304	3	FACETS	0.895	0.796	1	0.448	0.398	0.501	CLONAL	1	TRUE	1	0.584226220540285	3		364	420	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972484	81972484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761622324	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	290	482	1	ENST00000359376.3:c.3277G>A	p.Glu1093Lys	p.E1093K	ENST00000359376	NM_002661.3	1093	Gag/Aag	29/33	0.579513284896045	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.584226220540285	2		483	458	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654712	29654712	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	94	323	0	ENST00000356175.3:c.5401C>T	p.Gln1801Ter	p.Q1801*	ENST00000356175	NM_000267.3	1801	Cag/Tag	37/57	0.585129566581304	3	FACETS	0.91	0.814	1	0.455	0.407	0.506	CLONAL	1	TRUE	1	0.584226220540285	3		323	457	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665053	29665053	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691093	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	249	423	0	ENST00000356175.3:c.6652C>T	p.Gln2218Ter	p.Q2218*	ENST00000356175	NM_000267.3	2218	Caa/Taa	44/57	0.585129566581304	3	FACETS	0.996	0.94	1	0.996	0.94	1	CLONAL	2	TRUE	1	0.584226220540285	3		423	553	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650788	37650788	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	162	577	0	ENST00000447079.4:c.2260G>A	p.Ala754Thr	p.A754T	ENST00000447079	NM_015083.1	754	Gct/Act	5/14	0.585129566581304	3	FACETS	1	0.969	1	0.552	0.508	0.598	CLONAL	1	TRUE	1	0.584226220540285	3		577	649	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59820400	59820400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	120	400	0	ENST00000259008.2:c.2353C>T	p.Pro785Ser	p.P785S	ENST00000259008	NM_032043.2	785	Cct/Tct	16/20	0.585129566581304	3	FACETS	0.981	0.89	1	0.491	0.445	0.539	CLONAL	1	TRUE	1	0.584226220540285	3		400	541	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775164	73775164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867543814	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	471	586	0	ENST00000254810.4:c.92C>T	p.Pro31Leu	p.P31L	ENST00000254810	NM_005324.3	31	cCc/cTc	2/4	0.585129566581304	5	FACETS	0.962	0.923	1	0.962	0.923	1	CLONAL	3	TRUE	2	0.584226220540285	5		586	1048	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207092	1207092	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs778376925	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	852	789	3	ENST00000326873.7:c.180C>G	p.Tyr60Ter	p.Y60*	ENST00000326873	NM_000455.4	60	taC/taG	1/10	0.541335311776501	4	FACETS	0.993	0.972	1			1	CLONAL	4	TRUE	NA	0.584226220540285	4		792	1163	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138591	11138591	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	327	591	1	ENST00000358026.2:c.3347T>C	p.Phe1116Ser	p.F1116S	ENST00000358026	NM_001128849.1	1116	tTt/tCt	24/36	0.527646693635493	4	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	2	0.584226220540285	4		592	885	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965940	18965940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867974546	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	290	630	3	ENST00000262803.5:c.1433C>T	p.Ala478Val	p.A478V	ENST00000262803	NM_002911.3	478	gCc/gTc	11/24	0.527646693635493	4	FACETS	0.882	0.832	0.933	0.882	0.832	0.933	CLONAL	2	TRUE	2	0.584226220540285	4		633	892	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416557	29416557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	320	572	0	ENST00000389048.3:c.4396C>T	p.Pro1466Ser	p.P1466S	ENST00000389048	NM_004304.4	1466	Cct/Tct	29/29	0.585129566581304	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.584226220540285	4		572	809	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641445	47641445	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	230	458	0	ENST00000233146.2:c.830T>C	p.Leu277Ser	p.L277S	ENST00000233146	NM_000251.2	277	tTa/tCa	5/16	0.585129566581304	4	FACETS	0.948	0.889	1	0.948	0.889	1	CLONAL	2	TRUE	2	0.584226220540285	4		458	658	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634711	158634711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374836197	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	174	336	0	ENST00000263640.3:c.475C>T	p.Pro159Ser	p.P159S	ENST00000263640	NM_001105.4	159	Ccc/Tcc	5/11	0.585129566581304	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.584226220540285	3		336	365	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190717451	190717451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	221	362	0	ENST00000441310.2:c.770G>A	p.Arg257Lys	p.R257K	ENST00000441310	NM_000534.4	257	aGa/aAa	7/13	0.585129566581304	3	FACETS	0.993	0.935	1	0.993	0.935	1	CLONAL	2	TRUE	1	0.584226220540285	3		362	492	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483981	212483981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	196	431	0	ENST00000342788.4:c.2222G>A	p.Gly741Glu	p.G741E	ENST00000342788	NM_005235.2	741	gGa/gAa	19/28	0.585129566581304	3	FACETS	0.94	0.88	1	0.94	0.88	1	CLONAL	2	TRUE	1	0.584226220540285	3		431	461	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812196	212812196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	174	349	0	ENST00000342788.4:c.380G>A	p.Gly127Glu	p.G127E	ENST00000342788	NM_005235.2	127	gGa/gAa	3/28	0.585129566581304	3	FACETS	0.955	0.891	1	0.955	0.891	1	CLONAL	2	TRUE	1	0.584226220540285	3		349	403	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546761	9546761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768724288	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	180	295	1	ENST00000353224.5:c.1261G>A	p.Asp421Asn	p.D421N	ENST00000353224	NM_177990.2	421	Gac/Aac	5/10	0.585129566581304	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.584226220540285	4		296	458	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561102	9561102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	181	340	0	ENST00000353224.5:c.680C>T	p.Pro227Leu	p.P227L	ENST00000353224	NM_177990.2	227	cCt/cTt	4/10	0.585129566581304	4	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	2	0.584226220540285	4		340	483	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727125	40727125	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	314	587	0	ENST00000373198.4:c.3839G>T	p.Trp1280Leu	p.W1280L	ENST00000373198	NM_133170.3	1280	tGg/tTg	28/32	0.585129566581304	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.584226220540285	4		587	782	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264401	46264401	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	231	450	0	ENST00000371998.3:c.1448C>T	p.Ser483Phe	p.S483F	ENST00000371998		483	tCt/tTt	11/23	0.585129566581304	4	FACETS	0.949	0.89	1	0.949	0.89	1	CLONAL	2	TRUE	2	0.584226220540285	4		450	660	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164451	36164451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	61	321	1	ENST00000300305.3:c.1424C>T	p.Ala475Val	p.A475V	ENST00000300305		475	gCc/gTc	8/8	0.585129566581304	3	FACETS	0.93	0.809	1	0.465	0.404	0.53	CLONAL	1	TRUE	1	0.584226220540285	3		322	290	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860364	42860364	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	347	668	0	ENST00000398585.3:c.513T>A	p.Asp171Glu	p.D171E	ENST00000398585	NM_001135099.1	171	gaT/gaA	5/14	0.585129566581304	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.584226220540285	3		668	757	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447543	12447544	+	missense_variant	Missense_Mutation	DNP	CG	CG	TA	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	338	588	0	ENST00000287820.6:c.782_783delinsTA	p.Ala261Val	p.A261V	ENST00000287820	NM_015869.4	261	gCG/gTA	5/7	0.585129566581304	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	2	0.584226220540285	4		588	887	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713336	30713336	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	234	462	0	ENST00000295754.5:c.661G>A	p.Glu221Lys	p.E221K	ENST00000295754	NM_003242.5	221	Gaa/Aaa	4/7	0.585129566581304	4	FACETS	0.961	0.902	1	0.961	0.902	1	CLONAL	2	TRUE	2	0.584226220540285	4		462	660	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163694	47163694	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	226	358	0	ENST00000409792.3:c.2432A>T	p.Asn811Ile	p.N811I	ENST00000409792	NM_014159.6	811	aAt/aTt	3/21	0.585129566581304	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.584226220540285	4		358	589	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987040	69987040	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	303	588	0	ENST00000394351.3:c.101A>G	p.Gln34Arg	p.Q34R	ENST00000394351	NM_000248.3	34	cAg/cGg	2/9	0.585129566581304	4	FACETS	0.963	0.911	1	0.963	0.911	1	CLONAL	2	TRUE	2	0.584226220540285	4		588	853	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498451	89498451	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	162	329	0	ENST00000336596.2:c.2423G>A	p.Trp808Ter	p.W808*	ENST00000336596	NM_005233.5	808	tGg/tAg	14/17	0.585129566581304	4	FACETS	0.861	0.796	0.929	0.861	0.796	0.929	CLONAL	2	TRUE	2	0.584226220540285	4		329	510	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280115	142280115	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	225	463	0	ENST00000350721.4:c.1319C>T	p.Pro440Leu	p.P440L	ENST00000350721	NM_001184.3	440	cCt/cTt	5/47	0.585129566581304	4	FACETS	0.95	0.89	1	0.95	0.89	1	CLONAL	2	TRUE	2	0.584226220540285	4		463	642	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612250	189612250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749906547	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	209	388	0	ENST00000264731.3:c.2002C>T	p.Arg668Cys	p.R668C	ENST00000264731	NM_003722.4	668	Cgc/Tgc	14/14	0.585129566581304	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	2	0.584226220540285	4		388	526	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944588	38944588	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	214	382	0	ENST00000357387.3:c.4873A>T	p.Ser1625Cys	p.S1625C	ENST00000357387	NM_152756.3	1625	Agt/Tgt	36/38	0.585129566581304	4	FACETS	0.902	0.843	0.963	0.902	0.843	0.963	CLONAL	2	TRUE	2	0.584226220540285	4		382	643	SUCCESS
APC	324	MSKCC	GRCh37	5	112175780	112175781	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TA	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	130	301	0	ENST00000257430.4:c.4489_4490delinsTA	p.Pro1497Ter	p.P1497*	ENST00000257430	NM_000038.5	1497	CCa/TAa	16/16	0.585129566581304	4	FACETS	0.81	0.741	0.882	0.81	0.741	0.882	CLONAL	2	TRUE	2	0.584226220540285	4		301	435	SUCCESS
APC	324	MSKCC	GRCh37	5	112177425	112177425	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	195	358	1	ENST00000257430.4:c.6134C>T	p.Ser2045Phe	p.S2045F	ENST00000257430	NM_000038.5	2045	tCc/tTc	16/16	0.585129566581304	4	FACETS	0.987	0.92	1	0.987	0.92	1	CLONAL	2	TRUE	2	0.584226220540285	4		359	536	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509341	149509341	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	259	406	0	ENST00000261799.4:c.1558G>A	p.Glu520Lys	p.E520K	ENST00000261799	NM_002609.3	520	Gag/Aag	10/23	0.585129566581304	4	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	2	0.584226220540285	4		406	693	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180040018	180040018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370894507	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	362	710	0	ENST00000261937.6:c.3424C>T	p.Pro1142Ser	p.P1142S	ENST00000261937	NM_182925.4	1142	Ccc/Tcc	25/30	0.585129566581304	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	2	0.584226220540285	4		710	977	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671556	30671556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	153	692	0	ENST00000376406.3:c.5404G>A	p.Glu1802Lys	p.E1802K	ENST00000376406	NM_014641.2	1802	Gag/Aag	10/15	0.584226220540285	6	FACETS	0.919	0.839	1	0.23	0.209	0.251	CLONAL	1	TRUE	2	0.584226220540285	6		692	1236	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324160	31324160	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137854719	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	626	727	1	ENST00000412585.2:c.403C>T	p.Arg135Cys	p.R135C	ENST00000412585	NM_005514.6	135	Cgc/Tgc	3/8	0.584226220540285	6	FACETS	1	0.993	1	0.826	0.796	0.855	CLONAL	3	TRUE	2	0.584226220540285	6		728	1407	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982036	93982036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1165179670	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	84	369	0	ENST00000369303.4:c.1429G>A	p.Glu477Lys	p.E477K	ENST00000369303	NM_004440.3	477	Gaa/Aaa	6/17	1	2	FACETS	0.998	0.892	1	0.998	0.892	1	CLONAL	1	TRUE	1	0.584226220540285	2		369	288	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683852	117683852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	113	503	0	ENST00000368508.3:c.3295G>A	p.Glu1099Lys	p.E1099K	ENST00000368508	NM_002944.2	1099	Gaa/Aaa	21/43	1	2	FACETS	0.834	0.755	0.916	0.834	0.755	0.916	CLONAL	1	TRUE	1	0.584226220540285	2		503	464	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415566	152415566	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1356235501	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	158	568	0	ENST00000206249.3:c.1416G>C	p.Lys472Asn	p.K472N	ENST00000206249	NM_000125.3	472	aaG/aaC	7/8	1	2	FACETS	0.944	0.869	1	0.944	0.869	1	CLONAL	1	TRUE	1	0.584226220540285	2		568	573	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934283	68934283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773476490	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	253	486	0	ENST00000288368.4:c.349C>T	p.Arg117Cys	p.R117C	ENST00000288368	NM_024870.2	117	Cgt/Tgt	4/40	0.585129566581304	4	FACETS	0.958	0.901	1	0.958	0.901	1	CLONAL	2	TRUE	2	0.584226220540285	4		486	716	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939506	68939506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1309816810	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	241	793	0	ENST00000288368.4:c.491G>A	p.Gly164Glu	p.G164E	ENST00000288368	NM_024870.2	164	gGa/gAa	5/40	0.585129566581304	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.584226220540285	4		793	619	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68984765	68984765	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	174	451	0	ENST00000288368.4:c.1529T>A	p.Val510Glu	p.V510E	ENST00000288368	NM_024870.2	510	gTg/gAg	14/40	0.585129566581304	4	FACETS	0.885	0.821	0.951	0.885	0.821	0.951	CLONAL	2	TRUE	2	0.584226220540285	4		451	533	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21968234	21968234	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	164	353	0	ENST00000304494.5:c.465del	p.Asp156IlefsTer37	p.D156Ifs*37	ENST00000304494	NM_000077.4	155	ccC/cc	3/3	0.579513284896045	2	FACETS	0.93	0.871	0.987	0.93	0.871	0.987	CLONAL	2	TRUE	0	0.584226220540285	2		353	302	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27173241	27173241	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	292	635	1	ENST00000380036.4:c.782G>A	p.Gly261Asp	p.G261D	ENST00000380036	NM_000459.3	261	gGc/gAc	6/23	0.579513284896045	2	FACETS	0.992	0.947	1	0.992	0.947	1	CLONAL	2	TRUE	0	0.584226220540285	2		636	504	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409446	80409447	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	193	353	0	ENST00000286548.4:c.667_668delinsAA	p.Val223Asn	p.V223N	ENST00000286548	NM_002072.3	223	GTc/AAc	5/7	0.527646693635493	4	FACETS	0.928	0.864	0.993	0.928	0.864	0.993	CLONAL	2	TRUE	2	0.584226220540285	4		353	564	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760028	133760028	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	403	835	1	ENST00000318560.5:c.2351C>T	p.Pro784Leu	p.P784L	ENST00000318560	NM_005157.4	784	cCc/cTc	11/11	0.585129566581304	3	FACETS	0.956	0.914	0.999	0.956	0.914	0.999	CLONAL	2	TRUE	1	0.584226220540285	3		836	932	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937185	76937185	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	263	227	0	ENST00000373344.5:c.3563C>T	p.Ser1188Phe	p.S1188F	ENST00000373344	NM_000489.3	1188	tCc/tTc	9/35	0.541335311776501	2	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.584226220540285	2		227	371	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0028603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	1917	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.52114279013766	4	FACETS	1	0.996	1			1	CLONAL	4	TRUE	2	0.528454090640648	4		436	2699	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0028603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	449	346	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.479927297874046	2	FACETS	0.931	0.893	0.968	0.931	0.893	0.968	CLONAL	2	TRUE	0	0.528454090640648	2		346	913	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971153	21971153	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913383	NA	P-0028603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	200	539	0	ENST00000304494.5:c.205G>T	p.Glu69Ter	p.E69*	ENST00000304494	NM_000077.4	69	Gag/Tag	2/3	0.528454090640648	1	FACETS	0.974	0.908	1	0.974	0.908	1	CLONAL	1	TRUE	0	0.528454090640648	1		539	572	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44910996	44910999	+	frameshift_variant	Frame_Shift_Del	DEL	CAGA	CAGA	-	novel	NA	P-0028603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	256	322	0	ENST00000377967.4:c.701_704del	p.Thr234ArgfsTer7	p.T234Rfs*7	ENST00000377967	NM_021140.2	233	CAGAca/ca	9/29	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.528454090640648	1		322	491	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50827471	50827471	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1165672681	NA	P-0028603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	105	523	1	ENST00000398568.2:c.2356C>T	p.Arg786Trp	p.R786W	ENST00000398568	NM_001042412.1	786	Cgg/Tgg	16/18	0.242127752501565	3	FACETS	0.545	0.487	0.606	0.182	0.162	0.202	INDETERMINATE	1	TRUE	0	0.528454090640648	3		524	922	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0028740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	77	303	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.28	2		303	536	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361160	70361160	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs79912241	NA	P-0028740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	27	296	0	ENST00000374080.3:c.6348C>A	p.His2116Gln	p.H2116Q	ENST00000374080		2116	caC/caA	43/45	1	1	FACETS	0.586	0.467	0.721	0.586	0.467	0.721	SUBCLONAL	1	TRUE	0	0.28	1		296	283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576865	7576865	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	rs879254077	NA	P-0028775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	50	458	0	ENST00000269305.4:c.981T>G	p.Tyr327Ter	p.Y327*	ENST00000269305	NM_001126112.2	327	taT/taG	9/11	1	2	FACETS	0.928	0.787	1	0.928	0.787	1	CLONAL	1	TRUE	1	0.2	2		458	539	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333670	70333670	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	27	308	0	ENST00000373644.4:c.1575T>A	p.His525Gln	p.H525Q	ENST00000373644	NM_030625.2	525	caT/caA	2/12	1	2	FACETS	0.742	0.59	0.915	0.742	0.59	0.915	CLONAL	1	TRUE	1	0.2	2		308	364	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673698	37673698	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	54	356	0	ENST00000447079.4:c.2852T>C	p.Leu951Pro	p.L951P	ENST00000447079	NM_015083.1	951	cTt/cCt	10/14	1	2	FACETS	0.993	0.848	1	0.993	0.848	1	CLONAL	1	TRUE	1	0.2	2		356	544	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0028831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	539	741	1	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.82	2		742	1257	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0028955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	210	520	2	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.439860648638944	1	FACETS	0.981	0.914	1	0.981	0.914	1	CLONAL	1	TRUE	0	0.439860648638944	1		522	759	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831629	72831629	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	189	520	0	ENST00000268489.5:c.4952C>A	p.Thr1651Lys	p.T1651K	ENST00000268489	NM_006885.3	1651	aCg/aAg	9/10	0.366634062872247	3	FACETS	1	0.948	1	0.517	0.477	0.558	CLONAL	1	TRUE	1	0.439860648638944	3		520	1014	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0029168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	406	570	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.413982035266996	4	FACETS	0.902	0.862	0.943	0.902	0.862	0.943	CLONAL	3	TRUE	1	0.451966416608742	4		570	964	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578552	7578552	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	441	1247	0	ENST00000269305.4:c.378C>A	p.Tyr126Ter	p.Y126*	ENST00000269305	NM_001126112.2	126	taC/taA	5/11	0.43994339366511	2	FACETS	0.916	0.877	0.956	0.916	0.877	0.956	CLONAL	2	TRUE	0	0.451966416608742	2		1247	1065	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053347	37053348	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs63751653	NA	P-0029168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	150	467	0	ENST00000231790.2:c.588dup	p.Gln197ThrfsTer7	p.Q197Tfs*7	ENST00000231790	NM_000249.3	194	-/A	7/19	1	2	FACETS	0.899	0.823	0.979	0.899	0.823	0.979	CLONAL	1	TRUE	1	0.451966416608742	2		467	738	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0029280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	228	880	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA	2	FACETS	0.967	0.903	1			1	INDETERMINATE	2	TRUE	NA	0.278562850833292	2		880	846	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0029280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	94	500	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	0.271553267580226	2	FACETS	0.833	0.746	0.924	0.833	0.746	0.924	CLONAL	2	TRUE	0	0.278562850833292	2		500	405	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611845	1611845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1301102408	NA	P-0029280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	190	541	0	ENST00000344749.5:c.1817G>A	p.Arg606Gln	p.R606Q	ENST00000344749	NM_001136139.2	606	cGg/cAg	19/19	0.271553267580226	2	FACETS	0.955	0.886	1	0.955	0.886	1	CLONAL	2	TRUE	0	0.278562850833292	2		541	714	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878076	48878084	+	inframe_deletion	In_Frame_Del	DEL	GCCGCCACC	GCCGCCACC	-	rs759465865	NA	P-0029280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	22	151	0	ENST00000267163.4:c.34_42del	p.Thr12_Ala14del	p.T12_A14del	ENST00000267163	NM_000321.2	10	GCCGCCACC/-	1/27	0.278562850833292	5	FACETS	0.673	0.521	0.848	0.224	0.173	0.283	SUBCLONAL	1	TRUE	2	0.278562850833292	5		151	333	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162039	47162039	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	124	399	0	ENST00000409792.3:c.4087G>C	p.Asp1363His	p.D1363H	ENST00000409792	NM_014159.6	1363	Gac/Cac	3/21	0.253077861936919	3	FACETS	0.972	0.883	1	0.972	0.883	1	CLONAL	2	TRUE	1	0.278562850833292	3		399	522	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	192	468	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.98	0.908	1	0.98	0.908	1	CLONAL	1	TRUE	1	0.486979205687301	2		472	805	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101268	27101268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	185	506	1	ENST00000324856.7:c.4555del	p.Gln1519ArgfsTer8	p.Q1519Rfs*8	ENST00000324856	NM_006015.4	1517	gCc/gc	18/20	1	2	FACETS	0.909	0.84	0.98	0.909	0.84	0.98	CLONAL	1	TRUE	1	0.486979205687301	2		507	836	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	80	247	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.872	0.772	0.977	0.872	0.772	0.977	CLONAL	1	TRUE	1	0.486979205687301	2		247	377	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255883	16255883	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	49	389	2	ENST00000375759.3:c.3154del	p.Ile1052SerfsTer40	p.I1052Sfs*40	ENST00000375759	NM_015001.2	1050	Aaa/aa	11/15	1	2	FACETS	0.324	0.273	0.379	0.324	0.273	0.379	SUBCLONAL	1	TRUE	1	0.486979205687301	2		391	622	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	36	461	2	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.279	0.229	0.335	0.279	0.229	0.335	SUBCLONAL	1	TRUE	1	0.486979205687301	2		463	530	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128017009	128017009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151216904	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	50	498	1	ENST00000285398.2:c.2080G>A	p.Ala694Thr	p.A694T	ENST00000285398	NM_000122.1	694	Gct/Act	14/15	1	2	FACETS	0.286	0.242	0.335	0.286	0.242	0.335	SUBCLONAL	1	TRUE	1	0.486979205687301	2		499	718	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	161	548	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.99	0.911	1	0.99	0.911	1	CLONAL	1	TRUE	1	0.486979205687301	2		549	668	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653796	89653798	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs1554893765	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	47	518	0	ENST00000371953.3:c.97_99del	p.Ile33del	p.I33del	ENST00000371953	NM_000314.4	32	ATT/-	2/9	1	2	FACETS	0.35	0.295	0.41	0.35	0.295	0.41	SUBCLONAL	1	TRUE	1	0.486979205687301	2		518	552	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436127	56436127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138844366	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	218	545	0	ENST00000407977.2:c.1010G>A	p.Arg337Gln	p.R337Q	ENST00000407977		337	cGa/cAa	9/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.486979205687301	2		545	855	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37058999	37058999	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs63751194	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	135	379	2	ENST00000231790.2:c.793C>T	p.Arg265Cys	p.R265C	ENST00000231790	NM_000249.3	265	Cgt/Tgt	10/19	1	2	FACETS	0.951	0.868	1	0.951	0.868	1	CLONAL	1	TRUE	1	0.486979205687301	2		381	583	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70441157	70441157	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	rs764225020	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	48	372	0	ENST00000373644.4:c.4832del	p.Asn1611ThrfsTer13	p.N1611Tfs*13	ENST00000373644	NM_030625.2	1609	gAa/ga	9/12	1	2	FACETS	0.336	0.283	0.394	0.336	0.283	0.394	SUBCLONAL	1	TRUE	1	0.486979205687301	2		372	587	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	204	304	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.486979205687301	2		305	587	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552152	29552152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199474738	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	87	221	0	ENST00000356175.3:c.1885G>A	p.Gly629Arg	p.G629R	ENST00000356175	NM_000267.3	629	Ggg/Agg	17/57	1	2	FACETS	0.94	0.838	1	0.94	0.838	1	CLONAL	1	TRUE	1	0.486979205687301	2		221	380	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	224	633	5	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	0.83	0.772	0.89	0.83	0.772	0.89	CLONAL	1	TRUE	1	0.486979205687301	2		638	1108	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822563	72822564	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGC	rs376311468	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	95	401	0	ENST00000268489.5:c.9609_9611dup	p.Gln3204dup	p.Q3204dup	ENST00000268489	NM_006885.3	3204	caa/caGCAa	10/10	1	2	FACETS	0.686	0.612	0.764	0.686	0.612	0.764	SUBCLONAL	1	TRUE	1	0.486979205687301	2		401	569	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120115	70120115	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	36	151	0	ENST00000245479.2:c.1121del	p.Pro374ArgfsTer9	p.P374Rfs*9	ENST00000245479	NM_000346.3	373	Ccc/cc	3/3	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.486979205687301	2		151	135	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257144	19257144	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	172	438	2	ENST00000162023.5:c.819del	p.Thr274ProfsTer?	p.T274Pfs*?	ENST00000162023		273	ccC/cc	12/13	1	2	FACETS	0.989	0.913	1	0.989	0.913	1	CLONAL	1	TRUE	1	0.486979205687301	2		440	714	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793252	33793253	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs137852728	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	22	124	0	ENST00000498907.2:c.68dup	p.His24AlafsTer84	p.H24Afs*84	ENST00000498907	NM_004364.3	23	ccg/ccCg	1/1	1	2	FACETS	0.336	0.26	0.423	0.336	0.26	0.423	SUBCLONAL	1	TRUE	1	0.486979205687301	2		124	269	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	103	634	0	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	0.451	0.403	0.503	0.451	0.403	0.503	SUBCLONAL	1	TRUE	1	0.486979205687301	2		634	937	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856623	111856623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	57	141	0	ENST00000341259.2:c.674G>A	p.Arg225His	p.R225H	ENST00000341259	NM_005475.2	225	cGc/cAc	2/8	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.486979205687301	2		141	226	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957464	175957465	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	129	377	1	ENST00000367669.3:c.1931dup	p.Asn644LysfsTer17	p.N644Kfs*17	ENST00000367669	NM_022457.5	644	aac/aaAc	17/20	1	2	FACETS	0.855	0.777	0.936	0.855	0.777	0.936	CLONAL	1	TRUE	1	0.486979205687301	2		378	620	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132907	64132907	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	67	577	2	ENST00000334205.4:c.1046del	p.Pro349HisfsTer26	p.P349Hfs*26	ENST00000334205	NM_003942.2	347	agC/ag	9/17	1	2	FACETS	0.312	0.27	0.357	0.312	0.27	0.357	SUBCLONAL	1	TRUE	1	0.486979205687301	2		579	883	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416900	416900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377384081	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	92	348	0	ENST00000399788.2:c.3650G>A	p.Arg1217Gln	p.R1217Q	ENST00000399788	NM_001042603.1	1217	cGg/cAg	23/28	1	2	FACETS	0.71	0.633	0.792	0.71	0.633	0.792	SUBCLONAL	1	TRUE	1	0.486979205687301	2		348	532	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640853	3640853	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs117707719	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	205	654	0	ENST00000294008.3:c.2786C>T	p.Pro929Leu	p.P929L	ENST00000294008	NM_032444.2	929	cCg/cTg	12/15	1	2	FACETS	0.886	0.822	0.952	0.886	0.822	0.952	CLONAL	1	TRUE	1	0.486979205687301	2		654	950	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264348	46264348	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	32	344	0	ENST00000371998.3:c.1400del	p.Pro467HisfsTer15	p.P467Hfs*15	ENST00000371998		465	agC/ag	11/23	1	2	FACETS	0.252	0.204	0.306	0.252	0.204	0.306	SUBCLONAL	1	TRUE	1	0.486979205687301	2		344	522	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683558	29683558	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060500295	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	166	420	2	ENST00000356175.3:c.7638del	p.Met2548Ter	p.M2548*	ENST00000356175	NM_000267.3	2545	Ccc/cc	51/57	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.486979205687301	2		422	667	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225731	26225731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	203	486	0	ENST00000360408.1:c.349C>T	p.Arg117Cys	p.R117C	ENST00000360408	NM_003532.2	117	Cgc/Tgc	1/1	1	2	FACETS	0.96	0.892	1	0.96	0.892	1	CLONAL	1	TRUE	1	0.486979205687301	2		486	868	SUCCESS
APC	324	MSKCC	GRCh37	5	112173955	112173956	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	115	276	0	ENST00000257430.4:c.2667dup	p.Val890SerfsTer22	p.V890Sfs*22	ENST00000257430	NM_000038.5	888	-/A	16/16	1	2	FACETS	0.98	0.888	1	0.98	0.888	1	CLONAL	1	TRUE	1	0.486979205687301	2		276	482	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	292	936	0	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	1	2	FACETS	0.959	0.901	1	0.959	0.901	1	CLONAL	1	TRUE	1	0.486979205687301	2		936	1251	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021818	71021818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs869025203	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	63	140	0	ENST00000318789.4:c.1540C>T	p.Arg514Cys	p.R514C	ENST00000318789	NM_032682.5	514	Cgt/Tgt	18/21	1	2	FACETS	0.86	0.749	0.977	0.86	0.749	0.977	CLONAL	1	TRUE	1	0.486979205687301	2		140	301	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119769	70119769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	204	552	0	ENST00000245479.2:c.774del	p.Leu259CysfsTer20	p.L259Cfs*20	ENST00000245479	NM_000346.3	257	cgC/cg	3/3	1	2	FACETS	0.938	0.871	1	0.938	0.871	1	CLONAL	1	TRUE	1	0.486979205687301	2		552	893	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273026	18273026	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	169	672	2	ENST00000222254.8:c.921del	p.Lys308ArgfsTer33	p.K308Rfs*33	ENST00000222254	NM_005027.3	306	Ccc/cc	8/16	1	2	FACETS	0.659	0.605	0.716	0.659	0.605	0.716	SUBCLONAL	1	TRUE	1	0.486979205687301	2		674	1053	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440542	49440542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773033619	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	270	678	3	ENST00000301067.7:c.4268G>A	p.Arg1423His	p.R1423H	ENST00000301067	NM_003482.3	1423	cGt/cAt	15/54	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.486979205687301	2		681	1103	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753149	42753151	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs199960550	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	192	531	7	ENST00000222329.4:c.1113_1115del	p.Ser373del	p.S373del	ENST00000222329	NM_006494.2	371	tcTTCc/tcc	4/4	1	2	FACETS	0.909	0.842	0.979	0.909	0.842	0.979	CLONAL	1	TRUE	1	0.486979205687301	2		538	867	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40864479	40864479	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	228	600	0	ENST00000428826.2:c.1229C>T	p.Pro410Leu	p.P410L	ENST00000428826		410	cCc/cTc	12/21	1	2	FACETS	0.984	0.917	1	0.984	0.917	1	CLONAL	1	TRUE	1	0.486979205687301	2		600	952	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211883	36211883	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202218975	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	310	843	2	ENST00000222270.7:c.1634G>A	p.Arg545Gln	p.R545Q	ENST00000222270	NM_014727.1	545	cGa/cAa	3/37	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.486979205687301	2		845	1256	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438586	52438586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1466585782	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	100	337	4	ENST00000460680.1:c.1133C>T	p.Ala378Val	p.A378V	ENST00000460680	NM_004656.3	378	gCg/gTg	12/17	1	2	FACETS	0.683	0.612	0.759	0.683	0.612	0.759	SUBCLONAL	1	TRUE	1	0.486979205687301	2		341	601	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254933	16254933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779692614	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	157	399	4	ENST00000375759.3:c.2198G>A	p.Arg733His	p.R733H	ENST00000375759	NM_015001.2	733	cGt/cAt	11/15	1	2	FACETS	0.998	0.918	1	0.998	0.918	1	CLONAL	1	TRUE	1	0.486979205687301	2		403	646	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263810	16263810	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	67	497	0	ENST00000375759.3:c.10182del	p.Thr3395ProfsTer5	p.T3395Pfs*5	ENST00000375759	NM_015001.2	3393	aaG/aa	12/15	1	2	FACETS	0.358	0.31	0.41	0.358	0.31	0.41	SUBCLONAL	1	TRUE	1	0.486979205687301	2		497	769	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937950	36937950	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368300579	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	194	690	2	ENST00000361632.4:c.886G>A	p.Gly296Arg	p.G296R	ENST00000361632		296	Ggg/Agg	7/16	1	2	FACETS	0.722	0.668	0.779	0.722	0.668	0.779	SUBCLONAL	1	TRUE	1	0.486979205687301	2		692	1103	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203511	108203511	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	81	257	0	ENST00000278616.4:c.7811G>T	p.Arg2604Ile	p.R2604I	ENST00000278616	NM_000051.3	2604	aGa/aTa	53/63	1	2	FACETS	0.823	0.729	0.923	0.823	0.729	0.923	CLONAL	1	TRUE	1	0.486979205687301	2		257	404	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344821	118344821	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	93	302	0	ENST00000534358.1:c.2947C>A	p.Leu983Met	p.L983M	ENST00000534358	NM_005933.3	983	Ctg/Atg	3/36	1	2	FACETS	0.715	0.638	0.797	0.715	0.638	0.797	SUBCLONAL	1	TRUE	1	0.486979205687301	2		302	534	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864745	57864745	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	152	601	0	ENST00000228682.2:c.2222A>G	p.Glu741Gly	p.E741G	ENST00000228682	NM_005269.2	741	gAg/gGg	12/12	1	2	FACETS	0.677	0.619	0.738	0.677	0.619	0.738	SUBCLONAL	1	TRUE	1	0.486979205687301	2		601	922	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609880	81609880	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	91	252	0	ENST00000298171.2:c.1478G>A	p.Gly493Glu	p.G493E	ENST00000298171	NM_000369.2	493	gGg/gAg	10/10	1	2	FACETS	0.963	0.861	1	0.963	0.861	1	CLONAL	1	TRUE	1	0.486979205687301	2		252	388	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610452	81610452	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267604071	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	116	291	0	ENST00000298171.2:c.2050G>A	p.Ala684Thr	p.A684T	ENST00000298171	NM_000369.2	684	Gcc/Acc	10/10	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.486979205687301	2		291	476	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003773	45003773	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	301	356	1	ENST00000558401.1:c.29T>C	p.Leu10Pro	p.L10P	ENST00000558401	NM_004048.2	10	cTc/cCc	1/4	0.486979205687301	2	FACETS	0.978	0.93	1	0.978	0.93	1	CLONAL	2	TRUE	0	0.486979205687301	2		357	632	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632597	3632597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	236	650	0	ENST00000294008.3:c.5251G>A	p.Asp1751Asn	p.D1751N	ENST00000294008	NM_032444.2	1751	Gac/Aac	15/15	1	2	FACETS	0.943	0.88	1	0.943	0.88	1	CLONAL	1	TRUE	1	0.486979205687301	2		650	1028	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14021985	14021985	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1022507611	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	79	494	0	ENST00000311895.7:c.685A>G	p.Ile229Val	p.I229V	ENST00000311895	NM_005236.2	229	Ata/Gta	4/11	1	2	FACETS	0.401	0.352	0.453	0.401	0.352	0.453	SUBCLONAL	1	TRUE	1	0.486979205687301	2		494	810	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782248	56782248	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	162	397	0	ENST00000308159.5:c.89A>G	p.Glu30Gly	p.E30G	ENST00000308159	NM_014669.4	30	gAa/gGa	2/22	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.486979205687301	2		397	624	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870594	40870594	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	62	583	0	ENST00000428826.2:c.809C>A	p.Pro270His	p.P270H	ENST00000428826		270	cCc/cAc	9/21	1	2	FACETS	0.263	0.226	0.304	0.263	0.226	0.304	SUBCLONAL	1	TRUE	1	0.486979205687301	2		583	967	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436008	56436008	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	29	290	0	ENST00000407977.2:c.1129C>A	p.Pro377Thr	p.P377T	ENST00000407977		377	Cca/Aca	9/10	1	2	FACETS	0.262	0.21	0.321	0.262	0.21	0.321	SUBCLONAL	1	TRUE	1	0.486979205687301	2		290	455	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78599504	78599504	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	187	349	0	ENST00000306801.3:c.176G>A	p.Ser59Asn	p.S59N	ENST00000306801	NM_020761.2	59	aGt/aAt	2/34	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.486979205687301	2		349	614	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610211	10610211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749396788	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	265	643	0	ENST00000171111.5:c.499G>A	p.Val167Ile	p.V167I	ENST00000171111	NM_203500.1	167	Gtt/Att	2/6	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.486979205687301	2		643	1028	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152064	11152064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761083981	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	207	457	0	ENST00000358026.2:c.4348G>A	p.Asp1450Asn	p.D1450N	ENST00000358026	NM_001128849.1	1450	Gac/Aac	31/36	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.486979205687301	2		457	797	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945448	17945448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	70	559	0	ENST00000458235.1:c.2282C>T	p.Ala761Val	p.A761V	ENST00000458235	NM_000215.3	761	gCc/gTc	17/24	1	2	FACETS	0.28	0.243	0.32	0.28	0.243	0.32	SUBCLONAL	1	TRUE	1	0.486979205687301	2		559	1028	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523021	25523021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457666600	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	162	562	0	ENST00000264709.3:c.164G>A	p.Arg55His	p.R55H	ENST00000264709	NM_175629.2	55	cGc/cAc	3/23	1	2	FACETS	0.686	0.629	0.746	0.686	0.629	0.746	SUBCLONAL	1	TRUE	1	0.486979205687301	2		562	970	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46608817	46608817	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	177	630	0	ENST00000263734.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000263734	NM_001430.4	710	Cga/Tga	13/16	1	2	FACETS	0.763	0.703	0.825	0.763	0.703	0.825	SUBCLONAL	1	TRUE	1	0.486979205687301	2		630	953	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022247	31022247	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1569327372	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	105	273	0	ENST00000375687.4:c.1732C>T	p.Arg578Cys	p.R578C	ENST00000375687	NM_015338.5	578	Cgt/Tgt	13/13	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.486979205687301	2		273	408	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022680	31022680	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	142	592	0	ENST00000375687.4:c.2165C>A	p.Pro722His	p.P722H	ENST00000375687	NM_015338.5	722	cCt/cAt	13/13	1	2	FACETS	0.677	0.616	0.74	0.677	0.616	0.74	SUBCLONAL	1	TRUE	1	0.486979205687301	2		592	862	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368253	31368253	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	59	510	1	ENST00000328111.2:c.124C>A	p.Arg42Ser	p.R42S	ENST00000328111	NM_006892.3	42	Cgc/Agc	2/23	1	2	FACETS	0.265	0.227	0.307	0.265	0.227	0.307	SUBCLONAL	1	TRUE	1	0.486979205687301	2		511	913	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031586	36031586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774838914	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	166	489	2	ENST00000358208.4:c.1415G>A	p.Arg472His	p.R472H	ENST00000358208		472	cGc/cAc	12/12	1	2	FACETS	0.839	0.771	0.909	0.839	0.771	0.909	CLONAL	1	TRUE	1	0.486979205687301	2		491	813	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188272	10188272	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	194	556	0	ENST00000256474.2:c.415T>C	p.Ser139Pro	p.S139P	ENST00000256474	NM_000551.3	139	Tct/Cct	2/3	1	2	FACETS	0.884	0.819	0.952	0.884	0.819	0.952	CLONAL	1	TRUE	1	0.486979205687301	2		556	901	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156562	106156562	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs758328975	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	117	319	0	ENST00000380013.4:c.1463A>G	p.Asn488Ser	p.N488S	ENST00000380013	NM_001127208.2	488	aAt/aGt	3/11	1	2	FACETS	0.952	0.862	1	0.952	0.862	1	CLONAL	1	TRUE	1	0.486979205687301	2		319	505	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526618	31526618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	150	501	0	ENST00000344624.3:c.422C>T	p.Thr141Ile	p.T141I	ENST00000344624		141	aCt/aTt	2/33	1	2	FACETS	0.889	0.814	0.967	0.889	0.814	0.967	CLONAL	1	TRUE	1	0.486979205687301	2		501	693	SUCCESS
APC	324	MSKCC	GRCh37	5	112177922	112177922	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	49	330	0	ENST00000257430.4:c.6631G>T	p.Gly2211Cys	p.G2211C	ENST00000257430	NM_000038.5	2211	Ggc/Tgc	16/16	1	2	FACETS	0.343	0.29	0.402	0.343	0.29	0.402	SUBCLONAL	1	TRUE	1	0.486979205687301	2		330	586	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520479	176520479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749158608	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	278	660	1	ENST00000292408.4:c.1324G>A	p.Gly442Ser	p.G442S	ENST00000292408	NM_213647.1	442	Ggc/Agc	10/18	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.486979205687301	2		661	1077	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048157	180048157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768465100	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	69	598	2	ENST00000261937.6:c.2116G>A	p.Ala706Thr	p.A706T	ENST00000261937	NM_182925.4	706	Gcg/Acg	14/30	1	2	FACETS	0.274	0.238	0.314	0.274	0.238	0.314	SUBCLONAL	1	TRUE	1	0.486979205687301	2		600	1033	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778214	27778214	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	148	528	0	ENST00000369163.2:c.363G>T	p.Met121Ile	p.M121I	ENST00000369163	NM_003536.2	121	atG/atT	1/1	1	2	FACETS	0.883	0.809	0.961	0.883	0.809	0.961	CLONAL	1	TRUE	1	0.486979205687301	2		528	688	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289112	33289112	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	58	566	0	ENST00000374542.5:c.440del	p.Pro147LeufsTer82	p.P147Lfs*82	ENST00000374542	NM_001141970.1	147	cCt/ct	3/8	1	2	FACETS	0.26	0.222	0.301	0.26	0.222	0.301	SUBCLONAL	1	TRUE	1	0.486979205687301	2		566	917	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200459	138200460	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	46	423	0	ENST00000237289.4:c.1880_1881del	p.Cys627PhefsTer44	p.C627Ffs*44	ENST00000237289	NM_001270507.1	626	cTG/c	7/9	1	2	FACETS	0.288	0.242	0.339	0.288	0.242	0.339	SUBCLONAL	1	TRUE	1	0.486979205687301	2		423	656	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370942	55370942	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	209	615	2	ENST00000297316.4:c.244G>A	p.Glu82Lys	p.E82K	ENST00000297316	NM_022454.3	82	Gag/Aag	1/2	1	2	FACETS	0.967	0.898	1	0.967	0.898	1	CLONAL	1	TRUE	1	0.486979205687301	2		617	888	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760004	133760004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	85	740	0	ENST00000318560.5:c.2329del	p.Arg777GlufsTer4	p.R777Efs*4	ENST00000318560	NM_005157.4	776	aCc/ac	11/11	1	2	FACETS	0.304	0.267	0.343	0.304	0.267	0.343	SUBCLONAL	1	TRUE	1	0.486979205687301	2		740	1149	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771794	135771794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	241	546	1	ENST00000298552.3:c.3323G>A	p.Gly1108Asp	p.G1108D	ENST00000298552	NM_001162426.1	1108	gGc/gAc	23/23	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.486979205687301	2		547	946	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300005	137300005	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	96	547	1	ENST00000481739.1:c.290C>A	p.Pro97His	p.P97H	ENST00000481739	NM_002957.4	97	cCt/cAt	3/10	1	2	FACETS	0.428	0.38	0.478	0.428	0.38	0.478	SUBCLONAL	1	TRUE	1	0.486979205687301	2		548	922	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	231112	231112	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	37	245	0	ENST00000264932.6:c.892A>G	p.Thr298Ala	p.T298A	ENST00000264932	NM_004168.2	298	Aca/Gca	7/15	1	2	FACETS	0.349	0.287	0.417	0.349	0.287	0.417	SUBCLONAL	1	TRUE	1	0.486979205687301	2		245	436	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380570	31380570	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1158754730	NA	P-0029442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	113	572	1	ENST00000328111.2:c.1060C>T	p.Gln354Ter	p.Q354*	ENST00000328111	NM_006892.3	354	Caa/Taa	9/23	0.45701450917238	3	FACETS	0.653	0.588	0.723	0.327	0.294	0.362	SUBCLONAL	1	TRUE	1	0.542277859214179	3		573	811	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077476	30077486	+	frameshift_variant	Frame_Shift_Del	DEL	ACTCAAGACAG	ACTCAAGACAG	-	novel	NA	P-0029442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	306	666	1	ENST00000338641.4:c.1624_1634del	p.Leu542AsnfsTer19	p.L542Nfs*19	ENST00000338641	NM_000268.3	541	gaACTCAAGACAGaa/gaaa	15/16	0.466199245276625	2	FACETS	0.823	0.781	0.864	0.823	0.781	0.864	CLONAL	2	TRUE	0	0.542277859214179	2		667	686	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288770	33288771	+	inframe_insertion	In_Frame_Ins	INS	-	-	CACGGTAGGGGATGCGCTGCTCTATGA	novel	NA	P-0029442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	65	617	0	ENST00000374542.5:c.755_781dup	p.Val252_Arg260dup	p.V252_R260dup	ENST00000374542	NM_001141970.1	252	ggc/gTCATAGAGCAGCGCATCCCCTACCGTGgc	3/8	0.408179799615718	4	FACETS	0.377	0.326	0.433	0.189	0.163	0.217	SUBCLONAL	1	TRUE	2	0.542277859214179	4		617	980	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0029454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	746	663	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.677779955037142	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.79265785507338	3		664	1300	SUCCESS
APC	324	MSKCC	GRCh37	5	112175351	112175352	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0029454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	294	266	0	ENST00000257430.4:c.4062_4063del	p.Ser1355PhefsTer19	p.S1355Ffs*19	ENST00000257430	NM_000038.5	1354	TTt/t	16/16	0.766429763509015	3	FACETS	0.913	0.883	0.943	0.913	0.883	0.943	CLONAL	3	TRUE	0	0.79265785507338	3		266	378	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981540	201981540	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	726	832	2	ENST00000359651.3:c.454G>T	p.Glu152Ter	p.E152*	ENST00000359651		152	Gag/Tag	3/8	0.787923699723525	3	FACETS	0.958	0.929	0.987	0.958	0.929	0.987	CLONAL	2	TRUE	1	0.79265785507338	3		834	1335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572928	7572929	+	frameshift_variant,stop_lost	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	240	550	0	ENST00000269305.4:c.1180dup	p.Ter394LeufsTer77	p.*394Lfs*77	ENST00000269305	NM_001126112.2	394	tga/tTga	11/11	0.677779955037142	3	FACETS	0.951	0.89	1	0.476	0.445	0.507	CLONAL	1	TRUE	1	0.79265785507338	3		550	889	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	137	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.223366130360055	2	FACETS	1	0.986	1	0.722	0.658	0.789	CLONAL	1	TRUE	0	0.26987679312759	2		436	703	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109319958	109319958	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	52	430	0	ENST00000436639.2:c.730G>A	p.Gly244Arg	p.G244R	ENST00000436639	NM_014454.2	244	Gga/Aga	5/10	0.154919195938988	4	FACETS	0.801	0.681	0.932	0.4	0.34	0.466	INDETERMINATE	1	TRUE	2	0.26987679312759	4		430	611	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0029721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	42	302	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.15	2		302	423	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0029721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	16	225	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.469	0.345	0.618	0.469	0.345	0.618	SUBCLONAL	1	TRUE	1	0.15	2		225	455	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0029721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	27	364	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	1	2	FACETS	0.845	0.672	1	0.845	0.672	1	CLONAL	1	TRUE	1	0.15	2		364	426	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662539	227662539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	41	402	0	ENST00000305123.5:c.916G>A	p.Glu306Lys	p.E306K	ENST00000305123	NM_005544.2	306	Gag/Aag	1/2	1	2	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	TRUE	1	0.15	2		402	532	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861143	57861143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772799269	NA	P-0029721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	44	533	0	ENST00000228682.2:c.940C>T	p.Arg314Cys	p.R314C	ENST00000228682	NM_005269.2	314	Cgc/Tgc	9/12	0.0976316793287707	3	FACETS	0.993	0.832	1	0.497	0.416	0.587	CLONAL	1	TRUE	1	0.15	3		533	635	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057961	27057961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	57	575	1	ENST00000324856.7:c.1669C>T	p.Gln557Ter	p.Q557*	ENST00000324856	NM_006015.4	557	Cag/Tag	3/20	0.136277816249479	3	FACETS	1	0.899	1	0.531	0.455	0.615	CLONAL	1	TRUE	1	0.15	3		576	769	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026871	71026871	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	21	273	0	ENST00000318789.4:c.1351G>A	p.Asp451Asn	p.D451N	ENST00000318789	NM_032682.5	451	Gat/Aat	16/21	1	2	FACETS	0.918	0.707	1	0.918	0.707	1	CLONAL	1	TRUE	1	0.15	2		273	305	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818358	43818358	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	72	614	0	ENST00000372470.3:c.1823C>T	p.Pro608Leu	p.P608L	ENST00000372470	NM_005373.2	608	cCa/cTa	12/12	0.136277816249479	3	FACETS	1	0.969	1	0.696	0.608	0.792	CLONAL	1	TRUE	1	0.15	3		614	741	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247934	59247934	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	111	718	3	ENST00000371222.2:c.809G>T	p.Arg270Leu	p.R270L	ENST00000371222	NM_002228.3	270	cGa/cTa	1/1	0.136277816249479	3	FACETS	0.805	0.722	0.893	0.805	0.722	0.893	CLONAL	2	TRUE	1	0.15	3		721	988	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206669470	206669470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	36	571	0	ENST00000367120.3:c.2143G>A	p.Asp715Asn	p.D715N	ENST00000367120	NM_014002.3	715	Gat/Aat	22/22	0.136277816249479	3	FACETS	0.722	0.591	0.869	0.361	0.295	0.435	SUBCLONAL	1	TRUE	1	0.15	3		571	715	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724694	112724694	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	30	540	1	ENST00000369452.4:c.578C>T	p.Ser193Phe	p.S193F	ENST00000369452	NM_007373.3	193	tCt/tTt	2/9	1	2	FACETS	0.735	0.591	0.9	0.735	0.591	0.9	SUBCLONAL	1	TRUE	1	0.15	2		541	544	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41199678	41199678	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	45	723	0	ENST00000357654.3:c.5449G>C	p.Glu1817Gln	p.E1817Q	ENST00000357654	NM_007294.3	1817	Gag/Cag	22/23	0.136277816249479	3	FACETS	0.779	0.653	0.92	0.389	0.326	0.46	CLONAL	1	TRUE	1	0.15	3		723	828	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39595486	39595486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	19	402	0	ENST00000262039.4:c.1372C>T	p.Pro458Ser	p.P458S	ENST00000262039	NM_002647.2	458	Cct/Tct	12/25	1	2	FACETS	0.698	0.529	0.897	0.698	0.529	0.897	SUBCLONAL	1	TRUE	1	0.15	2		402	363	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264782	46264782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	25	494	0	ENST00000371998.3:c.1652C>T	p.Ser551Phe	p.S551F	ENST00000371998		551	tCt/tTt	12/23	1	2	FACETS	0.676	0.532	0.843	0.676	0.532	0.843	SUBCLONAL	1	TRUE	1	0.15	2		494	493	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098795	47098795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745996964	NA	P-0029721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	58	723	0	ENST00000409792.3:c.6479C>T	p.Pro2160Leu	p.P2160L	ENST00000409792	NM_014159.6	2160	cCg/cTg	15/21	1	2	FACETS	0.988	0.847	1	0.988	0.847	1	CLONAL	1	TRUE	1	0.15	2		723	783	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961452	1961452	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	42	495	0	ENST00000382891.5:c.3240G>C	p.Lys1080Asn	p.K1080N	ENST00000382891	NM_133335.3	1080	aaG/aaC	17/22	1	2	FACETS	1	0.839	1	1	0.839	1	CLONAL	1	TRUE	1	0.15	2		495	557	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177397	56177410	+	frameshift_variant	Frame_Shift_Del	DEL	GTATAAGAAGCTGC	GTATAAGAAGCTGC	CTA	novel	NA	P-0029721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	19	251	0	ENST00000399503.3:c.2370_2383delinsCTA	p.Arg790SerfsTer13	p.R790Sfs*13	ENST00000399503	NM_005921.1	790	agGTATAAGAAGCTGCtg/agCTAtg	14/20	0.0976316793287707	3	FACETS	0.893	0.678	1	0.446	0.339	0.573	CLONAL	1	TRUE	1	0.15	3		251	305	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878902	151878902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1412833343	NA	P-0029721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	33	514	0	ENST00000262189.6:c.6043G>A	p.Asp2015Asn	p.D2015N	ENST00000262189	NM_170606.2	2015	Gat/Aat	36/59	1	2	FACETS	0.894	0.728	1	0.894	0.728	1	CLONAL	1	TRUE	1	0.15	2		514	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782664	NA	P-0029743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	141	585	0	ENST00000269305.4:c.711G>C	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atC	7/11	0.259761383168332	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.278280806905847	1		585	833	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118870	70118870	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs886041242	NA	P-0029743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	55	371	0	ENST00000245479.2:c.442G>C	p.Glu148Gln	p.E148Q	ENST00000245479	NM_000346.3	148	Gag/Cag	2/3	0.268728982918503	3	FACETS	0.499	0.426	0.58	0.166	0.142	0.194	SUBCLONAL	1	TRUE	0	0.278280806905847	3		371	902	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156439	106156439	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	50	352	0	ENST00000380013.4:c.1340G>C	p.Arg447Thr	p.R447T	ENST00000380013	NM_001127208.2	447	aGg/aCg	3/11	1	2	FACETS	0.564	0.478	0.659	0.564	0.478	0.659	SUBCLONAL	1	TRUE	1	0.278280806905847	2		352	637	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0029819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	68	570	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.712	0.62	0.812	0.712	0.62	0.812	SUBCLONAL	1	TRUE	1	0.31	2		570	616	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575152	48575152	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	34	293	0	ENST00000342988.3:c.346C>T	p.Gln116Ter	p.Q116*	ENST00000342988	NM_005359.5	116	Cag/Tag	3/12	1	2	FACETS	0.532	0.435	0.642	0.532	0.435	0.642	SUBCLONAL	1	TRUE	1	0.31	2		293	412	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332628	153332628	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	49	391	0	ENST00000281708.4:c.328G>T	p.Glu110Ter	p.E110*	ENST00000281708	NM_033632.3	110	Gag/Tag	2/12	1	2	FACETS	0.668	0.566	0.78	0.668	0.566	0.78	SUBCLONAL	1	TRUE	1	0.31	2		391	473	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425073	49425073	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs768387349	NA	P-0029819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	79	716	0	ENST00000301067.7:c.13415T>C	p.Val4472Ala	p.V4472A	ENST00000301067	NM_003482.3	4472	gTg/gCg	39/54	1	2	FACETS	0.572	0.502	0.648	0.572	0.502	0.648	SUBCLONAL	1	TRUE	1	0.31	2		716	891	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913983	32913984	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs80359517	NA	P-0029819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	55	468	0	ENST00000380152.3:c.5492dup	p.Ser1832IlefsTer2	p.S1832Ifs*2	ENST00000380152		1831	ata/aTta	11/27	1	2	FACETS	0.52	0.444	0.603	0.52	0.444	0.603	SUBCLONAL	1	TRUE	1	0.31	2		468	683	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033405	48033405	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	60	448	0	ENST00000234420.5:c.3709G>C	p.Glu1237Gln	p.E1237Q	ENST00000234420	NM_000179.2	1237	Gag/Cag	8/10	1	2	FACETS	0.542	0.466	0.625	0.542	0.466	0.625	SUBCLONAL	1	TRUE	1	0.31	2		448	714	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68999981	68999981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	52	516	0	ENST00000288368.4:c.2050G>A	p.Ala684Thr	p.A684T	ENST00000288368	NM_024870.2	684	Gct/Act	19/40	1	2	FACETS	0.49	0.416	0.571	0.49	0.416	0.571	SUBCLONAL	1	TRUE	1	0.31	2		516	685	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249350	110249406	+	inframe_deletion	In_Frame_Del	DEL	GTGTAGGTTTTGCCGCAGCCCGCGTAATCACAAGTGTGGGTGGCGGTCCTTTTCCGG	GTGTAGGTTTTGCCGCAGCCCGCGTAATCACAAGTGTGGGTGGCGGTCCTTTTCCGG	-	novel	NA	P-0029819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	105	912	0	ENST00000374672.4:c.1167_1223del	p.Arg390_Thr408del	p.R390_T408del	ENST00000374672	NM_004235.4	389	ccCCGGAAAAGGACCGCCACCCACACTTGTGATTACGCGGGCTGCGGCAAAACCTACACa/cca	4/5	1	2	FACETS	0.594	0.531	0.662	0.594	0.531	0.662	SUBCLONAL	1	TRUE	1	0.31	2		912	1140	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913079	44913082	+	frameshift_variant	Frame_Shift_Del	DEL	ATGC	ATGC	-	novel	NA	P-0029819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	68	184	0	ENST00000377967.4:c.756_759del	p.Met252IlefsTer4	p.M252Ifs*4	ENST00000377967	NM_021140.2	252	ATGCat/at	10/29	1	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.31	1		184	263	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0029990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	126	303	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.105511587611242	5	FACETS	1	0.949	1	0.712	0.646	0.78	INDETERMINATE	2	FALSE	2	0.257797431302309	5		303	635	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0029990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	258	525	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.257797431302309	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	FALSE	0	0.257797431302309	2		525	959	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911534	101911534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111426349	NA	P-0029990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	154	384	0	ENST00000374994.4:c.1459C>T	p.Arg487Trp	p.R487W	ENST00000374994	NM_004612.2	487	Cgg/Tgg	9/9	0.257797431302309	2	FACETS	0.93	0.854	1	0.93	0.854	1	CLONAL	2	FALSE	0	0.257797431302309	2		384	642	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50810101	50810101	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	52	401	1	ENST00000398568.2:c.925C>T	p.Gln309Ter	p.Q309*	ENST00000398568	NM_001042412.1	309	Cag/Tag	6/18	0.105511587611242	5	FACETS	0.844	0.717	0.983	0.281	0.239	0.328	INDETERMINATE	1	FALSE	2	0.257797431302309	5		402	663	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437265	220437265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1224525818	NA	P-0029990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1226	170	654	3	ENST00000243786.2:c.169C>T	p.Arg57Trp	p.R57W	ENST00000243786	NM_002191.3	57	Cgg/Tgg	1/2	0.257797431302309	3	FACETS	1	0.957	1	0.533	0.489	0.58	CLONAL	1	FALSE	1	0.257797431302309	3		657	1396	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665315	117665315	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	36	338	0	ENST00000368508.3:c.4432del	p.Tyr1478MetfsTer26	p.Y1478Mfs*26	ENST00000368508	NM_002944.2	1478	Tat/at	27/43	1	2	FACETS	0.551	0.452	0.662	0.551	0.452	0.662	SUBCLONAL	1	FALSE	1	0.257797431302309	2		338	507	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0030014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	30	553	1	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.132038867841739	4	FACETS	0.226	0.181	0.277	0.113	0.09	0.139	INDETERMINATE	1	TRUE	2	0.39003307572941	4		554	947	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692835	89692835	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs57374291	NA	P-0030014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	106	195	0	ENST00000371953.3:c.319G>T	p.Asp107Tyr	p.D107Y	ENST00000371953	NM_000314.4	107	Gat/Tat	5/9	0.34894764009606	2	FACETS	0.971	0.884	1	0.971	0.884	1	CLONAL	2	TRUE	0	0.39003307572941	2		195	280	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46724370	46724370	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs138566817	NA	P-0030014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	279	619	0	ENST00000371975.4:c.223C>T	p.Arg75Ter	p.R75*	ENST00000371975	NM_003579.3	75	Cga/Tga	4/18	0.34894764009606	2	FACETS	0.892	0.841	0.944	0.892	0.841	0.944	CLONAL	2	TRUE	0	0.39003307572941	2		619	802	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	322	737	1	ENST00000269305.4:c.472C>A	p.Arg158Ser	p.R158S	ENST00000269305	NM_001126112.2	158	Cgc/Agc	5/11	0.36002336165764	2	FACETS	0.858	0.812	0.905	0.858	0.812	0.905	CLONAL	2	TRUE	0	0.39003307572941	2		738	962	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578445	7578450	+	inframe_deletion	In_Frame_Del	DEL	ATGGCC	ATGGCC	-	novel	NA	P-0030014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	300	709	0	ENST00000269305.4:c.480_485del	p.Met160_Ala161del	p.M160_A161del	ENST00000269305	NM_001126112.2	160	atGGCCATc/atc	5/11	0.36002336165764	2	FACETS	0.854	0.806	0.902	0.854	0.806	0.902	CLONAL	2	TRUE	0	0.39003307572941	2		709	901	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830731	156830731	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	20	88	0	ENST00000524377.1:c.5T>A	p.Leu2Gln	p.L2Q	ENST00000524377	NM_002529.3	2	cTg/cAg	1/17	0.39003307572941	5	FACETS	1	0.907	1			1	CLONAL	1	TRUE	NA	0.39003307572941	5		88	117	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432484	49432484	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	239	683	0	ENST00000301067.7:c.8655G>C	p.Gln2885His	p.Q2885H	ENST00000301067	NM_003482.3	2885	caG/caC	34/54	0.208822142284024	5	FACETS	0.836	0.78	0.894	0.557	0.52	0.596	INDETERMINATE	2	TRUE	2	0.39003307572941	5		683	1162	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448758	49448758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	243	522	0	ENST00000301067.7:c.101C>T	p.Pro34Leu	p.P34L	ENST00000301067	NM_003482.3	34	cCc/cTc	2/54	0.208822142284024	5	FACETS	0.887	0.828	0.948	0.592	0.552	0.632	INDETERMINATE	2	TRUE	2	0.39003307572941	5		522	1113	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50481248	50481248	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	178	413	0	ENST00000394963.4:c.634G>C	p.Glu212Gln	p.E212Q	ENST00000394963	NM_003076.4	212	Gaa/Caa	5/13	0.208822142284024	5	FACETS	0.912	0.842	0.985	0.608	0.561	0.657	INDETERMINATE	2	TRUE	2	0.39003307572941	5		413	793	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123627	11123627	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	120	579	0	ENST00000358026.2:c.2277C>G	p.Ile759Met	p.I759M	ENST00000358026	NM_001128849.1	759	atC/atG	16/36	0.193117305534307	3	FACETS	0.881	0.795	0.971	0.44	0.397	0.486	INDETERMINATE	1	TRUE	1	0.39003307572941	3		579	835	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36014531	36014531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	123	607	0	ENST00000358208.4:c.304G>A	p.Asp102Asn	p.D102N	ENST00000358208		102	Gac/Aac	3/12	0.33727426233339	6	FACETS	0.829	0.747	0.915	0.207	0.186	0.229	CLONAL	1	TRUE	2	0.39003307572941	6		607	1355	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36014552	36014552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1195	116	580	0	ENST00000358208.4:c.325G>A	p.Glu109Lys	p.E109K	ENST00000358208		109	Gag/Aag	3/12	0.33727426233339	6	FACETS	0.808	0.725	0.895	0.202	0.181	0.224	CLONAL	1	TRUE	2	0.39003307572941	6		580	1311	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998975	169998975	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	73	388	0	ENST00000295797.4:c.904G>C	p.Glu302Gln	p.E302Q	ENST00000295797	NM_002740.5	302	Gag/Cag	10/18	0.132038867841739	4	FACETS	0.852	0.745	0.966	0.426	0.372	0.483	INDETERMINATE	1	TRUE	2	0.39003307572941	4		388	611	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176618927	176618927	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	297	575	2	ENST00000439151.2:c.970G>A	p.Gly324Arg	p.G324R	ENST00000439151	NM_022455.4	324	Gga/Aga	3/23	0.36002336165764	2	FACETS	0.876	0.828	0.926	0.876	0.828	0.926	CLONAL	2	TRUE	0	0.39003307572941	2		577	869	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056065	26056065	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	283	318	0	ENST00000343677.2:c.592G>C	p.Ala198Pro	p.A198P	ENST00000343677	NM_005319.3	198	Gct/Cct	1/1	0.39003307572941	5	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	TRUE	2	0.39003307572941	5		318	735	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965690	90965690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	160	406	0	ENST00000265433.3:c.1627G>A	p.Glu543Lys	p.E543K	ENST00000265433	NM_002485.4	543	Gaa/Aaa	11/16	0.377731019006074	4	FACETS	1	0.987	1	0.697	0.64	0.757	CLONAL	1	TRUE	2	0.39003307572941	4		406	818	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	92	607	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.664	0.591	0.742	0.664	0.591	0.742	SUBCLONAL	1	TRUE	1	0.46105112237069	2		613	601	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	158	468	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.248906122468239	3	FACETS	1	0.945	1	0.52	0.477	0.565	INDETERMINATE	1	TRUE	1	0.46105112237069	3		472	811	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	197	665	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.46105112237069	2	FACETS	0.969	0.908	1	0.969	0.908	1	CLONAL	2	TRUE	0	0.46105112237069	2		665	441	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795103	242795104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs768249210	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	157	997	0	ENST00000334409.5:c.105dup	p.Thr36HisfsTer70	p.T36Hfs*70	ENST00000334409	NM_005018.2	35	-/C	2/5	1	2	FACETS	0.795	0.728	0.864	0.795	0.728	0.864	SUBCLONAL	1	TRUE	1	0.46105112237069	2		997	857	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209314	133209314	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs754630848	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	66	541	1	ENST00000320574.5:c.6072del	p.Val2025Ter	p.V2025*	ENST00000320574	NM_006231.2	2024	ccC/cc	44/49	1	2	FACETS	0.324	0.28	0.371	0.324	0.28	0.371	SUBCLONAL	1	TRUE	1	0.46105112237069	2		542	885	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	127	461	2	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.993	0.903	1	0.993	0.903	1	CLONAL	1	TRUE	1	0.46105112237069	2		463	555	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100175	27100176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	109	621	2	ENST00000324856.7:c.3977dup	p.Gln1327AlafsTer11	p.Q1327Afs*11	ENST00000324856	NM_006015.4	1324	tac/taCc	16/20	1	2	FACETS	0.793	0.714	0.877	0.793	0.714	0.877	SUBCLONAL	1	TRUE	1	0.46105112237069	2		623	596	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665752	29665755	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1555535032	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	117	300	0	ENST00000356175.3:c.6789_6792del	p.Tyr2264ThrfsTer5	p.Y2264Tfs*5	ENST00000356175	NM_000267.3	2263	ACTTac/ac	45/57	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.46105112237069	2		300	501	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	61	191	1	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.792	0.688	0.904	0.792	0.688	0.904	CLONAL	1	TRUE	1	0.46105112237069	2		192	334	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	199	694	2	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.46105112237069	2		696	844	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67459125	67459125	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	176	618	0	ENST00000327367.4:c.545del	p.Pro182LeufsTer4	p.P182Lfs*4	ENST00000327367	NM_005902.3	181	Ccc/cc	4/9	1	2	FACETS	0.867	0.799	0.937	0.867	0.799	0.937	CLONAL	1	TRUE	1	0.46105112237069	2		618	881	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764347	39764347	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	187	436	0	ENST00000288319.7:c.765del	p.Arg256GlyfsTer35	p.R256Gfs*35	ENST00000288319	NM_182918.3	255	ccC/cc	7/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.46105112237069	2		436	738	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132617	11132617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1445478818	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	232	566	1	ENST00000358026.2:c.2833G>A	p.Ala945Thr	p.A945T	ENST00000358026	NM_001128849.1	945	Gca/Aca	19/36	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.46105112237069	2		567	932	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533939	63533940	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs771001164	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	93	339	0	ENST00000307078.5:c.1214_1215del	p.Glu405GlyfsTer56	p.E405Gfs*56	ENST00000307078	NM_004655.3	405	gAG/g	6/11	0.248906122468239	3	FACETS	0.946	0.843	1	0.473	0.421	0.527	INDETERMINATE	1	TRUE	1	0.46105112237069	3		339	525	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519219	187519219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774367320	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	206	429	2	ENST00000441802.2:c.12164C>T	p.Pro4055Leu	p.P4055L	ENST00000441802	NM_005245.3	4055	cCg/cTg	23/27	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.46105112237069	2		431	839	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202148	67202148	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1265076720	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	84	552	4	ENST00000312629.5:c.1255del	p.Arg419GlyfsTer75	p.R419Gfs*75	ENST00000312629	NM_003952.2	417	agC/ag	14/15	1	2	FACETS	0.428	0.377	0.482	0.428	0.377	0.482	SUBCLONAL	1	TRUE	1	0.46105112237069	2		556	852	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114816	108114817	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	126	427	0	ENST00000278616.4:c.640dup	p.Ser214PhefsTer40	p.S214Ffs*40	ENST00000278616	NM_000051.3	211	-/T	6/63	1	2	FACETS	0.832	0.755	0.913	0.832	0.755	0.913	CLONAL	1	TRUE	1	0.46105112237069	2		427	657	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732984	30732984	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	48	266	0	ENST00000295754.5:c.1597T>C	p.Cys533Arg	p.C533R	ENST00000295754	NM_003242.5	533	Tgt/Cgt	7/7	0.46105112237069	2	FACETS	0.497	0.421	0.581	0.248	0.21	0.291	SUBCLONAL	1	TRUE	0	0.46105112237069	2		266	419	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119910	70119910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1297203260	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	70	387	1	ENST00000245479.2:c.916del	p.Val306CysfsTer77	p.V306Cfs*77	ENST00000245479	NM_000346.3	304	ccG/cc	3/3	0.248906122468239	3	FACETS	0.524	0.456	0.597	0.262	0.228	0.299	INDETERMINATE	1	TRUE	1	0.46105112237069	3		388	713	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	222	940	1	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.959	0.893	1	0.959	0.893	1	CLONAL	1	TRUE	1	0.46105112237069	2		941	1004	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874506	151874506	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	116	325	0	ENST00000262189.6:c.8032A>G	p.Thr2678Ala	p.T2678A	ENST00000262189	NM_170606.2	2678	Acc/Gcc	38/59	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.46105112237069	2		325	502	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324889	31324889	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs45585233	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	84	366	0	ENST00000412585.2:c.47C>G	p.Ala16Gly	p.A16G	ENST00000412585	NM_005514.6	16	gCc/gGc	1/8	1	2	FACETS	0.679	0.601	0.762	0.679	0.601	0.762	SUBCLONAL	1	TRUE	1	0.46105112237069	2		366	537	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324886	31324887	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760037174	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	84	374	0	ENST00000412585.2:c.49_50insG	p.Leu17ArgfsTer82	p.L17Rfs*82	ENST00000412585	NM_005514.6	17	ctg/cGtg	1/8	1	2	FACETS	0.671	0.594	0.753	0.671	0.594	0.753	SUBCLONAL	1	TRUE	1	0.46105112237069	2		374	543	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	319	798	29	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	1	2	FACETS	0.934	0.887	0.981	1	0.996	1	CLONAL	2	TRUE	1	0.46105112237069	2		827	741	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437701	49437701	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555194045	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	83	1202	4	ENST00000301067.7:c.5269C>T	p.Arg1757Ter	p.R1757*	ENST00000301067	NM_003482.3	1757	Cga/Tga	22/54	1	2	FACETS	0.401	0.353	0.453	0.401	0.353	0.453	SUBCLONAL	1	TRUE	1	0.46105112237069	2		1206	898	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415856	49415858	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	rs587783704	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	109	317	0	ENST00000301067.7:c.16489_16491del	p.Ile5497del	p.I5497del	ENST00000301067	NM_003482.3	5497	ATC/-	53/54	1	2	FACETS	0.896	0.807	0.988	0.896	0.807	0.988	CLONAL	1	TRUE	1	0.46105112237069	2		317	528	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128028913	128028913	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	160	379	1	ENST00000285398.2:c.1944del	p.Met650TrpfsTer32	p.M650Wfs*32	ENST00000285398	NM_000122.1	648	aaA/aa	12/15	1	2	FACETS	0.922	0.847	1	0.922	0.847	1	CLONAL	1	TRUE	1	0.46105112237069	2		380	753	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023715	27023716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	54	287	0	ENST00000324856.7:c.827dup	p.Gly277ArgfsTer123	p.G277Rfs*123	ENST00000324856	NM_006015.4	274	atg/atGg	1/20	1	2	FACETS	0.451	0.385	0.523	0.451	0.385	0.523	SUBCLONAL	1	TRUE	1	0.46105112237069	2		287	519	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212815	27212815	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1307510192	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	61	556	1	ENST00000380036.4:c.2797G>A	p.Ala933Thr	p.A933T	ENST00000380036	NM_000459.3	933	Gcg/Acg	17/23	1	2	FACETS	0.319	0.274	0.368	0.319	0.274	0.368	SUBCLONAL	1	TRUE	1	0.46105112237069	2		557	829	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501302	140501302	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs180177035	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	118	348	0	ENST00000288602.6:c.770A>G	p.Gln257Arg	p.Q257R	ENST00000288602	NM_004333.4	257	cAg/cGg	6/18	1	2	FACETS	0.939	0.851	1	0.939	0.851	1	CLONAL	1	TRUE	1	0.46105112237069	2		348	545	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268988	115268988	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	139	300	0	ENST00000438362.2:c.1622A>G	p.Asp541Gly	p.D541G	ENST00000438362	NM_001242891.1	541	gAc/gGc	14/20	1	2	FACETS	0.992	0.906	1	0.992	0.906	1	CLONAL	1	TRUE	1	0.46105112237069	2		300	608	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857874	57857874	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1389442591	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	166	374	0	ENST00000228682.2:c.193G>T	p.Gly65Cys	p.G65C	ENST00000228682	NM_005269.2	65	Ggc/Tgc	3/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.46105112237069	2		374	647	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914340	32914343	+	frameshift_variant	Frame_Shift_Del	DEL	GTTA	GTTA	-	rs80359543	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	65	429	0	ENST00000380152.3:c.5851_5854del	p.Ser1951TrpfsTer11	p.S1951Wfs*11	ENST00000380152		1950	GTTAgt/gt	11/27	1	2	FACETS	0.509	0.441	0.582	0.509	0.441	0.582	SUBCLONAL	1	TRUE	1	0.46105112237069	2		429	554	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308333	15308333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	98	580	0	ENST00000263388.2:c.175C>T	p.Pro59Ser	p.P59S	ENST00000263388	NM_000435.2	59	Ccc/Tcc	2/33	1	2	FACETS	0.451	0.401	0.504	0.451	0.401	0.504	SUBCLONAL	1	TRUE	1	0.46105112237069	2		580	943	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457206	25457206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	187	500	0	ENST00000264709.3:c.2681G>A	p.Ser894Asn	p.S894N	ENST00000264709	NM_175629.2	894	aGc/aAc	23/23	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.46105112237069	2		500	753	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143320	30143320	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769061878	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	99	494	0	ENST00000389048.3:c.206G>A	p.Arg69Gln	p.R69Q	ENST00000389048	NM_004304.4	69	cGg/cAg	1/29	1	2	FACETS	0.552	0.492	0.615	0.552	0.492	0.615	SUBCLONAL	1	TRUE	1	0.46105112237069	2		494	778	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046296	128046296	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs748138133	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	159	417	0	ENST00000285398.2:c.967A>G	p.Ser323Gly	p.S323G	ENST00000285398	NM_000122.1	323	Agc/Ggc	7/15	1	2	FACETS	0.967	0.889	1	0.967	0.889	1	CLONAL	1	TRUE	1	0.46105112237069	2		417	713	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321508	62321508	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs773705133	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	104	561	0	ENST00000360203.5:c.2210A>G	p.Asn737Ser	p.N737S	ENST00000360203	NM_001283009.1	737	aAc/aGc	25/35	0.241532353500392	5	FACETS	0.577	0.515	0.643	0.192	0.171	0.215	INDETERMINATE	1	TRUE	2	0.46105112237069	5		561	1323	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426031	138426031	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	136	400	0	ENST00000289153.2:c.1500del	p.Lys500AsnfsTer39	p.K500Nfs*39	ENST00000289153	NM_006219.2	500	aaA/aa	9/22	1	2	FACETS	0.871	0.794	0.952	0.871	0.794	0.952	CLONAL	1	TRUE	1	0.46105112237069	2		400	677	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268140	153268140	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs185892035	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	49	272	1	ENST00000281708.4:c.668G>A	p.Arg223His	p.R223H	ENST00000281708	NM_033632.3	223	cGc/cAc	4/12	1	2	FACETS	0.41	0.347	0.48	0.41	0.347	0.48	SUBCLONAL	1	TRUE	1	0.46105112237069	2		273	518	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524436	187524436	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	162	409	0	ENST00000441802.2:c.11244C>A	p.Cys3748Ter	p.C3748*	ENST00000441802	NM_005245.3	3748	tgC/tgA	19/27	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.46105112237069	2		409	664	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225746	26225746	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1365152477	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	77	492	0	ENST00000360408.1:c.364C>T	p.Pro122Ser	p.P122S	ENST00000360408	NM_003532.2	122	Cct/Tct	1/1	1	2	FACETS	0.443	0.388	0.502	0.443	0.388	0.502	SUBCLONAL	1	TRUE	1	0.46105112237069	2		492	754	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323992	31323992	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs41551517	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	16	10	0	ENST00000412585.2:c.571T>C	p.Trp191Arg	p.W191R	ENST00000412585	NM_005514.6	191	Tgg/Cgg	3/8	1	2	FACETS	1	0.833	1	1	0.951	1	CLONAL	3	TRUE	1	0.46105112237069	2		10	23	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820005	32820005	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	176	481	0	ENST00000354258.4:c.905A>G	p.Glu302Gly	p.E302G	ENST00000354258	NM_000593.5	302	gAg/gGg	3/11	1	2	FACETS	0.878	0.809	0.949	0.878	0.809	0.949	CLONAL	1	TRUE	1	0.46105112237069	2		481	870	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0030213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	121	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.424147618205201	2		436	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0030213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	200	346	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.383148991161332	1	FACETS	0.811	0.752	0.872	0.811	0.752	0.872	CLONAL	1	TRUE	0	0.424147618205201	1		346	916	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41219635	41219637	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	rs80358344	NA	P-0030213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	102	342	0	ENST00000357654.3:c.5062_5064del	p.Val1688del	p.V1688del	ENST00000357654	NM_007294.3	1688	GTT/-	16/23	0.381372365108398	3	FACETS	0.81	0.724	0.9	0.405	0.362	0.45	CLONAL	1	TRUE	1	0.424147618205201	3		342	720	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955121	17955121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769828760	NA	P-0030213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	232	491	1	ENST00000458235.1:c.106G>A	p.Gly36Arg	p.G36R	ENST00000458235	NM_000215.3	36	Ggg/Agg	2/24	1	2	FACETS	0.894	0.832	0.958	0.894	0.832	0.958	CLONAL	1	TRUE	1	0.424147618205201	2		492	1224	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940181	31940181	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1307450480	NA	P-0030213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1390	275	519	1	ENST00000375333.2:c.323C>T	p.Ser108Phe	p.S108F	ENST00000375333	NM_032454.1	108	tCc/tTc	2/8	0.333819796375737	3	FACETS	0.944	0.883	1	0.315	0.294	0.336	CLONAL	1	TRUE	0	0.424147618205201	3		520	1665	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020386	69020386	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	149	392	0	ENST00000288368.4:c.2758C>T	p.Gln920Ter	p.Q920*	ENST00000288368	NM_024870.2	920	Cag/Tag	24/40	0.381372365108398	3	FACETS	1	0.94	1	0.518	0.473	0.565	CLONAL	1	TRUE	1	0.424147618205201	3		392	822	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953893	32953896	+	frameshift_variant	Frame_Shift_Del	DEL	TGAG	TGAG	-	rs80359734	NA	P-0030289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	91	369	0	ENST00000380152.3:c.8961_8964del	p.Ser2988PhefsTer12	p.S2988Ffs*12	ENST00000380152		2987	cTGAGt/ct	23/27	1	2	FACETS	0.974	0.869	1	0.974	0.869	1	CLONAL	1	TRUE	1	0.400904367050415	2		369	466	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0030289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	254	570	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.961	1	1	0.995	1	CLONAL	2	TRUE	1	0.400904367050415	2		570	619	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023090	27023090	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	37	70	0	ENST00000324856.7:c.197del	p.Pro66ArgfsTer35	p.P66Rfs*35	ENST00000324856	NM_006015.4	66	Ccg/cg	1/20	0.370527157905488	1	FACETS	1	0.842	1	1	0.842	1	CLONAL	1	TRUE	0	0.400904367050415	1		70	147	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818427	43818427	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	165	552	0	ENST00000372470.3:c.1892A>G	p.Tyr631Cys	p.Y631C	ENST00000372470	NM_005373.2	631	tAt/tGt	12/12	1	2	FACETS	0.949	0.872	1	0.949	0.872	1	CLONAL	1	TRUE	1	0.400904367050415	2		552	867	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130282	2130285	+	frameshift_variant	Frame_Shift_Del	DEL	GGCA	GGCA	TT	novel	NA	P-0030289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	166	548	1	ENST00000219476.3:c.3514_3517delinsTT	p.Gly1172PhefsTer61	p.G1172Ffs*61	ENST00000219476	NM_000548.3	1172	GGCAcc/TTcc	30/42	1	2	FACETS	0.784	0.719	0.852	0.784	0.719	0.852	SUBCLONAL	1	TRUE	1	0.400904367050415	2		549	1056	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256250	41256278	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CTTTTTTGCAAAATTATAGCTGTTTGCAT	CTTTTTTGCAAAATTATAGCTGTTTGCAT	-	novel	NA	P-0030289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	82	310	0	ENST00000357654.3:c.302_330del	p.Tyr101Ter	p.Y101*	ENST00000357654	NM_007294.3	101	tATGCAAACAGCTATAATTTTGCAAAAAAG/t	6/23	1	2	FACETS	0.885	0.784	0.994	0.885	0.784	0.994	CLONAL	1	TRUE	1	0.400904367050415	2		310	462	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591885	48591885	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	134	448	0	ENST00000342988.3:c.1048G>T	p.Val350Phe	p.V350F	ENST00000342988	NM_005359.5	350	Gtt/Ttt	9/12	0.370527157905488	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.400904367050415	1		448	525	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589594	67589618	+	protein_altering_variant	In_Frame_Del	DEL	AACACTCAGTTTCAAGAAAAAAGTC	AACACTCAGTTTCAAGAAAAAAGTC	GATA	novel	NA	P-0030289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	75	410	1	ENST00000274335.5:c.1357_1381delinsGATA	p.Asn453_Ser460delinsAsp	p.N453_S460delinsD	ENST00000274335		453	AACACTCAGTTTCAAGAAAAAAGTCga/GATAga	10/15	0.400904367050415	1	FACETS	0.872	0.77	0.98	0.872	0.77	0.98	CLONAL	1	TRUE	0	0.400904367050415	1		411	343	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332825	152332825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	255	417	0	ENST00000206249.3:c.1132del	p.Leu378PhefsTer2	p.L378Ffs*2	ENST00000206249	NM_000125.3	377	caC/ca	5/8	0.400904367050415	2	FACETS	0.817	0.767	0.867	0.817	0.767	0.867	CLONAL	2	TRUE	0	0.400904367050415	2		417	779	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853342	151853342	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	139	396	0	ENST00000262189.6:c.11760del	p.Phe3920LeufsTer14	p.F3920Lfs*14	ENST00000262189	NM_170606.2	3920	ttT/tt	45/59	1	2	FACETS	0.96	0.876	1	0.96	0.876	1	CLONAL	1	TRUE	1	0.400904367050415	2		396	722	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034448	123034448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	132	467	0	ENST00000355640.3:c.1205G>A	p.Ser402Asn	p.S402N	ENST00000355640		402	aGc/aAc	6/7	NA	2	FACETS	0.998	0.908	1			1	INDETERMINATE	1	TRUE	NA	0.400904367050415	2		467	660	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555249	226555249	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	153	494	0	ENST00000366794.5:c.2338G>T	p.Gly780Ter	p.G780*	ENST00000366794	NM_001618.3	780	Gga/Tga	17/23	0.625568591419535	6	FACETS	0.869	0.793	0.949	0.174	0.158	0.19	CLONAL	1	TRUE	1	0.625568591419535	6		494	1267	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653846	89653846	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762518389	NA	P-0030343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	450	281	0	ENST00000371953.3:c.144C>A	p.Asn48Lys	p.N48K	ENST00000371953	NM_000314.4	48	aaC/aaA	2/9	0.615058221729958	3	FACETS	0.94	0.909	0.97	0.94	0.909	0.97	CLONAL	3	TRUE	0	0.625568591419535	3		281	670	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885908	59885908	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	195	457	1	ENST00000259008.2:c.838G>T	p.Asp280Tyr	p.D280Y	ENST00000259008	NM_032043.2	280	Gat/Tat	7/20	0.625568591419535	3	FACETS	0.983	0.911	1	0.491	0.455	0.529	CLONAL	1	TRUE	1	0.625568591419535	3		458	833	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547291	106547291	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	165	424	0	ENST00000369096.4:c.528T>G	p.Cys176Trp	p.C176W	ENST00000369096	NM_001198.3	176	tgT/tgG	4/7	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.625568591419535	2		424	524	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0030452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	156	253	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.557067165568397	3	FACETS	0.943	0.887	0.998	0.943	0.887	0.998	CLONAL	3	TRUE	0	0.557067165568397	3		253	253	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0030452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	306	586	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.557067165568397	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.557067165568397	2		586	530	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103385	2103385	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45517099	NA	P-0030452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	599	814	0	ENST00000219476.3:c.268C>T	p.Gln90Ter	p.Q90*	ENST00000219476	NM_000548.3	90	Cag/Tag	4/42	0.557067165568397	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.557067165568397	3		814	850	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633501	3633501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs560866356	NA	P-0030452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	531	740	0	ENST00000294008.3:c.4750C>T	p.Arg1584Cys	p.R1584C	ENST00000294008	NM_032444.2	1584	Cgc/Tgc	14/15	0.557067165568397	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	0	0.557067165568397	3		740	805	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678134	58678134	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0030452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	175	534	0	ENST00000305921.3:c.359T>A	p.Leu120Ter	p.L120*	ENST00000305921	NM_003620.3	120	tTg/tAg	1/6	0.495358344021582	4	FACETS	1	0.974	1	0.564	0.52	0.61	CLONAL	1	TRUE	2	0.557067165568397	4		534	867	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98011302	98011410	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCAGTCAATACCACAAGTCCCGATTCTGGGTGGCATTCTGTCTTGGTGAAATCTGGTAGAGTCCCTGAAGTCAGAAAATAATTTCATTATTCTGGTCCACTACTTACCA	TCAGTCAATACCACAAGTCCCGATTCTGGGTGGCATTCTGTCTTGGTGAAATCTGGTAGAGTCCCTGAAGTCAGAAAATAATTTCATTATTCTGGTCCACTACTTACCA	-	novel	NA	P-0030452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	82	130	0	ENST00000289081.3:c.164_165+107del		p.X55_splice	ENST00000289081	NM_000136.2	55		2/15	0.425420582323056	4	FACETS	0.888	0.805	0.972	1	0.979	1	CLONAL	3	TRUE	2	0.557067165568397	4		130	172	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0030540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	110	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.896	0.806	0.99	0.896	0.806	0.99	CLONAL	1	TRUE	1	0.391675986705917	2		436	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0030540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	190	611	1	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.391675986705917	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.391675986705917	1		612	766	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0030540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	211	370	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	0.350488409553133	2	FACETS	0.952	0.891	1	0.952	0.891	1	CLONAL	2	TRUE	0	0.391675986705917	2		370	566	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912143	114912145	+	frameshift_variant	Frame_Shift_Ins	INS	AAG	AAG	CTTC	novel	NA	P-0030540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	212	477	0	ENST00000543371.1:c.1213_1215delinsCTTC	p.Lys405LeufsTer18	p.K405Lfs*18	ENST00000543371	NM_001198531.1	405	AAG/CTTC	11/14	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.391675986705917	2		477	875	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140166	50140166	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1274073568	NA	P-0030540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	212	446	0	ENST00000246792.3:c.259C>G	p.Gln87Glu	p.Q87E	ENST00000246792	NM_006270.3	87	Cag/Gag	3/6	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.391675986705917	2		446	853	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343531	70343531	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	115	503	0	ENST00000374080.3:c.1705G>T	p.Val569Phe	p.V569F	ENST00000374080		569	Gtc/Ttc	12/45	0.130948034092519	0	FACETS	0.484	0.436	0.535			1	INDETERMINATE	1	TRUE	0	0.391675986705917	0		503	738	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76949404	76949404	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	27	321	1	ENST00000373344.5:c.393G>T	p.Glu131Asp	p.E131D	ENST00000373344	NM_000489.3	131	gaG/gaT	6/35	0.130948034092519	0	FACETS	0.214	0.17	0.265			1	INDETERMINATE	1	TRUE	0	0.391675986705917	0		322	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0030752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	373	346	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.303239555393611	2	FACETS	0.974	0.927	1	0.974	0.927	1	CLONAL	2	TRUE	0	0.400689479765512	2		346	956	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0030752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	139	336	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.397715101278455	1	FACETS	0.824	0.752	0.9	0.824	0.752	0.9	CLONAL	1	TRUE	0	0.400689479765512	1		336	673	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	56	290	2	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	0.383891882892814	2	FACETS	0.41	0.351	0.476	0.205	0.175	0.238	SUBCLONAL	1	TRUE	0	0.400689479765512	2		292	681	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0030752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	52	777	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	0.383891882892814	2	FACETS	0.269	0.228	0.314	0.134	0.114	0.157	SUBCLONAL	1	TRUE	0	0.400689479765512	2		777	965	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	T	rs1023835002	NA	P-0030752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	41	301	0	ENST00000558401.1:c.1A>T	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Ttg	1/4	0.397715101278455	1	FACETS	0.285	0.237	0.339	0.285	0.237	0.339	SUBCLONAL	1	TRUE	0	0.400689479765512	1		301	574	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557537	21557537	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	43	506	0	ENST00000382592.4:c.2308T>C	p.Phe770Leu	p.F770L	ENST00000382592	NM_014572.2	770	Ttc/Ctc	5/8	0.400689479765512	1	FACETS	0.21	0.174	0.249	0.21	0.174	0.249	SUBCLONAL	1	TRUE	0	0.400689479765512	1		506	819	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237688	133237688	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878854857	NA	P-0030752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	265	449	1	ENST00000320574.5:c.2927G>A	p.Arg976His	p.R976H	ENST00000320574	NM_006231.2	976	cGc/cAc	25/49	0.400689479765512	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.400689479765512	1		450	897	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264412	46264412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746670862	NA	P-0030752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	99	325	0	ENST00000371998.3:c.1459C>T	p.Arg487Cys	p.R487C	ENST00000371998		487	Cgt/Tgt	11/23	1	2	FACETS	0.788	0.705	0.877	0.788	0.705	0.877	SUBCLONAL	1	TRUE	1	0.400689479765512	2		325	627	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107231	193107231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	63	231	0	ENST00000367435.3:c.440G>A	p.Arg147His	p.R147H	ENST00000367435	NM_024529.4	147	cGc/cAc	6/17	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.400689479765512	NA		231	272	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746113	162746113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1364325806	NA	P-0030752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	125	248	0	ENST00000367921.3:c.2236C>T	p.Arg746Trp	p.R746W	ENST00000367921	NM_006182.2	746	Cgg/Tgg	16/18	0.331229062698735	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.400689479765512	1		248	397	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035190	30035192	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	rs1555987732	NA	P-0030752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	234	320	0	ENST00000338641.4:c.357_359del	p.Phe119del	p.F119del	ENST00000338641	NM_000268.3	118	TTC/-	3/16	0.383891882892814	2	FACETS	0.926	0.869	0.983	0.926	0.869	0.983	CLONAL	2	TRUE	0	0.400689479765512	2		320	631	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366676	40366676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1432125997	NA	P-0030752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	230	441	0	ENST00000397332.2:c.521C>T	p.Ala174Val	p.A174V	ENST00000397332	NM_001033082.2	174	gCc/gTc	2/3	0.400689479765512	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.400689479765512	1		441	719	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120469232	120469232	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs371580595	NA	P-0030752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	46	338	1	ENST00000256646.2:c.3895C>T	p.Arg1299Trp	p.R1299W	ENST00000256646	NM_024408.3	1299	Cgg/Tgg	24/34	0.331229062698735	1	FACETS	0.328	0.276	0.386	0.328	0.276	0.386	SUBCLONAL	1	TRUE	0	0.400689479765512	1		339	559	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557887	21557887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	174	399	0	ENST00000382592.4:c.1958C>T	p.Ser653Phe	p.S653F	ENST00000382592	NM_014572.2	653	tCt/tTt	5/8	0.400689479765512	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.400689479765512	1		399	619	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895673	28895673	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	40	448	0	ENST00000282397.4:c.3101A>G	p.Asn1034Ser	p.N1034S	ENST00000282397	NM_002019.4	1034	aAc/aGc	23/30	0.400689479765512	1	FACETS	0.256	0.212	0.306	0.256	0.212	0.306	SUBCLONAL	1	TRUE	0	0.400689479765512	1		448	623	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241994	105241994	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375990114	NA	P-0030752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	190	462	0	ENST00000349310.3:c.430C>T	p.Arg144Cys	p.R144C	ENST00000349310	NM_001014432.1	144	Cgc/Tgc	6/15	0.400689479765512	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.400689479765512	1		462	744	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988735	41988738	+	frameshift_variant	Frame_Shift_Del	DEL	TACA	TACA	-	novel	NA	P-0030752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	93	330	0	ENST00000219905.7:c.1532_1535del	p.Tyr511LeufsTer11	p.Y511Lfs*11	ENST00000219905	NM_001164273.1	509	ccTACA/cc	3/24	0.397715101278455	1	FACETS	0.786	0.702	0.875	0.786	0.702	0.875	SUBCLONAL	1	TRUE	0	0.400689479765512	1		330	472	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696467	47696468	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0030752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	176	337	0	ENST00000347630.2:c.355_356del	p.Gln120ThrfsTer4	p.Q120Tfs*4	ENST00000347630	NM_001007230.1	119	AGt/t	6/11	0.400689479765512	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.400689479765512	1		337	539	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707906	47707906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	25	345	0	ENST00000233146.2:c.2530G>A	p.Ala844Thr	p.A844T	ENST00000233146	NM_000251.2	844	Gct/Act	15/16	0.400689479765512	1	FACETS	0.222	0.174	0.277	0.222	0.174	0.277	SUBCLONAL	1	TRUE	0	0.400689479765512	1		345	450	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467997	66467997	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	54	207	0	ENST00000273854.3:c.272A>G	p.Glu91Gly	p.E91G	ENST00000273854	NM_004439.5	91	gAa/gGa	3/18	0.400689479765512	1	FACETS	0.823	0.709	0.945	0.823	0.709	0.945	CLONAL	1	TRUE	0	0.400689479765512	1		207	262	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599332	55599332	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519710	NA	P-0030781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	114	302	0	ENST00000288135.5:c.2458G>T	p.Asp820Tyr	p.D820Y	ENST00000288135	NM_000222.2	820	Gat/Tat	17/21	1	2	FACETS	0.91	0.831	0.991	0.91	0.831	0.991	CLONAL	1	TRUE	1	0.81614801838285	2		302	307	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006836	47006836	+	5_prime_UTR_variant	5'UTR	SNP	C	C	T	rs781915889	NA	P-0030828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	144	706	1	ENST00000377604.3:c.-45C>T		p.*15*	ENST00000377604	NM_001204468.1	-/852		2/24	0.241558336493919	4	FACETS	0.984	0.896	1	0.492	0.448	0.538	INDETERMINATE	1	FALSE	2	0.404841549138694	4		707	1016	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0030828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	196	979	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.241136306855267	3	FACETS	0.809	0.751	0.868	0.539	0.5	0.579	INDETERMINATE	2	FALSE	0	0.404841549138694	3		979	720	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0030828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	130	515	1	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	0.404841549138694	4	FACETS	0.887	0.816	0.96	0.887	0.816	0.96	CLONAL	3	FALSE	1	0.404841549138694	4		516	339	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447305	49447305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766543419	NA	P-0030828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	139	599	0	ENST00000301067.7:c.793C>T	p.Arg265Cys	p.R265C	ENST00000301067	NM_003482.3	265	Cgt/Tgt	6/54	0.404841549138694	4	FACETS	0.931	0.846	1	0.31	0.282	0.34	CLONAL	1	FALSE	1	0.404841549138694	4		599	1036	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711339	114711343	+	frameshift_variant	Frame_Shift_Del	DEL	CGGAT	CGGAT	-	novel	NA	P-0030828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	119	333	0	ENST00000543371.1:c.356_360del	p.Gly119AlafsTer24	p.G119Afs*24	ENST00000543371	NM_001198531.1	118	aaCGGATcg/aacg	3/14	0.148919504142119	3	FACETS	1	0.941	1	0.528	0.477	0.582	INDETERMINATE	1	FALSE	1	0.404841549138694	3		333	669	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715988	52715988	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	84	517	0	ENST00000322088.6:c.553G>T	p.Ala185Ser	p.A185S	ENST00000322088	NM_014225.5	185	Gca/Tca	5/15	NA	2	FACETS	0.549	0.484	0.618			1	INDETERMINATE	1	FALSE	NA	0.404841549138694	2		517	756	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427690	72427690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	39	279	0	ENST00000477973.2:c.800G>A	p.Arg267His	p.R267H	ENST00000477973	NM_012234.5	267	cGc/cAc	4/4	0.404841549138694	1	FACETS	0.408	0.338	0.485	0.408	0.338	0.485	SUBCLONAL	1	FALSE	0	0.404841549138694	1		279	377	SUCCESS
APC	324	MSKCC	GRCh37	5	112173249	112173249	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs863225321	NA	P-0030828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	10	151	0	ENST00000257430.4:c.1959-1G>A		p.X653_splice	ENST00000257430	NM_000038.5	653			1	2	FACETS	0.95	0.66	1	0.95	0.66	1	CLONAL	1	FALSE	1	0.404841549138694	2		151	52	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041169	47041169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782425783	NA	P-0030828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	158	774	1	ENST00000377604.3:c.1597G>A	p.Ala533Thr	p.A533T	ENST00000377604	NM_001204468.1	533	Gct/Act	15/24	0.241558336493919	4	FACETS	1	0.975	1	0.581	0.532	0.632	INDETERMINATE	1	FALSE	2	0.404841549138694	4		775	944	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0030851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	121	478	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.937	0.849	1	0.937	0.849	1	CLONAL	1	TRUE	1	0.436137058619025	2		478	592	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680698	88680698	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	95	681	0	ENST00000360948.2:c.559C>A	p.Leu187Ile	p.L187I	ENST00000360948	NM_001012338.2	187	Ctc/Atc	6/19	1	2	FACETS	0.286	0.254	0.32	0.286	0.254	0.32	SUBCLONAL	1	TRUE	1	0.782440000875824	2		681	850	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0030889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	223	570	0	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	0.63682411916122	1	FACETS	0.88	0.83	0.93	0.88	0.83	0.93	CLONAL	1	TRUE	0	0.72039182774821	1		570	450	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0031014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	85	949	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.899	0.795	1	0.899	0.795	1	CLONAL	1	TRUE	1	0.288565408129015	2		949	655	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919331	48919331	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1131690874	NA	P-0031014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	41	104	0	ENST00000267163.4:c.496G>T	p.Glu166Ter	p.E166*	ENST00000267163	NM_000321.2	166	Gaa/Taa	4/27	0.288565408129015	1	FACETS	0.95	0.797	1	0.95	0.797	1	CLONAL	1	TRUE	0	0.288565408129015	1		104	256	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221229	1221229	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881977	NA	P-0031014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	207	638	0	ENST00000326873.7:c.752G>A	p.Gly251Asp	p.G251D	ENST00000326873	NM_000455.4	251	gGt/gAt	6/10	0.274105162350714	2	FACETS	0.857	0.797	0.919	0.857	0.797	0.919	CLONAL	2	TRUE	0	0.288565408129015	2		638	837	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623821	28623821	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs550878210	NA	P-0031014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	101	469	0	ENST00000241453.7:c.833A>C	p.Asn278Thr	p.N278T	ENST00000241453	NM_004119.2	278	aAc/aCc	7/24	0.288565408129015	1	FACETS	0.868	0.777	0.965	0.868	0.777	0.965	CLONAL	1	TRUE	0	0.288565408129015	1		469	690	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382171	152382171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	89	374	0	ENST00000206249.3:c.1281G>A	p.Met427Ile	p.M427I	ENST00000206249	NM_000125.3	427	atG/atA	6/8	1	2	FACETS	0.978	0.868	1	0.978	0.868	1	CLONAL	1	TRUE	1	0.288565408129015	2		374	631	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874011	123874013	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs780061449	NA	P-0031135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	10	45	0	ENST00000330479.4:c.62_64del	p.Ala21del	p.A21del	ENST00000330479	NM_020382.3	14	gaGGCg/gag	2/9	0.38165295172679	4	FACETS	0.348	0.236	0.488	0.174	0.118	0.244	SUBCLONAL	1	TRUE	2	0.589167930814793	4		45	155	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246078851	246078851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61762672	NA	P-0031135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	130	604	2	ENST00000388985.4:c.794G>A	p.Arg265His	p.R265H	ENST00000388985		265	cGt/cAt	8/12	0.534513140486476	3	FACETS	1	0.987	1	0.736	0.675	0.8	CLONAL	1	TRUE	1	0.589167930814793	3		606	388	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782198	9782198	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	20	476	0	ENST00000377346.4:c.2221C>A	p.Leu741Met	p.L741M	ENST00000377346	NM_005026.3	741	Ctg/Atg	17/24	0.534513140486476	3	FACETS	0.231	0.176	0.296	0.116	0.088	0.148	SUBCLONAL	1	TRUE	1	0.589167930814793	3		476	380	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499742	18499742	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	16	368	0	ENST00000266497.5:c.1597C>T	p.His533Tyr	p.H533Y	ENST00000266497		533	Cac/Tac	10/31	0.527133118522676	1	FACETS	0.202	0.149	0.264	0.202	0.149	0.264	SUBCLONAL	1	TRUE	0	0.589167930814793	1		368	190	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508653	38508653	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	171	703	0	ENST00000254066.5:c.701A>T	p.Lys234Met	p.K234M	ENST00000254066	NM_000964.3	234	aAg/aTg	6/9	0.310861690094214	4	FACETS	0.824	0.762	0.887	0.824	0.762	0.887	INDETERMINATE	2	TRUE	2	0.589167930814793	4		703	560	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440284	187440285	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0031135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	23	482	0	ENST00000232014.4:c.2082dup	p.Ala695SerfsTer3	p.A695Sfs*3	ENST00000232014	NM_001130845.1	694	-/A	10/10	0.447054024917381	3	FACETS	0.225	0.175	0.284	0.113	0.087	0.142	SUBCLONAL	1	TRUE	1	0.589167930814793	3		482	449	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057092	180057092	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	25	645	0	ENST00000261937.6:c.527T>C	p.Leu176Pro	p.L176P	ENST00000261937	NM_182925.4	176	cTg/cCg	5/30	0.287062488632837	2	FACETS	0.291	0.229	0.361	0.145	0.114	0.181	INDETERMINATE	1	TRUE	0	0.589167930814793	2		645	292	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528868	157528868	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	95	534	0	ENST00000346085.5:c.6593C>G	p.Ala2198Gly	p.A2198G	ENST00000346085	NM_020732.3	2198	gCg/gGg	20/20	0.38165295172679	4	FACETS	1	0.947	1	0.548	0.49	0.609	CLONAL	1	TRUE	2	0.589167930814793	4		534	468	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951873	2951873	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	181	596	0	ENST00000396946.4:c.3077C>T	p.Ser1026Phe	p.S1026F	ENST00000396946	NM_032415.4	1026	tCc/tTc	23/25	0.300543774937599	3	FACETS	0.945	0.882	1	0.63	0.588	0.672	INDETERMINATE	2	TRUE	0	0.589167930814793	3		596	421	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214315	55214318	+	frameshift_variant	Frame_Shift_Del	DEL	CGTG	CGTG	-	novel	NA	P-0031135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	31	482	0	ENST00000275493.2:c.443_446del	p.Val148GlyfsTer19	p.V148Gfs*19	ENST00000275493	NM_005228.3	147	gcCGTG/gc	4/28	0.385303330905282	5	FACETS	0.393	0.317	0.479	0.131	0.105	0.16	SUBCLONAL	1	TRUE	2	0.589167930814793	5		482	505	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129198	2129198	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0031151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	229	767	1	ENST00000219476.3:c.3131+1G>T		p.X1044_splice	ENST00000219476	NM_000548.3	1044			0.599124819096135	3	FACETS	1	0.984	1	0.387	0.361	0.414	CLONAL	1	TRUE	0	0.595401165825086	3		768	860	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607619	46607619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	486	837	3	ENST00000263734.3:c.1808C>T	p.Pro603Leu	p.P603L	ENST00000263734	NM_001430.4	603	cCc/cTc	12/16	0.567959491196478	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.595401165825086	3		840	930	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345223	70345223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	161	599	1	ENST00000374080.3:c.2249G>A	p.Cys750Tyr	p.C750Y	ENST00000374080		750	tGc/tAc	16/45	0.523322958624719	3	FACETS	0.957	0.88	1			1	CLONAL	1	TRUE	NA	0.595401165825086	3		600	733	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252911	36252911	+	frameshift_variant	Frame_Shift_Ins	INS	T	T	AA	novel	NA	P-0031151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	230	431	0	ENST00000300305.3:c.451delinsTT	p.Met151PhefsTer9	p.M151Ffs*9	ENST00000300305		151	Atg/TTtg	4/8	0.599124819096135	5	FACETS	1	0.945	1	0.673	0.63	0.718	CLONAL	2	TRUE	2	0.595401165825086	5		431	724	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589143	67589150	+	frameshift_variant	Frame_Shift_Del	DEL	TAACAAAT	TAACAAAT	-	novel	NA	P-0031172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	12	216	0	ENST00000274335.5:c.1134_1141del	p.Lys379GlnfsTer13	p.K379Qfs*13	ENST00000274335		377	aaTAACAAATta/aata	9/15	1	2	FACETS	1	0.742	1	1	0.742	1	CLONAL	1	TRUE	1	0.16	2		216	142	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0031245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	103	455	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.166966800269391	3	FACETS	0.941	0.842	1			1	INDETERMINATE	1	TRUE	NA	0.337190138898747	3		455	759	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057520000	NA	P-0031245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	166	856	3	ENST00000269305.4:c.452C>A	p.Pro151His	p.P151H	ENST00000269305	NM_001126112.2	151	cCc/cAc	5/11	0.337190138898747	1	FACETS	0.979	0.9	1	0.979	0.9	1	CLONAL	1	TRUE	0	0.337190138898747	1		859	836	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713559	30713559	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0031245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	92	580	0	ENST00000295754.5:c.884C>G	p.Ser295Ter	p.S295*	ENST00000295754	NM_003242.5	295	tCa/tGa	4/7	0.317838848645037	1	FACETS	0.881	0.785	0.982	0.881	0.785	0.982	CLONAL	1	TRUE	0	0.337190138898747	1		580	515	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604736	48604736	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	106	541	0	ENST00000342988.3:c.1558G>T	p.Glu520Ter	p.E520*	ENST00000342988	NM_005359.5	520	Gaa/Taa	12/12	0.317838848645037	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	0	0.337190138898747	1		541	519	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129377	2129377	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs78956195	NA	P-0031245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	138	709	0	ENST00000219476.3:c.3232C>T	p.Arg1078Trp	p.R1078W	ENST00000219476	NM_000548.3	1078	Cgg/Tgg	28/42	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.337190138898747	2		709	760	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317275	87317275	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	141	525	0	ENST00000277120.3:c.300T>G	p.Asp100Glu	p.D100E	ENST00000277120		100	gaT/gaG	4/19	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.337190138898747	2		525	787	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	100	580	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.902	0.807	1	0.902	0.807	1	CLONAL	1	TRUE	1	0.34	2		580	652	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	91	423	1	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.88	0.783	0.984	0.88	0.783	0.984	CLONAL	1	TRUE	1	0.34	2		424	608	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	124	744	4	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.34	2		748	714	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441304	149441304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	103	659	1	ENST00000286301.3:c.1735C>T	p.Arg579Trp	p.R579W	ENST00000286301	NM_005211.3	579	Cgg/Tgg	12/22	1	2	FACETS	0.91	0.815	1	0.91	0.815	1	CLONAL	1	TRUE	1	0.34	2		660	666	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112154	115112154	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	45	485	0	ENST00000257566.3:c.1586del	p.Gly529AlafsTer103	p.G529Afs*103	ENST00000257566	NM_016569.3	529	gGc/gc	7/8	1	2	FACETS	0.408	0.342	0.481	0.408	0.342	0.481	SUBCLONAL	1	TRUE	1	0.34	2		485	649	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056588	26056590	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs751086925	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	40	227	0	ENST00000343677.2:c.67_69del	p.Lys23del	p.K23del	ENST00000343677	NM_005319.3	23	AAG/-	1/1	1	2	FACETS	0.68	0.567	0.806	0.68	0.567	0.806	SUBCLONAL	1	TRUE	1	0.34	2		227	346	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481857	56481857	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519817	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	150	547	0	ENST00000267101.3:c.785C>A	p.Pro262His	p.P262H	ENST00000267101	NM_001982.3	262	cCt/cAt	7/28	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.34	2		547	840	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	80	412	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	1	2	FACETS	0.816	0.719	0.919	0.816	0.719	0.919	CLONAL	1	TRUE	1	0.34	2		412	577	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267708	198267708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	96	464	0	ENST00000335508.6:c.1771G>A	p.Val591Met	p.V591M	ENST00000335508	NM_012433.2	591	Gtg/Atg	13/25	1	2	FACETS	0.727	0.647	0.812	0.727	0.647	0.812	SUBCLONAL	1	TRUE	1	0.34	2		464	777	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022332	31022332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778061	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	102	390	0	ENST00000375687.4:c.1817G>A	p.Arg606Gln	p.R606Q	ENST00000375687	NM_015338.5	606	cGg/cAg	13/13	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.34	2		390	522	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023091	33023091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	77	446	0	ENST00000300177.4:c.200C>T	p.Ala67Val	p.A67V	ENST00000300177	NM_001191322.1	67	gCc/gTc	2/2	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.34	2		446	449	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	127	640	3	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	1	2	FACETS	0.859	0.778	0.944	0.859	0.778	0.944	CLONAL	1	TRUE	1	0.34	2		643	870	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029576	14029576	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751782722	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	85	364	0	ENST00000311895.7:c.1787C>T	p.Ala596Val	p.A596V	ENST00000311895	NM_005236.2	596	gCg/gTg	8/11	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.34	2		364	491	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052629	42052629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	53	541	0	ENST00000219905.7:c.7300C>T	p.Arg2434Trp	p.R2434W	ENST00000219905	NM_001164273.1	2434	Cgg/Tgg	20/24	1	2	FACETS	0.392	0.333	0.456	0.392	0.333	0.456	SUBCLONAL	1	TRUE	1	0.34	2		541	796	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	95	751	3	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	0.818	0.729	0.913	0.818	0.729	0.913	CLONAL	1	TRUE	1	0.34	2		754	683	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217783	2217783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	116	598	1	ENST00000398665.3:c.2557C>T	p.Arg853Cys	p.R853C	ENST00000398665	NM_032482.2	853	Cgc/Tgc	22/28	1	2	FACETS	0.925	0.834	1	0.925	0.834	1	CLONAL	1	TRUE	1	0.34	2		599	738	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850704	63850705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	32	422	0	ENST00000279873.7:c.1489dup	p.Ile497AsnfsTer31	p.I497Nfs*31	ENST00000279873	NM_032199.2	494	-/A	10/10	1	2	FACETS	0.301	0.243	0.367	0.301	0.243	0.367	SUBCLONAL	1	TRUE	1	0.34	2		422	625	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870921	12870922	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	63	400	0	ENST00000228872.4:c.151_152del	p.Asp51HisfsTer73	p.D51Hfs*73	ENST00000228872	NM_004064.3	50	AGa/a	1/3	1	2	FACETS	0.8	0.694	0.915	0.8	0.694	0.915	CLONAL	1	TRUE	1	0.34	2		400	463	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820617	3820617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	84	698	0	ENST00000262367.5:c.2834C>T	p.Ser945Leu	p.S945L	ENST00000262367	NM_004380.2	945	tCg/tTg	14/31	1	2	FACETS	0.522	0.46	0.589	0.522	0.46	0.589	SUBCLONAL	1	TRUE	1	0.34	2		698	946	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117408	7117408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371841833	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	91	551	0	ENST00000302850.5:c.3808C>T	p.Arg1270Cys	p.R1270C	ENST00000302850	NM_000208.2	1270	Cgc/Tgc	22/22	1	2	FACETS	0.904	0.804	1	0.904	0.804	1	CLONAL	1	TRUE	1	0.34	2		551	592	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973736	15973736	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755143406	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	109	465	0	ENST00000268712.3:c.4256C>T	p.Pro1419Leu	p.P1419L	ENST00000268712	NM_006311.3	1419	cCg/cTg	31/46	1	2	FACETS	0.928	0.834	1	0.928	0.834	1	CLONAL	1	TRUE	1	0.34	2		465	691	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564074	139564074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773216266	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	154	691	1	ENST00000308874.7:c.214G>A	p.Ala72Thr	p.A72T	ENST00000308874		72	Gcc/Acc	5/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.34	2		692	777	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619370	1619370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs76459051	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	100	386	0	ENST00000344749.5:c.1271C>T	p.Ala424Val	p.A424V	ENST00000344749	NM_001136139.2	424	gCg/gTg	15/19	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.34	2		386	578	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885550	111885550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775891572	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	133	726	2	ENST00000341259.2:c.1327C>T	p.Arg443Cys	p.R443C	ENST00000341259	NM_005475.2	443	Cgc/Tgc	7/8	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.34	2		728	768	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416473	29416473	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199940609	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	134	763	4	ENST00000389048.3:c.4480G>A	p.Gly1494Arg	p.G1494R	ENST00000389048	NM_004304.4	1494	Gga/Aga	29/29	1	2	FACETS	0.838	0.76	0.919	0.838	0.76	0.919	CLONAL	1	TRUE	1	0.34	2		767	941	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	74	600	1	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	1	2	FACETS	0.654	0.572	0.742	0.654	0.572	0.742	SUBCLONAL	1	TRUE	1	0.34	2		601	666	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936093	178936093	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913275	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	94	555	0	ENST00000263967.3:c.1635G>C	p.Glu545Asp	p.E545D	ENST00000263967	NM_006218.2	545	gaG/gaC	10/21	1	2	FACETS	0.794	0.707	0.888	0.794	0.707	0.888	SUBCLONAL	1	TRUE	1	0.34	2		555	696	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635629	47635629	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63750318	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	116	636	0	ENST00000233146.2:c.301G>T	p.Glu101Ter	p.E101*	ENST00000233146	NM_000251.2	101	Gaa/Taa	2/16	1	2	FACETS	0.797	0.718	0.881	0.797	0.718	0.881	SUBCLONAL	1	TRUE	1	0.34	2		636	856	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249474	153249476	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	novel	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	106	592	0	ENST00000281708.4:c.1302_1304del	p.Ile435del	p.I435del	ENST00000281708	NM_033632.3	434	atCATt/att	9/12	1	2	FACETS	0.786	0.705	0.873	0.786	0.705	0.873	SUBCLONAL	1	TRUE	1	0.34	2		592	793	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874149	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	99	498	2	ENST00000262189.6:c.8389_8390del	p.Lys2797GlyfsTer11	p.K2797Gfs*11	ENST00000262189	NM_170606.2	2797	AAg/g	38/59	1	2	FACETS	0.844	0.754	0.94	0.844	0.754	0.94	CLONAL	1	TRUE	1	0.34	2		500	690	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748545	40748545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1054914884	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	132	749	2	ENST00000392038.2:c.337C>T	p.Arg113Trp	p.R113W	ENST00000392038	NM_001626.4	113	Cgg/Tgg	5/14	1	2	FACETS	0.992	0.901	1	0.992	0.901	1	CLONAL	1	TRUE	1	0.34	2		751	783	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002939	69002939	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773432628	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	87	359	0	ENST00000288368.4:c.2239C>T	p.Arg747Trp	p.R747W	ENST00000288368	NM_024870.2	747	Cgg/Tgg	20/40	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.34	2		359	506	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061726	38061726	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	52	287	3	ENST00000250448.2:c.263del	p.Gly88AlafsTer6	p.G88Afs*6	ENST00000250448	NM_004496.3	88	gGc/gc	2/2	1	2	FACETS	0.843	0.72	0.976	0.843	0.72	0.976	CLONAL	1	TRUE	1	0.34	2		290	363	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428681	49428681	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	133	609	2	ENST00000301067.7:c.10269del	p.Ile3424LeufsTer9	p.I3424Lfs*9	ENST00000301067	NM_003482.3	3423	ccC/cc	35/54	1	2	FACETS	0.925	0.84	1	0.925	0.84	1	CLONAL	1	TRUE	1	0.34	2		611	846	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117191	7117191	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	119	593	1	ENST00000302850.5:c.4025del	p.Gly1342AlafsTer23	p.G1342Afs*23	ENST00000302850	NM_000208.2	1342	gGc/gc	22/22	1	2	FACETS	0.888	0.802	0.98	0.888	0.802	0.98	CLONAL	1	TRUE	1	0.34	2		594	788	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383667	42383667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	114	611	0	ENST00000221972.3:c.442G>A	p.Glu148Lys	p.E148K	ENST00000221972	NM_021601.3	148	Gag/Aag	3/5	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.34	2		611	670	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261298	115261299	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	105	585	0	ENST00000438362.2:c.2422_2423del	p.Leu808GlyfsTer2	p.L808Gfs*2	ENST00000438362	NM_001242891.1	808	CTg/g	19/20	1	2	FACETS	0.885	0.793	0.982	0.885	0.793	0.982	CLONAL	1	TRUE	1	0.34	2		585	698	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648211	206648211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202128741	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	84	439	0	ENST00000367120.3:c.232G>A	p.Gly78Arg	p.G78R	ENST00000367120	NM_014002.3	78	Gga/Aga	5/22	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.34	2		439	424	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435164	18435164	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	92	555	0	ENST00000266497.5:c.149A>G	p.Lys50Arg	p.K50R	ENST00000266497		50	aAa/aGa	1/31	1	2	FACETS	0.881	0.784	0.985	0.881	0.784	0.985	CLONAL	1	TRUE	1	0.34	2		555	614	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109794	115109794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772126133	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	122	487	0	ENST00000257566.3:c.2084G>A	p.Arg695His	p.R695H	ENST00000257566	NM_016569.3	695	cGc/cAc	8/8	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.34	2		487	684	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957865	1957865	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	99	617	0	ENST00000382891.5:c.2834del	p.Gly945AlafsTer52	p.G945Afs*52	ENST00000382891	NM_133335.3	944	cGg/cg	15/22	1	2	FACETS	0.727	0.649	0.811	0.727	0.649	0.811	SUBCLONAL	1	TRUE	1	0.34	2		617	801	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874749	151874749	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	92	424	0	ENST00000262189.6:c.7789C>G	p.Pro2597Ala	p.P2597A	ENST00000262189	NM_170606.2	2597	Cca/Gca	38/59	1	2	FACETS	0.988	0.88	1	0.988	0.88	1	CLONAL	1	TRUE	1	0.34	2		424	548	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610125	43610125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	125	698	1	ENST00000355710.3:c.2077C>T	p.Arg693Cys	p.R693C	ENST00000355710	NM_020975.4	693	Cgc/Tgc	11/20	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.34	2		699	723	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437179	121437179	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372624970	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	158	747	1	ENST00000257555.6:c.1610C>T	p.Thr537Met	p.T537M	ENST00000257555		537	aCg/aTg	8/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.34	2		748	882	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644760	67644760	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	74	630	0	ENST00000264010.4:c.25A>G	p.Ile9Val	p.I9V	ENST00000264010	NM_006565.3	9	Att/Gtt	3/12	1	2	FACETS	0.519	0.453	0.59	0.519	0.453	0.59	SUBCLONAL	1	TRUE	1	0.34	2		630	839	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884254	37884254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778352367	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	38	617	0	ENST00000269571.5:c.3725C>T	p.Thr1242Met	p.T1242M	ENST00000269571		1242	aCg/aTg	27/27	1	2	FACETS	0.335	0.276	0.401	0.335	0.276	0.401	SUBCLONAL	1	TRUE	1	0.34	2		617	667	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78811771	78811773	+	inframe_deletion	In_Frame_Del	DEL	ATC	ATC	-	novel	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	62	511	0	ENST00000306801.3:c.1189_1191del	p.Ile397del	p.I397del	ENST00000306801	NM_020761.2	396	ATC/-	10/34	1	2	FACETS	0.497	0.428	0.572	0.497	0.428	0.572	SUBCLONAL	1	TRUE	1	0.34	2		511	734	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303298	15303298	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	155	809	0	ENST00000263388.2:c.230A>C	p.Gln77Pro	p.Q77P	ENST00000263388	NM_000435.2	77	cAg/cCg	3/33	1	2	FACETS	0.984	0.9	1	0.984	0.9	1	CLONAL	1	TRUE	1	0.34	2		809	927	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795851	42795851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749413984	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	149	674	0	ENST00000575354.2:c.2840C>T	p.Pro947Leu	p.P947L	ENST00000575354	NM_015125.3	947	cCg/cTg	11/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.34	2		674	813	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877435	40877435	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	35	552	0	ENST00000373198.4:c.2261T>C	p.Val754Ala	p.V754A	ENST00000373198	NM_133170.3	754	gTg/gCg	15/32	1	2	FACETS	0.323	0.264	0.389	0.323	0.264	0.389	SUBCLONAL	1	TRUE	1	0.34	2		552	638	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164000	47164000	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	64	465	0	ENST00000409792.3:c.2126del	p.Pro709LeufsTer58	p.P709Lfs*58	ENST00000409792	NM_014159.6	709	cCt/ct	3/21	1	2	FACETS	0.789	0.685	0.902	0.789	0.685	0.902	CLONAL	1	TRUE	1	0.34	2		465	477	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209423	98209423	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765348942	NA	P-0031332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	109	606	0	ENST00000331920.6:c.4115C>T	p.Thr1372Met	p.T1372M	ENST00000331920	NM_000264.3	1372	aCg/aTg	23/24	1	2	FACETS	0.907	0.815	1	0.907	0.815	1	CLONAL	1	TRUE	1	0.34	2		606	707	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	79	499	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	0.831	0.731	0.937	0.831	0.731	0.937	CLONAL	1	TRUE	1	0.317489218465692	2		499	599	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	54	580	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.77	0.659	0.891	0.77	0.659	0.891	SUBCLONAL	1	TRUE	1	0.317489218465692	2		580	442	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	46	468	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.317489218465692	2		472	241	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	25	536	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.932	0.741	1	0.932	0.741	1	CLONAL	1	TRUE	1	0.317489218465692	2		537	169	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	46	408	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.779	0.658	0.912	0.779	0.658	0.912	CLONAL	1	TRUE	1	0.317489218465692	2		408	372	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	39	423	1	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.317489218465692	2		424	238	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	76	789	8	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.317489218465692	2		797	468	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	56	744	4	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	0.972	0.836	1	0.972	0.836	1	CLONAL	1	TRUE	1	0.317489218465692	2		748	363	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441304	149441304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	16	659	1	ENST00000286301.3:c.1735C>T	p.Arg579Trp	p.R579W	ENST00000286301	NM_005211.3	579	Cgg/Tgg	12/22	0.18077387936625	1	FACETS	0.372	0.275	0.487	0.372	0.275	0.487	INDETERMINATE	1	TRUE	0	0.317489218465692	1		660	228	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481857	56481857	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519817	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	88	547	0	ENST00000267101.3:c.785C>A	p.Pro262His	p.P262H	ENST00000267101	NM_001982.3	262	cCt/cAt	7/28	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.317489218465692	2		547	522	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	52	412	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	1	2	FACETS	0.789	0.674	0.916	0.789	0.674	0.916	CLONAL	1	TRUE	1	0.317489218465692	2		412	415	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267708	198267708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	25	464	0	ENST00000335508.6:c.1771G>A	p.Val591Met	p.V591M	ENST00000335508	NM_012433.2	591	Gtg/Atg	13/25	0.234030219369949	3	FACETS	0.694	0.548	0.86	0.347	0.274	0.43	SUBCLONAL	1	TRUE	1	0.317489218465692	3		464	263	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	53	640	3	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	1	2	FACETS	0.954	0.817	1	0.954	0.817	1	CLONAL	1	TRUE	1	0.317489218465692	2		643	350	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029576	14029576	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751782722	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	56	364	0	ENST00000311895.7:c.1787C>T	p.Ala596Val	p.A596V	ENST00000311895	NM_005236.2	596	gCg/gTg	8/11	1	2	FACETS	0.882	0.758	1	0.882	0.758	1	CLONAL	1	TRUE	1	0.317489218465692	2		364	400	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217783	2217783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	16	598	1	ENST00000398665.3:c.2557C>T	p.Arg853Cys	p.R853C	ENST00000398665	NM_032482.2	853	Cgc/Tgc	22/28	1	2	FACETS	0.53	0.393	0.693	0.53	0.393	0.693	SUBCLONAL	1	TRUE	1	0.317489218465692	2		599	190	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416473	29416473	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199940609	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	85	763	4	ENST00000389048.3:c.4480G>A	p.Gly1494Arg	p.G1494R	ENST00000389048	NM_004304.4	1494	Gga/Aga	29/29	0.234030219369949	3	FACETS	1	0.964	1	0.608	0.539	0.682	CLONAL	1	TRUE	1	0.317489218465692	3		767	510	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635629	47635629	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63750318	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	36	636	0	ENST00000233146.2:c.301G>T	p.Glu101Ter	p.E101*	ENST00000233146	NM_000251.2	101	Gaa/Taa	2/16	0.134230764629328	0	FACETS	0.737	0.611	0.875			1	INDETERMINATE	1	TRUE	0	0.317489218465692	0		636	210	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249474	153249476	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	novel	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	82	592	0	ENST00000281708.4:c.1302_1304del	p.Ile435del	p.I435del	ENST00000281708	NM_033632.3	434	atCATt/att	9/12	1	2	FACETS	0.964	0.852	1	0.964	0.852	1	CLONAL	1	TRUE	1	0.317489218465692	2		592	536	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002939	69002939	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773432628	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	98	359	0	ENST00000288368.4:c.2239C>T	p.Arg747Trp	p.R747W	ENST00000288368	NM_024870.2	747	Cgg/Tgg	20/40	1	2	FACETS	0.893	0.798	0.995	0.893	0.798	0.995	CLONAL	1	TRUE	1	0.317489218465692	2		359	691	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061726	38061726	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	15	287	3	ENST00000250448.2:c.263del	p.Gly88AlafsTer6	p.G88Afs*6	ENST00000250448	NM_004496.3	88	gGc/gc	2/2	1	2	FACETS	0.883	0.654	1	0.883	0.654	1	CLONAL	1	TRUE	1	0.317489218465692	2		290	107	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428681	49428681	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	66	609	2	ENST00000301067.7:c.10269del	p.Ile3424LeufsTer9	p.I3424Lfs*9	ENST00000301067	NM_003482.3	3423	ccC/cc	35/54	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.317489218465692	2		611	363	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117191	7117191	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	22	593	1	ENST00000302850.5:c.4025del	p.Gly1342AlafsTer23	p.G1342Afs*23	ENST00000302850	NM_000208.2	1342	gGc/gc	22/22	1	2	FACETS	0.449	0.348	0.566	0.449	0.348	0.566	SUBCLONAL	1	TRUE	1	0.317489218465692	2		594	309	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261298	115261299	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	49	585	0	ENST00000438362.2:c.2422_2423del	p.Leu808GlyfsTer2	p.L808Gfs*2	ENST00000438362	NM_001242891.1	808	CTg/g	19/20	1	2	FACETS	0.633	0.536	0.739	0.633	0.536	0.739	SUBCLONAL	1	TRUE	1	0.317489218465692	2		585	488	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648211	206648211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202128741	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	37	439	0	ENST00000367120.3:c.232G>A	p.Gly78Arg	p.G78R	ENST00000367120	NM_014002.3	78	Gga/Aga	5/22	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.317489218465692	2		439	197	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435164	18435164	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	76	555	0	ENST00000266497.5:c.149A>G	p.Lys50Arg	p.K50R	ENST00000266497		50	aAa/aGa	1/31	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.317489218465692	2		555	434	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109794	115109794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772126133	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	40	487	0	ENST00000257566.3:c.2084G>A	p.Arg695His	p.R695H	ENST00000257566	NM_016569.3	695	cGc/cAc	8/8	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.317489218465692	2		487	175	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957865	1957865	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	90	617	0	ENST00000382891.5:c.2834del	p.Gly945AlafsTer52	p.G945Afs*52	ENST00000382891	NM_133335.3	944	cGg/cg	15/22	1	2	FACETS	0.919	0.816	1	0.919	0.816	1	CLONAL	1	TRUE	1	0.317489218465692	2		617	617	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874749	151874749	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	54	424	0	ENST00000262189.6:c.7789C>G	p.Pro2597Ala	p.P2597A	ENST00000262189	NM_170606.2	2597	Cca/Gca	38/59	1	2	FACETS	0.859	0.736	0.993	0.859	0.736	0.993	CLONAL	1	TRUE	1	0.317489218465692	2		424	396	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255883	16255883	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	43	389	2	ENST00000375759.3:c.3154del	p.Ile1052SerfsTer40	p.I1052Sfs*40	ENST00000375759	NM_015001.2	1050	Aaa/aa	11/15	1	2	FACETS	0.844	0.709	0.992	0.844	0.709	0.992	CLONAL	1	TRUE	1	0.317489218465692	2		391	321	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484813	57484813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555891595	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	53	657	0	ENST00000371085.3:c.793C>T	p.Arg265Cys	p.R265C	ENST00000371085	NM_000516.4	265	Cgc/Tgc	10/13	0.156041965379478	4	FACETS	1	0.953	1	0.643	0.551	0.743	INDETERMINATE	1	TRUE	2	0.317489218465692	4		657	342	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467573	66467573	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	58	461	0	ENST00000273854.3:c.696del	p.Lys232AsnfsTer36	p.K232Nfs*36	ENST00000273854	NM_004439.5	232	aaA/aa	3/18	1	2	FACETS	0.951	0.821	1	0.951	0.821	1	CLONAL	1	TRUE	1	0.317489218465692	2		461	384	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265049	46265049	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	89	499	1	ENST00000371998.3:c.1924del	p.Leu642Ter	p.L642*	ENST00000371998		640	tCc/tc	12/23	0.156041965379478	4	FACETS	0.855	0.762	0.953	0.855	0.762	0.953	INDETERMINATE	2	TRUE	2	0.317489218465692	4		500	432	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938499	76938501	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs1297294136	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	24	488	0	ENST00000373344.5:c.2247_2249del	p.Ser750del	p.S750del	ENST00000373344	NM_000489.3	749	tcTTCa/tca	9/35	1	2	FACETS	0.617	0.485	0.768	0.617	0.485	0.768	SUBCLONAL	1	TRUE	1	0.317489218465692	2		488	245	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260896	16260896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199693521	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	35	460	1	ENST00000375759.3:c.8161G>A	p.Ala2721Thr	p.A2721T	ENST00000375759	NM_015001.2	2721	Gcc/Acc	11/15	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.317489218465692	2		461	186	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371710	89371710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764805663	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	54	544	1	ENST00000301030.4:c.130C>T	p.Arg44Cys	p.R44C	ENST00000301030	NM_001256183.1	44	Cgt/Tgt	4/13	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.317489218465692	2		545	242	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935528	13935528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781723736	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	59	401	0	ENST00000405192.2:c.1328G>A	p.Cys443Tyr	p.C443Y	ENST00000405192	NM_001163147.1	443	tGc/tAc	12/12	1	2	FACETS	0.891	0.769	1	0.891	0.769	1	CLONAL	1	TRUE	1	0.317489218465692	2		401	417	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805298	89805298	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145148206	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	24	548	0	ENST00000389301.3:c.4252G>A	p.Val1418Met	p.V1418M	ENST00000389301	NM_000135.2	1418	Gtg/Atg	42/43	1	2	FACETS	0.652	0.513	0.81	0.652	0.513	0.81	SUBCLONAL	1	TRUE	1	0.317489218465692	2		548	232	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519504	137519505	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	49	416	0	ENST00000367739.4:c.1132_1133dup	p.Ser378ArgfsTer6	p.S378Rfs*6	ENST00000367739	NM_000416.2	378	agt/agAGt	7/7	1	2	FACETS	0.755	0.641	0.88	0.755	0.641	0.88	SUBCLONAL	1	TRUE	1	0.317489218465692	2		416	409	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197435	106197435	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	18	396	1	ENST00000380013.4:c.5772del	p.Ala1925ProfsTer25	p.A1925Pfs*25	ENST00000380013	NM_001127208.2	1923	gAa/ga	11/11	1	2	FACETS	0.391	0.294	0.505	0.391	0.294	0.505	SUBCLONAL	1	TRUE	1	0.317489218465692	2		397	290	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166608	118166608	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	79	324	0	ENST00000369448.3:c.1118T>C	p.Val373Ala	p.V373A	ENST00000369448	NM_017709.3	373	gTt/gCt	2/2	1	2	FACETS	0.861	0.766	0.961	1	0.982	1	CLONAL	2	TRUE	1	0.317489218465692	2		324	289	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406703	70406703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	42	527	0	ENST00000373644.4:c.4217C>T	p.Pro1406Leu	p.P1406L	ENST00000373644	NM_030625.2	1406	cCt/cTt	4/12	0.234030219369949	3	FACETS	1	0.91	1	0.564	0.473	0.662	CLONAL	1	TRUE	1	0.317489218465692	3		527	272	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742951	17742951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1332082680	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	29	432	0	ENST00000250003.3:c.859G>A	p.Ala287Thr	p.A287T	ENST00000250003	NM_002478.4	287	Gcc/Acc	3/3	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.317489218465692	2		432	148	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988824	41988824	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1185978488	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	18	596	0	ENST00000219905.7:c.1616T>C	p.Val539Ala	p.V539A	ENST00000219905	NM_001164273.1	539	gTg/gCg	3/24	1	2	FACETS	0.369	0.278	0.478	0.369	0.278	0.478	SUBCLONAL	1	TRUE	1	0.317489218465692	2		596	307	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99452038	99452038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771228557	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	48	511	0	ENST00000268035.6:c.1372G>A	p.Glu458Lys	p.E458K	ENST00000268035	NM_000875.3	458	Gaa/Aaa	6/21	1	2	FACETS	0.889	0.755	1	0.889	0.755	1	CLONAL	1	TRUE	1	0.317489218465692	2		511	340	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868087	56868087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150762291	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	71	531	1	ENST00000308159.5:c.1585G>A	p.Val529Met	p.V529M	ENST00000308159	NM_014669.4	529	Gtg/Atg	14/22	1	2	FACETS	0.944	0.826	1	0.944	0.826	1	CLONAL	1	TRUE	1	0.317489218465692	2		532	474	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81971411	81971411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs563473638	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	68	587	2	ENST00000359376.3:c.3101C>T	p.Thr1034Met	p.T1034M	ENST00000359376	NM_002661.3	1034	aCg/aTg	28/33	1	2	FACETS	0.958	0.836	1	0.958	0.836	1	CLONAL	1	TRUE	1	0.317489218465692	2		589	447	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89355048	89355048	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	37	600	1	ENST00000301030.4:c.632G>A	p.Arg211Gln	p.R211Q	ENST00000301030	NM_001256183.1	211	cGg/cAg	7/13	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.317489218465692	2		601	218	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983733	15983733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	58	459	0	ENST00000268712.3:c.3389G>A	p.Gly1130Asp	p.G1130D	ENST00000268712	NM_006311.3	1130	gGt/gAt	25/46	1	2	FACETS	0.632	0.543	0.729	0.632	0.543	0.729	SUBCLONAL	1	TRUE	1	0.317489218465692	2		459	578	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218626	36218626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780730597	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	21	642	0	ENST00000222270.7:c.4330C>T	p.Pro1444Ser	p.P1444S	ENST00000222270	NM_014727.1	1444	Cca/Tca	17/37	1	2	FACETS	0.652	0.504	0.822	0.652	0.504	0.822	SUBCLONAL	1	TRUE	1	0.317489218465692	2		642	203	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224282	36224282	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746054083	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	20	477	0	ENST00000222270.7:c.6832G>A	p.Val2278Ile	p.V2278I	ENST00000222270	NM_014727.1	2278	Gtc/Atc	28/37	1	2	FACETS	0.813	0.627	1	0.813	0.627	1	CLONAL	1	TRUE	1	0.317489218465692	2		477	155	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797002	42797002	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	28	766	0	ENST00000575354.2:c.3460A>G	p.Ser1154Gly	p.S1154G	ENST00000575354	NM_015125.3	1154	Agc/Ggc	14/20	1	2	FACETS	0.923	0.744	1	0.923	0.744	1	CLONAL	1	TRUE	1	0.317489218465692	2		766	191	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798196	42798196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1355435851	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	30	731	3	ENST00000575354.2:c.4150C>T	p.Arg1384Trp	p.R1384W	ENST00000575354	NM_015125.3	1384	Cgg/Tgg	17/20	1	2	FACETS	0.984	0.8	1	0.984	0.8	1	CLONAL	1	TRUE	1	0.317489218465692	2		734	192	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906823	50906823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1260247042	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	27	649	0	ENST00000440232.2:c.1211C>T	p.Pro404Leu	p.P404L	ENST00000440232	NM_002691.3	404	cCg/cTg	10/27	1	2	FACETS	0.686	0.548	0.842	0.686	0.548	0.842	SUBCLONAL	1	TRUE	1	0.317489218465692	2		649	248	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469578	25469578	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	41	757	0	ENST00000264709.3:c.1190A>C	p.Lys397Thr	p.K397T	ENST00000264709	NM_175629.2	397	aAg/aCg	10/23	0.234030219369949	3	FACETS	1	0.888	1	0.538	0.451	0.634	CLONAL	1	TRUE	1	0.317489218465692	3		757	278	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573177	41573177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747329417	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	33	709	0	ENST00000263253.7:c.5462G>A	p.Arg1821Gln	p.R1821Q	ENST00000263253	NM_001429.3	1821	cGa/cAa	31/31	1	2	FACETS	0.912	0.748	1	0.912	0.748	1	CLONAL	1	TRUE	1	0.317489218465692	2		709	228	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158131	47158131	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	31	595	0	ENST00000409792.3:c.4568G>A	p.Arg1523His	p.R1523H	ENST00000409792	NM_014159.6	1523	cGt/cAt	4/21	1	2	FACETS	0.676	0.548	0.819	0.676	0.548	0.819	SUBCLONAL	1	TRUE	1	0.317489218465692	2		595	289	SUCCESS
ATR	545	MSKCC	GRCh37	3	142203985	142203985	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	38	452	0	ENST00000350721.4:c.6218G>A	p.Gly2073Asp	p.G2073D	ENST00000350721	NM_001184.3	2073	gGc/gAc	36/47	1	2	FACETS	0.846	0.703	1	0.846	0.703	1	CLONAL	1	TRUE	1	0.317489218465692	2		452	283	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524447	187524448	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	37	529	0	ENST00000441802.2:c.11232dup	p.Trp3745LeufsTer6	p.W3745Lfs*6	ENST00000441802	NM_005245.3	3744	-/C	19/27	1	2	FACETS	0.453	0.373	0.543	0.453	0.373	0.543	SUBCLONAL	1	TRUE	1	0.317489218465692	2		529	514	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740617	145740617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	26	634	0	ENST00000428558.2:c.1400C>T	p.Ala467Val	p.A467V	ENST00000428558	NM_004260.3	467	gCt/gTt	8/22	1	2	FACETS	0.89	0.711	1	0.89	0.711	1	CLONAL	1	TRUE	1	0.317489218465692	2		634	184	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779171	135779171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199755731	NA	P-0031332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	55	499	0	ENST00000298552.3:c.2075G>A	p.Arg692Gln	p.R692Q	ENST00000298552	NM_001162426.1	692	cGa/cAa	17/23	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.317489218465692	2		499	338	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267439	7267439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1380670253	NA	P-0031348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	18	489	0	ENST00000302850.5:c.569C>T	p.Ala190Val	p.A190V	ENST00000302850	NM_000208.2	190	gCg/gTg	2/22	0.562372356035177	1	FACETS	0.63	0.487	0.79	0.63	0.487	0.79	SUBCLONAL	1	TRUE	0	0.562372356035177	1		489	73	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107030	11107030	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	92	473	0	ENST00000358026.2:c.1735G>T	p.Glu579Ter	p.E579*	ENST00000358026	NM_001128849.1	579	Gag/Tag	10/36	0.489345298748058	1	FACETS	0.835	0.765	0.905	1	0.987	1	CLONAL	2	TRUE	0	0.489345298748058	1		473	170	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578441	7578441	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1567553246	NA	P-0031410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	345	710	0	ENST00000269305.4:c.489C>G	p.Tyr163Ter	p.Y163*	ENST00000269305	NM_001126112.2	163	taC/taG	5/11	0.489345298748058	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	4	TRUE	0	0.489345298748058	4		710	482	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348536	89348536	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	31	785	0	ENST00000301030.4:c.4414G>A	p.Glu1472Lys	p.E1472K	ENST00000301030	NM_001256183.1	1472	Gag/Aag	9/13	0.489345298748058	2	FACETS	0.454	0.368	0.55	0.227	0.184	0.275	SUBCLONAL	1	TRUE	0	0.489345298748058	2		785	279	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508482	106508482	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	53	272	0	ENST00000359195.3:c.476G>T	p.Gly159Val	p.G159V	ENST00000359195	NM_002649.2	159	gGc/gTc	2/11	0.489345298748058	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	2	TRUE	0	0.489345298748058	2		272	103	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	101	188	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.686215033246267	2		188	224	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101268	27101268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	175	506	1	ENST00000324856.7:c.4555del	p.Gln1519ArgfsTer8	p.Q1519Rfs*8	ENST00000324856	NM_006015.4	1517	gCc/gc	18/20	1	2	FACETS	0.964	0.894	1	0.964	0.894	1	CLONAL	1	TRUE	1	0.686215033246267	2		507	529	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600393	10600393	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	345	826	0	ENST00000171111.5:c.1462G>T	p.Glu488Ter	p.E488*	ENST00000171111	NM_203500.1	488	Gag/Tag	4/6	0.686215033246267	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.686215033246267	1		826	592	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092977	27092978	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0031656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	87	309	0	ENST00000324856.7:c.2910dup	p.Gly971TrpfsTer36	p.G971Wfs*36	ENST00000324856	NM_006015.4	970	ctt/cTtt	10/20	1	2	FACETS	0.902	0.809	0.999	0.902	0.809	0.999	CLONAL	1	TRUE	1	0.686215033246267	2		309	281	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235838	108235838	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	95	416	0	ENST00000278616.4:c.8880G>C	p.Trp2960Cys	p.W2960C	ENST00000278616	NM_000051.3	2960	tgG/tgC	62/63	0.686215033246267	1	FACETS	0.942	0.861	1	0.942	0.861	1	CLONAL	1	TRUE	0	0.686215033246267	1		416	193	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287398	38287398	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	179	449	0	ENST00000425967.3:c.259C>G	p.Arg87Gly	p.R87G	ENST00000425967	NM_001174067.1	87	Cgc/Ggc	4/19	1	2	FACETS	0.918	0.852	0.987	0.918	0.852	0.987	CLONAL	1	TRUE	1	0.686215033246267	2		449	568	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105588	27105590	+	missense_variant	Missense_Mutation	TNP	GTA	GTA	TTC	novel	NA	P-0031656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	143	487	0	ENST00000324856.7:c.5199_5201delinsTTC	p.Glu1733_Tyr1734delinsAspSer	p.E1733_Y1734delinsDS	ENST00000324856	NM_006015.4	1733	gaGTAt/gaTTCt	20/20	1	2	FACETS	0.794	0.728	0.862	0.794	0.728	0.862	SUBCLONAL	1	TRUE	1	0.686215033246267	2		487	525	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145436	58145436	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	195	455	0	ENST00000257904.6:c.65A>T	p.Lys22Met	p.K22M	ENST00000257904	NM_000075.3	22	aAg/aTg	2/8	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.634974569294143	2		455	598	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061000	38061000	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	15	309	1	ENST00000250448.2:c.989C>T	p.Ala330Val	p.A330V	ENST00000250448	NM_004496.3	330	gCc/gTc	2/2	0.634974569294143	1	FACETS	0.14	0.102	0.186	0.14	0.102	0.186	SUBCLONAL	1	TRUE	0	0.634974569294143	1		310	230	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719132	190719132	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	154	359	0	ENST00000441310.2:c.1134G>T	p.Lys378Asn	p.K378N	ENST00000441310	NM_000534.4	378	aaG/aaT	9/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.634974569294143	2		359	413	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637917	176637917	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	275	566	0	ENST00000439151.2:c.2517del	p.Asn840ThrfsTer13	p.N840Tfs*13	ENST00000439151	NM_022455.4	839	ctG/ct	5/23	0.634974569294143	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.634974569294143	1		566	536	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683396	88683396	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	116	411	0	ENST00000372037.3:c.1519A>G	p.Asn507Asp	p.N507D	ENST00000372037	NM_004329.2	507	Aat/Gat	13/13	0.793215515083156	3	FACETS	0.98	0.89	1	0.49	0.445	0.537	CLONAL	1	TRUE	1	0.793215515083156	3		411	417	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573820	41573820	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	43	750	0	ENST00000263253.7:c.6105G>C	p.Gln2035His	p.Q2035H	ENST00000263253	NM_001429.3	2035	caG/caC	31/31	0.278483098886457	1	FACETS	0.138	0.115	0.163	0.138	0.115	0.163	INDETERMINATE	1	TRUE	0	0.793215515083156	1		750	474	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257973	19257973	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	119	514	0	ENST00000162023.5:c.413C>G	p.Pro138Arg	p.P138R	ENST00000162023		138	cCc/cGc	9/13	1	2	FACETS	0.539	0.488	0.592	0.539	0.488	0.592	SUBCLONAL	1	TRUE	1	0.808430555499558	2		514	546	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0031919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	54	451	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	NA	2	FACETS	0.863	0.75	0.982			1	INDETERMINATE	2	TRUE	NA	0.349590031144234	2		451	179	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	95	570	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.252238572926938	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.349590031144234	4		570	325	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0031919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	178	422	2	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.349590031144234	3	FACETS	0.997	0.951	1	1	0.994	1	CLONAL	5	TRUE	0	0.349590031144234	3		424	240	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141426	11141426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	45	581	3	ENST00000358026.2:c.3403C>T	p.Arg1135Trp	p.R1135W	ENST00000358026	NM_001128849.1	1135	Cgg/Tgg	25/36	1	2	FACETS	0.69	0.582	0.81	0.69	0.582	0.81	SUBCLONAL	1	TRUE	1	0.349590031144234	2		584	373	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11227537	11227537	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	70	650	0	ENST00000361445.4:c.4291G>A	p.Gly1431Arg	p.G1431R	ENST00000361445	NM_004958.3	1431	Gga/Aga	29/58	0.432288175840666	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.349590031144234	1		650	282	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512270	38512270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866777491	NA	P-0031919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	50	704	0	ENST00000254066.5:c.1181G>A	p.Arg394Gln	p.R394Q	ENST00000254066	NM_000964.3	394	cGg/cAg	9/9	0.349590031144234	7	FACETS	0.766	0.648	0.895			1	SUBCLONAL	1	TRUE	NA	0.349590031144234	7		704	700	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174440	11174440	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	36	699	1	ENST00000361445.4:c.7235A>T	p.Asp2412Val	p.D2412V	ENST00000361445	NM_004958.3	2412	gAc/gTc	53/58	0.432288175840666	1	FACETS	0.477	0.393	0.572	0.477	0.393	0.572	SUBCLONAL	1	TRUE	0	0.349590031144234	1		700	356	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115691	108115691	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782080	NA	P-0031919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	15	346	0	ENST00000278616.4:c.839T>C	p.Ile280Thr	p.I280T	ENST00000278616	NM_000051.3	280	aTt/aCt	7/63	1	2	FACETS	0.802	0.594	1	0.802	0.594	1	CLONAL	1	TRUE	1	0.349590031144234	2		346	107	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845573	72845574	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0031919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	89	729	0	ENST00000268489.5:c.3766_3767del	p.Leu1256ValfsTer24	p.L1256Vfs*24	ENST00000268489	NM_006885.3	1256	CTg/g	7/10	0.173915043538859	4	FACETS	0.755	0.673	0.842	0.755	0.673	0.842	INDETERMINATE	2	TRUE	2	0.349590031144234	4		729	455	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731529	47731529	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	10	34	0	ENST00000449228.1:c.263C>T	p.Ala88Val	p.A88V	ENST00000449228	NM_001127240.2	88	gCt/gTt	2/4	1	2	FACETS	0.325	0.22	0.457	0.325	0.22	0.457	SUBCLONAL	1	TRUE	1	0.349590031144234	2		34	176	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738381	190738381	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	41	307	0	ENST00000441310.2:c.2633A>T	p.Glu878Val	p.E878V	ENST00000441310	NM_000534.4	878	gAg/gTg	12/13	0.139007635142232	4	FACETS	1	0.869	1	1	0.869	1	INDETERMINATE	2	TRUE	2	0.349590031144234	4		307	154	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738348	133738348	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1216325712	NA	P-0031919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	10	459	0	ENST00000318560.5:c.748G>A	p.Gly250Arg	p.G250R	ENST00000318560	NM_005157.4	250	Ggg/Agg	4/11	1	2	FACETS	0.164	0.111	0.233	0.164	0.111	0.233	SUBCLONAL	1	TRUE	1	0.349590031144234	2		459	348	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0031964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	244	455	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.226630961426422	5	FACETS	0.915	0.858	0.974	0.915	0.858	0.974	CLONAL	4	TRUE	1	0.226630961426422	5		455	788	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0031964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	81	459	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.226630961426422	2		459	586	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974792	21974792	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs141798398	NA	P-0031964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	34	168	0	ENST00000304494.5:c.35C>A	p.Ser12Ter	p.S12*	ENST00000304494	NM_000077.4	12	tCg/tAg	1/3	0.226630961426422	1	FACETS	0.887	0.736	1	1	0.96	1	CLONAL	2	TRUE	0	0.226630961426422	1		168	150	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	105	686	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.226630961426422	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.226630961426422	1		686	704	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961059	55961059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530419081	NA	P-0031964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	46	711	0	ENST00000263923.4:c.2881C>T	p.Arg961Trp	p.R961W	ENST00000263923	NM_002253.2	961	Cgg/Tgg	21/30	1	2	FACETS	0.511	0.429	0.602	0.511	0.429	0.602	SUBCLONAL	1	TRUE	1	0.226630961426422	2		711	794	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868410	117868410	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	38	488	0	ENST00000297338.2:c.932T>A	p.Ile311Lys	p.I311K	ENST00000297338	NM_006265.2	311	aTa/aAa	8/14	1	2	FACETS	0.468	0.386	0.561	0.468	0.386	0.561	SUBCLONAL	1	TRUE	1	0.226630961426422	2		488	716	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	32	570	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.309337472378463	0	FACETS	0.476	0.388	0.576			1	SUBCLONAL	1	FALSE	0	0.309337472378463	0		570	300	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0032078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	32	137	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	0.30634920664885	1	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	FALSE	0	0.309337472378463	1		137	170	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522188	157522188	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370838091	NA	P-0032078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	46	457	1	ENST00000346085.5:c.4460C>T	p.Ala1487Val	p.A1487V	ENST00000346085	NM_020732.3	1487	gCg/gTg	18/20	1	2	FACETS	0.705	0.594	0.826	0.705	0.594	0.826	SUBCLONAL	1	FALSE	1	0.309337472378463	2		458	422	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193202184	193202184	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	19	296	0	ENST00000367435.3:c.1216C>G	p.Gln406Glu	p.Q406E	ENST00000367435	NM_024529.4	406	Caa/Gaa	14/17	1	2	FACETS	0.521	0.396	0.666	0.521	0.396	0.666	SUBCLONAL	1	FALSE	1	0.309337472378463	2		296	236	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577125	7577126	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	99	561	0	ENST00000269305.4:c.812dup	p.Val272GlyfsTer34	p.V272Gfs*34	ENST00000269305	NM_001126112.2	271	gag/gaAg	8/11	0.309337472378463	1	FACETS	0.97	0.868	1	0.97	0.868	1	CLONAL	1	FALSE	0	0.309337472378463	1		561	558	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028668	12028668	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	41	360	0	ENST00000353533.5:c.871T>A	p.Trp291Arg	p.W291R	ENST00000353533	NM_003010.3	291	Tgg/Agg	8/11	0.309337472378463	1	FACETS	0.886	0.743	1	0.886	0.743	1	CLONAL	1	FALSE	0	0.309337472378463	1		360	253	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	154	499	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.449913609917175	2		499	550	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	182	643	4	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	1	2	FACETS	0.819	0.755	0.885	0.819	0.755	0.885	CLONAL	1	TRUE	1	0.449913609917175	2		647	988	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	245	378	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.449913609917175	4	FACETS	0.966	0.912	1	0.966	0.912	1	CLONAL	3	TRUE	1	0.449913609917175	4		378	545	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703631	47703631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750636	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	186	594	0	ENST00000233146.2:c.2131C>T	p.Arg711Ter	p.R711*	ENST00000233146	NM_000251.2	711	Cga/Tga	13/16	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.449913609917175	2		594	812	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560815	9560815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388617807	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	176	555	1	ENST00000353224.5:c.967G>A	p.Glu323Lys	p.E323K	ENST00000353224	NM_177990.2	323	Gag/Aag	4/10	1	2	FACETS	0.953	0.879	1	0.953	0.879	1	CLONAL	1	TRUE	1	0.449913609917175	2		556	821	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	71	323	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.799	0.701	0.904	0.799	0.701	0.904	CLONAL	1	TRUE	1	0.449913609917175	2		323	395	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578341	212578341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1216559792	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	62	408	1	ENST00000342788.4:c.916C>T	p.Arg306Cys	p.R306C	ENST00000342788	NM_005235.2	306	Cgt/Tgt	8/28	1	2	FACETS	0.96	0.837	1	0.96	0.837	1	CLONAL	1	TRUE	1	0.449913609917175	2		409	287	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692981	89692982	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	88	479	0	ENST00000371953.3:c.469dup	p.Glu157GlyfsTer23	p.E157Gfs*23	ENST00000371953	NM_000314.4	155	-/G	5/9	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.449913609917175	2		479	353	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843595	156843595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139875058	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	255	788	1	ENST00000524377.1:c.1021G>A	p.Val341Met	p.V341M	ENST00000524377	NM_002529.3	341	Gtg/Atg	8/17	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.449913609917175	2		789	1113	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	332	885	0	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	0.433367238257889	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.449913609917175	2		885	729	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89815155	89815155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376089640	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	215	542	1	ENST00000389301.3:c.3260C>T	p.Ser1087Leu	p.S1087L	ENST00000389301	NM_000135.2	1087	tCg/tTg	33/43	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.449913609917175	2		543	943	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261555	142261555	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	18	490	3	ENST00000350721.4:c.3402del	p.Phe1134LeufsTer6	p.F1134Lfs*6	ENST00000350721	NM_001184.3	1134	ttT/tt	17/47	1	2	FACETS	0.238	0.179	0.308	0.238	0.179	0.308	SUBCLONAL	1	TRUE	1	0.449913609917175	2		493	336	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347484	91347484	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	154	805	1	ENST00000355112.3:c.3651del	p.Lys1217AsnfsTer62	p.K1217Nfs*62	ENST00000355112	NM_000057.2	1216	Aaa/aa	19/22	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.449913609917175	2		806	568	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202283	133202283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764457707	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	234	732	1	ENST00000320574.5:c.6605C>T	p.Thr2202Met	p.T2202M	ENST00000320574	NM_006231.2	2202	aCg/aTg	47/49	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.449913609917175	2		733	974	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303191	15303191	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs781622431	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	230	795	0	ENST00000263388.2:c.337C>T	p.Arg113Ter	p.R113*	ENST00000263388	NM_000435.2	113	Cga/Tga	3/33	1	2	FACETS	0.952	0.887	1	0.952	0.887	1	CLONAL	1	TRUE	1	0.449913609917175	2		795	1074	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138382756	138382756	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	160	464	3	ENST00000289153.2:c.2788del	p.Thr930LeufsTer62	p.T930Lfs*62	ENST00000289153	NM_006219.2	930	Act/ct	19/22	1	2	FACETS	0.936	0.86	1	0.936	0.86	1	CLONAL	1	TRUE	1	0.449913609917175	2		467	760	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476387	88476387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202056599	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	201	571	1	ENST00000360948.2:c.1745G>A	p.Arg582Gln	p.R582Q	ENST00000360948	NM_001012338.2	582	cGg/cAg	15/19	1	2	FACETS	0.978	0.907	1	0.978	0.907	1	CLONAL	1	TRUE	1	0.449913609917175	2		572	914	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126332	5126332	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	36	338	0	ENST00000381652.3:c.3178-1G>A		p.X1060_splice	ENST00000381652	NM_004972.3	1060			0.428820758187914	1	FACETS	0.743	0.619	0.877	0.743	0.619	0.877	SUBCLONAL	1	TRUE	0	0.449913609917175	1		338	167	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965643	93965643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762713500	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	117	574	2	ENST00000369303.4:c.2285G>A	p.Arg762His	p.R762H	ENST00000369303	NM_004440.3	762	cGc/cAc	13/17	1	2	FACETS	0.857	0.775	0.943	0.857	0.775	0.943	CLONAL	1	TRUE	1	0.449913609917175	2		576	607	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214871	36214871	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	222	814	3	ENST00000222270.7:c.3302del	p.Pro1101LeufsTer81	p.P1101Lfs*81	ENST00000222270	NM_014727.1	1099	ggC/gg	8/37	1	2	FACETS	0.908	0.845	0.973	0.908	0.845	0.973	CLONAL	1	TRUE	1	0.449913609917175	2		817	1087	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427522	49427522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201283589	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	182	659	2	ENST00000301067.7:c.10966C>T	p.Arg3656Cys	p.R3656C	ENST00000301067	NM_003482.3	3656	Cgc/Tgc	39/54	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.449913609917175	2		661	792	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624404	140624409	+	inframe_deletion	In_Frame_Del	DEL	CGGCGC	CGGCGC	-	rs397507458	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	47	118	0	ENST00000288602.6:c.95_100del	p.Gly32_Ala33del	p.G32_A33del	ENST00000288602	NM_004333.4	32	gGCGCCGcg/gcg	1/18	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.449913609917175	2		118	207	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593478	48593479	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs730881952	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	142	428	0	ENST00000342988.3:c.1231_1232del	p.Ser411LeufsTer17	p.S411Lfs*17	ENST00000342988	NM_005359.5	410	cAG/c	10/12	1	2	FACETS	0.98	0.896	1	0.98	0.896	1	CLONAL	1	TRUE	1	0.449913609917175	2		428	644	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006836	47006836	+	5_prime_UTR_variant	5'UTR	SNP	C	C	T	rs781915889	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	170	706	1	ENST00000377604.3:c.-45C>T		p.*15*	ENST00000377604	NM_001204468.1	-/852		2/24	1	2	FACETS	0.82	0.754	0.888	0.82	0.754	0.888	CLONAL	1	TRUE	1	0.449913609917175	2		707	922	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169361	11169361	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519777	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	149	565	0	ENST00000361445.4:c.7514G>A	p.Arg2505Gln	p.R2505Q	ENST00000361445	NM_004958.3	2505	cGa/cAa	56/58	0.449913609917175	1	FACETS	0.97	0.892	1	0.97	0.892	1	CLONAL	1	TRUE	0	0.449913609917175	1		565	529	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023826	27023827	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	139	306	0	ENST00000324856.7:c.936dup	p.Gly313ArgfsTer87	p.G313Rfs*87	ENST00000324856	NM_006015.4	311	tac/taCc	1/20	0.449913609917175	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.449913609917175	1		306	414	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114724320	114724320	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	180	566	1	ENST00000543371.1:c.390del	p.Gln131SerfsTer24	p.Q131Sfs*24	ENST00000543371	NM_001198531.1	129	caT/ca	4/14	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.449913609917175	2		567	761	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377000	118377000	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	157	447	0	ENST00000534358.1:c.10396del	p.Thr3466LeufsTer25	p.T3466Lfs*25	ENST00000534358	NM_005933.3	3465	Aaa/aa	27/36	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.449913609917175	2		447	683	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170318	119170318	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	128	305	0	ENST00000264033.4:c.2548G>A	p.Ala850Thr	p.A850T	ENST00000264033	NM_005188.3	850	Gct/Act	16/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.449913609917175	2		305	510	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912733	32912733	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs70953664	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	69	433	1	ENST00000380152.3:c.4241C>T	p.Thr1414Met	p.T1414M	ENST00000380152		1414	aCg/aTg	11/27	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.449913609917175	2		434	277	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41023374	41023374	+	stop_lost	Nonstop_Mutation	SNP	T	T	G	novel	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	147	503	0	ENST00000267868.3:c.1018T>G	p.Ter340GlyextTer8	p.*340Gext*8	ENST00000267868	NM_002875.4	340	Tga/Gga	10/10	1	2	FACETS	0.946	0.865	1	0.946	0.865	1	CLONAL	1	TRUE	1	0.449913609917175	2		503	691	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50818317	50818317	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	71	420	0	ENST00000398568.2:c.1895A>T	p.Glu632Val	p.E632V	ENST00000398568	NM_001042412.1	632	gAa/gTa	11/18	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.449913609917175	2		420	313	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56852575	56852575	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	39	570	0	ENST00000308159.5:c.490-1G>T		p.X164_splice	ENST00000308159	NM_014669.4	164			1	2	FACETS	0.223	0.184	0.266	0.223	0.184	0.266	SUBCLONAL	1	TRUE	1	0.449913609917175	2		570	779	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428251	33428251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150134822	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	177	509	0	ENST00000345365.6:c.872G>A	p.Arg291His	p.R291H	ENST00000345365	NM_002878.3	291	cGc/cAc	9/10	1	2	FACETS	0.901	0.831	0.974	0.901	0.831	0.974	CLONAL	1	TRUE	1	0.449913609917175	2		509	873	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857650	78857650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184854653	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	222	648	3	ENST00000306801.3:c.1720C>T	p.Arg574Cys	p.R574C	ENST00000306801	NM_020761.2	574	Cgc/Tgc	16/34	0.433367238257889	2	FACETS	0.971	0.904	1	0.486	0.452	0.521	CLONAL	1	TRUE	0	0.449913609917175	2		651	1016	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4094456	4094456	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	70	711	0	ENST00000262948.5:c.1087C>A	p.Leu363Ile	p.L363I	ENST00000262948	NM_030662.3	363	Ctc/Atc	10/11	1	2	FACETS	0.281	0.244	0.322	0.281	0.244	0.322	SUBCLONAL	1	TRUE	1	0.449913609917175	2		711	1106	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215336	5215336	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	45	586	2	ENST00000357368.4:c.4282T>C	p.Tyr1428His	p.Y1428H	ENST00000357368	NM_002850.3	1428	Tat/Cat	28/38	1	2	FACETS	0.222	0.186	0.263	0.222	0.186	0.263	SUBCLONAL	1	TRUE	1	0.449913609917175	2		588	900	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122963	7122963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1209792886	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	242	685	1	ENST00000302850.5:c.3296C>T	p.Thr1099Met	p.T1099M	ENST00000302850	NM_000208.2	1099	aCg/aTg	18/22	1	2	FACETS	0.985	0.92	1	0.985	0.92	1	CLONAL	1	TRUE	1	0.449913609917175	2		686	1092	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353791	15353791	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	161	499	0	ENST00000263377.2:c.3089del	p.Pro1030ArgfsTer38	p.P1030Rfs*38	ENST00000263377	NM_058243.2	1030	cCg/cg	14/20	1	2	FACETS	0.861	0.791	0.935	0.861	0.791	0.935	CLONAL	1	TRUE	1	0.449913609917175	2		499	831	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971687	18971687	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1273688735	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	264	667	0	ENST00000262803.5:c.2353G>A	p.Ala785Thr	p.A785T	ENST00000262803	NM_002911.3	785	Gcc/Acc	17/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.449913609917175	2		667	1031	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156011	99156011	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	196	657	0	ENST00000074304.5:c.691C>A	p.Arg231Ser	p.R231S	ENST00000074304	NM_001134224.1	231	Cgc/Agc	10/26	1	2	FACETS	0.878	0.813	0.946	0.878	0.813	0.946	CLONAL	1	TRUE	1	0.449913609917175	2		657	992	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663280	227663280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	157	594	0	ENST00000305123.5:c.175G>A	p.Ala59Thr	p.A59T	ENST00000305123	NM_005544.2	59	Gcc/Acc	1/2	1	2	FACETS	0.88	0.807	0.956	0.88	0.807	0.956	CLONAL	1	TRUE	1	0.449913609917175	2		594	793	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630861	187630861	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371144856	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	168	623	0	ENST00000441802.2:c.121G>A	p.Val41Ile	p.V41I	ENST00000441802	NM_005245.3	41	Gtc/Atc	2/27	1	2	FACETS	0.806	0.74	0.874	0.806	0.74	0.874	CLONAL	1	TRUE	1	0.449913609917175	2		623	927	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048821	180048821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368426530	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	300	837	0	ENST00000261937.6:c.1741G>A	p.Asp581Asn	p.D581N	ENST00000261937	NM_182925.4	581	Gac/Aac	13/30	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.449913609917175	2		837	1285	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158681	26158681	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	21	52	0	ENST00000289316.2:c.284T>A	p.Ile95Asn	p.I95N	ENST00000289316	NM_138720.2	95	aTc/aAc	1/2	1	2	FACETS	1	0.828	1	1	0.828	1	CLONAL	1	TRUE	1	0.449913609917175	2		52	88	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214311	55214311	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	235	520	0	ENST00000275493.2:c.437G>A	p.Gly146Asp	p.G146D	ENST00000275493	NM_005228.3	146	gGc/gAc	4/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.449913609917175	2		520	946	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884887	151884887	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	130	469	0	ENST00000262189.6:c.4706G>C	p.Ser1569Thr	p.S1569T	ENST00000262189	NM_170606.2	1569	aGt/aCt	32/59	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.449913609917175	2		469	549	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137326046	137326046	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	247	722	0	ENST00000481739.1:c.1234C>T	p.Pro412Ser	p.P412S	ENST00000481739	NM_002957.4	412	Ccg/Tcg	9/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.449913609917175	2		722	1054	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930900	39930900	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	45	519	0	ENST00000378444.4:c.3041C>T	p.Ala1014Val	p.A1014V	ENST00000378444	NM_001123385.1	1014	gCt/gTt	5/15	1	2	FACETS	0.669	0.565	0.782	0.669	0.565	0.782	SUBCLONAL	1	TRUE	1	0.449913609917175	2		519	299	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969422	44969423	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	121	559	0	ENST00000377967.4:c.4106dup	p.Leu1369PhefsTer20	p.L1369Ffs*20	ENST00000377967	NM_021140.2	1368	-/T	28/29	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.449913609917175	2		559	507	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0032154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	30	451	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.21	2		451	259	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0032154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	27	482	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	1	2	FACETS	0.799	0.636	0.984	0.799	0.636	0.984	CLONAL	1	TRUE	1	0.21	2		482	322	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300570	11300570	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764486955	NA	P-0032154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	53	655	0	ENST00000361445.4:c.1576C>T	p.Arg526Cys	p.R526C	ENST00000361445	NM_004958.3	526	Cgt/Tgt	11/58	1	2	FACETS	0.94	0.802	1	0.94	0.802	1	CLONAL	1	TRUE	1	0.21	2		655	537	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120713	115120731	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTCTTCGGGCTCCATGG	TCTTCTTCGGGCTCCATGG	-	novel	NA	P-0032154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	38	636	0	ENST00000257566.3:c.275_293del	p.Thr92ArgfsTer41	p.T92Rfs*41	ENST00000257566	NM_016569.3	92	aCCATGGAGCCCGAAGAAGAg/ag	1/8	0.3	4	FACETS	0.625	0.515	0.748			1	SUBCLONAL	1	TRUE	NA	0.21	4		636	701	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	232	664	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.284732740879616	4	FACETS	1	0.962	1	0.771	0.726	0.816	CLONAL	3	TRUE	0	0.390456631644295	4		665	536	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176710810	176710810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	56	488	0	ENST00000439151.2:c.6032C>T	p.Pro2011Leu	p.P2011L	ENST00000439151	NM_022455.4	2011	cCc/cTc	20/23	0.300921791496404	3	FACETS	0.79	0.686	0.901	0.79	0.686	0.901	CLONAL	2	TRUE	1	0.390456631644295	3		488	217	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961538	54961538	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1338142196	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	116	458	0	ENST00000312783.6:c.94C>T	p.Pro32Ser	p.P32S	ENST00000312783	NM_198436.1	32	Cct/Tct	4/10	0.390456631644295	6	FACETS	0.834	0.757	0.913	0.834	0.757	0.913	CLONAL	3	TRUE	3	0.390456631644295	6		458	423	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727098	40727098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	138	561	0	ENST00000373198.4:c.3866C>T	p.Ser1289Phe	p.S1289F	ENST00000373198	NM_133170.3	1289	tCc/tTc	28/32	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.390456631644295	2		561	542	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972913	55972913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	25	608	0	ENST00000263923.4:c.1477G>A	p.Gly493Arg	p.G493R	ENST00000263923	NM_002253.2	493	Gga/Aga	11/30	0.232117041900375	3	FACETS	0.814	0.657	0.985	0.814	0.657	0.985	INDETERMINATE	2	TRUE	1	0.390456631644295	3		608	94	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255496	16255496	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	146	504	0	ENST00000375759.3:c.2761C>T	p.Gln921Ter	p.Q921*	ENST00000375759	NM_015001.2	921	Cag/Tag	11/15	0.390456631644295	6	FACETS	0.951	0.881	1	0.951	0.881	1	CLONAL	4	TRUE	2	0.390456631644295	6		504	350	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244913	123244913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1224606327	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	92	786	0	ENST00000358487.5:c.2191G>A	p.Glu731Lys	p.E731K	ENST00000358487	NM_000141.4	731	Gaa/Aaa	16/18	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.390456631644295	2		786	440	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562641	29562641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854562	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	44	530	0	ENST00000356175.3:c.3721C>T	p.Arg1241Ter	p.R1241*	ENST00000356175	NM_000267.3	1241	Cga/Tga	28/57	0.284732740879616	4	FACETS	1	0.906	1	0.54	0.462	0.623	CLONAL	2	TRUE	0	0.390456631644295	4		530	145	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505128	149505128	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1483057981	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	61	523	0	ENST00000261799.4:c.1687G>A	p.Glu563Lys	p.E563K	ENST00000261799	NM_002609.3	563	Gag/Aag	12/23	0.300921791496404	3	FACETS	0.927	0.802	1	0.463	0.401	0.531	CLONAL	1	TRUE	1	0.390456631644295	3		523	403	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845688	68845688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	39	659	0	ENST00000261769.5:c.934C>T	p.Pro312Ser	p.P312S	ENST00000261769	NM_004360.3	312	Cct/Tct	7/16	0.390456631644295	3	FACETS	0.511	0.424	0.609	0.256	0.212	0.305	SUBCLONAL	1	TRUE	1	0.390456631644295	3		659	467	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271562	15271562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751851528	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	120	850	1	ENST00000263388.2:c.6877C>T	p.Pro2293Ser	p.P2293S	ENST00000263388	NM_000435.2	2293	Ccc/Tcc	33/33	1	2	FACETS	0.856	0.774	0.943	0.856	0.774	0.943	CLONAL	1	TRUE	1	0.390456631644295	2		851	718	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942825	68942825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753863699	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	93	597	0	ENST00000288368.4:c.637G>A	p.Glu213Lys	p.E213K	ENST00000288368	NM_024870.2	213	Gag/Aag	6/40	0.362684966780768	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	2	TRUE	0	0.390456631644295	2		597	234	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614833	23614833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200283306	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	97	576	0	ENST00000261584.4:c.3508C>T	p.His1170Tyr	p.H1170Y	ENST00000261584	NM_024675.3	1170	Cat/Tat	13/13	0.390456631644295	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.390456631644295	3		576	259	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950309	17950309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	116	669	0	ENST00000458235.1:c.1418C>T	p.Ser473Phe	p.S473F	ENST00000458235	NM_000215.3	473	tCc/tTc	10/24	1	2	FACETS	0.995	0.9	1	0.995	0.9	1	CLONAL	1	TRUE	1	0.390456631644295	2		669	597	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628376	187628376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	131	762	0	ENST00000441802.2:c.2606C>T	p.Ser869Leu	p.S869L	ENST00000441802	NM_005245.3	869	tCa/tTa	2/27	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.390456631644295	2		762	471	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763235	59763235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761639530	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	16	686	0	ENST00000259008.2:c.2867C>T	p.Ser956Leu	p.S956L	ENST00000259008	NM_032043.2	956	tCa/tTa	19/20	0.390456631644295	4	FACETS	0.991	0.741	1	0.248	0.185	0.321	CLONAL	1	TRUE	0	0.390456631644295	4		686	115	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451026	70451026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	51	573	0	ENST00000373644.4:c.5866C>T	p.Pro1956Ser	p.P1956S	ENST00000373644	NM_030625.2	1956	Cca/Tca	12/12	1	2	FACETS	0.859	0.735	0.994	0.859	0.735	0.994	CLONAL	1	TRUE	1	0.390456631644295	2		573	304	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291077	10291077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	94	684	0	ENST00000340748.4:c.394C>T	p.Leu132Phe	p.L132F	ENST00000340748		132	Ctt/Ttt	4/40	1	2	FACETS	0.912	0.814	1	0.912	0.814	1	CLONAL	1	TRUE	1	0.390456631644295	2		684	528	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980726	40980726	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	54	366	0	ENST00000373198.4:c.1760C>T	p.Ser587Leu	p.S587L	ENST00000373198	NM_133170.3	587	tCa/tTa	10/32	NA	2	FACETS	1	0.945	1			1	INDETERMINATE	1	TRUE	NA	0.390456631644295	2		366	232	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264143	46264143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746732554	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	66	312	0	ENST00000371998.3:c.1190C>T	p.Ser397Leu	p.S397L	ENST00000371998		397	tCg/tTg	11/23	0.390456631644295	6	FACETS	0.941	0.823	1	0.627	0.548	0.711	CLONAL	2	TRUE	3	0.390456631644295	6		312	320	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770629	40770629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	82	434	0	ENST00000373198.4:c.2753G>A	p.Gly918Glu	p.G918E	ENST00000373198	NM_133170.3	918	gGg/gAg	19/32	NA	2	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.390456631644295	2		434	290	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189879	11189879	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	30	439	0	ENST00000361445.4:c.5630T>A	p.Leu1877His	p.L1877H	ENST00000361445	NM_004958.3	1877	cTc/cAc	40/58	0.390456631644295	6	FACETS	0.564	0.454	0.69	0.141	0.113	0.173	SUBCLONAL	1	TRUE	2	0.390456631644295	6		439	485	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28601372	28601372	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1317298662	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	325	635	0	ENST00000253063.3:c.1057C>T	p.Gln353Ter	p.Q353*	ENST00000253063	NM_031459.4	353	Cag/Tag	8/10	0.390456631644295	3	FACETS	0.939	0.894	0.985	1	0.995	1	CLONAL	3	TRUE	1	0.390456631644295	3		635	706	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809739	36809739	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779143408	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	60	567	0	ENST00000373129.3:c.866C>T	p.Ala289Val	p.A289V	ENST00000373129	NM_032017.1	289	gCc/gTc	9/12	0.390456631644295	3	FACETS	0.706	0.609	0.812	0.353	0.304	0.406	SUBCLONAL	1	TRUE	1	0.390456631644295	3		567	520	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175996737	175996737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	34	475	0	ENST00000367669.3:c.1700C>T	p.Ser567Phe	p.S567F	ENST00000367669	NM_022457.5	567	tCc/tTc	15/20	0.30771717679779	3	FACETS	0.788	0.656	0.931	0.526	0.437	0.621	CLONAL	2	TRUE	0	0.390456631644295	3		475	132	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612826	228612827	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	67	654	0	ENST00000366696.1:c.200_201delinsTT	p.Pro67Leu	p.P67L	ENST00000366696	NM_003493.2	67	cCC/cTT	1/1	0.30771717679779	3	FACETS	0.736	0.64	0.84	0.245	0.213	0.28	SUBCLONAL	1	TRUE	0	0.390456631644295	3		654	557	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123324078	123324078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	33	571	0	ENST00000358487.5:c.392G>A	p.Gly131Glu	p.G131E	ENST00000358487	NM_000141.4	131	gGa/gAa	4/18	1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	1	0.390456631644295	2		571	164	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518530	69518530	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	245	492	0	ENST00000294312.3:c.115G>A	p.Gly39Ser	p.G39S	ENST00000294312	NM_005117.2	39	Ggc/Agc	1/3	0.390456631644295	3	FACETS	0.936	0.884	0.989	0.936	0.884	0.989	CLONAL	3	TRUE	0	0.390456631644295	3		492	534	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434663	49434663	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778904794	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	77	771	0	ENST00000301067.7:c.6890C>T	p.Pro2297Leu	p.P2297L	ENST00000301067	NM_003482.3	2297	cCt/cTt	31/54	0.390456631644295	4	FACETS	0.788	0.691	0.892	0.394	0.345	0.446	SUBCLONAL	1	TRUE	2	0.390456631644295	4		771	696	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431343	121431343	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	163	399	0	ENST00000257555.6:c.547G>A	p.Gly183Arg	p.G183R	ENST00000257555		183	Gga/Aga	3/10	0.390456631644295	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.390456631644295	2		399	378	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588650	28588650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	38	500	0	ENST00000241453.7:c.2798G>A	p.Arg933Gln	p.R933Q	ENST00000241453	NM_004119.2	933	cGg/cAg	23/24	0.322729085653682	0	FACETS	0.836	0.703	0.977			1	CLONAL	1	TRUE	0	0.390456631644295	0		500	142	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954045	32954045	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	22	449	0	ENST00000380152.3:c.9112C>G	p.Leu3038Val	p.L3038V	ENST00000380152		3038	Cta/Gta	23/27	0.315282094989761	4	FACETS	0.861	0.682	1	0.861	0.682	1	CLONAL	2	TRUE	2	0.390456631644295	4		449	91	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972611	32972611	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1566261240	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	20	454	0	ENST00000380152.3:c.9961C>T	p.Gln3321Ter	p.Q3321*	ENST00000380152		3321	Cag/Tag	27/27	0.315282094989761	4	FACETS	1	0.841	1	0.556	0.43	0.7	CLONAL	1	TRUE	2	0.390456631644295	4		454	128	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942734	48942734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	22	288	0	ENST00000267163.4:c.1121C>T	p.Pro374Leu	p.P374L	ENST00000267163	NM_000321.2	374	cCa/cTa	11/27	0.315282094989761	4	FACETS	1	0.922	1	0.725	0.572	0.897	CLONAL	1	TRUE	2	0.390456631644295	4		288	108	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675062	40675062	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1056073891	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	115	639	0	ENST00000249776.8:c.26T>C	p.Leu9Pro	p.L9P	ENST00000249776	NM_033286.3	9	cTg/cCg	1/9	0.390456631644295	3	FACETS	0.926	0.835	1	0.463	0.417	0.512	CLONAL	1	TRUE	1	0.390456631644295	3		639	760	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843456	3843456	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	153	561	0	ENST00000262367.5:c.1147C>T	p.Pro383Ser	p.P383S	ENST00000262367	NM_004380.2	383	Ccg/Tcg	4/31	0.390456631644295	3	FACETS	0.937	0.863	1	0.937	0.863	1	CLONAL	2	TRUE	1	0.390456631644295	3		561	500	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274136	10274136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866582475	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	133	553	0	ENST00000330684.3:c.133G>A	p.Asp45Asn	p.D45N	ENST00000330684	NM_001134407.1	45	Gac/Aac	2/13	0.390456631644295	3	FACETS	0.819	0.748	0.893	0.819	0.748	0.893	CLONAL	2	TRUE	1	0.390456631644295	3		553	497	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968283	15968283	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	49	384	0	ENST00000268712.3:c.5002G>A	p.Gly1668Arg	p.G1668R	ENST00000268712	NM_006311.3	1668	Ggg/Agg	34/46	0.284732740879616	4	FACETS	1	0.914	1	0.793	0.694	0.894	CLONAL	3	TRUE	0	0.390456631644295	4		384	110	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10264989	10264990	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	46	401	1	ENST00000340748.4:c.1950_1951delinsTT	p.Arg651Trp	p.R651W	ENST00000340748		650	cgCCgg/cgTTgg	21/40	1	2	FACETS	0.732	0.619	0.855	0.732	0.619	0.855	SUBCLONAL	1	TRUE	1	0.390456631644295	2		402	322	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355564	15355566	+	missense_variant	Missense_Mutation	TNP	GGA	GGA	AAT	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	53	637	1	ENST00000263377.2:c.2166_2168delinsATT	p.Pro723Leu	p.P723L	ENST00000263377	NM_058243.2	722	gcTCCg/gcATTg	12/20	1	2	FACETS	0.689	0.589	0.798	0.689	0.589	0.798	SUBCLONAL	1	TRUE	1	0.390456631644295	2		638	394	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213539	36213539	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs867685821	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	140	929	0	ENST00000222270.7:c.2641C>T	p.Gln881Ter	p.Q881*	ENST00000222270	NM_014727.1	881	Cag/Tag	5/37	0.390456631644295	3	FACETS	1	0.95	1	0.531	0.484	0.581	CLONAL	1	TRUE	1	0.390456631644295	3		929	807	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222498	39222498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	106	657	0	ENST00000402219.2:c.3112C>T	p.Pro1038Ser	p.P1038S	ENST00000402219	NM_005633.3	1038	Cct/Tct	20/23	0.390456631644295	3	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	1	0.390456631644295	3		657	306	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027076	48027076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	29	467	0	ENST00000234420.5:c.1954G>A	p.Gly652Arg	p.G652R	ENST00000234420	NM_000179.2	652	Ggg/Agg	4/10	0.390456631644295	3	FACETS	1	0.921	1	0.639	0.52	0.769	CLONAL	1	TRUE	1	0.390456631644295	3		467	139	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980390	55980390	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	12	405	0	ENST00000263923.4:c.701T>G	p.Ile234Ser	p.I234S	ENST00000263923	NM_002253.2	234	aTt/aGt	6/30	0.232117041900375	3	FACETS	0.735	0.522	0.99	0.367	0.261	0.495	INDETERMINATE	1	TRUE	1	0.390456631644295	3		405	100	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155150	106155150	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	34	364	0	ENST00000380013.4:c.51C>A	p.Phe17Leu	p.F17L	ENST00000380013	NM_001127208.2	17	ttC/ttA	3/11	0.390456631644295	1	FACETS	0.829	0.686	0.986	0.829	0.686	0.986	CLONAL	1	TRUE	0	0.390456631644295	1		364	169	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510330	187510330	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768414337	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	21	386	0	ENST00000441802.2:c.13183C>T	p.Pro4395Ser	p.P4395S	ENST00000441802	NM_005245.3	4395	Ccg/Tcg	27/27	1	2	FACETS	0.712	0.554	0.894	0.712	0.554	0.894	SUBCLONAL	1	TRUE	1	0.390456631644295	2		386	151	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876472	35876472	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	83	613	0	ENST00000303115.3:c.1264C>T	p.Gln422Ter	p.Q422*	ENST00000303115	NM_002185.3	422	Caa/Taa	8/8	0.300921791496404	3	FACETS	0.772	0.688	0.861	0.772	0.688	0.861	SUBCLONAL	2	TRUE	1	0.390456631644295	3		613	329	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754834	57754834	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	22	375	0	ENST00000274289.3:c.356C>T	p.Ala119Val	p.A119V	ENST00000274289	NM_006622.3	119	gCt/gTt	2/14	0.300921791496404	3	FACETS	0.935	0.733	1	0.468	0.366	0.583	CLONAL	1	TRUE	1	0.390456631644295	3		375	144	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449596	149449596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	174	632	0	ENST00000286301.3:c.1350G>A	p.Trp450Ter	p.W450*	ENST00000286301	NM_005211.3	450	tgG/tgA	10/22	0.300921791496404	3	FACETS	0.869	0.804	0.936	0.869	0.804	0.936	CLONAL	2	TRUE	1	0.390456631644295	3		632	613	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858177	27858177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1199392510	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	182	440	0	ENST00000359303.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000359303	NM_003535.2	132	Cgt/Tgt	1/1	0.390456631644295	13	FACETS	1	0.969	1			1	CLONAL	4	TRUE	NA	0.390456631644295	13		440	677	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948275	31948275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs140503088	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	251	720	0	ENST00000375333.2:c.863G>A	p.Trp288Ter	p.W288*	ENST00000375333	NM_032454.1	288	tGg/tAg	6/8	0.390456631644295	7	FACETS	1	0.943	1			1	CLONAL	3	TRUE	NA	0.390456631644295	7		720	842	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169192	32169192	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs952787215	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	292	672	0	ENST00000375023.3:c.3841G>A	p.Gly1281Arg	p.G1281R	ENST00000375023	NM_004557.3	1281	Gga/Aga	22/30	0.390456631644295	7	FACETS	0.877	0.828	0.926			1	CLONAL	4	TRUE	NA	0.390456631644295	7		672	843	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138201292	138201292	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	101	442	0	ENST00000237289.4:c.1991C>T	p.Thr664Ile	p.T664I	ENST00000237289	NM_001270507.1	664	aCc/aTc	8/9	0.390456631644295	3	FACETS	0.763	0.687	0.843	0.763	0.687	0.843	SUBCLONAL	2	TRUE	1	0.390456631644295	3		442	405	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771143	161771144	+	missense_variant	Missense_Mutation	DNP	CC	CC	TG	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	126	523	0	ENST00000366898.1:c.1385_1386delinsCA	p.Trp462Ser	p.W462S	ENST00000366898	NM_004562.2	462	tGG/tCA	12/12	0.390456631644295	3	FACETS	0.867	0.791	0.946	0.867	0.791	0.946	CLONAL	2	TRUE	1	0.390456631644295	3		523	445	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864404	162864404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	94	482	0	ENST00000366898.1:c.109C>T	p.Pro37Ser	p.P37S	ENST00000366898	NM_004562.2	37	Ccg/Tcg	2/12	0.390456631644295	3	FACETS	0.822	0.738	0.91	0.822	0.738	0.91	CLONAL	2	TRUE	1	0.390456631644295	3		482	350	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962855	2962855	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	149	668	0	ENST00000396946.4:c.2053G>A	p.Gly685Ser	p.G685S	ENST00000396946	NM_032415.4	685	Ggc/Agc	16/25	0.232117041900375	3	FACETS	1	0.983	1	0.648	0.593	0.705	INDETERMINATE	1	TRUE	1	0.390456631644295	3		668	704	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27213555	27213555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	29	602	0	ENST00000380036.4:c.2951G>A	p.Gly984Glu	p.G984E	ENST00000380036	NM_000459.3	984	gGa/gAa	18/23	0.390456631644295	1	FACETS	0.941	0.769	1	0.941	0.769	1	CLONAL	1	TRUE	0	0.390456631644295	1		602	127	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950087	44950087	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775880927	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	18	280	0	ENST00000377967.4:c.3856C>T	p.Pro1286Ser	p.P1286S	ENST00000377967	NM_021140.2	1286	Cca/Tca	26/29	0.323953717701354	2	FACETS	1	0.826	1			1	CLONAL	2	TRUE	NA	0.390456631644295	2		280	44	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813044	76813044	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	25	343	0	ENST00000373344.5:c.6577C>T	p.Gln2193Ter	p.Q2193*	ENST00000373344	NM_000489.3	2193	Cag/Tag	30/35	0.323953717701354	2	FACETS	0.854	0.712	0.995			1	CLONAL	3	TRUE	NA	0.390456631644295	2		343	50	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627386	37627386	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	64	637	0	ENST00000447079.4:c.1301C>T	p.Ser434Leu	p.S434L	ENST00000447079	NM_015083.1	434	tCa/tTa	2/14	0.284732740879616	4	FACETS	1	0.934	1	0.548	0.482	0.617	CLONAL	2	TRUE	0	0.390456631644295	4		637	208	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	89	570	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.190137869867135	2	FACETS	1	0.97	1	0.639	0.568	0.714	CLONAL	1	TRUE	0	0.254237038319281	2		570	548	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0032448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	162	663	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.190137869867135	2	FACETS	0.766	0.703	0.831	0.766	0.703	0.831	SUBCLONAL	2	TRUE	0	0.254237038319281	2		664	832	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435471	49435471	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	189	747	0	ENST00000301067.7:c.6201C>G	p.Asn2067Lys	p.N2067K	ENST00000301067	NM_003482.3	2067	aaC/aaG	30/54	0.251653925198248	4	FACETS	0.769	0.713	0.827	0.769	0.713	0.827	INDETERMINATE	2	TRUE	2	0.509438570589895	4		747	728	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118941	115118941	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	44	299	0	ENST00000257566.3:c.400C>A	p.Pro134Thr	p.P134T	ENST00000257566	NM_016569.3	134	Cct/Act	2/8	1	2	FACETS	0.919	0.781	1	0.919	0.781	1	CLONAL	1	TRUE	1	0.509438570589895	2		299	188	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953517	32953517	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0032480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	71	515	0	ENST00000380152.3:c.8818A>T	p.Lys2940Ter	p.K2940*	ENST00000380152		2940	Aaa/Taa	22/27	1	2	FACETS	0.825	0.725	0.931	0.825	0.725	0.931	CLONAL	1	TRUE	1	0.509438570589895	2		515	338	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791019	42791019	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	21	550	0	ENST00000575354.2:c.164C>G	p.Pro55Arg	p.P55R	ENST00000575354	NM_015125.3	55	cCg/cGg	2/20	1	2	FACETS	0.218	0.167	0.277	0.218	0.167	0.277	SUBCLONAL	1	TRUE	1	0.509438570589895	2		550	378	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279876	46279876	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	81	621	0	ENST00000371998.3:c.3802C>T	p.Gln1268Ter	p.Q1268*	ENST00000371998		1268	Caa/Taa	20/23	1	2	FACETS	0.546	0.482	0.615	0.546	0.482	0.615	SUBCLONAL	1	TRUE	1	0.509438570589895	2		621	582	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84384033	84384033	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1454080702	NA	P-0032480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	100	678	0	ENST00000321945.7:c.819C>A	p.Asp273Glu	p.D273E	ENST00000321945	NM_139076.2	273	gaC/gaA	9/9	0.177052710061184	3	FACETS	1	0.918	1	0.513	0.46	0.569	INDETERMINATE	1	TRUE	1	0.509438570589895	3		678	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577050	7577072	+	frameshift_variant	Frame_Shift_Del	DEL	GTGAGGCTCCCCTTTCTTGCGGA	GTGAGGCTCCCCTTTCTTGCGGA	-	novel	NA	P-0032528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	223	698	0	ENST00000269305.4:c.866_888del	p.Leu289ProfsTer9	p.L289Pfs*9	ENST00000269305	NM_001126112.2	289	cTCCGCAAGAAAGGGGAGCCTCAC/c	8/11	0.357104343047943	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.357104343047943	2		698	600	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282719	1282719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776459827	NA	P-0032528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	80	497	0	ENST00000310581.5:c.1594G>A	p.Ala532Thr	p.A532T	ENST00000310581	NM_198253.2	532	Gca/Aca	3/16	0.357104343047943	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.357104343047943	1		497	285	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	59	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.301974034309233	4	FACETS	0.967	0.854	1	0.967	0.854	1	CLONAL	3	TRUE	1	0.382602361305977	4		436	147	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	39	536	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.588	0.488	0.698	0.588	0.488	0.698	SUBCLONAL	1	TRUE	1	0.382602361305977	2		537	347	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	79	566	1	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.879	0.785	0.976	1	0.983	1	CLONAL	2	TRUE	1	0.382602361305977	2		567	235	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692981	89692982	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	23	479	0	ENST00000371953.3:c.469dup	p.Glu157GlyfsTer23	p.E157Gfs*23	ENST00000371953	NM_000314.4	155	-/G	5/9	0.27302859217037	3	FACETS	1	0.853	1	1	0.853	1	CLONAL	2	TRUE	1	0.382602361305977	3		479	67	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202627	67202627	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1028574404	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	51	595	0	ENST00000312629.5:c.1436G>A	p.Arg479His	p.R479H	ENST00000312629	NM_003952.2	479	cGt/cAt	15/15	1	2	FACETS	0.916	0.784	1	0.916	0.784	1	CLONAL	1	TRUE	1	0.382602361305977	2		595	291	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023559	27023560	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	54	391	0	ENST00000324856.7:c.671dup	p.Pro225AlafsTer175	p.P225Afs*175	ENST00000324856	NM_006015.4	222	tac/taCc	1/20	1	2	FACETS	0.728	0.623	0.841	0.728	0.623	0.841	SUBCLONAL	1	TRUE	1	0.382602361305977	2		391	388	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250883	153250883	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	23	423	0	ENST00000281708.4:c.1177C>T	p.Arg393Ter	p.R393*	ENST00000281708	NM_033632.3	393	Cga/Tga	8/12	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.382602361305977	2		423	84	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	24	148	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	0.859	0.681	1	0.859	0.681	1	CLONAL	1	TRUE	1	0.382602361305977	2		148	146	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	81	757	0	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	0.382602361305977	3	FACETS	1	0.952	1	0.573	0.507	0.643	CLONAL	1	TRUE	1	0.382602361305977	3		757	440	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436028	56436028	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	34	448	1	ENST00000407977.2:c.1109del	p.Pro370HisfsTer49	p.P370Hfs*49	ENST00000407977		370	cCa/ca	9/10	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.382602361305977	2		449	157	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881512	48881512	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	28	310	0	ENST00000267163.4:c.234G>A	p.Trp78Ter	p.W78*	ENST00000267163	NM_000321.2	78	tgG/tgA	2/27	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.382602361305977	2		310	108	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254594	1254594	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35719940	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	78	617	1	ENST00000310581.5:c.3184G>A	p.Ala1062Thr	p.A1062T	ENST00000310581	NM_198253.2	1062	Gcc/Acc	15/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.382602361305977	2		618	361	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	20	744	4	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	0.307	0.235	0.393	0.307	0.235	0.393	SUBCLONAL	1	TRUE	1	0.382602361305977	2		748	340	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619228	23619228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201657283	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	53	550	0	ENST00000261584.4:c.3307G>A	p.Val1103Met	p.V1103M	ENST00000261584	NM_024675.3	1103	Gtg/Atg	12/13	1	2	FACETS	0.952	0.818	1	0.952	0.818	1	CLONAL	1	TRUE	1	0.382602361305977	2		550	291	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265024	46265024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1172968588	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	17	504	0	ENST00000371998.3:c.1894C>T	p.Arg632Trp	p.R632W	ENST00000371998		632	Cgg/Tgg	12/23	1	2	FACETS	0.689	0.519	0.886	0.689	0.519	0.886	SUBCLONAL	1	TRUE	1	0.382602361305977	2		504	129	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33433425	33433425	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs387906843	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	83	647	1	ENST00000345365.6:c.556C>T	p.Arg186Ter	p.R186*	ENST00000345365	NM_002878.3	186	Cga/Tga	6/10	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.382602361305977	2		648	417	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798822	42798822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	118	783	1	ENST00000575354.2:c.4394G>A	p.Arg1465His	p.R1465H	ENST00000575354	NM_015125.3	1465	cGc/cAc	19/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.382602361305977	2		784	483	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351871	89351871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752417963	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	102	953	2	ENST00000301030.4:c.1079C>T	p.Pro360Leu	p.P360L	ENST00000301030	NM_001256183.1	360	cCg/cTg	9/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.382602361305977	2		955	421	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442811	442811	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	29	389	1	ENST00000399788.2:c.1495del	p.Glu499SerfsTer19	p.E499Sfs*19	ENST00000399788	NM_001042603.1	499	Gag/ag	12/28	0.301974034309233	4	FACETS	1	0.933	1	0.46	0.373	0.555	CLONAL	1	TRUE	1	0.382602361305977	4		390	152	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737698	145737698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560476442	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	64	713	0	ENST00000428558.2:c.3065G>A	p.Arg1022His	p.R1022H	ENST00000428558	NM_004260.3	1022	cGt/cAt	19/22	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.382602361305977	2		713	269	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444960	49444960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	74	558	3	ENST00000301067.7:c.2506del	p.Gln836SerfsTer94	p.Q836Sfs*94	ENST00000301067	NM_003482.3	836	Cag/ag	10/54	0.301974034309233	4	FACETS	1	0.97	1	0.451	0.397	0.509	CLONAL	1	TRUE	1	0.382602361305977	4		561	395	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941265	71941265	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144485030	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	109	769	2	ENST00000298229.2:c.1040G>A	p.Arg347Gln	p.R347Q	ENST00000298229	NM_001567.3	347	cGg/cAg	9/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.382602361305977	2		771	447	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425823	49425824	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs754290613	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	50	656	0	ENST00000301067.7:c.12662_12664dup	p.Gln4221dup	p.Q4221dup	ENST00000301067	NM_003482.3	4221	cta/cAGCta	39/54	0.301974034309233	4	FACETS	1	0.93	1	0.386	0.329	0.448	CLONAL	1	TRUE	1	0.382602361305977	4		656	312	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821572	72821572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457944892	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	11	232	0	ENST00000268489.5:c.10603G>A	p.Glu3535Lys	p.E3535K	ENST00000268489	NM_006885.3	3535	Gag/Aag	10/10	1	2	FACETS	0.414	0.287	0.57	0.414	0.287	0.57	SUBCLONAL	1	TRUE	1	0.382602361305977	2		232	139	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928074	178928074	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	32	559	0	ENST00000263967.3:c.1352G>T	p.Gly451Val	p.G451V	ENST00000263967	NM_006218.2	451	gGa/gTa	8/21	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.382602361305977	2		559	121	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042482	16042482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	23	558	1	ENST00000268712.3:c.1192C>T	p.Arg398Trp	p.R398W	ENST00000268712	NM_006311.3	398	Cgg/Tgg	12/46	1	2	FACETS	0.994	0.786	1	0.994	0.786	1	CLONAL	1	TRUE	1	0.382602361305977	2		559	121	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187222	38187222	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	61	964	3	ENST00000317025.8:c.1255del	p.Thr419ProfsTer8	p.T419Pfs*8	ENST00000317025	NM_023034.1	419	Acc/cc	6/24	1	2	FACETS	0.972	0.844	1	0.972	0.844	1	CLONAL	1	TRUE	1	0.382602361305977	2		967	328	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745624	162745624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765562219	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	31	439	0	ENST00000367921.3:c.2039G>A	p.Arg680His	p.R680H	ENST00000367921	NM_006182.2	680	cGc/cAc	15/18	1	2	FACETS	0.779	0.635	0.94	0.779	0.635	0.94	CLONAL	1	TRUE	1	0.382602361305977	2		439	208	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009121	27009126	+	inframe_deletion	In_Frame_Del	DEL	CCCGAC	CCCGAC	-	novel	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	39	99	0	ENST00000335756.4:c.66_71del	p.Thr23_Pro24del	p.T23_P24del	ENST00000335756	NM_001809.3	19	agCCCGACc/agc	1/5	0.382602361305977	3	FACETS	0.843	0.712	0.984	0.843	0.712	0.984	CLONAL	2	TRUE	1	0.382602361305977	3		99	144	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219406	1219406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555737824	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	92	630	0	ENST00000326873.7:c.458C>T	p.Ala153Val	p.A153V	ENST00000326873	NM_000455.4	153	gCc/gTc	3/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.382602361305977	2		630	428	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606184	93606184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201301123	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	25	500	0	ENST00000375746.1:c.4G>A	p.Ala2Thr	p.A2T	ENST00000375746	NM_001174167.1	2	Gcc/Acc	2/14	1	2	FACETS	0.411	0.324	0.511	0.411	0.324	0.511	SUBCLONAL	1	TRUE	1	0.382602361305977	2		500	318	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004808	16004808	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs76080188	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	52	698	0	ENST00000268712.3:c.2446G>A	p.Ala816Thr	p.A816T	ENST00000268712	NM_006311.3	816	Gct/Act	20/46	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.382602361305977	2		698	257	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246518362	246518362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142323814	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	23	511	0	ENST00000388985.4:c.199G>A	p.Val67Ile	p.V67I	ENST00000388985		67	Gtc/Atc	2/12	1	2	FACETS	0.716	0.563	0.89	0.716	0.563	0.89	SUBCLONAL	1	TRUE	1	0.382602361305977	2		511	168	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319325	11319325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	87	679	0	ENST00000361445.4:c.142G>A	p.Val48Ile	p.V48I	ENST00000361445	NM_004958.3	48	Gtc/Atc	2/58	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.382602361305977	2		679	341	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023542	27023542	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	69	447	0	ENST00000324856.7:c.651del	p.Asn218ThrfsTer14	p.N218Tfs*14	ENST00000324856	NM_006015.4	216	taC/ta	1/20	1	2	FACETS	0.906	0.793	1	0.906	0.793	1	CLONAL	1	TRUE	1	0.382602361305977	2		447	398	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692880	89692880	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	28	377	0	ENST00000371953.3:c.364A>T	p.Ile122Phe	p.I122F	ENST00000371953	NM_000314.4	122	Att/Ttt	5/9	0.27302859217037	3	FACETS	0.918	0.752	1	0.918	0.752	1	CLONAL	2	TRUE	1	0.382602361305977	3		377	95	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625374	69625374	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782226740	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	108	764	0	ENST00000334134.2:c.419C>T	p.Thr140Met	p.T140M	ENST00000334134	NM_005247.2	140	aCg/aTg	3/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.382602361305977	2		764	416	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94209471	94209471	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762424288	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	17	374	0	ENST00000323929.3:c.643G>A	p.Val215Met	p.V215M	ENST00000323929	NM_005591.3	215	Gtg/Atg	7/20	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.382602361305977	2		374	72	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352447	118352447	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	22	265	0	ENST00000534358.1:c.3656del	p.Lys1219SerfsTer16	p.K1219Sfs*16	ENST00000534358	NM_005933.3	1218	Aaa/aa	7/36	1	2	FACETS	0.777	0.62	0.947	1	0.934	1	CLONAL	2	TRUE	1	0.382602361305977	2		265	74	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435870	110435870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173972047	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	64	554	0	ENST00000375856.3:c.2531C>T	p.Thr844Met	p.T844M	ENST00000375856	NM_003749.2	844	aCg/aTg	1/2	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.382602361305977	2		554	331	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988304	41988304	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs563448726	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	64	697	0	ENST00000219905.7:c.1096C>T	p.Arg366Cys	p.R366C	ENST00000219905	NM_001164273.1	366	Cgt/Tgt	3/24	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.382602361305977	2		697	234	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14031682	14031682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs180919656	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	28	390	1	ENST00000311895.7:c.1871G>A	p.Arg624Gln	p.R624Q	ENST00000311895	NM_005236.2	624	cGg/cAg	9/11	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.382602361305977	2		391	117	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646552	23646553	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	19	589	0	ENST00000261584.4:c.1314dup	p.Gly439ArgfsTer3	p.G439Rfs*3	ENST00000261584	NM_024675.3	438	-/A	4/13	1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	1	0.382602361305977	2		589	92	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645163	67645163	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	35	628	0	ENST00000264010.4:c.428C>A	p.Ser143Tyr	p.S143Y	ENST00000264010	NM_006565.3	143	tCt/tAt	3/12	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.382602361305977	2		628	152	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867268	68867268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780121	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	46	538	0	ENST00000261769.5:c.2515G>A	p.Gly839Ser	p.G839S	ENST00000261769	NM_004360.3	839	Ggt/Agt	16/16	1	2	FACETS	0.936	0.794	1	0.936	0.794	1	CLONAL	1	TRUE	1	0.382602361305977	2		538	257	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830234	72830234	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	22	412	0	ENST00000268489.5:c.6347del	p.Pro2116ArgfsTer60	p.P2116Rfs*60	ENST00000268489	NM_006885.3	2116	cCg/cg	9/10	1	2	FACETS	0.635	0.496	0.795	0.635	0.496	0.795	SUBCLONAL	1	TRUE	1	0.382602361305977	2		412	181	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993882	72993882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	38	480	0	ENST00000268489.5:c.163G>A	p.Ala55Thr	p.A55T	ENST00000268489	NM_006885.3	55	Gcc/Acc	2/10	1	2	FACETS	0.924	0.771	1	0.924	0.771	1	CLONAL	1	TRUE	1	0.382602361305977	2		480	215	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619112	37619112	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	33	509	0	ENST00000447079.4:c.788A>G	p.Lys263Arg	p.K263R	ENST00000447079	NM_015083.1	263	aAg/aGg	1/14	1	2	FACETS	0.894	0.735	1	0.894	0.735	1	CLONAL	1	TRUE	1	0.382602361305977	2		509	193	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246517	41246517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658636	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	18	889	1	ENST00000357654.3:c.1031C>T	p.Ala344Val	p.A344V	ENST00000357654	NM_007294.3	344	gCt/gTt	10/23	1	2	FACETS	0.444	0.335	0.572	0.444	0.335	0.572	SUBCLONAL	1	TRUE	1	0.382602361305977	2		890	212	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434952	56434952	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	73	720	0	ENST00000407977.2:c.2185C>A	p.Leu729Met	p.L729M	ENST00000407977		729	Ctg/Atg	9/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.382602361305977	2		720	310	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897301	78897301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1466918945	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	53	666	0	ENST00000306801.3:c.2636C>T	p.Pro879Leu	p.P879L	ENST00000306801	NM_020761.2	879	cCg/cTg	23/34	1	2	FACETS	0.759	0.65	0.878	0.759	0.65	0.878	SUBCLONAL	1	TRUE	1	0.382602361305977	2		666	365	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303107	15303107	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	115	958	0	ENST00000263388.2:c.343C>T	p.Pro115Ser	p.P115S	ENST00000263388	NM_000435.2	115	Cct/Tct	4/33	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.382602361305977	2		958	482	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47672741	47672741	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	25	704	0	ENST00000233146.2:c.1331del	p.Arg444LeufsTer10	p.R444Lfs*10	ENST00000233146	NM_000251.2	444	cGt/ct	8/16	0.382602361305977	3	FACETS	0.782	0.62	0.966	0.391	0.31	0.483	CLONAL	1	TRUE	1	0.382602361305977	3		704	199	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028199	48028199	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	15	394	0	ENST00000234420.5:c.3077A>C	p.Asp1026Ala	p.D1026A	ENST00000234420	NM_000179.2	1026	gAt/gCt	4/10	0.382602361305977	3	FACETS	0.865	0.64	1	0.432	0.32	0.564	CLONAL	1	TRUE	1	0.382602361305977	3		394	108	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225362540	225362540	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770136825	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	37	546	0	ENST00000264414.4:c.1637G>A	p.Arg546Gln	p.R546Q	ENST00000264414	NM_003590.4	546	cGa/cAa	12/16	0.382602361305977	3	FACETS	1	0.94	1	0.655	0.546	0.772	CLONAL	1	TRUE	1	0.382602361305977	3		546	176	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015126	71015126	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1233821874	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	62	405	0	ENST00000318789.4:c.1804A>G	p.Ile602Val	p.I602V	ENST00000318789	NM_032682.5	602	Ata/Gta	20/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.382602361305977	2		405	241	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156685	55156685	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	26	456	0	ENST00000257290.5:c.3086C>A	p.Pro1029His	p.P1029H	ENST00000257290	NM_006206.4	1029	cCt/cAt	22/23	1	2	FACETS	0.786	0.628	0.963	0.786	0.628	0.963	CLONAL	1	TRUE	1	0.382602361305977	2		456	173	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538214	187538214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750202307	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	34	762	2	ENST00000441802.2:c.9020C>T	p.Ala3007Val	p.A3007V	ENST00000441802	NM_005245.3	3007	gCg/gTg	11/27	1	2	FACETS	0.78	0.641	0.933	0.78	0.641	0.933	CLONAL	1	TRUE	1	0.382602361305977	2		764	228	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515369	149515369	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	51	632	0	ENST00000261799.4:c.113del	p.Pro38ArgfsTer15	p.P38Rfs*15	ENST00000261799	NM_002609.3	38	cCg/cg	3/23	1	2	FACETS	0.919	0.787	1	0.919	0.787	1	CLONAL	1	TRUE	1	0.382602361305977	2		632	290	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128420027	128420027	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	45	877	0	ENST00000265960.3:c.401C>T	p.Pro134Leu	p.P134L	ENST00000265960	NM_001006617.1	134	cCa/cTa	4/12	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.382602361305977	2		877	226	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	50	570	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.275421551146683	1	FACETS	0.966	0.824	1	0.966	0.824	1	CLONAL	1	TRUE	0	0.275421551146683	1		570	324	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	35	329	0	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	0.275421551146683	1	FACETS	0.884	0.729	1	0.884	0.729	1	CLONAL	1	TRUE	0	0.275421551146683	1		329	248	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197443	106197443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1452689450	NA	P-0032627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	34	259	0	ENST00000380013.4:c.5776C>T	p.Arg1926Cys	p.R1926C	ENST00000380013	NM_001127208.2	1926	Cgt/Tgt	11/11	1	2	FACETS	0.968	0.795	1	0.968	0.795	1	CLONAL	1	TRUE	1	0.275421551146683	2		259	255	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196879	108196880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs773570504	NA	P-0032627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	58	356	0	ENST00000278616.4:c.6908dup	p.Glu2304GlyfsTer69	p.E2304Gfs*69	ENST00000278616	NM_000051.3	2301	gca/gcAa	47/63	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.275421551146683	2		356	413	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124712	108124712	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	40	403	1	ENST00000278616.4:c.2071del	p.Asp691IlefsTer12	p.D691Ifs*12	ENST00000278616	NM_000051.3	690	ctG/ct	13/63	1	2	FACETS	0.768	0.64	0.911	0.768	0.64	0.911	CLONAL	1	TRUE	1	0.275421551146683	2		404	378	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264527	30264527	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	206	163	0	ENST00000322652.5:c.262C>T	p.Gln88Ter	p.Q88*	ENST00000322652	NM_015355.2	88	Cag/Tag	1/16	0.847089890428531	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.847089890428531	1		163	249	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264527	30264527	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032893-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	199	163	0	ENST00000322652.5:c.262C>T	p.Gln88Ter	p.Q88*	ENST00000322652	NM_015355.2	88	Cag/Tag	1/16	0.724957588723098	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.724957588723098	2		163	267	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0032937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	102	302	0				ENST00000310581	NM_198253.2	-/1132			0.209266583706657	5	FACETS	0.931	0.84	1	0.931	0.84	1	CLONAL	3	TRUE	2	0.278503701732877	5		302	372	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0032937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	150	303	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.209266583706657	5	FACETS	0.904	0.831	0.98	0.904	0.831	0.98	CLONAL	3	TRUE	2	0.278503701732877	5		303	563	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486824	56486824	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1023742896	NA	P-0032937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	77	511	0	ENST00000267101.3:c.1238C>T	p.Ser413Phe	p.S413F	ENST00000267101	NM_001982.3	413	tCc/tTc	11/28	1	2	FACETS	0.661	0.579	0.749	0.661	0.579	0.749	SUBCLONAL	1	TRUE	1	0.278503701732877	2		511	837	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123889485	123889485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	51	226	0	ENST00000330479.4:c.712C>T	p.Arg238Trp	p.R238W	ENST00000330479	NM_020382.3	238	Cgg/Tgg	7/9	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.278503701732877	2		226	304	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211753	2211753	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	165	671	0	ENST00000398665.3:c.1469C>T	p.Ser490Phe	p.S490F	ENST00000398665	NM_032482.2	490	tCc/tTc	16/28	0.0644066577368558	3	FACETS	1	0.986	1	0.692	0.635	0.751	INDETERMINATE	1	TRUE	1	0.278503701732877	3		671	976	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354040	15354040	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	94	343	0	ENST00000263377.2:c.2840C>T	p.Ser947Phe	p.S947F	ENST00000263377	NM_058243.2	947	tCc/tTc	14/20	0.0644066577368558	3	FACETS	0.769	0.687	0.856	0.769	0.687	0.856	INDETERMINATE	2	TRUE	1	0.278503701732877	3		343	500	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867256	45867256	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780129241	NA	P-0032937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	128	521	1	ENST00000391945.4:c.937G>A	p.Glu313Lys	p.E313K	ENST00000391945	NM_000400.3	313	Gaa/Aaa	10/23	0.0644066577368558	3	FACETS	1	0.983	1	0.701	0.636	0.769	INDETERMINATE	1	TRUE	1	0.278503701732877	3		522	747	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133183	38133183	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	143	560	0	ENST00000317025.8:c.4290T>G	p.Asp1430Glu	p.D1430E	ENST00000317025	NM_023034.1	1430	gaT/gaG	24/24	0.0644066577368558	3	FACETS	1	0.983	1	0.665	0.606	0.727	INDETERMINATE	1	TRUE	1	0.278503701732877	3		560	880	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0032953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	157	880	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.457775575965075	1	FACETS	0.819	0.753	0.887	0.819	0.753	0.887	CLONAL	1	FALSE	0	0.457775575965075	1		880	646	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0032953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	129	468	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.936	0.852	1	0.936	0.852	1	CLONAL	1	FALSE	1	0.457775575965075	2		472	602	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584514	48584514	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	19	347	2	ENST00000342988.3:c.692del	p.Gly231AlafsTer10	p.G231Afs*10	ENST00000342988	NM_005359.5	229	ctG/ct	6/12	0.456296230935603	1	FACETS	0.184	0.139	0.237	0.184	0.139	0.237	SUBCLONAL	1	FALSE	0	0.457775575965075	1		349	348	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806119	1806119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931614	NA	P-0032953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	55	898	5	ENST00000260795.2:c.1138G>A	p.Gly380Arg	p.G380R	ENST00000260795		380	Ggg/Agg	8/17	1	2	FACETS	0.305	0.26	0.354	0.305	0.26	0.354	SUBCLONAL	1	FALSE	1	0.457775575965075	2		903	789	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781417	3781417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776549587	NA	P-0032953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	53	445	0	ENST00000262367.5:c.4948G>A	p.Val1650Ile	p.V1650I	ENST00000262367	NM_004380.2	1650	Gtc/Atc	30/31	1	2	FACETS	0.437	0.372	0.507	0.437	0.372	0.507	SUBCLONAL	1	FALSE	1	0.457775575965075	2		445	530	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720733	89720734	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	rs1564568350	NA	P-0032953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	12	158	0	ENST00000371953.3:c.885_886del	p.Cys296Ter	p.C296*	ENST00000371953	NM_000314.4	295	cTA/c	8/9	0.457775575965075	1	FACETS	0.275	0.194	0.374	0.275	0.194	0.374	SUBCLONAL	1	FALSE	0	0.457775575965075	1		158	147	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023290	27023290	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	20	53	0	ENST00000324856.7:c.400del	p.Ala134ArgfsTer98	p.A134Rfs*98	ENST00000324856	NM_006015.4	132	gtG/gt	1/20	1	2	FACETS	0.794	0.617	0.995	0.794	0.617	0.995	CLONAL	1	FALSE	1	0.457775575965075	2		53	110	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998128	169998128	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs753143066	NA	P-0032953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	141	578	3	ENST00000295797.4:c.826del	p.Thr276GlnfsTer7	p.T276Qfs*7	ENST00000295797	NM_002740.5	273	ttA/tt	9/18	1	2	FACETS	0.797	0.727	0.871	0.797	0.727	0.871	SUBCLONAL	1	FALSE	1	0.457775575965075	2		581	773	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348964	89348964	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	162	659	0	ENST00000301030.4:c.3986del	p.Pro1329LeufsTer16	p.P1329Lfs*16	ENST00000301030	NM_001256183.1	1329	cCt/ct	9/13	1	2	FACETS	0.918	0.844	0.995	0.918	0.844	0.995	CLONAL	1	FALSE	1	0.457775575965075	2		659	771	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46282157	46282157	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1170628032	NA	P-0032953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	64	279	0	ENST00000371998.3:c.4271G>A	p.Cys1424Tyr	p.C1424Y	ENST00000371998		1424	tGc/tAc	23/23	1	2	FACETS	0.637	0.553	0.727	0.637	0.553	0.727	SUBCLONAL	1	FALSE	1	0.457775575965075	2		279	439	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436278	110436278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	14	121	1	ENST00000375856.3:c.2123C>T	p.Ala708Val	p.A708V	ENST00000375856	NM_003749.2	708	gCg/gTg	1/2	1	2	FACETS	0.606	0.443	0.797	0.606	0.443	0.797	SUBCLONAL	1	FALSE	1	0.457775575965075	2		122	101	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115848	8115849	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0032953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	122	502	0	ENST00000346208.3:c.1197_1198del	p.Met400ValfsTer106	p.M400Vfs*106	ENST00000346208		398	agACac/agac	6/6	1	2	FACETS	0.818	0.74	0.898	0.818	0.74	0.898	CLONAL	1	FALSE	1	0.457775575965075	2		502	652	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500591	99500591	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1442885994	NA	P-0032953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	80	350	0	ENST00000268035.6:c.4024G>A	p.Glu1342Lys	p.E1342K	ENST00000268035	NM_000875.3	1342	Gag/Aag	21/21	1	2	FACETS	0.88	0.779	0.987	0.88	0.779	0.987	CLONAL	1	FALSE	1	0.457775575965075	2		350	397	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347447	89347447	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	110	474	2	ENST00000301030.4:c.5503C>A	p.Leu1835Met	p.L1835M	ENST00000301030	NM_001256183.1	1835	Ctg/Atg	9/13	1	2	FACETS	0.926	0.835	1	0.926	0.835	1	CLONAL	1	FALSE	1	0.457775575965075	2		476	519	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250417	10250417	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	24	412	0	ENST00000340748.4:c.3835G>C	p.Val1279Leu	p.V1279L	ENST00000340748		1279	Gtc/Ctc	33/40	1	2	FACETS	0.22	0.172	0.276	0.22	0.172	0.276	SUBCLONAL	1	FALSE	1	0.457775575965075	2		412	477	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026108	36026108	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	139	647	0	ENST00000358208.4:c.710C>T	p.Ala237Val	p.A237V	ENST00000358208		237	gCc/gTc	7/12	1	2	FACETS	0.917	0.837	1	0.917	0.837	1	CLONAL	1	FALSE	1	0.457775575965075	2		647	662	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181471	38181471	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	104	473	0	ENST00000396334.3:c.484A>G	p.Thr162Ala	p.T162A	ENST00000396334	NM_002468.4	162	Aca/Gca	2/5	0.456296230935603	1	FACETS	0.857	0.773	0.944	0.857	0.773	0.944	CLONAL	1	FALSE	0	0.457775575965075	1		473	409	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456492	189456492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	118	389	0	ENST00000264731.3:c.253G>A	p.Ala85Thr	p.A85T	ENST00000264731	NM_003722.4	85	Gcg/Acg	3/14	1	2	FACETS	0.833	0.753	0.917	0.833	0.753	0.917	CLONAL	1	FALSE	1	0.457775575965075	2		389	619	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710999	117710999	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	49	190	0	ENST00000368508.3:c.1273T>C	p.Tyr425His	p.Y425H	ENST00000368508	NM_002944.2	425	Tac/Cac	12/43	1	2	FACETS	0.978	0.837	1	0.978	0.837	1	CLONAL	1	FALSE	1	0.457775575965075	2		190	219	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0033061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	390	663	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.284127230343618	4	FACETS	1	0.968	1	1	0.996	1	CLONAL	3	FALSE	2	0.396043156915264	4		664	901	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0033061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	149	246	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.239124146777612	4	FACETS	0.9	0.832	0.969	1	0.987	1	CLONAL	3	FALSE	2	0.396043156915264	4		247	389	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197255	106197255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1222260506	NA	P-0033061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	160	311	1	ENST00000380013.4:c.5588C>T	p.Ala1863Val	p.A1863V	ENST00000380013	NM_001127208.2	1863	gCc/gTc	11/11	0.239124146777612	4	FACETS	1	0.957	1	1	0.991	1	CLONAL	3	FALSE	2	0.396043156915264	4		312	362	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572986	7572986	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555524156	NA	P-0033061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	330	467	1	ENST00000269305.4:c.1123C>T	p.Gln375Ter	p.Q375*	ENST00000269305	NM_001126112.2	375	Cag/Tag	11/11	0.284127230343618	4	FACETS	1	0.962	1	1	0.995	1	CLONAL	3	FALSE	2	0.396043156915264	4		468	765	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939340	76939343	+	frameshift_variant	Frame_Shift_Del	DEL	CTAC	CTAC	-	novel	NA	P-0033061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	328	397	0	ENST00000373344.5:c.1405_1408del	p.Val469IlefsTer44	p.V469Ifs*44	ENST00000373344	NM_000489.3	469	GTAGat/at	9/35	0.330354291326527	2	FACETS	1	0.981	1			1	CLONAL	4	FALSE	NA	0.396043156915264	2		397	408	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123873992	123873992	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	21	27	0	ENST00000330479.4:c.23C>T	p.Ser8Phe	p.S8F	ENST00000330479	NM_020382.3	8	tCc/tTc	2/9	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	FALSE	1	0.396043156915264	2		27	92	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0033172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	145	880	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.610648689642947	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.610648689642947	1		880	291	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	10	232	1	ENST00000257430.4:c.3919dup	p.Ile1307AsnfsTer8	p.I1307Nfs*8	ENST00000257430	NM_000038.5	1306	gaa/gAaa	16/16	1	2	FACETS	0.504	0.347	0.692	0.504	0.347	0.692	SUBCLONAL	1	TRUE	1	0.610648689642947	2		233	65	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395108	139395108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371414501	NA	P-0033172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	10	761	1	ENST00000277541.6:c.5830G>A	p.Ala1944Thr	p.A1944T	ENST00000277541	NM_017617.3	1944	Gcc/Acc	31/34	1	2	FACETS	0.074	0.05	0.106	0.074	0.05	0.106	SUBCLONAL	1	TRUE	1	0.610648689642947	2		762	440	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226677	2226677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763271310	NA	P-0033172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	11	818	0	ENST00000398665.3:c.4157G>A	p.Gly1386Asp	p.G1386D	ENST00000398665	NM_032482.2	1386	gGc/gAc	27/28	1	2	FACETS	0.08	0.055	0.112	0.08	0.055	0.112	SUBCLONAL	1	TRUE	1	0.610648689642947	2		818	448	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993104	72993104	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1469786547	NA	P-0033172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	20	928	0	ENST00000268489.5:c.941G>A	p.Arg314Gln	p.R314Q	ENST00000268489	NM_006885.3	314	cGg/cAg	2/10	0.343821639225927	1	FACETS	0.15	0.114	0.192	0.15	0.114	0.192	INDETERMINATE	1	TRUE	0	0.610648689642947	1		928	303	SUCCESS
APC	324	MSKCC	GRCh37	5	112174559	112174559	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	29	465	0	ENST00000257430.4:c.3268C>T	p.Gln1090Ter	p.Q1090*	ENST00000257430	NM_000038.5	1090	Caa/Taa	16/16	1	2	FACETS	0.959	0.789	1	0.959	0.789	1	CLONAL	1	TRUE	1	0.610648689642947	2		465	99	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998450	100998450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746718938	NA	P-0033172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	72	404	1	ENST00000325455.5:c.1352C>T	p.Ala451Val	p.A451V	ENST00000325455	NM_001202474.3	451	gCg/gTg	1/8	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.610648689642947	2		405	198	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155153	108155153	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555093708	NA	P-0033172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	28	584	0	ENST00000278616.4:c.3946A>G	p.Thr1316Ala	p.T1316A	ENST00000278616	NM_000051.3	1316	Acc/Gcc	26/63	1	2	FACETS	0.665	0.539	0.803	0.665	0.539	0.803	SUBCLONAL	1	TRUE	1	0.610648689642947	2		584	138	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0033174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	78	336	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.349564921909251	1	FACETS	0.774	0.682	0.872	0.774	0.682	0.872	SUBCLONAL	1	TRUE	0	0.349564921909251	1		336	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0033174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	283	520	2	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	0.929	0.876	0.984	1	0.995	1	CLONAL	2	TRUE	1	0.349564921909251	2		522	871	SUCCESS
APC	324	MSKCC	GRCh37	5	112175758	112175758	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	31	352	0	ENST00000257430.4:c.4467del	p.Leu1489PhefsTer18	p.L1489Ffs*18	ENST00000257430	NM_000038.5	1489	ttA/tt	16/16	1	2	FACETS	0.768	0.625	0.928	0.768	0.625	0.928	CLONAL	1	TRUE	1	0.349564921909251	2		352	231	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821594	72821596	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	rs374416547	NA	P-0033174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	10	93	0	ENST00000268489.5:c.10579_10581del	p.Gly3527del	p.G3527del	ENST00000268489	NM_006885.3	3527	GGC/-	10/10	0.234698036695837	3	FACETS	0.653	0.446	0.908	0.326	0.223	0.454	SUBCLONAL	1	TRUE	1	0.349564921909251	3		93	103	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119928	70119929	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0033174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	120	438	0	ENST00000245479.2:c.932dup	p.Gln312ProfsTer266	p.Q312Pfs*266	ENST00000245479	NM_000346.3	310	-/G	3/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.349564921909251	2		438	528	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117878	70117888	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCAGGCGGC	GCGCAGGCGGC	-	novel	NA	P-0033174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	28	427	0	ENST00000245479.2:c.353_363del	p.Ala118GlufsTer130	p.A118Efs*130	ENST00000245479	NM_000346.3	116	GCGCAGGCGGCg/g	1/3	1	2	FACETS	0.426	0.34	0.524	0.426	0.34	0.524	SUBCLONAL	1	TRUE	1	0.349564921909251	2		427	376	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858744	9858744	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs367543136	NA	P-0033174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	33	404	0	ENST00000330684.3:c.2657A>G	p.Asn886Ser	p.N886S	ENST00000330684	NM_001134407.1	886	aAt/aGt	13/13	0.349564921909251	1	FACETS	0.436	0.356	0.527	0.436	0.356	0.527	SUBCLONAL	1	TRUE	0	0.349564921909251	1		404	357	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604758	48604759	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCACTTACACCGGGCCCTCCAGCTCCTAG	novel	NA	P-0033174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	70	417	0	ENST00000342988.3:c.1581_1609dup	p.Asp537ValfsTer10	p.D537Vfs*10	ENST00000342988	NM_005359.5	527	att/atTCACTTACACCGGGCCCTCCAGCTCCTAGt	12/12	0.349564921909251	1	FACETS	0.798	0.699	0.905	0.798	0.699	0.905	CLONAL	1	TRUE	0	0.349564921909251	1		417	414	SUCCESS
APC	324	MSKCC	GRCh37	5	112174348	112174348	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	10	244	0	ENST00000257430.4:c.3057del	p.Glu1020AsnfsTer2	p.E1020Nfs*2	ENST00000257430	NM_000038.5	1019	ggA/gg	16/16	1	2	FACETS	0.724	0.497	1	0.724	0.497	1	CLONAL	1	TRUE	1	0.349564921909251	2		244	79	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0033204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	190	378	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.740898657906579	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.721956879848527	3		378	351	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127164	22127164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057519911	NA	P-0033204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	40	418	0	ENST00000215832.6:c.964G>A	p.Glu322Lys	p.E322K	ENST00000215832	NM_002745.4	322	Gag/Aag	7/9	1	2	FACETS	0.497	0.416	0.585	0.497	0.416	0.585	SUBCLONAL	1	TRUE	1	0.721956879848527	2		418	223	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577579	7577579	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	229	525	0	ENST00000269305.4:c.702C>A	p.Tyr234Ter	p.Y234*	ENST00000269305	NM_001126112.2	234	taC/taA	7/11	0.348980410145454	4	FACETS	0.942	0.907	0.975			1	INDETERMINATE	4	TRUE	NA	0.721956879848527	4		525	290	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0033204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	73	500	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	0.422161712684395	4	FACETS	0.902	0.805	1			1	INDETERMINATE	2	TRUE	NA	0.721956879848527	4		500	193	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589585	67589586	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATGAAT	novel	NA	P-0033204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	74	195	0	ENST00000274335.5:c.1351_1356dup	p.Glu451_Tyr452dup	p.E451_Y452dup	ENST00000274335		451	cat/cATGAATat	10/15	0.721956879848527	5	FACETS	0.776	0.687	0.87			1	SUBCLONAL	2	TRUE	NA	0.721956879848527	5		195	275	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457711	67457711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	103	337	0	ENST00000327367.4:c.521G>A	p.Ser174Asn	p.S174N	ENST00000327367	NM_005902.3	174	aGc/aAc	3/9	0.270951710092536	2	FACETS	0.771	0.711	0.831	0.771	0.711	0.831	INDETERMINATE	2	TRUE	0	0.721956879848527	2		337	185	SUCCESS
APC	324	MSKCC	GRCh37	5	112174294	112174294	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	58	242	0	ENST00000257430.4:c.3003del	p.Ala1002ProfsTer3	p.A1002Pfs*3	ENST00000257430	NM_000038.5	1001	ccA/cc	16/16	0.422161712684395	4	FACETS	0.764	0.669	0.864			1	INDETERMINATE	2	TRUE	NA	0.721956879848527	4		242	181	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678076	117678076	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs373090808	NA	P-0033242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	95	255	0	ENST00000368508.3:c.3857G>A	p.Arg1286His	p.R1286H	ENST00000368508	NM_002944.2	1286	cGc/cAc	25/43	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.788102291969436	2		255	240	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791796	42791796	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	154	462	0	ENST00000575354.2:c.682C>G	p.Arg228Gly	p.R228G	ENST00000575354	NM_015125.3	228	Cgg/Ggg	5/20	1	2	FACETS	0.882	0.815	0.951	0.882	0.815	0.951	CLONAL	1	TRUE	1	0.788102291969436	2		462	443	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591148	67591149	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGA	novel	NA	P-0033242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	111	235	0	ENST00000274335.5:c.1744_1745+1dup		p.L582_M583dup	ENST00000274335		582	ttg/tTGAtg	12/15	1	2	FACETS	0.992	0.906	1	0.992	0.906	1	CLONAL	1	TRUE	1	0.788102291969436	2		235	284	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465976	69465976	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	171	519	0	ENST00000227507.2:c.814G>T	p.Glu272Ter	p.E272*	ENST00000227507	NM_053056.2	272	Gag/Tag	5/5	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.788102291969436	2		519	410	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313314	65313314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	20	360	1	ENST00000342505.4:c.1800del	p.Thr601ProfsTer2	p.T601Pfs*2	ENST00000342505	NM_002227.2	600	ggG/gg	13/25	1	2	FACETS	0.128	0.097	0.163	0.128	0.097	0.163	SUBCLONAL	1	TRUE	1	0.788102291969436	2		361	398	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50821730	50821730	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	164	378	0	ENST00000398568.2:c.2066del	p.His689LeufsTer3	p.H689Lfs*3	ENST00000398568	NM_001042412.1	689	cAt/ct	13/18	0.788102291969436	1	FACETS	0.931	0.876	0.984	0.931	0.876	0.984	CLONAL	1	TRUE	0	0.788102291969436	1		378	271	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976431	25976431	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	205	487	0	ENST00000435504.4:c.1114del	p.Gln372AsnfsTer13	p.Q372Nfs*13	ENST00000435504		372	Caa/aa	11/13	0.788102291969436	1	FACETS	0.947	0.897	0.995	0.947	0.897	0.995	CLONAL	1	TRUE	0	0.788102291969436	1		487	333	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0033255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	118	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.424124252772659	4	FACETS	0.822	0.747	0.899	0.822	0.747	0.899	CLONAL	2	TRUE	2	0.501395895932389	4		436	430	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578520	7578520	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	296	591	1	ENST00000269305.4:c.410T>A	p.Leu137Gln	p.L137Q	ENST00000269305	NM_001126112.2	137	cTg/cAg	5/11	0.472021595460483	2	FACETS	0.989	0.94	1	0.989	0.94	1	CLONAL	2	TRUE	0	0.501395895932389	2		592	597	SUCCESS
CALR	811	MSKCC	GRCh37	19	13049949	13049949	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	25	242	0	ENST00000316448.5:c.93C>G	p.Asp31Glu	p.D31E	ENST00000316448	NM_004343.3	31	gaC/gaG	2/9	0.326068048123354	4	FACETS	0.412	0.325	0.513	0.206	0.162	0.257	SUBCLONAL	1	TRUE	2	0.501395895932389	4		242	363	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42851168	42851168	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	80	380	1	ENST00000398585.3:c.725G>A	p.Gly242Glu	p.G242E	ENST00000398585	NM_001135099.1	242	gGa/gAa	7/14	0.501492356489319	3	FACETS	1	0.916	1	0.521	0.461	0.584	CLONAL	1	TRUE	1	0.501395895932389	3		381	383	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268197	153268197	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	100	199	0	ENST00000281708.4:c.611C>T	p.Ala204Val	p.A204V	ENST00000281708	NM_033632.3	204	gCa/gTa	4/12	0.501492356489319	3	FACETS	0.857	0.776	0.941	0.857	0.776	0.941	CLONAL	2	TRUE	1	0.501395895932389	3		199	291	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80109427	80109427	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	79	311	0	ENST00000265081.6:c.2680A>G	p.Ile894Val	p.I894V	ENST00000265081	NM_002439.4	894	Att/Gtt	20/24	0.471923040961146	3	FACETS	1	0.952	1	0.571	0.506	0.64	CLONAL	1	TRUE	1	0.501395895932389	3		311	345	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	60	302	0				ENST00000310581	NM_198253.2	-/1132			0.24829853814946	3	FACETS	1	0.97	1	0.699	0.612	0.789	INDETERMINATE	1	TRUE	1	0.583939971353414	3		302	190	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622162	1622162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	74	384	0	ENST00000344749.5:c.713C>T	p.Pro238Leu	p.P238L	ENST00000344749	NM_001136139.2	238	cCc/cTc	10/19	0.538405874103214	1	FACETS	0.831	0.74	0.925	0.831	0.74	0.925	CLONAL	1	TRUE	0	0.583939971353414	1		384	216	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372040	45372040	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	73	327	0	ENST00000262160.6:c.1129C>T	p.Pro377Ser	p.P377S	ENST00000262160	NM_005901.5	377	Cca/Tca	9/11	1	2	FACETS	0.859	0.759	0.965	0.859	0.759	0.965	CLONAL	1	TRUE	1	0.583939971353414	2		327	291	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686267	117686267	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	38	230	1	ENST00000368508.3:c.3074G>A	p.Gly1025Glu	p.G1025E	ENST00000368508	NM_002944.2	1025	gGa/gAa	20/43	1	2	FACETS	0.654	0.546	0.772	0.654	0.546	0.772	SUBCLONAL	1	TRUE	1	0.583939971353414	2		231	199	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58701074	58701074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	87	406	0	ENST00000305921.3:c.665C>T	p.Pro222Leu	p.P222L	ENST00000305921	NM_003620.3	222	cCc/cTc	2/6	1	2	FACETS	0.937	0.838	1	0.937	0.838	1	CLONAL	1	TRUE	1	0.583939971353414	2		406	318	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136004	64136004	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	91	460	0	ENST00000334205.4:c.1265T>G	p.Phe422Cys	p.F422C	ENST00000334205	NM_003942.2	422	tTt/tGt	11/17	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.583939971353414	2		460	310	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445230	49445230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201896284	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	83	571	2	ENST00000301067.7:c.2236C>T	p.Arg746Trp	p.R746W	ENST00000301067	NM_003482.3	746	Cgg/Tgg	10/54	1	2	FACETS	0.736	0.654	0.824	0.736	0.654	0.824	SUBCLONAL	1	TRUE	1	0.583939971353414	2		573	386	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579312	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	115	312	1	ENST00000269305.4:c.375_375+1delinsAA		p.X125_splice	ENST00000269305	NM_001126112.2	125		4/11	0.528823769349875	2	FACETS	0.925	0.855	0.994	0.925	0.855	0.994	CLONAL	2	TRUE	0	0.583939971353414	2		313	213	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866441	42866441	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770444484	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	98	622	0	ENST00000398585.3:c.191C>T	p.Pro64Leu	p.P64L	ENST00000398585	NM_001135099.1	64	cCc/cTc	3/14	1	2	FACETS	0.85	0.764	0.94	0.85	0.764	0.94	CLONAL	1	TRUE	1	0.583939971353414	2		622	395	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940093	31940093	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	78	432	0	ENST00000375333.2:c.235G>A	p.Glu79Lys	p.E79K	ENST00000375333	NM_032454.1	79	Gag/Aag	2/8	1	2	FACETS	0.774	0.686	0.868	0.774	0.686	0.868	SUBCLONAL	1	TRUE	1	0.583939971353414	2		432	345	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263863	16263864	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	83	447	1	ENST00000375759.3:c.10232_10233delinsAA	p.Arg3411Lys	p.R3411K	ENST00000375759	NM_015001.2	3411	aGG/aAA	12/15	1	2	FACETS	0.88	0.784	0.981	0.88	0.784	0.981	CLONAL	1	TRUE	1	0.583939971353414	2		448	323	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532596	46532596	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	66	255	0	ENST00000262741.5:c.482C>T	p.Ser161Phe	p.S161F	ENST00000262741	NM_003629.3	161	tCc/tTc	4/10	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.583939971353414	2		255	209	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551637	150551637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771094920	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	71	310	0	ENST00000369026.2:c.370G>A	p.Glu124Lys	p.E124K	ENST00000369026	NM_021960.4	124	Gag/Aag	1/3	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.583939971353414	2		310	242	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606815	43606816	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	94	517	1	ENST00000355710.3:c.1424_1425delinsAA	p.Arg475Gln	p.R475Q	ENST00000355710	NM_020975.4	475	cGG/cAA	7/20	1	2	FACETS	0.904	0.812	1	0.904	0.812	1	CLONAL	1	TRUE	1	0.583939971353414	2		518	356	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615126	43615126	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	114	481	1	ENST00000355710.3:c.2540C>T	p.Thr847Ile	p.T847I	ENST00000355710	NM_020975.4	847	aCc/aTc	14/20	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.583939971353414	2		482	371	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342599	118342599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	46	160	0	ENST00000534358.1:c.725C>T	p.Ser242Leu	p.S242L	ENST00000534358	NM_005933.3	242	tCa/tTa	3/36	1	2	FACETS	0.911	0.779	1	0.911	0.779	1	CLONAL	1	TRUE	1	0.583939971353414	2		160	173	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155963	119155963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	91	412	0	ENST00000264033.4:c.1628C>T	p.Pro543Leu	p.P543L	ENST00000264033	NM_005188.3	543	cCa/cTa	11/16	1	2	FACETS	0.849	0.76	0.943	0.849	0.76	0.943	CLONAL	1	TRUE	1	0.583939971353414	2		412	367	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748789	43748790	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	94	613	1	ENST00000382044.4:c.2016_2017delinsTT	p.Pro673Ser	p.P673S	ENST00000382044	NM_001141980.1	672	atCCct/atTTct	12/28	1	2	FACETS	0.787	0.705	0.874	0.787	0.705	0.874	SUBCLONAL	1	TRUE	1	0.583939971353414	2		614	409	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934839	9934839	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	85	422	0	ENST00000330684.3:c.1451A>T	p.Lys484Met	p.K484M	ENST00000330684	NM_001134407.1	484	aAg/aTg	6/13	1	2	FACETS	0.844	0.752	0.94	0.844	0.752	0.94	CLONAL	1	TRUE	1	0.583939971353414	2		422	345	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649442	23649442	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	51	222	0	ENST00000261584.4:c.57G>C	p.Glu19Asp	p.E19D	ENST00000261584	NM_024675.3	19	gaG/gaC	2/13	1	2	FACETS	0.878	0.757	1	0.878	0.757	1	CLONAL	1	TRUE	1	0.583939971353414	2		222	199	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67132631	67132631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	92	372	0	ENST00000412916.2:c.514C>T	p.Pro172Ser	p.P172S	ENST00000412916		172	Cct/Tct	6/6	1	2	FACETS	0.847	0.759	0.94	0.847	0.759	0.94	CLONAL	1	TRUE	1	0.583939971353414	2		372	372	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992456	72992456	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	88	611	0	ENST00000268489.5:c.1589T>G	p.Ile530Ser	p.I530S	ENST00000268489	NM_006885.3	530	aTt/aGt	2/10	1	2	FACETS	0.777	0.693	0.865	0.777	0.693	0.865	SUBCLONAL	1	TRUE	1	0.583939971353414	2		611	388	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687598	29687598	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	94	458	0	ENST00000356175.3:c.8191G>A	p.Glu2731Lys	p.E2731K	ENST00000356175	NM_000267.3	2731	Gaa/Aaa	56/57	1	2	FACETS	0.961	0.864	1	0.961	0.864	1	CLONAL	1	TRUE	1	0.583939971353414	2		458	335	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245092	41245092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	94	637	0	ENST00000357654.3:c.2456C>T	p.Ser819Phe	p.S819F	ENST00000357654	NM_007294.3	819	tCc/tTc	10/23	1	2	FACETS	0.774	0.693	0.859	0.774	0.693	0.859	SUBCLONAL	1	TRUE	1	0.583939971353414	2		637	416	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584495	39584496	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	51	218	0	ENST00000262039.4:c.1160_1161delinsTT	p.Ala387Val	p.A387V	ENST00000262039	NM_002647.2	387	gCC/gTT	10/25	1	2	FACETS	0.905	0.781	1	0.905	0.781	1	CLONAL	1	TRUE	1	0.583939971353414	2		218	193	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919719	96919719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	140	342	0	ENST00000258439.3:c.544G>A	p.Gly182Arg	p.G182R	ENST00000258439	NM_001193304.2	182	Gga/Aga	4/4	0.430826998955771	3	FACETS	0.9	0.832	0.97	0.9	0.832	0.97	CLONAL	2	TRUE	1	0.583939971353414	3		342	344	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164277	47164277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372521251	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	57	322	0	ENST00000409792.3:c.1849C>T	p.Pro617Ser	p.P617S	ENST00000409792	NM_014159.6	617	Cca/Tca	3/21	0.538405874103214	1	FACETS	0.674	0.587	0.766	0.674	0.587	0.766	SUBCLONAL	1	TRUE	0	0.583939971353414	1		322	205	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445016	89445016	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	60	316	1	ENST00000336596.2:c.1336G>A	p.Asp446Asn	p.D446N	ENST00000336596	NM_005233.5	446	Gat/Aat	6/17	NA	2	FACETS	0.758	0.659	0.864			1	INDETERMINATE	1	TRUE	NA	0.583939971353414	2		317	271	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961237	1961237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	75	298	0	ENST00000382891.5:c.3025G>A	p.Asp1009Asn	p.D1009N	ENST00000382891	NM_133335.3	1009	Gat/Aat	17/22	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.583939971353414	2		298	247	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638204	176638204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	90	463	0	ENST00000439151.2:c.2804C>T	p.Ser935Phe	p.S935F	ENST00000439151	NM_022455.4	935	tCt/tTt	5/23	0.538405874103214	1	FACETS	0.856	0.771	0.943	0.856	0.771	0.943	CLONAL	1	TRUE	0	0.583939971353414	1		463	255	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066608	94066608	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	62	357	0	ENST00000369303.4:c.1151G>C	p.Ser384Thr	p.S384T	ENST00000369303	NM_004440.3	384	aGt/aCt	5/17	NA	2	FACETS	0.896	0.784	1			1	INDETERMINATE	1	TRUE	NA	0.583939971353414	2		357	237	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023060	150023060	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	70	558	0	ENST00000253339.5:c.203C>T	p.Pro68Leu	p.P68L	ENST00000253339		68	cCa/cTa	1/7	1	2	FACETS	0.74	0.65	0.835	0.74	0.65	0.835	SUBCLONAL	1	TRUE	1	0.583939971353414	2		558	324	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515111	148515111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	64	354	0	ENST00000320356.2:c.1098C>A	p.Asn366Lys	p.N366K	ENST00000320356	NM_004456.4	366	aaC/aaA	10/20	1	2	FACETS	0.743	0.649	0.843	0.743	0.649	0.843	SUBCLONAL	1	TRUE	1	0.583939971353414	2		354	295	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151882704	151882704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	17	263	0	ENST00000262189.6:c.5021G>A	p.Arg1674Lys	p.R1674K	ENST00000262189	NM_170606.2	1674	aGa/aAa	34/59	1	2	FACETS	0.287	0.214	0.372	0.287	0.214	0.372	SUBCLONAL	1	TRUE	1	0.583939971353414	2		263	203	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56912066	56912066	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	108	538	1	ENST00000519728.1:c.1294C>T	p.Leu432Phe	p.L432F	ENST00000519728	NM_002350.3	432	Ctc/Ttc	12/13	1	2	FACETS	0.941	0.852	1	0.941	0.852	1	CLONAL	1	TRUE	1	0.583939971353414	2		539	393	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220410	98220410	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	80	372	0	ENST00000331920.6:c.3053G>A	p.Trp1018Ter	p.W1018*	ENST00000331920	NM_000264.3	1018	tGg/tAg	18/24	0.538405874103214	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.583939971353414	1		372	187	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874407	76874407	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	84	199	0	ENST00000373344.5:c.5315C>T	p.Ser1772Phe	p.S1772F	ENST00000373344	NM_000489.3	1772	tCc/tTc	21/35	1	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.583939971353414	1		199	159	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0033290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	320	294	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.104249553920958	5	FACETS	0.963	0.91	1	0.642	0.607	0.678	INDETERMINATE	2	TRUE	2	0.632414026016643	5		294	1024	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797906	45797906	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	334	414	0	ENST00000450313.1:c.865G>T	p.Val289Leu	p.V289L	ENST00000450313	NM_012222.2	289	Gtg/Ttg	10/16	0.18762733353633	3	FACETS	1	0.993	1	0.673	0.637	0.709	INDETERMINATE	1	TRUE	1	0.632414026016643	3		414	1033	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0033375-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	21	499	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.23	0.176	0.294	0.23	0.176	0.294	SUBCLONAL	1	TRUE	1	0.21	2		500	869	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0033375-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	107	562	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.21	2		562	780	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690847	89690847	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587776667	NA	P-0033375-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	35	275	0	ENST00000371953.3:c.253+1G>T		p.X85_splice	ENST00000371953	NM_000314.4	85			1	2	FACETS	0.809	0.663	0.972	0.809	0.663	0.972	CLONAL	1	TRUE	1	0.21	2		275	412	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573217	64573217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906552	NA	P-0033375-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	69	635	0	ENST00000312049.6:c.1075G>A	p.Glu359Lys	p.E359K	ENST00000312049	NM_130799.2	359	Gag/Aag	8/10	1	2	FACETS	0.739	0.642	0.845	0.739	0.642	0.845	SUBCLONAL	1	TRUE	1	0.21	2		635	889	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226827	142226827	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033375-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	61	362	0	ENST00000350721.4:c.4977A>C	p.Glu1659Asp	p.E1659D	ENST00000350721	NM_001184.3	1659	gaA/gaC	28/47	1	2	FACETS	0.851	0.733	0.979	0.851	0.733	0.979	CLONAL	1	TRUE	1	0.21	2		362	683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0033395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	128	703	1	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.22	2		704	963	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063717	+	splice_donor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0033395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	35	243	0	ENST00000412916.2:c.165+1del		p.X55_splice	ENST00000412916		55			1	2	FACETS	0.907	0.744	1	0.907	0.744	1	CLONAL	1	TRUE	1	0.22	2		243	351	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347055	89347056	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0033395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	44	482	0	ENST00000301030.4:c.5893_5894dup	p.Thr1966AlafsTer7	p.T1966Afs*7	ENST00000301030	NM_001256183.1	1965	ggc/ggGGc	9/13	1	2	FACETS	0.599	0.501	0.708	0.599	0.501	0.708	SUBCLONAL	1	TRUE	1	0.22	2		482	668	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268959	55268959	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148019583	NA	P-0033395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	94	628	0	ENST00000275493.2:c.3025G>A	p.Asp1009Asn	p.D1009N	ENST00000275493	NM_005228.3	1009	Gac/Aac	25/28	1	2	FACETS	0.861	0.764	0.964	0.861	0.764	0.964	CLONAL	1	TRUE	1	0.22	2		628	993	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845743	151845743	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	47	602	0	ENST00000262189.6:c.13269C>A	p.Asp4423Glu	p.D4423E	ENST00000262189	NM_170606.2	4423	gaC/gaA	52/59	1	2	FACETS	0.506	0.425	0.595	0.506	0.425	0.595	SUBCLONAL	1	TRUE	1	0.22	2		602	845	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875059	151875060	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	32	183	0	ENST00000262189.6:c.7478_7479insT	p.Ser2494GlufsTer31	p.S2494Efs*31	ENST00000262189	NM_170606.2	2493	ccg/ccTg	38/59	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.22	2		183	255	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880997	37880998	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0033395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	100	705	0	ENST00000269571.5:c.2326_2327insTT	p.Gly776ValfsTer16	p.G776Vfs*16	ENST00000269571		776	ggt/gTTgt	20/27	1	2	FACETS	0.866	0.772	0.966	0.866	0.772	0.966	CLONAL	1	TRUE	1	0.22	2		705	1050	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0033409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	87	302	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.536502854758279	2		302	316	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0033409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	230	743	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	1	2	FACETS	0.893	0.833	0.955	0.893	0.833	0.955	CLONAL	1	TRUE	1	0.536502854758279	2		743	960	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576135	29576135	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs868573462	NA	P-0033409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	199	267	0	ENST00000356175.3:c.4108C>T	p.Gln1370Ter	p.Q1370*	ENST00000356175	NM_000267.3	1370	Cag/Tag	30/57	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.536502854758279	2		267	696	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435721	116435721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751186512	NA	P-0033409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	157	263	0	ENST00000397752.3:c.3811G>A	p.Val1271Met	p.V1271M	ENST00000397752	NM_000245.2	1271	Gtg/Atg	20/21	0.536502854758279	3	FACETS	0.966	0.887	1	0.483	0.443	0.525	CLONAL	1	TRUE	1	0.536502854758279	3		263	768	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554625	29554625	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1555614022	NA	P-0033409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	106	135	0	ENST00000356175.3:c.2409+1G>T		p.X803_splice	ENST00000356175	NM_000267.3	803			1	2	FACETS	0.932	0.841	1	0.932	0.841	1	CLONAL	1	TRUE	1	0.536502854758279	2		135	424	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970908	55970908	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	220	443	0	ENST00000263923.4:c.1889A>T	p.Lys630Met	p.K630M	ENST00000263923	NM_002253.2	630	aAg/aTg	13/30	1	2	FACETS	0.974	0.908	1	0.974	0.908	1	CLONAL	1	TRUE	1	0.536502854758279	2		443	842	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467944	66467944	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	171	259	0	ENST00000273854.3:c.325C>T	p.Gln109Ter	p.Q109*	ENST00000273854	NM_004439.5	109	Cag/Tag	3/18	1	2	FACETS	0.99	0.914	1	0.99	0.914	1	CLONAL	1	TRUE	1	0.536502854758279	2		259	644	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577533	7577534	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0033582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	209	763	1	ENST00000269305.4:c.747_748delinsTT	p.Arg249_Pro250delinsSerSer	p.R249_P250delinsSS	ENST00000269305	NM_001126112.2	249	agGCcc/agTTcc	7/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.286396208799831	2		764	1029	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78933885	78933885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	115	677	1	ENST00000306801.3:c.3485C>T	p.Pro1162Leu	p.P1162L	ENST00000306801	NM_020761.2	1162	cCt/cTt	30/34	1	2	FACETS	0.709	0.637	0.786	0.709	0.637	0.786	SUBCLONAL	1	TRUE	1	0.286396208799831	2		678	1132	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0033648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	497	422	2	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.662777319622916	4	FACETS	0.988	0.965	1			1	CLONAL	4	TRUE	NA	0.717182901605475	4		424	602	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578504	7578540	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTG	AGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTG	-	novel	NA	P-0033648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	309	782	1	ENST00000269305.4:c.390_426del	p.Asn131CysfsTer27	p.N131Cfs*27	ENST00000269305	NM_001126112.2	130	ctCAACAAGATGTTTTGCCAACTGGCCAAGACCTGCCCT/ct	5/11	0.707173357626343	2	FACETS	0.808	0.773	0.844	0.808	0.773	0.844	CLONAL	2	TRUE	0	0.717182901605475	2		783	533	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4123815	4123815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	63	339	0	ENST00000262948.5:c.58G>A	p.Glu20Lys	p.E20K	ENST00000262948	NM_030662.3	20	Gag/Aag	1/11	0.702547680360522	3	FACETS	0.654	0.568	0.746	0.327	0.284	0.373	SUBCLONAL	1	TRUE	1	0.717182901605475	3		339	365	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0033648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	87	379	1	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			0.717182901605475	9	FACETS	0.738	0.651	0.831			1	SUBCLONAL	1	TRUE	NA	0.717182901605475	9		380	1154	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939029	48939029	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0033648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	144	291	0	ENST00000267163.4:c.862-1G>A		p.X288_splice	ENST00000267163	NM_000321.2	288			0.707227517317571	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.717182901605475	2		291	190	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265115	46265115	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	113	394	0	ENST00000371998.3:c.1985C>G	p.Ser662Cys	p.S662C	ENST00000371998		662	tCt/tGt	12/23	0.576617431282724	4	FACETS	1	0.923	1	0.512	0.463	0.564	CLONAL	1	TRUE	2	0.717182901605475	4		394	528	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781411	135781411	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	23	416	0	ENST00000298552.3:c.1554G>C	p.Lys518Asn	p.K518N	ENST00000298552	NM_001162426.1	518	aaG/aaC	15/23	1	2	FACETS	0.181	0.14	0.227	0.181	0.14	0.227	SUBCLONAL	1	TRUE	1	0.717182901605475	2		416	355	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0033684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	60	294	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.187855556853602	5	FACETS	0.922	0.8	1	0.615	0.533	0.702	CLONAL	2	FALSE	2	0.309324950971977	5		294	308	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828504	72828504	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	372	680	1	ENST00000268489.5:c.8077C>T	p.Arg2693Ter	p.R2693*	ENST00000268489	NM_006885.3	2693	Cga/Tga	9/10	0.564333401764744	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.564333401764744	1		681	753	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720869	89720869	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1564568689	NA	P-0033701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	207	405	0	ENST00000371953.3:c.1023del	p.Phe341LeufsTer3	p.F341Lfs*3	ENST00000371953	NM_000314.4	340	aaT/aa	8/9	0.564333401764744	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.564333401764744	1		405	427	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420880	49420892	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGGGATGAGGC	CAGGGGATGAGGC	-	novel	NA	P-0033701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	242	569	1	ENST00000301067.7:c.14857_14869del	p.Ala4953AsnfsTer38	p.A4953Nfs*38	ENST00000301067	NM_003482.3	4953	GCCTCATCCCCTGaa/aa	48/54	0.3360917556359	1	FACETS	0.949	0.892	1	0.949	0.892	1	INDETERMINATE	1	TRUE	0	0.564333401764744	1		570	649	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909660	50909684	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTAGGTGCTGCTGCGGGAGTACAAG	CTAGGTGCTGCTGCGGGAGTACAAG	-	novel	NA	P-0033701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	135	627	0	ENST00000440232.2:c.1384-2_1406del		p.X462_splice	ENST00000440232	NM_002691.3	462		12/27	1	2	FACETS	0.48	0.436	0.527	0.48	0.436	0.527	SUBCLONAL	1	TRUE	1	0.564333401764744	2		627	996	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280272	1280272	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0033701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	458	729	1	ENST00000310581.5:c.1950+1G>C		p.X650_splice	ENST00000310581	NM_198253.2	650			0.564333401764744	3	FACETS	1	0.994	1	0.626	0.597	0.657	CLONAL	1	TRUE	1	0.564333401764744	3		730	1661	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982755	90982755	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	485	343	0	ENST00000265433.3:c.733G>A	p.Gly245Arg	p.G245R	ENST00000265433	NM_002485.4	245	Gga/Aga	7/16	0.564333401764744	5	FACETS	0.956	0.917	0.995	0.956	0.917	0.995	CLONAL	3	TRUE	2	0.564333401764744	5		343	1107	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914412	32914438	+	protein_altering_variant	In_Frame_Del	DEL	ACTTGTGGGATTTTTAGCACAGCAAGT	ACTTGTGGGATTTTTAGCACAGCAAGT	CTG	novel	NA	P-0033701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	139	607	0	ENST00000380152.3:c.5920_5946delinsCTG	p.Thr1974_Ser1982delinsLeu	p.T1974_S1982delinsL	ENST00000380152		1974	ACTTGTGGGATTTTTAGCACAGCAAGT/CTG	11/27	0.564333401764744	1	FACETS	0.52	0.474	0.568	0.52	0.474	0.568	SUBCLONAL	1	TRUE	0	0.564333401764744	1		607	680	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254992	16254992	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	127	343	0	ENST00000375759.3:c.2257A>G	p.Arg753Gly	p.R753G	ENST00000375759	NM_015001.2	753	Agg/Ggg	11/15	1	2	FACETS	0.937	0.859	1	0.937	0.859	1	CLONAL	1	TRUE	1	0.765599253202703	2		343	354	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263258	115263258	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	270	653	0	ENST00000438362.2:c.2092G>A	p.Val698Ile	p.V698I	ENST00000438362	NM_001242891.1	698	Gtc/Atc	17/20	NA	2	FACETS	1	0.945	1			1	INDETERMINATE	1	TRUE	NA	0.765599253202703	2		653	704	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175432	108175432	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1060501607	NA	P-0033711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	518	417	0	ENST00000278616.4:c.5527C>G	p.Pro1843Ala	p.P1843A	ENST00000278616	NM_000051.3	1843	Cca/Gca	37/63	0.767751067802538	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.765599253202703	3		417	608	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436293	110436293	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	65	173	0	ENST00000375856.3:c.2108C>A	p.Pro703His	p.P703H	ENST00000375856	NM_003749.2	703	cCt/cAt	1/2	0.767751067802538	5	FACETS	1	0.93	1	0.22	0.191	0.25	CLONAL	1	TRUE	0	0.765599253202703	5		173	332	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131662	2131662	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	258	660	0	ENST00000219476.3:c.3677T>G	p.Met1226Arg	p.M1226R	ENST00000219476	NM_000548.3	1226	aTg/aGg	31/42	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.765599253202703	2		660	653	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993437	72993437	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	237	697	0	ENST00000268489.5:c.608C>A	p.Ser203Tyr	p.S203Y	ENST00000268489	NM_006885.3	203	tCc/tAc	2/10	0.738856273286426	5	FACETS	0.935	0.87	1			1	CLONAL	1	TRUE	NA	0.765599253202703	5		697	1423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578393	7578393	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876660821	NA	P-0033711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	518	543	0	ENST00000269305.4:c.537T>A	p.His179Gln	p.H179Q	ENST00000269305	NM_001126112.2	179	caT/caA	5/11	0.767751067802538	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.765599253202703	2		543	618	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15365062	15365081	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAACTTTCTCAGCTGCAATC	CAACTTTCTCAGCTGCAATC	-	novel	NA	P-0033711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	149	572	0	ENST00000263377.2:c.2048-8_2059del		p.X683_splice	ENST00000263377	NM_058243.2	683		11/20	0.698622313723123	4	FACETS	0.72	0.657	0.785	0.36	0.328	0.393	SUBCLONAL	1	TRUE	2	0.765599253202703	4		572	955	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308324	30308324	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	197	521	0	ENST00000262643.3:c.338G>C	p.Arg113Thr	p.R113T	ENST00000262643	NM_001238.2	113	aGa/aCa	6/12	0.509488680436195	3	FACETS	0.903	0.838	0.97			1	CLONAL	1	TRUE	NA	0.765599253202703	3		521	788	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39237845	39237845	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0033711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	206	422	0	ENST00000402219.2:c.2391-1G>C		p.X797_splice	ENST00000402219	NM_005633.3	797			0.752862887950827	4	FACETS	1	0.943	1	0.339	0.315	0.365	CLONAL	1	TRUE	1	0.765599253202703	4		422	933	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067862	30067881	+	frameshift_variant	Frame_Shift_Del	DEL	TGAACGCACGAGGGATGAGT	TGAACGCACGAGGGATGAGT	-	novel	NA	P-0033711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	171	439	0	ENST00000338641.4:c.1049_1068del	p.Glu350GlyfsTer22	p.E350Gfs*22	ENST00000338641	NM_000268.3	349	gcTGAACGCACGAGGGATGAGTtg/gctg	11/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.765599253202703	2		439	399	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52612543	52613155	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCTGCTGTGTTTGCCATTCAACCATACTGTCATCCTTTTGTCATTTACTTGTTCATCAAATATCTGAGGCCCTACTATGTTTCATGCACTATGATTTGAGCAGGGAATACAAGGGTGAAACCTGACAATAACACAATGAACACCGATATGTGATATATACGCTAAGGAGAAGGAAATATGTGGTGCTTTGAGAGTGTGCAACAGGGAGACTTAACCCATTCTGCAGTGGACAGGAAAGACTTCCTTTTAAGAAAGTGTCACTTCAAATTTATGCTAAAGGAGTTTACTGTATGAAGTAGGCAGGGAGATTTCTGAGCTGAAAGTTCTGTAAATAGTGGAAGAAAACAAAAGAGCCCAAAGGGATAATTTAAGGAAGAAAGTGTGGTTGGAGGGGAACATGGTGTGAGAAGAAGCTGGAGAAACTGCCAGGGGAAGGACTTTTGTCTTCATCCGAAGGGTGACTAATTTCTACTGGTTCCAAATTTCTCAGATTCAACCTCATCTTCCCTAATTCAATGACACTCACCTGCCCACACGAGGACGCACCAGGCCATGGGACTTGATGAAGACACAGTCGCCAACCTTCAGCCACATGTCATTGTAATGGAGCTG	CTCTGCTGTGTTTGCCATTCAACCATACTGTCATCCTTTTGTCATTTACTTGTTCATCAAATATCTGAGGCCCTACTATGTTTCATGCACTATGATTTGAGCAGGGAATACAAGGGTGAAACCTGACAATAACACAATGAACACCGATATGTGATATATACGCTAAGGAGAAGGAAATATGTGGTGCTTTGAGAGTGTGCAACAGGGAGACTTAACCCATTCTGCAGTGGACAGGAAAGACTTCCTTTTAAGAAAGTGTCACTTCAAATTTATGCTAAAGGAGTTTACTGTATGAAGTAGGCAGGGAGATTTCTGAGCTGAAAGTTCTGTAAATAGTGGAAGAAAACAAAAGAGCCCAAAGGGATAATTTAAGGAAGAAAGTGTGGTTGGAGGGGAACATGGTGTGAGAAGAAGCTGGAGAAACTGCCAGGGGAAGGACTTTTGTCTTCATCCGAAGGGTGACTAATTTCTACTGGTTCCAAATTTCTCAGATTCAACCTCATCTTCCCTAATTCAATGACACTCACCTGCCCACACGAGGACGCACCAGGCCATGGGACTTGATGAAGACACAGTCGCCAACCTTCAGCCACATGTCATTGTAATGGAGCTG	-	novel	NA	P-0033711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4	198	0	0	ENST00000394830.3:c.3373_3458+527del		p.X1125_splice	ENST00000394830	NM_018313.4	1125		22/30	0.767751067802538	1	FACETS		NA	1	1	0.996	1	NA	2	TRUE	0	0.765599253202703	1		0	202	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505488	186505599	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGTGGGCTATACCACTTAGTATAGTTCGCTACTATTTTGTGGCCTACATGACAGGTGTCAAGTTTTTTTGAATCAATTTTTAAAACATGCCATTGTGTTTCAGGCTCGCGG	CAGTGGGCTATACCACTTAGTATAGTTCGCTACTATTTTGTGGCCTACATGACAGGTGTCAAGTTTTTTTGAATCAATTTTTAAAACATGCCATTGTGTTTCAGGCTCGCGG	-	novel	NA	P-0033711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	132	187	0	ENST00000323963.5:c.1000-104_1007del		p.X334_splice	ENST00000323963		334		10/11	0.765599253202703	6	FACETS	0.825	0.753	0.9	0.412	0.376	0.45	CLONAL	2	TRUE	2	0.765599253202703	6		187	529	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39074430	39074430	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0033711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	168	415	0	ENST00000357387.3:c.49+1G>A		p.X17_splice	ENST00000357387	NM_152756.3	17			0.637015833779462	5	FACETS	0.986	0.906	1			1	CLONAL	1	TRUE	NA	0.765599253202703	5		415	956	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642439	117642439	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	518	658	0	ENST00000368508.3:c.5760T>A	p.Asn1920Lys	p.N1920K	ENST00000368508	NM_002944.2	1920	aaT/aaA	35/43	0.591196835108739	4	FACETS	0.968	0.93	1	0.968	0.93	1	CLONAL	2	TRUE	2	0.765599253202703	4		658	1234	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450378	50450378	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	141	413	0	ENST00000331340.3:c.562C>A	p.Leu188Ile	p.L188I	ENST00000331340	NM_006060.4	188	Ctc/Atc	5/8	0.704515243732313	3	FACETS	1	0.923	1	0.503	0.461	0.547	CLONAL	1	TRUE	1	0.765599253202703	3		413	506	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509913	106509913	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0033711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	453	576	0	ENST00000359195.3:c.1907C>G	p.Ser636Ter	p.S636*	ENST00000359195	NM_002649.2	636	tCa/tGa	2/11	0.767751067802538	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.765599253202703	2		576	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0033729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	618	346	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.429583456809962	5	FACETS	1	0.992	1	1	0.992	1	CLONAL	5	TRUE	0	0.443389624359866	5		346	887	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465650	8465650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763141884	NA	P-0033729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	194	548	0	ENST00000356435.5:c.3530G>A	p.Arg1177His	p.R1177H	ENST00000356435		1177	cGc/cAc	21/35	0.443389624359866	2	FACETS	0.931	0.871	0.992	0.931	0.871	0.992	CLONAL	2	TRUE	0	0.443389624359866	2		548	470	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922276	39922276	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	64	504	0	ENST00000378444.4:c.3896C>A	p.Thr1299Asn	p.T1299N	ENST00000378444	NM_001123385.1	1299	aCc/aAc	9/15	0.179817867668776	5	FACETS	0.919	0.797	1	0.306	0.265	0.351	INDETERMINATE	1	TRUE	2	0.443389624359866	5		504	523	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986957	36986957	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	102	456	0	ENST00000354822.5:c.732C>A	p.Tyr244Ter	p.Y244*	ENST00000354822	NM_001079668.2	244	taC/taA	3/3	0.337375828853602	4	FACETS	1	0.943	1	0.539	0.483	0.599	CLONAL	1	TRUE	2	0.443389624359866	4		456	616	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797240	42797240	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778203	NA	P-0033729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	299	652	0	ENST00000575354.2:c.3602G>A	p.Gly1201Asp	p.G1201D	ENST00000575354	NM_015125.3	1201	gGc/gAc	15/20	0.443389624359866	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	3	TRUE	0	0.443389624359866	3		652	549	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	68	303	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.777	0.68	0.88	0.777	0.68	0.88	SUBCLONAL	1	TRUE	1	0.489047767756553	2		303	358	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	42	247	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.684	0.575	0.803	0.684	0.575	0.803	SUBCLONAL	1	TRUE	1	0.489047767756553	2		247	251	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406064	70406064	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	183	543	1	ENST00000373644.4:c.3578C>A	p.Ser1193Ter	p.S1193*	ENST00000373644	NM_030625.2	1193	tCg/tAg	4/12	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.489047767756553	2		544	701	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	141	644	1	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	1	2	FACETS	0.887	0.81	0.967	0.887	0.81	0.967	CLONAL	1	TRUE	1	0.489047767756553	2		645	650	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913283	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	96	481	0	ENST00000263967.3:c.3129G>T	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atT	21/21	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.489047767756553	2		481	389	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793710	89793710	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	101	319	0	ENST00000336032.3:c.779A>C	p.Lys260Thr	p.K260T	ENST00000336032	NM_006813.2	260	aAa/aCa	2/2	1	2	FACETS	0.939	0.844	1	0.939	0.844	1	CLONAL	1	TRUE	1	0.489047767756553	2		319	440	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	49	179	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	1	2	FACETS	0.792	0.677	0.917	0.792	0.677	0.917	CLONAL	1	TRUE	1	0.489047767756553	2		179	253	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911181	32911181	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs979372317	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	24	405	0	ENST00000380152.3:c.2689G>T	p.Glu897Ter	p.E897*	ENST00000380152		897	Gaa/Taa	11/27	1	2	FACETS	0.21	0.164	0.264	0.21	0.164	0.264	SUBCLONAL	1	TRUE	1	0.489047767756553	2		405	467	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520000	106520000	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs759433704	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	64	231	0	ENST00000359195.3:c.2428C>A	p.Pro810Thr	p.P810T	ENST00000359195	NM_002649.2	810	Cca/Aca	6/11	1	2	FACETS	0.991	0.868	1	0.991	0.868	1	CLONAL	1	TRUE	1	0.489047767756553	2		231	264	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913155	32913155	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	93	382	0	ENST00000380152.3:c.4663G>T	p.Glu1555Ter	p.E1555*	ENST00000380152		1555	Gaa/Taa	11/27	1	2	FACETS	0.903	0.808	1	0.903	0.808	1	CLONAL	1	TRUE	1	0.489047767756553	2		382	421	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681733	30681733	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs137893469	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	146	516	0	ENST00000376406.3:c.364C>A	p.Leu122Ile	p.L122I	ENST00000376406	NM_014641.2	122	Ctc/Atc	3/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.489047767756553	2		516	544	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332849	152332849	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	143	510	0	ENST00000206249.3:c.1155G>T	p.Glu385Asp	p.E385D	ENST00000206249	NM_000125.3	385	gaG/gaT	5/8	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.489047767756553	2		510	564	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16247393	16247393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747220001	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	55	215	0	ENST00000375759.3:c.1664C>T	p.Ala555Val	p.A555V	ENST00000375759	NM_015001.2	555	gCc/gTc	9/15	1	2	FACETS	0.728	0.627	0.837	0.728	0.627	0.837	SUBCLONAL	1	TRUE	1	0.489047767756553	2		215	309	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276860	15276861	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs753725730	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	134	670	3	ENST00000263388.2:c.5404dup	p.Ala1802GlyfsTer8	p.A1802Gfs*8	ENST00000263388	NM_000435.2	1802	gct/gGct	30/33	1	2	FACETS	0.934	0.851	1	0.934	0.851	1	CLONAL	1	TRUE	1	0.489047767756553	2		673	587	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910435	32910435	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	95	358	0	ENST00000380152.3:c.1943C>A	p.Ser648Ter	p.S648*	ENST00000380152		648	tCa/tAa	11/27	1	2	FACETS	0.768	0.686	0.854	0.768	0.686	0.854	SUBCLONAL	1	TRUE	1	0.489047767756553	2		358	506	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205711	108205711	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	58	287	0	ENST00000278616.4:c.8026G>T	p.Glu2676Ter	p.E2676*	ENST00000278616	NM_000051.3	2676	Gaa/Taa	55/63	1	2	FACETS	0.773	0.668	0.884	0.773	0.668	0.884	SUBCLONAL	1	TRUE	1	0.489047767756553	2		287	307	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231757	66231757	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	39	397	0	ENST00000273854.3:c.1943G>T	p.Arg648Ile	p.R648I	ENST00000273854	NM_004439.5	648	aGa/aTa	11/18	0.139055188993831	0	FACETS	0.221	0.184	0.263			1	INDETERMINATE	1	TRUE	0	0.489047767756553	0		397	368	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739790	41739790	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	44	595	0	ENST00000242208.4:c.183C>A	p.His61Gln	p.H61Q	ENST00000242208	NM_002192.2	61	caC/caA	2/3	1	2	FACETS	0.333	0.279	0.393	0.333	0.279	0.393	SUBCLONAL	1	TRUE	1	0.489047767756553	2		595	540	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922867	39922867	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	142	278	0	ENST00000378444.4:c.3841G>T	p.Glu1281Ter	p.E1281*	ENST00000378444	NM_001123385.1	1281	Gaa/Taa	8/15	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.489047767756553	1		278	297	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150330	108150330	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	103	343	0	ENST00000278616.4:c.3397G>T	p.Glu1133Ter	p.E1133*	ENST00000278616	NM_000051.3	1133	Gaa/Taa	23/63	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.489047767756553	2		343	390	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176614	56176614	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	111	336	0	ENST00000399503.3:c.2164G>T	p.Glu722Ter	p.E722*	ENST00000399503	NM_005921.1	722	Gaa/Taa	12/20	1	2	FACETS	0.928	0.839	1	0.928	0.839	1	CLONAL	1	TRUE	1	0.489047767756553	2		336	489	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610715	52610715	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	27	297	0	ENST00000394830.3:c.3459-1G>T		p.X1153_splice	ENST00000394830	NM_018313.4	1153			1	2	FACETS	0.264	0.209	0.326	0.264	0.209	0.326	SUBCLONAL	1	TRUE	1	0.489047767756553	2		297	419	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246158	46246158	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	25	390	0	ENST00000334344.6:c.4252G>T	p.Gly1418Ter	p.G1418*	ENST00000334344	NM_152641.2	1418	Gga/Tga	15/21	1	2	FACETS	0.233	0.183	0.29	0.233	0.183	0.29	SUBCLONAL	1	TRUE	1	0.489047767756553	2		390	439	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915295	32915295	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	140	606	0	ENST00000380152.3:c.6803G>T	p.Arg2268Ile	p.R2268I	ENST00000380152		2268	aGa/aTa	11/27	1	2	FACETS	0.844	0.771	0.921	0.844	0.771	0.921	CLONAL	1	TRUE	1	0.489047767756553	2		606	678	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056420	180056420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372030421	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	81	473	0	ENST00000261937.6:c.824G>A	p.Arg275Gln	p.R275Q	ENST00000261937	NM_182925.4	275	cGg/cAg	7/30	NA	2	FACETS	0.774	0.685	0.868			1	INDETERMINATE	1	TRUE	NA	0.489047767756553	2		473	428	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259479	16259480	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	27	424	1	ENST00000375759.3:c.6750dup	p.Ala2251ArgfsTer10	p.A2251Rfs*10	ENST00000375759	NM_015001.2	2248	-/C	11/15	1	2	FACETS	0.272	0.216	0.336	0.272	0.216	0.336	SUBCLONAL	1	TRUE	1	0.489047767756553	2		425	406	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65304224	65304224	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	144	422	0	ENST00000342505.4:c.2891T>G	p.Leu964Arg	p.L964R	ENST00000342505	NM_002227.2	964	cTt/cGt	21/25	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.489047767756553	2		422	567	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743292	162743292	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	96	324	0	ENST00000367921.3:c.1762T>A	p.Phe588Ile	p.F588I	ENST00000367921	NM_006182.2	588	Ttc/Atc	14/18	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.489047767756553	2		324	352	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317623	163317623	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs747173543	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	80	221	0	ENST00000271452.3:c.1019C>A	p.Ser340Ter	p.S340*	ENST00000271452	NM_145697.2	340	tCg/tAg	12/14	1	2	FACETS	0.988	0.878	1	0.988	0.878	1	CLONAL	1	TRUE	1	0.489047767756553	2		221	331	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193202172	193202172	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	104	268	0	ENST00000367435.3:c.1204G>T	p.Glu402Ter	p.E402*	ENST00000367435	NM_024529.4	402	Gaa/Taa	14/17	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.489047767756553	2		268	410	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226576395	226576395	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	51	528	0	ENST00000366794.5:c.679G>T	p.Glu227Ter	p.E227*	ENST00000366794	NM_001618.3	227	Gaa/Taa	5/23	1	2	FACETS	0.318	0.27	0.372	0.318	0.27	0.372	SUBCLONAL	1	TRUE	1	0.489047767756553	2		528	655	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680556	241680556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs769956664	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	136	577	0	ENST00000366560.3:c.193G>T	p.Asp65Tyr	p.D65Y	ENST00000366560	NM_000143.3	65	Gat/Tat	2/10	1	2	FACETS	0.807	0.735	0.882	0.807	0.735	0.882	CLONAL	1	TRUE	1	0.489047767756553	2		577	689	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912704	100912704	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	36	447	0	ENST00000325455.5:c.2618T>G	p.Leu873Arg	p.L873R	ENST00000325455	NM_001202474.3	873	cTt/cGt	7/8	1	2	FACETS	0.275	0.225	0.33	0.275	0.225	0.33	SUBCLONAL	1	TRUE	1	0.489047767756553	2		447	536	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236180	108236180	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	38	602	0	ENST00000278616.4:c.9116C>A	p.Ala3039Asp	p.A3039D	ENST00000278616	NM_000051.3	3039	gCc/gAc	63/63	1	2	FACETS	0.206	0.169	0.247	0.206	0.169	0.247	SUBCLONAL	1	TRUE	1	0.489047767756553	2		602	755	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505413	125505413	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	24	293	2	ENST00000428830.2:c.703G>T	p.Asp235Tyr	p.D235Y	ENST00000428830	NM_001114121.2	235	Gat/Tat	7/14	1	2	FACETS	0.249	0.195	0.312	0.249	0.195	0.312	SUBCLONAL	1	TRUE	1	0.489047767756553	2		295	394	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417122	417122	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	124	395	0	ENST00000399788.2:c.3428C>A	p.Ser1143Tyr	p.S1143Y	ENST00000399788	NM_001042603.1	1143	tCt/tAt	23/28	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.489047767756553	2		395	468	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641509	18641509	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	74	391	0	ENST00000266497.5:c.2508A>C	p.Lys836Asn	p.K836N	ENST00000266497		836	aaA/aaC	17/31	1	2	FACETS	0.751	0.661	0.847	0.751	0.661	0.847	SUBCLONAL	1	TRUE	1	0.489047767756553	2		391	403	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435178	49435178	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	24	414	0	ENST00000301067.7:c.6375C>A	p.Phe2125Leu	p.F2125L	ENST00000301067	NM_003482.3	2125	ttC/ttA	31/54	1	2	FACETS	0.271	0.212	0.339	0.271	0.212	0.339	SUBCLONAL	1	TRUE	1	0.489047767756553	2		414	362	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437468	49437468	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	126	565	0	ENST00000301067.7:c.5417C>A	p.Ala1806Asp	p.A1806D	ENST00000301067	NM_003482.3	1806	gCc/gAc	23/54	1	2	FACETS	0.887	0.806	0.972	0.887	0.806	0.972	CLONAL	1	TRUE	1	0.489047767756553	2		565	581	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233086	69233086	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	69	310	0	ENST00000462284.1:c.951G>T	p.Met317Ile	p.M317I	ENST00000462284	NM_002392.5	317	atG/atT	11/11	1	2	FACETS	0.737	0.645	0.835	0.737	0.645	0.835	SUBCLONAL	1	TRUE	1	0.489047767756553	2		310	383	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120785302	120785302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	71	541	0	ENST00000257552.2:c.806C>A	p.Ala269Asp	p.A269D	ENST00000257552	NM_002442.3	269	gCc/gAc	12/15	1	2	FACETS	0.521	0.455	0.592	0.521	0.455	0.592	SUBCLONAL	1	TRUE	1	0.489047767756553	2		541	557	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252691	133252691	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	26	475	0	ENST00000320574.5:c.1009G>T	p.Glu337Ter	p.E337*	ENST00000320574	NM_006231.2	337	Gaa/Taa	10/49	1	2	FACETS	0.208	0.164	0.259	0.208	0.164	0.259	SUBCLONAL	1	TRUE	1	0.489047767756553	2		475	511	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955403	48955403	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	77	295	0	ENST00000267163.4:c.1519G>T	p.Asp507Tyr	p.D507Y	ENST00000267163	NM_000321.2	507	Gat/Tat	17/27	1	2	FACETS	0.829	0.732	0.931	0.829	0.732	0.931	CLONAL	1	TRUE	1	0.489047767756553	2		295	380	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068922	30068922	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	126	689	0	ENST00000331968.5:c.2007G>T	p.Met669Ile	p.M669I	ENST00000331968	NM_002742.2	669	atG/atT	14/18	1	2	FACETS	0.647	0.586	0.712	0.647	0.586	0.712	SUBCLONAL	1	TRUE	1	0.489047767756553	2		689	796	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100166	30100166	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	202	562	0	ENST00000331968.5:c.1454A>T	p.Asn485Ile	p.N485I	ENST00000331968	NM_002742.2	485	aAt/aTt	10/18	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.489047767756553	2		562	670	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562226	95562226	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	152	371	0	ENST00000393063.1:c.5031C>A	p.Phe1677Leu	p.F1677L	ENST00000393063	NM_030621.3	1677	ttC/ttA	24/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.489047767756553	2		371	531	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41999995	41999995	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	78	658	0	ENST00000219905.7:c.2258C>A	p.Pro753His	p.P753H	ENST00000219905	NM_001164273.1	753	cCt/cAt	6/24	1	2	FACETS	0.436	0.382	0.493	0.436	0.382	0.493	SUBCLONAL	1	TRUE	1	0.489047767756553	2		658	732	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482814	67482814	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	137	628	1	ENST00000327367.4:c.1218G>T	p.Trp406Cys	p.W406C	ENST00000327367	NM_005902.3	406	tgG/tgT	9/9	1	2	FACETS	0.969	0.885	1	0.969	0.885	1	CLONAL	1	TRUE	1	0.489047767756553	2		629	578	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354334	354334	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	36	692	0	ENST00000262320.3:c.1224G>T	p.Lys408Asn	p.K408N	ENST00000262320	NM_003502.3	408	aaG/aaT	5/11	0.378351369277864	3	FACETS	0.255	0.209	0.307	0.128	0.104	0.154	SUBCLONAL	1	TRUE	1	0.489047767756553	3		692	718	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647697	3647697	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	108	654	0	ENST00000294008.3:c.1367-1G>T		p.X456_splice	ENST00000294008	NM_032444.2	456			0.378351369277864	3	FACETS	0.726	0.652	0.805	0.363	0.326	0.403	SUBCLONAL	1	TRUE	1	0.489047767756553	3		654	757	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641575	23641575	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	38	628	0	ENST00000261584.4:c.1900C>A	p.Pro634Thr	p.P634T	ENST00000261584	NM_024675.3	634	Cca/Aca	5/13	1	2	FACETS	0.233	0.191	0.279	0.233	0.191	0.279	SUBCLONAL	1	TRUE	1	0.489047767756553	2		628	668	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645377	67645377	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	115	376	0	ENST00000264010.4:c.642T>G	p.Tyr214Ter	p.Y214*	ENST00000264010	NM_006565.3	214	taT/taG	3/12	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.489047767756553	2		376	433	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650662	67650662	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	31	453	0	ENST00000264010.4:c.967A>G	p.Lys323Glu	p.K323E	ENST00000264010	NM_006565.3	323	Aag/Gag	5/12	1	2	FACETS	0.236	0.19	0.288	0.236	0.19	0.288	SUBCLONAL	1	TRUE	1	0.489047767756553	2		453	538	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671652	67671652	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	50	473	0	ENST00000264010.4:c.2061A>T	p.Glu687Asp	p.E687D	ENST00000264010	NM_006565.3	687	gaA/gaT	12/12	1	2	FACETS	0.416	0.353	0.486	0.416	0.353	0.486	SUBCLONAL	1	TRUE	1	0.489047767756553	2		473	491	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346627	89346627	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	66	452	0	ENST00000301030.4:c.6323G>T	p.Gly2108Val	p.G2108V	ENST00000301030	NM_001256183.1	2108	gGc/gTc	9/13	1	2	FACETS	0.871	0.762	0.987	0.871	0.762	0.987	CLONAL	1	TRUE	1	0.489047767756553	2		452	310	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348410	89348410	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	211	765	1	ENST00000301030.4:c.4540C>A	p.Leu1514Ile	p.L1514I	ENST00000301030	NM_001256183.1	1514	Ctc/Atc	9/13	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.489047767756553	2		766	720	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573997	7573997	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	41	686	0	ENST00000269305.4:c.1030C>A	p.Leu344Met	p.L344M	ENST00000269305	NM_001126112.2	344	Ctg/Atg	10/11	1	2	FACETS	0.241	0.2	0.286	0.241	0.2	0.286	SUBCLONAL	1	TRUE	1	0.489047767756553	2		686	697	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961030	15961030	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs767942246	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	136	373	0	ENST00000268712.3:c.6190G>T	p.Ala2064Ser	p.A2064S	ENST00000268712	NM_006311.3	2064	Gct/Tct	40/46	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.489047767756553	2		373	511	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40461433	40461433	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	58	696	0	ENST00000345506.4:c.2153C>A	p.Ala718Asp	p.A718D	ENST00000345506	NM_003152.3	718	gCc/gAc	19/20	1	2	FACETS	0.405	0.348	0.468	0.405	0.348	0.468	SUBCLONAL	1	TRUE	1	0.489047767756553	2		696	585	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40477068	40477068	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	93	440	2	ENST00000264657.5:c.1377G>T	p.Leu459Phe	p.L459F	ENST00000264657	NM_139276.2	459	ttG/ttT	16/24	1	2	FACETS	0.813	0.726	0.904	0.813	0.726	0.904	CLONAL	1	TRUE	1	0.489047767756553	2		442	468	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885860	59885860	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs876660125	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	136	480	0	ENST00000259008.2:c.886G>T	p.Glu296Ter	p.E296*	ENST00000259008	NM_032043.2	296	Gag/Tag	7/20	1	2	FACETS	0.951	0.868	1	0.951	0.868	1	CLONAL	1	TRUE	1	0.489047767756553	2		480	585	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526218	63526218	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1280152084	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	153	465	0	ENST00000307078.5:c.2408A>G	p.Tyr803Cys	p.Y803C	ENST00000307078	NM_004655.3	803	tAt/tGt	11/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.489047767756553	2		465	581	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57569903	57569903	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	57	258	0	ENST00000316660.6:c.83A>G	p.Gln28Arg	p.Q28R	ENST00000316660	NM_021127.2	28	cAa/cGa	2/2	1	2	FACETS	0.676	0.583	0.776	0.676	0.583	0.776	SUBCLONAL	1	TRUE	1	0.489047767756553	2		258	345	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4097329	4097329	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	27	451	0	ENST00000262948.5:c.932A>G	p.Asp311Gly	p.D311G	ENST00000262948	NM_030662.3	311	gAt/gGt	8/11	1	2	FACETS	0.213	0.169	0.264	0.213	0.169	0.264	SUBCLONAL	1	TRUE	1	0.489047767756553	2		451	518	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11015629	11015629	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	108	432	0	ENST00000327064.4:c.223G>T	p.Glu75Ter	p.E75*	ENST00000327064	NM_199141.1	75	Gaa/Taa	2/16	1	2	FACETS	0.876	0.79	0.967	0.876	0.79	0.967	CLONAL	1	TRUE	1	0.489047767756553	2		432	504	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39237792	39237792	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	167	464	1	ENST00000402219.2:c.2443G>T	p.Glu815Ter	p.E815*	ENST00000402219	NM_005633.3	815	Gaa/Taa	15/23	1	2	FACETS	0.997	0.919	1	0.997	0.919	1	CLONAL	1	TRUE	1	0.489047767756553	2		465	685	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241033	39241033	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	137	483	0	ENST00000402219.2:c.2038G>T	p.Glu680Ter	p.E680*	ENST00000402219	NM_005633.3	680	Gaa/Taa	12/23	1	2	FACETS	0.948	0.866	1	0.948	0.866	1	CLONAL	1	TRUE	1	0.489047767756553	2		483	591	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250011	39250011	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	145	597	0	ENST00000402219.2:c.1558G>C	p.Asp520His	p.D520H	ENST00000402219	NM_005633.3	520	Gat/Cat	10/23	1	2	FACETS	0.925	0.847	1	0.925	0.847	1	CLONAL	1	TRUE	1	0.489047767756553	2		597	641	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872974	136872974	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	84	381	0	ENST00000241393.3:c.524C>A	p.Ala175Asp	p.A175D	ENST00000241393	NM_003467.2	175	gCc/gAc	2/2	1	2	FACETS	0.859	0.763	0.96	0.859	0.763	0.96	CLONAL	1	TRUE	1	0.489047767756553	2		381	400	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158595035	158595035	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	145	425	0	ENST00000263640.3:c.1312G>T	p.Asp438Tyr	p.D438Y	ENST00000263640	NM_001105.4	438	Gac/Tac	10/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.489047767756553	2		425	512	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141693	202141693	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	27	264	0	ENST00000358485.4:c.979+2T>C		p.X327_splice	ENST00000358485	NM_001080125.1	327			0.378351369277864	3	FACETS	0.387	0.308	0.478	0.194	0.154	0.239	SUBCLONAL	1	TRUE	1	0.489047767756553	3		264	355	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570050	212570050	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	97	445	0	ENST00000342788.4:c.1191G>T	p.Glu397Asp	p.E397D	ENST00000342788	NM_005235.2	397	gaG/gaT	10/28	1	2	FACETS	0.784	0.702	0.871	0.784	0.702	0.871	SUBCLONAL	1	TRUE	1	0.489047767756553	2		445	506	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812165	212812165	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	59	294	0	ENST00000342788.4:c.411G>T	p.Lys137Asn	p.K137N	ENST00000342788	NM_005235.2	137	aaG/aaT	3/28	1	2	FACETS	0.727	0.629	0.832	0.727	0.629	0.832	SUBCLONAL	1	TRUE	1	0.489047767756553	2		294	332	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660757	227660757	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	93	547	0	ENST00000305123.5:c.2698G>T	p.Glu900Ter	p.E900*	ENST00000305123	NM_005544.2	900	Gaa/Taa	1/2	1	2	FACETS	0.761	0.679	0.847	0.761	0.679	0.847	SUBCLONAL	1	TRUE	1	0.489047767756553	2		547	500	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31020757	31020757	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	41	216	0	ENST00000375687.4:c.1054G>T	p.Glu352Ter	p.E352*	ENST00000375687	NM_015338.5	352	Gaa/Taa	11/13	1	2	FACETS	0.682	0.572	0.802	0.682	0.572	0.802	SUBCLONAL	1	TRUE	1	0.489047767756553	2		216	246	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31020765	31020765	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	55	205	0	ENST00000375687.4:c.1062C>A	p.Phe354Leu	p.F354L	ENST00000375687	NM_015338.5	354	ttC/ttA	11/13	1	2	FACETS	0.957	0.828	1	0.957	0.828	1	CLONAL	1	TRUE	1	0.489047767756553	2		205	235	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164731	36164731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	151	617	0	ENST00000300305.3:c.1144C>T	p.Pro382Ser	p.P382S	ENST00000300305		382	Ccg/Tcg	8/8	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.489047767756553	2		617	573	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288524	21288524	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	134	574	2	ENST00000354336.3:c.769G>T	p.Ala257Ser	p.A257S	ENST00000354336	NM_005207.3	257	Gca/Tca	2/3	1	2	FACETS	0.817	0.744	0.893	0.817	0.744	0.893	CLONAL	1	TRUE	1	0.489047767756553	2		576	671	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523732	41523732	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	42	662	0	ENST00000263253.7:c.1148A>G	p.Gln383Arg	p.Q383R	ENST00000263253	NM_001429.3	383	cAg/cGg	4/31	1	2	FACETS	0.236	0.196	0.28	0.236	0.196	0.28	SUBCLONAL	1	TRUE	1	0.489047767756553	2		662	728	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626671	12626671	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	126	519	0	ENST00000251849.4:c.1618G>T	p.Glu540Ter	p.E540*	ENST00000251849	NM_002880.3	540	Gaa/Taa	15/17	1	2	FACETS	0.872	0.792	0.955	0.872	0.792	0.955	CLONAL	1	TRUE	1	0.489047767756553	2		519	591	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924769	49924769	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	152	637	0	ENST00000296474.3:c.4174C>A	p.Pro1392Thr	p.P1392T	ENST00000296474	NM_002447.2	1392	Cca/Aca	20/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.489047767756553	2		637	588	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987202	69987202	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	89	345	0	ENST00000394351.3:c.261+2T>A		p.X87_splice	ENST00000394351	NM_000248.3	87			1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.489047767756553	2		345	356	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799734	72799734	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	174	628	0	ENST00000325599.8:c.1435G>T	p.Glu479Ter	p.E479*	ENST00000325599	NM_018130.2	479	Gaa/Taa	11/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.489047767756553	2		628	687	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72891457	72891457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	143	466	0	ENST00000325599.8:c.305C>T	p.Thr102Ile	p.T102I	ENST00000325599	NM_018130.2	102	aCa/aTa	3/11	1	2	FACETS	0.894	0.818	0.974	0.894	0.818	0.974	CLONAL	1	TRUE	1	0.489047767756553	2		466	654	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73047278	73047278	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	143	439	0	ENST00000356692.5:c.85C>A	p.Leu29Ile	p.L29I	ENST00000356692		29	Ctt/Att	2/9	1	2	FACETS	0.936	0.856	1	0.936	0.856	1	CLONAL	1	TRUE	1	0.489047767756553	2		439	625	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138431122	138431122	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	147	352	0	ENST00000289153.2:c.1327A>C	p.Thr443Pro	p.T443P	ENST00000289153	NM_006219.2	443	Acg/Ccg	8/22	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.489047767756553	2		352	536	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664867	138664867	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	15	99	0	ENST00000330315.3:c.698C>A	p.Ala233Asp	p.A233D	ENST00000330315	NM_023067.3	233	gCc/gAc	1/1	1	2	FACETS	0.558	0.412	0.728	0.558	0.412	0.728	SUBCLONAL	1	TRUE	1	0.489047767756553	2		99	110	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215241	142215241	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	27	439	0	ENST00000350721.4:c.5860G>T	p.Glu1954Ter	p.E1954*	ENST00000350721	NM_001184.3	1954	Gaa/Taa	34/47	1	2	FACETS	0.223	0.176	0.276	0.223	0.176	0.276	SUBCLONAL	1	TRUE	1	0.489047767756553	2		439	496	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430749	181430749	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	46	590	0	ENST00000325404.1:c.601G>T	p.Asp201Tyr	p.D201Y	ENST00000325404	NM_003106.3	201	Gac/Tac	1/1	1	2	FACETS	0.312	0.263	0.368	0.312	0.263	0.368	SUBCLONAL	1	TRUE	1	0.489047767756553	2		590	602	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504340	186504340	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	18	231	0	ENST00000323963.5:c.677A>C	p.Lys226Thr	p.K226T	ENST00000323963		226	aAa/aCa	7/11	1	2	FACETS	0.231	0.174	0.3	0.231	0.174	0.3	SUBCLONAL	1	TRUE	1	0.489047767756553	2		231	318	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506949	186506949	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	19	270	0	ENST00000323963.5:c.1115T>C	p.Val372Ala	p.V372A	ENST00000323963		372	gTg/gCg	11/11	1	2	FACETS	0.219	0.166	0.282	0.219	0.166	0.282	SUBCLONAL	1	TRUE	1	0.489047767756553	2		270	354	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806182	1806182	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762705505	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	140	655	0	ENST00000260795.2:c.1201C>A	p.Pro401Thr	p.P401T	ENST00000260795		401	Ccc/Acc	8/17	NA	2	FACETS	1	0.916	1			1	INDETERMINATE	1	TRUE	NA	0.489047767756553	2		655	572	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971117	55971117	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	136	593	0	ENST00000263923.4:c.1680G>T	p.Gln560His	p.Q560H	ENST00000263923	NM_002253.2	560	caG/caT	13/30	0.139055188993831	0	FACETS	0.495	0.452	0.54			1	INDETERMINATE	1	TRUE	0	0.489047767756553	0		593	574	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509932	187509932	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	105	381	3	ENST00000441802.2:c.13581C>A	p.Phe4527Leu	p.F4527L	ENST00000441802	NM_005245.3	4527	ttC/ttA	27/27	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.489047767756553	2		384	395	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524798	187524798	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	87	679	0	ENST00000441802.2:c.10882A>G	p.Thr3628Ala	p.T3628A	ENST00000441802	NM_005245.3	3628	Aca/Gca	19/27	1	2	FACETS	0.468	0.414	0.526	0.468	0.414	0.526	SUBCLONAL	1	TRUE	1	0.489047767756553	2		679	760	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38943046	38943046	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	40	279	0	ENST00000357387.3:c.4941T>A	p.Phe1647Leu	p.F1647L	ENST00000357387	NM_152756.3	1647	ttT/ttA	37/38	1	2	FACETS	0.433	0.36	0.513	0.433	0.36	0.513	SUBCLONAL	1	TRUE	1	0.489047767756553	2		279	378	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944618	38944618	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	37	426	0	ENST00000357387.3:c.4843G>T	p.Glu1615Ter	p.E1615*	ENST00000357387	NM_152756.3	1615	Gaa/Taa	36/38	1	2	FACETS	0.31	0.255	0.372	0.31	0.255	0.372	SUBCLONAL	1	TRUE	1	0.489047767756553	2		426	488	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945785	38945785	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	17	296	0	ENST00000357387.3:c.4441C>A	p.His1481Asn	p.H1481N	ENST00000357387	NM_152756.3	1481	Cac/Aac	34/38	1	2	FACETS	0.217	0.161	0.283	0.217	0.161	0.283	SUBCLONAL	1	TRUE	1	0.489047767756553	2		296	321	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752361	57752361	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	99	422	0	ENST00000274289.3:c.1212G>T	p.Lys404Asn	p.K404N	ENST00000274289	NM_006622.3	404	aaG/aaT	9/14	1	2	FACETS	0.81	0.726	0.898	0.81	0.726	0.898	CLONAL	1	TRUE	1	0.489047767756553	2		422	500	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80083394	80083394	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	56	598	1	ENST00000265081.6:c.2446G>T	p.Glu816Ter	p.E816*	ENST00000265081	NM_002439.4	816	Gaa/Taa	18/24	1	2	FACETS	0.321	0.274	0.372	0.321	0.274	0.372	SUBCLONAL	1	TRUE	1	0.489047767756553	2		599	713	SUCCESS
APC	324	MSKCC	GRCh37	5	112157678	112157678	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	29	431	0	ENST00000257430.4:c.1398G>T	p.Met466Ile	p.M466I	ENST00000257430	NM_000038.5	466	atG/atT	11/16	1	2	FACETS	0.227	0.181	0.279	0.227	0.181	0.279	SUBCLONAL	1	TRUE	1	0.489047767756553	2		431	523	SUCCESS
APC	324	MSKCC	GRCh37	5	112175806	112175806	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	69	278	0	ENST00000257430.4:c.4515C>A	p.Ser1505Arg	p.S1505R	ENST00000257430	NM_000038.5	1505	agC/agA	16/16	1	2	FACETS	0.913	0.802	1	0.913	0.802	1	CLONAL	1	TRUE	1	0.489047767756553	2		278	309	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638539	176638539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	140	621	0	ENST00000439151.2:c.3139G>T	p.Ala1047Ser	p.A1047S	ENST00000439151	NM_022455.4	1047	Gcc/Tcc	5/23	0.378351369277864	3	FACETS	0.892	0.813	0.975	0.446	0.406	0.488	CLONAL	1	TRUE	1	0.489047767756553	3		621	799	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721984	176721984	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	38	470	0	ENST00000439151.2:c.7615C>A	p.Leu2539Ile	p.L2539I	ENST00000439151	NM_022455.4	2539	Ctt/Att	23/23	0.378351369277864	3	FACETS	0.337	0.278	0.403	0.168	0.139	0.202	SUBCLONAL	1	TRUE	1	0.489047767756553	3		470	574	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190323	32190323	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	51	445	0	ENST00000375023.3:c.416G>C	p.Gly139Ala	p.G139A	ENST00000375023	NM_004557.3	139	gGc/gCc	3/30	1	2	FACETS	0.49	0.417	0.569	0.49	0.417	0.569	SUBCLONAL	1	TRUE	1	0.489047767756553	2		445	426	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798492	32798492	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	169	720	0	ENST00000374899.4:c.1364C>A	p.Ser455Ter	p.S455*	ENST00000374899	NM_018833.2	455	tCa/tAa	8/12	1	2	FACETS	0.912	0.84	0.986	0.912	0.84	0.986	CLONAL	1	TRUE	1	0.489047767756553	2		720	758	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800496	32800496	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	160	784	0	ENST00000374899.4:c.1051G>T	p.Glu351Ter	p.E351*	ENST00000374899	NM_018833.2	351	Gaa/Taa	6/12	1	2	FACETS	0.885	0.813	0.96	0.885	0.813	0.96	CLONAL	1	TRUE	1	0.489047767756553	2		784	739	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120887	94120887	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	61	389	0	ENST00000369303.4:c.164G>T	p.Trp55Leu	p.W55L	ENST00000369303	NM_004440.3	55	tGg/tTg	3/17	1	2	FACETS	0.671	0.581	0.767	0.671	0.581	0.767	SUBCLONAL	1	TRUE	1	0.489047767756553	2		389	372	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555065	106555065	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	154	482	0	ENST00000369096.4:c.2182G>T	p.Glu728Ter	p.E728*	ENST00000369096	NM_001198.3	728	Gaa/Taa	7/7	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.489047767756553	2		482	504	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555216	106555216	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	96	466	0	ENST00000369096.4:c.2333G>T	p.Arg778Ile	p.R778I	ENST00000369096	NM_001198.3	778	aGa/aTa	7/7	1	2	FACETS	0.734	0.656	0.816	0.734	0.656	0.816	SUBCLONAL	1	TRUE	1	0.489047767756553	2		466	535	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109415129	109415129	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	186	855	0	ENST00000436639.2:c.148T>A	p.Ser50Thr	p.S50T	ENST00000436639	NM_014454.2	50	Tca/Aca	1/10	1	2	FACETS	0.787	0.727	0.85	0.787	0.727	0.85	SUBCLONAL	1	TRUE	1	0.489047767756553	2		855	966	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001072	150001072	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	106	474	0	ENST00000253339.5:c.2532G>T	p.Leu844Phe	p.L844F	ENST00000253339		844	ttG/ttT	4/7	1	2	FACETS	0.771	0.694	0.853	0.771	0.694	0.853	SUBCLONAL	1	TRUE	1	0.489047767756553	2		474	562	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004238	150004238	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	109	350	0	ENST00000253339.5:c.1987C>A	p.Gln663Lys	p.Q663K	ENST00000253339		663	Caa/Aaa	3/7	1	2	FACETS	0.879	0.793	0.97	0.879	0.793	0.97	CLONAL	1	TRUE	1	0.489047767756553	2		350	507	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150022982	150022982	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	60	642	0	ENST00000253339.5:c.281C>A	p.Ser94Tyr	p.S94Y	ENST00000253339		94	tCt/tAt	1/7	1	2	FACETS	0.383	0.329	0.441	0.383	0.329	0.441	SUBCLONAL	1	TRUE	1	0.489047767756553	2		642	641	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026395	6026395	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	28	401	0	ENST00000265849.7:c.2001G>T	p.Glu667Asp	p.E667D	ENST00000265849	NM_000535.5	667	gaG/gaT	11/15	1	2	FACETS	0.221	0.176	0.272	0.221	0.176	0.272	SUBCLONAL	1	TRUE	1	0.489047767756553	2		401	519	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739888	41739888	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	89	357	1	ENST00000242208.4:c.85C>A	p.His29Asn	p.H29N	ENST00000242208	NM_002192.2	29	Cac/Aac	2/3	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.489047767756553	2		358	355	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50358679	50358679	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	57	251	0	ENST00000331340.3:c.22G>T	p.Asp8Tyr	p.D8Y	ENST00000331340	NM_006060.4	8	Gac/Tac	2/8	1	2	FACETS	0.742	0.641	0.851	0.742	0.641	0.851	SUBCLONAL	1	TRUE	1	0.489047767756553	2		251	314	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334756	81334756	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	150	552	0	ENST00000222390.5:c.1960G>T	p.Glu654Ter	p.E654*	ENST00000222390	NM_000601.4	654	Gag/Tag	17/18	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.489047767756553	2		552	604	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388044	81388044	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	70	452	0	ENST00000222390.5:c.331G>T	p.Glu111Ter	p.E111*	ENST00000222390	NM_000601.4	111	Gaa/Taa	3/18	1	2	FACETS	0.526	0.459	0.598	0.526	0.459	0.598	SUBCLONAL	1	TRUE	1	0.489047767756553	2		452	544	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508531	106508531	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	44	261	0	ENST00000359195.3:c.525C>A	p.Phe175Leu	p.F175L	ENST00000359195	NM_002649.2	175	ttC/ttA	2/11	1	2	FACETS	0.75	0.634	0.875	0.75	0.634	0.875	SUBCLONAL	1	TRUE	1	0.489047767756553	2		261	240	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371905	116371905	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	137	462	0	ENST00000397752.3:c.1384T>A	p.Phe462Ile	p.F462I	ENST00000397752	NM_000245.2	462	Ttc/Atc	3/21	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.489047767756553	2		462	559	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415062	116415062	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	36	553	0	ENST00000397752.3:c.3156C>G	p.His1052Gln	p.H1052Q	ENST00000397752	NM_000245.2	1052	caC/caG	15/21	1	2	FACETS	0.222	0.182	0.267	0.222	0.182	0.267	SUBCLONAL	1	TRUE	1	0.489047767756553	2		553	663	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133997	38133997	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	51	516	0	ENST00000317025.8:c.3889G>T	p.Glu1297Ter	p.E1297*	ENST00000317025	NM_023034.1	1297	Gaa/Taa	23/24	1	2	FACETS	0.346	0.294	0.404	0.346	0.294	0.404	SUBCLONAL	1	TRUE	1	0.489047767756553	2		516	602	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38194840	38194840	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	165	467	0	ENST00000317025.8:c.893C>A	p.Thr298Asn	p.T298N	ENST00000317025	NM_023034.1	298	aCt/aAt	4/24	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.489047767756553	2		467	637	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864899	117864899	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	35	477	0	ENST00000297338.2:c.1210A>G	p.Arg404Gly	p.R404G	ENST00000297338	NM_006265.2	404	Agg/Ggg	10/14	1	2	FACETS	0.267	0.218	0.322	0.267	0.218	0.322	SUBCLONAL	1	TRUE	1	0.489047767756553	2		477	536	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750835	128750835	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	25	553	0	ENST00000377970.2:c.372C>A	p.Asp124Glu	p.D124E	ENST00000377970	NM_002467.4	124	gaC/gaA	2/3	1	2	FACETS	0.213	0.167	0.266	0.213	0.167	0.266	SUBCLONAL	1	TRUE	1	0.489047767756553	2		553	480	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740578	145740578	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs767337200	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	38	656	0	ENST00000428558.2:c.1439C>A	p.Ala480Asp	p.A480D	ENST00000428558	NM_004260.3	480	gCc/gAc	8/22	1	2	FACETS	0.256	0.211	0.306	0.256	0.211	0.306	SUBCLONAL	1	TRUE	1	0.489047767756553	2		656	608	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484185	8484185	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	39	577	0	ENST00000356435.5:c.3347G>T	p.Gly1116Val	p.G1116V	ENST00000356435		1116	gGg/gTg	19/35	1	2	FACETS	0.269	0.222	0.321	0.269	0.222	0.321	SUBCLONAL	1	TRUE	1	0.489047767756553	2		577	594	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912370	97912370	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	102	265	0	ENST00000289081.3:c.522-1G>T		p.X174_splice	ENST00000289081	NM_000136.2	174			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.489047767756553	2		265	353	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891336	101891336	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	144	557	0	ENST00000374994.4:c.297T>A	p.Tyr99Ter	p.Y99*	ENST00000374994	NM_004612.2	99	taT/taA	2/9	1	2	FACETS	0.821	0.75	0.895	0.821	0.75	0.895	CLONAL	1	TRUE	1	0.489047767756553	2		557	717	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904821	101904821	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	40	348	0	ENST00000374994.4:c.809A>T	p.Asn270Ile	p.N270I	ENST00000374994	NM_004612.2	270	aAt/aTt	5/9	1	2	FACETS	0.377	0.313	0.448	0.377	0.313	0.448	SUBCLONAL	1	TRUE	1	0.489047767756553	2		348	434	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908816	101908816	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	130	445	0	ENST00000374994.4:c.1180G>T	p.Glu394Ter	p.E394*	ENST00000374994	NM_004612.2	394	Gaa/Taa	7/9	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.489047767756553	2		445	466	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912019	127912019	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	76	382	0	ENST00000373547.4:c.851T>G	p.Leu284Ter	p.L284*	ENST00000373547	NM_002721.4	284	tTa/tGa	7/7	1	2	FACETS	0.594	0.522	0.672	0.594	0.522	0.672	SUBCLONAL	1	TRUE	1	0.489047767756553	2		382	523	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750333	133750333	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	53	527	0	ENST00000318560.5:c.1164G>T	p.Met388Ile	p.M388I	ENST00000318560	NM_005157.4	388	atG/atT	7/11	1	2	FACETS	0.389	0.332	0.452	0.389	0.332	0.452	SUBCLONAL	1	TRUE	1	0.489047767756553	2		527	557	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759501	133759501	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	148	589	0	ENST00000318560.5:c.1824G>T	p.Lys608Asn	p.K608N	ENST00000318560	NM_005157.4	608	aaG/aaT	11/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.489047767756553	2		589	517	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760859	133760859	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	120	719	0	ENST00000318560.5:c.3182A>C	p.Lys1061Thr	p.K1061T	ENST00000318560	NM_005157.4	1061	aAa/aCa	11/11	1	2	FACETS	0.788	0.713	0.866	0.788	0.713	0.866	SUBCLONAL	1	TRUE	1	0.489047767756553	2		719	623	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933976	39933976	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	175	348	1	ENST00000378444.4:c.623A>T	p.Asp208Val	p.D208V	ENST00000378444	NM_001123385.1	208	gAc/gTc	4/15	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.489047767756553	1		349	392	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77043904	77043995	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTACAAGGCCTGGCAATAAAAATGGTGAATCACCTTGAGCTCCAAATGAGGCTCTCTCTTGTTCCCCATATACAAGTTCTAGAAATATGGTC	GTACAAGGCCTGGCAATAAAAATGGTGAATCACCTTGAGCTCCAAATGAGGCTCTCTCTTGTTCCCCATATACAAGTTCTAGAAATATGGTC	T	novel	NA	P-0033748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	65	601	0	ENST00000356341.3:c.1414-83_1422delinsA		p.X472_splice	ENST00000356341	NM_002576.4	472		14/15	1	2	FACETS	0.458	0.397	0.524	0.458	0.397	0.524	SUBCLONAL	1	TRUE	1	0.489047767756553	2		601	581	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261278	115261278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	354	558	0	ENST00000438362.2:c.2443C>T	p.Arg815Cys	p.R815C	ENST00000438362	NM_001242891.1	815	Cgc/Tgc	19/20	0.78257887606407	4	FACETS	0.968	0.922	1	0.968	0.922	1	CLONAL	2	TRUE	2	0.78257887606407	4		558	833	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-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6	90	58	0	ENST00000371953.3:c.1027-171_1092del		p.X343_splice	ENST00000371953	NM_000314.4	343		9/9	0.78257887606407	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.78257887606407	2		58	96	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316349	14316350	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0033767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	331	572	0	ENST00000256196.4:c.255_256delinsCT	p.Gly86Cys	p.G86C	ENST00000256196		85	acTGgc/acCTgc	3/6	0.660665250416983	4	FACETS	0.832	0.789	0.876	0.832	0.789	0.876	CLONAL	2	TRUE	2	0.78257887606407	4		572	906	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798103	32798105	+	frameshift_variant	Frame_Shift_Del	DEL	GTC	GTC	TT	novel	NA	P-0033767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	226	707	1	ENST00000374899.4:c.1574_1576delinsAA	p.Gly525GlufsTer36	p.G525Efs*36	ENST00000374899	NM_018833.2	525	gGACag/gAAag	9/12	0.732862800210479	4	FACETS	0.849	0.789	0.91	0.424	0.394	0.455	CLONAL	1	TRUE	2	0.78257887606407	4		708	1213	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681118	117681118	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	202	453	0	ENST00000368508.3:c.3502G>T	p.Asp1168Tyr	p.D1168Y	ENST00000368508	NM_002944.2	1168	Gat/Tat	23/43	0.78257887606407	3	FACETS	1	0.986	1	0.403	0.376	0.431	CLONAL	1	TRUE	0	0.78257887606407	3		453	594	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0033930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	71	294	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.145889779642592	4	FACETS	1	0.957	1	0.603	0.53	0.682	INDETERMINATE	1	TRUE	2	0.466249479109355	4		294	370	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584560	48584560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	16	504	0	ENST00000342988.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000342988	NM_005359.5	245	Cag/Tag	6/12	0.466249479109355	1	FACETS	0.166	0.122	0.219	0.166	0.122	0.219	SUBCLONAL	1	TRUE	0	0.466249479109355	1		504	317	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0033930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	168	649	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.466249479109355	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.466249479109355	1		649	387	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0033930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	116	265	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	0.256631128384317	3	FACETS	0.996	0.911	1	0.664	0.607	0.722	INDETERMINATE	2	TRUE	0	0.466249479109355	3		265	308	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0033930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	172	879	0	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	0.119650897077772	0	FACETS	0.583	0.538	0.629			1	INDETERMINATE	1	TRUE	0	0.466249479109355	0		879	676	SUCCESS
APC	324	MSKCC	GRCh37	5	112174086	112174086	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs878853432	NA	P-0033930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	58	394	0	ENST00000257430.4:c.2795C>G	p.Ser932Ter	p.S932*	ENST00000257430	NM_000038.5	932	tCa/tGa	16/16	0.145889779642592	4	FACETS	1	0.963	1	0.673	0.583	0.769	INDETERMINATE	1	TRUE	2	0.466249479109355	4		394	271	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129655	11129655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	117	605	1	ENST00000358026.2:c.2461G>A	p.Glu821Lys	p.E821K	ENST00000358026	NM_001128849.1	821	Gag/Aag	17/36	1	2	FACETS	0.901	0.815	0.991	0.901	0.815	0.991	CLONAL	1	TRUE	1	0.466249479109355	2		606	557	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453149	140453149	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913361	NA	P-0033930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	20	404	0	ENST00000288602.6:c.1786G>C	p.Gly596Arg	p.G596R	ENST00000288602	NM_004333.4	596	Ggt/Cgt	15/18	1	2	FACETS	0.21	0.16	0.269	0.21	0.16	0.269	SUBCLONAL	1	TRUE	1	0.466249479109355	2		404	408	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28595728	28595728	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769967309	NA	P-0033930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	123	685	0	ENST00000253063.3:c.125G>A	p.Arg42Gln	p.R42Q	ENST00000253063	NM_031459.4	42	cGa/cAa	2/10	0.326333899961462	4	FACETS	1	0.914	1	0.506	0.457	0.557	CLONAL	1	TRUE	2	0.466249479109355	4		685	765	SUCCESS
APC	324	MSKCC	GRCh37	5	112175907	112175907	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0033930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	39	288	0	ENST00000257430.4:c.4616C>G	p.Ser1539Ter	p.S1539*	ENST00000257430	NM_000038.5	1539	tCa/tGa	16/16	0.145889779642592	4	FACETS	0.767	0.645	0.897	0.767	0.645	0.897	INDETERMINATE	2	TRUE	2	0.466249479109355	4		288	160	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495465	56495465	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	165	664	0	ENST00000267101.3:c.3655G>A	p.Glu1219Lys	p.E1219K	ENST00000267101	NM_001982.3	1219	Gag/Aag	28/28	0.378286871756781	4	FACETS	1	0.988	1	0.71	0.653	0.769	CLONAL	1	TRUE	2	0.466249479109355	4		664	731	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032547	12032547	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	55	392	0	ENST00000353533.5:c.983T>A	p.Leu328Gln	p.L328Q	ENST00000353533	NM_003010.3	328	cTg/cAg	9/11	0.466249479109355	1	FACETS	0.754	0.652	0.863	0.754	0.652	0.863	SUBCLONAL	1	TRUE	0	0.466249479109355	1		392	240	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575080	48575080	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	82	488	0	ENST00000342988.3:c.274C>G	p.His92Asp	p.H92D	ENST00000342988	NM_005359.5	92	Cat/Gat	3/12	0.466249479109355	1	FACETS	0.674	0.598	0.755	0.674	0.598	0.755	SUBCLONAL	1	TRUE	0	0.466249479109355	1		488	400	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606137	47606137	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs878854493	NA	P-0033930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	41	566	0	ENST00000263735.4:c.601C>G	p.Gln201Glu	p.Q201E	ENST00000263735	NM_002354.2	201	Caa/Gaa	6/9	1	2	FACETS	0.324	0.269	0.385	0.324	0.269	0.385	SUBCLONAL	1	TRUE	1	0.466249479109355	2		566	543	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095721	178095721	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	148	558	0	ENST00000397062.3:c.1610A>C	p.Glu537Ala	p.E537A	ENST00000397062	NM_006164.4	537	gAa/gCa	5/5	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.466249479109355	2		558	565	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974804	21974805	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	24	138	0	ENST00000304494.5:c.22dup	p.Ser8LysfsTer7	p.S8Kfs*7	ENST00000304494	NM_000077.4	8	agc/aAgc	1/3	0.466249479109355	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.466249479109355	1		138	55	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137321007	137321007	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	104	646	0	ENST00000481739.1:c.964G>T	p.Asp322Tyr	p.D322Y	ENST00000481739	NM_002957.4	322	Gac/Tac	7/10	0.466249479109355	3	FACETS	0.993	0.892	1	0.496	0.446	0.55	CLONAL	1	TRUE	1	0.466249479109355	3		646	554	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0033993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	164	520	2	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.199044850573679	2	FACETS	0.826	0.757	0.897	0.826	0.757	0.897	CLONAL	2	TRUE	0	0.199044850573679	2		522	998	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610333	10610366	+	frameshift_variant	Frame_Shift_Del	DEL	TCAATGGACACCACCTCCATGCCCTGCTCCCGCA	TCAATGGACACCACCTCCATGCCCTGCTCCCGCA	-	novel	NA	P-0033993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	62	805	0	ENST00000171111.5:c.344_377del	p.Leu115ArgfsTer31	p.L115Rfs*31	ENST00000171111	NM_203500.1	115	cTGCGGGAGCAGGGCATGGAGGTGGTGTCCATTGAg/cg	2/6	1	2	FACETS	0.631	0.543	0.726	0.631	0.543	0.726	SUBCLONAL	1	TRUE	1	0.199044850573679	2		805	988	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213920	36213920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	45	689	0	ENST00000222270.7:c.2746G>A	p.Glu916Lys	p.E916K	ENST00000222270	NM_014727.1	916	Gag/Aag	6/37	1	2	FACETS	0.511	0.428	0.604	0.511	0.428	0.604	SUBCLONAL	1	TRUE	1	0.199044850573679	2		689	885	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033634	48033634	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	76	496	0	ENST00000234420.5:c.3845C>G	p.Thr1282Ser	p.T1282S	ENST00000234420	NM_000179.2	1282	aCt/aGt	9/10	0.199044850573679	3	FACETS	1	0.945	1	0.572	0.501	0.648	CLONAL	1	TRUE	1	0.199044850573679	3		496	734	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751251	128751251	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	46	343	0	ENST00000377970.2:c.788C>G	p.Thr263Ser	p.T263S	ENST00000377970	NM_002467.4	263	aCc/aGc	2/3	1	2	FACETS	0.936	0.788	1	0.936	0.788	1	CLONAL	1	TRUE	1	0.199044850573679	2		343	494	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	44	570	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.837	0.702	0.986	0.837	0.702	0.986	CLONAL	1	TRUE	1	0.210778295512589	2		570	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0034033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	84	663	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.210778295512589	1	FACETS	0.938	0.828	1	0.938	0.828	1	CLONAL	1	TRUE	0	0.210778295512589	1		664	760	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0034446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	989	652	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.883419696847609	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.885736098409296	3		652	1072	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869444	102869444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	178	341	0	ENST00000307046.8:c.197G>A	p.Cys66Tyr	p.C66Y	ENST00000307046	NM_001111285.1	66	tGt/tAt	2/4	1	2	FACETS	0.973	0.908	1	0.973	0.908	1	CLONAL	1	TRUE	1	0.885736098409296	2		341	413	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193519	99193519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	614	521	1	ENST00000074304.5:c.2714C>T	p.Ser905Leu	p.S905L	ENST00000074304	NM_001134224.1	905	tCg/tTg	25/26	0.881343677775084	2	FACETS	0.995	0.977	1	0.995	0.977	1	CLONAL	2	TRUE	0	0.885736098409296	2		522	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0034446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	334	688	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.0612608152649661	5	FACETS	1	0.976	1			1	INDETERMINATE	4	FALSE	NA	0.403685443109372	5		688	642	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197075	26197075	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	37	349	0	ENST00000356476.2:c.404G>T	p.Arg135Met	p.R135M	ENST00000356476		135	aGg/aTg	1/1	0.403685443109372	3	FACETS	0.344	0.283	0.413	0.115	0.094	0.138	SUBCLONAL	1	FALSE	0	0.403685443109372	3		349	640	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921512	39921512	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	181	319	0	ENST00000378444.4:c.4308C>A	p.Cys1436Ter	p.C1436*	ENST00000378444	NM_001123385.1	1436	tgC/tgA	10/15	1	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.596892237223519	1		319	408	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910686	32910686	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	69	572	0	ENST00000380152.3:c.2194G>T	p.Glu732Ter	p.E732*	ENST00000380152		732	Gag/Tag	11/27	1	2	FACETS	0.918	0.798	1	0.918	0.798	1	CLONAL	1	TRUE	1	0.2	2		572	752	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004633	150004633	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	82	729	0	ENST00000253339.5:c.1592del	p.Pro531LeufsTer10	p.P531Lfs*10	ENST00000253339		531	cCt/ct	3/7	1	2	FACETS	0.754	0.663	0.852	0.754	0.663	0.852	SUBCLONAL	1	TRUE	1	0.2	2		729	1088	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319920	8319920	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	81	509	0	ENST00000356435.5:c.5581T>A	p.Leu1861Met	p.L1861M	ENST00000356435		1861	Ttg/Atg	34/35	0.189944955782412	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.2	1		509	655	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033844	49033844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853294	NA	P-0034674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	141	367	0	ENST00000267163.4:c.1981C>T	p.Arg661Trp	p.R661W	ENST00000267163	NM_000321.2	661	Cgg/Tgg	20/27	0.604478763843576	1	FACETS	0.969	0.896	1	0.969	0.896	1	CLONAL	1	TRUE	0	0.604478763843576	1		367	336	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0034674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	87	276	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	0.316169398672874	6	FACETS	1	0.979	1	0.495	0.441	0.553	INDETERMINATE	1	TRUE	3	0.604478763843576	6		276	428	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432255	49432255	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	296	738	1	ENST00000301067.7:c.8884G>T	p.Glu2962Ter	p.E2962*	ENST00000301067	NM_003482.3	2962	Gag/Tag	34/54	0.604478763843576	3	FACETS	1	0.961	1	0.514	0.483	0.545	CLONAL	1	TRUE	1	0.604478763843576	3		739	1241	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007876	45007876	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0034674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	34	388	0	ENST00000558401.1:c.323C>G	p.Ser108Ter	p.S108*	ENST00000558401	NM_004048.2	108	tCa/tGa	2/4	0.604478763843576	1	FACETS	0.331	0.272	0.397	0.331	0.272	0.397	SUBCLONAL	1	TRUE	0	0.604478763843576	1		388	237	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829518	72829518	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	247	594	0	ENST00000268489.5:c.7063G>T	p.Glu2355Ter	p.E2355*	ENST00000268489	NM_006885.3	2355	Gag/Tag	9/10	0.604478763843576	3	FACETS	1	0.984	1	0.577	0.54	0.614	CLONAL	1	TRUE	1	0.604478763843576	3		594	923	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566487	41566487	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	38	336	0	ENST00000263253.7:c.4364A>T	p.Gln1455Leu	p.Q1455L	ENST00000263253	NM_001429.3	1455	cAg/cTg	27/31	0.604478763843576	2	FACETS	0.261	0.215	0.312	0.13	0.107	0.156	SUBCLONAL	1	TRUE	0	0.604478763843576	2		336	482	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709563	176709563	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs797045825	NA	P-0034674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	47	377	0	ENST00000439151.2:c.5990A>G	p.Tyr1997Cys	p.Y1997C	ENST00000439151	NM_022455.4	1997	tAt/tGt	19/23	0.604478763843576	3	FACETS	0.329	0.277	0.386	0.164	0.138	0.193	SUBCLONAL	1	TRUE	1	0.604478763843576	3		377	616	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120851	94120851	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	55	484	0	ENST00000369303.4:c.200C>G	p.Pro67Arg	p.P67R	ENST00000369303	NM_004440.3	67	cCg/cGg	3/17	0.604478763843576	3	FACETS	0.295	0.252	0.343	0.148	0.126	0.172	SUBCLONAL	1	TRUE	1	0.604478763843576	3		484	802	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164905	123164905	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	43	183	0	ENST00000218089.9:c.218A>C	p.His73Pro	p.H73P	ENST00000218089	NM_001042749.1	73	cAt/cCt	5/35	0.568403801702343	2	FACETS	0.418	0.351	0.492			1	SUBCLONAL	1	TRUE	NA	0.604478763843576	2		183	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0034731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	374	492	1	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.562610873587914	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.562610873587914	2		493	613	SUCCESS
APC	324	MSKCC	GRCh37	5	112175213	112175213	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0034731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	107	266	0	ENST00000257430.4:c.3922A>T	p.Lys1308Ter	p.K1308*	ENST00000257430	NM_000038.5	1308	Aaa/Taa	16/16	0.562610873587914	3	FACETS	0.934	0.866	0.999	0.934	0.866	0.999	CLONAL	3	TRUE	0	0.562610873587914	3		266	174	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443657	29443657	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	444	794	0	ENST00000389048.3:c.3560T>C	p.Leu1187Pro	p.L1187P	ENST00000389048	NM_004304.4	1187	cTg/cCg	23/29	0.562610873587914	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.562610873587914	3		794	918	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662128	227662128	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775603579	NA	P-0034731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	352	648	0	ENST00000305123.5:c.1327C>T	p.Arg443Cys	p.R443C	ENST00000305123	NM_005544.2	443	Cgc/Tgc	1/2	0.562610873587914	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.562610873587914	3		648	770	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812260	212812260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751175543	NA	P-0034770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	39	446	1	ENST00000342788.4:c.316C>T	p.Arg106Cys	p.R106C	ENST00000342788	NM_005235.2	106	Cgt/Tgt	3/28	1	2	FACETS	0.238	0.197	0.284	0.238	0.197	0.284	SUBCLONAL	1	TRUE	1	0.672286716487268	2		447	487	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0034770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	89	232	1	ENST00000257430.4:c.3919dup	p.Ile1307AsnfsTer8	p.I1307Nfs*8	ENST00000257430	NM_000038.5	1306	gaa/gAaa	16/16	1	2	FACETS	0.959	0.862	1	0.959	0.862	1	CLONAL	1	TRUE	1	0.672286716487268	2		233	276	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916946	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0034770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	185	459	0	ENST00000263967.3:c.332_334del	p.Lys111del	p.K111del	ENST00000263967	NM_006218.2	111	AAG/-	2/21	1	2	FACETS	0.962	0.894	1	0.962	0.894	1	CLONAL	1	TRUE	1	0.672286716487268	2		459	572	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0034770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	119	367	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.747	0.678	0.819	0.747	0.678	0.819	SUBCLONAL	1	TRUE	1	0.672286716487268	2		367	474	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0034770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	322	378	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.599901087061269	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.672286716487268	1		378	593	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41526008	41526008	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0034770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	65	460	0	ENST00000263253.7:c.1282+1G>A		p.X428_splice	ENST00000263253	NM_001429.3	428			0.43577555295582	1	FACETS	0.315	0.274	0.36	0.315	0.274	0.36	SUBCLONAL	1	TRUE	0	0.672286716487268	1		460	407	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942153	81942153	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	221	618	0	ENST00000359376.3:c.1690C>T	p.Arg564Trp	p.R564W	ENST00000359376	NM_002661.3	564	Cgg/Tgg	17/33	0.439453437090424	1	FACETS	0.885	0.833	0.938	0.885	0.833	0.938	CLONAL	1	TRUE	0	0.672286716487268	1		618	493	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845236	89845236	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775917892	NA	P-0034770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	100	617	0	ENST00000389301.3:c.1799G>A	p.Arg600His	p.R600H	ENST00000389301	NM_000135.2	600	cGt/cAt	20/43	0.439453437090424	1	FACETS	0.335	0.299	0.372	0.335	0.299	0.372	SUBCLONAL	1	TRUE	0	0.672286716487268	1		617	590	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673694	37673694	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	244	632	0	ENST00000447079.4:c.2848C>T	p.Arg950Ter	p.R950*	ENST00000447079	NM_015083.1	950	Cga/Tga	10/14	1	2	FACETS	0.958	0.898	1	0.958	0.898	1	CLONAL	1	TRUE	1	0.672286716487268	2		632	758	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059279	42059279	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	52	446	0	ENST00000219905.7:c.8999C>G	p.Ser3000Cys	p.S3000C	ENST00000219905	NM_001164273.1	3000	tCc/tGc	24/24	0.43577555295582	1	FACETS	0.262	0.223	0.304	0.262	0.223	0.304	SUBCLONAL	1	TRUE	0	0.672286716487268	1		446	392	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575209	48575209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767326	NA	P-0034900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	84	401	0	ENST00000342988.3:c.403C>T	p.Arg135Ter	p.R135*	ENST00000342988	NM_005359.5	135	Cga/Tga	3/12	0.695056554852361	1	FACETS	0.77	0.696	0.845	0.77	0.696	0.845	SUBCLONAL	1	TRUE	0	0.7198670051856	1		401	194	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372159	45372159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	105	471	0	ENST00000262160.6:c.1010G>A	p.Arg337His	p.R337H	ENST00000262160	NM_005901.5	337	cGc/cAc	9/11	0.7198670051856	3	FACETS	0.874	0.787	0.964	0.437	0.393	0.482	CLONAL	1	TRUE	1	0.7198670051856	3		471	454	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145494	24145561	+	protein_altering_variant	In_Frame_Del	DEL	TGACCCAGCTGTGATCCATGAGAACGCATCTCAGCCCGAGGTGCTGGTCCCCATCCGGCTGGACATGG	TGACCCAGCTGTGATCCATGAGAACGCATCTCAGCCCGAGGTGCTGGTCCCCATCCGGCTGGACATGG	CTTTC	novel	NA	P-0034900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	91	737	3	ENST00000263121.7:c.513_580delinsCTTTC	p.Asp172_Glu194delinsPheGln	p.D172_E194delinsFQ	ENST00000263121	NM_003073.3	171	caTGACCCAGCTGTGATCCATGAGAACGCATCTCAGCCCGAGGTGCTGGTCCCCATCCGGCTGGACATGGag/caCTTTCag	5/9	0.500773303819166	5	FACETS	0.606	0.537	0.679	0.202	0.179	0.227	SUBCLONAL	1	TRUE	2	0.7198670051856	5		740	868	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930153	68930153	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0034900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	80	346	0	ENST00000288368.4:c.213+1G>T		p.X71_splice	ENST00000288368	NM_024870.2	71			0.7198670051856	6	FACETS	0.772	0.68	0.872	0.257	0.226	0.291	SUBCLONAL	1	TRUE	3	0.7198670051856	6		346	702	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398827	398827	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0035075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	27	432	0	ENST00000380956.4:c.638-1G>T		p.X213_splice	ENST00000380956	NM_001195286.1	213			0.380343765490032	9	FACETS	0.853	0.684	1			1	CLONAL	2	TRUE	NA	0.380343765490032	9		432	194	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033949	49033949	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0035075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	25	379	0	ENST00000267163.4:c.2086A>T	p.Arg696Ter	p.R696*	ENST00000267163	NM_000321.2	696	Aga/Tga	20/27	0.387983147572595	3	FACETS	1	0.917	1	0.657	0.527	0.802	CLONAL	1	TRUE	1	0.380343765490032	3		379	119	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375274	118375274	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	27	398	0	ENST00000534358.1:c.8667T>G	p.Asn2889Lys	p.N2889K	ENST00000534358	NM_005933.3	2889	aaT/aaG	27/36	0.380582201737632	4	FACETS	0.951	0.774	1	0.951	0.774	1	CLONAL	2	TRUE	2	0.380343765490032	4		398	103	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687408	117687410	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0035075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	14	359	0	ENST00000368508.3:c.2641_2643del	p.Ser881del	p.S881del	ENST00000368508	NM_002944.2	881	TCT/-	18/43	0.387983147572595	0	FACETS	0.931	0.698	1			1	CLONAL	1	TRUE	0	0.380343765490032	0		359	49	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs1202793339	NA	P-0035119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	277	548	0	ENST00000269305.4:c.560-1G>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.596685073041184	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.863880978087227	1		548	334	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866098	37866098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs971655376	NA	P-0035119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	583	670	0	ENST00000269571.5:c.607C>T	p.Arg203Cys	p.R203C	ENST00000269571		203	Cgc/Tgc	5/27	0.167893963585259	3	FACETS	1	0.996	1	0.431	0.414	0.448	INDETERMINATE	1	TRUE	0	0.863880978087227	3		670	1495	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061113	38061185	+	frameshift_variant	Frame_Shift_Del	DEL	CTCAGGGCCGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCG	CTCAGGGCCGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCG	-	novel	NA	P-0035119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	434	110	1	ENST00000250448.2:c.804_876del	p.Cys268Ter	p.C268*	ENST00000250448	NM_004496.3	268	tgCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGCGGCGCCAAGGGCGGCCCTGAG/tg	2/2	0.466666334565476	3	FACETS	1	0.994	1	1	0.994	1	INDETERMINATE	2	TRUE	1	0.863880978087227	3		111	633	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81399235	81399249	+	inframe_deletion	In_Frame_Del	DEL	TGCAGGAGGACATGC	TGCAGGAGGACATGC	-	novel	NA	P-0035119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1206	193	596	0	ENST00000222390.5:c.39_53del	p.Gln13_Leu17del	p.Q13_L17del	ENST00000222390	NM_000601.4	13	caGCATGTCCTCCTGCAt/cat	1/18	0.466666334565476	3	FACETS	0.457	0.422	0.495	0.229	0.211	0.248	INDETERMINATE	1	TRUE	1	0.863880978087227	3		596	1399	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187288	38187288	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0035119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	90	744	0	ENST00000317025.8:c.1189A>T	p.Lys397Ter	p.K397*	ENST00000317025	NM_023034.1	397	Aaa/Taa	6/24	0.804820737433064	3	FACETS	0.471	0.418	0.528	0.236	0.209	0.264	SUBCLONAL	1	TRUE	1	0.863880978087227	3		744	633	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578433	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555526101	NA	P-0035123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	64	742	0	ENST00000269305.4:c.497C>G	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	166	tCa/tGa	5/11	0.191331979822318	3	FACETS	0.879	0.764	1	0.879	0.764	1	CLONAL	2	FALSE	1	0.191331979822318	3		742	417	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111498	8111499	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	88	575	0	ENST00000346208.3:c.985dup	p.Arg329LysfsTer23	p.R329Kfs*23	ENST00000346208		328	-/A	5/6	0.161662592518016	1	FACETS	0.914	0.814	1	1	0.984	1	CLONAL	2	FALSE	0	0.191331979822318	1		575	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0035205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	409	615	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	NA	2	FACETS	0.917	0.881	0.952			1	INDETERMINATE	2	TRUE	NA	0.61882579539031	2		615	721	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134228	2134228	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1085307853	NA	P-0035205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	116	497	0	ENST00000219476.3:c.4006-1G>A		p.X1336_splice	ENST00000219476	NM_000548.3	1336			0.607719247310383	1	FACETS	0.852	0.779	0.926	0.852	0.779	0.926	CLONAL	1	TRUE	0	0.61882579539031	1		497	304	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667851	37667851	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	333	421	0	ENST00000447079.4:c.2737del	p.Tyr913ThrfsTer5	p.Y913Tfs*5	ENST00000447079	NM_015083.1	912	cgT/cg	8/14	0.61882579539031	2	FACETS	0.951	0.911	0.99	0.951	0.911	0.99	CLONAL	2	TRUE	0	0.61882579539031	2		421	566	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937690	76937690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	136	535	0	ENST00000373344.5:c.3058C>T	p.Pro1020Ser	p.P1020S	ENST00000373344	NM_000489.3	1020	Cct/Tct	9/35	1	2	FACETS	0.674	0.614	0.737	0.674	0.614	0.737	SUBCLONAL	1	TRUE	1	0.61882579539031	2		535	652	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0035217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	73	303	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.348574862591266	1	FACETS	0.399	0.352	0.447	0.399	0.352	0.447	INDETERMINATE	1	TRUE	0	0.801289651168644	1		303	274	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0035217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	253	525	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.738292109894415	1	FACETS	0.916	0.873	0.959	0.916	0.873	0.959	CLONAL	1	TRUE	0	0.801289651168644	1		525	413	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0035217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	84	247	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.738292109894415	1	FACETS	0.8	0.73	0.871	0.8	0.73	0.871	SUBCLONAL	1	TRUE	0	0.801289651168644	1		247	157	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057627	180057627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756234174	NA	P-0035217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	272	707	0	ENST00000261937.6:c.328G>A	p.Val110Ile	p.V110I	ENST00000261937	NM_182925.4	110	Gtc/Atc	3/30	0.738292109894415	1	FACETS	0.902	0.861	0.943	0.902	0.861	0.943	CLONAL	1	TRUE	0	0.801289651168644	1		707	451	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711993	89711993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	140	275	0	ENST00000371953.3:c.611C>T	p.Pro204Leu	p.P204L	ENST00000371953	NM_000314.4	204	cCa/cTa	6/9	0.738292109894415	1	FACETS	0.919	0.861	0.975	0.919	0.861	0.975	CLONAL	1	TRUE	0	0.801289651168644	1		275	228	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336253	73336253	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	39	147	0	ENST00000377767.4:c.2150C>A	p.Thr717Lys	p.T717K	ENST00000377767	NM_014953.3	717	aCa/aAa	17/21	0.384391878689195	5	FACETS	0.729	0.607	0.864	0.146	0.121	0.173	INDETERMINATE	1	TRUE	0	0.801289651168644	5		147	294	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989562	212989562	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs755026855	NA	P-0035217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	56	253	0	ENST00000342788.4:c.149G>T	p.Arg50Leu	p.R50L	ENST00000342788	NM_005235.2	50	cGc/cTc	2/28	0.348574862591266	1	FACETS	0.33	0.285	0.378	0.33	0.285	0.378	INDETERMINATE	1	TRUE	0	0.801289651168644	1		253	254	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944557	40944557	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	140	351	0	ENST00000373198.4:c.1945C>A	p.Pro649Thr	p.P649T	ENST00000373198	NM_133170.3	649	Ccc/Acc	12/32	1	2	FACETS	0.917	0.845	0.991	0.917	0.845	0.991	CLONAL	1	TRUE	1	0.801289651168644	2		351	381	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56912090	56912090	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	644	498	0	ENST00000519728.1:c.1320del	p.Ile442PhefsTer11	p.I442Ffs*11	ENST00000519728	NM_002350.3	440	Ggg/gg	12/13	0.801289651168644	3	FACETS	0.856	0.834	0.876	0.856	0.834	0.876	CLONAL	3	TRUE	0	0.801289651168644	3		498	877	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0035484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	305	422	2	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.410744731774639	3	FACETS	0.9	0.855	0.945	0.9	0.855	0.945	CLONAL	3	TRUE	0	0.410744731774639	3		424	663	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0035484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	240	787	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.348872182675473	2	FACETS	0.764	0.716	0.813	0.764	0.716	0.813	SUBCLONAL	2	TRUE	0	0.410744731774639	2		787	765	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890105	76890105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	271	618	0	ENST00000373344.5:c.4789G>A	p.Gly1597Ser	p.G1597S	ENST00000373344	NM_000489.3	1597	Ggc/Agc	17/35	0.410744731774639	3	FACETS	0.93	0.875	0.986	0.62	0.583	0.658	CLONAL	2	TRUE	0	0.410744731774639	3		618	855	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44921918	44921918	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	200	576	1	ENST00000377967.4:c.1452A>T	p.Arg484Ser	p.R484S	ENST00000377967	NM_021140.2	484	agA/agT	15/29	NA	2	FACETS	0.798	0.744	0.854			1	INDETERMINATE	2	TRUE	NA	0.410744731774639	2		577	610	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572516	64572516	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	143	568	1	ENST00000312049.6:c.1340T>C	p.Phe447Ser	p.F447S	ENST00000312049	NM_130799.2	447	tTt/tCt	9/10	0.554589231303633	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.554589231303633	1		569	304	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218021	108218021	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	153	325	0	ENST00000278616.4:c.8600G>A	p.Gly2867Glu	p.G2867E	ENST00000278616	NM_000051.3	2867	gGa/gAa	59/63	0.554589231303633	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.554589231303633	1		325	365	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741882	162741882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1558078519	NA	P-0035530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	63	381	0	ENST00000367921.3:c.1573G>A	p.Asp525Asn	p.D525N	ENST00000367921	NM_006182.2	525	Gac/Aac	13/18	0.18095870943109	4	FACETS	1	0.899	1	0.522	0.452	0.598	INDETERMINATE	1	TRUE	2	0.318804418708084	4		381	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579477	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGGGA	GGGGGGA	-	novel	NA	P-0035530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	185	765	1	ENST00000269305.4:c.210_216del	p.Pro71TrpfsTer50	p.P71Wfs*50	ENST00000269305	NM_001126112.2	70	gcTCCCCCC/gc	4/11	0.246135334915617	2	FACETS	0.907	0.841	0.974	0.907	0.841	0.974	CLONAL	2	TRUE	0	0.318804418708084	2		766	640	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561229	9561229	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749532063	NA	P-0035530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	43	541	0	ENST00000353224.5:c.553G>A	p.Val185Met	p.V185M	ENST00000353224	NM_177990.2	185	Gtg/Atg	4/10	0.18095870943109	4	FACETS	0.586	0.49	0.693	0.293	0.245	0.347	INDETERMINATE	1	TRUE	2	0.318804418708084	4		541	607	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670230	134670230	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	53	340	0	ENST00000398015.3:c.141del	p.Tyr48ThrfsTer5	p.Y48Tfs*5	ENST00000398015	NM_004441.4	47	ggC/gg	3/16	0.318804418708084	3	FACETS	0.768	0.655	0.891	0.384	0.327	0.446	SUBCLONAL	1	TRUE	1	0.318804418708084	3		340	502	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371616	55371616	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0035530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	137	555	2	ENST00000297316.4:c.308-2A>G		p.X103_splice	ENST00000297316	NM_022454.3	103			0.315936945791885	4	FACETS	0.869	0.793	0.949	0.869	0.793	0.949	CLONAL	2	TRUE	2	0.318804418708084	4		557	652	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0035563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	216	528	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.343399844707551	1	FACETS	0.718	0.672	0.764	0.718	0.672	0.764	INDETERMINATE	1	TRUE	0	0.682445711729541	1		528	581	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0035563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	548	723	1	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	0.682445711729541	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.682445711729541	1		724	899	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14317382	14317382	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	213	407	0	ENST00000256196.4:c.128A>G	p.Tyr43Cys	p.Y43C	ENST00000256196		43	tAt/tGt	2/6	1	2	FACETS	0.921	0.859	0.983	0.921	0.859	0.983	CLONAL	1	TRUE	1	0.682445711729541	2		407	678	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560475	95560475	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	196	410	0	ENST00000393063.1:c.5114A>T	p.Glu1705Val	p.E1705V	ENST00000393063	NM_030621.3	1705	gAa/gTa	25/28	1	2	FACETS	0.868	0.807	0.93	0.868	0.807	0.93	CLONAL	1	TRUE	1	0.682445711729541	2		410	662	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591122	67591136	+	inframe_deletion	In_Frame_Del	DEL	AGCTGAGAAAGACGA	AGCTGAGAAAGACGA	-	novel	NA	P-0035563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	127	233	0	ENST00000274335.5:c.1715_1729del	p.Gln572_Thr576del	p.Q572_T576del	ENST00000274335		572	cAGCTGAGAAAGACGAga/cga	12/15	1	2	FACETS	0.874	0.798	0.952	0.874	0.798	0.952	CLONAL	1	TRUE	1	0.682445711729541	2		233	426	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288512	33288512	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0035563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	197	364	0	ENST00000374542.5:c.1039+1G>A		p.X347_splice	ENST00000374542	NM_001141970.1	347			0.682445711729541	3	FACETS	0.973	0.903	1			1	CLONAL	1	TRUE	NA	0.682445711729541	3		364	796	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274121	10274121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	95	642	0	ENST00000330684.3:c.148G>A	p.Glu50Lys	p.E50K	ENST00000330684	NM_001134407.1	50	Gaa/Aaa	2/13	1	2	FACETS	0.972	0.867	1	0.972	0.867	1	CLONAL	1	TRUE	1	0.31523060969396	2		642	620	SUCCESS
AR	367	MSKCC	GRCh37	X	66863125	66863125	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139524801	NA	P-0035625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	30	343	0	ENST00000374690.3:c.1644G>T	p.Leu548Phe	p.L548F	ENST00000374690	NM_000044.3	548	ttG/ttT	2/8	1	1	FACETS	0.474	0.383	0.578	0.474	0.383	0.578	SUBCLONAL	1	TRUE	0	0.31523060969396	1		343	338	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153469	108153469	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0035625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	178	611	0	ENST00000278616.4:c.3609T>A	p.Tyr1203Ter	p.Y1203*	ENST00000278616	NM_000051.3	1203	taT/taA	25/63	0.309580492272624	2	FACETS	0.911	0.843	0.98	0.911	0.843	0.98	CLONAL	2	TRUE	0	0.31523060969396	2		611	620	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973179	25973179	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	101	521	0	ENST00000435504.4:c.1246G>T	p.Glu416Ter	p.E416*	ENST00000435504		416	Gag/Tag	12/13	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.31523060969396	2		521	596	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518148	8518148	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	72	529	0	ENST00000356435.5:c.1243C>A	p.Gln415Lys	p.Q415K	ENST00000356435		415	Caa/Aaa	10/35	1	2	FACETS	0.86	0.753	0.976	0.86	0.753	0.976	CLONAL	1	TRUE	1	0.31523060969396	2		529	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587781702	NA	P-0035712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	349	576	0	ENST00000269305.4:c.920-1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.75066436218037	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.75066436218037	1		576	572	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	208	607	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	TRUE	1	0.379440594152219	2		613	451	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	150	468	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.379440594152219	2		472	693	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	253	665	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.379440594152219	2	FACETS	0.877	0.83	0.923	1	0.992	1	CLONAL	3	TRUE	0	0.379440594152219	2		665	507	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	222	336	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.379440594152219	2		336	940	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	131	566	1	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.991	0.901	1	0.991	0.901	1	CLONAL	1	TRUE	1	0.379440594152219	2		567	697	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	218	765	7	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.379440594152219	2		772	880	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	222	1022	0	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.379440594152219	2		1022	871	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852118	63852118	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	43	603	1	ENST00000279873.7:c.2901del	p.Lys967AsnfsTer15	p.K967Nfs*15	ENST00000279873	NM_032199.2	966	Aaa/aa	10/10	1	2	FACETS	0.36	0.3	0.426	0.36	0.3	0.426	SUBCLONAL	1	TRUE	1	0.379440594152219	2		604	630	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716032	243716032	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	109	643	0	ENST00000263826.5:c.1162C>T	p.Arg388Cys	p.R388C	ENST00000263826	NM_005465.4	388	Cgc/Tgc	10/13	1	2	FACETS	0.659	0.591	0.731	0.659	0.591	0.731	SUBCLONAL	1	TRUE	1	0.379440594152219	2		643	872	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	65	563	6	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	0.464	0.401	0.531	0.464	0.401	0.531	SUBCLONAL	1	TRUE	1	0.379440594152219	2		569	739	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178095	56178095	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374455781	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	114	393	0	ENST00000399503.3:c.3068G>A	p.Arg1023His	p.R1023H	ENST00000399503	NM_005921.1	1023	cGc/cAc	14/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.379440594152219	2		393	492	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099579	157099579	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1562376341	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	29	167	0	ENST00000346085.5:c.521del	p.Pro174ArgfsTer6	p.P174Rfs*6	ENST00000346085	NM_020732.3	172	gaC/ga	1/20	0.0824428162016451	3	FACETS	1	0.835	1	0.517	0.419	0.626	INDETERMINATE	1	TRUE	1	0.379440594152219	3		167	176	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106162524	106162524	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	119	351	1	ENST00000380013.4:c.3442del	p.Tyr1148IlefsTer4	p.Y1148Ifs*4	ENST00000380013	NM_001127208.2	1146	ccT/cc	4/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.379440594152219	2		352	519	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029445	16029446	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	218	520	6	ENST00000268712.3:c.1584dup	p.Glu529ArgfsTer7	p.E529Rfs*7	ENST00000268712	NM_006311.3	528	-/A	15/46	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.379440594152219	2		526	933	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120031	70120031	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	15	85	0	ENST00000245479.2:c.1037del	p.Pro346ArgfsTer37	p.P346Rfs*37	ENST00000245479	NM_000346.3	345	Ccc/cc	3/3	1	2	FACETS	0.941	0.701	1	0.941	0.701	1	CLONAL	1	TRUE	1	0.379440594152219	2		85	84	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202909	16202909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs975826717	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	164	629	0	ENST00000375759.3:c.617G>A	p.Arg206His	p.R206H	ENST00000375759	NM_015001.2	206	cGc/cAc	3/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.379440594152219	2		629	708	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840049	27840049	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	136	549	0	ENST00000328488.2:c.45A>T	p.Lys15Asn	p.K15N	ENST00000328488	NM_003533.2	15	aaA/aaT	1/1	0.1543560787635	6	FACETS	1	0.964	1	0.736	0.672	0.803	INDETERMINATE	2	TRUE	3	0.379440594152219	6		549	571	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094309	193094309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748952219	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	149	654	1	ENST00000367435.3:c.199G>A	p.Val67Met	p.V67M	ENST00000367435	NM_024529.4	67	Gtg/Atg	2/17	1	2	FACETS	0.871	0.795	0.95	0.871	0.795	0.95	CLONAL	1	TRUE	1	0.379440594152219	2		655	902	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050708	30050708	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	113	449	0	ENST00000338641.4:c.514del	p.Arg172GlyfsTer2	p.R172Gfs*2	ENST00000338641	NM_000268.3	170	ccA/cc	5/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.379440594152219	2		449	514	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257899	19257899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374422850	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	174	1038	4	ENST00000162023.5:c.487G>A	p.Ala163Thr	p.A163T	ENST00000162023		163	Gcc/Acc	9/13	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.379440594152219	2		1042	759	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324892	31324892	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs765875917	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	55	397	0	ENST00000412585.2:c.44del	p.Ala15GlyfsTer5	p.A15Gfs*5	ENST00000412585	NM_005514.6	15	gCg/gg	1/8	0.0824428162016451	3	FACETS	0.711	0.609	0.823	0.356	0.304	0.412	INDETERMINATE	1	TRUE	1	0.379440594152219	3		397	485	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998127	169998128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs753143066	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	218	854	7	ENST00000295797.4:c.826dup	p.Thr276AsnfsTer16	p.T276Nfs*16	ENST00000295797	NM_002740.5	273	tta/ttAa	9/18	1	2	FACETS	0.975	0.905	1	0.975	0.905	1	CLONAL	1	TRUE	1	0.379440594152219	2		861	1179	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	205	819	1	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	0.25735828650801	3	FACETS	1	0.981	1	0.585	0.542	0.63	CLONAL	1	TRUE	1	0.379440594152219	3		820	1098	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30099946	30099946	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs758403249	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	84	512	0	ENST00000331968.5:c.1672+2T>C		p.X558_splice	ENST00000331968	NM_002742.2	558			1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.379440594152219	2		512	438	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	129	981	2	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.958	0.87	1	0.958	0.87	1	CLONAL	1	TRUE	1	0.379440594152219	2		983	710	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779419	3779419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370389591	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	164	1069	2	ENST00000262367.5:c.5629G>A	p.Val1877Met	p.V1877M	ENST00000262367	NM_004380.2	1877	Gtg/Atg	31/31	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.379440594152219	2		1071	675	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	121	447	1	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.379440594152219	2		448	578	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38631981	38631981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1255149646	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	76	790	1	ENST00000299084.4:c.471del	p.Gln158SerfsTer16	p.Q158Sfs*16	ENST00000299084	NM_152594.2	156	cTt/ct	5/7	1	2	FACETS	0.366	0.32	0.416	0.366	0.32	0.416	SUBCLONAL	1	TRUE	1	0.379440594152219	2		791	1095	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933438	49933438	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	139	853	1	ENST00000296474.3:c.2752del	p.Leu918CysfsTer18	p.L918Cfs*18	ENST00000296474	NM_002447.2	918	Ctg/tg	11/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.379440594152219	2		854	541	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286238	66286238	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	162	623	0	ENST00000273854.3:c.1448del	p.Asn483ThrfsTer18	p.N483Tfs*18	ENST00000273854	NM_004439.5	483	aAc/ac	6/18	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.379440594152219	2		623	830	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007681	45007681	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	180	565	1	ENST00000558401.1:c.128T>C	p.Leu43Pro	p.L43P	ENST00000558401	NM_004048.2	43	cTg/cCg	2/4	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.379440594152219	2		566	764	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445149	49445149	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	175	873	4	ENST00000301067.7:c.2317del	p.Gln773SerfsTer157	p.Q773Sfs*157	ENST00000301067	NM_003482.3	773	Cag/ag	10/54	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.379440594152219	2		877	764	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978662	70978662	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	138	915	0	ENST00000276594.2:c.991G>A	p.Ala331Thr	p.A331T	ENST00000276594	NM_024504.3	331	Gcc/Acc	5/8	1	2	FACETS	0.935	0.851	1	0.935	0.851	1	CLONAL	1	TRUE	1	0.379440594152219	2		915	778	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983136	149983136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	245	853	1	ENST00000253339.5:c.3122C>T	p.Pro1041Leu	p.P1041L	ENST00000253339		1041	cCt/cTt	7/7	0.0824428162016451	3	FACETS	0.762	0.712	0.813	0.762	0.712	0.813	INDETERMINATE	2	TRUE	1	0.379440594152219	3		854	1008	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864218	57864218	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	124	678	0	ENST00000228682.2:c.1700del	p.Pro567LeufsTer46	p.P567Lfs*46	ENST00000228682	NM_005269.2	565	ttC/tt	12/12	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.379440594152219	2		678	509	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151315	202151315	+	stop_lost	Nonstop_Mutation	SNP	T	T	C	rs761997594	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	106	491	0	ENST00000358485.4:c.1615T>C	p.Ter539ArgextTer88	p.*539Rext*88	ENST00000358485	NM_001080125.1	539	Tga/Cga	9/9	1	2	FACETS	0.95	0.854	1	0.95	0.854	1	CLONAL	1	TRUE	1	0.379440594152219	2		491	588	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026115	71026115	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs797045584	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	199	569	0	ENST00000318789.4:c.1507C>T	p.Arg503Ter	p.R503*	ENST00000318789	NM_032682.5	503	Cga/Tga	17/21	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.379440594152219	2		569	795	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793888	89793888	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	149	433	0	ENST00000336032.3:c.961del	p.Thr321ArgfsTer16	p.T321Rfs*16	ENST00000336032	NM_006813.2	319	ttA/tt	2/2	0.0824428162016451	3	FACETS	1	0.985	1	0.684	0.626	0.744	INDETERMINATE	1	TRUE	1	0.379440594152219	3		433	683	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821889	72821890	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	82	400	1	ENST00000268489.5:c.10285dup	p.Arg3429ProfsTer2	p.R3429Pfs*2	ENST00000268489	NM_006885.3	3429	cgt/cCgt	10/10	1	2	FACETS	0.859	0.76	0.965	0.859	0.76	0.965	CLONAL	1	TRUE	1	0.379440594152219	2		401	503	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225480	26225480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	90	409	0	ENST00000360408.1:c.98C>T	p.Thr33Met	p.T33M	ENST00000360408	NM_003532.2	33	aCg/aTg	1/1	0.1543560787635	6	FACETS	0.917	0.817	1	0.611	0.545	0.682	INDETERMINATE	2	TRUE	3	0.379440594152219	6		409	455	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532613	63532613	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121908568	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	201	964	0	ENST00000307078.5:c.1966C>T	p.Arg656Ter	p.R656*	ENST00000307078	NM_004655.3	656	Cga/Tga	8/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.379440594152219	2		964	794	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621901	1621901	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	137	890	0	ENST00000344749.5:c.891del	p.Gly298GlufsTer96	p.G298Efs*96	ENST00000344749	NM_001136139.2	297	ccC/cc	11/19	0.379440594152219	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.379440594152219	1		890	558	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174884	11174884	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	175	677	0	ENST00000361445.4:c.7150A>G	p.Thr2384Ala	p.T2384A	ENST00000361445	NM_004958.3	2384	Acc/Gcc	52/58	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.379440594152219	2		677	777	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023462	27023462	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	158	688	2	ENST00000324856.7:c.572del	p.Gly191AlafsTer41	p.G191Afs*41	ENST00000324856	NM_006015.4	190	Ggg/gg	1/20	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.379440594152219	2		690	816	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845453	156845453	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	142	979	0	ENST00000524377.1:c.1496A>G	p.Asp499Gly	p.D499G	ENST00000524377	NM_002529.3	499	gAt/gGt	12/17	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.379440594152219	2		979	745	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318827	163318827	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	149	452	0	ENST00000271452.3:c.1217A>G	p.Gln406Arg	p.Q406R	ENST00000271452	NM_145697.2	406	cAa/cGa	13/14	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.379440594152219	2		452	703	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70412348	70412348	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	81	323	0	ENST00000373644.4:c.4458G>C	p.Lys1486Asn	p.K1486N	ENST00000373644	NM_030625.2	1486	aaG/aaC	6/12	1	2	FACETS	0.984	0.871	1	0.984	0.871	1	CLONAL	1	TRUE	1	0.379440594152219	2		323	434	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417817	32417817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1440971275	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	128	518	0	ENST00000332351.3:c.1235G>A	p.Ser412Asn	p.S412N	ENST00000332351	NM_024426.4	412	aGc/aAc	7/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.379440594152219	2		518	573	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347134	347134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200996293	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	188	1140	3	ENST00000262320.3:c.1877C>T	p.Ala626Val	p.A626V	ENST00000262320	NM_003502.3	626	gCg/gTg	7/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.379440594152219	2		1143	808	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396838	396838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759464398	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	50	772	1	ENST00000262320.3:c.188G>A	p.Arg63His	p.R63H	ENST00000262320	NM_003502.3	63	cGc/cAc	2/11	1	2	FACETS	0.436	0.37	0.51	0.436	0.37	0.51	SUBCLONAL	1	TRUE	1	0.379440594152219	2		773	604	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647828	3647828	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	135	958	2	ENST00000294008.3:c.1336G>A	p.Ala446Thr	p.A446T	ENST00000294008	NM_032444.2	446	Gcc/Acc	6/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.379440594152219	2		960	635	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670697	67670697	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749826586	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	118	520	0	ENST00000264010.4:c.1942G>A	p.Ala648Thr	p.A648T	ENST00000264010	NM_006565.3	648	Gcc/Acc	11/12	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.379440594152219	2		520	476	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856089	68856089	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	141	704	0	ENST00000261769.5:c.1900del	p.Ala634ArgfsTer19	p.A634Rfs*19	ENST00000261769	NM_004360.3	633	Ggg/gg	12/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.379440594152219	2		704	672	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831848	72831848	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	84	1162	1	ENST00000268489.5:c.4733A>G	p.Gln1578Arg	p.Q1578R	ENST00000268489	NM_006885.3	1578	cAa/cGa	9/10	1	2	FACETS	0.427	0.375	0.482	0.427	0.375	0.482	SUBCLONAL	1	TRUE	1	0.379440594152219	2		1163	1038	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990690	7990690	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs201575829	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	205	821	0	ENST00000319144.4:c.71T>C	p.Leu24Pro	p.L24P	ENST00000319144	NM_001139.2	24	cTg/cCg	1/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.379440594152219	2		821	842	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961331	15961331	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	210	712	0	ENST00000268712.3:c.6058C>T	p.Gln2020Ter	p.Q2020*	ENST00000268712	NM_006311.3	2020	Cag/Tag	39/46	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.379440594152219	2		712	900	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995271	15995271	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	84	695	0	ENST00000268712.3:c.2922G>T	p.Glu974Asp	p.E974D	ENST00000268712	NM_006311.3	974	gaG/gaT	22/46	1	2	FACETS	0.481	0.424	0.542	0.481	0.424	0.542	SUBCLONAL	1	TRUE	1	0.379440594152219	2		695	921	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552242	29552242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757512142	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	224	656	0	ENST00000356175.3:c.1975C>T	p.Arg659Trp	p.R659W	ENST00000356175	NM_000267.3	659	Cgg/Tgg	17/57	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.379440594152219	2		656	949	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63553964	63553964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	156	539	0	ENST00000307078.5:c.775G>A	p.Ala259Thr	p.A259T	ENST00000307078	NM_004655.3	259	Gcg/Acg	2/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.379440594152219	2		539	590	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39620649	39620649	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs750956513	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	186	563	0	ENST00000262039.4:c.2047C>T	p.Gln683Ter	p.Q683*	ENST00000262039	NM_002647.2	683	Cag/Tag	19/25	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.379440594152219	2		563	886	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2214480	2214480	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1285640382	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	43	729	3	ENST00000398665.3:c.1808G>A	p.Arg603His	p.R603H	ENST00000398665	NM_032482.2	603	cGc/cAc	19/28	0.379440594152219	1	FACETS	0.293	0.244	0.347	0.293	0.244	0.347	SUBCLONAL	1	TRUE	0	0.379440594152219	1		732	627	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152036	11152038	+	inframe_deletion	In_Frame_Del	DEL	ATC	ATC	-	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	81	531	0	ENST00000358026.2:c.4324_4326del	p.Ser1442del	p.S1442del	ENST00000358026	NM_001128849.1	1440	aaATCa/aaa	31/36	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.379440594152219	2		531	372	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143219	30143219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	48	758	0	ENST00000389048.3:c.307G>A	p.Gly103Arg	p.G103R	ENST00000389048	NM_004304.4	103	Ggg/Agg	1/29	1	2	FACETS	0.529	0.448	0.619	0.529	0.448	0.619	SUBCLONAL	1	TRUE	1	0.379440594152219	2		758	478	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702208	47702208	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs748797209	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	174	626	0	ENST00000233146.2:c.1804C>G	p.Leu602Val	p.L602V	ENST00000233146	NM_000251.2	602	Cta/Gta	12/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.379440594152219	2		626	794	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131424	202131424	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs746965223	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	153	608	0	ENST00000358485.4:c.392T>C	p.Leu131Pro	p.L131P	ENST00000358485	NM_001080125.1	131	cTg/cCg	2/9	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.379440594152219	2		608	714	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225343002	225343002	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1221	95	886	0	ENST00000264414.4:c.2090A>T	p.Asp697Val	p.D697V	ENST00000264414	NM_003590.4	697	gAc/gTc	15/16	1	2	FACETS	0.38	0.337	0.427	0.38	0.337	0.427	SUBCLONAL	1	TRUE	1	0.379440594152219	2		886	1316	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37059035	37059036	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	329	574	0	ENST00000231790.2:c.832dup	p.Thr278AsnfsTer29	p.T278Nfs*29	ENST00000231790	NM_000249.3	277	gaa/gAaa	10/19	0.379440594152219	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.379440594152219	2		574	710	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268763	41268763	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	221	588	0	ENST00000349496.5:c.1005del	p.Lys335AsnfsTer10	p.K335Nfs*10	ENST00000349496	NM_001904.3	334	gAa/ga	7/15	0.379440594152219	2	FACETS	1	0.992	1	0.734	0.685	0.785	CLONAL	1	TRUE	0	0.379440594152219	2		588	793	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933508	49933509	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	190	1155	0	ENST00000296474.3:c.2681_2682del	p.Val894GlyfsTer9	p.V894Gfs*9	ENST00000296474	NM_002447.2	894	gTG/g	11/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.379440594152219	2		1155	857	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916660	178916660	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	144	446	0	ENST00000263967.3:c.47T>C	p.Met16Thr	p.M16T	ENST00000263967	NM_006218.2	16	aTg/aCg	2/21	1	2	FACETS	0.756	0.694	0.82	1	0.988	1	SUBCLONAL	2	TRUE	1	0.379440594152219	2		446	502	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964878	55964878	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1139774	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	96	438	0	ENST00000263923.4:c.2359C>T	p.Arg787Trp	p.R787W	ENST00000263923	NM_002253.2	787	Cgg/Tgg	16/30	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.379440594152219	2		438	467	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84390219	84390219	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	195	611	0	ENST00000321945.7:c.562T>A	p.Ser188Thr	p.S188T	ENST00000321945	NM_139076.2	188	Tcc/Acc	6/9	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.379440594152219	2		611	749	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629490	187629490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200350035	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	281	838	1	ENST00000441802.2:c.1492G>A	p.Val498Met	p.V498M	ENST00000441802	NM_005245.3	498	Gtg/Atg	2/27	1	2	FACETS	0.763	0.718	0.809	1	0.994	1	SUBCLONAL	2	TRUE	1	0.379440594152219	2		839	971	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79968633	79968633	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201336852	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	169	560	1	ENST00000265081.6:c.983G>A	p.Arg328Gln	p.R328Q	ENST00000265081	NM_002439.4	328	cGg/cAg	6/24	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.379440594152219	2		561	871	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109311961	109311961	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	187	783	0	ENST00000436639.2:c.1311del	p.Lys437AsnfsTer38	p.K437Nfs*38	ENST00000436639	NM_014454.2	437	aaA/aa	8/10	0.0824428162016451	3	FACETS	1	0.988	1	0.671	0.62	0.724	INDETERMINATE	1	TRUE	1	0.379440594152219	3		783	874	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005399	150005399	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1045863115	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	70	780	0	ENST00000253339.5:c.826C>T	p.Arg276Cys	p.R276C	ENST00000253339		276	Cgc/Tgc	3/7	0.0824428162016451	3	FACETS	0.531	0.462	0.606	0.265	0.231	0.303	INDETERMINATE	1	TRUE	1	0.379440594152219	3		780	827	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522481	157522481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	170	874	0	ENST00000346085.5:c.4753C>T	p.Pro1585Ser	p.P1585S	ENST00000346085	NM_020732.3	1585	Ccc/Tcc	18/20	0.0824428162016451	3	FACETS	1	0.988	1	0.703	0.648	0.761	INDETERMINATE	1	TRUE	1	0.379440594152219	3		874	758	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877042	151877042	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	34	519	0	ENST00000262189.6:c.7319C>A	p.Pro2440His	p.P2440H	ENST00000262189	NM_170606.2	2440	cCt/cAt	37/59	0.25735828650801	3	FACETS	0.347	0.283	0.42	0.174	0.141	0.21	SUBCLONAL	1	TRUE	1	0.379440594152219	3		519	614	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877794	151877794	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	104	372	0	ENST00000262189.6:c.7149+2T>C		p.X2383_splice	ENST00000262189	NM_170606.2	2383			0.25735828650801	3	FACETS	1	0.978	1	0.67	0.602	0.74	CLONAL	1	TRUE	1	0.379440594152219	3		372	487	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412427	63412427	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	32	588	0	ENST00000330258.3:c.740C>A	p.Pro247Gln	p.P247Q	ENST00000330258	NM_152424.3	247	cCa/cAa	2/2	NA	2	FACETS	0.331	0.268	0.403			1	INDETERMINATE	1	TRUE	NA	0.379440594152219	2		588	509	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061218	38061235	+	inframe_deletion	In_Frame_Del	DEL	GCCGTTCTCGAACATGTT	GCCGTTCTCGAACATGTT	-	novel	NA	P-0035807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	315	551	0	ENST00000250448.2:c.754_771del	p.Asn252_Gly257del	p.N252_G257del	ENST00000250448	NM_004496.3	252	AACATGTTCGAGAACGGC/-	2/2	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.63544786159502	2		551	861	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578507	7578507	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	365	834	0	ENST00000269305.4:c.423C>A	p.Cys141Ter	p.C141*	ENST00000269305	NM_001126112.2	141	tgC/tgA	5/11	0.63544786159502	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.63544786159502	1		834	718	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943786	71943786	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	249	616	0	ENST00000298229.2:c.1829A>T	p.Tyr610Phe	p.Y610F	ENST00000298229	NM_001567.3	610	tAc/tTc	15/28	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.63544786159502	2		616	759	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020824	26020824	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	35	281	0	ENST00000357647.3:c.107T>A	p.Val36Glu	p.V36E	ENST00000357647	NM_003529.2	36	gTg/gAg	1/1	1	2	FACETS	0.32	0.263	0.384	0.32	0.263	0.384	SUBCLONAL	1	TRUE	1	0.63544786159502	2		281	344	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929592	44929592	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	94	111	0	ENST00000377967.4:c.2693del	p.Lys898ArgfsTer6	p.K898Rfs*6	ENST00000377967	NM_021140.2	898	Aag/ag	17/29	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.63544786159502	1		111	155	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0035818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	444	703	1	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.907225415207027	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.907225415207027	1		704	485	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32905070	32905070	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80359630	NA	P-0035818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	75	231	0	ENST00000380152.3:c.700del	p.Ser234ProfsTer7	p.S234Pfs*7	ENST00000380152		232	taT/ta	9/27	0.8584070622033	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.907225415207027	1		231	87	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881407	48881444	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTTGGTAGGCTTGAGTTTGAAGAAACAGAAGAACCTG	ATTTGGTAGGCTTGAGTTTGAAGAAACAGAAGAACCTG	-	novel	NA	P-0035818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	43	174	0	ENST00000267163.4:c.138-5_170del		p.X46_splice	ENST00000267163	NM_000321.2	46		2/27	0.8584070622033	1	FACETS	0.942	0.857	1	0.942	0.857	1	CLONAL	1	TRUE	0	0.907225415207027	1		174	55	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313204	30313204	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	69	838	0	ENST00000262643.3:c.898G>A	p.Ala300Thr	p.A300T	ENST00000262643	NM_001238.2	300	Gct/Act	10/12	1	2	FACETS	0.237	0.206	0.271	0.237	0.206	0.271	SUBCLONAL	1	TRUE	1	0.907225415207027	2		838	641	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578507	7578507	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	474	834	0	ENST00000269305.4:c.423C>A	p.Cys141Ter	p.C141*	ENST00000269305	NM_001126112.2	141	tgC/tgA	5/11	0.753792428850597	1	FACETS	0.981	0.946	1	0.981	0.946	1	CLONAL	1	TRUE	0	0.753792428850597	1		834	799	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562142	21562142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1421513550	NA	P-0035854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	539	989	0	ENST00000382592.4:c.1777C>T	p.Arg593Cys	p.R593C	ENST00000382592	NM_014572.2	593	Cgc/Tgc	4/8	1	2	FACETS	0.944	0.905	0.983	0.944	0.905	0.983	CLONAL	1	TRUE	1	0.753792428850597	2		989	1515	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012317	152012317	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	342	660	1	ENST00000262189.6:c.496C>T	p.Gln166Ter	p.Q166*	ENST00000262189	NM_170606.2	166	Caa/Taa	4/59	1	2	FACETS	0.966	0.917	1	0.966	0.917	1	CLONAL	1	TRUE	1	0.753792428850597	2		661	939	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	195	570	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.207441413809813	3	FACETS	1	0.989	1	0.711	0.658	0.766	CLONAL	1	TRUE	1	0.331980499539071	3		570	963	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs786203436	NA	P-0035856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	232	702	0	ENST00000269305.4:c.487T>A	p.Tyr163Asn	p.Y163N	ENST00000269305	NM_001126112.2	163	Tac/Aac	5/11	0.331980499539071	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.331980499539071	1		702	1010	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0035991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	89	346	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.328371870603123	1	FACETS	0.761	0.678	0.847	0.761	0.678	0.847	SUBCLONAL	1	TRUE	0	0.442338000088312	1		346	412	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245279	41245279	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs80357583	NA	P-0035991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	109	890	0	ENST00000357654.3:c.2269del	p.Val757PhefsTer8	p.V757Ffs*8	ENST00000357654	NM_007294.3	757	Gtt/tt	10/23	0.370446526000855	2	FACETS	1	0.984	1	0.727	0.66	0.796	CLONAL	1	TRUE	0	0.442338000088312	2		890	339	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588631	28588631	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	57	463	0	ENST00000241453.7:c.2817G>C	p.Leu939Phe	p.L939F	ENST00000241453	NM_004119.2	939	ttG/ttC	23/24	NA	2	FACETS	0.856	0.74	0.981			1	INDETERMINATE	1	TRUE	NA	0.442338000088312	2		463	301	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858266	59858266	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	60	724	0	ENST00000259008.2:c.1729A>C	p.Lys577Gln	p.K577Q	ENST00000259008	NM_032043.2	577	Aag/Cag	12/20	0.442338000088312	3	FACETS	0.936	0.811	1	0.312	0.27	0.357	CLONAL	1	TRUE	0	0.442338000088312	3		724	354	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965959	25965959	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	99	744	0	ENST00000435504.4:c.3247G>T	p.Val1083Leu	p.V1083L	ENST00000435504		1083	Gtg/Ttg	13/13	1	2	FACETS	0.995	0.893	1	0.995	0.893	1	CLONAL	1	TRUE	1	0.442338000088312	2		744	450	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928946	49928946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	87	875	0	ENST00000296474.3:c.3420C>A	p.His1140Gln	p.H1140Q	ENST00000296474	NM_002447.2	1140	caC/caA	16/20	0.421663798084958	1	FACETS	0.819	0.73	0.912	0.819	0.73	0.912	CLONAL	1	TRUE	0	0.442338000088312	1		875	374	SUCCESS
APC	324	MSKCC	GRCh37	5	112177566	112177566	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	27	388	0	ENST00000257430.4:c.6275T>C	p.Leu2092Pro	p.L2092P	ENST00000257430	NM_000038.5	2092	cTa/cCa	16/16	0.423359278644557	1	FACETS	0.97	0.791	1	0.97	0.791	1	CLONAL	1	TRUE	0	0.442338000088312	1		388	98	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151866334	151866334	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	20	343	0	ENST00000262189.6:c.9454G>C	p.Asp3152His	p.D3152H	ENST00000262189	NM_170606.2	3152	Gat/Cat	41/59	0.148193814382236	3	FACETS	0.591	0.454	0.749	0.295	0.227	0.375	INDETERMINATE	1	TRUE	1	0.442338000088312	3		343	187	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0036208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	335	294	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.3	5	FACETS	0.837	0.792	0.883	0.418	0.396	0.442	INDETERMINATE	2	TRUE	1	0.78	5		294	1114	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879331	151879331	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1563292120	NA	P-0036208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	262	461	0	ENST00000262189.6:c.5614C>T	p.Gln1872Ter	p.Q1872*	ENST00000262189	NM_170606.2	1872	Cag/Tag	36/59	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.78	2		461	605	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437848	52437848	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	123	656	2	ENST00000460680.1:c.1313C>A	p.Ser438Ter	p.S438*	ENST00000460680	NM_004656.3	438	tCa/tAa	13/17	0.273115570506079	4	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	2	0.273115570506079	4		658	547	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115758	8115846	+	frameshift_variant	Frame_Shift_Del	DEL	GTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAGAACAGCTCGTTTAACCCGGCCGCCCTCTCCA	GTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAGAACAGCTCGTTTAACCCGGCCGCCCTCTCCA	-	novel	NA	P-0036237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	249	480	0	ENST00000346208.3:c.1105_1193del	p.Ser369ThrfsTer108	p.S369Tfs*108	ENST00000346208		368	atGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAGAACAGCTCGTTTAACCCGGCCGCCCTCTCCAga/atga	6/6	NA	2	FACETS	1	0.952	1			1	INDETERMINATE	1	TRUE	NA	0.652563039489568	2		480	751	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720804	89720804	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	156	213	0	ENST00000371953.3:c.955del	p.Thr319LeufsTer2	p.T319Lfs*2	ENST00000371953	NM_000314.4	319	Act/ct	8/9	0.629951303810684	2	FACETS	0.824	0.771	0.877	0.824	0.771	0.877	CLONAL	2	TRUE	0	0.652563039489568	2		213	290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577102	7577102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793881	NA	P-0036292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	68	716	0	ENST00000269305.4:c.836G>A	p.Gly279Glu	p.G279E	ENST00000269305	NM_001126112.2	279	gGg/gAg	8/11	0.219510784900823	1	FACETS	0.527	0.457	0.603	0.527	0.457	0.603	SUBCLONAL	1	TRUE	0	0.261150913728283	1		716	859	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860035	151860035	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	23	429	0	ENST00000262189.6:c.10627A>C	p.Ser3543Arg	p.S3543R	ENST00000262189	NM_170606.2	3543	Agc/Cgc	43/59	0.227069366739697	5	FACETS	0.632	0.492	0.794	0.211	0.164	0.265	SUBCLONAL	1	TRUE	2	0.261150913728283	5		429	388	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622288	117622288	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	404	605	0	ENST00000368508.3:c.6582G>A	p.Met2194Ile	p.M2194I	ENST00000368508	NM_002944.2	2194	atG/atA	42/43	0.726899145017428	2	FACETS	0.957	0.925	0.988	0.957	0.925	0.988	CLONAL	2	TRUE	0	0.726899145017428	2		605	581	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156617	2156617	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	83	689	0	ENST00000434045.2:c.305G>C	p.Gly102Ala	p.G102A	ENST00000434045	NM_001127598.1	102	gGg/gCg	3/5	0.585491021286742	4	FACETS	0.453	0.399	0.512			1	SUBCLONAL	1	TRUE	NA	0.726899145017428	4		689	870	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86658367	86658367	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0036321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	52	160	0	ENST00000274376.6:c.1333-1G>C		p.X445_splice	ENST00000274376	NM_002890.2	445			0.565908299094755	2	FACETS	1	0.9	1	0.518	0.452	0.587	CLONAL	1	TRUE	0	0.726899145017428	2		160	138	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526068	189526068	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	47	542	1	ENST00000264731.3:c.332A>G	p.Tyr111Cys	p.Y111C	ENST00000264731	NM_003722.4	111	tAc/tGc	4/14	0.567495892278703	4	FACETS	0.303	0.254	0.356	0.151	0.127	0.178	SUBCLONAL	1	TRUE	2	0.726899145017428	4		543	738	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578178	7578178	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	714	711	0	ENST00000269305.4:c.671del	p.Glu224GlyfsTer23	p.E224Gfs*23	ENST00000269305	NM_001126112.2	224	gAg/gg	6/11	0.726899145017428	3	FACETS	0.989	0.968	1	0.989	0.968	1	CLONAL	3	TRUE	0	0.726899145017428	3		711	903	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639586	3639586	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	390	888	1	ENST00000294008.3:c.4053C>A	p.His1351Gln	p.H1351Q	ENST00000294008	NM_032444.2	1351	caC/caA	12/15	0.714826340051932	3	FACETS	0.917	0.877	0.956	0.611	0.585	0.638	CLONAL	2	TRUE	0	0.726899145017428	3		889	798	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197447	26197447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	115	359	0	ENST00000356476.2:c.32C>T	p.Ser11Phe	p.S11F	ENST00000356476		11	tCc/tTc	1/1	0.69509815703946	3	FACETS	1	0.982	1	0.444	0.405	0.484	CLONAL	1	TRUE	0	0.726899145017428	3		359	324	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622191	1622191	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	26	530	0	ENST00000344749.5:c.684G>C	p.Trp228Cys	p.W228C	ENST00000344749	NM_001136139.2	228	tgG/tgC	10/19	0.726899145017428	2	FACETS	0.181	0.143	0.224	0.09	0.071	0.112	SUBCLONAL	1	TRUE	0	0.726899145017428	2		530	396	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	211	294	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	NA	2	FACETS	0.929	0.864	0.996			1	INDETERMINATE	1	TRUE	NA	0.533658379998179	2		294	851	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	143	302	0				ENST00000310581	NM_198253.2	-/1132			0.309894096704336	3	FACETS	0.946	0.874	1	0.946	0.874	1	INDETERMINATE	2	TRUE	1	0.533658379998179	3		302	359	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817754	3817754	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	140	742	1	ENST00000262367.5:c.3217C>T	p.Gln1073Ter	p.Q1073*	ENST00000262367	NM_004380.2	1073	Cag/Tag	16/31	1	2	FACETS	0.513	0.466	0.562	0.513	0.466	0.562	SUBCLONAL	1	TRUE	1	0.533658379998179	2		743	1023	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	143	408	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.884	0.809	0.962	0.884	0.809	0.962	CLONAL	1	TRUE	1	0.533658379998179	2		408	606	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423511	88423511	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	105	639	0	ENST00000360948.2:c.2324C>G	p.Ser775Ter	p.S775*	ENST00000360948	NM_001012338.2	775	tCa/tGa	18/19	0.337242541729008	1	FACETS	0.405	0.362	0.449	0.405	0.362	0.449	SUBCLONAL	1	TRUE	0	0.533658379998179	1		639	713	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675183	30675183	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs748112559	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	210	617	0	ENST00000376406.3:c.3062G>C	p.Arg1021Thr	p.R1021T	ENST00000376406	NM_014641.2	1021	aGa/aCa	9/15	0.533658379998179	4	FACETS	0.873	0.809	0.941	0.437	0.404	0.471	CLONAL	1	TRUE	2	0.533658379998179	4		617	1382	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348945	11348945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	94	455	0	ENST00000332029.2:c.391C>G	p.Gln131Glu	p.Q131E	ENST00000332029	NM_003745.1	131	Cag/Gag	2/2	1	2	FACETS	0.541	0.482	0.604	0.541	0.482	0.604	SUBCLONAL	1	TRUE	1	0.533658379998179	2		455	651	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651292	52651292	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	208	536	0	ENST00000394830.3:c.1804G>A	p.Glu602Lys	p.E602K	ENST00000394830	NM_018313.4	602	Gag/Aag	15/30	1	2	FACETS	0.949	0.883	1	0.949	0.883	1	CLONAL	1	TRUE	1	0.533658379998179	2		536	821	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911194	29911194	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs41541518	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	106	457	0	ENST00000376809.5:c.493C>G	p.Gln165Glu	p.Q165E	ENST00000376809	NM_002116.7	165	Cag/Gag	3/8	0.533658379998179	4	FACETS	0.685	0.614	0.762	0.343	0.307	0.381	SUBCLONAL	1	TRUE	2	0.533658379998179	4		457	889	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445917	49445917	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	352	1097	0	ENST00000301067.7:c.1549G>T	p.Glu517Ter	p.E517*	ENST00000301067	NM_003482.3	517	Gag/Tag	10/54	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.533658379998179	2		1097	1302	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944503	40944503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	188	579	0	ENST00000373198.4:c.1999G>A	p.Glu667Lys	p.E667K	ENST00000373198	NM_133170.3	667	Gag/Aag	12/32	NA	2	FACETS	1	0.935	1			1	INDETERMINATE	1	TRUE	NA	0.533658379998179	2		579	698	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462782	69462782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	176	603	1	ENST00000227507.2:c.595C>T	p.Pro199Ser	p.P199S	ENST00000227507	NM_053056.2	199	Ccg/Tcg	4/5	1	2	FACETS	0.907	0.838	0.979	0.907	0.838	0.979	CLONAL	1	TRUE	1	0.533658379998179	2		604	727	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38178687	38178687	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761714577	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	95	443	1	ENST00000317025.8:c.1712C>T	p.Ser571Leu	p.S571L	ENST00000317025	NM_023034.1	571	tCa/tTa	8/24	1	2	FACETS	0.483	0.43	0.54	0.483	0.43	0.54	SUBCLONAL	1	TRUE	1	0.533658379998179	2		444	737	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926549	59926549	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762701532	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	328	872	0	ENST00000259008.2:c.448G>A	p.Glu150Lys	p.E150K	ENST00000259008	NM_032043.2	150	Gaa/Aaa	5/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.533658379998179	2		872	1083	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088724	27088724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	264	626	0	ENST00000324856.7:c.2333G>A	p.Gly778Glu	p.G778E	ENST00000324856	NM_006015.4	778	gGa/gAa	7/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.533658379998179	2		626	947	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196062	67196062	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	101	510	0	ENST00000312629.5:c.46G>T	p.Glu16Ter	p.E16*	ENST00000312629	NM_003952.2	16	Gag/Tag	1/15	1	2	FACETS	0.584	0.523	0.649	0.584	0.523	0.649	SUBCLONAL	1	TRUE	1	0.533658379998179	2		510	648	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196074	67196074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	98	495	0	ENST00000312629.5:c.58G>A	p.Glu20Lys	p.E20K	ENST00000312629	NM_003952.2	20	Gag/Aag	1/15	1	2	FACETS	0.56	0.5	0.624	0.56	0.5	0.624	SUBCLONAL	1	TRUE	1	0.533658379998179	2		495	656	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144637	119144637	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1414264462	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	193	538	0	ENST00000264033.4:c.650C>G	p.Ser217Cys	p.S217C	ENST00000264033	NM_005188.3	217	tCt/tGt	4/16	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.533658379998179	2		538	721	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144732	119144732	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	160	385	0	ENST00000264033.4:c.745C>G	p.Gln249Glu	p.Q249E	ENST00000264033	NM_005188.3	249	Cag/Gag	4/16	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.533658379998179	2		385	599	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244016	46244016	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	193	558	0	ENST00000334344.6:c.2110C>G	p.Gln704Glu	p.Q704E	ENST00000334344	NM_152641.2	704	Caa/Gaa	15/21	1	2	FACETS	0.865	0.802	0.931	0.865	0.802	0.931	CLONAL	1	TRUE	1	0.533658379998179	2		558	836	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442937	49442937	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	217	601	0	ENST00000301067.7:c.3971G>C	p.Arg1324Thr	p.R1324T	ENST00000301067	NM_003482.3	1324	aGa/aCa	12/54	1	2	FACETS	0.976	0.91	1	0.976	0.91	1	CLONAL	1	TRUE	1	0.533658379998179	2		601	833	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068252	30068252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	76	513	0	ENST00000331968.5:c.2147C>T	p.Ser716Leu	p.S716L	ENST00000331968	NM_002742.2	716	tCa/tTa	15/18	1	2	FACETS	0.419	0.368	0.475	0.419	0.368	0.475	SUBCLONAL	1	TRUE	1	0.533658379998179	2		513	679	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100023	30100023	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	117	651	0	ENST00000331968.5:c.1597G>T	p.Glu533Ter	p.E533*	ENST00000331968	NM_002742.2	533	Gag/Tag	10/18	1	2	FACETS	0.507	0.457	0.56	0.507	0.457	0.56	SUBCLONAL	1	TRUE	1	0.533658379998179	2		651	865	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987188	36987188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	123	699	0	ENST00000354822.5:c.501G>A	p.Met167Ile	p.M167I	ENST00000354822	NM_001079668.2	167	atG/atA	3/3	1	2	FACETS	0.562	0.508	0.619	0.562	0.508	0.619	SUBCLONAL	1	TRUE	1	0.533658379998179	2		699	820	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95583961	95583961	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	rs137852977	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	144	466	0	ENST00000393063.1:c.1507G>T	p.Glu503Ter	p.E503*	ENST00000393063	NM_030621.3	503	Gag/Tag	10/28	1	2	FACETS	0.913	0.836	0.993	0.913	0.836	0.993	CLONAL	1	TRUE	1	0.533658379998179	2		466	591	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43738651	43738651	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	135	685	0	ENST00000382044.4:c.2974C>G	p.Leu992Val	p.L992V	ENST00000382044	NM_001141980.1	992	Cta/Gta	14/28	0.337242541729008	1	FACETS	0.446	0.405	0.489	0.446	0.405	0.489	SUBCLONAL	1	TRUE	0	0.533658379998179	1		685	832	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358391	91358391	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	92	587	0	ENST00000355112.3:c.4136C>G	p.Ser1379Cys	p.S1379C	ENST00000355112	NM_000057.2	1379	tCc/tGc	22/22	0.337242541729008	1	FACETS	0.354	0.314	0.396	0.354	0.314	0.396	SUBCLONAL	1	TRUE	0	0.533658379998179	1		587	714	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358414	91358414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	103	622	0	ENST00000355112.3:c.4159C>T	p.Gln1387Ter	p.Q1387*	ENST00000355112	NM_000057.2	1387	Caa/Taa	22/22	0.337242541729008	1	FACETS	0.386	0.345	0.429	0.386	0.345	0.429	SUBCLONAL	1	TRUE	0	0.533658379998179	1		622	733	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358483	91358483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	79	551	0	ENST00000355112.3:c.4228C>T	p.Leu1410Phe	p.L1410F	ENST00000355112	NM_000057.2	1410	Ctt/Ttt	22/22	0.337242541729008	1	FACETS	0.343	0.301	0.387	0.343	0.301	0.387	SUBCLONAL	1	TRUE	0	0.533658379998179	1		551	633	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657527	37657527	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	104	609	1	ENST00000447079.4:c.2444A>T	p.Tyr815Phe	p.Y815F	ENST00000447079	NM_015083.1	815	tAt/tTt	6/14	1	2	FACETS	0.445	0.398	0.495	0.445	0.398	0.495	SUBCLONAL	1	TRUE	1	0.533658379998179	2		610	876	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244679	41244679	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	348	897	0	ENST00000357654.3:c.2869C>G	p.Gln957Glu	p.Q957E	ENST00000357654	NM_007294.3	957	Cag/Gag	10/23	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.533658379998179	2		897	1170	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7152901	7152901	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	209	618	0	ENST00000302850.5:c.2067C>G	p.Phe689Leu	p.F689L	ENST00000302850	NM_000208.2	689	ttC/ttG	10/22	1	2	FACETS	0.956	0.89	1	0.956	0.89	1	CLONAL	1	TRUE	1	0.533658379998179	2		618	819	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032829	30032829	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	124	421	0	ENST00000338641.4:c.204C>G	p.Ile68Met	p.I68M	ENST00000338641	NM_000268.3	68	atC/atG	2/16	1	2	FACETS	0.928	0.844	1	0.928	0.844	1	CLONAL	1	TRUE	1	0.533658379998179	2		421	501	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226923	142226923	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	158	510	1	ENST00000350721.4:c.4881G>T	p.Gln1627His	p.Q1627H	ENST00000350721	NM_001184.3	1627	caG/caT	28/47	1	2	FACETS	0.817	0.75	0.886	0.817	0.75	0.886	CLONAL	1	TRUE	1	0.533658379998179	2		511	725	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539549	187539549	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1237866299	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	89	499	0	ENST00000441802.2:c.8191G>A	p.Gly2731Arg	p.G2731R	ENST00000441802	NM_005245.3	2731	Ggg/Agg	10/27	0.303366568722414	1	FACETS	0.482	0.429	0.539	0.482	0.429	0.539	INDETERMINATE	1	TRUE	0	0.533658379998179	1		499	507	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235293	235293	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs780941330	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	313	515	1	ENST00000264932.6:c.1099C>T	p.Gln367Ter	p.Q367*	ENST00000264932	NM_004168.2	367	Cag/Tag	9/15	0.309894096704336	3	FACETS	0.935	0.886	0.984	0.935	0.886	0.984	INDETERMINATE	2	TRUE	1	0.533658379998179	3		516	795	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871211	35871211	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	87	450	0	ENST00000303115.3:c.433G>C	p.Asp145His	p.D145H	ENST00000303115	NM_002185.3	145	Gac/Cac	4/8	0.309894096704336	3	FACETS	0.571	0.505	0.642	0.286	0.252	0.321	INDETERMINATE	1	TRUE	1	0.533658379998179	3		450	723	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30676075	30676075	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	176	430	0	ENST00000376406.3:c.2281G>C	p.Glu761Gln	p.E761Q	ENST00000376406	NM_014641.2	761	Gag/Cag	8/15	0.533658379998179	4	FACETS	0.924	0.85	1	0.462	0.425	0.501	CLONAL	1	TRUE	2	0.533658379998179	4		430	1095	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266499	55266499	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	234	638	0	ENST00000275493.2:c.2791G>C	p.Glu931Gln	p.E931Q	ENST00000275493	NM_005228.3	931	Gaa/Caa	23/28	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.533658379998179	2		638	836	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835888	151835888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	164	461	0	ENST00000262189.6:c.14636G>A	p.Gly4879Glu	p.G4879E	ENST00000262189	NM_170606.2	4879	gGa/gAa	58/59	1	2	FACETS	0.905	0.834	0.979	0.905	0.834	0.979	CLONAL	1	TRUE	1	0.533658379998179	2		461	679	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027786	152027786	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	302	794	1	ENST00000262189.6:c.289G>T	p.Glu97Ter	p.E97*	ENST00000262189	NM_170606.2	97	Gaa/Taa	3/59	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.533658379998179	2		795	1114	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90990497	90990497	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1293382034	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	190	577	0	ENST00000265433.3:c.535G>T	p.Glu179Ter	p.E179*	ENST00000265433	NM_002485.4	179	Gaa/Taa	5/16	1	2	FACETS	0.778	0.72	0.839	0.778	0.72	0.839	SUBCLONAL	1	TRUE	1	0.533658379998179	2		577	915	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27203085	27203085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1367866328	NA	P-0036403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	179	542	0	ENST00000380036.4:c.2177C>T	p.Ser726Phe	p.S726F	ENST00000380036	NM_000459.3	726	tCt/tTt	13/23	0.385678553937217	1	FACETS	0.747	0.692	0.805	0.747	0.692	0.805	SUBCLONAL	1	TRUE	0	0.533658379998179	1		542	658	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0036564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	26	626	17	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.483	0.381	0.601	0.483	0.381	0.601	SUBCLONAL	1	TRUE	1	0.14	2		643	769	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856178	111856178	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1319912702	NA	P-0036564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	29	410	1	ENST00000341259.2:c.229C>T	p.Arg77Cys	p.R77C	ENST00000341259	NM_005475.2	77	Cgc/Tgc	2/8	1	2	FACETS	0.913	0.732	1	0.913	0.732	1	CLONAL	1	TRUE	1	0.14	2		411	454	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55229255	55229255	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs2227983	NA	P-0036564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	27	518	0	ENST00000275493.2:c.1562G>T	p.Arg521Met	p.R521M	ENST00000275493	NM_005228.3	521	aGg/aTg	13/28	1	2	FACETS	0.716	0.568	0.885	0.716	0.568	0.885	SUBCLONAL	1	TRUE	1	0.14	2		518	539	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0036569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	215	570	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.608497933647404	4	FACETS	0.974	0.912	1	0.649	0.608	0.692	CLONAL	2	TRUE	1	0.617671469829665	4		570	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0036569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	771	586	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.617671469829665	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	4	TRUE	0	0.617671469829665	4		586	984	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741757	17741757	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	195	562	1	ENST00000250003.3:c.428G>A	p.Arg143Gln	p.R143Q	ENST00000250003	NM_002478.4	143	cGg/cAg	1/3	0.617671469829665	3	FACETS	1	0.978	1	0.567	0.526	0.609	CLONAL	1	TRUE	1	0.617671469829665	3		563	729	SUCCESS
APC	324	MSKCC	GRCh37	5	112175754	112175755	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	98	354	0	ENST00000257430.4:c.4464dup	p.Leu1489IlefsTer25	p.L1489Ifs*25	ENST00000257430	NM_000038.5	1488	tta/ttAa	16/16	0.617671469829665	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.617671469829665	1		354	217	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0036779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	257	562	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.691669143182504	1	FACETS	0.946	0.896	0.995	0.946	0.896	0.995	CLONAL	1	TRUE	0	0.691669143182504	1		562	514	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754873	57754875	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	novel	NA	P-0036779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	173	346	0	ENST00000274289.3:c.315_317del	p.Asn105del	p.N105del	ENST00000274289	NM_006622.3	105	aaCAAa/aaa	2/14	0.691669143182504	1	FACETS	0.852	0.795	0.909	0.852	0.795	0.909	CLONAL	1	TRUE	0	0.691669143182504	1		346	384	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970904	70970904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	268	556	0	ENST00000276594.2:c.1357C>T	p.His453Tyr	p.H453Y	ENST00000276594	NM_024504.3	453	Cat/Tat	6/8	0.691669143182504	3	FACETS	0.885	0.829	0.942	0.442	0.414	0.471	CLONAL	1	TRUE	1	0.691669143182504	3		556	1179	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004873	150004873	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	226	497	0	ENST00000253339.5:c.1352T>C	p.Ile451Thr	p.I451T	ENST00000253339		451	aTc/aCc	3/7	0.691669143182504	1	FACETS	0.925	0.873	0.978	0.925	0.873	0.978	CLONAL	1	TRUE	0	0.691669143182504	1		497	462	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004869	150004872	+	frameshift_variant	Frame_Shift_Del	DEL	AGGG	AGGG	-	novel	NA	P-0036779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	227	494	0	ENST00000253339.5:c.1353_1356del	p.Pro452HisfsTer8	p.P452Hfs*8	ENST00000253339		451	atCCCT/at	3/7	0.691669143182504	1	FACETS	0.921	0.869	0.974	0.921	0.869	0.974	CLONAL	1	TRUE	0	0.691669143182504	1		494	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0036814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	494	559	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.735795133074742	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.754867668795766	2		559	611	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163309223	163309223	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	43	458	0	ENST00000271452.3:c.562C>G	p.Gln188Glu	p.Q188E	ENST00000271452	NM_145697.2	188	Cag/Gag	8/14	0.211602208908016	6	FACETS	0.399	0.333	0.473	0.067	0.055	0.079	INDETERMINATE	1	TRUE	0	0.754867668795766	6		458	716	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729793	41729793	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	96	387	1	ENST00000242208.4:c.736C>T	p.Gln246Ter	p.Q246*	ENST00000242208	NM_002192.2	246	Cag/Tag	3/3	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.754867668795766	2		388	226	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932289	39932289	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	334	844	0	ENST00000378444.4:c.2310del	p.Ser771AlafsTer15	p.S771Afs*15	ENST00000378444	NM_001123385.1	770	acT/ac	4/15	0.445222114178933	1	FACETS	0.772	0.735	0.808	0.772	0.735	0.808	INDETERMINATE	1	TRUE	0	0.754867668795766	1		844	714	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0036878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	48	464	1	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.1	2		465	792	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0036878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	30	590	2	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	0.821	0.659	1	0.821	0.659	1	CLONAL	1	TRUE	1	0.1	2		592	731	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0036878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	40	618	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.88	0.729	1	0.88	0.729	1	CLONAL	1	TRUE	1	0.1	2		618	909	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	9	304	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	0.418	0.275	0.601	0.418	0.275	0.601	SUBCLONAL	1	TRUE	1	0.1	2		304	431	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670755	67670755	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0036878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	30	358	1	ENST00000264010.4:c.1999+1G>A		p.X667_splice	ENST00000264010	NM_006565.3	667			1	2	FACETS	1	0.826	1	1	0.826	1	CLONAL	1	TRUE	1	0.1	2		359	583	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041214	29041214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758936491	NA	P-0036878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	43	609	0	ENST00000282397.4:c.214G>A	p.Glu72Lys	p.E72K	ENST00000282397	NM_002019.4	72	Gaa/Aaa	3/30	1	2	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	TRUE	1	0.1	2		609	853	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	132	188	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.557022677600151	2		188	323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0036905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	236	898	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.557022677600151	2		898	829	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	210	826	0	ENST00000269305.4:c.472C>G	p.Arg158Gly	p.R158G	ENST00000269305	NM_001126112.2	158	Cgc/Ggc	5/11	1	2	FACETS	0.954	0.889	1	0.954	0.889	1	CLONAL	1	TRUE	1	0.557022677600151	2		826	790	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0036905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	667	650	1	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	0.557022677600151	4	FACETS	0.9	0.875	0.925			1	CLONAL	4	TRUE	NA	0.557022677600151	4		651	1036	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926248	112926248	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs121918468	NA	P-0036905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	249	619	0	ENST00000351677.2:c.1381G>A	p.Ala461Thr	p.A461T	ENST00000351677	NM_002834.3	461	Gct/Act	12/16	1	2	FACETS	0.776	0.732	0.82	1	0.994	1	SUBCLONAL	2	TRUE	1	0.557022677600151	2		619	576	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273029	55273029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770749711	NA	P-0036905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	73	585	0	ENST00000275493.2:c.3352G>A	p.Ala1118Thr	p.A1118T	ENST00000275493	NM_005228.3	1118	Gcg/Acg	28/28	0.425696961408297	1	FACETS	0.409	0.359	0.463	0.409	0.359	0.463	SUBCLONAL	1	TRUE	0	0.557022677600151	1		585	462	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490204	29490204	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	115	306	0	ENST00000356175.3:c.289C>T	p.Gln97Ter	p.Q97*	ENST00000356175	NM_000267.3	97	Caa/Taa	4/57	0.287015962425477	2	FACETS	1	0.975	1	0.598	0.545	0.653	INDETERMINATE	1	TRUE	0	0.557022677600151	2		306	345	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683532	29683538	+	frameshift_variant	Frame_Shift_Del	DEL	AAGAAAT	AAGAAAT	-	novel	NA	P-0036905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	46	363	0	ENST00000356175.3:c.7607_7613del	p.Gln2536ArgfsTer11	p.Q2536Rfs*11	ENST00000356175	NM_000267.3	2536	cAAGAAATg/cg	51/57	0.287015962425477	2	FACETS	0.455	0.384	0.533	0.227	0.192	0.267	INDETERMINATE	1	TRUE	0	0.557022677600151	2		363	363	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932150	39932150	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	327	439	2	ENST00000378444.4:c.2449del	p.Thr817LeufsTer39	p.T817Lfs*39	ENST00000378444	NM_001123385.1	817	Act/ct	4/15	1	1	FACETS	1	0.993	1	1	0.997	1	CLONAL	2	TRUE	0	0.557022677600151	1		441	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0036961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	141	567	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.440964692462848	2	FACETS	0.861	0.795	0.927	0.861	0.795	0.927	CLONAL	2	TRUE	0	0.480444874750841	2		567	341	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742837	17742837	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	18	599	0	ENST00000250003.3:c.745C>A	p.Leu249Ile	p.L249I	ENST00000250003	NM_002478.4	249	Cta/Ata	3/3	0.436872465865415	2	FACETS	0.314	0.236	0.405	0.157	0.118	0.203	SUBCLONAL	1	TRUE	0	0.480444874750841	2		599	239	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625335	69625335	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	20	619	0	ENST00000334134.2:c.458G>A	p.Trp153Ter	p.W153*	ENST00000334134	NM_005247.2	153	tGg/tAg	3/3	0.420976429653992	4	FACETS	0.365	0.278	0.466	0.182	0.139	0.233	SUBCLONAL	1	TRUE	2	0.480444874750841	4		619	338	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628495	21628495	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	28	530	0	ENST00000421138.2:c.1123G>A	p.Gly375Ser	p.G375S	ENST00000421138		375	Ggt/Agt	11/16	0.358719550842745	3	FACETS	0.297	0.237	0.367	0.149	0.118	0.184	SUBCLONAL	1	TRUE	1	0.480444874750841	3		530	486	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495770	56495770	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	70	448	0	ENST00000267101.3:c.3960C>G	p.Asp1320Glu	p.D1320E	ENST00000267101	NM_001982.3	1320	gaC/gaG	28/28	0.449206062650195	3	FACETS	1	0.955	1	0.396	0.348	0.447	CLONAL	1	TRUE	0	0.480444874750841	3		448	304	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991265	41991275	+	frameshift_variant	Frame_Shift_Del	DEL	ACAGAGCAAGA	ACAGAGCAAGA	-	novel	NA	P-0036961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	49	420	0	ENST00000219905.7:c.2097_2107del	p.Arg700PhefsTer41	p.R700Ffs*41	ENST00000219905	NM_001164273.1	699	tACAGAGCAAGA/t	5/24	0.480444874750841	1	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	0	0.480444874750841	1		420	155	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003599	45003784	+	coding_sequence_variant,5_prime_UTR_variant	In_Frame_Del	DEL	CTCTCTCTAACCTGGCACTGCGTCGCTGGCTTGGAGACAGGTGACGGTCCCTGCGGGCCTTGTCCTGATTGGCTGGGCACGCGTTTAATATAAGTGGAGGCGTCGCGCTGGCGGGCATTCCTGAAGCTGACAGCATTCGGGCCGAGATGTCTCGCTCCGTGGCCTTAGCTGTGCTCGCGCTACTCT	CTCTCTCTAACCTGGCACTGCGTCGCTGGCTTGGAGACAGGTGACGGTCCCTGCGGGCCTTGTCCTGATTGGCTGGGCACGCGTTTAATATAAGTGGAGGCGTCGCGCTGGCGGGCATTCCTGAAGCTGACAGCATTCGGGCCGAGATGTCTCGCTCCGTGGCCTTAGCTGTGCTCGCGCTACTCT	-	novel	NA	P-0036961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	112	33	0				ENST00000558401	NM_004048.2	?-14/119		1/4	0.480444874750841	1	FACETS	1	0.983	1	1	0.992	1	CLONAL	2	TRUE	0	0.480444874750841	1		33	154	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324177	62324177	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761295679	NA	P-0036961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	36	533	0	ENST00000360203.5:c.2672C>T	p.Ala891Val	p.A891V	ENST00000360203	NM_001283009.1	891	gCa/gTa	29/35	0.420976429653992	4	FACETS	0.432	0.354	0.519	0.216	0.177	0.26	SUBCLONAL	1	TRUE	2	0.480444874750841	4		533	514	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0036999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	166	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.550047757888215	2		436	486	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0036999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	101	383	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.550047757888215	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	0	0.550047757888215	1		383	266	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577531	7577531	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567549203	NA	P-0036999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	378	604	0	ENST00000269305.4:c.750del	p.Ile251SerfsTer94	p.I251Sfs*94	ENST00000269305	NM_001126112.2	250	ccC/cc	7/11	0.550047757888215	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.550047757888215	1		604	773	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151895	108151895	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	121	306	0	ENST00000278616.4:c.3576G>C	p.Lys1192Asn	p.K1192N	ENST00000278616	NM_000051.3	1192	aaG/aaC	24/63	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.550047757888215	2		306	343	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146710	185146710	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	201	582	0	ENST00000265026.3:c.341A>G	p.Glu114Gly	p.E114G	ENST00000265026	NM_004721.4	114	gAa/gGa	2/14	0.28123419944698	1	FACETS	0.658	0.611	0.707	0.658	0.611	0.707	INDETERMINATE	1	TRUE	0	0.550047757888215	1		582	805	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526390	31526390	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1273	86	868	0	ENST00000344624.3:c.650G>C	p.Ser217Thr	p.S217T	ENST00000344624		217	aGt/aCt	2/33	0.321826542872813	1	FACETS	0.167	0.147	0.189	0.167	0.147	0.189	INDETERMINATE	1	TRUE	0	0.550047757888215	1		868	1359	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0037712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	111	294	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	0.575232025202785	2		294	334	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0037712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	31	451	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.98	0.811	1	0.98	0.811	1	CLONAL	1	TRUE	1	0.575232025202785	2		451	110	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0037712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	145	455	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.575232025202785	2	FACETS	0.91	0.848	0.972	0.91	0.848	0.972	CLONAL	2	TRUE	0	0.575232025202785	2		455	277	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374935	45374935	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	149	477	0	ENST00000262160.6:c.908C>G	p.Thr303Arg	p.T303R	ENST00000262160	NM_005901.5	303	aCa/aGa	8/11	0.575110269458985	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.575232025202785	2		477	248	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249460	153249460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	151	481	1	ENST00000281708.4:c.1318G>A	p.Asp440Asn	p.D440N	ENST00000281708	NM_033632.3	440	Gat/Aat	9/12	1	2	FACETS	0.972	0.91	1	1	0.993	1	CLONAL	2	TRUE	1	0.575232025202785	2		482	270	SUCCESS
APC	324	MSKCC	GRCh37	5	112174814	112174814	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085081	NA	P-0037712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	25	229	0	ENST00000257430.4:c.3523C>T	p.Gln1175Ter	p.Q1175*	ENST00000257430	NM_000038.5	1175	Cag/Tag	16/16	1	2	FACETS	1	0.818	1	1	0.818	1	CLONAL	1	TRUE	1	0.575232025202785	2		229	86	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793269	33793269	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	53	109	0	ENST00000498907.2:c.52C>T	p.His18Tyr	p.H18Y	ENST00000498907	NM_004364.3	18	Cac/Tac	1/1	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.575232025202785	2		109	143	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243048	105243048	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519804	NA	P-0037871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	351	838	1	ENST00000349310.3:c.235C>A	p.Gln79Lys	p.Q79K	ENST00000349310	NM_001014432.1	79	Cag/Aag	5/15	0.458369249645561	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	FALSE	0	0.458369249645561	1		839	948	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217230	11217230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786205165	NA	P-0037871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	123	525	0	ENST00000361445.4:c.4448G>A	p.Cys1483Tyr	p.C1483Y	ENST00000361445	NM_004958.3	1483	tGc/tAc	30/58	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	FALSE	1	0.458369249645561	2		525	533	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445246	49445250	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCT	CCCCT	-	novel	NA	P-0037871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	194	906	0	ENST00000301067.7:c.2216_2220del	p.Glu739AlafsTer8	p.E739Afs*8	ENST00000301067	NM_003482.3	739	gAGGGG/g	10/54	0.252992879802173	3	FACETS	0.95	0.878	1	0.475	0.439	0.513	INDETERMINATE	1	FALSE	1	0.458369249645561	3		906	1095	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640279	3640279	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	192	945	1	ENST00000294008.3:c.3360A>C	p.Lys1120Asn	p.K1120N	ENST00000294008	NM_032444.2	1120	aaA/aaC	12/15	1	2	FACETS	0.897	0.83	0.967	0.897	0.83	0.967	CLONAL	1	FALSE	1	0.458369249645561	2		946	934	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829212	72829212	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	176	689	0	ENST00000268489.5:c.7369del	p.Gln2457LysfsTer71	p.Q2457Kfs*71	ENST00000268489	NM_006885.3	2457	Caa/aa	9/10	0.416607601108026	1	FACETS	0.98	0.907	1	0.98	0.907	1	CLONAL	1	FALSE	0	0.458369249645561	1		689	604	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1485978447	NA	P-0037916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	162	440	0	ENST00000324856.7:c.5164C>T	p.Arg1722Ter	p.R1722*	ENST00000324856	NM_006015.4	1722	Cga/Tga	20/20	0.390516459576098	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.390516459576098	1		440	608	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186599	108186599	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876658415	NA	P-0037916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	208	451	0	ENST00000278616.4:c.6056A>G	p.Tyr2019Cys	p.Y2019C	ENST00000278616	NM_000051.3	2019	tAt/tGt	41/63	0.390516459576098	3	FACETS	0.823	0.765	0.881	0.823	0.765	0.881	CLONAL	2	TRUE	1	0.390516459576098	3		451	774	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551745	150551745	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760318078	NA	P-0037916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	43	246	1	ENST00000369026.2:c.262G>A	p.Asp88Asn	p.D88N	ENST00000369026	NM_021960.4	88	Gac/Aac	1/3	1	2	FACETS	0.615	0.516	0.724	0.615	0.516	0.724	SUBCLONAL	1	TRUE	1	0.390516459576098	2		247	358	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148925	119149173	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAATATGTGCTGAAAATGATAAGGATGTAAAGATTGAGCCCTGTGGACACCTCATGTGCACATCCTGTCTTACATCCTGGCAGGTACGGATCTAAACAGCGACTTTTTTCAGCTATGTAATAACCTTGGAAAATTCGGTATTATATAGCCTTTACTGATACAAGGGGTGGCCTGGCTTTTGGGGTTAGGTTTAAACTTTTACTTTTTTTTGATCTCTAGGAAATGTATTTTCTAGTAGATTAATATTTT	AAATATGTGCTGAAAATGATAAGGATGTAAAGATTGAGCCCTGTGGACACCTCATGTGCACATCCTGTCTTACATCCTGGCAGGTACGGATCTAAACAGCGACTTTTTTCAGCTATGTAATAACCTTGGAAAATTCGGTATTATATAGCCTTTACTGATACAAGGGGTGGCCTGGCTTTTGGGGTTAGGTTTAAACTTTTACTTTTTTTTGATCTCTAGGAAATGTATTTTCTAGTAGATTAATATTTT	-	novel	NA	P-0037916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	212	532	0	ENST00000264033.4:c.1147_1228-45del		p.X383_splice	ENST00000264033	NM_005188.3	383		8/16	0.390516459576098	3	FACETS	0.779	0.725	0.835	0.779	0.725	0.835	SUBCLONAL	2	TRUE	1	0.390516459576098	3		532	833	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828186	72828186	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	194	782	1	ENST00000268489.5:c.8395C>A	p.Leu2799Ile	p.L2799I	ENST00000268489	NM_006885.3	2799	Ctt/Att	9/10	0.252640521366018	1	FACETS	0.89	0.824	0.959	0.89	0.824	0.959	CLONAL	1	TRUE	0	0.390516459576098	1		783	898	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678746	52678749	+	frameshift_variant	Frame_Shift_Del	DEL	TTCA	TTCA	-	novel	NA	P-0037916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	105	518	1	ENST00000394830.3:c.870_873del	p.His290GlnfsTer9	p.H290Qfs*9	ENST00000394830	NM_018313.4	290	caTGAA/ca	9/30	0.390516459576098	1	FACETS	0.86	0.774	0.951	0.86	0.774	0.951	CLONAL	1	TRUE	0	0.390516459576098	1		519	503	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	258	530	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.983	0.922	1	0.983	0.922	1	CLONAL	1	TRUE	1	0.594615897191612	2		534	883	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101402	27101402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	140	508	3	ENST00000324856.7:c.4689del	p.Met1564Ter	p.M1564*	ENST00000324856	NM_006015.4	1562	Ccc/cc	18/20	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.594615897191612	2		511	471	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161907	47161907	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	136	352	0	ENST00000409792.3:c.4219del	p.Arg1407GlyfsTer5	p.R1407Gfs*5	ENST00000409792	NM_014159.6	1407	Agg/gg	3/21	1	2	FACETS	0.926	0.847	1	0.926	0.847	1	CLONAL	1	TRUE	1	0.594615897191612	2		352	494	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	170	466	2	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.813	0.75	0.879	0.813	0.75	0.879	CLONAL	1	TRUE	1	0.594615897191612	2		468	703	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	154	580	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.844	0.775	0.915	0.844	0.775	0.915	CLONAL	1	TRUE	1	0.594615897191612	2		580	614	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	209	626	17	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.956	0.891	1	0.956	0.891	1	CLONAL	1	TRUE	1	0.594615897191612	2		643	735	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	388	468	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.895	0.858	0.932	1	0.997	1	CLONAL	2	TRUE	1	0.594615897191612	2		472	729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555526097	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	249	821	1	ENST00000269305.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000269305	NM_001126112.2	167	Cag/Tag	5/11	1	2	FACETS	0.978	0.917	1	0.978	0.917	1	CLONAL	1	TRUE	1	0.594615897191612	2		822	856	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	167	707	28	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.835	0.769	0.902	0.835	0.769	0.902	CLONAL	1	TRUE	1	0.594615897191612	2		735	673	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	150	438	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	1	2	FACETS	0.895	0.822	0.97	0.895	0.822	0.97	CLONAL	1	TRUE	1	0.594615897191612	2		438	564	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	211	464	1	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.953	0.888	1	0.953	0.888	1	CLONAL	1	TRUE	1	0.594615897191612	2		465	745	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346884	73346884	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	92	273	0	ENST00000377767.4:c.1333del	p.Ser445HisfsTer20	p.S445Hfs*20	ENST00000377767	NM_014953.3	445	Tca/ca	9/21	1	2	FACETS	0.843	0.755	0.935	0.843	0.755	0.935	CLONAL	1	TRUE	1	0.594615897191612	2		273	367	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	217	499	1	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	0.594615897191612	2		500	762	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549752	187549752	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	136	440	0	ENST00000441802.2:c.4489A>G	p.Arg1497Gly	p.R1497G	ENST00000441802	NM_005245.3	1497	Aga/Gga	8/27	1	2	FACETS	0.899	0.822	0.978	0.899	0.822	0.978	CLONAL	1	TRUE	1	0.594615897191612	2		440	509	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349730	15349730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750347317	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	182	863	1	ENST00000263377.2:c.3844C>T	p.Arg1282Cys	p.R1282C	ENST00000263377	NM_058243.2	1282	Cgc/Tgc	19/20	1	2	FACETS	0.882	0.817	0.95	0.882	0.817	0.95	CLONAL	1	TRUE	1	0.594615897191612	2		864	694	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	236	643	4	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	1	2	FACETS	0.967	0.905	1	0.967	0.905	1	CLONAL	1	TRUE	1	0.594615897191612	2		647	821	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698146	47698147	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs63750393	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	120	352	0	ENST00000233146.2:c.1705_1706del	p.Glu569IlefsTer2	p.E569Ifs*2	ENST00000233146	NM_000251.2	568	acAGaa/acaa	11/16	1	2	FACETS	0.881	0.801	0.965	0.881	0.801	0.965	CLONAL	1	TRUE	1	0.594615897191612	2		352	458	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800900	18800900	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs372507637	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	120	399	0	ENST00000266497.5:c.4276C>T	p.Arg1426Ter	p.R1426*	ENST00000266497		1426	Cga/Tga	31/31	1	2	FACETS	0.891	0.81	0.975	0.891	0.81	0.975	CLONAL	1	TRUE	1	0.594615897191612	2		399	453	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851717	134851717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150028142	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	160	602	0	ENST00000398015.3:c.1123G>A	p.Asp375Asn	p.D375N	ENST00000398015	NM_004441.4	375	Gac/Aac	5/16	1	2	FACETS	0.959	0.885	1	0.959	0.885	1	CLONAL	1	TRUE	1	0.594615897191612	2		602	561	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487277	56487277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035001455	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	157	509	0	ENST00000267101.3:c.1423C>T	p.Arg475Trp	p.R475W	ENST00000267101	NM_001982.3	475	Cgg/Tgg	12/28	1	2	FACETS	0.866	0.796	0.937	0.866	0.796	0.937	CLONAL	1	TRUE	1	0.594615897191612	2		509	610	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906958	32906958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358423	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	150	434	1	ENST00000380152.3:c.1343G>A	p.Arg448His	p.R448H	ENST00000380152		448	cGt/cAt	10/27	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.594615897191612	2		435	488	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408879	41408879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776612407	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	159	496	1	ENST00000373198.4:c.547C>T	p.Arg183Trp	p.R183W	ENST00000373198	NM_133170.3	183	Cgg/Tgg	4/32	1	2	FACETS	0.998	0.92	1	0.998	0.92	1	CLONAL	1	TRUE	1	0.594615897191612	2		497	536	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	138	542	6	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.791	0.722	0.862	0.791	0.722	0.862	SUBCLONAL	1	TRUE	1	0.594615897191612	2		548	587	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134251	11134251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1218643327	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	179	709	1	ENST00000358026.2:c.2917C>T	p.Arg973Trp	p.R973W	ENST00000358026	NM_001128849.1	973	Cgg/Tgg	20/36	1	2	FACETS	0.816	0.754	0.88	0.816	0.754	0.88	CLONAL	1	TRUE	1	0.594615897191612	2		710	738	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56872937	56872937	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	116	310	3	ENST00000308159.5:c.2097del	p.Phe699LeufsTer19	p.F699Lfs*19	ENST00000308159	NM_014669.4	698	Ttt/tt	19/22	1	2	FACETS	0.863	0.783	0.947	0.863	0.783	0.947	CLONAL	1	TRUE	1	0.594615897191612	2		313	452	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755427	39755427	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	152	543	4	ENST00000288319.7:c.1338del	p.Phe446LeufsTer59	p.F446Lfs*59	ENST00000288319	NM_182918.3	446	ttT/tt	10/10	1	2	FACETS	0.908	0.835	0.984	0.908	0.835	0.984	CLONAL	1	TRUE	1	0.594615897191612	2		547	563	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058747	180058748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755445139	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	175	767	1	ENST00000261937.6:c.89dup	p.Thr31AspfsTer15	p.T31Dfs*15	ENST00000261937	NM_182925.4	30	ccg/ccCg	2/30	0.202928639167689	0	FACETS	0.328	0.303	0.355			1	INDETERMINATE	1	TRUE	0	0.594615897191612	0		768	727	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543606	148543606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	181	469	0	ENST00000320356.2:c.202G>A	p.Val68Met	p.V68M	ENST00000320356	NM_004456.4	68	Gtg/Atg	3/20	1	2	FACETS	0.88	0.814	0.947	0.88	0.814	0.947	CLONAL	1	TRUE	1	0.594615897191612	2		469	692	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394380	162394380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554256339	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	119	365	2	ENST00000366898.1:c.688G>A	p.Ala230Thr	p.A230T	ENST00000366898	NM_004562.2	230	Gca/Aca	6/12	1	2	FACETS	0.87	0.79	0.953	0.87	0.79	0.953	CLONAL	1	TRUE	1	0.594615897191612	2		367	460	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209504	98209504	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766315655	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	166	353	1	ENST00000331920.6:c.4034G>A	p.Arg1345His	p.R1345H	ENST00000331920	NM_000264.3	1345	cGt/cAt	23/24	1	2	FACETS	0.881	0.812	0.951	0.881	0.812	0.951	CLONAL	1	TRUE	1	0.594615897191612	2		354	634	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	273	879	1	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.855	0.803	0.909	0.855	0.803	0.909	CLONAL	1	TRUE	1	0.594615897191612	2		880	1074	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	171	536	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.853	0.788	0.921	0.853	0.788	0.921	CLONAL	1	TRUE	1	0.594615897191612	2		537	674	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27213538	27213538	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	157	469	0	ENST00000380036.4:c.2938del	p.Ile980Ter	p.I980*	ENST00000380036	NM_000459.3	978	gcA/gc	18/23	1	2	FACETS	0.807	0.742	0.875	0.807	0.742	0.875	CLONAL	1	TRUE	1	0.594615897191612	2		469	654	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193850	106193850	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	111	314	1	ENST00000380013.4:c.4317del	p.Lys1439AsnfsTer9	p.K1439Nfs*9	ENST00000380013	NM_001127208.2	1438	Aaa/aa	10/11	1	2	FACETS	0.762	0.688	0.839	0.762	0.688	0.839	SUBCLONAL	1	TRUE	1	0.594615897191612	2		315	490	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218668	98218668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	141	370	0	ENST00000331920.6:c.3196G>A	p.Glu1066Lys	p.E1066K	ENST00000331920	NM_000264.3	1066	Gag/Aag	19/24	1	2	FACETS	0.897	0.821	0.974	0.897	0.821	0.974	CLONAL	1	TRUE	1	0.594615897191612	2		370	529	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980604	70980604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1036596459	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	181	624	0	ENST00000276594.2:c.773C>T	p.Thr258Met	p.T258M	ENST00000276594	NM_024504.3	258	aCg/aTg	4/8	1	2	FACETS	0.938	0.869	1	0.938	0.869	1	CLONAL	1	TRUE	1	0.594615897191612	2		624	649	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717712	89717712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782350	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	170	431	0	ENST00000371953.3:c.737C>T	p.Pro246Leu	p.P246L	ENST00000371953	NM_000314.4	246	cCg/cTg	7/9	1	2	FACETS	0.909	0.84	0.981	0.909	0.84	0.981	CLONAL	1	TRUE	1	0.594615897191612	2		431	629	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447773	49447773	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	205	554	0	ENST00000301067.7:c.661del	p.Ala221LeufsTer40	p.A221Lfs*40	ENST00000301067	NM_003482.3	221	Gct/ct	5/54	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.594615897191612	2		554	597	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316397	14316397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782457908	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	150	767	0	ENST00000256196.4:c.208G>A	p.Ala70Thr	p.A70T	ENST00000256196		70	Gca/Aca	3/6	1	2	FACETS	0.868	0.797	0.942	0.868	0.797	0.942	CLONAL	1	TRUE	1	0.594615897191612	2		767	581	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31405819	31405819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	89	450	1	ENST00000344624.3:c.3959C>T	p.Ala1320Val	p.A1320V	ENST00000344624		1320	gCg/gTg	32/33	1	2	FACETS	0.76	0.678	0.846	0.76	0.678	0.846	SUBCLONAL	1	TRUE	1	0.594615897191612	2		451	394	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210893	36210893	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	211	810	4	ENST00000222270.7:c.649del	p.Arg217GlyfsTer22	p.R217Gfs*22	ENST00000222270	NM_014727.1	215	aCc/ac	3/37	1	2	FACETS	0.89	0.829	0.954	0.89	0.829	0.954	CLONAL	1	TRUE	1	0.594615897191612	2		814	797	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120560	2120560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397515296	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	266	904	1	ENST00000219476.3:c.1820C>T	p.Ala607Val	p.A607V	ENST00000219476	NM_000548.3	607	gCg/gTg	17/42	1	2	FACETS	0.986	0.927	1	0.986	0.927	1	CLONAL	1	TRUE	1	0.594615897191612	2		905	907	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349471	73349471	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777245855	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	160	454	1	ENST00000377767.4:c.865G>A	p.Glu289Lys	p.E289K	ENST00000377767	NM_014953.3	289	Gaa/Aaa	6/21	1	2	FACETS	0.912	0.84	0.986	0.912	0.84	0.986	CLONAL	1	TRUE	1	0.594615897191612	2		455	590	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131930584	131930584	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs749083001	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	72	229	0	ENST00000265335.6:c.1817A>G	p.Gln606Arg	p.Q606R	ENST00000265335		606	cAg/cGg	12/25	1	2	FACETS	0.743	0.654	0.837	0.743	0.654	0.837	SUBCLONAL	1	TRUE	1	0.594615897191612	2		229	326	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510219	187510219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1276553545	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	182	485	1	ENST00000441802.2:c.13294G>A	p.Glu4432Lys	p.E4432K	ENST00000441802	NM_005245.3	4432	Gaa/Aaa	27/27	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.594615897191612	2		486	599	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244326	5244326	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	212	914	1	ENST00000357368.4:c.1156C>T	p.Arg386Cys	p.R386C	ENST00000357368	NM_002850.3	386	Cgt/Tgt	11/38	1	2	FACETS	0.807	0.75	0.865	0.807	0.75	0.865	CLONAL	1	TRUE	1	0.594615897191612	2		915	884	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031619	36031619	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753395244	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	180	814	4	ENST00000358208.4:c.1448G>A	p.Arg483Gln	p.R483Q	ENST00000358208		483	cGg/cAg	12/12	1	2	FACETS	0.893	0.826	0.962	0.893	0.826	0.962	CLONAL	1	TRUE	1	0.594615897191612	2		818	678	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456466	99456466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764375938	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	123	502	0	ENST00000268035.6:c.1783C>T	p.Arg595Cys	p.R595C	ENST00000268035	NM_000875.3	595	Cgt/Tgt	8/21	1	2	FACETS	0.797	0.724	0.873	0.797	0.724	0.873	SUBCLONAL	1	TRUE	1	0.594615897191612	2		502	519	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957465	175957465	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	180	514	0	ENST00000367669.3:c.1931A>G	p.Asn644Ser	p.N644S	ENST00000367669	NM_022457.5	644	aAc/aGc	17/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.594615897191612	2		514	561	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918482	94918482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368962287	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	181	485	1	ENST00000536441.1:c.700G>A	p.Val234Ile	p.V234I	ENST00000536441	NM_144665.3	234	Gtt/Att	5/10	1	2	FACETS	0.901	0.834	0.97	0.901	0.834	0.97	CLONAL	1	TRUE	1	0.594615897191612	2		486	676	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557791	21557791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	234	746	1	ENST00000382592.4:c.2054C>T	p.Ala685Val	p.A685V	ENST00000382592	NM_014572.2	685	gCt/gTt	5/8	1	2	FACETS	0.949	0.888	1	0.949	0.888	1	CLONAL	1	TRUE	1	0.594615897191612	2		747	829	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712713	43712713	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	236	806	0	ENST00000382044.4:c.4471T>G	p.Phe1491Val	p.F1491V	ENST00000382044	NM_001141980.1	1491	Ttt/Gtt	21/28	1	2	FACETS	0.944	0.883	1	0.944	0.883	1	CLONAL	1	TRUE	1	0.594615897191612	2		806	841	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969788	81969788	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1278946830	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	154	537	0	ENST00000359376.3:c.2857C>T	p.Arg953Ter	p.R953*	ENST00000359376	NM_002661.3	953	Cga/Tga	27/33	1	2	FACETS	0.959	0.883	1	0.959	0.883	1	CLONAL	1	TRUE	1	0.594615897191612	2		537	540	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66525125	66525125	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	116	245	0	ENST00000358598.2:c.887del	p.Leu296Ter	p.L296*	ENST00000358598	NM_212471.2	295	aTt/at	9/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.594615897191612	2		245	372	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603021	48603021	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	120	274	0	ENST00000342988.3:c.1322G>A	p.Arg441His	p.R441H	ENST00000342988	NM_005359.5	441	cGt/cAt	11/12	1	2	FACETS	0.905	0.823	0.99	0.905	0.823	0.99	CLONAL	1	TRUE	1	0.594615897191612	2		274	446	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094846	11094846	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	160	980	0	ENST00000358026.2:c.22del	p.Leu8TrpfsTer35	p.L8Wfs*35	ENST00000358026	NM_001128849.1	7	Ccc/cc	2/36	1	2	FACETS	0.609	0.558	0.662	0.609	0.558	0.662	SUBCLONAL	1	TRUE	1	0.594615897191612	2		980	884	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229010	36229010	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	268	745	0	ENST00000222270.7:c.7790C>T	p.Ala2597Val	p.A2597V	ENST00000222270	NM_014727.1	2597	gCg/gTg	36/37	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.594615897191612	2		745	889	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735524	204735524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	122	520	1	ENST00000302823.3:c.325G>A	p.Gly109Arg	p.G109R	ENST00000302823	NM_005214.4	109	Gga/Aga	2/4	1	2	FACETS	0.716	0.65	0.786	0.716	0.65	0.786	SUBCLONAL	1	TRUE	1	0.594615897191612	2		521	573	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144527	55144527	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	113	387	0	ENST00000257290.5:c.2003-2A>G		p.X668_splice	ENST00000257290	NM_006206.4	668			1	2	FACETS	0.814	0.737	0.895	0.814	0.737	0.895	CLONAL	1	TRUE	1	0.594615897191612	2		387	467	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156805	106156805	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	188	521	0	ENST00000380013.4:c.1709del	p.Pro570LeufsTer10	p.P570Lfs*10	ENST00000380013	NM_001127208.2	569	gCc/gc	3/11	1	2	FACETS	0.99	0.919	1	0.99	0.919	1	CLONAL	1	TRUE	1	0.594615897191612	2		521	639	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183279	56183279	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	197	544	0	ENST00000399503.3:c.4189T>G	p.Ser1397Ala	p.S1397A	ENST00000399503	NM_005921.1	1397	Tca/Gca	18/20	1	2	FACETS	0.916	0.851	0.984	0.916	0.851	0.984	CLONAL	1	TRUE	1	0.594615897191612	2		544	723	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564686	86564686	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	165	765	0	ENST00000274376.6:c.422del	p.Pro141LeufsTer33	p.P141Lfs*33	ENST00000274376	NM_002890.2	140	Ccc/cc	1/25	1	2	FACETS	0.813	0.748	0.879	0.813	0.748	0.879	CLONAL	1	TRUE	1	0.594615897191612	2		765	683	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056044	26056044	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745914791	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	99	335	0	ENST00000343677.2:c.613C>T	p.Pro205Ser	p.P205S	ENST00000343677	NM_005319.3	205	Cct/Tct	1/1	1	2	FACETS	0.835	0.75	0.923	0.835	0.75	0.923	CLONAL	1	TRUE	1	0.594615897191612	2		335	399	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468060	50468060	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	114	484	0	ENST00000331340.3:c.1295A>G	p.His432Arg	p.H432R	ENST00000331340	NM_006060.4	432	cAc/cGc	8/8	1	2	FACETS	0.839	0.76	0.921	0.839	0.76	0.921	CLONAL	1	TRUE	1	0.594615897191612	2		484	457	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508275	106508275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749392283	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	118	399	0	ENST00000359195.3:c.269G>A	p.Arg90Gln	p.R90Q	ENST00000359195	NM_002649.2	90	cGg/cAg	2/11	1	2	FACETS	0.978	0.89	1	0.978	0.89	1	CLONAL	1	TRUE	1	0.594615897191612	2		399	406	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151164275	151164275	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	163	570	0	ENST00000262187.5:c.485G>T	p.Arg162Met	p.R162M	ENST00000262187	NM_005614.3	162	aGg/aTg	8/8	1	2	FACETS	0.899	0.829	0.971	0.899	0.829	0.971	CLONAL	1	TRUE	1	0.594615897191612	2		570	610	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542189	141542189	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	249	641	2	ENST00000220592.5:c.2534C>T	p.Ala845Val	p.A845V	ENST00000220592	NM_012154.3	845	gCg/gTg	19/19	1	2	FACETS	0.947	0.888	1	0.947	0.888	1	CLONAL	1	TRUE	1	0.594615897191612	2		643	884	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	103	188	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.897	0.815	0.98	0.897	0.815	0.98	CLONAL	1	TRUE	1	0.847898103021402	2		188	271	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0038185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	23511	1019	4	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.847898103021402	34	FACETS	1	0.999	1			1	CLONAL	33	TRUE	NA	0.847898103021402	34		1023	24332	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418346	139418346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532574807	NA	P-0038185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	541	1063	0	ENST00000277541.6:c.226G>A	p.Val76Met	p.V76M	ENST00000277541	NM_017617.3	76	Gtg/Atg	3/34	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.847898103021402	2		1063	1183	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592078	67592212	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AACAAAGCTGAAAACCTGTTGCGAGGGAAGCGAGATGGCACTTTTCTTGTCCGGGAGAGCAGTAAACAGGGCTGCTATGCCTGCTCTGTAGTGTATGTATCTCCAGCAAACTTTTCTTTACAACATCTCATGAAG	AACAAAGCTGAAAACCTGTTGCGAGGGAAGCGAGATGGCACTTTTCTTGTCCGGGAGAGCAGTAAACAGGGCTGCTATGCCTGCTCTGTAGTGTATGTATCTCCAGCAAACTTTTCTTTACAACATCTCATGAAG	-	novel	NA	P-0038185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	63	481	0	ENST00000274335.5:c.1895_1985+44del		p.X632_splice	ENST00000274335		632		14/15	1	2	FACETS	0.319	0.276	0.365	0.319	0.276	0.365	SUBCLONAL	1	TRUE	1	0.847898103021402	2		481	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0038262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	88	880	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.867	0.767	0.974	0.867	0.767	0.974	CLONAL	1	TRUE	1	0.25	2		880	812	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225839	2225839	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	59	598	0	ENST00000326181.6:c.1633del	p.Asp545ThrfsTer23	p.D545Tfs*23	ENST00000326181	NM_032271.2	544	tGg/tg	18/21	1	2	FACETS	0.866	0.746	0.997	0.866	0.746	0.997	CLONAL	1	TRUE	1	0.25	2		598	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0038427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	135	652	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.320091284551391	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	3	TRUE	0	0.354130001870784	3		652	283	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649566	206649566	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	41	761	0	ENST00000367120.3:c.401G>C	p.Arg134Pro	p.R134P	ENST00000367120	NM_014002.3	134	cGc/cCc	6/22	0.319694132964229	3	FACETS	0.595	0.496	0.706	0.298	0.248	0.353	SUBCLONAL	1	TRUE	1	0.354130001870784	3		761	458	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856482	111856482	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1337144150	NA	P-0038427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	19	250	0	ENST00000341259.2:c.533T>C	p.Leu178Pro	p.L178P	ENST00000341259	NM_005475.2	178	cTg/cCg	2/8	0.113778393334151	5	FACETS	0.865	0.66	1	0.216	0.165	0.276	INDETERMINATE	1	TRUE	1	0.354130001870784	5		250	190	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865899	56865899	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs779103749	NA	P-0038427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	18	456	0	ENST00000308159.5:c.1231G>C	p.Glu411Gln	p.E411Q	ENST00000308159	NM_014669.4	411	Gag/Cag	11/22	1	2	FACETS	0.458	0.345	0.59	0.458	0.345	0.59	SUBCLONAL	1	TRUE	1	0.354130001870784	2		456	222	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320304	30320304	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	27	449	0	ENST00000322652.5:c.1245A>T	p.Glu415Asp	p.E415D	ENST00000322652	NM_015355.2	415	gaA/gaT	11/16	0.354130001870784	1	FACETS	0.701	0.563	0.856	0.701	0.563	0.856	SUBCLONAL	1	TRUE	0	0.354130001870784	1		449	179	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618186	37618187	+	upstream_gene_variant	5'Flank	INS	-	-	T	novel	NA	P-0038427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	13	97	0				ENST00000447079	NM_015083.1	-/1490			0.354130001870784	2	FACETS	1	0.785	1	1	0.785	1	CLONAL	2	TRUE	0	0.354130001870784	2		97	35	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619319	37619320	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AG	novel	NA	P-0038427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	27	615	1	ENST00000447079.4:c.995_996delinsAG	p.Ser332Ter	p.S332*	ENST00000447079	NM_015083.1	332	tCC/tAG	1/14	0.354130001870784	2	FACETS	0.404	0.322	0.499	0.202	0.161	0.25	SUBCLONAL	1	TRUE	0	0.354130001870784	2		616	377	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229338	5229338	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	30	747	0	ENST00000357368.4:c.2365A>T	p.Thr789Ser	p.T789S	ENST00000357368	NM_002850.3	789	Acg/Tcg	16/38	0.354130001870784	1	FACETS	0.677	0.549	0.819	0.677	0.549	0.819	SUBCLONAL	1	TRUE	0	0.354130001870784	1		747	206	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589819	55589819	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	18	519	0	ENST00000288135.5:c.1301C>T	p.Pro434Leu	p.P434L	ENST00000288135	NM_000222.2	434	cCa/cTa	8/21	0.337199812090831	2	FACETS	0.425	0.321	0.549	0.213	0.16	0.275	SUBCLONAL	1	TRUE	0	0.354130001870784	2		519	239	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184043	123184043	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	10	397	0	ENST00000218089.9:c.901A>C	p.Ile301Leu	p.I301L	ENST00000218089	NM_001042749.1	301	Ata/Cta	11/35	0.224378798643571	2	FACETS	0.372	0.252	0.521	0.186	0.126	0.261	SUBCLONAL	1	TRUE	0	0.354130001870784	2		397	152	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101412	27101418	+	frameshift_variant	Frame_Shift_Del	DEL	CAAGGCC	CAAGGCC	-	novel	NA	P-0038558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	220	463	0	ENST00000324856.7:c.4695_4701del	p.Arg1566LeufsTer44	p.R1566Lfs*44	ENST00000324856	NM_006015.4	1565	aCAAGGCCc/ac	18/20	0.49590064948632	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.556334077251824	2		463	388	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100211	30100211	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	78	367	0	ENST00000331968.5:c.1409A>C	p.Glu470Ala	p.E470A	ENST00000331968	NM_002742.2	470	gAa/gCa	10/18	0.217357546462069	3	FACETS	1	0.952	1	0.571	0.506	0.639	INDETERMINATE	1	TRUE	1	0.556334077251824	3		367	314	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098037	178098037	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	85	333	0	ENST00000397062.3:c.343T>A	p.Tyr115Asn	p.Y115N	ENST00000397062	NM_006164.4	115	Tac/Aac	3/5	0.500132698427443	2	FACETS	0.876	0.78	0.976	0.438	0.39	0.488	CLONAL	1	TRUE	0	0.556334077251824	2		333	349	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0038626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	68	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.942	0.822	1	0.942	0.822	1	CLONAL	1	TRUE	1	0.335029514467373	2		436	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0038626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	122	1020	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.335029514467373	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.335029514467373	1		1020	575	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857910	9857910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	76	573	1	ENST00000330684.3:c.3491C>T	p.Thr1164Met	p.T1164M	ENST00000330684	NM_001134407.1	1164	aCg/aTg	13/13	0.312668435433369	3	FACETS	0.923	0.81	1	0.461	0.405	0.522	CLONAL	1	TRUE	1	0.335029514467373	3		574	574	SUCCESS
APC	324	MSKCC	GRCh37	5	112175271	112175271	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1554085429	NA	P-0038626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	77	273	0	ENST00000257430.4:c.3980C>G	p.Ser1327Ter	p.S1327*	ENST00000257430	NM_000038.5	1327	tCa/tGa	16/16	0.254508529377052	3	FACETS	0.994	0.883	1	0.663	0.589	0.74	CLONAL	2	TRUE	0	0.335029514467373	3		273	270	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584725	48584725	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	74	450	0	ENST00000342988.3:c.803G>A	p.Trp268Ter	p.W268*	ENST00000342988	NM_005359.5	268	tGg/tAg	7/12	0.324409210428405	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.335029514467373	1		450	341	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869492	102869492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	73	585	1	ENST00000307046.8:c.149C>T	p.Pro50Leu	p.P50L	ENST00000307046	NM_001111285.1	50	cCg/cTg	2/4	1	2	FACETS	0.988	0.868	1	0.988	0.868	1	CLONAL	1	TRUE	1	0.335029514467373	2		586	441	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876491	59876491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	69	477	0	ENST00000259008.2:c.1310C>T	p.Pro437Leu	p.P437L	ENST00000259008	NM_032043.2	437	cCc/cTc	9/20	0.335029514467373	1	FACETS	0.895	0.784	1	0.895	0.784	1	CLONAL	1	TRUE	0	0.335029514467373	1		477	383	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0038674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	247	478	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.45461489004099	5	FACETS	1	0.982	1	1	0.982	1	CLONAL	5	TRUE	0	0.578112439520259	5		478	310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0038674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	628	742	1	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.578112439520259	NA		743	1076	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99180083	99180083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777486763	NA	P-0038674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	155	527	2	ENST00000074304.5:c.2026G>A	p.Val676Met	p.V676M	ENST00000074304	NM_001134224.1	676	Gtg/Atg	19/26	0.510633286595656	3	FACETS	0.811	0.743	0.883	0.406	0.371	0.442	CLONAL	1	TRUE	1	0.578112439520259	3		529	852	SUCCESS
CBL	867	MSKCC	GRCh37	11	119077305	119077305	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	273	694	1	ENST00000264033.4:c.178T>A	p.Trp60Arg	p.W60R	ENST00000264033	NM_005188.3	60	Tgg/Agg	1/16	0.198301675876604	1	FACETS	0.676	0.635	0.718	0.676	0.635	0.718	INDETERMINATE	1	TRUE	0	0.578112439520259	1		695	994	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194802	30194802	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	80	583	1	ENST00000331968.5:c.343C>A	p.Gln115Lys	p.Q115K	ENST00000331968	NM_002742.2	115	Cag/Aag	2/18	0.577381564642728	2	FACETS	0.69	0.611	0.774	0.345	0.305	0.387	SUBCLONAL	1	TRUE	0	0.578112439520259	2		584	401	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2164155	2164211	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	AGCATGGTGCGGCGGCCGCGCGCGCGGACATGGGGGAGAAGCTGGAGCTGAGACTGA	AGCATGGTGCGGCGGCCGCGCGCGCGGACATGGGGGAGAAGCTGGAGCTGAGACTGA	-	novel	NA	P-0038674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	110	265	0	ENST00000398665.3:c.-27_30del		p.*9*	ENST00000398665	NM_032482.2	?-10/1537		1/28	0.577756039698598	2	FACETS	1	0.984	1	0.694	0.634	0.756	CLONAL	1	TRUE	0	0.578112439520259	2		265	274	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225732	26225732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	112	572	0	ENST00000360408.1:c.350G>A	p.Arg117His	p.R117H	ENST00000360408	NM_003532.2	117	cGc/cAc	1/1	0.578112439520259	3	FACETS	0.408	0.366	0.454			1	SUBCLONAL	1	TRUE	NA	0.578112439520259	3		572	1223	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958897	2959073	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGGGCTTCTCTATAAGCCCCTCTGCTGATGTTCGTGGCATCCGCAGCCTCCTGCCTGGTCCTCCATAGACTCAGGGAAATGGAGGCCCCGCCCTGATTCTGGCCTCACCGGCTGTAGCTGGGTATGGTGCCCATATCCAGGTCATGGTCTGTGAAAGGGTCGACCCGCGCGCACAG	CTGGGCTTCTCTATAAGCCCCTCTGCTGATGTTCGTGGCATCCGCAGCCTCCTGCCTGGTCCTCCATAGACTCAGGGAAATGGAGGCCCCGCCCTGATTCTGGCCTCACCGGCTGTAGCTGGGTATGGTGCCCATATCCAGGTCATGGTCTGTGAAAGGGTCGACCCGCGCGCACAG	-	novel	NA	P-0038674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	70	169	0	ENST00000396946.4:c.2443_2510+109del		p.X815_splice	ENST00000396946	NM_032415.4	815		18/25	0.577756039698598	2	FACETS	0.835	0.75	0.92	0.835	0.75	0.92	CLONAL	2	TRUE	0	0.578112439520259	2		169	145	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0038757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	127	663	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.24934421113358	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.24934421113358	1		664	734	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0038757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	95	455	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.24934421113358	2		455	681	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528739	157528770	+	frameshift_variant	Frame_Shift_Del	DEL	GCATTGGAAACTTGATAAGCTTCCTAGAGGAT	GCATTGGAAACTTGATAAGCTTCCTAGAGGAT	-	novel	NA	P-0038757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	100	599	0	ENST00000346085.5:c.6465_6496del	p.Ser2155ArgfsTer26	p.S2155Rfs*26	ENST00000346085	NM_020732.3	2155	aGCATTGGAAACTTGATAAGCTTCCTAGAGGAT/a	20/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.24934421113358	2		599	645	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913476	NA	P-0038758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	220	679	0	ENST00000358487.5:c.1647T>G	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaG	12/18	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.56362535794995	2		679	683	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	176	499	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	0.932	0.862	1	0.932	0.862	1	CLONAL	1	TRUE	1	0.56362535794995	2		499	670	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0038758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	175	435	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	0.973	0.9	1	0.973	0.9	1	CLONAL	1	TRUE	1	0.56362535794995	2		435	638	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557629	95557629	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	205	617	0	ENST00000393063.1:c.5438A>G	p.Glu1813Gly	p.E1813G	ENST00000393063	NM_030621.3	1813	gAg/gGg	26/28	1	2	FACETS	0.983	0.915	1	0.983	0.915	1	CLONAL	1	TRUE	1	0.56362535794995	2		617	740	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1485978447	NA	P-0038758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	193	440	0	ENST00000324856.7:c.5164C>T	p.Arg1722Ter	p.R1722*	ENST00000324856	NM_006015.4	1722	Cga/Tga	20/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.56362535794995	2		440	656	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692803	89692803	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	116	402	1	ENST00000371953.3:c.287C>A	p.Pro96Gln	p.P96Q	ENST00000371953	NM_000314.4	96	cCa/cAa	5/9	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.56362535794995	2		403	355	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943739	9943739	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1489261681	NA	P-0038758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	216	707	0	ENST00000330684.3:c.1202C>T	p.Pro401Leu	p.P401L	ENST00000330684	NM_001134407.1	401	cCg/cTg	5/13	1	2	FACETS	0.859	0.8	0.921	0.859	0.8	0.921	CLONAL	1	TRUE	1	0.56362535794995	2		707	892	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821400	72821401	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGC	novel	NA	P-0038758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	210	535	0	ENST00000268489.5:c.10771_10774dup	p.His3592ArgfsTer75	p.H3592Rfs*75	ENST00000268489	NM_006885.3	3592	cac/cGCTCac	10/10	1	2	FACETS	0.898	0.835	0.962	0.898	0.835	0.962	CLONAL	1	TRUE	1	0.56362535794995	2		535	830	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990307	81990307	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0038758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	139	456	0	ENST00000359376.3:c.3579del	p.Glu1194ArgfsTer10	p.E1194Rfs*10	ENST00000359376	NM_002661.3	1193	gAa/ga	32/33	1	2	FACETS	0.87	0.795	0.947	0.87	0.795	0.947	CLONAL	1	TRUE	1	0.56362535794995	2		456	567	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953083	2953083	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1322611135	NA	P-0038758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	253	738	0	ENST00000396946.4:c.2857G>A	p.Glu953Lys	p.E953K	ENST00000396946	NM_032415.4	953	Gag/Aag	22/25	1	2	FACETS	0.942	0.883	1	0.942	0.883	1	CLONAL	1	TRUE	1	0.56362535794995	2		738	953	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0038817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	145	311	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.708982796211089	1	FACETS	0.982	0.916	1	0.982	0.916	1	CLONAL	1	TRUE	0	0.708982796211089	1		311	269	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525104	9525104	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	201	459	1	ENST00000353224.5:c.1781C>T	p.Ser594Phe	p.S594F	ENST00000353224	NM_177990.2	594	tCc/tTc	8/10	1	2	FACETS	0.922	0.859	0.986	0.922	0.859	0.986	CLONAL	1	TRUE	1	0.708982796211089	2		460	615	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781440	135781440	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203542	NA	P-0038817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	58	524	1	ENST00000298552.3:c.1525C>T	p.Arg509Ter	p.R509*	ENST00000298552	NM_001162426.1	509	Cga/Tga	15/23	0.708982796211089	1	FACETS	0.267	0.23	0.308	0.267	0.23	0.308	SUBCLONAL	1	TRUE	0	0.708982796211089	1		525	395	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692968	89692968	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	217	498	2	ENST00000371953.3:c.452C>A	p.Ala151Asp	p.A151D	ENST00000371953	NM_000314.4	151	gCc/gAc	5/9	0.708982796211089	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.708982796211089	1		500	389	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0038817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	219	302	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.708982796211089	2		302	615	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346978	73346978	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0038817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	96	241	0	ENST00000377767.4:c.1240-1G>A		p.X414_splice	ENST00000377767	NM_014953.3	414			1	2	FACETS	0.833	0.75	0.919	0.833	0.75	0.919	CLONAL	1	TRUE	1	0.708982796211089	2		241	325	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729084	66729101	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CTAATTCATCTGGAGATC	CTAATTCATCTGGAGATC	-	novel	NA	P-0038817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	409	582	0	ENST00000307102.5:c.292_309del	p.Leu98_Ile103del	p.L98_I103del	ENST00000307102	NM_002755.3	98	CTAATTCATCTGGAGATC/-	3/11	0.703386534385425	3	FACETS	0.876	0.838	0.914	0.876	0.838	0.914	CLONAL	2	TRUE	1	0.708982796211089	3		582	892	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754451	41754451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	326	714	0	ENST00000301178.4:c.1570G>A	p.Glu524Lys	p.E524K	ENST00000301178	NM_021913.4	524	Gag/Aag	13/20	1	2	FACETS	0.978	0.927	1	0.978	0.927	1	CLONAL	1	TRUE	1	0.708982796211089	2		714	940	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55225400	55225400	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1390766480	NA	P-0038817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	230	473	1	ENST00000275493.2:c.1252C>T	p.His418Tyr	p.H418Y	ENST00000275493	NM_005228.3	418	Cat/Tat	11/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.708982796211089	2		474	589	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0038832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	72	684	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.432	0.378	0.49	0.432	0.378	0.49	SUBCLONAL	1	TRUE	1	0.655505132808731	2		684	509	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135703	64135703	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	114	581	0	ENST00000334205.4:c.1171G>C	p.Ala391Pro	p.A391P	ENST00000334205	NM_003942.2	391	Gca/Cca	10/17	1	2	FACETS	0.538	0.485	0.593	0.538	0.485	0.593	SUBCLONAL	1	TRUE	1	0.655505132808731	2		581	647	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005565	42005567	+	frameshift_variant	Frame_Shift_Del	DEL	AGG	AGG	TT	novel	NA	P-0038832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	92	388	1	ENST00000219905.7:c.3301_3303delinsTT	p.Arg1101LeufsTer32	p.R1101Lfs*32	ENST00000219905	NM_001164273.1	1101	AGG/TT	9/24	1	2	FACETS	0.586	0.523	0.653	0.586	0.523	0.653	SUBCLONAL	1	TRUE	1	0.655505132808731	2		389	479	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166381	7166381	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	108	598	1	ENST00000302850.5:c.1645G>T	p.Asp549Tyr	p.D549Y	ENST00000302850	NM_000208.2	549	Gat/Tat	8/22	1	2	FACETS	0.545	0.49	0.603	0.545	0.49	0.603	SUBCLONAL	1	TRUE	1	0.655505132808731	2		599	605	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942795	44942796	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	105	419	0	ENST00000377967.4:c.3376dup	p.Ile1126AsnfsTer25	p.I1126Nfs*25	ENST00000377967	NM_021140.2	1125	-/A	23/29	1	2	FACETS	0.518	0.465	0.575	0.518	0.465	0.575	SUBCLONAL	1	TRUE	1	0.655505132808731	2		419	618	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205173	123205173	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	40	233	0	ENST00000218089.9:c.2533G>A	p.Asp845Asn	p.D845N	ENST00000218089	NM_001042749.1	845	Gat/Aat	25/35	1	2	FACETS	0.425	0.355	0.503	0.425	0.355	0.503	SUBCLONAL	1	TRUE	1	0.655505132808731	2		233	287	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0038990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	406	758	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.319554947046863	3	FACETS	0.958	0.915	1	0.958	0.915	1	CLONAL	3	TRUE	0	0.345942745609055	3		759	958	SUCCESS
APC	324	MSKCC	GRCh37	5	112162803	112162803	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1064794163	NA	P-0038990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	156	285	1	ENST00000257430.4:c.1409-2A>G		p.X470_splice	ENST00000257430	NM_000038.5	470			0.319554947046863	3	FACETS	1	0.984	1	0.828	0.766	0.891	CLONAL	2	TRUE	0	0.345942745609055	3		286	426	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478916	56478916	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	375	783	0	ENST00000267101.3:c.372C>A	p.Asn124Lys	p.N124K	ENST00000267101	NM_001982.3	124	aaC/aaA	3/28	0.308545153518653	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.345942745609055	3		783	1259	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593388	48593388	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0038990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	123	275	0	ENST00000342988.3:c.1140-1G>T		p.X380_splice	ENST00000342988	NM_005359.5	380			0.345942745609055	2	FACETS	0.971	0.888	1	0.971	0.888	1	CLONAL	2	TRUE	0	0.345942745609055	2		275	366	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467161	25467161	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	80	574	1	ENST00000264709.3:c.1714G>T	p.Ala572Ser	p.A572S	ENST00000264709	NM_175629.2	572	Gcc/Tcc	15/23	0.227121001307503	3	FACETS	0.609	0.535	0.689	0.203	0.178	0.23	SUBCLONAL	1	TRUE	0	0.345942745609055	3		575	891	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0038990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	88	523	1	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	0.252209097568867	3	FACETS	0.84	0.745	0.943	0.42	0.372	0.472	CLONAL	1	TRUE	1	0.345942745609055	3		524	710	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0038990-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	323	758	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.556634462842265	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.556634462842265	1		759	746	SUCCESS
APC	324	MSKCC	GRCh37	5	112162803	112162803	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1064794163	NA	P-0038990-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	155	285	1	ENST00000257430.4:c.1409-2A>G		p.X470_splice	ENST00000257430	NM_000038.5	470			0.556634462842265	2	FACETS	0.944	0.882	1	0.944	0.882	1	CLONAL	2	TRUE	0	0.556634462842265	2		286	295	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276726	15276726	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs956073860	NA	P-0038990-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	217	712	0	ENST00000263388.2:c.5539G>T	p.Ala1847Ser	p.A1847S	ENST00000263388	NM_000435.2	1847	Gcc/Tcc	30/33	1	2	FACETS	0.987	0.92	1	0.987	0.92	1	CLONAL	1	TRUE	1	0.556634462842265	2		712	790	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478916	56478916	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038990-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	280	783	0	ENST00000267101.3:c.372C>A	p.Asn124Lys	p.N124K	ENST00000267101	NM_001982.3	124	aaC/aaA	3/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.556634462842265	2		783	946	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593388	48593388	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0038990-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	134	275	0	ENST00000342988.3:c.1140-1G>T		p.X380_splice	ENST00000342988	NM_005359.5	380			0.556634462842265	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.556634462842265	1		275	303	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467161	25467161	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038990-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	245	574	1	ENST00000264709.3:c.1714G>T	p.Ala572Ser	p.A572S	ENST00000264709	NM_175629.2	572	Gcc/Tcc	15/23	0.151924599806709	2	FACETS	1	0.992	1	0.69	0.649	0.731	INDETERMINATE	1	TRUE	0	0.556634462842265	2		575	638	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16203019	16203019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217055650	NA	P-0039273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	79	512	22	ENST00000375759.3:c.727C>T	p.Arg243Trp	p.R243W	ENST00000375759	NM_015001.2	243	Cgg/Tgg	3/15	0.19007389717744	2	FACETS	0.996	0.893	1	0.498	0.446	0.552	INDETERMINATE	1	TRUE	0	0.740956015803775	2		534	214	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248011	59248011	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	139	493	0	ENST00000371222.2:c.732del	p.Ile245SerfsTer16	p.I245Sfs*16	ENST00000371222	NM_002228.3	244	ccC/cc	1/1	0.19007389717744	2	FACETS	0.915	0.841	0.991	0.458	0.42	0.496	INDETERMINATE	1	TRUE	0	0.740956015803775	2		493	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577056	7577060	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCC	CTCCC	-	novel	NA	P-0039273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	159	721	0	ENST00000269305.4:c.878_882del	p.Gly293AlafsTer11	p.G293Afs*11	ENST00000269305	NM_001126112.2	293	gGGGAG/g	8/11	0.740956015803775	1	FACETS	0.951	0.892	1	0.951	0.892	1	CLONAL	1	TRUE	0	0.740956015803775	1		721	284	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577067	7577067	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	154	723	0	ENST00000269305.4:c.871A>C	p.Lys291Gln	p.K291Q	ENST00000269305	NM_001126112.2	291	Aag/Cag	8/11	0.740956015803775	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.740956015803775	1		723	253	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006605	62006605	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	214	607	0	ENST00000392795.3:c.674A>C	p.Glu225Ala	p.E225A	ENST00000392795	NM_001039933.1	225	gAg/gCg	6/6	0.648512811071813	3	FACETS	0.929	0.891	0.966	0.929	0.891	0.966	CLONAL	3	TRUE	0	0.740956015803775	3		607	284	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413214	139413214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	23	590	1	ENST00000277541.6:c.928G>A	p.Gly310Arg	p.G310R	ENST00000277541	NM_017617.3	310	Ggg/Agg	6/34	0.142295297545805	2	FACETS	0.202	0.157	0.255	0.101	0.078	0.128	INDETERMINATE	1	TRUE	0	0.600958575562626	2		591	378	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641050	117641050	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	101	420	0	ENST00000368508.3:c.5921A>G	p.Glu1974Gly	p.E1974G	ENST00000368508	NM_002944.2	1974	gAa/gGa	36/43	0.398212376511547	2	FACETS	0.857	0.787	0.928	0.857	0.787	0.928	CLONAL	2	TRUE	0	0.600958575562626	2		420	196	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405159	139405159	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	24	588	0	ENST00000277541.6:c.2686C>T	p.Gln896Ter	p.Q896*	ENST00000277541	NM_017617.3	896	Cag/Tag	17/34	0.142295297545805	2	FACETS	0.269	0.211	0.336	0.134	0.105	0.168	INDETERMINATE	1	TRUE	0	0.600958575562626	2		588	297	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061447	38061448	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0039499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	12	672	0	ENST00000250448.2:c.541_542del	p.Met181GlyfsTer45	p.M181Gfs*45	ENST00000250448	NM_004496.3	181	ATg/g	2/2	0.158592474055567	3	FACETS	0.638	0.451	0.867	0.319	0.225	0.434	INDETERMINATE	1	FALSE	1	0.307712356277619	3		672	141	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428401	72428401	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0039499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	36	481	0	ENST00000477973.2:c.600+1G>T		p.X200_splice	ENST00000477973	NM_012234.5	200			0.169119862471439	4	FACETS	1	0.912	1	1	0.912	1	INDETERMINATE	2	FALSE	2	0.307712356277619	4		481	134	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132711	152132714	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TTCT	TTCT	-	novel	NA	P-0039499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	19	216	0	ENST00000262189.6:c.158_161del	p.Lys53AsnfsTer51	p.K53Nfs*51	ENST00000262189	NM_170606.2	53	aAGAAa/aa	1/59	0.307712356277619	4	FACETS	1	0.874	1	1	0.874	1	CLONAL	3	FALSE	1	0.307712356277619	4		216	47	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589168	67589168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	44	410	0	ENST00000274335.5:c.1156C>T	p.Arg386Ter	p.R386*	ENST00000274335		386	Cga/Tga	9/15	1	2	FACETS	0.983	0.826	1	0.983	0.826	1	CLONAL	1	TRUE	1	0.217212538074841	2		410	412	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0039608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	79	432	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.217212538074841	2		432	684	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0039608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	137	582	2	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.217212538074841	2		584	1191	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424695	49424695	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0039608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	95	814	2	ENST00000301067.7:c.13652T>A	p.Leu4551Ter	p.L4551*	ENST00000301067	NM_003482.3	4551	tTg/tAg	40/54	1	2	FACETS	0.807	0.717	0.904	0.807	0.717	0.904	CLONAL	1	TRUE	1	0.217212538074841	2		816	1084	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578448	7578449	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0039608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	276	1053	0	ENST00000269305.4:c.481_482del	p.Ala161HisfsTer19	p.A161Hfs*19	ENST00000269305	NM_001126112.2	161	GCc/c	5/11	1	2	FACETS	0.94	0.881	1	1	0.995	1	CLONAL	2	TRUE	1	0.217212538074841	2		1053	1352	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252723	10252723	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	85	921	0	ENST00000340748.4:c.3242A>G	p.Asn1081Ser	p.N1081S	ENST00000340748		1081	aAc/aGc	29/40	0.189505260036348	3	FACETS	0.708	0.624	0.799	0.354	0.312	0.4	SUBCLONAL	1	TRUE	1	0.217212538074841	3		921	1225	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678751	52678751	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	38	426	0	ENST00000394830.3:c.868C>A	p.His290Asn	p.H290N	ENST00000394830	NM_018313.4	290	Cat/Aat	9/30	1	2	FACETS	0.48	0.395	0.575	0.48	0.395	0.575	SUBCLONAL	1	TRUE	1	0.217212538074841	2		426	729	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86667956	86667957	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0039608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	38	365	1	ENST00000274376.6:c.1721dup	p.Phe575IlefsTer8	p.F575Ifs*8	ENST00000274376	NM_002890.2	574	gca/gCca	13/25	1	2	FACETS	0.839	0.694	1	0.839	0.694	1	CLONAL	1	TRUE	1	0.217212538074841	2		366	417	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683755	162683755	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	52	528	0	ENST00000366898.1:c.214A>G	p.Arg72Gly	p.R72G	ENST00000366898	NM_004562.2	72	Aga/Gga	3/12	0.189505260036348	3	FACETS	0.687	0.583	0.801	0.343	0.291	0.401	SUBCLONAL	1	TRUE	1	0.217212538074841	3		528	773	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273455	5273455	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs758669308	NA	P-0039630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	250	923	1	ENST00000357368.4:c.377G>A	p.Arg126Gln	p.R126Q	ENST00000357368	NM_002850.3	126	cGa/cAa	4/38	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.510090687258455	2		924	864	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171709	36171736	+	frameshift_variant	Frame_Shift_Del	DEL	GGTAGGACTGATCGTAGGACCACGGTGG	GGTAGGACTGATCGTAGGACCACGGTGG	-	novel	NA	P-0039630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	47	594	0	ENST00000300305.3:c.829_856del	p.Pro277AsnfsTer25	p.P277Nfs*25	ENST00000300305		277	CCACCGTGGTCCTACGATCAGTCCTACCaa/aa	7/8	1	2	FACETS	0.291	0.245	0.342	0.291	0.245	0.342	SUBCLONAL	1	TRUE	1	0.510090687258455	2		594	634	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979529	2979529	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	153	666	0	ENST00000396946.4:c.718G>C	p.Glu240Gln	p.E240Q	ENST00000396946	NM_032415.4	240	Gag/Cag	6/25	0.510090687258455	1	FACETS	0.974	0.898	1	0.974	0.898	1	CLONAL	1	TRUE	0	0.510090687258455	1		666	459	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	161	188	0				ENST00000310581	NM_198253.2	-/1132			0.615398922288437	1	FACETS	0.725	0.678	0.772	0.725	0.678	0.772	SUBCLONAL	1	TRUE	0	0.833313505616287	1		188	311	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911445	134911445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571583026	NA	P-0039645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	252	626	0	ENST00000398015.3:c.1910G>A	p.Arg637His	p.R637H	ENST00000398015	NM_004441.4	637	cGt/cAt	11/16	1	2	FACETS	0.996	0.94	1	0.996	0.94	1	CLONAL	1	TRUE	1	0.833313505616287	2		626	607	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720858	89720858	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1564568660	NA	P-0039645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	255	433	0	ENST00000371953.3:c.1012del	p.Ser338LeufsTer6	p.S338Lfs*6	ENST00000371953	NM_000314.4	337	Ttt/tt	8/9	0.833313505616287	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.833313505616287	1		433	337	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280332	1280332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194223999	NA	P-0039645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	195	1035	3	ENST00000310581.5:c.1891C>T	p.Arg631Trp	p.R631W	ENST00000310581	NM_198253.2	631	Cgg/Tgg	4/16	0.615398922288437	1	FACETS	0.346	0.32	0.372	0.346	0.32	0.372	SUBCLONAL	1	TRUE	0	0.833313505616287	1		1038	790	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847282	68847282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	138	742	0	ENST00000261769.5:c.1204G>A	p.Asp402Asn	p.D402N	ENST00000261769	NM_004360.3	402	Gat/Aat	9/16	0.444886129460073	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.444886129460073	1		742	477	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850816	63850816	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	122	554	0	ENST00000279873.7:c.1594G>T	p.Glu532Ter	p.E532*	ENST00000279873	NM_032199.2	532	Gag/Tag	10/10	0.444886129460073	5	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.444886129460073	5		554	713	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs587781433	NA	P-0000012-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	114	569	0	ENST00000269305.4:c.766A>C	p.Thr256Pro	p.T256P	ENST00000269305	NM_001126112.2	256	Aca/Cca	7/11	0.320469393214047	3	FACETS	1	0.94	1	1	0.94	1	CLONAL	3	TRUE	0	0.391264952233406	3		569	227	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521514	46521514	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000012-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	129	1243	0	ENST00000262741.5:c.894C>G	p.Ile298Met	p.I298M	ENST00000262741	NM_003629.3	298	atC/atG	7/10	0.208038583453887	5	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.446994272435647	5		1243	733	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178126	142178126	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs759327414	NA	P-0000012-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	84	580	1	ENST00000350721.4:c.7292G>T	p.Arg2431Met	p.R2431M	ENST00000350721	NM_001184.3	2431	aGg/aTg	43/47	0.394029357088039	3	FACETS	0.954	0.846	1	0.477	0.423	0.535	CLONAL	1	TRUE	1	0.446994272435647	3		581	482	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139732	55139732	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000012-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	116	811	0	ENST00000257290.5:c.1393T>A	p.Leu465Met	p.L465M	ENST00000257290	NM_006206.4	465	Ttg/Atg	10/23	0.289646909716039	6	FACETS	0.862	0.78	0.949			1	CLONAL	2	TRUE	NA	0.446994272435647	6		811	570	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249542	153249542	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0000012-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	85	458	0	ENST00000281708.4:c.1237-1G>T		p.X413_splice	ENST00000281708	NM_033632.3	413			0.169754075984315	2	FACETS	1	0.956	1	0.571	0.509	0.636	INDETERMINATE	1	TRUE	0	0.446994272435647	2		458	333	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332775	153332775	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000012-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	130	908	0	ENST00000281708.4:c.181G>T	p.Gly61Ter	p.G61*	ENST00000281708	NM_033632.3	61	Gga/Tga	2/12	0.169754075984315	2	FACETS	1	0.927	1	0.51	0.464	0.558	INDETERMINATE	1	TRUE	0	0.446994272435647	2		908	570	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	240484	240484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1205384855	NA	P-0000012-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	28	343	0	ENST00000264932.6:c.1444C>T	p.Pro482Ser	p.P482S	ENST00000264932	NM_004168.2	482	Cct/Tct	11/15	0.446994272435647	5	FACETS	0.799	0.641	0.978	0.266	0.213	0.326	CLONAL	1	TRUE	2	0.446994272435647	5		343	262	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160630	56160630	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000012-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	72	641	2	ENST00000399503.3:c.904G>T	p.Glu302Ter	p.E302*	ENST00000399503	NM_005921.1	302	Gag/Tag	4/20	0.370097890679603	2	FACETS	0.78	0.684	0.882	0.39	0.342	0.441	SUBCLONAL	1	TRUE	0	0.446994272435647	2		643	413	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174930	56174930	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0000012-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	57	427	0	ENST00000399503.3:c.2087+2T>G		p.X696_splice	ENST00000399503	NM_005921.1	696			0.370097890679603	2	FACETS	0.898	0.777	1	0.449	0.388	0.514	CLONAL	1	TRUE	0	0.446994272435647	2		427	284	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696637	176696637	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000012-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	60	763	0	ENST00000439151.2:c.5338G>T	p.Val1780Phe	p.V1780F	ENST00000439151	NM_022455.4	1780	Gtt/Ttt	16/23	0.446994272435647	1	FACETS	0.675	0.585	0.77	0.675	0.585	0.77	SUBCLONAL	1	TRUE	0	0.446994272435647	1		763	309	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056365	180056365	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000012-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	42	788	0	ENST00000261937.6:c.879C>A	p.Ser293Arg	p.S293R	ENST00000261937	NM_182925.4	293	agC/agA	7/30	0.446994272435647	1	FACETS	0.621	0.523	0.728	0.621	0.523	0.728	SUBCLONAL	1	TRUE	0	0.446994272435647	1		788	235	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151871275	151871275	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000012-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	95	897	0	ENST00000262189.6:c.9315A>T	p.Lys3105Asn	p.K3105N	ENST00000262189	NM_170606.2	3105	aaA/aaT	39/59	NA	2	FACETS	0.799	0.714	0.889			1	INDETERMINATE	1	TRUE	NA	0.446994272435647	2		897	532	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436666	8436666	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs775630094	NA	P-0000012-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	135	686	0	ENST00000356435.5:c.4012C>A	p.Pro1338Thr	p.P1338T	ENST00000356435		1338	Ccc/Acc	24/35	0.111692781746209	5	FACETS	1	0.968	1			1	INDETERMINATE	2	TRUE	NA	0.446994272435647	5		686	453	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486074	8486074	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000012-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	94	921	0	ENST00000356435.5:c.2743G>T	p.Glu915Ter	p.E915*	ENST00000356435		915	Gaa/Taa	17/35	0.111692781746209	5	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.446994272435647	5		921	533	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609039	43609039	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1486769344	NA	P-0000012-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	46	480	0	ENST00000355710.3:c.1795C>A	p.Pro599Thr	p.P599T	ENST00000355710	NM_020975.4	599	Ccc/Acc	10/20	0.394029357088039	3	FACETS	1	0.879	1	0.52	0.442	0.605	CLONAL	1	TRUE	1	0.446994272435647	3		480	242	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	472166	472166	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000012-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	87	835	0	ENST00000399788.2:c.635A>T	p.Asn212Ile	p.N212I	ENST00000399788	NM_001042603.1	212	aAc/aTc	5/28	NA	2	FACETS	0.966	0.86	1			1	INDETERMINATE	1	TRUE	NA	0.446994272435647	2		835	403	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719971	18719971	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000012-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	112	627	0	ENST00000266497.5:c.3868G>T	p.Val1290Leu	p.V1290L	ENST00000266497		1290	Gta/Tta	27/31	0.394029357088039	3	FACETS	1	0.98	1	0.662	0.599	0.728	CLONAL	1	TRUE	1	0.446994272435647	3		627	463	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422025	81422025	+	start_lost	Translation_Start_Site	SNP	A	A	T	novel	NA	P-0000012-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	42	457	0	ENST00000298171.2:c.1A>T	p.Met1?	p.M1?	ENST00000298171	NM_000369.2	1	Atg/Ttg	1/10	0.446994272435647	3	FACETS	0.688	0.577	0.811	0.344	0.288	0.406	SUBCLONAL	1	TRUE	1	0.446994272435647	3		457	334	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778565	3778565	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000012-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	67	640	0	ENST00000262367.5:c.6483G>T	p.Met2161Ile	p.M2161I	ENST00000262367	NM_004380.2	2161	atG/atT	31/31	0.315034552865455	1	FACETS	0.862	0.757	0.973	0.862	0.757	0.973	CLONAL	1	TRUE	0	0.446994272435647	1		640	270	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876623	59876623	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000012-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	92	791	0	ENST00000259008.2:c.1178A>T	p.Asp393Val	p.D393V	ENST00000259008	NM_032043.2	393	gAt/gTt	9/20	0.297659986513738	4	FACETS	0.945	0.841	1	0.473	0.42	0.529	CLONAL	1	TRUE	2	0.446994272435647	4		791	630	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534396	63534396	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs748945736	NA	P-0000012-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	89	885	0	ENST00000307078.5:c.1125C>G	p.Ile375Met	p.I375M	ENST00000307078	NM_004655.3	375	atC/atG	5/11	0.297659986513738	4	FACETS	0.886	0.787	0.993	0.443	0.393	0.497	CLONAL	1	TRUE	2	0.446994272435647	4		885	650	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207631	2207631	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000012-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	61	958	0	ENST00000398665.3:c.915G>T	p.Trp305Cys	p.W305C	ENST00000398665	NM_032482.2	305	tgG/tgT	11/28	0.111692781746209	5	FACETS	1	0.946	1			1	INDETERMINATE	1	TRUE	NA	0.446994272435647	5		958	385	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211674	5211674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1351895585	NA	P-0000012-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	42	806	5	ENST00000357368.4:c.5161C>T	p.Arg1721Trp	p.R1721W	ENST00000357368	NM_002850.3	1721	Cgg/Tgg	33/38	0.446994272435647	1	FACETS	0.491	0.412	0.578	0.491	0.412	0.578	SUBCLONAL	1	TRUE	0	0.446994272435647	1		811	297	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144050	11144050	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000012-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	82	894	4	ENST00000358026.2:c.3631G>T	p.Glu1211Ter	p.E1211*	ENST00000358026	NM_001128849.1	1211	Gag/Tag	26/36	0.446994272435647	1	FACETS	0.721	0.64	0.808	0.721	0.64	0.808	SUBCLONAL	1	TRUE	0	0.446994272435647	1		898	395	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303904	30303904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000012-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	39	571	0	ENST00000262643.3:c.140C>T	p.Ala47Val	p.A47V	ENST00000262643	NM_001238.2	47	gCc/gTc	4/12	NA	2	FACETS	0.669	0.557	0.791			1	INDETERMINATE	1	TRUE	NA	0.446994272435647	2		571	261	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739128	40739128	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0000012-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	13	420	0	ENST00000373198.4:c.3157-1G>C		p.X1053_splice	ENST00000373198	NM_133170.3	1053			0.169754075984315	2	FACETS	0.227	0.162	0.307	0.114	0.081	0.154	INDETERMINATE	1	TRUE	0	0.446994272435647	2		420	256	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748610	40748610	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000012-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	63	769	0	ENST00000373198.4:c.2906G>T	p.Gly969Val	p.G969V	ENST00000373198	NM_133170.3	969	gGa/gTa	21/32	0.169754075984315	2	FACETS	0.636	0.552	0.728	0.318	0.276	0.364	INDETERMINATE	1	TRUE	0	0.446994272435647	2		769	443	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937801	76937801	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0000012-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	110	1451	0	ENST00000373344.5:c.2947A>T	p.Lys983Ter	p.K983*	ENST00000373344	NM_000489.3	983	Aag/Tag	9/35	NA	2	FACETS	0.885	0.798	0.977			1	INDETERMINATE	1	TRUE	NA	0.446994272435647	2		1451	556	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335719	81335719	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000012-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	83	655	0	ENST00000222390.5:c.1641del	p.Trp547CysfsTer35	p.W547Cfs*35	ENST00000222390	NM_000601.4	547	tgG/tg	15/18	0.169754075984315	2	FACETS	0.632	0.558	0.71	0.316	0.279	0.355	INDETERMINATE	1	TRUE	0	0.446994272435647	2		655	588	SUCCESS
BLM	641	MSKCC	GRCh37	15	91298168	91298168	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000012-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	43	411	0	ENST00000355112.3:c.1087+1del		p.A363fs	ENST00000355112	NM_000057.2	363	Gct/ct	5/22	0.394029357088039	3	FACETS	0.699	0.586	0.822	0.349	0.293	0.411	SUBCLONAL	1	TRUE	1	0.446994272435647	3		411	337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579487	7579487	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000012-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	88	544	0	ENST00000269305.4:c.200del	p.Pro67GlnfsTer56	p.P67Qfs*56	ENST00000269305	NM_001126112.2	67	cCa/ca	4/11	0.37899743422431	2	FACETS	0.899	0.812	0.988	0.899	0.812	0.988	CLONAL	2	TRUE	0	0.446994272435647	2		544	219	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434179	49434179	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000067-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	200	334	0	ENST00000301067.7:c.7374G>T	p.Gln2458His	p.Q2458H	ENST00000301067	NM_003482.3	2458	caG/caT	31/54	1	2	FACETS	0.988	0.924	1	0.988	0.924	1	CLONAL	1	TRUE	1	0.809989660178635	2		334	500	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947579	48947579	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs587778845	NA	P-0000067-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	1328	373	2	ENST00000267163.4:c.1166T>A	p.Leu389Ter	p.L389*	ENST00000267163	NM_000321.2	389	tTa/tAa	12/27	0.809989660178635	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.809989660178635	2		375	1597	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2111969	2111969	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000067-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	176	295	0	ENST00000219476.3:c.1217G>A	p.Arg406Lys	p.R406K	ENST00000219476	NM_000548.3	406	aGa/aAa	12/42	0.809989660178635	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.809989660178635	1		295	234	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0000067-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	163	268	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.809989660178635	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.809989660178635	1		268	235	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0000082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	343	262	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	0.55028473828034	2		262	1155	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176132107	176132107	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	248	406	0	ENST00000367669.3:c.660G>T	p.Gln220His	p.Q220H	ENST00000367669	NM_022457.5	220	caG/caT	5/20	0.525503604447288	3	FACETS	1	0.954	1	0.513	0.479	0.548	CLONAL	1	TRUE	1	0.55028473828034	3		406	1120	SUCCESS
REL	5966	MSKCC	GRCh37	2	61121637	61121637	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	157	341	2	ENST00000295025.8:c.259G>T	p.Gly87Cys	p.G87C	ENST00000295025	NM_002908.2	87	Ggc/Tgc	3/11	1	2	FACETS	0.831	0.763	0.901	0.831	0.763	0.901	CLONAL	1	TRUE	1	0.55028473828034	2		343	687	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660531	227660531	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	171	263	0	ENST00000305123.5:c.2924T>C	p.Ile975Thr	p.I975T	ENST00000305123	NM_005544.2	975	aTt/aCt	1/2	0.525503604447288	3	FACETS	1	0.97	1	0.552	0.509	0.597	CLONAL	1	TRUE	1	0.55028473828034	3		263	718	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405633	139405635	+	missense_variant	Missense_Mutation	TNP	AAG	AAG	CTC	novel	NA	P-0000082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	144	424	0	ENST00000277541.6:c.2556_2558delinsGAG	p.Ser852_Phe853delinsArgSer	p.S852_F853delinsRS	ENST00000277541	NM_017617.3	852	agCTTc/agGAGc	16/34	1	2	FACETS	0.677	0.618	0.739	0.677	0.618	0.739	SUBCLONAL	1	TRUE	1	0.55028473828034	2		424	773	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413143	139413143	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	213	354	0	ENST00000277541.6:c.999C>G	p.Ser333Arg	p.S333R	ENST00000277541	NM_017617.3	333	agC/agG	6/34	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.55028473828034	2		354	759	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597822	43597822	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0000082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	382	643	0	ENST00000355710.3:c.370A>T	p.Lys124Ter	p.K124*	ENST00000355710	NM_020975.4	124	Aag/Tag	3/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.55028473828034	2		643	1365	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719941	18719941	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	213	474	0	ENST00000266497.5:c.3838C>G	p.Leu1280Val	p.L1280V	ENST00000266497		1280	Cta/Gta	27/31	1	2	FACETS	0.804	0.747	0.863	0.804	0.747	0.863	CLONAL	1	TRUE	1	0.55028473828034	2		474	963	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18762501	18762501	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	352	492	0	ENST00000266497.5:c.3997C>G	p.Gln1333Glu	p.Q1333E	ENST00000266497		1333	Cag/Gag	29/31	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.55028473828034	2		492	1104	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549284	21549285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0000082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	334	609	0	ENST00000382592.4:c.2991_2992delinsAT	p.Met997_Asp998delinsIleTyr	p.M997_D998delinsIY	ENST00000382592	NM_014572.2	997	atGGac/atATac	8/8	0.55028473828034	1	FACETS	0.951	0.902	1	0.951	0.902	1	CLONAL	1	TRUE	0	0.55028473828034	1		609	925	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134449	2134449	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768684515	NA	P-0000082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	174	565	0	ENST00000219476.3:c.4226G>A	p.Arg1409Gln	p.R1409Q	ENST00000219476	NM_000548.3	1409	cGg/cAg	34/42	0.55028473828034	1	FACETS	0.565	0.521	0.611	0.565	0.521	0.611	SUBCLONAL	1	TRUE	0	0.55028473828034	1		565	811	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0000082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	171	294	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.55028473828034	1	FACETS	0.981	0.912	1	0.981	0.912	1	CLONAL	1	TRUE	0	0.55028473828034	1		294	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0000127-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	35	153	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.319506436183575	1	FACETS	0.81	0.67	0.964	0.81	0.67	0.964	CLONAL	1	TRUE	0	0.350866788856759	1		153	203	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22143076	22143076	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000127-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	144	222	0	ENST00000215832.6:c.631A>G	p.Ile211Val	p.I211V	ENST00000215832	NM_002745.4	211	Att/Gtt	5/9	0.350866788856759	3	FACETS	1	0.982	1			1	CLONAL	2	TRUE	NA	0.350866788856759	3		222	393	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165983	118165983	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000130-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	47	446	0	ENST00000369448.3:c.493G>T	p.Val165Leu	p.V165L	ENST00000369448	NM_017709.3	165	Gtg/Ttg	2/2	0.17686740715717	2	FACETS	0.813	0.705	0.925	0.813	0.705	0.925	INDETERMINATE	2	TRUE	0	0.473856543094643	2		446	122	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050864	49050864	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886042935	NA	P-0000130-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	146	175	0	ENST00000267163.4:c.2548C>T	p.Gln850Ter	p.Q850*	ENST00000267163	NM_000321.2	850	Cag/Tag	25/27	0.419885087841378	3	FACETS	1	0.98	1	0.777	0.72	0.834	CLONAL	2	TRUE	0	0.473856543094643	3		175	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0000130-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	15	281	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.17686740715717	2	FACETS	1	0.871	1	0.633	0.48	0.801	INDETERMINATE	1	TRUE	0	0.473856543094643	2		281	50	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554098	63554098	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000130-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	35	616	0	ENST00000307078.5:c.641del	p.Gly214AspfsTer5	p.G214Dfs*5	ENST00000307078	NM_004655.3	214	gGa/ga	2/11	0.17686740715717	2	FACETS	1	0.896	1	0.551	0.46	0.649	INDETERMINATE	1	TRUE	0	0.473856543094643	2		616	134	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0000134-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	570	991	2	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.65853654147557	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.65853654147557	1		993	1019	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951149	48951149	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000134-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	92	398	0	ENST00000267163.4:c.1312del	p.Cys438ValfsTer19	p.C438Vfs*19	ENST00000267163	NM_000321.2	437	ggT/gg	13/27	0.510562005347345	0	FACETS	0.346	0.311	0.381			1	SUBCLONAL	1	TRUE	0	0.65853654147557	0		398	276	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0000174-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	562	796	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	NA	2	FACETS	0.94	0.905	0.976			1	INDETERMINATE	1	TRUE	NA	0.935312478121148	2		796	1278	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31020771	31020771	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000228-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	34	504	1	ENST00000375687.4:c.1068A>T	p.Glu356Asp	p.E356D	ENST00000375687	NM_015338.5	356	gaA/gaT	11/13	1	2	FACETS	0.452	0.368	0.547	0.452	0.368	0.547	SUBCLONAL	1	TRUE	1	0.230215330832727	2		505	653	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	465700	465701	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0000228-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	35	356	0	ENST00000399788.2:c.675dup	p.Glu226ArgfsTer7	p.E226Rfs*7	ENST00000399788	NM_001042603.1	225	-/A	6/28	1	2	FACETS	0.639	0.523	0.769	0.639	0.523	0.769	SUBCLONAL	1	TRUE	1	0.230215330832727	2		356	476	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592216	55592216	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000228-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	31	392	0	ENST00000288135.5:c.1540G>A	p.Glu514Lys	p.E514K	ENST00000288135	NM_000222.2	514	Gag/Aag	9/21	0.230215330832727	1	FACETS	0.516	0.417	0.628	0.516	0.417	0.628	SUBCLONAL	1	TRUE	0	0.230215330832727	1		392	462	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793565	89793565	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000228-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	37	323	0	ENST00000336032.3:c.634A>C	p.Asn212His	p.N212H	ENST00000336032	NM_006813.2	212	Aac/Cac	2/2	1	2	FACETS	0.599	0.493	0.717	0.599	0.493	0.717	SUBCLONAL	1	TRUE	1	0.230215330832727	2		323	537	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117874103	117874103	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000228-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	197	723	0	ENST00000297338.2:c.351T>A	p.Phe117Leu	p.F117L	ENST00000297338	NM_006265.2	117	ttT/ttA	4/14	0.230215330832727	4	FACETS	1	0.973	1	0.738	0.683	0.795	CLONAL	2	TRUE	1	0.230215330832727	4		723	951	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822178	72822178	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000228-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	70	877	3	ENST00000268489.5:c.9997C>T	p.Gln3333Ter	p.Q3333*	ENST00000268489	NM_006885.3	3333	Cag/Tag	10/10	0.230215330832727	1	FACETS	0.469	0.407	0.536	0.469	0.407	0.536	SUBCLONAL	1	TRUE	0	0.230215330832727	1		880	1148	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0000246-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	59	266	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.241888706381172	4	FACETS	0.835	0.721	0.958	0.418	0.36	0.479	INDETERMINATE	1	FALSE	2	0.568027787984487	4		266	390	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599320	55599320	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913506	NA	P-0000246-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	190	249	0	ENST00000288135.5:c.2446G>C	p.Asp816His	p.D816H	ENST00000288135	NM_000222.2	816	Gac/Cac	17/21	0.568027787984487	3	FACETS	0.9	0.851	0.949	0.9	0.851	0.949	CLONAL	3	FALSE	0	0.568027787984487	3		249	318	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235853	108235853	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200899512	NA	P-0000246-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	83	343	0	ENST00000278616.4:c.8895G>T	p.Leu2965Phe	p.L2965F	ENST00000278616	NM_000051.3	2965	ttG/ttT	62/63	0.21062901259551	5	FACETS	1	0.971	1	0.436	0.386	0.488	INDETERMINATE	1	FALSE	2	0.568027787984487	5		343	414	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398262	25398262	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913538	NA	P-0000246-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	112	442	0	ENST00000311936.3:c.57G>C	p.Leu19Phe	p.L19F	ENST00000311936	NM_004985.3	19	ttG/ttC	2/5	0.461916326754368	4	FACETS	1	0.983	1	0.48	0.435	0.528	CLONAL	1	FALSE	1	0.568027787984487	4		442	429	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0000320-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	22	779	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.542	0.418	0.687	0.542	0.418	0.687	SUBCLONAL	1	TRUE	1	0.12	2		779	677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0000320-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	25	689	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	1	2	FACETS	0.689	0.541	0.86	0.689	0.541	0.86	SUBCLONAL	1	TRUE	1	0.12	2		689	605	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038190	30038190	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0000320-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	55	705	0	ENST00000338641.4:c.364-1G>C		p.X122_splice	ENST00000338641	NM_000268.3	122			1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.12	2		705	703	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0000407-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	305	225	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.709380886774906	2	FACETS	0.977	0.941	1	0.977	0.941	1	CLONAL	2	TRUE	0	0.725731372953142	2		225	430	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425050	49425050	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000407-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	206	383	0	ENST00000301067.7:c.13438T>G	p.Ser4480Ala	p.S4480A	ENST00000301067	NM_003482.3	4480	Tcc/Gcc	39/54	NA	2	FACETS	0.934	0.872	0.997			1	INDETERMINATE	1	TRUE	NA	0.725731372953142	2		383	608	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473780	67473780	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730880214	NA	P-0000407-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	59	203	0	ENST00000327367.4:c.860G>A	p.Arg287Gln	p.R287Q	ENST00000327367	NM_005902.3	287	cGg/cAg	6/9	0.63381235750079	2	FACETS	0.559	0.484	0.638	0.279	0.242	0.319	SUBCLONAL	1	TRUE	0	0.725731372953142	2		203	291	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791346	42791346	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000407-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	180	279	0	ENST00000575354.2:c.406G>T	p.Gly136Ter	p.G136*	ENST00000575354	NM_015125.3	136	Gga/Tga	3/20	0.507510342714064	1	FACETS	0.961	0.903	1	0.961	0.903	1	CLONAL	1	TRUE	0	0.725731372953142	1		279	329	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202444	123202444	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0000407-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	391	451	0	ENST00000218089.9:c.2296A>T	p.Arg766Ter	p.R766*	ENST00000218089	NM_001042749.1	766	Aga/Tga	24/35	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	1	TRUE	NA	0.725731372953142	2		451	810	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26911720	26911735	+	frameshift_variant	Frame_Shift_Del	DEL	TATGCTTTAAAACAAA	TATGCTTTAAAACAAA	-	novel	NA	P-0000407-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	103	263	0	ENST00000381527.3:c.147_162del	p.Tyr49Ter	p.Y49*	ENST00000381527	NM_001260.1	49	TATGCTTTAAAACAAAta/ta	2/13	NA	2	FACETS	0.558	0.501	0.617			1	INDETERMINATE	1	TRUE	NA	0.725731372953142	2		263	509	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252880	36252881	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0000432-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	165	145	0	ENST00000300305.3:c.481dup	p.Leu161ProfsTer52	p.L161Pfs*52	ENST00000300305		161	ctc/cCtc	4/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.366012335830107	2		145	689	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000435-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	102	486	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	0.725505191991098	2		486	268	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0000435-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	215	334	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.725505191991098	2		334	579	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259439	55259439	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000435-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	116	190	0	ENST00000275493.2:c.2497T>A	p.Leu833Met	p.L833M	ENST00000275493	NM_005228.3	833	Ttg/Atg	21/28	0.725505191991098	3	FACETS	0.899	0.814	0.987	0.449	0.407	0.494	CLONAL	1	TRUE	1	0.725505191991098	3		190	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0000550-T05-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	46	457	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.3	3	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	3		457	831	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0000586-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	63	240	0	ENST00000269305.4:c.559+1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.358845195662234	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.548726244387695	1		240	125	SUCCESS
FH	2271	MSKCC	GRCh37	1	241665855	241665855	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000586-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	61	485	1	ENST00000366560.3:c.1124C>G	p.Thr375Ser	p.T375S	ENST00000366560	NM_000143.3	375	aCt/aGt	8/10	0.302501932253371	3	FACETS	0.701	0.607	0.803	0.234	0.202	0.268	INDETERMINATE	1	TRUE	0	0.548726244387695	3		486	404	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718717	190718717	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1288595603	NA	P-0000586-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	304	587	0	ENST00000441310.2:c.875A>G	p.Tyr292Cys	p.Y292C	ENST00000441310	NM_000534.4	292	tAt/tGt	8/13	0.262934623138394	5	FACETS	1	0.987	1	0.666	0.633	0.698	INDETERMINATE	3	TRUE	0	0.548726244387695	5		587	607	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586432	189586432	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000586-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	96	217	0	ENST00000264731.3:c.1056G>T	p.Arg352Ser	p.R352S	ENST00000264731	NM_003722.4	352	agG/agT	8/14	0.330671633297278	6	FACETS	0.844	0.762	0.928	0.633	0.571	0.696	CLONAL	3	TRUE	2	0.548726244387695	6		217	290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0000775-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	138	470	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.359117508369141	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.359117508369141	1		470	526	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624272	89624273	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs876661009	NA	P-0000775-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	23	88	0	ENST00000371953.3:c.47dup	p.Tyr16Ter	p.Y16*	ENST00000371953	NM_000314.4	16	tat/tAat	1/9	0.276210848578515	1	FACETS	0.489	0.383	0.61	0.489	0.383	0.61	SUBCLONAL	1	TRUE	0	0.359117508369141	1		88	215	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023007	27023008	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGC	rs587779737	NA	P-0000835-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	15	5	0	ENST00000324856.7:c.126_128dup	p.Ala45dup	p.A45dup	ENST00000324856	NM_006015.4	45	gag/gaGGCg	1/20	0.266682416656547	1	FACETS	0.936	0.712	1	1	0.923	1	CLONAL	2	TRUE	0	0.286098209455633	1		5	48	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0000897-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	223	262	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.24036488995234	3	FACETS	1	0.992	1	0.707	0.663	0.752	INDETERMINATE	1	TRUE	1	0.734717240048462	3		262	587	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915589	131915589	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000897-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	179	135	0	ENST00000265335.6:c.587G>T	p.Arg196Leu	p.R196L	ENST00000265335		196	cGt/cTt	5/25	NA	2	FACETS	0.978	0.931	1			1	INDETERMINATE	2	TRUE	NA	0.734717240048462	2		135	249	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0000897-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	153	341	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.734717240048462	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.734717240048462	1		341	250	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781596	9781596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000897-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	112	389	0	ENST00000377346.4:c.1906C>T	p.Arg636Trp	p.R636W	ENST00000377346	NM_005026.3	636	Cgg/Tgg	15/24	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.734717240048462	2		389	304	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162722951	162722951	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000897-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	128	411	0	ENST00000367921.3:c.149G>A	p.Ser50Asn	p.S50N	ENST00000367921	NM_006182.2	50	aGt/aAt	4/18	1	2	FACETS	0.96	0.88	1	0.96	0.88	1	CLONAL	1	TRUE	1	0.734717240048462	2		411	363	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107223	193107223	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000897-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	121	159	0	ENST00000367435.3:c.432G>T	p.Glu144Asp	p.E144D	ENST00000367435	NM_024529.4	144	gaG/gaT	6/17	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.734717240048462	2		159	305	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566745	212566745	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000897-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	175	342	0	ENST00000342788.4:c.1436G>T	p.Ser479Ile	p.S479I	ENST00000342788	NM_005235.2	479	aGc/aTc	12/28	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.734717240048462	2		342	475	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575633	55575633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000897-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	284	463	0	ENST00000288135.5:c.1159G>A	p.Gly387Arg	p.G387R	ENST00000288135	NM_000222.2	387	Gga/Aga	7/21	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.734717240048462	2		463	644	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231742	66231742	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000897-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	120	371	0	ENST00000273854.3:c.1958C>A	p.Pro653Gln	p.P653Q	ENST00000273854	NM_004439.5	653	cCa/cAa	11/18	1	2	FACETS	0.91	0.831	0.991	0.91	0.831	0.991	CLONAL	1	TRUE	1	0.734717240048462	2		371	359	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521865	157521865	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763386213	NA	P-0000897-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	237	247	1	ENST00000346085.5:c.4137G>A	p.Met1379Ile	p.M1379I	ENST00000346085	NM_020732.3	1379	atG/atA	18/20	0.161949774401463	5	FACETS	1	0.981	1	0.737	0.693	0.782	INDETERMINATE	2	TRUE	2	0.734717240048462	5		248	613	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90633783	90633783	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000897-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	198	440	0	ENST00000330062.3:c.301G>C	p.Ala101Pro	p.A101P	ENST00000330062	NM_002168.2	101	Gca/Cca	3/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.734717240048462	2		440	488	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220622	1220622	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690923	NA	P-0000897-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	148	438	0	ENST00000326873.7:c.640C>T	p.Gln214Ter	p.Q214*	ENST00000326873	NM_000455.4	214	Cag/Tag	5/10	0.584282685199238	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.734717240048462	1		438	234	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597395	10597395	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000897-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	139	429	0	ENST00000171111.5:c.1808G>T	p.Gly603Val	p.G603V	ENST00000171111	NM_203500.1	603	gGg/gTg	6/6	0.734717240048462	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.734717240048462	1		429	234	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899093	40899093	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000897-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	143	566	0	ENST00000373198.4:c.2177C>T	p.Ala726Val	p.A726V	ENST00000373198	NM_133170.3	726	gCa/gTa	14/32	1	2	FACETS	0.891	0.819	0.964	0.891	0.819	0.964	CLONAL	1	TRUE	1	0.734717240048462	2		566	437	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778801	76778801	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000897-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	124	664	0	ENST00000373344.5:c.6778C>A	p.His2260Asn	p.H2260N	ENST00000373344	NM_000489.3	2260	Cac/Aac	31/35	0.489273876458868	0	FACETS		NA	1			1	NA	1	TRUE	0	0.734717240048462	0		664	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0001104-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	299	405	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.487323885368389	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.487323885368389	1		406	884	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0001104-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	263	779	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.487323885368389	1	FACETS	0.993	0.934	1	0.993	0.934	1	CLONAL	1	TRUE	0	0.487323885368389	1		779	822	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038912	12038912	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001104-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	139	399	0	ENST00000396373.4:c.1205A>G	p.Tyr402Cys	p.Y402C	ENST00000396373	NM_001987.4	402	tAc/tGc	7/8	0.355874603943162	3	FACETS	0.654	0.594	0.717	0.327	0.297	0.359	SUBCLONAL	1	TRUE	1	0.487323885368389	3		399	1085	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782654	9782654	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001104-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	239	345	0	ENST00000377346.4:c.2416C>A	p.Leu806Met	p.L806M	ENST00000377346	NM_005026.3	806	Ctg/Atg	19/24	0.487323885368389	1	FACETS	0.886	0.83	0.945	0.886	0.83	0.945	CLONAL	1	TRUE	0	0.487323885368389	1		345	837	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917797	29917797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748854412	NA	P-0001104-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	232	353	0	ENST00000389048.3:c.871C>T	p.Arg291Cys	p.R291C	ENST00000389048	NM_004304.4	291	Cgc/Tgc	3/29	1	2	FACETS	0.975	0.909	1	0.975	0.909	1	CLONAL	1	TRUE	1	0.487323885368389	2		353	977	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808647	1808647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373425119	NA	P-0001104-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	225	305	0	ENST00000260795.2:c.2260G>A	p.Val754Met	p.V754M	ENST00000260795		754	Gtg/Atg	16/17	0.30097102173688	1	FACETS	0.686	0.639	0.735	0.686	0.639	0.735	SUBCLONAL	1	TRUE	0	0.487323885368389	1		305	1018	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213909	66213909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001104-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	177	361	2	ENST00000273854.3:c.2521C>T	p.Pro841Ser	p.P841S	ENST00000273854	NM_004439.5	841	Cca/Tca	15/18	0.30097102173688	1	FACETS	0.562	0.518	0.609	0.562	0.518	0.609	SUBCLONAL	1	TRUE	0	0.487323885368389	1		363	977	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468029	50468029	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001104-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	213	254	1	ENST00000331340.3:c.1264G>A	p.Ala422Thr	p.A422T	ENST00000331340	NM_006060.4	422	Gcg/Acg	8/8	0.225574079906535	3	FACETS	1	0.988	1	0.646	0.601	0.693	INDETERMINATE	1	TRUE	1	0.487323885368389	3		255	841	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504378	8504378	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001104-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	146	307	0	ENST00000356435.5:c.1705T>A	p.Ser569Thr	p.S569T	ENST00000356435		569	Tca/Aca	12/35	0.487323885368389	1	FACETS	0.752	0.689	0.817	0.752	0.689	0.817	SUBCLONAL	1	TRUE	0	0.487323885368389	1		307	603	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231337	46231337	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001104-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	114	296	0	ENST00000334344.6:c.1177G>A	p.Glu393Lys	p.E393K	ENST00000334344	NM_152641.2	393	Gaa/Aaa	10/21	0.487323885368389	1	FACETS	0.402	0.361	0.445	0.402	0.361	0.445	SUBCLONAL	1	TRUE	0	0.487323885368389	1		296	880	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432110	121432110	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001104-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	216	340	0	ENST00000257555.6:c.857A>T	p.Tyr286Phe	p.Y286F	ENST00000257555		286	tAc/tTc	4/10	0.406625082729155	1	FACETS	0.782	0.728	0.838	0.782	0.728	0.838	SUBCLONAL	1	TRUE	0	0.487323885368389	1		340	857	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2218120	2218120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001104-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	141	360	0	ENST00000326181.6:c.182C>T	p.Ser61Phe	p.S61F	ENST00000326181	NM_032271.2	61	tCc/tTc	4/21	0.406625082729155	1	FACETS	0.42	0.382	0.461	0.42	0.382	0.461	SUBCLONAL	1	TRUE	0	0.487323885368389	1		360	1041	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857029	9857029	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001104-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	147	375	0	ENST00000330684.3:c.4372C>G	p.Pro1458Ala	p.P1458A	ENST00000330684	NM_001134407.1	1458	Cct/Gct	13/13	0.406625082729155	1	FACETS	0.502	0.458	0.548	0.502	0.458	0.548	SUBCLONAL	1	TRUE	0	0.487323885368389	1		375	909	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439988	56439993	+	frameshift_variant	Frame_Shift_Ins	INS	GGATCC	GGATCC	TCATAATCTG	novel	NA	P-0001104-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	114	313	0	ENST00000407977.2:c.599_604delinsCAGATTATGA	p.Trp200SerfsTer60	p.W200Sfs*60	ENST00000407977		200	tGGATCCta/tCAGATTATGAta	6/10	0.487323885368389	1	FACETS	0.568	0.512	0.627	0.568	0.512	0.627	SUBCLONAL	1	TRUE	0	0.487323885368389	1		313	623	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661692	227661693	+	stop_gained	Nonsense_Mutation	DNP	TC	TC	CA	novel	NA	P-0001104-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	83	279	0	ENST00000305123.5:c.1762_1763delinsTG	p.Glu588Ter	p.E588*	ENST00000305123	NM_005544.2	588	GAa/TGa	1/2	1	2	FACETS	0.367	0.323	0.414	0.367	0.323	0.414	SUBCLONAL	1	TRUE	1	0.487323885368389	2		279	929	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612272	189612272	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001176-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	52	367	1	ENST00000264731.3:c.2024T>G	p.Ile675Ser	p.I675S	ENST00000264731	NM_003722.4	675	aTc/aGc	14/14	0.184951226184235	5	FACETS	0.757	0.655	0.865	0.505	0.436	0.577	INDETERMINATE	2	TRUE	2	0.818015012674113	5		368	187	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005305	29005305	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs547950624	NA	P-0001176-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	118	640	0	ENST00000282397.4:c.956T>A	p.Phe319Tyr	p.F319Y	ENST00000282397	NM_002019.4	319	tTc/tAc	7/30	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.818015012674113	2		640	266	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589595	67589600	+	inframe_deletion	In_Frame_Del	DEL	ACACTC	ACACTC	-	novel	NA	P-0001176-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	147	445	0	ENST00000274335.5:c.1359_1364del	p.Asn453_Gln455delinsLys	p.N453_Q455delinsK	ENST00000274335		453	aACACTCag/aag	10/15	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.818015012674113	2		445	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579329	7579332	+	frameshift_variant	Frame_Shift_Del	DEL	TGGC	TGGC	-	novel	NA	P-0001176-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	74	498	0	ENST00000269305.4:c.355_358del	p.Ala119SerfsTer3	p.A119Sfs*3	ENST00000269305	NM_001126112.2	119	GCCAag/ag	4/11	0.818015012674113	1	FACETS	0.938	0.86	1	0.938	0.86	1	CLONAL	1	TRUE	0	0.818015012674113	1		498	114	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347191	70347191	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001332-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	396	201	1	ENST00000374080.3:c.2855G>A	p.Cys952Tyr	p.C952Y	ENST00000374080		952	tGt/tAt	21/45	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.691916101547512	1		202	582	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913396	NA	P-0001336-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	46	440	0	ENST00000349496.5:c.95A>T	p.Asp32Val	p.D32V	ENST00000349496	NM_001904.3	32	gAc/gTc	3/15	1	2	FACETS	0.535	0.449	0.63	0.535	0.449	0.63	SUBCLONAL	1	TRUE	1	0.227641897210437	2		440	756	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524993	8524993	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001336-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	99	567	0	ENST00000356435.5:c.611A>T	p.Lys204Ile	p.K204I	ENST00000356435		204	aAa/aTa	7/35	1	2	FACETS	0.915	0.815	1	0.915	0.815	1	CLONAL	1	TRUE	1	0.227641897210437	2		567	951	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950396	15950396	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201721277	NA	P-0001336-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	110	437	0	ENST00000268712.3:c.6548G>A	p.Arg2183His	p.R2183H	ENST00000268712	NM_006311.3	2183	cGc/cAc	42/46	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.227641897210437	2		437	812	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791356	42791356	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760049446	NA	P-0001336-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	170	381	0	ENST00000575354.2:c.416G>A	p.Arg139Gln	p.R139Q	ENST00000575354	NM_015125.3	139	cGg/cAg	3/20	0.164180127969625	1	FACETS	0.867	0.799	0.938	1	0.991	1	CLONAL	2	TRUE	0	0.227641897210437	1		381	763	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0001338-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	350	618	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.465147595423335	2	FACETS	0.981	0.936	1	0.981	0.936	1	CLONAL	2	TRUE	0	0.492974938460067	2		618	724	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0001338-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	176	237	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.492974938460067	2		237	699	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0001338-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	244	251	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.465147595423335	2	FACETS	0.998	0.944	1	0.998	0.944	1	CLONAL	2	TRUE	0	0.492974938460067	2		251	496	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610560	215610560	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001340-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	85	363	0	ENST00000260947.4:c.1696A>G	p.Arg566Gly	p.R566G	ENST00000260947	NM_000465.2	566	Agg/Ggg	8/11	1	2	FACETS	0.925	0.816	1	0.925	0.816	1	CLONAL	1	TRUE	1	0.174275030263457	2		363	1054	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056541	26056541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763803622	NA	P-0001340-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	93	169	0	ENST00000343677.2:c.116C>T	p.Pro39Leu	p.P39L	ENST00000343677	NM_005319.3	39	cCg/cTg	1/1	1	2	FACETS	1	0.92	1	1	0.987	1	CLONAL	2	TRUE	1	0.174275030263457	2		169	514	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270504	98270504	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001340-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	65	290	0	ENST00000331920.6:c.140G>A	p.Arg47Gln	p.R47Q	ENST00000331920	NM_000264.3	47	cGg/cAg	1/24	0.158049735522851	2	FACETS	1	0.958	1	0.636	0.552	0.728	CLONAL	1	TRUE	0	0.174275030263457	2		290	586	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691039	NA	P-0001340-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	56	303	0	ENST00000269305.4:c.919+1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			1	2	FACETS	0.975	0.835	1	0.975	0.835	1	CLONAL	1	TRUE	1	0.174275030263457	2		303	659	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663658	29663658	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001340-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	97	433	0	ENST00000356175.3:c.6090T>G	p.Ile2030Met	p.I2030M	ENST00000356175	NM_000267.3	2030	atT/atG	41/57	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.174275030263457	2		433	1083	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763410	41763410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001340-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	84	538	0	ENST00000301178.4:c.2209G>A	p.Val737Met	p.V737M	ENST00000301178	NM_021913.4	737	Gtg/Atg	19/20	1	2	FACETS	0.954	0.84	1	0.954	0.84	1	CLONAL	1	TRUE	1	0.174275030263457	2		538	1011	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94201058	94201058	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001341-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	151	504	0	ENST00000323929.3:c.1019T>C	p.Ile340Thr	p.I340T	ENST00000323929	NM_005591.3	340	aTt/aCt	10/20	0.647248164645243	3	FACETS	0.987	0.905	1			1	CLONAL	1	TRUE	NA	0.6	3		504	663	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012157	16012157	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001341-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	338	550	0	ENST00000268712.3:c.2125C>T	p.Gln709Ter	p.Q709*	ENST00000268712	NM_006311.3	709	Cag/Tag	19/46	0.647248164645243	2	FACETS	1	0.983	1			1	CLONAL	2	TRUE	NA	0.6	2		550	540	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76812991	76812991	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001341-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	142	625	1	ENST00000373344.5:c.6630T>G	p.Phe2210Leu	p.F2210L	ENST00000373344	NM_000489.3	2210	ttT/ttG	30/35	0.647248164645243	2	FACETS	0.757	0.692	0.825			1	SUBCLONAL	1	TRUE	NA	0.6	2		626	625	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837904	156837904	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001348-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	62	364	1	ENST00000524377.1:c.437C>A	p.Ser146Ter	p.S146*	ENST00000524377	NM_002529.3	146	tCg/tAg	5/17	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.14	2		365	746	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746110	162746110	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001348-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	40	289	2	ENST00000367921.3:c.2233G>T	p.Gly745Cys	p.G745C	ENST00000367921	NM_006182.2	745	Ggc/Tgc	16/18	1	2	FACETS	0.871	0.722	1	0.871	0.722	1	CLONAL	1	TRUE	1	0.14	2		291	656	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32191699	32191699	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1046272476	NA	P-0001348-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	68	398	0	ENST00000375023.3:c.7C>G	p.Pro3Ala	p.P3A	ENST00000375023	NM_004557.3	3	Ccc/Gcc	1/30	0.206814400112032	3	FACETS	1	0.939	1	0.572	0.496	0.654	CLONAL	1	TRUE	1	0.14	3		398	909	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33446586	33446586	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs797044943	NA	P-0001348-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	59	579	0	ENST00000345365.6:c.47T>C	p.Met16Thr	p.M16T	ENST00000345365	NM_002878.3	16	aTg/aCg	1/10	1	2	FACETS	0.918	0.788	1	0.918	0.788	1	CLONAL	1	TRUE	1	0.14	2		579	918	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222983	1222983	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs398123406	NA	P-0001348-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	27	196	0	ENST00000326873.7:c.921-1G>T		p.X307_splice	ENST00000326873	NM_000455.4	307			0.165351468305365	1	FACETS	0.967	0.769	1	0.967	0.769	1	CLONAL	1	TRUE	0	0.14	1		196	371	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602773	10602773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001348-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	43	382	0	ENST00000171111.5:c.805C>T	p.Arg269Trp	p.R269W	ENST00000171111	NM_203500.1	269	Cgg/Tgg	3/6	0.165351468305365	1	FACETS	0.797	0.665	0.944	0.797	0.665	0.944	CLONAL	1	TRUE	0	0.14	1		382	717	SUCCESS
APC	324	MSKCC	GRCh37	5	112173629	112173630	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	T	novel	NA	P-0001348-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	41	328	0	ENST00000257430.4:c.2338_2339delinsT	p.Ser780PhefsTer40	p.S780Ffs*40	ENST00000257430	NM_000038.5	780	AGt/Tt	16/16	1	2	FACETS	0.891	0.741	1	0.891	0.741	1	CLONAL	1	TRUE	1	0.14	2		328	657	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0001365-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	290	379	0	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	0.503981456567065	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.722408213724603	1		379	489	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054221	30054221	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001365-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	381	446	1	ENST00000338641.4:c.643G>T	p.Glu215Ter	p.E215*	ENST00000338641	NM_000268.3	215	Gag/Tag	7/16	0.722408213724603	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.722408213724603	1		447	646	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794475	242794475	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs774374376	NA	P-0001365-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	327	355	0	ENST00000334409.5:c.467C>A	p.Pro156His	p.P156H	ENST00000334409	NM_005018.2	156	cCc/cAc	3/5	0.722408213724603	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.722408213724603	1		355	511	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434531	49434531	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001365-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	206	173	0	ENST00000301067.7:c.7022A>G	p.Gln2341Arg	p.Q2341R	ENST00000301067	NM_003482.3	2341	cAg/cGg	31/54	0.69979926129736	2	FACETS	0.905	0.86	0.949	0.905	0.86	0.949	CLONAL	2	TRUE	0	0.722408213724603	2		173	315	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748606	40748606	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001365-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	265	393	0	ENST00000373198.4:c.2910C>A	p.Tyr970Ter	p.Y970*	ENST00000373198	NM_133170.3	970	taC/taA	21/32	NA	2	FACETS	1	0.958	1			1	INDETERMINATE	1	TRUE	NA	0.722408213724603	2		393	719	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520017	NA	P-0001365-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	29	688	0	ENST00000326873.7:c.647C>T	p.Ser216Phe	p.S216F	ENST00000326873	NM_000455.4	216	tCc/tTc	5/10	0.310636188775607	1	FACETS	0.304	0.244	0.374	0.304	0.244	0.374	SUBCLONAL	1	TRUE	0	0.310636188775607	1		688	518	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602493	10602493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001365-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	23	555	0	ENST00000171111.5:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000171111	NM_203500.1	362	cGg/cAg	3/6	0.310636188775607	1	FACETS	0.322	0.25	0.404	0.322	0.25	0.404	SUBCLONAL	1	TRUE	0	0.310636188775607	1		555	389	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662313	227662313	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001365-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	71	477	0	ENST00000305123.5:c.1142G>T	p.Arg381Leu	p.R381L	ENST00000305123	NM_005544.2	381	cGc/cTc	1/2	1	2	FACETS	0.874	0.764	0.992	0.874	0.764	0.992	CLONAL	1	TRUE	1	0.310636188775607	2		477	523	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52692291	52692291	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001365-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	35	641	0	ENST00000394830.3:c.569T>C	p.Leu190Pro	p.L190P	ENST00000394830	NM_018313.4	190	cTt/cCt	6/30	0.235768958043993	0	FACETS	0.271	0.221	0.326			1	SUBCLONAL	1	TRUE	0	0.310636188775607	0		641	574	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193985	106193985	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1178437123	NA	P-0001365-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	42	550	0	ENST00000380013.4:c.4447G>T	p.Glu1483Ter	p.E1483*	ENST00000380013	NM_001127208.2	1483	Gag/Tag	10/11	1	2	FACETS	0.478	0.398	0.566	0.478	0.398	0.566	SUBCLONAL	1	TRUE	1	0.310636188775607	2		550	566	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244091	153244091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001365-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	22	575	0	ENST00000281708.4:c.2066G>A	p.Arg689Gln	p.R689Q	ENST00000281708	NM_033632.3	689	cGg/cAg	12/12	1	2	FACETS	0.24	0.185	0.305	0.24	0.185	0.305	SUBCLONAL	1	TRUE	1	0.310636188775607	2		575	589	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245425	153245425	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001365-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	49	583	0	ENST00000281708.4:c.1766T>C	p.Leu589Pro	p.L589P	ENST00000281708	NM_033632.3	589	cTc/cCc	11/12	1	2	FACETS	0.558	0.472	0.653	0.558	0.472	0.653	SUBCLONAL	1	TRUE	1	0.310636188775607	2		583	565	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779264	3779264	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001365-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	56	352	0	ENST00000262367.5:c.5784G>T	p.Gln1928His	p.Q1928H	ENST00000262367	NM_004380.2	1928	caG/caT	31/31	1	2	FACETS	0.951	0.818	1	0.951	0.818	1	CLONAL	1	TRUE	1	0.310636188775607	2		352	379	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858892	89858892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773687142	NA	P-0001365-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	28	498	0	ENST00000389301.3:c.1070C>T	p.Ser357Leu	p.S357L	ENST00000389301	NM_000135.2	357	tCa/tTa	12/43	NA	2	FACETS	0.34	0.27	0.419			1	INDETERMINATE	1	TRUE	NA	0.310636188775607	2		498	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882025	NA	P-0001365-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	74	764	0	ENST00000269305.4:c.646G>T	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ttg	6/11	0.310636188775607	1	FACETS	0.732	0.641	0.829	0.732	0.641	0.829	SUBCLONAL	1	TRUE	0	0.310636188775607	1		764	550	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220640	1220640	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690940	NA	P-0001365-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	29	715	0	ENST00000326873.7:c.658C>T	p.Gln220Ter	p.Q220*	ENST00000326873	NM_000455.4	220	Cag/Tag	5/10	0.310636188775607	1	FACETS	0.307	0.246	0.378	0.307	0.246	0.378	SUBCLONAL	1	TRUE	0	0.310636188775607	1		715	513	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0001368-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	156	248	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	0.529972732932901	2		248	586	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0001368-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	170	300	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.530289396553574	3	FACETS	1	0.984	1	0.621	0.573	0.671	CLONAL	1	TRUE	1	0.529972732932901	3		300	653	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612029	189612029	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	22	285	0	ENST00000264731.3:c.1781G>T	p.Arg594Leu	p.R594L	ENST00000264731	NM_003722.4	594	cGa/cTa	14/14	0.30019302721351	2	FACETS	0.552	0.429	0.693	0.276	0.214	0.347	SUBCLONAL	1	TRUE	0	0.372650031359061	2		285	214	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875096	151875096	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0001372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	43	101	0	ENST00000262189.6:c.7443-1G>T		p.X2481_splice	ENST00000262189	NM_170606.2	2481			0.263019043851164	3	FACETS	1	0.948	1	0.822	0.708	0.94	CLONAL	2	TRUE	0	0.372650031359061	3		101	111	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352470	118352470	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	30	189	0	ENST00000534358.1:c.3675G>T	p.Lys1225Asn	p.K1225N	ENST00000534358	NM_005933.3	1225	aaG/aaT	7/36	0.243349452117592	3	FACETS	1	0.871	1	0.546	0.444	0.658	CLONAL	1	TRUE	1	0.372650031359061	3		189	175	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435931	49435931	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	46	586	0	ENST00000301067.7:c.6050C>G	p.Thr2017Ser	p.T2017S	ENST00000301067	NM_003482.3	2017	aCc/aGc	28/54	NA	2	FACETS	0.802	0.678	0.936			1	INDETERMINATE	1	TRUE	NA	0.372650031359061	2		586	308	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69210676	69210676	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	39	294	0	ENST00000462284.1:c.259C>A	p.Leu87Ile	p.L87I	ENST00000462284	NM_002392.5	87	Ctt/Att	4/11	0.372650031359061	5	FACETS	0.556	0.46	0.663	0.185	0.153	0.221	SUBCLONAL	1	TRUE	2	0.372650031359061	5		294	587	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222562	69222562	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	43	296	0	ENST00000462284.1:c.535G>T	p.Asp179Tyr	p.D179Y	ENST00000462284	NM_002392.5	179	Gat/Tat	8/11	0.372650031359061	5	FACETS	0.693	0.58	0.819	0.231	0.193	0.273	SUBCLONAL	1	TRUE	2	0.372650031359061	5		296	519	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108765	2108765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755631210	NA	P-0001372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	73	557	1	ENST00000219476.3:c.866C>T	p.Ala289Val	p.A289V	ENST00000219476	NM_000548.3	289	gCg/gTg	10/42	0.222233142775162	1	FACETS	1	0.974	1	1	0.974	1	INDETERMINATE	1	TRUE	0	0.372650031359061	1		558	231	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349200	70349200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	63	822	0	ENST00000374080.3:c.3612C>A	p.Asp1204Glu	p.D1204E	ENST00000374080		1204	gaC/gaA	26/45	0.266326780970648	0	FACETS	0.647	0.563	0.736			1	SUBCLONAL	1	TRUE	0	0.372650031359061	0		822	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577146	7577147	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0001372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	86	467	0	ENST00000269305.4:c.791dup	p.Leu265ThrfsTer7	p.L265Tfs*7	ENST00000269305	NM_001126112.2	264	cta/ctTa	8/11	0.372650031359061	1	FACETS	0.789	0.71	0.871	1	0.983	1	SUBCLONAL	2	TRUE	0	0.372650031359061	1		467	238	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0001385-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	33	360	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.408	0.331	0.495	0.408	0.331	0.495	SUBCLONAL	1	TRUE	1	0.266572933124188	2		360	607	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45800152	45800152	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553131563	NA	P-0001385-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	93	472	0	ENST00000450313.1:c.68G>A	p.Gly23Glu	p.G23E	ENST00000450313	NM_012222.2	23	gGa/gAa	2/16	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.266572933124188	2		472	663	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225360595	225360595	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001385-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	98	501	0	ENST00000264414.4:c.1796T>G	p.Met599Arg	p.M599R	ENST00000264414	NM_003590.4	599	aTg/aGg	13/16	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.266572933124188	2		501	730	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201686	66201686	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001385-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	114	638	0	ENST00000273854.3:c.2816C>G	p.Pro939Arg	p.P939R	ENST00000273854	NM_004439.5	939	cCa/cGa	16/18	0.266572933124188	1	FACETS	0.834	0.75	0.923	0.834	0.75	0.923	CLONAL	1	TRUE	0	0.266572933124188	1		638	889	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517807	187517807	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001385-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	61	299	0	ENST00000441802.2:c.12887G>T	p.Arg4296Leu	p.R4296L	ENST00000441802	NM_005245.3	4296	cGa/cTa	25/27	0.266572933124188	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.266572933124188	1		299	330	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334991	81334991	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001385-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	52	383	0	ENST00000222390.5:c.1836C>A	p.Cys612Ter	p.C612*	ENST00000222390	NM_000601.4	612	tgC/tgA	16/18	1	2	FACETS	0.628	0.534	0.732	0.628	0.534	0.732	SUBCLONAL	1	TRUE	1	0.266572933124188	2		383	621	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913535	NA	P-0001385-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	290	479	0	ENST00000311936.3:c.37G>C	p.Gly13Arg	p.G13R	ENST00000311936	NM_004985.3	13	Ggc/Cgc	2/5	0.234248795687722	5	FACETS	1	0.97	1			1	CLONAL	3	TRUE	NA	0.266572933124188	5		479	972	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882287	89882287	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001385-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	109	495	0	ENST00000389301.3:c.187G>C	p.Glu63Gln	p.E63Q	ENST00000389301	NM_000135.2	63	Gag/Cag	2/43	0.197815992499806	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.266572933124188	1		495	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913343	NA	P-0001385-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	191	462	0	ENST00000269305.4:c.817C>G	p.Arg273Gly	p.R273G	ENST00000269305	NM_001126112.2	273	Cgt/Ggt	8/11	1	2	FACETS	1	0.933	1	1	0.993	1	CLONAL	2	TRUE	1	0.266572933124188	2		462	712	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221947	1221947	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs863224448	NA	P-0001385-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	120	359	0	ENST00000326873.7:c.863-1G>A		p.X288_splice	ENST00000326873	NM_000455.4	288			NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.266572933124188	2		359	635	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610154	10610154	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001385-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	79	351	0	ENST00000171111.5:c.556G>T	p.Gly186Cys	p.G186C	ENST00000171111	NM_203500.1	186	Ggc/Tgc	2/6	0.266572933124188	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.266572933124188	1		351	471	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349664	70349664	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001385-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	67	499	0	ENST00000374080.3:c.3826G>T	p.Asp1276Tyr	p.D1276Y	ENST00000374080		1276	Gat/Tat	27/45	0.217723274264432	0	FACETS	0.507	0.44	0.58			1	SUBCLONAL	1	TRUE	0	0.266572933124188	0		499	727	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944336	76944336	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001385-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	99	729	0	ENST00000373344.5:c.569C>A	p.Pro190His	p.P190H	ENST00000373344	NM_000489.3	190	cCt/cAt	7/35	0.217723274264432	0	FACETS	0.602	0.536	0.672			1	SUBCLONAL	1	TRUE	0	0.266572933124188	0		729	905	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161284210	161284210	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001397-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	137	515	0	ENST00000367975.2:c.15G>C	p.Leu5Phe	p.L5F	ENST00000367975	NM_003001.3	5	ttG/ttC	1/6	0.33283194586261	4	FACETS	1	0.966	1	0.377	0.342	0.413	CLONAL	1	TRUE	1	0.36899783372485	4		515	900	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629517	187629517	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001397-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	95	458	0	ENST00000441802.2:c.1465G>T	p.Asp489Tyr	p.D489Y	ENST00000441802	NM_005245.3	489	Gac/Tac	2/27	0.36899783372485	1	FACETS	0.986	0.883	1	0.986	0.883	1	CLONAL	1	TRUE	0	0.36899783372485	1		458	426	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004345	150004345	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001397-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	291	676	0	ENST00000253339.5:c.1880G>T	p.Arg627Met	p.R627M	ENST00000253339		627	aGg/aTg	3/7	0.36899783372485	0	FACETS	0.761	0.721	0.801			1	SUBCLONAL	2	TRUE	0	0.36899783372485	0		676	654	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336639	81336639	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001397-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	336	418	0	ENST00000222390.5:c.1583G>T	p.Trp528Leu	p.W528L	ENST00000222390	NM_000601.4	528	tGg/tTg	14/18	1	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	1	0.36899783372485	2		418	756	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845814	151845814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001397-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	236	458	0	ENST00000262189.6:c.13198C>T	p.Arg4400Trp	p.R4400W	ENST00000262189	NM_170606.2	4400	Cgg/Tgg	52/59	0.36899783372485	0	FACETS	0.717	0.683	0.751			1	SUBCLONAL	3	TRUE	0	0.36899783372485	0		458	375	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285506	38285506	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001397-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	215	486	0	ENST00000425967.3:c.647A>C	p.Asn216Thr	p.N216T	ENST00000425967	NM_001174067.1	216	aAc/aCc	6/19	0.36899783372485	9	FACETS	0.981	0.91	1			1	CLONAL	2	TRUE	NA	0.36899783372485	9		486	1361	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015192	37015192	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0001397-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	87	421	0	ENST00000358127.4:c.213-1G>T		p.X71_splice	ENST00000358127	NM_001280556.1	71			0.36899783372485	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.36899783372485	1		421	357	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28897059	28897059	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001397-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	88	314	0	ENST00000282397.4:c.2821A>G	p.Lys941Glu	p.K941E	ENST00000282397	NM_002019.4	941	Aag/Gag	21/30	0.342584732191153	0	FACETS	0.909	0.813	1			1	CLONAL	1	TRUE	0	0.36899783372485	0		314	331	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690565	88690565	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0001397-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	148	307	0	ENST00000360948.2:c.464+1G>A		p.X155_splice	ENST00000360948	NM_001012338.2	155			0.36899783372485	1	FACETS	0.954	0.884	1	1	0.992	1	CLONAL	2	TRUE	0	0.36899783372485	1		307	343	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832771	3832771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001397-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	171	331	0	ENST00000262367.5:c.1487C>T	p.Pro496Leu	p.P496L	ENST00000262367	NM_004380.2	496	cCc/cTc	6/31	0.186359024420838	1	FACETS	0.893	0.831	0.956	1	0.992	1	INDETERMINATE	2	TRUE	0	0.36899783372485	1		331	423	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556173	29556173	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs199474747	NA	P-0001397-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	73	162	0	ENST00000356175.3:c.2540T>G	p.Leu847Arg	p.L847R	ENST00000356175	NM_000267.3	847	cTt/cGt	21/57	0.186359024420838	1	FACETS	0.791	0.705	0.88	1	0.98	1	INDETERMINATE	2	TRUE	0	0.36899783372485	1		162	204	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934037	39934037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001397-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	134	522	2	ENST00000378444.4:c.562C>T	p.Arg188Trp	p.R188W	ENST00000378444	NM_001123385.1	188	Cgg/Tgg	4/15	0.36899783372485	0	FACETS	0.994	0.91	1			1	CLONAL	1	TRUE	0	0.36899783372485	0		524	461	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223431	53223431	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001397-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	98	494	0	ENST00000375401.3:c.3928G>T	p.Glu1310Ter	p.E1310*	ENST00000375401	NM_004187.3	1310	Gag/Tag	23/26	0.36899783372485	0	FACETS	0.98	0.883	1			1	CLONAL	1	TRUE	0	0.36899783372485	0		494	342	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80646037	80646037	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001397-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	106	245	0	ENST00000286548.4:c.115del	p.Glu39SerfsTer21	p.E39Sfs*21	ENST00000286548	NM_002072.3	39	Gag/ag	1/7	0.36899783372485	1	FACETS	0.933	0.852	1	1	0.989	1	CLONAL	2	TRUE	0	0.36899783372485	1		245	251	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341242	341243	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0001397-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	120	424	0	ENST00000262320.3:c.2241_2242del	p.Pro748GlyfsTer33	p.P748Gfs*33	ENST00000262320	NM_003502.3	747	gcGCcg/gccg	9/11	0.342584732191153	0	FACETS	1	0.952	1			1	CLONAL	1	TRUE	0	0.36899783372485	0		424	385	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653027	29653028	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0001397-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	298	613	0	ENST00000356175.3:c.4963_4964del	p.Ala1655SerfsTer5	p.A1655Sfs*5	ENST00000356175	NM_000267.3	1654	tcCGca/tcca	36/57	0.186359024420838	1	FACETS	0.828	0.784	0.874	1	0.995	1	INDETERMINATE	2	TRUE	0	0.36899783372485	1		613	795	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609620	81609621	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0001397-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	187	417	0	ENST00000298171.2:c.1218_1219delinsAA	p.Asn406_Pro407delinsLysThr	p.N406_P407delinsKT	ENST00000298171	NM_000369.2	406	aaCCcg/aaAAcg	10/10	1	2	FACETS	0.926	0.862	0.992	1	0.993	1	CLONAL	2	TRUE	1	0.36899783372485	2		417	547	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0001454-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	48	262	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.274388477553769	4	FACETS	1	0.894	1	0.539	0.454	0.634	CLONAL	1	TRUE	2	0.11	4		262	898	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145430	58145430	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894340	NA	P-0001454-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	17	685	0	ENST00000257904.6:c.71G>T	p.Arg24Leu	p.R24L	ENST00000257904	NM_000075.3	24	cGt/cTt	2/8	0.274388477553769	4	FACETS	0.66	0.49	0.863	0.33	0.245	0.432	SUBCLONAL	1	TRUE	2	0.11	4		685	520	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444326	50444326	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001454-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	20	479	1	ENST00000331340.3:c.256G>T	p.Asp86Tyr	p.D86Y	ENST00000331340	NM_006060.4	86	Gat/Tat	4/8	0.274388477553769	4	FACETS	1	0.807	1	0.533	0.406	0.681	CLONAL	1	TRUE	2	0.11	4		480	379	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044595	47044595	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001454-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	10	452	0	ENST00000377604.3:c.2092G>T	p.Glu698Ter	p.E698*	ENST00000377604	NM_001204468.1	698	Gag/Tag	18/24	0.3	2	FACETS	0.909	0.616	1	0.455	0.308	0.639	CLONAL	1	TRUE	0	0.11	2		452	200	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372744	81372744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1168082930	NA	P-0001586-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	249	443	0	ENST00000222390.5:c.790G>A	p.Asp264Asn	p.D264N	ENST00000222390	NM_000601.4	264	Gat/Aat	7/18	0.763465865994398	4	FACETS	0.938	0.884	0.992	0.938	0.884	0.992	CLONAL	2	TRUE	2	0.800702072128902	4		443	597	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790038	40790038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757402269	NA	P-0001586-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	178	341	0	ENST00000373198.4:c.2693C>T	p.Thr898Met	p.T898M	ENST00000373198	NM_133170.3	898	aCg/aTg	18/32	0.732040945693535	4	FACETS	0.968	0.893	1	0.484	0.446	0.523	CLONAL	1	TRUE	2	0.800702072128902	4		341	827	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974795	21974818	+	inframe_deletion	In_Frame_Del	DEL	GGCTCCATGCTGCTCCCCGCCGCC	GGCTCCATGCTGCTCCCCGCCGCC	-	rs587780668	NA	P-0001586-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	27	170	0	ENST00000304494.5:c.9_32del	p.Ala4_Pro11del	p.A4_P11del	ENST00000304494	NM_000077.4	3	ccGGCGGCGGGGAGCAGCATGGAGCCt/cct	1/3	0.800702072128902	1	FACETS	0.293	0.236	0.356	0.293	0.236	0.356	SUBCLONAL	1	TRUE	0	0.800702072128902	1		170	138	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs121913468	NA	P-0001586-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	17347	472	2	ENST00000269571.5:c.2305G>C	p.Asp769His	p.D769H	ENST00000269571		769	Gac/Cac	19/27	0.800702072128902	28	FACETS	0.999	0.997	1			1	CLONAL	28	TRUE	NA	0.800702072128902	28		474	17673	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481856	56481856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001586-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	205	480	0	ENST00000267101.3:c.784C>T	p.Pro262Ser	p.P262S	ENST00000267101	NM_001982.3	262	Cct/Tct	7/28	0.800702072128902	3	FACETS	1	0.961	1	0.523	0.487	0.56	CLONAL	1	TRUE	1	0.800702072128902	3		480	686	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0001599-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	29	228	0	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	1	2	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	TRUE	1	0.146566971237609	2		228	375	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023312	27023312	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001599-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	33	30	0	ENST00000324856.7:c.418G>A	p.Ala140Thr	p.A140T	ENST00000324856	NM_006015.4	140	Gcg/Acg	1/20	1	2	FACETS	1	0.883	1	1	0.976	1	CLONAL	5	TRUE	1	0.146566971237609	2		30	85	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443574	29443574	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001599-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	36	193	0	ENST00000389048.3:c.3643C>A	p.Pro1215Thr	p.P1215T	ENST00000389048	NM_004304.4	1215	Ccg/Acg	23/29	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.146566971237609	2		193	386	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422565	225422565	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001599-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	40	189	0	ENST00000264414.4:c.75G>T	p.Met25Ile	p.M25I	ENST00000264414	NM_003590.4	25	atG/atT	2/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.146566971237609	2		189	389	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973981	55973981	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0001599-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	54	231	0	ENST00000263923.4:c.1335T>A	p.Cys445Ter	p.C445*	ENST00000263923	NM_002253.2	445	tgT/tgA	10/30	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.146566971237609	2		231	546	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459672	149459672	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1362664764	NA	P-0001599-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	75	318	0	ENST00000286301.3:c.535G>A	p.Ala179Thr	p.A179T	ENST00000286301	NM_005211.3	179	Gcc/Acc	4/22	1	2	FACETS	0.844	0.74	0.956	1	0.979	1	CLONAL	2	TRUE	1	0.146566971237609	2		318	606	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001245	150001245	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001599-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	53	473	0	ENST00000253339.5:c.2359G>C	p.Gly787Arg	p.G787R	ENST00000253339		787	Ggg/Cgg	4/7	1	2	FACETS	0.948	0.807	1	0.948	0.807	1	CLONAL	1	TRUE	1	0.146566971237609	2		473	763	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579478	7579478	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567556594	NA	P-0001599-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	36	229	0	ENST00000269305.4:c.209C>T	p.Ala70Val	p.A70V	ENST00000269305	NM_001126112.2	70	gCt/gTt	4/11	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.146566971237609	2		229	364	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533309	29533309	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs752789273	NA	P-0001599-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	62	324	0	ENST00000356175.3:c.1312G>T	p.Glu438Ter	p.E438*	ENST00000356175	NM_000267.3	438	Gaa/Taa	12/57	1	2	FACETS	0.785	0.678	0.9	1	0.972	1	SUBCLONAL	2	TRUE	1	0.146566971237609	2		324	539	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645134	86645134	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0001599-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	25	282	0	ENST00000274376.6:c.1206T>A	p.Cys402Ter	p.C402*	ENST00000274376	NM_002890.2	402	tgT/tgA	8/25	0.146566971237609	1	FACETS	0.848	0.668	1	0.848	0.668	1	CLONAL	1	TRUE	0	0.146566971237609	1		282	373	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0001613-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	326	391	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.3	6	FACETS	1	0.985	1	0.877	0.833	0.922	CLONAL	4	FALSE	1	0.3	6		391	793	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241677	55241677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504256	NA	P-0001613-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	42	427	1	ENST00000275493.2:c.2125G>A	p.Glu709Lys	p.E709K	ENST00000275493	NM_005228.3	709	Gaa/Aaa	18/28	0.3	6	FACETS	0.599	0.499	0.711	0.12	0.099	0.143	SUBCLONAL	1	FALSE	1	0.3	6		428	748	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630504	47630504	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs372189599	NA	P-0001613-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	28	404	0	ENST00000233146.2:c.174C>G	p.Phe58Leu	p.F58L	ENST00000233146	NM_000251.2	58	ttC/ttG	1/16	1	2	FACETS	0.417	0.332	0.513	0.417	0.332	0.513	SUBCLONAL	1	FALSE	1	0.3	2		404	448	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2949706	2949706	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001613-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	36	456	0	ENST00000396946.4:c.3238G>C	p.Glu1080Gln	p.E1080Q	ENST00000396946	NM_032415.4	1080	Gag/Cag	24/25	0.3	3	FACETS	0.496	0.407	0.597	0.248	0.203	0.299	SUBCLONAL	1	FALSE	1	0.3	3		456	556	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782664	NA	P-0001613-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	35	367	0	ENST00000269305.4:c.711G>C	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atC	7/11	1	2	FACETS	0.585	0.479	0.703	0.585	0.479	0.703	SUBCLONAL	1	FALSE	1	0.3	2		367	399	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001632-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	444	486	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.600857251042008	3	FACETS	1	0.995	1	0.44	0.42	0.461	CLONAL	1	TRUE	0	0.724177179110485	3		486	1265	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151893024	151893024	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0001632-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	370	482	0	ENST00000262189.6:c.4346C>G	p.Ser1449Ter	p.S1449*	ENST00000262189	NM_170606.2	1449	tCa/tGa	28/59	NA	2	FACETS	0.933	0.887	0.981			1	INDETERMINATE	1	TRUE	NA	0.724177179110485	2		482	1095	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835596	68835596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587783047	NA	P-0001632-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	783	488	0	ENST00000261769.5:c.187C>T	p.Arg63Ter	p.R63*	ENST00000261769	NM_004360.3	63	Cga/Tga	3/16	0.608901499737666	3	FACETS	0.915	0.894	0.935	0.915	0.894	0.935	CLONAL	3	TRUE	0	0.724177179110485	3		488	1073	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0001697-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	43	306	1	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	0.179417144891197	2	FACETS	0.808	0.686	0.939	0.808	0.686	0.939	INDETERMINATE	2	TRUE	0	0.305739185063058	2		307	174	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032055	26032055	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs754817747	NA	P-0001697-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	43	241	0	ENST00000244661.2:c.234C>G	p.Asp78Glu	p.D78E	ENST00000244661	NM_003537.3	78	gaC/gaG	1/1	0.305739185063058	2	FACETS	0.818	0.695	0.95	0.818	0.695	0.95	CLONAL	2	TRUE	0	0.305739185063058	2		241	172	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449610	187449610	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001697-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	38	296	0	ENST00000232014.4:c.270G>T	p.Met90Ile	p.M90I	ENST00000232014	NM_001130845.1	90	atG/atT	4/10	0.305739185063058	3	FACETS	1	0.886	1	0.543	0.451	0.644	CLONAL	1	TRUE	1	0.305739185063058	3		296	264	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0001724-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	90	796	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.134062578353521	4	FACETS	1	0.977	1	0.694	0.619	0.773	INDETERMINATE	1	TRUE	2	0.422236012470477	4		796	437	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098804	178098804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553487942	NA	P-0001724-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	201	904	0	ENST00000397062.3:c.241G>A	p.Gly81Ser	p.G81S	ENST00000397062	NM_006164.4	81	Ggt/Agt	2/5	0.248194474038553	5	FACETS	0.873	0.814	0.933			1	INDETERMINATE	3	TRUE	NA	0.422236012470477	5		904	594	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628184	187628184	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs61733570	NA	P-0001724-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	129	699	0	ENST00000441802.2:c.2798G>T	p.Arg933Leu	p.R933L	ENST00000441802	NM_005245.3	933	cGt/cTt	2/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.422236012470477	2		699	481	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220717	1220717	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587782018	NA	P-0001724-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	100	490	0	ENST00000326873.7:c.734+1G>T		p.X245_splice	ENST00000326873	NM_000455.4	245			0.422236012470477	1	FACETS	0.816	0.744	0.889	1	0.987	1	CLONAL	2	TRUE	0	0.422236012470477	1		490	229	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156717	20156717	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs967472465	NA	P-0001724-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	101	430	2	ENST00000379607.5:c.40A>G	p.Arg14Gly	p.R14G	ENST00000379607	NM_001412.3	14	Agg/Ggg	2/7	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.422236012470477	1		432	252	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0001731-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	188	322	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.93617576038411	2		324	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0001731-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	262	559	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.93617576038411	2		560	541	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131161	55131161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001731-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	368	685	0	ENST00000257290.5:c.704G>A	p.Cys235Tyr	p.C235Y	ENST00000257290	NM_006206.4	235	tGt/tAt	5/23	0.135665984798296	4	FACETS	1	0.958	1	1	0.958	1	INDETERMINATE	2	FALSE	2	0.93617576038411	4		685	759	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457692	67457692	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs548756379	NA	P-0001731-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	216	551	0	ENST00000327367.4:c.502G>C	p.Ala168Pro	p.A168P	ENST00000327367	NM_005902.3	168	Gca/Cca	3/9	1	2	FACETS	0.988	0.93	1	0.988	0.93	1	CLONAL	1	FALSE	1	0.93617576038411	2		551	467	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938085	76938085	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001731-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	358	373	0	ENST00000373344.5:c.2663del	p.Phe888SerfsTer17	p.F888Sfs*17	ENST00000373344	NM_000489.3	888	tTc/tc	9/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	FALSE	0	0.93617576038411	1		373	381	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0001778-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	181	512	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.417273411399206	3	FACETS	1	0.939	1	0.511	0.47	0.552	CLONAL	1	TRUE	1	0.430420992108245	3		512	1001	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0001778-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	174	454	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.430420992108245	2	FACETS	0.853	0.792	0.914	0.853	0.792	0.914	CLONAL	2	TRUE	0	0.430420992108245	2		454	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577107	7577107	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1057523347	NA	P-0001778-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	328	684	2	ENST00000269305.4:c.831T>A	p.Cys277Ter	p.C277*	ENST00000269305	NM_001126112.2	277	tgT/tgA	8/11	0.430420992108245	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.430420992108245	2		686	682	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114679	108114679	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs778624615	NA	P-0001778-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	165	317	0	ENST00000278616.4:c.497-1G>C		p.X166_splice	ENST00000278616	NM_000051.3	166			0.430420992108245	2	FACETS	0.98	0.912	1	0.98	0.912	1	CLONAL	2	TRUE	0	0.430420992108245	2		317	391	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427377	49427377	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001778-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	69	560	0	ENST00000301067.7:c.11111T>G	p.Leu3704Arg	p.L3704R	ENST00000301067	NM_003482.3	3704	cTt/cGt	39/54	0.417273411399206	3	FACETS	0.52	0.452	0.594	0.26	0.226	0.297	SUBCLONAL	1	TRUE	1	0.430420992108245	3		560	749	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256748	19256748	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001778-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	26	461	0	ENST00000162023.5:c.965G>A	p.Arg322His	p.R322H	ENST00000162023		322	cGc/cAc	13/13	0.150834547453864	5	FACETS	0.402	0.317	0.499	0.1	0.079	0.125	INDETERMINATE	1	TRUE	1	0.430420992108245	5		461	495	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931634	39931634	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001778-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	42	335	0	ENST00000378444.4:c.2965A>C	p.Ser989Arg	p.S989R	ENST00000378444	NM_001123385.1	989	Agt/Cgt	4/15	0.229278085077933	2	FACETS	0.323	0.269	0.383			1	INDETERMINATE	1	TRUE	NA	0.430420992108245	2		335	605	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875982	76875982	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001778-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	276	375	0	ENST00000373344.5:c.5153G>T	p.Cys1718Phe	p.C1718F	ENST00000373344	NM_000489.3	1718	tGt/tTt	20/35	1	1	FACETS	0.889	0.844	0.935	1	0.995	1	CLONAL	2	TRUE	0	0.430420992108245	1		375	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578517	7578517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750600586	NA	P-0001823-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	1961	321	0	ENST00000269305.4:c.413C>T	p.Ala138Val	p.A138V	ENST00000269305	NM_001126112.2	138	gCc/gTc	5/11	0.266940256395406	8	FACETS	0.976	0.969	0.983			1	CLONAL	13	FALSE	2	0.266940256395406	8		321	2085	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0001823-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	337	308	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.26898105978586	4	FACETS	0.868	0.82	0.916	0.868	0.82	0.916	CLONAL	3	FALSE	1	0.266940256395406	4		309	1229	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397695	116397695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001823-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1357	16238	416	2	ENST00000397752.3:c.1969C>T	p.Pro657Ser	p.P657S	ENST00000397752	NM_000245.2	657	Cct/Tct	8/21	0.266940256395406	36	FACETS	1	0.999	1			1	CLONAL	38	FALSE	NA	0.266940256395406	36		418	17595	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517201	NA	P-0001846-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	86	142	0	ENST00000263967.3:c.1637A>C	p.Gln546Pro	p.Q546P	ENST00000263967	NM_006218.2	546	cAg/cCg	10/21	1	2	FACETS	0.95	0.845	1	0.95	0.845	1	CLONAL	1	TRUE	1	0.429173272072315	2		142	422	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525110	187525110	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001846-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	54	101	0	ENST00000441802.2:c.10570C>G	p.Gln3524Glu	p.Q3524E	ENST00000441802	NM_005245.3	3524	Cag/Gag	19/27	0.429173272072315	1	FACETS	0.827	0.714	0.948	0.827	0.714	0.948	CLONAL	1	TRUE	0	0.429173272072315	1		101	239	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030367	49030368	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0001846-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	120	204	0	ENST00000267163.4:c.1848dup	p.Gly617ArgfsTer36	p.G617Rfs*36	ENST00000267163	NM_000321.2	614	-/A	19/27	0.404139964942666	1	FACETS	0.819	0.743	0.899	0.819	0.743	0.899	CLONAL	1	TRUE	0	0.429173272072315	1		204	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0001916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	174	341	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.3791907008204	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.386867455503268	1		341	624	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913351	NA	P-0001916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	137	318	0	ENST00000288602.6:c.1397G>T	p.Gly466Val	p.G466V	ENST00000288602	NM_004333.4	466	gGa/gTa	11/18	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.386867455503268	2		318	525	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533378	29533378	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs878853865	NA	P-0001916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	167	188	0	ENST00000356175.3:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000356175	NM_000267.3	461	Cga/Tga	12/57	0.279954333819625	3	FACETS	1	0.974	1			1	CLONAL	2	TRUE	NA	0.386867455503268	3		188	464	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551710	150551710	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	67	98	0	ENST00000369026.2:c.297C>A	p.Phe99Leu	p.F99L	ENST00000369026	NM_021960.4	99	ttC/ttA	1/3	0.365631199587887	3	FACETS	0.783	0.688	0.883	0.783	0.688	0.883	SUBCLONAL	2	TRUE	1	0.386867455503268	3		98	264	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471043	25471043	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	170	314	2	ENST00000264709.3:c.718G>T	p.Glu240Ter	p.E240*	ENST00000264709	NM_175629.2	240	Gag/Tag	7/23	0.165741568803813	2	FACETS	1	0.989	1	0.724	0.669	0.781	INDETERMINATE	1	TRUE	0	0.386867455503268	2		316	607	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541541	187541541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs980333559	NA	P-0001916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	51	299	1	ENST00000441802.2:c.6199G>A	p.Val2067Met	p.V2067M	ENST00000441802	NM_005245.3	2067	Gtg/Atg	10/27	0.267797396010276	1	FACETS	0.436	0.37	0.507	0.436	0.37	0.507	SUBCLONAL	1	TRUE	0	0.386867455503268	1		300	488	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952502	38952502	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	80	165	0	ENST00000357387.3:c.2923A>G	p.Ile975Val	p.I975V	ENST00000357387	NM_152756.3	975	Ata/Gta	30/38	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.386867455503268	2		165	408	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615005	43615005	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	79	275	0	ENST00000355710.3:c.2419G>C	p.Ala807Pro	p.A807P	ENST00000355710	NM_020975.4	807	Gcc/Ccc	14/20	0.222093787691412	3	FACETS	0.979	0.863	1	0.489	0.431	0.551	INDETERMINATE	1	TRUE	1	0.386867455503268	3		275	498	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008226	29008226	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	84	304	0	ENST00000282397.4:c.645G>T	p.Leu215Phe	p.L215F	ENST00000282397	NM_002019.4	215	ttG/ttT	5/30	0.386867455503268	1	FACETS	0.768	0.681	0.86	0.768	0.681	0.86	SUBCLONAL	1	TRUE	0	0.386867455503268	1		304	456	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923390	9923390	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	59	336	0	ENST00000330684.3:c.1897G>C	p.Val633Leu	p.V633L	ENST00000330684	NM_001134407.1	633	Gta/Cta	9/13	0.192024962314993	1	FACETS	0.531	0.458	0.611	0.531	0.458	0.611	INDETERMINATE	1	TRUE	0	0.386867455503268	1		336	463	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220443	1220443	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	121	286	0	ENST00000326873.7:c.536C>A	p.Pro179Gln	p.P179Q	ENST00000326873	NM_000455.4	179	cCg/cAg	4/10	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.386867455503268	2		286	477	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602871	10602871	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	144	256	0	ENST00000171111.5:c.707A>T	p.Asp236Val	p.D236V	ENST00000171111	NM_203500.1	236	gAc/gTc	3/6	0.386867455503268	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.386867455503268	1		256	504	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141495	11141495	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	139	291	0	ENST00000358026.2:c.3472G>C	p.Ala1158Pro	p.A1158P	ENST00000358026	NM_001128849.1	1158	Gct/Cct	25/36	0.386867455503268	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.386867455503268	1		291	497	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276713	15276713	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	134	302	0	ENST00000263388.2:c.5552G>T	p.Arg1851Leu	p.R1851L	ENST00000263388	NM_000435.2	1851	cGt/cTt	30/33	0.386867455503268	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.386867455503268	1		302	488	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276768	15276768	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	145	324	0	ENST00000263388.2:c.5497G>T	p.Ala1833Ser	p.A1833S	ENST00000263388	NM_000435.2	1833	Gca/Tca	30/33	0.386867455503268	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.386867455503268	1		324	466	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561552	9561552	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	24	191	0	ENST00000353224.5:c.230G>T	p.Cys77Phe	p.C77F	ENST00000353224	NM_177990.2	77	tGc/tTc	4/10	0.249314962080261	0	FACETS	0.302	0.237	0.376			1	SUBCLONAL	1	TRUE	0	0.386867455503268	0		191	252	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513232	44513232	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	37	96	0	ENST00000291552.4:c.703G>C	p.Glu235Gln	p.E235Q	ENST00000291552	NM_006758.2	235	Gaa/Caa	8/8	0.386867455503268	3	FACETS	1	0.908	1			1	CLONAL	1	TRUE	NA	0.386867455503268	3		96	200	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0001920-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	168	272	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.684963924723515	2		272	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0001920-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	300	618	0	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	0.684963924723515	2		618	713	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0001920-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	237	308	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.155143075782129	3	FACETS	1	0.992	1	0.702	0.659	0.746	INDETERMINATE	1	TRUE	1	0.684963924723515	3		309	662	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0001944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	92	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.14	2		341	983	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628053	187628053	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	99	518	0	ENST00000441802.2:c.2929G>T	p.Asp977Tyr	p.D977Y	ENST00000441802	NM_005245.3	977	Gat/Tat	2/27	1	2	FACETS	0.806	0.719	0.9	1	0.983	1	CLONAL	2	TRUE	1	0.14	2		518	877	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220371	1220371	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0001944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	67	314	0	ENST00000326873.7:c.465-1G>T		p.X155_splice	ENST00000326873	NM_000455.4	155			0.209809910052775	1	FACETS	0.853	0.742	0.972	1	0.977	1	CLONAL	2	TRUE	0	0.14	1		314	522	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597396	10597396	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	57	438	0	ENST00000171111.5:c.1807G>T	p.Gly603Trp	p.G603W	ENST00000171111	NM_203500.1	603	Ggg/Tgg	6/6	0.276158792326604	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.14	1		438	543	SUCCESS
AR	367	MSKCC	GRCh37	X	66937319	66937319	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0001944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	65	453	0	ENST00000374690.3:c.2174-1G>C		p.X725_splice	ENST00000374690	NM_000044.3	725			0.3	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.14	1		453	718	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589370	28589370	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001959-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	113	444	0	ENST00000241453.7:c.2677C>A	p.Pro893Thr	p.P893T	ENST00000241453	NM_004119.2	893	Ccg/Acg	22/24	NA	2	FACETS	0.527	0.476	0.581			1	INDETERMINATE	1	TRUE	NA	0.783716048332647	2		444	547	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933586	39933586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1397661727	NA	P-0001959-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	193	357	0	ENST00000378444.4:c.1013G>A	p.Arg338Gln	p.R338Q	ENST00000378444	NM_001123385.1	338	cGg/cAg	4/15	NA	2	FACETS	0.747	0.694	0.802			1	INDETERMINATE	1	TRUE	NA	0.783716048332647	2		357	659	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587163	212587163	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	107	752	2	ENST00000342788.4:c.838A>G	p.Asn280Asp	p.N280D	ENST00000342788	NM_005235.2	280	Aat/Gat	7/28	1	2	FACETS	0.804	0.726	0.885	1	0.985	1	CLONAL	2	TRUE	1	0.322280162607784	2		754	413	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538372	9538375	+	frameshift_variant	Frame_Shift_Del	DEL	TTCA	TTCA	-	novel	NA	P-0001998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	29	535	0	ENST00000353224.5:c.1623_1626del	p.Asn541LysfsTer4	p.N541Kfs*4	ENST00000353224	NM_177990.2	541	aaTGAA/aa	7/10	1	2	FACETS	0.586	0.471	0.716	0.586	0.471	0.716	SUBCLONAL	1	TRUE	1	0.322280162607784	2		535	307	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0002026-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	112	515	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	1	2	FACETS	0.784	0.705	0.868	1	0.984	1	SUBCLONAL	2	TRUE	1	0.175914213467399	2		515	812	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0002026-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	192	473	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.175914213467399	8	FACETS	1	0.933	1	0.606	0.56	0.655	CLONAL	3	TRUE	3	0.175914213467399	8		473	1100	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11301680	11301680	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002026-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	65	473	0	ENST00000361445.4:c.1471C>T	p.Arg491Ter	p.R491*	ENST00000361445	NM_004958.3	491	Cga/Tga	10/58	0.175914213467399	3	FACETS	0.907	0.785	1	0.454	0.392	0.521	CLONAL	1	TRUE	1	0.175914213467399	3		473	886	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224526	224526	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002026-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	79	221	1	ENST00000264932.6:c.202G>T	p.Gly68Cys	p.G68C	ENST00000264932	NM_004168.2	68	Ggc/Tgc	3/15	NA	2	FACETS	1	0.959	1			1	INDETERMINATE	2	TRUE	NA	0.175914213467399	2		222	377	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030326	180030326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150279372	NA	P-0002026-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	175	528	1	ENST00000261937.6:c.3958C>T	p.Arg1320Trp	p.R1320W	ENST00000261937	NM_182925.4	1320	Cgg/Tgg	30/30	1	2	FACETS	1	0.962	1	1	0.993	1	CLONAL	2	TRUE	1	0.175914213467399	2		529	928	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680730	30680730	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002026-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	67	535	0	ENST00000376406.3:c.989A>G	p.Asp330Gly	p.D330G	ENST00000376406	NM_014641.2	330	gAc/gGc	5/15	1	2	FACETS	0.875	0.758	1	0.875	0.758	1	CLONAL	1	TRUE	1	0.175914213467399	2		535	871	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93636564	93636564	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002026-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	66	343	0	ENST00000375746.1:c.994G>T	p.Ala332Ser	p.A332S	ENST00000375746	NM_001174167.1	332	Gca/Tca	8/14	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.175914213467399	2		343	672	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620407	43620407	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002026-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	148	373	0	ENST00000355710.3:c.3016G>T	p.Glu1006Ter	p.E1006*	ENST00000355710	NM_020975.4	1006	Gag/Tag	18/20	0.175914213467399	4	FACETS	1	0.977	1	0.798	0.73	0.871	CLONAL	2	TRUE	1	0.175914213467399	4		373	826	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670436	88670436	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002026-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	75	445	1	ENST00000360948.2:c.1250C>A	p.Pro417His	p.P417H	ENST00000360948	NM_001012338.2	417	cCt/cAt	11/19	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.175914213467399	2		446	830	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs11575997	NA	P-0002026-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	62	526	0	ENST00000269305.4:c.993+1G>T		p.X331_splice	ENST00000269305	NM_001126112.2	331			1	2	FACETS	0.931	0.803	1	0.931	0.803	1	CLONAL	1	TRUE	1	0.175914213467399	2		526	757	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281164	15281164	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002026-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	57	453	0	ENST00000263388.2:c.5092G>T	p.Gly1698Cys	p.G1698C	ENST00000263388	NM_000435.2	1698	Ggc/Tgc	27/33	0.175914213467399	1	FACETS	0.941	0.807	1	0.941	0.807	1	CLONAL	1	TRUE	0	0.175914213467399	1		453	628	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408858	41408858	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0002026-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	144	462	0	ENST00000373198.4:c.568A>T	p.Arg190Ter	p.R190*	ENST00000373198	NM_133170.3	190	Aga/Tga	4/32	0.175914213467399	3	FACETS	0.904	0.824	0.989	0.904	0.824	0.989	CLONAL	2	TRUE	1	0.175914213467399	3		462	985	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410700	32410700	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002026-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	50	504	0	ENST00000332351.3:c.1458del	p.Trp486CysfsTer14	p.W486Cfs*14	ENST00000332351	NM_024426.4	486	tgG/tg	10/10	0.175914213467399	3	FACETS	0.763	0.645	0.892	0.381	0.322	0.446	SUBCLONAL	1	TRUE	1	0.175914213467399	3		504	811	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0002027-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	99	327	1	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.28	2		328	498	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258070	123258070	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519799	NA	P-0002027-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	65	480	1	ENST00000358487.5:c.1611G>A	p.Met537Ile	p.M537I	ENST00000358487	NM_000141.4	537	atG/atA	12/18	1	2	FACETS	0.865	0.75	0.988	0.865	0.75	0.988	CLONAL	1	TRUE	1	0.28	2		481	537	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432693	49432693	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002027-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	18	292	2	ENST00000301067.7:c.8446C>T	p.Gln2816Ter	p.Q2816*	ENST00000301067	NM_003482.3	2816	Caa/Taa	34/54	1	2	FACETS	0.386	0.29	0.5	0.386	0.29	0.5	SUBCLONAL	1	TRUE	1	0.28	2		294	333	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088774	27088805	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTATGGTCCCCAGGGGGGTCAGTATGGCCC	AGCTATGGTCCCCAGGGGGGTCAGTATGGCCC	-	novel	NA	P-0002027-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	40	299	0	ENST00000324856.7:c.2384_2415del	p.Ser795ThrfsTer11	p.S795Tfs*11	ENST00000324856	NM_006015.4	795	AGCTATGGTCCCCAGGGGGGTCAGTATGGCCCa/a	7/20	1	2	FACETS	0.713	0.593	0.845	0.713	0.593	0.845	SUBCLONAL	1	TRUE	1	0.28	2		299	401	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396372	396372	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002027-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	25	406	0	ENST00000262320.3:c.654del	p.Val220SerfsTer22	p.V220Sfs*22	ENST00000262320	NM_003502.3	218	ccC/cc	2/11	0.27276693370035	1	FACETS	0.363	0.285	0.452	0.363	0.285	0.452	SUBCLONAL	1	TRUE	0	0.28	1		406	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0002028-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	133	469	0	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.270849332238269	1	FACETS	1	0.917	1	1	0.991	1	CLONAL	2	TRUE	0	0.270849332238269	1		469	424	SUCCESS
APC	324	MSKCC	GRCh37	5	112173538	112173538	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002028-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	134	384	2	ENST00000257430.4:c.2247G>T	p.Leu749Phe	p.L749F	ENST00000257430	NM_000038.5	749	ttG/ttT	16/16	0.270849332238269	2	FACETS	0.93	0.849	1	0.93	0.849	1	CLONAL	2	TRUE	0	0.270849332238269	2		386	532	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720649	89720649	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0002028-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	61	88	0	ENST00000371953.3:c.802-2A>C		p.X268_splice	ENST00000371953	NM_000314.4	268			0.270849332238269	3	FACETS	0.902	0.792	1	0.902	0.792	1	CLONAL	3	TRUE	0	0.270849332238269	3		88	189	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479268	50479268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002028-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	103	191	0	ENST00000394963.4:c.116G>A	p.Arg39Gln	p.R39Q	ENST00000394963	NM_003076.4	39	cGa/cAa	1/13	0.270849332238269	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.270849332238269	3		191	362	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39570459	39570459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002028-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	84	451	0	ENST00000262039.4:c.655G>A	p.Val219Ile	p.V219I	ENST00000262039	NM_002647.2	219	Gtt/Att	6/25	0.270849332238269	3	FACETS	0.799	0.705	0.901	0.4	0.352	0.451	CLONAL	1	TRUE	1	0.270849332238269	3		451	881	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057221	30057221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002028-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	159	451	1	ENST00000338641.4:c.703G>A	p.Gly235Arg	p.G235R	ENST00000338641	NM_000268.3	235	Gga/Aga	8/16	0.270849332238269	3	FACETS	0.903	0.829	0.98	0.903	0.829	0.98	CLONAL	2	TRUE	1	0.270849332238269	3		452	738	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0002032-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	98	393	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.510678532274176	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.510678532274176	1		393	231	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0002032-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	334	306	1	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	0.510678532274176	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	4	TRUE	0	0.510678532274176	4		307	473	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976745	2976745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748839211	NA	P-0002032-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	128	502	1	ENST00000396946.4:c.1267C>T	p.Arg423Trp	p.R423W	ENST00000396946	NM_032415.4	423	Cgg/Tgg	9/25	0.510678532274176	3	FACETS	1	0.978	1	0.617	0.562	0.674	CLONAL	1	TRUE	1	0.510678532274176	3		503	510	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230571	46230571	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002032-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	150	460	0	ENST00000334344.6:c.820C>T	p.Arg274Ter	p.R274*	ENST00000334344	NM_152641.2	274	Cga/Tga	8/21	0.204323436546947	4	FACETS	0.94	0.866	1	0.94	0.866	1	INDETERMINATE	2	TRUE	2	0.510678532274176	4		460	472	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604790	48604790	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1568211615	NA	P-0002032-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	325	375	0	ENST00000342988.3:c.1612G>T	p.Glu538Ter	p.E538*	ENST00000342988	NM_005359.5	538	Gaa/Taa	12/12	0.47334076045995	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.510678532274176	3		375	502	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748914	41748914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751855310	NA	P-0002032-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	98	397	0	ENST00000301178.4:c.1439G>A	p.Arg480His	p.R480H	ENST00000301178	NM_021913.4	480	cGt/cAt	11/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.510678532274176	2		397	336	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183322	56183323	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002032-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	123	329	0	ENST00000399503.3:c.4232_4233insT	p.Thr1412AspfsTer8	p.T1412Dfs*8	ENST00000399503	NM_005921.1	1411	ggg/ggTg	18/20	0.510678532274176	4	FACETS	1	0.981	1	0.44	0.399	0.483	CLONAL	1	TRUE	1	0.510678532274176	4		329	551	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0002033-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	99	348	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.847	0.755	0.945	0.847	0.755	0.945	CLONAL	1	TRUE	1	0.259125981665425	2		348	902	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217245	66217245	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0002033-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	83	296	0	ENST00000273854.3:c.2370C>G	p.Tyr790Ter	p.Y790*	ENST00000273854	NM_004439.5	790	taC/taG	14/18	0.189996432099682	1	FACETS	0.678	0.597	0.764	0.678	0.597	0.764	SUBCLONAL	1	TRUE	0	0.259125981665425	1		296	823	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032408	10032408	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1555455852	NA	P-0002033-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	38	89	0	ENST00000330684.3:c.415G>T	p.Asp139Tyr	p.D139Y	ENST00000330684	NM_001134407.1	139	Gat/Tat	3/13	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.259125981665425	2		89	251	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220370	1220370	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0002033-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	142	251	0	ENST00000326873.7:c.465-2A>G		p.X155_splice	ENST00000326873	NM_000455.4	155			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.259125981665425	2		251	895	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610243	10610243	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002033-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	149	399	0	ENST00000171111.5:c.467T>C	p.Met156Thr	p.M156T	ENST00000171111	NM_203500.1	156	aTg/aCg	2/6	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.259125981665425	2		399	1132	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557859	29557859	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0002033-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	44	131	0	ENST00000356175.3:c.3114del		p.X1038_splice	ENST00000356175	NM_000267.3	1038			1	2	FACETS	0.908	0.763	1	0.908	0.763	1	CLONAL	1	TRUE	1	0.259125981665425	2		131	374	SUCCESS
APC	324	MSKCC	GRCh37	5	112174217	112174217	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0002035-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	66	371	0	ENST00000257430.4:c.2926A>T	p.Arg976Ter	p.R976*	ENST00000257430	NM_000038.5	976	Aga/Tga	16/16	1	2	FACETS	0.859	0.751	0.974	0.859	0.751	0.974	CLONAL	1	TRUE	1	0.460113570203276	2		371	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578419	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002035-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	53	208	0	ENST00000269305.4:c.511del	p.Glu171ArgfsTer3	p.E171Rfs*3	ENST00000269305	NM_001126112.2	171	Gag/ag	5/11	0.368252624464977	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.460113570203276	1		208	161	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0002036-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	257	257	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.63744150204105	2	FACETS	0.992	0.948	1	0.992	0.948	1	CLONAL	2	TRUE	0	0.64918882930551	2		257	399	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0002036-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	279	476	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	0.63744150204105	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.64918882930551	2		476	427	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0002037-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	17	162	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.528	0.395	0.686	0.528	0.395	0.686	SUBCLONAL	1	TRUE	1	0.28	2		162	230	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220649	1220649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060499964	NA	P-0002037-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	142	356	0	ENST00000326873.7:c.667G>A	p.Glu223Lys	p.E223K	ENST00000326873	NM_000455.4	223	Gag/Aag	5/10	0.3	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.28	1		356	624	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578453	7578458	+	inframe_deletion	In_Frame_Del	DEL	GGCGCG	GGCGCG	-	novel	NA	P-0002037-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	109	344	0	ENST00000269305.4:c.472_477del	p.Arg158_Ala159del	p.R158_A159del	ENST00000269305	NM_001126112.2	158	CGCGCC/-	5/11	0.275168692388591	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.28	1		344	622	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38975702	38975702	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002038-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	61	337	0	ENST00000357387.3:c.826G>C	p.Asp276His	p.D276H	ENST00000357387	NM_152756.3	276	Gac/Cac	10/38	0.250596568683038	3	FACETS	0.63	0.543	0.726	0.315	0.271	0.363	SUBCLONAL	1	TRUE	1	0.312134894379892	3		337	717	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70442723	70442723	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002038-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	68	423	0	ENST00000373644.4:c.5045G>T	p.Ser1682Ile	p.S1682I	ENST00000373644	NM_030625.2	1682	aGc/aTc	10/12	0.195504595554183	1	FACETS	0.638	0.556	0.728	0.638	0.556	0.728	SUBCLONAL	1	TRUE	0	0.312134894379892	1		423	576	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434214	121434214	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs1490866595	NA	P-0002038-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	102	269	0	ENST00000257555.6:c.1105C>G	p.Leu369Val	p.L369V	ENST00000257555		369	Ctg/Gtg	5/10	0.278617973025788	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.312134894379892	1		269	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576863	7576863	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002038-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	106	353	0	ENST00000269305.4:c.983del	p.Phe328SerfsTer17	p.F328Sfs*17	ENST00000269305	NM_001126112.2	328	tTc/tc	9/11	0.240238698098656	1	FACETS	0.929	0.835	1	0.929	0.835	1	CLONAL	1	TRUE	0	0.312134894379892	1		353	617	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242470	+	missense_variant	Missense_Mutation	DNP	TT	TT	CC	rs397517096	NA	P-0002038-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	113	347	0	ENST00000275493.2:c.2239_2240delinsCC	p.Leu747Pro	p.L747P	ENST00000275493	NM_005228.3	747	TTa/CCa	19/28	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.312134894379892	2		347	704	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913499	NA	P-0002043-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	241	320	0	ENST00000345146.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000345146	NM_005896.2	132	Cgt/Ggt	4/10	0.172894725381181	4	FACETS	1	0.97	1	1	0.993	1	INDETERMINATE	3	TRUE	2	0.294994804212887	4		320	671	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133729472	133729472	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002043-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	146	336	0	ENST00000318560.5:c.101C>G	p.Ala34Gly	p.A34G	ENST00000318560	NM_005157.4	34	gCa/gGa	2/11	0.118020360771794	4	FACETS	1	0.969	1	1	0.969	1	INDETERMINATE	2	TRUE	2	0.294994804212887	4		336	574	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907621	76907621	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002043-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	45	233	0	ENST00000373344.5:c.4540C>T	p.Arg1514Ter	p.R1514*	ENST00000373344	NM_000489.3	1514	Cga/Tga	15/35	1	1	FACETS	0.583	0.49	0.685	0.583	0.49	0.685	SUBCLONAL	1	TRUE	0	0.294994804212887	1		233	446	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918980	76918981	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTGTATCTTGGCTTCTTAGATTCTTC	novel	NA	P-0002043-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	195	234	0	ENST00000373344.5:c.3985_4010dup	p.His1338LysfsTer17	p.H1338Kfs*17	ENST00000373344	NM_000489.3	1337	aga/agGAAGAATCTAAGAAGCCAAGATACAGa	12/35	1	1	FACETS	1	0.982	1	1	0.994	1	CLONAL	2	TRUE	0	0.294994804212887	1		234	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0002045-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	25	272	0	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	1	2	FACETS	0.393	0.31	0.489	0.393	0.31	0.489	SUBCLONAL	1	TRUE	1	0.41	2		272	310	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0002086-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	449	469	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	0.646258743213606	3	FACETS	0.948	0.909	0.987			1	CLONAL	2	TRUE	NA	0.646258743213606	3		469	970	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204513738	204513738	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002086-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	117	372	0	ENST00000367182.3:c.748G>A	p.Gly250Ser	p.G250S	ENST00000367182	NM_001278516.1	250	Ggt/Agt	9/11	0.321614775997001	1	FACETS	0.429	0.388	0.472	0.429	0.388	0.472	INDETERMINATE	1	TRUE	0	0.646258743213606	1		372	571	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149218	119149218	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs727504426	NA	P-0002086-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	132	512	0	ENST00000264033.4:c.1228-2A>G		p.X410_splice	ENST00000264033	NM_005188.3	410			0.320193791912031	1	FACETS	0.414	0.376	0.453	0.414	0.376	0.453	INDETERMINATE	1	TRUE	0	0.646258743213606	1		512	668	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088730	27088733	+	frameshift_variant	Frame_Shift_Del	DEL	AGAT	AGAT	-	novel	NA	P-0002086-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	250	433	0	ENST00000324856.7:c.2340_2343del	p.Gln780HisfsTer52	p.Q780Hfs*52	ENST00000324856	NM_006015.4	780	cAGATa/ca	7/20	0.350689773565232	1	FACETS	0.797	0.75	0.845	0.797	0.75	0.845	INDETERMINATE	1	TRUE	0	0.646258743213606	1		433	657	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17349219	17349219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200245469	NA	P-0002130-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	81	215	0	ENST00000375499.3:c.649C>T	p.Arg217Cys	p.R217C	ENST00000375499	NM_003000.2	217	Cgc/Tgc	7/8	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.602089457874408	2		215	254	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021754	71021754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002130-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	250	549	1	ENST00000318789.4:c.1604C>T	p.Thr535Ile	p.T535I	ENST00000318789	NM_032682.5	535	aCa/aTa	18/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.602089457874408	2		550	795	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932180	39932181	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0002130-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	185	300	0	ENST00000378444.4:c.2417_2418dup	p.Asp807Ter	p.D807*	ENST00000378444	NM_001123385.1	806	-/TA	4/15	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.602089457874408	1		300	327	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0002143-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	275	714	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.761	0.715	0.809	1	0.993	1	SUBCLONAL	2	TRUE	1	0.342209050006847	2		714	1056	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0002143-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	175	266	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	0.342209050006847	2		266	838	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105676	27105676	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002143-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	67	314	1	ENST00000324856.7:c.5287G>T	p.Glu1763Ter	p.E1763*	ENST00000324856	NM_006015.4	1763	Gaa/Taa	20/20	0.342209050006847	1	FACETS	0.658	0.573	0.75	0.658	0.573	0.75	SUBCLONAL	1	TRUE	0	0.342209050006847	1		315	493	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884485	151884485	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002143-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	101	372	0	ENST00000262189.6:c.4870G>T	p.Gly1624Ter	p.G1624*	ENST00000262189	NM_170606.2	1624	Gga/Tga	33/59	0.0978465383633567	4	FACETS	0.686	0.611	0.766	0.343	0.305	0.383	INDETERMINATE	1	TRUE	2	0.342209050006847	4		372	1155	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0002174-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	463	429	0	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	0.387898329255392	2	FACETS	0.911	0.873	0.95	0.911	0.873	0.95	CLONAL	2	TRUE	0	0.463511232835736	2		429	1096	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142956	47142956	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002174-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	135	386	0	ENST00000409792.3:c.5007G>T	p.Gln1669His	p.Q1669H	ENST00000409792	NM_014159.6	1669	caG/caT	8/21	0.248659756790093	1	FACETS	0.392	0.355	0.431	0.392	0.355	0.431	INDETERMINATE	1	TRUE	0	0.463511232835736	1		386	1141	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952498	38952498	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002174-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	93	205	0	ENST00000357387.3:c.2927C>G	p.Ala976Gly	p.A976G	ENST00000357387	NM_152756.3	976	gCt/gGt	30/38	1	2	FACETS	0.511	0.454	0.572	0.511	0.454	0.572	SUBCLONAL	1	TRUE	1	0.463511232835736	2		205	785	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641608	23641608	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002179-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	32	364	0	ENST00000261584.4:c.1867A>C	p.Lys623Gln	p.K623Q	ENST00000261584	NM_024675.3	623	Aag/Cag	5/13	1	2	FACETS	0.199	0.161	0.242	0.199	0.161	0.242	SUBCLONAL	1	TRUE	1	0.826532488872365	2		364	389	SUCCESS
APC	324	MSKCC	GRCh37	5	112103053	112103053	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002302-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	13	318	0	ENST00000257430.4:c.388A>C	p.Ser130Arg	p.S130R	ENST00000257430	NM_000038.5	130	Agt/Cgt	4/16	1	2	FACETS	0.455	0.33	0.601	0.455	0.33	0.601	SUBCLONAL	1	TRUE	1	0.761877178930913	2		318	75	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685304	89685304	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002302-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	57	221	0	ENST00000371953.3:c.199A>G	p.Ile67Val	p.I67V	ENST00000371953	NM_000314.4	67	Ata/Gta	3/9	0.761877178930913	3	FACETS	1	0.974	1	0.749	0.66	0.839	CLONAL	1	TRUE	1	0.761877178930913	3		221	138	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579559	7579559	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1555526777	NA	P-0002302-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	89	333	0	ENST00000269305.4:c.128T>A	p.Leu43Ter	p.L43*	ENST00000269305	NM_001126112.2	43	tTg/tAg	4/11	0.72079751963449	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.761877178930913	2		333	112	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0002340-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	181	262	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.405486612905525	2		262	871	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164951	47164951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769535379	NA	P-0002340-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	205	415	0	ENST00000409792.3:c.1175C>T	p.Ser392Phe	p.S392F	ENST00000409792	NM_014159.6	392	tCc/tTc	3/21	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.405486612905525	2		415	812	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209282	98209282	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002340-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	197	562	0	ENST00000331920.6:c.4256G>T	p.Arg1419Leu	p.R1419L	ENST00000331920	NM_000264.3	1419	cGg/cTg	23/24	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.405486612905525	2		562	871	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033916	49033916	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs878853949	NA	P-0002340-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	211	494	0	ENST00000267163.4:c.2053C>T	p.Gln685Ter	p.Q685*	ENST00000267163	NM_000321.2	685	Cag/Tag	20/27	0.405486612905525	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.405486612905525	1		494	778	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162082	22162082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002340-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	124	397	0	ENST00000215832.6:c.173C>T	p.Pro58Leu	p.P58L	ENST00000215832	NM_002745.4	58	cCc/cTc	2/9	1	2	FACETS	0.966	0.876	1	0.966	0.876	1	CLONAL	1	TRUE	1	0.405486612905525	2		397	633	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41560056	41560056	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0002340-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	179	525	0	ENST00000263253.7:c.3729-1G>T		p.X1243_splice	ENST00000263253	NM_001429.3	1243			1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.405486612905525	2		525	850	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207076	1207077	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs121913319	NA	P-0002340-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	133	461	1	ENST00000326873.7:c.169dup	p.Glu57GlyfsTer106	p.E57Gfs*106	ENST00000326873	NM_000455.4	55	ctg/ctGg	1/10	0.405486612905525	1	FACETS	0.991	0.904	1	0.991	0.904	1	CLONAL	1	TRUE	0	0.405486612905525	1		462	528	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610265	10610269	+	stop_gained	Nonsense_Mutation	ONP	CGCCC	CGCCC	AGCCA	novel	NA	P-0002340-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	170	504	0	ENST00000171111.5:c.441_445delinsTGGCT	p.Met147_Glu149delinsIleGlyTer	p.M147_E149delinsIG*	ENST00000171111	NM_203500.1	147	atGGGCGag/atTGGCTag	2/6	0.405486612905525	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.405486612905525	1		504	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579349	7579349	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1567555667	NA	P-0002368-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	62	304	0	ENST00000269305.4:c.338T>G	p.Phe113Cys	p.F113C	ENST00000269305	NM_001126112.2	113	tTc/tGc	4/11	0.256753038319463	2	FACETS	0.814	0.707	0.928	0.407	0.353	0.464	INDETERMINATE	1	TRUE	0	0.446968208225284	2		304	341	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533656	41533656	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002398-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	46	387	0	ENST00000263253.7:c.1623-1G>A		p.X541_splice	ENST00000263253	NM_001429.3	541			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		387	155	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439883	52439883	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002402-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	123	334	0	ENST00000460680.1:c.829C>T	p.Gln277Ter	p.Q277*	ENST00000460680	NM_004656.3	277	Caa/Taa	10/17	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.29	2		334	771	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440295	52440295	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs776240891	NA	P-0002402-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	106	350	0	ENST00000460680.1:c.757C>T	p.Gln253Ter	p.Q253*	ENST00000460680	NM_004656.3	253	Cag/Tag	9/17	1	2	FACETS	0.889	0.797	0.988	0.889	0.797	0.988	CLONAL	1	TRUE	1	0.29	2		350	822	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343619	118343619	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002402-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	59	283	0	ENST00000534358.1:c.1745C>A	p.Thr582Lys	p.T582K	ENST00000534358	NM_005933.3	582	aCa/aAa	3/36	1	2	FACETS	0.604	0.519	0.696	0.604	0.519	0.696	SUBCLONAL	1	TRUE	1	0.29	2		283	674	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256535	115256535	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002404-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	295	536	0	ENST00000369535.4:c.176C>A	p.Ala59Asp	p.A59D	ENST00000369535	NM_002524.4	59	gCt/gAt	3/7	1	2	FACETS	0.962	0.91	1	0.962	0.91	1	CLONAL	1	TRUE	1	0.784277348195201	2		536	782	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441815	49441816	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs756471180	NA	P-0002404-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	364	426	1	ENST00000301067.7:c.4168dup	p.Ala1390GlyfsTer42	p.A1390Gfs*42	ENST00000301067	NM_003482.3	1390	gca/gGca	14/54	0.473734838133206	3	FACETS	0.928	0.888	0.968	0.928	0.888	0.968	CLONAL	2	TRUE	1	0.784277348195201	3		427	696	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578393	7578405	+	frameshift_variant	Frame_Shift_Del	DEL	ATGGTGGGGGCAG	ATGGTGGGGGCAG	-	novel	NA	P-0002404-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	233	285	0	ENST00000269305.4:c.525_537del	p.Cys176SerfsTer67	p.C176Sfs*67	ENST00000269305	NM_001126112.2	175	cgCTGCCCCCACCAT/cg	5/11	0.784277348195201	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.784277348195201	1		285	285	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662885	227662885	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002406-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	328	524	0	ENST00000305123.5:c.570G>C	p.Lys190Asn	p.K190N	ENST00000305123	NM_005544.2	190	aaG/aaC	1/2	1	2	FACETS	0.897	0.851	0.943	0.897	0.851	0.943	CLONAL	1	TRUE	1	0.859420339965224	2		524	851	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467988	66467988	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002406-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	391	433	1	ENST00000273854.3:c.281C>A	p.Ala94Asp	p.A94D	ENST00000273854	NM_004439.5	94	gCc/gAc	3/18	NA	2	FACETS	0.892	0.85	0.935			1	INDETERMINATE	1	TRUE	NA	0.859420339965224	2		434	1020	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541627	187541627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002406-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	347	394	0	ENST00000441802.2:c.6113C>T	p.Pro2038Leu	p.P2038L	ENST00000441802	NM_005245.3	2038	cCc/cTc	10/27	0.859420339965224	2	FACETS	1	0.989	1	0.558	0.532	0.584	CLONAL	1	TRUE	0	0.859420339965224	2		394	724	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436011	116436011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1258671501	NA	P-0002406-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	530	634	0	ENST00000397752.3:c.4006C>T	p.Arg1336Trp	p.R1336W	ENST00000397752	NM_000245.2	1336	Cgg/Tgg	21/21	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.859420339965224	2		634	1153	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5467853	5467853	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002406-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	649	495	0	ENST00000381577.3:c.864G>T	p.Glu288Asp	p.E288D	ENST00000381577	NM_014143.3	288	gaG/gaT	7/7	0.859420339965224	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.859420339965224	2		495	741	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432063	121432063	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002406-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	96	496	0	ENST00000257555.6:c.810C>G	p.Asn270Lys	p.N270K	ENST00000257555		270	aaC/aaG	4/10	1	2	FACETS	0.256	0.227	0.286	0.256	0.227	0.286	SUBCLONAL	1	TRUE	1	0.859420339965224	2		496	873	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133236017	133236017	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002406-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	358	490	0	ENST00000320574.5:c.3139G>T	p.Gly1047Trp	p.G1047W	ENST00000320574	NM_006231.2	1047	Ggg/Tgg	26/49	1	2	FACETS	0.954	0.908	1	0.954	0.908	1	CLONAL	1	TRUE	1	0.859420339965224	2		490	873	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574026	7574026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002406-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	416	526	0	ENST00000269305.4:c.1001G>T	p.Gly334Val	p.G334V	ENST00000269305	NM_001126112.2	334	gGg/gTg	10/11	0.859420339965224	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.859420339965224	1		526	505	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776037	9776037	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002406-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	256	394	3	ENST00000377346.4:c.505del	p.Leu169CysfsTer48	p.L169Cfs*48	ENST00000377346	NM_005026.3	167	ttC/tt	5/24	1	2	FACETS	0.893	0.841	0.946	0.893	0.841	0.946	CLONAL	1	TRUE	1	0.859420339965224	2		397	667	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055897	180055897	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002406-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	198	327	1	ENST00000261937.6:c.1088del	p.Pro363ArgfsTer27	p.P363Rfs*27	ENST00000261937	NM_182925.4	363	cCg/cg	8/30	1	2	FACETS	0.997	0.934	1	0.997	0.934	1	CLONAL	1	TRUE	1	0.859420339965224	2		328	462	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098434	11098434	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	TT	novel	NA	P-0002406-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	238	156	0	ENST00000358026.2:c.952delinsTT	p.Val318PhefsTer69	p.V318Ffs*69	ENST00000358026	NM_001128849.1	318	Gtc/TTtc	6/36	0.859420339965224	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.859420339965224	1		156	266	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0002407-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	226	555	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.164137850480287	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.257117681295467	2		557	850	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248397	59248397	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002407-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	57	248	0	ENST00000371222.2:c.346C>G	p.Arg116Gly	p.R116G	ENST00000371222	NM_002228.3	116	Cgc/Ggc	1/1	0.217613545301953	3	FACETS	1	0.938	1	0.585	0.503	0.673	CLONAL	1	TRUE	1	0.257117681295467	3		248	428	SUCCESS
APC	324	MSKCC	GRCh37	5	112174112	112174112	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002407-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	108	277	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	0.257117681295467	2		277	815	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248120	110248120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002407-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	102	440	0	ENST00000374672.4:c.1352C>T	p.Thr451Met	p.T451M	ENST00000374672	NM_004235.4	451	aCg/aTg	5/5	0.257117681295467	2	FACETS	1	0.947	1	0.546	0.489	0.608	CLONAL	1	TRUE	0	0.257117681295467	2		440	726	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260241	10260241	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555690467	NA	P-0002407-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	51	815	1	ENST00000340748.4:c.2426C>T	p.Ser809Leu	p.S809L	ENST00000340748		809	tCg/tTg	25/40	0.198216645113575	2	FACETS	0.546	0.463	0.638	0.273	0.231	0.319	SUBCLONAL	1	TRUE	0	0.257117681295467	2		816	726	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578289	28578289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373674960	NA	P-0002408-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	151	316	2	ENST00000241453.7:c.2882G>A	p.Arg961His	p.R961H	ENST00000241453	NM_004119.2	961	cGt/cAt	24/24	0.326629260766764	2	FACETS	0.895	0.819	0.975	0.448	0.409	0.488	CLONAL	1	TRUE	0	0.400695583598925	2		318	842	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594258	55594258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913523	NA	P-0002409-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	378	541	0	ENST00000288135.5:c.1961T>C	p.Val654Ala	p.V654A	ENST00000288135	NM_000222.2	654	gTg/gCg	13/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.749886353550766	2		541	988	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303765	65303765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1427072320	NA	P-0002409-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	331	315	0	ENST00000342505.4:c.2990G>A	p.Arg997Gln	p.R997Q	ENST00000342505	NM_002227.2	997	cGg/cAg	22/25	NA	2	FACETS	0.973	0.923	1			1	INDETERMINATE	1	TRUE	NA	0.749886353550766	2		315	907	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-0002409-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	375	426	1	ENST00000288135.5:c.1648-6_1672del		p.K550_K558del	ENST00000288135	NM_000222.2	550		11/21	1	2	FACETS	0.913	0.868	0.959	0.913	0.868	0.959	CLONAL	1	TRUE	1	0.749886353550766	2		427	1095	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096159	71096160	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	AG	novel	NA	P-0002443-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	63	337	0	ENST00000318789.4:c.597_598delinsCT	p.Leu199_Gln200delinsPheTer	p.L199_Q200delinsF*	ENST00000318789	NM_032682.5	199	ttGCag/ttCTag	10/21	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.429779857374681	2		337	205	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247366	71247366	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002443-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	65	304	0	ENST00000318789.4:c.167del	p.Gln56ArgfsTer26	p.Q56Rfs*26	ENST00000318789	NM_032682.5	56	cAg/cg	6/21	1	2	FACETS	0.776	0.685	0.87	1	0.977	1	SUBCLONAL	2	TRUE	1	0.429779857374681	2		304	195	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0002444-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	271	262	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.31534238942699	4	FACETS	0.887	0.833	0.943	0.887	0.833	0.943	CLONAL	2	TRUE	2	0.395913712691514	4		262	1077	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0002444-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	296	604	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.31534238942699	4	FACETS	0.961	0.905	1	0.961	0.905	1	CLONAL	2	TRUE	2	0.395913712691514	4		604	1086	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643368	52643368	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002444-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	175	321	0	ENST00000394830.3:c.2528A>T	p.His843Leu	p.H843L	ENST00000394830	NM_018313.4	843	cAt/cTt	17/30	0.39532536040146	3	FACETS	0.999	0.919	1	0.5	0.459	0.542	CLONAL	1	TRUE	1	0.395913712691514	3		321	1060	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468500	89468501	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0002444-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	154	200	0	ENST00000336596.2:c.2034_2035delinsAT	p.Asp678_His679delinsGluTyr	p.D678_H679delinsEY	ENST00000336596	NM_005233.5	678	gaCCac/gaATac	11/17	0.39532536040146	3	FACETS	1	0.986	1	0.697	0.639	0.756	CLONAL	1	TRUE	1	0.395913712691514	3		200	669	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602904	55602904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002444-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	246	216	0	ENST00000288135.5:c.2614G>A	p.Gly872Arg	p.G872R	ENST00000288135	NM_000222.2	872	Gga/Aga	19/21	0.39532536040146	3	FACETS	0.936	0.878	0.996	0.936	0.878	0.996	CLONAL	2	TRUE	1	0.395913712691514	3		216	795	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143191928	143191928	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0002444-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	215	188	0	ENST00000262992.4:c.504-1G>A		p.X168_splice	ENST00000262992	NM_001101669.1	168			0.39532536040146	3	FACETS	0.907	0.847	0.97	0.907	0.847	0.97	CLONAL	2	TRUE	1	0.395913712691514	3		188	717	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433947	149433947	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002444-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	285	212	0	ENST00000286301.3:c.2701C>A	p.Pro901Thr	p.P901T	ENST00000286301	NM_005211.3	901	Ccc/Acc	21/22	0.39532536040146	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.395913712691514	3		212	788	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517973	8517973	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002444-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	279	319	0	ENST00000356435.5:c.1418A>T	p.Asp473Val	p.D473V	ENST00000356435		473	gAc/gTc	10/35	0.395913712691514	2	FACETS	0.945	0.892	0.998	0.945	0.892	0.998	CLONAL	2	TRUE	0	0.395913712691514	2		319	746	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971173	21971173	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002444-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	81	58	0	ENST00000304494.5:c.185T>C	p.Leu62Pro	p.L62P	ENST00000304494	NM_000077.4	62	cTg/cCg	2/3	0.395913712691514	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.395913712691514	2		58	186	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346335	73346335	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002444-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	144	245	0	ENST00000377767.4:c.1465G>A	p.Ala489Thr	p.A489T	ENST00000377767	NM_014953.3	489	Gct/Act	10/21	1	2	FACETS	0.988	0.903	1	0.988	0.903	1	CLONAL	1	TRUE	1	0.395913712691514	2		245	736	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637632	23637632	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs78179744	NA	P-0002444-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	165	406	0	ENST00000261584.4:c.2673C>G	p.Cys891Trp	p.C891W	ENST00000261584	NM_024675.3	891	tgC/tgG	7/13	0.39532536040146	3	FACETS	0.927	0.85	1	0.464	0.425	0.504	CLONAL	1	TRUE	1	0.395913712691514	3		406	1077	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78811722	78811722	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002444-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	254	249	0	ENST00000306801.3:c.1137G>T	p.Trp379Cys	p.W379C	ENST00000306801	NM_020761.2	379	tgG/tgT	10/34	0.31534238942699	4	FACETS	0.976	0.915	1	0.976	0.915	1	CLONAL	2	TRUE	2	0.395913712691514	4		249	918	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221995	1221995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201090	NA	P-0002444-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	239	211	0	ENST00000326873.7:c.910C>T	p.Arg304Trp	p.R304W	ENST00000326873	NM_000455.4	304	Cgg/Tgg	7/10	0.395913712691514	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.395913712691514	2		211	599	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100110	11100110	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002444-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	220	196	0	ENST00000358026.2:c.1237del	p.Gln413ArgfsTer88	p.Q413Rfs*88	ENST00000358026	NM_001128849.1	412	ttC/tt	7/36	0.395913712691514	2	FACETS	0.947	0.887	1	0.947	0.887	1	CLONAL	2	TRUE	0	0.395913712691514	2		196	587	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602564	10602565	+	missense_variant	Missense_Mutation	DNP	CG	CG	AA	novel	NA	P-0002444-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	166	192	0	ENST00000171111.5:c.1013_1014delinsTT	p.Ser338Phe	p.S338F	ENST00000171111	NM_203500.1	338	tCG/tTT	3/6	0.395913712691514	2	FACETS	0.856	0.792	0.92	0.856	0.792	0.92	CLONAL	2	TRUE	0	0.395913712691514	2		192	490	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0002446-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	321	443	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.443173146836454	NA		443	639	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502651	149502651	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371341863	NA	P-0002446-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	62	319	1	ENST00000261799.4:c.2137G>A	p.Ala713Thr	p.A713T	ENST00000261799	NM_002609.3	713	Gcg/Acg	15/23	0.361576207640996	3	FACETS	0.949	0.824	1	0.475	0.412	0.542	CLONAL	1	FALSE	1	0.443173146836454	3		320	360	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738801	145738801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747445357	NA	P-0002446-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	68	291	0	ENST00000428558.2:c.2264G>A	p.Arg755Gln	p.R755Q	ENST00000428558	NM_004260.3	755	cGg/cAg	14/22	0.382030084274283	4	FACETS	0.776	0.675	0.884	0.388	0.337	0.442	SUBCLONAL	1	FALSE	2	0.443173146836454	4		291	571	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981895	101981895	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002446-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	60	402	0	ENST00000282441.5:c.316C>G	p.Arg106Gly	p.R106G	ENST00000282441	NM_001130145.2	106	Cga/Gga	1/9	0.430949820604664	3	FACETS	0.696	0.601	0.8	0.232	0.2	0.267	SUBCLONAL	1	FALSE	0	0.443173146836454	3		402	475	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524597	103524597	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002446-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	103	476	0	ENST00000355739.4:c.2728C>A	p.His910Asn	p.H910N	ENST00000355739	NM_000123.3	910	Cat/Aat	13/15	0.445267092852303	3	FACETS	1	0.936	1	0.529	0.475	0.586	CLONAL	1	FALSE	1	0.443173146836454	3		476	537	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099920	27099921	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0002446-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	147	346	0	ENST00000324856.7:c.3800_3801del	p.Gly1267AlafsTer19	p.G1267Afs*19	ENST00000324856	NM_006015.4	1267	GGg/g	15/20	0.445267092852303	4	FACETS	1	0.935	1	0.679	0.625	0.735	CLONAL	2	FALSE	1	0.443173146836454	4		346	470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574002	7574022	+	inframe_deletion	In_Frame_Del	DEL	CGGAACATCTCGAAGCGCTCA	CGGAACATCTCGAAGCGCTCA	-	novel	NA	P-0002446-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	239	634	0	ENST00000269305.4:c.1005_1025del	p.Arg337_Glu343del	p.R337_E343del	ENST00000269305	NM_001126112.2	335	cgTGAGCGCTTCGAGATGTTCCGa/cga	10/11	0.342783125557891	3	FACETS	1	0.986	1	0.762	0.718	0.808	CLONAL	2	FALSE	0	0.443173146836454	3		634	576	SUCCESS
APC	324	MSKCC	GRCh37	5	112174202	112174202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002447-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	32	452	0	ENST00000257430.4:c.2911G>A	p.Asp971Asn	p.D971N	ENST00000257430	NM_000038.5	971	Gat/Aat	16/16	1	2	FACETS	0.617	0.51	0.734	0.617	0.51	0.734	SUBCLONAL	1	TRUE	1	0.797614486272033	2		452	130	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552758	106552758	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002447-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	28	454	0	ENST00000369096.4:c.723G>C	p.Lys241Asn	p.K241N	ENST00000369096	NM_001198.3	241	aaG/aaC	5/7	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.797614486272033	NA		454	139	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513558	41513558	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002447-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	17	332	0	ENST00000263253.7:c.462G>A	p.Met154Ile	p.M154I	ENST00000263253	NM_001429.3	154	atG/atA	2/31	NA	2	FACETS	0.347	0.261	0.446			1	INDETERMINATE	1	TRUE	NA	0.797614486272033	2		332	123	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248998	55248999	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCCAGCG	rs727504263	NA	P-0002451-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	214	352	0	ENST00000275493.2:c.2300_2308dup	p.Ala767_Val769dup	p.A767_V769dup	ENST00000275493	NM_005228.3	767	atg/aTGGCCAGCGtg	20/28	0.423153974878091	4	FACETS	1	0.973	1			1	CLONAL	2	TRUE	NA	0.474909141306899	4		352	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0002451-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	192	240	0	ENST00000269305.4:c.559+1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.4678972304331	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.474909141306899	2		240	351	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681705	78681705	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1452445269	NA	P-0002451-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	122	436	0	ENST00000306801.3:c.413G>A	p.Arg138His	p.R138H	ENST00000306801	NM_020761.2	138	cGt/cAt	4/34	0.423473270424428	5	FACETS	1	0.97	1	0.237	0.214	0.261	CLONAL	1	TRUE	0	0.474909141306899	5		436	744	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691022	NA	P-0002454-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	240	434	0	ENST00000269305.4:c.1024del	p.Arg342GlufsTer3	p.R342Efs*3	ENST00000269305	NM_001126112.2	342	Cga/ga	10/11	0.377654665254076	2	FACETS	0.927	0.873	0.981	0.927	0.873	0.981	CLONAL	2	TRUE	0	0.457567561411488	2		434	566	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499832	8499832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002454-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	74	307	0	ENST00000356435.5:c.2137G>A	p.Gly713Ser	p.G713S	ENST00000356435		713	Ggt/Agt	14/35	0.385730640399126	1	FACETS	0.558	0.49	0.631	0.558	0.49	0.631	SUBCLONAL	1	TRUE	0	0.457567561411488	1		307	447	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971098	21971098	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs878853647	NA	P-0002454-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	162	173	0	ENST00000304494.5:c.260G>C	p.Arg87Pro	p.R87P	ENST00000304494	NM_000077.4	87	cGg/cCg	2/3	0.101808361736222	4	FACETS	0.969	0.903	1			1	INDETERMINATE	3	TRUE	NA	0.457567561411488	4		173	355	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625251	69625251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782147248	NA	P-0002454-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	97	394	0	ENST00000334134.2:c.542G>A	p.Arg181His	p.R181H	ENST00000334134	NM_005247.2	181	cGc/cAc	3/3	NA	2	FACETS	0.674	0.602	0.751			1	INDETERMINATE	1	TRUE	NA	0.457567561411488	2		394	629	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299833	15299833	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002454-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	196	354	0	ENST00000263388.2:c.1345C>T	p.Arg449Cys	p.R449C	ENST00000263388	NM_000435.2	449	Cgc/Tgc	8/33	0.316444101916251	3	FACETS	0.901	0.84	0.964	0.901	0.84	0.964	CLONAL	2	TRUE	1	0.457567561411488	3		354	584	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	256	632	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.45453928017276	3	FACETS	0.871	0.833	0.908			1	CLONAL	3	TRUE	NA	0.68	3		635	386	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197506	106197506	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	269	503	1	ENST00000380013.4:c.5844del	p.Val1949Ter	p.V1949*	ENST00000380013	NM_001127208.2	1947	Aaa/aa	11/11	0.107889792585987	3	FACETS	1	0.994	1	0.739	0.697	0.782	INDETERMINATE	1	TRUE	1	0.68	3		504	717	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	190	779	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.946	0.879	1	0.946	0.879	1	CLONAL	1	TRUE	1	0.68	2		779	591	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	224	454	1	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.68	2		455	586	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263973	104263974	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776579	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	108	176	6	ENST00000369902.3:c.71dup	p.Ala25GlyfsTer23	p.A25Gfs*23	ENST00000369902	NM_016169.3	22	gcc/gCcc	1/12	0.45453928017276	3	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.68	3		182	314	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	253	563	1	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.68	2		564	637	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	240	650	2	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	0.45453928017276	0	FACETS		NA	1			1	NA	1	TRUE	0	0.68	0		652	385	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552144	29552144	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	273	419	2	ENST00000356175.3:c.1882del	p.Tyr628ThrfsTer3	p.Y628Tfs*3	ENST00000356175	NM_000267.3	626	cTt/ct	17/57	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.68	2		421	727	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433673	149433673	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1467770819	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	203	458	0	ENST00000286301.3:c.2878G>A	p.Ala960Thr	p.A960T	ENST00000286301	NM_005211.3	960	Gcc/Acc	22/22	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.68	2		458	526	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436297	110436299	+	inframe_deletion	In_Frame_Del	DEL	CGG	CGG	-	rs34412495	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	45	59	2	ENST00000375856.3:c.2102_2104del	p.Ala701del	p.A701del	ENST00000375856	NM_003749.2	701	gCCGtg/gtg	1/2	0.185178511581276	4	FACETS	1	0.954	1	0.666	0.569	0.769	INDETERMINATE	1	TRUE	2	0.68	4		61	167	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	55	113	1	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	0.107889792585987	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.68	0		114	156	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001358	150001358	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	296	562	0	ENST00000253339.5:c.2246A>G	p.His749Arg	p.H749R	ENST00000253339		749	cAt/cGt	4/7	0.107889792585987	3	FACETS	0.78	0.738	0.822	0.78	0.738	0.822	INDETERMINATE	2	TRUE	1	0.68	3		562	748	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	135	216	2	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.68	2		218	310	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	113	253	3	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	0.45453928017276	1	FACETS	0.754	0.689	0.82	0.754	0.689	0.82	SUBCLONAL	1	TRUE	0	0.68	1		256	291	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	195	471	2	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	0.107889792585987	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.68	0		473	504	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776561	9776561	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772233114	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	134	360	0	ENST00000377346.4:c.664C>T	p.Arg222Trp	p.R222W	ENST00000377346	NM_005026.3	222	Cgg/Tgg	6/24	0.45453928017276	2	FACETS	0.894	0.819	0.971			1	CLONAL	1	TRUE	NA	0.68	2		360	441	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298067	11298067	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143201596	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	201	322	0	ENST00000361445.4:c.2041G>A	p.Glu681Lys	p.E681K	ENST00000361445	NM_004958.3	681	Gag/Aag	13/58	0.45453928017276	1	FACETS	0.798	0.747	0.85	0.798	0.747	0.85	SUBCLONAL	1	TRUE	0	0.68	1		322	489	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261372	16261372	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	160	350	0	ENST00000375759.3:c.8637C>G	p.Asn2879Lys	p.N2879K	ENST00000375759	NM_015001.2	2879	aaC/aaG	11/15	0.107889792585987	3	FACETS	0.771	0.715	0.828	0.771	0.715	0.828	INDETERMINATE	2	TRUE	1	0.68	3		350	409	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265840	16265840	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	231	479	0	ENST00000375759.3:c.10913A>G	p.His3638Arg	p.H3638R	ENST00000375759	NM_015001.2	3638	cAc/cGc	15/15	0.107889792585987	3	FACETS	0.803	0.755	0.851	0.803	0.755	0.851	INDETERMINATE	2	TRUE	1	0.68	3		479	567	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798458	45798458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750592289	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	264	518	2	ENST00000450313.1:c.553C>T	p.Arg185Trp	p.R185W	ENST00000450313	NM_012222.2	185	Cgg/Tgg	7/16	0.107889792585987	3	FACETS	0.798	0.753	0.843	0.798	0.753	0.843	INDETERMINATE	2	TRUE	1	0.68	3		520	652	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309779	65309779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1456930967	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	232	398	0	ENST00000342505.4:c.2371G>A	p.Glu791Lys	p.E791K	ENST00000342505	NM_002227.2	791	Gag/Aag	17/25	0.107889792585987	3	FACETS	0.78	0.733	0.828	0.78	0.733	0.828	INDETERMINATE	2	TRUE	1	0.68	3		398	586	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464977	120464977	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs374318244	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	204	282	0	ENST00000256646.2:c.5095A>G	p.Met1699Val	p.M1699V	ENST00000256646	NM_024408.3	1699	Atg/Gtg	28/34	0.45453928017276	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.68	1		282	302	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724626	162724626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879065950	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	158	297	0	ENST00000367921.3:c.398G>A	p.Arg133Gln	p.R133Q	ENST00000367921	NM_006182.2	133	cGg/cAg	5/18	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.68	2		297	439	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027046	48027046	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	234	294	0	ENST00000234420.5:c.1924T>C	p.Tyr642His	p.Y642H	ENST00000234420	NM_000179.2	642	Tat/Cat	4/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.68	2		294	575	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738317	190738317	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1181192737	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	202	290	0	ENST00000441310.2:c.2569A>G	p.Ile857Val	p.I857V	ENST00000441310	NM_000534.4	857	Ata/Gta	12/13	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.68	2		290	491	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383999	84383999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150371881	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	153	242	0	ENST00000321945.7:c.853C>T	p.Arg285Trp	p.R285W	ENST00000321945	NM_139076.2	285	Cgg/Tgg	9/9	0.107889792585987	3	FACETS	1	0.989	1	0.732	0.677	0.788	INDETERMINATE	1	TRUE	1	0.68	3		242	412	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521103	187521103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs183364307	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	247	352	0	ENST00000441802.2:c.12052G>A	p.Ala4018Thr	p.A4018T	ENST00000441802	NM_005245.3	4018	Gcc/Acc	22/27	0.107889792585987	3	FACETS	0.822	0.775	0.87	0.822	0.775	0.87	INDETERMINATE	2	TRUE	1	0.68	3		352	592	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755729	57755729	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	282	306	1	ENST00000274289.3:c.58C>T	p.Gln20Ter	p.Q20*	ENST00000274289	NM_006622.3	20	Cag/Tag	1/14	0.185178511581276	4	FACETS	1	0.988	1	1	0.988	1	INDETERMINATE	2	TRUE	2	0.68	4		307	615	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176662878	176662878	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1562242197	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	256	339	0	ENST00000439151.2:c.3853A>G	p.Thr1285Ala	p.T1285A	ENST00000439151	NM_022455.4	1285	Aca/Gca	6/23	0.45453928017276	2	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.68	2		339	596	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289107	33289107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760147301	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	251	325	1	ENST00000374542.5:c.445G>A	p.Ala149Thr	p.A149T	ENST00000374542	NM_001141970.1	149	Gcc/Acc	3/8	0.45453928017276	4	FACETS	0.986	0.929	1	0.986	0.929	1	CLONAL	2	TRUE	2	0.68	4		326	629	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536164	106536164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	213	302	2	ENST00000369096.4:c.131C>T	p.Ala44Val	p.A44V	ENST00000369096	NM_001198.3	44	gCg/gTg	2/7	0.45453928017276	4	FACETS	0.857	0.801	0.914	0.857	0.801	0.914	CLONAL	2	TRUE	2	0.68	4		304	614	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683806	117683806	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	198	371	0	ENST00000368508.3:c.3341A>G	p.Gln1114Arg	p.Q1114R	ENST00000368508	NM_002944.2	1114	cAa/cGa	21/43	0.45453928017276	1	FACETS	0.739	0.69	0.789	0.739	0.69	0.789	SUBCLONAL	1	TRUE	0	0.68	1		371	520	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528720	157528720	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	240	337	0	ENST00000346085.5:c.6445A>G	p.Ile2149Val	p.I2149V	ENST00000346085	NM_020732.3	2149	Ata/Gta	20/20	0.107889792585987	3	FACETS	1	0.993	1	0.741	0.697	0.787	INDETERMINATE	1	TRUE	1	0.68	3		337	638	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971238	13971238	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	237	398	0	ENST00000405192.2:c.691T>C	p.Tyr231His	p.Y231H	ENST00000405192	NM_001163147.1	231	Tac/Cac	8/12	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.68	2		398	647	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459530	50459530	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	182	284	0	ENST00000331340.3:c.819A>C	p.Lys273Asn	p.K273N	ENST00000331340	NM_006060.4	273	aaA/aaC	7/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.68	2		284	470	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467849	50467849	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	128	283	0	ENST00000331340.3:c.1084A>G	p.Asn362Asp	p.N362D	ENST00000331340	NM_006060.4	362	Aac/Gac	8/8	1	2	FACETS	0.988	0.905	1	0.988	0.905	1	CLONAL	1	TRUE	1	0.68	2		283	381	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739581	145739581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375100228	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	413	298	0	ENST00000428558.2:c.1870G>A	p.Val624Ile	p.V624I	ENST00000428558	NM_004260.3	624	Gtc/Atc	11/22	0.654212927290296	4	FACETS	0.977	0.941	1	0.977	0.941	1	CLONAL	3	TRUE	1	0.68	4		298	696	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636820	8636820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369741244	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	227	318	0	ENST00000356435.5:c.89C>T	p.Pro30Leu	p.P30L	ENST00000356435		30	cCc/cTc	2/35	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.68	2		318	632	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268722	98268722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776424978	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	280	491	0	ENST00000331920.6:c.361C>T	p.Leu121Phe	p.L121F	ENST00000331920	NM_000264.3	121	Ctc/Ttc	2/24	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.68	2		491	718	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104353441	104353441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	208	304	2	ENST00000369902.3:c.646G>A	p.Gly216Arg	p.G216R	ENST00000369902	NM_016169.3	216	Ggg/Agg	5/12	0.45453928017276	3	FACETS	0.818	0.767	0.87			1	CLONAL	2	TRUE	NA	0.68	3		306	501	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201682	67201682	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1205436797	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	213	543	0	ENST00000312629.5:c.983T>C	p.Phe328Ser	p.F328S	ENST00000312629	NM_003952.2	328	tTc/tCc	12/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.68	2		543	567	SUCCESS
EED	8726	MSKCC	GRCh37	11	85979574	85979574	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1301151502	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	274	342	0	ENST00000263360.6:c.937C>T	p.Arg313Ter	p.R313*	ENST00000263360	NM_003797.3	313	Cga/Tga	9/12	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.68	2		342	732	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374073	118374073	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	209	442	0	ENST00000534358.1:c.7466A>C	p.Lys2489Thr	p.K2489T	ENST00000534358	NM_005933.3	2489	aAg/aCg	27/36	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.68	2		442	578	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420448	49420448	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	83	282	0	ENST00000301067.7:c.15301A>G	p.Thr5101Ala	p.T5101A	ENST00000301067	NM_003482.3	5101	Acc/Gcc	48/54	0.45453928017276	5	FACETS	0.743	0.655	0.836			1	SUBCLONAL	1	TRUE	NA	0.68	5		282	664	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432375	49432375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751964761	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	330	326	0	ENST00000301067.7:c.8764C>T	p.Arg2922Trp	p.R2922W	ENST00000301067	NM_003482.3	2922	Cgg/Tgg	34/54	0.45453928017276	5	FACETS	0.878	0.841	0.915			1	CLONAL	4	TRUE	NA	0.68	5		326	558	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50483736	50483736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768972786	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	266	407	0	ENST00000394963.4:c.841C>T	p.Arg281Trp	p.R281W	ENST00000394963	NM_003076.4	281	Cgg/Tgg	7/13	0.45453928017276	5	FACETS	0.814	0.764	0.865			1	CLONAL	2	TRUE	NA	0.68	5		407	971	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563021	21563021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	134	353	2	ENST00000382592.4:c.898G>A	p.Ala300Thr	p.A300T	ENST00000382592	NM_014572.2	300	Gcc/Acc	4/8	0.45453928017276	1	FACETS	0.733	0.674	0.793	0.733	0.674	0.793	SUBCLONAL	1	TRUE	0	0.68	1		355	355	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26978094	26978094	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1160704856	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	313	598	1	ENST00000381527.3:c.1271G>A	p.Arg424His	p.R424H	ENST00000381527	NM_001260.1	424	cGt/cAt	13/13	0.45453928017276	1	FACETS	0.861	0.818	0.904	0.861	0.818	0.904	CLONAL	1	TRUE	0	0.68	1		599	706	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543211	65543211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768360710	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	629	416	0	ENST00000358664.4:c.466C>T	p.Arg156Trp	p.R156W	ENST00000358664	NM_002382.4	156	Cgg/Tgg	5/5	0.45453928017276	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	TRUE	1	0.68	4		416	1030	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560394	95560394	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	47	206	0	ENST00000393063.1:c.5195T>C	p.Leu1732Pro	p.L1732P	ENST00000393063	NM_030621.3	1732	cTg/cCg	25/28	0.45453928017276	4	FACETS	0.35	0.295	0.412	0.117	0.098	0.138	SUBCLONAL	1	TRUE	1	0.68	4		206	663	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680686	88680686	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	183	455	0	ENST00000360948.2:c.571A>G	p.Asn191Asp	p.N191D	ENST00000360948	NM_001012338.2	191	Aac/Gac	6/19	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.68	2		455	461	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15943797	15943797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	201	345	0	ENST00000268712.3:c.6691C>T	p.Pro2231Ser	p.P2231S	ENST00000268712	NM_006311.3	2231	Cca/Tca	43/46	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.68	2		345	498	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439924	56439924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780231969	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	131	163	0	ENST00000407977.2:c.668G>A	p.Arg223His	p.R223H	ENST00000407977		223	cGc/cAc	6/10	0.45453928017276	3	FACETS	0.782	0.72	0.846			1	SUBCLONAL	2	TRUE	NA	0.68	3		163	330	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5225809	5225809	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748896771	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	138	378	2	ENST00000357368.4:c.2423C>T	p.Thr808Met	p.T808M	ENST00000357368	NM_002850.3	808	aCg/aTg	17/38	0.185178511581276	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.68	0		380	356	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117273	7117273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1300273034	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	219	468	0	ENST00000302850.5:c.3943G>A	p.Glu1315Lys	p.E1315K	ENST00000302850	NM_000208.2	1315	Gag/Aag	22/22	0.185178511581276	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.68	0		468	547	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270347	10270347	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	182	392	2	ENST00000340748.4:c.1219C>A	p.Leu407Met	p.L407M	ENST00000340748		407	Ctg/Atg	16/40	0.185178511581276	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.68	0		394	484	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170792	11170792	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568565971	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	98	284	1	ENST00000358026.2:c.4936C>T	p.Arg1646Trp	p.R1646W	ENST00000358026	NM_001128849.1	1646	Cgg/Tgg	35/36	0.107889792585987	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.68	0		285	298	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281523	15281523	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	113	405	0	ENST00000263388.2:c.4850T>C	p.Val1617Ala	p.V1617A	ENST00000263388	NM_000435.2	1617	gTg/gCg	26/33	0.107889792585987	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.68	0		405	303	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945695	17945695	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1322146058	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	144	361	0	ENST00000458235.1:c.2165T>C	p.Val722Ala	p.V722A	ENST00000458235	NM_000215.3	722	gTc/gCc	16/24	0.107889792585987	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.68	0		361	388	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279911	18279911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	158	355	0	ENST00000222254.8:c.1994C>T	p.Thr665Ile	p.T665I	ENST00000222254	NM_005027.3	665	aCc/aTc	16/16	0.107889792585987	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.68	0		355	444	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019408	31019408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769717271	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	246	336	0	ENST00000375687.4:c.905G>A	p.Arg302His	p.R302H	ENST00000375687	NM_015338.5	302	cGt/cAt	10/13	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.68	2		336	615	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40709541	40709541	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	177	573	0	ENST00000373198.4:c.4361T>A	p.Leu1454Gln	p.L1454Q	ENST00000373198	NM_133170.3	1454	cTg/cAg	32/32	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.68	2		573	438	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231812	36231812	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	219	312	0	ENST00000300305.3:c.572G>T	p.Arg191Ile	p.R191I	ENST00000300305		191	aGa/aTa	5/8	0.185178511581276	5	FACETS	1	0.982	1	0.748	0.701	0.796	INDETERMINATE	2	TRUE	2	0.68	5		312	580	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044992	47044992	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556781995	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	167	371	1	ENST00000377604.3:c.2318C>T	p.Ala773Val	p.A773V	ENST00000377604	NM_001204468.1	773	gCg/gTg	20/24	0.45453928017276	0	FACETS		NA	1			1	NA	1	TRUE	0	0.68	0		372	252	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143045	30143045	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	147	486	0	ENST00000389048.3:c.481del	p.Ala161ArgfsTer25	p.A161Rfs*25	ENST00000389048	NM_004304.4	161	Gcg/cg	1/29	1	2	FACETS	0.974	0.897	1	0.974	0.897	1	CLONAL	1	TRUE	1	0.68	2		486	444	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719640	190719640	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	107	244	0	ENST00000441310.2:c.1647del	p.Lys549AsnfsTer4	p.K549Nfs*4	ENST00000441310	NM_000534.4	548	Aaa/aa	9/13	1	2	FACETS	0.561	0.505	0.62	0.561	0.505	0.62	SUBCLONAL	1	TRUE	1	0.68	2		244	561	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645983	215645984	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1559425604	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	207	469	0	ENST00000260947.4:c.614dup	p.Gln206AlafsTer8	p.Q206Afs*8	ENST00000260947	NM_000465.2	205	aag/aaAg	4/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.68	2		469	592	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643943	52643943	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	178	304	0	ENST00000394830.3:c.1953del	p.Lys651AsnfsTer5	p.K651Nfs*5	ENST00000394830	NM_018313.4	651	aaA/aa	17/30	0.45453928017276	2	FACETS	1	0.963	1			1	CLONAL	1	TRUE	NA	0.68	2		304	496	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664989	138664989	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	41	56	0	ENST00000330315.3:c.576del	p.Lys193SerfsTer78	p.K193Sfs*78	ENST00000330315	NM_023067.3	192	ccC/cc	1/1	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.68	2		56	118	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447335	187447335	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	173	268	0	ENST00000232014.4:c.858del	p.Ser287GlnfsTer37	p.S287Qfs*37	ENST00000232014	NM_001130845.1	286	ccC/cc	5/10	0.185178511581276	4	FACETS	1	0.978	1	1	0.978	1	INDETERMINATE	2	TRUE	2	0.68	4		268	385	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521299	187521299	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1166479124	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	228	747	2	ENST00000441802.2:c.11856del	p.Phe3952LeufsTer31	p.F3952Lfs*31	ENST00000441802	NM_005245.3	3952	ttT/tt	22/27	0.107889792585987	3	FACETS	1	0.992	1	0.694	0.651	0.739	INDETERMINATE	1	TRUE	1	0.68	3		749	647	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542109	187542110	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1560943587	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	195	346	0	ENST00000441802.2:c.5630dup	p.Val1878CysfsTer8	p.V1878Cfs*8	ENST00000441802	NM_005245.3	1877	cct/ccCt	10/27	0.107889792585987	3	FACETS	1	0.99	1	0.685	0.638	0.733	INDETERMINATE	1	TRUE	1	0.68	3		346	561	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755670	57755670	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	243	311	1	ENST00000274289.3:c.117del	p.Glu40ArgfsTer60	p.E40Rfs*60	ENST00000274289	NM_006622.3	39	ccC/cc	1/14	0.185178511581276	4	FACETS	1	0.967	1	1	0.967	1	INDETERMINATE	2	TRUE	2	0.68	4		312	579	SUCCESS
APC	324	MSKCC	GRCh37	5	112176345	112176345	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	183	253	0	ENST00000257430.4:c.5058del	p.Lys1686AsnfsTer23	p.K1686Nfs*23	ENST00000257430	NM_000038.5	1685	gAa/ga	16/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.68	2		253	497	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099421	157099426	+	inframe_deletion	In_Frame_Del	DEL	CAGCAA	CAGCAA	-	rs750911844	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	74	96	1	ENST00000346085.5:c.363_368del	p.Gln130_Gln131del	p.Q130_Q131del	ENST00000346085	NM_020732.3	120	CAGCAA/-	1/20	0.107889792585987	3	FACETS	0.956	0.845	1	0.478	0.422	0.537	INDETERMINATE	1	TRUE	1	0.68	3		97	305	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6036958	6036958	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	234	434	0	ENST00000265849.7:c.802del	p.Tyr268ThrfsTer39	p.Y268Tfs*39	ENST00000265849	NM_000535.5	268	Tac/ac	7/15	0.45453928017276	1	FACETS	0.748	0.703	0.794	0.748	0.703	0.794	SUBCLONAL	1	TRUE	0	0.68	1		434	607	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446284	70446284	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	235	545	0	ENST00000373644.4:c.5230del	p.Arg1744GlufsTer18	p.R1744Efs*18	ENST00000373644	NM_030625.2	1742	Aaa/aa	11/12	0.45453928017276	1	FACETS	0.712	0.668	0.756	0.712	0.668	0.756	SUBCLONAL	1	TRUE	0	0.68	1		545	641	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556102	29556103	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	138	205	0	ENST00000356175.3:c.2471dup	p.Ser825IlefsTer6	p.S825Ifs*6	ENST00000356175	NM_000267.3	823	-/G	21/57	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.68	2		205	370	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532517	63532517	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	162	268	0	ENST00000307078.5:c.2062del	p.Leu688Ter	p.L688*	ENST00000307078	NM_004655.3	688	Ctg/tg	8/11	0.45453928017276	1	FACETS	0.78	0.724	0.837	0.78	0.724	0.837	SUBCLONAL	1	TRUE	0	0.68	1		268	403	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141540	11141541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	178	400	0	ENST00000358026.2:c.3522dup	p.Asp1175Ter	p.D1175*	ENST00000358026	NM_001128849.1	1173	att/aTtt	25/36	0.107889792585987	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.68	0		400	496	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	50	153	0	ENST00000375687.4:c.1933_1934dup	p.Gly646ValfsTer58	p.G646Vfs*58	ENST00000375687	NM_015338.5	642	-/GG	13/13	1	2	FACETS	0.665	0.571	0.767	0.665	0.571	0.767	SUBCLONAL	1	TRUE	1	0.68	2		153	221	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934127	39934127	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	260	554	0	ENST00000378444.4:c.472del	p.Ser158ValfsTer3	p.S158Vfs*3	ENST00000378444	NM_001123385.1	158	Agt/gt	4/15	0.45453928017276	0	FACETS		NA	1			1	NA	1	TRUE	0	0.68	0		554	369	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0002456-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	27	418	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.396999293412548	3	FACETS	0.171	0.135	0.212	0.057	0.045	0.071	SUBCLONAL	1	TRUE	0	0.475250817196478	3		418	824	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248482	212248482	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002456-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	223	358	0	ENST00000342788.4:c.3785A>G	p.Tyr1262Cys	p.Y1262C	ENST00000342788	NM_005235.2	1262	tAc/tGc	28/28	0.361788094403021	5	FACETS	1	0.989	1	0.445	0.413	0.478	CLONAL	1	TRUE	2	0.475250817196478	5		358	1204	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921551	178921551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002456-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	16	265	0	ENST00000263967.3:c.1033A>G	p.Asn345Asp	p.N345D	ENST00000263967	NM_006218.2	345	Aat/Gat	5/21	0.201679738924209	6	FACETS	0.247	0.182	0.326			1	INDETERMINATE	1	TRUE	NA	0.475250817196478	6		265	531	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541727	187541727	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002456-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	175	383	0	ENST00000441802.2:c.6013G>C	p.Gly2005Arg	p.G2005R	ENST00000441802	NM_005245.3	2005	Ggg/Cgg	10/27	0.475250817196478	2	FACETS	0.943	0.87	1	0.471	0.435	0.51	CLONAL	1	TRUE	0	0.475250817196478	2		383	781	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118355640	118355640	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002456-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	80	400	0	ENST00000534358.1:c.4282A>G	p.Ile1428Val	p.I1428V	ENST00000534358	NM_005933.3	1428	Ata/Gta	10/36	0.475250817196478	2	FACETS	0.825	0.73	0.926	0.413	0.365	0.463	CLONAL	1	TRUE	0	0.475250817196478	2		400	408	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435689	110435689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002456-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	51	96	0	ENST00000375856.3:c.2712G>A	p.Met904Ile	p.M904I	ENST00000375856	NM_003749.2	904	atG/atA	1/2	0.200747681926092	3	FACETS	0.516	0.438	0.601	0.258	0.219	0.301	INDETERMINATE	1	TRUE	1	0.475250817196478	3		96	515	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42788861	42788861	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002456-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	153	211	0	ENST00000575354.2:c.5A>G	p.Tyr2Cys	p.Y2C	ENST00000575354	NM_015125.3	2	tAt/tGt	1/20	0.4602428407685	3	FACETS	0.779	0.712	0.849	0.389	0.356	0.425	SUBCLONAL	1	TRUE	1	0.475250817196478	3		211	1023	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0002457-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	681	508	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.57567879448097	4	FACETS	1	0.989	1			1	CLONAL	3	TRUE	NA	0.57567879448097	4		508	1194	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0002457-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	348	283	0	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	0.57567879448097	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.57567879448097	2		283	568	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0002459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	1070	554	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.389141933213572	5	FACETS	0.961	0.942	0.98	1	0.999	1	CLONAL	5	TRUE	2	0.529691974498375	5		554	1509	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812465	43812465	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs373621350	NA	P-0002459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	116	398	1	ENST00000372470.3:c.1168C>T	p.Arg390Cys	p.R390C	ENST00000372470	NM_005373.2	390	Cgc/Tgc	8/12	0.509364849310477	2	FACETS	1	0.965	1	0.562	0.511	0.614	CLONAL	1	TRUE	0	0.529691974498375	2		399	390	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966995	25966996	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0002459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	120	559	1	ENST00000435504.4:c.2210_2211delinsTT	p.Arg737Ile	p.R737I	ENST00000435504		737	aGG/aTT	13/13	0.530114049016042	3	FACETS	0.895	0.81	0.985	0.448	0.405	0.493	CLONAL	1	TRUE	1	0.529691974498375	3		560	640	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096600	178096600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415279225	NA	P-0002459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	141	449	0	ENST00000397062.3:c.731C>T	p.Pro244Leu	p.P244L	ENST00000397062	NM_006164.4	244	cCa/cTa	5/5	0.389141933213572	5	FACETS	1	0.983	1	0.442	0.403	0.482	CLONAL	1	TRUE	2	0.529691974498375	5		449	721	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576866	212576866	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	105	464	0	ENST00000342788.4:c.1033G>T	p.Ala345Ser	p.A345S	ENST00000342788	NM_005235.2	345	Gct/Tct	9/28	0.530114049016042	3	FACETS	0.929	0.835	1	0.464	0.417	0.514	CLONAL	1	TRUE	1	0.529691974498375	3		464	540	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188333	142188333	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	249	633	0	ENST00000350721.4:c.6398T>C	p.Leu2133Ser	p.L2133S	ENST00000350721	NM_001184.3	2133	tTa/tCa	38/47	0.332691923796514	5	FACETS	1	0.975	1	0.716	0.672	0.762	CLONAL	2	TRUE	2	0.529691974498375	5		633	785	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554966	187554966	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs774134398	NA	P-0002459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	179	533	0	ENST00000441802.2:c.4195G>T	p.Asp1399Tyr	p.D1399Y	ENST00000441802	NM_005245.3	1399	Gac/Tac	7/27	0.3969029996645	4	FACETS	0.795	0.736	0.856	0.795	0.736	0.856	SUBCLONAL	2	TRUE	2	0.529691974498375	4		533	650	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293621	1293621	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	197	389	0	ENST00000310581.5:c.1380G>T	p.Gln460His	p.Q460H	ENST00000310581	NM_198253.2	460	caG/caT	2/16	0.413606606311569	5	FACETS	0.951	0.89	1	0.951	0.89	1	CLONAL	3	TRUE	2	0.529691974498375	5		389	468	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170866	56170866	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	242	453	0	ENST00000399503.3:c.1694G>T	p.Gly565Val	p.G565V	ENST00000399503	NM_005921.1	565	gGa/gTa	10/20	0.530114049016042	4	FACETS	0.909	0.852	0.967	0.909	0.852	0.967	CLONAL	2	TRUE	2	0.529691974498375	4		453	769	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468059	50468059	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	171	378	0	ENST00000331340.3:c.1294C>A	p.His432Asn	p.H432N	ENST00000331340	NM_006060.4	432	Cac/Aac	8/8	0.530114049016042	4	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	2	0.529691974498375	4		378	480	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945465	151945465	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	202	446	1	ENST00000262189.6:c.2054C>T	p.Pro685Leu	p.P685L	ENST00000262189	NM_170606.2	685	cCa/cTa	14/59	0.530114049016042	4	FACETS	0.838	0.78	0.898	0.838	0.78	0.898	CLONAL	2	TRUE	2	0.529691974498375	4		447	696	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484339	8484339	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	124	569	1	ENST00000356435.5:c.3193G>T	p.Gly1065Cys	p.G1065C	ENST00000356435		1065	Ggc/Tgc	19/35	0.388553790177486	6	FACETS	1	0.952	1	0.362	0.327	0.399	CLONAL	1	TRUE	3	0.529691974498375	6		570	888	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528777	8528777	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	184	394	1	ENST00000356435.5:c.355G>T	p.Asp119Tyr	p.D119Y	ENST00000356435		119	Gat/Tat	4/35	0.388553790177486	6	FACETS	1	0.972	1	0.733	0.679	0.788	CLONAL	2	TRUE	3	0.529691974498375	6		395	651	SUCCESS
ATM	472	MSKCC	GRCh37	11	108213985	108213985	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	235	482	0	ENST00000278616.4:c.8305T>C	p.Trp2769Arg	p.W2769R	ENST00000278616	NM_000051.3	2769	Tgg/Cgg	57/63	0.509364849310477	2	FACETS	0.952	0.9	1	0.952	0.9	1	CLONAL	2	TRUE	0	0.529691974498375	2		482	466	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527708	103527708	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	167	462	0	ENST00000355739.4:c.3016G>C	p.Asp1006His	p.D1006H	ENST00000355739	NM_000123.3	1006	Gat/Cat	15/15	0.394609187827072	3	FACETS	1	0.989	1	0.473	0.437	0.51	CLONAL	1	TRUE	0	0.529691974498375	3		462	562	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670428	88670428	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	208	581	0	ENST00000360948.2:c.1258A>T	p.Thr420Ser	p.T420S	ENST00000360948	NM_001012338.2	420	Act/Tct	11/19	0.529691974498375	2	FACETS	0.994	0.938	1	0.994	0.938	1	CLONAL	2	TRUE	0	0.529691974498375	2		581	395	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99473513	99473513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	86	346	0	ENST00000268035.6:c.2935G>A	p.Glu979Lys	p.E979K	ENST00000268035	NM_000875.3	979	Gag/Aag	15/21	0.529691974498375	2	FACETS	0.944	0.842	1	0.472	0.421	0.526	CLONAL	1	TRUE	0	0.529691974498375	2		346	344	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52705201	52705201	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	130	601	0	ENST00000322088.6:c.83G>T	p.Arg28Leu	p.R28L	ENST00000322088	NM_014225.5	28	cGc/cTc	2/15	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.529691974498375	2		601	462	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630232	100630232	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057520682	NA	P-0002459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	107	733	0	ENST00000308731.7:c.41C>A	p.Ser14Tyr	p.S14Y	ENST00000308731	NM_000061.2	14	tCc/tAc	2/19	0.240075780116052	3	FACETS	0.748	0.672	0.829			1	INDETERMINATE	1	TRUE	NA	0.529691974498375	3		733	683	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179050	123179050	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	162	706	0	ENST00000218089.9:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000218089	NM_001042749.1	167	Cag/Tag	8/35	0.356822623436414	1	FACETS	0.73	0.673	0.789	0.73	0.673	0.789	SUBCLONAL	1	TRUE	0	0.529691974498375	1		706	616	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561131	9561132	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0002459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	205	444	1	ENST00000353224.5:c.650_651insC	p.Trp217CysfsTer9	p.W217Cfs*9	ENST00000353224	NM_177990.2	217	tgg/tgCg	4/10	0.240075780116052	3	FACETS	1	0.984	1			1	INDETERMINATE	2	TRUE	NA	0.529691974498375	3		445	432	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24133945	24133945	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	73	254	0	ENST00000263121.7:c.98del	p.Gly33GlufsTer22	p.G33Efs*22	ENST00000263121	NM_003073.3	32	gtG/gt	2/9	0.164081528269025	5	FACETS	0.768	0.677	0.864			1	INDETERMINATE	2	TRUE	NA	0.529691974498375	5		254	322	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568859	212568859	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002460-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	59	453	0	ENST00000342788.4:c.1259T>C	p.Leu420Pro	p.L420P	ENST00000342788	NM_005235.2	420	cTg/cCg	11/28	0.371294321007047	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.405811392920587	1		453	217	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497552	125497552	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs367942205	NA	P-0002460-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	65	235	0	ENST00000428830.2:c.116T>C	p.Ile39Thr	p.I39T	ENST00000428830	NM_001114121.2	39	aTt/aCt	3/14	0.221871127770645	4	FACETS	1	0.946	1	0.389	0.338	0.443	INDETERMINATE	1	TRUE	1	0.405811392920587	4		235	386	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578220	7578221	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	rs587776768	NA	P-0002460-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	155	445	0	ENST00000269305.4:c.628_629del	p.Asn210HisfsTer5	p.N210Hfs*5	ENST00000269305	NM_001126112.2	210	AAc/c	6/11	0.350447512359949	2	FACETS	0.952	0.882	1	0.952	0.882	1	CLONAL	2	TRUE	0	0.405811392920587	2		445	401	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	222	248	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.759	0.707	0.813	0.759	0.707	0.813	SUBCLONAL	1	TRUE	1	0.635087720393358	2		248	921	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1432	138	508	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.150025550402209	5	FACETS	0.541	0.49	0.594			1	INDETERMINATE	1	TRUE	NA	0.635087720393358	5		508	1570	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	224	779	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.782	0.729	0.837	0.782	0.729	0.837	SUBCLONAL	1	TRUE	1	0.635087720393358	2		779	902	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	356	563	1	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	NA	2	FACETS	0.817	0.773	0.861			1	INDETERMINATE	1	TRUE	NA	0.635087720393358	2		564	1373	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	376	600	1	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	0.822	0.779	0.866	0.822	0.779	0.866	CLONAL	1	TRUE	1	0.635087720393358	2		601	1440	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	124	189	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.908	0.828	0.991	0.908	0.828	0.991	CLONAL	1	TRUE	1	0.635087720393358	2		189	430	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412375	139412375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1341448592	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	179	274	0	ENST00000277541.6:c.1270G>A	p.Glu424Lys	p.E424K	ENST00000277541	NM_017617.3	424	Gag/Aag	8/34	1	2	FACETS	0.852	0.788	0.917	0.852	0.788	0.917	CLONAL	1	TRUE	1	0.635087720393358	2		274	662	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474110	29474110	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	212	403	0	ENST00000389048.3:c.2065G>T	p.Gly689Trp	p.G689W	ENST00000389048	NM_004304.4	689	Ggg/Tgg	12/29	1	2	FACETS	0.844	0.786	0.904	0.844	0.786	0.904	CLONAL	1	TRUE	1	0.635087720393358	2		403	791	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165831	118165831	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	225	343	0	ENST00000369448.3:c.341G>A	p.Cys114Tyr	p.C114Y	ENST00000369448	NM_017709.3	114	tGt/tAt	2/2	1	2	FACETS	0.805	0.751	0.861	0.805	0.751	0.861	CLONAL	1	TRUE	1	0.635087720393358	2		343	880	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724560	162724560	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	294	427	0	ENST00000367921.3:c.332G>A	p.Gly111Asp	p.G111D	ENST00000367921	NM_006182.2	111	gGc/gAc	5/18	1	2	FACETS	0.814	0.766	0.864	0.814	0.766	0.864	CLONAL	1	TRUE	1	0.635087720393358	2		427	1137	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956168	175956168	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	118	595	0	ENST00000367669.3:c.2044A>G	p.Thr682Ala	p.T682A	ENST00000367669	NM_022457.5	682	Aca/Gca	18/20	1	2	FACETS	0.312	0.28	0.346	0.312	0.28	0.346	SUBCLONAL	1	TRUE	1	0.635087720393358	2		595	1191	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104571	193104571	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	319	478	0	ENST00000367435.3:c.358C>T	p.Arg120Ter	p.R120*	ENST00000367435	NM_024529.4	120	Cga/Tga	4/17	1	2	FACETS	0.811	0.765	0.859	0.811	0.765	0.859	CLONAL	1	TRUE	1	0.635087720393358	2		478	1238	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293184	212293184	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	238	386	0	ENST00000342788.4:c.2668G>T	p.Glu890Ter	p.E890*	ENST00000342788	NM_005235.2	890	Gag/Tag	22/28	1	2	FACETS	0.706	0.659	0.754	0.706	0.659	0.754	SUBCLONAL	1	TRUE	1	0.635087720393358	2		386	1062	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662389	227662389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773817315	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	130	249	0	ENST00000305123.5:c.1066G>A	p.Ala356Thr	p.A356T	ENST00000305123	NM_005544.2	356	Gcc/Acc	1/2	1	2	FACETS	0.669	0.609	0.732	0.669	0.609	0.732	SUBCLONAL	1	TRUE	1	0.635087720393358	2		249	612	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582380	119582380	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs753950587	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	107	409	0	ENST00000316626.5:c.1021C>T	p.Arg341Ter	p.R341*	ENST00000316626		341	Cga/Tga	10/12	1	2	FACETS	0.366	0.327	0.407	0.366	0.327	0.407	SUBCLONAL	1	TRUE	1	0.635087720393358	2		409	921	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549916	187549916	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	215	291	0	ENST00000441802.2:c.4325T>C	p.Val1442Ala	p.V1442A	ENST00000441802	NM_005245.3	1442	gTa/gCa	8/27	1	2	FACETS	0.783	0.729	0.839	0.783	0.729	0.839	SUBCLONAL	1	TRUE	1	0.635087720393358	2		291	865	SUCCESS
APC	324	MSKCC	GRCh37	5	112177725	112177725	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	49	284	0	ENST00000257430.4:c.6434G>A	p.Gly2145Glu	p.G2145E	ENST00000257430	NM_000038.5	2145	gGa/gAa	16/16	1	2	FACETS	0.197	0.166	0.231	0.197	0.166	0.231	SUBCLONAL	1	TRUE	1	0.635087720393358	2		284	785	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435645	149435645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780804532	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	302	477	0	ENST00000286301.3:c.2498C>T	p.Thr833Met	p.T833M	ENST00000286301	NM_005211.3	833	aCg/aTg	19/22	1	2	FACETS	0.836	0.787	0.885	0.836	0.787	0.885	CLONAL	1	TRUE	1	0.635087720393358	2		477	1138	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449504	149449504	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs374872712	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	282	415	0	ENST00000286301.3:c.1442A>G	p.Gln481Arg	p.Q481R	ENST00000286301	NM_005211.3	481	cAa/cGa	10/22	1	2	FACETS	0.818	0.769	0.869	0.818	0.769	0.869	CLONAL	1	TRUE	1	0.635087720393358	2		415	1085	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515229	149515229	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1414956735	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	270	476	0	ENST00000261799.4:c.253C>T	p.Leu85Phe	p.L85F	ENST00000261799	NM_002609.3	85	Ctc/Ttc	3/23	1	2	FACETS	0.752	0.706	0.801	0.752	0.706	0.801	SUBCLONAL	1	TRUE	1	0.635087720393358	2		476	1130	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158662	26158662	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	34	24	0	ENST00000289316.2:c.265A>G	p.Thr89Ala	p.T89A	ENST00000289316	NM_138720.2	89	Acc/Gcc	1/2	0.150025550402209	5	FACETS	1	0.914	1			1	INDETERMINATE	2	TRUE	NA	0.635087720393358	5		24	92	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015133	37015133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223489007	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	251	614	0	ENST00000358127.4:c.271G>A	p.Ala91Thr	p.A91T	ENST00000358127	NM_001280556.1	91	Gcc/Acc	3/10	1	2	FACETS	0.67	0.626	0.716	0.67	0.626	0.716	SUBCLONAL	1	TRUE	1	0.635087720393358	2		614	1179	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80646042	80646042	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	122	210	1	ENST00000286548.4:c.110G>A	p.Arg37His	p.R37H	ENST00000286548	NM_002072.3	37	cGc/cAc	1/7	1	2	FACETS	0.833	0.758	0.912	0.833	0.758	0.912	CLONAL	1	TRUE	1	0.635087720393358	2		211	461	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249983	110249983	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	120	227	0	ENST00000374672.4:c.692T>A	p.Leu231Gln	p.L231Q	ENST00000374672	NM_004235.4	231	cTg/cAg	3/5	1	2	FACETS	0.741	0.672	0.813	0.741	0.672	0.813	SUBCLONAL	1	TRUE	1	0.635087720393358	2		227	510	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413964	139413964	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	372	518	0	ENST00000277541.6:c.796T>G	p.Cys266Gly	p.C266G	ENST00000277541	NM_017617.3	266	Tgc/Ggc	5/34	1	2	FACETS	0.909	0.862	0.957	0.909	0.862	0.957	CLONAL	1	TRUE	1	0.635087720393358	2		518	1289	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247618	123247618	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1466101220	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	268	486	0	ENST00000358487.5:c.1873C>T	p.Arg625Ter	p.R625*	ENST00000358487	NM_000141.4	625	Cga/Tga	14/18	1	2	FACETS	0.744	0.698	0.792	0.744	0.698	0.792	SUBCLONAL	1	TRUE	1	0.635087720393358	2		486	1134	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202788	133202788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201165149	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	240	443	0	ENST00000320574.5:c.6446G>A	p.Arg2149His	p.R2149H	ENST00000320574	NM_006231.2	2149	cGc/cAc	46/49	0.573763832193141	3	FACETS	0.813	0.758	0.87	0.406	0.379	0.435	CLONAL	1	TRUE	1	0.635087720393358	3		443	1225	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337696	73337696	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	316	505	0	ENST00000377767.4:c.2020G>T	p.Val674Phe	p.V674F	ENST00000377767	NM_014953.3	674	Gtt/Ttt	16/21	1	2	FACETS	0.781	0.736	0.827	0.781	0.736	0.827	SUBCLONAL	1	TRUE	1	0.635087720393358	2		505	1274	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457322	67457322	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	132	436	0	ENST00000327367.4:c.296G>A	p.Ser99Asn	p.S99N	ENST00000327367	NM_005902.3	99	aGc/aAc	2/9	1	2	FACETS	0.346	0.313	0.381	0.346	0.313	0.381	SUBCLONAL	1	TRUE	1	0.635087720393358	2		436	1200	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129668	2129668	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs137854074	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	256	427	0	ENST00000219476.3:c.3395C>T	p.Ser1132Leu	p.S1132L	ENST00000219476	NM_000548.3	1132	tCg/tTg	29/42	1	2	FACETS	0.871	0.816	0.926	0.871	0.816	0.926	CLONAL	1	TRUE	1	0.635087720393358	2		427	926	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849631	68849631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659244	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	320	508	0	ENST00000261769.5:c.1534G>A	p.Glu512Lys	p.E512K	ENST00000261769	NM_004360.3	512	Gag/Aag	10/16	1	2	FACETS	0.876	0.827	0.926	0.876	0.827	0.926	CLONAL	1	TRUE	1	0.635087720393358	2		508	1150	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15960949	15960949	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199804512	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	295	391	0	ENST00000268712.3:c.6271A>G	p.Thr2091Ala	p.T2091A	ENST00000268712	NM_006311.3	2091	Aca/Gca	40/46	1	2	FACETS	0.856	0.806	0.907	0.856	0.806	0.907	CLONAL	1	TRUE	1	0.635087720393358	2		391	1085	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78704462	78704462	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	197	392	0	ENST00000306801.3:c.610A>G	p.Lys204Glu	p.K204E	ENST00000306801	NM_020761.2	204	Aag/Gag	5/34	1	2	FACETS	0.701	0.65	0.754	0.701	0.65	0.754	SUBCLONAL	1	TRUE	1	0.635087720393358	2		392	885	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375038	45375038	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	382	320	0	ENST00000262160.6:c.805T>C	p.Ser269Pro	p.S269P	ENST00000262160	NM_005901.5	269	Tca/Cca	8/11	0.573763832193141	3	FACETS	0.86	0.82	0.9	0.86	0.82	0.9	CLONAL	2	TRUE	1	0.635087720393358	3		320	922	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226989	2226989	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	192	261	0	ENST00000398665.3:c.4469G>A	p.Gly1490Asp	p.G1490D	ENST00000398665	NM_032482.2	1490	gGc/gAc	27/28	NA	2	FACETS	0.915	0.85	0.982			1	INDETERMINATE	1	TRUE	NA	0.635087720393358	2		261	661	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5216740	5216740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	279	525	0	ENST00000357368.4:c.4087C>T	p.His1363Tyr	p.H1363Y	ENST00000357368	NM_002850.3	1363	Cac/Tac	26/38	1	2	FACETS	0.808	0.759	0.859	0.808	0.759	0.859	CLONAL	1	TRUE	1	0.635087720393358	2		525	1087	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145644	11145644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555785374	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	206	310	0	ENST00000358026.2:c.4006C>T	p.Arg1336Cys	p.R1336C	ENST00000358026	NM_001128849.1	1336	Cgc/Tgc	29/36	1	2	FACETS	0.845	0.786	0.905	0.845	0.786	0.905	CLONAL	1	TRUE	1	0.635087720393358	2		310	768	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152065	11152065	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	191	329	0	ENST00000358026.2:c.4349A>G	p.Asp1450Gly	p.D1450G	ENST00000358026	NM_001128849.1	1450	gAc/gGc	31/36	1	2	FACETS	0.732	0.678	0.788	0.732	0.678	0.788	SUBCLONAL	1	TRUE	1	0.635087720393358	2		329	822	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276202	15276202	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	254	497	0	ENST00000263388.2:c.5792A>T	p.Asp1931Val	p.D1931V	ENST00000263388	NM_000435.2	1931	gAt/gTt	31/33	1	2	FACETS	0.793	0.742	0.845	0.793	0.742	0.845	SUBCLONAL	1	TRUE	1	0.635087720393358	2		497	1009	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302456	15302456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749561286	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	281	444	0	ENST00000263388.2:c.815C>T	p.Thr272Met	p.T272M	ENST00000263388	NM_000435.2	272	aCg/aTg	6/33	1	2	FACETS	0.913	0.859	0.968	0.913	0.859	0.968	CLONAL	1	TRUE	1	0.635087720393358	2		444	969	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795716	42795716	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	317	587	1	ENST00000575354.2:c.2705C>A	p.Ser902Ter	p.S902*	ENST00000575354	NM_015125.3	902	tCa/tAa	11/20	1	2	FACETS	0.785	0.74	0.831	0.785	0.74	0.831	SUBCLONAL	1	TRUE	1	0.635087720393358	2		588	1272	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855603	45855603	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	233	400	0	ENST00000391945.4:c.2054C>G	p.Ala685Gly	p.A685G	ENST00000391945	NM_000400.3	685	gCc/gGc	22/23	1	2	FACETS	0.859	0.803	0.917	0.859	0.803	0.917	CLONAL	1	TRUE	1	0.635087720393358	2		400	854	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478776	57478776	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	216	327	0	ENST00000371085.3:c.362A>G	p.Asn121Ser	p.N121S	ENST00000371085	NM_000516.4	121	aAc/aGc	5/13	1	2	FACETS	0.748	0.696	0.802	0.748	0.696	0.802	SUBCLONAL	1	TRUE	1	0.635087720393358	2		327	909	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655447	45655447	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	119	190	0	ENST00000407780.3:c.407-2A>G		p.X136_splice	ENST00000407780	NM_001283052.1	136			NA	2	FACETS	0.77	0.698	0.844			1	INDETERMINATE	1	TRUE	NA	0.635087720393358	2		190	487	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176118141	176118142	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	262	433	0	ENST00000367669.3:c.830_831dup	p.Gln278SerfsTer10	p.Q278Sfs*10	ENST00000367669	NM_022457.5	277	-/AG		1	2	FACETS	0.818	0.767	0.87	0.818	0.767	0.87	CLONAL	1	TRUE	1	0.635087720393358	2		433	1009	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403253	213403254	+	frameshift_variant,start_lost,start_retained_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	283	503	0	ENST00000342788.4:c.1dup	p.Met1?	p.M1?	ENST00000342788	NM_005235.2	1	atg/aAtg	1/28	1	2	FACETS	0.78	0.733	0.829	0.78	0.733	0.829	SUBCLONAL	1	TRUE	1	0.635087720393358	2		503	1142	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795103	242795104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs768249210	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	186	314	1	ENST00000334409.5:c.105dup	p.Thr36HisfsTer70	p.T36Hfs*70	ENST00000334409	NM_005018.2	35	-/C	2/5	1	2	FACETS	0.724	0.67	0.78	0.724	0.67	0.78	SUBCLONAL	1	TRUE	1	0.635087720393358	2		315	809	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056076	26056076	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	266	357	0	ENST00000343677.2:c.581del	p.Lys194SerfsTer?	p.K194Sfs*?	ENST00000343677	NM_005319.3	194	aAg/ag	1/1	0.150025550402209	5	FACETS	0.772	0.724	0.822			1	INDETERMINATE	2	TRUE	NA	0.635087720393358	5		357	1059	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636729	8636729	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	213	383	0	ENST00000356435.5:c.180del	p.Gly61GlufsTer11	p.G61Efs*11	ENST00000356435		60	aaA/aa	2/35	1	2	FACETS	0.808	0.752	0.866	0.808	0.752	0.866	CLONAL	1	TRUE	1	0.635087720393358	2		383	830	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209616	98209617	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761353734	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	120	179	0	ENST00000331920.6:c.3921dup	p.Arg1308GlnfsTer17	p.R1308Qfs*17	ENST00000331920	NM_000264.3	1307	-/C	23/24	1	2	FACETS	0.779	0.708	0.854	0.779	0.708	0.854	SUBCLONAL	1	TRUE	1	0.635087720393358	2		179	485	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244454	46244454	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs751704736	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	595	548	0	ENST00000334344.6:c.2552del	p.Pro851HisfsTer4	p.P851Hfs*4	ENST00000334344	NM_152641.2	850	Ccc/cc	15/21	0.150025550402209	5	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.635087720393358	5		548	1586	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420204	49420204	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	252	406	0	ENST00000301067.7:c.15545del	p.Gly5182AlafsTer61	p.G5182Afs*61	ENST00000301067	NM_003482.3	5182	gGc/gc	48/54	0.150025550402209	5	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.635087720393358	5		406	1188	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67459125	67459125	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	375	583	0	ENST00000327367.4:c.545del	p.Pro182LeufsTer4	p.P182Lfs*4	ENST00000327367	NM_005902.3	181	Ccc/cc	4/9	1	2	FACETS	0.832	0.789	0.877	0.832	0.789	0.877	CLONAL	1	TRUE	1	0.635087720393358	2		583	1419	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832688	3832688	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	273	383	2	ENST00000262367.5:c.1570del	p.Leu524TrpfsTer6	p.L524Wfs*6	ENST00000262367	NM_004380.2	524	Ctg/tg	6/31	1	2	FACETS	0.891	0.837	0.946	0.891	0.837	0.946	CLONAL	1	TRUE	1	0.635087720393358	2		385	965	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349090	11349090	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	112	154	0	ENST00000332029.2:c.246del	p.Leu84Ter	p.L84*	ENST00000332029	NM_003745.1	82	ggG/gg	2/2	1	2	FACETS	0.743	0.671	0.817	0.743	0.671	0.817	SUBCLONAL	1	TRUE	1	0.635087720393358	2		154	475	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223376	2223376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	354	560	3	ENST00000398665.3:c.3492del	p.Val1165CysfsTer8	p.V1165Cfs*8	ENST00000398665	NM_032482.2	1163	Ccc/cc	25/28	NA	2	FACETS	0.867	0.821	0.914			1	INDETERMINATE	1	TRUE	NA	0.635087720393358	2		563	1286	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938173	76938174	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1218	292	755	0	ENST00000373344.5:c.2574dup	p.Gly859ArgfsTer4	p.G859Rfs*4	ENST00000373344	NM_000489.3	858	-/A	9/35	0.401969227011865	1	FACETS	0.416	0.39	0.442	0.416	0.39	0.442	SUBCLONAL	1	TRUE	0	0.635087720393358	1		755	1510	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0002465-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	569	470	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.627959600273114	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.631649904040915	2		470	847	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176684120	176684120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002465-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	194	478	0	ENST00000439151.2:c.4934C>T	p.Ala1645Val	p.A1645V	ENST00000439151	NM_022455.4	1645	gCt/gTt	13/23	0.421453835118201	3	FACETS	0.85	0.787	0.916			1	CLONAL	1	TRUE	NA	0.631649904040915	3		478	951	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460444	8460444	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002465-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	207	404	0	ENST00000356435.5:c.3842T>G	p.Ile1281Ser	p.I1281S	ENST00000356435		1281	aTc/aGc	22/35	NA	2	FACETS	0.992	0.925	1			1	INDETERMINATE	1	TRUE	NA	0.631649904040915	2		404	661	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229455	98229455	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002465-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	237	503	0	ENST00000331920.6:c.2503G>T	p.Glu835Ter	p.E835*	ENST00000331920	NM_000264.3	835	Gaa/Taa	15/24	0.608650918202677	3	FACETS	0.934	0.872	0.999	0.311	0.29	0.333	CLONAL	1	TRUE	0	0.631649904040915	3		503	1057	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405571	70405571	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002465-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	165	329	0	ENST00000373644.4:c.3085G>C	p.Asp1029His	p.D1029H	ENST00000373644	NM_030625.2	1029	Gac/Cac	4/12	NA	2	FACETS	0.901	0.832	0.972			1	INDETERMINATE	1	TRUE	NA	0.631649904040915	2		329	580	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437989	49437989	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370969225	NA	P-0002465-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	269	404	0	ENST00000301067.7:c.5182G>A	p.Asp1728Asn	p.D1728N	ENST00000301067	NM_003482.3	1728	Gac/Aac	21/54	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.631649904040915	2		404	797	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008271	29008271	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002465-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	241	573	0	ENST00000282397.4:c.600A>T	p.Lys200Asn	p.K200N	ENST00000282397	NM_002019.4	200	aaA/aaT	5/30	0.206308808438768	5	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.631649904040915	5		573	1088	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2132442	2132442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs534533805	NA	P-0002465-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	234	432	0	ENST00000219476.3:c.3820T>C	p.Ser1274Pro	p.S1274P	ENST00000219476	NM_000548.3	1274	Tct/Cct	32/42	0.631649904040915	3	FACETS	0.931	0.869	0.996	0.31	0.289	0.332	CLONAL	1	TRUE	0	0.631649904040915	3		432	1047	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604779	48604779	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002465-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	202	410	0	ENST00000342988.3:c.1601A>C	p.Gln534Pro	p.Q534P	ENST00000342988	NM_005359.5	534	cAg/cCg	12/12	0.596946373197675	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.631649904040915	1		410	434	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525131	9525132	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0002465-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	181	460	0	ENST00000353224.5:c.1753_1754delinsAT	p.Ser585Ile	p.S585I	ENST00000353224	NM_177990.2	585	TCt/ATt	8/10	0.631649904040915	3	FACETS	0.766	0.707	0.829	0.383	0.353	0.415	SUBCLONAL	1	TRUE	1	0.631649904040915	3		460	984	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243778438	243778439	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0002465-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	202	413	0	ENST00000263826.5:c.586dup	p.Glu196GlyfsTer9	p.E196Gfs*9	ENST00000263826	NM_005465.4	196	gaa/gGaa	6/13	0.631649904040915	2	FACETS	0.752	0.698	0.807	0.376	0.349	0.404	SUBCLONAL	1	TRUE	0	0.631649904040915	2		413	851	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680513	30680513	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002469-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	108	449	0	ENST00000376406.3:c.1206C>A	p.Ser402Arg	p.S402R	ENST00000376406	NM_014641.2	402	agC/agA	5/15	NA	2	FACETS	0.878	0.788	0.973			1	INDETERMINATE	1	TRUE	NA	0.32	2		449	769	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412282	139412282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002469-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	99	411	0	ENST00000277541.6:c.1363G>A	p.Glu455Lys	p.E455K	ENST00000277541	NM_017617.3	455	Gag/Aag	8/34	0.197181773039664	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	0	0.32	1		411	513	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562702	95562702	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002469-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	118	497	0	ENST00000393063.1:c.4555G>A	p.Glu1519Lys	p.E1519K	ENST00000393063	NM_030621.3	1519	Gaa/Aaa	24/28	1	2	FACETS	0.979	0.884	1	0.979	0.884	1	CLONAL	1	TRUE	1	0.32	2		497	753	SUCCESS
FH	2271	MSKCC	GRCh37	1	241665867	241665867	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1553340891	NA	P-0002470-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	226	541	0	ENST00000366560.3:c.1112A>G	p.Lys371Arg	p.K371R	ENST00000366560	NM_000143.3	371	aAg/aGg	8/10	0.299591661317268	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.299591661317268	2		541	723	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573563	48573564	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs786203560	NA	P-0002470-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	83	384	0	ENST00000342988.3:c.153dup	p.Asp52ArgfsTer2	p.D52Rfs*2	ENST00000342988	NM_005359.5	49	-/A	2/12	0.278222179785691	1	FACETS	0.821	0.725	0.923	0.821	0.725	0.923	CLONAL	1	TRUE	0	0.299591661317268	1		384	574	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0002473-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	82	272	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.294160118570117	4	FACETS	1	0.972	1	0.444	0.393	0.498	CLONAL	1	TRUE	1	0.393587432609947	4		272	436	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156825	106156825	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1305714370	NA	P-0002473-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	31	269	0	ENST00000380013.4:c.1726G>T	p.Glu576Ter	p.E576*	ENST00000380013	NM_001127208.2	576	Gaa/Taa	3/11	0.346530217001475	4	FACETS	0.369	0.297	0.45	0.123	0.099	0.15	SUBCLONAL	1	TRUE	1	0.393587432609947	4		269	595	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056280	27056281	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0002473-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	55	184	0	ENST00000324856.7:c.1280dup	p.Gln428AlafsTer195	p.Q428Afs*195	ENST00000324856	NM_006015.4	426	acc/aCcc	2/20	1	2	FACETS	0.899	0.774	1	0.899	0.774	1	CLONAL	1	TRUE	1	0.393587432609947	2		184	311	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111540	8111541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0002473-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	189	268	0	ENST00000346208.3:c.1029_1030dup	p.Tyr344SerfsTer12	p.Y344Sfs*12	ENST00000346208		342	-/CT	5/6	0.393587432609947	5	FACETS	1	0.957	1	1	0.957	1	CLONAL	3	TRUE	2	0.393587432609947	5		268	492	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063715	67063717	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TCG	TCG	-	novel	NA	P-0002473-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	106	108	0	ENST00000412916.2:c.165_165+2del		p.X55_splice	ENST00000412916		55		2/6	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.393587432609947	NA		108	216	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654857	29654857	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002473-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	132	155	0	ENST00000356175.3:c.5546+1del		p.R1849fs	ENST00000356175	NM_000267.3	1849	cGg/cg	37/57	0.393587432609947	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	2	TRUE	0	0.393587432609947	2		155	335	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0002475-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	295	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.872	0.822	0.922	0.872	0.822	0.922	CLONAL	1	TRUE	1	0.721584832123289	2		341	938	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0002475-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	353	604	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.721584832123289	2		604	940	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0002475-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	232	250	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.977	0.917	1	0.977	0.917	1	CLONAL	1	TRUE	1	0.721584832123289	2		250	658	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0002475-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	295	398	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.721584832123289	2		398	810	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455075	50455075	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002475-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	301	330	0	ENST00000331340.3:c.622C>T	p.Arg208Ter	p.R208*	ENST00000331340	NM_006060.4	208	Cga/Tga	6/8	1	2	FACETS	0.939	0.888	0.992	0.939	0.888	0.992	CLONAL	1	TRUE	1	0.721584832123289	2		330	888	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118339539	118339539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002475-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	106	455	0	ENST00000534358.1:c.482G>T	p.Ser161Ile	p.S161I	ENST00000534358	NM_005933.3	161	aGt/aTt	2/36	1	2	FACETS	0.264	0.236	0.295	0.264	0.236	0.295	SUBCLONAL	1	TRUE	1	0.721584832123289	2		455	1111	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002475-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	252	425	0	ENST00000342988.3:c.1067C>A	p.Pro356His	p.P356H	ENST00000342988	NM_005359.5	356	cCt/cAt	9/12	0.721584832123289	1	FACETS	0.771	0.728	0.815	0.771	0.728	0.815	SUBCLONAL	1	TRUE	0	0.721584832123289	1		425	579	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593405	48593405	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002475-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	14	291	0	ENST00000342988.3:c.1156G>C	p.Gly386Arg	p.G386R	ENST00000342988	NM_005359.5	386	Ggt/Cgt	10/12	0.721584832123289	1	FACETS	0.055	0.039	0.074	0.055	0.039	0.074	SUBCLONAL	1	TRUE	0	0.721584832123289	1		291	450	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141502	11141502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002475-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	328	367	0	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	0.721584832123289	2		367	835	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594258	55594258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913523	NA	P-0002477-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	174	541	0	ENST00000288135.5:c.1961T>C	p.Val654Ala	p.V654A	ENST00000288135	NM_000222.2	654	gTg/gCg	13/21	0.174932511140081	4	FACETS	1	0.924	1	0.501	0.462	0.541	INDETERMINATE	1	TRUE	2	0.835706750867995	4		541	763	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0002477-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	326	492	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	0.174932511140081	4	FACETS	0.999	0.95	1	0.999	0.95	1	INDETERMINATE	2	TRUE	2	0.835706750867995	4		492	717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0002478-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	160	559	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.467251155703003	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.56123023084146	1		560	376	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685305	89685305	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002478-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	176	212	0	ENST00000371953.3:c.200T>C	p.Ile67Thr	p.I67T	ENST00000371953	NM_000314.4	67	aTa/aCa	3/9	0.236796850788246	4	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.56123023084146	4		212	772	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518562	69518562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002478-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	52	112	0	ENST00000294312.3:c.83C>T	p.Ser28Leu	p.S28L	ENST00000294312	NM_005117.2	28	tCg/tTg	1/3	0.372411182428594	0	FACETS	0.403	0.347	0.461			1	SUBCLONAL	1	TRUE	0	0.56123023084146	0		112	202	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510710	38510713	+	missense_variant	Missense_Mutation	ONP	GATG	GATG	AATT	novel	NA	P-0002478-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	145	207	0	ENST00000254066.5:c.964_967delinsAATT	p.Asp322_Asp323delinsAsnTyr	p.D322_D323delinsNY	ENST00000254066	NM_000964.3	322	GATGat/AATTat	7/9	0.56123023084146	8	FACETS	0.797	0.727	0.87			1	SUBCLONAL	2	TRUE	NA	0.56123023084146	8		207	870	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511523	38511523	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002478-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	123	168	0	ENST00000254066.5:c.1021G>T	p.Asp341Tyr	p.D341Y	ENST00000254066	NM_000964.3	341	Gac/Tac	8/9	0.56123023084146	8	FACETS	0.766	0.693	0.843			1	SUBCLONAL	2	TRUE	NA	0.56123023084146	8		168	768	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511538	38511538	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002478-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	130	196	0	ENST00000254066.5:c.1036G>C	p.Asp346His	p.D346H	ENST00000254066	NM_000964.3	346	Gac/Cac	8/9	0.56123023084146	8	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.56123023084146	8		196	863	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849425	68849426	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002478-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	138	341	0	ENST00000261769.5:c.1332dup	p.Glu445Ter	p.E445*	ENST00000261769	NM_004360.3	443	gat/gaTt	10/16	0.511647396434336	1	FACETS	0.988	0.911	1	0.988	0.911	1	CLONAL	1	TRUE	0	0.56123023084146	1		341	358	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0002479-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	131	357	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	0.24951833428855	3	FACETS	1	0.986	1	0.741	0.676	0.809	CLONAL	1	TRUE	1	0.399238750323435	3		357	531	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286829	212286829	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002479-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	171	357	0	ENST00000342788.4:c.2867G>T	p.Cys956Phe	p.C956F	ENST00000342788	NM_005235.2	956	tGt/tTt	24/28	0.24951833428855	3	FACETS	0.808	0.746	0.872	0.808	0.746	0.872	CLONAL	2	TRUE	1	0.399238750323435	3		357	636	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469672	NA	P-0002479-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	146	426	0	ENST00000374080.3:c.131G>A	p.Gly44Asp	p.G44D	ENST00000374080		44	gGt/gAt	2/45	0.205869329436177	0	FACETS	0.915	0.842	0.991			1	INDETERMINATE	1	TRUE	0	0.399238750323435	0		426	480	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0002485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	107	411	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.201757987106787	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.31	1		411	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578463	7578463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371524413	NA	P-0002485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	37	390	0	ENST00000269305.4:c.467G>A	p.Arg156His	p.R156H	ENST00000269305	NM_001126112.2	156	cGc/cAc	5/11	1	2	FACETS	0.443	0.364	0.531	0.443	0.364	0.531	SUBCLONAL	1	TRUE	1	0.31	2		390	539	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683196	88683197	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	48	211	0	ENST00000372037.3:c.1407dup	p.Met470TyrfsTer3	p.M470Yfs*3	ENST00000372037	NM_004329.2	469	gat/gaTt	12/13	0.201757987106787	1	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	0	0.31	1		211	261	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0002488-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	587	354	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.772514370187361	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.772514370187361	2		354	660	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0002488-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	447	391	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.4349703137905	3	FACETS	1	0.977	1			1	INDETERMINATE	2	TRUE	NA	0.772514370187361	3		391	786	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0002488-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	503	635	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.772514370187361	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.772514370187361	2		635	610	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002488-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	179	365	1	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	1	2	FACETS	0.866	0.804	0.93	0.866	0.804	0.93	CLONAL	1	TRUE	1	0.772514370187361	2		366	535	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157192784	157192784	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002488-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	221	400	0	ENST00000346085.5:c.1774T>G	p.Leu592Val	p.L592V	ENST00000346085	NM_020732.3	592	Ttg/Gtg	3/20	0.772514370187361	2	FACETS	0.913	0.854	0.972	0.456	0.427	0.486	CLONAL	1	TRUE	0	0.772514370187361	2		400	627	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120226	70120226	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002488-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	561	314	1	ENST00000245479.2:c.1228C>T	p.Gln410Ter	p.Q410*	ENST00000245479	NM_000346.3	410	Cag/Tag	3/3	0.217440515452231	4	FACETS	0.974	0.954	0.992			1	INDETERMINATE	4	TRUE	NA	0.772514370187361	4		315	661	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119325	3119325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002488-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	245	366	0	ENST00000078429.4:c.857C>T	p.Ser286Leu	p.S286L	ENST00000078429	NM_002067.2	286	tCg/tTg	6/7	0.110510735137362	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.772514370187361	0		366	586	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374390	31374390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773207465	NA	P-0002488-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	229	399	0	ENST00000328111.2:c.389G>A	p.Arg130His	p.R130H	ENST00000328111	NM_006892.3	130	cGc/cAc	5/23	0.708530490621113	4	FACETS	0.941	0.876	1	0.47	0.438	0.504	CLONAL	1	TRUE	2	0.772514370187361	4		399	1117	SUCCESS
APC	324	MSKCC	GRCh37	5	112175068	112175069	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0002488-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	167	355	0	ENST00000257430.4:c.3778_3779del	p.Gln1260AspfsTer15	p.Q1260Dfs*15	ENST00000257430	NM_000038.5	1259	atACag/atag	16/16	1	2	FACETS	0.893	0.828	0.96	0.893	0.828	0.96	CLONAL	1	TRUE	1	0.772514370187361	2		355	484	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121913370	NA	P-0002495-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	16	274	0	ENST00000288602.6:c.1742A>G	p.Asn581Ser	p.N581S	ENST00000288602	NM_004333.4	581	aAt/aGt	15/18	1	2	FACETS	0.287	0.211	0.379	0.287	0.211	0.379	SUBCLONAL	1	TRUE	1	0.19	2		274	587	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223814	2223814	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567252663	NA	P-0002495-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	23	299	0	ENST00000326181.6:c.1112G>A	p.Arg371Gln	p.R371Q	ENST00000326181	NM_032271.2	371	cGg/cAg	12/21	1	2	FACETS	0.786	0.613	0.986	0.786	0.613	0.986	CLONAL	1	TRUE	1	0.19	2		299	308	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973916	131973916	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587781925	NA	P-0002497-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	78	253	0	ENST00000265335.6:c.3618+1G>A		p.X1206_splice	ENST00000265335		1206			1	2	FACETS	0.85	0.75	0.957	0.85	0.75	0.957	CLONAL	1	TRUE	1	0.413371587768151	2		253	444	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381502	81381502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002497-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	110	514	0	ENST00000222390.5:c.559C>T	p.Pro187Ser	p.P187S	ENST00000222390	NM_000601.4	187	Ccc/Tcc	5/18	0.254174209435811	5	FACETS	1	0.955	1	0.371	0.333	0.411	CLONAL	1	TRUE	2	0.413371587768151	5		514	775	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523592	106523592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1383854511	NA	P-0002497-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	115	356	1	ENST00000359195.3:c.2744C>T	p.Ser915Phe	p.S915F	ENST00000359195	NM_002649.2	915	tCc/tTc	8/11	0.254174209435811	5	FACETS	1	0.975	1	0.418	0.377	0.462	CLONAL	1	TRUE	2	0.413371587768151	5		357	718	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380041	116380041	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002497-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	97	539	0	ENST00000397752.3:c.1430T>G	p.Val477Gly	p.V477G	ENST00000397752	NM_000245.2	477	gTg/gGg	4/21	0.254174209435811	5	FACETS	0.999	0.891	1	0.333	0.297	0.372	CLONAL	1	TRUE	2	0.413371587768151	5		539	761	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514301	69514301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148589027	NA	P-0002497-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	235	420	0	ENST00000294312.3:c.380G>A	p.Arg127His	p.R127H	ENST00000294312	NM_005117.2	127	cGc/cAc	3/3	0.403748050556734	4	FACETS	1	0.959	1	0.689	0.644	0.734	CLONAL	2	TRUE	1	0.413371587768151	4		420	778	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	418992	418992	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002497-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	73	666	0	ENST00000399788.2:c.3355G>A	p.Glu1119Lys	p.E1119K	ENST00000399788	NM_001042603.1	1119	Gaa/Aaa	22/28	0.413371587768151	5	FACETS	0.761	0.665	0.865			1	SUBCLONAL	1	TRUE	NA	0.413371587768151	5		666	752	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438288	49438288	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002497-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	111	333	0	ENST00000301067.7:c.4981G>A	p.Glu1661Lys	p.E1661K	ENST00000301067	NM_003482.3	1661	Gag/Aag	20/54	0.375087136674338	3	FACETS	0.983	0.885	1	0.492	0.442	0.544	CLONAL	1	TRUE	1	0.413371587768151	3		333	659	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	360032	360032	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs796665119	NA	P-0002497-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	75	357	1	ENST00000262320.3:c.1057C>T	p.Arg353Cys	p.R353C	ENST00000262320	NM_003502.3	353	Cgc/Tgc	4/11	0.413371587768151	6	FACETS	0.617	0.539	0.701			1	SUBCLONAL	1	TRUE	NA	0.413371587768151	6		358	1075	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654535	29654535	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002497-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	237	451	0	ENST00000356175.3:c.5224C>T	p.Gln1742Ter	p.Q1742*	ENST00000356175	NM_000267.3	1742	Caa/Taa	37/57	0.413371587768151	2	FACETS	0.904	0.85	0.96	0.904	0.85	0.96	CLONAL	2	TRUE	0	0.413371587768151	2		451	634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577573	7577573	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002497-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	243	351	0	ENST00000269305.4:c.708del	p.Tyr236Ter	p.Y236*	ENST00000269305	NM_001126112.2	236	taC/ta	7/11	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	2	TRUE	NA	0.413371587768151	2		351	558	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0002499-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	94	357	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.23	2		357	700	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460354	149460354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437040009	NA	P-0002499-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	43	459	0	ENST00000286301.3:c.283G>A	p.Ala95Thr	p.A95T	ENST00000286301	NM_005211.3	95	Gcc/Acc	3/22	1	2	FACETS	0.752	0.629	0.889	0.752	0.629	0.889	SUBCLONAL	1	TRUE	1	0.23	2		459	497	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676341	37676341	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002499-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	71	407	0	ENST00000447079.4:c.3095+1G>A		p.X1032_splice	ENST00000447079	NM_015083.1	1032			1	2	FACETS	0.823	0.718	0.937	0.823	0.718	0.937	CLONAL	1	TRUE	1	0.23	2		407	750	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0002499-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	56	357	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	1	2	FACETS	0.819	0.702	0.947	0.819	0.702	0.947	CLONAL	1	TRUE	1	0.255008963066071	2		357	536	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460354	149460354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437040009	NA	P-0002499-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	57	459	0	ENST00000286301.3:c.283G>A	p.Ala95Thr	p.A95T	ENST00000286301	NM_005211.3	95	Gcc/Acc	3/22	0.154881103501862	0	FACETS	0.541	0.463	0.625			1	SUBCLONAL	1	TRUE	0	0.255008963066071	0		459	616	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676341	37676341	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002499-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	76	407	0	ENST00000447079.4:c.3095+1G>A		p.X1032_splice	ENST00000447079	NM_015083.1	1032			1	2	FACETS	0.894	0.784	1	0.894	0.784	1	CLONAL	1	TRUE	1	0.255008963066071	2		407	667	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	443492	443492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002499-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	68	398	0	ENST00000399788.2:c.1405C>T	p.Pro469Ser	p.P469S	ENST00000399788	NM_001042603.1	469	Ccg/Tcg	11/28	0.221768567855633	3	FACETS	0.845	0.734	0.964			1	CLONAL	1	TRUE	NA	0.255008963066071	3		398	712	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657676	37658063	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTTTGCTGAATAACAGGTAACATAGTAACCAAATAAGATTAAGCACTTTCCTCTTCTCCTCTGACCTTTTTAGTTTCAAATGGTTAATTGGTATTATAATTAGACCTAATAGTGCAGTATTCACACACTATTTAGTGATATTTCCTACGTTCAGTGTGGGAGAAACATACCTGCTCCTTTAGCTGTTCTTGAGCCTTTTCTCAGTTACCAGCTTTCTGAGTAAACATTGATGTGCAGTTGGTGATTGGCCTTTTCTGCCTAGTACTTACTCCTAGGTTTTAATAGCGTAAACAAACAGGAATCTGGTTATGAACAGGTGTTAATTCATCAGAAGTTTTTATCATTTGCTTTCTTCTTTTCTGTTTATTTGCCTATACTGCATTGGTA	ATTTTGCTGAATAACAGGTAACATAGTAACCAAATAAGATTAAGCACTTTCCTCTTCTCCTCTGACCTTTTTAGTTTCAAATGGTTAATTGGTATTATAATTAGACCTAATAGTGCAGTATTCACACACTATTTAGTGATATTTCCTACGTTCAGTGTGGGAGAAACATACCTGCTCCTTTAGCTGTTCTTGAGCCTTTTCTCAGTTACCAGCTTTCTGAGTAAACATTGATGTGCAGTTGGTGATTGGCCTTTTCTGCCTAGTACTTACTCCTAGGTTTTAATAGCGTAAACAAACAGGAATCTGGTTATGAACAGGTGTTAATTCATCAGAAGTTTTTATCATTTGCTTTCTTCTTTTCTGTTTATTTGCCTATACTGCATTGGTA	-	novel	NA	P-0002499-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	27	348	0	ENST00000447079.4:c.2595_2609+373del		p.X865_splice	ENST00000447079	NM_015083.1	865		6/14	1	2	FACETS	0.478	0.38	0.591	0.478	0.38	0.591	SUBCLONAL	1	TRUE	1	0.255008963066071	2		348	443	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435318	110435318	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	51	76	0	ENST00000375856.3:c.3083C>T	p.Ser1028Phe	p.S1028F	ENST00000375856	NM_003749.2	1028	tCt/tTt	1/2	1	2	FACETS	0.889	0.761	1	0.889	0.761	1	CLONAL	1	TRUE	1	0.39985885366556	2		76	287	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435814	110435814	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762937636	NA	P-0002500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	43	54	0	ENST00000375856.3:c.2587C>T	p.His863Tyr	p.H863Y	ENST00000375856	NM_003749.2	863	Cac/Tac	1/2	1	2	FACETS	0.991	0.838	1	0.991	0.838	1	CLONAL	1	TRUE	1	0.39985885366556	2		54	217	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030487	49030487	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0002501-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	163	307	0	ENST00000267163.4:c.1960+2T>G		p.X654_splice	ENST00000267163	NM_000321.2	654			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		307	316	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0002503-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	43	257	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.455171822026775	1	FACETS	0.512	0.431	0.601	0.512	0.431	0.601	SUBCLONAL	1	TRUE	0	0.455171822026775	1		257	285	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0002503-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	44	293	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.531	0.446	0.624	0.531	0.446	0.624	SUBCLONAL	1	TRUE	1	0.455171822026775	2		293	364	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0002503-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	108	415	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.301832720114489	3	FACETS	0.902	0.819	0.987	0.902	0.819	0.987	CLONAL	2	TRUE	1	0.455171822026775	3		415	323	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287315	46287315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1565642121	NA	P-0002503-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	11	302	0	ENST00000334344.6:c.5260C>T	p.Arg1754Ter	p.R1754*	ENST00000334344	NM_152641.2	1754	Cga/Tga	19/21	0.282409192643028	1	FACETS	0.174	0.12	0.242	0.174	0.12	0.242	SUBCLONAL	1	TRUE	0	0.455171822026775	1		302	214	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603023	48603023	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555687378	NA	P-0002503-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	45	231	0	ENST00000342988.3:c.1324C>T	p.Gln442Ter	p.Q442*	ENST00000342988	NM_005359.5	442	Cag/Tag	11/12	0.282409192643028	1	FACETS	0.527	0.445	0.616	0.527	0.445	0.616	SUBCLONAL	1	TRUE	0	0.455171822026775	1		231	290	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659587	88659589	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0002503-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	42	310	0	ENST00000372037.3:c.373_375del	p.Cys125del	p.C125del	ENST00000372037	NM_004329.2	124	TGT/-	6/13	1	2	FACETS	0.809	0.682	0.948	0.809	0.682	0.948	CLONAL	1	TRUE	1	0.455171822026775	2		310	228	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0002505-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	113	330	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	0.978	0.886	1	0.978	0.886	1	CLONAL	1	TRUE	1	0.53	2		330	436	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728573	190728573	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002505-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	140	413	0	ENST00000441310.2:c.1961T>G	p.Ile654Arg	p.I654R	ENST00000441310	NM_000534.4	654	aTa/aGa	10/13	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.53	2		413	516	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0002507-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	233	330	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	0.69348677562938	3	FACETS	0.932	0.87	0.996	0.466	0.435	0.498	CLONAL	1	TRUE	1	0.720261313655827	3		330	944	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0002507-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	676	345	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	0.69348677562938	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.720261313655827	3		345	1270	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953737	48953737	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002507-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	338	394	0	ENST00000267163.4:c.1340A>T	p.Lys447Ile	p.K447I	ENST00000267163	NM_000321.2	447	aAa/aTa	14/27	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.720261313655827	2		394	847	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953758	48953758	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1281607292	NA	P-0002507-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	322	392	0	ENST00000267163.4:c.1361A>G	p.Tyr454Cys	p.Y454C	ENST00000267163	NM_000321.2	454	tAc/tGc	14/27	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.720261313655827	2		392	856	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546081	29546081	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002507-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	311	405	0	ENST00000356175.3:c.1586T>C	p.Leu529Pro	p.L529P	ENST00000356175	NM_000267.3	529	cTc/cCc	14/57	0.720873695775192	1	FACETS	0.976	0.932	1	0.976	0.932	1	CLONAL	1	TRUE	0	0.720261313655827	1		405	566	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141006	55141006	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0002514-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	33	408	0	ENST00000257290.5:c.1654-2A>G		p.X552_splice	ENST00000257290	NM_006206.4	552			0.252694750873676	1	FACETS	0.821	0.68	0.974	1	0.956	1	CLONAL	2	TRUE	0	0.252694750873676	1		408	139	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78933971	78933971	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771723844	NA	P-0002514-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	23	403	0	ENST00000306801.3:c.3571C>T	p.Arg1191Cys	p.R1191C	ENST00000306801	NM_020761.2	1191	Cgc/Tgc	30/34	0.252694750873676	0	FACETS	1	0.807	1			1	CLONAL	2	TRUE	0	0.252694750873676	0		403	68	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574011	7574012	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGAAGCGCTCA	novel	NA	P-0002514-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	23	425	0	ENST00000269305.4:c.1005_1015dup	p.Glu339ValfsTer10	p.E339Vfs*10	ENST00000269305	NM_001126112.2	339	gag/gTGAGCGCTTCGag	10/11	0.252694750873676	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.252694750873676	1		425	107	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0002517-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	254	330	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	0.998	0.938	1	0.998	0.938	1	CLONAL	1	TRUE	1	0.663595412082372	2		330	767	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0002517-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	225	351	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	0.977	0.914	1	0.977	0.914	1	CLONAL	1	TRUE	1	0.663595412082372	2		351	694	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0002526-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	54	468	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.414966881661265	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.414966881661265	1		468	186	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12043978	12043978	+	stop_lost	Nonstop_Mutation	SNP	T	T	G	novel	NA	P-0002526-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	48	265	0	ENST00000396373.4:c.1357T>G	p.Ter453GlyextTer30	p.*453Gext*30	ENST00000396373	NM_001987.4	453	Tga/Gga	8/8	0.414966881661265	7	FACETS	0.775	0.659	0.902			1	CLONAL	2	TRUE	NA	0.414966881661265	7		265	304	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0002531-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	114	248	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.277858836827144	4	FACETS	1	0.956	1	0.555	0.5	0.614	CLONAL	1	TRUE	2	0.355305952151356	4		248	783	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934874	NA	P-0002548-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	84	322	0	ENST00000269305.4:c.451C>G	p.Pro151Ala	p.P151A	ENST00000269305	NM_001126112.2	151	Ccc/Gcc	5/11	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.186656174157376	2		322	846	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913255	NA	P-0002548-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	97	504	0	ENST00000369535.4:c.183A>T	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caT	3/7	1	2	FACETS	0.919	0.817	1	0.919	0.817	1	CLONAL	1	TRUE	1	0.186656174157376	2		504	1131	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143326410	143326410	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002548-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	69	388	0	ENST00000262992.4:c.204C>G	p.Ile68Met	p.I68M	ENST00000262992	NM_001101669.1	68	atC/atG	4/24	1	2	FACETS	0.849	0.738	0.97	0.849	0.738	0.97	CLONAL	1	TRUE	1	0.186656174157376	2		388	871	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001347	150001347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002548-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	94	614	0	ENST00000253339.5:c.2257G>A	p.Glu753Lys	p.E753K	ENST00000253339		753	Gag/Aag	4/7	0.186656174157376	1	FACETS	0.78	0.692	0.874	0.78	0.692	0.874	SUBCLONAL	1	TRUE	0	0.186656174157376	1		614	1171	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615101	43615101	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002548-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	72	416	0	ENST00000355710.3:c.2515G>A	p.Asp839Asn	p.D839N	ENST00000355710	NM_020975.4	839	Gac/Aac	14/20	1	2	FACETS	0.836	0.728	0.952	0.836	0.728	0.952	CLONAL	1	TRUE	1	0.186656174157376	2		416	923	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835584	68835584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002548-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	79	421	0	ENST00000261769.5:c.175G>A	p.Asp59Asn	p.D59N	ENST00000261769	NM_004360.3	59	Gat/Aat	3/16	1	2	FACETS	0.983	0.863	1	0.983	0.863	1	CLONAL	1	TRUE	1	0.186656174157376	2		421	861	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002548-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	70	336	0	ENST00000269305.4:c.438G>C	p.Trp146Cys	p.W146C	ENST00000269305	NM_001126112.2	146	tgG/tgC	5/11	1	2	FACETS	0.888	0.772	1	0.888	0.772	1	CLONAL	1	TRUE	1	0.186656174157376	2		336	845	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222986	1222986	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs864622488	NA	P-0002548-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	95	222	0	ENST00000326873.7:c.923G>T	p.Trp308Leu	p.W308L	ENST00000326873	NM_000455.4	308	tGg/tTg	8/10	1	2	FACETS	0.847	0.755	0.944	1	0.984	1	CLONAL	2	TRUE	1	0.186656174157376	2		222	601	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20152121	20152121	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002548-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	99	310	0	ENST00000379607.5:c.209G>T	p.Trp70Leu	p.W70L	ENST00000379607	NM_001412.3	70	tGg/tTg	4/7	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.186656174157376	1		310	648	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098951	178098953	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0002548-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	66	426	0	ENST00000397062.3:c.92_94del	p.Gly31del	p.G31del	ENST00000397062	NM_006164.4	31	gGAGta/gta	2/5	1	2	FACETS	0.731	0.633	0.839	0.731	0.633	0.839	SUBCLONAL	1	TRUE	1	0.186656174157376	2		426	967	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803850	43803850	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002551-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	78	337	0	ENST00000372470.3:c.160G>T	p.Glu54Ter	p.E54*	ENST00000372470	NM_005373.2	54	Gag/Tag	2/12	0.268458188261166	1	FACETS	0.35	0.307	0.396	0.35	0.307	0.396	INDETERMINATE	1	TRUE	0	0.47822988861339	1		337	709	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270189	66270189	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002551-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	61	332	0	ENST00000273854.3:c.1693G>T	p.Ala565Ser	p.A565S	ENST00000273854	NM_004439.5	565	Gca/Tca	8/18	0.220145182432793	0	FACETS	0.301	0.26	0.345			1	INDETERMINATE	1	TRUE	0	0.47822988861339	0		332	442	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170233	32170233	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002551-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	75	286	0	ENST00000375023.3:c.3375C>A	p.Cys1125Ter	p.C1125*	ENST00000375023	NM_004557.3	1125	tgC/tgA	21/30	0.273924918362685	3	FACETS	0.592	0.519	0.672	0.296	0.259	0.336	INDETERMINATE	1	TRUE	1	0.47822988861339	3		286	656	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954915	2954915	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002551-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	334	357	0	ENST00000396946.4:c.2795G>T	p.Arg932Leu	p.R932L	ENST00000396946	NM_032415.4	932	cGg/cTg	21/25	0.39606696566151	3	FACETS	0.897	0.85	0.944	0.897	0.85	0.944	CLONAL	2	TRUE	1	0.47822988861339	3		357	965	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170461	108170462	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0002551-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	139	376	1	ENST00000278616.4:c.5026_5027delinsTT	p.Gly1676Leu	p.G1676L	ENST00000278616	NM_000051.3	1676	GGa/TTa	34/63	0.273924918362685	3	FACETS	0.934	0.851	1	0.467	0.425	0.511	INDETERMINATE	1	TRUE	1	0.47822988861339	3		377	771	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012483	29012483	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0002551-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	53	299	0	ENST00000282397.4:c.389-1G>C		p.X130_splice	ENST00000282397	NM_002019.4	130			0.47822988861339	1	FACETS	0.439	0.376	0.508	0.439	0.376	0.508	SUBCLONAL	1	TRUE	0	0.47822988861339	1		299	384	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562971	95562971	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002551-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	90	449	0	ENST00000393063.1:c.4286G>T	p.Trp1429Leu	p.W1429L	ENST00000393063	NM_030621.3	1429	tGg/tTg	24/28	0.329623578281516	1	FACETS	0.441	0.391	0.493	0.441	0.391	0.493	SUBCLONAL	1	TRUE	0	0.47822988861339	1		449	650	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566234	95566234	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002551-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	84	353	0	ENST00000393063.1:c.4089G>T	p.Lys1363Asn	p.K1363N	ENST00000393063	NM_030621.3	1363	aaG/aaT	23/28	0.329623578281516	1	FACETS	0.454	0.401	0.51	0.454	0.401	0.51	SUBCLONAL	1	TRUE	0	0.47822988861339	1		353	589	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2125848	2125848	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002551-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	211	427	0	ENST00000219476.3:c.2594A>G	p.Tyr865Cys	p.Y865C	ENST00000219476	NM_000548.3	865	tAt/tGt	23/42	NA	2	FACETS	0.972	0.903	1			1	INDETERMINATE	1	TRUE	NA	0.47822988861339	2		427	908	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900342	3900342	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002551-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	343	404	0	ENST00000262367.5:c.754G>T	p.Gly252Cys	p.G252C	ENST00000262367	NM_004380.2	252	Ggt/Tgt	2/31	0.273924918362685	3	FACETS	0.777	0.735	0.819	0.777	0.735	0.819	INDETERMINATE	2	TRUE	1	0.47822988861339	3		404	1144	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916159	9916159	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002551-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	72	442	0	ENST00000330684.3:c.2130G>T	p.Gln710His	p.Q710H	ENST00000330684	NM_001134407.1	710	caG/caT	10/13	0.273924918362685	3	FACETS	0.469	0.409	0.534	0.235	0.204	0.267	INDETERMINATE	1	TRUE	1	0.47822988861339	3		442	795	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763323	59763323	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002551-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	191	514	0	ENST00000259008.2:c.2779A>G	p.Ser927Gly	p.S927G	ENST00000259008	NM_032043.2	927	Agt/Ggt	19/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.47822988861339	2		514	790	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591825	48591825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767342	NA	P-0002551-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	85	453	0	ENST00000342988.3:c.988G>A	p.Glu330Lys	p.E330K	ENST00000342988	NM_005359.5	330	Gaa/Aaa	9/12	0.366574645124495	0	FACETS	0.407	0.361	0.455			1	SUBCLONAL	1	TRUE	0	0.47822988861339	0		453	456	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955145	17955145	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002551-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	84	321	0	ENST00000458235.1:c.82G>T	p.Val28Leu	p.V28L	ENST00000458235	NM_000215.3	28	Gtg/Ttg	2/24	0.329623578281516	1	FACETS	0.448	0.396	0.503	0.448	0.396	0.503	SUBCLONAL	1	TRUE	0	0.47822988861339	1		321	597	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714370	40714370	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs956451753	NA	P-0002551-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	73	286	0	ENST00000373198.4:c.4027C>T	p.Arg1343Trp	p.R1343W	ENST00000373198	NM_133170.3	1343	Cgg/Tgg	29/32	0.329623578281516	1	FACETS	0.41	0.358	0.465	0.41	0.358	0.465	SUBCLONAL	1	TRUE	0	0.47822988861339	1		286	567	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795436	39795436	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002551-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	136	392	0	ENST00000288319.7:c.284del	p.Gly95AlafsTer8	p.G95Afs*8	ENST00000288319	NM_182918.3	95	gGc/gc	3/10	0.220145182432793	0	FACETS	0.392	0.357	0.429			1	INDETERMINATE	1	TRUE	0	0.47822988861339	0		392	757	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0002559-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	227	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.41806871811758	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.41806871811758	1		341	814	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534259	534259	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121917757	NA	P-0002603-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	149	885	0	ENST00000451590.1:c.64C>A	p.Gln22Lys	p.Q22K	ENST00000451590	NM_001130442.1	22	Cag/Aag	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		885	793	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340156	116340156	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002603-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	36	493	0	ENST00000397752.3:c.1018G>C	p.Asp340His	p.D340H	ENST00000397752	NM_000245.2	340	Gac/Cac	2/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		493	535	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046293	69046293	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002603-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	91	483	0	ENST00000288368.4:c.3767-1G>A		p.X1256_splice	ENST00000288368	NM_024870.2	1256			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		483	585	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971040	21971672	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CACGTCCAGCCGCGCCCCGGCCCGGTGCAGCACCACCAGCGTGTCCAGGAAGCCCTCCCGGGCAGCGTCGTGCACGGGTCGGGTGAGAGTGGCGGGGTCGGCGCAGTTGGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCTGCCCATCATCATGACCTGCCAGAGAGAACAGAATGGTCAGAGCCAGGGTGGGGGCCGGCATGACGGAAAGGAAGCTTGTGTAGAGCCCCCTCACCGCCAAGCAGACCCCCACACAAGCCCCAGGTGTCTAATTACCCCTACATTTGCTTCCAGTTTCCAATTTCCTTCTTGAGTTCTCTATCCATTCTTCAGTACACAATGAATTCCATTATATCCTCCGAACTTCTGCGGAGCTGTCGTCACAGGCAGAGAGCACTGTGAGGCACGGGCAAAATAGCAAAGGGGCAGGGACAGACTGACTTTTACTCCAGGCTAACTTCCTGTATTTCCCCTGAGATACAACTACTGAAATTTCTTCCTGAAATTATGTTAGGCCTGGAGATTTTTTTTTTTTTTTTTGTTCACTGCTGTATATCCAAGCGCAGAATGTGGTAATTGTTAAAAAGAGAAAACTTGTTTGTTTGTTAAAACAAATTCTCA	CACGTCCAGCCGCGCCCCGGCCCGGTGCAGCACCACCAGCGTGTCCAGGAAGCCCTCCCGGGCAGCGTCGTGCACGGGTCGGGTGAGAGTGGCGGGGTCGGCGCAGTTGGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCTGCCCATCATCATGACCTGCCAGAGAGAACAGAATGGTCAGAGCCAGGGTGGGGGCCGGCATGACGGAAAGGAAGCTTGTGTAGAGCCCCCTCACCGCCAAGCAGACCCCCACACAAGCCCCAGGTGTCTAATTACCCCTACATTTGCTTCCAGTTTCCAATTTCCTTCTTGAGTTCTCTATCCATTCTTCAGTACACAATGAATTCCATTATATCCTCCGAACTTCTGCGGAGCTGTCGTCACAGGCAGAGAGCACTGTGAGGCACGGGCAAAATAGCAAAGGGGCAGGGACAGACTGACTTTTACTCCAGGCTAACTTCCTGTATTTCCCCTGAGATACAACTACTGAAATTTCTTCCTGAAATTATGTTAGGCCTGGAGATTTTTTTTTTTTTTTTTGTTCACTGCTGTATATCCAAGCGCAGAATGTGGTAATTGTTAAAAAGAGAAAACTTGTTTGTTTGTTAAAACAAATTCTCA	-	novel	NA	P-0002603-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	122	287	0	ENST00000304494.5:c.151-465_318del		p.X51_splice	ENST00000304494	NM_000077.4	51		2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		287	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519988	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	113	478	0	ENST00000269305.4:c.808T>G	p.Phe270Val	p.F270V	ENST00000269305	NM_001126112.2	270	Ttt/Gtt	8/11	0.239997990848416	2	FACETS	0.929	0.84	1	0.929	0.84	1	CLONAL	2	FALSE	0	0.2456503364355	2		478	495	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775780	9775780	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs765031777	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	25	263	0	ENST00000377346.4:c.323G>T	p.Arg108Leu	p.R108L	ENST00000377346	NM_005026.3	108	cGc/cTc	4/24	0.114580956237085	3	FACETS	0.644	0.507	0.801			1	INDETERMINATE	1	FALSE	NA	0.2456503364355	3		263	355	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255709	16255709	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	28	208	0	ENST00000375759.3:c.2974A>T	p.Asn992Tyr	p.N992Y	ENST00000375759	NM_015001.2	992	Aat/Tat	11/15	1	2	FACETS	0.823	0.66	1	0.823	0.66	1	CLONAL	1	FALSE	1	0.2456503364355	2		208	277	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143226	30143226	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	33	175	0	ENST00000389048.3:c.300G>T	p.Arg100Ser	p.R100S	ENST00000389048	NM_004304.4	100	agG/agT	1/29	0.164325650852474	4	FACETS	1	0.896	1	0.573	0.468	0.69	CLONAL	1	FALSE	2	0.2456503364355	4		175	292	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61708412	61708412	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	34	319	1	ENST00000401558.2:c.2977C>G	p.Gln993Glu	p.Q993E	ENST00000401558	NM_003400.3	993	Caa/Gaa	24/25	0.164325650852474	4	FACETS	0.724	0.591	0.874	0.362	0.295	0.437	SUBCLONAL	1	FALSE	2	0.2456503364355	4		320	476	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61729416	61729416	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	38	425	0	ENST00000401558.2:c.331A>G	p.Ile111Val	p.I111V	ENST00000401558	NM_003400.3	111	Atc/Gtc	5/25	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.2456503364355	NA		425	684	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131354	202131354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	28	277	0	ENST00000358485.4:c.322C>T	p.Gln108Ter	p.Q108*	ENST00000358485	NM_001080125.1	108	Cag/Tag	2/9	0.164325650852474	4	FACETS	0.621	0.496	0.765	0.311	0.248	0.383	SUBCLONAL	1	FALSE	2	0.2456503364355	4		277	457	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286731	212286731	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	62	257	0	ENST00000342788.4:c.2964+1G>T		p.X988_splice	ENST00000342788	NM_005235.2	988			0.164325650852474	4	FACETS	1	0.968	1	0.716	0.62	0.82	CLONAL	1	FALSE	2	0.2456503364355	4		257	439	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295801	212295801	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1423325504	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	68	374	0	ENST00000342788.4:c.2512C>T	p.Arg838Ter	p.R838*	ENST00000342788	NM_005235.2	838	Cga/Tga	21/28	0.164325650852474	4	FACETS	1	0.96	1	0.637	0.555	0.726	CLONAL	1	FALSE	2	0.2456503364355	4		374	541	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488692	212488692	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	89	354	0	ENST00000342788.4:c.2157G>T	p.Lys719Asn	p.K719N	ENST00000342788	NM_005235.2	719	aaG/aaT	18/28	0.164325650852474	4	FACETS	1	0.975	1	0.69	0.612	0.773	CLONAL	1	FALSE	2	0.2456503364355	4		354	654	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587173	212587173	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	89	396	0	ENST00000342788.4:c.828G>T	p.Glu276Asp	p.E276D	ENST00000342788	NM_005235.2	276	gaG/gaT	7/28	0.164325650852474	4	FACETS	1	0.976	1	0.707	0.628	0.792	CLONAL	1	FALSE	2	0.2456503364355	4		396	638	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715714	30715714	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	63	273	0	ENST00000295754.5:c.1372A>T	p.Thr458Ser	p.T458S	ENST00000295754	NM_003242.5	458	Aca/Tca	5/7	0.239997990848416	2	FACETS	1	0.971	1	0.746	0.649	0.849	CLONAL	1	FALSE	0	0.2456503364355	2		273	344	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72897455	72897455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs769998067	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	33	291	0	ENST00000325599.8:c.37G>C	p.Asp13His	p.D13H	ENST00000325599	NM_018130.2	13	Gac/Cac	1/11	1	2	FACETS	0.85	0.694	1	0.85	0.694	1	CLONAL	1	FALSE	1	0.2456503364355	2		291	316	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457269	89457269	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	81	294	0	ENST00000336596.2:c.1750G>T	p.Gly584Cys	p.G584C	ENST00000336596	NM_005233.5	584	Ggc/Tgc	9/17	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.2456503364355	2		294	468	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499382	89499382	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	88	267	0	ENST00000336596.2:c.2552C>A	p.Ala851Asp	p.A851D	ENST00000336596	NM_005233.5	851	gCt/gAt	15/17	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.2456503364355	2		267	494	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664694	138664694	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	14	16	0	ENST00000330315.3:c.871C>A	p.His291Asn	p.H291N	ENST00000330315	NM_023067.3	291	Cac/Aac	1/1	1	2	FACETS	1	0.834	1	1	0.928	1	CLONAL	2	FALSE	1	0.2456503364355	2		16	49	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665244	138665244	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	46	477	0	ENST00000330315.3:c.321C>G	p.Ser107Arg	p.S107R	ENST00000330315	NM_023067.3	107	agC/agG	1/1	1	2	FACETS	0.724	0.61	0.851	0.724	0.61	0.851	SUBCLONAL	1	FALSE	1	0.2456503364355	2		477	517	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007344	143007344	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	40	336	0	ENST00000262992.4:c.2440C>G	p.Gln814Glu	p.Q814E	ENST00000262992	NM_001101669.1	814	Caa/Gaa	22/24	1	2	FACETS	0.68	0.565	0.808	0.68	0.565	0.808	SUBCLONAL	1	FALSE	1	0.2456503364355	2		336	479	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449582	149449582	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	68	373	0	ENST00000286301.3:c.1364C>A	p.Pro455His	p.P455H	ENST00000286301	NM_005211.3	455	cCt/cAt	10/22	0.196645430939196	2	FACETS	1	0.972	1	0.728	0.637	0.826	CLONAL	1	FALSE	0	0.2456503364355	2		373	380	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818789	170818789	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	66	225	0	ENST00000296930.5:c.338G>T	p.Gly113Val	p.G113V	ENST00000296930	NM_002520.6	113	gGa/gTa	4/11	0.2456503364355	3	FACETS	1	0.969	1	0.468	0.407	0.533	CLONAL	1	FALSE	0	0.2456503364355	3		225	430	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176719036	176719036	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	151	303	0	ENST00000439151.2:c.6340A>T	p.Thr2114Ser	p.T2114S	ENST00000439151	NM_022455.4	2114	Aca/Tca	22/23	0.2456503364355	3	FACETS	0.941	0.867	1	0.941	0.867	1	CLONAL	3	FALSE	0	0.2456503364355	3		303	489	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790898	89790898	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	24	225	0	ENST00000336032.3:c.285G>C	p.Lys95Asn	p.K95N	ENST00000336032	NM_006813.2	95	aaG/aaC	1/2	0.2456503364355	4	FACETS	0.708	0.555	0.884	0.354	0.277	0.442	SUBCLONAL	1	FALSE	2	0.2456503364355	4		225	344	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6029549	6029549	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	101	391	0	ENST00000265849.7:c.1026A>T	p.Gln342His	p.Q342H	ENST00000265849	NM_000535.5	342	caA/caT	10/15	0.2456503364355	5	FACETS	0.753	0.673	0.838	0.502	0.449	0.559	SUBCLONAL	2	FALSE	2	0.2456503364355	5		391	747	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509227	106509227	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	118	348	0	ENST00000359195.3:c.1221G>C	p.Glu407Asp	p.E407D	ENST00000359195	NM_002649.2	407	gaG/gaC	2/11	0.2456503364355	3	FACETS	0.943	0.854	1	0.629	0.569	0.691	CLONAL	2	FALSE	0	0.2456503364355	3		348	572	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148516738	148516738	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	26	270	0	ENST00000320356.2:c.949G>A	p.Glu317Lys	p.E317K	ENST00000320356	NM_004456.4	317	Gaa/Aaa	9/20	0.2456503364355	3	FACETS	0.558	0.441	0.692	0.186	0.147	0.231	SUBCLONAL	1	FALSE	0	0.2456503364355	3		270	426	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148529808	148529808	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	114	342	0	ENST00000320356.2:c.281A>G	p.Gln94Arg	p.Q94R	ENST00000320356	NM_004456.4	94	cAa/cGa	4/20	0.2456503364355	3	FACETS	1	0.941	1	0.703	0.636	0.773	CLONAL	2	FALSE	0	0.2456503364355	3		342	494	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836311	151836311	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	31	260	0	ENST00000262189.6:c.14494G>T	p.Asp4832Tyr	p.D4832Y	ENST00000262189	NM_170606.2	4832	Gac/Tac	57/59	0.2456503364355	3	FACETS	0.732	0.592	0.89	0.244	0.197	0.297	SUBCLONAL	1	FALSE	0	0.2456503364355	3		260	387	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874784	151874784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1283067830	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	111	289	0	ENST00000262189.6:c.7754C>T	p.Ser2585Phe	p.S2585F	ENST00000262189	NM_170606.2	2585	tCt/tTt	38/59	0.2456503364355	3	FACETS	0.907	0.823	0.994	0.907	0.823	0.994	CLONAL	3	FALSE	0	0.2456503364355	3		289	373	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879178	151879178	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	118	431	0	ENST00000262189.6:c.5767G>T	p.Val1923Leu	p.V1923L	ENST00000262189	NM_170606.2	1923	Gtg/Ttg	36/59	0.2456503364355	3	FACETS	1	0.943	1	0.704	0.638	0.772	CLONAL	2	FALSE	0	0.2456503364355	3		431	511	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275466	38275466	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	93	409	0	ENST00000425967.3:c.1567G>T	p.Val523Leu	p.V523L	ENST00000425967	NM_001174067.1	523	Gtg/Ttg	12/19	0.114580956237085	3	FACETS	0.901	0.804	1			1	INDETERMINATE	2	FALSE	NA	0.2456503364355	3		409	472	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958472	90958472	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	68	308	0	ENST00000265433.3:c.1966T>A	p.Leu656Met	p.L656M	ENST00000265433	NM_002485.4	656	Ttg/Atg	13/16	0.2456503364355	5	FACETS	0.794	0.693	0.903	0.529	0.462	0.602	CLONAL	2	FALSE	2	0.2456503364355	5		308	477	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069158	5069158	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	41	360	0	ENST00000381652.3:c.1463C>G	p.Ser488Ter	p.S488*	ENST00000381652	NM_004972.3	488	tCa/tGa	11/25	0.2456503364355	1	FACETS	0.651	0.542	0.771	0.651	0.542	0.771	SUBCLONAL	1	FALSE	0	0.2456503364355	1		360	450	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450613	70450613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772501728	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	45	518	1	ENST00000373644.4:c.5453C>T	p.Pro1818Leu	p.P1818L	ENST00000373644	NM_030625.2	1818	cCc/cTc	12/12	1	2	FACETS	0.624	0.524	0.735	0.624	0.524	0.735	SUBCLONAL	1	FALSE	1	0.2456503364355	2		519	587	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725091	89725091	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	20	175	1	ENST00000371953.3:c.1074G>T	p.Glu358Asp	p.E358D	ENST00000371953	NM_000314.4	358	gaG/gaT	9/9	1	2	FACETS	0.835	0.642	1	0.835	0.642	1	CLONAL	1	FALSE	1	0.2456503364355	2		176	195	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741765	17741765	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1240833046	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	60	316	0	ENST00000250003.3:c.436A>G	p.Lys146Glu	p.K146E	ENST00000250003	NM_002478.4	146	Aag/Gag	1/3	0.164325650852474	4	FACETS	0.874	0.757	1	0.874	0.757	1	CLONAL	2	FALSE	2	0.2456503364355	4		316	348	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344222	118344222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	31	274	0	ENST00000534358.1:c.2348C>T	p.Ser783Phe	p.S783F	ENST00000534358	NM_005933.3	783	tCt/tTt	3/36	0.164325650852474	4	FACETS	0.788	0.637	0.958	0.394	0.318	0.479	CLONAL	1	FALSE	2	0.2456503364355	4		274	399	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246437	46246437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	82	413	0	ENST00000334344.6:c.4531G>A	p.Glu1511Lys	p.E1511K	ENST00000334344	NM_152641.2	1511	Gaa/Aaa	15/21	0.2456503364355	4	FACETS	1	0.966	1	0.632	0.557	0.712	CLONAL	1	FALSE	2	0.2456503364355	4		413	658	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246473	46246473	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	73	374	0	ENST00000334344.6:c.4567G>C	p.Asp1523His	p.D1523H	ENST00000334344	NM_152641.2	1523	Gat/Cat	15/21	0.2456503364355	4	FACETS	1	0.96	1	0.621	0.543	0.705	CLONAL	1	FALSE	2	0.2456503364355	4		374	596	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432521	49432521	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	116	311	0	ENST00000301067.7:c.8618G>T	p.Gly2873Val	p.G2873V	ENST00000301067	NM_003482.3	2873	gGt/gTt	34/54	0.2456503364355	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	FALSE	2	0.2456503364355	4		311	540	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557681	21557681	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	109	482	0	ENST00000382592.4:c.2164G>T	p.Glu722Ter	p.E722*	ENST00000382592	NM_014572.2	722	Gag/Tag	5/8	0.239997990848416	2	FACETS	0.952	0.86	1	0.952	0.86	1	CLONAL	2	FALSE	0	0.2456503364355	2		482	466	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915256	32915256	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	89	278	2	ENST00000380152.3:c.6764C>A	p.Thr2255Lys	p.T2255K	ENST00000380152		2255	aCa/aAa	11/27	0.239997990848416	2	FACETS	0.789	0.703	0.881	0.789	0.703	0.881	SUBCLONAL	2	FALSE	0	0.2456503364355	2		280	459	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105237181	105237181	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	51	281	0	ENST00000349310.3:c.1264A>C	p.Ser422Arg	p.S422R	ENST00000349310	NM_001014432.1	422	Agc/Cgc	14/15	0.164325650852474	4	FACETS	1	0.964	1	0.745	0.636	0.864	CLONAL	1	FALSE	2	0.2456503364355	4		281	347	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031852	10031852	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	35	278	0	ENST00000330684.3:c.971T>A	p.Met324Lys	p.M324K	ENST00000330684	NM_001134407.1	324	aTg/aAg	3/13	1	2	FACETS	0.803	0.659	0.963	0.803	0.659	0.963	CLONAL	1	FALSE	1	0.2456503364355	2		278	355	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646639	23646639	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	64	244	0	ENST00000261584.4:c.1228G>T	p.Val410Phe	p.V410F	ENST00000261584	NM_024675.3	410	Gtt/Ttt	4/13	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.2456503364355	2		244	383	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882377	89882377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	35	407	1	ENST00000389301.3:c.97G>A	p.Glu33Lys	p.E33K	ENST00000389301	NM_000135.2	33	Gaa/Aaa	2/43	1	2	FACETS	0.592	0.485	0.713	0.592	0.485	0.713	SUBCLONAL	1	FALSE	1	0.2456503364355	2		408	481	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602932	10602932	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	90	291	0	ENST00000171111.5:c.646A>T	p.Lys216Ter	p.K216*	ENST00000171111	NM_203500.1	216	Aag/Tag	3/6	0.239997990848416	2	FACETS	0.998	0.893	1	0.998	0.893	1	CLONAL	2	FALSE	0	0.2456503364355	2		291	367	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386335	31386335	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	41	375	0	ENST00000328111.2:c.1560G>T	p.Glu520Asp	p.E520D	ENST00000328111	NM_006892.3	520	gaG/gaT	15/23	1	2	FACETS	0.951	0.794	1	0.951	0.794	1	CLONAL	1	FALSE	1	0.2456503364355	2		375	351	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306625	41306625	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	26	354	0	ENST00000373198.4:c.1034A>G	p.Tyr345Cys	p.Y345C	ENST00000373198	NM_133170.3	345	tAt/tGt	7/32	1	2	FACETS	0.484	0.383	0.601	0.484	0.383	0.601	SUBCLONAL	1	FALSE	1	0.2456503364355	2		354	437	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419972	41419972	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	36	389	0	ENST00000373198.4:c.349C>A	p.Pro117Thr	p.P117T	ENST00000373198	NM_133170.3	117	Cca/Aca	3/32	1	2	FACETS	0.596	0.489	0.715	0.596	0.489	0.715	SUBCLONAL	1	FALSE	1	0.2456503364355	2		389	492	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419987	41419987	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	28	383	0	ENST00000373198.4:c.334C>A	p.Arg112Ser	p.R112S	ENST00000373198	NM_133170.3	112	Cgt/Agt	3/32	1	2	FACETS	0.489	0.39	0.602	0.489	0.39	0.602	SUBCLONAL	1	FALSE	1	0.2456503364355	2		383	466	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422699	47422699	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	26	372	0	ENST00000377045.4:c.171C>G	p.Asp57Glu	p.D57E	ENST00000377045	NM_001654.4	57	gaC/gaG	3/16	NA	2	FACETS	0.446	0.352	0.553			1	INDETERMINATE	1	FALSE	NA	0.2456503364355	2		372	475	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430759	47430759	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	26	460	0	ENST00000377045.4:c.1724C>A	p.Pro575His	p.P575H	ENST00000377045	NM_001654.4	575	cCc/cAc	16/16	NA	2	FACETS	0.423	0.334	0.526			1	INDETERMINATE	1	FALSE	NA	0.2456503364355	2		460	500	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239994	53239995	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	76	450	0	ENST00000375401.3:c.1446_1447delinsTT	p.Leu482_Glu483delinsPheTer	p.L482_E483delinsF*	ENST00000375401	NM_004187.3	482	ttGGaa/ttTTaa	11/26	NA	2	FACETS	1	0.957	1			1	INDETERMINATE	1	FALSE	NA	0.2456503364355	2		450	514	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345298	70345298	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	33	449	0	ENST00000374080.3:c.2324C>T	p.Thr775Ile	p.T775I	ENST00000374080		775	aCc/aTc	16/45	NA	2	FACETS	0.578	0.47	0.699			1	INDETERMINATE	1	FALSE	NA	0.2456503364355	2		449	465	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937193	76937193	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	97	552	2	ENST00000373344.5:c.3555G>T	p.Lys1185Asn	p.K1185N	ENST00000373344	NM_000489.3	1185	aaG/aaT	9/35	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.2456503364355	2		554	669	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617608	100617608	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	78	436	0	ENST00000308731.7:c.461G>T	p.Cys154Phe	p.C154F	ENST00000308731	NM_000061.2	154	tGc/tTc	6/19	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.2456503364355	2		436	530	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764347	39764347	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	23	201	0	ENST00000288319.7:c.765del	p.Arg256GlyfsTer35	p.R256Gfs*35	ENST00000288319	NM_182918.3	255	ccC/cc	7/10	0.185140176342837	4	FACETS	0.666	0.519	0.837	0.333	0.259	0.419	SUBCLONAL	1	FALSE	2	0.2456503364355	4		201	350	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0002622-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	114	540	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.18	2		540	904	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917707	151917707	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0002622-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	13	101	0	ENST00000262189.6:c.3613A>T	p.Lys1205Ter	p.K1205*	ENST00000262189	NM_170606.2	1205	Aaa/Taa	23/59	1	2	FACETS	0.521	0.371	0.705	0.521	0.371	0.705	SUBCLONAL	1	TRUE	1	0.18	2		101	277	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070594	67070594	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002622-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	83	396	0	ENST00000412916.2:c.218G>A	p.Trp73Ter	p.W73*	ENST00000412916		73	tGg/tAg	3/6	0.152394733993677	1	FACETS	0.698	0.613	0.788	0.698	0.613	0.788	SUBCLONAL	1	TRUE	0	0.18	1		396	1203	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654689	29654690	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0002622-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	83	351	0	ENST00000356175.3:c.5380dup	p.Gln1794ProfsTer4	p.Q1794Pfs*4	ENST00000356175	NM_000267.3	1793	cac/caCc	37/57	0.152394733993677	1	FACETS	0.774	0.681	0.874	0.774	0.681	0.874	SUBCLONAL	1	TRUE	0	0.18	1		351	1084	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792819	33792819	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002622-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	48	142	0	ENST00000498907.2:c.502G>A	p.Asp168Asn	p.D168N	ENST00000498907	NM_004364.3	168	Gat/Aat	1/1	0.152394733993677	1	FACETS	0.954	0.806	1	0.954	0.806	1	CLONAL	1	TRUE	0	0.18	1		142	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577041	7577137	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCTCGTGGTGAGGCTCCCCTTTCTTGCGGAGATTCTCTTCCTCTGTGCGCCGGTCTCTCCCAGGACAGGCACAAACACGCACCTCAAAGCTGTTC	CAGCTCGTGGTGAGGCTCCCCTTTCTTGCGGAGATTCTCTTCCTCTGTGCGCCGGTCTCTCCCAGGACAGGCACAAACACGCACCTCAAAGCTGTTC	-	novel	NA	P-0002622-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	56	322	0	ENST00000269305.4:c.801_897del	p.Asn268ProfsTer45	p.N268Pfs*45	ENST00000269305	NM_001126112.2	267	cgGAACAGCTTTGAGGTGCGTGTTTGTGCCTGTCCTGGGAGAGACCGGCGCACAGAGGAAGAGAATCTCCGCAAGAAAGGGGAGCCTCACCACGAGCTG/cg	8/11	0.152394733993677	1	FACETS	0.563	0.48	0.654	0.563	0.48	0.654	SUBCLONAL	1	TRUE	0	0.18	1		322	1006	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0002648-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	257	308	1	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	0.621432586697326	2		309	787	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691003	NA	P-0002648-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	268	297	0	ENST00000269305.4:c.96+1G>T		p.X32_splice	ENST00000269305	NM_001126112.2	32			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.621432586697326	2		297	782	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577146	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0002648-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	295	363	0	ENST00000269305.4:c.792_794del	p.Leu265del	p.L265del	ENST00000269305	NM_001126112.2	264	ctACTg/ctg	8/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.621432586697326	2		363	831	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47088075	47088075	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002749-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	44	584	1	ENST00000409792.3:c.7000C>A	p.Gln2334Lys	p.Q2334K	ENST00000409792	NM_014159.6	2334	Caa/Aaa	16/21	0.216971553486208	1	FACETS	0.602	0.504	0.71	0.602	0.504	0.71	SUBCLONAL	1	FALSE	0	0.216971553486208	1		585	601	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806119	1806119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931614	NA	P-0002750-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	51	687	0	ENST00000260795.2:c.1138G>A	p.Gly380Arg	p.G380R	ENST00000260795		380	Ggg/Agg	8/17	1	2	FACETS	0.195	0.164	0.228	0.195	0.164	0.228	SUBCLONAL	1	TRUE	1	0.63330966305296	2		687	828	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002750-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	241	594	0	ENST00000397062.3:c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	NM_006164.4	34	Cga/Gga	2/5	0.187495205211789	4	FACETS	0.963	0.898	1			1	INDETERMINATE	1	TRUE	NA	0.63330966305296	4		594	1291	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014134	70014134	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002750-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	224	876	1	ENST00000394351.3:c.995A>T	p.His332Leu	p.H332L	ENST00000394351	NM_000248.3	332	cAt/cTt	9/9	1	2	FACETS	0.897	0.837	0.958	0.897	0.837	0.958	CLONAL	1	TRUE	1	0.63330966305296	2		877	789	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626124	12626147	+	inframe_deletion	In_Frame_Del	DEL	AGAGTGTTGGAGCAGCTCAATGGA	AGAGTGTTGGAGCAGCTCAATGGA	-	novel	NA	P-0002750-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	88	494	0	ENST00000251849.4:c.1813_1836del	p.Ser605_Ser612del	p.S605_S612del	ENST00000251849	NM_002880.3	605	TCCATTGAGCTGCTCCAACACTCT/-	17/17	1	2	FACETS	0.59	0.525	0.659	0.59	0.525	0.659	SUBCLONAL	1	TRUE	1	0.63330966305296	2		494	471	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0002766-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	113	714	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.274711929822254	1	FACETS	0.946	0.852	1	0.946	0.852	1	CLONAL	1	TRUE	0	0.274711929822254	1		714	750	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610229	10610229	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002766-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	102	373	0	ENST00000171111.5:c.481A>G	p.Met161Val	p.M161V	ENST00000171111	NM_203500.1	161	Atg/Gtg	2/6	0.274711929822254	1	FACETS	0.847	0.758	0.943	0.847	0.758	0.943	CLONAL	1	TRUE	0	0.274711929822254	1		373	756	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132522	11132522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778175819	NA	P-0002766-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	54	334	0	ENST00000358026.2:c.2738C>T	p.Pro913Leu	p.P913L	ENST00000358026	NM_001128849.1	913	cCg/cTg	19/36	0.274711929822254	1	FACETS	0.482	0.411	0.561	0.482	0.411	0.561	SUBCLONAL	1	TRUE	0	0.274711929822254	1		334	703	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974727	21974744	+	inframe_deletion	In_Frame_Del	DEL	CCTCCAGCAGCGCCCGCA	CCTCCAGCAGCGCCCGCA	-	novel	NA	P-0002766-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	28	264	0	ENST00000304494.5:c.83_100del	p.Val28_Glu33del	p.V28_E33del	ENST00000304494	NM_000077.4	28	gTGCGGGCGCTGCTGGAGGcg/gcg	1/3	0.274711929822254	1	FACETS	0.366	0.291	0.45	0.366	0.291	0.45	SUBCLONAL	1	TRUE	0	0.274711929822254	1		264	481	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207077	1207077	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs121913319	NA	P-0002766-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	110	316	0	ENST00000326873.7:c.169del	p.Glu57LysfsTer7	p.E57Kfs*7	ENST00000326873	NM_000455.4	55	ctG/ct	1/10	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.274711929822254	2		316	622	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0002769-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	182	322	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.504971290547178	2	FACETS	0.974	0.914	1	0.974	0.914	1	CLONAL	2	TRUE	0	0.517705909842347	2		324	361	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26911760	26911760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002769-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	50	352	0	ENST00000381527.3:c.185C>T	p.Ser62Leu	p.S62L	ENST00000381527	NM_001260.1	62	tCg/tTg	2/13	0.467056097777171	3	FACETS	0.308	0.26	0.36	0.103	0.086	0.12	SUBCLONAL	1	TRUE	0	0.517705909842347	3		352	790	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0002793-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	23	453	1	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	0.073	0.056	0.093	0.073	0.056	0.093	SUBCLONAL	1	FALSE	1	0.756694493000046	2		454	833	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0002793-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	262	330	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	0.177976366028591	3	FACETS	1	0.994	1	0.733	0.692	0.775	INDETERMINATE	1	FALSE	1	0.756694493000046	3		330	651	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703662	47703662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002793-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	251	353	1	ENST00000233146.2:c.2162G>T	p.Gly721Val	p.G721V	ENST00000233146	NM_000251.2	721	gGa/gTa	13/16	0.50851882743661	3	FACETS	1	0.987	1	0.588	0.552	0.624	CLONAL	1	FALSE	1	0.756694493000046	3		354	778	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638139	176638139	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002793-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	190	275	0	ENST00000439151.2:c.2739G>A	p.Met913Ile	p.M913I	ENST00000439151	NM_022455.4	913	atG/atA	5/23	0.756694493000046	3	FACETS	0.864	0.8	0.93	0.432	0.4	0.465	CLONAL	1	FALSE	1	0.756694493000046	3		275	801	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0002818-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	131	802	5	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	NA	2	FACETS	0.791	0.723	0.862			1	INDETERMINATE	2	TRUE	NA	0.36	2		807	460	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0002818-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	65	411	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.287114139006063	2	FACETS	0.795	0.699	0.896	0.795	0.699	0.896	SUBCLONAL	2	TRUE	0	0.36	2		411	227	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0002818-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	152	697	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	0.298001224150276	4	FACETS	1	0.97	1	0.74	0.681	0.801	CLONAL	2	TRUE	1	0.36	4		697	517	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17124889	17124889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748031634	NA	P-0002818-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	174	551	0	ENST00000285071.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000285071	NM_144997.5	278	cCg/cTg	8/14	0.298001224150276	3	FACETS	0.933	0.864	1			1	CLONAL	2	TRUE	NA	0.36	3		551	611	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16247377	16247377	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748683309	NA	P-0002818-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	90	393	0	ENST00000375759.3:c.1648C>T	p.Arg550Cys	p.R550C	ENST00000375759	NM_015001.2	550	Cgc/Tgc	9/15	0.298001224150276	3	FACETS	1	0.979	1	0.73	0.652	0.813	CLONAL	1	TRUE	1	0.36	3		393	404	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258670	16258670	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002818-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	160	418	0	ENST00000375759.3:c.5935G>C	p.Glu1979Gln	p.E1979Q	ENST00000375759	NM_015001.2	1979	Gag/Cag	11/15	0.298001224150276	3	FACETS	0.906	0.835	0.979	0.906	0.835	0.979	CLONAL	2	TRUE	1	0.36	3		418	579	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183604	185183604	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002818-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	126	506	0	ENST00000265026.3:c.1458G>C	p.Leu486Phe	p.L486F	ENST00000265026	NM_004721.4	486	ttG/ttC	9/14	0.298001224150276	2	FACETS	0.812	0.741	0.885	0.812	0.741	0.885	CLONAL	2	TRUE	0	0.36	2		506	431	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130094	143130094	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs140724729	NA	P-0002818-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	121	555	0	ENST00000262992.4:c.922G>C	p.Val308Leu	p.V308L	ENST00000262992	NM_001101669.1	308	Gtg/Ctg	11/24	0.298001224150276	2	FACETS	0.936	0.855	1	0.936	0.855	1	CLONAL	2	TRUE	0	0.36	2		555	359	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332694	153332694	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002818-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	104	652	0	ENST00000281708.4:c.262G>A	p.Asp88Asn	p.D88N	ENST00000281708	NM_033632.3	88	Gat/Aat	2/12	0.298001224150276	2	FACETS	0.787	0.711	0.866	0.787	0.711	0.866	SUBCLONAL	2	TRUE	0	0.36	2		652	367	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519749	137519749	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002818-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	28	411	0	ENST00000367739.4:c.889G>C	p.Glu297Gln	p.E297Q	ENST00000367739	NM_000416.2	297	Gag/Cag	7/7	1	2	FACETS	0.608	0.487	0.744	0.608	0.487	0.744	SUBCLONAL	1	TRUE	1	0.36	2		411	256	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026586	6026586	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002818-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	92	754	0	ENST00000265849.7:c.1810C>T	p.Gln604Ter	p.Q604*	ENST00000265849	NM_000535.5	604	Cag/Tag	11/15	0.270128692716618	3	FACETS	0.737	0.654	0.826	0.369	0.327	0.413	SUBCLONAL	1	TRUE	1	0.36	3		754	818	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425839	49425839	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002818-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	84	501	1	ENST00000301067.7:c.12649C>T	p.Gln4217Ter	p.Q4217*	ENST00000301067	NM_003482.3	4217	Cag/Tag	39/54	0.298001224150276	3	FACETS	0.882	0.78	0.992	0.441	0.39	0.496	CLONAL	1	TRUE	1	0.36	3		502	624	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426709	49426709	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002818-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	41	169	0	ENST00000301067.7:c.11779C>T	p.Gln3927Ter	p.Q3927*	ENST00000301067	NM_003482.3	3927	Cag/Tag	39/54	0.298001224150276	3	FACETS	1	0.956	1	0.723	0.609	0.845	CLONAL	1	TRUE	1	0.36	3		169	186	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030468	49030468	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0002818-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	140	388	0	ENST00000267163.4:c.1943C>G	p.Ser648Ter	p.S648*	ENST00000267163	NM_000321.2	648	tCa/tGa	19/27	0.298001224150276	3	FACETS	1	0.98	1			1	CLONAL	2	TRUE	NA	0.36	3		388	380	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520114	9520114	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002818-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	28	387	0	ENST00000353224.5:c.2155C>T	p.His719Tyr	p.H719Y	ENST00000353224	NM_177990.2	719	Cac/Tac	10/10	0.298001224150276	5	FACETS	0.634	0.506	0.779	0.211	0.168	0.26	SUBCLONAL	1	TRUE	2	0.36	5		387	378	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652501	48652501	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002818-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	108	581	0	ENST00000376670.3:c.1172C>G	p.Thr391Arg	p.T391R	ENST00000376670	NM_002049.3	391	aCg/aGg	6/6	NA	2	FACETS	0.958	0.862	1			1	INDETERMINATE	1	TRUE	NA	0.36	2		581	626	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979395	2979396	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCAG	novel	NA	P-0002818-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	128	553	0	ENST00000396946.4:c.847_851dup	p.Gln284HisfsTer84	p.Q284Hfs*84	ENST00000396946	NM_032415.4	284	cag/caCTGCAg	6/25	0.270128692716618	3	FACETS	1	0.978	1	0.63	0.572	0.691	CLONAL	1	TRUE	1	0.36	3		553	666	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988345	36988345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002818-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	47	178	0	ENST00000354822.5:c.308del	p.Ala103GlyfsTer22	p.A103Gfs*22	ENST00000354822	NM_001079668.2	103	gCg/gg	2/3	0.298001224150276	4	FACETS	1	0.859	1	0.338	0.286	0.395	CLONAL	1	TRUE	1	0.36	4		178	350	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203561	108203561	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002824-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	95	404	2	ENST00000278616.4:c.7861G>T	p.Glu2621Ter	p.E2621*	ENST00000278616	NM_000051.3	2621	Gag/Tag	53/63	0.187668033367326	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	0	0.219019890460891	1		406	675	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556699	41556699	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0002824-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	71	338	0	ENST00000263253.7:c.3644T>A	p.Leu1215Ter	p.L1215*	ENST00000263253	NM_001429.3	1215	tTg/tAg	20/31	1	2	FACETS	0.959	0.837	1	0.959	0.837	1	CLONAL	1	FALSE	1	0.219019890460891	2		338	676	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436878	49436879	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0002824-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	111	645	0	ENST00000301067.7:c.5624dup	p.Leu1875PhefsTer28	p.L1875Ffs*28	ENST00000301067	NM_003482.3	1875	tta/ttTa	25/54	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.219019890460891	2		645	853	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444363	49444366	+	frameshift_variant	Frame_Shift_Del	DEL	GGGG	GGGG	-	novel	NA	P-0002824-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	37	307	0	ENST00000301067.7:c.3005_3008del	p.Pro1002HisfsTer14	p.P1002Hfs*14	ENST00000301067	NM_003482.3	1002	cCCCCa/ca	11/54	1	2	FACETS	0.882	0.728	1	0.882	0.728	1	CLONAL	1	FALSE	1	0.219019890460891	2		307	383	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0002835-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	832	453	1	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.761967783903939	2	FACETS	0.974	0.953	0.994	0.974	0.953	0.994	CLONAL	2	TRUE	0	0.761967783903939	2		454	1121	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0002835-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	519	379	0	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	1	2	FACETS	1	0.977	1	1	0.998	1	CLONAL	2	TRUE	1	0.761967783903939	2		379	679	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0002835-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	338	467	1	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.989	0.939	1	0.989	0.939	1	CLONAL	1	TRUE	1	0.761967783903939	2		468	897	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699320	117699320	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002835-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	61	521	0	ENST00000369458.3:c.321A>C	p.Gln107His	p.Q107H	ENST00000369458	NM_024626.3	107	caA/caC	3/6	0.761967783903939	2	FACETS	0.14	0.12	0.163	0.07	0.06	0.082	SUBCLONAL	1	TRUE	0	0.761967783903939	2		521	1140	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280669	41280669	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002835-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	365	524	0	ENST00000349496.5:c.2182G>A	p.Ala728Thr	p.A728T	ENST00000349496	NM_001904.3	728	Gcc/Acc	15/15	0.761967783903939	3	FACETS	0.961	0.91	1	0.48	0.455	0.507	CLONAL	1	TRUE	1	0.761967783903939	3		524	1377	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687346	117687346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002835-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	396	513	0	ENST00000368508.3:c.2705G>A	p.Arg902Lys	p.R902K	ENST00000368508	NM_002944.2	902	aGg/aAg	18/43	0.218224206722219	6	FACETS	0.895	0.85	0.942			1	INDETERMINATE	2	TRUE	NA	0.761967783903939	6		513	1465	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563107	21563107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542237961	NA	P-0002835-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1300	276	383	0	ENST00000382592.4:c.812G>A	p.Arg271His	p.R271H	ENST00000382592	NM_014572.2	271	cGc/cAc	4/8	0.68626048676958	5	FACETS	0.985	0.922	1	0.328	0.307	0.35	CLONAL	1	TRUE	2	0.761967783903939	5		383	1576	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575663	48575663	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0002835-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	27	364	0	ENST00000342988.3:c.425-2A>G		p.X142_splice	ENST00000342988	NM_005359.5	142			0.761967783903939	1	FACETS	0.114	0.09	0.141	0.114	0.09	0.141	SUBCLONAL	1	TRUE	0	0.761967783903939	1		364	385	SUCCESS
APC	324	MSKCC	GRCh37	5	112175548	112175548	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002835-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	320	426	0	ENST00000257430.4:c.4260del	p.Ser1421ValfsTer52	p.S1421Vfs*52	ENST00000257430	NM_000038.5	1419	agC/ag	16/16	1	2	FACETS	0.951	0.901	1	0.951	0.901	1	CLONAL	1	TRUE	1	0.761967783903939	2		426	883	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0002868-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	24	571	1	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		572	547	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532696	46532696	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002877-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	71	380	0	ENST00000262741.5:c.382C>G	p.Leu128Val	p.L128V	ENST00000262741	NM_003629.3	128	Ctg/Gtg	4/10	0.28195215816931	3	FACETS	0.751	0.654	0.856	0.375	0.327	0.428	SUBCLONAL	1	TRUE	1	0.26	3		380	822	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682971	241682971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002877-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	68	276	0	ENST00000366560.3:c.52C>T	p.Pro18Ser	p.P18S	ENST00000366560	NM_000143.3	18	Cca/Tca	1/10	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.26	2		276	466	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586425	189586425	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002877-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	43	203	0	ENST00000264731.3:c.1049G>C	p.Arg350Thr	p.R350T	ENST00000264731	NM_003722.4	350	aGa/aCa	8/14	1	2	FACETS	0.78	0.654	0.92	0.78	0.654	0.92	CLONAL	1	TRUE	1	0.26	2		203	424	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38942417	38942417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002877-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	73	309	0	ENST00000357387.3:c.5116G>A	p.Ala1706Thr	p.A1706T	ENST00000357387	NM_152756.3	1706	Gct/Act	38/38	0.3	3	FACETS	0.755	0.659	0.859	0.378	0.329	0.43	SUBCLONAL	1	TRUE	1	0.26	3		309	840	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557414	21557414	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1284836425	NA	P-0002877-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	42	457	0	ENST00000382592.4:c.2431G>A	p.Gly811Ser	p.G811S	ENST00000382592	NM_014572.2	811	Ggc/Agc	5/8	1	2	FACETS	0.397	0.33	0.472	0.397	0.33	0.472	SUBCLONAL	1	TRUE	1	0.26	2		457	814	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103789	47103789	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002877-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	131	554	0	ENST00000409792.3:c.6157del	p.Ala2053ProfsTer94	p.A2053Pfs*94	ENST00000409792	NM_014159.6	2053	Gcc/cc	14/21	0.290245224055563	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.26	1		554	813	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098973	178098973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002881-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	70	329	0	ENST00000397062.3:c.72G>C	p.Trp24Cys	p.W24C	ENST00000397062	NM_006164.4	24	tgG/tgC	2/5	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.439463543160331	2		329	309	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86637132	86637132	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002881-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	59	267	0	ENST00000274376.6:c.1043G>C	p.Gly348Ala	p.G348A	ENST00000274376	NM_002890.2	348	gGa/gCa	6/25	NA	2	FACETS	1	0.909	1			1	INDETERMINATE	1	TRUE	NA	0.439463543160331	2		267	254	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333105	70333105	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002881-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	137	502	0	ENST00000373644.4:c.1010C>G	p.Ala337Gly	p.A337G	ENST00000373644	NM_030625.2	337	gCg/gGg	2/12	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.439463543160331	2		502	580	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441780	49441780	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555195442	NA	P-0002881-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	162	440	0	ENST00000301067.7:c.4204C>T	p.Gln1402Ter	p.Q1402*	ENST00000301067	NM_003482.3	1402	Cag/Tag	14/54	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.439463543160331	2		440	664	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608116	28608116	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002901-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	55	528	0	ENST00000241453.7:c.1850G>T	p.Gly617Val	p.G617V	ENST00000241453	NM_004119.2	617	gGa/gTa	15/24	0.381288092577977	1	FACETS	0.51	0.439	0.587	0.51	0.439	0.587	SUBCLONAL	1	TRUE	0	0.516106256170273	1		528	310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555525857	NA	P-0002912-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	8	446	0	ENST00000269305.4:c.596G>A	p.Gly199Glu	p.G199E	ENST00000269305	NM_001126112.2	199	gGa/gAa	6/11	0.318168234457355	1	FACETS	0.124	0.079	0.183	0.124	0.079	0.183	SUBCLONAL	1	TRUE	0	0.318168234457355	1		446	340	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721214	176721214	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002912-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	50	285	0	ENST00000439151.2:c.6845C>A	p.Pro2282His	p.P2282H	ENST00000439151	NM_022455.4	2282	cCt/cAt	23/23	1	2	FACETS	0.658	0.558	0.766	0.658	0.558	0.766	SUBCLONAL	1	TRUE	1	0.318168234457355	2		285	478	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678409	88678409	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	49	792	0	ENST00000360948.2:c.1127A>G	p.Tyr376Cys	p.Y376C	ENST00000360948	NM_001012338.2	376	tAt/tGt	9/19	0.344191077918291	1	FACETS	0.349	0.295	0.408	0.349	0.295	0.408	SUBCLONAL	1	TRUE	0	0.397357051479221	1		792	567	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739031	40739031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1358914349	NA	P-0002916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	87	482	1	ENST00000373198.4:c.3253G>A	p.Val1085Ile	p.V1085I	ENST00000373198	NM_133170.3	1085	Gtc/Atc	24/32	0.3525367521043	3	FACETS	0.967	0.858	1	0.322	0.286	0.361	CLONAL	1	TRUE	0	0.397357051479221	3		483	543	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241679	55241681	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	rs397517086	NA	P-0002916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	211	600	0	ENST00000275493.2:c.2127_2129del	p.Glu709_Thr710delinsAsp	p.E709_T710delinsD	ENST00000275493	NM_005228.3	709	gaAACt/gat	18/28	0.375820040183699	5	FACETS	1	0.966	1	0.706	0.657	0.757	CLONAL	2	TRUE	2	0.397357051479221	5		600	800	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519988	NA	P-0002943-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	173	478	0	ENST00000269305.4:c.808T>G	p.Phe270Val	p.F270V	ENST00000269305	NM_001126112.2	270	Ttt/Gtt	8/11	0.812538239412212	1	FACETS	0.965	0.913	1	0.965	0.913	1	CLONAL	1	TRUE	0	0.812538239412212	1		478	262	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955535	48955535	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002943-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	232	464	0	ENST00000267163.4:c.1651G>T	p.Glu551Ter	p.E551*	ENST00000267163	NM_000321.2	551	Gaa/Taa	17/27	0.812538239412212	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.812538239412212	1		464	327	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118502	17118502	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs879255678	NA	P-0002943-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	93	353	0	ENST00000285071.4:c.1429C>T	p.Arg477Ter	p.R477*	ENST00000285071	NM_144997.5	477	Cga/Tga	12/14	0.812538239412212	1	FACETS	0.992	0.921	1	0.992	0.921	1	CLONAL	1	TRUE	0	0.812538239412212	1		353	137	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352297	70352297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002943-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	34	604	0	ENST00000374080.3:c.4324C>T	p.His1442Tyr	p.H1442Y	ENST00000374080		1442	Cat/Tat	31/45	1	2	FACETS	0.162	0.132	0.196	0.162	0.132	0.196	SUBCLONAL	1	TRUE	1	0.812538239412212	2		604	516	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76953113	76953113	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002943-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	328	594	3	ENST00000373344.5:c.200C>A	p.Ser67Tyr	p.S67Y	ENST00000373344	NM_000489.3	67	tCt/tAt	4/35	1	2	FACETS	0.953	0.904	1	0.953	0.904	1	CLONAL	1	TRUE	1	0.812538239412212	2		597	847	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750684	128750684	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002978-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	210	363	0	ENST00000377970.2:c.221C>A	p.Pro74Gln	p.P74Q	ENST00000377970	NM_002467.4	74	cCg/cAg	2/3	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.667097814936738	2		363	614	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878081	48878112	+	frameshift_variant	Frame_Shift_Del	DEL	CACCGCCGCCGCTGCCGCCGCGGAACCCCCGG	CACCGCCGCCGCTGCCGCCGCGGAACCCCCGG	-	novel	NA	P-0002978-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	134	60	0	ENST00000267163.4:c.45_76del	p.Ala17ProfsTer3	p.A17Pfs*3	ENST00000267163	NM_000321.2	11	gcCACCGCCGCCGCTGCCGCCGCGGAACCCCCGGca/gcca	1/27	0.650477901858061	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.667097814936738	1		60	213	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0002990-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	142	246	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.442949470483944	4	FACETS	0.997	0.915	1	0.997	0.915	1	CLONAL	2	TRUE	2	0.44181741521644	4		246	465	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421807	49421808	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0002990-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	258	729	0	ENST00000301067.7:c.14499_14500del	p.Glu4834SerfsTer2	p.E4834Sfs*2	ENST00000301067	NM_003482.3	4833	ggGGaa/ggaa	46/54	0.42460930387142	4	FACETS	0.794	0.744	0.846	0.794	0.744	0.846	SUBCLONAL	2	TRUE	2	0.44181741521644	4		729	1060	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266997	18266998	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0002990-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	11	85	0	ENST00000222254.8:c.308_309delinsTT	p.Gly103Val	p.G103V	ENST00000222254	NM_005027.3	103	gGG/gTT	2/16	0.442949470483944	4	FACETS	0.565	0.393	0.777	0.283	0.196	0.389	SUBCLONAL	1	TRUE	2	0.44181741521644	4		85	127	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0002996-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	56	473	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.866	0.74	1	0.866	0.74	1	CLONAL	1	TRUE	1	0.16034602578976	2		473	807	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578538	7578538	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1131691037	NA	P-0002996-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	45	380	0	ENST00000269305.4:c.392A>T	p.Asn131Ile	p.N131I	ENST00000269305	NM_001126112.2	131	aAc/aTc	5/11	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.16034602578976	2		380	524	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220649	1220649	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002996-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	120	496	2	ENST00000326873.7:c.667G>T	p.Glu223Ter	p.E223*	ENST00000326873	NM_000455.4	223	Gag/Tag	5/10	0.153800999763813	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.16034602578976	3		498	687	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442833	187442833	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002996-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	43	378	0	ENST00000232014.4:c.1873A>T	p.Thr625Ser	p.T625S	ENST00000232014	NM_001130845.1	625	Act/Tct	9/10	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.16034602578976	2		378	484	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628055	187628055	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002996-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	74	600	0	ENST00000441802.2:c.2927T>C	p.Val976Ala	p.V976A	ENST00000441802	NM_005245.3	976	gTg/gCg	2/27	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.16034602578976	2		600	804	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132839	152132839	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002996-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	48	382	0	ENST00000262189.6:c.33G>T	p.Gln11His	p.Q11H	ENST00000262189	NM_170606.2	11	caG/caT	1/59	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.16034602578976	2		382	544	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602355	28602355	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002996-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	42	599	2	ENST00000241453.7:c.2013C>A	p.His671Gln	p.H671Q	ENST00000241453	NM_004119.2	671	caC/caA	16/24	1	2	FACETS	0.662	0.551	0.786	0.662	0.551	0.786	SUBCLONAL	1	TRUE	1	0.16034602578976	2		601	791	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577595	7577595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793603	NA	P-0002996-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	58	350	0	ENST00000269305.4:c.686G>A	p.Cys229Tyr	p.C229Y	ENST00000269305	NM_001126112.2	229	tGt/tAt	7/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.16034602578976	2		350	536	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63537649	63537649	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002996-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	50	551	0	ENST00000307078.5:c.983G>T	p.Gly328Val	p.G328V	ENST00000307078	NM_004655.3	328	gGc/gTc	4/11	1	2	FACETS	0.774	0.655	0.905	0.774	0.655	0.905	CLONAL	1	TRUE	1	0.16034602578976	2		551	806	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385223	41385223	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002996-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	117	525	0	ENST00000373198.4:c.738G>T	p.Arg246Ser	p.R246S	ENST00000373198	NM_133170.3	246	agG/agT	6/32	1	2	FACETS	1	0.938	1	1	0.989	1	CLONAL	2	TRUE	1	0.16034602578976	2		525	693	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811611	102811611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002996-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	101	840	0	ENST00000307046.8:c.573del	p.Gly194GlufsTer8	p.G194Efs*8	ENST00000307046	NM_001111285.1	191	ggC/gg	4/4	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.16034602578976	2		840	948	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913255	NA	P-0003034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	233	504	0	ENST00000369535.4:c.183A>T	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caT	3/7	0.396426319732681	3	FACETS	1	0.981	1	0.57	0.531	0.61	CLONAL	1	TRUE	1	0.459946926926465	3		504	1093	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0003034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	290	369	1	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	0.345287838191657	3	FACETS	1	0.99	1	0.781	0.74	0.822	CLONAL	2	TRUE	0	0.459946926926465	3		370	662	SUCCESS
INSRR	3645	MSKCC	GRCh37	1	156811916	156811916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035402024	NA	P-0003034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	191	593	0	ENST00000368195.3:c.3385G>A	p.Val1129Ile	p.V1129I	ENST00000368195	NM_014215.2	1129	Gtc/Atc	19/22	0.460608682891944	3	FACETS	0.893	0.824	0.964	0.446	0.412	0.482	CLONAL	1	TRUE	1	0.459946926926465	3		593	1144	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932747	49932747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144684048	NA	P-0003034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	277	877	0	ENST00000296474.3:c.3124G>A	p.Asp1042Asn	p.D1042N	ENST00000296474	NM_002447.2	1042	Gat/Aat	14/20	0.345287838191657	3	FACETS	1	0.986	1	0.392	0.367	0.417	CLONAL	1	TRUE	0	0.459946926926465	3		877	1260	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157893	106157893	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	149	485	0	ENST00000380013.4:c.2794G>C	p.Asp932His	p.D932H	ENST00000380013	NM_001127208.2	932	Gac/Cac	3/11	0.273073798494232	5	FACETS	1	0.98	1	0.414	0.378	0.452	INDETERMINATE	1	TRUE	2	0.459946926926465	5		485	881	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753942	57753942	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	237	507	0	ENST00000274289.3:c.682G>A	p.Ala228Thr	p.A228T	ENST00000274289	NM_006622.3	228	Gcc/Acc	5/14	0.459946926926465	2	FACETS	1	0.99	1	0.643	0.602	0.686	CLONAL	1	TRUE	0	0.459946926926465	2		507	801	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562442	176562442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	672	530	0	ENST00000439151.2:c.338G>A	p.Cys113Tyr	p.C113Y	ENST00000439151	NM_022455.4	113	tGc/tAc	2/23	0.460608682891944	3	FACETS	1	0.976	1			1	CLONAL	3	TRUE	NA	0.459946926926465	3		530	1189	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051032	180051032	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	134	436	0	ENST00000261937.6:c.1451C>A	p.Pro484Gln	p.P484Q	ENST00000261937	NM_182925.4	484	cCa/cAa	11/30	0.189814355291094	3	FACETS	0.916	0.833	1			1	INDETERMINATE	1	TRUE	NA	0.459946926926465	3		436	782	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858315	27858315	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1612	103	1125	0	ENST00000359303.2:c.256C>G	p.Gln86Glu	p.Q86E	ENST00000359303	NM_003535.2	86	Cag/Gag	1/1	0.369883977531511	3	FACETS	0.321	0.286	0.359	0.107	0.095	0.12	SUBCLONAL	1	TRUE	0	0.459946926926465	3		1125	1715	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912174	29912174	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	rs199474643	NA	P-0003034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	103	133	0	ENST00000376809.5:c.895G>T	p.Glu299Ter	p.E299*	ENST00000376809	NM_002116.7	299	Gag/Tag	4/8	0.369883977531511	3	FACETS	0.838	0.768	0.91	0.838	0.768	0.91	CLONAL	3	TRUE	0	0.459946926926465	3		133	219	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680887	30680887	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	590	838	0	ENST00000376406.3:c.832G>T	p.Ala278Ser	p.A278S	ENST00000376406	NM_014641.2	278	Gca/Tca	5/15	0.369883977531511	3	FACETS	1	0.994	1	0.774	0.745	0.803	CLONAL	2	TRUE	0	0.459946926926465	3		838	1359	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265487	152265487	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	273	363	1	ENST00000206249.3:c.940C>A	p.Gln314Lys	p.Q314K	ENST00000206249	NM_000125.3	314	Cag/Aag	4/8	0.25471289707992	3	FACETS	1	0.969	1	0.692	0.654	0.732	INDETERMINATE	2	TRUE	0	0.459946926926465	3		364	703	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762944	40762944	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	252	384	0	ENST00000392038.2:c.64T>C	p.Trp22Arg	p.W22R	ENST00000392038	NM_001626.4	22	Tgg/Cgg	3/14	0.273073798494232	5	FACETS	1	0.976	1	0.72	0.675	0.766	INDETERMINATE	2	TRUE	2	0.459946926926465	5		384	857	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432347	49432347	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	396	433	0	ENST00000301067.7:c.8792del	p.Pro2931HisfsTer12	p.P2931Hfs*12	ENST00000301067	NM_003482.3	2931	cCa/ca	34/54	0.460608682891944	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.459946926926465	3		433	985	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0003041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	1828	618	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.859398603231889	4	FACETS	1	0.998	1	1	0.998	1	CLONAL	4	FALSE	0	0.860666553171412	4		618	1936	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0003041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	449	308	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.808652918671124	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	FALSE	2	0.860666553171412	4		309	958	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956552	93956552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754119070	NA	P-0003041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1169	260	585	1	ENST00000369303.4:c.2684G>A	p.Arg895Gln	p.R895Q	ENST00000369303	NM_004440.3	895	cGa/cAa	15/17	0.629381090429687	4	FACETS	0.787	0.735	0.84	0.393	0.367	0.42	SUBCLONAL	1	FALSE	2	0.860666553171412	4		586	1429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0003057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	172	328	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.418937533225737	1	FACETS	0.751	0.699	0.804	1	0.991	1	SUBCLONAL	2	TRUE	0	0.418937533225737	1		328	432	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630000	187630000	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	63	236	0	ENST00000441802.2:c.982C>A	p.His328Asn	p.H328N	ENST00000441802	NM_005245.3	328	Cat/Aat	2/27	NA	2	FACETS	0.688	0.597	0.787			1	INDETERMINATE	1	TRUE	NA	0.418937533225737	2		236	437	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518715	176518715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	55	201	0	ENST00000292408.4:c.633G>A	p.Met211Ile	p.M211I	ENST00000292408	NM_213647.1	211	atG/atA	6/18	0.362594163261631	3	FACETS	1	0.892	1			1	CLONAL	1	TRUE	NA	0.418937533225737	3		201	305	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056997	180056997	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	48	271	0	ENST00000261937.6:c.622A>G	p.Thr208Ala	p.T208A	ENST00000261937	NM_182925.4	208	Acc/Gcc	5/30	NA	2	FACETS	0.574	0.486	0.671			1	INDETERMINATE	1	TRUE	NA	0.418937533225737	2		271	399	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0003101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	148	165	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.539146001516547	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.539146001516547	2		165	255	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857047	9857047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568622613	NA	P-0003101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	166	352	0	ENST00000330684.3:c.4354C>T	p.Arg1452Cys	p.R1452C	ENST00000330684	NM_001134407.1	1452	Cgc/Tgc	13/13	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.539146001516547	2		352	558	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417868	138417868	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	155	344	0	ENST00000289153.2:c.1651T>C	p.Cys551Arg	p.C551R	ENST00000289153	NM_006219.2	551	Tgt/Cgt	11/22	0.338404999760416	3	FACETS	1	0.981	1	0.61	0.561	0.661	CLONAL	1	TRUE	1	0.539146001516547	3		344	598	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881505	48881505	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0003101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	141	231	0	ENST00000267163.4:c.227T>G	p.Leu76Ter	p.L76*	ENST00000267163	NM_000321.2	76	tTa/tGa	2/27	0.508529148192636	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.539146001516547	1		231	358	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577043	7577046	+	frameshift_variant	Frame_Shift_Del	DEL	GCTC	GCTC	-	novel	NA	P-0003101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	143	271	0	ENST00000269305.4:c.892_895del	p.Glu298CysfsTer46	p.E298Cfs*46	ENST00000269305	NM_001126112.2	298	GAGCtg/tg	8/11	0.539146001516547	1	FACETS	0.971	0.895	1	0.971	0.895	1	CLONAL	1	TRUE	0	0.539146001516547	1		271	399	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0003102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	58	618	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	NA	2	FACETS	0.795	0.706	0.885			1	INDETERMINATE	2	TRUE	NA	0.597676456905338	2		619	122	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	29	162	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.562922259748453	4	FACETS	1	0.933	1	0.861	0.745	0.969	CLONAL	3	TRUE	0	0.597676456905338	4		162	45	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0003102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	26	319	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.429632678538185	4	FACETS	1	0.825	1	0.515	0.413	0.628	CLONAL	1	TRUE	2	0.597676456905338	4		319	135	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023307	27023307	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	37	90	0	ENST00000324856.7:c.413C>A	p.Ser138Ter	p.S138*	ENST00000324856	NM_006015.4	138	tCa/tAa	1/20	0.479063995533072	3	FACETS	1	0.927	1	1	0.927	1	CLONAL	3	TRUE	0	0.597676456905338	3		90	51	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066611	94066611	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	35	494	0	ENST00000369303.4:c.1148G>T	p.Gly383Val	p.G383V	ENST00000369303	NM_004440.3	383	gGg/gTg	5/17	0.597676456905338	1	FACETS	0.507	0.421	0.6	0.507	0.421	0.6	SUBCLONAL	1	TRUE	0	0.597676456905338	1		494	162	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112919996	112919996	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0003102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	25	198	0	ENST00000351677.2:c.1211C>G	p.Ser404Ter	p.S404*	ENST00000351677	NM_002834.3	404	tCa/tGa	10/16	0.597676456905338	3	FACETS	0.929	0.745	1	0.464	0.372	0.566	CLONAL	1	TRUE	1	0.597676456905338	3		198	117	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0003106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	11	126	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.353	0.243	0.492	0.353	0.243	0.492	SUBCLONAL	1	TRUE	1	0.12	2		126	519	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974767	21974771	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGG	CGCGG	-	novel	NA	P-0003106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	24	155	0	ENST00000304494.5:c.56_60del	p.Ala19GlyfsTer23	p.A19Gfs*23	ENST00000304494	NM_000077.4	19	gCCGCG/g	1/3	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.12	2		155	345	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519902	29519902	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs200364883	NA	P-0003127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	56	243	0	ENST00000389048.3:c.1669C>G	p.Arg557Gly	p.R557G	ENST00000389048	NM_004304.4	557	Cgt/Ggt	9/29	0.150535326921677	4	FACETS	0.987	0.846	1	0.493	0.423	0.571	INDETERMINATE	1	TRUE	2	0.26	4		243	550	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86667998	86667998	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0003127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	52	251	0	ENST00000274376.6:c.1762A>T	p.Lys588Ter	p.K588*	ENST00000274376	NM_002890.2	588	Aaa/Taa	13/25	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.26	2		251	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0003135-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	51	618	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.819	0.697	0.953	1	0.968	1	CLONAL	2	TRUE	1	0.13	2		619	479	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70355083	70355083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779481901	NA	P-0003135-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	53	377	0	ENST00000374080.3:c.5005G>A	p.Asp1669Asn	p.D1669N	ENST00000374080		1669	Gat/Aat	36/45	1	1	FACETS	0.897	0.767	1	1	0.973	1	CLONAL	2	TRUE	0	0.13	1		377	425	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003187-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	83	333	0				ENST00000310581	NM_198253.2	-/1132			0.24545633805096	3	FACETS	0.879	0.779	0.984	0.879	0.779	0.984	CLONAL	2	TRUE	1	0.24545633805096	3		333	432	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566883	212566883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003187-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	34	270	0	ENST00000342788.4:c.1298C>T	p.Ser433Phe	p.S433F	ENST00000342788	NM_005235.2	433	tCc/tTc	12/28	1	2	FACETS	0.774	0.633	0.931	0.774	0.633	0.931	CLONAL	1	TRUE	1	0.24545633805096	2		270	358	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444055	49444055	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003187-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	52	380	0	ENST00000301067.7:c.3316C>T	p.Pro1106Ser	p.P1106S	ENST00000301067	NM_003482.3	1106	Ccc/Tcc	11/54	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.24545633805096	2		380	393	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7126597	7126597	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003187-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	52	608	0	ENST00000302850.5:c.3011A>G	p.Asp1004Gly	p.D1004G	ENST00000302850	NM_000208.2	1004	gAt/gGt	16/22	1	2	FACETS	0.626	0.532	0.729	0.626	0.532	0.729	SUBCLONAL	1	TRUE	1	0.24545633805096	2		608	677	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812190	43812191	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	ATATGCAATTCTGTCAT	novel	NA	P-0003187-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	50	613	0	ENST00000372470.3:c.1055_1056insATATGCAATTCTGTCAT	p.Cys352Ter	p.C352*	ENST00000372470	NM_005373.2	352	tgc/tgATATGCAATTCTGTCATc	7/12	1	2	FACETS	0.476	0.403	0.558	0.476	0.403	0.558	SUBCLONAL	1	TRUE	1	0.24545633805096	2		613	855	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0003198-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	55	802	5	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.250064082708066	1	FACETS	1	0.94	1	1	0.94	1	INDETERMINATE	1	FALSE	0	0.4290032153393	1		807	176	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426988	70426988	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003198-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	70	286	1	ENST00000373644.4:c.4648G>T	p.Asp1550Tyr	p.D1550Y	ENST00000373644	NM_030625.2	1550	Gac/Tac	7/12	0.4290032153393	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	0	0.4290032153393	1		287	181	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0003273-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	345	415	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.738023201743612	10	FACETS	0.996	0.97	1			1	CLONAL	9	TRUE	NA	0.738023201743612	10		415	412	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933385	39933385	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003290-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	172	287	0	ENST00000378444.4:c.1214C>A	p.Pro405Gln	p.P405Q	ENST00000378444	NM_001123385.1	405	cCa/cAa	4/15	0.336980274858092	1	FACETS	0.529	0.492	0.567	0.529	0.492	0.567	INDETERMINATE	1	TRUE	0	0.846304646632789	1		287	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577525	7577526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0003290-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	426	218	0	ENST00000269305.4:c.755_756insA	p.Thr253HisfsTer11	p.T253Hfs*11	ENST00000269305	NM_001126112.2	252	ctc/ctAc	7/11	0.477899602488289	4	FACETS	0.97	0.95	0.988			1	INDETERMINATE	4	TRUE	NA	0.846304646632789	4		218	479	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224551	123224552	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0003290-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	204	406	0	ENST00000218089.9:c.3406dup	p.Asp1136GlyfsTer2	p.D1136Gfs*2	ENST00000218089	NM_001042749.1	1135	gag/gaGg	31/35	0.336980274858092	1	FACETS	0.633	0.595	0.672	0.633	0.595	0.672	INDETERMINATE	1	TRUE	0	0.846304646632789	1		406	439	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576910	7576910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003342-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	124	204	0	ENST00000269305.4:c.936del	p.Ser313AlafsTer32	p.S313Afs*32	ENST00000269305	NM_001126112.2	312	acC/ac	9/11	0.531241001718662	2	FACETS	0.869	0.805	0.932	0.869	0.805	0.932	CLONAL	2	TRUE	0	0.60478992088049	2		204	236	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720805	89720808	+	frameshift_variant	Frame_Shift_Del	DEL	CTTT	CTTT	-	rs398123330	NA	P-0003376-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	56	116	0	ENST00000371953.3:c.956_959del	p.Thr319LysfsTer24	p.T319Kfs*24	ENST00000371953	NM_000314.4	319	aCTTTa/aa	8/9	0.570710800112998	3	FACETS	0.883	0.794	0.969	0.883	0.794	0.969	CLONAL	3	TRUE	0	0.596618855686851	3		116	92	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0003376-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	61	367	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.596618855686851	1	FACETS	0.78	0.709	0.846	1	0.982	1	SUBCLONAL	2	TRUE	0	0.596618855686851	1		367	92	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128018908	128018908	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003376-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	31	334	0	ENST00000285398.2:c.1960G>C	p.Glu654Gln	p.E654Q	ENST00000285398	NM_000122.1	654	Gag/Cag	13/15	NA	2	FACETS	1	0.884	1			1	INDETERMINATE	1	TRUE	NA	0.596618855686851	2		334	96	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90995013	90995013	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003376-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	74	308	0	ENST00000265433.3:c.108A>C	p.Glu36Asp	p.E36D	ENST00000265433	NM_002485.4	36	gaA/gaC	2/16	0.330148940392641	4	FACETS	1	0.972	1	0.676	0.598	0.758	INDETERMINATE	1	TRUE	2	0.596618855686851	4		308	293	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557393	29557393	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1567849891	NA	P-0003376-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	24	221	0	ENST00000356175.3:c.3106A>T	p.Lys1036Ter	p.K1036*	ENST00000356175	NM_000267.3	1036	Aaa/Taa	23/57	0.596618855686851	1	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	0	0.596618855686851	1		221	51	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0003425-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	30	422	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.3	5	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	5		423	733	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691039	NA	P-0003425-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	22	303	0	ENST00000269305.4:c.919+1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		303	393	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597493	52597493	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003425-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	15	296	0	ENST00000394830.3:c.3817C>T	p.Gln1273Ter	p.Q1273*	ENST00000394830	NM_018313.4	1273	Cag/Tag	25/30	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		296	232	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044840	47044840	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0003425-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	18	240	0	ENST00000377604.3:c.2167-1G>T		p.X723_splice	ENST00000377604	NM_001204468.1	723			0.229735954656927	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		240	313	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242481	+	inframe_deletion	In_Frame_Del	DEL	AATTAAGAGAAGCAA	AATTAAGAGAAGCAA	-	rs121913425	NA	P-0003425-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	124	281	0	ENST00000275493.2:c.2237_2251del	p.Glu746_Thr751delinsAla	p.E746_T751delinsA	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAAca/gca	19/28	0.3	5	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	5		281	478	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0003455-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	21	473	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.658	0.505	0.837	0.658	0.505	0.837	SUBCLONAL	1	TRUE	1	0.14	2		473	456	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449595	149449595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003455-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	27	457	0	ENST00000286301.3:c.1351G>A	p.Asp451Asn	p.D451N	ENST00000286301	NM_005211.3	451	Gat/Aat	10/22	1	2	FACETS	0.964	0.767	1	0.964	0.767	1	CLONAL	1	TRUE	1	0.14	2		457	400	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444281	50444281	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs748435863	NA	P-0003455-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	20	189	0	ENST00000331340.3:c.211T>C	p.Cys71Arg	p.C71R	ENST00000331340	NM_006060.4	71	Tgt/Cgt	4/8	1	2	FACETS	1	0.809	1	1	0.809	1	CLONAL	1	TRUE	1	0.14	2		189	268	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603042	48603042	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0003455-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	17	205	0	ENST00000342988.3:c.1343del	p.Gln448ArgfsTer28	p.Q448Rfs*28	ENST00000342988	NM_005359.5	448	cAg/cg	11/12	1	2	FACETS	0.952	0.711	1	0.952	0.711	1	CLONAL	1	TRUE	1	0.14	2		205	255	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0003458-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	110	618	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.937	0.844	1	0.937	0.844	1	CLONAL	1	TRUE	1	0.4	2		618	587	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761304	59761304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45437094	NA	P-0003458-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	126	593	0	ENST00000259008.2:c.3103C>T	p.Arg1035Cys	p.R1035C	ENST00000259008	NM_032043.2	1035	Cgt/Tgt	20/20	1	2	FACETS	0.905	0.821	0.994	0.905	0.821	0.994	CLONAL	1	TRUE	1	0.4	2		593	696	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665752	29665755	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1555535032	NA	P-0003458-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	122	473	1	ENST00000356175.3:c.6789_6792del	p.Tyr2264ThrfsTer5	p.Y2264Tfs*5	ENST00000356175	NM_000267.3	2263	ACTTac/ac	45/57	1	2	FACETS	0.814	0.737	0.896	0.814	0.737	0.896	CLONAL	1	TRUE	1	0.4	2		474	749	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131402	17131402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398124537	NA	P-0003458-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	62	472	1	ENST00000285071.4:c.50G>A	p.Arg17His	p.R17H	ENST00000285071	NM_144997.5	17	cGc/cAc	4/14	1	2	FACETS	0.934	0.812	1	0.934	0.812	1	CLONAL	1	TRUE	1	0.4	2		473	332	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176118143	176118143	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003458-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	74	383	0	ENST00000367669.3:c.830A>G	p.Glu277Gly	p.E277G	ENST00000367669	NM_022457.5	277	gAg/gGg	6/20	1	2	FACETS	0.579	0.507	0.657	0.579	0.507	0.657	SUBCLONAL	1	TRUE	1	0.4	2		383	639	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61709632	61709632	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003458-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	90	364	0	ENST00000401558.2:c.2855T>C	p.Leu952Ser	p.L952S	ENST00000401558	NM_003400.3	952	tTg/tCg	23/25	1	2	FACETS	0.753	0.669	0.842	0.753	0.669	0.842	SUBCLONAL	1	TRUE	1	0.4	2		364	598	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042043	14042043	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778284	NA	P-0003458-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	66	447	0	ENST00000311895.7:c.2590C>T	p.Arg864Cys	p.R864C	ENST00000311895	NM_005236.2	864	Cgc/Tgc	11/11	0.3	1	FACETS	0.539	0.468	0.615	0.539	0.468	0.615	SUBCLONAL	1	TRUE	0	0.4	1		447	490	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59770824	59770824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45572934	NA	P-0003458-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	136	511	2	ENST00000259008.2:c.2542C>T	p.Arg848Cys	p.R848C	ENST00000259008	NM_032043.2	848	Cgc/Tgc	18/20	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.4	2		513	664	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244433	5244433	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003458-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	29	250	0	ENST00000357368.4:c.1049T>A	p.Ile350Asn	p.I350N	ENST00000357368	NM_002850.3	350	aTc/aAc	11/38	0.3	0	FACETS	0.46	0.372	0.558			1	SUBCLONAL	1	TRUE	0	0.4	0		250	189	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303305	15303305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762164861	NA	P-0003458-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	53	473	1	ENST00000263388.2:c.223C>T	p.Arg75Trp	p.R75W	ENST00000263388	NM_000435.2	75	Cgg/Tgg	3/33	0.206498469566114	0	FACETS	0.546	0.469	0.63			1	INDETERMINATE	1	TRUE	0	0.4	0		474	291	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743865	40743865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758531464	NA	P-0003458-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	85	472	0	ENST00000373198.4:c.3130G>A	p.Val1044Ile	p.V1044I	ENST00000373198	NM_133170.3	1044	Gtc/Atc	23/32	0.113538745608716	0	FACETS	0.63	0.56	0.704			1	INDETERMINATE	1	TRUE	0	0.4	0		472	405	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562657	29562660	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs1064794276	NA	P-0003458-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	123	591	0	ENST00000356175.3:c.3739_3742del	p.Phe1247IlefsTer18	p.F1247Ifs*18	ENST00000356175	NM_000267.3	1246	cTGTTt/ct	28/57	1	2	FACETS	0.904	0.819	0.994	0.904	0.819	0.994	CLONAL	1	TRUE	1	0.4	2		591	680	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627788	37627790	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs587778181	NA	P-0003458-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	128	662	0	ENST00000447079.4:c.1705_1707del	p.Ser569del	p.S569del	ENST00000447079	NM_015083.1	568	cCTTct/cct	2/14	1	2	FACETS	0.979	0.889	1	0.979	0.889	1	CLONAL	1	TRUE	1	0.4	2		662	654	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165280	47165283	+	frameshift_variant	Frame_Shift_Del	DEL	TTCT	TTCT	-	novel	NA	P-0003458-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	207	333	0	ENST00000409792.3:c.843_846del	p.Glu282IlefsTer18	p.E282Ifs*18	ENST00000409792	NM_014159.6	281	aaAGAA/aa	3/21	0.3	2	FACETS	1	0.956	1			1	CLONAL	2	TRUE	NA	0.4	2		333	505	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0003461-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	1116	819	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.523288174509487	17	FACETS	1	0.989	1			1	CLONAL	16	TRUE	NA	0.523288174509487	17		819	1307	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0003461-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	70	360	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.523288174509487	3	FACETS	1	0.932	1	0.544	0.479	0.614	CLONAL	1	TRUE	1	0.523288174509487	3		360	310	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370709	55370709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003461-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	43	164	0	ENST00000297316.4:c.11C>T	p.Pro4Leu	p.P4L	ENST00000297316	NM_022454.3	4	cCg/cTg	1/2	0.523288174509487	3	FACETS	0.938	0.793	1	0.469	0.396	0.548	CLONAL	1	TRUE	1	0.523288174509487	3		164	221	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs864622237	NA	P-0003461-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	125	370	0	ENST00000269305.4:c.700T>A	p.Tyr234Asn	p.Y234N	ENST00000269305	NM_001126112.2	234	Tac/Aac	7/11	1	2	FACETS	1	0.97	1	1	0.992	1	CLONAL	2	TRUE	1	0.523288174509487	2		370	221	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004992	16004992	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs755777616	NA	P-0003461-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	178	422	0	ENST00000268712.3:c.2262G>T	p.Glu754Asp	p.E754D	ENST00000268712	NM_006311.3	754	gaG/gaT	20/46	1	2	FACETS	0.846	0.802	0.889	1	0.995	1	CLONAL	3	TRUE	1	0.523288174509487	2		422	268	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131282	17131282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749770193	NA	P-0003461-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	94	658	0	ENST00000285071.4:c.170G>A	p.Arg57Gln	p.R57Q	ENST00000285071	NM_144997.5	57	cGg/cAg	4/14	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.523288174509487	2		658	340	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510606	38510606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003461-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	547	680	1	ENST00000254066.5:c.860C>T	p.Ser287Leu	p.S287L	ENST00000254066	NM_000964.3	287	tCg/tTg	7/9	0.523288174509487	4	FACETS	1	0.988	1	1	0.997	1	CLONAL	4	TRUE	1	0.523288174509487	4		681	774	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589773	55589773	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752354428	NA	P-0003463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	48	276	0	ENST00000288135.5:c.1255G>A	p.Asp419Asn	p.D419N	ENST00000288135	NM_000222.2	419	Gac/Aac	8/21	0.727826076559545	2	FACETS	0.393	0.333	0.457	0.196	0.166	0.229	SUBCLONAL	1	TRUE	0	0.727826076559545	2		276	336	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681757	30681757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779352833	NA	P-0003463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	163	302	0	ENST00000376406.3:c.340C>T	p.Arg114Cys	p.R114C	ENST00000376406	NM_014641.2	114	Cgt/Tgt	3/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.727826076559545	2		302	411	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372683	81372683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	115	322	0	ENST00000222390.5:c.851C>T	p.Ala284Val	p.A284V	ENST00000222390	NM_000601.4	284	gCa/gTa	7/18	0.707659202267959	3	FACETS	0.876	0.793	0.963	0.438	0.396	0.482	CLONAL	1	TRUE	1	0.727826076559545	3		322	492	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340245	116340245	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0003463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	24	250	0	ENST00000397752.3:c.1107T>A	p.Tyr369Ter	p.Y369*	ENST00000397752	NM_000245.2	369	taT/taA	2/21	0.707659202267959	3	FACETS	0.286	0.224	0.358	0.143	0.112	0.179	SUBCLONAL	1	TRUE	1	0.727826076559545	3		250	314	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134755	41134756	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0003464-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	249	700	0	ENST00000379561.5:c.872dup	p.Phe292ValfsTer14	p.F292Vfs*14	ENST00000379561	NM_002015.3	291	cag/caAg	2/3	0.382837025355362	1	FACETS	0.777	0.731	0.824	1	0.994	1	SUBCLONAL	2	TRUE	0	0.382837025355362	1		700	677	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984849	11984849	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0003481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	22	192	0	ENST00000353533.5:c.393+2T>A		p.X131_splice	ENST00000353533	NM_003010.3	131			0.525929929431626	3	FACETS	0.452	0.352	0.566			1	SUBCLONAL	1	FALSE	NA	0.724468443000349	3		192	183	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115905	8115912	+	frameshift_variant	Frame_Shift_Del	DEL	CACGCCCA	CACGCCCA	-	novel	NA	P-0003481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	138	307	0	ENST00000346208.3:c.1252_1259del	p.Thr418AlafsTer86	p.T418Afs*86	ENST00000346208		417	acCACGCCCAcg/accg	6/6	0.724468443000349	10	FACETS	1	0.943	1			1	CLONAL	4	FALSE	NA	0.724468443000349	10		307	361	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577361	64577373	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCCAGGCGGGT	CCGCCAGGCGGGT	-	novel	NA	P-0003481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	50	307	0	ENST00000312049.6:c.209_221del	p.Asp70AlafsTer45	p.D70Afs*45	ENST00000312049	NM_130799.2	70	gACCCGCCTGGCGGc/gc	2/10	0.738676452771335	4	FACETS	0.976	0.852	1			1	CLONAL	2	FALSE	NA	0.724468443000349	4		307	122	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0003505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	349	262	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.978	0.928	1	0.978	0.928	1	CLONAL	1	TRUE	1	0.726961097812365	2		262	982	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220371	1220372	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	TT	novel	NA	P-0003505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	173	270	0	ENST00000326873.7:c.465-1_465delinsTT		p.X155_splice	ENST00000326873	NM_000455.4	155		4/10	0.726961097812365	1	FACETS	0.971	0.912	1	0.971	0.912	1	CLONAL	1	TRUE	0	0.726961097812365	1		270	312	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204515988	204515988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	83	309	0	ENST00000367182.3:c.886G>A	p.Val296Ile	p.V296I	ENST00000367182	NM_001278516.1	296	Gta/Ata	10/11	0.400300980270942	2	FACETS	0.315	0.278	0.356	0.158	0.139	0.178	INDETERMINATE	1	TRUE	0	0.726961097812365	2		309	724	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086076	16086076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760647298	NA	P-0003505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	190	318	1	ENST00000281043.3:c.1252G>A	p.Ala418Thr	p.A418T	ENST00000281043	NM_005378.4	418	Gcc/Acc	3/3	0.726961097812365	1	FACETS	0.97	0.914	1	0.97	0.914	1	CLONAL	1	TRUE	0	0.726961097812365	1		319	343	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505524	25505524	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	243	366	0	ENST00000264709.3:c.234G>T	p.Met78Ile	p.M78I	ENST00000264709	NM_175629.2	78	atG/atT	4/23	0.726961097812365	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.726961097812365	1		366	385	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751390	57751390	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	151	263	0	ENST00000274289.3:c.1601A>T	p.His534Leu	p.H534L	ENST00000274289	NM_006622.3	534	cAc/cTc	11/14	0.183080932789661	2	FACETS	0.667	0.612	0.724	0.333	0.306	0.362	INDETERMINATE	1	TRUE	0	0.726961097812365	2		263	623	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956610	93956610	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	232	506	1	ENST00000369303.4:c.2626G>T	p.Glu876Ter	p.E876*	ENST00000369303	NM_004440.3	876	Gag/Tag	15/17	0.726961097812365	1	FACETS	0.544	0.509	0.58	0.544	0.509	0.58	SUBCLONAL	1	TRUE	0	0.726961097812365	1		507	747	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729688	41729688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	310	464	0	ENST00000242208.4:c.841G>A	p.Ala281Thr	p.A281T	ENST00000242208	NM_002192.2	281	Gca/Aca	3/3	0.353350201623049	1	FACETS	0.758	0.72	0.797	0.758	0.72	0.797	INDETERMINATE	1	TRUE	0	0.726961097812365	1		464	716	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750701	128750701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1460265619	NA	P-0003505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	275	342	0	ENST00000377970.2:c.238C>T	p.Arg80Cys	p.R80C	ENST00000377970	NM_002467.4	80	Cgc/Tgc	2/3	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.726961097812365	2		342	673	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072573	5072573	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	254	243	0	ENST00000381652.3:c.1723G>T	p.Glu575Ter	p.E575*	ENST00000381652	NM_004972.3	575	Gaa/Taa	13/25	0.726961097812365	1	FACETS	0.991	0.942	1	0.991	0.942	1	CLONAL	1	TRUE	0	0.726961097812365	1		243	449	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741925	17741925	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	50	36	0	ENST00000250003.3:c.596C>A	p.Ala199Glu	p.A199E	ENST00000250003	NM_002478.4	199	gCg/gAg	1/3	0.421605403175612	3	FACETS	0.998	0.883	1	0.998	0.883	1	INDETERMINATE	2	TRUE	1	0.726961097812365	3		36	94	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28897004	28897004	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	239	334	1	ENST00000282397.4:c.2876G>A	p.Ser959Asn	p.S959N	ENST00000282397	NM_002019.4	959	aGc/aAc	21/30	0.402779761441606	1	FACETS	0.787	0.742	0.832	0.787	0.742	0.832	INDETERMINATE	1	TRUE	0	0.726961097812365	1		335	532	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346338	73346338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	364	326	0	ENST00000377767.4:c.1462G>A	p.Asp488Asn	p.D488N	ENST00000377767	NM_014953.3	488	Gat/Aat	10/21	0.183080932789661	2	FACETS	1	0.995	1	0.678	0.648	0.709	INDETERMINATE	1	TRUE	0	0.726961097812365	2		326	738	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576214	88576214	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	171	192	0	ENST00000360948.2:c.1459G>C	p.Gly487Arg	p.G487R	ENST00000360948	NM_001012338.2	487	Ggc/Cgc	13/19	1	2	FACETS	0.986	0.915	1	0.986	0.915	1	CLONAL	1	TRUE	1	0.726961097812365	2		192	477	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610208	10610208	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	239	360	0	ENST00000171111.5:c.502G>T	p.Val168Phe	p.V168F	ENST00000171111	NM_203500.1	168	Gtc/Ttc	2/6	0.726961097812365	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.726961097812365	1		360	387	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459458	50459458	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	105	240	0	ENST00000331340.3:c.748del	p.Ala250GlnfsTer7	p.A250Qfs*7	ENST00000331340	NM_006060.4	249	atG/at	7/8	0.353350201623049	1	FACETS	0.342	0.308	0.379	0.342	0.308	0.379	INDETERMINATE	1	TRUE	0	0.726961097812365	1		240	537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0003521-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	101	802	5	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.234510143912285	2	FACETS	0.86	0.778	0.945	0.86	0.778	0.945	CLONAL	2	TRUE	0	0.38	2		807	309	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533093	63533093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750354919	NA	P-0003521-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	97	320	2	ENST00000307078.5:c.1801G>A	p.Gly601Ser	p.G601S	ENST00000307078	NM_004655.3	601	Ggc/Agc	7/11	0.234510143912285	3	FACETS	0.828	0.744	0.915	0.828	0.744	0.915	CLONAL	2	TRUE	1	0.38	3		322	367	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133980	41133980	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003521-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	37	475	0	ENST00000379561.5:c.1648T>C	p.Ser550Pro	p.S550P	ENST00000379561	NM_002015.3	550	Tcg/Ccg	2/3	0.311611643117744	3	FACETS	0.367	0.301	0.44	0.122	0.1	0.147	SUBCLONAL	1	TRUE	0	0.38	3		475	632	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353785	68353785	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003521-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	108	265	0	ENST00000487270.1:c.620T>C	p.Val207Ala	p.V207A	ENST00000487270	NM_133509.3	207	gTg/gCg	7/11	0.372702980755233	3	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.38	3		265	491	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743881	40743881	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003521-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	67	285	0	ENST00000373198.4:c.3114G>T	p.Glu1038Asp	p.E1038D	ENST00000373198	NM_133170.3	1038	gaG/gaT	23/32	0.372702980755233	1	FACETS	0.84	0.735	0.952	0.84	0.735	0.952	CLONAL	1	TRUE	0	0.38	1		285	340	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41560049	41560061	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTTCCAGGTTTG	TCTTCCAGGTTTG	-	novel	NA	P-0003521-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	97	281	0	ENST00000263253.7:c.3729-7_3734del		p.X1243_splice	ENST00000263253	NM_001429.3	1243		22/31	0.234510143912285	2	FACETS	1	0.975	1	0.641	0.576	0.71	CLONAL	1	TRUE	0	0.38	2		281	398	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78435674	78435674	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003521-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	39	246	0	ENST00000370768.2:c.146C>G	p.Ala49Gly	p.A49G	ENST00000370768	NM_003902.3	49	gCa/gGa	2/20	0.372702980755233	6	FACETS	0.47	0.388	0.562			1	SUBCLONAL	1	TRUE	NA	0.38	6		246	768	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACAACCCCC	rs397517115	NA	P-0003530-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	51	382	0	ENST00000275493.2:c.2311_2319dup	p.Asn771_His773dup	p.N771_H773dup	ENST00000275493	NM_005228.3	771	gac/gACAACCCCCac	20/28	0.669763335971548	5	FACETS	0.887	0.793	0.979			1	CLONAL	4	TRUE	NA	0.669763335971548	5		382	86	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143063	58143063	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755502728	NA	P-0003530-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	100	212	0	ENST00000257904.6:c.721G>A	p.Asp241Asn	p.D241N	ENST00000257904	NM_000075.3	241	Gat/Aat	7/8	0.669763335971548	35	FACETS	1	0.909	1			1	CLONAL	11	TRUE	NA	0.669763335971548	35		212	325	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775907	9775907	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	272	319	12	ENST00000377346.4:c.371G>A	p.Gly124Asp	p.G124D	ENST00000377346	NM_005026.3	124	gGc/gAc	5/24	0.384393060768211	4	FACETS	1	0.99	1			1	INDETERMINATE	4	TRUE	NA	0.662378840588946	4		331	325	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578499	7578499	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	280	390	14	ENST00000269305.4:c.431del	p.Gln144ArgfsTer26	p.Q144Rfs*26	ENST00000269305	NM_001126112.2	144	cAg/cg	5/11	0.255774147680695	3	FACETS	1	0.988	1	1	0.996	1	INDETERMINATE	3	TRUE	1	0.662378840588946	3		404	357	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712615	52712615	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0003590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	174	247	0	ENST00000394830.3:c.139-2A>G		p.X47_splice	ENST00000394830	NM_018313.4	47			0.544382199302208	1	FACETS	0.977	0.917	1	0.977	0.917	1	CLONAL	1	TRUE	0	0.710837601813065	1		247	323	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106162520	106162520	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	147	259	0	ENST00000380013.4:c.3434G>T	p.Gly1145Val	p.G1145V	ENST00000380013	NM_001127208.2	1145	gGt/gTt	4/11	0.544382199302208	1	FACETS	0.846	0.786	0.907	0.846	0.786	0.907	CLONAL	1	TRUE	0	0.710837601813065	1		259	315	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	510	284	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.214943991254078	13	FACETS	0.993	0.957	1			1	CLONAL	11	FALSE	NA	0.214943991254078	13		284	948	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578433	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555526101	NA	P-0003627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	33	266	0	ENST00000269305.4:c.497C>G	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	166	tCa/tGa	5/11	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	FALSE	1	0.214943991254078	2		266	256	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228613026	228613026	+	start_lost	Translation_Start_Site	SNP	T	T	C	rs146533230	NA	P-0003627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	35	482	0	ENST00000366696.1:c.1A>G	p.Met1?	p.M1?	ENST00000366696	NM_003493.2	1	Atg/Gtg	1/1	0.0756620616251924	4	FACETS	0.912	0.747	1			1	INDETERMINATE	1	FALSE	NA	0.214943991254078	4		482	434	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136270	2136270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1371745883	NA	P-0003627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	19	408	0	ENST00000219476.3:c.4739G>A	p.Arg1580Gln	p.R1580Q	ENST00000219476	NM_000548.3	1580	cGg/cAg	37/42	1	2	FACETS	0.599	0.455	0.769	0.599	0.455	0.769	SUBCLONAL	1	FALSE	1	0.214943991254078	2		408	295	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0003656-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	103	562	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.439697814673774	5	FACETS	0.903	0.82	0.988			1	CLONAL	3	FALSE	NA	0.439697814673774	5		562	287	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0003656-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	62	605	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	0.351629317919966	3	FACETS	0.771	0.676	0.872			1	SUBCLONAL	2	FALSE	NA	0.439697814673774	3		605	223	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150547	157150547	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554256749	NA	P-0003656-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	59	231	0	ENST00000346085.5:c.1729C>T	p.Gln577Ter	p.Q577*	ENST00000346085	NM_020732.3	577	Cag/Tag	2/20	0.439697814673774	5	FACETS	1	0.948	1			1	CLONAL	2	FALSE	NA	0.439697814673774	5		231	191	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692961	89692961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060500122	NA	P-0003656-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	70	289	0	ENST00000371953.3:c.445C>T	p.Gln149Ter	p.Q149*	ENST00000371953	NM_000314.4	149	Caa/Taa	5/9	NA	2	FACETS	1	0.954	1			1	INDETERMINATE	2	FALSE	NA	0.439697814673774	2		289	143	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856020	68856020	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003656-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	67	479	0	ENST00000261769.5:c.1828C>T	p.Gln610Ter	p.Q610*	ENST00000261769	NM_004360.3	610	Cag/Tag	12/16	0.247049381171205	1	FACETS	0.922	0.829	1	1	0.983	1	INDETERMINATE	2	FALSE	0	0.439697814673774	1		479	129	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982779	7982779	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003656-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	46	459	1	ENST00000319144.4:c.1006C>A	p.His336Asn	p.H336N	ENST00000319144	NM_001139.2	336	Cac/Aac	8/15	0.389330438048426	5	FACETS	1	0.93	1	0.761	0.654	0.875	CLONAL	2	FALSE	2	0.439697814673774	5		460	152	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24158967	24158967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003656-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	44	407	0	ENST00000263121.7:c.639G>A	p.Met213Ile	p.M213I	ENST00000263121	NM_003073.3	213	atG/atA	6/9	0.311087499708623	5	FACETS	0.918	0.78	1	0.612	0.52	0.71	CLONAL	2	FALSE	2	0.439697814673774	5		407	181	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176085811	176085811	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0003656-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	71	413	0	ENST00000367669.3:c.975del	p.Ile326LeufsTer28	p.I326Lfs*28	ENST00000367669	NM_022457.5	325	atT/at	9/20	0.439697814673774	8	FACETS	1	0.888	1	0.337	0.296	0.382	CLONAL	2	FALSE	2	0.439697814673774	8		413	370	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223621	55223621	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139429793	NA	P-0003702-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	11	187	0	ENST00000275493.2:c.988G>A	p.Glu330Lys	p.E330K	ENST00000275493	NM_005228.3	330	Gaa/Aaa	8/28	0.313670501470552	1	FACETS	0.645	0.451	0.879	0.645	0.451	0.879	SUBCLONAL	1	TRUE	0	0.330877924540251	1		187	86	SUCCESS
EED	8726	MSKCC	GRCh37	11	85956352	85956352	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003702-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	10	155	0	ENST00000263360.6:c.81G>C	p.Glu27Asp	p.E27D	ENST00000263360	NM_003797.3	27	gaG/gaC	1/12	0.330877924540251	3	FACETS	0.452	0.306	0.633	0.226	0.153	0.317	SUBCLONAL	1	TRUE	1	0.330877924540251	3		155	156	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573988	7573988	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003702-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	43	407	1	ENST00000269305.4:c.1039G>C	p.Ala347Pro	p.A347P	ENST00000269305	NM_001126112.2	347	Gcc/Ccc	10/11	1	2	FACETS	0.788	0.67	0.914	1	0.964	1	CLONAL	2	TRUE	1	0.330877924540251	2		408	165	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123505212	123505212	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003702-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	17	281	0	ENST00000371139.4:c.358G>C	p.Asp120His	p.D120H	ENST00000371139	NM_001114937.2	120	Gat/Cat	4/4	NA	2	FACETS	0.584	0.438	0.756			1	INDETERMINATE	1	TRUE	NA	0.330877924540251	2		281	176	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7152900	7152900	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003702-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	11	252	0	ENST00000302850.5:c.2068G>A	p.Glu690Lys	p.E690K	ENST00000302850	NM_000208.2	690	Gag/Aag	10/22	0.16808250003022	1	FACETS	0.292	0.202	0.404	0.292	0.202	0.404	INDETERMINATE	1	TRUE	0	0.330877924540251	1		252	190	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980832	40980832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465279954	NA	P-0003743-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	29	296	0	ENST00000373198.4:c.1654C>T	p.Leu552Phe	p.L552F	ENST00000373198	NM_133170.3	552	Ctc/Ttc	10/32	0.3	1	FACETS	0.671	0.537	0.824	0.671	0.537	0.824	SUBCLONAL	1	TRUE	0	0.15	1		296	533	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539512	187539512	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003743-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	42	355	0	ENST00000441802.2:c.8228C>T	p.Pro2743Leu	p.P2743L	ENST00000441802	NM_005245.3	2743	cCa/cTa	10/27	0.3	2	FACETS	0.867	0.722	1			1	CLONAL	1	TRUE	NA	0.15	2		355	646	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133761036	133761036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1456042173	NA	P-0003743-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	69	376	1	ENST00000318560.5:c.3359C>T	p.Ser1120Leu	p.S1120L	ENST00000318560	NM_005157.4	1120	tCg/tTg	11/11	0.182956672624471	2	FACETS	0.983	0.858	1	0.983	0.858	1	CLONAL	2	TRUE	0	0.15	2		377	468	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115874	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752977342	NA	P-0003743-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	34	383	0	ENST00000346208.3:c.1220C>T	p.Ser407Leu	p.S407L	ENST00000346208		407	tCg/tTg	6/6	1	2	FACETS	0.776	0.633	0.938	0.776	0.633	0.938	CLONAL	1	TRUE	1	0.15	2		383	584	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402169	402169	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003743-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	80	586	0	ENST00000399788.2:c.4622G>C	p.Gly1541Ala	p.G1541A	ENST00000399788	NM_001042603.1	1541	gGt/gCt	27/28	0.3	2	FACETS	0.871	0.764	0.987			1	CLONAL	1	TRUE	NA	0.15	2		586	1224	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716431	18716431	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003743-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	36	291	0	ENST00000266497.5:c.3778G>A	p.Glu1260Lys	p.E1260K	ENST00000266497		1260	Gag/Aag	26/31	0.3	2	FACETS	0.679	0.556	0.817			1	SUBCLONAL	1	TRUE	NA	0.15	2		291	707	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120535069	120535069	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003743-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	71	549	0	ENST00000229340.5:c.586C>T	p.Arg196Ter	p.R196*	ENST00000229340	NM_006861.6	196	Cga/Tga	6/6	0.3	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.15	1		549	723	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572483	95572483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003743-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	48	255	0	ENST00000393063.1:c.2882C>T	p.Pro961Leu	p.P961L	ENST00000393063	NM_030621.3	961	cCt/cTt	19/28	1	2	FACETS	0.703	0.592	0.826	0.703	0.592	0.826	SUBCLONAL	1	TRUE	1	0.15	2		255	910	SUCCESS
AR	367	MSKCC	GRCh37	X	66765655	66765655	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1036966197	NA	P-0003743-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	47	243	0	ENST00000374690.3:c.667G>A	p.Asp223Asn	p.D223N	ENST00000374690	NM_000044.3	223	Gac/Aac	1/8	1	1	FACETS	0.816	0.691	0.953	1	0.966	1	CLONAL	2	TRUE	0	0.15	1		243	355	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205160	128205160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003745-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	90	632	0	ENST00000341105.2:c.281G>A	p.Gly94Asp	p.G94D	ENST00000341105	NM_032638.4	94	gGt/gAt	3/6	1	2	FACETS	0.672	0.595	0.755	0.672	0.595	0.755	SUBCLONAL	1	TRUE	1	0.277386010496205	2		632	965	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003781-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	26	333	0				ENST00000310581	NM_198253.2	-/1132			0.14526794066047	1	FACETS	0.863	0.687	1	0.863	0.687	1	CLONAL	1	TRUE	0	0.229863854372053	1		333	232	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003781-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	45	162	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	TRUE	1	0.229863854372053	2		162	390	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237686	133237686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142563997	NA	P-0003781-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	101	597	0	ENST00000320574.5:c.2929G>A	p.Gly977Arg	p.G977R	ENST00000320574	NM_006231.2	977	Ggg/Agg	25/49	1	2	FACETS	0.823	0.734	0.918	0.823	0.734	0.918	CLONAL	1	TRUE	1	0.229863854372053	2		597	1068	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657517	29657517	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs876658854	NA	P-0003781-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	41	181	0	ENST00000356175.3:c.5749+1G>A		p.X1917_splice	ENST00000356175	NM_000267.3	1917			0.229863854372053	1	FACETS	0.723	0.602	0.856	0.723	0.602	0.856	SUBCLONAL	1	TRUE	0	0.229863854372053	1		181	437	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003866-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	124	284	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	FALSE	1	0.445555558020061	2		284	540	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003866-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	122	486	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.445555558020061	1	FACETS	0.367	0.331	0.406	0.367	0.331	0.406	SUBCLONAL	1	FALSE	0	0.445555558020061	1		486	1159	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870839	12870840	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0003866-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	73	284	0	ENST00000228872.4:c.67dup	p.His23ProfsTer102	p.H23Pfs*102	ENST00000228872	NM_004064.3	22	-/C	1/3	0.445555558020061	1	FACETS	0.887	0.784	0.996	0.887	0.784	0.996	CLONAL	1	FALSE	0	0.445555558020061	1		284	287	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003866-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	32	825	0	ENST00000206249.3:c.1609T>C	p.Tyr537His	p.Y537H	ENST00000206249	NM_000125.3	537	Tat/Cat	8/8	0.445555558020061	1	FACETS	0.096	0.077	0.118	0.096	0.077	0.118	SUBCLONAL	1	FALSE	0	0.445555558020061	1		825	1162	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005333	150005333	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003866-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	134	651	0	ENST00000253339.5:c.892G>C	p.Glu298Gln	p.E298Q	ENST00000253339		298	Gag/Cag	3/7	0.445555558020061	1	FACETS	0.458	0.416	0.503	0.458	0.416	0.503	SUBCLONAL	1	FALSE	0	0.445555558020061	1		651	1020	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003866-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	214	284	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	0.68871779997725	2		284	587	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003866-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	188	486	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.68871779997725	1	FACETS	0.612	0.569	0.656	0.612	0.569	0.656	SUBCLONAL	1	TRUE	0	0.68871779997725	1		486	585	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870839	12870840	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0003866-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	69	284	0	ENST00000228872.4:c.67dup	p.His23ProfsTer102	p.H23Pfs*102	ENST00000228872	NM_004064.3	22	-/C	1/3	0.68871779997725	1	FACETS	0.882	0.79	0.974	0.882	0.79	0.974	CLONAL	1	TRUE	0	0.68871779997725	1		284	149	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005333	150005333	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003866-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	215	651	0	ENST00000253339.5:c.892G>C	p.Glu298Gln	p.E298Q	ENST00000253339		298	Gag/Cag	3/7	0.68871779997725	1	FACETS	0.74	0.694	0.788	0.74	0.694	0.788	SUBCLONAL	1	TRUE	0	0.68871779997725	1		651	553	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4123815	4123815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003866-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	176	402	0	ENST00000262948.5:c.58G>A	p.Glu20Lys	p.E20K	ENST00000262948	NM_030662.3	20	Gag/Aag	1/11	1	2	FACETS	0.659	0.608	0.712	0.659	0.608	0.712	SUBCLONAL	1	TRUE	1	0.68871779997725	2		402	775	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070577	67070578	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0003918-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	122	551	0	ENST00000412916.2:c.207dup	p.Pro70SerfsTer13	p.P70Sfs*13	ENST00000412916		67	-/T	3/6	1	2	FACETS	0.994	0.896	1	0.994	0.896	1	CLONAL	1	TRUE	1	0.210740354393577	2		551	1165	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443576	29443576	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750194005	NA	P-0003918-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	45	270	0	ENST00000389048.3:c.3641G>A	p.Arg1214His	p.R1214H	ENST00000389048	NM_004304.4	1214	cGc/cAc	23/29	1	2	FACETS	0.913	0.767	1	0.913	0.767	1	CLONAL	1	TRUE	1	0.210740354393577	2		270	468	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246666	46246666	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003918-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	82	84	0	ENST00000334344.6:c.4760A>G	p.Asn1587Ser	p.N1587S	ENST00000334344	NM_152641.2	1587	aAt/aGt	15/21	0.210740354393577	4	FACETS	1	0.896	1			1	CLONAL	3	TRUE	NA	0.210740354393577	4		84	312	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846130	68846131	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003918-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	110	544	0	ENST00000261769.5:c.1102dup	p.Thr368AsnfsTer4	p.T368Nfs*4	ENST00000261769	NM_004360.3	367	-/A	8/16	0.210740354393577	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.210740354393577	1		544	908	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641188	117641188	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003929-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	131	483	0	ENST00000368508.3:c.5783T>C	p.Leu1928Pro	p.L1928P	ENST00000368508	NM_002944.2	1928	cTt/cCt	36/43	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.233950198926829	2		483	852	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199594	138199594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003929-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	66	244	0	ENST00000237289.4:c.1012G>A	p.Glu338Lys	p.E338K	ENST00000237289	NM_001270507.1	338	Gaa/Aaa	7/9	0.233950198926829	6	FACETS	1	0.966	1			1	CLONAL	1	TRUE	NA	0.233950198926829	6		244	605	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428260	33428260	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003929-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	68	265	0	ENST00000345365.6:c.863G>A	p.Gly288Asp	p.G288D	ENST00000345365	NM_002878.3	288	gGc/gAc	9/10	0.233950198926829	2	FACETS	0.866	0.753	0.989	0.433	0.376	0.495	CLONAL	1	TRUE	0	0.233950198926829	2		265	671	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0003933-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	301	248	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.961	0.907	1	0.961	0.907	1	CLONAL	1	TRUE	1	0.681922016783809	2		248	919	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856020	68856020	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003933-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	359	479	0	ENST00000261769.5:c.1828C>T	p.Gln610Ter	p.Q610*	ENST00000261769	NM_004360.3	610	Cag/Tag	12/16	0.681922016783809	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.681922016783809	1		479	676	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851325	156851325	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201891311	NA	P-0003933-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	161	296	2	ENST00000524377.1:c.2282G>A	p.Arg761Gln	p.R761Q	ENST00000524377	NM_002529.3	761	cGg/cAg	17/17	0.50195592535486	3	FACETS	0.813	0.747	0.882			1	CLONAL	1	TRUE	NA	0.681922016783809	3		298	779	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945694	38945694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1175194099	NA	P-0003933-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	413	370	0	ENST00000357387.3:c.4532G>A	p.Gly1511Glu	p.G1511E	ENST00000357387	NM_152756.3	1511	gGa/gAa	34/38	NA	2	FACETS	0.948	0.903	0.994			1	INDETERMINATE	1	TRUE	NA	0.681922016783809	2		370	1278	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003943-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	217	284	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.864242925715523	3	FACETS	0.87	0.81	0.931	0.435	0.405	0.466	CLONAL	1	TRUE	1	0.864242925715523	3		284	827	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0003943-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	203	281	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.864242925715523	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.864242925715523	1		281	244	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288936	11288936	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003943-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	177	233	0	ENST00000361445.4:c.2819A>C	p.Asn940Thr	p.N940T	ENST00000361445	NM_004958.3	940	aAc/aCc	19/58	1	2	FACETS	0.929	0.865	0.993	0.929	0.865	0.993	CLONAL	1	TRUE	1	0.864242925715523	2		233	441	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731154	162731154	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003943-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	418	467	0	ENST00000367921.3:c.1009C>A	p.Pro337Thr	p.P337T	ENST00000367921	NM_006182.2	337	Cct/Act	9/18	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.864242925715523	2		467	919	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170915	99170915	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs750621338	NA	P-0003943-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	232	345	0	ENST00000074304.5:c.1544G>T	p.Arg515Leu	p.R515L	ENST00000074304	NM_001134224.1	515	cGa/cTa	16/26	1	2	FACETS	0.998	0.94	1	0.998	0.94	1	CLONAL	1	TRUE	1	0.864242925715523	2		345	538	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205868	128205868	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003943-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	42	184	0	ENST00000341105.2:c.7G>C	p.Val3Leu	p.V3L	ENST00000341105	NM_032638.4	3	Gtg/Ctg	2/6	0.864242925715523	3	FACETS	0.819	0.694	0.953	0.409	0.347	0.477	CLONAL	1	TRUE	1	0.864242925715523	3		184	170	SUCCESS
FIP1L1	81608	MSKCC	GRCh37	4	54280853	54280853	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003943-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	387	290	0	ENST00000358575.5:c.842A>T	p.Gln281Leu	p.Q281L	ENST00000358575	NM_001134937.1	281	cAg/cTg	10/18	0.308174626413287	1	FACETS	0.508	0.483	0.532	0.508	0.483	0.532	INDETERMINATE	1	TRUE	0	0.864242925715523	1		290	1002	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592128	55592128	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003943-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	415	379	0	ENST00000288135.5:c.1452G>T	p.Lys484Asn	p.K484N	ENST00000288135	NM_000222.2	484	aaG/aaT	9/21	0.308174626413287	1	FACETS	0.597	0.571	0.623	0.597	0.571	0.623	INDETERMINATE	1	TRUE	0	0.864242925715523	1		379	913	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508364	106508364	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003943-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	92	114	0	ENST00000359195.3:c.358G>T	p.Asp120Tyr	p.D120Y	ENST00000359195	NM_002649.2	120	Gac/Tac	2/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.864242925715523	2		114	172	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637031	93637031	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0003943-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	350	334	0	ENST00000375746.1:c.1081A>T	p.Lys361Ter	p.K361*	ENST00000375746	NM_001174167.1	361	Aag/Tag	9/14	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.864242925715523	2		334	749	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	463306	463306	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003943-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	459	467	0	ENST00000399788.2:c.965G>T	p.Cys322Phe	p.C322F	ENST00000399788	NM_001042603.1	322	tGt/tTt	8/28	0.864242925715523	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.864242925715523	1		467	581	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254668	46254668	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003943-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	467	411	0	ENST00000334344.6:c.4858C>T	p.Gln1620Ter	p.Q1620*	ENST00000334344	NM_152641.2	1620	Cag/Tag	16/21	NA	2	FACETS	0.947	0.907	0.987			1	INDETERMINATE	1	TRUE	NA	0.864242925715523	2		411	1141	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039190	49039190	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0003943-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	474	294	0	ENST00000267163.4:c.2268T>G	p.Tyr756Ter	p.Y756*	ENST00000267163	NM_000321.2	756	taT/taG	22/27	0.864242925715523	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.864242925715523	1		294	589	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019385	31019385	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs74414530	NA	P-0003943-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	313	386	1	ENST00000375687.4:c.883-1G>A		p.X295_splice	ENST00000375687	NM_015338.5	295			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.864242925715523	2		387	709	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429027	47429027	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003943-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	207	434	2	ENST00000377045.4:c.1390G>T	p.Glu464Ter	p.E464*	ENST00000377045	NM_001654.4	464	Gag/Tag	13/16	0.415974102904555	1	FACETS	0.53	0.497	0.564	0.53	0.497	0.564	INDETERMINATE	1	TRUE	0	0.864242925715523	1		436	513	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222362	53222362	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003943-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	214	569	0	ENST00000375401.3:c.4470G>T	p.Glu1490Asp	p.E1490D	ENST00000375401	NM_004187.3	1490	gaG/gaT	26/26	0.415974102904555	1	FACETS	0.572	0.537	0.607	0.572	0.537	0.607	INDETERMINATE	1	TRUE	0	0.864242925715523	1		569	492	SUCCESS
APC	324	MSKCC	GRCh37	5	112175315	112175319	+	frameshift_variant	Frame_Shift_Del	DEL	TTATC	TTATC	-	novel	NA	P-0003943-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	196	262	0	ENST00000257430.4:c.4026_4030del	p.Leu1342PhefsTer10	p.L1342Ffs*10	ENST00000257430	NM_000038.5	1342	TTATCt/t	16/16	0.864242925715523	1	FACETS	0.847	0.804	0.89	0.847	0.804	0.89	CLONAL	1	TRUE	0	0.864242925715523	1		262	304	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657442	29657442	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003947-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	290	610	0	ENST00000356175.3:c.5675A>T	p.Lys1892Met	p.K1892M	ENST00000356175	NM_000267.3	1892	aAg/aTg	38/57	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.580467984971939	2		610	926	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881414	37881414	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1131692237	NA	P-0003947-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	137	295	2	ENST00000269571.5:c.2606T>G	p.Leu869Arg	p.L869R	ENST00000269571		869	cTg/cGg	21/27	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.580467984971939	2		297	444	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061101	38061135	+	frameshift_variant	Frame_Shift_Del	DEL	GTCCTTGCGGCTCTCAGGGCCGCCCTTGGCGCCGC	GTCCTTGCGGCTCTCAGGGCCGCCCTTGGCGCCGC	-	novel	NA	P-0003947-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	19	63	0	ENST00000250448.2:c.854_888del	p.Ser285ThrfsTer6	p.S285Tfs*6	ENST00000250448	NM_004496.3	285	aGCGGCGCCAAGGGCGGCCCTGAGAGCCGCAAGGAC/a	2/2	1	2	FACETS	0.682	0.527	0.857	0.682	0.527	0.857	SUBCLONAL	1	TRUE	1	0.580467984971939	2		63	96	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862143	68862144	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003947-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	230	482	0	ENST00000261769.5:c.2232dup	p.Glu745ArgfsTer3	p.E745Rfs*3	ENST00000261769	NM_004360.3	744	cca/ccAa	14/16	0.580467984971939	1	FACETS	0.975	0.916	1	0.975	0.916	1	CLONAL	1	TRUE	0	0.580467984971939	1		482	577	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003958-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	26	486	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.667094737588866	1	FACETS	0.167	0.132	0.206	0.167	0.132	0.206	SUBCLONAL	1	TRUE	0	0.667094737588866	1		486	312	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003958-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	144	502	0	ENST00000206249.3:c.1610A>G	p.Tyr537Cys	p.Y537C	ENST00000206249	NM_000125.3	537	tAt/tGt	8/8	0.667094737588866	1	FACETS	0.931	0.864	0.999	0.931	0.864	0.999	CLONAL	1	TRUE	0	0.667094737588866	1		502	309	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873888	151873888	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003958-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	82	802	0	ENST00000262189.6:c.8650C>T	p.Arg2884Ter	p.R2884*	ENST00000262189	NM_170606.2	2884	Cga/Tga	38/59	0.202461752556636	5	FACETS	0.536	0.471	0.605	0.179	0.157	0.202	INDETERMINATE	1	TRUE	2	0.667094737588866	5		802	918	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100613	67100613	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003958-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	371	846	2	ENST00000412916.2:c.311A>G	p.Asn104Ser	p.N104S	ENST00000412916		104	aAt/aGt	4/6	0.667094737588866	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.667094737588866	1		848	594	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891104	151891104	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003958-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	54	528	0	ENST00000262189.6:c.4650del	p.His1551ThrfsTer12	p.H1551Tfs*12	ENST00000262189	NM_170606.2	1550	atA/at	31/59	0.202461752556636	5	FACETS	0.378	0.322	0.44	0.126	0.107	0.147	INDETERMINATE	1	TRUE	2	0.667094737588866	5		528	856	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842343	68842344	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0003958-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	333	983	0	ENST00000261769.5:c.406dup	p.Gln136ProfsTer32	p.Q136Pfs*32	ENST00000261769	NM_004360.3	135	atc/atCc	4/16	0.667094737588866	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.667094737588866	1		983	639	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115873	8115874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0003961-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	231	472	0	ENST00000346208.3:c.1220dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tCcg	6/6	0.384180370104076	6	FACETS	1	0.98	1	0.827	0.776	0.879	CLONAL	3	TRUE	2	0.384180370104076	6		472	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579345	7579346	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003977-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	81	408	0	ENST00000269305.4:c.341dup	p.Leu114PhefsTer35	p.L114Ffs*35	ENST00000269305	NM_001126112.2	114	ttg/ttTg	4/11	0.334250192065284	1	FACETS	0.632	0.557	0.712	0.632	0.557	0.712	SUBCLONAL	1	TRUE	0	0.334250192065284	1		408	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0003978-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	360	311	6	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.962576017456701	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.962576017456701	1		317	385	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401426	139401426	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003978-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	357	172	2	ENST00000277541.6:c.3644-1G>A		p.X1215_splice	ENST00000277541	NM_017617.3	1215			0.962576017456701	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.962576017456701	2		174	369	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955502	48955502	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003978-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	539	408	6	ENST00000267163.4:c.1619del	p.Gly540AlafsTer3	p.G540Afs*3	ENST00000267163	NM_000321.2	540	Ggc/gc	17/27	0.962576017456701	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.962576017456701	1		414	573	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469672	NA	P-0003980-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	341	426	0	ENST00000374080.3:c.131G>A	p.Gly44Asp	p.G44D	ENST00000374080		44	gGt/gAt	2/45	0.106473672169394	0	FACETS	0.534	0.507	0.563			1	INDETERMINATE	1	TRUE	0	0.561630346859976	0		426	996	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0003980-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	184	342	0	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.561630346859976	2		342	648	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0003982-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	49	170	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.292451913235808	4	FACETS	0.875	0.756	1	0.583	0.504	0.667	INDETERMINATE	2	TRUE	1	0.56	4		170	156	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0003982-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	80	446	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.21416434697521	0	FACETS	0.364	0.323	0.408			1	INDETERMINATE	1	TRUE	0	0.56	0		446	345	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560464	95560464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003982-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	25	102	0	ENST00000393063.1:c.5125G>A	p.Asp1709Asn	p.D1709N	ENST00000393063	NM_030621.3	1709	Gat/Aat	25/28	1	2	FACETS	0.72	0.576	0.88	0.72	0.576	0.88	SUBCLONAL	1	TRUE	1	0.56	2		102	124	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591282	67591282	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003982-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	25	156	0	ENST00000274335.5:c.1780T>G	p.Leu594Val	p.L594V	ENST00000274335		594	Ttg/Gtg	13/15	1	2	FACETS	0.562	0.447	0.69	0.562	0.447	0.69	SUBCLONAL	1	TRUE	1	0.56	2		156	159	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054569	5054569	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003982-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	27	155	0	ENST00000381652.3:c.621G>C	p.Lys207Asn	p.K207N	ENST00000381652	NM_004972.3	207	aaG/aaC	7/25	1	2	FACETS	0.994	0.81	1	0.994	0.81	1	CLONAL	1	TRUE	1	0.56	2		155	97	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37856540	37856540	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1307888184	NA	P-0003982-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	86	259	0	ENST00000269571.5:c.49C>T	p.Pro17Ser	p.P17S	ENST00000269571		17	Ccc/Tcc	1/27	1	2	FACETS	0.991	0.886	1	0.991	0.886	1	CLONAL	1	TRUE	1	0.56	2		259	310	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105611	27105612	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0003982-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	34	307	0	ENST00000324856.7:c.5225_5226del	p.Arg1742AsnfsTer13	p.R1742Nfs*13	ENST00000324856	NM_006015.4	1741	cAG/c	20/20	0.164586813520297	3	FACETS	0.703	0.579	0.841	0.352	0.289	0.421	INDETERMINATE	1	TRUE	1	0.56	3		307	221	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562482	21562483	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGGCG	rs550642106	NA	P-0003983-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	11	69	0	ENST00000382592.4:c.1431_1436dup	p.Pro479_Ala480dup	p.P479_A480dup	ENST00000382592	NM_014572.2	479	ccg/ccCGCCCCg	4/8	1	2	FACETS	0.7	0.486	0.964	0.7	0.486	0.964	SUBCLONAL	1	TRUE	1	0.219720747923973	2		69	143	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0003983-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	232	471	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.219720747923973	3	FACETS	0.903	0.844	0.964	1	0.99	1	CLONAL	3	TRUE	1	0.219720747923973	3		471	865	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858992	243858992	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003983-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	110	549	0	ENST00000263826.5:c.73A>G	p.Arg25Gly	p.R25G	ENST00000263826	NM_005465.4	25	Aga/Gga	2/13	0.175535855745821	2	FACETS	0.83	0.748	0.917	0.83	0.748	0.917	CLONAL	2	TRUE	0	0.219720747923973	2		549	603	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278100	41278100	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003983-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1228	191	812	0	ENST00000349496.5:c.1976T>C	p.Leu659Ser	p.L659S	ENST00000349496	NM_001904.3	659	tTg/tCg	13/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.219720747923973	2		812	1419	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259526	89259526	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003983-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	127	614	0	ENST00000336596.2:c.670G>T	p.Val224Leu	p.V224L	ENST00000336596	NM_005233.5	224	Gtg/Ttg	3/17	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.219720747923973	2		614	944	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258979	153258979	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003983-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	52	721	0	ENST00000281708.4:c.836A>G	p.Asp279Gly	p.D279G	ENST00000281708	NM_033632.3	279	gAc/gGc	5/12	1	2	FACETS	0.679	0.577	0.791	0.679	0.577	0.791	SUBCLONAL	1	TRUE	1	0.219720747923973	2		721	697	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959365	38959365	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003983-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	68	669	0	ENST00000357387.3:c.2110A>G	p.Ser704Gly	p.S704G	ENST00000357387	NM_152756.3	704	Agc/Ggc	22/38	1	2	FACETS	0.731	0.634	0.836	0.731	0.634	0.836	SUBCLONAL	1	TRUE	1	0.219720747923973	2		669	847	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781181	161781181	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003983-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	82	815	0	ENST00000366898.1:c.1224A>C	p.Lys408Asn	p.K408N	ENST00000366898	NM_004562.2	408	aaA/aaC	11/12	1	2	FACETS	0.614	0.54	0.695	0.614	0.54	0.695	SUBCLONAL	1	TRUE	1	0.219720747923973	2		815	1215	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080600	5080600	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003983-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1239	90	819	0	ENST00000381652.3:c.2351T>G	p.Ile784Arg	p.I784R	ENST00000381652	NM_004972.3	784	aTa/aGa	18/25	1	2	FACETS	0.616	0.545	0.694	0.616	0.545	0.694	SUBCLONAL	1	TRUE	1	0.219720747923973	2		819	1329	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434428	110434428	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003983-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	156	692	0	ENST00000375856.3:c.3973T>G	p.Phe1325Val	p.F1325V	ENST00000375856	NM_003749.2	1325	Ttc/Gtc	1/2	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.219720747923973	2		692	1252	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944487	40944487	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003983-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	79	770	0	ENST00000373198.4:c.2015A>G	p.Asn672Ser	p.N672S	ENST00000373198	NM_133170.3	672	aAc/aGc	12/32	NA	2	FACETS	0.578	0.506	0.655			1	INDETERMINATE	1	TRUE	NA	0.219720747923973	2		770	1245	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0004015-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	82	320	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.821	0.724	0.926	0.821	0.724	0.926	CLONAL	1	TRUE	1	0.26	2		320	768	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6439806	6439806	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004015-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	123	268	0	ENST00000356142.4:c.332A>T	p.Asn111Ile	p.N111I	ENST00000356142	NM_018890.3	111	aAt/aTt	5/7	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.26	2		268	727	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424418	49424418	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004015-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	57	331	0	ENST00000301067.7:c.13805C>G	p.Thr4602Ser	p.T4602S	ENST00000301067	NM_003482.3	4602	aCt/aGt	41/54	1	2	FACETS	0.652	0.558	0.754	0.652	0.558	0.754	SUBCLONAL	1	TRUE	1	0.26	2		331	673	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610105	81610105	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004015-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	79	250	0	ENST00000298171.2:c.1703T>C	p.Ile568Thr	p.I568T	ENST00000298171	NM_000369.2	568	aTc/aCc	10/10	1	2	FACETS	0.921	0.81	1	0.921	0.81	1	CLONAL	1	TRUE	1	0.26	2		250	660	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156732	20156732	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004015-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	119	199	0	ENST00000379607.5:c.25G>C	p.Gly9Arg	p.G9R	ENST00000379607	NM_001412.3	9	Ggt/Cgt	2/7	1	1	FACETS	0.959	0.873	1	1	0.989	1	CLONAL	2	TRUE	0	0.26	1		199	415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578207	+	missense_variant	Missense_Mutation	TNP	CTA	CTA	TTT	novel	NA	P-0004015-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	92	392	0	ENST00000269305.4:c.642_644delinsAAA	p.His214_Ser215delinsGlnAsn	p.H214_S215delinsQN	ENST00000269305	NM_001126112.2	214	caTAGt/caAAAt	6/11	0.299993634852178	1	FACETS	0.787	0.699	0.882	0.787	0.699	0.882	SUBCLONAL	1	TRUE	0	0.26	1		392	782	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0004018-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	216	274	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.108401926935476	4	FACETS	0.824	0.77	0.878	0.824	0.77	0.878	INDETERMINATE	2	TRUE	2	0.694233956654014	4		274	640	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0004018-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	422	430	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.171917106186018	1	FACETS	1	0.995	1	1	0.995	1	INDETERMINATE	1	TRUE	0	0.694233956654014	1		430	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0004018-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	247	463	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.694233956654014	1	FACETS	0.962	0.911	1	0.962	0.911	1	CLONAL	1	TRUE	0	0.694233956654014	1		463	483	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31369176	31369176	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760640013	NA	P-0004018-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	230	399	0	ENST00000328111.2:c.160C>T	p.Arg54Ter	p.R54*	ENST00000328111	NM_006892.3	54	Cga/Tga	3/23	1	2	FACETS	0.979	0.917	1	0.979	0.917	1	CLONAL	1	TRUE	1	0.694233956654014	2		399	677	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0004018-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	134	147	1	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	0.108401926935476	4	FACETS	0.826	0.758	0.895	0.826	0.758	0.895	INDETERMINATE	2	TRUE	2	0.694233956654014	4		148	396	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004018-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	263	411	0	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	0.694233956654014	1	FACETS	0.933	0.885	0.982	0.933	0.885	0.982	CLONAL	1	TRUE	0	0.694233956654014	1		411	530	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675646	30675646	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004018-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	215	678	0	ENST00000376406.3:c.2710C>G	p.Gln904Glu	p.Q904E	ENST00000376406	NM_014641.2	904	Caa/Gaa	8/15	0.368070915352682	3	FACETS	1	0.976	1	0.55	0.513	0.589	INDETERMINATE	1	TRUE	1	0.694233956654014	3		678	758	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840622	36840622	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004018-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	68	284	0	ENST00000358127.4:c.1111T>G	p.Tyr371Asp	p.Y371D	ENST00000358127	NM_001280556.1	371	Tat/Gat	10/10	0.611517859744823	3	FACETS	0.453	0.394	0.517	0.227	0.197	0.259	SUBCLONAL	1	TRUE	1	0.694233956654014	3		284	582	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245795	5245795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368461283	NA	P-0004018-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	120	261	0	ENST00000357368.4:c.980C>T	p.Thr327Met	p.T327M	ENST00000357368	NM_002850.3	327	aCg/aTg	10/38	1	2	FACETS	0.937	0.855	1	0.937	0.855	1	CLONAL	1	TRUE	1	0.694233956654014	2		261	369	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164616	36164616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1442265949	NA	P-0004018-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	157	291	0	ENST00000300305.3:c.1259G>A	p.Gly420Asp	p.G420D	ENST00000300305		420	gGc/gAc	8/8	0.368070915352682	3	FACETS	1	0.975	1	0.569	0.525	0.616	INDETERMINATE	1	TRUE	1	0.694233956654014	3		291	535	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514857	44514857	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004018-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	300	408	0	ENST00000291552.4:c.390G>C	p.Leu130Phe	p.L130F	ENST00000291552	NM_006758.2	130	ttG/ttC	6/8	NA	2	FACETS	1	0.963	1			1	INDETERMINATE	1	TRUE	NA	0.694233956654014	2		408	844	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652398	48652398	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004018-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	200	277	0	ENST00000376670.3:c.1069C>T	p.Pro357Ser	p.P357S	ENST00000376670	NM_002049.3	357	Ccc/Tcc	6/6	0.318931875798049	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	NA	0.694233956654014	0		277	299	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125034	46125035	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0004031-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	131	624	0	ENST00000334344.6:c.221_222del	p.Glu74GlyfsTer10	p.E74Gfs*10	ENST00000334344	NM_152641.2	74	gAA/g	3/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.457100540275222	2		624	433	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741502	145741502	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004031-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	90	617	0	ENST00000428558.2:c.1001A>T	p.Glu334Val	p.E334V	ENST00000428558	NM_004260.3	334	gAg/gTg	5/22	0.288090821522527	5	FACETS	0.858	0.773	0.945	0.858	0.773	0.945	CLONAL	3	TRUE	2	0.457100540275222	5		617	258	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115714	8115717	+	frameshift_variant	Frame_Shift_Del	DEL	CTGA	CTGA	-	novel	NA	P-0004031-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	104	570	0	ENST00000346208.3:c.1062_1065del	p.Thr355Ter	p.T355*	ENST00000346208		354	CTGAct/ct	6/6	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.457100540275222	2		570	331	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230746	46230746	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004031-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	99	525	0	ENST00000334344.6:c.996del	p.Asp333ThrfsTer3	p.D333Tfs*3	ENST00000334344	NM_152641.2	332	cTt/ct	8/21	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.457100540275222	2		525	304	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0004050-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	71	344	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	0.508412163125206	3	FACETS	0.803	0.704	0.909	0.402	0.352	0.455	CLONAL	1	TRUE	1	0.56730181108722	3		344	400	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163971	47163971	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs115859828	NA	P-0004050-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	144	324	0	ENST00000409792.3:c.2155A>G	p.Asn719Asp	p.N719D	ENST00000409792	NM_014159.6	719	Aat/Gat	3/21	0.508412163125206	3	FACETS	0.867	0.8	0.934	0.867	0.8	0.934	CLONAL	2	TRUE	1	0.56730181108722	3		324	376	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239915	53239915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004050-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	173	267	0	ENST00000375401.3:c.1526C>T	p.Ser509Leu	p.S509L	ENST00000375401	NM_004187.3	509	tCa/tTa	11/26	0.56730181108722	2	FACETS	1	0.987	1			1	CLONAL	2	TRUE	NA	0.56730181108722	2		267	263	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014379	70014379	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004050-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	36	158	0	ENST00000394351.3:c.1240G>T	p.Glu414Ter	p.E414*	ENST00000394351	NM_000248.3	414	Gag/Tag	9/9	0.508412163125206	3	FACETS	0.942	0.784	1	0.471	0.392	0.557	CLONAL	1	TRUE	1	0.56730181108722	3		158	173	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259064	89259064	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004050-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	40	238	0	ENST00000336596.2:c.208G>C	p.Val70Leu	p.V70L	ENST00000336596	NM_005233.5	70	Gtg/Ctg	3/17	0.508412163125206	3	FACETS	0.724	0.606	0.854	0.362	0.303	0.427	SUBCLONAL	1	TRUE	1	0.56730181108722	3		238	250	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160718	56160718	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004050-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	102	395	0	ENST00000399503.3:c.992G>T	p.Gly331Val	p.G331V	ENST00000399503	NM_005921.1	331	gGa/gTa	4/20	0.112619353177765	4	FACETS	0.883	0.799	0.97	0.883	0.799	0.97	INDETERMINATE	2	TRUE	2	0.56730181108722	4		395	319	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36846853	36846853	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004050-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	65	336	1	ENST00000358127.4:c.1086C>A	p.Asn362Lys	p.N362K	ENST00000358127	NM_001280556.1	362	aaC/aaA	9/10	0.354543881107174	3	FACETS	0.937	0.818	1			1	CLONAL	1	TRUE	NA	0.56730181108722	3		337	314	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953623	32953623	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004050-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	52	211	0	ENST00000380152.3:c.8924T>C	p.Val2975Ala	p.V2975A	ENST00000380152		2975	gTa/gCa	22/27	0.286647849262081	3	FACETS	1	0.927	1	0.56	0.483	0.643	INDETERMINATE	1	TRUE	1	0.56730181108722	3		211	210	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782082	NA	P-0004050-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	161	256	0	ENST00000269305.4:c.745A>T	p.Arg249Trp	p.R249W	ENST00000269305	NM_001126112.2	249	Agg/Tgg	7/11	0.0999541389781993	4	FACETS	1	0.969	1			1	INDETERMINATE	3	TRUE	NA	0.56730181108722	4		256	282	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918491	44918491	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0004050-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	240	259	0	ENST00000377967.4:c.975-1G>A		p.X325_splice	ENST00000377967	NM_021140.2	325			0.56730181108722	2	FACETS	0.852	0.817	0.886			1	CLONAL	3	TRUE	NA	0.56730181108722	2		259	331	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937980	76937980	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004050-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	105	266	0	ENST00000373344.5:c.2768A>C	p.Lys923Thr	p.K923T	ENST00000373344	NM_000489.3	923	aAg/aCg	9/35	0.29130452770393	0	FACETS	0.861	0.795	0.926			1	INDETERMINATE	1	TRUE	NA	0.56730181108722	0		266	186	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0004072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	98	618	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.249677669613966	2	FACETS	1	0.962	1	0.583	0.521	0.648	CLONAL	1	TRUE	0	0.290537293845173	2		619	579	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106648	27106648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553153748	NA	P-0004072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	249	288	0	ENST00000324856.7:c.6259G>A	p.Gly2087Arg	p.G2087R	ENST00000324856	NM_006015.4	2087	Gga/Aga	20/20	0.249677669613966	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.290537293845173	2		288	766	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259476	89259476	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs763655362	NA	P-0004072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	91	315	0	ENST00000336596.2:c.620A>G	p.Lys207Arg	p.K207R	ENST00000336596	NM_005233.5	207	aAg/aGg	3/17	0.281453734303767	3	FACETS	1	0.892	1	0.502	0.446	0.563	CLONAL	1	TRUE	1	0.290537293845173	3		315	714	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169272	32169272	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	135	188	0	ENST00000375023.3:c.3761C>A	p.Ala1254Asp	p.A1254D	ENST00000375023	NM_004557.3	1254	gCc/gAc	22/30	0.290485767191911	4	FACETS	0.873	0.795	0.954	0.873	0.795	0.954	CLONAL	2	TRUE	2	0.290537293845173	4		188	687	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411930	116411930	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	172	244	0	ENST00000397752.3:c.2915A>C	p.Asp972Ala	p.D972A	ENST00000397752	NM_000245.2	972	gAt/gCt	14/21	0.281453734303767	3	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	1	0.290537293845173	3		244	661	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727454	66727454	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519909	NA	P-0004072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	17	276	0	ENST00000307102.5:c.170A>C	p.Lys57Thr	p.K57T	ENST00000307102	NM_002755.3	57	aAg/aCg	2/11	0.249677669613966	2	FACETS	0.192	0.142	0.251	0.096	0.071	0.126	SUBCLONAL	1	TRUE	0	0.290537293845173	2		276	611	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299062	15299062	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	177	315	0	ENST00000263388.2:c.1476C>G	p.Ser492Arg	p.S492R	ENST00000263388	NM_000435.2	492	agC/agG	9/33	0.281453734303767	3	FACETS	0.818	0.754	0.884	0.818	0.754	0.884	CLONAL	2	TRUE	1	0.290537293845173	3		315	853	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952149	178952150	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTCA	novel	NA	P-0004072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	118	182	0	ENST00000263967.3:c.3205_3206insTCAT	p.Ter1069PhefsTer5	p.*1069Ffs*5	ENST00000263967	NM_006218.2	1068	-/TTCA	21/21	0.281453734303767	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.290537293845173	3		182	419	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0004115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	963	508	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.436252373118527	12	FACETS	1	0.991	1			1	CLONAL	10	TRUE	NA	0.436252373118527	12		508	1375	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0004115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	91	236	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.371880146995175	2	FACETS	0.79	0.712	0.871	0.79	0.712	0.871	SUBCLONAL	2	TRUE	0	0.436252373118527	2		236	264	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343507	343507	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567261095	NA	P-0004115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	172	233	0	ENST00000262320.3:c.2167C>T	p.Arg723Ter	p.R723*	ENST00000262320	NM_003502.3	723	Cga/Tga	8/11	0.436252373118527	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.436252373118527	2		233	363	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764146326	NA	P-0004115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	172	341	0	ENST00000269305.4:c.841G>T	p.Asp281Tyr	p.D281Y	ENST00000269305	NM_001126112.2	281	Gac/Tac	8/11	NA	2	FACETS	0.761	0.706	0.818			1	INDETERMINATE	2	TRUE	NA	0.436252373118527	2		341	518	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771163	161771163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755627153	NA	P-0004115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	62	250	2	ENST00000366898.1:c.1366G>A	p.Val456Ile	p.V456I	ENST00000366898	NM_004562.2	456	Gtc/Atc	12/12	0.303310484694233	4	FACETS	0.781	0.675	0.895	0.195	0.168	0.224	SUBCLONAL	1	TRUE	0	0.436252373118527	4		252	523	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879856	37879856	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	143	175	0	ENST00000269571.5:c.2151G>C	p.Glu717Asp	p.E717D	ENST00000269571		717	gaG/gaC	18/27	0.436252373118527	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	1	0.436252373118527	3		175	387	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0004454-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	98	779	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.924	0.828	1	1	0.986	1	CLONAL	2	TRUE	1	0.211259851527865	2		779	502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0004454-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	139	365	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.188100321029836	0	FACETS	0.854	0.786	0.925			1	CLONAL	3	TRUE	0	0.211259851527865	0		365	405	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0004454-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	132	470	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	1	0.949	1	1	0.991	1	CLONAL	2	TRUE	1	0.211259851527865	2		470	589	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944944	31944944	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144139961	NA	P-0004454-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	79	228	0	ENST00000340398.3:c.157C>T	p.Arg53Cys	p.R53C	ENST00000340398	NM_001013699.2	53	Cgt/Tgt	1/1	1	2	FACETS	1	0.892	1	1	0.984	1	CLONAL	2	TRUE	1	0.211259851527865	2		228	371	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271913	18271913	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004454-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	99	223	0	ENST00000222254.8:c.516C>A	p.Asp172Glu	p.D172E	ENST00000222254	NM_005027.3	172	gaC/gaA	5/16	1	2	FACETS	0.87	0.784	0.96	1	0.989	1	CLONAL	3	TRUE	1	0.211259851527865	2		223	359	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492789	56492790	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACTCTGATAACAGCTTTCT	novel	NA	P-0004454-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	114	370	0	ENST00000407977.2:c.149_150insAGAAAGCTGTTATCAGAGT	p.Ile51GlufsTer30	p.I51Efs*30	ENST00000407977		50	gtg/gtAGAAAGCTGTTATCAGAGTg	2/10	0.211259851527865	0	FACETS	0.946	0.857	1			1	CLONAL	2	TRUE	0	0.211259851527865	0		370	450	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0004478-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	87	473	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.366563610216839	4	FACETS	0.781	0.692	0.876	0.39	0.346	0.438	SUBCLONAL	1	FALSE	2	0.556869939396361	4		473	623	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199836	108199836	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004478-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	114	468	0	ENST00000278616.4:c.7178T>C	p.Phe2393Ser	p.F2393S	ENST00000278616	NM_000051.3	2393	tTt/tCt	49/63	0.366563610216839	4	FACETS	0.882	0.794	0.974	0.441	0.397	0.487	CLONAL	1	FALSE	2	0.556869939396361	4		468	723	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531765	46531766	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	TCTTTAG	novel	NA	P-0004478-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	48	654	0	ENST00000262741.5:c.581_582insCTAAAGA	p.Glu194AspfsTer2	p.E194Dfs*2	ENST00000262741	NM_003629.3	194	gag/gaCTAAAGAg	5/10	0.366563610216839	4	FACETS	0.303	0.255	0.357	0.152	0.127	0.179	SUBCLONAL	1	FALSE	2	0.556869939396361	4		654	885	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0004716-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	173	473	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.898	0.831	0.966	0.898	0.831	0.966	CLONAL	1	TRUE	1	0.679521599434602	2		473	567	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593504	48593504	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004716-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	174	310	0	ENST00000342988.3:c.1255G>A	p.Gly419Arg	p.G419R	ENST00000342988	NM_005359.5	419	Ggg/Agg	10/12	0.679521599434602	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.679521599434602	1		310	320	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0004716-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	260	361	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	0.679521599434602	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.679521599434602	1		361	477	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469507	25469507	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004716-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	174	489	0	ENST00000264709.3:c.1261G>C	p.Gly421Arg	p.G421R	ENST00000264709	NM_175629.2	421	Ggc/Cgc	10/23	1	2	FACETS	0.975	0.905	1	0.975	0.905	1	CLONAL	1	TRUE	1	0.679521599434602	2		489	525	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0004716-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	125	182	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.679521599434602	1	FACETS	0.987	0.914	1	0.987	0.914	1	CLONAL	1	TRUE	0	0.679521599434602	1		182	246	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61213514	61213514	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004716-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	215	326	0	ENST00000301761.2:c.472C>A	p.Leu158Ile	p.L158I	ENST00000301761	NM_017841.2	158	Ctt/Att	4/4	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.679521599434602	2		326	576	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143284	108143284	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004716-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	213	336	0	ENST00000278616.4:c.3103A>G	p.Ile1035Val	p.I1035V	ENST00000278616	NM_000051.3	1035	Ata/Gta	21/63	0.679521599434602	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.679521599434602	1		336	403	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205217	46205217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004716-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	185	333	0	ENST00000334344.6:c.301G>A	p.Glu101Lys	p.E101K	ENST00000334344	NM_152641.2	101	Gag/Aag	4/21	1	2	FACETS	0.904	0.84	0.971	0.904	0.84	0.971	CLONAL	1	TRUE	1	0.679521599434602	2		333	602	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807359	3807359	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1200092189	NA	P-0004716-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	192	341	0	ENST00000262367.5:c.3628A>G	p.Thr1210Ala	p.T1210A	ENST00000262367	NM_004380.2	1210	Act/Gct	19/31	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.679521599434602	2		341	553	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53253974	53253974	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004716-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	291	533	0	ENST00000375401.3:c.98A>C	p.Lys33Thr	p.K33T	ENST00000375401	NM_004187.3	33	aAa/aCa	1/26	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.679521599434602	2		533	737	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411818	63411818	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004716-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	254	624	0	ENST00000330258.3:c.1349del	p.Pro450LeufsTer5	p.P450Lfs*5	ENST00000330258	NM_152424.3	450	cCt/ct	2/2	1	2	FACETS	0.95	0.892	1	0.95	0.892	1	CLONAL	1	TRUE	1	0.679521599434602	2		624	787	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0004729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	143	391	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.412502511259539	3	FACETS	1	0.952	1	0.532	0.485	0.581	CLONAL	1	TRUE	1	0.412502511259539	3		391	786	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0004729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	198	301	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.412502511259539	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	1	0.412502511259539	3		301	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0004729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	204	410	0	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.412502511259539	2	FACETS	0.949	0.888	1	0.949	0.888	1	CLONAL	2	TRUE	0	0.412502511259539	2		410	521	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726905	61726905	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	139	439	0	ENST00000401558.2:c.533T>C	p.Val178Ala	p.V178A	ENST00000401558	NM_003400.3	178	gTa/gCa	7/25	0.412502511259539	3	FACETS	0.921	0.838	1	0.46	0.419	0.504	CLONAL	1	TRUE	1	0.412502511259539	3		439	883	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72861891	72861891	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	103	388	0	ENST00000325599.8:c.991T>G	p.Tyr331Asp	p.Y331D	ENST00000325599	NM_018130.2	331	Tac/Gac	9/11	0.412502511259539	3	FACETS	0.877	0.785	0.974	0.438	0.392	0.487	CLONAL	1	TRUE	1	0.412502511259539	3		388	687	SUCCESS
APC	324	MSKCC	GRCh37	5	112174682	112174682	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs878853438	NA	P-0004729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	133	432	1	ENST00000257430.4:c.3391C>T	p.Gln1131Ter	p.Q1131*	ENST00000257430	NM_000038.5	1131	Caa/Taa	16/16	0.412502511259539	1	FACETS	0.882	0.805	0.964	0.882	0.805	0.964	CLONAL	1	TRUE	0	0.412502511259539	1		433	580	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966554	36966554	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1288922202	NA	P-0004729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	147	351	0	ENST00000358127.4:c.772C>A	p.Pro258Thr	p.P258T	ENST00000358127	NM_001280556.1	258	Ccc/Acc	6/10	0.412502511259539	2	FACETS	0.95	0.879	1	0.95	0.879	1	CLONAL	2	TRUE	0	0.412502511259539	2		351	375	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493736	56493736	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	131	514	0	ENST00000267101.3:c.3052G>T	p.Glu1018Ter	p.E1018*	ENST00000267101	NM_001982.3	1018	Gag/Tag	25/28	0.412502511259539	3	FACETS	1	0.958	1	0.546	0.496	0.598	CLONAL	1	TRUE	1	0.412502511259539	3		514	702	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112035	115112035	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	87	364	0	ENST00000257566.3:c.1705G>C	p.Gly569Arg	p.G569R	ENST00000257566	NM_016569.3	569	Gga/Cga	7/8	0.412502511259539	2	FACETS	1	0.896	1	0.503	0.448	0.562	CLONAL	1	TRUE	0	0.412502511259539	2		364	419	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340935	70340935	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	135	589	0	ENST00000374080.3:c.668C>A	p.Pro223His	p.P223H	ENST00000374080		223	cCc/cAc	5/45	1	2	FACETS	0.998	0.909	1	0.998	0.909	1	CLONAL	1	TRUE	1	0.412502511259539	2		589	656	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604697	48604697	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	88	416	0	ENST00000342988.3:c.1521del	p.Gly508AlafsTer29	p.G508Afs*29	ENST00000342988	NM_005359.5	507	Aaa/aa	12/12	0.211676386253205	0	FACETS	0.597	0.532	0.666			1	INDETERMINATE	1	TRUE	0	0.412502511259539	0		416	420	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0004733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	354	418	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.739738638664343	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.739738638664343	1		418	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555526097	NA	P-0004733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	242	369	0	ENST00000269305.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000269305	NM_001126112.2	167	Cag/Tag	5/11	0.739738638664343	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.739738638664343	1		369	368	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115111972	115111972	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	99	185	0	ENST00000257566.3:c.1768C>T	p.Gln590Ter	p.Q590*	ENST00000257566	NM_016569.3	590	Cag/Tag	7/8	1	2	FACETS	0.892	0.807	0.98	0.892	0.807	0.98	CLONAL	1	TRUE	1	0.739738638664343	2		185	300	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804268	43804268	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs763144679	NA	P-0004733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	291	465	1	ENST00000372470.3:c.268C>T	p.Arg90Ter	p.R90*	ENST00000372470	NM_005373.2	90	Cga/Tga	3/12	1	2	FACETS	0.866	0.817	0.917	0.866	0.817	0.917	CLONAL	1	TRUE	1	0.739738638664343	2		466	908	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335081	65335081	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	288	466	0	ENST00000342505.4:c.560A>G	p.Asn187Ser	p.N187S	ENST00000342505	NM_002227.2	187	aAc/aGc	6/25	1	2	FACETS	0.855	0.806	0.905	0.855	0.806	0.905	CLONAL	1	TRUE	1	0.739738638664343	2		466	911	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091349	193091349	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	188	302	0	ENST00000367435.3:c.19G>T	p.Val7Phe	p.V7F	ENST00000367435	NM_024529.4	7	Gtc/Ttc	1/17	1	2	FACETS	0.906	0.843	0.971	0.906	0.843	0.971	CLONAL	1	TRUE	1	0.739738638664343	2		302	561	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965256	25965256	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	224	319	0	ENST00000435504.4:c.3950A>G	p.Tyr1317Cys	p.Y1317C	ENST00000435504		1317	tAt/tGt	13/13	0.739738638664343	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.739738638664343	1		319	356	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968250	134968250	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs765393605	NA	P-0004733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	303	476	0	ENST00000398015.3:c.2763C>A	p.Ser921Arg	p.S921R	ENST00000398015	NM_004441.4	921	agC/agA	15/16	1	2	FACETS	0.967	0.915	1	0.967	0.915	1	CLONAL	1	TRUE	1	0.739738638664343	2		476	847	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430429	181430429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	438	516	0	ENST00000325404.1:c.281C>T	p.Ala94Val	p.A94V	ENST00000325404	NM_003106.3	94	gCt/gTt	1/1	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.739738638664343	2		516	1073	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164084	106164084	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	220	309	1	ENST00000380013.4:c.3594G>T	p.Trp1198Cys	p.W1198C	ENST00000380013	NM_001127208.2	1198	tgG/tgT	5/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.739738638664343	2		310	573	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540003	187540003	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	276	427	0	ENST00000441802.2:c.7737C>A	p.Phe2579Leu	p.F2579L	ENST00000441802	NM_005245.3	2579	ttC/ttA	10/27	1	2	FACETS	0.995	0.939	1	0.995	0.939	1	CLONAL	1	TRUE	1	0.739738638664343	2		427	750	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750451	57750451	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	304	528	0	ENST00000274289.3:c.2017A>G	p.Met673Val	p.M673V	ENST00000274289	NM_006622.3	673	Atg/Gtg	14/14	1	2	FACETS	0.921	0.871	0.973	0.921	0.871	0.973	CLONAL	1	TRUE	1	0.739738638664343	2		528	892	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750740	57750740	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	230	432	0	ENST00000274289.3:c.1864C>G	p.Gln622Glu	p.Q622E	ENST00000274289	NM_006622.3	622	Cag/Gag	13/14	1	2	FACETS	0.927	0.869	0.986	0.927	0.869	0.986	CLONAL	1	TRUE	1	0.739738638664343	2		432	671	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048229	180048229	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	188	326	0	ENST00000261937.6:c.2044C>A	p.Gln682Lys	p.Q682K	ENST00000261937	NM_182925.4	682	Cag/Aag	14/30	1	2	FACETS	0.993	0.925	1	0.993	0.925	1	CLONAL	1	TRUE	1	0.739738638664343	2		326	512	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004912	150004912	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1295040914	NA	P-0004733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	402	611	1	ENST00000253339.5:c.1313C>T	p.Ser438Phe	p.S438F	ENST00000253339		438	tCt/tTt	3/7	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.739738638664343	2		612	1082	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403521	139403521	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1054240778	NA	P-0004733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	198	321	0	ENST00000277541.6:c.2972C>T	p.Ser991Phe	p.S991F	ENST00000277541	NM_017617.3	991	tCc/tTc	19/34	0.739738638664343	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.739738638664343	1		321	332	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245035	133245035	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	231	391	0	ENST00000320574.5:c.2080A>G	p.Lys694Glu	p.K694E	ENST00000320574	NM_006231.2	694	Aag/Gag	19/49	1	2	FACETS	0.962	0.903	1	0.962	0.903	1	CLONAL	1	TRUE	1	0.739738638664343	2		391	649	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602370	10602370	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	409	539	0	ENST00000171111.5:c.1208G>T	p.Trp403Leu	p.W403L	ENST00000171111	NM_203500.1	403	tGg/tTg	3/6	0.739738638664343	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.739738638664343	1		539	649	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145591	11145591	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	141	185	0	ENST00000358026.2:c.3953G>C	p.Arg1318Pro	p.R1318P	ENST00000358026	NM_001128849.1	1318	cGc/cCc	29/36	0.739738638664343	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.739738638664343	1		185	213	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953870	17953870	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	304	451	0	ENST00000458235.1:c.532G>T	p.Ala178Ser	p.A178S	ENST00000458235	NM_000215.3	178	Gcc/Tcc	5/24	0.739738638664343	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.739738638664343	1		451	470	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889128	76889128	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	520	412	0	ENST00000373344.5:c.4882C>G	p.Leu1628Val	p.L1628V	ENST00000373344	NM_000489.3	1628	Ctt/Gtt	18/35	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.739738638664343	1		412	673	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665436	138665436	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	119	257	0	ENST00000330315.3:c.129del	p.Thr44GlnfsTer106	p.T44Qfs*106	ENST00000330315	NM_023067.3	43	ggG/gg	1/1	1	2	FACETS	0.946	0.865	1	0.946	0.865	1	CLONAL	1	TRUE	1	0.739738638664343	2		257	340	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971082	21971083	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	125	207	0	ENST00000304494.5:c.275dup	p.Asp92GlufsTer28	p.D92Efs*28	ENST00000304494	NM_000077.4	92	gac/gaAc	2/3	0.739738638664343	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.739738638664343	1		207	199	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55154992	55154993	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	318	555	0	ENST00000257290.5:c.2702dup	p.Asp902GlyfsTer7	p.D902Gfs*7	ENST00000257290	NM_006206.4	901	gtg/gTtg	20/23	1	2	FACETS	0.87	0.823	0.918	0.87	0.823	0.918	CLONAL	1	TRUE	1	0.739738638664343	2		555	988	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239840	53239856	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CCCCAGGGTCCCACTCA	CCCCAGGGTCCCACTCA	-	novel	NA	P-0004733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	326	273	0	ENST00000375401.3:c.1583+2_1583+18del		p.X528_splice	ENST00000375401	NM_004187.3	528			1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.739738638664343	1		273	451	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0004802-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	1114	262	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.27420680383517	11	FACETS	0.969	0.947	0.991			1	CLONAL	10	TRUE	NA	0.27420680383517	11		262	1873	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs786202525	NA	P-0004802-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	119	283	0	ENST00000269305.4:c.532del	p.His178ThrfsTer69	p.H178Tfs*69	ENST00000269305	NM_001126112.2	178	Cac/ac	5/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.27420680383517	2		283	729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578528	7578528	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004802-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	66	333	0	ENST00000269305.4:c.402T>G	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	ttT/ttG	5/11	1	2	FACETS	0.538	0.466	0.617	0.538	0.466	0.617	SUBCLONAL	1	TRUE	1	0.27420680383517	2		333	894	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796231	45796231	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0004802-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	337	455	0	ENST00000450313.1:c.1477-2A>C		p.X493_splice	ENST00000450313	NM_012222.2	493			0.215905059583269	3	FACETS	0.836	0.791	0.881	0.836	0.791	0.881	CLONAL	3	TRUE	0	0.27420680383517	3		455	1115	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613145	52613145	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004802-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	83	433	0	ENST00000394830.3:c.3383A>G	p.Tyr1128Cys	p.Y1128C	ENST00000394830	NM_018313.4	1128	tAc/tGc	22/30	1	2	FACETS	0.622	0.547	0.702	0.622	0.547	0.702	SUBCLONAL	1	TRUE	1	0.27420680383517	2		433	974	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294142	1294142	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004802-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	122	310	0	ENST00000310581.5:c.859G>T	p.Gly287Cys	p.G287C	ENST00000310581	NM_198253.2	287	Ggt/Tgt	2/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.27420680383517	2		310	807	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138187	64138187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1418251990	NA	P-0004802-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	153	307	0	ENST00000334205.4:c.2110G>A	p.Ala704Thr	p.A704T	ENST00000334205	NM_003942.2	704	Gcc/Acc	16/17	0.27420680383517	3	FACETS	1	0.986	1	0.704	0.644	0.767	CLONAL	1	TRUE	1	0.27420680383517	3		307	901	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114790	108114790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004802-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	95	247	0	ENST00000278616.4:c.607G>A	p.Asp203Asn	p.D203N	ENST00000278616	NM_000051.3	203	Gac/Aac	6/63	0.27420680383517	3	FACETS	0.973	0.865	1	0.486	0.432	0.544	CLONAL	1	TRUE	1	0.27420680383517	3		247	810	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109852	115109852	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1013102657	NA	P-0004802-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	84	190	0	ENST00000257566.3:c.2026G>T	p.Ala676Ser	p.A676S	ENST00000257566	NM_016569.3	676	Gcc/Tcc	8/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.27420680383517	2		190	433	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17949144	17949144	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004802-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	100	446	0	ENST00000458235.1:c.1497G>T	p.Leu499Phe	p.L499F	ENST00000458235	NM_000215.3	499	ttG/ttT	11/24	1	2	FACETS	0.623	0.555	0.696	0.623	0.555	0.696	SUBCLONAL	1	TRUE	1	0.27420680383517	2		446	1170	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748538	40748538	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1203244050	NA	P-0004802-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	92	432	1	ENST00000392038.2:c.344C>T	p.Pro115Leu	p.P115L	ENST00000392038	NM_001626.4	115	cCa/cTa	5/14	1	2	FACETS	0.666	0.59	0.747	0.666	0.59	0.747	SUBCLONAL	1	TRUE	1	0.27420680383517	2		433	1008	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664761	138664761	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs797044528	NA	P-0004802-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	20	20	0	ENST00000330315.3:c.804del	p.Gly269AlafsTer2	p.G269Afs*2	ENST00000330315	NM_023067.3	268	ccC/cc	1/1	1	2	FACETS	0.752	0.586	0.938	1	0.92	1	CLONAL	2	TRUE	1	0.27420680383517	2		20	97	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105684	27105688	+	frameshift_variant	Frame_Shift_Del	DEL	AGAAG	AGAAG	C	novel	NA	P-0004802-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	248	334	0	ENST00000324856.7:c.5295_5299delinsC	p.Glu1765AspfsTer4	p.E1765Dfs*4	ENST00000324856	NM_006015.4	1765	gaAGAAGaa/gaCaa	20/20	0.215905059583269	3	FACETS	1	0.975	1	0.722	0.675	0.769	CLONAL	2	TRUE	0	0.27420680383517	3		334	950	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152093	55152093	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121908585	NA	P-0004828-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	327	358	0	ENST00000257290.5:c.2525A>T	p.Asp842Val	p.D842V	ENST00000257290	NM_006206.4	842	gAc/gTc	18/23	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.918701864191922	2		358	707	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431628	6431628	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	41	279	0	ENST00000356142.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000356142	NM_018890.3	61	Caa/Aaa	3/7	0.427387132039246	8	FACETS	1	0.835	1	0.167	0.139	0.198	CLONAL	1	TRUE	2	0.427387132039246	8		279	437	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0004897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	271	308	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.387830862823741	7	FACETS	0.958	0.912	1			1	CLONAL	6	TRUE	NA	0.387830862823741	7		308	479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0004897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	406	559	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.383488928289382	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.387830862823741	2		560	903	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851754	134851754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56396912	NA	P-0004897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	139	515	3	ENST00000398015.3:c.1160C>T	p.Thr387Met	p.T387M	ENST00000398015	NM_004441.4	387	aCg/aTg	5/16	0.387830862823741	3	FACETS	1	0.933	1	0.514	0.468	0.563	CLONAL	1	TRUE	1	0.387830862823741	3		518	832	SUCCESS
APC	324	MSKCC	GRCh37	5	112111408	112111411	+	frameshift_variant	Frame_Shift_Del	DEL	ATAG	ATAG	-	rs387906231	NA	P-0004897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	87	444	0	ENST00000257430.4:c.509_512del	p.Asp170ValfsTer4	p.D170Vfs*4	ENST00000257430	NM_000038.5	169	ATAGat/at	5/16	0.387830862823741	2	FACETS	0.935	0.841	1	0.935	0.841	1	CLONAL	2	TRUE	0	0.387830862823741	2		444	240	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959351	26959351	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	87	321	0	ENST00000381527.3:c.518A>G	p.Asp173Gly	p.D173G	ENST00000381527	NM_001260.1	173	gAc/gGc	6/13	0.387830862823741	7	FACETS	1	0.889	1	0.4	0.355	0.447	CLONAL	2	TRUE	2	0.387830862823741	7		321	442	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44515848	44515848	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	144	629	1	ENST00000291552.4:c.205G>T	p.Val69Leu	p.V69L	ENST00000291552	NM_006758.2	69	Gtg/Ttg	4/8	0.387830862823741	3	FACETS	0.981	0.902	1	0.981	0.902	1	CLONAL	2	TRUE	1	0.387830862823741	3		630	452	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913125	32913126	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	142	825	1	ENST00000380152.3:c.4633_4634insG	p.Leu1545ArgfsTer3	p.L1545Rfs*3	ENST00000380152		1545	ctt/cGtt	11/27	0.387830862823741	3	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.387830862823741	3		826	646	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0005057-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	57	473	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.861	0.74	0.991	0.861	0.74	0.991	CLONAL	1	TRUE	1	0.32	2		473	414	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046364	128046364	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005057-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	58	584	0	ENST00000285398.2:c.899A>G	p.Asp300Gly	p.D300G	ENST00000285398	NM_000122.1	300	gAt/gGt	7/15	1	2	FACETS	0.751	0.646	0.864	0.751	0.646	0.864	SUBCLONAL	1	TRUE	1	0.32	2		584	483	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606432	93606452	+	inframe_deletion	In_Frame_Del	DEL	CCCCGCCGACCTCTGCCACTA	CCCCGCCGACCTCTGCCACTA	-	novel	NA	P-0005057-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	51	444	0	ENST00000375746.1:c.254_274del	p.Pro85_Tyr91del	p.P85_Y91del	ENST00000375746	NM_001174167.1	84	agCCCCGCCGACCTCTGCCACTAc/agc	2/14	1	2	FACETS	0.649	0.552	0.756	0.649	0.552	0.756	SUBCLONAL	1	TRUE	1	0.32	2		444	491	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641307	23641308	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs587776416	NA	P-0005057-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	74	508	0	ENST00000261584.4:c.2167_2168del	p.Met723ValfsTer21	p.M723Vfs*21	ENST00000261584	NM_024675.3	723	ATg/g	5/13	1	2	FACETS	0.988	0.868	1	0.988	0.868	1	CLONAL	1	TRUE	1	0.32	2		508	468	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434157	121434157	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	450	547	0	ENST00000257555.6:c.1048C>T	p.Gln350Ter	p.Q350*	ENST00000257555		350	Caa/Taa	5/10	1	2	FACETS	0.936	0.896	0.976	0.936	0.896	0.976	CLONAL	1	TRUE	1	0.918568335880123	2		547	1047	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289516	33289517	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0005101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	378	530	0	ENST00000374542.5:c.186_187delinsTT	p.Glu62_Asn63delinsAspTyr	p.E62_N63delinsDY	ENST00000374542	NM_001141970.1	62	gaGAat/gaTTat	2/8	1	2	FACETS	0.896	0.854	0.938	0.896	0.854	0.938	CLONAL	1	TRUE	1	0.918568335880123	2		530	919	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215230	123215231	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005119-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	187	363	0	ENST00000218089.9:c.2781dup	p.Asn928Ter	p.N928*	ENST00000218089	NM_001042749.1	926	ctt/cTtt	28/35	1	2	FACETS	0.94	0.882	0.998	1	0.995	1	CLONAL	3	TRUE	1	0.35	2		363	379	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539884	187539884	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005121-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	173	381	0	ENST00000441802.2:c.7856T>G	p.Leu2619Arg	p.L2619R	ENST00000441802	NM_005245.3	2619	cTt/cGt	10/27	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.449316276214022	2		381	725	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81971404	81971404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1428917927	NA	P-0005121-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	276	549	0	ENST00000359376.3:c.3094G>A	p.Gly1032Arg	p.G1032R	ENST00000359376	NM_002661.3	1032	Ggg/Agg	28/33	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.449316276214022	2		549	1140	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720803	89720804	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs786204892	NA	P-0005121-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	51	99	0	ENST00000371953.3:c.955dup	p.Thr319AsnfsTer6	p.T319Nfs*6	ENST00000371953	NM_000314.4	318	-/A	8/9	0.449316276214022	1	FACETS	0.819	0.704	0.941	0.819	0.704	0.941	CLONAL	1	TRUE	0	0.449316276214022	1		99	215	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577576	7577578	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	novel	NA	P-0005137-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	439	499	0	ENST00000269305.4:c.703_705del	p.Asn235del	p.N235del	ENST00000269305	NM_001126112.2	235	AAC/-	7/11	NA	2	FACETS	0.93	0.9	0.959			1	INDETERMINATE	2	TRUE	NA	0.738710209679313	2		499	639	SUCCESS
APC	324	MSKCC	GRCh37	5	112175211	112175212	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005137-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	86	254	0	ENST00000257430.4:c.3924dup	p.Glu1309ArgfsTer6	p.E1309Rfs*6	ENST00000257430	NM_000038.5	1307	ata/atAa	16/16	1	2	FACETS	0.875	0.785	0.969	0.875	0.785	0.969	CLONAL	1	TRUE	1	0.738710209679313	2		254	266	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366982	40366982	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005137-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	208	471	0	ENST00000397332.2:c.215C>A	p.Ser72Ter	p.S72*	ENST00000397332	NM_001033082.2	72	tCg/tAg	2/3	0.738710209679313	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.738710209679313	1		471	349	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412464	63412464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005137-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	290	895	1	ENST00000330258.3:c.703C>T	p.Pro235Ser	p.P235S	ENST00000330258	NM_152424.3	235	Cct/Tct	2/2	0.117135634125026	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.738710209679313	0		896	861	SUCCESS
APC	324	MSKCC	GRCh37	5	112173502	112173506	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CAAGG	CAAGG	-	novel	NA	P-0005137-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	102	408	0	ENST00000257430.4:c.2211_2215del	p.Tyr737Ter	p.Y737*	ENST00000257430	NM_000038.5	737	taCAAGGat/taat	16/16	1	2	FACETS	0.791	0.715	0.871	0.791	0.715	0.871	SUBCLONAL	1	TRUE	1	0.738710209679313	2		408	349	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576761	67576762	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005137-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	91	164	0	ENST00000274335.5:c.845dup	p.Asn282LysfsTer3	p.N282Kfs*3	ENST00000274335		281	-/A	6/15	0.738710209679313	1	FACETS	0.965	0.886	1	0.965	0.886	1	CLONAL	1	TRUE	0	0.738710209679313	1		164	161	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0005152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	215	237	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.220073085636193	9	FACETS	0.95	0.892	1			1	CLONAL	7	FALSE	NA	0.220073085636193	9		237	520	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543627	9543627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1047406889	NA	P-0005152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	30	423	0	ENST00000353224.5:c.1527G>A	p.Met509Ile	p.M509I	ENST00000353224	NM_177990.2	509	atG/atA	6/10	0.220073085636193	3	FACETS	0.633	0.509	0.774	0.317	0.254	0.387	SUBCLONAL	1	FALSE	1	0.220073085636193	3		423	478	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411072	63411072	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1464385859	NA	P-0005152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	48	468	0	ENST00000330258.3:c.2095C>T	p.Arg699Cys	p.R699C	ENST00000330258	NM_152424.3	699	Cgt/Tgt	2/2	1	2	FACETS	0.676	0.571	0.793	0.676	0.571	0.793	SUBCLONAL	1	FALSE	1	0.220073085636193	2		468	645	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0005164-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	283	508	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.806771693489152	2		508	676	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005164-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	310	411	0	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	0.471091911947403	1	FACETS	0.662	0.628	0.695	0.662	0.628	0.695	INDETERMINATE	1	TRUE	0	0.806771693489152	1		411	693	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956221	55956221	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs767542615	NA	P-0005164-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	296	572	0	ENST00000263923.4:c.3094C>T	p.Arg1032Ter	p.R1032*	ENST00000263923	NM_002253.2	1032	Cga/Tga	23/30	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.806771693489152	2		572	727	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001463	150001463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005164-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	381	796	0	ENST00000253339.5:c.2141G>A	p.Gly714Glu	p.G714E	ENST00000253339		714	gGa/gAa	4/7	1	2	FACETS	0.976	0.93	1	0.976	0.93	1	CLONAL	1	TRUE	1	0.806771693489152	2		796	968	SUCCESS
APC	324	MSKCC	GRCh37	5	112175756	112175756	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005164-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	195	389	0	ENST00000257430.4:c.4466del	p.Leu1489TyrfsTer18	p.L1489Yfs*18	ENST00000257430	NM_000038.5	1489	Tta/ta	16/16	1	2	FACETS	0.931	0.869	0.994	0.931	0.869	0.994	CLONAL	1	TRUE	1	0.806771693489152	2		389	519	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38991050	38991050	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0005164-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	223	482	0	ENST00000357387.3:c.583+1G>T		p.X195_splice	ENST00000357387	NM_152756.3	195			1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.806771693489152	2		482	549	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157488319	157488319	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005164-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	86	406	0	ENST00000346085.5:c.3025G>A	p.Ala1009Thr	p.A1009T	ENST00000346085	NM_020732.3	1009	Gca/Aca	10/20	1	2	FACETS	0.421	0.373	0.471	0.421	0.373	0.471	SUBCLONAL	1	TRUE	1	0.806771693489152	2		406	507	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005200-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	169	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.547531822936877	2		341	555	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0005200-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	13	126	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.135	0.095	0.183	0.135	0.095	0.183	SUBCLONAL	1	TRUE	1	0.547531822936877	2		126	353	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0005200-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	29	137	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.509344681449314	1	FACETS	0.177	0.141	0.217	0.177	0.141	0.217	SUBCLONAL	1	TRUE	0	0.547531822936877	1		137	435	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0005200-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	233	191	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	0.509344681449314	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.547531822936877	1		191	467	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478043	138478043	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1374478281	NA	P-0005200-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	173	237	0	ENST00000289153.2:c.143G>A	p.Arg48Gln	p.R48Q	ENST00000289153	NM_006219.2	48	cGg/cAg	1/22	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.547531822936877	2		237	599	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423646	88423646	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005200-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	27	144	0	ENST00000360948.2:c.2189C>G	p.Thr730Ser	p.T730S	ENST00000360948	NM_001012338.2	730	aCc/aGc	18/19	0.547531822936877	1	FACETS	0.269	0.215	0.331	0.269	0.215	0.331	SUBCLONAL	1	TRUE	0	0.547531822936877	1		144	266	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604706	48604706	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005200-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	142	210	0	ENST00000342988.3:c.1528G>A	p.Gly510Arg	p.G510R	ENST00000342988	NM_005359.5	510	Gga/Aga	12/12	0.418258495524976	0	FACETS	0.665	0.614	0.717			1	SUBCLONAL	1	TRUE	0	0.547531822936877	0		210	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0005237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	71	635	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.202372607442045	2	FACETS	1	0.972	1	0.72	0.631	0.816	CLONAL	1	FALSE	0	0.227667632766563	2		635	433	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	137	641	7	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	0.202372607442045	2	FACETS	0.777	0.708	0.851	0.777	0.708	0.851	SUBCLONAL	2	FALSE	0	0.227667632766563	2		648	774	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508805	106508805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762805000	NA	P-0005237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	79	605	1	ENST00000359195.3:c.799G>A	p.Glu267Lys	p.E267K	ENST00000359195	NM_002649.2	267	Gaa/Aaa	2/11	0.227667632766563	5	FACETS	0.786	0.692	0.887	0.524	0.461	0.592	SUBCLONAL	2	FALSE	2	0.227667632766563	5		606	592	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432664	29432664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113994087	NA	P-0005237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	44	569	1	ENST00000389048.3:c.3824G>A	p.Arg1275Gln	p.R1275Q	ENST00000389048	NM_004304.4	1275	cGa/cAa	25/29	1	2	FACETS	0.554	0.463	0.655	0.554	0.463	0.655	SUBCLONAL	1	FALSE	1	0.227667632766563	2		570	698	SUCCESS
APC	324	MSKCC	GRCh37	5	112174094	112174095	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs863225332	NA	P-0005237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	123	605	0	ENST00000257430.4:c.2804dup	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	tac/tAac	16/16	1	2	FACETS	0.902	0.818	0.99	1	0.988	1	CLONAL	2	FALSE	1	0.227667632766563	2		605	599	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466324	120466324	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	50	524	0	ENST00000256646.2:c.4795G>T	p.Ala1599Ser	p.A1599S	ENST00000256646	NM_024408.3	1599	Gct/Tct	26/34	0.175132201122825	3	FACETS	0.944	0.802	1	0.472	0.401	0.551	CLONAL	1	FALSE	1	0.227667632766563	3		524	518	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858467	27858467	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113019637	NA	P-0005237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	80	918	0	ENST00000359303.2:c.104G>A	p.Gly35Asp	p.G35D	ENST00000359303	NM_003535.2	35	gGt/gAt	1/1	0.227667632766563	6	FACETS	1	0.963	1	0.415	0.365	0.47	CLONAL	1	FALSE	3	0.227667632766563	6		918	821	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840565	36840565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1227199851	NA	P-0005237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	26	514	1	ENST00000358127.4:c.1168C>T	p.Arg390Cys	p.R390C	ENST00000358127	NM_001280556.1	390	Cgt/Tgt	10/10	0.175132201122825	3	FACETS	0.677	0.536	0.838	0.338	0.268	0.419	SUBCLONAL	1	FALSE	1	0.227667632766563	3		515	376	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864515	57864515	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	82	737	2	ENST00000228682.2:c.1992T>A	p.His664Gln	p.H664Q	ENST00000228682	NM_005269.2	664	caT/caA	12/12	0.149676206499722	5	FACETS	0.982	0.869	1	0.655	0.579	0.735	CLONAL	2	FALSE	2	0.227667632766563	5		739	492	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866663	37866663	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	103	619	1	ENST00000269571.5:c.830A>T	p.Asp277Val	p.D277V	ENST00000269571		277	gAc/gTc	7/27	0.202372607442045	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	FALSE	0	0.227667632766563	2		620	415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0005240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	158	322	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.361500249202115	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.406111895606695	2		324	347	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448592	89448592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543425684	NA	P-0005240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	455	519	0	ENST00000336596.2:c.1556C>T	p.Thr519Met	p.T519M	ENST00000336596	NM_005233.5	519	aCg/aTg	7/17	0.406111895606695	3	FACETS	1	0.994	1	0.801	0.766	0.836	CLONAL	2	TRUE	0	0.406111895606695	3		519	1122	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953229	81953229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	163	696	0	ENST00000359376.3:c.2195G>A	p.Arg732His	p.R732H	ENST00000359376	NM_002661.3	732	cGc/cAc	20/33	0.164620355321388	2	FACETS	0.781	0.716	0.849	0.39	0.358	0.425	INDETERMINATE	1	TRUE	0	0.406111895606695	2		696	1028	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034385	123034385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1308142786	NA	P-0005240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	131	357	0	ENST00000355640.3:c.1142G>A	p.Arg381Gln	p.R381Q	ENST00000355640		381	cGa/cAa	6/7	0.406111895606695	4	FACETS	0.845	0.766	0.93			1	CLONAL	1	TRUE	NA	0.406111895606695	4		357	1073	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38968098	38968098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777143677	NA	P-0005240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1258	147	563	0	ENST00000357387.3:c.1007G>A	p.Arg336His	p.R336H	ENST00000357387	NM_152756.3	336	cGt/cAt	12/38	0.406111895606695	5	FACETS	0.829	0.755	0.908			1	CLONAL	1	TRUE	NA	0.406111895606695	5		563	1405	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394848	394848	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1302327519	NA	P-0005240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	95	428	0	ENST00000380956.4:c.244C>T	p.Arg82Ter	p.R82*	ENST00000380956	NM_001195286.1	82	Cga/Tga	3/9	NA	2	FACETS	0.771	0.687	0.859			1	INDETERMINATE	1	TRUE	NA	0.406111895606695	2		428	607	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38315029	38315029	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	107	495	0	ENST00000425967.3:c.35A>T	p.Glu12Val	p.E12V	ENST00000425967	NM_001174067.1	12	gAg/gTg	3/19	0.370316563679519	1	FACETS	0.555	0.498	0.616	0.555	0.498	0.616	SUBCLONAL	1	TRUE	0	0.406111895606695	1		495	756	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710517	114710517	+	start_lost	Translation_Start_Site	SNP	T	T	A	novel	NA	P-0005240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1324	328	599	0	ENST00000543371.1:c.2T>A	p.Met1?	p.M1?	ENST00000543371	NM_001198531.1	1	aTg/aAg	1/14	0.396637273206001	3	FACETS	1	0.988	1	0.588	0.554	0.623	CLONAL	1	TRUE	1	0.406111895606695	3		599	1652	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912541	32912541	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1861	205	823	0	ENST00000380152.3:c.4049A>G	p.His1350Arg	p.H1350R	ENST00000380152		1350	cAt/cGt	11/27	0.406111895606695	5	FACETS	0.786	0.726	0.85	0.197	0.181	0.213	SUBCLONAL	1	TRUE	1	0.406111895606695	5		823	2066	SUCCESS
APC	324	MSKCC	GRCh37	5	112151245	112151246	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs1114167567	NA	P-0005240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	333	567	0	ENST00000257430.4:c.893_894del	p.His298LeufsTer28	p.H298Lfs*28	ENST00000257430	NM_000038.5	296	agCAca/agca	9/16	0.336066363436471	3	FACETS	1	0.988	1	0.754	0.716	0.793	CLONAL	2	TRUE	0	0.406111895606695	3		567	872	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0005313-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	419	570	0	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	0.707516259656843	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.707516259656843	1		570	583	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798137	45798137	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005313-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	588	467	0	ENST00000450313.1:c.714C>G	p.Asn238Lys	p.N238K	ENST00000450313	NM_012222.2	238	aaC/aaG	9/16	0.707516259656843	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.707516259656843	2		467	805	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117057	193117057	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005313-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	242	518	0	ENST00000367435.3:c.790G>T	p.Ala264Ser	p.A264S	ENST00000367435	NM_024529.4	264	Gca/Tca	8/17	NA	2	FACETS	0.587	0.547	0.627			1	INDETERMINATE	1	TRUE	NA	0.707516259656843	2		518	1166	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520444	176520444	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005313-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	498	453	0	ENST00000292408.4:c.1289C>A	p.Ser430Ter	p.S430*	ENST00000292408	NM_213647.1	430	tCa/tAa	10/18	0.187877791207246	5	FACETS	1	0.994	1	0.787	0.755	0.82	INDETERMINATE	2	TRUE	2	0.707516259656843	5		453	1229	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023007	150023007	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005313-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	534	653	0	ENST00000253339.5:c.256C>A	p.Leu86Ile	p.L86I	ENST00000253339		86	Ctt/Att	1/7	0.151869860025303	4	FACETS	0.846	0.811	0.881	0.846	0.811	0.881	INDETERMINATE	2	TRUE	2	0.707516259656843	4		653	1524	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467984	50467984	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005313-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	284	549	0	ENST00000331340.3:c.1219C>A	p.Gln407Lys	p.Q407K	ENST00000331340	NM_006060.4	407	Cag/Aag	8/8	0.151869860025303	4	FACETS	0.82	0.773	0.867	0.82	0.773	0.867	INDETERMINATE	2	TRUE	2	0.707516259656843	4		549	836	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375024	118375024	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005313-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	340	419	0	ENST00000534358.1:c.8417C>A	p.Ser2806Ter	p.S2806*	ENST00000534358	NM_005933.3	2806	tCa/tAa	27/36	0.707516259656843	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.707516259656843	1		419	542	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910435	32910435	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005313-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	446	845	0	ENST00000380152.3:c.1943C>A	p.Ser648Ter	p.S648*	ENST00000380152		648	tCa/tAa	11/27	0.623352456792358	2	FACETS	0.89	0.849	0.932	0.445	0.424	0.466	CLONAL	1	TRUE	0	0.707516259656843	2		845	1417	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033957	49033957	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005313-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	479	505	0	ENST00000267163.4:c.2094G>T	p.Arg698Ser	p.R698S	ENST00000267163	NM_000321.2	698	agG/agT	20/27	0.623352456792358	2	FACETS	0.875	0.845	0.904	0.875	0.845	0.904	CLONAL	2	TRUE	0	0.707516259656843	2		505	774	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56873468	56873468	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005313-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	575	1030	2	ENST00000308159.5:c.2172G>T	p.Gln724His	p.Q724H	ENST00000308159	NM_014669.4	724	caG/caT	20/22	0.128633874769346	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.707516259656843	0		1032	1571	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81904507	81904507	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005313-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	474	776	2	ENST00000359376.3:c.615C>A	p.Phe205Leu	p.F205L	ENST00000359376	NM_002661.3	205	ttC/ttA	7/33	0.128633874769346	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.707516259656843	0		778	1455	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559158	29559158	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005313-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	441	391	1	ENST00000356175.3:c.3265G>T	p.Glu1089Ter	p.E1089*	ENST00000356175	NM_000267.3	1089	Gaa/Taa	25/57	0.707516259656843	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.707516259656843	1		392	731	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726609	41726609	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005313-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	280	708	0	ENST00000301178.4:c.154G>T	p.Gly52Cys	p.G52C	ENST00000301178	NM_021913.4	52	Ggc/Tgc	2/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.707516259656843	2		708	756	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939304	76939304	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005313-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	636	591	0	ENST00000373344.5:c.1444G>T	p.Glu482Ter	p.E482*	ENST00000373344	NM_000489.3	482	Gaa/Taa	9/35	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.707516259656843	2		591	1450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578250	7578250	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1131691011	NA	P-0006495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	971	556	0	ENST00000269305.4:c.599del	p.Asn200IlefsTer47	p.N200Ifs*47	ENST00000269305	NM_001126112.2	200	aAt/at	6/11	0.396600597522685	4	FACETS	0.928	0.905	0.952	0.928	0.905	0.952	CLONAL	4	TRUE	0	0.434268063333695	4		556	1727	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972916	55972916	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	122	429	0	ENST00000263923.4:c.1474C>T	p.Gln492Ter	p.Q492*	ENST00000263923	NM_002253.2	492	Cag/Tag	11/30	0.203661716263227	2	FACETS	0.531	0.478	0.586	0.265	0.239	0.293	INDETERMINATE	1	TRUE	0	0.434268063333695	2		429	1059	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741345	17741345	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	120	285	0	ENST00000250003.3:c.16C>G	p.Pro6Ala	p.P6A	ENST00000250003	NM_002478.4	6	Cca/Gca	1/3	0.316127118235701	5	FACETS	0.802	0.722	0.886	0.267	0.24	0.296	CLONAL	1	TRUE	2	0.434268063333695	5		285	1138	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410449	139410463	+	frameshift_variant	Frame_Shift_Del	DEL	GGTGTAAGTGTTGGG	GGTGTAAGTGTTGGG	C	novel	NA	P-0006495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	422	441	0	ENST00000277541.6:c.1639_1653delinsG	p.Pro547ValfsTer18	p.P547Vfs*18	ENST00000277541	NM_017617.3	547	CCCAACACTTACACC/G	10/34	0.321346102621377	3	FACETS	1	0.99	1	0.743	0.71	0.777	CLONAL	2	TRUE	0	0.434268063333695	3		441	1061	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645922	67645922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	417	486	0	ENST00000264010.4:c.850C>T	p.His284Tyr	p.H284Y	ENST00000264010	NM_006565.3	284	Cac/Tac	4/12	0.758500960286719	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.758500960286719	1		486	661	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100436	8100436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1220437638	NA	P-0006558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	608	460	0	ENST00000346208.3:c.410C>T	p.Ser137Leu	p.S137L	ENST00000346208		137	tCg/tTg	3/6	1	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	1	0.758500960286719	2		460	1153	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041713	47041713	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1593	236	589	0	ENST00000377604.3:c.1938G>C	p.Lys646Asn	p.K646N	ENST00000377604	NM_001204468.1	646	aaG/aaC	17/24	0.44405846094605	5	FACETS	0.727	0.676	0.781			1	INDETERMINATE	1	TRUE	NA	0.758500960286719	5		589	1829	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653863	89653865	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TAA	TAA	-	novel	NA	P-0006558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1735	337	308	0	ENST00000371953.3:c.161_163del	p.Val54_Arg55delinsGly	p.V54_R55delinsG	ENST00000371953	NM_000314.4	54	gTAAgg/ggg	2/9	0.453371631283986	5	FACETS	0.917	0.863	0.972			1	INDETERMINATE	1	TRUE	NA	0.758500960286719	5		308	2072	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0006603-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	302	153	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.936380018646032	2		153	319	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006659-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	188	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.968	0.894	1	0.968	0.894	1	CLONAL	1	TRUE	1	0.373847910860939	2		341	1039	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0006659-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	276	405	1	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.373847910860939	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.373847910860939	1		406	935	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0006659-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	176	274	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.933	0.859	1	0.933	0.859	1	CLONAL	1	TRUE	1	0.373847910860939	2		274	1009	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912188	114912188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006659-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1311	297	567	3	ENST00000543371.1:c.1258C>T	p.Arg420Trp	p.R420W	ENST00000543371	NM_001198531.1	420	Cgg/Tgg	11/14	1	2	FACETS	0.988	0.928	1	0.988	0.928	1	CLONAL	1	TRUE	1	0.373847910860939	2		570	1608	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157488227	157488227	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs913734487	NA	P-0006659-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	267	438	0	ENST00000346085.5:c.2933C>A	p.Pro978His	p.P978H	ENST00000346085	NM_020732.3	978	cCc/cAc	10/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.373847910860939	2		438	1179	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920392	114920392	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006659-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1264	303	495	0	ENST00000543371.1:c.1333A>G	p.Lys445Glu	p.K445E	ENST00000543371	NM_001198531.1	445	Aag/Gag	13/14	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.373847910860939	2		495	1567	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912463	32912463	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006659-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1697	295	650	0	ENST00000380152.3:c.3971A>C	p.Tyr1324Ser	p.Y1324S	ENST00000380152		1324	tAt/tCt	11/27	0.274158447265929	3	FACETS	0.94	0.881	1	0.47	0.44	0.501	CLONAL	1	TRUE	1	0.373847910860939	3		650	1992	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003095	42003095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs769752495	NA	P-0006659-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	459	624	0	ENST00000219905.7:c.2632A>G	p.Ile878Val	p.I878V	ENST00000219905	NM_001164273.1	878	Att/Gtt	8/24	0.373847910860939	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.373847910860939	1		624	1485	SUCCESS
APC	324	MSKCC	GRCh37	5	112175745	112175753	+	frameshift_variant	Frame_Shift_Del	DEL	CTGATACTT	CTGATACTT	A	novel	NA	P-0006659-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	157	365	0	ENST00000257430.4:c.4454_4462delinsA	p.Ala1485AspfsTer26	p.A1485Dfs*26	ENST00000257430	NM_000038.5	1485	gCTGATACTTta/gAta	16/16	1	2	FACETS	0.963	0.883	1	0.963	0.883	1	CLONAL	1	TRUE	1	0.373847910860939	2		365	872	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183724	10183724	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs869025616	NA	P-0006738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	60	469	0	ENST00000256474.2:c.193T>C	p.Ser65Pro	p.S65P	ENST00000256474	NM_000551.3	65	Tcg/Ccg	1/3	1	2	FACETS	0.847	0.729	0.977	0.847	0.729	0.977	CLONAL	1	TRUE	1	0.182981771253315	2		469	774	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441255	52441255	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	67	549	2	ENST00000460680.1:c.515G>A	p.Ser172Asn	p.S172N	ENST00000460680	NM_004656.3	172	aGc/aAc	7/17	0.182981771253315	1	FACETS	0.73	0.632	0.835	0.73	0.632	0.835	SUBCLONAL	1	TRUE	0	0.182981771253315	1		551	912	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222200	2222200	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367688361	NA	P-0006738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	56	512	0	ENST00000398665.3:c.3032G>A	p.Arg1011Gln	p.R1011Q	ENST00000398665	NM_032482.2	1011	cGg/cAg	24/28	NA	2	FACETS	0.835	0.714	0.968			1	INDETERMINATE	1	TRUE	NA	0.182981771253315	2		512	733	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352765	70352765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759105512	NA	P-0006738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	142	361	1	ENST00000374080.3:c.4486C>T	p.Arg1496Cys	p.R1496C	ENST00000374080		1496	Cgc/Tgc	32/45	1	1	FACETS	0.886	0.808	0.967	1	0.99	1	CLONAL	2	TRUE	0	0.182981771253315	1		362	796	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0006878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	160	262	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.762	0.701	0.825	1	0.989	1	SUBCLONAL	2	TRUE	1	0.322587892211267	2		262	651	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222006	1222006	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0006878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	190	216	0	ENST00000326873.7:c.920+1G>T		p.X307_splice	ENST00000326873	NM_000455.4	307			0.322587892211267	1	FACETS	0.933	0.862	1	0.933	0.862	1	CLONAL	1	TRUE	0	0.322587892211267	1		216	1059	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602488	10602488	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1397945617	NA	P-0006878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	179	203	0	ENST00000171111.5:c.1090G>T	p.Gly364Cys	p.G364C	ENST00000171111	NM_203500.1	364	Ggc/Tgc	3/6	0.322587892211267	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.322587892211267	1		203	916	SUCCESS
ATR	545	MSKCC	GRCh37	3	142257340	142257340	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	41	216	1	ENST00000350721.4:c.3709C>A	p.Leu1237Ile	p.L1237I	ENST00000350721	NM_001184.3	1237	Ctc/Atc	19/47	1	2	FACETS	0.445	0.37	0.529	0.445	0.37	0.529	SUBCLONAL	1	TRUE	1	0.322587892211267	2		217	571	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968187	15968187	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	104	253	0	ENST00000268712.3:c.5098C>G	p.Pro1700Ala	p.P1700A	ENST00000268712	NM_006311.3	1700	Cca/Gca	34/46	1	2	FACETS	0.622	0.556	0.693	0.622	0.556	0.693	SUBCLONAL	1	TRUE	1	0.322587892211267	2		253	1036	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913315	NA	P-0007638-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	193	719	1	ENST00000326873.7:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000326873	NM_000455.4	194	Gac/Tac	4/10	0.252180159043909	2	FACETS	0.94	0.871	1	0.94	0.871	1	CLONAL	2	TRUE	0	0.252180159043909	2		720	814	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233140	66233140	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs769393148	NA	P-0007638-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	142	522	0	ENST00000273854.3:c.1859G>A	p.Arg620Gln	p.R620Q	ENST00000273854	NM_004439.5	620	cGg/cAg	10/18	0.191288117441787	4	FACETS	0.975	0.89	1	0.975	0.89	1	CLONAL	2	TRUE	2	0.252180159043909	4		522	723	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034465	47034465	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007638-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	99	731	0	ENST00000377604.3:c.550G>T	p.Ala184Ser	p.A184S	ENST00000377604	NM_001204468.1	184	Gct/Tct	6/24	1	2	FACETS	0.874	0.779	0.976	0.874	0.779	0.976	CLONAL	1	TRUE	1	0.252180159043909	2		731	898	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199444	11199444	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1358692215	NA	P-0007638-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	202	716	0	ENST00000361445.4:c.5047C>T	p.Arg1683Trp	p.R1683W	ENST00000361445	NM_004958.3	1683	Cgg/Tgg	36/58	0.234475585167802	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	1	0.252180159043909	3		716	870	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602848	10602848	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007638-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	251	914	0	ENST00000171111.5:c.730G>T	p.Glu244Ter	p.E244*	ENST00000171111	NM_203500.1	244	Gag/Tag	3/6	0.252180159043909	2	FACETS	0.995	0.932	1	0.995	0.932	1	CLONAL	2	TRUE	0	0.252180159043909	2		914	1000	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524588	176524588	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs752951653	NA	P-0007638-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	190	859	0	ENST00000292408.4:c.2320A>T	p.Thr774Ser	p.T774S	ENST00000292408	NM_213647.1	774	Acc/Tcc	18/18	0.191288117441787	4	FACETS	0.905	0.836	0.977	0.905	0.836	0.977	CLONAL	2	TRUE	2	0.252180159043909	4		859	1042	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0009122-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	133	284	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.247864179132204	4	FACETS	0.84	0.765	0.919	0.42	0.382	0.46	CLONAL	2	TRUE	0	0.310615363944959	4		284	668	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11999013	11999013	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0009122-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	117	324	0	ENST00000353533.5:c.513+2T>C		p.X171_splice	ENST00000353533	NM_003010.3	171			0.245323153942888	2	FACETS	0.839	0.762	0.919	0.839	0.762	0.919	CLONAL	2	TRUE	0	0.310615363944959	2		324	449	SUCCESS
ATR	545	MSKCC	GRCh37	3	142172040	142172040	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009122-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	359	583	1	ENST00000350721.4:c.7691A>G	p.Glu2564Gly	p.E2564G	ENST00000350721	NM_001184.3	2564	gAa/gGa	46/47	0.247864179132204	4	FACETS	1	0.984	1	0.811	0.771	0.851	CLONAL	3	TRUE	0	0.310615363944959	4		584	934	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1555525585	NA	P-0009122-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	171	568	0	ENST00000269305.4:c.673-2A>G		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.245323153942888	2	FACETS	0.753	0.694	0.814	0.753	0.694	0.814	SUBCLONAL	2	TRUE	0	0.310615363944959	2		568	731	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982361	201982361	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755079997	NA	P-0009122-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1268	131	764	1	ENST00000359651.3:c.740G>A	p.Arg247Gln	p.R247Q	ENST00000359651		247	cGa/cAa	6/8	0.091029408235775	4	FACETS	0.79	0.715	0.87	0.395	0.357	0.435	INDETERMINATE	1	TRUE	2	0.310615363944959	4		765	1399	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686994	37686994	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009122-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	91	489	2	ENST00000447079.4:c.3898G>T	p.Ala1300Ser	p.A1300S	ENST00000447079	NM_015083.1	1300	Gcc/Tcc	14/14	0.247864179132204	4	FACETS	0.799	0.708	0.897	0.2	0.177	0.225	SUBCLONAL	1	TRUE	0	0.310615363944959	4		491	961	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671990	30671990	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009122-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1271	135	903	0	ENST00000376406.3:c.4970C>A	p.Ala1657Asp	p.A1657D	ENST00000376406	NM_014641.2	1657	gCc/gAc	10/15	0.149831403591089	4	FACETS	0.81	0.734	0.891	0.405	0.367	0.446	INDETERMINATE	1	TRUE	2	0.310615363944959	4		903	1406	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0009396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	54	473	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.13	2		473	801	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604778	48604778	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767383	NA	P-0009396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1265	80	557	0	ENST00000342988.3:c.1600C>T	p.Gln534Ter	p.Q534*	ENST00000342988	NM_005359.5	534	Cag/Tag	12/12	1	2	FACETS	0.915	0.802	1	0.915	0.802	1	CLONAL	1	TRUE	1	0.13	2		557	1345	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916143	9916143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762659685	NA	P-0009396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	78	560	0	ENST00000330684.3:c.2146G>A	p.Ala716Thr	p.A716T	ENST00000330684	NM_001134407.1	716	Gcc/Acc	10/13	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.13	2		560	1161	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	43	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.346	0.29	0.408	0.346	0.29	0.408	SUBCLONAL	1	TRUE	1	0.637899648008289	2		341	390	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30061018	30061022	+	frameshift_variant	Frame_Shift_Del	DEL	AAGTT	AAGTT	-	novel	NA	P-0009788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	125	484	0	ENST00000338641.4:c.850_854del	p.Lys284Ter	p.K284*	ENST00000338641	NM_000268.3	284	AAGTTt/t	9/16	0.637899648008289	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.637899648008289	1		484	257	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0010387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	9	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.578	0.382	0.83	0.578	0.382	0.83	SUBCLONAL	1	TRUE	1	0.11	2		341	283	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119726	108119726	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	15	335	0	ENST00000278616.4:c.1132del	p.Ser378ValfsTer12	p.S378Vfs*12	ENST00000278616	NM_000051.3	378	Agt/gt	9/63	1	2	FACETS	0.934	0.682	1	0.934	0.682	1	CLONAL	1	TRUE	1	0.11	2		335	292	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0010809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	85	284	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.387294819787734	3	FACETS	1	0.949	1			1	CLONAL	2	TRUE	NA	0.397793998170393	3		284	235	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	268	375	0	ENST00000269305.4:c.166G>T	p.Glu56Ter	p.E56*	ENST00000269305	NM_001126112.2	56	Gaa/Taa	4/11	0.397793998170393	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.397793998170393	2		375	601	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031925	26031925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	392	728	0	ENST00000244661.2:c.364C>T	p.Pro122Ser	p.P122S	ENST00000244661	NM_003537.3	122	Ccc/Tcc	1/1	0.397793998170393	3	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	1	0.397793998170393	3		728	1182	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420213	49420213	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	142	445	0	ENST00000301067.7:c.15536G>C	p.Arg5179Pro	p.R5179P	ENST00000301067	NM_003482.3	5179	cGt/cCt	48/54	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.397793998170393	2		445	669	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863561	68863562	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0010809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	519	423	0	ENST00000261769.5:c.2300_2301insC	p.Asp768Ter	p.D768*	ENST00000261769	NM_004360.3	767	ttt/ttCt	15/16	0.387294819787734	3	FACETS	1	0.99	1			1	CLONAL	3	TRUE	NA	0.397793998170393	3		423	972	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185227	123185230	+	frameshift_variant	Frame_Shift_Del	DEL	ACTC	ACTC	-	novel	NA	P-0010809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	95	473	0	ENST00000218089.9:c.1183_1186del	p.Thr395LeufsTer29	p.T395Lfs*29	ENST00000218089	NM_001042749.1	393	ttACTC/tt	13/35	0.397793998170393	2	FACETS	0.735	0.655	0.82	0.367	0.327	0.41	SUBCLONAL	1	TRUE	0	0.397793998170393	2		473	650	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0011307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	19	162	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.677	0.52	0.856	0.677	0.52	0.856	SUBCLONAL	1	TRUE	1	0.456613001433309	2		162	123	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588144	67588145	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0011307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	100	282	0	ENST00000274335.5:c.976_977del	p.Met326ValfsTer6	p.M326Vfs*6	ENST00000274335		325	aAT/a	7/15	0.142671072181877	3	FACETS	1	0.972	1	0.618	0.556	0.684	INDETERMINATE	1	TRUE	1	0.456613001433309	3		282	435	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643786	52643786	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0011307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	183	355	0	ENST00000394830.3:c.2110del	p.Met704TrpfsTer10	p.M704Wfs*10	ENST00000394830	NM_018313.4	704	Atg/tg	17/30	0.456613001433309	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.456613001433309	1		355	461	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162795	47162805	+	frameshift_variant	Frame_Shift_Del	DEL	GTCTCCTTGAC	GTCTCCTTGAC	-	novel	NA	P-0011307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	103	278	0	ENST00000409792.3:c.3321_3331del	p.Ser1108PhefsTer3	p.S1108Ffs*3	ENST00000409792	NM_014159.6	1107	gaGTCAAGGAGACat/gaat	3/21	0.456613001433309	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.456613001433309	1		278	293	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191546	10191553	+	frameshift_variant	Frame_Shift_Del	DEL	TCGTCAGG	TCGTCAGG	-	novel	NA	P-0011307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	190	307	0	ENST00000256474.2:c.542_549del	p.Val181AlafsTer72	p.V181Afs*72	ENST00000256474	NM_000551.3	180	aTCGTCAGG/a	3/3	0.456613001433309	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.456613001433309	1		307	577	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11193207	11193207	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	409	818	0	ENST00000361445.4:c.5294A>G	p.Asn1765Ser	p.N1765S	ENST00000361445	NM_004958.3	1765	aAt/aGt	38/58	0.702773970671014	1	FACETS	0.979	0.94	1	0.979	0.94	1	CLONAL	1	TRUE	0	0.702773970671014	1		818	771	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037923	49037924	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	278	615	0	ENST00000267163.4:c.2167dup	p.Ile723AsnfsTer28	p.I723Nfs*28	ENST00000267163	NM_000321.2	721	-/A	21/27	0.702773970671014	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.702773970671014	1		615	509	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593607	55593608	+	protein_altering_variant	In_Frame_Ins	INS	-	-	TCC	novel	NA	P-0012248-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	334	548	0	ENST00000288135.5:c.1673_1674insTCC	p.Lys558delinsAsnPro	p.K558delinsNP	ENST00000288135	NM_000222.2	558	aag/aaTCCg	11/21	0.715729269701321	3	FACETS	0.892	0.85	0.935	0.892	0.85	0.935	CLONAL	2	TRUE	1	0.715729269701321	3		548	710	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297716	15297716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568359179	NA	P-0012248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	204	711	2	ENST00000263388.2:c.1924G>A	p.Asp642Asn	p.D642N	ENST00000263388	NM_000435.2	642	Gac/Aac	12/33	1	2	FACETS	0.983	0.91	1	0.983	0.91	1	CLONAL	1	TRUE	1	0.350797936105785	2		713	1183	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191480	10191480	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913346	NA	P-0012248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	127	345	0	ENST00000256474.2:c.473T>C	p.Leu158Pro	p.L158P	ENST00000256474	NM_000551.3	158	cTg/cCg	3/3	0.333003206694618	1	FACETS	0.917	0.833	1	0.917	0.833	1	CLONAL	1	TRUE	0	0.350797936105785	1		345	651	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248234	59248234	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	13	22	0	ENST00000371222.2:c.509A>G	p.Tyr170Cys	p.Y170C	ENST00000371222	NM_002228.3	170	tAc/tGc	1/1	1	2	FACETS	1	0.766	1	1	0.766	1	CLONAL	1	TRUE	1	0.350797936105785	2		22	70	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870813	12870813	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	60	153	0	ENST00000228872.4:c.40G>T	p.Glu14Ter	p.E14*	ENST00000228872	NM_004064.3	14	Gag/Tag	1/3	0.337306596623333	3	FACETS	0.935	0.808	1	0.468	0.404	0.537	CLONAL	1	TRUE	1	0.350797936105785	3		153	430	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52692244	52692244	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	138	436	0	ENST00000394830.3:c.616G>T	p.Glu206Ter	p.E206*	ENST00000394830	NM_018313.4	206	Gaa/Taa	6/30	0.333003206694618	1	FACETS	0.844	0.768	0.923	0.844	0.768	0.923	CLONAL	1	TRUE	0	0.350797936105785	1		436	769	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180616	56180616	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	149	466	3	ENST00000399503.3:c.3945G>T	p.Glu1315Asp	p.E1315D	ENST00000399503	NM_005921.1	1315	gaG/gaT	16/20	0.337306596623333	3	FACETS	0.967	0.882	1	0.483	0.441	0.528	CLONAL	1	TRUE	1	0.350797936105785	3		469	1033	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240967	53240967	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0012248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	318	250	0	ENST00000375401.3:c.1242+2T>G		p.X414_splice	ENST00000375401	NM_004187.3	414			0.334486767778682	2	FACETS	0.97	0.925	1			1	CLONAL	3	TRUE	NA	0.350797936105785	2		250	623	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0012380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	25	284	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.339	0.266	0.422	0.339	0.266	0.422	SUBCLONAL	1	FALSE	1	0.337933011739709	2		284	437	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0012380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	88	512	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.529	0.468	0.595	0.529	0.468	0.595	SUBCLONAL	1	FALSE	1	0.337933011739709	2		512	984	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244091	153244091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	97	575	0	ENST00000281708.4:c.2066G>A	p.Arg689Gln	p.R689Q	ENST00000281708	NM_033632.3	689	cGg/cAg	12/12	1	2	FACETS	0.496	0.44	0.555	0.496	0.44	0.555	SUBCLONAL	1	FALSE	1	0.337933011739709	2		575	1158	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0012380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	95	492	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.564	0.501	0.631	0.564	0.501	0.631	SUBCLONAL	1	FALSE	1	0.337933011739709	2		492	997	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267491	198267491	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs763149798	NA	P-0012380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	67	461	0	ENST00000335508.6:c.1866G>C	p.Glu622Asp	p.E622D	ENST00000335508	NM_012433.2	622	gaG/gaC	14/25	1	2	FACETS	0.452	0.392	0.518	0.452	0.392	0.518	SUBCLONAL	1	FALSE	1	0.337933011739709	2		461	877	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140507763	140507763	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	113	484	0	ENST00000288602.6:c.708C>G	p.Asn236Lys	p.N236K	ENST00000288602	NM_004333.4	236	aaC/aaG	5/18	0.211057689407104	3	FACETS	0.879	0.791	0.974	0.44	0.395	0.487	CLONAL	1	FALSE	1	0.337933011739709	3		484	889	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248150	110248150	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	82	473	0	ENST00000374672.4:c.1322A>G	p.Asp441Gly	p.D441G	ENST00000374672	NM_004235.4	441	gAt/gGt	5/5	1	2	FACETS	0.59	0.52	0.666	0.59	0.52	0.666	SUBCLONAL	1	FALSE	1	0.337933011739709	2		473	822	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	288	399	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.471690959629495	2		399	882	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261554	142261555	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1043355995	NA	P-0012542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	120	445	0	ENST00000350721.4:c.3402dup	p.Asn1135Ter	p.N1135*	ENST00000350721	NM_001184.3	1134	-/T	17/47	1	2	FACETS	0.641	0.579	0.706	0.641	0.579	0.706	SUBCLONAL	1	TRUE	1	0.471690959629495	2		445	794	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0012542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	177	728	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	0.684	0.629	0.741	0.684	0.629	0.741	SUBCLONAL	1	TRUE	1	0.471690959629495	2		728	1098	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	98	307	5	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.661	0.59	0.735	0.661	0.59	0.735	SUBCLONAL	1	TRUE	1	0.471690959629495	2		312	629	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086001	16086001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	172	391	1	ENST00000281043.3:c.1177C>T	p.Arg393Cys	p.R393C	ENST00000281043	NM_005378.4	393	Cgc/Tgc	3/3	1	2	FACETS	0.94	0.866	1	0.94	0.866	1	CLONAL	1	TRUE	1	0.471690959629495	2		392	776	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106072	27106072	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	109	323	1	ENST00000324856.7:c.5683G>T	p.Glu1895Ter	p.E1895*	ENST00000324856	NM_006015.4	1895	Gag/Tag	20/20	1	2	FACETS	0.848	0.764	0.936	0.848	0.764	0.936	CLONAL	1	TRUE	1	0.471690959629495	2		324	545	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599359	55599359	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0012542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	54	307	0	ENST00000288135.5:c.2484+1G>A		p.X828_splice	ENST00000288135	NM_000222.2	828			1	2	FACETS	0.471	0.403	0.546	0.471	0.403	0.546	SUBCLONAL	1	TRUE	1	0.471690959629495	2		307	486	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950303	38950303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561445386	NA	P-0012542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	98	461	1	ENST00000357387.3:c.3647G>A	p.Arg1216His	p.R1216H	ENST00000357387	NM_152756.3	1216	cGt/cAt	31/38	1	2	FACETS	0.628	0.56	0.699	0.628	0.56	0.699	SUBCLONAL	1	TRUE	1	0.471690959629495	2		462	662	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962857	2962857	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	132	445	1	ENST00000396946.4:c.2051G>T	p.Gly684Val	p.G684V	ENST00000396946	NM_032415.4	684	gGg/gTg	16/25	1	2	FACETS	0.753	0.684	0.825	0.753	0.684	0.825	SUBCLONAL	1	TRUE	1	0.471690959629495	2		446	743	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423410	116423410	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs768125521	NA	P-0012542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	77	422	0	ENST00000397752.3:c.3685A>G	p.Met1229Val	p.M1229V	ENST00000397752	NM_000245.2	1229	Atg/Gtg	19/21	1	2	FACETS	0.507	0.445	0.574	0.507	0.445	0.574	SUBCLONAL	1	TRUE	1	0.471690959629495	2		422	644	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692985	89692985	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121909220	NA	P-0012542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	67	259	0	ENST00000371953.3:c.469G>T	p.Glu157Ter	p.E157*	ENST00000371953	NM_000314.4	157	Gaa/Taa	5/9	0.343515360221017	3	FACETS	0.765	0.666	0.871	0.382	0.333	0.436	SUBCLONAL	1	TRUE	1	0.471690959629495	3		259	459	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432464	49432464	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	189	580	1	ENST00000301067.7:c.8675del	p.Gly2892AlafsTer18	p.G2892Afs*18	ENST00000301067	NM_003482.3	2892	gGc/gc	34/54	1	2	FACETS	0.851	0.786	0.918	0.851	0.786	0.918	CLONAL	1	TRUE	1	0.471690959629495	2		581	942	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692918	89692918	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	110	335	0	ENST00000371953.3:c.402del	p.Met134IlefsTer13	p.M134Ifs*13	ENST00000371953	NM_000314.4	134	atG/at	5/9	0.343515360221017	3	FACETS	1	0.956	1	0.553	0.499	0.61	CLONAL	1	TRUE	1	0.471690959629495	3		335	521	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0012895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	112	391	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.294590468557893	3	FACETS	0.897	0.807	0.994	0.449	0.403	0.497	CLONAL	1	TRUE	1	0.34	3		391	859	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343020	70343020	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	225	642	0	ENST00000374080.3:c.1561C>T	p.Arg521Cys	p.R521C	ENST00000374080		521	Cgt/Tgt	11/45	0.249614968641867	4	FACETS	0.963	0.898	1	0.963	0.898	1	CLONAL	2	TRUE	2	0.34	4		642	921	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660144	227660144	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	128	748	0	ENST00000305123.5:c.3311del	p.Phe1104SerfsTer22	p.F1104Sfs*22	ENST00000305123	NM_005544.2	1104	tTc/tc	1/2	0.294590468557893	3	FACETS	1	0.921	1	0.509	0.461	0.56	CLONAL	1	TRUE	1	0.34	3		748	865	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045115	47045115	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	201	770	1	ENST00000377604.3:c.2356C>T	p.Gln786Ter	p.Q786*	ENST00000377604	NM_001204468.1	786	Caa/Taa	21/24	0.125487915682002	3	FACETS	0.837	0.777	0.899			1	INDETERMINATE	2	TRUE	NA	0.34	3		771	826	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913517	NA	P-0013114-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	218	443	0	ENST00000288135.5:c.1676T>A	p.Val559Asp	p.V559D	ENST00000288135	NM_000222.2	559	gTt/gAt	11/21	1	2	FACETS	0.921	0.861	0.981	0.921	0.861	0.981	CLONAL	1	TRUE	1	0.756554504957345	2		443	626	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594258	55594258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913523	NA	P-0013114-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	237	541	0	ENST00000288135.5:c.1961T>C	p.Val654Ala	p.V654A	ENST00000288135	NM_000222.2	654	gTg/gCg	13/21	1	2	FACETS	0.994	0.934	1	0.994	0.934	1	CLONAL	1	TRUE	1	0.756554504957345	2		541	630	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711883	89711883	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013114-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	77	393	0	ENST00000371953.3:c.501del	p.Ile168PhefsTer15	p.I168Ffs*15	ENST00000371953	NM_000314.4	167	acT/ac	6/9	0.756554504957345	1	FACETS	0.349	0.308	0.392	0.349	0.308	0.392	SUBCLONAL	1	TRUE	0	0.756554504957345	1		393	363	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741637	17741637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013697-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	87	130	0	ENST00000250003.3:c.308G>A	p.Arg103His	p.R103H	ENST00000250003	NM_002478.4	103	cGc/cAc	1/3	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.604422138322313	2		130	265	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439659	51439659	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013697-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	260	511	0	ENST00000262662.1:c.224A>G	p.His75Arg	p.H75R	ENST00000262662		75	cAt/cGt	4/4	0.604422138322313	1	FACETS	0.961	0.907	1	0.961	0.907	1	CLONAL	1	TRUE	0	0.604422138322313	1		511	625	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350416	89350416	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0013697-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	570	1105	0	ENST00000301030.4:c.2534T>A	p.Leu845Ter	p.L845*	ENST00000301030	NM_001256183.1	845	tTg/tAg	9/13	0.604422138322313	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.604422138322313	1		1105	1247	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636766	8636766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776233840	NA	P-0013697-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	256	398	0	ENST00000356435.5:c.143C>T	p.Thr48Met	p.T48M	ENST00000356435		48	aCg/aTg	2/35	0.604422138322313	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.604422138322313	1		398	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0014259-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	13	405	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.522585285118274	1	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	0	0.522585285118274	1		406	25	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs11575997	NA	P-0014438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	405	526	0	ENST00000269305.4:c.993+1G>T		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.849952148312833	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.854829825105521	1		526	533	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996839	100996839	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	390	598	0	ENST00000325455.5:c.1688C>T	p.Pro563Leu	p.P563L	ENST00000325455	NM_001202474.3	563	cCt/cTt	2/8	0.854829825105521	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.854829825105521	1		598	495	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962304	2962304	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs895009948	NA	P-0014438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	406	706	1	ENST00000396946.4:c.2233G>A	p.Gly745Ser	p.G745S	ENST00000396946	NM_032415.4	745	Ggc/Agc	17/25	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	1	TRUE	NA	0.854829825105521	2		707	716	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416680	121416680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014808-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	252	634	0	ENST00000257555.6:c.109C>T	p.Leu37Phe	p.L37F	ENST00000257555		37	Ctc/Ttc	1/10	0.411749632684091	4	FACETS	1	0.989	1	0.648	0.605	0.692	CLONAL	1	TRUE	2	0.412790159320026	4		634	1331	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520126	9520126	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014808-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	126	400	0	ENST00000353224.5:c.2143C>A	p.Gln715Lys	p.Q715K	ENST00000353224	NM_177990.2	715	Caa/Aaa	10/10	0.412790159320026	3	FACETS	0.997	0.903	1	0.498	0.451	0.548	CLONAL	1	TRUE	1	0.412790159320026	3		400	739	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719690	190719690	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014808-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	74	255	0	ENST00000441310.2:c.1692T>A	p.Asp564Glu	p.D564E	ENST00000441310	NM_000534.4	564	gaT/gaA	9/13	0.410284213693885	4	FACETS	1	0.975	1	0.736	0.649	0.829	CLONAL	1	TRUE	2	0.412790159320026	4		255	344	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435697	149435697	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014808-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	169	589	0	ENST00000286301.3:c.2446C>T	p.Arg816Cys	p.R816C	ENST00000286301	NM_005211.3	816	Cgc/Tgc	19/22	0.412790159320026	4	FACETS	0.926	0.85	1	0.309	0.283	0.336	CLONAL	1	TRUE	1	0.412790159320026	4		589	1249	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0015009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	106	554	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	0.975	0.876	1	1	0.987	1	CLONAL	2	TRUE	1	0.18	2		554	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578426	7578426	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	64	647	0	ENST00000269305.4:c.504del	p.His168GlnfsTer2	p.H168Qfs*2	ENST00000269305	NM_001126112.2	168	caC/ca	5/11	1	2	FACETS	0.883	0.763	1	0.883	0.763	1	CLONAL	1	TRUE	1	0.18	2		647	805	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879626	151879628	+	frameshift_variant	Frame_Shift_Del	DEL	AAG	AAG	T	novel	NA	P-0015009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	18	272	0	ENST00000262189.6:c.5317_5319delinsA	p.Leu1773ArgfsTer6	p.L1773Rfs*6	ENST00000262189	NM_170606.2	1773	CTT/A	36/59	1	2	FACETS	0.608	0.457	0.786	0.608	0.457	0.786	SUBCLONAL	1	TRUE	1	0.18	2		272	329	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856116	111856116	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1314581870	NA	P-0015131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	99	449	0	ENST00000341259.2:c.167C>T	p.Ala56Val	p.A56V	ENST00000341259	NM_005475.2	56	gCg/gTg	2/8	1	2	FACETS	0.974	0.867	1	0.974	0.867	1	CLONAL	1	TRUE	1	0.183350997542552	2		449	1109	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37856477	37856510	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	GCCGCAGTGAGCACCATGGAGCTGGCGGCCTTGT	GCCGCAGTGAGCACCATGGAGCTGGCGGCCTTGT	-	novel	NA	P-0015131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	34	255	0	ENST00000269571.5:c.-10_24del		p.*4*	ENST00000269571		?-7/1255		1/27	1	2	FACETS	0.803	0.656	0.969	0.803	0.656	0.969	CLONAL	1	TRUE	1	0.183350997542552	2		255	462	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	61	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.133603029896519	3	FACETS	0.955	0.824	1			1	INDETERMINATE	1	TRUE	NA	0.233069705001809	3		341	612	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0015477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	74	262	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.233069705001809	3	FACETS	0.798	0.702	0.902	0.798	0.702	0.902	CLONAL	2	TRUE	1	0.233069705001809	3		262	444	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0015477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	32	250	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.145396612764431	4	FACETS	0.851	0.691	1	0.425	0.345	0.516	CLONAL	1	TRUE	2	0.233069705001809	4		250	398	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0015477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	54	311	2	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.129623095629295	3	FACETS	1	0.906	1	0.54	0.462	0.626	INDETERMINATE	1	TRUE	1	0.233069705001809	3		313	479	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0015477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	17	147	1	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	0.145396612764431	4	FACETS	0.814	0.609	1	0.407	0.304	0.528	CLONAL	1	TRUE	2	0.233069705001809	4		148	221	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	65	411	0	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	0.129623095629295	3	FACETS	1	0.953	1	0.611	0.53	0.698	INDETERMINATE	1	TRUE	1	0.233069705001809	3		411	510	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741838	17741838	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	21	140	0	ENST00000250003.3:c.509C>T	p.Ala170Val	p.A170V	ENST00000250003	NM_002478.4	170	gCg/gTg	1/3	0.129623095629295	3	FACETS	0.906	0.709	1	0.906	0.709	1	INDETERMINATE	2	TRUE	1	0.233069705001809	3		140	111	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822709	72822709	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs774756480	NA	P-0015477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	49	451	0	ENST00000268489.5:c.9466A>G	p.Ser3156Gly	p.S3156G	ENST00000268489	NM_006885.3	3156	Agc/Ggc	10/10	0.177260895882885	0	FACETS	0.794	0.674	0.926			1	CLONAL	1	TRUE	0	0.233069705001809	0		451	406	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858244	27858244	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs763088293	NA	P-0015477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	58	382	0	ENST00000359303.2:c.327C>A	p.Asn109Lys	p.N109K	ENST00000359303	NM_003535.2	109	aaC/aaA	1/1	0.233069705001809	13	FACETS	1	0.887	1			1	CLONAL	2	TRUE	NA	0.233069705001809	13		382	548	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920182	76920182	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	34	406	0	ENST00000373344.5:c.3895G>T	p.Gly1299Trp	p.G1299W	ENST00000373344	NM_000489.3	1299	Ggg/Tgg	11/35	0.123496491916545	0	FACETS	0.48	0.392	0.58			1	INDETERMINATE	1	TRUE	0	0.233069705001809	0		406	466	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	49	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.448	0.379	0.525	0.448	0.379	0.525	SUBCLONAL	1	TRUE	1	0.34	2		341	643	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	59	632	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.492	0.423	0.568	0.492	0.423	0.568	SUBCLONAL	1	TRUE	1	0.34	2		635	705	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	104	604	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.959	0.86	1	0.959	0.86	1	CLONAL	1	TRUE	1	0.34	2		604	638	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	113	551	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.34	2		551	579	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	215	626	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.924	0.863	0.987	1	0.994	1	CLONAL	2	TRUE	1	0.34	2		626	684	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	169	609	6	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.34	2		615	707	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	167	580	1	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	0.831	0.767	0.897	1	0.991	1	CLONAL	2	TRUE	1	0.34	2		581	591	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	56	272	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	0.34	2		272	292	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161222	56161222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	40	629	0	ENST00000399503.3:c.1091G>A	p.Arg364Gln	p.R364Q	ENST00000399503	NM_005921.1	364	cGg/cAg	5/20	1	2	FACETS	0.357	0.295	0.425	0.357	0.295	0.425	SUBCLONAL	1	TRUE	1	0.34	2		629	660	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	279	779	1	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	1	2	FACETS	0.88	0.828	0.932	1	0.995	1	CLONAL	2	TRUE	1	0.34	2		780	933	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	11	239	2	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	2	FACETS	0.274	0.189	0.38	0.274	0.189	0.38	SUBCLONAL	1	TRUE	1	0.34	2		241	236	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928425	69928425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781567478	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	96	538	0	ENST00000352241.4:c.245C>T	p.Ala82Val	p.A82V	ENST00000352241	NM_198159.2	82	gCg/gTg	2/10	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.34	2		538	551	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521285	187521285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200468783	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	71	763	0	ENST00000441802.2:c.11870G>A	p.Arg3957His	p.R3957H	ENST00000441802	NM_005245.3	3957	cGt/cAt	22/27	1	2	FACETS	0.482	0.42	0.55	0.482	0.42	0.55	SUBCLONAL	1	TRUE	1	0.34	2		763	866	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654642	67654642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	61	654	0	ENST00000264010.4:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000264010	NM_006565.3	377	Cgt/Tgt	6/12	1	2	FACETS	0.444	0.382	0.512	0.444	0.382	0.512	SUBCLONAL	1	TRUE	1	0.34	2		654	808	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	89	546	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.887	0.788	0.993	0.887	0.788	0.993	CLONAL	1	TRUE	1	0.34	2		546	590	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40742171	40742171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1206035617	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	224	718	1	ENST00000392038.2:c.953C>T	p.Ala318Val	p.A318V	ENST00000392038	NM_001626.4	318	gCg/gTg	10/14	1	2	FACETS	0.83	0.775	0.886	1	0.993	1	CLONAL	2	TRUE	1	0.34	2		719	794	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795597	42795597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142397024	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	95	877	0	ENST00000575354.2:c.2677C>T	p.Pro893Ser	p.P893S	ENST00000575354	NM_015125.3	893	Ccc/Tcc	10/20	1	2	FACETS	0.623	0.554	0.697	0.623	0.554	0.697	SUBCLONAL	1	TRUE	1	0.34	2		877	897	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101300	27101300	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	128	740	0	ENST00000324856.7:c.4582C>T	p.Arg1528Ter	p.R1528*	ENST00000324856	NM_006015.4	1528	Cga/Tga	18/20	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.34	2		740	723	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752960	128752960	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	69	525	0	ENST00000377970.2:c.1121A>G	p.His374Arg	p.H374R	ENST00000377970	NM_002467.4	374	cAc/cGc	3/3	1	2	FACETS	0.613	0.534	0.699	0.613	0.534	0.699	SUBCLONAL	1	TRUE	1	0.34	2		525	662	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115837	8115837	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200935603	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	66	751	2	ENST00000346208.3:c.1183G>A	p.Ala395Thr	p.A395T	ENST00000346208		395	Gcc/Acc	6/6	1	2	FACETS	0.454	0.393	0.52	0.454	0.393	0.52	SUBCLONAL	1	TRUE	1	0.34	2		753	855	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672177	30672177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762832250	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	55	660	2	ENST00000376406.3:c.4783C>T	p.Arg1595Trp	p.R1595W	ENST00000376406	NM_014641.2	1595	Cgg/Tgg	10/15	1	2	FACETS	0.453	0.387	0.526	0.453	0.387	0.526	SUBCLONAL	1	TRUE	1	0.34	2		662	714	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5225773	5225773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1012604149	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	111	765	4	ENST00000357368.4:c.2459G>A	p.Arg820His	p.R820H	ENST00000357368	NM_002850.3	820	cGc/cAc	17/38	1	2	FACETS	0.715	0.642	0.793	0.715	0.642	0.793	SUBCLONAL	1	TRUE	1	0.34	2		769	913	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422384	47422384	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	50	576	0	ENST00000377045.4:c.23del	p.Pro8LeufsTer26	p.P8Lfs*26	ENST00000377045	NM_001654.4	6	ggC/gg	2/16	1	2	FACETS	0.495	0.42	0.578	0.495	0.42	0.578	SUBCLONAL	1	TRUE	1	0.34	2		576	594	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313336	65313336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1163622258	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	59	549	1	ENST00000342505.4:c.1778C>T	p.Thr593Met	p.T593M	ENST00000342505	NM_002227.2	593	aCg/aTg	13/25	1	2	FACETS	0.529	0.455	0.61	0.529	0.455	0.61	SUBCLONAL	1	TRUE	1	0.34	2		550	656	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317160	11317160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	57	688	1	ENST00000361445.4:c.334C>T	p.Arg112Trp	p.R112W	ENST00000361445	NM_004958.3	112	Cgg/Tgg	4/58	1	2	FACETS	0.459	0.393	0.532	0.459	0.393	0.532	SUBCLONAL	1	TRUE	1	0.34	2		689	730	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910549	29910549	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45585732	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	15	223	2	ENST00000376809.5:c.89G>A	p.Arg30Lys	p.R30K	ENST00000376809	NM_002116.7	30	aGg/aAg	2/8	1	2	FACETS	0.33	0.241	0.438	0.33	0.241	0.438	SUBCLONAL	1	TRUE	1	0.34	2		225	267	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	360046	360046	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	55	672	0	ENST00000262320.3:c.1043T>C	p.Ile348Thr	p.I348T	ENST00000262320	NM_003502.3	348	aTc/aCc	4/11	1	2	FACETS	0.465	0.397	0.539	0.465	0.397	0.539	SUBCLONAL	1	TRUE	1	0.34	2		672	696	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94201025	94201025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780133	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	44	450	0	ENST00000323929.3:c.1052G>A	p.Arg351His	p.R351H	ENST00000323929	NM_005591.3	351	cGt/cAt	10/20	1	2	FACETS	0.448	0.375	0.529	0.448	0.375	0.529	SUBCLONAL	1	TRUE	1	0.34	2		450	578	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10279006	10279006	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs779634956	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	137	616	0	ENST00000340748.4:c.755C>T	p.Pro252Leu	p.P252L	ENST00000340748		252	cCa/cTa	9/40	1	2	FACETS	0.95	0.864	1	0.95	0.864	1	CLONAL	1	TRUE	1	0.34	2		616	848	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260188	16260188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368603571	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	106	527	2	ENST00000375759.3:c.7453G>A	p.Ala2485Thr	p.A2485T	ENST00000375759	NM_015001.2	2485	Gcc/Acc	11/15	1	2	FACETS	0.994	0.893	1	0.994	0.893	1	CLONAL	1	TRUE	1	0.34	2		529	627	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553539	106553539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762241140	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	130	343	0	ENST00000369096.4:c.1504G>A	p.Ala502Thr	p.A502T	ENST00000369096	NM_001198.3	502	Gcc/Acc	5/7	1	2	FACETS	0.963	0.882	1	1	0.99	1	CLONAL	2	TRUE	1	0.34	2		343	397	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845633	63845634	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	33	338	0	ENST00000279873.7:c.1376dup	p.Pro461AlafsTer26	p.P461Afs*26	ENST00000279873	NM_032199.2	458	gcc/gCcc	9/10	1	2	FACETS	0.512	0.417	0.619	0.512	0.417	0.619	SUBCLONAL	1	TRUE	1	0.34	2		338	379	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683201	88683201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771452619	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	46	377	0	ENST00000372037.3:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000372037	NM_004329.2	471	Cgt/Tgt	12/13	1	2	FACETS	0.621	0.523	0.728	0.621	0.523	0.728	SUBCLONAL	1	TRUE	1	0.34	2		377	436	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760714	133760714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755821709	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	97	880	0	ENST00000318560.5:c.3037C>T	p.Arg1013Trp	p.R1013W	ENST00000318560	NM_005157.4	1013	Cgg/Tgg	11/11	1	2	FACETS	0.576	0.513	0.644	0.576	0.513	0.644	SUBCLONAL	1	TRUE	1	0.34	2		880	990	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107008	27107008	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	172	409	0	ENST00000324856.7:c.6619C>T	p.Gln2207Ter	p.Q2207*	ENST00000324856	NM_006015.4	2207	Cag/Tag	20/20	1	2	FACETS	0.877	0.811	0.944	1	0.992	1	CLONAL	2	TRUE	1	0.34	2		409	577	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692940	89692940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746152219	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	86	657	1	ENST00000371953.3:c.424C>T	p.Arg142Trp	p.R142W	ENST00000371953	NM_000314.4	142	Cgg/Tgg	5/9	1	2	FACETS	0.716	0.633	0.804	0.716	0.633	0.804	SUBCLONAL	1	TRUE	1	0.34	2		658	707	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261134	16261134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367966477	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	89	397	0	ENST00000375759.3:c.8399C>T	p.Ala2800Val	p.A2800V	ENST00000375759	NM_015001.2	2800	gCg/gTg	11/15	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.34	2		397	518	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261146	16261146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769982439	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	46	395	1	ENST00000375759.3:c.8411C>T	p.Ala2804Val	p.A2804V	ENST00000375759	NM_015001.2	2804	gCg/gTg	11/15	1	2	FACETS	0.566	0.477	0.665	0.566	0.477	0.665	SUBCLONAL	1	TRUE	1	0.34	2		396	478	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807477	36807477	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139437228	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	69	697	1	ENST00000373129.3:c.1187G>A	p.Arg396Gln	p.R396Q	ENST00000373129	NM_032017.1	396	cGg/cAg	12/12	1	2	FACETS	0.486	0.422	0.555	0.486	0.422	0.555	SUBCLONAL	1	TRUE	1	0.34	2		698	835	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725454	162725454	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	43	528	0	ENST00000367921.3:c.566A>G	p.Asp189Gly	p.D189G	ENST00000367921	NM_006182.2	189	gAt/gGt	7/18	1	2	FACETS	0.432	0.361	0.512	0.432	0.361	0.512	SUBCLONAL	1	TRUE	1	0.34	2		528	585	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421555	32421555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	112	631	0	ENST00000332351.3:c.1037C>T	p.Thr346Met	p.T346M	ENST00000332351	NM_024426.4	346	aCg/aTg	6/10	1	2	FACETS	0.907	0.817	1	0.907	0.817	1	CLONAL	1	TRUE	1	0.34	2		631	726	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949351	71949351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	140	691	1	ENST00000298229.2:c.3731C>T	p.Pro1244Leu	p.P1244L	ENST00000298229	NM_001567.3	1244	cCg/cTg	28/28	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.34	2		692	749	SUCCESS
EED	8726	MSKCC	GRCh37	11	85967532	85967532	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	47	421	1	ENST00000263360.6:c.530C>A	p.Pro177His	p.P177H	ENST00000263360	NM_003797.3	177	cCt/cAt	5/12	1	2	FACETS	0.751	0.636	0.878	0.751	0.636	0.878	SUBCLONAL	1	TRUE	1	0.34	2		422	368	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888166	112888166	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121918461	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	64	717	0	ENST00000351677.2:c.182A>C	p.Asp61Ala	p.D61A	ENST00000351677	NM_002834.3	61	gAt/gCt	3/16	1	2	FACETS	0.476	0.411	0.546	0.476	0.411	0.546	SUBCLONAL	1	TRUE	1	0.34	2		717	791	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237644	133237644	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	88	780	0	ENST00000320574.5:c.2971G>A	p.Glu991Lys	p.E991K	ENST00000320574	NM_006231.2	991	Gag/Aag	25/49	1	2	FACETS	0.598	0.529	0.673	0.598	0.529	0.673	SUBCLONAL	1	TRUE	1	0.34	2		780	865	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514431	103514431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	46	309	2	ENST00000355739.4:c.932C>T	p.Ser311Phe	p.S311F	ENST00000355739	NM_000123.3	311	tCc/tTc	8/15	1	2	FACETS	0.689	0.581	0.807	0.689	0.581	0.807	SUBCLONAL	1	TRUE	1	0.34	2		311	393	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132999	30132999	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749612527	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	65	671	1	ENST00000331968.5:c.602G>A	p.Arg201Gln	p.R201Q	ENST00000331968	NM_002742.2	201	cGg/cAg	4/18	1	2	FACETS	0.557	0.482	0.638	0.557	0.482	0.638	SUBCLONAL	1	TRUE	1	0.34	2		672	687	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610144	81610144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1305132938	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	101	442	0	ENST00000298171.2:c.1742C>T	p.Ala581Val	p.A581V	ENST00000298171	NM_000369.2	581	gCa/gTa	10/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.34	2		442	481	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358662	67358662	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	98	739	0	ENST00000327367.4:c.170C>T	p.Thr57Met	p.T57M	ENST00000327367	NM_005902.3	57	aCg/aTg	1/9	1	2	FACETS	0.717	0.639	0.8	0.717	0.639	0.8	SUBCLONAL	1	TRUE	1	0.34	2		739	804	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14021959	14021959	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	50	704	0	ENST00000311895.7:c.659C>A	p.Pro220His	p.P220H	ENST00000311895	NM_005236.2	220	cCt/cAt	4/11	1	2	FACETS	0.46	0.39	0.538	0.46	0.39	0.538	SUBCLONAL	1	TRUE	1	0.34	2		704	639	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804348	46804348	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	71	548	0	ENST00000290295.7:c.659G>A	p.Arg220His	p.R220H	ENST00000290295	NM_006361.5	220	cGc/cAc	2/2	1	2	FACETS	0.648	0.565	0.737	0.648	0.565	0.737	SUBCLONAL	1	TRUE	1	0.34	2		548	645	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437510	56437510	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	59	678	0	ENST00000407977.2:c.952G>T	p.Glu318Ter	p.E318*	ENST00000407977		318	Gag/Tag	8/10	1	2	FACETS	0.447	0.383	0.516	0.447	0.383	0.516	SUBCLONAL	1	TRUE	1	0.34	2		678	777	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439931	56439931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748533737	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	170	651	2	ENST00000407977.2:c.661C>T	p.Arg221Trp	p.R221W	ENST00000407977		221	Cgg/Tgg	6/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.34	2		653	868	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78858811	78858811	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1440436634	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	55	463	0	ENST00000306801.3:c.1846C>T	p.Arg616Cys	p.R616C	ENST00000306801	NM_020761.2	616	Cgc/Tgc	17/34	1	2	FACETS	0.495	0.423	0.575	0.495	0.423	0.575	SUBCLONAL	1	TRUE	1	0.34	2		463	653	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78931492	78931492	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs564814581	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	65	632	0	ENST00000306801.3:c.3439G>A	p.Val1147Ile	p.V1147I	ENST00000306801	NM_020761.2	1147	Gtc/Atc	29/34	1	2	FACETS	0.524	0.454	0.601	0.524	0.454	0.601	SUBCLONAL	1	TRUE	1	0.34	2		632	729	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211145	2211145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775729505	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	291	908	1	ENST00000398665.3:c.1399G>A	p.Val467Met	p.V467M	ENST00000398665	NM_032482.2	467	Gtg/Atg	15/28	1	2	FACETS	0.912	0.86	0.966	1	0.995	1	CLONAL	2	TRUE	1	0.34	2		909	938	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	86	905	1	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	1	2	FACETS	0.47	0.414	0.53	0.47	0.414	0.53	SUBCLONAL	1	TRUE	1	0.34	2		906	1077	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519792	29519792	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	192	721	0	ENST00000389048.3:c.1779G>T	p.Trp593Cys	p.W593C	ENST00000389048	NM_004304.4	593	tgG/tgT	9/29	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.34	2		721	766	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158636847	158636847	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	120	414	0	ENST00000263640.3:c.331+2T>G		p.X111_splice	ENST00000263640	NM_001105.4	111			1	2	FACETS	0.754	0.685	0.826	1	0.986	1	SUBCLONAL	2	TRUE	1	0.34	2		414	468	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321649	62321649	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs938432778	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	123	617	0	ENST00000360203.5:c.2268G>A	p.Met756Ile	p.M756I	ENST00000360203	NM_001283009.1	756	atG/atA	26/35	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.34	2		617	648	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29083929	29083929	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1444665408	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	17	221	2	ENST00000328354.6:c.1588G>A	p.Ala530Thr	p.A530T	ENST00000328354	NM_007194.3	530	Gcc/Acc	15/15	1	2	FACETS	0.422	0.315	0.548	0.422	0.315	0.548	SUBCLONAL	1	TRUE	1	0.34	2		223	237	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259517	89259517	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	72	466	2	ENST00000336596.2:c.661C>T	p.Gln221Ter	p.Q221*	ENST00000336596	NM_005233.5	221	Cag/Tag	3/17	1	2	FACETS	0.913	0.8	1	0.913	0.8	1	CLONAL	1	TRUE	1	0.34	2		468	464	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670718	134670718	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	50	562	0	ENST00000398015.3:c.629T>C	p.Met210Thr	p.M210T	ENST00000398015	NM_004441.4	210	aTg/aCg	3/16	1	2	FACETS	0.438	0.371	0.512	0.438	0.371	0.512	SUBCLONAL	1	TRUE	1	0.34	2		562	671	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523735	176523735	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	57	615	0	ENST00000292408.4:c.2146C>A	p.Pro716Thr	p.P716T	ENST00000292408	NM_213647.1	716	Cca/Aca	16/18	1	2	FACETS	0.504	0.432	0.583	0.504	0.432	0.583	SUBCLONAL	1	TRUE	1	0.34	2		615	665	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524306	176524306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201490532	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	77	779	4	ENST00000292408.4:c.2167C>T	p.Arg723Cys	p.R723C	ENST00000292408	NM_213647.1	723	Cgt/Tgt	17/18	1	2	FACETS	0.519	0.455	0.589	0.519	0.455	0.589	SUBCLONAL	1	TRUE	1	0.34	2		783	872	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694608	176694608	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750040600	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	62	575	1	ENST00000439151.2:c.5192G>A	p.Arg1731His	p.R1731H	ENST00000439151	NM_022455.4	1731	cGt/cAt	15/23	1	2	FACETS	0.575	0.496	0.661	0.575	0.496	0.661	SUBCLONAL	1	TRUE	1	0.34	2		576	634	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176710839	176710839	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	40	555	0	ENST00000439151.2:c.6061C>T	p.His2021Tyr	p.H2021Y	ENST00000439151	NM_022455.4	2021	Cat/Tat	20/23	1	2	FACETS	0.335	0.277	0.4	0.335	0.277	0.4	SUBCLONAL	1	TRUE	1	0.34	2		555	702	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481530	20481530	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	55	421	0	ENST00000346618.3:c.599G>T	p.Gly200Val	p.G200V	ENST00000346618	NM_001949.4	200	gGg/gTg	3/7	1	2	FACETS	0.601	0.514	0.696	0.601	0.514	0.696	SUBCLONAL	1	TRUE	1	0.34	2		421	538	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777962	27777962	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	26	291	0	ENST00000369163.2:c.111G>T	p.Lys37Asn	p.K37N	ENST00000369163	NM_003536.2	37	aaG/aaT	1/1	1	2	FACETS	0.52	0.413	0.643	0.52	0.413	0.643	SUBCLONAL	1	TRUE	1	0.34	2		291	294	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323261	31323261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576012253	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	17	242	0	ENST00000412585.2:c.728G>A	p.Arg243Gln	p.R243Q	ENST00000412585	NM_005514.6	243	cGg/cAg	4/8	1	2	FACETS	0.369	0.275	0.48	0.369	0.275	0.48	SUBCLONAL	1	TRUE	1	0.34	2		242	271	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469889	157469889	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	36	592	0	ENST00000346085.5:c.2683C>A	p.Pro895Thr	p.P895T	ENST00000346085	NM_020732.3	895	Ccc/Acc	9/20	1	2	FACETS	0.319	0.262	0.385	0.319	0.262	0.385	SUBCLONAL	1	TRUE	1	0.34	2		592	663	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394338	162394338	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771259513	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	84	388	1	ENST00000366898.1:c.730G>A	p.Val244Ile	p.V244I	ENST00000366898	NM_004562.2	244	Gtc/Atc	6/12	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.34	2		389	455	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864370	162864370	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	52	502	0	ENST00000366898.1:c.143A>G	p.Lys48Arg	p.K48R	ENST00000366898	NM_004562.2	48	aAg/aGg	2/12	1	2	FACETS	0.52	0.442	0.606	0.52	0.442	0.606	SUBCLONAL	1	TRUE	1	0.34	2		502	588	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211013	55211013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	59	463	1	ENST00000275493.2:c.256G>A	p.Ala86Thr	p.A86T	ENST00000275493	NM_005228.3	86	Gct/Act	3/28	1	2	FACETS	0.608	0.523	0.7	0.608	0.523	0.7	SUBCLONAL	1	TRUE	1	0.34	2		464	571	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843336	128843336	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	165	778	0	ENST00000249373.3:c.443A>G	p.Gln148Arg	p.Q148R	ENST00000249373	NM_005631.4	148	cAg/cGg	2/12	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.34	2		778	828	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939479	68939479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778971988	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	124	561	0	ENST00000288368.4:c.464G>A	p.Arg155Gln	p.R155Q	ENST00000288368	NM_024870.2	155	cGg/cAg	5/40	1	2	FACETS	0.802	0.73	0.876	1	0.987	1	CLONAL	2	TRUE	1	0.34	2		561	455	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542217	141542217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	40	583	0	ENST00000220592.5:c.2506G>A	p.Gly836Arg	p.G836R	ENST00000220592	NM_012154.3	836	Ggg/Agg	19/19	1	2	FACETS	0.347	0.287	0.413	0.347	0.287	0.413	SUBCLONAL	1	TRUE	1	0.34	2		583	679	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739691	145739691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747307935	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	229	706	2	ENST00000428558.2:c.1760C>T	p.Ala587Val	p.A587V	ENST00000428558	NM_004260.3	587	gCg/gTg	11/22	1	2	FACETS	0.876	0.819	0.934	1	0.994	1	CLONAL	2	TRUE	1	0.34	2		708	769	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27192600	27192600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs539332352	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	121	546	0	ENST00000380036.4:c.1603C>T	p.Arg535Cys	p.R535C	ENST00000380036	NM_000459.3	535	Cgc/Tgc	11/23	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.34	2		546	642	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407858	139407858	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750859847	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	83	639	2	ENST00000277541.6:c.2339G>A	p.Arg780Gln	p.R780Q	ENST00000277541	NM_017617.3	780	cGg/cAg	14/34	1	2	FACETS	0.636	0.56	0.717	0.636	0.56	0.717	SUBCLONAL	1	TRUE	1	0.34	2		641	768	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413893	139413893	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	71	493	0	ENST00000277541.6:c.865+2C>G		p.X289_splice	ENST00000277541	NM_017617.3	289			1	2	FACETS	0.657	0.573	0.747	0.657	0.573	0.747	SUBCLONAL	1	TRUE	1	0.34	2		493	636	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045551	47045551	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1365868137	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	38	651	3	ENST00000377604.3:c.2518G>A	p.Gly840Ser	p.G840S	ENST00000377604	NM_001204468.1	840	Ggc/Agc	22/24	1	2	FACETS	0.307	0.253	0.369	0.307	0.253	0.369	SUBCLONAL	1	TRUE	1	0.34	2		654	727	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424213	47424213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	72	636	3	ENST00000377045.4:c.218C>T	p.Ala73Val	p.A73V	ENST00000377045	NM_001654.4	73	gCc/gTc	4/16	1	2	FACETS	0.623	0.544	0.708	0.623	0.544	0.708	SUBCLONAL	1	TRUE	1	0.34	2		639	680	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527850	103527850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774653208	NA	P-0015885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	69	481	0	ENST00000355739.4:c.3158G>A	p.Gly1053Glu	p.G1053E	ENST00000355739	NM_000123.3	1053	gGa/gAa	15/15	1	2	FACETS	0.683	0.595	0.778	0.683	0.595	0.778	SUBCLONAL	1	TRUE	1	0.34	2		481	594	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0015886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	44	688	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	1	2	FACETS	0.75	0.627	0.888	0.75	0.627	0.888	SUBCLONAL	1	TRUE	1	0.13	2		688	902	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0015886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	25	441	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.626	0.492	0.782	0.626	0.492	0.782	SUBCLONAL	1	TRUE	1	0.13	2		441	614	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339286	70339286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	42	250	0	ENST00000374080.3:c.163G>A	p.Glu55Lys	p.E55K	ENST00000374080		55	Gag/Aag	2/45	1	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.13	1		250	427	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266531	115266531	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	36	536	1	ENST00000438362.2:c.1984C>T	p.Gln662Ter	p.Q662*	ENST00000438362	NM_001242891.1	662	Caa/Taa	16/20	1	2	FACETS	0.781	0.64	0.94	0.781	0.64	0.94	CLONAL	1	TRUE	1	0.13	2		537	709	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77064592	77064592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	41	554	0	ENST00000356341.3:c.825G>T	p.Lys275Asn	p.K275N	ENST00000356341	NM_002576.4	275	aaG/aaT	8/15	1	2	FACETS	0.842	0.699	1	0.842	0.699	1	CLONAL	1	TRUE	1	0.13	2		554	749	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375936	118375936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	27	440	0	ENST00000534358.1:c.9329C>T	p.Ser3110Phe	p.S3110F	ENST00000534358	NM_005933.3	3110	tCt/tTt	27/36	1	2	FACETS	0.827	0.657	1	0.827	0.657	1	CLONAL	1	TRUE	1	0.13	2		440	502	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69203049	69203049	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	33	471	0	ENST00000462284.1:c.76C>G	p.Pro26Ala	p.P26A	ENST00000462284	NM_002392.5	26	Cca/Gca	2/11	1	2	FACETS	0.853	0.693	1	0.853	0.693	1	CLONAL	1	TRUE	1	0.13	2		471	595	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983225	7983225	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	36	536	0	ENST00000319144.4:c.789C>G	p.Phe263Leu	p.F263L	ENST00000319144	NM_001139.2	263	ttC/ttG	7/15	1	2	FACETS	0.851	0.698	1	0.851	0.698	1	CLONAL	1	TRUE	1	0.13	2		536	651	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170016852	170016852	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	55	582	1	ENST00000295797.4:c.1657G>A	p.Asp553Asn	p.D553N	ENST00000295797	NM_002740.5	553	Gat/Aat	17/18	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.13	2		583	757	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928321	178928321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	33	461	0	ENST00000263967.3:c.1507G>A	p.Glu503Lys	p.E503K	ENST00000263967	NM_006218.2	503	Gaa/Aaa	9/21	1	2	FACETS	0.883	0.718	1	0.883	0.718	1	CLONAL	1	TRUE	1	0.13	2		461	575	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501488	149501488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771923448	NA	P-0015886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	52	746	0	ENST00000261799.4:c.2299G>A	p.Glu767Lys	p.E767K	ENST00000261799	NM_002609.3	767	Gag/Aag	16/23	1	2	FACETS	0.978	0.831	1	0.978	0.831	1	CLONAL	1	TRUE	1	0.13	2		746	818	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900158	101900158	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	20	251	0	ENST00000374994.4:c.592C>T	p.Gln198Ter	p.Q198*	ENST00000374994	NM_004612.2	198	Cag/Tag	4/9	1	2	FACETS	0.965	0.738	1	0.965	0.738	1	CLONAL	1	TRUE	1	0.13	2		251	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520006	NA	P-0017023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	448	589	1	ENST00000269305.4:c.821T>G	p.Val274Gly	p.V274G	ENST00000269305	NM_001126112.2	274	gTt/gGt	8/11	NA	2	FACETS	0.969	0.938	0.999			1	INDETERMINATE	2	TRUE	NA	0.709394472476917	2		590	652	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821598	72821618	+	inframe_deletion	In_Frame_Del	DEL	CCGCCGCCGCCGCCGCCGCCA	CCGCCGCCGCCGCCGCCGCCA	-	rs781609559	NA	P-0017023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	53	71	1	ENST00000268489.5:c.10557_10577del	p.Gly3521_Gly3527del	p.G3521_G3527del	ENST00000268489	NM_006885.3	3519	ggTGGCGGCGGCGGCGGCGGCGGc/ggc	10/10	NA	2	FACETS	0.844	0.733	0.962			1	INDETERMINATE	1	TRUE	NA	0.709394472476917	2		72	177	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	459	605	0	ENST00000322088.6:c.767C>A	p.Ser256Tyr	p.S256Y	ENST00000322088	NM_014225.5	256	tCc/tAc	6/15	0.709394472476917	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.709394472476917	3		605	838	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495384	56495384	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	70	577	0	ENST00000267101.3:c.3574G>C	p.Asp1192His	p.D1192H	ENST00000267101	NM_001982.3	1192	Gat/Cat	28/28	0.709394472476917	4	FACETS	0.353	0.307	0.403			1	SUBCLONAL	1	TRUE	NA	0.709394472476917	4		577	956	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605868	46605868	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745977062	NA	P-0017023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	208	591	0	ENST00000263734.3:c.1516G>A	p.Ala506Thr	p.A506T	ENST00000263734	NM_001430.4	506	Gcc/Acc	11/16	0.709394472476917	3	FACETS	0.82	0.761	0.881	0.41	0.38	0.441	CLONAL	1	TRUE	1	0.709394472476917	3		591	969	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518806	204518806	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	47	247	0	ENST00000367182.3:c.1469C>A	p.Ala490Glu	p.A490E	ENST00000367182	NM_001278516.1	490	gCa/gAa	11/11	0.709394472476917	4	FACETS	0.412	0.347	0.483	0.137	0.115	0.161	SUBCLONAL	1	TRUE	1	0.709394472476917	4		247	550	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110590	4110590	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	95	644	0	ENST00000262948.5:c.367C>A	p.His123Asn	p.H123N	ENST00000262948	NM_030662.3	123	Cac/Aac	3/11	0.683318541735743	2	FACETS	0.435	0.387	0.485	0.217	0.193	0.243	SUBCLONAL	1	TRUE	0	0.709394472476917	2		644	616	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740380	145740380	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	106	742	0	ENST00000428558.2:c.1560C>A	p.Ser520Arg	p.S520R	ENST00000428558	NM_004260.3	520	agC/agA	9/22	0.401742648457761	5	FACETS	0.553	0.494	0.616	0.184	0.164	0.206	INDETERMINATE	1	TRUE	2	0.709394472476917	5		742	1115	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391901	139391901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	211	778	0	ENST00000277541.6:c.6290C>T	p.Pro2097Leu	p.P2097L	ENST00000277541	NM_017617.3	2097	cCg/cTg	34/34	0.709394472476917	3	FACETS	0.843	0.783	0.905	0.421	0.391	0.453	CLONAL	1	TRUE	1	0.709394472476917	3		778	956	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0017042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	289	284	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	0.661002851975005	2		284	829	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0017042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	213	398	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.661002851975005	2		398	634	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46527739	46527740	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	146	247	0	ENST00000262741.5:c.625dup	p.Ile209AsnfsTer12	p.I209Nfs*12	ENST00000262741	NM_003629.3	209	ata/aAta	6/10	1	2	FACETS	0.84	0.771	0.911	0.84	0.771	0.911	CLONAL	1	TRUE	1	0.661002851975005	2		247	526	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186501401	186501401	+	start_lost	Translation_Start_Site	SNP	T	T	A	novel	NA	P-0017042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	122	214	0	ENST00000323963.5:c.2T>A	p.Met1?	p.M1?	ENST00000323963		1	aTg/aAg	1/11	1	2	FACETS	0.761	0.692	0.833	0.761	0.692	0.833	SUBCLONAL	1	TRUE	1	0.661002851975005	2		214	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577107	7577107	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1057523347	NA	P-0017365-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1268	107	684	2	ENST00000269305.4:c.831T>A	p.Cys277Ter	p.C277*	ENST00000269305	NM_001126112.2	277	tgT/tgA	8/11	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.143134257468785	2		686	1375	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0017598-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	92	631	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	0.320096551186008	1	FACETS	0.973	0.868	1	0.973	0.868	1	CLONAL	1	TRUE	0	0.320096551186008	1		631	496	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0017752-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	9	284	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.561	0.379	0.782	0.561	0.379	0.782	SUBCLONAL	1	FALSE	1	0.572743740043007	2		284	56	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876476	35876476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017752-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	11	618	0	ENST00000303115.3:c.1268C>T	p.Ser423Phe	p.S423F	ENST00000303115	NM_002185.3	423	tCt/tTt	8/8	0.289957099982255	0	FACETS	0.155	0.107	0.212			1	INDETERMINATE	1	FALSE	0	0.572743740043007	0		618	106	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100523	157100527	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCG	GCCCG	-	novel	NA	P-0017752-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	56	252	0	ENST00000346085.5:c.1463_1467del	p.Pro488LeufsTer45	p.P488Lfs*45	ENST00000346085	NM_020732.3	487	aGCCCG/a	1/20	0.112445683370842	4	FACETS	0.732	0.629	0.844	0.366	0.314	0.422	INDETERMINATE	1	FALSE	2	0.572743740043007	4		252	420	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265667	10265667	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017752-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	25	662	0	ENST00000340748.4:c.1510G>C	p.Glu504Gln	p.E504Q	ENST00000340748		504	Gag/Cag	19/40	0.501106366101685	4	FACETS	0.452	0.356	0.561	0.226	0.178	0.281	SUBCLONAL	1	FALSE	2	0.572743740043007	4		662	304	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148675	20148675	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017752-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	11	215	0	ENST00000379607.5:c.388C>T	p.Gln130Ter	p.Q130*	ENST00000379607	NM_001412.3	130	Cag/Tag	6/7	0.561232139123432	2	FACETS	0.784	0.558	1			1	CLONAL	1	FALSE	NA	0.572743740043007	2		215	49	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	74	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.364231301136513	2		341	380	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0018013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	158	546	1	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	0.364231301136513	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.364231301136513	1		547	646	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644591	3644591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767473953	NA	P-0018013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	129	536	0	ENST00000294008.3:c.2023G>A	p.Gly675Arg	p.G675R	ENST00000294008	NM_032444.2	675	Ggg/Agg	10/15	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.364231301136513	2		536	666	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781871	3781871	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	150	580	0	ENST00000262367.5:c.4796G>A	p.Ser1599Asn	p.S1599N	ENST00000262367	NM_004380.2	1599	aGc/aAc	29/31	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.364231301136513	2		580	776	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974742	21974743	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0018013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	85	233	0	ENST00000304494.5:c.84dup	p.Arg29AlafsTer15	p.R29Afs*15	ENST00000304494	NM_000077.4	28	-/G	1/3	0.364231301136513	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.364231301136513	1		233	320	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904887	101904888	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	69	414	0	ENST00000374994.4:c.878dup	p.Asn293LysfsTer40	p.N293Kfs*40	ENST00000374994	NM_004612.2	292	tta/ttAa	5/9	0.364231301136513	1	FACETS	0.75	0.656	0.851	0.75	0.656	0.851	SUBCLONAL	1	TRUE	0	0.364231301136513	1		414	413	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938552	44938553	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0018013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	108	317	0	ENST00000377967.4:c.3101_3102del	p.Lys1034IlefsTer18	p.K1034Ifs*18	ENST00000377967	NM_021140.2	1034	AAa/a	20/29	1	1	FACETS	0.857	0.781	0.935	1	0.988	1	CLONAL	2	TRUE	0	0.364231301136513	1		317	283	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380276	+	missense_variant	Missense_Mutation	DNP	TT	TT	GC	novel	NA	P-0018457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	175	544	0	ENST00000311936.3:c.182_183delinsGC	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAA/cGC	3/5	1	2	FACETS	0.942	0.87	1	0.942	0.87	1	CLONAL	1	TRUE	1	0.517618356918707	2		544	718	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737107	145737109	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs780986647	NA	P-0018457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	117	601	0	ENST00000428558.2:c.3457_3459del	p.Glu1153del	p.E1153del	ENST00000428558	NM_004260.3	1153	GAG/-	21/22	0.51830918398013	4	FACETS	0.914	0.824	1	0.305	0.274	0.336	CLONAL	1	TRUE	1	0.517618356918707	4		601	751	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22412955	22412955	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	65	195	0	ENST00000344548.3:c.202C>T	p.Arg68Ter	p.R68*	ENST00000344548	NM_001039802.1	68	Cga/Tga	5/7	0.508554787062282	1	FACETS	0.96	0.847	1	0.96	0.847	1	CLONAL	1	TRUE	0	0.517618356918707	1		195	194	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0018488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	258	262	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.587551628065291	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.587551628065291	3		262	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0018488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	428	618	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.587551628065291	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.587551628065291	2		618	680	SUCCESS
APC	324	MSKCC	GRCh37	5	112175328	112175328	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	201	210	0	ENST00000257430.4:c.4037C>A	p.Ser1346Ter	p.S1346*	ENST00000257430	NM_000038.5	1346	tCa/tAa	16/16	0.587551628065291	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	0	0.587551628065291	3		210	286	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857680	9857680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303700994	NA	P-0018488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	104	378	1	ENST00000330684.3:c.3721C>T	p.Arg1241Trp	p.R1241W	ENST00000330684	NM_001134407.1	1241	Cgg/Tgg	13/13	0.587551628065291	3	FACETS	1	0.953	1	0.548	0.494	0.604	CLONAL	1	TRUE	1	0.587551628065291	3		379	418	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024380	31024380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201302084	NA	P-0018488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	512	624	0	ENST00000375687.4:c.3865C>T	p.Arg1289Trp	p.R1289W	ENST00000375687	NM_015338.5	1289	Cgg/Tgg	13/13	0.587551628065291	7	FACETS	0.945	0.905	0.986	0.567	0.543	0.592	CLONAL	3	TRUE	2	0.587551628065291	7		624	1517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0020714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	249	927	1	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.367834969738405	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.378040292812812	2		928	635	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979323	40979323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	462	871	2	ENST00000373198.4:c.1810G>T	p.Asp604Tyr	p.D604Y	ENST00000373198	NM_133170.3	604	Gac/Tac	11/32	0.378040292812812	4	FACETS	0.956	0.919	0.992	0.956	0.919	0.992	CLONAL	4	TRUE	0	0.378040292812812	4		873	881	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439781	52439781	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	200	754	1	ENST00000460680.1:c.931G>A	p.Asp311Asn	p.D311N	ENST00000460680	NM_004656.3	311	Gat/Aat	10/17	0.367834969738405	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	0	0.378040292812812	2		755	524	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696644	47696644	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519964	NA	P-0021931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	88	635	0	ENST00000347630.2:c.304T>G	p.Phe102Val	p.F102V	ENST00000347630	NM_001007230.1	102	Ttc/Gtc	5/11	1	2	FACETS	0.85	0.753	0.953	0.85	0.753	0.953	CLONAL	1	TRUE	1	0.31	2		635	668	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0022187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	118	779	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		779	315	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0022198-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	1830	391	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.416874196907276	13	FACETS	1	0.99	1	1	0.99	1	CLONAL	11	TRUE	2	0.416874196907276	13		391	2607	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423407	116423407	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913671	NA	P-0022198-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1813	486	351	0	ENST00000397752.3:c.3682G>C	p.Asp1228His	p.D1228H	ENST00000397752	NM_000245.2	1228	Gac/Cac	19/21	0.416874196907276	21	FACETS	1	0.958	1			1	CLONAL	5	TRUE	NA	0.416874196907276	21		351	2299	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988529	41988529	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022198-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	117	573	0	ENST00000219905.7:c.1321C>G	p.Leu441Val	p.L441V	ENST00000219905	NM_001164273.1	441	Cta/Gta	3/24	1	2	FACETS	0.742	0.669	0.818	0.742	0.669	0.818	SUBCLONAL	1	TRUE	1	0.416874196907276	2		573	757	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500902	8500902	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022198-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	96	543	1	ENST00000356435.5:c.1980C>A	p.His660Gln	p.H660Q	ENST00000356435		660	caC/caA	13/35	0.398277443838705	1	FACETS	0.697	0.623	0.775	0.697	0.623	0.775	SUBCLONAL	1	TRUE	0	0.416874196907276	1		544	523	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248067	110248067	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022198-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	93	561	0	ENST00000374672.4:c.1405G>C	p.Asp469His	p.D469H	ENST00000374672	NM_004235.4	469	Gac/Cac	5/5	NA	2	FACETS	0.507	0.45	0.568			1	INDETERMINATE	1	TRUE	NA	0.416874196907276	2		561	880	SUCCESS
MET	4233	MSKCC	GRCh37	7	116417457	116417457	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786202724	NA	P-0022198-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1297	1041	383	0	ENST00000397752.3:c.3274G>A	p.Val1092Ile	p.V1092I	ENST00000397752	NM_000245.2	1092	Gta/Ata	16/21	0.416874196907276	21	FACETS	0.963	0.937	0.99			1	CLONAL	11	TRUE	NA	0.416874196907276	21		383	2338	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938159	76938159	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022198-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	63	629	0	ENST00000373344.5:c.2589A>C	p.Gln863His	p.Q863H	ENST00000373344	NM_000489.3	863	caA/caC	9/35	0.343665758000476	2	FACETS	0.393	0.339	0.452	0.197	0.169	0.226	SUBCLONAL	1	TRUE	0	0.416874196907276	2		629	769	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0022839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	169	492	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.519256975242425	2		492	630	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780684	56780684	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	196	513	0	ENST00000337432.4:c.699C>G	p.His233Gln	p.H233Q	ENST00000337432	NM_058216.2	233	caC/caG	4/9	1	2	FACETS	0.907	0.841	0.976	0.907	0.841	0.976	CLONAL	1	TRUE	1	0.519256975242425	2		513	832	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0023157-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	530	300	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.61318918186796	6	FACETS	1	0.994	1	0.892	0.863	0.921	CLONAL	4	TRUE	1	0.61318918186796	6		300	863	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0023157-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	745	422	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.61318918186796	6	FACETS	1	0.995	1	0.673	0.651	0.695	CLONAL	3	TRUE	1	0.61318918186796	6		423	1608	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851074	63851074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143074852	NA	P-0023157-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	179	748	1	ENST00000279873.7:c.1852G>A	p.Ala618Thr	p.A618T	ENST00000279873	NM_032199.2	618	Gcc/Acc	10/10	0.595287079781754	3	FACETS	0.942	0.869	1	0.471	0.434	0.509	CLONAL	1	TRUE	1	0.61318918186796	3		749	810	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0023157-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	455	828	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	0.602132675204311	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.61318918186796	2		828	737	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729601	41729601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023157-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	161	655	1	ENST00000242208.4:c.928C>T	p.Arg310Trp	p.R310W	ENST00000242208	NM_002192.2	310	Cgg/Tgg	3/3	0.61318918186796	6	FACETS	0.922	0.844	1	0.184	0.168	0.201	CLONAL	1	TRUE	1	0.61318918186796	6		656	1268	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223144	5223144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1007529586	NA	P-0023157-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	52	1200	1	ENST00000357368.4:c.2659G>A	p.Glu887Lys	p.E887K	ENST00000357368	NM_002850.3	887	Gag/Aag	18/38	0.602132675204311	2	FACETS	0.176	0.149	0.206	0.088	0.074	0.103	SUBCLONAL	1	TRUE	0	0.61318918186796	2		1201	962	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249091	55249091	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519861	NA	P-0023157-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1386	336	862	0	ENST00000275493.2:c.2389T>A	p.Cys797Ser	p.C797S	ENST00000275493	NM_005228.3	797	Tgc/Agc	20/28	0.61318918186796	6	FACETS	1	0.994	1	0.283	0.267	0.3	CLONAL	1	TRUE	1	0.61318918186796	6		862	1722	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267276	41267299	+	inframe_deletion	In_Frame_Del	DEL	ACAAAACAAATGTTAAATTCTTGG	ACAAAACAAATGTTAAATTCTTGG	-	novel	NA	P-0023157-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	133	439	0	ENST00000349496.5:c.860_883del	p.Asn287_Ala295delinsThr	p.N287_A295delinsT	ENST00000349496	NM_001904.3	287	aACAAAACAAATGTTAAATTCTTGGct/act	6/15	0.576092968032375	3	FACETS	1	0.976	1	0.396	0.362	0.432	CLONAL	1	TRUE	0	0.61318918186796	3		439	477	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023278-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	129	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.815	0.742	0.891	0.815	0.742	0.891	CLONAL	1	TRUE	1	0.561134894929591	2		341	564	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0023278-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	164	126	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.941	0.868	1	0.941	0.868	1	CLONAL	1	TRUE	1	0.561134894929591	2		126	621	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180629	32180629	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1278741655	NA	P-0023278-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	121	538	0	ENST00000375023.3:c.2498C>T	p.Pro833Leu	p.P833L	ENST00000375023	NM_004557.3	833	cCc/cTc	16/30	1	2	FACETS	0.5	0.452	0.552	0.5	0.452	0.552	SUBCLONAL	1	TRUE	1	0.561134894929591	2		538	862	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659850	227659850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1486271813	NA	P-0023278-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	260	550	0	ENST00000305123.5:c.3605C>T	p.Pro1202Leu	p.P1202L	ENST00000305123	NM_005544.2	1202	cCc/cTc	1/2	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.561134894929591	2		550	805	SUCCESS
BTK	695	MSKCC	GRCh37	X	100609652	100609652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023278-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	176	469	1	ENST00000308731.7:c.1597G>A	p.Gly533Arg	p.G533R	ENST00000308731	NM_000061.2	533	Gga/Aga	16/19	1	2	FACETS	0.866	0.8	0.935	0.866	0.8	0.935	CLONAL	1	TRUE	1	0.561134894929591	2		470	724	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	507	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.698555774370994	3	FACETS	0.991	0.955	1	0.991	0.955	1	CLONAL	2	TRUE	1	0.698555774370994	3		341	988	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0023682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	587	917	1	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.693954590416832	2	FACETS	0.954	0.926	0.981	0.954	0.926	0.981	CLONAL	2	TRUE	0	0.698555774370994	2		918	881	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249635	110249635	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	732	1129	0	ENST00000374672.4:c.1040A>G	p.Asn347Ser	p.N347S	ENST00000374672	NM_004235.4	347	aAt/aGt	3/5	0.698555774370994	2	FACETS	0.998	0.973	1	0.998	0.973	1	CLONAL	2	TRUE	0	0.698555774370994	2		1129	1050	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023151	27023179	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	-	novel	NA	P-0023682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	385	104	0	ENST00000324856.7:c.267_295del	p.Ser90ProfsTer11	p.S90Pfs*11	ENST00000324856	NM_006015.4	86	gGCGGAGCCGGCAGCGGCGGCGGGCCCGGC/g	1/20	NA	2	FACETS	1	0.997	1			1	INDETERMINATE	2	TRUE	NA	0.698555774370994	2		104	446	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	375	274	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	0.659024587874237	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.698555774370994	2		274	469	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175996744	175996769	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTGAATTTAACACAGCACACATTA	GGCTGAATTTAACACAGCACACATTA	-	novel	NA	P-0023682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	338	622	2	ENST00000367669.3:c.1668_1693del	p.Asn557LeufsTer19	p.N557Lfs*19	ENST00000367669	NM_022457.5	556	gcTAATGTGTGCTGTGTTAAATTCAGCCcc/gccc	15/20	0.694790767039194	3	FACETS	0.834	0.793	0.875	0.834	0.793	0.875	CLONAL	2	TRUE	1	0.698555774370994	3		624	783	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78831606	78831606	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	314	681	1	ENST00000306801.3:c.1415T>C	p.Ile472Thr	p.I472T	ENST00000306801	NM_020761.2	472	aTc/aCc	13/34	0.644992357738108	4	FACETS	1	0.994	1	0.748	0.706	0.79	CLONAL	1	TRUE	2	0.698555774370994	4		682	1021	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815709	32815709	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1328042727	NA	P-0023682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	324	805	0	ENST00000354258.4:c.1907A>G	p.Tyr636Cys	p.Y636C	ENST00000354258	NM_000593.5	636	tAc/tGc	8/11	0.698555774370994	3	FACETS	1	0.978	1	0.533	0.503	0.564	CLONAL	1	TRUE	1	0.698555774370994	3		805	1174	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0023748-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	124	284	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.189949161281021	5	FACETS	0.932	0.843	1	0.466	0.421	0.514	CLONAL	2	TRUE	1	0.189949161281021	5		284	900	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0023748-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	161	248	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.189949161281021	5	FACETS	0.983	0.907	1	0.983	0.907	1	CLONAL	4	TRUE	1	0.189949161281021	5		248	554	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182641	38182641	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs387907272	NA	P-0023748-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	14	368	0	ENST00000396334.3:c.794T>C	p.Leu265Pro	p.L265P	ENST00000396334	NM_002468.4	265	cTg/cCg	5/5	0.149313190491393	1	FACETS	0.389	0.28	0.521	0.389	0.28	0.521	SUBCLONAL	1	TRUE	0	0.189949161281021	1		368	343	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832398	72832398	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023748-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	37	546	0	ENST00000268489.5:c.4183G>C	p.Asp1395His	p.D1395H	ENST00000268489	NM_006885.3	1395	Gat/Cat	9/10	0.189949161281021	2	FACETS	0.838	0.69	1	0.419	0.345	0.502	CLONAL	1	TRUE	0	0.189949161281021	2		546	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577596	7577597	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0023748-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	40	609	0	ENST00000269305.4:c.683_684dup	p.Cys229ThrfsTer19	p.C229Tfs*19	ENST00000269305	NM_001126112.2	228	-/AC	7/11	0.189949161281021	1	FACETS	0.689	0.572	0.82	0.689	0.572	0.82	SUBCLONAL	1	TRUE	0	0.189949161281021	1		609	553	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526700	106526700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023748-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	47	577	0	ENST00000359195.3:c.2993C>T	p.Ser998Phe	p.S998F	ENST00000359195	NM_002649.2	998	tCt/tTt	10/11	1	2	FACETS	0.884	0.745	1	0.884	0.745	1	CLONAL	1	TRUE	1	0.189949161281021	2		577	560	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0023910-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	60	391	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.834462864195563	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	3	TRUE	0	0.833952311814442	3		391	67	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0023910-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	13	422	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.834462864195563	3	FACETS	0.502	0.363	0.666	0.167	0.121	0.222	SUBCLONAL	1	TRUE	0	0.833952311814442	3		423	88	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445007	89445007	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023910-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	46	385	1	ENST00000336596.2:c.1327A>G	p.Ile443Val	p.I443V	ENST00000336596	NM_005233.5	443	Att/Gtt	6/17	0.834462864195563	3	FACETS	0.942	0.831	1	0.942	0.831	1	CLONAL	2	TRUE	1	0.833952311814442	3		386	83	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280314	1280314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561203868	NA	P-0023910-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	106	829	0	ENST00000310581.5:c.1909G>A	p.Asp637Asn	p.D637N	ENST00000310581	NM_198253.2	637	Gac/Aac	4/16	0.833952311814442	8	FACETS	1	0.957	1			1	CLONAL	4	TRUE	NA	0.833952311814442	8		829	209	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039380	47039380	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0023910-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3	62	749	0	ENST00000377604.3:c.1003A>T	p.Lys335Ter	p.K335*	ENST00000377604	NM_001204468.1	335	Aag/Tag	10/24	0.800961769915967	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.833952311814442	2		749	65	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	218	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.931	0.869	0.995	0.931	0.869	0.995	CLONAL	1	TRUE	1	0.629188856973131	2		341	744	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0023924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	45	473	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.192	0.161	0.227	0.192	0.161	0.227	SUBCLONAL	1	TRUE	1	0.629188856973131	2		473	744	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0023924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	162	802	5	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.524292698205435	1	FACETS	0.668	0.617	0.721	0.668	0.617	0.721	SUBCLONAL	1	TRUE	0	0.629188856973131	1		807	528	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039133	49039133	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0023924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	40	305	0	ENST00000267163.4:c.2212-1G>C		p.X738_splice	ENST00000267163	NM_000321.2	738			1	2	FACETS	0.505	0.422	0.595	0.505	0.422	0.595	SUBCLONAL	1	TRUE	1	0.629188856973131	2		305	252	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498433	89498433	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369423490	NA	P-0023924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	34	521	2	ENST00000336596.2:c.2405C>T	p.Thr802Met	p.T802M	ENST00000336596	NM_005233.5	802	aCg/aTg	14/17	1	2	FACETS	0.219	0.179	0.265	0.219	0.179	0.265	SUBCLONAL	1	TRUE	1	0.629188856973131	2		523	493	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057904	27057904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	272	827	4	ENST00000324856.7:c.1612C>T	p.Gln538Ter	p.Q538*	ENST00000324856	NM_006015.4	538	Cag/Tag	3/20	1	2	FACETS	0.997	0.938	1	0.997	0.938	1	CLONAL	1	TRUE	1	0.629188856973131	2		831	867	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623569	43623569	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	32	486	0	ENST00000355710.3:c.3197A>C	p.Asp1066Ala	p.D1066A	ENST00000355710	NM_020975.4	1066	gAc/gCc	20/20	1	2	FACETS	0.2	0.162	0.243	0.2	0.162	0.243	SUBCLONAL	1	TRUE	1	0.629188856973131	2		486	509	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999546	100999546	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868723861	NA	P-0023924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	45	973	3	ENST00000325455.5:c.256G>A	p.Ala86Thr	p.A86T	ENST00000325455	NM_001202474.3	86	Gca/Aca	1/8	1	2	FACETS	0.177	0.148	0.21	0.177	0.148	0.21	SUBCLONAL	1	TRUE	1	0.629188856973131	2		976	807	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042725	42042725	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	42	604	1	ENST00000219905.7:c.6920A>G	p.Asp2307Gly	p.D2307G	ENST00000219905	NM_001164273.1	2307	gAt/gGt	17/24	1	2	FACETS	0.21	0.175	0.25	0.21	0.175	0.25	SUBCLONAL	1	TRUE	1	0.629188856973131	2		605	635	SUCCESS
APC	324	MSKCC	GRCh37	5	112175189	112175199	+	frameshift_variant	Frame_Shift_Del	DEL	AATACCCTGCA	AATACCCTGCA	-	novel	NA	P-0023924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	208	328	1	ENST00000257430.4:c.3902_3912del	p.Thr1301SerfsTer10	p.T1301Sfs*10	ENST00000257430	NM_000038.5	1300	AATACCCTGCAa/a	16/16	0.629188856973131	2	FACETS	0.859	0.811	0.906	0.859	0.811	0.906	CLONAL	2	TRUE	0	0.629188856973131	2		329	385	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0024302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	43	473	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.370696173067812	3	FACETS	0.828	0.704	0.961	0.828	0.704	0.961	CLONAL	2	FALSE	1	0.370696173067812	3		473	166	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578277	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs1555525902	NA	P-0024302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	71	754	0	ENST00000269305.4:c.572_574del	p.Pro191del	p.P191del	ENST00000269305	NM_001126112.2	191	cCTCag/cag	6/11	0.327727421821379	2	FACETS	0.883	0.783	0.986	0.883	0.783	0.986	CLONAL	2	FALSE	0	0.370696173067812	2		754	217	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932980	39932980	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238996683	NA	P-0024302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	67	750	0	ENST00000378444.4:c.1619G>A	p.Arg540Gln	p.R540Q	ENST00000378444	NM_001123385.1	540	cGg/cAg	4/15	0.242117685347126	3	FACETS	1	0.873	1	0.501	0.436	0.57	CLONAL	1	FALSE	1	0.370696173067812	3		750	428	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0024302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	39	688	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	0.370696173067812	3	FACETS	1	0.949	1	0.685	0.575	0.805	CLONAL	1	FALSE	1	0.370696173067812	3		688	182	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827927	40827927	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536150112	NA	P-0024302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	223	659	0	ENST00000373198.4:c.2501G>A	p.Arg834His	p.R834H	ENST00000373198	NM_133170.3	834	cGc/cAc	17/32	0.370696173067812	5	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	FALSE	2	0.370696173067812	5		659	563	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593520	48593520	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	24	300	0	ENST00000342988.3:c.1271A>T	p.Asp424Val	p.D424V	ENST00000342988	NM_005359.5	424	gAt/gTt	10/12	0.370696173067812	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	0	0.370696173067812	1		300	75	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11301617	11301617	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	76	819	0	ENST00000361445.4:c.1534G>C	p.Gly512Arg	p.G512R	ENST00000361445	NM_004958.3	512	Gga/Cga	10/58	1	2	FACETS	0.954	0.84	1	0.954	0.84	1	CLONAL	1	FALSE	1	0.370696173067812	2		819	430	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911953	32911953	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202212	NA	P-0024302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	37	667	0	ENST00000380152.3:c.3461C>T	p.Thr1154Ile	p.T1154I	ENST00000380152		1154	aCc/aTc	11/27	0.370696173067812	3	FACETS	0.794	0.666	0.933	0.794	0.666	0.933	CLONAL	2	FALSE	1	0.370696173067812	3		667	149	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247367	153247368	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0024302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	17	352	0	ENST00000281708.4:c.1434_1435del	p.Asp480CysfsTer4	p.D480Cfs*4	ENST00000281708	NM_033632.3	478	tcTCga/tcga	10/12	1	2	FACETS	1	0.797	1	1	0.797	1	CLONAL	1	FALSE	1	0.370696173067812	2		352	87	SUCCESS
APC	324	MSKCC	GRCh37	5	112175218	112175219	+	stop_gained	Nonsense_Mutation	DNP	AA	AA	TT	novel	NA	P-0024302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	25	271	2	ENST00000257430.4:c.3927_3928inv	p.Glu1309_Lys1310delinsAspTer	p.E1309_K1310delinsD*	ENST00000257430	NM_000038.5	1309	gaAAag/gaTTag	16/16	0.370696173067812	3	FACETS	1	0.88	1	1	0.88	1	CLONAL	2	FALSE	1	0.370696173067812	3		273	72	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128432165	128432165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1371596131	NA	P-0024302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	60	694	1	ENST00000265960.3:c.281G>A	p.Arg94Gln	p.R94Q	ENST00000265960	NM_001006617.1	94	cGa/cAa	3/12	0.370696173067812	3	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	FALSE	1	0.370696173067812	3		695	169	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056449	26056449	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs760498539	NA	P-0024734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	164	297	0	ENST00000343677.2:c.208G>C	p.Gly70Arg	p.G70R	ENST00000343677	NM_005319.3	70	Ggc/Cgc	1/1	0.641127336186523	4	FACETS	0.917	0.841	0.995	0.306	0.28	0.332	CLONAL	1	TRUE	1	0.641127336186523	4		297	916	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155102	108155102	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	205	612	0	ENST00000278616.4:c.3895G>C	p.Ala1299Pro	p.A1299P	ENST00000278616	NM_000051.3	1299	Gcc/Ccc	26/63	0.636198609480068	2	FACETS	0.894	0.833	0.958	0.447	0.416	0.479	CLONAL	1	TRUE	0	0.641127336186523	2		612	715	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281471	49281471	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	310	664	0	ENST00000282018.3:c.518T>C	p.Leu173Pro	p.L173P	ENST00000282018	NM_020377.2	173	cTc/cCc	1/1	NA	2	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.641127336186523	2		664	935	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943631	9943631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770071260	NA	P-0024734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	283	635	2	ENST00000330684.3:c.1310G>A	p.Arg437Gln	p.R437Q	ENST00000330684	NM_001134407.1	437	cGg/cAg	5/13	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.641127336186523	2		637	840	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579360	7579361	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0024734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	372	777	0	ENST00000269305.4:c.326dup	p.Arg110ProfsTer39	p.R110Pfs*39	ENST00000269305	NM_001126112.2	109	ttc/ttTc	4/11	0.641127336186523	1	FACETS	0.993	0.948	1	0.993	0.948	1	CLONAL	1	TRUE	0	0.641127336186523	1		777	794	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556301	29556301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771012891	NA	P-0024734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	269	608	0	ENST00000356175.3:c.2668C>T	p.Pro890Ser	p.P890S	ENST00000356175	NM_000267.3	890	Cct/Tct	21/57	0.641127336186523	3	FACETS	0.919	0.861	0.978	0.306	0.287	0.326	CLONAL	1	TRUE	0	0.641127336186523	3		608	1206	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30310106	30310106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	17	59	0	ENST00000322652.5:c.1006A>G	p.Thr336Ala	p.T336A	ENST00000322652	NM_015355.2	336	Act/Gct	9/16	0.641127336186523	3	FACETS	0.62	0.468	0.795	0.207	0.156	0.265	SUBCLONAL	1	TRUE	0	0.641127336186523	3		59	113	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259582	89259582	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	159	331	0	ENST00000336596.2:c.726G>A	p.Met242Ile	p.M242I	ENST00000336596	NM_005233.5	242	atG/atA	3/17	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.641127336186523	2		331	454	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166467	32166467	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1972	493	843	0	ENST00000375023.3:c.4576G>C	p.Val1526Leu	p.V1526L	ENST00000375023	NM_004557.3	1526	Gtg/Ctg	25/30	0.641127336186523	5	FACETS	1	0.993	1	0.306	0.291	0.321	CLONAL	1	TRUE	1	0.641127336186523	5		843	2465	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187504	32187504	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1608	671	811	1	ENST00000375023.3:c.1375T>A	p.Phe459Ile	p.F459I	ENST00000375023	NM_004557.3	459	Ttc/Atc	8/30	0.641127336186523	5	FACETS	0.901	0.866	0.936	0.45	0.433	0.468	CLONAL	2	TRUE	1	0.641127336186523	5		812	2279	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444267	50444267	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	265	314	0	ENST00000331340.3:c.197A>G	p.Glu66Gly	p.E66G	ENST00000331340	NM_006060.4	66	gAg/gGg	4/8	0.465014207784107	3	FACETS	0.899	0.85	0.949			1	CLONAL	2	TRUE	NA	0.641127336186523	3		314	607	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759596	133759596	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	362	798	0	ENST00000318560.5:c.1919A>G	p.Asp640Gly	p.D640G	ENST00000318560	NM_005157.4	640	gAc/gGc	11/11	0.641127336186523	2	FACETS	1	0.953	1	0.502	0.476	0.529	CLONAL	1	TRUE	0	0.641127336186523	2		798	1124	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	213	792	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.925	0.86	0.992	1	0.993	1	CLONAL	2	TRUE	1	0.24656046857151	2		796	934	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	127	936	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.943	0.853	1	0.943	0.853	1	CLONAL	1	TRUE	1	0.24656046857151	2		936	1092	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	69	819	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.701	0.61	0.801	0.701	0.61	0.801	SUBCLONAL	1	TRUE	1	0.24656046857151	2		819	798	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	53	461	1	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.773	0.659	0.898	0.773	0.659	0.898	SUBCLONAL	1	TRUE	1	0.24656046857151	2		462	556	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	145	969	4	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.939	0.854	1	0.939	0.854	1	CLONAL	1	TRUE	1	0.24656046857151	2		973	1253	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260241	10260241	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555690467	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	144	815	1	ENST00000340748.4:c.2426C>T	p.Ser809Leu	p.S809L	ENST00000340748		809	tCg/tTg	25/40	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.24656046857151	2		816	1098	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521299	187521299	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1166479124	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	69	747	2	ENST00000441802.2:c.11856del	p.Phe3952LeufsTer31	p.F3952Lfs*31	ENST00000441802	NM_005245.3	3952	ttT/tt	22/27	1	2	FACETS	0.64	0.556	0.731	0.64	0.556	0.731	SUBCLONAL	1	TRUE	1	0.24656046857151	2		749	875	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	40	323	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	0.906	0.755	1	0.906	0.755	1	CLONAL	1	TRUE	1	0.24656046857151	2		323	358	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	103	873	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.889	0.794	0.99	0.889	0.794	0.99	CLONAL	1	TRUE	1	0.24656046857151	2		874	940	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	77	661	6	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.678	0.594	0.769	0.678	0.594	0.769	SUBCLONAL	1	TRUE	1	0.24656046857151	2		667	921	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	67	390	0	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.887	0.771	1	0.887	0.771	1	CLONAL	1	TRUE	1	0.24656046857151	2		390	613	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107258	193107258	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	45	382	0	ENST00000367435.3:c.467G>A	p.Arg156His	p.R156H	ENST00000367435	NM_024529.4	156	cGt/cAt	6/17	1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	1	0.24656046857151	2		382	365	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78811795	78811795	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	44	576	0	ENST00000306801.3:c.1210C>T	p.Arg404Trp	p.R404W	ENST00000306801	NM_020761.2	404	Cgg/Tgg	10/34	1	2	FACETS	0.45	0.376	0.532	0.45	0.376	0.532	SUBCLONAL	1	TRUE	1	0.24656046857151	2		576	793	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576098	29576098	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1135402852	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	89	716	0	ENST00000356175.3:c.4076del	p.Pro1359LeufsTer26	p.P1359Lfs*26	ENST00000356175	NM_000267.3	1357	ttC/tt	30/57	1	2	FACETS	0.795	0.704	0.893	0.795	0.704	0.893	SUBCLONAL	1	TRUE	1	0.24656046857151	2		716	908	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224583	108224583	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881329	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	50	330	1	ENST00000278616.4:c.8762C>T	p.Thr2921Met	p.T2921M	ENST00000278616	NM_000051.3	2921	aCg/aTg	60/63	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.24656046857151	2		331	366	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957465	175957465	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	65	552	0	ENST00000367669.3:c.1931del	p.Asn644ThrfsTer3	p.N644Tfs*3	ENST00000367669	NM_022457.5	644	aAc/ac	17/20	1	2	FACETS	0.749	0.649	0.858	0.749	0.649	0.858	SUBCLONAL	1	TRUE	1	0.24656046857151	2		552	704	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588972	67588972	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	48	412	0	ENST00000274335.5:c.1067del	p.Leu356TrpfsTer17	p.L356Wfs*17	ENST00000274335		355	Ttt/tt	8/15	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.24656046857151	2		412	365	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235935	108235935	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770641163	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	60	430	1	ENST00000278616.4:c.8977C>T	p.Arg2993Ter	p.R2993*	ENST00000278616	NM_000051.3	2993	Cga/Tga	62/63	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.24656046857151	2		431	484	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030631	48030631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs191109849	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	85	574	2	ENST00000234420.5:c.3245C>T	p.Pro1082Leu	p.P1082L	ENST00000234420	NM_000179.2	1082	cCg/cTg	5/10	1	2	FACETS	0.793	0.7	0.894	0.793	0.7	0.894	SUBCLONAL	1	TRUE	1	0.24656046857151	2		576	869	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981721	101981721	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555075353	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	43	407	3	ENST00000282441.5:c.147del	p.Ala50ProfsTer24	p.A50Pfs*24	ENST00000282441	NM_001130145.2	48	Ccc/cc	1/9	1	2	FACETS	0.722	0.604	0.853	0.722	0.604	0.853	SUBCLONAL	1	TRUE	1	0.24656046857151	2		410	483	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209593	98209593	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	101	647	1	ENST00000331920.6:c.3945del	p.Tyr1316ThrfsTer56	p.Y1316Tfs*56	ENST00000331920	NM_000264.3	1315	ccC/cc	23/24	1	2	FACETS	0.999	0.892	1	0.999	0.892	1	CLONAL	1	TRUE	1	0.24656046857151	2		648	820	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468398	89468398	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1467832547	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	40	253	0	ENST00000336596.2:c.1938del	p.Glu647ArgfsTer9	p.E647Rfs*9	ENST00000336596	NM_005233.5	644	tcA/tc	11/17	1	2	FACETS	1	0.845	1	1	0.845	1	CLONAL	1	TRUE	1	0.24656046857151	2		253	320	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750678	128750678	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	86	689	0	ENST00000377970.2:c.215C>A	p.Pro72His	p.P72H	ENST00000377970	NM_002467.4	72	cCc/cAc	2/3	1	2	FACETS	0.905	0.8	1	0.905	0.8	1	CLONAL	1	TRUE	1	0.24656046857151	2		689	771	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478220	99478220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	80	469	0	ENST00000268035.6:c.3124C>T	p.Arg1042Cys	p.R1042C	ENST00000268035	NM_000875.3	1042	Cgt/Tgt	16/21	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.24656046857151	2		469	635	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500476	99500476	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	97	776	0	ENST00000268035.6:c.3913del	p.Leu1305TrpfsTer45	p.L1305Wfs*45	ENST00000268035	NM_000875.3	1303	gtC/gt	21/21	1	2	FACETS	0.816	0.726	0.912	0.816	0.726	0.912	CLONAL	1	TRUE	1	0.24656046857151	2		776	964	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606678	29606678	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs188859061	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	105	743	2	ENST00000389048.3:c.1202G>A	p.Arg401Gln	p.R401Q	ENST00000389048	NM_004304.4	401	cGa/cAa	5/29	1	2	FACETS	0.927	0.829	1	0.927	0.829	1	CLONAL	1	TRUE	1	0.24656046857151	2		745	919	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363141	40363141	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	51	618	0	ENST00000397332.2:c.1088T>C	p.Leu363Pro	p.L363P	ENST00000397332	NM_001033082.2	363	cTg/cCg	3/3	1	2	FACETS	0.494	0.419	0.578	0.494	0.419	0.578	SUBCLONAL	1	TRUE	1	0.24656046857151	2		618	837	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798843	45798843	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs372267274	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	121	696	0	ENST00000450313.1:c.389-1G>C		p.X130_splice	ENST00000450313	NM_012222.2	130			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.24656046857151	2		696	805	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268911	115268911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	93	735	0	ENST00000438362.2:c.1699G>A	p.Gly567Ser	p.G567S	ENST00000438362	NM_001242891.1	567	Ggt/Agt	14/20	1	2	FACETS	0.941	0.836	1	0.941	0.836	1	CLONAL	1	TRUE	1	0.24656046857151	2		735	802	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100690	8100690	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	136	966	1	ENST00000346208.3:c.664T>C	p.Tyr222His	p.Y222H	ENST00000346208		222	Tac/Cac	3/6	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.24656046857151	2		967	1101	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944697	71944697	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	96	916	0	ENST00000298229.2:c.2123-2A>C		p.X708_splice	ENST00000298229	NM_001567.3	708			1	2	FACETS	0.728	0.647	0.815	0.728	0.647	0.815	SUBCLONAL	1	TRUE	1	0.24656046857151	2		916	1070	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998342	100998342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	12	33	0	ENST00000325455.5:c.1460G>A	p.Gly487Asp	p.G487D	ENST00000325455	NM_001202474.3	487	gGc/gAc	1/8	1	2	FACETS	1	0.751	1	1	0.909	1	CLONAL	2	TRUE	1	0.24656046857151	2		33	47	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871836	35871836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1183733796	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	90	624	0	ENST00000216797.5:c.670G>A	p.Ala224Thr	p.A224T	ENST00000216797	NM_020529.2	224	Gca/Aca	5/6	1	2	FACETS	0.944	0.837	1	0.944	0.837	1	CLONAL	1	TRUE	1	0.24656046857151	2		624	773	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060587	38060587	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1258	137	1095	1	ENST00000250448.2:c.1402G>A	p.Val468Ile	p.V468I	ENST00000250448	NM_004496.3	468	Gtc/Atc	2/2	1	2	FACETS	0.797	0.722	0.875	0.797	0.722	0.875	SUBCLONAL	1	TRUE	1	0.24656046857151	2		1096	1395	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59871029	59871029	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1369814158	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	87	671	0	ENST00000259008.2:c.1402T>C	p.Trp468Arg	p.W468R	ENST00000259008	NM_032043.2	468	Tgg/Cgg	10/20	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.24656046857151	2		671	699	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575053	48575054	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	A	novel	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	28	377	0	ENST00000342988.3:c.250-2dup		p.X84_splice	ENST00000342988	NM_005359.5	84			1	2	FACETS	0.575	0.459	0.707	0.575	0.459	0.707	SUBCLONAL	1	TRUE	1	0.24656046857151	2		377	395	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098425	11098425	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	135	621	2	ENST00000358026.2:c.947del	p.Pro316LeufsTer10	p.P316Lfs*10	ENST00000358026	NM_001128849.1	315	Ccc/cc	6/36	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.24656046857151	2		623	1015	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314638	30314638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	109	697	1	ENST00000262643.3:c.1187C>T	p.Pro396Leu	p.P396L	ENST00000262643	NM_001238.2	396	cCg/cTg	12/12	1	2	FACETS	0.855	0.766	0.95	0.855	0.766	0.95	CLONAL	1	TRUE	1	0.24656046857151	2		698	1034	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249914	39249914	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs397517154	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	96	840	0	ENST00000402219.2:c.1655G>T	p.Arg552Met	p.R552M	ENST00000402219	NM_005633.3	552	aGg/aTg	10/23	1	2	FACETS	0.925	0.823	1	0.925	0.823	1	CLONAL	1	TRUE	1	0.24656046857151	2		840	842	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116180	209116180	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	63	568	0	ENST00000345146.2:c.96del	p.Tyr34ThrfsTer11	p.Y34Tfs*11	ENST00000345146	NM_005896.2	32	ttT/tt	3/10	1	2	FACETS	0.789	0.682	0.905	0.789	0.682	0.905	CLONAL	1	TRUE	1	0.24656046857151	2		568	648	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181894	38181894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772707495	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	46	345	0	ENST00000396334.3:c.518G>A	p.Arg173His	p.R173H	ENST00000396334	NM_002468.4	173	cGt/cAt	3/5	0.24656046857151	2	FACETS	0.662	0.557	0.778	0.331	0.278	0.389	SUBCLONAL	1	TRUE	0	0.24656046857151	2		345	564	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939983	49939983	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1347342848	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	73	820	0	ENST00000296474.3:c.1060A>G	p.Lys354Glu	p.K354E	ENST00000296474	NM_002447.2	354	Aag/Gag	1/20	1	2	FACETS	0.5	0.436	0.57	0.5	0.436	0.57	SUBCLONAL	1	TRUE	1	0.24656046857151	2		820	1184	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805327	32805327	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	120	441	0	ENST00000374899.4:c.595T>C	p.Phe199Leu	p.F199L	ENST00000374899	NM_018833.2	199	Ttc/Ctc	3/12	0.198183936628704	2	FACETS	0.782	0.708	0.86	0.782	0.708	0.86	SUBCLONAL	2	TRUE	0	0.24656046857151	2		441	622	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0025381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	70	514	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.85	0.743	0.966	0.85	0.743	0.966	CLONAL	1	FALSE	1	0.335958289778413	2		514	490	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682399	52682400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	75	484	0	ENST00000394830.3:c.773dup	p.Asn258LysfsTer6	p.N258Kfs*6	ENST00000394830	NM_018313.4	258	aat/aaAt	8/30	1	2	FACETS	0.841	0.738	0.951	0.841	0.738	0.951	CLONAL	1	FALSE	1	0.335958289778413	2		484	531	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211473	46211473	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	41	329	0	ENST00000334344.6:c.439G>A	p.Gly147Arg	p.G147R	ENST00000334344	NM_152641.2	147	Ggg/Agg	5/21	0.170477408180321	3	FACETS	0.666	0.555	0.789	0.333	0.277	0.395	INDETERMINATE	1	FALSE	1	0.335958289778413	3		329	428	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109949	115109949	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0025381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	50	690	0	ENST00000257566.3:c.1929C>G	p.Tyr643Ter	p.Y643*	ENST00000257566	NM_016569.3	643	taC/taG	8/8	0.335958289778413	1	FACETS	0.485	0.411	0.565	0.485	0.411	0.565	SUBCLONAL	1	FALSE	0	0.335958289778413	1		690	511	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019575	42019575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	46	555	0	ENST00000219905.7:c.3628C>T	p.Arg1210Trp	p.R1210W	ENST00000219905	NM_001164273.1	1210	Cgg/Tgg	10/24	0.150762607871691	0	FACETS	0.364	0.306	0.427			1	INDETERMINATE	1	FALSE	0	0.335958289778413	0		555	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882000	NA	P-0025381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	10	658	0	ENST00000269305.4:c.475G>A	p.Ala159Thr	p.A159T	ENST00000269305	NM_001126112.2	159	Gcc/Acc	5/11	NA	2	FACETS	0.12	0.081	0.171			1	INDETERMINATE	1	FALSE	NA	0.335958289778413	2		658	495	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170147	32170147	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs577534927	NA	P-0025705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	21	759	0	ENST00000375023.3:c.3461G>T	p.Gly1154Val	p.G1154V	ENST00000375023	NM_004557.3	1154	gGc/gTc	21/30	1	2	FACETS	0.977	0.765	1	0.977	0.765	1	CLONAL	1	TRUE	1	0.405583101197939	2		759	106	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878020	151878020	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	12	269	0	ENST00000262189.6:c.6925C>T	p.Gln2309Ter	p.Q2309*	ENST00000262189	NM_170606.2	2309	Cag/Tag	36/59	1	2	FACETS	0.897	0.643	1	0.897	0.643	1	CLONAL	1	TRUE	1	0.405583101197939	2		269	66	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0025837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	464	618	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.625290563824218	2	FACETS	0.982	0.949	1	0.982	0.949	1	CLONAL	2	TRUE	0	0.646967866561961	2		619	730	SUCCESS
APC	324	MSKCC	GRCh37	5	112175513	112175513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	312	355	0	ENST00000257430.4:c.4222G>T	p.Glu1408Ter	p.E1408*	ENST00000257430	NM_000038.5	1408	Gaa/Taa	16/16	NA	2	FACETS	0.974	0.934	1			1	INDETERMINATE	2	TRUE	NA	0.646967866561961	2		355	495	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971292	13971292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772105404	NA	P-0025837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	216	461	2	ENST00000405192.2:c.637C>T	p.Arg213Cys	p.R213C	ENST00000405192	NM_001163147.1	213	Cgc/Tgc	8/12	0.637512294806775	4	FACETS	0.986	0.916	1	0.329	0.305	0.353	CLONAL	1	TRUE	1	0.646967866561961	4		463	1115	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143138	24143138	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0025837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	201	456	0	ENST00000263121.7:c.370A>T	p.Lys124Ter	p.K124*	ENST00000263121	NM_003073.3	124	Aag/Tag	4/9	1	2	FACETS	0.991	0.924	1	0.991	0.924	1	CLONAL	1	TRUE	1	0.646967866561961	2		456	627	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0025853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	453	779	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.599875809876836	3	FACETS	0.976	0.935	1	0.976	0.935	1	CLONAL	2	TRUE	1	0.599875809876836	3		779	1006	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508728	148508728	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs267601395	NA	P-0025853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	234	411	0	ENST00000320356.2:c.1936T>A	p.Tyr646Asn	p.Y646N	ENST00000320356	NM_004456.4	646	Tac/Aac	16/20	0.599875809876836	3	FACETS	0.978	0.912	1	0.489	0.456	0.523	CLONAL	1	TRUE	1	0.599875809876836	3		411	1037	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243484	46243484	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	437	397	0	ENST00000334344.6:c.1837C>T	p.Gln613Ter	p.Q613*	ENST00000334344	NM_152641.2	613	Cag/Tag	14/21	0.596312788986753	2	FACETS	0.962	0.926	0.998	0.962	0.926	0.998	CLONAL	2	TRUE	0	0.599875809876836	2		397	757	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097132	11097132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769756381	NA	P-0025853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	263	550	1	ENST00000358026.2:c.623G>A	p.Arg208Gln	p.R208Q	ENST00000358026	NM_001128849.1	208	cGg/cAg	4/36	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.599875809876836	2		551	833	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949093	151949120	+	frameshift_variant	Frame_Shift_Del	DEL	TACAATACATGCAGATATACTCTTCTTT	TACAATACATGCAGATATACTCTTCTTT	AA	novel	NA	P-0025853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	247	554	3	ENST00000262189.6:c.1525_1552delinsTT	p.Lys509LeufsTer6	p.K509Lfs*6	ENST00000262189	NM_170606.2	509	AAAGAAGAGTATATCTGCATGTATTGTAaa/TTaa	11/59	0.599875809876836	3	FACETS	0.916	0.855	0.978	0.458	0.427	0.489	CLONAL	1	TRUE	1	0.599875809876836	3		557	1169	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485927	8485927	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	182	371	0	ENST00000356435.5:c.2890C>G	p.Pro964Ala	p.P964A	ENST00000356435		964	Ccc/Gcc	17/35	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.599875809876836	2		371	572	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226162	53226186	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGGCAGTGAGGCCAGGGCCTCAC	GAGGGCAGTGAGGCCAGGGCCTCAC	-	novel	NA	P-0025853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	266	264	0	ENST00000375401.3:c.2663_2687del	p.Arg888ProfsTer39	p.R888Pfs*39	ENST00000375401	NM_004187.3	888	cGTGAGGCCCTGGCCTCACTGCCCTCc/cc	19/26	1	1	FACETS	0.761	0.728	0.793	1	0.995	1	SUBCLONAL	2	TRUE	0	0.599875809876836	1		264	408	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0026352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	68	473	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.256136288878998	2	FACETS	0.867	0.761	0.98	0.867	0.761	0.98	CLONAL	2	TRUE	0	0.259653024211245	2		473	302	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0026352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	37	216	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.259653024211245	1	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	0	0.259653024211245	1		216	219	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248049	59248052	+	frameshift_variant	Frame_Shift_Del	DEL	CTGT	CTGT	-	novel	NA	P-0026352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	35	238	0	ENST00000371222.2:c.691_694del	p.Thr231CysfsTer29	p.T231Cfs*29	ENST00000371222	NM_002228.3	231	ACAGtg/tg	1/1	0.259653024211245	1	FACETS	0.829	0.682	0.992	0.829	0.682	0.992	CLONAL	1	TRUE	0	0.259653024211245	1		238	283	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054467	42054469	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0026352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	17	293	0	ENST00000219905.7:c.7654_7656del	p.Ser2552del	p.S2552del	ENST00000219905	NM_001164273.1	2551	TCT/-	22/24	0.196807925233741	1	FACETS	0.42	0.314	0.547	0.42	0.314	0.547	SUBCLONAL	1	TRUE	0	0.259653024211245	1		293	271	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578404	+	inframe_deletion	In_Frame_Del	DEL	GCA	GCA	-	novel	NA	P-0026352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	87	270	0	ENST00000269305.4:c.526_528del	p.Cys176del	p.C176del	ENST00000269305	NM_001126112.2	176	TGC/-	5/11	0.256136288878998	2	FACETS	0.777	0.692	0.868	0.777	0.692	0.868	SUBCLONAL	2	TRUE	0	0.259653024211245	2		270	431	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441311	52441312	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1559590613	NA	P-0026352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	52	335	0	ENST00000460680.1:c.458_459del	p.Pro153ArgfsTer7	p.P153Rfs*7	ENST00000460680	NM_004656.3	153	cCT/c	7/17	0.259653024211245	1	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	0	0.259653024211245	1		335	339	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654515	29654515	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs1555533548	NA	P-0026565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	114	240	0	ENST00000356175.3:c.5206-2A>T		p.X1736_splice	ENST00000356175	NM_000267.3	1736			1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.65963705590218	2		240	339	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992930	72992930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1398839726	NA	P-0026605-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	51	731	1	ENST00000268489.5:c.1115G>A	p.Arg372Gln	p.R372Q	ENST00000268489	NM_006885.3	372	cGa/cAa	2/10	0.811165432752112	2	FACETS	0.165	0.14	0.193	0.083	0.07	0.097	SUBCLONAL	1	TRUE	0	0.820657622394171	2		732	753	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016634	12016634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026605-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	190	314	0	ENST00000353533.5:c.770C>T	p.Ser257Phe	p.S257F	ENST00000353533	NM_003010.3	257	tCt/tTt	7/11	0.820657622394171	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.820657622394171	1		314	261	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467502	25467502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026605-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	163	567	1	ENST00000264709.3:c.1574C>T	p.Ala525Val	p.A525V	ENST00000264709	NM_175629.2	525	gCg/gTg	14/23	0.273492714694569	2	FACETS	0.6	0.552	0.649	0.3	0.276	0.325	INDETERMINATE	1	TRUE	0	0.820657622394171	2		568	662	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291915	15291915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775964142	NA	P-0026605-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	98	793	1	ENST00000263388.2:c.2851C>T	p.Arg951Cys	p.R951C	ENST00000263388	NM_000435.2	951	Cgt/Tgt	18/33	0.273492714694569	2	FACETS	0.294	0.262	0.328	0.147	0.131	0.164	INDETERMINATE	1	TRUE	0	0.820657622394171	2		794	812	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	105	284	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		284	338	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518770	176518770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	59	605	0	ENST00000292408.4:c.688G>A	p.Val230Met	p.V230M	ENST00000292408	NM_213647.1	230	Gtg/Atg	6/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		605	842	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	144	262	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		262	388	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	136	399	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		399	444	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	66	632	3	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		635	759	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100175	27100176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	37	459	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		459	589	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696802	176696802	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	23	254	0	ENST00000439151.2:c.5508del	p.Ala1837LeufsTer12	p.A1837Lfs*12	ENST00000439151	NM_022455.4	1835	Aaa/aa	16/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		254	301	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934152	48934152	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	25	260	0	ENST00000267163.4:c.610del		p.X204_splice	ENST00000267163	NM_000321.2	204			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		260	185	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	48	355	0	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		355	560	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	81	455	0	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		455	637	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560514	65560514	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	220	368	0	ENST00000358664.4:c.83A>G	p.His28Arg	p.H28R	ENST00000358664	NM_002382.4	28	cAt/cGt	3/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		368	615	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101268	27101268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	32	551	1	ENST00000324856.7:c.4555del	p.Gln1519ArgfsTer8	p.Q1519Rfs*8	ENST00000324856	NM_006015.4	1517	gCc/gc	18/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		552	615	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850705	63850705	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs201178069	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	39	355	1	ENST00000279873.7:c.1489del	p.Ile497Ter	p.I497*	ENST00000279873	NM_032199.2	495	Aaa/aa	10/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		356	435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	50	811	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		812	781	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930634	32930634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56070345	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	37	393	1	ENST00000380152.3:c.7505G>A	p.Arg2502His	p.R2502H	ENST00000380152		2502	cGc/cAc	15/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		394	583	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197506	106197506	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	37	503	1	ENST00000380013.4:c.5844del	p.Val1949Ter	p.V1949*	ENST00000380013	NM_001127208.2	1947	Aaa/aa	11/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		504	479	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	154	342	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		342	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577524	7577524	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	54	571	0	ENST00000269305.4:c.757A>G	p.Thr253Ala	p.T253A	ENST00000269305	NM_001126112.2	253	Acc/Gcc	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		571	836	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245587	41245587	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357522	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	41	622	2	ENST00000357654.3:c.1961del	p.Lys654SerfsTer47	p.K654Sfs*47	ENST00000357654	NM_007294.3	654	aAg/ag	10/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		624	539	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28611336	28611336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201905189	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	23	427	0	ENST00000241453.7:c.1295C>T	p.Thr432Met	p.T432M	ENST00000241453	NM_004119.2	432	aCg/aTg	10/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		427	397	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796882	42796883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761345552	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	61	809	2	ENST00000575354.2:c.3347dup	p.Ser1117LysfsTer34	p.S1117Kfs*34	ENST00000575354	NM_015125.3	1114	gcc/gCcc	14/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		811	875	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145645	11145645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	68	637	0	ENST00000358026.2:c.4007G>A	p.Arg1336His	p.R1336H	ENST00000358026	NM_001128849.1	1336	cGc/cAc	29/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		637	818	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910346	29910346	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	49	469	0	ENST00000376809.5:c.19del	p.Arg7GlufsTer13	p.R7Efs*13	ENST00000376809	NM_002116.7	6	Ccc/cc	1/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		469	658	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436227	110436227	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1394911868	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	34	263	0	ENST00000375856.3:c.2174del	p.Gly725AlafsTer102	p.G725Afs*102	ENST00000375856	NM_003749.2	725	gGc/gc	1/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		263	394	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690584	88690584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368222977	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	91	472	0	ENST00000360948.2:c.446C>T	p.Thr149Met	p.T149M	ENST00000360948	NM_001012338.2	149	aCg/aTg	5/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		472	670	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169182	119169182	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757530036	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	44	497	0	ENST00000264033.4:c.2366C>T	p.Thr789Ile	p.T789I	ENST00000264033	NM_005188.3	789	aCt/aTt	15/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		497	797	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606334	93606334	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs796052158	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	47	574	2	ENST00000375746.1:c.154G>A	p.Ala52Thr	p.A52T	ENST00000375746	NM_001174167.1	52	Gcc/Acc	2/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		576	742	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256321	16256321	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	45	537	0	ENST00000375759.3:c.3591del	p.Asp1198MetfsTer2	p.D1198Mfs*2	ENST00000375759	NM_015001.2	1196	Aaa/aa	11/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		537	556	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	84	792	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		796	503	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129350	64129351	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1166600152	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	46	594	0	ENST00000334205.4:c.788dup	p.Arg264SerfsTer16	p.R264Sfs*16	ENST00000334205	NM_003942.2	261	ttc/ttCc	8/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		594	729	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	74	711	1	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		712	881	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106333	27106333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201604768	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	62	536	0	ENST00000324856.7:c.5944G>A	p.Val1982Ile	p.V1982I	ENST00000324856	NM_006015.4	1982	Gtc/Atc	20/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		536	785	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	57	611	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		612	711	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212166	5212166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775731386	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	61	692	0	ENST00000357368.4:c.4865C>T	p.Thr1622Met	p.T1622M	ENST00000357368	NM_002850.3	1622	aCg/aTg	32/38	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		692	857	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860770	45860770	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141457460	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	43	665	0	ENST00000391945.4:c.1339G>A	p.Val447Ile	p.V447I	ENST00000391945	NM_000400.3	447	Gta/Ata	14/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		665	782	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432420	49432420	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	67	715	0	ENST00000301067.7:c.8719del	p.Tyr2907ThrfsTer3	p.Y2907Tfs*3	ENST00000301067	NM_003482.3	2907	Tac/ac	34/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		715	910	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	66	681	2	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		683	1072	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352727	70352727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1488661030	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	34	473	0	ENST00000374080.3:c.4448C>T	p.Ser1483Leu	p.S1483L	ENST00000374080		1483	tCg/tTg	32/45	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		473	658	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383774	15383774	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	44	536	0	ENST00000263377.2:c.137del	p.Pro46ArgfsTer47	p.P46Rfs*47	ENST00000263377	NM_058243.2	46	cCg/cg	2/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		536	716	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335837	73335837	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372878316	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	34	356	0	ENST00000377767.4:c.2458C>T	p.Arg820Trp	p.R820W	ENST00000377767	NM_014953.3	820	Cgg/Tgg	18/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		356	401	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692809	89692809	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	181	285	0	ENST00000371953.3:c.293del	p.Leu98GlnfsTer15	p.L98Qfs*15	ENST00000371953	NM_000314.4	98	cTa/ca	5/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		285	242	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519135	103519136	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	33	403	0	ENST00000355739.4:c.2477_2478del	p.Phe826Ter	p.F826*	ENST00000355739	NM_000123.3	825	TTt/t	11/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		403	531	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99454619	99454619	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373427868	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	274	550	2	ENST00000268035.6:c.1538G>A	p.Arg513Gln	p.R513Q	ENST00000268035	NM_000875.3	513	cGg/cAg	7/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		552	777	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287371	33287371	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	47	485	0	ENST00000374542.5:c.1726C>A	p.Leu576Met	p.L576M	ENST00000374542	NM_001141970.1	576	Ctg/Atg	6/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		485	591	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778059	135778059	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	233	556	0	ENST00000298552.3:c.2324T>C	p.Leu775Pro	p.L775P	ENST00000298552	NM_001162426.1	775	cTc/cCc	18/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		556	753	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191805	123191805	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	22	329	0	ENST00000218089.9:c.1400del	p.Phe467SerfsTer3	p.F467Sfs*3	ENST00000218089	NM_001042749.1	465	gTt/gt	15/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		329	291	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006836	47006836	+	5_prime_UTR_variant	5'UTR	SNP	C	C	T	rs781915889	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	43	597	4	ENST00000377604.3:c.-45C>T		p.*15*	ENST00000377604	NM_001204468.1	-/852		2/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		601	805	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067433	37067433	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	51	454	0	ENST00000231790.2:c.1348del	p.Asp450IlefsTer41	p.D450Ifs*41	ENST00000231790	NM_000249.3	448	gaG/ga	12/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		454	656	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99192851	99192851	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	45	333	0	ENST00000268035.6:c.45del	p.Leu16SerfsTer31	p.L16Sfs*31	ENST00000268035	NM_000875.3	14	tGg/tg	1/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		333	554	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057962	27057962	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	53	524	0	ENST00000324856.7:c.1670A>G	p.Gln557Arg	p.Q557R	ENST00000324856	NM_006015.4	557	cAg/cGg	3/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		524	752	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276740	115276740	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	18	283	0	ENST00000438362.2:c.721-2A>G		p.X241_splice	ENST00000438362	NM_001242891.1	241			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		283	191	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841437	156841437	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1265775208	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	54	512	0	ENST00000524377.1:c.740T>C	p.Leu247Pro	p.L247P	ENST00000524377	NM_002529.3	247	cTg/cCg	7/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		512	655	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333273	70333273	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	64	590	0	ENST00000373644.4:c.1178C>A	p.Pro393Gln	p.P393Q	ENST00000373644	NM_030625.2	393	cCa/cAa	2/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		590	727	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14303214	14303214	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	50	535	0	ENST00000256196.4:c.461T>C	p.Met154Thr	p.M154T	ENST00000256196		154	aTg/aCg	5/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		535	509	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121536	108121537	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	36	438	0	ENST00000278616.4:c.1348dup	p.Glu450GlyfsTer37	p.E450Gfs*37	ENST00000278616	NM_000051.3	448	-/G	10/63	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		438	557	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112209	115112209	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	25	334	1	ENST00000257566.3:c.1531C>T	p.Gln511Ter	p.Q511*	ENST00000257566	NM_016569.3	511	Cag/Tag	7/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		335	393	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32899291	32899291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	27	292	1	ENST00000380152.3:c.395G>A	p.Cys132Tyr	p.C132Y	ENST00000380152		132	tGt/tAt	4/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		293	274	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913911	32913911	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	20	449	0	ENST00000380152.3:c.5419G>T	p.Asp1807Tyr	p.D1807Y	ENST00000380152		1807	Gat/Tat	11/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		449	301	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727398	66727398	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	55	372	0	ENST00000307102.5:c.114G>T	p.Glu38Asp	p.E38D	ENST00000307102	NM_002755.3	38	gaG/gaT	2/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		372	550	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807871	3807871	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	33	484	0	ENST00000262367.5:c.3548A>G	p.Glu1183Gly	p.E1183G	ENST00000262367	NM_004380.2	1183	gAg/gGg	18/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		484	617	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857365	9857365	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	44	468	1	ENST00000330684.3:c.4036del	p.Gln1346LysfsTer51	p.Q1346Kfs*51	ENST00000330684	NM_001134407.1	1346	Caa/aa	13/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		469	620	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644825	67644826	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	40	534	0	ENST00000264010.4:c.95dup	p.Gln33ProfsTer17	p.Q33Pfs*17	ENST00000264010	NM_006565.3	30	-/G	3/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		534	720	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645065	67645065	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	67	637	0	ENST00000264010.4:c.330A>G	p.Ile110Met	p.I110M	ENST00000264010	NM_006565.3	110	atA/atG	3/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		637	689	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483058	29483058	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	24	403	1	ENST00000356175.3:c.118A>G	p.Lys40Glu	p.K40E	ENST00000356175	NM_000267.3	40	Aag/Gag	2/57	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		404	308	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664397	29664397	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	20	346	0	ENST00000356175.3:c.6376C>T	p.Gln2126Ter	p.Q2126*	ENST00000356175	NM_000267.3	2126	Caa/Taa	42/57	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		346	381	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610204	10610204	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	72	692	0	ENST00000171111.5:c.506del	p.Arg169LeufsTer61	p.R169Lfs*61	ENST00000171111	NM_203500.1	169	cGt/ct	2/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		692	916	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11018736	11018736	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	61	591	0	ENST00000327064.4:c.368T>C	p.Ile123Thr	p.I123T	ENST00000327064	NM_199141.1	123	aTc/aCc	3/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		591	934	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257630	19257630	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	72	623	1	ENST00000162023.5:c.596del	p.Pro199HisfsTer24	p.P199Hfs*24	ENST00000162023		199	cCa/ca	10/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		624	924	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42381400	42381400	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs781968364	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	56	576	0	ENST00000221972.3:c.26A>G	p.Gln9Arg	p.Q9R	ENST00000221972	NM_021601.3	9	cAa/cGa	1/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		576	795	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921139	50921139	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	57	519	0	ENST00000440232.2:c.3259A>G	p.Lys1087Glu	p.K1087E	ENST00000440232	NM_002691.3	1087	Aag/Gag	27/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		519	863	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376098	225376098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	31	451	0	ENST00000264414.4:c.856C>T	p.His286Tyr	p.H286Y	ENST00000264414	NM_003590.4	286	Cat/Tat	6/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		451	294	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054216	30054216	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	51	387	0	ENST00000338641.4:c.638A>G	p.Asp213Gly	p.D213G	ENST00000338641	NM_000268.3	213	gAc/gGc	7/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		387	619	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035118	37035118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138705565	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	43	412	0	ENST00000231790.2:c.80G>A	p.Arg27Gln	p.R27Q	ENST00000231790	NM_000249.3	27	cGg/cAg	1/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		412	626	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939932	49939933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	52	740	0	ENST00000296474.3:c.1110dup	p.Ile371HisfsTer2	p.I371Hfs*2	ENST00000296474	NM_002447.2	370	-/C	1/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		740	966	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643671	52643671	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	36	464	0	ENST00000394830.3:c.2225A>G	p.Glu742Gly	p.E742G	ENST00000394830	NM_018313.4	742	gAg/gGg	17/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		464	490	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478096	138478096	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	36	494	0	ENST00000289153.2:c.90A>G	p.Ile30Met	p.I30M	ENST00000289153	NM_006219.2	30	atA/atG	1/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		494	570	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430546	181430546	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	41	190	0	ENST00000325404.1:c.402del	p.Gly135AlafsTer19	p.G135Afs*19	ENST00000325404	NM_003106.3	133	gCc/gc	1/1	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		190	408	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1978346	1978346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024380548	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	57	588	1	ENST00000382891.5:c.3766C>T	p.Arg1256Cys	p.R1256C	ENST00000382891	NM_133335.3	1256	Cgc/Tgc	21/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		589	910	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251924	153251924	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	20	424	0	ENST00000281708.4:c.1082T>C	p.Ile361Thr	p.I361T	ENST00000281708	NM_033632.3	361	aTt/aCt	7/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		424	307	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630482	187630482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	74	566	0	ENST00000441802.2:c.500G>A	p.Ser167Asn	p.S167N	ENST00000441802	NM_005245.3	167	aGt/aAt	2/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		566	760	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755752	57755752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	36	524	1	ENST00000274289.3:c.35C>T	p.Ala12Val	p.A12V	ENST00000274289	NM_006622.3	12	gCc/gTc	1/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		525	641	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449564	149449564	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	68	592	0	ENST00000286301.3:c.1382A>G	p.Glu461Gly	p.E461G	ENST00000286301	NM_005211.3	461	gAg/gGg	10/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		592	768	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056386	26056386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750602586	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	30	379	0	ENST00000343677.2:c.271G>A	p.Gly91Ser	p.G91S	ENST00000343677	NM_005319.3	91	Ggc/Agc	1/1	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		379	409	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522386	157522386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762698567	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	43	599	0	ENST00000346085.5:c.4658C>T	p.Ala1553Val	p.A1553V	ENST00000346085	NM_020732.3	1553	gCg/gTg	18/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		599	761	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006000	22006000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026935-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	38	427	0	ENST00000276925.6:c.403G>A	p.Ala135Thr	p.A135T	ENST00000276925	NM_004936.3	135	Gcc/Acc	2/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		427	669	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0026942-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	357	272	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.39658480649466	3	FACETS	0.857	0.82	0.893	0.857	0.82	0.893	CLONAL	3	TRUE	0	0.536082915801358	3		272	657	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0026942-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	244	295	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.536082915801358	6	FACETS	1	0.986	1			1	CLONAL	2	TRUE	NA	0.536082915801358	6		295	805	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14628978	14628978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026942-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	95	299	0	ENST00000254322.2:c.184G>A	p.Glu62Lys	p.E62K	ENST00000254322	NM_006145.1	62	Gag/Aag	1/3	0.536082915801358	3	FACETS	0.629	0.56	0.702	0.21	0.186	0.234	SUBCLONAL	1	TRUE	0	0.536082915801358	3		299	715	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246861	10246861	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026942-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	128	417	0	ENST00000340748.4:c.4544G>A	p.Gly1515Glu	p.G1515E	ENST00000340748		1515	gGa/gAa	37/40	0.536082915801358	3	FACETS	0.772	0.7	0.848	0.257	0.233	0.283	SUBCLONAL	1	TRUE	0	0.536082915801358	3		417	784	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858005	152858005	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026942-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	46	87	0	ENST00000406277.2:c.610G>C	p.Glu204Gln	p.E204Q	ENST00000406277	NM_152274.4	204	Gag/Cag	6/7	0.49703193323806	2	FACETS	0.733	0.623	0.852			1	SUBCLONAL	1	TRUE	NA	0.536082915801358	2		87	234	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330590	65330590	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026942-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	101	287	0	ENST00000342505.4:c.1056G>C	p.Lys352Asn	p.K352N	ENST00000342505	NM_002227.2	352	aaG/aaC	8/25	0.442534649078671	4	FACETS	0.857	0.767	0.953	0.429	0.383	0.477	CLONAL	1	TRUE	2	0.536082915801358	4		287	675	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953210	81953210	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026942-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	73	217	0	ENST00000359376.3:c.2176T>A	p.Tyr726Asn	p.Y726N	ENST00000359376	NM_002661.3	726	Tac/Aac	20/33	0.536082915801358	3	FACETS	0.716	0.628	0.811	0.239	0.209	0.271	SUBCLONAL	1	TRUE	0	0.536082915801358	3		217	482	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246804	10246804	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026942-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	121	378	0	ENST00000340748.4:c.4601G>A	p.Gly1534Asp	p.G1534D	ENST00000340748		1534	gGc/gAc	37/40	0.536082915801358	3	FACETS	0.76	0.687	0.837	0.253	0.229	0.279	SUBCLONAL	1	TRUE	0	0.536082915801358	3		378	753	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319060	62319060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1472407817	NA	P-0026942-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1280	118	443	1	ENST00000360203.5:c.1418G>A	p.Arg473His	p.R473H	ENST00000360203	NM_001283009.1	473	cGc/cAc	17/35	0.536082915801358	6	FACETS	0.653	0.586	0.723	0.218	0.195	0.241	SUBCLONAL	1	TRUE	3	0.536082915801358	6		444	1398	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251205	251205	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026942-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	54	192	0	ENST00000264932.6:c.1650G>C	p.Lys550Asn	p.K550N	ENST00000264932	NM_004168.2	550	aaG/aaC	12/15	0.426594831334884	3	FACETS	0.866	0.745	0.996	0.433	0.372	0.498	CLONAL	1	TRUE	1	0.536082915801358	3		192	295	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945111	151945111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026942-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	26	184	0	ENST00000262189.6:c.2408C>A	p.Ala803Asp	p.A803D	ENST00000262189	NM_170606.2	803	gCt/gAt	14/59	0.418512967190283	5	FACETS	0.501	0.397	0.621	0.167	0.132	0.207	SUBCLONAL	1	TRUE	2	0.536082915801358	5		184	349	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0027127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	70	714	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.2	2		714	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0027127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	26	763	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	1	2	FACETS	0.408	0.322	0.508	0.408	0.322	0.508	SUBCLONAL	1	TRUE	1	0.2	2		763	637	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085659	16085659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs794727503	NA	P-0027127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	52	816	0	ENST00000281043.3:c.835G>A	p.Val279Met	p.V279M	ENST00000281043	NM_005378.4	279	Gtg/Atg	3/3	1	2	FACETS	0.799	0.679	0.93	0.799	0.679	0.93	CLONAL	1	TRUE	1	0.2	2		816	651	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	537	632	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.921	0.888	0.954	1	0.997	1	CLONAL	2	TRUE	1	0.57	2		635	1023	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	325	792	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.932	0.88	0.985	0.932	0.88	0.985	CLONAL	1	TRUE	1	0.57	2		796	1224	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	221	540	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.926	0.864	0.991	0.926	0.864	0.991	CLONAL	1	TRUE	1	0.57	2		540	837	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	218	779	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.876	0.816	0.938	0.876	0.816	0.938	CLONAL	1	TRUE	1	0.57	2		779	873	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	181	936	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.481	0.442	0.521	0.481	0.442	0.521	SUBCLONAL	1	TRUE	1	0.57	2		936	1321	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	362	776	3	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.57	2		779	1165	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151289	202151290	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	73	522	0	ENST00000358485.4:c.1596dup	p.Leu533ThrfsTer6	p.L533Tfs*6	ENST00000358485	NM_001080125.1	530	aga/agAa	9/9	1	2	FACETS	0.287	0.25	0.327	0.287	0.25	0.327	SUBCLONAL	1	TRUE	1	0.57	2		522	892	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965666	90965666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	157	368	0	ENST00000265433.3:c.1651del	p.Arg551GlyfsTer8	p.R551Gfs*8	ENST00000265433	NM_002485.4	551	Agg/gg	11/16	1	2	FACETS	0.886	0.815	0.959	0.886	0.815	0.959	CLONAL	1	TRUE	1	0.57	2		368	622	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867541	35867541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	199	460	6	ENST00000303115.3:c.361del	p.Ile121Ter	p.I121*	ENST00000303115	NM_002185.3	119	Aaa/aa	3/8	1	2	FACETS	0.915	0.85	0.982	0.915	0.85	0.982	CLONAL	1	TRUE	1	0.57	2		466	763	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	196	537	2	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	1	2	FACETS	0.895	0.831	0.962	0.895	0.831	0.962	CLONAL	1	TRUE	1	0.57	2		539	768	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243668598	243668598	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776935	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	214	512	0	ENST00000263826.5:c.1393C>T	p.Arg465Trp	p.R465W	ENST00000263826	NM_005465.4	465	Cgg/Tgg	13/13	1	2	FACETS	0.9	0.838	0.964	0.9	0.838	0.964	CLONAL	1	TRUE	1	0.57	2		512	834	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61729435	61729435	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	69	538	2	ENST00000401558.2:c.312del	p.Lys104AsnfsTer17	p.K104Nfs*17	ENST00000401558	NM_003400.3	104	aaA/aa	5/25	1	2	FACETS	0.301	0.261	0.344	0.301	0.261	0.344	SUBCLONAL	1	TRUE	1	0.57	2		540	804	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781122	161781122	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	277	502	0	ENST00000366898.1:c.1283del	p.Asn428MetfsTer7	p.N428Mfs*7	ENST00000366898	NM_004562.2	428	aAt/at	11/12	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.57	2		502	860	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39629562	39629562	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	162	432	0	ENST00000262039.4:c.2260del	p.Thr754GlnfsTer7	p.T754Qfs*7	ENST00000262039	NM_002647.2	752	acA/ac	21/25	1	2	FACETS	0.82	0.755	0.888	0.82	0.755	0.888	CLONAL	1	TRUE	1	0.57	2		432	693	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148516773	148516773	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	137	293	0	ENST00000320356.2:c.914A>G	p.His305Arg	p.H305R	ENST00000320356	NM_004456.4	305	cAt/cGt	9/20	1	2	FACETS	0.963	0.882	1	0.963	0.882	1	CLONAL	1	TRUE	1	0.57	2		293	499	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589698	69589698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	89	208	1	ENST00000168712.1:c.155C>T	p.Ala52Val	p.A52V	ENST00000168712	NM_002007.2	52	gCg/gTg	1/3	1	2	FACETS	0.935	0.837	1	0.935	0.837	1	CLONAL	1	TRUE	1	0.57	2		209	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572991	7572991	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	110	470	0	ENST00000269305.4:c.1118del	p.Lys373ArgfsTer49	p.K373Rfs*49	ENST00000269305	NM_001126112.2	373	aAg/ag	11/11	1	2	FACETS	0.603	0.543	0.667	0.603	0.543	0.667	SUBCLONAL	1	TRUE	1	0.57	2		470	640	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263974	104263974	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776579	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	180	392	0	ENST00000369902.3:c.71del	p.Pro24ArgfsTer72	p.P24Rfs*72	ENST00000369902	NM_016169.3	22	gCc/gc	1/12	1	2	FACETS	0.975	0.903	1	0.975	0.903	1	CLONAL	1	TRUE	1	0.57	2		392	648	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993014	72993014	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	390	934	0	ENST00000268489.5:c.1031del	p.Asn344ThrfsTer8	p.N344Tfs*8	ENST00000268489	NM_006885.3	344	aAc/ac	2/10	1	2	FACETS	0.962	0.913	1	0.962	0.913	1	CLONAL	1	TRUE	1	0.57	2		934	1422	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	361	924	0	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.966	0.915	1	0.966	0.915	1	CLONAL	1	TRUE	1	0.57	2		924	1311	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610561	10610561	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766652922	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	326	707	1	ENST00000171111.5:c.149G>A	p.Arg50His	p.R50H	ENST00000171111	NM_203500.1	50	cGc/cAc	2/6	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.57	2		708	1137	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740376	58740376	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1064797099	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	200	464	0	ENST00000305921.3:c.1281G>A	p.Trp427Ter	p.W427*	ENST00000305921	NM_003620.3	427	tgG/tgA	6/6	1	2	FACETS	0.902	0.838	0.968	0.902	0.838	0.968	CLONAL	1	TRUE	1	0.57	2		464	778	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599970	10599970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749651891	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	340	831	4	ENST00000171111.5:c.1606C>T	p.Arg536Cys	p.R536C	ENST00000171111	NM_203500.1	536	Cgc/Tgc	5/6	1	2	FACETS	0.939	0.887	0.991	0.939	0.887	0.991	CLONAL	1	TRUE	1	0.57	2		835	1271	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216189	36216189	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	266	645	6	ENST00000222270.7:c.3602del	p.Pro1201ArgfsTer154	p.P1201Rfs*154	ENST00000222270	NM_014727.1	1199	ggC/gg	11/37	1	2	FACETS	0.983	0.924	1	0.983	0.924	1	CLONAL	1	TRUE	1	0.57	2		651	949	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829014	128829014	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	52	98	0	ENST00000249373.3:c.22C>T	p.Arg8Trp	p.R8W	ENST00000249373	NM_005631.4	8	Cgg/Tgg	1/12	1	2	FACETS	0.865	0.746	0.992	0.865	0.746	0.992	CLONAL	1	TRUE	1	0.57	2		98	211	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27168574	27168576	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	310	637	0	ENST00000380036.4:c.453_455del	p.Glu151del	p.E151del	ENST00000380036	NM_000459.3	149	aAAGaa/aaa	3/23	1	2	FACETS	0.991	0.935	1	0.991	0.935	1	CLONAL	1	TRUE	1	0.57	2		637	1098	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17350485	17350485	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	320	675	0	ENST00000375499.3:c.625C>G	p.Pro209Ala	p.P209A	ENST00000375499	NM_003000.2	209	Cct/Gct	6/8	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.57	2		675	1122	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675283	241675283	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs863224015	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	182	429	0	ENST00000366560.3:c.539A>G	p.His180Arg	p.H180R	ENST00000366560	NM_000143.3	180	cAt/cGt	4/10	1	2	FACETS	0.826	0.764	0.891	0.826	0.764	0.891	CLONAL	1	TRUE	1	0.57	2		429	773	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451522	70451522	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	126	718	0	ENST00000373644.4:c.6362C>G	p.Ser2121Cys	p.S2121C	ENST00000373644	NM_030625.2	2121	tCc/tGc	12/12	1	2	FACETS	0.37	0.334	0.408	0.37	0.334	0.408	SUBCLONAL	1	TRUE	1	0.57	2		718	1195	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343529	118343529	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	141	420	1	ENST00000534358.1:c.1660del	p.Gln554SerfsTer13	p.Q554Sfs*13	ENST00000534358	NM_005933.3	552	gCc/gc	3/36	1	2	FACETS	0.756	0.691	0.825	0.756	0.691	0.825	SUBCLONAL	1	TRUE	1	0.57	2		421	654	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233172	46233172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376273452	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	161	369	1	ENST00000334344.6:c.1391C>T	p.Ala464Val	p.A464V	ENST00000334344	NM_152641.2	464	gCg/gTg	11/21	1	2	FACETS	0.991	0.914	1	0.991	0.914	1	CLONAL	1	TRUE	1	0.57	2		370	570	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431961	49431962	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1173	89	825	0	ENST00000301067.7:c.9177_9178del	p.Asp3061GlnfsTer7	p.D3061Qfs*7	ENST00000301067	NM_003482.3	3059	acTGgg/acgg	34/54	1	2	FACETS	0.247	0.218	0.279	0.247	0.218	0.279	SUBCLONAL	1	TRUE	1	0.57	2		825	1262	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444363	49444363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	103	728	2	ENST00000301067.7:c.3008del	p.Pro1003HisfsTer14	p.P1003Hfs*14	ENST00000301067	NM_003482.3	1003	cCa/ca	11/54	1	2	FACETS	0.348	0.31	0.388	0.348	0.31	0.388	SUBCLONAL	1	TRUE	1	0.57	2		730	1039	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240165	41240165	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	97	186	0	ENST00000379561.5:c.185C>A	p.Ser62Ter	p.S62*	ENST00000379561	NM_002015.3	62	tCg/tAg	1/3	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.57	2		186	291	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987219	36987219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757129857	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	278	699	0	ENST00000354822.5:c.470G>A	p.Arg157His	p.R157H	ENST00000354822	NM_001079668.2	157	cGc/cAc	3/3	1	2	FACETS	0.976	0.918	1	0.976	0.918	1	CLONAL	1	TRUE	1	0.57	2		699	999	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828771	3828771	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	260	649	1	ENST00000262367.5:c.1871G>A	p.Arg624His	p.R624H	ENST00000262367	NM_004380.2	624	cGc/cAc	9/31	1	2	FACETS	0.912	0.855	0.971	0.912	0.855	0.971	CLONAL	1	TRUE	1	0.57	2		650	1000	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533766	63533766	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060502150	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	247	534	1	ENST00000307078.5:c.1388G>A	p.Arg463His	p.R463H	ENST00000307078	NM_004655.3	463	cGc/cAc	6/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.57	2		535	846	SUCCESS
YES1	7525	MSKCC	GRCh37	18	742983	742983	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1462023222	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	204	524	0	ENST00000314574.4:c.995T>C	p.Leu332Pro	p.L332P	ENST00000314574	NM_005433.3	332	cTt/cCt	8/12	1	2	FACETS	0.787	0.731	0.846	0.787	0.731	0.846	SUBCLONAL	1	TRUE	1	0.57	2		524	909	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214724	5214724	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	199	629	0	ENST00000357368.4:c.4342A>G	p.Asn1448Asp	p.N1448D	ENST00000357368	NM_002850.3	1448	Aat/Gat	29/38	1	2	FACETS	0.819	0.759	0.88	0.819	0.759	0.88	CLONAL	1	TRUE	1	0.57	2		629	853	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277088	18277088	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	304	577	0	ENST00000222254.8:c.1535A>G	p.Glu512Gly	p.E512G	ENST00000222254	NM_005027.3	512	gAg/gGg	12/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.57	2		577	993	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209065	36209065	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	90	170	0	ENST00000222270.7:c.145del	p.Arg49AlafsTer118	p.R49Afs*118	ENST00000222270	NM_014727.1	49	Cgc/gc	1/37	1	2	FACETS	0.999	0.896	1	0.999	0.896	1	CLONAL	1	TRUE	1	0.57	2		170	316	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212189	36212189	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	272	627	0	ENST00000222270.7:c.1940T>C	p.Leu647Pro	p.L647P	ENST00000222270	NM_014727.1	647	cTt/cCt	3/37	1	2	FACETS	0.998	0.938	1	0.998	0.938	1	CLONAL	1	TRUE	1	0.57	2		627	956	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028289	48028289	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	149	373	0	ENST00000234420.5:c.3167T>C	p.Val1056Ala	p.V1056A	ENST00000234420	NM_000179.2	1056	gTg/gCg	4/10	1	2	FACETS	0.819	0.751	0.89	0.819	0.751	0.89	CLONAL	1	TRUE	1	0.57	2		373	638	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662767	227662767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	340	709	0	ENST00000305123.5:c.688G>A	p.Val230Met	p.V230M	ENST00000305123	NM_005544.2	230	Gtg/Atg	1/2	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.57	2		709	1180	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159067	24159067	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	234	543	0	ENST00000263121.7:c.739T>C	p.Ser247Pro	p.S247P	ENST00000263121	NM_003073.3	247	Tcc/Ccc	6/9	1	2	FACETS	0.873	0.815	0.932	0.873	0.815	0.932	CLONAL	1	TRUE	1	0.57	2		543	941	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713851	30713853	+	inframe_deletion	In_Frame_Del	DEL	CTG	CTG	-	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	271	683	0	ENST00000295754.5:c.1180_1182del	p.Cys394del	p.C394del	ENST00000295754	NM_003242.5	392	acCTGc/acc	4/7	1	2	FACETS	0.883	0.829	0.939	0.883	0.829	0.939	CLONAL	1	TRUE	1	0.57	2		683	1077	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430228	181430228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	244	490	0	ENST00000325404.1:c.80C>T	p.Ala27Val	p.A27V	ENST00000325404	NM_003106.3	27	gCg/gTg	1/1	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.57	2		490	732	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628581	187628581	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	346	731	1	ENST00000441802.2:c.2401C>T	p.Gln801Ter	p.Q801*	ENST00000441802	NM_005245.3	801	Cag/Tag	2/27	1	2	FACETS	0.938	0.887	0.99	0.938	0.887	0.99	CLONAL	1	TRUE	1	0.57	2		732	1294	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31493328	31493328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	175	401	0	ENST00000344624.3:c.1828G>A	p.Ala610Thr	p.A610T	ENST00000344624		610	Gcc/Acc	10/33	1	2	FACETS	0.925	0.855	0.997	0.925	0.855	0.997	CLONAL	1	TRUE	1	0.57	2		401	664	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871249	35871249	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	225	541	0	ENST00000303115.3:c.471G>T	p.Lys157Asn	p.K157N	ENST00000303115	NM_002185.3	157	aaG/aaT	4/8	1	2	FACETS	0.916	0.854	0.979	0.916	0.854	0.979	CLONAL	1	TRUE	1	0.57	2		541	862	SUCCESS
APC	324	MSKCC	GRCh37	5	112151265	112151265	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	182	377	0	ENST00000257430.4:c.908G>T	p.Arg303Met	p.R303M	ENST00000257430	NM_000038.5	303	aGg/aTg	9/16	1	2	FACETS	0.883	0.817	0.952	0.883	0.817	0.952	CLONAL	1	TRUE	1	0.57	2		377	723	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196093	138196093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1405321250	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	166	351	0	ENST00000237289.4:c.407G>A	p.Arg136His	p.R136H	ENST00000237289	NM_001270507.1	136	cGc/cAc	3/9	1	2	FACETS	0.946	0.872	1	0.946	0.872	1	CLONAL	1	TRUE	1	0.57	2		351	616	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509879	106509879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776574072	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	271	661	0	ENST00000359195.3:c.1873G>A	p.Gly625Arg	p.G625R	ENST00000359195	NM_002649.2	625	Ggg/Agg	2/11	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.57	2		661	942	SUCCESS
MET	4233	MSKCC	GRCh37	7	116417506	116417506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	146	346	1	ENST00000397752.3:c.3323C>T	p.Ala1108Val	p.A1108V	ENST00000397752	NM_000245.2	1108	gCt/gTt	16/21	1	2	FACETS	0.83	0.761	0.903	0.83	0.761	0.903	CLONAL	1	TRUE	1	0.57	2		347	617	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231381	98231382	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	96	542	0	ENST00000331920.6:c.1901_1902del	p.His634ArgfsTer19	p.H634Rfs*19	ENST00000331920	NM_000264.3	634	cAC/c	14/24	1	2	FACETS	0.36	0.32	0.403	0.36	0.32	0.403	SUBCLONAL	1	TRUE	1	0.57	2		542	935	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772972	135772972	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1449821288	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	110	292	0	ENST00000298552.3:c.2651A>G	p.Tyr884Cys	p.Y884C	ENST00000298552	NM_001162426.1	884	tAt/tGt	21/23	1	2	FACETS	0.865	0.782	0.952	0.865	0.782	0.952	CLONAL	1	TRUE	1	0.57	2		292	446	SUCCESS
AR	367	MSKCC	GRCh37	X	66863121	66863122	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTTGCCC	novel	NA	P-0027438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	85	607	0	ENST00000374690.3:c.1641_1647dup	p.Ile550PhefsTer4	p.I550Ffs*4	ENST00000374690	NM_000044.3	547	gtt/gtTTTGCCCt	2/8	1	2	FACETS	0.323	0.284	0.364	0.323	0.284	0.364	SUBCLONAL	1	TRUE	1	0.57	2		607	924	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0028362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	25	684	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	1	2	FACETS	0.274	0.214	0.343	0.274	0.214	0.343	SUBCLONAL	1	TRUE	1	0.15	2		684	1218	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0028362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	43	403	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	1	2	FACETS	0.854	0.713	1	0.854	0.713	1	CLONAL	1	TRUE	1	0.15	2		403	671	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	CT	rs121913227	NA	P-0028362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	45	587	0	ENST00000288602.6:c.1798_1799delinsAG	p.Val600Arg	p.V600R	ENST00000288602	NM_004333.4	600	GTg/AGg	15/18	1	2	FACETS	0.984	0.826	1	0.984	0.826	1	CLONAL	1	TRUE	1	0.15	2		587	610	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936806	32936806	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80359689	NA	P-0028362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	52	513	0	ENST00000380152.3:c.7954del	p.Val2652CysfsTer5	p.V2652Cfs*5	ENST00000380152		2651	aGg/ag	17/27	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.15	2		513	675	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760743	59760743	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	44	699	0	ENST00000259008.2:c.3664G>C	p.Glu1222Gln	p.E1222Q	ENST00000259008	NM_032043.2	1222	Gaa/Caa	20/20	1	2	FACETS	0.715	0.598	0.846	0.715	0.598	0.846	SUBCLONAL	1	TRUE	1	0.15	2		699	820	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0028422-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	1490	248	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.370969410105099	26	FACETS	1	0.988	1			1	CLONAL	25	TRUE	NA	0.370969410105099	26		248	1750	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741836	145741836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028422-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1369	127	663	1	ENST00000428558.2:c.667G>A	p.Gly223Ser	p.G223S	ENST00000428558	NM_004260.3	223	Ggt/Agt	5/22	0.370969410105099	7	FACETS	0.882	0.796	0.973			1	CLONAL	1	TRUE	NA	0.370969410105099	7		664	1496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579592	7579592	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0028422-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	211	481	0	ENST00000269305.4:c.97-2A>T		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.363010405155807	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.370969410105099	2		481	559	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55225416	55225416	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028422-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	57	391	0	ENST00000275493.2:c.1268T>G	p.Leu423Arg	p.L423R	ENST00000275493	NM_005228.3	423	cTa/cGa	11/28	0.370396290611884	3	FACETS	0.664	0.569	0.766	0.332	0.284	0.383	SUBCLONAL	1	TRUE	1	0.370969410105099	3		391	549	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149450048	149450048	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028422-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	113	482	0	ENST00000286301.3:c.1169G>C	p.Arg390Thr	p.R390T	ENST00000286301	NM_005211.3	390	aGa/aCa	8/22	0.370969410105099	3	FACETS	0.998	0.898	1	0.499	0.449	0.551	CLONAL	1	TRUE	1	0.370969410105099	3		482	724	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839799	27839799	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028422-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	53	489	0	ENST00000328488.2:c.295del	p.Ala99ProfsTer?	p.A99Pfs*?	ENST00000328488	NM_003533.2	99	Gcc/cc	1/1	0.370396290611884	3	FACETS	0.505	0.43	0.587	0.252	0.215	0.294	SUBCLONAL	1	TRUE	1	0.370969410105099	3		489	671	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647509	117647509	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028422-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	84	426	0	ENST00000368508.3:c.5435G>T	p.Ser1812Ile	p.S1812I	ENST00000368508	NM_002944.2	1812	aGt/aTt	33/43	0.370396290611884	3	FACETS	1	0.946	1	0.558	0.494	0.626	CLONAL	1	TRUE	1	0.370969410105099	3		426	481	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412949	49412949	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028591-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	200	860	0	ENST00000418115.1:c.74T>G	p.Phe25Cys	p.F25C	ENST00000418115	NM_001664.2	25	tTc/tGc	2/5	1	2	FACETS	0.726	0.672	0.783	0.726	0.672	0.783	SUBCLONAL	1	FALSE	1	0.493896636889774	2		860	1115	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170009676	170009676	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028591-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	80	433	0	ENST00000295797.4:c.1238T>C	p.Phe413Ser	p.F413S	ENST00000295797	NM_002740.5	413	tTc/tCc	13/18	1	2	FACETS	0.752	0.665	0.844	0.752	0.665	0.844	SUBCLONAL	1	FALSE	1	0.493896636889774	2		433	431	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417356	139417356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1027492078	NA	P-0028591-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	159	450	9	ENST00000277541.6:c.688G>A	p.Gly230Arg	p.G230R	ENST00000277541	NM_017617.3	230	Ggg/Agg	4/34	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	1	0.493896636889774	2		459	642	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0028711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	327	300	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		300	990	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577049	7577049	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	292	1140	0	ENST00000269305.4:c.889del	p.His297ThrfsTer48	p.H297Tfs*48	ENST00000269305	NM_001126112.2	297	Cac/ac	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1140	922	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401642	401642	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210576093	NA	P-0028711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	79	848	0	ENST00000380956.4:c.964G>A	p.Asp322Asn	p.D322N	ENST00000380956	NM_001195286.1	322	Gac/Aac	7/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		848	741	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151893043	151893043	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1406863036	NA	P-0028711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	45	732	0	ENST00000262189.6:c.4327G>A	p.Asp1443Asn	p.D1443N	ENST00000262189	NM_170606.2	1443	Gac/Aac	28/59	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		732	839	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924617	94924617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1433012201	NA	P-0028711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1236	86	1159	4	ENST00000536441.1:c.293G>A	p.Arg98His	p.R98H	ENST00000536441	NM_144665.3	98	cGc/cAc	3/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1163	1322	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432688	29432688	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	91	940	0	ENST00000389048.3:c.3800A>G	p.Lys1267Arg	p.K1267R	ENST00000389048	NM_004304.4	1267	aAg/aGg	25/29	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		940	757	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198262804	198262804	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	70	683	0	ENST00000335508.6:c.3171G>T	p.Arg1057Ser	p.R1057S	ENST00000335508	NM_012433.2	1057	agG/agT	22/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		683	590	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72881634	72881634	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0028711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	39	664	0	ENST00000325599.8:c.487-2A>G		p.X163_splice	ENST00000325599	NM_018130.2	163			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		664	513	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715831	117715839	+	inframe_deletion	In_Frame_Del	DEL	TAAATGTTT	TAAATGTTT	-	novel	NA	P-0028711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	58	778	0	ENST00000368508.3:c.919_927del	p.Lys307_Leu309del	p.K307_L309del	ENST00000368508	NM_002944.2	307	AAACATTTA/-	9/43	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		778	590	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415160	116415160	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1562931818	NA	P-0028711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	75	825	2	ENST00000397752.3:c.3254G>A	p.Gly1085Glu	p.G1085E	ENST00000397752	NM_000245.2	1085	gGa/gAa	15/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		827	987	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477858	140477858	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	177	844	0	ENST00000288602.6:c.1450A>G	p.Met484Val	p.M484V	ENST00000288602	NM_004333.4	484	Atg/Gtg	12/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		844	866	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266110	41266110	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	79	309	0	ENST00000349496.5:c.107A>C	p.His36Pro	p.H36P	ENST00000349496	NM_001904.3	36	cAt/cCt	3/15	1	2	FACETS	0.88	0.785	0.978	0.88	0.785	0.978	CLONAL	1	TRUE	1	0.730223352921112	2		309	246	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857974	9857974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61758996	NA	P-0028835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	119	438	1	ENST00000330684.3:c.3427G>A	p.Glu1143Lys	p.E1143K	ENST00000330684	NM_001134407.1	1143	Gag/Aag	13/13	1	2	FACETS	0.771	0.701	0.843	0.771	0.701	0.843	SUBCLONAL	1	TRUE	1	0.730223352921112	2		439	423	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0029218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	289	716	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	1	2	FACETS	0.935	0.879	0.993	0.935	0.879	0.993	CLONAL	1	TRUE	1	0.530985564713503	2		716	1164	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533772	41533772	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853038	NA	P-0029218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	199	557	0	ENST00000263253.7:c.1738C>T	p.Arg580Ter	p.R580*	ENST00000263253	NM_001429.3	580	Cga/Tga	8/31	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.530985564713503	2		557	724	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257336	16257336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557759530	NA	P-0029218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	221	680	0	ENST00000375759.3:c.4601C>T	p.Ser1534Leu	p.S1534L	ENST00000375759	NM_015001.2	1534	tCa/tTa	11/15	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.530985564713503	2		680	651	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925543	114925543	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774534267	NA	P-0029218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	214	575	0	ENST00000543371.1:c.1621G>A	p.Ala541Thr	p.A541T	ENST00000543371	NM_001198531.1	541	Gct/Act	14/14	0.520182340688817	2	FACETS	0.999	0.93	1	0.499	0.465	0.535	CLONAL	1	TRUE	0	0.530985564713503	2		575	807	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118301	17118301	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	304	580	0	ENST00000285071.4:c.1536G>A	p.Met512Ile	p.M512I	ENST00000285071	NM_144997.5	512	atG/atA	13/14	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.530985564713503	2		580	974	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	303	473	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.924	0.873	0.975	0.924	0.873	0.975	CLONAL	1	TRUE	1	0.76107399966574	2		473	862	SUCCESS
APC	324	MSKCC	GRCh37	5	112175650	112175651	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	196	578	0	ENST00000257430.4:c.4364dup	p.Asn1455LysfsTer2	p.N1455Kfs*2	ENST00000257430	NM_000038.5	1453	-/A	16/16	0.744164596256153	1	FACETS	0.865	0.814	0.915	0.865	0.814	0.915	CLONAL	1	TRUE	0	0.76107399966574	1		578	369	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243237	123243237	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	371	1088	1	ENST00000358487.5:c.2276G>T	p.Arg759Leu	p.R759L	ENST00000358487	NM_000141.4	759	cGa/cTa	17/18	0.76107399966574	1	FACETS	0.942	0.904	0.98	0.942	0.904	0.98	CLONAL	1	TRUE	0	0.76107399966574	1		1089	641	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467185	25467185	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	367	779	1	ENST00000264709.3:c.1690G>T	p.Asp564Tyr	p.D564Y	ENST00000264709	NM_175629.2	564	Gac/Tac	15/23	0.560336999498628	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.76107399966574	1		780	546	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29115429	29115429	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	313	802	1	ENST00000328354.6:c.637C>T	p.Pro213Ser	p.P213S	ENST00000328354	NM_007194.3	213	Cct/Tct	5/15	1	2	FACETS	0.898	0.849	0.947	0.898	0.849	0.947	CLONAL	1	TRUE	1	0.76107399966574	2		803	916	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509835	187509835	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	121	397	0	ENST00000441802.2:c.13678A>G	p.Met4560Val	p.M4560V	ENST00000441802	NM_005245.3	4560	Atg/Gtg	27/27	0.744164596256153	1	FACETS	0.831	0.768	0.894	0.831	0.768	0.894	CLONAL	1	TRUE	0	0.76107399966574	1		397	237	SUCCESS
MET	4233	MSKCC	GRCh37	7	116409843	116409869	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGGTGGGATTCCTGCATTCCTCTCAT	GAGGTGGGATTCCTGCATTCCTCTCAT	-	novel	NA	P-0029627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	125	486	0	ENST00000397752.3:c.2730_2730+26del		p.X910_splice	ENST00000397752	NM_000245.2	910		12/21	1	2	FACETS	0.702	0.639	0.767	0.702	0.639	0.767	SUBCLONAL	1	TRUE	1	0.76107399966574	2		486	468	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0029938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	148	284	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	0.985	1	CLONAL	1	TRUE	1	0.515675161072377	2		284	439	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	97	333	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.962	0.864	1	0.962	0.864	1	CLONAL	1	TRUE	1	0.515675161072377	2		333	391	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0029938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	34	480	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.226	0.184	0.273	0.226	0.184	0.273	SUBCLONAL	1	TRUE	1	0.515675161072377	2		480	584	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888189	112888189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507511	NA	P-0029938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	32	593	0	ENST00000351677.2:c.205G>A	p.Glu69Lys	p.E69K	ENST00000351677	NM_002834.3	69	Gag/Aag	3/16	0.515675161072377	1	FACETS	0.155	0.125	0.189	0.155	0.125	0.189	SUBCLONAL	1	TRUE	0	0.515675161072377	1		593	595	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779187	135779187	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	204	408	0	ENST00000298552.3:c.2059G>T	p.Glu687Ter	p.E687*	ENST00000298552	NM_001162426.1	687	Gag/Tag	17/23	0.370865339262961	3	FACETS	0.801	0.747	0.857	0.801	0.747	0.857	CLONAL	2	TRUE	1	0.515675161072377	3		408	621	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426955	49426955	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	43	519	0	ENST00000301067.7:c.11533C>T	p.Gln3845Ter	p.Q3845*	ENST00000301067	NM_003482.3	3845	Cag/Tag	39/54	0.515675161072377	1	FACETS	0.279	0.233	0.329	0.279	0.233	0.329	SUBCLONAL	1	TRUE	0	0.515675161072377	1		519	444	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63662083	63662083	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	133	359	0	ENST00000279873.7:c.187G>C	p.Glu63Gln	p.E63Q	ENST00000279873	NM_032199.2	63	Gag/Cag	2/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.515675161072377	2		359	484	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006384	12006384	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	137	436	0	ENST00000396373.4:c.352C>T	p.Gln118Ter	p.Q118*	ENST00000396373	NM_001987.4	118	Cag/Tag	4/8	0.515675161072377	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.515675161072377	1		436	376	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81563044	81563044	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	104	337	0	ENST00000298171.2:c.607G>C	p.Asp203His	p.D203H	ENST00000298171	NM_000369.2	203	Gat/Cat	7/10	1	2	FACETS	0.839	0.755	0.927	0.839	0.755	0.927	CLONAL	1	TRUE	1	0.515675161072377	2		337	481	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43767830	43767830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	207	614	0	ENST00000382044.4:c.1018C>T	p.Pro340Ser	p.P340S	ENST00000382044	NM_001141980.1	340	Cct/Tct	9/28	1	2	FACETS	0.997	0.928	1	0.997	0.928	1	CLONAL	1	TRUE	1	0.515675161072377	2		614	805	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654788	29654788	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	111	361	0	ENST00000356175.3:c.5477C>A	p.Pro1826Gln	p.P1826Q	ENST00000356175	NM_000267.3	1826	cCa/cAa	37/57	1	2	FACETS	0.901	0.814	0.991	0.901	0.814	0.991	CLONAL	1	TRUE	1	0.515675161072377	2		361	478	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45377695	45377695	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	68	258	0	ENST00000262160.6:c.734C>T	p.Ser245Phe	p.S245F	ENST00000262160	NM_005901.5	245	tCt/tTt	7/11	1	2	FACETS	0.956	0.84	1	0.956	0.84	1	CLONAL	1	TRUE	1	0.515675161072377	2		258	276	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978892	25978892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	84	361	0	ENST00000435504.4:c.1031C>T	p.Ser344Leu	p.S344L	ENST00000435504		344	tCa/tTa	10/13	1	2	FACETS	0.737	0.654	0.825	0.737	0.654	0.825	SUBCLONAL	1	TRUE	1	0.515675161072377	2		361	442	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73108264	73108264	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	46	147	0	ENST00000356692.5:c.364C>T	p.Leu122Phe	p.L122F	ENST00000356692		122	Ctc/Ttc	4/9	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.515675161072377	2		147	157	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	207	604	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.983	0.917	1	0.983	0.917	1	CLONAL	1	TRUE	1	0.647685970360698	2		604	650	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	216	559	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.647685970360698	1	FACETS	0.942	0.885	0.998	0.942	0.885	0.998	CLONAL	1	TRUE	0	0.647685970360698	1		560	479	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	177	434	7	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.992	0.92	1	0.992	0.92	1	CLONAL	1	TRUE	1	0.647685970360698	2		441	551	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	179	514	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.647685970360698	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.647685970360698	1		514	371	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592108	67592108	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1419325070	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	128	286	0	ENST00000274335.5:c.1924C>T	p.Arg642Ter	p.R642*	ENST00000274335		642	Cga/Tga	14/15	1	2	FACETS	0.876	0.8	0.955	0.876	0.8	0.955	CLONAL	1	TRUE	1	0.647685970360698	2		286	451	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	249	658	1	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	1	2	FACETS	0.921	0.863	0.98	0.921	0.863	0.98	CLONAL	1	TRUE	1	0.647685970360698	2		659	835	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354509	91354509	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730880251	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	198	409	0	ENST00000355112.3:c.3949G>A	p.Glu1317Lys	p.E1317K	ENST00000355112	NM_000057.2	1317	Gag/Aag	21/22	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.647685970360698	2		409	580	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675571	86675571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1561325048	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	171	258	0	ENST00000274376.6:c.2513del	p.Asn838MetfsTer4	p.N838Mfs*4	ENST00000274376	NM_002890.2	836	gAa/ga	19/25	1	2	FACETS	0.967	0.895	1	0.967	0.895	1	CLONAL	1	TRUE	1	0.647685970360698	2		258	546	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015230	128015230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs189511674	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	219	398	0	ENST00000285398.2:c.2291C>T	p.Ser764Leu	p.S764L	ENST00000285398	NM_000122.1	764	tCg/tTg	15/15	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.647685970360698	2		398	626	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882050	36882050	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs780753361	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	229	627	6	ENST00000358127.4:c.963del	p.Ala322LeufsTer11	p.A322Lfs*11	ENST00000358127	NM_001280556.1	321	ccC/cc	8/10	1	2	FACETS	0.934	0.874	0.996	0.934	0.874	0.996	CLONAL	1	TRUE	1	0.647685970360698	2		633	757	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	145	289	2	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	0.647685970360698	1	FACETS	0.915	0.848	0.982	0.915	0.848	0.982	CLONAL	1	TRUE	0	0.647685970360698	1		291	331	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637539	52637540	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	202	365	0	ENST00000394830.3:c.2776dup	p.Arg926LysfsTer4	p.R926Kfs*4	ENST00000394830	NM_018313.4	926	aga/aAga	18/30	0.647685970360698	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.647685970360698	1		365	414	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622039	43622039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1371891301	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	121	270	0	ENST00000355710.3:c.3056C>T	p.Ala1019Val	p.A1019V	ENST00000355710	NM_020975.4	1019	gCg/gTg	19/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.647685970360698	2		270	327	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	360055	360055	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	166	469	0	ENST00000262320.3:c.1034del	p.Pro345HisfsTer69	p.P345Hfs*69	ENST00000262320	NM_003502.3	345	cCa/ca	4/11	1	2	FACETS	0.967	0.894	1	0.967	0.894	1	CLONAL	1	TRUE	1	0.647685970360698	2		469	530	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505443	157505443	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554231830	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	181	397	0	ENST00000346085.5:c.3428del	p.Lys1143SerfsTer68	p.K1143Sfs*68	ENST00000346085	NM_020732.3	1142	Aaa/aa	13/20	1	2	FACETS	0.946	0.877	1	0.946	0.877	1	CLONAL	1	TRUE	1	0.647685970360698	2		397	591	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891687	28891687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	210	520	1	ENST00000282397.4:c.3334C>T	p.Arg1112Cys	p.R1112C	ENST00000282397	NM_002019.4	1112	Cgc/Tgc	25/30	1	2	FACETS	0.951	0.887	1	0.951	0.887	1	CLONAL	1	TRUE	1	0.647685970360698	2		521	682	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202351	138202351	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	181	458	1	ENST00000237289.4:c.2274del	p.Lys759SerfsTer57	p.K759Sfs*57	ENST00000237289	NM_001270507.1	756	gaC/ga	9/9	1	2	FACETS	0.83	0.769	0.894	0.83	0.769	0.894	CLONAL	1	TRUE	1	0.647685970360698	2		459	673	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416952	416953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs771545848	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	163	345	6	ENST00000399788.2:c.3597dup	p.Gly1200ArgfsTer7	p.G1200Rfs*7	ENST00000399788	NM_001042603.1	1199	-/A	23/28	NA	2	FACETS	0.857	0.791	0.926			1	INDETERMINATE	1	TRUE	NA	0.647685970360698	2		351	587	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483963	212483963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	266	396	1	ENST00000342788.4:c.2240C>T	p.Pro747Leu	p.P747L	ENST00000342788	NM_005235.2	747	cCt/cTt	19/28	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.647685970360698	2		397	805	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117632201	117632201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779401784	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	283	505	1	ENST00000368508.3:c.6215G>A	p.Arg2072Gln	p.R2072Q	ENST00000368508	NM_002944.2	2072	cGg/cAg	39/43	1	2	FACETS	0.962	0.907	1	0.962	0.907	1	CLONAL	1	TRUE	1	0.647685970360698	2		506	908	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137321073	137321073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768721235	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	150	419	0	ENST00000481739.1:c.1030G>A	p.Ala344Thr	p.A344T	ENST00000481739	NM_002957.4	344	Gcc/Acc	7/10	1	2	FACETS	0.994	0.916	1	0.994	0.916	1	CLONAL	1	TRUE	1	0.647685970360698	2		419	466	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396234	396234	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	229	471	4	ENST00000262320.3:c.792del	p.Gly265GlufsTer149	p.G265Efs*149	ENST00000262320	NM_003502.3	264	ccC/cc	2/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.647685970360698	2		475	631	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214866	36214866	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568372429	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	225	658	5	ENST00000222270.7:c.3296del	p.Gly1099AlafsTer83	p.G1099Afs*83	ENST00000222270	NM_014727.1	1098	Ggg/gg	8/37	1	2	FACETS	0.92	0.86	0.982	0.92	0.86	0.982	CLONAL	1	TRUE	1	0.647685970360698	2		663	755	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187059	38187059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1460044917	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	216	545	0	ENST00000317025.8:c.1418C>T	p.Ala473Val	p.A473V	ENST00000317025	NM_023034.1	473	gCg/gTg	6/24	1	2	FACETS	0.809	0.754	0.866	0.809	0.754	0.866	CLONAL	1	TRUE	1	0.647685970360698	2		545	824	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156918	89156920	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	rs768142526	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	198	380	0	ENST00000336596.2:c.27_29del	p.Leu11del	p.L11del	ENST00000336596	NM_005233.5	7	aTCCtc/atc	1/17	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.647685970360698	2		380	556	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647098	23647098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780824	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	344	611	0	ENST00000261584.4:c.769G>A	p.Gly257Ser	p.G257S	ENST00000261584	NM_024675.3	257	Ggt/Agt	4/13	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.647685970360698	2		611	939	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310518	65310518	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1307956862	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	236	427	0	ENST00000342505.4:c.2170C>T	p.Arg724Cys	p.R724C	ENST00000342505	NM_002227.2	724	Cgt/Tgt	16/25	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.647685970360698	2		427	634	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341193	8341193	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	166	370	0	ENST00000356435.5:c.5023C>A	p.Leu1675Ile	p.L1675I	ENST00000356435		1675	Ctt/Att	30/35	1	2	FACETS	0.946	0.874	1	0.946	0.874	1	CLONAL	1	TRUE	1	0.647685970360698	2		370	542	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612809	228612809	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773691912	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	209	467	0	ENST00000366696.1:c.218G>A	p.Arg73His	p.R73H	ENST00000366696	NM_003493.2	73	cGc/cAc	1/1	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.647685970360698	2		467	602	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138075	64138075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	165	492	0	ENST00000334205.4:c.2000del	p.Gly667AspfsTer53	p.G667Dfs*53	ENST00000334205	NM_003942.2	666	gaG/ga	16/17	1	2	FACETS	0.886	0.818	0.956	0.886	0.818	0.956	CLONAL	1	TRUE	1	0.647685970360698	2		492	575	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225528	133225528	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	191	441	0	ENST00000320574.5:c.4136C>T	p.Ala1379Val	p.A1379V	ENST00000320574	NM_006231.2	1379	gCt/gTt	32/49	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.647685970360698	2		441	558	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78765291	78765291	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	161	247	0	ENST00000306801.3:c.872C>T	p.Thr291Ile	p.T291I	ENST00000306801	NM_020761.2	291	aCa/aTa	7/34	0.618190365043737	3	FACETS	0.997	0.918	1	0.499	0.459	0.54	CLONAL	1	TRUE	1	0.647685970360698	3		247	660	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212567	36212567	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	262	635	2	ENST00000222270.7:c.2322del	p.Ala775ProfsTer14	p.A775Pfs*14	ENST00000222270	NM_014727.1	773	gAa/ga	3/37	1	2	FACETS	0.975	0.916	1	0.975	0.916	1	CLONAL	1	TRUE	1	0.647685970360698	2		637	830	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082191	16082191	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370558211	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	246	569	1	ENST00000281043.3:c.5C>T	p.Pro2Leu	p.P2L	ENST00000281043	NM_005378.4	2	cCg/cTg	2/3	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.647685970360698	2		570	722	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660016	227660017	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	205	442	0	ENST00000305123.5:c.3438dup	p.Glu1147Ter	p.E1147*	ENST00000305123	NM_005544.2	1146	-/T	1/2	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.647685970360698	2		442	556	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495355	149495355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600485	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	153	525	0	ENST00000261799.4:c.3292C>T	p.Arg1098Trp	p.R1098W	ENST00000261799	NM_002609.3	1098	Cgg/Tgg	23/23	1	2	FACETS	0.951	0.876	1	0.951	0.876	1	CLONAL	1	TRUE	1	0.647685970360698	2		525	497	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048561	180048562	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	191	462	0	ENST00000261937.6:c.2000dup	p.Lys668GlufsTer104	p.K668Efs*104	ENST00000261937	NM_182925.4	667	aag/aaAg	13/30	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.647685970360698	2		462	530	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056155	26056155	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	222	373	0	ENST00000343677.2:c.502A>G	p.Lys168Glu	p.K168E	ENST00000343677	NM_005319.3	168	Aag/Gag	1/1	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.647685970360698	2		373	610	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439613	140439614	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	227	464	0	ENST00000288602.6:c.2125dup	p.Gln709ProfsTer7	p.Q709Pfs*7	ENST00000288602	NM_004333.4	709	caa/cCaa	17/18	1	2	FACETS	0.884	0.826	0.944	0.884	0.826	0.944	CLONAL	1	TRUE	1	0.647685970360698	2		464	793	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136840	69136840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746734356	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	177	306	0	ENST00000288368.4:c.4754G>A	p.Arg1585Gln	p.R1585Q	ENST00000288368	NM_024870.2	1585	cGg/cAg	39/40	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.647685970360698	2		306	544	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561430	141561430	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	166	331	0	ENST00000220592.5:c.1375del	p.Gln459SerfsTer9	p.Q459Sfs*9	ENST00000220592	NM_012154.3	459	Cag/ag	11/19	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.647685970360698	2		331	462	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471057	8471057	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	209	292	0	ENST00000356435.5:c.3442A>G	p.Lys1148Glu	p.K1148E	ENST00000356435		1148	Aag/Gag	20/35	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.647685970360698	2		292	541	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390696	139390697	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	214	681	0	ENST00000277541.6:c.7494dup	p.Ser2499GlnfsTer8	p.S2499Qfs*8	ENST00000277541	NM_017617.3	2498	-/C	34/34	1	2	FACETS	0.908	0.847	0.97	0.908	0.847	0.97	CLONAL	1	TRUE	1	0.647685970360698	2		681	728	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15826384	15826384	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	161	362	0	ENST00000307771.7:c.428C>T	p.Ala143Val	p.A143V	ENST00000307771	NM_005089.3	143	gCt/gTt	6/11	1	2	FACETS	0.815	0.751	0.881	0.815	0.751	0.881	CLONAL	1	TRUE	1	0.647685970360698	2		362	610	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325856	65325856	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030371-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	47	514	0	ENST00000342505.4:c.1266C>A	p.Tyr422Ter	p.Y422*	ENST00000342505	NM_002227.2	422	taC/taA	9/25	1	2	FACETS	0.592	0.5	0.694	0.592	0.5	0.694	SUBCLONAL	1	FALSE	1	0.329170528768826	2		514	482	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0030482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	138	248	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.225731830067087	4	FACETS	0.861	0.791	0.933	0.861	0.791	0.933	CLONAL	3	TRUE	1	0.34	4		248	421	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788618	3788618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398124146	NA	P-0030482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	35	283	0	ENST00000262367.5:c.4336C>T	p.Arg1446Cys	p.R1446C	ENST00000262367	NM_004380.2	1446	Cgc/Tgc	26/31	0.205880870722013	3	FACETS	0.476	0.39	0.573	0.238	0.195	0.287	SUBCLONAL	1	TRUE	1	0.34	3		283	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579310	7579310	+	splice_donor_variant	Splice_Site	SNP	A	A	T	rs1555526469	NA	P-0030482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	95	325	0	ENST00000269305.4:c.375+2T>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.3	1	FACETS	0.966	0.864	1	0.966	0.864	1	CLONAL	1	TRUE	0	0.34	1		325	480	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805371	46805371	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	2989	617	0	ENST00000290295.7:c.585G>C	p.Trp195Cys	p.W195C	ENST00000290295	NM_006361.5	195	tgG/tgC	1/2	0.3	20	FACETS	1	0.996	1			1	CLONAL	19	TRUE	NA	0.34	20		617	3716	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805399	46805400	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TA	novel	NA	P-0030482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	2968	658	2	ENST00000290295.7:c.556_557delinsTA	p.Gly186Ter	p.G186*	ENST00000290295	NM_006361.5	186	GGa/TAa	1/2	0.3	20	FACETS	1	0.991	1			1	CLONAL	19	TRUE	NA	0.34	20		660	3727	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805601	46805601	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	3417	572	0	ENST00000290295.7:c.355G>C	p.Glu119Gln	p.E119Q	ENST00000290295	NM_006361.5	119	Gag/Cag	1/2	0.3	20	FACETS	0.998	0.99	1			1	CLONAL	20	TRUE	NA	0.34	20		572	4087	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688772	47688772	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	873	267	0	ENST00000347630.2:c.528G>C	p.Met176Ile	p.M176I	ENST00000347630	NM_001007230.1	176	atG/atC	7/11	0.3	20	FACETS	0.97	0.944	0.996			1	CLONAL	14	TRUE	NA	0.34	20		267	1535	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500339	99500339	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs368065238	NA	P-0030482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	203	616	0	ENST00000268035.6:c.3772T>G	p.Ser1258Ala	p.S1258A	ENST00000268035	NM_000875.3	1258	Tcc/Gcc	21/21	0.270372673809054	4	FACETS	0.813	0.754	0.874			1	CLONAL	2	TRUE	NA	0.34	4		616	984	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0030734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	33	819	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.238	0.193	0.29	0.238	0.193	0.29	SUBCLONAL	1	TRUE	1	0.248283496616774	2		819	1116	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845477	72845477	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	74	435	1	ENST00000268489.5:c.3863C>A	p.Thr1288Lys	p.T1288K	ENST00000268489	NM_006885.3	1288	aCg/aAg	7/10	0.248283496616774	3	FACETS	1	0.939	1	0.56	0.491	0.635	CLONAL	1	TRUE	1	0.248283496616774	3		436	598	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483085	29483085	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs764367878	NA	P-0030734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	125	612	0	ENST00000356175.3:c.145T>A	p.Tyr49Asn	p.Y49N	ENST00000356175	NM_000267.3	49	Tac/Aac	2/57	0.248283496616774	3	FACETS	0.992	0.896	1	0.496	0.448	0.547	CLONAL	1	TRUE	1	0.248283496616774	3		612	1141	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682359	37682359	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	167	596	0	ENST00000447079.4:c.3550T>G	p.Ser1184Ala	p.S1184A	ENST00000447079	NM_015083.1	1184	Tct/Gct	13/14	0.248283496616774	3	FACETS	0.933	0.859	1	0.933	0.859	1	CLONAL	2	TRUE	1	0.248283496616774	3		596	810	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511595	66511595	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	153	411	0	ENST00000358598.2:c.55G>T	p.Glu19Ter	p.E19*	ENST00000358598	NM_212471.2	19	Gag/Tag	2/11	0.248283496616774	3	FACETS	0.963	0.883	1	0.963	0.883	1	CLONAL	2	TRUE	1	0.248283496616774	3		411	719	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270434	10270434	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	213	602	0	ENST00000340748.4:c.1132C>G	p.Pro378Ala	p.P378A	ENST00000340748		378	Cca/Gca	16/40	0.190341822958557	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	2	0.248283496616774	4		602	996	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523361	9523361	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs149977525	NA	P-0030734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	137	403	0	ENST00000353224.5:c.1876A>G	p.Ile626Val	p.I626V	ENST00000353224	NM_177990.2	626	Atc/Gtc	9/10	0.248283496616774	3	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	1	0.248283496616774	3		403	608	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967330	38967330	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0030734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	182	421	0	ENST00000357387.3:c.1152-1G>A		p.X384_splice	ENST00000357387	NM_152756.3	384			0.248283496616774	5	FACETS	1	0.97	1	0.549	0.507	0.593	CLONAL	2	TRUE	1	0.248283496616774	5		421	916	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911524	131911524	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659915	NA	P-0030734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	120	503	0	ENST00000265335.6:c.269A>G	p.Asn90Ser	p.N90S	ENST00000265335		90	aAt/aGt	3/25	0.206931654780517	4	FACETS	1	0.967	1	0.389	0.35	0.43	CLONAL	1	TRUE	1	0.248283496616774	4		503	1035	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840048	27840048	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	31	309	0	ENST00000328488.2:c.46G>T	p.Ala16Ser	p.A16S	ENST00000328488	NM_003533.2	16	Gcg/Tcg	1/1	0.248283496616774	3	FACETS	0.628	0.507	0.765	0.314	0.253	0.383	SUBCLONAL	1	TRUE	1	0.248283496616774	3		309	447	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27205058	27205058	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	75	557	0	ENST00000380036.4:c.2359A>T	p.Asn787Tyr	p.N787Y	ENST00000380036	NM_000459.3	787	Aac/Tac	14/23	1	2	FACETS	0.83	0.727	0.941	0.83	0.727	0.941	CLONAL	1	TRUE	1	0.248283496616774	2		557	728	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229429	98229429	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	82	406	0	ENST00000331920.6:c.2529G>C	p.Met843Ile	p.M843I	ENST00000331920	NM_000264.3	843	atG/atC	15/24	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.248283496616774	2		406	601	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	77	355	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.38	2		355	392	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	103	250	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.837	0.757	0.919	1	0.986	1	CLONAL	2	TRUE	1	0.38	2		250	324	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	72	308	1	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	0.38	2		309	285	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	56	665	2	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.475	0.407	0.55	0.475	0.407	0.55	SUBCLONAL	1	TRUE	1	0.38	2		667	620	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	84	293	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.781	0.698	0.867	1	0.981	1	SUBCLONAL	2	TRUE	1	0.38	2		293	283	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	47	580	1	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	0.423	0.356	0.496	0.423	0.356	0.496	SUBCLONAL	1	TRUE	1	0.38	2		581	585	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491309	2491309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750864649	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	152	739	0	ENST00000355716.4:c.352G>A	p.Val118Met	p.V118M	ENST00000355716	NM_003820.2	118	Gtg/Atg	4/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.38	2		739	597	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073804	8073804	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1557463619	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	88	362	0	ENST00000377482.5:c.855del	p.Arg286GlufsTer9	p.R286Efs*9	ENST00000377482	NM_018948.3	285	ccC/cc	4/4	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.38	2		362	367	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257968	16257968	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	23	473	0	ENST00000375759.3:c.5233G>A	p.Ala1745Thr	p.A1745T	ENST00000375759	NM_015001.2	1745	Gca/Aca	11/15	1	2	FACETS	0.276	0.215	0.348	0.276	0.215	0.348	SUBCLONAL	1	TRUE	1	0.38	2		473	438	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264487	16264487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1228222000	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	37	485	2	ENST00000375759.3:c.10690G>A	p.Ala3564Thr	p.A3564T	ENST00000375759	NM_015001.2	3564	Gcc/Acc	13/15	1	2	FACETS	0.429	0.353	0.513	0.429	0.353	0.513	SUBCLONAL	1	TRUE	1	0.38	2		487	454	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056211	27056211	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs878853088	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	32	450	0	ENST00000324856.7:c.1207C>T	p.Gln403Ter	p.Q403*	ENST00000324856	NM_006015.4	403	Cag/Tag	2/20	1	2	FACETS	0.323	0.262	0.393	0.323	0.262	0.393	SUBCLONAL	1	TRUE	1	0.38	2		450	521	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058018	27058018	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	115	462	0	ENST00000324856.7:c.1726C>T	p.Gln576Ter	p.Q576*	ENST00000324856	NM_006015.4	576	Cag/Tag	3/20	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.38	2		462	579	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100946	27100946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	106	530	1	ENST00000324856.7:c.4228C>T	p.Pro1410Ser	p.P1410S	ENST00000324856	NM_006015.4	1410	Ccc/Tcc	18/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.38	2		531	500	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106105	27106105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	33	479	1	ENST00000324856.7:c.5716C>T	p.Arg1906Trp	p.R1906W	ENST00000324856	NM_006015.4	1906	Cgg/Tgg	20/20	1	2	FACETS	0.389	0.316	0.47	0.389	0.316	0.47	SUBCLONAL	1	TRUE	1	0.38	2		480	447	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107159	27107159	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	51	603	0	ENST00000324856.7:c.6770G>T	p.Arg2257Leu	p.R2257L	ENST00000324856	NM_006015.4	2257	cGg/cTg	20/20	1	2	FACETS	0.403	0.342	0.47	0.403	0.342	0.47	SUBCLONAL	1	TRUE	1	0.38	2		603	666	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809476	36809476	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	35	605	1	ENST00000373129.3:c.989C>T	p.Ala330Val	p.A330V	ENST00000373129	NM_032017.1	330	gCc/gTc	10/12	1	2	FACETS	0.318	0.26	0.384	0.318	0.26	0.384	SUBCLONAL	1	TRUE	1	0.38	2		606	579	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935319	36935319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748675453	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	153	759	0	ENST00000361632.4:c.1408G>A	p.Ala470Thr	p.A470T	ENST00000361632		470	Gcg/Acg	10/16	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.38	2		759	593	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726435	46726435	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142433634	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	35	425	0	ENST00000371975.4:c.514C>T	p.Arg172Cys	p.R172C	ENST00000371975	NM_003579.3	172	Cgc/Tgc	7/18	1	2	FACETS	0.485	0.398	0.582	0.485	0.398	0.582	SUBCLONAL	1	TRUE	1	0.38	2		425	380	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247938	59247938	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	155	731	0	ENST00000371222.2:c.805T>C	p.Cys269Arg	p.C269R	ENST00000371222	NM_002228.3	269	Tgc/Cgc	1/1	1	2	FACETS	0.997	0.914	1	0.997	0.914	1	CLONAL	1	TRUE	1	0.38	2		731	818	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65349076	65349076	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs768272377	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	134	584	0	ENST00000342505.4:c.89A>G	p.Glu30Gly	p.E30G	ENST00000342505	NM_002227.2	30	gAg/gGg	3/25	1	2	FACETS	0.995	0.905	1	0.995	0.905	1	CLONAL	1	TRUE	1	0.38	2		584	709	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258681	115258681	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	79	308	0	ENST00000369535.4:c.101C>A	p.Pro34His	p.P34H	ENST00000369535	NM_002524.4	34	cCc/cAc	2/7	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.38	2		308	370	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268831	115268831	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	106	514	3	ENST00000438362.2:c.1778+1G>A		p.X593_splice	ENST00000438362	NM_001242891.1	593			1	2	FACETS	0.979	0.88	1	0.979	0.88	1	CLONAL	1	TRUE	1	0.38	2		517	570	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166296	118166296	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	82	327	0	ENST00000369448.3:c.806A>G	p.Tyr269Cys	p.Y269C	ENST00000369448	NM_017709.3	269	tAc/tGc	2/2	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.38	2		327	319	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459239	120459239	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	105	473	1	ENST00000256646.2:c.6106C>T	p.Arg2036Ter	p.R2036*	ENST00000256646	NM_024408.3	2036	Cga/Tga	34/34	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.38	2		474	509	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120508081	120508081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	62	301	0	ENST00000256646.2:c.1676C>T	p.Ala559Val	p.A559V	ENST00000256646	NM_024408.3	559	gCc/gTc	10/34	1	2	FACETS	0.88	0.763	1	0.88	0.763	1	CLONAL	1	TRUE	1	0.38	2		301	371	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729614	162729614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773580613	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	31	457	0	ENST00000367921.3:c.700G>A	p.Asp234Asn	p.D234N	ENST00000367921	NM_006182.2	234	Gat/Aat	8/18	1	2	FACETS	0.338	0.273	0.412	0.338	0.273	0.412	SUBCLONAL	1	TRUE	1	0.38	2		457	483	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175916376	175916376	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	14	296	0	ENST00000367669.3:c.2134-1G>A		p.X712_splice	ENST00000367669	NM_022457.5	712			1	2	FACETS	0.278	0.201	0.372	0.278	0.201	0.372	SUBCLONAL	1	TRUE	1	0.38	2		296	265	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176104161	176104161	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	22	378	0	ENST00000367669.3:c.953C>A	p.Pro318His	p.P318H	ENST00000367669	NM_022457.5	318	cCt/cAt	8/20	1	2	FACETS	0.349	0.27	0.44	0.349	0.27	0.44	SUBCLONAL	1	TRUE	1	0.38	2		378	332	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206646592	206646592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	47	790	0	ENST00000367120.3:c.22C>A	p.Leu8Met	p.L8M	ENST00000367120	NM_014002.3	8	Ctg/Atg	3/22	1	2	FACETS	0.383	0.322	0.45	0.383	0.322	0.45	SUBCLONAL	1	TRUE	1	0.38	2		790	646	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652302	206652302	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	125	634	0	ENST00000367120.3:c.1009G>T	p.Glu337Ter	p.E337*	ENST00000367120	NM_014002.3	337	Gag/Tag	10/22	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.38	2		634	603	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612776	228612776	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	142	663	0	ENST00000366696.1:c.251G>A	p.Arg84His	p.R84H	ENST00000366696	NM_003493.2	84	cGc/cAc	1/1	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.38	2		663	539	SUCCESS
FH	2271	MSKCC	GRCh37	1	241669413	241669413	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	131	434	4	ENST00000366560.3:c.794C>T	p.Ala265Val	p.A265V	ENST00000366560	NM_000143.3	265	gCc/gTc	6/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.38	2		438	530	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097820	8097820	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	30	541	0	ENST00000346208.3:c.202G>A	p.Val68Ile	p.V68I	ENST00000346208		68	Gtc/Atc	2/6	1	2	FACETS	0.367	0.295	0.449	0.367	0.295	0.449	SUBCLONAL	1	TRUE	1	0.38	2		541	430	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106003	8106003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	121	398	0	ENST00000346208.3:c.823C>T	p.Arg275Trp	p.R275W	ENST00000346208		275	Cgg/Tgg	4/6	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.38	2		398	430	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63661933	63661933	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1313253636	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	100	361	0	ENST00000279873.7:c.37T>C	p.Cys13Arg	p.C13R	ENST00000279873	NM_032199.2	13	Tgt/Cgt	2/10	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.38	2		361	494	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852217	63852217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	39	511	1	ENST00000279873.7:c.2995C>T	p.Arg999Trp	p.R999W	ENST00000279873	NM_032199.2	999	Cgg/Tgg	10/10	1	2	FACETS	0.395	0.327	0.471	0.395	0.327	0.471	SUBCLONAL	1	TRUE	1	0.38	2		512	520	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332152	70332153	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1196853334	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	36	222	0	ENST00000373644.4:c.65dup	p.Lys23GlufsTer37	p.K23Efs*37	ENST00000373644	NM_030625.2	19	-/A	2/12	1	2	FACETS	0.842	0.698	1	0.842	0.698	1	CLONAL	1	TRUE	1	0.38	2		222	225	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649890	88649890	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	38	402	0	ENST00000372037.3:c.139G>A	p.Gly47Arg	p.G47R	ENST00000372037	NM_004329.2	47	Gga/Aga	4/13	1	2	FACETS	0.506	0.419	0.604	0.506	0.419	0.604	SUBCLONAL	1	TRUE	1	0.38	2		402	395	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88672119	88672119	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	102	517	1	ENST00000372037.3:c.653G>T	p.Ser218Ile	p.S218I	ENST00000372037	NM_004329.2	218	aGt/aTt	8/13	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.38	2		518	465	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712007	89712007	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs765433422	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	15	319	0	ENST00000371953.3:c.625G>T	p.Gly209Ter	p.G209*	ENST00000371953	NM_000314.4	209	Gga/Tga	6/9	1	2	FACETS	0.297	0.217	0.393	0.297	0.217	0.393	SUBCLONAL	1	TRUE	1	0.38	2		319	266	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725076	89725076	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	28	166	0	ENST00000371953.3:c.1059G>T	p.Glu353Asp	p.E353D	ENST00000371953	NM_000314.4	353	gaG/gaT	9/9	1	2	FACETS	0.915	0.74	1	0.915	0.74	1	CLONAL	1	TRUE	1	0.38	2		166	161	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104356980	104356981	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1477199832	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	34	527	0	ENST00000369902.3:c.846dup	p.Glu283ArgfsTer3	p.E283Rfs*3	ENST00000369902	NM_016169.3	280	-/C	7/12	1	2	FACETS	0.345	0.281	0.417	0.345	0.281	0.417	SUBCLONAL	1	TRUE	1	0.38	2		527	519	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741382	17741382	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	74	837	1	ENST00000250003.3:c.53G>A	p.Gly18Asp	p.G18D	ENST00000250003	NM_002478.4	18	gGc/gAc	1/3	1	2	FACETS	0.542	0.474	0.616	0.542	0.474	0.616	SUBCLONAL	1	TRUE	1	0.38	2		838	718	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137271	64137271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	196	628	0	ENST00000334205.4:c.1703C>T	p.Thr568Met	p.T568M	ENST00000334205	NM_003942.2	568	aCg/aTg	14/17	1	2	FACETS	0.837	0.779	0.897	1	0.992	1	CLONAL	2	TRUE	1	0.38	2		628	616	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631162	69631162	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	89	603	0	ENST00000334134.2:c.250G>T	p.Gly84Cys	p.G84C	ENST00000334134	NM_005247.2	84	Ggc/Tgc	2/3	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.38	2		603	467	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939791	71939791	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	120	726	0	ENST00000298229.2:c.418C>T	p.Pro140Ser	p.P140S	ENST00000298229	NM_001567.3	140	Ccg/Tcg	4/28	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.38	2		726	605	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948250	71948250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770973654	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	49	949	1	ENST00000298229.2:c.2962G>A	p.Val988Ile	p.V988I	ENST00000298229	NM_001567.3	988	Gtc/Atc	26/28	1	2	FACETS	0.338	0.285	0.396	0.338	0.285	0.396	SUBCLONAL	1	TRUE	1	0.38	2		950	764	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948745	71948745	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	37	709	2	ENST00000298229.2:c.3457C>T	p.Gln1153Ter	p.Q1153*	ENST00000298229	NM_001567.3	1153	Cag/Tag	26/28	1	2	FACETS	0.412	0.339	0.493	0.412	0.339	0.493	SUBCLONAL	1	TRUE	1	0.38	2		711	473	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94910884	94910884	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	27	412	0	ENST00000536441.1:c.1246A>G	p.Arg416Gly	p.R416G	ENST00000536441	NM_144665.3	416	Agg/Ggg	8/10	1	2	FACETS	0.363	0.288	0.448	0.363	0.288	0.448	SUBCLONAL	1	TRUE	1	0.38	2		412	392	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920723	100920723	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	149	523	0	ENST00000325455.5:c.2425G>T	p.Val809Phe	p.V809F	ENST00000325455	NM_001202474.3	809	Gtc/Ttc	6/8	1	2	FACETS	0.906	0.835	0.978	1	0.991	1	CLONAL	2	TRUE	1	0.38	2		523	433	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102033189	102033189	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	43	466	0	ENST00000282441.5:c.575A>G	p.His192Arg	p.H192R	ENST00000282441	NM_001130145.2	192	cAc/cGc	3/9	1	2	FACETS	0.39	0.326	0.462	0.39	0.326	0.462	SUBCLONAL	1	TRUE	1	0.38	2		466	580	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151894	108151894	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1555091451	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	101	293	0	ENST00000278616.4:c.3575A>G	p.Lys1192Arg	p.K1192R	ENST00000278616	NM_000051.3	1192	aAg/aGg	24/63	1	2	FACETS	0.823	0.744	0.905	1	0.986	1	CLONAL	2	TRUE	1	0.38	2		293	323	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343871	118343871	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs782290578	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	44	503	0	ENST00000534358.1:c.1997G>T	p.Gly666Val	p.G666V	ENST00000534358	NM_005933.3	666	gGt/gTt	3/36	1	2	FACETS	0.419	0.351	0.494	0.419	0.351	0.494	SUBCLONAL	1	TRUE	1	0.38	2		503	553	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348835	118348835	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	66	309	0	ENST00000534358.1:c.3488T>C	p.Val1163Ala	p.V1163A	ENST00000534358	NM_005933.3	1163	gTg/gCg	5/36	1	2	FACETS	0.97	0.847	1	0.97	0.847	1	CLONAL	1	TRUE	1	0.38	2		309	358	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366606	118366606	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	82	324	1	ENST00000534358.1:c.5555T>C	p.Leu1852Ser	p.L1852S	ENST00000534358	NM_005933.3	1852	tTg/tCg	19/36	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.38	2		325	338	SUCCESS
CBL	867	MSKCC	GRCh37	11	119146721	119146721	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	30	536	0	ENST00000264033.4:c.884T>C	p.Leu295Pro	p.L295P	ENST00000264033	NM_005188.3	295	cTg/cCg	6/16	1	2	FACETS	0.292	0.234	0.357	0.292	0.234	0.357	SUBCLONAL	1	TRUE	1	0.38	2		536	541	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503194	125503194	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	58	405	0	ENST00000428830.2:c.561A>C	p.Glu187Asp	p.E187D	ENST00000428830	NM_001114121.2	187	gaA/gaC	6/14	1	2	FACETS	0.746	0.643	0.858	0.746	0.643	0.858	SUBCLONAL	1	TRUE	1	0.38	2		405	409	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	401925	401925	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	22	349	0	ENST00000399788.2:c.4866G>T	p.Lys1622Asn	p.K1622N	ENST00000399788	NM_001042603.1	1622	aaG/aaT	27/28	1	2	FACETS	0.329	0.254	0.415	0.329	0.254	0.415	SUBCLONAL	1	TRUE	1	0.38	2		349	352	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402086	402086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1285618565	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	107	599	0	ENST00000399788.2:c.4705G>A	p.Ala1569Thr	p.A1569T	ENST00000399788	NM_001042603.1	1569	Gct/Act	27/28	1	2	FACETS	0.939	0.844	1	0.939	0.844	1	CLONAL	1	TRUE	1	0.38	2		599	600	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406317	406318	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	37	497	0	ENST00000399788.2:c.4123dup	p.Cys1375LeufsTer2	p.C1375Lfs*2	ENST00000399788	NM_001042603.1	1375	tgt/tTgt	25/28	1	2	FACETS	0.402	0.331	0.481	0.402	0.331	0.481	SUBCLONAL	1	TRUE	1	0.38	2		497	485	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432317	432317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1247040869	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	33	406	2	ENST00000399788.2:c.2206G>A	p.Ala736Thr	p.A736T	ENST00000399788	NM_001042603.1	736	Gca/Aca	16/28	1	2	FACETS	0.396	0.322	0.479	0.396	0.322	0.479	SUBCLONAL	1	TRUE	1	0.38	2		408	439	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022447	12022447	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	50	806	2	ENST00000396373.4:c.553C>T	p.Pro185Ser	p.P185S	ENST00000396373	NM_001987.4	185	Cct/Tct	5/8	0.165677961718858	4	FACETS	0.421	0.356	0.493	0.21	0.178	0.247	INDETERMINATE	1	TRUE	2	0.38	4		808	863	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435238	18435238	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	60	323	1	ENST00000266497.5:c.223G>T	p.Gly75Trp	p.G75W	ENST00000266497		75	Ggg/Tgg	1/31	0.3	1	FACETS	0.879	0.764	1	0.879	0.764	1	CLONAL	1	TRUE	0	0.38	1		324	291	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524149	18524149	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	87	449	0	ENST00000266497.5:c.1661G>T	p.Arg554Met	p.R554M	ENST00000266497		554	aGg/aTg	11/31	0.3	1	FACETS	0.885	0.788	0.988	0.885	0.788	0.988	CLONAL	1	TRUE	0	0.38	1		449	419	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534753	18534753	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	83	434	0	ENST00000266497.5:c.1811C>T	p.Pro604Leu	p.P604L	ENST00000266497		604	cCc/cTc	12/31	0.3	1	FACETS	0.774	0.686	0.868	0.774	0.686	0.868	SUBCLONAL	1	TRUE	0	0.38	1		434	457	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650580	18650580	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765083759	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	27	523	0	ENST00000266497.5:c.2791C>T	p.Leu931Phe	p.L931F	ENST00000266497		931	Ctt/Ttt	20/31	0.3	1	FACETS	0.237	0.188	0.293	0.237	0.188	0.293	SUBCLONAL	1	TRUE	0	0.38	1		523	486	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21630876	21630876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	43	522	0	ENST00000421138.2:c.728G>A	p.Arg243Gln	p.R243Q	ENST00000421138		243	cGg/cAg	8/16	0.3	1	FACETS	0.285	0.238	0.338	0.285	0.238	0.338	SUBCLONAL	1	TRUE	0	0.38	1		522	643	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25368455	25368455	+	intron_variant	Intron	SNP	G	G	A	rs200186819	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	102	418	0	ENST00000311936.3:c.451-5610C>T		p.*151*	ENST00000311936	NM_004985.3	164/189			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.38	2		418	453	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945049	31945049	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs754427138	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	153	711	0	ENST00000340398.3:c.52del	p.Arg18AlafsTer19	p.R18Afs*19	ENST00000340398	NM_001013699.2	18	Cgc/gc	1/1	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.38	2		711	768	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244773	46244773	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	59	598	0	ENST00000334344.6:c.2867C>T	p.Ala956Val	p.A956V	ENST00000334344	NM_152641.2	956	gCt/gTt	15/21	1	2	FACETS	0.615	0.53	0.708	0.615	0.53	0.708	SUBCLONAL	1	TRUE	1	0.38	2		598	505	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285701	46285701	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	75	403	0	ENST00000334344.6:c.5061G>T	p.Gln1687His	p.Q1687H	ENST00000334344	NM_152641.2	1687	caG/caT	17/21	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.38	2		403	382	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418727	49418727	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs398123731	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	122	361	0	ENST00000301067.7:c.15787G>A	p.Val5263Met	p.V5263M	ENST00000301067	NM_003482.3	5263	Gtg/Atg	49/54	1	2	FACETS	0.781	0.712	0.853	1	0.987	1	SUBCLONAL	2	TRUE	1	0.38	2		361	411	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420528	49420528	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	37	648	1	ENST00000301067.7:c.15221G>A	p.Gly5074Asp	p.G5074D	ENST00000301067	NM_003482.3	5074	gGc/gAc	48/54	1	2	FACETS	0.36	0.296	0.432	0.36	0.296	0.432	SUBCLONAL	1	TRUE	1	0.38	2		649	541	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420748	49420748	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	35	572	0	ENST00000301067.7:c.15001G>T	p.Gly5001Trp	p.G5001W	ENST00000301067	NM_003482.3	5001	Ggg/Tgg	48/54	1	2	FACETS	0.325	0.266	0.392	0.325	0.266	0.392	SUBCLONAL	1	TRUE	1	0.38	2		572	566	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433554	49433554	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	192	960	0	ENST00000301067.7:c.7999C>A	p.Pro2667Thr	p.P2667T	ENST00000301067	NM_003482.3	2667	Cca/Aca	31/54	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.38	2		960	851	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434849	49434849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs551403860	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	208	824	2	ENST00000301067.7:c.6704G>A	p.Arg2235Lys	p.R2235K	ENST00000301067	NM_003482.3	2235	aGa/aAa	31/54	1	2	FACETS	0.807	0.753	0.863	1	0.992	1	CLONAL	2	TRUE	1	0.38	2		826	678	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435032	49435032	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs557789686	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	23	462	0	ENST00000301067.7:c.6521A>G	p.Gln2174Arg	p.Q2174R	ENST00000301067	NM_003482.3	2174	cAg/cGg	31/54	1	2	FACETS	0.366	0.285	0.459	0.366	0.285	0.459	SUBCLONAL	1	TRUE	1	0.38	2		462	331	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493968	56493968	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	138	538	0	ENST00000267101.3:c.3140T>G	p.Leu1047Arg	p.L1047R	ENST00000267101	NM_001982.3	1047	cTt/cGt	26/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.38	2		538	615	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915695	112915695	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	34	482	0	ENST00000351677.2:c.968C>A	p.Pro323His	p.P323H	ENST00000351677	NM_002834.3	323	cCc/cAc	9/16	1	2	FACETS	0.384	0.313	0.464	0.384	0.313	0.464	SUBCLONAL	1	TRUE	1	0.38	2		482	466	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112017	115112017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1156821376	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	109	636	2	ENST00000257566.3:c.1723G>A	p.Ala575Thr	p.A575T	ENST00000257566	NM_016569.3	575	Gcg/Acg	7/8	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.38	2		638	549	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112326	115112326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1302202171	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	45	214	0	ENST00000257566.3:c.1414G>A	p.Ala472Thr	p.A472T	ENST00000257566	NM_016569.3	472	Gcg/Acg	7/8	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.38	2		214	169	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416574	121416574	+	start_lost	Translation_Start_Site	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	33	497	1	ENST00000257555.6:c.3G>T	p.Met1?	p.M1?	ENST00000257555		1	atG/atT	1/10	1	2	FACETS	0.484	0.394	0.584	0.484	0.394	0.584	SUBCLONAL	1	TRUE	1	0.38	2		498	359	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123868748	123868748	+	start_lost	Translation_Start_Site	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	30	602	0	ENST00000330479.4:c.3G>T	p.Met1?	p.M1?	ENST00000330479	NM_020382.3	1	atG/atT	1/9	1	2	FACETS	0.277	0.222	0.339	0.277	0.222	0.339	SUBCLONAL	1	TRUE	1	0.38	2		602	570	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210855	133210855	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	156	733	0	ENST00000320574.5:c.5921A>G	p.Asp1974Gly	p.D1974G	ENST00000320574	NM_006231.2	1974	gAt/gGt	43/49	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.38	2		733	639	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214612	133214612	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	88	423	0	ENST00000320574.5:c.5666A>G	p.Tyr1889Cys	p.Y1889C	ENST00000320574	NM_006231.2	1889	tAc/tGc	41/49	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.38	2		423	417	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215886	133215886	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	18	356	0	ENST00000320574.5:c.5379-2A>G		p.X1793_splice	ENST00000320574	NM_006231.2	1793			1	2	FACETS	0.464	0.351	0.598	0.464	0.351	0.598	SUBCLONAL	1	TRUE	1	0.38	2		356	204	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219579	133219579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542430685	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	69	422	2	ENST00000320574.5:c.4555C>T	p.Arg1519Cys	p.R1519C	ENST00000320574	NM_006231.2	1519	Cgc/Tgc	36/49	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.38	2		424	336	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226035	133226035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200398117	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	96	624	1	ENST00000320574.5:c.3862G>A	p.Ala1288Thr	p.A1288T	ENST00000320574	NM_006231.2	1288	Gcc/Acc	31/49	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.38	2		625	487	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133236097	133236097	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	18	338	0	ENST00000320574.5:c.3061-2A>G		p.X1021_splice	ENST00000320574	NM_006231.2	1021			1	2	FACETS	0.308	0.231	0.398	0.308	0.231	0.398	SUBCLONAL	1	TRUE	1	0.38	2		338	308	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133238237	133238237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754311081	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	89	426	0	ENST00000320574.5:c.2740G>A	p.Ala914Thr	p.A914T	ENST00000320574	NM_006231.2	914	Gct/Act	24/49	1	2	FACETS	0.946	0.842	1	0.946	0.842	1	CLONAL	1	TRUE	1	0.38	2		426	495	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240730	133240730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555226454	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	132	564	0	ENST00000320574.5:c.2566C>T	p.Pro856Ser	p.P856S	ENST00000320574	NM_006231.2	856	Ccc/Tcc	23/49	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.38	2		564	493	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555788	21555788	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	41	548	0	ENST00000382592.4:c.2483-1G>A		p.X828_splice	ENST00000382592	NM_014572.2	828			NA	2	FACETS	0.443	0.369	0.526			1	INDETERMINATE	1	TRUE	NA	0.38	2		548	487	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562215	21562215	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	188	906	1	ENST00000382592.4:c.1704G>T	p.Lys568Asn	p.K568N	ENST00000382592	NM_014572.2	568	aaG/aaT	4/8	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.38	2		907	858	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562789	21562789	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766346109	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	120	594	1	ENST00000382592.4:c.1130G>A	p.Arg377His	p.R377H	ENST00000382592	NM_014572.2	377	cGc/cAc	4/8	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.38	2		595	448	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26978093	26978093	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	114	565	4	ENST00000381527.3:c.1270C>T	p.Arg424Cys	p.R424C	ENST00000381527	NM_001260.1	424	Cgt/Tgt	13/13	0.220339615780378	0	FACETS	0.647	0.584	0.713			1	INDETERMINATE	1	TRUE	0	0.38	0		569	575	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589320	28589320	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	74	424	0	ENST00000241453.7:c.2727T>A	p.Asp909Glu	p.D909E	ENST00000241453	NM_004119.2	909	gaT/gaA	22/24	0.220339615780378	0	FACETS	0.598	0.526	0.674			1	INDETERMINATE	1	TRUE	0	0.38	0		424	404	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610143	28610143	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	123	453	0	ENST00000241453.7:c.1347G>T	p.Gln449His	p.Q449H	ENST00000241453	NM_004119.2	449	caG/caT	11/24	0.220339615780378	0	FACETS	0.84	0.764	0.918			1	INDETERMINATE	1	TRUE	0	0.38	0		453	478	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896975	28896975	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	135	536	0	ENST00000282397.4:c.2905T>C	p.Ser969Pro	p.S969P	ENST00000282397	NM_002019.4	969	Tcc/Ccc	21/30	0.220339615780378	0	FACETS	0.742	0.676	0.81			1	INDETERMINATE	1	TRUE	0	0.38	0		536	594	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964143	28964143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766569666	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	85	514	0	ENST00000282397.4:c.1759G>A	p.Val587Ile	p.V587I	ENST00000282397	NM_002019.4	587	Gtt/Att	13/30	0.220339615780378	0	FACETS	0.619	0.55	0.693			1	INDETERMINATE	1	TRUE	0	0.38	0		514	448	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914994	32914994	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs886040660	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	63	483	0	ENST00000380152.3:c.6502G>T	p.Gly2168Ter	p.G2168*	ENST00000380152		2168	Gga/Tga	11/27	1	2	FACETS	0.752	0.652	0.86	0.752	0.652	0.86	SUBCLONAL	1	TRUE	1	0.38	2		483	441	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133787	41133787	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	67	366	0	ENST00000379561.5:c.1841T>C	p.Met614Thr	p.M614T	ENST00000379561	NM_002015.3	614	aTg/aCg	2/3	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.38	2		366	334	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953751	48953751	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	91	268	0	ENST00000267163.4:c.1354T>A	p.Leu452Met	p.L452M	ENST00000267163	NM_000321.2	452	Ttg/Atg	14/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.38	2		268	329	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281278	49281278	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	35	798	0	ENST00000282018.3:c.325C>A	p.Leu109Met	p.L109M	ENST00000282018	NM_020377.2	109	Ctg/Atg	1/1	1	2	FACETS	0.279	0.228	0.337	0.279	0.228	0.337	SUBCLONAL	1	TRUE	1	0.38	2		798	660	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281701	49281701	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	44	853	0	ENST00000282018.3:c.748A>G	p.Ile250Val	p.I250V	ENST00000282018	NM_020377.2	250	Atc/Gtc	1/1	1	2	FACETS	0.281	0.234	0.332	0.281	0.234	0.332	SUBCLONAL	1	TRUE	1	0.38	2		853	825	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518082	103518082	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	36	253	0	ENST00000355739.4:c.2020T>C	p.Ser674Pro	p.S674P	ENST00000355739	NM_000123.3	674	Tcc/Ccc	9/15	1	2	FACETS	0.623	0.514	0.745	0.623	0.514	0.745	SUBCLONAL	1	TRUE	1	0.38	2		253	304	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435135	110435135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758318243	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	35	684	0	ENST00000375856.3:c.3266C>T	p.Ala1089Val	p.A1089V	ENST00000375856	NM_003749.2	1089	gCc/gTc	1/2	1	2	FACETS	0.331	0.271	0.399	0.331	0.271	0.399	SUBCLONAL	1	TRUE	1	0.38	2		684	556	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068315	30068315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141649026	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	86	328	0	ENST00000331968.5:c.2084G>A	p.Arg695Gln	p.R695Q	ENST00000331968	NM_002742.2	695	cGg/cAg	15/18	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.38	2		328	339	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068902	30068902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	110	742	1	ENST00000331968.5:c.2027G>A	p.Gly676Asp	p.G676D	ENST00000331968	NM_002742.2	676	gGc/gAc	14/18	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.38	2		743	553	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396469	30396469	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs756773077	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	76	394	0	ENST00000331968.5:c.250A>G	p.Ile84Val	p.I84V	ENST00000331968	NM_002742.2	84	Att/Gtt	1/18	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.38	2		394	385	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061474	38061474	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	101	495	0	ENST00000250448.2:c.515C>A	p.Pro172His	p.P172H	ENST00000250448	NM_004496.3	172	cCc/cAc	2/2	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.38	2		495	475	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610483	81610483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760244433	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	26	391	0	ENST00000298171.2:c.2081G>A	p.Ser694Asn	p.S694N	ENST00000298171	NM_000369.2	694	aGc/aAc	10/10	1	2	FACETS	0.359	0.284	0.445	0.359	0.284	0.445	SUBCLONAL	1	TRUE	1	0.38	2		391	381	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570006	95570006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	91	547	0	ENST00000393063.1:c.3727C>T	p.Leu1243Phe	p.L1243F	ENST00000393063	NM_030621.3	1243	Ctt/Ttt	22/28	1	2	FACETS	0.902	0.803	1	0.902	0.803	1	CLONAL	1	TRUE	1	0.38	2		547	531	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241276	105241276	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	35	648	0	ENST00000349310.3:c.632C>T	p.Thr211Ile	p.T211I	ENST00000349310	NM_001014432.1	211	aCa/aTa	8/15	1	2	FACETS	0.386	0.316	0.465	0.386	0.316	0.465	SUBCLONAL	1	TRUE	1	0.38	2		648	477	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991125	41991125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	37	570	0	ENST00000219905.7:c.2078C>T	p.Thr693Ile	p.T693I	ENST00000219905	NM_001164273.1	693	aCc/aTc	4/24	1	2	FACETS	0.337	0.277	0.405	0.337	0.277	0.405	SUBCLONAL	1	TRUE	1	0.38	2		570	577	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003228	42003228	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	112	633	1	ENST00000219905.7:c.2765C>A	p.Pro922His	p.P922H	ENST00000219905	NM_001164273.1	922	cCt/cAt	8/24	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.38	2		634	571	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019595	42019596	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	71	436	0	ENST00000219905.7:c.3650dup	p.Asn1217LysfsTer17	p.N1217Kfs*17	ENST00000219905	NM_001164273.1	1216	-/A	10/24	1	2	FACETS	0.951	0.834	1	0.951	0.834	1	CLONAL	1	TRUE	1	0.38	2		436	393	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032257	42032257	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	34	591	0	ENST00000219905.7:c.4441T>C	p.Ser1481Pro	p.S1481P	ENST00000219905	NM_001164273.1	1481	Tcc/Ccc	14/24	1	2	FACETS	0.309	0.251	0.373	0.309	0.251	0.373	SUBCLONAL	1	TRUE	1	0.38	2		591	580	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712701	43712701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1483739038	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	130	769	3	ENST00000382044.4:c.4483C>T	p.Arg1495Cys	p.R1495C	ENST00000382044	NM_001141980.1	1495	Cgt/Tgt	21/28	1	2	FACETS	0.958	0.87	1	0.958	0.87	1	CLONAL	1	TRUE	1	0.38	2		772	714	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749040	43749040	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	245	922	0	ENST00000382044.4:c.1766A>T	p.Asp589Val	p.D589V	ENST00000382044	NM_001141980.1	589	gAc/gTc	12/28	1	2	FACETS	0.782	0.733	0.833	1	0.993	1	SUBCLONAL	2	TRUE	1	0.38	2		922	824	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749099	43749100	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	152	858	0	ENST00000382044.4:c.1706dup	p.Asn569LysfsTer2	p.N569Kfs*2	ENST00000382044	NM_001141980.1	569	aat/aaAt	12/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.38	2		858	704	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66781568	66781568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	125	604	1	ENST00000307102.5:c.976C>T	p.Pro326Ser	p.P326S	ENST00000307102	NM_002755.3	326	Ccc/Tcc	9/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.38	2		605	549	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457274	67457274	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	103	641	2	ENST00000327367.4:c.248T>C	p.Leu83Pro	p.L83P	ENST00000327367	NM_005902.3	83	cTc/cCc	2/9	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.38	2		643	510	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690581	88690581	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	24	352	0	ENST00000360948.2:c.449T>C	p.Leu150Pro	p.L150P	ENST00000360948	NM_001012338.2	150	cTg/cCg	5/19	1	2	FACETS	0.281	0.22	0.352	0.281	0.22	0.352	SUBCLONAL	1	TRUE	1	0.38	2		352	449	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727513	88727513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374069724	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	32	457	0	ENST00000360948.2:c.266G>A	p.Arg89His	p.R89H	ENST00000360948	NM_001012338.2	89	cGc/cAc	3/19	1	2	FACETS	0.365	0.295	0.443	0.365	0.295	0.443	SUBCLONAL	1	TRUE	1	0.38	2		457	462	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628112	90628112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756680721	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	44	746	1	ENST00000330062.3:c.1207G>A	p.Val403Met	p.V403M	ENST00000330062	NM_002168.2	403	Gtg/Atg	10/11	1	2	FACETS	0.351	0.294	0.415	0.351	0.294	0.415	SUBCLONAL	1	TRUE	1	0.38	2		747	659	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303410	91303410	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs776225502	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	96	376	0	ENST00000355112.3:c.1121A>G	p.His374Arg	p.H374R	ENST00000355112	NM_000057.2	374	cAt/cGt	6/22	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.38	2		376	386	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304000	91304000	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	124	655	0	ENST00000355112.3:c.1397G>T	p.Gly466Val	p.G466V	ENST00000355112	NM_000057.2	466	gGg/gTg	7/22	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.38	2		655	549	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99192878	99192878	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	83	317	0	ENST00000268035.6:c.68T>C	p.Leu23Pro	p.L23P	ENST00000268035	NM_000875.3	23	cTc/cCc	1/21	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.38	2		317	403	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99451944	99451944	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	29	335	1	ENST00000268035.6:c.1278G>T	p.Gln426His	p.Q426H	ENST00000268035	NM_000875.3	426	caG/caT	6/21	1	2	FACETS	0.376	0.301	0.461	0.376	0.301	0.461	SUBCLONAL	1	TRUE	1	0.38	2		336	406	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465471	99465471	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	25	412	0	ENST00000268035.6:c.2296A>C	p.Thr766Pro	p.T766P	ENST00000268035	NM_000875.3	766	Acc/Ccc	11/21	1	2	FACETS	0.272	0.214	0.34	0.272	0.214	0.34	SUBCLONAL	1	TRUE	1	0.38	2		412	483	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467227	99467227	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372672370	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	16	288	0	ENST00000268035.6:c.2608G>A	p.Gly870Arg	p.G870R	ENST00000268035	NM_000875.3	870	Gga/Aga	12/21	1	2	FACETS	0.354	0.262	0.464	0.354	0.262	0.464	SUBCLONAL	1	TRUE	1	0.38	2		288	238	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347078	347078	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	49	758	0	ENST00000262320.3:c.1933A>G	p.Arg645Gly	p.R645G	ENST00000262320	NM_003502.3	645	Agg/Ggg	7/11	1	2	FACETS	0.373	0.315	0.437	0.373	0.315	0.437	SUBCLONAL	1	TRUE	1	0.38	2		758	691	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396466	396466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	41	872	0	ENST00000262320.3:c.560C>T	p.Thr187Ile	p.T187I	ENST00000262320	NM_003502.3	187	aCc/aTc	2/11	1	2	FACETS	0.29	0.241	0.346	0.29	0.241	0.346	SUBCLONAL	1	TRUE	1	0.38	2		872	743	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106687	2106687	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	156	737	0	ENST00000219476.3:c.691C>A	p.Leu231Met	p.L231M	ENST00000219476	NM_000548.3	231	Ctg/Atg	8/42	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.38	2		737	689	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108863	2108863	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	34	689	0	ENST00000219476.3:c.964T>C	p.Ser322Pro	p.S322P	ENST00000219476	NM_000548.3	322	Tca/Cca	10/42	1	2	FACETS	0.288	0.235	0.349	0.288	0.235	0.349	SUBCLONAL	1	TRUE	1	0.38	2		689	621	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136258	2136258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45437192	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	111	588	0	ENST00000219476.3:c.4727C>T	p.Thr1576Met	p.T1576M	ENST00000219476	NM_000548.3	1576	aCg/aTg	37/42	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.38	2		588	538	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138532	2138532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	44	643	1	ENST00000219476.3:c.5345C>T	p.Ala1782Val	p.A1782V	ENST00000219476	NM_000548.3	1782	gCc/gTc	42/42	1	2	FACETS	0.411	0.344	0.485	0.411	0.344	0.485	SUBCLONAL	1	TRUE	1	0.38	2		644	564	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213947	2213947	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	161	605	0	ENST00000326181.6:c.26A>G	p.Tyr9Cys	p.Y9C	ENST00000326181	NM_032271.2	9	tAc/tGc	2/21	1	2	FACETS	0.796	0.735	0.859	1	0.99	1	SUBCLONAL	2	TRUE	1	0.38	2		605	532	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223834	2223834	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	136	880	0	ENST00000326181.6:c.1132G>T	p.Gly378Cys	p.G378C	ENST00000326181	NM_032271.2	378	Ggc/Tgc	12/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.38	2		880	573	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642800	3642800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747832147	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	136	653	0	ENST00000294008.3:c.2227G>A	p.Val743Met	p.V743M	ENST00000294008	NM_032444.2	743	Gtg/Atg	11/15	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.38	2		653	665	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807966	3807966	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs533778365	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	37	635	0	ENST00000262367.5:c.3453G>T	p.Trp1151Cys	p.W1151C	ENST00000262367	NM_004380.2	1151	tgG/tgT	18/31	1	2	FACETS	0.3	0.246	0.36	0.3	0.246	0.36	SUBCLONAL	1	TRUE	1	0.38	2		635	650	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828051	3828051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1289765861	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	46	597	0	ENST00000262367.5:c.2074C>T	p.Pro692Ser	p.P692S	ENST00000262367	NM_004380.2	692	Ccc/Tcc	10/31	1	2	FACETS	0.342	0.287	0.403	0.342	0.287	0.403	SUBCLONAL	1	TRUE	1	0.38	2		597	707	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831226	3831226	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398406959	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	168	450	0	ENST00000262367.5:c.1655C>T	p.Pro552Leu	p.P552L	ENST00000262367	NM_004380.2	552	cCg/cTg	7/31	1	2	FACETS	0.862	0.798	0.927	1	0.992	1	CLONAL	2	TRUE	1	0.38	2		450	513	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858417	9858417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777687136	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	82	509	0	ENST00000330684.3:c.2984C>T	p.Thr995Met	p.T995M	ENST00000330684	NM_001134407.1	995	aCg/aTg	13/13	1	2	FACETS	0.895	0.792	1	0.895	0.792	1	CLONAL	1	TRUE	1	0.38	2		509	482	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862922	9862922	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	95	568	0	ENST00000330684.3:c.2381T>C	p.Leu794Pro	p.L794P	ENST00000330684	NM_001134407.1	794	cTg/cCg	12/13	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.38	2		568	478	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892161	9892161	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	25	473	0	ENST00000330684.3:c.2329C>A	p.Leu777Met	p.L777M	ENST00000330684	NM_001134407.1	777	Ctg/Atg	11/13	1	2	FACETS	0.296	0.233	0.37	0.296	0.233	0.37	SUBCLONAL	1	TRUE	1	0.38	2		473	444	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934854	9934854	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	119	608	0	ENST00000330684.3:c.1436T>C	p.Leu479Pro	p.L479P	ENST00000330684	NM_001134407.1	479	cTg/cCg	6/13	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.38	2		608	562	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943787	9943787	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	86	446	1	ENST00000330684.3:c.1154T>C	p.Leu385Pro	p.L385P	ENST00000330684	NM_001134407.1	385	cTg/cCg	5/13	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.38	2		447	378	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031919	10031919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs901717931	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	132	607	1	ENST00000330684.3:c.904G>A	p.Ala302Thr	p.A302T	ENST00000330684	NM_001134407.1	302	Gct/Act	3/13	1	2	FACETS	0.757	0.692	0.824	1	0.987	1	SUBCLONAL	2	TRUE	1	0.38	2		608	459	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128989	30128989	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1178214091	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	86	477	0	ENST00000263025.4:c.775+2T>C		p.X259_splice	ENST00000263025	NM_002746.2	259			1	2	FACETS	0.978	0.868	1	0.978	0.868	1	CLONAL	1	TRUE	1	0.38	2		477	463	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56867184	56867184	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	34	624	0	ENST00000308159.5:c.1403T>C	p.Leu468Pro	p.L468P	ENST00000308159	NM_014669.4	468	cTg/cCg	13/22	1	2	FACETS	0.284	0.232	0.344	0.284	0.232	0.344	SUBCLONAL	1	TRUE	1	0.38	2		624	629	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663337	67663337	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	80	410	0	ENST00000264010.4:c.1738C>A	p.Pro580Thr	p.P580T	ENST00000264010	NM_006565.3	580	Cca/Aca	10/12	1	2	FACETS	0.988	0.874	1	0.988	0.874	1	CLONAL	1	TRUE	1	0.38	2		410	426	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991503	72991503	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	153	778	1	ENST00000268489.5:c.2542C>A	p.Leu848Met	p.L848M	ENST00000268489	NM_006885.3	848	Ctg/Atg	2/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.38	2		779	737	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942115	81942115	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	33	549	0	ENST00000359376.3:c.1652G>A	p.Cys551Tyr	p.C551Y	ENST00000359376	NM_002661.3	551	tGc/tAc	17/33	1	2	FACETS	0.364	0.296	0.441	0.364	0.296	0.441	SUBCLONAL	1	TRUE	1	0.38	2		549	477	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347627	89347627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559618415	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	84	578	0	ENST00000301030.4:c.5323G>A	p.Ala1775Thr	p.A1775T	ENST00000301030	NM_001256183.1	1775	Gcc/Acc	9/13	1	2	FACETS	0.933	0.827	1	0.933	0.827	1	CLONAL	1	TRUE	1	0.38	2		578	474	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858914	89858914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150290184	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	139	547	1	ENST00000389301.3:c.1048C>T	p.Arg350Trp	p.R350W	ENST00000389301	NM_000135.2	350	Cgg/Tgg	12/43	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.38	2		548	592	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958286	11958286	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	64	379	0	ENST00000353533.5:c.196A>C	p.Thr66Pro	p.T66P	ENST00000353533	NM_003010.3	66	Aca/Cca	2/11	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.38	2		379	295	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028685	12028686	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	32	389	0	ENST00000353533.5:c.890dup	p.Leu297PhefsTer3	p.L297Ffs*3	ENST00000353533	NM_003010.3	296	-/T	8/11	1	2	FACETS	0.347	0.281	0.421	0.347	0.281	0.421	SUBCLONAL	1	TRUE	1	0.38	2		389	486	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17125975	17125975	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	83	415	0	ENST00000285071.4:c.619G>A	p.Val207Met	p.V207M	ENST00000285071	NM_144997.5	207	Gtg/Atg	7/14	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.38	2		415	417	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652959	29652959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876659922	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	95	497	0	ENST00000356175.3:c.4894C>T	p.Arg1632Cys	p.R1632C	ENST00000356175	NM_000267.3	1632	Cgc/Tgc	36/57	1	2	FACETS	0.882	0.787	0.982	0.882	0.787	0.982	CLONAL	1	TRUE	1	0.38	2		497	567	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653115	29653115	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	28	364	0	ENST00000356175.3:c.5050A>G	p.Arg1684Gly	p.R1684G	ENST00000356175	NM_000267.3	1684	Agg/Ggg	36/57	1	2	FACETS	0.332	0.265	0.409	0.332	0.265	0.409	SUBCLONAL	1	TRUE	1	0.38	2		364	444	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667663	29667663	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	25	433	0	ENST00000356175.3:c.6999G>T	p.Lys2333Asn	p.K2333N	ENST00000356175	NM_000267.3	2333	aaG/aaT	46/57	1	2	FACETS	0.317	0.249	0.395	0.317	0.249	0.395	SUBCLONAL	1	TRUE	1	0.38	2		433	415	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627811	37627811	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1453484766	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	133	677	0	ENST00000447079.4:c.1726G>A	p.Val576Ile	p.V576I	ENST00000447079	NM_015083.1	576	Gtt/Att	2/14	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.38	2		677	688	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682211	37682211	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	113	540	0	ENST00000447079.4:c.3402G>T	p.Met1134Ile	p.M1134I	ENST00000447079	NM_015083.1	1134	atG/atT	13/14	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.38	2		540	550	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682349	37682349	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	93	580	0	ENST00000447079.4:c.3540G>T	p.Lys1180Asn	p.K1180N	ENST00000447079	NM_015083.1	1180	aaG/aaT	13/14	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.38	2		580	481	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370244	40370244	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	111	699	1	ENST00000293328.3:c.1094A>C	p.Asn365Thr	p.N365T	ENST00000293328	NM_012448.3	365	aAc/aCc	9/19	1	2	FACETS	0.895	0.806	0.989	0.895	0.806	0.989	CLONAL	1	TRUE	1	0.38	2		700	653	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375562	40375562	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	89	486	0	ENST00000293328.3:c.388G>A	p.Ala130Thr	p.A130T	ENST00000293328	NM_012448.3	130	Gct/Act	5/19	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.38	2		486	463	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805918	46805918	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	83	318	0	ENST00000290295.7:c.38A>G	p.Lys13Arg	p.K13R	ENST00000290295	NM_006361.5	13	aAg/aGg	1/2	1	2	FACETS	0.95	0.853	1	1	0.985	1	CLONAL	2	TRUE	1	0.38	2		318	230	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696602	47696602	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	79	460	0	ENST00000347630.2:c.346G>T	p.Ala116Ser	p.A116S	ENST00000347630	NM_001007230.1	116	Gct/Tct	5/11	1	2	FACETS	0.89	0.786	1	0.89	0.786	1	CLONAL	1	TRUE	1	0.38	2		460	467	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56432348	56432348	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	86	360	0	ENST00000407977.2:c.2309-1G>T		p.X770_splice	ENST00000407977		770			1	2	FACETS	0.959	0.852	1	0.959	0.852	1	CLONAL	1	TRUE	1	0.38	2		360	472	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677917	58677917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	63	339	0	ENST00000305921.3:c.142C>T	p.Pro48Ser	p.P48S	ENST00000305921	NM_003620.3	48	Ccg/Tcg	1/6	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.38	2		339	287	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740542	58740542	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	46	550	0	ENST00000305921.3:c.1447A>G	p.Thr483Ala	p.T483A	ENST00000305921	NM_003620.3	483	Act/Gct	6/6	1	2	FACETS	0.497	0.419	0.584	0.497	0.419	0.584	SUBCLONAL	1	TRUE	1	0.38	2		550	487	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740809	58740809	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs765769406	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	193	437	0	ENST00000305921.3:c.1714C>T	p.Arg572Ter	p.R572*	ENST00000305921	NM_003620.3	572	Cga/Tga	6/6	1	2	FACETS	0.876	0.815	0.937	1	0.993	1	CLONAL	2	TRUE	1	0.38	2		437	580	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761130	59761130	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	94	634	0	ENST00000259008.2:c.3277C>A	p.Leu1093Ile	p.L1093I	ENST00000259008	NM_032043.2	1093	Ctc/Atc	20/20	1	2	FACETS	0.843	0.751	0.94	0.843	0.751	0.94	CLONAL	1	TRUE	1	0.38	2		634	587	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853773	59853773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	56	360	0	ENST00000259008.2:c.2086C>T	p.Pro696Ser	p.P696S	ENST00000259008	NM_032043.2	696	Cca/Tca	14/20	1	2	FACETS	0.939	0.809	1	0.939	0.809	1	CLONAL	1	TRUE	1	0.38	2		360	314	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885827	59885827	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs587781655	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	37	370	0	ENST00000259008.2:c.918+1G>A		p.X306_splice	ENST00000259008	NM_032043.2	306			1	2	FACETS	0.474	0.391	0.567	0.474	0.391	0.567	SUBCLONAL	1	TRUE	1	0.38	2		370	411	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66518934	66518934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	72	305	1	ENST00000358598.2:c.215G>A	p.Gly72Asp	p.G72D	ENST00000358598	NM_212471.2	72	gGc/gAc	3/11	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.38	2		306	377	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117918	70117918	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	88	369	0	ENST00000245479.2:c.386A>G	p.His129Arg	p.H129R	ENST00000245479	NM_000346.3	129	cAc/cGc	1/3	1	2	FACETS	0.759	0.68	0.842	1	0.981	1	SUBCLONAL	2	TRUE	1	0.38	2		369	305	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78829307	78829307	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	143	622	0	ENST00000306801.3:c.1358T>A	p.Leu453His	p.L453H	ENST00000306801	NM_020761.2	453	cTt/cAt	12/34	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.38	2		622	658	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857650	78857650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184854653	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	107	663	1	ENST00000306801.3:c.1720C>T	p.Arg574Cys	p.R574C	ENST00000306801	NM_020761.2	574	Cgc/Tgc	16/34	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.38	2		664	533	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857725	78857725	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	99	635	0	ENST00000306801.3:c.1795A>G	p.Ser599Gly	p.S599G	ENST00000306801	NM_020761.2	599	Agc/Ggc	16/34	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.38	2		635	521	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604661	48604661	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	23	350	0	ENST00000342988.3:c.1483C>A	p.Leu495Ile	p.L495I	ENST00000342988	NM_005359.5	495	Ctt/Att	12/12	1	2	FACETS	0.325	0.253	0.409	0.325	0.253	0.409	SUBCLONAL	1	TRUE	1	0.38	2		350	372	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60795959	60795959	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748122615	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	96	430	0	ENST00000333681.4:c.619C>T	p.Arg207Trp	p.R207W	ENST00000333681		207	Cgg/Tgg	3/3	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.38	2		430	458	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226569	1226569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368466538	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	46	565	0	ENST00000326873.7:c.1225C>T	p.Arg409Trp	p.R409W	ENST00000326873	NM_000455.4	409	Cgg/Tgg	9/10	1	2	FACETS	0.457	0.384	0.537	0.457	0.384	0.537	SUBCLONAL	1	TRUE	1	0.38	2		565	530	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622318	1622318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774052015	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	111	694	1	ENST00000344749.5:c.646G>A	p.Val216Met	p.V216M	ENST00000344749	NM_001136139.2	216	Gtg/Atg	9/19	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.38	2		695	516	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217048	2217048	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	115	651	1	ENST00000398665.3:c.2503C>A	p.Pro835Thr	p.P835T	ENST00000398665	NM_032482.2	835	Cct/Act	21/28	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.38	2		652	541	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226323	2226323	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	180	886	1	ENST00000398665.3:c.3803G>A	p.Ser1268Asn	p.S1268N	ENST00000398665	NM_032482.2	1268	aGc/aAc	27/28	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.38	2		887	722	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226704	2226704	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750419812	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	131	677	0	ENST00000398665.3:c.4184C>T	p.Pro1395Leu	p.P1395L	ENST00000398665	NM_032482.2	1395	cCg/cTg	27/28	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.38	2		677	552	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226883	2226883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	19	282	1	ENST00000398665.3:c.4363G>A	p.Ala1455Thr	p.A1455T	ENST00000398665	NM_032482.2	1455	Gcg/Acg	27/28	1	2	FACETS	0.341	0.259	0.438	0.341	0.259	0.438	SUBCLONAL	1	TRUE	1	0.38	2		283	293	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110554	4110554	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	125	610	0	ENST00000262948.5:c.403G>T	p.Gly135Trp	p.G135W	ENST00000262948	NM_030662.3	135	Ggg/Tgg	3/11	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.38	2		610	617	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210778	5210778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374377699	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	121	675	1	ENST00000357368.4:c.5273C>T	p.Ala1758Val	p.A1758V	ENST00000357368	NM_002850.3	1758	gCg/gTg	34/38	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.38	2		676	547	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212242	5212242	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	112	563	0	ENST00000357368.4:c.4789G>T	p.Gly1597Cys	p.G1597C	ENST00000357368	NM_002850.3	1597	Ggc/Tgc	32/38	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.38	2		563	403	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220117	5220117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1390942862	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	125	510	0	ENST00000357368.4:c.3598C>T	p.Arg1200Cys	p.R1200C	ENST00000357368	NM_002850.3	1200	Cgt/Tgt	22/38	1	2	FACETS	0.861	0.787	0.937	1	0.989	1	CLONAL	2	TRUE	1	0.38	2		510	382	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245891	5245891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1045893958	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	152	836	1	ENST00000357368.4:c.884G>A	p.Arg295Gln	p.R295Q	ENST00000357368	NM_002850.3	295	cGg/cAg	10/38	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.38	2		837	702	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7120676	7120676	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	132	709	0	ENST00000302850.5:c.3614C>A	p.Pro1205Gln	p.P1205Q	ENST00000302850	NM_000208.2	1205	cCg/cAg	20/22	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.38	2		709	623	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254557	10254557	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	118	628	0	ENST00000340748.4:c.2953C>A	p.Leu985Met	p.L985M	ENST00000340748		985	Ctg/Atg	28/40	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.38	2		628	589	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262088	10262088	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1381758934	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	46	657	1	ENST00000340748.4:c.2203G>A	p.Gly735Arg	p.G735R	ENST00000340748		735	Gga/Aga	23/40	1	2	FACETS	0.406	0.341	0.478	0.406	0.341	0.478	SUBCLONAL	1	TRUE	1	0.38	2		658	596	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599907	10599907	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	45	667	0	ENST00000171111.5:c.1669C>A	p.Leu557Met	p.L557M	ENST00000171111	NM_203500.1	557	Ctg/Atg	5/6	1	2	FACETS	0.335	0.28	0.395	0.335	0.28	0.395	SUBCLONAL	1	TRUE	1	0.38	2		667	708	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600479	10600479	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145311080	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	132	625	1	ENST00000171111.5:c.1376G>A	p.Arg459Gln	p.R459Q	ENST00000171111	NM_203500.1	459	cGa/cAa	4/6	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.38	2		626	621	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11022965	11022965	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	117	580	0	ENST00000327064.4:c.664G>A	p.Ala222Thr	p.A222T	ENST00000327064	NM_199141.1	222	Gct/Act	5/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.38	2		580	486	SUCCESS
CALR	811	MSKCC	GRCh37	19	13049552	13049552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	117	744	0	ENST00000316448.5:c.59C>T	p.Ala20Val	p.A20V	ENST00000316448	NM_004343.3	20	gCc/gTc	1/9	1	2	FACETS	0.906	0.818	0.998	0.906	0.818	0.998	CLONAL	1	TRUE	1	0.38	2		744	680	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051105	13051105	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	41	442	0	ENST00000316448.5:c.541A>G	p.Thr181Ala	p.T181A	ENST00000316448	NM_004343.3	181	Acc/Gcc	5/9	1	2	FACETS	0.399	0.332	0.474	0.399	0.332	0.474	SUBCLONAL	1	TRUE	1	0.38	2		442	541	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289723	15289723	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	153	742	3	ENST00000263388.2:c.3748T>C	p.Cys1250Arg	p.C1250R	ENST00000263388	NM_000435.2	1250	Tgc/Cgc	23/33	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.38	2		745	601	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300082	15300082	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs112788166	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	74	578	0	ENST00000263388.2:c.1192+2T>C		p.X398_splice	ENST00000263388	NM_000435.2	398			1	2	FACETS	0.962	0.846	1	0.962	0.846	1	CLONAL	1	TRUE	1	0.38	2		578	405	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303224	15303224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753596637	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	160	814	1	ENST00000263388.2:c.304G>A	p.Ala102Thr	p.A102T	ENST00000263388	NM_000435.2	102	Gcc/Acc	3/33	1	2	FACETS	0.764	0.705	0.825	1	0.989	1	SUBCLONAL	2	TRUE	1	0.38	2		815	551	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965815	18965815	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	97	573	0	ENST00000262803.5:c.1393G>T	p.Ala465Ser	p.A465S	ENST00000262803	NM_002911.3	465	Gcg/Tcg	10/24	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.38	2		573	444	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974297	18974297	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	96	549	0	ENST00000262803.5:c.2651T>C	p.Leu884Pro	p.L884P	ENST00000262803	NM_002911.3	884	cTc/cCc	19/24	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.38	2		549	468	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258587	19258587	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	56	794	1	ENST00000162023.5:c.313G>T	p.Gly105Trp	p.G105W	ENST00000162023		105	Ggg/Tgg	8/13	1	2	FACETS	0.484	0.414	0.56	0.484	0.414	0.56	SUBCLONAL	1	TRUE	1	0.38	2		795	609	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792794	33792794	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs957167825	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	44	158	0	ENST00000498907.2:c.527C>T	p.Ala176Val	p.A176V	ENST00000498907	NM_004364.3	176	gCc/gTc	1/1	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.38	2		158	171	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218066	36218066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	84	357	0	ENST00000222270.7:c.4013G>A	p.Cys1338Tyr	p.C1338Y	ENST00000222270	NM_014727.1	1338	tGc/tAc	15/37	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.38	2		357	307	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219002	36219002	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	126	612	0	ENST00000222270.7:c.4501C>A	p.Leu1501Ile	p.L1501I	ENST00000222270	NM_014727.1	1501	Cta/Ata	19/37	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.38	2		612	628	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222925	36222925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746346674	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	172	929	2	ENST00000222270.7:c.5554G>A	p.Ala1852Thr	p.A1852T	ENST00000222270	NM_014727.1	1852	Gcc/Acc	27/37	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.38	2		931	779	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223562	36223562	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	108	902	0	ENST00000222270.7:c.6112C>A	p.Pro2038Thr	p.P2038T	ENST00000222270	NM_014727.1	2038	Cct/Act	28/37	1	2	FACETS	0.852	0.766	0.944	0.852	0.766	0.944	CLONAL	1	TRUE	1	0.38	2		902	667	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754720	41754720	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs913467939	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	178	557	0	ENST00000301178.4:c.1706T>C	p.Met569Thr	p.M569T	ENST00000301178	NM_021913.4	569	aTg/aCg	14/20	1	2	FACETS	0.836	0.776	0.899	1	0.992	1	CLONAL	2	TRUE	1	0.38	2		557	560	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791393	42791393	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	115	677	1	ENST00000575354.2:c.452+1G>A		p.X151_splice	ENST00000575354	NM_015125.3	151			1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.38	2		678	600	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795620	42795620	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	50	776	0	ENST00000575354.2:c.2698+2T>C		p.X900_splice	ENST00000575354	NM_015125.3	900			1	2	FACETS	0.42	0.356	0.491	0.42	0.356	0.491	SUBCLONAL	1	TRUE	1	0.38	2		776	626	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797278	42797278	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs968289754	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	175	672	0	ENST00000575354.2:c.3640C>T	p.Arg1214Ter	p.R1214*	ENST00000575354	NM_015125.3	1214	Cga/Tga	15/20	1	2	FACETS	0.881	0.817	0.946	1	0.992	1	CLONAL	2	TRUE	1	0.38	2		672	523	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917108	50917108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs199783227	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	136	838	0	ENST00000440232.2:c.2360C>A	p.Pro787Gln	p.P787Q	ENST00000440232	NM_002691.3	787	cCg/cAg	19/27	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.38	2		838	708	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918759	50918759	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555793039	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	201	730	0	ENST00000440232.2:c.2629G>A	p.Asp877Asn	p.D877N	ENST00000440232	NM_002691.3	877	Gat/Aat	21/27	1	2	FACETS	0.92	0.858	0.983	1	0.993	1	CLONAL	2	TRUE	1	0.38	2		730	575	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919734	50919734	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878854545	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	145	709	0	ENST00000440232.2:c.2902C>T	p.Arg968Cys	p.R968C	ENST00000440232	NM_002691.3	968	Cgc/Tgc	23/27	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.38	2		709	572	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52709291	52709291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	76	477	0	ENST00000322088.6:c.245G>A	p.Gly82Asp	p.G82D	ENST00000322088	NM_014225.5	82	gGc/gAc	3/15	1	2	FACETS	0.998	0.88	1	0.998	0.88	1	CLONAL	1	TRUE	1	0.38	2		477	401	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464483	25464483	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	106	551	0	ENST00000264709.3:c.2030A>G	p.His677Arg	p.H677R	ENST00000264709	NM_175629.2	677	cAc/cGc	17/23	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.38	2		551	492	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469540	25469540	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764880874	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	113	700	0	ENST00000264709.3:c.1228G>A	p.Ala410Thr	p.A410T	ENST00000264709	NM_175629.2	410	Gcc/Acc	10/23	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.38	2		700	591	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523052	25523052	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	43	677	0	ENST00000264709.3:c.133G>A	p.Ala45Thr	p.A45T	ENST00000264709	NM_175629.2	45	Gca/Aca	3/23	1	2	FACETS	0.373	0.311	0.441	0.373	0.311	0.441	SUBCLONAL	1	TRUE	1	0.38	2		677	607	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982389	25982389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	70	375	0	ENST00000435504.4:c.901C>T	p.Gln301Ter	p.Q301*	ENST00000435504		301	Caa/Taa	9/13	1	2	FACETS	0.907	0.795	1	0.907	0.795	1	CLONAL	1	TRUE	1	0.38	2		375	406	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029183	26029183	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	27	404	0	ENST00000435504.4:c.167T>C	p.Leu56Pro	p.L56P	ENST00000435504		56	cTg/cCg	4/13	1	2	FACETS	0.337	0.267	0.416	0.337	0.267	0.416	SUBCLONAL	1	TRUE	1	0.38	2		404	422	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416406	29416406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	224	803	0	ENST00000389048.3:c.4547C>T	p.Thr1516Ile	p.T1516I	ENST00000389048	NM_004304.4	1516	aCc/aTc	29/29	1	2	FACETS	0.842	0.788	0.898	1	0.993	1	CLONAL	2	TRUE	1	0.38	2		803	700	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443655	29443655	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	27	621	3	ENST00000389048.3:c.3562C>T	p.Gln1188Ter	p.Q1188*	ENST00000389048	NM_004304.4	1188	Caa/Taa	23/29	1	2	FACETS	0.269	0.213	0.333	0.269	0.213	0.333	SUBCLONAL	1	TRUE	1	0.38	2		624	528	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143421	30143421	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	26	452	0	ENST00000389048.3:c.105del	p.Pro36ArgfsTer45	p.P36Rfs*45	ENST00000389048	NM_004304.4	35	ggG/gg	1/29	0.3	0	FACETS	0.238	0.188	0.295			1	SUBCLONAL	1	TRUE	0	0.38	0		452	356	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607420	46607420	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137853036	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	119	735	2	ENST00000263734.3:c.1609G>A	p.Gly537Arg	p.G537R	ENST00000263734	NM_001430.4	537	Ggg/Agg	12/16	0.3	0	FACETS	0.828	0.752	0.907			1	CLONAL	1	TRUE	0	0.38	0		737	469	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61709561	61709561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	34	402	0	ENST00000401558.2:c.2926G>A	p.Glu976Lys	p.E976K	ENST00000401558	NM_003400.3	976	Gaa/Aaa	23/25	1	2	FACETS	0.364	0.297	0.439	0.364	0.297	0.439	SUBCLONAL	1	TRUE	1	0.38	2		402	492	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96930969	96930969	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	174	554	0	ENST00000258439.3:c.151C>T	p.Pro51Ser	p.P51S	ENST00000258439	NM_001193304.2	51	Ccc/Tcc	2/4	1	2	FACETS	0.869	0.806	0.934	1	0.992	1	CLONAL	2	TRUE	1	0.38	2		554	527	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128016984	128016984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs563550613	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	110	555	2	ENST00000285398.2:c.2105C>T	p.Ala702Val	p.A702V	ENST00000285398	NM_000122.1	702	gCg/gTg	14/15	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.38	2		557	563	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128017001	128017001	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	101	542	0	ENST00000285398.2:c.2088G>T	p.Met696Ile	p.M696I	ENST00000285398	NM_000122.1	696	atG/atT	14/15	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.38	2		542	501	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622571	158622571	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	124	546	1	ENST00000263640.3:c.928C>A	p.Leu310Met	p.L310M	ENST00000263640	NM_001105.4	310	Ctg/Atg	8/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.38	2		547	549	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634710	158634710	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	104	381	0	ENST00000263640.3:c.476C>A	p.Pro159His	p.P159H	ENST00000263640	NM_001105.4	159	cCc/cAc	5/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.38	2		381	474	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098061	178098061	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	76	309	0	ENST00000397062.3:c.319C>A	p.His107Asn	p.H107N	ENST00000397062	NM_006164.4	107	Cac/Aac	3/5	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.38	2		309	381	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131282	202131282	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	25	453	1	ENST00000358485.4:c.250C>A	p.Leu84Met	p.L84M	ENST00000358485	NM_001080125.1	84	Ctg/Atg	2/9	1	2	FACETS	0.281	0.22	0.35	0.281	0.22	0.35	SUBCLONAL	1	TRUE	1	0.38	2		454	469	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285224	212285224	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	43	496	1	ENST00000342788.4:c.3077A>G	p.Gln1026Arg	p.Q1026R	ENST00000342788	NM_005235.2	1026	cAg/cGg	25/28	1	2	FACETS	0.512	0.429	0.604	0.512	0.429	0.604	SUBCLONAL	1	TRUE	1	0.38	2		497	442	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610551	215610551	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	84	468	0	ENST00000260947.4:c.1705C>T	p.Pro569Ser	p.P569S	ENST00000260947	NM_000465.2	569	Cct/Tct	8/11	1	2	FACETS	0.923	0.818	1	0.923	0.818	1	CLONAL	1	TRUE	1	0.38	2		468	479	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439518	220439518	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	117	647	0	ENST00000243786.2:c.371G>T	p.Arg124Leu	p.R124L	ENST00000243786	NM_002191.3	124	cGc/cTc	2/2	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.38	2		647	432	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368487	225368487	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	32	471	0	ENST00000264414.4:c.1259G>T	p.Arg420Met	p.R420M	ENST00000264414	NM_003590.4	420	aGg/aTg	9/16	1	2	FACETS	0.354	0.287	0.43	0.354	0.287	0.43	SUBCLONAL	1	TRUE	1	0.38	2		471	476	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662521	227662521	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	52	492	0	ENST00000305123.5:c.934T>C	p.Ser312Pro	p.S312P	ENST00000305123	NM_005544.2	312	Tcc/Ccc	1/2	1	2	FACETS	0.805	0.689	0.931	0.805	0.689	0.931	CLONAL	1	TRUE	1	0.38	2		492	340	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561289	9561289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985722631	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	85	496	1	ENST00000353224.5:c.493G>A	p.Ala165Thr	p.A165T	ENST00000353224	NM_177990.2	165	Gca/Aca	4/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.38	2		497	408	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979293	40979293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750102292	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	58	582	1	ENST00000373198.4:c.1840G>A	p.Ala614Thr	p.A614T	ENST00000373198	NM_133170.3	614	Gct/Act	11/32	0.3	0	FACETS	0.373	0.32	0.43			1	SUBCLONAL	1	TRUE	0	0.38	0		583	508	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306793	41306793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	21	290	0	ENST00000373198.4:c.866C>T	p.Pro289Leu	p.P289L	ENST00000373198	NM_133170.3	289	cCc/cTc	7/32	0.3	0	FACETS	0.275	0.212	0.348			1	SUBCLONAL	1	TRUE	0	0.38	0		290	249	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419887	41419887	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	120	479	0	ENST00000373198.4:c.434G>T	p.Gly145Val	p.G145V	ENST00000373198	NM_133170.3	145	gGc/gTc	3/32	0.3	0	FACETS	0.967	0.881	1			1	CLONAL	1	TRUE	0	0.38	0		479	405	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265048	46265049	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	71	495	0	ENST00000371998.3:c.1924dup	p.Leu642ProfsTer6	p.L642Pfs*6	ENST00000371998		640	tcc/tCcc	12/23	1	2	FACETS	0.818	0.716	0.927	0.818	0.716	0.927	CLONAL	1	TRUE	1	0.38	2		495	457	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46277793	46277793	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	29	403	0	ENST00000371998.3:c.3591C>A	p.Asn1197Lys	p.N1197K	ENST00000371998		1197	aaC/aaA	19/23	1	2	FACETS	0.318	0.255	0.39	0.318	0.255	0.39	SUBCLONAL	1	TRUE	1	0.38	2		403	480	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62303913	62303913	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs549397879	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	102	551	2	ENST00000360203.5:c.704G>A	p.Arg235His	p.R235H	ENST00000360203	NM_001283009.1	235	cGc/cAc	9/35	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.38	2		553	505	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44527574	44527574	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	67	455	0	ENST00000291552.4:c.31A>G	p.Thr11Ala	p.T11A	ENST00000291552	NM_006758.2	11	Acc/Gcc	1/8	0.133086375453015	3	FACETS	0.98	0.855	1	0.49	0.427	0.558	INDETERMINATE	1	TRUE	1	0.38	3		455	428	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627421	37627421	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	40	674	0	ENST00000249071.6:c.298G>T	p.Glu100Ter	p.E100*	ENST00000249071	NM_002872.4	100	Gaa/Taa	5/7	1	2	FACETS	0.389	0.323	0.463	0.389	0.323	0.463	SUBCLONAL	1	TRUE	1	0.38	2		674	541	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523630	41523630	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	46	657	0	ENST00000263253.7:c.1046A>G	p.His349Arg	p.H349R	ENST00000263253	NM_001429.3	349	cAc/cGc	4/31	1	2	FACETS	0.346	0.29	0.407	0.346	0.29	0.407	SUBCLONAL	1	TRUE	1	0.38	2		657	700	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533739	41533739	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	43	518	0	ENST00000263253.7:c.1705A>G	p.Lys569Glu	p.K569E	ENST00000263253	NM_001429.3	569	Aaa/Gaa	8/31	1	2	FACETS	0.386	0.322	0.457	0.386	0.322	0.457	SUBCLONAL	1	TRUE	1	0.38	2		518	586	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568502	41568502	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	42	357	0	ENST00000263253.7:c.4453-1G>T		p.X1485_splice	ENST00000263253	NM_001429.3	1485			1	2	FACETS	0.643	0.538	0.758	0.643	0.538	0.758	SUBCLONAL	1	TRUE	1	0.38	2		357	344	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569711	41569711	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	61	285	0	ENST00000263253.7:c.4702A>G	p.Lys1568Glu	p.K1568E	ENST00000263253	NM_001429.3	1568	Aag/Gag	29/31	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.38	2		285	312	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574678	41574679	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs754418509	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	46	848	5	ENST00000263253.7:c.6970dup	p.His2324ProfsTer55	p.H2324Pfs*55	ENST00000263253	NM_001429.3	2321	-/C	31/31	1	2	FACETS	0.341	0.286	0.401	0.341	0.286	0.401	SUBCLONAL	1	TRUE	1	0.38	2		853	711	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641700	12641700	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746992885	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	51	534	0	ENST00000251849.4:c.941C>T	p.Ala314Val	p.A314V	ENST00000251849	NM_002880.3	314	gCa/gTa	9/17	1	2	FACETS	0.445	0.378	0.519	0.445	0.378	0.519	SUBCLONAL	1	TRUE	1	0.38	2		534	603	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267350	41267350	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	50	234	0	ENST00000349496.5:c.934A>G	p.Lys312Glu	p.K312E	ENST00000349496	NM_001904.3	312	Aag/Gag	6/15	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.38	2		234	262	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098956	47098957	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	114	552	0	ENST00000409792.3:c.6317dup	p.Lys2107GlufsTer5	p.K2107Efs*5	ENST00000409792	NM_014159.6	2106	aag/aaAg	15/21	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.38	2		552	598	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127765	47127765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758473163	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	179	437	0	ENST00000409792.3:c.5317C>T	p.Arg1773Cys	p.R1773C	ENST00000409792	NM_014159.6	1773	Cgt/Tgt	11/21	1	2	FACETS	0.77	0.713	0.828	1	0.991	1	SUBCLONAL	2	TRUE	1	0.38	2		437	612	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163333	47163333	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	91	449	0	ENST00000409792.3:c.2793A>T	p.Glu931Asp	p.E931D	ENST00000409792	NM_014159.6	931	gaA/gaT	3/21	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.38	2		449	376	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928639	49928639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1008363508	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	47	657	0	ENST00000296474.3:c.3635G>A	p.Arg1212Gln	p.R1212Q	ENST00000296474	NM_002447.2	1212	cGg/cAg	17/20	1	2	FACETS	0.386	0.325	0.453	0.386	0.325	0.453	SUBCLONAL	1	TRUE	1	0.38	2		657	641	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940064	49940064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200757776	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	185	648	1	ENST00000296474.3:c.979G>A	p.Ala327Thr	p.A327T	ENST00000296474	NM_002447.2	327	Gct/Act	1/20	1	2	FACETS	0.842	0.782	0.904	1	0.992	1	CLONAL	2	TRUE	1	0.38	2		649	578	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436380	52436380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	36	639	0	ENST00000460680.1:c.2114G>A	p.Ser705Asn	p.S705N	ENST00000460680	NM_004656.3	705	aGc/aAc	17/17	1	2	FACETS	0.339	0.278	0.408	0.339	0.278	0.408	SUBCLONAL	1	TRUE	1	0.38	2		639	559	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439792	52439792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	36	542	0	ENST00000460680.1:c.920G>A	p.Gly307Asp	p.G307D	ENST00000460680	NM_004656.3	307	gGc/gAc	10/17	1	2	FACETS	0.387	0.318	0.465	0.387	0.318	0.465	SUBCLONAL	1	TRUE	1	0.38	2		542	489	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643716	52643716	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	39	654	0	ENST00000394830.3:c.2180A>G	p.Asp727Gly	p.D727G	ENST00000394830	NM_018313.4	727	gAc/gGc	17/30	1	2	FACETS	0.329	0.272	0.394	0.329	0.272	0.394	SUBCLONAL	1	TRUE	1	0.38	2		654	623	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799640	72799640	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762002222	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	32	602	1	ENST00000325599.8:c.1529G>A	p.Arg510His	p.R510H	ENST00000325599	NM_018130.2	510	cGc/cAc	11/11	1	2	FACETS	0.314	0.254	0.382	0.314	0.254	0.382	SUBCLONAL	1	TRUE	1	0.38	2		603	536	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72891455	72891455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs529476695	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	40	513	1	ENST00000325599.8:c.307G>A	p.Ala103Thr	p.A103T	ENST00000325599	NM_018130.2	103	Gca/Aca	3/11	1	2	FACETS	0.381	0.316	0.453	0.381	0.316	0.453	SUBCLONAL	1	TRUE	1	0.38	2		514	553	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73112898	73112898	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	85	370	0	ENST00000356692.5:c.494G>A	p.Arg165Lys	p.R165K	ENST00000356692		165	aGg/aAg	6/9	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.38	2		370	375	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119634966	119634966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	53	231	0	ENST00000316626.5:c.533G>A	p.Cys178Tyr	p.C178Y	ENST00000316626		178	tGc/tAc	5/12	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.38	2		231	252	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204639	128204639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764747992	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	125	618	0	ENST00000341105.2:c.802G>A	p.Gly268Arg	p.G268R	ENST00000341105	NM_032638.4	268	Gga/Aga	3/6	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.38	2		618	518	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205017	128205017	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	150	611	0	ENST00000341105.2:c.424C>A	p.Pro142Thr	p.P142T	ENST00000341105	NM_032638.4	142	Cca/Aca	3/6	1	2	FACETS	0.918	0.847	0.991	1	0.991	1	CLONAL	2	TRUE	1	0.38	2		611	430	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670774	134670774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1435725610	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	87	433	0	ENST00000398015.3:c.685G>A	p.Ala229Thr	p.A229T	ENST00000398015	NM_004441.4	229	Gca/Aca	3/16	0.3	1	FACETS	0.851	0.757	0.95	0.851	0.757	0.95	CLONAL	1	TRUE	0	0.38	1		433	436	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825361	134825361	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	83	442	0	ENST00000398015.3:c.877T>C	p.Ser293Pro	p.S293P	ENST00000398015	NM_004441.4	293	Tcc/Ccc	4/16	0.3	1	FACETS	0.835	0.74	0.935	0.835	0.74	0.935	CLONAL	1	TRUE	0	0.38	1		442	424	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134881006	134881006	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	136	450	0	ENST00000398015.3:c.1569C>A	p.Phe523Leu	p.F523L	ENST00000398015	NM_004441.4	523	ttC/ttA	7/16	0.3	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.38	1		450	420	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272236	142272236	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367864862	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	25	291	0	ENST00000350721.4:c.2638G>A	p.Ala880Thr	p.A880T	ENST00000350721	NM_001184.3	880	Gca/Aca	13/47	1	2	FACETS	0.393	0.309	0.488	0.393	0.309	0.488	SUBCLONAL	1	TRUE	1	0.38	2		291	335	SUCCESS
ATR	545	MSKCC	GRCh37	3	142286929	142286929	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	150	449	0	ENST00000350721.4:c.127C>T	p.Arg43Trp	p.R43W	ENST00000350721	NM_001184.3	43	Cgg/Tgg	2/47	1	2	FACETS	0.84	0.774	0.908	1	0.99	1	CLONAL	2	TRUE	1	0.38	2		449	470	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374825	149374825	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	69	367	0	ENST00000360632.3:c.269C>T	p.Ser90Leu	p.S90L	ENST00000360632	NM_015472.4	90	tCg/tTg	2/7	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.38	2		367	312	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169953109	169953109	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	99	503	1	ENST00000295797.4:c.193C>A	p.Leu65Ile	p.L65I	ENST00000295797	NM_002740.5	65	Ctc/Atc	2/18	1	2	FACETS	0.921	0.824	1	0.921	0.824	1	CLONAL	1	TRUE	1	0.38	2		504	566	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952075	178952075	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	24	375	0	ENST00000263967.3:c.3130A>G	p.Asn1044Asp	p.N1044D	ENST00000263967	NM_006218.2	1044	Aat/Gat	21/21	1	2	FACETS	0.362	0.283	0.452	0.362	0.283	0.452	SUBCLONAL	1	TRUE	1	0.38	2		375	349	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182662910	182662910	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	65	570	0	ENST00000292782.4:c.752T>A	p.Ile251Asn	p.I251N	ENST00000292782	NM_020640.2	251	aTt/aAt	7/7	1	2	FACETS	0.627	0.544	0.716	0.627	0.544	0.716	SUBCLONAL	1	TRUE	1	0.38	2		570	546	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446953	187446953	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	166	687	0	ENST00000232014.4:c.1240T>A	p.Cys414Ser	p.C414S	ENST00000232014	NM_001130845.1	414	Tgc/Agc	5/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.38	2		687	640	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447519	187447519	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	92	549	0	ENST00000232014.4:c.674C>A	p.Pro225His	p.P225H	ENST00000232014	NM_001130845.1	225	cCc/cAc	5/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.38	2		549	446	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801184	1801184	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	166	779	1	ENST00000260795.2:c.313G>C	p.Gly105Arg	p.G105R	ENST00000260795		105	Ggg/Cgg	2/17	1	2	FACETS	0.82	0.758	0.883	1	0.991	1	CLONAL	2	TRUE	1	0.38	2		780	533	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747964	41747964	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	11	179	0	ENST00000226382.2:c.805C>A	p.Pro269Thr	p.P269T	ENST00000226382	NM_003924.3	269	Cct/Act	3/3	1	2	FACETS	0.353	0.244	0.487	0.353	0.244	0.487	SUBCLONAL	1	TRUE	1	0.38	2		179	164	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592204	55592204	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	26	493	0	ENST00000288135.5:c.1528G>T	p.Gly510Cys	p.G510C	ENST00000288135	NM_000222.2	510	Ggt/Tgt	9/21	1	2	FACETS	0.303	0.239	0.376	0.303	0.239	0.376	SUBCLONAL	1	TRUE	1	0.38	2		493	452	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55962494	55962494	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	93	454	1	ENST00000263923.4:c.2630G>A	p.Ser877Asn	p.S877N	ENST00000263923	NM_002253.2	877	aGt/aAt	19/30	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.38	2		455	454	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979515	55979515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	171	574	0	ENST00000263923.4:c.932G>A	p.Ser311Asn	p.S311N	ENST00000263923	NM_002253.2	311	aGt/aAt	7/30	1	2	FACETS	0.817	0.756	0.879	1	0.991	1	CLONAL	2	TRUE	1	0.38	2		574	551	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55987273	55987273	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	103	472	0	ENST00000263923.4:c.152T>A	p.Ile51Asn	p.I51N	ENST00000263923	NM_002253.2	51	aTt/aAt	2/30	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.38	2		472	476	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156355	106156355	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	64	285	0	ENST00000380013.4:c.1256C>A	p.Pro419His	p.P419H	ENST00000380013	NM_001127208.2	419	cCt/cAt	3/11	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.38	2		285	318	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157665	106157665	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	15	254	0	ENST00000380013.4:c.2566G>T	p.Gly856Ter	p.G856*	ENST00000380013	NM_001127208.2	856	Gga/Tga	3/11	1	2	FACETS	0.29	0.212	0.385	0.29	0.212	0.385	SUBCLONAL	1	TRUE	1	0.38	2		254	272	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106194022	106194022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	101	238	0	ENST00000380013.4:c.4484C>T	p.Ala1495Val	p.A1495V	ENST00000380013	NM_001127208.2	1495	gCc/gTc	10/11	1	2	FACETS	0.828	0.749	0.91	1	0.986	1	CLONAL	2	TRUE	1	0.38	2		238	321	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	22	252	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.421	0.327	0.53	0.421	0.327	0.53	SUBCLONAL	1	TRUE	1	0.38	2		252	275	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540628	187540628	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	105	355	0	ENST00000441802.2:c.7112G>A	p.Ser2371Asn	p.S2371N	ENST00000441802	NM_005245.3	2371	aGc/aAc	10/27	1	2	FACETS	0.757	0.685	0.832	1	0.984	1	SUBCLONAL	2	TRUE	1	0.38	2		355	365	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630465	187630465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1439256953	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	179	748	1	ENST00000441802.2:c.517G>A	p.Ala173Thr	p.A173T	ENST00000441802	NM_005245.3	173	Gcc/Acc	2/27	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.38	2		749	812	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233651	233651	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs377509915	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	42	223	0	ENST00000264932.6:c.955A>G	p.Ile319Val	p.I319V	ENST00000264932	NM_004168.2	319	Att/Gtt	8/15	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.38	2		223	192	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1253917	1253917	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	92	621	0	ENST00000310581.5:c.3325G>T	p.Gly1109Trp	p.G1109W	ENST00000310581	NM_198253.2	1109	Ggg/Tgg	16/16	1	2	FACETS	0.998	0.891	1	0.998	0.891	1	CLONAL	1	TRUE	1	0.38	2		621	485	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278878	1278878	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	125	600	0	ENST00000310581.5:c.2164C>T	p.Gln722Ter	p.Q722*	ENST00000310581	NM_198253.2	722	Cag/Tag	6/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.38	2		600	520	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293833	1293833	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	58	945	5	ENST00000310581.5:c.1168C>T	p.Arg390Trp	p.R390W	ENST00000310581	NM_198253.2	390	Cgg/Tgg	2/16	1	2	FACETS	0.485	0.416	0.56	0.485	0.416	0.56	SUBCLONAL	1	TRUE	1	0.38	2		950	630	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526216	31526216	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	207	839	0	ENST00000344624.3:c.824C>A	p.Pro275Gln	p.P275Q	ENST00000344624		275	cCa/cAa	2/33	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.38	2		839	871	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867520	35867520	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	50	251	0	ENST00000303115.3:c.334G>T	p.Gly112Ter	p.G112*	ENST00000303115	NM_002185.3	112	Gga/Tga	3/8	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.38	2		251	245	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875622	35875622	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866550601	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	51	325	0	ENST00000303115.3:c.809C>A	p.Pro270His	p.P270H	ENST00000303115	NM_002185.3	270	cCt/cAt	7/8	1	2	FACETS	0.787	0.672	0.912	0.787	0.672	0.912	CLONAL	1	TRUE	1	0.38	2		325	341	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953120	38953120	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	18	271	0	ENST00000357387.3:c.2864T>G	p.Leu955Arg	p.L955R	ENST00000357387	NM_152756.3	955	cTt/cGt	29/38	1	2	FACETS	0.307	0.23	0.397	0.307	0.23	0.397	SUBCLONAL	1	TRUE	1	0.38	2		271	309	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160664	56160664	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200705994	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	127	340	0	ENST00000399503.3:c.938G>A	p.Arg313Gln	p.R313Q	ENST00000399503	NM_005921.1	313	cGg/cAg	4/20	1	2	FACETS	0.772	0.705	0.841	1	0.987	1	SUBCLONAL	2	TRUE	1	0.38	2		340	433	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178664	56178664	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	19	205	0	ENST00000399503.3:c.3637G>T	p.Gly1213Ter	p.G1213*	ENST00000399503	NM_005921.1	1213	Gga/Tga	14/20	1	2	FACETS	0.433	0.329	0.554	0.433	0.329	0.554	SUBCLONAL	1	TRUE	1	0.38	2		205	231	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576486	67576487	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	31	359	0	ENST00000274335.5:c.770dup	p.Asn257LysfsTer10	p.N257Kfs*10	ENST00000274335		255	-/A	5/15	1	2	FACETS	0.347	0.28	0.423	0.347	0.28	0.423	SUBCLONAL	1	TRUE	1	0.38	2		359	470	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588928	67588928	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	14	247	0	ENST00000274335.5:c.1020-1G>T		p.X340_splice	ENST00000274335		340			1	2	FACETS	0.273	0.197	0.365	0.273	0.197	0.365	SUBCLONAL	1	TRUE	1	0.38	2		247	270	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591007	67591007	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	18	174	1	ENST00000274335.5:c.1600C>T	p.Arg534Ter	p.R534*	ENST00000274335		534	Cga/Tga	12/15	1	2	FACETS	0.449	0.339	0.578	0.449	0.339	0.578	SUBCLONAL	1	TRUE	1	0.38	2		175	211	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675570	86675571	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	53	247	0	ENST00000274376.6:c.2513dup	p.Asn838LysfsTer2	p.N838Kfs*2	ENST00000274376	NM_002890.2	836	gaa/gAaa	19/25	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.38	2		247	250	SUCCESS
APC	324	MSKCC	GRCh37	5	112178717	112178717	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	82	495	0	ENST00000257430.4:c.7426A>G	p.Arg2476Gly	p.R2476G	ENST00000257430	NM_000038.5	2476	Agg/Ggg	16/16	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.38	2		495	409	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911514	131911514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143802516	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	33	413	0	ENST00000265335.6:c.259C>T	p.Arg87Cys	p.R87C	ENST00000265335		87	Cgt/Tgt	3/25	1	2	FACETS	0.41	0.333	0.496	0.41	0.333	0.496	SUBCLONAL	1	TRUE	1	0.38	2		413	424	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915589	131915589	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764784659	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	10	240	0	ENST00000265335.6:c.587G>A	p.Arg196His	p.R196H	ENST00000265335		196	cGt/cAt	5/25	1	2	FACETS	0.274	0.185	0.385	0.274	0.185	0.385	SUBCLONAL	1	TRUE	1	0.38	2		240	192	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502737	149502737	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	32	537	0	ENST00000261799.4:c.2051G>A	p.Cys684Tyr	p.C684Y	ENST00000261799	NM_002609.3	684	tGc/tAc	15/23	1	2	FACETS	0.304	0.246	0.37	0.304	0.246	0.37	SUBCLONAL	1	TRUE	1	0.38	2		537	554	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504289	149504289	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	114	545	0	ENST00000261799.4:c.1912+1G>A		p.X638_splice	ENST00000261799	NM_002609.3	638			1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.38	2		545	578	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504328	149504328	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	115	585	0	ENST00000261799.4:c.1874C>A	p.Ser625Tyr	p.S625Y	ENST00000261799	NM_002609.3	625	tCt/tAt	13/23	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.38	2		585	577	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149506081	149506081	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	80	522	0	ENST00000261799.4:c.1674+2T>C		p.X558_splice	ENST00000261799	NM_002609.3	558			1	2	FACETS	0.885	0.781	0.995	0.885	0.781	0.995	CLONAL	1	TRUE	1	0.38	2		522	476	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512472	149512472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374208706	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	78	483	1	ENST00000261799.4:c.968G>A	p.Gly323Asp	p.G323D	ENST00000261799	NM_002609.3	323	gGc/gAc	7/23	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.38	2		484	400	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176516650	176516650	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	108	604	0	ENST00000292408.4:c.47G>T	p.Gly16Val	p.G16V	ENST00000292408	NM_213647.1	16	gGg/gTg	2/18	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.38	2		604	553	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517612	176517612	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	129	900	2	ENST00000292408.4:c.313G>T	p.Gly105Cys	p.G105C	ENST00000292408	NM_213647.1	105	Ggc/Tgc	3/18	1	2	FACETS	0.997	0.906	1	0.997	0.906	1	CLONAL	1	TRUE	1	0.38	2		902	681	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522596	176522596	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754440305	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	120	701	0	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	0.38	2		701	491	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636644	176636644	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	27	293	0	ENST00000439151.2:c.1244A>G	p.Gln415Arg	p.Q415R	ENST00000439151	NM_022455.4	415	cAg/cGg	5/23	1	2	FACETS	0.472	0.376	0.581	0.472	0.376	0.581	SUBCLONAL	1	TRUE	1	0.38	2		293	301	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638953	176638953	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	44	498	0	ENST00000439151.2:c.3553T>C	p.Cys1185Arg	p.C1185R	ENST00000439151	NM_022455.4	1185	Tgt/Cgt	5/23	1	2	FACETS	0.376	0.315	0.444	0.376	0.315	0.444	SUBCLONAL	1	TRUE	1	0.38	2		498	616	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030325	180030325	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115824945	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	167	717	2	ENST00000261937.6:c.3959G>A	p.Arg1320Gln	p.R1320Q	ENST00000261937	NM_182925.4	1320	cGg/cAg	30/30	0.3	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.38	1		719	542	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045804	180045804	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	118	681	1	ENST00000261937.6:c.2967G>T	p.Glu989Asp	p.E989D	ENST00000261937	NM_182925.4	989	gaG/gaT	21/30	0.3	1	FACETS	0.932	0.844	1	0.932	0.844	1	CLONAL	1	TRUE	0	0.38	1		682	540	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047694	180047694	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	36	554	0	ENST00000261937.6:c.2321T>C	p.Met774Thr	p.M774T	ENST00000261937	NM_182925.4	774	aTg/aCg	16/30	0.3	1	FACETS	0.322	0.264	0.386	0.322	0.264	0.386	SUBCLONAL	1	TRUE	0	0.38	1		554	477	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057736	180057736	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	42	630	0	ENST00000261937.6:c.219G>T	p.Lys73Asn	p.K73N	ENST00000261937	NM_182925.4	73	aaG/aaT	3/30	0.3	1	FACETS	0.39	0.326	0.462	0.39	0.326	0.462	SUBCLONAL	1	TRUE	0	0.38	1		630	459	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056274	26056274	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	128	523	0	ENST00000343677.2:c.383C>A	p.Pro128His	p.P128H	ENST00000343677	NM_005319.3	128	cCt/cAt	1/1	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.38	2		523	640	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911136	29911136	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	31	533	1	ENST00000376809.5:c.435G>T	p.Lys145Asn	p.K145N	ENST00000376809	NM_002116.7	145	aaG/aaT	3/8	1	2	FACETS	0.364	0.294	0.444	0.364	0.294	0.444	SUBCLONAL	1	TRUE	1	0.38	2		534	448	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672782	30672782	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	141	787	0	ENST00000376406.3:c.4178G>T	p.Arg1393Met	p.R1393M	ENST00000376406	NM_014641.2	1393	aGg/aTg	10/15	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.38	2		787	732	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673724	30673724	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61733207	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	45	632	0	ENST00000376406.3:c.3236G>A	p.Arg1079His	p.R1079H	ENST00000376406	NM_014641.2	1079	cGt/cAt	10/15	1	2	FACETS	0.381	0.32	0.45	0.381	0.32	0.45	SUBCLONAL	1	TRUE	1	0.38	2		632	621	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680192	30680192	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	167	779	2	ENST00000376406.3:c.1527C>A	p.His509Gln	p.H509Q	ENST00000376406	NM_014641.2	509	caC/caA	5/15	1	2	FACETS	0.997	0.916	1	0.997	0.916	1	CLONAL	1	TRUE	1	0.38	2		781	882	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324165	31324165	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	36	267	0	ENST00000412585.2:c.398T>C	p.Leu133Pro	p.L133P	ENST00000412585	NM_005514.6	133	cTc/cCc	3/8	1	2	FACETS	0.81	0.67	0.963	0.81	0.67	0.963	CLONAL	1	TRUE	1	0.38	2		267	234	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185034	32185034	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	91	537	0	ENST00000375023.3:c.1634G>A	p.Gly545Asp	p.G545D	ENST00000375023	NM_004557.3	545	gGc/gAc	10/30	1	2	FACETS	0.96	0.855	1	0.96	0.855	1	CLONAL	1	TRUE	1	0.38	2		537	499	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188850	32188850	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	29	624	0	ENST00000375023.3:c.704C>T	p.Ala235Val	p.A235V	ENST00000375023	NM_004557.3	235	gCa/gTa	4/30	1	2	FACETS	0.339	0.272	0.416	0.339	0.272	0.416	SUBCLONAL	1	TRUE	1	0.38	2		624	450	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800429	32800429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750440758	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	284	844	3	ENST00000374899.4:c.1118G>A	p.Arg373His	p.R373H	ENST00000374899	NM_018833.2	373	cGc/cAc	6/12	1	2	FACETS	0.827	0.779	0.876	1	0.995	1	CLONAL	2	TRUE	1	0.38	2		847	904	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816544	32816544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376553490	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	58	786	1	ENST00000354258.4:c.1631G>A	p.Arg544His	p.R544H	ENST00000354258	NM_000593.5	544	cGc/cAc	7/11	1	2	FACETS	0.376	0.322	0.435	0.376	0.322	0.435	SUBCLONAL	1	TRUE	1	0.38	2		787	812	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820999	32820999	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	49	900	1	ENST00000354258.4:c.595G>A	p.Ala199Thr	p.A199T	ENST00000354258	NM_000593.5	199	Gcc/Acc	1/11	1	2	FACETS	0.343	0.289	0.402	0.343	0.289	0.402	SUBCLONAL	1	TRUE	1	0.38	2		901	752	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287212	33287213	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1268651006	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	109	523	1	ENST00000374542.5:c.1884dup	p.Cys629LeufsTer29	p.C629Lfs*29	ENST00000374542	NM_001141970.1	628	-/C	6/8	1	2	FACETS	0.967	0.871	1	0.967	0.871	1	CLONAL	1	TRUE	1	0.38	2		524	593	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139163	37139163	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	32	435	0	ENST00000373509.5:c.503T>C	p.Ile168Thr	p.I168T	ENST00000373509	NM_002648.3	168	aTc/aCc	4/6	1	2	FACETS	0.423	0.343	0.513	0.423	0.343	0.513	SUBCLONAL	1	TRUE	1	0.38	2		435	398	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982076	93982076	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	112	488	0	ENST00000369303.4:c.1389G>A	p.Trp463Ter	p.W463*	ENST00000369303	NM_004440.3	463	tgG/tgA	6/17	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.38	2		488	566	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015606	112015606	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	42	491	0	ENST00000368678.4:c.1236A>G	p.Ile412Met	p.I412M	ENST00000368678		412	atA/atG	11/13	1	2	FACETS	0.421	0.351	0.499	0.421	0.351	0.499	SUBCLONAL	1	TRUE	1	0.38	2		491	525	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642471	117642471	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs750354810	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	245	691	0	ENST00000368508.3:c.5728C>T	p.Arg1910Ter	p.R1910*	ENST00000368508	NM_002944.2	1910	Cga/Tga	35/43	1	2	FACETS	0.849	0.797	0.903	1	0.994	1	CLONAL	2	TRUE	1	0.38	2		691	759	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663697	117663697	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	51	372	0	ENST00000368508.3:c.4535A>T	p.Asp1512Val	p.D1512V	ENST00000368508	NM_002944.2	1512	gAc/gTc	28/43	1	2	FACETS	0.987	0.845	1	0.987	0.845	1	CLONAL	1	TRUE	1	0.38	2		372	272	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674333	117674333	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	58	373	0	ENST00000368508.3:c.4142-1G>A		p.X1381_splice	ENST00000368508	NM_002944.2	1381			1	2	FACETS	0.85	0.734	0.976	0.85	0.734	0.976	CLONAL	1	TRUE	1	0.38	2		373	359	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681061	117681061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749977900	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	93	534	0	ENST00000368508.3:c.3559G>A	p.Val1187Ile	p.V1187I	ENST00000368508	NM_002944.2	1187	Gtt/Att	23/43	1	2	FACETS	0.956	0.853	1	0.956	0.853	1	CLONAL	1	TRUE	1	0.38	2		534	512	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725441	117725441	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	75	458	0	ENST00000368508.3:c.438+2T>C		p.X146_splice	ENST00000368508	NM_002944.2	146			1	2	FACETS	0.868	0.763	0.979	0.868	0.763	0.979	CLONAL	1	TRUE	1	0.38	2		458	455	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199820	138199820	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	97	425	1	ENST00000237289.4:c.1238A>G	p.Lys413Arg	p.K413R	ENST00000237289	NM_001270507.1	413	aAg/aGg	7/9	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.38	2		426	496	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202200	138202200	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3734553	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	30	426	0	ENST00000237289.4:c.2117G>A	p.Arg706Gln	p.R706Q	ENST00000237289	NM_001270507.1	706	cGa/cAa	9/9	1	2	FACETS	0.373	0.3	0.456	0.373	0.3	0.456	SUBCLONAL	1	TRUE	1	0.38	2		426	423	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001241	150001241	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	36	585	0	ENST00000253339.5:c.2363del	p.Gly788ValfsTer3	p.G788Vfs*3	ENST00000253339		788	gGt/gt	4/7	1	2	FACETS	0.388	0.319	0.466	0.388	0.319	0.466	SUBCLONAL	1	TRUE	1	0.38	2		585	488	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023204	150023204	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	34	684	1	ENST00000253339.5:c.59C>T	p.Ala20Val	p.A20V	ENST00000253339		20	gCc/gTc	1/7	1	2	FACETS	0.312	0.254	0.378	0.312	0.254	0.378	SUBCLONAL	1	TRUE	1	0.38	2		685	573	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129417	152129417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	77	380	0	ENST00000206249.3:c.370C>T	p.His124Tyr	p.H124Y	ENST00000206249	NM_000125.3	124	Cac/Tac	1/8	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.38	2		380	347	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265307	152265307	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	53	248	0	ENST00000206249.3:c.761-1G>T		p.X254_splice	ENST00000206249	NM_000125.3	254			1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.38	2		248	245	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150545	157150545	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	31	374	0	ENST00000346085.5:c.1727C>A	p.Pro576His	p.P576H	ENST00000346085	NM_020732.3	576	cCt/cAt	2/20	1	2	FACETS	0.363	0.293	0.443	0.363	0.293	0.443	SUBCLONAL	1	TRUE	1	0.38	2		374	449	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781239	161781239	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1393283491	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	43	440	0	ENST00000366898.1:c.1168-2A>G		p.X390_splice	ENST00000366898	NM_004562.2	390			1	2	FACETS	0.486	0.406	0.573	0.486	0.406	0.573	SUBCLONAL	1	TRUE	1	0.38	2		440	466	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683713	162683713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747891099	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	171	548	0	ENST00000366898.1:c.256G>A	p.Asp86Asn	p.D86N	ENST00000366898	NM_004562.2	86	Gac/Aac	3/12	1	2	FACETS	0.83	0.769	0.893	1	0.991	1	CLONAL	2	TRUE	1	0.38	2		548	542	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	163148694	163148694	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	26	485	0	ENST00000366898.1:c.7G>T	p.Val3Leu	p.V3L	ENST00000366898	NM_004562.2	3	Gtg/Ttg	1/12	1	2	FACETS	0.344	0.272	0.426	0.344	0.272	0.426	SUBCLONAL	1	TRUE	1	0.38	2		485	398	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953016	2953016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764229454	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	216	704	1	ENST00000396946.4:c.2924G>A	p.Arg975Gln	p.R975Q	ENST00000396946	NM_032415.4	975	cGg/cAg	22/25	1	2	FACETS	0.917	0.858	0.977	1	0.994	1	CLONAL	2	TRUE	1	0.38	2		705	620	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450369	50450369	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	133	404	0	ENST00000331340.3:c.553A>G	p.Arg185Gly	p.R185G	ENST00000331340	NM_006060.4	185	Agg/Ggg	5/8	1	2	FACETS	0.845	0.775	0.918	1	0.989	1	CLONAL	2	TRUE	1	0.38	2		404	414	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468014	50468014	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	24	480	0	ENST00000331340.3:c.1249C>T	p.His417Tyr	p.H417Y	ENST00000331340	NM_006060.4	417	Cac/Tac	8/8	1	2	FACETS	0.344	0.269	0.43	0.344	0.269	0.43	SUBCLONAL	1	TRUE	1	0.38	2		480	367	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340234	116340234	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	33	321	0	ENST00000397752.3:c.1096C>A	p.Pro366Thr	p.P366T	ENST00000397752	NM_000245.2	366	Cct/Act	2/21	1	2	FACETS	0.487	0.397	0.588	0.487	0.397	0.588	SUBCLONAL	1	TRUE	1	0.38	2		321	357	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128849213	128849213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	141	583	2	ENST00000249373.3:c.1441G>A	p.Glu481Lys	p.E481K	ENST00000249373	NM_005631.4	481	Gag/Aag	8/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.38	2		585	579	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481389	140481389	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	21	410	0	ENST00000288602.6:c.1419G>T	p.Lys473Asn	p.K473N	ENST00000288602	NM_004333.4	473	aaG/aaT	11/18	1	2	FACETS	0.309	0.237	0.392	0.309	0.237	0.392	SUBCLONAL	1	TRUE	1	0.38	2		410	358	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842373	151842373	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	17	164	0	ENST00000262189.6:c.14039G>T	p.Gly4680Val	p.G4680V	ENST00000262189	NM_170606.2	4680	gGg/gTg	54/59	1	2	FACETS	0.452	0.338	0.586	0.452	0.338	0.586	SUBCLONAL	1	TRUE	1	0.38	2		164	198	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845352	151845352	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	46	595	0	ENST00000262189.6:c.13660A>G	p.Ile4554Val	p.I4554V	ENST00000262189	NM_170606.2	4554	Atc/Gtc	52/59	1	2	FACETS	0.41	0.345	0.483	0.41	0.345	0.483	SUBCLONAL	1	TRUE	1	0.38	2		595	590	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	142	673	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	0.38	2		673	670	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151871294	151871294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	95	482	0	ENST00000262189.6:c.9296C>T	p.Ala3099Val	p.A3099V	ENST00000262189	NM_170606.2	3099	gCc/gTc	39/59	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.38	2		482	498	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873531	151873531	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	37	597	0	ENST00000262189.6:c.9007A>G	p.Ser3003Gly	p.S3003G	ENST00000262189	NM_170606.2	3003	Agt/Ggt	38/59	1	2	FACETS	0.306	0.251	0.367	0.306	0.251	0.367	SUBCLONAL	1	TRUE	1	0.38	2		597	637	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877114	151877114	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	32	447	0	ENST00000262189.6:c.7247A>G	p.His2416Arg	p.H2416R	ENST00000262189	NM_170606.2	2416	cAt/cGt	37/59	1	2	FACETS	0.338	0.274	0.411	0.338	0.274	0.411	SUBCLONAL	1	TRUE	1	0.38	2		447	498	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187129	38187129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	265	784	0	ENST00000317025.8:c.1348C>T	p.His450Tyr	p.H450Y	ENST00000317025	NM_023034.1	450	Cat/Tat	6/24	0.3	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.38	1		784	763	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273414	38273414	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	163	864	2	ENST00000425967.3:c.1921G>T	p.Gly641Cys	p.G641C	ENST00000425967	NM_001174067.1	641	Ggc/Tgc	14/19	0.3	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.38	1		866	628	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38314984	38314984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	210	813	0	ENST00000425967.3:c.80C>T	p.Thr27Ile	p.T27I	ENST00000425967	NM_001174067.1	27	aCc/aTc	3/19	0.3	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.38	1		813	653	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992721	68992721	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs764112302	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	38	642	3	ENST00000288368.4:c.1693del	p.Ser565ArgfsTer10	p.S565Rfs*10	ENST00000288368	NM_024870.2	562	cgT/cg	16/40	1	2	FACETS	0.322	0.265	0.385	0.322	0.265	0.385	SUBCLONAL	1	TRUE	1	0.38	2		645	622	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964443	70964443	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	112	617	0	ENST00000276594.2:c.1585C>A	p.His529Asn	p.H529N	ENST00000276594	NM_024504.3	529	Cat/Aat	8/8	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.38	2		617	552	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978681	70978681	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	140	600	0	ENST00000276594.2:c.972G>T	p.Trp324Cys	p.W324C	ENST00000276594	NM_024504.3	324	tgG/tgT	5/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.38	2		600	638	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981933	70981933	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	36	768	2	ENST00000276594.2:c.163C>T	p.Gln55Ter	p.Q55*	ENST00000276594	NM_024504.3	55	Cag/Tag	2/8	1	2	FACETS	0.327	0.268	0.393	0.327	0.268	0.393	SUBCLONAL	1	TRUE	1	0.38	2		770	580	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955551	90955551	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	36	516	0	ENST00000265433.3:c.2114G>T	p.Gly705Val	p.G705V	ENST00000265433	NM_002485.4	705	gGa/gTa	14/16	1	2	FACETS	0.364	0.298	0.437	0.364	0.298	0.437	SUBCLONAL	1	TRUE	1	0.38	2		516	521	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967689	90967689	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	87	428	0	ENST00000265433.3:c.1219T>C	p.Cys407Arg	p.C407R	ENST00000265433	NM_002485.4	407	Tgc/Cgc	10/16	1	2	FACETS	0.816	0.724	0.914	0.816	0.724	0.914	CLONAL	1	TRUE	1	0.38	2		428	561	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90996756	90996756	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	133	470	0	ENST00000265433.3:c.34G>T	p.Gly12Ter	p.G12*	ENST00000265433	NM_002485.4	12	Gga/Tga	1/16	1	2	FACETS	0.768	0.702	0.835	1	0.988	1	SUBCLONAL	2	TRUE	1	0.38	2		470	456	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864938	117864938	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1259968025	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	124	342	0	ENST00000297338.2:c.1171C>T	p.Arg391Cys	p.R391C	ENST00000297338	NM_006265.2	391	Cgc/Tgc	10/14	1	2	FACETS	0.924	0.846	1	1	0.99	1	CLONAL	2	TRUE	1	0.38	2		342	353	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869671	117869671	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	77	448	0	ENST00000297338.2:c.523A>G	p.Ser175Gly	p.S175G	ENST00000297338	NM_006265.2	175	Agt/Ggt	6/14	1	2	FACETS	0.853	0.751	0.962	0.853	0.751	0.962	CLONAL	1	TRUE	1	0.38	2		448	475	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742084	145742084	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1406864413	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	140	630	0	ENST00000428558.2:c.419del	p.Pro140GlnfsTer40	p.P140Qfs*40	ENST00000428558	NM_004260.3	140	cCa/ca	5/22	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.38	2		630	664	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022168	5022168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1439413818	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	87	568	0	ENST00000381652.3:c.181G>A	p.Glu61Lys	p.E61K	ENST00000381652	NM_004972.3	61	Gag/Aag	3/25	1	2	FACETS	0.879	0.78	0.984	0.879	0.78	0.984	CLONAL	1	TRUE	1	0.38	2		568	521	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375939	8375939	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	18	246	1	ENST00000356435.5:c.4658G>A	p.Cys1553Tyr	p.C1553Y	ENST00000356435		1553	tGc/tAc	28/35	1	2	FACETS	0.313	0.235	0.404	0.313	0.235	0.404	SUBCLONAL	1	TRUE	1	0.38	2		247	303	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27203012	27203012	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	53	561	0	ENST00000380036.4:c.2104C>A	p.Leu702Ile	p.L702I	ENST00000380036	NM_000459.3	702	Cta/Ata	13/23	1	2	FACETS	0.507	0.432	0.589	0.507	0.432	0.589	SUBCLONAL	1	TRUE	1	0.38	2		561	550	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27205046	27205046	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	99	498	0	ENST00000380036.4:c.2347C>A	p.Gln783Lys	p.Q783K	ENST00000380036	NM_000459.3	783	Caa/Aaa	14/23	1	2	FACETS	0.944	0.845	1	0.944	0.845	1	CLONAL	1	TRUE	1	0.38	2		498	552	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37006523	37006523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	29	424	0	ENST00000358127.4:c.422C>T	p.Thr141Ile	p.T141I	ENST00000358127	NM_001280556.1	141	aCa/aTa	4/10	1	2	FACETS	0.373	0.299	0.457	0.373	0.299	0.457	SUBCLONAL	1	TRUE	1	0.38	2		424	409	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336430	80336430	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	64	328	0	ENST00000286548.4:c.890-1G>T		p.X297_splice	ENST00000286548	NM_002072.3	297			1	2	FACETS	0.997	0.869	1	0.997	0.869	1	CLONAL	1	TRUE	1	0.38	2		328	338	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87338486	87338486	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	74	374	0	ENST00000277120.3:c.584-2A>G		p.X195_splice	ENST00000277120		195			1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.38	2		374	369	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635188	87635188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	151	472	1	ENST00000277120.3:c.2240C>T	p.Thr747Met	p.T747M	ENST00000277120		747	aCg/aTg	18/19	1	2	FACETS	0.758	0.698	0.821	1	0.989	1	SUBCLONAL	2	TRUE	1	0.38	2		473	524	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641094	93641094	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	106	569	2	ENST00000375746.1:c.1440G>T	p.Met480Ile	p.M480I	ENST00000375746	NM_001174167.1	480	atG/atT	11/14	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.38	2		571	528	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229496	98229496	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	43	503	0	ENST00000331920.6:c.2462A>G	p.Asp821Gly	p.D821G	ENST00000331920	NM_000264.3	821	gAc/gGc	15/24	1	2	FACETS	0.451	0.377	0.533	0.451	0.377	0.533	SUBCLONAL	1	TRUE	1	0.38	2		503	502	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738156	133738156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756003964	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	77	401	0	ENST00000318560.5:c.556G>A	p.Val186Ile	p.V186I	ENST00000318560	NM_005157.4	186	Gtc/Atc	4/11	1	2	FACETS	0.917	0.808	1	0.917	0.808	1	CLONAL	1	TRUE	1	0.38	2		401	442	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787818	135787818	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	24	410	0	ENST00000298552.3:c.764T>C	p.Val255Ala	p.V255A	ENST00000298552	NM_001162426.1	255	gTt/gCt	9/23	1	2	FACETS	0.284	0.222	0.356	0.284	0.222	0.356	SUBCLONAL	1	TRUE	1	0.38	2		410	445	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797313	135797313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1279777367	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	27	219	1	ENST00000298552.3:c.556G>A	p.Ala186Thr	p.A186T	ENST00000298552	NM_001162426.1	186	Gca/Aca	7/23	1	2	FACETS	0.521	0.415	0.64	0.521	0.415	0.64	SUBCLONAL	1	TRUE	1	0.38	2		220	273	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309069	137309069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756234164	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	121	825	0	ENST00000481739.1:c.676G>A	p.Ala226Thr	p.A226T	ENST00000481739	NM_002957.4	226	Gcc/Acc	5/10	1	2	FACETS	0.966	0.875	1	0.966	0.875	1	CLONAL	1	TRUE	1	0.38	2		825	659	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418430	139418430	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	94	551	0	ENST00000277541.6:c.142T>C	p.Cys48Arg	p.C48R	ENST00000277541	NM_017617.3	48	Tgt/Cgt	3/34	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.38	2		551	489	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793255	139793255	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	46	669	1	ENST00000247668.2:c.63G>T	p.Lys21Asn	p.K21N	ENST00000247668	NM_021138.3	21	aaG/aaT	2/11	1	2	FACETS	0.333	0.28	0.393	0.333	0.28	0.393	SUBCLONAL	1	TRUE	1	0.38	2		670	726	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814714	139814714	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	37	492	0	ENST00000247668.2:c.707A>G	p.Glu236Gly	p.E236G	ENST00000247668	NM_021138.3	236	gAg/gGg	8/11	1	2	FACETS	0.352	0.29	0.422	0.352	0.29	0.422	SUBCLONAL	1	TRUE	1	0.38	2		492	553	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932060	39932060	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	61	384	0	ENST00000378444.4:c.2539C>T	p.Gln847Ter	p.Q847*	ENST00000378444	NM_001123385.1	847	Cag/Tag	4/15	1	1	FACETS	0.749	0.65	0.856	0.749	0.65	0.856	SUBCLONAL	1	TRUE	0	0.38	1		384	347	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922690	44922690	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	81	170	0	ENST00000377967.4:c.1551G>T	p.Gln517His	p.Q517H	ENST00000377967	NM_021140.2	517	caG/caT	16/29	1	1	FACETS	0.959	0.866	1	1	0.986	1	CLONAL	2	TRUE	0	0.38	1		170	180	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945109	44945109	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	104	212	1	ENST00000377967.4:c.3434-1G>T		p.X1145_splice	ENST00000377967	NM_021140.2	1145			1	1	FACETS	0.849	0.786	0.911	1	0.991	1	CLONAL	3	TRUE	0	0.38	1		213	174	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247025	53247025	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556852786	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	56	323	0	ENST00000375401.3:c.475C>T	p.Arg159Cys	p.R159C	ENST00000375401	NM_004187.3	159	Cgc/Tgc	4/26	1	1	FACETS	0.694	0.598	0.798	0.694	0.598	0.798	SUBCLONAL	1	TRUE	0	0.38	1		323	344	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412044	63412044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	32	418	0	ENST00000330258.3:c.1123C>T	p.Pro375Ser	p.P375S	ENST00000330258	NM_152424.3	375	Cca/Tca	2/2	1	1	FACETS	0.513	0.418	0.619	0.513	0.418	0.619	SUBCLONAL	1	TRUE	0	0.38	1		418	266	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412110	63412110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852216	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	216	462	0	ENST00000330258.3:c.1057C>T	p.Arg353Ter	p.R353*	ENST00000330258	NM_152424.3	353	Cga/Tga	2/2	1	1	FACETS	0.85	0.806	0.894	1	0.995	1	CLONAL	3	TRUE	0	0.38	1		462	361	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343505	70343505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	165	328	0	ENST00000374080.3:c.1679C>T	p.Ala560Val	p.A560V	ENST00000374080		560	gCt/gTt	12/45	1	1	FACETS	0.928	0.864	0.993	1	0.993	1	CLONAL	2	TRUE	0	0.38	1		328	379	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347277	70347277	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	20	271	0	ENST00000374080.3:c.2941T>C	p.Ser981Pro	p.S981P	ENST00000374080		981	Tcc/Ccc	21/45	1	1	FACETS	0.316	0.241	0.403	0.316	0.241	0.403	SUBCLONAL	1	TRUE	0	0.38	1		271	270	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351421	70351421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1474736821	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	183	341	0	ENST00000374080.3:c.4069C>T	p.Arg1357Cys	p.R1357C	ENST00000374080		1357	Cgc/Tgc	29/45	1	1	FACETS	0.853	0.805	0.9	1	0.995	1	CLONAL	3	TRUE	0	0.38	1		341	305	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938134	76938134	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	212	387	0	ENST00000373344.5:c.2614C>G	p.Gln872Glu	p.Q872E	ENST00000373344	NM_000489.3	872	Caa/Gaa	9/35	1	1	FACETS	0.858	0.814	0.902	1	0.995	1	CLONAL	3	TRUE	0	0.38	1		387	351	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938538	76938538	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	46	332	0	ENST00000373344.5:c.2210T>C	p.Ile737Thr	p.I737T	ENST00000373344	NM_000489.3	737	aTc/aCc	9/35	1	1	FACETS	0.769	0.653	0.895	0.769	0.653	0.895	SUBCLONAL	1	TRUE	0	0.38	1		332	255	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196978	123196978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	76	226	0	ENST00000218089.9:c.1744G>A	p.Ala582Thr	p.A582T	ENST00000218089	NM_001042749.1	582	Gca/Aca	19/35	1	1	FACETS	0.876	0.786	0.968	1	0.983	1	CLONAL	2	TRUE	0	0.38	1		226	185	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78599563	78599563	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	43	510	1	ENST00000306801.3:c.235A>G	p.Thr79Ala	p.T79A	ENST00000306801	NM_020761.2	79	Acg/Gcg	2/34	1	2	FACETS	0.424	0.354	0.501	0.424	0.354	0.501	SUBCLONAL	1	TRUE	1	0.38	2		511	534	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040624	47040624	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	87	369	0	ENST00000377604.3:c.1259G>A	p.Gly420Asp	p.G420D	ENST00000377604	NM_001204468.1	420	gGt/gAt	13/24	1	2	FACETS	0.323	0.286	0.363	0.323	0.286	0.363	SUBCLONAL	1	TRUE	1	0.867907410450245	2		369	620	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577232	64577242	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTCACGGCT	AGCTCACGGCT	-	novel	NA	P-0031836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	364	616	0	ENST00000312049.6:c.340_350del	p.Ser114GlyfsTer62	p.S114Gfs*62	ENST00000312049	NM_130799.2	114	AGCCGTGAGCTg/g	2/10	0.867907410450245	1	FACETS	0.899	0.867	0.93	0.899	0.867	0.93	CLONAL	1	TRUE	0	0.867907410450245	1		616	528	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120442	70120442	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs865937701	NA	P-0031836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1297	115	840	1	ENST00000245479.2:c.1444G>A	p.Asp482Asn	p.D482N	ENST00000245479	NM_000346.3	482	Gac/Aac	3/3	1	2	FACETS	0.188	0.168	0.209	0.188	0.168	0.209	SUBCLONAL	1	TRUE	1	0.867907410450245	2		841	1412	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778788	76778788	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	294	588	0	ENST00000373344.5:c.6791A>C	p.Glu2264Ala	p.E2264A	ENST00000373344	NM_000489.3	2264	gAa/gCa	31/35	1	2	FACETS	0.965	0.914	1	0.965	0.914	1	CLONAL	1	TRUE	1	0.867907410450245	2		588	702	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0031927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	218	540	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.973	0.907	1	0.973	0.907	1	CLONAL	1	TRUE	1	0.567919559126253	2		540	789	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0031927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	159	396	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.896	0.824	0.97	0.896	0.824	0.97	CLONAL	1	TRUE	1	0.567919559126253	2		396	625	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594221	55594221	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913512	NA	P-0031969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	316	465	1	ENST00000288135.5:c.1924A>G	p.Lys642Glu	p.K642E	ENST00000288135	NM_000222.2	642	Aaa/Gaa	13/21	0.617704218482628	3	FACETS	0.977	0.94	1	0.977	0.94	1	CLONAL	3	TRUE	0	0.617704218482628	3		466	457	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0032008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	222	630	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.599586838421978	2		630	592	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350248	15350248	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	89	855	0	ENST00000263377.2:c.3531G>T	p.Lys1177Asn	p.K1177N	ENST00000263377	NM_058243.2	1177	aaG/aaT	17/20	0.566908346983864	2	FACETS	0.409	0.363	0.459	0.205	0.181	0.23	SUBCLONAL	1	TRUE	0	0.599586838421978	2		855	725	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094925	11094925	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	31	844	1	ENST00000358026.2:c.98G>T	p.Gly33Val	p.G33V	ENST00000358026	NM_001128849.1	33	gGt/gTt	2/36	0.566908346983864	2	FACETS	0.244	0.197	0.298	0.122	0.098	0.149	SUBCLONAL	1	TRUE	0	0.599586838421978	2		845	423	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158474	26158475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0032008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	214	730	0	ENST00000289316.2:c.78dup	p.Gly27ArgfsTer117	p.G27Rfs*117	ENST00000289316	NM_138720.2	26	gac/gaCc	1/2	0.264116938601031	4	FACETS	0.846	0.79	0.903	0.846	0.79	0.903	INDETERMINATE	2	TRUE	2	0.599586838421978	4		730	675	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983463	90983463	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	209	406	0	ENST00000265433.3:c.640G>T	p.Gly214Ter	p.G214*	ENST00000265433	NM_002485.4	214	Gga/Tga	6/16	0.280677878022869	6	FACETS	1	0.977	1	0.552	0.515	0.591	INDETERMINATE	2	TRUE	2	0.599586838421978	6		406	694	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549130	87549130	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	169	588	0	ENST00000277120.3:c.1687G>T	p.Gly563Ter	p.G563*	ENST00000277120		563	Gga/Tga	15/19	0.238853046167203	1	FACETS	0.804	0.745	0.864	0.804	0.745	0.864	INDETERMINATE	1	TRUE	0	0.599586838421978	1		588	491	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127920662	127920662	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0032008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	136	366	1	ENST00000373547.4:c.238-1G>A		p.X80_splice	ENST00000373547	NM_002721.4	80			0.238853046167203	1	FACETS	0.915	0.844	0.989	0.915	0.844	0.989	INDETERMINATE	1	TRUE	0	0.599586838421978	1		367	347	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0032012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	151	262	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.634538056089471	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.634538056089471	2		262	218	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974695	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691187	NA	P-0032012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	135	399	0	ENST00000304494.5:c.132del	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	taC/ta	1/3	0.634538056089471	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.634538056089471	1		399	278	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs863224499	NA	P-0032012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	208	610	1	ENST00000269305.4:c.672+1G>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.624350229696929	1	FACETS	0.925	0.868	0.983	0.925	0.868	0.983	CLONAL	1	TRUE	0	0.634538056089471	1		611	484	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420342	49420342	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	414	662	0	ENST00000301067.7:c.15407A>G	p.His5136Arg	p.H5136R	ENST00000301067	NM_003482.3	5136	cAt/cGt	48/54	0.634538056089471	2	FACETS	0.936	0.901	0.971	0.936	0.901	0.971	CLONAL	2	TRUE	0	0.634538056089471	2		662	697	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478783	57478783	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	144	412	0	ENST00000371085.3:c.369G>C	p.Glu123Asp	p.E123D	ENST00000371085	NM_000516.4	123	gaG/gaC	5/13	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.634538056089471	2		412	442	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213896	66213896	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	10	428	0	ENST00000273854.3:c.2534C>A	p.Thr845Asn	p.T845N	ENST00000273854	NM_004439.5	845	aCt/aAt	15/18	0.479133450272007	1	FACETS	0.189	0.128	0.264	0.189	0.128	0.264	SUBCLONAL	1	TRUE	0	0.634538056089471	1		428	114	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578517	7578517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750600586	NA	P-0032050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	315	321	0	ENST00000269305.4:c.413C>T	p.Ala138Val	p.A138V	ENST00000269305	NM_001126112.2	138	gCc/gTc	5/11	0.375269155690833	2	FACETS	0.756	0.716	0.797	0.756	0.716	0.797	SUBCLONAL	2	TRUE	0	0.483846138418902	2		321	861	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991632	72991632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781454634	NA	P-0032050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	135	568	4	ENST00000268489.5:c.2413C>T	p.Arg805Trp	p.R805W	ENST00000268489	NM_006885.3	805	Cgg/Tgg	2/10	1	2	FACETS	0.894	0.815	0.977	0.894	0.815	0.977	CLONAL	1	TRUE	1	0.483846138418902	2		572	624	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748510	162748510	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs765660823	NA	P-0032050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	88	313	0	ENST00000367921.3:c.2424A>C	p.Gln808His	p.Q808H	ENST00000367921	NM_006182.2	808	caA/caC	17/18	0.392110809779286	3	FACETS	1	0.916	1	0.517	0.46	0.577	CLONAL	1	TRUE	1	0.483846138418902	3		313	437	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118367012	118367013	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0032050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	95	457	0	ENST00000534358.1:c.5596_5597dup	p.Pro1867HisfsTer5	p.P1867Hfs*5	ENST00000534358	NM_005933.3	1865	aac/aaCCc	20/36	0.483846138418902	3	FACETS	0.779	0.695	0.869	0.39	0.347	0.435	SUBCLONAL	1	TRUE	1	0.483846138418902	3		457	626	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139503	47139503	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	124	589	0	ENST00000409792.3:c.5084T>G	p.Val1695Gly	p.V1695G	ENST00000409792	NM_014159.6	1695	gTc/gGc	9/21	1	2	FACETS	0.764	0.692	0.839	0.764	0.692	0.839	SUBCLONAL	1	TRUE	1	0.483846138418902	2		589	671	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1956968	1956968	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143360610	NA	P-0032050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	136	699	3	ENST00000382891.5:c.2419G>A	p.Ala807Thr	p.A807T	ENST00000382891	NM_133335.3	807	Gcc/Acc	13/22	1	2	FACETS	0.821	0.748	0.897	0.821	0.748	0.897	CLONAL	1	TRUE	1	0.483846138418902	2		702	685	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0032053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	61	391	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.525946367321885	3	FACETS	0.385	0.331	0.444	0.192	0.165	0.222	SUBCLONAL	1	TRUE	1	0.525946367321885	3		391	761	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578247	7578247	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0032053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	59	475	1	ENST00000269305.4:c.602T>A	p.Leu201Ter	p.L201*	ENST00000269305	NM_001126112.2	201	tTg/tAg	6/11	1	2	FACETS	0.314	0.269	0.362	0.314	0.269	0.362	SUBCLONAL	1	TRUE	1	0.525946367321885	2		476	715	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136926	64136932	+	frameshift_variant	Frame_Shift_Del	DEL	GTACCTG	GTACCTG	-	novel	NA	P-0032053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	38	352	0	ENST00000334205.4:c.1439_1445del	p.Tyr480SerfsTer36	p.Y480Sfs*36	ENST00000334205	NM_003942.2	479	acGTACCTG/ac	13/17	1	2	FACETS	0.287	0.237	0.344	0.287	0.237	0.344	SUBCLONAL	1	TRUE	1	0.525946367321885	2		352	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579550	7579550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	59	563	0	ENST00000269305.4:c.137C>A	p.Ser46Tyr	p.S46Y	ENST00000269305	NM_001126112.2	46	tCc/tAc	4/11	1	2	FACETS	0.339	0.291	0.392	0.339	0.291	0.392	SUBCLONAL	1	TRUE	1	0.525946367321885	2		563	661	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031196	11031196	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	34	565	0	ENST00000327064.4:c.1281C>A	p.Phe427Leu	p.F427L	ENST00000327064	NM_199141.1	427	ttC/ttA	11/16	1	2	FACETS	0.191	0.155	0.231	0.191	0.155	0.231	SUBCLONAL	1	TRUE	1	0.525946367321885	2		565	677	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0032054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	114	198	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	0.551800009295556	3	FACETS	1	0.973	1	0.596	0.541	0.653	CLONAL	1	TRUE	1	0.64943014623585	3		198	390	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511575	38511575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866375031	NA	P-0032054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	174	537	0	ENST00000254066.5:c.1073C>T	p.Ala358Val	p.A358V	ENST00000254066	NM_000964.3	358	gCg/gTg	8/9	1	2	FACETS	0.973	0.901	1	0.973	0.901	1	CLONAL	1	TRUE	1	0.64943014623585	2		537	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28934577	NA	P-0032054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	443	676	0	ENST00000269305.4:c.770T>C	p.Leu257Pro	p.L257P	ENST00000269305	NM_001126112.2	257	cTg/cCg	7/11	0.641816754349765	2	FACETS	0.969	0.935	1	0.969	0.935	1	CLONAL	2	TRUE	0	0.64943014623585	2		676	704	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692835	89692835	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs57374291	NA	P-0032054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	98	182	0	ENST00000371953.3:c.319G>T	p.Asp107Tyr	p.D107Y	ENST00000371953	NM_000314.4	107	Gat/Tat	5/9	0.64943014623585	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.64943014623585	1		182	180	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295338	1295338	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0032054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	32	386	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.248	0.201	0.301	0.248	0.201	0.301	SUBCLONAL	1	TRUE	1	0.64943014623585	2		386	398	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981549	201981549	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	227	747	0	ENST00000359651.3:c.463G>A	p.Asp155Asn	p.D155N	ENST00000359651		155	Gac/Aac	3/8	1	2	FACETS	0.996	0.932	1	0.996	0.932	1	CLONAL	1	TRUE	1	0.64943014623585	2		747	702	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881475	48881476	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	141	277	0	ENST00000267163.4:c.198dup	p.Pro67ThrfsTer43	p.P67Tfs*43	ENST00000267163	NM_000321.2	66	ata/atAa	2/27	0.64943014623585	1	FACETS	0.961	0.891	1	0.961	0.891	1	CLONAL	1	TRUE	0	0.64943014623585	1		277	305	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911616	134911616	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	35	523	0	ENST00000398015.3:c.2081T>C	p.Met694Thr	p.M694T	ENST00000398015	NM_004441.4	694	aTg/aCg	11/16	1	2	FACETS	0.233	0.19	0.28	0.233	0.19	0.28	SUBCLONAL	1	TRUE	1	0.64943014623585	2		523	463	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139009	37139009	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	49	628	0	ENST00000373509.5:c.349G>T	p.Val117Phe	p.V117F	ENST00000373509	NM_002648.3	117	Gtc/Ttc	4/6	1	2	FACETS	0.2	0.168	0.235	0.2	0.168	0.235	SUBCLONAL	1	TRUE	1	0.64943014623585	2		628	755	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846013	128846013	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765279156	NA	P-0032054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	135	595	0	ENST00000249373.3:c.943G>A	p.Val315Ile	p.V315I	ENST00000249373	NM_005631.4	315	Gtc/Atc	5/12	0.382264552457357	5	FACETS	0.873	0.793	0.958	0.291	0.264	0.32	INDETERMINATE	1	TRUE	2	0.64943014623585	5		595	940	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888695	76888695	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	185	453	0	ENST00000373344.5:c.5134G>A	p.Gly1712Ser	p.G1712S	ENST00000373344	NM_000489.3	1712	Ggc/Agc	19/35	1	2	FACETS	0.998	0.927	1	0.998	0.927	1	CLONAL	1	TRUE	1	0.64943014623585	2		453	571	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239419	105239419	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	110	467	0	ENST00000349310.3:c.968A>G	p.Asp323Gly	p.D323G	ENST00000349310	NM_001014432.1	323	gAc/gGc	12/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.351899606333891	2		467	565	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871798	12871798	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	38	130	0	ENST00000228872.4:c.518del	p.Asn173MetfsTer52	p.N173Mfs*52	ENST00000228872	NM_004064.3	172	gAa/ga	2/3	1	2	FACETS	0.943	0.786	1	0.943	0.786	1	CLONAL	1	TRUE	1	0.351899606333891	2		130	229	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55962511	55962511	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0032068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	19	309	0	ENST00000263923.4:c.2615-2A>G		p.X872_splice	ENST00000263923	NM_002253.2	872			0.351899606333891	1	FACETS	0.259	0.196	0.333	0.259	0.196	0.333	SUBCLONAL	1	TRUE	0	0.351899606333891	1		309	344	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923063	44923063	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0032068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	17	188	0	ENST00000377967.4:c.1923+1G>A		p.X641_splice	ENST00000377967	NM_021140.2	641			1	1	FACETS	0.275	0.205	0.359	0.275	0.205	0.359	SUBCLONAL	1	TRUE	0	0.351899606333891	1		188	289	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0032077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	174	592	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.38808434727227	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.38808434727227	1		592	621	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0032077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	133	348	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.109554045258368	4	FACETS	0.911	0.832	0.994	0.911	0.832	0.994	INDETERMINATE	2	TRUE	2	0.38808434727227	4		348	522	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0032077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	130	407	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.38808434727227	2		407	501	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579533	7579533	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	175	702	2	ENST00000269305.4:c.154C>T	p.Gln52Ter	p.Q52*	ENST00000269305	NM_001126112.2	52	Caa/Taa	4/11	0.196356296865514	2	FACETS	0.915	0.844	0.989	0.915	0.844	0.989	CLONAL	2	TRUE	0	0.231243420127078	2		704	827	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665721	29665721	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0032133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	45	222	0	ENST00000356175.3:c.6757-1G>A		p.X2253_splice	ENST00000356175	NM_000267.3	2253			0.173597114280795	4	FACETS	0.791	0.668	0.925			1	CLONAL	2	TRUE	NA	0.231243420127078	4		222	303	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581314	48581315	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0032133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	55	529	0	ENST00000342988.3:c.618_619del	p.Asn207CysfsTer27	p.N207Cfs*27	ENST00000342988	NM_005359.5	206	tcTAat/tcat	5/12	0.211136735011961	1	FACETS	0.654	0.559	0.759	0.654	0.559	0.759	SUBCLONAL	1	TRUE	0	0.231243420127078	1		529	643	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	50	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.67	0.566	0.784	0.67	0.566	0.784	SUBCLONAL	1	FALSE	1	0.171612840501799	2		341	870	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0032135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	78	262	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.171612840501799	2		262	759	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0032135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	72	640	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	1	2	FACETS	0.997	0.869	1	0.997	0.869	1	CLONAL	1	FALSE	1	0.171612840501799	2		640	842	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052636	42052636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1054243525	NA	P-0032135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	45	557	0	ENST00000219905.7:c.7307G>A	p.Arg2436His	p.R2436H	ENST00000219905	NM_001164273.1	2436	cGt/cAt	20/24	1	2	FACETS	0.614	0.514	0.725	0.614	0.514	0.725	SUBCLONAL	1	FALSE	1	0.171612840501799	2		557	854	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536713	120536713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748118400	NA	P-0032135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	65	661	1	ENST00000229340.5:c.379C>T	p.Arg127Trp	p.R127W	ENST00000229340	NM_006861.6	127	Cgg/Tgg	5/6	1	2	FACETS	0.874	0.756	1	0.874	0.756	1	CLONAL	1	FALSE	1	0.171612840501799	2		662	867	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119750	70119751	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0032135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	43	575	0	ENST00000245479.2:c.754dup	p.Leu252ProfsTer44	p.L252Pfs*44	ENST00000245479	NM_000346.3	251	gac/gaCc	3/3	1	2	FACETS	0.692	0.578	0.82	0.692	0.578	0.82	SUBCLONAL	1	FALSE	1	0.171612840501799	2		575	724	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374866	45374866	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	70	565	0	ENST00000262160.6:c.977A>G	p.Glu326Gly	p.E326G	ENST00000262160	NM_005901.5	326	gAa/gGa	8/11	1	2	FACETS	0.924	0.804	1	0.924	0.804	1	CLONAL	1	FALSE	1	0.171612840501799	2		565	883	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265418	10265418	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	81	683	0	ENST00000340748.4:c.1628A>G	p.Asn543Ser	p.N543S	ENST00000340748		543	aAc/aGc	20/40	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	1	0.171612840501799	2		683	823	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713647	30713649	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0032135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	77	438	0	ENST00000295754.5:c.973_975del	p.Thr325del	p.T325del	ENST00000295754	NM_003242.5	324	atCACc/atc	4/7	0.171612840501799	2	FACETS	0.782	0.687	0.883	0.782	0.687	0.883	SUBCLONAL	2	FALSE	0	0.171612840501799	2		438	574	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403570	138403570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	95	715	0	ENST00000289153.2:c.2212G>A	p.Gly738Arg	p.G738R	ENST00000289153	NM_006219.2	738	Ggg/Agg	15/22	1	2	FACETS	0.954	0.847	1	0.954	0.847	1	CLONAL	1	FALSE	1	0.171612840501799	2		715	1160	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651881	36651881	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0032135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	56	564	1	ENST00000244741.5:c.3G>A	p.Met1?	p.M1?	ENST00000244741	NM_000389.4	1	atG/atA	2/3	1	2	FACETS	0.986	0.844	1	0.986	0.844	1	CLONAL	1	FALSE	1	0.171612840501799	2		565	662	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332892	152332892	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	57	545	2	ENST00000206249.3:c.1198G>T	p.Gly400Trp	p.G400W	ENST00000206249	NM_000125.3	400	Ggg/Tgg	5/8	1	2	FACETS	0.846	0.724	0.98	0.846	0.724	0.98	CLONAL	1	FALSE	1	0.171612840501799	2		547	785	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	8	397	0	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	1	2	FACETS	0.184	0.118	0.271	0.184	0.118	0.271	SUBCLONAL	1	TRUE	1	0.24	2		397	362	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845613	68845619	+	frameshift_variant	Frame_Shift_Del	DEL	ACAGACG	ACAGACG	-	novel	NA	P-0032139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	123	477	0	ENST00000261769.5:c.859_865del	p.Thr287ArgfsTer5	p.T287Rfs*5	ENST00000261769	NM_004360.3	287	ACAGACGcg/cg	7/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.24	2		477	734	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629848	187629848	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	61	704	0	ENST00000441802.2:c.1134A>C	p.Glu378Asp	p.E378D	ENST00000441802	NM_005245.3	378	gaA/gaC	2/27	1	2	FACETS	0.621	0.534	0.715	0.621	0.534	0.715	SUBCLONAL	1	TRUE	1	0.24	2		704	819	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678541	88678541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145157285	NA	P-0032152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	199	328	0	ENST00000360948.2:c.995C>T	p.Thr332Met	p.T332M	ENST00000360948	NM_001012338.2	332	aCg/aTg	9/19	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.656400965768172	2		328	589	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	43	333	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.975	0.832	1	1	0.972	1	CLONAL	2	TRUE	1	0.29	2		333	152	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112769504	112769504	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	49	446	1	ENST00000369452.4:c.1456C>T	p.Leu486Phe	p.L486F	ENST00000369452	NM_007373.3	486	Ctt/Ttt	8/9	0.3	1	FACETS	0.501	0.424	0.586	0.501	0.424	0.586	SUBCLONAL	1	TRUE	0	0.29	1		447	577	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420281	49420292	+	inframe_deletion	In_Frame_Del	DEL	GTAGACCCGCCG	GTAGACCCGCCG	-	novel	NA	P-0032155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	60	568	0	ENST00000301067.7:c.15457_15468del	p.Arg5153_Tyr5156del	p.R5153_Y5156del	ENST00000301067	NM_003482.3	5153	CGGCGGGTCTAC/-	48/54	0.20466710319695	5	FACETS	0.782	0.673	0.902	0.261	0.224	0.301	CLONAL	1	TRUE	2	0.29	5		568	759	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881523	48881523	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	71	250	0	ENST00000267163.4:c.245C>A	p.Ser82Ter	p.S82*	ENST00000267163	NM_000321.2	82	tCa/tAa	2/27	0.249434684647596	4	FACETS	1	0.95	1			1	CLONAL	1	TRUE	NA	0.29	4		250	538	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577588	7577588	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	127	492	0	ENST00000269305.4:c.693del	p.Ile232SerfsTer15	p.I232Sfs*15	ENST00000269305	NM_001126112.2	231	acC/ac	7/11	0.153103985725956	3	FACETS	0.932	0.848	1	0.621	0.565	0.68	INDETERMINATE	2	TRUE	0	0.29	3		492	538	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170002380	170002380	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	66	249	0	ENST00000295797.4:c.1199G>T	p.Cys400Phe	p.C400F	ENST00000295797	NM_002740.5	400	tGt/tTt	12/18	0.161952855302534	3	FACETS	1	0.973	1	0.747	0.652	0.848	INDETERMINATE	1	TRUE	1	0.29	3		249	349	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652083	36652084	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0032155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	221	598	0	ENST00000244741.5:c.209dup	p.Leu71ProfsTer18	p.L71Pfs*18	ENST00000244741	NM_000389.4	69	cgg/cGgg	2/3	0.283075514592202	4	FACETS	0.843	0.787	0.901	0.843	0.787	0.901	CLONAL	3	TRUE	1	0.29	4		598	777	SUCCESS
AR	367	MSKCC	GRCh37	X	66941796	66941796	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	13	387	0	ENST00000374690.3:c.2440T>G	p.Phe814Val	p.F814V	ENST00000374690	NM_000044.3	814	Ttc/Gtc	6/8	0.3	1	FACETS	0.326	0.232	0.441	0.326	0.232	0.441	SUBCLONAL	1	TRUE	0	0.29	1		387	235	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0032160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	27	457	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	0.641	0.508	0.794	0.641	0.508	0.794	SUBCLONAL	1	TRUE	1	0.12	2		457	702	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0032160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	27	437	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			1	2	FACETS	0.833	0.662	1	0.833	0.662	1	CLONAL	1	TRUE	1	0.12	2		437	540	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373293	118373293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	23	350	0	ENST00000534358.1:c.6686C>T	p.Ser2229Leu	p.S2229L	ENST00000534358	NM_005933.3	2229	tCa/tTa	27/36	1	2	FACETS	0.937	0.73	1	0.937	0.73	1	CLONAL	1	TRUE	1	0.12	2		350	409	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373312	118373313	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	T	novel	NA	P-0032160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	23	352	0	ENST00000534358.1:c.6705_6706delinsT	p.Ala2236LeufsTer10	p.A2236Lfs*10	ENST00000534358	NM_005933.3	2235	acCGct/acTct	27/36	1	2	FACETS	0.924	0.719	1	0.924	0.719	1	CLONAL	1	TRUE	1	0.12	2		352	415	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0032161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	143	604	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.3126790940093	4	FACETS	0.937	0.858	1	0.937	0.858	1	CLONAL	2	TRUE	2	0.351381815227655	4		604	587	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220382	1220382	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	228	467	0	ENST00000326873.7:c.475C>T	p.Gln159Ter	p.Q159*	ENST00000326873	NM_000455.4	159	Cag/Tag	4/10	0.276636458361078	3	FACETS	1	0.987	1	0.8	0.75	0.851	CLONAL	2	TRUE	0	0.351381815227655	3		467	636	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687566	29687566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144178015	NA	P-0032161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	97	500	1	ENST00000356175.3:c.8159C>T	p.Thr2720Met	p.T2720M	ENST00000356175	NM_000267.3	2720	aCg/aTg	56/57	0.285590416244635	3	FACETS	0.917	0.818	1	0.458	0.409	0.511	CLONAL	1	TRUE	1	0.351381815227655	3		501	708	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292749	91292749	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	101	428	0	ENST00000355112.3:c.251A>G	p.Gln84Arg	p.Q84R	ENST00000355112	NM_000057.2	84	cAa/cGa	3/22	0.285590416244635	3	FACETS	1	0.929	1	0.524	0.469	0.582	CLONAL	1	TRUE	1	0.351381815227655	3		428	645	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602478	10602478	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	236	468	0	ENST00000171111.5:c.1100del	p.Gly367AlafsTer33	p.G367Afs*33	ENST00000171111	NM_203500.1	367	gGc/gc	3/6	0.276636458361078	3	FACETS	0.917	0.863	0.972	0.917	0.863	0.972	CLONAL	3	TRUE	0	0.351381815227655	3		468	574	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132572	11132572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	259	682	1	ENST00000358026.2:c.2788C>T	p.Pro930Ser	p.P930S	ENST00000358026	NM_001128849.1	930	Ccc/Tcc	19/36	0.276636458361078	3	FACETS	1	0.982	1	0.739	0.695	0.784	CLONAL	2	TRUE	0	0.351381815227655	3		683	782	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031894	26031894	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	46	222	0	ENST00000244661.2:c.395G>C	p.Arg132Pro	p.R132P	ENST00000244661	NM_003537.3	132	cGc/cCc	1/1	1	2	FACETS	0.823	0.697	0.962	0.823	0.697	0.962	CLONAL	1	TRUE	1	0.351381815227655	2		222	318	SUCCESS
AR	367	MSKCC	GRCh37	X	66765466	66765466	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	209	648	0	ENST00000374690.3:c.478G>T	p.Ala160Ser	p.A160S	ENST00000374690	NM_000044.3	160	Gcc/Tcc	1/8	0.253326745924879	4	FACETS	0.925	0.86	0.992	0.925	0.86	0.992	CLONAL	2	TRUE	2	0.351381815227655	4		648	869	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061249	38061249	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	111	526	0	ENST00000250448.2:c.740A>G	p.His247Arg	p.H247R	ENST00000250448	NM_004496.3	247	cAc/cGc	2/2	1	2	FACETS	0.876	0.787	0.969	0.876	0.787	0.969	CLONAL	1	TRUE	1	0.330482814934646	2		526	767	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095620	178095620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	105	487	0	ENST00000397062.3:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000397062	NM_006164.4	571	Gaa/Aaa	5/5	0.330482814934646	7	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.330482814934646	7		487	817	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420637	49420637	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	115	522	0	ENST00000301067.7:c.15112G>T	p.Glu5038Ter	p.E5038*	ENST00000301067	NM_003482.3	5038	Gag/Tag	48/54	0.134159172995614	3	FACETS	0.976	0.879	1	0.488	0.439	0.54	INDETERMINATE	1	TRUE	1	0.330482814934646	3		522	831	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576250	7577272	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AACCTCATCTCTACTAAAAAAAAAAATAAATAAATAACAAAAAATTAGCTGGGCGTCGGGGCAGGTGCCTGTAATCCCAGCTACTCAGTGGGCTGAGGCAGGAGAATCGCTTGAACCCAGAAGGCGGAGGTTGCAGTGAGCCGAGATCCCGCCACTGCACTCCAGCCTGGGTGACAGAGTGAGACTCTGTCTCCAAAAAAAAAAAAAAAAAAAGCAGGCTAGGCTAAGCTATGATGTTCCTTAGATTAGGTGTATTAAATCCATTTTCAACTTACAATATTTTCAACTTACGACGAGTTTATCAGGAAGTAACACCATCGTAAGTCAAGTAGCATCTGTATCAGGCAAAGTCATAGAACCATTTTCATGCTCTCTTTAACAATTTTCTTTTTGAAAGCTGGTCTGGTCCTTTAAAATATATATTATGGTATAAGTTGGTGTTCTGAAGTTAGTTAGCTACAACCAGGAGCCATTGTCTTTGAGGCATCACTGCCCCCTGATGGCAAATGCCCCAATTGCAGGTAAAACAGTCAAGAAGAAAACGGCATTTTGAGTGTTAGACTGGAAACTTTCCACTTGATAAGAGGTCCCAAGACTTAGTACCTGAAGGGTGAAATATTCTCCATCCAGTGGTTTCTTCTTTGGCTGGGGAGAGGAGCTGGTGTTGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAAAGTGAATCTGAGGCATAACTGCACCCTTGGTCTCCTCCACCGCTTCTTGTCCTGCTTGCTTACCTCGCTTAGTGCTCCCTGGGGGCAGCTCGTGGTGAGGCTCCCCTTTCTTGCGGAGATTCTCTTCCTCTGTGCGCCGGTCTCTCCCAGGACAGGCACAAACACGCACCTCAAAGCTGTTCCGTCCCAGTAGATTACCACTACTCAGGATAGGAAAAGAGAAGCAAGAGGCAGTAAGGAAATCAGGTCCTACCTGTCCCATTTAAAAAACCAGGCTCCATCTACTCCCAACCACCCTTGTCCTTTCTGGAGCCTAA	AACCTCATCTCTACTAAAAAAAAAAATAAATAAATAACAAAAAATTAGCTGGGCGTCGGGGCAGGTGCCTGTAATCCCAGCTACTCAGTGGGCTGAGGCAGGAGAATCGCTTGAACCCAGAAGGCGGAGGTTGCAGTGAGCCGAGATCCCGCCACTGCACTCCAGCCTGGGTGACAGAGTGAGACTCTGTCTCCAAAAAAAAAAAAAAAAAAAGCAGGCTAGGCTAAGCTATGATGTTCCTTAGATTAGGTGTATTAAATCCATTTTCAACTTACAATATTTTCAACTTACGACGAGTTTATCAGGAAGTAACACCATCGTAAGTCAAGTAGCATCTGTATCAGGCAAAGTCATAGAACCATTTTCATGCTCTCTTTAACAATTTTCTTTTTGAAAGCTGGTCTGGTCCTTTAAAATATATATTATGGTATAAGTTGGTGTTCTGAAGTTAGTTAGCTACAACCAGGAGCCATTGTCTTTGAGGCATCACTGCCCCCTGATGGCAAATGCCCCAATTGCAGGTAAAACAGTCAAGAAGAAAACGGCATTTTGAGTGTTAGACTGGAAACTTTCCACTTGATAAGAGGTCCCAAGACTTAGTACCTGAAGGGTGAAATATTCTCCATCCAGTGGTTTCTTCTTTGGCTGGGGAGAGGAGCTGGTGTTGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAAAGTGAATCTGAGGCATAACTGCACCCTTGGTCTCCTCCACCGCTTCTTGTCCTGCTTGCTTACCTCGCTTAGTGCTCCCTGGGGGCAGCTCGTGGTGAGGCTCCCCTTTCTTGCGGAGATTCTCTTCCTCTGTGCGCCGGTCTCTCCCAGGACAGGCACAAACACGCACCTCAAAGCTGTTCCGTCCCAGTAGATTACCACTACTCAGGATAGGAAAAGAGAAGCAAGAGGCAGTAAGGAAATCAGGTCCTACCTGTCCCATTTAAAAAACCAGGCTCCATCTACTCCCAACCACCCTTGTCCTTTCTGGAGCCTAA	-	novel	NA	P-0032187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	33	6	0	ENST00000269305.4:c.783-116_993+604del		p.X261_splice	ENST00000269305	NM_001126112.2	261		8-9/11	0.306543488978506	2	FACETS	0.999	0.904	1	1	0.976	1	CLONAL	5	TRUE	0	0.330482814934646	2		6	40	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278061	18278061	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	128	577	0	ENST00000222254.8:c.1681A>T	p.Asn561Tyr	p.N561Y	ENST00000222254	NM_005027.3	561	Aac/Tac	13/16	1	2	FACETS	0.775	0.701	0.852	0.775	0.701	0.852	SUBCLONAL	1	TRUE	1	0.330482814934646	2		577	1000	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277990	41278077	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTAAGTAAAAAGGAACCAAAGCCTTTAGCAGATGTGTACATTGAAGTCTCAGTTTTTCCTCAAGGGCCTTTTTCTCCTTGTCTCTTA	GGTAAGTAAAAAGGAACCAAAGCCTTTAGCAGATGTGTACATTGAAGTCTCAGTTTTTCCTCAAGGGCCTTTTTCTCCTTGTCTCTTA	-	novel	NA	P-0032187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	61	373	0	ENST00000349496.5:c.1954+1_1955-1del		p.X652_splice	ENST00000349496	NM_001904.3	652		12/15	0.330482814934646	1	FACETS	0.664	0.574	0.762	0.664	0.574	0.762	SUBCLONAL	1	TRUE	0	0.330482814934646	1		373	464	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41279567	41280589	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTATGTGTCTCATATTTCTCGATTAACTCCAGATCAAGCTAAAGTTCTAAAACTTTTATCAGAAGAGCCGGTTTGCTCATCTGGGAAACCAGTGTTGGCAGAAAAGTAGTGGCTTCAATTAAAAGCAGTTCTTAAATTCCAGTCAGCAACAGTATCTTTAATGGAGCACAGGGAATTCAGAGCCACACAATGAGTAGCAGTAGGATTACACCACCAACAAATACATGCTACTGCTAGGCCTCTGCAGTGCAGGATGTTACAATTTACCTGGCTTTTTATTCTCTTTTTGGCCAGAGGACTCATAATACCTTTGTCTACAAGCTACCCAAGGAAGATAGGAAAACTCCTGTTTCTAGGCTCAGATCTCGGGTGGGTTTTTACATAGTTGCATTATCATCAGGGTTTTCTTGAAAAGCTAATTTAAATCTGGGTAATGAACATGGAGGATGGCATAGACCACTAACAATTATAACTGTCTTACATTTATAACCGCATCTGCTTCTACCTAATTATGAAACCACTAAAGCGCAGATTCTTACTGTGAGAAATAACATGTCAACCCTAAGATAAAATATGTTGAGGTTTCATGGAAATAGTGCCTTTCCTTAGTACTTTTGTGGGTGTCACTTGGCCTTTTTGTCAAGATAGATTACACCTGCCAGACCTCATTATTGTCTTAATCCTCCTTCCCATGACTTCTCACTGCCTAGGTGGTCACACAGTAGATTCCTGCTTCTTCTCCTCGGGAACCCCAAGTCTCTTGACAGGGGTAAATGCAGAGTGTTCAGGGTTAGACTAATGATGTGACTAGGCCCTGCTGGTGTGCCTGTCTGATGGAAATAGATGTTATTTGTGTAGTCTCATGGGTGGCCTGGCACTGAGTAATTACTTGGCTAAAGAAAGCTGGAGGTTGAAGAGGCTAGAAAGCGTTGTTTTCTGACAAGTTTGCTGCTGAACTTTGGATGCCCTAACCTCAGTGTTAACGTCTATGTCTGCTTCTCTCCTCTCTCTTTTGCCTTCCT	GGTATGTGTCTCATATTTCTCGATTAACTCCAGATCAAGCTAAAGTTCTAAAACTTTTATCAGAAGAGCCGGTTTGCTCATCTGGGAAACCAGTGTTGGCAGAAAAGTAGTGGCTTCAATTAAAAGCAGTTCTTAAATTCCAGTCAGCAACAGTATCTTTAATGGAGCACAGGGAATTCAGAGCCACACAATGAGTAGCAGTAGGATTACACCACCAACAAATACATGCTACTGCTAGGCCTCTGCAGTGCAGGATGTTACAATTTACCTGGCTTTTTATTCTCTTTTTGGCCAGAGGACTCATAATACCTTTGTCTACAAGCTACCCAAGGAAGATAGGAAAACTCCTGTTTCTAGGCTCAGATCTCGGGTGGGTTTTTACATAGTTGCATTATCATCAGGGTTTTCTTGAAAAGCTAATTTAAATCTGGGTAATGAACATGGAGGATGGCATAGACCACTAACAATTATAACTGTCTTACATTTATAACCGCATCTGCTTCTACCTAATTATGAAACCACTAAAGCGCAGATTCTTACTGTGAGAAATAACATGTCAACCCTAAGATAAAATATGTTGAGGTTTCATGGAAATAGTGCCTTTCCTTAGTACTTTTGTGGGTGTCACTTGGCCTTTTTGTCAAGATAGATTACACCTGCCAGACCTCATTATTGTCTTAATCCTCCTTCCCATGACTTCTCACTGCCTAGGTGGTCACACAGTAGATTCCTGCTTCTTCTCCTCGGGAACCCCAAGTCTCTTGACAGGGGTAAATGCAGAGTGTTCAGGGTTAGACTAATGATGTGACTAGGCCCTGCTGGTGTGCCTGTCTGATGGAAATAGATGTTATTTGTGTAGTCTCATGGGTGGCCTGGCACTGAGTAATTACTTGGCTAAAGAAAGCTGGAGGTTGAAGAGGCTAGAAAGCGTTGTTTTCTGACAAGTTTGCTGCTGAACTTTGGATGCCCTAACCTCAGTGTTAACGTCTATGTCTGCTTCTCTCCTCTCTCTTTTGCCTTCCT	-	novel	NA	P-0032187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	56	440	0	ENST00000349496.5:c.2137_2138-36del		p.X713_splice	ENST00000349496	NM_001904.3	713		14/15	0.330482814934646	1	FACETS	0.545	0.467	0.63	0.545	0.467	0.63	SUBCLONAL	1	TRUE	0	0.330482814934646	1		440	519	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518086	187518086	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	109	538	0	ENST00000441802.2:c.12608G>T	p.Arg4203Leu	p.R4203L	ENST00000441802	NM_005245.3	4203	cGt/cTt	25/27	0.330482814934646	1	FACETS	0.963	0.867	1	0.963	0.867	1	CLONAL	1	TRUE	0	0.330482814934646	1		538	572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0032188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	132	405	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.19057893206508	2	FACETS	0.904	0.822	0.991	0.904	0.822	0.991	CLONAL	2	TRUE	0	0.19057893206508	2		406	766	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984914	9984914	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	38	459	0	ENST00000330684.3:c.1051A>G	p.Thr351Ala	p.T351A	ENST00000330684	NM_001134407.1	351	Act/Gct	4/13	0.155022747650213	3	FACETS	0.657	0.542	0.786	0.328	0.271	0.393	SUBCLONAL	1	TRUE	1	0.19057893206508	3		459	665	SUCCESS
APC	324	MSKCC	GRCh37	5	112175900	112175901	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0032188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	55	208	0	ENST00000257430.4:c.4610dup	p.Glu1538ArgfsTer6	p.E1538Rfs*6	ENST00000257430	NM_000038.5	1537	aca/aCca	16/16	0.19057893206508	2	FACETS	0.962	0.829	1	0.962	0.829	1	CLONAL	2	TRUE	0	0.19057893206508	2		208	300	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939182	131939182	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0032188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	84	436	2	ENST00000265335.6:c.2397+1G>C		p.X799_splice	ENST00000265335		799			0.19057893206508	2	FACETS	0.973	0.863	1	0.973	0.863	1	CLONAL	2	TRUE	0	0.19057893206508	2		438	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0032189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	155	618	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.239404953462594	2	FACETS	0.907	0.833	0.983	0.907	0.833	0.983	CLONAL	2	TRUE	0	0.265430437695851	2		618	644	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491389	18491390	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	96	204	0	ENST00000266497.5:c.1309dup	p.Ile437AsnfsTer19	p.I437Nfs*19	ENST00000266497		434	-/A	8/31	0.216620284538889	3	FACETS	0.969	0.868	1	0.969	0.868	1	CLONAL	2	TRUE	1	0.265430437695851	3		204	423	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11270931	11270931	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	71	312	0	ENST00000361445.4:c.3594del	p.Leu1199TrpfsTer32	p.L1199Wfs*32	ENST00000361445	NM_004958.3	1198	gtT/gt	24/58	1	2	FACETS	0.902	0.788	1	0.902	0.788	1	CLONAL	1	TRUE	1	0.265430437695851	2		312	593	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127769	64127770	+	missense_variant	Missense_Mutation	DNP	GT	GT	TG	novel	NA	P-0032189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	95	377	0	ENST00000334205.4:c.262_263delinsTG	p.Val88Trp	p.V88W	ENST00000334205	NM_003942.2	88	GTg/TGg	3/17	0.239404953462594	2	FACETS	1	0.98	1	0.723	0.646	0.804	CLONAL	1	TRUE	0	0.265430437695851	2		377	495	SUCCESS
APC	324	MSKCC	GRCh37	5	112163698	112163698	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	28	245	0	ENST00000257430.4:c.1621del	p.Gln541SerfsTer8	p.Q541Sfs*8	ENST00000257430	NM_000038.5	541	Cag/ag	13/16	1	2	FACETS	0.67	0.536	0.822	0.67	0.536	0.822	SUBCLONAL	1	TRUE	1	0.265430437695851	2		245	315	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	51	473	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.189256438787376	3	FACETS	0.883	0.751	1	0.883	0.751	1	CLONAL	2	TRUE	1	0.12	3		473	510	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0032190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	32	547	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	1	2	FACETS	0.56	0.453	0.683	0.56	0.453	0.683	SUBCLONAL	1	TRUE	1	0.12	2		547	952	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295222	1295222	+	upstream_gene_variant	5'Flank	SNP	C	C	A	rs907929058	NA	P-0032190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	41	218	0				ENST00000310581	NM_198253.2	-/1132			0.189256438787376	3	FACETS	0.924	0.771	1	0.924	0.771	1	CLONAL	2	TRUE	1	0.12	3		218	392	SUCCESS
AR	367	MSKCC	GRCh37	X	66765142	66765142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747293337	NA	P-0032191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	49	139	0	ENST00000374690.3:c.154G>A	p.Ala52Thr	p.A52T	ENST00000374690	NM_000044.3	52	Gcc/Acc	1/8	1	1	FACETS	0.984	0.85	1	1	0.976	1	CLONAL	2	TRUE	0	0.28	1		139	153	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0032191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	43	250	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.753	0.631	0.887	0.753	0.631	0.887	SUBCLONAL	1	TRUE	1	0.28	2		250	408	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0032191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	120	311	6	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.297300329682666	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.28	1		317	683	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735407	204735407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs606231422	NA	P-0032191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	80	309	0	ENST00000302823.3:c.208C>T	p.Arg70Trp	p.R70W	ENST00000302823	NM_005214.4	70	Cgg/Tgg	2/4	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.28	2		309	462	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593504	48593504	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	68	310	0	ENST00000342988.3:c.1255G>A	p.Gly419Arg	p.G419R	ENST00000342988	NM_005359.5	419	Ggg/Agg	10/12	0.297300329682666	1	FACETS	0.926	0.808	1	0.926	0.808	1	CLONAL	1	TRUE	0	0.28	1		310	451	SUCCESS
APC	324	MSKCC	GRCh37	5	112128175	112128175	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	32	295	0	ENST00000257430.4:c.679del	p.Asp227ThrfsTer66	p.D227Tfs*66	ENST00000257430	NM_000038.5	226	aaG/aa	7/16	1	2	FACETS	0.417	0.338	0.507	0.417	0.338	0.507	SUBCLONAL	1	TRUE	1	0.28	2		295	548	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	299	409	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.623480571092104	2	FACETS	0.993	0.95	1	0.993	0.95	1	CLONAL	2	TRUE	0	0.623480571092104	2		409	483	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950724	79950725	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCGCAGCGC	rs1554066076	NA	P-0032192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	10	176	1	ENST00000265081.6:c.181_189dup	p.Ala61_Pro63dup	p.A61_P63dup	ENST00000265081	NM_002439.4	61	gcc/gCCGCAGCGCcc	1/24	0.623480571092104	1	FACETS	0.219	0.149	0.304	0.219	0.149	0.304	SUBCLONAL	1	TRUE	0	0.623480571092104	1		177	101	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	348	473	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.232128734352214	8	FACETS	1	0.953	1			1	CLONAL	5	TRUE	NA	0.232128734352214	8		473	1012	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0032195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	109	555	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.232128734352214	2		557	726	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0032195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	36	162	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	0.232128734352214	1	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	0	0.232128734352214	1		162	241	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604776	48604776	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs377767382	NA	P-0032195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	98	335	0	ENST00000342988.3:c.1598T>C	p.Leu533Pro	p.L533P	ENST00000342988	NM_005359.5	533	cTc/cCc	12/12	1	2	FACETS	0.831	0.744	0.923	1	0.984	1	CLONAL	2	TRUE	1	0.232128734352214	2		335	508	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0032214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	59	779	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		779	281	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732969	30732969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893810	NA	P-0032227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	22	329	1	ENST00000295754.5:c.1582C>T	p.Arg528Cys	p.R528C	ENST00000295754	NM_003242.5	528	Cgt/Tgt	7/7	0.281322127286135	1	FACETS	0.644	0.501	0.807	0.644	0.501	0.807	SUBCLONAL	1	TRUE	0	0.28	1		330	210	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164508	47164508	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs201756643	NA	P-0032227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	31	420	0	ENST00000409792.3:c.1618C>T	p.Arg540Ter	p.R540*	ENST00000409792	NM_014159.6	540	Cga/Tga	3/21	0.281322127286135	1	FACETS	0.7	0.568	0.848	0.7	0.568	0.848	SUBCLONAL	1	TRUE	0	0.28	1		420	272	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761468	59761468	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781622986	NA	P-0032227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	48	423	0	ENST00000259008.2:c.2939C>T	p.Ala980Val	p.A980V	ENST00000259008	NM_032043.2	980	gCa/gTa	20/20	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.28	2		423	339	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490422	20490422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	20	430	0	ENST00000346618.3:c.1159C>T	p.His387Tyr	p.H387Y	ENST00000346618	NM_001949.4	387	Cat/Tat	7/7	0.233569894822204	3	FACETS	0.498	0.381	0.636	0.249	0.19	0.318	SUBCLONAL	1	TRUE	1	0.28	3		430	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577575	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782289	NA	P-0032230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	228	579	0	ENST00000269305.4:c.706T>C	p.Tyr236His	p.Y236H	ENST00000269305	NM_001126112.2	236	Tac/Cac	7/11	0.200208183641131	3	FACETS	0.839	0.784	0.896	0.839	0.784	0.896	CLONAL	3	TRUE	0	0.263065287637086	3		579	779	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602967	55602967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	19	266	0	ENST00000288135.5:c.2677G>A	p.Glu893Lys	p.E893K	ENST00000288135	NM_000222.2	893	Gaa/Aaa	19/21	1	2	FACETS	0.41	0.311	0.528	0.41	0.311	0.528	SUBCLONAL	1	TRUE	1	0.263065287637086	2		266	352	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991999	72991999	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0032230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	44	558	0	ENST00000268489.5:c.2046C>G	p.Tyr682Ter	p.Y682*	ENST00000268489	NM_006885.3	682	taC/taG	2/10	1	2	FACETS	0.691	0.58	0.815	0.691	0.58	0.815	SUBCLONAL	1	TRUE	1	0.263065287637086	2		558	484	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	46	792	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.195019737293731	2	FACETS	1	0.95	1	0.65	0.553	0.755	CLONAL	1	TRUE	0	0.32	2		796	221	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501461	149501461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751904503	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	48	558	0	ENST00000261799.4:c.2326G>A	p.Asp776Asn	p.D776N	ENST00000261799	NM_002609.3	776	Gat/Aat	16/23	0.3	1	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	0	0.32	1		558	242	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	28	434	2	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	0.792	0.637	0.967	0.792	0.637	0.967	CLONAL	1	TRUE	1	0.32	2		436	221	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	27	551	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	1	0.821	1	1	0.821	1	CLONAL	1	TRUE	1	0.32	2		551	165	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	66	714	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.787	0.691	0.889	1	0.976	1	SUBCLONAL	2	TRUE	1	0.32	2		714	262	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578177	7578177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs267605076	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	50	471	0	ENST00000269305.4:c.672G>T	p.Glu224Asp	p.E224D	ENST00000269305	NM_001126112.2	224	gaG/gaT	6/11	0.221637423070748	1	FACETS	0.844	0.72	0.978	0.844	0.72	0.978	CLONAL	1	TRUE	0	0.32	1		471	311	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729968	30729968	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs863223852	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	26	239	0	ENST00000295754.5:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000295754	NM_003242.5	497	Cga/Tga	6/7	0.172774995021055	3	FACETS	0.769	0.612	0.949	0.385	0.306	0.475	INDETERMINATE	1	TRUE	1	0.32	3		239	245	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74000769	74000769	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369418465	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	32	519	2	ENST00000318443.5:c.1459G>A	p.Val487Met	p.V487M	ENST00000318443	NM_001024736.1	487	Gtg/Atg	7/10	1	2	FACETS	0.604	0.491	0.731	0.604	0.491	0.731	SUBCLONAL	1	TRUE	1	0.32	2		521	331	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371801	55371801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746536924	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	23	144	0	ENST00000297316.4:c.491C>T	p.Ala164Val	p.A164V	ENST00000297316	NM_022454.3	164	gCg/gTg	2/2	1	2	FACETS	0.946	0.76	1	1	0.948	1	CLONAL	2	TRUE	1	0.32	2		144	76	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118924	70118926	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	68	517	0	ENST00000245479.2:c.499_501del	p.Lys167del	p.K167del	ENST00000245479	NM_000346.3	166	AAG/-	2/3	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.32	2		517	334	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873081	134873081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	29	478	3	ENST00000398015.3:c.1385G>A	p.Gly462Asp	p.G462D	ENST00000398015	NM_004441.4	462	gGc/gAc	6/16	0.3	1	FACETS	0.677	0.546	0.823	0.677	0.546	0.823	SUBCLONAL	1	TRUE	0	0.32	1		481	225	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913836	32913837	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359507	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	30	362	0	ENST00000380152.3:c.5351dup	p.Asn1784LysfsTer3	p.N1784Kfs*3	ENST00000380152		1782	caa/cAaa	11/27	0.172774995021055	3	FACETS	1	0.859	1	0.536	0.435	0.648	INDETERMINATE	1	TRUE	1	0.32	3		362	203	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793054	33793056	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs747773004	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	10	217	0	ENST00000498907.2:c.265_267del	p.Glu89del	p.E89del	ENST00000498907	NM_004364.3	89	GAG/-	1/1	0.221637423070748	1	FACETS	0.505	0.344	0.703	0.505	0.344	0.703	SUBCLONAL	1	TRUE	0	0.32	1		217	104	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298723	46298724	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	30	257	0	ENST00000334344.6:c.5371_5372del	p.Lys1791GlufsTer3	p.K1791Efs*3	ENST00000334344	NM_152641.2	1790	ttAAag/ttag	21/21	0.172774995021055	3	FACETS	1	0.942	1	0.73	0.596	0.877	INDETERMINATE	1	TRUE	1	0.32	3		257	149	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170147	32170147	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	24	597	2	ENST00000375023.3:c.3461del	p.Gly1154AlafsTer150	p.G1154Afs*150	ENST00000375023	NM_004557.3	1154	gGc/gc	21/30	0.221637423070748	1	FACETS	0.458	0.36	0.571	0.458	0.36	0.571	SUBCLONAL	1	TRUE	0	0.32	1		599	275	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120805882	120805882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	58	557	1	ENST00000257552.2:c.196G>A	p.Val66Ile	p.V66I	ENST00000257552	NM_002442.3	66	Gtc/Atc	4/15	0.221637423070748	1	FACETS	0.848	0.732	0.973	0.848	0.732	0.973	CLONAL	1	TRUE	0	0.32	1		558	359	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970971	21970971	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	61	486	0	ENST00000304494.5:c.387C>G	p.Tyr129Ter	p.Y129*	ENST00000304494	NM_000077.4	129	taC/taG	2/3	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.32	2		486	331	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941486	71941486	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	55	611	0	ENST00000298229.2:c.1171A>G	p.Lys391Glu	p.K391E	ENST00000298229	NM_001567.3	391	Aag/Gag	10/28	0.3	1	FACETS	0.785	0.674	0.905	0.785	0.674	0.905	CLONAL	1	TRUE	0	0.32	1		611	368	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378639	25378639	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	53	505	0	ENST00000311936.3:c.359T>C	p.Leu120Ser	p.L120S	ENST00000311936	NM_004985.3	120	tTg/tCg	4/5	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.32	2		505	246	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123891	46123892	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	28	225	0	ENST00000334344.6:c.159_160del	p.Arg53SerfsTer12	p.R53Sfs*12	ENST00000334344	NM_152641.2	53	AGa/a	2/21	0.172774995021055	3	FACETS	0.829	0.665	1	0.414	0.332	0.507	INDETERMINATE	1	TRUE	1	0.32	3		225	245	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964084	28964084	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	24	463	0	ENST00000282397.4:c.1818G>T	p.Lys606Asn	p.K606N	ENST00000282397	NM_002019.4	606	aaG/aaT	13/30	0.3	1	FACETS	0.724	0.572	0.896	0.724	0.572	0.896	SUBCLONAL	1	TRUE	0	0.32	1		463	174	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823801	3823801	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1260458096	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	39	372	0	ENST00000262367.5:c.2414C>T	p.Ala805Val	p.A805V	ENST00000262367	NM_004380.2	805	gCg/gTg	13/31	1	2	FACETS	0.762	0.634	0.904	0.762	0.634	0.904	CLONAL	1	TRUE	1	0.32	2		372	320	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004808	16004808	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs76080188	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	51	538	1	ENST00000268712.3:c.2446G>A	p.Ala816Thr	p.A816T	ENST00000268712	NM_006311.3	816	Gct/Act	20/46	0.221637423070748	1	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	0	0.32	1		539	254	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56409168	56409168	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	35	426	0	ENST00000348428.3:c.1675G>T	p.Ala559Ser	p.A559S	ENST00000348428	NM_006785.3	559	Gca/Tca	14/17	0.172774995021055	3	FACETS	1	0.907	1	0.579	0.478	0.691	INDETERMINATE	1	TRUE	1	0.32	3		426	219	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140378	50140378	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368625677	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	33	356	0	ENST00000246792.3:c.163G>A	p.Val55Met	p.V55M	ENST00000246792	NM_006270.3	55	Gtg/Atg	2/6	0.221637423070748	1	FACETS	0.585	0.478	0.705	0.585	0.478	0.705	SUBCLONAL	1	TRUE	0	0.32	1		356	296	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474012	29474012	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	30	613	0	ENST00000389048.3:c.2163A>C	p.Lys721Asn	p.K721N	ENST00000389048	NM_004304.4	721	aaA/aaC	12/29	0.3	0	FACETS	0.508	0.411	0.617			1	SUBCLONAL	1	TRUE	0	0.32	0		613	251	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564470	55564470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	32	351	0	ENST00000288135.5:c.358G>A	p.Val120Ile	p.V120I	ENST00000288135	NM_000222.2	120	Gtt/Att	3/21	0.221637423070748	1	FACETS	0.812	0.664	0.975	0.812	0.664	0.975	CLONAL	1	TRUE	0	0.32	1		351	207	SUCCESS
APC	324	MSKCC	GRCh37	5	112174990	112174996	+	frameshift_variant	Frame_Shift_Del	DEL	AAGTTCT	AAGTTCT	-	novel	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	17	200	0	ENST00000257430.4:c.3699_3705del	p.Ser1234HisfsTer29	p.S1234Hfs*29	ENST00000257430	NM_000038.5	1233	ccAAGTTCT/cc	16/16	0.195019737293731	2	FACETS	1	0.852	1	0.59	0.448	0.752	CLONAL	1	TRUE	0	0.32	2		200	90	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680172	30680172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	61	658	0	ENST00000376406.3:c.1547C>T	p.Ser516Phe	p.S516F	ENST00000376406	NM_014641.2	516	tCc/tTc	5/15	0.3	3	FACETS	1	0.895	1			1	CLONAL	1	TRUE	NA	0.32	3		658	425	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187531	32187531	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769779477	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	23	565	1	ENST00000375023.3:c.1348G>A	p.Gly450Ser	p.G450S	ENST00000375023	NM_004557.3	450	Ggt/Agt	8/30	0.221637423070748	1	FACETS	0.414	0.323	0.518	0.414	0.323	0.518	SUBCLONAL	1	TRUE	0	0.32	1		566	292	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813532	32813532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747716612	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	63	326	0	ENST00000354258.4:c.2251C>T	p.Arg751Trp	p.R751W	ENST00000354258	NM_000593.5	751	Cgg/Tgg	11/11	0.172288079270222	4	FACETS	1	0.967	1	0.693	0.602	0.791	INDETERMINATE	1	TRUE	2	0.32	4		326	375	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339709	116339709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs530932258	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	47	292	0	ENST00000397752.3:c.571C>T	p.Arg191Trp	p.R191W	ENST00000397752	NM_000245.2	191	Cgg/Tgg	2/21	0.130224969414108	4	FACETS	0.818	0.697	0.949	0.818	0.697	0.949	INDETERMINATE	2	TRUE	2	0.32	4		292	237	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955584	90955584	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	26	367	0	ENST00000265433.3:c.2081C>A	p.Pro694His	p.P694H	ENST00000265433	NM_002485.4	694	cCt/cAt	14/16	1	2	FACETS	0.825	0.658	1	0.825	0.658	1	CLONAL	1	TRUE	1	0.32	2		367	197	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460511	8460511	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	20	417	1	ENST00000356435.5:c.3775C>T	p.Pro1259Ser	p.P1259S	ENST00000356435		1259	Cca/Tca	22/35	1	2	FACETS	0.41	0.313	0.523	0.41	0.313	0.523	SUBCLONAL	1	TRUE	1	0.32	2		418	305	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114905849	114905849	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	12	342	0	ENST00000543371.1:c.868A>G	p.Met290Val	p.M290V	ENST00000543371	NM_001198531.1	290	Atg/Gtg	8/14	0.3	1	FACETS	0.281	0.197	0.384	0.281	0.197	0.384	SUBCLONAL	1	TRUE	0	0.32	1		342	224	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434898	110434898	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	44	727	0	ENST00000375856.3:c.3503A>G	p.Asn1168Ser	p.N1168S	ENST00000375856	NM_003749.2	1168	aAc/aGc	1/2	0.172774995021055	3	FACETS	0.881	0.741	1	0.441	0.37	0.518	INDETERMINATE	1	TRUE	1	0.32	3		727	362	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996131	73996131	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	27	686	1	ENST00000318443.5:c.865G>T	p.Asp289Tyr	p.D289Y	ENST00000318443	NM_001024736.1	289	Gac/Tac	5/10	1	2	FACETS	0.662	0.528	0.813	0.662	0.528	0.813	SUBCLONAL	1	TRUE	1	0.32	2		687	255	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030080	36030080	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	32	401	0	ENST00000358208.4:c.1115A>G	p.Gln372Arg	p.Q372R	ENST00000358208		372	cAg/cGg	9/12	0.172288079270222	4	FACETS	1	0.881	1	0.555	0.453	0.668	INDETERMINATE	1	TRUE	2	0.32	4		401	238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0032260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	155	257	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.444774637323282	2	FACETS	0.995	0.925	1	0.995	0.925	1	CLONAL	2	TRUE	0	0.463750666252055	2		257	336	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481806	56481806	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	148	499	0	ENST00000267101.3:c.734C>T	p.Ala245Val	p.A245V	ENST00000267101	NM_001982.3	245	gCc/gTc	7/28	0.382137979264221	3	FACETS	0.929	0.857	1	0.929	0.857	1	CLONAL	2	TRUE	1	0.463750666252055	3		499	423	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696730	47696730	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	169	311	0	ENST00000347630.2:c.218C>G	p.Pro73Arg	p.P73R	ENST00000347630	NM_001007230.1	73	cCc/cGc	5/11	0.464289834617494	3	FACETS	0.855	0.799	0.911	0.855	0.799	0.911	CLONAL	3	TRUE	0	0.463750666252055	3		311	350	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	95	473	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.579741765853554	3	FACETS	0.919	0.834	1	0.919	0.834	1	CLONAL	2	TRUE	1	0.579741765853554	3		473	230	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934874	NA	P-0032262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	261	322	0	ENST00000269305.4:c.451C>G	p.Pro151Ala	p.P151A	ENST00000269305	NM_001126112.2	151	Ccc/Gcc	5/11	0.57580674501937	2	FACETS	0.917	0.871	0.963	0.917	0.871	0.963	CLONAL	2	TRUE	0	0.579741765853554	2		322	491	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039668	47039668	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	52	382	0	ENST00000377604.3:c.1121del	p.Gly374AlafsTer111	p.G374Afs*111	ENST00000377604	NM_001204468.1	374	Ggc/gc	11/24	1	1	FACETS	0.945	0.806	1	0.945	0.806	1	CLONAL	1	TRUE	0	0.22	1		382	445	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411902	116411902	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0032270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	256	727	1	ENST00000397752.3:c.2888-1G>A		p.X963_splice	ENST00000397752	NM_000245.2	963			0.145291315406752	3	FACETS	1	0.985	1	0.777	0.727	0.829	CLONAL	2	TRUE	0	0.22	3		728	1108	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003311	42003311	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	41	559	0	ENST00000219905.7:c.2848C>T	p.Gln950Ter	p.Q950*	ENST00000219905	NM_001164273.1	950	Cag/Tag	8/24	1	2	FACETS	0.56	0.466	0.666	0.56	0.466	0.666	SUBCLONAL	1	TRUE	1	0.22	2		559	665	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165719	118165719	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	22	377	0	ENST00000369448.3:c.229G>A	p.Gly77Ser	p.G77S	ENST00000369448	NM_017709.3	77	Ggc/Agc	2/2	1	2	FACETS	0.559	0.433	0.705	0.559	0.433	0.705	SUBCLONAL	1	TRUE	1	0.22	2		377	358	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112230	115112230	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs780531262	NA	P-0032270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	17	246	0	ENST00000257566.3:c.1510G>T	p.Ala504Ser	p.A504S	ENST00000257566	NM_016569.3	504	Gcc/Tcc	7/8	1	2	FACETS	0.623	0.465	0.81	0.623	0.465	0.81	SUBCLONAL	1	TRUE	1	0.22	2		246	248	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654656	29654656	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	29	264	0	ENST00000356175.3:c.5346del	p.Ile1782MetfsTer60	p.I1782Mfs*60	ENST00000356175	NM_000267.3	1782	aTt/at	37/57	1	2	FACETS	0.821	0.66	1	0.821	0.66	1	CLONAL	1	TRUE	1	0.22	2		264	321	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0032273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	31	779	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.157666311506846	4	FACETS	0.934	0.779	1	0.934	0.779	1	INDETERMINATE	2	FALSE	2	0.594289063400506	4		779	89	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0032273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	15	301	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.157666311506846	4	FACETS	0.781	0.579	1	0.391	0.289	0.509	INDETERMINATE	1	FALSE	2	0.594289063400506	4		301	103	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696642	47696642	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519965	NA	P-0032314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	115	553	0	ENST00000347630.2:c.306C>G	p.Phe102Leu	p.F102L	ENST00000347630	NM_001007230.1	102	ttC/ttG	5/11	1	2	FACETS	0.943	0.85	1	0.943	0.85	1	CLONAL	1	FALSE	1	0.323830516308806	2		553	753	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094324	193094324	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	129	476	0	ENST00000367435.3:c.214C>A	p.Pro72Thr	p.P72T	ENST00000367435	NM_024529.4	72	Cct/Act	2/17	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	1	0.323830516308806	2		476	752	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246117	46246117	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	67	373	0	ENST00000334344.6:c.4211A>C	p.Gln1404Pro	p.Q1404P	ENST00000334344	NM_152641.2	1404	cAa/cCa	15/21	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	1	0.323830516308806	2		373	383	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495646	72495646	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0032314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	62	289	0	ENST00000477973.2:c.423+1G>C		p.X141_splice	ENST00000477973	NM_012234.5	141			1	2	FACETS	0.884	0.766	1	0.884	0.766	1	CLONAL	1	FALSE	1	0.323830516308806	2		289	433	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0032317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	107	311	2	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.751	0.676	0.829	0.751	0.676	0.829	SUBCLONAL	1	TRUE	1	0.538951202794526	2		313	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0032317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	239	776	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.433251993261085	1	FACETS	0.618	0.577	0.661	0.618	0.577	0.661	SUBCLONAL	1	TRUE	0	0.538951202794526	1		776	1048	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249016	55249017	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCCACG	rs397517114	NA	P-0032317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	526	180	0	ENST00000275493.2:c.2315_2320dup	p.His773_Val774insAlaHis	p.H773_V774insAH	ENST00000275493	NM_005228.3	772	ccc/cCCCACGcc	20/28	0.498665860515269	5	FACETS	0.929	0.892	0.966	0.697	0.669	0.724	CLONAL	3	TRUE	1	0.538951202794526	5		180	1267	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0032338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	32	272	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.567	0.458	0.69	0.567	0.458	0.69	SUBCLONAL	1	TRUE	1	0.15	2		272	753	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555687605	NA	P-0032338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	20	290	0	ENST00000342988.3:c.1610A>G	p.Asp537Gly	p.D537G	ENST00000342988	NM_005359.5	537	gAc/gGc	12/12	1	2	FACETS	0.626	0.478	0.801	0.626	0.478	0.801	SUBCLONAL	1	TRUE	1	0.15	2		290	426	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224792	123224792	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs777611309	NA	P-0032338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	25	164	0	ENST00000218089.9:c.3556C>T	p.Arg1186Ter	p.R1186*	ENST00000218089	NM_001042749.1	1186	Cga/Tga	32/35	0.105764655149237	2	FACETS	1	0.835	1			1	CLONAL	1	TRUE	NA	0.15	2		164	312	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505300	186505302	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0032354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	36	383	0	ENST00000323963.5:c.928_930del	p.Lys310del	p.K310del	ENST00000323963		309	cAGAag/cag	9/11	0.226274966902609	3	FACETS	0.628	0.516	0.753	0.314	0.258	0.377	SUBCLONAL	1	TRUE	1	0.295948101164794	3		383	445	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535284	66535284	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs55860557	NA	P-0032354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	40	567	0	ENST00000273854.3:c.177C>G	p.Asn59Lys	p.N59K	ENST00000273854	NM_004439.5	59	aaC/aaG	1/18	1	2	FACETS	0.505	0.419	0.601	0.505	0.419	0.601	SUBCLONAL	1	TRUE	1	0.295948101164794	2		567	535	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0032358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	305	717	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.671953533124066	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.671953533124066	1		717	596	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0032358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	4663	362	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.671953533124066	26	FACETS	0.987	0.982	0.993			1	CLONAL	25	TRUE	NA	0.671953533124066	26		362	5097	SUCCESS
APC	324	MSKCC	GRCh37	5	112090657	112090657	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs145945630	NA	P-0032358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	60	277	0	ENST00000257430.4:c.70C>T	p.Arg24Ter	p.R24*	ENST00000257430	NM_000038.5	24	Cga/Tga	2/16	0.614444772158715	2	FACETS	0.516	0.447	0.591	0.258	0.223	0.296	SUBCLONAL	1	TRUE	0	0.671953533124066	2		277	346	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248526	59248526	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	315	554	0	ENST00000371222.2:c.217T>G	p.Ser73Ala	p.S73A	ENST00000371222	NM_002228.3	73	Tcg/Gcg	1/1	1	2	FACETS	0.975	0.922	1	0.975	0.922	1	CLONAL	1	TRUE	1	0.671953533124066	2		554	962	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037924	49037924	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	203	406	0	ENST00000267163.4:c.2167del	p.Ile723SerfsTer3	p.I723Sfs*3	ENST00000267163	NM_000321.2	722	Aaa/aa	21/27	0.671953533124066	1	FACETS	0.964	0.907	1	0.964	0.907	1	CLONAL	1	TRUE	0	0.671953533124066	1		406	416	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021290	31021290	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0032358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	91	486	0	ENST00000375687.4:c.1289C>G	p.Ser430Ter	p.S430*	ENST00000375687	NM_015338.5	430	tCa/tGa	12/13	1	2	FACETS	0.41	0.364	0.459	0.41	0.364	0.459	SUBCLONAL	1	TRUE	1	0.671953533124066	2		486	661	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32790075	32790075	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	30	201	0	ENST00000374899.4:c.1953G>A	p.Met651Ile	p.M651I	ENST00000374899	NM_018833.2	651	atG/atA	12/12	0.671953533124066	3	FACETS	0.292	0.235	0.357	0.146	0.117	0.179	SUBCLONAL	1	TRUE	1	0.671953533124066	3		201	408	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0032426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	101	512	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.262482264551377	4	FACETS	0.921	0.823	1	0.461	0.411	0.513	CLONAL	1	TRUE	2	0.375762305769749	4		512	803	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0032426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	93	802	5	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.175448355971364	3	FACETS	0.941	0.838	1	0.47	0.419	0.526	INDETERMINATE	1	TRUE	1	0.375762305769749	3		807	625	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593502	48593502	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	27	256	0	ENST00000342988.3:c.1253del	p.Ala418ValfsTer18	p.A418Vfs*18	ENST00000342988	NM_005359.5	418	gCt/gt	10/12	1	2	FACETS	0.424	0.337	0.523	0.424	0.337	0.523	SUBCLONAL	1	TRUE	1	0.375762305769749	2		256	339	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511638	66511639	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0032431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	294	381	0	ENST00000358598.2:c.99_100dup	p.Ser34PhefsTer96	p.S34Ffs*96	ENST00000358598	NM_212471.2	33	gat/gaTTt	2/11	0.904102946718093	1	FACETS	0.94	0.908	0.971	0.94	0.908	0.971	CLONAL	1	TRUE	0	0.904102946718093	1		381	379	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45391463	45391476	+	frameshift_variant	Frame_Shift_Del	DEL	TTGTTTCTCCATCT	TTGTTTCTCCATCT	-	novel	NA	P-0032431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	65	485	0	ENST00000262160.6:c.684_697del	p.Asp229Ter	p.D229*	ENST00000262160	NM_005901.5	228	gaAGATGGAGAAACAAgt/gagt	6/11	0.904102946718093	1	FACETS	0.392	0.345	0.44	0.392	0.345	0.44	SUBCLONAL	1	TRUE	0	0.904102946718093	1		485	201	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626948	14626949	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0032431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	184	609	0	ENST00000254322.2:c.826_827del	p.Leu276GlyfsTer41	p.L276Gfs*41	ENST00000254322	NM_006145.1	276	CTg/g	3/3	1	2	FACETS	0.442	0.408	0.478	0.442	0.408	0.478	SUBCLONAL	1	TRUE	1	0.904102946718093	2		609	920	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026248	48026249	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0032431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	92	339	0	ENST00000234420.5:c.1126_1127delinsAT	p.Glu376Ile	p.E376I	ENST00000234420	NM_000179.2	376	GAa/ATa	4/10	0.884299317807015	2	FACETS	0.617	0.553	0.683	0.308	0.276	0.342	SUBCLONAL	1	TRUE	0	0.904102946718093	2		339	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0032778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	279	468	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.33281224881732	2		468	722	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692912	89692970	+	frameshift_variant	Frame_Shift_Del	DEL	TGTAATGATATGTGCATATTTATTACATCGGGGCAAATTTTTAAAGGCACAAGAGGCCC	TGTAATGATATGTGCATATTTATTACATCGGGGCAAATTTTTAAAGGCACAAGAGGCCC	-	novel	NA	P-0032778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	19	357	0	ENST00000371953.3:c.397_455del	p.Val133ArgfsTer27	p.V133Rfs*27	ENST00000371953	NM_000314.4	132	ggTGTAATGATATGTGCATATTTATTACATCGGGGCAAATTTTTAAAGGCACAAGAGGCCCta/ggta	5/9	0.33281224881732	1	FACETS	0.439	0.334	0.561	0.439	0.334	0.561	SUBCLONAL	1	TRUE	0	0.33281224881732	1		357	217	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	438	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.484770085435519	3	FACETS	0.97	0.93	1			1	CLONAL	2	TRUE	NA	0.639618868062806	3		341	932	SUCCESS
APC	324	MSKCC	GRCh37	5	112174112	112174112	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	110	277	0	ENST00000257430.4:c.2821G>T	p.Glu941Ter	p.E941*	ENST00000257430	NM_000038.5	941	Gaa/Taa	16/16	1	2	FACETS	0.922	0.836	1	0.922	0.836	1	CLONAL	1	TRUE	1	0.639618868062806	2		277	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0032824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	410	542	1	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.608850221462256	2	FACETS	0.95	0.914	0.984	0.95	0.914	0.984	CLONAL	2	TRUE	0	0.639618868062806	2		543	675	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591931	48591931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	179	430	1	ENST00000342988.3:c.1094G>A	p.Gly365Asp	p.G365D	ENST00000342988	NM_005359.5	365	gGt/gAt	9/12	0.639618868062806	1	FACETS	0.877	0.818	0.937	0.877	0.818	0.937	CLONAL	1	TRUE	0	0.639618868062806	1		431	434	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175951	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1392778905	NA	P-0032824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	88	203	0	ENST00000257430.4:c.4660G>T	p.Glu1554Ter	p.E1554*	ENST00000257430	NM_000038.5	1554	Gaa/Taa	16/16	1	2	FACETS	0.885	0.792	0.981	0.885	0.792	0.981	CLONAL	1	TRUE	1	0.639618868062806	2		203	311	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859658	57859658	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746017407	NA	P-0032824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	192	434	0	ENST00000228682.2:c.712C>T	p.Arg238Cys	p.R238C	ENST00000228682	NM_005269.2	238	Cgt/Tgt	7/12	1	2	FACETS	0.986	0.917	1	0.986	0.917	1	CLONAL	1	TRUE	1	0.639618868062806	2		434	609	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119941	70119942	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0032824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	266	304	1	ENST00000245479.2:c.944dup	p.Tyr315Ter	p.Y315*	ENST00000245479	NM_000346.3	315	tac/tAac	3/3	0.222732948184888	3	FACETS	0.975	0.923	1	0.65	0.615	0.685	INDETERMINATE	2	TRUE	0	0.639618868062806	3		305	563	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707946	47707946	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	216	415	0	ENST00000233146.2:c.2570T>C	p.Ile857Thr	p.I857T	ENST00000233146	NM_000251.2	857	aTt/aCt	15/16	0.314286416184913	1	FACETS	0.771	0.721	0.821	0.771	0.721	0.821	INDETERMINATE	1	TRUE	0	0.639618868062806	1		415	596	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209101885	209101885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs566072712	NA	P-0032824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	96	346	0	ENST00000345146.2:c.1163G>A	p.Arg388His	p.R388H	ENST00000345146	NM_005896.2	388	cGt/cAt	10/10	0.314286416184913	1	FACETS	0.409	0.366	0.455	0.409	0.366	0.455	INDETERMINATE	1	TRUE	0	0.639618868062806	1		346	499	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55991418	55991418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1023303395	NA	P-0032824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	118	602	4	ENST00000263923.4:c.43G>A	p.Val15Met	p.V15M	ENST00000263923	NM_002253.2	15	Gtg/Atg	1/30	0.51211390879602	1	FACETS	0.416	0.376	0.458	0.416	0.376	0.458	SUBCLONAL	1	TRUE	0	0.639618868062806	1		606	603	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202420	138202420	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	99	562	1	ENST00000237289.4:c.2337C>A	p.Cys779Ter	p.C779*	ENST00000237289	NM_001270507.1	779	tgC/tgA	9/9	1	2	FACETS	0.406	0.362	0.453	0.406	0.362	0.453	SUBCLONAL	1	TRUE	1	0.639618868062806	2		563	762	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411622	63411622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	471	710	2	ENST00000330258.3:c.1545del	p.Glu516ArgfsTer25	p.E516Rfs*25	ENST00000330258	NM_152424.3	515	ctT/ct	2/2	NA	2	FACETS	0.788	0.757	0.818			1	INDETERMINATE	2	TRUE	NA	0.639618868062806	2		712	935	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032824-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	396	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.234813557921419	6	FACETS	0.962	0.922	1			1	INDETERMINATE	4	TRUE	NA	0.569233516442679	6		341	773	SUCCESS
APC	324	MSKCC	GRCh37	5	112174112	112174112	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032824-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	84	277	0	ENST00000257430.4:c.2821G>T	p.Glu941Ter	p.E941*	ENST00000257430	NM_000038.5	941	Gaa/Taa	16/16	1	2	FACETS	0.9	0.802	1	0.9	0.802	1	CLONAL	1	TRUE	1	0.569233516442679	2		277	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0032824-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	281	542	1	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.52437085075049	2	FACETS	0.901	0.856	0.945	0.901	0.856	0.945	CLONAL	2	TRUE	0	0.569233516442679	2		543	548	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591931	48591931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032824-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	128	430	1	ENST00000342988.3:c.1094G>A	p.Gly365Asp	p.G365D	ENST00000342988	NM_005359.5	365	gGt/gAt	9/12	0.569233516442679	1	FACETS	0.896	0.822	0.972	0.896	0.822	0.972	CLONAL	1	TRUE	0	0.569233516442679	1		431	359	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175951	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1392778905	NA	P-0032824-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	78	203	0	ENST00000257430.4:c.4660G>T	p.Glu1554Ter	p.E1554*	ENST00000257430	NM_000038.5	1554	Gaa/Taa	16/16	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.569233516442679	2		203	248	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859658	57859658	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746017407	NA	P-0032824-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	159	434	0	ENST00000228682.2:c.712C>T	p.Arg238Cys	p.R238C	ENST00000228682	NM_005269.2	238	Cgt/Tgt	7/12	0.318735876121868	3	FACETS	1	0.984	1	0.636	0.586	0.688	INDETERMINATE	1	TRUE	1	0.569233516442679	3		434	564	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119941	70119942	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0032824-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	161	304	1	ENST00000245479.2:c.944dup	p.Tyr315Ter	p.Y315*	ENST00000245479	NM_000346.3	315	tac/tAac	3/3	0.290613420609165	2	FACETS	1	0.99	1	0.742	0.69	0.795	INDETERMINATE	1	TRUE	0	0.569233516442679	2		305	381	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707946	47707946	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032824-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	149	415	0	ENST00000233146.2:c.2570T>C	p.Ile857Thr	p.I857T	ENST00000233146	NM_000251.2	857	aTt/aCt	15/16	1	2	FACETS	0.988	0.908	1	0.988	0.908	1	CLONAL	1	TRUE	1	0.569233516442679	2		415	530	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209101885	209101885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs566072712	NA	P-0032824-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	113	346	0	ENST00000345146.2:c.1163G>A	p.Arg388His	p.R388H	ENST00000345146	NM_005896.2	388	cGt/cAt	10/10	1	2	FACETS	0.919	0.833	1	0.919	0.833	1	CLONAL	1	TRUE	1	0.569233516442679	2		346	432	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55991418	55991418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1023303395	NA	P-0032824-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	178	602	4	ENST00000263923.4:c.43G>A	p.Val15Met	p.V15M	ENST00000263923	NM_002253.2	15	Gtg/Atg	1/30	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.569233516442679	2		606	557	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411622	63411622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032824-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	404	710	2	ENST00000330258.3:c.1545del	p.Glu516ArgfsTer25	p.E516Rfs*25	ENST00000330258	NM_152424.3	515	ctT/ct	2/2	0.569233516442679	3	FACETS	0.932	0.89	0.975	0.932	0.89	0.975	CLONAL	2	TRUE	1	0.569233516442679	3		712	978	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0033318-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	363	405	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.39035844294595	2	FACETS	0.814	0.775	0.855	0.814	0.775	0.855	CLONAL	2	TRUE	0	0.464243432923209	2		406	960	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42790946	42790946	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033318-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	281	800	0	ENST00000575354.2:c.91T>A	p.Ser31Thr	p.S31T	ENST00000575354	NM_015125.3	31	Tct/Act	2/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.464243432923209	2		800	1018	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577599	7577600	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1567550002	NA	P-0033437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	248	527	0	ENST00000269305.4:c.681dup	p.Asp228Ter	p.D228*	ENST00000269305	NM_001126112.2	227	-/T	7/11	0.798252864886892	2	FACETS	0.975	0.943	1	0.975	0.943	1	CLONAL	2	FALSE	0	0.844613600816381	2		527	301	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445084	49445085	+	missense_variant	Missense_Mutation	DNP	TC	TC	CT	novel	NA	P-0033437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	30	462	0	ENST00000301067.7:c.2381_2382delinsAG	p.Gly794Glu	p.G794E	ENST00000301067	NM_003482.3	794	gGA/gAG	10/54	0.752901593483423	3	FACETS	0.307	0.248	0.374	0.102	0.082	0.125	SUBCLONAL	1	FALSE	0	0.844613600816381	3		462	329	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445096	49445134	+	protein_altering_variant	In_Frame_Del	DEL	GGGGGACAAGTGTGGCTCCTCAGGCACAGCGCATAGGCA	GGGGGACAAGTGTGGCTCCTCAGGCACAGCGCATAGGCA	CGGAGATAGGTG	novel	NA	P-0033437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	24	543	2	ENST00000301067.7:c.2332_2370delinsCACCTATCTCCG	p.Cys778_Pro786del	p.C778_P786del	ENST00000301067	NM_003482.3	778	TGCCTATGCGCTGTGCCTGAGGAGCCACACTTGTCCCCC/CACCTATCTCCG	10/54	0.752901593483423	3	FACETS	0.222	0.174	0.278	0.074	0.058	0.093	SUBCLONAL	1	FALSE	0	0.844613600816381	3		545	364	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243451	41243493	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CCTAAGTTTGAATCCATGCTTTGCTCTTCTTGATTATTTTCTT	CCTAAGTTTGAATCCATGCTTTGCTCTTCTTGATTATTTTCTT	-	novel	NA	P-0033437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	15	534	0	ENST00000357654.3:c.4055_4096+1del		p.X1352_splice	ENST00000357654	NM_007294.3	1352		10/23	0.798252864886892	2	FACETS	0.161	0.117	0.213	0.08	0.058	0.107	SUBCLONAL	1	FALSE	0	0.844613600816381	2		534	221	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243456	41243456	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	13	527	0	ENST00000357654.3:c.4092C>G	p.Asn1364Lys	p.N1364K	ENST00000357654	NM_007294.3	1364	aaC/aaG	10/23	0.798252864886892	2	FACETS	0.133	0.095	0.18	0.067	0.047	0.09	SUBCLONAL	1	FALSE	0	0.844613600816381	2		527	231	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220599	1220602	+	frameshift_variant	Frame_Shift_Del	DEL	CGGA	CGGA	-	novel	NA	P-0033437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	412	355	0	ENST00000326873.7:c.619_622del	p.Asp207ThrfsTer79	p.D207Tfs*79	ENST00000326873	NM_000455.4	206	gCGGAc/gc	5/10	0.827785361187385	4	FACETS	0.947	0.926	0.967	0.947	0.926	0.967	CLONAL	4	FALSE	0	0.844613600816381	4		355	475	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15273335	15273335	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	180	618	0	ENST00000263388.2:c.5854G>C	p.Val1952Leu	p.V1952L	ENST00000263388	NM_000435.2	1952	Gtg/Ctg	32/33	0.777080731562928	6	FACETS	1	0.976	1	0.229	0.211	0.248	CLONAL	1	FALSE	1	0.844613600816381	6		618	1000	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532590	187532590	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	62	389	0	ENST00000441802.2:c.9803C>T	p.Ser3268Leu	p.S3268L	ENST00000441802	NM_005245.3	3268	tCa/tTa	14/27	0.844613600816381	3	FACETS	0.928	0.813	1	0.464	0.406	0.525	CLONAL	1	FALSE	1	0.844613600816381	3		389	225	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932196	39932211	+	frameshift_variant	Frame_Shift_Del	DEL	GTCGCTTTTGACAACA	GTCGCTTTTGACAACA	-	novel	NA	P-0033437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	268	818	0	ENST00000378444.4:c.2388_2403del	p.Val797SerfsTer5	p.V797Sfs*5	ENST00000378444	NM_001123385.1	796	acTGTTGTCAAAAGCGAC/ac	4/15	0.792746262275064	1	FACETS	0.919	0.88	0.957	0.919	0.88	0.957	CLONAL	1	FALSE	0	0.844613600816381	1		818	399	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0033534-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	367	665	2	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	0.674983679269443	3	FACETS	0.98	0.93	1			1	CLONAL	1	TRUE	NA	0.93297822838987	3		667	1177	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0033534-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	240	559	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.674983679269443	3	FACETS	0.814	0.761	0.868			1	CLONAL	1	TRUE	NA	0.93297822838987	3		559	927	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772316	68772316	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0033534-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	420	783	0	ENST00000261769.5:c.163+2T>C		p.X55_splice	ENST00000261769	NM_004360.3	55			0.93297822838987	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.93297822838987	1		783	463	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114147	115114148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0033534-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	384	610	0	ENST00000257566.3:c.1069dup	p.Ala357GlyfsTer18	p.A357Gfs*18	ENST00000257566	NM_016569.3	357	gcc/gGcc	6/8	0.222922932291989	3	FACETS	0.755	0.722	0.789	0.755	0.722	0.789	INDETERMINATE	2	TRUE	1	0.93297822838987	3		610	799	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100687	67100689	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0033534-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	220	445	0	ENST00000412916.2:c.388_390del	p.Glu130del	p.E130del	ENST00000412916		129	GAG/-	4/6	0.93297822838987	1	FACETS	0.971	0.94	1	0.971	0.94	1	CLONAL	1	TRUE	0	0.93297822838987	1		445	259	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578432	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033534-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	420	751	0	ENST00000269305.4:c.498dup	p.Gln167ThrfsTer14	p.Q167Tfs*14	ENST00000269305	NM_001126112.2	166	-/A	5/11	0.93297822838987	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.93297822838987	1		751	455	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456650	138456650	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs750830394	NA	P-0033534-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	169	390	0	ENST00000289153.2:c.700A>G	p.Ile234Val	p.I234V	ENST00000289153	NM_006219.2	234	Att/Gtt	4/22	0.843182440283111	3	FACETS	0.927	0.857	0.999	0.464	0.428	0.5	CLONAL	1	TRUE	1	0.93297822838987	3		390	573	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974727	21974727	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033534-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	354	354	0	ENST00000304494.5:c.100G>C	p.Ala34Pro	p.A34P	ENST00000304494	NM_000077.4	34	Gcg/Ccg	1/3	0.882652997611756	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.93297822838987	1		354	377	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0033534-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1371	459	665	2	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	0.699778873801741	3	FACETS	0.968	0.922	1			1	CLONAL	1	TRUE	NA	0.699778873801741	3		667	1830	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0033534-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	323	559	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.699778873801741	3	FACETS	0.959	0.905	1			1	CLONAL	1	TRUE	NA	0.699778873801741	3		559	1299	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772316	68772316	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0033534-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	452	783	0	ENST00000261769.5:c.163+2T>C		p.X55_splice	ENST00000261769	NM_004360.3	55			0.699778873801741	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.699778873801741	1		783	818	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114147	115114148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0033534-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	331	610	0	ENST00000257566.3:c.1069dup	p.Ala357GlyfsTer18	p.A357Gfs*18	ENST00000257566	NM_016569.3	357	gcc/gGcc	6/8	1	2	FACETS	0.956	0.905	1	0.956	0.905	1	CLONAL	1	TRUE	1	0.699778873801741	2		610	990	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100687	67100689	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0033534-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	222	445	0	ENST00000412916.2:c.388_390del	p.Glu130del	p.E130del	ENST00000412916		129	GAG/-	4/6	0.699778873801741	1	FACETS	0.889	0.838	0.94	0.889	0.838	0.94	CLONAL	1	TRUE	0	0.699778873801741	1		445	464	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578432	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033534-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	476	751	0	ENST00000269305.4:c.498dup	p.Gln167ThrfsTer14	p.Q167Tfs*14	ENST00000269305	NM_001126112.2	166	-/A	5/11	0.689357874880607	1	FACETS	0.964	0.928	1	0.964	0.928	1	CLONAL	1	TRUE	0	0.699778873801741	1		751	917	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456650	138456650	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs750830394	NA	P-0033534-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	248	390	0	ENST00000289153.2:c.700A>G	p.Ile234Val	p.I234V	ENST00000289153	NM_006219.2	234	Att/Gtt	4/22	0.699778873801741	3	FACETS	1	0.955	1	0.512	0.479	0.546	CLONAL	1	TRUE	1	0.699778873801741	3		390	934	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974727	21974727	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033534-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	209	354	0	ENST00000304494.5:c.100G>C	p.Ala34Pro	p.A34P	ENST00000304494	NM_000077.4	34	Gcg/Ccg	1/3	0.689357874880607	1	FACETS	0.966	0.911	1	0.966	0.911	1	CLONAL	1	TRUE	0	0.699778873801741	1		354	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0033783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	38	735	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.178212443859269	3	FACETS	0.59	0.486	0.708	0.295	0.243	0.354	SUBCLONAL	1	TRUE	1	0.16	3		735	869	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0033791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	368	567	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.573594469483088	2	FACETS	0.87	0.834	0.906	0.87	0.834	0.906	CLONAL	2	TRUE	0	0.640980873505385	2		567	660	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624269	89624269	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0033791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	234	353	0	ENST00000371953.3:c.43A>T	p.Arg15Ter	p.R15*	ENST00000371953	NM_000314.4	15	Aga/Tga	1/9	0.557270338758119	2	FACETS	0.924	0.878	0.97	0.924	0.878	0.97	CLONAL	2	TRUE	0	0.640980873505385	2		353	395	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436102	110436102	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	51	794	0	ENST00000375856.3:c.2299C>G	p.Leu767Val	p.L767V	ENST00000375856	NM_003749.2	767	Ctc/Gtc	1/2	0.542541075752689	2	FACETS	0.19	0.161	0.222	0.095	0.08	0.111	SUBCLONAL	1	TRUE	0	0.640980873505385	2		794	838	SUCCESS
BLM	641	MSKCC	GRCh37	15	91333931	91333931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772585415	NA	P-0033791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	371	580	0	ENST00000355112.3:c.2876G>A	p.Arg959Gln	p.R959Q	ENST00000355112	NM_000057.2	959	cGa/cAa	15/22	0.635006375335818	5	FACETS	1	0.983	1	0.429	0.407	0.451	CLONAL	2	TRUE	0	0.640980873505385	5		580	1059	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526144	63526144	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	1218	642	0	ENST00000307078.5:c.2482C>T	p.Leu828Phe	p.L828F	ENST00000307078	NM_004655.3	828	Ctc/Ttc	11/11	0.575690311761186	5	FACETS	0.981	0.965	0.996	0.981	0.965	0.996	CLONAL	5	TRUE	0	0.640980873505385	5		642	1520	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149705	202149705	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	338	588	0	ENST00000358485.4:c.1146C>G	p.Ile382Met	p.I382M	ENST00000358485	NM_001080125.1	382	atC/atG	8/9	0.591752800838305	2	FACETS	0.933	0.895	0.971	0.933	0.895	0.971	CLONAL	2	TRUE	0	0.640980873505385	2		588	565	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474618	138474629	+	inframe_deletion	In_Frame_Del	DEL	TTTTGAGTCTAA	TTTTGAGTCTAA	-	novel	NA	P-0033791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	183	368	0	ENST00000289153.2:c.364_375del	p.Leu122_Lys125del	p.L122_K125del	ENST00000289153	NM_006219.2	122	TTAGACTCAAAA/-	2/22	0.624553874374803	3	FACETS	1	0.973	1	0.368	0.341	0.396	CLONAL	1	TRUE	0	0.640980873505385	3		368	683	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526261	189526261	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1374	296	631	0	ENST00000264731.3:c.525C>G	p.His175Gln	p.H175Q	ENST00000264731	NM_003722.4	175	caC/caG	4/14	0.640980873505385	5	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.640980873505385	5		631	1670	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044850	47044850	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	385	782	0	ENST00000377604.3:c.2176C>G	p.Arg726Gly	p.R726G	ENST00000377604	NM_001204468.1	726	Cga/Gga	20/24	0.33894119485371	3	FACETS	0.901	0.86	0.942	0.901	0.86	0.942	INDETERMINATE	2	TRUE	1	0.640980873505385	3		782	880	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778779	3778779	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	458	904	0	ENST00000262367.5:c.6269del	p.Leu2090ProfsTer7	p.L2090Pfs*7	ENST00000262367	NM_004380.2	2090	cTc/cc	31/31	0.660753903726972	3	FACETS	0.923	0.886	0.96			1	CLONAL	2	TRUE	NA	0.725696912949799	3		904	932	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779167	3779167	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	246	602	3	ENST00000262367.5:c.5881C>T	p.Gln1961Ter	p.Q1961*	ENST00000262367	NM_004380.2	1961	Cag/Tag	31/31	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.725696912949799	NA		605	498	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820960	3820960	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	315	678	0	ENST00000262367.5:c.2491A>G	p.Asn831Asp	p.N831D	ENST00000262367	NM_004380.2	831	Aac/Gac	14/31	0.537933172082243	4	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.725696912949799	4		678	672	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962941	2962941	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1571	185	988	0	ENST00000396946.4:c.1967del	p.Val656GlyfsTer16	p.V656Gfs*16	ENST00000396946	NM_032415.4	656	gTg/gg	16/25	0.725696912949799	6	FACETS	0.712	0.654	0.772	0.142	0.13	0.155	SUBCLONAL	1	TRUE	1	0.725696912949799	6		988	1756	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696637	47696637	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	46	655	0	ENST00000347630.2:c.311T>G	p.Phe104Cys	p.F104C	ENST00000347630	NM_001007230.1	104	tTc/tGc	5/11	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.19	2		655	437	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019411	42019411	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	23	704	2	ENST00000219905.7:c.3464G>T	p.Arg1155Leu	p.R1155L	ENST00000219905	NM_001164273.1	1155	cGa/cTa	10/24	1	2	FACETS	0.71	0.553	0.891	0.71	0.553	0.891	SUBCLONAL	1	TRUE	1	0.19	2		706	341	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061018	38061033	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGCGCCCTCTAGCT	GGCGCGCCCTCTAGCT	-	novel	NA	P-0034085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	29	157	0	ENST00000250448.2:c.956_971del	p.Gln319ArgfsTer26	p.Q319Rfs*26	ENST00000250448	NM_004496.3	319	cAGCTAGAGGGCGCGCCg/cg	2/2	1	2	FACETS	0.867	0.703	1	1	0.951	1	CLONAL	2	TRUE	1	0.19	2		157	176	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0034264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	60	284	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.231993766616336	2		284	505	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0034264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	44	274	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.231993766616336	2		274	324	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103498674	103498674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761699560	NA	P-0034264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	59	362	0	ENST00000355739.4:c.58G>A	p.Glu20Lys	p.E20K	ENST00000355739	NM_000123.3	20	Gaa/Aaa	1/15	0.13589400341551	3	FACETS	0.975	0.839	1	0.488	0.419	0.562	INDETERMINATE	1	TRUE	1	0.231993766616336	3		362	582	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578264	7578265	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATA	novel	NA	P-0034264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	88	459	0	ENST00000269305.4:c.582_584dup	p.Ile195dup	p.I195dup	ENST00000269305	NM_001126112.2	195	atc/atTATc	6/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.231993766616336	2		459	604	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372423	55372423	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	115	714	2	ENST00000297316.4:c.1113C>A	p.Cys371Ter	p.C371*	ENST00000297316	NM_022454.3	371	tgC/tgA	2/2	0.231993766616336	1	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	0	0.231993766616336	1		716	874	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150030	202150030	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs931648756	NA	P-0036303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	167	541	0	ENST00000358485.4:c.1471C>T	p.Arg491Ter	p.R491*	ENST00000358485	NM_001080125.1	491	Cga/Tga	8/9	0.263086379663283	5	FACETS	1	0.979	1	0.778	0.718	0.84	CLONAL	2	TRUE	2	0.355827866255858	5		541	617	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624245	89624245	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554890335	NA	P-0036303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	20	199	0	ENST00000371953.3:c.19G>T	p.Glu7Ter	p.E7*	ENST00000371953	NM_000314.4	7	Gag/Tag	1/9	0.355827866255858	1	FACETS	0.604	0.466	0.763	0.604	0.466	0.763	SUBCLONAL	1	TRUE	0	0.355827866255858	1		199	153	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752724	42752724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764618715	NA	P-0036303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	171	693	1	ENST00000222329.4:c.1540C>T	p.Arg514Cys	p.R514C	ENST00000222329	NM_006494.2	514	Cgt/Tgt	4/4	0.308569394409014	4	FACETS	0.875	0.806	0.945	0.875	0.806	0.945	CLONAL	2	TRUE	2	0.355827866255858	4		694	745	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	171	618	1	ENST00000269305.4:c.548C>A	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tAa	5/11	0.343724733734611	2	FACETS	0.983	0.912	1	0.983	0.912	1	CLONAL	2	TRUE	0	0.355827866255858	2		619	489	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148529772	148529772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	40	380	0	ENST00000320356.2:c.317C>T	p.Ser106Leu	p.S106L	ENST00000320356	NM_004456.4	106	tCa/tTa	4/20	0.355827866255858	3	FACETS	0.74	0.616	0.877	0.37	0.308	0.439	SUBCLONAL	1	TRUE	1	0.355827866255858	3		380	358	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375699	118375699	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	65	536	0	ENST00000534358.1:c.9095del	p.Pro3032LeufsTer43	p.P3032Lfs*43	ENST00000534358	NM_005933.3	3031	aCc/ac	27/36	0.309049407193819	5	FACETS	1	0.898	1			1	CLONAL	1	TRUE	NA	0.355827866255858	5		536	538	SUCCESS
REL	5966	MSKCC	GRCh37	2	61128209	61128223	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCATTCAATGGTAAG	CCATTCAATGGTAAG	TT	novel	NA	P-0036303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	39	183	1	ENST00000295025.8:c.385_394+5delinsTT		p.X129_splice	ENST00000295025	NM_002908.2	129		4/11	0.351079787477208	4	FACETS	1	0.954	1			1	CLONAL	1	TRUE	NA	0.355827866255858	4		184	203	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61709590	61709615	+	frameshift_variant	Frame_Shift_Del	DEL	TTTCCAGGATTTAATGATGTACTTAT	TTTCCAGGATTTAATGATGTACTTAT	-	novel	NA	P-0036303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	63	373	0	ENST00000401558.2:c.2872_2897del	p.Ile958SerfsTer3	p.I958Sfs*3	ENST00000401558	NM_003400.3	958	ATAAGTACATCATTAAATCCTGGAAAt/t	23/25	0.351079787477208	4	FACETS	1	0.961	1			1	CLONAL	1	TRUE	NA	0.355827866255858	4		373	370	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055670	152055670	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0036371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	179	655	0	ENST00000262189.6:c.250+2T>C		p.X84_splice	ENST00000262189	NM_170606.2	84			1	2	FACETS	0.718	0.662	0.776	0.718	0.662	0.776	SUBCLONAL	1	TRUE	1	0.557003719469795	2		655	895	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838020	156838020	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	189	704	0	ENST00000524377.1:c.553C>T	p.His185Tyr	p.H185Y	ENST00000524377	NM_002529.3	185	Cac/Tac	5/17	1	2	FACETS	0.834	0.772	0.898	0.834	0.772	0.898	CLONAL	1	TRUE	1	0.557003719469795	2		704	814	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830824	72830824	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	249	680	0	ENST00000268489.5:c.5757del	p.Glu1920SerfsTer77	p.E1920Sfs*77	ENST00000268489	NM_006885.3	1919	aaA/aa	9/10	0.557003719469795	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.557003719469795	1		680	580	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0036379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	149	352	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		352	391	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0036389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	33	779	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.916	0.749	1	0.916	0.749	1	CLONAL	1	TRUE	1	0.253756533901832	2		779	284	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068283	30068283	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	34	343	0	ENST00000331968.5:c.2116G>T	p.Asp706Tyr	p.D706Y	ENST00000331968	NM_002742.2	706	Gac/Tac	15/18	1	2	FACETS	0.687	0.562	0.828	0.687	0.562	0.828	SUBCLONAL	1	TRUE	1	0.253756533901832	2		343	390	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435924	56435925	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0036389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	39	377	0	ENST00000407977.2:c.1211_1212dup	p.Leu405AlafsTer15	p.L405Afs*15	ENST00000407977		404	-/GC	9/10	0.253756533901832	1	FACETS	0.938	0.782	1	0.938	0.782	1	CLONAL	1	TRUE	0	0.253756533901832	1		377	286	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484233	8484233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200684369	NA	P-0036389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	52	517	0	ENST00000356435.5:c.3299C>T	p.Thr1100Met	p.T1100M	ENST00000356435		1100	aCg/aTg	19/35	0.253756533901832	1	FACETS	0.592	0.504	0.69	0.592	0.504	0.69	SUBCLONAL	1	TRUE	0	0.253756533901832	1		517	604	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342671	70342671	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	77	316	0	ENST00000374080.3:c.1432G>C	p.Asp478His	p.D478H	ENST00000374080		478	Gac/Cac	10/45	1	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.253756533901832	1		316	364	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100884	27100884	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036400-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	143	536	0	ENST00000324856.7:c.4166del	p.Tyr1389SerfsTer92	p.Y1389Sfs*92	ENST00000324856	NM_006015.4	1389	tAc/tc	18/20	1	2	FACETS	0.48	0.438	0.522	0.48	0.438	0.522	SUBCLONAL	1	TRUE	1	0.939223228179859	2		536	635	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141517	11141517	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036400-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	132	607	0	ENST00000358026.2:c.3494T>A	p.Leu1165His	p.L1165H	ENST00000358026	NM_001128849.1	1165	cTc/cAc	25/36	1	2	FACETS	0.551	0.5	0.605	0.551	0.5	0.605	SUBCLONAL	1	TRUE	1	0.579093250710456	2		607	827	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0036534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	143	473	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.20506694437566	3	FACETS	0.957	0.883	1	0.638	0.589	0.688	INDETERMINATE	2	TRUE	0	0.506149738463887	3		473	370	SUCCESS
APC	324	MSKCC	GRCh37	5	112175147	112175147	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	47	223	0	ENST00000257430.4:c.3856G>T	p.Glu1286Ter	p.E1286*	ENST00000257430	NM_000038.5	1286	Gaa/Taa	16/16	0.506149738463887	2	FACETS	0.815	0.709	0.923	0.815	0.709	0.923	CLONAL	2	TRUE	0	0.506149738463887	2		223	114	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481882	56481882	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	142	609	0	ENST00000267101.3:c.810C>G	p.Phe270Leu	p.F270L	ENST00000267101	NM_001982.3	270	ttC/ttG	7/28	0.506149738463887	3	FACETS	1	0.961	1	0.544	0.497	0.593	CLONAL	1	TRUE	1	0.506149738463887	3		609	646	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225669	225669	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542980860	NA	P-0036534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	145	687	1	ENST00000264932.6:c.448G>A	p.Val150Met	p.V150M	ENST00000264932	NM_004168.2	150	Gtg/Atg	4/15	1	2	FACETS	0.947	0.867	1	0.947	0.867	1	CLONAL	1	TRUE	1	0.506149738463887	2		688	605	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711367	114711367	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0036534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	66	136	0	ENST00000543371.1:c.381+1G>C		p.X127_splice	ENST00000543371	NM_001198531.1	127			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.506149738463887	2		136	209	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39726924	39726924	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	37	203	0	ENST00000361337.2:c.922T>C	p.Tyr308His	p.Y308H	ENST00000361337	NM_003286.2	308	Tat/Cat	11/21	0.288457446255749	3	FACETS	0.974	0.813	1	0.487	0.406	0.576	INDETERMINATE	1	TRUE	1	0.506149738463887	3		203	188	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747836	41747836	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	83	328	0	ENST00000226382.2:c.933C>A	p.Ser311Arg	p.S311R	ENST00000226382	NM_003924.3	311	agC/agA	3/3	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.506149738463887	2		328	322	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421909	49421909	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	138	527	5	ENST00000301067.7:c.14398A>T	p.Met4800Leu	p.M4800L	ENST00000301067	NM_003482.3	4800	Atg/Ttg	46/54	0.262114013860632	4	FACETS	0.912	0.832	0.996	0.912	0.832	0.996	CLONAL	2	TRUE	2	0.29	4		532	673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934578	NA	P-0036637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	66	652	0	ENST00000269305.4:c.524G>T	p.Arg175Leu	p.R175L	ENST00000269305	NM_001126112.2	175	cGc/cTc	5/11	1	2	FACETS	0.482	0.418	0.551	0.482	0.418	0.551	SUBCLONAL	1	TRUE	1	0.43	2		652	637	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255016	16255016	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	24	385	0	ENST00000375759.3:c.2281G>A	p.Asp761Asn	p.D761N	ENST00000375759	NM_015001.2	761	Gac/Aac	11/15	1	2	FACETS	0.257	0.201	0.322	0.257	0.201	0.322	SUBCLONAL	1	TRUE	1	0.43	2		385	434	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255058	16255058	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	29	403	0	ENST00000375759.3:c.2323G>C	p.Glu775Gln	p.E775Q	ENST00000375759	NM_015001.2	775	Gag/Cag	11/15	1	2	FACETS	0.33	0.264	0.404	0.33	0.264	0.404	SUBCLONAL	1	TRUE	1	0.43	2		403	409	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40467819	40467819	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0036637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	35	459	0	ENST00000264657.5:c.2258-1G>A		p.X753_splice	ENST00000264657	NM_139276.2	753			1	2	FACETS	0.287	0.234	0.346	0.287	0.234	0.346	SUBCLONAL	1	TRUE	1	0.43	2		459	568	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152446	56152447	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	68	203	0	ENST00000399503.3:c.505dup	p.Thr169AsnfsTer10	p.T169Nfs*10	ENST00000399503	NM_005921.1	168	gaa/gAaa	2/20	0.236853067598176	3	FACETS	1	0.941	1	0.563	0.493	0.638	INDETERMINATE	1	TRUE	1	0.43	3		203	341	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536224	106536224	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	49	510	0	ENST00000369096.4:c.191A>T	p.Asp64Val	p.D64V	ENST00000369096	NM_001198.3	64	gAc/gTc	2/7	1	2	FACETS	0.352	0.297	0.412	0.352	0.297	0.412	SUBCLONAL	1	TRUE	1	0.43	2		510	648	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922994	44922994	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	43	602	0	ENST00000377967.4:c.1855C>T	p.His619Tyr	p.H619Y	ENST00000377967	NM_021140.2	619	Cat/Tat	16/29	1	2	FACETS	0.257	0.214	0.305	0.257	0.214	0.305	SUBCLONAL	1	TRUE	1	0.43	2		602	779	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603048	48603049	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCGGCTACTGCACAAGCTGCAGCAGCT	novel	NA	P-0036737-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	25	376	0	ENST00000342988.3:c.1351_1378dup	p.Ala460GlyfsTer43	p.A460Gfs*43	ENST00000342988	NM_005359.5	450	cag/caGGCGGCTACTGCACAAGCTGCAGCAGCTg	11/12	0.244348950006314	1	FACETS	0.28	0.221	0.349	0.28	0.221	0.349	INDETERMINATE	1	TRUE	0	0.421423100733785	1		376	334	SUCCESS
APC	324	MSKCC	GRCh37	5	112175991	112175991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036737-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	30	285	0	ENST00000257430.4:c.4700C>T	p.Ser1567Leu	p.S1567L	ENST00000257430	NM_000038.5	1567	tCa/tTa	16/16	0.219353238814362	4	FACETS	0.688	0.556	0.837	0.344	0.278	0.419	INDETERMINATE	1	TRUE	2	0.421423100733785	4		285	294	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023905	27023905	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	10	76	0	ENST00000324856.7:c.1011G>A	p.Trp337Ter	p.W337*	ENST00000324856	NM_006015.4	337	tgG/tgA	1/20	NA	2	FACETS	0.22	0.149	0.307			1	INDETERMINATE	1	TRUE	NA	0.798252927901642	2		76	114	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578540	7578542	+	frameshift_variant	Frame_Shift_Del	DEL	GAG	GAG	CA	novel	NA	P-0036828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	351	795	2	ENST00000269305.4:c.388_390delinsTG	p.Leu130Ter	p.L130*	ENST00000269305	NM_001126112.2	130	CTC/TG	5/11	0.798252927901642	1	FACETS	0.954	0.917	0.99	0.954	0.917	0.99	CLONAL	1	TRUE	0	0.798252927901642	1		797	554	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860368	42860368	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	61	670	0	ENST00000398585.3:c.509G>A	p.Cys170Tyr	p.C170Y	ENST00000398585	NM_001135099.1	170	tGt/tAt	5/14	1	2	FACETS	0.2	0.171	0.23	0.2	0.171	0.23	SUBCLONAL	1	TRUE	1	0.798252927901642	2		670	766	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796856	42796856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	106	855	0	ENST00000575354.2:c.3314C>T	p.Ser1105Leu	p.S1105L	ENST00000575354	NM_015125.3	1105	tCa/tTa	14/20	1	2	FACETS	0.87	0.781	0.964	0.87	0.781	0.964	CLONAL	1	TRUE	1	0.378873916922514	2		855	643	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948665	71948665	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	66	742	0	ENST00000298229.2:c.3377T>C	p.Met1126Thr	p.M1126T	ENST00000298229	NM_001567.3	1126	aTg/aCg	26/28	0.1078574914105	3	FACETS	0.776	0.674	0.886	0.259	0.224	0.296	INDETERMINATE	1	TRUE	0	0.378873916922514	3		742	534	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623605	43623605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762952212	NA	P-0037494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	60	415	0	ENST00000355710.3:c.3233C>T	p.Thr1078Met	p.T1078M	ENST00000355710	NM_020975.4	1078	aCg/aTg	20/20	0.175116008004326	3	FACETS	0.84	0.723	0.969	0.42	0.361	0.485	CLONAL	1	TRUE	1	0.214555862346593	3		415	737	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56878417	56878417	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs190188561	NA	P-0037494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	52	338	0	ENST00000308159.5:c.2356C>T	p.Arg786Ter	p.R786*	ENST00000308159	NM_014669.4	786	Cga/Tga	22/22	0.14092932994508	4	FACETS	0.883	0.75	1	0.441	0.375	0.514	CLONAL	1	TRUE	2	0.214555862346593	4		338	667	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971304	15971304	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	54	465	0	ENST00000268712.3:c.4645C>G	p.Pro1549Ala	p.P1549A	ENST00000268712	NM_006311.3	1549	Ccc/Gcc	32/46	0.165015075605581	2	FACETS	0.779	0.665	0.905	0.39	0.332	0.453	CLONAL	1	TRUE	0	0.214555862346593	2		465	646	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31946698	31946698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	51	415	0	ENST00000375333.2:c.586G>A	p.Gly196Arg	p.G196R	ENST00000375333	NM_032454.1	196	Ggg/Agg	4/8	1	2	FACETS	0.736	0.625	0.858	0.736	0.625	0.858	SUBCLONAL	1	TRUE	1	0.214555862346593	2		415	646	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279815	46279850	+	inframe_deletion	In_Frame_Del	DEL	GCAGCAGCAGCAGCAGCAGCAACAGCAGCAGCAGCA	GCAGCAGCAGCAGCAGCAGCAACAGCAGCAGCAGCA	-	rs1299097534	NA	P-0037494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	53	396	1	ENST00000371998.3:c.3756_3791del	p.Gln1265_Gln1276del	p.Q1265_Q1276del	ENST00000371998		1247	atGCAGCAGCAGCAGCAGCAGCAACAGCAGCAGCAGCAg/atg	20/23	1	2	FACETS	0.728	0.619	0.846	0.728	0.619	0.846	SUBCLONAL	1	TRUE	1	0.214555862346593	2		397	679	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842344	151842344	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs749571160	NA	P-0037587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	43	355	0	ENST00000262189.6:c.14068C>T	p.Arg4690Ter	p.R4690*	ENST00000262189	NM_170606.2	4690	Cga/Tga	54/59	1	2	FACETS	0.844	0.707	0.994	0.844	0.707	0.994	CLONAL	1	TRUE	1	0.256117947682783	2		355	398	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0037587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	47	445	0	ENST00000311936.3:c.34_35delinsTA	p.Gly12Tyr	p.G12Y	ENST00000311936	NM_004985.3	12	GGt/TAt	2/5	1	2	FACETS	0.647	0.546	0.76	0.647	0.546	0.76	SUBCLONAL	1	TRUE	1	0.256117947682783	2		445	567	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28979956	28979956	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	44	560	1	ENST00000282397.4:c.1512C>A	p.Ser504Arg	p.S504R	ENST00000282397	NM_002019.4	504	agC/agA	11/30	1	2	FACETS	0.61	0.511	0.72	0.61	0.511	0.72	SUBCLONAL	1	TRUE	1	0.256117947682783	2		561	563	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005641	42005641	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	60	380	0	ENST00000219905.7:c.3379del	p.Glu1127ArgfsTer6	p.E1127Rfs*6	ENST00000219905	NM_001164273.1	1126	aGg/ag	9/24	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.256117947682783	2		380	394	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600426	10600426	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766297018	NA	P-0037587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	87	688	0	ENST00000171111.5:c.1429G>A	p.Gly477Ser	p.G477S	ENST00000171111	NM_203500.1	477	Ggc/Agc	4/6	1	2	FACETS	0.937	0.829	1	0.937	0.829	1	CLONAL	1	TRUE	1	0.256117947682783	2		688	725	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143352321	143352321	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0037587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	31	503	0	ENST00000262992.4:c.91+1del		p.X31_splice	ENST00000262992	NM_001101669.1	31			1	2	FACETS	0.466	0.376	0.568	0.466	0.376	0.568	SUBCLONAL	1	TRUE	1	0.256117947682783	2		503	520	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227998	53227998	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	177	541	0	ENST00000375401.3:c.2316del	p.Trp773GlyfsTer22	p.W773Gfs*22	ENST00000375401	NM_004187.3	772	acC/ac	16/26	0.104003338918745	2	FACETS	1	0.985	1			1	INDETERMINATE	2	FALSE	NA	0.276669499569364	2		541	521	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100115	157100115	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1015605215	NA	P-0037986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	11	34	0	ENST00000346085.5:c.1052G>C	p.Gly351Ala	p.G351A	ENST00000346085	NM_020732.3	351	gGa/gCa	1/20	0.268545769233052	3	FACETS	0.978	0.683	1	0.489	0.341	0.668	CLONAL	1	FALSE	1	0.268545769233052	3		34	95	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0038053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	14	418	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.815	1	1	0.924	1	CLONAL	2	TRUE	1	0.161499924419454	2		418	76	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326695	62326695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140411308	NA	P-0038053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	13	963	0	ENST00000360203.5:c.3514G>A	p.Glu1172Lys	p.E1172K	ENST00000360203	NM_001283009.1	1172	Gag/Aag	34/35	1	2	FACETS	0.91	0.666	1	1	0.926	1	CLONAL	3	TRUE	1	0.161499924419454	2		963	59	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519717	NA	P-0038237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	396	565	0	ENST00000206249.3:c.1607T>G	p.Leu536Arg	p.L536R	ENST00000206249	NM_000125.3	536	cTc/cGc	8/8	1	2	FACETS	0.972	0.928	1	0.972	0.928	1	CLONAL	1	TRUE	1	0.883044827702064	2		565	923	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112276	115112292	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGTCCGTCTGCACCG	CGCGTCCGTCTGCACCG	-	novel	NA	P-0038237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	43	56	0	ENST00000257566.3:c.1448_1464del	p.Thr483SerfsTer203	p.T483Sfs*203	ENST00000257566	NM_016569.3	483	aCGGTGCAGACGGACGCG/a	7/8	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.883044827702064	2		56	86	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15978934	15978935	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0038237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	344	601	1	ENST00000268712.3:c.3583_3584del	p.Ser1195GlnfsTer3	p.S1195Qfs*3	ENST00000268712	NM_006311.3	1195	AGc/c	27/46	0.883044827702064	1	FACETS	0.93	0.898	0.96	0.93	0.898	0.96	CLONAL	1	TRUE	0	0.883044827702064	1		602	468	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398107	4398107	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	252	537	0	ENST00000261254.3:c.671C>G	p.Thr224Ser	p.T224S	ENST00000261254	NM_001759.3	224	aCt/aGt	4/5	1	2	FACETS	0.612	0.573	0.652	0.612	0.573	0.652	SUBCLONAL	1	TRUE	1	0.883044827702064	2		537	933	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	54	333	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.648893601093861	2		333	149	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509186	106509186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	97	632	0	ENST00000359195.3:c.1180C>T	p.Leu394Phe	p.L394F	ENST00000359195	NM_002649.2	394	Ctt/Ttt	2/11	0.14798791469182	4	FACETS	0.787	0.71	0.868	0.787	0.71	0.868	INDETERMINATE	2	TRUE	2	0.648893601093861	4		632	313	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796882	42796883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761345552	NA	P-0038313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	48	809	2	ENST00000575354.2:c.3347dup	p.Ser1117LysfsTer34	p.S1117Kfs*34	ENST00000575354	NM_015125.3	1114	gcc/gCcc	14/20	0.597083319169637	1	FACETS	0.185	0.155	0.217	0.185	0.155	0.217	SUBCLONAL	1	TRUE	0	0.597083319169637	1		811	611	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	37	333	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.805	0.674	0.946	0.805	0.674	0.946	CLONAL	1	TRUE	1	0.597083319169637	2		333	154	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0038313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	104	308	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.597083319169637	2		309	335	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444667	78444692	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	GCACTGTTGAATAGTCTGCCATGGTT	GCACTGTTGAATAGTCTGCCATGGTT	-	novel	NA	P-0038313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	95	440	0	ENST00000370768.2:c.-4_22del		p.*2*	ENST00000370768	NM_003902.3	?-8/644		1/20	0.597083319169637	1	FACETS	0.647	0.581	0.715	0.647	0.581	0.715	SUBCLONAL	1	TRUE	0	0.597083319169637	1		440	345	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94910964	94910964	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	176	565	0	ENST00000536441.1:c.1166C>G	p.Thr389Ser	p.T389S	ENST00000536441	NM_144665.3	389	aCt/aGt	8/10	1	2	FACETS	0.937	0.867	1	0.937	0.867	1	CLONAL	1	TRUE	1	0.597083319169637	2		565	629	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348161	89348161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	267	782	0	ENST00000301030.4:c.4789C>T	p.Arg1597Cys	p.R1597C	ENST00000301030	NM_001256183.1	1597	Cgc/Tgc	9/13	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.597083319169637	2		782	851	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	225	632	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.762	0.711	0.814	1	0.992	1	SUBCLONAL	2	TRUE	1	0.357805501998817	2		635	825	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	161	828	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.357805501998817	2		828	662	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	86	609	6	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.763	0.676	0.857	0.763	0.676	0.857	SUBCLONAL	1	TRUE	1	0.357805501998817	2		615	630	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	104	847	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	0.815	0.73	0.905	0.815	0.73	0.905	CLONAL	1	TRUE	1	0.357805501998817	2		847	713	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	82	716	6	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.542	0.477	0.612	0.542	0.477	0.612	SUBCLONAL	1	TRUE	1	0.357805501998817	2		722	846	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	170	665	2	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.962	0.884	1	0.962	0.884	1	CLONAL	1	TRUE	1	0.357805501998817	2		667	988	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	149	712	1	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	0.212430328853166	4	FACETS	0.763	0.698	0.831	0.763	0.698	0.831	INDETERMINATE	2	TRUE	2	0.357805501998817	4		713	741	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	57	485	1	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	1	2	FACETS	0.819	0.705	0.942	0.819	0.705	0.942	CLONAL	1	TRUE	1	0.357805501998817	2		486	389	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671655	67671655	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1400980130	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	38	700	0	ENST00000264010.4:c.2070del	p.Glu691SerfsTer30	p.E691Sfs*30	ENST00000264010	NM_006565.3	688	gtA/gt	12/12	0.357805501998817	1	FACETS	0.312	0.257	0.373	0.312	0.257	0.373	SUBCLONAL	1	TRUE	0	0.357805501998817	1		700	559	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	137	665	0	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	0.762	0.692	0.836	0.762	0.692	0.836	SUBCLONAL	1	TRUE	1	0.357805501998817	2		665	1005	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374881	45374881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	82	795	0	ENST00000262160.6:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000262160	NM_005901.5	321	cGa/cAa	8/11	0.221856219541869	1	FACETS	0.808	0.715	0.906	0.808	0.715	0.906	CLONAL	1	TRUE	0	0.357805501998817	1		795	466	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	116	771	7	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	0.259145192511255	0	FACETS	0.729	0.659	0.803			1	SUBCLONAL	1	TRUE	0	0.357805501998817	0		778	571	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149596	202149596	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	38	626	0	ENST00000358485.4:c.1037G>A	p.Cys346Tyr	p.C346Y	ENST00000358485	NM_001080125.1	346	tGc/tAc	8/9	1	2	FACETS	0.439	0.362	0.524	0.439	0.362	0.524	SUBCLONAL	1	TRUE	1	0.357805501998817	2		626	484	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056053	26056067	+	inframe_deletion	In_Frame_Del	DEL	CCTTGGGCTTAGCGG	CCTTGGGCTTAGCGG	-	rs756916945	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	87	531	0	ENST00000343677.2:c.590_604del	p.Ala197_Lys201del	p.A197_K201del	ENST00000343677	NM_005319.3	197	gCCGCTAAGCCCAAGGtt/gtt	1/1	0.357805501998817	7	FACETS	1	0.976	1			1	CLONAL	1	TRUE	NA	0.357805501998817	7		531	655	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057937	27057937	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	132	796	0	ENST00000324856.7:c.1650del	p.Tyr551ThrfsTer68	p.Y551Tfs*68	ENST00000324856	NM_006015.4	549	Ccc/cc	3/20	0.326630970241583	1	FACETS	0.976	0.888	1	0.976	0.888	1	CLONAL	1	TRUE	0	0.357805501998817	1		796	621	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843724	156843724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	188	1134	2	ENST00000524377.1:c.1150G>A	p.Glu384Lys	p.E384K	ENST00000524377	NM_002529.3	384	Gag/Aag	8/17	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.357805501998817	2		1136	919	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132465	11132465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	137	965	1	ENST00000358026.2:c.2681C>T	p.Thr894Met	p.T894M	ENST00000358026	NM_001128849.1	894	aCg/aTg	19/36	1	2	FACETS	0.905	0.823	0.991	0.905	0.823	0.991	CLONAL	1	TRUE	1	0.357805501998817	2		966	846	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1272311	1272311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141425941	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	80	807	0	ENST00000310581.5:c.2371G>A	p.Val791Ile	p.V791I	ENST00000310581	NM_198253.2	791	Gtc/Atc	7/16	0.221856219541869	1	FACETS	0.649	0.572	0.731	0.649	0.572	0.731	SUBCLONAL	1	TRUE	0	0.357805501998817	1		807	566	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244155	153244156	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	112	721	0	ENST00000281708.4:c.2001dup	p.Ser668GlufsTer26	p.S668Efs*26	ENST00000281708	NM_033632.3	667	-/G	12/12	1	2	FACETS	0.865	0.778	0.956	0.865	0.778	0.956	CLONAL	1	TRUE	1	0.357805501998817	2		721	724	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549439	187549439	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	167	754	0	ENST00000441802.2:c.4679del	p.Pro1560ArgfsTer25	p.P1560Rfs*25	ENST00000441802	NM_005245.3	1560	cCg/cg	9/27	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.357805501998817	2		754	872	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508461	106508461	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762164881	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	38	496	0	ENST00000359195.3:c.455G>A	p.Arg152Gln	p.R152Q	ENST00000359195	NM_002649.2	152	cGg/cAg	2/11	1	2	FACETS	0.602	0.498	0.716	0.602	0.498	0.716	SUBCLONAL	1	TRUE	1	0.357805501998817	2		496	353	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033352	48033352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750949	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	74	597	0	ENST00000234420.5:c.3656C>T	p.Thr1219Ile	p.T1219I	ENST00000234420	NM_000179.2	1219	aCt/aTt	8/10	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.357805501998817	2		597	374	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414263	32414263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121907906	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	45	688	0	ENST00000332351.3:c.1288C>T	p.Arg430Ter	p.R430*	ENST00000332351	NM_024426.4	430	Cga/Tga	8/10	1	2	FACETS	0.451	0.378	0.531	0.451	0.378	0.531	SUBCLONAL	1	TRUE	1	0.357805501998817	2		688	558	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260485	16260486	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	90	702	2	ENST00000375759.3:c.7756dup	p.Thr2586AsnfsTer10	p.T2586Nfs*10	ENST00000375759	NM_015001.2	2584	gaa/gAaa	11/15	0.326630970241583	1	FACETS	0.886	0.79	0.988	0.886	0.79	0.988	CLONAL	1	TRUE	0	0.357805501998817	1		704	466	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383183	42383183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782507150	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	128	989	2	ENST00000221972.3:c.203G>A	p.Arg68His	p.R68H	ENST00000221972	NM_021601.3	68	cGc/cAc	2/5	1	2	FACETS	0.828	0.75	0.91	0.828	0.75	0.91	CLONAL	1	TRUE	1	0.357805501998817	2		991	864	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524347	187524347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773283301	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	122	702	1	ENST00000441802.2:c.11333C>T	p.Ala3778Val	p.A3778V	ENST00000441802	NM_005245.3	3778	gCg/gTg	19/27	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.357805501998817	2		703	651	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288788	15288789	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	37	96	0	ENST00000263388.2:c.3950dup	p.Gly1318ArgfsTer245	p.G1318Rfs*245	ENST00000263388	NM_000435.2	1317	cca/ccCa	24/33	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.357805501998817	2		96	200	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900661	3900661	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	34	813	0	ENST00000262367.5:c.435del	p.Ala146LeufsTer6	p.A146Lfs*6	ENST00000262367	NM_004380.2	145	ccC/cc	2/31	1	2	FACETS	0.299	0.244	0.362	0.299	0.244	0.362	SUBCLONAL	1	TRUE	1	0.357805501998817	2		813	635	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128420047	128420047	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	60	870	3	ENST00000265960.3:c.381del	p.Lys127AsnfsTer20	p.K127Nfs*20	ENST00000265960	NM_001006617.1	127	aaA/aa	4/12	0.221856219541869	1	FACETS	0.483	0.416	0.556	0.483	0.416	0.556	SUBCLONAL	1	TRUE	0	0.357805501998817	1		873	570	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058536	69058536	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61753703	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	110	849	1	ENST00000288368.4:c.4180C>T	p.Arg1394Trp	p.R1394W	ENST00000288368	NM_024870.2	1394	Cgg/Tgg	34/40	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.357805501998817	2		850	587	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211504	36211504	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	78	597	0	ENST00000222270.7:c.1259del	p.Pro420LeufsTer55	p.P420Lfs*55	ENST00000222270	NM_014727.1	419	Ccc/cc	3/37	1	2	FACETS	0.862	0.759	0.971	0.862	0.759	0.971	CLONAL	1	TRUE	1	0.357805501998817	2		597	506	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013719	170013719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388201066	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	92	571	0	ENST00000295797.4:c.1438C>T	p.Arg480Cys	p.R480C	ENST00000295797	NM_002740.5	480	Cgc/Tgc	15/18	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.357805501998817	2		571	470	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	83	936	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.212430328853166	4	FACETS	0.818	0.721	0.922	0.409	0.36	0.461	INDETERMINATE	1	TRUE	2	0.357805501998817	4		936	770	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158026	27158026	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	150	874	0	ENST00000380036.4:c.255del	p.Val86LeufsTer31	p.V86Lfs*31	ENST00000380036	NM_000459.3	84	Aaa/aa	2/23	0.221856219541869	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.357805501998817	1		874	678	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963985	2963985	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200736339	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	130	905	0	ENST00000396946.4:c.1822C>T	p.Arg608Cys	p.R608C	ENST00000396946	NM_032415.4	608	Cgc/Tgc	15/25	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.357805501998817	2		905	653	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210725	36210725	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	159	978	2	ENST00000222270.7:c.481del	p.Leu161PhefsTer6	p.L161Ffs*6	ENST00000222270	NM_014727.1	159	aCc/ac	3/37	1	2	FACETS	0.958	0.878	1	0.958	0.878	1	CLONAL	1	TRUE	1	0.357805501998817	2		980	928	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446317	70446317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1371245854	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	86	842	1	ENST00000373644.4:c.5257C>T	p.Arg1753Cys	p.R1753C	ENST00000373644	NM_030625.2	1753	Cgt/Tgt	11/12	1	2	FACETS	0.554	0.489	0.623	0.554	0.489	0.623	SUBCLONAL	1	TRUE	1	0.357805501998817	2		843	868	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476388	88476388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374759890	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	117	728	0	ENST00000360948.2:c.1744C>T	p.Arg582Trp	p.R582W	ENST00000360948	NM_001012338.2	582	Cgg/Tgg	15/19	0.357805501998817	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.357805501998817	1		728	530	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223375	2223376	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	127	845	0	ENST00000398665.3:c.3492dup	p.Val1165ArgfsTer28	p.V1165Rfs*28	ENST00000398665	NM_032482.2	1162	-/C	25/28	1	2	FACETS	0.824	0.746	0.906	0.824	0.746	0.906	CLONAL	1	TRUE	1	0.357805501998817	2		845	862	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796080	78796080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	130	733	1	ENST00000306801.3:c.970G>A	p.Ala324Thr	p.A324T	ENST00000306801	NM_020761.2	324	Gcg/Acg	8/34	1	2	FACETS	0.897	0.814	0.985	0.897	0.814	0.985	CLONAL	1	TRUE	1	0.357805501998817	2		734	810	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743757	46743757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774695182	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	180	978	0	ENST00000371975.4:c.2047C>T	p.Arg683Cys	p.R683C	ENST00000371975	NM_003579.3	683	Cgt/Tgt	18/18	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.357805501998817	2		978	942	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957514	175957514	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	84	649	0	ENST00000367669.3:c.1882G>T	p.Gly628Trp	p.G628W	ENST00000367669	NM_022457.5	628	Ggg/Tgg	17/20	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.357805501998817	2		649	445	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243778465	243778465	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	16	384	0	ENST00000263826.5:c.562-2A>G		p.X188_splice	ENST00000263826	NM_005465.4	188			1	2	FACETS	0.296	0.218	0.389	0.296	0.218	0.389	SUBCLONAL	1	TRUE	1	0.357805501998817	2		384	302	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670434	246670434	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	165	703	0	ENST00000388985.4:c.86T>C	p.Leu29Pro	p.L29P	ENST00000388985		29	cTa/cCa	1/12	0.240512283932166	1	FACETS	0.878	0.806	0.952	0.878	0.806	0.952	CLONAL	1	TRUE	0	0.357805501998817	1		703	863	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154234	2154234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1363016357	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	49	912	0	ENST00000434045.2:c.694G>A	p.Ala232Thr	p.A232T	ENST00000434045	NM_001127598.1	232	Gcc/Acc	5/5	1	2	FACETS	0.427	0.361	0.5	0.427	0.361	0.5	SUBCLONAL	1	TRUE	1	0.357805501998817	2		912	642	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71947004	71947005	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	159	1074	0	ENST00000298229.2:c.2857dup	p.Arg953ProfsTer16	p.R953Pfs*16	ENST00000298229	NM_001567.3	951	-/C	25/28	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.357805501998817	2		1074	889	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123689	46123689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	53	425	0	ENST00000334344.6:c.70C>T	p.Arg24Trp	p.R24W	ENST00000334344	NM_152641.2	24	Cgg/Tgg	1/21	0.212430328853166	4	FACETS	0.612	0.521	0.712	0.306	0.26	0.356	INDETERMINATE	1	TRUE	2	0.357805501998817	4		425	657	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245394	46245394	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	44	759	0	ENST00000334344.6:c.3491del	p.Phe1164SerfsTer9	p.F1164Sfs*9	ENST00000334344	NM_152641.2	1163	aTt/at	15/21	0.212430328853166	4	FACETS	0.596	0.499	0.704	0.298	0.249	0.352	INDETERMINATE	1	TRUE	2	0.357805501998817	4		759	560	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226079	133226079	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs377324348	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	140	987	1	ENST00000320574.5:c.3818G>T	p.Arg1273Leu	p.R1273L	ENST00000320574	NM_006231.2	1273	cGg/cTg	31/49	0.333582980757135	1	FACETS	0.935	0.854	1	0.935	0.854	1	CLONAL	1	TRUE	0	0.357805501998817	1		988	687	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872488	35872488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	127	805	1	ENST00000216797.5:c.415C>T	p.Leu139Phe	p.L139F	ENST00000216797	NM_020529.2	139	Ctc/Ttc	3/6	1	2	FACETS	0.738	0.668	0.812	0.738	0.668	0.812	SUBCLONAL	1	TRUE	1	0.357805501998817	2		806	962	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99451954	99451954	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	122	629	2	ENST00000268035.6:c.1288C>T	p.Gln430Ter	p.Q430*	ENST00000268035	NM_000875.3	430	Caa/Taa	6/21	0.357805501998817	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.357805501998817	1		631	472	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830763	3830763	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	106	689	1	ENST00000262367.5:c.1793A>G	p.Gln598Arg	p.Q598R	ENST00000262367	NM_004380.2	598	cAg/cGg	8/31	1	2	FACETS	0.967	0.868	1	0.967	0.868	1	CLONAL	1	TRUE	1	0.357805501998817	2		690	613	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611720	1611720	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149962284	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	163	922	0	ENST00000344749.5:c.1942G>A	p.Ala648Thr	p.A648T	ENST00000344749	NM_001136139.2	648	Gcc/Acc	19/19	1	2	FACETS	0.978	0.897	1	0.978	0.897	1	CLONAL	1	TRUE	1	0.357805501998817	2		922	932	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10244891	10244891	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	116	858	0	ENST00000340748.4:c.4816+2T>C		p.X1606_splice	ENST00000340748		1606			1	2	FACETS	0.961	0.867	1	0.961	0.867	1	CLONAL	1	TRUE	1	0.357805501998817	2		858	675	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17382428	17382428	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	129	852	1	ENST00000359435.4:c.308A>G	p.Glu103Gly	p.E103G	ENST00000359435	NM_001033549.1	103	gAg/gGg	3/9	1	2	FACETS	0.868	0.787	0.953	0.868	0.787	0.953	CLONAL	1	TRUE	1	0.357805501998817	2		853	831	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42381390	42381390	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	112	815	0	ENST00000221972.3:c.16G>T	p.Gly6Ter	p.G6*	ENST00000221972	NM_021601.3	6	Gga/Tga	1/5	1	2	FACETS	0.762	0.685	0.843	0.762	0.685	0.843	SUBCLONAL	1	TRUE	1	0.357805501998817	2		815	822	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794868	42794868	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143994466	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	115	963	2	ENST00000575354.2:c.1948G>A	p.Ala650Thr	p.A650T	ENST00000575354	NM_015125.3	650	Gcc/Acc	10/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.357805501998817	2		965	595	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919055	50919055	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555793174	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	134	879	0	ENST00000440232.2:c.2792A>G	p.Lys931Arg	p.K931R	ENST00000440232	NM_002691.3	931	aAg/aGg	22/27	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.357805501998817	2		879	693	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714579	52714579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113545781	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	155	924	0	ENST00000322088.6:c.337C>T	p.Arg113Trp	p.R113W	ENST00000322088	NM_014225.5	113	Cgg/Tgg	4/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.357805501998817	2		924	716	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470922	25470922	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	74	868	0	ENST00000264709.3:c.839A>G	p.Asp280Gly	p.D280G	ENST00000264709	NM_175629.2	280	gAc/gGc	7/23	1	2	FACETS	0.487	0.425	0.553	0.487	0.425	0.553	SUBCLONAL	1	TRUE	1	0.357805501998817	2		868	850	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378314	225378314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	70	480	0	ENST00000264414.4:c.581G>A	p.Gly194Asp	p.G194D	ENST00000264414	NM_003590.4	194	gGt/gAt	5/16	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.357805501998817	2		480	353	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663330	227663330	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	164	715	0	ENST00000305123.5:c.125C>T	p.Ala42Val	p.A42V	ENST00000305123	NM_005544.2	42	gCg/gTg	1/2	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.357805501998817	2		715	707	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651187	45651187	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs749300015	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	76	759	1	ENST00000407780.3:c.838C>T	p.Arg280Ter	p.R280*	ENST00000407780	NM_001283052.1	280	Cga/Tga	5/7	1	2	FACETS	0.566	0.495	0.641	0.566	0.495	0.641	SUBCLONAL	1	TRUE	1	0.357805501998817	2		760	751	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101764	71101764	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	60	325	0	ENST00000318789.4:c.434A>G	p.Glu145Gly	p.E145G	ENST00000318789	NM_032682.5	145	gAg/gGg	9/21	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.357805501998817	2		325	301	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259454	89259454	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	45	718	0	ENST00000336596.2:c.602del	p.Lys201SerfsTer6	p.K201Sfs*6	ENST00000336596	NM_005233.5	200	Aaa/aa	3/17	1	2	FACETS	0.414	0.347	0.488	0.414	0.347	0.488	SUBCLONAL	1	TRUE	1	0.357805501998817	2		718	608	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665499	176665499	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	112	608	0	ENST00000439151.2:c.4186del	p.Thr1396ArgfsTer23	p.T1396Rfs*23	ENST00000439151	NM_022455.4	1395	Aaa/aa	7/23	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.357805501998817	2		608	620	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031934	26031934	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	100	498	0	ENST00000244661.2:c.355A>G	p.Thr119Ala	p.T119A	ENST00000244661	NM_003537.3	119	Act/Gct	1/1	0.357805501998817	7	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.357805501998817	7		498	713	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940207	31940207	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	181	1103	1	ENST00000375333.2:c.349C>A	p.His117Asn	p.H117N	ENST00000375333	NM_032454.1	117	Cac/Aac	2/8	0.212430328853166	4	FACETS	1	0.976	1	0.573	0.528	0.621	INDETERMINATE	1	TRUE	2	0.357805501998817	4		1104	1198	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004668	150004668	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	123	809	0	ENST00000253339.5:c.1557G>T	p.Trp519Cys	p.W519C	ENST00000253339		519	tgG/tgT	3/7	0.212430328853166	4	FACETS	1	0.981	1	0.676	0.613	0.744	INDETERMINATE	1	TRUE	2	0.357805501998817	4		809	690	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2969640	2969640	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	63	783	0	ENST00000396946.4:c.1639T>C	p.Ser547Pro	p.S547P	ENST00000396946	NM_032415.4	547	Tcc/Ccc	12/25	1	2	FACETS	0.51	0.441	0.586	0.51	0.441	0.586	SUBCLONAL	1	TRUE	1	0.357805501998817	2		783	690	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358972	81358972	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	37	777	1	ENST00000222390.5:c.989A>G	p.Asp330Gly	p.D330G	ENST00000222390	NM_000601.4	330	gAt/gGt	8/18	1	2	FACETS	0.345	0.283	0.414	0.345	0.283	0.414	SUBCLONAL	1	TRUE	1	0.357805501998817	2		778	600	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162224	38162224	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	105	686	0	ENST00000317025.8:c.2492C>T	p.Ala831Val	p.A831V	ENST00000317025	NM_023034.1	831	gCt/gTt	14/24	1	2	FACETS	0.911	0.818	1	0.911	0.818	1	CLONAL	1	TRUE	1	0.357805501998817	2		686	644	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187218	38187218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766932248	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	190	958	2	ENST00000317025.8:c.1259G>A	p.Arg420Gln	p.R420Q	ENST00000317025	NM_023034.1	420	cGa/cAa	6/24	1	2	FACETS	0.998	0.922	1	0.998	0.922	1	CLONAL	1	TRUE	1	0.357805501998817	2		960	1064	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27228303	27228303	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	42	583	0	ENST00000380036.4:c.3300G>T	p.Lys1100Asn	p.K1100N	ENST00000380036	NM_000459.3	1100	aaG/aaT	22/23	0.221856219541869	1	FACETS	0.49	0.41	0.579	0.49	0.41	0.579	SUBCLONAL	1	TRUE	0	0.357805501998817	1		583	393	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966706	36966706	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759872013	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	102	623	0	ENST00000358127.4:c.620C>T	p.Pro207Leu	p.P207L	ENST00000358127	NM_001280556.1	207	cCg/cTg	6/10	0.221856219541869	1	FACETS	0.952	0.855	1	0.952	0.855	1	CLONAL	1	TRUE	0	0.357805501998817	1		623	492	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430649	80430649	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	59	534	0	ENST00000286548.4:c.359A>G	p.Lys120Arg	p.K120R	ENST00000286548	NM_002072.3	120	aAg/aGg	3/7	0.221856219541869	1	FACETS	0.778	0.673	0.891	0.778	0.673	0.891	SUBCLONAL	1	TRUE	0	0.357805501998817	1		534	348	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399780	139399780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367589813	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	89	865	0	ENST00000277541.6:c.4568G>A	p.Arg1523His	p.R1523H	ENST00000277541	NM_017617.3	1523	cGt/cAt	25/34	0.221856219541869	1	FACETS	0.5	0.443	0.561	0.5	0.443	0.561	SUBCLONAL	1	TRUE	0	0.357805501998817	1		865	817	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923666	39923666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	74	941	0	ENST00000378444.4:c.3425G>A	p.Ser1142Asn	p.S1142N	ENST00000378444	NM_001123385.1	1142	aGc/aAc	7/15	0.333582980757135	1	FACETS	0.493	0.431	0.56	0.493	0.431	0.56	SUBCLONAL	1	TRUE	0	0.357805501998817	1		941	689	SUCCESS
AR	367	MSKCC	GRCh37	X	66765427	66765427	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	50	924	0	ENST00000374690.3:c.439C>T	p.Gln147Ter	p.Q147*	ENST00000374690	NM_000044.3	147	Cag/Tag	1/8	0.333582980757135	1	FACETS	0.394	0.333	0.46	0.394	0.333	0.46	SUBCLONAL	1	TRUE	0	0.357805501998817	1		924	583	SUCCESS
AR	367	MSKCC	GRCh37	X	66766583	66766583	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	70	870	0	ENST00000374690.3:c.1595C>T	p.Ser532Phe	p.S532F	ENST00000374690	NM_000044.3	532	tCc/tTc	1/8	0.333582980757135	1	FACETS	0.46	0.401	0.525	0.46	0.401	0.525	SUBCLONAL	1	TRUE	0	0.357805501998817	1		870	698	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341473	70341473	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1157525906	NA	P-0038424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	156	968	2	ENST00000374080.3:c.908G>A	p.Arg303Gln	p.R303Q	ENST00000374080		303	cGg/cAg	7/45	0.333582980757135	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.357805501998817	1		970	646	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0038428-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	104	262	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.390945686753244	2		262	499	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544640	65544640	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038428-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	127	531	0	ENST00000358664.4:c.286G>T	p.Glu96Ter	p.E96*	ENST00000358664	NM_002382.4	96	Gag/Tag	4/5	1	2	FACETS	0.802	0.727	0.882	0.802	0.727	0.882	CLONAL	1	TRUE	1	0.390945686753244	2		531	810	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544712	65544712	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038428-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	162	701	0	ENST00000358664.4:c.214C>T	p.Gln72Ter	p.Q72*	ENST00000358664	NM_002382.4	72	Cag/Tag	4/5	1	2	FACETS	0.844	0.774	0.917	0.844	0.774	0.917	CLONAL	1	TRUE	1	0.390945686753244	2		701	982	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777990	3777990	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038428-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	241	1143	0	ENST00000262367.5:c.7058G>T	p.Arg2353Leu	p.R2353L	ENST00000262367	NM_004380.2	2353	cGg/cTg	31/31	1	2	FACETS	0.886	0.825	0.948	0.886	0.825	0.948	CLONAL	1	TRUE	1	0.390945686753244	2		1143	1392	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688805	47688805	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038428-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	78	354	0	ENST00000347630.2:c.495A>T	p.Gln165His	p.Q165H	ENST00000347630	NM_001007230.1	165	caA/caT	7/11	1	2	FACETS	0.617	0.542	0.697	0.617	0.542	0.697	SUBCLONAL	1	TRUE	1	0.390945686753244	2		354	647	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346615	225346615	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038428-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	85	373	0	ENST00000264414.4:c.2023C>T	p.Gln675Ter	p.Q675*	ENST00000264414	NM_003590.4	675	Caa/Taa	14/16	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.390945686753244	2		373	404	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661342	227661342	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038428-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	164	812	0	ENST00000305123.5:c.2113G>T	p.Gly705Cys	p.G705C	ENST00000305123	NM_005544.2	705	Ggc/Tgc	1/2	1	2	FACETS	0.865	0.794	0.94	0.865	0.794	0.94	CLONAL	1	TRUE	1	0.390945686753244	2		812	970	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933270	49933270	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038428-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	203	969	0	ENST00000296474.3:c.2840G>T	p.Arg947Leu	p.R947L	ENST00000296474	NM_002447.2	947	cGg/cTg	12/20	1	2	FACETS	0.948	0.879	1	0.948	0.879	1	CLONAL	1	TRUE	1	0.390945686753244	2		969	1095	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498395	89498395	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038428-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	46	298	0	ENST00000336596.2:c.2367G>T	p.Arg789Ser	p.R789S	ENST00000336596	NM_005233.5	789	agG/agT	14/17	1	2	FACETS	0.619	0.523	0.725	0.619	0.523	0.725	SUBCLONAL	1	TRUE	1	0.390945686753244	2		298	380	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0038472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	225	405	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.308248487813818	1	FACETS	0.982	0.916	1	0.982	0.916	1	CLONAL	1	TRUE	0	0.418608630753131	1		406	866	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916937	+	inframe_deletion	In_Frame_Del	DEL	GGCAACCGT	GGCAACCGT	-	novel	NA	P-0038472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	94	372	0	ENST00000263967.3:c.317_325del	p.Gly106_Arg108del	p.G106_R108del	ENST00000263967	NM_006218.2	106	GGCAACCGT/-	2/21	1	2	FACETS	0.926	0.827	1	0.926	0.827	1	CLONAL	1	TRUE	1	0.418608630753131	2		372	485	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046305	128046305	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	52	515	0	ENST00000285398.2:c.958C>G	p.Gln320Glu	p.Q320E	ENST00000285398	NM_000122.1	320	Cag/Gag	7/15	1	2	FACETS	0.351	0.298	0.41	0.351	0.298	0.41	SUBCLONAL	1	TRUE	1	0.418608630753131	2		515	707	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487214	56487214	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	175	614	0	ENST00000267101.3:c.1360A>G	p.Ile454Val	p.I454V	ENST00000267101	NM_001982.3	454	Atc/Gtc	12/28	0.119097333049954	5	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.418608630753131	5		614	916	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037934	49037935	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	15	301	0	ENST00000267163.4:c.2176dup	p.Thr726AsnfsTer25	p.T726Nfs*25	ENST00000267163	NM_000321.2	725	gta/gtAa	21/27	0.247974782603761	1	FACETS	0.208	0.151	0.275	0.208	0.151	0.275	INDETERMINATE	1	TRUE	0	0.418608630753131	1		301	273	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021133	31021133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	90	542	0	ENST00000375687.4:c.1132G>A	p.Glu378Lys	p.E378K	ENST00000375687	NM_015338.5	378	Gag/Aag	12/13	1	2	FACETS	0.47	0.416	0.528	0.47	0.416	0.528	SUBCLONAL	1	TRUE	1	0.418608630753131	2		542	915	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0038485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	492	540	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.163240829241074	6	FACETS	1	0.993	1			1	INDETERMINATE	3	TRUE	NA	0.689813736747633	6		540	993	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325900	30325900	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	111	337	0	ENST00000322652.5:c.2098G>C	p.Glu700Gln	p.E700Q	ENST00000322652	NM_015355.2	700	Gaa/Caa	16/16	0.689813736747633	1	FACETS	0.905	0.831	0.979	0.905	0.831	0.979	CLONAL	1	TRUE	0	0.689813736747633	1		337	233	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	127	399	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.824	0.752	0.9	0.824	0.752	0.9	CLONAL	1	TRUE	1	0.65	2		399	474	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	243	632	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.929	0.87	0.989	0.929	0.87	0.989	CLONAL	1	TRUE	1	0.65	2		635	805	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	187	355	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.874	0.811	0.94	0.874	0.811	0.94	CLONAL	1	TRUE	1	0.65	2		355	658	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796882	42796883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761345552	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	242	809	2	ENST00000575354.2:c.3347dup	p.Ser1117LysfsTer34	p.S1117Kfs*34	ENST00000575354	NM_015125.3	1114	gcc/gCcc	14/20	1	2	FACETS	0.759	0.709	0.81	0.759	0.709	0.81	SUBCLONAL	1	TRUE	1	0.65	2		811	981	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	184	626	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.95	0.882	1	0.95	0.882	1	CLONAL	1	TRUE	1	0.65	2		626	596	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	131	609	6	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.703	0.641	0.769	0.703	0.641	0.769	SUBCLONAL	1	TRUE	1	0.65	2		615	573	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	253	665	2	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.94	0.882	0.999	0.94	0.882	0.999	CLONAL	1	TRUE	1	0.65	2		667	828	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944516	71944516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293622519	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	227	609	0	ENST00000298229.2:c.2072G>A	p.Arg691Gln	p.R691Q	ENST00000298229	NM_001567.3	691	cGg/cAg	18/28	1	2	FACETS	0.85	0.794	0.907	0.85	0.794	0.907	CLONAL	1	TRUE	1	0.65	2		609	822	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	217	790	2	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.773	0.72	0.828	0.773	0.72	0.828	SUBCLONAL	1	TRUE	1	0.65	2		792	864	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	213	650	2	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	2	FACETS	0.764	0.711	0.819	0.764	0.711	0.819	SUBCLONAL	1	TRUE	1	0.65	2		652	858	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383232	31383232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35846833	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	160	397	0	ENST00000328111.2:c.1144C>T	p.Arg382Cys	p.R382C	ENST00000328111	NM_006892.3	382	Cgc/Tgc	11/23	1	2	FACETS	0.856	0.789	0.925	0.856	0.789	0.925	CLONAL	1	TRUE	1	0.65	2		397	575	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	102	323	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	0.954	0.863	1	0.954	0.863	1	CLONAL	1	TRUE	1	0.65	2		323	329	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	171	382	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.65	2		382	498	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	140	349	0	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.896	0.821	0.972	0.896	0.821	0.972	CLONAL	1	TRUE	1	0.65	2		349	481	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592099	67592099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	126	226	0	ENST00000274335.5:c.1915C>T	p.Arg639Ter	p.R639*	ENST00000274335		639	Cga/Tga	14/15	1	2	FACETS	0.955	0.873	1	0.955	0.873	1	CLONAL	1	TRUE	1	0.65	2		226	406	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435128	110435129	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs772322568	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	220	525	3	ENST00000375856.3:c.3272dup	p.Lys1092GlufsTer233	p.K1092Efs*233	ENST00000375856	NM_003749.2	1091	ccg/ccCg	1/2	1	2	FACETS	0.804	0.749	0.86	0.804	0.749	0.86	CLONAL	1	TRUE	1	0.65	2		528	842	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	174	412	0	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.65	2		412	496	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535351	66535351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs963468479	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	241	544	0	ENST00000273854.3:c.110G>A	p.Arg37Gln	p.R37Q	ENST00000273854	NM_004439.5	37	cGg/cAg	1/18	1	2	FACETS	0.976	0.915	1	0.976	0.915	1	CLONAL	1	TRUE	1	0.65	2		544	760	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	188	419	1	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.65	2		420	535	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099103	27099103	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	144	402	0	ENST00000324856.7:c.3524del	p.Pro1175HisfsTer5	p.P1175Hfs*5	ENST00000324856	NM_006015.4	1173	atC/at	13/20	1	2	FACETS	0.821	0.752	0.891	0.821	0.752	0.891	CLONAL	1	TRUE	1	0.65	2		402	540	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058747	180058748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755445139	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	231	669	0	ENST00000261937.6:c.89dup	p.Thr31AspfsTer15	p.T31Dfs*15	ENST00000261937	NM_182925.4	30	ccg/ccCg	2/30	1	2	FACETS	0.808	0.754	0.863	0.808	0.754	0.863	CLONAL	1	TRUE	1	0.65	2		669	880	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105892	27105892	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	201	492	1	ENST00000324856.7:c.5503C>T	p.Gln1835Ter	p.Q1835*	ENST00000324856	NM_006015.4	1835	Cag/Tag	20/20	1	2	FACETS	0.927	0.863	0.993	0.927	0.863	0.993	CLONAL	1	TRUE	1	0.65	2		493	667	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528849	157528849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761204913	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	216	515	0	ENST00000346085.5:c.6574G>A	p.Val2192Ile	p.V2192I	ENST00000346085	NM_020732.3	2192	Gta/Ata	20/20	1	2	FACETS	0.94	0.878	1	0.94	0.878	1	CLONAL	1	TRUE	1	0.65	2		515	707	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885577	111885577	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1416067054	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	305	678	4	ENST00000341259.2:c.1354G>A	p.Ala452Thr	p.A452T	ENST00000341259	NM_005475.2	452	Gcc/Acc	7/8	1	2	FACETS	0.931	0.879	0.984	0.931	0.879	0.984	CLONAL	1	TRUE	1	0.65	2		682	1008	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521525	46521525	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	226	439	0	ENST00000262741.5:c.883del	p.Met295Ter	p.M295*	ENST00000262741	NM_003629.3	295	Atg/tg	7/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.65	2		439	638	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442811	442811	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	114	274	1	ENST00000399788.2:c.1495del	p.Glu499SerfsTer19	p.E499Sfs*19	ENST00000399788	NM_001042603.1	499	Gag/ag	12/28	1	2	FACETS	0.837	0.759	0.918	0.837	0.759	0.918	CLONAL	1	TRUE	1	0.65	2		275	419	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	261	873	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.936	0.879	0.994	0.936	0.879	0.994	CLONAL	1	TRUE	1	0.65	2		874	858	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223175	36223175	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	367	922	0	ENST00000222270.7:c.5730del	p.Arg1911AspfsTer23	p.R1911Dfs*23	ENST00000222270	NM_014727.1	1909	Ccc/cc	28/37	1	2	FACETS	0.97	0.921	1	0.97	0.921	1	CLONAL	1	TRUE	1	0.65	2		922	1164	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	216	509	6	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.889	0.829	0.95	0.889	0.829	0.95	CLONAL	1	TRUE	1	0.65	2		515	748	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644874	67644874	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	216	480	0	ENST00000264010.4:c.143del	p.Gly48ValfsTer14	p.G48Vfs*14	ENST00000264010	NM_006565.3	47	Ggg/gg	3/12	1	2	FACETS	0.891	0.831	0.952	0.891	0.831	0.952	CLONAL	1	TRUE	1	0.65	2		480	746	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856448	111856448	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1445323886	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	108	197	0	ENST00000341259.2:c.499G>A	p.Gly167Arg	p.G167R	ENST00000341259	NM_005475.2	167	Gga/Aga	2/8	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.65	2		197	329	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523067	176523067	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs969219254	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	238	592	0	ENST00000292408.4:c.1831C>T	p.Arg611Trp	p.R611W	ENST00000292408	NM_213647.1	611	Cgg/Tgg	14/18	1	2	FACETS	0.947	0.887	1	0.947	0.887	1	CLONAL	1	TRUE	1	0.65	2		592	773	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349565	15349565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	311	829	0	ENST00000263377.2:c.4009C>T	p.Arg1337Cys	p.R1337C	ENST00000263377	NM_058243.2	1337	Cgc/Tgc	19/20	1	2	FACETS	0.961	0.908	1	0.961	0.908	1	CLONAL	1	TRUE	1	0.65	2		829	996	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573312	41573312	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763290593	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	283	741	0	ENST00000263253.7:c.5597C>T	p.Pro1866Leu	p.P1866L	ENST00000263253	NM_001429.3	1866	cCg/cTg	31/31	1	2	FACETS	0.945	0.89	1	0.945	0.89	1	CLONAL	1	TRUE	1	0.65	2		741	921	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425230	49425230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199797812	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	285	671	0	ENST00000301067.7:c.13258C>T	p.Arg4420Trp	p.R4420W	ENST00000301067	NM_003482.3	4420	Cgg/Tgg	39/54	1	2	FACETS	0.963	0.907	1	0.963	0.907	1	CLONAL	1	TRUE	1	0.65	2		671	911	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379453	225379453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	125	428	0	ENST00000264414.4:c.415G>A	p.Val139Ile	p.V139I	ENST00000264414	NM_003590.4	139	Gtc/Atc	4/16	1	2	FACETS	0.971	0.888	1	0.971	0.888	1	CLONAL	1	TRUE	1	0.65	2		428	396	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308365	15308365	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1362111590	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	316	764	0	ENST00000263388.2:c.143C>T	p.Pro48Leu	p.P48L	ENST00000263388	NM_000435.2	48	cCg/cTg	2/33	1	2	FACETS	0.941	0.889	0.994	0.941	0.889	0.994	CLONAL	1	TRUE	1	0.65	2		764	1033	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437265	220437265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1224525818	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	337	741	2	ENST00000243786.2:c.169C>T	p.Arg57Trp	p.R57W	ENST00000243786	NM_002191.3	57	Cgg/Tgg	1/2	1	2	FACETS	0.938	0.888	0.99	0.938	0.888	0.99	CLONAL	1	TRUE	1	0.65	2		743	1105	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467373	66467373	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	65	175	0	ENST00000273854.3:c.896del	p.Asn299MetfsTer123	p.N299Mfs*123	ENST00000273854	NM_004439.5	299	aAt/at	3/18	1	2	FACETS	0.847	0.744	0.956	0.847	0.744	0.956	CLONAL	1	TRUE	1	0.65	2		175	236	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073587	8073587	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs111953442	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	160	340	0	ENST00000377482.5:c.1072T>C	p.Tyr358His	p.Y358H	ENST00000377482	NM_018948.3	358	Tat/Cat	4/4	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.65	2		340	464	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775993	9775993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779489980	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	256	626	0	ENST00000377346.4:c.457C>T	p.Arg153Cys	p.R153C	ENST00000377346	NM_005026.3	153	Cgc/Tgc	5/24	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.65	2		626	782	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11193181	11193181	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	216	479	0	ENST00000361445.4:c.5320C>T	p.Gln1774Ter	p.Q1774*	ENST00000361445	NM_004958.3	1774	Cag/Tag	38/58	1	2	FACETS	0.871	0.812	0.931	0.871	0.812	0.931	CLONAL	1	TRUE	1	0.65	2		479	763	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28607299	28607299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149879215	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	191	439	1	ENST00000253063.3:c.1429C>T	p.Arg477Cys	p.R477C	ENST00000253063	NM_031459.4	477	Cgc/Tgc	10/10	1	2	FACETS	0.867	0.805	0.931	0.867	0.805	0.931	CLONAL	1	TRUE	1	0.65	2		440	678	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818399	43818399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	269	603	1	ENST00000372470.3:c.1864G>A	p.Ala622Thr	p.A622T	ENST00000372470	NM_005373.2	622	Gcc/Acc	12/12	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.65	2		604	800	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796925	45796925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779701238	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	222	550	0	ENST00000450313.1:c.1405G>A	p.Val469Ile	p.V469I	ENST00000450313	NM_012222.2	469	Gta/Ata	14/16	1	2	FACETS	0.857	0.8	0.916	0.857	0.8	0.916	CLONAL	1	TRUE	1	0.65	2		550	797	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193116998	193116998	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	126	237	0	ENST00000367435.3:c.731A>T	p.Asn244Ile	p.N244I	ENST00000367435	NM_024529.4	244	aAt/aTt	8/17	1	2	FACETS	0.972	0.888	1	0.972	0.888	1	CLONAL	1	TRUE	1	0.65	2		237	399	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405988	70405988	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	197	472	0	ENST00000373644.4:c.3502T>C	p.Tyr1168His	p.Y1168H	ENST00000373644	NM_030625.2	1168	Tat/Cat	4/12	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.65	2		472	600	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	532668	532668	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772602067	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	258	783	1	ENST00000451590.1:c.538G>A	p.Gly180Ser	p.G180S	ENST00000451590	NM_001130442.1	180	Ggc/Agc	5/5	1	2	FACETS	0.855	0.802	0.91	0.855	0.802	0.91	CLONAL	1	TRUE	1	0.65	2		784	928	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998883	100998883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	239	673	0	ENST00000325455.5:c.919C>T	p.Pro307Ser	p.P307S	ENST00000325455	NM_001202474.3	307	Cct/Tct	1/8	1	2	FACETS	0.882	0.825	0.94	0.882	0.825	0.94	CLONAL	1	TRUE	1	0.65	2		673	834	SUCCESS
ATM	472	MSKCC	GRCh37	11	108159786	108159786	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	71	221	0	ENST00000278616.4:c.4195del	p.Thr1399ProfsTer3	p.T1399Pfs*3	ENST00000278616	NM_000051.3	1398	Aaa/aa	28/63	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.65	2		221	202	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164203	108164203	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1565463405	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	56	121	0	ENST00000278616.4:c.4775A>G	p.Glu1592Gly	p.E1592G	ENST00000278616	NM_000051.3	1592	gAg/gGg	31/63	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.65	2		121	170	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434958	49434959	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	186	545	0	ENST00000301067.7:c.6594_6595insA	p.Tyr2199IlefsTer3	p.Y2199Ifs*3	ENST00000301067	NM_003482.3	2198	-/A	31/54	1	2	FACETS	0.867	0.804	0.932	0.867	0.804	0.932	CLONAL	1	TRUE	1	0.65	2		545	660	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448528	49448529	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	194	427	0	ENST00000301067.7:c.182dup	p.Pro62SerfsTer9	p.P62Sfs*9	ENST00000301067	NM_003482.3	61	ggt/ggGt	3/54	1	2	FACETS	0.934	0.869	1	0.934	0.869	1	CLONAL	1	TRUE	1	0.65	2		427	639	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895640	28895640	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139361304	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	117	446	2	ENST00000282397.4:c.3134G>A	p.Arg1045Gln	p.R1045Q	ENST00000282397	NM_002019.4	1045	cGg/cAg	23/30	1	2	FACETS	0.811	0.736	0.889	0.811	0.736	0.889	CLONAL	1	TRUE	1	0.65	2		448	444	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30133050	30133050	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	139	381	0	ENST00000331968.5:c.551A>G	p.Tyr184Cys	p.Y184C	ENST00000331968	NM_002742.2	184	tAc/tGc	4/18	1	2	FACETS	0.857	0.785	0.932	0.857	0.785	0.932	CLONAL	1	TRUE	1	0.65	2		381	499	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242073	105242075	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs768025881	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	232	737	10	ENST00000349310.3:c.349_351del	p.Glu117del	p.E117del	ENST00000349310	NM_001014432.1	117	GAG/-	6/15	1	2	FACETS	0.757	0.706	0.809	0.757	0.706	0.809	SUBCLONAL	1	TRUE	1	0.65	2		747	943	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658505	3658505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778404827	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	275	611	0	ENST00000294008.3:c.461G>A	p.Arg154Gln	p.R154Q	ENST00000294008	NM_032444.2	154	cGg/cAg	2/15	1	2	FACETS	0.954	0.898	1	0.954	0.898	1	CLONAL	1	TRUE	1	0.65	2		611	887	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15975530	15975530	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	111	346	0	ENST00000268712.3:c.3824G>C	p.Arg1275Pro	p.R1275P	ENST00000268712	NM_006311.3	1275	cGa/cCa	29/46	1	2	FACETS	0.951	0.864	1	0.951	0.864	1	CLONAL	1	TRUE	1	0.65	2		346	359	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858039	40858039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	254	583	1	ENST00000428826.2:c.1825C>T	p.Arg609Cys	p.R609C	ENST00000428826		609	Cgt/Tgt	16/21	1	2	FACETS	0.921	0.864	0.979	0.921	0.864	0.979	CLONAL	1	TRUE	1	0.65	2		584	849	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756661	756661	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	217	486	0	ENST00000314574.4:c.167G>C	p.Ser56Thr	p.S56T	ENST00000314574	NM_005433.3	56	aGt/aCt	2/12	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.65	2		486	653	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5207964	5207964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	308	682	2	ENST00000357368.4:c.5747G>A	p.Arg1916Gln	p.R1916Q	ENST00000357368	NM_002850.3	1916	cGa/cAa	37/38	1	2	FACETS	0.969	0.915	1	0.969	0.915	1	CLONAL	1	TRUE	1	0.65	2		684	978	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290208	15290208	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs60373464	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	297	754	1	ENST00000263388.2:c.3427C>T	p.Arg1143Cys	p.R1143C	ENST00000263388	NM_000435.2	1143	Cgc/Tgc	21/33	1	2	FACETS	0.962	0.908	1	0.962	0.908	1	CLONAL	1	TRUE	1	0.65	2		755	950	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220899	36220899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555731828	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	91	260	0	ENST00000222270.7:c.4949C>T	p.Thr1650Met	p.T1650M	ENST00000222270	NM_014727.1	1650	aCg/aTg	23/37	1	2	FACETS	0.9	0.808	0.996	0.9	0.808	0.996	CLONAL	1	TRUE	1	0.65	2		260	311	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794914	42794914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	267	698	1	ENST00000575354.2:c.1994C>T	p.Ser665Phe	p.S665F	ENST00000575354	NM_015125.3	665	tCc/tTc	10/20	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.65	2		699	818	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867528	45867528	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	309	759	0	ENST00000391945.4:c.780G>T	p.Gln260His	p.Q260H	ENST00000391945	NM_000400.3	260	caG/caT	9/23	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.65	2		759	924	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690207	47690217	+	frameshift_variant	Frame_Shift_Del	DEL	ATCCTAATCTC	ATCCTAATCTC	-	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	121	350	0	ENST00000233146.2:c.1425_1435del	p.Asp475GlufsTer2	p.D475Efs*2	ENST00000233146	NM_000251.2	475	gATCCTAATCTC/g	9/16	1	2	FACETS	0.801	0.728	0.876	0.801	0.728	0.876	CLONAL	1	TRUE	1	0.65	2		350	465	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582242	52582242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879167521	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	109	215	0	ENST00000394830.3:c.4586G>A	p.Arg1529His	p.R1529H	ENST00000394830	NM_018313.4	1529	cGc/cAc	30/30	1	2	FACETS	0.953	0.865	1	0.953	0.865	1	CLONAL	1	TRUE	1	0.65	2		215	352	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149375032	149375032	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	361	745	0	ENST00000360632.3:c.62C>T	p.Thr21Met	p.T21M	ENST00000360632	NM_015472.4	21	aCg/aTg	2/7	1	2	FACETS	0.953	0.904	1	0.953	0.904	1	CLONAL	1	TRUE	1	0.65	2		745	1165	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638779	176638780	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs587784101	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	219	579	0	ENST00000439151.2:c.3383_3384del	p.Ser1128PhefsTer2	p.S1128Ffs*2	ENST00000439151	NM_022455.4	1127	CTc/c	5/23	1	2	FACETS	0.853	0.796	0.912	0.853	0.796	0.912	CLONAL	1	TRUE	1	0.65	2		579	790	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956955	2956955	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	264	555	0	ENST00000396946.4:c.2672G>A	p.Arg891Gln	p.R891Q	ENST00000396946	NM_032415.4	891	cGa/cAa	20/25	1	2	FACETS	0.992	0.933	1	0.992	0.933	1	CLONAL	1	TRUE	1	0.65	2		555	819	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370978	55370978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	276	576	0	ENST00000297316.4:c.280C>T	p.His94Tyr	p.H94Y	ENST00000297316	NM_022454.3	94	Cac/Tac	1/2	1	2	FACETS	0.983	0.926	1	0.983	0.926	1	CLONAL	1	TRUE	1	0.65	2		576	864	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549475	5549475	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	346	662	0	ENST00000397747.3:c.502A>G	p.Arg168Gly	p.R168G	ENST00000397747	NM_025239.3	168	Agg/Ggg	4/7	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.65	2		662	991	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485311	8485312	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	129	345	0	ENST00000356435.5:c.3068dup	p.Asn1023LysfsTer23	p.N1023Kfs*23	ENST00000356435		1023	aat/aaAt	18/35	1	2	FACETS	0.908	0.83	0.989	0.908	0.83	0.989	CLONAL	1	TRUE	1	0.65	2		345	437	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937812	76937812	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	164	417	0	ENST00000373344.5:c.2936A>T	p.Glu979Val	p.E979V	ENST00000373344	NM_000489.3	979	gAa/gTa	9/35	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.65	2		417	476	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371708	225371708	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	103	489	0	ENST00000264414.4:c.896T>G	p.Met299Arg	p.M299R	ENST00000264414	NM_003590.4	299	aTg/aGg	7/16	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.312055369608004	2		489	581	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63817057	63817057	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	44	229	0	ENST00000279873.7:c.1028C>G	p.Pro343Arg	p.P343R	ENST00000279873	NM_032199.2	343	cCc/cGc	6/10	1	2	FACETS	0.949	0.801	1	0.949	0.801	1	CLONAL	1	TRUE	1	0.312055369608004	2		229	297	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715678	30715678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039551	NA	P-0039008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	136	345	1	ENST00000295754.5:c.1336G>A	p.Asp446Asn	p.D446N	ENST00000295754	NM_003242.5	446	Gat/Aat	5/7	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.531199129126228	2		346	404	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022917	27022939	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCCGCCAGCAGCCTGGGCAAC	CCGCCGCCAGCAGCCTGGGCAAC	-	novel	NA	P-0039008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	13	21	0	ENST00000324856.7:c.31_53del	p.Ser11AlafsTer92	p.S11Afs*92	ENST00000324856	NM_006015.4	8	gCCGCCGCCAGCAGCCTGGGCAAC/g	1/20	0.531199129126228	1	FACETS	1	0.81	1	1	0.81	1	CLONAL	1	TRUE	0	0.531199129126228	1		21	33	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226767	2226767	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	181	326	1	ENST00000398665.3:c.4247G>A	p.Arg1416His	p.R1416H	ENST00000398665	NM_032482.2	1416	cGc/cAc	27/28	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.531199129126228	2		327	619	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448439	49448439	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	205	594	0	ENST00000301067.7:c.272G>A	p.Trp91Ter	p.W91*	ENST00000301067	NM_003482.3	91	tGg/tAg	3/54	1	2	FACETS	0.939	0.873	1	0.939	0.873	1	CLONAL	1	TRUE	1	0.531199129126228	2		594	822	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434903	56434921	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGGCCCCTCCCCAGGTG	GAAGGCCCCTCCCCAGGTG	-	novel	NA	P-0039008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	127	596	0	ENST00000407977.2:c.2216_2234del	p.Pro739LeufsTer82	p.P739Lfs*82	ENST00000407977		739	cCACCTGGGGAGGGGCCTTCt/ct	9/10	0.531199129126228	1	FACETS	0.642	0.584	0.702	0.642	0.584	0.702	SUBCLONAL	1	TRUE	0	0.531199129126228	1		596	547	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971164	13971164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	123	329	0	ENST00000405192.2:c.765G>A	p.Met255Ile	p.M255I	ENST00000405192	NM_001163147.1	255	atG/atA	8/12	0.414886325644935	3	FACETS	0.964	0.874	1	0.482	0.437	0.529	CLONAL	1	TRUE	1	0.531199129126228	3		329	608	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787684	135787684	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs796053456	NA	P-0039008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	145	477	0	ENST00000298552.3:c.898A>G	p.Thr300Ala	p.T300A	ENST00000298552	NM_001162426.1	300	Aca/Gca	9/23	0.531199129126228	1	FACETS	0.808	0.742	0.876	0.808	0.742	0.876	CLONAL	1	TRUE	0	0.531199129126228	1		477	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0039086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	163	652	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		652	537	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0039086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	52	250	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		250	267	SUCCESS
APC	324	MSKCC	GRCh37	5	112175328	112175328	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	65	210	0	ENST00000257430.4:c.4037C>A	p.Ser1346Ter	p.S1346*	ENST00000257430	NM_000038.5	1346	tCa/tAa	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		210	280	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324496	31324496	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs2308559	NA	P-0039086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	11	321	0	ENST00000412585.2:c.312C>A	p.Asn104Lys	p.N104K	ENST00000412585	NM_005514.6	104	aaC/aaA	2/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		321	211	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857645	9857645	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	75	363	1	ENST00000330684.3:c.3756G>T	p.Gln1252His	p.Q1252H	ENST00000330684	NM_001134407.1	1252	caG/caT	13/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		364	374	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72994041	72994041	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	128	521	0	ENST00000268489.5:c.4G>T	p.Glu2Ter	p.E2*	ENST00000268489	NM_006885.3	2	Gaa/Taa	2/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		521	575	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93953170	93953170	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	46	313	0	ENST00000369303.4:c.2971T>A	p.Leu991Ile	p.L991I	ENST00000369303	NM_004440.3	991	Tta/Ata	17/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		313	228	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	164	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.439010918702741	2		341	502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576891	7576891	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0039093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	133	521	0	ENST00000269305.4:c.955A>T	p.Lys319Ter	p.K319*	ENST00000269305	NM_001126112.2	319	Aag/Tag	9/11	0.439010918702741	1	FACETS	0.787	0.717	0.86	0.787	0.717	0.86	SUBCLONAL	1	TRUE	0	0.439010918702741	1		521	601	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593558	48593558	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587781618	NA	P-0039093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	60	152	1	ENST00000342988.3:c.1308+1G>T		p.X436_splice	ENST00000342988	NM_005359.5	436			0.439010918702741	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.439010918702741	1		153	200	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369238	118369238	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	73	243	0	ENST00000534358.1:c.5956G>C	p.Gly1986Arg	p.G1986R	ENST00000534358	NM_005933.3	1986	Ggc/Cgc	22/36	0.439010918702741	3	FACETS	0.863	0.757	0.976	0.431	0.378	0.488	CLONAL	1	TRUE	1	0.439010918702741	3		243	470	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030460	49030516	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCTCTTTCACTGTTTTATAAAAAAGGTTAGTAGATGATTATTTTCAAGAGCATGGA	CTCTCTTTCACTGTTTTATAAAAAAGGTTAGTAGATGATTATTTTCAAGAGCATGGA	-	novel	NA	P-0039093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	60	326	0	ENST00000267163.4:c.1939_1960+35del		p.X647_splice	ENST00000267163	NM_000321.2	647		19/27	0.439010918702741	1	FACETS	0.679	0.589	0.776	0.679	0.589	0.776	SUBCLONAL	1	TRUE	0	0.439010918702741	1		326	314	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372087	55372087	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	121	243	1	ENST00000297316.4:c.777C>A	p.Tyr259Ter	p.Y259*	ENST00000297316	NM_022454.3	259	taC/taA	2/2	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.439010918702741	2		244	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0039122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	164	748	0	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	0.399104422822151	3	FACETS	0.888	0.827	0.95	1	0.988	1	CLONAL	3	FALSE	1	0.399104422822151	3		748	370	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968266	2968266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773909937	NA	P-0039122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	160	751	0	ENST00000396946.4:c.1720G>A	p.Val574Ile	p.V574I	ENST00000396946	NM_032415.4	574	Gtc/Atc	13/25	0.355072165581325	5	FACETS	1	0.951	1	0.696	0.641	0.753	CLONAL	2	FALSE	2	0.399104422822151	5		751	614	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303621	65303625	+	frameshift_variant	Frame_Shift_Del	DEL	ACAGG	ACAGG	-	novel	NA	P-0039122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	22	512	0	ENST00000342505.4:c.3130_3134del	p.Pro1044ValfsTer12	p.P1044Vfs*12	ENST00000342505	NM_002227.2	1044	CCTGTg/g	22/25	0.252525416209923	4	FACETS	0.563	0.437	0.709	0.281	0.218	0.355	SUBCLONAL	1	FALSE	2	0.399104422822151	4		512	274	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093362	30093362	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	69	510	2	ENST00000331968.5:c.1901T>C	p.Leu634Pro	p.L634P	ENST00000331968	NM_002742.2	634	cTa/cCa	13/18	0.334233395412399	3	FACETS	1	0.926	1	0.705	0.626	0.788	CLONAL	2	FALSE	0	0.399104422822151	3		512	196	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562459	95562459	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	50	481	0	ENST00000393063.1:c.4798del	p.Glu1600LysfsTer20	p.E1600Kfs*20	ENST00000393063	NM_030621.3	1600	Gaa/aa	24/28	0.334233395412399	3	FACETS	1	0.941	1	0.401	0.343	0.463	CLONAL	1	FALSE	0	0.399104422822151	3		481	250	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945773	38945773	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	11	262	0	ENST00000357387.3:c.4453C>T	p.Gln1485Ter	p.Q1485*	ENST00000357387	NM_152756.3	1485	Cag/Tag	34/38	0.334233395412399	3	FACETS	0.396	0.274	0.547	0.132	0.091	0.183	SUBCLONAL	1	FALSE	0	0.399104422822151	3		262	167	SUCCESS
APC	324	MSKCC	GRCh37	5	112175349	112175377	+	frameshift_variant	Frame_Shift_Del	DEL	AATTTTCTTCAGGAGCGAAATCTCCCTCC	AATTTTCTTCAGGAGCGAAATCTCCCTCC	-	novel	NA	P-0039122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	42	265	0	ENST00000257430.4:c.4060_4088del	p.Phe1354LysfsTer11	p.F1354Kfs*11	ENST00000257430	NM_000038.5	1353	gAATTTTCTTCAGGAGCGAAATCTCCCTCC/g	16/16	0.334233395412399	3	FACETS	1	0.934	1	0.772	0.664	0.884	CLONAL	2	FALSE	0	0.399104422822151	3		265	109	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662739	117662739	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs200762545	NA	P-0039122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	20	333	0	ENST00000368508.3:c.4726A>G	p.Ile1576Val	p.I1576V	ENST00000368508	NM_002944.2	1576	Ata/Gta	29/43	0.399104422822151	3	FACETS	0.871	0.673	1	0.436	0.336	0.549	CLONAL	1	FALSE	1	0.399104422822151	3		333	138	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	78	333	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		333	480	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	10	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.564	0.381	0.794	0.564	0.381	0.794	SUBCLONAL	1	TRUE	1	0.13	2		341	273	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584593	48584593	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	27	319	0	ENST00000342988.3:c.766C>T	p.Gln256Ter	p.Q256*	ENST00000342988	NM_005359.5	256	Cag/Tag	6/12	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.13	2		319	369	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14300947	14300947	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1384357948	NA	P-0039271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	18	280	0	ENST00000256196.4:c.551C>G	p.Pro184Arg	p.P184R	ENST00000256196		184	cCt/cGt	6/6	1	2	FACETS	0.847	0.637	1	0.847	0.637	1	CLONAL	1	TRUE	1	0.13	2		280	327	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464578	25464578	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0039271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	26	444	0	ENST00000264709.3:c.1937-2A>T		p.X646_splice	ENST00000264709	NM_175629.2	646			1	2	FACETS	0.911	0.721	1	0.911	0.721	1	CLONAL	1	TRUE	1	0.13	2		444	439	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	109	333	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.579960420310371	2		333	338	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524179	18524179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	160	348	0	ENST00000266497.5:c.1691G>A	p.Gly564Glu	p.G564E	ENST00000266497		564	gGg/gAg	11/31	1	2	FACETS	0.963	0.888	1	0.963	0.888	1	CLONAL	1	TRUE	1	0.579960420310371	2		348	573	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445192	49445192	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	137	598	0	ENST00000301067.7:c.2274G>T	p.Glu758Asp	p.E758D	ENST00000301067	NM_003482.3	758	gaG/gaT	10/54	1	2	FACETS	0.676	0.616	0.739	0.676	0.616	0.739	SUBCLONAL	1	TRUE	1	0.579960420310371	2		598	699	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98011507	98011507	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	201	436	0	ENST00000289081.3:c.67G>A	p.Asp23Asn	p.D23N	ENST00000289081	NM_000136.2	23	Gat/Aat	2/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.579960420310371	2		436	628	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0039301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	189	153	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.68341432649458	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.68341432649458	1		153	345	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	200	492	0	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.68341432649458	2		492	575	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425221	49425221	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	37	617	0	ENST00000301067.7:c.13267C>A	p.Pro4423Thr	p.P4423T	ENST00000301067	NM_003482.3	4423	Cca/Aca	39/54	1	2	FACETS	0.155	0.127	0.187	0.155	0.127	0.187	SUBCLONAL	1	TRUE	1	0.68341432649458	2		617	697	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663360	227663360	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	158	388	0	ENST00000305123.5:c.95T>A	p.Leu32Gln	p.L32Q	ENST00000305123	NM_005544.2	32	cTg/cAg	1/2	1	2	FACETS	0.916	0.845	0.988	0.916	0.845	0.988	CLONAL	1	TRUE	1	0.68341432649458	2		388	505	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163077	47163077	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	63	310	0	ENST00000409792.3:c.3049del	p.Tyr1017MetfsTer3	p.Y1017Mfs*3	ENST00000409792	NM_014159.6	1017	Tat/at	3/21	1	2	FACETS	0.988	0.858	1	0.988	0.858	1	CLONAL	1	TRUE	1	0.328718116547282	2		310	388	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165722	47165722	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0039458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	56	389	0	ENST00000409792.3:c.404C>G	p.Ser135Ter	p.S135*	ENST00000409792	NM_014159.6	135	tCa/tGa	3/21	1	2	FACETS	0.78	0.669	0.899	0.78	0.669	0.899	SUBCLONAL	1	TRUE	1	0.328718116547282	2		389	437	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884811	151884811	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0039458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	50	284	0	ENST00000262189.6:c.4782T>G	p.Tyr1594Ter	p.Y1594*	ENST00000262189	NM_170606.2	1594	taT/taG	32/59	1	2	FACETS	0.852	0.726	0.99	0.852	0.726	0.99	CLONAL	1	TRUE	1	0.328718116547282	2		284	357	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	87	473	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.31147432460865	2		473	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0039474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	263	618	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.31147432460865	2	FACETS	0.876	0.822	0.931	0.876	0.822	0.931	CLONAL	2	TRUE	0	0.31147432460865	2		619	964	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158198	47158198	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	93	438	1	ENST00000409792.3:c.4501T>C	p.Cys1501Arg	p.C1501R	ENST00000409792	NM_014159.6	1501	Tgt/Cgt	4/21	0.201033755943722	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.31147432460865	1		439	402	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860714	3860714	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	132	653	0	ENST00000262367.5:c.865G>T	p.Gly289Ter	p.G289*	ENST00000262367	NM_004380.2	289	Gga/Tga	3/31	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.31147432460865	2		653	751	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256439	46256439	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	263	456	0	ENST00000371998.3:c.667A>T	p.Thr223Ser	p.T223S	ENST00000371998		223	Aca/Tca	7/23	0.31147432460865	3	FACETS	0.986	0.93	1	0.986	0.93	1	CLONAL	3	TRUE	0	0.31147432460865	3		456	660	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0039474-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	472	618	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.555729215968067	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.555729215968067	2		619	805	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158198	47158198	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039474-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	198	438	1	ENST00000409792.3:c.4501T>C	p.Cys1501Arg	p.C1501R	ENST00000409792	NM_014159.6	1501	Tgt/Cgt	4/21	0.47256415038215	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.555729215968067	1		439	466	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860714	3860714	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039474-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	215	653	0	ENST00000262367.5:c.865G>T	p.Gly289Ter	p.G289*	ENST00000262367	NM_004380.2	289	Gga/Tga	3/31	1	2	FACETS	0.941	0.877	1	0.941	0.877	1	CLONAL	1	TRUE	1	0.555729215968067	2		653	822	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256439	46256439	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039474-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	502	456	0	ENST00000371998.3:c.667A>T	p.Thr223Ser	p.T223S	ENST00000371998		223	Aca/Tca	7/23	0.555729215968067	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	0	0.555729215968067	3		456	754	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447384	187447384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780987785	NA	P-0039548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	215	523	0	ENST00000232014.4:c.809G>A	p.Arg270Gln	p.R270Q	ENST00000232014	NM_001130845.1	270	cGa/cAa	5/10	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		523	966	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0039559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	553	228	0	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	0.703119091903824	2	FACETS	0.994	0.966	1	0.994	0.966	1	CLONAL	2	TRUE	0	0.703119091903824	2		228	791	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0039559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	283	454	1	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	0.703119091903824	2	FACETS	0.884	0.832	0.936	0.442	0.416	0.468	CLONAL	1	TRUE	0	0.703119091903824	2		455	911	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057924	27057924	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	278	629	0	ENST00000324856.7:c.1636del	p.Gln546ArgfsTer73	p.Q546Rfs*73	ENST00000324856	NM_006015.4	544	caC/ca	3/20	0.703119091903824	2	FACETS	1	0.969	1	0.52	0.49	0.55	CLONAL	1	TRUE	0	0.703119091903824	2		629	761	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007332	143007332	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	73	376	1	ENST00000262992.4:c.2452del	p.Arg818GlufsTer4	p.R818Efs*4	ENST00000262992	NM_001101669.1	818	Aga/ga	22/24	0.703119091903824	2	FACETS	0.429	0.376	0.486	0.215	0.188	0.243	SUBCLONAL	1	TRUE	0	0.703119091903824	2		377	484	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0039559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	237	301	10	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	0.703119091903824	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.703119091903824	2		311	325	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890149	76890150	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	251	247	1	ENST00000373344.5:c.4744dup	p.Thr1582AsnfsTer19	p.T1582Nfs*19	ENST00000373344	NM_000489.3	1582	aca/aAca	17/35	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.703119091903824	1		248	407	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776783	NA	P-0039559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	244	296	0	ENST00000267163.4:c.1215+1G>A		p.X405_splice	ENST00000267163	NM_000321.2	405			0.703119091903824	2	FACETS	0.911	0.869	0.952	0.911	0.869	0.952	CLONAL	2	TRUE	0	0.703119091903824	2		296	381	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586502	189586502	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757536818	NA	P-0039559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	194	402	0	ENST00000264731.3:c.1126C>T	p.Arg376Cys	p.R376C	ENST00000264731	NM_003722.4	376	Cgc/Tgc	8/14	0.703119091903824	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.703119091903824	1		402	329	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165663	118165663	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776281952	NA	P-0039559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	182	431	0	ENST00000369448.3:c.173G>A	p.Arg58Gln	p.R58Q	ENST00000369448	NM_017709.3	58	cGg/cAg	2/2	0.703119091903824	2	FACETS	1	0.98	1	0.568	0.529	0.607	CLONAL	1	TRUE	0	0.703119091903824	2		431	456	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971324	13971324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752431857	NA	P-0039559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	428	523	1	ENST00000405192.2:c.605C>T	p.Thr202Met	p.T202M	ENST00000405192	NM_001163147.1	202	aCg/aTg	8/12	0.362761154680255	3	FACETS	1	0.993	1	0.751	0.723	0.779	INDETERMINATE	2	TRUE	0	0.703119091903824	3		524	730	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966872	25966873	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	209	599	1	ENST00000435504.4:c.2333dup	p.Val779SerfsTer25	p.V779Sfs*25	ENST00000435504		778	cca/ccCa	13/13	0.703119091903824	2	FACETS	0.885	0.825	0.946	0.442	0.412	0.473	CLONAL	1	TRUE	0	0.703119091903824	2		600	672	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572092	64572093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs767319284	NA	P-0039559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	517	711	0	ENST00000312049.6:c.1546dup	p.Arg516ProfsTer15	p.R516Pfs*15	ENST00000312049	NM_130799.2	516	cgg/cCgg	10/10	0.703119091903824	2	FACETS	0.887	0.858	0.915	0.887	0.858	0.915	CLONAL	2	TRUE	0	0.703119091903824	2		711	829	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082313	16082314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs780080562	NA	P-0039559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	232	749	2	ENST00000281043.3:c.134dup	p.Glu47GlyfsTer8	p.E47Gfs*8	ENST00000281043	NM_005378.4	43	acc/aCcc	2/3	0.703119091903824	2	FACETS	0.778	0.727	0.831	0.389	0.363	0.416	SUBCLONAL	1	TRUE	0	0.703119091903824	2		751	848	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214666	5214666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs116660613	NA	P-0039559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	303	842	0	ENST00000357368.4:c.4400C>T	p.Pro1467Leu	p.P1467L	ENST00000357368	NM_002850.3	1467	cCg/cTg	29/38	0.703119091903824	3	FACETS	1	0.96	1	0.511	0.482	0.542	CLONAL	1	TRUE	1	0.703119091903824	3		842	1139	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	508	740	0	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	0.703119091903824	2	FACETS	0.867	0.838	0.896	0.867	0.838	0.896	CLONAL	2	TRUE	0	0.703119091903824	2		740	833	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0039559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	266	797	3	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	0.703119091903824	2	FACETS	0.93	0.875	0.986	0.465	0.437	0.493	CLONAL	1	TRUE	0	0.703119091903824	2		800	814	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840564	36840564	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771002648	NA	P-0039559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	546	813	0	ENST00000358127.4:c.1169G>A	p.Arg390His	p.R390H	ENST00000358127	NM_001280556.1	390	cGt/cAt	10/10	0.703119091903824	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.703119091903824	2		813	730	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164465	47164465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375514539	NA	P-0039559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	332	342	0	ENST00000409792.3:c.1661G>A	p.Arg554His	p.R554H	ENST00000409792	NM_014159.6	554	cGt/cAt	3/21	0.703119091903824	2	FACETS	0.931	0.895	0.967	0.931	0.895	0.967	CLONAL	2	TRUE	0	0.703119091903824	2		342	507	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523271	9523271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775109543	NA	P-0039559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	308	603	0	ENST00000353224.5:c.1966C>T	p.Arg656Trp	p.R656W	ENST00000353224	NM_177990.2	656	Cgg/Tgg	9/10	0.703119091903824	2	FACETS	1	0.988	1	0.566	0.536	0.596	CLONAL	1	TRUE	0	0.703119091903824	2		603	774	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612188	189612188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774550896	NA	P-0039559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	277	574	0	ENST00000264731.3:c.1940G>A	p.Arg647His	p.R647H	ENST00000264731	NM_003722.4	647	cGc/cAc	14/14	0.703119091903824	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.703119091903824	1		574	447	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131926920	131926920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776949511	NA	P-0039559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	93	191	0	ENST00000265335.6:c.1457G>A	p.Arg486His	p.R486H	ENST00000265335		486	cGt/cAt	10/25	0.703119091903824	2	FACETS	0.955	0.861	1	0.478	0.43	0.526	CLONAL	1	TRUE	0	0.703119091903824	2		191	277	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724487	162724487	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	261	584	0	ENST00000367921.3:c.259C>A	p.Leu87Met	p.L87M	ENST00000367921	NM_006182.2	87	Ctg/Atg	5/18	0.703119091903824	2	FACETS	1	0.973	1	0.528	0.497	0.559	CLONAL	1	TRUE	0	0.703119091903824	2		584	703	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415825	49415827	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CCT	CCT	-	novel	NA	P-0039559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	169	397	0	ENST00000301067.7:c.16520_16521+1del		p.X5507_splice	ENST00000301067	NM_003482.3	5507		53/54	0.703119091903824	2	FACETS	1	0.963	1	0.529	0.491	0.568	CLONAL	1	TRUE	0	0.703119091903824	2		397	454	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348078	348078	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	130	846	0	ENST00000262320.3:c.1428G>T	p.Gln476His	p.Q476H	ENST00000262320	NM_003502.3	476	caG/caT	6/11	0.703119091903824	2	FACETS	0.466	0.422	0.511	0.233	0.211	0.256	SUBCLONAL	1	TRUE	0	0.703119091903824	2		846	794	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879626	37879626	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	607	787	1	ENST00000269571.5:c.2005del	p.Val669TrpfsTer32	p.V669Wfs*32	ENST00000269571		667	ttG/tt	17/27	0.703119091903824	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.703119091903824	2		788	863	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4090610	4090610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730880516	NA	P-0039559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	395	562	1	ENST00000262948.5:c.1189C>T	p.Arg397Cys	p.R397C	ENST00000262948	NM_030662.3	397	Cgc/Tgc	11/11	0.703119091903824	3	FACETS	0.943	0.903	0.984	0.943	0.903	0.984	CLONAL	2	TRUE	1	0.703119091903824	3		563	805	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808323	1808323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	61	903	1	ENST00000260795.2:c.2081C>T	p.Pro694Leu	p.P694L	ENST00000260795		694	cCg/cTg	15/17	0.703119091903824	2	FACETS	0.188	0.162	0.217	0.094	0.081	0.109	SUBCLONAL	1	TRUE	0	0.703119091903824	2		904	922	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149437076	149437078	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0039559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	640	689	0	ENST00000286301.3:c.2210_2212del	p.Phe737del	p.F737del	ENST00000286301	NM_005211.3	737	tTCTct/tct	16/22	0.703119091903824	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.703119091903824	2		689	888	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670918	30670918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148600920	NA	P-0039559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	53	732	0	ENST00000376406.3:c.5828G>A	p.Arg1943Gln	p.R1943Q	ENST00000376406	NM_014641.2	1943	cGg/cAg	12/15	0.703119091903824	2	FACETS	0.176	0.149	0.206	0.088	0.074	0.103	SUBCLONAL	1	TRUE	0	0.703119091903824	2		732	856	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672566	30672566	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	59	632	0	ENST00000376406.3:c.4394T>C	p.Val1465Ala	p.V1465A	ENST00000376406	NM_014641.2	1465	gTt/gCt	10/15	0.703119091903824	2	FACETS	0.248	0.213	0.287	0.124	0.106	0.144	SUBCLONAL	1	TRUE	0	0.703119091903824	2		632	676	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100309	157100309	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	44	283	0	ENST00000346085.5:c.1246A>T	p.Thr416Ser	p.T416S	ENST00000346085	NM_020732.3	416	Acc/Tcc	1/20	0.354753979606366	3	FACETS	0.461	0.387	0.542	0.154	0.129	0.181	INDETERMINATE	1	TRUE	0	0.711312731492206	3		283	364	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944334	76944334	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	109	410	0	ENST00000373344.5:c.571T>C	p.Ser191Pro	p.S191P	ENST00000373344	NM_000489.3	191	Tca/Cca	7/35	0.341508087788155	3	FACETS	0.532	0.477	0.59	0.266	0.238	0.295	INDETERMINATE	1	TRUE	1	0.711312731492206	3		410	781	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	166	301	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.979	0.903	1	0.979	0.903	1	CLONAL	1	TRUE	1	0.53	2		301	640	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913403	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	96	344	0	ENST00000349496.5:c.110C>A	p.Ser37Tyr	p.S37Y	ENST00000349496	NM_001904.3	37	tCt/tAt	3/15	1	2	FACETS	0.82	0.734	0.909	0.82	0.734	0.909	CLONAL	1	TRUE	1	0.53	2		344	442	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104712	193104712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	81	309	0	ENST00000367435.3:c.416G>A	p.Arg139Gln	p.R139Q	ENST00000367435	NM_024529.4	139	cGa/cAa	5/17	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.53	2		309	277	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	112	165	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.976	0.884	1	0.976	0.884	1	CLONAL	1	TRUE	1	0.53	2		165	433	SUCCESS
APC	324	MSKCC	GRCh37	5	112177049	112177049	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	74	423	0	ENST00000257430.4:c.5758C>T	p.Arg1920Ter	p.R1920*	ENST00000257430	NM_000038.5	1920	Cga/Tga	16/16	1	2	FACETS	0.662	0.582	0.747	0.662	0.582	0.747	SUBCLONAL	1	TRUE	1	0.53	2		423	422	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453486	138453486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451809865	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	49	363	0	ENST00000289153.2:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000289153	NM_006219.2	321	cGa/cAa	5/22	1	2	FACETS	0.547	0.465	0.636	0.547	0.465	0.636	SUBCLONAL	1	TRUE	1	0.53	2		363	338	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916248	9916248	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397518472	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	94	385	0	ENST00000330684.3:c.2041C>T	p.Arg681Ter	p.R681*	ENST00000330684	NM_001134407.1	681	Cga/Tga	10/13	1	2	FACETS	0.812	0.726	0.902	0.812	0.726	0.902	CLONAL	1	TRUE	1	0.53	2		385	437	SUCCESS
AR	367	MSKCC	GRCh37	X	66942700	66942700	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs200801099	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	127	456	0	ENST00000374690.3:c.2481C>A	p.Phe827Leu	p.F827L	ENST00000374690	NM_000044.3	827	ttC/ttA	7/8	1	2	FACETS	0.816	0.742	0.894	0.816	0.742	0.894	CLONAL	1	TRUE	1	0.53	2		456	587	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	147	819	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.934	0.856	1	0.934	0.856	1	CLONAL	1	TRUE	1	0.53	2		819	594	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720744	89720744	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167674	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	10	223	1	ENST00000371953.3:c.895G>T	p.Glu299Ter	p.E299*	ENST00000371953	NM_000314.4	299	Gaa/Taa	8/9	1	2	FACETS	0.252	0.171	0.353	0.252	0.171	0.353	SUBCLONAL	1	TRUE	1	0.53	2		224	150	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81941311	81941311	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	209	615	1	ENST00000359376.3:c.1489G>A	p.Ala497Thr	p.A497T	ENST00000359376	NM_002661.3	497	Gcc/Acc	16/33	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.53	2		616	774	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	125	524	0	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	1	2	FACETS	0.841	0.764	0.921	0.841	0.764	0.921	CLONAL	1	TRUE	1	0.53	2		524	561	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650710	67650710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243010179	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	263	618	1	ENST00000264010.4:c.1015C>T	p.Arg339Trp	p.R339W	ENST00000264010	NM_006565.3	339	Cgg/Tgg	5/12	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.53	2		619	969	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876659802	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	276	844	0	ENST00000269305.4:c.833C>A	p.Pro278His	p.P278H	ENST00000269305	NM_001126112.2	278	cCt/cAt	8/11	1	2	FACETS	0.96	0.901	1	0.96	0.901	1	CLONAL	1	TRUE	1	0.53	2		844	1085	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955481	48955481	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237070816	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	95	384	0	ENST00000267163.4:c.1597G>A	p.Glu533Lys	p.E533K	ENST00000267163	NM_000321.2	533	Gaa/Aaa	17/27	1	2	FACETS	0.922	0.827	1	0.922	0.827	1	CLONAL	1	TRUE	1	0.53	2		384	389	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942751	44942751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763592177	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	115	524	1	ENST00000377967.4:c.3331C>T	p.Arg1111Cys	p.R1111C	ENST00000377967	NM_021140.2	1111	Cgt/Tgt	23/29	1	2	FACETS	0.799	0.723	0.879	0.799	0.723	0.879	SUBCLONAL	1	TRUE	1	0.53	2		525	543	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952049	178952049	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1242945375	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	84	395	0	ENST00000263967.3:c.3104C>T	p.Ala1035Val	p.A1035V	ENST00000263967	NM_006218.2	1035	gCt/gTt	21/21	1	2	FACETS	0.943	0.841	1	0.943	0.841	1	CLONAL	1	TRUE	1	0.53	2		395	336	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81973613	81973613	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	172	611	0	ENST00000359376.3:c.3430G>A	p.Asp1144Asn	p.D1144N	ENST00000359376	NM_002661.3	1144	Gat/Aat	30/33	1	2	FACETS	0.966	0.892	1	0.966	0.892	1	CLONAL	1	TRUE	1	0.53	2		611	672	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148504761	148504761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397515548	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	154	550	0	ENST00000320356.2:c.2233G>A	p.Glu745Lys	p.E745K	ENST00000320356	NM_004456.4	745	Gaa/Aaa	20/20	1	2	FACETS	0.9	0.826	0.976	0.9	0.826	0.976	CLONAL	1	TRUE	1	0.53	2		550	646	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858253	59858253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778133	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	127	500	0	ENST00000259008.2:c.1742G>A	p.Arg581Gln	p.R581Q	ENST00000259008	NM_032043.2	581	cGa/cAa	12/20	1	2	FACETS	0.955	0.87	1	0.955	0.87	1	CLONAL	1	TRUE	1	0.53	2		500	502	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944523	40944523	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	159	529	0	ENST00000373198.4:c.1979C>A	p.Ser660Tyr	p.S660Y	ENST00000373198	NM_133170.3	660	tCt/tAt	12/32	1	2	FACETS	0.919	0.845	0.995	0.919	0.845	0.995	CLONAL	1	TRUE	1	0.53	2		529	653	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740668	58740668	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs759850701	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	152	606	0	ENST00000305921.3:c.1573G>T	p.Glu525Ter	p.E525*	ENST00000305921	NM_003620.3	525	Gaa/Taa	6/6	1	2	FACETS	0.945	0.868	1	0.945	0.868	1	CLONAL	1	TRUE	1	0.53	2		606	607	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788637	3788637	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	166	499	0	ENST00000262367.5:c.4317C>A	p.Phe1439Leu	p.F1439L	ENST00000262367	NM_004380.2	1439	ttC/ttA	26/31	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.53	2		499	611	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381567	81381567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370760302	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	65	251	2	ENST00000222390.5:c.494C>T	p.Ser165Leu	p.S165L	ENST00000222390	NM_000601.4	165	tCg/tTg	5/18	1	2	FACETS	0.855	0.748	0.968	0.855	0.748	0.968	CLONAL	1	TRUE	1	0.53	2		253	287	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58701094	58701094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	151	529	0	ENST00000305921.3:c.685G>A	p.Glu229Lys	p.E229K	ENST00000305921	NM_003620.3	229	Gaa/Aaa	2/6	1	2	FACETS	0.842	0.772	0.915	0.842	0.772	0.915	CLONAL	1	TRUE	1	0.53	2		529	677	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480443	57480443	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	94	274	0	ENST00000371085.3:c.438C>A	p.Phe146Leu	p.F146L	ENST00000371085	NM_000516.4	146	ttC/ttA	6/13	1	2	FACETS	0.812	0.726	0.902	0.812	0.726	0.902	CLONAL	1	TRUE	1	0.53	2		274	437	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020225	123020225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	131	625	0	ENST00000355640.3:c.713G>A	p.Arg238Gln	p.R238Q	ENST00000355640		238	cGa/cAa	2/7	1	2	FACETS	0.808	0.735	0.884	0.808	0.735	0.884	CLONAL	1	TRUE	1	0.53	2		625	612	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344954	118344955	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	87	263	0	ENST00000534358.1:c.3086dup	p.Ala1030GlyfsTer9	p.A1030Gfs*9	ENST00000534358	NM_005933.3	1027	cta/ctAa	3/36	1	2	FACETS	0.949	0.847	1	0.949	0.847	1	CLONAL	1	TRUE	1	0.53	2		263	346	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1255456	1255456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374968697	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	197	683	2	ENST00000310581.5:c.3103G>A	p.Val1035Ile	p.V1035I	ENST00000310581	NM_198253.2	1035	Gtc/Atc	14/16	1	2	FACETS	0.732	0.678	0.789	0.732	0.678	0.789	SUBCLONAL	1	TRUE	1	0.53	2		685	1015	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433059	49433059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	82	855	0	ENST00000301067.7:c.8312G>A	p.Arg2771Gln	p.R2771Q	ENST00000301067	NM_003482.3	2771	cGa/cAa	33/54	1	2	FACETS	0.283	0.248	0.32	0.283	0.248	0.32	SUBCLONAL	1	TRUE	1	0.53	2		855	1095	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273218	115273218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	155	571	0	ENST00000438362.2:c.1240C>T	p.Arg414Cys	p.R414C	ENST00000438362	NM_001242891.1	414	Cgt/Tgt	11/20	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.53	2		571	573	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750453	57750453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	93	457	0	ENST00000274289.3:c.2015G>A	p.Arg672Gln	p.R672Q	ENST00000274289	NM_006622.3	672	cGa/cAa	14/14	1	2	FACETS	0.902	0.808	1	0.902	0.808	1	CLONAL	1	TRUE	1	0.53	2		457	389	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673712	176673712	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751194525	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	100	348	0	ENST00000439151.2:c.4412G>A	p.Arg1471Gln	p.R1471Q	ENST00000439151	NM_022455.4	1471	cGa/cAa	10/23	1	2	FACETS	0.844	0.758	0.934	0.844	0.758	0.934	CLONAL	1	TRUE	1	0.53	2		348	447	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646257	23646257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142103232	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	196	630	0	ENST00000261584.4:c.1610C>T	p.Ser537Leu	p.S537L	ENST00000261584	NM_024675.3	537	tCg/tTg	4/13	1	2	FACETS	0.933	0.865	1	0.933	0.865	1	CLONAL	1	TRUE	1	0.53	2		630	793	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710875	117710875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140178288	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	126	415	0	ENST00000368508.3:c.1397G>A	p.Arg466Gln	p.R466Q	ENST00000368508	NM_002944.2	466	cGa/cAa	12/43	1	2	FACETS	0.916	0.834	1	0.916	0.834	1	CLONAL	1	TRUE	1	0.53	2		415	519	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416411	49416411	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	179	563	1	ENST00000301067.7:c.16300G>A	p.Glu5434Lys	p.E5434K	ENST00000301067	NM_003482.3	5434	Gag/Aag	51/54	1	2	FACETS	0.957	0.885	1	0.957	0.885	1	CLONAL	1	TRUE	1	0.53	2		564	706	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266560	115266560	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	157	598	0	ENST00000438362.2:c.1955G>T	p.Arg652Met	p.R652M	ENST00000438362	NM_001242891.1	652	aGg/aTg	16/20	1	2	FACETS	0.949	0.873	1	0.949	0.873	1	CLONAL	1	TRUE	1	0.53	2		598	624	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451374	70451374	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	161	596	0	ENST00000373644.4:c.6214G>T	p.Glu2072Ter	p.E2072*	ENST00000373644	NM_030625.2	2072	Gaa/Taa	12/12	1	2	FACETS	0.957	0.881	1	0.957	0.881	1	CLONAL	1	TRUE	1	0.53	2		596	635	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922191	100922191	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	109	458	0	ENST00000325455.5:c.2321A>C	p.Gln774Pro	p.Q774P	ENST00000325455	NM_001202474.3	774	cAg/cCg	5/8	1	2	FACETS	0.996	0.901	1	0.996	0.901	1	CLONAL	1	TRUE	1	0.53	2		458	413	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151837	108151837	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	119	453	0	ENST00000278616.4:c.3518T>G	p.Leu1173Trp	p.L1173W	ENST00000278616	NM_000051.3	1173	tTg/tGg	24/63	1	2	FACETS	0.937	0.851	1	0.937	0.851	1	CLONAL	1	TRUE	1	0.53	2		453	479	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173699	108173699	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	80	413	0	ENST00000278616.4:c.5439T>A	p.Phe1813Leu	p.F1813L	ENST00000278616	NM_000051.3	1813	ttT/ttA	36/63	1	2	FACETS	0.807	0.715	0.904	0.807	0.715	0.904	CLONAL	1	TRUE	1	0.53	2		413	374	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552608	18552608	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs760027403	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	64	392	0	ENST00000266497.5:c.2019G>T	p.Lys673Asn	p.K673N	ENST00000266497		673	aaG/aaT	14/31	1	2	FACETS	0.717	0.624	0.815	0.717	0.624	0.815	SUBCLONAL	1	TRUE	1	0.53	2		392	337	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914550	32914550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358842	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	119	616	0	ENST00000380152.3:c.6058G>A	p.Glu2020Lys	p.E2020K	ENST00000380152		2020	Gaa/Aaa	11/27	1	2	FACETS	0.936	0.849	1	0.936	0.849	1	CLONAL	1	TRUE	1	0.53	2		616	480	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422106	81422106	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253500374	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	138	549	0	ENST00000298171.2:c.82C>T	p.Pro28Ser	p.P28S	ENST00000298171	NM_000369.2	28	Ccc/Tcc	1/10	1	2	FACETS	0.694	0.632	0.759	0.694	0.632	0.759	SUBCLONAL	1	TRUE	1	0.53	2		549	750	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58700895	58700895	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	79	519	0	ENST00000305921.3:c.486G>T	p.Lys162Asn	p.K162N	ENST00000305921	NM_003620.3	162	aaG/aaT	2/6	1	2	FACETS	0.556	0.49	0.627	0.556	0.49	0.627	SUBCLONAL	1	TRUE	1	0.53	2		519	536	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940449	29940449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375097381	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	75	334	0	ENST00000389048.3:c.782G>A	p.Arg261Gln	p.R261Q	ENST00000389048	NM_004304.4	261	cGa/cAa	2/29	1	2	FACETS	0.907	0.802	1	0.907	0.802	1	CLONAL	1	TRUE	1	0.53	2		334	312	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131400	202131400	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1163102643	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	101	537	0	ENST00000358485.4:c.368A>G	p.Glu123Gly	p.E123G	ENST00000358485	NM_001080125.1	123	gAg/gGg	2/9	1	2	FACETS	0.737	0.661	0.817	0.737	0.661	0.817	SUBCLONAL	1	TRUE	1	0.53	2		537	517	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37059087	37059087	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	100	354	0	ENST00000231790.2:c.881T>C	p.Leu294Pro	p.L294P	ENST00000231790	NM_000249.3	294	cTc/cCc	10/19	1	2	FACETS	0.842	0.757	0.932	0.842	0.757	0.932	CLONAL	1	TRUE	1	0.53	2		354	448	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612035	189612035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773237715	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	48	553	3	ENST00000264731.3:c.1787C>T	p.Ala596Val	p.A596V	ENST00000264731	NM_003722.4	596	gCg/gTg	14/14	1	2	FACETS	0.261	0.22	0.306	0.261	0.22	0.306	SUBCLONAL	1	TRUE	1	0.53	2		556	694	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467571	66467571	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	94	377	0	ENST00000273854.3:c.698G>A	p.Cys233Tyr	p.C233Y	ENST00000273854	NM_004439.5	233	tGc/tAc	3/18	1	2	FACETS	0.912	0.817	1	0.912	0.817	1	CLONAL	1	TRUE	1	0.53	2		377	389	SUCCESS
APC	324	MSKCC	GRCh37	5	112173909	112173909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	102	395	0	ENST00000257430.4:c.2618C>A	p.Ser873Tyr	p.S873Y	ENST00000257430	NM_000038.5	873	tCt/tAt	16/16	1	2	FACETS	0.81	0.728	0.897	0.81	0.728	0.897	CLONAL	1	TRUE	1	0.53	2		395	475	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401586	401586	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	163	589	0	ENST00000380956.4:c.908A>G	p.Asn303Ser	p.N303S	ENST00000380956	NM_001195286.1	303	aAc/aGc	7/9	1	2	FACETS	0.881	0.811	0.954	0.881	0.811	0.954	CLONAL	1	TRUE	1	0.53	2		589	698	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658374	117658374	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	143	700	0	ENST00000368508.3:c.5209G>T	p.Glu1737Ter	p.E1737*	ENST00000368508	NM_002944.2	1737	Gaa/Taa	31/43	1	2	FACETS	0.99	0.907	1	0.99	0.907	1	CLONAL	1	TRUE	1	0.53	2		700	545	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876917	151876917	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	61	241	0	ENST00000262189.6:c.7442+2T>C		p.X2481_splice	ENST00000262189	NM_170606.2	2481			1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.53	2		241	225	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945335	151945335	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	49	207	0	ENST00000262189.6:c.2184A>C	p.Glu728Asp	p.E728D	ENST00000262189	NM_170606.2	728	gaA/gaC	14/59	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.53	2		207	177	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005885	69005885	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	124	513	0	ENST00000288368.4:c.2296G>T	p.Glu766Ter	p.E766*	ENST00000288368	NM_024870.2	766	Gaa/Taa	21/40	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.53	2		513	461	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964333	70964333	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	81	294	0	ENST00000276594.2:c.1695G>T	p.Met565Ile	p.M565I	ENST00000276594	NM_024504.3	565	atG/atT	8/8	1	2	FACETS	0.844	0.749	0.945	0.844	0.749	0.945	CLONAL	1	TRUE	1	0.53	2		294	362	SUCCESS
BTK	695	MSKCC	GRCh37	X	100612553	100612553	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	104	391	0	ENST00000308731.7:c.1121A>C	p.Lys374Thr	p.K374T	ENST00000308731	NM_000061.2	374	aAa/aCa	13/19	1	2	FACETS	0.833	0.75	0.921	0.833	0.75	0.921	CLONAL	1	TRUE	1	0.53	2		391	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0039797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	227	1030	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.54486624192784	1	FACETS	0.914	0.857	0.973	0.914	0.857	0.973	CLONAL	1	TRUE	0	0.54486624192784	1		1030	663	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041886	14041886	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	132	518	0	ENST00000311895.7:c.2433G>C	p.Glu811Asp	p.E811D	ENST00000311895	NM_005236.2	811	gaG/gaC	11/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.54486624192784	2		518	458	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151640	55151640	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	164	822	0	ENST00000257290.5:c.2426T>C	p.Leu809Ser	p.L809S	ENST00000257290	NM_006206.4	809	tTg/tCg	17/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.54486624192784	2		822	513	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270134	66270418	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTCCCACTGTCACAGACACAGCAATTACAGGAATCTGGCTTTGATCGCTGGATGCTGCAACTGCTGATAGGAGATACAGAAAATGGAGCTTGTGGTTAAAGTGATCACATGCATTCAAAATAAAAGTTGCTTAATAGACAGTAATCAATTCATGATTTAAGCAATTTACCCACACTTAGCTGAAATTTCCCCTAATATCCTTTCTTAAAAGTGTGTAATTGAAAAGTCATCTATAATAGAAAATATTTACTTTCCAAATAGAGATTTGAGAGCATCACTAAGTC	ACTCCCACTGTCACAGACACAGCAATTACAGGAATCTGGCTTTGATCGCTGGATGCTGCAACTGCTGATAGGAGATACAGAAAATGGAGCTTGTGGTTAAAGTGATCACATGCATTCAAAATAAAAGTTGCTTAATAGACAGTAATCAATTCATGATTTAAGCAATTTACCCACACTTAGCTGAAATTTCCCCTAATATCCTTTCTTAAAAGTGTGTAATTGAAAAGTCATCTATAATAGAAAATATTTACTTTCCAAATAGAGATTTGAGAGCATCACTAAGTC	-	novel	NA	P-0039797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	56	520	0	ENST00000273854.3:c.1688-224_1748del		p.X563_splice	ENST00000273854	NM_004439.5	563		8/18	1	2	FACETS	0.483	0.414	0.557	0.483	0.414	0.557	SUBCLONAL	1	TRUE	1	0.54486624192784	2		520	426	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	119	333	0				ENST00000310581	NM_198253.2	-/1132			0.269229221368432	1	FACETS	1	0.925	1	1	0.925	1	INDETERMINATE	1	TRUE	0	0.481854307341548	1		333	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	105	409	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.481854307341548	1	FACETS	0.942	0.853	1	0.942	0.853	1	CLONAL	1	TRUE	0	0.481854307341548	1		409	351	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0039881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	79	162	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.997	0.884	1	0.997	0.884	1	CLONAL	1	TRUE	1	0.481854307341548	2		162	329	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716051	243716051	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	96	517	0	ENST00000263826.5:c.1143G>C	p.Leu381Phe	p.L381F	ENST00000263826	NM_005465.4	381	ttG/ttC	10/13	0.322647741795518	2	FACETS	0.781	0.699	0.869	0.391	0.349	0.435	SUBCLONAL	1	TRUE	0	0.481854307341548	2		517	510	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845243	151845243	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1323051494	NA	P-0039881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	55	684	1	ENST00000262189.6:c.13769G>A	p.Arg4590His	p.R4590H	ENST00000262189	NM_170606.2	4590	cGc/cAc	52/59	0.296631441353572	3	FACETS	0.553	0.473	0.64	0.184	0.157	0.214	SUBCLONAL	1	TRUE	0	0.481854307341548	3		685	512	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982329	201982329	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	271	1052	0	ENST00000359651.3:c.708G>C	p.Lys236Asn	p.K236N	ENST00000359651		236	aaG/aaC	6/8	0.322647741795518	2	FACETS	1	0.953	1	0.509	0.477	0.542	CLONAL	1	TRUE	0	0.481854307341548	2		1052	1105	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992750	68992750	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0039881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	34	558	0	ENST00000288368.4:c.1715C>G	p.Ser572Ter	p.S572*	ENST00000288368	NM_024870.2	572	tCa/tGa	16/40	0.353049699081894	3	FACETS	0.363	0.296	0.439	0.121	0.098	0.147	SUBCLONAL	1	TRUE	0	0.481854307341548	3		558	482	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075622	8075622	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	66	569	0	ENST00000377482.5:c.58C>G	p.Leu20Val	p.L20V	ENST00000377482	NM_018948.3	20	Cta/Gta	2/4	0.238657156260993	1	FACETS	0.354	0.307	0.404	0.354	0.307	0.404	INDETERMINATE	1	TRUE	0	0.481854307341548	1		569	588	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981791	201981791	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	210	1016	0	ENST00000359651.3:c.502G>T	p.Glu168Ter	p.E168*	ENST00000359651		168	Gag/Tag	4/8	0.322647741795518	2	FACETS	0.941	0.875	1	0.471	0.437	0.505	CLONAL	1	TRUE	0	0.481854307341548	2		1016	926	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983111	201983111	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	207	895	0	ENST00000359651.3:c.960G>C	p.Lys320Asn	p.K320N	ENST00000359651		320	aaG/aaC	7/8	0.322647741795518	2	FACETS	1	0.935	1	0.503	0.467	0.54	CLONAL	1	TRUE	0	0.481854307341548	2		895	854	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14317377	14317377	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	44	482	0	ENST00000256196.4:c.133C>G	p.Pro45Ala	p.P45A	ENST00000256196		45	Cca/Gca	2/6	0.376685887267858	0	FACETS	0.298	0.25	0.349			1	SUBCLONAL	1	TRUE	0	0.481854307341548	0		482	318	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832523	72832523	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	140	626	0	ENST00000268489.5:c.4058C>G	p.Ser1353Cys	p.S1353C	ENST00000268489	NM_006885.3	1353	tCt/tGt	9/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.481854307341548	2		626	450	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40864387	40864387	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	83	964	0	ENST00000428826.2:c.1321C>G	p.Leu441Val	p.L441V	ENST00000428826		441	Ctt/Gtt	12/21	1	2	FACETS	0.487	0.429	0.548	0.487	0.429	0.548	SUBCLONAL	1	TRUE	1	0.481854307341548	2		964	708	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40864393	40864393	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	82	982	0	ENST00000428826.2:c.1315G>C	p.Glu439Gln	p.E439Q	ENST00000428826		439	Gaa/Caa	12/21	1	2	FACETS	0.49	0.432	0.552	0.49	0.432	0.552	SUBCLONAL	1	TRUE	1	0.481854307341548	2		982	695	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250119	39250119	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	49	663	0	ENST00000402219.2:c.1450A>T	p.Ser484Cys	p.S484C	ENST00000402219	NM_005633.3	484	Agc/Tgc	10/23	0.20845872102264	3	FACETS	0.426	0.36	0.499	0.213	0.18	0.25	INDETERMINATE	1	TRUE	1	0.481854307341548	3		663	592	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488724	212488724	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	127	626	0	ENST00000342788.4:c.2125C>G	p.Gln709Glu	p.Q709E	ENST00000342788	NM_005235.2	709	Caa/Gaa	18/28	0.20845872102264	3	FACETS	1	0.92	1	0.507	0.46	0.556	INDETERMINATE	1	TRUE	1	0.481854307341548	3		626	645	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385204	41385204	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	68	878	0	ENST00000373198.4:c.757A>T	p.Ser253Cys	p.S253C	ENST00000373198	NM_133170.3	253	Agt/Tgt	6/32	0.481854307341548	0	FACETS	0.268	0.233	0.305			1	SUBCLONAL	1	TRUE	0	0.481854307341548	0		878	546	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156150	106156150	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	58	497	0	ENST00000380013.4:c.1051G>C	p.Glu351Gln	p.E351Q	ENST00000380013	NM_001127208.2	351	Gaa/Caa	3/11	1	2	FACETS	0.676	0.584	0.776	0.676	0.584	0.776	SUBCLONAL	1	TRUE	1	0.481854307341548	2		497	356	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005324	150005324	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	64	751	0	ENST00000253339.5:c.901C>T	p.Pro301Ser	p.P301S	ENST00000253339		301	Cct/Tct	3/7	1	2	FACETS	0.51	0.442	0.583	0.51	0.442	0.583	SUBCLONAL	1	TRUE	1	0.481854307341548	2		751	521	SUCCESS
AR	367	MSKCC	GRCh37	X	66765289	66765289	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	168	446	0	ENST00000374690.3:c.301C>G	p.Arg101Gly	p.R101G	ENST00000374690	NM_000044.3	101	Cgt/Ggt	1/8	1	1	FACETS	0.942	0.887	0.996	1	0.994	1	CLONAL	2	TRUE	0	0.481854307341548	1		446	281	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923029	44923029	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	48	397	0	ENST00000377967.4:c.1890del	p.Glu630AspfsTer61	p.E630Dfs*61	ENST00000377967	NM_021140.2	630	gaG/ga	16/29	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		397	448	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918342	44918343	+	frameshift_variant	Frame_Shift_Ins	INS	TC	TC	CCA	novel	NA	P-0039882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	16	239	0	ENST00000377967.4:c.967_968delinsCCA	p.Ser323ProfsTer41	p.S323Pfs*41	ENST00000377967	NM_021140.2	323	TCa/CCAa	11/29	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		239	243	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	64	248	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.81	0.702	0.927	0.81	0.702	0.927	CLONAL	1	TRUE	1	0.29	2		248	545	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	79	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.712	0.626	0.805	0.712	0.626	0.805	SUBCLONAL	1	TRUE	1	0.29	2		341	765	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	118	811	1	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	1	2	FACETS	0.802	0.722	0.886	0.802	0.722	0.886	CLONAL	1	TRUE	1	0.29	2		812	1015	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429978	78429978	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	69	447	0	ENST00000370768.2:c.901del	p.Ile301TyrfsTer22	p.I301Yfs*22	ENST00000370768	NM_003902.3	301	Ata/ta	11/20	1	2	FACETS	0.71	0.618	0.81	0.71	0.618	0.81	SUBCLONAL	1	TRUE	1	0.29	2		447	670	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	73	293	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.29	2		293	499	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779180	135779180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200827913	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	107	632	2	ENST00000298552.3:c.2066G>A	p.Arg689His	p.R689H	ENST00000298552	NM_001162426.1	689	cGc/cAc	17/23	1	2	FACETS	0.873	0.783	0.969	0.873	0.783	0.969	CLONAL	1	TRUE	1	0.29	2		634	845	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732996	30732996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893809	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	89	637	0	ENST00000295754.5:c.1609C>T	p.Arg537Cys	p.R537C	ENST00000295754	NM_003242.5	537	Cgc/Tgc	7/7	1	2	FACETS	0.798	0.707	0.896	0.798	0.707	0.896	SUBCLONAL	1	TRUE	1	0.29	2		637	769	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	134	790	2	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	0.299436178938759	3	FACETS	0.794	0.719	0.873	0.397	0.359	0.437	SUBCLONAL	1	TRUE	1	0.29	3		792	1333	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755554	39755554	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	112	637	2	ENST00000288319.7:c.1211del	p.Pro404ArgfsTer25	p.P404Rfs*25	ENST00000288319	NM_182918.3	404	cCg/cg	10/10	1	2	FACETS	0.925	0.832	1	0.925	0.832	1	CLONAL	1	TRUE	1	0.29	2		639	835	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	140	969	2	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.821	0.746	0.9	0.821	0.746	0.9	CLONAL	1	TRUE	1	0.29	2		971	1176	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272337	15272337	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs771517374	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	165	955	15	ENST00000263388.2:c.6102del	p.Gly2035ValfsTer50	p.G2035Vfs*50	ENST00000263388	NM_000435.2	2034	ccC/cc	33/33	1	2	FACETS	0.947	0.868	1	0.947	0.868	1	CLONAL	1	TRUE	1	0.29	2		970	1202	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257144	19257144	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	127	603	1	ENST00000162023.5:c.819del	p.Thr274ProfsTer?	p.T274Pfs*?	ENST00000162023		273	ccC/cc	12/13	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.29	2		604	840	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	113	461	1	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.828	0.744	0.917	0.828	0.744	0.917	CLONAL	1	TRUE	1	0.29	2		462	941	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806180	1806181	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760502257	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	156	1009	3	ENST00000260795.2:c.1206dup	p.Lys403GlnfsTer93	p.K403Qfs*93	ENST00000260795		400	agc/agCc	8/17	1	2	FACETS	0.938	0.857	1	0.938	0.857	1	CLONAL	1	TRUE	1	0.29	2		1012	1147	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443612	29443612	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	133	852	3	ENST00000389048.3:c.3605del	p.Gly1202GlufsTer56	p.G1202Efs*56	ENST00000389048	NM_004304.4	1202	gGa/ga	23/29	0.299436178938759	3	FACETS	0.876	0.793	0.963	0.438	0.396	0.482	CLONAL	1	TRUE	1	0.29	3		855	1199	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21304066	21304066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444326760	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	121	760	1	ENST00000354336.3:c.845G>A	p.Arg282His	p.R282H	ENST00000354336	NM_005207.3	282	cGc/cAc	3/3	1	2	FACETS	0.729	0.657	0.806	0.729	0.657	0.806	SUBCLONAL	1	TRUE	1	0.29	2		761	1144	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860518	151860518	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375738474	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	121	790	0	ENST00000262189.6:c.10144C>T	p.Arg3382Trp	p.R3382W	ENST00000262189	NM_170606.2	3382	Cgg/Tgg	43/59	1	2	FACETS	0.949	0.857	1	0.949	0.857	1	CLONAL	1	TRUE	1	0.29	2		790	879	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094798	2094798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370228590	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	140	773	1	ENST00000219066.1:c.382C>T	p.Arg128Cys	p.R128C	ENST00000219066	NM_002528.5	128	Cgc/Tgc	3/6	1	2	FACETS	0.95	0.864	1	0.95	0.864	1	CLONAL	1	TRUE	1	0.29	2		774	1016	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355047	73355047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	89	551	1	ENST00000377767.4:c.323G>A	p.Arg108His	p.R108H	ENST00000377767	NM_014953.3	108	cGc/cAc	2/21	1	2	FACETS	0.829	0.735	0.93	0.829	0.735	0.93	CLONAL	1	TRUE	1	0.29	2		552	740	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409089	139409089	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs79782048	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	150	1047	0	ENST00000277541.6:c.2080G>A	p.Glu694Lys	p.E694K	ENST00000277541	NM_017617.3	694	Gag/Aag	13/34	1	2	FACETS	0.803	0.732	0.878	0.803	0.732	0.878	CLONAL	1	TRUE	1	0.29	2		1047	1288	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777114	9777114	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs754116182	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	177	1035	0	ENST00000377346.4:c.883del	p.Gln295ArgfsTer39	p.Q295Rfs*39	ENST00000377346	NM_005026.3	293	gCc/gc	7/24	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.29	2		1035	1205	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578316	226578316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs193238922	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	110	684	1	ENST00000366794.5:c.412C>T	p.Arg138Cys	p.R138C	ENST00000366794	NM_001618.3	138	Cgc/Tgc	4/23	0.3	1	FACETS	0.751	0.674	0.832	0.751	0.674	0.832	SUBCLONAL	1	TRUE	0	0.29	1		685	864	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131665	2131665	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	140	934	0	ENST00000219476.3:c.3680C>T	p.Pro1227Leu	p.P1227L	ENST00000219476	NM_000548.3	1227	cCc/cTc	31/42	1	2	FACETS	0.815	0.741	0.894	0.815	0.741	0.894	CLONAL	1	TRUE	1	0.29	2		934	1184	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219692	36219692	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	155	831	3	ENST00000222270.7:c.4589C>T	p.Ala1530Val	p.A1530V	ENST00000222270	NM_014727.1	1530	gCg/gTg	20/37	1	2	FACETS	0.943	0.861	1	0.943	0.861	1	CLONAL	1	TRUE	1	0.29	2		834	1134	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860074	57860075	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs759448855	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	119	1030	2	ENST00000228682.2:c.821dup	p.Cys275LeufsTer32	p.C275Lfs*32	ENST00000228682	NM_005269.2	272	tgg/tGgg	8/12	1	2	FACETS	0.663	0.597	0.734	0.663	0.597	0.734	SUBCLONAL	1	TRUE	1	0.29	2		1032	1237	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94067986	94067986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150543233	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	45	390	0	ENST00000369303.4:c.976G>A	p.Val326Ile	p.V326I	ENST00000369303	NM_004440.3	326	Gtt/Att	4/17	1	2	FACETS	0.622	0.523	0.732	0.622	0.523	0.732	SUBCLONAL	1	TRUE	1	0.29	2		390	499	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614583	38614583	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121434312	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	89	648	0	ENST00000299084.4:c.349C>T	p.Arg117Ter	p.R117*	ENST00000299084	NM_152594.2	117	Cga/Tga	3/7	1	2	FACETS	0.787	0.697	0.883	0.787	0.697	0.883	SUBCLONAL	1	TRUE	1	0.29	2		648	780	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505431	25505431	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	117	802	2	ENST00000264709.3:c.327del	p.Gln110ArgfsTer52	p.Q110Rfs*52	ENST00000264709	NM_175629.2	109	ggG/gg	4/23	0.299436178938759	3	FACETS	0.969	0.873	1	0.485	0.436	0.536	CLONAL	1	TRUE	1	0.29	3		804	953	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426991	49426991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1002386392	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	106	822	1	ENST00000301067.7:c.11497C>T	p.Arg3833Trp	p.R3833W	ENST00000301067	NM_003482.3	3833	Cgg/Tgg	39/54	1	2	FACETS	0.754	0.675	0.839	0.754	0.675	0.839	SUBCLONAL	1	TRUE	1	0.29	2		823	969	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775990	9775990	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138463758	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	160	845	2	ENST00000377346.4:c.454G>A	p.Ala152Thr	p.A152T	ENST00000377346	NM_005026.3	152	Gcc/Acc	5/24	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.29	2		847	1006	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301171	65301171	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	48	308	0	ENST00000342505.4:c.3277G>T	p.Gly1093Cys	p.G1093C	ENST00000342505	NM_002227.2	1093	Ggc/Tgc	24/25	1	2	FACETS	0.736	0.623	0.86	0.736	0.623	0.86	SUBCLONAL	1	TRUE	1	0.29	2		308	450	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400821	72400821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	79	473	0	ENST00000357731.5:c.350C>T	p.Thr117Met	p.T117M	ENST00000357731	NM_173808.2	117	aCg/aTg	2/7	1	2	FACETS	0.828	0.728	0.935	0.828	0.728	0.935	CLONAL	1	TRUE	1	0.29	2		473	658	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737120	162737120	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	92	528	0	ENST00000367921.3:c.1264A>T	p.Arg422Trp	p.R422W	ENST00000367921	NM_006182.2	422	Agg/Tgg	11/18	1	2	FACETS	0.859	0.763	0.961	0.859	0.763	0.961	CLONAL	1	TRUE	1	0.29	2		528	739	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945728	206945728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	135	662	0	ENST00000423557.1:c.53C>T	p.Ala18Val	p.A18V	ENST00000423557	NM_000572.2	18	gCc/gTc	1/5	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.29	2		662	880	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589705	69589705	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	33	184	0	ENST00000168712.1:c.148C>A	p.Leu50Met	p.L50M	ENST00000168712	NM_002007.2	50	Ctg/Atg	1/3	1	2	FACETS	0.846	0.692	1	0.846	0.692	1	CLONAL	1	TRUE	1	0.29	2		184	269	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115676	108115677	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	45	422	0	ENST00000278616.4:c.828dup	p.Glu277ArgfsTer5	p.E277Rfs*5	ENST00000278616	NM_000051.3	275	tta/ttAa	7/63	1	2	FACETS	0.685	0.576	0.805	0.685	0.576	0.805	SUBCLONAL	1	TRUE	1	0.29	2		422	453	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881423	48881423	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	37	202	0	ENST00000267163.4:c.145T>C	p.Phe49Leu	p.F49L	ENST00000267163	NM_000321.2	49	Ttt/Ctt	2/27	1	2	FACETS	0.963	0.798	1	0.963	0.798	1	CLONAL	1	TRUE	1	0.29	2		202	265	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640889	3640889	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	161	910	0	ENST00000294008.3:c.2750C>T	p.Ala917Val	p.A917V	ENST00000294008	NM_032444.2	917	gCc/gTc	12/15	1	2	FACETS	0.878	0.804	0.957	0.878	0.804	0.957	CLONAL	1	TRUE	1	0.29	2		910	1264	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993165	72993165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202133340	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	170	1002	0	ENST00000268489.5:c.880G>A	p.Val294Ile	p.V294I	ENST00000268489	NM_006885.3	294	Gtc/Atc	2/10	1	2	FACETS	0.913	0.838	0.992	0.913	0.838	0.992	CLONAL	1	TRUE	1	0.29	2		1002	1284	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993752	72993752	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	89	722	0	ENST00000268489.5:c.293A>T	p.His98Leu	p.H98L	ENST00000268489	NM_006885.3	98	cAc/cTc	2/10	1	2	FACETS	0.809	0.717	0.907	0.809	0.717	0.907	CLONAL	1	TRUE	1	0.29	2		722	759	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350060	89350060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375695945	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	147	947	0	ENST00000301030.4:c.2890G>A	p.Gly964Ser	p.G964S	ENST00000301030	NM_001256183.1	964	Ggc/Agc	9/13	1	2	FACETS	0.867	0.79	0.949	0.867	0.79	0.949	CLONAL	1	TRUE	1	0.29	2		947	1169	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857866	89857866	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501879	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	154	938	3	ENST00000389301.3:c.1304G>A	p.Arg435His	p.R435H	ENST00000389301	NM_000135.2	435	cGc/cAc	14/43	1	2	FACETS	0.913	0.834	0.996	0.913	0.834	0.996	CLONAL	1	TRUE	1	0.29	2		941	1163	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579539	7579539	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	109	945	0	ENST00000269305.4:c.148A>G	p.Ile50Val	p.I50V	ENST00000269305	NM_001126112.2	50	Att/Gtt	4/11	1	2	FACETS	0.616	0.552	0.685	0.616	0.552	0.685	SUBCLONAL	1	TRUE	1	0.29	2		945	1220	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244017	41244017	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80357621	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	108	702	2	ENST00000357654.3:c.3531del	p.Phe1177LeufsTer33	p.F1177Lfs*33	ENST00000357654	NM_007294.3	1177	ttT/tt	10/23	1	2	FACETS	0.824	0.739	0.915	0.824	0.739	0.915	CLONAL	1	TRUE	1	0.29	2		704	904	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223105	5223105	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	154	895	0	ENST00000357368.4:c.2698A>T	p.Thr900Ser	p.T900S	ENST00000357368	NM_002850.3	900	Acg/Tcg	18/38	1	2	FACETS	0.898	0.82	0.98	0.898	0.82	0.98	CLONAL	1	TRUE	1	0.29	2		895	1183	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271676	15271676	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1220775151	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	163	1126	0	ENST00000263388.2:c.6763T>C	p.Trp2255Arg	p.W2255R	ENST00000263388	NM_000435.2	2255	Tgg/Cgg	33/33	1	2	FACETS	0.86	0.787	0.937	0.86	0.787	0.937	CLONAL	1	TRUE	1	0.29	2		1126	1307	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748480	40748480	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	153	956	0	ENST00000392038.2:c.402G>T	p.Glu134Asp	p.E134D	ENST00000392038	NM_001626.4	134	gaG/gaT	5/14	1	2	FACETS	0.862	0.787	0.941	0.862	0.787	0.941	CLONAL	1	TRUE	1	0.29	2		956	1224	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498070	29498070	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	105	746	0	ENST00000389048.3:c.1936C>T	p.Gln646Ter	p.Q646*	ENST00000389048	NM_004304.4	646	Cag/Tag	11/29	0.299436178938759	3	FACETS	0.748	0.669	0.833	0.374	0.334	0.417	SUBCLONAL	1	TRUE	1	0.29	3		746	1108	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639562	47639562	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	104	419	0	ENST00000233146.2:c.655A>T	p.Arg219Ter	p.R219*	ENST00000233146	NM_000251.2	219	Aga/Tga	4/16	0.239348298578967	2	FACETS	0.75	0.675	0.829	0.75	0.675	0.829	SUBCLONAL	2	TRUE	0	0.29	2		419	478	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394061	31394062	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	108	603	0	ENST00000328111.2:c.2352dup	p.Lys785GlufsTer20	p.K785Efs*20	ENST00000328111	NM_006892.3	783	cag/caGg	22/23	1	2	FACETS	0.889	0.797	0.986	0.889	0.797	0.986	CLONAL	1	TRUE	1	0.29	2		603	838	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721688	176721688	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	117	652	0	ENST00000439151.2:c.7319G>T	p.Arg2440Met	p.R2440M	ENST00000439151	NM_022455.4	2440	aGg/aTg	23/23	1	2	FACETS	0.978	0.882	1	0.978	0.882	1	CLONAL	1	TRUE	1	0.29	2		652	825	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324542	31324543	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	129	797	0	ENST00000412585.2:c.265_266del	p.Gln89AspfsTer9	p.Q89Dfs*9	ENST00000412585	NM_005514.6	89	CAg/g	2/8	0.248710273443385	2	FACETS	0.993	0.9	1	0.496	0.45	0.546	CLONAL	1	TRUE	0	0.29	2		797	896	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120465	94120465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs944145438	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	62	541	1	ENST00000369303.4:c.586G>A	p.Val196Ile	p.V196I	ENST00000369303	NM_004440.3	196	Gtt/Att	3/17	1	2	FACETS	0.745	0.644	0.855	0.745	0.644	0.855	SUBCLONAL	1	TRUE	1	0.29	2		542	574	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873741	151873741	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	121	739	1	ENST00000262189.6:c.8797A>T	p.Arg2933Trp	p.R2933W	ENST00000262189	NM_170606.2	2933	Agg/Tgg	38/59	1	2	FACETS	0.978	0.883	1	0.978	0.883	1	CLONAL	1	TRUE	1	0.29	2		740	853	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242821	98242821	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	103	638	0	ENST00000331920.6:c.796G>T	p.Glu266Ter	p.E266*	ENST00000331920	NM_000264.3	266	Gaa/Taa	6/24	1	2	FACETS	0.844	0.754	0.939	0.844	0.754	0.939	CLONAL	1	TRUE	1	0.29	2		638	842	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250292	110250292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760546357	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	144	1026	0	ENST00000374672.4:c.383C>T	p.Ala128Val	p.A128V	ENST00000374672	NM_004235.4	128	gCg/gTg	3/5	1	2	FACETS	0.914	0.833	1	0.914	0.833	1	CLONAL	1	TRUE	1	0.29	2		1026	1086	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396542	139396542	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	95	831	0	ENST00000277541.6:c.5385-2A>C		p.X1795_splice	ENST00000277541	NM_017617.3	1795			1	2	FACETS	0.748	0.665	0.837	0.748	0.665	0.837	SUBCLONAL	1	TRUE	1	0.29	2		831	876	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400293	139400293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	60	943	0	ENST00000277541.6:c.4055G>A	p.Cys1352Tyr	p.C1352Y	ENST00000277541	NM_017617.3	1352	tGc/tAc	25/34	1	2	FACETS	0.375	0.322	0.434	0.375	0.322	0.434	SUBCLONAL	1	TRUE	1	0.29	2		943	1103	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815534	139815534	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	174	919	1	ENST00000247668.2:c.1005G>A	p.Met335Ile	p.M335I	ENST00000247668	NM_021138.3	335	atG/atA	9/11	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.29	2		920	1200	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0039946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	341	703	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.391818040393251	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.391818040393251	2		703	782	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	301	662	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.391818040393251	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.391818040393251	3		662	760	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478815	56478815	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	384	657	0	ENST00000267101.3:c.271A>G	p.Met91Val	p.M91V	ENST00000267101	NM_001982.3	91	Atg/Gtg	3/28	0.391818040393251	5	FACETS	0.96	0.913	1	0.96	0.913	1	CLONAL	3	TRUE	2	0.391818040393251	5		657	1081	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239830	41239830	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	134	522	0	ENST00000379561.5:c.520G>C	p.Glu174Gln	p.E174Q	ENST00000379561	NM_002015.3	174	Gag/Cag	1/3	0.391818040393251	3	FACETS	1	0.983	1	0.449	0.409	0.491	CLONAL	1	TRUE	0	0.391818040393251	3		522	607	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045714	26045714	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs768776957	NA	P-0039946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	76	304	0	ENST00000540144.1:c.76G>T	p.Ala26Ser	p.A26S	ENST00000540144	NM_003531.2	26	Gcc/Tcc	1/1	0.17091454157799	6	FACETS	0.945	0.835	1	0.63	0.556	0.709	INDETERMINATE	2	TRUE	3	0.391818040393251	6		304	366	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	116	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.851	0.768	0.938	0.851	0.768	0.938	CLONAL	1	TRUE	1	0.40750095767394	2		341	669	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578538	7578538	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1131691037	NA	P-0039947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	244	380	0	ENST00000269305.4:c.392A>T	p.Asn131Ile	p.N131I	ENST00000269305	NM_001126112.2	131	aAc/aTc	5/11	0.396255783855182	1	FACETS	0.9	0.841	0.96	0.9	0.841	0.96	CLONAL	1	TRUE	0	0.40750095767394	1		380	1060	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023769	27023769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	401	488	0	ENST00000324856.7:c.879del	p.Thr294ProfsTer69	p.T294Pfs*69	ENST00000324856	NM_006015.4	292	aCc/ac	1/20	0.356247227362593	2	FACETS	0.964	0.919	1	0.964	0.919	1	CLONAL	2	TRUE	0	0.40750095767394	2		488	1021	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039420	47039420	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	196	333	0	ENST00000377604.3:c.1043T>G	p.Ile348Ser	p.I348S	ENST00000377604	NM_001204468.1	348	aTc/aGc	10/24	1	1	FACETS	0.757	0.707	0.808	1	0.992	1	SUBCLONAL	2	TRUE	0	0.40750095767394	1		333	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0039949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	460	559	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.511907178689516	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	FALSE	0	0.511907178689516	1		560	927	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46512292	46512292	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	85	444	0	ENST00000262741.5:c.947T>C	p.Leu316Pro	p.L316P	ENST00000262741	NM_003629.3	316	cTc/cCc	8/10	1	2	FACETS	0.858	0.763	0.958	0.858	0.763	0.958	CLONAL	1	FALSE	1	0.511907178689516	2		444	387	SUCCESS
APC	324	MSKCC	GRCh37	5	112116486	112116486	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0039972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	69	196	0	ENST00000257430.4:c.532-1G>T		p.X178_splice	ENST00000257430	NM_000038.5	178			0.351435190093623	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.351435190093623	1		196	235	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636884	2636884	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	52	726	0	ENST00000342085.4:c.1333G>A	p.Gly445Arg	p.G445R	ENST00000342085	NM_002613.4	445	Gga/Aga	11/14	0.276963234209595	2	FACETS	0.373	0.316	0.435	0.186	0.158	0.218	SUBCLONAL	1	TRUE	0	0.351435190093623	2		726	794	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267327	198267327	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	81	375	0	ENST00000335508.6:c.2030G>C	p.Cys677Ser	p.C677S	ENST00000335508	NM_012433.2	677	tGt/tCt	14/25	0.193432423729164	3	FACETS	1	0.908	1	0.516	0.456	0.581	INDETERMINATE	1	TRUE	1	0.351435190093623	3		375	525	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391010	89391010	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	43	446	0	ENST00000336596.2:c.1076T>A	p.Phe359Tyr	p.F359Y	ENST00000336596	NM_005233.5	359	tTc/tAc	5/17	0.351435190093623	2	FACETS	0.402	0.335	0.476	0.201	0.167	0.238	SUBCLONAL	1	TRUE	0	0.351435190093623	2		446	609	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950225	38950225	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	44	420	0	ENST00000357387.3:c.3725G>T	p.Gly1242Val	p.G1242V	ENST00000357387	NM_152756.3	1242	gGt/gTt	31/38	0.351435190093623	2	FACETS	0.459	0.384	0.541	0.229	0.192	0.271	SUBCLONAL	1	TRUE	0	0.351435190093623	2		420	546	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636848	176636848	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	47	413	0	ENST00000439151.2:c.1448C>G	p.Ser483Cys	p.S483C	ENST00000439151	NM_022455.4	483	tCt/tGt	5/23	0.351435190093623	2	FACETS	0.495	0.418	0.581	0.248	0.209	0.291	SUBCLONAL	1	TRUE	0	0.351435190093623	2		413	540	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0039991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	17	248	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.386	0.288	0.504	0.386	0.288	0.504	SUBCLONAL	1	TRUE	1	0.25	2		248	352	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111474	8111499	+	frameshift_variant	Frame_Shift_Del	DEL	TCAGACCACCACAACCACACTCTGGA	TCAGACCACCACAACCACACTCTGGA	-	novel	NA	P-0039991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	48	542	0	ENST00000346208.3:c.960_985del	p.Cys320TrpfsTer23	p.C320Wfs*23	ENST00000346208		320	tgTCAGACCACCACAACCACACTCTGGAgg/tggg	5/6	1	2	FACETS	0.459	0.387	0.54	0.459	0.387	0.54	SUBCLONAL	1	TRUE	1	0.25	2		542	836	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944516	71944516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293622519	NA	P-0039993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	53	609	0	ENST00000298229.2:c.2072G>A	p.Arg691Gln	p.R691Q	ENST00000298229	NM_001567.3	691	cGg/cAg	18/28	0.283881287560596	3	FACETS	0.574	0.491	0.666	0.191	0.163	0.222	INDETERMINATE	1	TRUE	0	0.544897559601515	3		609	431	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11227530	11227530	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	40	452	0	ENST00000361445.4:c.4298T>C	p.Leu1433Ser	p.L1433S	ENST00000361445	NM_004958.3	1433	tTa/tCa	29/58	0.406153648061666	1	FACETS	0.257	0.213	0.305	0.257	0.213	0.305	SUBCLONAL	1	TRUE	0	0.544897559601515	1		452	416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578404	+	frameshift_variant	Frame_Shift_Del	DEL	GGTGGGGGCA	GGTGGGGGCA	-	novel	NA	P-0039993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	88	507	0	ENST00000269305.4:c.526_535del	p.Cys176MetfsTer68	p.C176Mfs*68	ENST00000269305	NM_001126112.2	176	TGCCCCCACCat/at	5/11	0.45923971601831	1	FACETS	0.836	0.751	0.925	0.836	0.751	0.925	CLONAL	1	TRUE	0	0.544897559601515	1		507	281	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870050	40870050	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	56	380	0	ENST00000428826.2:c.967A>C	p.Asn323His	p.N323H	ENST00000428826		323	Aat/Cat	10/21	0.509912989002267	2	FACETS	0.581	0.5	0.668	0.29	0.25	0.334	SUBCLONAL	1	TRUE	0	0.544897559601515	2		380	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0039994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	64	457	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	0.696	0.601	0.799	0.696	0.601	0.799	SUBCLONAL	1	TRUE	1	0.21	2		457	876	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0039994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	43	354	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.559	0.467	0.663	0.559	0.467	0.663	SUBCLONAL	1	TRUE	1	0.21	2		354	732	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551085	41551085	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	43	498	0	ENST00000263253.7:c.3229C>T	p.Gln1077Ter	p.Q1077*	ENST00000263253	NM_001429.3	1077	Caa/Taa	17/31	1	2	FACETS	0.49	0.408	0.581	0.49	0.408	0.581	SUBCLONAL	1	TRUE	1	0.21	2		498	836	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420927	49420928	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0039994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	82	561	0	ENST00000301067.7:c.14821_14822del	p.Leu4941GlyfsTer2	p.L4941Gfs*2	ENST00000301067	NM_003482.3	4941	TTg/g	48/54	1	2	FACETS	0.99	0.872	1	0.99	0.872	1	CLONAL	1	TRUE	1	0.21	2		561	789	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299836	15299836	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	58	693	0	ENST00000263388.2:c.1342G>T	p.Asp448Tyr	p.D448Y	ENST00000263388	NM_000435.2	448	Gac/Tac	8/33	1	2	FACETS	0.612	0.524	0.708	0.612	0.524	0.708	SUBCLONAL	1	TRUE	1	0.21	2		693	903	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292751	62292751	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	78	477	0	ENST00000360203.5:c.203C>T	p.Ser68Phe	p.S68F	ENST00000360203	NM_001283009.1	68	tCt/tTt	3/35	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.21	2		477	603	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31511180	31511180	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755611158	NA	P-0039994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	117	560	0	ENST00000344624.3:c.1394C>T	p.Pro465Leu	p.P465L	ENST00000344624		465	cCg/cTg	6/33	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.21	2		560	932	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250145	110250145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	51	597	0	ENST00000374672.4:c.530C>T	p.Ser177Phe	p.S177F	ENST00000374672	NM_004235.4	177	tCc/tTc	3/5	1	2	FACETS	0.696	0.59	0.812	0.696	0.59	0.812	SUBCLONAL	1	TRUE	1	0.21	2		597	698	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249016	55249017	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCCACG	rs397517114	NA	P-0039995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	81	180	0	ENST00000275493.2:c.2315_2320dup	p.His773_Val774insAlaHis	p.H773_V774insAH	ENST00000275493	NM_005228.3	772	ccc/cCCCACGcc	20/28	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.326645803168885	2		180	414	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	131	486	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.987	0.905	1	0.987	0.905	1	CLONAL	1	TRUE	1	0.697065126578474	2		486	381	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115873	8115874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0040001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	167	472	0	ENST00000346208.3:c.1220dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tCcg	6/6	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.697065126578474	2		472	434	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057936	27057937	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0040001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	131	564	0	ENST00000324856.7:c.1649_1650dup	p.Tyr551ProfsTer69	p.Y551Pfs*69	ENST00000324856	NM_006015.4	548	-/CC	3/20	1	2	FACETS	0.821	0.75	0.894	0.821	0.75	0.894	CLONAL	1	TRUE	1	0.697065126578474	2		564	458	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0040004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	155	126	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.265263389959521	2		126	935	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	123	984	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.265263389959521	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.265263389959521	1		984	686	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838350	156838350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745366033	NA	P-0040004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	67	1025	0	ENST00000524377.1:c.628G>A	p.Asp210Asn	p.D210N	ENST00000524377	NM_002529.3	210	Gac/Aac	6/17	0.146001182091853	3	FACETS	0.465	0.402	0.534	0.155	0.134	0.178	INDETERMINATE	1	TRUE	0	0.265263389959521	3		1025	1230	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374999	118374999	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	60	478	0	ENST00000534358.1:c.8392G>C	p.Asp2798His	p.D2798H	ENST00000534358	NM_005933.3	2798	Gat/Cat	27/36	0.265263389959521	1	FACETS	0.801	0.691	0.92	0.801	0.691	0.92	CLONAL	1	TRUE	0	0.265263389959521	1		478	490	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490518	20490518	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	74	727	0	ENST00000346618.3:c.1255G>C	p.Glu419Gln	p.E419Q	ENST00000346618	NM_001949.4	419	Gaa/Caa	7/7	1	2	FACETS	0.704	0.616	0.8	0.704	0.616	0.8	SUBCLONAL	1	TRUE	1	0.265263389959521	2		727	792	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158109	27158109	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	50	586	0	ENST00000380036.4:c.333C>G	p.Ile111Met	p.I111M	ENST00000380036	NM_000459.3	111	atC/atG	2/23	1	2	FACETS	0.588	0.498	0.687	0.588	0.498	0.687	SUBCLONAL	1	TRUE	1	0.265263389959521	2		586	641	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0040010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	62	508	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.226587438750643	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.226587438750643	1		508	445	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450882	70450882	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200074832	NA	P-0040010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	97	644	0	ENST00000373644.4:c.5722G>T	p.Ala1908Ser	p.A1908S	ENST00000373644	NM_030625.2	1908	Gct/Tct	12/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.226587438750643	2		644	656	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0040011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	101	300	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	0.75	0.928	0.836	0.75	0.928	CLONAL	1	TRUE	1	0.425197349951466	2		300	568	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604673	48604673	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060500738	NA	P-0040011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	24	435	0	ENST00000342988.3:c.1495T>C	p.Cys499Arg	p.C499R	ENST00000342988	NM_005359.5	499	Tgc/Cgc	12/12	0.413401146120383	1	FACETS	0.233	0.182	0.291	0.233	0.182	0.291	SUBCLONAL	1	TRUE	0	0.425197349951466	1		435	382	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610695	52610695	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	27	435	0	ENST00000394830.3:c.3478C>T	p.Arg1160Ter	p.R1160*	ENST00000394830	NM_018313.4	1160	Cga/Tga	23/30	0.389840079714144	1	FACETS	0.274	0.218	0.338	0.274	0.218	0.338	SUBCLONAL	1	TRUE	0	0.425197349951466	1		435	365	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657633	37657633	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0040011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	98	623	0	ENST00000447079.4:c.2550T>A	p.Cys850Ter	p.C850*	ENST00000447079	NM_015083.1	850	tgT/tgA	6/14	1	2	FACETS	0.706	0.63	0.786	0.706	0.63	0.786	SUBCLONAL	1	TRUE	1	0.425197349951466	2		623	653	SUCCESS
APC	324	MSKCC	GRCh37	5	112174412	112174413	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	37	320	0	ENST00000257430.4:c.3124dup	p.Ser1042LysfsTer6	p.S1042Kfs*6	ENST00000257430	NM_000038.5	1041	caa/cAaa	16/16	0.354642724899533	1	FACETS	0.531	0.44	0.631	0.531	0.44	0.631	SUBCLONAL	1	TRUE	0	0.425197349951466	1		320	258	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840091	27840091	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0040011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	63	407	0	ENST00000328488.2:c.3G>A	p.Met1?	p.M1?	ENST00000328488	NM_003533.2	1	atG/atA	1/1	1	2	FACETS	0.788	0.685	0.899	0.788	0.685	0.899	SUBCLONAL	1	TRUE	1	0.425197349951466	2		407	376	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0040019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	44	262	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.848	0.713	0.998	0.848	0.713	0.998	CLONAL	1	TRUE	1	0.26	2		262	399	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0040019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	53	651	0	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	NA	2	FACETS	0.671	0.571	0.779			1	INDETERMINATE	1	TRUE	NA	0.26	2		651	608	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724460	162724460	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1189436808	NA	P-0040019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	46	474	0	ENST00000367921.3:c.232G>A	p.Val78Met	p.V78M	ENST00000367921	NM_006182.2	78	Gtg/Atg	5/18	0.140884149488727	3	FACETS	0.772	0.65	0.907	0.386	0.325	0.454	INDETERMINATE	1	TRUE	1	0.26	3		474	518	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318853	163318853	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	22	192	0	ENST00000271452.3:c.1243G>T	p.Glu415Ter	p.E415*	ENST00000271452	NM_145697.2	415	Gag/Tag	13/14	0.140884149488727	3	FACETS	0.611	0.474	0.77	0.305	0.237	0.385	INDETERMINATE	1	TRUE	1	0.26	3		192	313	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988511	41988511	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	55	405	0	ENST00000219905.7:c.1303A>C	p.Asn435His	p.N435H	ENST00000219905	NM_001164273.1	435	Aac/Cac	3/24	1	2	FACETS	0.68	0.581	0.788	0.68	0.581	0.788	SUBCLONAL	1	TRUE	1	0.26	2		405	622	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645529	215645529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1559424056	NA	P-0040019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	66	457	0	ENST00000260947.4:c.1069A>G	p.Ile357Val	p.I357V	ENST00000260947	NM_000465.2	357	Ata/Gta	4/11	1	2	FACETS	0.827	0.718	0.945	0.827	0.718	0.945	CLONAL	1	TRUE	1	0.26	2		457	614	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026858	6026858	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	96	584	0	ENST00000265849.7:c.1538G>T	p.Ser513Ile	p.S513I	ENST00000265849	NM_000535.5	513	aGt/aTt	11/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.26	2		584	618	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69012040	69012040	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	79	319	0	ENST00000288368.4:c.2677A>G	p.Ile893Val	p.I893V	ENST00000288368	NM_024870.2	893	Att/Gtt	23/40	1	2	FACETS	0.996	0.877	1	0.996	0.877	1	CLONAL	1	TRUE	1	0.26	2		319	610	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	132	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.932	0.849	1	0.932	0.849	1	CLONAL	1	TRUE	1	0.470372381036479	2		341	602	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0040033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	269	618	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.470372381036479	1	FACETS	0.985	0.926	1	0.985	0.926	1	CLONAL	1	TRUE	0	0.470372381036479	1		618	888	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967263	134967263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	438	662	1	ENST00000398015.3:c.2602C>T	p.Arg868Trp	p.R868W	ENST00000398015	NM_004441.4	868	Cgg/Tgg	14/16	0.470372381036479	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.470372381036479	3		663	1143	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0040054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	80	274	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.108535736752839	3	FACETS	1	0.956	1	0.389	0.344	0.437	INDETERMINATE	1	TRUE	0	0.402769472926613	3		274	409	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0040054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	87	453	1	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.402769472926613	2		454	408	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526498	66526498	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	266	388	0	ENST00000358598.2:c.1054C>T	p.Arg352Ter	p.R352*	ENST00000358598	NM_212471.2	352	Cga/Tga	11/11	0.403980803669735	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.402769472926613	3		388	642	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724766	43724766	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	46	486	0	ENST00000382044.4:c.3301G>T	p.Val1101Phe	p.V1101F	ENST00000382044	NM_001141980.1	1101	Gtc/Ttc	17/28	1	2	FACETS	0.467	0.393	0.549	0.467	0.393	0.549	SUBCLONAL	1	TRUE	1	0.402769472926613	2		486	489	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17125842	17125842	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255663	NA	P-0040054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	194	610	1	ENST00000285071.4:c.752G>A	p.Trp251Ter	p.W251*	ENST00000285071	NM_144997.5	251	tGg/tAg	7/14	0.403980803669735	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.402769472926613	1		611	596	SUCCESS
APC	324	MSKCC	GRCh37	5	112175136	112175136	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0040054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	83	159	0	ENST00000257430.4:c.3845C>G	p.Ser1282Ter	p.S1282*	ENST00000257430	NM_000038.5	1282	tCa/tGa	16/16	0.108535736752839	3	FACETS	1	0.958	1	0.754	0.678	0.832	INDETERMINATE	2	TRUE	0	0.402769472926613	3		159	219	SUCCESS
APC	324	MSKCC	GRCh37	5	112177241	112177244	+	frameshift_variant	Frame_Shift_Del	DEL	AATG	AATG	-	rs1057517544	NA	P-0040054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	60	265	0	ENST00000257430.4:c.5952_5955del	p.Glu1985LeufsTer58	p.E1985Lfs*58	ENST00000257430	NM_000038.5	1984	AATGaa/aa	16/16	0.108535736752839	3	FACETS	1	0.946	1	0.394	0.342	0.45	INDETERMINATE	1	TRUE	0	0.402769472926613	3		265	303	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0040055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	169	300	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.183638459559198	4	FACETS	0.806	0.744	0.87	0.537	0.496	0.58	INDETERMINATE	2	TRUE	1	0.480688272899062	4		300	646	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591891	48591891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912581	NA	P-0040055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	66	318	0	ENST00000342988.3:c.1054G>A	p.Gly352Arg	p.G352R	ENST00000342988	NM_005359.5	352	Gga/Aga	9/12	0.480688272899062	1	FACETS	0.49	0.426	0.558	0.49	0.426	0.558	SUBCLONAL	1	TRUE	0	0.480688272899062	1		318	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0040055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	388	549	1	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	0.478853798643472	2	FACETS	0.933	0.891	0.975	0.933	0.891	0.975	CLONAL	2	TRUE	0	0.480688272899062	2		550	865	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-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	147	184	0	ENST00000334344.6:c.4916_4922+13del		p.X1639_splice	ENST00000334344	NM_152641.2	1639		16/21	0.475420479197966	2	FACETS	0.886	0.821	0.952	0.886	0.821	0.952	CLONAL	2	TRUE	0	0.480688272899062	2		184	345	SUCCESS
APC	324	MSKCC	GRCh37	5	112163652	112163652	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	74	187	0	ENST00000257430.4:c.1575C>A	p.Cys525Ter	p.C525*	ENST00000257430	NM_000038.5	525	tgC/tgA	13/16	0.480688272899062	1	FACETS	0.907	0.804	1	0.907	0.804	1	CLONAL	1	TRUE	0	0.480688272899062	1		187	258	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340823	70340823	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	207	364	0	ENST00000374080.3:c.556T>C	p.Trp186Arg	p.W186R	ENST00000374080		186	Tgg/Cgg	5/45	1	2	FACETS	0.759	0.71	0.81	1	0.992	1	SUBCLONAL	2	TRUE	1	0.480688272899062	2		364	567	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0040056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	236	626	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.783129526058149	2	FACETS	0.99	0.93	1	0.495	0.465	0.525	CLONAL	1	TRUE	0	0.783129526058149	2		626	609	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816888	32816888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	737	396	0	ENST00000354258.4:c.1436G>A	p.Gly479Asp	p.G479D	ENST00000354258	NM_000593.5	479	gGt/gAt	6/11	0.779494654248323	5	FACETS	0.984	0.96	1	0.984	0.96	1	CLONAL	4	TRUE	1	0.783129526058149	5		396	1040	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0040076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	87	779	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.0957947129816119	3	FACETS	0.859	0.765	0.958	0.859	0.765	0.958	INDETERMINATE	2	FALSE	1	0.285790012641605	3		779	405	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0040076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	49	352	0				ENST00000310581	NM_198253.2	-/1132			0.285790012641605	0	FACETS	0.671	0.57	0.781			1	SUBCLONAL	1	FALSE	0	0.285790012641605	0		352	365	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713470	40713470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318044562	NA	P-0040076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	44	657	0	ENST00000373198.4:c.4045C>T	p.Arg1349Cys	p.R1349C	ENST00000373198	NM_133170.3	1349	Cgt/Tgt	30/32	0.285790012641605	0	FACETS	0.477	0.4	0.562			1	SUBCLONAL	1	FALSE	0	0.285790012641605	0		657	461	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790158	40790158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781621750	NA	P-0040076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	54	610	0	ENST00000373198.4:c.2573C>T	p.Ser858Phe	p.S858F	ENST00000373198	NM_133170.3	858	tCc/tTc	18/32	0.285790012641605	0	FACETS	0.608	0.52	0.704			1	SUBCLONAL	1	FALSE	0	0.285790012641605	0		610	444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577523	7577523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	40	588	0	ENST00000269305.4:c.758C>T	p.Thr253Ile	p.T253I	ENST00000269305	NM_001126112.2	253	aCc/aTc	7/11	1	2	FACETS	0.353	0.292	0.421	0.353	0.292	0.421	SUBCLONAL	1	FALSE	1	0.285790012641605	2		588	793	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610068	81610068	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	25	354	0	ENST00000298171.2:c.1666C>T	p.Pro556Ser	p.P556S	ENST00000298171	NM_000369.2	556	Cct/Tct	10/10	0.285790012641605	1	FACETS	0.446	0.352	0.555	0.446	0.352	0.555	SUBCLONAL	1	FALSE	0	0.285790012641605	1		354	336	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316114	11316114	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746557535	NA	P-0040076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	118	608	0	ENST00000361445.4:c.640C>T	p.Arg214Cys	p.R214C	ENST00000361445	NM_004958.3	214	Cgt/Tgt	5/58	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.285790012641605	2		608	698	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163805	72163805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	36	293	0	ENST00000357731.5:c.553G>A	p.Gly185Arg	p.G185R	ENST00000357731	NM_173808.2	185	Gga/Aga	4/7	1	2	FACETS	0.969	0.801	1	0.969	0.801	1	CLONAL	1	FALSE	1	0.285790012641605	2		293	260	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711894	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGAG	novel	NA	P-0040076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	52	357	0	ENST00000371953.3:c.512_515dup	p.Arg173GlufsTer8	p.R173Efs*8	ENST00000371953	NM_000314.4	171	cag/cAGAGag	6/9	1	2	FACETS	0.781	0.666	0.907	0.781	0.666	0.907	CLONAL	1	FALSE	1	0.285790012641605	2		357	466	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348822	118348822	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	52	300	0	ENST00000534358.1:c.3475C>T	p.Pro1159Ser	p.P1159S	ENST00000534358	NM_005933.3	1159	Ccc/Tcc	5/36	0.0957947129816119	3	FACETS	0.881	0.751	1	0.441	0.375	0.512	INDETERMINATE	1	FALSE	1	0.285790012641605	3		300	472	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523255	9523255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	34	575	1	ENST00000353224.5:c.1982C>T	p.Pro661Leu	p.P661L	ENST00000353224	NM_177990.2	661	cCa/cTa	9/10	0.285790012641605	1	FACETS	0.394	0.321	0.476	0.394	0.321	0.476	SUBCLONAL	1	FALSE	0	0.285790012641605	1		576	518	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582180	189582180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553856553	NA	P-0040076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	70	399	0	ENST00000264731.3:c.739C>T	p.His247Tyr	p.H247Y	ENST00000264731	NM_003722.4	247	Cat/Tat	5/14	1	2	FACETS	0.911	0.795	1	0.911	0.795	1	CLONAL	1	FALSE	1	0.285790012641605	2		399	538	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555731	21555732	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	73	685	0	ENST00000382592.4:c.2538dup	p.Asn847Ter	p.N847*	ENST00000382592	NM_014572.2	846	-/T	6/8	0.29240234569019	1	FACETS	0.585	0.511	0.665	0.585	0.511	0.665	SUBCLONAL	1	TRUE	0	0.293450609136677	1		685	726	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997447	149997449	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	novel	NA	P-0040077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	105	516	0	ENST00000253339.5:c.2830_2832del	p.Leu944del	p.L944del	ENST00000253339		944	TTG/-	6/7	0.293450609136677	1	FACETS	0.756	0.677	0.84	0.756	0.677	0.84	SUBCLONAL	1	TRUE	0	0.293450609136677	1		516	808	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345115	73345115	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	60	294	0	ENST00000377767.4:c.1682C>T	p.Ser561Leu	p.S561L	ENST00000377767	NM_014953.3	561	tCa/tTa	13/21	0.29240234569019	1	FACETS	0.881	0.762	1	0.881	0.762	1	CLONAL	1	TRUE	0	0.293450609136677	1		294	396	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607426	46607426	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	101	860	0	ENST00000263734.3:c.1615G>C	p.Asp539His	p.D539H	ENST00000263734	NM_001430.4	539	Gac/Cac	12/16	0.174465970217647	3	FACETS	0.727	0.648	0.811	0.363	0.324	0.406	INDETERMINATE	1	TRUE	1	0.293450609136677	3		860	1086	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0040081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	572	284	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.586934220802946	4	FACETS	0.842	0.814	0.87	1	0.996	1	CLONAL	3	TRUE	2	0.808728754709823	4		284	1013	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0040081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	1054	718	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.808728754709823	2		718	1286	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416523	49416710	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTCCATTCGGTGCGCAGCCGCCGGTACTGAGATGACTTGGAGTGCACAAACTGCTTGCTGTAGGGGGTGTTGGTCTCGCCTGTGAAGGTGCTCTGATATGCCTTAGACATGCTGGTGCTGTTCAGGGTATGGGGCCTGGGAGGTGATATAATCCATGACAAGACAGCTCTCCCTCAGACCAAGTACA	CTTCCATTCGGTGCGCAGCCGCCGGTACTGAGATGACTTGGAGTGCACAAACTGCTTGCTGTAGGGGGTGTTGGTCTCGCCTGTGAAGGTGCTCTGATATGCCTTAGACATGCTGGTGCTGTTCAGGGTATGGGGCCTGGGAGGTGATATAATCCATGACAAGACAGCTCTCCCTCAGACCAAGTACA	-	novel	NA	P-0040081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	190	518	0	ENST00000301067.7:c.16053-52_16188del		p.X5351_splice	ENST00000301067	NM_003482.3	5351		51/54	1	2	FACETS	0.528	0.488	0.569	0.528	0.488	0.569	SUBCLONAL	1	TRUE	1	0.808728754709823	2		518	890	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48952978	48953737	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTGTTAGATATGCAGTCAGTTATTGACCAAAAACGTTGTTATGCGGTGCATGATTATATATGAGATTTTTGCTCTTAGTTTGGAAGGAAATAATATGGTGTGTGTTTATATTTCTAAAATTTGGTTATTCTTTCAAATAATGGGAACTAGTTATTTGGCTAAAACTTCTTGCTCATAAGGTCAGTTTGATCTGATTTTTGCCTGTGTCAGTTTTACTAAATTTATGGACAAAGACTGTCCTCTTAATCCTGGACAGCTATCTTGAAAATACATGTCCTAGGTCATGAGAAATGTTATATAAGGTACATAAAGTGCTTAAAATAGTACTGGGCACATAACCTATCTTTAGTATGAATGATATAAACTGAAATGGAGTTAAGGAAATCCAGGTACTGGACCTACCCTCTTGTTAATTTACTTGGGAATGTTAATCACCACTTAATACTTAAGTTGTGAGTTTTAGACAAGCTAGCTTTTGTGTTGTCTTGGCGGCCATATTTGTAAGAAGGGTGAGAAGTATGTTTTAAGAAAAGGCTTTTTAAAAAATTTTAGTAATTGTCAGCTGGGTATAGTGGTACATGCCTATAATCCCAGCCTCTTGGGAGGCCAAAGCAGGAGGATCTCTTGAGCCCAGGAGTGTGAAGGCCAGCCTGGGCAAAACAGTGAGACTCCATCTCAAAAAAAAAAAAAATTTCATAATTGTGATTTTCTAAAATAGCAGGCTCTTATTTTTCTTTTTGTTTGTTTGTAGCGATACAA	ACTGTTAGATATGCAGTCAGTTATTGACCAAAAACGTTGTTATGCGGTGCATGATTATATATGAGATTTTTGCTCTTAGTTTGGAAGGAAATAATATGGTGTGTGTTTATATTTCTAAAATTTGGTTATTCTTTCAAATAATGGGAACTAGTTATTTGGCTAAAACTTCTTGCTCATAAGGTCAGTTTGATCTGATTTTTGCCTGTGTCAGTTTTACTAAATTTATGGACAAAGACTGTCCTCTTAATCCTGGACAGCTATCTTGAAAATACATGTCCTAGGTCATGAGAAATGTTATATAAGGTACATAAAGTGCTTAAAATAGTACTGGGCACATAACCTATCTTTAGTATGAATGATATAAACTGAAATGGAGTTAAGGAAATCCAGGTACTGGACCTACCCTCTTGTTAATTTACTTGGGAATGTTAATCACCACTTAATACTTAAGTTGTGAGTTTTAGACAAGCTAGCTTTTGTGTTGTCTTGGCGGCCATATTTGTAAGAAGGGTGAGAAGTATGTTTTAAGAAAAGGCTTTTTAAAAAATTTTAGTAATTGTCAGCTGGGTATAGTGGTACATGCCTATAATCCCAGCCTCTTGGGAGGCCAAAGCAGGAGGATCTCTTGAGCCCAGGAGTGTGAAGGCCAGCCTGGGCAAAACAGTGAGACTCCATCTCAAAAAAAAAAAAAATTTCATAATTGTGATTTTCTAAAATAGCAGGCTCTTATTTTTCTTTTTGTTTGTTTGTAGCGATACAA	-	novel	NA	P-0040081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	0	70	0	0	ENST00000267163.4:c.1333-749_1343del		p.X445_splice	ENST00000267163	NM_000321.2	445		14/27	0.808728754709823	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.808728754709823	1		0	70	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828969	72828979	+	frameshift_variant	Frame_Shift_Del	DEL	CCAACTTACAC	CCAACTTACAC	-	novel	NA	P-0040081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	455	691	0	ENST00000268489.5:c.7602_7612del	p.Gln2534HisfsTer6	p.Q2534Hfs*6	ENST00000268489	NM_006885.3	2534	caGTGTAAGTTGGca/caca	9/10	0.808728754709823	1	FACETS	0.952	0.92	0.983	0.952	0.92	0.983	CLONAL	1	TRUE	0	0.808728754709823	1		691	704	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0040082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	32	207	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	0.256257581290557	1	FACETS	0.642	0.522	0.778	0.642	0.522	0.778	SUBCLONAL	1	TRUE	0	0.259563653906907	1		207	334	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226309	2226309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	49	625	1	ENST00000326181.6:c.1922G>A	p.Arg641His	p.R641H	ENST00000326181	NM_032271.2	641	cGt/cAt	20/21	1	2	FACETS	0.561	0.474	0.657	0.561	0.474	0.657	SUBCLONAL	1	TRUE	1	0.259563653906907	2		626	673	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873634	35873634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778404	NA	P-0040082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	30	192	0	ENST00000303115.3:c.590C>T	p.Pro197Leu	p.P197L	ENST00000303115	NM_002185.3	197	cCg/cTg	5/8	0.256257581290557	1	FACETS	0.867	0.703	1	0.867	0.703	1	CLONAL	1	TRUE	0	0.259563653906907	1		192	232	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795422	39795422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140580933	NA	P-0040082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	101	585	0	ENST00000288319.7:c.298G>A	p.Val100Ile	p.V100I	ENST00000288319	NM_182918.3	100	Gtt/Att	3/10	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.259563653906907	2		585	745	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41267780	41267780	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	57	365	0	ENST00000357654.3:c.97G>A	p.Glu33Lys	p.E33K	ENST00000357654	NM_007294.3	33	Gaa/Aaa	3/23	0.259563653906907	3	FACETS	0.795	0.682	0.919			1	CLONAL	1	TRUE	NA	0.259563653906907	3		365	624	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117324	7117324	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	76	594	0	ENST00000302850.5:c.3892T>A	p.Phe1298Ile	p.F1298I	ENST00000302850	NM_000208.2	1298	Ttt/Att	22/22	1	2	FACETS	0.82	0.719	0.929	0.82	0.719	0.929	CLONAL	1	TRUE	1	0.259563653906907	2		594	714	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020725	26020725	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	31	166	0	ENST00000357647.3:c.8G>T	p.Arg3Leu	p.R3L	ENST00000357647	NM_003529.2	3	cGc/cTc	1/1	1	2	FACETS	0.979	0.796	1	0.979	0.796	1	CLONAL	1	TRUE	1	0.259563653906907	2		166	244	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0040093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	108	714	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.263005016865199	3	FACETS	0.631	0.567	0.7			1	INDETERMINATE	1	TRUE	NA	0.579847384476804	3		714	761	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0040093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	384	570	0	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	0.514882924673113	2	FACETS	0.869	0.832	0.906	0.869	0.832	0.906	CLONAL	2	TRUE	0	0.579847384476804	2		570	762	SUCCESS
APC	324	MSKCC	GRCh37	5	112175360	112175360	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	65	107	0	ENST00000257430.4:c.4069G>T	p.Gly1357Ter	p.G1357*	ENST00000257430	NM_000038.5	1357	Gga/Tga	16/16	0.513435341380421	3	FACETS	0.797	0.694	0.906	0.398	0.347	0.453	CLONAL	1	TRUE	1	0.579847384476804	3		107	363	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851754	134851754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56396912	NA	P-0040093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	308	515	3	ENST00000398015.3:c.1160C>T	p.Thr387Met	p.T387M	ENST00000398015	NM_004441.4	387	aCg/aTg	5/16	0.181032475582159	4	FACETS	1	0.986	1	0.743	0.704	0.782	INDETERMINATE	2	TRUE	1	0.579847384476804	4		518	753	SUCCESS
APC	324	MSKCC	GRCh37	5	112174171	112174171	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	155	160	0	ENST00000257430.4:c.2882del	p.Asn961MetfsTer4	p.N961Mfs*4	ENST00000257430	NM_000038.5	960	tcA/tc	16/16	0.513435341380421	3	FACETS	0.813	0.752	0.876	0.813	0.752	0.876	CLONAL	2	TRUE	1	0.579847384476804	3		160	424	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439632	220439632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	530	268	0	ENST00000243786.2:c.485C>T	p.Pro162Leu	p.P162L	ENST00000243786	NM_002191.3	162	cCc/cTc	2/2	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.579847384476804	2		268	1367	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938287	36938287	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	204	225	0	ENST00000361632.4:c.674T>A	p.Val225Glu	p.V225E	ENST00000361632		225	gTg/gAg	6/16	0.330399818868693	1	FACETS	0.547	0.508	0.588	0.547	0.508	0.588	INDETERMINATE	1	TRUE	0	0.579847384476804	1		225	913	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923213	26923213	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	28	96	0	ENST00000381527.3:c.209T>G	p.Leu70Arg	p.L70R	ENST00000381527	NM_001260.1	70	cTt/cGt	3/13	0.310525419342917	6	FACETS	0.435	0.347	0.536	0.145	0.115	0.179	INDETERMINATE	1	TRUE	3	0.579847384476804	6		96	479	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28611324	28611324	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	213	140	0	ENST00000241453.7:c.1307G>A	p.Arg436Lys	p.R436K	ENST00000241453	NM_004119.2	436	aGa/aAa	10/24	0.310525419342917	6	FACETS	0.981	0.913	1	0.654	0.609	0.7	INDETERMINATE	2	TRUE	3	0.579847384476804	6		140	809	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457302	67457302	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	182	248	0	ENST00000327367.4:c.276G>C	p.Trp92Cys	p.W92C	ENST00000327367	NM_005902.3	92	tgG/tgC	2/9	0.579847384476804	1	FACETS	0.541	0.5	0.584	0.541	0.5	0.584	SUBCLONAL	1	TRUE	0	0.579847384476804	1		248	824	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943340	17943340	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	197	205	0	ENST00000458235.1:c.2668A>C	p.Ser890Arg	p.S890R	ENST00000458235	NM_000215.3	890	Agc/Cgc	19/24	0.579847384476804	3	FACETS	0.872	0.807	0.939	0.436	0.403	0.47	CLONAL	1	TRUE	1	0.579847384476804	3		205	1005	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480328	89480328	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	83	83	0	ENST00000336596.2:c.2165A>T	p.Gln722Leu	p.Q722L	ENST00000336596	NM_005233.5	722	cAg/cTg	13/17	0.181032475582159	4	FACETS	1	0.967	1	0.415	0.369	0.464	INDETERMINATE	1	TRUE	1	0.579847384476804	4		83	363	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955930	55955930	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	111	193	0	ENST00000263923.4:c.3232T>G	p.Phe1078Val	p.F1078V	ENST00000263923	NM_002253.2	1078	Ttt/Gtt	24/30	0.263005016865199	3	FACETS	0.851	0.768	0.94			1	INDETERMINATE	1	TRUE	NA	0.579847384476804	3		193	580	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140879	37140879	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	186	202	0	ENST00000373509.5:c.715G>T	p.Asp239Tyr	p.D239Y	ENST00000373509	NM_002648.3	239	Gat/Tat	5/6	0.579847384476804	3	FACETS	0.878	0.811	0.947	0.439	0.405	0.474	CLONAL	1	TRUE	1	0.579847384476804	3		202	943	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0040097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	52	262	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.263074813997796	2		262	301	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0040097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	83	360	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.263074813997796	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	1	0.263074813997796	3		360	322	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544748	65544748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	71	134	0	ENST00000358664.4:c.178C>T	p.Arg60Trp	p.R60W	ENST00000358664	NM_002382.4	60	Cgg/Tgg	4/5	0.253988762994939	0	FACETS	1	0.953	1			1	CLONAL	1	TRUE	0	0.263074813997796	0		134	338	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206648	108206648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881321	NA	P-0040097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	39	114	0	ENST00000278616.4:c.8228C>T	p.Thr2743Met	p.T2743M	ENST00000278616	NM_000051.3	2743	aCg/aTg	56/63	0.24212295663961	0	FACETS	1	0.922	1			1	CLONAL	1	TRUE	0	0.263074813997796	0		114	186	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134652	41134652	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	51	125	0	ENST00000379561.5:c.976G>T	p.Gly326Trp	p.G326W	ENST00000379561	NM_002015.3	326	Ggg/Tgg	2/3	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.263074813997796	2		125	312	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986878	36986878	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	119	59	0	ENST00000354822.5:c.811G>T	p.Gly271Cys	p.G271C	ENST00000354822	NM_001079668.2	271	Ggc/Tgc	3/3	0.0696670515464248	3	FACETS	0.975	0.884	1			1	INDETERMINATE	2	TRUE	NA	0.263074813997796	3		59	525	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662299	227662299	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	171	181	0	ENST00000305123.5:c.1156G>C	p.Ala386Pro	p.A386P	ENST00000305123	NM_005544.2	386	Gcc/Ccc	1/2	1	2	FACETS	0.802	0.739	0.868	1	0.99	1	CLONAL	2	TRUE	1	0.263074813997796	2		181	810	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264430	46264430	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748672566	NA	P-0040097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	54	115	0	ENST00000371998.3:c.1477G>A	p.Ala493Thr	p.A493T	ENST00000371998		493	Gcc/Acc	11/23	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.263074813997796	2		115	332	SUCCESS
APC	324	MSKCC	GRCh37	5	112163703	112163703	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	30	75	0	ENST00000257430.4:c.1626G>T	p.Gln542His	p.Q542H	ENST00000257430	NM_000038.5	542	caG/caT	13/16	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.263074813997796	2		75	188	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056743	180056743	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	212	181	0	ENST00000261937.6:c.769G>C	p.Glu257Gln	p.E257Q	ENST00000261937	NM_182925.4	257	Gag/Cag	6/30	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.263074813997796	2		181	1116	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450310	50450310	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	121	169	0	ENST00000331340.3:c.494A>T	p.Lys165Met	p.K165M	ENST00000331340	NM_006060.4	165	aAg/aTg	5/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.263074813997796	2		169	660	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578528	7578528	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1210	183	1004	0	ENST00000269305.4:c.402T>A	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	ttT/ttA	5/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.25	2		1004	1393	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922154	100922154	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0040099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	45	329	0	ENST00000325455.5:c.2357+1G>A		p.X786_splice	ENST00000325455	NM_001202474.3	786			1	2	FACETS	0.923	0.778	1	0.923	0.778	1	CLONAL	1	TRUE	1	0.25	2		329	390	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864717	57864717	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	124	984	0	ENST00000228682.2:c.2194T>C	p.Tyr732His	p.Y732H	ENST00000228682	NM_005269.2	732	Tat/Cat	12/12	1	2	FACETS	0.925	0.835	1	0.925	0.835	1	CLONAL	1	TRUE	1	0.25	2		984	1073	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660544	227660544	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	110	686	1	ENST00000305123.5:c.2911G>T	p.Gly971Trp	p.G971W	ENST00000305123	NM_005544.2	971	Ggg/Tgg	1/2	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.25	2		687	781	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608279	100608279	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	107	810	0	ENST00000308731.7:c.1811G>C	p.Ser604Thr	p.S604T	ENST00000308731	NM_000061.2	604	aGt/aCt	18/19	0.264380737215418	3	FACETS	0.901	0.806	1	0.45	0.403	0.501	CLONAL	1	TRUE	1	0.25	3		810	1069	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0040105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	227	529	1	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.88	2		530	426	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0040105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	144	352	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.88	2		352	303	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872213	45872213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	236	711	0	ENST00000391945.4:c.221C>T	p.Ser74Leu	p.S74L	ENST00000391945	NM_000400.3	74	tCa/tTa	4/23	1	2	FACETS	0.977	0.92	1	0.977	0.92	1	CLONAL	1	TRUE	1	0.88	2		711	549	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174420	11174420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587777900	NA	P-0040105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	245	645	0	ENST00000361445.4:c.7255G>A	p.Glu2419Lys	p.E2419K	ENST00000361445	NM_004958.3	2419	Gaa/Aaa	53/58	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.88	2		645	557	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870966	12870966	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	116	376	0	ENST00000228872.4:c.193C>T	p.Gln65Ter	p.Q65*	ENST00000228872	NM_004064.3	65	Cag/Tag	1/3	1	2	FACETS	0.775	0.707	0.846	0.775	0.707	0.846	SUBCLONAL	1	TRUE	1	0.88	2		376	340	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440372	52440372	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	29	573	1	ENST00000460680.1:c.680G>T	p.Arg227Leu	p.R227L	ENST00000460680	NM_004656.3	227	cGc/cTc	9/17	1	2	FACETS	0.139	0.111	0.171	0.139	0.111	0.171	SUBCLONAL	1	TRUE	1	0.88	2		574	475	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100661	8100661	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	259	877	2	ENST00000346208.3:c.635C>T	p.Ser212Phe	p.S212F	ENST00000346208		212	tCc/tTc	3/6	1	2	FACETS	0.931	0.879	0.985	0.931	0.879	0.985	CLONAL	1	TRUE	1	0.88	2		879	632	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40742005	40742005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	195	701	0	ENST00000392038.2:c.967G>A	p.Glu323Lys	p.E323K	ENST00000392038	NM_001626.4	323	Gag/Aag	11/14	1	2	FACETS	0.849	0.792	0.907	0.849	0.792	0.907	CLONAL	1	TRUE	1	0.88	2		701	522	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041576	47041576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	252	326	1	ENST00000377604.3:c.1801C>T	p.Gln601Ter	p.Q601*	ENST00000377604	NM_001204468.1	601	Cag/Tag	17/24	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.88	1		327	303	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089767	27089777	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TCCAAAACAGG	TCCAAAACAGG	-	novel	NA	P-0040105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	38	552	1	ENST00000324856.7:c.2724_2732+2del		p.X908_splice	ENST00000324856	NM_006015.4	908		8/20	1	2	FACETS	0.178	0.147	0.213	0.178	0.147	0.213	SUBCLONAL	1	TRUE	1	0.88	2		553	485	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105610	27105611	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	178	504	0	ENST00000324856.7:c.5222dup	p.Arg1742GlufsTer14	p.R1742Efs*14	ENST00000324856	NM_006015.4	1741	cag/cAag	20/20	1	2	FACETS	0.811	0.753	0.869	0.811	0.753	0.869	CLONAL	1	TRUE	1	0.88	2		504	499	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160402	108160402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1227046364	NA	P-0040105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	122	303	0	ENST00000278616.4:c.4310G>A	p.Arg1437Lys	p.R1437K	ENST00000278616	NM_000051.3	1437	aGa/aAa	29/63	1	2	FACETS	0.883	0.81	0.958	0.883	0.81	0.958	CLONAL	1	TRUE	1	0.88	2		303	314	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961753	41961753	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	177	452	0	ENST00000219905.7:c.661C>G	p.Pro221Ala	p.P221A	ENST00000219905	NM_001164273.1	221	Cct/Gct	2/24	1	2	FACETS	0.931	0.868	0.995	0.931	0.868	0.995	CLONAL	1	TRUE	1	0.88	2		452	432	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40860019	40860019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	224	551	0	ENST00000428826.2:c.1617G>A	p.Met539Ile	p.M539I	ENST00000428826		539	atG/atA	15/21	1	2	FACETS	0.85	0.797	0.904	0.85	0.797	0.904	CLONAL	1	TRUE	1	0.88	2		551	599	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101057	26101057	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	30	558	1	ENST00000435504.4:c.35C>T	p.Thr12Ile	p.T12I	ENST00000435504		12	aCc/aTc	1/13	1	2	FACETS	0.134	0.108	0.165	0.134	0.108	0.165	SUBCLONAL	1	TRUE	1	0.88	2		559	507	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794999	242794999	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424422486	NA	P-0040105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	298	947	0	ENST00000334409.5:c.210G>A	p.Met70Ile	p.M70I	ENST00000334409	NM_005018.2	70	atG/atA	2/5	0.3	1	FACETS	0.586	0.556	0.616	0.586	0.556	0.616	INDETERMINATE	1	TRUE	0	0.88	1		947	647	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30310003	30310003	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1320914743	NA	P-0040105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	166	432	1	ENST00000307677.4:c.19G>A	p.Glu7Lys	p.E7K	ENST00000307677	NM_138578.1	7	Gag/Aag	2/3	1	2	FACETS	0.852	0.79	0.914	0.852	0.79	0.914	CLONAL	1	TRUE	1	0.88	2		433	443	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440393	52440393	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0040105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	152	469	0	ENST00000460680.1:c.660-1G>A		p.X220_splice	ENST00000460680	NM_004656.3	220			1	2	FACETS	0.902	0.835	0.97	0.902	0.835	0.97	CLONAL	1	TRUE	1	0.88	2		469	383	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528459	157528459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	206	544	0	ENST00000346085.5:c.6184G>A	p.Glu2062Lys	p.E2062K	ENST00000346085	NM_020732.3	2062	Gag/Aag	20/20	1	2	FACETS	0.904	0.846	0.962	0.904	0.846	0.962	CLONAL	1	TRUE	1	0.88	2		544	518	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771804	135771804	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	261	699	0	ENST00000298552.3:c.3313G>A	p.Asp1105Asn	p.D1105N	ENST00000298552	NM_001162426.1	1105	Gat/Aat	23/23	1	2	FACETS	0.968	0.914	1	0.968	0.914	1	CLONAL	1	TRUE	1	0.88	2		699	613	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922808	44922808	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	196	226	0	ENST00000377967.4:c.1669G>T	p.Gly557Ter	p.G557*	ENST00000377967	NM_021140.2	557	Gga/Tga	16/29	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.88	1		226	232	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	137	248	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.927	0.849	1	0.927	0.849	1	CLONAL	1	TRUE	1	0.622155913251818	2		248	475	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	149	274	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.943	0.867	1	0.943	0.867	1	CLONAL	1	TRUE	1	0.622155913251818	2		274	508	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	170	779	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.622155913251818	3	FACETS	1	0.939	1	0.51	0.47	0.552	CLONAL	1	TRUE	1	0.622155913251818	3		779	702	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	199	453	1	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.622155913251818	2		454	606	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318754	163318755	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	157	364	0	ENST00000271452.3:c.1150dup	p.Arg384LysfsTer6	p.R384Kfs*6	ENST00000271452	NM_145697.2	382	gaa/gAaa	13/14	1	2	FACETS	0.984	0.907	1	0.984	0.907	1	CLONAL	1	TRUE	1	0.622155913251818	2		364	513	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570793	226570793	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749502012	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	230	540	1	ENST00000366794.5:c.1103C>T	p.Thr368Met	p.T368M	ENST00000366794	NM_001618.3	368	aCg/aTg	8/23	1	2	FACETS	0.937	0.876	1	0.937	0.876	1	CLONAL	1	TRUE	1	0.622155913251818	2		541	789	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	166	358	7	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.923	0.853	0.996	0.923	0.853	0.996	CLONAL	1	TRUE	1	0.622155913251818	2		365	578	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417947	32417947	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1423753702	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	254	405	0	ENST00000332351.3:c.1105C>T	p.Arg369Ter	p.R369*	ENST00000332351	NM_024426.4	369	Cga/Tga	7/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.622155913251818	2		405	773	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	187	339	0	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.622155913251818	2		339	573	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999062	100999062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	203	498	0	ENST00000325455.5:c.740C>T	p.Ala247Val	p.A247V	ENST00000325455	NM_001202474.3	247	gCg/gTg	1/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.622155913251818	2		498	549	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371742	118371742	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	30	238	0	ENST00000534358.1:c.6199C>T	p.Arg2067Cys	p.R2067C	ENST00000534358	NM_005933.3	2067	Cgc/Tgc	25/36	1	2	FACETS	0.222	0.179	0.272	0.222	0.179	0.272	SUBCLONAL	1	TRUE	1	0.622155913251818	2		238	434	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487211	56487211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776335440	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	220	506	0	ENST00000267101.3:c.1357C>T	p.Arg453Cys	p.R453C	ENST00000267101	NM_001982.3	453	Cgt/Tgt	12/28	1	2	FACETS	0.929	0.867	0.993	0.929	0.867	0.993	CLONAL	1	TRUE	1	0.622155913251818	2		506	761	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	341	969	4	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	0.622155913251818	2		973	1086	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214688	133214688	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	250	531	0	ENST00000320574.5:c.5590A>G	p.Ile1864Val	p.I1864V	ENST00000320574	NM_006231.2	1864	Atc/Gtc	41/49	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.622155913251818	2		531	788	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515036	103515036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775996769	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	134	278	0	ENST00000355739.4:c.1537G>A	p.Ala513Thr	p.A513T	ENST00000355739	NM_000123.3	513	Gca/Aca	8/15	1	2	FACETS	0.957	0.877	1	0.957	0.877	1	CLONAL	1	TRUE	1	0.622155913251818	2		278	450	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246478	105246478	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766000895	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	59	683	0	ENST00000349310.3:c.122G>A	p.Arg41Gln	p.R41Q	ENST00000349310	NM_001014432.1	41	cGg/cAg	4/15	1	2	FACETS	0.204	0.175	0.237	0.204	0.175	0.237	SUBCLONAL	1	TRUE	1	0.622155913251818	2		683	928	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007740	45007740	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	163	326	0	ENST00000558401.1:c.187G>T	p.Gly63Ter	p.G63*	ENST00000558401	NM_004048.2	63	Gga/Tga	2/4	1	2	FACETS	0.981	0.906	1	0.981	0.906	1	CLONAL	1	TRUE	1	0.622155913251818	2		326	534	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007825	45007825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	185	329	0	ENST00000558401.1:c.276del	p.Thr93LeufsTer10	p.T93Lfs*10	ENST00000558401	NM_004048.2	91	aCc/ac	2/4	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.622155913251818	2		329	528	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640313	3640313	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	377	885	0	ENST00000294008.3:c.3326G>A	p.Cys1109Tyr	p.C1109Y	ENST00000294008	NM_032444.2	1109	tGc/tAc	12/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.622155913251818	2		885	1103	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820581	3820581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	317	643	0	ENST00000262367.5:c.2870C>T	p.Pro957Leu	p.P957L	ENST00000262367	NM_004380.2	957	cCt/cTt	14/31	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.622155913251818	2		643	989	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821343	72821344	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs771413197	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	94	372	0	ENST00000268489.5:c.10831dup	p.His3611ProfsTer55	p.H3611Pfs*55	ENST00000268489	NM_006885.3	3611	cac/cCac	10/10	1	2	FACETS	0.624	0.558	0.695	0.624	0.558	0.695	SUBCLONAL	1	TRUE	1	0.622155913251818	2		372	484	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828662	72828662	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	326	584	0	ENST00000268489.5:c.7919G>A	p.Arg2640Lys	p.R2640K	ENST00000268489	NM_006885.3	2640	aGa/aAa	9/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.622155913251818	2		584	974	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925131	81925131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1382212475	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	159	479	1	ENST00000359376.3:c.922G>A	p.Ala308Thr	p.A308T	ENST00000359376	NM_002661.3	308	Gcg/Acg	11/33	1	2	FACETS	0.669	0.614	0.726	0.669	0.614	0.726	SUBCLONAL	1	TRUE	1	0.622155913251818	2		480	764	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982763	7982763	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	254	644	1	ENST00000319144.4:c.1022G>A	p.Cys341Tyr	p.C341Y	ENST00000319144	NM_001139.2	341	tGc/tAc	8/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.622155913251818	2		645	789	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585444	29585444	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	43	465	0	ENST00000356175.3:c.4193T>C	p.Val1398Ala	p.V1398A	ENST00000356175	NM_000267.3	1398	gTc/gCc	31/57	1	2	FACETS	0.189	0.157	0.224	0.189	0.157	0.224	SUBCLONAL	1	TRUE	1	0.622155913251818	2		465	733	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864772	37864772	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	213	413	0	ENST00000269571.5:c.424C>A	p.Leu142Ile	p.L142I	ENST00000269571		142	Ctt/Att	3/27	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.622155913251818	2		413	558	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858072	40858072	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	257	575	0	ENST00000428826.2:c.1792A>G	p.Lys598Glu	p.K598E	ENST00000428826		598	Aag/Gag	16/21	1	2	FACETS	0.92	0.863	0.978	0.92	0.863	0.978	CLONAL	1	TRUE	1	0.622155913251818	2		575	898	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435162	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	298	660	0	ENST00000407977.2:c.1975_1976del	p.Gly659SerfsTer87	p.G659Sfs*87	ENST00000407977		659	GGt/t	9/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.622155913251818	2		660	888	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	204	492	0	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	0.819	0.761	0.878	0.819	0.761	0.878	CLONAL	1	TRUE	1	0.622155913251818	2		492	801	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	308	776	3	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	0.622155913251818	2		779	950	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1623979	1623979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746631584	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	49	607	0	ENST00000344749.5:c.520C>T	p.Arg174Trp	p.R174W	ENST00000344749	NM_001136139.2	174	Cgg/Tgg	8/19	1	2	FACETS	0.179	0.151	0.21	0.179	0.151	0.21	SUBCLONAL	1	TRUE	1	0.622155913251818	2		607	880	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4123835	4123835	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756416031	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	135	340	0	ENST00000262948.5:c.38C>T	p.Thr13Ile	p.T13I	ENST00000262948	NM_030662.3	13	aCc/aTc	1/11	1	2	FACETS	0.887	0.812	0.966	0.887	0.812	0.966	CLONAL	1	TRUE	1	0.622155913251818	2		340	489	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222730	5222731	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs756013055	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	40	449	1	ENST00000357368.4:c.3072dup	p.Val1025ArgfsTer34	p.V1025Rfs*34	ENST00000357368	NM_002850.3	1024	-/C	18/38	1	2	FACETS	0.2	0.165	0.239	0.2	0.165	0.239	SUBCLONAL	1	TRUE	1	0.622155913251818	2		450	643	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222936	5222936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	178	329	0	ENST00000357368.4:c.2867C>T	p.Ala956Val	p.A956V	ENST00000357368	NM_002850.3	956	gCc/gTc	18/38	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.622155913251818	2		329	563	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260622	10260622	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	218	458	0	ENST00000340748.4:c.2240A>G	p.Tyr747Cys	p.Y747C	ENST00000340748		747	tAt/tGt	24/40	1	2	FACETS	0.961	0.897	1	0.961	0.897	1	CLONAL	1	TRUE	1	0.622155913251818	2		458	729	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793280	33793280	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1443423632	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	83	140	2	ENST00000498907.2:c.41del	p.Pro14ArgfsTer2	p.P14Rfs*2	ENST00000498907	NM_004364.3	14	cCg/cg	1/1	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.622155913251818	2		142	257	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449864	29449864	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	340	892	0	ENST00000389048.3:c.2991G>T	p.Met997Ile	p.M997I	ENST00000389048	NM_004304.4	997	atG/atT	18/29	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.622155913251818	2		892	1060	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158594993	158594993	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	190	431	0	ENST00000263640.3:c.1354C>T	p.Gln452Ter	p.Q452*	ENST00000263640	NM_001105.4	452	Caa/Taa	10/11	1	2	FACETS	0.931	0.865	1	0.931	0.865	1	CLONAL	1	TRUE	1	0.622155913251818	2		431	656	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587117	212587117	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	141	268	0	ENST00000342788.4:c.883+1G>A		p.X295_splice	ENST00000342788	NM_005235.2	295			1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.622155913251818	2		268	446	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339038	225339038	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	200	385	0	ENST00000264414.4:c.2231G>A	p.Arg744His	p.R744H	ENST00000264414	NM_003590.4	744	cGt/cAt	16/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.622155913251818	2		385	553	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389156	31389156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568859258	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	241	526	2	ENST00000328111.2:c.2069G>A	p.Arg690Gln	p.R690Q	ENST00000328111	NM_006892.3	690	cGg/cAg	19/23	1	2	FACETS	0.92	0.861	0.98	0.92	0.861	0.98	CLONAL	1	TRUE	1	0.622155913251818	2		528	842	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032801	30032801	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	224	366	0	ENST00000338641.4:c.176C>T	p.Thr59Ile	p.T59I	ENST00000338641	NM_000268.3	59	aCc/aTc	2/16	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.622155913251818	2		366	705	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523722	41523722	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	240	678	0	ENST00000263253.7:c.1138A>G	p.Thr380Ala	p.T380A	ENST00000263253	NM_001429.3	380	Aca/Gca	4/31	1	2	FACETS	0.727	0.679	0.777	0.727	0.679	0.777	SUBCLONAL	1	TRUE	1	0.622155913251818	2		678	1061	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	164	318	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.962	0.889	1	0.962	0.889	1	CLONAL	1	TRUE	1	0.622155913251818	2		318	548	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236708	236708	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	89	158	0	ENST00000264932.6:c.1426A>G	p.Arg476Gly	p.R476G	ENST00000264932	NM_004168.2	476	Agg/Ggg	10/15	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.622155913251818	2		158	260	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161221	56161221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781300314	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	213	384	0	ENST00000399503.3:c.1090C>T	p.Arg364Trp	p.R364W	ENST00000399503	NM_005921.1	364	Cgg/Tgg	5/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.622155913251818	2		384	623	SUCCESS
APC	324	MSKCC	GRCh37	5	112170772	112170772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765557332	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	240	532	1	ENST00000257430.4:c.1868G>A	p.Arg623Gln	p.R623Q	ENST00000257430	NM_000038.5	623	cGg/cAg	15/16	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.622155913251818	2		533	754	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	142	216	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.622155913251818	2		216	442	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953842	131953842	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	96	342	0	ENST00000265335.6:c.3245A>G	p.Glu1082Gly	p.E1082G	ENST00000265335		1082	gAa/gGa	21/25	1	2	FACETS	0.535	0.477	0.596	0.535	0.477	0.596	SUBCLONAL	1	TRUE	1	0.622155913251818	2		342	577	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271534	26271534	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	273	315	0	ENST00000305910.3:c.79C>T	p.Arg27Trp	p.R27W	ENST00000305910	NM_003534.2	27	Cgg/Tgg	1/1	0.622155913251818	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.622155913251818	2		315	439	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32191658	32191659	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGCAGC	rs35795312	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	230	683	0	ENST00000375023.3:c.42_47dup	p.Leu15_Leu16dup	p.L15_L16dup	ENST00000375023	NM_004557.3	15	cta/ctGCTGCTa	1/30	0.622155913251818	2	FACETS	0.893	0.834	0.953	0.446	0.417	0.477	CLONAL	1	TRUE	0	0.622155913251818	2		683	828	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798477	32798477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269566347	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	649	687	0	ENST00000374899.4:c.1379C>T	p.Ala460Val	p.A460V	ENST00000374899	NM_018833.2	460	gCc/gTc	8/12	0.622155913251818	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.622155913251818	2		687	982	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43749743	43749743	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376388064	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	69	491	0	ENST00000523873.1:c.596C>T	p.Pro199Leu	p.P199L	ENST00000523873		199	cCg/cTg	7/8	1	2	FACETS	0.234	0.203	0.267	0.234	0.203	0.267	SUBCLONAL	1	TRUE	1	0.622155913251818	2		491	949	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129310	152129310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	251	548	0	ENST00000206249.3:c.263C>T	p.Ala88Val	p.A88V	ENST00000206249	NM_000125.3	88	gCg/gTg	1/8	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.622155913251818	2		548	692	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968322	2968323	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs762770988	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	341	631	1	ENST00000396946.4:c.1663dup	p.Arg555ProfsTer38	p.R555Pfs*38	ENST00000396946	NM_032415.4	555	cgg/cCgg	13/25	0.622155913251818	3	FACETS	1	0.994	1	0.684	0.648	0.721	CLONAL	1	TRUE	1	0.622155913251818	3		632	1050	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729384	41729384	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	250	502	0	ENST00000242208.4:c.1145G>A	p.Ser382Asn	p.S382N	ENST00000242208	NM_002192.2	382	aGc/aAc	3/3	0.622155913251818	3	FACETS	1	0.957	1	0.514	0.481	0.549	CLONAL	1	TRUE	1	0.622155913251818	3		502	1024	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882057	36882057	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	314	708	1	ENST00000358127.4:c.956T>C	p.Val319Ala	p.V319A	ENST00000358127	NM_001280556.1	319	gTc/gCc	8/10	1	2	FACETS	0.97	0.916	1	0.97	0.916	1	CLONAL	1	TRUE	1	0.622155913251818	2		709	1041	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93607789	93607789	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	159	352	2	ENST00000375746.1:c.496del	p.Met166CysfsTer18	p.M166Cfs*18	ENST00000375746	NM_001174167.1	164	gAa/ga	3/14	1	2	FACETS	0.987	0.911	1	0.987	0.911	1	CLONAL	1	TRUE	1	0.622155913251818	2		354	518	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418253	139418253	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	377	759	0	ENST00000277541.6:c.319C>A	p.Leu107Ile	p.L107I	ENST00000277541	NM_017617.3	107	Ctc/Atc	3/34	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.622155913251818	2		759	1150	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412473	63412473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	278	802	0	ENST00000330258.3:c.694del	p.Gln232LysfsTer50	p.Q232Kfs*50	ENST00000330258	NM_152424.3	232	Caa/aa	2/2	1	2	FACETS	0.958	0.901	1	0.958	0.901	1	CLONAL	1	TRUE	1	0.622155913251818	2		802	933	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763872	76763872	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	264	533	0	ENST00000373344.5:c.7436T>A	p.Met2479Lys	p.M2479K	ENST00000373344	NM_000489.3	2479	aTg/aAg	35/35	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.622155913251818	2		533	796	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776354	76776354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	191	462	1	ENST00000373344.5:c.7112C>T	p.Ala2371Val	p.A2371V	ENST00000373344	NM_000489.3	2371	gCg/gTg	34/35	1	2	FACETS	0.979	0.91	1	0.979	0.91	1	CLONAL	1	TRUE	1	0.622155913251818	2		463	627	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0040116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	114	311	2	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.916	0.83	1	0.916	0.83	1	CLONAL	1	TRUE	1	0.538481076973503	2		313	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0040116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	291	635	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.538481076973503	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.538481076973503	1		635	674	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0040116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	73	411	1	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	0.847	0.747	0.953	0.847	0.747	0.953	CLONAL	1	TRUE	1	0.538481076973503	2		412	320	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0040116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	72	454	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.538481076973503	2		454	237	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777676	9777676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	179	525	1	ENST00000377346.4:c.1012C>T	p.Arg338Trp	p.R338W	ENST00000377346	NM_005026.3	338	Cgg/Tgg	8/24	1	2	FACETS	0.861	0.795	0.929	0.861	0.795	0.929	CLONAL	1	TRUE	1	0.538481076973503	2		526	772	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120469123	120469123	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs746314617	NA	P-0040116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	161	364	0	ENST00000256646.2:c.4004C>T	p.Pro1335Leu	p.P1335L	ENST00000256646	NM_024408.3	1335	cCg/cTg	24/34	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.538481076973503	2		364	590	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94224036	94224036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	97	409	0	ENST00000323929.3:c.116C>T	p.Thr39Ile	p.T39I	ENST00000323929	NM_005591.3	39	aCa/aTa	3/20	1	2	FACETS	0.881	0.791	0.975	0.881	0.791	0.975	CLONAL	1	TRUE	1	0.538481076973503	2		409	409	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125499143	125499143	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	86	386	0	ENST00000428830.2:c.306G>T	p.Met102Ile	p.M102I	ENST00000428830	NM_001114121.2	102	atG/atT	4/14	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.538481076973503	2		386	309	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981632	70981632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1439	292	759	0	ENST00000276594.2:c.464C>T	p.Ala155Val	p.A155V	ENST00000276594	NM_024504.3	155	gCg/gTg	2/8	0.508494253954933	5	FACETS	1	0.983	1	0.283	0.265	0.302	CLONAL	1	TRUE	1	0.538481076973503	5		759	1731	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	92	333	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.864	0.771	0.963	0.864	0.771	0.963	CLONAL	1	TRUE	1	0.449134479918415	2		333	474	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0040117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	144	729	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	0.449134479918415	2		729	544	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164462	36164463	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0040117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	78	321	0	ENST00000300305.3:c.1412_1413del	p.Arg471ProfsTer128	p.R471Pfs*128	ENST00000300305		471	cGC/c	8/8	1	2	FACETS	0.86	0.759	0.966	0.86	0.759	0.966	CLONAL	1	TRUE	1	0.449134479918415	2		321	404	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946152	55946152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1383334001	NA	P-0040117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	75	365	1	ENST00000263923.4:c.4027C>T	p.Leu1343Phe	p.L1343F	ENST00000263923	NM_002253.2	1343	Ctc/Ttc	30/30	1	2	FACETS	0.841	0.741	0.948	0.841	0.741	0.948	CLONAL	1	TRUE	1	0.449134479918415	2		366	397	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444370	49444370	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	123	656	0	ENST00000301067.7:c.3001del	p.Leu1001PhefsTer16	p.L1001Ffs*16	ENST00000301067	NM_003482.3	1001	Ctt/tt	11/54	1	2	FACETS	0.807	0.731	0.887	0.807	0.731	0.887	CLONAL	1	TRUE	1	0.449134479918415	2		656	679	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383376	4383376	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	108	545	0	ENST00000261254.3:c.170G>C	p.Arg57Thr	p.R57T	ENST00000261254	NM_001759.3	57	aGa/aCa	1/5	1	2	FACETS	0.874	0.787	0.966	0.874	0.787	0.966	CLONAL	1	TRUE	1	0.449134479918415	2		545	550	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551216	29551216	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs749263944	NA	P-0040117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	85	507	0	ENST00000389048.3:c.1414C>T	p.Arg472Trp	p.R472W	ENST00000389048	NM_004304.4	472	Cgg/Tgg	6/29	1	2	FACETS	0.856	0.76	0.958	0.856	0.76	0.958	CLONAL	1	TRUE	1	0.449134479918415	2		507	442	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948320	71948320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	166	790	0	ENST00000298229.2:c.3032C>T	p.Ser1011Phe	p.S1011F	ENST00000298229	NM_001567.3	1011	tCt/tTt	26/28	1	2	FACETS	0.895	0.823	0.97	0.895	0.823	0.97	CLONAL	1	TRUE	1	0.449134479918415	2		790	826	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893343	32893343	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	54	304	0	ENST00000380152.3:c.197A>G	p.Gln66Arg	p.Q66R	ENST00000380152		66	cAa/cGa	3/27	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.449134479918415	2		304	177	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274078	18274078	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1263607860	NA	P-0040117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	38	544	0	ENST00000222254.8:c.1296G>C	p.Gln432His	p.Q432H	ENST00000222254	NM_005027.3	432	caG/caC	11/16	1	2	FACETS	0.308	0.254	0.368	0.308	0.254	0.368	SUBCLONAL	1	TRUE	1	0.449134479918415	2		544	550	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152241	99152241	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs780855388	NA	P-0040117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	37	248	0	ENST00000074304.5:c.320C>G	p.Ser107Cys	p.S107C	ENST00000074304	NM_001134224.1	107	tCt/tGt	6/26	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.449134479918415	2		248	160	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412985	49412985	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	82	626	0	ENST00000418115.1:c.38A>G	p.Asp13Gly	p.D13G	ENST00000418115	NM_001664.2	13	gAt/gGt	2/5	1	2	FACETS	0.804	0.712	0.902	0.804	0.712	0.902	CLONAL	1	TRUE	1	0.449134479918415	2		626	454	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942707	44942707	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	38	386	0	ENST00000377967.4:c.3288del	p.Trp1096Ter	p.W1096*	ENST00000377967	NM_021140.2	1096	tGg/tg	23/29	1	2	FACETS	0.945	0.791	1	0.945	0.791	1	CLONAL	1	TRUE	1	0.449134479918415	2		386	179	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966776	44966776	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	49	407	0	ENST00000377967.4:c.4000T>A	p.Cys1334Ser	p.C1334S	ENST00000377967	NM_021140.2	1334	Tgt/Agt	27/29	1	2	FACETS	0.974	0.834	1	0.974	0.834	1	CLONAL	1	TRUE	1	0.449134479918415	2		407	224	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101179	41101179	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770753852	NA	P-0040127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	138	752	0	ENST00000373198.4:c.1177G>A	p.Val393Met	p.V393M	ENST00000373198	NM_133170.3	393	Gtg/Atg	8/32	0.668482897669736	3	FACETS	0.912	0.833	0.994	0.456	0.416	0.497	CLONAL	1	TRUE	1	0.668482897669736	3		752	604	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39233628	39233628	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	36	622	0	ENST00000402219.2:c.2716G>A	p.Glu906Lys	p.E906K	ENST00000402219	NM_005633.3	906	Gaa/Aaa	17/23	0.567581824630135	4	FACETS	0.644	0.532	0.769	0.322	0.266	0.385	SUBCLONAL	1	TRUE	2	0.668482897669736	4		622	279	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39233637	39233637	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	37	586	0	ENST00000402219.2:c.2707G>C	p.Glu903Gln	p.E903Q	ENST00000402219	NM_005633.3	903	Gaa/Caa	17/23	0.567581824630135	4	FACETS	0.708	0.587	0.841	0.354	0.293	0.421	SUBCLONAL	1	TRUE	2	0.668482897669736	4		586	261	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411881	116411882	+	intron_variant	Intron	INS	-	-	TAGA	novel	NA	P-0040127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	498	912	0	ENST00000397752.3:c.2888-21_2888-20insAGAT		p.*963*	ENST00000397752	NM_000245.2	-/1390			0.656228075917645	4	FACETS	0.93	0.905	0.955	0.93	0.905	0.955	CLONAL	4	TRUE	0	0.668482897669736	4		912	668	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0040129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	89	473	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.87	0.773	0.973	0.87	0.773	0.973	CLONAL	1	TRUE	1	0.353454474662698	2		473	579	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	80	333	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.353454474662698	2		333	390	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0040129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	62	281	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.816	0.707	0.934	0.816	0.707	0.934	CLONAL	1	TRUE	1	0.353454474662698	2		281	430	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477807	140477807	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs180177038	NA	P-0040129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	125	525	0	ENST00000288602.6:c.1501G>A	p.Glu501Lys	p.E501K	ENST00000288602	NM_004333.4	501	Gaa/Aaa	12/18	0.30530034568118	3	FACETS	1	0.984	1	0.709	0.644	0.777	CLONAL	1	TRUE	1	0.353454474662698	3		525	587	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0040129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	77	207	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	1	2	FACETS	0.943	0.831	1	0.943	0.831	1	CLONAL	1	TRUE	1	0.353454474662698	2		207	462	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214696	5214696	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369756620	NA	P-0040129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	179	713	0	ENST00000357368.4:c.4370G>A	p.Cys1457Tyr	p.C1457Y	ENST00000357368	NM_002850.3	1457	tGt/tAt	29/38	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.353454474662698	2		713	969	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	234	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.556323963561901	6	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	3	0.625094520259843	6		341	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	334	614	0	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	0.56379774862258	2	FACETS	0.912	0.873	0.951	0.912	0.873	0.951	CLONAL	2	TRUE	0	0.625094520259843	2		614	586	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0040131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	105	284	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.365795638466815	2		284	569	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0040131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	178	512	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.338835542365669	3	FACETS	0.955	0.884	1	0.955	0.884	1	CLONAL	2	TRUE	1	0.365795638466815	3		512	603	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149071	61149071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772899527	NA	P-0040131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	76	449	0	ENST00000295025.8:c.1261C>T	p.Arg421Cys	p.R421C	ENST00000295025	NM_002908.2	421	Cgc/Tgc	11/11	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.365795638466815	2		449	401	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248877	133248878	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCTGCAGCAGGAAGTCAAAG	novel	NA	P-0040131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	116	657	0	ENST00000320574.5:c.1698_1717dup	p.Arg573ProfsTer45	p.R573Pfs*45	ENST00000320574	NM_006231.2	573	cgg/cCTTTGACTTCCTGCTGCAGCgg	16/49	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.365795638466815	2		657	599	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78935210	78935210	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1034257924	NA	P-0040131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	69	637	0	ENST00000306801.3:c.3622C>T	p.Arg1208Trp	p.R1208W	ENST00000306801	NM_020761.2	1208	Cgg/Tgg	31/34	0.365795638466815	1	FACETS	0.617	0.538	0.701	0.617	0.538	0.701	SUBCLONAL	1	TRUE	0	0.365795638466815	1		637	500	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0040132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	234	308	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.56551120486279	4	FACETS	0.964	0.922	1	0.964	0.922	1	CLONAL	4	TRUE	0	0.56551120486279	4		308	336	SUCCESS
APC	324	MSKCC	GRCh37	5	112175755	112175755	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	81	301	0	ENST00000257430.4:c.4464del	p.Leu1488PhefsTer19	p.L1488Ffs*19	ENST00000257430	NM_000038.5	1488	ttA/tt	16/16	0.56551120486279	3	FACETS	0.896	0.794	1	0.448	0.397	0.503	CLONAL	1	TRUE	1	0.56551120486279	3		301	410	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121649	108121649	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	247	440	2	ENST00000278616.4:c.1457A>C	p.Lys486Thr	p.K486T	ENST00000278616	NM_000051.3	486	aAa/aCa	10/63	0.56551120486279	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.56551120486279	4		442	628	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578158	7578389	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCCAGTTGCAAACCAGACCTCAGGCGGCTCATAGGGCACCACCACACTATGTCGAAAAGTGTTTCTGTCATCCAAATACTCCACACGCAAATTTCCTTCCACTCGGATAAGATGCTGAGGAGGGGCCAGACCTAAGAGCAATCAGTGAGGAATCAGAGGCCTGGGGACCCTGGGCAACCAGCCCTGTCGTCTCTCCAGCCCCAGCTGCTCACCATCGCTATCTGAGCAGCG	CCCCAGTTGCAAACCAGACCTCAGGCGGCTCATAGGGCACCACCACACTATGTCGAAAAGTGTTTCTGTCATCCAAATACTCCACACGCAAATTTCCTTCCACTCGGATAAGATGCTGAGGAGGGGCCAGACCTAAGAGCAATCAGTGAGGAATCAGAGGCCTGGGGACCCTGGGCAACCAGCCCTGTCGTCTCTCCAGCCCCAGCTGCTCACCATCGCTATCTGAGCAGCG	-	novel	NA	P-0040132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	329	598	0	ENST00000269305.4:c.541_672+19del		p.X181_splice	ENST00000269305	NM_001126112.2	181		5-6/11	0.526683149708792	2	FACETS	0.892	0.851	0.934	0.892	0.851	0.934	CLONAL	2	TRUE	0	0.56551120486279	2		598	652	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247265	153247265	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	308	321	0	ENST00000281708.4:c.1537A>T	p.Arg513Trp	p.R513W	ENST00000281708	NM_033632.3	513	Agg/Tgg	10/12	0.541800955929395	3	FACETS	0.919	0.879	0.957	0.919	0.879	0.957	CLONAL	3	TRUE	0	0.56551120486279	3		321	507	SUCCESS
APC	324	MSKCC	GRCh37	5	112174013	112174014	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTACCACTGAATTACATTGTGTGACAGATGAGAGAAATGCACTTAGAAGAAGCTCTGCTGCC	novel	NA	P-0040132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	61	336	0	ENST00000257430.4:c.2724_2785dup	p.His929LeufsTer8	p.H929Lfs*8	ENST00000257430	NM_000038.5	908	tct/tCTACCACTGAATTACATTGTGTGACAGATGAGAGAAATGCACTTAGAAGAAGCTCTGCTGCCct	16/16	0.56551120486279	3	FACETS	0.479	0.413	0.55	0.239	0.206	0.275	SUBCLONAL	1	TRUE	1	0.56551120486279	3		336	578	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964435	93964435	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	98	475	1	ENST00000369303.4:c.2462G>T	p.Ser821Ile	p.S821I	ENST00000369303	NM_004440.3	821	aGc/aTc	14/17	0.56551120486279	3	FACETS	0.792	0.709	0.881	0.396	0.354	0.441	SUBCLONAL	1	TRUE	1	0.56551120486279	3		476	561	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27192621	27192621	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs768209145	NA	P-0040132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	233	377	0	ENST00000380036.4:c.1624G>A	p.Gly542Arg	p.G542R	ENST00000380036	NM_000459.3	542	Gga/Aga	11/23	0.555900133945149	2	FACETS	0.894	0.845	0.943	0.894	0.845	0.943	CLONAL	2	TRUE	0	0.56551120486279	2		377	461	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843572	156843572	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	179	802	1	ENST00000524377.1:c.998T>A	p.Leu333Gln	p.L333Q	ENST00000524377	NM_002529.3	333	cTg/cAg	8/17	1	2	FACETS	0.988	0.91	1	0.988	0.91	1	CLONAL	1	TRUE	1	0.331558184724954	2		803	1093	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281506	49281506	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	177	504	0	ENST00000282018.3:c.553A>T	p.Thr185Ser	p.T185S	ENST00000282018	NM_020377.2	185	Aca/Tca	1/1	0.425051660619086	3	FACETS	1	0.987	1	0.639	0.593	0.686	INDETERMINATE	1	TRUE	1	0.71793617359634	3		504	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0040143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	513	620	1	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.685160277389439	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.71793617359634	2		621	707	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	44	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		341	448	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412008	116412023	+	protein_altering_variant	In_Frame_Del	DEL	ATGAATCTGTAGACTA	ATGAATCTGTAGACTA	G	novel	NA	P-0040161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	93	659	0	ENST00000397752.3:c.2993_3008delinsG	p.Asn998_Tyr1003delinsSer	p.N998_Y1003delinsS	ENST00000397752	NM_000245.2	998	aATGAATCTGTAGACTAc/aGc	14/21	1	2	FACETS	0.452	0.401	0.506	0.452	0.401	0.506	SUBCLONAL	1	TRUE	1	0.48	2		659	858	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248998	55248999	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCCAGCG	rs727504263	NA	P-0040162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	115	352	0	ENST00000275493.2:c.2300_2308dup	p.Ala767_Val769dup	p.A767_V769dup	ENST00000275493	NM_005228.3	767	atg/aTGGCCAGCGtg	20/28	0.276773038603773	2	FACETS	1	0.952	1	0.545	0.492	0.601	CLONAL	1	TRUE	0	0.330542322794012	2		352	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1555525429	NA	P-0040162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	159	608	0	ENST00000269305.4:c.782+1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.278393456913481	3	FACETS	0.983	0.906	1	0.656	0.604	0.709	CLONAL	2	TRUE	0	0.330542322794012	3		608	570	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725069	162725069	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	33	404	0	ENST00000367921.3:c.541G>C	p.Glu181Gln	p.E181Q	ENST00000367921	NM_006182.2	181	Gag/Cag	6/18	0.314573450463386	3	FACETS	0.732	0.597	0.882	0.366	0.298	0.441	SUBCLONAL	1	TRUE	1	0.330542322794012	3		404	318	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577505	7577505	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	168	610	0	ENST00000269305.4:c.776A>C	p.Asp259Ala	p.D259A	ENST00000269305	NM_001126112.2	259	gAc/gCc	7/11	0.278393456913481	3	FACETS	0.99	0.915	1	0.66	0.61	0.712	CLONAL	2	TRUE	0	0.330542322794012	3		610	598	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018257	48018257	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	39	462	0	ENST00000234420.5:c.452A>G	p.Tyr151Cys	p.Y151C	ENST00000234420	NM_000179.2	151	tAt/tGt	2/10	1	2	FACETS	0.69	0.573	0.819	0.69	0.573	0.819	SUBCLONAL	1	TRUE	1	0.330542322794012	2		462	342	SUCCESS
APC	324	MSKCC	GRCh37	5	112178376	112178376	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs756740976	NA	P-0040162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	12	411	0	ENST00000257430.4:c.7085G>T	p.Gly2362Val	p.G2362V	ENST00000257430	NM_000038.5	2362	gGa/gTa	16/16	1	2	FACETS	0.511	0.361	0.694	0.511	0.361	0.694	SUBCLONAL	1	TRUE	1	0.330542322794012	2		411	142	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410792	63410792	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	56	639	1	ENST00000330258.3:c.2375C>T	p.Ser792Phe	p.S792F	ENST00000330258	NM_152424.3	792	tCt/tTt	2/2	1	2	FACETS	0.692	0.593	0.799	0.692	0.593	0.799	SUBCLONAL	1	TRUE	1	0.330542322794012	2		640	490	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46276041	46276044	+	protein_altering_variant	In_Frame_Del	DEL	CATG	CATG	T	novel	NA	P-0040162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	73	559	0	ENST00000371998.3:c.3477_3480delinsT	p.Met1160del	p.M1160del	ENST00000371998		1159	atCATG/atT	18/23	0.250632085031064	2	FACETS	0.962	0.844	1	0.481	0.422	0.545	CLONAL	1	TRUE	0	0.330542322794012	2		559	459	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624616	93624616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201857010	NA	P-0040168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	199	507	0	ENST00000375746.1:c.707C>T	p.Thr236Met	p.T236M	ENST00000375746	NM_001174167.1	236	aCg/aTg	4/14	0.232807562990838	3	FACETS	0.983	0.919	1	0.656	0.612	0.699	INDETERMINATE	2	TRUE	0	0.480867659381624	3		507	522	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30293197	30293197	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	19	384	0	ENST00000322652.5:c.487G>A	p.Gly163Ser	p.G163S	ENST00000322652	NM_015355.2	163	Ggt/Agt	5/16	0.232807562990838	3	FACETS	0.284	0.215	0.365	0.095	0.071	0.122	INDETERMINATE	1	TRUE	0	0.480867659381624	3		384	345	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564766	41564766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303184977	NA	P-0040175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	83	521	0	ENST00000263253.7:c.4067G>A	p.Arg1356Gln	p.R1356Q	ENST00000263253	NM_001429.3	1356	cGa/cAa	25/31	1	2	FACETS	0.797	0.705	0.896	0.797	0.705	0.896	SUBCLONAL	1	TRUE	1	0.383416199206217	2		521	543	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248532	59248532	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	136	615	1	ENST00000371222.2:c.211C>G	p.Leu71Val	p.L71V	ENST00000371222	NM_002228.3	71	Ctg/Gtg	1/1	1	2	FACETS	0.981	0.894	1	0.981	0.894	1	CLONAL	1	TRUE	1	0.383416199206217	2		616	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934576	NA	P-0040176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	600	580	0	ENST00000269305.4:c.818G>C	p.Arg273Pro	p.R273P	ENST00000269305	NM_001126112.2	273	cGt/cCt	8/11	0.720501569127254	2	FACETS	0.913	0.888	0.938	0.913	0.888	0.938	CLONAL	2	TRUE	0	0.760487967839364	2		580	864	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022904	27022905	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	109	62	0	ENST00000324856.7:c.11dup	p.Val5GlyfsTer106	p.V5Gfs*106	ENST00000324856	NM_006015.4	4	cag/cAag	1/20	0.760487967839364	4	FACETS	0.967	0.884	1	0.967	0.884	1	CLONAL	2	TRUE	2	0.760487967839364	4		62	261	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881425	37881425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	443	586	0	ENST00000269571.5:c.2617G>A	p.Asp873Asn	p.D873N	ENST00000269571		873	Gac/Aac	21/27	0.354877735592091	6	FACETS	0.837	0.8	0.875	0.837	0.8	0.875	INDETERMINATE	3	TRUE	3	0.760487967839364	6		586	1169	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0040177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	1066	620	1	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.429806840406241	5	FACETS	0.947	0.928	0.965			1	CLONAL	5	TRUE	NA	0.565761102541317	5		621	1472	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158731	26158731	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	68	285	0	ENST00000289316.2:c.334G>T	p.Val112Leu	p.V112L	ENST00000289316	NM_138720.2	112	Gtg/Ttg	1/2	0.35360048298494	5	FACETS	0.777	0.676	0.886	0.259	0.225	0.296	SUBCLONAL	1	TRUE	2	0.565761102541317	5		285	572	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676286	37676286	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	283	480	0	ENST00000447079.4:c.3043del	p.Leu1015TyrfsTer42	p.L1015Yfs*42	ENST00000447079	NM_015083.1	1014	aCc/ac	11/14	0.529284403284449	2	FACETS	0.867	0.823	0.911	0.867	0.823	0.911	CLONAL	2	TRUE	0	0.565761102541317	2		480	577	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215661819	215661819	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	33	261	0	ENST00000260947.4:c.181G>A	p.Val61Met	p.V61M	ENST00000260947	NM_000465.2	61	Gtg/Atg	2/11	1	2	FACETS	0.645	0.53	0.77	0.645	0.53	0.77	SUBCLONAL	1	TRUE	1	0.565761102541317	2		261	181	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	106	333	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.877	0.792	0.966	0.877	0.792	0.966	CLONAL	1	TRUE	1	0.598203210751524	2		333	404	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249017	55249018	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCA	rs1554350381	NA	P-0040181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	151	510	0	ENST00000275493.2:c.2317_2319dup	p.His773dup	p.H773dup	ENST00000275493	NM_005228.3	773	ccc/ccCCAc	20/28	1	2	FACETS	0.947	0.871	1	0.947	0.871	1	CLONAL	1	TRUE	1	0.598203210751524	2		510	533	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829404	72829404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200268844	NA	P-0040181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	38	541	0	ENST00000268489.5:c.7177G>A	p.Ala2393Thr	p.A2393T	ENST00000268489	NM_006885.3	2393	Gcc/Acc	9/10	0.243639939882604	2	FACETS	0.202	0.166	0.242	0.101	0.083	0.121	INDETERMINATE	1	TRUE	0	0.598203210751524	2		541	628	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880449	155880449	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs869025189	NA	P-0040181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	117	468	0	ENST00000368323.3:c.104G>C	p.Ser35Thr	p.S35T	ENST00000368323	NM_006912.5	35	aGt/aCt	2/6	1	2	FACETS	0.747	0.676	0.82	0.747	0.676	0.82	SUBCLONAL	1	TRUE	1	0.598203210751524	2		468	524	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985725	60985725	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	25	225	0	ENST00000333681.4:c.175C>G	p.Pro59Ala	p.P59A	ENST00000333681		59	Cca/Gca	2/3	1	2	FACETS	0.338	0.267	0.419	0.338	0.267	0.419	SUBCLONAL	1	TRUE	1	0.598203210751524	2		225	247	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043387	180043387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760757893	NA	P-0040181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	85	535	0	ENST00000261937.6:c.3199G>A	p.Asp1067Asn	p.D1067N	ENST00000261937	NM_182925.4	1067	Gac/Aac	23/30	0.447620735141992	1	FACETS	0.354	0.313	0.397	0.354	0.313	0.397	SUBCLONAL	1	TRUE	0	0.598203210751524	1		535	563	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035232	42035232	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	59	537	0	ENST00000219905.7:c.5074T>C	p.Ser1692Pro	p.S1692P	ENST00000219905	NM_001164273.1	1692	Tcc/Ccc	15/24	0.368148250098379	1	FACETS	0.237	0.203	0.273	0.237	0.203	0.273	SUBCLONAL	1	TRUE	0	0.598203210751524	1		537	584	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349018	89349018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs534628110	NA	P-0040181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	341	615	1	ENST00000301030.4:c.3932G>A	p.Arg1311Gln	p.R1311Q	ENST00000301030	NM_001256183.1	1311	cGa/cAa	9/13	0.243639939882604	2	FACETS	0.797	0.76	0.835	0.797	0.76	0.835	INDETERMINATE	2	TRUE	0	0.598203210751524	2		616	715	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096091	71096091	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0040181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	126	213	0	ENST00000318789.4:c.664+2T>C		p.X222_splice	ENST00000318789	NM_032682.5	222			0.447620735141992	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.598203210751524	1		213	235	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395564	116395564	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	92	245	0	ENST00000397752.3:c.1857G>C	p.Met619Ile	p.M619I	ENST00000397752	NM_000245.2	619	atG/atC	6/21	1	2	FACETS	0.955	0.858	1	0.955	0.858	1	CLONAL	1	TRUE	1	0.598203210751524	2		245	322	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0040184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	82	352	0				ENST00000310581	NM_198253.2	-/1132			0.270460314516824	4	FACETS	0.78	0.692	0.873	0.78	0.692	0.873	SUBCLONAL	2	TRUE	2	0.362805849659244	4		352	395	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023307	27023307	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0040184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	67	227	0	ENST00000324856.7:c.413C>G	p.Ser138Ter	p.S138*	ENST00000324856	NM_006015.4	138	tCa/tGa	1/20	0.317501447250035	3	FACETS	0.992	0.875	1	0.992	0.875	1	CLONAL	2	TRUE	1	0.362805849659244	3		227	220	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577543	7577543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1019340046	NA	P-0040184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	137	553	0	ENST00000269305.4:c.738G>A	p.Met246Ile	p.M246I	ENST00000269305	NM_001126112.2	246	atG/atA	7/11	0.287913730461634	2	FACETS	0.826	0.757	0.897	0.826	0.757	0.897	CLONAL	2	TRUE	0	0.362805849659244	2		553	457	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023609	27023609	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	103	603	0	ENST00000324856.7:c.715C>G	p.Pro239Ala	p.P239A	ENST00000324856	NM_006015.4	239	Ccg/Gcg	1/20	0.317501447250035	3	FACETS	0.793	0.714	0.875	0.793	0.714	0.875	SUBCLONAL	2	TRUE	1	0.362805849659244	3		603	423	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0040184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	195	402	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	0.362805849659244	5	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	2	0.362805849659244	5		402	501	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950082	44950082	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0040184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	143	193	0	ENST00000377967.4:c.3851C>G	p.Ser1284Ter	p.S1284*	ENST00000377967	NM_021140.2	1284	tCa/tGa	26/29	0.362805849659244	3	FACETS	1	0.967	1			1	CLONAL	3	TRUE	NA	0.362805849659244	3		193	290	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572621	141572621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748022421	NA	P-0040184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	62	640	0	ENST00000220592.5:c.449G>A	p.Arg150Gln	p.R150Q	ENST00000220592	NM_012154.3	150	cGg/cAg	4/19	0.230352335263077	3	FACETS	0.87	0.753	0.997	0.435	0.376	0.499	CLONAL	1	TRUE	1	0.362805849659244	3		640	464	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	464403	464403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	159	367	1	ENST00000399788.2:c.791G>A	p.Arg264Gln	p.R264Q	ENST00000399788	NM_001042603.1	264	cGa/cAa	7/28	0.362805849659244	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.362805849659244	3		368	452	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321250	65321250	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	145	547	0	ENST00000342505.4:c.1590C>G	p.Ile530Met	p.I530M	ENST00000342505	NM_002227.2	530	atC/atG	11/25	0.317501447250035	3	FACETS	0.922	0.847	1	0.922	0.847	1	CLONAL	2	TRUE	1	0.362805849659244	3		547	512	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354380	40354380	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372734271	NA	P-0040184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	204	978	0	ENST00000293328.3:c.2215C>T	p.His739Tyr	p.H739Y	ENST00000293328	NM_012448.3	739	Cac/Tac	18/19	0.270460314516824	4	FACETS	0.855	0.794	0.919	0.855	0.794	0.919	CLONAL	2	TRUE	2	0.362805849659244	4		978	896	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40498592	40498592	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	80	315	0	ENST00000264657.5:c.268C>T	p.Leu90Phe	p.L90F	ENST00000264657	NM_139276.2	90	Ctt/Ttt	3/24	0.270460314516824	4	FACETS	1	0.972	1	0.674	0.595	0.757	CLONAL	1	TRUE	2	0.362805849659244	4		315	446	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732491	74732491	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	18	259	0	ENST00000359995.5:c.418A>C	p.Ser140Arg	p.S140R	ENST00000359995	NM_001195427.1	140	Agc/Cgc	2/3	0.270460314516824	4	FACETS	0.436	0.328	0.564	0.218	0.164	0.282	SUBCLONAL	1	TRUE	2	0.362805849659244	4		259	310	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276858	15276858	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	165	659	0	ENST00000263388.2:c.5407C>G	p.Leu1803Val	p.L1803V	ENST00000263388	NM_000435.2	1803	Ctg/Gtg	30/33	0.270460314516824	4	FACETS	0.835	0.769	0.905	0.835	0.769	0.905	CLONAL	2	TRUE	2	0.362805849659244	4		659	742	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912435	50912435	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0040184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	90	721	0	ENST00000440232.2:c.1949C>G	p.Ser650Ter	p.S650*	ENST00000440232	NM_002691.3	650	tCa/tGa	16/27	NA	2	FACETS	0.79	0.702	0.884			1	INDETERMINATE	1	TRUE	NA	0.362805849659244	2		721	628	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852406	42852406	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	189	539	0	ENST00000398585.3:c.680A>G	p.Tyr227Cys	p.Y227C	ENST00000398585	NM_001135099.1	227	tAt/tGt	6/14	0.317501447250035	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.362805849659244	3		539	559	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162516	47162528	+	frameshift_variant	Frame_Shift_Del	DEL	TTGGCAGCTCTTC	TTGGCAGCTCTTC	-	novel	NA	P-0040184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	90	298	0	ENST00000409792.3:c.3598_3610del	p.Glu1200PhefsTer32	p.E1200Ffs*32	ENST00000409792	NM_014159.6	1200	GAAGAGCTGCCAAtt/tt	3/21	0.362805849659244	3	FACETS	0.828	0.741	0.919	0.828	0.741	0.919	CLONAL	2	TRUE	1	0.362805849659244	3		298	354	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156201	106156201	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	75	280	0	ENST00000380013.4:c.1102G>A	p.Glu368Lys	p.E368K	ENST00000380013	NM_001127208.2	368	Gaa/Aaa	3/11	0.276175764236497	3	FACETS	1	0.948	1	0.74	0.659	0.824	CLONAL	2	TRUE	0	0.362805849659244	3		280	220	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670570	30670570	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	124	499	0	ENST00000376406.3:c.5950C>G	p.Gln1984Glu	p.Q1984E	ENST00000376406	NM_014641.2	1984	Caa/Gaa	13/15	0.317501447250035	3	FACETS	0.866	0.789	0.947	0.866	0.789	0.947	CLONAL	2	TRUE	1	0.362805849659244	3		499	466	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324187	31324187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151341223	NA	P-0040184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	88	457	0	ENST00000412585.2:c.376G>A	p.Asp126Asn	p.D126N	ENST00000412585	NM_005514.6	126	Gac/Aac	3/8	0.317501447250035	3	FACETS	1	0.902	1	1	0.902	1	CLONAL	2	TRUE	1	0.362805849659244	3		457	285	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900261	101900261	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	28	355	0	ENST00000374994.4:c.695A>G	p.Lys232Arg	p.K232R	ENST00000374994	NM_004612.2	232	aAg/aGg	4/9	0.362805849659244	1	FACETS	0.463	0.371	0.567	0.463	0.371	0.567	SUBCLONAL	1	TRUE	0	0.362805849659244	1		355	273	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040905	47040905	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0040184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	274	344	0	ENST00000377604.3:c.1436-1G>A		p.X479_splice	ENST00000377604	NM_001204468.1	479			0.362805849659244	3	FACETS	0.949	0.905	0.993			1	CLONAL	4	TRUE	NA	0.362805849659244	3		344	470	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	205	333	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.846981958901356	2		333	370	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0040190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	73	308	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.846981958901356	2		309	163	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413100	139413100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201236538	NA	P-0040190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	159	1048	3	ENST00000277541.6:c.1042G>A	p.Ala348Thr	p.A348T	ENST00000277541	NM_017617.3	348	Gcc/Acc	6/34	1	2	FACETS	0.342	0.313	0.373	0.342	0.313	0.373	SUBCLONAL	1	TRUE	1	0.846981958901356	2		1051	1098	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0040191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	143	798	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	1	2	FACETS	0.908	0.826	0.994	0.908	0.826	0.994	CLONAL	1	TRUE	1	0.264557698774434	2		798	1191	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482169	87482169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201028496	NA	P-0040191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	186	930	0	ENST00000277120.3:c.1456G>A	p.Val486Ile	p.V486I	ENST00000277120		486	Gtt/Att	14/19	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.264557698774434	2		930	1290	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0040192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	245	796	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.975	0.92	1	1	0.996	1	CLONAL	5	FALSE	1	0.179815793187245	2		796	559	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148726	20148726	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0040192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	156	433	0	ENST00000379607.5:c.338-1G>A		p.X113_splice	ENST00000379607	NM_001412.3	113			0.257690930843308	1	FACETS	1	0.971	1	1	0.995	1	CLONAL	5	FALSE	0	0.179815793187245	1		433	295	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0040200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	186	248	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.876	0.813	0.942	0.876	0.813	0.942	CLONAL	1	TRUE	1	0.639297134011752	2		248	664	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	299	235	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	NA	2	FACETS	0.983	0.927	1			1	INDETERMINATE	1	TRUE	NA	0.639297134011752	2		235	952	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577045	7577045	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	352	289	0	ENST00000269305.4:c.893del	p.Glu298GlyfsTer47	p.E298Gfs*47	ENST00000269305	NM_001126112.2	298	gAg/gg	8/11	0.639297134011752	1	FACETS	0.996	0.95	1	0.996	0.95	1	CLONAL	1	TRUE	0	0.639297134011752	1		289	752	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922196	39922196	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	313	205	0	ENST00000378444.4:c.3976G>T	p.Glu1326Ter	p.E1326*	ENST00000378444	NM_001123385.1	1326	Gaa/Taa	9/15	1	2	FACETS	0.999	0.944	1	0.999	0.944	1	CLONAL	1	TRUE	1	0.639297134011752	2		205	980	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0040201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	979	618	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.361841112790498	4	FACETS	1	0.995	1			1	INDETERMINATE	4	TRUE	NA	0.893982510822346	4		618	1029	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0040201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	146	308	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.229666595987886	4	FACETS	0.915	0.848	0.983	0.915	0.848	0.983	INDETERMINATE	2	TRUE	2	0.893982510822346	4		309	338	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937596	76937596	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1557138081	NA	P-0040201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	190	230	0	ENST00000373344.5:c.3152A>G	p.Asp1051Gly	p.D1051G	ENST00000373344	NM_000489.3	1051	gAt/gGt	9/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.893982510822346	1		230	205	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115723	8115724	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACAT	novel	NA	P-0040203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	114	489	0	ENST00000346208.3:c.1070_1071insCATA	p.Lys357AsnfsTer15	p.K357Nfs*15	ENST00000346208		357	aag/aACATag	6/6	0.199298481727433	3	FACETS	1	0.977	1	0.425	0.384	0.468	INDETERMINATE	1	TRUE	0	0.401722324245291	3		489	535	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063360	67063375	+	frameshift_variant	Frame_Shift_Del	DEL	TTTTTAGGAAGCTGAG	TTTTTAGGAAGCTGAG	-	novel	NA	P-0040203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	127	513	0	ENST00000412916.2:c.50_65del	p.Phe17SerfsTer67	p.F17Sfs*67	ENST00000412916		17	tTTTTTAGGAAGCTGAGc/tc	1/6	0.401722324245291	2	FACETS	0.985	0.905	1	0.985	0.905	1	CLONAL	2	TRUE	0	0.401722324245291	2		513	321	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131345	202131345	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	157	691	0	ENST00000358485.4:c.313C>T	p.Gln105Ter	p.Q105*	ENST00000358485	NM_001080125.1	105	Cag/Tag	2/9	0.354800165235274	1	FACETS	0.964	0.885	1	0.964	0.885	1	CLONAL	1	TRUE	0	0.354800165235274	1		691	755	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120611957	120611957	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs868921483	NA	P-0040205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	25	92	0	ENST00000256646.2:c.64C>G	p.Pro22Ala	p.P22A	ENST00000256646	NM_024408.3	22	Ccc/Gcc	1/34	0.354800165235274	7	FACETS	1	0.911	1	0.218	0.173	0.27	CLONAL	1	TRUE	1	0.354800165235274	7		92	203	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562669	95562669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	127	536	0	ENST00000393063.1:c.4588C>A	p.Pro1530Thr	p.P1530T	ENST00000393063	NM_030621.3	1530	Cca/Aca	24/28	0.354800165235274	1	FACETS	0.988	0.898	1	0.988	0.898	1	CLONAL	1	TRUE	0	0.354800165235274	1		536	596	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600356	10600356	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	232	957	0	ENST00000171111.5:c.1499T>C	p.Ile500Thr	p.I500T	ENST00000171111	NM_203500.1	500	aTc/aCc	4/6	1	2	FACETS	0.908	0.845	0.974	0.908	0.845	0.974	CLONAL	1	TRUE	1	0.354800165235274	2		957	1440	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143129620	143129620	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	115	482	0	ENST00000262992.4:c.1030C>A	p.Leu344Ile	p.L344I	ENST00000262992	NM_001101669.1	344	Cta/Ata	12/24	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.354800165235274	2		482	638	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0040206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	977	729	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.993	0.98	1	1	0.999	1	CLONAL	2	TRUE	1	0.892804885554367	2		729	1102	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789661	3789661	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	537	750	0	ENST00000262367.5:c.4198G>C	p.Glu1400Gln	p.E1400Q	ENST00000262367	NM_004380.2	1400	Gag/Cag	25/31	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.892804885554367	2		750	1185	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438535	52438535	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0040206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	623	773	0	ENST00000460680.1:c.1184C>G	p.Ser395Ter	p.S395*	ENST00000460680	NM_004656.3	395	tCa/tGa	12/17	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.892804885554367	2		773	1337	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273878	10273878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	107	884	4	ENST00000330684.3:c.391G>A	p.Ala131Thr	p.A131T	ENST00000330684	NM_001134407.1	131	Gca/Aca	2/13	1	2	FACETS	0.185	0.165	0.206	0.185	0.165	0.206	SUBCLONAL	1	TRUE	1	0.892804885554367	2		888	1297	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437315	52437315	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0040206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	474	787	0	ENST00000460680.1:c.1730-1G>C		p.X577_splice	ENST00000460680	NM_004656.3	577			1	2	FACETS	0.951	0.912	0.991	0.951	0.912	0.991	CLONAL	1	TRUE	1	0.892804885554367	2		787	1116	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427900	49427900	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	631	876	0	ENST00000301067.7:c.10690C>G	p.Leu3564Val	p.L3564V	ENST00000301067	NM_003482.3	3564	Ctc/Gtc	38/54	1	2	FACETS	0.988	0.953	1	0.988	0.953	1	CLONAL	1	TRUE	1	0.892804885554367	2		876	1431	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936802	32936802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	239	500	0	ENST00000380152.3:c.7948G>A	p.Glu2650Lys	p.E2650K	ENST00000380152		2650	Gaa/Aaa	17/27	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.892804885554367	2		500	527	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216786	7216786	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs748835899	NA	P-0040206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	381	619	0	ENST00000380728.2:c.637C>T	p.Pro213Ser	p.P213S	ENST00000380728		213	Cct/Tct	8/11	1	2	FACETS	0.892	0.85	0.934	0.892	0.85	0.934	CLONAL	1	TRUE	1	0.892804885554367	2		619	957	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137650	202137650	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	232	469	0	ENST00000358485.4:c.757G>C	p.Asp253His	p.D253H	ENST00000358485	NM_001080125.1	253	Gat/Cat	5/9	1	2	FACETS	0.882	0.829	0.936	0.882	0.829	0.936	CLONAL	1	TRUE	1	0.892804885554367	2		469	589	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610510	215610511	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	263	611	0	ENST00000260947.4:c.1745dup	p.Lys583GlufsTer5	p.K583Efs*5	ENST00000260947	NM_000465.2	582	cag/caAg	8/11	1	2	FACETS	0.881	0.831	0.931	0.881	0.831	0.931	CLONAL	1	TRUE	1	0.892804885554367	2		611	669	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339015	225339015	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	237	628	0	ENST00000264414.4:c.2254G>A	p.Glu752Lys	p.E752K	ENST00000264414	NM_003590.4	752	Gaa/Aaa	16/16	1	2	FACETS	0.878	0.825	0.931	0.878	0.825	0.931	CLONAL	1	TRUE	1	0.892804885554367	2		628	605	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339021	225339021	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	237	648	0	ENST00000264414.4:c.2248G>C	p.Glu750Gln	p.E750Q	ENST00000264414	NM_003590.4	750	Gag/Cag	16/16	1	2	FACETS	0.862	0.81	0.914	0.862	0.81	0.914	CLONAL	1	TRUE	1	0.892804885554367	2		648	616	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091126	29091126	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	385	838	0	ENST00000328354.6:c.1364T>G	p.Val455Gly	p.V455G	ENST00000328354	NM_007194.3	455	gTc/gGc	12/15	1	2	FACETS	0.981	0.937	1	0.981	0.937	1	CLONAL	1	TRUE	1	0.892804885554367	2		838	879	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547882	41547882	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	400	672	0	ENST00000263253.7:c.2863C>A	p.Pro955Thr	p.P955T	ENST00000263253	NM_001429.3	955	Cca/Aca	15/31	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.892804885554367	2		672	893	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565459	41565566	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTGACCTGACTTTTTTTTTCCTCTTCATTTCTCTTCATTTTGTATAGGAGAGTATACATATCTTACCTCGATAGTGTTCATTTCTTCCGTCCTAAATGCTTGAGGAC	TGTGACCTGACTTTTTTTTTCCTCTTCATTTCTCTTCATTTTGTATAGGAGAGTATACATATCTTACCTCGATAGTGTTCATTTCTTCCGTCCTAAATGCTTGAGGAC	-	novel	NA	P-0040206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	101	215	0	ENST00000263253.7:c.4173-46_4234del		p.X1391_splice	ENST00000263253	NM_001429.3	1391		26/31	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.892804885554367	2		215	206	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565509	41565509	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	181	387	0	ENST00000263253.7:c.4175G>C	p.Arg1392Thr	p.R1392T	ENST00000263253	NM_001429.3	1392	aGa/aCa	26/31	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.892804885554367	2		387	312	SUCCESS
ATR	545	MSKCC	GRCh37	3	142234351	142234351	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	171	430	0	ENST00000350721.4:c.4389G>C	p.Lys1463Asn	p.K1463N	ENST00000350721	NM_001184.3	1463	aaG/aaC	25/47	1	2	FACETS	0.958	0.892	1	0.958	0.892	1	CLONAL	1	TRUE	1	0.892804885554367	2		430	400	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155701	56155701	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	414	531	0	ENST00000399503.3:c.793G>C	p.Glu265Gln	p.E265Q	ENST00000399503	NM_005921.1	265	Gaa/Caa	3/20	0.194598541398576	3	FACETS	0.756	0.724	0.789	0.756	0.724	0.789	INDETERMINATE	2	TRUE	1	0.892804885554367	3		531	887	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0040223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	310	652	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.353587021276654	2	FACETS	0.94	0.89	0.992	0.94	0.89	0.992	CLONAL	2	TRUE	0	0.376844462932397	2		652	875	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745539	162745539	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	61	535	0	ENST00000367921.3:c.1954A>G	p.Met652Val	p.M652V	ENST00000367921	NM_006182.2	652	Atg/Gtg	15/18	1	2	FACETS	0.629	0.543	0.722	0.629	0.543	0.722	SUBCLONAL	1	TRUE	1	0.376844462932397	2		535	515	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510217	120510217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	105	476	0	ENST00000256646.2:c.1292G>A	p.Gly431Glu	p.G431E	ENST00000256646	NM_024408.3	431	gGa/gAa	8/34	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.376844462932397	2		476	519	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937116	76937116	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	99	260	0	ENST00000373344.5:c.3632A>G	p.Asp1211Gly	p.D1211G	ENST00000373344	NM_000489.3	1211	gAt/gGt	9/35	1	1	FACETS	0.802	0.727	0.878	1	0.985	1	CLONAL	2	TRUE	0	0.376844462932397	1		260	266	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0040224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	539	717	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	NA	2	FACETS	0.966	0.936	0.995			1	INDETERMINATE	2	TRUE	NA	0.673211084495588	2		717	829	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2493216	2493216	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	151	603	2	ENST00000355716.4:c.656T>G	p.Val219Gly	p.V219G	ENST00000355716	NM_003820.2	219	gTt/gGt	6/8	0.655403771177587	2	FACETS	0.892	0.821	0.965	0.446	0.41	0.483	CLONAL	1	TRUE	0	0.673211084495588	2		605	503	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351984	70351984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	416	782	0	ENST00000374080.3:c.4181C>T	p.Ala1394Val	p.A1394V	ENST00000374080		1394	gCa/gTa	30/45	0.622625981957339	4	FACETS	0.973	0.929	1	0.973	0.929	1	CLONAL	2	TRUE	2	0.673211084495588	4		782	1063	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0040225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	49	540	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.13	2		540	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0040225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	36	470	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	0.629	0.515	0.758	0.629	0.515	0.758	SUBCLONAL	1	TRUE	1	0.13	2		470	880	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0040251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	21	469	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	0.213779049121766	1	FACETS	0.191	0.146	0.243	0.191	0.146	0.243	INDETERMINATE	1	TRUE	0	0.42172903746166	1		469	412	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913351	NA	P-0040251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	131	316	0	ENST00000288602.6:c.1397G>C	p.Gly466Ala	p.G466A	ENST00000288602	NM_004333.4	466	gGa/gCa	11/18	0.213779049121766	1	FACETS	0.979	0.893	1	0.979	0.893	1	INDETERMINATE	1	TRUE	0	0.42172903746166	1		316	501	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132500	11132500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs898406635	NA	P-0040251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	113	634	0	ENST00000358026.2:c.2716C>T	p.Arg906Cys	p.R906C	ENST00000358026	NM_001128849.1	906	Cgc/Tgc	19/36	0.254995317536124	1	FACETS	0.46	0.413	0.509	0.46	0.413	0.509	SUBCLONAL	1	TRUE	0	0.42172903746166	1		634	920	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844801	156844801	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs764771898	NA	P-0040251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	418	616	0	ENST00000524377.1:c.1354+1G>T		p.X452_splice	ENST00000524377	NM_002529.3	452			0.418655104381676	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.42172903746166	3		616	1147	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543537	9543537	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0040251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	63	327	0	ENST00000353224.5:c.1616+1G>T		p.X539_splice	ENST00000353224	NM_177990.2	539			0.42172903746166	1	FACETS	0.503	0.436	0.575	0.503	0.436	0.575	SUBCLONAL	1	TRUE	0	0.42172903746166	1		327	469	SUCCESS
FH	2271	MSKCC	GRCh37	1	241672078	241672078	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	96	245	0	ENST00000366560.3:c.563A>G	p.Asn188Ser	p.N188S	ENST00000366560	NM_000143.3	188	aAt/aGt	5/10	0.418655104381676	3	FACETS	1	0.894	1	0.5	0.447	0.557	CLONAL	1	TRUE	1	0.42172903746166	3		245	551	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932420	36932420	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	221	562	0	ENST00000361632.4:c.2049C>A	p.Phe683Leu	p.F683L	ENST00000361632		683	ttC/ttA	16/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.42172903746166	2		562	981	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998952	100998952	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	200	510	0	ENST00000325455.5:c.850G>T	p.Glu284Ter	p.E284*	ENST00000325455	NM_001202474.3	284	Gag/Tag	1/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.42172903746166	2		510	775	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112329	115112329	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	58	184	0	ENST00000257566.3:c.1411C>A	p.Arg471Ser	p.R471S	ENST00000257566	NM_016569.3	471	Cgc/Agc	7/8	0.213779049121766	1	FACETS	0.731	0.633	0.836	0.731	0.633	0.836	INDETERMINATE	1	TRUE	0	0.42172903746166	1		184	297	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201397	133201397	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0040251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	103	559	0	ENST00000320574.5:c.6748-1G>T		p.X2250_splice	ENST00000320574	NM_006231.2	2250			0.213779049121766	1	FACETS	0.439	0.392	0.488	0.439	0.392	0.488	INDETERMINATE	1	TRUE	0	0.42172903746166	1		559	879	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42057119	42057119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	210	521	1	ENST00000219905.7:c.7780G>A	p.Ala2594Thr	p.A2594T	ENST00000219905	NM_001164273.1	2594	Gcc/Acc	23/24	0.42172903746166	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.42172903746166	1		522	763	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923461	9923462	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	79	399	0	ENST00000330684.3:c.1825dup	p.Trp609LeufsTer7	p.W609Lfs*7	ENST00000330684	NM_001134407.1	609	tgg/tTgg	9/13	0.213779049121766	1	FACETS	0.464	0.408	0.524	0.464	0.408	0.524	INDETERMINATE	1	TRUE	0	0.42172903746166	1		399	637	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548868	29548868	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	59	522	0	ENST00000356175.3:c.1642G>T	p.Ala548Ser	p.A548S	ENST00000356175	NM_000267.3	548	Gct/Tct	15/57	0.338565030181341	3	FACETS	0.429	0.368	0.495			1	SUBCLONAL	1	TRUE	NA	0.42172903746166	3		522	790	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548939	29548940	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0040251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	74	282	0	ENST00000356175.3:c.1713_1714delinsTT	p.Trp571_Glu572delinsCysTer	p.W571_E572delinsC*	ENST00000356175	NM_000267.3	571	tgGGag/tgTTag	15/57	0.338565030181341	3	FACETS	1	0.969	1			1	CLONAL	1	TRUE	NA	0.42172903746166	3		282	323	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536221	41536221	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	76	393	0	ENST00000263253.7:c.1838G>C	p.Arg613Pro	p.R613P	ENST00000263253	NM_001429.3	613	cGg/cCg	9/31	0.42172903746166	1	FACETS	0.41	0.359	0.464	0.41	0.359	0.464	SUBCLONAL	1	TRUE	0	0.42172903746166	1		393	694	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851557	134851557	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	53	338	0	ENST00000398015.3:c.963C>A	p.Ser321Arg	p.S321R	ENST00000398015	NM_004441.4	321	agC/agA	5/16	0.213779049121766	1	FACETS	0.354	0.301	0.411	0.354	0.301	0.411	INDETERMINATE	1	TRUE	0	0.42172903746166	1		338	561	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66468001	66468001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	27	203	0	ENST00000273854.3:c.268G>A	p.Asp90Asn	p.D90N	ENST00000273854	NM_004439.5	90	Gat/Aat	3/18	0.213779049121766	1	FACETS	0.335	0.266	0.412	0.335	0.266	0.412	INDETERMINATE	1	TRUE	0	0.42172903746166	1		203	302	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681131	117681131	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	139	343	1	ENST00000368508.3:c.3489G>T	p.Lys1163Asn	p.K1163N	ENST00000368508	NM_002944.2	1163	aaG/aaT	23/43	0.42172903746166	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.42172903746166	1		344	495	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355239	81355239	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200948659	NA	P-0040251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	38	221	2	ENST00000222390.5:c.1135C>A	p.Gln379Lys	p.Q379K	ENST00000222390	NM_000601.4	379	Caa/Aaa	9/18	0.213779049121766	1	FACETS	0.379	0.314	0.452	0.379	0.314	0.452	INDETERMINATE	1	TRUE	0	0.42172903746166	1		223	375	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500864	8500864	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs779550244	NA	P-0040251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	63	388	0	ENST00000356435.5:c.2018T>A	p.Leu673His	p.L673H	ENST00000356435		673	cTt/cAt	13/35	0.374080095768993	2	FACETS	0.436	0.377	0.501	0.218	0.188	0.251	SUBCLONAL	1	TRUE	0	0.42172903746166	2		388	685	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038749	47038749	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	107	686	0	ENST00000377604.3:c.756G>T	p.Arg252Ser	p.R252S	ENST00000377604	NM_001204468.1	252	agG/agT	9/24	0.254995317536124	1	FACETS	0.424	0.379	0.471	0.424	0.379	0.471	SUBCLONAL	1	TRUE	0	0.42172903746166	1		686	945	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411773	63411773	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	158	669	1	ENST00000330258.3:c.1394C>G	p.Pro465Arg	p.P465R	ENST00000330258	NM_152424.3	465	cCc/cGc	2/2	0.254995317536124	1	FACETS	0.53	0.485	0.578	0.53	0.485	0.578	SUBCLONAL	1	TRUE	0	0.42172903746166	1		670	1115	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0040279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5372	3280	509	0	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.762201923504789	25	FACETS	0.971	0.955	0.988			1	CLONAL	10	TRUE	NA	0.762201923504789	25		509	8652	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692930	89692930	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1554898163	NA	P-0040279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	304	543	0	ENST00000371953.3:c.416del	p.Leu139TyrfsTer8	p.L139Yfs*8	ENST00000371953	NM_000314.4	138	taT/ta	5/9	0.762201923504789	1	FACETS	0.995	0.953	1	0.995	0.953	1	CLONAL	1	TRUE	0	0.762201923504789	1		543	496	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061223	38061228	+	inframe_deletion	In_Frame_Del	DEL	TCTCGA	TCTCGA	-	novel	NA	P-0040293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	89	620	1	ENST00000250448.2:c.761_766del	p.Phe254_Asn256delinsTyr	p.F254_N256delinsY	ENST00000250448	NM_004496.3	254	tTCGAGAac/tac	2/2	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.51161332745301	2		621	306	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579547	7579547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567557016	NA	P-0040300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	438	711	0	ENST00000269305.4:c.140del	p.Pro47ArgfsTer76	p.P47Rfs*76	ENST00000269305	NM_001126112.2	47	cCg/cg	4/11	0.340006070337694	3	FACETS	1	0.991	1	0.761	0.728	0.795	CLONAL	2	TRUE	0	0.415424979509418	3		711	1115	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175728	176175733	+	inframe_deletion	In_Frame_Del	DEL	GTCCTC	GTCCTC	-	novel	NA	P-0040300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	263	783	1	ENST00000367669.3:c.382_387del	p.Glu128_Asp129del	p.E128_D129del	ENST00000367669	NM_022457.5	128	GAGGAC/-	1/20	1	2	FACETS	0.935	0.875	0.998	0.935	0.875	0.998	CLONAL	1	TRUE	1	0.415424979509418	2		784	1354	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849437	68849437	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	69	566	0	ENST00000261769.5:c.1340A>C	p.Lys447Thr	p.K447T	ENST00000261769	NM_004360.3	447	aAg/aCg	10/16	0.415424979509418	3	FACETS	0.365	0.317	0.418			1	SUBCLONAL	1	TRUE	NA	0.415424979509418	3		566	1098	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728637	190728637	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	56	440	0	ENST00000441310.2:c.2025A>C	p.Gln675His	p.Q675H	ENST00000441310	NM_000534.4	675	caA/caC	10/13	0.377256970678583	3	FACETS	0.488	0.417	0.566	0.163	0.139	0.189	SUBCLONAL	1	TRUE	0	0.415424979509418	3		440	667	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56171058	56171058	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	128	275	0	ENST00000399503.3:c.1886G>T	p.Gly629Val	p.G629V	ENST00000399503	NM_005921.1	629	gGa/gTa	10/20	0.365730051387344	2	FACETS	0.891	0.817	0.965	0.891	0.817	0.965	CLONAL	2	TRUE	0	0.415424979509418	2		275	346	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066486	94066486	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	36	323	0	ENST00000369303.4:c.1273A>G	p.Ser425Gly	p.S425G	ENST00000369303	NM_004440.3	425	Agc/Ggc	5/17	1	2	FACETS	0.368	0.302	0.442	0.368	0.302	0.442	SUBCLONAL	1	TRUE	1	0.415424979509418	2		323	471	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486284	8486284	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	48	321	0	ENST00000356435.5:c.2533C>G	p.Pro845Ala	p.P845A	ENST00000356435		845	Cct/Gct	17/35	1	2	FACETS	0.465	0.393	0.544	0.465	0.393	0.544	SUBCLONAL	1	TRUE	1	0.415424979509418	2		321	497	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128347978	128347978	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	98	754	0	ENST00000265960.3:c.527A>C	p.Lys176Thr	p.K176T	ENST00000265960	NM_001006617.1	176	aAg/aCg	5/12	1	2	FACETS	0.446	0.397	0.499	0.446	0.397	0.499	SUBCLONAL	1	TRUE	1	0.415424979509418	2		754	1057	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645155	67645156	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	A	novel	NA	P-0040300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1321	231	644	0	ENST00000264010.4:c.420_421delinsA	p.Asn140LysfsTer14	p.N140Kfs*14	ENST00000264010	NM_006565.3	140	aaTGaa/aaAaa	3/12	0.415424979509418	3	FACETS	0.865	0.804	0.929			1	CLONAL	1	TRUE	NA	0.415424979509418	3		644	1552	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965068	25965068	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	126	508	1	ENST00000435504.4:c.4138C>T	p.Gln1380Ter	p.Q1380*	ENST00000435504		1380	Cag/Tag	13/13	0.3	0	FACETS	0.81	0.742	0.88			1	CLONAL	2	FALSE	0	0.3	0		509	363	SUCCESS
APC	324	MSKCC	GRCh37	5	112175864	112175865	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0040301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	52	198	0	ENST00000257430.4:c.4573_4574del	p.Met1525AlafsTer7	p.M1525Afs*7	ENST00000257430	NM_000038.5	1525	ATg/g	16/16	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.3	2		198	267	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	51	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.953	0.81	1	0.953	0.81	1	CLONAL	1	TRUE	1	0.2	2		341	535	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0040302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	62	705	1	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	1	2	FACETS	0.978	0.844	1	0.978	0.844	1	CLONAL	1	TRUE	1	0.2	2		706	634	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97934360	97934360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	50	396	0	ENST00000289081.3:c.415G>A	p.Gly139Arg	p.G139R	ENST00000289081	NM_000136.2	139	Ggg/Agg	5/15	1	2	FACETS	0.914	0.775	1	0.914	0.775	1	CLONAL	1	TRUE	1	0.2	2		396	547	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0040338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	27	802	5	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		807	850	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781371	NA	P-0040338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	43	622	0	ENST00000269305.4:c.328C>T	p.Arg110Cys	p.R110C	ENST00000269305	NM_001126112.2	110	Cgt/Tgt	4/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		622	990	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793270	242793270	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	29	402	0	ENST00000334409.5:c.807C>A	p.Asp269Glu	p.D269E	ENST00000334409	NM_005018.2	269	gaC/gaA	5/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		402	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0040371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	226	322	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.502870460887435	2	FACETS	0.968	0.914	1	0.968	0.914	1	CLONAL	2	TRUE	0	0.516357160918166	2		324	452	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0040371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	247	828	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	0.516357160918166	3	FACETS	0.898	0.845	0.953	0.898	0.845	0.953	CLONAL	2	TRUE	1	0.516357160918166	3		828	670	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741579	17741579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1220240848	NA	P-0040371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	97	246	1	ENST00000250003.3:c.250C>T	p.Pro84Ser	p.P84S	ENST00000250003	NM_002478.4	84	Ccc/Tcc	1/3	0.503669868887486	3	FACETS	1	0.98	1	0.691	0.622	0.763	CLONAL	1	TRUE	1	0.516357160918166	3		247	342	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022792	31022792	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	205	398	0	ENST00000375687.4:c.2277C>A	p.Cys759Ter	p.C759*	ENST00000375687	NM_015338.5	759	tgC/tgA	13/13	0.516357160918166	7	FACETS	0.917	0.85	0.986	0.367	0.34	0.395	CLONAL	2	TRUE	2	0.516357160918166	7		398	992	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468363	89468363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	25	155	0	ENST00000336596.2:c.1897G>A	p.Gly633Arg	p.G633R	ENST00000336596	NM_005233.5	633	Gga/Aga	11/17	0.516357160918166	3	FACETS	0.666	0.529	0.821	0.333	0.264	0.411	SUBCLONAL	1	TRUE	1	0.516357160918166	3		155	183	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374930	149374930	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	140	401	0	ENST00000360632.3:c.164A>G	p.Glu55Gly	p.E55G	ENST00000360632	NM_015472.4	55	gAg/gGg	2/7	0.516357160918166	3	FACETS	1	0.963	1	0.55	0.503	0.6	CLONAL	1	TRUE	1	0.516357160918166	3		401	620	SUCCESS
APC	324	MSKCC	GRCh37	5	112175707	112175755	+	frameshift_variant	Frame_Shift_Del	DEL	AAATGCTGCAGTTCAGAGGGTCCAGGTTCTTCCAGATGCTGATACTTTA	AAATGCTGCAGTTCAGAGGGTCCAGGTTCTTCCAGATGCTGATACTTTA	-	novel	NA	P-0040371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	97	223	0	ENST00000257430.4:c.4416_4464del	p.Asn1473TyrfsTer18	p.N1473Yfs*18	ENST00000257430	NM_000038.5	1472	gtAAATGCTGCAGTTCAGAGGGTCCAGGTTCTTCCAGATGCTGATACTTTA/gt	16/16	0.516357160918166	2	FACETS	0.908	0.828	0.987	0.908	0.828	0.987	CLONAL	2	TRUE	0	0.516357160918166	2		223	207	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43738986	43738986	+	start_lost	Translation_Start_Site	SNP	G	G	T	novel	NA	P-0040371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	176	296	0	ENST00000523873.1:c.3G>T	p.Met1?	p.M1?	ENST00000523873		1	atG/atT	1/8	0.516357160918166	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.516357160918166	3		296	408	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955046	93955046	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	35	195	0	ENST00000369303.4:c.2852C>A	p.Ser951Tyr	p.S951Y	ENST00000369303	NM_004440.3	951	tCc/tAc	16/17	0.516357160918166	3	FACETS	0.969	0.804	1	0.485	0.402	0.575	CLONAL	1	TRUE	1	0.516357160918166	3		195	176	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0040374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	169	473	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.483710089496371	3	FACETS	0.851	0.788	0.915	0.851	0.788	0.915	CLONAL	2	TRUE	1	0.483710089496371	3		473	510	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913315	NA	P-0040374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	107	719	1	ENST00000326873.7:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000326873	NM_000455.4	194	Gac/Tac	4/10	0.483710089496371	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.483710089496371	1		720	318	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597431	10597431	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	162	447	1	ENST00000171111.5:c.1772G>A	p.Trp591Ter	p.W591*	ENST00000171111	NM_203500.1	591	tGg/tAg	6/6	0.483710089496371	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.483710089496371	1		448	455	SUCCESS
ALK	238	MSKCC	GRCh37	2	29419652	29419652	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1558606063	NA	P-0040374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	43	280	0	ENST00000389048.3:c.4148T>C	p.Ile1383Thr	p.I1383T	ENST00000389048	NM_004304.4	1383	aTt/aCt	28/29	0.250248865153204	1	FACETS	0.369	0.31	0.435	0.369	0.31	0.435	INDETERMINATE	1	TRUE	0	0.483710089496371	1		280	365	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508850	31508850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	22	363	1	ENST00000344624.3:c.1465G>A	p.Glu489Lys	p.E489K	ENST00000344624		489	Gag/Aag	7/33	0.250248865153204	1	FACETS	0.158	0.122	0.2	0.158	0.122	0.2	INDETERMINATE	1	TRUE	0	0.483710089496371	1		364	437	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863290	56863290	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	131	380	0	ENST00000519728.1:c.434C>A	p.Ala145Glu	p.A145E	ENST00000519728	NM_002350.3	145	gCa/gAa	6/13	0.256423993572593	3	FACETS	1	0.954	1	0.538	0.49	0.589	INDETERMINATE	1	TRUE	1	0.483710089496371	3		380	625	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858210	9858210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756930722	NA	P-0040376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	68	316	1	ENST00000330684.3:c.3191C>T	p.Thr1064Met	p.T1064M	ENST00000330684	NM_001134407.1	1064	aCg/aTg	13/13	0.444109374401013	3	FACETS	0.95	0.831	1	0.475	0.415	0.539	CLONAL	1	TRUE	1	0.471632950217198	3		317	375	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455623	189455623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	86	320	0	ENST00000264731.3:c.157G>A	p.Glu53Lys	p.E53K	ENST00000264731	NM_003722.4	53	Gag/Aag	2/14	1	2	FACETS	0.957	0.853	1	0.957	0.853	1	CLONAL	1	TRUE	1	0.471632950217198	2		320	381	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0040377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	193	529	1	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	0.881	0.823	0.939	0.881	0.823	0.939	CLONAL	1	TRUE	1	0.90942866805944	2		530	482	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045000	47045000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556782020	NA	P-0040377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	298	271	0	ENST00000377604.3:c.2326C>T	p.Arg776Trp	p.R776W	ENST00000377604	NM_001204468.1	776	Cgg/Tgg	20/24	1	1	FACETS	0.998	0.969	1	0.998	0.969	1	CLONAL	1	TRUE	0	0.90942866805944	1		271	358	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196143	108196143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564652222	NA	P-0040377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	102	324	2	ENST00000278616.4:c.6679C>T	p.Arg2227Cys	p.R2227C	ENST00000278616	NM_000051.3	2227	Cgc/Tgc	46/63	1	2	FACETS	0.856	0.779	0.935	0.856	0.779	0.935	CLONAL	1	TRUE	1	0.90942866805944	2		326	262	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602293	10602293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1320679251	NA	P-0040377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	287	520	0	ENST00000171111.5:c.1285G>A	p.Gly429Ser	p.G429S	ENST00000171111	NM_203500.1	429	Ggc/Agc	3/6	0.857918242541468	3	FACETS	0.898	0.845	0.952	0.449	0.422	0.476	CLONAL	1	TRUE	1	0.90942866805944	3		520	1023	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0040377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	321	352	0				ENST00000310581	NM_198253.2	-/1132			0.152279952484226	6	FACETS	0.925	0.885	0.964			1	INDETERMINATE	4	TRUE	NA	0.90942866805944	6		352	538	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981186	201981187	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0040377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	306	542	1	ENST00000359651.3:c.267dup	p.Ile90HisfsTer2	p.I90Hfs*2	ENST00000359651		89	gcc/gCcc	2/8	1	2	FACETS	0.981	0.932	1	0.981	0.932	1	CLONAL	1	TRUE	1	0.90942866805944	2		543	686	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981788	201981788	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	258	564	0	ENST00000359651.3:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000359651		167	Cag/Tag	4/8	1	2	FACETS	0.918	0.867	0.97	0.918	0.867	0.97	CLONAL	1	TRUE	1	0.90942866805944	2		564	618	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654709	67654709	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	145	307	0	ENST00000264010.4:c.1196G>A	p.Arg399Lys	p.R399K	ENST00000264010	NM_006565.3	399	aGa/aAa	6/12	1	2	FACETS	0.903	0.836	0.972	0.903	0.836	0.972	CLONAL	1	TRUE	1	0.90942866805944	2		307	353	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957889	1957889	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	198	357	0	ENST00000382891.5:c.2855G>C	p.Arg952Thr	p.R952T	ENST00000382891	NM_133335.3	952	aGa/aCa	15/22	1	2	FACETS	0.878	0.821	0.936	0.878	0.821	0.936	CLONAL	1	TRUE	1	0.90942866805944	2		357	496	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845886	151845886	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	249	436	0	ENST00000262189.6:c.13126G>T	p.Glu4376Ter	p.E4376*	ENST00000262189	NM_170606.2	4376	Gag/Tag	52/59	0.833567464065953	3	FACETS	0.87	0.825	0.914	0.87	0.825	0.914	CLONAL	2	TRUE	1	0.90942866805944	3		436	458	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845947	151845947	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	290	379	0	ENST00000262189.6:c.13065G>C	p.Met4355Ile	p.M4355I	ENST00000262189	NM_170606.2	4355	atG/atC	52/59	0.833567464065953	3	FACETS	0.933	0.891	0.975	0.933	0.891	0.975	CLONAL	2	TRUE	1	0.90942866805944	3		379	497	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942804	44942810	+	frameshift_variant	Frame_Shift_Del	DEL	CATGAAC	CATGAAC	-	novel	NA	P-0040377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	103	209	0	ENST00000377967.4:c.3384_3390del	p.Met1129GlnfsTer6	p.M1129Qfs*6	ENST00000377967	NM_021140.2	1128	ggCATGAAC/gg	23/29	1	1	FACETS	0.895	0.84	0.946	0.895	0.84	0.946	CLONAL	1	TRUE	0	0.90942866805944	1		209	138	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587781525	NA	P-0040379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	483	452	0	ENST00000269305.4:c.842A>G	p.Asp281Gly	p.D281G	ENST00000269305	NM_001126112.2	281	gAc/gGc	8/11	0.536990918504208	3	FACETS	0.968	0.937	0.999	0.968	0.937	0.999	CLONAL	3	TRUE	0	0.579635975444867	3		452	740	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220371	1220372	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	TT	novel	NA	P-0040379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	306	270	0	ENST00000326873.7:c.465-1_465delinsTT		p.X155_splice	ENST00000326873	NM_000455.4	155		4/10	0.579635975444867	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.579635975444867	2		270	501	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602748	10602748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	450	474	0	ENST00000171111.5:c.830C>T	p.Thr277Met	p.T277M	ENST00000171111	NM_203500.1	277	aCg/aTg	3/6	0.579635975444867	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.579635975444867	2		474	755	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258610	16258610	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200615625	NA	P-0040379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	153	364	2	ENST00000375759.3:c.5875C>T	p.Arg1959Ter	p.R1959*	ENST00000375759	NM_015001.2	1959	Cga/Tga	11/15	0.579635975444867	3	FACETS	1	0.919	1	0.501	0.459	0.544	CLONAL	1	TRUE	1	0.579635975444867	3		366	680	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263303	115263303	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	61	386	0	ENST00000438362.2:c.2047G>C	p.Val683Leu	p.V683L	ENST00000438362	NM_001242891.1	683	Gtt/Ctt	17/20	0.570364423249902	5	FACETS	0.417	0.359	0.481	0.139	0.119	0.161	SUBCLONAL	1	TRUE	2	0.579635975444867	5		386	943	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612146	43612147	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0040379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	81	225	1	ENST00000355710.3:c.2251_2252delinsCT	p.Gly751Leu	p.G751L	ENST00000355710	NM_020975.4	751	GGg/CTg	12/20	0.579635975444867	3	FACETS	1	0.911	1	0.515	0.457	0.576	CLONAL	1	TRUE	1	0.579635975444867	3		226	350	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426952	49426952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	199	390	0	ENST00000301067.7:c.11536G>A	p.Gly3846Ser	p.G3846S	ENST00000301067	NM_003482.3	3846	Ggc/Agc	39/54	0.208425811981375	5	FACETS	0.98	0.912	1	0.653	0.608	0.7	INDETERMINATE	2	TRUE	2	0.579635975444867	5		390	655	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133238138	133238138	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	179	320	0	ENST00000320574.5:c.2839del	p.Glu947LysfsTer6	p.E947Kfs*6	ENST00000320574	NM_006231.2	947	Gaa/aa	24/49	0.57489272434723	4	FACETS	1	0.987	1	0.445	0.412	0.481	CLONAL	1	TRUE	1	0.579635975444867	4		320	730	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041474	42041474	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	137	341	0	ENST00000219905.7:c.5669G>C	p.Gly1890Ala	p.G1890A	ENST00000219905	NM_001164273.1	1890	gGa/gCa	17/24	1	2	FACETS	0.918	0.84	0.999	0.918	0.84	0.999	CLONAL	1	TRUE	1	0.579635975444867	2		341	515	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724302	117724302	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	121	312	0	ENST00000368508.3:c.577G>C	p.Val193Leu	p.V193L	ENST00000368508	NM_002944.2	193	Gtt/Ctt	6/43	0.579635975444867	3	FACETS	1	0.908	1	0.5	0.454	0.549	CLONAL	1	TRUE	1	0.579635975444867	3		312	538	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729433	41729433	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	117	384	0	ENST00000242208.4:c.1096C>G	p.Leu366Val	p.L366V	ENST00000242208	NM_002192.2	366	Ctg/Gtg	3/3	0.579635975444867	2	FACETS	0.775	0.702	0.851	0.387	0.351	0.426	SUBCLONAL	1	TRUE	0	0.579635975444867	2		384	521	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020282	123020282	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	217	289	0	ENST00000355640.3:c.770C>G	p.Pro257Arg	p.P257R	ENST00000355640		257	cCa/cGa	2/7	0.323735103162985	4	FACETS	1	0.983	1			1	INDETERMINATE	2	TRUE	NA	0.579635975444867	4		289	525	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220522	123220522	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs763848087	NA	P-0040379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	271	343	1	ENST00000218089.9:c.3179T>C	p.Ile1060Thr	p.I1060T	ENST00000218089	NM_001042749.1	1060	aTt/aCt	30/35	0.323735103162985	4	FACETS	0.959	0.904	1			1	INDETERMINATE	2	TRUE	NA	0.579635975444867	4		344	770	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	18	333	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.15	2		333	189	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0040412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	28	457	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	0.458	0.364	0.566	0.458	0.364	0.566	SUBCLONAL	1	TRUE	1	0.15	2		457	815	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0040412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	46	354	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.89	0.748	1	0.89	0.748	1	CLONAL	1	TRUE	1	0.15	2		354	689	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094488	27094488	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	28	467	0	ENST00000324856.7:c.3196C>T	p.Gln1066Ter	p.Q1066*	ENST00000324856	NM_006015.4	1066	Cag/Tag	11/20	1	2	FACETS	0.784	0.626	0.966	0.784	0.626	0.966	CLONAL	1	TRUE	1	0.15	2		467	476	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632588	3632588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755406950	NA	P-0040412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	37	687	0	ENST00000294008.3:c.5260G>A	p.Glu1754Lys	p.E1754K	ENST00000294008	NM_032444.2	1754	Gag/Aag	15/15	1	2	FACETS	0.704	0.578	0.845	0.704	0.578	0.845	SUBCLONAL	1	TRUE	1	0.15	2		687	701	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119978	70119979	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCGGCA	novel	NA	P-0000631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	55	216	0	ENST00000245479.2:c.986_987insACCCGGC	p.Ser330ProfsTer250	p.S330Pfs*250	ENST00000245479	NM_000346.3	327	acc/acCCCGGCAc	3/3	0.476340903364578	3	FACETS	0.934	0.806	1	0.467	0.403	0.536	CLONAL	1	TRUE	1	0.555092539714699	3		216	271	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791853	42791853	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	209	950	0	ENST00000575354.2:c.739del	p.Gln247ArgfsTer10	p.Q247Rfs*10	ENST00000575354	NM_015125.3	247	Cag/ag	5/20	1	2	FACETS	0.979	0.912	1	0.979	0.912	1	CLONAL	1	TRUE	1	0.555092539714699	2		950	769	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100379	157100379	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	34	143	0	ENST00000346085.5:c.1316A>G	p.Glu439Gly	p.E439G	ENST00000346085	NM_020732.3	439	gAg/gGg	1/20	1	2	FACETS	0.521	0.429	0.624	0.521	0.429	0.624	SUBCLONAL	1	TRUE	1	0.555092539714699	2		143	235	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0005330-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	434	481	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	0.271525498054307	5	FACETS	0.869	0.83	0.909	0.869	0.83	0.909	INDETERMINATE	3	TRUE	2	0.475017819051559	5		481	1200	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594258	55594258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913523	NA	P-0005330-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	313	346	0	ENST00000288135.5:c.1961T>C	p.Val654Ala	p.V654A	ENST00000288135	NM_000222.2	654	gTg/gCg	13/21	0.271525498054307	5	FACETS	0.847	0.802	0.893	0.847	0.802	0.893	INDETERMINATE	3	TRUE	2	0.475017819051559	5		346	888	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226572	2226572	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005330-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	127	631	0	ENST00000326181.6:c.2010C>G	p.Cys670Trp	p.C670W	ENST00000326181	NM_032271.2	670	tgC/tgG	21/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.475017819051559	2		631	399	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512280	38512281	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTGAAGATGGAGATCC	novel	NA	P-0121458-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	33	461	0	ENST00000254066.5:c.1193_1208dup	p.Gly404GlufsTer47	p.G404Efs*47	ENST00000254066	NM_000964.3	397	-/CTGAAGATGGAGATCC	9/9	0.162467420697983	0	FACETS		NA	1			1	NA	NA	NA	0	NA	0		461	463	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	104	236	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.583546447516249	2		236	255	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0005367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	111	627	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.583546447516249	2		627	369	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0005367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	149	444	3	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.583546447516249	2		447	485	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778004	27778004	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	341	814	0	ENST00000369163.2:c.153G>C	p.Glu51Asp	p.E51D	ENST00000369163	NM_003536.2	51	gaG/gaC	1/1	1	2	FACETS	0.887	0.838	0.936	0.887	0.838	0.936	CLONAL	1	TRUE	1	0.583546447516249	2		814	1318	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056160	27056160	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	299	388	4	ENST00000324856.7:c.1156C>T	p.Gln386Ter	p.Q386*	ENST00000324856	NM_006015.4	386	Cag/Tag	2/20	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.583546447516249	2		392	753	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719140	190719140	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0005367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	157	276	0	ENST00000441310.2:c.1142C>G	p.Ser381Ter	p.S381*	ENST00000441310	NM_000534.4	381	tCa/tGa	9/13	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.583546447516249	2		276	489	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492919	8492919	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	69	472	1	ENST00000356435.5:c.2410A>G	p.Thr804Ala	p.T804A	ENST00000356435		804	Aca/Gca	16/35	0.583546447516249	1	FACETS	0.3	0.261	0.342	0.3	0.261	0.342	SUBCLONAL	1	TRUE	0	0.583546447516249	1		473	558	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380271	25380271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	221	389	0	ENST00000311936.3:c.187G>A	p.Glu63Lys	p.E63K	ENST00000311936	NM_004985.3	63	Gag/Aag	3/5	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.583546447516249	2		389	738	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287422	46287422	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	207	331	0	ENST00000334344.6:c.5281G>C	p.Glu1761Gln	p.E1761Q	ENST00000334344	NM_152641.2	1761	Gag/Cag	20/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.583546447516249	2		331	594	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44896902	44896902	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	387	258	0	ENST00000377967.4:c.622C>T	p.Gln208Ter	p.Q208*	ENST00000377967	NM_021140.2	208	Caa/Taa	8/29	1	1	FACETS	0.893	0.864	0.92	1	0.997	1	CLONAL	2	TRUE	0	0.583546447516249	1		258	526	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404371	139404371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764921648	NA	P-0005447-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	83	702	2	ENST00000277541.6:c.2783C>T	p.Thr928Met	p.T928M	ENST00000277541	NM_017617.3	928	aCg/aTg	18/34	1	2	FACETS	0.889	0.792	0.991	0.889	0.792	0.991	CLONAL	1	TRUE	1	0.574661869644261	2		704	325	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0005461-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	234	178	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.379803913343364	2		178	1180	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0005461-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	272	464	1	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.379803913343364	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.379803913343364	1		465	979	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715819	18715819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1379181643	NA	P-0005461-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	140	441	0	ENST00000266497.5:c.3650C>T	p.Ser1217Phe	p.S1217F	ENST00000266497		1217	tCc/tTc	25/31	1	2	FACETS	0.885	0.806	0.968	0.885	0.806	0.968	CLONAL	1	TRUE	1	0.379803913343364	2		441	833	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478227	99478228	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAT	novel	NA	P-0005461-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1273	256	484	0	ENST00000268035.6:c.3132_3134dup	p.Arg1044_Ile1045insMet	p.R1044_I1045insM	ENST00000268035	NM_000875.3	1044	agg/agGATg	16/21	1	2	FACETS	0.882	0.823	0.942	0.882	0.823	0.942	CLONAL	1	TRUE	1	0.379803913343364	2		484	1529	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400033	49400033	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005530-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1428	425	551	0	ENST00000418115.1:c.304G>A	p.Glu102Lys	p.E102K	ENST00000418115	NM_001664.2	102	Gaa/Aaa	4/5	1	2	FACETS	0.879	0.835	0.924	0.879	0.835	0.924	CLONAL	1	TRUE	1	0.521671251384575	2		551	1853	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486112	29486112	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0005530-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	158	249	0	ENST00000356175.3:c.288+1G>A		p.X96_splice	ENST00000356175	NM_000267.3	96			0.456422290206748	1	FACETS	0.885	0.817	0.955	0.885	0.817	0.955	CLONAL	1	TRUE	0	0.521671251384575	1		249	506	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123707	11123707	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005530-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	349	441	0	ENST00000358026.2:c.2357C>T	p.Thr786Ile	p.T786I	ENST00000358026	NM_001128849.1	786	aCc/aTc	16/36	0.521671251384575	1	FACETS	0.933	0.885	0.982	0.933	0.885	0.982	CLONAL	1	TRUE	0	0.521671251384575	1		441	1060	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290271	15290271	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005530-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1548	524	675	0	ENST00000263388.2:c.3364G>C	p.Asp1122His	p.D1122H	ENST00000263388	NM_000435.2	1122	Gac/Cac	21/33	1	2	FACETS	0.97	0.926	1	0.97	0.926	1	CLONAL	1	TRUE	1	0.521671251384575	2		675	2072	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252909	36252909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005530-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	276	346	0	ENST00000300305.3:c.453G>A	p.Met151Ile	p.M151I	ENST00000300305		151	atG/atA	4/8	1	2	FACETS	0.847	0.794	0.901	0.847	0.794	0.901	CLONAL	1	TRUE	1	0.521671251384575	2		346	1249	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219386	1219414	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	GCGTTTCCCAGTGTGCCAGGCCCACGGGT	GCGTTTCCCAGTGTGCCAGGCCCACGGGT	-	novel	NA	P-0005530-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	195	501	0	ENST00000326873.7:c.442_464+6del		p.X148_splice	ENST00000326873	NM_000455.4	148		3/10	0.521671251384575	1	FACETS	0.643	0.595	0.692	0.643	0.595	0.692	SUBCLONAL	1	TRUE	0	0.521671251384575	1		501	860	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610310	10610311	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005530-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	498	563	0	ENST00000171111.5:c.399_400insA	p.Glu134ArgfsTer5	p.E134Rfs*5	ENST00000171111	NM_203500.1	133	-/A	2/6	0.521671251384575	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.521671251384575	1		563	1376	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156747	106156747	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs572712965	NA	P-0005534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	265	606	0	ENST00000380013.4:c.1648C>T	p.Arg550Ter	p.R550*	ENST00000380013	NM_001127208.2	550	Cga/Tga	3/11	1	2	FACETS	0.918	0.862	0.976	0.918	0.862	0.976	CLONAL	1	TRUE	1	0.610733703668721	2		606	945	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441431	52441431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	270	675	0	ENST00000460680.1:c.421C>T	p.His141Tyr	p.H141Y	ENST00000460680	NM_004656.3	141	Cat/Tat	6/17	0.602408262615323	1	FACETS	0.827	0.779	0.875	0.827	0.779	0.875	CLONAL	1	TRUE	0	0.610733703668721	1		675	743	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65316570	65316570	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	61	629	0	ENST00000342505.4:c.1672A>G	p.Thr558Ala	p.T558A	ENST00000342505	NM_002227.2	558	Act/Gct	12/25	1	2	FACETS	0.227	0.195	0.262	0.227	0.195	0.262	SUBCLONAL	1	TRUE	1	0.610733703668721	2		629	879	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041459	42041459	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1223	70	1015	0	ENST00000219905.7:c.5654C>A	p.Ser1885Ter	p.S1885*	ENST00000219905	NM_001164273.1	1885	tCa/tAa	17/24	1	2	FACETS	0.177	0.154	0.203	0.177	0.154	0.203	SUBCLONAL	1	TRUE	1	0.610733703668721	2		1015	1293	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176330	24176330	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1057517825	NA	P-0005534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	260	586	2	ENST00000263121.7:c.1121G>A	p.Arg374Gln	p.R374Q	ENST00000263121	NM_003073.3	374	cGg/cAg	9/9	1	2	FACETS	0.946	0.888	1	0.946	0.888	1	CLONAL	1	TRUE	1	0.610733703668721	2		588	900	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0005541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	47	444	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.814	0.685	0.958	0.814	0.685	0.958	CLONAL	1	TRUE	1	0.12	2		444	962	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340263	116340263	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs776693512	NA	P-0005541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	46	418	0	ENST00000397752.3:c.1125C>A	p.Asn375Lys	p.N375K	ENST00000397752	NM_000245.2	375	aaC/aaA	2/21	1	2	FACETS	0.975	0.819	1	0.975	0.819	1	CLONAL	1	TRUE	1	0.12	2		418	786	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207533	102207533	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs576590633	NA	P-0005541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1287	81	608	0	ENST00000263464.3:c.1621+1G>T		p.X541_splice	ENST00000263464	NM_001165.4	541			1	2	FACETS	0.987	0.866	1	0.987	0.866	1	CLONAL	1	TRUE	1	0.12	2		608	1368	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727894	78727894	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	61	419	0	ENST00000306801.3:c.739G>T	p.Glu247Ter	p.E247*	ENST00000306801	NM_020761.2	247	Gag/Tag	6/34	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.12	2		419	993	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424664	47424664	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	42	348	0	ENST00000377045.4:c.472G>T	p.Val158Phe	p.V158F	ENST00000377045	NM_001654.4	158	Gtc/Ttc	6/16	1	1	FACETS	0.846	0.704	1	0.846	0.704	1	CLONAL	1	TRUE	0	0.12	1		348	778	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0005543-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	73	1192	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.150720416475597	3	FACETS	1	0.969	1	0.685	0.6	0.776	CLONAL	1	TRUE	1	0.219010124842631	3		1192	540	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0005543-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	56	306	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.150720416475597	3	FACETS	1	0.881	1	0.516	0.442	0.597	CLONAL	1	TRUE	1	0.219010124842631	3		306	550	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532739	46532739	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs200819515	NA	P-0005543-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	92	301	0	ENST00000262741.5:c.339A>G	p.Ile113Met	p.I113M	ENST00000262741	NM_003629.3	113	atA/atG	4/10	1	2	FACETS	0.799	0.712	0.891	1	0.982	1	SUBCLONAL	2	TRUE	1	0.219010124842631	2		301	526	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226561959	226561959	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005543-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	93	428	0	ENST00000366794.5:c.2038G>A	p.Glu680Lys	p.E680K	ENST00000366794	NM_001618.3	680	Gaa/Aaa	14/23	0.219010124842631	2	FACETS	1	0.976	1	0.682	0.607	0.761	CLONAL	1	TRUE	0	0.219010124842631	2		428	623	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948143	178948143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553825480	NA	P-0005543-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	89	261	0	ENST00000263967.3:c.2915C>T	p.Thr972Ile	p.T972I	ENST00000263967	NM_006218.2	972	aCa/aTa	20/21	0.119488566937019	4	FACETS	0.807	0.716	0.903	0.807	0.716	0.903	INDETERMINATE	2	TRUE	2	0.219010124842631	4		261	614	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043638	6043638	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005543-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	26	257	0	ENST00000265849.7:c.215G>C	p.Gly72Ala	p.G72A	ENST00000265849	NM_000535.5	72	gGa/gCa	3/15	0.150720416475597	3	FACETS	0.618	0.489	0.767	0.309	0.244	0.384	SUBCLONAL	1	TRUE	1	0.219010124842631	3		257	426	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69456273	69456273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005543-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	49	273	0	ENST00000227507.2:c.192G>A	p.Met64Ile	p.M64I	ENST00000227507	NM_053056.2	64	atG/atA	1/5	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.219010124842631	NA		273	531	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562168	21562168	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005543-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1264	173	669	0	ENST00000382592.4:c.1751G>T	p.Ser584Ile	p.S584I	ENST00000382592	NM_014572.2	584	aGc/aTc	4/8	0.119488566937019	4	FACETS	1	0.986	1	0.67	0.615	0.728	INDETERMINATE	1	TRUE	2	0.219010124842631	4		669	1437	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989018	41989018	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005543-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	180	728	0	ENST00000219905.7:c.1810C>T	p.Gln604Ter	p.Q604*	ENST00000219905	NM_001164273.1	604	Cag/Tag	3/24	0.219010124842631	3	FACETS	0.872	0.803	0.943	0.872	0.803	0.943	CLONAL	2	TRUE	1	0.219010124842631	3		728	1046	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612340	1612340	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005543-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	138	724	0	ENST00000344749.5:c.1679G>T	p.Arg560Leu	p.R560L	ENST00000344749	NM_001136139.2	560	cGg/cTg	18/19	0.219010124842631	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.219010124842631	1		724	816	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610239	10610239	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005543-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	127	631	0	ENST00000171111.5:c.471C>A	p.Asn157Lys	p.N157K	ENST00000171111	NM_203500.1	157	aaC/aaA	2/6	0.219010124842631	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.219010124842631	1		631	820	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164889	36164889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1358657401	NA	P-0005543-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	36	275	0	ENST00000300305.3:c.986C>T	p.Ala329Val	p.A329V	ENST00000300305		329	gCg/gTg	8/8	0.219010124842631	3	FACETS	0.973	0.801	1	0.486	0.4	0.583	CLONAL	1	TRUE	1	0.219010124842631	3		275	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578470	7578471	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	A	novel	NA	P-0005543-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	68	442	0	ENST00000269305.4:c.459_460delinsT	p.Gly154AlafsTer16	p.G154Afs*16	ENST00000269305	NM_001126112.2	153	ccCGgc/ccTgc	5/11	0.150720416475597	3	FACETS	1	0.952	1	0.603	0.525	0.688	CLONAL	1	TRUE	1	0.219010124842631	3		442	571	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803818	43803818	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005551-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	354	659	0	ENST00000372470.3:c.128G>C	p.Arg43Pro	p.R43P	ENST00000372470	NM_005373.2	43	cGa/cCa	2/12	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.609548387919529	2		659	1060	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165971	47165971	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005551-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	206	409	0	ENST00000409792.3:c.155G>A	p.Ser52Asn	p.S52N	ENST00000409792	NM_014159.6	52	aGt/aAt	3/21	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.609548387919529	2		409	672	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803102	1803102	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005551-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	199	462	0	ENST00000260795.2:c.454T>C	p.Tyr152His	p.Y152H	ENST00000260795		152	Tac/Cac	4/17	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.609548387919529	2		462	641	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562019	21562019	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0005551-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	325	570	0	ENST00000382592.4:c.1899+1G>C		p.X633_splice	ENST00000382592	NM_014572.2	633			1	2	FACETS	0.955	0.902	1	0.955	0.902	1	CLONAL	1	TRUE	1	0.609548387919529	2		570	1117	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725047	47725047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs184609559	NA	P-0005551-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	272	599	0	ENST00000449228.1:c.697C>T	p.Arg233Cys	p.R233C	ENST00000449228	NM_001127240.2	233	Cgc/Tgc	4/4	1	2	FACETS	0.906	0.851	0.962	0.906	0.851	0.962	CLONAL	1	TRUE	1	0.609548387919529	2		599	985	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771764	135771764	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005551-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	304	647	0	ENST00000298552.3:c.3353del	p.Lys1118ArgfsTer16	p.K1118Rfs*16	ENST00000298552	NM_001162426.1	1118	aAg/ag	23/23	0.609548387919529	1	FACETS	0.978	0.928	1	0.978	0.928	1	CLONAL	1	TRUE	0	0.609548387919529	1		647	709	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0005563-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	285	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.819664890993596	3	FACETS	0.922	0.867	0.979	0.461	0.433	0.49	CLONAL	1	FALSE	1	0.819664890993596	3		371	1063	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0005563-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	328	849	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	0.784	0.742	0.827	0.784	0.742	0.827	SUBCLONAL	1	FALSE	1	0.819664890993596	2		850	1021	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0005563-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	342	442	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.975	0.927	1	0.975	0.927	1	CLONAL	1	FALSE	1	0.819664890993596	2		443	856	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226568861	226568861	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150379323	NA	P-0005563-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	242	383	1	ENST00000366794.5:c.1208G>A	p.Arg403Gln	p.R403Q	ENST00000366794	NM_001618.3	403	cGg/cAg	9/23	1	2	FACETS	0.547	0.511	0.585	0.547	0.511	0.585	SUBCLONAL	1	FALSE	1	0.819664890993596	2		384	1079	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032181	10032181	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005563-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	199	414	0	ENST00000330684.3:c.642G>T	p.Lys214Asn	p.K214N	ENST00000330684	NM_001134407.1	214	aaG/aaT	3/13	1	2	FACETS	0.534	0.495	0.575	0.534	0.495	0.575	SUBCLONAL	1	FALSE	1	0.819664890993596	2		414	909	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287889	33287891	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs749346133	NA	P-0005563-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	131	355	0	ENST00000374542.5:c.1362_1364del	p.Glu457del	p.E457del	ENST00000374542	NM_001141970.1	454	gaAGAg/gag	5/8	1	2	FACETS	0.326	0.296	0.359	0.326	0.296	0.359	SUBCLONAL	1	FALSE	1	0.819664890993596	2		355	979	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0005572-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	838	330	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.805633506029721	5	FACETS	1	0.981	1	0.758	0.737	0.779	CLONAL	3	TRUE	1	0.806328591285422	5		330	1514	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443610	52443610	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005573-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	400	294	0	ENST00000460680.1:c.82C>T	p.Gln28Ter	p.Q28*	ENST00000460680	NM_004656.3	28	Caa/Taa	3/17	0.455037529013566	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.455037529013566	2		294	779	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272113	15272113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243104564	NA	P-0005573-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	76	141	0	ENST00000263388.2:c.6326G>A	p.Arg2109Gln	p.R2109Q	ENST00000263388	NM_000435.2	2109	cGg/cAg	33/33	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.455037529013566	2		141	278	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874410	76874410	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005573-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	127	440	0	ENST00000373344.5:c.5312G>C	p.Gly1771Ala	p.G1771A	ENST00000373344	NM_000489.3	1771	gGa/gCa	21/35	0.445504208889401	4	FACETS	0.764	0.691	0.842	0.255	0.23	0.281	SUBCLONAL	1	TRUE	1	0.455037529013566	4		440	1063	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0005583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	193	178	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.949	0.885	1	0.949	0.885	1	CLONAL	1	TRUE	1	0.76888756697811	2		178	529	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0005583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	674	326	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.713637129332284	4	FACETS	1	0.987	1			1	CLONAL	3	TRUE	NA	0.76888756697811	4		326	1010	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209103871	209103871	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	303	484	0	ENST00000345146.2:c.1078G>A	p.Glu360Lys	p.E360K	ENST00000345146	NM_005896.2	360	Gaa/Aaa	9/10	1	2	FACETS	0.968	0.916	1	0.968	0.916	1	CLONAL	1	TRUE	1	0.76888756697811	2		484	814	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522569	106522569	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746783339	NA	P-0005583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	253	340	0	ENST00000359195.3:c.2546G>A	p.Arg849Gln	p.R849Q	ENST00000359195	NM_002649.2	849	cGa/cAa	7/11	0.756642289085583	3	FACETS	1	0.983	1	0.564	0.529	0.599	CLONAL	1	TRUE	1	0.76888756697811	3		340	808	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032089	10032089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	309	534	0	ENST00000330684.3:c.734C>T	p.Ser245Phe	p.S245F	ENST00000330684	NM_001134407.1	245	tCc/tTc	3/13	1	2	FACETS	0.841	0.794	0.888	0.841	0.794	0.888	CLONAL	1	TRUE	1	0.76888756697811	2		534	956	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007672	45007673	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	210	322	0	ENST00000558401.1:c.122dup	p.Asn41LysfsTer16	p.N41Kfs*16	ENST00000558401	NM_004048.2	40	tca/tcAa	2/4	0.76888756697811	1	FACETS	0.885	0.836	0.933	0.885	0.836	0.933	CLONAL	1	TRUE	0	0.76888756697811	1		322	380	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779210	3779211	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs587783507	NA	P-0005583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	107	218	0	ENST00000262367.5:c.5837dup	p.Pro1947ThrfsTer19	p.P1947Tfs*19	ENST00000262367	NM_004380.2	1946	cca/ccCa	31/31	1	2	FACETS	0.767	0.694	0.842	0.767	0.694	0.842	SUBCLONAL	1	TRUE	1	0.76888756697811	2		218	363	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577595	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0005622-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	117	415	0	ENST00000269305.4:c.686_687del	p.Cys229TyrfsTer10	p.C229Yfs*10	ENST00000269305	NM_001126112.2	229	tGT/t	7/11	0.334095094161537	2	FACETS	0.792	0.721	0.865	0.792	0.721	0.865	SUBCLONAL	2	TRUE	0	0.391726885388215	2		415	377	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052972	180052972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1367683600	NA	P-0005622-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	159	657	0	ENST00000261937.6:c.1318C>T	p.Arg440Cys	p.R440C	ENST00000261937	NM_182925.4	440	Cgc/Tgc	10/30	0.27917822677586	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.391726885388215	1		657	577	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0005645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	264	417	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.376240709054808	3	FACETS	1	0.979	1	0.721	0.679	0.764	CLONAL	2	TRUE	0	0.400691982874375	3		417	731	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260036	16260036	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	92	275	0	ENST00000375759.3:c.7301C>T	p.Pro2434Leu	p.P2434L	ENST00000375759	NM_015001.2	2434	cCt/cTt	11/15	1	2	FACETS	0.622	0.553	0.697	0.622	0.553	0.697	SUBCLONAL	1	TRUE	1	0.400691982874375	2		275	738	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433868	78433868	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	96	241	0	ENST00000370768.2:c.231A>T	p.Lys77Asn	p.K77N	ENST00000370768	NM_003902.3	77	aaA/aaT	3/20	1	2	FACETS	0.642	0.572	0.717	0.642	0.572	0.717	SUBCLONAL	1	TRUE	1	0.400691982874375	2		241	746	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446862	187446862	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	114	286	0	ENST00000232014.4:c.1331G>T	p.Ser444Ile	p.S444I	ENST00000232014	NM_001130845.1	444	aGc/aTc	5/10	1	2	FACETS	0.664	0.597	0.735	0.664	0.597	0.735	SUBCLONAL	1	TRUE	1	0.400691982874375	2		286	857	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505133	149505133	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	129	393	0	ENST00000261799.4:c.1682G>C	p.Arg561Pro	p.R561P	ENST00000261799	NM_002609.3	561	cGt/cCt	12/23	0.267477324821067	3	FACETS	0.728	0.659	0.802	0.364	0.329	0.401	SUBCLONAL	1	TRUE	1	0.400691982874375	3		393	1061	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114835	108114835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555066551	NA	P-0005645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	185	135	0	ENST00000278616.4:c.652C>T	p.Gln218Ter	p.Q218*	ENST00000278616	NM_000051.3	218	Cag/Tag	6/63	0.28277975508282	3	FACETS	0.907	0.842	0.974	0.605	0.561	0.649	CLONAL	2	TRUE	0	0.400691982874375	3		135	611	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984829	72984829	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	230	464	0	ENST00000268489.5:c.2755G>T	p.Gly919Cys	p.G919C	ENST00000268489	NM_006885.3	919	Ggc/Tgc	3/10	0.190329190518804	2	FACETS	1	0.984	1	0.587	0.547	0.628	INDETERMINATE	1	TRUE	0	0.400691982874375	2		464	978	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342600	70342600	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	76	364	1	ENST00000374080.3:c.1361G>T	p.Gly454Val	p.G454V	ENST00000374080		454	gGa/gTa	10/45	1	2	FACETS	0.371	0.324	0.422	0.371	0.324	0.422	SUBCLONAL	1	TRUE	1	0.400691982874375	2		365	1022	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0005697-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	153	352	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	1	2	FACETS	0.946	0.867	1	0.946	0.867	1	CLONAL	1	TRUE	1	0.468274550976964	2		352	691	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs28934577	NA	P-0005697-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	175	407	0	ENST00000269305.4:c.770T>A	p.Leu257Gln	p.L257Q	ENST00000269305	NM_001126112.2	257	cTg/cAg	7/11	0.468274550976964	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.468274550976964	1		407	507	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857475	9857475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005726-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	176	341	1	ENST00000330684.3:c.3926G>A	p.Arg1309Gln	p.R1309Q	ENST00000330684	NM_001134407.1	1309	cGg/cAg	13/13	0.365849487244003	5	FACETS	0.842	0.778	0.909	0.561	0.518	0.606	CLONAL	2	TRUE	2	0.509305897596483	5		342	724	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055689	152055690	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0005726-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	303	543	1	ENST00000262189.6:c.232_233del	p.Glu78AsnfsTer17	p.E78Nfs*17	ENST00000262189	NM_170606.2	78	GAa/a	2/59	0.236820244924756	5	FACETS	0.995	0.938	1	0.663	0.625	0.702	INDETERMINATE	2	TRUE	2	0.509305897596483	5		544	1055	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226564835	226564836	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0005726-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	235	375	0	ENST00000366794.5:c.1914_1915del	p.Phe638LeufsTer6	p.F638Lfs*6	ENST00000366794	NM_001618.3	638	ttCTac/ttac	13/23	0.509305897596483	5	FACETS	0.808	0.754	0.864	0.539	0.503	0.576	CLONAL	2	TRUE	2	0.509305897596483	5		375	1007	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349905	89349905	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005726-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	254	1021	1	ENST00000301030.4:c.3045del	p.Asp1016IlefsTer302	p.D1016Ifs*302	ENST00000301030	NM_001256183.1	1015	ccC/cc	9/13	0.434935561867062	2	FACETS	0.866	0.81	0.924	0.433	0.405	0.462	CLONAL	1	TRUE	0	0.509305897596483	2		1022	1152	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115435	115115437	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	rs1319662056	NA	P-0005726-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	263	501	0	ENST00000257566.3:c.889_891del	p.Asn297del	p.N297del	ENST00000257566	NM_016569.3	297	AAC/-	5/8	0.236820244924756	5	FACETS	0.906	0.85	0.964	0.604	0.567	0.643	INDETERMINATE	2	TRUE	2	0.509305897596483	5		501	1005	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0005730-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	363	456	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.451242968598435	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	FALSE	0	0.451242968598435	2		456	772	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0005730-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	122	197	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.451242968598435	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	3	FALSE	0	0.451242968598435	3		197	216	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880920	134880920	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005730-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	55	443	0	ENST00000398015.3:c.1483G>T	p.Gly495Trp	p.G495W	ENST00000398015	NM_004441.4	495	Ggg/Tgg	7/16	0.42855255542308	4	FACETS	0.401	0.342	0.466	0.201	0.171	0.233	SUBCLONAL	1	FALSE	2	0.451242968598435	4		443	882	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467835	50467835	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs751623054	NA	P-0005730-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	234	413	0	ENST00000331340.3:c.1070G>T	p.Gly357Val	p.G357V	ENST00000331340	NM_006060.4	357	gGc/gTc	8/8	0.451242968598435	7	FACETS	1	0.974	1	0.435	0.406	0.465	CLONAL	2	FALSE	2	0.451242968598435	7		413	1015	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857656	9857656	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754286517	NA	P-0005730-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	175	402	2	ENST00000330684.3:c.3745G>A	p.Asp1249Asn	p.D1249N	ENST00000330684	NM_001134407.1	1249	Gat/Aat	13/13	0.302217786399825	4	FACETS	0.886	0.82	0.955	0.886	0.82	0.955	CLONAL	2	FALSE	2	0.451242968598435	4		404	635	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0005734-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	70	946	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.216642796879188	1	FACETS	0.979	0.855	1	0.979	0.855	1	CLONAL	1	TRUE	0	0.233851363721945	1		946	540	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947596	48947596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1566196458	NA	P-0005734-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	50	223	0	ENST00000267163.4:c.1183C>T	p.Gln395Ter	p.Q395*	ENST00000267163	NM_000321.2	395	Caa/Taa	12/27	0.233851363721945	2	FACETS	1	0.944	1	0.618	0.526	0.718	CLONAL	1	TRUE	0	0.233851363721945	2		223	346	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794995	242794995	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005734-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	100	458	0	ENST00000334409.5:c.214C>A	p.Pro72Thr	p.P72T	ENST00000334409	NM_005018.2	72	Ccc/Acc	2/5	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.233851363721945	2		458	743	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169567	11169567	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0005734-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	53	297	0	ENST00000358026.2:c.4731+2T>A		p.X1577_splice	ENST00000358026	NM_001128849.1	1577			0.216642796879188	1	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	0	0.233851363721945	1		297	379	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288456	15288456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005734-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	59	191	1	ENST00000263388.2:c.4283G>A	p.Cys1428Tyr	p.C1428Y	ENST00000263388	NM_000435.2	1428	tGc/tAc	24/33	0.216642796879188	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.233851363721945	1		192	375	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300195	15300195	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005734-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	96	450	0	ENST00000263388.2:c.1081C>G	p.His361Asp	p.H361D	ENST00000263388	NM_000435.2	361	Cac/Gac	7/33	0.221061555064495	3	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.233851363721945	3		450	650	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76777859	76777859	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005734-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	41	173	0	ENST00000373344.5:c.6857C>G	p.Thr2286Ser	p.T2286S	ENST00000373344	NM_000489.3	2286	aCc/aGc	32/35	0.233851363721945	0	FACETS	1	0.923	1			1	CLONAL	1	TRUE	NA	0.233851363721945	0		173	229	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0005737-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	380	481	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	0.722276950579502	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.739151722605326	3		481	661	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741925	145741925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747963862	NA	P-0005737-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	342	385	0	ENST00000428558.2:c.578G>A	p.Arg193Gln	p.R193Q	ENST00000428558	NM_004260.3	193	cGa/cAa	5/22	0.668538756416331	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.739151722605326	4		385	768	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094468	27094470	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs767284798	NA	P-0005737-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	23	355	0	ENST00000324856.7:c.3178_3180del	p.Glu1060del	p.E1060del	ENST00000324856	NM_006015.4	1059	aAGGag/aag	11/20	0.739151722605326	2	FACETS	0.186	0.145	0.234	0.093	0.072	0.117	SUBCLONAL	1	TRUE	0	0.739151722605326	2		355	334	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0005738-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	91	371	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	0.987	1	CLONAL	2	TRUE	1	0.19	2		371	433	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0005739-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	28	321	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.559	0.446	0.689	0.559	0.446	0.689	SUBCLONAL	1	TRUE	1	0.199169870275975	2		322	503	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917797	29917797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748854412	NA	P-0005739-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	35	465	0	ENST00000389048.3:c.871C>T	p.Arg291Cys	p.R291C	ENST00000389048	NM_004304.4	291	Cgc/Tgc	3/29	0.199169870275975	1	FACETS	0.666	0.546	0.802	0.666	0.546	0.802	SUBCLONAL	1	TRUE	0	0.199169870275975	1		465	475	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0005739-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	129	315	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	1	0.933	1	1	0.99	1	CLONAL	2	TRUE	1	0.199169870275975	2		315	628	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164773	106164773	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765414159	NA	P-0005739-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	36	400	3	ENST00000380013.4:c.3641G>A	p.Arg1214Gln	p.R1214Q	ENST00000380013	NM_001127208.2	1214	cGg/cAg	6/11	1	2	FACETS	0.658	0.54	0.791	0.658	0.54	0.791	SUBCLONAL	1	TRUE	1	0.199169870275975	2		403	549	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538978	23538978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749394163	NA	P-0005739-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	40	428	0	ENST00000380871.4:c.461G>A	p.Arg154Gln	p.R154Q	ENST00000380871	NM_006167.3	154	cGg/cAg	2/2	1	2	FACETS	0.856	0.712	1	0.856	0.712	1	CLONAL	1	TRUE	1	0.199169870275975	2		428	469	SUCCESS
APC	324	MSKCC	GRCh37	5	112174374	112174374	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005739-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	22	293	0	ENST00000257430.4:c.3083del	p.Ser1028IlefsTer9	p.S1028Ifs*9	ENST00000257430	NM_000038.5	1028	aGt/at	16/16	1	2	FACETS	0.615	0.476	0.777	0.615	0.476	0.777	SUBCLONAL	1	TRUE	1	0.199169870275975	2		293	359	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0005743-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	68	628	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.3	1	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	FALSE	0	0.3	1		629	376	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003313	143003313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754717740	NA	P-0005743-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	60	338	0	ENST00000262992.4:c.2513G>A	p.Arg838His	p.R838H	ENST00000262992	NM_001101669.1	838	cGt/cAt	23/24	0.0785658901697666	4	FACETS	0.965	0.832	1	0.482	0.416	0.555	INDETERMINATE	1	FALSE	2	0.3	4		338	539	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346363	89346363	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005743-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	73	523	1	ENST00000301030.4:c.6587C>A	p.Ser2196Tyr	p.S2196Y	ENST00000301030	NM_001256183.1	2196	tCc/tAc	9/13	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	FALSE	1	0.3	2		524	457	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199466	11199466	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	75	1026	0	ENST00000361445.4:c.5025G>T	p.Leu1675Phe	p.L1675F	ENST00000361445	NM_004958.3	1675	ttG/ttT	36/58	0.444395555900735	1	FACETS	0.746	0.658	0.839	0.746	0.658	0.839	SUBCLONAL	1	TRUE	0	0.444395555900735	1		1026	352	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183794	10183794	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs119103277	NA	P-0005747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	52	557	3	ENST00000256474.2:c.263G>A	p.Trp88Ter	p.W88*	ENST00000256474	NM_000551.3	88	tGg/tAg	1/3	0.377302868898514	1	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	0	0.444395555900735	1		560	180	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668742	52668742	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	113	933	0	ENST00000394830.3:c.1177G>T	p.Val393Phe	p.V393F	ENST00000394830	NM_018313.4	393	Gtt/Ttt	12/30	0.358052584274754	0	FACETS	0.8	0.728	0.875			1	SUBCLONAL	1	TRUE	0	0.444395555900735	0		933	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0005767-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	17	546	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.39126146134811	2	FACETS	0.155	0.115	0.203	0.078	0.057	0.102	SUBCLONAL	1	TRUE	0	0.408611811467534	2		547	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0005767-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	206	523	1	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.39126146134811	2	FACETS	0.951	0.89	1	0.951	0.89	1	CLONAL	2	TRUE	0	0.408611811467534	2		524	530	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432895	432895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005767-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	122	407	1	ENST00000399788.2:c.2021G>A	p.Arg674Gln	p.R674Q	ENST00000399788	NM_001042603.1	674	cGg/cAg	15/28	0.386912589762864	3	FACETS	1	0.953	1			1	CLONAL	1	TRUE	NA	0.408611811467534	3		408	663	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226846	142226846	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005767-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	81	389	2	ENST00000350721.4:c.4958G>A	p.Arg1653Gln	p.R1653Q	ENST00000350721	NM_001184.3	1653	cGa/cAa	28/47	0.339464012907779	5	FACETS	0.855	0.753	0.965			1	CLONAL	1	TRUE	NA	0.408611811467534	5		391	748	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371617	55371617	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0005767-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	59	402	0	ENST00000297316.4:c.308-1G>A		p.X103_splice	ENST00000297316	NM_022454.3	103			1	2	FACETS	0.591	0.509	0.679	0.591	0.509	0.679	SUBCLONAL	1	TRUE	1	0.408611811467534	2		402	489	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971107	21971107	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs587782792	NA	P-0005767-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	100	320	0	ENST00000304494.5:c.251A>C	p.Asp84Ala	p.D84A	ENST00000304494	NM_000077.4	84	gAc/gCc	2/3	0.408611811467534	3	FACETS	0.963	0.871	1	0.963	0.871	1	CLONAL	2	TRUE	1	0.408611811467534	3		320	306	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121173	11121173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005767-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	76	552	0	ENST00000358026.2:c.2240C>T	p.Ala747Val	p.A747V	ENST00000358026	NM_001128849.1	747	gCg/gTg	15/36	0.288787315874306	4	FACETS	0.684	0.599	0.776	0.342	0.299	0.388	SUBCLONAL	1	TRUE	2	0.408611811467534	4		552	766	SUCCESS
APC	324	MSKCC	GRCh37	5	112176064	112176064	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554086185	NA	P-0005768-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	42	410	0	ENST00000257430.4:c.4778del	p.Lys1593SerfsTer57	p.K1593Sfs*57	ENST00000257430	NM_000038.5	1591	gcA/gc	16/16	0.809491967381607	1	FACETS	0.191	0.16	0.226	0.191	0.16	0.226	SUBCLONAL	1	TRUE	0	0.822734673922051	1		410	314	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591288	67591288	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005768-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	41	431	0	ENST00000274335.5:c.1786G>T	p.Glu596Ter	p.E596*	ENST00000274335		596	Gag/Tag	13/15	0.809491967381607	1	FACETS	0.166	0.138	0.196	0.166	0.138	0.196	SUBCLONAL	1	TRUE	0	0.822734673922051	1		431	354	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845336	151845336	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005768-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	36	418	0	ENST00000262189.6:c.13676G>A	p.Gly4559Asp	p.G4559D	ENST00000262189	NM_170606.2	4559	gGt/gAt	52/59	1	2	FACETS	0.204	0.167	0.244	0.204	0.167	0.244	SUBCLONAL	1	TRUE	1	0.822734673922051	2		418	430	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005770-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	104	236	0				ENST00000310581	NM_198253.2	-/1132			0.163424135961894	3	FACETS	1	0.972	1			1	INDETERMINATE	2	FALSE	NA	0.3	3		236	333	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0005770-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	39	291	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	0.274441891106269	3	FACETS	0.602	0.498	0.717	0.301	0.249	0.359	SUBCLONAL	1	FALSE	1	0.3	3		291	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0005770-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	47	474	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.271626228309213	3	FACETS	1	0.945	1	0.63	0.535	0.733	CLONAL	1	FALSE	1	0.3	3		474	286	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056400	180056400	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005770-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	23	489	1	ENST00000261937.6:c.844C>T	p.Arg282Ter	p.R282*	ENST00000261937	NM_182925.4	282	Cga/Tga	7/30	0.271626228309213	3	FACETS	0.58	0.452	0.727	0.29	0.226	0.364	SUBCLONAL	1	FALSE	1	0.3	3		490	304	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881457	48881457	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0005770-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	60	384	0	ENST00000267163.4:c.179T>A	p.Leu60Ter	p.L60*	ENST00000267163	NM_000321.2	60	tTa/tAa	2/27	0.274441891106269	3	FACETS	1	0.952	1	0.617	0.534	0.706	CLONAL	1	FALSE	1	0.3	3		384	373	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618879	37618879	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005770-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	56	568	0	ENST00000447079.4:c.555G>C	p.Arg185Ser	p.R185S	ENST00000447079	NM_015083.1	185	agG/agC	1/14	0.271626228309213	3	FACETS	0.748	0.641	0.865	0.374	0.32	0.433	SUBCLONAL	1	FALSE	1	0.3	3		568	574	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651951	36651952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005770-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	25	392	0	ENST00000244741.5:c.74dup	p.Asp26GlyfsTer10	p.D26Gfs*10	ENST00000244741	NM_000389.4	25	gtg/gTtg	2/3	0.274441891106269	3	FACETS	0.498	0.392	0.62	0.249	0.196	0.31	SUBCLONAL	1	FALSE	1	0.3	3		392	385	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061208	38061208	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1292426539	NA	P-0005771-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	279	265	0	ENST00000250448.2:c.781C>G	p.Arg261Gly	p.R261G	ENST00000250448	NM_004496.3	261	Cgc/Ggc	2/2	0.197826360881796	4	FACETS	1	0.953	1	0.671	0.635	0.706	INDETERMINATE	2	TRUE	1	0.828900460741833	4		265	612	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657645	37657645	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005771-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	571	460	0	ENST00000447079.4:c.2564del	p.Phe855SerfsTer13	p.F855Sfs*13	ENST00000447079	NM_015083.1	854	aaT/aa	6/14	0.509106591331006	5	FACETS	1	0.995	1			1	CLONAL	3	TRUE	NA	0.828900460741833	5		460	904	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676313	37676313	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005771-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	233	449	0	ENST00000447079.4:c.3068del	p.Val1023AlafsTer34	p.V1023Afs*34	ENST00000447079	NM_015083.1	1023	gTc/gc	11/14	0.509106591331006	5	FACETS	0.751	0.702	0.801			1	SUBCLONAL	2	TRUE	NA	0.828900460741833	5		449	840	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916929	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519931	NA	P-0005773-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	378	798	0	ENST00000263967.3:c.316G>C	p.Gly106Arg	p.G106R	ENST00000263967	NM_006218.2	106	Ggc/Cgc	2/21	0.12820439257095	3	FACETS	1	0.994	1	0.651	0.619	0.684	INDETERMINATE	1	TRUE	1	0.705174528667015	3		798	1114	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0005773-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	160	503	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.705174528667015	2		503	423	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226574091	226574091	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0005773-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	114	664	0	ENST00000366794.5:c.770C>G	p.Ser257Ter	p.S257*	ENST00000366794	NM_001618.3	257	tCa/tGa	6/23	0.56619642207692	3	FACETS	0.648	0.584	0.715	0.324	0.292	0.358	SUBCLONAL	1	TRUE	1	0.705174528667015	3		664	675	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095941	178095941	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005773-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	102	399	0	ENST00000397062.3:c.1390C>G	p.Leu464Val	p.L464V	ENST00000397062	NM_006164.4	464	Ctc/Gtc	5/5	0.411848699390208	1	FACETS	0.45	0.405	0.497	0.45	0.405	0.497	INDETERMINATE	1	TRUE	0	0.705174528667015	1		399	416	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884825	134884825	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005773-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	172	500	0	ENST00000398015.3:c.1601A>C	p.Glu534Ala	p.E534A	ENST00000398015	NM_004441.4	534	gAg/gCg	8/16	0.12820439257095	3	FACETS	1	0.99	1	0.732	0.68	0.784	INDETERMINATE	1	TRUE	1	0.705174528667015	3		500	451	SUCCESS
ATR	545	MSKCC	GRCh37	3	142180886	142180886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142918229	NA	P-0005773-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	120	463	0	ENST00000350721.4:c.7088G>A	p.Arg2363Gln	p.R2363Q	ENST00000350721	NM_001184.3	2363	cGa/cAa	42/47	0.705174528667015	1	FACETS	0.584	0.533	0.638	0.584	0.533	0.638	SUBCLONAL	1	TRUE	0	0.705174528667015	1		463	377	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056533	26056533	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1332170864	NA	P-0005773-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	75	206	0	ENST00000343677.2:c.124G>C	p.Glu42Gln	p.E42Q	ENST00000343677	NM_005319.3	42	Gag/Cag	1/1	0.287059271841388	2	FACETS	0.765	0.678	0.857	0.383	0.339	0.429	INDETERMINATE	1	TRUE	0	0.705174528667015	2		206	278	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929243	32929243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398122578	NA	P-0005773-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	192	892	0	ENST00000380152.3:c.7253G>A	p.Arg2418Lys	p.R2418K	ENST00000380152		2418	aGa/aAa	14/27	0.705174528667015	1	FACETS	0.569	0.529	0.61	0.569	0.529	0.61	SUBCLONAL	1	TRUE	0	0.705174528667015	1		892	620	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061478	38061478	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005773-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	955	466	0	ENST00000250448.2:c.511C>T	p.Pro171Ser	p.P171S	ENST00000250448	NM_004496.3	171	Ccg/Tcg	2/2	0.705174528667015	6	FACETS	0.971	0.946	0.996			1	CLONAL	4	TRUE	NA	0.705174528667015	6		466	1681	SUCCESS
BTK	695	MSKCC	GRCh37	X	100625001	100625001	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005773-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	91	287	0	ENST00000308731.7:c.376C>T	p.His126Tyr	p.H126Y	ENST00000308731	NM_000061.2	126	Cac/Tac	5/19	1	1	FACETS	0.566	0.509	0.626	0.566	0.509	0.626	SUBCLONAL	1	TRUE	0	0.705174528667015	1		287	295	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937801	76937801	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0005775-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	63	463	0	ENST00000373344.5:c.2947A>T	p.Lys983Ter	p.K983*	ENST00000373344	NM_000489.3	983	Aag/Tag	9/35	0.433514911822286	0	FACETS	0.373	0.324	0.426			1	SUBCLONAL	1	TRUE	0	0.47312768478115	0		463	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057520000	NA	P-0005775-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	132	400	0	ENST00000269305.4:c.452C>G	p.Pro151Arg	p.P151R	ENST00000269305	NM_001126112.2	151	cCc/cGc	5/11	0.47312768478115	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.47312768478115	1		400	385	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913250	NA	P-0005777-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	589	433	0	ENST00000369535.4:c.34G>A	p.Gly12Ser	p.G12S	ENST00000369535	NM_002524.4	12	Ggt/Agt	2/7	0.737649703204115	6	FACETS	1	0.995	1	1	0.998	1	CLONAL	6	TRUE	2	0.737649703204115	6		433	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253911	NA	P-0005777-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	160	331	0	ENST00000269305.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000269305	NM_001126112.2	180	Gag/Aag	5/11	0.442428883740621	5	FACETS	1	0.973	1			1	INDETERMINATE	5	TRUE	NA	0.737649703204115	5		331	181	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149002	119149002	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs755557498	NA	P-0005777-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	229	448	0	ENST00000264033.4:c.1222T>C	p.Trp408Arg	p.W408R	ENST00000264033	NM_005188.3	408	Tgg/Cgg	8/16	0.727643356099848	4	FACETS	0.905	0.87	0.938	0.905	0.87	0.938	CLONAL	4	TRUE	0	0.737649703204115	4		448	298	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005868-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	256	417	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.370176794046379	2	FACETS	0.9	0.846	0.955	0.9	0.846	0.955	CLONAL	2	TRUE	0	0.373143207288593	2		417	762	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221320	1221320	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587776656	NA	P-0005868-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	106	444	0	ENST00000326873.7:c.843del	p.Leu282SerfsTer5	p.L282Sfs*5	ENST00000326873	NM_000455.4	281	ccG/cc	6/10	0.373143207288593	1	FACETS	0.854	0.768	0.945	0.854	0.768	0.945	CLONAL	1	TRUE	0	0.373143207288593	1		444	541	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602496	10602496	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750532889	NA	P-0005868-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	106	364	0	ENST00000171111.5:c.1082C>T	p.Pro361Leu	p.P361L	ENST00000171111	NM_203500.1	361	cCg/cTg	3/6	0.373143207288593	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.373143207288593	1		364	428	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997780	149997780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148506316	NA	P-0005868-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	151	390	0	ENST00000253339.5:c.2687G>A	p.Arg896Gln	p.R896Q	ENST00000253339		896	cGg/cAg	5/7	0.373143207288593	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.373143207288593	1		390	632	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562561	176562561	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005875-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	228	520	0	ENST00000439151.2:c.457T>G	p.Phe153Val	p.F153V	ENST00000439151	NM_022455.4	153	Ttt/Gtt	2/23	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.735858865300588	2		520	595	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0005881-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	71	370	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	0.15	2		370	657	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0005881-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	66	579	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.15	2		579	792	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145430	58145430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894340	NA	P-0005881-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	53	452	1	ENST00000257904.6:c.71G>A	p.Arg24His	p.R24H	ENST00000257904	NM_000075.3	24	cGt/cAt	2/8	1	2	FACETS	0.936	0.797	1	0.936	0.797	1	CLONAL	1	TRUE	1	0.15	2		453	755	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101353	27101353	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005881-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	43	554	1	ENST00000324856.7:c.4635G>A	p.Trp1545Ter	p.W1545*	ENST00000324856	NM_006015.4	1545	tgG/tgA	18/20	1	2	FACETS	0.674	0.562	0.799	0.674	0.562	0.799	SUBCLONAL	1	TRUE	1	0.15	2		555	851	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178023	56178023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005881-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	31	405	0	ENST00000399503.3:c.2996C>T	p.Thr999Ile	p.T999I	ENST00000399503	NM_005921.1	999	aCa/aTa	14/20	1	2	FACETS	0.672	0.542	0.82	0.672	0.542	0.82	SUBCLONAL	1	TRUE	1	0.15	2		405	615	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500395	99500395	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005881-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	51	659	0	ENST00000268035.6:c.3828G>T	p.Glu1276Asp	p.E1276D	ENST00000268035	NM_000875.3	1276	gaG/gaT	21/21	1	2	FACETS	0.69	0.585	0.807	0.69	0.585	0.807	SUBCLONAL	1	TRUE	1	0.15	2		659	985	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0005887-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	245	416	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.331464171456224	3	FACETS	0.763	0.717	0.809	0.763	0.717	0.809	INDETERMINATE	2	TRUE	1	0.656162321345672	3		416	650	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0005887-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	418	780	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.656162321345672	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.656162321345672	1		780	837	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201833	66201833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778795902	NA	P-0005887-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	61	163	0	ENST00000273854.3:c.2669C>T	p.Ala890Val	p.A890V	ENST00000273854	NM_004439.5	890	gCg/gTg	16/18	0.436264545262755	1	FACETS	0.376	0.326	0.43	0.376	0.326	0.43	SUBCLONAL	1	TRUE	0	0.656162321345672	1		163	332	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385113	41385113	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005887-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	355	302	1	ENST00000373198.4:c.848T>A	p.Leu283Gln	p.L283Q	ENST00000373198	NM_133170.3	283	cTg/cAg	6/32	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.656162321345672	2		303	1034	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023289	27023290	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005887-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	78	92	0	ENST00000324856.7:c.400dup	p.Ala134GlyfsTer266	p.A134Gfs*266	ENST00000324856	NM_006015.4	132	gtg/gtGg	1/20	0.323062735942309	1	FACETS	0.619	0.551	0.69	0.619	0.551	0.69	INDETERMINATE	1	TRUE	0	0.656162321345672	1		92	258	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0005925-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	105	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.25532892787322	2	FACETS	1	0.976	1	0.645	0.58	0.715	CLONAL	1	TRUE	0	0.291525097706214	2		371	558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0005925-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	187	946	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.291525097706214	2		946	1091	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0005925-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	20	383	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.54	0.414	0.688	0.54	0.414	0.688	SUBCLONAL	1	TRUE	1	0.291525097706214	2		383	254	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604778	48604778	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767383	NA	P-0005925-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	83	377	0	ENST00000342988.3:c.1600C>T	p.Gln534Ter	p.Q534*	ENST00000342988	NM_005359.5	534	Cag/Tag	12/12	0.240446702027175	2	FACETS	0.868	0.766	0.977	0.434	0.383	0.489	CLONAL	1	TRUE	0	0.291525097706214	2		377	656	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437669	52437669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005925-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1740	152	684	0	ENST00000460680.1:c.1492G>A	p.Glu498Lys	p.E498K	ENST00000460680	NM_004656.3	498	Gag/Aag	13/17	1	2	FACETS	0.551	0.502	0.604	0.551	0.502	0.604	SUBCLONAL	1	TRUE	1	0.291525097706214	2		684	1892	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455584	189455584	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs757932730	NA	P-0005925-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	104	363	0	ENST00000264731.3:c.118A>G	p.Met40Val	p.M40V	ENST00000264731	NM_003722.4	40	Atg/Gtg	2/14	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.291525097706214	2		363	522	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001043	150001043	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005925-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	60	422	0	ENST00000253339.5:c.2561G>C	p.Arg854Thr	p.R854T	ENST00000253339		854	aGa/aCa	4/7	1	2	FACETS	0.593	0.51	0.684	0.593	0.51	0.684	SUBCLONAL	1	TRUE	1	0.291525097706214	2		422	694	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109697	115109697	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005925-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	259	470	0	ENST00000257566.3:c.2181G>T	p.Leu727Phe	p.L727F	ENST00000257566	NM_016569.3	727	ttG/ttT	8/8	0.240446702027175	2	FACETS	1	0.992	1	0.721	0.674	0.769	CLONAL	1	TRUE	0	0.291525097706214	2		470	1233	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233721	133233721	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0005925-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	185	340	0	ENST00000320574.5:c.3582+1G>T		p.X1194_splice	ENST00000320574	NM_006231.2	1194			0.240446702027175	2	FACETS	0.781	0.722	0.841	0.781	0.722	0.841	SUBCLONAL	2	TRUE	0	0.291525097706214	2		340	813	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136299	2136299	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005925-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1350	92	487	0	ENST00000219476.3:c.4768G>A	p.Asp1590Asn	p.D1590N	ENST00000219476	NM_000548.3	1590	Gac/Aac	37/42	1	2	FACETS	0.438	0.387	0.492	0.438	0.387	0.492	SUBCLONAL	1	TRUE	1	0.291525097706214	2		487	1442	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857556	9857556	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1480366023	NA	P-0005925-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	40	310	0	ENST00000330684.3:c.3845A>G	p.Asn1282Ser	p.N1282S	ENST00000330684	NM_001134407.1	1282	aAc/aGc	13/13	1	2	FACETS	0.462	0.383	0.55	0.462	0.383	0.55	SUBCLONAL	1	TRUE	1	0.291525097706214	2		310	594	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390322	56390322	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005925-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	160	641	2	ENST00000348428.3:c.1061G>T	p.Arg354Leu	p.R354L	ENST00000348428	NM_006785.3	354	cGg/cTg	10/17	0.240446702027175	2	FACETS	1	0.981	1	0.615	0.563	0.668	CLONAL	1	TRUE	0	0.291525097706214	2		643	893	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748549	40748549	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005925-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	70	466	0	ENST00000392038.2:c.333G>T	p.Lys111Asn	p.K111N	ENST00000392038	NM_001626.4	111	aaG/aaT	5/14	1	2	FACETS	0.456	0.397	0.522	0.456	0.397	0.522	SUBCLONAL	1	TRUE	1	0.291525097706214	2		466	1052	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101612	27101612	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005925-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	69	357	0	ENST00000324856.7:c.4899del	p.Met1634Ter	p.M1634*	ENST00000324856	NM_006015.4	1632	Ccc/cc	18/20	1	2	FACETS	0.513	0.445	0.586	0.513	0.445	0.586	SUBCLONAL	1	TRUE	1	0.291525097706214	2		357	923	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204737513	204737513	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005925-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	48	326	0	ENST00000302823.3:c.650C>G	p.Pro217Arg	p.P217R	ENST00000302823	NM_005214.4	217	cCt/cGt	4/4	0.192890695340029	3	FACETS	0.578	0.488	0.678	0.193	0.162	0.226	SUBCLONAL	1	TRUE	0	0.291525097706214	3		326	653	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878287	151878287	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005925-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	62	456	0	ENST00000262189.6:c.6658C>T	p.Gln2220Ter	p.Q2220*	ENST00000262189	NM_170606.2	2220	Cag/Tag	36/59	0.160354501972142	3	FACETS	0.503	0.433	0.58	0.252	0.216	0.29	INDETERMINATE	1	TRUE	1	0.291525097706214	3		456	968	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0006000-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	106	552	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.482112857600368	2	FACETS	0.546	0.488	0.607			1	SUBCLONAL	1	TRUE	NA	0.4	2		552	971	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0006000-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	45	201	0	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	1	2	FACETS	0.434	0.364	0.51	0.434	0.364	0.51	SUBCLONAL	1	TRUE	1	0.4	2		201	519	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031697	36031697	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006000-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	60	445	1	ENST00000358208.4:c.1526G>A	p.Arg509Gln	p.R509Q	ENST00000358208		509	cGg/cAg	12/12	0.162975975470357	3	FACETS	0.33	0.283	0.381	0.165	0.141	0.191	INDETERMINATE	1	TRUE	1	0.4	3		446	1092	SUCCESS
APC	324	MSKCC	GRCh37	5	112174998	112174999	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs1554085246	NA	P-0006000-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	47	271	0	ENST00000257430.4:c.3709_3710del	p.Gln1237GlufsTer2	p.Q1237Efs*2	ENST00000257430	NM_000038.5	1236	gCA/g	16/16	1	2	FACETS	0.399	0.336	0.469	0.399	0.336	0.469	SUBCLONAL	1	TRUE	1	0.4	2		271	589	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572552	64572552	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	261	376	1	ENST00000312049.6:c.1304del	p.Gly435AlafsTer10	p.G435Afs*10	ENST00000312049	NM_130799.2	435	gGc/gc	9/10	0.469925518511978	2	FACETS	0.966	0.914	1	0.966	0.914	1	CLONAL	2	TRUE	0	0.469925518511978	2		377	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0006023-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	132	478	5	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.996	0.907	1	0.996	0.907	1	CLONAL	1	TRUE	1	0.426992562446569	2		483	621	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0006023-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	182	698	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.853	0.787	0.923	0.853	0.787	0.923	CLONAL	1	TRUE	1	0.426992562446569	2		698	999	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0006023-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	66	252	2	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.616	0.535	0.703	0.616	0.535	0.703	SUBCLONAL	1	TRUE	1	0.426992562446569	2		254	502	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266970	18266970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757629395	NA	P-0006023-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	32	64	0	ENST00000222254.8:c.281G>A	p.Arg94His	p.R94H	ENST00000222254	NM_005027.3	94	cGc/cAc	2/16	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.426992562446569	2		64	127	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484814	57484814	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006023-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	933	477	0	ENST00000371085.3:c.794G>T	p.Arg265Leu	p.R265L	ENST00000371085	NM_000516.4	265	cGc/cTc	10/13	0.426992562446569	6	FACETS	0.928	0.906	0.95	0.928	0.906	0.95	CLONAL	6	TRUE	0	0.426992562446569	6		477	1455	SUCCESS
AR	367	MSKCC	GRCh37	X	66766193	66766193	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866450936	NA	P-0006023-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	173	142	1	ENST00000374690.3:c.1205C>T	p.Ala402Val	p.A402V	ENST00000374690	NM_000044.3	402	gCg/gTg	1/8	0.36159638064186	2	FACETS	0.931	0.878	0.984			1	CLONAL	3	TRUE	NA	0.426992562446569	2		143	290	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557814	187557814	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006023-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	148	565	0	ENST00000441802.2:c.3897del	p.Lys1299AsnfsTer69	p.K1299Nfs*69	ENST00000441802	NM_005245.3	1299	aaA/aa	5/27	1	2	FACETS	0.894	0.818	0.975	0.894	0.818	0.975	CLONAL	1	TRUE	1	0.426992562446569	2		565	775	SUCCESS
APC	324	MSKCC	GRCh37	5	112176013	112176016	+	frameshift_variant	Frame_Shift_Del	DEL	ACTA	ACTA	-	novel	NA	P-0006023-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	92	357	0	ENST00000257430.4:c.4722_4725del	p.Ile1574MetfsTer75	p.I1574Mfs*75	ENST00000257430	NM_000038.5	1574	atACTA/at	16/16	1	2	FACETS	0.955	0.853	1	0.955	0.853	1	CLONAL	1	TRUE	1	0.426992562446569	2		357	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0006048-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	258	796	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	NA	2	FACETS	0.983	0.953	1			1	INDETERMINATE	2	TRUE	NA	0.860617383239834	2		796	305	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725043	89725043	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1057517809	NA	P-0006048-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	122	660	0	ENST00000371953.3:c.1027-1G>A		p.X343_splice	ENST00000371953	NM_000314.4	343			0.845776254897468	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.860617383239834	2		660	139	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416700	29416700	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006048-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	131	488	2	ENST00000389048.3:c.4253C>A	p.Pro1418His	p.P1418H	ENST00000389048	NM_004304.4	1418	cCt/cAt	29/29	0.860617383239834	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.860617383239834	3		490	202	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191490	185191490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372313966	NA	P-0006048-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	59	524	2	ENST00000265026.3:c.2371G>A	p.Gly791Ser	p.G791S	ENST00000265026	NM_004721.4	791	Ggc/Agc	11/14	0.860617383239834	5	FACETS	0.861	0.744	0.986	0.287	0.248	0.329	CLONAL	1	TRUE	2	0.860617383239834	5		526	365	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440398	49440398	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006048-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	122	527	0	ENST00000301067.7:c.4412G>T	p.Cys1471Phe	p.C1471F	ENST00000301067	NM_003482.3	1471	tGc/tTc	15/54	0.360470885682548	3	FACETS	1	0.982	1	0.759	0.713	0.804	INDETERMINATE	2	TRUE	0	0.860617383239834	3		527	178	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861913	57861913	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs114543757	NA	P-0006048-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	108	1289	1	ENST00000228682.2:c.1214G>A	p.Arg405Gln	p.R405Q	ENST00000228682	NM_005269.2	405	cGg/cAg	10/12	0.360470885682548	3	FACETS	0.853	0.771	0.938	0.284	0.257	0.313	INDETERMINATE	1	TRUE	0	0.860617383239834	3		1290	421	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222494	2222494	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1212009257	NA	P-0006048-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	119	683	1	ENST00000326181.6:c.688C>T	p.Pro230Ser	p.P230S	ENST00000326181	NM_032271.2	230	Cct/Tct	9/21	0.748480881549139	5	FACETS	0.941	0.851	1	0.235	0.212	0.259	CLONAL	1	TRUE	1	0.860617383239834	5		684	673	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788650	3788650	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs200207299	NA	P-0006048-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	290	805	0	ENST00000262367.5:c.4304A>G	p.Asp1435Gly	p.D1435G	ENST00000262367	NM_004380.2	1435	gAt/gGt	26/31	0.748480881549139	5	FACETS	1	0.971	1	1	0.971	1	CLONAL	4	TRUE	1	0.860617383239834	5		805	383	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533342	29533342	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0006048-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	169	621	1	ENST00000356175.3:c.1345A>T	p.Lys449Ter	p.K449*	ENST00000356175	NM_000267.3	449	Aaa/Taa	12/57	0.504997122065563	5	FACETS	1	0.986	1			1	INDETERMINATE	3	TRUE	NA	0.860617383239834	5		622	263	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54959363	54959363	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006048-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	121	549	0	ENST00000312783.6:c.337G>A	p.Glu113Lys	p.E113K	ENST00000312783	NM_198436.1	113	Gaa/Aaa	5/10	0.727529843993714	4	FACETS	0.915	0.84	0.99	0.915	0.84	0.99	CLONAL	2	TRUE	2	0.860617383239834	4		549	286	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297767	15297768	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0006048-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	112	948	1	ENST00000263388.2:c.1872_1873del	p.Ala625GlnfsTer11	p.A625Qfs*11	ENST00000263388	NM_000435.2	624	tgTGcc/tgcc	12/33	0.727529843993714	4	FACETS	0.95	0.858	1	0.475	0.429	0.523	CLONAL	1	TRUE	2	0.860617383239834	4		949	510	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576097	29576098	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0006048-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	90	851	2	ENST00000356175.3:c.4076dup	p.Gln1360SerfsTer14	p.Q1360Sfs*14	ENST00000356175	NM_000267.3	1357	ttc/ttCc	30/57	0.504997122065563	5	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.860617383239834	5		853	340	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106543538	106543538	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006048-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	15	470	1	ENST00000369096.4:c.340G>A	p.Gly114Arg	p.G114R	ENST00000369096	NM_001198.3	114	Gga/Aga	3/7	0.531594528504034	4	FACETS	0.312	0.228	0.412	0.104	0.076	0.138	SUBCLONAL	1	TRUE	1	0.860617383239834	4		471	208	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738651	145738651	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006048-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	20	389	0	ENST00000428558.2:c.2413del	p.Ala805ProfsTer38	p.A805Pfs*38	ENST00000428558	NM_004260.3	805	Gcc/cc	15/22	0.840685840894567	4	FACETS	0.222	0.169	0.284	0.111	0.084	0.142	SUBCLONAL	1	TRUE	2	0.860617383239834	4		389	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0006112-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	535	448	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.36927512314161	3	FACETS	0.938	0.906	0.971	0.938	0.906	0.971	CLONAL	3	TRUE	0	0.482992579964051	3		448	977	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132465	11132465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006112-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	350	454	0	ENST00000358026.2:c.2681C>T	p.Thr894Met	p.T894M	ENST00000358026	NM_001128849.1	894	aCg/aTg	19/36	0.180194594806846	2	FACETS	1	0.995	1	0.736	0.699	0.774	INDETERMINATE	1	TRUE	0	0.482992579964051	2		454	984	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971007	21971018	+	inframe_deletion	In_Frame_Del	DEL	CAGGTCCACGGG	CAGGTCCACGGG	-	novel	NA	P-0006112-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	196	343	0	ENST00000304494.5:c.340_351del	p.Pro114_Leu117del	p.P114_L117del	ENST00000304494	NM_000077.4	114	CCCGTGGACCTG/-	2/3	0.482992579964051	2	FACETS	0.751	0.701	0.803	0.751	0.701	0.803	SUBCLONAL	2	TRUE	0	0.482992579964051	2		343	540	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139211	37139211	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006121-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	10	163	0	ENST00000373509.5:c.551T>A	p.Leu184His	p.L184H	ENST00000373509	NM_002648.3	184	cTc/cAc	4/6	0.27402265583615	6	FACETS	0.579	0.392	0.814			1	SUBCLONAL	1	TRUE	NA	0.27402265583615	6		163	195	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500661	99500661	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006121-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	24	242	0	ENST00000268035.6:c.4094C>G	p.Ser1365Trp	p.S1365W	ENST00000268035	NM_000875.3	1365	tCg/tGg	21/21	1	2	FACETS	0.979	0.773	1	0.979	0.773	1	CLONAL	1	TRUE	1	0.27402265583615	2		242	179	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398288	+	missense_variant	Missense_Mutation	ONP	CCAGC	CCAGC	TCAGT	novel	NA	P-0006121-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	1042	380	0	ENST00000311936.3:c.31_35delinsACTGA	p.Ala11_Gly12delinsThrAsp	p.A11_G12delinsTD	ENST00000311936	NM_004985.3	11	GCTGGt/ACTGAt	2/5	0.27402265583615	15	FACETS	1	0.987	1			1	CLONAL	13	TRUE	NA	0.27402265583615	15		380	1605	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0006149-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	160	592	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.205552770415419	3	FACETS	1	0.979	1	0.793	0.728	0.859	CLONAL	2	FALSE	0	0.205552770415419	3		592	722	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013741	12013741	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006149-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	35	309	0	ENST00000353533.5:c.683G>C	p.Arg228Thr	p.R228T	ENST00000353533	NM_003010.3	228	aGa/aCa	6/11	0.205552770415419	1	FACETS	0.641	0.525	0.771	0.641	0.525	0.771	SUBCLONAL	1	FALSE	0	0.205552770415419	1		309	477	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939727	131939727	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006149-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	107	336	0	ENST00000265335.6:c.2513A>C	p.Lys838Thr	p.K838T	ENST00000265335		838	aAg/aCg	15/25	1	2	FACETS	0.836	0.751	0.925	1	0.985	1	CLONAL	2	FALSE	1	0.205552770415419	2		336	623	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853050	151853050	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006149-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	68	194	0	ENST00000262189.6:c.11905G>A	p.Val3969Ile	p.V3969I	ENST00000262189	NM_170606.2	3969	Gtt/Att	46/59	0.205552770415419	3	FACETS	0.82	0.715	0.932	0.82	0.715	0.932	CLONAL	2	FALSE	1	0.205552770415419	3		194	445	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0006194-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	107	114	0				ENST00000310581	NM_198253.2	-/1132			0.483661305317603	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	2	0.472630713612017	4		114	308	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0006194-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	170	665	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.472630713612017	2	FACETS	0.954	0.89	1	0.954	0.89	1	CLONAL	2	TRUE	0	0.472630713612017	2		665	377	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346669	225346669	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006194-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	64	395	1	ENST00000264414.4:c.1969C>T	p.His657Tyr	p.H657Y	ENST00000264414	NM_003590.4	657	Cat/Tat	14/16	0.422011644523822	4	FACETS	0.956	0.831	1	0.478	0.415	0.546	CLONAL	1	TRUE	2	0.472630713612017	4		396	417	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843416	3843416	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006194-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	56	353	1	ENST00000262367.5:c.1187C>A	p.Thr396Lys	p.T396K	ENST00000262367	NM_004380.2	396	aCg/aAg	4/31	0.152021204250883	3	FACETS	0.986	0.851	1	0.329	0.283	0.378	INDETERMINATE	1	TRUE	0	0.472630713612017	3		354	297	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490346	29490346	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006194-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	84	460	0	ENST00000356175.3:c.431C>G	p.Ser144Cys	p.S144C	ENST00000356175	NM_000267.3	144	tCt/tGt	4/57	0.250687853316556	4	FACETS	1	0.932	1	0.536	0.475	0.601	INDETERMINATE	1	TRUE	2	0.472630713612017	4		460	488	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797271	135797272	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0006194-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	143	263	0	ENST00000298552.3:c.597dup	p.Val200ArgfsTer18	p.V200Rfs*18	ENST00000298552	NM_001162426.1	199	-/C	7/23	0.472630713612017	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.472630713612017	2		263	276	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976422	25976422	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006194-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	32	423	0	ENST00000435504.4:c.1123G>C	p.Glu375Gln	p.E375Q	ENST00000435504		375	Gaa/Caa	11/13	1	2	FACETS	0.359	0.291	0.435	0.359	0.291	0.435	SUBCLONAL	1	TRUE	1	0.472630713612017	2		423	377	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233114	66233114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs561015414	NA	P-0006194-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	27	417	0	ENST00000273854.3:c.1885G>T	p.Asp629Tyr	p.D629Y	ENST00000273854	NM_004439.5	629	Gat/Tat	10/18	0.483661305317603	3	FACETS	0.283	0.224	0.35	0.142	0.112	0.175	SUBCLONAL	1	TRUE	1	0.472630713612017	3		417	499	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137313580	137313580	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006194-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	248	915	3	ENST00000481739.1:c.839T>A	p.Val280Glu	p.V280E	ENST00000481739	NM_002957.4	280	gTg/gAg	6/10	0.472630713612017	2	FACETS	0.999	0.945	1	0.999	0.945	1	CLONAL	2	TRUE	0	0.472630713612017	2		918	525	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18649063	18649063	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761182298	NA	P-0006196-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	250	448	2	ENST00000266497.5:c.2738G>A	p.Gly913Asp	p.G913D	ENST00000266497		913	gGc/gAc	19/31	NA	2	FACETS	0.986	0.93	1			1	INDETERMINATE	1	TRUE	NA	0.827094892073196	2		450	613	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0006246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	56	383	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.682540031989209	3	FACETS	0.568	0.489	0.655	0.284	0.244	0.328	SUBCLONAL	1	TRUE	1	0.690285253814488	3		383	384	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337650	73337650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	220	484	0	ENST00000377767.4:c.2066G>A	p.Arg689Gln	p.R689Q	ENST00000377767	NM_014953.3	689	cGa/cAa	16/21	0.527571430936602	4	FACETS	0.934	0.868	1	0.467	0.434	0.501	CLONAL	1	TRUE	2	0.690285253814488	4		484	1154	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237610	16237610	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	200	336	0	ENST00000375759.3:c.1057G>T	p.Asp353Tyr	p.D353Y	ENST00000375759	NM_015001.2	353	Gat/Tat	5/15	1	2	FACETS	0.959	0.894	1	0.959	0.894	1	CLONAL	1	TRUE	1	0.690285253814488	2		336	604	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562204	95562204	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886037721	NA	P-0006246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	248	608	0	ENST00000393063.1:c.5053C>T	p.Gln1685Ter	p.Q1685*	ENST00000393063	NM_030621.3	1685	Cag/Tag	24/28	1	2	FACETS	0.776	0.727	0.827	0.776	0.727	0.827	SUBCLONAL	1	TRUE	1	0.690285253814488	2		608	926	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348742	89348743	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0006246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	373	981	0	ENST00000301030.4:c.4207_4208delinsTT	p.Gly1403Leu	p.G1403L	ENST00000301030	NM_001256183.1	1403	GGa/TTa	9/13	1	2	FACETS	0.69	0.653	0.728	0.69	0.653	0.728	SUBCLONAL	1	TRUE	1	0.690285253814488	2		981	1566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0006261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	183	953	10	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.186233904828367	3	FACETS	0.964	0.897	1	0.964	0.897	1	CLONAL	3	TRUE	0	0.279407550298698	3		963	516	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0006261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	190	304	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	0.279407550298698	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.279407550298698	2		304	656	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174929	11174929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	178	561	0	ENST00000361445.4:c.7105G>A	p.Glu2369Lys	p.E2369K	ENST00000361445	NM_004958.3	2369	Gag/Aag	52/58	0.279407550298698	2	FACETS	0.959	0.888	1	0.959	0.888	1	CLONAL	2	TRUE	0	0.279407550298698	2		561	664	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154321	2154321	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150866176	NA	P-0006261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	171	654	0	ENST00000434045.2:c.607G>A	p.Glu203Lys	p.E203K	ENST00000434045	NM_001127598.1	203	Gag/Aag	5/5	0.180352698491111	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.279407550298698	4		654	700	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0006335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	211	427	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	TRUE	1	0.804347329478069	2		427	508	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0006335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	322	357	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	0.804347329478069	2		357	785	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741707	145741707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543009701	NA	P-0006335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	323	345	0	ENST00000428558.2:c.796G>A	p.Glu266Lys	p.E266K	ENST00000428558	NM_004260.3	266	Gag/Aag	5/22	1	2	FACETS	0.965	0.916	1	0.965	0.916	1	CLONAL	1	TRUE	1	0.804347329478069	2		345	832	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115111972	115111972	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	312	234	0	ENST00000257566.3:c.1768C>T	p.Gln590Ter	p.Q590*	ENST00000257566	NM_016569.3	590	Cag/Tag	7/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.804347329478069	2		234	734	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012331	176012331	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1278	176	474	0	ENST00000367669.3:c.1603G>A	p.Asp535Asn	p.D535N	ENST00000367669	NM_022457.5	535	Gat/Aat	14/20	0.805378545350249	3	FACETS	0.422	0.387	0.458	0.211	0.193	0.229	SUBCLONAL	1	TRUE	1	0.804347329478069	3		474	1454	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564677	86564677	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	341	343	0	ENST00000274376.6:c.409C>G	p.Leu137Val	p.L137V	ENST00000274376	NM_002890.2	137	Ctg/Gtg	1/25	0.173054317352405	4	FACETS	0.916	0.871	0.962	0.916	0.871	0.962	INDETERMINATE	2	TRUE	2	0.804347329478069	4		343	835	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860485	151860485	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	295	402	1	ENST00000262189.6:c.10177G>T	p.Glu3393Ter	p.E3393*	ENST00000262189	NM_170606.2	3393	Gaa/Taa	43/59	NA	2	FACETS	0.907	0.857	0.957			1	INDETERMINATE	1	TRUE	NA	0.804347329478069	2		403	809	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865468	57865468	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752275003	NA	P-0006335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	341	693	0	ENST00000228682.2:c.2945C>T	p.Ser982Leu	p.S982L	ENST00000228682	NM_005269.2	982	tCa/tTa	12/12	1	2	FACETS	0.952	0.904	1	0.952	0.904	1	CLONAL	1	TRUE	1	0.804347329478069	2		693	891	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913942	32913942	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs759741090	NA	P-0006335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	503	673	0	ENST00000380152.3:c.5450C>G	p.Ser1817Cys	p.S1817C	ENST00000380152		1817	tCt/tGt	11/27	1	2	FACETS	0.952	0.912	0.992	0.952	0.912	0.992	CLONAL	1	TRUE	1	0.804347329478069	2		673	1314	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937315	32937315	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs81002874	NA	P-0006335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	107	245	0	ENST00000380152.3:c.7977-1G>A		p.X2659_splice	ENST00000380152		2659			1	2	FACETS	0.478	0.43	0.528	0.478	0.43	0.528	SUBCLONAL	1	TRUE	1	0.804347329478069	2		245	557	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832769	3832769	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	291	511	0	ENST00000262367.5:c.1489C>T	p.Gln497Ter	p.Q497*	ENST00000262367	NM_004380.2	497	Cag/Tag	6/31	1	2	FACETS	0.925	0.875	0.977	0.925	0.875	0.977	CLONAL	1	TRUE	1	0.804347329478069	2		511	782	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40458263	40458263	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	300	595	0	ENST00000345506.4:c.1478G>C	p.Arg493Thr	p.R493T	ENST00000345506	NM_003152.3	493	aGg/aCg	14/20	NA	2	FACETS	0.871	0.824	0.92			1	INDETERMINATE	1	TRUE	NA	0.804347329478069	2		595	856	SUCCESS
AR	367	MSKCC	GRCh37	X	66942707	66942707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	123	670	0	ENST00000374690.3:c.2488G>A	p.Glu830Lys	p.E830K	ENST00000374690	NM_000044.3	830	Gaa/Aaa	7/8	NA	2	FACETS	0.329	0.297	0.363			1	INDETERMINATE	1	TRUE	NA	0.804347329478069	2		670	929	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862138	68862139	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0006335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	359	476	0	ENST00000261769.5:c.2231dup	p.Glu745ArgfsTer3	p.E745Rfs*3	ENST00000261769	NM_004360.3	742	-/C	14/16	0.805378545350249	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.804347329478069	1		476	529	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584426	39584440	+	inframe_deletion	In_Frame_Del	DEL	TGGAGCTGTTATCCT	TGGAGCTGTTATCCT	-	novel	NA	P-0006335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	336	446	0	ENST00000262039.4:c.1091_1105del	p.Leu364_Ser368del	p.L364_S368del	ENST00000262039	NM_002647.2	364	tTGGAGCTGTTATCCTct/tct	10/25	1	2	FACETS	0.948	0.9	0.997	0.948	0.9	0.997	CLONAL	1	TRUE	1	0.804347329478069	2		446	881	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089765	27089772	+	frameshift_variant	Frame_Shift_Del	DEL	TATCCAAA	TATCCAAA	G	novel	NA	P-0006335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	276	144	0	ENST00000324856.7:c.2721_2728delinsG	p.Ile908ThrfsTer9	p.I908Tfs*9	ENST00000324856	NM_006015.4	907	tcTATCCAAAac/tcGac	8/20	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.804347329478069	2		144	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0006504-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	466	764	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.328176558301047	3	FACETS	1	0.979	1	0.688	0.659	0.717	CLONAL	2	TRUE	0	0.532854143831631	3		765	1073	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205077	128205077	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006504-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	346	486	2	ENST00000341105.2:c.364T>A	p.Ser122Thr	p.S122T	ENST00000341105	NM_032638.4	122	Tcc/Acc	3/6	0.532854143831631	3	FACETS	1	0.994	1			1	CLONAL	1	TRUE	NA	0.532854143831631	3		488	1139	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193892	106193892	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1049545383	NA	P-0006504-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	122	489	0	ENST00000380013.4:c.4354C>T	p.Arg1452Ter	p.R1452*	ENST00000380013	NM_001127208.2	1452	Cga/Tga	10/11	0.484704388724926	2	FACETS	0.828	0.751	0.908	0.414	0.375	0.454	CLONAL	1	TRUE	0	0.532854143831631	2		489	553	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983114	111983114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006504-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1684	413	605	1	ENST00000368678.4:c.1433G>A	p.Arg478Gln	p.R478Q	ENST00000368678		478	cGa/cAa	13/13	0.532854143831631	6	FACETS	0.764	0.724	0.804	0.382	0.362	0.402	SUBCLONAL	2	TRUE	2	0.532854143831631	6		606	2097	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993434	72993434	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006504-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	291	749	0	ENST00000268489.5:c.611T>G	p.Phe204Cys	p.F204C	ENST00000268489	NM_006885.3	204	tTc/tGc	2/10	0.484704388724926	2	FACETS	0.938	0.883	0.996	0.469	0.441	0.498	CLONAL	1	TRUE	0	0.532854143831631	2		749	1164	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246466	41246476	+	frameshift_variant	Frame_Shift_Del	DEL	GAGCATGGCAG	GAGCATGGCAG	T	novel	NA	P-0006504-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	359	537	0	ENST00000357654.3:c.1072_1082delinsA	p.Leu358LysfsTer13	p.L358Kfs*13	ENST00000357654	NM_007294.3	358	CTGCCATGCTCa/Aa	10/23	0.328176558301047	3	FACETS	1	0.992	1	0.777	0.742	0.812	CLONAL	2	TRUE	0	0.532854143831631	3		537	732	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427451	427451	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006530-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	48	530	0	ENST00000399788.2:c.2718A>C	p.Glu906Asp	p.E906D	ENST00000399788	NM_001042603.1	906	gaA/gaC	19/28	1	2	FACETS	0.731	0.618	0.854	0.731	0.618	0.854	SUBCLONAL	1	TRUE	1	0.29	2		530	453	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0006561-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	104	417	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	NA	2	FACETS	1	0.924	1			1	INDETERMINATE	1	TRUE	NA	0.400332028355668	2		417	503	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0006561-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	110	498	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.87	0.783	0.961	0.87	0.783	0.961	CLONAL	1	TRUE	1	0.400332028355668	2		498	632	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0006561-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	60	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.210544147336443	3	FACETS	0.877	0.759	1	0.439	0.379	0.503	INDETERMINATE	1	TRUE	1	0.400332028355668	3		326	410	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911542	101911542	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006561-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	117	436	0	ENST00000374994.4:c.1467G>C	p.Lys489Asn	p.K489N	ENST00000374994	NM_004612.2	489	aaG/aaC	9/9	0.260427636090339	2	FACETS	1	0.967	1	0.573	0.519	0.63	CLONAL	1	TRUE	0	0.400332028355668	2		436	510	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099939	27099940	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0006561-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	142	557	0	ENST00000324856.7:c.3821dup	p.Pro1275ThrfsTer12	p.P1275Tfs*12	ENST00000324856	NM_006015.4	1273	atg/atGg	15/20	0.189383766272925	3	FACETS	1	0.943	1	0.523	0.477	0.572	INDETERMINATE	1	TRUE	1	0.400332028355668	3		557	814	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041669	47041669	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006561-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	137	590	0	ENST00000377604.3:c.1896del	p.Ser633ArgfsTer71	p.S633Rfs*71	ENST00000377604	NM_001204468.1	632	Ccc/cc	17/24	NA	2	FACETS	0.896	0.816	0.98			1	INDETERMINATE	1	TRUE	NA	0.400332028355668	2		590	764	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106377	27106378	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AATG	novel	NA	P-0006561-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	79	563	1	ENST00000324856.7:c.5990_5993dup	p.Asp1998GlufsTer2	p.D1998Efs*2	ENST00000324856	NM_006015.4	1996	-/AATG	20/20	0.189383766272925	3	FACETS	0.637	0.559	0.72	0.318	0.279	0.36	INDETERMINATE	1	TRUE	1	0.400332028355668	3		564	744	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0006584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	72	298	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.637607160109796	1	FACETS	0.989	0.89	1	0.989	0.89	1	CLONAL	1	TRUE	0	0.644660007156959	1		298	153	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285715	87285715	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	203	533	8	ENST00000277120.3:c.52T>C	p.Phe18Leu	p.F18L	ENST00000277120		18	Ttc/Ctc	2/19	1	2	FACETS	0.967	0.901	1	0.967	0.901	1	CLONAL	1	TRUE	1	0.644660007156959	2		541	651	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28963936	28963936	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs748105326	NA	P-0006584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	287	502	0	ENST00000282397.4:c.1966A>T	p.Arg656Ter	p.R656*	ENST00000282397	NM_002019.4	656	Aga/Tga	13/30	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.644660007156959	2		502	850	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578502	7578502	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006592-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	635	439	0	ENST00000269305.4:c.428T>C	p.Val143Ala	p.V143A	ENST00000269305	NM_001126112.2	143	gTg/gCg	5/11	0.876326756120693	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.876326756120693	1		439	766	SUCCESS
APC	324	MSKCC	GRCh37	5	112162804	112162804	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs863225313	NA	P-0006592-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	109	311	0	ENST00000257430.4:c.1409-1G>A		p.X470_splice	ENST00000257430	NM_000038.5	470			0.876326756120693	1	FACETS	0.822	0.765	0.877	0.822	0.765	0.877	CLONAL	1	TRUE	0	0.876326756120693	1		311	170	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569733	41569733	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs144547088	NA	P-0006592-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	349	491	0	ENST00000263253.7:c.4724A>G	p.Asn1575Ser	p.N1575S	ENST00000263253	NM_001429.3	1575	aAt/aGt	29/31	0.684745994538281	1	FACETS	0.397	0.376	0.419	0.397	0.376	0.419	SUBCLONAL	1	TRUE	0	0.876326756120693	1		491	1126	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0006631-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	92	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.256778499940667	1	FACETS	0.884	0.799	0.972	0.884	0.799	0.972	INDETERMINATE	1	TRUE	0	0.592777160359757	1		326	247	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849442	68849442	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006631-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	77	466	0	ENST00000261769.5:c.1345C>T	p.Gln449Ter	p.Q449*	ENST00000261769	NM_004360.3	449	Cag/Tag	10/16	0.592777160359757	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.592777160359757	1		466	153	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0006646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	58	197	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.538	0.462	0.62	0.538	0.462	0.62	SUBCLONAL	1	TRUE	1	0.398635527236582	2		197	541	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0006646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	90	463	0	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	NA	2	FACETS	0.653	0.58	0.732			1	INDETERMINATE	1	TRUE	NA	0.398635527236582	2		463	691	SUCCESS
APC	324	MSKCC	GRCh37	5	112170777	112170777	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876659517	NA	P-0006646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	89	586	2	ENST00000257430.4:c.1873C>T	p.Gln625Ter	p.Q625*	ENST00000257430	NM_000038.5	625	Cag/Tag	15/16	1	2	FACETS	0.585	0.518	0.657	0.585	0.518	0.657	SUBCLONAL	1	TRUE	1	0.398635527236582	2		588	763	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912200	114912200	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0006646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	125	609	0	ENST00000543371.1:c.1269+1G>A		p.X423_splice	ENST00000543371	NM_001198531.1	423			1	2	FACETS	0.56	0.506	0.618	0.56	0.506	0.618	SUBCLONAL	1	TRUE	1	0.398635527236582	2		609	1119	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015108	37015109	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	96	476	0	ENST00000358127.4:c.295dup	p.Ile99AsnfsTer3	p.I99Nfs*3	ENST00000358127	NM_001280556.1	99	atc/aAtc	3/10	1	2	FACETS	0.526	0.468	0.589	0.526	0.468	0.589	SUBCLONAL	1	TRUE	1	0.398635527236582	2		476	915	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0006681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	151	464	1	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.765372084677112	2		465	374	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129662	47129662	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057523157	NA	P-0006681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	324	635	1	ENST00000409792.3:c.5218C>T	p.Arg1740Trp	p.R1740W	ENST00000409792	NM_014159.6	1740	Cgg/Tgg	10/21	1	2	FACETS	0.881	0.834	0.929	0.881	0.834	0.929	CLONAL	1	TRUE	1	0.765372084677112	2		636	961	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007901	45007901	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0006681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	158	241	0	ENST00000558401.1:c.346+2T>C		p.X116_splice	ENST00000558401	NM_004048.2	116			0.765372084677112	1	FACETS	0.958	0.9	1	0.958	0.9	1	CLONAL	1	TRUE	0	0.765372084677112	1		241	266	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577125	7577133	+	inframe_deletion	In_Frame_Del	DEL	CTCAAAGCT	CTCAAAGCT	-	novel	NA	P-0006681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	312	587	0	ENST00000269305.4:c.805_813del	p.Ser269_Glu271del	p.S269_E271del	ENST00000269305	NM_001126112.2	269	AGCTTTGAG/-	8/11	0.765372084677112	1	FACETS	0.951	0.91	0.992	0.951	0.91	0.992	CLONAL	1	TRUE	0	0.765372084677112	1		587	529	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0006683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	15	306	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	0.382	0.278	0.508	0.382	0.278	0.508	SUBCLONAL	1	TRUE	1	0.17	2		306	462	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0006683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	21	197	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.1226176877869	3	FACETS	0.698	0.537	0.887	0.349	0.268	0.444	SUBCLONAL	1	TRUE	1	0.17	3		197	384	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0006683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	32	441	2	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.1226176877869	3	FACETS	0.751	0.608	0.913	0.375	0.304	0.457	CLONAL	1	TRUE	1	0.17	3		443	544	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679171	88679172	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CG	novel	NA	P-0006683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	24	465	0	ENST00000360948.2:c.864_865dup	p.Val289AlafsTer5	p.V289Afs*5	ENST00000360948	NM_001012338.2	289	gtg/gCGtg	8/19	1	2	FACETS	0.83	0.651	1	0.83	0.651	1	CLONAL	1	TRUE	1	0.17	2		465	340	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910830	114910830	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	69	679	0	ENST00000543371.1:c.950del	p.Pro317GlnfsTer34	p.P317Qfs*34	ENST00000543371	NM_001198531.1	317	Cca/ca	9/14	0.1226176877869	1	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	0	0.17	1		679	709	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578422	7578424	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	novel	NA	P-0006683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	43	323	2	ENST00000269305.4:c.506_508del	p.Met169del	p.M169del	ENST00000269305	NM_001126112.2	169	aTGAcg/acg	5/11	1	2	FACETS	0.79	0.664	0.929	1	0.961	1	CLONAL	2	TRUE	1	0.17	2		325	320	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0006685-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	233	471	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.21668413635456	2	FACETS	0.92	0.858	0.983	0.92	0.858	0.983	CLONAL	2	TRUE	0	0.260151058897726	2		471	974	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473722	67473722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs794727798	NA	P-0006685-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	184	450	1	ENST00000327367.4:c.802C>T	p.Arg268Cys	p.R268C	ENST00000327367	NM_005902.3	268	Cgc/Tgc	6/9	0.21668413635456	2	FACETS	0.837	0.773	0.903	0.837	0.773	0.903	CLONAL	2	TRUE	0	0.260151058897726	2		451	845	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0006685-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	68	274	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	1	2	FACETS	0.888	0.773	1	0.888	0.773	1	CLONAL	1	TRUE	1	0.260151058897726	2		274	589	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971367	13971367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755892534	NA	P-0006685-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	162	399	0	ENST00000405192.2:c.562C>T	p.Arg188Cys	p.R188C	ENST00000405192	NM_001163147.1	188	Cgc/Tgc	8/12	0.220666459526752	3	FACETS	0.766	0.702	0.832	0.766	0.702	0.832	SUBCLONAL	2	TRUE	1	0.260151058897726	3		399	919	SUCCESS
APC	324	MSKCC	GRCh37	5	112174982	112174983	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006685-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	81	326	0	ENST00000257430.4:c.3692dup	p.His1232ProfsTer8	p.H1232Pfs*8	ENST00000257430	NM_000038.5	1231	ctc/cTtc	16/16	1	2	FACETS	0.713	0.627	0.806	0.713	0.627	0.806	SUBCLONAL	1	TRUE	1	0.260151058897726	2		326	873	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0006698-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1974	232	627	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.482373979164257	9	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.482373979164257	9		627	2206	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589599	67589604	+	inframe_deletion	In_Frame_Del	DEL	TCAGTT	TCAGTT	-	novel	NA	P-0006698-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	235	367	0	ENST00000274335.5:c.1365_1370del	p.Phe456_Gln457del	p.F456_Q457del	ENST00000274335		454	acTCAGTTt/act	10/15	0.483946817096121	3	FACETS	0.875	0.821	0.931	0.875	0.821	0.931	CLONAL	2	TRUE	1	0.482373979164257	3		367	691	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127678	2127678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780981335	NA	P-0006698-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1432	211	583	0	ENST00000219476.3:c.2917G>A	p.Glu973Lys	p.E973K	ENST00000219476	NM_000548.3	973	Gag/Aag	26/42	0.482373979164257	5	FACETS	0.918	0.849	0.989	0.306	0.283	0.33	CLONAL	1	TRUE	2	0.482373979164257	5		583	1643	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678053	58678053	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1446153777	NA	P-0006698-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	185	379	0	ENST00000305921.3:c.278G>A	p.Arg93His	p.R93H	ENST00000305921	NM_003620.3	93	cGc/cAc	1/6	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.482373979164257	2		379	645	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579438	7579439	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0006698-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	432	345	1	ENST00000269305.4:c.248dup	p.Ala84GlyfsTer65	p.A84Gfs*65	ENST00000269305	NM_001126112.2	83	gcg/gcCg	4/11	0.483946817096121	3	FACETS	0.943	0.906	0.979	0.943	0.906	0.979	CLONAL	3	TRUE	0	0.482373979164257	3		346	786	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349052	89349052	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006698-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1348	340	803	0	ENST00000301030.4:c.3898del	p.Ile1300SerfsTer18	p.I1300Sfs*18	ENST00000301030	NM_001256183.1	1300	Atc/tc	9/13	0.483946817096121	3	FACETS	1	0.968	1	0.518	0.489	0.549	CLONAL	1	TRUE	1	0.482373979164257	3		803	1688	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591086	67591087	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0006698-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	135	325	0	ENST00000274335.5:c.1680dup	p.Lys561GlnfsTer7	p.K561Qfs*7	ENST00000274335		560	gac/gaCc	12/15	0.483946817096121	3	FACETS	1	0.939	1	0.519	0.473	0.568	CLONAL	1	TRUE	1	0.482373979164257	3		325	669	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740615	145740629	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGCCGGCGTCTCTG	CAGCCGGCGTCTCTG	-	novel	NA	P-0006698-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	190	412	0	ENST00000428558.2:c.1391-3_1402del		p.X464_splice	ENST00000428558	NM_004260.3	464		8/22	0.483946817096121	4	FACETS	0.996	0.919	1	0.332	0.306	0.359	CLONAL	1	TRUE	1	0.482373979164257	4		412	1173	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868313	45868314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGTGGGGCAGG	novel	NA	P-0006698-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	149	472	0	ENST00000391945.4:c.453_463dup	p.Cys155SerfsTer30	p.C155Sfs*30	ENST00000391945	NM_000400.3	155	tgc/tCCTGCCCCACTgc	6/23	0.23009416797767	6	FACETS	1	0.914	1			1	INDETERMINATE	1	TRUE	NA	0.482373979164257	6		472	1210	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873223	71873223	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	239	563	0	ENST00000357731.5:c.971G>C	p.Gly324Ala	p.G324A	ENST00000357731	NM_173808.2	324	gGg/gCg	7/7	1	2	FACETS	0.875	0.817	0.935	0.875	0.817	0.935	CLONAL	1	TRUE	1	0.506840866358509	2		563	1078	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145573	24145573	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	261	346	0	ENST00000263121.7:c.592C>T	p.Gln198Ter	p.Q198*	ENST00000263121	NM_003073.3	198	Cag/Tag	5/9	0.506840866358509	2	FACETS	0.913	0.864	0.962	0.913	0.864	0.962	CLONAL	2	TRUE	0	0.506840866358509	2		346	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0006862-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	19	499	2	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.245990670125905	4	FACETS	0.417	0.316	0.536	0.208	0.158	0.268	SUBCLONAL	1	FALSE	2	0.388160173318065	4		501	326	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0006862-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	70	582	2	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	1	2	FACETS	0.476	0.414	0.543	0.476	0.414	0.543	SUBCLONAL	1	FALSE	1	0.388160173318065	2		584	758	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268766	41268766	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006999-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	153	626	2	ENST00000349496.5:c.1004A>T	p.Lys335Ile	p.K335I	ENST00000349496	NM_001904.3	335	aAa/aTa	7/15	0.498699720238863	4	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	2	0.529631839737496	4		628	419	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0006999-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	81	279	1	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	0.529631839737496	3	FACETS	0.982	0.884	1	0.655	0.589	0.721	CLONAL	2	TRUE	0	0.529631839737496	3		280	197	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579592	7579592	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0006999-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	68	312	0	ENST00000269305.4:c.97-2A>T		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.36408735652772	3	FACETS	1	0.968	1	0.808	0.727	0.889	CLONAL	2	TRUE	0	0.529631839737496	3		312	134	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522452	157522452	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006999-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	20	521	0	ENST00000346085.5:c.4724T>C	p.Leu1575Pro	p.L1575P	ENST00000346085	NM_020732.3	1575	cTg/cCg	18/20	0.529631839737496	3	FACETS	0.257	0.196	0.328	0.128	0.098	0.164	SUBCLONAL	1	TRUE	1	0.529631839737496	3		521	372	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128603	30128604	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	AT	AT	TG	novel	NA	P-0006999-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	87	683	0	ENST00000263025.4:c.778_779delinsCA	p.Ile260His	p.I260H	ENST00000263025	NM_002746.2	260	ATc/CAc	6/9	0.423334346559186	3	FACETS	0.896	0.796	1	0.448	0.398	0.501	CLONAL	1	TRUE	1	0.529631839737496	3		683	464	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572261	64572261	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs104894267	NA	P-0007076-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	651	547	0	ENST00000312049.6:c.1378C>T	p.Arg460Ter	p.R460*	ENST00000312049	NM_130799.2	460	Cga/Tga	10/10	0.884145423796598	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.884145423796598	1		547	783	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12647769	12647769	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs756643623	NA	P-0007076-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	165	598	0	ENST00000251849.4:c.611G>C	p.Ser204Thr	p.S204T	ENST00000251849	NM_002880.3	204	aGt/aCt	6/17	0.884145423796598	1	FACETS	0.231	0.212	0.251	0.231	0.212	0.251	SUBCLONAL	1	TRUE	0	0.884145423796598	1		598	900	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288602	33288602	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007076-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	336	239	0	ENST00000374542.5:c.950T>C	p.Phe317Ser	p.F317S	ENST00000374542	NM_001141970.1	317	tTc/tCc	3/8	0.884145423796598	1	FACETS	0.936	0.904	0.967	0.936	0.904	0.967	CLONAL	1	TRUE	0	0.884145423796598	1		239	453	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685281	89685281	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007076-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	701	302	0	ENST00000371953.3:c.176C>A	p.Ser59Ter	p.S59*	ENST00000371953	NM_000314.4	59	tCa/tAa	3/9	0.882556306207974	1	FACETS	0.971	0.95	0.992	0.971	0.95	0.992	CLONAL	1	TRUE	0	0.884145423796598	1		302	911	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025944	1025944	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs554221618	NA	P-0007076-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	241	627	0	ENST00000358495.3:c.586C>G	p.Leu196Val	p.L196V	ENST00000358495	NM_134424.2	196	Ctt/Gtt	8/12	NA	2	FACETS	0.422	0.393	0.451			1	INDETERMINATE	1	TRUE	NA	0.884145423796598	2		627	1293	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687601	29687601	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007076-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1533	184	526	0	ENST00000356175.3:c.8194G>T	p.Glu2732Ter	p.E2732*	ENST00000356175	NM_000267.3	2732	Gaa/Taa	56/57	1	2	FACETS	0.242	0.223	0.263	0.242	0.223	0.263	SUBCLONAL	1	TRUE	1	0.884145423796598	2		526	1717	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222107	2222107	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007076-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	90	450	0	ENST00000398665.3:c.2939C>A	p.Ser980Tyr	p.S980Y	ENST00000398665	NM_032482.2	980	tCc/tAc	24/28	0.389583713071933	1	FACETS	0.129	0.114	0.146	0.129	0.114	0.146	INDETERMINATE	1	TRUE	0	0.884145423796598	1		450	878	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577144	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs879253942	NA	P-0007078-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	328	910	0	ENST00000269305.4:c.794T>C	p.Leu265Pro	p.L265P	ENST00000269305	NM_001126112.2	265	cTg/cCg	8/11	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.318361755690176	2		910	1560	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745617	162745617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759124429	NA	P-0007078-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1337	280	760	2	ENST00000367921.3:c.2032G>A	p.Asp678Asn	p.D678N	ENST00000367921	NM_006182.2	678	Gat/Aat	15/18	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.318361755690176	2		762	1617	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	266	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.294465625521823	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.294465625521823	3		371	1015	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0007079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	122	252	2	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.925	0.835	1	0.925	0.835	1	CLONAL	1	TRUE	1	0.294465625521823	2		254	896	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0007079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	70	427	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.294465625521823	3	FACETS	0.942	0.822	1	0.471	0.411	0.536	CLONAL	1	TRUE	1	0.294465625521823	3		427	579	SUCCESS
EED	8726	MSKCC	GRCh37	11	85961399	85961399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1343373792	NA	P-0007079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	144	612	0	ENST00000263360.6:c.176C>T	p.Thr59Met	p.T59M	ENST00000263360	NM_003797.3	59	aCg/aTg	2/12	1	2	FACETS	0.845	0.769	0.925	0.845	0.769	0.925	CLONAL	1	TRUE	1	0.294465625521823	2		612	1158	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795187	42795187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377759151	NA	P-0007079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	153	532	0	ENST00000575354.2:c.2267C>T	p.Ala756Val	p.A756V	ENST00000575354	NM_015125.3	756	gCg/gTg	10/20	0.294465625521823	3	FACETS	1	0.986	1	0.7	0.64	0.762	CLONAL	1	TRUE	1	0.294465625521823	3		532	852	SUCCESS
APC	324	MSKCC	GRCh37	5	112175424	112175425	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0007079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	104	382	0	ENST00000257430.4:c.4135dup	p.Glu1379GlyfsTer7	p.E1379Gfs*7	ENST00000257430	NM_000038.5	1378	cag/caGg	16/16	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.294465625521823	2		382	704	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177023	56177023	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	111	370	0	ENST00000399503.3:c.2293T>A	p.Leu765Met	p.L765M	ENST00000399503	NM_005921.1	765	Ttg/Atg	13/20	1	2	FACETS	0.96	0.863	1	0.96	0.863	1	CLONAL	1	TRUE	1	0.294465625521823	2		370	785	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0007080-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	1093	780	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.711731288595726	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.722735329941671	2		780	1465	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007080-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	599	538	0	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	0.271165674452302	2	FACETS	1	0.997	1	0.673	0.649	0.696	INDETERMINATE	1	TRUE	0	0.722735329941671	2		538	1232	SUCCESS
APC	324	MSKCC	GRCh37	5	112154963	112154963	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660802	NA	P-0007080-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	484	398	0	ENST00000257430.4:c.1234C>T	p.Gln412Ter	p.Q412*	ENST00000257430	NM_000038.5	412	Cag/Tag	10/16	0.314417804219246	1	FACETS	0.669	0.64	0.698	0.669	0.64	0.698	INDETERMINATE	1	TRUE	0	0.722735329941671	1		398	1279	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972992	25972992	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007080-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	123	424	1	ENST00000435504.4:c.1433T>A	p.Leu478His	p.L478H	ENST00000435504		478	cTt/cAt	12/13	0.262232875150702	3	FACETS	0.376	0.338	0.415	0.125	0.112	0.139	INDETERMINATE	1	TRUE	0	0.722735329941671	3		425	1234	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429386	47429386	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007080-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	128	477	0	ENST00000377045.4:c.1514G>C	p.Gly505Ala	p.G505A	ENST00000377045	NM_001654.4	505	gGc/gCc	14/16	0.555093609164069	1	FACETS	0.214	0.193	0.236	0.214	0.193	0.236	SUBCLONAL	1	TRUE	0	0.722735329941671	1		477	1058	SUCCESS
APC	324	MSKCC	GRCh37	5	112174834	112174834	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007080-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	321	473	0	ENST00000257430.4:c.3546del	p.Lys1182AsnfsTer83	p.K1182Nfs*83	ENST00000257430	NM_000038.5	1181	ttA/tt	16/16	1	2	FACETS	0.787	0.743	0.832	0.787	0.743	0.832	SUBCLONAL	1	TRUE	1	0.722735329941671	2		473	1129	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144589	55144589	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007080-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	142	465	0	ENST00000257290.5:c.2063A>C	p.Lys688Thr	p.K688T	ENST00000257290	NM_006206.4	688	aAg/aCg	15/23	0.247684944628915	1	FACETS	0.214	0.194	0.235	0.214	0.194	0.235	INDETERMINATE	1	TRUE	0	0.722735329941671	1		465	1171	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs11575997	NA	P-0007081-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	471	655	0	ENST00000269305.4:c.993+1G>T		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.507782014237184	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.507782014237184	2		655	820	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482242	87482242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007081-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	447	641	0	ENST00000277120.3:c.1529C>T	p.Ser510Leu	p.S510L	ENST00000277120		510	tCg/tTg	14/19	0.507782014237184	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.507782014237184	3		641	1026	SUCCESS
APC	324	MSKCC	GRCh37	5	112175389	112175390	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGACAC	novel	NA	P-0007081-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	147	424	0	ENST00000257430.4:c.4100_4106dup	p.Lys1370AspfsTer7	p.K1370Dfs*7	ENST00000257430	NM_000038.5	1366	-/CAGACAC	16/16	0.507782014237184	3	FACETS	0.996	0.911	1	0.498	0.455	0.543	CLONAL	1	TRUE	1	0.507782014237184	3		424	729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0007084-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	47	953	10	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.32151897588823	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.419735183967334	1		963	159	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0007084-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	55	573	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.419735183967334	1		573	144	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241726	55241726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767505234	NA	P-0007084-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	105	226	0	ENST00000275493.2:c.2174C>T	p.Thr725Met	p.T725M	ENST00000275493	NM_005228.3	725	aCg/aTg	18/28	0.419735183967334	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.419735183967334	3		226	260	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0007084-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	86	578	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.419735183967334	2		578	399	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715625	30715625	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007084-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	49	276	0	ENST00000295754.5:c.1283A>G	p.Glu428Gly	p.E428G	ENST00000295754	NM_003242.5	428	gAa/gGa	5/7	0.387990477428516	3	FACETS	0.757	0.643	0.882	0.379	0.321	0.441	SUBCLONAL	1	TRUE	1	0.419735183967334	3		276	373	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55087007	55087007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007084-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	75	190	0	ENST00000275493.2:c.37G>A	p.Ala13Thr	p.A13T	ENST00000275493	NM_005228.3	13	Gcg/Acg	1/28	0.419735183967334	3	FACETS	0.918	0.828	1	1	0.978	1	CLONAL	3	TRUE	1	0.419735183967334	3		190	157	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274934	38274934	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs774678297	NA	P-0007084-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	30	324	0	ENST00000425967.3:c.1646C>T	p.Ser549Leu	p.S549L	ENST00000425967	NM_001174067.1	549	tCg/tTg	13/19	0.362729471144396	1	FACETS	0.511	0.414	0.619	0.511	0.414	0.619	SUBCLONAL	1	TRUE	0	0.419735183967334	1		324	221	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905325	50905325	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007084-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	39	372	1	ENST00000440232.2:c.533G>T	p.Gly178Val	p.G178V	ENST00000440232	NM_002691.3	178	gGg/gTg	5/27	1	2	FACETS	0.963	0.807	1	0.963	0.807	1	CLONAL	1	TRUE	1	0.419735183967334	2		373	193	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560491	65560496	+	inframe_deletion	In_Frame_Del	DEL	TACGTT	TACGTT	-	novel	NA	P-0007084-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	72	344	0	ENST00000358664.4:c.101_106del	p.Lys34_Arg35del	p.K34_R35del	ENST00000358664	NM_002382.4	34	aAACGTAgg/agg	3/5	0.288511999035774	2	FACETS	1	0.966	1	0.635	0.561	0.713	CLONAL	1	TRUE	0	0.419735183967334	2		344	270	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0007085-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	302	252	2	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.408672649162945	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.448937166480844	1		254	1008	SUCCESS
APC	324	MSKCC	GRCh37	5	112175749	112175750	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007085-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	58	282	0	ENST00000257430.4:c.4459dup	p.Thr1487AsnfsTer27	p.T1487Nfs*27	ENST00000257430	NM_000038.5	1486	-/A	16/16	0.408672649162945	1	FACETS	0.223	0.191	0.259	0.223	0.191	0.259	SUBCLONAL	1	TRUE	0	0.448937166480844	1		282	897	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056053	26056067	+	inframe_deletion	In_Frame_Del	DEL	CCTTGGGCTTAGCGG	CCTTGGGCTTAGCGG	-	rs756916945	NA	P-0007085-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	231	168	0	ENST00000343677.2:c.590_604del	p.Ala197_Lys201del	p.A197_K201del	ENST00000343677	NM_005319.3	197	gCCGCTAAGCCCAAGGtt/gtt	1/1	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.448937166480844	2		168	894	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578463	7578463	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371524413	NA	P-0007085-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	227	245	0	ENST00000269305.4:c.467G>C	p.Arg156Pro	p.R156P	ENST00000269305	NM_001126112.2	156	cGc/cCc	5/11	0.448937166480844	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.448937166480844	1		245	719	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325831	30325831	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007085-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	329	345	0	ENST00000322652.5:c.2029G>C	p.Ala677Pro	p.A677P	ENST00000322652	NM_015355.2	677	Gct/Cct	16/16	0.251181713927283	2	FACETS	1	0.976	1	0.531	0.501	0.562	INDETERMINATE	1	TRUE	0	0.448937166480844	2		345	1379	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027006	71027007	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0007085-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	117	198	0	ENST00000318789.4:c.1320dup	p.Asp441ArgfsTer20	p.D441Rfs*20	ENST00000318789	NM_032682.5	440	-/A	15/21	1	2	FACETS	0.66	0.595	0.728	0.66	0.595	0.728	SUBCLONAL	1	TRUE	1	0.448937166480844	2		198	790	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0007088-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	240	541	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.219217177086751	5	FACETS	0.842	0.787	0.898	0.561	0.524	0.599	INDETERMINATE	2	TRUE	2	0.544812932391967	5		542	951	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0007088-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	396	264	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.219217177086751	5	FACETS	0.913	0.871	0.955	0.913	0.871	0.955	INDETERMINATE	3	TRUE	2	0.544812932391967	5		264	965	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691039	NA	P-0007088-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	178	736	0	ENST00000269305.4:c.919+1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.544812932391967	1	FACETS	0.909	0.844	0.975	0.909	0.844	0.975	CLONAL	1	TRUE	0	0.544812932391967	1		736	523	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241672	55241672	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007088-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	454	294	0	ENST00000275493.2:c.2120T>G	p.Leu707Trp	p.L707W	ENST00000275493	NM_005228.3	707	tTg/tGg	18/28	0.219217177086751	5	FACETS	0.901	0.862	0.94	0.901	0.862	0.94	INDETERMINATE	3	TRUE	2	0.544812932391967	5		294	1121	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154357	2154357	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1459983752	NA	P-0007088-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	430	301	0	ENST00000434045.2:c.571C>T	p.Arg191Cys	p.R191C	ENST00000434045	NM_001127598.1	191	Cgt/Tgt	5/5	0.531599062591619	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.544812932391967	2		301	722	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057936	27057937	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1415146710	NA	P-0007089-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	77	304	0	ENST00000324856.7:c.1650dup	p.Tyr551LeufsTer72	p.Y551Lfs*72	ENST00000324856	NM_006015.4	548	-/C	3/20	0.659951986491668	2	FACETS	1	0.898	1	0.503	0.449	0.56	CLONAL	1	TRUE	0	0.665476318815185	2		304	230	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115888	8115889	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0007089-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	161	480	0	ENST00000346208.3:c.1236dup	p.Ser413GlnfsTer94	p.S413Qfs*94	ENST00000346208		412	tcc/tCcc	6/6	0.38881608090609	6	FACETS	1	0.984	1	0.824	0.763	0.887	INDETERMINATE	2	TRUE	3	0.665476318815185	6		480	456	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367867	15367867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1454979767	NA	P-0007089-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	135	347	1	ENST00000263377.2:c.1459G>A	p.Asp487Asn	p.D487N	ENST00000263377	NM_058243.2	487	Gac/Aac	8/20	0.659951986491668	2	FACETS	0.906	0.847	0.963	0.906	0.847	0.963	CLONAL	2	TRUE	0	0.665476318815185	2		348	224	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739958	41739958	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007089-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	104	525	0	ENST00000242208.4:c.15G>C	p.Trp5Cys	p.W5C	ENST00000242208	NM_002192.2	5	tgG/tgC	2/3	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.665476318815185	2		525	294	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244722	46244722	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007089-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	231	542	0	ENST00000334344.6:c.2816A>C	p.Tyr939Ser	p.Y939S	ENST00000334344	NM_152641.2	939	tAt/tCt	15/21	0.386698515561456	4	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.665476318815185	4		542	465	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0007090-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	179	326	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.29924943636517	6	FACETS	0.767	0.706	0.83	0.383	0.353	0.415	SUBCLONAL	2	TRUE	2	0.38	6		326	1081	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0007090-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	117	427	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.202446986877044	5	FACETS	1	0.981	1	0.455	0.41	0.501	INDETERMINATE	1	TRUE	2	0.38	5		427	709	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0007090-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	127	822	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.183755444187516	2	FACETS	1	0.982	1	0.666	0.606	0.728	INDETERMINATE	1	TRUE	0	0.38	2		822	502	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0007090-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	78	939	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.516	0.453	0.585	0.516	0.453	0.585	SUBCLONAL	1	TRUE	1	0.38	2		939	795	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0007090-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	57	294	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.519	0.445	0.6	0.519	0.445	0.6	SUBCLONAL	1	TRUE	1	0.38	2		294	578	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272496	11272496	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007156-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	22	561	1	ENST00000361445.4:c.3434C>T	p.Ser1145Phe	p.S1145F	ENST00000361445	NM_004958.3	1145	tCc/tTc	23/58	0.23915941453777	3	FACETS	1	0.896	1	0.64	0.5	0.799	CLONAL	1	TRUE	1	0.23915941453777	3		562	161	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937537	76937537	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143621153	NA	P-0007156-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	13	451	0	ENST00000373344.5:c.3211G>A	p.Gly1071Arg	p.G1071R	ENST00000373344	NM_000489.3	1071	Gga/Aga	9/35	1	1	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	0	0.23915941453777	1		451	69	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661035	227661035	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007289-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	32	183	0	ENST00000305123.5:c.2420C>A	p.Ser807Tyr	p.S807Y	ENST00000305123	NM_005544.2	807	tCt/tAt	1/2	0.677927597961298	3	FACETS	0.389	0.317	0.47			1	SUBCLONAL	1	TRUE	NA	0.780322163822672	3		183	293	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775219	73775219	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007289-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1162	247	454	0	ENST00000254810.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000254810	NM_005324.3	13	Ggt/Cgt	2/4	0.780322163822672	5	FACETS	0.975	0.91	1	0.325	0.303	0.348	CLONAL	1	TRUE	2	0.780322163822672	5		454	1409	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30954226	30954226	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1192808397	NA	P-0007289-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	129	333	0	ENST00000375687.4:c.97C>G	p.Gln33Glu	p.Q33E	ENST00000375687	NM_015338.5	33	Cag/Gag	2/13	0.780322163822672	3	FACETS	0.694	0.631	0.761	0.347	0.315	0.381	SUBCLONAL	1	TRUE	1	0.780322163822672	3		333	662	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576926	7576947	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTAGGAAAGAGGCAAGGAAAG	GCTAGGAAAGAGGCAAGGAAAG	-	novel	NA	P-0007289-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	229	274	0	ENST00000269305.4:c.920-21_920del		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	0.780322163822672	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.780322163822672	2		274	274	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186507000	186507001	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GACTTTCT	novel	NA	P-0007289-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	194	527	0	ENST00000323963.5:c.1167_1174dup	p.Tyr392Ter	p.Y392*	ENST00000323963		389	gag/gaGACTTTCTg	11/11	0.780322163822672	4	FACETS	0.626	0.577	0.677			1	SUBCLONAL	1	TRUE	NA	0.780322163822672	4		527	1414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0007294-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	217	478	5	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.425298534484736	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.426477676398098	2		483	488	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0007294-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	259	294	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.381567615987818	2	FACETS	0.841	0.792	0.891	0.841	0.792	0.891	CLONAL	2	TRUE	0	0.426477676398098	2		294	722	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0007294-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	212	482	1	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.426477676398098	2		483	864	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680531	241680531	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007294-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	225	491	0	ENST00000366560.3:c.218T>C	p.Val73Ala	p.V73A	ENST00000366560	NM_000143.3	73	gTg/gCg	2/10	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.426477676398098	2		491	1017	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523486	106523486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750632554	NA	P-0007294-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	129	345	0	ENST00000359195.3:c.2638G>A	p.Glu880Lys	p.E880K	ENST00000359195	NM_002649.2	880	Gag/Aag	8/11	0.422496188574983	3	FACETS	0.861	0.781	0.946	0.431	0.39	0.473	CLONAL	1	TRUE	1	0.426477676398098	3		345	852	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120450	70120451	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0007294-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	405	727	0	ENST00000245479.2:c.1456dup	p.Val486GlyfsTer92	p.V486Gfs*92	ENST00000245479	NM_000346.3	484	-/G	3/3	0.426477676398098	2	FACETS	0.934	0.891	0.977	0.934	0.891	0.977	CLONAL	2	TRUE	0	0.426477676398098	2		727	1017	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045918	180045920	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CTC	CTC	-	rs746341092	NA	P-0007297-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	48	220	0	ENST00000261937.6:c.2851_2853del	p.Glu951del	p.E951del	ENST00000261937	NM_182925.4	951	GAG/-	21/30	1	2	FACETS	0.896	0.759	1	0.896	0.759	1	CLONAL	1	FALSE	1	0.254360555348266	2		220	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574002	7574002	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs375338359	NA	P-0007297-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	206	574	0	ENST00000269305.4:c.1025G>C	p.Arg342Pro	p.R342P	ENST00000269305	NM_001126112.2	342	cGa/cCa	10/11	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	FALSE	NA	0.254360555348266	2		574	1118	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106049	27106049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756198362	NA	P-0007297-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	48	280	0	ENST00000324856.7:c.5660G>A	p.Gly1887Asp	p.G1887D	ENST00000324856	NM_006015.4	1887	gGt/gAt	20/20	1	2	FACETS	0.608	0.513	0.712	0.608	0.513	0.712	SUBCLONAL	1	FALSE	1	0.254360555348266	2		280	621	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436717	110436717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007297-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	59	520	0	ENST00000375856.3:c.1684G>A	p.Asp562Asn	p.D562N	ENST00000375856	NM_003749.2	562	Gac/Aac	1/2	0.171874337658417	3	FACETS	0.557	0.478	0.645	0.279	0.239	0.323	SUBCLONAL	1	FALSE	1	0.254360555348266	3		520	938	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946443	2946445	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0007297-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	55	580	0	ENST00000396946.4:c.3292_3294del	p.Glu1098del	p.E1098del	ENST00000396946	NM_032415.4	1098	GAG/-	25/25	1	2	FACETS	0.433	0.369	0.503	0.433	0.369	0.503	SUBCLONAL	1	FALSE	1	0.254360555348266	2		580	999	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	76	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.9	0.788	1	0.9	0.788	1	CLONAL	1	TRUE	1	0.17	2		371	993	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0007300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	93	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.146040462649163	3	FACETS	0.984	0.873	1	0.492	0.436	0.552	CLONAL	1	TRUE	1	0.17	3		326	1206	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440757	56440757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774211426	NA	P-0007300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	44	428	0	ENST00000407977.2:c.461C>T	p.Pro154Leu	p.P154L	ENST00000407977		154	cCg/cTg	5/10	1	2	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	TRUE	1	0.17	2		428	506	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0007300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	91	343	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.17	2		343	1018	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251912	153251912	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	94	523	0	ENST00000281708.4:c.1094G>A	p.Trp365Ter	p.W365*	ENST00000281708	NM_033632.3	365	tGg/tAg	7/12	1	2	FACETS	0.806	0.718	0.901	0.806	0.718	0.901	CLONAL	1	TRUE	1	0.319780626925503	2		523	729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577560	7577568	+	inframe_deletion	In_Frame_Del	DEL	AACTGTTAC	AACTGTTAC	-	novel	NA	P-0007334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	84	440	0	ENST00000269305.4:c.713_721del	p.Cys238_Ser240del	p.C238_S240del	ENST00000269305	NM_001126112.2	238	tGTAACAGTTcc/tcc	7/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.319780626925503	2		440	421	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589617	67589628	+	inframe_deletion	In_Frame_Del	DEL	TCGAGAATATGA	TCGAGAATATGA	-	novel	NA	P-0007334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	56	366	0	ENST00000274335.5:c.1381_1392del	p.Glu462_Arg465del	p.E462_R465del	ENST00000274335		460	agTCGAGAATATGAt/agt	10/15	0.310620055899782	2	FACETS	0.655	0.561	0.757	0.327	0.28	0.379	SUBCLONAL	1	TRUE	0	0.319780626925503	2		366	535	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958231	11958231	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	40	206	0	ENST00000353533.5:c.144del	p.Phe48LeufsTer14	p.F48Lfs*14	ENST00000353533	NM_003010.3	47	aaT/aa	2/11	1	2	FACETS	0.86	0.718	1	0.86	0.718	1	CLONAL	1	TRUE	1	0.319780626925503	2		206	291	SUCCESS
APC	324	MSKCC	GRCh37	5	112154967	112154968	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs879254088	NA	P-0007334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	222	494	0	ENST00000257430.4:c.1239dup	p.Arg414ThrfsTer5	p.R414Tfs*5	ENST00000257430	NM_000038.5	413	ata/atAa	10/16	0.310620055899782	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.319780626925503	2		494	663	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0007368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	85	378	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.933	0.826	1	0.933	0.826	1	CLONAL	1	TRUE	1	0.31	2		379	588	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0007368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	61	263	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.996	0.863	1	0.996	0.863	1	CLONAL	1	TRUE	1	0.31	2		263	395	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0007368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	95	350	1	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.81	0.721	0.905	0.81	0.721	0.905	CLONAL	1	TRUE	1	0.31	2		351	757	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519456	176519456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752008617	NA	P-0007368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	92	602	0	ENST00000292408.4:c.862G>A	p.Val288Ile	p.V288I	ENST00000292408	NM_213647.1	288	Gtc/Atc	7/18	1	2	FACETS	0.906	0.806	1	0.906	0.806	1	CLONAL	1	TRUE	1	0.31	2		602	655	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037445	12037445	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	182	497	0	ENST00000396373.4:c.1076G>T	p.Arg359Leu	p.R359L	ENST00000396373	NM_001987.4	359	cGa/cTa	6/8	0.289051374870083	3	FACETS	0.934	0.864	1	0.934	0.864	1	CLONAL	2	TRUE	1	0.31	3		497	726	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	87	477	0	ENST00000257430.4:c.4285del	p.Gln1429LysfsTer44	p.Q1429Kfs*44	ENST00000257430	NM_000038.5	1429	Caa/aa	16/16	1	2	FACETS	0.898	0.796	1	0.898	0.796	1	CLONAL	1	TRUE	1	0.31	2		477	625	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120114	70120115	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0007368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	24	65	0	ENST00000245479.2:c.1120_1121dup	p.Gln375ArgfsTer9	p.Q375Rfs*9	ENST00000245479	NM_000346.3	372	-/CC	3/3	0.289227614458642	4	FACETS	1	0.844	1	0.78	0.635	0.933	CLONAL	3	TRUE	0	0.31	4		65	65	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0007373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	92	758	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.279376794675752	2	FACETS	1	0.951	1	0.549	0.493	0.607	INDETERMINATE	1	TRUE	0	0.539083753453522	2		759	311	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0007373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	130	452	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.269400112953654	3	FACETS	1	0.95	1	0.532	0.484	0.581	INDETERMINATE	1	TRUE	1	0.539083753453522	3		452	576	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467500	66467500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757521167	NA	P-0007373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	157	477	1	ENST00000273854.3:c.769G>A	p.Glu257Lys	p.E257K	ENST00000273854	NM_004439.5	257	Gaa/Aaa	3/18	0.269400112953654	3	FACETS	1	0.981	1	0.606	0.557	0.657	INDETERMINATE	1	TRUE	1	0.539083753453522	3		478	610	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245945	46245945	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	113	425	0	ENST00000334344.6:c.4039C>A	p.Gln1347Lys	p.Q1347K	ENST00000334344	NM_152641.2	1347	Caa/Aaa	15/21	0.252485669957624	3	FACETS	1	0.968	1	0.58	0.525	0.637	INDETERMINATE	1	TRUE	1	0.539083753453522	3		425	459	SUCCESS
AR	367	MSKCC	GRCh37	X	66765736	66765736	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	90	372	0	ENST00000374690.3:c.748G>T	p.Gly250Cys	p.G250C	ENST00000374690	NM_000044.3	250	Ggt/Tgt	1/8	0.428710969895136	2	FACETS	0.872	0.779	0.969			1	CLONAL	1	TRUE	NA	0.539083753453522	2		372	383	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0007377-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	452	371	0	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	0.858670649490593	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.858670649490593	2		371	501	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925316	114925317	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs745872748	NA	P-0007377-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	753	718	19	ENST00000543371.1:c.1403dup	p.Cys469ValfsTer8	p.C469Vfs*8	ENST00000543371	NM_001198531.1	465	aga/agAa	14/14	0.858670649490593	2	FACETS	0.867	0.848	0.886	0.867	0.848	0.886	CLONAL	2	TRUE	0	0.858670649490593	2		737	1011	SUCCESS
APC	324	MSKCC	GRCh37	5	112175756	112175756	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007377-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	215	386	1	ENST00000257430.4:c.4466del	p.Leu1489TyrfsTer18	p.L1489Yfs*18	ENST00000257430	NM_000038.5	1489	Tta/ta	16/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.858670649490593	2		387	445	SUCCESS
APC	324	MSKCC	GRCh37	5	112155031	112155032	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007377-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	197	373	0	ENST00000257430.4:c.1307dup	p.Asn436LysfsTer8	p.N436Kfs*8	ENST00000257430	NM_000038.5	434	-/A	10/16	1	2	FACETS	0.935	0.874	0.996	0.935	0.874	0.996	CLONAL	1	TRUE	1	0.858670649490593	2		373	491	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445008	89445008	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007377-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	265	476	1	ENST00000336596.2:c.1328T>C	p.Ile443Thr	p.I443T	ENST00000336596	NM_005233.5	443	aTt/aCt	6/17	0.739872622586532	3	FACETS	1	0.972	1	0.528	0.496	0.56	CLONAL	1	TRUE	1	0.858670649490593	3		477	836	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350071	81350071	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007377-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	286	594	0	ENST00000222390.5:c.1261G>T	p.Asp421Tyr	p.D421Y	ENST00000222390	NM_000601.4	421	Gac/Tac	10/18	0.818865873441252	4	FACETS	0.869	0.816	0.925	0.435	0.408	0.463	CLONAL	1	TRUE	2	0.858670649490593	4		594	1424	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589692	69589692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs924238902	NA	P-0007377-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	88	219	0	ENST00000168712.1:c.161C>T	p.Ser54Leu	p.S54L	ENST00000168712	NM_002007.2	54	tCg/tTg	1/3	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.858670649490593	2		219	201	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835687	68835687	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007377-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	377	745	1	ENST00000261769.5:c.278A>G	p.Asn93Ser	p.N93S	ENST00000261769	NM_004360.3	93	aAc/aGc	3/16	0.858670649490593	3	FACETS	0.942	0.893	0.991	0.471	0.446	0.496	CLONAL	1	TRUE	1	0.858670649490593	3		746	1333	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950432	17950432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749143191	NA	P-0007377-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	238	391	0	ENST00000458235.1:c.1295G>A	p.Arg432His	p.R432H	ENST00000458235	NM_000215.3	432	cGc/cAc	10/24	0.858670649490593	3	FACETS	1	0.988	1	0.598	0.562	0.636	CLONAL	1	TRUE	1	0.858670649490593	3		391	662	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31020700	31020700	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007377-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	215	410	1	ENST00000375687.4:c.997A>T	p.Met333Leu	p.M333L	ENST00000375687	NM_015338.5	333	Atg/Ttg	11/13	0.858670649490593	6	FACETS	0.99	0.918	1	0.248	0.229	0.267	CLONAL	1	TRUE	2	0.858670649490593	6		411	1374	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	67	236	0				ENST00000310581	NM_198253.2	-/1132			0.143374447790166	1	FACETS	0.817	0.727	0.909	0.817	0.727	0.909	INDETERMINATE	1	TRUE	0	0.666747219392555	1		236	164	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259601	89259601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773846066	NA	P-0007397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	128	154	0	ENST00000336596.2:c.745G>A	p.Glu249Lys	p.E249K	ENST00000336596	NM_005233.5	249	Gaa/Aaa	3/17	0.666747219392555	3	FACETS	1	0.974	1			1	CLONAL	1	TRUE	NA	0.666747219392555	3		154	436	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589663	67589663	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs587777709	NA	P-0007397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	143	133	0	ENST00000274335.5:c.1425+1G>C		p.X475_splice	ENST00000274335		475			0.110727962948341	4	FACETS	0.837	0.77	0.906	0.837	0.77	0.906	INDETERMINATE	2	TRUE	2	0.666747219392555	4		133	427	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692977	89692977	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	224	224	0	ENST00000371953.3:c.461T>G	p.Phe154Cys	p.F154C	ENST00000371953	NM_000314.4	154	tTc/tGc	5/9	0.666747219392555	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.666747219392555	1		224	392	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28903809	28903809	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	34	396	0	ENST00000282397.4:c.2650C>A	p.His884Asn	p.H884N	ENST00000282397	NM_002019.4	884	Cac/Aac	19/30	0.666747219392555	1	FACETS	0.198	0.161	0.238	0.198	0.161	0.238	SUBCLONAL	1	TRUE	0	0.666747219392555	1		396	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0007483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	62	758	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.644	0.556	0.74	0.644	0.556	0.74	SUBCLONAL	1	FALSE	1	0.314597910909362	2		759	612	SUCCESS
APC	324	MSKCC	GRCh37	5	112175621	112175621	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	126	319	1	ENST00000257430.4:c.4330C>T	p.Gln1444Ter	p.Q1444*	ENST00000257430	NM_000038.5	1444	Caa/Taa	16/16	1	2	FACETS	0.76	0.687	0.837	0.76	0.687	0.837	SUBCLONAL	1	FALSE	1	0.314597910909362	2		320	1054	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259328	11259328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	81	225	0	ENST00000361445.4:c.4240G>A	p.Glu1414Lys	p.E1414K	ENST00000361445	NM_004958.3	1414	Gaa/Aaa	28/58	1	2	FACETS	0.578	0.508	0.653	0.578	0.508	0.653	SUBCLONAL	1	FALSE	1	0.314597910909362	2		225	891	SUCCESS
APC	324	MSKCC	GRCh37	5	112175449	112175449	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	58	163	0	ENST00000257430.4:c.4158A>T	p.Arg1386Ser	p.R1386S	ENST00000257430	NM_000038.5	1386	agA/agT	16/16	1	2	FACETS	0.607	0.522	0.701	0.607	0.522	0.701	SUBCLONAL	1	FALSE	1	0.314597910909362	2		163	607	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845262	151845262	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747850540	NA	P-0007483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	48	139	0	ENST00000262189.6:c.13750C>T	p.Arg4584Trp	p.R4584W	ENST00000262189	NM_170606.2	4584	Cgg/Tgg	52/59	0.223064776285903	3	FACETS	0.634	0.536	0.743	0.317	0.268	0.372	SUBCLONAL	1	FALSE	1	0.314597910909362	3		139	557	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401342	139401342	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	64	190	0	ENST00000277541.6:c.3727A>G	p.Thr1243Ala	p.T1243A	ENST00000277541	NM_017617.3	1243	Acc/Gcc	23/34	1	2	FACETS	0.651	0.563	0.746	0.651	0.563	0.746	SUBCLONAL	1	FALSE	1	0.314597910909362	2		190	625	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434889	49434889	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555192676	NA	P-0007483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	22	136	0	ENST00000301067.7:c.6664C>T	p.Gln2222Ter	p.Q2222*	ENST00000301067	NM_003482.3	2222	Cag/Tag	31/54	1	2	FACETS	0.402	0.311	0.507	0.402	0.311	0.507	SUBCLONAL	1	FALSE	1	0.314597910909362	2		136	348	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223813	2223813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567252659	NA	P-0007483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	49	203	0	ENST00000326181.6:c.1111C>T	p.Arg371Trp	p.R371W	ENST00000326181	NM_032271.2	371	Cgg/Tgg	12/21	1	2	FACETS	0.664	0.563	0.775	0.664	0.563	0.775	SUBCLONAL	1	FALSE	1	0.314597910909362	2		203	469	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561495	9561495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559966028	NA	P-0007483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	103	159	1	ENST00000353224.5:c.287G>A	p.Arg96His	p.R96H	ENST00000353224	NM_177990.2	96	cGc/cAc	4/10	0.223064776285903	3	FACETS	1	0.966	1	0.593	0.531	0.658	CLONAL	1	FALSE	1	0.314597910909362	3		160	639	SUCCESS
AR	367	MSKCC	GRCh37	X	66765350	66765350	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	89	120	0	ENST00000374690.3:c.362C>A	p.Ser121Ter	p.S121*	ENST00000374690	NM_000044.3	121	tCg/tAg	1/8	0.314597910909362	2	FACETS	1	0.974	1			1	CLONAL	1	FALSE	NA	0.314597910909362	2		120	428	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0007486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	108	384	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	1	2	FACETS	0.967	0.875	1	0.967	0.875	1	CLONAL	1	TRUE	1	0.542059568535555	2		384	412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0007486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	101	152	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.542059568535555	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.542059568535555	1		152	236	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940127	49940127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs553617101	NA	P-0007486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	187	353	1	ENST00000296474.3:c.916C>T	p.Arg306Cys	p.R306C	ENST00000296474	NM_002447.2	306	Cgc/Tgc	1/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.542059568535555	2		354	617	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933389	100933389	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	56	457	1	ENST00000325455.5:c.2001A>T	p.Gln667His	p.Q667H	ENST00000325455	NM_001202474.3	667	caA/caT	4/8	1	2	FACETS	0.209	0.178	0.243	0.209	0.178	0.243	SUBCLONAL	1	TRUE	1	0.542059568535555	2		458	987	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974936	15974936	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	169	279	0	ENST00000268712.3:c.3939del	p.Lys1313AsnfsTer48	p.K1313Nfs*48	ENST00000268712	NM_006311.3	1313	aaA/aa	30/46	0.542059568535555	1	FACETS	0.978	0.907	1	0.978	0.907	1	CLONAL	1	TRUE	0	0.542059568535555	1		279	465	SUCCESS
APC	324	MSKCC	GRCh37	5	112174590	112174590	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	155	276	0	ENST00000257430.4:c.3299del	p.Ser1100PhefsTer26	p.S1100Ffs*26	ENST00000257430	NM_000038.5	1100	tCt/tt	16/16	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.542059568535555	2		276	568	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	39	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.959	0.793	1	0.959	0.793	1	CLONAL	1	TRUE	1	0.12	2		371	678	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0007488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	11	427	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.569	0.392	0.791	0.569	0.392	0.791	SUBCLONAL	1	TRUE	1	0.12	2		427	322	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038479	180038479	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	21	185	0	ENST00000261937.6:c.3538G>A	p.Glu1180Lys	p.E1180K	ENST00000261937	NM_182925.4	1180	Gag/Aag	27/30	1	2	FACETS	1	0.78	1	1	0.78	1	CLONAL	1	TRUE	1	0.12	2		185	345	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0007489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	154	822	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.672871916177411	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.672871916177411	1		822	286	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0007489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	113	393	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.672871916177411	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.672871916177411	2		393	156	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198264983	198264983	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	14	246	0	ENST00000335508.6:c.2894G>C	p.Cys965Ser	p.C965S	ENST00000335508	NM_012433.2	965	tGt/tCt	19/25	0.649277614227944	3	FACETS	0.242	0.174	0.323	0.121	0.087	0.162	SUBCLONAL	1	TRUE	1	0.672871916177411	3		246	230	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226290	133226291	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0007489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	24	345	0	ENST00000320574.5:c.3767_3768del	p.Gly1256AlafsTer98	p.G1256Afs*98	ENST00000320574	NM_006231.2	1256	gGG/g	30/49	1	2	FACETS	0.179	0.14	0.225	0.179	0.14	0.225	SUBCLONAL	1	TRUE	1	0.672871916177411	2		345	398	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593525	48593526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0007489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	65	220	0	ENST00000342988.3:c.1278dup	p.His427SerfsTer2	p.H427Sfs*2	ENST00000342988	NM_005359.5	426	gtt/gTtt	10/12	0.672871916177411	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.672871916177411	1		220	98	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0007492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	168	326	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	0.43713611675475	2		326	532	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653814	89653814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780004	NA	P-0007492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	110	339	1	ENST00000371953.3:c.112C>T	p.Pro38Ser	p.P38S	ENST00000371953	NM_000314.4	38	Cct/Tct	2/9	0.43713611675475	1	FACETS	0.988	0.895	1	0.988	0.895	1	CLONAL	1	TRUE	0	0.43713611675475	1		340	398	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455097	50455097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	117	332	0	ENST00000331340.3:c.644C>T	p.Ser215Phe	p.S215F	ENST00000331340	NM_006060.4	215	tCt/tTt	6/8	1	2	FACETS	0.984	0.891	1	0.984	0.891	1	CLONAL	1	TRUE	1	0.43713611675475	2		332	544	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012115	16012115	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	177	487	0	ENST00000268712.3:c.2167C>T	p.Pro723Ser	p.P723S	ENST00000268712	NM_006311.3	723	Cca/Tca	19/46	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.43713611675475	2		487	740	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144747	11144812	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCCGCCCACCCCGGCCCCTCCTCAGCGGCACTGACAGTTTGCAATCTTATAGGAGGAAGACGAGGT	GCCGCCCACCCCGGCCCCTCCTCAGCGGCACTGACAGTTTGCAATCTTATAGGAGGAAGACGAGGT	-	novel	NA	P-0007492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	73	164	0	ENST00000358026.2:c.3874-49_3890del		p.X1292_splice	ENST00000358026	NM_001128849.1	1292		28/36	0.158112457684702	1	FACETS	0.85	0.75	0.956	0.85	0.75	0.956	INDETERMINATE	1	TRUE	0	0.43713611675475	1		164	307	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512401	38512402	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs745553450	NA	P-0007526-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	110	303	0	ENST00000254066.5:c.1319dup	p.Pro441AlafsTer5	p.P441Afs*5	ENST00000254066	NM_000964.3	438	gcc/gCcc	9/9	0.527947290134081	2	FACETS	0.775	0.7	0.854	0.388	0.35	0.427	SUBCLONAL	1	TRUE	0	0.581693052655453	2		303	488	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068081	94068081	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007526-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	265	869	1	ENST00000369303.4:c.881C>A	p.Ser294Tyr	p.S294Y	ENST00000369303	NM_004440.3	294	tCt/tAt	4/17	0.525808460907965	3	FACETS	0.858	0.803	0.915	0.286	0.267	0.305	CLONAL	1	TRUE	0	0.581693052655453	3		870	1371	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0007530-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	776	478	5	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.77847554069605	3	FACETS	0.988	0.971	1	0.988	0.971	1	CLONAL	3	TRUE	0	0.793808291413154	3		483	921	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796937	45796937	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007530-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	1085	373	0	ENST00000450313.1:c.1393C>A	p.Pro465Thr	p.P465T	ENST00000450313	NM_012222.2	465	Cca/Aca	14/16	0.545793401912578	3	FACETS	1	0.996	1			1	CLONAL	3	TRUE	NA	0.793808291413154	3		373	1242	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	98	417	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.852	0.759	0.951	0.852	0.759	0.951	CLONAL	1	TRUE	1	0.278557229251663	2		417	826	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0007554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	45	478	5	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.278557229251663	1	FACETS	0.983	0.831	1	0.983	0.831	1	CLONAL	1	TRUE	0	0.278557229251663	1		483	283	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0007554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	63	294	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.906	0.785	1	0.906	0.785	1	CLONAL	1	TRUE	1	0.278557229251663	2		294	499	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562363	21562363	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202040927	NA	P-0007554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	65	211	0	ENST00000382592.4:c.1556C>T	p.Pro519Leu	p.P519L	ENST00000382592	NM_014572.2	519	cCg/cTg	4/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.278557229251663	2		211	329	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411291	63411291	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1408150272	NA	P-0007554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	119	423	0	ENST00000330258.3:c.1876C>T	p.Arg626Ter	p.R626*	ENST00000330258	NM_152424.3	626	Cga/Tga	2/2	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.278557229251663	2		423	742	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737329	145737329	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs776023102	NA	P-0007554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	98	338	0	ENST00000428558.2:c.3358G>C	p.Glu1120Gln	p.E1120Q	ENST00000428558	NM_004260.3	1120	Gag/Cag	20/22	0.193340583831749	3	FACETS	1	0.965	1	0.398	0.355	0.443	CLONAL	1	TRUE	0	0.278557229251663	3		338	672	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239868	41239868	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	103	275	0	ENST00000379561.5:c.482G>A	p.Gly161Asp	p.G161D	ENST00000379561	NM_002015.3	161	gGc/gAc	1/3	0.20871148789973	4	FACETS	1	0.956	1	0.565	0.505	0.629	CLONAL	1	TRUE	2	0.278557229251663	4		275	837	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435312	56435312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139405076	NA	P-0007554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	92	195	0	ENST00000407977.2:c.1825C>T	p.Arg609Trp	p.R609W	ENST00000407977		609	Cgg/Tgg	9/10	0.278557229251663	1	FACETS	0.796	0.714	0.883	1	0.983	1	SUBCLONAL	2	TRUE	0	0.278557229251663	1		195	357	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604731	48604731	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	94	289	0	ENST00000342988.3:c.1553T>A	p.Ile518Asn	p.I518N	ENST00000342988	NM_005359.5	518	aTc/aAc	12/12	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.278557229251663	2		289	633	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020108	123020108	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	170	467	0	ENST00000355640.3:c.596A>C	p.Gln199Pro	p.Q199P	ENST00000355640		199	cAg/cCg	2/7	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.278557229251663	2		467	1189	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118720	115118721	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0007554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	92	402	0	ENST00000257566.3:c.620_621del	p.Leu207GlnfsTer19	p.L207Qfs*19	ENST00000257566	NM_016569.3	207	cTG/c	2/8	1	2	FACETS	0.694	0.615	0.778	0.694	0.615	0.778	SUBCLONAL	1	TRUE	1	0.278557229251663	2		402	952	SUCCESS
APC	324	MSKCC	GRCh37	5	112175686	112175686	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	74	325	0	ENST00000257430.4:c.4395del	p.Ser1465ArgfsTer8	p.S1465Rfs*8	ENST00000257430	NM_000038.5	1465	agT/ag	16/16	1	2	FACETS	0.743	0.65	0.844	0.743	0.65	0.844	SUBCLONAL	1	TRUE	1	0.278557229251663	2		325	715	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0007590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	89	330	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.145615494178869	2	FACETS	1	0.903	1	0.509	0.452	0.57	INDETERMINATE	1	TRUE	0	0.286482666747637	2		330	610	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0007590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	118	279	1	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	0.286482666747637	2	FACETS	0.936	0.851	1	0.936	0.851	1	CLONAL	2	TRUE	0	0.286482666747637	2		280	440	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578214	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs864309495	NA	P-0007590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	247	501	2	ENST00000269305.4:c.635_636del	p.Phe212SerfsTer3	p.F212Sfs*3	ENST00000269305	NM_001126112.2	212	tTT/t	6/11	0.286482666747637	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.286482666747637	2		503	816	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879673	151879673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	11	116	0	ENST00000262189.6:c.5272C>T	p.Arg1758Cys	p.R1758C	ENST00000262189	NM_170606.2	1758	Cgt/Tgt	36/59	0.246895199802863	4	FACETS	0.52	0.359	0.719	0.173	0.119	0.24	SUBCLONAL	1	TRUE	1	0.286482666747637	4		116	190	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967242	93967242	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0007590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	96	356	0	ENST00000369303.4:c.2111-1G>T		p.X704_splice	ENST00000369303	NM_004440.3	704			0.196850477221575	4	FACETS	0.754	0.673	0.839	0.754	0.673	0.839	SUBCLONAL	2	TRUE	2	0.286482666747637	4		356	572	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355310	81355310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	180	371	0	ENST00000222390.5:c.1064G>A	p.Arg355Gln	p.R355Q	ENST00000222390	NM_000601.4	355	cGa/cAa	9/18	0.246895199802863	4	FACETS	0.882	0.817	0.948	0.882	0.817	0.948	CLONAL	3	TRUE	1	0.286482666747637	4		371	611	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252748	133252748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775365628	NA	P-0007590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	93	362	0	ENST00000320574.5:c.952G>A	p.Glu318Lys	p.E318K	ENST00000320574	NM_006231.2	318	Gaa/Aaa	10/49	0.145615494178869	2	FACETS	1	0.943	1	0.547	0.487	0.61	INDETERMINATE	1	TRUE	0	0.286482666747637	2		362	594	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117957	70117957	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	69	127	0	ENST00000245479.2:c.425T>G	p.Leu142Arg	p.L142R	ENST00000245479	NM_000346.3	142	cTc/cGc	1/3	0.286482666747637	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	0	0.286482666747637	2		127	221	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604665	48604665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660045	NA	P-0007590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	128	283	0	ENST00000342988.3:c.1487G>A	p.Arg496His	p.R496H	ENST00000342988	NM_005359.5	496	cGt/cAt	12/12	0.286482666747637	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	2	TRUE	0	0.286482666747637	2		283	443	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0007591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	207	252	2	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.781	0.727	0.837	0.781	0.727	0.837	SUBCLONAL	1	TRUE	1	0.706868296451002	2		254	750	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0007591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	197	269	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	1	2	FACETS	0.997	0.93	1	0.997	0.93	1	CLONAL	1	TRUE	1	0.706868296451002	2		269	559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0007591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	235	346	0	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	0.706868296451002	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.706868296451002	1		346	424	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014221	14014221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	113	139	0	ENST00000311895.7:c.199G>A	p.Ala67Thr	p.A67T	ENST00000311895	NM_005236.2	67	Gcc/Acc	1/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.706868296451002	2		139	264	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347225	70347225	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1308	328	635	0	ENST00000374080.3:c.2889T>A	p.Asp963Glu	p.D963E	ENST00000374080		963	gaT/gaA	21/45	0.546884457115357	3	FACETS	0.768	0.723	0.814	0.384	0.361	0.407	SUBCLONAL	1	TRUE	1	0.706868296451002	3		635	1636	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918999	76918999	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	390	524	0	ENST00000373344.5:c.3992C>A	p.Ser1331Tyr	p.S1331Y	ENST00000373344	NM_000489.3	1331	tCt/tAt	12/35	0.546884457115357	3	FACETS	0.954	0.905	1	0.477	0.452	0.503	CLONAL	1	TRUE	1	0.706868296451002	3		524	1565	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0007592-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	272	417	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.92	0.864	0.977	0.92	0.864	0.977	CLONAL	1	TRUE	1	0.616101167544656	2		417	960	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0007592-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	347	378	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.986	0.934	1	0.986	0.934	1	CLONAL	1	TRUE	1	0.616101167544656	2		379	1142	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0007592-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	72	652	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.698	0.614	0.786	0.698	0.614	0.786	SUBCLONAL	1	TRUE	1	0.616101167544656	2		652	335	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555687605	NA	P-0007592-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	198	334	0	ENST00000342988.3:c.1610A>G	p.Asp537Gly	p.D537G	ENST00000342988	NM_005359.5	537	gAc/gGc	12/12	0.585190931640231	1	FACETS	0.822	0.767	0.878	0.822	0.767	0.878	CLONAL	1	TRUE	0	0.616101167544656	1		334	541	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0007592-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	160	207	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.842	0.775	0.911	0.842	0.775	0.911	CLONAL	1	TRUE	1	0.616101167544656	2		207	617	SUCCESS
APC	324	MSKCC	GRCh37	5	112173656	112173656	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123117	NA	P-0007592-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	176	332	0	ENST00000257430.4:c.2365C>T	p.Gln789Ter	p.Q789*	ENST00000257430	NM_000038.5	789	Cag/Tag	16/16	0.616101167544656	3	FACETS	1	0.924	1	0.5	0.462	0.54	CLONAL	1	TRUE	1	0.616101167544656	3		332	747	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114905771	114905771	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007592-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	303	529	3	ENST00000543371.1:c.790C>T	p.Gln264Ter	p.Q264*	ENST00000543371	NM_001198531.1	264	Caa/Taa	8/14	1	2	FACETS	0.83	0.782	0.88	0.83	0.782	0.88	CLONAL	1	TRUE	1	0.616101167544656	2		532	1185	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552647	18552647	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007592-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	285	490	0	ENST00000266497.5:c.2058T>A	p.Asn686Lys	p.N686K	ENST00000266497		686	aaT/aaA	14/31	1	2	FACETS	0.87	0.818	0.923	0.87	0.818	0.923	CLONAL	1	TRUE	1	0.616101167544656	2		490	1064	SUCCESS
APC	324	MSKCC	GRCh37	5	112176024	112176024	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007592-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	263	263	0	ENST00000257430.4:c.4733del	p.Cys1578LeufsTer72	p.C1578Lfs*72	ENST00000257430	NM_000038.5	1578	tGt/tt	16/16	0.616101167544656	3	FACETS	0.935	0.884	0.987	0.935	0.884	0.987	CLONAL	2	TRUE	1	0.616101167544656	3		263	597	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	89	417	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.247566193316084	3	FACETS	0.813	0.723	0.908	0.813	0.723	0.908	CLONAL	2	TRUE	1	0.247566193316084	3		417	497	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	45	195	0	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	0.247566193316084	3	FACETS	0.851	0.716	1	0.426	0.358	0.501	CLONAL	1	TRUE	1	0.247566193316084	3		195	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0007593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	194	749	1	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.247566193316084	3	FACETS	1	0.978	1	0.759	0.704	0.816	CLONAL	2	TRUE	0	0.247566193316084	3		750	773	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519446	137519446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	37	180	1	ENST00000367739.4:c.1192C>T	p.His398Tyr	p.H398Y	ENST00000367739	NM_000416.2	398	Cac/Tac	7/7	1	2	FACETS	0.967	0.8	1	0.967	0.8	1	CLONAL	1	TRUE	1	0.247566193316084	2		181	309	SUCCESS
AR	367	MSKCC	GRCh37	X	66766238	66766238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1327366080	NA	P-0007593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	70	173	0	ENST00000374690.3:c.1250C>T	p.Ala417Val	p.A417V	ENST00000374690	NM_000044.3	417	gCg/gTg	1/8	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.247566193316084	2		173	521	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346550	81346550	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs148293411	NA	P-0007593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	58	276	0	ENST00000222390.5:c.1403G>A	p.Arg468His	p.R468H	ENST00000222390	NM_000601.4	468	cGt/cAt	11/18	0.247566193316084	3	FACETS	1	0.958	1	0.657	0.566	0.755	CLONAL	1	TRUE	1	0.247566193316084	3		276	401	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468158	50468158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	93	190	0	ENST00000331340.3:c.1393G>A	p.Glu465Lys	p.E465K	ENST00000331340	NM_006060.4	465	Gaa/Aaa	8/8	0.247566193316084	3	FACETS	0.81	0.723	0.903	0.81	0.723	0.903	CLONAL	2	TRUE	1	0.247566193316084	3		190	521	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442854	187442854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867576130	NA	P-0007593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	8	149	0	ENST00000232014.4:c.1852C>T	p.Arg618Cys	p.R618C	ENST00000232014	NM_001130845.1	618	Cgt/Tgt	9/10	0.247566193316084	3	FACETS	0.188	0.12	0.277	0.094	0.06	0.139	SUBCLONAL	1	TRUE	1	0.247566193316084	3		149	386	SUCCESS
APC	324	MSKCC	GRCh37	5	112174058	112174058	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0007593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	44	295	0	ENST00000257430.4:c.2767A>T	p.Arg923Ter	p.R923*	ENST00000257430	NM_000038.5	923	Aga/Tga	16/16	0.247566193316084	3	FACETS	1	0.938	1	0.622	0.524	0.73	CLONAL	1	TRUE	1	0.247566193316084	3		295	321	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166872	32166872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770780305	NA	P-0007593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	90	153	0	ENST00000375023.3:c.4366G>A	p.Gly1456Arg	p.G1456R	ENST00000375023	NM_004557.3	1456	Ggg/Agg	24/30	0.247566193316084	6	FACETS	0.995	0.886	1	0.498	0.443	0.556	CLONAL	2	TRUE	2	0.247566193316084	6		153	546	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943692	9943692	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749504561	NA	P-0007593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	56	269	0	ENST00000330684.3:c.1249G>A	p.Val417Ile	p.V417I	ENST00000330684	NM_001134407.1	417	Gtc/Atc	5/13	0.247566193316084	3	FACETS	0.931	0.798	1	0.466	0.399	0.539	CLONAL	1	TRUE	1	0.247566193316084	3		269	546	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794655	42794655	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	42	241	0	ENST00000575354.2:c.1739del	p.Gly580ValfsTer148	p.G580Vfs*148	ENST00000575354	NM_015125.3	579	Ggg/gg	10/20	0.247566193316084	3	FACETS	0.769	0.642	0.91	0.384	0.321	0.455	CLONAL	1	TRUE	1	0.247566193316084	3		241	496	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	162	417	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.165995135524786	3	FACETS	0.812	0.746	0.88	0.271	0.248	0.294	INDETERMINATE	1	TRUE	0	0.72	3		417	754	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0007620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	94	383	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.302992785424069	5	FACETS	1	0.961	1			1	INDETERMINATE	1	TRUE	NA	0.72	5		383	467	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257536	16257536	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	73	317	0	ENST00000375759.3:c.4801G>C	p.Asp1601His	p.D1601H	ENST00000375759	NM_015001.2	1601	Gac/Cac	11/15	0.302992785424069	6	FACETS	0.719	0.629	0.817			1	INDETERMINATE	1	TRUE	NA	0.72	6		317	688	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037923	49037923	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	103	379	0	ENST00000267163.4:c.2163C>A	p.Phe721Leu	p.F721L	ENST00000267163	NM_000321.2	721	ttC/ttA	21/27	0.302992785424069	3	FACETS	0.588	0.526	0.653	0.294	0.263	0.327	INDETERMINATE	1	TRUE	1	0.72	3		379	662	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039161	49039161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	83	263	0	ENST00000267163.4:c.2239G>A	p.Glu747Lys	p.E747K	ENST00000267163	NM_000321.2	747	Gag/Aag	22/27	0.302992785424069	3	FACETS	0.514	0.454	0.578	0.257	0.227	0.289	INDETERMINATE	1	TRUE	1	0.72	3		263	610	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128216	30128216	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	118	370	0	ENST00000263025.4:c.1016A>T	p.Glu339Val	p.E339V	ENST00000263025	NM_002746.2	339	gAg/gTg	7/9	1	2	FACETS	0.519	0.469	0.572	0.519	0.469	0.572	SUBCLONAL	1	TRUE	1	0.72	2		370	631	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0007631-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	82	427	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.951	0.853	1	0.951	0.853	1	CLONAL	1	TRUE	1	0.727295658102027	2		427	237	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0007631-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	319	311	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.727295658102027	1	FACETS	0.974	0.931	1	0.974	0.931	1	CLONAL	1	TRUE	0	0.727295658102027	1		311	573	SUCCESS
APC	324	MSKCC	GRCh37	5	112174670	112174670	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007631-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	210	404	0	ENST00000257430.4:c.3379C>T	p.Gln1127Ter	p.Q1127*	ENST00000257430	NM_000038.5	1127	Cag/Tag	16/16	1	2	FACETS	0.979	0.915	1	0.979	0.915	1	CLONAL	1	TRUE	1	0.727295658102027	2		404	590	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923778	131923778	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007631-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	98	300	0	ENST00000265335.6:c.1048C>T	p.Gln350Ter	p.Q350*	ENST00000265335		350	Cag/Tag	7/25	1	2	FACETS	0.819	0.739	0.903	0.819	0.739	0.903	CLONAL	1	TRUE	1	0.727295658102027	2		300	329	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508461	106508461	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762164881	NA	P-0007631-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	86	69	0	ENST00000359195.3:c.455G>A	p.Arg152Gln	p.R152Q	ENST00000359195	NM_002649.2	152	cGg/cAg	2/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.727295658102027	2		69	204	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18747474	18747474	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs561351298	NA	P-0007631-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	106	350	0	ENST00000266497.5:c.3935C>G	p.Thr1312Arg	p.T1312R	ENST00000266497		1312	aCa/aGa	28/31	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.727295658102027	2		350	286	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1404	196	417	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.301837899023838	3	FACETS	0.819	0.756	0.886			1	CLONAL	1	TRUE	NA	0.35153700006964	3		417	1600	SUCCESS
APC	324	MSKCC	GRCh37	5	112175198	112175198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	227	303	0	ENST00000257430.4:c.3907C>T	p.Gln1303Ter	p.Q1303*	ENST00000257430	NM_000038.5	1303	Caa/Taa	16/16	0.35153700006964	2	FACETS	0.916	0.857	0.976	0.916	0.857	0.976	CLONAL	2	TRUE	0	0.35153700006964	2		303	705	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161324	55161324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514550	NA	P-0007664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	152	424	0	ENST00000257290.5:c.3155C>T	p.Thr1052Met	p.T1052M	ENST00000257290	NM_006206.4	1052	aCg/aTg	23/23	1	2	FACETS	0.925	0.845	1	0.925	0.845	1	CLONAL	1	TRUE	1	0.35153700006964	2		424	935	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149619	202149619	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	186	449	0	ENST00000358485.4:c.1060A>T	p.Ile354Phe	p.I354F	ENST00000358485	NM_001080125.1	354	Att/Ttt	8/9	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.35153700006964	2		449	977	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750765	128750765	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	272	359	0	ENST00000377970.2:c.302A>G	p.Asn101Ser	p.N101S	ENST00000377970	NM_002467.4	101	aAc/aGc	2/3	0.35153700006964	3	FACETS	0.991	0.932	1	0.991	0.932	1	CLONAL	2	TRUE	1	0.35153700006964	3		359	918	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894992	101894992	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	252	530	0	ENST00000374994.4:c.545A>G	p.Tyr182Cys	p.Y182C	ENST00000374994	NM_004612.2	182	tAt/tGt	3/9	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.35153700006964	2		530	1412	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218035	108218035	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	393	460	0	ENST00000278616.4:c.8614C>G	p.His2872Asp	p.H2872D	ENST00000278616	NM_000051.3	2872	Cat/Gat	59/63	0.35153700006964	2	FACETS	0.865	0.822	0.909	0.865	0.822	0.909	CLONAL	2	TRUE	0	0.35153700006964	2		460	1292	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7218300	7218300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	140	437	1	ENST00000380728.2:c.72G>A	p.Met24Ile	p.M24I	ENST00000380728		24	atG/atA	2/11	0.35153700006964	1	FACETS	0.916	0.835	1	0.916	0.835	1	CLONAL	1	TRUE	0	0.35153700006964	1		438	717	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436101	51436101	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007669-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	315	338	2	ENST00000262662.1:c.61C>T	p.Leu21Phe	p.L21F	ENST00000262662		21	Ctt/Ttt	3/4	1	2	FACETS	0.807	0.761	0.853	0.807	0.761	0.853	CLONAL	1	TRUE	1	0.677419824885163	2		340	1153	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572971	7572971	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007669-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	723	640	0	ENST00000269305.4:c.1138del	p.His380IlefsTer42	p.H380Ifs*42	ENST00000269305	NM_001126112.2	380	Cat/at	11/11	0.677419824885163	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.677419824885163	1		640	1386	SUCCESS
APC	324	MSKCC	GRCh37	5	112175349	112175353	+	frameshift_variant	Frame_Shift_Del	DEL	AATTT	AATTT	-	novel	NA	P-0007669-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	531	291	0	ENST00000257430.4:c.4058_4062del	p.Glu1353ValfsTer20	p.E1353Vfs*20	ENST00000257430	NM_000038.5	1353	gAATTT/g	16/16	NA	2	FACETS	0.864	0.835	0.893			1	INDETERMINATE	2	TRUE	NA	0.677419824885163	2		291	907	SUCCESS
APC	324	MSKCC	GRCh37	5	112175343	112175344	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGGCACAA	novel	NA	P-0007669-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	543	291	0	ENST00000257430.4:c.4052_4053insCAGGCACAA	p.Ala1351_Val1352insArgHisAsn	p.A1351_V1352insRHN	ENST00000257430	NM_000038.5	1351	gct/gcCAGGCACAAt	16/16	NA	2	FACETS	0.855	0.826	0.883			1	INDETERMINATE	2	TRUE	NA	0.677419824885163	2		291	938	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021542	42021543	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	TA	novel	NA	P-0007669-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2023	143	695	2	ENST00000219905.7:c.3838_3839delinsTA	p.Ala1280Ter	p.A1280*	ENST00000219905	NM_001164273.1	1280	GCa/TAa	11/24	0.659568260234142	2	FACETS	0.195	0.176	0.215	0.097	0.088	0.108	SUBCLONAL	1	TRUE	0	0.677419824885163	2		697	2166	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0007680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	252	939	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.853778997102362	1	FACETS	0.831	0.792	0.869	0.831	0.792	0.869	CLONAL	1	TRUE	0	0.853778997102362	1		939	407	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0007680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	138	482	1	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.443897500729073	1	FACETS	0.493	0.453	0.533	0.493	0.453	0.533	INDETERMINATE	1	TRUE	0	0.853778997102362	1		483	376	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519893	NA	P-0007680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1693	671	781	0	ENST00000267101.3:c.310G>T	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ttg	3/28	0.233378118832761	5	FACETS	0.758	0.729	0.788			1	INDETERMINATE	2	TRUE	NA	0.853778997102362	5		781	2364	SUCCESS
ATM	472	MSKCC	GRCh37	11	108213967	108213967	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876659872	NA	P-0007680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	174	323	0	ENST00000278616.4:c.8287C>T	p.Arg2763Ter	p.R2763*	ENST00000278616	NM_000051.3	2763	Cga/Tga	57/63	1	2	FACETS	0.884	0.822	0.947	0.884	0.822	0.947	CLONAL	1	TRUE	1	0.853778997102362	2		323	461	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469564	25469564	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs796065342	NA	P-0007680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	1080	514	0	ENST00000264709.3:c.1204C>T	p.Gln402Ter	p.Q402*	ENST00000264709	NM_175629.2	402	Cag/Tag	10/23	0.622763652462905	3	FACETS	0.858	0.836	0.88	0.858	0.836	0.88	CLONAL	2	TRUE	1	0.853778997102362	3		514	2104	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821870	59821870	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	407	572	2	ENST00000259008.2:c.2180C>A	p.Pro727Gln	p.P727Q	ENST00000259008	NM_032043.2	727	cCa/cAa	15/20	0.8175775681428	2	FACETS	0.962	0.919	1	0.481	0.459	0.503	CLONAL	1	TRUE	0	0.853778997102362	2		574	991	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019464	31019464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	32	287	0	ENST00000375687.4:c.961C>T	p.Arg321Trp	p.R321W	ENST00000375687	NM_015338.5	321	Cgg/Tgg	10/13	0.747054172624247	1	FACETS	0.071	0.057	0.087	0.071	0.057	0.087	SUBCLONAL	1	TRUE	0	0.853778997102362	1		287	602	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577557	7577558	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0007680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	500	366	0	ENST00000269305.4:c.723dup	p.Cys242LeufsTer22	p.C242Lfs*22	ENST00000269305	NM_001126112.2	241	-/C	7/11	0.820121659823434	1	FACETS	0.906	0.878	0.933	0.906	0.878	0.933	CLONAL	1	TRUE	0	0.853778997102362	1		366	741	SUCCESS
APC	324	MSKCC	GRCh37	5	112175983	112175991	+	inframe_deletion	In_Frame_Del	DEL	AGATGATTC	AGATGATTC	-	novel	NA	P-0007680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	137	301	0	ENST00000257430.4:c.4699_4707del	p.Ser1567_Asp1569del	p.S1567_D1569del	ENST00000257430	NM_000038.5	1564	ttAGATGATTCa/tta	16/16	0.853778997102362	1	FACETS	0.893	0.839	0.944	0.893	0.839	0.944	CLONAL	1	TRUE	0	0.853778997102362	1		301	206	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007737-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	627	538	0	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	0.452272042913718	3	FACETS	0.946	0.916	0.975	1	0.997	1	CLONAL	3	TRUE	1	0.502919199086329	3		538	1100	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0007737-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	246	294	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.919	0.868	0.971	1	0.995	1	CLONAL	2	TRUE	1	0.502919199086329	2		294	532	SUCCESS
APC	324	MSKCC	GRCh37	5	112162819	112162819	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007737-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	252	390	0	ENST00000257430.4:c.1423A>T	p.Ile475Phe	p.I475F	ENST00000257430	NM_000038.5	475	Att/Ttt	12/16	1	2	FACETS	0.862	0.814	0.911	1	0.995	1	CLONAL	2	TRUE	1	0.502919199086329	2		390	581	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341596	89341596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007737-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	234	296	0	ENST00000301030.4:c.7474G>A	p.Ala2492Thr	p.A2492T	ENST00000301030	NM_001256183.1	2492	Gca/Aca	10/13	1	2	FACETS	0.866	0.816	0.917	1	0.994	1	CLONAL	2	TRUE	1	0.502919199086329	2		296	537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0007737-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	253	304	0	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	0.476407886554054	0	FACETS		NA	1			1	NA	3	TRUE	0	0.502919199086329	0		304	300	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117774	70117774	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007737-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	262	549	2	ENST00000245479.2:c.242T>C	p.Leu81Pro	p.L81P	ENST00000245479	NM_000346.3	81	cTc/cCc	1/3	1	2	FACETS	1	0.99	1	1	0.997	1	CLONAL	3	TRUE	1	0.502919199086329	2		551	325	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368304	45368304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007737-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	364	508	0	ENST00000262160.6:c.1298G>A	p.Ser433Asn	p.S433N	ENST00000262160	NM_005901.5	433	aGt/aAt	11/11	1	2	FACETS	0.916	0.874	0.958	1	0.996	1	CLONAL	2	TRUE	1	0.502919199086329	2		508	790	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937134	76937134	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007737-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	723	832	2	ENST00000373344.5:c.3614C>A	p.Ser1205Tyr	p.S1205Y	ENST00000373344	NM_000489.3	1205	tCt/tAt	9/35	0.502919199086329	1	FACETS		NA	1	1	0.998	1	NA	3	TRUE	0	0.502919199086329	1		834	829	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0007737-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	197	73	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.765	0.715	0.816	1	0.992	1	SUBCLONAL	2	TRUE	1	0.502919199086329	2		73	512	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222865	5222865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	35	181	0	ENST00000357368.4:c.2938G>A	p.Glu980Lys	p.E980K	ENST00000357368	NM_002850.3	980	Gag/Aag	18/38	0.396572504101691	4	FACETS	0.441	0.361	0.531	0.147	0.12	0.177	SUBCLONAL	1	TRUE	1	0.425353409137419	4		181	532	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	95	639	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.981	0.884	1	1	0.99	1	CLONAL	3	TRUE	1	0.206860698342831	2		645	312	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671655	67671655	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1400980130	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	57	409	0	ENST00000264010.4:c.2070del	p.Glu691SerfsTer30	p.E691Sfs*30	ENST00000264010	NM_006565.3	688	gtA/gt	12/12	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.206860698342831	2		409	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	144	564	1	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	1	2	FACETS	0.757	0.69	0.828	1	0.987	1	SUBCLONAL	2	TRUE	1	0.206860698342831	2		565	919	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	447	565	16	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	0.00479274575642896	4	FACETS	0.883	0.842	0.925	1	0.997	1	INDETERMINATE	4	TRUE	2	0.206860698342831	4		581	1477	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	50	473	3	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.767	0.655	0.89	1	0.965	1	SUBCLONAL	2	TRUE	1	0.206860698342831	2		476	315	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	105	309	1	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.796	0.714	0.882	1	0.984	1	SUBCLONAL	2	TRUE	1	0.206860698342831	2		310	638	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988348	36988348	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs546402304	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	19	118	1	ENST00000354822.5:c.305C>T	p.Ala102Val	p.A102V	ENST00000354822	NM_001079668.2	102	gCg/gTg	2/3	1	2	FACETS	0.765	0.588	0.968	1	0.915	1	CLONAL	2	TRUE	1	0.206860698342831	2		119	120	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043349	6043349	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781716	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	47	204	0	ENST00000265849.7:c.325del	p.Glu109LysfsTer3	p.E109Kfs*3	ENST00000265849	NM_000535.5	109	Gaa/aa	4/15	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.206860698342831	2		204	365	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186733	11186733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	104	558	0	ENST00000361445.4:c.6472C>T	p.Pro2158Ser	p.P2158S	ENST00000361445	NM_004958.3	2158	Ccg/Tcg	46/58	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.206860698342831	2		558	852	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747937	41747937	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	59	310	1	ENST00000226382.2:c.832G>T	p.Gly278Cys	p.G278C	ENST00000226382	NM_003924.3	278	Ggc/Tgc	3/3	1	2	FACETS	0.757	0.654	0.868	1	0.97	1	SUBCLONAL	2	TRUE	1	0.206860698342831	2		311	377	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555104	106555104	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778518932	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	92	333	0	ENST00000369096.4:c.2221C>T	p.Arg741Trp	p.R741W	ENST00000369096	NM_001198.3	741	Cgg/Tgg	7/7	0.206860698342831	3	FACETS	0.851	0.757	0.95	0.851	0.757	0.95	CLONAL	2	TRUE	1	0.206860698342831	3		333	577	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875067	151875067	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	56	219	0	ENST00000262189.6:c.7471A>G	p.Thr2491Ala	p.T2491A	ENST00000262189	NM_170606.2	2491	Acc/Gcc	38/59	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.206860698342831	2		219	475	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417575	139417575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	78	465	2	ENST00000277541.6:c.469C>T	p.Pro157Ser	p.P157S	ENST00000277541	NM_017617.3	157	Ccc/Tcc	4/34	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.206860698342831	2		467	685	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649849	88649849	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	48	219	0	ENST00000372037.3:c.98C>T	p.Thr33Ile	p.T33I	ENST00000372037	NM_004329.2	33	aCt/aTt	4/13	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.206860698342831	2		219	411	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625393	69625393	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1408391209	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	86	480	0	ENST00000334134.2:c.400T>C	p.Tyr134His	p.Y134H	ENST00000334134	NM_005247.2	134	Tac/Cac	3/3	1	2	FACETS	0.936	0.832	1	1	0.984	1	CLONAL	2	TRUE	1	0.206860698342831	2		480	444	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94211958	94211958	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	168	525	1	ENST00000323929.3:c.487G>A	p.Asp163Asn	p.D163N	ENST00000323929	NM_005591.3	163	Gac/Aac	6/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.206860698342831	2		526	1273	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490875	56490875	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	105	440	0	ENST00000267101.3:c.2321T>C	p.Leu774Pro	p.L774P	ENST00000267101	NM_001982.3	774	cTg/cCg	20/28	0.206860698342831	3	FACETS	0.863	0.774	0.957	0.863	0.774	0.957	CLONAL	2	TRUE	1	0.206860698342831	3		440	649	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145108	58145108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	117	358	0	ENST00000257904.6:c.236C>T	p.Ala79Val	p.A79V	ENST00000257904	NM_000075.3	79	gCc/gTc	3/8	0.206860698342831	3	FACETS	0.911	0.823	1	0.911	0.823	1	CLONAL	2	TRUE	1	0.206860698342831	3		358	685	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112329	115112329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1295791270	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	15	100	0	ENST00000257566.3:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000257566	NM_016569.3	471	Cgc/Tgc	7/8	0.206860698342831	3	FACETS	0.808	0.599	1	0.808	0.599	1	CLONAL	2	TRUE	1	0.206860698342831	3		100	99	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005402	29005402	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	197	406	0	ENST00000282397.4:c.859T>C	p.Ser287Pro	p.S287P	ENST00000282397	NM_002019.4	287	Tcc/Ccc	7/30	0.00479274575642896	4	FACETS	1	0.947	1	1	0.947	1	INDETERMINATE	2	TRUE	2	0.206860698342831	4		406	1117	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346401	73346401	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs143362001	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	198	351	1	ENST00000377767.4:c.1399C>T	p.Arg467Ter	p.R467*	ENST00000377767	NM_014953.3	467	Cga/Tga	10/21	0.00479274575642896	4	FACETS	0.894	0.829	0.962	1	0.988	1	INDETERMINATE	3	TRUE	2	0.206860698342831	4		352	861	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994739	73994739	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	79	526	1	ENST00000318443.5:c.223C>A	p.Leu75Met	p.L75M	ENST00000318443	NM_001024736.1	75	Ctg/Atg	3/10	1	2	FACETS	0.768	0.678	0.865	1	0.978	1	SUBCLONAL	2	TRUE	1	0.206860698342831	2		527	497	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56867238	56867238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377453680	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	123	619	1	ENST00000308159.5:c.1457G>A	p.Arg486His	p.R486H	ENST00000308159	NM_014669.4	486	cGc/cAc	13/22	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.206860698342831	2		620	961	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855952	68855952	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	131	591	0	ENST00000261769.5:c.1760A>G	p.Asp587Gly	p.D587G	ENST00000261769	NM_004360.3	587	gAt/gGt	12/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.206860698342831	2		591	936	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615698	1615698	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs145878545	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	134	984	4	ENST00000344749.5:c.1573C>G	p.Arg525Gly	p.R525G	ENST00000344749	NM_001136139.2	525	Cgg/Ggg	17/19	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.206860698342831	2		988	1001	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273017	18273017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	117	486	0	ENST00000222254.8:c.907C>T	p.Pro303Ser	p.P303S	ENST00000222254	NM_005027.3	303	Ccg/Tcg	8/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.206860698342831	2		486	787	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39935759	39935759	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1257	261	814	1	ENST00000378444.4:c.113C>T	p.Ala38Val	p.A38V	ENST00000378444	NM_001123385.1	38	gCt/gTt	3/15	0.206860698342831	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.206860698342831	1		815	1518	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914632	39914632	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	256	711	0	ENST00000378444.4:c.4730del	p.Lys1577SerfsTer3	p.K1577Sfs*3	ENST00000378444	NM_001123385.1	1577	aAg/ag	12/15	0.206860698342831	1	FACETS	0.829	0.774	0.885	1	0.994	1	CLONAL	2	TRUE	0	0.206860698342831	1		711	1339	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222626	157222631	+	inframe_deletion	In_Frame_Del	DEL	GTCCCA	GTCCCA	-	novel	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	66	304	0	ENST00000346085.5:c.1900_1905del	p.Ser634_Gln635del	p.S634_Q635del	ENST00000346085	NM_020732.3	631	ccGTCCCAg/ccg	4/20	0.206860698342831	3	FACETS	1	0.957	1	0.628	0.545	0.717	CLONAL	1	TRUE	1	0.206860698342831	3		304	561	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830551	72830551	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	200	900	1	ENST00000268489.5:c.6030del	p.Pro2011LeufsTer22	p.P2011Lfs*22	ENST00000268489	NM_006885.3	2010	ttT/tt	9/10	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.206860698342831	2		901	1336	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100260	157100260	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1554248082	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	57	131	0	ENST00000346085.5:c.1202del	p.Gly401AlafsTer29	p.G401Afs*29	ENST00000346085	NM_020732.3	399	gcG/gc	1/20	0.206860698342831	3	FACETS	1	0.915	1	1	0.915	1	CLONAL	2	TRUE	1	0.206860698342831	3		131	282	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098363	11098363	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	124	476	0	ENST00000358026.2:c.885del	p.Thr296ArgfsTer7	p.T296Rfs*7	ENST00000358026	NM_001128849.1	294	gCc/gc	6/36	1	2	FACETS	0.82	0.743	0.902	1	0.987	1	CLONAL	2	TRUE	1	0.206860698342831	2		476	731	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615692	1615692	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	135	978	0	ENST00000344749.5:c.1579del	p.Arg527GlyfsTer16	p.R527Gfs*16	ENST00000344749	NM_001136139.2	527	Cgg/gg	17/19	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.206860698342831	2		978	990	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526209	189526210	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1462944177	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	114	546	0	ENST00000264731.3:c.480_481del	p.Pro161IlefsTer36	p.P161Ifs*36	ENST00000264731	NM_003722.4	158	gCT/g	4/14	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.206860698342831	2		546	786	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	43	330	0	ENST00000269305.4:c.517del	p.Val173Ter	p.V173*	ENST00000269305	NM_001126112.2	173	Gtg/tg	5/11	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.206860698342831	2		330	305	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217557	142217557	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1268253442	NA	P-0007739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	142	448	1	ENST00000350721.4:c.5440del	p.Arg1814GlufsTer10	p.R1814Efs*10	ENST00000350721	NM_001184.3	1814	Aga/ga	32/47	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.206860698342831	2		449	1148	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0007740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	212	478	5	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.615826439354408	2	FACETS	0.956	0.906	1	0.956	0.906	1	CLONAL	2	TRUE	0	0.615826439354408	2		483	360	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0007740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	441	441	2	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.615826439354408	3	FACETS	0.994	0.963	1	0.994	0.963	1	CLONAL	3	TRUE	0	0.615826439354408	3		443	628	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528615	89528615	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	159	372	0	ENST00000336596.2:c.2915T>A	p.Leu972Gln	p.L972Q	ENST00000336596	NM_005233.5	972	cTa/cAa	17/17	0.601819423765563	4	FACETS	0.946	0.867	1	0.473	0.433	0.514	CLONAL	1	TRUE	2	0.615826439354408	4		372	882	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374907	45374907	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	431	557	0	ENST00000262160.6:c.936C>G	p.Cys312Trp	p.C312W	ENST00000262160	NM_005901.5	312	tgC/tgG	8/11	0.615826439354408	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.615826439354408	2		557	691	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224452	123224452	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	507	720	0	ENST00000218089.9:c.3305T>A	p.Met1102Lys	p.M1102K	ENST00000218089	NM_001042749.1	1102	aTg/aAg	31/35	0.489594740959419	4	FACETS	0.884	0.846	0.922	0.884	0.846	0.922	CLONAL	2	TRUE	2	0.615826439354408	4		720	1505	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	25	236	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		236	303	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092825	27092825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867253777	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	97	358	0	ENST00000324856.7:c.2846C>T	p.Ser949Phe	p.S949F	ENST00000324856	NM_006015.4	949	tCc/tTc	9/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		358	902	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546314	46546314	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	142	442	0	ENST00000262741.5:c.215G>A	p.Arg72Lys	p.R72K	ENST00000262741	NM_003629.3	72	aGg/aAg	2/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		442	1030	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076812	72076812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	116	430	0	ENST00000357731.5:c.685G>A	p.Glu229Lys	p.E229K	ENST00000357731	NM_173808.2	229	Gaa/Aaa	5/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		430	990	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433335	78433335	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	32	267	0	ENST00000370768.2:c.266T>A	p.Leu89Ter	p.L89*	ENST00000370768	NM_003902.3	89	tTa/tAa	4/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		267	639	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47613717	47613717	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	55	428	0	ENST00000263735.4:c.910G>A	p.Glu304Lys	p.E304K	ENST00000263735	NM_002354.2	304	Gag/Aag	9/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		428	862	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702212	47702212	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs267607985	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	63	439	0	ENST00000233146.2:c.1808A>G	p.Asp603Gly	p.D603G	ENST00000233146	NM_000251.2	603	gAt/gGt	12/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		439	914	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248486	212248486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1178525913	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	56	477	1	ENST00000342788.4:c.3781G>A	p.Glu1261Lys	p.E1261K	ENST00000342788	NM_005235.2	1261	Gag/Aag	28/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		478	968	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448571	89448571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	73	491	0	ENST00000336596.2:c.1535G>A	p.Arg512Gln	p.R512Q	ENST00000336596	NM_005233.5	512	cGa/cAa	7/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		491	1116	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528553	89528553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	26	233	0	ENST00000336596.2:c.2853G>A	p.Met951Ile	p.M951I	ENST00000336596	NM_005233.5	951	atG/atA	17/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		233	517	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587175	189587175	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	51	363	0	ENST00000264731.3:c.1192G>A	p.Asp398Asn	p.D398N	ENST00000264731	NM_003722.4	398	Gat/Aat	9/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		363	816	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808030	1808030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773089715	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	38	349	1	ENST00000260795.2:c.2006G>A	p.Arg669Gln	p.R669Q	ENST00000260795		669	cGa/cAa	14/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		350	631	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	223682	223682	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs369321221	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	46	397	0	ENST00000264932.6:c.149C>T	p.Ser50Phe	p.S50F	ENST00000264932	NM_004168.2	50	tCc/tTc	2/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		397	790	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945123	38945123	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	66	351	0	ENST00000357387.3:c.4681A>C	p.Asn1561His	p.N1561H	ENST00000357387	NM_152756.3	1561	Aat/Cat	35/38	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		351	922	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715890	117715890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371206741	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	54	403	0	ENST00000368508.3:c.868G>A	p.Glu290Lys	p.E290K	ENST00000368508	NM_002944.2	290	Gaa/Aaa	9/43	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		403	925	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729679	41729679	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1452	83	913	0	ENST00000242208.4:c.850G>C	p.Glu284Gln	p.E284Q	ENST00000242208	NM_002192.2	284	Gaa/Caa	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		913	1535	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730099	41730099	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1517	96	858	0	ENST00000242208.4:c.430G>A	p.Gly144Ser	p.G144S	ENST00000242208	NM_002192.2	144	Ggc/Agc	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		858	1613	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5029863	5029863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	47	414	0	ENST00000381652.3:c.307C>T	p.His103Tyr	p.H103Y	ENST00000381652	NM_004972.3	103	Cat/Tat	4/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		414	812	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601906	43601906	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs760322514	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	59	465	0	ENST00000355710.3:c.950C>G	p.Thr317Arg	p.T317R	ENST00000355710	NM_020975.4	317	aCg/aGg	5/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		465	865	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344279	118344279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	23	156	0	ENST00000534358.1:c.2405C>T	p.Ser802Phe	p.S802F	ENST00000534358	NM_005933.3	802	tCc/tTc	3/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		156	361	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373751	118373751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs387907275	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	45	316	0	ENST00000534358.1:c.7144C>T	p.Arg2382Ter	p.R2382*	ENST00000534358	NM_005933.3	2382	Cga/Tga	27/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		316	604	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658349	18658349	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	63	419	0	ENST00000266497.5:c.3154T>A	p.Phe1052Ile	p.F1052I	ENST00000266497		1052	Ttt/Att	22/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		419	842	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230641	46230641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	89	500	1	ENST00000334344.6:c.890C>T	p.Ser297Phe	p.S297F	ENST00000334344	NM_152641.2	297	tCc/tTc	8/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		501	1179	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246350	46246350	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1275863291	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	59	341	0	ENST00000334344.6:c.4444C>T	p.Gln1482Ter	p.Q1482*	ENST00000334344	NM_152641.2	1482	Caa/Taa	15/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		341	792	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426423	49426423	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	91	553	0	ENST00000301067.7:c.12065C>G	p.Thr4022Arg	p.T4022R	ENST00000301067	NM_003482.3	4022	aCg/aGg	39/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		553	1143	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446388	49446389	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	42	383	0	ENST00000301067.7:c.1216_1217delinsTT	p.Pro406Phe	p.P406F	ENST00000301067	NM_003482.3	406	CCc/TTc	9/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		383	816	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869552	102869552	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766508915	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	32	212	0	ENST00000307046.8:c.89C>T	p.Ser30Leu	p.S30L	ENST00000307046	NM_001111285.1	30	tCg/tTg	2/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		212	485	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129658	2129658	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1028039505	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	59	518	0	ENST00000219476.3:c.3385C>T	p.Arg1129Cys	p.R1129C	ENST00000219476	NM_000548.3	1129	Cgt/Tgt	29/42	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		518	899	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9927998	9927998	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	63	382	0	ENST00000330684.3:c.1741C>T	p.Pro581Ser	p.P581S	ENST00000330684	NM_001134407.1	581	Cct/Tct	8/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		382	877	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348752	11348752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	59	371	0	ENST00000332029.2:c.584C>T	p.Pro195Leu	p.P195L	ENST00000332029	NM_003745.1	195	cCc/cTc	2/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		371	710	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646434	23646434	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786203879	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	65	398	0	ENST00000261584.4:c.1433C>T	p.Ser478Phe	p.S478F	ENST00000261584	NM_024675.3	478	tCt/tTt	4/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		398	877	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337290	89337290	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	65	414	0	ENST00000301030.4:c.7741C>T	p.Arg2581Cys	p.R2581C	ENST00000301030	NM_001256183.1	2581	Cgt/Tgt	12/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		414	812	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350758	89350758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1761	129	1051	0	ENST00000301030.4:c.2192C>T	p.Ser731Phe	p.S731F	ENST00000301030	NM_001256183.1	731	tCt/tTt	9/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1051	1890	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577594	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	57	246	0	ENST00000269305.4:c.687T>A	p.Cys229Ter	p.C229*	ENST00000269305	NM_001126112.2	229	tgT/tgA	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		246	504	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40368109	40368109	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	145	703	0	ENST00000293328.3:c.1396G>A	p.Val466Met	p.V466M	ENST00000293328	NM_012448.3	466	Gtg/Atg	12/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		703	1313	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226925	2226926	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	25	173	0	ENST00000398665.3:c.4405_4406delinsTT	p.Pro1469Leu	p.P1469L	ENST00000398665	NM_032482.2	1469	CCg/TTg	27/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		173	411	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097626	11097627	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	84	583	1	ENST00000358026.2:c.806_807delinsTT	p.Pro269Leu	p.P269L	ENST00000358026	NM_001128849.1	269	cCC/cTT	5/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		584	1039	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14628998	14628998	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	83	648	0	ENST00000254322.2:c.164T>G	p.Leu55Arg	p.L55R	ENST00000254322	NM_006145.1	55	cTc/cGc	1/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		648	1160	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272342	15272342	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375213868	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	29	301	0	ENST00000263388.2:c.6097C>T	p.Pro2033Ser	p.P2033S	ENST00000263388	NM_000435.2	2033	Ccc/Tcc	33/33	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		301	562	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733295	40733295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	33	242	0	ENST00000373198.4:c.3511C>T	p.Pro1171Ser	p.P1171S	ENST00000373198	NM_133170.3	1171	Cct/Tct	26/32	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		242	459	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944415	40944415	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	64	528	1	ENST00000373198.4:c.2087C>T	p.Ser696Phe	p.S696F	ENST00000373198	NM_133170.3	696	tCt/tTt	12/32	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		529	1013	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076940	41076940	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	56	440	0	ENST00000373198.4:c.1480C>T	p.Gln494Ter	p.Q494*	ENST00000373198	NM_133170.3	494	Caa/Taa	9/32	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		440	895	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164518	36164518	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1256636876	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	49	230	0	ENST00000300305.3:c.1357G>A	p.Val453Met	p.V453M	ENST00000300305		453	Gtg/Atg	8/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		230	482	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775563	39775563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007810-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	63	360	0	ENST00000288319.7:c.457C>T	p.Pro153Ser	p.P153S	ENST00000288319	NM_182918.3	153	Cca/Tca	4/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		360	695	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0007868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	154	456	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.543012729113206	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.543012729113206	1		456	355	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0007868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	168	990	1	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.543012729113206	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.543012729113206	1		991	430	SUCCESS
APC	324	MSKCC	GRCh37	5	112174720	112174720	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0007868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	98	416	0	ENST00000257430.4:c.3429T>G	p.Tyr1143Ter	p.Y1143*	ENST00000257430	NM_000038.5	1143	taT/taG	16/16	0.406813235377417	1	FACETS	0.722	0.65	0.798	0.722	0.65	0.798	SUBCLONAL	1	TRUE	0	0.543012729113206	1		416	364	SUCCESS
APC	324	MSKCC	GRCh37	5	112175447	112175447	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0007868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	50	373	0	ENST00000257430.4:c.4156A>T	p.Arg1386Ter	p.R1386*	ENST00000257430	NM_000038.5	1386	Aga/Tga	16/16	0.406813235377417	1	FACETS	0.386	0.328	0.448	0.386	0.328	0.448	SUBCLONAL	1	TRUE	0	0.543012729113206	1		373	348	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235939	108235939	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	30	350	0	ENST00000278616.4:c.8981A>G	p.Asn2994Ser	p.N2994S	ENST00000278616	NM_000051.3	2994	aAt/aGt	62/63	1	2	FACETS	0.304	0.244	0.37	0.304	0.244	0.37	SUBCLONAL	1	TRUE	1	0.543012729113206	2		350	364	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867334	45867334	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1222183146	NA	P-0007868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	64	204	0	ENST00000391945.4:c.859C>T	p.Arg287Cys	p.R287C	ENST00000391945	NM_000400.3	287	Cgt/Tgt	10/23	0.406813235377417	1	FACETS	0.859	0.756	0.965	0.859	0.756	0.965	CLONAL	1	TRUE	0	0.543012729113206	1		204	200	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713386	40713386	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	61	451	3	ENST00000373198.4:c.4129C>T	p.Arg1377Ter	p.R1377*	ENST00000373198	NM_133170.3	1377	Cga/Tga	30/32	0.105567412839576	5	FACETS	0.642	0.553	0.738			1	INDETERMINATE	1	TRUE	NA	0.543012729113206	5		454	635	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573381	41573381	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	28	564	1	ENST00000263253.7:c.5666G>T	p.Arg1889Met	p.R1889M	ENST00000263253	NM_001429.3	1889	aGg/aTg	31/31	0.368449684071966	1	FACETS	0.158	0.126	0.195	0.158	0.126	0.195	SUBCLONAL	1	TRUE	0	0.543012729113206	1		565	475	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0007879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	417	417	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.20864101028898	3	FACETS	1	0.99	1			1	CLONAL	3	TRUE	NA	0.337769375733671	3		417	872	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560500	65560500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs387906651	NA	P-0007879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	299	421	0	ENST00000358664.4:c.97C>T	p.Arg33Ter	p.R33*	ENST00000358664	NM_002382.4	33	Cga/Tga	3/5	0.331413847450263	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.337769375733671	2		421	826	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463289	25463289	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs147828672	NA	P-0007879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	104	303	0	ENST00000264709.3:c.2204A>G	p.Tyr735Cys	p.Y735C	ENST00000264709	NM_175629.2	735	tAc/tGc	19/23	0.308734966643239	4	FACETS	1	0.969	1	0.406	0.363	0.45	CLONAL	1	TRUE	1	0.337769375733671	4		303	677	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873421	136873421	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	148	668	1	ENST00000241393.3:c.77A>T	p.Glu26Val	p.E26V	ENST00000241393	NM_003467.2	26	gAa/gTa	2/2	0.337769375733671	3	FACETS	0.925	0.844	1	0.463	0.422	0.506	CLONAL	1	TRUE	1	0.337769375733671	3		669	1107	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542681	187542681	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	321	488	0	ENST00000441802.2:c.5059G>T	p.Gly1687Trp	p.G1687W	ENST00000441802	NM_005245.3	1687	Ggg/Tgg	10/27	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.337769375733671	2		488	809	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056437	26056437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781281855	NA	P-0007879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	58	197	0	ENST00000343677.2:c.220G>A	p.Glu74Lys	p.E74K	ENST00000343677	NM_005319.3	74	Gag/Aag	1/1	0.337769375733671	3	FACETS	0.814	0.7	0.938	0.407	0.35	0.469	CLONAL	1	TRUE	1	0.337769375733671	3		197	493	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540386	23540386	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	48	86	0	ENST00000380871.4:c.17A>T	p.Glu6Val	p.E6V	ENST00000380871	NM_006167.3	6	gAg/gTg	1/2	0.331413847450263	2	FACETS	0.917	0.79	1	0.917	0.79	1	CLONAL	2	TRUE	0	0.337769375733671	2		86	155	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891211	101891211	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	121	416	0	ENST00000374994.4:c.172G>T	p.Val58Phe	p.V58F	ENST00000374994	NM_004612.2	58	Gtc/Ttc	2/9	1	2	FACETS	0.897	0.81	0.988	0.897	0.81	0.988	CLONAL	1	TRUE	1	0.337769375733671	2		416	799	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391998	139391998	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	59	309	0	ENST00000277541.6:c.6193C>G	p.Leu2065Val	p.L2065V	ENST00000277541	NM_017617.3	2065	Ctg/Gtg	34/34	1	2	FACETS	0.753	0.649	0.866	0.753	0.649	0.866	SUBCLONAL	1	TRUE	1	0.337769375733671	2		309	464	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041209	47041285	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTTCTGCTCTCCCACCGGCTACCAGCCCCACTGCCCAGGAATCCTACAGCCAGTACCGTGAGTAGCCACAGCCTGTG	GTTCTGCTCTCCCACCGGCTACCAGCCCCACTGCCCAGGAATCCTACAGCCAGTACCGTGAGTAGCCACAGCCTGTG	-	novel	NA	P-0007879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	267	564	0	ENST00000377604.3:c.1638_1693+21del		p.X546_splice	ENST00000377604	NM_001204468.1	546		15/24	NA	2	FACETS	0.992	0.934	1			1	INDETERMINATE	2	TRUE	NA	0.337769375733671	2		564	797	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0007883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	619	546	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.704071734881925	3	FACETS	0.996	0.972	1	0.996	0.972	1	CLONAL	3	TRUE	0	0.704071734881925	3		547	796	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0007883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	216	473	0	ENST00000262160.6:c.1391C>G	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tGa	11/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.704071734881925	2		473	602	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937887	36937887	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	291	611	0	ENST00000361632.4:c.949C>A	p.His317Asn	p.H317N	ENST00000361632		317	Cac/Aac	7/16	0.522566441685636	3	FACETS	0.874	0.821	0.928			1	CLONAL	1	TRUE	NA	0.704071734881925	3		611	1279	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804274	43804274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1215318596	NA	P-0007883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	252	515	0	ENST00000372470.3:c.274G>A	p.Val92Met	p.V92M	ENST00000372470	NM_005373.2	92	Gtg/Atg	3/12	0.522566441685636	3	FACETS	0.85	0.794	0.907			1	CLONAL	1	TRUE	NA	0.704071734881925	3		515	1139	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267681	198267681	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	159	409	0	ENST00000335508.6:c.1798T>A	p.Leu600Met	p.L600M	ENST00000335508	NM_012433.2	600	Ttg/Atg	13/25	0.689671323244352	4	FACETS	0.962	0.883	1	0.241	0.22	0.262	CLONAL	1	TRUE	0	0.704071734881925	4		409	800	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032541	12032541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267604739	NA	P-0007883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	483	310	0	ENST00000353533.5:c.977C>T	p.Pro326Leu	p.P326L	ENST00000353533	NM_003010.3	326	cCg/cTg	9/11	0.704071734881925	3	FACETS	0.975	0.949	1	0.975	0.949	1	CLONAL	3	TRUE	0	0.704071734881925	3		310	634	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371784	45371784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	229	488	0	ENST00000262160.6:c.1207G>A	p.Glu403Lys	p.E403K	ENST00000262160	NM_005901.5	403	Gaa/Aaa	10/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.704071734881925	2		488	589	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757428	40757428	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763638227	NA	P-0007883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1856	230	481	1	ENST00000373198.4:c.2870C>T	p.Pro957Leu	p.P957L	ENST00000373198	NM_133170.3	957	cCg/cTg	20/32	0.704071734881925	8	FACETS	0.975	0.904	1	0.162	0.15	0.175	CLONAL	1	TRUE	2	0.704071734881925	8		482	2086	SUCCESS
APC	324	MSKCC	GRCh37	5	112175472	112175472	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	404	398	0	ENST00000257430.4:c.4181del	p.Asp1394ValfsTer21	p.D1394Vfs*21	ENST00000257430	NM_000038.5	1394	gAt/gt	16/16	0.699897382771541	2	FACETS	0.991	0.958	1	0.991	0.958	1	CLONAL	2	TRUE	0	0.704071734881925	2		398	579	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0007911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	238	370	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	0.343958055091093	2		370	1122	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153609	55153609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501520	NA	P-0007911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1293	314	602	0	ENST00000257290.5:c.2575G>A	p.Val859Met	p.V859M	ENST00000257290	NM_006206.4	859	Gtg/Atg	19/23	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.343958055091093	2		602	1607	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515215	149515215	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1247	230	645	0	ENST00000261799.4:c.267C>A	p.Asn89Lys	p.N89K	ENST00000261799	NM_002609.3	89	aaC/aaA	3/23	1	2	FACETS	0.905	0.842	0.972	0.905	0.842	0.972	CLONAL	1	TRUE	1	0.343958055091093	2		645	1477	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068126	94068126	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1543	209	825	0	ENST00000369303.4:c.836G>T	p.Cys279Phe	p.C279F	ENST00000369303	NM_004440.3	279	tGt/tTt	4/17	0.213708820641844	1	FACETS	0.574	0.531	0.62	0.574	0.531	0.62	SUBCLONAL	1	TRUE	0	0.343958055091093	1		825	1752	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522169	157522169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1368764248	NA	P-0007911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	121	318	1	ENST00000346085.5:c.4441C>T	p.Pro1481Ser	p.P1481S	ENST00000346085	NM_020732.3	1481	Cct/Tct	18/20	1	2	FACETS	0.87	0.786	0.958	0.87	0.786	0.958	CLONAL	1	TRUE	1	0.343958055091093	2		319	809	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646831	23646831	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0007911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1405	1102	781	1	ENST00000261584.4:c.1036A>T	p.Lys346Ter	p.K346*	ENST00000261584	NM_024675.3	346	Aaa/Taa	4/13	0.343958055091093	4	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	1	0.343958055091093	4		782	2507	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042359	16042359	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	285	613	0	ENST00000268712.3:c.1315G>A	p.Val439Ile	p.V439I	ENST00000268712	NM_006311.3	439	Gtt/Att	12/46	0.343958055091093	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.343958055091093	1		613	1210	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564828	41564828	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	145	482	1	ENST00000263253.7:c.4129C>T	p.His1377Tyr	p.H1377Y	ENST00000263253	NM_001429.3	1377	Cat/Tat	25/31	1	2	FACETS	0.679	0.618	0.743	0.679	0.618	0.743	SUBCLONAL	1	TRUE	1	0.343958055091093	2		483	1242	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354667	70354667	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1569482153	NA	P-0007926-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	135	617	0	ENST00000374080.3:c.4832G>A	p.Arg1611His	p.R1611H	ENST00000374080		1611	cGt/cAt	35/45	1	2	FACETS	0.932	0.847	1	0.932	0.847	1	CLONAL	1	TRUE	1	0.335952301105054	2		617	862	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576888	7576889	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007926-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	97	419	0	ENST00000269305.4:c.957_958insT	p.Lys320Ter	p.K320*	ENST00000269305	NM_001126112.2	319	-/T	9/11	0.311451642601929	1	FACETS	0.82	0.733	0.913	0.82	0.733	0.913	CLONAL	1	TRUE	0	0.335952301105054	1		419	586	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952149	178952150	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTTT	novel	NA	P-0007926-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	102	221	0	ENST00000263967.3:c.3205_3206insTTTT	p.Ter1069PhefsTer5	p.*1069Ffs*5	ENST00000263967	NM_006218.2	1068	-/TTTT	21/21	0.335952301105054	3	FACETS	1	0.981	1	0.727	0.653	0.804	CLONAL	1	TRUE	1	0.335952301105054	3		221	488	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0007976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	508	481	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	0.811153309372789	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.861495980551193	1		481	652	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599341	55599341	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519761	NA	P-0007976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	335	389	0	ENST00000288135.5:c.2467T>G	p.Tyr823Asp	p.Y823D	ENST00000288135	NM_000222.2	823	Tat/Gat	17/21	0.811153309372789	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.861495980551193	1		389	430	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0008022-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	177	546	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.603843260551807	2		547	543	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555687605	NA	P-0008022-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	289	334	0	ENST00000342988.3:c.1610A>G	p.Asp537Gly	p.D537G	ENST00000342988	NM_005359.5	537	gAc/gGc	12/12	0.603843260551807	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	0	0.603843260551807	1		334	607	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117799	108117799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202160435	NA	P-0008022-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	209	288	2	ENST00000278616.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000278616	NM_000051.3	337	cGt/cAt	8/63	1	2	FACETS	0.999	0.931	1	0.999	0.931	1	CLONAL	1	FALSE	1	0.603843260551807	2		290	693	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0008022-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	177	286	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	1	2	FACETS	0.875	0.809	0.943	0.875	0.809	0.943	CLONAL	1	FALSE	1	0.603843260551807	2		286	670	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578538	7578538	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008022-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	167	1084	0	ENST00000269305.4:c.392A>G	p.Asn131Ser	p.N131S	ENST00000269305	NM_001126112.2	131	aAc/aGc	5/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.603843260551807	2		1084	493	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100976	27100976	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008022-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	142	306	0	ENST00000324856.7:c.4258C>T	p.Gln1420Ter	p.Q1420*	ENST00000324856	NM_006015.4	1420	Cag/Tag	18/20	1	2	FACETS	0.891	0.816	0.968	0.891	0.816	0.968	CLONAL	1	FALSE	1	0.603843260551807	2		306	528	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026147	36026147	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767829559	NA	P-0008022-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	515	406	0	ENST00000358208.4:c.749C>T	p.Thr250Met	p.T250M	ENST00000358208		250	aCg/aTg	7/12	0.420015120027719	6	FACETS	0.894	0.86	0.928			1	CLONAL	4	FALSE	NA	0.603843260551807	6		406	1053	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0008308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	337	452	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.704194443448995	2		452	955	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014097	70014097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757354709	NA	P-0008308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	231	802	0	ENST00000394351.3:c.958G>A	p.Val320Ile	p.V320I	ENST00000394351	NM_000248.3	320	Gtt/Att	9/9	0.356024943420455	1	FACETS	0.357	0.332	0.383	0.357	0.332	0.383	INDETERMINATE	1	TRUE	0	0.704194443448995	1		802	1191	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710666	114710666	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	436	763	0	ENST00000543371.1:c.151G>T	p.Glu51Ter	p.E51*	ENST00000543371	NM_001198531.1	51	Gaa/Taa	1/14	0.356024943420455	1	FACETS	0.731	0.698	0.763	0.731	0.698	0.763	INDETERMINATE	1	TRUE	0	0.704194443448995	1		763	1098	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2221281	2221281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1313697003	NA	P-0008308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	317	502	3	ENST00000326181.6:c.365C>T	p.Ala122Val	p.A122V	ENST00000326181	NM_032271.2	122	gCg/gTg	6/21	0.397019351023411	1	FACETS	0.881	0.839	0.924	0.881	0.839	0.924	INDETERMINATE	1	TRUE	0	0.704194443448995	1		505	662	SUCCESS
AR	367	MSKCC	GRCh37	X	66941679	66941679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852562	NA	P-0008308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	446	403	0	ENST00000374690.3:c.2323C>T	p.Arg775Cys	p.R775C	ENST00000374690	NM_000044.3	775	Cgc/Tgc	6/8	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.704194443448995	1		403	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578266	7578267	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0008308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	323	661	0	ENST00000269305.4:c.582dup	p.Ile195TyrfsTer14	p.I195Yfs*14	ENST00000269305	NM_001126112.2	194	-/T	6/11	0.704194443448995	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.704194443448995	1		661	564	SUCCESS
APC	324	MSKCC	GRCh37	5	112175213	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	rs876659647	NA	P-0008308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	137	247	0	ENST00000257430.4:c.3925_3928del	p.Glu1309ArgfsTer11	p.E1309Rfs*11	ENST00000257430	NM_000038.5	1308	AAAGaa/aa	16/16	1	2	FACETS	0.869	0.796	0.943	0.869	0.796	0.943	CLONAL	1	TRUE	1	0.704194443448995	2		247	448	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591892	48591894	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	novel	NA	P-0008308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	456	630	0	ENST00000342988.3:c.1055_1057del	p.Gly352_Tyr353delinsAsp	p.G352_Y353delinsD	ENST00000342988	NM_005359.5	352	gGATac/gac	9/12	0.704194443448995	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.704194443448995	1		630	759	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	116	236	0				ENST00000310581	NM_198253.2	-/1132			0.704997824475207	1	FACETS	0.718	0.667	0.767	0.718	0.667	0.767	SUBCLONAL	1	TRUE	0	0.91164344316551	1		236	193	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344018	70344018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747113641	NA	P-0008341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	226	943	1	ENST00000374080.3:c.1754G>A	p.Arg585Gln	p.R585Q	ENST00000374080		585	cGa/cAa	13/45	0.574912661467597	1	FACETS	0.268	0.25	0.287	0.268	0.25	0.287	SUBCLONAL	1	TRUE	0	0.91164344316551	1		944	1006	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888165	112888165	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397507510	NA	P-0008341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	212	664	0	ENST00000351677.2:c.181G>T	p.Asp61Tyr	p.D61Y	ENST00000351677	NM_002834.3	61	Gat/Tat	3/16	NA	2	FACETS	0.599	0.557	0.641			1	INDETERMINATE	1	TRUE	NA	0.91164344316551	2		664	777	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106922	11106922	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	320	673	0	ENST00000358026.2:c.1627G>T	p.Asp543Tyr	p.D543Y	ENST00000358026	NM_001128849.1	543	Gac/Tac	10/36	0.780591859923943	1	FACETS	0.66	0.63	0.689	0.66	0.63	0.689	SUBCLONAL	1	TRUE	0	0.91164344316551	1		673	579	SUCCESS
APC	324	MSKCC	GRCh37	5	112128207	112128207	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	592	571	0	ENST00000257430.4:c.712del	p.Gln238LysfsTer55	p.Q238Kfs*55	ENST00000257430	NM_000038.5	237	tCc/tc	7/16	0.433551818485501	1	FACETS	0.649	0.627	0.671	0.649	0.627	0.671	INDETERMINATE	1	TRUE	0	0.91164344316551	1		571	1089	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0008350-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	70	326	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.318188311323055	5	FACETS	0.983	0.877	1	0.983	0.877	1	CLONAL	3	TRUE	2	0.457015596724517	5		326	175	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604787	48604787	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519741	NA	P-0008350-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	40	261	0	ENST00000342988.3:c.1609G>T	p.Asp537Tyr	p.D537Y	ENST00000342988	NM_005359.5	537	Gac/Tac	12/12	0.457015596724517	2	FACETS	1	0.957	1	0.706	0.6	0.817	CLONAL	1	TRUE	0	0.457015596724517	2		261	124	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682869	190682869	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008350-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	43	227	0	ENST00000441310.2:c.545T>G	p.Leu182Arg	p.L182R	ENST00000441310	NM_000534.4	182	cTt/cGt	5/13	0.457015596724517	3	FACETS	1	0.925	1	0.581	0.492	0.677	CLONAL	1	TRUE	1	0.457015596724517	3		227	199	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437275	220437275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370513243	NA	P-0008350-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	51	455	1	ENST00000243786.2:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000243786	NM_002191.3	60	cGa/cAa	1/2	0.457015596724517	3	FACETS	1	0.914	1	0.546	0.468	0.63	CLONAL	1	TRUE	1	0.457015596724517	3		456	251	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233142	66233142	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1316940637	NA	P-0008350-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	49	282	0	ENST00000273854.3:c.1857G>A	p.Trp619Ter	p.W619*	ENST00000273854	NM_004439.5	619	tgG/tgA	10/18	0.457015596724517	2	FACETS	1	0.947	1	0.613	0.527	0.703	CLONAL	1	TRUE	0	0.457015596724517	2		282	175	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484372	8484372	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008350-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	26	194	0	ENST00000356435.5:c.3160T>C	p.Tyr1054His	p.Y1054H	ENST00000356435		1054	Tat/Cat	19/35	1	2	FACETS	0.925	0.745	1	0.925	0.745	1	CLONAL	1	TRUE	1	0.457015596724517	2		194	123	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201369	133201369	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866548835	NA	P-0008350-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	38	289	0	ENST00000320574.5:c.6775C>T	p.Arg2259Trp	p.R2259W	ENST00000320574	NM_006231.2	2259	Cgg/Tgg	49/49	0.176066968392884	2	FACETS	1	0.948	1	0.665	0.562	0.775	INDETERMINATE	1	TRUE	0	0.457015596724517	2		289	125	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677306	29677306	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008350-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	44	270	0	ENST00000356175.3:c.7364A>T	p.Tyr2455Phe	p.Y2455F	ENST00000356175	NM_000267.3	2455	tAt/tTt	49/57	0.457015596724517	2	FACETS	0.891	0.771	1	0.891	0.771	1	CLONAL	2	TRUE	0	0.457015596724517	2		270	108	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435815	56435815	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755967475	NA	P-0008350-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	31	168	0	ENST00000407977.2:c.1322del	p.Pro441LeufsTer61	p.P441Lfs*61	ENST00000407977		441	cCt/ct	9/10	0.457015596724517	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	2	TRUE	0	0.457015596724517	2		168	65	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73342922	73342923	+	inframe_insertion,splice_region_variant	In_Frame_Ins	INS	-	-	CCT	novel	NA	P-0008350-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	61	283	0	ENST00000377767.4:c.1881_1883dup	p.Gly628dup	p.G628dup	ENST00000377767	NM_014953.3	628	ggg/ggAGGg		0.304335752976491	4	FACETS	0.817	0.714	0.927	0.817	0.714	0.927	CLONAL	2	TRUE	2	0.457015596724517	4		283	238	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570841	226570841	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008350-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	10	230	0	ENST00000366794.5:c.1055A>C	p.Lys352Thr	p.K352T	ENST00000366794	NM_001618.3	352	aAa/aCa	8/23	0.432967496486188	3	FACETS	0.379	0.257	0.53	0.189	0.128	0.265	SUBCLONAL	1	TRUE	1	0.457015596724517	3		230	142	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522403	157522403	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008350-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	11	263	0	ENST00000346085.5:c.4675T>G	p.Phe1559Val	p.F1559V	ENST00000346085	NM_020732.3	1559	Ttc/Gtc	18/20	0.216646314049639	4	FACETS	0.458	0.317	0.632	0.153	0.105	0.211	INDETERMINATE	1	TRUE	1	0.457015596724517	4		263	153	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69456108	69456108	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008350-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	10	281	0	ENST00000227507.2:c.27A>T	p.Glu9Asp	p.E9D	ENST00000227507	NM_053056.2	9	gaA/gaT	1/5	0.432967496486188	3	FACETS	0.437	0.297	0.61	0.219	0.148	0.305	SUBCLONAL	1	TRUE	1	0.457015596724517	3		281	123	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350338	89350338	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008350-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	19	551	0	ENST00000301030.4:c.2612A>C	p.Asp871Ala	p.D871A	ENST00000301030	NM_001256183.1	871	gAc/gCc	9/13	1	2	FACETS	0.376	0.286	0.481	0.376	0.286	0.481	SUBCLONAL	1	TRUE	1	0.457015596724517	2		551	221	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0008458-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	14	416	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.294288834626114	3	FACETS	0.87	0.636	1	0.435	0.318	0.573	CLONAL	1	TRUE	1	0.361800809479056	3		416	105	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0008458-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	11	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.579	0.403	0.793	0.579	0.403	0.793	SUBCLONAL	1	TRUE	1	0.361800809479056	2		326	105	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461135	120461135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008458-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	26	300	0	ENST00000256646.2:c.5823G>A	p.Met1941Ile	p.M1941I	ENST00000256646	NM_024408.3	1941	atG/atA	32/34	0.278330489970086	1	FACETS	0.623	0.497	0.765	0.623	0.497	0.765	SUBCLONAL	1	TRUE	0	0.361800809479056	1		300	189	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845956	151845956	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008458-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	34	389	0	ENST00000262189.6:c.13056G>A	p.Trp4352Ter	p.W4352*	ENST00000262189	NM_170606.2	4352	tgG/tgA	52/59	0.33988814670768	1	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	0	0.361800809479056	1		389	147	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0008458-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	79	426	0	ENST00000269305.4:c.375+1G>T		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.247599905552054	0	FACETS	0.799	0.708	0.895			1	SUBCLONAL	1	TRUE	0	0.361800809479056	0		426	349	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435549	56435549	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008458-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	59	424	1	ENST00000407977.2:c.1588C>T	p.Pro530Ser	p.P530S	ENST00000407977		530	Cct/Tct	9/10	1	2	FACETS	0.811	0.7	0.931	0.811	0.7	0.931	CLONAL	1	TRUE	1	0.361800809479056	2		425	402	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715688	30715689	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008458-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	22	295	0	ENST00000295754.5:c.1346_1347insT	p.Met450HisfsTer13	p.M450Hfs*13	ENST00000295754	NM_003242.5	449	tcc/tcTc	5/7	0.292181467213246	0	FACETS	0.558	0.437	0.695			1	SUBCLONAL	1	TRUE	0	0.361800809479056	0		295	139	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188309	10188309	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs869025655	NA	P-0008459-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	234	363	0	ENST00000256474.2:c.452T>G	p.Ile151Ser	p.I151S	ENST00000256474	NM_000551.3	151	aTc/aGc	2/3	0.492958426827216	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.492958426827216	1		363	705	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	62	236	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.763	0.66	0.874			1	INDETERMINATE	1	TRUE	NA	0.32	2		236	508	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	226	417	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.782	0.729	0.836	1	0.992	1	SUBCLONAL	2	TRUE	1	0.32	2		417	903	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809240	243809240	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs374658863	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1460	97	641	0	ENST00000263826.5:c.384A>G	p.Ile128Met	p.I128M	ENST00000263826	NM_005465.4	128	atA/atG	4/13	0.3	3	FACETS	0.452	0.401	0.506	0.226	0.2	0.253	SUBCLONAL	1	TRUE	1	0.32	3		641	1557	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543861	212543861	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	55	380	0	ENST00000342788.4:c.1538G>T	p.Trp513Leu	p.W513L	ENST00000342788	NM_005235.2	513	tGg/tTg	13/28	0.3	3	FACETS	0.428	0.365	0.498	0.214	0.182	0.249	SUBCLONAL	1	TRUE	1	0.32	3		380	931	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576787	212576787	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1317408332	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	158	441	1	ENST00000342788.4:c.1112C>A	p.Thr371Asn	p.T371N	ENST00000342788	NM_005235.2	371	aCt/aAt	9/28	0.3	3	FACETS	1	0.948	1	0.524	0.48	0.572	CLONAL	1	TRUE	1	0.32	3		442	1092	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498373	89498373	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	75	307	0	ENST00000336596.2:c.2347-2A>T		p.X783_splice	ENST00000336596	NM_005233.5	783			0.180084322652968	2	FACETS	0.818	0.718	0.926	0.409	0.359	0.463	INDETERMINATE	1	TRUE	0	0.32	2		307	573	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670841	134670841	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	31	176	0	ENST00000398015.3:c.752G>T	p.Gly251Val	p.G251V	ENST00000398015	NM_004441.4	251	gGg/gTg	3/16	0.209478477908833	3	FACETS	0.614	0.497	0.746	0.307	0.248	0.373	SUBCLONAL	1	TRUE	1	0.32	3		176	366	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825298	134825298	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	65	368	0	ENST00000398015.3:c.814G>C	p.Ala272Pro	p.A272P	ENST00000398015	NM_004441.4	272	Gca/Cca	4/16	0.209478477908833	3	FACETS	0.601	0.52	0.689	0.301	0.26	0.345	SUBCLONAL	1	TRUE	1	0.32	3		368	784	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919111	178919111	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	53	302	0	ENST00000263967.3:c.596C>G	p.Ser199Cys	p.S199C	ENST00000263967	NM_006218.2	199	tCt/tGt	4/21	0.209478477908833	3	FACETS	0.514	0.438	0.599	0.257	0.219	0.3	SUBCLONAL	1	TRUE	1	0.32	3		302	747	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151593	55151593	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1202	81	544	0	ENST00000257290.5:c.2379G>C	p.Leu793Phe	p.L793F	ENST00000257290	NM_006206.4	793	ttG/ttC	17/23	0.3	3	FACETS	0.458	0.402	0.518	0.229	0.201	0.259	SUBCLONAL	1	TRUE	1	0.32	3		544	1283	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007355	143007355	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	177	369	0	ENST00000262992.4:c.2429T>A	p.Leu810His	p.L810H	ENST00000262992	NM_001101669.1	810	cTt/cAt	22/24	0.3	3	FACETS	1	0.987	1	0.683	0.629	0.739	CLONAL	1	TRUE	1	0.32	3		369	940	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517745	187517745	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	103	210	0	ENST00000441802.2:c.12949C>A	p.Pro4317Thr	p.P4317T	ENST00000441802	NM_005245.3	4317	Cct/Act	25/27	0.3	3	FACETS	0.81	0.729	0.895	0.81	0.729	0.895	CLONAL	2	TRUE	1	0.32	3		210	461	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157470075	157470075	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	21	102	0	ENST00000346085.5:c.2869G>T	p.Ala957Ser	p.A957S	ENST00000346085	NM_020732.3	957	Gca/Tca	9/20	0.209478477908833	3	FACETS	0.659	0.509	0.833	0.33	0.254	0.417	SUBCLONAL	1	TRUE	1	0.32	3		102	231	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467792	50467792	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	61	474	1	ENST00000331340.3:c.1027G>T	p.Val343Phe	p.V343F	ENST00000331340	NM_006060.4	343	Gtc/Ttc	8/8	0.209478477908833	3	FACETS	0.522	0.449	0.602	0.261	0.224	0.301	SUBCLONAL	1	TRUE	1	0.32	3		475	847	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335070	81335070	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	38	259	0	ENST00000222390.5:c.1758-1G>C		p.X586_splice	ENST00000222390	NM_000601.4	586			0.253034272687811	4	FACETS	0.486	0.401	0.582	0.243	0.2	0.291	SUBCLONAL	1	TRUE	2	0.32	4		259	645	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339283	116339283	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1447	99	544	0	ENST00000397752.3:c.145G>T	p.Glu49Ter	p.E49*	ENST00000397752	NM_000245.2	49	Gaa/Taa	2/21	0.253034272687811	4	FACETS	0.528	0.469	0.591	0.264	0.234	0.296	SUBCLONAL	1	TRUE	2	0.32	4		544	1546	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436685	8436685	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	59	367	0	ENST00000356435.5:c.3993G>C	p.Met1331Ile	p.M1331I	ENST00000356435		1331	atG/atC	24/35	1	2	FACETS	0.452	0.388	0.523	0.452	0.388	0.523	SUBCLONAL	1	TRUE	1	0.32	2		367	815	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135780996	135780996	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1403	428	862	0	ENST00000298552.3:c.1969G>T	p.Ala657Ser	p.A657S	ENST00000298552	NM_001162426.1	657	Gca/Tca	15/23	0.185129172928366	3	FACETS	0.847	0.805	0.891	0.565	0.537	0.594	INDETERMINATE	2	TRUE	0	0.32	3		862	1831	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100747	8100748	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	106	326	0	ENST00000346208.3:c.721_722delinsTT	p.Gly241Phe	p.G241F	ENST00000346208		241	GGc/TTc	3/6	0.265429214546356	3	FACETS	0.973	0.872	1	0.486	0.436	0.54	CLONAL	1	TRUE	1	0.32	3		326	790	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066737	77066737	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1174	173	558	0	ENST00000356341.3:c.748G>C	p.Asp250His	p.D250H	ENST00000356341	NM_002576.4	250	Gat/Cat	7/15	0.3	3	FACETS	0.931	0.855	1	0.31	0.285	0.337	CLONAL	1	TRUE	0	0.32	3		558	1347	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076656	102076656	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	185	303	0	ENST00000282441.5:c.835G>T	p.Val279Leu	p.V279L	ENST00000282441	NM_001130145.2	279	Gtg/Ttg	5/9	0.3	3	FACETS	0.988	0.915	1	0.658	0.61	0.708	CLONAL	2	TRUE	0	0.32	3		303	679	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885884	111885884	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1703	149	825	1	ENST00000341259.2:c.1506T>A	p.Ser502Arg	p.S502R	ENST00000341259	NM_005475.2	502	agT/agA	8/8	1	2	FACETS	0.503	0.457	0.551	0.503	0.457	0.551	SUBCLONAL	1	TRUE	1	0.32	2		826	1852	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202738	133202738	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs759795841	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	191	543	0	ENST00000320574.5:c.6496G>T	p.Asp2166Tyr	p.D2166Y	ENST00000320574	NM_006231.2	2166	Gac/Tac	46/49	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.32	2		543	1026	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608451	28608451	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	64	448	0	ENST00000241453.7:c.1691A>T	p.His564Leu	p.H564L	ENST00000241453	NM_004119.2	564	cAc/cTc	13/24	0.209478477908833	3	FACETS	0.514	0.444	0.591	0.257	0.222	0.296	SUBCLONAL	1	TRUE	1	0.32	3		448	902	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346365	73346365	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	144	412	0	ENST00000377767.4:c.1435G>T	p.Asp479Tyr	p.D479Y	ENST00000377767	NM_014953.3	479	Gac/Tac	10/21	0.209478477908833	3	FACETS	1	0.965	1	0.558	0.509	0.61	CLONAL	1	TRUE	1	0.32	3		412	935	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103520576	103520576	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	135	513	0	ENST00000355739.4:c.2647G>T	p.Gly883Trp	p.G883W	ENST00000355739	NM_000123.3	883	Ggg/Tgg	12/15	0.209478477908833	3	FACETS	0.907	0.823	0.996	0.454	0.411	0.498	CLONAL	1	TRUE	1	0.32	3		513	1079	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576175	88576175	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	58	383	1	ENST00000360948.2:c.1498A>T	p.Thr500Ser	p.T500S	ENST00000360948	NM_001012338.2	500	Act/Tct	13/19	1	2	FACETS	0.438	0.375	0.507	0.438	0.375	0.507	SUBCLONAL	1	TRUE	1	0.32	2		384	828	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680705	88680705	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	73	505	0	ENST00000360948.2:c.552C>A	p.Ser184Arg	p.S184R	ENST00000360948	NM_001012338.2	184	agC/agA	6/19	1	2	FACETS	0.437	0.38	0.498	0.437	0.38	0.498	SUBCLONAL	1	TRUE	1	0.32	2		505	1045	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726685	88726685	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	57	406	0	ENST00000360948.2:c.359C>A	p.Pro120His	p.P120H	ENST00000360948	NM_001012338.2	120	cCc/cAc	4/19	1	2	FACETS	0.464	0.397	0.537	0.464	0.397	0.537	SUBCLONAL	1	TRUE	1	0.32	2		406	768	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943749	9943749	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	114	368	0	ENST00000330684.3:c.1192G>T	p.Asp398Tyr	p.D398Y	ENST00000330684	NM_001134407.1	398	Gac/Tac	5/13	0.180746525024975	2	FACETS	1	0.949	1	0.541	0.488	0.598	INDETERMINATE	1	TRUE	0	0.32	2		368	658	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	154	401	1	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.180746525024975	2	FACETS	1	0.98	1	0.611	0.559	0.664	INDETERMINATE	1	TRUE	0	0.32	2		402	788	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016579	12016579	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	140	390	0	ENST00000353533.5:c.715A>T	p.Arg239Ter	p.R239*	ENST00000353533	NM_003010.3	239	Aga/Tga	7/11	0.180746525024975	2	FACETS	1	0.915	1	0.502	0.457	0.55	INDETERMINATE	1	TRUE	0	0.32	2		390	871	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562942	29562942	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	185	550	3	ENST00000356175.3:c.3877G>T	p.Gly1293Cys	p.G1293C	ENST00000356175	NM_000267.3	1293	Ggt/Tgt	29/57	0.163888207625147	4	FACETS	1	0.977	1	0.579	0.533	0.627	INDETERMINATE	1	TRUE	2	0.32	4		553	1318	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41222955	41222955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1292	233	673	0	ENST00000357654.3:c.4976C>T	p.Pro1659Leu	p.P1659L	ENST00000357654	NM_007294.3	1659	cCa/cTa	15/23	0.163888207625147	4	FACETS	1	0.987	1	0.63	0.586	0.676	INDETERMINATE	1	TRUE	2	0.32	4		673	1525	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243818	41243818	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	131	385	0	ENST00000357654.3:c.3730C>T	p.His1244Tyr	p.H1244Y	ENST00000357654	NM_007294.3	1244	Cat/Tat	10/23	0.163888207625147	4	FACETS	1	0.978	1	0.632	0.573	0.694	INDETERMINATE	1	TRUE	2	0.32	4		385	855	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190081	123190081	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	71	280	0	ENST00000218089.9:c.1300A>C	p.Lys434Gln	p.K434Q	ENST00000218089	NM_001042749.1	434	Aaa/Caa	14/35	0.3	2	FACETS	0.624	0.544	0.711			1	SUBCLONAL	1	TRUE	NA	0.32	2		280	711	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578336	212578336	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	61	389	0	ENST00000342788.4:c.921del	p.Cys308AlafsTer8	p.C308Afs*8	ENST00000342788	NM_005235.2	307	gcC/gc	8/28	0.3	3	FACETS	0.485	0.417	0.559	0.242	0.208	0.28	SUBCLONAL	1	TRUE	1	0.32	3		389	912	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907073	101907073	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008465-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	148	383	0	ENST00000374994.4:c.1034del	p.Gly345GlufsTer8	p.G345Efs*8	ENST00000374994	NM_004612.2	345	Gga/ga	6/9	0.185129172928366	3	FACETS	1	0.98	1	0.417	0.381	0.455	INDETERMINATE	1	TRUE	0	0.32	3		383	857	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0008481-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	39	121	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	NA	2	FACETS	1	0.944	1			1	INDETERMINATE	1	TRUE	NA	0.571410290604697	2		121	109	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842693	68842693	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008481-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	129	635	0	ENST00000261769.5:c.631del	p.Thr211GlnfsTer4	p.T211Qfs*4	ENST00000261769	NM_004360.3	210	gAa/ga	5/16	0.571410290604697	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.571410290604697	1		635	294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138729528	NA	P-0008488-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	85	203	0	ENST00000269305.4:c.523C>G	p.Arg175Gly	p.R175G	ENST00000269305	NM_001126112.2	175	Cgc/Ggc	5/11	0.210894902574066	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.210894902574066	1		203	570	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440222	220440222	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008488-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	281	589	1	ENST00000243786.2:c.1075C>A	p.Leu359Ile	p.L359I	ENST00000243786	NM_002191.3	359	Ctc/Atc	2/2	0.208841171882686	2	FACETS	0.961	0.901	1	0.961	0.901	1	CLONAL	2	TRUE	0	0.210894902574066	2		590	1386	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1272334	1272334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008488-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	186	368	0	ENST00000310581.5:c.2348C>A	p.Thr783Asn	p.T783N	ENST00000310581	NM_198253.2	783	aCc/aAc	7/16	NA	2	FACETS	0.99	0.915	1			1	INDETERMINATE	2	TRUE	NA	0.210894902574066	2		368	891	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3799652	3799652	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008488-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	69	429	0	ENST00000262367.5:c.3812A>G	p.Lys1271Arg	p.K1271R	ENST00000262367	NM_004380.2	1271	aAa/aGa	21/31	1	2	FACETS	0.528	0.458	0.605	0.528	0.458	0.605	SUBCLONAL	1	TRUE	1	0.210894902574066	2		429	1239	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867270	45867270	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008488-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	65	175	2	ENST00000391945.4:c.923C>A	p.Pro308His	p.P308H	ENST00000391945	NM_000400.3	308	cCc/cAc	10/23	0.210600361789228	4	FACETS	1	0.969	1	0.723	0.628	0.826	CLONAL	1	TRUE	2	0.210894902574066	4		177	516	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841228	15841228	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008488-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	207	373	0	ENST00000307771.7:c.1312G>T	p.Gly438Cys	p.G438C	ENST00000307771	NM_005089.3	438	Ggc/Tgc	11/11	1	2	FACETS	0.928	0.86	0.998	1	0.993	1	CLONAL	2	TRUE	1	0.210894902574066	2		373	1058	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268448	142268448	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs564283952	NA	P-0008488-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	48	253	0	ENST00000350721.4:c.3044G>C	p.Arg1015Pro	p.R1015P	ENST00000350721	NM_001184.3	1015	cGa/cCa	15/47	0.203504110615879	3	FACETS	0.582	0.49	0.683			1	SUBCLONAL	1	TRUE	NA	0.210894902574066	3		253	865	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968577	55968577	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008488-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	70	354	0	ENST00000263923.4:c.2086C>A	p.Pro696Thr	p.P696T	ENST00000263923	NM_002253.2	696	Cca/Aca	14/30	0.210894902574066	3	FACETS	0.654	0.568	0.747	0.327	0.284	0.374	SUBCLONAL	1	TRUE	1	0.210894902574066	3		354	1122	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0008492-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	70	326	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	0.403584427149085	2		326	333	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815564	139815564	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008492-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1735	353	606	0	ENST00000247668.2:c.1035G>A	p.Met345Ile	p.M345I	ENST00000247668	NM_021138.3	345	atG/atA	9/11	0.382441416888689	3	FACETS	1	0.949	1	0.336	0.316	0.356	CLONAL	1	TRUE	0	0.403584427149085	3		606	2088	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815568	139815568	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008492-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1739	343	582	2	ENST00000247668.2:c.1039G>A	p.Ala347Thr	p.A347T	ENST00000247668	NM_021138.3	347	Gca/Aca	9/11	0.382441416888689	3	FACETS	0.981	0.925	1	0.327	0.308	0.347	CLONAL	1	TRUE	0	0.403584427149085	3		584	2082	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008531-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	147	236	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.973	0.898	1	0.973	0.898	1	CLONAL	1	TRUE	1	0.757380364769506	2		236	399	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0008531-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	251	316	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.757380364769506	2		316	624	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161888	47161891	+	frameshift_variant	Frame_Shift_Del	DEL	CTCT	CTCT	-	rs771527963	NA	P-0008531-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	295	518	0	ENST00000409792.3:c.4235_4238del	p.Glu1412ValfsTer19	p.E1412Vfs*19	ENST00000409792	NM_014159.6	1412	gAGAGt/gt	3/21	1	2	FACETS	0.899	0.848	0.949	0.899	0.848	0.949	CLONAL	1	TRUE	1	0.757380364769506	2		518	867	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799060	42799060	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008531-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	113	332	1	ENST00000575354.2:c.4544G>A	p.Arg1515His	p.R1515H	ENST00000575354	NM_015125.3	1515	cGc/cAc	20/20	0.755746119934793	1	FACETS	0.492	0.447	0.539	0.492	0.447	0.539	SUBCLONAL	1	TRUE	0	0.757380364769506	1		333	377	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794714	42794714	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008531-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	37	439	0	ENST00000575354.2:c.1795del	p.Arg599GlyfsTer129	p.R599Gfs*129	ENST00000575354	NM_015125.3	598	ttC/tt	10/20	0.755746119934793	1	FACETS	0.141	0.115	0.168	0.141	0.115	0.168	SUBCLONAL	1	TRUE	0	0.757380364769506	1		439	432	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082349	16082349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008531-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	137	396	0	ENST00000281043.3:c.163C>A	p.Leu55Met	p.L55M	ENST00000281043	NM_005378.4	55	Ctg/Atg	2/3	1	2	FACETS	0.489	0.445	0.535	0.489	0.445	0.535	SUBCLONAL	1	TRUE	1	0.757380364769506	2		396	740	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158212	47158212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553699111	NA	P-0008531-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	145	323	0	ENST00000409792.3:c.4487G>A	p.Arg1496Gln	p.R1496Q	ENST00000409792	NM_014159.6	1496	cGa/cAa	4/21	1	2	FACETS	0.592	0.541	0.644	0.592	0.541	0.644	SUBCLONAL	1	TRUE	1	0.757380364769506	2		323	647	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732969	74732969	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008531-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	178	355	0	ENST00000359995.5:c.274T>C	p.Tyr92His	p.Y92H	ENST00000359995	NM_001195427.1	92	Tac/Cac	1/3	1	2	FACETS	0.855	0.793	0.918	0.855	0.793	0.918	CLONAL	1	TRUE	1	0.757380364769506	2		355	550	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589583	67589584	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACA	novel	NA	P-0008531-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	128	334	0	ENST00000274335.5:c.1347_1349dup	p.Leu449_His450insGln	p.L449_H450insQ	ENST00000274335		449	tta/ttACAa	10/15	1	2	FACETS	0.476	0.432	0.523	0.476	0.432	0.523	SUBCLONAL	1	TRUE	1	0.757380364769506	2		334	710	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522604	67522605	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0008531-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	39	349	0	ENST00000274335.5:c.102_103dup	p.Gly35GlufsTer4	p.G35Efs*4	ENST00000274335		34	aaa/aaAGa	1/15	1	2	FACETS	0.135	0.111	0.162	0.135	0.111	0.162	SUBCLONAL	1	TRUE	1	0.757380364769506	2		349	761	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs864622237	NA	P-0008536-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	272	301	0	ENST00000269305.4:c.700T>C	p.Tyr234His	p.Y234H	ENST00000269305	NM_001126112.2	234	Tac/Cac	7/11	0.555942442368797	2	FACETS	0.961	0.914	1	0.961	0.914	1	CLONAL	2	TRUE	0	0.561386292051277	2		301	504	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591891	48591891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912581	NA	P-0008536-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	159	542	0	ENST00000342988.3:c.1054G>A	p.Gly352Arg	p.G352R	ENST00000342988	NM_005359.5	352	Gga/Aga	9/12	0.561386292051277	1	FACETS	0.963	0.892	1	0.963	0.892	1	CLONAL	1	TRUE	0	0.561386292051277	1		542	423	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317147	87317147	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008536-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	84	370	1	ENST00000277120.3:c.286C>A	p.Leu96Met	p.L96M	ENST00000277120		96	Ctg/Atg	3/19	0.561386292051277	4	FACETS	0.99	0.878	1	0.495	0.439	0.555	CLONAL	1	TRUE	2	0.561386292051277	4		371	472	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557725	21557725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs915063122	NA	P-0008536-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	160	516	1	ENST00000382592.4:c.2120G>A	p.Arg707Gln	p.R707Q	ENST00000382592	NM_014572.2	707	cGg/cAg	5/8	0.561386292051277	3	FACETS	0.899	0.825	0.976	0.45	0.412	0.488	CLONAL	1	TRUE	1	0.561386292051277	3		517	812	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993250	72993250	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008536-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	244	751	2	ENST00000268489.5:c.795C>A	p.Asp265Glu	p.D265E	ENST00000268489	NM_006885.3	265	gaC/gaA	2/10	1	2	FACETS	0.967	0.905	1	0.967	0.905	1	CLONAL	1	TRUE	1	0.561386292051277	2		753	899	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200072	138200072	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008544-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	25	198	0	ENST00000237289.4:c.1490G>T	p.Arg497Leu	p.R497L	ENST00000237289	NM_001270507.1	497	cGt/cTt	7/9	1	2	FACETS	0.452	0.356	0.563	0.452	0.356	0.563	SUBCLONAL	1	TRUE	1	0.267101745527358	2		198	414	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0008549-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	312	379	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.384488935333197	5	FACETS	1	0.991	1	0.833	0.787	0.88	CLONAL	2	TRUE	2	0.384488935333197	5		379	1024	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193121548	193121548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008549-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1243	133	499	0	ENST00000367435.3:c.946C>T	p.His316Tyr	p.H316Y	ENST00000367435	NM_024529.4	316	Cat/Tat	10/17	0.384488935333197	6	FACETS	0.889	0.805	0.979	0.222	0.201	0.245	CLONAL	1	TRUE	2	0.384488935333197	6		499	1376	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184592	11184592	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs774204282	NA	P-0008549-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	273	815	0	ENST00000361445.4:c.6625C>G	p.Leu2209Val	p.L2209V	ENST00000361445	NM_004958.3	2209	Ctg/Gtg	47/58	0.384488935333197	4	FACETS	0.868	0.815	0.924	0.868	0.815	0.924	CLONAL	2	TRUE	2	0.384488935333197	4		815	1132	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409016	139409016	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008558-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	472	550	0	ENST00000277541.6:c.2153A>G	p.Asn718Ser	p.N718S	ENST00000277541	NM_017617.3	718	aAt/aGt	13/34	0.311397993466866	3	FACETS	0.998	0.959	1	0.666	0.639	0.692	INDETERMINATE	2	TRUE	0	0.64084477330767	3		550	974	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396806	396806	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008558-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	494	530	0	ENST00000262320.3:c.220G>A	p.Gly74Ser	p.G74S	ENST00000262320	NM_003502.3	74	Ggc/Agc	2/11	0.64084477330767	3	FACETS	0.95	0.913	0.988	0.95	0.913	0.988	CLONAL	2	TRUE	1	0.64084477330767	3		530	1071	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2215919	2215919	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008558-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1365	389	943	0	ENST00000326181.6:c.121G>T	p.Val41Phe	p.V41F	ENST00000326181	NM_032271.2	41	Gtc/Ttc	3/21	0.64084477330767	3	FACETS	0.914	0.866	0.963	0.457	0.433	0.482	CLONAL	1	TRUE	1	0.64084477330767	3		943	1754	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7141814	7141814	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008558-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	712	551	0	ENST00000302850.5:c.2556C>G	p.Asp852Glu	p.D852E	ENST00000302850	NM_000208.2	852	gaC/gaG	13/22	0.630164903191516	3	FACETS	0.979	0.955	1	0.979	0.955	1	CLONAL	3	TRUE	0	0.64084477330767	3		551	999	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578371	7578382	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CATCGCTATCTG	CATCGCTATCTG	-	novel	NA	P-0008558-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	340	312	0	ENST00000269305.4:c.548_559del	p.Ser183_Gly187delinsCys	p.S183_G187delinsC	ENST00000269305	NM_001126112.2	183	tCAGATAGCGATGgt/tgt	5/11	0.64084477330767	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.64084477330767	2		312	503	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916774	48916775	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs587778825	NA	P-0008558-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	309	586	0	ENST00000267163.4:c.305_306del	p.Cys102TyrfsTer7	p.C102Yfs*7	ENST00000267163	NM_000321.2	102	TGt/t	3/27	0.637669183571837	2	FACETS	0.962	0.922	1	0.962	0.922	1	CLONAL	2	TRUE	0	0.64084477330767	2		586	501	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0008679-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	368	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.934	0.89	0.979	0.934	0.89	0.979	CLONAL	1	TRUE	1	0.892152068840614	2		326	883	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519938	NA	P-0008679-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	365	306	0	ENST00000263967.3:c.1034A>T	p.Asn345Ile	p.N345I	ENST00000263967	NM_006218.2	345	aAt/aTt	5/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.892152068840614	2		306	801	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437431	121437431	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0008679-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	252	166	0	ENST00000257555.6:c.1768+1G>A		p.X590_splice	ENST00000257555		590			1	2	FACETS	0.995	0.939	1	0.995	0.939	1	CLONAL	1	TRUE	1	0.892152068840614	2		166	568	SUCCESS
APC	324	MSKCC	GRCh37	5	112177587	112177587	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008758-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	32	309	0	ENST00000257430.4:c.6296T>G	p.Phe2099Cys	p.F2099C	ENST00000257430	NM_000038.5	2099	tTt/tGt	16/16	0.142967585340004	3	FACETS	0.439	0.355	0.534	0.219	0.177	0.267	INDETERMINATE	1	TRUE	1	0.3	3		309	559	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036041	180036041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008758-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	37	531	0	ENST00000261937.6:c.3820G>A	p.Asp1274Asn	p.D1274N	ENST00000261937	NM_182925.4	1274	Gac/Aac	29/30	0.3	0	FACETS	0.38	0.313	0.455			1	SUBCLONAL	1	TRUE	0	0.3	0		531	454	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692936	89692936	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008758-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	55	349	0	ENST00000371953.3:c.420A>T	p.Leu140Phe	p.L140F	ENST00000371953	NM_000314.4	140	ttA/ttT	5/9	0.3	3	FACETS	0.607	0.518	0.704			1	SUBCLONAL	1	TRUE	NA	0.3	3		349	695	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94169023	94169023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008758-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	35	466	0	ENST00000323929.3:c.1969C>T	p.Pro657Ser	p.P657S	ENST00000323929	NM_005591.3	657	Cct/Tct	18/20	0.3	3	FACETS	0.393	0.321	0.475			1	SUBCLONAL	1	TRUE	NA	0.3	3		466	682	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996021	73996021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008758-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	24	329	0	ENST00000318443.5:c.755C>T	p.Pro252Leu	p.P252L	ENST00000318443	NM_001024736.1	252	cCt/cTt	5/10	0.200138428003773	3	FACETS	0.401	0.313	0.502	0.2	0.156	0.251	SUBCLONAL	1	TRUE	1	0.3	3		329	459	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791709	42791709	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008758-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	63	334	0	ENST00000575354.2:c.595C>G	p.His199Asp	p.H199D	ENST00000575354	NM_015125.3	199	Cac/Gac	5/20	1	2	FACETS	0.618	0.534	0.709	0.618	0.534	0.709	SUBCLONAL	1	TRUE	1	0.3	2		334	680	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008759-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	61	236	0				ENST00000310581	NM_198253.2	-/1132			0.223754572689971	3	FACETS	1	0.955	1	0.633	0.547	0.727	CLONAL	1	TRUE	1	0.22	3		236	486	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0008759-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	269	503	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.251949039955927	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	1	0.22	3		503	1330	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148726	20148726	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0008759-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	94	351	0	ENST00000379607.5:c.338-1G>A		p.X113_splice	ENST00000379607	NM_001412.3	113			1	2	FACETS	0.783	0.695	0.878	0.783	0.695	0.878	SUBCLONAL	1	TRUE	1	0.22	2		351	1091	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0008759-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	275	625	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.21102279070497	2	FACETS	0.864	0.809	0.92	0.864	0.809	0.92	CLONAL	2	TRUE	0	0.22	2		625	1447	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731485	47731485	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008759-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	15	62	0	ENST00000449228.1:c.307C>T	p.His103Tyr	p.H103Y	ENST00000449228	NM_001127240.2	103	Cac/Tac	2/4	1	2	FACETS	0.988	0.728	1	0.988	0.728	1	CLONAL	1	TRUE	1	0.22	2		62	138	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0008761-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	640	582	2	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.333502530015059	5	FACETS	0.971	0.94	1	0.776	0.752	0.801	CLONAL	4	TRUE	0	0.496174219421139	5		584	1159	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0008761-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	393	758	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.411178189675169	3	FACETS	0.876	0.834	0.919	0.584	0.556	0.613	CLONAL	2	TRUE	0	0.496174219421139	3		759	1128	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416767	29416767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201768549	NA	P-0008761-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	279	384	0	ENST00000389048.3:c.4186G>A	p.Ala1396Thr	p.A1396T	ENST00000389048	NM_004304.4	1396	Gct/Act	29/29	0.344589602691669	3	FACETS	1	0.983	1	0.725	0.687	0.765	CLONAL	2	TRUE	0	0.496174219421139	3		384	645	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418847	116418847	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008761-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	321	707	1	ENST00000397752.3:c.3358G>T	p.Glu1120Ter	p.E1120*	ENST00000397752	NM_000245.2	1120	Gaa/Taa	17/21	0.496174219421139	3	FACETS	1	0.992	1	0.429	0.404	0.454	CLONAL	1	TRUE	0	0.496174219421139	3		708	1256	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954283	32954283	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs81002883	NA	P-0008769-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	129	404	0	ENST00000380152.3:c.9256+1G>C		p.X3086_splice	ENST00000380152		3086			0.397121120197347	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.397121120197347	1		404	493	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312710	91312725	+	frameshift_variant	Frame_Shift_Del	DEL	CTTCGCCAGAAGTTTC	CTTCGCCAGAAGTTTC	-	novel	NA	P-0008769-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	193	522	0	ENST00000355112.3:c.2453_2468del	p.Arg818LeufsTer4	p.R818Lfs*4	ENST00000355112	NM_000057.2	817	CTTCGCCAGAAGTTTCct/ct	12/22	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.397121120197347	2		522	897	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155712	119155712	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008769-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	83	576	0	ENST00000264033.4:c.1465C>T	p.Pro489Ser	p.P489S	ENST00000264033	NM_005188.3	489	Cca/Tca	10/16	1	2	FACETS	0.515	0.454	0.581	0.515	0.454	0.581	SUBCLONAL	1	TRUE	1	0.397121120197347	2		576	811	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49449085	49449103	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGCCAGCTTCTGGCTGT	CCAGCCAGCTTCTGGCTGT	-	novel	NA	P-0008769-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	109	452	0	ENST00000301067.7:c.5_23del	p.Asp2ValfsTer122	p.D2Vfs*122	ENST00000301067	NM_003482.3	2	gACAGCCAGAAGCTGGCTGGt/gt	1/54	1	2	FACETS	0.706	0.633	0.782	0.706	0.633	0.782	SUBCLONAL	1	TRUE	1	0.397121120197347	2		452	778	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0009159-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	48	202	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	0.3	3	FACETS	0.436	0.368	0.511			1	SUBCLONAL	1	TRUE	NA	0.48	3		202	569	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405932	49405932	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009159-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1295	144	554	0	ENST00000418115.1:c.206T>G	p.Leu69Arg	p.L69R	ENST00000418115	NM_001664.2	69	cTg/cGg	3/5	0.237933529758548	4	FACETS	0.617	0.561	0.677	0.309	0.28	0.339	INDETERMINATE	1	TRUE	2	0.48	4		554	1439	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917107	50917107	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009175-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	10	668	0	ENST00000440232.2:c.2359C>T	p.Pro787Ser	p.P787S	ENST00000440232	NM_002691.3	787	Ccg/Tcg	19/27	1	2	FACETS	0.203	0.137	0.286	0.203	0.137	0.286	SUBCLONAL	1	TRUE	1	0.491980112057153	2		668	200	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060765	38061235	+	inframe_deletion	In_Frame_Del	DEL	GGAGGACATGAGGTTGTTGATGGAGAACGGGTGGTTGAAGGAGTAGTGGGGGTCCCCTTTCAGGTGCAGCTGGGACTCGTGGGGTGCCAAGCCGTGTGCCGGGTGAGAGGCGGGCACAGAGGCCAGCGCCCCGGGCCCGGAGCTTATGGGGGGCGCAGTTGAGGAGGCTGGAGTCTTCAACTCCGAGGCGCCCCCTGTCGCCGTCGCCCCACTGTGGTCCAGAGTCTGGGGGCTGGCGGCGGGCCCGGGGGCCGGCGCGCCCTCTAGCTGGCCGGTCTTCCCGTGCACACCCCGATGGAGGGGCGAGTCGGCGCTGGGGTTAGAGGCGCCAGAGGGGTCCTTGCGGCTCTCAGGGCCGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTGGCGGCGCAAGTAGCAGCCGTTCTCGAACATGTT	GGAGGACATGAGGTTGTTGATGGAGAACGGGTGGTTGAAGGAGTAGTGGGGGTCCCCTTTCAGGTGCAGCTGGGACTCGTGGGGTGCCAAGCCGTGTGCCGGGTGAGAGGCGGGCACAGAGGCCAGCGCCCCGGGCCCGGAGCTTATGGGGGGCGCAGTTGAGGAGGCTGGAGTCTTCAACTCCGAGGCGCCCCCTGTCGCCGTCGCCCCACTGTGGTCCAGAGTCTGGGGGCTGGCGGCGGGCCCGGGGGCCGGCGCGCCCTCTAGCTGGCCGGTCTTCCCGTGCACACCCCGATGGAGGGGCGAGTCGGCGCTGGGGTTAGAGGCGCCAGAGGGGTCCTTGCGGCTCTCAGGGCCGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTGGCGGCGCAAGTAGCAGCCGTTCTCGAACATGTT	-	novel	NA	P-0009175-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	144	800	0	ENST00000250448.2:c.754_1224del	p.Asn252_Ser408del	p.N252_S408del	ENST00000250448	NM_004496.3	252	AACATGTTCGAGAACGGCTGCTACTTGCGCCGCCAGAAGCGCTTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGCGGCGCCAAGGGCGGCCCTGAGAGCCGCAAGGACCCCTCTGGCGCCTCTAACCCCAGCGCCGACTCGCCCCTCCATCGGGGTGTGCACGGGAAGACCGGCCAGCTAGAGGGCGCGCCGGCCCCCGGGCCCGCCGCCAGCCCCCAGACTCTGGACCACAGTGGGGCGACGGCGACAGGGGGCGCCTCGGAGTTGAAGACTCCAGCCTCCTCAACTGCGCCCCCCATAAGCTCCGGGCCCGGGGCGCTGGCCTCTGTGCCCGCCTCTCACCCGGCACACGGCTTGGCACCCCACGAGTCCCAGCTGCACCTGAAAGGGGACCCCCACTACTCCTTCAACCACCCGTTCTCCATCAACAACCTCATGTCCTCC/-	2/2	0.239170621755822	3	FACETS	1	0.934	1	0.513	0.468	0.559	INDETERMINATE	1	TRUE	1	0.491980112057153	3		800	711	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256325	16256325	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1248208637	NA	P-0009199-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	104	450	0	ENST00000375759.3:c.3590A>C	p.Lys1197Thr	p.K1197T	ENST00000375759	NM_015001.2	1197	aAa/aCa	11/15	0.345056131784725	1	FACETS	0.961	0.864	1	0.961	0.864	1	CLONAL	1	FALSE	0	0.348955417375512	1		450	512	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972771	32972771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56309455	NA	P-0009199-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	89	450	0	ENST00000380152.3:c.10121C>T	p.Thr3374Ile	p.T3374I	ENST00000380152		3374	aCc/aTc	27/27	0.262487645757922	2	FACETS	1	0.939	1	0.54	0.481	0.603	CLONAL	1	FALSE	0	0.348955417375512	2		450	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0009214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1282	199	837	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.190824993161557	2		837	1481	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509312	106509312	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	84	404	0	ENST00000359195.3:c.1306G>T	p.Gly436Cys	p.G436C	ENST00000359195	NM_002649.2	436	Ggt/Tgt	2/11	0.190824993161557	3	FACETS	0.787	0.692	0.888			1	SUBCLONAL	1	TRUE	NA	0.190824993161557	3		404	1226	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691905	30691905	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	85	335	0	ENST00000295754.5:c.407G>A	p.Cys136Tyr	p.C136Y	ENST00000295754	NM_003242.5	136	tGt/tAt	3/7	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.190824993161557	2		335	677	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356152	66356152	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370633345	NA	P-0009214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	57	449	0	ENST00000273854.3:c.1345G>A	p.Asp449Asn	p.D449N	ENST00000273854	NM_004439.5	449	Gac/Aac	5/18	1	2	FACETS	0.631	0.539	0.731	0.631	0.539	0.731	SUBCLONAL	1	TRUE	1	0.190824993161557	2		449	947	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361223	66361223	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	55	349	0	ENST00000273854.3:c.949C>A	p.Gln317Lys	p.Q317K	ENST00000273854	NM_004439.5	317	Cag/Aag	4/18	1	2	FACETS	0.79	0.674	0.916	0.79	0.674	0.916	CLONAL	1	TRUE	1	0.190824993161557	2		349	730	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541733	120541733	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1572	194	680	0	ENST00000229340.5:c.124G>T	p.Gly42Ter	p.G42*	ENST00000229340	NM_006861.6	42	Gga/Tga	3/6	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.190824993161557	2		680	1766	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984514	72984514	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1626	91	769	0	ENST00000268489.5:c.3070G>T	p.Ala1024Ser	p.A1024S	ENST00000268489	NM_006885.3	1024	Gcc/Tcc	3/10	1	2	FACETS	0.555	0.491	0.625	0.555	0.491	0.625	SUBCLONAL	1	TRUE	1	0.190824993161557	2		769	1717	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602581	10602582	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0009214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	109	323	0	ENST00000171111.5:c.996_997del	p.Gly333LeufsTer16	p.G333Lfs*16	ENST00000171111	NM_203500.1	332	ggCGgc/gggc	3/6	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.190824993161557	2		323	815	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0009224-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	85	582	2	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	1	2	FACETS	0.846	0.749	0.95	0.846	0.749	0.95	CLONAL	1	TRUE	1	0.341555356340635	2		584	588	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0009224-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	225	446	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.341555356340635	3	FACETS	0.81	0.755	0.867	0.81	0.755	0.867	CLONAL	2	TRUE	1	0.341555356340635	3		446	952	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555526097	NA	P-0009224-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	81	263	0	ENST00000269305.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000269305	NM_001126112.2	167	Cag/Tag	5/11	0.341555356340635	1	FACETS	0.748	0.66	0.841	0.748	0.66	0.841	SUBCLONAL	1	TRUE	0	0.341555356340635	1		263	526	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653807	89653807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554893782	NA	P-0009224-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	70	356	0	ENST00000371953.3:c.105G>A	p.Met35Ile	p.M35I	ENST00000371953	NM_000314.4	35	atG/atA	2/9	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.341555356340635	2		356	353	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145742	61145742	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0009224-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	44	216	0	ENST00000295025.8:c.853+1G>A		p.X285_splice	ENST00000295025	NM_002908.2	285			1	2	FACETS	0.783	0.659	0.919	0.783	0.659	0.919	CLONAL	1	TRUE	1	0.341555356340635	2		216	329	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412323	63412323	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009224-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	101	285	0	ENST00000330258.3:c.844G>T	p.Glu282Ter	p.E282*	ENST00000330258	NM_152424.3	282	Gag/Tag	2/2	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.341555356340635	1		285	336	SUCCESS
APC	324	MSKCC	GRCh37	5	112170768	112170769	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0009224-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	54	517	0	ENST00000257430.4:c.1865dup	p.Tyr622Ter	p.Y622*	ENST00000257430	NM_000038.5	622	tac/tAac	15/16	0.341555356340635	3	FACETS	0.477	0.406	0.555	0.239	0.203	0.278	SUBCLONAL	1	TRUE	1	0.341555356340635	3		517	776	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0009226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	383	732	1	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.409499363737011	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.409499363737011	2		733	810	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0009226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	185	404	0	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	0.962	0.889	1	0.962	0.889	1	CLONAL	1	TRUE	1	0.409499363737011	2		404	939	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097808	27097808	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	145	312	1	ENST00000324856.7:c.3397C>A	p.Pro1133Thr	p.P1133T	ENST00000324856	NM_006015.4	1133	Ccc/Acc	12/20	1	2	FACETS	0.988	0.903	1	0.988	0.903	1	CLONAL	1	TRUE	1	0.409499363737011	2		313	717	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653245	206653245	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	156	346	0	ENST00000367120.3:c.1216G>A	p.Val406Met	p.V406M	ENST00000367120	NM_014002.3	406	Gtg/Atg	11/22	0.404163400097103	4	FACETS	0.971	0.888	1	0.324	0.296	0.353	CLONAL	1	TRUE	1	0.409499363737011	4		346	1106	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248399	212248399	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	307	374	0	ENST00000342788.4:c.3868C>A	p.Leu1290Met	p.L1290M	ENST00000342788	NM_005235.2	1290	Ctg/Atg	28/28	0.205036205764605	5	FACETS	1	0.973	1	0.702	0.661	0.743	INDETERMINATE	2	TRUE	2	0.409499363737011	5		374	1150	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294216	1294216	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150277224	NA	P-0009226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	305	371	0	ENST00000310581.5:c.785C>T	p.Thr262Met	p.T262M	ENST00000310581	NM_198253.2	262	aCg/aTg	2/16	0.35338230700297	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	2	0.409499363737011	4		371	992	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876154	35876154	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	382	408	0	ENST00000303115.3:c.946G>T	p.Ala316Ser	p.A316S	ENST00000303115	NM_002185.3	316	Gct/Tct	8/8	0.35338230700297	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.409499363737011	4		408	1278	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056698	180056698	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	202	424	1	ENST00000261937.6:c.814C>T	p.Gln272Ter	p.Q272*	ENST00000261937	NM_182925.4	272	Cag/Tag	6/30	0.385827399344811	3	FACETS	1	0.969	1	0.543	0.502	0.585	CLONAL	1	TRUE	1	0.409499363737011	3		425	1095	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057629	180057629	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1411	246	642	0	ENST00000261937.6:c.326A>G	p.Tyr109Cys	p.Y109C	ENST00000261937	NM_182925.4	109	tAc/tGc	3/30	0.385827399344811	3	FACETS	0.874	0.814	0.936	0.437	0.407	0.468	CLONAL	1	TRUE	1	0.409499363737011	3		642	1657	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031970	26031970	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1649	242	625	0	ENST00000244661.2:c.319G>T	p.Asp107Tyr	p.D107Y	ENST00000244661	NM_003537.3	107	Gac/Tac	1/1	0.205036205764605	5	FACETS	1	0.938	1	0.336	0.313	0.361	INDETERMINATE	1	TRUE	2	0.409499363737011	5		625	1891	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032020	26032020	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1517	507	721	0	ENST00000244661.2:c.269T>C	p.Val90Ala	p.V90A	ENST00000244661	NM_003537.3	90	gTg/gCg	1/1	0.205036205764605	5	FACETS	0.987	0.943	1	0.658	0.628	0.689	INDETERMINATE	2	TRUE	2	0.409499363737011	5		721	2024	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521892	157521892	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs889402710	NA	P-0009226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	145	301	0	ENST00000346085.5:c.4164G>C	p.Glu1388Asp	p.E1388D	ENST00000346085	NM_020732.3	1388	gaG/gaC	18/20	0.205036205764605	5	FACETS	1	0.911	1	0.334	0.303	0.365	INDETERMINATE	1	TRUE	2	0.409499363737011	5		301	1142	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36846882	36846882	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	1374	482	4	ENST00000358127.4:c.1057T>C	p.Ser353Pro	p.S353P	ENST00000358127	NM_001280556.1	353	Tcg/Ccg	9/10	0.409499363737011	7	FACETS	0.973	0.955	0.991			1	CLONAL	7	TRUE	NA	0.409499363737011	7		486	1994	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333088	70333088	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1527	248	560	0	ENST00000373644.4:c.993G>T	p.Leu331Phe	p.L331F	ENST00000373644	NM_030625.2	331	ttG/ttT	2/12	0.404163400097103	4	FACETS	0.962	0.896	1	0.321	0.298	0.344	CLONAL	1	TRUE	1	0.409499363737011	4		560	1775	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206713	102206713	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1423	531	455	0	ENST00000263464.3:c.1341C>G	p.Ile447Met	p.I447M	ENST00000263464	NM_001165.4	447	atC/atG	7/9	0.402053401186009	4	FACETS	0.935	0.894	0.977	0.935	0.894	0.977	CLONAL	2	TRUE	2	0.409499363737011	4		455	1954	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953258	81953258	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1483	578	646	1	ENST00000359376.3:c.2224C>A	p.Arg742Ser	p.R742S	ENST00000359376	NM_002661.3	742	Cgc/Agc	20/33	0.35338230700297	4	FACETS	0.965	0.925	1	0.965	0.925	1	CLONAL	2	TRUE	2	0.409499363737011	4		647	2061	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78858807	78858807	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0009226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	305	361	0	ENST00000306801.3:c.1843-1G>T		p.X615_splice	ENST00000306801	NM_020761.2	615			0.402053401186009	4	FACETS	0.989	0.933	1	0.989	0.933	1	CLONAL	2	TRUE	2	0.409499363737011	4		361	1061	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145614	11145614	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	265	287	1	ENST00000358026.2:c.3976G>T	p.Glu1326Ter	p.E1326*	ENST00000358026	NM_001128849.1	1326	Gag/Tag	29/36	0.409499363737011	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.409499363737011	2		288	579	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46255871	46255871	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1785	322	646	0	ENST00000371998.3:c.483A>T	p.Leu161Phe	p.L161F	ENST00000371998		161	ttA/ttT	6/23	0.205036205764605	5	FACETS	1	0.989	1	0.402	0.377	0.427	INDETERMINATE	1	TRUE	2	0.409499363737011	5		646	2107	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860366	42860366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	495	532	1	ENST00000398585.3:c.511G>T	p.Asp171Tyr	p.D171Y	ENST00000398585	NM_001135099.1	171	Gat/Tat	5/14	0.409499363737011	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.409499363737011	4		533	1635	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552779	18552780	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0009226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	157	235	0	ENST00000266497.5:c.2191dup	p.Ser731LysfsTer9	p.S731Kfs*9	ENST00000266497		730	-/A	14/31	0.385827399344811	3	FACETS	0.762	0.701	0.825	0.762	0.701	0.825	SUBCLONAL	2	TRUE	1	0.409499363737011	3		235	606	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207026	1207038	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCCGCAAGCGG	GCGCCGCAAGCGG	-	novel	NA	P-0009226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	290	308	0	ENST00000326873.7:c.116_128del	p.Arg39ProfsTer8	p.R39Pfs*8	ENST00000326873	NM_000455.4	38	ccGCGCCGCAAGCGG/cc	1/10	0.409499363737011	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.409499363737011	2		308	683	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645693	12645695	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	novel	NA	P-0009226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	311	356	0	ENST00000251849.4:c.774_776del	p.Ser259del	p.S259del	ENST00000251849	NM_002880.3	258	acATCc/acc	7/17	0.409499363737011	2	FACETS	0.927	0.878	0.977	0.927	0.878	0.977	CLONAL	2	TRUE	0	0.409499363737011	2		356	819	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020162	123020163	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0009226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1282	464	560	0	ENST00000355640.3:c.650_651insT	p.Trp217CysfsTer10	p.W217Cfs*10	ENST00000355640		217	tgg/tgTg	2/7	0.205036205764605	5	FACETS	1	0.979	1	0.698	0.666	0.732	INDETERMINATE	2	TRUE	2	0.409499363737011	5		560	1746	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152102	55152104	+	missense_variant	Missense_Mutation	TNP	ATG	ATG	CTA	novel	NA	P-0009250-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	256	419	0	ENST00000257290.5:c.2534_2536delinsCTA	p.His845_Asp846delinsProAsn	p.H845_D846delinsPN	ENST00000257290	NM_006206.4	845	cATGat/cCTAat	18/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		419	825	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879888	37879888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	349	445	0	ENST00000269571.5:c.2183C>T	p.Ser728Phe	p.S728F	ENST00000269571		728	tCt/tTt	18/27	0.341664802553465	3	FACETS	0.917	0.871	0.964	0.917	0.871	0.964	CLONAL	2	TRUE	1	0.494476194234072	3		445	960	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266513	198266513	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	163	456	0	ENST00000335508.6:c.2323C>G	p.Arg775Gly	p.R775G	ENST00000335508	NM_012433.2	775	Cga/Gga	16/25	0.246546083011385	4	FACETS	0.917	0.847	0.989	0.917	0.847	0.989	INDETERMINATE	2	TRUE	2	0.494476194234072	4		456	537	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267447	198267447	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	126	359	0	ENST00000335508.6:c.1910C>G	p.Ser637Cys	p.S637C	ENST00000335508	NM_012433.2	637	tCt/tGt	14/25	0.246546083011385	4	FACETS	0.852	0.777	0.929	0.852	0.777	0.929	INDETERMINATE	2	TRUE	2	0.494476194234072	4		359	447	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602800	10602800	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	55	432	0	ENST00000171111.5:c.778C>T	p.Arg260Ter	p.R260*	ENST00000171111	NM_203500.1	260	Cga/Tga	3/6	0.494476194234072	2	FACETS	0.28	0.238	0.325	0.14	0.119	0.163	SUBCLONAL	1	TRUE	0	0.494476194234072	2		432	795	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0009324-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	223	178	0				ENST00000310581	NM_198253.2	-/1132			0.534188794117979	3	FACETS	0.954	0.899	1	0.954	0.899	1	CLONAL	2	TRUE	1	0.659765474771999	3		178	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0009324-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	549	878	2	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	0.94	0.91	0.97	1	0.998	1	CLONAL	2	TRUE	1	0.659765474771999	2		880	885	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827993	40827993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1328809133	NA	P-0009324-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	146	212	0	ENST00000373198.4:c.2435G>A	p.Gly812Glu	p.G812E	ENST00000373198	NM_133170.3	812	gGa/gAa	17/32	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.659765474771999	2		212	402	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630411	187630411	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009324-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	298	367	0	ENST00000441802.2:c.571C>T	p.Arg191Ter	p.R191*	ENST00000441802	NM_005245.3	191	Cga/Tga	2/27	1	2	FACETS	0.918	0.866	0.971	0.918	0.866	0.971	CLONAL	1	TRUE	1	0.659765474771999	2		367	984	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468149	120468149	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009324-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	152	194	0	ENST00000256646.2:c.4290T>G	p.Cys1430Trp	p.C1430W	ENST00000256646	NM_024408.3	1430	tgT/tgG	25/34	1	2	FACETS	0.895	0.824	0.968	0.895	0.824	0.968	CLONAL	1	TRUE	1	0.659765474771999	2		194	515	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243675697	243675697	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009324-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	237	312	0	ENST00000263826.5:c.1283C>T	p.Ser428Phe	p.S428F	ENST00000263826	NM_005465.4	428	tCt/tTt	12/13	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.659765474771999	2		312	684	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456506	29456506	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009324-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	359	503	0	ENST00000389048.3:c.2412A>T	p.Glu804Asp	p.E804D	ENST00000389048	NM_004304.4	804	gaA/gaT	14/29	0.443980035410301	1	FACETS	0.782	0.743	0.82	0.782	0.743	0.82	SUBCLONAL	1	TRUE	0	0.659765474771999	1		503	933	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1795734	1795734	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009324-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	112	178	0	ENST00000260795.2:c.73T>A	p.Leu25Met	p.L25M	ENST00000260795		25	Ttg/Atg	1/17	1	2	FACETS	0.875	0.794	0.959	0.875	0.794	0.959	CLONAL	1	TRUE	1	0.659765474771999	2		178	388	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467472	66467472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009324-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	147	260	0	ENST00000273854.3:c.797C>T	p.Ser266Phe	p.S266F	ENST00000273854	NM_004439.5	266	tCt/tTt	3/18	1	2	FACETS	0.952	0.876	1	0.952	0.876	1	CLONAL	1	TRUE	1	0.659765474771999	2		260	468	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397225	397225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009324-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	175	252	0	ENST00000380956.4:c.610C>T	p.His204Tyr	p.H204Y	ENST00000380956	NM_001195286.1	204	Cac/Tac	5/9	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.659765474771999	2		252	529	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964390	93964390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009324-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	322	492	0	ENST00000369303.4:c.2507C>T	p.Pro836Leu	p.P836L	ENST00000369303	NM_004440.3	836	cCt/cTt	14/17	1	2	FACETS	0.95	0.898	1	0.95	0.898	1	CLONAL	1	TRUE	1	0.659765474771999	2		492	1028	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964510	93964510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1435219791	NA	P-0009324-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	243	370	0	ENST00000369303.4:c.2387G>A	p.Gly796Glu	p.G796E	ENST00000369303	NM_004440.3	796	gGa/gAa	14/17	1	2	FACETS	0.954	0.895	1	0.954	0.895	1	CLONAL	1	TRUE	1	0.659765474771999	2		370	772	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715868	117715868	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009324-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	300	410	1	ENST00000368508.3:c.890G>A	p.Arg297Lys	p.R297K	ENST00000368508	NM_002944.2	297	aGa/aAa	9/43	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.659765474771999	2		411	903	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974703	21974703	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009324-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	194	300	0	ENST00000304494.5:c.124A>T	p.Asn42Tyr	p.N42Y	ENST00000304494	NM_000077.4	42	Aat/Tat	1/3	0.659765474771999	1	FACETS	0.882	0.825	0.938	0.882	0.825	0.938	CLONAL	1	TRUE	0	0.659765474771999	1		300	447	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137029	64137029	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009324-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	171	187	0	ENST00000334205.4:c.1540G>T	p.Val514Leu	p.V514L	ENST00000334205	NM_003942.2	514	Gtg/Ttg	13/17	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.659765474771999	2		187	453	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375564	118375564	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009324-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	181	221	0	ENST00000534358.1:c.8957C>A	p.Pro2986Gln	p.P2986Q	ENST00000534358	NM_005933.3	2986	cCa/cAa	27/36	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.659765474771999	2		221	524	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78829331	78829331	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009324-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	185	266	1	ENST00000306801.3:c.1382C>T	p.Pro461Leu	p.P461L	ENST00000306801	NM_020761.2	461	cCc/cTc	12/34	1	2	FACETS	0.984	0.914	1	0.984	0.914	1	CLONAL	1	TRUE	1	0.659765474771999	2		267	570	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309610	30309610	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009324-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	342	344	0	ENST00000307677.4:c.412G>A	p.Gly138Ser	p.G138S	ENST00000307677	NM_138578.1	138	Ggt/Agt	2/3	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.659765474771999	2		344	960	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021623	31021627	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTT	GGCTT	-	novel	NA	P-0009324-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	129	207	1	ENST00000375687.4:c.1623_1627del	p.Leu542ArgfsTer7	p.L542Rfs*7	ENST00000375687	NM_015338.5	541	cGGCTT/c	12/13	1	2	FACETS	0.995	0.911	1	0.995	0.911	1	CLONAL	1	TRUE	1	0.659765474771999	2		208	393	SUCCESS
EED	8726	MSKCC	GRCh37	11	85977143	85977166	+	inframe_deletion	In_Frame_Del	DEL	GAAAAAATAATGTCCTGTGGTATG	GAAAAAATAATGTCCTGTGGTATG	-	novel	NA	P-0009324-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	59	336	0	ENST00000263360.6:c.747_770del	p.Glu249_Met256del	p.E249_M256del	ENST00000263360	NM_003797.3	249	GAAAAAATAATGTCCTGTGGTATG/-	8/12	1	2	FACETS	0.302	0.26	0.348	0.302	0.26	0.348	SUBCLONAL	1	TRUE	1	0.659765474771999	2		336	592	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402447	139402448	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0009324-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	251	355	1	ENST00000277541.6:c.3469_3470delinsAA	p.Gly1157Lys	p.G1157K	ENST00000277541	NM_017617.3	1157	GGg/AAg	21/34	1	2	FACETS	0.942	0.884	1	0.942	0.884	1	CLONAL	1	TRUE	1	0.659765474771999	2		356	808	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412266	139412267	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009324-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	222	280	0	ENST00000277541.6:c.1378_1379delinsTT	p.Pro460Leu	p.P460L	ENST00000277541	NM_017617.3	460	CCg/TTg	8/34	1	2	FACETS	0.884	0.826	0.944	0.884	0.826	0.944	CLONAL	1	TRUE	1	0.659765474771999	2		280	761	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831219	3831220	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009324-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	259	298	0	ENST00000262367.5:c.1661_1662delinsTT	p.Ser554Phe	p.S554F	ENST00000262367	NM_004380.2	554	tCC/tTT	7/31	0.659765474771999	1	FACETS	0.982	0.93	1	0.982	0.93	1	CLONAL	1	TRUE	0	0.659765474771999	1		298	536	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931463	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622007	NA	P-0009402-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	332	307	0	ENST00000374690.3:c.2105T>A	p.Leu702His	p.L702H	ENST00000374690	NM_000044.3	702	cTc/cAc	4/8	0.592459714410062	4	FACETS	0.804	0.76	0.848			1	CLONAL	2	TRUE	NA	0.592459714410062	4		307	1110	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061223	38061231	+	inframe_deletion	In_Frame_Del	DEL	TCTCGAACA	TCTCGAACA	-	novel	NA	P-0009402-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	228	505	0	ENST00000250448.2:c.758_766del	p.Met253_Glu255del	p.M253_E255del	ENST00000250448	NM_004496.3	253	aTGTTCGAGAac/aac	2/2	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.592459714410062	2		505	661	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828767	72828767	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0009402-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	203	595	0	ENST00000268489.5:c.7814C>G	p.Ser2605Ter	p.S2605*	ENST00000268489	NM_006885.3	2605	tCa/tGa	9/10	1	2	FACETS	0.962	0.896	1	0.962	0.896	1	CLONAL	1	TRUE	1	0.592459714410062	2		595	712	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619370	37619370	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009402-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	125	286	0	ENST00000447079.4:c.1046+1del		p.S349fs	ENST00000447079	NM_015083.1	349	aGt/at	1/14	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.592459714410062	2		286	386	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37665974	37665975	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0009402-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	123	426	0	ENST00000447079.4:c.2626_2627delinsTT	p.Ala876Leu	p.A876L	ENST00000447079	NM_015083.1	876	GCa/TTa	7/14	1	2	FACETS	0.775	0.704	0.849	0.775	0.704	0.849	SUBCLONAL	1	TRUE	1	0.592459714410062	2		426	536	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456463	99456463	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs758765712	NA	P-0009450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	120	270	0	ENST00000268035.6:c.1780A>G	p.Ile594Val	p.I594V	ENST00000268035	NM_000875.3	594	Atc/Gtc	8/21	0.475579393785635	2	FACETS	0.448	0.406	0.493	0.224	0.203	0.247	INDETERMINATE	1	TRUE	0	0.920241498097994	2		270	582	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578498	7578499	+	missense_variant	Missense_Mutation	DNP	CT	CT	GG	novel	NA	P-0009450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	299	290	0	ENST00000269305.4:c.431_432delinsCC	p.Gln144Pro	p.Q144P	ENST00000269305	NM_001126112.2	144	cAG/cCC	5/11	0.920241498097994	2	FACETS	0.985	0.962	1	0.985	0.962	1	CLONAL	2	TRUE	0	0.920241498097994	2		290	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0009741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	216	467	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.548642057516957	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.611645162047166	1		468	471	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0009741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	314	345	1	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	0.611645162047166	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.611645162047166	3		346	645	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584497	48584497	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	189	262	1	ENST00000342988.3:c.670C>T	p.Gln224Ter	p.Q224*	ENST00000342988	NM_005359.5	224	Cag/Tag	6/12	0.370870414671276	3	FACETS	0.964	0.916	1			1	CLONAL	3	TRUE	NA	0.611645162047166	3		263	279	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943724	17943724	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	36	261	0	ENST00000458235.1:c.2365T>G	p.Ser789Ala	p.S789A	ENST00000458235	NM_000215.3	789	Tca/Gca	18/24	0.247591618541288	5	FACETS	0.423	0.347	0.509	0.141	0.115	0.17	INDETERMINATE	1	TRUE	2	0.611645162047166	5		261	533	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409115	4409122	+	frameshift_variant	Frame_Shift_Del	DEL	GTCGGAGG	GTCGGAGG	-	novel	NA	P-0009741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	181	455	1	ENST00000261254.3:c.810_817del	p.Ser271Ter	p.S271*	ENST00000261254	NM_001759.3	270	aaGTCGGAGGat/aaat	5/5	0.548335869853218	3	FACETS	1	0.959	1	0.527	0.487	0.568	CLONAL	1	TRUE	1	0.611645162047166	3		456	733	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120007	70120007	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	60	44	0	ENST00000245479.2:c.1009del	p.Ser337ProfsTer46	p.S337Pfs*46	ENST00000245479	NM_000346.3	337	Tcc/cc	3/3	0.611645162047166	4	FACETS	0.843	0.751	0.936	0.843	0.751	0.936	CLONAL	3	TRUE	1	0.611645162047166	4		44	125	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0010074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	140	552	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.183997255532301	3	FACETS	0.803	0.731	0.878	0.803	0.731	0.878	CLONAL	2	TRUE	1	0.233514890011335	3		552	834	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0010074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	55	482	1	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.654	0.559	0.759	0.654	0.559	0.759	SUBCLONAL	1	TRUE	1	0.233514890011335	2		483	720	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167577	NA	P-0010074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	88	444	1	ENST00000257430.4:c.4463del	p.Leu1488TyrfsTer19	p.L1488Yfs*19	ENST00000257430	NM_000038.5	1487	acT/ac	16/16	0.233514890011335	2	FACETS	1	0.972	1	0.658	0.584	0.736	CLONAL	1	TRUE	0	0.233514890011335	2		445	573	SUCCESS
RET	5979	MSKCC	GRCh37	10	43572717	43572717	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	64	201	0	ENST00000355710.3:c.11C>A	p.Ala4Glu	p.A4E	ENST00000355710	NM_020975.4	4	gCg/gAg	1/20	0.116330964279987	5	FACETS	1	0.893	1	0.26	0.224	0.298	INDETERMINATE	1	TRUE	1	0.233514890011335	5		201	713	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106648	27106648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553153748	NA	P-0010096-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	282	686	0	ENST00000324856.7:c.6259G>A	p.Gly2087Arg	p.G2087R	ENST00000324856	NM_006015.4	2087	Gga/Aga	20/20	0.409509341472782	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	FALSE	2	0.510532980724252	4		686	807	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0010096-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	171	498	1	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	0.449143072325998	4	FACETS	1	0.989	1			1	CLONAL	1	FALSE	NA	0.510532980724252	4		499	702	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438535	52438535	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0010096-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	259	656	0	ENST00000460680.1:c.1184C>G	p.Ser395Ter	p.S395*	ENST00000460680	NM_004656.3	395	tCa/tGa	12/17	0.516016613086716	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	FALSE	0	0.510532980724252	2		656	470	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464388	120464388	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010096-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	119	665	0	ENST00000256646.2:c.5258G>C	p.Gly1753Ala	p.G1753A	ENST00000256646	NM_024408.3	1753	gGa/gCa	29/34	0.516016613086716	4	FACETS	0.835	0.754	0.922			1	CLONAL	1	FALSE	NA	0.510532980724252	4		665	843	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941234	71941234	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010096-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	656	890	0	ENST00000298229.2:c.1009G>C	p.Asp337His	p.D337H	ENST00000298229	NM_001567.3	337	Gat/Cat	9/28	0.510532980724252	6	FACETS	0.956	0.924	0.988			1	CLONAL	4	FALSE	NA	0.510532980724252	6		890	1358	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941285	71941285	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010096-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	625	849	0	ENST00000298229.2:c.1060G>T	p.Glu354Ter	p.E354*	ENST00000298229	NM_001567.3	354	Gag/Tag	9/28	0.510532980724252	6	FACETS	0.987	0.954	1			1	CLONAL	4	FALSE	NA	0.510532980724252	6		849	1253	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385326	4385340	+	inframe_deletion	In_Frame_Del	DEL	GCTGACCGCGGAGAA	GCTGACCGCGGAGAA	-	novel	NA	P-0010096-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	43	455	0	ENST00000261254.3:c.355_369del	p.Thr119_Leu123del	p.T119_L123del	ENST00000261254	NM_001759.3	117	ccGCTGACCGCGGAGAAg/ccg	2/5	0.510532980724252	5	FACETS	0.507	0.423	0.599	0.169	0.141	0.2	SUBCLONAL	1	FALSE	2	0.510532980724252	5		455	587	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245268	133245268	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010096-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	133	813	0	ENST00000320574.5:c.1979G>C	p.Gly660Ala	p.G660A	ENST00000320574	NM_006231.2	660	gGa/gCa	18/49	0.406169245016209	1	FACETS	0.776	0.709	0.846	0.776	0.709	0.846	SUBCLONAL	1	FALSE	0	0.510532980724252	1		813	500	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032249	10032249	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010096-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	86	701	0	ENST00000330684.3:c.574G>C	p.Asp192His	p.D192H	ENST00000330684	NM_001134407.1	192	Gac/Cac	3/13	0.516016613086716	3	FACETS	0.722	0.639	0.81	0.361	0.319	0.405	SUBCLONAL	1	FALSE	1	0.510532980724252	3		701	586	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637660	23637660	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010096-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	98	628	0	ENST00000261584.4:c.2645G>C	p.Cys882Ser	p.C882S	ENST00000261584	NM_024675.3	882	tGt/tCt	7/13	0.516016613086716	3	FACETS	0.97	0.869	1	0.485	0.434	0.538	CLONAL	1	FALSE	1	0.510532980724252	3		628	497	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663756	29663756	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010096-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	115	579	0	ENST00000356175.3:c.6188A>T	p.Tyr2063Phe	p.Y2063F	ENST00000356175	NM_000267.3	2063	tAc/tTc	41/57	0.384840982251992	5	FACETS	1	0.974	1	0.412	0.371	0.454	CLONAL	1	FALSE	2	0.510532980724252	5		579	644	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210830	2210830	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs751935862	NA	P-0010096-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	67	556	0	ENST00000398665.3:c.1327C>G	p.Gln443Glu	p.Q443E	ENST00000398665	NM_032482.2	443	Cag/Gag	14/28	0.384840982251992	5	FACETS	0.795	0.691	0.907	0.265	0.23	0.303	CLONAL	1	FALSE	2	0.510532980724252	5		556	583	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280082	18280082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1463912510	NA	P-0010096-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	51	66	0	ENST00000222254.8:c.2165G>A	p.Gly722Asp	p.G722D	ENST00000222254	NM_005027.3	722	gGc/gAc	16/16	0.384840982251992	5	FACETS	0.933	0.816	1	0.933	0.816	1	CLONAL	3	FALSE	2	0.510532980724252	5		66	126	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151203	202151203	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010096-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	213	303	0	ENST00000358485.4:c.1503C>G	p.Ile501Met	p.I501M	ENST00000358485	NM_001080125.1	501	atC/atG	9/9	0.516016613086716	5	FACETS	1	0.97	1	1	0.97	1	CLONAL	4	FALSE	1	0.510532980724252	5		303	356	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451389	187451389	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010096-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	105	432	0	ENST00000232014.4:c.93G>C	p.Leu31Phe	p.L31F	ENST00000232014	NM_001130845.1	31	ttG/ttC	3/10	0.510532980724252	11	FACETS	1	0.949	1	0.158	0.14	0.176	CLONAL	1	FALSE	4	0.510532980724252	11		432	1229	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143326389	143326424	+	inframe_deletion	In_Frame_Del	DEL	CAGACTCTGCTCCACGGGGTGGATTACGGAGATCTG	CAGACTCTGCTCCACGGGGTGGATTACGGAGATCTG	-	novel	NA	P-0010096-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	45	449	0	ENST00000262992.4:c.190_225del	p.Gln64_Leu75del	p.Q64_L75del	ENST00000262992	NM_001101669.1	64	CAGATCTCCGTAATCCACCCCGTGGAGCAGAGTCTG/-	4/24	0.516016613086716	3	FACETS	0.485	0.408	0.571	0.243	0.204	0.286	SUBCLONAL	1	FALSE	1	0.510532980724252	3		449	456	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064733	80064733	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010096-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	120	449	0	ENST00000265081.6:c.2164G>C	p.Val722Leu	p.V722L	ENST00000265081	NM_002439.4	722	Gtt/Ctt	15/24	0.143694855205293	3	FACETS	0.922	0.844	1	0.615	0.563	0.668	INDETERMINATE	2	FALSE	0	0.510532980724252	3		449	320	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821041	32821041	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010096-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	79	912	1	ENST00000354258.4:c.553G>T	p.Ala185Ser	p.A185S	ENST00000354258	NM_000593.5	185	Gcg/Tcg	1/11	0.192593607408225	6	FACETS	0.718	0.63	0.813			1	INDETERMINATE	1	FALSE	NA	0.510532980724252	6		913	871	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917694	151917694	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010096-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	77	325	0	ENST00000262189.6:c.3626T>C	p.Ile1209Thr	p.I1209T	ENST00000262189	NM_170606.2	1209	aTa/aCa	23/59	0.516016613086716	4	FACETS	0.822	0.73	0.919	0.411	0.365	0.46	CLONAL	2	FALSE	0	0.510532980724252	4		325	277	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0010180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1753	189	894	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.222072996073025	5	FACETS	1	0.978	1	0.389	0.358	0.422	CLONAL	1	TRUE	2	0.222072996073025	5		894	1942	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717699	89717699	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554825210	NA	P-0010180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	179	345	0	ENST00000371953.3:c.724G>T	p.Glu242Ter	p.E242*	ENST00000371953	NM_000314.4	242	Gag/Tag	7/9	0.205226848691704	3	FACETS	0.883	0.817	0.951	0.883	0.817	0.951	CLONAL	3	TRUE	0	0.222072996073025	3		345	676	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453187	140453187	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	35	494	0	ENST00000288602.6:c.1748T>G	p.Phe583Cys	p.F583C	ENST00000288602	NM_004333.4	583	tTt/tGt	15/18	0.222072996073025	5	FACETS	0.656	0.536	0.791	0.219	0.178	0.264	SUBCLONAL	1	TRUE	2	0.222072996073025	5		494	641	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010234-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	391	471	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.840629483476517	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.840629483476517	1		471	511	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845367	151845367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010234-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	319	450	0	ENST00000262189.6:c.13645C>T	p.Arg4549Cys	p.R4549C	ENST00000262189	NM_170606.2	4549	Cgc/Tgc	52/59	NA	2	FACETS	0.983	0.955	1			1	INDETERMINATE	2	TRUE	NA	0.840629483476517	2		450	386	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115871	8115872	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0010234-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	419	588	0	ENST00000346208.3:c.1219_1220del	p.Ser407AlafsTer99	p.S407Afs*99	ENST00000346208		406	aTC/a	6/6	1	2	FACETS	0.802	0.764	0.84	0.802	0.764	0.84	CLONAL	1	TRUE	1	0.840629483476517	2		588	1243	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	69061276	69061276	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010234-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	10	104	0	ENST00000487270.1:c.1111C>T	p.Gln371Ter	p.Q371*	ENST00000487270	NM_133509.3	371	Cag/Tag	11/11	1	2	FACETS	0.209	0.142	0.291	0.209	0.142	0.291	SUBCLONAL	1	TRUE	1	0.840629483476517	2		104	114	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0010332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	32	392	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.235570210078876	3	FACETS	1	0.871	1	0.544	0.443	0.658	CLONAL	1	TRUE	1	0.23	3		392	285	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0010332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	109	320	0	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.23	2		320	792	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92462418	92462418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	55	329	0	ENST00000265734.4:c.220C>T	p.Pro74Ser	p.P74S	ENST00000265734	NM_001259.6	74	Ccc/Tcc	2/8	1	2	FACETS	0.704	0.602	0.817	0.704	0.602	0.817	SUBCLONAL	1	TRUE	1	0.23	2		329	679	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939103	36939103	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1435	208	680	0	ENST00000361632.4:c.606G>T	p.Trp202Cys	p.W202C	ENST00000361632		202	tgG/tgT	5/16	0.235570210078876	3	FACETS	1	0.984	1	0.614	0.567	0.662	CLONAL	1	TRUE	1	0.23	3		680	1643	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40367115	40367115	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	81	360	0	ENST00000397332.2:c.82G>A	p.Gly28Arg	p.G28R	ENST00000397332	NM_001033082.2	28	Gga/Aga	2/3	0.235570210078876	3	FACETS	0.872	0.766	0.985	0.436	0.383	0.493	CLONAL	1	TRUE	1	0.23	3		360	901	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429324	78429324	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	55	378	1	ENST00000370768.2:c.1118C>T	p.Pro373Leu	p.P373L	ENST00000370768	NM_003902.3	373	cCt/cTt	13/20	1	2	FACETS	0.74	0.633	0.858	0.74	0.633	0.858	SUBCLONAL	1	TRUE	1	0.23	2		379	646	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587235	212587235	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	45	342	0	ENST00000342788.4:c.766G>T	p.Gly256Ter	p.G256*	ENST00000342788	NM_005235.2	256	Gga/Tga	7/28	1	2	FACETS	0.553	0.464	0.653	0.553	0.464	0.653	SUBCLONAL	1	TRUE	1	0.23	2		342	707	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645456	215645456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	95	687	0	ENST00000260947.4:c.1142G>A	p.Ser381Asn	p.S381N	ENST00000260947	NM_000465.2	381	aGt/aAt	4/11	1	2	FACETS	0.853	0.758	0.955	0.853	0.758	0.955	CLONAL	1	TRUE	1	0.23	2		687	968	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442502	52442502	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	33	136	0	ENST00000460680.1:c.243C>G	p.Phe81Leu	p.F81L	ENST00000460680	NM_004656.3	81	ttC/ttG	4/17	1	2	FACETS	1	0.834	1	1	0.834	1	CLONAL	1	TRUE	1	0.23	2		136	281	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541364	187541364	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	49	376	0	ENST00000441802.2:c.6376C>A	p.His2126Asn	p.H2126N	ENST00000441802	NM_005245.3	2126	Cac/Aac	10/27	1	2	FACETS	0.598	0.506	0.701	0.598	0.506	0.701	SUBCLONAL	1	TRUE	1	0.23	2		376	712	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876278	35876278	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	40	292	0	ENST00000303115.3:c.1070C>G	p.Thr357Ser	p.T357S	ENST00000303115	NM_002185.3	357	aCt/aGt	8/8	1	2	FACETS	0.764	0.635	0.908	0.764	0.635	0.908	CLONAL	1	TRUE	1	0.23	2		292	455	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876401	35876401	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	34	230	0	ENST00000303115.3:c.1193C>A	p.Pro398His	p.P398H	ENST00000303115	NM_002185.3	398	cCt/cAt	8/8	1	2	FACETS	0.824	0.674	0.991	0.824	0.674	0.991	CLONAL	1	TRUE	1	0.23	2		230	359	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196966	138196966	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs758353383	NA	P-0010332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	35	168	0	ENST00000237289.4:c.628A>T	p.Ile210Phe	p.I210F	ENST00000237289	NM_001270507.1	210	Att/Ttt	4/9	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.23	2		168	289	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729816	41729816	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1273	141	582	0	ENST00000242208.4:c.713T>A	p.Leu238Gln	p.L238Q	ENST00000242208	NM_002192.2	238	cTg/cAg	3/3	1	2	FACETS	0.867	0.787	0.951	0.867	0.787	0.951	CLONAL	1	TRUE	1	0.23	2		582	1414	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521468	8521468	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	52	257	0	ENST00000356435.5:c.770G>T	p.Cys257Phe	p.C257F	ENST00000356435		257	tGt/tTt	9/35	0.3	1	FACETS	0.998	0.852	1	0.998	0.852	1	CLONAL	1	TRUE	0	0.23	1		257	401	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342871	87342871	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	16	135	0	ENST00000277120.3:c.1156G>C	p.Asp386His	p.D386H	ENST00000277120		386	Gat/Cat	9/19	1	2	FACETS	0.65	0.481	0.851	0.65	0.481	0.851	SUBCLONAL	1	TRUE	1	0.23	2		135	214	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534722	18534722	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	78	378	0	ENST00000266497.5:c.1780C>A	p.Leu594Met	p.L594M	ENST00000266497		594	Ctg/Atg	12/31	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.23	2		378	672	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245844	46245844	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	66	322	0	ENST00000334344.6:c.3938A>T	p.Gln1313Leu	p.Q1313L	ENST00000334344	NM_152641.2	1313	cAa/cTa	15/21	1	2	FACETS	0.938	0.814	1	0.938	0.814	1	CLONAL	1	TRUE	1	0.23	2		322	612	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610078	81610078	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	50	339	2	ENST00000298171.2:c.1676G>T	p.Gly559Val	p.G559V	ENST00000298171	NM_000369.2	559	gGa/gTa	10/10	1	2	FACETS	0.492	0.416	0.576	0.492	0.416	0.576	SUBCLONAL	1	TRUE	1	0.23	2		341	884	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982728	7982728	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	66	267	0	ENST00000319144.4:c.1057C>A	p.Pro353Thr	p.P353T	ENST00000319144	NM_001139.2	353	Ccc/Acc	8/15	1	2	FACETS	0.912	0.792	1	0.912	0.792	1	CLONAL	1	TRUE	1	0.23	2		267	629	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33433430	33433430	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1060502960	NA	P-0010332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	47	206	0	ENST00000345365.6:c.551A>T	p.Glu184Val	p.E184V	ENST00000345365	NM_002878.3	184	gAg/gTg	6/10	0.235570210078876	3	FACETS	0.814	0.686	0.955	0.407	0.343	0.478	CLONAL	1	TRUE	1	0.23	3		206	560	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006684	62006684	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	75	341	0	ENST00000392795.3:c.595G>T	p.Gly199Cys	p.G199C	ENST00000392795	NM_001039933.1	199	Ggc/Tgc	6/6	0.235570210078876	3	FACETS	0.79	0.69	0.897	0.395	0.345	0.449	SUBCLONAL	1	TRUE	1	0.23	3		341	921	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980783	40980783	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	66	398	2	ENST00000373198.4:c.1703C>A	p.Ala568Asp	p.A568D	ENST00000373198	NM_133170.3	568	gCc/gAc	10/32	0.3	2	FACETS	0.799	0.693	0.915			1	CLONAL	1	TRUE	NA	0.23	2		400	718	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933751	39933751	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	94	460	0	ENST00000378444.4:c.848C>A	p.Ala283Glu	p.A283E	ENST00000378444	NM_001123385.1	283	gCa/gAa	4/15	1	2	FACETS	0.725	0.643	0.812	0.725	0.643	0.812	SUBCLONAL	1	TRUE	1	0.23	2		460	1128	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409937	63409937	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	145	560	1	ENST00000330258.3:c.3230C>A	p.Pro1077His	p.P1077H	ENST00000330258	NM_152424.3	1077	cCt/cAt	2/2	0.3	1	FACETS	0.997	0.908	1	0.997	0.908	1	CLONAL	1	TRUE	0	0.23	1		561	1119	SUCCESS
AR	367	MSKCC	GRCh37	X	66765480	66765480	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	69	276	0	ENST00000374690.3:c.492G>T	p.Leu164Phe	p.L164F	ENST00000374690	NM_000044.3	164	ttG/ttT	1/8	0.3	1	FACETS	0.714	0.621	0.814	0.714	0.621	0.814	SUBCLONAL	1	TRUE	0	0.23	1		276	744	SUCCESS
AR	367	MSKCC	GRCh37	X	66937395	66937395	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	122	626	0	ENST00000374690.3:c.2249T>A	p.Met750Lys	p.M750K	ENST00000374690	NM_000044.3	750	aTg/aAg	5/8	0.3	1	FACETS	0.723	0.652	0.799	0.723	0.652	0.799	SUBCLONAL	1	TRUE	0	0.23	1		626	1298	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776957	76776957	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	97	582	1	ENST00000373344.5:c.6995G>T	p.Arg2332Ile	p.R2332I	ENST00000373344	NM_000489.3	2332	aGa/aTa	33/35	1	2	FACETS	0.829	0.738	0.927	0.829	0.738	0.927	CLONAL	1	TRUE	1	0.23	2		583	1017	SUCCESS
ATRX	546	MSKCC	GRCh37	X	77041467	77041467	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0010332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	128	469	0	ENST00000373344.5:c.20+1G>T		p.X7_splice	ENST00000373344	NM_000489.3	7			1	2	FACETS	0.942	0.851	1	0.942	0.851	1	CLONAL	1	TRUE	1	0.23	2		469	1182	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215294	123215294	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	107	598	0	ENST00000218089.9:c.2840G>C	p.Gly947Ala	p.G947A	ENST00000218089	NM_001042749.1	947	gGc/gCc	28/35	1	2	FACETS	0.75	0.671	0.835	0.75	0.671	0.835	SUBCLONAL	1	TRUE	1	0.23	2		598	1240	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220201	1220383	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCAGGTGTGGCTCCCTGCTGGACCTAGCCTTTCCTCTGTCCTGTGTGCCTGGACTTCTGTGACTTCCCAGCTGGGCCTGTGGTGTTTGGGAGGCTCCCAGGCAGCTGCAAAGGGGACCCCTGTGAGGGGCAGGGAGGCCTCGGCCCCAGGACGGGTGTGTGCTGCCCGCAGGTACTTCTGTCA	GCAGGTGTGGCTCCCTGCTGGACCTAGCCTTTCCTCTGTCCTGTGTGCCTGGACTTCTGTGACTTCCCAGCTGGGCCTGTGGTGTTTGGGAGGCTCCCAGGCAGCTGCAAAGGGGACCCCTGTGAGGGGCAGGGAGGCCTCGGCCCCAGGACGGGTGTGTGCTGCCCGCAGGTACTTCTGTCA	-	novel	NA	P-0010332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	52	23	0	ENST00000326873.7:c.465-169_478del		p.X155_splice	ENST00000326873	NM_000455.4	155		4/10	1	2	FACETS	0.962	0.856	1	1	0.985	1	CLONAL	5	TRUE	1	0.23	2		23	94	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566781	212566782	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	50	464	0	ENST00000342788.4:c.1399dup	p.Cys467LeufsTer7	p.C467Lfs*7	ENST00000342788	NM_005235.2	467	tgt/tTgt	12/28	1	2	FACETS	0.472	0.399	0.552	0.472	0.399	0.552	SUBCLONAL	1	TRUE	1	0.23	2		464	922	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610153	10610154	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0010332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	93	331	0	ENST00000171111.5:c.556_557delinsTT	p.Gly186Phe	p.G186F	ENST00000171111	NM_203500.1	186	GGc/TTc	2/6	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.23	2		331	753	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343060	70343062	+	frameshift_variant	Frame_Shift_Del	DEL	CGG	CGG	A	novel	NA	P-0010332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	41	367	0	ENST00000374080.3:c.1601_1603delinsA	p.Ala534GlufsTer3	p.A534Efs*3	ENST00000374080		534	gCGGag/gAag	11/45	0.3	1	FACETS	0.519	0.431	0.617	0.519	0.431	0.617	SUBCLONAL	1	TRUE	0	0.23	1		367	608	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0010525-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	42	370	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.673	0.561	0.798	0.673	0.561	0.798	SUBCLONAL	1	TRUE	1	0.195372032703303	2		370	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0010525-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	50	764	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.195372032703303	1	FACETS	0.731	0.619	0.854	0.731	0.619	0.854	SUBCLONAL	1	TRUE	0	0.195372032703303	1		765	632	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148922	119148922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768898787	NA	P-0010525-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	29	441	0	ENST00000264033.4:c.1142G>A	p.Cys381Tyr	p.C381Y	ENST00000264033	NM_005188.3	381	tGt/tAt	8/16	0.195372032703303	1	FACETS	0.515	0.412	0.632	0.515	0.412	0.632	SUBCLONAL	1	TRUE	0	0.195372032703303	1		441	520	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855288	76855288	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010525-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	41	397	0	ENST00000373344.5:c.5699G>T	p.Gly1900Val	p.G1900V	ENST00000373344	NM_000489.3	1900	gGt/gTt	24/35	1	2	FACETS	0.828	0.689	0.982	0.828	0.689	0.982	CLONAL	1	TRUE	1	0.195372032703303	2		397	507	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194859	30194859	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010525-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	40	530	0	ENST00000331968.5:c.286G>T	p.Gly96Ter	p.G96*	ENST00000331968	NM_002742.2	96	Gga/Tga	2/18	1	2	FACETS	0.718	0.596	0.855	0.718	0.596	0.855	SUBCLONAL	1	TRUE	1	0.195372032703303	2		530	570	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584552	48584552	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0010525-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	26	566	0	ENST00000342988.3:c.725C>G	p.Ser242Ter	p.S242*	ENST00000342988	NM_005359.5	242	tCa/tGa	6/12	1	2	FACETS	0.541	0.427	0.672	0.541	0.427	0.672	SUBCLONAL	1	TRUE	1	0.195372032703303	2		566	492	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78426146	78426162	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGGTACAGGTGGCCC	TGGGGTACAGGTGGCCC	-	novel	NA	P-0010525-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	23	356	0	ENST00000370768.2:c.1363_1379del	p.Gly455TrpfsTer30	p.G455Wfs*30	ENST00000370768	NM_003902.3	455	GGGCCACCTGTACCCCAt/t	15/20	1	2	FACETS	0.658	0.512	0.826	0.658	0.512	0.826	SUBCLONAL	1	TRUE	1	0.195372032703303	2		356	358	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420124	49420124	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010525-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	31	623	0	ENST00000301067.7:c.15625G>T	p.Gly5209Cys	p.G5209C	ENST00000301067	NM_003482.3	5209	Ggc/Tgc	48/54	1	2	FACETS	0.631	0.509	0.769	0.631	0.509	0.769	SUBCLONAL	1	TRUE	1	0.195372032703303	2		623	503	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483037	29483037	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1060500324	NA	P-0010525-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	40	486	1	ENST00000356175.3:c.97A>T	p.Lys33Ter	p.K33*	ENST00000356175	NM_000267.3	33	Aaa/Taa	2/57	1	2	FACETS	0.64	0.53	0.762	0.64	0.53	0.762	SUBCLONAL	1	TRUE	1	0.195372032703303	2		487	640	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249994	39249994	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010525-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	66	686	0	ENST00000402219.2:c.1575A>G	p.Ile525Met	p.I525M	ENST00000402219	NM_005633.3	525	atA/atG	10/23	1	2	FACETS	0.856	0.742	0.981	0.856	0.742	0.981	CLONAL	1	TRUE	1	0.195372032703303	2		686	789	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026100	36026100	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0010525-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	46	664	1	ENST00000358208.4:c.704-2A>T		p.X235_splice	ENST00000358208		235			1	2	FACETS	0.831	0.699	0.976	0.831	0.699	0.976	CLONAL	1	TRUE	1	0.195372032703303	2		665	567	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898776	134898776	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0010525-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	39	534	0	ENST00000398015.3:c.1834A>T	p.Lys612Ter	p.K612*	ENST00000398015	NM_004441.4	612	Aag/Tag	10/16	0.195372032703303	1	FACETS	0.771	0.639	0.919	0.771	0.639	0.919	CLONAL	1	TRUE	0	0.195372032703303	1		534	467	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920439	134920439	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010525-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	40	772	0	ENST00000398015.3:c.2254G>T	p.Val752Phe	p.V752F	ENST00000398015	NM_004441.4	752	Gtc/Ttc	12/16	0.195372032703303	1	FACETS	0.53	0.439	0.632	0.53	0.439	0.632	SUBCLONAL	1	TRUE	0	0.195372032703303	1		772	697	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871220	35871220	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010525-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	91	390	1	ENST00000303115.3:c.442G>T	p.Val148Leu	p.V148L	ENST00000303115	NM_002185.3	148	Gtg/Ttg	4/8	0.195372032703303	3	FACETS	0.908	0.808	1	0.908	0.808	1	CLONAL	2	TRUE	1	0.195372032703303	3		391	563	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010525-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	37	443	0	ENST00000257430.4:c.4189G>A	p.Glu1397Lys	p.E1397K	ENST00000257430	NM_000038.5	1397	Gag/Aag	16/16	0.195372032703303	3	FACETS	0.741	0.61	0.888	0.371	0.305	0.444	SUBCLONAL	1	TRUE	1	0.195372032703303	3		443	561	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342665	87342665	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010525-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	48	622	0	ENST00000277120.3:c.950G>T	p.Trp317Leu	p.W317L	ENST00000277120		317	tGg/tTg	9/19	1	2	FACETS	0.773	0.652	0.906	0.773	0.652	0.906	CLONAL	1	TRUE	1	0.195372032703303	2		622	636	SUCCESS
AR	367	MSKCC	GRCh37	X	66765112	66765112	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010525-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	32	579	0	ENST00000374690.3:c.124C>A	p.Pro42Thr	p.P42T	ENST00000374690	NM_000044.3	42	Cca/Aca	1/8	1	2	FACETS	0.731	0.593	0.887	0.731	0.593	0.887	SUBCLONAL	1	TRUE	1	0.195372032703303	2		579	448	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0011043-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	19	383	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.202755038995082	3	FACETS	0.335	0.253	0.432	0.112	0.084	0.144	SUBCLONAL	1	TRUE	0	0.225434455369847	3		383	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0011043-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	121	398	0	ENST00000269305.4:c.376-1G>T		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.225434455369847	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.225434455369847	1		398	776	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183162	32183162	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011043-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	58	420	0	ENST00000375023.3:c.1862G>A	p.Gly621Asp	p.G621D	ENST00000375023	NM_004557.3	621	gGc/gAc	12/30	1	2	FACETS	0.587	0.503	0.68	0.587	0.503	0.68	SUBCLONAL	1	TRUE	1	0.225434455369847	2		420	876	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66735696	66735696	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1240248728	NA	P-0011043-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	97	434	0	ENST00000307102.5:c.516+1G>A		p.X172_splice	ENST00000307102	NM_002755.3	172			1	2	FACETS	0.851	0.757	0.952	0.851	0.757	0.952	CLONAL	1	TRUE	1	0.225434455369847	2		434	1011	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527488	41527488	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011043-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	95	584	0	ENST00000263253.7:c.1379A>T	p.Asp460Val	p.D460V	ENST00000263253	NM_001429.3	460	gAt/gTt	6/31	1	2	FACETS	0.703	0.624	0.788	0.703	0.624	0.788	SUBCLONAL	1	TRUE	1	0.225434455369847	2		584	1199	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164773	106164773	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765414159	NA	P-0012067-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	327	400	3	ENST00000380013.4:c.3641G>A	p.Arg1214Gln	p.R1214Q	ENST00000380013	NM_001127208.2	1214	cGg/cAg	6/11	1	2	FACETS	0.926	0.879	0.972	0.926	0.879	0.972	CLONAL	1	TRUE	1	0.9	2		403	785	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732959	74732959	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs751713049	NA	P-0012067-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	228	592	0	ENST00000359995.5:c.284C>G	p.Pro95Arg	p.P95R	ENST00000359995	NM_001195427.1	95	cCc/cGc	1/3	1	2	FACETS	0.944	0.888	1	0.944	0.888	1	CLONAL	1	TRUE	1	0.9	2		592	537	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260061	16260061	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012067-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	463	880	0	ENST00000375759.3:c.7326G>C	p.Glu2442Asp	p.E2442D	ENST00000375759	NM_015001.2	2442	gaG/gaC	11/15	1	2	FACETS	0.997	0.956	1	0.997	0.956	1	CLONAL	1	TRUE	1	0.9	2		880	1032	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164919	106164919	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012067-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	240	579	2	ENST00000380013.4:c.3787T>G	p.Cys1263Gly	p.C1263G	ENST00000380013	NM_001127208.2	1263	Tgt/Ggt	6/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.9	2		581	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0012426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	350	764	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.174215854860029	3	FACETS	1	0.973	1	1	0.994	1	CLONAL	4	FALSE	0	0.174215854860029	3		765	1052	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0012426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	77	441	2	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.141179702138165	4	FACETS	1	0.946	1	0.573	0.502	0.65	CLONAL	1	FALSE	2	0.174215854860029	4		443	905	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948198	55948198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147627339	NA	P-0012426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	153	558	2	ENST00000263923.4:c.3773C>T	p.Thr1258Met	p.T1258M	ENST00000263923	NM_002253.2	1258	aCg/aTg	29/30	1	2	FACETS	0.886	0.81	0.966	1	0.99	1	CLONAL	2	FALSE	1	0.174215854860029	2		560	991	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508932	106508932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	25	245	0	ENST00000359195.3:c.926C>T	p.Thr309Met	p.T309M	ENST00000359195	NM_002649.2	309	aCg/aTg	2/11	0.174215854860029	3	FACETS	0.821	0.647	1	0.411	0.323	0.511	CLONAL	1	FALSE	1	0.174215854860029	3		245	380	SUCCESS
APC	324	MSKCC	GRCh37	5	112175399	112175400	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0012426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	100	380	0	ENST00000257430.4:c.4110_4111del	p.Pro1372ThrfsTer2	p.P1372Tfs*2	ENST00000257430	NM_000038.5	1370	AAa/a	16/16	0.141179702138165	4	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	FALSE	2	0.174215854860029	4		380	577	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508511	106508511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	100	242	0	ENST00000359195.3:c.505C>T	p.His169Tyr	p.H169Y	ENST00000359195	NM_002649.2	169	Cac/Tac	2/11	0.134838096122118	3	FACETS	1	0.982	1	0.474	0.43	0.521	INDETERMINATE	1	TRUE	0	0.651264187098578	3		242	286	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs121913468	NA	P-0012526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	406	433	0	ENST00000269571.5:c.2305G>A	p.Asp769Asn	p.D769N	ENST00000269571		769	Gac/Aac	19/27	0.651264187098578	4	FACETS	0.944	0.907	0.981	0.944	0.907	0.981	CLONAL	3	TRUE	1	0.651264187098578	4		433	727	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81916879	81916879	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs760446087	NA	P-0012526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	74	681	0	ENST00000359376.3:c.698C>G	p.Thr233Ser	p.T233S	ENST00000359376	NM_002661.3	233	aCt/aGt	9/33	0.428420583290813	3	FACETS	0.26	0.227	0.297	0.13	0.113	0.149	SUBCLONAL	1	TRUE	1	0.651264187098578	3		681	1158	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081523	143081523	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	29	475	0	ENST00000262992.4:c.1551T>A	p.Asp517Glu	p.D517E	ENST00000262992	NM_001101669.1	517	gaT/gaA	15/24	0.518197751099515	2	FACETS	0.18	0.144	0.222	0.09	0.072	0.111	SUBCLONAL	1	TRUE	0	0.651264187098578	2		475	494	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27173353	27173353	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	87	568	0	ENST00000380036.4:c.894C>A	p.Cys298Ter	p.C298*	ENST00000380036	NM_000459.3	298	tgC/tgA	6/23	0.118967055067676	5	FACETS	0.534	0.471	0.601	0.178	0.157	0.201	INDETERMINATE	1	TRUE	2	0.651264187098578	5		568	990	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25458621	25458633	+	frameshift_variant	Frame_Shift_Del	DEL	AAGACAGGAAAAT	AAGACAGGAAAAT	-	novel	NA	P-0012765-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	99	523	7	ENST00000264709.3:c.2540_2552del	p.His847ProfsTer2	p.H847Pfs*2	ENST00000264709	NM_175629.2	847	cATTTTCCTGTCTTc/cc	22/23	1	2	FACETS	0.219	0.195	0.245	0.219	0.195	0.245	SUBCLONAL	1	FALSE	1	0.931338913566522	2		530	970	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740749	58740749	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs779070661	NA	P-0012765-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	103	529	8	ENST00000305921.3:c.1654C>T	p.Arg552Ter	p.R552*	ENST00000305921	NM_003620.3	552	Cga/Tga	6/6	1	2	FACETS	0.247	0.22	0.275	0.247	0.22	0.275	SUBCLONAL	1	FALSE	1	0.931338913566522	2		537	897	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317042	11317042	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014014-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	75	548	0	ENST00000361445.4:c.452G>A	p.Arg151Gln	p.R151Q	ENST00000361445	NM_004958.3	151	cGa/cAa	4/58	0.396109946217021	2	FACETS	1	0.908	1	0.517	0.456	0.582	CLONAL	1	FALSE	0	0.396109946217021	2		548	366	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165942	118165942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749332682	NA	P-0014132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	12	369	0	ENST00000369448.3:c.452G>A	p.Arg151His	p.R151H	ENST00000369448	NM_017709.3	151	cGc/cAc	2/2	1	2	FACETS	0.375	0.263	0.513	0.375	0.263	0.513	SUBCLONAL	1	FALSE	1	0.281863297637701	2		369	227	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0014701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	251	618	2	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	0.558019595593646	1	FACETS	0.877	0.827	0.927	0.877	0.827	0.927	CLONAL	1	TRUE	0	0.644485594417762	1		620	602	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0014701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	196	777	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.644485594417762	1	FACETS	0.636	0.592	0.682	0.636	0.592	0.682	SUBCLONAL	1	TRUE	0	0.644485594417762	1		777	648	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991668	25991668	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	211	523	0	ENST00000435504.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000435504		192	Cag/Tag	7/13	0.598420037687061	1	FACETS	0.881	0.826	0.936	0.881	0.826	0.936	CLONAL	1	TRUE	0	0.644485594417762	1		523	504	SUCCESS
AR	367	MSKCC	GRCh37	X	66937372	66937372	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	163	346	1	ENST00000374690.3:c.2226G>C	p.Trp742Cys	p.W742C	ENST00000374690	NM_000044.3	742	tgG/tgC	5/8	1	1	FACETS	0.634	0.585	0.684	0.634	0.585	0.684	SUBCLONAL	1	TRUE	0	0.644485594417762	1		347	541	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807521	1807521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	345	760	1	ENST00000260795.2:c.1690C>T	p.Arg564Trp	p.R564W	ENST00000260795		564	Cgg/Tgg	12/17	0.348488794336111	1	FACETS	0.724	0.687	0.762	0.724	0.687	0.762	INDETERMINATE	1	TRUE	0	0.644485594417762	1		761	1002	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0015189-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	382	467	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.869191491662316	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.864379034703073	2		468	423	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729734	162729734	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015189-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	309	439	0	ENST00000367921.3:c.820G>T	p.Glu274Ter	p.E274*	ENST00000367921	NM_006182.2	274	Gaa/Taa	8/18	0.868210771061716	4	FACETS	0.982	0.933	1	0.982	0.933	1	CLONAL	2	TRUE	2	0.864379034703073	4		439	679	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582897	95582897	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015189-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	214	163	0	ENST00000393063.1:c.1645T>C	p.Ser549Pro	p.S549P	ENST00000393063	NM_030621.3	549	Tct/Cct	11/28	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.864379034703073	2		163	235	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510706	38510706	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015189-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	209	451	0	ENST00000254066.5:c.960G>T	p.Glu320Asp	p.E320D	ENST00000254066	NM_000964.3	320	gaG/gaT	7/9	NA	2	FACETS	0.995	0.963	1			1	INDETERMINATE	2	TRUE	NA	0.864379034703073	2		451	243	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401469	401469	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015189-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	86	256	0	ENST00000380956.4:c.791A>T	p.Lys264Met	p.K264M	ENST00000380956	NM_001195286.1	264	aAg/aTg	7/9	0.320622366552391	1	FACETS	1	0.988	1	1	0.988	1	INDETERMINATE	1	TRUE	0	0.864379034703073	1		256	94	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959168	2959168	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015189-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	274	569	0	ENST00000396946.4:c.2348A>G	p.Asn783Ser	p.N783S	ENST00000396946	NM_032415.4	783	aAc/aGc	18/25	0.864379034703073	7	FACETS	0.98	0.921	1	0.327	0.307	0.347	CLONAL	2	TRUE	1	0.864379034703073	7		569	1022	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541543	29541543	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1567841799	NA	P-0015189-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	248	207	0	ENST00000356175.3:c.1467T>A	p.Tyr489Ter	p.Y489*	ENST00000356175	NM_000267.3	489	taT/taA	13/57	0.869191491662316	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.864379034703073	2		207	278	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159041	24159042	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0016457-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	194	680	0	ENST00000263121.7:c.716_717dup	p.Ala240LeufsTer28	p.A240Lfs*28	ENST00000263121	NM_003073.3	238	gcc/gcCTc	6/9	0.148026587033636	0	FACETS	0.921	0.861	0.982			1	CLONAL	5	FALSE	0	0.148026587033636	0		680	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519975	NA	P-0017605-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	519	805	0	ENST00000269305.4:c.403T>C	p.Cys135Arg	p.C135R	ENST00000269305	NM_001126112.2	135	Tgc/Cgc	5/11	0.289222559377755	3	FACETS	0.837	0.805	0.869			1	CLONAL	3	FALSE	NA	0.458189443550981	3		805	1109	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911387	32911387	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017605-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	147	403	0	ENST00000380152.3:c.2895G>T	p.Met965Ile	p.M965I	ENST00000380152		965	atG/atT	11/27	0.396219487821927	2	FACETS	0.804	0.742	0.867	0.804	0.742	0.867	CLONAL	2	FALSE	0	0.458189443550981	2		403	399	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0018022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	132	498	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.282261764268319	3	FACETS	1	0.982	1	0.663	0.602	0.726	CLONAL	1	TRUE	1	0.310500407401395	3		498	741	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0018022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	82	541	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.282261764268319	3	FACETS	0.82	0.723	0.925	0.41	0.361	0.463	CLONAL	1	TRUE	1	0.310500407401395	3		542	744	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138384011	138384011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759151757	NA	P-0018022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	43	306	0	ENST00000289153.2:c.2539C>T	p.Arg847Cys	p.R847C	ENST00000289153	NM_006219.2	847	Cgc/Tgc	18/22	0.211664121539711	3	FACETS	0.664	0.555	0.784	0.221	0.185	0.262	SUBCLONAL	1	TRUE	0	0.310500407401395	3		306	482	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989202	41989202	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	57	403	0	ENST00000219905.7:c.1994T>G	p.Phe665Cys	p.F665C	ENST00000219905	NM_001164273.1	665	tTt/tGt	3/24	0.233323455089661	2	FACETS	0.691	0.593	0.798	0.346	0.296	0.399	SUBCLONAL	1	TRUE	0	0.310500407401395	2		403	531	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688761	47688761	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	58	307	0	ENST00000347630.2:c.539A>C	p.Lys180Thr	p.K180T	ENST00000347630	NM_001007230.1	180	aAg/aCg	7/11	0.274480599770685	4	FACETS	0.913	0.785	1	0.304	0.261	0.351	CLONAL	1	TRUE	1	0.310500407401395	4		307	536	SUCCESS
APC	324	MSKCC	GRCh37	5	112175163	112175163	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	25	135	0	ENST00000257430.4:c.3872A>G	p.Gln1291Arg	p.Q1291R	ENST00000257430	NM_000038.5	1291	cAg/cGg	16/16	0.310500407401395	3	FACETS	0.853	0.676	1	0.427	0.338	0.528	CLONAL	1	TRUE	1	0.310500407401395	3		135	218	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41267780	41267780	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs80357066	NA	P-0018022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	41	391	0	ENST00000357654.3:c.97G>C	p.Glu33Gln	p.E33Q	ENST00000357654	NM_007294.3	33	Gaa/Caa	3/23	0.274480599770685	4	FACETS	0.636	0.529	0.755	0.212	0.176	0.252	SUBCLONAL	1	TRUE	1	0.310500407401395	4		391	544	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229210	36229210	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	58	468	0	ENST00000222270.7:c.7900G>C	p.Asp2634His	p.D2634H	ENST00000222270	NM_014727.1	2634	Gat/Cat	37/37	0.211664121539711	3	FACETS	0.579	0.497	0.67	0.193	0.165	0.224	SUBCLONAL	1	TRUE	0	0.310500407401395	3		468	745	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675844	30675844	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	72	578	0	ENST00000376406.3:c.2512C>G	p.Leu838Val	p.L838V	ENST00000376406	NM_014641.2	838	Ctg/Gtg	8/15	0.227108084893532	3	FACETS	0.653	0.569	0.743	0.218	0.189	0.248	SUBCLONAL	1	TRUE	0	0.310500407401395	3		578	821	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	59	326	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.227779965068945	4	FACETS	0.851	0.741	0.969	1	0.959	1	CLONAL	3	FALSE	2	0.227779965068945	4		326	249	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	175	639	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.227779965068945	6	FACETS	0.954	0.884	1	0.954	0.884	1	CLONAL	4	FALSE	2	0.227779965068945	6		645	586	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307997	11307997	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	69	497	0	ENST00000361445.4:c.995G>T	p.Gly332Val	p.G332V	ENST00000361445	NM_004958.3	332	gGg/gTg	7/58	1	2	FACETS	1	0.926	1	1	0.983	1	CLONAL	2	FALSE	1	0.227779965068945	2		497	282	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254996	16254996	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	52	294	0	ENST00000375759.3:c.2261G>T	p.Arg754Met	p.R754M	ENST00000375759	NM_015001.2	754	aGg/aTg	11/15	0.227779965068945	7	FACETS	1	0.949	1	0.624	0.535	0.72	CLONAL	2	FALSE	3	0.227779965068945	7		294	287	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436168	51436168	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	rs1377714753	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	103	225	0	ENST00000262662.1:c.128A>C	p.Gln43Pro	p.Q43P	ENST00000262662		43	cAg/cCg	3/4	0.227779965068945	7	FACETS	0.988	0.888	1			1	CLONAL	3	FALSE	NA	0.227779965068945	7		225	479	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85741996	85741996	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	196	571	0	ENST00000370580.1:c.40A>G	p.Thr14Ala	p.T14A	ENST00000370580	NM_003921.4	14	Act/Gct	1/3	0.18022646620728	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	FALSE	1	0.227779965068945	3		571	860	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458276	120458276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1378776407	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	35	553	0	ENST00000256646.2:c.7069A>G	p.Met2357Val	p.M2357V	ENST00000256646	NM_024408.3	2357	Atg/Gtg	34/34	0.18022646620728	3	FACETS	1	0.892	1	0.561	0.461	0.672	CLONAL	1	FALSE	1	0.227779965068945	3		553	305	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458452	120458452	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140832430	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	60	463	0	ENST00000256646.2:c.6893G>A	p.Arg2298Gln	p.R2298Q	ENST00000256646	NM_024408.3	2298	cGg/cAg	34/34	0.18022646620728	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	FALSE	1	0.227779965068945	3		463	244	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318779	163318779	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs116669228	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	38	338	1	ENST00000271452.3:c.1169G>A	p.Arg390Gln	p.R390Q	ENST00000271452	NM_145697.2	390	cGa/cAa	13/14	0.18022646620728	3	FACETS	1	0.95	1	0.717	0.597	0.851	CLONAL	1	FALSE	1	0.227779965068945	3		339	259	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70441157	70441157	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	rs764225020	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	43	387	0	ENST00000373644.4:c.4832del	p.Asn1611ThrfsTer13	p.N1611Tfs*13	ENST00000373644	NM_030625.2	1609	gAa/ga	9/12	0.227779965068945	6	FACETS	0.974	0.82	1	0.65	0.547	0.762	CLONAL	2	FALSE	3	0.227779965068945	6		387	282	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88635800	88635800	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	97	387	0	ENST00000372037.3:c.25A>G	p.Arg9Gly	p.R9G	ENST00000372037	NM_004329.2	9	Aga/Gga	3/13	0.227779965068945	6	FACETS	0.984	0.883	1	0.984	0.883	1	CLONAL	3	FALSE	3	0.227779965068945	6		387	420	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	68	609	4	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.92	1	1	0.983	1	CLONAL	2	FALSE	1	0.227779965068945	2		613	281	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625456	69625456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781938977	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	88	659	0	ENST00000334134.2:c.337G>A	p.Ala113Thr	p.A113T	ENST00000334134	NM_005247.2	113	Gcc/Acc	3/3	0.14677420455029	4	FACETS	0.927	0.829	1	1	0.977	1	CLONAL	3	FALSE	2	0.227779965068945	4		659	341	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948208	71948209	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs749079348	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	161	917	4	ENST00000298229.2:c.2927dup	p.Pro977ThrfsTer7	p.P977Tfs*7	ENST00000298229	NM_001567.3	974	gcc/gCcc	26/28	0.14677420455029	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	FALSE	2	0.227779965068945	4		921	751	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427411	49427411	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	114	694	0	ENST00000301067.7:c.11077G>T	p.Ala3693Ser	p.A3693S	ENST00000301067	NM_003482.3	3693	Gct/Tct	39/54	0.227779965068945	8	FACETS	0.909	0.82	1	0.682	0.615	0.752	CLONAL	3	FALSE	4	0.227779965068945	8		694	618	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120621	115120621	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	197	699	0	ENST00000257566.3:c.385G>T	p.Gly129Ter	p.G129*	ENST00000257566	NM_016569.3	129	Gga/Tga	1/8	1	2	FACETS	1	0.979	1	1	0.994	1	CLONAL	2	FALSE	1	0.227779965068945	2		699	761	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434367	121434367	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	120	308	2	ENST00000257555.6:c.1136del	p.Pro379LeufsTer5	p.P379Lfs*5	ENST00000257555		377	ctC/ct	6/10	1	2	FACETS	1	0.964	1	1	0.99	1	CLONAL	2	FALSE	1	0.227779965068945	2		310	469	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241504	105241504	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	95	652	1	ENST00000349310.3:c.476G>A	p.Gly159Asp	p.G159D	ENST00000349310	NM_001014432.1	159	gGc/gAc	7/15	1	2	FACETS	0.925	0.828	1	1	0.986	1	CLONAL	2	FALSE	1	0.227779965068945	2		653	451	SUCCESS
BLM	641	MSKCC	GRCh37	15	91337481	91337481	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1288025724	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	147	481	0	ENST00000355112.3:c.3104A>G	p.Glu1035Gly	p.E1035G	ENST00000355112	NM_000057.2	1035	gAa/gGa	16/22	0.227779965068945	11	FACETS	1	0.924	1			1	CLONAL	4	FALSE	NA	0.227779965068945	11		481	647	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396724	396724	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	84	496	0	ENST00000262320.3:c.302T>C	p.Leu101Pro	p.L101P	ENST00000262320	NM_003502.3	101	cTg/cCg	2/11	1	2	FACETS	0.927	0.823	1	1	0.984	1	CLONAL	2	FALSE	1	0.227779965068945	2		496	398	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637567	23637567	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	64	510	0	ENST00000261584.4:c.2738A>G	p.His913Arg	p.H913R	ENST00000261584	NM_024675.3	913	cAc/cGc	7/13	1	2	FACETS	0.803	0.699	0.914	1	0.975	1	CLONAL	2	FALSE	1	0.227779965068945	2		510	350	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993731	72993731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	59	453	0	ENST00000268489.5:c.314del	p.Pro105ArgfsTer4	p.P105Rfs*4	ENST00000268489	NM_006885.3	105	cCg/cg	2/10	1	2	FACETS	1	0.948	1	1	0.982	1	CLONAL	2	FALSE	1	0.227779965068945	2		453	220	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831344	89831345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	119	566	0	ENST00000389301.3:c.2730_2731dup	p.Trp911SerfsTer11	p.W911Sfs*11	ENST00000389301	NM_000135.2	911	tgg/tCTgg	28/43	0.192910327091952	5	FACETS	0.997	0.901	1	0.665	0.601	0.732	CLONAL	2	FALSE	2	0.227779965068945	5		566	703	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16052823	16052823	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	86	327	0	ENST00000268712.3:c.851T>C	p.Val284Ala	p.V284A	ENST00000268712	NM_006311.3	284	gTg/gCg	9/46	0.227779965068945	6	FACETS	1	0.931	1	0.794	0.708	0.884	CLONAL	3	FALSE	2	0.227779965068945	6		327	346	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	38	686	2	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	0.227779965068945	6	FACETS	0.869	0.717	1	0.217	0.179	0.26	CLONAL	1	FALSE	2	0.227779965068945	6		688	559	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119790	70119790	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	156	535	0	ENST00000245479.2:c.792A>T	p.Arg264Ser	p.R264S	ENST00000245479	NM_000346.3	264	agA/agT	3/3	0.227779965068945	6	FACETS	0.939	0.865	1	0.939	0.865	1	CLONAL	4	FALSE	2	0.227779965068945	6		535	531	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57567468	57567468	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	80	297	0	ENST00000316660.6:c.58+1G>A		p.X20_splice	ENST00000316660	NM_021127.2	20			1	2	FACETS	1	0.916	1	1	0.985	1	CLONAL	2	FALSE	1	0.227779965068945	2		297	338	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271744	18271744	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	148	648	0	ENST00000222254.8:c.431C>T	p.Ser144Phe	p.S144F	ENST00000222254	NM_005027.3	144	tCt/tTt	4/16	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.227779965068945	2		648	934	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224130	36224130	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200908859	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	73	701	0	ENST00000222270.7:c.6680C>T	p.Thr2227Met	p.T2227M	ENST00000222270	NM_014727.1	2227	aCg/aTg	28/37	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.227779965068945	2		701	480	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50138855	50138855	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	213	882	3	ENST00000246792.3:c.635del	p.Gly212AlafsTer22	p.G212Afs*22	ENST00000246792	NM_006270.3	212	gGc/gc	6/6	NA	2	FACETS	0.909	0.844	0.976			1	INDETERMINATE	2	FALSE	NA	0.227779965068945	2		885	1029	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910258	50910258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1271321739	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	95	574	1	ENST00000440232.2:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000440232	NM_002691.3	505	Cgc/Tgc	13/27	NA	2	FACETS	1	0.951	1			1	INDETERMINATE	2	FALSE	NA	0.227779965068945	2		575	379	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918709	50918709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501818	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	47	435	0	ENST00000440232.2:c.2579C>T	p.Ala860Val	p.A860V	ENST00000440232	NM_002691.3	860	gCg/gTg	21/27	NA	2	FACETS	0.829	0.705	0.962			1	INDETERMINATE	2	FALSE	NA	0.227779965068945	2		435	249	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39294893	39294893	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	51	292	0	ENST00000402219.2:c.89T>C	p.Val30Ala	p.V30A	ENST00000402219	NM_005633.3	30	gTc/gCc	2/23	1	2	FACETS	0.982	0.844	1	1	0.976	1	CLONAL	2	FALSE	1	0.227779965068945	2		292	228	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030613	48030613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779617676	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	97	506	0	ENST00000234420.5:c.3227G>A	p.Arg1076His	p.R1076H	ENST00000234420	NM_000179.2	1076	cGc/cAc	5/10	1	2	FACETS	0.959	0.86	1	1	0.986	1	CLONAL	2	FALSE	1	0.227779965068945	2		506	444	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919674	96919674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140860906	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	83	471	1	ENST00000258439.3:c.589C>T	p.Arg197Cys	p.R197C	ENST00000258439	NM_001193304.2	197	Cgc/Tgc	4/4	1	2	FACETS	0.808	0.716	0.906	1	0.981	1	CLONAL	2	FALSE	1	0.227779965068945	2		472	451	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131228	202131228	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	69	395	0	ENST00000358485.4:c.196C>A	p.Leu66Ile	p.L66I	ENST00000358485	NM_001080125.1	66	Ctt/Att	2/9	1	2	FACETS	0.921	0.808	1	1	0.98	1	CLONAL	2	FALSE	1	0.227779965068945	2		395	329	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385064	31385064	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	79	608	0	ENST00000328111.2:c.1449G>T	p.Glu483Asp	p.E483D	ENST00000328111	NM_006892.3	483	gaG/gaT	14/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.227779965068945	2		608	465	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	22	390	0	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	0.227779965068945	0	FACETS	1	0.794	1			1	CLONAL	1	FALSE	0	0.227779965068945	0		390	147	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42840387	42840387	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs756502093	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	149	482	0	ENST00000398585.3:c.1361A>G	p.Asp454Gly	p.D454G	ENST00000398585	NM_001135099.1	454	gAc/gGc	12/14	0.211877091079058	1	FACETS	1	0.937	1	1	0.992	1	CLONAL	2	FALSE	0	0.227779965068945	1		482	566	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160171	22160171	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	54	337	0	ENST00000215832.6:c.460A>G	p.Asn154Asp	p.N154D	ENST00000215832	NM_002745.4	154	Aac/Gac	3/9	0.227779965068945	0	FACETS	1	0.908	1			1	CLONAL	1	FALSE	0	0.227779965068945	0		337	340	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548348	41548348	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	47	271	0	ENST00000263253.7:c.3140del	p.Lys1047ArgfsTer12	p.K1047Rfs*12	ENST00000263253	NM_001429.3	1046	Aaa/aa	16/31	0.227779965068945	5	FACETS	0.905	0.768	1	0.603	0.512	0.703	CLONAL	2	FALSE	2	0.227779965068945	5		271	306	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458270	12458270	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	132	562	1	ENST00000287820.6:c.892del	p.Leu298CysfsTer38	p.L298Cfs*38	ENST00000287820	NM_015869.4	296	aCc/ac	6/7	0.227779965068945	5	FACETS	1	0.976	1	0.811	0.738	0.887	CLONAL	2	FALSE	2	0.227779965068945	5		563	639	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940115	49940115	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	170	640	0	ENST00000296474.3:c.928G>T	p.Gly310Trp	p.G310W	ENST00000296474	NM_002447.2	310	Ggg/Tgg	1/20	0.227779965068945	5	FACETS	1	0.949	1	1	0.949	1	CLONAL	3	FALSE	2	0.227779965068945	5		640	645	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231210	142231211	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs1464095818	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	93	506	0	ENST00000350721.4:c.4743_4744del	p.Phe1582LeufsTer4	p.F1582Lfs*4	ENST00000350721	NM_001184.3	1581	gtGTtc/gttc	27/47	0.227779965068945	5	FACETS	1	0.956	1	0.758	0.676	0.844	CLONAL	2	FALSE	2	0.227779965068945	5		506	482	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	93	310	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.227779965068945	4	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	FALSE	2	0.227779965068945	4		311	467	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681714	30681714	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	126	455	0	ENST00000376406.3:c.383G>T	p.Cys128Phe	p.C128F	ENST00000376406	NM_014641.2	128	tGc/tTc	3/15	0.227779965068945	6	FACETS	0.852	0.773	0.934	0.852	0.773	0.934	CLONAL	3	FALSE	3	0.227779965068945	6		455	630	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323289	31323289	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	13	130	0	ENST00000412585.2:c.700C>A	p.Pro234Thr	p.P234T	ENST00000412585	NM_005514.6	234	Cct/Act	4/8	0.227779965068945	6	FACETS	1	0.742	1	0.346	0.248	0.465	CLONAL	1	FALSE	3	0.227779965068945	6		130	160	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940100	31940100	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	189	719	0	ENST00000375333.2:c.242T>A	p.Val81Glu	p.V81E	ENST00000375333	NM_032454.1	81	gTa/gAa	2/8	0.227779965068945	6	FACETS	1	0.98	1	0.785	0.725	0.847	CLONAL	2	FALSE	3	0.227779965068945	6		719	1026	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864489	162864490	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	17	347	0	ENST00000366898.1:c.23dup	p.Asn8LysfsTer13	p.N8Kfs*13	ENST00000366898	NM_004562.2	8	aac/aaAc	2/12	0.227779965068945	5	FACETS	1	0.891	1	0.7	0.527	0.903	CLONAL	1	FALSE	3	0.227779965068945	5		347	143	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	33	613	0	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	0.227779965068945	0	FACETS	0.717	0.586	0.865			1	SUBCLONAL	1	FALSE	0	0.227779965068945	0		613	312	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879594	151879596	+	inframe_deletion	In_Frame_Del	DEL	TGC	TGC	-	novel	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	17	298	2	ENST00000262189.6:c.5349_5351del	p.Gln1787del	p.Q1787del	ENST00000262189	NM_170606.2	1783	caGCAa/caa	36/59	0.227779965068945	4	FACETS	0.804	0.601	1	0.402	0.3	0.522	CLONAL	1	FALSE	2	0.227779965068945	4		300	228	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046323	69046323	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	38	472	0	ENST00000288368.4:c.3796G>T	p.Val1266Phe	p.V1266F	ENST00000288368	NM_024870.2	1266	Gtt/Ttt	32/40	1	2	FACETS	0.751	0.626	0.889	1	0.954	1	SUBCLONAL	2	FALSE	1	0.227779965068945	2		472	222	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485909	8485909	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1165957484	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	33	404	0	ENST00000356435.5:c.2908C>T	p.Gln970Ter	p.Q970*	ENST00000356435		970	Cag/Tag	17/35	0.18022646620728	3	FACETS	0.849	0.699	1	0.849	0.699	1	CLONAL	2	FALSE	1	0.227779965068945	3		404	190	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359956	87359956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137873897	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	55	286	0	ENST00000277120.3:c.1264G>A	p.Val422Ile	p.V422I	ENST00000277120		422	Gtc/Atc	11/19	0.18022646620728	3	FACETS	1	0.913	1	1	0.913	1	CLONAL	2	FALSE	1	0.227779965068945	3		286	250	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907165	101907165	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	29	306	0	ENST00000374994.4:c.1129del	p.Arg377GlyfsTer12	p.R377Gfs*12	ENST00000374994	NM_004612.2	375	acA/ac	6/9	0.18022646620728	3	FACETS	0.771	0.624	0.934	0.771	0.624	0.934	CLONAL	2	FALSE	1	0.227779965068945	3		306	184	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249927	110249927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	130	530	0	ENST00000374672.4:c.748G>A	p.Val250Ile	p.V250I	ENST00000374672	NM_004235.4	250	Gtc/Atc	3/5	0.18022646620728	3	FACETS	0.948	0.867	1	1	0.986	1	CLONAL	3	FALSE	1	0.227779965068945	3		530	447	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417370	139417370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs553542677	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	161	644	1	ENST00000277541.6:c.674C>T	p.Ser225Leu	p.S225L	ENST00000277541	NM_017617.3	225	tCg/tTg	4/34	0.18022646620728	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	FALSE	1	0.227779965068945	3		645	645	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246393	53246393	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	93	741	0	ENST00000375401.3:c.589del	p.Leu197TyrfsTer37	p.L197Yfs*37	ENST00000375401	NM_004187.3	197	Cta/ta	5/26	0.227779965068945	0	FACETS	0.72	0.643	0.8			1	SUBCLONAL	2	FALSE	0	0.227779965068945	0		741	438	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438316	110438317	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTTGTT	rs532810290	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	32	192	0	ENST00000375856.3:c.79_84dup	p.Asn27_Asn28dup	p.N27_N28dup	ENST00000375856	NM_003749.2	27	-/AACAAC	1/2	1	2	FACETS	0.912	0.742	1	0.912	0.742	1	CLONAL	1	FALSE	1	0.227779965068945	2		192	308	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962610	100962610	+	splice_region_variant,intron_variant	Splice_Region	DEL	A	A	-	rs761514775	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	37	337	0	ENST00000325455.5:c.1790-3del		p.X597_splice	ENST00000325455	NM_001202474.3	597			0.14677420455029	4	FACETS	0.863	0.717	1	0.863	0.717	1	CLONAL	2	FALSE	2	0.227779965068945	4		337	231	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836879	151836879	+	splice_region_variant,intron_variant	Splice_Region	DEL	A	A	-	rs369965395	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	125	434	3	ENST00000262189.6:c.14344-3del		p.X4782_splice	ENST00000262189	NM_170606.2	4782			0.227779965068945	4	FACETS	1	0.949	1	1	0.991	1	CLONAL	4	FALSE	2	0.227779965068945	4		437	322	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52676064	52676067	+	splice_region_variant,intron_variant	Splice_Region	DEL	ACAA	ACAA	-	novel	NA	P-0018118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	40	267	0	ENST00000394830.3:c.996-6_996-3del		p.X332_splice	ENST00000394830	NM_018313.4	332			0.227779965068945	5	FACETS	1	0.935	1	0.822	0.691	0.964	CLONAL	2	FALSE	2	0.227779965068945	5		267	191	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32439122	32439122	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs771527206	NA	P-0019019-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	324	630	0	ENST00000332351.3:c.950+1G>A		p.X317_splice	ENST00000332351	NM_024426.4	317			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		630	692	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891405	76891405	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0019019-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	232	427	0	ENST00000373344.5:c.4699+1G>C		p.X1567_splice	ENST00000373344	NM_000489.3	1567			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		427	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0019102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	271	478	5	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.53569116332568	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.53569116332568	1		483	620	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0019102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	95	350	1	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.278173363316871	1	FACETS	0.792	0.712	0.874	0.792	0.712	0.874	INDETERMINATE	1	TRUE	0	0.53569116332568	1		351	328	SUCCESS
APC	324	MSKCC	GRCh37	5	112175162	112175162	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561588104	NA	P-0019102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	33	179	0	ENST00000257430.4:c.3871C>T	p.Gln1291Ter	p.Q1291*	ENST00000257430	NM_000038.5	1291	Cag/Tag	16/16	0.278173363316871	1	FACETS	0.444	0.365	0.532	0.444	0.365	0.532	INDETERMINATE	1	TRUE	0	0.53569116332568	1		179	203	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564615	55564615	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149092990	NA	P-0019102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	98	510	0	ENST00000288135.5:c.503C>T	p.Ala168Val	p.A168V	ENST00000288135	NM_000222.2	168	gCg/gTg	3/21	0.53569116332568	1	FACETS	0.58	0.52	0.643	0.58	0.52	0.643	SUBCLONAL	1	TRUE	0	0.53569116332568	1		510	462	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911548	114911548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	135	365	0	ENST00000543371.1:c.1066G>A	p.Ala356Thr	p.A356T	ENST00000543371	NM_001198531.1	356	Gca/Aca	10/14	0.319419137666793	1	FACETS	0.858	0.787	0.932	0.858	0.787	0.932	INDETERMINATE	1	TRUE	0	0.53569116332568	1		365	430	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859609	57859610	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	rs1566559797	NA	P-0019102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	126	530	0	ENST00000228682.2:c.671_672dup	p.Glu225ArgfsTer56	p.E225Rfs*56	ENST00000228682	NM_005269.2	221	-/GA	7/12	0.278173363316871	1	FACETS	0.545	0.495	0.598	0.545	0.495	0.598	INDETERMINATE	1	TRUE	0	0.53569116332568	1		530	632	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37680994	37680994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	84	458	0	ENST00000447079.4:c.3163G>A	p.Val1055Ile	p.V1055I	ENST00000447079	NM_015083.1	1055	Gtt/Att	12/14	0.178144869631871	4	FACETS	0.679	0.6	0.765	0.34	0.3	0.383	INDETERMINATE	1	TRUE	2	0.53569116332568	4		458	709	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40864884	40864884	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	62	350	0	ENST00000373198.4:c.2384C>A	p.Ser795Tyr	p.S795Y	ENST00000373198	NM_133170.3	795	tCc/tAc	16/32	0.53569116332568	3	FACETS	0.62	0.537	0.711	0.31	0.268	0.356	SUBCLONAL	1	TRUE	1	0.53569116332568	3		350	473	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450345	50450345	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	82	513	0	ENST00000331340.3:c.529C>G	p.Leu177Val	p.L177V	ENST00000331340	NM_006060.4	177	Ctc/Gtc	5/8	1	2	FACETS	0.417	0.367	0.471	0.417	0.367	0.471	SUBCLONAL	1	TRUE	1	0.53569116332568	2		513	734	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541405	187541405	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	44	360	0	ENST00000441802.2:c.6335G>C	p.Arg2112Thr	p.R2112T	ENST00000441802	NM_005245.3	2112	aGa/aCa	10/27	0.53569116332568	1	FACETS	0.4	0.337	0.469	0.4	0.337	0.469	SUBCLONAL	1	TRUE	0	0.53569116332568	1		360	301	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262004	16262004	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	81	393	1	ENST00000375759.3:c.9269del	p.Leu3090ArgfsTer9	p.L3090Rfs*9	ENST00000375759	NM_015001.2	3090	cTg/cg	11/15	0.298520147289891	1	FACETS	0.486	0.429	0.545	0.486	0.429	0.545	INDETERMINATE	1	TRUE	0	0.53569116332568	1		394	456	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834581	156834581	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	115	774	2	ENST00000524377.1:c.349C>T	p.Leu117Phe	p.L117F	ENST00000524377	NM_002529.3	117	Ctc/Ttc	3/17	0.298520147289891	1	FACETS	0.399	0.36	0.442	0.399	0.36	0.442	INDETERMINATE	1	TRUE	0	0.53569116332568	1		776	787	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137767	64137767	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	97	889	0	ENST00000334205.4:c.1868A>G	p.Glu623Gly	p.E623G	ENST00000334205	NM_003942.2	623	gAg/gGg	15/17	0.278173363316871	1	FACETS	0.273	0.242	0.305	0.273	0.242	0.305	INDETERMINATE	1	TRUE	0	0.53569116332568	1		889	972	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813342	102813342	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	93	527	0	ENST00000307046.8:c.347A>G	p.Lys116Arg	p.K116R	ENST00000307046	NM_001111285.1	116	aAg/aGg	3/4	0.278173363316871	1	FACETS	0.423	0.376	0.472	0.423	0.376	0.472	INDETERMINATE	1	TRUE	0	0.53569116332568	1		527	601	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202767	133202767	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	114	600	0	ENST00000320574.5:c.6467T>A	p.Val2156Asp	p.V2156D	ENST00000320574	NM_006231.2	2156	gTc/gAc	46/49	0.278173363316871	1	FACETS	0.482	0.434	0.532	0.482	0.434	0.532	INDETERMINATE	1	TRUE	0	0.53569116332568	1		600	647	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528238	103528238	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	42	260	0	ENST00000355739.4:c.3546A>T	p.Arg1182Ser	p.R1182S	ENST00000355739	NM_000123.3	1182	agA/agT	15/15	1	2	FACETS	0.399	0.333	0.471	0.399	0.333	0.471	SUBCLONAL	1	TRUE	1	0.53569116332568	2		260	393	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085661	16085661	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	123	559	0	ENST00000281043.3:c.838del	p.Val280SerfsTer39	p.V280Sfs*39	ENST00000281043	NM_005378.4	279	gtG/gt	3/3	0.278173363316871	1	FACETS	0.526	0.477	0.578	0.526	0.477	0.578	INDETERMINATE	1	TRUE	0	0.53569116332568	1		559	639	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682802	190682802	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	45	279	0	ENST00000441310.2:c.478T>A	p.Ser160Thr	p.S160T	ENST00000441310	NM_000534.4	160	Tca/Aca	5/13	0.268181800184169	2	FACETS	0.483	0.407	0.566	0.241	0.203	0.283	INDETERMINATE	1	TRUE	0	0.53569116332568	2		279	348	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539448	187539448	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	39	304	0	ENST00000441802.2:c.8292G>C	p.Lys2764Asn	p.K2764N	ENST00000441802	NM_005245.3	2764	aaG/aaC	10/27	0.53569116332568	1	FACETS	0.357	0.297	0.423	0.357	0.297	0.423	SUBCLONAL	1	TRUE	0	0.53569116332568	1		304	299	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395007	395007	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	47	401	0	ENST00000380956.4:c.403G>T	p.Gly135Ter	p.G135*	ENST00000380956	NM_001195286.1	135	Gga/Tga	3/9	NA	2	FACETS	0.445	0.376	0.521			1	INDETERMINATE	1	TRUE	NA	0.53569116332568	2		401	394	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188877	32188877	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	95	690	0	ENST00000375023.3:c.677A>T	p.Gln226Leu	p.Q226L	ENST00000375023	NM_004557.3	226	cAg/cTg	4/30	0.422345249656933	3	FACETS	0.523	0.465	0.586	0.262	0.232	0.293	SUBCLONAL	1	TRUE	1	0.53569116332568	3		690	859	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979541	2979541	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	72	415	0	ENST00000396946.4:c.706T>G	p.Leu236Val	p.L236V	ENST00000396946	NM_032415.4	236	Ttg/Gtg	6/25	NA	2	FACETS	0.553	0.484	0.627			1	INDETERMINATE	1	TRUE	NA	0.53569116332568	2		415	486	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752861	128752861	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	62	295	0	ENST00000377970.2:c.1022A>C	p.Lys341Thr	p.K341T	ENST00000377970	NM_002467.4	341	aAg/aCg	3/3	0.278173363316871	1	FACETS	0.31	0.267	0.356	0.31	0.267	0.356	INDETERMINATE	1	TRUE	0	0.53569116332568	1		295	547	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566457	139566457	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1564285709	NA	P-0019102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	154	661	0	ENST00000308874.7:c.716T>C	p.Leu239Pro	p.L239P	ENST00000308874		239	cTc/cCc	9/10	0.298520147289891	1	FACETS	0.506	0.463	0.551	0.506	0.463	0.551	INDETERMINATE	1	TRUE	0	0.53569116332568	1		661	832	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836816	151836816	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	234	568	2	ENST00000262189.6:c.14404G>A	p.Gly4802Arg	p.G4802R	ENST00000262189	NM_170606.2	4802	Ggg/Agg	56/59	0.746376067996125	3	FACETS	0.939	0.877	1	0.469	0.438	0.502	CLONAL	1	TRUE	1	0.746376067996125	3		570	917	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28624235	28624235	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	436	565	0	ENST00000241453.7:c.739A>G	p.Ile247Val	p.I247V	ENST00000241453	NM_004119.2	247	Ata/Gta	6/24	0.746376067996125	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.746376067996125	3		565	754	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs879253911	NA	P-0019783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	540	633	0	ENST00000269305.4:c.538G>T	p.Glu180Ter	p.E180*	ENST00000269305	NM_001126112.2	180	Gag/Tag	5/11	0.790106587580119	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.790106587580119	2		633	650	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671286	30671286	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	425	373	0	ENST00000376406.3:c.5591G>C	p.Arg1864Thr	p.R1864T	ENST00000376406	NM_014641.2	1864	aGa/aCa	11/15	0.790106587580119	6	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	3	0.790106587580119	6		373	869	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450397	50450397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	126	379	0	ENST00000331340.3:c.581C>T	p.Thr194Met	p.T194M	ENST00000331340	NM_006060.4	194	aCg/aTg	5/8	0.790106587580119	6	FACETS	0.834	0.754	0.918	0.208	0.188	0.23	CLONAL	1	TRUE	2	0.790106587580119	6		379	987	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670422	246670422	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1195	714	626	0	ENST00000388985.4:c.98C>G	p.Ser33Trp	p.S33W	ENST00000388985		33	tCg/tGg	1/12	0.790106587580119	7	FACETS	0.939	0.906	0.972	0.563	0.543	0.584	CLONAL	3	TRUE	2	0.790106587580119	7		626	1909	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433614	49433614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	671	925	1	ENST00000301067.7:c.7939G>A	p.Asp2647Asn	p.D2647N	ENST00000301067	NM_003482.3	2647	Gac/Aac	31/54	0.467132766548151	6	FACETS	0.95	0.918	0.983	0.95	0.918	0.983	INDETERMINATE	3	TRUE	3	0.790106587580119	6		926	1537	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434849	49434849	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	633	731	0	ENST00000301067.7:c.6704G>C	p.Arg2235Thr	p.R2235T	ENST00000301067	NM_003482.3	2235	aGa/aCa	31/54	0.467132766548151	6	FACETS	0.943	0.909	0.976	0.943	0.909	0.976	INDETERMINATE	3	TRUE	3	0.790106587580119	6		731	1462	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435312	49435312	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	505	651	0	ENST00000301067.7:c.6241G>A	p.Glu2081Lys	p.E2081K	ENST00000301067	NM_003482.3	2081	Gag/Aag	31/54	0.467132766548151	6	FACETS	0.975	0.936	1	0.975	0.936	1	INDETERMINATE	3	TRUE	3	0.790106587580119	6		651	1128	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436602	49436602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	564	642	0	ENST00000301067.7:c.5704G>A	p.Glu1902Lys	p.E1902K	ENST00000301067	NM_003482.3	1902	Gaa/Aaa	26/54	0.467132766548151	6	FACETS	0.942	0.907	0.978	0.942	0.907	0.978	INDETERMINATE	3	TRUE	3	0.790106587580119	6		642	1303	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41011054	41011054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	259	591	0	ENST00000267868.3:c.487G>A	p.Glu163Lys	p.E163K	ENST00000267868	NM_002875.4	163	Gag/Aag	6/10	0.790106587580119	3	FACETS	0.989	0.928	1	0.494	0.464	0.526	CLONAL	1	TRUE	1	0.790106587580119	3		591	925	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855969	68855969	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	379	493	2	ENST00000261769.5:c.1777C>A	p.Pro593Thr	p.P593T	ENST00000261769	NM_004360.3	593	Ccc/Acc	12/16	0.790106587580119	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.790106587580119	2		495	468	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004871	16004871	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	497	526	0	ENST00000268712.3:c.2383C>T	p.Gln795Ter	p.Q795*	ENST00000268712	NM_006311.3	795	Cag/Tag	20/46	0.467132766548151	6	FACETS	1	0.991	1	1	0.991	1	INDETERMINATE	3	TRUE	3	0.790106587580119	6		526	995	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277027	18277027	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	389	483	0	ENST00000222254.8:c.1474G>C	p.Glu492Gln	p.E492Q	ENST00000222254	NM_005027.3	492	Gaa/Caa	12/16	0.790106587580119	3	FACETS	0.973	0.933	1	0.973	0.933	1	CLONAL	2	TRUE	1	0.790106587580119	3		483	706	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245175	46245175	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	181	450	0	ENST00000334344.6:c.3269C>A	p.Ala1090Glu	p.A1090E	ENST00000334344	NM_152641.2	1090	gCa/gAa	15/21	0.467132766548151	6	FACETS	1	0.989	1	0.479	0.442	0.517	INDETERMINATE	1	TRUE	3	0.790106587580119	6		450	823	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940457	13940457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	132	216	0	ENST00000405192.2:c.1049G>A	p.Arg350Gln	p.R350Q	ENST00000405192	NM_001163147.1	350	cGa/cAa	11/12	0.790106587580119	6	FACETS	1	0.96	1	0.275	0.25	0.302	CLONAL	1	TRUE	2	0.790106587580119	6		216	783	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520006	NA	P-0020632-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	195	742	0	ENST00000269305.4:c.821T>C	p.Val274Ala	p.V274A	ENST00000269305	NM_001126112.2	274	gTt/gCt	8/11	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.483375254586719	2		742	602	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020632-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	148	382	6	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	0.339578441761069	3	FACETS	0.807	0.743	0.873	0.807	0.743	0.873	CLONAL	2	TRUE	1	0.483375254586719	3		388	471	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348329	89348329	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020632-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	102	979	0	ENST00000301030.4:c.4621G>T	p.Glu1541Ter	p.E1541*	ENST00000301030	NM_001256183.1	1541	Gaa/Taa	9/13	0.483375254586719	3	FACETS	0.58	0.518	0.647	0.29	0.259	0.324	SUBCLONAL	1	TRUE	1	0.483375254586719	3		979	903	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779258	3779258	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020632-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	72	444	1	ENST00000262367.5:c.5790del	p.Thr1931ProfsTer45	p.T1931Pfs*45	ENST00000262367	NM_004380.2	1930	ccC/cc	31/31	0.339578441761069	3	FACETS	0.833	0.73	0.943	0.417	0.365	0.472	CLONAL	1	TRUE	1	0.483375254586719	3		445	444	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982372	201982372	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1258691938	NA	P-0020632-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	42	709	0	ENST00000359651.3:c.751C>T	p.Arg251Ter	p.R251*	ENST00000359651		251	Cga/Tga	6/8	0.440651640293692	3	FACETS	0.287	0.239	0.341	0.143	0.119	0.171	SUBCLONAL	1	TRUE	1	0.483375254586719	3		709	752	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380272	25380273	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCTTGACCTGCTGTGTCGAGAATATCCAAGAGACAGGTTTCT	novel	NA	P-0020632-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	87	670	0	ENST00000311936.3:c.144_185dup	p.Thr50_Glu63dup	p.T50_E63dup	ENST00000311936	NM_004985.3	50	gag/gaAGAAACCTGTCTCTTGGATATTCTCGACACAGCAGGTCAAGAg	3/5	0.206240888795342	2	FACETS	0.709	0.629	0.793	0.354	0.314	0.397	INDETERMINATE	1	TRUE	0	0.483375254586719	2		670	508	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211073	36211073	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020632-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	111	810	0	ENST00000222270.7:c.824G>C	p.Gly275Ala	p.G275A	ENST00000222270	NM_014727.1	275	gGa/gCa	3/37	1	2	FACETS	0.531	0.477	0.588	0.531	0.477	0.588	SUBCLONAL	1	TRUE	1	0.483375254586719	2		810	865	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40828013	40828013	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020632-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	113	401	0	ENST00000373198.4:c.2415G>T	p.Lys805Asn	p.K805N	ENST00000373198	NM_133170.3	805	aaG/aaT	17/32	0.483375254586719	5	FACETS	0.767	0.693	0.844	0.511	0.462	0.563	SUBCLONAL	2	TRUE	2	0.483375254586719	5		401	526	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205156	128205156	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020632-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	250	634	1	ENST00000341105.2:c.285G>C	p.Leu95Phe	p.L95F	ENST00000341105	NM_032638.4	95	ttG/ttC	3/6	0.370580412940906	5	FACETS	1	0.987	1	0.783	0.735	0.831	CLONAL	2	TRUE	2	0.483375254586719	5		635	760	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741905	17741905	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020632-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	26	146	0	ENST00000250003.3:c.576C>G	p.His192Gln	p.H192Q	ENST00000250003	NM_002478.4	192	caC/caG	1/3	0.371552787860316	2	FACETS	0.476	0.379	0.586	0.238	0.189	0.293	SUBCLONAL	1	TRUE	0	0.483375254586719	2		146	226	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3842044	3842044	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567316683	NA	P-0020632-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	70	559	2	ENST00000262367.5:c.1268C>T	p.Thr423Ile	p.T423I	ENST00000262367	NM_004380.2	423	aCa/aTa	5/31	0.339578441761069	3	FACETS	0.772	0.675	0.876	0.386	0.337	0.438	SUBCLONAL	1	TRUE	1	0.483375254586719	3		561	466	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548934	29548934	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020632-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	18	413	0	ENST00000356175.3:c.1708T>G	p.Phe570Val	p.F570V	ENST00000356175	NM_000267.3	570	Ttt/Gtt	15/57	0.381700215584297	2	FACETS	0.493	0.374	0.632	0.247	0.187	0.316	SUBCLONAL	1	TRUE	0	0.483375254586719	2		413	151	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17382396	17382479	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TACCTTGCAGATTATCTGCCTGGACCTGTCAGAGGAAATGTCACTGCCAAAGCTGGAGTCGTTCAACGGGTAAGAGGGACATTT	TACCTTGCAGATTATCTGCCTGGACCTGTCAGAGGAAATGTCACTGCCAAAGCTGGAGTCGTTCAACGGGTAAGAGGGACATTT	-	novel	NA	P-0020632-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	27	566	0	ENST00000359435.4:c.286-8_344+17del		p.X96_splice	ENST00000359435	NM_001033549.1	96		3/9	1	2	FACETS	0.275	0.218	0.34	0.275	0.218	0.34	SUBCLONAL	1	TRUE	1	0.483375254586719	2		566	406	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162475142	162475142	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020632-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	62	521	0	ENST00000366898.1:c.599A>G	p.His200Arg	p.H200R	ENST00000366898	NM_004562.2	200	cAc/cGc	5/12	0.440651640293692	3	FACETS	0.711	0.616	0.814	0.356	0.308	0.407	SUBCLONAL	1	TRUE	1	0.483375254586719	3		521	448	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166282	7166282	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021506-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	150	1131	0	ENST00000302850.5:c.1744G>T	p.Gly582Cys	p.G582C	ENST00000302850	NM_000208.2	582	Ggt/Tgt	8/22	0.879865535878369	2	FACETS	0.568	0.521	0.617	0.284	0.26	0.309	SUBCLONAL	1	TRUE	0	0.879865535878369	2		1131	600	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577123	7577123	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876660333	NA	P-0021506-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	572	1064	0	ENST00000269305.4:c.815T>A	p.Val272Glu	p.V272E	ENST00000269305	NM_001126112.2	272	gTg/gAg	8/11	0.879865535878369	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.879865535878369	2		1064	635	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763843	76763843	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021506-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	406	740	0	ENST00000373344.5:c.7465G>T	p.Gly2489Trp	p.G2489W	ENST00000373344	NM_000489.3	2489	Ggg/Tgg	35/35	0.638728585318113	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.879865535878369	4		740	849	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923091	48923091	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0021506-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	125	90	0	ENST00000267163.4:c.540-1G>T		p.X180_splice	ENST00000267163	NM_000321.2	180			0.879865535878369	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.879865535878369	2		90	139	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646184	23646184	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021506-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	155	368	0	ENST00000261584.4:c.1683A>C	p.Lys561Asn	p.K561N	ENST00000261584	NM_024675.3	561	aaA/aaC	4/13	0.879865535878369	3	FACETS	1	0.967	1	0.543	0.501	0.586	CLONAL	1	TRUE	1	0.879865535878369	3		368	467	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111852	56111852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021506-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	34	30	0	ENST00000399503.3:c.452C>T	p.Ala151Val	p.A151V	ENST00000399503	NM_005921.1	151	gCc/gTc	1/20	0.879865535878369	8	FACETS	0.885	0.742	1			1	CLONAL	3	TRUE	NA	0.879865535878369	8		30	106	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519427	137519427	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021506-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	180	205	0	ENST00000367739.4:c.1211A>C	p.Glu404Ala	p.E404A	ENST00000367739	NM_000416.2	404	gAg/gCg	7/7	0.747004043795894	4	FACETS	0.994	0.93	1	0.994	0.93	1	CLONAL	2	TRUE	2	0.879865535878369	4		205	387	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339544	116339544	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021506-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	126	433	0	ENST00000397752.3:c.406G>C	p.Val136Leu	p.V136L	ENST00000397752	NM_000245.2	136	Gtc/Ctc	2/21	0.879865535878369	3	FACETS	1	0.974	1	0.579	0.531	0.629	CLONAL	1	TRUE	1	0.879865535878369	3		433	356	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845880	151845880	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021506-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	180	680	0	ENST00000262189.6:c.13132G>T	p.Glu4378Ter	p.E4378*	ENST00000262189	NM_170606.2	4378	Gaa/Taa	52/59	0.879865535878369	3	FACETS	0.89	0.824	0.958	0.445	0.412	0.479	CLONAL	1	TRUE	1	0.879865535878369	3		680	662	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341092	8341092	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021506-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	102	263	0	ENST00000356435.5:c.5124C>A	p.Tyr1708Ter	p.Y1708*	ENST00000356435		1708	taC/taA	30/35	1	2	FACETS	0.962	0.877	1	0.962	0.877	1	CLONAL	1	TRUE	1	0.879865535878369	2		263	241	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578393	7578393	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876660821	NA	P-0022050-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	134	673	0	ENST00000269305.4:c.537T>G	p.His179Gln	p.H179Q	ENST00000269305	NM_001126112.2	179	caT/caG	5/11	0.523439410552076	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.538192395043694	1		673	327	SUCCESS
APC	324	MSKCC	GRCh37	5	112173377	112173377	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022050-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	45	260	0	ENST00000257430.4:c.2086G>T	p.Glu696Ter	p.E696*	ENST00000257430	NM_000038.5	696	Gaa/Taa	16/16	1	2	FACETS	0.74	0.628	0.861	0.74	0.628	0.861	SUBCLONAL	1	TRUE	1	0.538192395043694	2		260	226	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117909	70117911	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0022050-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	94	393	0	ENST00000245479.2:c.378_380del	p.Gln126_Tyr127delinsHis	p.Q126_Y127delinsH	ENST00000245479	NM_000346.3	126	cAGTac/cac	1/3	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.538192395043694	2		393	321	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0022504-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	53	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.328	0.279	0.382	0.328	0.279	0.382	SUBCLONAL	1	TRUE	1	0.381188672919416	2		371	848	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0022504-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	73	546	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.359	0.313	0.41	0.359	0.313	0.41	SUBCLONAL	1	TRUE	1	0.381188672919416	2		547	1066	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26974650	26974650	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022504-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	62	843	0	ENST00000381527.3:c.994G>A	p.Asp332Asn	p.D332N	ENST00000381527	NM_001260.1	332	Gac/Aac	10/13	1	2	FACETS	0.293	0.252	0.338	0.293	0.252	0.338	SUBCLONAL	1	TRUE	1	0.381188672919416	2		843	1109	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0022602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	298	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.69702964613758	2		371	843	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988310	41988310	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	349	807	2	ENST00000219905.7:c.1102G>T	p.Ala368Ser	p.A368S	ENST00000219905	NM_001164273.1	368	Gcc/Tcc	3/24	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.69702964613758	2		809	968	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063316	67063319	+	missense_variant	Missense_Mutation	ONP	GCGC	GCGC	TCTG	novel	NA	P-0022602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	158	492	1	ENST00000412916.2:c.6_9delinsTCTG	p.Arg3Leu	p.R3L	ENST00000412916		2	ccGCGC/ccTCTG	1/6	1	2	FACETS	0.652	0.599	0.708	0.652	0.599	0.708	SUBCLONAL	1	TRUE	1	0.69702964613758	2		493	695	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220579	1220579	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0022602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	362	908	0	ENST00000326873.7:c.598-1G>T		p.X200_splice	ENST00000326873	NM_000455.4	200			0.69702964613758	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.69702964613758	1		908	667	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259209	36259210	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0022602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	329	1048	3	ENST00000300305.3:c.281_282delinsAA	p.Ser94Lys	p.S94K	ENST00000300305		94	aGC/aAA	3/8	1	2	FACETS	0.898	0.85	0.947	0.898	0.85	0.947	CLONAL	1	TRUE	1	0.69702964613758	2		1051	1051	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054229	30054229	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	228	704	0	ENST00000338641.4:c.651C>A	p.Tyr217Ter	p.Y217*	ENST00000338641	NM_000268.3	217	taC/taA	7/16	1	2	FACETS	0.9	0.842	0.959	0.9	0.842	0.959	CLONAL	1	TRUE	1	0.69702964613758	2		704	727	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508950	106508950	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	210	523	1	ENST00000359195.3:c.944T>C	p.Leu315Pro	p.L315P	ENST00000359195	NM_002649.2	315	cTa/cCa	2/11	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.69702964613758	2		524	602	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485897	8485897	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	186	501	0	ENST00000356435.5:c.2920C>A	p.Pro974Thr	p.P974T	ENST00000356435		974	Cca/Aca	17/35	0.171554878430054	2	FACETS	0.95	0.883	1	0.475	0.441	0.509	INDETERMINATE	1	TRUE	0	0.69702964613758	2		501	562	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0022602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	282	760	1	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	0.69702964613758	1	FACETS	0.971	0.923	1	0.971	0.923	1	CLONAL	1	TRUE	0	0.69702964613758	1		761	543	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411315	63411315	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	342	1089	0	ENST00000330258.3:c.1852G>C	p.Ala618Pro	p.A618P	ENST00000330258	NM_152424.3	618	Gct/Cct	2/2	1	2	FACETS	0.953	0.903	1	0.953	0.903	1	CLONAL	1	TRUE	1	0.69702964613758	2		1089	1030	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022760-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	74	417	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	0.18156806904287	2		417	690	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0022760-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	136	822	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.18156806904287	2		822	1180	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0022760-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	57	343	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.18156806904287	1	FACETS	0.884	0.757	1	0.884	0.757	1	CLONAL	1	TRUE	0	0.18156806904287	1		343	646	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058705	47058706	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022760-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	48	459	0	ENST00000409792.3:c.7572dup	p.Lys2525Ter	p.K2525*	ENST00000409792	NM_014159.6	2524	-/T	21/21	1	2	FACETS	0.703	0.593	0.825	0.703	0.593	0.825	SUBCLONAL	1	TRUE	1	0.18156806904287	2		459	752	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951168	48951168	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022760-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	78	386	0	ENST00000267163.4:c.1330C>T	p.Gln444Ter	p.Q444*	ENST00000267163	NM_000321.2	444	Cag/Tag	13/27	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.18156806904287	2		386	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0023941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	87	822	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.501097208695325	1	FACETS	0.801	0.718	0.887	0.801	0.718	0.887	CLONAL	1	FALSE	0	0.549200495379489	1		822	287	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0023941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2265	176	516	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.549200495379489	25	FACETS	0.96	0.88	1			1	CLONAL	2	FALSE	NA	0.549200495379489	25		516	2441	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912580	NA	P-0023941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	69	406	0	ENST00000342988.3:c.1157G>A	p.Gly386Asp	p.G386D	ENST00000342988	NM_005359.5	386	gGt/gAt	10/12	0.501097208695325	1	FACETS	0.799	0.707	0.897	0.799	0.707	0.897	SUBCLONAL	1	FALSE	0	0.549200495379489	1		406	228	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971170	21971170	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	160	485	0	ENST00000304494.5:c.188T>C	p.Leu63Pro	p.L63P	ENST00000304494	NM_000077.4	63	cTg/cCg	2/3	0.523236659803266	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	FALSE	0	0.549200495379489	2		485	275	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777898	3777898	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1189062800	NA	P-0023941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	81	866	0	ENST00000262367.5:c.7150C>T	p.His2384Tyr	p.H2384Y	ENST00000262367	NM_004380.2	2384	Cac/Tac	31/31	1	2	FACETS	0.808	0.717	0.904	0.808	0.717	0.904	CLONAL	1	FALSE	1	0.549200495379489	2		866	365	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713640	30713640	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	80	528	0	ENST00000295754.5:c.965G>A	p.Trp322Ter	p.W322*	ENST00000295754	NM_003242.5	322	tGg/tAg	4/7	0.501097208695325	1	FACETS	0.923	0.826	1	0.923	0.826	1	CLONAL	1	FALSE	0	0.549200495379489	1		528	229	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0023958-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	392	849	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.814991423816616	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.814991423816616	2		850	450	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0023958-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	99	73	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.814991423816616	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.814991423816616	1		73	130	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100645	8100645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1218595084	NA	P-0023958-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	155	163	0	ENST00000346208.3:c.619G>A	p.Ala207Thr	p.A207T	ENST00000346208		207	Gcc/Acc	3/6	0.630719845710573	4	FACETS	0.943	0.865	1	0.472	0.432	0.512	CLONAL	1	TRUE	2	0.814991423816616	4		163	732	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025261-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	101	236	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.903	0.816	0.994	1	0.987	1	CLONAL	2	TRUE	1	0.326040287293168	2		236	343	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944587	40944587	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025261-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	54	432	0	ENST00000373198.4:c.1915G>T	p.Ala639Ser	p.A639S	ENST00000373198	NM_133170.3	639	Gca/Tca	12/32	1	2	FACETS	0.73	0.624	0.845	0.73	0.624	0.845	SUBCLONAL	1	TRUE	1	0.326040287293168	2		432	454	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405950	49405950	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025261-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	50	650	1	ENST00000418115.1:c.188A>T	p.Gln63Leu	p.Q63L	ENST00000418115	NM_001664.2	63	cAg/cTg	3/5	1	2	FACETS	0.399	0.338	0.467	0.399	0.338	0.467	SUBCLONAL	1	TRUE	1	0.326040287293168	2		651	768	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683652	162683652	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1288568218	NA	P-0025261-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	54	665	0	ENST00000366898.1:c.317A>T	p.Asp106Val	p.D106V	ENST00000366898	NM_004562.2	106	gAc/gTc	3/12	0.326040287293168	2	FACETS	0.456	0.389	0.53	0.228	0.194	0.265	SUBCLONAL	1	TRUE	0	0.326040287293168	2		665	726	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169019	32169019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	173	830	0	ENST00000375023.3:c.4014G>A	p.Met1338Ile	p.M1338I	ENST00000375023	NM_004557.3	1338	atG/atA	22/30	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.262796928830829	2		830	1184	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248980	55248981	+	splice_region_variant,intron_variant	In_Frame_Ins	INS	-	-	TCCAGGAAGCCT	rs397517106	NA	P-0025284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1397	399	469	0	ENST00000275493.2:c.2284-5_2290dup		p.A763_Y764insFQEA	ENST00000275493	NM_005228.3	763			0.262796928830829	17	FACETS	1	0.952	1			1	CLONAL	5	TRUE	NA	0.262796928830829	17		469	1796	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873717	151873717	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	89	473	0	ENST00000262189.6:c.8821C>A	p.Pro2941Thr	p.P2941T	ENST00000262189	NM_170606.2	2941	Cca/Aca	38/59	1	2	FACETS	0.934	0.828	1	0.934	0.828	1	CLONAL	1	TRUE	1	0.262796928830829	2		473	725	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0025745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	245	822	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.976	1	1	0.995	1	CLONAL	2	TRUE	1	0.262567761808798	2		822	860	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	123	600	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.262567761808798	2		600	661	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916957	178916957	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200018596	NA	P-0025745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	1032	341	0	ENST00000263967.3:c.344G>T	p.Arg115Leu	p.R115L	ENST00000263967	NM_006218.2	115	cGa/cTa	2/21	0.262567761808798	28	FACETS	0.983	0.965	1			1	CLONAL	26	TRUE	NA	0.262567761808798	28		341	1357	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	1226	384	0	ENST00000263967.3:c.331A>C	p.Lys111Gln	p.K111Q	ENST00000263967	NM_006218.2	111	Aag/Cag	2/21	0.262567761808798	28	FACETS	1	0.993	1			1	CLONAL	25	TRUE	NA	0.262567761808798	28		384	1617	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692895	89692895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781255	NA	P-0025745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	54	408	0	ENST00000371953.3:c.379G>A	p.Gly127Arg	p.G127R	ENST00000371953	NM_000314.4	127	Gga/Aga	5/9	0.262567761808798	1	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	0	0.262567761808798	1		408	332	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105872	27105872	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0025745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	83	524	0	ENST00000324856.7:c.5483C>G	p.Ser1828Ter	p.S1828*	ENST00000324856	NM_006015.4	1828	tCa/tGa	20/20	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.262567761808798	2		524	558	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798191	42798191	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026198-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	397	763	1	ENST00000575354.2:c.4145C>T	p.Ser1382Leu	p.S1382L	ENST00000575354	NM_015125.3	1382	tCa/tTa	17/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.762442622609888	2		764	990	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78923242	78923242	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0026198-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	252	525	0	ENST00000306801.3:c.3266-1G>A		p.X1089_splice	ENST00000306801	NM_020761.2	1089			0.762442622609888	3	FACETS	0.951	0.891	1	0.476	0.445	0.507	CLONAL	1	TRUE	1	0.762442622609888	3		525	960	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028127	69028127	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026198-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	241	551	1	ENST00000288368.4:c.3286G>T	p.Asp1096Tyr	p.D1096Y	ENST00000288368	NM_024870.2	1096	Gat/Tat	26/40	1	2	FACETS	0.902	0.846	0.958	0.902	0.846	0.958	CLONAL	1	TRUE	1	0.762442622609888	2		552	701	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46736378	46736378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1347233260	NA	P-0026198-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	53	458	0	ENST00000371975.4:c.1090G>A	p.Gly364Ser	p.G364S	ENST00000371975	NM_003579.3	364	Ggt/Agt	10/18	1	2	FACETS	0.207	0.176	0.241	0.207	0.176	0.241	SUBCLONAL	1	TRUE	1	0.762442622609888	2		458	673	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940500	76940500	+	splice_acceptor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0026492-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	365	467	0	ENST00000373344.5:c.595-2del		p.X199_splice	ENST00000373344	NM_000489.3	199			0.645866702604885	6	FACETS	1	0.983	1			1	CLONAL	3	TRUE	NA	0.645866702604885	6		467	814	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599880	10599880	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026492-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	255	1208	0	ENST00000171111.5:c.1696A>T	p.Ile566Phe	p.I566F	ENST00000171111	NM_203500.1	566	Atc/Ttc	5/6	0.645866702604885	3	FACETS	0.968	0.906	1	0.484	0.453	0.516	CLONAL	1	TRUE	1	0.645866702604885	3		1208	1079	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0026989-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	21	370	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		370	616	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0026989-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1348	35	849	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.3	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		849	1383	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0027319-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	74	464	1	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.283678180422136	2		465	514	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027319-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	43	417	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.283678180422136	2		417	254	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0027319-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	114	698	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.272492887720864	1	FACETS	0.845	0.761	0.935	0.845	0.761	0.935	CLONAL	1	TRUE	0	0.283678180422136	1		698	816	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593399	48593400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0027319-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	49	368	0	ENST00000342988.3:c.1151_1152dup	p.Lys385AlafsTer31	p.K385Afs*31	ENST00000342988	NM_005359.5	384	ggc/gGCgc	10/12	0.272492887720864	1	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	0	0.283678180422136	1		368	278	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879131	151879131	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027319-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	57	582	0	ENST00000262189.6:c.5814G>A	p.Met1938Ile	p.M1938I	ENST00000262189	NM_170606.2	1938	atG/atA	36/59	1	2	FACETS	0.741	0.636	0.856	0.741	0.636	0.856	SUBCLONAL	1	TRUE	1	0.283678180422136	2		582	542	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912580	NA	P-0027619-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	119	406	0	ENST00000342988.3:c.1157G>A	p.Gly386Asp	p.G386D	ENST00000342988	NM_005359.5	386	gGt/gAt	10/12	0.259300003264798	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	0	0.275723396473672	1		406	680	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0027619-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1173	122	746	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	0.275723396473672	3	FACETS	0.778	0.701	0.859	0.259	0.233	0.287	SUBCLONAL	1	FALSE	0	0.275723396473672	3		746	1295	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102132	27102132	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027619-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	166	692	0	ENST00000324856.7:c.5058G>A	p.Trp1686Ter	p.W1686*	ENST00000324856	NM_006015.4	1686	tgG/tgA	19/20	0.275723396473672	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	0	0.275723396473672	1		692	956	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842471	68842471	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1131690808	NA	P-0027619-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	107	568	0	ENST00000261769.5:c.531+1G>T		p.X177_splice	ENST00000261769	NM_004360.3	177			0.259300003264798	1	FACETS	0.875	0.785	0.97	0.875	0.785	0.97	CLONAL	1	FALSE	0	0.275723396473672	1		568	765	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523719	41523719	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027619-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1264	155	857	0	ENST00000263253.7:c.1135A>G	p.Met379Val	p.M379V	ENST00000263253	NM_001429.3	379	Atg/Gtg	4/31	0.190201038214353	3	FACETS	0.902	0.823	0.985	0.451	0.411	0.493	CLONAL	1	FALSE	1	0.275723396473672	3		857	1419	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859308	151859309	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0027619-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	52	331	0	ENST00000262189.6:c.11353_11354del	p.Lys3785ValfsTer10	p.K3785Vfs*10	ENST00000262189	NM_170606.2	3785	AAg/g	43/59	1	2	FACETS	0.834	0.712	0.969	0.834	0.712	0.969	CLONAL	1	FALSE	1	0.275723396473672	2		331	452	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0028070-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	150	519	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.341078111148823	3	FACETS	0.977	0.893	1	0.489	0.446	0.533	CLONAL	1	TRUE	1	0.440766211176927	3		519	850	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0028070-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	474	736	3	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.440766211176927	2		739	939	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692839	89692839	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028070-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	115	209	0	ENST00000371953.3:c.323T>G	p.Leu108Arg	p.L108R	ENST00000371953	NM_000314.4	108	cTt/cGt	5/9	0.440766211176927	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.440766211176927	2		209	246	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47735799	47735799	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028070-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	191	571	0	ENST00000449228.1:c.61A>T	p.Thr21Ser	p.T21S	ENST00000449228	NM_001127240.2	21	Acg/Tcg	1/4	0.332270097819897	4	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.440766211176927	4		571	1063	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265542	198265542	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1402437917	NA	P-0028070-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	148	589	0	ENST00000335508.6:c.2615T>C	p.Ile872Thr	p.I872T	ENST00000335508	NM_012433.2	872	aTt/aCt	18/25	0.375653747207881	3	FACETS	1	0.981	1	0.628	0.575	0.682	CLONAL	1	TRUE	1	0.440766211176927	3		589	653	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589139	67589140	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAATAACAAATTAATCA	novel	NA	P-0028070-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	22	255	0	ENST00000274335.5:c.1133_1149dup	p.Phe384ThrfsTer3	p.F384Tfs*3	ENST00000274335		376	gga/ggAAATAACAAATTAATCAa	9/15	1	2	FACETS	0.574	0.448	0.718	0.574	0.448	0.718	SUBCLONAL	1	TRUE	1	0.440766211176927	2		255	174	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589580	67589588	+	inframe_deletion	In_Frame_Del	DEL	AATTACATG	AATTACATG	-	novel	NA	P-0028070-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	17	141	0	ENST00000274335.5:c.1346_1354del	p.Leu449_Glu451del	p.L449_E451del	ENST00000274335		448	aAATTACATGaa/aaa	10/15	1	2	FACETS	0.989	0.755	1	0.989	0.755	1	CLONAL	1	TRUE	1	0.440766211176927	2		141	78	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026415	6026415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778531080	NA	P-0028070-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	48	383	0	ENST00000265849.7:c.1981G>A	p.Glu661Lys	p.E661K	ENST00000265849	NM_000535.5	661	Gaa/Aaa	11/15	0.375653747207881	3	FACETS	0.536	0.453	0.627	0.268	0.226	0.314	SUBCLONAL	1	TRUE	1	0.440766211176927	3		383	496	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0028935-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	296	417	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.847438968068422	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.847438968068422	4		417	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0028935-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	507	631	1	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.847438968068422	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.847438968068422	2		632	558	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804988	43804988	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028935-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	210	422	0	ENST00000372470.3:c.438G>T	p.Gln146His	p.Q146H	ENST00000372470	NM_005373.2	146	caG/caT	4/12	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.847438968068422	2		422	489	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046637	30046637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771109503	NA	P-0028935-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	260	574	1	ENST00000331968.5:c.2546G>A	p.Arg849Gln	p.R849Q	ENST00000331968	NM_002742.2	849	cGa/cAa	18/18	1	2	FACETS	0.972	0.918	1	0.972	0.918	1	CLONAL	1	TRUE	1	0.847438968068422	2		575	631	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660837	227660837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200073898	NA	P-0028935-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	271	525	2	ENST00000305123.5:c.2618G>A	p.Arg873Gln	p.R873Q	ENST00000305123	NM_005544.2	873	cGg/cAg	1/2	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.847438968068422	2		527	583	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265789	41266324	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTA	CAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTA	-	novel	NA	P-0028935-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	85	74	0	ENST00000349496.5:c.13+217_241+80del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.847438968068422	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.847438968068422	2		74	90	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029159-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	56	236	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.523421461732072	2		236	199	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242470	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs397517097	NA	P-0029159-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5962	200	334	0	ENST00000275493.2:c.2240T>C	p.Leu747Ser	p.L747S	ENST00000275493	NM_005228.3	747	tTa/tCa	19/28	0.523421461732072	42	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.523421461732072	42		334	6162	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74868172	74868172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1563677151	NA	P-0029159-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	39	141	0	ENST00000284811.8:c.122C>T	p.Thr41Met	p.T41M	ENST00000284811		41	aCg/aTg	3/4	1	2	FACETS	0.877	0.737	1	0.877	0.737	1	CLONAL	1	TRUE	1	0.523421461732072	2		141	170	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162701	47162701	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029159-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	150	452	0	ENST00000409792.3:c.3425A>G	p.Glu1142Gly	p.E1142G	ENST00000409792	NM_014159.6	1142	gAa/gGa	3/21	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.523421461732072	2		452	570	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0030001-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	30	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.823	0.664	1	0.823	0.664	1	CLONAL	1	TRUE	1	0.217577067051823	2		326	335	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164701	36164701	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030001-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	121	705	0	ENST00000300305.3:c.1174C>T	p.Gln392Ter	p.Q392*	ENST00000300305		392	Cag/Tag	8/8	0.202710372609481	2	FACETS	0.844	0.764	0.928	0.844	0.764	0.928	CLONAL	2	TRUE	0	0.217577067051823	2		705	659	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0030001-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	36	358	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.768	0.631	0.921	0.768	0.631	0.921	CLONAL	1	TRUE	1	0.217577067051823	2		358	431	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120806010	120806010	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030001-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	116	658	2	ENST00000257552.2:c.167T>A	p.Leu56Gln	p.L56Q	ENST00000257552	NM_002442.3	56	cTg/cAg	3/15	0.217577067051823	1	FACETS	0.855	0.773	0.94	1	0.987	1	CLONAL	2	TRUE	0	0.217577067051823	1		660	556	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838145	89838145	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030001-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	114	618	0	ENST00000389301.3:c.2092G>C	p.Glu698Gln	p.E698Q	ENST00000389301	NM_000135.2	698	Gag/Cag	23/43	0.202710372609481	2	FACETS	0.764	0.688	0.843	0.764	0.688	0.843	SUBCLONAL	2	TRUE	0	0.217577067051823	2		618	686	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115888	8115889	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0030342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	65	480	0	ENST00000346208.3:c.1236dup	p.Ser413GlnfsTer94	p.S413Qfs*94	ENST00000346208		412	tcc/tCcc	6/6	1	2	FACETS	0.838	0.726	0.961	0.838	0.726	0.961	CLONAL	1	TRUE	1	0.19	2		480	816	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412905	49412905	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519951	NA	P-0030342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	72	668	0	ENST00000418115.1:c.118G>C	p.Glu40Gln	p.E40Q	ENST00000418115	NM_001664.2	40	Gag/Cag	2/5	1	2	FACETS	0.866	0.755	0.986	0.866	0.755	0.986	CLONAL	1	TRUE	1	0.19	2		668	875	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577068	7577071	+	frameshift_variant	Frame_Shift_Del	DEL	GCGG	GCGG	-	novel	NA	P-0030342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	92	673	0	ENST00000269305.4:c.867_870del	p.Lys292GlyfsTer52	p.K292Gfs*52	ENST00000269305	NM_001126112.2	289	ctCCGC/ct	8/11	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.19	2		673	908	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097625	8097625	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	24	179	0	ENST00000346208.3:c.7G>A	p.Val3Met	p.V3M	ENST00000346208		3	Gtg/Atg	2/6	1	2	FACETS	0.871	0.684	1	0.871	0.684	1	CLONAL	1	TRUE	1	0.19	2		179	290	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097640	8097640	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	27	204	0	ENST00000346208.3:c.22C>T	p.Pro8Ser	p.P8S	ENST00000346208		8	Ccg/Tcg	2/6	1	2	FACETS	0.807	0.643	0.995	0.807	0.643	0.995	CLONAL	1	TRUE	1	0.19	2		204	352	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097782	8097782	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	73	547	1	ENST00000346208.3:c.164G>T	p.Gly55Val	p.G55V	ENST00000346208		55	gGt/gTt	2/6	1	2	FACETS	0.894	0.78	1	0.894	0.78	1	CLONAL	1	TRUE	1	0.19	2		548	860	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097847	8097847	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1325423656	NA	P-0030342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	65	383	0	ENST00000346208.3:c.229C>T	p.Pro77Ser	p.P77S	ENST00000346208		77	Ccg/Tcg	2/6	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.19	2		383	629	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100349	8100350	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0030342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	59	671	1	ENST00000346208.3:c.323_324delinsTT	p.Thr108Ile	p.T108I	ENST00000346208		108	aCC/aTT	3/6	1	2	FACETS	0.639	0.548	0.739	0.639	0.548	0.739	SUBCLONAL	1	TRUE	1	0.19	2		672	972	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320287	30320287	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	38	272	0	ENST00000322652.5:c.1228C>G	p.Leu410Val	p.L410V	ENST00000322652	NM_015355.2	410	Cta/Gta	11/16	0.3	6	FACETS	0.872	0.719	1			1	CLONAL	1	TRUE	NA	0.19	6		272	633	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40743920	40743920	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	60	501	0	ENST00000392038.2:c.787C>G	p.Leu263Val	p.L263V	ENST00000392038	NM_001626.4	263	Ctt/Gtt	9/14	1	2	FACETS	0.83	0.714	0.957	0.83	0.714	0.957	CLONAL	1	TRUE	1	0.19	2		501	761	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755642	57755642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144564763	NA	P-0030342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	80	589	0	ENST00000274289.3:c.145G>A	p.Ala49Thr	p.A49T	ENST00000274289	NM_006622.3	49	Gcg/Acg	1/14	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.19	2		589	837	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207392	29207392	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1229264590	NA	P-0030342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	64	403	2	ENST00000240100.2:c.404C>A	p.Ala135Asp	p.A135D	ENST00000240100	NM_001394.6	135	gCc/gAc	1/4	0.200812152672376	1	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	0	0.19	1		405	570	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207519	29207519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	46	452	0	ENST00000240100.2:c.277G>A	p.Val93Ile	p.V93I	ENST00000240100	NM_001394.6	93	Gta/Ata	1/4	0.200812152672376	1	FACETS	0.646	0.543	0.761	0.646	0.543	0.761	SUBCLONAL	1	TRUE	0	0.19	1		452	678	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111510	8111511	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	77	489	0	ENST00000346208.3:c.998dup	p.Asn333LysfsTer19	p.N333Kfs*19	ENST00000346208		332	-/A	5/6	0.321888854586482	3	FACETS	0.698	0.614	0.789	0.349	0.307	0.395	SUBCLONAL	1	TRUE	1	0.469565851923506	3		489	580	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	129	236	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.923	0.847	1	0.923	0.847	1	CLONAL	1	TRUE	1	0.784805910297334	2		236	356	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0030460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	251	627	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.784805910297334	2		627	571	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753158	42753158	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	262	837	0	ENST00000222329.4:c.1106C>G	p.Ser369Cys	p.S369C	ENST00000222329	NM_006494.2	369	tCt/tGt	4/4	1	2	FACETS	0.923	0.87	0.978	0.923	0.87	0.978	CLONAL	1	TRUE	1	0.784805910297334	2		837	723	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022373	26022373	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0030460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	653	709	0	ENST00000435504.4:c.284C>G	p.Ser95Ter	p.S95*	ENST00000435504		95	tCa/tGa	5/13	0.775674233637632	2	FACETS	0.969	0.946	0.991	0.969	0.946	0.991	CLONAL	2	TRUE	0	0.784805910297334	2		709	859	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569772	41569772	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057521737	NA	P-0030460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	234	245	1	ENST00000263253.7:c.4763T>C	p.Met1588Thr	p.M1588T	ENST00000263253	NM_001429.3	1588	aTg/aCg	29/31	0.775674233637632	2	FACETS	0.968	0.93	1	0.968	0.93	1	CLONAL	2	TRUE	0	0.784805910297334	2		246	308	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942820	44942821	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	317	829	0	ENST00000377967.4:c.3401dup	p.Tyr1135IlefsTer16	p.Y1135Ifs*16	ENST00000377967	NM_021140.2	1134	cta/cTta	23/29	1	2	FACETS	0.908	0.859	0.957	0.908	0.859	0.957	CLONAL	1	TRUE	1	0.784805910297334	2		829	890	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665752	29665755	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1555535032	NA	P-0030555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	66	171	0	ENST00000356175.3:c.6789_6792del	p.Tyr2264ThrfsTer5	p.Y2264Tfs*5	ENST00000356175	NM_000267.3	2263	ACTTac/ac	45/57	0.173875193292128	4	FACETS	0.856	0.748	0.972	0.856	0.748	0.972	CLONAL	3	TRUE	1	0.173875193292128	4		171	347	SUCCESS
APC	324	MSKCC	GRCh37	5	112178747	112178747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768537235	NA	P-0030555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	127	529	0	ENST00000257430.4:c.7456C>T	p.Pro2486Ser	p.P2486S	ENST00000257430	NM_000038.5	2486	Cct/Tct	16/16	0.173875193292128	3	FACETS	1	0.971	1	0.782	0.709	0.858	CLONAL	2	TRUE	0	0.173875193292128	3		529	677	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035196	30035196	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	121	445	0	ENST00000338641.4:c.359del	p.Leu120TyrfsTer3	p.L120Yfs*3	ENST00000338641	NM_000268.3	120	Tta/ta	3/16	0.173875193292128	4	FACETS	0.863	0.782	0.949	0.863	0.782	0.949	CLONAL	3	TRUE	1	0.173875193292128	4		445	631	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805537	32805537	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	175	727	9	ENST00000374899.4:c.474C>A	p.Phe158Leu	p.F158L	ENST00000374899	NM_018833.2	158	ttC/ttA	2/12	0.173875193292128	4	FACETS	0.866	0.798	0.938	0.866	0.798	0.938	CLONAL	3	TRUE	1	0.173875193292128	4		736	909	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562134	21562134	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	251	1010	0	ENST00000382592.4:c.1785G>C	p.Lys595Asn	p.K595N	ENST00000382592	NM_014572.2	595	aaG/aaC	4/8	0.173875193292128	4	FACETS	0.976	0.913	1	0.976	0.913	1	CLONAL	3	TRUE	1	0.173875193292128	4		1010	1157	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562163	21562163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	246	1009	1	ENST00000382592.4:c.1756G>A	p.Asp586Asn	p.D586N	ENST00000382592	NM_014572.2	586	Gac/Aac	4/8	0.173875193292128	4	FACETS	0.955	0.892	1	0.955	0.892	1	CLONAL	3	TRUE	1	0.173875193292128	4		1010	1159	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	170	473	3	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.941	0.875	1	0.941	0.875	1	CLONAL	1	TRUE	1	0.842648208649344	2		476	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	249	736	3	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.941	0.886	0.996	0.941	0.886	0.996	CLONAL	1	TRUE	1	0.842648208649344	2		739	628	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	165	286	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.948	0.881	1	0.948	0.881	1	CLONAL	1	TRUE	1	0.842648208649344	2		286	413	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	213	439	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.991	0.93	1	0.991	0.93	1	CLONAL	1	TRUE	1	0.842648208649344	2		440	510	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261554	142261555	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1043355995	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	198	443	1	ENST00000350721.4:c.3402dup	p.Asn1135Ter	p.N1135*	ENST00000350721	NM_001184.3	1134	-/T	17/47	1	2	FACETS	0.859	0.802	0.918	0.859	0.802	0.918	CLONAL	1	TRUE	1	0.842648208649344	2		444	547	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	231	545	0	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	1	2	FACETS	0.99	0.931	1	0.99	0.931	1	CLONAL	1	TRUE	1	0.842648208649344	2		545	554	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650770	67650770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1363179074	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	220	455	1	ENST00000264010.4:c.1075G>A	p.Ala359Thr	p.A359T	ENST00000264010	NM_006565.3	359	Gcc/Acc	5/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.842648208649344	2		456	492	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	126	436	0	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	0.885	0.812	0.96	0.885	0.812	0.96	CLONAL	1	TRUE	1	0.842648208649344	2		436	338	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692911	89692911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909241	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	417	562	1	ENST00000371953.3:c.395G>A	p.Gly132Asp	p.G132D	ENST00000371953	NM_000314.4	132	gGt/gAt	5/9	0.842648208649344	3	FACETS	0.938	0.901	0.974	0.938	0.901	0.974	CLONAL	2	TRUE	1	0.842648208649344	3		563	750	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	442	470	0	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	0.842648208649344	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.842648208649344	3		470	741	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	112	259	2	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.939	0.858	1	0.939	0.858	1	CLONAL	1	TRUE	1	0.842648208649344	2		261	283	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370236	40370236	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs761761205	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	152	702	9	ENST00000293328.3:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000293328	NM_012448.3	368	Cag/ag	9/19	1	2	FACETS	0.598	0.549	0.649	0.598	0.549	0.649	SUBCLONAL	1	TRUE	1	0.842648208649344	2		711	603	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	122	532	1	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	1	2	FACETS	0.472	0.428	0.519	0.472	0.428	0.519	SUBCLONAL	1	TRUE	1	0.842648208649344	2		533	613	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444659	78444659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs908264837	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	157	442	0	ENST00000370768.2:c.30del	p.Ser11LeufsTer43	p.S11Lfs*43	ENST00000370768	NM_003902.3	10	ccC/cc	1/20	1	2	FACETS	0.881	0.816	0.948	0.881	0.816	0.948	CLONAL	1	TRUE	1	0.842648208649344	2		442	423	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468032	50468032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757907717	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	282	425	0	ENST00000331340.3:c.1267C>T	p.Arg423Cys	p.R423C	ENST00000331340	NM_006060.4	423	Cgc/Tgc	8/8	0.842648208649344	4	FACETS	0.906	0.857	0.955	0.604	0.571	0.637	CLONAL	2	TRUE	1	0.842648208649344	4		425	681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577569	7577569	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519981	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	18	534	0	ENST00000269305.4:c.712T>C	p.Cys238Arg	p.C238R	ENST00000269305	NM_001126112.2	238	Tgt/Cgt	7/11	1	2	FACETS	0.083	0.062	0.108	0.083	0.062	0.108	SUBCLONAL	1	TRUE	1	0.842648208649344	2		534	513	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	270	545	10	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.983	0.929	1	0.983	0.929	1	CLONAL	1	TRUE	1	0.842648208649344	2		555	652	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330610	65330611	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	172	418	1	ENST00000342505.4:c.1035dup	p.Leu346ThrfsTer4	p.L346Tfs*4	ENST00000342505	NM_002227.2	345	-/A	8/25	1	2	FACETS	0.863	0.801	0.926	0.863	0.801	0.926	CLONAL	1	TRUE	1	0.842648208649344	2		419	473	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435417	56435417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112997544	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	255	600	0	ENST00000407977.2:c.1720G>A	p.Gly574Arg	p.G574R	ENST00000407977		574	Gga/Aga	9/10	1	2	FACETS	0.95	0.896	1	0.95	0.896	1	CLONAL	1	TRUE	1	0.842648208649344	2		600	637	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245024	133245024	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs752846614	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	260	330	2	ENST00000320574.5:c.2091del	p.Leu698CysfsTer94	p.L698Cfs*94	ENST00000320574	NM_006231.2	697	ccC/cc	19/49	1	2	FACETS	0.969	0.914	1	0.969	0.914	1	CLONAL	1	TRUE	1	0.842648208649344	2		332	637	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123246893	123246893	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	473	547	0	ENST00000358487.5:c.2032A>G	p.Arg678Gly	p.R678G	ENST00000358487	NM_000141.4	678	Aga/Gga	15/18	0.842648208649344	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.842648208649344	3		547	771	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337684	73337684	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771690280	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	120	249	3	ENST00000377767.4:c.2032del	p.Ile678PhefsTer59	p.I678Ffs*59	ENST00000377767	NM_014953.3	678	Att/tt	16/21	1	2	FACETS	0.937	0.859	1	0.937	0.859	1	CLONAL	1	TRUE	1	0.842648208649344	2		252	304	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345769	152345769	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs759063323	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	178	308	0	ENST00000359321.1:c.801del	p.Lys267AsnfsTer30	p.K267Nfs*30	ENST00000359321	NM_005431.1	267	aaA/aa	3/3	0.842648208649344	4	FACETS	1	0.926	1	0.334	0.308	0.361	CLONAL	1	TRUE	1	0.842648208649344	4		308	776	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173696	108173696	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	196	393	1	ENST00000278616.4:c.5441del	p.Leu1814TrpfsTer14	p.L1814Wfs*14	ENST00000278616	NM_000051.3	1812	gcT/gc	36/63	1	2	FACETS	0.923	0.862	0.985	0.923	0.862	0.985	CLONAL	1	TRUE	1	0.842648208649344	2		394	504	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97933361	97933361	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs755283850	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	182	388	0	ENST00000289081.3:c.521G>A	p.Arg174Gln	p.R174Q	ENST00000289081	NM_000136.2	174	cGa/cAa	6/15	1	2	FACETS	0.956	0.891	1	0.956	0.891	1	CLONAL	1	TRUE	1	0.842648208649344	2		388	452	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117712788	117712788	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	165	399	2	ENST00000369458.3:c.38T>A	p.Ile13Asn	p.I13N	ENST00000369458	NM_024626.3	13	aTt/aAt	2/6	1	2	FACETS	0.884	0.82	0.949	0.884	0.82	0.949	CLONAL	1	TRUE	1	0.842648208649344	2		401	443	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528486	157528486	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554237969	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	248	472	0	ENST00000346085.5:c.6211G>T	p.Gly2071Ter	p.G2071*	ENST00000346085	NM_020732.3	2071	Gga/Tga	20/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.842648208649344	2		472	575	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386388	31386388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	259	539	2	ENST00000328111.2:c.1613G>A	p.Arg538His	p.R538H	ENST00000328111	NM_006892.3	538	cGc/cAc	15/23	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.842648208649344	2		541	565	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790072	40790072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61753667	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	218	538	2	ENST00000373198.4:c.2659G>A	p.Ala887Thr	p.A887T	ENST00000373198	NM_133170.3	887	Gcc/Acc	18/32	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.842648208649344	2		540	497	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	327	1058	3	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.842648208649344	2		1061	775	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88672029	88672029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749780872	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	215	419	0	ENST00000372037.3:c.563G>A	p.Arg188His	p.R188H	ENST00000372037	NM_004329.2	188	cGt/cAt	8/13	0.842648208649344	3	FACETS	1	0.959	1	0.519	0.484	0.554	CLONAL	1	TRUE	1	0.842648208649344	3		419	699	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	270	613	2	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.962	0.909	1	0.962	0.909	1	CLONAL	1	TRUE	1	0.842648208649344	2		615	666	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341589	89341589	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	214	400	0	ENST00000301030.4:c.7481del	p.Pro2494LeufsTer8	p.P2494Lfs*8	ENST00000301030	NM_001256183.1	2494	cCt/ct	10/13	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.842648208649344	2		400	440	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944121	71944123	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	270	567	1	ENST00000298229.2:c.1960_1962del	p.Glu654del	p.E654del	ENST00000298229	NM_001567.3	652	GAG/-	17/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.842648208649344	2		568	618	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352674	68352674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199981178	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	203	395	0	ENST00000487270.1:c.541C>T	p.Arg181Trp	p.R181W	ENST00000487270	NM_133509.3	181	Cgg/Tgg	6/11	1	2	FACETS	0.956	0.895	1	0.956	0.895	1	CLONAL	1	TRUE	1	0.842648208649344	2		395	504	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512098	148512098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	180	531	1	ENST00000320356.2:c.1580C>T	p.Pro527Leu	p.P527L	ENST00000320356	NM_004456.4	527	cCc/cTc	14/20	0.842648208649344	4	FACETS	0.851	0.785	0.92	0.284	0.261	0.307	CLONAL	1	TRUE	1	0.842648208649344	4		532	925	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874149	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	226	472	1	ENST00000262189.6:c.8389_8390del	p.Lys2797GlyfsTer11	p.K2797Gfs*11	ENST00000262189	NM_170606.2	2797	AAg/g	38/59	0.842648208649344	4	FACETS	0.941	0.877	1	0.314	0.292	0.336	CLONAL	1	TRUE	1	0.842648208649344	4		473	1050	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434561	49434562	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	207	663	0	ENST00000301067.7:c.6991dup	p.Leu2331ProfsTer46	p.L2331Pfs*46	ENST00000301067	NM_003482.3	2331	ctg/cCtg	31/54	1	2	FACETS	0.795	0.742	0.849	0.795	0.742	0.849	SUBCLONAL	1	TRUE	1	0.842648208649344	2		663	618	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725043	89725043	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	93	239	0	ENST00000371953.3:c.1027-1G>T		p.X343_splice	ENST00000371953	NM_000314.4	343			0.842648208649344	3	FACETS	0.767	0.686	0.852	0.384	0.343	0.426	SUBCLONAL	1	TRUE	1	0.842648208649344	3		239	409	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554937	106554937	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs565965311	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	207	448	1	ENST00000369096.4:c.2054G>A	p.Arg685Gln	p.R685Q	ENST00000369096	NM_001198.3	685	cGg/cAg	7/7	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.842648208649344	2		449	490	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975459	13975459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80157564	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	365	351	1	ENST00000405192.2:c.428C>T	p.Thr143Met	p.T143M	ENST00000405192	NM_001163147.1	143	aCg/aTg	7/12	0.842648208649344	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	TRUE	1	0.842648208649344	4		352	529	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101601	27101601	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	282	723	2	ENST00000324856.7:c.4886del	p.Pro1629LeufsTer6	p.P1629Lfs*6	ENST00000324856	NM_006015.4	1628	gCc/gc	18/20	1	2	FACETS	0.989	0.936	1	0.989	0.936	1	CLONAL	1	TRUE	1	0.842648208649344	2		725	677	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439617	51439617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	176	338	0	ENST00000262662.1:c.182C>T	p.Ala61Val	p.A61V	ENST00000262662		61	gCt/gTt	4/4	1	2	FACETS	0.96	0.895	1	0.96	0.895	1	CLONAL	1	TRUE	1	0.842648208649344	2		338	435	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262347	115262347	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	156	392	0	ENST00000438362.2:c.2207A>G	p.Tyr736Cys	p.Y736C	ENST00000438362	NM_001242891.1	736	tAt/tGt	18/20	1	2	FACETS	0.935	0.867	1	0.935	0.867	1	CLONAL	1	TRUE	1	0.842648208649344	2		392	396	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596008	43596009	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	249	622	0	ENST00000355710.3:c.179dup	p.Glu61Ter	p.E61*	ENST00000355710	NM_020975.4	59	gcc/gCcc	2/20	0.842648208649344	3	FACETS	0.995	0.933	1	0.498	0.466	0.53	CLONAL	1	TRUE	1	0.842648208649344	3		622	844	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725078	89725078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375709098	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	51	168	0	ENST00000371953.3:c.1061C>T	p.Pro354Leu	p.P354L	ENST00000371953	NM_000314.4	354	cCg/cTg	9/9	0.842648208649344	3	FACETS	0.64	0.548	0.739	0.32	0.274	0.37	SUBCLONAL	1	TRUE	1	0.842648208649344	3		168	269	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856626	111856626	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	73	151	1	ENST00000341259.2:c.677G>T	p.Arg226Leu	p.R226L	ENST00000341259	NM_005475.2	226	cGg/cTg	2/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.842648208649344	2		152	138	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225552	133225552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs535074635	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	274	550	0	ENST00000320574.5:c.4112G>A	p.Arg1371Gln	p.R1371Q	ENST00000320574	NM_006231.2	1371	cGa/cAa	32/49	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.842648208649344	2		550	596	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896445	28896445	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	203	437	0	ENST00000282397.4:c.3005A>G	p.Tyr1002Cys	p.Y1002C	ENST00000282397	NM_002019.4	1002	tAc/tGc	22/30	1	2	FACETS	0.964	0.902	1	0.964	0.902	1	CLONAL	1	TRUE	1	0.842648208649344	2		437	500	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041169	29041169	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	220	622	0	ENST00000282397.4:c.259C>T	p.Gln87Ter	p.Q87*	ENST00000282397	NM_002019.4	87	Caa/Taa	3/30	1	2	FACETS	0.931	0.873	0.989	0.931	0.873	0.989	CLONAL	1	TRUE	1	0.842648208649344	2		622	561	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133697	41133697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554193370	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	160	362	1	ENST00000379561.5:c.1931G>A	p.Ser644Asn	p.S644N	ENST00000379561	NM_002015.3	644	aGt/aAt	2/3	1	2	FACETS	0.992	0.921	1	0.992	0.921	1	CLONAL	1	TRUE	1	0.842648208649344	2		363	383	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701215	43701215	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	288	576	0	ENST00000382044.4:c.5480G>T	p.Gly1827Val	p.G1827V	ENST00000382044	NM_001141980.1	1827	gGg/gTg	26/28	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.842648208649344	2		576	611	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663418	67663418	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	176	365	0	ENST00000264010.4:c.1819G>T	p.Glu607Ter	p.E607*	ENST00000264010	NM_006565.3	607	Gaa/Taa	10/12	1	2	FACETS	0.906	0.843	0.97	0.906	0.843	0.97	CLONAL	1	TRUE	1	0.842648208649344	2		365	461	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553543	29553543	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	158	331	1	ENST00000356175.3:c.2092C>A	p.Pro698Thr	p.P698T	ENST00000356175	NM_000267.3	698	Cct/Act	18/57	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.842648208649344	2		332	341	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512279	38512279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	260	747	2	ENST00000254066.5:c.1190C>T	p.Thr397Met	p.T397M	ENST00000254066	NM_000964.3	397	aCg/aTg	9/9	1	2	FACETS	0.972	0.917	1	0.972	0.917	1	CLONAL	1	TRUE	1	0.842648208649344	2		749	635	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245972	5245972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	252	669	0	ENST00000357368.4:c.803C>T	p.Ala268Val	p.A268V	ENST00000357368	NM_002850.3	268	gCc/gTc	10/38	1	2	FACETS	0.965	0.909	1	0.965	0.909	1	CLONAL	1	TRUE	1	0.842648208649344	2		669	620	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228762	36228762	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1377607028	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	286	652	1	ENST00000222270.7:c.7661G>A	p.Arg2554His	p.R2554H	ENST00000222270	NM_014727.1	2554	cGt/cAt	35/37	1	2	FACETS	0.997	0.944	1	0.997	0.944	1	CLONAL	1	TRUE	1	0.842648208649344	2		653	681	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678768	52678768	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	176	397	1	ENST00000394830.3:c.851del	p.Lys284ArgfsTer16	p.K284Rfs*16	ENST00000394830	NM_018313.4	284	aAg/ag	9/30	1	2	FACETS	0.908	0.845	0.972	0.908	0.845	0.972	CLONAL	1	TRUE	1	0.842648208649344	2		398	460	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670532	134670532	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	93	597	0	ENST00000398015.3:c.443A>G	p.Gln148Arg	p.Q148R	ENST00000398015	NM_004441.4	148	cAg/cGg	3/16	1	2	FACETS	0.364	0.324	0.407	0.364	0.324	0.407	SUBCLONAL	1	TRUE	1	0.842648208649344	2		597	606	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825317	134825317	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	122	316	0	ENST00000398015.3:c.833G>A	p.Ser278Asn	p.S278N	ENST00000398015	NM_004441.4	278	aGc/aAc	4/16	1	2	FACETS	0.902	0.827	0.979	0.902	0.827	0.979	CLONAL	1	TRUE	1	0.842648208649344	2		316	321	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1955067	1955067	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	205	612	0	ENST00000382891.5:c.2154C>A	p.Phe718Leu	p.F718L	ENST00000382891	NM_133335.3	718	ttC/ttA	12/22	1	2	FACETS	0.848	0.792	0.905	0.848	0.792	0.905	CLONAL	1	TRUE	1	0.842648208649344	2		612	574	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696742	176696742	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	222	355	0	ENST00000439151.2:c.5443T>G	p.Tyr1815Asp	p.Y1815D	ENST00000439151	NM_022455.4	1815	Tac/Gac	16/23	0.723600137234371	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.842648208649344	1		355	296	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382182	152382182	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs981690419	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	161	391	0	ENST00000206249.3:c.1292C>T	p.Thr431Ile	p.T431I	ENST00000206249	NM_000125.3	431	aCa/aTa	6/8	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.842648208649344	2		391	377	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157454179	157454179	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554301197	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	197	431	0	ENST00000346085.5:c.2389C>T	p.Gln797Ter	p.Q797*	ENST00000346085	NM_020732.3	797	Caa/Taa	8/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.842648208649344	2		431	455	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968322	2968322	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	215	545	1	ENST00000396946.4:c.1664G>T	p.Arg555Leu	p.R555L	ENST00000396946	NM_032415.4	555	cGg/cTg	13/25	0.842648208649344	4	FACETS	1	0.949	1	0.341	0.317	0.366	CLONAL	1	TRUE	1	0.842648208649344	4		546	918	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729598	41729598	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	190	457	0	ENST00000242208.4:c.931G>T	p.Gly311Cys	p.G311C	ENST00000242208	NM_002192.2	311	Ggc/Tgc	3/3	0.842648208649344	4	FACETS	0.982	0.909	1	0.327	0.303	0.353	CLONAL	1	TRUE	1	0.842648208649344	4		457	846	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148526847	148526847	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	176	360	0	ENST00000320356.2:c.457T>C	p.Tyr153His	p.Y153H	ENST00000320356	NM_004456.4	153	Tat/Cat	5/20	0.842648208649344	4	FACETS	0.96	0.885	1	0.32	0.295	0.346	CLONAL	1	TRUE	1	0.842648208649344	4		360	802	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860328	151860330	+	inframe_deletion	In_Frame_Del	DEL	CTA	CTA	-	rs1381682036	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	176	445	0	ENST00000262189.6:c.10332_10334del	p.Ser3444del	p.S3444del	ENST00000262189	NM_170606.2	3444	agTAGg/agg	43/59	0.842648208649344	4	FACETS	0.846	0.779	0.915	0.282	0.259	0.305	CLONAL	1	TRUE	1	0.842648208649344	4		445	910	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212173	98212173	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	200	450	0	ENST00000331920.6:c.3499G>T	p.Gly1167Trp	p.G1167W	ENST00000331920	NM_000264.3	1167	Ggg/Tgg	21/24	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.842648208649344	2		450	469	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0030874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	389	352	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	0.726029443100551	5	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	2	0.726029443100551	5		352	670	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484858	57485003	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTTTGTGGAGTGACCGCCCACCCCCTGCGCTTGCCCAGGAGGCCCTGGTCTGCACTGTTTATAGAGAAGAACCCCGTGCAAGCATTCCAGACCCCTGGCCGAAAGCGCGCTTCTCCCAAGCATTCACACGGCCTCCCTTCTTGT	AGGTTTGTGGAGTGACCGCCCACCCCCTGCGCTTGCCCAGGAGGCCCTGGTCTGCACTGTTTATAGAGAAGAACCCCGTGCAAGCATTCCAGACCCCTGGCCGAAAGCGCGCTTCTCCCAAGCATTCACACGGCCTCCCTTCTTGT	-	novel	NA	P-0030874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1442	169	395	0	ENST00000371085.3:c.839+1_840-1del		p.X280_splice	ENST00000371085	NM_000516.4	280		10/13	0.726029443100551	7	FACETS	0.813	0.745	0.885	0.163	0.149	0.177	CLONAL	1	TRUE	2	0.726029443100551	7		395	1611	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-0030874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	153	281	0	ENST00000371085.3:c.970+1_971-1del		p.X324_splice	ENST00000371085	NM_000516.4	324		11/13	0.726029443100551	7	FACETS	0.985	0.9	1	0.197	0.18	0.216	CLONAL	1	TRUE	2	0.726029443100551	7		281	1204	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380346	14380346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	119	174	0	ENST00000256196.4:c.71G>A	p.Gly24Asp	p.G24D	ENST00000256196		24	gGc/gAc	1/6	0.404661741215931	5	FACETS	0.793	0.721	0.867	0.528	0.48	0.578	INDETERMINATE	2	TRUE	2	0.726029443100551	5		174	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-0030874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1252	146	273	1	ENST00000371085.3:c.1038+1_1039-1del		p.X346_splice	ENST00000371085	NM_000516.4	346		12/13	0.726029443100551	7	FACETS	0.81	0.737	0.887	0.162	0.147	0.178	CLONAL	1	TRUE	2	0.726029443100551	7		274	1398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578202	7578204	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0030874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	432	522	0	ENST00000269305.4:c.645_647del	p.Ser215_Val216delinsArg	p.S215_V216delinsR	ENST00000269305	NM_001126112.2	215	agTGTg/agg	6/11	0.72272002775612	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.726029443100551	2		522	574	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281963	39281963	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs397517174	NA	P-0030874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	147	220	0	ENST00000402219.2:c.512T>C	p.Val171Ala	p.V171A	ENST00000402219	NM_005633.3	171	gTa/gCa	5/23	0.726029443100551	5	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	TRUE	2	0.726029443100551	5		220	263	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023004	150023004	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	313	487	0	ENST00000253339.5:c.259C>T	p.Pro87Ser	p.P87S	ENST00000253339		87	Cca/Tca	1/7	0.706433287856183	4	FACETS	0.953	0.903	1	0.953	0.903	1	CLONAL	2	TRUE	2	0.726029443100551	4		487	781	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80343484	80343484	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	199	355	0	ENST00000286548.4:c.835C>G	p.Leu279Val	p.L279V	ENST00000286548	NM_002072.3	279	Cta/Gta	6/7	0.72272002775612	2	FACETS	0.986	0.941	1	0.986	0.941	1	CLONAL	2	TRUE	0	0.726029443100551	2		355	278	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0031225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	349	573	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.66118302042903	1		573	511	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026959	6026959	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs63750685	NA	P-0031225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	12	357	0	ENST00000265849.7:c.1437C>G	p.His479Gln	p.H479Q	ENST00000265849	NM_000535.5	479	caC/caG	11/15	1	2	FACETS	0.21	0.147	0.286	0.21	0.147	0.286	SUBCLONAL	1	TRUE	1	0.66118302042903	2		357	173	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719836	52719836	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	426	1504	0	ENST00000322088.6:c.1048A>G	p.Met350Val	p.M350V	ENST00000322088	NM_014225.5	350	Atg/Gtg	9/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.66118302042903	2		1504	1243	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829195	128829195	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs767938975	NA	P-0031264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	31	212	0	ENST00000249373.3:c.203C>G	p.Ala68Gly	p.A68G	ENST00000249373	NM_005631.4	68	gCc/gGc	1/12	NA	2	FACETS	0.98	0.815	1			1	INDETERMINATE	1	TRUE	NA	0.673297891287516	2		212	94	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46733200	46733200	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	79	616	1	ENST00000371975.4:c.961G>T	p.Val321Leu	p.V321L	ENST00000371975	NM_003579.3	321	Gtg/Ttg	9/18	0.673297891287516	3	FACETS	0.651	0.574	0.733	0.217	0.191	0.245	SUBCLONAL	1	TRUE	0	0.673297891287516	3		617	482	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999645	100999645	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	137	939	0	ENST00000325455.5:c.157A>T	p.Ile53Phe	p.I53F	ENST00000325455	NM_001202474.3	53	Atc/Ttc	1/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.673297891287516	2		939	356	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562919	21562919	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	85	459	0	ENST00000382592.4:c.1000del	p.Arg334AlafsTer99	p.R334Afs*99	ENST00000382592	NM_014572.2	334	Cgc/gc	4/8	0.210728547812462	3	FACETS	1	0.953	1	0.374	0.334	0.416	INDETERMINATE	1	TRUE	0	0.673297891287516	3		459	301	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	120	236	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.987	0.905	1	0.987	0.905	1	CLONAL	1	TRUE	1	0.792055207746378	2		236	307	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0031278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	281	478	5	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.792055207746378	2		483	709	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509435	106509435	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138344795	NA	P-0031278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	83	665	1	ENST00000359195.3:c.1429C>T	p.Arg477Cys	p.R477C	ENST00000359195	NM_002649.2	477	Cgt/Tgt	2/11	0.786710001378678	4	FACETS	0.304	0.267	0.344	0.101	0.089	0.115	SUBCLONAL	1	TRUE	1	0.792055207746378	4		666	1236	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974121	2974121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760308478	NA	P-0031278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	189	499	0	ENST00000396946.4:c.1484C>T	p.Pro495Leu	p.P495L	ENST00000396946	NM_032415.4	495	cCg/cTg	10/25	0.792055207746378	3	FACETS	0.999	0.927	1	0.499	0.463	0.537	CLONAL	1	TRUE	1	0.792055207746378	3		499	667	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1131691023	NA	P-0031278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	363	1081	0	ENST00000269305.4:c.470T>A	p.Val157Asp	p.V157D	ENST00000269305	NM_001126112.2	157	gTc/gAc	5/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.792055207746378	2		1081	902	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955569	48955569	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	153	410	2	ENST00000267163.4:c.1685C>A	p.Ala562Glu	p.A562E	ENST00000267163	NM_000321.2	562	gCa/gAa	17/27	0.792055207746378	1	FACETS	0.864	0.809	0.918	0.864	0.809	0.918	CLONAL	1	TRUE	0	0.792055207746378	1		412	270	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522706	67522706	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	153	317	0	ENST00000274335.5:c.203del	p.Asp68AlafsTer7	p.D68Afs*7	ENST00000274335		68	gAc/gc	1/15	1	2	FACETS	0.926	0.857	0.998	0.926	0.857	0.998	CLONAL	1	TRUE	1	0.792055207746378	2		317	417	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152853852	152853852	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	142	365	0	ENST00000406277.2:c.712A>G	p.Ile238Val	p.I238V	ENST00000406277	NM_152274.4	238	Att/Gtt	7/7	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.792055207746378	2		365	351	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121452	108121452	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	168	309	0	ENST00000278616.4:c.1260A>G	p.Ile420Met	p.I420M	ENST00000278616	NM_000051.3	420	atA/atG	10/63	0.837447198319106	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.837447198319106	2		309	185	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	128	236	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.66736158846954	2		236	325	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926900	112926900	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs886039463	NA	P-0032061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	113	563	0	ENST00000351677.2:c.1520C>A	p.Thr507Lys	p.T507K	ENST00000351677	NM_002834.3	507	aCa/aAa	13/16	1	2	FACETS	0.534	0.481	0.59	0.534	0.481	0.59	SUBCLONAL	1	TRUE	1	0.66736158846954	2		563	634	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426123	138426123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217537873	NA	P-0032061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	167	380	0	ENST00000289153.2:c.1408G>A	p.Glu470Lys	p.E470K	ENST00000289153	NM_006219.2	470	Gaa/Aaa	9/22	1	2	FACETS	0.887	0.82	0.957	0.887	0.82	0.957	CLONAL	1	TRUE	1	0.66736158846954	2		380	564	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624303	89624303	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs786204853	NA	P-0032061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	217	513	0	ENST00000371953.3:c.77C>T	p.Thr26Ile	p.T26I	ENST00000371953	NM_000314.4	26	aCc/aTc	1/9	0.66736158846954	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.66736158846954	1		513	431	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161807896	161807896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761213043	NA	P-0032061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	122	388	0	ENST00000366898.1:c.1097G>A	p.Arg366Gln	p.R366Q	ENST00000366898	NM_004562.2	366	cGg/cAg	10/12	1	2	FACETS	0.835	0.76	0.912	0.835	0.76	0.912	CLONAL	1	TRUE	1	0.66736158846954	2		388	438	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133529	55133537	+	inframe_deletion	In_Frame_Del	DEL	CCGAGGCCA	CCGAGGCCA	-	novel	NA	P-0032061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	41	418	0	ENST00000257290.5:c.834_842del	p.Glu279_Thr281del	p.E279_T281del	ENST00000257290	NM_006206.4	278	cCCGAGGCCAcg/ccg	6/23	1	2	FACETS	0.222	0.185	0.264	0.222	0.185	0.264	SUBCLONAL	1	TRUE	1	0.66736158846954	2		418	553	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141084	55141084	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	56	404	0	ENST00000257290.5:c.1730C>G	p.Pro577Arg	p.P577R	ENST00000257290	NM_006206.4	577	cCg/cGg	12/23	1	2	FACETS	0.318	0.273	0.368	0.318	0.273	0.368	SUBCLONAL	1	TRUE	1	0.66736158846954	2		404	527	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0032123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	444	370	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.679822272362114	2	FACETS	0.964	0.932	0.996	0.964	0.932	0.996	CLONAL	2	TRUE	0	0.680361704614184	2		370	677	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184592	11184592	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs774204282	NA	P-0032123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	325	815	0	ENST00000361445.4:c.6625C>G	p.Leu2209Val	p.L2209V	ENST00000361445	NM_004958.3	2209	Ctg/Gtg	47/58	1	2	FACETS	0.912	0.862	0.962	0.912	0.862	0.962	CLONAL	1	TRUE	1	0.680361704614184	2		815	1048	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0032123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	134	446	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.809	0.74	0.881	0.809	0.74	0.881	CLONAL	1	TRUE	1	0.680361704614184	2		446	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0032123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	358	736	3	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.680361704614184	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.680361704614184	1		739	694	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592108	67592108	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1419325070	NA	P-0032123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	38	362	0	ENST00000274335.5:c.1924C>T	p.Arg642Ter	p.R642*	ENST00000274335		642	Cga/Tga	14/15	1	2	FACETS	0.242	0.2	0.29	0.242	0.2	0.29	SUBCLONAL	1	TRUE	1	0.680361704614184	2		362	461	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976476	25976476	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	249	680	0	ENST00000435504.4:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000435504		357	Cga/Tga	11/13	1	2	FACETS	0.843	0.79	0.898	0.843	0.79	0.898	CLONAL	1	TRUE	1	0.680361704614184	2		680	868	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268138	153268138	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1406877044	NA	P-0032123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	204	538	0	ENST00000281708.4:c.670C>T	p.Arg224Ter	p.R224*	ENST00000281708	NM_033632.3	224	Cga/Tga	4/12	1	2	FACETS	0.815	0.758	0.873	0.815	0.758	0.873	CLONAL	1	TRUE	1	0.680361704614184	2		538	736	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211091	36211091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373603029	NA	P-0032123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	363	1000	1	ENST00000222270.7:c.842G>A	p.Arg281His	p.R281H	ENST00000222270	NM_014727.1	281	cGt/cAt	3/37	0.680361704614184	3	FACETS	1	0.956	1	0.506	0.479	0.533	CLONAL	1	TRUE	1	0.680361704614184	3		1001	1414	SUCCESS
APC	324	MSKCC	GRCh37	5	112173655	112173656	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0032123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	153	484	0	ENST00000257430.4:c.2364_2365del	p.Gln789GlufsTer9	p.Q789Efs*9	ENST00000257430	NM_000038.5	788	aaGCag/aaag	16/16	1	2	FACETS	0.815	0.749	0.882	0.815	0.749	0.882	CLONAL	1	TRUE	1	0.680361704614184	2		484	552	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40998441	40998441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	28	617	0	ENST00000267868.3:c.292G>A	p.Glu98Lys	p.E98K	ENST00000267868	NM_002875.4	98	Gag/Aag	4/10	1	2	FACETS	1	0.835	1	1	0.835	1	CLONAL	1	TRUE	1	0.18	2		617	297	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	13	315	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.571	0.407	0.771	0.571	0.407	0.771	SUBCLONAL	1	TRUE	1	0.18	2		315	253	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	35	727	0	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	1	2	FACETS	0.778	0.637	0.936	0.778	0.637	0.936	CLONAL	1	TRUE	1	0.18	2		727	500	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023037	33023037	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	41	447	0	ENST00000300177.4:c.146C>T	p.Ser49Leu	p.S49L	ENST00000300177	NM_001191322.1	49	tCg/tTg	2/2	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.18	2		447	422	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6048638	6048638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	38	555	0	ENST00000265849.7:c.13G>A	p.Glu5Lys	p.E5K	ENST00000265849	NM_000535.5	5	Gag/Aag	1/15	1	2	FACETS	0.896	0.741	1	0.896	0.741	1	CLONAL	1	TRUE	1	0.18	2		555	471	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	20	403	0	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	0.109883579254124	3	FACETS	0.682	0.521	0.871	0.341	0.26	0.436	SUBCLONAL	1	TRUE	1	0.18	3		403	355	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663346	227663346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024227751	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	45	469	0	ENST00000305123.5:c.109G>A	p.Glu37Lys	p.E37K	ENST00000305123	NM_005544.2	37	Gag/Aag	1/2	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.18	2		469	424	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270162	198270162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	10	348	0	ENST00000335508.6:c.1274G>A	p.Arg425Gln	p.R425Q	ENST00000335508	NM_012433.2	425	cGa/cAa	10/25	1	2	FACETS	0.65	0.441	0.912	0.65	0.441	0.912	SUBCLONAL	1	TRUE	1	0.18	2		348	171	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143441	30143441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326321652	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	25	350	2	ENST00000389048.3:c.85G>A	p.Ala29Thr	p.A29T	ENST00000389048	NM_004304.4	29	Gcg/Acg	1/29	1	2	FACETS	0.696	0.548	0.867	0.696	0.548	0.867	SUBCLONAL	1	TRUE	1	0.18	2		352	399	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	29	184	1	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.3	1	FACETS	0.598	0.479	0.734	0.598	0.479	0.734	SUBCLONAL	1	TRUE	0	0.18	1		185	490	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117755	70117755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	41	642	0	ENST00000245479.2:c.223G>A	p.Glu75Lys	p.E75K	ENST00000245479	NM_000346.3	75	Gag/Aag	1/3	1	2	FACETS	0.746	0.62	0.886	0.746	0.62	0.886	SUBCLONAL	1	TRUE	1	0.18	2		642	611	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156687	55156687	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	29	429	0	ENST00000257290.5:c.3088G>C	p.Glu1030Gln	p.E1030Q	ENST00000257290	NM_006206.4	1030	Gag/Cag	22/23	0.109883579254124	3	FACETS	0.823	0.66	1	0.411	0.33	0.504	CLONAL	1	TRUE	1	0.18	3		429	427	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922814	44922814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761667415	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	52	206	0	ENST00000377967.4:c.1675C>T	p.Arg559Cys	p.R559C	ENST00000377967	NM_021140.2	559	Cgt/Tgt	16/29	0.100632417999746	2	FACETS	1	0.923	1			1	INDETERMINATE	2	TRUE	NA	0.18	2		206	259	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372400	55372400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	33	745	0	ENST00000297316.4:c.1090G>A	p.Glu364Lys	p.E364K	ENST00000297316	NM_022454.3	364	Gaa/Aaa	2/2	1	2	FACETS	0.599	0.487	0.727	0.599	0.487	0.727	SUBCLONAL	1	TRUE	1	0.18	2		745	612	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396541	30396541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746045993	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	36	347	0	ENST00000331968.5:c.178G>A	p.Glu60Lys	p.E60K	ENST00000331968	NM_002742.2	60	Gag/Aag	1/18	1	2	FACETS	0.943	0.776	1	0.943	0.776	1	CLONAL	1	TRUE	1	0.18	2		347	424	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780677	56780677	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060502588	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	25	398	1	ENST00000337432.4:c.692C>T	p.Ser231Leu	p.S231L	ENST00000337432	NM_058216.2	231	tCa/tTa	4/9	1	2	FACETS	0.755	0.599	0.931	1	0.932	1	CLONAL	2	TRUE	1	0.18	2		399	184	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675046	40675046	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	58	629	1	ENST00000249776.8:c.10C>T	p.Pro4Ser	p.P4S	ENST00000249776	NM_033286.3	4	Ccc/Tcc	1/9	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.18	2		630	484	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266816	18266816	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750768114	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	34	535	0	ENST00000222254.8:c.127G>A	p.Val43Met	p.V43M	ENST00000222254	NM_005027.3	43	Gtg/Atg	2/16	1	2	FACETS	0.895	0.732	1	0.895	0.732	1	CLONAL	1	TRUE	1	0.18	2		535	422	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242640	16242640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	10	424	0	ENST00000375759.3:c.1261G>A	p.Glu421Lys	p.E421K	ENST00000375759	NM_015001.2	421	Gaa/Aaa	6/15	1	2	FACETS	0.708	0.48	0.992	0.708	0.48	0.992	CLONAL	1	TRUE	1	0.18	2		424	157	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17349200	17349200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	37	388	0	ENST00000375499.3:c.668G>A	p.Arg223Lys	p.R223K	ENST00000375499	NM_003000.2	223	aGa/aAa	7/8	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.18	2		388	388	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023471	27023471	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs967763683	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	24	387	0	ENST00000324856.7:c.577G>A	p.Glu193Lys	p.E193K	ENST00000324856	NM_006015.4	193	Gag/Aag	1/20	1	2	FACETS	0.587	0.46	0.735	0.587	0.46	0.735	SUBCLONAL	1	TRUE	1	0.18	2		387	454	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598814	28598814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	34	710	0	ENST00000253063.3:c.374G>A	p.Cys125Tyr	p.C125Y	ENST00000253063	NM_031459.4	125	tGt/tAt	4/10	1	2	FACETS	0.698	0.57	0.844	0.698	0.57	0.844	SUBCLONAL	1	TRUE	1	0.18	2		710	541	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695881	117695881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	30	662	0	ENST00000369458.3:c.556G>A	p.Asp186Asn	p.D186N	ENST00000369458	NM_024626.3	186	Gac/Aac	4/6	1	2	FACETS	0.664	0.534	0.812	0.664	0.534	0.812	SUBCLONAL	1	TRUE	1	0.18	2		662	502	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551491	150551492	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCC	rs759789515	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	35	790	0	ENST00000369026.2:c.513_515dup	p.Glu171dup	p.E171dup	ENST00000369026	NM_021960.4	171	gac/gaGGAc	1/3	1	2	FACETS	0.802	0.657	0.965	0.802	0.657	0.965	CLONAL	1	TRUE	1	0.18	2		790	485	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939543	71939543	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	64	827	0	ENST00000298229.2:c.397+1G>A		p.X133_splice	ENST00000298229	NM_001567.3	133			1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.18	2		827	586	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100435	102100435	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	14	401	0	ENST00000282441.5:c.1279G>A	p.Asp427Asn	p.D427N	ENST00000282441	NM_001130145.2	427	Gat/Aat	9/9	1	2	FACETS	0.617	0.446	0.825	0.617	0.446	0.825	SUBCLONAL	1	TRUE	1	0.18	2		401	252	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195629	102195629	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs147101958	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	29	387	0	ENST00000263464.3:c.389A>C	p.Asn130Thr	p.N130T	ENST00000263464	NM_001165.4	130	aAc/aCc	2/9	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.18	2		387	243	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038954	12038954	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	13	276	0	ENST00000396373.4:c.1247T>C	p.Leu416Ser	p.L416S	ENST00000396373	NM_001987.4	416	tTg/tCg	7/8	1	2	FACETS	0.798	0.571	1	0.798	0.571	1	CLONAL	1	TRUE	1	0.18	2		276	181	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716371	18716371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773501044	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	10	313	0	ENST00000266497.5:c.3718G>A	p.Glu1240Lys	p.E1240K	ENST00000266497		1240	Gag/Aag	26/31	1	2	FACETS	0.712	0.484	0.998	0.712	0.484	0.998	CLONAL	1	TRUE	1	0.18	2		313	156	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434880	49434880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	38	751	0	ENST00000301067.7:c.6673G>A	p.Glu2225Lys	p.E2225K	ENST00000301067	NM_003482.3	2225	Gaa/Aaa	31/54	1	2	FACETS	0.804	0.664	0.961	0.804	0.664	0.961	CLONAL	1	TRUE	1	0.18	2		751	525	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487891	56487891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759562930	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	27	528	0	ENST00000267101.3:c.1622G>A	p.Arg541Gln	p.R541Q	ENST00000267101	NM_001982.3	541	cGa/cAa	14/28	1	2	FACETS	0.642	0.51	0.794	0.642	0.51	0.794	SUBCLONAL	1	TRUE	1	0.18	2		528	467	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253950	133253950	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	14	508	0	ENST00000320574.5:c.800C>T	p.Pro267Leu	p.P267L	ENST00000320574	NM_006231.2	267	cCt/cTt	8/49	1	2	FACETS	0.625	0.451	0.835	0.625	0.451	0.835	SUBCLONAL	1	TRUE	1	0.18	2		508	249	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923311	26923311	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	11	296	0	ENST00000381527.3:c.307G>A	p.Asp103Asn	p.D103N	ENST00000381527	NM_001260.1	103	Gac/Aac	3/13	1	2	FACETS	0.861	0.597	1	0.861	0.597	1	CLONAL	1	TRUE	1	0.18	2		296	142	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134873	41134873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	16	330	0	ENST00000379561.5:c.755G>A	p.Arg252Lys	p.R252K	ENST00000379561	NM_002015.3	252	aGa/aAa	2/3	1	2	FACETS	0.573	0.423	0.753	0.573	0.423	0.753	SUBCLONAL	1	TRUE	1	0.18	2		330	310	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614968	23614968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	14	340	0	ENST00000261584.4:c.3373G>A	p.Asp1125Asn	p.D1125N	ENST00000261584	NM_024675.3	1125	Gat/Aat	13/13	0.109883579254124	3	FACETS	0.804	0.582	1	0.402	0.291	0.536	CLONAL	1	TRUE	1	0.18	3		340	211	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816263	89816264	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	26	516	0	ENST00000389301.3:c.3113_3114del	p.Leu1038ArgfsTer12	p.L1038Rfs*12	ENST00000389301	NM_000135.2	1038	cTC/c	32/43	0.27569842401298	1	FACETS	0.584	0.462	0.725	0.584	0.462	0.725	SUBCLONAL	1	TRUE	0	0.18	1		516	450	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654589	29654589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	18	307	0	ENST00000356175.3:c.5278G>A	p.Asp1760Asn	p.D1760N	ENST00000356175	NM_000267.3	1760	Gac/Aac	37/57	1	2	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	TRUE	1	0.18	2		307	171	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56367746	56367746	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	18	354	0	ENST00000348428.3:c.572G>T	p.Arg191Leu	p.R191L	ENST00000348428	NM_006785.3	191	cGa/cTa	4/17	0.231279275930226	3	FACETS	1	0.812	1	0.545	0.412	0.701	CLONAL	1	TRUE	1	0.18	3		354	200	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191099	2191099	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	24	656	0	ENST00000398665.3:c.353C>G	p.Ser118Trp	p.S118W	ENST00000398665	NM_032482.2	118	tCg/tGg	5/28	1	2	FACETS	0.595	0.466	0.745	0.595	0.466	0.745	SUBCLONAL	1	TRUE	1	0.18	2		656	448	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051440	13051440	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769245573	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	24	533	0	ENST00000316448.5:c.788C>T	p.Pro263Leu	p.P263L	ENST00000316448	NM_004343.3	263	cCc/cTc	6/9	1	2	FACETS	0.866	0.68	1	0.866	0.68	1	CLONAL	1	TRUE	1	0.18	2		533	308	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281581	15281581	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	46	831	1	ENST00000263388.2:c.4792G>A	p.Asp1598Asn	p.D1598N	ENST00000263388	NM_000435.2	1598	Gat/Aat	26/33	1	2	FACETS	0.839	0.706	0.987	0.839	0.706	0.987	CLONAL	1	TRUE	1	0.18	2		832	609	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17389843	17389843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	34	748	1	ENST00000359435.4:c.976G>A	p.Glu326Lys	p.E326K	ENST00000359435	NM_001033549.1	326	Gag/Aag	9/9	1	2	FACETS	0.779	0.636	0.94	0.779	0.636	0.94	CLONAL	1	TRUE	1	0.18	2		749	485	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762361	41762361	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	31	484	0	ENST00000301178.4:c.2042del	p.Asn681MetfsTer41	p.N681Mfs*41	ENST00000301178	NM_021913.4	681	Aat/at	18/20	1	2	FACETS	0.89	0.72	1	0.89	0.72	1	CLONAL	1	TRUE	1	0.18	2		484	387	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46588072	46588072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	33	641	0	ENST00000263734.3:c.622C>T	p.His208Tyr	p.H208Y	ENST00000263734	NM_001430.4	208	Cac/Tac	6/16	1	2	FACETS	0.769	0.625	0.93	0.769	0.625	0.93	CLONAL	1	TRUE	1	0.18	2		641	477	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47612312	47612312	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs864622286	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	11	397	0	ENST00000263735.4:c.866C>T	p.Ser289Phe	p.S289F	ENST00000263735	NM_002354.2	289	tCc/tTc	8/9	1	2	FACETS	0.694	0.48	0.959	0.694	0.48	0.959	SUBCLONAL	1	TRUE	1	0.18	2		397	176	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442080	52442080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	30	516	0	ENST00000460680.1:c.269C>T	p.Ser90Phe	p.S90F	ENST00000460680	NM_004656.3	90	tCt/tTt	5/17	1	2	FACETS	0.817	0.658	0.997	0.817	0.658	0.997	CLONAL	1	TRUE	1	0.18	2		516	408	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799680	72799680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867810225	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	23	573	0	ENST00000325599.8:c.1489G>A	p.Glu497Lys	p.E497K	ENST00000325599	NM_018130.2	497	Gaa/Aaa	11/11	1	2	FACETS	0.728	0.567	0.914	0.728	0.567	0.914	CLONAL	1	TRUE	1	0.18	2		573	351	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205859	128205859	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760132552	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	41	354	0	ENST00000341105.2:c.16G>A	p.Glu6Lys	p.E6K	ENST00000341105	NM_032638.4	6	Gag/Aag	2/6	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.18	2		354	329	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231240	142231240	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	21	450	0	ENST00000350721.4:c.4714G>A	p.Asp1572Asn	p.D1572N	ENST00000350721	NM_001184.3	1572	Gat/Aat	27/47	1	2	FACETS	0.864	0.666	1	0.864	0.666	1	CLONAL	1	TRUE	1	0.18	2		450	270	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161268	185161268	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	24	528	0	ENST00000265026.3:c.695T>C	p.Ile232Thr	p.I232T	ENST00000265026	NM_004721.4	232	aTc/aCc	4/14	1	2	FACETS	0.813	0.638	1	0.813	0.638	1	CLONAL	1	TRUE	1	0.18	2		528	328	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564797	86564797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	28	703	0	ENST00000274376.6:c.529C>T	p.Pro177Ser	p.P177S	ENST00000274376	NM_002890.2	177	Cca/Tca	1/25	1	2	FACETS	0.814	0.651	1	0.814	0.651	1	CLONAL	1	TRUE	1	0.18	2		703	382	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721708	176721708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	16	444	0	ENST00000439151.2:c.7339C>T	p.Gln2447Ter	p.Q2447*	ENST00000439151	NM_022455.4	2447	Cag/Tag	23/23	1	2	FACETS	0.583	0.43	0.766	0.583	0.43	0.766	SUBCLONAL	1	TRUE	1	0.18	2		444	305	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288543	33288543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	15	477	1	ENST00000374542.5:c.1009G>A	p.Gly337Ser	p.G337S	ENST00000374542	NM_001141970.1	337	Ggc/Agc	3/8	1	2	FACETS	0.575	0.42	0.761	0.575	0.42	0.761	SUBCLONAL	1	TRUE	1	0.18	2		478	290	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222592	157222601	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCGCACCT	CCCCGCACCT	-	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	31	533	0	ENST00000346085.5:c.1862_1871del	p.Pro621HisfsTer44	p.P621Hfs*44	ENST00000346085	NM_020732.3	620	cCCCCGCACCTc/cc	4/20	0.231279275930226	3	FACETS	0.673	0.543	0.821	0.336	0.271	0.411	SUBCLONAL	1	TRUE	1	0.18	3		533	558	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339695	116339695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	39	360	0	ENST00000397752.3:c.557C>T	p.Ser186Leu	p.S186L	ENST00000397752	NM_000245.2	186	tCa/tTa	2/21	0.3	3	FACETS	1	0.951	1	0.729	0.606	0.865	CLONAL	1	TRUE	1	0.18	3		360	324	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172285	38172285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	21	321	0	ENST00000317025.8:c.2122G>A	p.Glu708Lys	p.E708K	ENST00000317025	NM_023034.1	708	Gaa/Aaa	12/24	1	2	FACETS	1	0.802	1	1	0.802	1	CLONAL	1	TRUE	1	0.18	2		321	224	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272080	38272080	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	22	601	0	ENST00000425967.3:c.2138A>G	p.Asp713Gly	p.D713G	ENST00000425967	NM_001174067.1	713	gAt/gGt	16/19	1	2	FACETS	0.679	0.526	0.857	0.679	0.526	0.857	SUBCLONAL	1	TRUE	1	0.18	2		601	360	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270502	98270502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	38	441	0	ENST00000331920.6:c.142G>A	p.Asp48Asn	p.D48N	ENST00000331920	NM_000264.3	48	Gac/Aac	1/24	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.18	2		441	383	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224133	53224133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	46	373	0	ENST00000375401.3:c.3418C>T	p.Leu1140Phe	p.L1140F	ENST00000375401	NM_004187.3	1140	Ctc/Ttc	22/26	0.100632417999746	2	FACETS	0.806	0.682	0.942			1	INDETERMINATE	2	TRUE	NA	0.18	2		373	317	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224144	53224144	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	45	378	0	ENST00000375401.3:c.3407C>G	p.Ser1136Cys	p.S1136C	ENST00000375401	NM_004187.3	1136	tCt/tGt	22/26	0.100632417999746	2	FACETS	0.794	0.67	0.929			1	INDETERMINATE	2	TRUE	NA	0.18	2		378	315	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53254068	53254068	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	31	207	0	ENST00000375401.3:c.4G>A	p.Glu2Lys	p.E2K	ENST00000375401	NM_004187.3	2	Gag/Aag	1/26	0.100632417999746	2	FACETS	0.936	0.764	1			1	INDETERMINATE	2	TRUE	NA	0.18	2		207	184	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349237	70349237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	20	305	0	ENST00000374080.3:c.3649G>A	p.Asp1217Asn	p.D1217N	ENST00000374080		1217	Gat/Aat	26/45	0.100632417999746	2	FACETS	0.743	0.568	0.948			1	INDETERMINATE	1	TRUE	NA	0.18	2		305	299	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-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	19	336	0	ENST00000300305.3:c.806-35_814del		p.X269_splice	ENST00000300305		269		7/8	1	2	FACETS	1	0.762	1	1	0.762	1	CLONAL	1	TRUE	1	0.18	2		336	211	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0032305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	200	447	2	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.37	2		449	962	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740809	58740809	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs765769406	NA	P-0032305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	159	743	1	ENST00000305921.3:c.1714C>T	p.Arg572Ter	p.R572*	ENST00000305921	NM_003620.3	572	Cga/Tga	6/6	1	2	FACETS	0.88	0.806	0.957	0.88	0.806	0.957	CLONAL	1	TRUE	1	0.37	2		744	977	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0032363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	153	426	0	ENST00000269305.4:c.375+1G>T		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.406385382736121	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.433141640235421	1		426	542	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913237	NA	P-0032363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	335	464	0	ENST00000369535.4:c.35G>T	p.Gly12Val	p.G12V	ENST00000369535	NM_002524.4	12	gGt/gTt	2/7	0.241736214716539	4	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.433141640235421	4		464	993	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939999	76939999	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	196	298	1	ENST00000373344.5:c.749G>A	p.Arg250Gln	p.R250Q	ENST00000373344	NM_000489.3	250	cGa/cAa	9/35	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.433141640235421	1		299	490	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120707	115120707	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	126	679	0	ENST00000257566.3:c.299A>C	p.Glu100Ala	p.E100A	ENST00000257566	NM_016569.3	100	gAg/gCg	1/8	0.232384759846544	1	FACETS	0.43	0.389	0.474	0.43	0.389	0.474	INDETERMINATE	1	TRUE	0	0.433141640235421	1		679	1059	SUCCESS
APC	324	MSKCC	GRCh37	5	112175222	112175223	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0032363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	46	222	0	ENST00000257430.4:c.3932_3933dup	p.Gly1312LeufsTer10	p.G1312Lfs*10	ENST00000257430	NM_000038.5	1311	att/aTTtt	16/16	0.232384759846544	1	FACETS	0.547	0.463	0.639	0.547	0.463	0.639	INDETERMINATE	1	TRUE	0	0.433141640235421	1		222	304	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945052	151945052	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	49	596	0	ENST00000262189.6:c.2467A>T	p.Ile823Phe	p.I823F	ENST00000262189	NM_170606.2	823	Att/Ttt	14/59	1	2	FACETS	0.257	0.216	0.301	0.257	0.216	0.301	SUBCLONAL	1	TRUE	1	0.433141640235421	2		596	882	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5066746	5066746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	63	347	0	ENST00000381652.3:c.1283G>A	p.Ser428Asn	p.S428N	ENST00000381652	NM_004972.3	428	aGt/aAt	10/25	1	2	FACETS	0.817	0.711	0.931	0.817	0.711	0.931	CLONAL	1	TRUE	1	0.433141640235421	2		347	356	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911614	114911614	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	CCGGC	novel	NA	P-0032363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	97	503	0	ENST00000543371.1:c.1132delinsCCGGC	p.Ala378ProfsTer46	p.A378Pfs*46	ENST00000543371	NM_001198531.1	378	Gcg/CCGGCcg	10/14	1	2	FACETS	0.651	0.581	0.726	0.651	0.581	0.726	SUBCLONAL	1	TRUE	1	0.433141640235421	2		503	688	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0032774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	182	325	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	0.708518294419818	4	FACETS	0.975	0.911	1	0.975	0.911	1	CLONAL	2	TRUE	2	0.77635319709666	4		325	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578493	7578493	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1206165503	NA	P-0032774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	659	665	0	ENST00000269305.4:c.437G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tGg/tAg	5/11	0.77635319709666	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.77635319709666	2		665	812	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057874	27057874	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1503	500	593	1	ENST00000324856.7:c.1582C>T	p.Gln528Ter	p.Q528*	ENST00000324856	NM_006015.4	528	Cag/Tag	3/20	0.77635319709666	7	FACETS	0.946	0.902	0.99			1	CLONAL	2	TRUE	NA	0.77635319709666	7		594	2003	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56787259	56787259	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28363311	NA	P-0032774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	309	519	0	ENST00000337432.4:c.745C>T	p.Arg249Cys	p.R249C	ENST00000337432	NM_058216.2	249	Cgt/Tgt	5/9	0.77635319709666	2	FACETS	0.939	0.905	0.971	0.939	0.905	0.971	CLONAL	2	TRUE	0	0.77635319709666	2		519	424	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867256	45867256	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780129241	NA	P-0032774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	424	608	0	ENST00000391945.4:c.937G>A	p.Glu313Lys	p.E313K	ENST00000391945	NM_000400.3	313	Gaa/Aaa	10/23	0.77635319709666	3	FACETS	0.937	0.9	0.975	0.937	0.9	0.975	CLONAL	2	TRUE	1	0.77635319709666	3		608	809	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612176	189612176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	417	466	0	ENST00000264731.3:c.1928G>A	p.Arg643Gln	p.R643Q	ENST00000264731	NM_003722.4	643	cGa/cAa	14/14	0.771696758649947	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.77635319709666	2		466	503	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588877	69588877	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1179344852	NA	P-0032774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	363	442	0	ENST00000168712.1:c.359C>T	p.Pro120Leu	p.P120L	ENST00000168712	NM_002007.2	120	cCc/cTc	2/3	0.750832000803099	5	FACETS	0.992	0.943	1			1	CLONAL	2	TRUE	NA	0.77635319709666	5		442	1020	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341785	8341785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776356704	NA	P-0032774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	422	617	0	ENST00000356435.5:c.4855G>A	p.Glu1619Lys	p.E1619K	ENST00000356435		1619	Gaa/Aaa	29/35	0.771696758649947	2	FACETS	0.981	0.953	1	0.981	0.953	1	CLONAL	2	TRUE	0	0.77635319709666	2		617	554	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245057	46245057	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	340	429	0	ENST00000334344.6:c.3151C>T	p.Gln1051Ter	p.Q1051*	ENST00000334344	NM_152641.2	1051	Cag/Tag	15/21	0.77635319709666	2	FACETS	0.982	0.95	1	0.982	0.95	1	CLONAL	2	TRUE	0	0.77635319709666	2		429	446	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008329	29008329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	204	260	0	ENST00000282397.4:c.542G>A	p.Gly181Glu	p.G181E	ENST00000282397	NM_002019.4	181	gGa/gAa	5/30	0.443303710194281	4	FACETS	1	0.978	1	1	0.978	1	INDETERMINATE	2	TRUE	2	0.77635319709666	4		260	430	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263314	123263314	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	141	329	0	ENST00000358487.5:c.1429C>T	p.Pro477Ser	p.P477S	ENST00000358487	NM_000141.4	477	Cca/Tca	10/18	0.77635319709666	3	FACETS	1	0.961	1	0.54	0.495	0.586	CLONAL	1	TRUE	1	0.77635319709666	3		329	467	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085798	16085798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	312	338	0	ENST00000281043.3:c.974C>T	p.Pro325Leu	p.P325L	ENST00000281043	NM_005378.4	325	cCc/cTc	3/3	0.77635319709666	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.77635319709666	3		338	534	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0032774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	164	114	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.77635319709666	2		114	402	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023917	27023918	+	missense_variant	Missense_Mutation	DNP	GG	GG	TA	novel	NA	P-0032774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	56	32	0	ENST00000324856.7:c.1023_1024delinsTA	p.Ala342Thr	p.A342T	ENST00000324856	NM_006015.4	341	gcGGcg/gcTAcg	1/20	0.77635319709666	7	FACETS	0.842	0.736	0.953			1	CLONAL	3	TRUE	NA	0.77635319709666	7		32	168	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332949	70332949	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	162	553	0	ENST00000373644.4:c.854C>T	p.Ser285Phe	p.S285F	ENST00000373644	NM_030625.2	285	tCt/tTt	2/12	0.77635319709666	3	FACETS	0.793	0.729	0.859	0.396	0.364	0.43	SUBCLONAL	1	TRUE	1	0.77635319709666	3		553	731	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373196	118373196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377156559	NA	P-0032774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	246	328	1	ENST00000534358.1:c.6589C>T	p.Arg2197Cys	p.R2197C	ENST00000534358	NM_005933.3	2197	Cgt/Tgt	27/36	0.771696758649947	2	FACETS	0.987	0.95	1	0.987	0.95	1	CLONAL	2	TRUE	0	0.77635319709666	2		329	321	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975715	26975715	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	170	316	0	ENST00000381527.3:c.1223C>T	p.Pro408Leu	p.P408L	ENST00000381527	NM_001260.1	408	cCt/cTt	12/13	0.443303710194281	4	FACETS	1	0.99	1	0.73	0.676	0.785	INDETERMINATE	1	TRUE	2	0.77635319709666	4		316	533	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73343010	73343010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	166	304	0	ENST00000377767.4:c.1796C>T	p.Ser599Leu	p.S599L	ENST00000377767	NM_014953.3	599	tCa/tTa	14/21	0.443303710194281	4	FACETS	1	0.971	1	1	0.971	1	INDETERMINATE	2	TRUE	2	0.77635319709666	4		304	354	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058300	42058300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	194	272	0	ENST00000219905.7:c.8020G>A	p.Glu2674Lys	p.E2674K	ENST00000219905	NM_001164273.1	2674	Gaa/Aaa	24/24	0.616785102887257	4	FACETS	0.86	0.803	0.919	0.86	0.803	0.919	CLONAL	2	TRUE	2	0.77635319709666	4		272	516	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992613	72992613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	354	465	0	ENST00000268489.5:c.1432G>A	p.Glu478Lys	p.E478K	ENST00000268489	NM_006885.3	478	Gaa/Aaa	2/10	0.77635319709666	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.77635319709666	2		465	442	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979566	7979566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	428	475	0	ENST00000319144.4:c.1459G>A	p.Glu487Lys	p.E487K	ENST00000319144	NM_001139.2	487	Gag/Aag	11/15	0.77635319709666	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.77635319709666	2		475	522	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979995	7979995	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	424	576	1	ENST00000319144.4:c.1342G>A	p.Glu448Lys	p.E448K	ENST00000319144	NM_001139.2	448	Gag/Aag	10/15	0.77635319709666	2	FACETS	0.993	0.965	1	0.993	0.965	1	CLONAL	2	TRUE	0	0.77635319709666	2		577	550	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42384964	42384964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	171	475	0	ENST00000221972.3:c.598G>A	p.Glu200Lys	p.E200K	ENST00000221972	NM_021601.3	200	Gag/Aag	5/5	0.77635319709666	3	FACETS	0.969	0.895	1	0.485	0.447	0.523	CLONAL	1	TRUE	1	0.77635319709666	3		475	631	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321174	62321175	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0032774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	416	654	2	ENST00000360203.5:c.2097_2098delinsTT	p.Arg700Trp	p.R700W	ENST00000360203	NM_001283009.1	699	atCCgg/atTTgg	24/35	0.616785102887257	4	FACETS	0.861	0.822	0.901	0.861	0.822	0.901	CLONAL	2	TRUE	2	0.77635319709666	4		656	1105	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42861441	42861441	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	262	329	1	ENST00000398585.3:c.429G>A	p.Trp143Ter	p.W143*	ENST00000398585	NM_001135099.1	143	tgG/tgA	4/14	0.708518294419818	4	FACETS	0.935	0.883	0.988	0.935	0.883	0.988	CLONAL	2	TRUE	2	0.77635319709666	4		330	641	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961160	79961160	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750366331	NA	P-0032774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	117	426	0	ENST00000265081.6:c.557C>T	p.Ser186Leu	p.S186L	ENST00000265081	NM_002439.4	186	tCg/tTg	3/24	1	2	FACETS	0.701	0.637	0.768	0.701	0.637	0.768	SUBCLONAL	1	TRUE	1	0.77635319709666	2		426	430	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515406	149515406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	188	430	1	ENST00000261799.4:c.76G>A	p.Glu26Lys	p.E26K	ENST00000261799	NM_002609.3	26	Gaa/Aaa	3/23	0.77635319709666	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.77635319709666	1		431	276	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43739003	43739004	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0032774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	175	388	1	ENST00000523873.1:c.20_21delinsAA	p.Trp7Ter	p.W7*	ENST00000523873		7	tGG/tAA	1/8	0.77635319709666	3	FACETS	0.963	0.89	1	0.481	0.445	0.519	CLONAL	1	TRUE	1	0.77635319709666	3		389	650	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64288881	64288881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369392023	NA	P-0032774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	406	551	0	ENST00000370651.3:c.277C>T	p.Arg93Cys	p.R93C	ENST00000370651	NM_003463.4	93	Cgt/Tgt	4/6	0.77635319709666	3	FACETS	0.972	0.933	1	0.972	0.933	1	CLONAL	2	TRUE	1	0.77635319709666	3		551	747	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922637	56922637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	163	432	0	ENST00000519728.1:c.1507G>A	p.Ala503Thr	p.A503T	ENST00000519728	NM_002350.3	503	Gcc/Acc	13/13	0.77635319709666	3	FACETS	0.897	0.826	0.97	0.448	0.413	0.485	CLONAL	1	TRUE	1	0.77635319709666	3		432	650	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058544	69058544	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	137	569	0	ENST00000288368.4:c.4188A>C	p.Lys1396Asn	p.K1396N	ENST00000288368	NM_024870.2	1396	aaA/aaC	34/40	0.77635319709666	3	FACETS	0.878	0.802	0.957	0.439	0.401	0.479	CLONAL	1	TRUE	1	0.77635319709666	3		569	558	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966647	36966647	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	406	509	0	ENST00000358127.4:c.679G>T	p.Asp227Tyr	p.D227Y	ENST00000358127	NM_001280556.1	227	Gac/Tac	6/10	0.616785102887257	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.77635319709666	4		509	916	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606247	93606247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	393	517	0	ENST00000375746.1:c.67G>A	p.Glu23Lys	p.E23K	ENST00000375746	NM_001174167.1	23	Gag/Aag	2/14	0.616785102887257	4	FACETS	0.962	0.918	1	0.962	0.918	1	CLONAL	2	TRUE	2	0.77635319709666	4		517	935	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178199	142178199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746049210	NA	P-0033018-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	126	274	0	ENST00000350721.4:c.7219C>T	p.Arg2407Cys	p.R2407C	ENST00000350721	NM_001184.3	2407	Cgc/Tgc	43/47	1	2	FACETS	0.906	0.826	0.989	0.906	0.826	0.989	CLONAL	1	TRUE	1	0.600873898337507	2		274	463	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748093	43748093	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033018-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	194	398	0	ENST00000382044.4:c.2713A>G	p.Ser905Gly	p.S905G	ENST00000382044	NM_001141980.1	905	Agt/Ggt	12/28	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.600873898337507	2		398	646	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644474	3644474	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033018-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	288	669	0	ENST00000294008.3:c.2140T>G	p.Cys714Gly	p.C714G	ENST00000294008	NM_032444.2	714	Tgc/Ggc	10/15	1	2	FACETS	0.944	0.889	1	0.944	0.889	1	CLONAL	1	TRUE	1	0.600873898337507	2		669	1015	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0033222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	222	370	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.3	4	FACETS	0.923	0.861	0.987			1	CLONAL	5	TRUE	NA	0.13	4		370	836	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587780070	NA	P-0033222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	56	547	0	ENST00000269305.4:c.535C>A	p.His179Asn	p.H179N	ENST00000269305	NM_001126112.2	179	Cat/Aat	5/11	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.13	2		547	717	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512393	38512393	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1403898124	NA	P-0033222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	49	562	0	ENST00000254066.5:c.1304G>A	p.Gly435Asp	p.G435D	ENST00000254066	NM_000964.3	435	gGt/gAt	9/9	1	2	FACETS	0.997	0.843	1	0.997	0.843	1	CLONAL	1	TRUE	1	0.13	2		562	756	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553497	106553497	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	21	275	0	ENST00000369096.4:c.1462C>A	p.Leu488Ile	p.L488I	ENST00000369096	NM_001198.3	488	Ctt/Att	5/7	1	2	FACETS	0.92	0.708	1	0.92	0.708	1	CLONAL	1	TRUE	1	0.13	2		275	351	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033599-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	43	417	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.918	0.768	1	0.918	0.768	1	CLONAL	1	TRUE	1	0.19	2		417	493	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068375	26068375	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033599-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	29	490	0	ENST00000435504.4:c.115C>T	p.Gln39Ter	p.Q39*	ENST00000435504		39	Cag/Tag	2/13	1	2	FACETS	0.55	0.44	0.675	0.55	0.44	0.675	SUBCLONAL	1	TRUE	1	0.19	2		490	555	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987087	36987087	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033599-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	63	635	2	ENST00000354822.5:c.602C>T	p.Ala201Val	p.A201V	ENST00000354822	NM_001079668.2	201	gCg/gTg	3/3	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.19	2		637	589	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610135	43610135	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564496520	NA	P-0033599-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	35	605	0	ENST00000355710.3:c.2087C>T	p.Ser696Leu	p.S696L	ENST00000355710	NM_020975.4	696	tCg/tTg	11/20	1	2	FACETS	0.693	0.567	0.834	0.693	0.567	0.834	SUBCLONAL	1	TRUE	1	0.19	2		605	532	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226385	2226385	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033599-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	59	706	0	ENST00000326181.6:c.1998G>T	p.Lys666Asn	p.K666N	ENST00000326181	NM_032271.2	666	aaG/aaT	20/21	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.19	2		706	600	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0033683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	196	379	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.625458741662999	5	FACETS	0.881	0.829	0.933	0.881	0.829	0.933	CLONAL	3	TRUE	2	0.953786658056516	5		379	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0033683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	157	487	1	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.953786658056516	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.953786658056516	1		488	165	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510620	38510620	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	196	544	0	ENST00000254066.5:c.874C>G	p.Leu292Val	p.L292V	ENST00000254066	NM_000964.3	292	Ctg/Gtg	7/9	0.309089827883549	3	FACETS	1	0.991	1	0.693	0.649	0.737	INDETERMINATE	1	TRUE	1	0.953786658056516	3		544	438	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399350	139399350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755124691	NA	P-0033683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	49	578	1	ENST00000277541.6:c.4793G>A	p.Arg1598His	p.R1598H	ENST00000277541	NM_017617.3	1598	cGc/cAc	26/34	0.309089827883549	3	FACETS	0.488	0.415	0.567	0.244	0.207	0.284	INDETERMINATE	1	TRUE	1	0.953786658056516	3		579	311	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294603	1294603	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	16	170	0	ENST00000310581.5:c.398G>C	p.Gly133Ala	p.G133A	ENST00000310581	NM_198253.2	133	gGg/gCg	2/16	0.456950527231768	2	FACETS	0.541	0.412	0.686	0.271	0.206	0.343	INDETERMINATE	1	TRUE	0	0.953786658056516	2		170	62	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446212	70446212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	83	608	0	ENST00000373644.4:c.5152G>A	p.Glu1718Lys	p.E1718K	ENST00000373644	NM_030625.2	1718	Gag/Aag	11/12	0.533675033256933	1	FACETS	0.404	0.357	0.454	0.404	0.357	0.454	SUBCLONAL	1	TRUE	0	0.533675033256933	1		608	565	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035154	30035154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	206	606	0	ENST00000338641.4:c.316G>A	p.Glu106Lys	p.E106K	ENST00000338641	NM_000268.3	106	Gaa/Aaa	3/16	1	2	FACETS	0.982	0.914	1	0.982	0.914	1	CLONAL	1	TRUE	1	0.533675033256933	2		606	786	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058705	47058706	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	237	459	0	ENST00000409792.3:c.7572dup	p.Lys2525Ter	p.K2525*	ENST00000409792	NM_014159.6	2524	-/T	21/21	0.533675033256933	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.533675033256933	1		459	577	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838389	156838389	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	85	755	0	ENST00000524377.1:c.667G>C	p.Glu223Gln	p.E223Q	ENST00000524377	NM_002529.3	223	Gag/Cag	6/17	0.502561152465139	3	FACETS	0.354	0.311	0.399	0.177	0.155	0.2	SUBCLONAL	1	TRUE	1	0.533675033256933	3		755	1141	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953288	17953288	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs941028266	NA	P-0033700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	153	704	1	ENST00000458235.1:c.698C>G	p.Ser233Trp	p.S233W	ENST00000458235	NM_000215.3	233	tCg/tGg	6/24	0.360587412993812	4	FACETS	0.667	0.608	0.728			1	SUBCLONAL	1	TRUE	NA	0.533675033256933	4		705	1319	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226568830	226568830	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs772391589	NA	P-0033700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	82	742	0	ENST00000366794.5:c.1239G>C	p.Glu413Asp	p.E413D	ENST00000366794	NM_001618.3	413	gaG/gaC	9/23	0.502561152465139	3	FACETS	0.337	0.296	0.381	0.169	0.148	0.191	SUBCLONAL	1	TRUE	1	0.533675033256933	3		742	1155	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434211	49434211	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	291	968	0	ENST00000301067.7:c.7342G>C	p.Asp2448His	p.D2448H	ENST00000301067	NM_003482.3	2448	Gac/Cac	31/54	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.533675033256933	2		968	1090	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69229748	69229748	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	38	376	0	ENST00000462284.1:c.824C>T	p.Ser275Leu	p.S275L	ENST00000462284	NM_002392.5	275	tCa/tTa	9/11	1	2	FACETS	0.272	0.224	0.325	0.272	0.224	0.325	SUBCLONAL	1	TRUE	1	0.533675033256933	2		376	524	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346334	89346334	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	133	462	0	ENST00000301030.4:c.6616G>C	p.Glu2206Gln	p.E2206Q	ENST00000301030	NM_001256183.1	2206	Gag/Cag	9/13	0.533675033256933	1	FACETS	0.944	0.867	1	0.944	0.867	1	CLONAL	1	TRUE	0	0.533675033256933	1		462	387	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757422	40757422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	98	672	0	ENST00000373198.4:c.2876C>T	p.Ser959Phe	p.S959F	ENST00000373198	NM_133170.3	959	tCt/tTt	20/32	1	2	FACETS	0.464	0.413	0.517	0.464	0.413	0.517	SUBCLONAL	1	TRUE	1	0.533675033256933	2		672	792	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41525947	41525947	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0033700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	211	602	0	ENST00000263253.7:c.1222A>T	p.Arg408Ter	p.R408*	ENST00000263253	NM_001429.3	408	Aga/Tga	5/31	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.533675033256933	2		602	771	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480346	89480346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748206093	NA	P-0033700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	32	361	0	ENST00000336596.2:c.2183G>A	p.Arg728Gln	p.R728Q	ENST00000336596	NM_005233.5	728	cGa/cAa	13/17	0.502561152465139	3	FACETS	0.271	0.219	0.33	0.136	0.109	0.165	SUBCLONAL	1	TRUE	1	0.533675033256933	3		361	560	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149375021	149375021	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1294	130	816	0	ENST00000360632.3:c.73G>C	p.Asp25His	p.D25H	ENST00000360632	NM_015472.4	25	Gac/Cac	2/7	0.502561152465139	3	FACETS	0.433	0.392	0.478	0.217	0.196	0.239	SUBCLONAL	1	TRUE	1	0.533675033256933	3		816	1424	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167750	185167750	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	187	594	0	ENST00000265026.3:c.1073C>T	p.Ser358Phe	p.S358F	ENST00000265026	NM_004721.4	358	tCt/tTt	6/14	0.502561152465139	3	FACETS	0.899	0.83	0.97	0.449	0.415	0.485	CLONAL	1	TRUE	1	0.533675033256933	3		594	988	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191235	185191235	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	149	518	0	ENST00000265026.3:c.2116G>C	p.Asp706His	p.D706H	ENST00000265026	NM_004721.4	706	Gac/Cac	11/14	0.502561152465139	3	FACETS	0.874	0.799	0.953	0.437	0.399	0.477	CLONAL	1	TRUE	1	0.533675033256933	3		518	809	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191361	185191361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	242	679	0	ENST00000265026.3:c.2242G>A	p.Ala748Thr	p.A748T	ENST00000265026	NM_004721.4	748	Gct/Act	11/14	0.502561152465139	3	FACETS	1	0.955	1	0.515	0.48	0.55	CLONAL	1	TRUE	1	0.533675033256933	3		679	1116	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0033998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	143	573	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.202132608250021	2	FACETS	1	0.924	1			1	CLONAL	3	TRUE	NA	0.222765104789436	2		573	426	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100677	8100677	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	115	839	0	ENST00000346208.3:c.651C>A	p.His217Gln	p.H217Q	ENST00000346208		217	caC/caA	3/6	0.189023174253096	4	FACETS	1	0.962	1	0.573	0.515	0.635	CLONAL	1	TRUE	2	0.222765104789436	4		839	1101	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221211	1221211	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0033998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	168	615	0	ENST00000326873.7:c.735-1G>T		p.X245_splice	ENST00000326873	NM_000455.4	245			0.222765104789436	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.222765104789436	2		615	702	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600380	10600380	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	206	879	1	ENST00000171111.5:c.1475del	p.Pro492GlnfsTer8	p.P492Qfs*8	ENST00000171111	NM_203500.1	492	cCa/ca	4/6	0.222765104789436	2	FACETS	0.95	0.882	1	0.95	0.882	1	CLONAL	2	TRUE	0	0.222765104789436	2		880	973	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966754	18966754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568279022	NA	P-0033998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	92	752	2	ENST00000262803.5:c.1565C>T	p.Pro522Leu	p.P522L	ENST00000262803	NM_002911.3	522	cCg/cTg	12/24	0.222765104789436	2	FACETS	0.807	0.716	0.906	0.404	0.358	0.453	CLONAL	1	TRUE	0	0.222765104789436	2		754	1023	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798206	42798253	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGGCTCTTACCGCAAGAAGAGGAAGAACTCCACGGGTAGGCGAGCAT	TGGGCTCTTACCGCAAGAAGAGGAAGAACTCCACGGGTAGGCGAGCAT	-	novel	NA	P-0033998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	91	760	1	ENST00000575354.2:c.4165_4195+17del		p.X1389_splice	ENST00000575354	NM_015125.3	1389		17/20	0.222765104789436	2	FACETS	1	0.905	1	0.511	0.453	0.573	CLONAL	1	TRUE	0	0.222765104789436	2		761	799	SUCCESS
APC	324	MSKCC	GRCh37	5	112136975	112136975	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0033998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	89	358	0	ENST00000257430.4:c.730-1G>A		p.X244_splice	ENST00000257430	NM_000038.5	244			0.222765104789436	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	2	TRUE	0	0.222765104789436	2		358	392	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944368	131944368	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	26	213	0	ENST00000265335.6:c.2781del	p.Glu928AsnfsTer2	p.E928Nfs*2	ENST00000265335		927	gAa/ga	17/25	0.249454831938353	1	FACETS	0.59	0.468	0.73	0.59	0.468	0.73	SUBCLONAL	1	FALSE	0	0.249454831938353	1		213	309	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0034088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	67	197	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.425927327097067	4	FACETS	1	0.974	1	0.74	0.65	0.835	CLONAL	1	TRUE	2	0.510164654500729	4		197	268	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0034088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	401	698	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.510164654500729	2	FACETS	0.986	0.945	1	0.986	0.945	1	CLONAL	2	TRUE	0	0.510164654500729	2		698	797	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372184	55372184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs915105324	NA	P-0034088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	137	184	0	ENST00000297316.4:c.874G>A	p.Ala292Thr	p.A292T	ENST00000297316	NM_022454.3	292	Gcc/Acc	2/2	0.458735666976448	5	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.510164654500729	5		184	712	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0034088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	266	506	0	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	0.510164654500729	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.510164654500729	3		506	589	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46587863	46587863	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747275399	NA	P-0034088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	97	451	1	ENST00000263734.3:c.541C>T	p.Arg181Cys	p.R181C	ENST00000263734	NM_001430.4	181	Cgt/Tgt	5/16	0.510164654500729	3	FACETS	0.906	0.81	1	0.453	0.405	0.504	CLONAL	1	TRUE	1	0.510164654500729	3		452	527	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942874	15942875	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0034088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	212	456	1	ENST00000268712.3:c.6827_6828del	p.Asp2276GlyfsTer4	p.D2276Gfs*4	ENST00000268712	NM_006311.3	2276	gAT/g	44/46	0.510164654500729	2	FACETS	0.938	0.883	0.993	0.938	0.883	0.993	CLONAL	2	TRUE	0	0.510164654500729	2		457	443	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587142	212587142	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	63	442	0	ENST00000342788.4:c.859G>A	p.Ala287Thr	p.A287T	ENST00000342788	NM_005235.2	287	Gca/Aca	7/28	0.510164654500729	3	FACETS	0.719	0.624	0.822	0.36	0.312	0.411	SUBCLONAL	1	TRUE	1	0.510164654500729	3		442	431	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAAT	novel	NA	P-0034088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	78	217	0	ENST00000257430.4:c.3920_3923dup	p.Lys1308AsnfsTer8	p.K1308Nfs*8	ENST00000257430	NM_000038.5	1306	gaa/gAAATaa	16/16	0.425927327097067	4	FACETS	0.891	0.794	0.993	0.891	0.794	0.993	CLONAL	2	TRUE	2	0.510164654500729	4		217	259	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982010	70982011	+	missense_variant	Missense_Mutation	DNP	TA	TA	GT	novel	NA	P-0034088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1825	216	1022	1	ENST00000276594.2:c.85_86delinsAC	p.Tyr29Thr	p.Y29T	ENST00000276594	NM_024504.3	29	TAc/ACc	2/8	0.510164654500729	7	FACETS	0.944	0.874	1	0.189	0.174	0.204	CLONAL	1	TRUE	2	0.510164654500729	7		1023	2041	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0034112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	147	481	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	0.745565828370274	1	FACETS	0.959	0.897	1	0.959	0.897	1	CLONAL	1	TRUE	0	0.745565828370274	1		481	258	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652404	206652404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17021877	NA	P-0034113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	45	636	1	ENST00000367120.3:c.1111G>A	p.Ala371Thr	p.A371T	ENST00000367120	NM_014002.3	371	Gcc/Acc	10/22	1	2	FACETS	0.872	0.731	1	0.872	0.731	1	CLONAL	1	TRUE	1	0.15	2		637	688	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0121536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	73	732	1	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	1	2	FACETS	0.728	0.635	0.828	0.728	0.635	0.828	SUBCLONAL	1	NA	1	0.23	2		733	872	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939577	76939577	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0121536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	65	341	0	ENST00000373344.5:c.1171C>T	p.Gln391Ter	p.Q391*	ENST00000373344	NM_000489.3	391	Cag/Tag	9/35	1	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	NA	0	0.23	1		341	442	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865794	56865794	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0121536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	31	302	0	ENST00000308159.5:c.1126C>G	p.Arg376Gly	p.R376G	ENST00000308159	NM_014669.4	376	Cgt/Ggt	11/22	1	2	FACETS	0.772	0.625	0.938	0.772	0.625	0.938	CLONAL	1	NA	1	0.23	2		302	349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0034144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	92	546	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.969	1	1	0.988	1	CLONAL	2	TRUE	1	0.13	2		547	568	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242478	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAG	AATTAAGAGAAG	CAC	rs727503015	NA	P-0034144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	78	343	0	ENST00000275493.2:c.2237_2248delinsCAC	p.Glu746_Ala750delinsAlaPro	p.E746_A750delinsAP	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGca/gCACca	19/28	0.3	3	FACETS	1	0.899	1	1	0.978	1	CLONAL	3	TRUE	1	0.13	3		343	418	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610038	43610038	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1357060080	NA	P-0034144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	27	683	0	ENST00000355710.3:c.1990G>T	p.Ala664Ser	p.A664S	ENST00000355710	NM_020975.4	664	Gcc/Tcc	11/20	1	2	FACETS	0.796	0.632	0.984	0.796	0.632	0.984	CLONAL	1	TRUE	1	0.13	2		683	522	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31372646	31372646	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs775213720	NA	P-0034144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	23	430	0	ENST00000328111.2:c.287C>G	p.Thr96Ser	p.T96S	ENST00000328111	NM_006892.3	96	aCt/aGt	4/23	1	2	FACETS	0.91	0.708	1	0.91	0.708	1	CLONAL	1	TRUE	1	0.13	2		430	389	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48922000	48922000	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1566187856	NA	P-0034220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	115	192	0	ENST00000267163.4:c.539+1G>A		p.X180_splice	ENST00000267163	NM_000321.2	180			0.516459583507291	2	FACETS	0.823	0.755	0.891	0.823	0.755	0.891	CLONAL	2	TRUE	0	0.539820880116414	2		192	259	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426679	49426696	+	inframe_deletion	In_Frame_Del	DEL	GCTGTTGCTGCTGTTGAA	GCTGTTGCTGCTGTTGAA	-	rs752843878	NA	P-0034220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	74	277	0	ENST00000301067.7:c.11792_11809del	p.Leu3931_Gln3936del	p.L3931_Q3936del	ENST00000301067	NM_003482.3	3931	cTTCAACAGCAGCAACAGCag/cag	39/54	0.380172080337719	4	FACETS	0.91	0.799	1	0.455	0.399	0.514	CLONAL	1	TRUE	2	0.539820880116414	4		277	464	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481405	140481405	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397507473	NA	P-0034220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	201	337	0	ENST00000288602.6:c.1403T>C	p.Phe468Ser	p.F468S	ENST00000288602	NM_004333.4	468	tTt/tCt	11/18	0.317866022744952	4	FACETS	1	0.983	1	1	0.983	1	INDETERMINATE	2	TRUE	2	0.539820880116414	4		337	501	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246442	46246443	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0034220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	68	244	0	ENST00000334344.6:c.4540dup	p.Thr1514AsnfsTer10	p.T1514Nfs*10	ENST00000334344	NM_152641.2	1512	-/A	15/21	0.380172080337719	4	FACETS	1	0.887	1	0.508	0.444	0.576	CLONAL	1	TRUE	2	0.539820880116414	4		244	382	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752903	128752903	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	100	309	0	ENST00000377970.2:c.1064G>A	p.Arg355Gln	p.R355Q	ENST00000377970	NM_002467.4	355	cGa/cAa	3/3	0.539820880116414	13	FACETS	1	0.963	1			1	CLONAL	1	TRUE	NA	0.539820880116414	13		309	1234	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061221	38061232	+	inframe_deletion	In_Frame_Del	DEL	GTTCTCGAACAT	GTTCTCGAACAT	-	novel	NA	P-0034300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	164	749	0	ENST00000250448.2:c.757_768del	p.Met253_Asn256del	p.M253_N256del	ENST00000250448	NM_004496.3	253	ATGTTCGAGAAC/-	2/2	1	2	FACETS	0.887	0.819	0.958	0.887	0.819	0.958	CLONAL	1	TRUE	1	0.629817318270705	2		749	587	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927408	245927408	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	412	695	0	ENST00000388985.4:c.1120A>G	p.Met374Val	p.M374V	ENST00000388985		374	Atg/Gtg	11/12	0.629817318270705	3	FACETS	0.991	0.949	1	0.991	0.949	1	CLONAL	2	TRUE	1	0.629817318270705	3		695	868	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911964	32911964	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	205	749	0	ENST00000380152.3:c.3472G>T	p.Glu1158Ter	p.E1158*	ENST00000380152		1158	Gaa/Taa	11/27	0.629817318270705	1	FACETS	0.896	0.839	0.953	0.896	0.839	0.953	CLONAL	1	TRUE	0	0.629817318270705	1		749	498	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430853	181430853	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	312	1128	3	ENST00000325404.1:c.705G>A	p.Met235Ile	p.M235I	ENST00000325404	NM_003106.3	235	atG/atA	1/1	0.629817318270705	3	FACETS	0.994	0.937	1	0.497	0.468	0.527	CLONAL	1	TRUE	1	0.629817318270705	3		1131	1310	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289512	33289512	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1300176657	NA	P-0034300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	343	1153	0	ENST00000374542.5:c.191A>G	p.Glu64Gly	p.E64G	ENST00000374542	NM_001141970.1	64	gAg/gGg	2/8	NA	2	FACETS	0.994	0.941	1			1	INDETERMINATE	1	TRUE	NA	0.629817318270705	2		1153	1096	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268987	55268987	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	291	887	0	ENST00000275493.2:c.3053T>A	p.Ile1018Asn	p.I1018N	ENST00000275493	NM_005228.3	1018	aTc/aAc	25/28	0.629817318270705	3	FACETS	1	0.96	1	0.514	0.483	0.545	CLONAL	1	TRUE	1	0.629817318270705	3		887	1183	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923358	36923358	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	189	751	0	ENST00000358127.4:c.904G>T	p.Val302Leu	p.V302L	ENST00000358127	NM_001280556.1	302	Gtg/Ttg	7/10	0.629817318270705	3	FACETS	1	0.938	1	0.507	0.47	0.546	CLONAL	1	TRUE	1	0.629817318270705	3		751	778	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760448	133760448	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	158	823	0	ENST00000318560.5:c.2771G>C	p.Gly924Ala	p.G924A	ENST00000318560	NM_005157.4	924	gGg/gCg	11/11	0.629817318270705	3	FACETS	0.83	0.761	0.901	0.415	0.38	0.451	CLONAL	1	TRUE	1	0.629817318270705	3		823	795	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0034303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	245	114	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.928525025265915	2		114	522	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528489	29528489	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764079291	NA	P-0034303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	173	628	0	ENST00000356175.3:c.1246C>T	p.Arg416Ter	p.R416*	ENST00000356175	NM_000267.3	416	Cga/Tga	11/57	1	2	FACETS	0.911	0.849	0.974	0.911	0.849	0.974	CLONAL	1	TRUE	1	0.928525025265915	2		628	409	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0034303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	367	766	4	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	0.889	0.847	0.932	0.889	0.847	0.932	CLONAL	1	TRUE	1	0.928525025265915	2		770	889	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781440	135781440	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203542	NA	P-0034303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	47	575	1	ENST00000298552.3:c.1525C>T	p.Arg509Ter	p.R509*	ENST00000298552	NM_001162426.1	509	Cga/Tga	15/23	0.928525025265915	1	FACETS	0.134	0.113	0.157	0.134	0.113	0.157	SUBCLONAL	1	TRUE	0	0.928525025265915	1		576	406	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974312	93974312	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	119	462	0	ENST00000369303.4:c.1742G>A	p.Arg581Lys	p.R581K	ENST00000369303	NM_004440.3	581	aGg/aAg	8/17	0.914841813441118	1	FACETS	0.981	0.937	1	0.981	0.937	1	CLONAL	1	TRUE	0	0.928525025265915	1		462	140	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699356	18699356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	108	410	0	ENST00000266497.5:c.3457C>T	p.His1153Tyr	p.H1153Y	ENST00000266497		1153	Cat/Tat	24/31	0.122149868151822	4	FACETS	0.837	0.764	0.911	0.837	0.764	0.911	INDETERMINATE	2	TRUE	2	0.928525025265915	4		410	268	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874562	35874562	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	184	622	0	ENST00000303115.3:c.718C>T	p.Pro240Ser	p.P240S	ENST00000303115	NM_002185.3	240	Cct/Tct	6/8	1	2	FACETS	0.751	0.698	0.804	0.751	0.698	0.804	SUBCLONAL	1	TRUE	1	0.928525025265915	2		622	528	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155731	119155731	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373989524	NA	P-0034303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	447	747	2	ENST00000264033.4:c.1484C>T	p.Pro495Leu	p.P495L	ENST00000264033	NM_005188.3	495	cCg/cTg	10/16	0.914841813441118	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.928525025265915	1		749	495	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798734	135798734	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs118203390	NA	P-0034303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	19	312	0	ENST00000298552.3:c.508+1G>A		p.X170_splice	ENST00000298552	NM_001162426.1	170			0.928525025265915	1	FACETS	0.147	0.112	0.187	0.147	0.112	0.187	SUBCLONAL	1	TRUE	0	0.928525025265915	1		312	149	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264143	46264143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746732554	NA	P-0034303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	94	277	0	ENST00000371998.3:c.1190C>T	p.Ser397Leu	p.S397L	ENST00000371998		397	tCg/tTg	11/23	1	2	FACETS	0.833	0.755	0.914	0.833	0.755	0.914	CLONAL	1	TRUE	1	0.928525025265915	2		277	243	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813380	102813381	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0034303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	316	622	0	ENST00000307046.8:c.308_309delinsAA	p.Arg103Lys	p.R103K	ENST00000307046	NM_001111285.1	103	aGG/aAA	3/4	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.928525025265915	2		622	637	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926257	112926258	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0034303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	286	728	2	ENST00000351677.2:c.1390_1391delinsAA	p.Gly464Asn	p.G464N	ENST00000351677	NM_002834.3	464	GGc/AAc	12/16	1	2	FACETS	0.881	0.834	0.929	0.881	0.834	0.929	CLONAL	1	TRUE	1	0.928525025265915	2		730	699	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066916	30066916	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	252	525	0	ENST00000331968.5:c.2215T>G	p.Phe739Val	p.F739V	ENST00000331968	NM_002742.2	739	Ttc/Gtc	16/18	1	2	FACETS	0.92	0.868	0.972	0.92	0.868	0.972	CLONAL	1	TRUE	1	0.928525025265915	2		525	590	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3645679	3645679	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	425	835	0	ENST00000294008.3:c.1940C>T	p.Pro647Leu	p.P647L	ENST00000294008	NM_032444.2	647	cCc/cTc	9/15	1	2	FACETS	0.96	0.918	1	0.96	0.918	1	CLONAL	1	TRUE	1	0.928525025265915	2		835	954	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39644758	39644759	+	missense_variant	Missense_Mutation	DNP	AG	AG	CT	novel	NA	P-0034303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	147	453	1	ENST00000262039.4:c.2487_2488inv	p.Asp830Tyr	p.D830Y	ENST00000262039	NM_002647.2	829	ccAGat/ccCTat	23/25	1	2	FACETS	0.929	0.86	0.997	0.929	0.86	0.997	CLONAL	1	TRUE	1	0.928525025265915	2		454	341	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523702	176523702	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	406	873	0	ENST00000292408.4:c.2113G>A	p.Gly705Arg	p.G705R	ENST00000292408	NM_213647.1	705	Gga/Aga	16/18	1	2	FACETS	0.999	0.956	1	0.999	0.956	1	CLONAL	1	TRUE	1	0.928525025265915	2		873	875	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995542	68995542	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	244	925	0	ENST00000288368.4:c.1946T>C	p.Phe649Ser	p.F649S	ENST00000288368	NM_024870.2	649	tTc/tCc	18/40	0.865330209570461	4	FACETS	1	0.942	1	0.336	0.314	0.359	CLONAL	1	TRUE	1	0.928525025265915	4		925	1006	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781241	135781242	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0034303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	264	734	0	ENST00000298552.3:c.1723dup	p.Ser575PhefsTer13	p.S575Ffs*13	ENST00000298552	NM_001162426.1	575	tct/tTct	15/23	0.928525025265915	1	FACETS	0.645	0.614	0.677	0.645	0.614	0.677	SUBCLONAL	1	TRUE	0	0.928525025265915	1		734	472	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	262	417	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.226120261748558	3	FACETS	0.981	0.921	1	0.981	0.921	1	CLONAL	2	TRUE	1	0.33	3		417	943	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0034305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	73	207	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.33	2		207	386	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	137	382	6	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.33	2		388	813	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0034305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	330	1096	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	0.226120261748558	3	FACETS	0.791	0.746	0.838	0.791	0.746	0.838	SUBCLONAL	2	TRUE	1	0.33	3		1096	1472	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358683	67358683	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	104	223	0	ENST00000327367.4:c.191G>T	p.Cys64Phe	p.C64F	ENST00000327367	NM_005902.3	64	tGc/tTc	1/9	0.3	2	FACETS	1	0.958	1	0.563	0.505	0.623	CLONAL	1	TRUE	0	0.33	2		223	560	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457640	67457640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs863223759	NA	P-0034305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	173	434	3	ENST00000327367.4:c.455del	p.Pro152HisfsTer34	p.P152Hfs*34	ENST00000327367	NM_005902.3	150	ttC/tt	3/9	0.3	2	FACETS	1	0.94	1	0.513	0.472	0.557	CLONAL	1	TRUE	0	0.33	2		437	1021	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821601	72821618	+	inframe_deletion	In_Frame_Del	DEL	CCGCCGCCGCCGCCGCCA	CCGCCGCCGCCGCCGCCA	-	rs778016374	NA	P-0034305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	28	46	0	ENST00000268489.5:c.10557_10574del	p.Gly3522_Gly3527del	p.G3522_G3527del	ENST00000268489	NM_006885.3	3519	ggTGGCGGCGGCGGCGGCGGc/ggc	10/10	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.33	2		46	124	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554542	63554542	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	173	288	0	ENST00000307078.5:c.197A>T	p.Glu66Val	p.E66V	ENST00000307078	NM_004655.3	66	gAg/gTg	2/11	1	2	FACETS	0.793	0.733	0.856	1	0.991	1	SUBCLONAL	2	TRUE	1	0.33	2		288	661	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368202	45368202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	208	271	0	ENST00000262160.6:c.1400C>T	p.Ser467Leu	p.S467L	ENST00000262160	NM_005901.5	467	tCa/tTa	11/11	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	1	0.33	2		271	531	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229207	36229207	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	210	405	0	ENST00000222270.7:c.7897A>G	p.Met2633Val	p.M2633V	ENST00000222270	NM_014727.1	2633	Atg/Gtg	37/37	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.33	2		405	945	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277254	41277254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs797044875	NA	P-0034305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	63	282	0	ENST00000349496.5:c.1723G>A	p.Gly575Arg	p.G575R	ENST00000349496	NM_001904.3	575	Gga/Aga	11/15	1	2	FACETS	0.539	0.465	0.619	0.539	0.465	0.619	SUBCLONAL	1	TRUE	1	0.33	2		282	709	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127447	55127447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1333247214	NA	P-0034305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	160	375	0	ENST00000257290.5:c.235G>A	p.Gly79Ser	p.G79S	ENST00000257290	NM_006206.4	79	Ggc/Agc	3/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.33	2		375	849	SUCCESS
APC	324	MSKCC	GRCh37	5	112173368	112173368	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs773985321	NA	P-0034305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	94	226	1	ENST00000257430.4:c.2077A>T	p.Lys693Ter	p.K693*	ENST00000257430	NM_000038.5	693	Aaa/Taa	16/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.33	2		227	473	SUCCESS
APC	324	MSKCC	GRCh37	5	112175753	112175754	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0034305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	103	220	0	ENST00000257430.4:c.4464_4465dup	p.Leu1489TyrfsTer19	p.L1489Yfs*19	ENST00000257430	NM_000038.5	1488	tta/tTAta	16/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.33	2		220	535	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839802	27839802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	171	366	0	ENST00000328488.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000328488	NM_003533.2	98	Gag/Aag	1/1	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.33	2		366	844	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020754	37020754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	44	302	2	ENST00000358127.4:c.91C>T	p.Arg31Trp	p.R31W	ENST00000358127	NM_001280556.1	31	Cgg/Tgg	2/10	1	2	FACETS	0.372	0.311	0.44	0.372	0.311	0.44	SUBCLONAL	1	TRUE	1	0.33	2		304	716	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356727	70356727	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0034305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	135	183	0	ENST00000374080.3:c.5401-2A>G		p.X1801_splice	ENST00000374080		1801			1	1	FACETS	1	0.961	1	1	0.992	1	CLONAL	2	TRUE	0	0.33	1		183	320	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0034307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	305	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.649429718141744	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.649429718141744	1		371	485	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201843	66201843	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	103	471	0	ENST00000273854.3:c.2659G>T	p.Val887Leu	p.V887L	ENST00000273854	NM_004439.5	887	Gtg/Ttg	16/18	0.544193087987137	3	FACETS	0.991	0.893	1	0.496	0.446	0.547	CLONAL	1	TRUE	1	0.649429718141744	3		471	424	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526658	106526658	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	135	635	0	ENST00000359195.3:c.2951C>T	p.Pro984Leu	p.P984L	ENST00000359195	NM_002649.2	984	cCa/cTa	10/11	0.574843175961619	4	FACETS	0.815	0.741	0.893	0.408	0.37	0.447	CLONAL	1	TRUE	2	0.649429718141744	4		635	841	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858304	9858304	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	275	638	0	ENST00000330684.3:c.3097del	p.Gln1033ArgfsTer14	p.Q1033Rfs*14	ENST00000330684	NM_001134407.1	1033	Cag/ag	13/13	0.544193087987137	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.649429718141744	3		638	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7579045	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACGCGGGTGCCGGGCGGGGGTGTGGAATCAACCCACAGCTGCACAGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAAGCAACTGGAAGACGGCAGCAAAGAAACAAACATGCGTAAGCACCTCCTGCAACCCACTAGCGAGCTAGAGAGAGTTGGCGTCTACACCTCAGGAGCTTTTCTTTTTTTTTTTTTTTTTTGAGATAGGGTCTTGCTCTGTCACTCAGGCTGGAGCACAGTGGTGTGATCACAGCTCACTGCAGCCTCCATCTCCTGGCCTCAAGTGATCTTCCCACCTCAGCCTCCTAAGTGGCTGGGACTATAGGTGTGCACCACCATGCCTGGCTAATTTTTTGTATTTTTTTGTAGAGACGAGGTTTCATCATGTTACCCAGGCTGGTCTTGAACTCCTGGGCTCAGGTGATCTGCCTGCCTTGGCCTCTTTGAGAGTGCTGGGATTGCAGGTGTGAGCCACCAAGCCTGGTCAGGAGCTTATTTTCAAAAGCCAAGGAATAC	ACGCGGGTGCCGGGCGGGGGTGTGGAATCAACCCACAGCTGCACAGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAAGCAACTGGAAGACGGCAGCAAAGAAACAAACATGCGTAAGCACCTCCTGCAACCCACTAGCGAGCTAGAGAGAGTTGGCGTCTACACCTCAGGAGCTTTTCTTTTTTTTTTTTTTTTTTGAGATAGGGTCTTGCTCTGTCACTCAGGCTGGAGCACAGTGGTGTGATCACAGCTCACTGCAGCCTCCATCTCCTGGCCTCAAGTGATCTTCCCACCTCAGCCTCCTAAGTGGCTGGGACTATAGGTGTGCACCACCATGCCTGGCTAATTTTTTGTATTTTTTTGTAGAGACGAGGTTTCATCATGTTACCCAGGCTGGTCTTGAACTCCTGGGCTCAGGTGATCTGCCTGCCTTGGCCTCTTTGAGAGTGCTGGGATTGCAGGTGTGAGCCACCAAGCCTGGTCAGGAGCTTATTTTCAAAAGCCAAGGAATAC	-	novel	NA	P-0034307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	291	1024	0	ENST00000269305.4:c.375+267_470del		p.X125_splice	ENST00000269305	NM_001126112.2	125		5/11	0.612581998959295	2	FACETS	0.806	0.767	0.845	0.806	0.767	0.845	CLONAL	2	TRUE	0	0.649429718141744	2		1024	556	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55478801	55478801	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	518	628	0	ENST00000284073.2:c.374A>G	p.Asp125Gly	p.D125G	ENST00000284073	NM_138962.2	125	gAt/gGt	6/14	0.641212042141038	3	FACETS	0.996	0.969	1	0.996	0.969	1	CLONAL	3	TRUE	0	0.649429718141744	3		628	707	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602878	10602878	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	284	1143	0	ENST00000171111.5:c.700C>G	p.Arg234Gly	p.R234G	ENST00000171111	NM_203500.1	234	Cgg/Ggg	3/6	0.649429718141744	2	FACETS	0.953	0.898	1	0.476	0.449	0.505	CLONAL	1	TRUE	0	0.649429718141744	2		1143	918	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155197	55155197	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	314	706	0	ENST00000257290.5:c.2796C>A	p.Cys932Ter	p.C932*	ENST00000257290	NM_006206.4	932	tgC/tgA	21/23	0.544193087987137	3	FACETS	0.988	0.941	1	0.988	0.941	1	CLONAL	2	TRUE	1	0.649429718141744	3		706	648	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652306	36652307	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0034307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	193	625	0	ENST00000244741.5:c.428_429delinsTT	p.Arg143Leu	p.R143L	ENST00000244741	NM_000389.4	143	cGG/cTT	2/3	0.513853543131777	4	FACETS	0.784	0.729	0.841	0.784	0.729	0.841	SUBCLONAL	2	TRUE	2	0.649429718141744	4		625	625	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141567295	141567295	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1876	175	715	1	ENST00000220592.5:c.919A>C	p.Thr307Pro	p.T307P	ENST00000220592	NM_012154.3	307	Acg/Ccg	8/19	0.649429718141744	11	FACETS	1	0.94	1	0.115	0.105	0.125	CLONAL	1	TRUE	2	0.649429718141744	11		716	2051	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022403	31022425	+	frameshift_variant	Frame_Shift_Del	DEL	CACCACTGCCATAGAGAGGCGGC	CACCACTGCCATAGAGAGGCGGC	-	rs766433101	NA	P-0034335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	36	334	0	ENST00000375687.4:c.1900_1922del	p.Glu635ArgfsTer15	p.E635Rfs*15	ENST00000375687	NM_015338.5	630	CACCACTGCCATAGAGAGGCGGCc/c	13/13	1	2	FACETS	0.785	0.646	0.94	1	0.953	1	CLONAL	2	FALSE	1	0.126705554365317	2		334	362	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964925	55964925	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	41	438	0	ENST00000263923.4:c.2312C>G	p.Thr771Arg	p.T771R	ENST00000263923	NM_002253.2	771	aCg/aGg	16/30	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	FALSE	1	0.126705554365317	2		438	595	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0034351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	150	583	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.368869846187577	2		583	595	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939051	48939068	+	inframe_deletion	In_Frame_Del	DEL	AATTTTATACCTTTTATG	AATTTTATACCTTTTATG	-	novel	NA	P-0034351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	26	429	0	ENST00000267163.4:c.887_904del	p.Phe296_Asn301del	p.F296_N301del	ENST00000267163	NM_000321.2	295	AATTTTATACCTTTTATG/-	9/27	0.368869846187577	1	FACETS	0.289	0.228	0.358	0.289	0.228	0.358	SUBCLONAL	1	TRUE	0	0.368869846187577	1		429	398	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599338	55599338	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	258	573	0	ENST00000288135.5:c.2464A>T	p.Asn822Tyr	p.N822Y	ENST00000288135	NM_000222.2	822	Aat/Tat	17/21	1	2	FACETS	0.967	0.913	1	0.967	0.913	1	CLONAL	1	TRUE	1	0.884821902291785	2		573	603	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0034355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	113	427	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.473	0.426	0.522	0.473	0.426	0.522	SUBCLONAL	1	TRUE	1	0.723458464419452	2		427	661	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	144	846	2	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.529328362546091	1	FACETS	0.515	0.473	0.559	0.515	0.473	0.559	SUBCLONAL	1	TRUE	0	0.723458464419452	1		848	493	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845261	151845261	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	94	506	0	ENST00000262189.6:c.13751G>A	p.Arg4584Gln	p.R4584Q	ENST00000262189	NM_170606.2	4584	cGg/cAg	52/59	1	2	FACETS	0.626	0.561	0.695	0.626	0.561	0.695	SUBCLONAL	1	TRUE	1	0.723458464419452	2		506	415	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0034357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	104	464	1	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.172293217709369	2	FACETS	0.794	0.714	0.878	0.794	0.714	0.878	SUBCLONAL	2	TRUE	0	0.265809381906387	2		465	493	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843595	156843595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139875058	NA	P-0034357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	95	826	1	ENST00000524377.1:c.1021G>A	p.Val341Met	p.V341M	ENST00000524377	NM_002529.3	341	Gtg/Atg	8/17	1	2	FACETS	0.785	0.697	0.878	0.785	0.697	0.878	SUBCLONAL	1	TRUE	1	0.265809381906387	2		827	911	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29422337	29422337	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	64	392	0	ENST00000356175.3:c.10C>T	p.His4Tyr	p.H4Y	ENST00000356175	NM_000267.3	4	Cac/Tac	1/57	1	2	FACETS	0.91	0.789	1	0.91	0.789	1	CLONAL	1	TRUE	1	0.265809381906387	2		392	529	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602679	10602679	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	124	805	0	ENST00000171111.5:c.899A>G	p.Tyr300Cys	p.Y300C	ENST00000171111	NM_203500.1	300	tAc/tGc	3/6	0.265809381906387	1	FACETS	0.892	0.806	0.982	0.892	0.806	0.982	CLONAL	1	TRUE	0	0.265809381906387	1		805	907	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101834	11101841	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGGTGG	GGAGGTGG	-	novel	NA	P-0034357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	80	666	0	ENST00000358026.2:c.1254_1261del	p.Gln418HisfsTer17	p.Q418Hfs*17	ENST00000358026	NM_001128849.1	418	caGGAGGTGGtg/catg	8/36	0.265809381906387	1	FACETS	0.718	0.632	0.811	0.718	0.632	0.811	SUBCLONAL	1	TRUE	0	0.265809381906387	1		666	727	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206678	27206678	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	82	479	0	ENST00000380036.4:c.2463G>C	p.Trp821Cys	p.W821C	ENST00000380036	NM_000459.3	821	tgG/tgC	15/23	0.172293217709369	2	FACETS	0.914	0.806	1	0.457	0.403	0.515	CLONAL	1	TRUE	0	0.265809381906387	2		479	675	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143994	11143994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	162	584	2	ENST00000358026.2:c.3575G>A	p.Arg1192His	p.R1192H	ENST00000358026	NM_001128849.1	1192	cGc/cAc	26/36	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.597049912163771	2		586	541	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346139	89346139	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	57	230	0	ENST00000301030.4:c.6811C>T	p.Pro2271Ser	p.P2271S	ENST00000301030	NM_001256183.1	2271	Cct/Tct	9/13	1	2	FACETS	0.964	0.84	1	0.964	0.84	1	CLONAL	1	TRUE	1	0.597049912163771	2		230	198	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0034373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	235	370	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.766263956935155	4	FACETS	0.974	0.917	1	0.974	0.917	1	CLONAL	2	TRUE	2	0.766263956935155	4		370	556	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0034373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	326	515	0	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	0.766263956935155	2	FACETS	0.999	0.966	1	0.999	0.966	1	CLONAL	2	TRUE	0	0.766263956935155	2		515	426	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045016	47045016	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0034373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	135	279	0	ENST00000377604.3:c.2342C>G	p.Ser781Ter	p.S781*	ENST00000377604	NM_001204468.1	781	tCa/tGa	20/24	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.766263956935155	1		279	188	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18576885	18576885	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	53	429	2	ENST00000266497.5:c.2293A>C	p.Lys765Gln	p.K765Q	ENST00000266497		765	Aag/Cag	16/31	0.492485210488317	4	FACETS	0.393	0.334	0.457			1	SUBCLONAL	1	TRUE	NA	0.766263956935155	4		431	622	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473618	67473618	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	503	485	0	ENST00000327367.4:c.698G>T	p.Cys233Phe	p.C233F	ENST00000327367	NM_005902.3	233	tGc/tTc	6/9	0.766263956935155	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	4	TRUE	0	0.766263956935155	4		485	560	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794449	42794449	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	377	683	0	ENST00000575354.2:c.1529T>A	p.Leu510Gln	p.L510Q	ENST00000575354	NM_015125.3	510	cTg/cAg	10/20	0.766263956935155	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.766263956935155	2		683	459	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670774	134670774	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	226	396	1	ENST00000398015.3:c.685G>T	p.Ala229Ser	p.A229S	ENST00000398015	NM_004441.4	229	Gca/Tca	3/16	NA	2	FACETS	0.764	0.725	0.803			1	INDETERMINATE	2	TRUE	NA	0.766263956935155	2		397	386	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880959	134880959	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	121	459	0	ENST00000398015.3:c.1522G>T	p.Ala508Ser	p.A508S	ENST00000398015	NM_004441.4	508	Gcc/Tcc	7/16	NA	2	FACETS	0.74	0.673	0.808			1	INDETERMINATE	1	TRUE	NA	0.766263956935155	2		459	427	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138431116	138431116	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	214	334	0	ENST00000289153.2:c.1333G>T	p.Val445Phe	p.V445F	ENST00000289153	NM_006219.2	445	Gtt/Ttt	8/22	0.766263956935155	3	FACETS	0.968	0.914	1	0.968	0.914	1	CLONAL	2	TRUE	1	0.766263956935155	3		334	399	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193827	106193827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	191	299	0	ENST00000380013.4:c.4289G>T	p.Gly1430Val	p.G1430V	ENST00000380013	NM_001127208.2	1430	gGg/gTg	10/11	0.766263956935155	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.766263956935155	3		299	328	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876931	151876931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	147	256	0	ENST00000262189.6:c.7430C>T	p.Pro2477Leu	p.P2477L	ENST00000262189	NM_170606.2	2477	cCt/cTt	37/59	0.741302396485509	4	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	2	0.766263956935155	4		256	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0034383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	194	635	2	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.536538368300464	2	FACETS	0.791	0.744	0.839	0.791	0.744	0.839	SUBCLONAL	2	TRUE	0	0.630186156624089	2		637	389	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204633	108204633	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	43	306	0	ENST00000278616.4:c.7948G>C	p.Asp2650His	p.D2650H	ENST00000278616	NM_000051.3	2650	Gac/Cac	54/63	0.52978755432069	5	FACETS	0.797	0.67	0.938	0.159	0.134	0.188	CLONAL	1	TRUE	0	0.630186156624089	5		306	333	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929025	44929025	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	162	506	0	ENST00000377967.4:c.2125C>T	p.Gln709Ter	p.Q709*	ENST00000377967	NM_021140.2	709	Caa/Taa	17/29	0.370392165232992	3	FACETS	0.827	0.767	0.887	0.827	0.767	0.887	INDETERMINATE	2	TRUE	1	0.630186156624089	3		506	409	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615730	100615730	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	69	626	0	ENST00000308731.7:c.602C>A	p.Pro201Gln	p.P201Q	ENST00000308731	NM_000061.2	201	cCa/cAa	8/19	0.500751299592476	1	FACETS	0.457	0.401	0.517	0.457	0.401	0.517	SUBCLONAL	1	TRUE	0	0.630186156624089	1		626	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	165	547	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.38239880435224	2		547	714	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151863	108151863	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs377349886	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	198	428	0	ENST00000278616.4:c.3544G>C	p.Glu1182Gln	p.E1182Q	ENST00000278616	NM_000051.3	1182	Gag/Cag	24/63	0.345318595499412	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.38239880435224	4		428	579	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443940	18443940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866374517	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	106	312	1	ENST00000266497.5:c.913C>T	p.Pro305Ser	p.P305S	ENST00000266497		305	Cca/Tca	3/31	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.38239880435224	2		313	372	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038130	128038130	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	143	438	0	ENST00000285398.2:c.1420G>C	p.Asp474His	p.D474H	ENST00000285398	NM_000122.1	474	Gat/Cat	9/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.38239880435224	2		438	626	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238339	98238339	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	132	370	0	ENST00000331920.6:c.1705G>T	p.Ala569Ser	p.A569S	ENST00000331920	NM_000264.3	569	Gct/Tct	12/24	0.38239880435224	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.38239880435224	1		370	516	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896455	28896455	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	45	320	0	ENST00000282397.4:c.2995C>A	p.Leu999Met	p.L999M	ENST00000282397	NM_002019.4	999	Ctg/Atg	22/30	0.221446368312219	1	FACETS	0.467	0.393	0.548	0.467	0.393	0.548	INDETERMINATE	1	TRUE	0	0.38239880435224	1		320	408	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11308028	11308028	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	72	531	0	ENST00000361445.4:c.964G>C	p.Val322Leu	p.V322L	ENST00000361445	NM_004958.3	322	Gta/Cta	7/58	1	2	FACETS	0.519	0.453	0.591	0.519	0.453	0.591	SUBCLONAL	1	TRUE	1	0.38239880435224	2		531	725	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097736	27097737	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	129	460	0	ENST00000324856.7:c.3329dup	p.Glu1111ArgfsTer12	p.E1111Rfs*12	ENST00000324856	NM_006015.4	1109	cgg/cGgg	12/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.38239880435224	2		460	615	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241855	72241855	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	92	253	0	ENST00000357731.5:c.535G>T	p.Ala179Ser	p.A179S	ENST00000357731	NM_173808.2	179	Gca/Tca	3/7	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.38239880435224	2		253	398	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054925	176054925	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	117	380	0	ENST00000367669.3:c.1128G>T	p.Met376Ile	p.M376I	ENST00000367669	NM_022457.5	376	atG/atT	10/20	0.153734442343295	4	FACETS	0.813	0.737	0.894	0.813	0.737	0.894	INDETERMINATE	2	TRUE	2	0.38239880435224	4		380	520	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70432660	70432660	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	154	396	0	ENST00000373644.4:c.4682G>T	p.Cys1561Phe	p.C1561F	ENST00000373644	NM_030625.2	1561	tGt/tTt	8/12	0.38239880435224	1	FACETS	0.777	0.719	0.837	1	0.99	1	SUBCLONAL	2	TRUE	0	0.38239880435224	1		396	419	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414299	32414299	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	129	383	0	ENST00000332351.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000332351	NM_024426.4	418	Gag/Aag	8/10	0.316241371602771	2	FACETS	1	0.982	1	0.66	0.602	0.721	CLONAL	1	TRUE	0	0.38239880435224	2		383	511	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948755	71948755	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	353	615	0	ENST00000298229.2:c.3467G>T	p.Arg1156Leu	p.R1156L	ENST00000298229	NM_001567.3	1156	cGg/cTg	26/28	0.345318595499412	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	2	0.38239880435224	4		615	1083	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163459	108163459	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	183	614	0	ENST00000278616.4:c.4550T>A	p.Leu1517His	p.L1517H	ENST00000278616	NM_000051.3	1517	cTt/cAt	30/63	0.345318595499412	4	FACETS	1	0.988	1	0.705	0.65	0.761	CLONAL	1	TRUE	2	0.38239880435224	4		614	939	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343561	118343561	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	238	386	0	ENST00000534358.1:c.1687C>G	p.Pro563Ala	p.P563A	ENST00000534358	NM_005933.3	563	Cca/Gca	3/36	0.345318595499412	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.38239880435224	4		386	767	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344660	118344660	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	236	404	0	ENST00000534358.1:c.2786A>T	p.Lys929Ile	p.K929I	ENST00000534358	NM_005933.3	929	aAa/aTa	3/36	0.345318595499412	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.38239880435224	4		404	734	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1022596	1022596	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1415589794	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	46	535	1	ENST00000358495.3:c.1218G>C	p.Lys406Asn	p.K406N	ENST00000358495	NM_134424.2	406	aaG/aaC	12/12	1	2	FACETS	0.308	0.258	0.363	0.308	0.258	0.363	SUBCLONAL	1	TRUE	1	0.38239880435224	2		536	781	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858895	57858895	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	205	496	0	ENST00000228682.2:c.391C>A	p.Pro131Thr	p.P131T	ENST00000228682	NM_005269.2	131	Cca/Aca	5/12	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.38239880435224	2		496	762	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861886	57861886	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	120	444	0	ENST00000228682.2:c.1187G>T	p.Arg396Leu	p.R396L	ENST00000228682	NM_005269.2	396	cGg/cTg	10/12	1	2	FACETS	0.928	0.84	1	0.928	0.84	1	CLONAL	1	TRUE	1	0.38239880435224	2		444	676	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218396	69218396	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1340897471	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	64	448	0	ENST00000462284.1:c.488C>G	p.Ser163Cys	p.S163C	ENST00000462284	NM_002392.5	163	tCt/tGt	7/11	1	2	FACETS	0.6	0.52	0.687	0.6	0.52	0.687	SUBCLONAL	1	TRUE	1	0.38239880435224	2		448	558	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562234	21562234	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	78	784	1	ENST00000382592.4:c.1685A>T	p.Lys562Met	p.K562M	ENST00000382592	NM_014572.2	562	aAg/aTg	4/8	0.221446368312219	1	FACETS	0.37	0.324	0.419	0.37	0.324	0.419	INDETERMINATE	1	TRUE	0	0.38239880435224	1		785	892	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423579	88423579	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	171	516	0	ENST00000360948.2:c.2256T>A	p.Asp752Glu	p.D752E	ENST00000360948	NM_001012338.2	752	gaT/gaA	18/19	0.38239880435224	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.38239880435224	1		516	637	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641506	23641506	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	102	634	1	ENST00000261584.4:c.1969G>T	p.Glu657Ter	p.E657*	ENST00000261584	NM_024675.3	657	Gag/Tag	5/13	0.221446368312219	1	FACETS	0.571	0.511	0.636	0.571	0.511	0.636	INDETERMINATE	1	TRUE	0	0.38239880435224	1		635	755	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660599	67660599	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	70	595	2	ENST00000264010.4:c.1499G>T	p.Cys500Phe	p.C500F	ENST00000264010	NM_006565.3	500	tGt/tTt	8/12	0.187211220800771	0	FACETS	0.377	0.329	0.43			1	INDETERMINATE	1	TRUE	0	0.38239880435224	0		597	599	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671698	67671698	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	71	524	0	ENST00000264010.4:c.2107G>T	p.Glu703Ter	p.E703*	ENST00000264010	NM_006565.3	703	Gag/Tag	12/12	0.187211220800771	0	FACETS	0.417	0.364	0.474			1	INDETERMINATE	1	TRUE	0	0.38239880435224	0		524	550	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972454	81972454	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	82	478	0	ENST00000359376.3:c.3247C>A	p.Pro1083Thr	p.P1083T	ENST00000359376	NM_002661.3	1083	Ccc/Acc	29/33	0.187211220800771	0	FACETS	0.512	0.453	0.576			1	INDETERMINATE	1	TRUE	0	0.38239880435224	0		478	517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577339	7578192	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTGAGTGGGAGCAGTAAGGAGATTCCCCGCCGGGGATGTGATGAGAGGTGGATGGGTAGTAGTATGGAAGAAATCGGTAAGAGGTGGGCCCAGGGGTCAGAGGCAAGCAGAGGCTGGGGCACAGCAGGCCAGTGTGCAGGGTGGCAAGTGGCTCCTGACCTGGAGTCTTCCAGTGTGATGATGGTGAGGATGGGCCTCCGGTTCATGCCGCCCATGCAGGAACTGTTACACATGTAGTTGTAGTGGATGGTGGTACAGTCAGAGCCAACCTAGGAGATAACACAGGCCCAAGATGAGGCCAGTGCGCCTTGGGGAGACCTGTGGCAAGCAGGGGAGGCCTTTTTTTTTTTTTTTTGAGATGGAATCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGTGATCTCAGCTCACTGCAAGCTCCACCGCCCAGGTTCACGCCATTCTCCTTCCTCAGCCTCCCGAGTAGCTGGGACTACAGGTGCCCAGCACCACGCCCGGCTAATTTTTTTTTGTATTTTTCAGTAGAGACGGGGTTTCACCGTTAGCCAGGATGGTCTCGATCTCCCAACCTCGTGATCCGCCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACTGCGCCCAGCCAAGCAGGGGAGGCCCTTAGCCTCTGTAAGCTTCAGTTTTTTCAACTGTGCAATAGTTAAACCCATTTACTTTGCACATCTCATGGGGTTATAGGGAGGTCAAATAAGCAGCAGGAGAAAGCCCCCCTACTGCTCACCTGGAGGGCCACTGACAACCACCCTTAACCCCTCCTCCCAGAGACCCCAGTTGCAAACCAGACCTCAGGCGGCTCATAG	ACTGAGTGGGAGCAGTAAGGAGATTCCCCGCCGGGGATGTGATGAGAGGTGGATGGGTAGTAGTATGGAAGAAATCGGTAAGAGGTGGGCCCAGGGGTCAGAGGCAAGCAGAGGCTGGGGCACAGCAGGCCAGTGTGCAGGGTGGCAAGTGGCTCCTGACCTGGAGTCTTCCAGTGTGATGATGGTGAGGATGGGCCTCCGGTTCATGCCGCCCATGCAGGAACTGTTACACATGTAGTTGTAGTGGATGGTGGTACAGTCAGAGCCAACCTAGGAGATAACACAGGCCCAAGATGAGGCCAGTGCGCCTTGGGGAGACCTGTGGCAAGCAGGGGAGGCCTTTTTTTTTTTTTTTTGAGATGGAATCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGTGATCTCAGCTCACTGCAAGCTCCACCGCCCAGGTTCACGCCATTCTCCTTCCTCAGCCTCCCGAGTAGCTGGGACTACAGGTGCCCAGCACCACGCCCGGCTAATTTTTTTTTGTATTTTTCAGTAGAGACGGGGTTTCACCGTTAGCCAGGATGGTCTCGATCTCCCAACCTCGTGATCCGCCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACTGCGCCCAGCCAAGCAGGGGAGGCCCTTAGCCTCTGTAAGCTTCAGTTTTTTCAACTGTGCAATAGTTAAACCCATTTACTTTGCACATCTCATGGGGTTATAGGGAGGTCAAATAAGCAGCAGGAGAAAGCCCCCCTACTGCTCACCTGGAGGGCCACTGACAACCACCCTTAACCCCTCCTCCCAGAGACCCCAGTTGCAAACCAGACCTCAGGCGGCTCATAG	-	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	90	146	0	ENST00000269305.4:c.657_782+160del		p.X219_splice	ENST00000269305	NM_001126112.2	219		6-7/11	1	2	FACETS	0.892	0.803	0.983	1	0.986	1	CLONAL	2	TRUE	1	0.38239880435224	2		146	264	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556167	29556167	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	21	99	1	ENST00000356175.3:c.2534G>T	p.Cys845Phe	p.C845F	ENST00000356175	NM_000267.3	845	tGt/tTt	21/57	1	2	FACETS	0.742	0.577	0.931	0.742	0.577	0.931	CLONAL	1	TRUE	1	0.38239880435224	2		100	148	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246107	41246107	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1397842308	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	128	623	0	ENST00000357654.3:c.1441C>G	p.Leu481Val	p.L481V	ENST00000357654	NM_007294.3	481	Cta/Gta	10/23	1	2	FACETS	0.867	0.786	0.952	0.867	0.786	0.952	CLONAL	1	TRUE	1	0.38239880435224	2		623	772	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41251895	41251895	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	84	408	0	ENST00000357654.3:c.444G>T	p.Gln148His	p.Q148H	ENST00000357654	NM_007294.3	148	caG/caT	7/23	1	2	FACETS	0.829	0.734	0.93	0.829	0.734	0.93	CLONAL	1	TRUE	1	0.38239880435224	2		408	530	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727845	78727845	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	67	611	0	ENST00000306801.3:c.690G>C	p.Gln230His	p.Q230H	ENST00000306801	NM_020761.2	230	caG/caC	6/34	1	2	FACETS	0.401	0.347	0.459	0.401	0.347	0.459	SUBCLONAL	1	TRUE	1	0.38239880435224	2		611	874	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584318	39584318	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	62	223	0	ENST00000262039.4:c.985-2A>T		p.X329_splice	ENST00000262039	NM_002647.2	329			0.38239880435224	1	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	0	0.38239880435224	1		223	256	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218439	1218439	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	159	525	0	ENST00000326873.7:c.314T>C	p.Leu105Ser	p.L105S	ENST00000326873	NM_000455.4	105	tTa/tCa	2/10	0.38239880435224	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.38239880435224	1		525	567	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599904	10599904	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	175	558	0	ENST00000171111.5:c.1672G>T	p.Gly558Trp	p.G558W	ENST00000171111	NM_203500.1	558	Ggg/Tgg	5/6	0.38239880435224	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.38239880435224	1		558	730	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741876	40741876	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	222	580	0	ENST00000392038.2:c.1096G>C	p.Glu366Gln	p.E366Q	ENST00000392038	NM_001626.4	366	Gag/Cag	11/14	0.153734442343295	4	FACETS	0.891	0.83	0.953	0.891	0.83	0.953	INDETERMINATE	2	TRUE	2	0.38239880435224	4		580	901	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753534	42753534	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	192	555	0	ENST00000222329.4:c.730C>A	p.Pro244Thr	p.P244T	ENST00000222329	NM_006494.2	244	Ccc/Acc	4/4	0.153734442343295	4	FACETS	1	0.989	1	0.702	0.649	0.757	INDETERMINATE	1	TRUE	2	0.38239880435224	4		555	989	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52705251	52705251	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	142	468	1	ENST00000322088.6:c.133G>A	p.Glu45Lys	p.E45K	ENST00000322088	NM_014225.5	45	Gaa/Aaa	2/15	0.153734442343295	4	FACETS	1	0.987	1	0.745	0.68	0.813	INDETERMINATE	1	TRUE	2	0.38239880435224	4		469	689	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967075	25967075	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	205	495	0	ENST00000435504.4:c.2131A>G	p.Arg711Gly	p.R711G	ENST00000435504		711	Aga/Gga	13/13	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.38239880435224	2		495	736	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719490	61719490	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	192	518	0	ENST00000401558.2:c.1693G>C	p.Val565Leu	p.V565L	ENST00000401558	NM_003400.3	565	Gta/Cta	15/25	1	2	FACETS	0.906	0.844	0.97	1	0.993	1	CLONAL	2	TRUE	1	0.38239880435224	2		518	554	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172074	99172074	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	179	482	0	ENST00000074304.5:c.1640A>T	p.Lys547Met	p.K547M	ENST00000074304	NM_001134224.1	547	aAg/aTg	17/26	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.38239880435224	2		482	651	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198272771	198272771	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	64	540	0	ENST00000335508.6:c.1190G>T	p.Arg397Leu	p.R397L	ENST00000335508	NM_012433.2	397	cGc/cTc	9/25	1	2	FACETS	0.536	0.463	0.614	0.536	0.463	0.614	SUBCLONAL	1	TRUE	1	0.38239880435224	2		540	625	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433518	138433518	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	153	392	0	ENST00000289153.2:c.1094G>T	p.Cys365Phe	p.C365F	ENST00000289153	NM_006219.2	365	tGt/tTt	7/22	0.153734442343295	4	FACETS	0.998	0.918	1	0.998	0.918	1	INDETERMINATE	2	TRUE	2	0.38239880435224	4		392	554	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215310	142215310	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	143	458	1	ENST00000350721.4:c.5791G>T	p.Ala1931Ser	p.A1931S	ENST00000350721	NM_001184.3	1931	Gct/Tct	34/47	0.153734442343295	4	FACETS	1	0.986	1	0.714	0.652	0.779	INDETERMINATE	1	TRUE	2	0.38239880435224	4		459	724	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157518	106157518	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	86	276	0	ENST00000380013.4:c.2419G>T	p.Glu807Ter	p.E807*	ENST00000380013	NM_001127208.2	807	Gag/Tag	3/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.38239880435224	2		276	369	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250840	153250840	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	44	373	0	ENST00000281708.4:c.1220C>G	p.Ser407Ter	p.S407*	ENST00000281708	NM_033632.3	407	tCa/tGa	8/12	0.362592489511721	1	FACETS	0.597	0.502	0.7	0.597	0.502	0.7	SUBCLONAL	1	TRUE	0	0.38239880435224	1		373	312	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876434	35876435	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	148	559	1	ENST00000303115.3:c.1226_1227delinsTT	p.Gly409Val	p.G409V	ENST00000303115	NM_002185.3	409	gGG/gTT	8/8	NA	2	FACETS	0.889	0.812	0.969			1	INDETERMINATE	1	TRUE	NA	0.38239880435224	2		560	871	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751153	57751153	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	55	342	0	ENST00000274289.3:c.1714C>A	p.Leu572Met	p.L572M	ENST00000274289	NM_006622.3	572	Ctg/Atg	12/14	0.38239880435224	1	FACETS	0.669	0.575	0.77	0.669	0.575	0.77	SUBCLONAL	1	TRUE	0	0.38239880435224	1		342	348	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79965947	79965947	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs570136307	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	112	497	0	ENST00000265081.6:c.611G>T	p.Gly204Val	p.G204V	ENST00000265081	NM_002439.4	204	gGa/gTa	4/24	0.38239880435224	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.38239880435224	1		497	437	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109415091	109415091	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	181	697	0	ENST00000436639.2:c.186G>T	p.Leu62Phe	p.L62F	ENST00000436639	NM_014454.2	62	ttG/ttT	1/10	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.38239880435224	2		697	762	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099508	157099508	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	50	230	0	ENST00000346085.5:c.445C>A	p.Gln149Lys	p.Q149K	ENST00000346085	NM_020732.3	149	Cag/Aag	1/20	0.371550497344985	2	FACETS	0.747	0.636	0.868	0.374	0.318	0.434	SUBCLONAL	1	TRUE	0	0.38239880435224	2		230	350	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2998134	2998134	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	136	685	2	ENST00000396946.4:c.7G>T	p.Gly3Ter	p.G3*	ENST00000396946	NM_032415.4	3	Gga/Tga	2/25	0.326090447911069	3	FACETS	0.785	0.712	0.861			1	SUBCLONAL	1	TRUE	NA	0.38239880435224	3		687	1080	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508374	106508374	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	144	249	0	ENST00000359195.3:c.368G>T	p.Arg123Leu	p.R123L	ENST00000359195	NM_002649.2	123	cGc/cTc	2/11	0.371550497344985	2	FACETS	0.991	0.915	1	0.991	0.915	1	CLONAL	2	TRUE	0	0.38239880435224	2		249	380	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74868221	74868221	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	69	225	0	ENST00000284811.8:c.73G>T	p.Asp25Tyr	p.D25Y	ENST00000284811		25	Gat/Tat	3/4	0.232767963302721	3	FACETS	1	0.973	1	0.724	0.636	0.817	CLONAL	1	TRUE	1	0.38239880435224	3		225	297	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404593	8404593	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	41	337	0	ENST00000356435.5:c.4154G>C	p.Arg1385Thr	p.R1385T	ENST00000356435		1385	aGa/aCa	25/35	0.38239880435224	1	FACETS	0.447	0.373	0.529	0.447	0.373	0.529	SUBCLONAL	1	TRUE	0	0.38239880435224	1		337	388	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500815	8500816	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	150	425	0	ENST00000356435.5:c.2066_2067delinsAA	p.Ala689Glu	p.A689E	ENST00000356435		689	gCC/gAA	13/35	0.38239880435224	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.38239880435224	1		425	582	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760186	133760186	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	123	467	0	ENST00000318560.5:c.2509G>T	p.Gly837Ter	p.G837*	ENST00000318560	NM_005157.4	837	Gga/Tga	11/11	0.38239880435224	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	0	0.38239880435224	1		467	520	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239959	53239959	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	159	303	0	ENST00000375401.3:c.1482C>G	p.Ile494Met	p.I494M	ENST00000375401	NM_004187.3	494	atC/atG	11/26	1	1	FACETS	0.795	0.736	0.855	1	0.991	1	SUBCLONAL	2	TRUE	0	0.38239880435224	1		303	423	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164773	106164773	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765414159	NA	P-0034441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	138	400	3	ENST00000380013.4:c.3641G>A	p.Arg1214Gln	p.R1214Q	ENST00000380013	NM_001127208.2	1214	cGg/cAg	6/11	1	2	FACETS	0.887	0.812	0.966	0.887	0.812	0.966	CLONAL	1	TRUE	1	0.57807939740161	2		403	538	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491645	56491645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	154	520	0	ENST00000267101.3:c.2537G>T	p.Ser846Ile	p.S846I	ENST00000267101	NM_001982.3	846	aGt/aTt	21/28	0.57807939740161	5	FACETS	0.826	0.754	0.902			1	CLONAL	1	TRUE	NA	0.57807939740161	5		520	1204	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220644	1220644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1167609100	NA	P-0034441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	238	827	1	ENST00000326873.7:c.662C>T	p.Pro221Leu	p.P221L	ENST00000326873	NM_000455.4	221	cCg/cTg	5/10	0.57807939740161	1	FACETS	0.938	0.882	0.995	0.938	0.882	0.995	CLONAL	1	TRUE	0	0.57807939740161	1		828	624	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135319	30135319	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	21	458	0	ENST00000331968.5:c.499C>G	p.Leu167Val	p.L167V	ENST00000331968	NM_002742.2	167	Ctg/Gtg	3/18	0.710144406614688	1	FACETS	0.105	0.08	0.133	0.105	0.08	0.133	SUBCLONAL	1	TRUE	0	0.710144406614688	1		458	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574026	7574026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	464	555	0	ENST00000269305.4:c.1001G>T	p.Gly334Val	p.G334V	ENST00000269305	NM_001126112.2	334	gGg/gTg	10/11	0.762373158890248	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.764630029474696	1		555	726	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484634	57484634	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	417	493	0	ENST00000371085.3:c.718G>T	p.Asp240Tyr	p.D240Y	ENST00000371085	NM_000516.4	240	Gat/Tat	9/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.764630029474696	2		493	1027	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0034479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	186	326	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.985	0.917	1	0.985	0.917	1	CLONAL	1	TRUE	1	0.728965518778636	2		326	518	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888165	112888165	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397507510	NA	P-0121577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	299	664	0	ENST00000351677.2:c.181G>T	p.Asp61Tyr	p.D61Y	ENST00000351677	NM_002834.3	61	Gat/Tat	3/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	NA	1	0.659876396177402	2		664	846	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206648	108206648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881321	NA	P-0121577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	188	372	1	ENST00000278616.4:c.8228C>T	p.Thr2743Met	p.T2743M	ENST00000278616	NM_000051.3	2743	aCg/aTg	56/63	0.393226585416702	1	FACETS	0.807	0.753	0.862	0.807	0.753	0.862	INDETERMINATE	1	NA	0	0.659876396177402	1		373	473	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647142	2647142	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0121577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	203	481	0	ENST00000342085.4:c.1420C>G	p.Arg474Gly	p.R474G	ENST00000342085	NM_002613.4	474	Cga/Gga	13/14	1	2	FACETS	0.944	0.879	1	0.944	0.879	1	CLONAL	1	NA	1	0.659876396177402	2		481	652	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0034494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	357	711	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	1	2	FACETS	0.999	0.95	1	0.999	0.95	1	CLONAL	1	TRUE	1	0.780888018946629	2		711	915	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578224	7578224	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1429743956	NA	P-0034494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	355	559	0	ENST00000269305.4:c.625A>T	p.Arg209Ter	p.R209*	ENST00000269305	NM_001126112.2	209	Aga/Tga	6/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.780888018946629	2		559	881	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639279	3639290	+	inframe_deletion	In_Frame_Del	DEL	GGCTGCTGGTGC	GGCTGCTGGTGC	-	novel	NA	P-0034494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	349	694	0	ENST00000294008.3:c.4349_4360del	p.Ser1450_Pro1454delinsThr	p.S1450_P1454delinsT	ENST00000294008	NM_032444.2	1450	aGCACCAGCAGCCcc/acc	12/15	1	2	FACETS	0.941	0.894	0.989	0.941	0.894	0.989	CLONAL	1	TRUE	1	0.780888018946629	2		694	950	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180314	32180314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760538818	NA	P-0034494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	120	560	1	ENST00000375023.3:c.2617G>A	p.Gly873Arg	p.G873R	ENST00000375023	NM_004557.3	873	Gga/Aga	17/30	0.780888018946629	1	FACETS	0.399	0.363	0.438	0.399	0.363	0.438	SUBCLONAL	1	TRUE	0	0.780888018946629	1		561	469	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735457	40735457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775419119	NA	P-0034495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	66	669	0	ENST00000373198.4:c.3416G>A	p.Arg1139Gln	p.R1139Q	ENST00000373198	NM_133170.3	1139	cGg/cAg	25/32	1	2	FACETS	0.418	0.361	0.479	0.418	0.361	0.479	SUBCLONAL	1	TRUE	1	0.338471128485963	2		669	934	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028646	12028646	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	103	371	0	ENST00000353533.5:c.849del	p.Tyr284MetfsTer34	p.Y284Mfs*34	ENST00000353533	NM_003010.3	283	ggA/gg	8/11	0.338471128485963	1	FACETS	0.999	0.898	1	0.999	0.898	1	CLONAL	1	TRUE	0	0.338471128485963	1		371	506	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061249	38061249	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	287	522	1	ENST00000250448.2:c.740A>G	p.His247Arg	p.H247R	ENST00000250448	NM_004496.3	247	cAc/cGc	2/2	1	2	FACETS	0.986	0.935	1	0.986	0.935	1	CLONAL	1	TRUE	1	0.9214381254815	2		523	632	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163749	152163760	+	protein_altering_variant	In_Frame_Del	DEL	GACGCCAGGGTG	GACGCCAGGGTG	CAC	novel	NA	P-0034496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	174	417	1	ENST00000206249.3:c.470_481delinsCAC	p.Arg157_Gly161delinsProArg	p.R157_G161delinsPR	ENST00000206249	NM_000125.3	157	cGACGCCAGGGTGgc/cCACgc	2/8	0.9214381254815	1	FACETS	0.909	0.869	0.947	0.909	0.869	0.947	CLONAL	1	TRUE	0	0.9214381254815	1		418	224	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	215	417	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.358630470438732	2	FACETS	0.999	0.935	1	0.999	0.935	1	CLONAL	2	TRUE	0	0.358630470438732	2		417	600	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0034497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	524	478	5	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.358630470438732	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	TRUE	0	0.358630470438732	3		483	1140	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432923	432925	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs1221939206	NA	P-0034497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	102	470	0	ENST00000399788.2:c.1991_1993del	p.Glu664del	p.E664del	ENST00000399788	NM_001042603.1	664	gAAGtg/gtg	15/28	0.358630470438732	2	FACETS	0.874	0.782	0.971	0.437	0.391	0.486	CLONAL	1	TRUE	0	0.358630470438732	2		470	651	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911155	29911155	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs45482492	NA	P-0034498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	103	488	0	ENST00000376809.5:c.454G>T	p.Glu152Ter	p.E152*	ENST00000376809	NM_002116.7	152	Gag/Tag	3/8	0.340897813645844	2	FACETS	1	0.976	1	0.643	0.578	0.71	CLONAL	1	TRUE	0	0.343947790293011	2		488	466	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665043	29665043	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	218	468	0	ENST00000356175.3:c.6642del	p.Arg2214SerfsTer30	p.R2214Sfs*30	ENST00000356175	NM_000267.3	2214	agA/ag	44/57	0.343947790293011	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.343947790293011	3		468	683	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911284	29911285	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0034498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	20	271	0	ENST00000376809.5:c.584dup	p.Tyr195Ter	p.Y195*	ENST00000376809	NM_002116.7	195	tac/tAac	3/8	0.340897813645844	2	FACETS	0.375	0.287	0.479	0.188	0.143	0.24	SUBCLONAL	1	TRUE	0	0.343947790293011	2		271	310	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776371	76776372	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0034498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	215	544	0	ENST00000373344.5:c.7094_7095del	p.Ser2365Ter	p.S2365*	ENST00000373344	NM_000489.3	2365	tCA/t	34/35	0.263831079833778	5	FACETS	1	0.981	1	0.759	0.707	0.813	CLONAL	2	TRUE	2	0.343947790293011	5		544	832	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0034502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	95	513	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.467813863922991	3	FACETS	1	0.958	1	0.569	0.51	0.632	CLONAL	1	TRUE	1	0.467813863922991	3		513	440	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519988	NA	P-0034502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	92	724	0	ENST00000269305.4:c.808T>G	p.Phe270Val	p.F270V	ENST00000269305	NM_001126112.2	270	Ttt/Gtt	8/11	1	2	FACETS	0.658	0.585	0.735	0.658	0.585	0.735	SUBCLONAL	1	TRUE	1	0.467813863922991	2		724	598	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692792	89692792	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	43	416	0	ENST00000371953.3:c.277del	p.His93IlefsTer6	p.H93Ifs*6	ENST00000371953	NM_000314.4	92	gaC/ga	5/9	1	2	FACETS	0.479	0.401	0.564	0.479	0.401	0.564	SUBCLONAL	1	TRUE	1	0.467813863922991	2		416	384	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0034512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	235	652	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.114662430514581	3	FACETS	0.849	0.797	0.902	0.849	0.797	0.902	INDETERMINATE	3	TRUE	0	0.34	3		652	635	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0034517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	124	573	0	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	0.268855525958592	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	0	0.340775209216005	3		573	253	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724360	52724360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	53	453	1	ENST00000322088.6:c.1492C>T	p.Arg498Cys	p.R498C	ENST00000322088	NM_014225.5	498	Cgc/Tgc	12/15	NA	2	FACETS	1	0.927	1			1	INDETERMINATE	1	TRUE	NA	0.340775209216005	2		454	276	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155322	185155322	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779365471	NA	P-0034518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	121	393	0	ENST00000265026.3:c.563G>A	p.Arg188Gln	p.R188Q	ENST00000265026	NM_004721.4	188	cGg/cAg	3/14	0.51945189998225	5	FACETS	1	0.954	1			1	CLONAL	1	TRUE	NA	0.586710466406673	5		393	711	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131976443	131976443	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	435	512	0	ENST00000265335.6:c.3698C>T	p.Pro1233Leu	p.P1233L	ENST00000265335		1233	cCa/cTa	24/25	0.586710466406673	3	FACETS	0.973	0.94	1	0.973	0.94	1	CLONAL	3	TRUE	0	0.586710466406673	3		512	657	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404194	139404194	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	128	562	0	ENST00000277541.6:c.2960G>T	p.Cys987Phe	p.C987F	ENST00000277541	NM_017617.3	987	tGc/tTc	18/34	0.586710466406673	5	FACETS	0.68	0.614	0.749	0.17	0.153	0.188	SUBCLONAL	1	TRUE	1	0.586710466406673	5		562	1207	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	39	236	0				ENST00000310581	NM_198253.2	-/1132			0.0566898008899772	3	FACETS	0.799	0.669	0.94	0.799	0.669	0.94	INDETERMINATE	2	TRUE	1	0.273349246357904	3		236	203	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0034519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	318	467	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.27108699491772	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	3	TRUE	0	0.273349246357904	3		468	865	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0034538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	10	516	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.221665175563796	1	FACETS	0.074	0.049	0.105	0.074	0.049	0.105	INDETERMINATE	1	TRUE	0	0.432616056703887	1		516	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203436	NA	P-0034538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	173	493	0	ENST00000269305.4:c.487T>C	p.Tyr163His	p.Y163H	ENST00000269305	NM_001126112.2	163	Tac/Cac	5/11	0.390824919414271	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.432616056703887	1		493	620	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0034541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	111	383	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.566667779912937	3	FACETS	0.854	0.769	0.942	0.427	0.384	0.471	CLONAL	1	TRUE	1	0.566667779912937	3		383	589	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405103	70405103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199844508	NA	P-0034541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	150	462	0	ENST00000373644.4:c.2617G>A	p.Val873Ile	p.V873I	ENST00000373644	NM_030625.2	873	Gtt/Att	4/12	1	2	FACETS	0.98	0.901	1	0.98	0.901	1	CLONAL	1	TRUE	1	0.566667779912937	2		462	540	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061240	38061240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	177	506	0	ENST00000250448.2:c.749C>T	p.Ser250Phe	p.S250F	ENST00000250448	NM_004496.3	250	tCc/tTc	2/2	0.566667779912937	3	FACETS	0.967	0.892	1			1	CLONAL	1	TRUE	NA	0.566667779912937	3		506	829	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092809	27092809	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	317	512	0	ENST00000324856.7:c.2830C>T	p.Gln944Ter	p.Q944*	ENST00000324856	NM_006015.4	944	Cag/Tag	9/20	0.566667779912937	3	FACETS	0.952	0.904	1	0.952	0.904	1	CLONAL	2	TRUE	1	0.566667779912937	3		512	754	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061191	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	138	359	0	ENST00000250448.2:c.798C>G	p.Phe266Leu	p.F266L	ENST00000250448	NM_004496.3	266	ttC/ttG	2/2	0.566667779912937	3	FACETS	1	0.967	1			1	CLONAL	1	TRUE	NA	0.566667779912937	3		359	561	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239420	105239420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	310	465	0	ENST00000349310.3:c.967G>A	p.Asp323Asn	p.D323N	ENST00000349310	NM_001014432.1	323	Gac/Aac	12/15	0.566667779912937	3	FACETS	0.993	0.943	1	0.662	0.628	0.696	CLONAL	2	TRUE	0	0.566667779912937	3		465	707	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178143	56178143	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0034541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	202	309	0	ENST00000399503.3:c.3116C>G	p.Ser1039Ter	p.S1039*	ENST00000399503	NM_005921.1	1039	tCa/tGa	14/20	0.566667779912937	3	FACETS	0.988	0.926	1	0.988	0.926	1	CLONAL	2	TRUE	1	0.566667779912937	3		309	463	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11314000	11314000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	349	562	0	ENST00000361445.4:c.736G>A	p.Asp246Asn	p.D246N	ENST00000361445	NM_004958.3	246	Gat/Aat	6/58	0.566667779912937	3	FACETS	0.97	0.923	1	0.97	0.923	1	CLONAL	2	TRUE	1	0.566667779912937	3		562	815	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999768	100999768	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	184	524	0	ENST00000325455.5:c.34C>T	p.Pro12Ser	p.P12S	ENST00000325455	NM_001202474.3	12	Ccc/Tcc	1/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.566667779912937	2		524	587	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620105	21620105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	136	558	0	ENST00000382592.4:c.61G>A	p.Glu21Lys	p.E21K	ENST00000382592	NM_014572.2	21	Gag/Aag	2/8	1	2	FACETS	0.86	0.786	0.938	0.86	0.786	0.938	CLONAL	1	TRUE	1	0.566667779912937	2		558	558	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292865	91292865	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	135	519	0	ENST00000355112.3:c.367C>G	p.Gln123Glu	p.Q123E	ENST00000355112	NM_000057.2	123	Caa/Gaa	3/22	1	2	FACETS	0.918	0.839	1	0.918	0.839	1	CLONAL	1	TRUE	1	0.566667779912937	2		519	519	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217638	7217638	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	173	511	0	ENST00000380728.2:c.289G>T	p.Glu97Ter	p.E97*	ENST00000380728		97	Gaa/Taa	4/11	0.548856058229059	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.566667779912937	1		511	402	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217855	7217858	+	frameshift_variant	Frame_Shift_Del	DEL	CTTC	CTTC	-	novel	NA	P-0034541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	182	587	0	ENST00000380728.2:c.153_156del	p.Lys53ArgfsTer9	p.K53Rfs*9	ENST00000380728		51	agGAAG/ag	3/11	0.548856058229059	1	FACETS	0.923	0.859	0.988	0.923	0.859	0.988	CLONAL	1	TRUE	0	0.566667779912937	1		587	499	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667516	29667530	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTGCCAGGACTCGCC	TTGCCAGGACTCGCC	-	novel	NA	P-0034541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	150	389	0	ENST00000356175.3:c.6859-6_6867del		p.X2287_splice	ENST00000356175	NM_000267.3	2287		46/57	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.566667779912937	2		389	493	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5207935	5207935	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	134	522	0	ENST00000357368.4:c.5776G>T	p.Glu1926Ter	p.E1926*	ENST00000357368	NM_002850.3	1926	Gag/Tag	37/38	1	2	FACETS	0.926	0.846	1	0.926	0.846	1	CLONAL	1	TRUE	1	0.566667779912937	2		522	511	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098742	178098742	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	163	513	0	ENST00000397062.3:c.303C>G	p.Asn101Lys	p.N101K	ENST00000397062	NM_006164.4	101	aaC/aaG	2/5	1	2	FACETS	0.977	0.901	1	0.977	0.901	1	CLONAL	1	TRUE	1	0.566667779912937	2		513	589	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0034543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	191	551	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.557101109567286	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.557101109567286	1		551	446	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342597	70342597	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	99	592	0	ENST00000374080.3:c.1358T>C	p.Ile453Thr	p.I453T	ENST00000374080		453	aTt/aCt	10/45	0.454176135491275	1	FACETS	0.502	0.449	0.557	0.502	0.449	0.557	SUBCLONAL	1	TRUE	0	0.557101109567286	1		592	511	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106072	27106072	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	103	407	0	ENST00000324856.7:c.5683G>T	p.Glu1895Ter	p.E1895*	ENST00000324856	NM_006015.4	1895	Gag/Tag	20/20	0.2484664916547	2	FACETS	1	0.949	1	0.547	0.491	0.607	CLONAL	1	TRUE	0	0.325788274573029	2		407	578	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333873	70333873	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	57	259	1	ENST00000373644.4:c.1778T>C	p.Val593Ala	p.V593A	ENST00000373644	NM_030625.2	593	gTc/gCc	2/12	0.225859450863687	3	FACETS	0.822	0.706	0.948	0.411	0.353	0.474	CLONAL	1	TRUE	1	0.325788274573029	3		260	495	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374618	118374619	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0034557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	102	329	0	ENST00000534358.1:c.8013dup	p.Asp2672ArgfsTer2	p.D2672Rfs*2	ENST00000534358	NM_005933.3	2671	gcc/gCcc	27/36	0.166781078287072	3	FACETS	0.77	0.692	0.852			1	INDETERMINATE	2	TRUE	NA	0.325788274573029	3		329	473	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281165	49281165	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	180	592	1	ENST00000282018.3:c.212C>G	p.Thr71Arg	p.T71R	ENST00000282018	NM_020377.2	71	aCa/aGa	1/1	0.225859450863687	3	FACETS	1	0.975	1	0.57	0.524	0.617	CLONAL	1	TRUE	1	0.325788274573029	3		593	1128	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449624	187449624	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	70	359	0	ENST00000232014.4:c.256C>T	p.Leu86Phe	p.L86F	ENST00000232014	NM_001130845.1	86	Ctc/Ttc	4/10	1	2	FACETS	0.666	0.581	0.759	0.666	0.581	0.759	SUBCLONAL	1	TRUE	1	0.325788274573029	2		359	645	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133737085	133738107	+	intron_variant	Intron	DEL	CTGAATGCCTAGTCATGATTTTAAGTCTTCTTTCCACCTTCAGTGATGGTTGGCTACCCTGAGCAAGCCAGTAGATTCAGTTATGTGCCTGGAGTCCAGATGTTTTATGTGGATTTTTCATGTGGAATTGTTTTTGGTAAGGAAGTATTCCCTTGCCACACCAATGAAAAGAGAAGAAAACAGGTAGCTGGCACCCACTGCATTGTTGCTTTCTGCCAGCCTGCTCCTTCTCCTTCCTCTCCAGCTCTGTTGTGTCCAGATGCAAACTCTACATGCAGGGTTTGACCCTAGGTCCTCACCTGCTGTAGCTCTCACACGGGGACCGAATGCTCTTGTGTCGTAAATCCTTCCTTTTGCTTCCTCGTGTTGGATGTGTTTAGTGGTTTTCATCTTCTGGTCACTATTTCATTCTAGGTTTATCCCCTTTAAATTATAAATTAAATGAATTCTTCGCTTTTCCTACCAGCAACTACCCACCAAGTTCTACCATGTGTTAATTTAATCAACAGTTATTTATTGAGTACTTATTACATGTTGATTTCCTGTTCTCAACATTGGAATGAAGACAGCTTAGGGTTCTGCTTTCATGAAGCTTGCATGCTCTTAGGTGGAGACAGACAGTAATTAAGCAGATAAACAGGAAATTATGAGCTAGTAGTGGGTCCATTGCTGAGAAGTAAGACAGGTGGTAGGATGACCCGTGCCGTGTGATGACTTTAGATTGGGTGGTTGGGGAAGACTTCACGGACCTTAAAACTGGCCTTGGAACGGGAAGCGAGAACTGGGCACGGAAGATGAGGGAGTGGGAGATTTCAGGCAGAGGGAGCAGCAGCAGGTACAGAGGCCCTGAGGCCTTTTATTGTGTCTTTTTGCTTGAGCGAGTAACTTAGAGCACACGTAGAGAAAGACAGCAGAAGTGATCTTCTAAACACTCTGTCCTGTGTGGAGAGCTCCTTATGTGAGATTTTGCTGTGTAGTGAATTAAGGCTCAGCCAAACTGGCTCACGTGAGCTCTTTGAGCTT	CTGAATGCCTAGTCATGATTTTAAGTCTTCTTTCCACCTTCAGTGATGGTTGGCTACCCTGAGCAAGCCAGTAGATTCAGTTATGTGCCTGGAGTCCAGATGTTTTATGTGGATTTTTCATGTGGAATTGTTTTTGGTAAGGAAGTATTCCCTTGCCACACCAATGAAAAGAGAAGAAAACAGGTAGCTGGCACCCACTGCATTGTTGCTTTCTGCCAGCCTGCTCCTTCTCCTTCCTCTCCAGCTCTGTTGTGTCCAGATGCAAACTCTACATGCAGGGTTTGACCCTAGGTCCTCACCTGCTGTAGCTCTCACACGGGGACCGAATGCTCTTGTGTCGTAAATCCTTCCTTTTGCTTCCTCGTGTTGGATGTGTTTAGTGGTTTTCATCTTCTGGTCACTATTTCATTCTAGGTTTATCCCCTTTAAATTATAAATTAAATGAATTCTTCGCTTTTCCTACCAGCAACTACCCACCAAGTTCTACCATGTGTTAATTTAATCAACAGTTATTTATTGAGTACTTATTACATGTTGATTTCCTGTTCTCAACATTGGAATGAAGACAGCTTAGGGTTCTGCTTTCATGAAGCTTGCATGCTCTTAGGTGGAGACAGACAGTAATTAAGCAGATAAACAGGAAATTATGAGCTAGTAGTGGGTCCATTGCTGAGAAGTAAGACAGGTGGTAGGATGACCCGTGCCGTGTGATGACTTTAGATTGGGTGGTTGGGGAAGACTTCACGGACCTTAAAACTGGCCTTGGAACGGGAAGCGAGAACTGGGCACGGAAGATGAGGGAGTGGGAGATTTCAGGCAGAGGGAGCAGCAGCAGGTACAGAGGCCCTGAGGCCTTTTATTGTGTCTTTTTGCTTGAGCGAGTAACTTAGAGCACACGTAGAGAAAGACAGCAGAAGTGATCTTCTAAACACTCTGTCCTGTGTGGAGAGCTCCTTATGTGAGATTTTGCTGTGTAGTGAATTAAGGCTCAGCCAAACTGGCTCACGTGAGCTCTTTGAGCTT	-	novel	NA	P-0034557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	0	23	0	0	ENST00000318560.5:c.550-1065_550-43del		p.*184*	ENST00000318560	NM_005157.4	-/1130			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	6	TRUE	1	0.325788274573029	2		0	23	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933945	39933945	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0034557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	159	322	0	ENST00000378444.4:c.654C>G	p.Tyr218Ter	p.Y218*	ENST00000378444	NM_001123385.1	218	taC/taG	4/15	0.166781078287072	2	FACETS	0.944	0.871	1			1	INDETERMINATE	2	TRUE	NA	0.325788274573029	2		322	517	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	171	417	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.190189961454371	2	FACETS	0.869	0.802	0.937	0.869	0.802	0.937	CLONAL	2	TRUE	0	0.31	2		417	635	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0034566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	194	467	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.212750104950664	2	FACETS	0.829	0.769	0.891	0.829	0.769	0.891	CLONAL	2	TRUE	0	0.31	2		468	755	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0034566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	86	331	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.212750104950664	2	FACETS	1	0.965	1	0.61	0.542	0.682	CLONAL	1	TRUE	0	0.31	2		331	455	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411735	63411735	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	132	354	0	ENST00000330258.3:c.1432G>T	p.Gly478Ter	p.G478*	ENST00000330258	NM_152424.3	478	Gga/Tga	2/2	0.103750053294174	2	FACETS	0.955	0.874	1			1	INDETERMINATE	2	TRUE	NA	0.31	2		354	446	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0034579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	302	347	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.660673156024463	4	FACETS	0.859	0.82	0.897	0.859	0.82	0.897	CLONAL	3	TRUE	1	0.818406213774548	4		347	521	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520177	9520177	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	280	464	0	ENST00000353224.5:c.2092C>T	p.Pro698Ser	p.P698S	ENST00000353224	NM_177990.2	698	Cca/Tca	10/10	0.497401541901199	3	FACETS	0.92	0.875	0.965	0.92	0.875	0.965	CLONAL	2	TRUE	1	0.818406213774548	3		464	524	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653842	89653842	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057518425	NA	P-0034579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	185	466	0	ENST00000371953.3:c.140G>A	p.Arg47Lys	p.R47K	ENST00000371953	NM_000314.4	47	aGg/aAg	2/9	0.818406213774548	1	FACETS	0.989	0.94	1	0.989	0.94	1	CLONAL	1	TRUE	0	0.818406213774548	1		466	270	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0034579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	103	213	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.871	0.791	0.954	0.871	0.791	0.954	CLONAL	1	TRUE	1	0.818406213774548	2		213	289	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037463	12037463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	179	468	2	ENST00000396373.4:c.1094C>T	p.Ser365Phe	p.S365F	ENST00000396373	NM_001987.4	365	tCc/tTc	6/8	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.818406213774548	NA		470	467	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562997	29562997	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782894	NA	P-0034579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	224	600	0	ENST00000356175.3:c.3932C>T	p.Ser1311Phe	p.S1311F	ENST00000356175	NM_000267.3	1311	tCc/tTc	29/57	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.818406213774548	2		600	517	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15379805	15379805	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0034579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	245	614	0	ENST00000263377.2:c.334A>T	p.Lys112Ter	p.K112*	ENST00000263377	NM_058243.2	112	Aag/Tag	3/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.818406213774548	2		614	570	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035124	37035124	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs63750216	NA	P-0034579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	189	403	0	ENST00000231790.2:c.86C>G	p.Ala29Gly	p.A29G	ENST00000231790	NM_000249.3	29	gCt/gGt	1/19	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.818406213774548	2		403	421	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979469	2979469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	253	684	1	ENST00000396946.4:c.778C>T	p.Arg260Trp	p.R260W	ENST00000396946	NM_032415.4	260	Cgg/Tgg	6/25	1	2	FACETS	0.968	0.912	1	0.968	0.912	1	CLONAL	1	TRUE	1	0.818406213774548	2		685	639	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403103	116403103	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0034579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	153	404	0	ENST00000397752.3:c.2365-1G>C		p.X789_splice	ENST00000397752	NM_000245.2	789			0.660673156024463	4	FACETS	0.963	0.883	1	0.321	0.294	0.349	CLONAL	1	TRUE	1	0.818406213774548	4		404	706	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15840867	15840867	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	43	184	0	ENST00000307771.7:c.951A>G	p.Ile317Met	p.I317M	ENST00000307771	NM_005089.3	317	atA/atG	11/11	1	1	FACETS	0.306	0.259	0.357	0.306	0.259	0.357	SUBCLONAL	1	TRUE	0	0.818406213774548	1		184	203	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348712	118348712	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	167	222	0	ENST00000534358.1:c.3365C>G	p.Ala1122Gly	p.A1122G	ENST00000534358	NM_005933.3	1122	gCt/gGt	5/36	1	2	FACETS	0.916	0.853	0.98	0.916	0.853	0.98	CLONAL	1	TRUE	1	0.942104694338137	2		222	387	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732996	30732997	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0034586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	215	308	0	ENST00000295754.5:c.1610_1611del	p.Arg537LeufsTer3	p.R537Lfs*3	ENST00000295754	NM_003242.5	537	CGc/c	7/7	0.942104694338137	1	FACETS	0.884	0.85	0.916	0.884	0.85	0.916	CLONAL	1	TRUE	0	0.942104694338137	1		308	273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0034587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	445	849	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.64945319839749	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.64945319839749	2		850	680	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0034587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	179	300	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.64945319839749	2		300	399	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971029	21971029	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519852	NA	P-0034587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	208	472	0	ENST00000304494.5:c.329G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tGg/tAg	2/3	0.64945319839749	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.64945319839749	1		472	365	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44948987	44948987	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs796568156	NA	P-0034587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	134	174	0	ENST00000377967.4:c.3549-1G>A		p.X1183_splice	ENST00000377967	NM_021140.2	1183			1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.64945319839749	1		174	224	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325881	65325881	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	136	294	0	ENST00000342505.4:c.1241G>T	p.Arg414Leu	p.R414L	ENST00000342505	NM_002227.2	414	cGg/cTg	9/25	1	2	FACETS	0.839	0.768	0.913	0.839	0.768	0.913	CLONAL	1	TRUE	1	0.64945319839749	2		294	499	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8246247	8246247	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	98	409	0	ENST00000335790.3:c.387C>G	p.Phe129Leu	p.F129L	ENST00000335790	NM_002315.2	129	ttC/ttG	4/4	1	2	FACETS	0.743	0.668	0.823	0.743	0.668	0.823	SUBCLONAL	1	TRUE	1	0.64945319839749	2		409	406	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18478033	18478033	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0034587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	116	306	1	ENST00000266497.5:c.1272+1G>T		p.X424_splice	ENST00000266497		424			0.157566546999674	5	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.64945319839749	5		307	535	SUCCESS
BLM	641	MSKCC	GRCh37	15	91333970	91333970	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs150475674	NA	P-0034587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	153	493	0	ENST00000355112.3:c.2915G>T	p.Gly972Val	p.G972V	ENST00000355112	NM_000057.2	972	gGt/gTt	15/22	1	2	FACETS	0.874	0.804	0.946	0.874	0.804	0.946	CLONAL	1	TRUE	1	0.64945319839749	2		493	539	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357037	89357037	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	125	411	0	ENST00000301030.4:c.597C>G	p.Phe199Leu	p.F199L	ENST00000301030	NM_001256183.1	199	ttC/ttG	6/13	1	2	FACETS	0.844	0.769	0.922	0.844	0.769	0.922	CLONAL	1	TRUE	1	0.64945319839749	2		411	456	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989741	15989741	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	121	273	0	ENST00000268712.3:c.3032C>T	p.Pro1011Leu	p.P1011L	ENST00000268712	NM_006311.3	1011	cCa/cTa	23/46	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.64945319839749	2		273	363	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568898	212568898	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	80	327	0	ENST00000342788.4:c.1220G>T	p.Trp407Leu	p.W407L	ENST00000342788	NM_005235.2	407	tGg/tTg	11/28	1	2	FACETS	0.795	0.706	0.887	0.795	0.706	0.887	SUBCLONAL	1	TRUE	1	0.64945319839749	2		327	310	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445055	89445055	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	83	379	0	ENST00000336596.2:c.1375G>C	p.Glu459Gln	p.E459Q	ENST00000336596	NM_005233.5	459	Gaa/Caa	6/17	0.643241489425706	1	FACETS	0.661	0.592	0.734	0.661	0.592	0.734	SUBCLONAL	1	TRUE	0	0.64945319839749	1		379	261	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505297	186505297	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	123	295	0	ENST00000323963.5:c.923A>G	p.Asp308Gly	p.D308G	ENST00000323963		308	gAc/gGc	9/11	0.64945319839749	4	FACETS	0.928	0.841	1	0.464	0.42	0.51	CLONAL	1	TRUE	2	0.64945319839749	4		295	673	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80074586	80074586	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs10067975	NA	P-0034587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	177	449	0	ENST00000265081.6:c.2366A>G	p.Tyr789Cys	p.Y789C	ENST00000265081	NM_002439.4	789	tAc/tGc	17/24	1	2	FACETS	0.881	0.815	0.948	0.881	0.815	0.948	CLONAL	1	TRUE	1	0.64945319839749	2		449	619	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80074600	80074600	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	190	464	0	ENST00000265081.6:c.2380C>G	p.Gln794Glu	p.Q794E	ENST00000265081	NM_002439.4	794	Cag/Gag	17/24	1	2	FACETS	0.927	0.861	0.995	0.927	0.861	0.995	CLONAL	1	TRUE	1	0.64945319839749	2		464	631	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839834	27839834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs549064212	NA	P-0034587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	135	459	0	ENST00000328488.2:c.260G>A	p.Ser87Asn	p.S87N	ENST00000328488	NM_003533.2	87	aGc/aAc	1/1	0.64945319839749	3	FACETS	0.89	0.811	0.972	0.445	0.405	0.486	CLONAL	1	TRUE	1	0.64945319839749	3		459	619	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982046	93982046	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	119	410	0	ENST00000369303.4:c.1419C>G	p.Ile473Met	p.I473M	ENST00000369303	NM_004440.3	473	atC/atG	6/17	1	2	FACETS	0.862	0.784	0.943	0.862	0.784	0.943	CLONAL	1	TRUE	1	0.64945319839749	2		410	425	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413133	139413134	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0034587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	554	744	0	ENST00000277541.6:c.1008dup	p.Asp337Ter	p.D337*	ENST00000277541	NM_017617.3	336	-/T	6/34	0.64945319839749	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.64945319839749	2		744	846	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942733	44942733	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	192	297	0	ENST00000377967.4:c.3313A>G	p.Lys1105Glu	p.K1105E	ENST00000377967	NM_021140.2	1105	Aaa/Gaa	23/29	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.64945319839749	1		297	334	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0034590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	142	427	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	0.528188534707303	2		427	388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0034590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	11	479	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.534271823781191	1	FACETS	0.087	0.06	0.122	0.087	0.06	0.122	SUBCLONAL	1	TRUE	0	0.528188534707303	1		479	351	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860398	42860398	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	27	503	0	ENST00000398585.3:c.479C>T	p.Ser160Leu	p.S160L	ENST00000398585	NM_001135099.1	160	tCa/tTa	5/14	1	2	FACETS	0.195	0.154	0.241	0.195	0.154	0.241	SUBCLONAL	1	TRUE	1	0.528188534707303	2		503	525	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861085	35861085	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	20	297	0	ENST00000303115.3:c.214G>A	p.Glu72Lys	p.E72K	ENST00000303115	NM_002185.3	72	Gaa/Aaa	2/8	1	2	FACETS	0.234	0.178	0.299	0.234	0.178	0.299	SUBCLONAL	1	TRUE	1	0.528188534707303	2		297	324	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224498	108224498	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	103	212	0	ENST00000278616.4:c.8677G>C	p.Ala2893Pro	p.A2893P	ENST00000278616	NM_000051.3	2893	Gct/Cct	60/63	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.540426637270465	2		212	324	SUCCESS
AR	367	MSKCC	GRCh37	X	66765173	66765173	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs746341152	NA	P-0034597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	15	216	1	ENST00000374690.3:c.185A>T	p.Gln62Leu	p.Q62L	ENST00000374690	NM_000044.3	62	cAg/cTg	1/8	NA	2	FACETS	0.207	0.151	0.275			1	INDETERMINATE	1	TRUE	NA	0.540426637270465	2		217	268	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508526	106508526	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	147	251	1	ENST00000359195.3:c.520G>T	p.Glu174Ter	p.E174*	ENST00000359195	NM_002649.2	174	Gag/Tag	2/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.540426637270465	2		252	378	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890135	76890135	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	225	477	0	ENST00000373344.5:c.4759G>T	p.Gly1587Cys	p.G1587C	ENST00000373344	NM_000489.3	1587	Ggt/Tgt	17/35	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.540426637270465	2		477	739	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574025	7574025	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	406	482	0	ENST00000269305.4:c.1002del	p.Arg335ValfsTer10	p.R335Vfs*10	ENST00000269305	NM_001126112.2	334	ggG/gg	10/11	0.540426637270465	1	FACETS	0.945	0.914	0.976	1	0.997	1	CLONAL	2	TRUE	0	0.540426637270465	1		482	580	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725039	162725039	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	277	431	0	ENST00000367921.3:c.511G>C	p.Asp171His	p.D171H	ENST00000367921	NM_006182.2	171	Gac/Cac	6/18	1	2	FACETS	0.791	0.748	0.834	1	0.995	1	SUBCLONAL	2	TRUE	1	0.540426637270465	2		431	648	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050375	176050375	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	157	287	0	ENST00000367669.3:c.1190C>A	p.Ser397Tyr	p.S397Y	ENST00000367669	NM_022457.5	397	tCc/tAc	11/20	1	2	FACETS	0.769	0.713	0.825	1	0.99	1	SUBCLONAL	2	TRUE	1	0.540426637270465	2		287	378	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919262	48919262	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0034597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	103	179	0	ENST00000267163.4:c.427A>T	p.Lys143Ter	p.K143*	ENST00000267163	NM_000321.2	143	Aaa/Taa	4/27	0.540426637270465	1	FACETS	0.927	0.865	0.986	1	0.99	1	CLONAL	2	TRUE	0	0.540426637270465	1		179	150	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032200	10032200	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	398	605	0	ENST00000330684.3:c.623C>A	p.Thr208Asn	p.T208N	ENST00000330684	NM_001134407.1	208	aCt/aAt	3/13	0.1480764251402	3	FACETS	0.983	0.938	1	0.983	0.938	1	INDETERMINATE	2	TRUE	1	0.540426637270465	3		605	952	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564834	41564834	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	351	564	0	ENST00000263253.7:c.4135C>A	p.Gln1379Lys	p.Q1379K	ENST00000263253	NM_001429.3	1379	Caa/Aaa	25/31	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.540426637270465	2		564	869	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102918	71102918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	158	209	0	ENST00000318789.4:c.289del	p.Val97CysfsTer5	p.V97Cfs*5	ENST00000318789	NM_032682.5	97	Gtg/tg	8/21	0.540426637270465	1	FACETS	0.889	0.839	0.937	1	0.993	1	CLONAL	2	TRUE	0	0.540426637270465	1		209	240	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73046189	73046189	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1224564140	NA	P-0034597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	258	304	0	ENST00000356692.5:c.1A>G	p.Met1?	p.M1?	ENST00000356692		1	Atg/Gtg	1/9	0.540426637270465	1	FACETS	0.987	0.948	1	1	0.996	1	CLONAL	2	TRUE	0	0.540426637270465	1		304	353	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629167	187629167	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	289	559	0	ENST00000441802.2:c.1815G>T	p.Gln605His	p.Q605H	ENST00000441802	NM_005245.3	605	caG/caT	2/27	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.540426637270465	2		559	715	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527854	157527854	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	276	391	0	ENST00000346085.5:c.5579A>T	p.Glu1860Val	p.E1860V	ENST00000346085	NM_020732.3	1860	gAa/gTa	20/20	1	2	FACETS	0.853	0.808	0.898	1	0.995	1	CLONAL	2	TRUE	1	0.540426637270465	2		391	599	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412874	116412874	+	intron_variant	Intron	SNP	A	A	T	novel	NA	P-0034597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	454	780	0	ENST00000397752.3:c.3028+831A>T		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.777	0.744	0.81	1	0.996	1	SUBCLONAL	2	TRUE	1	0.540426637270465	2		780	1081	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187237	38187237	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs777879948	NA	P-0034597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	559	716	1	ENST00000317025.8:c.1240A>G	p.Thr414Ala	p.T414A	ENST00000317025	NM_023034.1	414	Acc/Gcc	6/24	NA	2	FACETS	0.799	0.768	0.829			1	INDETERMINATE	2	TRUE	NA	0.540426637270465	2		717	1295	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983499	90983499	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	123	204	0	ENST00000265433.3:c.604G>C	p.Glu202Gln	p.E202Q	ENST00000265433	NM_002485.4	202	Gaa/Caa	6/16	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.540426637270465	2		204	327	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499652	8499652	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	231	392	0	ENST00000356435.5:c.2317G>T	p.Ala773Ser	p.A773S	ENST00000356435		773	Gca/Tca	14/35	1	2	FACETS	0.765	0.719	0.811	1	0.993	1	SUBCLONAL	2	TRUE	1	0.540426637270465	2		392	559	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649659	48649659	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1223699669	NA	P-0034597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	344	652	1	ENST00000376670.3:c.143C>A	p.Thr48Asn	p.T48N	ENST00000376670	NM_002049.3	48	aCt/aAt	2/6	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.540426637270465	2		653	1017	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341557	70341557	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1283598954	NA	P-0034597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	519	654	0	ENST00000374080.3:c.992C>T	p.Thr331Ile	p.T331I	ENST00000374080		331	aCc/aTc	7/45	1	2	FACETS	0.868	0.834	0.901	1	0.997	1	CLONAL	2	TRUE	1	0.540426637270465	2		654	1107	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191799	123191799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	151	317	0	ENST00000218089.9:c.1388C>A	p.Thr463Lys	p.T463K	ENST00000218089	NM_001042749.1	463	aCa/aAa	15/35	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.540426637270465	2		317	508	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196840	123196840	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	130	334	0	ENST00000218089.9:c.1727C>G	p.Ala576Gly	p.A576G	ENST00000218089	NM_001042749.1	576	gCa/gGa	18/35	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.540426637270465	2		334	417	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600326	10600326	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	50	643	0	ENST00000171111.5:c.1529C>T	p.Ala510Val	p.A510V	ENST00000171111	NM_203500.1	510	gCa/gTa	4/6	0.265536784302795	3	FACETS	0.514	0.435	0.602			1	SUBCLONAL	1	TRUE	NA	0.265536784302795	3		643	830	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971137	21971137	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	45	423	1	ENST00000304494.5:c.221A>G	p.Asp74Gly	p.D74G	ENST00000304494	NM_000077.4	74	gAc/gGc	2/3	0.265536784302795	5	FACETS	0.587	0.491	0.692	0.196	0.163	0.231	SUBCLONAL	1	TRUE	2	0.265536784302795	5		424	808	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578503	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	228	856	0	ENST00000269305.4:c.427del	p.Val143CysfsTer27	p.V143Cfs*27	ENST00000269305	NM_001126112.2	143	Gtg/tg	5/11	0.222686851261334	2	FACETS	0.799	0.744	0.855	0.799	0.744	0.855	SUBCLONAL	2	TRUE	0	0.265536784302795	2		856	1075	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437782	110437782	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	58	609	0	ENST00000375856.3:c.619C>G	p.Leu207Val	p.L207V	ENST00000375856	NM_003749.2	207	Ctg/Gtg	1/2	0.232069584461488	3	FACETS	0.537	0.46	0.621	0.179	0.153	0.207	SUBCLONAL	1	TRUE	0	0.265536784302795	3		609	922	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299049	15299049	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	57	567	0	ENST00000263388.2:c.1489T>C	p.Ser497Pro	p.S497P	ENST00000263388	NM_000435.2	497	Tcg/Ccg	9/33	0.202759897743596	4	FACETS	0.593	0.507	0.687	0.297	0.253	0.344	SUBCLONAL	1	TRUE	2	0.265536784302795	4		567	916	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845798	151845798	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	225	778	0	ENST00000262189.6:c.13214G>C	p.Cys4405Ser	p.C4405S	ENST00000262189	NM_170606.2	4405	tGt/tCt	52/59	0.265536784302795	4	FACETS	0.945	0.879	1	0.945	0.879	1	CLONAL	2	TRUE	2	0.265536784302795	4		778	1135	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411717	63411717	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	66	924	0	ENST00000330258.3:c.1450G>C	p.Gly484Arg	p.G484R	ENST00000330258	NM_152424.3	484	Ggt/Cgt	2/2	0.170037644047863	2	FACETS	0.523	0.452	0.599	0.261	0.226	0.3	SUBCLONAL	1	TRUE	0	0.265536784302795	2		924	951	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0034615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	102	326	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.999	0.899	1	0.999	0.899	1	CLONAL	1	TRUE	1	0.459807134188447	2		326	444	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0034621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	25	213	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.282	0.221	0.352	0.282	0.221	0.352	SUBCLONAL	1	TRUE	1	0.378367874368122	2		213	469	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230571	46230571	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	36	467	0	ENST00000334344.6:c.820C>T	p.Arg274Ter	p.R274*	ENST00000334344	NM_152641.2	274	Cga/Tga	8/21	1	2	FACETS	0.408	0.335	0.49	0.408	0.335	0.49	SUBCLONAL	1	TRUE	1	0.378367874368122	2		467	466	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724328	117724328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	59	477	0	ENST00000368508.3:c.551C>T	p.Pro184Leu	p.P184L	ENST00000368508	NM_002944.2	184	cCc/cTc	6/43	1	2	FACETS	0.397	0.34	0.458	0.397	0.34	0.458	SUBCLONAL	1	TRUE	1	0.378367874368122	2		477	786	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99179952	99179952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1394330959	NA	P-0034621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	62	647	0	ENST00000074304.5:c.1895C>T	p.Pro632Leu	p.P632L	ENST00000074304	NM_001134224.1	632	cCg/cTg	19/26	1	2	FACETS	0.331	0.285	0.382	0.331	0.285	0.382	SUBCLONAL	1	TRUE	1	0.378367874368122	2		647	989	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851391	156851391	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	76	592	0	ENST00000524377.1:c.2348C>T	p.Ala783Val	p.A783V	ENST00000524377	NM_002529.3	783	gCc/gTc	17/17	1	2	FACETS	0.46	0.403	0.522	0.46	0.403	0.522	SUBCLONAL	1	TRUE	1	0.378367874368122	2		592	873	SUCCESS
RET	5979	MSKCC	GRCh37	10	43572774	43572774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554815546	NA	P-0034621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	37	151	0	ENST00000355710.3:c.68G>A	p.Gly23Asp	p.G23D	ENST00000355710	NM_020975.4	23	gGc/gAc	1/20	1	2	FACETS	0.526	0.434	0.628	0.526	0.434	0.628	SUBCLONAL	1	TRUE	1	0.378367874368122	2		151	372	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112767346	112767346	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	21	509	0	ENST00000369452.4:c.1219T>A	p.Leu407Met	p.L407M	ENST00000369452	NM_007373.3	407	Ttg/Atg	6/9	1	2	FACETS	0.324	0.249	0.411	0.324	0.249	0.411	SUBCLONAL	1	TRUE	1	0.378367874368122	2		509	343	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344357	118344357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	35	282	0	ENST00000534358.1:c.2483C>T	p.Ser828Leu	p.S828L	ENST00000534358	NM_005933.3	828	tCa/tTa	3/36	1	2	FACETS	0.473	0.388	0.569	0.473	0.388	0.569	SUBCLONAL	1	TRUE	1	0.378367874368122	2		282	391	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656319	18656319	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	20	409	0	ENST00000266497.5:c.2998C>T	p.Gln1000Ter	p.Q1000*	ENST00000266497		1000	Cag/Tag	21/31	1	2	FACETS	0.344	0.263	0.439	0.344	0.263	0.439	SUBCLONAL	1	TRUE	1	0.378367874368122	2		409	307	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246246	46246246	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0034621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	46	415	0	ENST00000334344.6:c.4340T>A	p.Leu1447Ter	p.L1447*	ENST00000334344	NM_152641.2	1447	tTg/tAg	15/21	1	2	FACETS	0.465	0.391	0.546	0.465	0.391	0.546	SUBCLONAL	1	TRUE	1	0.378367874368122	2		415	523	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415864	49415864	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	55	457	0	ENST00000301067.7:c.16483A>G	p.Ile5495Val	p.I5495V	ENST00000301067	NM_003482.3	5495	Atc/Gtc	53/54	1	2	FACETS	0.397	0.339	0.461	0.397	0.339	0.461	SUBCLONAL	1	TRUE	1	0.378367874368122	2		457	732	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354615	91354615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	44	375	0	ENST00000355112.3:c.4055C>T	p.Ser1352Phe	p.S1352F	ENST00000355112	NM_000057.2	1352	tCc/tTc	21/22	1	2	FACETS	0.437	0.366	0.516	0.437	0.366	0.516	SUBCLONAL	1	TRUE	1	0.378367874368122	2		375	532	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428323	33428323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793702	NA	P-0034621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	88	475	1	ENST00000345365.6:c.800C>T	p.Ser267Phe	p.S267F	ENST00000345365	NM_002878.3	267	tCc/tTc	9/10	1	2	FACETS	0.48	0.424	0.54	0.48	0.424	0.54	SUBCLONAL	1	TRUE	1	0.378367874368122	2		476	969	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734071	58734071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	51	486	0	ENST00000305921.3:c.1129C>T	p.Pro377Ser	p.P377S	ENST00000305921	NM_003620.3	377	Cca/Tca	5/6	1	2	FACETS	0.401	0.34	0.468	0.401	0.34	0.468	SUBCLONAL	1	TRUE	1	0.378367874368122	2		486	673	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223454	36223454	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	85	724	0	ENST00000222270.7:c.6004C>T	p.Pro2002Ser	p.P2002S	ENST00000222270	NM_014727.1	2002	Ccc/Tcc	28/37	1	2	FACETS	0.414	0.365	0.467	0.414	0.365	0.467	SUBCLONAL	1	TRUE	1	0.378367874368122	2		724	1085	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248765	212248765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	25	323	0	ENST00000342788.4:c.3502G>A	p.Glu1168Lys	p.E1168K	ENST00000342788	NM_005235.2	1168	Gag/Aag	28/28	1	2	FACETS	0.424	0.334	0.526	0.424	0.334	0.526	SUBCLONAL	1	TRUE	1	0.378367874368122	2		323	312	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661957	227661957	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	52	574	0	ENST00000305123.5:c.1498T>G	p.Leu500Val	p.L500V	ENST00000305123	NM_005544.2	500	Ttg/Gtg	1/2	1	2	FACETS	0.354	0.3	0.413	0.354	0.3	0.413	SUBCLONAL	1	TRUE	1	0.378367874368122	2		574	777	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259606	89259606	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	34	362	0	ENST00000336596.2:c.750G>A	p.Trp250Ter	p.W250*	ENST00000336596	NM_005233.5	250	tgG/tgA	3/17	1	2	FACETS	0.444	0.363	0.535	0.444	0.363	0.535	SUBCLONAL	1	TRUE	1	0.378367874368122	2		362	405	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948154	55948154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	40	504	0	ENST00000263923.4:c.3817G>A	p.Glu1273Lys	p.E1273K	ENST00000263923	NM_002253.2	1273	Gaa/Aaa	29/30	1	2	FACETS	0.514	0.428	0.611	0.514	0.428	0.611	SUBCLONAL	1	TRUE	1	0.378367874368122	2		504	411	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155515	106155515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	21	335	0	ENST00000380013.4:c.416C>T	p.Pro139Leu	p.P139L	ENST00000380013	NM_001127208.2	139	cCa/cTa	3/11	1	2	FACETS	0.276	0.212	0.351	0.276	0.212	0.351	SUBCLONAL	1	TRUE	1	0.378367874368122	2		335	402	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181548	32181548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	74	573	0	ENST00000375023.3:c.2237C>T	p.Pro746Leu	p.P746L	ENST00000375023	NM_004557.3	746	cCt/cTt	14/30	0.339804749824461	3	FACETS	0.393	0.343	0.448	0.197	0.171	0.224	SUBCLONAL	1	TRUE	1	0.378367874368122	3		573	1183	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188545	32188545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752931284	NA	P-0034621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	184	525	0	ENST00000375023.3:c.910G>A	p.Glu304Lys	p.E304K	ENST00000375023	NM_004557.3	304	Gaa/Aaa	5/30	0.339804749824461	3	FACETS	1	0.985	1	0.64	0.591	0.691	CLONAL	1	TRUE	1	0.378367874368122	3		525	904	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426710	47426710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	79	590	0	ENST00000377045.4:c.955G>A	p.Gly319Ser	p.G319S	ENST00000377045	NM_001654.4	319	Ggc/Agc	10/16	1	2	FACETS	0.409	0.358	0.464	0.409	0.358	0.464	SUBCLONAL	1	TRUE	1	0.378367874368122	2		590	1021	SUCCESS
AR	367	MSKCC	GRCh37	X	66766312	66766312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1410383824	NA	P-0034621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	40	233	1	ENST00000374690.3:c.1324G>A	p.Glu442Lys	p.E442K	ENST00000374690	NM_000044.3	442	Gaa/Aaa	1/8	1	2	FACETS	0.488	0.406	0.58	0.488	0.406	0.58	SUBCLONAL	1	TRUE	1	0.378367874368122	2		234	433	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	41	417	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.43	0.357	0.512	0.43	0.357	0.512	SUBCLONAL	1	TRUE	1	0.24	2		417	794	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0034626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	41	447	2	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.0945875826589136	0	FACETS	0.376	0.312	0.447			1	INDETERMINATE	1	TRUE	0	0.24	0		449	691	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943380	71943380	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1394942069	NA	P-0034626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	46	604	0	ENST00000298229.2:c.1712G>A	p.Arg571Gln	p.R571Q	ENST00000298229	NM_001567.3	571	cGg/cAg	14/28	1	2	FACETS	0.56	0.471	0.66	0.56	0.471	0.66	SUBCLONAL	1	TRUE	1	0.24	2		604	684	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662085	227662085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755583840	NA	P-0034626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	40	678	0	ENST00000305123.5:c.1370G>A	p.Arg457His	p.R457H	ENST00000305123	NM_005544.2	457	cGc/cAc	1/2	1	2	FACETS	0.523	0.434	0.623	0.523	0.434	0.623	SUBCLONAL	1	TRUE	1	0.24	2		678	637	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732964	30732965	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0034626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	30	458	0	ENST00000295754.5:c.1579dup	p.Ala527GlyfsTer14	p.A527Gfs*14	ENST00000295754	NM_003242.5	526	gag/gaGg	7/7	1	2	FACETS	0.595	0.479	0.727	0.595	0.479	0.727	SUBCLONAL	1	TRUE	1	0.24	2		458	420	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413952	139413952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	56	854	0	ENST00000277541.6:c.808G>A	p.Gly270Ser	p.G270S	ENST00000277541	NM_017617.3	270	Ggt/Agt	5/34	1	2	FACETS	0.489	0.417	0.567	0.489	0.417	0.567	SUBCLONAL	1	TRUE	1	0.24	2		854	955	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855290	76855290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0034628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	116	214	0	ENST00000373344.5:c.5698-1G>A		p.X1900_splice	ENST00000373344	NM_000489.3	1900			1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.599646123849648	1		214	204	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574544	64574564	+	frameshift_variant	Frame_Shift_Del	DEL	GCCAGGTTCCCTAAGGCCATG	GCCAGGTTCCCTAAGGCCATG	CCCAGGCCAT	novel	NA	P-0034628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	445	716	2	ENST00000312049.6:c.831_851delinsATGGCCTGGG	p.Met278TrpfsTer35	p.M278Wfs*35	ENST00000312049	NM_130799.2	277	ccCATGGCCTTAGGGAACCTGGCa/ccATGGCCTGGGa	6/10	0.599646123849648	2	FACETS	0.9	0.865	0.934	0.9	0.865	0.934	CLONAL	2	TRUE	0	0.599646123849648	2		718	825	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643399	38643399	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0034628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	189	608	0	ENST00000299084.4:c.869C>G	p.Ser290Ter	p.S290*	ENST00000299084	NM_152594.2	290	tCa/tGa	7/7	1	2	FACETS	0.934	0.867	1	0.934	0.867	1	CLONAL	1	TRUE	1	0.599646123849648	2		608	675	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574564	64574564	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	397	680	0	ENST00000312049.6:c.831del	p.Met278TrpfsTer3	p.M278Wfs*3	ENST00000312049	NM_130799.2	277	ccC/cc	6/10	0.599646123849648	2	FACETS	0.896	0.859	0.932	0.896	0.859	0.932	CLONAL	2	TRUE	0	0.599646123849648	2		680	739	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0034631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	43	384	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.0608859553068579	4	FACETS	0.87	0.728	1	0.435	0.364	0.514	INDETERMINATE	1	TRUE	2	0.264887681748843	4		384	472	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376803	118376803	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	37	460	0	ENST00000534358.1:c.10196C>A	p.Pro3399His	p.P3399H	ENST00000534358	NM_005933.3	3399	cCt/cAt	27/36	0.259354523388013	3	FACETS	0.727	0.6	0.87	0.364	0.3	0.435	SUBCLONAL	1	TRUE	1	0.264887681748843	3		460	435	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711908	89711910	+	inframe_deletion	In_Frame_Del	DEL	TAT	TAT	-	rs587780711	NA	P-0034633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	142	771	0	ENST00000371953.3:c.532_534del	p.Tyr178del	p.Y178del	ENST00000371953	NM_000314.4	176	TAT/-	6/9	0.720872771695759	1	FACETS	0.603	0.555	0.652	0.603	0.555	0.652	SUBCLONAL	1	TRUE	0	0.720872771695759	1		771	418	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130363	2130364	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0034633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	111	842	0	ENST00000219476.3:c.3596_3597dup	p.Arg1200SerfsTer11	p.R1200Sfs*11	ENST00000219476	NM_000548.3	1199	gtc/gTCtc	30/42	1	2	FACETS	0.425	0.382	0.471	0.425	0.382	0.471	SUBCLONAL	1	TRUE	1	0.720872771695759	2		842	724	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385226	41385267	+	inframe_deletion	In_Frame_Del	DEL	GTGGTTGACCACACGGGTGACCATCAGGGCCGTGTCCCTGCC	GTGGTTGACCACACGGGTGACCATCAGGGCCGTGTCCCTGCC	-	novel	NA	P-0034633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	111	785	1	ENST00000373198.4:c.694_735del	p.Gly232_His245del	p.G232_H245del	ENST00000373198	NM_133170.3	232	GGCAGGGACACGGCCCTGATGGTCACCCGTGTGGTCAACCAC/-	6/32	0.176195582724097	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.720872771695759	0		786	490	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918596	44918597	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0034639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	191	279	0	ENST00000377967.4:c.1083_1084del	p.Tyr362Ter	p.Y362*	ENST00000377967	NM_021140.2	360	aCT/a	12/29	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.620108927364102	1		279	341	SUCCESS
APC	324	MSKCC	GRCh37	5	112175921	112175921	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	52	226	0	ENST00000257430.4:c.4630G>T	p.Glu1544Ter	p.E1544*	ENST00000257430	NM_000038.5	1544	Gaa/Taa	16/16	0.600335562220634	1	FACETS	0.693	0.601	0.789	0.693	0.601	0.789	SUBCLONAL	1	TRUE	0	0.620108927364102	1		226	167	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0034639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	27	308	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	0.600335562220634	1	FACETS	0.236	0.188	0.29	0.236	0.188	0.29	SUBCLONAL	1	TRUE	0	0.620108927364102	1		308	255	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696644	47696644	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	184	477	1	ENST00000347630.2:c.304T>A	p.Phe102Ile	p.F102I	ENST00000347630	NM_001007230.1	102	Ttc/Atc	5/11	1	2	FACETS	0.938	0.869	1	0.938	0.869	1	CLONAL	1	TRUE	1	0.620108927364102	2		478	633	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47108606	47108606	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	140	311	0	ENST00000409792.3:c.6063G>C	p.Glu2021Asp	p.E2021D	ENST00000409792	NM_014159.6	2021	gaG/gaC	13/21	1	2	FACETS	0.967	0.887	1	0.967	0.887	1	CLONAL	1	TRUE	1	0.620108927364102	2		311	467	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	139	417	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.544829143075076	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	4	TRUE	0	0.544829143075076	4		417	187	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0034641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	205	625	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.544829143075076	2	FACETS	0.982	0.927	1	0.982	0.927	1	CLONAL	2	TRUE	0	0.544829143075076	2		625	383	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159112	24159112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1341827515	NA	P-0034641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	158	319	0	ENST00000263121.7:c.784G>A	p.Val262Ile	p.V262I	ENST00000263121	NM_003073.3	262	Gtc/Atc	6/9	0.179988753344652	3	FACETS	1	0.982	1	0.771	0.719	0.823	INDETERMINATE	2	TRUE	0	0.544829143075076	3		319	319	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0034642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	9	330	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.13	0.085	0.187	0.13	0.085	0.187	SUBCLONAL	1	FALSE	1	0.337405641238146	2		330	411	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196791	108196791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039471	NA	P-0034642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	34	274	0	ENST00000278616.4:c.6814G>A	p.Glu2272Lys	p.E2272K	ENST00000278616	NM_000051.3	2272	Gaa/Aaa	47/63	1	2	FACETS	0.561	0.459	0.676	0.561	0.459	0.676	SUBCLONAL	1	FALSE	1	0.337405641238146	2		274	359	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347299	89347299	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0034642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	53	592	0	ENST00000301030.4:c.5651C>G	p.Ser1884Ter	p.S1884*	ENST00000301030	NM_001256183.1	1884	tCa/tGa	9/13	1	2	FACETS	0.437	0.372	0.509	0.437	0.372	0.509	SUBCLONAL	1	FALSE	1	0.337405641238146	2		592	719	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106495	27106495	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	47	591	0	ENST00000324856.7:c.6106G>T	p.Glu2036Ter	p.E2036*	ENST00000324856	NM_006015.4	2036	Gaa/Taa	20/20	1	2	FACETS	0.34	0.286	0.4	0.34	0.286	0.4	SUBCLONAL	1	FALSE	1	0.337405641238146	2		591	820	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335085	65335085	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	39	546	0	ENST00000342505.4:c.556G>C	p.Glu186Gln	p.E186Q	ENST00000342505	NM_002227.2	186	Gag/Cag	6/25	1	2	FACETS	0.321	0.265	0.383	0.321	0.265	0.383	SUBCLONAL	1	FALSE	1	0.337405641238146	2		546	721	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871005	12871005	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	27	278	0	ENST00000228872.4:c.232G>C	p.Glu78Gln	p.E78Q	ENST00000228872	NM_004064.3	78	Gag/Cag	1/3	1	2	FACETS	0.43	0.342	0.531	0.43	0.342	0.531	SUBCLONAL	1	FALSE	1	0.337405641238146	2		278	372	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482566	56482566	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	47	536	0	ENST00000267101.3:c.1023G>C	p.Gln341His	p.Q341H	ENST00000267101	NM_001982.3	341	caG/caC	9/28	1	2	FACETS	0.33	0.277	0.388	0.33	0.277	0.388	SUBCLONAL	1	FALSE	1	0.337405641238146	2		536	845	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69788806	69788806	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	24	286	0	ENST00000352241.4:c.58G>C	p.Glu20Gln	p.E20Q	ENST00000352241	NM_198159.2	20	Gag/Cag	1/10	1	2	FACETS	0.331	0.259	0.414	0.331	0.259	0.414	SUBCLONAL	1	FALSE	1	0.337405641238146	2		286	430	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31521236	31521236	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	43	592	0	ENST00000344624.3:c.941C>G	p.Ser314Cys	p.S314C	ENST00000344624		314	tCt/tGt	3/33	1	2	FACETS	0.341	0.284	0.404	0.341	0.284	0.404	SUBCLONAL	1	FALSE	1	0.337405641238146	2		592	748	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132522	11132522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778175819	NA	P-0034644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	58	554	0	ENST00000358026.2:c.2738C>T	p.Pro913Leu	p.P913L	ENST00000358026	NM_001128849.1	913	cCg/cTg	19/36	0.431115055919273	2	FACETS	0.701	0.605	0.804	0.35	0.302	0.402	SUBCLONAL	1	TRUE	0	0.454898036390842	2		554	364	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742704	39742704	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	162	394	0	ENST00000361337.2:c.1547C>G	p.Pro516Arg	p.P516R	ENST00000361337	NM_003286.2	516	cCa/cGa	15/21	0.276446132411528	4	FACETS	0.974	0.899	1	0.974	0.899	1	CLONAL	2	TRUE	2	0.454898036390842	4		394	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577540	7577554	+	inframe_deletion	In_Frame_Del	DEL	GTTCATGCCGCCCAT	GTTCATGCCGCCCAT	-	novel	NA	P-0034644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	387	604	0	ENST00000269305.4:c.727_741del	p.Met243_Asn247del	p.M243_N247del	ENST00000269305	NM_001126112.2	243	ATGGGCGGCATGAAC/-	7/11	0.454898036390842	4	FACETS	0.9	0.863	0.935	0.9	0.863	0.935	CLONAL	4	TRUE	0	0.454898036390842	4		604	688	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355107	15355107	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	231	788	0	ENST00000263377.2:c.2516T>C	p.Leu839Pro	p.L839P	ENST00000263377	NM_058243.2	839	cTg/cCg	13/20	0.431115055919273	2	FACETS	0.93	0.875	0.986	0.93	0.875	0.986	CLONAL	2	TRUE	0	0.454898036390842	2		788	546	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607552	46607552	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	208	704	0	ENST00000263734.3:c.1741A>T	p.Ser581Cys	p.S581C	ENST00000263734	NM_001430.4	581	Agt/Tgt	12/16	0.394771449824333	4	FACETS	0.933	0.869	0.998	0.933	0.869	0.998	CLONAL	2	TRUE	2	0.454898036390842	4		704	713	SUCCESS
ATR	545	MSKCC	GRCh37	3	142177873	142177873	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	53	299	0	ENST00000350721.4:c.7430A>G	p.His2477Arg	p.H2477R	ENST00000350721	NM_001184.3	2477	cAt/cGt	44/47	0.395511109950647	4	FACETS	1	0.923	1	0.559	0.48	0.645	CLONAL	1	TRUE	2	0.454898036390842	4		299	303	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152071	55152071	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	177	564	0	ENST00000257290.5:c.2503T>G	p.Cys835Gly	p.C835G	ENST00000257290	NM_006206.4	835	Tgt/Ggt	18/23	0.276446132411528	4	FACETS	0.968	0.897	1	0.968	0.897	1	CLONAL	2	TRUE	2	0.454898036390842	4		564	585	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630302	187630302	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	162	572	0	ENST00000441802.2:c.680G>T	p.Arg227Leu	p.R227L	ENST00000441802	NM_005245.3	227	cGt/cTt	2/27	0.161515251893386	2	FACETS	0.85	0.788	0.913	0.85	0.788	0.913	INDETERMINATE	2	TRUE	0	0.454898036390842	2		572	419	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372097	55372097	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	334	431	1	ENST00000297316.4:c.787C>A	p.Pro263Thr	p.P263T	ENST00000297316	NM_022454.3	263	Ccg/Acg	2/2	0.454898036390842	5	FACETS	0.988	0.944	1			1	CLONAL	4	TRUE	NA	0.454898036390842	5		432	625	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0034645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	193	582	2	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.360136944348603	2		584	826	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0034645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	77	316	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.928	0.817	1	0.928	0.817	1	CLONAL	1	TRUE	1	0.360136944348603	2		316	461	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481399	140481399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	106	382	0	ENST00000288602.6:c.1409C>T	p.Thr470Ile	p.T470I	ENST00000288602	NM_004333.4	470	aCa/aTa	11/18	1	2	FACETS	0.94	0.845	1	0.94	0.845	1	CLONAL	1	TRUE	1	0.360136944348603	2		382	626	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0034650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	306	370	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.235792805689037	4	FACETS	1	0.984	1			1	CLONAL	3	TRUE	NA	0.270731931004081	4		370	869	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0034650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	262	841	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	1	2	FACETS	0.923	0.866	0.983	1	0.995	1	CLONAL	2	TRUE	1	0.270731931004081	2		841	1048	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0034650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	400	899	1	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	0.270731931004081	3	FACETS	0.992	0.945	1	0.992	0.945	1	CLONAL	3	TRUE	0	0.270731931004081	3		900	1127	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950005	44950005	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	70	293	0	ENST00000377967.4:c.3774G>A	p.Trp1258Ter	p.W1258*	ENST00000377967	NM_021140.2	1258	tgG/tgA	26/29	1	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.270731931004081	1		293	315	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926878	112926878	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	112	781	0	ENST00000351677.2:c.1498C>T	p.Gln500Ter	p.Q500*	ENST00000351677	NM_002834.3	500	Cag/Tag	13/16	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.270731931004081	2		781	747	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514570	41514570	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	45	461	0	ENST00000373198.4:c.91G>T	p.Gly31Cys	p.G31C	ENST00000373198	NM_133170.3	31	Ggc/Tgc	2/32	0.270731931004081	1	FACETS	0.613	0.515	0.721	0.613	0.515	0.721	SUBCLONAL	1	TRUE	0	0.270731931004081	1		461	469	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259513	16259513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	72	491	0	ENST00000375759.3:c.6778G>A	p.Glu2260Lys	p.E2260K	ENST00000375759	NM_015001.2	2260	Gag/Aag	11/15	0.265802785267324	2	FACETS	1	0.946	1	0.573	0.502	0.649	CLONAL	1	TRUE	0	0.270731931004081	2		491	464	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518541	204518541	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	103	305	0	ENST00000367182.3:c.1204G>C	p.Glu402Gln	p.E402Q	ENST00000367182	NM_001278516.1	402	Gaa/Caa	11/11	0.270731931004081	3	FACETS	0.956	0.86	1	0.956	0.86	1	CLONAL	2	TRUE	1	0.270731931004081	3		305	452	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144732	119144732	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	74	413	0	ENST00000264033.4:c.745C>T	p.Gln249Ter	p.Q249*	ENST00000264033	NM_005188.3	249	Cag/Tag	4/16	0.270731931004081	3	FACETS	0.95	0.832	1	0.475	0.416	0.539	CLONAL	1	TRUE	1	0.270731931004081	3		413	653	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863463	57863463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	88	506	0	ENST00000228682.2:c.1558C>T	p.Pro520Ser	p.P520S	ENST00000228682	NM_005269.2	520	Ccc/Tcc	11/12	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.270731931004081	2		506	554	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68290324	68290324	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	158	480	0	ENST00000487270.1:c.64C>A	p.His22Asn	p.H22N	ENST00000487270	NM_133509.3	22	Cat/Aat	2/11	1	2	FACETS	0.998	0.919	1	1	0.992	1	CLONAL	2	TRUE	1	0.270731931004081	2		480	585	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028438	42028438	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	132	476	1	ENST00000219905.7:c.3976del	p.Gln1326ArgfsTer10	p.Q1326Rfs*10	ENST00000219905	NM_001164273.1	1326	Cag/ag	13/24	0.270731931004081	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	2	TRUE	0	0.270731931004081	2		477	485	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829935	72829935	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs748630143	NA	P-0034650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	109	766	0	ENST00000268489.5:c.6646A>G	p.Ile2216Val	p.I2216V	ENST00000268489	NM_006885.3	2216	Atc/Gtc	9/10	NA	2	FACETS	1	0.936	1			1	INDETERMINATE	1	TRUE	NA	0.270731931004081	2		766	762	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341546	89341546	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	79	597	0	ENST00000301030.4:c.7524G>T	p.Gln2508His	p.Q2508H	ENST00000301030	NM_001256183.1	2508	caG/caT	10/13	0.270731931004081	1	FACETS	0.882	0.777	0.995	0.882	0.777	0.995	CLONAL	1	TRUE	0	0.270731931004081	1		597	572	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61711222	61711222	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	85	507	0	ENST00000401558.2:c.2527G>T	p.Glu843Ter	p.E843*	ENST00000401558	NM_003400.3	843	Gaa/Taa	21/25	0.270731931004081	3	FACETS	1	0.893	1	0.506	0.447	0.569	CLONAL	1	TRUE	1	0.270731931004081	3		507	705	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015280	128015280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	46	502	1	ENST00000285398.2:c.2241G>A	p.Met747Ile	p.M747I	ENST00000285398	NM_000122.1	747	atG/atA	15/15	1	2	FACETS	0.6	0.505	0.706	0.6	0.505	0.706	SUBCLONAL	1	TRUE	1	0.270731931004081	2		503	566	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408903	41408904	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0034650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	55	414	0	ENST00000373198.4:c.522dup	p.Gly175TrpfsTer49	p.G175Wfs*49	ENST00000373198	NM_133170.3	174	-/T	4/32	0.270731931004081	1	FACETS	0.789	0.677	0.912	0.789	0.677	0.912	CLONAL	1	TRUE	0	0.270731931004081	1		414	445	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31401618	31401618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	117	676	0	ENST00000344624.3:c.4046G>A	p.Arg1349Lys	p.R1349K	ENST00000344624		1349	aGa/aAa	33/33	0.270731931004081	5	FACETS	1	0.938	1	0.265	0.238	0.293	CLONAL	1	TRUE	1	0.270731931004081	5		676	1148	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180513	56180513	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	39	321	0	ENST00000399503.3:c.3842C>A	p.Ser1281Tyr	p.S1281Y	ENST00000399503	NM_005921.1	1281	tCt/tAt	16/20	0.240200504557392	2	FACETS	0.762	0.633	0.906	0.381	0.316	0.453	CLONAL	1	TRUE	0	0.270731931004081	2		321	378	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517497	176517497	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	129	935	0	ENST00000292408.4:c.198G>C	p.Trp66Cys	p.W66C	ENST00000292408	NM_213647.1	66	tgG/tgC	3/18	0.270731931004081	2	FACETS	1	0.953	1	0.541	0.49	0.595	CLONAL	1	TRUE	0	0.270731931004081	2		935	881	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820834	32820834	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	98	812	0	ENST00000354258.4:c.760G>T	p.Val254Leu	p.V254L	ENST00000354258	NM_000593.5	254	Gtg/Ttg	1/11	0.265802785267324	2	FACETS	0.871	0.777	0.972	0.436	0.388	0.486	CLONAL	1	TRUE	0	0.270731931004081	2		812	831	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141570582	141570582	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	118	535	0	ENST00000220592.5:c.546C>G	p.Phe182Leu	p.F182L	ENST00000220592	NM_012154.3	182	ttC/ttG	5/19	0.270731931004081	5	FACETS	0.866	0.782	0.954	0.577	0.521	0.636	CLONAL	2	TRUE	2	0.270731931004081	5		535	708	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5055739	5055739	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0034650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	153	453	0	ENST00000381652.3:c.1007C>G	p.Ser336Ter	p.S336*	ENST00000381652	NM_004972.3	336	tCa/tGa	8/25	0.270731931004081	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	2	TRUE	0	0.270731931004081	2		453	564	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0034668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	20	498	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.393	0.299	0.504	0.393	0.299	0.504	SUBCLONAL	1	TRUE	1	0.15	2		498	678	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056349	27056349	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	23	304	0	ENST00000324856.7:c.1345C>T	p.Gln449Ter	p.Q449*	ENST00000324856	NM_006015.4	449	Cag/Tag	2/20	1	2	FACETS	0.757	0.59	0.952	0.757	0.59	0.952	CLONAL	1	TRUE	1	0.15	2		304	405	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69456221	69456221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	63	540	0	ENST00000227507.2:c.140G>A	p.Cys47Tyr	p.C47Y	ENST00000227507	NM_053056.2	47	tGt/tAt	1/5	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.15	2		540	834	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69456211	69456213	+	missense_variant	Missense_Mutation	TNP	TAC	TAC	CAG	novel	NA	P-0034668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	58	552	0	ENST00000227507.2:c.130_132delinsCAG	p.Tyr44Gln	p.Y44Q	ENST00000227507	NM_053056.2	44	TAC/CAG	1/5	1	2	FACETS	0.904	0.775	1	0.904	0.775	1	CLONAL	1	TRUE	1	0.15	2		552	855	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0034669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	41	114	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.779	0.659	0.908	0.779	0.659	0.908	CLONAL	1	TRUE	1	0.634001700139451	2		114	166	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375235	31375235	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	131	690	0	ENST00000328111.2:c.632A>G	p.Asp211Gly	p.D211G	ENST00000328111	NM_006892.3	211	gAt/gGt	6/23	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.634001700139451	2		690	377	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191784	123191784	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	84	383	0	ENST00000218089.9:c.1374del	p.Asn459ThrfsTer11	p.N459Tfs*11	ENST00000218089	NM_001042749.1	458	gCc/gc	15/35	1	2	FACETS	0.911	0.814	1	0.911	0.814	1	CLONAL	1	TRUE	1	0.634001700139451	2		383	291	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0034673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	53	383	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	0.19	2		383	545	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0034673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	20	291	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.529	0.404	0.676	0.529	0.404	0.676	SUBCLONAL	1	TRUE	1	0.19	2		291	398	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0034673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	58	548	2	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.86	0.738	0.994	0.86	0.738	0.994	CLONAL	1	TRUE	1	0.19	2		550	710	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717695	89717696	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1060500115	NA	P-0034673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	27	426	0	ENST00000371953.3:c.723dup	p.Glu242Ter	p.E242*	ENST00000371953	NM_000314.4	240	-/T	7/9	1	2	FACETS	0.548	0.435	0.677	0.548	0.435	0.677	SUBCLONAL	1	TRUE	1	0.19	2		426	519	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712018	89712018	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0034673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	32	300	0	ENST00000371953.3:c.634+2T>A		p.X212_splice	ENST00000371953	NM_000314.4	212			1	2	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	1	0.19	2		300	321	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119069	70119069	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	31	390	0	ENST00000245479.2:c.642del	p.Ser215ProfsTer4	p.S215Pfs*4	ENST00000245479	NM_000346.3	214	tCc/tc	2/3	1	2	FACETS	0.773	0.625	0.941	0.773	0.625	0.941	CLONAL	1	TRUE	1	0.19	2		390	422	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023781	27023782	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0034673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	34	363	0	ENST00000324856.7:c.889dup	p.Gln297ProfsTer103	p.Q297Pfs*103	ENST00000324856	NM_006015.4	296	aac/aaCc	1/20	1	2	FACETS	0.626	0.51	0.756	0.626	0.51	0.756	SUBCLONAL	1	TRUE	1	0.19	2		363	572	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673733	176673734	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0034673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	44	363	0	ENST00000439151.2:c.4434dup	p.Ala1479SerfsTer6	p.A1479Sfs*6	ENST00000439151	NM_022455.4	1478	gca/gcAa	10/23	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.19	2		363	449	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	37	236	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.837	1	1	0.837	1	CLONAL	1	TRUE	1	0.15	2		236	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0034675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	79	703	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.15	2		703	991	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196653	67196653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	45	445	1	ENST00000312629.5:c.182G>A	p.Arg61His	p.R61H	ENST00000312629	NM_003952.2	61	cGc/cAc	3/15	1	2	FACETS	0.796	0.667	0.939	0.796	0.667	0.939	CLONAL	1	TRUE	1	0.15	2		446	754	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110175	3110175	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	43	503	0	ENST00000078429.4:c.165C>A	p.Phe55Leu	p.F55L	ENST00000078429	NM_002067.2	55	ttC/ttA	2/7	1	2	FACETS	0.846	0.706	1	0.846	0.706	1	CLONAL	1	TRUE	1	0.15	2		503	678	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240362	98240362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767273237	NA	P-0034676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	164	432	0	ENST00000331920.6:c.1322G>A	p.Arg441His	p.R441H	ENST00000331920	NM_000264.3	441	cGc/cAc	9/24	0.264999298762827	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.348262986522655	4		432	543	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874199	155874199	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	133	641	0	ENST00000368323.3:c.332T>A	p.Val111Asp	p.V111D	ENST00000368323	NM_006912.5	111	gTt/gAt	5/6	0.318371978010607	4	FACETS	1	0.94	1	0.524	0.475	0.575	CLONAL	1	TRUE	2	0.348262986522655	4		641	983	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749901	162749901	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0034676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	73	449	0	ENST00000367921.3:c.2434-1G>C		p.X812_splice	ENST00000367921	NM_006182.2	812			0.318371978010607	4	FACETS	1	0.886	1	0.506	0.443	0.574	CLONAL	1	TRUE	2	0.348262986522655	4		449	558	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0034678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	141	222	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.564558804879039	2		222	455	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244016	46244016	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	167	399	0	ENST00000334344.6:c.2110C>T	p.Gln704Ter	p.Q704*	ENST00000334344	NM_152641.2	704	Caa/Taa	15/21	1	2	FACETS	0.854	0.787	0.923	0.854	0.787	0.923	CLONAL	1	TRUE	1	0.564558804879039	2		399	693	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245868	46245868	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	140	254	0	ENST00000334344.6:c.3962del	p.Leu1321GlnfsTer10	p.L1321Qfs*10	ENST00000334344	NM_152641.2	1321	cTa/ca	15/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.564558804879039	2		254	452	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643642	38643642	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1178736205	NA	P-0034678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	228	504	1	ENST00000299084.4:c.1112G>A	p.Cys371Tyr	p.C371Y	ENST00000299084	NM_152594.2	371	tGt/tAt	7/7	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.564558804879039	2		505	803	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274897	41274897	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	192	394	0	ENST00000349496.5:c.1147T>G	p.Trp383Gly	p.W383G	ENST00000349496	NM_001904.3	383	Tgg/Ggg	8/15	1	2	FACETS	0.951	0.883	1	0.951	0.883	1	CLONAL	1	TRUE	1	0.564558804879039	2		394	715	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924527	131924528	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0034678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	133	328	0	ENST00000265335.6:c.1208_1209del	p.Arg403ThrfsTer14	p.R403Tfs*14	ENST00000265335		400	gtGAga/gtga	8/25	1	2	FACETS	0.796	0.725	0.869	0.796	0.725	0.869	SUBCLONAL	1	TRUE	1	0.564558804879039	2		328	592	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69143603	69143603	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	93	223	0	ENST00000288368.4:c.4811G>C	p.Gly1604Ala	p.G1604A	ENST00000288368	NM_024870.2	1604	gGa/gCa	40/40	1	2	FACETS	0.872	0.781	0.967	0.872	0.781	0.967	CLONAL	1	TRUE	1	0.564558804879039	2		223	378	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0034683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	1162	652	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.256964661462952	11	FACETS	1	0.987	1	1	0.987	1	CLONAL	11	TRUE	0	0.256964661462952	11		652	1753	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287446	46287446	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs774801990	NA	P-0034683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	143	354	0	ENST00000334344.6:c.5305C>T	p.Arg1769Ter	p.R1769*	ENST00000334344	NM_152641.2	1769	Cga/Tga	20/21	0.252019384736352	2	FACETS	0.971	0.889	1	0.971	0.889	1	CLONAL	2	TRUE	0	0.256964661462952	2		354	573	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201873	152201873	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779180038	NA	P-0034683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	45	326	0	ENST00000206249.3:c.727C>T	p.Arg243Cys	p.R243C	ENST00000206249	NM_000125.3	243	Cgt/Tgt	3/8	1	2	FACETS	0.773	0.65	0.909	0.773	0.65	0.909	CLONAL	1	TRUE	1	0.256964661462952	2		326	453	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36989302	36989303	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0034683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	48	561	0	ENST00000354822.5:c.32_33insT	p.Trp12LeufsTer34	p.W12Lfs*34	ENST00000354822	NM_001079668.2	11	ggc/ggTc	1/3	1	2	FACETS	0.483	0.407	0.567	0.483	0.407	0.567	SUBCLONAL	1	TRUE	1	0.256964661462952	2		561	774	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574013	7574014	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAGCGCTCA	novel	NA	P-0034683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	145	756	0	ENST00000269305.4:c.1005_1013dup	p.Arg337_Glu339dup	p.R337_E339dup	ENST00000269305	NM_001126112.2	337	ttc/ttTGAGCGCTTc	10/11	0.256964661462952	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.256964661462952	1		756	895	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660661	227660661	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	65	692	1	ENST00000305123.5:c.2794A>G	p.Arg932Gly	p.R932G	ENST00000305123	NM_005544.2	932	Aga/Gga	1/2	1	2	FACETS	0.58	0.501	0.665	0.58	0.501	0.665	SUBCLONAL	1	TRUE	1	0.256964661462952	2		693	873	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62320991	62320991	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1405025025	NA	P-0034683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	61	723	0	ENST00000360203.5:c.2015C>T	p.Ala672Val	p.A672V	ENST00000360203	NM_001283009.1	672	gCt/gTt	23/35	1	2	FACETS	0.477	0.41	0.551	0.477	0.41	0.551	SUBCLONAL	1	TRUE	1	0.256964661462952	2		723	995	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271371	26271421	+	inframe_deletion	In_Frame_Del	DEL	GTCTTGAAGTCCTGAGCGATTTCTCGCACCAGGCGTTGGAAAGGCAACTTG	GTCTTGAAGTCCTGAGCGATTTCTCGCACCAGGCGTTGGAAAGGCAACTTG	-	novel	NA	P-0034683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	76	649	0	ENST00000305910.3:c.192_242del	p.Lys65_Thr81del	p.K65_T81del	ENST00000305910	NM_003534.2	64	cgCAAGTTGCCTTTCCAACGCCTGGTGCGAGAAATCGCTCAGGACTTCAAGACa/cga	1/1	0.220831909389664	3	FACETS	0.695	0.608	0.79	0.348	0.304	0.395	SUBCLONAL	1	TRUE	1	0.256964661462952	3		649	960	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578266	7578267	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0034685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	412	661	0	ENST00000269305.4:c.582dup	p.Ile195TyrfsTer14	p.I195Yfs*14	ENST00000269305	NM_001126112.2	194	-/T	6/11	0.473328327307825	2	FACETS	0.999	0.957	1	0.999	0.957	1	CLONAL	2	TRUE	0	0.473437598450675	2		661	871	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443674	49443674	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	157	654	0	ENST00000301067.7:c.3697G>T	p.Glu1233Ter	p.E1233*	ENST00000301067	NM_003482.3	1233	Gag/Tag	11/54	NA	2	FACETS	0.813	0.745	0.883			1	INDETERMINATE	1	TRUE	NA	0.473437598450675	2		654	816	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14016045	14016045	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	77	211	0	ENST00000311895.7:c.365G>C	p.Arg122Thr	p.R122T	ENST00000311895	NM_005236.2	122	aGa/aCa	2/11	NA	2	FACETS	0.927	0.82	1			1	INDETERMINATE	1	TRUE	NA	0.473437598450675	2		211	351	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245091	41245091	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80357669	NA	P-0034685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	564	758	0	ENST00000357654.3:c.2457del	p.Asp821IlefsTer25	p.D821Ifs*25	ENST00000357654	NM_007294.3	819	tcC/tc	10/23	0.473328327307825	2	FACETS	0.986	0.95	1	0.986	0.95	1	CLONAL	2	TRUE	0	0.473437598450675	2		758	1208	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0034692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	149	417	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.514545830863215	2		417	516	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220502	1220502	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	rs121913317	NA	P-0034692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	265	681	0	ENST00000326873.7:c.595G>T	p.Glu199Ter	p.E199*	ENST00000326873	NM_000455.4	199	Gag/Tag	4/10	0.514545830863215	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.514545830863215	1		681	704	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637684	52637684	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	208	462	0	ENST00000394830.3:c.2632G>T	p.Glu878Ter	p.E878*	ENST00000394830	NM_018313.4	878	Gaa/Taa	18/30	0.514545830863215	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.514545830863215	1		462	515	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137357	64137357	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	136	611	0	ENST00000334205.4:c.1789G>C	p.Val597Leu	p.V597L	ENST00000334205	NM_003942.2	597	Gtc/Ctc	14/17	1	2	FACETS	0.745	0.678	0.814	0.745	0.678	0.814	SUBCLONAL	1	TRUE	1	0.514545830863215	2		611	710	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599897	10599907	+	frameshift_variant	Frame_Shift_Del	DEL	GTGATCCCCAG	GTGATCCCCAG	-	novel	NA	P-0034692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	296	701	0	ENST00000171111.5:c.1669_1679del	p.Leu557CysfsTer13	p.L557Cfs*13	ENST00000171111	NM_203500.1	557	CTGGGGATCACt/t	5/6	0.514545830863215	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.514545830863215	1		701	679	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141546	11141546	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	252	616	0	ENST00000358026.2:c.3523G>T	p.Asp1175Tyr	p.D1175Y	ENST00000358026	NM_001128849.1	1175	Gac/Tac	25/36	0.514545830863215	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.514545830863215	1		616	629	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733244	40733244	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	203	692	0	ENST00000373198.4:c.3562C>A	p.Gln1188Lys	p.Q1188K	ENST00000373198	NM_133170.3	1188	Cag/Aag	26/32	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.514545830863215	2		692	737	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0034694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	24	383	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.265	0.207	0.333	0.265	0.207	0.333	SUBCLONAL	1	FALSE	1	0.260945293006045	2		383	694	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0034694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	23	392	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.29	0.225	0.366	0.29	0.225	0.366	SUBCLONAL	1	FALSE	1	0.260945293006045	2		392	607	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023211	27023220	+	frameshift_variant	Frame_Shift_Del	DEL	ACGCGGGCCC	ACGCGGGCCC	-	novel	NA	P-0034694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	42	191	0	ENST00000324856.7:c.317_326del	p.Asn106IlefsTer5	p.N106Ifs*5	ENST00000324856	NM_006015.4	106	aACGCGGGCCCt/at	1/20	1	2	FACETS	0.93	0.779	1	0.93	0.779	1	CLONAL	1	FALSE	1	0.260945293006045	2		191	346	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480320	56480320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	116	400	0	ENST00000267101.3:c.427C>A	p.Leu143Met	p.L143M	ENST00000267101	NM_001982.3	143	Ctg/Atg	4/28	0.105224826714187	3	FACETS	0.833	0.753	0.918	0.556	0.502	0.612	INDETERMINATE	2	FALSE	0	0.260945293006045	3		400	603	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880257	37880257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	103	432	0	ENST00000269571.5:c.2301C>G	p.Ile767Met	p.I767M	ENST00000269571		767	atC/atG	19/27	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.260945293006045	2		432	600	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265021	5265021	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	42	596	0	ENST00000357368.4:c.566C>T	p.Ser189Leu	p.S189L	ENST00000357368	NM_002850.3	189	tCa/tTa	5/38	0.260945293006045	1	FACETS	0.408	0.34	0.484	0.408	0.34	0.484	SUBCLONAL	1	FALSE	0	0.260945293006045	1		596	686	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442562	52442573	+	inframe_deletion	In_Frame_Del	DEL	CTTTCGCCGGGA	CTTTCGCCGGGA	-	novel	NA	P-0034694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	55	365	0	ENST00000460680.1:c.172_183del	p.Ser58_Lys61del	p.S58_K61del	ENST00000460680	NM_004656.3	58	TCCCGGCGAAAG/-	4/17	1	2	FACETS	0.808	0.691	0.935	0.808	0.691	0.935	CLONAL	1	FALSE	1	0.260945293006045	2		365	522	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71008403	71008403	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	53	280	0	ENST00000318789.4:c.2029G>C	p.Glu677Gln	p.E677Q	ENST00000318789	NM_032682.5	677	Gag/Cag	21/21	1	2	FACETS	0.832	0.711	0.966	0.832	0.711	0.966	CLONAL	1	FALSE	1	0.260945293006045	2		280	488	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419957	41419957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369230837	NA	P-0034699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	47	474	1	ENST00000373198.4:c.364G>A	p.Val122Ile	p.V122I	ENST00000373198	NM_133170.3	122	Gtc/Atc	3/32	1	2	FACETS	0.422	0.356	0.495	0.422	0.356	0.495	SUBCLONAL	1	TRUE	1	0.397116563008988	2		475	561	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183714	10183715	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0034699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	112	581	0	ENST00000256474.2:c.184_185insAG	p.Val62GlufsTer6	p.V62Efs*6	ENST00000256474	NM_000551.3	61	-/GA	1/3	0.397116563008988	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.397116563008988	1		581	423	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588814	52588814	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	72	388	0	ENST00000394830.3:c.4214del	p.Pro1405HisfsTer27	p.P1405Hfs*27	ENST00000394830	NM_018313.4	1405	cCa/ca	27/30	0.397116563008988	1	FACETS	0.833	0.732	0.939	0.833	0.732	0.939	CLONAL	1	TRUE	0	0.397116563008988	1		388	349	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818239	32818239	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	128	587	1	ENST00000354258.4:c.1286A>T	p.Glu429Val	p.E429V	ENST00000354258	NM_000593.5	429	gAg/gTg	5/11	1	2	FACETS	0.984	0.894	1	0.984	0.894	1	CLONAL	1	TRUE	1	0.397116563008988	2		588	655	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820254	139820254	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	136	549	0	ENST00000247668.2:c.1411del	p.Leu471SerfsTer28	p.L471Sfs*28	ENST00000247668	NM_021138.3	469	tgC/tg	11/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.397116563008988	2		549	632	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579381	7579381	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	161	690	0	ENST00000269305.4:c.306del	p.Tyr103ThrfsTer20	p.Y103Tfs*20	ENST00000269305	NM_001126112.2	102	acC/ac	4/11	NA	2	FACETS	0.92	0.845	0.997			1	INDETERMINATE	2	TRUE	NA	0.228254032911113	2		690	767	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878176	151878176	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	90	558	0	ENST00000262189.6:c.6769C>T	p.Arg2257Ter	p.R2257*	ENST00000262189	NM_170606.2	2257	Cga/Tga	36/59	0.228254032911113	3	FACETS	1	0.974	1	0.678	0.602	0.759	CLONAL	1	TRUE	1	0.228254032911113	3		558	648	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242481	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAA	AATTAAGAGAAGCAA	TCC	novel	NA	P-0034706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	114	413	2	ENST00000275493.2:c.2237_2251delinsTCC	p.Glu746_Thr751delinsValPro	p.E746_T751delinsVP	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAAca/gTCCca	19/28	0.197331580819776	7	FACETS	0.93	0.842	1	0.93	0.842	1	CLONAL	4	FALSE	3	0.197331580819776	7		415	464	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80168933	80168933	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0034706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	97	804	1	ENST00000265081.6:c.3131-2A>T		p.X1044_splice	ENST00000265081	NM_002439.4	1044			0.197331580819776	8	FACETS	0.89	0.793	0.994	0.297	0.264	0.332	CLONAL	2	FALSE	2	0.197331580819776	8		805	879	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0034711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	554	498	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.592728655506135	4	FACETS	0.973	0.942	1	0.973	0.942	1	CLONAL	3	TRUE	1	0.723605682521002	4		498	904	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0034711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	540	736	3	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.723605682521002	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.723605682521002	2		739	726	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0034711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	141	291	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.723605682521002	2		291	361	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164610	47164610	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	144	380	0	ENST00000409792.3:c.1516A>G	p.Arg506Gly	p.R506G	ENST00000409792	NM_014159.6	506	Aga/Gga	3/21	1	2	FACETS	0.911	0.838	0.985	0.911	0.838	0.985	CLONAL	1	TRUE	1	0.723605682521002	2		380	437	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532645	187532645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	109	487	0	ENST00000441802.2:c.9748C>T	p.Leu3250Phe	p.L3250F	ENST00000441802	NM_005245.3	3250	Ctt/Ttt	14/27	0.723605682521002	2	FACETS	0.629	0.568	0.693	0.314	0.284	0.347	SUBCLONAL	1	TRUE	0	0.723605682521002	2		487	479	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86682702	86682703	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0034711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	101	234	0	ENST00000274376.6:c.2912dup	p.Leu971PhefsTer3	p.L971Ffs*3	ENST00000274376	NM_002890.2	969	-/T	23/25	0.723605682521002	3	FACETS	0.975	0.878	1	0.487	0.439	0.538	CLONAL	1	TRUE	1	0.723605682521002	3		234	390	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	109	417	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.190361925124814	3	FACETS	1	0.983	1	0.745	0.671	0.823	CLONAL	1	FALSE	1	0.3	3		417	561	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579493	7579493	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	211	840	0	ENST00000269305.4:c.194del	p.Arg65LysfsTer58	p.R65Kfs*58	ENST00000269305	NM_001126112.2	65	aGa/aa	4/11	0.182093366356142	2	FACETS	1	0.981	1	0.585	0.542	0.63	CLONAL	1	FALSE	0	0.3	2		840	1202	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860125	151860125	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	44	570	0	ENST00000262189.6:c.10537C>T	p.Pro3513Ser	p.P3513S	ENST00000262189	NM_170606.2	3513	Cct/Tct	43/59	0.210175194761616	4	FACETS	0.508	0.424	0.6	0.254	0.212	0.3	SUBCLONAL	1	FALSE	2	0.3	4		570	751	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205644	38205644	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	158	986	0	ENST00000317025.8:c.46A>G	p.Ile16Val	p.I16V	ENST00000317025	NM_023034.1	16	Att/Gtt	2/24	0.190361925124814	3	FACETS	0.972	0.889	1	0.486	0.444	0.53	CLONAL	1	FALSE	1	0.3	3		986	1246	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0034728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	50	427	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.862	0.731	1	0.862	0.731	1	CLONAL	1	FALSE	1	0.215345761822074	2		427	539	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244091	153244091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	60	503	0	ENST00000281708.4:c.2066G>A	p.Arg689Gln	p.R689Q	ENST00000281708	NM_033632.3	689	cGg/cAg	12/12	0.0976409977144446	3	FACETS	1	0.905	1	0.532	0.458	0.612	INDETERMINATE	1	FALSE	1	0.215345761822074	3		503	580	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073947	8073947	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs994703930	NA	P-0034728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	41	485	0	ENST00000377482.5:c.712C>T	p.Pro238Ser	p.P238S	ENST00000377482	NM_018948.3	238	Cct/Tct	4/4	1	2	FACETS	0.703	0.585	0.834	0.703	0.585	0.834	SUBCLONAL	1	FALSE	1	0.215345761822074	2		485	542	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827828	72827828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	57	695	0	ENST00000268489.5:c.8753C>T	p.Ser2918Leu	p.S2918L	ENST00000268489	NM_006885.3	2918	tCa/tTa	9/10	1	2	FACETS	0.805	0.69	0.93	0.805	0.69	0.93	CLONAL	1	FALSE	1	0.215345761822074	2		695	658	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944572	40944572	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	34	413	0	ENST00000373198.4:c.1930G>C	p.Glu644Gln	p.E644Q	ENST00000373198	NM_133170.3	644	Gag/Cag	12/32	0.215345761822074	0	FACETS	0.642	0.525	0.773			1	SUBCLONAL	1	FALSE	0	0.215345761822074	0		413	386	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180614	56180614	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	CC	novel	NA	P-0034728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	41	384	0	ENST00000399503.3:c.3943delinsCC	p.Glu1315ProfsTer10	p.E1315Pfs*10	ENST00000399503	NM_005921.1	1315	Gag/CCag	16/20	0.0976409977144446	3	FACETS	0.805	0.67	0.955	0.402	0.335	0.478	INDETERMINATE	1	FALSE	1	0.215345761822074	3		384	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0034729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1231	112	732	1	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	1	2	FACETS	0.408	0.366	0.453	0.408	0.366	0.453	SUBCLONAL	1	TRUE	1	0.408717912790667	2		733	1343	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	40	315	0	ENST00000397062.3:c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	NM_006164.4	34	Cga/Gga	2/5	1	2	FACETS	0.332	0.275	0.395	0.332	0.275	0.395	SUBCLONAL	1	TRUE	1	0.408717912790667	2		315	590	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971138	21971138	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs760640852	NA	P-0034729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	141	396	0	ENST00000304494.5:c.220G>T	p.Asp74Tyr	p.D74Y	ENST00000304494	NM_000077.4	74	Gac/Tac	2/3	1	2	FACETS	0.869	0.792	0.949	0.869	0.792	0.949	CLONAL	1	TRUE	1	0.408717912790667	2		396	794	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390917	89390917	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	51	328	0	ENST00000336596.2:c.983C>A	p.Ser328Ter	p.S328*	ENST00000336596	NM_005233.5	328	tCa/tAa	5/17	1	2	FACETS	0.482	0.409	0.561	0.482	0.409	0.561	SUBCLONAL	1	TRUE	1	0.408717912790667	2		328	518	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174441	11174441	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	66	661	0	ENST00000361445.4:c.7234G>T	p.Asp2412Tyr	p.D2412Y	ENST00000361445	NM_004958.3	2412	Gac/Tac	53/58	1	2	FACETS	0.276	0.238	0.317	0.276	0.238	0.317	SUBCLONAL	1	TRUE	1	0.408717912790667	2		661	1171	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247230	153247230	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	55	382	0	ENST00000281708.4:c.1572G>C	p.Lys524Asn	p.K524N	ENST00000281708	NM_033632.3	524	aaG/aaC	10/12	1	2	FACETS	0.418	0.357	0.485	0.418	0.357	0.485	SUBCLONAL	1	TRUE	1	0.408717912790667	2		382	644	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275858	38275858	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	74	506	0	ENST00000425967.3:c.1411G>A	p.Gly471Arg	p.G471R	ENST00000425967	NM_001174067.1	471	Ggg/Agg	11/19	NA	2	FACETS	0.352	0.307	0.4			1	INDETERMINATE	1	TRUE	NA	0.408717912790667	2		506	1030	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0034735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	120	442	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.923	0.835	1	0.923	0.835	1	CLONAL	1	FALSE	1	0.393822572780391	2		443	660	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0034735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	168	316	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.963	1	1	0.993	1	CLONAL	2	FALSE	1	0.393822572780391	2		316	405	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814303	76814306	+	frameshift_variant	Frame_Shift_Del	DEL	ATAA	ATAA	-	novel	NA	P-0034735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	147	135	0	ENST00000373344.5:c.6338_6341del	p.Phe2113SerfsTer9	p.F2113Sfs*9	ENST00000373344	NM_000489.3	2113	tTTATc/tc	29/35	1	1	FACETS	1	0.988	1	1	0.994	1	CLONAL	3	FALSE	0	0.393822572780391	1		135	179	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106916	27106917	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0034735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	98	380	0	ENST00000324856.7:c.6527_6528del	p.Gln2176ArgfsTer48	p.Q2176Rfs*48	ENST00000324856	NM_006015.4	2176	cAG/c	20/20	1	2	FACETS	0.764	0.683	0.851	0.764	0.683	0.851	SUBCLONAL	1	FALSE	1	0.393822572780391	2		380	651	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774735	73774736	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0034735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	91	174	0	ENST00000254810.4:c.351_352del	p.Arg117SerfsTer30	p.R117Sfs*30	ENST00000254810	NM_005324.3	117	agAGtc/agtc	4/4	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.393822572780391	2		174	353	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317533	1317533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199794164	NA	P-0034735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	95	455	1	ENST00000400841.2:c.532G>A	p.Glu178Lys	p.E178K	ENST00000400841		178	Gag/Aag	5/6	0.387547101156283	0	FACETS	0.364	0.323	0.407			1	SUBCLONAL	1	FALSE	NA	0.393822572780391	0		456	804	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574022	7574023	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGCCCC	novel	NA	P-0034735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	804	546	0	ENST00000269305.4:c.1004_1005insGGGGCG	p.Gly334_Arg335dup	p.G334_R335dup	ENST00000269305	NM_001126112.2	334	cgt/cgGGGGCGt	10/11	0.393822572780391	2	FACETS	1	0.993	1	1	0.998	1	CLONAL	4	FALSE	0	0.393822572780391	2		546	995	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404313	139404315	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	novel	NA	P-0034735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	170	682	0	ENST00000277541.6:c.2839_2841del	p.Asn947del	p.N947del	ENST00000277541	NM_017617.3	947	AAC/-	18/34	1	2	FACETS	0.739	0.678	0.802	0.739	0.678	0.802	SUBCLONAL	1	FALSE	1	0.393822572780391	2		682	1169	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0034751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	74	698	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.927	0.809	1	0.927	0.809	1	CLONAL	1	TRUE	1	0.16	2		698	998	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0034751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	17	263	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.409	0.304	0.535	0.409	0.304	0.535	SUBCLONAL	1	TRUE	1	0.16	2		263	519	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739064	40739064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780908301	NA	P-0034751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	33	568	0	ENST00000373198.4:c.3220G>A	p.Val1074Ile	p.V1074I	ENST00000373198	NM_133170.3	1074	Gtt/Att	24/32	1	2	FACETS	0.667	0.542	0.809	0.667	0.542	0.809	SUBCLONAL	1	TRUE	1	0.16	2		568	618	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831226	3831226	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398406959	NA	P-0034751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	63	530	0	ENST00000262367.5:c.1655C>T	p.Pro552Leu	p.P552L	ENST00000262367	NM_004380.2	552	cCg/cTg	7/31	1	2	FACETS	0.966	0.834	1	0.966	0.834	1	CLONAL	1	TRUE	1	0.16	2		530	815	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864658	68864658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1418006656	NA	P-0034751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	36	302	0	ENST00000288368.4:c.29G>A	p.Arg10His	p.R10H	ENST00000288368	NM_024870.2	10	cGc/cAc	1/40	1	2	FACETS	0.84	0.694	1	1	0.958	1	CLONAL	2	TRUE	1	0.16	2		302	268	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950049	44950049	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	44	379	0	ENST00000377967.4:c.3818T>G	p.Leu1273Arg	p.L1273R	ENST00000377967	NM_021140.2	1273	cTt/cGt	26/29	0.3	2	FACETS	1	0.926	1	0.594	0.498	0.7	CLONAL	1	TRUE	0	0.16	2		379	463	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0034752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1237	74	984	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	1	2	FACETS	0.753	0.656	0.857	0.753	0.656	0.857	SUBCLONAL	1	TRUE	1	0.15	2		984	1311	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7168066	7168066	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	46	596	0	ENST00000302850.5:c.1523C>G	p.Ser508Cys	p.S508C	ENST00000302850	NM_000208.2	508	tCt/tGt	7/22	1	2	FACETS	0.805	0.676	0.948	0.805	0.676	0.948	CLONAL	1	TRUE	1	0.15	2		596	762	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750897	128750897	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	123	667	1	ENST00000377970.2:c.434T>A	p.Ile145Asn	p.I145N	ENST00000377970	NM_002467.4	145	aTc/aAc	2/3	0.3	3	FACETS	1	0.933	1	1	0.933	1	CLONAL	2	TRUE	1	0.15	3		668	847	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411895	116411919	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTTTTAAGATCTGGGCAGTGAATTA	GTTTTAAGATCTGGGCAGTGAATTA	-	novel	NA	P-0034752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1312	334	1039	0	ENST00000397752.3:c.2888-5_2907del		p.X963_splice	ENST00000397752	NM_000245.2	963		14/21	0.3	3	FACETS	0.969	0.914	1	1	0.994	1	CLONAL	3	TRUE	1	0.15	3		1039	1646	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0034753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	529	578	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.56931293012729	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.56931293012729	2		578	903	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0034753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	150	350	1	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.929	0.854	1	0.929	0.854	1	CLONAL	1	TRUE	1	0.56931293012729	2		351	567	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0034753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	176	506	0	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	0.56931293012729	1	FACETS	0.943	0.877	1	0.943	0.877	1	CLONAL	1	TRUE	0	0.56931293012729	1		506	469	SUCCESS
APC	324	MSKCC	GRCh37	5	112175171	112175171	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085373	NA	P-0034753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	88	267	0	ENST00000257430.4:c.3880C>T	p.Gln1294Ter	p.Q1294*	ENST00000257430	NM_000038.5	1294	Cag/Tag	16/16	1	2	FACETS	0.928	0.83	1	0.928	0.83	1	CLONAL	1	TRUE	1	0.56931293012729	2		267	333	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236087	108236087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781894	NA	P-0034753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	200	519	1	ENST00000278616.4:c.9023G>A	p.Arg3008His	p.R3008H	ENST00000278616	NM_000051.3	3008	cGt/cAt	63/63	0.56931293012729	1	FACETS	0.98	0.916	1	0.98	0.916	1	CLONAL	1	TRUE	0	0.56931293012729	1		520	513	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0034753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	175	326	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.56931293012729	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.56931293012729	1		326	373	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046611	30046611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556530827	NA	P-0034753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	252	663	0	ENST00000331968.5:c.2572C>T	p.Arg858Cys	p.R858C	ENST00000331968	NM_002742.2	858	Cgc/Tgc	18/18	1	2	FACETS	0.994	0.931	1	0.994	0.931	1	CLONAL	1	TRUE	1	0.56931293012729	2		663	891	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609672	117609672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	144	447	1	ENST00000368508.3:c.7027G>A	p.Gly2343Arg	p.G2343R	ENST00000368508	NM_002944.2	2343	Gga/Aga	43/43	1	2	FACETS	0.958	0.879	1	0.958	0.879	1	CLONAL	1	TRUE	1	0.56931293012729	2		448	528	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560052	29560052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	133	316	0	ENST00000356175.3:c.3529G>A	p.Ala1177Thr	p.A1177T	ENST00000356175	NM_000267.3	1177	Gct/Act	27/57	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.56931293012729	2		316	435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0034754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	195	822	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.436561476274024	1	FACETS	0.95	0.883	1	0.95	0.883	1	CLONAL	1	TRUE	0	0.464163709353778	1		822	679	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786715	3786715	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	129	768	0	ENST00000262367.5:c.4496T>C	p.Leu1499Pro	p.L1499P	ENST00000262367	NM_004380.2	1499	cTg/cCg	27/31	0.238996554962395	1	FACETS	0.526	0.476	0.577	0.526	0.476	0.577	INDETERMINATE	1	TRUE	0	0.464163709353778	1		768	812	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020429	14020429	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	60	390	0	ENST00000311895.7:c.400T>C	p.Tyr134His	p.Y134H	ENST00000311895	NM_005236.2	134	Tat/Cat	3/11	0.238996554962395	1	FACETS	0.462	0.399	0.53	0.462	0.399	0.53	INDETERMINATE	1	TRUE	0	0.464163709353778	1		390	430	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278060	18278060	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	203	723	1	ENST00000222254.8:c.1680G>T	p.Met560Ile	p.M560I	ENST00000222254	NM_005027.3	560	atG/atT	13/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.464163709353778	2		724	763	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205620	38205620	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	186	929	0	ENST00000317025.8:c.70G>C	p.Asp24His	p.D24H	ENST00000317025	NM_023034.1	24	Gac/Cac	2/24	1	2	FACETS	0.811	0.749	0.876	0.811	0.749	0.876	CLONAL	1	TRUE	1	0.464163709353778	2		929	988	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564485	41564485	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	28	424	0	ENST00000263253.7:c.3907G>C	p.Glu1303Gln	p.E1303Q	ENST00000263253	NM_001429.3	1303	Gag/Cag	24/31	1	2	FACETS	0.228	0.181	0.281	0.228	0.181	0.281	SUBCLONAL	1	TRUE	1	0.464163709353778	2		424	530	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115928	8115929	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0034764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	147	469	0	ENST00000346208.3:c.1275dup	p.Ser426IlefsTer81	p.S426Ifs*81	ENST00000346208		425	cca/ccAa	6/6	0.515724953807706	3	FACETS	0.867	0.794	0.944	0.434	0.397	0.472	CLONAL	1	TRUE	1	0.665150184577104	3		469	679	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843495	3843495	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	139	667	3	ENST00000262367.5:c.1108C>T	p.Arg370Ter	p.R370*	ENST00000262367	NM_004380.2	370	Cga/Tga	4/31	0.251040529208682	2	FACETS	0.603	0.55	0.659	0.302	0.275	0.33	INDETERMINATE	1	TRUE	0	0.665150184577104	2		670	693	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156713	20156713	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	147	668	0	ENST00000379607.5:c.44G>T	p.Gly15Val	p.G15V	ENST00000379607	NM_001412.3	15	gGt/gTt	2/7	1	2	FACETS	0.619	0.566	0.674	0.619	0.566	0.674	SUBCLONAL	1	TRUE	1	0.665150184577104	2		668	714	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814153	76814153	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	45	303	0	ENST00000373344.5:c.6491G>A	p.Arg2164Lys	p.R2164K	ENST00000373344	NM_000489.3	2164	aGg/aAg	29/35	1	2	FACETS	0.462	0.39	0.54	0.462	0.39	0.54	SUBCLONAL	1	TRUE	1	0.665150184577104	2		303	293	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667795	37667795	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	103	474	0	ENST00000447079.4:c.2680A>G	p.Asn894Asp	p.N894D	ENST00000447079	NM_015083.1	894	Aac/Gac	8/14	0.295996079076312	4	FACETS	1	0.964	1	0.287	0.258	0.317	INDETERMINATE	1	TRUE	0	0.764419943037336	4		474	414	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537132	41537133	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAGC	novel	NA	P-0034766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	119	498	0	ENST00000263253.7:c.1961_1964dup	p.Asn656AlafsTer20	p.N656Afs*20	ENST00000263253	NM_001429.3	653	-/AAGC	10/31	0.713119231990553	2	FACETS	0.875	0.798	0.953	0.437	0.399	0.477	CLONAL	1	TRUE	0	0.764419943037336	2		498	356	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272543	142272543	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	30	768	0	ENST00000350721.4:c.2572C>A	p.Gln858Lys	p.Q858K	ENST00000350721	NM_001184.3	858	Caa/Aaa	12/47	0.247232356344662	4	FACETS	0.246	0.197	0.301	0.123	0.098	0.151	INDETERMINATE	1	TRUE	2	0.764419943037336	4		768	563	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272570	142272570	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0034766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	81	691	0	ENST00000350721.4:c.2545A>T	p.Arg849Ter	p.R849*	ENST00000350721	NM_001184.3	849	Aga/Tga	12/47	0.247232356344662	4	FACETS	0.864	0.764	0.969	0.432	0.382	0.485	INDETERMINATE	1	TRUE	2	0.764419943037336	4		691	433	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0034776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	15	298	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.0993574516804979	3	FACETS	1	0.733	1	0.501	0.366	0.664	CLONAL	1	TRUE	1	0.11	3		298	287	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0034776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	23	573	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.0993574516804979	0	FACETS	0.777	0.604	0.978			1	CLONAL	1	TRUE	0	0.11	0		573	479	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264985	46264985	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	22	451	0	ENST00000371998.3:c.1860del	p.Lys620AsnfsTer18	p.K620Nfs*18	ENST00000371998		619	Aaa/aa	12/23	1	2	FACETS	0.941	0.728	1	0.941	0.728	1	CLONAL	1	TRUE	1	0.11	2		451	425	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0034776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	26	788	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.967	0.764	1	0.967	0.764	1	CLONAL	1	TRUE	1	0.11	2		790	489	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591004	67591005	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0034776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	16	248	0	ENST00000274335.5:c.1599_1600del	p.Arg534AsnfsTer3	p.R534Nfs*3	ENST00000274335		533	TCt/t	12/15	0.1677178763158	3	FACETS	1	0.796	1	0.546	0.403	0.717	CLONAL	1	TRUE	1	0.11	3		248	281	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509517	106509517	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	39	622	0	ENST00000359195.3:c.1511C>A	p.Ser504Tyr	p.S504Y	ENST00000359195	NM_002649.2	504	tCt/tAt	2/11	0.670784627677878	3	FACETS	0.255	0.21	0.304	0.127	0.105	0.152	SUBCLONAL	1	TRUE	1	0.670784627677878	3		622	610	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699362	47699362	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	297	460	0	ENST00000347630.2:c.146G>T	p.Gly49Val	p.G49V	ENST00000347630	NM_001007230.1	49	gGt/gTt	4/11	0.670784627677878	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	4	TRUE	0	0.670784627677878	4		460	360	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639596	47639596	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1553351592	NA	P-0034780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	50	326	0	ENST00000233146.2:c.689C>G	p.Ala230Gly	p.A230G	ENST00000233146	NM_000251.2	230	gCt/gGt	4/16	1	2	FACETS	0.948	0.805	1	0.948	0.805	1	CLONAL	1	TRUE	1	0.209317281937182	2		326	504	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622651	158622651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	81	410	0	ENST00000263640.3:c.848C>T	p.Thr283Ile	p.T283I	ENST00000263640	NM_001105.4	283	aCa/aTa	8/11	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.209317281937182	2		410	730	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266048	41266049	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0034780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	60	293	0	ENST00000349496.5:c.47dup	p.Asp17ArgfsTer7	p.D17Rfs*7	ENST00000349496	NM_001904.3	15	-/C	3/15	0.15227765044326	2	FACETS	1	0.966	1	0.706	0.61	0.809	CLONAL	1	TRUE	0	0.209317281937182	2		293	406	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50830234	50830271	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GGTGGTCAGAATGGCTTCAACATTCCTCAAGTCACCCC	GGTGGTCAGAATGGCTTCAACATTCCTCAAGTCACCCC	T	novel	NA	P-0034780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	48	331	0	ENST00000398568.2:c.2678-1_2714delinsT		p.X893_splice	ENST00000398568	NM_001042412.1	893		18/18	0.178842386242899	1	FACETS	0.815	0.689	0.953	0.815	0.689	0.953	CLONAL	1	TRUE	0	0.209317281937182	1		331	504	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143020	47143020	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	50	474	0	ENST00000409792.3:c.4943T>A	p.Val1648Asp	p.V1648D	ENST00000409792	NM_014159.6	1648	gTt/gAt	8/21	1	2	FACETS	0.415	0.351	0.486	0.415	0.351	0.486	SUBCLONAL	1	FALSE	1	0.3	2		474	803	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815419	32815419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	65	612	0	ENST00000354258.4:c.1954G>A	p.Gly652Arg	p.G652R	ENST00000354258	NM_000593.5	652	Gga/Aga	9/11	1	2	FACETS	0.471	0.407	0.54	0.471	0.407	0.54	SUBCLONAL	1	FALSE	1	0.3	2		612	921	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0034783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	66	263	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.437926129868126	3	FACETS	0.852	0.742	0.971	0.426	0.371	0.486	CLONAL	1	TRUE	1	0.437926129868126	3		263	431	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692816	89692817	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554898084	NA	P-0034783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	167	292	0	ENST00000371953.3:c.301dup	p.Ile101AsnfsTer6	p.I101Nfs*6	ENST00000371953	NM_000314.4	100	-/A	5/9	0.437926129868126	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.437926129868126	2		292	335	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247361	71247361	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	258	522	0	ENST00000318789.4:c.172C>T	p.Gln58Ter	p.Q58*	ENST00000318789	NM_032682.5	58	Cag/Tag	6/21	0.437926129868126	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.437926129868126	2		522	530	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0034785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	229	498	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.525451786379938	3	FACETS	0.925	0.869	0.983	0.925	0.869	0.983	CLONAL	2	TRUE	1	0.53068187288158	3		498	590	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223550	55223550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	293	542	1	ENST00000275493.2:c.917C>T	p.Ser306Leu	p.S306L	ENST00000275493	NM_005228.3	306	tCg/tTg	8/28	0.525451786379938	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.53068187288158	3		543	674	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273793	18273793	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs886041591	NA	P-0034785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	152	466	0	ENST00000222254.8:c.1126A>G	p.Lys376Glu	p.K376E	ENST00000222254	NM_005027.3	376	Aag/Gag	10/16	0.53068187288158	2	FACETS	1	0.97	1	0.556	0.512	0.602	CLONAL	1	TRUE	0	0.53068187288158	2		466	515	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643663	38643663	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	145	661	0	ENST00000299084.4:c.1133A>G	p.His378Arg	p.H378R	ENST00000299084	NM_152594.2	378	cAt/cGt	7/7	1	2	FACETS	0.9	0.825	0.979	0.9	0.825	0.979	CLONAL	1	TRUE	1	0.53068187288158	2		661	607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0034789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	528	546	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.32742065192762	2	FACETS	0.963	0.939	0.985	1	0.998	1	CLONAL	5	TRUE	0	0.32742065192762	2		547	670	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0034789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	114	316	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.951	1	1	0.99	1	CLONAL	2	TRUE	1	0.32742065192762	2		316	327	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891404	76891404	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0034789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	194	206	0	ENST00000373344.5:c.4699+2T>C		p.X1567_splice	ENST00000373344	NM_000489.3	1567			1	1	FACETS	0.949	0.907	0.989	1	0.996	1	CLONAL	4	TRUE	0	0.32742065192762	1		206	261	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0034812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	575	546	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.654289765883002	3	FACETS	0.998	0.972	1	0.998	0.972	1	CLONAL	3	TRUE	0	0.654289765883002	3		547	779	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31423033	31423033	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	150	607	0	ENST00000344624.3:c.3280G>T	p.Asp1094Tyr	p.D1094Y	ENST00000344624		1094	Gat/Tat	26/33	0.443537457021839	4	FACETS	1	0.938	1	0.507	0.469	0.546	CLONAL	2	TRUE	0	0.654289765883002	4		607	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691039	NA	P-0034816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	971	629	0	ENST00000269305.4:c.919+1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.830193795674913	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.830193795674913	3		629	1092	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447841	49447841	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748834953	NA	P-0034816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	283	578	1	ENST00000301067.7:c.593C>T	p.Ala198Val	p.A198V	ENST00000301067	NM_003482.3	198	gCg/gTg	5/54	NA	2	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.830193795674913	2		579	644	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434475	110434475	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	429	573	0	ENST00000375856.3:c.3926C>T	p.Pro1309Leu	p.P1309L	ENST00000375856	NM_003749.2	1309	cCg/cTg	1/2	0.390238655617355	2	FACETS	0.754	0.727	0.781	0.754	0.727	0.781	INDETERMINATE	2	TRUE	0	0.830193795674913	2		573	685	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0034818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	327	557	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	0.914	0.866	0.962	0.914	0.866	0.962	CLONAL	1	TRUE	1	0.80678411367478	2		557	887	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808870	1808870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs560280646	NA	P-0034818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	755	649	5	ENST00000260795.2:c.2302G>A	p.Glu768Lys	p.E768K	ENST00000260795		768	Gag/Aag	17/17	NA	2	FACETS	1	0.998	1			1	INDETERMINATE	1	TRUE	NA	0.80678411367478	2		654	1349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0034818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	408	685	3	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.80678411367478	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.80678411367478	1		688	575	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562298	21562298	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	266	707	1	ENST00000382592.4:c.1621G>T	p.Glu541Ter	p.E541*	ENST00000382592	NM_014572.2	541	Gag/Tag	4/8	0.80678411367478	1	FACETS	0.649	0.614	0.685	0.649	0.614	0.685	SUBCLONAL	1	TRUE	0	0.80678411367478	1		708	606	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70412308	70412308	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	185	310	1	ENST00000373644.4:c.4418G>T	p.Gly1473Val	p.G1473V	ENST00000373644	NM_030625.2	1473	gGt/gTt	6/12	1	2	FACETS	0.915	0.853	0.979	0.915	0.853	0.979	CLONAL	1	TRUE	1	0.80678411367478	2		311	501	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123681	46123682	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGAG	novel	NA	P-0034818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	324	306	0	ENST00000334344.6:c.64_67dup	p.Leu23ArgfsTer14	p.L23Rfs*14	ENST00000334344	NM_152641.2	21	gac/gaCGAGc	1/21	0.461303676006301	3	FACETS	0.892	0.851	0.933			1	INDETERMINATE	2	TRUE	NA	0.80678411367478	3		306	632	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562031	21562031	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	285	907	0	ENST00000382592.4:c.1888G>C	p.Glu630Gln	p.E630Q	ENST00000382592	NM_014572.2	630	Gaa/Caa	4/8	0.80678411367478	1	FACETS	0.588	0.556	0.62	0.588	0.556	0.62	SUBCLONAL	1	TRUE	0	0.80678411367478	1		907	717	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434426	110434426	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	405	644	0	ENST00000375856.3:c.3975C>G	p.Phe1325Leu	p.F1325L	ENST00000375856	NM_003749.2	1325	ttC/ttG	1/2	0.80678411367478	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.80678411367478	1		644	550	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792651	33792651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	88	118	0	ENST00000498907.2:c.670C>T	p.His224Tyr	p.H224Y	ENST00000498907	NM_004364.3	224	Cac/Tac	1/1	0.153933149935305	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.80678411367478	0		118	191	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1253896	1253896	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1196160200	NA	P-0034818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	72	537	0	ENST00000310581.5:c.3346G>C	p.Glu1116Gln	p.E1116Q	ENST00000310581	NM_198253.2	1116	Gag/Cag	16/16	0.752754621867544	3	FACETS	0.227	0.197	0.259	0.113	0.098	0.13	SUBCLONAL	1	TRUE	1	0.80678411367478	3		537	1104	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123687	46123687	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	334	291	0	ENST00000334344.6:c.68T>G	p.Leu23Arg	p.L23R	ENST00000334344	NM_152641.2	23	cTg/cGg	1/21	0.461303676006301	3	FACETS	0.983	0.941	1			1	INDETERMINATE	2	TRUE	NA	0.80678411367478	3		291	591	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0034819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	27	263	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.203720145328933	2		263	234	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0034819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	58	706	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	0.203720145328933	1	FACETS	0.828	0.711	0.955	0.828	0.711	0.955	CLONAL	1	TRUE	0	0.203720145328933	1		706	618	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	534	673	0	ENST00000269571.5:c.829G>C	p.Asp277His	p.D277H	ENST00000269571		277	Gac/Cac	7/27	0.646464276988568	4	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.646464276988568	4		673	1122	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921555	178921555	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	209	326	0	ENST00000263967.3:c.1037T>G	p.Val346Gly	p.V346G	ENST00000263967	NM_006218.2	346	gTa/gGa	5/21	0.646464276988568	4	FACETS	1	0.963	1	1	0.963	1	CLONAL	3	TRUE	1	0.646464276988568	4		326	348	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002734	37002734	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	47	484	1	ENST00000358127.4:c.515C>T	p.Thr172Met	p.T172M	ENST00000358127	NM_001280556.1	172	aCg/aTg	5/10	0.227191327845627	3	FACETS	0.356	0.3	0.418	0.119	0.1	0.14	INDETERMINATE	1	TRUE	0	0.646464276988568	3		485	540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1555525585	NA	P-0034820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	301	452	2	ENST00000269305.4:c.673-2A>G		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.646464276988568	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.646464276988568	2		454	426	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266753	142266753	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0034820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	257	368	0	ENST00000350721.4:c.3172-1G>C		p.X1058_splice	ENST00000350721	NM_001184.3	1058			0.568941240007354	6	FACETS	1	0.975	1			1	CLONAL	3	TRUE	NA	0.646464276988568	6		368	576	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45377650	45377650	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	124	251	0	ENST00000262160.6:c.779G>C	p.Ser260Thr	p.S260T	ENST00000262160	NM_005901.5	260	aGc/aCc	7/11	0.597804282718496	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.646464276988568	2		251	180	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917035	50917035	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	166	616	0	ENST00000440232.2:c.2288del	p.Phe763SerfsTer125	p.F763Sfs*125	ENST00000440232	NM_002691.3	763	Ttc/tc	19/27	NA	2	FACETS	1	0.928	1			1	INDETERMINATE	1	TRUE	NA	0.646464276988568	2		616	512	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31401656	31401656	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	284	418	0	ENST00000344624.3:c.4008G>C	p.Gln1336His	p.Q1336H	ENST00000344624		1336	caG/caC	33/33	0.400074421179278	5	FACETS	0.893	0.846	0.94	0.893	0.846	0.94	CLONAL	3	TRUE	2	0.646464276988568	5		418	646	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127911993	127911993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	140	451	0	ENST00000373547.4:c.877C>T	p.Arg293Cys	p.R293C	ENST00000373547	NM_002721.4	293	Cgt/Tgt	7/7	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.646464276988568	2		451	427	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938330	76938330	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs782580387	NA	P-0034820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	111	696	0	ENST00000373344.5:c.2418G>C	p.Lys806Asn	p.K806N	ENST00000373344	NM_000489.3	806	aaG/aaC	9/35	0.227191327845627	3	FACETS	0.881	0.795	0.97	0.294	0.265	0.324	INDETERMINATE	1	TRUE	0	0.646464276988568	3		696	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578548	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0034846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	200	797	0	ENST00000269305.4:c.382_383del	p.Pro128CysfsTer20	p.P128Cfs*20	ENST00000269305	NM_001126112.2	128	CCt/t	5/11	0.497706157228529	1	FACETS	0.92	0.857	0.985	0.92	0.857	0.985	CLONAL	1	TRUE	0	0.497706157228529	1		797	656	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624483	21624483	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	241	700	0	ENST00000421138.2:c.1546A>G	p.Ile516Val	p.I516V	ENST00000421138		516	Att/Gtt	14/16	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.497706157228529	2		700	954	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131632	2131632	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	34	590	0	ENST00000219476.3:c.3647T>A	p.Leu1216His	p.L1216H	ENST00000219476	NM_000548.3	1216	cTc/cAc	31/42	1	2	FACETS	0.232	0.188	0.28	0.232	0.188	0.28	SUBCLONAL	1	TRUE	1	0.497706157228529	2		590	590	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031141	11031141	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	146	691	0	ENST00000327064.4:c.1226C>G	p.Thr409Arg	p.T409R	ENST00000327064	NM_199141.1	409	aCa/aGa	11/16	1	2	FACETS	0.93	0.851	1	0.93	0.851	1	CLONAL	1	TRUE	1	0.497706157228529	2		691	631	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742767	39742790	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	ACTATAACAAGGTCCCTGTTGAGA	ACTATAACAAGGTCCCTGTTGAGA	-	novel	NA	P-0034846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	86	437	0	ENST00000361337.2:c.1611_1634del	p.Tyr537_Lys545delinsTer	p.Y537_K545delins*	ENST00000361337	NM_003286.2	537	tACTATAACAAGGTCCCTGTTGAGAaa/taa	15/21	0.497706157228529	3	FACETS	0.563	0.497	0.633	0.281	0.248	0.317	SUBCLONAL	1	TRUE	1	0.497706157228529	3		437	767	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381560	81381560	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0034846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	71	286	0	ENST00000222390.5:c.501T>G	p.Tyr167Ter	p.Y167*	ENST00000222390	NM_000601.4	167	taT/taG	5/18	1	2	FACETS	0.757	0.664	0.856	0.757	0.664	0.856	SUBCLONAL	1	TRUE	1	0.497706157228529	2		286	377	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133325	38133325	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1184541530	NA	P-0034846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	114	492	0	ENST00000317025.8:c.4148A>G	p.His1383Arg	p.H1383R	ENST00000317025	NM_023034.1	1383	cAt/cGt	24/24	1	2	FACETS	0.78	0.705	0.86	0.78	0.705	0.86	SUBCLONAL	1	TRUE	1	0.497706157228529	2		492	587	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0034848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	159	371	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	0.557051783518918	2		371	517	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0034848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	41	383	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.292356831092208	3	FACETS	0.293	0.243	0.348	0.146	0.121	0.174	INDETERMINATE	1	TRUE	1	0.557051783518918	3		383	643	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0034848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	92	447	2	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.425648431032478	3	FACETS	0.482	0.428	0.54	0.241	0.214	0.27	SUBCLONAL	1	TRUE	1	0.557051783518918	3		449	876	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0034848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	191	458	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.425648431032478	3	FACETS	1	0.932	1	0.504	0.466	0.543	CLONAL	1	TRUE	1	0.557051783518918	3		459	870	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224583	108224583	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881329	NA	P-0034848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	97	278	0	ENST00000278616.4:c.8762C>T	p.Thr2921Met	p.T2921M	ENST00000278616	NM_000051.3	2921	aCg/aTg	60/63	1	2	FACETS	0.86	0.772	0.952	0.86	0.772	0.952	CLONAL	1	TRUE	1	0.557051783518918	2		278	405	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984448	201984449	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0034848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	152	387	0	ENST00000359651.3:c.1114dup	p.Ter372LeufsTer99	p.*372Lfs*99	ENST00000359651		371	-/T	8/8	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.557051783518918	2		387	497	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298012	15298012	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	252	730	0	ENST00000263388.2:c.1744C>G	p.Gln582Glu	p.Q582E	ENST00000263388	NM_000435.2	582	Cag/Gag	11/33	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.557051783518918	2		730	861	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0034853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	155	546	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.402099010957413	1	FACETS	0.792	0.726	0.86	0.792	0.726	0.86	SUBCLONAL	1	TRUE	0	0.422366647757627	1		547	731	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0034853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	147	427	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.872	0.797	0.951	0.872	0.797	0.951	CLONAL	1	TRUE	1	0.422366647757627	2		427	798	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0034853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	189	325	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	0.235749565621558	3	FACETS	1	0.973	1	0.724	0.675	0.774	INDETERMINATE	2	TRUE	0	0.422366647757627	3		325	499	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25990499	25990503	+	frameshift_variant	Frame_Shift_Del	DEL	AGTAA	AGTAA	-	novel	NA	P-0034853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	247	530	0	ENST00000435504.4:c.724_728del	p.Leu242ArgfsTer11	p.L242Rfs*11	ENST00000435504		242	TTACTa/a	8/13	0.37992089702396	2	FACETS	0.851	0.8	0.903	0.851	0.8	0.903	CLONAL	2	TRUE	0	0.422366647757627	2		530	687	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968610	55968610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374980446	NA	P-0034853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	135	635	0	ENST00000263923.4:c.2053G>A	p.Glu685Lys	p.E685K	ENST00000263923	NM_002253.2	685	Gaa/Aaa	14/30	1	2	FACETS	0.776	0.705	0.85	0.776	0.705	0.85	SUBCLONAL	1	TRUE	1	0.422366647757627	2		635	824	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838032	156838032	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	145	767	0	ENST00000524377.1:c.565G>C	p.Ala189Pro	p.A189P	ENST00000524377	NM_002529.3	189	Gcc/Ccc	5/17	1	2	FACETS	0.826	0.754	0.902	0.826	0.754	0.902	CLONAL	1	TRUE	1	0.422366647757627	2		767	831	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477083	67477083	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	102	447	0	ENST00000327367.4:c.890A>G	p.Tyr297Cys	p.Y297C	ENST00000327367	NM_005902.3	297	tAc/tGc	7/9	1	2	FACETS	0.938	0.842	1	0.938	0.842	1	CLONAL	1	TRUE	1	0.422366647757627	2		447	515	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966760	18966760	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	58	695	0	ENST00000262803.5:c.1571A>T	p.Asn524Ile	p.N524I	ENST00000262803	NM_002911.3	524	aAc/aTc	12/24	1	2	FACETS	0.283	0.242	0.328	0.283	0.242	0.328	SUBCLONAL	1	TRUE	1	0.422366647757627	2		695	969	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911551	134911551	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	118	465	0	ENST00000398015.3:c.2016G>A	p.Met672Ile	p.M672I	ENST00000398015	NM_004441.4	672	atG/atA	11/16	1	2	FACETS	0.834	0.754	0.919	0.834	0.754	0.919	CLONAL	1	TRUE	1	0.422366647757627	2		465	670	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604607	55604607	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	52	467	0	ENST00000288135.5:c.2815T>G	p.Leu939Val	p.L939V	ENST00000288135	NM_000222.2	939	Tta/Gta	21/21	1	2	FACETS	0.347	0.295	0.405	0.347	0.295	0.405	SUBCLONAL	1	TRUE	1	0.422366647757627	2		467	709	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652231	36652231	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	133	530	0	ENST00000244741.5:c.355del	p.Val120CysfsTer28	p.V120Cfs*28	ENST00000244741	NM_000389.4	118	aCc/ac	2/3	1	2	FACETS	0.973	0.886	1	0.973	0.886	1	CLONAL	1	TRUE	1	0.422366647757627	2		530	647	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0034854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	104	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.89	0.798	0.987	0.89	0.798	0.987	CLONAL	1	TRUE	1	0.378765706797111	2		371	617	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0034854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	136	343	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.378765706797111	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.378765706797111	1		343	547	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502382	186502384	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1171371205	NA	P-0034854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	52	426	0	ENST00000323963.5:c.109_111del	p.Asp37del	p.D37del	ENST00000323963		35	ttTGAt/ttt	3/11	1	2	FACETS	0.43	0.366	0.501	0.43	0.366	0.501	SUBCLONAL	1	TRUE	1	0.378765706797111	2		426	638	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399128	139399128	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372830543	NA	P-0034854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	149	500	0	ENST00000277541.6:c.5015G>A	p.Arg1672His	p.R1672H	ENST00000277541	NM_017617.3	1672	cGc/cAc	26/34	1	2	FACETS	0.906	0.828	0.988	0.906	0.828	0.988	CLONAL	1	TRUE	1	0.378765706797111	2		500	868	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118683	115118683	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0034854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	126	497	0	ENST00000257566.3:c.657+1G>T		p.X219_splice	ENST00000257566	NM_016569.3	219			1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.378765706797111	2		497	642	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119060	70119060	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	250	382	0	ENST00000245479.2:c.632C>A	p.Ser211Ter	p.S211*	ENST00000245479	NM_000346.3	211	tCg/tAg	2/3	0.378765706797111	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.378765706797111	2		382	591	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933243	49933243	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767098895	NA	P-0034854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	183	664	1	ENST00000296474.3:c.2867G>A	p.Ser956Asn	p.S956N	ENST00000296474	NM_002447.2	956	aGc/aAc	12/20	1	2	FACETS	0.899	0.829	0.972	0.899	0.829	0.972	CLONAL	1	TRUE	1	0.378765706797111	2		665	1075	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0034855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	173	444	3	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	1	2	FACETS	0.972	0.899	1	0.972	0.899	1	CLONAL	1	TRUE	1	0.55	2		447	647	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	160	417	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.915	0.842	0.99	0.915	0.842	0.99	CLONAL	1	TRUE	1	0.55	2		417	636	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0034855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	181	427	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.869	0.804	0.937	0.869	0.804	0.937	CLONAL	1	TRUE	1	0.55	2		427	757	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218084	108218084	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs760955058	NA	P-0034855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	116	405	0	ENST00000278616.4:c.8663T>C	p.Ile2888Thr	p.I2888T	ENST00000278616	NM_000051.3	2888	aTa/aCa	59/63	1	2	FACETS	0.821	0.743	0.902	0.821	0.743	0.902	CLONAL	1	TRUE	1	0.55	2		405	514	SUCCESS
ATM	472	MSKCC	GRCh37	11	108183216	108183216	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	74	208	0	ENST00000278616.4:c.5998del	p.Ser2000ValfsTer7	p.S2000Vfs*7	ENST00000278616	NM_000051.3	1999	atA/at	40/63	1	2	FACETS	0.941	0.832	1	0.941	0.832	1	CLONAL	1	TRUE	1	0.55	2		208	286	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245520	46245520	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	98	330	0	ENST00000334344.6:c.3614G>T	p.Gly1205Val	p.G1205V	ENST00000334344	NM_152641.2	1205	gGa/gTa	15/21	1	2	FACETS	0.909	0.817	1	0.909	0.817	1	CLONAL	1	TRUE	1	0.55	2		330	392	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512090	148512090	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	165	426	0	ENST00000320356.2:c.1588C>A	p.His530Asn	p.H530N	ENST00000320356	NM_004456.4	530	Cat/Aat	14/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.55	2		426	563	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732962	44733984	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGGGCCGCCGTCACTCGCCCGGTCGGCTCCGGACGGGCAGTAGCCGCTCTCCCGGGAGGACCGAGCGCGGCTTGTCTCTGGCGGCGGCGGGGCGGGCACCTCGGTTTGGCGCTCTTCGCGCCGCCTCCGCTGGGGCCTCGGGCTCGGGCAGGGACGGGTCGGTGGCGTTCCCTGAGCGTTAACGAGTAAACTGTGTCTGTCTCCACAGCCGCCTCTTTGGGTTCGTGAGATTTCATGAAGATGGCGCCAGGACGAAGGCCCTACTGGGCAAGGTAAGGCAGCTGCGAGTCGGAGCGCGGACACCGTCTCCCTGGCCGGCGCCGCGCTCGCCCCGGGCCCCGCGGCCGGGTCTGTGCTCATTGTGGCCACGGACGATGGTCGAGGGGCTTCCGGAAACTATTTCCTGCCTCTGCTCTCCCCCCACCCCCGGGTACCCTGCTTGCTCCCTTGCGAAATCGCTCTTTTCCTCTTGTAGCTGGAGGAACAGAGACGGGATCGCTTTGGGGCCGGGCTCAACTGGGTCGACACAACTGCCTGCTATTTTACAGCTTTTTGAGGGTAGGCCGATGATCTTCGAGGTGCCTGTTTAGGGTCAAGGGATCGTGAGTGTGTTCAGATTTTCCCAAATTTCGGACTTAACTTGCCTCTACGGGTTTAAAAAAATTCTTTTCCTTCAAGCAGGCTGTTCGTGATGCCTACTGCTAACCAAATGTTTTAGGCTTTCTTGTGTCCCCGCTCCCAGAAGGGGGAAGTTTCACGGAGTTTAGGTCGGTGAAGAGTTTGCATTGGGCTGTTGACATGTATCTCGATTGCAGTGTGTGTTACCTGAAGTTAGGTGACTTGTTTACTTTTTGGGTCTTTTTGGCATAGAAATACCGTAGTTATTTGTAAACGTGTTCTCTTCCTGGAGCCTCATTTCCTGTGTGTCTGACAGGGGAGGCTGGGGAGGATTCGGGGTGTAGTCTTTTTTTATTTGTGTGGAAAGTTGTTGGCACTGTCATTTAGTTAAGTAATGGCTGCTCC	CGGGCCGCCGTCACTCGCCCGGTCGGCTCCGGACGGGCAGTAGCCGCTCTCCCGGGAGGACCGAGCGCGGCTTGTCTCTGGCGGCGGCGGGGCGGGCACCTCGGTTTGGCGCTCTTCGCGCCGCCTCCGCTGGGGCCTCGGGCTCGGGCAGGGACGGGTCGGTGGCGTTCCCTGAGCGTTAACGAGTAAACTGTGTCTGTCTCCACAGCCGCCTCTTTGGGTTCGTGAGATTTCATGAAGATGGCGCCAGGACGAAGGCCCTACTGGGCAAGGTAAGGCAGCTGCGAGTCGGAGCGCGGACACCGTCTCCCTGGCCGGCGCCGCGCTCGCCCCGGGCCCCGCGGCCGGGTCTGTGCTCATTGTGGCCACGGACGATGGTCGAGGGGCTTCCGGAAACTATTTCCTGCCTCTGCTCTCCCCCCACCCCCGGGTACCCTGCTTGCTCCCTTGCGAAATCGCTCTTTTCCTCTTGTAGCTGGAGGAACAGAGACGGGATCGCTTTGGGGCCGGGCTCAACTGGGTCGACACAACTGCCTGCTATTTTACAGCTTTTTGAGGGTAGGCCGATGATCTTCGAGGTGCCTGTTTAGGGTCAAGGGATCGTGAGTGTGTTCAGATTTTCCCAAATTTCGGACTTAACTTGCCTCTACGGGTTTAAAAAAATTCTTTTCCTTCAAGCAGGCTGTTCGTGATGCCTACTGCTAACCAAATGTTTTAGGCTTTCTTGTGTCCCCGCTCCCAGAAGGGGGAAGTTTCACGGAGTTTAGGTCGGTGAAGAGTTTGCATTGGGCTGTTGACATGTATCTCGATTGCAGTGTGTGTTACCTGAAGTTAGGTGACTTGTTTACTTTTTGGGTCTTTTTGGCATAGAAATACCGTAGTTATTTGTAAACGTGTTCTCTTCCTGGAGCCTCATTTCCTGTGTGTCTGACAGGGGAGGCTGGGGAGGATTCGGGGTGTAGTCTTTTTTTATTTGTGTGGAAAGTTGTTGGCACTGTCATTTAGTTAAGTAATGGCTGCTCC	-	novel	NA	P-0034855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	103	324	0	ENST00000377967.4:c.161+4_225+751del		p.X54_splice	ENST00000377967	NM_021140.2	54		2/29	1	2	FACETS	0.946	0.853	1	0.946	0.853	1	CLONAL	1	TRUE	1	0.55	2		324	396	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0034856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	169	583	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	1	2	FACETS	0.909	0.838	0.982	0.909	0.838	0.982	CLONAL	1	TRUE	1	0.535180415303488	2		583	695	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520437	176520437	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	144	611	0	ENST00000292408.4:c.1282T>A	p.Ser428Thr	p.S428T	ENST00000292408	NM_213647.1	428	Tca/Aca	10/18	NA	2	FACETS	1	0.934	1			1	INDETERMINATE	1	TRUE	NA	0.535180415303488	2		611	527	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0034878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	228	459	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.741714308585695	2		459	615	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115279407	115279407	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs765189129	NA	P-0034878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	300	493	1	ENST00000438362.2:c.610A>G	p.Ile204Val	p.I204V	ENST00000438362	NM_001242891.1	204	Ata/Gta	6/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.741714308585695	2		494	760	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004609	150004609	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1283527874	NA	P-0034878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	304	738	0	ENST00000253339.5:c.1616A>G	p.Asn539Ser	p.N539S	ENST00000253339		539	aAt/aGt	3/7	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.741714308585695	2		738	795	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040984	47040990	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGCAT	CTGGCAT	-	novel	NA	P-0034878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	276	830	0	ENST00000377604.3:c.1516_1522del	p.Gly506ThrfsTer196	p.G506Tfs*196	ENST00000377604	NM_001204468.1	505	cCTGGCATc/cc	14/24	1	2	FACETS	0.969	0.914	1	0.969	0.914	1	CLONAL	1	TRUE	1	0.741714308585695	2		830	768	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064370	30064370	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	174	400	0	ENST00000338641.4:c.936del	p.Ala313ProfsTer9	p.A313Pfs*9	ENST00000338641	NM_000268.3	312	Aaa/aa	10/16	0.817175472009053	1	FACETS	0.988	0.937	1	0.988	0.937	1	CLONAL	1	TRUE	0	0.817175472009053	1		400	255	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2193702	2193702	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	289	685	0	ENST00000398665.3:c.508G>A	p.Val170Met	p.V170M	ENST00000398665	NM_032482.2	170	Gtg/Atg	6/28	0.817175472009053	1	FACETS	0.923	0.884	0.962	0.923	0.884	0.962	CLONAL	1	TRUE	0	0.817175472009053	1		685	453	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0034880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	147	291	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.936	0.863	1	0.936	0.863	1	CLONAL	1	TRUE	1	0.708675893397979	2		291	443	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0034880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	151	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.708675893397979	2		326	378	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106336	27106337	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0034880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	535	614	0	ENST00000324856.7:c.5952_5953del	p.Ser1985GlnfsTer13	p.S1985Qfs*13	ENST00000324856	NM_006015.4	1983	TGt/t	20/20	0.708675893397979	2	FACETS	0.937	0.908	0.965	0.937	0.908	0.965	CLONAL	2	TRUE	0	0.708675893397979	2		614	806	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653796	89653798	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs1554893765	NA	P-0034880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	154	418	0	ENST00000371953.3:c.97_99del	p.Ile33del	p.I33del	ENST00000371953	NM_000314.4	32	ATT/-	2/9	1	2	FACETS	0.949	0.876	1	0.949	0.876	1	CLONAL	1	TRUE	1	0.708675893397979	2		418	458	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466023	69466052	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	CACCGACGTGCGGGACGTGGACATCTGAGG	CACCGACGTGCGGGACGTGGACATCTGAGG	-	novel	NA	P-0034880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	151	645	0	ENST00000227507.2:c.861_*2del		p.*287*	ENST00000227507	NM_053056.2	287		5/5	1	2	FACETS	0.588	0.538	0.639	0.588	0.538	0.639	SUBCLONAL	1	TRUE	1	0.708675893397979	2		645	725	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67646003	67646003	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	198	417	0	ENST00000264010.4:c.932del	p.Asn311IlefsTer22	p.N311Ifs*22	ENST00000264010	NM_006565.3	311	Aat/at	4/12	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.708675893397979	2		417	553	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022288	31022288	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs371369583	NA	P-0034880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	169	335	0	ENST00000375687.4:c.1773C>A	p.Tyr591Ter	p.Y591*	ENST00000375687	NM_015338.5	591	taC/taA	13/13	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.708675893397979	2		335	465	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505541	157505576	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCAGCCCAAGCTCCAGCCGCCATCTCCTGGTAAGTG	GCAGCCCAAGCTCCAGCCGCCATCTCCTGGTAAGTG	-	novel	NA	P-0034880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	20	235	0	ENST00000346085.5:c.3524_3550+9del		p.X1175_splice	ENST00000346085	NM_020732.3	1175		13/20	1	2	FACETS	0.192	0.146	0.245	0.192	0.146	0.245	SUBCLONAL	1	TRUE	1	0.708675893397979	2		235	294	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	132	417	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.236147419622734	2	FACETS	0.901	0.823	0.982	0.901	0.823	0.982	CLONAL	2	TRUE	0	0.289487849874868	2		417	506	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218164	69218164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1152	143	477	0	ENST00000462284.1:c.380C>T	p.Ser127Phe	p.S127F	ENST00000462284	NM_002392.5	127	tCt/tTt	6/11	0.289487849874868	14	FACETS	1	0.94	1			1	CLONAL	2	TRUE	NA	0.289487849874868	14		477	1295	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40861892	40861892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	45	772	2	ENST00000428826.2:c.1465C>T	p.Pro489Ser	p.P489S	ENST00000428826		489	Ccc/Tcc	13/21	1	2	FACETS	0.538	0.451	0.634	0.538	0.451	0.634	SUBCLONAL	1	TRUE	1	0.289487849874868	2		774	578	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010569	48010569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881812	NA	P-0034884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	39	330	0	ENST00000234420.5:c.197C>T	p.Pro66Leu	p.P66L	ENST00000234420	NM_000179.2	66	cCg/cTg	1/10	0.290066897560972	3	FACETS	0.989	0.823	1	0.494	0.411	0.586	CLONAL	1	TRUE	1	0.289487849874868	3		330	312	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522771	67522772	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0034884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	38	275	0	ENST00000274335.5:c.270dup	p.Pro91AlafsTer15	p.P91Afs*15	ENST00000274335		90	cgg/cGgg	1/15	0.235749621316987	4	FACETS	1	0.911	1	0.58	0.481	0.689	CLONAL	1	TRUE	2	0.289487849874868	4		275	292	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242297	98242297	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs780256480	NA	P-0034884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	49	655	0	ENST00000331920.6:c.1021T>A	p.Leu341Met	p.L341M	ENST00000331920	NM_000264.3	341	Ttg/Atg	7/24	1	2	FACETS	0.622	0.527	0.727	0.622	0.527	0.727	SUBCLONAL	1	TRUE	1	0.289487849874868	2		655	544	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966680	44966680	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1556375815	NA	P-0034886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	22	399	1	ENST00000377967.4:c.3904C>T	p.Gln1302Ter	p.Q1302*	ENST00000377967	NM_021140.2	1302	Caa/Taa	27/29	0.528350196007703	1	FACETS	0.166	0.128	0.21	0.166	0.128	0.21	SUBCLONAL	1	TRUE	0	0.528350196007703	1		400	369	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870995	12870995	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	211	337	0	ENST00000228872.4:c.222C>A	p.Tyr74Ter	p.Y74*	ENST00000228872	NM_004064.3	74	taC/taA	1/3	0.499450329538816	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	0	0.528350196007703	2		337	397	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248069	110248069	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0121609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	149	428	1	ENST00000374672.4:c.1403C>A	p.Ser468Ter	p.S468*	ENST00000374672	NM_004235.4	468	tCg/tAg	5/5	1	2	FACETS	0.527	0.483	0.574	0.527	0.483	0.574	SUBCLONAL	1	NA	1	0.84958713202137	2		429	665	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518418	69518418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	22	60	0	ENST00000294312.3:c.227C>T	p.Ala76Val	p.A76V	ENST00000294312	NM_005117.2	76	gCg/gTg	1/3	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.487778449866379	2		60	79	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44920662	44920662	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	17	191	0	ENST00000377967.4:c.1423del	p.Gln475SerfsTer13	p.Q475Sfs*13	ENST00000377967	NM_021140.2	475	Cag/ag	14/29	1	1	FACETS	0.207	0.154	0.269	0.207	0.154	0.269	SUBCLONAL	1	TRUE	0	0.487778449866379	1		191	255	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0034894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	849	658	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.517451527530788	3	FACETS	1	0.991	1			1	CLONAL	3	TRUE	NA	0.740442877258786	3		658	1032	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636809	2636809	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	217	617	1	ENST00000342085.4:c.1258G>T	p.Asp420Tyr	p.D420Y	ENST00000342085	NM_002613.4	420	Gac/Tac	11/14	0.680587532987841	5	FACETS	0.97	0.901	1	0.323	0.3	0.348	CLONAL	1	TRUE	2	0.740442877258786	5		618	1275	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	171	236	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.897721688748485	2		236	349	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961370	15961370	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	349	494	0	ENST00000268712.3:c.6019A>T	p.Thr2007Ser	p.T2007S	ENST00000268712	NM_006311.3	2007	Acc/Tcc	39/46	1	2	FACETS	0.98	0.934	1	0.98	0.934	1	CLONAL	1	TRUE	1	0.897721688748485	2		494	793	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926888	112926888	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397507546	NA	P-0121510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	179	621	0	ENST00000351677.2:c.1508G>C	p.Gly503Ala	p.G503A	ENST00000351677	NM_002834.3	503	gGg/gCg	13/16	0.736498783296329	4	FACETS	0.572	0.525	0.62	0.191	0.175	0.207	SUBCLONAL	1	NA	1	0.880133516773039	4		621	1338	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166244	118166244	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	67	277	0	ENST00000369448.3:c.754G>T	p.Val252Leu	p.V252L	ENST00000369448	NM_017709.3	252	Gtg/Ttg	2/2	0.150210454204907	5	FACETS	0.73	0.636	0.831	0.243	0.212	0.277	INDETERMINATE	1	NA	2	0.880133516773039	5		277	484	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433109	49433109	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	147	653	0	ENST00000301067.7:c.8262C>A	p.Ser2754Arg	p.S2754R	ENST00000301067	NM_003482.3	2754	agC/agA	33/54	1	2	FACETS	0.528	0.483	0.574	0.528	0.483	0.574	SUBCLONAL	1	NA	1	0.880133516773039	2		653	633	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415519	152415519	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0121510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	90	420	1	ENST00000206249.3:c.1370-1G>T		p.X457_splice	ENST00000206249	NM_000125.3	457			0.213252967190099	5	FACETS	0.775	0.689	0.868	0.155	0.137	0.174	INDETERMINATE	1	NA	0	0.880133516773039	5		421	612	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0034901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	28	503	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		503	670	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484150	50484150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	57	593	0	ENST00000394963.4:c.1000C>T	p.Arg334Trp	p.R334W	ENST00000394963	NM_003076.4	334	Cgg/Tgg	8/13	1	2	FACETS	0.473	0.404	0.548	0.473	0.404	0.548	SUBCLONAL	1	TRUE	1	0.27	2		593	893	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0034944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	84	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.287458790763725	4	FACETS	0.943	0.838	1	0.943	0.838	1	CLONAL	2	TRUE	2	0.287458790763725	4		326	399	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061274	38061274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	370	654	0	ENST00000250448.2:c.715G>A	p.Gly239Ser	p.G239S	ENST00000250448	NM_004496.3	239	Ggc/Agc	2/2	0.274912372958853	5	FACETS	0.986	0.935	1	0.986	0.935	1	CLONAL	3	TRUE	2	0.287458790763725	5		654	1246	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663659	29663659	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	94	267	0	ENST00000356175.3:c.6091G>T	p.Gly2031Ter	p.G2031*	ENST00000356175	NM_000267.3	2031	Gga/Tga	41/57	0.26991709693665	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	2	TRUE	0	0.287458790763725	2		267	321	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813027	89813027	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1164540064	NA	P-0034944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	122	642	0	ENST00000389301.3:c.3478C>T	p.Gln1160Ter	p.Q1160*	ENST00000389301	NM_000135.2	1160	Cag/Tag	35/43	0.287458790763725	4	FACETS	0.933	0.841	1	0.467	0.42	0.516	CLONAL	1	TRUE	2	0.287458790763725	4		642	1171	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630803	187630803	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	287	614	0	ENST00000441802.2:c.179G>C	p.Gly60Ala	p.G60A	ENST00000441802	NM_005245.3	60	gGt/gCt	2/27	0.287458790763725	5	FACETS	0.869	0.817	0.922	0.869	0.817	0.922	CLONAL	3	TRUE	2	0.287458790763725	5		614	1096	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172163	32172163	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	117	653	1	ENST00000375023.3:c.2869G>T	p.Ala957Ser	p.A957S	ENST00000375023	NM_004557.3	957	Gcc/Tcc	19/30	0.287458790763725	3	FACETS	0.928	0.836	1	0.464	0.418	0.514	CLONAL	1	TRUE	1	0.287458790763725	3		654	1003	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123026582	123026582	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	56	205	0	ENST00000355640.3:c.1058T>G	p.Val353Gly	p.V353G	ENST00000355640		353	gTa/gGa	5/7	0.287458790763725	2	FACETS	1	0.96	1	0.667	0.576	0.765	CLONAL	1	TRUE	0	0.287458790763725	2		205	292	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577126	+	protein_altering_variant	In_Frame_Del	DEL	CGCACCT	CGCACCT	A	novel	NA	P-0034944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	229	698	0	ENST00000269305.4:c.812_818delinsT	p.Glu271_Arg273delinsVal	p.E271_R273delinsV	ENST00000269305	NM_001126112.2	271	gAGGTGCGt/gTt	8/11	0.26991709693665	2	FACETS	0.83	0.774	0.888	0.83	0.774	0.888	CLONAL	2	TRUE	0	0.287458790763725	2		698	960	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0034947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	142	627	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.948	0.869	1	0.948	0.869	1	CLONAL	1	TRUE	1	0.547449432747495	2		627	547	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942739	44942739	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	234	301	0	ENST00000377967.4:c.3320del	p.Pro1107LeufsTer13	p.P1107Lfs*13	ENST00000377967	NM_021140.2	1107	Cct/ct	23/29	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.547449432747495	1		301	474	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199896	108199896	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	73	205	0	ENST00000278616.4:c.7238A>G	p.Lys2413Arg	p.K2413R	ENST00000278616	NM_000051.3	2413	aAg/aGg	49/63	1	2	FACETS	0.91	0.804	1	0.91	0.804	1	CLONAL	1	TRUE	1	0.547449432747495	2		205	293	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459148	120459148	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs758985315	NA	P-0034947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	230	630	0	ENST00000256646.2:c.6197A>G	p.Asn2066Ser	p.N2066S	ENST00000256646	NM_024408.3	2066	aAt/aGt	34/34	1	2	FACETS	0.88	0.821	0.941	0.88	0.821	0.941	CLONAL	1	TRUE	1	0.547449432747495	2		630	955	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555974	226555974	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	198	470	0	ENST00000366794.5:c.2203C>A	p.Arg735Ser	p.R735S	ENST00000366794	NM_001618.3	735	Cgc/Agc	16/23	1	2	FACETS	0.924	0.858	0.992	0.924	0.858	0.992	CLONAL	1	TRUE	1	0.547449432747495	2		470	783	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201059	108201062	+	frameshift_variant	Frame_Shift_Del	DEL	AGTG	AGTG	-	novel	NA	P-0034947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	116	442	0	ENST00000278616.4:c.7426_7429del	p.Ser2476GlufsTer27	p.S2476Efs*27	ENST00000278616	NM_000051.3	2476	AGTGga/ga	50/63	1	2	FACETS	0.838	0.758	0.92	0.838	0.758	0.92	CLONAL	1	TRUE	1	0.547449432747495	2		442	506	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190031	123190032	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0034947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	184	280	0	ENST00000218089.9:c.1251_1252del	p.Tyr418PhefsTer22	p.Y418Ffs*22	ENST00000218089	NM_001042749.1	417	gTT/g	14/35	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.547449432747495	1		280	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0034948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	350	711	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.348555029947656	0	FACETS	0.53	0.505	0.555			1	INDETERMINATE	1	TRUE	0	0.636179469525533	0		711	755	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600447	10600447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	354	696	0	ENST00000171111.5:c.1408C>T	p.Arg470Cys	p.R470C	ENST00000171111	NM_203500.1	470	Cgt/Tgt	4/6	0.636179469525533	1	FACETS	0.989	0.944	1	0.989	0.944	1	CLONAL	1	TRUE	0	0.636179469525533	1		696	767	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969137	93969137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	40	390	0	ENST00000369303.4:c.1859C>T	p.Ala620Val	p.A620V	ENST00000369303	NM_004440.3	620	gCt/gTt	10/17	0.636179469525533	1	FACETS	0.501	0.422	0.587	0.501	0.422	0.587	SUBCLONAL	1	TRUE	0	0.636179469525533	1		390	171	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106508	27106508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	125	635	0	ENST00000324856.7:c.6119G>A	p.Gly2040Glu	p.G2040E	ENST00000324856	NM_006015.4	2040	gGg/gAg	20/20	1	2	FACETS	0.446	0.403	0.491	0.446	0.403	0.491	SUBCLONAL	1	TRUE	1	0.636179469525533	2		635	882	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65311261	65311261	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	139	512	0	ENST00000342505.4:c.2050G>T	p.Asp684Tyr	p.D684Y	ENST00000342505	NM_002227.2	684	Gat/Tat	15/25	0.636179469525533	1	FACETS	0.892	0.824	0.961	0.892	0.824	0.961	CLONAL	1	TRUE	0	0.636179469525533	1		512	334	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166577	118166577	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs773285739	NA	P-0034948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	160	320	0	ENST00000369448.3:c.1087G>T	p.Val363Phe	p.V363F	ENST00000369448	NM_017709.3	363	Gtc/Ttc	2/2	0.636179469525533	1	FACETS	0.969	0.902	1	0.969	0.902	1	CLONAL	1	TRUE	0	0.636179469525533	1		320	354	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431079	49431079	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	144	615	0	ENST00000301067.7:c.10060G>T	p.Gly3354Trp	p.G3354W	ENST00000301067	NM_003482.3	3354	Ggg/Tgg	34/54	NA	2	FACETS	0.639	0.584	0.697			1	INDETERMINATE	1	TRUE	NA	0.636179469525533	2		615	708	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89871793	89871793	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	247	508	0	ENST00000389301.3:c.604G>C	p.Asp202His	p.D202H	ENST00000389301	NM_000135.2	202	Gac/Cac	7/43	0.598256178499421	1	FACETS	0.954	0.901	1	0.954	0.901	1	CLONAL	1	TRUE	0	0.636179469525533	1		508	555	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222348	39222348	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	235	665	0	ENST00000402219.2:c.3262A>T	p.Thr1088Ser	p.T1088S	ENST00000402219	NM_005633.3	1088	Aca/Tca	20/23	0.353717729923335	1	FACETS	0.681	0.638	0.725	0.681	0.638	0.725	INDETERMINATE	1	TRUE	0	0.636179469525533	1		665	740	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495267	212495267	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs775987436	NA	P-0034948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	70	335	0	ENST00000342788.4:c.1999G>C	p.Val667Leu	p.V667L	ENST00000342788	NM_005235.2	667	Gtg/Ctg	17/28	0.353717729923335	1	FACETS	0.705	0.625	0.788	0.705	0.625	0.788	INDETERMINATE	1	TRUE	0	0.636179469525533	1		335	213	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70005682	70005682	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0034948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	44	144	0	ENST00000394351.3:c.710+1G>T		p.X237_splice	ENST00000394351	NM_000248.3	237			0.312368470380096	1	FACETS	0.767	0.66	0.878	0.767	0.66	0.878	INDETERMINATE	1	TRUE	0	0.636179469525533	1		144	123	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462330	89462330	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	76	296	0	ENST00000336596.2:c.1802C>A	p.Thr601Lys	p.T601K	ENST00000336596	NM_005233.5	601	aCa/aAa	10/17	0.312368470380096	1	FACETS	0.849	0.76	0.939	0.849	0.76	0.939	INDETERMINATE	1	TRUE	0	0.636179469525533	1		296	192	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151604	55151604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	111	496	0	ENST00000257290.5:c.2390G>A	p.Ser797Asn	p.S797N	ENST00000257290	NM_006206.4	797	aGc/aAc	17/23	0.312368470380096	1	FACETS	0.468	0.422	0.515	0.468	0.422	0.515	INDETERMINATE	1	TRUE	0	0.636179469525533	1		496	509	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562942	176562942	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	39	279	0	ENST00000439151.2:c.838G>C	p.Asp280His	p.D280H	ENST00000439151	NM_022455.4	280	Gat/Cat	2/23	0.353717729923335	1	FACETS	0.37	0.309	0.437	0.37	0.309	0.437	INDETERMINATE	1	TRUE	0	0.636179469525533	1		279	226	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239759	53239759	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0034948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	270	504	0	ENST00000375401.3:c.1584-1G>T		p.X528_splice	ENST00000375401	NM_004187.3	528			0.598105927629145	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.636179469525533	1		504	541	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572505	64572505	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs863223311	NA	P-0034949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	309	555	0	ENST00000312049.6:c.1350+1G>A		p.X450_splice	ENST00000312049	NM_130799.2	450			0.906433807449063	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.906433807449063	1		555	344	SUCCESS
ATM	472	MSKCC	GRCh37	11	108159769	108159770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0034949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	112	354	0	ENST00000278616.4:c.4176dup	p.Ile1393TyrfsTer6	p.I1393Yfs*6	ENST00000278616	NM_000051.3	1392	tat/taTt	28/63	0.906433807449063	1	FACETS	0.958	0.907	1	0.958	0.907	1	CLONAL	1	TRUE	0	0.906433807449063	1		354	141	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855829	45855829	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	479	768	1	ENST00000391945.4:c.1981G>T	p.Ala661Ser	p.A661S	ENST00000391945	NM_000400.3	661	Gcc/Tcc	21/23	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.906433807449063	2		769	1029	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	79	326	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.487713688304781	2		326	324	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	129	310	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.487713688304781	2		311	521	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345769	152345769	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs759063323	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	52	308	0	ENST00000359321.1:c.801del	p.Lys267AsnfsTer30	p.K267Nfs*30	ENST00000359321	NM_005431.1	267	aaA/aa	3/3	1	2	FACETS	0.529	0.452	0.614	0.529	0.452	0.614	SUBCLONAL	1	TRUE	1	0.487713688304781	2		308	403	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	101	788	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.465	0.415	0.519	0.465	0.415	0.519	SUBCLONAL	1	TRUE	1	0.487713688304781	2		790	890	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	117	331	1	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	1	2	FACETS	0.893	0.809	0.982	0.893	0.809	0.982	CLONAL	1	TRUE	1	0.487713688304781	2		332	537	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659550	88659550	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	128	443	0	ENST00000372037.3:c.334-1G>T		p.X112_splice	ENST00000372037	NM_004329.2	112			0.487713688304781	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.487713688304781	1		443	394	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	98	408	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.487713688304781	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.487713688304781	1		408	280	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	80	287	2	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.982	0.872	1	0.982	0.872	1	CLONAL	1	TRUE	1	0.487713688304781	2		289	334	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	148	559	2	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	1	2	FACETS	0.945	0.866	1	0.945	0.866	1	CLONAL	1	TRUE	1	0.487713688304781	2		561	642	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401528	401528	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767774669	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	129	347	1	ENST00000380956.4:c.850G>A	p.Ala284Thr	p.A284T	ENST00000380956	NM_001195286.1	284	Gcc/Acc	7/9	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.487713688304781	2		348	478	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755554	39755554	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	145	500	2	ENST00000288319.7:c.1211del	p.Pro404ArgfsTer25	p.P404Rfs*25	ENST00000288319	NM_182918.3	404	cCg/cg	10/10	1	2	FACETS	0.965	0.884	1	0.965	0.884	1	CLONAL	1	TRUE	1	0.487713688304781	2		502	616	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870985	12870986	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1555085549	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	84	341	0	ENST00000228872.4:c.215dup	p.Lys73GlnfsTer52	p.K73Qfs*52	ENST00000228872	NM_004064.3	71	gag/gaGg	1/3	1	2	FACETS	0.876	0.779	0.98	0.876	0.779	0.98	CLONAL	1	TRUE	1	0.487713688304781	2		341	393	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	134	470	14	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	NA	2	FACETS	0.836	0.762	0.914			1	INDETERMINATE	1	TRUE	NA	0.487713688304781	2		484	657	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225365174	225365174	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	149	410	0	ENST00000264414.4:c.1516C>T	p.Arg506Trp	p.R506W	ENST00000264414	NM_003590.4	506	Cgg/Tgg	11/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.487713688304781	2		410	553	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652118	36652118	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	205	665	0	ENST00000244741.5:c.243del	p.Arg83GlyfsTer65	p.R83Gfs*65	ENST00000244741	NM_000389.4	80	acG/ac	2/3	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.487713688304781	2		665	840	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391799	139391799	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1455334351	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	137	632	2	ENST00000277541.6:c.6392del	p.Gly2131AlafsTer117	p.G2131Afs*117	ENST00000277541	NM_017617.3	2131	gGc/gc	34/34	1	2	FACETS	0.777	0.708	0.85	0.777	0.708	0.85	SUBCLONAL	1	TRUE	1	0.487713688304781	2		634	723	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436026	56436026	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771831816	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	94	454	0	ENST00000407977.2:c.1111C>T	p.Arg371Ter	p.R371*	ENST00000407977		371	Cga/Tga	9/10	1	2	FACETS	0.882	0.789	0.98	0.882	0.789	0.98	CLONAL	1	TRUE	1	0.487713688304781	2		454	437	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972439	81972439	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	159	489	2	ENST00000359376.3:c.3232C>T	p.Arg1078Ter	p.R1078*	ENST00000359376	NM_002661.3	1078	Cga/Tga	29/33	1	2	FACETS	0.942	0.866	1	0.942	0.866	1	CLONAL	1	TRUE	1	0.487713688304781	2		491	692	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302390	15302390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146578114	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	316	925	2	ENST00000263388.2:c.881C>T	p.Thr294Met	p.T294M	ENST00000263388	NM_000435.2	294	aCg/aTg	6/33	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.487713688304781	2		927	1208	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811605	102811605	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1565968684	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	338	611	0	ENST00000307046.8:c.579del	p.Gly194GlufsTer8	p.G194Efs*8	ENST00000307046	NM_001111285.1	193	aaA/aa	4/4	0.393182642673628	2	FACETS	0.859	0.817	0.901	0.859	0.817	0.901	CLONAL	2	TRUE	0	0.487713688304781	2		611	807	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053348	37053348	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63751653	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	112	380	1	ENST00000231790.2:c.588del	p.Lys196AsnfsTer6	p.K196Nfs*6	ENST00000231790	NM_000249.3	195	Aaa/aa	7/19	1	2	FACETS	0.971	0.878	1	0.971	0.878	1	CLONAL	1	TRUE	1	0.487713688304781	2		381	473	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920466	50920466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs980793204	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	355	643	1	ENST00000440232.2:c.3158G>A	p.Arg1053His	p.R1053H	ENST00000440232	NM_002691.3	1053	cGc/cAc	26/27	0.474690539792965	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.487713688304781	3		644	898	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087513	27087513	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	248	796	0	ENST00000324856.7:c.2090del	p.Pro697ArgfsTer45	p.P697Rfs*45	ENST00000324856	NM_006015.4	696	tCc/tc	5/20	1	2	FACETS	0.94	0.879	1	0.94	0.879	1	CLONAL	1	TRUE	1	0.487713688304781	2		796	1082	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992721	68992721	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs764112302	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	101	408	1	ENST00000288368.4:c.1693del	p.Ser565ArgfsTer10	p.S565Rfs*10	ENST00000288368	NM_024870.2	562	cgT/cg	16/40	1	2	FACETS	0.863	0.775	0.955	0.863	0.775	0.955	CLONAL	1	TRUE	1	0.487713688304781	2		409	480	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200877	67200877	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	197	596	1	ENST00000312629.5:c.870del	p.Tyr291ThrfsTer14	p.Y291Tfs*14	ENST00000312629	NM_003952.2	289	Ccc/cc	10/15	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.487713688304781	2		597	786	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323362	31323363	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748204482	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	201	494	1	ENST00000412585.2:c.626dup	p.Thr211AspfsTer10	p.T211Dfs*10	ENST00000412585	NM_005514.6	209	cca/ccCa	4/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.487713688304781	2		495	683	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29701087	29701087	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	118	394	0	ENST00000356175.3:c.8371C>T	p.Arg2791Ter	p.R2791*	ENST00000356175	NM_000267.3	2791	Cga/Tga	57/57	1	2	FACETS	0.842	0.762	0.925	0.842	0.762	0.925	CLONAL	1	TRUE	1	0.487713688304781	2		394	575	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646980	23646981	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	184	610	0	ENST00000261584.4:c.886dup	p.Met296AsnfsTer7	p.M296Nfs*7	ENST00000261584	NM_024675.3	296	atg/aAtg	4/13	1	2	FACETS	0.984	0.91	1	0.984	0.91	1	CLONAL	1	TRUE	1	0.487713688304781	2		610	767	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302611	15302611	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	231	818	0	ENST00000263388.2:c.747del	p.Thr250HisfsTer122	p.T250Hfs*122	ENST00000263388	NM_000435.2	249	ggG/gg	5/33	1	2	FACETS	0.867	0.808	0.929	0.867	0.808	0.929	CLONAL	1	TRUE	1	0.487713688304781	2		818	1092	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231215	98231215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750970743	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	256	761	0	ENST00000331920.6:c.2068G>A	p.Val690Ile	p.V690I	ENST00000331920	NM_000264.3	690	Gtc/Atc	14/24	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.487713688304781	2		761	954	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111167	193111167	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	57	281	1	ENST00000367435.3:c.700C>T	p.Arg234Ter	p.R234*	ENST00000367435	NM_024529.4	234	Cga/Tga	7/17	1	2	FACETS	0.82	0.709	0.939	0.82	0.709	0.939	CLONAL	1	TRUE	1	0.487713688304781	2		282	285	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988426	36988426	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1341967476	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	85	240	0	ENST00000354822.5:c.227C>T	p.Ala76Val	p.A76V	ENST00000354822	NM_001079668.2	76	gCg/gTg	2/3	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.487713688304781	2		240	336	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138127	64138127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1412221175	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	201	492	0	ENST00000334205.4:c.2050C>T	p.Pro684Ser	p.P684S	ENST00000334205	NM_003942.2	684	Ccg/Tcg	16/17	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.487713688304781	2		492	667	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224532	36224532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759167832	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1240	316	987	0	ENST00000222270.7:c.6994C>T	p.Arg2332Cys	p.R2332C	ENST00000222270	NM_014727.1	2332	Cgt/Tgt	29/37	0.474690539792965	3	FACETS	1	0.965	1	0.518	0.487	0.55	CLONAL	1	TRUE	1	0.487713688304781	3		987	1556	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046022	180046022	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	43	90	0	ENST00000261937.6:c.2849C>T	p.Ala950Val	p.A950V	ENST00000261937	NM_182925.4	950	gCg/gTg	20/30	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.487713688304781	2		90	146	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944732	71944732	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	117	865	0	ENST00000298229.2:c.2160del	p.Val721CysfsTer37	p.V721Cfs*37	ENST00000298229	NM_001567.3	719	tCc/tc	19/28	1	2	FACETS	0.419	0.377	0.464	0.419	0.377	0.464	SUBCLONAL	1	TRUE	1	0.487713688304781	2		865	1145	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478609	99478609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1330526325	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	188	566	0	ENST00000268035.6:c.3251G>A	p.Arg1084Gln	p.R1084Q	ENST00000268035	NM_000875.3	1084	cGg/cAg	17/21	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.487713688304781	2		566	703	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78435687	78435687	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	72	272	0	ENST00000370768.2:c.133del	p.Ile45LeufsTer9	p.I45Lfs*9	ENST00000370768	NM_003902.3	45	Att/tt	2/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.487713688304781	2		272	271	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599165	28599165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	274	906	0	ENST00000253063.3:c.611G>A	p.Cys204Tyr	p.C204Y	ENST00000253063	NM_031459.4	204	tGc/tAc	5/10	1	2	FACETS	0.995	0.934	1	0.995	0.934	1	CLONAL	1	TRUE	1	0.487713688304781	2		906	1129	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805659	43805659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	168	472	0	ENST00000372470.3:c.715G>A	p.Gly239Arg	p.G239R	ENST00000372470	NM_005373.2	239	Gga/Aga	5/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.487713688304781	2		472	632	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248636	8248636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	133	635	1	ENST00000335790.3:c.251C>T	p.Thr84Ile	p.T84I	ENST00000335790	NM_002315.2	84	aCc/aTc	3/4	1	2	FACETS	0.859	0.782	0.939	0.859	0.782	0.939	CLONAL	1	TRUE	1	0.487713688304781	2		636	635	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94926640	94926640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	91	318	0	ENST00000536441.1:c.125C>T	p.Ala42Val	p.A42V	ENST00000536441	NM_144665.3	42	gCc/gTc	2/10	1	2	FACETS	0.808	0.72	0.9	0.808	0.72	0.9	CLONAL	1	TRUE	1	0.487713688304781	2		318	462	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448379	49448379	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	189	651	0	ENST00000301067.7:c.332C>A	p.Pro111His	p.P111H	ENST00000301067	NM_003482.3	111	cCc/cAc	3/54	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.487713688304781	2		651	774	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225618	133225618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536988344	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	43	632	1	ENST00000320574.5:c.4046C>T	p.Ala1349Val	p.A1349V	ENST00000320574	NM_006231.2	1349	gCg/gTg	32/49	0.393182642673628	2	FACETS	0.234	0.195	0.277	0.117	0.097	0.139	SUBCLONAL	1	TRUE	0	0.487713688304781	2		633	754	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896487	28896487	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149241190	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	86	329	0	ENST00000282397.4:c.2963G>A	p.Gly988Asp	p.G988D	ENST00000282397	NM_002019.4	988	gGt/gAt	22/30	1	2	FACETS	0.953	0.849	1	0.953	0.849	1	CLONAL	1	TRUE	1	0.487713688304781	2		329	370	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194817	30194817	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	46	596	1	ENST00000331968.5:c.328T>A	p.Ser110Thr	p.S110T	ENST00000331968	NM_002742.2	110	Tct/Act	2/18	1	2	FACETS	0.256	0.215	0.302	0.256	0.215	0.302	SUBCLONAL	1	TRUE	1	0.487713688304781	2		597	737	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989044	41989044	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	148	525	1	ENST00000219905.7:c.1840del	p.Arg614GlufsTer7	p.R614Efs*7	ENST00000219905	NM_001164273.1	612	ggA/gg	3/24	1	2	FACETS	0.993	0.911	1	0.993	0.911	1	CLONAL	1	TRUE	1	0.487713688304781	2		526	611	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632770	23632770	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs180177131	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	45	467	1	ENST00000261584.4:c.3026del	p.Pro1009LeufsTer6	p.P1009Lfs*6	ENST00000261584	NM_024675.3	1009	cCt/ct	10/13	1	2	FACETS	0.374	0.314	0.44	0.374	0.314	0.44	SUBCLONAL	1	TRUE	1	0.487713688304781	2		468	494	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821959	72821960	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	75	407	0	ENST00000268489.5:c.10214_10215dup	p.Gly3406ProfsTer80	p.G3406Pfs*80	ENST00000268489	NM_006885.3	3405	-/CC	10/10	1	2	FACETS	0.595	0.522	0.673	0.595	0.522	0.673	SUBCLONAL	1	TRUE	1	0.487713688304781	2		407	517	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438293	56438293	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs776193125	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	148	744	0	ENST00000407977.2:c.700C>T	p.Gln234Ter	p.Q234*	ENST00000407977		234	Cag/Tag	7/10	1	2	FACETS	0.845	0.773	0.92	0.845	0.773	0.92	CLONAL	1	TRUE	1	0.487713688304781	2		744	718	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78921062	78921062	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	188	665	0	ENST00000306801.3:c.3176A>G	p.Tyr1059Cys	p.Y1059C	ENST00000306801	NM_020761.2	1059	tAt/tGt	27/34	1	2	FACETS	0.909	0.841	0.98	0.909	0.841	0.98	CLONAL	1	TRUE	1	0.487713688304781	2		665	848	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30311686	30311686	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	128	428	0	ENST00000262643.3:c.540A>C	p.Gln180His	p.Q180H	ENST00000262643	NM_001238.2	180	caA/caC	7/12	0.474690539792965	3	FACETS	1	0.939	1	0.521	0.474	0.571	CLONAL	1	TRUE	1	0.487713688304781	3		428	626	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741863	40741863	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	165	677	0	ENST00000392038.2:c.1109del	p.Pro370ArgfsTer205	p.P370Rfs*205	ENST00000392038	NM_001626.4	370	cCg/cg	11/14	0.474690539792965	3	FACETS	0.833	0.765	0.905	0.417	0.382	0.453	CLONAL	1	TRUE	1	0.487713688304781	3		677	1010	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991710	25991710	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	203	458	0	ENST00000435504.4:c.532C>A	p.Gln178Lys	p.Q178K	ENST00000435504		178	Cag/Aag	7/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.487713688304781	2		458	758	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309744	30309744	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	46	650	0	ENST00000307677.4:c.278C>G	p.Ala93Gly	p.A93G	ENST00000307677	NM_138578.1	93	gCa/gGa	2/3	1	2	FACETS	0.242	0.203	0.286	0.242	0.203	0.286	SUBCLONAL	1	TRUE	1	0.487713688304781	2		650	778	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928730	49928730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771218531	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	121	919	1	ENST00000296474.3:c.3544G>A	p.Val1182Met	p.V1182M	ENST00000296474	NM_002447.2	1182	Gtg/Atg	17/20	1	2	FACETS	0.467	0.421	0.516	0.467	0.421	0.516	SUBCLONAL	1	TRUE	1	0.487713688304781	2		920	1063	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430478	181430478	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	40	514	0	ENST00000325404.1:c.330C>A	p.Tyr110Ter	p.Y110*	ENST00000325404	NM_003106.3	110	taC/taA	1/1	1	2	FACETS	0.227	0.188	0.271	0.227	0.188	0.271	SUBCLONAL	1	TRUE	1	0.487713688304781	2		514	723	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176719015	176719015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1321310131	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	80	306	0	ENST00000439151.2:c.6319C>T	p.Arg2107Cys	p.R2107C	ENST00000439151	NM_022455.4	2107	Cgc/Tgc	22/23	1	2	FACETS	0.87	0.771	0.975	0.87	0.771	0.975	CLONAL	1	TRUE	1	0.487713688304781	2		306	377	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13949265	13949265	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	54	196	0	ENST00000405192.2:c.863A>G	p.Lys288Arg	p.K288R	ENST00000405192	NM_001163147.1	288	aAa/aGa	9/12	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.487713688304781	2		196	215	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339164	116339164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1355886011	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	118	345	0	ENST00000397752.3:c.26C>T	p.Pro9Leu	p.P9L	ENST00000397752	NM_000245.2	9	cCt/cTt	2/21	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.487713688304781	2		345	467	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129910	69129910	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	45	303	0	ENST00000288368.4:c.4664C>A	p.Pro1555Gln	p.P1555Q	ENST00000288368	NM_024870.2	1555	cCa/cAa	38/40	1	2	FACETS	0.407	0.342	0.479	0.407	0.342	0.479	SUBCLONAL	1	TRUE	1	0.487713688304781	2		303	453	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983427	90983427	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1563561558	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	72	211	0	ENST00000265433.3:c.676del	p.Thr226HisfsTer5	p.T226Hfs*5	ENST00000265433	NM_002485.4	226	Aca/ca	6/16	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.487713688304781	2		211	266	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549536	5549536	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	235	740	0	ENST00000397747.3:c.563G>C	p.Arg188Thr	p.R188T	ENST00000397747	NM_025239.3	188	aGa/aCa	4/7	1	2	FACETS	0.99	0.925	1	0.99	0.925	1	CLONAL	1	TRUE	1	0.487713688304781	2		740	973	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633347	8633347	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1182127602	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	150	512	1	ENST00000356435.5:c.322A>G	p.Ser108Gly	p.S108G	ENST00000356435		108	Agt/Ggt	3/35	1	2	FACETS	0.951	0.872	1	0.951	0.872	1	CLONAL	1	TRUE	1	0.487713688304781	2		513	647	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231272	98231272	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	294	792	0	ENST00000331920.6:c.2011C>A	p.His671Asn	p.H671N	ENST00000331920	NM_000264.3	671	Cac/Aac	14/24	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.487713688304781	2		792	1085	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0035063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	63	583	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	NA	2	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.235275280550127	2		583	442	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399155	139399155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749490844	NA	P-0035063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	58	838	2	ENST00000277541.6:c.4988G>A	p.Arg1663Gln	p.R1663Q	ENST00000277541	NM_017617.3	1663	cGg/cAg	26/34	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.235275280550127	2		840	459	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916920	178916928	+	inframe_deletion	In_Frame_Del	DEL	GAACCAGTA	GAACCAGTA	-	novel	NA	P-0035063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	220	543	1	ENST00000263967.3:c.308_316del	p.Glu103_Val105del	p.E103_V105del	ENST00000263967	NM_006218.2	103	GAACCAGTA/-	2/21	0.235275280550127	8	FACETS	0.974	0.917	1			1	CLONAL	7	TRUE	NA	0.235275280550127	8		544	468	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967846	93967846	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	41	496	0	ENST00000369303.4:c.2081T>C	p.Val694Ala	p.V694A	ENST00000369303	NM_004440.3	694	gTt/gCt	11/17	0.235275280550127	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.235275280550127	1		496	265	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625218	69625218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1168737490	NA	P-0035722-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	95	1178	5	ENST00000334134.2:c.575G>A	p.Arg192Gln	p.R192Q	ENST00000334134	NM_005247.2	192	cGg/cAg	3/3	0.72227593025574	3	FACETS	0.349	0.31	0.391	0.174	0.155	0.196	SUBCLONAL	1	TRUE	1	0.72227593025574	3		1183	1026	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211661	5211661	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035722-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1375	160	872	1	ENST00000357368.4:c.5174A>G	p.Gln1725Arg	p.Q1725R	ENST00000357368	NM_002850.3	1725	cAa/cGa	33/38	0.50696374925667	5	FACETS	0.601	0.549	0.656	0.2	0.183	0.219	SUBCLONAL	1	TRUE	2	0.72227593025574	5		873	1535	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986994	36986994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035722-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	212	648	0	ENST00000354822.5:c.695C>T	p.Pro232Leu	p.P232L	ENST00000354822	NM_001079668.2	232	cCc/cTc	3/3	0.209368773473796	6	FACETS	0.872	0.812	0.934	0.581	0.541	0.623	INDETERMINATE	2	TRUE	3	0.72227593025574	6		648	823	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56911060	56911060	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0035722-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	165	568	0	ENST00000519728.1:c.1204+2T>C		p.X402_splice	ENST00000519728	NM_002350.3	402			0.209368773473796	6	FACETS	1	0.979	1	0.4	0.367	0.434	INDETERMINATE	1	TRUE	3	0.72227593025574	6		568	931	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	144	236	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.845	0.776	0.916	1	0.99	1	CLONAL	2	TRUE	1	0.353505250481752	2		236	482	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0036214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	76	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.352452010619787	3	FACETS	1	0.894	1	0.509	0.447	0.575	CLONAL	1	TRUE	1	0.353505250481752	3		326	497	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721018	176721018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	317	338	0	ENST00000439151.2:c.6649G>A	p.Glu2217Lys	p.E2217K	ENST00000439151	NM_022455.4	2217	Gag/Aag	23/23	0.282643689260778	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.353505250481752	2		338	740	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273838	18273838	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	144	508	1	ENST00000222254.8:c.1171G>A	p.Glu391Lys	p.E391K	ENST00000222254	NM_005027.3	391	Gag/Aag	10/16	1	2	FACETS	0.756	0.688	0.827	0.756	0.688	0.827	SUBCLONAL	1	TRUE	1	0.353505250481752	2		509	1078	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480522	57480522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	71	229	0	ENST00000371085.3:c.517G>A	p.Asp173Asn	p.D173N	ENST00000371085	NM_000516.4	173	Gac/Aac	6/13	1	2	FACETS	0.61	0.532	0.694	0.61	0.532	0.694	SUBCLONAL	1	TRUE	1	0.353505250481752	2		229	659	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484787	57484789	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	novel	NA	P-0036214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	122	384	0	ENST00000371085.3:c.769_771del	p.Ile257del	p.I257del	ENST00000371085	NM_000516.4	256	gTCAtc/gtc	10/13	1	2	FACETS	0.749	0.676	0.826	0.749	0.676	0.826	SUBCLONAL	1	TRUE	1	0.353505250481752	2		384	922	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434367	121434367	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	177	308	2	ENST00000257555.6:c.1136del	p.Pro379LeufsTer5	p.P379Lfs*5	ENST00000257555		377	ctC/ct	6/10	0.382144325963338	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.382144325963338	3		310	494	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	70	310	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.99	0.868	1	0.99	0.868	1	CLONAL	1	TRUE	1	0.382144325963338	2		311	370	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	98	286	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.382144325963338	2		286	414	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245024	133245024	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs752846614	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	173	330	2	ENST00000320574.5:c.2091del	p.Leu698CysfsTer94	p.L698Cfs*94	ENST00000320574	NM_006231.2	697	ccC/cc	19/49	0.382144325963338	3	FACETS	0.963	0.892	1	0.963	0.892	1	CLONAL	2	TRUE	1	0.382144325963338	3		332	560	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	79	300	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.962	0.85	1	0.962	0.85	1	CLONAL	1	TRUE	1	0.382144325963338	2		300	430	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	147	222	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.382144325963338	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.382144325963338	2		222	346	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	38	788	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.487	0.403	0.581	0.487	0.403	0.581	SUBCLONAL	1	TRUE	1	0.382144325963338	2		790	408	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	65	316	1	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.768	0.668	0.876	0.768	0.668	0.876	SUBCLONAL	1	TRUE	1	0.382144325963338	2		317	443	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	102	323	0	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.382144325963338	2		323	497	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	43	242	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.95	0.801	1	0.95	0.801	1	CLONAL	1	TRUE	1	0.382144325963338	2		242	237	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	39	147	1	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.382144325963338	2		148	161	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749415085	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	11	282	0	ENST00000263967.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000263967	NM_006218.2	38	Cgt/Tgt	2/21	1	2	FACETS	0.212	0.146	0.294	0.212	0.146	0.294	SUBCLONAL	1	TRUE	1	0.382144325963338	2		282	272	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	43	146	1	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	1	2	FACETS	0.911	0.768	1	0.911	0.768	1	CLONAL	1	TRUE	1	0.382144325963338	2		147	247	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097200	11097205	+	inframe_deletion	In_Frame_Del	DEL	GGCCCT	GGCCCT	-	rs372601826	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	54	294	1	ENST00000358026.2:c.708_713del	p.Gly243_Pro244del	p.G243_P244del	ENST00000358026	NM_001128849.1	231	GGCCCT/-	4/36	1	2	FACETS	0.678	0.58	0.784	0.678	0.58	0.784	SUBCLONAL	1	TRUE	1	0.382144325963338	2		295	417	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777898	3777898	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	130	402	0	ENST00000262367.5:c.7150del	p.His2384ThrfsTer12	p.H2384Tfs*12	ENST00000262367	NM_004380.2	2384	Cac/ac	31/31	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.382144325963338	2		402	472	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	8	387	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.118	0.075	0.174	0.118	0.075	0.174	SUBCLONAL	1	TRUE	1	0.382144325963338	2		387	355	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287469	46287469	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	126	332	0	ENST00000334344.6:c.5333del	p.Asn1778IlefsTer13	p.N1778Ifs*13	ENST00000334344	NM_152641.2	1776	ttA/tt	20/21	0.382144325963338	3	FACETS	0.972	0.888	1	0.972	0.888	1	CLONAL	2	TRUE	1	0.382144325963338	3		332	404	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222449	53222451	+	inframe_deletion	In_Frame_Del	DEL	CCG	CCG	-	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	84	354	2	ENST00000375401.3:c.4381_4383del	p.Arg1461del	p.R1461del	ENST00000375401	NM_004187.3	1461	CGG/-	26/26	1	2	FACETS	0.927	0.822	1	0.927	0.822	1	CLONAL	1	TRUE	1	0.382144325963338	2		356	474	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482927	140482927	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	76	336	4	ENST00000288602.6:c.1208del	p.Pro403LeufsTer8	p.P403Lfs*8	ENST00000288602	NM_004333.4	403	cCt/ct	10/18	1	2	FACETS	0.932	0.821	1	0.932	0.821	1	CLONAL	1	TRUE	1	0.382144325963338	2		340	427	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528825	157528825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	86	268	1	ENST00000346085.5:c.6554del	p.Pro2185ArgfsTer8	p.P2185Rfs*8	ENST00000346085	NM_020732.3	2184	Ccc/cc	20/20	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.382144325963338	2		269	410	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979551	55979551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375035755	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	79	326	0	ENST00000263923.4:c.896G>A	p.Arg299Gln	p.R299Q	ENST00000263923	NM_002253.2	299	cGg/cAg	7/30	1	2	FACETS	0.946	0.836	1	0.946	0.836	1	CLONAL	1	TRUE	1	0.382144325963338	2		326	437	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	78	277	3	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.382144325963338	2		280	397	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911443	32911443	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359365	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	34	280	0	ENST00000380152.3:c.2957del	p.Asn986IlefsTer5	p.N986Ifs*5	ENST00000380152		984	gAa/ga	11/27	1	2	FACETS	0.913	0.753	1	0.913	0.753	1	CLONAL	1	TRUE	1	0.382144325963338	2		280	195	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003813	45003813	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	44	277	1	ENST00000558401.1:c.67+2T>C		p.X23_splice	ENST00000558401	NM_004048.2	23			1	2	FACETS	0.59	0.496	0.694	0.59	0.496	0.694	SUBCLONAL	1	TRUE	1	0.382144325963338	2		278	390	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120115	70120115	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	13	42	1	ENST00000245479.2:c.1121del	p.Pro374ArgfsTer9	p.P374Rfs*9	ENST00000245479	NM_000346.3	373	Ccc/cc	3/3	1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	1	0.382144325963338	2		43	54	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255142	16255143	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	rs764595221	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	89	203	0	ENST00000375759.3:c.2417_2418del	p.Arg806ThrfsTer14	p.R806Tfs*14	ENST00000375759	NM_015001.2	803	GAg/g	11/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.382144325963338	2		203	354	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	64	263	1	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	1	2	FACETS	0.881	0.767	1	0.881	0.767	1	CLONAL	1	TRUE	1	0.382144325963338	2		264	380	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865794	56865794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs990904998	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	54	238	0	ENST00000308159.5:c.1126C>T	p.Arg376Cys	p.R376C	ENST00000308159	NM_014669.4	376	Cgt/Tgt	11/22	1	2	FACETS	0.883	0.759	1	0.883	0.759	1	CLONAL	1	TRUE	1	0.382144325963338	2		238	320	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829454	72829454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771717307	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	93	338	0	ENST00000268489.5:c.7127C>T	p.Thr2376Met	p.T2376M	ENST00000268489	NM_006885.3	2376	aCg/aTg	9/10	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.382144325963338	2		338	458	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	108	450	1	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.382144325963338	2		451	495	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825519	50825519	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	45	322	2	ENST00000398568.2:c.2156del	p.Asn719MetfsTer13	p.N719Mfs*13	ENST00000398568	NM_001042412.1	717	gAa/ga	14/18	1	2	FACETS	0.994	0.843	1	0.994	0.843	1	CLONAL	1	TRUE	1	0.382144325963338	2		324	237	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	109	363	0	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.382144325963338	2		363	508	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177984	56177986	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs754402779	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	79	271	0	ENST00000399503.3:c.2965_2967del	p.Ser989del	p.S989del	ENST00000399503	NM_005921.1	986	cCTTct/cct	14/20	1	2	FACETS	0.984	0.87	1	0.984	0.87	1	CLONAL	1	TRUE	1	0.382144325963338	2		271	420	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	122	350	2	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.382144325963338	2		352	522	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591246	67591246	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	44	240	0	ENST00000274335.5:c.1746-2A>G		p.X582_splice	ENST00000274335		582			1	2	FACETS	0.627	0.528	0.737	0.627	0.528	0.737	SUBCLONAL	1	TRUE	1	0.382144325963338	2		240	367	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906370	50906370	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs749601227	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	79	758	2	ENST00000440232.2:c.1036del	p.Glu346SerfsTer47	p.E346Sfs*47	ENST00000440232	NM_002691.3	344	tGg/tg	9/27	1	2	FACETS	0.977	0.864	1	0.977	0.864	1	CLONAL	1	TRUE	1	0.382144325963338	2		760	423	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	181	328	1	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.382144325963338	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.382144325963338	3		329	520	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38616977	38616977	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	67	280	0	ENST00000299084.4:c.395del	p.Asn132MetfsTer20	p.N132Mfs*20	ENST00000299084	NM_152594.2	130	tcA/tc	4/7	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.382144325963338	2		280	281	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655248	45655248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs533193731	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	105	328	0	ENST00000407780.3:c.604G>A	p.Val202Met	p.V202M	ENST00000407780	NM_001283052.1	202	Gtg/Atg	4/7	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.382144325963338	2		328	503	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1620979	1620979	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1329397192	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	99	350	2	ENST00000344749.5:c.1081del	p.Gln361ArgfsTer33	p.Q361Rfs*33	ENST00000344749	NM_001136139.2	361	Cag/ag	13/19	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.382144325963338	2		352	486	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205092	38205092	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	74	368	5	ENST00000317025.8:c.598del	p.Ser200AlafsTer20	p.S200Afs*20	ENST00000317025	NM_023034.1	200	Agc/gc	2/24	1	2	FACETS	0.968	0.852	1	0.968	0.852	1	CLONAL	1	TRUE	1	0.382144325963338	2		373	400	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860074	57860075	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs759448855	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	88	331	1	ENST00000228682.2:c.821dup	p.Cys275LeufsTer32	p.C275Lfs*32	ENST00000228682	NM_005269.2	272	tgg/tGgg	8/12	0.382144325963338	3	FACETS	0.964	0.856	1	0.482	0.428	0.54	CLONAL	1	TRUE	1	0.382144325963338	3		332	569	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175996765	175996765	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	21	320	0	ENST00000367669.3:c.1672G>T	p.Val558Leu	p.V558L	ENST00000367669	NM_022457.5	558	Gtg/Ttg	15/20	1	2	FACETS	0.262	0.201	0.333	0.262	0.201	0.333	SUBCLONAL	1	TRUE	1	0.382144325963338	2		320	420	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541733	120541733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	98	338	0	ENST00000229340.5:c.124G>A	p.Gly42Arg	p.G42R	ENST00000229340	NM_006861.6	42	Gga/Aga	3/6	0.382144325963338	3	FACETS	1	0.949	1	0.551	0.493	0.613	CLONAL	1	TRUE	1	0.382144325963338	3		338	554	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928893	49928893	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	106	358	0	ENST00000296474.3:c.3473A>G	p.His1158Arg	p.H1158R	ENST00000296474	NM_002447.2	1158	cAt/cGt	16/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.382144325963338	2		358	487	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303359	11303359	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	84	277	0	ENST00000361445.4:c.1226-2A>G		p.X409_splice	ENST00000361445	NM_004958.3	409			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.382144325963338	2		277	348	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256107	16256108	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	87	299	0	ENST00000375759.3:c.3379_3380del	p.Glu1127ArgfsTer3	p.E1127Rfs*3	ENST00000375759	NM_015001.2	1124	ccAGag/ccag	11/15	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.382144325963338	2		299	452	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933741	36933741	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	97	358	0	ENST00000361632.4:c.1658A>G	p.Glu553Gly	p.E553G	ENST00000361632		553	gAg/gGg	12/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.382144325963338	2		358	454	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690314	117690314	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	23	289	0	ENST00000369458.3:c.815T>C	p.Leu272Pro	p.L272P	ENST00000369458	NM_024626.3	272	cTt/cCt	5/6	1	2	FACETS	0.315	0.245	0.396	0.315	0.245	0.396	SUBCLONAL	1	TRUE	1	0.382144325963338	2		289	382	SUCCESS
ATM	472	MSKCC	GRCh37	11	108183191	108183191	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	34	201	0	ENST00000278616.4:c.5977del	p.Ser1993ValfsTer7	p.S1993Vfs*7	ENST00000278616	NM_000051.3	1991	gAa/ga	40/63	1	2	FACETS	0.735	0.604	0.881	0.735	0.604	0.881	SUBCLONAL	1	TRUE	1	0.382144325963338	2		201	242	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	461421	461421	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	70	302	0	ENST00000399788.2:c.1099G>T	p.Gly367Ter	p.G367*	ENST00000399788	NM_001042603.1	367	Gga/Tga	9/28	0.382144325963338	3	FACETS	0.959	0.839	1	0.48	0.419	0.544	CLONAL	1	TRUE	1	0.382144325963338	3		302	455	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650592	18650593	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	74	351	0	ENST00000266497.5:c.2805dup	p.Ile936TyrfsTer21	p.I936Yfs*21	ENST00000266497		935	ctt/cTtt	20/31	0.382144325963338	3	FACETS	1	0.945	1	0.565	0.497	0.638	CLONAL	1	TRUE	1	0.382144325963338	3		351	408	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245882	46245882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	113	232	0	ENST00000334344.6:c.3976C>T	p.Pro1326Ser	p.P1326S	ENST00000334344	NM_152641.2	1326	Cca/Tca	15/21	0.382144325963338	3	FACETS	0.984	0.895	1	0.984	0.895	1	CLONAL	2	TRUE	1	0.382144325963338	3		232	358	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527868	103527868	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1349676548	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	56	195	0	ENST00000355739.4:c.3176G>A	p.Gly1059Asp	p.G1059D	ENST00000355739	NM_000123.3	1059	gGc/gAc	15/15	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.382144325963338	2		195	288	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986566	36986566	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	21	217	0	ENST00000354822.5:c.1123T>C	p.Ser375Pro	p.S375P	ENST00000354822	NM_001079668.2	375	Tcc/Ccc	3/3	1	2	FACETS	0.334	0.257	0.424	0.334	0.257	0.424	SUBCLONAL	1	TRUE	1	0.382144325963338	2		217	329	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353736	68353736	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	44	166	0	ENST00000487270.1:c.573-2A>G		p.X191_splice	ENST00000487270	NM_133509.3	191			1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.382144325963338	2		166	199	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007893	45007893	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	24	248	0	ENST00000558401.1:c.340A>T	p.Lys114Ter	p.K114*	ENST00000558401	NM_004048.2	114	Aag/Tag	2/4	1	2	FACETS	0.346	0.271	0.433	0.346	0.271	0.433	SUBCLONAL	1	TRUE	1	0.382144325963338	2		248	363	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729210	66729210	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	24	352	0	ENST00000307102.5:c.418A>C	p.Ser140Arg	p.S140R	ENST00000307102	NM_002755.3	140	Agt/Cgt	3/11	1	2	FACETS	0.287	0.225	0.36	0.287	0.225	0.36	SUBCLONAL	1	TRUE	1	0.382144325963338	2		352	437	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434833	99434834	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	86	246	0	ENST00000268035.6:c.924dup	p.Ser309LeufsTer17	p.S309Lfs*17	ENST00000268035	NM_000875.3	307	tgc/tgCc	3/21	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.382144325963338	2		246	405	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136361	2136361	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs45517372	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	95	329	0	ENST00000219476.3:c.4830G>A	p.Trp1610Ter	p.W1610*	ENST00000219476	NM_000548.3	1610	tgG/tgA	37/42	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.382144325963338	2		329	451	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778207	3778207	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	91	331	0	ENST00000262367.5:c.6841del	p.Ala2281GlnfsTer21	p.A2281Qfs*21	ENST00000262367	NM_004380.2	2281	Gca/ca	31/31	1	2	FACETS	0.976	0.87	1	0.976	0.87	1	CLONAL	1	TRUE	1	0.382144325963338	2		331	488	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993735	72993735	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	101	244	0	ENST00000268489.5:c.310C>G	p.Pro104Ala	p.P104A	ENST00000268489	NM_006885.3	104	Ccc/Gcc	2/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.382144325963338	2		244	368	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40462592	40462592	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1029737475	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	96	332	0	ENST00000345506.4:c.2290G>T	p.Val764Leu	p.V764L	ENST00000345506	NM_003152.3	764	Gtg/Ttg	20/20	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.382144325963338	2		332	465	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435921	56435921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	67	258	0	ENST00000407977.2:c.1216G>A	p.Ala406Thr	p.A406T	ENST00000407977		406	Gca/Aca	9/10	1	2	FACETS	0.953	0.833	1	0.953	0.833	1	CLONAL	1	TRUE	1	0.382144325963338	2		258	368	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78854243	78854243	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs76608178	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	98	335	0	ENST00000306801.3:c.1538A>C	p.Asn513Thr	p.N513T	ENST00000306801	NM_020761.2	513	aAc/aCc	14/34	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.382144325963338	2		335	459	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56376790	56376790	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	40	218	0	ENST00000348428.3:c.828+2T>C		p.X276_splice	ENST00000348428	NM_006785.3	276			1	2	FACETS	0.799	0.668	0.943	0.799	0.668	0.943	CLONAL	1	TRUE	1	0.382144325963338	2		218	262	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267424	7267424	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	42	262	0	ENST00000302850.5:c.584A>G	p.Asn195Ser	p.N195S	ENST00000302850	NM_000208.2	195	aAc/aGc	2/22	1	2	FACETS	0.424	0.353	0.502	0.424	0.353	0.502	SUBCLONAL	1	TRUE	1	0.382144325963338	2		262	519	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288441	15288441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	62	198	0	ENST00000263388.2:c.4298G>A	p.Cys1433Tyr	p.C1433Y	ENST00000263388	NM_000435.2	1433	tGc/tAc	24/33	1	2	FACETS	0.758	0.665	0.856	1	0.974	1	SUBCLONAL	2	TRUE	1	0.382144325963338	2		198	214	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227811	36227811	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	128	343	0	ENST00000222270.7:c.7298-2A>G		p.X2433_splice	ENST00000222270	NM_014727.1	2433			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.382144325963338	2		343	537	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753544	42753545	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	109	318	0	ENST00000222329.4:c.719dup	p.Gly241TrpfsTer3	p.G241Wfs*3	ENST00000222329	NM_006494.2	240	ggt/ggGt	4/4	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.382144325963338	2		318	427	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792089	42792089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1451774836	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	81	259	0	ENST00000575354.2:c.893G>A	p.Arg298Gln	p.R298Q	ENST00000575354	NM_015125.3	298	cGg/cAg	6/20	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.382144325963338	2		259	402	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645495	215645495	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	100	366	0	ENST00000260947.4:c.1103G>A	p.Cys368Tyr	p.C368Y	ENST00000260947	NM_000465.2	368	tGc/tAc	4/11	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.382144325963338	2		366	481	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39704816	39704817	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	37	102	0	ENST00000361337.2:c.162_163del	p.His54GlnfsTer4	p.H54Qfs*4	ENST00000361337	NM_003286.2	54	cAT/c	4/21	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.382144325963338	2		102	159	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546064	41546065	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	101	314	0	ENST00000263253.7:c.2683dup	p.Gln895ProfsTer14	p.Q895Pfs*14	ENST00000263253	NM_001429.3	893	-/C	14/31	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.382144325963338	2		314	488	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275323	41275323	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	17	282	0	ENST00000349496.5:c.1489C>G	p.Leu497Val	p.L497V	ENST00000349496	NM_001904.3	497	Ctc/Gtc	9/15	0.382144325963338	2	FACETS	0.272	0.202	0.355	0.136	0.101	0.178	SUBCLONAL	1	TRUE	0	0.382144325963338	2		282	327	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808651	1808651	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752294041	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	61	403	1	ENST00000260795.2:c.2264C>T	p.Thr755Met	p.T755M	ENST00000260795		755	aCg/aTg	16/17	NA	2	FACETS	0.724	0.626	0.83			1	INDETERMINATE	1	TRUE	NA	0.382144325963338	2		404	441	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268222	153268222	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1473413902	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	63	137	0	ENST00000281708.4:c.586A>G	p.Thr196Ala	p.T196A	ENST00000281708	NM_033632.3	196	Acc/Gcc	4/12	1	2	FACETS	0.841	0.74	0.946	1	0.978	1	CLONAL	2	TRUE	1	0.382144325963338	2		137	196	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294050	1294050	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	72	370	0	ENST00000310581.5:c.951G>T	p.Trp317Cys	p.W317C	ENST00000310581	NM_198253.2	317	tgG/tgT	2/16	1	2	FACETS	0.821	0.72	0.93	0.821	0.72	0.93	CLONAL	1	TRUE	1	0.382144325963338	2		370	459	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38957774	38957775	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	43	276	0	ENST00000357387.3:c.2478dup	p.Gln827ThrfsTer15	p.Q827Tfs*15	ENST00000357387	NM_152756.3	826	-/A	25/38	1	2	FACETS	0.846	0.713	0.992	0.846	0.713	0.992	CLONAL	1	TRUE	1	0.382144325963338	2		276	266	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659282	86659282	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	47	201	0	ENST00000274376.6:c.1571T>C	p.Val524Ala	p.V524A	ENST00000274376	NM_002890.2	524	gTa/gCa	11/25	1	2	FACETS	0.976	0.831	1	0.976	0.831	1	CLONAL	1	TRUE	1	0.382144325963338	2		201	252	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176719025	176719025	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs754837409	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	68	206	0	ENST00000439151.2:c.6329A>G	p.Gln2110Arg	p.Q2110R	ENST00000439151	NM_022455.4	2110	cAg/cGg	22/23	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.382144325963338	2		206	337	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778216	27778216	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	80	297	0	ENST00000369163.2:c.365C>T	p.Pro122Leu	p.P122L	ENST00000369163	NM_003536.2	122	cCc/cTc	1/1	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.382144325963338	2		297	415	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468191	50468191	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs751951646	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	94	305	0	ENST00000331340.3:c.1426A>G	p.Met476Val	p.M476V	ENST00000331340	NM_006060.4	476	Atg/Gtg	8/8	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.382144325963338	2		305	441	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508538	106508538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1157393554	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	76	183	0	ENST00000359195.3:c.532C>T	p.Arg178Cys	p.R178C	ENST00000359195	NM_002649.2	178	Cgt/Tgt	2/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.382144325963338	2		183	308	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740787	145740787	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	113	372	0	ENST00000428558.2:c.1313A>G	p.Gln438Arg	p.Q438R	ENST00000428558	NM_004260.3	438	cAa/cGa	7/22	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.382144325963338	2		372	494	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245132	53245133	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	80	307	0	ENST00000375401.3:c.807dup	p.Thr270HisfsTer20	p.T270Hfs*20	ENST00000375401	NM_004187.3	269	-/C	7/26	1	2	FACETS	0.935	0.826	1	0.935	0.826	1	CLONAL	1	TRUE	1	0.382144325963338	2		307	448	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412775	63412775	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	90	300	0	ENST00000330258.3:c.392A>G	p.Gln131Arg	p.Q131R	ENST00000330258	NM_152424.3	131	cAg/cGg	2/2	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.382144325963338	2		300	413	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412839	63412839	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	100	329	0	ENST00000330258.3:c.328G>A	p.Val110Ile	p.V110I	ENST00000330258	NM_152424.3	110	Gtc/Atc	2/2	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.382144325963338	2		329	481	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0037447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	299	417	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.421342905652444	5	FACETS	0.837	0.792	0.883	0.837	0.792	0.883	CLONAL	3	TRUE	2	0.563037606987025	5		417	780	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0037447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	55	197	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.88	0.762	1	0.88	0.762	1	CLONAL	1	TRUE	1	0.563037606987025	2		197	222	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0037447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	317	478	5	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.541126140448516	2	FACETS	0.932	0.889	0.975	0.932	0.889	0.975	CLONAL	2	TRUE	0	0.563037606987025	2		483	604	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0037447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	58	252	2	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.744	0.645	0.85	0.744	0.645	0.85	SUBCLONAL	1	TRUE	1	0.563037606987025	2		254	277	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106089	27106090	+	stop_gained	Nonsense_Mutation	DNP	TG	TG	AT	novel	NA	P-0037447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	89	406	2	ENST00000324856.7:c.5700_5701delinsAT	p.Asp1900_Gly1901delinsGluTer	p.D1900_G1901delinsE*	ENST00000324856	NM_006015.4	1900	gaTGga/gaATga	20/20	0.559870457473195	3	FACETS	0.79	0.702	0.882	0.395	0.351	0.441	SUBCLONAL	1	TRUE	1	0.563037606987025	3		408	513	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633486	3633486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs181782315	NA	P-0037447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	318	576	2	ENST00000294008.3:c.4765C>T	p.Arg1589Cys	p.R1589C	ENST00000294008	NM_032444.2	1589	Cgc/Tgc	14/15	0.417909157987049	4	FACETS	0.855	0.808	0.902	0.855	0.808	0.902	CLONAL	2	TRUE	2	0.563037606987025	4		578	1033	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223251	5223251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199604489	NA	P-0037447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	142	391	0	ENST00000357368.4:c.2552G>A	p.Arg851His	p.R851H	ENST00000357368	NM_002850.3	851	cGc/cAc	18/38	0.559870457473195	3	FACETS	0.996	0.91	1	0.498	0.455	0.543	CLONAL	1	TRUE	1	0.563037606987025	3		391	649	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0037449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	210	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.573401892730334	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	FALSE	1	0.573401892730334	3		326	417	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100436	8100436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1220437638	NA	P-0037449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	40	609	0	ENST00000346208.3:c.410C>T	p.Ser137Leu	p.S137L	ENST00000346208		137	tCg/tTg	3/6	0.408343360407088	4	FACETS	0.287	0.237	0.342	0.143	0.118	0.171	SUBCLONAL	1	FALSE	2	0.573401892730334	4		609	766	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339968	116339968	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	103	384	0	ENST00000397752.3:c.830G>C	p.Arg277Thr	p.R277T	ENST00000397752	NM_000245.2	277	aGa/aCa	2/21	0.408343360407088	4	FACETS	1	0.961	1	0.57	0.512	0.631	CLONAL	1	FALSE	2	0.573401892730334	4		384	496	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992054	72992054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	279	596	0	ENST00000268489.5:c.1991C>T	p.Ser664Phe	p.S664F	ENST00000268489	NM_006885.3	664	tCt/tTt	2/10	0.573401892730334	3	FACETS	1	0.968	1	0.686	0.65	0.723	CLONAL	2	FALSE	0	0.573401892730334	3		596	608	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115386	115115386	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	288	570	2	ENST00000257566.3:c.940del	p.Arg314GlufsTer9	p.R314Efs*9	ENST00000257566	NM_016569.3	314	Aga/ga	5/8	0.573401892730334	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	FALSE	1	0.573401892730334	3		572	572	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482606	56482606	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1157	329	620	1	ENST00000267101.3:c.1063A>C	p.Thr355Pro	p.T355P	ENST00000267101	NM_001982.3	355	Acc/Ccc	9/28	0.573401892730334	8	FACETS	1	0.972	1	0.35	0.33	0.371	CLONAL	2	FALSE	2	0.573401892730334	8		621	1486	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842363	68842363	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	347	482	0	ENST00000261769.5:c.426del	p.Asn144ThrfsTer71	p.N144Tfs*71	ENST00000261769	NM_004360.3	142	Ttt/tt	4/16	0.573401892730334	3	FACETS	0.996	0.959	1	0.996	0.959	1	CLONAL	3	FALSE	0	0.573401892730334	3		482	521	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532645	46532645	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	84	411	0	ENST00000262741.5:c.433C>G	p.Leu145Val	p.L145V	ENST00000262741	NM_003629.3	145	Ctt/Gtt	4/10	0.573401892730334	3	FACETS	0.752	0.667	0.844	0.376	0.333	0.422	SUBCLONAL	1	FALSE	1	0.573401892730334	3		411	501	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731039	162731039	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	113	409	0	ENST00000367921.3:c.894C>G	p.Ile298Met	p.I298M	ENST00000367921	NM_006182.2	298	atC/atG	9/18	0.573401892730334	7	FACETS	1	0.95	1	0.182	0.163	0.202	CLONAL	1	FALSE	1	0.573401892730334	7		409	878	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945424	71945424	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	43	636	1	ENST00000298229.2:c.2312C>T	p.Ser771Phe	p.S771F	ENST00000298229	NM_001567.3	771	tCt/tTt	20/28	0.573401892730334	3	FACETS	0.307	0.256	0.363	0.153	0.128	0.182	SUBCLONAL	1	FALSE	1	0.573401892730334	3		637	629	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94153295	94153295	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393301068	NA	P-0037449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	43	434	0	ENST00000323929.3:c.2123G>A	p.Arg708Lys	p.R708K	ENST00000323929	NM_005591.3	708	aGa/aAa	20/20	0.573401892730334	3	FACETS	0.436	0.365	0.514	0.218	0.182	0.257	SUBCLONAL	1	FALSE	1	0.573401892730334	3		434	443	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117753	108117753	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	71	306	1	ENST00000278616.4:c.964G>T	p.Glu322Ter	p.E322*	ENST00000278616	NM_000051.3	322	Gag/Tag	8/63	0.573401892730334	3	FACETS	0.88	0.773	0.994	0.44	0.386	0.497	CLONAL	1	FALSE	1	0.573401892730334	3		307	362	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39607441	39607441	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	57	258	0	ENST00000262039.4:c.1519C>T	p.Gln507Ter	p.Q507*	ENST00000262039	NM_002647.2	507	Cag/Tag	14/25	1	2	FACETS	0.984	0.857	1	0.984	0.857	1	CLONAL	1	FALSE	1	0.573401892730334	2		258	202	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228160	36228160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	114	587	0	ENST00000222270.7:c.7546C>T	p.Leu2516Phe	p.L2516F	ENST00000222270	NM_014727.1	2516	Ctc/Ttc	33/37	0.408343360407088	4	FACETS	0.978	0.882	1	0.489	0.441	0.539	CLONAL	1	FALSE	2	0.573401892730334	4		587	640	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280107	66280107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs77407591	NA	P-0037449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	93	410	0	ENST00000273854.3:c.1582G>A	p.Glu528Lys	p.E528K	ENST00000273854	NM_004439.5	528	Gag/Aag	7/18	0.573401892730334	4	FACETS	0.967	0.862	1	0.483	0.431	0.539	CLONAL	1	FALSE	2	0.573401892730334	4		410	528	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212845	27212845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143080429	NA	P-0037449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	151	616	1	ENST00000380036.4:c.2827C>T	p.His943Tyr	p.H943Y	ENST00000380036	NM_000459.3	943	Cac/Tac	17/23	0.573401892730334	3	FACETS	1	0.968	1	0.554	0.508	0.601	CLONAL	1	FALSE	1	0.573401892730334	3		617	612	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890189	76890189	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	124	430	0	ENST00000373344.5:c.4705C>T	p.Gln1569Ter	p.Q1569*	ENST00000373344	NM_000489.3	1569	Cag/Tag	17/35	0.216458020321971	5	FACETS	1	0.983	1	0.461	0.418	0.505	INDETERMINATE	1	FALSE	2	0.573401892730334	5		430	582	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394990	394990	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	191	311	0	ENST00000380956.4:c.386C>A	p.Pro129His	p.P129H	ENST00000380956	NM_001195286.1	129	cCt/cAt	3/9	0.606685741759249	24	FACETS	0.992	0.934	1			1	CLONAL	14	FALSE	NA	0.606685741759249	24		311	348	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391000	89391000	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	21	422	0	ENST00000336596.2:c.1066G>A	p.Asp356Asn	p.D356N	ENST00000336596	NM_005233.5	356	Gat/Aat	5/17	0.439762823387763	5	FACETS	1	0.877	1	0.76	0.609	0.92	CLONAL	2	FALSE	2	0.606685741759249	5		422	58	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939418	76939418	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2	28	702	0	ENST00000373344.5:c.1330C>T	p.Arg444Ter	p.R444*	ENST00000373344	NM_000489.3	444	Cga/Tga	9/35	0.60856337888478	1	FACETS	1	0.958	1	1	0.974	1	CLONAL	2	FALSE	0	0.606685741759249	1		702	30	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521939	157521939	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs372833448	NA	P-0037713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	29	362	0	ENST00000346085.5:c.4211A>G	p.Tyr1404Cys	p.Y1404C	ENST00000346085	NM_020732.3	1404	tAc/tGc	18/20	0.60856337888478	4	FACETS	1	0.87	1	1	0.87	1	CLONAL	2	FALSE	2	0.606685741759249	4		362	73	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822405	72822405	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	13	821	0	ENST00000268489.5:c.9770C>G	p.Pro3257Arg	p.P3257R	ENST00000268489	NM_006885.3	3257	cCc/cGc	10/10	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.606685741759249	NA		821	36	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654532	29654532	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	24	203	0	ENST00000356175.3:c.5221del	p.Val1741SerfsTer3	p.V1741Sfs*3	ENST00000356175	NM_000267.3	1741	Gtc/tc	37/57	0.60856337888478	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	2	FALSE	0	0.606685741759249	2		203	38	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243963	5243963	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4	25	458	0	ENST00000357368.4:c.1519G>C	p.Val507Leu	p.V507L	ENST00000357368	NM_002850.3	507	Gtc/Ctc	11/38	0.607676279276665	2	FACETS	0.947	0.852	1	1	0.964	1	CLONAL	3	FALSE	0	0.606685741759249	2		458	29	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169977829	169977829	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs781289139	NA	P-0037713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	21	473	0	ENST00000295797.4:c.296C>G	p.Ser99Cys	p.S99C	ENST00000295797	NM_002740.5	99	tCt/tGt	3/18	0.408650469351183	5	FACETS	1	0.818	1	1	0.818	1	CLONAL	3	FALSE	2	0.606685741759249	5		473	44	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670651	30670651	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770859881	NA	P-0037713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	58	348	0	ENST00000376406.3:c.5869C>T	p.Arg1957Cys	p.R1957C	ENST00000376406	NM_014641.2	1957	Cgc/Tgc	13/15	0.606685741759249	6	FACETS	0.966	0.894	1	0.966	0.894	1	CLONAL	6	FALSE	0	0.606685741759249	6		348	73	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	33	417	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.728	0.592	0.883	0.728	0.592	0.883	SUBCLONAL	1	TRUE	1	0.15	2		417	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555526268	NA	P-0037715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	67	705	0	ENST00000269305.4:c.406C>G	p.Gln136Glu	p.Q136E	ENST00000269305	NM_001126112.2	136	Caa/Gaa	5/11	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.15	2		705	855	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435300	110435302	+	inframe_deletion	In_Frame_Del	DEL	GGT	GGT	-	rs765493638	NA	P-0037715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	11	64	0	ENST00000375856.3:c.3099_3101del	p.Pro1036del	p.P1036del	ENST00000375856	NM_003749.2	1033	ccACCg/ccg	1/2	1	2	FACETS	0.797	0.557	1	1	0.868	1	CLONAL	2	TRUE	1	0.15	2		64	92	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0037716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	68	114	0				ENST00000310581	NM_198253.2	-/1132			0.408920776966799	3	FACETS	1	0.952	1	0.747	0.667	0.828	CLONAL	2	FALSE	0	0.490849626548212	3		114	154	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120502102	120502102	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	32	276	0	ENST00000256646.2:c.1939G>C	p.Asp647His	p.D647H	ENST00000256646	NM_024408.3	647	Gat/Cat	12/34	0.226952575911439	3	FACETS	0.562	0.457	0.679	0.281	0.228	0.34	INDETERMINATE	1	FALSE	1	0.490849626548212	3		276	289	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94908721	94908721	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	37	482	0	ENST00000536441.1:c.1333G>A	p.Glu445Lys	p.E445K	ENST00000536441	NM_144665.3	445	Gag/Aag	9/10	0.314274067481243	3	FACETS	0.429	0.353	0.513	0.214	0.176	0.257	SUBCLONAL	1	FALSE	1	0.490849626548212	3		482	438	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342446	118342446	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0037716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	39	151	0	ENST00000534358.1:c.572C>G	p.Ser191Ter	p.S191*	ENST00000534358	NM_005933.3	191	tCa/tGa	3/36	0.115158473211192	4	FACETS	1	0.934	1	0.62	0.52	0.729	INDETERMINATE	1	FALSE	2	0.490849626548212	4		151	191	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934254	48934254	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1131690904	NA	P-0037716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	85	344	0	ENST00000267163.4:c.709G>T	p.Glu237Ter	p.E237*	ENST00000267163	NM_000321.2	237	Gaa/Taa	7/27	0.115158473211192	4	FACETS	1	0.979	1	0.733	0.653	0.818	INDETERMINATE	1	FALSE	2	0.490849626548212	4		344	352	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30047529	30047529	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	16	320	0	ENST00000331968.5:c.2472G>C	p.Met824Ile	p.M824I	ENST00000331968	NM_002742.2	824	atG/atC	17/18	0.115158473211192	4	FACETS	0.398	0.294	0.522	0.199	0.147	0.261	INDETERMINATE	1	FALSE	2	0.490849626548212	4		320	244	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942068	81942068	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	28	353	0	ENST00000359376.3:c.1605G>C	p.Lys535Asn	p.K535N	ENST00000359376	NM_002661.3	535	aaG/aaC	17/33	0.405065777535825	1	FACETS	0.395	0.317	0.482	0.395	0.317	0.482	SUBCLONAL	1	FALSE	0	0.490849626548212	1		353	218	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942088	81942088	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	35	366	0	ENST00000359376.3:c.1625G>C	p.Ser542Thr	p.S542T	ENST00000359376	NM_002661.3	542	aGt/aCt	17/33	0.405065777535825	1	FACETS	0.464	0.383	0.554	0.464	0.383	0.554	SUBCLONAL	1	FALSE	0	0.490849626548212	1		366	232	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16090003	16090003	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0037716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	48	162	0	ENST00000268712.3:c.109-2A>G		p.X37_splice	ENST00000268712	NM_006311.3	37			0.271674250340809	2	FACETS	0.914	0.782	1	0.457	0.391	0.528	INDETERMINATE	1	FALSE	0	0.490849626548212	2		162	214	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56809896	56809896	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	81	373	0	ENST00000337432.4:c.1017T>G	p.Phe339Leu	p.F339L	ENST00000337432	NM_058216.2	339	ttT/ttG	8/9	0.115158473211192	4	FACETS	1	0.976	1	0.707	0.628	0.791	INDETERMINATE	1	FALSE	2	0.490849626548212	4		373	348	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118872	70118872	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	31	331	0	ENST00000245479.2:c.444G>C	p.Glu148Asp	p.E148D	ENST00000245479	NM_000346.3	148	gaG/gaC	2/3	0.115158473211192	4	FACETS	1	0.924	1	0.632	0.518	0.757	INDETERMINATE	1	FALSE	2	0.490849626548212	4		331	149	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118878	70118878	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1465795705	NA	P-0037716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	31	352	0	ENST00000245479.2:c.450G>C	p.Glu150Asp	p.E150D	ENST00000245479	NM_000346.3	150	gaG/gaC	2/3	0.115158473211192	4	FACETS	1	0.903	1	0.585	0.479	0.702	INDETERMINATE	1	FALSE	2	0.490849626548212	4		352	161	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56402488	56402488	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	16	193	0	ENST00000348428.3:c.1530C>G	p.Ile510Met	p.I510M	ENST00000348428	NM_006785.3	510	atC/atG	13/17	1	2	FACETS	0.282	0.209	0.37	0.282	0.209	0.37	SUBCLONAL	1	FALSE	1	0.490849626548212	2		193	231	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302346	15302346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1386908989	NA	P-0037716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	22	621	1	ENST00000263388.2:c.925G>A	p.Glu309Lys	p.E309K	ENST00000263388	NM_000435.2	309	Gag/Aag	6/33	0.180590789550398	5	FACETS	0.378	0.292	0.478	0.126	0.097	0.16	INDETERMINATE	1	FALSE	2	0.490849626548212	5		622	412	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916755	178916755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	41	271	0	ENST00000263967.3:c.142G>A	p.Glu48Lys	p.E48K	ENST00000263967	NM_006218.2	48	Gaa/Aaa	2/21	0.115158473211192	4	FACETS	0.712	0.594	0.841	0.356	0.297	0.421	INDETERMINATE	1	FALSE	2	0.490849626548212	4		271	350	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55974025	55974025	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1379812941	NA	P-0037716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	20	326	0	ENST00000263923.4:c.1291C>T	p.Pro431Ser	p.P431S	ENST00000263923	NM_002253.2	431	Cct/Tct	10/30	0.275811678722002	1	FACETS	0.283	0.217	0.36	0.283	0.217	0.36	INDETERMINATE	1	FALSE	0	0.490849626548212	1		326	217	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950121	38950121	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	34	373	0	ENST00000357387.3:c.3829C>G	p.Leu1277Val	p.L1277V	ENST00000357387	NM_152756.3	1277	Ctg/Gtg	31/38	0.490849626548212	6	FACETS	0.507	0.413	0.612			1	SUBCLONAL	1	FALSE	NA	0.490849626548212	6		373	542	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753376	57753376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	14	342	0	ENST00000274289.3:c.748G>A	p.Glu250Lys	p.E250K	ENST00000274289	NM_006622.3	250	Gaa/Aaa	6/14	0.314274067481243	3	FACETS	0.355	0.257	0.474	0.178	0.128	0.237	SUBCLONAL	1	FALSE	1	0.490849626548212	3		342	200	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80171619	80171619	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	16	306	0	ENST00000265081.6:c.3352G>C	p.Asp1118His	p.D1118H	ENST00000265081	NM_002439.4	1118	Gac/Cac	24/24	0.314274067481243	3	FACETS	0.376	0.278	0.492	0.188	0.139	0.246	SUBCLONAL	1	FALSE	1	0.490849626548212	3		306	216	SUCCESS
APC	324	MSKCC	GRCh37	5	112178922	112178922	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	39	210	0	ENST00000257430.4:c.7631C>A	p.Ser2544Ter	p.S2544*	ENST00000257430	NM_000038.5	2544	tCa/tAa	16/16	0.314274067481243	3	FACETS	1	0.933	1	0.611	0.514	0.715	CLONAL	1	FALSE	1	0.490849626548212	3		210	162	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031973	26031973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	36	255	0	ENST00000244661.2:c.316G>A	p.Glu106Lys	p.E106K	ENST00000244661	NM_003537.3	106	Gag/Aag	1/1	0.490849626548212	7	FACETS	0.791	0.651	0.948	0.198	0.162	0.237	CLONAL	1	FALSE	3	0.490849626548212	7		255	413	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032069	26032069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	36	274	0	ENST00000244661.2:c.220G>A	p.Glu74Lys	p.E74K	ENST00000244661	NM_003537.3	74	Gaa/Aaa	1/1	0.490849626548212	7	FACETS	0.78	0.641	0.935	0.195	0.16	0.234	CLONAL	1	FALSE	3	0.490849626548212	7		274	419	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641147	117641147	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370269692	NA	P-0037716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	49	447	1	ENST00000368508.3:c.5824C>T	p.Arg1942Trp	p.R1942W	ENST00000368508	NM_002944.2	1942	Cgg/Tgg	36/43	0.4138169682108	0	FACETS	0.527	0.452	0.606			1	SUBCLONAL	1	FALSE	0	0.490849626548212	0		448	193	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001166	150001167	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0037716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	18	384	0	ENST00000253339.5:c.2437dup	p.Thr813AsnfsTer5	p.T813Nfs*5	ENST00000253339		813	acc/aAcc	4/7	0.441783900074529	3	FACETS	0.293	0.22	0.379			1	SUBCLONAL	1	FALSE	NA	0.490849626548212	3		384	312	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001595	150001595	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0037716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	45	279	0	ENST00000253339.5:c.2011-2A>G		p.X671_splice	ENST00000253339		671			0.441783900074529	3	FACETS	0.936	0.793	1			1	CLONAL	1	FALSE	NA	0.490849626548212	3		279	244	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034517	123034517	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	24	291	0	ENST00000355640.3:c.1274A>G	p.Glu425Gly	p.E425G	ENST00000355640		425	gAg/gGg	6/7	1	2	FACETS	0.459	0.362	0.57	0.459	0.362	0.57	SUBCLONAL	1	FALSE	1	0.490849626548212	2		291	213	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732533	74732533	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	16	89	0	ENST00000359995.5:c.376C>T	p.Arg126Cys	p.R126C	ENST00000359995	NM_001195427.1	126	Cgc/Tgc	2/3	0.115158473211192	4	FACETS	0.81	0.605	1	0.405	0.302	0.525	INDETERMINATE	1	FALSE	2	0.490849626548212	4		89	120	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81941320	81941320	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762012909	NA	P-0037716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	41	424	0	ENST00000359376.3:c.1498G>A	p.Asp500Asn	p.D500N	ENST00000359376	NM_002661.3	500	Gat/Aat	16/33	0.405065777535825	1	FACETS	0.534	0.448	0.628	0.534	0.448	0.628	SUBCLONAL	1	FALSE	0	0.490849626548212	1		424	236	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	85	236	0				ENST00000310581	NM_198253.2	-/1132			0.346705563772339	3	FACETS	0.913	0.824	1	1	0.979	1	CLONAL	3	TRUE	1	0.346705563772339	3		236	210	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0037717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	76	326	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	0.346705563772339	2		326	386	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412022	116412022	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	221	633	1	ENST00000397752.3:c.3007T>A	p.Tyr1003Asn	p.Y1003N	ENST00000397752	NM_000245.2	1003	Tac/Aac	14/21	0.254935425737229	3	FACETS	0.889	0.83	0.949	0.889	0.83	0.949	CLONAL	3	TRUE	0	0.254935425737229	3		634	733	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72897386	72897386	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	30	270	0	ENST00000325599.8:c.106T>G	p.Ser36Ala	p.S36A	ENST00000325599	NM_018130.2	36	Tct/Gct	1/11	1	2	FACETS	0.795	0.642	0.967	0.795	0.642	0.967	CLONAL	1	TRUE	1	0.254935425737229	2		270	296	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	36	236	0				ENST00000310581	NM_198253.2	-/1132			0.611440449221897	3	FACETS	0.818	0.68	0.969	0.409	0.34	0.485	CLONAL	1	TRUE	1	0.611440449221897	3		236	188	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0037720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	10688	478	5	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.611440449221897	57	FACETS	0.995	0.992	0.999			1	CLONAL	55	TRUE	NA	0.611440449221897	57		483	11376	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227863	36227863	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	188	852	0	ENST00000222270.7:c.7348C>G	p.Arg2450Gly	p.R2450G	ENST00000222270	NM_014727.1	2450	Cga/Gga	32/37	0.611440449221897	3	FACETS	0.98	0.907	1	0.49	0.453	0.528	CLONAL	1	TRUE	1	0.611440449221897	3		852	819	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	144	309	1	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	0.721124146908791	2		310	399	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859308	151859309	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	189	331	0	ENST00000262189.6:c.11353_11354del	p.Lys3785ValfsTer10	p.K3785Vfs*10	ENST00000262189	NM_170606.2	3785	AAg/g	43/59	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.721124146908791	2		331	508	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779218	3779218	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	18	356	0	ENST00000262367.5:c.5830G>C	p.Ala1944Pro	p.A1944P	ENST00000262367	NM_004380.2	1944	Gcc/Ccc	31/31	1	2	FACETS	0.15	0.112	0.194	0.15	0.112	0.194	SUBCLONAL	1	TRUE	1	0.721124146908791	2		356	333	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	35	487	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.721124146908791	2	FACETS	0.16	0.13	0.193	0.08	0.065	0.097	SUBCLONAL	1	TRUE	0	0.721124146908791	2		487	607	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	120	267	0	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	1	2	FACETS	0.999	0.914	1	0.999	0.914	1	CLONAL	1	TRUE	1	0.721124146908791	2		267	333	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	361	322	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	0.721124146908791	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.721124146908791	2		322	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	206	424	0	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	1	2	FACETS	0.867	0.808	0.927	0.867	0.808	0.927	CLONAL	1	TRUE	1	0.721124146908791	2		424	659	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856532	45856532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201165309	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	48	594	2	ENST00000391945.4:c.1726G>A	p.Glu576Lys	p.E576K	ENST00000391945	NM_000400.3	576	Gaa/Aaa	18/23	1	2	FACETS	0.188	0.158	0.221	0.188	0.158	0.221	SUBCLONAL	1	TRUE	1	0.721124146908791	2		596	707	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482926	140482927	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs777474487	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	188	476	0	ENST00000288602.6:c.1208dup	p.Ala404CysfsTer9	p.A404Cfs*9	ENST00000288602	NM_004333.4	403	cct/ccCt	10/18	1	2	FACETS	0.832	0.772	0.893	0.832	0.772	0.893	CLONAL	1	TRUE	1	0.721124146908791	2		476	627	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370985	55370985	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	194	444	0	ENST00000297316.4:c.287C>G	p.Ala96Gly	p.A96G	ENST00000297316	NM_022454.3	96	gCc/gGc	1/2	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.721124146908791	2		444	523	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134267	11134267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1180804356	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	200	410	0	ENST00000358026.2:c.2933G>A	p.Arg978Gln	p.R978Q	ENST00000358026	NM_001128849.1	978	cGa/cAa	20/36	1	2	FACETS	0.942	0.878	1	0.942	0.878	1	CLONAL	1	TRUE	1	0.721124146908791	2		410	589	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828257	72828257	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	35	534	0	ENST00000268489.5:c.8324del	p.Pro2775GlnfsTer14	p.P2775Qfs*14	ENST00000268489	NM_006885.3	2775	cCa/ca	9/10	1	2	FACETS	0.164	0.134	0.198	0.164	0.134	0.198	SUBCLONAL	1	TRUE	1	0.721124146908791	2		534	592	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528252	157528252	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554237801	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	415	433	0	ENST00000346085.5:c.5977C>T	p.Gln1993Ter	p.Q1993*	ENST00000346085	NM_020732.3	1993	Cag/Tag	20/20	0.703306490346497	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.721124146908791	2		433	557	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752673	128752675	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	193	194	0	ENST00000377970.2:c.838_840del	p.Val280del	p.V280del	ENST00000377970	NM_002467.4	278	gaTGTt/gat	3/3	0.721124146908791	3	FACETS	0.899	0.844	0.955	0.899	0.844	0.955	CLONAL	2	TRUE	1	0.721124146908791	3		194	405	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279450	1279450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs973201915	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	46	654	1	ENST00000310581.5:c.2086C>T	p.Arg696Cys	p.R696C	ENST00000310581	NM_198253.2	696	Cgt/Tgt	5/16	1	2	FACETS	0.199	0.167	0.235	0.199	0.167	0.235	SUBCLONAL	1	TRUE	1	0.721124146908791	2		655	640	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925621	114925621	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763934346	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	222	459	3	ENST00000543371.1:c.1699G>A	p.Ala567Thr	p.A567T	ENST00000543371	NM_001198531.1	567	Gcc/Acc	14/14	0.721124146908791	2	FACETS	0.931	0.872	0.993	0.466	0.436	0.497	CLONAL	1	TRUE	0	0.721124146908791	2		462	661	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059207	27059207	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	34	400	0	ENST00000324856.7:c.1848del	p.Ser617GlnfsTer2	p.S617Qfs*2	ENST00000324856	NM_006015.4	615	gCc/gc	4/20	1	2	FACETS	0.165	0.134	0.2	0.165	0.134	0.2	SUBCLONAL	1	TRUE	1	0.721124146908791	2		400	572	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412899	49412899	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	47	482	0	ENST00000418115.1:c.124T>A	p.Tyr42Asn	p.Y42N	ENST00000418115	NM_001664.2	42	Tat/Aat	2/5	1	2	FACETS	0.165	0.138	0.194	0.165	0.138	0.194	SUBCLONAL	1	TRUE	1	0.721124146908791	2		482	791	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989633	68989633	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs866647316	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	35	402	0	ENST00000288368.4:c.1571G>A	p.Gly524Glu	p.G524E	ENST00000288368	NM_024870.2	524	gGa/gAa	15/40	1	2	FACETS	0.179	0.146	0.217	0.179	0.146	0.217	SUBCLONAL	1	TRUE	1	0.721124146908791	2		402	541	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466000	69466000	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	37	513	0	ENST00000227507.2:c.838G>T	p.Glu280Ter	p.E280*	ENST00000227507	NM_053056.2	280	Gag/Tag	5/5	1	2	FACETS	0.17	0.139	0.204	0.17	0.139	0.204	SUBCLONAL	1	TRUE	1	0.721124146908791	2		513	605	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380431	31380431	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	146	290	0	ENST00000328111.2:c.922-1G>A		p.X308_splice	ENST00000328111	NM_006892.3	308			1	2	FACETS	0.997	0.92	1	0.997	0.92	1	CLONAL	1	TRUE	1	0.721124146908791	2		290	406	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845649	68845649	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	257	455	0	ENST00000261769.5:c.895G>A	p.Ala299Thr	p.A299T	ENST00000261769	NM_004360.3	299	Gcc/Acc	7/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.721124146908791	2		455	681	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819212	3819212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	216	395	0	ENST00000262367.5:c.3023C>T	p.Pro1008Leu	p.P1008L	ENST00000262367	NM_004380.2	1008	cCc/cTc	15/31	1	2	FACETS	0.974	0.911	1	0.974	0.911	1	CLONAL	1	TRUE	1	0.721124146908791	2		395	615	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717727	89717727	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	390	395	1	ENST00000371953.3:c.752G>A	p.Gly251Asp	p.G251D	ENST00000371953	NM_000314.4	251	gGt/gAt	7/9	0.721124146908791	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.721124146908791	2		396	508	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219414	133219414	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878854876	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	41	644	1	ENST00000320574.5:c.4720G>A	p.Ala1574Thr	p.A1574T	ENST00000320574	NM_006231.2	1574	Gcc/Acc	36/49	1	2	FACETS	0.163	0.135	0.194	0.163	0.135	0.194	SUBCLONAL	1	TRUE	1	0.721124146908791	2		645	698	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370951	55370952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	244	457	0	ENST00000297316.4:c.255dup	p.Leu86AlafsTer76	p.L86Afs*76	ENST00000297316	NM_022454.3	85	cgg/cGgg	1/2	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.721124146908791	2		457	591	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023539	27023539	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	162	253	0	ENST00000324856.7:c.645C>A	p.Tyr215Ter	p.Y215*	ENST00000324856	NM_006015.4	215	taC/taA	1/20	1	2	FACETS	0.948	0.877	1	0.948	0.877	1	CLONAL	1	TRUE	1	0.721124146908791	2		253	474	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106572	27106581	+	frameshift_variant	Frame_Shift_Del	DEL	GGTTACACTC	GGTTACACTC	-	novel	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	212	492	0	ENST00000324856.7:c.6184_6193del	p.Val2062ProfsTer70	p.V2062Pfs*70	ENST00000324856	NM_006015.4	2061	ttGGTTACACTC/tt	20/20	1	2	FACETS	0.907	0.847	0.969	0.907	0.847	0.969	CLONAL	1	TRUE	1	0.721124146908791	2		492	648	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39321516	39321516	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	214	458	0	ENST00000373001.3:c.505C>A	p.Pro169Thr	p.P169T	ENST00000373001	NM_022157.3	169	Cca/Aca	3/7	1	2	FACETS	0.962	0.9	1	0.962	0.9	1	CLONAL	1	TRUE	1	0.721124146908791	2		458	617	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851378	156851378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374957692	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	218	542	0	ENST00000524377.1:c.2335G>A	p.Ala779Thr	p.A779T	ENST00000524377	NM_002529.3	779	Gcc/Acc	17/17	0.721124146908791	3	FACETS	0.944	0.88	1	0.472	0.44	0.506	CLONAL	1	TRUE	1	0.721124146908791	3		542	871	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615620	43615620	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	150	361	0	ENST00000355710.3:c.2699A>G	p.Tyr900Cys	p.Y900C	ENST00000355710	NM_020975.4	900	tAt/tGt	15/20	1	2	FACETS	0.941	0.868	1	0.941	0.868	1	CLONAL	1	TRUE	1	0.721124146908791	2		361	442	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447257	49447257	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	191	448	0	ENST00000301067.7:c.839+2T>C		p.X280_splice	ENST00000301067	NM_003482.3	280			1	2	FACETS	0.96	0.894	1	0.96	0.894	1	CLONAL	1	TRUE	1	0.721124146908791	2		448	552	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434602	110434602	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	171	302	0	ENST00000375856.3:c.3799del	p.Gln1267SerfsTer64	p.Q1267Sfs*64	ENST00000375856	NM_003749.2	1267	Cag/ag	1/2	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.721124146908791	2		302	440	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459360	99459360	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	28	243	0	ENST00000268035.6:c.1996G>T	p.Asp666Tyr	p.D666Y	ENST00000268035	NM_000875.3	666	Gac/Tac	9/21	1	2	FACETS	0.23	0.183	0.282	0.23	0.183	0.282	SUBCLONAL	1	TRUE	1	0.721124146908791	2		243	338	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658518	3658518	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	47	623	0	ENST00000294008.3:c.448C>A	p.Pro150Thr	p.P150T	ENST00000294008	NM_032444.2	150	Cca/Aca	2/15	1	2	FACETS	0.167	0.14	0.196	0.167	0.14	0.196	SUBCLONAL	1	TRUE	1	0.721124146908791	2		623	782	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349547	89349547	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	54	652	0	ENST00000301030.4:c.3403T>C	p.Phe1135Leu	p.F1135L	ENST00000301030	NM_001256183.1	1135	Ttc/Ctc	9/13	1	2	FACETS	0.182	0.155	0.212	0.182	0.155	0.212	SUBCLONAL	1	TRUE	1	0.721124146908791	2		652	822	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40476807	40476807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	214	482	0	ENST00000264657.5:c.1522C>A	p.Leu508Met	p.L508M	ENST00000264657	NM_139276.2	508	Ctg/Atg	17/24	1	2	FACETS	0.95	0.888	1	0.95	0.888	1	CLONAL	1	TRUE	1	0.721124146908791	2		482	625	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753545	42753545	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1254035180	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	224	629	0	ENST00000222329.4:c.719del	p.Gly240ValfsTer31	p.G240Vfs*31	ENST00000222329	NM_006494.2	240	gGt/gt	4/4	1	2	FACETS	0.948	0.888	1	0.948	0.888	1	CLONAL	1	TRUE	1	0.721124146908791	2		629	655	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574122	46574122	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1376666026	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	52	571	0	ENST00000263734.3:c.137G>A	p.Ser46Asn	p.S46N	ENST00000263734	NM_001430.4	46	aGt/aAt	2/16	1	2	FACETS	0.223	0.189	0.26	0.223	0.189	0.26	SUBCLONAL	1	TRUE	1	0.721124146908791	2		571	647	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753325	57753325	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1251040408	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	31	417	0	ENST00000274289.3:c.799G>T	p.Gly267Cys	p.G267C	ENST00000274289	NM_006622.3	267	Ggc/Tgc	6/14	1	2	FACETS	0.152	0.122	0.185	0.152	0.122	0.185	SUBCLONAL	1	TRUE	1	0.721124146908791	2		417	567	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864364	162864364	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	98	257	0	ENST00000366898.1:c.149T>C	p.Leu50Pro	p.L50P	ENST00000366898	NM_004562.2	50	cTg/cCg	2/12	0.703306490346497	2	FACETS	0.816	0.736	0.9	0.408	0.368	0.45	CLONAL	1	TRUE	0	0.721124146908791	2		257	333	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151868426	151868426	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	123	321	0	ENST00000262189.6:c.9376T>A	p.Phe3126Ile	p.F3126I	ENST00000262189	NM_170606.2	3126	Ttc/Atc	40/59	1	2	FACETS	0.799	0.728	0.872	0.799	0.728	0.872	SUBCLONAL	1	TRUE	1	0.721124146908791	2		321	427	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376008	8376008	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	153	254	0	ENST00000356435.5:c.4589C>A	p.Pro1530His	p.P1530H	ENST00000356435		1530	cCt/cAt	28/35	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.721124146908791	2		254	341	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969373	44969373	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	186	376	0	ENST00000377967.4:c.4055A>C	p.Lys1352Thr	p.K1352T	ENST00000377967	NM_021140.2	1352	aAg/aCg	28/29	1	2	FACETS	0.95	0.884	1	0.95	0.884	1	CLONAL	1	TRUE	1	0.721124146908791	2		376	543	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937630	76937630	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	43	397	0	ENST00000373344.5:c.3118A>T	p.Thr1040Ser	p.T1040S	ENST00000373344	NM_000489.3	1040	Act/Tct	9/35	1	2	FACETS	0.222	0.185	0.263	0.222	0.185	0.263	SUBCLONAL	1	TRUE	1	0.721124146908791	2		397	537	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0037722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	145	357	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	0.227387748345476	3	FACETS	1	0.95	1	1	0.95	1	CLONAL	3	TRUE	0	0.286545815789847	3		357	372	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0037722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	100	467	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.153890408917527	2	FACETS	1	0.979	1	0.698	0.626	0.774	INDETERMINATE	1	TRUE	0	0.286545815789847	2		468	500	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871800	12871800	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	51	120	0	ENST00000228872.4:c.517A>C	p.Asn173His	p.N173H	ENST00000228872	NM_004064.3	173	Aat/Cat	2/3	0.117310421859451	3	FACETS	1	0.872	1	1	0.872	1	INDETERMINATE	2	TRUE	1	0.286545815789847	3		120	201	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640004	3640004	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	34	580	0	ENST00000294008.3:c.3635C>A	p.Ala1212Asp	p.A1212D	ENST00000294008	NM_032444.2	1212	gCt/gAt	12/15	0.227387748345476	3	FACETS	0.418	0.34	0.506	0.139	0.113	0.169	SUBCLONAL	1	TRUE	0	0.286545815789847	3		580	649	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813048	89813048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753036862	NA	P-0037722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	35	415	0	ENST00000389301.3:c.3457G>A	p.Asp1153Asn	p.D1153N	ENST00000389301	NM_000135.2	1153	Gac/Aac	35/43	0.153890408917527	2	FACETS	0.543	0.445	0.653	0.271	0.222	0.327	INDETERMINATE	1	TRUE	0	0.286545815789847	2		415	450	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716329	52716329	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	136	435	0	ENST00000322088.6:c.773G>T	p.Arg258Leu	p.R258L	ENST00000322088	NM_014225.5	258	cGc/cTc	6/15	0.0426687778757269	3	FACETS	0.917	0.837	1			1	INDETERMINATE	2	TRUE	NA	0.286545815789847	3		435	592	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0037724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	16	383	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.57	0.42	0.751	0.57	0.42	0.751	SUBCLONAL	1	TRUE	1	0.12	2		383	468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577146	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0037724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	29	449	0	ENST00000269305.4:c.792_794del	p.Leu265del	p.L265del	ENST00000269305	NM_001126112.2	264	ctACTg/ctg	8/11	1	2	FACETS	0.912	0.73	1	0.912	0.73	1	CLONAL	1	TRUE	1	0.12	2		449	530	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672668	30672669	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0037724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	57	572	0	ENST00000376406.3:c.4291_4292del	p.Gln1431GlyfsTer8	p.Q1431Gfs*8	ENST00000376406	NM_014641.2	1431	CAg/g	10/15	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.12	2		572	780	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	40	236	0				ENST00000310581	NM_198253.2	-/1132			0.3	0	FACETS	0.981	0.854	1			1	CLONAL	6	TRUE	0	0.15	0		236	77	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0037731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	53	326	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.904	1	1	0.985	1	CLONAL	5	TRUE	1	0.15	2		326	136	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577069	7577069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55819519	NA	P-0037731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	8	742	0	ENST00000269305.4:c.869G>A	p.Arg290His	p.R290H	ENST00000269305	NM_001126112.2	290	cGc/cAc	8/11	1	2	FACETS	0.319	0.205	0.469	0.319	0.205	0.469	SUBCLONAL	1	TRUE	1	0.15	2		742	334	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1956899	1956899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	14	714	1	ENST00000382891.5:c.2350C>T	p.Arg784Trp	p.R784W	ENST00000382891	NM_133335.3	784	Cgg/Tgg	13/22	1	2	FACETS	0.798	0.577	1	0.798	0.577	1	CLONAL	1	TRUE	1	0.15	2		715	234	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279668	123279668	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	86	404	0	ENST00000358487.5:c.764G>T	p.Arg255Leu	p.R255L	ENST00000358487	NM_000141.4	255	cGg/cTg	7/18	0.863366937750052	4	FACETS	0.779	0.692	0.87	0.389	0.346	0.435	SUBCLONAL	1	TRUE	2	0.956179456469812	4		404	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579370	7579419	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCCCTGGTAGGTTTTCTGGGAAGGGACAGAAGATGACAGGGGCCAGGA	CTGCCCTGGTAGGTTTTCTGGGAAGGGACAGAAGATGACAGGGGCCAGGA	-	novel	NA	P-0037733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	456	833	1	ENST00000269305.4:c.268_317del	p.Ser90LeufsTer42	p.S90Lfs*42	ENST00000269305	NM_001126112.2	90	TCCTGGCCCCTGTCATCTTCTGTCCCTTCCCAGAAAACCTACCAGGGCAGc/c	4/11	0.956179456469812	3	FACETS	0.899	0.88	0.916	0.899	0.88	0.916	CLONAL	3	TRUE	0	0.956179456469812	3		834	523	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627719	37627719	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	134	621	0	ENST00000447079.4:c.1634C>G	p.Pro545Arg	p.P545R	ENST00000447079	NM_015083.1	545	cCa/cGa	2/14	0.956179456469812	3	FACETS	0.666	0.607	0.728	0.222	0.202	0.243	SUBCLONAL	1	TRUE	0	0.956179456469812	3		621	622	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0038040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	75	370	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.360833348655444	2		370	411	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11181324	11181324	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	94	526	0	ENST00000361445.4:c.6912G>T	p.Trp2304Cys	p.W2304C	ENST00000361445	NM_004958.3	2304	tgG/tgT	49/58	1	2	FACETS	0.929	0.828	1	0.929	0.828	1	CLONAL	1	TRUE	1	0.360833348655444	2		526	561	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170461	108170461	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	54	306	0	ENST00000278616.4:c.5026G>T	p.Gly1676Ter	p.G1676*	ENST00000278616	NM_000051.3	1676	Gga/Tga	34/63	0.360833348655444	1	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	0	0.360833348655444	1		306	242	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544137	18544137	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	60	291	0	ENST00000266497.5:c.1954G>T	p.Glu652Ter	p.E652*	ENST00000266497		652	Gag/Tag	13/31	1	2	FACETS	0.924	0.8	1	0.924	0.8	1	CLONAL	1	TRUE	1	0.360833348655444	2		291	360	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865032	57865032	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	136	828	0	ENST00000228682.2:c.2509C>A	p.Pro837Thr	p.P837T	ENST00000228682	NM_005269.2	837	Ccc/Acc	12/12	1	2	FACETS	0.948	0.863	1	0.948	0.863	1	CLONAL	1	TRUE	1	0.360833348655444	2		828	795	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210953	133210953	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	57	516	0	ENST00000320574.5:c.5823G>C	p.Gln1941His	p.Q1941H	ENST00000320574	NM_006231.2	1941	caG/caC	43/49	1	2	FACETS	0.541	0.464	0.625	0.541	0.464	0.625	SUBCLONAL	1	TRUE	1	0.360833348655444	2		516	584	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042100	42042100	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	45	529	0	ENST00000219905.7:c.6295C>T	p.Gln2099Ter	p.Q2099*	ENST00000219905	NM_001164273.1	2099	Caa/Taa	17/24	0.360833348655444	1	FACETS	0.428	0.359	0.503	0.428	0.359	0.503	SUBCLONAL	1	TRUE	0	0.360833348655444	1		529	478	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054049	42054049	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0038040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	27	249	0	ENST00000219905.7:c.7510+1G>T		p.X2504_splice	ENST00000219905	NM_001164273.1	2504			0.360833348655444	1	FACETS	0.56	0.448	0.687	0.56	0.448	0.687	SUBCLONAL	1	TRUE	0	0.360833348655444	1		249	219	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339479	339479	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	103	798	0	ENST00000262320.3:c.2423G>T	p.Gly808Val	p.G808V	ENST00000262320	NM_003502.3	808	gGc/gTc	10/11	0.335700841149943	1	FACETS	0.539	0.482	0.6	0.539	0.482	0.6	SUBCLONAL	1	TRUE	0	0.360833348655444	1		798	868	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991913	72991913	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	146	509	0	ENST00000268489.5:c.2132C>G	p.Pro711Arg	p.P711R	ENST00000268489	NM_006885.3	711	cCc/cGc	2/10	0.335700841149943	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.360833348655444	1		509	576	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243932	41243932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	154	583	0	ENST00000357654.3:c.3616G>A	p.Ala1206Thr	p.A1206T	ENST00000357654	NM_007294.3	1206	Gcc/Acc	10/23	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.360833348655444	2		583	678	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965864	25965864	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	93	618	0	ENST00000435504.4:c.3342G>T	p.Arg1114Ser	p.R1114S	ENST00000435504		1114	agG/agT	13/13	1	2	FACETS	0.758	0.674	0.847	0.758	0.674	0.847	SUBCLONAL	1	TRUE	1	0.360833348655444	2		618	680	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183020	32183020	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	88	651	0	ENST00000375023.3:c.2004C>A	p.His668Gln	p.H668Q	ENST00000375023	NM_004557.3	668	caC/caA	12/30	1	2	FACETS	0.696	0.616	0.781	0.696	0.616	0.781	SUBCLONAL	1	TRUE	1	0.360833348655444	2		651	701	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797253	32797253	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	147	847	1	ENST00000374899.4:c.1856G>T	p.Arg619Leu	p.R619L	ENST00000374899	NM_018833.2	619	cGg/cTg	11/12	1	2	FACETS	0.809	0.738	0.884	0.809	0.738	0.884	CLONAL	1	TRUE	1	0.360833348655444	2		848	1007	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907160	101907160	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	30	308	0	ENST00000374994.4:c.1120G>T	p.Gly374Ter	p.G374*	ENST00000374994	NM_004612.2	374	Gga/Tga	6/9	0.335700841149943	1	FACETS	0.468	0.378	0.57	0.468	0.378	0.57	SUBCLONAL	1	TRUE	0	0.360833348655444	1		308	291	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249906	110249906	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	109	443	0	ENST00000374672.4:c.769G>T	p.Gly257Cys	p.G257C	ENST00000374672	NM_004235.4	257	Ggc/Tgc	3/5	0.335700841149943	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.360833348655444	1		443	437	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841229	15841229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	82	167	0	ENST00000307771.7:c.1313G>A	p.Gly438Asp	p.G438D	ENST00000307771	NM_005089.3	438	gGc/gAc	11/11	NA	2	FACETS	1	0.945	1			1	INDETERMINATE	2	TRUE	NA	0.360833348655444	2		167	211	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0038226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1447	72	736	3	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.243	0.211	0.278	0.243	0.211	0.278	SUBCLONAL	1	TRUE	1	0.39	2		739	1519	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942685	48942685	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913301	NA	P-0038226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	39	332	0	ENST00000267163.4:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000267163	NM_000321.2	358	Cga/Tga	11/27	1	2	FACETS	0.281	0.232	0.335	0.281	0.232	0.335	SUBCLONAL	1	TRUE	1	0.39	2		332	713	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519893	NA	P-0038226-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	100	781	0	ENST00000267101.3:c.310G>T	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ttg	3/28	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.168386043279905	2		781	1074	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0038226-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	161	736	3	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.869	0.796	0.946	1	0.99	1	CLONAL	2	TRUE	1	0.168386043279905	2		739	1100	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942685	48942685	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913301	NA	P-0038226-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	42	332	0	ENST00000267163.4:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000267163	NM_000321.2	358	Cga/Tga	11/27	1	2	FACETS	0.863	0.724	1	1	0.965	1	CLONAL	2	TRUE	1	0.168386043279905	2		332	289	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393194	393194	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038226-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	37	500	0	ENST00000380956.4:c.42G>C	p.Met14Ile	p.M14I	ENST00000380956	NM_001195286.1	14	atG/atC	2/9	1	2	FACETS	0.772	0.636	0.926	0.772	0.636	0.926	CLONAL	1	TRUE	1	0.168386043279905	2		500	569	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101267	27101276	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCCCCAGG	GCCCCCCAGG	-	novel	NA	P-0038226-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	74	695	0	ENST00000324856.7:c.4554_4563del	p.Gln1519ProfsTer5	p.Q1519Pfs*5	ENST00000324856	NM_006015.4	1517	GCCCCCCAGGgc/gc	18/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.168386043279905	2		695	714	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474652	138474652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038226-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	38	549	0	ENST00000289153.2:c.341G>A	p.Arg114Lys	p.R114K	ENST00000289153	NM_006219.2	114	aGa/aAa	2/22	1	2	FACETS	0.865	0.714	1	0.865	0.714	1	CLONAL	1	TRUE	1	0.168386043279905	2		549	522	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0038634-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	1238	780	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.754756582822939	3	FACETS	0.991	0.98	1			1	CLONAL	3	TRUE	NA	0.862326599334385	3		780	1382	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39321417	39321417	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038634-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	228	487	0	ENST00000373001.3:c.604G>C	p.Asp202His	p.D202H	ENST00000373001	NM_022157.3	202	Gac/Cac	3/7	0.862338728452131	3	FACETS	0.896	0.836	0.957	0.448	0.418	0.479	CLONAL	1	TRUE	1	0.862326599334385	3		487	845	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562999	21562999	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038634-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	382	733	0	ENST00000382592.4:c.920C>T	p.Pro307Leu	p.P307L	ENST00000382592	NM_014572.2	307	cCt/cTt	4/8	0.862338728452131	3	FACETS	0.934	0.886	0.982			1	CLONAL	1	TRUE	NA	0.862326599334385	3		733	1358	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682152	37682152	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038634-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	305	485	0	ENST00000447079.4:c.3343G>A	p.Glu1115Lys	p.E1115K	ENST00000447079	NM_015083.1	1115	Gaa/Aaa	13/14	0.856568141972279	2	FACETS	1	0.962	1	0.508	0.482	0.534	CLONAL	1	TRUE	0	0.862326599334385	2		485	696	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0038752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	82	416	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	0.234423505722709	2		416	644	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578530	7578530	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs267605077	NA	P-0038752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	166	1014	0	ENST00000269305.4:c.400T>C	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	Ttt/Ctt	5/11	0.234423505722709	1	FACETS	0.932	0.853	1	0.932	0.853	1	CLONAL	1	TRUE	0	0.234423505722709	1		1014	1342	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46602960	46602960	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	113	794	0	ENST00000263734.3:c.1018G>T	p.Val340Phe	p.V340F	ENST00000263734	NM_001430.4	340	Gtc/Ttc	8/16	1	2	FACETS	0.932	0.837	1	0.932	0.837	1	CLONAL	1	TRUE	1	0.234423505722709	2		794	1034	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0039044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	64	498	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.293	0.253	0.337	0.293	0.253	0.337	SUBCLONAL	1	TRUE	1	0.44	2		498	992	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	96	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.242199889071937	3	FACETS	0.924	0.827	1	0.924	0.827	1	CLONAL	2	TRUE	1	0.242199889071937	3		371	481	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0039049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	159	546	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	0.242199889071937	2		547	998	SUCCESS
APC	324	MSKCC	GRCh37	5	112170682	112170682	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1064794226	NA	P-0039049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	71	487	0	ENST00000257430.4:c.1778G>A	p.Trp593Ter	p.W593*	ENST00000257430	NM_000038.5	593	tGg/tAg	15/16	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.242199889071937	2		487	559	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109311924	109311924	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	75	660	0	ENST00000436639.2:c.1348G>A	p.Ala450Thr	p.A450T	ENST00000436639	NM_014454.2	450	Gca/Aca	8/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.242199889071937	2		660	528	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508616	106508616	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	61	587	0	ENST00000359195.3:c.610T>G	p.Ser204Ala	p.S204A	ENST00000359195	NM_002649.2	204	Tcc/Gcc	2/11	0.0703082506826223	4	FACETS	0.732	0.63	0.843	0.366	0.315	0.422	INDETERMINATE	1	TRUE	2	0.242199889071937	4		587	855	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141498	11141498	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	460	984	1	ENST00000358026.2:c.3475G>T	p.Gly1159Trp	p.G1159W	ENST00000358026	NM_001128849.1	1159	Ggg/Tgg	25/36	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.72	2		985	1264	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100819	27100819	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0039056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	283	537	0	ENST00000324856.7:c.4102-1G>A		p.X1368_splice	ENST00000324856	NM_006015.4	1368			0.732997446536711	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.72	1		537	490	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913255	NA	P-0039056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	339	673	0	ENST00000369535.4:c.183A>C	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caC	3/7	1	2	FACETS	0.972	0.922	1	0.972	0.922	1	CLONAL	1	TRUE	1	0.72	2		673	969	SUCCESS
AR	367	MSKCC	GRCh37	X	66765190	66765190	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	236	202	0	ENST00000374690.3:c.202C>T	p.Gln68Ter	p.Q68*	ENST00000374690	NM_000044.3	68	Cag/Tag	1/8	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.72	1		202	341	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348175	348175	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	936	1019	1	ENST00000262320.3:c.1331G>A	p.Trp444Ter	p.W444*	ENST00000262320	NM_003502.3	444	tGg/tAg	6/11	0.732997446536711	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.72	2		1020	1247	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs879253911	NA	P-0039131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	87	633	0	ENST00000269305.4:c.538G>T	p.Glu180Ter	p.E180*	ENST00000269305	NM_001126112.2	180	Gag/Tag	5/11	0.302298594015413	1	FACETS	0.756	0.671	0.847	0.756	0.671	0.847	SUBCLONAL	1	TRUE	0	0.36	1		633	524	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099479	27099479	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0039131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	47	378	0	ENST00000324856.7:c.3715+1G>A		p.X1239_splice	ENST00000324856	NM_006015.4	1239			1	2	FACETS	0.853	0.724	0.994	0.853	0.724	0.994	CLONAL	1	TRUE	1	0.36	2		378	306	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285570	46285570	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs78222561	NA	P-0039131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	26	241	0	ENST00000334344.6:c.4930C>T	p.Gln1644Ter	p.Q1644*	ENST00000334344	NM_152641.2	1644	Cag/Tag	17/21	1	2	FACETS	0.712	0.567	0.875	0.712	0.567	0.875	SUBCLONAL	1	TRUE	1	0.36	2		241	203	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111528	8111529	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AATGCCTGTGGGCTCTACTACA	novel	NA	P-0039131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	57	573	0	ENST00000346208.3:c.1016_1037dup	p.Leu347CysfsTer12	p.L347Cfs*12	ENST00000346208		338	-/AATGCCTGTGGGCTCTACTACA	5/6	1	2	FACETS	0.595	0.511	0.687	0.595	0.511	0.687	SUBCLONAL	1	TRUE	1	0.36	2		573	532	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749136	43749136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	91	725	0	ENST00000382044.4:c.1670C>T	p.Ser557Phe	p.S557F	ENST00000382044	NM_001141980.1	557	tCt/tTt	12/28	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.36	2		725	481	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027008	71027008	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0039131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	84	517	0	ENST00000318789.4:c.1319C>G	p.Ser440Ter	p.S440*	ENST00000318789	NM_032682.5	440	tCa/tGa	15/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.36	2		517	424	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0039235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	10	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.132	0.089	0.188	0.132	0.089	0.188	SUBCLONAL	1	TRUE	1	0.30789678973052	2		326	491	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061208	38061208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	130	476	0	ENST00000250448.2:c.781C>T	p.Arg261Cys	p.R261C	ENST00000250448	NM_004496.3	261	Cgc/Tgc	2/2	1	2	FACETS	0.954	0.865	1	0.954	0.865	1	CLONAL	1	TRUE	1	0.30789678973052	2		476	885	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692791	89692791	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	73	308	0	ENST00000371953.3:c.275A>T	p.Asp92Val	p.D92V	ENST00000371953	NM_000314.4	92	gAc/gTc	5/9	1	2	FACETS	0.895	0.784	1	0.895	0.784	1	CLONAL	1	TRUE	1	0.30789678973052	2		308	530	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907432	32907432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80358469	NA	P-0039235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	69	270	0	ENST00000380152.3:c.1817C>T	p.Pro606Leu	p.P606L	ENST00000380152		606	cCg/cTg	10/27	0.30789678973052	1	FACETS	0.884	0.773	1	0.884	0.773	1	CLONAL	1	TRUE	0	0.30789678973052	1		270	429	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405953	49405953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039255-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	204	565	0	ENST00000418115.1:c.185G>A	p.Gly62Glu	p.G62E	ENST00000418115	NM_001664.2	62	gGg/gAg	3/5	0.187339122643526	3	FACETS	0.826	0.767	0.887	0.551	0.511	0.591	INDETERMINATE	2	TRUE	0	0.344628575197724	3		565	840	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662939	52662939	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039255-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	114	330	0	ENST00000394830.3:c.1414C>T	p.Arg472Ter	p.R472*	ENST00000394830	NM_018313.4	472	Cga/Tga	13/30	1	2	FACETS	0.815	0.74	0.893	1	0.987	1	CLONAL	2	TRUE	1	0.344628575197724	2		330	406	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981879	201981879	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039255-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	262	700	0	ENST00000359651.3:c.591del	p.Thr198ProfsTer56	p.T198Pfs*56	ENST00000359651		197	tCc/tc	4/8	1	2	FACETS	0.767	0.719	0.816	1	0.993	1	SUBCLONAL	2	TRUE	1	0.344628575197724	2		700	991	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716237	243716237	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039255-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	48	397	0	ENST00000263826.5:c.957A>C	p.Glu319Asp	p.E319D	ENST00000263826	NM_005465.4	319	gaA/gaC	10/13	0.344628575197724	1	FACETS	0.407	0.344	0.477	0.407	0.344	0.477	SUBCLONAL	1	TRUE	0	0.344628575197724	1		397	566	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858555	57858555	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039255-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	110	702	0	ENST00000228682.2:c.293T>C	p.Val98Ala	p.V98A	ENST00000228682	NM_005269.2	98	gTt/gCt	4/12	0.154197467975858	4	FACETS	0.941	0.845	1	0.471	0.422	0.522	INDETERMINATE	1	TRUE	2	0.344628575197724	4		702	912	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442757	99442757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1484576897	NA	P-0039255-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	105	609	0	ENST00000268035.6:c.1154C>T	p.Thr385Met	p.T385M	ENST00000268035	NM_000875.3	385	aCg/aTg	5/21	0.180879890468617	3	FACETS	1	0.935	1	0.529	0.474	0.587	INDETERMINATE	1	TRUE	1	0.344628575197724	3		609	675	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643389	52643389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761573345	NA	P-0039255-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	31	352	0	ENST00000394830.3:c.2507G>A	p.Arg836Gln	p.R836Q	ENST00000394830	NM_018313.4	836	cGg/cAg	17/30	1	2	FACETS	0.347	0.28	0.423	0.347	0.28	0.423	SUBCLONAL	1	TRUE	1	0.344628575197724	2		352	519	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0039263-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	30	370	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.848	0.684	1	0.848	0.684	1	CLONAL	1	TRUE	1	0.206195604383194	2		370	343	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772950	135772951	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs118203724	NA	P-0039263-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	24	403	0	ENST00000298552.3:c.2672dup	p.Asn891LysfsTer13	p.N891Kfs*13	ENST00000298552	NM_001162426.1	891	aac/aaAc	21/23	1	2	FACETS	0.654	0.512	0.817	0.654	0.512	0.817	SUBCLONAL	1	TRUE	1	0.206195604383194	2		403	356	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222983	1222983	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs398123406	NA	P-0039263-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	70	619	0	ENST00000326873.7:c.921-1G>C		p.X307_splice	ENST00000326873	NM_000455.4	307			0.155758310575618	2	FACETS	1	0.971	1	0.712	0.622	0.808	CLONAL	1	TRUE	0	0.206195604383194	2		619	477	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602818	10602818	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0039263-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	107	986	0	ENST00000171111.5:c.760A>T	p.Lys254Ter	p.K254*	ENST00000171111	NM_203500.1	254	Aag/Tag	3/6	0.155758310575618	2	FACETS	0.765	0.687	0.848	0.765	0.687	0.848	SUBCLONAL	2	TRUE	0	0.206195604383194	2		986	678	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602281	10602281	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039263-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	95	860	0	ENST00000171111.5:c.1297G>T	p.Gly433Cys	p.G433C	ENST00000171111	NM_203500.1	433	Ggc/Tgc	3/6	0.155758310575618	2	FACETS	0.792	0.706	0.882	0.792	0.706	0.882	SUBCLONAL	2	TRUE	0	0.206195604383194	2		860	582	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786880	135786880	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039263-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	32	492	0	ENST00000298552.3:c.989T>G	p.Leu330Arg	p.L330R	ENST00000298552	NM_001162426.1	330	cTg/cGg	10/23	1	2	FACETS	0.786	0.638	0.953	0.786	0.638	0.953	CLONAL	1	TRUE	1	0.206195604383194	2		492	395	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788651	3788651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	160	379	0	ENST00000262367.5:c.4303G>A	p.Asp1435Asn	p.D1435N	ENST00000262367	NM_004380.2	1435	Gat/Aat	26/31	0.486119236071974	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.486119236071974	1		379	459	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435061	18435061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267603400	NA	P-0039425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	40	270	0	ENST00000266497.5:c.46G>A	p.Glu16Lys	p.E16K	ENST00000266497		16	Gaa/Aaa	1/31	0.258721974279062	1	FACETS	0.414	0.345	0.49	0.414	0.345	0.49	INDETERMINATE	1	TRUE	0	0.486119236071974	1		270	301	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489571	56489571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	183	475	0	ENST00000267101.3:c.2036G>A	p.Arg679Gln	p.R679Q	ENST00000267101	NM_001982.3	679	cGa/cAa	17/28	0.258721974279062	1	FACETS	0.816	0.756	0.879	0.816	0.756	0.879	INDETERMINATE	1	TRUE	0	0.486119236071974	1		475	698	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946319	2946319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373819371	NA	P-0039425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	402	775	0	ENST00000396946.4:c.3418G>A	p.Gly1140Ser	p.G1140S	ENST00000396946	NM_032415.4	1140	Ggc/Agc	25/25	0.290655499301958	1	FACETS	0.914	0.869	0.961	0.914	0.869	0.961	INDETERMINATE	1	TRUE	0	0.486119236071974	1		775	1369	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550932	150550932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	119	327	0	ENST00000369026.2:c.724G>A	p.Asp242Asn	p.D242N	ENST00000369026	NM_021960.4	242	Gat/Aat	2/3	1	2	FACETS	0.771	0.697	0.848	0.771	0.697	0.848	SUBCLONAL	1	TRUE	1	0.486119236071974	2		327	635	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0039425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	283	156	0				ENST00000310581	NM_198253.2	-/1132			0.276217238290451	3	FACETS	0.801	0.755	0.849	0.801	0.755	0.849	INDETERMINATE	2	TRUE	1	0.486119236071974	3		156	903	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627969	187627969	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	207	559	0	ENST00000441802.2:c.3013G>C	p.Asp1005His	p.D1005H	ENST00000441802	NM_005245.3	1005	Gac/Cac	2/27	0.486119236071974	1	FACETS	0.98	0.914	1	0.98	0.914	1	CLONAL	1	TRUE	0	0.486119236071974	1		559	658	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398032	4398032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	95	451	0	ENST00000261254.3:c.596C>T	p.Pro199Leu	p.P199L	ENST00000261254	NM_001759.3	199	cCg/cTg	4/5	0.258721974279062	1	FACETS	0.386	0.343	0.431	0.386	0.343	0.431	INDETERMINATE	1	TRUE	0	0.486119236071974	1		451	767	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369196	118369196	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	59	303	0	ENST00000534358.1:c.5914G>T	p.Asp1972Tyr	p.D1972Y	ENST00000534358	NM_005933.3	1972	Gat/Tat	22/36	0.290655499301958	1	FACETS	0.401	0.346	0.461	0.401	0.346	0.461	INDETERMINATE	1	TRUE	0	0.486119236071974	1		303	458	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149361	119149361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	72	330	0	ENST00000264033.4:c.1369G>A	p.Asp457Asn	p.D457N	ENST00000264033	NM_005188.3	457	Gat/Aat	9/16	0.290655499301958	1	FACETS	0.424	0.371	0.481	0.424	0.371	0.481	INDETERMINATE	1	TRUE	0	0.486119236071974	1		330	529	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913160	32913160	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	110	456	0	ENST00000380152.3:c.4668C>G	p.Ile1556Met	p.I1556M	ENST00000380152		1556	atC/atG	11/27	0.205926455454829	0	FACETS	0.469	0.423	0.517			1	INDETERMINATE	1	TRUE	0	0.486119236071974	0		456	496	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32969063	32969063	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	51	218	0	ENST00000380152.3:c.9494C>A	p.Thr3165Asn	p.T3165N	ENST00000380152		3165	aCt/aAt	25/27	0.205926455454829	0	FACETS	0.437	0.374	0.503			1	INDETERMINATE	1	TRUE	0	0.486119236071974	0		218	247	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972384	32972384	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	104	452	1	ENST00000380152.3:c.9734C>T	p.Ser3245Leu	p.S3245L	ENST00000380152		3245	tCa/tTa	27/27	0.205926455454829	0	FACETS	0.507	0.456	0.559			1	INDETERMINATE	1	TRUE	0	0.486119236071974	0		453	434	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519159	103519159	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	155	364	0	ENST00000355739.4:c.2497G>A	p.Glu833Lys	p.E833K	ENST00000355739	NM_000123.3	833	Gaa/Aaa	11/15	0.204988710596511	2	FACETS	1	0.987	1	0.68	0.627	0.734	INDETERMINATE	1	TRUE	0	0.486119236071974	2		364	469	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434817	110434817	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	335	520	1	ENST00000375856.3:c.3584G>C	p.Gly1195Ala	p.G1195A	ENST00000375856	NM_003749.2	1195	gGa/gCa	1/2	0.204988710596511	2	FACETS	1	0.991	1	0.613	0.58	0.647	INDETERMINATE	1	TRUE	0	0.486119236071974	2		521	1124	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961873	41961873	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	124	339	0	ENST00000219905.7:c.781G>A	p.Asp261Asn	p.D261N	ENST00000219905	NM_001164273.1	261	Gat/Aat	2/24	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.486119236071974	2		339	417	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829646	72829646	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767087836	NA	P-0039425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	229	589	0	ENST00000268489.5:c.6935G>A	p.Arg2312Gln	p.R2312Q	ENST00000268489	NM_006885.3	2312	cGg/cAg	9/10	0.486119236071974	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.486119236071974	1		589	694	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221297	36221297	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	341	798	0	ENST00000222270.7:c.5131G>C	p.Glu1711Gln	p.E1711Q	ENST00000222270	NM_014727.1	1711	Gag/Cag	24/37	1	2	FACETS	0.946	0.893	1	0.946	0.893	1	CLONAL	1	TRUE	1	0.486119236071974	2		798	1483	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149246	61149246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	93	290	0	ENST00000295025.8:c.1436C>T	p.Ser479Leu	p.S479L	ENST00000295025	NM_002908.2	479	tCa/tTa	11/11	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.486119236071974	2		290	376	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52663008	52663008	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1188691461	NA	P-0039425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	90	245	0	ENST00000394830.3:c.1345G>C	p.Glu449Gln	p.E449Q	ENST00000394830	NM_018313.4	449	Gag/Cag	13/30	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.486119236071974	2		245	282	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156944	89156944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	216	552	0	ENST00000336596.2:c.46C>T	p.Leu16Phe	p.L16F	ENST00000336596	NM_005233.5	16	Ctc/Ttc	1/17	1	2	FACETS	0.934	0.869	1	0.934	0.869	1	CLONAL	1	TRUE	1	0.486119236071974	2		552	951	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250889	153250895	+	frameshift_variant	Frame_Shift_Del	DEL	CACAAAA	CACAAAA	-	novel	NA	P-0039425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	70	310	0	ENST00000281708.4:c.1165_1171del	p.Phe389ValfsTer4	p.F389Vfs*4	ENST00000281708	NM_033632.3	389	TTTTGTGgt/gt	8/12	0.486119236071974	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.486119236071974	1		310	208	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628134	187628134	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	240	619	0	ENST00000441802.2:c.2848G>C	p.Glu950Gln	p.E950Q	ENST00000441802	NM_005245.3	950	Gaa/Caa	2/27	0.486119236071974	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.486119236071974	1		619	684	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628287	187628287	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	260	590	0	ENST00000441802.2:c.2695G>T	p.Asp899Tyr	p.D899Y	ENST00000441802	NM_005245.3	899	Gac/Tac	2/27	0.486119236071974	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.486119236071974	1		590	744	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32814921	32814921	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	594	634	0	ENST00000354258.4:c.2144G>C	p.Arg715Pro	p.R715P	ENST00000354258	NM_000593.5	715	cGa/cCa	10/11	0.475269605933009	2	FACETS	0.902	0.869	0.936	0.902	0.869	0.936	CLONAL	2	TRUE	0	0.486119236071974	2		634	1354	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287406	33287406	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	394	475	0	ENST00000374542.5:c.1691C>G	p.Ser564Cys	p.S564C	ENST00000374542	NM_001141970.1	564	tCt/tGt	6/8	0.475269605933009	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.486119236071974	2		475	807	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525543	137525543	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	247	468	0	ENST00000367739.4:c.472G>T	p.Glu158Ter	p.E158*	ENST00000367739	NM_000416.2	158	Gaa/Taa	4/7	0.475269605933009	2	FACETS	0.953	0.901	1	0.953	0.901	1	CLONAL	2	TRUE	0	0.486119236071974	2		468	533	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864287	151864287	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	132	485	0	ENST00000262189.6:c.9694G>C	p.Glu3232Gln	p.E3232Q	ENST00000262189	NM_170606.2	3232	Gaa/Caa	42/59	0.290655499301958	1	FACETS	0.812	0.742	0.886	0.812	0.742	0.886	INDETERMINATE	1	TRUE	0	0.486119236071974	1		485	506	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	5	417	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.29	0.163	0.468	0.29	0.163	0.468	SUBCLONAL	1	TRUE	1	0.11	2		417	314	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974770	21974775	+	inframe_deletion	In_Frame_Del	DEL	GGCCGT	GGCCGT	-	novel	NA	P-0039457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	15	266	0	ENST00000304494.5:c.52_57del	p.Thr18_Ala19del	p.T18_A19del	ENST00000304494	NM_000077.4	18	ACGGCC/-	1/3	1	2	FACETS	0.988	0.722	1	0.988	0.722	1	CLONAL	1	TRUE	1	0.11	2		266	276	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	67	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.25	2		371	397	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0039462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	128	565	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.281080573680073	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.25	2		565	457	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0039462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	74	404	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.975	0.854	1	0.975	0.854	1	CLONAL	1	TRUE	1	0.25	2		404	607	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727483	66727483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504317	NA	P-0039462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	36	344	0	ENST00000307102.5:c.199G>A	p.Asp67Asn	p.D67N	ENST00000307102	NM_002755.3	67	Gac/Aac	2/11	1	2	FACETS	0.512	0.42	0.615	0.512	0.42	0.615	SUBCLONAL	1	TRUE	1	0.25	2		344	563	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148516750	148516750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	38	229	0	ENST00000320356.2:c.937C>T	p.Arg313Trp	p.R313W	ENST00000320356	NM_004456.4	313	Cgg/Tgg	9/20	0.183875945800751	3	FACETS	0.864	0.715	1	0.432	0.357	0.515	CLONAL	1	TRUE	1	0.25	3		229	396	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097782	27097783	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0039462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	70	337	0	ENST00000324856.7:c.3372_3373del	p.Lys1125ValfsTer67	p.K1125Vfs*67	ENST00000324856	NM_006015.4	1124	aAG/a	12/20	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.25	2		337	544	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797428	45797428	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780741	NA	P-0039462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	100	665	0	ENST00000450313.1:c.1091G>A	p.Arg364His	p.R364H	ENST00000450313	NM_012222.2	364	cGc/cAc	12/16	1	2	FACETS	0.936	0.835	1	0.936	0.835	1	CLONAL	1	TRUE	1	0.25	2		665	855	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591118	67591119	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	54	218	0	ENST00000274335.5:c.1712dup	p.Gln572ProfsTer30	p.Q572Pfs*30	ENST00000274335		571	atc/aTtc	12/15	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.25	2		218	359	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	92	298	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.489965108543419	2		298	342	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	41	639	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.25	0.208	0.298	0.25	0.208	0.298	SUBCLONAL	1	TRUE	1	0.489965108543419	2		645	669	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717699	89717699	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554825210	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	93	345	0	ENST00000371953.3:c.724G>T	p.Glu242Ter	p.E242*	ENST00000371953	NM_000314.4	242	Gag/Tag	7/9	1	2	FACETS	0.951	0.852	1	0.951	0.852	1	CLONAL	1	TRUE	1	0.489965108543419	2		345	399	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	32	516	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	0.219	0.177	0.267	0.219	0.177	0.267	SUBCLONAL	1	TRUE	1	0.489965108543419	2		516	596	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	64	286	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.639	0.555	0.729	0.639	0.555	0.729	SUBCLONAL	1	TRUE	1	0.489965108543419	2		286	409	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	100	1058	3	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.427	0.38	0.476	0.427	0.38	0.476	SUBCLONAL	1	TRUE	1	0.489965108543419	2		1061	957	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	94	291	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	0.489965108543419	2		291	346	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	179	788	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.489965108543419	2		790	686	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	14	271	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	1	2	FACETS	0.235	0.17	0.314	0.235	0.17	0.314	SUBCLONAL	1	TRUE	1	0.489965108543419	2		271	243	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749415085	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	19	282	0	ENST00000263967.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000263967	NM_006218.2	38	Cgt/Tgt	2/21	1	2	FACETS	0.301	0.228	0.385	0.301	0.228	0.385	SUBCLONAL	1	TRUE	1	0.489965108543419	2		282	258	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906370	50906370	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs749601227	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	91	758	2	ENST00000440232.2:c.1036del	p.Glu346SerfsTer47	p.E346Sfs*47	ENST00000440232	NM_002691.3	344	tGg/tg	9/27	1	2	FACETS	0.473	0.42	0.53	0.473	0.42	0.53	SUBCLONAL	1	TRUE	1	0.489965108543419	2		760	785	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094416	27094416	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	281	466	0	ENST00000324856.7:c.3125del	p.Pro1042LeufsTer17	p.P1042Lfs*17	ENST00000324856	NM_006015.4	1042	Cct/ct	11/20	0.489965108543419	2	FACETS	0.966	0.916	1	0.966	0.916	1	CLONAL	2	TRUE	0	0.489965108543419	2		466	594	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339093	65339093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	35	361	0	ENST00000342505.4:c.443del	p.Pro148LeufsTer20	p.P148Lfs*20	ENST00000342505	NM_002227.2	148	cCt/ct	5/25	1	2	FACETS	0.308	0.252	0.371	0.308	0.252	0.371	SUBCLONAL	1	TRUE	1	0.489965108543419	2		361	464	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465042	120465042	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	21	341	1	ENST00000256646.2:c.5030A>G	p.Gln1677Arg	p.Q1677R	ENST00000256646	NM_024408.3	1677	cAg/cGg	28/34	1	2	FACETS	0.21	0.161	0.267	0.21	0.161	0.267	SUBCLONAL	1	TRUE	1	0.489965108543419	2		342	408	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156848931	156848931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	39	611	2	ENST00000524377.1:c.1823C>T	p.Ala608Val	p.A608V	ENST00000524377	NM_002529.3	608	gCc/gTc	15/17	1	2	FACETS	0.247	0.204	0.295	0.247	0.204	0.295	SUBCLONAL	1	TRUE	1	0.489965108543419	2		613	644	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243668637	243668637	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	15	238	0	ENST00000263826.5:c.1355-1G>A		p.X452_splice	ENST00000263826	NM_005465.4	452			1	2	FACETS	0.212	0.154	0.281	0.212	0.154	0.281	SUBCLONAL	1	TRUE	1	0.489965108543419	2		238	289	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205478	61205478	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs766035180	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	23	335	0	ENST00000301761.2:c.267del	p.Phe89LeufsTer9	p.F89Lfs*9	ENST00000301761	NM_017841.2	88	cTt/ct	3/4	1	2	FACETS	0.256	0.199	0.322	0.256	0.199	0.322	SUBCLONAL	1	TRUE	1	0.489965108543419	2		335	367	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466003	69466038	+	inframe_deletion	In_Frame_Del	DEL	GTGGACCTGGCTTGCACACCCACCGACGTGCGGGAC	GTGGACCTGGCTTGCACACCCACCGACGTGCGGGAC	-	novel	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	36	765	0	ENST00000227507.2:c.847_882del	p.Leu283_Asp294del	p.L283_D294del	ENST00000227507	NM_053056.2	281	GTGGACCTGGCTTGCACACCCACCGACGTGCGGGAC/-	5/5	1	2	FACETS	0.239	0.196	0.288	0.239	0.196	0.288	SUBCLONAL	1	TRUE	1	0.489965108543419	2		765	615	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939843	71939843	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1474702365	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	106	731	1	ENST00000298229.2:c.470G>A	p.Ser157Asn	p.S157N	ENST00000298229	NM_001567.3	157	aGc/aAc	4/28	1	2	FACETS	0.514	0.461	0.572	0.514	0.461	0.572	SUBCLONAL	1	TRUE	1	0.489965108543419	2		732	841	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948755	71948755	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1565399032	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	80	805	2	ENST00000298229.2:c.3470del	p.Gly1157AspfsTer45	p.G1157Dfs*45	ENST00000298229	NM_001567.3	1156	cGg/cg	26/28	1	2	FACETS	0.475	0.418	0.536	0.475	0.418	0.536	SUBCLONAL	1	TRUE	1	0.489965108543419	2		807	688	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219109	94219109	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	51	275	1	ENST00000323929.3:c.295G>A	p.Val99Ile	p.V99I	ENST00000323929	NM_005591.3	99	Gtc/Atc	4/20	1	2	FACETS	0.541	0.461	0.628	0.541	0.461	0.628	SUBCLONAL	1	TRUE	1	0.489965108543419	2		276	385	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360507	118360507	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	22	249	0	ENST00000534358.1:c.4480C>T	p.Gln1494Ter	p.Q1494*	ENST00000534358	NM_005933.3	1494	Cag/Tag	12/36	1	2	FACETS	0.302	0.234	0.381	0.302	0.234	0.381	SUBCLONAL	1	TRUE	1	0.489965108543419	2		249	297	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369100	118369101	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	25	244	0	ENST00000534358.1:c.5822dup	p.Pro1942AlafsTer31	p.P1942Afs*31	ENST00000534358	NM_005933.3	1940	caa/cAaa	22/36	1	2	FACETS	0.27	0.212	0.336	0.27	0.212	0.336	SUBCLONAL	1	TRUE	1	0.489965108543419	2		244	378	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444960	49444960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	36	527	0	ENST00000301067.7:c.2506del	p.Gln836SerfsTer94	p.Q836Sfs*94	ENST00000301067	NM_003482.3	836	Cag/ag	10/54	1	2	FACETS	0.282	0.231	0.339	0.282	0.231	0.339	SUBCLONAL	1	TRUE	1	0.489965108543419	2		527	521	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856434	111856434	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs776317487	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	24	259	0	ENST00000341259.2:c.489del	p.Thr165ProfsTer32	p.T165Pfs*32	ENST00000341259	NM_005475.2	162	gCc/gc	2/8	1	2	FACETS	0.286	0.224	0.358	0.286	0.224	0.358	SUBCLONAL	1	TRUE	1	0.489965108543419	2		259	342	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226120	2226120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759516773	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	87	781	0	ENST00000326181.6:c.1817C>T	p.Ala606Val	p.A606V	ENST00000326181	NM_032271.2	606	gCg/gTg	19/21	1	2	FACETS	0.423	0.374	0.476	0.423	0.374	0.476	SUBCLONAL	1	TRUE	1	0.489965108543419	2		781	840	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779136	3779136	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	34	630	0	ENST00000262367.5:c.5912A>G	p.His1971Arg	p.H1971R	ENST00000262367	NM_004380.2	1971	cAc/cGc	31/31	1	2	FACETS	0.247	0.201	0.299	0.247	0.201	0.299	SUBCLONAL	1	TRUE	1	0.489965108543419	2		630	562	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644874	67644874	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	31	453	0	ENST00000264010.4:c.143del	p.Gly48ValfsTer14	p.G48Vfs*14	ENST00000264010	NM_006565.3	47	Ggg/gg	3/12	1	2	FACETS	0.212	0.171	0.259	0.212	0.171	0.259	SUBCLONAL	1	TRUE	1	0.489965108543419	2		453	596	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650710	67650710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243010179	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	166	432	0	ENST00000264010.4:c.1015C>T	p.Arg339Trp	p.R339W	ENST00000264010	NM_006565.3	339	Cgg/Tgg	5/12	1	2	FACETS	0.9	0.828	0.974	0.9	0.828	0.974	CLONAL	1	TRUE	1	0.489965108543419	2		432	753	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40497609	40497609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs964892419	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	92	576	1	ENST00000264657.5:c.340C>T	p.Arg114Cys	p.R114C	ENST00000264657	NM_139276.2	114	Cgc/Tgc	4/24	1	2	FACETS	0.446	0.396	0.5	0.446	0.396	0.5	SUBCLONAL	1	TRUE	1	0.489965108543419	2		577	842	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804373	46804373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145059285	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	39	459	1	ENST00000290295.7:c.634G>A	p.Ala212Thr	p.A212T	ENST00000290295	NM_006361.5	212	Gcc/Acc	2/2	1	2	FACETS	0.283	0.234	0.338	0.283	0.234	0.338	SUBCLONAL	1	TRUE	1	0.489965108543419	2		460	563	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856039	45856039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372960848	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	55	692	1	ENST00000391945.4:c.1867G>A	p.Val623Ile	p.V623I	ENST00000391945	NM_000400.3	623	Gtc/Atc	20/23	1	2	FACETS	0.264	0.225	0.307	0.264	0.225	0.307	SUBCLONAL	1	TRUE	1	0.489965108543419	2		693	850	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416646	29416646	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs544926207	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	32	367	0	ENST00000389048.3:c.4307G>A	p.Arg1436His	p.R1436H	ENST00000389048	NM_004304.4	1436	cGc/cAc	29/29	1	2	FACETS	0.296	0.24	0.36	0.296	0.24	0.36	SUBCLONAL	1	TRUE	1	0.489965108543419	2		367	441	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920691	96920691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752938517	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	35	415	1	ENST00000258439.3:c.289G>A	p.Ala97Thr	p.A97T	ENST00000258439	NM_001193304.2	97	Gcc/Acc	3/4	1	2	FACETS	0.262	0.214	0.316	0.262	0.214	0.316	SUBCLONAL	1	TRUE	1	0.489965108543419	2		416	546	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189323	99189323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173310435	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	49	411	0	ENST00000074304.5:c.2579G>A	p.Arg860Gln	p.R860Q	ENST00000074304	NM_001134224.1	860	cGg/cAg	24/26	1	2	FACETS	0.313	0.264	0.367	0.313	0.264	0.367	SUBCLONAL	1	TRUE	1	0.489965108543419	2		411	639	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630626	158630626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912678	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	19	228	0	ENST00000263640.3:c.617G>A	p.Arg206His	p.R206H	ENST00000263640	NM_001105.4	206	cGc/cAc	6/11	1	2	FACETS	0.259	0.197	0.333	0.259	0.197	0.333	SUBCLONAL	1	TRUE	1	0.489965108543419	2		228	299	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439529	220439529	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	32	639	0	ENST00000243786.2:c.382T>C	p.Ser128Pro	p.S128P	ENST00000243786	NM_002191.3	128	Tca/Cca	2/2	1	2	FACETS	0.224	0.181	0.273	0.224	0.181	0.273	SUBCLONAL	1	TRUE	1	0.489965108543419	2		639	582	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125763	47125763	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144171734	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	19	281	0	ENST00000409792.3:c.5507C>T	p.Pro1836Leu	p.P1836L	ENST00000409792	NM_014159.6	1836	cCg/cTg	12/21	1	2	FACETS	0.209	0.158	0.269	0.209	0.158	0.269	SUBCLONAL	1	TRUE	1	0.489965108543419	2		281	371	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390125	89390125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	21	262	0	ENST00000336596.2:c.874C>T	p.Pro292Ser	p.P292S	ENST00000336596	NM_005233.5	292	Cct/Tct	4/17	1	2	FACETS	0.29	0.223	0.367	0.29	0.223	0.367	SUBCLONAL	1	TRUE	1	0.489965108543419	2		262	296	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998128	169998128	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs753143066	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	39	554	3	ENST00000295797.4:c.826del	p.Thr276GlnfsTer7	p.T276Qfs*7	ENST00000295797	NM_002740.5	273	ttA/tt	9/18	1	2	FACETS	0.23	0.19	0.275	0.23	0.19	0.275	SUBCLONAL	1	TRUE	1	0.489965108543419	2		557	693	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916726	178916726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772110575	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	33	282	0	ENST00000263967.3:c.113G>A	p.Arg38His	p.R38H	ENST00000263967	NM_006218.2	38	cGt/cAt	2/21	1	2	FACETS	0.528	0.432	0.635	0.528	0.432	0.635	SUBCLONAL	1	TRUE	1	0.489965108543419	2		282	255	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253823	153253823	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	21	277	0	ENST00000281708.4:c.910G>T	p.Ala304Ser	p.A304S	ENST00000281708	NM_033632.3	304	Gca/Tca	6/12	1	2	FACETS	0.256	0.197	0.325	0.256	0.197	0.325	SUBCLONAL	1	TRUE	1	0.489965108543419	2		277	335	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867418	35867418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200687605	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	14	215	0	ENST00000303115.3:c.232G>A	p.Val78Met	p.V78M	ENST00000303115	NM_002185.3	78	Gtg/Atg	3/8	1	2	FACETS	0.233	0.168	0.312	0.233	0.168	0.312	SUBCLONAL	1	TRUE	1	0.489965108543419	2		215	245	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628428	86628428	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	12	163	0	ENST00000274376.6:c.801del	p.Lys267AsnfsTer12	p.K267Nfs*12	ENST00000274376	NM_002890.2	266	gAa/ga	3/25	1	2	FACETS	0.244	0.171	0.333	0.244	0.171	0.333	SUBCLONAL	1	TRUE	1	0.489965108543419	2		163	201	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176715859	176715859	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	43	459	0	ENST00000439151.2:c.6191G>T	p.Gly2064Val	p.G2064V	ENST00000439151	NM_022455.4	2064	gGg/gTg	21/23	1	2	FACETS	0.273	0.228	0.323	0.273	0.228	0.323	SUBCLONAL	1	TRUE	1	0.489965108543419	2		459	643	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020979	26020979	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	25	351	0	ENST00000357647.3:c.262T>C	p.Ser88Pro	p.S88P	ENST00000357647	NM_003529.2	88	Tcc/Ccc	1/1	1	2	FACETS	0.281	0.221	0.35	0.281	0.221	0.35	SUBCLONAL	1	TRUE	1	0.489965108543419	2		351	363	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099468	157099470	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	rs1429292576	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	21	326	0	ENST00000346085.5:c.413_415del	p.Asn138del	p.N138del	ENST00000346085	NM_020732.3	135	tcCAAc/tcc	1/20	1	2	FACETS	0.236	0.181	0.3	0.236	0.181	0.3	SUBCLONAL	1	TRUE	1	0.489965108543419	2		326	363	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971299	13971299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	28	359	0	ENST00000405192.2:c.630G>A	p.Met210Ile	p.M210I	ENST00000405192	NM_001163147.1	210	atG/atA	8/12	1	2	FACETS	0.228	0.182	0.281	0.228	0.182	0.281	SUBCLONAL	1	TRUE	1	0.489965108543419	2		359	501	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859207	151859207	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	17	267	0	ENST00000262189.6:c.11455G>T	p.Gly3819Ter	p.G3819*	ENST00000262189	NM_170606.2	3819	Gga/Tga	43/59	1	2	FACETS	0.246	0.183	0.321	0.246	0.183	0.321	SUBCLONAL	1	TRUE	1	0.489965108543419	2		267	282	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860833	151860833	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1487130537	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	36	333	0	ENST00000262189.6:c.9829C>A	p.Pro3277Thr	p.P3277T	ENST00000262189	NM_170606.2	3277	Cca/Aca	43/59	1	2	FACETS	0.426	0.351	0.51	0.426	0.351	0.51	SUBCLONAL	1	TRUE	1	0.489965108543419	2		333	345	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878694	151878694	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	18	320	0	ENST00000262189.6:c.6251A>T	p.Asn2084Ile	p.N2084I	ENST00000262189	NM_170606.2	2084	aAt/aTt	36/59	1	2	FACETS	0.234	0.176	0.303	0.234	0.176	0.303	SUBCLONAL	1	TRUE	1	0.489965108543419	2		320	314	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370919	55370920	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	192	685	0	ENST00000297316.4:c.224dup	p.Met76HisfsTer5	p.M76Hfs*5	ENST00000297316	NM_022454.3	74	gct/gcTt	1/2	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.489965108543419	2		685	780	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	56	792	1	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	1	2	FACETS	0.218	0.185	0.253	0.218	0.185	0.253	SUBCLONAL	1	TRUE	1	0.489965108543419	2		793	1050	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141583008	141583008	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	71	544	0	ENST00000220592.5:c.239A>G	p.Gln80Arg	p.Q80R	ENST00000220592	NM_012154.3	80	cAg/cGg	3/19	1	2	FACETS	0.404	0.352	0.46	0.404	0.352	0.46	SUBCLONAL	1	TRUE	1	0.489965108543419	2		544	717	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759623	133759623	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	57	758	1	ENST00000318560.5:c.1950del	p.Leu651TrpfsTer43	p.L651Wfs*43	ENST00000318560	NM_005157.4	649	aCc/ac	11/11	1	2	FACETS	0.295	0.252	0.341	0.295	0.252	0.341	SUBCLONAL	1	TRUE	1	0.489965108543419	2		759	790	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760024	133760024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	51	798	4	ENST00000318560.5:c.2352del	p.Arg785GlyfsTer3	p.R785Gfs*3	ENST00000318560	NM_005157.4	783	Ccc/cc	11/11	1	2	FACETS	0.233	0.197	0.273	0.233	0.197	0.273	SUBCLONAL	1	TRUE	1	0.489965108543419	2		802	893	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139438500	139438500	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747994799	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	58	782	2	ENST00000277541.6:c.116C>T	p.Ala39Val	p.A39V	ENST00000277541	NM_017617.3	39	gCg/gTg	2/34	1	2	FACETS	0.268	0.23	0.311	0.268	0.23	0.311	SUBCLONAL	1	TRUE	1	0.489965108543419	2		784	882	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931690	39931690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771757019	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	55	622	1	ENST00000378444.4:c.2909C>T	p.Ala970Val	p.A970V	ENST00000378444	NM_001123385.1	970	gCg/gTg	4/15	1	2	FACETS	0.306	0.261	0.356	0.306	0.261	0.356	SUBCLONAL	1	TRUE	1	0.489965108543419	2		623	733	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922901	44922901	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	48	454	0	ENST00000377967.4:c.1762A>G	p.Thr588Ala	p.T588A	ENST00000377967	NM_021140.2	588	Aca/Gca	16/29	1	2	FACETS	0.368	0.31	0.431	0.368	0.31	0.431	SUBCLONAL	1	TRUE	1	0.489965108543419	2		454	533	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045888	47045889	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	32	644	0	ENST00000377604.3:c.2687dup	p.Ser897LeufsTer83	p.S897Lfs*83	ENST00000377604	NM_001204468.1	895	cgg/cGgg	24/24	1	2	FACETS	0.205	0.166	0.25	0.205	0.166	0.25	SUBCLONAL	1	TRUE	1	0.489965108543419	2		644	637	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426675	47426675	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	67	687	0	ENST00000377045.4:c.920C>A	p.Pro307His	p.P307H	ENST00000377045	NM_001654.4	307	cCc/cAc	10/16	1	2	FACETS	0.373	0.323	0.426	0.373	0.323	0.426	SUBCLONAL	1	TRUE	1	0.489965108543419	2		687	734	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349632	70349632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	67	628	2	ENST00000374080.3:c.3794G>A	p.Gly1265Asp	p.G1265D	ENST00000374080		1265	gGc/gAc	27/45	1	2	FACETS	0.36	0.312	0.412	0.36	0.312	0.412	SUBCLONAL	1	TRUE	1	0.489965108543419	2		630	759	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814170	76814171	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	13	233	0	ENST00000373344.5:c.6473dup	p.Pro2159AlafsTer6	p.P2159Afs*6	ENST00000373344	NM_000489.3	2158	aag/aaAg	29/35	1	2	FACETS	0.241	0.172	0.326	0.241	0.172	0.326	SUBCLONAL	1	TRUE	1	0.489965108543419	2		233	220	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185016	123185016	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	33	326	0	ENST00000218089.9:c.1063T>C	p.Tyr355His	p.Y355H	ENST00000218089	NM_001042749.1	355	Tat/Cat	12/35	1	2	FACETS	0.411	0.335	0.496	0.411	0.335	0.496	SUBCLONAL	1	TRUE	1	0.489965108543419	2		326	328	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0039469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	221	211	1	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	0.829907634363996	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.83046179343843	2		212	254	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279438	38279438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1563475734	NA	P-0039469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2293	176	527	0	ENST00000425967.3:c.1051G>A	p.Asp351Asn	p.D351N	ENST00000425967	NM_001174067.1	351	Gac/Aac	9/19	0.83046179343843	10	FACETS	0.742	0.68	0.808			1	SUBCLONAL	1	TRUE	NA	0.83046179343843	10		527	2469	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828002	72828002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	726	771	0	ENST00000268489.5:c.8579G>A	p.Gly2860Glu	p.G2860E	ENST00000268489	NM_006885.3	2860	gGa/gAa	9/10	0.83046179343843	3	FACETS	1	0.984	1			1	CLONAL	2	TRUE	NA	0.83046179343843	3		771	1215	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007240	62007240	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	263	679	1	ENST00000392795.3:c.442A>T	p.Thr148Ser	p.T148S	ENST00000392795	NM_001039933.1	148	Acc/Tcc	4/6	0.823921704217546	3	FACETS	0.89	0.835	0.947	0.297	0.278	0.316	CLONAL	1	TRUE	0	0.83046179343843	3		680	1007	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0039475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	252	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.479110367810115	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.479110367810115	3		326	394	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120663	115120663	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	463	892	0	ENST00000257566.3:c.343C>T	p.Gln115Ter	p.Q115*	ENST00000257566	NM_016569.3	115	Cag/Tag	1/8	0.245647811482859	3	FACETS	0.867	0.828	0.907	0.867	0.828	0.907	INDETERMINATE	2	TRUE	1	0.479110367810115	3		892	1381	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859878	117859878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780692465	NA	P-0039475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	63	232	0	ENST00000297338.2:c.1757G>A	p.Arg586Gln	p.R586Q	ENST00000297338	NM_006265.2	586	cGa/cAa	14/14	0.479110367810115	3	FACETS	0.891	0.774	1	0.445	0.387	0.508	CLONAL	1	TRUE	1	0.479110367810115	3		232	366	SUCCESS
APC	324	MSKCC	GRCh37	5	112102958	112102958	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	154	428	0	ENST00000257430.4:c.293G>T	p.Ser98Ile	p.S98I	ENST00000257430	NM_000038.5	98	aGc/aTc	4/16	0.203244641152643	4	FACETS	0.849	0.781	0.919	0.849	0.781	0.919	INDETERMINATE	2	TRUE	2	0.479110367810115	4		428	560	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437684	52437685	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0039475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	576	729	0	ENST00000460680.1:c.1476_1477insG	p.Thr493AspfsTer6	p.T493Dfs*6	ENST00000460680	NM_004656.3	492	-/G	13/17	0.479110367810115	3	FACETS	0.894	0.863	0.925	0.894	0.863	0.925	CLONAL	3	TRUE	0	0.479110367810115	3		729	1111	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268144	153268144	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs920052554	NA	P-0039547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	38	329	1	ENST00000281708.4:c.664C>T	p.Arg222Ter	p.R222*	ENST00000281708	NM_033632.3	222	Cga/Tga	4/12	1	2	FACETS	0.778	0.643	0.93	0.778	0.643	0.93	CLONAL	1	TRUE	1	0.19	2		330	514	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657523	37657523	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1234	590	415	0	ENST00000447079.4:c.2440G>C	p.Glu814Gln	p.E814Q	ENST00000447079	NM_015083.1	814	Gag/Cag	6/14	0.3	6	FACETS	0.94	0.902	0.978			1	CLONAL	5	TRUE	NA	0.19	6		415	1824	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0039547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	46	473	0	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	0.792	0.666	0.932	0.792	0.666	0.932	CLONAL	1	TRUE	1	0.19	2		473	611	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272449	11272449	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	40	490	0	ENST00000361445.4:c.3481C>T	p.Arg1161Ter	p.R1161*	ENST00000361445	NM_004958.3	1161	Cga/Tga	23/58	1	2	FACETS	0.608	0.504	0.725	0.608	0.504	0.725	SUBCLONAL	1	TRUE	1	0.19	2		490	692	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0039550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	106	574	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	1	2	FACETS	0.845	0.765	0.928	1	0.986	1	CLONAL	2	TRUE	1	0.352463071603896	2		574	356	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023090	27023090	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs962566886	NA	P-0039550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	22	99	0	ENST00000324856.7:c.196C>A	p.Pro66Thr	p.P66T	ENST00000324856	NM_006015.4	66	Ccg/Acg	1/20	0.352463071603896	1	FACETS	0.745	0.584	0.928	0.745	0.584	0.928	CLONAL	1	TRUE	0	0.352463071603896	1		99	138	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722065	176722065	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs778841211	NA	P-0039550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	52	445	0	ENST00000439151.2:c.7696A>G	p.Thr2566Ala	p.T2566A	ENST00000439151	NM_022455.4	2566	Acc/Gcc	23/23	1	2	FACETS	0.881	0.754	1	0.881	0.754	1	CLONAL	1	TRUE	1	0.352463071603896	2		445	335	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	147	236	0				ENST00000310581	NM_198253.2	-/1132			0.34468385744223	5	FACETS	0.839	0.767	0.915	0.42	0.383	0.458	CLONAL	2	TRUE	1	0.34468385744223	5		236	771	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0039551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	332	467	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.29518099013271	3	FACETS	0.954	0.907	1	0.954	0.907	1	CLONAL	3	TRUE	0	0.34468385744223	3		468	789	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0039551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	142	271	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	0.34468385744223	4	FACETS	0.97	0.888	1			1	CLONAL	2	TRUE	NA	0.34468385744223	4		271	571	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115595	108115595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769166447	NA	P-0039551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	131	363	0	ENST00000278616.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000278616	NM_000051.3	248	cGa/cAa	7/63	0.255286905595561	3	FACETS	0.898	0.82	0.98	0.898	0.82	0.98	CLONAL	2	TRUE	1	0.34468385744223	3		363	496	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319439	11319440	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	54	531	0	ENST00000361445.4:c.27dup	p.Thr10HisfsTer8	p.T10Hfs*8	ENST00000361445	NM_004958.3	9	-/C	2/58	0.238659579489667	3	FACETS	0.449	0.382	0.522			1	SUBCLONAL	1	TRUE	NA	0.34468385744223	3		531	818	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089494	27089494	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	64	573	0	ENST00000324856.7:c.2451del	p.Leu818CysfsTer15	p.L818Cfs*15	ENST00000324856	NM_006015.4	817	gCc/gc	8/20	0.212605056452563	3	FACETS	0.518	0.448	0.595	0.173	0.149	0.199	SUBCLONAL	1	TRUE	0	0.34468385744223	3		573	840	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039386	49039386	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	248	482	0	ENST00000267163.4:c.2372del	p.Lys791SerfsTer19	p.K791Sfs*19	ENST00000267163	NM_000321.2	791	Aag/ag	23/27	0.255286905595561	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.34468385744223	3		482	805	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645620	215645621	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	178	519	0	ENST00000260947.4:c.977dup	p.Asn326LysfsTer2	p.N326Kfs*2	ENST00000260947	NM_000465.2	326	aat/aaAt	4/11	0.34468385744223	2	FACETS	0.802	0.742	0.863	0.802	0.742	0.863	CLONAL	2	TRUE	0	0.34468385744223	2		519	644	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722083	176722112	+	inframe_deletion	In_Frame_Del	DEL	CAATCCCCGGGCCTGGTGAAGCAGGCGAAG	CAATCCCCGGGCCTGGTGAAGCAGGCGAAG	-	novel	NA	P-0039551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	39	470	0	ENST00000439151.2:c.7716_7745del	p.Ser2573_Gln2582del	p.S2573_Q2582del	ENST00000439151	NM_022455.4	2572	CAATCCCCGGGCCTGGTGAAGCAGGCGAAG/-	23/23	0.34468385744223	2	FACETS	0.392	0.324	0.467	0.196	0.162	0.234	SUBCLONAL	1	TRUE	0	0.34468385744223	2		470	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0039553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	189	552	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.438369660166815	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.438689795817894	2		552	427	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026078	48026078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs188252826	NA	P-0039553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	60	364	0	ENST00000234420.5:c.956C>T	p.Thr319Met	p.T319M	ENST00000234420	NM_000179.2	319	aCg/aTg	4/10	0.438689795817894	3	FACETS	0.855	0.74	0.98	0.428	0.37	0.49	CLONAL	1	TRUE	1	0.438689795817894	3		364	390	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513197	41513197	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	69	372	0	ENST00000263253.7:c.101G>C	p.Gly34Ala	p.G34A	ENST00000263253	NM_001429.3	34	gGc/gCc	2/31	0.39796373293156	3	FACETS	1	0.969	1	0.45	0.396	0.508	CLONAL	1	TRUE	0	0.438689795817894	3		372	284	SUCCESS
APC	324	MSKCC	GRCh37	5	112128212	112128213	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAACA	novel	NA	P-0039553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	41	306	0	ENST00000257430.4:c.716_720dup	p.Glu241GlnfsTer54	p.E241Qfs*54	ENST00000257430	NM_000038.5	239	gca/gCAACAca	7/16	1	2	FACETS	0.834	0.701	0.979	0.834	0.701	0.979	CLONAL	1	TRUE	1	0.438689795817894	2		306	224	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431628	6431628	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	99	333	0	ENST00000356142.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000356142	NM_018890.3	61	Caa/Aaa	3/7	0.39656893002132	3	FACETS	1	0.969	1	0.6	0.539	0.663	CLONAL	1	TRUE	1	0.507222779226863	3		333	408	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631589	119631589	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	21	381	0	ENST00000316626.5:c.677A>T	p.Glu226Val	p.E226V	ENST00000316626		226	gAg/gTg	6/12	0.507222779226863	2	FACETS	0.231	0.177	0.293	0.115	0.088	0.147	SUBCLONAL	1	TRUE	0	0.507222779226863	2		381	359	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0039555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	64	427	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.358459895030055	3	FACETS	0.859	0.746	0.982	0.43	0.373	0.491	CLONAL	1	TRUE	1	0.358459895030055	3		427	490	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027160	49027160	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0039555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	14	313	0	ENST00000267163.4:c.1727C>G	p.Ser576Ter	p.S576*	ENST00000267163	NM_000321.2	576	tCa/tGa	18/27	1	2	FACETS	0.288	0.208	0.386	0.288	0.208	0.386	SUBCLONAL	1	TRUE	1	0.358459895030055	2		313	271	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101909995	101909995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	22	217	0	ENST00000374994.4:c.1315G>A	p.Glu439Lys	p.E439K	ENST00000374994	NM_004612.2	439	Gaa/Aaa	8/9	1	2	FACETS	0.671	0.523	0.84	0.671	0.523	0.84	SUBCLONAL	1	TRUE	1	0.358459895030055	2		217	183	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022592	31022592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs373221034	NA	P-0039555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	108	504	0	ENST00000375687.4:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000375687	NM_015338.5	693	Cga/Tga	13/13	1	2	FACETS	0.844	0.758	0.935	0.844	0.758	0.935	CLONAL	1	TRUE	1	0.358459895030055	2		504	714	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609111	43609111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767402	NA	P-0039555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	141	648	2	ENST00000355710.3:c.1867G>A	p.Glu623Lys	p.E623K	ENST00000355710	NM_020975.4	623	Gaa/Aaa	10/20	0.172790640483877	3	FACETS	0.989	0.9	1	0.495	0.45	0.541	INDETERMINATE	1	TRUE	1	0.358459895030055	3		650	938	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437448	49437448	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	103	514	0	ENST00000301067.7:c.5437G>A	p.Glu1813Lys	p.E1813K	ENST00000301067	NM_003482.3	1813	Gaa/Aaa	23/54	0.172790640483877	3	FACETS	0.949	0.85	1	0.475	0.425	0.527	INDETERMINATE	1	TRUE	1	0.358459895030055	3		514	714	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441413	149441413	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0039555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	93	391	0	ENST00000286301.3:c.1627-1G>A		p.X543_splice	ENST00000286301	NM_005211.3	543			1	2	FACETS	0.89	0.793	0.993	0.89	0.793	0.993	CLONAL	1	TRUE	1	0.358459895030055	2		391	583	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0039557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	80	330	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.241631128847771	2		330	473	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0039557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	141	304	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	0.241631128847771	3	FACETS	0.877	0.804	0.953	0.877	0.804	0.953	CLONAL	3	TRUE	0	0.241631128847771	3		304	497	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0039557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	87	343	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.202639367941841	2	FACETS	0.797	0.708	0.89	0.797	0.708	0.89	SUBCLONAL	2	TRUE	0	0.241631128847771	2		343	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577571	7577571	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs765848205	NA	P-0039557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	161	447	0	ENST00000269305.4:c.710T>A	p.Met237Lys	p.M237K	ENST00000269305	NM_001126112.2	237	aTg/aAg	7/11	0.188148505268914	2	FACETS	0.973	0.895	1	0.973	0.895	1	CLONAL	2	TRUE	0	0.241631128847771	2		447	685	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851995	63851995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	96	448	1	ENST00000279873.7:c.2773G>A	p.Ala925Thr	p.A925T	ENST00000279873	NM_032199.2	925	Gct/Act	10/10	0.170288301711282	3	FACETS	1	0.975	1	0.672	0.599	0.749	CLONAL	1	TRUE	1	0.241631128847771	3		449	663	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280666	41280666	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1157	202	566	0	ENST00000349496.5:c.2179G>C	p.Asp727His	p.D727H	ENST00000349496	NM_001904.3	727	Gat/Cat	15/15	0.172162671254242	6	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.592976211253266	6		566	1359	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795022	45795022	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	312	618	1	ENST00000450313.1:c.1606C>G	p.His536Asp	p.H536D	ENST00000450313	NM_012222.2	536	Cac/Gac	16/16	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.592976211253266	2		619	923	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577557	7577557	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519982	NA	P-0039562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	402	558	3	ENST00000269305.4:c.724T>A	p.Cys242Ser	p.C242S	ENST00000269305	NM_001126112.2	242	Tgc/Agc	7/11	0.598030276905987	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.592976211253266	1		561	679	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1040433	1040433	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	438	610	0	ENST00000358495.3:c.139C>G	p.Leu47Val	p.L47V	ENST00000358495	NM_134424.2	47	Ctg/Gtg	3/12	0.598030276905987	3	FACETS	0.939	0.899	0.979	0.626	0.599	0.653	CLONAL	2	TRUE	0	0.592976211253266	3		610	1020	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186501425	186501425	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1418086849	NA	P-0039562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	93	282	0	ENST00000323963.5:c.26A>G	p.Asn9Ser	p.N9S	ENST00000323963		9	aAc/aGc	1/11	0.256179170094669	4	FACETS	0.86	0.766	0.96	0.43	0.383	0.48	INDETERMINATE	1	TRUE	2	0.592976211253266	4		282	581	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875002	151875012	+	frameshift_variant	Frame_Shift_Del	DEL	TGGAGAAACTC	TGGAGAAACTC	ATCTTCTTA	novel	NA	P-0039562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	87	226	1	ENST00000262189.6:c.7526_7536delinsTAAGAAGAT	p.Gly2509ValfsTer15	p.G2509Vfs*15	ENST00000262189	NM_170606.2	2509	gGAGTTTCTCCA/gTAAGAAGAT	38/59	0.547152900716901	4	FACETS	0.827	0.734	0.927	0.276	0.244	0.309	CLONAL	1	TRUE	1	0.592976211253266	4		227	565	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0039565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	56	379	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	0.723	0.619	0.838	0.723	0.619	0.838	SUBCLONAL	1	TRUE	1	0.243410351907145	2		379	636	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0039566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	147	384	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.293228933952461	3	FACETS	0.9	0.827	0.976	0.9	0.827	0.976	CLONAL	2	TRUE	1	0.36762087245116	3		384	526	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197347	106197347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	79	398	0	ENST00000380013.4:c.5680C>T	p.Pro1894Ser	p.P1894S	ENST00000380013	NM_001127208.2	1894	Ccc/Tcc	11/11	1	2	FACETS	0.938	0.828	1	0.938	0.828	1	CLONAL	1	TRUE	1	0.36762087245116	2		398	458	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	83	417	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.951	0.842	1	0.951	0.842	1	CLONAL	1	TRUE	1	0.36	2		417	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0039568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	131	478	5	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.359726842533662	1	FACETS	0.941	0.857	1	0.941	0.857	1	CLONAL	1	TRUE	0	0.36	1		483	634	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945109	44945109	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0039568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	62	265	0	ENST00000377967.4:c.3434-1G>T		p.X1145_splice	ENST00000377967	NM_021140.2	1145			0.359726842533662	1	FACETS	0.974	0.849	1	0.974	0.849	1	CLONAL	1	TRUE	0	0.36	1		265	290	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435267	49435267	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	147	685	0	ENST00000301067.7:c.6286A>G	p.Lys2096Glu	p.K2096E	ENST00000301067	NM_003482.3	2096	Aag/Gag	31/54	1	2	FACETS	0.965	0.882	1	0.965	0.882	1	CLONAL	1	TRUE	1	0.36	2		685	846	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56787266	56787266	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	122	496	0	ENST00000337432.4:c.752A>G	p.Asp251Gly	p.D251G	ENST00000337432	NM_058216.2	251	gAc/gGc	5/9	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.36	2		496	645	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100936	41100936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757806313	NA	P-0039569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	159	483	1	ENST00000373198.4:c.1420G>A	p.Glu474Lys	p.E474K	ENST00000373198	NM_133170.3	474	Gag/Aag	8/32	0.477557825385946	4	FACETS	0.789	0.722	0.858	0.394	0.361	0.429	SUBCLONAL	1	TRUE	2	0.683267816514135	4		484	993	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577113	7577113	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	572	591	0	ENST00000269305.4:c.825del	p.Cys275TrpfsTer70	p.C275Wfs*70	ENST00000269305	NM_001126112.2	275	tgT/tg	8/11	0.683267816514135	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.683267816514135	2		591	806	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589220	67589255	+	inframe_deletion	In_Frame_Del	DEL	AATTAATAAACCACTACCGGAATGAATCTCTAGCTC	AATTAATAAACCACTACCGGAATGAATCTCTAGCTC	-	novel	NA	P-0039569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	150	312	0	ENST00000274335.5:c.1209_1244del	p.Leu404_Gln415del	p.L404_Q415del	ENST00000274335		403	gAATTAATAAACCACTACCGGAATGAATCTCTAGCTCag/gag	9/15	0.683267816514135	2	FACETS	0.848	0.794	0.9	0.848	0.794	0.9	CLONAL	2	TRUE	0	0.683267816514135	2		312	259	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115972	8115973	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0039575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	71	361	0	ENST00000346208.3:c.1320dup	p.Ala441ArgfsTer66	p.A441Rfs*66	ENST00000346208		440	acc/aCcc	6/6	0.376027026876623	3	FACETS	0.898	0.786	1	0.449	0.393	0.51	CLONAL	1	TRUE	1	0.387492561143147	3		361	487	SUCCESS
APC	324	MSKCC	GRCh37	5	112179432	112179432	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	48	482	0	ENST00000257430.4:c.8141G>C	p.Arg2714Pro	p.R2714P	ENST00000257430	NM_000038.5	2714	cGt/cCt	16/16	0.176768633800881	3	FACETS	0.479	0.404	0.562	0.24	0.202	0.281	INDETERMINATE	1	TRUE	1	0.387492561143147	3		482	617	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763509	59763509	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs578022079	NA	P-0039583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	72	521	1	ENST00000259008.2:c.2593C>T	p.Arg865Trp	p.R865W	ENST00000259008	NM_032043.2	865	Cgg/Tgg	19/20	0.502627763314492	3	FACETS	0.711	0.622	0.805	0.237	0.207	0.269	SUBCLONAL	1	FALSE	0	0.522588192093184	3		522	489	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574004	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAACATCTCGAAGCGCTCAC	novel	NA	P-0039583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	190	1013	1	ENST00000269305.4:c.1004_1023dup	p.Arg342ValfsTer10	p.R342Vfs*10	ENST00000269305	NM_001126112.2	341	-/GTGAGCGCTTCGAGATGTTC	10/11	0.497220173791023	1	FACETS	0.685	0.635	0.737	0.685	0.635	0.737	SUBCLONAL	1	FALSE	0	0.522588192093184	1		1014	784	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0039584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	139	513	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.168441863495651	6	FACETS	1	0.986	1	0.489	0.445	0.535	INDETERMINATE	1	FALSE	3	0.456213611705988	6		513	794	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578188	7578188	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201592	NA	P-0039584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	397	805	0	ENST00000269305.4:c.661G>T	p.Glu221Ter	p.E221*	ENST00000269305	NM_001126112.2	221	Gag/Tag	6/11	0.398994063629959	2	FACETS	0.881	0.84	0.922	0.881	0.84	0.922	CLONAL	2	FALSE	0	0.456213611705988	2		805	988	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191199	2191199	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	53	893	0	ENST00000398665.3:c.453C>G	p.Ile151Met	p.I151M	ENST00000398665	NM_032482.2	151	atC/atG	5/28	0.456213611705988	1	FACETS	0.21	0.178	0.244	0.21	0.178	0.244	SUBCLONAL	1	FALSE	0	0.456213611705988	1		893	856	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45422944	45422944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	21	372	0	ENST00000262160.6:c.184G>A	p.Glu62Lys	p.E62K	ENST00000262160	NM_005901.5	62	Gag/Aag	2/11	0.456213611705988	1	FACETS	0.177	0.136	0.225	0.177	0.136	0.225	SUBCLONAL	1	FALSE	0	0.456213611705988	1		372	402	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603047	48603047	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	30	386	0	ENST00000342988.3:c.1348C>T	p.Gln450Ter	p.Q450*	ENST00000342988	NM_005359.5	450	Cag/Tag	11/12	0.456213611705988	1	FACETS	0.238	0.192	0.291	0.238	0.192	0.291	SUBCLONAL	1	FALSE	0	0.456213611705988	1		386	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0039586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	326	1003	0	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	0.375561988822708	2	FACETS	0.849	0.803	0.895	0.849	0.803	0.895	CLONAL	2	TRUE	0	0.375561988822708	2		1003	1023	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138376590	138376590	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	218	618	0	ENST00000289153.2:c.2884T>A	p.Tyr962Asn	p.Y962N	ENST00000289153	NM_006219.2	962	Tat/Aat	20/22	0.375561988822708	3	FACETS	0.829	0.772	0.887	0.829	0.772	0.887	CLONAL	2	TRUE	1	0.375561988822708	3		618	832	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281645	49281645	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	476	959	0	ENST00000282018.3:c.692T>C	p.Val231Ala	p.V231A	ENST00000282018	NM_020377.2	231	gTg/gCg	1/1	0.375561988822708	4	FACETS	1	0.99	1	0.752	0.718	0.786	CLONAL	2	TRUE	1	0.375561988822708	4		959	1546	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639605	3639605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757202686	NA	P-0039586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	190	1301	0	ENST00000294008.3:c.4034G>A	p.Arg1345His	p.R1345H	ENST00000294008	NM_032444.2	1345	cGt/cAt	12/15	0.17655509854146	3	FACETS	0.88	0.812	0.952	0.293	0.27	0.318	INDETERMINATE	1	TRUE	0	0.375561988822708	3		1301	1365	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	60	417	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.679	0.585	0.78	0.679	0.585	0.78	SUBCLONAL	1	TRUE	1	0.355741163242894	2		417	497	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253176	133253176	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	33	613	1	ENST00000320574.5:c.865G>A	p.Glu289Lys	p.E289K	ENST00000320574	NM_006231.2	289	Gag/Aag	9/49	1	2	FACETS	0.349	0.283	0.423	0.349	0.283	0.423	SUBCLONAL	1	TRUE	1	0.355741163242894	2		614	532	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420315	88420315	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	58	506	0	ENST00000360948.2:c.2371C>G	p.Arg791Gly	p.R791G	ENST00000360948	NM_001012338.2	791	Cgg/Ggg	19/19	1	2	FACETS	0.583	0.501	0.673	0.583	0.501	0.673	SUBCLONAL	1	TRUE	1	0.355741163242894	2		506	559	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561114	9561114	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	67	459	0	ENST00000353224.5:c.668C>A	p.Ser223Ter	p.S223*	ENST00000353224	NM_177990.2	223	tCg/tAg	4/10	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.355741163242894	2		459	346	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405093	405093	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	280	659	0	ENST00000380956.4:c.1175C>G	p.Pro392Arg	p.P392R	ENST00000380956	NM_001195286.1	392	cCa/cGa	8/9	0.188341488583833	3	FACETS	1	0.989	1	1	0.989	1	INDETERMINATE	2	TRUE	1	0.355741163242894	3		659	778	SUCCESS
AR	367	MSKCC	GRCh37	X	66765891	66765891	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	44	1264	0	ENST00000374690.3:c.903G>C	p.Lys301Asn	p.K301N	ENST00000374690	NM_000044.3	301	aaG/aaC	1/8	0.354438408699077	1	FACETS	0.246	0.205	0.291	0.246	0.205	0.291	SUBCLONAL	1	TRUE	0	0.355741163242894	1		1264	827	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	125	417	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.854	0.777	0.934	1	0.988	1	CLONAL	2	TRUE	1	0.29	2		417	505	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0039590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	59	330	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.825	0.711	0.949	0.825	0.711	0.949	CLONAL	1	TRUE	1	0.29	2		330	493	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0039590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	191	565	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.3	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.29	3		565	665	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597433	52597433	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199643728	NA	P-0039590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	106	547	1	ENST00000394830.3:c.3877G>A	p.Glu1293Lys	p.E1293K	ENST00000394830	NM_018313.4	1293	Gag/Aag	25/30	1	2	FACETS	0.985	0.884	1	0.985	0.884	1	CLONAL	1	TRUE	1	0.29	2		548	742	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440660	56440660	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	175	761	0	ENST00000407977.2:c.558del	p.Ile186MetfsTer3	p.I186Mfs*3	ENST00000407977		186	atT/at	5/10	1	2	FACETS	0.976	0.897	1	0.976	0.897	1	CLONAL	1	TRUE	1	0.29	2		761	1237	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851694	134851694	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749032472	NA	P-0039591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	74	670	0	ENST00000398015.3:c.1100G>A	p.Arg367His	p.R367H	ENST00000398015	NM_004441.4	367	cGc/cAc	5/16	0.209964104478484	3	FACETS	1	0.964	1	0.638	0.559	0.723	CLONAL	1	TRUE	1	0.220394489609562	3		670	584	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525054	9525054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	84	543	0	ENST00000353224.5:c.1831G>A	p.Ala611Thr	p.A611T	ENST00000353224	NM_177990.2	611	Gcc/Acc	8/10	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.220394489609562	2		543	646	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271256	1271256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	27	520	0	ENST00000310581.5:c.2446C>T	p.His816Tyr	p.H816Y	ENST00000310581	NM_198253.2	816	Cac/Tac	8/16	0.220394489609562	6	FACETS	0.657	0.522	0.813	0.131	0.104	0.163	SUBCLONAL	1	TRUE	1	0.220394489609562	6		520	537	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411889	116411904	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCTCTGTTTTAAGAT	CTCTCTGTTTTAAGAT	GAA	novel	NA	P-0039591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	274	1021	1	ENST00000397752.3:c.2888-14_2889delinsGAA		p.X963_splice	ENST00000397752	NM_000245.2	963		14/21	0.220394489609562	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.220394489609562	2		1022	1024	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0039595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	235	459	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	1	2	FACETS	0.942	0.883	1	0.942	0.883	1	CLONAL	1	TRUE	1	0.699515209908493	2		459	713	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023790	27023790	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	221	558	0	ENST00000324856.7:c.896T>G	p.Leu299Arg	p.L299R	ENST00000324856	NM_006015.4	299	cTc/cGc	1/20	1	2	FACETS	0.806	0.752	0.861	0.806	0.752	0.861	CLONAL	1	TRUE	1	0.699515209908493	2		558	784	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743534	46743534	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	332	671	0	ENST00000371975.4:c.1915A>C	p.Lys639Gln	p.K639Q	ENST00000371975	NM_003579.3	639	Aag/Cag	17/18	0.65582596715489	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.699515209908493	1		671	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0039597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	97	849	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	0.811	0.721	0.907	0.811	0.721	0.907	CLONAL	1	FALSE	1	0.230437441955405	2		850	1038	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578538	7578538	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1269	117	1084	0	ENST00000269305.4:c.392A>G	p.Asn131Ser	p.N131S	ENST00000269305	NM_001126112.2	131	aAc/aGc	5/11	1	2	FACETS	0.733	0.658	0.812	0.733	0.658	0.812	SUBCLONAL	1	FALSE	1	0.230437441955405	2		1084	1386	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0039597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	90	114	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.230437441955405	2		114	588	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570814	226570814	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	69	629	1	ENST00000366794.5:c.1082C>A	p.Thr361Asn	p.T361N	ENST00000366794	NM_001618.3	361	aCc/aAc	8/23	1	2	FACETS	0.728	0.632	0.831	0.728	0.632	0.831	SUBCLONAL	1	FALSE	1	0.230437441955405	2		630	823	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979624	55979624	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	39	505	0	ENST00000263923.4:c.823C>T	p.Arg275Ter	p.R275*	ENST00000263923	NM_002253.2	275	Cga/Tga	7/30	1	2	FACETS	0.549	0.454	0.656	0.549	0.454	0.656	SUBCLONAL	1	FALSE	1	0.230437441955405	2		505	616	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964909	25964909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	43	436	0	ENST00000435504.4:c.4297G>A	p.Val1433Ile	p.V1433I	ENST00000435504		1433	Gtc/Atc	13/13	1	2	FACETS	0.738	0.617	0.871	0.738	0.617	0.871	SUBCLONAL	1	FALSE	1	0.230437441955405	2		436	506	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950588	38950588	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	53	437	0	ENST00000357387.3:c.3362C>T	p.Ser1121Leu	p.S1121L	ENST00000357387	NM_152756.3	1121	tCa/tTa	31/38	1	2	FACETS	0.646	0.55	0.752	0.646	0.55	0.752	SUBCLONAL	1	FALSE	1	0.230437441955405	2		437	712	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249015	55249016	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGT	novel	NA	P-0039598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	247	582	0	ENST00000275493.2:c.2313_2314insGGT	p.Asn771_Pro772insGly	p.N771_P772insG	ENST00000275493	NM_005228.3	771	-/GGT	20/28	0.343052403859629	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.343052403859629	3		582	727	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205368	38205368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	68	777	0	ENST00000317025.8:c.322C>T	p.Pro108Ser	p.P108S	ENST00000317025	NM_023034.1	108	Ccc/Tcc	2/24	0.343052403859629	1	FACETS	0.43	0.373	0.491	0.43	0.373	0.491	SUBCLONAL	1	TRUE	0	0.343052403859629	1		777	764	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444659	78444659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs908264837	NA	P-0039599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	196	442	0	ENST00000370768.2:c.30del	p.Ser11LeufsTer43	p.S11Lfs*43	ENST00000370768	NM_003902.3	10	ccC/cc	1/20	1	2	FACETS	0.97	0.902	1	0.97	0.902	1	CLONAL	1	TRUE	1	0.618068702144876	2		442	654	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	472	1058	3	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.618068702144876	2		1061	1285	SUCCESS
APC	324	MSKCC	GRCh37	5	112177091	112177091	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1131691253	NA	P-0039599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	134	413	0	ENST00000257430.4:c.5803del	p.Gln1935SerfsTer35	p.Q1935Sfs*35	ENST00000257430	NM_000038.5	1934	Ccc/cc	16/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.618068702144876	2		413	393	SUCCESS
APC	324	MSKCC	GRCh37	5	112174783	112174783	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	71	248	0	ENST00000257430.4:c.3495del	p.Lys1165AsnfsTer17	p.K1165Nfs*17	ENST00000257430	NM_000038.5	1164	atA/at	16/16	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.618068702144876	2		248	222	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882050	36882050	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs780753361	NA	P-0039599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	404	822	9	ENST00000358127.4:c.963del	p.Ala322LeufsTer11	p.A322Lfs*11	ENST00000358127	NM_001280556.1	321	ccC/cc	8/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.618068702144876	2		831	1236	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692896	89692896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123322	NA	P-0039599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	135	424	0	ENST00000371953.3:c.380G>A	p.Gly127Glu	p.G127E	ENST00000371953	NM_000314.4	127	gGa/gAa	5/9	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.618068702144876	2		424	389	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922301	178922301	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	83	307	0	ENST00000263967.3:c.1070G>T	p.Arg357Leu	p.R357L	ENST00000263967	NM_006218.2	357	cGa/cTa	6/21	1	2	FACETS	0.901	0.804	1	0.901	0.804	1	CLONAL	1	TRUE	1	0.618068702144876	2		307	298	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753385	42753385	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555750642	NA	P-0039599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	111	908	4	ENST00000222329.4:c.879del	p.Ser295AlafsTer16	p.S295Afs*16	ENST00000222329	NM_006494.2	293	ggG/gg	4/4	1	2	FACETS	0.344	0.309	0.382	0.344	0.309	0.382	SUBCLONAL	1	TRUE	1	0.618068702144876	2		912	1043	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716029	243716029	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0039599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	98	446	0	ENST00000263826.5:c.1163+2T>C		p.X388_splice	ENST00000263826	NM_005465.4	388			0.618068702144876	3	FACETS	0.791	0.708	0.878	0.395	0.354	0.439	SUBCLONAL	1	TRUE	1	0.618068702144876	3		446	525	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724726	112724726	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	156	467	0	ENST00000369452.4:c.610A>T	p.Ile204Leu	p.I204L	ENST00000369452	NM_007373.3	204	Ata/Tta	2/9	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.618068702144876	2		467	451	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533461	533461	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	277	861	0	ENST00000451590.1:c.442A>G	p.Thr148Ala	p.T148A	ENST00000451590	NM_001130442.1	148	Acc/Gcc	4/5	1	2	FACETS	0.98	0.922	1	0.98	0.922	1	CLONAL	1	TRUE	1	0.618068702144876	2		861	915	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948732	71948732	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	271	907	1	ENST00000298229.2:c.3448del	p.Leu1150TrpfsTer52	p.L1150Wfs*52	ENST00000298229	NM_001567.3	1148	ggC/gg	26/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.618068702144876	2		908	797	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831411	72831411	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	144	465	0	ENST00000268489.5:c.5170C>T	p.Gln1724Ter	p.Q1724*	ENST00000268489	NM_006885.3	1724	Cag/Tag	9/10	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.618068702144876	2		465	455	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59924475	59924475	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	102	279	0	ENST00000259008.2:c.614T>G	p.Phe205Cys	p.F205C	ENST00000259008	NM_032043.2	205	tTt/tGt	6/20	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.618068702144876	2		279	312	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543636	148543636	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	64	393	0	ENST00000320356.2:c.172C>T	p.Gln58Ter	p.Q58*	ENST00000320356	NM_004456.4	58	Caa/Taa	3/20	0.618068702144876	3	FACETS	0.331	0.286	0.38	0.166	0.143	0.19	SUBCLONAL	1	TRUE	1	0.618068702144876	3		393	819	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753073	128753073	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	112	438	0	ENST00000377970.2:c.1239del	p.Ala414ProfsTer29	p.A414Pfs*29	ENST00000377970	NM_002467.4	412	Aaa/aa	3/3	1	2	FACETS	0.612	0.552	0.676	0.612	0.552	0.676	SUBCLONAL	1	TRUE	1	0.618068702144876	2		438	592	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575521	64575521	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1565648511	NA	P-0039607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	622	810	1	ENST00000312049.6:c.496C>T	p.Gln166Ter	p.Q166*	ENST00000312049	NM_130799.2	166	Cag/Tag	3/10	0.974345867370402	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.974345867370402	1		811	645	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374727	118374727	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1327510788	NA	P-0039607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	368	512	0	ENST00000534358.1:c.8120G>A	p.Arg2707Gln	p.R2707Q	ENST00000534358	NM_005933.3	2707	cGg/cAg	27/36	0.974345867370402	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.974345867370402	1		512	380	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562719	21562719	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	606	794	1	ENST00000382592.4:c.1200C>A	p.Cys400Ter	p.C400*	ENST00000382592	NM_014572.2	400	tgC/tgA	4/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.974345867370402	2		795	1185	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162720	47162720	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	349	487	0	ENST00000409792.3:c.3406G>T	p.Gly1136Ter	p.G1136*	ENST00000409792	NM_014159.6	1136	Gga/Tga	3/21	0.974345867370402	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.974345867370402	1		487	361	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642554	117642554	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	523	751	0	ENST00000368508.3:c.5645G>A	p.Trp1882Ter	p.W1882*	ENST00000368508	NM_002944.2	1882	tGg/tAg	35/43	0.974345867370402	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.974345867370402	1		751	539	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518351	8518351	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	252	330	0	ENST00000356435.5:c.1040A>C	p.Asn347Thr	p.N347T	ENST00000356435		347	aAc/aCc	10/35	1	2	FACETS	0.993	0.94	1	0.993	0.94	1	CLONAL	1	TRUE	1	0.974345867370402	2		330	521	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37672062	37672062	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0121537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	94	378	0	ENST00000447079.4:c.2846+1G>A		p.X949_splice	ENST00000447079	NM_015083.1	949			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		378	827	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41522009	41522009	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0121537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	353	471	0	ENST00000263253.7:c.871A>T	p.Lys291Ter	p.K291*	ENST00000263253	NM_001429.3	291	Aaa/Taa	3/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		471	884	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0039611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	21	764	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		765	792	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0039613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	246	583	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	0.826	0.939	0.882	0.826	0.939	CLONAL	1	TRUE	1	0.651989555406533	2		583	856	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434506	110434506	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1019316102	NA	P-0039613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	336	854	1	ENST00000375856.3:c.3895G>A	p.Val1299Ile	p.V1299I	ENST00000375856	NM_003749.2	1299	Gtc/Atc	1/2	0.651989555406533	1	FACETS	0.901	0.857	0.945	0.901	0.857	0.945	CLONAL	1	TRUE	0	0.651989555406533	1		855	771	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057976	27057976	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	111	668	0	ENST00000324856.7:c.1684C>T	p.Gln562Ter	p.Q562*	ENST00000324856	NM_006015.4	562	Cag/Tag	3/20	0.295805842193751	1	FACETS	0.702	0.632	0.777	0.702	0.632	0.777	SUBCLONAL	1	TRUE	0	0.383059587541289	1		668	667	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577508	7577509	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	106	591	0	ENST00000269305.4:c.772_773insC	p.Glu258AlafsTer6	p.E258Afs*6	ENST00000269305	NM_001126112.2	258	gaa/gCaa	7/11	0.295805842193751	1	FACETS	0.753	0.677	0.834	0.753	0.677	0.834	SUBCLONAL	1	TRUE	0	0.383059587541289	1		591	594	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321584	30321584	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	27	215	0	ENST00000322652.5:c.1439A>G	p.Tyr480Cys	p.Y480C	ENST00000322652	NM_015355.2	480	tAt/tGt	13/16	0.295805842193751	1	FACETS	0.857	0.692	1	0.857	0.692	1	CLONAL	1	TRUE	0	0.383059587541289	1		215	133	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787769	135787769	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0039614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	149	455	0	ENST00000298552.3:c.813T>G	p.Tyr271Ter	p.Y271*	ENST00000298552	NM_001162426.1	271	taT/taG	9/23	0.318199262338201	2	FACETS	0.804	0.74	0.87	0.804	0.74	0.87	CLONAL	2	TRUE	0	0.383059587541289	2		455	484	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	286	236	0				ENST00000310581	NM_198253.2	-/1132			0.211775204506052	5	FACETS	0.986	0.929	1	0.986	0.929	1	CLONAL	3	TRUE	2	0.31	5		236	914	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0039617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	253	370	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.3	4	FACETS	1	0.942	1	1	0.942	1	CLONAL	3	TRUE	1	0.31	4		370	712	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0039617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	156	376	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.3	5	FACETS	0.878	0.804	0.954	0.878	0.804	0.954	CLONAL	2	TRUE	3	0.31	5		376	840	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0039617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	79	765	1	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	0.180515958743718	3	FACETS	0.599	0.525	0.678	0.2	0.175	0.226	INDETERMINATE	1	TRUE	0	0.31	3		766	983	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579717	7579717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs922736614	NA	P-0039617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	71	678	0	ENST00000269305.4:c.79C>T	p.Pro27Ser	p.P27S	ENST00000269305	NM_001126112.2	27	Cct/Tct	3/11	0.180515958743718	3	FACETS	0.629	0.548	0.717	0.21	0.182	0.239	INDETERMINATE	1	TRUE	0	0.31	3		678	841	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2224003	2224003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1227	110	957	0	ENST00000326181.6:c.1217C>T	p.Ser406Phe	p.S406F	ENST00000326181	NM_032271.2	406	tCc/tTc	13/21	1	2	FACETS	0.531	0.475	0.59	0.531	0.475	0.59	SUBCLONAL	1	TRUE	1	0.31	2		957	1337	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909954	100909954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	77	373	0	ENST00000325455.5:c.2695C>T	p.Arg899Trp	p.R899W	ENST00000325455	NM_001202474.3	899	Cgg/Tgg	8/8	0.297742532331954	3	FACETS	1	0.958	1	0.601	0.53	0.678	CLONAL	1	TRUE	1	0.31	3		373	477	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680776	88680776	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	107	736	0	ENST00000360948.2:c.481T>G	p.Phe161Val	p.F161V	ENST00000360948	NM_001012338.2	161	Ttt/Gtt	6/19	NA	2	FACETS	0.651	0.582	0.724			1	INDETERMINATE	1	TRUE	NA	0.31	2		736	1061	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303184	11303184	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	127	736	1	ENST00000361445.4:c.1399G>T	p.Asp467Tyr	p.D467Y	ENST00000361445	NM_004958.3	467	Gac/Tac	9/58	NA	2	FACETS	0.881	0.797	0.969			1	INDETERMINATE	1	TRUE	NA	0.31	2		737	930	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356413	66356413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764384268	NA	P-0039617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	125	352	0	ENST00000273854.3:c.1084C>T	p.Arg362Trp	p.R362W	ENST00000273854	NM_004439.5	362	Cgg/Tgg	5/18	0.3	3	FACETS	0.807	0.733	0.885	0.807	0.733	0.885	CLONAL	2	TRUE	1	0.31	3		352	577	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798967	45798968	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0039617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1312	96	875	1	ENST00000450313.1:c.377_378delinsCT	p.Arg126Pro	p.R126P	ENST00000450313	NM_012222.2	126	cGG/cCT	4/16	0.186842401566158	4	FACETS	0.576	0.511	0.646	0.288	0.255	0.323	SUBCLONAL	1	TRUE	2	0.31	4		876	1408	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276702	115276702	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	41	370	0	ENST00000438362.2:c.757A>G	p.Lys253Glu	p.K253E	ENST00000438362	NM_001242891.1	253	Aaa/Gaa	8/20	1	2	FACETS	0.542	0.451	0.643	0.542	0.451	0.643	SUBCLONAL	1	TRUE	1	0.31	2		370	488	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610009	43610009	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	327	1008	0	ENST00000355710.3:c.1962del	p.Phe655SerfsTer20	p.F655Sfs*20	ENST00000355710	NM_020975.4	654	gCc/gc	11/20	0.180515958743718	3	FACETS	0.9	0.849	0.952	0.6	0.566	0.635	INDETERMINATE	2	TRUE	0	0.31	3		1008	1354	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946919	71946938	+	frameshift_variant	Frame_Shift_Del	DEL	AGGCCTCCTGCCCGCTCTCC	AGGCCTCCTGCCCGCTCTCC	-	novel	NA	P-0039617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1344	158	1106	0	ENST00000298229.2:c.2771_2790del	p.Ala924ValfsTer3	p.A924Vfs*3	ENST00000298229	NM_001567.3	923	gAGGCCTCCTGCCCGCTCTCC/g	25/28	0.297742532331954	3	FACETS	0.784	0.716	0.856	0.392	0.358	0.428	SUBCLONAL	1	TRUE	1	0.31	3		1106	1502	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480638	50480638	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	53	381	0	ENST00000394963.4:c.508G>C	p.Glu170Gln	p.E170Q	ENST00000394963	NM_003076.4	170	Gag/Cag	4/13	0.3	3	FACETS	0.555	0.472	0.646	0.277	0.236	0.323	SUBCLONAL	1	TRUE	1	0.31	3		381	712	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489094	56489094	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	91	443	0	ENST00000267101.3:c.1913G>T	p.Gly638Val	p.G638V	ENST00000267101	NM_001982.3	638	gGc/gTc	16/28	0.3	3	FACETS	0.817	0.725	0.916	0.408	0.362	0.458	CLONAL	1	TRUE	1	0.31	3		443	830	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28903867	28903867	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0039617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	206	661	0	ENST00000282397.4:c.2594-2A>C		p.X865_splice	ENST00000282397	NM_002019.4	865			0.180515958743718	3	FACETS	0.956	0.889	1	0.637	0.592	0.683	INDETERMINATE	2	TRUE	0	0.31	3		661	803	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579563	7579563	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	96	859	0	ENST00000269305.4:c.124G>C	p.Asp42His	p.D42H	ENST00000269305	NM_001126112.2	42	Gat/Cat	4/11	0.180515958743718	3	FACETS	0.727	0.646	0.813	0.242	0.215	0.271	INDETERMINATE	1	TRUE	0	0.31	3		859	984	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928435	69928435	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	301	720	0	ENST00000352241.4:c.255C>G	p.Phe85Leu	p.F85L	ENST00000352241	NM_198159.2	85	ttC/ttG	2/10	0.3	4	FACETS	1	0.983	1	0.737	0.694	0.781	CLONAL	2	TRUE	1	0.31	4		720	1150	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188911	32188911	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	243	919	0	ENST00000375023.3:c.643C>A	p.Leu215Met	p.L215M	ENST00000375023	NM_004557.3	215	Ctg/Atg	4/30	0.225790124648319	2	FACETS	1	0.991	1	0.679	0.634	0.726	CLONAL	1	TRUE	0	0.31	2		919	1154	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553158	106553158	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	84	688	1	ENST00000369096.4:c.1123G>T	p.Ala375Ser	p.A375S	ENST00000369096	NM_001198.3	375	Gct/Tct	5/7	1	2	FACETS	0.578	0.51	0.652	0.578	0.51	0.652	SUBCLONAL	1	TRUE	1	0.31	2		689	937	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38283664	38283664	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	138	599	0	ENST00000425967.3:c.814C>A	p.His272Asn	p.H272N	ENST00000425967	NM_001174067.1	272	Cac/Aac	7/19	1	2	FACETS	0.97	0.882	1	0.97	0.882	1	CLONAL	1	TRUE	1	0.31	2		599	918	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331607	8331607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	167	486	0	ENST00000356435.5:c.5509G>A	p.Asp1837Asn	p.D1837N	ENST00000356435		1837	Gat/Aat	33/35	0.180515958743718	3	FACETS	0.891	0.821	0.964	0.594	0.547	0.643	INDETERMINATE	2	TRUE	0	0.31	3		486	698	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399458	139399458	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	262	966	0	ENST00000277541.6:c.4685C>G	p.Ala1562Gly	p.A1562G	ENST00000277541	NM_017617.3	1562	gCg/gGg	26/34	0.225790124648319	2	FACETS	1	0.988	1	0.616	0.575	0.657	CLONAL	1	TRUE	0	0.31	2		966	1373	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	189	236	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.979	0.914	1	0.979	0.914	1	CLONAL	1	TRUE	1	0.799313544213582	2		236	483	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692800	89692800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204856	NA	P-0039621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	230	402	0	ENST00000371953.3:c.284C>T	p.Pro95Leu	p.P95L	ENST00000371953	NM_000314.4	95	cCa/cTa	5/9	0.799313544213582	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.799313544213582	1		402	308	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022839	31022839	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs752263134	NA	P-0039621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	254	609	0	ENST00000375687.4:c.2324T>G	p.Leu775Ter	p.L775*	ENST00000375687	NM_015338.5	775	tTa/tGa	13/13	1	2	FACETS	0.956	0.9	1	0.956	0.9	1	CLONAL	1	TRUE	1	0.799313544213582	2		609	665	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	59	146	0	ENST00000366813.1:c.83A>C	p.Lys28Thr	p.K28T	ENST00000366813		28	aAg/aCg	1/3	1	2	FACETS	0.934	0.823	1	0.934	0.823	1	CLONAL	1	TRUE	1	0.799313544213582	2		146	158	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	98	236	0				ENST00000310581	NM_198253.2	-/1132			0.713121972373913	5	FACETS	1	0.949	1	0.712	0.647	0.779	CLONAL	2	TRUE	2	0.82300984347425	5		236	249	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0039626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	141	383	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.82300984347425	6	FACETS	0.959	0.873	1	0.24	0.218	0.263	CLONAL	1	TRUE	2	0.82300984347425	6		383	945	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983044	201983044	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs778191104	NA	P-0039626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	300	1145	2	ENST00000359651.3:c.893G>C	p.Arg298Pro	p.R298P	ENST00000359651		298	cGg/cCg	7/8	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.82300984347425	2		1147	546	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428005	49428005	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	114	942	0	ENST00000301067.7:c.10585G>C	p.Glu3529Gln	p.E3529Q	ENST00000301067	NM_003482.3	3529	Gag/Cag	38/54	0.617936976169534	4	FACETS	1	0.976	1	0.413	0.374	0.452	CLONAL	1	TRUE	1	0.82300984347425	4		942	408	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428074	49428074	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	115	841	0	ENST00000301067.7:c.10516G>C	p.Asp3506His	p.D3506H	ENST00000301067	NM_003482.3	3506	Gac/Cac	38/54	0.617936976169534	4	FACETS	1	0.983	1	0.464	0.422	0.507	CLONAL	1	TRUE	1	0.82300984347425	4		841	366	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647873	3647873	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	108	1238	0	ENST00000294008.3:c.1291G>C	p.Glu431Gln	p.E431Q	ENST00000294008	NM_032444.2	431	Gag/Cag	6/15	0.717271960829652	4	FACETS	0.87	0.783	0.961	0.435	0.391	0.481	CLONAL	1	TRUE	2	0.82300984347425	4		1238	550	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916269	9916269	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1555491681	NA	P-0039626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	99	586	0	ENST00000330684.3:c.2020C>A	p.His674Asn	p.H674N	ENST00000330684	NM_001134407.1	674	Cat/Aat	10/13	0.717271960829652	4	FACETS	1	0.944	1	0.537	0.483	0.595	CLONAL	1	TRUE	2	0.82300984347425	4		586	408	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374892	45374893	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0039626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	111	728	3	ENST00000262160.6:c.950_951delinsTT	p.Ser317Phe	p.S317F	ENST00000262160	NM_005901.5	317	tCC/tTT	8/11	0.82300984347425	3	FACETS	0.81	0.732	0.891	0.405	0.366	0.446	CLONAL	1	TRUE	1	0.82300984347425	3		731	470	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164509	36164509	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	98	703	0	ENST00000300305.3:c.1366G>A	p.Glu456Lys	p.E456K	ENST00000300305		456	Gag/Aag	8/8	0.691969502703431	5	FACETS	1	0.967	1	0.299	0.268	0.332	CLONAL	1	TRUE	1	0.82300984347425	5		703	445	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259439	89259439	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	85	730	1	ENST00000336596.2:c.583G>C	p.Val195Leu	p.V195L	ENST00000336596	NM_005233.5	195	Gtg/Ctg	3/17	0.717271960829652	4	FACETS	0.868	0.771	0.97	0.434	0.385	0.485	CLONAL	1	TRUE	2	0.82300984347425	4		731	434	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652266	36652267	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0039626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	307	821	0	ENST00000244741.5:c.392dup	p.Gly132ArgfsTer65	p.G132Rfs*65	ENST00000244741	NM_000389.4	130	tcc/tCcc	2/3	0.82300984347425	4	FACETS	0.994	0.944	1	0.994	0.944	1	CLONAL	2	TRUE	2	0.82300984347425	4		821	684	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146156	38146156	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	172	1001	0	ENST00000317025.8:c.3350G>A	p.Arg1117Lys	p.R1117K	ENST00000317025	NM_023034.1	1117	aGa/aAa	19/24	0.82300984347425	3	FACETS	0.925	0.854	0.997	0.462	0.427	0.499	CLONAL	1	TRUE	1	0.82300984347425	3		1001	638	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022050	5022050	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1319914611	NA	P-0039626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	31	573	0	ENST00000381652.3:c.63G>C	p.Gln21His	p.Q21H	ENST00000381652	NM_004972.3	21	caG/caC	3/25	0.82300984347425	3	FACETS	0.333	0.27	0.405	0.167	0.135	0.203	SUBCLONAL	1	TRUE	1	0.82300984347425	3		573	319	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727522	66727522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	168	719	1	ENST00000307102.5:c.238G>A	p.Gly80Ser	p.G80S	ENST00000307102	NM_002755.3	80	Ggt/Agt	2/11	1	2	FACETS	0.649	0.596	0.703	0.649	0.596	0.703	SUBCLONAL	1	TRUE	1	0.573131320935901	2		720	904	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952457	17952457	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1766	226	1032	0	ENST00000458235.1:c.976C>A	p.Gln326Lys	p.Q326K	ENST00000458235	NM_000215.3	326	Cag/Aag	7/24	0.419851356950416	4	FACETS	0.623	0.577	0.67	0.156	0.144	0.168	SUBCLONAL	1	TRUE	0	0.573131320935901	4		1032	1992	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457283	5457283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778072834	NA	P-0039627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	66	398	2	ENST00000381577.3:c.257G>A	p.Arg86Gln	p.R86Q	ENST00000381577	NM_014143.3	86	cGg/cAg	3/7	0.454051958664293	0	FACETS	0.354	0.31	0.4			1	SUBCLONAL	1	TRUE	0	0.573131320935901	0		400	278	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443697	29443697	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs281864719	NA	P-0121598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	230	743	0	ENST00000389048.3:c.3520T>A	p.Phe1174Ile	p.F1174I	ENST00000389048	NM_004304.4	1174	Ttc/Atc	23/29	0.472119615529221	1	FACETS	0.344	0.321	0.367	0.344	0.321	0.367	INDETERMINATE	1	NA	0	0.938321170663659	1		743	757	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0039640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	84	676	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	1	2	FACETS	0.886	0.781	0.999	0.886	0.781	0.999	CLONAL	1	TRUE	1	0.2	2		676	948	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0039642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	40	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.122413835413531	3	FACETS	1	0.95	1	0.705	0.588	0.833	CLONAL	1	TRUE	1	0.20090180705326	3		326	311	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0039642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	97	878	2	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.20090180705326	2	FACETS	1	0.965	1	0.602	0.536	0.672	CLONAL	1	TRUE	0	0.20090180705326	2		880	802	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0039642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	24	405	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.18717091152698	1	FACETS	0.793	0.623	0.988	0.793	0.623	0.988	CLONAL	1	TRUE	0	0.20090180705326	1		405	271	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205807	108205807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782719	NA	P-0039642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	35	383	2	ENST00000278616.4:c.8122G>A	p.Asp2708Asn	p.D2708N	ENST00000278616	NM_000051.3	2708	Gat/Aat	55/63	0.20090180705326	1	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	0	0.20090180705326	1		385	262	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041007	47041007	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	126	896	0	ENST00000377604.3:c.1537G>T	p.Glu513Ter	p.E513*	ENST00000377604	NM_001204468.1	513	Gag/Tag	14/24	0.18717091152698	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.20090180705326	1		896	753	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679408	29679408	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555536372	NA	P-0039642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	60	441	0	ENST00000356175.3:c.7528C>T	p.Gln2510Ter	p.Q2510*	ENST00000356175	NM_000267.3	2510	Cag/Tag	50/57	0.20090180705326	2	FACETS	1	0.97	1	0.749	0.647	0.858	CLONAL	1	TRUE	0	0.20090180705326	2		441	399	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645064	86645064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	13	322	1	ENST00000274376.6:c.1136C>T	p.Ser379Leu	p.S379L	ENST00000274376	NM_002890.2	379	tCa/tTa	8/25	0.122413835413531	3	FACETS	0.762	0.544	1	0.381	0.272	0.513	CLONAL	1	TRUE	1	0.20090180705326	3		323	187	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447499	12447499	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	88	625	0	ENST00000287820.6:c.738G>T	p.Leu246Phe	p.L246F	ENST00000287820	NM_015869.4	246	ttG/ttT	5/7	0.122413835413531	3	FACETS	1	0.978	1	0.736	0.652	0.825	CLONAL	1	TRUE	1	0.20090180705326	3		625	655	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs17849781	NA	P-0039643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	818	751	0	ENST00000269305.4:c.832C>G	p.Pro278Ala	p.P278A	ENST00000269305	NM_001126112.2	278	Cct/Gct	8/11	0.862295207764157	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.873400189366883	2		751	933	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777972	27777972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	99	385	0	ENST00000369163.2:c.121C>T	p.Arg41Cys	p.R41C	ENST00000369163	NM_003536.2	41	Cgc/Tgc	1/1	0.862295207764157	2	FACETS	0.525	0.471	0.581	0.262	0.235	0.291	SUBCLONAL	1	TRUE	0	0.873400189366883	2		385	432	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047494	49047495	+	splice_acceptor_variant	Splice_Site	DEL	AG	AG	-	novel	NA	P-0039643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	92	248	0	ENST00000267163.4:c.2490-1_2490del		p.X830_splice	ENST00000267163	NM_000321.2	830			0.873400189366883	1	FACETS	0.899	0.836	0.958	0.899	0.836	0.958	CLONAL	1	TRUE	0	0.873400189366883	1		248	132	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10277294	10277294	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	684	795	0	ENST00000340748.4:c.823G>C	p.Asp275His	p.D275H	ENST00000340748		275	Gac/Cac	10/40	0.439740887694159	4	FACETS	0.98	0.947	1	0.49	0.473	0.507	INDETERMINATE	2	TRUE	0	0.873400189366883	4		795	1497	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228985	36228985	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1347	239	807	0	ENST00000222270.7:c.7765C>G	p.Leu2589Val	p.L2589V	ENST00000222270	NM_014727.1	2589	Ctg/Gtg	36/37	0.650869628210903	3	FACETS	0.496	0.461	0.532	0.165	0.153	0.178	SUBCLONAL	1	TRUE	0	0.873400189366883	3		807	1586	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792124	42792124	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	797	520	0	ENST00000575354.2:c.931+1del		p.G310fs	ENST00000575354	NM_015125.3	310	Ggg/gg	6/20	0.650869628210903	3	FACETS	1	0.998	1	0.827	0.809	0.844	CLONAL	2	TRUE	0	0.873400189366883	3		520	1057	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319388	62319388	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1315	284	968	0	ENST00000360203.5:c.1580C>G	p.Ser527Cys	p.S527C	ENST00000360203	NM_001283009.1	527	tCc/tGc	18/35	0.195904175829185	3	FACETS	0.584	0.547	0.622	0.195	0.182	0.208	INDETERMINATE	1	TRUE	0	0.873400189366883	3		968	1599	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818153	32818153	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0039643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	244	714	1	ENST00000354258.4:c.1372A>T	p.Lys458Ter	p.K458*	ENST00000354258	NM_000593.5	458	Aag/Tag	5/11	0.856533363118787	2	FACETS	0.601	0.562	0.641	0.3	0.281	0.321	SUBCLONAL	1	TRUE	0	0.873400189366883	2		715	930	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0039644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	378	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.374117629195118	7	FACETS	1	0.984	1			1	CLONAL	5	TRUE	NA	0.374117629195118	7		326	741	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0039644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	263	823	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.374117629195118	1	FACETS	0.786	0.74	0.833	1	0.994	1	SUBCLONAL	2	TRUE	0	0.374117629195118	1		823	727	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224357	36224357	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1640	205	1142	0	ENST00000222270.7:c.6907G>C	p.Asp2303His	p.D2303H	ENST00000222270	NM_014727.1	2303	Gat/Cat	28/37	0.374117629195118	7	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.374117629195118	7		1142	1845	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	73	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.237880792616645	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.237880792616645	1		371	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578519	7578520	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGTTGGCAA	novel	NA	P-0039646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	114	924	0	ENST00000269305.4:c.402_410dup	p.Cys135_Leu137dup	p.C135_L137dup	ENST00000269305	NM_001126112.2	135	ctg/ctTTGCCAACTg	5/11	0.237880792616645	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.237880792616645	1		924	763	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617739	39617739	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	18	365	0	ENST00000262039.4:c.1923A>T	p.Leu641Phe	p.L641F	ENST00000262039	NM_002647.2	641	ttA/ttT	17/25	1	2	FACETS	0.432	0.325	0.56	0.432	0.325	0.56	SUBCLONAL	1	TRUE	1	0.237880792616645	2		365	350	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711883	89711886	+	frameshift_variant	Frame_Shift_Del	DEL	TATT	TATT	-	novel	NA	P-0039648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	226	467	0	ENST00000371953.3:c.501_504del	p.Ile168ProfsTer14	p.I168Pfs*14	ENST00000371953	NM_000314.4	167	acTATT/ac	6/9	0.737827042298146	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.737827042298146	1		467	377	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946199	71946201	+	inframe_deletion	In_Frame_Del	DEL	CAG	CAG	-	novel	NA	P-0039648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	442	852	0	ENST00000298229.2:c.2457_2459del	p.Gln819del	p.Q819del	ENST00000298229	NM_001567.3	819	CAG/-	22/28	0.737827042298146	1	FACETS	0.918	0.882	0.953	0.918	0.882	0.953	CLONAL	1	TRUE	0	0.737827042298146	1		852	824	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878076	48878087	+	inframe_deletion	In_Frame_Del	DEL	GCCGCCACCGCC	GCCGCCACCGCC	-	novel	NA	P-0039648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	459	199	0	ENST00000267163.4:c.33_44del	p.Thr12_Ala15del	p.T12_A15del	ENST00000267163	NM_000321.2	10	GCCGCCACCGCC/-	1/27	0.737827042298146	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.737827042298146	2		199	616	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434556	110434557	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCT	novel	NA	P-0039648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	351	710	0	ENST00000375856.3:c.3842_3844dup	p.Lys1281dup	p.K1281dup	ENST00000375856	NM_003749.2	1281	agc/aAGAgc	1/2	0.737827042298146	3	FACETS	0.94	0.889	0.992	0.47	0.444	0.496	CLONAL	1	TRUE	1	0.737827042298146	3		710	1386	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873716	35873717	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATCT	novel	NA	P-0039648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	381	629	1	ENST00000216797.5:c.131_134dup	p.Met45IlefsTer42	p.M45Ifs*42	ENST00000216797	NM_020529.2	45	atg/atAGATg	1/6	1	2	FACETS	0.872	0.829	0.916	0.872	0.829	0.916	CLONAL	1	TRUE	1	0.737827042298146	2		630	1184	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437508	56437508	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0039648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	385	724	0	ENST00000407977.2:c.952+2T>A		p.X318_splice	ENST00000407977		318			0.737827042298146	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.737827042298146	1		724	651	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0039649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	1271	849	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.951909651764294	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.953554777873268	3		850	1310	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100462	8100462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752779081	NA	P-0039649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	448	1015	0	ENST00000346208.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000346208		146	Gcc/Acc	3/6	0.17948100281165	3	FACETS	1	0.979	1	0.348	0.331	0.364	INDETERMINATE	1	TRUE	0	0.953554777873268	3		1015	1331	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566442	41566442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6	366	393	0	ENST00000263253.7:c.4319C>T	p.Pro1440Leu	p.P1440L	ENST00000263253	NM_001429.3	1440	cCa/cTa	27/31	0.947457488601993	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.953554777873268	2		393	372	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860940	45860940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs574002154	NA	P-0039649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	386	858	0	ENST00000391945.4:c.1255G>A	p.Glu419Lys	p.E419K	ENST00000391945	NM_000400.3	419	Gag/Aag	13/23	0.951472517570733	2	FACETS	0.97	0.927	1	0.485	0.463	0.507	CLONAL	1	TRUE	0	0.953554777873268	2		858	835	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220489	98220489	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	698	640	0	ENST00000331920.6:c.2974G>A	p.Glu992Lys	p.E992K	ENST00000331920	NM_000264.3	992	Gaa/Aaa	18/24	0.947457488601993	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.953554777873268	2		640	723	SUCCESS
AR	367	MSKCC	GRCh37	X	66766008	66766008	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1282227912	NA	P-0039649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	476	489	0	ENST00000374690.3:c.1020A>C	p.Glu340Asp	p.E340D	ENST00000374690	NM_000044.3	340	gaA/gaC	1/8	0.709777587164814	2	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.953554777873268	2		489	949	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0039651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	385	444	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.131996359698738	4	FACETS	1	0.989	1			1	INDETERMINATE	4	TRUE	NA	0.433683305393003	4		444	596	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923703	39923703	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	182	891	0	ENST00000378444.4:c.3388C>A	p.Leu1130Ile	p.L1130I	ENST00000378444	NM_001123385.1	1130	Ctc/Atc	7/15	0.391433601059104	3	FACETS	1	0.937	1	0.509	0.469	0.551	CLONAL	1	TRUE	1	0.433683305393003	3		891	1003	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99491840	99491840	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	207	556	2	ENST00000268035.6:c.3625G>T	p.Ala1209Ser	p.A1209S	ENST00000268035	NM_000875.3	1209	Gcc/Tcc	20/21	0.391433601059104	3	FACETS	0.88	0.821	0.941	0.88	0.821	0.941	CLONAL	2	TRUE	1	0.433683305393003	3		558	660	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508461	29508461	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	136	388	0	ENST00000356175.3:c.608C>G	p.Ala203Gly	p.A203G	ENST00000356175	NM_000267.3	203	gCc/gGc	6/57	0.411676928640488	2	FACETS	0.971	0.896	1	0.971	0.896	1	CLONAL	2	TRUE	0	0.433683305393003	2		388	323	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618832	37618832	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	263	656	0	ENST00000447079.4:c.508A>T	p.Ser170Cys	p.S170C	ENST00000447079	NM_015083.1	170	Agc/Tgc	1/14	0.333668195752198	4	FACETS	0.93	0.873	0.988	0.93	0.873	0.988	CLONAL	2	TRUE	2	0.433683305393003	4		656	935	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761399	59761399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	104	479	0	ENST00000259008.2:c.3008C>T	p.Ser1003Leu	p.S1003L	ENST00000259008	NM_032043.2	1003	tCa/tTa	20/20	0.333668195752198	4	FACETS	1	0.932	1	0.526	0.471	0.583	CLONAL	1	TRUE	2	0.433683305393003	4		479	654	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606604	29606604	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	221	395	0	ENST00000389048.3:c.1276A>T	p.Ser426Cys	p.S426C	ENST00000389048	NM_004304.4	426	Agt/Tgt	5/29	0.348137343757212	5	FACETS	0.842	0.788	0.898	0.842	0.788	0.898	CLONAL	3	TRUE	2	0.433683305393003	5		395	666	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715735	30715735	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs144766594	NA	P-0039651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	199	328	2	ENST00000295754.5:c.1393G>T	p.Gly465Ter	p.G465*	ENST00000295754	NM_003242.5	465	Gga/Tga	5/7	0.422097385206833	3	FACETS	0.903	0.849	0.958	0.903	0.849	0.958	CLONAL	3	TRUE	0	0.433683305393003	3		330	412	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231287	98231287	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	260	795	1	ENST00000331920.6:c.1996A>T	p.Thr666Ser	p.T666S	ENST00000331920	NM_000264.3	666	Acg/Tcg	14/24	0.391433601059104	3	FACETS	0.822	0.772	0.874	0.822	0.772	0.874	CLONAL	2	TRUE	1	0.433683305393003	3		796	887	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123025086	123025086	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0039651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	162	461	0	ENST00000355640.3:c.978-2A>T		p.X326_splice	ENST00000355640		326			0.307069377807282	4	FACETS	0.846	0.779	0.915	0.846	0.779	0.915	CLONAL	2	TRUE	2	0.433683305393003	4		461	633	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894230	NA	P-0039652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	34	756	2	ENST00000451590.1:c.35G>A	p.Gly12Asp	p.G12D	ENST00000451590	NM_001130442.1	12	gGc/gAc	2/5	1	2	FACETS	1	0.826	1	1	0.826	1	CLONAL	1	TRUE	1	0.12	2		758	559	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949076	44949076	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	34	588	1	ENST00000377967.4:c.3637C>T	p.Arg1213Ter	p.R1213*	ENST00000377967	NM_021140.2	1213	Cga/Tga	25/29	1	2	FACETS	0.847	0.69	1	0.847	0.69	1	CLONAL	1	TRUE	1	0.12	2		589	669	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0039654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	39	427	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.428	0.355	0.509	0.428	0.355	0.509	SUBCLONAL	1	TRUE	1	0.49	2		427	372	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0039654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	44	652	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.544	0.458	0.639	0.544	0.458	0.639	SUBCLONAL	1	TRUE	1	0.49	2		652	330	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0039654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	102	670	3	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.895	0.805	0.99	0.895	0.805	0.99	CLONAL	1	TRUE	1	0.49	2		673	465	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732969	30732969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893810	NA	P-0039654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	135	382	1	ENST00000295754.5:c.1582C>T	p.Arg528Cys	p.R528C	ENST00000295754	NM_003242.5	528	Cgt/Tgt	7/7	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.49	2		383	513	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0039654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	373	405	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.3	1	FACETS	0.762	0.729	0.796	1	0.996	1	SUBCLONAL	2	TRUE	0	0.49	1		405	754	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715678	30715678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039551	NA	P-0039654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	109	336	1	ENST00000295754.5:c.1336G>A	p.Asp446Asn	p.D446N	ENST00000295754	NM_003242.5	446	Gat/Aat	5/7	1	2	FACETS	0.768	0.692	0.849	0.768	0.692	0.849	SUBCLONAL	1	TRUE	1	0.49	2		337	579	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208356	5208356	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1257575436	NA	P-0039654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	76	612	5	ENST00000357368.4:c.5534C>T	p.Pro1845Leu	p.P1845L	ENST00000357368	NM_002850.3	1845	cCg/cTg	36/38	1	2	FACETS	0.721	0.635	0.813	0.721	0.635	0.813	SUBCLONAL	1	TRUE	1	0.49	2		617	430	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101054	27101064	+	frameshift_variant	Frame_Shift_Del	DEL	CGACCAGCAGG	CGACCAGCAGG	-	novel	NA	P-0039654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	89	665	0	ENST00000324856.7:c.4338_4348del	p.Ala1448ProfsTer39	p.A1448Pfs*39	ENST00000324856	NM_006015.4	1446	CGACCAGCAGGc/c	18/20	1	2	FACETS	0.791	0.705	0.883	0.791	0.705	0.883	SUBCLONAL	1	TRUE	1	0.49	2		665	459	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524608	103524608	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	56	344	0	ENST00000355739.4:c.2739A>C	p.Lys913Asn	p.K913N	ENST00000355739	NM_000123.3	913	aaA/aaC	13/15	1	2	FACETS	0.436	0.374	0.504	0.436	0.374	0.504	SUBCLONAL	1	TRUE	1	0.49	2		344	524	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120402	70120402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	137	825	0	ENST00000245479.2:c.1404del	p.Tyr468Ter	p.Y468*	ENST00000245479	NM_000346.3	468	taC/ta	3/3	1	2	FACETS	0.888	0.81	0.969	0.888	0.81	0.969	CLONAL	1	TRUE	1	0.49	2		825	630	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2185903	2185903	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	140	604	1	ENST00000398665.3:c.175G>A	p.Val59Ile	p.V59I	ENST00000398665	NM_032482.2	59	Gtt/Att	3/28	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.49	2		605	549	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164544	36164544	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	70	432	2	ENST00000300305.3:c.1331C>T	p.Pro444Leu	p.P444L	ENST00000300305		444	cCc/cTc	8/8	0.19634521177223	0	FACETS	0.519	0.457	0.584			1	INDETERMINATE	1	TRUE	0	0.49	0		434	281	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266065	41266501	+	splice_donor_variant,splice_acceptor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	CTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCC	CTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCC	-	novel	NA	P-0039654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	89	324	0	ENST00000349496.5:c.65_301del		p.X22_splice	ENST00000349496	NM_001904.3	22	gCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCct/gct	3-4/15	1	2	FACETS	0.766	0.682	0.856	0.766	0.682	0.856	SUBCLONAL	1	TRUE	1	0.49	2		324	474	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247246	153247247	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	42	397	0	ENST00000281708.4:c.1555dup	p.Tyr519LeufsTer2	p.Y519Lfs*2	ENST00000281708	NM_033632.3	519	tat/tTat	10/12	1	2	FACETS	0.282	0.235	0.335	0.282	0.235	0.335	SUBCLONAL	1	TRUE	1	0.49	2		397	608	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940455	13940455	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758057612	NA	P-0039654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	146	263	1	ENST00000405192.2:c.1051C>T	p.Arg351Cys	p.R351C	ENST00000405192	NM_001163147.1	351	Cgt/Tgt	11/12	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.49	2		264	529	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900261	101900261	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	55	383	0	ENST00000374994.4:c.695A>T	p.Lys232Met	p.K232M	ENST00000374994	NM_004612.2	232	aAg/aTg	4/9	1	2	FACETS	0.325	0.277	0.377	0.325	0.277	0.377	SUBCLONAL	1	TRUE	1	0.49	2		383	691	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068424	26068425	+	stop_gained,inframe_insertion	Nonsense_Mutation	INS	-	-	TAGTAATAATTATAATAC	novel	NA	P-0039654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	12	245	1	ENST00000435504.4:c.65_66insGTATTATAATTATTACTA	p.Glu22_Lys23insTyrTyrAsnTyrTyrTer	p.E22_K23insYYNYY*	ENST00000435504		22	gaa/gaGTATTATAATTATTACTAa	2/13	0.116562987369458	0	FACETS	0.117	0.082	0.16			1	INDETERMINATE	1	TRUE	0	0.49	0		246	214	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	99	236	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.973	1	1	0.989	1	CLONAL	2	TRUE	1	0.243541444536218	2		236	329	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0039655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	150	427	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	0.992	1	CLONAL	2	TRUE	1	0.243541444536218	2		427	580	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7978925	7978925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397514532	NA	P-0039655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	157	362	0	ENST00000319144.4:c.1642C>T	p.Arg548Trp	p.R548W	ENST00000319144	NM_001139.2	548	Cgg/Tgg	12/15	1	2	FACETS	1	0.983	1	1	0.993	1	CLONAL	2	TRUE	1	0.243541444536218	2		362	521	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248514	59248514	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	303	527	1	ENST00000371222.2:c.229G>T	p.Glu77Ter	p.E77*	ENST00000371222	NM_002228.3	77	Gag/Tag	1/1	0.700553705103243	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.700553705103243	1		528	508	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375690	118375690	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	219	469	0	ENST00000534358.1:c.9083A>T	p.Asn3028Ile	p.N3028I	ENST00000534358	NM_005933.3	3028	aAc/aTc	27/36	0.38894843043376	1	FACETS	0.801	0.753	0.85	0.801	0.753	0.85	INDETERMINATE	1	TRUE	0	0.700553705103243	1		469	507	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944575	32944575	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs80359081	NA	P-0039656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	301	481	1	ENST00000380152.3:c.8368A>T	p.Thr2790Ser	p.T2790S	ENST00000380152		2790	Acc/Tcc	19/27	0.374605135903809	1	FACETS	0.833	0.791	0.876	0.833	0.791	0.876	INDETERMINATE	1	TRUE	0	0.700553705103243	1		482	670	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032280	10032280	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	312	507	1	ENST00000330684.3:c.543G>T	p.Arg181Ser	p.R181S	ENST00000330684	NM_001134407.1	181	agG/agT	3/13	0.374605135903809	1	FACETS	0.83	0.789	0.872	0.83	0.789	0.872	INDETERMINATE	1	TRUE	0	0.700553705103243	1		508	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397516435	NA	P-0039656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	296	595	0	ENST00000269305.4:c.586C>G	p.Arg196Gly	p.R196G	ENST00000269305	NM_001126112.2	196	Cga/Gga	6/11	0.700553705103243	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.700553705103243	1		595	531	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533379	29533379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555611606	NA	P-0039656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	130	188	0	ENST00000356175.3:c.1382G>A	p.Arg461Gln	p.R461Q	ENST00000356175	NM_000267.3	461	cGa/cAa	12/57	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.700553705103243	2		188	365	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576058	29576058	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	305	442	0	ENST00000356175.3:c.4031A>T	p.Glu1344Val	p.E1344V	ENST00000356175	NM_000267.3	1344	gAa/gTa	30/57	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.700553705103243	2		442	805	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031789	11031789	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	275	636	2	ENST00000327064.4:c.1601A>T	p.Asn534Ile	p.N534I	ENST00000327064	NM_199141.1	534	aAc/aTc	14/16	1	2	FACETS	0.955	0.9	1	0.955	0.9	1	CLONAL	1	TRUE	1	0.700553705103243	2		638	822	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051666	13051666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318523776	NA	P-0039656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	254	510	0	ENST00000316448.5:c.925G>A	p.Asp309Asn	p.D309N	ENST00000316448	NM_004343.3	309	Gat/Aat	7/9	1	2	FACETS	0.944	0.887	1	0.944	0.887	1	CLONAL	1	TRUE	1	0.700553705103243	2		510	768	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943499	17943499	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	289	569	1	ENST00000458235.1:c.2509G>C	p.Glu837Gln	p.E837Q	ENST00000458235	NM_000215.3	837	Gag/Cag	19/24	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.700553705103243	2		570	821	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038071	128038071	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	96	376	0	ENST00000285398.2:c.1479G>A	p.Trp493Ter	p.W493*	ENST00000285398	NM_000122.1	493	tgG/tgA	9/15	0.38894843043376	1	FACETS	0.355	0.317	0.395	0.355	0.317	0.395	INDETERMINATE	1	TRUE	0	0.700553705103243	1		376	502	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499424	89499424	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	226	379	0	ENST00000336596.2:c.2594G>C	p.Arg865Thr	p.R865T	ENST00000336596	NM_005233.5	865	aGg/aCg	15/17	0.700553705103243	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.700553705103243	1		379	410	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138431121	138431121	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	150	380	0	ENST00000289153.2:c.1328C>G	p.Thr443Arg	p.T443R	ENST00000289153	NM_006219.2	443	aCg/aGg	8/22	1	2	FACETS	0.632	0.579	0.687	0.632	0.579	0.687	SUBCLONAL	1	TRUE	1	0.700553705103243	2		380	678	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549435	187549435	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs758123411	NA	P-0039656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	335	529	0	ENST00000441802.2:c.4683G>T	p.Trp1561Cys	p.W1561C	ENST00000441802	NM_005245.3	1561	tgG/tgT	9/27	0.700553705103243	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.700553705103243	1		529	565	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670549	30670549	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1262512315	NA	P-0039656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	239	471	0	ENST00000376406.3:c.5971C>T	p.Arg1991Trp	p.R1991W	ENST00000376406	NM_014641.2	1991	Cgg/Tgg	13/15	1	2	FACETS	0.985	0.924	1	0.985	0.924	1	CLONAL	1	TRUE	1	0.700553705103243	2		471	693	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170117	32170117	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	287	737	0	ENST00000375023.3:c.3491G>T	p.Ser1164Ile	p.S1164I	ENST00000375023	NM_004557.3	1164	aGc/aTc	21/30	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.700553705103243	2		737	813	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409910	63409910	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	116	422	0	ENST00000330258.3:c.3257A>T	p.Gln1086Leu	p.Q1086L	ENST00000330258	NM_152424.3	1086	cAg/cTg	2/2	0.39926131253359	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.700553705103243	0		422	380	SUCCESS
AR	367	MSKCC	GRCh37	X	66863151	66863151	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	134	542	0	ENST00000374690.3:c.1670A>G	p.Gln557Arg	p.Q557R	ENST00000374690	NM_000044.3	557	cAg/cGg	2/8	0.39926131253359	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.700553705103243	0		542	513	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344013	70344013	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	165	578	0	ENST00000374080.3:c.1749C>A	p.Asp583Glu	p.D583E	ENST00000374080		583	gaC/gaA	13/45	0.39926131253359	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.700553705103243	0		578	594	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348541	70348541	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	166	489	0	ENST00000374080.3:c.3448G>T	p.Ala1150Ser	p.A1150S	ENST00000374080		1150	Gct/Tct	24/45	0.39926131253359	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.700553705103243	0		489	542	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76949370	76949370	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	81	352	0	ENST00000373344.5:c.427G>T	p.Gly143Trp	p.G143W	ENST00000373344	NM_000489.3	143	Ggg/Tgg	6/35	0.39926131253359	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.700553705103243	0		352	365	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229223	123229223	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	92	267	0	ENST00000218089.9:c.3707C>A	p.Pro1236Gln	p.P1236Q	ENST00000218089	NM_001042749.1	1236	cCa/cAa	34/35	0.39926131253359	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.700553705103243	0		267	276	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0039657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	53	283	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		286	212	SUCCESS
APC	324	MSKCC	GRCh37	5	112174112	112174112	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	120	386	0	ENST00000257430.4:c.2821G>T	p.Glu941Ter	p.E941*	ENST00000257430	NM_000038.5	941	Gaa/Taa	16/16	1	2	FACETS	0.867	0.788	0.95	0.867	0.788	0.95	CLONAL	1	TRUE	1	0.595000900142109	2		386	465	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175481	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0039659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	130	380	0	ENST00000257430.4:c.4192_4193del	p.Arg1399PhefsTer9	p.R1399Ffs*9	ENST00000257430	NM_000038.5	1397	GAg/g	16/16	1	2	FACETS	0.958	0.876	1	0.958	0.876	1	CLONAL	1	TRUE	1	0.595000900142109	2		380	456	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532867	187532867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762890230	NA	P-0039659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	44	481	0	ENST00000441802.2:c.9526G>A	p.Glu3176Lys	p.E3176K	ENST00000441802	NM_005245.3	3176	Gaa/Aaa	14/27	0.372045306759124	1	FACETS	0.166	0.138	0.196	0.166	0.138	0.196	SUBCLONAL	1	TRUE	0	0.595000900142109	1		481	627	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857425	9857425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1268143219	NA	P-0039659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	175	645	0	ENST00000330684.3:c.3976G>A	p.Gly1326Ser	p.G1326S	ENST00000330684	NM_001134407.1	1326	Ggc/Agc	13/13	1	2	FACETS	0.967	0.895	1	0.967	0.895	1	CLONAL	1	TRUE	1	0.595000900142109	2		645	608	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382159	152382159	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	110	429	0	ENST00000206249.3:c.1269G>C	p.Glu423Asp	p.E423D	ENST00000206249	NM_000125.3	423	gaG/gaC	6/8	0.372045306759124	1	FACETS	0.506	0.457	0.558	0.506	0.457	0.558	SUBCLONAL	1	TRUE	0	0.595000900142109	1		429	513	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346139	152346139	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	377	587	0	ENST00000359321.1:c.431G>A	p.Cys144Tyr	p.C144Y	ENST00000359321	NM_005431.1	144	tGc/tAc	3/3	0.239744497601764	2	FACETS	0.861	0.824	0.898	0.861	0.824	0.898	INDETERMINATE	2	TRUE	0	0.595000900142109	2		587	736	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs760043106	NA	P-0039662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	13	653	0	ENST00000269305.4:c.584T>A	p.Ile195Asn	p.I195N	ENST00000269305	NM_001126112.2	195	aTc/aAc	6/11	1	2	FACETS	0.981	0.719	1	1	0.911	1	CLONAL	2	TRUE	1	0.228465057363835	2		653	58	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245994	46245994	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	16	347	0	ENST00000334344.6:c.4088A>T	p.Asp1363Val	p.D1363V	ENST00000334344	NM_152641.2	1363	gAt/gTt	15/21	0.199084605177087	3	FACETS	1	0.825	1	1	0.825	1	CLONAL	2	TRUE	1	0.228465057363835	3		347	70	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112007	115112007	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	77	668	0	ENST00000257566.3:c.1733T>C	p.Leu578Pro	p.L578P	ENST00000257566	NM_016569.3	578	cTg/cCg	7/8	0.199084605177087	3	FACETS	1	0.898	1	1	0.898	1	CLONAL	2	TRUE	1	0.228465057363835	3		668	369	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678589	88678589	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	11	388	0	ENST00000360948.2:c.947G>C	p.Arg316Pro	p.R316P	ENST00000360948	NM_001012338.2	316	cGc/cCc	9/19	1	2	FACETS	0.845	0.598	1	1	0.88	1	CLONAL	2	TRUE	1	0.228465057363835	2		388	57	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645219	67645219	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	21	673	0	ENST00000264010.4:c.484G>A	p.Glu162Lys	p.E162K	ENST00000264010	NM_006565.3	162	Gaa/Aaa	3/12	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.228465057363835	2		673	127	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013741	170013741	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	11	377	0	ENST00000295797.4:c.1460T>G	p.Val487Gly	p.V487G	ENST00000295797	NM_002740.5	487	gTa/gGa	15/18	0.228465057363835	9	FACETS	0.788	0.544	1	0.098	0.068	0.137	CLONAL	1	TRUE	1	0.228465057363835	9		377	220	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157520007	157520007	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	18	600	0	ENST00000346085.5:c.4076G>C	p.Gly1359Ala	p.G1359A	ENST00000346085	NM_020732.3	1359	gGa/gCa	17/20	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.228465057363835	2		600	119	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0039675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	158	503	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.763	0.703	0.824	1	0.989	1	SUBCLONAL	2	TRUE	1	0.39	2		503	531	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740610	58740611	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	29	542	0	ENST00000305921.3:c.1516dup	p.Thr506AsnfsTer22	p.T506Nfs*22	ENST00000305921	NM_003620.3	505	-/A	6/6	1	2	FACETS	0.444	0.357	0.543	0.444	0.357	0.543	SUBCLONAL	1	TRUE	1	0.39	2		542	335	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884491	151884491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	101	319	1	ENST00000262189.6:c.4864G>A	p.Val1622Met	p.V1622M	ENST00000262189	NM_170606.2	1622	Gtg/Atg	33/59	1	2	FACETS	0.794	0.718	0.874	1	0.985	1	SUBCLONAL	2	TRUE	1	0.39	2		320	326	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0039676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	168	592	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.216147604054613	3	FACETS	1	0.988	1	0.693	0.639	0.748	INDETERMINATE	1	TRUE	1	0.449466523052338	3		592	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574007	7574011	+	frameshift_variant	Frame_Shift_Del	DEL	CATCT	CATCT	-	novel	NA	P-0039676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	247	733	0	ENST00000269305.4:c.1016_1020del	p.Glu339ValfsTer6	p.E339Vfs*6	ENST00000269305	NM_001126112.2	339	gAGATG/g	10/11	0.449466523052338	2	FACETS	0.908	0.856	0.961	0.908	0.856	0.961	CLONAL	2	TRUE	0	0.449466523052338	2		733	605	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416562	29416562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500213	NA	P-0039676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	69	558	0	ENST00000389048.3:c.4391G>A	p.Arg1464Gln	p.R1464Q	ENST00000389048	NM_004304.4	1464	cGa/cAa	29/29	0.449466523052338	4	FACETS	0.654	0.57	0.746	0.218	0.19	0.249	SUBCLONAL	1	TRUE	1	0.449466523052338	4		558	680	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142482	119142482	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs776426602	NA	P-0039677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	78	436	0	ENST00000264033.4:c.481A>C	p.Met161Leu	p.M161L	ENST00000264033	NM_005188.3	161	Atg/Ctg	3/16	1	2	FACETS	0.681	0.599	0.768	0.681	0.599	0.768	SUBCLONAL	1	FALSE	1	0.439027722523469	2		436	522	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370236	40370236	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs761761205	NA	P-0039679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	289	702	9	ENST00000293328.3:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000293328	NM_012448.3	368	Cag/ag	9/19	1	2	FACETS	0.694	0.655	0.734	0.694	0.655	0.734	SUBCLONAL	1	TRUE	1	0.966156784407221	2		711	862	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574000	7574000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	496	613	0	ENST00000269305.4:c.1027G>T	p.Glu343Ter	p.E343*	ENST00000269305	NM_001126112.2	343	Gag/Tag	10/11	0.966156784407221	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.966156784407221	1		613	517	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484339	8484339	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	202	385	0	ENST00000356435.5:c.3193G>T	p.Gly1065Cys	p.G1065C	ENST00000356435		1065	Ggc/Tgc	19/35	0.400166644976757	1	FACETS	0.457	0.428	0.486	0.457	0.428	0.486	INDETERMINATE	1	TRUE	0	0.966156784407221	1		385	473	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027133	49027133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853292	NA	P-0039679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	147	264	0	ENST00000267163.4:c.1700C>T	p.Ser567Leu	p.S567L	ENST00000267163	NM_000321.2	567	tCa/tTa	18/27	0.966156784407221	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.966156784407221	1		264	155	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470536	25470536	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1204478457	NA	P-0039679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	493	651	0	ENST00000264709.3:c.938G>A	p.Trp313Ter	p.W313*	ENST00000264709	NM_175629.2	313	tGg/tAg	8/23	0.400166644976757	1	FACETS	0.571	0.55	0.592	0.571	0.55	0.592	INDETERMINATE	1	TRUE	0	0.966156784407221	1		651	924	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023723	27023723	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	36	266	0	ENST00000324856.7:c.829G>C	p.Gly277Arg	p.G277R	ENST00000324856	NM_006015.4	277	Ggc/Cgc	1/20	1	2	FACETS	0.14	0.114	0.168	0.14	0.114	0.168	SUBCLONAL	1	TRUE	1	0.966156784407221	2		266	534	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114917781	114917781	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	178	285	0	ENST00000543371.1:c.1271G>A	p.Gly424Glu	p.G424E	ENST00000543371	NM_001198531.1	424	gGa/gAa	12/14	0.966156784407221	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.966156784407221	1		285	186	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857694	9857694	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	211	438	0	ENST00000330684.3:c.3707G>C	p.Cys1236Ser	p.C1236S	ENST00000330684	NM_001134407.1	1236	tGc/tCc	13/13	0.476905782297843	1	FACETS	0.604	0.571	0.636	0.604	0.571	0.636	INDETERMINATE	1	TRUE	0	0.966156784407221	1		438	374	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753887	42753887	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs778205341	NA	P-0039679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	525	636	0	ENST00000222329.4:c.377G>T	p.Gly126Val	p.G126V	ENST00000222329	NM_006494.2	126	gGt/gTt	4/4	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.966156784407221	2		636	1026	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293136	212293136	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	139	288	0	ENST00000342788.4:c.2716T>C	p.Tyr906His	p.Y906H	ENST00000342788	NM_005235.2	906	Tat/Cat	22/28	0.400166644976757	1	FACETS	0.412	0.38	0.445	0.412	0.38	0.445	INDETERMINATE	1	TRUE	0	0.966156784407221	1		288	361	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368540	225368540	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0039679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	115	226	0	ENST00000264414.4:c.1207-1G>C		p.X403_splice	ENST00000264414	NM_003590.4	403			0.400166644976757	1	FACETS	0.559	0.516	0.602	0.559	0.516	0.602	INDETERMINATE	1	TRUE	0	0.966156784407221	1		226	220	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385255	41385255	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	362	561	0	ENST00000373198.4:c.706G>A	p.Ala236Thr	p.A236T	ENST00000373198	NM_133170.3	236	Gcc/Acc	6/32	1	2	FACETS	0.996	0.952	1	0.996	0.952	1	CLONAL	1	TRUE	1	0.966156784407221	2		561	752	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439213	52439213	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	533	672	0	ENST00000460680.1:c.1029del	p.Asn344MetfsTer18	p.N344Mfs*18	ENST00000460680	NM_004656.3	343	ctC/ct	11/17	0.966156784407221	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.966156784407221	1		672	567	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169940465	169940465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	257	399	0	ENST00000295797.4:c.8C>T	p.Thr3Ile	p.T3I	ENST00000295797	NM_002740.5	3	aCc/aTc	1/18	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.966156784407221	2		399	499	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099114	157099114	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	132	135	0	ENST00000346085.5:c.51G>C	p.Lys17Asn	p.K17N	ENST00000346085	NM_020732.3	17	aaG/aaC	1/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.966156784407221	2		135	269	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282086	38282086	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs767977802	NA	P-0039679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	432	788	0	ENST00000425967.3:c.970A>G	p.Ile324Val	p.I324V	ENST00000425967	NM_001174067.1	324	Atc/Gtc	8/19	0.476905782297843	1	FACETS	0.533	0.511	0.555	0.533	0.511	0.555	INDETERMINATE	1	TRUE	0	0.966156784407221	1		788	867	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412715	63412715	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	22	614	0	ENST00000330258.3:c.452C>G	p.Thr151Arg	p.T151R	ENST00000330258	NM_152424.3	151	aCa/aGa	2/2	0.890255744044954	1	FACETS	0.08	0.061	0.101	0.08	0.061	0.101	SUBCLONAL	1	TRUE	0	0.966156784407221	1		614	295	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413127	63413127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	46	639	1	ENST00000330258.3:c.40G>A	p.Ala14Thr	p.A14T	ENST00000330258	NM_152424.3	14	Gct/Act	2/2	0.890255744044954	1	FACETS	0.111	0.093	0.131	0.111	0.093	0.131	SUBCLONAL	1	TRUE	0	0.966156784407221	1		640	442	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348204	70348204	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	419	664	0	ENST00000374080.3:c.3268G>T	p.Ala1090Ser	p.A1090S	ENST00000374080		1090	Gca/Tca	23/45	0.890255744044954	1	FACETS	0.981	0.963	0.997	0.981	0.963	0.997	CLONAL	1	TRUE	0	0.966156784407221	1		664	457	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829760	76829760	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	38	510	0	ENST00000373344.5:c.6281C>A	p.Ser2094Ter	p.S2094*	ENST00000373344	NM_000489.3	2094	tCa/tAa	28/35	0.890255744044954	1	FACETS	0.099	0.081	0.118	0.099	0.081	0.118	SUBCLONAL	1	TRUE	0	0.966156784407221	1		510	412	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0039680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	434	370	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.520013907997263	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.520013907997263	3		370	662	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547874	41547874	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0039680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	123	453	0	ENST00000263253.7:c.2855C>G	p.Ser952Ter	p.S952*	ENST00000263253	NM_001429.3	952	tCa/tGa	15/31	0.491406747156999	2	FACETS	0.967	0.88	1	0.484	0.44	0.53	CLONAL	1	TRUE	0	0.520013907997263	2		453	489	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36024580	36024580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	193	678	0	ENST00000358208.4:c.569C>T	p.Ser190Leu	p.S190L	ENST00000358208		190	tCa/tTa	6/12	0.44647719788378	3	FACETS	1	0.966	1	0.537	0.497	0.578	CLONAL	1	TRUE	1	0.520013907997263	3		678	871	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374298	138374298	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	143	580	0	ENST00000289153.2:c.3146T>G	p.Leu1049Arg	p.L1049R	ENST00000289153	NM_006219.2	1049	cTc/cGc	22/22	1	2	FACETS	0.866	0.792	0.943	0.866	0.792	0.943	CLONAL	1	TRUE	1	0.520013907997263	2		580	635	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056617	26056617	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs751385999	NA	P-0039680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	60	273	0	ENST00000343677.2:c.40C>G	p.Pro14Ala	p.P14A	ENST00000343677	NM_005319.3	14	Cct/Gct	1/1	1	2	FACETS	0.861	0.749	0.98	0.861	0.749	0.98	CLONAL	1	TRUE	1	0.520013907997263	2		273	268	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216664	36216664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558770050	NA	P-0039680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	161	661	4	ENST00000222270.7:c.3830C>T	p.Pro1277Leu	p.P1277L	ENST00000222270	NM_014727.1	1277	cCg/cTg	13/37	1	2	FACETS	0.962	0.885	1	0.962	0.885	1	CLONAL	1	TRUE	1	0.520013907997263	2		665	644	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28586412	28586412	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	132	471	0	ENST00000253063.3:c.54C>G	p.Phe18Leu	p.F18L	ENST00000253063	NM_031459.4	18	ttC/ttG	1/10	1	2	FACETS	0.978	0.893	1	0.978	0.893	1	CLONAL	1	TRUE	1	0.520013907997263	2		471	519	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834168	156834168	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	185	701	0	ENST00000524377.1:c.235C>G	p.Leu79Val	p.L79V	ENST00000524377	NM_002529.3	79	Ctg/Gtg	2/17	0.44647719788378	3	FACETS	0.973	0.899	1	0.487	0.449	0.526	CLONAL	1	TRUE	1	0.520013907997263	3		701	921	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552603	18552603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	125	327	0	ENST00000266497.5:c.2014G>A	p.Glu672Lys	p.E672K	ENST00000266497		672	Gaa/Aaa	14/31	0.520013907997263	3	FACETS	1	0.973	1	0.395	0.359	0.433	CLONAL	1	TRUE	0	0.520013907997263	3		327	511	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217824	7217824	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	180	536	0	ENST00000380728.2:c.187G>C	p.Glu63Gln	p.E63Q	ENST00000380728		63	Gag/Cag	3/11	1	2	FACETS	0.891	0.823	0.961	0.891	0.823	0.961	CLONAL	1	TRUE	1	0.520013907997263	2		536	777	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246215	41246215	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs80356915	NA	P-0039680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	125	433	0	ENST00000357654.3:c.1333G>C	p.Glu445Gln	p.E445Q	ENST00000357654	NM_007294.3	445	Gaa/Caa	10/23	1	2	FACETS	0.941	0.856	1	0.941	0.856	1	CLONAL	1	TRUE	1	0.520013907997263	2		433	511	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41247890	41247890	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	115	454	0	ENST00000357654.3:c.643G>T	p.Glu215Ter	p.E215*	ENST00000357654	NM_007294.3	215	Gaa/Taa	9/23	1	2	FACETS	0.904	0.819	0.994	0.904	0.819	0.994	CLONAL	1	TRUE	1	0.520013907997263	2		454	489	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250158	39250158	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	172	591	0	ENST00000402219.2:c.1411T>C	p.Cys471Arg	p.C471R	ENST00000402219	NM_005633.3	471	Tgt/Cgt	10/23	0.520013907997263	2	FACETS	1	0.95	1	0.518	0.479	0.559	CLONAL	1	TRUE	0	0.520013907997263	2		591	638	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39690058	39690058	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	56	207	0	ENST00000361337.2:c.83A>G	p.His28Arg	p.H28R	ENST00000361337	NM_003286.2	28	cAc/cGc	3/21	0.44647719788378	3	FACETS	0.787	0.677	0.905	0.393	0.338	0.453	CLONAL	1	TRUE	1	0.520013907997263	3		207	345	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39746907	39746907	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	111	344	0	ENST00000361337.2:c.1921G>A	p.Glu641Lys	p.E641K	ENST00000361337	NM_003286.2	641	Gag/Aag	18/21	0.44647719788378	3	FACETS	1	0.921	1	0.511	0.461	0.564	CLONAL	1	TRUE	1	0.520013907997263	3		344	526	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551011	41551011	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	97	380	0	ENST00000263253.7:c.3155A>C	p.Glu1052Ala	p.E1052A	ENST00000263253	NM_001429.3	1052	gAa/gCa	17/31	0.491406747156999	2	FACETS	0.876	0.786	0.97	0.438	0.393	0.485	CLONAL	1	TRUE	0	0.520013907997263	2		380	426	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551118	41551118	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0039680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	123	377	0	ENST00000263253.7:c.3261+1G>A		p.X1087_splice	ENST00000263253	NM_001429.3	1087			0.491406747156999	2	FACETS	0.876	0.796	0.96	0.438	0.398	0.48	CLONAL	1	TRUE	0	0.520013907997263	2		377	540	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927388	178927388	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	93	261	0	ENST00000263967.3:c.1151A>G	p.Asn384Ser	p.N384S	ENST00000263967	NM_006218.2	384	aAt/aGt	7/21	1	2	FACETS	0.985	0.884	1	0.985	0.884	1	CLONAL	1	TRUE	1	0.520013907997263	2		261	363	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961036	55961036	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	129	598	0	ENST00000263923.4:c.2904T>G	p.Ser968Arg	p.S968R	ENST00000263923	NM_002253.2	968	agT/agG	21/30	1	2	FACETS	0.799	0.726	0.875	0.799	0.726	0.875	SUBCLONAL	1	TRUE	1	0.520013907997263	2		598	621	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967461	38967461	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	113	345	0	ENST00000357387.3:c.1129C>G	p.Leu377Val	p.L377V	ENST00000357387	NM_152756.3	377	Ctt/Gtt	13/38	0.507781956479732	4	FACETS	0.912	0.822	1	0.304	0.274	0.336	CLONAL	1	TRUE	1	0.520013907997263	4		345	724	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80171652	80171652	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	110	446	0	ENST00000265081.6:c.3385G>A	p.Glu1129Lys	p.E1129K	ENST00000265081	NM_002439.4	1129	Gaa/Aaa	24/24	1	2	FACETS	0.815	0.735	0.899	0.815	0.735	0.899	CLONAL	1	TRUE	1	0.520013907997263	2		446	519	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505081	149505081	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	132	609	0	ENST00000261799.4:c.1734G>C	p.Glu578Asp	p.E578D	ENST00000261799	NM_002609.3	578	gaG/gaC	12/23	1	2	FACETS	0.886	0.808	0.968	0.886	0.808	0.968	CLONAL	1	TRUE	1	0.520013907997263	2		609	573	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016339	150016339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751789340	NA	P-0039680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	114	371	0	ENST00000253339.5:c.367C>T	p.Leu123Phe	p.L123F	ENST00000253339		123	Ctt/Ttt	2/7	1	2	FACETS	0.939	0.85	1	0.939	0.85	1	CLONAL	1	TRUE	1	0.520013907997263	2		371	467	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527871	157527871	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	116	413	0	ENST00000346085.5:c.5596G>A	p.Glu1866Lys	p.E1866K	ENST00000346085	NM_020732.3	1866	Gaa/Aaa	20/20	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.520013907997263	2		413	443	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151927394	151927394	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	18	49	0	ENST00000262189.6:c.2782G>C	p.Asp928His	p.D928H	ENST00000262189	NM_170606.2	928	Gat/Cat	17/59	0.511296942015905	2	FACETS	1	0.809	1	0.524	0.406	0.655	CLONAL	1	TRUE	0	0.520013907997263	2		49	66	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218592	98218592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	139	484	0	ENST00000331920.6:c.3272G>T	p.Gly1091Val	p.G1091V	ENST00000331920	NM_000264.3	1091	gGc/gTc	19/24	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.520013907997263	2		484	485	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248148	110248148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	180	553	0	ENST00000374672.4:c.1324G>A	p.Glu442Lys	p.E442K	ENST00000374672	NM_004235.4	442	Gaa/Aaa	5/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.520013907997263	2		553	604	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340908	70340908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1261616099	NA	P-0039680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	116	645	0	ENST00000374080.3:c.641G>A	p.Gly214Asp	p.G214D	ENST00000374080		214	gGc/gAc	5/45	0.520013907997263	3	FACETS	0.696	0.627	0.769	0.348	0.313	0.385	SUBCLONAL	1	TRUE	1	0.520013907997263	3		645	808	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123156514	123156514	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	80	259	0	ENST00000218089.9:c.37C>G	p.Leu13Val	p.L13V	ENST00000218089	NM_001042749.1	13	Cta/Gta	3/35	0.520013907997263	3	FACETS	0.858	0.758	0.964	0.429	0.379	0.482	CLONAL	1	TRUE	1	0.520013907997263	3		259	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0039681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	294	764	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.282799256374839	3	FACETS	0.896	0.85	0.942			1	CLONAL	3	TRUE	NA	0.404643263535101	3		765	650	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870969	12870970	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	TCTG	novel	NA	P-0039681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	109	371	0	ENST00000228872.4:c.196_197insTCTG	p.Asn66IlefsTer2	p.N66Ifs*2	ENST00000228872	NM_004064.3	66	aat/aTCTGat	1/3	0.325460546072779	4	FACETS	1	0.978	1	0.66	0.595	0.73	CLONAL	1	TRUE	2	0.404643263535101	4		371	573	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996813	73996813	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	81	339	0	ENST00000318443.5:c.1369G>A	p.Gly457Arg	p.G457R	ENST00000318443	NM_001024736.1	457	Ggg/Agg	6/10	0.240092892812371	0	FACETS	0.66	0.586	0.739			1	INDETERMINATE	1	TRUE	0	0.404643263535101	0		339	361	SUCCESS
APC	324	MSKCC	GRCh37	5	112173779	112173779	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1554084209	NA	P-0039681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	12	307	0	ENST00000257430.4:c.2488G>C	p.Val830Leu	p.V830L	ENST00000257430	NM_000038.5	830	Gtg/Ctg	16/16	0.307824354880471	1	FACETS	0.532	0.378	0.715	0.532	0.378	0.715	SUBCLONAL	1	TRUE	0	0.404643263535101	1		307	89	SUCCESS
APC	324	MSKCC	GRCh37	5	112175189	112175204	+	frameshift_variant	Frame_Shift_Del	DEL	AATACCCTGCAAATAG	AATACCCTGCAAATAG	-	novel	NA	P-0039681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	12	179	0	ENST00000257430.4:c.3898_3913del	p.Asn1300GlnfsTer3	p.N1300Qfs*3	ENST00000257430	NM_000038.5	1300	AATACCCTGCAAATAGca/ca	16/16	0.307824354880471	1	FACETS	0.739	0.531	0.983	0.739	0.531	0.983	CLONAL	1	TRUE	0	0.404643263535101	1		179	64	SUCCESS
APC	324	MSKCC	GRCh37	5	112173804	112173806	+	frameshift_variant	Frame_Shift_Del	DEL	GAG	GAG	A	novel	NA	P-0039681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	14	303	0	ENST00000257430.4:c.2513_2515delinsA	p.Arg838LysfsTer5	p.R838Kfs*5	ENST00000257430	NM_000038.5	838	aGAGga/aAga	16/16	0.307824354880471	1	FACETS	0.627	0.46	0.822	0.627	0.46	0.822	SUBCLONAL	1	TRUE	0	0.404643263535101	1		303	88	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	105	236	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.758073097712745	2		236	265	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0039682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	136	326	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.922	0.848	0.999	0.922	0.848	0.999	CLONAL	1	TRUE	1	0.758073097712745	2		326	389	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141567	11141567	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	211	644	0	ENST00000358026.2:c.3544C>T	p.Gln1182Ter	p.Q1182*	ENST00000358026	NM_001128849.1	1182	Cag/Tag	25/36	1	2	FACETS	0.973	0.911	1	0.973	0.911	1	CLONAL	1	TRUE	1	0.758073097712745	2		644	572	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696431	47696431	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519969	NA	P-0039689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	33	587	0	ENST00000347630.2:c.392G>C	p.Trp131Ser	p.W131S	ENST00000347630	NM_001007230.1	131	tGg/tCg	6/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		587	446	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060691	38060692	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	ACCT	novel	NA	P-0039689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	82	745	0	ENST00000250448.2:c.1297_1298insAGGT	p.Leu433Ter	p.L433*	ENST00000250448	NM_004496.3	433	ttg/tAGGTtg	2/2	0.0916484829864397	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		745	685	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0039690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	12	399	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	0.19	0.132	0.261	0.19	0.132	0.261	SUBCLONAL	1	TRUE	1	0.223160912520229	2		399	567	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553483	29553483	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs758691069	NA	P-0039690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	99	519	0	ENST00000356175.3:c.2032C>A	p.Pro678Thr	p.P678T	ENST00000356175	NM_000267.3	678	Ccg/Acg	18/57	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.223160912520229	2		519	783	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828303	72828303	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs770675303	NA	P-0039690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	80	497	0	ENST00000268489.5:c.8278A>G	p.Met2760Val	p.M2760V	ENST00000268489	NM_006885.3	2760	Atg/Gtg	9/10	1	2	FACETS	0.946	0.832	1	0.946	0.832	1	CLONAL	1	TRUE	1	0.223160912520229	2		497	758	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113368	209113368	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	35	267	0	ENST00000345146.2:c.139G>A	p.Glu47Lys	p.E47K	ENST00000345146	NM_005896.2	47	Gag/Aag	4/10	1	2	FACETS	0.752	0.617	0.904	0.752	0.617	0.904	CLONAL	1	TRUE	1	0.223160912520229	2		267	417	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265016	46265016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568744962	NA	P-0039690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	41	490	0	ENST00000371998.3:c.1886C>T	p.Ser629Phe	p.S629F	ENST00000371998		629	tCt/tTt	12/23	1	2	FACETS	0.562	0.467	0.668	0.562	0.467	0.668	SUBCLONAL	1	TRUE	1	0.223160912520229	2		490	654	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162474	47162474	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	55	430	0	ENST00000409792.3:c.3652C>G	p.Gln1218Glu	p.Q1218E	ENST00000409792	NM_014159.6	1218	Caa/Gaa	3/21	1	2	FACETS	0.965	0.826	1	0.965	0.826	1	CLONAL	1	TRUE	1	0.223160912520229	2		430	511	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519422	137519422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	23	299	0	ENST00000367739.4:c.1216G>A	p.Asp406Asn	p.D406N	ENST00000367739	NM_000416.2	406	Gat/Aat	7/7	1	2	FACETS	0.538	0.419	0.676	0.538	0.419	0.676	SUBCLONAL	1	TRUE	1	0.223160912520229	2		299	383	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172230	38172230	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	70	399	0	ENST00000317025.8:c.2177A>T	p.His726Leu	p.H726L	ENST00000317025	NM_023034.1	726	cAc/cTc	12/24	0.223160912520229	5	FACETS	0.903	0.786	1			1	CLONAL	1	TRUE	NA	0.223160912520229	5		399	927	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141582964	141582964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	95	699	0	ENST00000220592.5:c.283G>A	p.Asp95Asn	p.D95N	ENST00000220592	NM_012154.3	95	Gac/Aac	3/19	1	2	FACETS	0.784	0.696	0.878	0.784	0.696	0.878	SUBCLONAL	1	TRUE	1	0.223160912520229	2		699	1086	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579417	7579426	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGGGGGCT	GGAGGGGGCT	-	novel	NA	P-0039690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	63	605	0	ENST00000269305.4:c.261_270del	p.Ala88GlyfsTer32	p.A88Gfs*32	ENST00000269305	NM_001126112.2	87	ccAGCCCCCTCC/cc	4/11	1	2	FACETS	0.786	0.679	0.903	0.786	0.679	0.903	CLONAL	1	TRUE	1	0.223160912520229	2		605	718	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	154	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.506499879259237	1	FACETS	0.756	0.71	0.802	0.756	0.71	0.802	INDETERMINATE	1	TRUE	0	0.882373482146967	1		371	258	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0039695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	531	546	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.882373482146967	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.882373482146967	1		547	631	SUCCESS
APC	324	MSKCC	GRCh37	5	112175344	112175344	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	237	277	0	ENST00000257430.4:c.4053del	p.Val1352LeufsTer63	p.V1352Lfs*63	ENST00000257430	NM_000038.5	1351	gcT/gc	16/16	0.506499879259237	1	FACETS	0.718	0.681	0.755	0.718	0.681	0.755	INDETERMINATE	1	TRUE	0	0.882373482146967	1		277	418	SUCCESS
APC	324	MSKCC	GRCh37	5	112175985	112175985	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	110	259	0	ENST00000257430.4:c.4694del	p.Asp1565ValfsTer11	p.D1565Vfs*11	ENST00000257430	NM_000038.5	1565	gAt/gt	16/16	0.506499879259237	1	FACETS	0.382	0.346	0.419	0.382	0.346	0.419	INDETERMINATE	1	TRUE	0	0.882373482146967	1		259	365	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111499	8111500	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	104	813	0	ENST00000346208.3:c.987dup	p.Arg330GlufsTer22	p.R330Efs*22	ENST00000346208		329	agg/aGgg	5/6	1	2	FACETS	0.827	0.748	0.909	0.827	0.748	0.909	CLONAL	1	TRUE	1	0.712542706443477	2		813	353	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	9	1185	1	ENST00000281043.3:c.131C>A	p.Pro44His	p.P44H	ENST00000281043	NM_005378.4	44	cCc/cAc	2/3	1	2	FACETS	0.092	0.06	0.133	0.092	0.06	0.133	SUBCLONAL	1	TRUE	1	0.712542706443477	2		1186	274	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	37	236	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.847	0.697	1	0.847	0.697	1	CLONAL	1	TRUE	1	0.14	2		236	624	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0039699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	67	326	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	0.14	2		326	741	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937619	17937619	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	62	941	0	ENST00000458235.1:c.3308G>T	p.Arg1103Leu	p.R1103L	ENST00000458235	NM_000215.3	1103	cGg/cTg	24/24	1	2	FACETS	0.765	0.658	0.882	0.765	0.658	0.882	SUBCLONAL	1	TRUE	1	0.14	2		941	1158	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163832	152163832	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	52	571	0	ENST00000206249.3:c.553T>A	p.Cys185Ser	p.C185S	ENST00000206249	NM_000125.3	185	Tgt/Agt	2/8	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.14	2		571	694	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0039700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	97	669	0	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	0.241196998027077	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.241196998027077	1		669	601	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873020	136873020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147198552	NA	P-0039700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	81	512	0	ENST00000241393.3:c.478G>A	p.Val160Ile	p.V160I	ENST00000241393	NM_003467.2	160	Gtc/Atc	2/2	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.241196998027077	2		512	667	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280380	1280380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112614087	NA	P-0039700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	127	973	1	ENST00000310581.5:c.1843G>A	p.Ala615Thr	p.A615T	ENST00000310581	NM_198253.2	615	Gcc/Acc	4/16	0.163605968758084	4	FACETS	1	0.923	1	0.341	0.308	0.377	CLONAL	1	TRUE	1	0.241196998027077	4		974	1276	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720806	89720806	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167682	NA	P-0039700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	31	423	0	ENST00000371953.3:c.959del	p.Leu320Ter	p.L320*	ENST00000371953	NM_000314.4	319	acT/ac	8/9	0.241196998027077	1	FACETS	0.502	0.406	0.612	0.502	0.406	0.612	SUBCLONAL	1	TRUE	0	0.241196998027077	1		423	450	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	338208	338208	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	86	842	0	ENST00000262320.3:c.2503del	p.Val835TrpfsTer103	p.V835Wfs*103	ENST00000262320	NM_003502.3	835	Gtg/tg	11/11	0.241196998027077	1	FACETS	0.685	0.605	0.772	0.685	0.605	0.772	SUBCLONAL	1	TRUE	0	0.241196998027077	1		842	915	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137733	64137733	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	103	1093	0	ENST00000334205.4:c.1834G>C	p.Ala612Pro	p.A612P	ENST00000334205	NM_003942.2	612	Gcc/Ccc	15/17	1	2	FACETS	0.793	0.708	0.884	0.793	0.708	0.884	SUBCLONAL	1	TRUE	1	0.241196998027077	2		1093	1077	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579583	7579583	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	103	748	0	ENST00000269305.4:c.104del	p.Leu35CysfsTer9	p.L35Cfs*9	ENST00000269305	NM_001126112.2	35	tTg/tg	4/11	0.241196998027077	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.241196998027077	1		748	717	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131893077	131893077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	86	426	0	ENST00000265335.6:c.61G>A	p.Asp21Asn	p.D21N	ENST00000265335		21	Gat/Aat	1/25	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.241196998027077	2		426	537	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127916221	127916226	+	inframe_deletion	In_Frame_Del	DEL	GTATCT	GTATCT	-	novel	NA	P-0039700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	60	587	0	ENST00000373547.4:c.418_423del	p.Arg140_Tyr141del	p.R140_Y141del	ENST00000373547	NM_002721.4	140	AGATAC/-	5/7	0.231504805503403	2	FACETS	0.701	0.603	0.808	0.35	0.301	0.404	SUBCLONAL	1	TRUE	0	0.241196998027077	2		587	710	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039339	47039339	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	91	958	0	ENST00000377604.3:c.962C>A	p.Ala321Glu	p.A321E	ENST00000377604	NM_001204468.1	321	gCa/gAa	10/24	1	2	FACETS	0.73	0.646	0.819	0.73	0.646	0.819	SUBCLONAL	1	TRUE	1	0.241196998027077	2		958	1034	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0039714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	288	628	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	1	0.785585193302808	2		628	731	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	81	417	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.307964541977749	1	FACETS	0.765	0.675	0.861	0.765	0.675	0.861	SUBCLONAL	1	TRUE	0	0.307964541977749	1		417	582	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0039715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	70	393	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.307964541977749	1	FACETS	0.936	0.819	1	0.936	0.819	1	CLONAL	1	TRUE	0	0.307964541977749	1		393	411	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46740279	46740279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150315374	NA	P-0039715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	111	514	0	ENST00000371975.4:c.1759C>T	p.Arg587Trp	p.R587W	ENST00000371975	NM_003579.3	587	Cgg/Tgg	16/18	1	2	FACETS	0.914	0.821	1	0.914	0.821	1	CLONAL	1	TRUE	1	0.307964541977749	2		514	789	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578195	7578197	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0039715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	181	660	0	ENST00000269305.4:c.652_654del	p.Val218del	p.V218del	ENST00000269305	NM_001126112.2	218	GTG/-	6/11	0.307964541977749	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.307964541977749	1		660	946	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106539	27106539	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	159	711	0	ENST00000324856.7:c.6150G>A	p.Trp2050Ter	p.W2050*	ENST00000324856	NM_006015.4	2050	tgG/tgA	20/20	1	2	FACETS	0.899	0.823	0.98	0.899	0.823	0.98	CLONAL	1	TRUE	1	0.307964541977749	2		711	1148	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944471	40944471	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	248	636	0	ENST00000373198.4:c.2031G>T	p.Gln677His	p.Q677H	ENST00000373198	NM_133170.3	677	caG/caT	12/32	0.307964541977749	3	FACETS	0.971	0.909	1	0.971	0.909	1	CLONAL	2	TRUE	1	0.307964541977749	3		636	957	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0039716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	432	379	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.741218609577877	5	FACETS	1	0.972	1	0.684	0.653	0.715	CLONAL	2	TRUE	2	0.741218609577877	5		379	1200	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576857	7576857	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	252	566	0	ENST00000269305.4:c.989T>G	p.Leu330Arg	p.L330R	ENST00000269305	NM_001126112.2	330	cTt/cGt	9/11	0.534410789075396	1	FACETS	0.825	0.78	0.869	0.825	0.78	0.869	CLONAL	1	TRUE	0	0.741218609577877	1		566	519	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358946	81358946	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1246	77	619	1	ENST00000222390.5:c.1015A>T	p.Met339Leu	p.M339L	ENST00000222390	NM_000601.4	339	Atg/Ttg	8/18	0.741218609577877	5	FACETS	0.332	0.29	0.377	0.111	0.096	0.126	SUBCLONAL	1	TRUE	2	0.741218609577877	5		620	1323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0039727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	214	953	10	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.333286237837393	2	FACETS	0.986	0.923	1	0.986	0.923	1	CLONAL	2	TRUE	0	0.369603073412803	2		963	587	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206646650	206646650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553384304	NA	P-0039727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	102	703	2	ENST00000367120.3:c.80G>A	p.Arg27His	p.R27H	ENST00000367120	NM_014002.3	27	cGc/cAc	3/22	0.274675272987054	3	FACETS	0.928	0.83	1	0.464	0.415	0.516	CLONAL	1	TRUE	1	0.369603073412803	3		705	705	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023253	27023265	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCCGGCGGCGG	CGCCCGGCGGCGG	-	novel	NA	P-0039727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	35	218	0	ENST00000324856.7:c.361_373del	p.Pro121ValfsTer107	p.P121Vfs*107	ENST00000324856	NM_006015.4	120	cCGCCCGGCGGCGGc/cc	1/20	1	2	FACETS	0.796	0.657	0.95	0.796	0.657	0.95	CLONAL	1	TRUE	1	0.369603073412803	2		218	238	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933988	39933988	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	82	586	0	ENST00000378444.4:c.611A>C	p.Tyr204Ser	p.Y204S	ENST00000378444	NM_001123385.1	204	tAc/tCc	4/15	0.309520090744007	5	FACETS	0.776	0.683	0.876	0.259	0.227	0.292	SUBCLONAL	1	TRUE	2	0.369603073412803	5		586	889	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0039728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	485	628	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.869714894263655	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.869714894263655	2		629	531	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027244	49027244	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	135	56	0	ENST00000267163.4:c.1811A>G	p.Asp604Gly	p.D604G	ENST00000267163	NM_000321.2	604	gAt/gGt	18/27	0.869714894263655	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.869714894263655	2		56	152	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015081	27015081	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	574	390	0	ENST00000335756.4:c.183G>T	p.Leu61Phe	p.L61F	ENST00000335756	NM_001809.3	61	ttG/ttT	2/5	0.869714894263655	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.869714894263655	3		390	619	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428618	49428618	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	530	506	0	ENST00000301067.7:c.10332T>G	p.Ile3444Met	p.I3444M	ENST00000301067	NM_003482.3	3444	atT/atG	35/54	0.577127258677602	6	FACETS	0.986	0.949	1	0.986	0.949	1	CLONAL	3	TRUE	3	0.869714894263655	6		506	1129	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097218	11097218	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	597	741	0	ENST00000358026.2:c.709G>T	p.Gly237Cys	p.G237C	ENST00000358026	NM_001128849.1	237	Ggc/Tgc	4/36	0.527201818226382	5	FACETS	0.895	0.864	0.925	0.895	0.864	0.925	CLONAL	3	TRUE	2	0.869714894263655	5		741	1179	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743886	40743886	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	135	399	0	ENST00000373198.4:c.3109A>G	p.Thr1037Ala	p.T1037A	ENST00000373198	NM_133170.3	1037	Aca/Gca	23/32	NA	2	FACETS	0.518	0.473	0.566			1	INDETERMINATE	1	TRUE	NA	0.869714894263655	2		399	599	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230911	66230911	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	115	59	0	ENST00000273854.3:c.2060G>T	p.Gly687Val	p.G687V	ENST00000273854	NM_004439.5	687	gGt/gTt	12/18	0.869714894263655	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.869714894263655	2		59	126	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401876	139401876	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	630	723	1	ENST00000277541.6:c.3524A>T	p.Tyr1175Phe	p.Y1175F	ENST00000277541	NM_017617.3	1175	tAc/tTc	22/34	0.869714894263655	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	2	0.869714894263655	4		724	1277	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731176	162731176	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs775649903	NA	P-0039737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1550	234	418	0	ENST00000367921.3:c.1031G>C	p.Ser344Thr	p.S344T	ENST00000367921	NM_006182.2	344	aGt/aCt	9/18	0.664805359028056	10	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.664805359028056	10		418	1784	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32449606	32449606	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0039737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	360	739	1	ENST00000332351.3:c.770-2A>T		p.X257_splice	ENST00000332351	NM_024426.4	257			1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.664805359028056	2		740	729	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465976	69465987	+	inframe_deletion	In_Frame_Del	DEL	GAGGAGGAGGAA	GAGGAGGAGGAA	-	rs1565073771	NA	P-0039737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	145	932	0	ENST00000227507.2:c.825_836del	p.Glu277_Glu280del	p.E277_E280del	ENST00000227507	NM_053056.2	272	GAGGAGGAGGAA/-	5/5	0.337081274322854	3	FACETS	0.476	0.433	0.522	0.159	0.144	0.174	INDETERMINATE	1	TRUE	0	0.664805359028056	3		932	1220	SUCCESS
ATM	472	MSKCC	GRCh37	11	108128211	108128211	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs756522395	NA	P-0039737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	46	118	0	ENST00000278616.4:c.2254C>G	p.Leu752Val	p.L752V	ENST00000278616	NM_000051.3	752	Cta/Gta	15/63	0.428878166015108	3	FACETS	0.834	0.71	0.968	0.417	0.355	0.484	CLONAL	1	TRUE	1	0.664805359028056	3		118	221	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160468	108160468	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	79	268	1	ENST00000278616.4:c.4376G>T	p.Gly1459Val	p.G1459V	ENST00000278616	NM_000051.3	1459	gGa/gTa	29/63	0.428878166015108	3	FACETS	0.875	0.775	0.981	0.437	0.387	0.491	CLONAL	1	TRUE	1	0.664805359028056	3		269	362	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118355607	118355607	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	95	487	0	ENST00000534358.1:c.4249A>T	p.Met1417Leu	p.M1417L	ENST00000534358	NM_005933.3	1417	Atg/Ttg	10/36	0.428878166015108	3	FACETS	0.56	0.499	0.625	0.28	0.249	0.313	SUBCLONAL	1	TRUE	1	0.664805359028056	3		487	680	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107905	30107905	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	78	447	0	ENST00000331968.5:c.902G>T	p.Cys301Phe	p.C301F	ENST00000331968	NM_002742.2	301	tGc/tTc	5/18	0.337081274322854	3	FACETS	0.552	0.486	0.624	0.184	0.162	0.208	INDETERMINATE	1	TRUE	0	0.664805359028056	3		447	566	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107907	30107907	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	76	465	0	ENST00000331968.5:c.900G>T	p.Gln300His	p.Q300H	ENST00000331968	NM_002742.2	300	caG/caT	5/18	0.337081274322854	3	FACETS	0.528	0.463	0.597	0.176	0.154	0.199	INDETERMINATE	1	TRUE	0	0.664805359028056	3		465	577	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646303	23646303	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs373876101	NA	P-0039737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	134	632	0	ENST00000261584.4:c.1564C>G	p.Pro522Ala	p.P522A	ENST00000261584	NM_024675.3	522	Cca/Gca	4/13	0.616308502507395	2	FACETS	0.696	0.635	0.76	0.348	0.317	0.38	SUBCLONAL	1	TRUE	0	0.664805359028056	2		632	579	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993245	72993245	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1355004353	NA	P-0039737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	179	958	0	ENST00000268489.5:c.800C>T	p.Ser267Phe	p.S267F	ENST00000268489	NM_006885.3	267	tCc/tTc	2/10	0.657875852116272	2	FACETS	0.471	0.433	0.51	0.235	0.216	0.255	SUBCLONAL	1	TRUE	0	0.664805359028056	2		958	1144	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029399	16029400	+	missense_variant	Missense_Mutation	DNP	GA	GA	AG	novel	NA	P-0039737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	37	154	0	ENST00000268712.3:c.1630_1631delinsCT	p.Ser544Leu	p.S544L	ENST00000268712	NM_006311.3	544	TCc/CTc	15/46	0.616308502507395	2	FACETS	0.608	0.507	0.718	0.304	0.253	0.359	SUBCLONAL	1	TRUE	0	0.664805359028056	2		154	183	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602445	10602445	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	538	911	0	ENST00000171111.5:c.1133del	p.Gly378AlafsTer22	p.G378Afs*22	ENST00000171111	NM_203500.1	378	gGc/gc	3/6	0.621014312281841	2	FACETS	0.929	0.899	0.959	0.929	0.899	0.959	CLONAL	2	TRUE	0	0.664805359028056	2		911	871	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136146	11136146	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	636	858	0	ENST00000358026.2:c.3131del	p.Lys1044ArgfsTer62	p.K1044Rfs*62	ENST00000358026	NM_001128849.1	1044	Aag/ag	22/36	0.664805359028056	2	FACETS	0.984	0.957	1	0.984	0.957	1	CLONAL	2	TRUE	0	0.664805359028056	2		858	972	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285015	15285015	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1337308187	NA	P-0039737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1617	211	952	2	ENST00000263388.2:c.4600C>T	p.Arg1534Trp	p.R1534W	ENST00000263388	NM_000435.2	1534	Cgg/Tgg	25/33	0.601246850543882	4	FACETS	0.578	0.535	0.624			1	SUBCLONAL	1	TRUE	NA	0.664805359028056	4		954	1828	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457191	25457197	+	frameshift_variant	Frame_Shift_Del	DEL	CGGATGA	CGGATGA	-	novel	NA	P-0039737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	159	697	0	ENST00000264709.3:c.2690_2696del	p.Val897AlafsTer7	p.V897Afs*7	ENST00000264709	NM_175629.2	897	gTCATCCGc/gc	23/23	0.319909353925569	2	FACETS	0.533	0.489	0.58	0.267	0.244	0.29	INDETERMINATE	1	TRUE	0	0.664805359028056	2		697	897	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189356	99189356	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	341	616	0	ENST00000074304.5:c.2612A>G	p.Asn871Ser	p.N871S	ENST00000074304	NM_001134224.1	871	aAt/aGt	24/26	0.514439564869222	4	FACETS	1	0.993	1			1	CLONAL	1	TRUE	NA	0.664805359028056	4		616	1289	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561201	9561201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	67	425	0	ENST00000353224.5:c.581G>A	p.Arg194Lys	p.R194K	ENST00000353224	NM_177990.2	194	aGa/aAa	4/10	0.664805359028056	1	FACETS	0.489	0.429	0.553	0.489	0.429	0.553	SUBCLONAL	1	TRUE	0	0.664805359028056	1		425	275	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443288	187443288	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	29	225	0	ENST00000232014.4:c.1838A>T	p.Gln613Leu	p.Q613L	ENST00000232014	NM_001130845.1	613	cAg/cTg	8/10	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.664805359028056	NA		225	305	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226121	226121	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	522	965	0	ENST00000264932.6:c.580G>C	p.Asp194His	p.D194H	ENST00000264932	NM_004168.2	194	Gat/Cat	5/15	NA	2	FACETS	1	0.997	1			1	INDETERMINATE	1	TRUE	NA	0.664805359028056	2		965	1055	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295299	1295299	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0039737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	360	595	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.996	1			1	INDETERMINATE	1	TRUE	NA	0.664805359028056	2		595	727	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401717	401717	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	352	629	0	ENST00000380956.4:c.1041del	p.Asn348ThrfsTer36	p.N348Tfs*36	ENST00000380956	NM_001195286.1	347	Ccc/cc	7/9	0.314446202062114	3	FACETS	0.794	0.755	0.833	0.794	0.755	0.833	INDETERMINATE	2	TRUE	1	0.664805359028056	3		629	889	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372752	81372752	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	66	343	0	ENST00000222390.5:c.782G>C	p.Arg261Pro	p.R261P	ENST00000222390	NM_000601.4	261	cGc/cCc	7/18	NA	2	FACETS	0.527	0.459	0.599			1	INDETERMINATE	1	TRUE	NA	0.664805359028056	2		343	377	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878067	151878067	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	73	418	0	ENST00000262189.6:c.6878C>A	p.Ser2293Tyr	p.S2293Y	ENST00000262189	NM_170606.2	2293	tCt/tAt	36/59	1	2	FACETS	0.512	0.449	0.579	0.512	0.449	0.579	SUBCLONAL	1	TRUE	1	0.664805359028056	2		418	429	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992720	68992720	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	30	294	0	ENST00000288368.4:c.1685G>T	p.Arg562Leu	p.R562L	ENST00000288368	NM_024870.2	562	cGt/cTt	16/40	0.34521417652045	3	FACETS	0.281	0.226	0.343	0.094	0.075	0.115	INDETERMINATE	1	TRUE	0	0.664805359028056	3		294	428	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633346	8633346	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	134	468	0	ENST00000356435.5:c.323G>T	p.Ser108Ile	p.S108I	ENST00000356435		108	aGt/aTt	3/35	0.664805359028056	1	FACETS	0.938	0.868	1	0.938	0.868	1	CLONAL	1	TRUE	0	0.664805359028056	1		468	287	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412434	63412434	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	293	446	0	ENST00000330258.3:c.733C>T	p.Pro245Ser	p.P245S	ENST00000330258	NM_152424.3	245	Cct/Tct	2/2	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.664805359028056	1		446	428	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	56	236	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.28	2		236	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691039	NA	P-0039740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	157	736	0	ENST00000269305.4:c.919+1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.155516903705884	2	FACETS	1	0.986	1	0.686	0.629	0.746	INDETERMINATE	1	TRUE	0	0.28	2		736	817	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24158974	24158974	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	61	593	0	ENST00000263121.7:c.646G>C	p.Glu216Gln	p.E216Q	ENST00000263121	NM_003073.3	216	Gag/Cag	6/9	0.3	2	FACETS	0.57	0.491	0.657	0.285	0.245	0.329	SUBCLONAL	1	TRUE	0	0.28	2		593	764	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443402	187443402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1262719853	NA	P-0039740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	35	313	0	ENST00000232014.4:c.1724G>A	p.Arg575His	p.R575H	ENST00000232014	NM_001130845.1	575	cGt/cAt	8/10	1	2	FACETS	0.608	0.499	0.731	0.608	0.499	0.731	SUBCLONAL	1	TRUE	1	0.28	2		313	411	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63662153	63662153	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	25	280	0	ENST00000279873.7:c.257G>C	p.Arg86Thr	p.R86T	ENST00000279873	NM_032199.2	86	aGa/aCa	2/10	1	2	FACETS	0.428	0.337	0.533	0.428	0.337	0.533	SUBCLONAL	1	TRUE	1	0.28	2		280	417	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453459	40453459	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	121	667	0	ENST00000345506.4:c.1156G>C	p.Glu386Gln	p.E386Q	ENST00000345506	NM_003152.3	386	Gag/Cag	10/20	0.155516903705884	2	FACETS	1	0.914	1	0.507	0.457	0.559	INDETERMINATE	1	TRUE	0	0.28	2		667	853	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0039746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	431	417	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.349276653671122	5	FACETS	0.975	0.934	1			1	CLONAL	4	TRUE	NA	0.386357043686313	5		417	904	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0039746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	114	39	0	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	0.37908123565686	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.386357043686313	2		39	259	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962846	2962846	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	78	153	0	ENST00000396946.4:c.2062C>T	p.Arg688Ter	p.R688*	ENST00000396946	NM_032415.4	688	Cga/Tga	16/25	0.386357043686313	4	FACETS	0.772	0.678	0.873	0.386	0.339	0.437	SUBCLONAL	1	TRUE	2	0.386357043686313	4		153	725	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601353	28601353	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0039746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	95	47	0	ENST00000241453.7:c.2079C>G	p.Tyr693Ter	p.Y693*	ENST00000241453	NM_004119.2	693	taC/taG	17/24	0.386357043686313	3	FACETS	1	0.98	1	0.719	0.644	0.797	CLONAL	1	TRUE	1	0.386357043686313	3		47	408	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92462475	92462475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867580762	NA	P-0039746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	71	115	0	ENST00000265734.4:c.163C>T	p.Pro55Ser	p.P55S	ENST00000265734	NM_001259.6	55	Ccg/Tcg	2/8	0.386357043686313	4	FACETS	0.813	0.709	0.924	0.406	0.354	0.462	CLONAL	1	TRUE	2	0.386357043686313	4		115	627	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913517	NA	P-0039747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	150	405	0	ENST00000288135.5:c.1676T>A	p.Val559Asp	p.V559D	ENST00000288135	NM_000222.2	559	gTt/gAt	11/21	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.826607999467627	2		405	349	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	177	236	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.731141921417834	2		236	450	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223531	55223533	+	inframe_deletion	In_Frame_Del	DEL	GTG	GTG	-	novel	NA	P-0039748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7693	13065	592	0	ENST00000275493.2:c.901_903del	p.Val301del	p.V301del	ENST00000275493	NM_005228.3	300	GTG/-	8/28	0.731141921417834	36	FACETS	1	0.997	1			1	CLONAL	23	TRUE	NA	0.731141921417834	36		592	20758	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950724	79950725	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCGCAGCGC	rs1554066076	NA	P-0039750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	19	116	1	ENST00000265081.6:c.181_189dup	p.Ala61_Pro63dup	p.A61_P63dup	ENST00000265081	NM_002439.4	61	gcc/gCCGCAGCGCcc	1/24	0.85500406547584	3	FACETS	0.316	0.24	0.403	0.158	0.12	0.202	SUBCLONAL	1	TRUE	1	0.85500406547584	3		117	201	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214457	5214457	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	73	648	1	ENST00000357368.4:c.4529C>A	p.Thr1510Lys	p.T1510K	ENST00000357368	NM_002850.3	1510	aCg/aAg	30/38	0.85500406547584	3	FACETS	0.302	0.263	0.343	0.151	0.131	0.172	SUBCLONAL	1	TRUE	1	0.85500406547584	3		649	808	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281307	15281307	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	303	708	0	ENST00000263388.2:c.4949G>A	p.Gly1650Asp	p.G1650D	ENST00000263388	NM_000435.2	1650	gGc/gAc	27/33	0.85500406547584	3	FACETS	1	0.959	1	0.509	0.481	0.539	CLONAL	1	TRUE	1	0.85500406547584	3		708	993	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137524755	137524762	+	frameshift_variant	Frame_Shift_Del	DEL	GGAATCGC	GGAATCGC	TTAA	novel	NA	P-0039750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	141	412	1	ENST00000367739.4:c.607_614delinsTTAA	p.Ala203LeufsTer6	p.A203Lfs*6	ENST00000367739	NM_000416.2	203	GCGATTCCa/TTAAa	5/7	0.625092562621443	5	FACETS	0.77	0.706	0.836	0.513	0.47	0.557	SUBCLONAL	2	TRUE	2	0.85500406547584	5		413	489	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339210	70339254	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTCCTGCCTCAGGATGAACTGACGGCCTTGAATGTAAAACAAGG	TTTCCTGCCTCAGGATGAACTGACGGCCTTGAATGTAAAACAAGG	-	novel	NA	P-0039750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	376	498	0	ENST00000374080.3:c.100-9_135del		p.X34_splice	ENST00000374080		34		2/45	0.85500406547584	5	FACETS	1	0.993	1	0.846	0.814	0.878	CLONAL	3	TRUE	1	0.85500406547584	5		498	593	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	90	417	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.191177166504607	4	FACETS	0.988	0.882	1	0.659	0.588	0.733	CLONAL	2	TRUE	1	0.28377122513666	4		417	412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0039766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	135	736	3	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.19890709139776	3	FACETS	1	0.961	1	0.726	0.664	0.79	CLONAL	2	TRUE	0	0.28377122513666	3		739	499	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0039766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	44	489	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	0.28377122513666	5	FACETS	1	0.957	1	0.483	0.407	0.567	CLONAL	1	TRUE	2	0.28377122513666	5		489	305	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593505	48593505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	67	414	0	ENST00000342988.3:c.1256G>A	p.Gly419Glu	p.G419E	ENST00000342988	NM_005359.5	419	gGg/gAg	10/12	0.19890709139776	3	FACETS	0.98	0.861	1	0.654	0.574	0.738	CLONAL	2	TRUE	0	0.28377122513666	3		414	275	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223356	2223356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1376643409	NA	P-0039766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	143	1072	0	ENST00000326181.6:c.968C>T	p.Ser323Leu	p.S323L	ENST00000326181	NM_032271.2	323	tCg/tTg	10/21	0.28377122513666	5	FACETS	0.874	0.801	0.95	0.874	0.801	0.95	CLONAL	3	TRUE	2	0.28377122513666	5		1072	548	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204849	128204849	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	119	1275	0	ENST00000341105.2:c.592G>A	p.Ala198Thr	p.A198T	ENST00000341105	NM_032638.4	198	Gcg/Acg	3/6	1	2	FACETS	0.805	0.73	0.883	1	0.987	1	CLONAL	2	TRUE	1	0.28377122513666	2		1275	521	SUCCESS
APC	324	MSKCC	GRCh37	5	112174268	112174269	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGTTTTGC	novel	NA	P-0039766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	55	420	0	ENST00000257430.4:c.2982_2989dup	p.Tyr997PhefsTer11	p.Y997Ffs*11	ENST00000257430	NM_000038.5	993	aag/aAGTTTTGCag	16/16	0.28377122513666	5	FACETS	0.85	0.731	0.978	0.567	0.487	0.652	CLONAL	2	TRUE	2	0.28377122513666	5		420	325	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039766-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	66	417	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	4	FACETS	1	0.964	1	0.672	0.583	0.769	INDETERMINATE	1	TRUE	2	0.173173758232188	4		417	665	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0039766-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	178	736	3	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.173173758232188	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	0	0.173173758232188	2		739	1025	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0039766-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	67	489	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	NA	4	FACETS	0.848	0.738	0.967	0.848	0.738	0.967	INDETERMINATE	2	TRUE	2	0.173173758232188	4		489	535	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593505	48593505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039766-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	76	414	0	ENST00000342988.3:c.1256G>A	p.Gly419Glu	p.G419E	ENST00000342988	NM_005359.5	419	gGg/gAg	10/12	0.148922360863242	2	FACETS	0.924	0.813	1	0.924	0.813	1	CLONAL	2	TRUE	0	0.173173758232188	2		414	475	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223356	2223356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1376643409	NA	P-0039766-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	132	1072	0	ENST00000326181.6:c.968C>T	p.Ser323Leu	p.S323L	ENST00000326181	NM_032271.2	323	tCg/tTg	10/21	NA	4	FACETS	0.928	0.841	1	0.928	0.841	1	INDETERMINATE	2	TRUE	2	0.173173758232188	4		1072	964	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204849	128204849	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039766-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	98	1275	0	ENST00000341105.2:c.592G>A	p.Ala198Thr	p.A198T	ENST00000341105	NM_032638.4	198	Gcg/Acg	3/6	1	2	FACETS	0.998	0.888	1	0.998	0.888	1	CLONAL	1	TRUE	1	0.173173758232188	2		1275	1134	SUCCESS
APC	324	MSKCC	GRCh37	5	112174268	112174269	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGTTTTGC	novel	NA	P-0039766-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	56	420	0	ENST00000257430.4:c.2982_2989dup	p.Tyr997PhefsTer11	p.Y997Ffs*11	ENST00000257430	NM_000038.5	993	aag/aAGTTTTGCag	16/16	NA	4	FACETS	1	0.967	1	0.75	0.643	0.866	INDETERMINATE	1	TRUE	2	0.173173758232188	4		420	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579445	7579475	+	frameshift_variant	Frame_Shift_Del	DEL	GTAGGAGCTGCTGGTGCAGGGGCCACGGGGG	GTAGGAGCTGCTGGTGCAGGGGCCACGGGGG	-	novel	NA	P-0039767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	215	781	0	ENST00000269305.4:c.212_242del	p.Pro71HisfsTer42	p.P71Hfs*42	ENST00000269305	NM_001126112.2	71	cCCCCCGTGGCCCCTGCACCAGCAGCTCCTACa/ca	4/11	0.229251109321327	4	FACETS	1	0.963	1	0.785	0.733	0.839	CLONAL	3	TRUE	0	0.240527760360501	4		781	706	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0039771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	138	736	3	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.904	0.823	0.989	0.904	0.823	0.989	CLONAL	1	TRUE	1	0.367745765575221	2		739	830	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509828	106509828	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	116	649	0	ENST00000359195.3:c.1822T>C	p.Tyr608His	p.Y608H	ENST00000359195	NM_002649.2	608	Tac/Cac	2/11	1	2	FACETS	0.829	0.747	0.915	0.829	0.747	0.915	CLONAL	1	TRUE	1	0.367745765575221	2		649	761	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250155	110250156	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATAG	novel	NA	P-0039771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	47	797	0	ENST00000374672.4:c.516_519dup	p.Gly174LeufsTer84	p.G174Lfs*84	ENST00000374672	NM_004235.4	173	-/CTAT	3/5	1	2	FACETS	0.326	0.274	0.384	0.326	0.274	0.384	SUBCLONAL	1	TRUE	1	0.367745765575221	2		797	784	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0039780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	84	321	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.40565873845546	4	FACETS	1	0.957	1			1	CLONAL	2	TRUE	NA	0.40565873845546	4		322	257	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0039780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	191	546	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.235931167766507	5	FACETS	0.975	0.909	1	0.585	0.545	0.625	INDETERMINATE	3	TRUE	0	0.40565873845546	5		547	518	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0039780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	246	627	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.235931167766507	5	FACETS	0.94	0.888	0.991	0.752	0.71	0.793	INDETERMINATE	4	TRUE	0	0.40565873845546	5		627	519	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0039780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	62	458	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.248093367331117	5	FACETS	1	0.969	1	0.476	0.414	0.544	CLONAL	1	TRUE	2	0.40565873845546	5		459	344	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0039780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	41	405	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.248093367331117	5	FACETS	1	0.935	1	0.415	0.348	0.489	CLONAL	1	TRUE	2	0.40565873845546	5		405	261	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572520	64572520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	79	628	0	ENST00000312049.6:c.1336C>T	p.Arg446Cys	p.R446C	ENST00000312049	NM_130799.2	446	Cgt/Tgt	9/10	0.318874564434729	3	FACETS	0.84	0.74	0.947	0.28	0.246	0.316	CLONAL	1	TRUE	0	0.40565873845546	3		628	558	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176560	142176560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151162347	NA	P-0039780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	22	412	0	ENST00000350721.4:c.7541G>A	p.Arg2514His	p.R2514H	ENST00000350721	NM_001184.3	2514	cGc/cAc	45/47	0.318874564434729	3	FACETS	0.453	0.351	0.571	0.151	0.117	0.191	SUBCLONAL	1	TRUE	0	0.40565873845546	3		412	288	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143137	30143137	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1553380330	NA	P-0039780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	63	510	1	ENST00000389048.3:c.389G>T	p.Gly130Val	p.G130V	ENST00000389048	NM_004304.4	130	gGc/gTc	1/29	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.40565873845546	2		511	286	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55960975	55960975	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	60	449	1	ENST00000263923.4:c.2965G>T	p.Glu989Ter	p.E989*	ENST00000263923	NM_002253.2	989	Gag/Tag	21/30	0.210554485647962	3	FACETS	1	0.97	1	0.482	0.42	0.548	INDETERMINATE	1	TRUE	0	0.40565873845546	3		450	246	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157180	106157180	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	33	370	0	ENST00000380013.4:c.2081T>G	p.Leu694Arg	p.L694R	ENST00000380013	NM_001127208.2	694	cTt/cGt	3/11	0.210554485647962	3	FACETS	0.878	0.72	1	0.293	0.24	0.351	INDETERMINATE	1	TRUE	0	0.40565873845546	3		370	223	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532640	187532640	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	41	389	0	ENST00000441802.2:c.9753A>C	p.Gln3251His	p.Q3251H	ENST00000441802	NM_005245.3	3251	caA/caC	14/27	0.40565873845546	3	FACETS	0.924	0.775	1	0.462	0.387	0.544	CLONAL	1	TRUE	1	0.40565873845546	3		389	263	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460475	149460476	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs753211296	NA	P-0039780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	78	726	0	ENST00000286301.3:c.161dup	p.Ser55IlefsTer9	p.S55Ifs*9	ENST00000286301	NM_005211.3	54	cca/ccCa	3/22	1	2	FACETS	0.945	0.835	1	0.945	0.835	1	CLONAL	1	TRUE	1	0.40565873845546	2		726	407	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431079	49431079	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	191	615	0	ENST00000301067.7:c.10060G>T	p.Gly3354Trp	p.G3354W	ENST00000301067	NM_003482.3	3354	Ggg/Tgg	34/54	0.502481490838004	4	FACETS	0.894	0.826	0.965			1	CLONAL	1	TRUE	NA	0.635181938788355	4		615	1100	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0039785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	559	897	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.635181938788355	2	FACETS	0.95	0.92	0.981	0.95	0.92	0.981	CLONAL	2	TRUE	0	0.635181938788355	2		897	926	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821594	72821602	+	inframe_deletion	In_Frame_Del	DEL	GCCGCCGCC	GCCGCCGCC	-	rs374416547	NA	P-0039785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	62	132	0	ENST00000268489.5:c.10573_10581del	p.Gly3525_Gly3527del	p.G3525_G3527del	ENST00000268489	NM_006885.3	3525	GGCGGCGGC/-	10/10	0.629809780797028	3	FACETS	1	0.97	1	0.461	0.405	0.519	CLONAL	1	TRUE	0	0.635181938788355	3		132	186	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602322	10602322	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	573	848	0	ENST00000171111.5:c.1256G>T	p.Gly419Val	p.G419V	ENST00000171111	NM_203500.1	419	gGg/gTg	3/6	0.635181938788355	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.635181938788355	2		848	899	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194706	29194706	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs974286158	NA	P-0039785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	185	803	0	ENST00000240100.2:c.1022C>T	p.Ala341Val	p.A341V	ENST00000240100	NM_001394.6	341	gCg/gTg	4/4	1	2	FACETS	0.591	0.545	0.638	0.591	0.545	0.638	SUBCLONAL	1	TRUE	1	0.635181938788355	2		803	986	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175916356	175916356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	182	296	1	ENST00000367669.3:c.2153C>T	p.Ala718Val	p.A718V	ENST00000367669	NM_022457.5	718	gCt/gTt	19/20	0.635181938788355	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	1	0.635181938788355	3		297	370	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312699	91312699	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1274275865	NA	P-0039785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	111	307	0	ENST00000355112.3:c.2438G>C	p.Arg813Thr	p.R813T	ENST00000355112	NM_000057.2	813	aGa/aCa	12/22	0.635181938788355	5	FACETS	1	0.922	1	0.257	0.231	0.284	CLONAL	1	TRUE	1	0.635181938788355	5		307	664	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207142	1207243	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCAAGATCCTCAAGAAGAAGAAGTTGCGAAGGATCCCCAACGGGGAGGCCAACGTGAAGAAGTAAGTATGGCTTGCTGGGGTCGGGGCCGGGCCGGGCCAGT	TCAAGATCCTCAAGAAGAAGAAGTTGCGAAGGATCCCCAACGGGGAGGCCAACGTGAAGAAGTAAGTATGGCTTGCTGGGGTCGGGGCCGGGCCGGGCCAGT	-	novel	NA	P-0039785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	425	842	0	ENST00000326873.7:c.230_290+41del		p.X77_splice	ENST00000326873	NM_000455.4	77		1/10	0.635181938788355	2	FACETS	0.857	0.823	0.89	0.857	0.823	0.89	CLONAL	2	TRUE	0	0.635181938788355	2		842	781	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	184	236	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.462068965102153	2		236	771	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0039787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	136	326	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.22907142500708	4	FACETS	1	0.987	1	0.75	0.684	0.818	INDETERMINATE	1	TRUE	2	0.462068965102153	4		326	574	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992180	11992180	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	91	377	0	ENST00000396373.4:c.270T>G	p.Asn90Lys	p.N90K	ENST00000396373	NM_001987.4	90	aaT/aaG	3/8	0.239326595416692	1	FACETS	0.474	0.421	0.53	0.474	0.421	0.53	INDETERMINATE	1	TRUE	0	0.462068965102153	1		377	639	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442892	49442892	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	223	549	0	ENST00000301067.7:c.4016T>A	p.Leu1339Gln	p.L1339Q	ENST00000301067	NM_003482.3	1339	cTg/cAg	12/54	0.239326595416692	1	FACETS	0.872	0.813	0.933	0.872	0.813	0.933	INDETERMINATE	1	TRUE	0	0.462068965102153	1		549	851	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892256	9892256	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	70	450	0	ENST00000330684.3:c.2234G>T	p.Cys745Phe	p.C745F	ENST00000330684	NM_001134407.1	745	tGc/tTc	11/13	1	2	FACETS	0.372	0.323	0.424	0.372	0.323	0.424	SUBCLONAL	1	TRUE	1	0.462068965102153	2		450	815	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56912104	56912104	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	89	504	0	ENST00000519728.1:c.1334del	p.Pro445GlnfsTer8	p.P445Qfs*8	ENST00000519728	NM_002350.3	444	taC/ta	12/13	1	2	FACETS	0.482	0.427	0.541	0.482	0.427	0.541	SUBCLONAL	1	TRUE	1	0.462068965102153	2		504	799	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992680	68992680	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	93	387	0	ENST00000288368.4:c.1645C>T	p.Leu549Phe	p.L549F	ENST00000288368	NM_024870.2	549	Ctt/Ttt	16/40	1	2	FACETS	0.758	0.676	0.845	0.758	0.676	0.845	SUBCLONAL	1	TRUE	1	0.462068965102153	2		387	531	SUCCESS
AR	367	MSKCC	GRCh37	X	66766343	66766343	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1485244725	NA	P-0039787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	27	100	0	ENST00000374690.3:c.1355G>T	p.Gly452Val	p.G452V	ENST00000374690	NM_000044.3	452	gGt/gTt	1/8	1	1	FACETS	0.505	0.405	0.617	0.505	0.405	0.617	SUBCLONAL	1	TRUE	0	0.462068965102153	1		100	178	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0039793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	166	487	1	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.220796943128505	2	FACETS	0.933	0.86	1	0.933	0.86	1	CLONAL	2	TRUE	0	0.277664069678465	2		488	641	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129428	64129428	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61736650	NA	P-0039793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	271	657	0	ENST00000334205.4:c.860C>T	p.Ala287Val	p.A287V	ENST00000334205	NM_003942.2	287	gCg/gTg	8/17	0.277664069678465	3	FACETS	0.966	0.911	1	0.966	0.911	1	CLONAL	3	TRUE	0	0.277664069678465	3		657	767	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041046	29041046	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	47	262	0	ENST00000282397.4:c.382A>G	p.Ile128Val	p.I128V	ENST00000282397	NM_002019.4	128	Att/Gtt	3/30	1	2	FACETS	0.976	0.826	1	0.976	0.826	1	CLONAL	1	TRUE	1	0.277664069678465	2		262	347	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628366	86628366	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	72	164	0	ENST00000274376.6:c.739del	p.Ser247LeufsTer6	p.S247Lfs*6	ENST00000274376	NM_002890.2	245	cgT/cg	3/25	0.18802679934914	3	FACETS	0.956	0.842	1	0.637	0.561	0.717	CLONAL	2	TRUE	0	0.277664069678465	3		164	309	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023603	27023603	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1010624759	NA	P-0039793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	43	515	0	ENST00000324856.7:c.709G>A	p.Gly237Ser	p.G237S	ENST00000324856	NM_006015.4	237	Ggc/Agc	1/20	1	2	FACETS	0.58	0.485	0.686	0.58	0.485	0.686	SUBCLONAL	1	TRUE	1	0.277664069678465	2		515	534	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239375	123239375	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	20	302	0	ENST00000358487.5:c.2462C>A	p.Thr821Lys	p.T821K	ENST00000358487	NM_000141.4	821	aCa/aAa	18/18	1	2	FACETS	0.477	0.365	0.608	0.477	0.365	0.608	SUBCLONAL	1	TRUE	1	0.277664069678465	2		302	302	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129428	64129429	+	missense_variant	Missense_Mutation	DNP	CG	CG	TT	novel	NA	P-0039793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	271	659	1	ENST00000334205.4:c.860_861delinsTT	p.Ala287Val	p.A287V	ENST00000334205	NM_003942.2	287	gCG/gTT	8/17	0.277664069678465	3	FACETS	0.966	0.911	1	0.966	0.911	1	CLONAL	3	TRUE	0	0.277664069678465	3		660	767	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245973	46245973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142127790	NA	P-0039793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	86	232	1	ENST00000334344.6:c.4067C>T	p.Pro1356Leu	p.P1356L	ENST00000334344	NM_152641.2	1356	cCg/cTg	15/21	0.18802679934914	3	FACETS	1	0.944	1	0.726	0.648	0.807	CLONAL	2	TRUE	0	0.277664069678465	3		233	324	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974745	15974745	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	32	282	0	ENST00000268712.3:c.4130T>A	p.Ile1377Lys	p.I1377K	ENST00000268712	NM_006311.3	1377	aTa/aAa	30/46	0.220796943128505	2	FACETS	0.455	0.368	0.552	0.227	0.184	0.276	SUBCLONAL	1	TRUE	0	0.277664069678465	2		282	507	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687505	29687505	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	92	269	0	ENST00000356175.3:c.8098C>T	p.Gln2700Ter	p.Q2700*	ENST00000356175	NM_000267.3	2700	Caa/Taa	56/57	0.220796943128505	2	FACETS	0.793	0.709	0.881	0.793	0.709	0.881	SUBCLONAL	2	TRUE	0	0.277664069678465	2		269	418	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687382	37687382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	28	425	0	ENST00000447079.4:c.4286C>T	p.Ser1429Phe	p.S1429F	ENST00000447079	NM_015083.1	1429	tCt/tTt	14/14	0.220796943128505	2	FACETS	0.456	0.364	0.562	0.228	0.182	0.281	SUBCLONAL	1	TRUE	0	0.277664069678465	2		425	442	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602551	10602551	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	184	607	0	ENST00000171111.5:c.1027G>T	p.Glu343Ter	p.E343*	ENST00000171111	NM_203500.1	343	Gag/Tag	3/6	0.271383214137036	2	FACETS	0.932	0.863	1	0.932	0.863	1	CLONAL	2	TRUE	0	0.277664069678465	2		607	711	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628335	187628335	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	175	491	0	ENST00000441802.2:c.2647C>G	p.Leu883Val	p.L883V	ENST00000441802	NM_005245.3	883	Ctg/Gtg	2/27	0.220796943128505	2	FACETS	0.873	0.806	0.942	0.873	0.806	0.942	CLONAL	2	TRUE	0	0.277664069678465	2		491	722	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32806006	32806006	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1198620573	NA	P-0039793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	121	486	1	ENST00000374899.4:c.5G>T	p.Arg2Leu	p.R2L	ENST00000374899	NM_018833.2	2	cGg/cTg	2/12	0.218830611436555	2	FACETS	0.858	0.779	0.94	0.858	0.779	0.94	CLONAL	2	TRUE	0	0.277664069678465	2		487	508	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148516729	148516729	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs6954744	NA	P-0039793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	149	278	0	ENST00000320356.2:c.958C>G	p.Leu320Val	p.L320V	ENST00000320356	NM_004456.4	320	Cta/Gta	9/20	0.277664069678465	6	FACETS	0.918	0.842	0.997	0.689	0.632	0.748	CLONAL	3	TRUE	2	0.277664069678465	6		278	606	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112433	115112433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	226	592	2	ENST00000257566.3:c.1307G>A	p.Arg436His	p.R436H	ENST00000257566	NM_016569.3	436	cGc/cAc	7/8	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.553502955684041	2		594	744	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	70	73	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.31	2		73	417	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	133	639	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.974	0.884	1	0.974	0.884	1	CLONAL	1	TRUE	1	0.31	2		645	881	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	159	609	4	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.852	0.784	0.922	1	0.991	1	CLONAL	2	TRUE	1	0.31	2		613	602	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	254	310	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.772	0.722	0.822	1	0.993	1	SUBCLONAL	2	TRUE	1	0.31	2		311	1062	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	136	1096	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.728	0.66	0.799	0.728	0.66	0.799	SUBCLONAL	1	TRUE	1	0.31	2		1096	1206	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	120	788	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.823	0.742	0.908	0.823	0.742	0.908	CLONAL	1	TRUE	1	0.31	2		790	941	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	102	405	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.943	0.844	1	0.943	0.844	1	CLONAL	1	TRUE	1	0.31	2		405	698	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	85	591	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.674	0.595	0.759	0.674	0.595	0.759	SUBCLONAL	1	TRUE	1	0.31	2		593	814	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	98	591	1	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	0.957	0.854	1	0.957	0.854	1	CLONAL	1	TRUE	1	0.31	2		592	661	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781324	3781326	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs587783502	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	180	1245	0	ENST00000262367.5:c.5039_5041del	p.Ser1680del	p.S1680del	ENST00000262367	NM_004380.2	1680	tCCTtg/ttg	30/31	1	2	FACETS	0.966	0.889	1	0.966	0.889	1	CLONAL	1	TRUE	1	0.31	2		1245	1202	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131402	17131402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398124537	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	125	969	2	ENST00000285071.4:c.50G>A	p.Arg17His	p.R17H	ENST00000285071	NM_144997.5	17	cGc/cAc	4/14	1	2	FACETS	0.922	0.834	1	0.922	0.834	1	CLONAL	1	TRUE	1	0.31	2		971	875	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440943	56440943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786205215	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	157	821	1	ENST00000407977.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000407977		132	Cga/Tga	4/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.31	2		822	924	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849467	68849467	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778170	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	133	863	0	ENST00000261769.5:c.1370C>T	p.Thr457Met	p.T457M	ENST00000261769	NM_004360.3	457	aCg/aTg	10/16	1	2	FACETS	0.884	0.802	0.97	0.884	0.802	0.97	CLONAL	1	TRUE	1	0.31	2		863	971	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817813	3817813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142008620	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	111	752	0	ENST00000262367.5:c.3158C>T	p.Pro1053Leu	p.P1053L	ENST00000262367	NM_004380.2	1053	cCt/cTt	16/31	1	2	FACETS	0.816	0.732	0.904	0.816	0.732	0.904	CLONAL	1	TRUE	1	0.31	2		752	878	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867540	35867541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs869312857	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	58	469	1	ENST00000303115.3:c.361dup	p.Ile121AsnfsTer8	p.I121Nfs*8	ENST00000303115	NM_002185.3	118	-/A	3/8	1	2	FACETS	0.674	0.579	0.778	0.674	0.579	0.778	SUBCLONAL	1	TRUE	1	0.31	2		470	555	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874637	35874637	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	77	514	4	ENST00000303115.3:c.799del	p.Arg267GlyfsTer28	p.R267Gfs*28	ENST00000303115	NM_002185.3	265	Aaa/aa	6/8	1	2	FACETS	0.827	0.726	0.934	0.827	0.726	0.934	CLONAL	1	TRUE	1	0.31	2		518	601	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687471	37687472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs760014508	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	48	534	1	ENST00000447079.4:c.4382dup	p.Thr1463AsnfsTer50	p.T1463Nfs*50	ENST00000447079	NM_015083.1	1459	tgg/tGgg	14/14	1	2	FACETS	0.665	0.562	0.777	0.665	0.562	0.777	SUBCLONAL	1	TRUE	1	0.31	2		535	466	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40384055	40384055	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	93	628	0	ENST00000293328.3:c.91C>T	p.Arg31Trp	p.R31W	ENST00000293328	NM_012448.3	31	Cgg/Tgg	2/19	1	2	FACETS	0.744	0.661	0.833	0.744	0.661	0.833	SUBCLONAL	1	TRUE	1	0.31	2		628	806	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209298	133209298	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060500809	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	98	1059	2	ENST00000320574.5:c.6088del	p.Ala2030ProfsTer18	p.A2030Pfs*18	ENST00000320574	NM_006231.2	2030	Gcc/cc	44/49	1	2	FACETS	0.735	0.655	0.821	0.735	0.655	0.821	SUBCLONAL	1	TRUE	1	0.31	2		1061	860	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097625	11097625	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	181	1272	4	ENST00000358026.2:c.810del	p.Met272CysfsTer31	p.M272Cfs*31	ENST00000358026	NM_001128849.1	269	Ccc/cc	5/36	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.31	2		1276	1084	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052632	42052632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779811318	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	115	681	0	ENST00000219905.7:c.7303C>T	p.Arg2435Trp	p.R2435W	ENST00000219905	NM_001164273.1	2435	Cgg/Tgg	20/24	1	2	FACETS	0.94	0.847	1	0.94	0.847	1	CLONAL	1	TRUE	1	0.31	2		681	789	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919007	50919007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1483458869	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	118	816	3	ENST00000440232.2:c.2744C>T	p.Ala915Val	p.A915V	ENST00000440232	NM_002691.3	915	gCg/gTg	22/27	1	2	FACETS	0.858	0.774	0.948	0.858	0.774	0.948	CLONAL	1	TRUE	1	0.31	2		819	887	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	107	833	2	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	0.697	0.624	0.775	0.697	0.624	0.775	SUBCLONAL	1	TRUE	1	0.31	2		835	990	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982386	25982386	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	68	367	0	ENST00000435504.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000435504		302	Cga/Tga	9/13	1	2	FACETS	0.829	0.722	0.945	0.829	0.722	0.945	CLONAL	1	TRUE	1	0.31	2		367	529	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837949	156837949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150271893	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	178	1120	1	ENST00000524377.1:c.482G>A	p.Arg161His	p.R161H	ENST00000524377	NM_002529.3	161	cGc/cAc	5/17	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.31	2		1121	1058	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194859	30194859	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1186546402	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	85	691	0	ENST00000331968.5:c.286G>A	p.Gly96Arg	p.G96R	ENST00000331968	NM_002742.2	96	Gga/Aga	2/18	1	2	FACETS	0.727	0.642	0.818	0.727	0.642	0.818	SUBCLONAL	1	TRUE	1	0.31	2		691	754	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025856	48025857	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs267608041	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	56	388	0	ENST00000234420.5:c.741dup	p.Arg248ThrfsTer8	p.R248Tfs*8	ENST00000234420	NM_000179.2	245	ata/atAa	4/10	1	2	FACETS	0.693	0.594	0.802	0.693	0.594	0.802	SUBCLONAL	1	TRUE	1	0.31	2		388	521	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209267	133209267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs5745021	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	99	1031	1	ENST00000320574.5:c.6119C>T	p.Ala2040Val	p.A2040V	ENST00000320574	NM_006231.2	2040	gCg/gTg	44/49	1	2	FACETS	0.743	0.662	0.829	0.743	0.662	0.829	SUBCLONAL	1	TRUE	1	0.31	2		1032	860	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178943755	178943755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200671228	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	57	378	0	ENST00000263967.3:c.2422C>T	p.Arg808Trp	p.R808W	ENST00000263967	NM_006218.2	808	Cgg/Tgg	17/21	1	2	FACETS	0.728	0.625	0.84	0.728	0.625	0.84	SUBCLONAL	1	TRUE	1	0.31	2		378	505	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716331	52716331	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	118	882	2	ENST00000322088.6:c.775G>A	p.Val259Ile	p.V259I	ENST00000322088	NM_014225.5	259	Gtc/Atc	6/15	1	2	FACETS	0.871	0.785	0.962	0.871	0.785	0.962	CLONAL	1	TRUE	1	0.31	2		884	874	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004232	29004232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763071731	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	89	528	0	ENST00000282397.4:c.1061G>A	p.Arg354Gln	p.R354Q	ENST00000282397	NM_002019.4	354	cGg/cAg	8/30	1	2	FACETS	0.812	0.72	0.911	0.812	0.72	0.911	CLONAL	1	TRUE	1	0.31	2		528	707	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090086	37090086	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63751310	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	80	690	0	ENST00000231790.2:c.1975C>T	p.Arg659Ter	p.R659*	ENST00000231790	NM_000249.3	659	Cga/Tga	17/19	1	2	FACETS	0.748	0.658	0.844	0.748	0.658	0.844	SUBCLONAL	1	TRUE	1	0.31	2		690	690	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809802	36809802	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	126	1061	0	ENST00000373129.3:c.803T>G	p.Leu268Arg	p.L268R	ENST00000373129	NM_032017.1	268	cTg/cGg	9/12	1	2	FACETS	0.858	0.776	0.945	0.858	0.776	0.945	CLONAL	1	TRUE	1	0.31	2		1061	947	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458044	120458045	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	103	828	0	ENST00000256646.2:c.7300dup	p.Ser2434PhefsTer2	p.S2434Ffs*2	ENST00000256646	NM_024408.3	2434	tct/tTct	34/34	1	2	FACETS	0.816	0.73	0.908	0.816	0.73	0.908	CLONAL	1	TRUE	1	0.31	2		828	814	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99440125	99440125	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	75	483	0	ENST00000268035.6:c.1093C>T	p.Arg365Ter	p.R365*	ENST00000268035	NM_000875.3	365	Cga/Tga	4/21	1	2	FACETS	0.773	0.678	0.876	0.773	0.678	0.876	SUBCLONAL	1	TRUE	1	0.31	2		483	626	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992505	72992505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150708008	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	123	1037	7	ENST00000268489.5:c.1540G>A	p.Ala514Thr	p.A514T	ENST00000268489	NM_006885.3	514	Gca/Aca	2/10	1	2	FACETS	0.776	0.701	0.856	0.776	0.701	0.856	SUBCLONAL	1	TRUE	1	0.31	2		1044	1022	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346879	89346879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760859183	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	74	409	0	ENST00000301030.4:c.6071C>T	p.Pro2024Leu	p.P2024L	ENST00000301030	NM_001256183.1	2024	cCg/cTg	9/13	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.31	2		409	372	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979649	7979649	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774946794	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	87	623	1	ENST00000319144.4:c.1376G>A	p.Gly459Asp	p.G459D	ENST00000319144	NM_001139.2	459	gGc/gAc	11/15	1	2	FACETS	0.858	0.76	0.963	0.858	0.76	0.963	CLONAL	1	TRUE	1	0.31	2		624	654	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368254	45368254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	79	597	0	ENST00000262160.6:c.1348G>A	p.Asp450Asn	p.D450N	ENST00000262160	NM_005901.5	450	Gac/Aac	11/11	1	2	FACETS	0.793	0.697	0.895	0.793	0.697	0.895	SUBCLONAL	1	TRUE	1	0.31	2		597	643	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591940	48591940	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	84	524	0	ENST00000342988.3:c.1103C>A	p.Ser368Tyr	p.S368Y	ENST00000342988	NM_005359.5	368	tCc/tAc	9/12	1	2	FACETS	0.911	0.806	1	0.911	0.806	1	CLONAL	1	TRUE	1	0.31	2		524	595	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101854	11101854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377549345	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	135	1089	0	ENST00000358026.2:c.1274G>A	p.Arg425Gln	p.R425Q	ENST00000358026	NM_001128849.1	425	cGg/cAg	8/36	1	2	FACETS	0.862	0.783	0.946	0.862	0.783	0.946	CLONAL	1	TRUE	1	0.31	2		1089	1010	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302926	15302926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	119	1267	0	ENST00000263388.2:c.524T>C	p.Leu175Pro	p.L175P	ENST00000263388	NM_000435.2	175	cTc/cCc	4/33	1	2	FACETS	0.757	0.682	0.837	0.757	0.682	0.837	SUBCLONAL	1	TRUE	1	0.31	2		1267	1014	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745116	41745116	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	125	995	1	ENST00000301178.4:c.1186del	p.Asp396ThrfsTer7	p.D396Tfs*7	ENST00000301178	NM_021913.4	394	caG/ca	9/20	1	2	FACETS	0.83	0.75	0.914	0.83	0.75	0.914	CLONAL	1	TRUE	1	0.31	2		996	972	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430687	181430688	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	91	695	0	ENST00000325404.1:c.542dup	p.Gln182AlafsTer128	p.Q182Afs*128	ENST00000325404	NM_003106.3	180	tac/taCc	1/1	1	2	FACETS	0.865	0.768	0.968	0.865	0.768	0.968	CLONAL	1	TRUE	1	0.31	2		695	679	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518113	187518113	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	115	685	1	ENST00000441802.2:c.12581del	p.Leu4194TyrfsTer12	p.L4194Yfs*12	ENST00000441802	NM_005245.3	4194	tTa/ta	25/27	1	2	FACETS	0.882	0.794	0.975	0.882	0.794	0.975	CLONAL	1	TRUE	1	0.31	2		686	841	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836863	151836863	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	117	727	0	ENST00000262189.6:c.14357A>G	p.Tyr4786Cys	p.Y4786C	ENST00000262189	NM_170606.2	4786	tAt/tGt	56/59	1	2	FACETS	0.97	0.875	1	0.97	0.875	1	CLONAL	1	TRUE	1	0.31	2		727	778	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391962	139391962	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759749364	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	120	1006	3	ENST00000277541.6:c.6229G>A	p.Ala2077Thr	p.A2077T	ENST00000277541	NM_017617.3	2077	Gcc/Acc	34/34	1	2	FACETS	0.772	0.696	0.852	0.772	0.696	0.852	SUBCLONAL	1	TRUE	1	0.31	2		1009	1003	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325419	1325419	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	113	730	0	ENST00000400841.2:c.256C>A	p.Leu86Ile	p.L86I	ENST00000400841		86	Cta/Ata	3/6	1	1	FACETS	0.804	0.724	0.889	0.804	0.724	0.889	CLONAL	1	TRUE	0	0.31	1		730	766	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953228	81953228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369760877	NA	P-0039803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	41	438	2	ENST00000359376.3:c.2194C>T	p.Arg732Cys	p.R732C	ENST00000359376	NM_002661.3	732	Cgc/Tgc	20/33	1	2	FACETS	0.609	0.508	0.721	0.609	0.508	0.721	SUBCLONAL	1	FALSE	1	0.36177051956852	2		440	372	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560934	9560934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	38	650	0	ENST00000353224.5:c.848G>A	p.Arg283Gln	p.R283Q	ENST00000353224	NM_177990.2	283	cGg/cAg	4/10	0.36177051956852	3	FACETS	0.551	0.456	0.658	0.276	0.228	0.329	SUBCLONAL	1	FALSE	1	0.36177051956852	3		650	450	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877423	28877423	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750346448	NA	P-0039803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	87	704	2	ENST00000282397.4:c.3898G>A	p.Val1300Ile	p.V1300I	ENST00000282397	NM_002019.4	1300	Gtc/Atc	30/30	0.36177051956852	4	FACETS	0.946	0.838	1	0.315	0.279	0.354	CLONAL	1	FALSE	1	0.36177051956852	4		706	692	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579415	7579478	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTGCAGGGGCCACGGGGGGAG	CAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTGCAGGGGCCACGGGGGGAG	-	novel	NA	P-0039803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	211	1113	0	ENST00000269305.4:c.209_272del	p.Ala70GlyfsTer32	p.A70Gfs*32	ENST00000269305	NM_001126112.2	70	gCTCCCCCCGTGGCCCCTGCACCAGCAGCTCCTACACCGGCGGCCCCTGCACCAGCCCCCTCCTGg/gg	4/11	0.36177051956852	1	FACETS	0.812	0.76	0.866	1	0.993	1	CLONAL	2	FALSE	0	0.36177051956852	1		1113	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0039805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	628	1192	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.611384050075824	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.611384050075824	2		1192	917	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720711	89720712	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	65	219	0	ENST00000371953.3:c.867dup	p.Val290SerfsTer8	p.V290Sfs*8	ENST00000371953	NM_000314.4	288	gaa/gAaa	8/9	NA	2	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.611384050075824	2		219	185	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178642	108178642	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370680798	NA	P-0039805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	70	282	0	ENST00000278616.4:c.5693G>A	p.Arg1898Gln	p.R1898Q	ENST00000278616	NM_000051.3	1898	cGa/cAa	38/63	0.611384050075824	7	FACETS	0.858	0.747	0.977			1	CLONAL	1	TRUE	NA	0.611384050075824	7		282	675	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289871	15289871	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	492	1239	1	ENST00000263388.2:c.3683G>A	p.Gly1228Glu	p.G1228E	ENST00000263388	NM_000435.2	1228	gGa/gAa	22/33	0.299583697768826	2	FACETS	0.806	0.775	0.837	0.806	0.775	0.837	INDETERMINATE	2	TRUE	0	0.611384050075824	2		1240	998	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0039806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	147	383	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	0.279778855500616	2		383	979	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0039806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	194	639	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	0.279778855500616	2		645	1284	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1555525429	NA	P-0039806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	187	696	0	ENST00000269305.4:c.782+1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.279778855500616	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.279778855500616	1		696	943	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508152	106508152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1446853033	NA	P-0039806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	31	318	0	ENST00000359195.3:c.146G>A	p.Arg49His	p.R49H	ENST00000359195	NM_002649.2	49	cGc/cAc	2/11	1	2	FACETS	0.483	0.39	0.588	0.483	0.39	0.588	SUBCLONAL	1	TRUE	1	0.279778855500616	2		318	459	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358475	91358475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs557057587	NA	P-0039806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	151	598	1	ENST00000355112.3:c.4220G>A	p.Arg1407Lys	p.R1407K	ENST00000355112	NM_000057.2	1407	aGa/aAa	22/22	0.251090920213971	3	FACETS	1	0.956	1	0.538	0.491	0.588	CLONAL	1	TRUE	1	0.279778855500616	3		599	1143	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089691	27089701	+	frameshift_variant	Frame_Shift_Del	DEL	ATGTGTCCCCC	ATGTGTCCCCC	-	novel	NA	P-0039806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	188	757	0	ENST00000324856.7:c.2648_2658del	p.Met883ThrfsTer49	p.M883Tfs*49	ENST00000324856	NM_006015.4	883	ATGTGTCCCCCa/a	8/20	0.279778855500616	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.279778855500616	1		757	1118	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610549	81610549	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	35	407	0	ENST00000298171.2:c.2147G>C	p.Ser716Thr	p.S716T	ENST00000298171	NM_000369.2	716	aGc/aCc	10/10	0.226482277556544	1	FACETS	0.358	0.293	0.432	0.358	0.293	0.432	SUBCLONAL	1	TRUE	0	0.279778855500616	1		407	601	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572100	95572100	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	68	516	0	ENST00000393063.1:c.3008G>A	p.Arg1003Gln	p.R1003Q	ENST00000393063	NM_030621.3	1003	cGa/cAa	20/28	0.226482277556544	1	FACETS	0.549	0.476	0.627	0.549	0.476	0.627	SUBCLONAL	1	TRUE	0	0.279778855500616	1		516	762	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703656	47703656	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	119	554	0	ENST00000233146.2:c.2156T>C	p.Leu719Ser	p.L719S	ENST00000233146	NM_000251.2	719	tTg/tCg	13/16	1	2	FACETS	0.985	0.888	1	0.985	0.888	1	CLONAL	1	TRUE	1	0.279778855500616	2		554	864	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38156968	38156968	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	119	447	0	ENST00000317025.8:c.2752G>C	p.Glu918Gln	p.E918Q	ENST00000317025	NM_023034.1	918	Gag/Cag	15/24	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.279778855500616	2		447	823	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1131691023	NA	P-0039807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	462	1081	0	ENST00000269305.4:c.470T>A	p.Val157Asp	p.V157D	ENST00000269305	NM_001126112.2	157	gTc/gAc	5/11	0.433231248672545	2	FACETS	0.839	0.805	0.873	0.839	0.805	0.873	CLONAL	2	TRUE	0	0.545277024215336	2		1081	1010	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720805	89720808	+	frameshift_variant	Frame_Shift_Del	DEL	CTTT	CTTT	-	rs398123330	NA	P-0039807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	67	410	0	ENST00000371953.3:c.956_959del	p.Thr319LysfsTer24	p.T319Kfs*24	ENST00000371953	NM_000314.4	319	aCTTTa/aa	8/9	0.545277024215336	1	FACETS	0.843	0.745	0.946	0.843	0.745	0.946	CLONAL	1	TRUE	0	0.545277024215336	1		410	212	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587172	212587172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	116	648	0	ENST00000342788.4:c.829C>T	p.His277Tyr	p.H277Y	ENST00000342788	NM_005235.2	277	Cac/Tac	7/28	1	2	FACETS	0.577	0.52	0.637	0.577	0.52	0.637	SUBCLONAL	1	TRUE	1	0.545277024215336	2		648	737	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638917	176638917	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749199217	NA	P-0039808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	253	782	0	ENST00000439151.2:c.3517C>T	p.Arg1173Cys	p.R1173C	ENST00000439151	NM_022455.4	1173	Cgc/Tgc	5/23	0.592662371991058	3	FACETS	0.973	0.91	1	0.486	0.455	0.519	CLONAL	1	TRUE	1	0.592662371991058	3		782	1138	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163313565	163313565	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs769098815	NA	P-0039808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	79	371	0	ENST00000271452.3:c.712G>C	p.Glu238Gln	p.E238Q	ENST00000271452	NM_145697.2	238	Gag/Cag	10/14	0.396863776867045	3	FACETS	0.789	0.697	0.887	0.263	0.232	0.296	SUBCLONAL	1	TRUE	0	0.592662371991058	3		371	438	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226553743	226553743	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs755163226	NA	P-0039808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	118	396	0	ENST00000366794.5:c.2417G>C	p.Arg806Thr	p.R806T	ENST00000366794	NM_001618.3	806	aGa/aCa	18/23	0.555092399398412	3	FACETS	1	0.918	1	0.338	0.306	0.371	CLONAL	1	TRUE	0	0.592662371991058	3		396	509	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115877	8115877	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	273	716	0	ENST00000346208.3:c.1223C>A	p.Pro408His	p.P408H	ENST00000346208		408	cCc/cAc	6/6	NA	2	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.592662371991058	2		716	853	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851418	63851418	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	217	666	0	ENST00000279873.7:c.2196G>C	p.Leu732Phe	p.L732F	ENST00000279873	NM_032199.2	732	ttG/ttC	10/10	0.353625197897854	5	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.592662371991058	5		666	1066	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144069	11144069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	331	1060	0	ENST00000358026.2:c.3650C>T	p.Ala1217Val	p.A1217V	ENST00000358026	NM_001128849.1	1217	gCa/gTa	26/36	0.36348586290033	1	FACETS	0.779	0.738	0.821	0.779	0.738	0.821	SUBCLONAL	1	TRUE	0	0.592662371991058	1		1060	1009	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960024	134960024	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1407516775	NA	P-0039808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	103	707	0	ENST00000398015.3:c.2381A>G	p.Glu794Gly	p.E794G	ENST00000398015	NM_004441.4	794	gAg/gGg	13/16	0.300715534570111	3	FACETS	0.501	0.448	0.558	0.167	0.149	0.186	INDETERMINATE	1	TRUE	0	0.592662371991058	3		707	899	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664918	138664918	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	109	243	0	ENST00000330315.3:c.647C>G	p.Ala216Gly	p.A216G	ENST00000330315	NM_023067.3	216	gCc/gGc	1/1	0.300715534570111	3	FACETS	1	0.978	1	0.428	0.388	0.47	INDETERMINATE	1	TRUE	0	0.592662371991058	3		243	371	SUCCESS
APC	324	MSKCC	GRCh37	5	112175401	112175406	+	inframe_deletion	In_Frame_Del	DEL	AAGTCC	AAGTCC	-	novel	NA	P-0039808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	93	413	0	ENST00000257430.4:c.4111_4116del	p.Ser1371_Pro1372del	p.S1371_P1372del	ENST00000257430	NM_000038.5	1370	aaAAGTCCa/aaa	16/16	0.592662371991058	3	FACETS	0.902	0.806	1	0.451	0.403	0.502	CLONAL	1	TRUE	1	0.592662371991058	3		413	451	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910331	29910331	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1482193506	NA	P-0039808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	620	848	0	ENST00000376809.5:c.1A>G	p.Met1?	p.M1?	ENST00000376809	NM_002116.7	1	Atg/Gtg	1/8	0.563717270432489	3	FACETS	0.849	0.822	0.875	0.849	0.822	0.875	CLONAL	3	TRUE	0	0.592662371991058	3		848	1065	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671858	30671858	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	483	1077	1	ENST00000376406.3:c.5102A>C	p.Gln1701Pro	p.Q1701P	ENST00000376406	NM_014641.2	1701	cAa/cCa	10/15	0.563717270432489	3	FACETS	0.811	0.776	0.846	0.541	0.517	0.564	CLONAL	2	TRUE	0	0.592662371991058	3		1078	1303	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683622	162683622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	254	696	0	ENST00000366898.1:c.347C>T	p.Ser116Phe	p.S116F	ENST00000366898	NM_004562.2	116	tCt/tTt	3/12	0.569206232857004	3	FACETS	1	0.985	1	0.578	0.541	0.616	CLONAL	1	TRUE	1	0.592662371991058	3		696	961	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729472	41729472	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	553	814	1	ENST00000242208.4:c.1057G>C	p.Glu353Gln	p.E353Q	ENST00000242208	NM_002192.2	353	Gag/Cag	3/3	0.592662371991058	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.592662371991058	3		815	1119	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815652	139815652	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	235	730	0	ENST00000247668.2:c.1123G>T	p.Ala375Ser	p.A375S	ENST00000247668	NM_021138.3	375	Gcc/Tcc	9/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.592662371991058	2		730	747	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111496	8111497	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0039809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	39	920	0	ENST00000346208.3:c.982_983del	p.Trp328GlufsTer23	p.W328Efs*23	ENST00000346208		328	TGg/g	5/6	1	2	FACETS	0.502	0.415	0.6	0.502	0.415	0.6	SUBCLONAL	1	TRUE	1	0.200956427824513	2		920	773	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578247	7578247	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0039811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	781	868	0	ENST00000269305.4:c.602T>A	p.Leu201Ter	p.L201*	ENST00000269305	NM_001126112.2	201	tTg/tAg	6/11	0.629114621303635	7	FACETS	0.958	0.94	0.975	0.958	0.94	0.975	CLONAL	7	FALSE	0	0.629114621303635	7		868	953	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18747471	18747471	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs368190625	NA	P-0039811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	74	442	0	ENST00000266497.5:c.3932A>C	p.Gln1311Pro	p.Q1311P	ENST00000266497		1311	cAa/cCa	28/31	0.377692086986439	5	FACETS	0.799	0.707	0.896	0.533	0.471	0.598	SUBCLONAL	2	FALSE	2	0.629114621303635	5		442	286	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636057	28636057	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	173	824	1	ENST00000241453.7:c.315G>T	p.Trp105Cys	p.W105C	ENST00000241453	NM_004119.2	105	tgG/tgT	3/24	0.545430363323135	4	FACETS	0.816	0.756	0.878	0.408	0.378	0.439	CLONAL	2	FALSE	0	0.629114621303635	4		825	549	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211904	+	frameshift_variant	Frame_Shift_Del	DEL	ACCCCCC	ACCCCCC	-	novel	NA	P-0039811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1538	165	1212	0	ENST00000222270.7:c.1649_1655del	p.Asp550AlafsTer53	p.D550Afs*53	ENST00000222270	NM_014727.1	550	gACCCCCCc/gc	3/37	0.629114621303635	9	FACETS	0.986	0.902	1			1	CLONAL	1	FALSE	NA	0.629114621303635	9		1212	1703	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956125	55956125	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	160	492	0	ENST00000263923.4:c.3190G>T	p.Asp1064Tyr	p.D1064Y	ENST00000263923	NM_002253.2	1064	Gat/Tat	23/30	0.619975889141544	3	FACETS	0.91	0.859	0.959	0.91	0.859	0.959	CLONAL	3	FALSE	0	0.629114621303635	3		492	245	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259428	55259428	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	158	521	0	ENST00000275493.2:c.2486A>T	p.Glu829Val	p.E829V	ENST00000275493	NM_005228.3	829	gAg/gTg	21/28	0.629114621303635	7	FACETS	0.889	0.816	0.964	0.356	0.326	0.386	CLONAL	2	FALSE	2	0.629114621303635	7		521	727	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115873	8115874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0039813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	160	715	0	ENST00000346208.3:c.1220dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tCcg	6/6	1	2	FACETS	0.907	0.833	0.985	0.907	0.833	0.985	CLONAL	1	TRUE	1	0.448187558411487	2		715	787	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591104	67591115	+	inframe_deletion	In_Frame_Del	DEL	TTAAACCAGACC	TTAAACCAGACC	-	novel	NA	P-0039813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	27	353	0	ENST00000274335.5:c.1700_1711del	p.Lys567_Leu570del	p.K567_L570del	ENST00000274335		566	aTTAAACCAGACCtt/att	12/15	1	2	FACETS	0.231	0.183	0.286	0.231	0.183	0.286	SUBCLONAL	1	TRUE	1	0.448187558411487	2		353	521	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141801	108141801	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	131	394	0	ENST00000278616.4:c.2849T>C	p.Leu950Pro	p.L950P	ENST00000278616	NM_000051.3	950	cTt/cCt	19/63	0.81818580454443	3	FACETS	0.972	0.89	1	0.486	0.445	0.529	CLONAL	1	TRUE	1	0.882460378171219	3		394	440	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937035	48937035	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	239	370	0	ENST00000267163.4:c.806del	p.Asn269MetfsTer17	p.N269Mfs*17	ENST00000267163	NM_000321.2	268	gAa/ga	8/27	0.882460378171219	2	FACETS	0.981	0.952	1	0.981	0.952	1	CLONAL	2	TRUE	0	0.882460378171219	2		370	276	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0039831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	55	264	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.9	0.788	1	0.9	0.788	1	CLONAL	1	TRUE	1	0.804089653957485	2		264	152	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696708	47696708	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	133	436	0	ENST00000347630.2:c.240C>G	p.Ser80Arg	p.S80R	ENST00000347630	NM_001007230.1	80	agC/agG	5/11	1	2	FACETS	0.911	0.838	0.987	0.911	0.838	0.987	CLONAL	1	TRUE	1	0.804089653957485	2		436	363	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519886	NA	P-0039831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	88	321	0	ENST00000349496.5:c.97T>G	p.Ser33Ala	p.S33A	ENST00000349496	NM_001904.3	33	Tct/Gct	3/15	1	2	FACETS	0.879	0.791	0.969	0.879	0.791	0.969	CLONAL	1	TRUE	1	0.804089653957485	2		321	249	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105967	27105967	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	106	544	0	ENST00000324856.7:c.5578G>T	p.Glu1860Ter	p.E1860*	ENST00000324856	NM_006015.4	1860	Gag/Tag	20/20	1	2	FACETS	0.867	0.788	0.949	0.867	0.788	0.949	CLONAL	1	TRUE	1	0.804089653957485	2		544	304	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426172	49426172	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	82	706	0	ENST00000301067.7:c.12316A>G	p.Ser4106Gly	p.S4106G	ENST00000301067	NM_003482.3	4106	Agc/Ggc	39/54	0.735698429379903	3	FACETS	0.573	0.507	0.644	0.287	0.253	0.322	SUBCLONAL	1	TRUE	1	0.804089653957485	3		706	499	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	129	417	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.232970281581067	3	FACETS	1	0.979	1	0.829	0.757	0.903	CLONAL	2	TRUE	0	0.260697830151257	3		417	450	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729743	162729743	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	94	582	0	ENST00000367921.3:c.829C>G	p.Arg277Gly	p.R277G	ENST00000367921	NM_006182.2	277	Cgc/Ggc	8/18	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.260697830151257	2		582	651	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77054889	77054889	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1389156966	NA	P-0039832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	35	405	0	ENST00000356341.3:c.973C>G	p.Pro325Ala	p.P325A	ENST00000356341	NM_002576.4	325	Cca/Gca	10/15	1	2	FACETS	0.624	0.512	0.751	0.624	0.512	0.751	SUBCLONAL	1	TRUE	1	0.260697830151257	2		405	430	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230671	46230671	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	101	397	0	ENST00000334344.6:c.920C>T	p.Ala307Val	p.A307V	ENST00000334344	NM_152641.2	307	gCa/gTa	8/21	0.232439351196474	2	FACETS	0.94	0.846	1	0.94	0.846	1	CLONAL	2	TRUE	0	0.260697830151257	2		397	412	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039494	49039494	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	61	441	0	ENST00000267163.4:c.2480del	p.Pro827GlnfsTer6	p.P827Qfs*6	ENST00000267163	NM_000321.2	827	Cca/ca	23/27	0.260697830151257	1	FACETS	0.906	0.784	1	0.906	0.784	1	CLONAL	1	TRUE	0	0.260697830151257	1		441	449	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40682108	40682108	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	93	547	0	ENST00000249776.8:c.663G>T	p.Leu221Phe	p.L221F	ENST00000249776	NM_033286.3	221	ttG/ttT	6/9	0.260697830151257	1	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	0	0.260697830151257	1		547	616	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40682117	40682117	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	93	526	0	ENST00000249776.8:c.672G>T	p.Lys224Asn	p.K224N	ENST00000249776	NM_033286.3	224	aaG/aaT	6/9	0.260697830151257	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.260697830151257	1		526	600	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	116	721	1	ENST00000269305.4:c.313G>T	p.Gly105Cys	p.G105C	ENST00000269305	NM_001126112.2	105	Ggc/Tgc	4/11	0.260697830151257	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.260697830151257	1		722	742	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170723	7170723	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	39	784	1	ENST00000302850.5:c.1308G>T	p.Arg436Ser	p.R436S	ENST00000302850	NM_000208.2	436	agG/agT	6/22	0.260697830151257	1	FACETS	0.366	0.303	0.438	0.366	0.303	0.438	SUBCLONAL	1	TRUE	0	0.260697830151257	1		785	710	SUCCESS
APC	324	MSKCC	GRCh37	5	112176538	112176538	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1397709973	NA	P-0039832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	32	301	0	ENST00000257430.4:c.5247G>T	p.Gln1749His	p.Q1749H	ENST00000257430	NM_000038.5	1749	caG/caT	16/16	1	2	FACETS	0.684	0.556	0.828	0.684	0.556	0.828	SUBCLONAL	1	TRUE	1	0.260697830151257	2		301	359	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978575	70978575	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	127	563	0	ENST00000276594.2:c.1078C>G	p.Gln360Glu	p.Q360E	ENST00000276594	NM_024504.3	360	Caa/Gaa	5/8	0.13772782138719	4	FACETS	0.791	0.717	0.869	0.791	0.717	0.869	INDETERMINATE	2	TRUE	2	0.260697830151257	4		563	776	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742547	145742547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	159	697	0	ENST00000428558.2:c.241C>T	p.His81Tyr	p.H81Y	ENST00000428558	NM_004260.3	81	Cat/Tat	4/22	0.13772782138719	4	FACETS	0.939	0.861	1	0.939	0.861	1	INDETERMINATE	2	TRUE	2	0.260697830151257	4		697	819	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485860	8485860	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs778486665	NA	P-0039832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	36	337	0	ENST00000356435.5:c.2957C>A	p.Pro986Gln	p.P986Q	ENST00000356435		986	cCa/cAa	17/35	1	2	FACETS	0.746	0.614	0.894	0.746	0.614	0.894	SUBCLONAL	1	TRUE	1	0.260697830151257	2		337	370	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248118	98248118	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554702186	NA	P-0039832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	72	488	0	ENST00000331920.6:c.433C>T	p.Gln145Ter	p.Q145*	ENST00000331920	NM_000264.3	145	Cag/Tag	3/24	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.260697830151257	2		488	491	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	112	236	0				ENST00000310581	NM_198253.2	-/1132			0.40022878209251	3	FACETS	0.973	0.885	1	0.973	0.885	1	CLONAL	2	TRUE	1	0.40022878209251	3		236	345	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0039849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	115	652	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.958	0.865	1	0.958	0.865	1	CLONAL	1	TRUE	1	0.40022878209251	2		652	600	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217299	11217299	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519779	NA	P-0039849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	184	832	0	ENST00000361445.4:c.4379T>C	p.Leu1460Pro	p.L1460P	ENST00000361445	NM_004958.3	1460	cTt/cCt	30/58	1	2	FACETS	0.983	0.908	1	0.983	0.908	1	CLONAL	1	TRUE	1	0.40022878209251	2		832	935	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549482	5549482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	206	849	1	ENST00000397747.3:c.509C>T	p.Pro170Leu	p.P170L	ENST00000397747	NM_025239.3	170	cCt/cTt	4/7	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.40022878209251	2		850	996	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0039851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	644	953	10	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.968566229580379	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.969131366989833	2		963	656	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612091	189612091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	233	879	3	ENST00000264731.3:c.1843C>T	p.His615Tyr	p.H615Y	ENST00000264731	NM_003722.4	615	Cat/Tat	14/14	0.902240947685825	5	FACETS	0.879	0.818	0.942	0.22	0.204	0.236	CLONAL	1	TRUE	1	0.969131366989833	5		882	1342	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649561	48649561	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	352	1209	8	ENST00000376670.3:c.49del	p.Gln17SerfsTer120	p.Q17Sfs*120	ENST00000376670	NM_002049.3	15	ctC/ct	2/6	0.421460470604956	4	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.969131366989833	4		1217	1038	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658283	18658283	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	196	593	1	ENST00000266497.5:c.3088G>T	p.Gly1030Ter	p.G1030*	ENST00000266497		1030	Gga/Tga	22/31	0.669145899531242	4	FACETS	0.946	0.877	1			1	CLONAL	1	TRUE	NA	0.969131366989833	4		594	842	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919295	48919295	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0039851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4	287	246	3	ENST00000267163.4:c.460A>T	p.Lys154Ter	p.K154*	ENST00000267163	NM_000321.2	154	Aag/Tag	4/27	0.969131366989833	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.969131366989833	2		249	291	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211845	123211845	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	193	540	0	ENST00000218089.9:c.2712G>T	p.Met904Ile	p.M904I	ENST00000218089	NM_001042749.1	904	atG/atT	27/35	0.969131366989833	3	FACETS	0.897	0.834	0.963	0.449	0.417	0.482	CLONAL	1	TRUE	1	0.969131366989833	3		540	659	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456608	32456608	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	52	96	0	ENST00000332351.3:c.284C>A	p.Pro95His	p.P95H	ENST00000332351	NM_024426.4	95	cCt/cAt	1/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.969131366989833	2		96	81	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577347	64577347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	315	946	7	ENST00000312049.6:c.235C>T	p.Pro79Ser	p.P79S	ENST00000312049	NM_130799.2	79	Ccc/Tcc	2/10	1	2	FACETS	0.976	0.929	1	0.976	0.929	1	CLONAL	1	TRUE	1	0.969131366989833	2		953	666	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858556	9858556	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	215	646	3	ENST00000330684.3:c.2845T>C	p.Phe949Leu	p.F949L	ENST00000330684	NM_001134407.1	949	Ttt/Ctt	13/13	0.932484231852023	3	FACETS	0.966	0.902	1	0.483	0.451	0.516	CLONAL	1	TRUE	1	0.969131366989833	3		649	682	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515613	31515613	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1561283913	NA	P-0039851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	205	605	4	ENST00000344624.3:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000344624		336	Gag/Tag	4/33	0.895425036308697	4	FACETS	0.905	0.841	0.973	0.453	0.42	0.487	CLONAL	1	TRUE	2	0.969131366989833	4		609	920	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971243	13971243	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	249	654	5	ENST00000405192.2:c.686A>T	p.Gln229Leu	p.Q229L	ENST00000405192	NM_001163147.1	229	cAg/cTg	8/12	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.969131366989833	2		659	512	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140449139	140449139	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1562939198	NA	P-0039851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	235	541	0	ENST00000288602.6:c.1940A>G	p.Tyr647Cys	p.Y647C	ENST00000288602	NM_004333.4	647	tAt/tGt	16/18	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.969131366989833	2		541	482	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1331520	1331520	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	226	647	2	ENST00000400841.2:c.8G>T	p.Arg3Leu	p.R3L	ENST00000400841		3	cGg/cTg	1/6	0.790670240960603	4	FACETS	0.832	0.774	0.891			1	CLONAL	1	TRUE	NA	0.969131366989833	4		649	1104	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	210	383	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.538117182439915	3	FACETS	1	0.95	1	1	0.95	1	CLONAL	3	FALSE	0	0.540319416099325	3		383	329	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099397	27099397	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	90	684	0	ENST00000324856.7:c.3634C>T	p.Gln1212Ter	p.Q1212*	ENST00000324856	NM_006015.4	1212	Cag/Tag	14/20	0.474741841592099	4	FACETS	1	0.979	1	0.353	0.316	0.393	CLONAL	1	FALSE	0	0.540319416099325	4		684	363	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309866	65309866	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	173	520	0	ENST00000342505.4:c.2284G>C	p.Glu762Gln	p.E762Q	ENST00000342505	NM_002227.2	762	Gag/Cag	17/25	0.523373878333172	2	FACETS	0.991	0.93	1	0.991	0.93	1	CLONAL	2	FALSE	0	0.540319416099325	2		520	323	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429779	78429779	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	71	419	0	ENST00000370768.2:c.1009G>C	p.Glu337Gln	p.E337Q	ENST00000370768	NM_003902.3	337	Gaa/Caa	12/20	0.523373878333172	2	FACETS	0.826	0.741	0.913	0.826	0.741	0.913	CLONAL	2	FALSE	0	0.540319416099325	2		419	159	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243708880	243708880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	60	441	0	ENST00000263826.5:c.1183G>A	p.Asp395Asn	p.D395N	ENST00000263826	NM_005465.4	395	Gat/Aat	11/13	0.540319416099325	5	FACETS	1	0.961	1	0.437	0.379	0.499	CLONAL	1	FALSE	2	0.540319416099325	5		441	307	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61197641	61197641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	177	568	0	ENST00000301761.2:c.23C>T	p.Ser8Leu	p.S8L	ENST00000301761	NM_017841.2	8	tCg/tTg	1/4	0.282414282501567	5	FACETS	1	0.966	1	0.714	0.662	0.767	INDETERMINATE	2	FALSE	2	0.540319416099325	5		568	554	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196471	67196471	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs546014798	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	155	689	0	ENST00000312629.5:c.97G>A	p.Glu33Lys	p.E33K	ENST00000312629	NM_003952.2	33	Gag/Aag	2/15	0.282414282501567	5	FACETS	1	0.983	1	0.432	0.395	0.47	INDETERMINATE	1	FALSE	2	0.540319416099325	5		689	802	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200506	67200506	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	167	791	0	ENST00000312629.5:c.700G>A	p.Glu234Lys	p.E234K	ENST00000312629	NM_003952.2	234	Gag/Aag	8/15	0.282414282501567	5	FACETS	1	0.984	1	0.426	0.391	0.462	INDETERMINATE	1	FALSE	2	0.540319416099325	5		791	876	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172408	108172408	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	74	473	0	ENST00000278616.4:c.5211G>C	p.Leu1737Phe	p.L1737F	ENST00000278616	NM_000051.3	1737	ttG/ttC	35/63	0.282414282501567	5	FACETS	1	0.921	1	0.697	0.62	0.779	INDETERMINATE	2	FALSE	2	0.540319416099325	5		473	237	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202721	108202721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758128730	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	54	387	0	ENST00000278616.4:c.7745G>A	p.Arg2582Lys	p.R2582K	ENST00000278616	NM_000051.3	2582	aGa/aAa	52/63	0.282414282501567	5	FACETS	0.757	0.654	0.868	0.505	0.436	0.579	INDETERMINATE	2	FALSE	2	0.540319416099325	5		387	239	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236120	108236120	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	137	626	0	ENST00000278616.4:c.9056G>C	p.Gly3019Ala	p.G3019A	ENST00000278616	NM_000051.3	3019	gGa/gCa	63/63	0.282414282501567	5	FACETS	1	0.964	1	0.727	0.667	0.788	INDETERMINATE	2	FALSE	2	0.540319416099325	5		626	421	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432863	432863	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	130	586	0	ENST00000399788.2:c.2053C>G	p.Leu685Val	p.L685V	ENST00000399788	NM_001042603.1	685	Ctc/Gtc	15/28	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	1	FALSE	NA	0.540319416099325	2		586	409	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	441043	441043	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1164949015	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	114	520	0	ENST00000399788.2:c.1715C>G	p.Ser572Cys	p.S572C	ENST00000399788	NM_001042603.1	572	tCt/tGt	13/28	NA	2	FACETS	1	0.95	1			1	INDETERMINATE	1	FALSE	NA	0.540319416099325	2		520	395	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245376	46245376	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	88	563	0	ENST00000334344.6:c.3470C>G	p.Ser1157Ter	p.S1157*	ENST00000334344	NM_152641.2	1157	tCa/tGa	15/21	0.540319416099325	4	FACETS	0.791	0.708	0.878	0.791	0.708	0.878	SUBCLONAL	2	FALSE	2	0.540319416099325	4		563	317	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415831	49415831	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	119	451	0	ENST00000301067.7:c.16516G>C	p.Glu5506Gln	p.E5506Q	ENST00000301067	NM_003482.3	5506	Gag/Cag	53/54	0.540319416099325	4	FACETS	1	0.979	1	0.644	0.583	0.707	CLONAL	1	FALSE	2	0.540319416099325	4		451	527	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415882	49415882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	120	514	0	ENST00000301067.7:c.16465G>A	p.Asp5489Asn	p.D5489N	ENST00000301067	NM_003482.3	5489	Gac/Aac	53/54	0.540319416099325	4	FACETS	1	0.969	1	0.583	0.528	0.64	CLONAL	1	FALSE	2	0.540319416099325	4		514	587	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111855952	111855952	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	253	576	0	ENST00000341259.2:c.3G>A	p.Met1?	p.M1?	ENST00000341259	NM_005475.2	1	atG/atA	2/8	0.475338713686978	4	FACETS	0.922	0.866	0.98	0.922	0.866	0.98	CLONAL	2	FALSE	2	0.540319416099325	4		576	782	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536716	120536716	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	188	841	0	ENST00000229340.5:c.376G>C	p.Glu126Gln	p.E126Q	ENST00000229340	NM_006861.6	126	Gag/Cag	5/6	0.475338713686978	4	FACETS	0.907	0.843	0.972	0.907	0.843	0.972	CLONAL	2	FALSE	2	0.540319416099325	4		841	591	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252685	133252685	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149029910	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	29	564	0	ENST00000320574.5:c.1015G>A	p.Asp339Asn	p.D339N	ENST00000320574	NM_006231.2	339	Gat/Aat	10/49	0.475338713686978	4	FACETS	0.515	0.414	0.63	0.258	0.207	0.315	SUBCLONAL	1	FALSE	2	0.540319416099325	4		564	321	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597546	28597546	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	82	704	0	ENST00000241453.7:c.2359G>C	p.Asp787His	p.D787H	ENST00000241453	NM_004119.2	787	Gat/Cat	19/24	0.475338713686978	4	FACETS	0.759	0.676	0.846	0.759	0.676	0.846	SUBCLONAL	2	FALSE	2	0.540319416099325	4		704	308	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912304	32912304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	45	516	0	ENST00000380152.3:c.3812C>T	p.Ser1271Leu	p.S1271L	ENST00000380152		1271	tCa/tTa	11/27	0.475338713686978	4	FACETS	1	0.933	1	0.594	0.504	0.691	CLONAL	1	FALSE	2	0.540319416099325	4		516	216	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915220	32915220	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs876659031	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	77	708	0	ENST00000380152.3:c.6728C>G	p.Ser2243Cys	p.S2243C	ENST00000380152		2243	tCt/tGt	11/27	0.475338713686978	4	FACETS	0.825	0.734	0.921	0.825	0.734	0.921	CLONAL	2	FALSE	2	0.540319416099325	4		708	266	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046637	30046637	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	150	565	0	ENST00000331968.5:c.2546G>C	p.Arg849Pro	p.R849P	ENST00000331968	NM_002742.2	849	cGa/cCa	18/18	0.475338713686978	4	FACETS	0.938	0.864	1	0.938	0.864	1	CLONAL	2	FALSE	2	0.540319416099325	4		565	456	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061115	38061115	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	24	83	0	ENST00000250448.2:c.874G>T	p.Glu292Ter	p.E292*	ENST00000250448	NM_004496.3	292	Gag/Tag	2/2	0.475338713686978	4	FACETS	1	0.878	1	1	0.878	1	CLONAL	2	FALSE	2	0.540319416099325	4		83	62	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422130	81422130	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	177	605	0	ENST00000298171.2:c.106G>T	p.Asp36Tyr	p.D36Y	ENST00000298171	NM_000369.2	36	Gac/Tac	1/10	0.475338713686978	4	FACETS	0.87	0.806	0.935	0.87	0.806	0.935	CLONAL	2	FALSE	2	0.540319416099325	4		605	580	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610315	81610315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1324770985	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	84	551	0	ENST00000298171.2:c.1913C>T	p.Ala638Val	p.A638V	ENST00000298171	NM_000369.2	638	gCc/gTc	10/10	0.475338713686978	4	FACETS	0.858	0.768	0.953	0.858	0.768	0.953	CLONAL	2	FALSE	2	0.540319416099325	4		551	279	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90634818	90634818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	161	699	0	ENST00000330062.3:c.174G>A	p.Met58Ile	p.M58I	ENST00000330062	NM_002168.2	58	atG/atA	2/11	0.280861698381906	4	FACETS	0.759	0.699	0.82	0.759	0.699	0.82	INDETERMINATE	2	FALSE	2	0.540319416099325	4		699	605	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90634838	90634838	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	161	689	0	ENST00000330062.3:c.154G>A	p.Glu52Lys	p.E52K	ENST00000330062	NM_002168.2	52	Gag/Aag	2/11	0.280861698381906	4	FACETS	1	0.988	1	0.723	0.665	0.782	INDETERMINATE	1	FALSE	2	0.540319416099325	4		689	635	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639265	3639265	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1168844302	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	260	903	0	ENST00000294008.3:c.4374G>C	p.Met1458Ile	p.M1458I	ENST00000294008	NM_032444.2	1458	atG/atC	12/15	0.212249796952973	5	FACETS	1	0.957	1	0.682	0.64	0.724	INDETERMINATE	2	FALSE	2	0.540319416099325	5		903	852	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346169	89346169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770262960	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	84	310	0	ENST00000301030.4:c.6781G>A	p.Glu2261Lys	p.E2261K	ENST00000301030	NM_001256183.1	2261	Gaa/Aaa	9/13	0.212249796952973	5	FACETS	1	0.962	1	0.772	0.693	0.854	INDETERMINATE	2	FALSE	2	0.540319416099325	5		310	243	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216889	7216889	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	118	595	0	ENST00000380728.2:c.632G>A	p.Arg211Lys	p.R211K	ENST00000380728		211	aGa/aAa	7/11	0.540319416099325	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	0	0.540319416099325	1		595	286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578259	7578260	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTCGGATAAGATGCTG	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	125	743	0	ENST00000269305.4:c.574_589dup	p.Val197AlafsTer17	p.V197Afs*17	ENST00000269305	NM_001126112.2	197	gtg/gCAGCATCTTATCCGAGtg	6/11	0.540319416099325	1	FACETS	0.877	0.802	0.955	0.877	0.802	0.955	CLONAL	1	FALSE	0	0.540319416099325	1		743	385	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496952	29496952	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	47	405	0	ENST00000356175.3:c.523C>G	p.His175Asp	p.H175D	ENST00000356175	NM_000267.3	175	Cat/Gat	5/57	0.540319416099325	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	FALSE	0	0.540319416099325	1		405	113	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683977	29683977	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	78	512	0	ENST00000356175.3:c.7676-1G>A		p.X2559_splice	ENST00000356175	NM_000267.3	2559			0.540319416099325	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	FALSE	0	0.540319416099325	1		512	193	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881588	37881588	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	270	780	0	ENST00000269571.5:c.2658C>G	p.Ile886Met	p.I886M	ENST00000269571		886	atC/atG	22/27	0.540319416099325	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	0	0.540319416099325	1		780	570	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37882913	37882913	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs112493843	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	153	755	0	ENST00000269571.5:c.2970+1G>A		p.X990_splice	ENST00000269571		990			0.540319416099325	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	0	0.540319416099325	1		755	326	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804406	46804406	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	157	513	0	ENST00000290295.7:c.602-1G>T		p.X201_splice	ENST00000290295	NM_006361.5	201			0.540319416099325	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	0	0.540319416099325	1		513	297	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118578	11118578	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	94	392	0	ENST00000358026.2:c.2002G>C	p.Glu668Gln	p.E668Q	ENST00000358026	NM_001128849.1	668	Gag/Cag	14/36	0.475338713686978	4	FACETS	0.807	0.725	0.892	0.807	0.725	0.892	CLONAL	2	FALSE	2	0.540319416099325	4		392	332	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118653	11118653	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	269	804	0	ENST00000358026.2:c.2077C>G	p.Pro693Ala	p.P693A	ENST00000358026	NM_001128849.1	693	Cca/Gca	14/36	0.475338713686978	4	FACETS	0.802	0.753	0.852	0.802	0.753	0.852	CLONAL	2	FALSE	2	0.540319416099325	4		804	956	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912096	50912096	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	281	1006	0	ENST00000440232.2:c.1830C>G	p.Ile610Met	p.I610M	ENST00000440232	NM_002691.3	610	atC/atG	15/27	0.475338713686978	4	FACETS	0.945	0.89	1	0.945	0.89	1	CLONAL	2	FALSE	2	0.540319416099325	4		1006	848	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469041	25469041	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	51	810	0	ENST00000264709.3:c.1417G>T	p.Glu473Ter	p.E473*	ENST00000264709	NM_175629.2	473	Gag/Tag	11/23	0.240369082461232	5	FACETS	0.521	0.442	0.608	0.174	0.147	0.203	INDETERMINATE	1	FALSE	2	0.540319416099325	5		810	656	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026971	48026971	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	69	446	0	ENST00000234420.5:c.1849C>G	p.Leu617Val	p.L617V	ENST00000234420	NM_000179.2	617	Ctt/Gtt	4/10	0.240369082461232	5	FACETS	1	0.944	1	0.741	0.656	0.829	INDETERMINATE	2	FALSE	2	0.540319416099325	5		446	208	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61725920	61725920	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs928432127	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	41	454	0	ENST00000401558.2:c.647C>G	p.Ser216Cys	p.S216C	ENST00000401558	NM_003400.3	216	tCt/tGt	9/25	0.240369082461232	5	FACETS	1	0.958	1	0.495	0.417	0.579	INDETERMINATE	1	FALSE	2	0.540319416099325	5		454	185	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812182	212812182	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	45	329	0	ENST00000342788.4:c.394C>G	p.Gln132Glu	p.Q132E	ENST00000342788	NM_005235.2	132	Caa/Gaa	3/28	0.240369082461232	5	FACETS	0.833	0.71	0.964	0.555	0.473	0.643	INDETERMINATE	2	FALSE	2	0.540319416099325	5		329	181	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560998	9560998	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	138	461	0	ENST00000353224.5:c.784G>A	p.Asp262Asn	p.D262N	ENST00000353224	NM_177990.2	262	Gat/Aat	4/10	0.282414282501567	5	FACETS	1	0.979	1	0.795	0.731	0.86	INDETERMINATE	2	FALSE	2	0.540319416099325	5		461	388	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30946621	30946621	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	32	195	0	ENST00000375687.4:c.43G>C	p.Glu15Gln	p.E15Q	ENST00000375687	NM_015338.5	15	Gag/Cag	1/13	0.282414282501567	5	FACETS	0.459	0.372	0.558	0.153	0.124	0.186	INDETERMINATE	1	FALSE	2	0.540319416099325	5		195	467	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39751917	39751917	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	132	491	0	ENST00000361337.2:c.2278G>C	p.Asp760His	p.D760H	ENST00000361337	NM_003286.2	760	Gat/Cat	21/21	0.282414282501567	5	FACETS	1	0.939	1	0.687	0.629	0.747	INDETERMINATE	2	FALSE	2	0.540319416099325	5		491	429	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860377	42860377	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	292	879	0	ENST00000398585.3:c.500C>G	p.Ser167Cys	p.S167C	ENST00000398585	NM_001135099.1	167	tCt/tGt	5/14	0.371847667240871	2	FACETS	0.932	0.886	0.977	0.932	0.886	0.977	CLONAL	2	FALSE	0	0.540319416099325	2		879	580	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127167	22127167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	108	493	0	ENST00000215832.6:c.961G>A	p.Asp321Asn	p.D321N	ENST00000215832	NM_002745.4	321	Gac/Aac	7/9	0.240369082461232	5	FACETS	0.889	0.804	0.978	0.593	0.536	0.652	INDETERMINATE	2	FALSE	2	0.540319416099325	5		493	407	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051626	30051626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1234052589	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	93	367	0	ENST00000338641.4:c.560G>A	p.Arg187Lys	p.R187K	ENST00000338641	NM_000268.3	187	aGa/aAa	6/16	0.240369082461232	5	FACETS	0.82	0.735	0.91	0.547	0.49	0.607	INDETERMINATE	2	FALSE	2	0.540319416099325	5		367	380	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138452271	138452271	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	49	423	0	ENST00000289153.2:c.982G>T	p.Glu328Ter	p.E328*	ENST00000289153	NM_006219.2	328	Gaa/Taa	6/22	0.538117182439915	3	FACETS	1	0.964	1	0.471	0.406	0.54	CLONAL	1	FALSE	0	0.540319416099325	3		423	163	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198132	185198132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763283780	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	140	617	0	ENST00000265026.3:c.2614G>A	p.Glu872Lys	p.E872K	ENST00000265026	NM_004721.4	872	Gag/Aag	13/14	0.538117182439915	3	FACETS	1	0.986	1	0.467	0.428	0.507	CLONAL	1	FALSE	0	0.540319416099325	3		617	470	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506980	186506980	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	51	357	0	ENST00000323963.5:c.1146G>C	p.Lys382Asn	p.K382N	ENST00000323963		382	aaG/aaC	11/11	0.538117182439915	3	FACETS	1	0.947	1	0.406	0.349	0.465	CLONAL	1	FALSE	0	0.540319416099325	3		357	197	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55987277	55987277	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	52	467	0	ENST00000263923.4:c.148C>G	p.Gln50Glu	p.Q50E	ENST00000263923	NM_002253.2	50	Caa/Gaa	2/30	0.212249796952973	5	FACETS	0.803	0.692	0.921	0.535	0.461	0.614	INDETERMINATE	2	FALSE	2	0.540319416099325	5		467	217	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280043	66280043	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs551656821	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	66	317	0	ENST00000273854.3:c.1646G>A	p.Gly549Asp	p.G549D	ENST00000273854	NM_004439.5	549	gGt/gAt	7/18	0.212249796952973	5	FACETS	1	0.971	1	0.479	0.419	0.543	INDETERMINATE	1	FALSE	2	0.540319416099325	5		317	308	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143043324	143043324	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	61	461	0	ENST00000262992.4:c.2092G>T	p.Glu698Ter	p.E698*	ENST00000262992	NM_001101669.1	698	Gaa/Taa	19/24	0.344048452311259	3	FACETS	0.975	0.864	1	0.65	0.576	0.726	CLONAL	2	FALSE	0	0.540319416099325	3		461	147	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542590	187542590	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	50	565	0	ENST00000441802.2:c.5150G>A	p.Gly1717Glu	p.G1717E	ENST00000441802	NM_005245.3	1717	gGa/gAa	10/27	0.344048452311259	3	FACETS	0.794	0.689	0.904	0.529	0.459	0.603	CLONAL	2	FALSE	0	0.540319416099325	3		565	148	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56171105	56171105	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	16	329	0	ENST00000399503.3:c.1933G>C	p.Asp645His	p.D645H	ENST00000399503	NM_005921.1	645	Gac/Cac	10/20	0.240369082461232	5	FACETS	0.348	0.257	0.457	0.116	0.085	0.153	INDETERMINATE	1	FALSE	2	0.540319416099325	5		329	308	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590490	67590490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	43	276	0	ENST00000274335.5:c.1552G>A	p.Glu518Lys	p.E518K	ENST00000274335		518	Gag/Aag	11/15	0.240369082461232	5	FACETS	0.853	0.725	0.989	0.568	0.483	0.66	INDETERMINATE	2	FALSE	2	0.540319416099325	5		276	169	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645088	86645088	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	60	421	0	ENST00000274376.6:c.1160C>A	p.Ser387Ter	p.S387*	ENST00000274376	NM_002890.2	387	tCa/tAa	8/25	0.240369082461232	5	FACETS	0.91	0.795	1	0.606	0.53	0.688	INDETERMINATE	2	FALSE	2	0.540319416099325	5		421	221	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665482	176665482	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	207	507	0	ENST00000439151.2:c.4166C>G	p.Ser1389Cys	p.S1389C	ENST00000439151	NM_022455.4	1389	tCt/tGt	7/23	0.240369082461232	5	FACETS	1	0.984	1	0.78	0.728	0.832	INDETERMINATE	2	FALSE	2	0.540319416099325	5		507	593	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176678749	176678749	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	102	446	0	ENST00000439151.2:c.4660G>A	p.Glu1554Lys	p.E1554K	ENST00000439151	NM_022455.4	1554	Gag/Aag	12/23	0.240369082461232	5	FACETS	0.859	0.774	0.947	0.572	0.516	0.632	INDETERMINATE	2	FALSE	2	0.540319416099325	5		446	398	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176718993	176718993	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	97	382	0	ENST00000439151.2:c.6297C>A	p.Phe2099Leu	p.F2099L	ENST00000439151	NM_022455.4	2099	ttC/ttA	22/23	0.240369082461232	5	FACETS	0.956	0.861	1	0.637	0.574	0.703	INDETERMINATE	2	FALSE	2	0.540319416099325	5		382	340	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032205	26032205	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	86	408	0	ENST00000244661.2:c.84G>C	p.Lys28Asn	p.K28N	ENST00000244661	NM_003537.3	28	aaG/aaC	1/1	0.475338713686978	4	FACETS	0.799	0.714	0.887	0.799	0.714	0.887	SUBCLONAL	2	FALSE	2	0.540319416099325	4		408	307	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680121	30680121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs117708355	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	159	761	0	ENST00000376406.3:c.1598C>T	p.Ser533Leu	p.S533L	ENST00000376406	NM_014641.2	533	tCa/tTa	5/15	0.475338713686978	4	FACETS	0.884	0.816	0.954	0.884	0.816	0.954	CLONAL	2	FALSE	2	0.540319416099325	4		761	513	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169887	32169887	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	231	861	0	ENST00000375023.3:c.3721G>C	p.Asp1241His	p.D1241H	ENST00000375023	NM_004557.3	1241	Gat/Cat	21/30	0.475338713686978	4	FACETS	0.807	0.754	0.861	0.807	0.754	0.861	CLONAL	2	FALSE	2	0.540319416099325	4		861	816	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170164	32170164	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1015983606	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	266	979	0	ENST00000375023.3:c.3444G>C	p.Glu1148Asp	p.E1148D	ENST00000375023	NM_004557.3	1148	gaG/gaC	21/30	0.475338713686978	4	FACETS	0.994	0.936	1	0.994	0.936	1	CLONAL	2	FALSE	2	0.540319416099325	4		979	763	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287239	33287239	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	156	693	0	ENST00000374542.5:c.1858C>G	p.His620Asp	p.H620D	ENST00000374542	NM_001141970.1	620	Cac/Gac	6/8	0.475338713686978	4	FACETS	0.827	0.762	0.894	0.827	0.762	0.894	CLONAL	2	FALSE	2	0.540319416099325	4		693	538	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109322556	109322556	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	105	677	0	ENST00000436639.2:c.481C>T	p.Gln161Ter	p.Q161*	ENST00000436639	NM_014454.2	161	Cag/Tag	3/10	0.475338713686978	4	FACETS	0.79	0.714	0.869	0.79	0.714	0.869	SUBCLONAL	2	FALSE	2	0.540319416099325	4		677	379	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129076	152129076	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	214	819	0	ENST00000206249.3:c.29C>G	p.Ser10Cys	p.S10C	ENST00000206249	NM_000125.3	10	tCt/tGt	1/8	0.475338713686978	4	FACETS	0.997	0.932	1	0.997	0.932	1	CLONAL	2	FALSE	2	0.540319416099325	4		819	612	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265364	152265364	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775405192	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	30	609	0	ENST00000206249.3:c.817G>A	p.Asp273Asn	p.D273N	ENST00000206249	NM_000125.3	273	Gat/Aat	4/8	0.475338713686978	4	FACETS	0.387	0.311	0.473	0.193	0.155	0.237	SUBCLONAL	1	FALSE	2	0.540319416099325	4		609	442	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6048638	6048638	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs372539944	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	217	703	0	ENST00000265849.7:c.13G>C	p.Glu5Gln	p.E5Q	ENST00000265849	NM_000535.5	5	Gag/Cag	1/15	0.475338713686978	4	FACETS	0.776	0.724	0.83	0.776	0.724	0.83	SUBCLONAL	2	FALSE	2	0.540319416099325	4		703	797	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879331	151879331	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1563292120	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	115	552	1	ENST00000262189.6:c.5614C>T	p.Gln1872Ter	p.Q1872*	ENST00000262189	NM_170606.2	1872	Cag/Tag	36/59	0.344048452311259	3	FACETS	0.994	0.911	1	0.663	0.607	0.719	CLONAL	2	FALSE	0	0.540319416099325	3		553	272	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753178	128753178	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	89	361	0	ENST00000377970.2:c.1339G>C	p.Glu447Gln	p.E447Q	ENST00000377970	NM_002467.4	447	Gaa/Caa	3/3	0.212249796952973	5	FACETS	0.95	0.851	1	0.633	0.567	0.702	INDETERMINATE	2	FALSE	2	0.540319416099325	5		361	314	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5073724	5073724	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	41	354	0	ENST00000381652.3:c.1803G>T	p.Met601Ile	p.M601I	ENST00000381652	NM_004972.3	601	atG/atT	14/25	0.280861698381906	4	FACETS	1	0.943	1	0.639	0.539	0.746	INDETERMINATE	1	FALSE	2	0.540319416099325	4		354	183	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486089	8486089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	117	609	0	ENST00000356435.5:c.2728G>A	p.Glu910Lys	p.E910K	ENST00000356435		910	Gag/Aag	17/35	0.280861698381906	4	FACETS	0.787	0.715	0.861	0.787	0.715	0.861	INDETERMINATE	2	FALSE	2	0.540319416099325	4		609	424	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27173273	27173273	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1172998434	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	182	784	0	ENST00000380036.4:c.814G>A	p.Glu272Lys	p.E272K	ENST00000380036	NM_000459.3	272	Gag/Aag	6/23	0.280861698381906	4	FACETS	0.966	0.898	1	0.966	0.898	1	INDETERMINATE	2	FALSE	2	0.540319416099325	4		784	537	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128432184	128432184	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	20	426	0	ENST00000265960.3:c.262C>G	p.Gln88Glu	p.Q88E	ENST00000265960	NM_001006617.1	88	Caa/Gaa	3/12	0.280861698381906	4	FACETS	0.402	0.307	0.512	0.201	0.153	0.256	INDETERMINATE	1	FALSE	2	0.540319416099325	4		426	284	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139563050	139563050	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	271	899	0	ENST00000308874.7:c.122C>G	p.Ser41Cys	p.S41C	ENST00000308874		41	tCc/tGc	4/10	0.280861698381906	4	FACETS	0.87	0.818	0.923	0.87	0.818	0.923	INDETERMINATE	2	FALSE	2	0.540319416099325	4		899	888	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410441	63410441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	170	810	0	ENST00000330258.3:c.2726C>T	p.Ser909Phe	p.S909F	ENST00000330258	NM_152424.3	909	tCc/tTc	2/2	0.282414282501567	5	FACETS	0.953	0.88	1	0.635	0.587	0.685	INDETERMINATE	2	FALSE	2	0.540319416099325	5		810	598	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185066	123185066	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	70	596	0	ENST00000218089.9:c.1113C>G	p.Phe371Leu	p.F371L	ENST00000218089	NM_001042749.1	371	ttC/ttG	12/35	0.282414282501567	5	FACETS	0.844	0.743	0.95	0.562	0.495	0.633	INDETERMINATE	2	FALSE	2	0.540319416099325	5		596	278	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0039859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	12	343	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.300671948451133	1	FACETS	0.199	0.139	0.273	0.199	0.139	0.273	SUBCLONAL	1	TRUE	0	0.29	1		343	356	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0039859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	145	379	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.199926987209582	3	FACETS	1	0.924	1	0.672	0.616	0.73	CLONAL	2	TRUE	0	0.29	3		379	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0039859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	298	930	0	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	0.206829218499797	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.29	2		930	993	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57470669	57470669	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	35	290	0	ENST00000371085.3:c.142G>T	p.Ala48Ser	p.A48S	ENST00000371085	NM_000516.4	48	Gct/Tct	2/13	0.300671948451133	5	FACETS	0.619	0.506	0.745	0.155	0.126	0.187	SUBCLONAL	1	TRUE	1	0.29	5		290	560	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708981	117708981	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	31	585	0	ENST00000368508.3:c.1976C>G	p.Pro659Arg	p.P659R	ENST00000368508	NM_002944.2	659	cCc/cGc	13/43	1	2	FACETS	0.464	0.374	0.565	0.464	0.374	0.565	SUBCLONAL	1	TRUE	1	0.29	2		585	461	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244406	5244406	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	355	797	0	ENST00000357368.4:c.1076C>A	p.Pro359His	p.P359H	ENST00000357368	NM_002850.3	359	cCt/cAt	11/38	1	2	FACETS	0.961	0.915	1	1	0.996	1	CLONAL	2	TRUE	1	0.436245428104853	2		797	847	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828051	3828051	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	161	610	0	ENST00000262367.5:c.2074C>A	p.Pro692Thr	p.P692T	ENST00000262367	NM_004380.2	692	Ccc/Acc	10/31	0.436245428104853	0	FACETS	0.771	0.711	0.832			1	SUBCLONAL	1	TRUE	0	0.436245428104853	0		610	540	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31466297	31466297	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	244	698	0	ENST00000344624.3:c.2458C>T	p.Gln820Ter	p.Q820*	ENST00000344624		820	Cag/Tag	16/33	0.436245428104853	1	FACETS	0.959	0.898	1	0.959	0.898	1	CLONAL	1	TRUE	0	0.436245428104853	1		698	912	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435355	18435355	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	155	394	0	ENST00000266497.5:c.340T>G	p.Leu114Val	p.L114V	ENST00000266497		114	Tta/Gta	1/31	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.427364991147322	2		394	555	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	202	236	0				ENST00000310581	NM_198253.2	-/1132			0.384161842237653	5	FACETS	0.982	0.912	1	0.655	0.608	0.703	CLONAL	2	TRUE	2	0.384161842237653	5		236	844	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0039926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	341	184	1	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.384161842237653	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.384161842237653	2		185	830	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0039926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	134	209	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.282742812081818	4	FACETS	0.958	0.869	1	0.479	0.434	0.526	CLONAL	1	TRUE	2	0.384161842237653	4		209	1008	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0039926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	30	178	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	0.384161842237653	5	FACETS	0.396	0.318	0.486			1	SUBCLONAL	1	TRUE	NA	0.384161842237653	5		178	621	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868682	37868682	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	122	174	0	ENST00000269571.5:c.1129C>G	p.Leu377Val	p.L377V	ENST00000269571		377	Ctg/Gtg	9/27	0.282742812081818	4	FACETS	0.991	0.895	1	0.496	0.447	0.546	CLONAL	1	TRUE	2	0.384161842237653	4		174	887	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548276	41548276	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	74	134	0	ENST00000263253.7:c.3064G>T	p.Glu1022Ter	p.E1022*	ENST00000263253	NM_001429.3	1022	Gaa/Taa	16/31	0.384161842237653	5	FACETS	1	0.9	1			1	CLONAL	1	TRUE	NA	0.384161842237653	5		134	589	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342379	118342385	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	AAAACTA	AAAACTA	TAGTT	novel	NA	P-0039926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	87	108	1	ENST00000534358.1:c.505_511delinsTAGTT	p.Lys169Ter	p.K169*	ENST00000534358	NM_005933.3	169	AAAACTAgt/TAGTTgt	3/36	0.349374893186583	4	FACETS	0.812	0.724	0.905			1	CLONAL	2	TRUE	NA	0.384161842237653	4		109	386	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285839	46285839	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	169	164	0	ENST00000334344.6:c.5107G>C	p.Asp1703His	p.D1703H	ENST00000334344	NM_152641.2	1703	Gat/Cat	18/21	0.282742812081818	4	FACETS	0.91	0.84	0.983	0.91	0.84	0.983	CLONAL	2	TRUE	2	0.384161842237653	4		164	669	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264345	30264346	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	51	69	0	ENST00000322652.5:c.82dup	p.Ser28PhefsTer55	p.S28Ffs*55	ENST00000322652	NM_015355.2	27	ggt/ggTt	1/16	0.282742812081818	4	FACETS	0.962	0.82	1	0.481	0.41	0.559	CLONAL	1	TRUE	2	0.384161842237653	4		69	382	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265468	198265468	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	99	188	0	ENST00000335508.6:c.2689C>T	p.Leu897Phe	p.L897F	ENST00000335508	NM_012433.2	897	Ctt/Ttt	18/25	0.384161842237653	6	FACETS	0.996	0.888	1			1	CLONAL	1	TRUE	NA	0.384161842237653	6		188	915	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091210	29091210	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	34	41	0	ENST00000328354.6:c.1280T>G	p.Phe427Cys	p.F427C	ENST00000328354	NM_007194.3	427	tTc/tGc	12/15	0.230799441820946	4	FACETS	0.761	0.63	0.904	0.507	0.42	0.603	CLONAL	2	TRUE	1	0.384161842237653	4		41	161	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934807	49934807	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767641458	NA	P-0039926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	186	255	0	ENST00000296474.3:c.2089G>A	p.Ala697Thr	p.A697T	ENST00000296474	NM_002447.2	697	Gca/Aca	7/20	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.384161842237653	2		255	811	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157431693	157431693	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	105	214	0	ENST00000346085.5:c.2369G>C	p.Arg790Thr	p.R790T	ENST00000346085	NM_020732.3	790	aGa/aCa	7/20	0.209573015285592	2	FACETS	0.838	0.752	0.93	0.419	0.376	0.465	INDETERMINATE	1	TRUE	0	0.384161842237653	2		214	652	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0039928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	113	552	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.264986630366464	2		552	772	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0039928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	59	822	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.472	0.405	0.546	0.472	0.405	0.546	SUBCLONAL	1	TRUE	1	0.264986630366464	2		822	943	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0039928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	90	452	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.264986630366464	1	FACETS	0.979	0.87	1	0.979	0.87	1	CLONAL	1	TRUE	0	0.264986630366464	1		452	602	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0039928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	133	405	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.175141376793471	2	FACETS	0.885	0.807	0.966	0.885	0.807	0.966	CLONAL	2	TRUE	0	0.264986630366464	2		405	567	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211778	5211778	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs370553812	NA	P-0039928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	130	677	0	ENST00000357368.4:c.5057G>A	p.Arg1686Gln	p.R1686Q	ENST00000357368	NM_002850.3	1686	cGg/cAg	33/38	0.171400352564696	3	FACETS	0.759	0.689	0.832	0.759	0.689	0.832	SUBCLONAL	2	TRUE	1	0.264986630366464	3		677	732	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	19	236	0				ENST00000310581	NM_198253.2	-/1132			0.125479132590263	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		236	185	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696674	47696674	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	42	453	0	ENST00000347630.2:c.274A>C	p.Ser92Arg	p.S92R	ENST00000347630	NM_001007230.1	92	Agc/Cgc	5/11	0.0926719276244685	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		453	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0039970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	188	478	5	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.20119628644874	2	FACETS	0.838	0.777	0.9	1	0.986	1	CLONAL	3	TRUE	0	0.219069566033945	2		483	683	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0039970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	36	345	1	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	1	2	FACETS	0.856	0.704	1	0.856	0.704	1	CLONAL	1	TRUE	1	0.219069566033945	2		346	384	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851324	156851324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759637817	NA	P-0039970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	94	741	0	ENST00000524377.1:c.2281C>T	p.Arg761Trp	p.R761W	ENST00000524377	NM_002529.3	761	Cgg/Tgg	17/17	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.219069566033945	2		741	698	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872969	136872969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767830104	NA	P-0039970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	49	412	0	ENST00000241393.3:c.529G>A	p.Val177Ile	p.V177I	ENST00000241393	NM_003467.2	177	Gtc/Atc	2/2	0.219069566033945	3	FACETS	1	0.919	1	0.565	0.479	0.66	CLONAL	1	TRUE	1	0.219069566033945	3		412	439	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40384105	40384105	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	80	439	0	ENST00000293328.3:c.41C>G	p.Ala14Gly	p.A14G	ENST00000293328	NM_012448.3	14	gCc/gGc	2/19	0.219069566033945	3	FACETS	1	0.966	1	0.64	0.564	0.722	CLONAL	1	TRUE	1	0.219069566033945	3		439	633	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617538	158617538	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	63	529	0	ENST00000263640.3:c.1118A>C	p.Asn373Thr	p.N373T	ENST00000263640	NM_001105.4	373	aAt/aCt	9/11	0.219069566033945	3	FACETS	1	0.911	1	0.535	0.463	0.614	CLONAL	1	TRUE	1	0.219069566033945	3		529	596	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067371	37067371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs989382971	NA	P-0039970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	29	486	0	ENST00000231790.2:c.1282G>A	p.Asp428Asn	p.D428N	ENST00000231790	NM_000249.3	428	Gat/Aat	12/19	1	2	FACETS	0.562	0.45	0.69	0.562	0.45	0.69	SUBCLONAL	1	TRUE	1	0.219069566033945	2		486	471	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670595	134670595	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	79	787	0	ENST00000398015.3:c.506C>A	p.Thr169Asn	p.T169N	ENST00000398015	NM_004441.4	169	aCt/aAt	3/16	1	2	FACETS	0.984	0.865	1	0.984	0.865	1	CLONAL	1	TRUE	1	0.219069566033945	2		787	733	SUCCESS
APC	324	MSKCC	GRCh37	5	112175343	112175344	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	30	229	0	ENST00000257430.4:c.4053dup	p.Val1352CysfsTer2	p.V1352Cfs*2	ENST00000257430	NM_000038.5	1351	gct/gcTt	16/16	1	2	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	TRUE	1	0.219069566033945	2		229	260	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288734	33288734	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778068396	NA	P-0039970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	36	464	0	ENST00000374542.5:c.818G>A	p.Arg273Gln	p.R273Q	ENST00000374542	NM_001141970.1	273	cGg/cAg	3/8	0.219069566033945	3	FACETS	0.585	0.48	0.704	0.293	0.24	0.352	SUBCLONAL	1	TRUE	1	0.219069566033945	3		464	623	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0039973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	55	526	1	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	0.568	0.485	0.658	0.568	0.485	0.658	SUBCLONAL	1	TRUE	1	0.34	2		527	570	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098965	178098965	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	22	244	0	ENST00000397062.3:c.80A>G	p.Asp27Gly	p.D27G	ENST00000397062	NM_006164.4	27	gAt/gGt	2/5	1	2	FACETS	0.5	0.388	0.629	0.5	0.388	0.629	SUBCLONAL	1	TRUE	1	0.34	2		244	259	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279522	123279522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370877537	NA	P-0039973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	43	694	1	ENST00000358487.5:c.910G>A	p.Asp304Asn	p.D304N	ENST00000358487	NM_000141.4	304	Gac/Aac	7/18	1	2	FACETS	0.392	0.327	0.464	0.392	0.327	0.464	SUBCLONAL	1	TRUE	1	0.34	2		695	645	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986973	36986973	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	48	497	1	ENST00000354822.5:c.716del	p.Phe239SerfsTer8	p.F239Sfs*8	ENST00000354822	NM_001079668.2	239	tTc/tc	3/3	1	2	FACETS	0.635	0.537	0.742	0.635	0.537	0.742	SUBCLONAL	1	TRUE	1	0.34	2		498	445	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987010	36987010	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	37	537	0	ENST00000354822.5:c.679del	p.Met227Ter	p.M227*	ENST00000354822	NM_001079668.2	227	Atg/tg	3/3	1	2	FACETS	0.471	0.388	0.564	0.471	0.388	0.564	SUBCLONAL	1	TRUE	1	0.34	2		537	462	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0039974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	264	627	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.746121544007731	2		627	700	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0039974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	399	114	0				ENST00000310581	NM_198253.2	-/1132			0.652745047141717	3	FACETS	1	0.987	1			1	CLONAL	2	TRUE	NA	0.746121544007731	3		114	690	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782131	135782131	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	22	455	0	ENST00000298552.3:c.1425del	p.Asp476IlefsTer56	p.D476Ifs*56	ENST00000298552	NM_001162426.1	475	aaA/aa	14/23	0.746121544007731	1	FACETS	0.13	0.1	0.164	0.13	0.1	0.164	SUBCLONAL	1	TRUE	0	0.746121544007731	1		455	285	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440208	49440208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0039974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	250	566	0	ENST00000301067.7:c.4419-1G>A		p.X1473_splice	ENST00000301067	NM_003482.3	1473			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.746121544007731	2		566	646	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918267	44918267	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	125	380	0	ENST00000377967.4:c.894del	p.Val300PhefsTer25	p.V300Ffs*25	ENST00000377967	NM_021140.2	298	Ggg/gg	11/29	1	2	FACETS	0.997	0.915	1	0.997	0.915	1	CLONAL	1	TRUE	1	0.746121544007731	2		380	336	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191729	123191729	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0039974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	148	378	0	ENST00000218089.9:c.1318A>T	p.Arg440Ter	p.R440*	ENST00000218089	NM_001042749.1	440	Aga/Tga	15/35	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.746121544007731	2		378	364	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947827	178947827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	126	243	0	ENST00000263967.3:c.2702G>T	p.Cys901Phe	p.C901F	ENST00000263967	NM_006218.2	901	tGt/tTt	19/21	0.809088584994616	2	FACETS	0.933	0.882	0.98	0.933	0.882	0.98	CLONAL	2	TRUE	0	0.809088584994616	2		243	167	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574005	7574005	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	477	640	0	ENST00000269305.4:c.1022T>G	p.Phe341Cys	p.F341C	ENST00000269305	NM_001126112.2	341	tTc/tGc	10/11	0.315065428338479	3	FACETS	0.87	0.836	0.903	0.87	0.836	0.903	INDETERMINATE	2	TRUE	1	0.809088584994616	3		640	952	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231585	5231585	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779378586	NA	P-0039975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	14	246	0	ENST00000357368.4:c.1891C>T	p.Arg631Cys	p.R631C	ENST00000357368	NM_002850.3	631	Cgc/Tgc	14/38	0.808701604563017	1	FACETS	0.075	0.053	0.1	0.075	0.053	0.1	SUBCLONAL	1	TRUE	0	0.809088584994616	1		246	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574035	7574035	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0039975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	292	546	0	ENST00000269305.4:c.994-2A>C		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.315065428338479	3	FACETS	1	0.992	1	0.646	0.61	0.682	INDETERMINATE	1	TRUE	1	0.809088584994616	3		546	785	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292541	15292541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1481	765	714	1	ENST00000263388.2:c.2638G>A	p.Ala880Thr	p.A880T	ENST00000263388	NM_000435.2	880	Gcc/Acc	17/33	0.809088584994616	5	FACETS	0.932	0.899	0.965	0.621	0.599	0.643	CLONAL	2	TRUE	2	0.809088584994616	5		715	2246	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30061041	30061041	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	335	295	0	ENST00000338641.4:c.873del	p.Val292LeufsTer4	p.V292Lfs*4	ENST00000338641	NM_000268.3	291	cgT/cg	9/16	0.809088584994616	2	FACETS	0.979	0.949	1	0.979	0.949	1	CLONAL	2	TRUE	0	0.809088584994616	2		295	423	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31423042	31423042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	104	393	0	ENST00000344624.3:c.3271C>T	p.Pro1091Ser	p.P1091S	ENST00000344624		1091	Cca/Tca	26/33	0.799469657022465	3	FACETS	0.824	0.743	0.91	0.412	0.371	0.455	CLONAL	1	TRUE	1	0.809088584994616	3		393	438	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370709	55370709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	61	498	1	ENST00000297316.4:c.11C>T	p.Pro4Leu	p.P4L	ENST00000297316	NM_022454.3	4	cCg/cTg	1/2	1	2	FACETS	0.601	0.519	0.69	0.601	0.519	0.69	SUBCLONAL	1	TRUE	1	0.403591803488205	2		499	503	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281876	49281876	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751133878	NA	P-0039977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	85	650	1	ENST00000282018.3:c.923C>T	p.Ala308Val	p.A308V	ENST00000282018	NM_020377.2	308	gCt/gTt	1/1	0.367549551995197	2	FACETS	0.904	0.802	1	0.452	0.401	0.506	CLONAL	1	TRUE	0	0.403591803488205	2		651	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0039978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	1014	837	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.635358873179245	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	4	TRUE	0	0.674837435966831	4		837	1238	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161326556	161326556	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	44	185	0	ENST00000367975.2:c.331G>T	p.Ala111Ser	p.A111S	ENST00000367975	NM_003001.3	111	Gca/Tca	5/6	0.674837435966831	3	FACETS	0.758	0.642	0.885	0.379	0.321	0.443	SUBCLONAL	1	TRUE	1	0.674837435966831	3		185	230	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162722914	162722914	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	328	624	0	ENST00000367921.3:c.112G>T	p.Gly38Ter	p.G38*	ENST00000367921	NM_006182.2	38	Gga/Tga	4/18	0.674837435966831	3	FACETS	0.953	0.908	0.998	0.953	0.908	0.998	CLONAL	2	TRUE	1	0.674837435966831	3		624	682	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716134	243716134	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	144	625	0	ENST00000263826.5:c.1060C>G	p.Leu354Val	p.L354V	ENST00000263826	NM_005465.4	354	Ctt/Gtt	10/13	NA	2	FACETS	0.885	0.813	0.96			1	INDETERMINATE	1	TRUE	NA	0.674837435966831	2		625	482	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115790	8115790	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	420	630	0	ENST00000346208.3:c.1136A>T	p.His379Leu	p.H379L	ENST00000346208		379	cAt/cTt	6/6	0.674837435966831	2	FACETS	0.982	0.948	1	0.982	0.948	1	CLONAL	2	TRUE	0	0.674837435966831	2		630	634	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115803	8115803	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	315	619	0	ENST00000346208.3:c.1149G>T	p.Glu383Asp	p.E383D	ENST00000346208		383	gaG/gaT	6/6	0.674837435966831	2	FACETS	1	0.995	1	0.724	0.689	0.759	CLONAL	1	TRUE	0	0.674837435966831	2		619	645	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448089	49448089	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0039978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	140	496	0	ENST00000301067.7:c.510+1G>A		p.X170_splice	ENST00000301067	NM_003482.3	170			0.674837435966831	3	FACETS	0.96	0.878	1	0.48	0.439	0.523	CLONAL	1	TRUE	1	0.674837435966831	3		496	578	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233078	69233078	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	131	330	0	ENST00000462284.1:c.943A>G	p.Asn315Asp	p.N315D	ENST00000462284	NM_002392.5	315	Aat/Gat	11/11	0.674837435966831	3	FACETS	0.927	0.857	0.997	0.927	0.857	0.997	CLONAL	2	TRUE	1	0.674837435966831	3		330	280	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528225	103528225	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	92	321	0	ENST00000355739.4:c.3533G>T	p.Arg1178Leu	p.R1178L	ENST00000355739	NM_000123.3	1178	cGt/cTt	15/15	0.674837435966831	1	FACETS	0.796	0.721	0.872	0.796	0.721	0.872	SUBCLONAL	1	TRUE	0	0.674837435966831	1		321	227	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032128	10032128	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	89	709	0	ENST00000330684.3:c.695C>G	p.Ser232Cys	p.S232C	ENST00000330684	NM_001134407.1	232	tCc/tGc	3/13	0.674837435966831	2	FACETS	0.395	0.351	0.443	0.198	0.175	0.222	SUBCLONAL	1	TRUE	0	0.674837435966831	2		709	667	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129400	30129400	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	86	772	0	ENST00000263025.4:c.628T>C	p.Tyr210His	p.Y210H	ENST00000263025	NM_002746.2	210	Tac/Cac	4/9	0.607364071631966	4	FACETS	0.575	0.508	0.646			1	SUBCLONAL	1	TRUE	NA	0.674837435966831	4		772	743	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59861713	59861713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567816972	NA	P-0039978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	228	496	0	ENST00000259008.2:c.1546G>A	p.Val516Ile	p.V516I	ENST00000259008	NM_032043.2	516	Gta/Ata	11/20	0.567516678298546	4	FACETS	0.971	0.912	1	0.971	0.912	1	CLONAL	2	TRUE	2	0.674837435966831	4		496	583	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129661	11129661	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	514	747	1	ENST00000358026.2:c.2467G>A	p.Asp823Asn	p.D823N	ENST00000358026	NM_001128849.1	823	Gac/Aac	17/36	0.674837435966831	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.674837435966831	2		748	714	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023962	31023962	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	177	666	0	ENST00000375687.4:c.3447G>A	p.Met1149Ile	p.M1149I	ENST00000375687	NM_015338.5	1149	atG/atA	13/13	0.396786808083374	3	FACETS	0.939	0.867	1	0.313	0.289	0.338	INDETERMINATE	1	TRUE	0	0.674837435966831	3		666	747	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514823	44514823	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	200	583	0	ENST00000291552.4:c.424G>T	p.Ala142Ser	p.A142S	ENST00000291552	NM_006758.2	142	Gcc/Tcc	6/8	0.669152992879195	3	FACETS	1	0.947	1	0.511	0.475	0.549	CLONAL	1	TRUE	1	0.674837435966831	3		583	775	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526100	189526100	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	639	642	0	ENST00000264731.3:c.364C>A	p.Gln122Lys	p.Q122K	ENST00000264731	NM_003722.4	122	Cag/Aag	4/14	0.597406480801504	5	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	2	0.674837435966831	5		642	1214	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254515	1254524	+	frameshift_variant	Frame_Shift_Del	DEL	GTGACACGGT	GTGACACGGT	-	novel	NA	P-0039978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1862	104	981	0	ENST00000310581.5:c.3254_3263del	p.His1085ProfsTer16	p.H1085Pfs*16	ENST00000310581	NM_198253.2	1085	cACCGTGTCACc/cc	15/16	0.674837435966831	6	FACETS	0.368	0.328	0.412	0.092	0.082	0.103	SUBCLONAL	1	TRUE	2	0.674837435966831	6		981	1966	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279534	1279534	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1810	250	961	0	ENST00000310581.5:c.2002G>T	p.Glu668Ter	p.E668*	ENST00000310581	NM_198253.2	668	Gag/Tag	5/16	0.674837435966831	6	FACETS	0.845	0.787	0.906	0.211	0.196	0.227	CLONAL	1	TRUE	2	0.674837435966831	6		961	2060	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184096	56184096	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	33	406	0	ENST00000399503.3:c.4301G>T	p.Ser1434Ile	p.S1434I	ENST00000399503	NM_005921.1	1434	aGt/aTt	19/20	NA	2	FACETS	0.375	0.306	0.451			1	INDETERMINATE	1	TRUE	NA	0.674837435966831	2		406	261	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651959	36651959	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762818650	NA	P-0039978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	212	671	1	ENST00000244741.5:c.81C>A	p.Ser27Arg	p.S27R	ENST00000244741	NM_000389.4	27	agC/agA	2/3	0.528532322639206	4	FACETS	1	0.966	1	0.532	0.494	0.571	CLONAL	1	TRUE	2	0.674837435966831	4		672	989	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953012	2953012	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	215	798	0	ENST00000396946.4:c.2928del	p.Val977CysfsTer88	p.V977Cfs*88	ENST00000396946	NM_032415.4	976	ccC/cc	22/25	1	2	FACETS	0.733	0.682	0.786	0.733	0.682	0.786	SUBCLONAL	1	TRUE	1	0.674837435966831	2		798	869	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340029	116340029	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	78	334	0	ENST00000397752.3:c.891G>T	p.Glu297Asp	p.E297D	ENST00000397752	NM_000245.2	297	gaG/gaT	2/21	0.654939798665507	3	FACETS	1	0.904	1	0.51	0.453	0.571	CLONAL	1	TRUE	1	0.674837435966831	3		334	303	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412055	63412055	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747944110	NA	P-0039978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	186	812	0	ENST00000330258.3:c.1112A>G	p.Glu371Gly	p.E371G	ENST00000330258	NM_152424.3	371	gAg/gGg	2/2	0.674837435966831	2	FACETS	0.84	0.779	0.903	0.42	0.389	0.452	CLONAL	1	TRUE	0	0.674837435966831	2		812	656	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0039980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	245	330	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.172175722065166	7	FACETS	1	0.974	1			1	CLONAL	5	FALSE	NA	0.172175722065166	7		330	761	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0039980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	28	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.170345342189356	3	FACETS	0.768	0.613	0.945	0.384	0.306	0.473	CLONAL	1	FALSE	1	0.172175722065166	3		326	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0039980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	146	749	1	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	1	2	FACETS	0.858	0.782	0.938	1	0.989	1	CLONAL	2	FALSE	1	0.172175722065166	2		750	988	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439494	220439494	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764382434	NA	P-0039980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	114	530	0	ENST00000243786.2:c.347G>A	p.Arg116Gln	p.R116Q	ENST00000243786	NM_002191.3	116	cGg/cAg	2/2	1	2	FACETS	0.818	0.737	0.905	1	0.985	1	CLONAL	2	FALSE	1	0.172175722065166	2		530	809	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986820	36986821	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0039980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	35	113	0	ENST00000354822.5:c.868dup	p.Val290GlyfsTer149	p.V290Gfs*149	ENST00000354822	NM_001079668.2	290	gtg/gGtg	3/3	1	2	FACETS	0.83	0.684	0.991	1	0.956	1	CLONAL	2	FALSE	1	0.172175722065166	2		113	245	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652087	36652087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769049147	NA	P-0039980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	130	700	0	ENST00000244741.5:c.209G>A	p.Gly70Asp	p.G70D	ENST00000244741	NM_000389.4	70	gGc/gAc	2/3	0.170345342189356	3	FACETS	0.752	0.68	0.827	0.752	0.68	0.827	SUBCLONAL	2	FALSE	1	0.172175722065166	3		700	1091	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	52	417	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.875	0.748	1	0.875	0.748	1	CLONAL	1	TRUE	1	0.33	2		417	360	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	319	920	0	ENST00000269305.4:c.403del	p.Cys135AlafsTer35	p.C135Afs*35	ENST00000269305	NM_001126112.2	135	Tgc/gc	5/11	0.249396489882639	2	FACETS	0.967	0.914	1	0.967	0.914	1	CLONAL	2	TRUE	0	0.33	2		920	1000	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974762	21974763	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	72	294	0	ENST00000304494.5:c.64dup	p.Arg22ProfsTer22	p.R22Pfs*22	ENST00000304494	NM_000077.4	22	cgg/cCgg	1/3	0.303095531241111	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.33	1		294	274	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128983	64128984	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0039984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	73	793	0	ENST00000334205.4:c.618dup	p.Glu207ArgfsTer5	p.E207Rfs*5	ENST00000334205	NM_003942.2	205	gcc/gCcc	6/17	0.303095531241111	1	FACETS	0.525	0.458	0.596	0.525	0.458	0.596	SUBCLONAL	1	TRUE	0	0.33	1		793	704	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	107	417	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.849	0.765	0.938	0.849	0.765	0.938	CLONAL	1	TRUE	1	0.503937204058303	2		417	500	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444042	49444042	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	245	630	1	ENST00000301067.7:c.3329del	p.Pro1110GlnfsTer9	p.P1110Qfs*9	ENST00000301067	NM_003482.3	1110	cCa/ca	11/54	1	2	FACETS	0.975	0.912	1	0.975	0.912	1	CLONAL	1	TRUE	1	0.503937204058303	2		631	997	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224505	108224505	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	70	241	0	ENST00000278616.4:c.8684A>T	p.Glu2895Val	p.E2895V	ENST00000278616	NM_000051.3	2895	gAa/gTa	60/63	1	2	FACETS	0.743	0.651	0.841	0.743	0.651	0.841	SUBCLONAL	1	TRUE	1	0.503937204058303	2		241	374	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023637	27023638	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTCCAAGCCGC	novel	NA	P-0039986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	105	376	0	ENST00000324856.7:c.748_758dup	p.Ser255ArgfsTer112	p.S255Rfs*112	ENST00000324856	NM_006015.4	248	ggc/ggCTCCAAGCCGCc	1/20	1	2	FACETS	0.649	0.582	0.72	0.649	0.582	0.72	SUBCLONAL	1	TRUE	1	0.503937204058303	2		376	642	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066840	30066840	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	141	609	0	ENST00000331968.5:c.2291T>C	p.Leu764Pro	p.L764P	ENST00000331968	NM_002742.2	764	cTa/cCa	16/18	1	2	FACETS	0.713	0.65	0.779	0.713	0.65	0.779	SUBCLONAL	1	TRUE	1	0.503937204058303	2		609	785	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156655	55156655	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	200	484	0	ENST00000257290.5:c.3056T>C	p.Ile1019Thr	p.I1019T	ENST00000257290	NM_006206.4	1019	aTc/aCc	22/23	1	2	FACETS	0.94	0.873	1	0.94	0.873	1	CLONAL	1	TRUE	1	0.503937204058303	2		484	844	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879670	151879670	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	75	176	0	ENST00000262189.6:c.5275C>T	p.Gln1759Ter	p.Q1759*	ENST00000262189	NM_170606.2	1759	Cag/Tag	36/59	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.503937204058303	2		176	287	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0039987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	103	383	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.482	0.434	0.532	0.482	0.434	0.532	SUBCLONAL	1	TRUE	1	0.996066591037126	2		383	429	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258036	123258036	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	56	388	0	ENST00000358487.5:c.1645A>G	p.Asn549Asp	p.N549D	ENST00000358487	NM_000141.4	549	Aat/Gat	12/18	1	2	FACETS	0.215	0.184	0.249	0.215	0.184	0.249	SUBCLONAL	1	TRUE	1	0.996066591037126	2		388	523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0039988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	338	946	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	1	2	FACETS	0.967	0.915	1	0.967	0.915	1	CLONAL	1	TRUE	1	0.612686427963746	2		946	1141	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519989	NA	P-0039988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	250	630	0	ENST00000269305.4:c.730G>C	p.Gly244Arg	p.G244R	ENST00000269305	NM_001126112.2	244	Ggc/Cgc	7/11	1	2	FACETS	0.996	0.935	1	0.996	0.935	1	CLONAL	1	TRUE	1	0.612686427963746	2		630	819	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005852	69005852	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	157	349	0	ENST00000288368.4:c.2263C>A	p.Gln755Lys	p.Q755K	ENST00000288368	NM_024870.2	755	Caa/Aaa	21/40	0.319683351087318	1	FACETS	0.804	0.744	0.866	0.804	0.744	0.866	INDETERMINATE	1	TRUE	0	0.612686427963746	1		349	442	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481403	140481403	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913357	NA	P-0039988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	165	414	0	ENST00000288602.6:c.1405G>C	p.Gly469Arg	p.G469R	ENST00000288602	NM_004333.4	469	Gga/Cga	11/18	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.612686427963746	2		414	518	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148529772	148529772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	134	398	0	ENST00000320356.2:c.317C>T	p.Ser106Leu	p.S106L	ENST00000320356	NM_004456.4	106	tCa/tTa	4/20	1	2	FACETS	0.937	0.857	1	0.937	0.857	1	CLONAL	1	TRUE	1	0.612686427963746	2		398	467	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797510	45797510	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	335	844	0	ENST00000450313.1:c.1009G>T	p.Gly337Ter	p.G337*	ENST00000450313	NM_012222.2	337	Gga/Tga	12/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.612686427963746	2		844	1024	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46725723	46725723	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1210724853	NA	P-0039988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	201	521	0	ENST00000371975.4:c.359T>C	p.Leu120Pro	p.L120P	ENST00000371975	NM_003579.3	120	cTg/cCg	5/18	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.612686427963746	2		521	576	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414921	78414921	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	154	418	0	ENST00000370768.2:c.1845G>A	p.Trp615Ter	p.W615*	ENST00000370768	NM_003902.3	615	tgG/tgA	19/20	1	2	FACETS	0.916	0.843	0.991	0.916	0.843	0.991	CLONAL	1	TRUE	1	0.612686427963746	2		418	549	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666681	206666681	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1322042486	NA	P-0039988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	239	761	0	ENST00000367120.3:c.2015C>G	p.Pro672Arg	p.P672R	ENST00000367120	NM_014002.3	672	cCc/cGc	20/22	1	2	FACETS	0.916	0.857	0.976	0.916	0.857	0.976	CLONAL	1	TRUE	1	0.612686427963746	2		761	852	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667486	241667486	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	124	281	0	ENST00000366560.3:c.964G>T	p.Val322Phe	p.V322F	ENST00000366560	NM_000143.3	322	Gtt/Ttt	7/10	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.612686427963746	2		281	324	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944761	31944761	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	112	298	0	ENST00000340398.3:c.340G>T	p.Ala114Ser	p.A114S	ENST00000340398	NM_001013699.2	114	Gct/Tct	1/1	0.612686427963746	1	FACETS	0.983	0.901	1	0.983	0.901	1	CLONAL	1	TRUE	0	0.612686427963746	1		298	258	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975477	26975477	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	133	333	0	ENST00000381527.3:c.1103G>T	p.Gly368Val	p.G368V	ENST00000381527	NM_001260.1	368	gGa/gTa	11/13	0.319683351087318	1	FACETS	0.751	0.689	0.815	0.751	0.689	0.815	INDETERMINATE	1	TRUE	0	0.612686427963746	1		333	401	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955568	48955568	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	43	275	0	ENST00000267163.4:c.1684G>T	p.Ala562Ser	p.A562S	ENST00000267163	NM_000321.2	562	Gca/Tca	17/27	0.319683351087318	1	FACETS	0.342	0.287	0.401	0.342	0.287	0.401	INDETERMINATE	1	TRUE	0	0.612686427963746	1		275	285	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56871574	56871574	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	304	565	0	ENST00000308159.5:c.1954C>G	p.Gln652Glu	p.Q652E	ENST00000308159	NM_014669.4	652	Cag/Gag	18/22	0.583888543329059	2	FACETS	0.866	0.825	0.906	0.866	0.825	0.906	CLONAL	2	TRUE	0	0.612686427963746	2		565	573	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508800	29508800	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	91	360	0	ENST00000356175.3:c.727G>T	p.Ala243Ser	p.A243S	ENST00000356175	NM_000267.3	243	Gct/Tct	7/57	1	2	FACETS	0.701	0.626	0.78	0.701	0.626	0.78	SUBCLONAL	1	TRUE	1	0.612686427963746	2		360	424	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211193	2211193	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1452632751	NA	P-0039988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	378	868	2	ENST00000398665.3:c.1447G>T	p.Ala483Ser	p.A483S	ENST00000398665	NM_032482.2	483	Gcg/Tcg	15/28	0.612686427963746	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.612686427963746	1		870	718	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170928	99170928	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	260	718	0	ENST00000074304.5:c.1557G>T	p.Gln519His	p.Q519H	ENST00000074304	NM_001134224.1	519	caG/caT	16/26	0.319683351087318	1	FACETS	0.84	0.791	0.889	0.84	0.791	0.889	INDETERMINATE	1	TRUE	0	0.612686427963746	1		718	701	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468393	89468394	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0039988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	80	218	1	ENST00000336596.2:c.1927_1928delinsAA	p.Pro643Asn	p.P643N	ENST00000336596	NM_005233.5	643	CCt/AAt	11/17	0.612686427963746	1	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	0	0.612686427963746	1		219	180	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275285	142275285	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	199	558	0	ENST00000350721.4:c.2018G>T	p.Ser673Ile	p.S673I	ENST00000350721	NM_001184.3	673	aGt/aTt	9/47	0.313588914529598	3	FACETS	1	0.968	1	0.536	0.498	0.576	INDETERMINATE	1	TRUE	1	0.612686427963746	3		558	791	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582149	189582149	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	351	511	0	ENST00000264731.3:c.708C>G	p.His236Gln	p.H236Q	ENST00000264731	NM_003722.4	236	caC/caG	5/14	0.313588914529598	3	FACETS	0.941	0.897	0.986	0.941	0.897	0.986	INDETERMINATE	2	TRUE	1	0.612686427963746	3		511	795	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129858	55129858	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	163	470	0	ENST00000257290.5:c.392T>C	p.Leu131Pro	p.L131P	ENST00000257290	NM_006206.4	131	cTa/cCa	4/23	1	2	FACETS	0.991	0.915	1	0.991	0.915	1	CLONAL	1	TRUE	1	0.612686427963746	2		470	537	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55154981	55154981	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	135	529	0	ENST00000257290.5:c.2690C>A	p.Pro897His	p.P897H	ENST00000257290	NM_006206.4	897	cCc/cAc	20/23	1	2	FACETS	0.795	0.726	0.867	0.795	0.726	0.867	SUBCLONAL	1	TRUE	1	0.612686427963746	2		529	554	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970810	55970810	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	164	418	0	ENST00000263923.4:c.1987G>T	p.Glu663Ter	p.E663*	ENST00000263923	NM_002253.2	663	Gag/Tag	13/30	1	2	FACETS	0.98	0.906	1	0.98	0.906	1	CLONAL	1	TRUE	1	0.612686427963746	2		418	546	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979595	55979595	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs962180771	NA	P-0039988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	182	487	0	ENST00000263923.4:c.852G>C	p.Glu284Asp	p.E284D	ENST00000263923	NM_002253.2	284	gaG/gaC	7/30	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.612686427963746	2		487	557	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236663	236663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	858	597	0	ENST00000264932.6:c.1381G>A	p.Val461Ile	p.V461I	ENST00000264932	NM_004168.2	461	Gtt/Att	10/15	0.607978508333338	5	FACETS	0.959	0.934	0.983	0.959	0.934	0.983	CLONAL	4	TRUE	1	0.612686427963746	5		597	1401	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382159	152382159	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	122	343	0	ENST00000206249.3:c.1269G>T	p.Glu423Asp	p.E423D	ENST00000206249	NM_000125.3	423	gaG/gaT	6/8	1	2	FACETS	0.868	0.789	0.949	0.868	0.789	0.949	CLONAL	1	TRUE	1	0.612686427963746	2		343	459	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559315	141559315	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	120	805	1	ENST00000220592.5:c.1486C>T	p.Gln496Ter	p.Q496*	ENST00000220592	NM_012154.3	496	Cag/Tag	12/19	0.329993675585561	2	FACETS	0.406	0.365	0.448	0.203	0.182	0.224	INDETERMINATE	1	TRUE	0	0.612686427963746	2		806	966	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518050	8518050	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	139	424	0	ENST00000356435.5:c.1341G>T	p.Gln447His	p.Q447H	ENST00000356435		447	caG/caT	10/35	0.612686427963746	1	FACETS	0.915	0.845	0.986	0.915	0.845	0.986	CLONAL	1	TRUE	0	0.612686427963746	1		424	344	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0039989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	255	503	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.77192696233054	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.77192696233054	1		503	398	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156732	20156732	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	173	341	0	ENST00000379607.5:c.25G>C	p.Gly9Arg	p.G9R	ENST00000379607	NM_001412.3	9	Ggt/Cgt	2/7	0.77192696233054	1	FACETS	0.976	0.921	1	0.976	0.921	1	CLONAL	1	TRUE	0	0.77192696233054	1		341	282	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0039989-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	68	503	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		503	510	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156732	20156732	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039989-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	54	341	0	ENST00000379607.5:c.25G>C	p.Gly9Arg	p.G9R	ENST00000379607	NM_001412.3	9	Ggt/Cgt	2/7	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		341	388	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	64	236	0				ENST00000310581	NM_198253.2	-/1132			0.316700966556134	3	FACETS	1	0.913	1	0.533	0.463	0.609	CLONAL	1	TRUE	1	0.316700966556134	3		236	439	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	95	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.316700966556134	3	FACETS	0.893	0.801	0.99	0.893	0.801	0.99	CLONAL	2	TRUE	1	0.316700966556134	3		371	389	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477080	67477080	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	79	411	0	ENST00000327367.4:c.887T>G	p.Leu296Arg	p.L296R	ENST00000327367	NM_005902.3	296	cTc/cGc	7/9	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.316700966556134	2		411	475	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482860	67482860	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	69	419	1	ENST00000327367.4:c.1264T>C	p.Ser422Pro	p.S422P	ENST00000327367	NM_005902.3	422	Tcc/Ccc	9/9	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.316700966556134	2		420	414	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902657	50902657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141319800	NA	P-0039990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	144	728	0	ENST00000440232.2:c.232C>T	p.Arg78Cys	p.R78C	ENST00000440232	NM_002691.3	78	Cgc/Tgc	3/27	0.316700966556134	3	FACETS	1	0.981	1	0.635	0.579	0.693	CLONAL	1	TRUE	1	0.316700966556134	3		728	830	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265608	41266240	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTCTGCTTCGTTGCCATTAAGCCAGTCTGGCTGAGATCCCCCTGCTTTCCTCTCTCCCTGCTTACTTGTCAGGCTACCTTTTGCTCCATTTTCTGCTCACTCCTCCTAATGGCTTGGTGAAATAGCAAACAAGCCACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTA	GCTCTGCTTCGTTGCCATTAAGCCAGTCTGGCTGAGATCCCCCTGCTTTCCTCTCTCCCTGCTTACTTGTCAGGCTACCTTTTGCTCCATTTTCTGCTCACTCCTCCTAATGGCTTGGTGAAATAGCAAACAAGCCACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTA	-	novel	NA	P-0039990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	87	246	0	ENST00000349496.5:c.13+39_240del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.316700966556134	3	FACETS	1	0.971	1	0.822	0.739	0.909	CLONAL	2	TRUE	0	0.316700966556134	3		246	258	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939021	131939021	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	36	262	0	ENST00000265335.6:c.2237A>G	p.Glu746Gly	p.E746G	ENST00000265335		746	gAa/gGa	14/25	0.316700966556134	3	FACETS	0.954	0.788	1	0.477	0.394	0.569	CLONAL	1	TRUE	1	0.316700966556134	3		262	276	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462360	89462360	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000604-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1181	98	343	0	ENST00000336596.2:c.1832A>C	p.Glu611Ala	p.E611A	ENST00000336596	NM_005233.5	611	gAg/gCg	10/17	0.272212409675504	3	FACETS	0.629	0.56	0.704	0.315	0.28	0.352	SUBCLONAL	1	TRUE	1	0.277190132958694	3		343	1279	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133747572	133747572	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000604-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	55	273	0	ENST00000318560.5:c.879C>G	p.Ile293Met	p.I293M	ENST00000318560	NM_005157.4	293	atC/atG	5/11	0.15989447874022	2	FACETS	0.569	0.485	0.66	0.284	0.242	0.33	INDETERMINATE	1	TRUE	0	0.277190132958694	2		273	698	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090381	77090381	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369339512	NA	P-0000604-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1332	148	493	1	ENST00000356341.3:c.344C>T	p.Ser115Leu	p.S115L	ENST00000356341	NM_002576.4	115	tCg/tTg	4/15	0.246924597877114	1	FACETS	0.622	0.566	0.681	0.622	0.566	0.681	SUBCLONAL	1	TRUE	0	0.277190132958694	1		494	1480	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877454	40877454	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000604-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	52	204	0	ENST00000373198.4:c.2242A>G	p.Thr748Ala	p.T748A	ENST00000373198	NM_133170.3	748	Acc/Gcc	15/32	1	2	FACETS	0.604	0.514	0.704	0.604	0.514	0.704	SUBCLONAL	1	TRUE	1	0.277190132958694	2		204	621	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000758-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	30	174	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.887	1			1	INDETERMINATE	1	TRUE	NA	0.740859032103013	2		174	75	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934574	NA	P-0000758-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	402	556	0	ENST00000269305.4:c.844C>G	p.Arg282Gly	p.R282G	ENST00000269305	NM_001126112.2	282	Cgg/Ggg	8/11	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.740859032103013	2		556	508	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685298	86685298	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000758-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	55	256	0	ENST00000274376.6:c.3014A>G	p.His1005Arg	p.H1005R	ENST00000274376	NM_002890.2	1005	cAt/cGt	24/25	0.157812809836452	3	FACETS	0.548	0.471	0.633	0.274	0.235	0.317	INDETERMINATE	1	TRUE	1	0.740859032103013	3		256	371	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226474	133226474	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000758-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	61	371	0	ENST00000320574.5:c.3584T>C	p.Val1195Ala	p.V1195A	ENST00000320574	NM_006231.2	1195	gTc/gCc	30/49	NA	2	FACETS	0.695	0.607	0.788			1	INDETERMINATE	1	TRUE	NA	0.740859032103013	2		371	237	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279556	18279556	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1398647764	NA	P-0000758-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	108	381	0	ENST00000222254.8:c.1829A>G	p.Asp610Gly	p.D610G	ENST00000222254	NM_005027.3	610	gAc/gGc	15/16	0.740859032103013	3	FACETS	0.949	0.858	1	0.475	0.429	0.522	CLONAL	1	TRUE	1	0.740859032103013	3		381	421	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994251	21994251	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001288-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	202	283	0	ENST00000579755.1:c.80T>G	p.Ile27Ser	p.I27S	ENST00000579755		27	aTc/aGc	1/3	1		FACETS		0.891	1				CLONAL	1	TRUE	1	0.719267417985085	2		283	588	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69229647	69229647	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001288-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	174	162	0	ENST00000462284.1:c.723G>C	p.Trp241Cys	p.W241C	ENST00000462284	NM_002392.5	241	tgG/tgC	9/11	0.124274797244586	4	FACETS	1	0.99	1	0.734	0.679	0.789	INDETERMINATE	1	TRUE	2	0.719267417985085	4		162	567	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457159	5457159	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001288-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	213	197	0	ENST00000381577.3:c.133del	p.Glu45LysfsTer4	p.E45Kfs*4	ENST00000381577	NM_014143.3	45	Gaa/aa	3/7	1	2	FACETS	0.853	0.796	0.912	0.853	0.796	0.912	CLONAL	1	TRUE	1	0.719267417985085	2		197	694	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0001449-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	316	530	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.898485156431366	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.898485156431366	1		530	383	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751237	57751237	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001449-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	274	414	0	ENST00000274289.3:c.1630G>C	p.Val544Leu	p.V544L	ENST00000274289	NM_006622.3	544	Gtt/Ctt	12/14	1	2	FACETS	0.99	0.937	1	0.99	0.937	1	CLONAL	1	TRUE	1	0.898485156431366	2		414	616	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	443454	443454	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001449-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	455	651	0	ENST00000399788.2:c.1443C>A	p.Cys481Ter	p.C481*	ENST00000399788	NM_001042603.1	481	tgC/tgA	11/28	0.898485156431366	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.898485156431366	1		651	536	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879904	44879904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs912069418	NA	P-0001449-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	425	296	1	ENST00000377967.4:c.493C>T	p.Arg165Ter	p.R165*	ENST00000377967	NM_021140.2	165	Cga/Tga	6/29	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.898485156431366	1		297	470	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781441	3781441	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001449-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	301	442	1	ENST00000262367.5:c.4924G>C	p.Val1642Leu	p.V1642L	ENST00000262367	NM_004380.2	1642	Gtc/Ctc	30/31	0.846098500483349	3	FACETS	0.947	0.893	1	0.474	0.446	0.501	CLONAL	1	TRUE	1	0.898485156431366	3		443	1025	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351782	89351782	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001449-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	637	957	0	ENST00000301030.4:c.1168del	p.Ser390ValfsTer37	p.S390Vfs*37	ENST00000301030	NM_001256183.1	390	Agt/gt	9/13	0.898485156431366	1	FACETS	0.995	0.974	1	0.995	0.974	1	CLONAL	1	TRUE	0	0.898485156431366	1		957	785	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027146	48027150	+	frameshift_variant	Frame_Shift_Del	DEL	AGAAA	AGAAA	-	novel	NA	P-0001449-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	404	547	0	ENST00000234420.5:c.2026_2030del	p.Lys676Ter	p.K676*	ENST00000234420	NM_000179.2	675	gAGAAA/g	4/10	0.898485156431366	1	FACETS	0.993	0.966	1	0.993	0.966	1	CLONAL	1	TRUE	0	0.898485156431366	1		547	499	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509484	106509484	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001449-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	463	757	0	ENST00000359195.3:c.1478A>T	p.Asp493Val	p.D493V	ENST00000359195	NM_002649.2	493	gAc/gTc	2/11	0.898485156431366	3	FACETS	0.983	0.938	1	0.492	0.469	0.515	CLONAL	1	TRUE	1	0.898485156431366	3		757	1519	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0001507-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	200	307	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.86210175190654	2	FACETS	1	0.983	1	0.564	0.53	0.599	CLONAL	1	TRUE	0	0.86210175190654	2		307	411	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612062	189612062	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142981128	NA	P-0001507-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	171	456	0	ENST00000264731.3:c.1814G>A	p.Arg605Gln	p.R605Q	ENST00000264731	NM_003722.4	605	cGg/cAg	14/14	1	2	FACETS	0.933	0.868	0.999	0.933	0.868	0.999	CLONAL	1	TRUE	1	0.86210175190654	2		456	425	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099796	157099796	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001507-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	96	229	0	ENST00000346085.5:c.733G>C	p.Gly245Arg	p.G245R	ENST00000346085	NM_020732.3	245	Ggc/Cgc	1/20	0.86210175190654	3	FACETS	1	0.976	1	0.625	0.566	0.685	CLONAL	1	TRUE	1	0.86210175190654	3		229	255	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862189	68862205	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AGGCGGAGAAGAGGACC	AGGCGGAGAAGAGGACC	-	novel	NA	P-0001507-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	91	356	0	ENST00000261769.5:c.2280_2295+1del		p.GGGEEDQ759fs	ENST00000261769	NM_004360.3	759	ggAGGCGGAGAAGAGGACCag/ggag	14/16	NA	2	FACETS	0.605	0.542	0.671			1	INDETERMINATE	1	TRUE	NA	0.86210175190654	2		356	349	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121230	29121230	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs121908698	NA	P-0001712-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	225	674	0	ENST00000328354.6:c.444+1G>A		p.X148_splice	ENST00000328354	NM_007194.3	148			0.506880123117497	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.506880123117497	1		674	661	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732932	74732933	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0001712-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	131	461	0	ENST00000359995.5:c.310_311delinsTT	p.Gly104Leu	p.G104L	ENST00000359995	NM_001195427.1	104	GGa/TTa	1/3	1	2	FACETS	0.827	0.753	0.905	0.827	0.753	0.905	CLONAL	1	TRUE	1	0.506880123117497	2		461	625	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176132111	176132111	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001835-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	199	502	1	ENST00000367669.3:c.656G>T	p.Trp219Leu	p.W219L	ENST00000367669	NM_022457.5	219	tGg/tTg	5/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		503	546	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47087991	47087991	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001835-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	148	485	0	ENST00000409792.3:c.7084C>T	p.Gln2362Ter	p.Q2362*	ENST00000409792	NM_014159.6	2362	Cag/Tag	16/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		485	303	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637186	176637186	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001835-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	158	456	0	ENST00000439151.2:c.1786G>A	p.Gly596Ser	p.G596S	ENST00000439151	NM_022455.4	596	Ggt/Agt	5/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		456	441	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78865554	78865554	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001835-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	151	486	0	ENST00000306801.3:c.2018A>C	p.Gln673Pro	p.Q673P	ENST00000306801	NM_020761.2	673	cAg/cCg	18/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		486	471	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582075	52582093	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	GTGATTAAACATTTTCTAG	GTGATTAAACATTTTCTAG	-	novel	NA	P-0001835-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	106	370	0	ENST00000394830.3:c.4735_*4del		p.*1579*	ENST00000394830	NM_018313.4	1579		30/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		370	242	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038213	30038213	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001835-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	189	589	0	ENST00000338641.4:c.389del	p.Lys130ArgfsTer44	p.K130Rfs*44	ENST00000338641	NM_000268.3	129	gAa/ga	4/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		589	339	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63816909	63816909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001835-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	28	369	0	ENST00000279873.7:c.880C>A	p.Pro294Thr	p.P294T	ENST00000279873	NM_032199.2	294	Ccg/Acg	6/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		369	474	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0002042-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	608	327	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.519696237688535	4	FACETS	0.92	0.887	0.952	0.92	0.887	0.952	CLONAL	3	TRUE	1	0.519696237688535	4		327	1289	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002042-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	103	317	0	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	0.519696237688535	1	FACETS	0.583	0.524	0.646	0.583	0.524	0.646	SUBCLONAL	1	TRUE	0	0.519696237688535	1		317	503	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023720	27023720	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002042-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	246	229	0	ENST00000324856.7:c.826G>T	p.Gly276Ter	p.G276*	ENST00000324856	NM_006015.4	276	Gga/Tga	1/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.519696237688535	2		229	931	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643329	52643329	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1457764063	NA	P-0002042-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	107	324	0	ENST00000394830.3:c.2567G>A	p.Arg856Gln	p.R856Q	ENST00000394830	NM_018313.4	856	cGg/cAg	17/30	1	2	FACETS	0.778	0.701	0.86	0.778	0.701	0.86	SUBCLONAL	1	TRUE	1	0.519696237688535	2		324	529	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202187	108202187	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002042-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	132	249	0	ENST00000278616.4:c.7532T>C	p.Ile2511Thr	p.I2511T	ENST00000278616	NM_000051.3	2511	aTt/aCt	51/63	1	2	FACETS	0.91	0.83	0.994	0.91	0.83	0.994	CLONAL	1	TRUE	1	0.519696237688535	2		249	558	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037441	12037441	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1235766887	NA	P-0002042-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	216	286	0	ENST00000396373.4:c.1072A>G	p.Ile358Val	p.I358V	ENST00000396373	NM_001987.4	358	Atc/Gtc	6/8	0.519696237688535	8	FACETS	0.826	0.766	0.888			1	CLONAL	2	TRUE	NA	0.519696237688535	8		286	1288	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421833	49421833	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758494772	NA	P-0002042-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	57	342	1	ENST00000301067.7:c.14474G>A	p.Arg4825Gln	p.R4825Q	ENST00000301067	NM_003482.3	4825	cGg/cAg	46/54	0.519696237688535	4	FACETS	0.324	0.277	0.376	0.108	0.092	0.126	SUBCLONAL	1	TRUE	1	0.519696237688535	4		343	1029	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473653	67473653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223737	NA	P-0002042-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	284	367	0	ENST00000327367.4:c.733G>A	p.Gly245Arg	p.G245R	ENST00000327367	NM_005902.3	245	Ggg/Agg	6/9	0.426601072363761	2	FACETS	0.782	0.739	0.825	0.782	0.739	0.825	SUBCLONAL	2	TRUE	0	0.519696237688535	2		367	699	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220116	5220116	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781371580	NA	P-0002042-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	72	244	0	ENST00000357368.4:c.3599G>A	p.Arg1200His	p.R1200H	ENST00000357368	NM_002850.3	1200	cGt/cAt	22/38	1	2	FACETS	0.676	0.593	0.764	0.676	0.593	0.764	SUBCLONAL	1	TRUE	1	0.519696237688535	2		244	410	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368195	45368206	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	GCTTTATGACAT	GCTTTATGACAT	-	novel	NA	P-0002042-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	218	276	1	ENST00000262160.6:c.1396_*3del		p.*466*	ENST00000262160	NM_005901.5	466		11/11	0.3170575002139	3	FACETS	1	0.946	1	0.672	0.631	0.714	CLONAL	2	TRUE	0	0.519696237688535	3		277	524	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002508-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	61	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.275	0.236	0.317	0.275	0.236	0.317	SUBCLONAL	1	TRUE	1	0.533446383750942	2		174	833	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097819	27097819	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0002508-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	162	406	0	ENST00000324856.7:c.3406+2T>A		p.X1136_splice	ENST00000324856	NM_006015.4	1136			0.532787425261043	1	FACETS	0.983	0.911	1	0.983	0.911	1	CLONAL	1	TRUE	0	0.533446383750942	1		406	453	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220443	1220443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202466	NA	P-0002508-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	346	996	0	ENST00000326873.7:c.536C>T	p.Pro179Leu	p.P179L	ENST00000326873	NM_000455.4	179	cCg/cTg	4/10	0.533446383750942	1	FACETS	0.961	0.912	1	0.961	0.912	1	CLONAL	1	TRUE	0	0.533446383750942	1		996	990	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002681-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	213	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.993	0.928	1	0.993	0.928	1	CLONAL	1	TRUE	1	0.67	2		174	640	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0002681-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	202	318	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.921	0.858	0.985	0.921	0.858	0.985	CLONAL	1	TRUE	1	0.67	2		318	655	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0002681-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	196	300	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.985	0.917	1	0.985	0.917	1	CLONAL	1	TRUE	1	0.67	2		300	594	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532735	187532736	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002681-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	253	566	0	ENST00000441802.2:c.9657dup	p.Val3220SerfsTer3	p.V3220Sfs*3	ENST00000441802	NM_005245.3	3219	-/A	14/27	1	2	FACETS	0.982	0.923	1	0.982	0.923	1	CLONAL	1	TRUE	1	0.67	2		566	769	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0002793-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	149	332	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	NA	2	FACETS	0.866	0.798	0.935			1	INDETERMINATE	1	TRUE	NA	0.785900297863305	2		332	438	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703662	47703662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002793-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	189	341	0	ENST00000233146.2:c.2162G>T	p.Gly721Val	p.G721V	ENST00000233146	NM_000251.2	721	gGa/gTa	13/16	0.785900297863305	3	FACETS	0.904	0.838	0.973	0.452	0.419	0.487	CLONAL	1	TRUE	1	0.785900297863305	3		341	741	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638139	176638139	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002793-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	215	382	0	ENST00000439151.2:c.2739G>A	p.Met913Ile	p.M913I	ENST00000439151	NM_022455.4	913	atG/atA	5/23	0.785900297863305	3	FACETS	0.906	0.844	0.97	0.453	0.422	0.485	CLONAL	1	TRUE	1	0.785900297863305	3		382	841	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578374	7578374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501206	NA	P-0002793-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	26	327	1	ENST00000269305.4:c.556G>A	p.Asp186Asn	p.D186N	ENST00000269305	NM_001126112.2	186	Gat/Aat	5/11	1	2	FACETS	0.16	0.126	0.199	0.16	0.126	0.199	SUBCLONAL	1	TRUE	1	0.785900297863305	2		328	414	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002838-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	60	174	0				ENST00000310581	NM_198253.2	-/1132			0.177087757486547	1	FACETS	0.632	0.548	0.722	0.632	0.548	0.722	INDETERMINATE	1	TRUE	0	0.45	1		174	327	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0002838-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	198	318	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	0.45	2		318	869	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0002838-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	122	515	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.955	0.866	1	0.955	0.866	1	CLONAL	1	TRUE	1	0.45	2		515	568	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151927396	151927396	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002838-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	22	30	0	ENST00000262189.6:c.2780C>T	p.Ala927Val	p.A927V	ENST00000262189	NM_170606.2	927	gCa/gTa	17/59	1	2	FACETS	0.998	0.789	1	0.998	0.789	1	CLONAL	1	TRUE	1	0.45	2		30	98	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	38	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.753230726414274	2		174	89	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920413	134920413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1338928289	NA	P-0003068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	195	436	0	ENST00000398015.3:c.2228G>A	p.Arg743Gln	p.R743Q	ENST00000398015	NM_004441.4	743	cGg/cAg	12/16	1	2	FACETS	0.982	0.917	1	0.982	0.917	1	CLONAL	1	TRUE	1	0.753230726414274	2		436	527	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224307	55224307	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	13092	340	4	ENST00000275493.2:c.1088C>A	p.Thr363Asn	p.T363N	ENST00000275493	NM_005228.3	363	aCc/aAc	9/28	0.753230726414274	31	FACETS	0.987	0.985	0.99	0.987	0.985	0.99	CLONAL	31	TRUE	0	0.753230726414274	31		344	13541	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691094	18691094	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs201586034	NA	P-0003068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	168	313	0	ENST00000266497.5:c.3205C>T	p.Arg1069Ter	p.R1069*	ENST00000266497		1069	Cga/Tga	23/31	1	2	FACETS	0.961	0.892	1	0.961	0.892	1	CLONAL	1	TRUE	1	0.753230726414274	2		313	464	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	34	769	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.954	1			1	INDETERMINATE	1	TRUE	NA	0.700272583031725	2		769	71	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749986	162749986	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	153	335	0	ENST00000367921.3:c.2518C>T	p.Pro840Ser	p.P840S	ENST00000367921	NM_006182.2	840	Ccc/Tcc	18/18	0.597560039489827	3	FACETS	1	0.985	1	0.644	0.594	0.695	CLONAL	1	TRUE	1	0.700272583031725	3		335	458	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517930	187517930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	142	320	0	ENST00000441802.2:c.12764C>T	p.Ser4255Phe	p.S4255F	ENST00000441802	NM_005245.3	4255	tCc/tTc	25/27	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.700272583031725	2		320	335	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	773	365	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.700272583031725	7	FACETS	1	0.993	1			1	CLONAL	6	TRUE	NA	0.700272583031725	7		365	983	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608053	28608053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	126	425	0	ENST00000241453.7:c.1913C>T	p.Ser638Leu	p.S638L	ENST00000241453	NM_004119.2	638	tCa/tTa	15/24	0.460796450002239	3	FACETS	1	0.959	1	0.543	0.496	0.593	CLONAL	1	TRUE	1	0.700272583031725	3		425	447	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843593	156843593	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	109	385	0	ENST00000524377.1:c.1019C>T	p.Thr340Ile	p.T340I	ENST00000524377	NM_002529.3	340	aCc/aTc	8/17	0.597560039489827	3	FACETS	1	0.934	1	0.52	0.471	0.572	CLONAL	1	TRUE	1	0.700272583031725	3		385	404	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662151	227662151	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1250279823	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	108	282	0	ENST00000305123.5:c.1304C>T	p.Pro435Leu	p.P435L	ENST00000305123	NM_005544.2	435	cCc/cTc	1/2	1	2	FACETS	0.961	0.873	1	0.961	0.873	1	CLONAL	1	TRUE	1	0.700272583031725	2		282	321	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795096	242795096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1243031095	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	87	268	0	ENST00000334409.5:c.113C>T	p.Ser38Phe	p.S38F	ENST00000334409	NM_005018.2	38	tCc/tTc	2/5	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.700272583031725	2		268	194	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890312	72890312	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	162	368	0	ENST00000325599.8:c.370G>A	p.Glu124Lys	p.E124K	ENST00000325599	NM_018130.2	124	Gag/Aag	4/11	0.136473352627554	4	FACETS	0.791	0.732	0.853	0.791	0.732	0.853	INDETERMINATE	2	TRUE	2	0.700272583031725	4		368	497	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119624643	119624643	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	153	428	0	ENST00000316626.5:c.772C>T	p.Pro258Ser	p.P258S	ENST00000316626		258	Cca/Tca	7/12	0.136473352627554	4	FACETS	0.822	0.759	0.887	0.822	0.759	0.887	INDETERMINATE	2	TRUE	2	0.700272583031725	4		428	452	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628000	187628000	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs926336062	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	161	425	0	ENST00000441802.2:c.2982G>C	p.Lys994Asn	p.K994N	ENST00000441802	NM_005245.3	994	aaG/aaC	2/27	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.700272583031725	2		425	397	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876305	35876305	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778728560	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	99	264	0	ENST00000303115.3:c.1097C>T	p.Ser366Phe	p.S366F	ENST00000303115	NM_002185.3	366	tCc/tTc	8/8	1	2	FACETS	0.939	0.849	1	0.939	0.849	1	CLONAL	1	TRUE	1	0.700272583031725	2		264	301	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505094	149505094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	102	354	0	ENST00000261799.4:c.1721C>T	p.Ser574Phe	p.S574F	ENST00000261799	NM_002609.3	574	tCt/tTt	12/23	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.700272583031725	2		354	291	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958208	2958208	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1162658658	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	37	257	0	ENST00000396946.4:c.2524C>T	p.Leu842Phe	p.L842F	ENST00000396946	NM_032415.4	842	Ctc/Ttc	19/25	0.191332569605077	5	FACETS	0.669	0.553	0.797			1	INDETERMINATE	1	TRUE	NA	0.700272583031725	5		257	324	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381516	81381516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	265	475	0	ENST00000222390.5:c.545G>A	p.Gly182Glu	p.G182E	ENST00000222390	NM_000601.4	182	gGg/gAg	5/18	0.33568154302838	6	FACETS	1	0.974	1	0.531	0.499	0.564	INDETERMINATE	2	TRUE	2	0.700272583031725	6		475	855	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913355	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	290	351	0	ENST00000288602.6:c.1406G>A	p.Gly469Glu	p.G469E	ENST00000288602	NM_004333.4	469	gGa/gAa	11/18	0.453234941644643	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	2	0.700272583031725	4		351	606	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231226	98231226	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1373585633	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	34	236	0	ENST00000331920.6:c.2057C>T	p.Ser686Phe	p.S686F	ENST00000331920	NM_000264.3	686	tCt/tTt	14/24	0.463264042667868	1	FACETS	0.351	0.289	0.418	0.351	0.289	0.418	SUBCLONAL	1	TRUE	0	0.700272583031725	1		236	180	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114901048	114901048	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	167	518	0	ENST00000543371.1:c.658T>A	p.Leu220Ile	p.L220I	ENST00000543371	NM_001198531.1	220	Tta/Ata	6/14	NA	2	FACETS	1	0.948	1			1	INDETERMINATE	1	TRUE	NA	0.700272583031725	2		518	464	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999068	100999068	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1185502243	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	122	436	1	ENST00000325455.5:c.734G>A	p.Gly245Asp	p.G245D	ENST00000325455	NM_001202474.3	245	gGt/gAt	1/8	0.700272583031725	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.700272583031725	1		437	207	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344314	118344314	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	64	159	0	ENST00000534358.1:c.2440C>T	p.Gln814Ter	p.Q814*	ENST00000534358	NM_005933.3	814	Cag/Tag	3/36	0.579995047565224	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.700272583031725	1		159	116	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563269	21563269	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	200	322	0	ENST00000382592.4:c.650C>T	p.Pro217Leu	p.P217L	ENST00000382592	NM_014572.2	217	cCc/cTc	4/8	0.460796450002239	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.700272583031725	3		322	372	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680724	88680724	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	111	308	0	ENST00000360948.2:c.533G>A	p.Gly178Glu	p.G178E	ENST00000360948	NM_001012338.2	178	gGg/gAg	6/19	NA	2	FACETS	1	0.972	1			1	INDETERMINATE	1	TRUE	NA	0.700272583031725	2		308	275	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226054	2226054	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	93	297	0	ENST00000326181.6:c.1751G>T	p.Trp584Leu	p.W584L	ENST00000326181	NM_032271.2	584	tGg/tTg	19/21	0.187730906090755	3	FACETS	1	0.949	1	0.547	0.491	0.605	INDETERMINATE	1	TRUE	1	0.700272583031725	3		297	328	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592302	29592302	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	347	325	0	ENST00000356175.3:c.4717T>C	p.Tyr1573His	p.Y1573H	ENST00000356175	NM_000267.3	1573	Tac/Cac	35/57	1	2	FACETS	1	0.994	1	1	0.997	1	CLONAL	2	TRUE	1	0.700272583031725	2		325	447	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39613898	39613898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	163	338	0	ENST00000262039.4:c.1816C>T	p.Pro606Ser	p.P606S	ENST00000262039	NM_002647.2	606	Ccg/Tcg	16/25	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.700272583031725	2		338	411	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099273	4099274	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	86	328	0	ENST00000262948.5:c.844_845delinsTT	p.Pro282Phe	p.P282F	ENST00000262948	NM_030662.3	282	CCc/TTc	7/11	1	2	FACETS	0.948	0.851	1	0.948	0.851	1	CLONAL	1	TRUE	1	0.700272583031725	2		328	259	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272063	15272063	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762210622	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	25	76	0	ENST00000263388.2:c.6376C>T	p.Pro2126Ser	p.P2126S	ENST00000263388	NM_000435.2	2126	Ccc/Tcc	33/33	1	2	FACETS	0.752	0.606	0.91	0.752	0.606	0.91	CLONAL	1	TRUE	1	0.700272583031725	2		76	95	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350015	15350015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	130	305	0	ENST00000263377.2:c.3637C>T	p.Pro1213Ser	p.P1213S	ENST00000263377	NM_058243.2	1213	Ccc/Tcc	18/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.700272583031725	2		305	309	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793280	33793280	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	67	127	0	ENST00000498907.2:c.41C>T	p.Pro14Leu	p.P14L	ENST00000498907	NM_004364.3	14	cCg/cTg	1/1	0.452400604904587	3	FACETS	1	0.944	1	0.712	0.642	0.78	CLONAL	2	TRUE	0	0.700272583031725	3		127	121	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743903	41743903	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	253	385	0	ENST00000301178.4:c.838G>A	p.Glu280Lys	p.E280K	ENST00000301178	NM_021913.4	280	Gag/Aag	7/20	0.452400604904587	3	FACETS	0.856	0.818	0.892	0.856	0.818	0.892	CLONAL	3	TRUE	0	0.700272583031725	3		385	380	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525059	9525059	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	161	429	0	ENST00000353224.5:c.1826G>A	p.Trp609Ter	p.W609*	ENST00000353224	NM_177990.2	609	tGg/tAg	8/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.700272583031725	2		429	392	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561102	9561102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	74	267	0	ENST00000353224.5:c.680C>T	p.Pro227Leu	p.P227L	ENST00000353224	NM_177990.2	227	cCt/cTt	4/10	1	2	FACETS	0.969	0.863	1	0.969	0.863	1	CLONAL	1	TRUE	1	0.700272583031725	2		267	218	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929022	44929022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	203	510	0	ENST00000377967.4:c.2122G>A	p.Gly708Arg	p.G708R	ENST00000377967	NM_021140.2	708	Gga/Aga	17/29	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.700272583031725	2		510	539	SUCCESS
AR	367	MSKCC	GRCh37	X	66931406	66931406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	172	487	0	ENST00000374690.3:c.2048C>T	p.Pro683Leu	p.P683L	ENST00000374690	NM_000044.3	683	cCa/cTa	4/8	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.700272583031725	2		487	430	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480568	123480568	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	112	118	0	ENST00000371139.4:c.76G>A	p.Asp26Asn	p.D26N	ENST00000371139	NM_001114937.2	26	Gat/Aat	1/4	NA	2	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.700272583031725	2		118	294	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252782	10252783	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0003069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	80	206	0	ENST00000340748.4:c.3182_3183delinsTT	p.Thr1061Ile	p.T1061I	ENST00000340748		1061	aCC/aTT	29/40	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.700272583031725	2		206	222	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0003071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	69	769	0				ENST00000310581	NM_198253.2	-/1132			0.388500538216021	4	FACETS	1	0.92	1	1	0.92	1	CLONAL	2	TRUE	2	0.425135204912786	4		769	220	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs17849781	NA	P-0003071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	494	409	0	ENST00000269305.4:c.832C>G	p.Pro278Ala	p.P278A	ENST00000269305	NM_001126112.2	278	Cct/Gct	8/11	0.425135204912786	3	FACETS	0.977	0.941	1	0.977	0.941	1	CLONAL	3	TRUE	0	0.425135204912786	3		409	961	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463181	25463181	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757823678	NA	P-0003071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	280	358	1	ENST00000264709.3:c.2312G>A	p.Arg771Gln	p.R771Q	ENST00000264709	NM_175629.2	771	cGa/cAa	19/23	0.364161558354534	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.425135204912786	4		359	898	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911535	101911535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113605875	NA	P-0003071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	376	408	0	ENST00000374994.4:c.1460G>A	p.Arg487Gln	p.R487Q	ENST00000374994	NM_004612.2	487	cGg/cAg	9/9	0.407018791736381	3	FACETS	0.947	0.906	0.988	0.947	0.906	0.988	CLONAL	3	TRUE	0	0.425135204912786	3		408	755	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45873425	45873425	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	214	288	0	ENST00000391945.4:c.71A>G	p.Tyr24Cys	p.Y24C	ENST00000391945	NM_000400.3	24	tAc/tGc	2/23	0.373350284142933	5	FACETS	0.996	0.927	1	0.664	0.618	0.711	CLONAL	2	TRUE	2	0.425135204912786	5		288	828	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44920586	44920586	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	407	270	0	ENST00000377967.4:c.1347G>A	p.Trp449Ter	p.W449*	ENST00000377967	NM_021140.2	449	tgG/tgA	14/29	0.345007717484943	2	FACETS	0.877	0.842	0.911			1	CLONAL	3	TRUE	NA	0.425135204912786	2		270	728	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	24	174	0				ENST00000310581	NM_198253.2	-/1132			0.273404009549994	1	FACETS	0.926	0.761	1	1	0.954	1	CLONAL	2	TRUE	0	0.381528051937773	1		174	55	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0003075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	113	318	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.381528051937773	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.381528051937773	1		318	324	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0003075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	124	440	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.381528107629629	1	FACETS	0.862	0.792	0.934	1	0.989	1	CLONAL	2	TRUE	0	0.381528051937773	1		440	305	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0003075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	211	932	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.381528051937773	2		932	751	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656884	47656884	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	76	341	0	ENST00000233146.2:c.1080G>C	p.Leu360Phe	p.L360F	ENST00000233146	NM_000251.2	360	ttG/ttC	7/16	0.179168072387974	1	FACETS	1	0.926	1	1	0.926	1	INDETERMINATE	1	TRUE	0	0.381528051937773	1		341	304	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821890	72821890	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	192	638	0	ENST00000268489.5:c.10285del	p.Arg3429ValfsTer56	p.R3429Vfs*56	ENST00000268489	NM_006885.3	3429	Cgt/gt	10/10	0.381528107629629	1	FACETS	0.756	0.704	0.808	1	0.991	1	SUBCLONAL	2	TRUE	0	0.381528051937773	1		638	539	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241677	55241677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504256	NA	P-0003107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	275	280	0	ENST00000275493.2:c.2125G>A	p.Glu709Lys	p.E709K	ENST00000275493	NM_005228.3	709	Gaa/Aaa	18/28	0.252653729799822	4	FACETS	0.946	0.886	1	0.946	0.886	1	CLONAL	2	TRUE	2	0.252653729799822	4		280	1441	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0003107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	240	639	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.252653729799822	4	FACETS	0.924	0.861	0.989	0.924	0.861	0.989	CLONAL	2	TRUE	2	0.252653729799822	4		639	1288	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874257	155874257	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	67	256	0	ENST00000368323.3:c.274G>T	p.Ala92Ser	p.A92S	ENST00000368323	NM_006912.5	92	Gca/Tca	5/6	0.252653729799822	6	FACETS	0.986	0.855	1			1	CLONAL	1	TRUE	NA	0.252653729799822	6		256	810	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423511	88423511	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0003107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	90	356	0	ENST00000360948.2:c.2324C>G	p.Ser775Ter	p.S775*	ENST00000360948	NM_001012338.2	775	tCa/tGa	18/19	0.203334409395956	3	FACETS	0.862	0.763	0.968	0.431	0.381	0.484	CLONAL	1	TRUE	1	0.252653729799822	3		356	931	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534457	63534457	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555578556	NA	P-0003107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	63	134	0	ENST00000307078.5:c.1064C>T	p.Thr355Ile	p.T355I	ENST00000307078	NM_004655.3	355	aCc/aTc	5/11	0.252653729799822	4	FACETS	0.904	0.781	1	0.452	0.39	0.519	CLONAL	1	TRUE	2	0.252653729799822	4		134	691	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604699	48604699	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	178	275	0	ENST00000342988.3:c.1521A>C	p.Lys507Asn	p.K507N	ENST00000342988	NM_005359.5	507	aaA/aaC	12/12	0.219679584878757	4	FACETS	0.845	0.782	0.911			1	CLONAL	3	TRUE	NA	0.252653729799822	4		275	696	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420094	152420112	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	CGGTCTGAGAGCTCCCTGG	CGGTCTGAGAGCTCCCTGG	-	novel	NA	P-0003107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	127	162	0	ENST00000206249.3:c.1782_*12del		p.*594*	ENST00000206249	NM_000125.3	594		8/8	0.252653729799822	4	FACETS	0.858	0.778	0.942	0.858	0.778	0.942	CLONAL	2	TRUE	2	0.252653729799822	4		162	734	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0003167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	148	927	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.190144851521428	3	FACETS	0.961	0.878	1	0.961	0.878	1	CLONAL	2	TRUE	1	0.190144851521428	3		927	887	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0003167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	75	366	1	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.190144851521428	2		367	752	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971098	21971098	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs878853647	NA	P-0003167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	43	196	0	ENST00000304494.5:c.260G>C	p.Arg87Pro	p.R87P	ENST00000304494	NM_000077.4	87	cGg/cCg	2/3	0.190144851521428	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.190144851521428	1		196	315	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247866	59247866	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	62	629	0	ENST00000371222.2:c.877G>A	p.Glu293Lys	p.E293K	ENST00000371222	NM_002228.3	293	Gag/Aag	1/1	1	2	FACETS	0.593	0.51	0.683	0.593	0.51	0.683	SUBCLONAL	1	TRUE	1	0.190144851521428	2		629	1100	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022334	26022334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	60	609	0	ENST00000435504.4:c.323C>T	p.Ser108Phe	p.S108F	ENST00000435504		108	tCc/tTc	5/13	1	2	FACETS	0.606	0.52	0.7	0.606	0.52	0.7	SUBCLONAL	1	TRUE	1	0.190144851521428	2		609	1042	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61729133	61729133	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	53	496	0	ENST00000401558.2:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000401558	NM_003400.3	136	Cag/Tag	6/25	1	2	FACETS	0.538	0.457	0.628	0.538	0.457	0.628	SUBCLONAL	1	TRUE	1	0.190144851521428	2		496	1036	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646062	215646062	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0003167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	47	490	0	ENST00000260947.4:c.536C>G	p.Ser179Ter	p.S179*	ENST00000260947	NM_000465.2	179	tCa/tGa	4/11	1	2	FACETS	0.687	0.578	0.807	0.687	0.578	0.807	SUBCLONAL	1	TRUE	1	0.190144851521428	2		490	720	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220432056	220432056	+	upstream_gene_variant	5'Flank	SNP	G	G	C	novel	NA	P-0003167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	61	584	0				ENST00000243786	NM_002191.3	592/1896			1	2	FACETS	0.713	0.613	0.822	0.713	0.613	0.822	SUBCLONAL	1	TRUE	1	0.190144851521428	2		584	900	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37092022	37092022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	92	542	1	ENST00000231790.2:c.2149G>A	p.Glu717Lys	p.E717K	ENST00000231790	NM_000249.3	717	Gaa/Aaa	19/19	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.190144851521428	2		543	838	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504350	186504350	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	40	317	0	ENST00000323963.5:c.687G>A	p.Met229Ile	p.M229I	ENST00000323963		229	atG/atA	7/11	1	2	FACETS	0.795	0.66	0.946	0.795	0.66	0.946	CLONAL	1	TRUE	1	0.190144851521428	2		317	529	SUCCESS
APC	324	MSKCC	GRCh37	5	112176008	112176008	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	33	311	0	ENST00000257430.4:c.4717G>A	p.Glu1573Lys	p.E1573K	ENST00000257430	NM_000038.5	1573	Gaa/Aaa	16/16	1	2	FACETS	0.611	0.497	0.741	0.611	0.497	0.741	SUBCLONAL	1	TRUE	1	0.190144851521428	2		311	568	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910744	29910744	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0003167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	158	423	0	ENST00000376809.5:c.284C>G	p.Ser95Ter	p.S95*	ENST00000376809	NM_002116.7	95	tCa/tGa	2/8	0.144069535293026	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.190144851521428	2		423	763	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505484	157505484	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	33	319	0	ENST00000346085.5:c.3465G>C	p.Lys1155Asn	p.K1155N	ENST00000346085	NM_020732.3	1155	aaG/aaC	13/20	1	2	FACETS	0.57	0.463	0.691	0.57	0.463	0.691	SUBCLONAL	1	TRUE	1	0.190144851521428	2		319	609	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334776	81334776	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	39	503	0	ENST00000222390.5:c.1940G>C	p.Arg647Pro	p.R647P	ENST00000222390	NM_000601.4	647	cGa/cCa	17/18	1	2	FACETS	0.59	0.488	0.705	0.59	0.488	0.705	SUBCLONAL	1	TRUE	1	0.190144851521428	2		503	695	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852173	128852173	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	66	491	0	ENST00000249373.3:c.2245C>G	p.Leu749Val	p.L749V	ENST00000249373	NM_005631.4	749	Ctg/Gtg	12/12	1	2	FACETS	0.954	0.827	1	0.954	0.827	1	CLONAL	1	TRUE	1	0.190144851521428	2		491	728	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101909995	101909995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	74	327	0	ENST00000374994.4:c.1315G>A	p.Glu439Lys	p.E439K	ENST00000374994	NM_004612.2	439	Gaa/Aaa	8/9	0.190144851521428	1	FACETS	0.968	0.846	1	0.968	0.846	1	CLONAL	1	TRUE	0	0.190144851521428	1		327	728	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760819	133760819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769953778	NA	P-0003167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	38	464	1	ENST00000318560.5:c.3142G>A	p.Glu1048Lys	p.E1048K	ENST00000318560	NM_005157.4	1048	Gag/Aag	11/11	0.190144851521428	1	FACETS	0.565	0.466	0.676	0.565	0.466	0.676	SUBCLONAL	1	TRUE	0	0.190144851521428	1		465	640	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845588	63845588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774238244	NA	P-0003167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	40	289	0	ENST00000279873.7:c.1327C>T	p.Arg443Cys	p.R443C	ENST00000279873	NM_032199.2	443	Cgc/Tgc	9/10	0.144069535293026	2	FACETS	0.559	0.463	0.666	0.279	0.231	0.333	SUBCLONAL	1	TRUE	0	0.190144851521428	2		289	753	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333593	70333593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	118	411	0	ENST00000373644.4:c.1498G>A	p.Glu500Lys	p.E500K	ENST00000373644	NM_030625.2	500	Gag/Aag	2/12	0.144069535293026	2	FACETS	0.884	0.798	0.974	0.884	0.798	0.974	CLONAL	2	TRUE	0	0.190144851521428	2		411	702	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375770	118375770	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	89	474	0	ENST00000534358.1:c.9163G>C	p.Asp3055His	p.D3055H	ENST00000534358	NM_005933.3	3055	Gat/Cat	27/36	1	2	FACETS	0.995	0.88	1	0.995	0.88	1	CLONAL	1	TRUE	1	0.190144851521428	2		474	941	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650565	18650565	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	40	342	0	ENST00000266497.5:c.2776C>G	p.Leu926Val	p.L926V	ENST00000266497		926	Ctt/Gtt	20/31	1	2	FACETS	0.751	0.623	0.894	0.751	0.623	0.894	SUBCLONAL	1	TRUE	1	0.190144851521428	2		342	560	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671683	67671683	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	30	325	0	ENST00000264010.4:c.2092G>T	p.Glu698Ter	p.E698*	ENST00000264010	NM_006565.3	698	Gag/Tag	12/12	1	2	FACETS	0.531	0.427	0.65	0.531	0.427	0.65	SUBCLONAL	1	TRUE	1	0.190144851521428	2		325	594	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862145	68862145	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	89	338	0	ENST00000261769.5:c.2233G>C	p.Glu745Gln	p.E745Q	ENST00000261769	NM_004360.3	745	Gag/Cag	14/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.190144851521428	2		338	721	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437520	56437520	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	66	287	0	ENST00000407977.2:c.942C>G	p.Phe314Leu	p.F314L	ENST00000407977		314	ttC/ttG	8/10	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.190144851521428	2		287	600	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917133	50917133	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	75	495	0	ENST00000440232.2:c.2385G>C	p.Glu795Asp	p.E795D	ENST00000440232	NM_002691.3	795	gaG/gaC	19/27	0.190144851521428	1	FACETS	0.997	0.873	1	0.997	0.873	1	CLONAL	1	TRUE	0	0.190144851521428	1		495	716	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46270961	46270961	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	54	583	0	ENST00000371998.3:c.3085C>G	p.Leu1029Val	p.L1029V	ENST00000371998		1029	Ctt/Gtt	17/23	1	2	FACETS	0.535	0.455	0.624	0.535	0.455	0.624	SUBCLONAL	1	TRUE	1	0.190144851521428	2		583	1061	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424413	47424413	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	40	279	0	ENST00000377045.4:c.333C>G	p.Phe111Leu	p.F111L	ENST00000377045	NM_001654.4	111	ttC/ttG	5/16	1	1	FACETS	0.751	0.624	0.893	0.751	0.624	0.893	SUBCLONAL	1	TRUE	0	0.190144851521428	1		279	507	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602580	10602581	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0003167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	59	297	0	ENST00000171111.5:c.997_998delinsTT	p.Gly333Phe	p.G333F	ENST00000171111	NM_203500.1	333	GGc/TTc	3/6	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.190144851521428	2		297	521	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	53	174	0				ENST00000310581	NM_198253.2	-/1132			0.336201980730305	4	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	2	0.35925991406402	4		174	179	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0003176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	51	318	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.326805580628591	3	FACETS	1	0.859	1	0.503	0.429	0.583	CLONAL	1	TRUE	1	0.35925991406402	3		318	333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0003176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	285	725	0	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	0.349858777941475	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	4	TRUE	0	0.35925991406402	4		725	529	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0003176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	198	394	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	0.35925991406402	5	FACETS	0.942	0.883	1	0.942	0.883	1	CLONAL	4	TRUE	1	0.35925991406402	5		394	450	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	109	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.815032870315506	2		174	228	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0003178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	24	300	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.084	0.065	0.106	0.084	0.065	0.106	SUBCLONAL	1	TRUE	1	0.815032870315506	2		300	703	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0003178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	355	687	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.993	0.945	1	0.993	0.945	1	CLONAL	1	TRUE	1	0.815032870315506	2		687	877	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0003178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	8	249	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.052	0.033	0.077	0.052	0.033	0.077	SUBCLONAL	1	TRUE	1	0.815032870315506	2		249	378	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	60	638	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.678	0.593	0.769	0.678	0.593	0.769	SUBCLONAL	1	TRUE	1	0.815032870315506	2		639	217	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0003188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	45	769	0				ENST00000310581	NM_198253.2	-/1132			0.123115512114716	3	FACETS	1	0.959	1	0.733	0.62	0.855	INDETERMINATE	1	TRUE	1	0.26213934401159	3		769	265	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	94	515	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.26213934401159	3	FACETS	0.856	0.765	0.952	0.856	0.765	0.952	CLONAL	2	TRUE	1	0.26213934401159	3		515	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0003188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	113	440	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.26213934401159	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.26213934401159	1		440	732	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394992	394992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	91	170	0	ENST00000380956.4:c.388G>A	p.Glu130Lys	p.E130K	ENST00000380956	NM_001195286.1	130	Gag/Aag	3/9	0.206952797401774	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.26213934401159	1		170	414	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960145	151960145	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	147	376	0	ENST00000262189.6:c.1255C>T	p.Gln419Ter	p.Q419*	ENST00000262189	NM_170606.2	419	Caa/Taa	9/59	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.26213934401159	2		376	962	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759870	133759870	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	152	289	0	ENST00000318560.5:c.2193G>A	p.Trp731Ter	p.W731*	ENST00000318560	NM_005157.4	731	tgG/tgA	11/11	0.260309617134329	2	FACETS	0.978	0.898	1	0.978	0.898	1	CLONAL	2	TRUE	0	0.26213934401159	2		289	593	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426775	49426775	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886042253	NA	P-0003188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	46	144	0	ENST00000301067.7:c.11713C>T	p.Gln3905Ter	p.Q3905*	ENST00000301067	NM_003482.3	3905	Cag/Tag	39/54	1	2	FACETS	0.991	0.838	1	0.991	0.838	1	CLONAL	1	TRUE	1	0.26213934401159	2		144	354	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346814	91346814	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs770370129	NA	P-0003188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	72	363	0	ENST00000355112.3:c.3422A>G	p.Asn1141Ser	p.N1141S	ENST00000355112	NM_000057.2	1141	aAt/aGt	18/22	1	2	FACETS	0.599	0.522	0.683	0.599	0.522	0.683	SUBCLONAL	1	TRUE	1	0.26213934401159	2		363	917	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136336	2136336	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	116	356	0	ENST00000219476.3:c.4805A>G	p.Glu1602Gly	p.E1602G	ENST00000219476	NM_000548.3	1602	gAg/gGg	37/42	0.26213934401159	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.26213934401159	1		356	648	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220714	2220714	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754251548	NA	P-0003188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	96	273	0	ENST00000326181.6:c.331G>A	p.Glu111Lys	p.E111K	ENST00000326181	NM_032271.2	111	Gag/Aag	5/21	0.26213934401159	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.26213934401159	1		273	545	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808962	3808962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	118	238	0	ENST00000262367.5:c.3262G>A	p.Glu1088Lys	p.E1088K	ENST00000262367	NM_004380.2	1088	Gag/Aag	17/31	0.26213934401159	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.26213934401159	1		238	568	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821349	72821349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567505140	NA	P-0003188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	146	350	0	ENST00000268489.5:c.10826C>T	p.Ser3609Phe	p.S3609F	ENST00000268489	NM_006885.3	3609	tCc/tTc	10/10	0.26213934401159	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.26213934401159	1		350	665	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47679263	47679263	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	74	305	0	ENST00000347630.2:c.944A>G	p.Asp315Gly	p.D315G	ENST00000347630	NM_001007230.1	315	gAt/gGt	10/11	1	2	FACETS	0.62	0.542	0.706	0.62	0.542	0.706	SUBCLONAL	1	TRUE	1	0.26213934401159	2		305	910	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5260818	5260818	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs747842113	NA	P-0003188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	27	166	0	ENST00000357368.4:c.593G>C	p.Arg198Pro	p.R198P	ENST00000357368	NM_002850.3	198	cGa/cCa	7/38	1	2	FACETS	0.436	0.346	0.54	0.436	0.346	0.54	SUBCLONAL	1	TRUE	1	0.26213934401159	2		166	472	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121153	11121153	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	75	352	0	ENST00000358026.2:c.2220G>C	p.Glu740Asp	p.E740D	ENST00000358026	NM_001128849.1	740	gaG/gaC	15/36	1	2	FACETS	0.672	0.587	0.763	0.672	0.587	0.763	SUBCLONAL	1	TRUE	1	0.26213934401159	2		352	852	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872214	45872214	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	79	310	0	ENST00000391945.4:c.220T>C	p.Ser74Pro	p.S74P	ENST00000391945	NM_000400.3	74	Tca/Cca	4/23	1	2	FACETS	0.743	0.653	0.841	0.743	0.653	0.841	SUBCLONAL	1	TRUE	1	0.26213934401159	2		310	811	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76953120	76953120	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	117	477	0	ENST00000373344.5:c.193A>C	p.Thr65Pro	p.T65P	ENST00000373344	NM_000489.3	65	Act/Cct	4/35	0.26213934401159	1	FACETS	0.697	0.627	0.771	0.697	0.627	0.771	SUBCLONAL	1	TRUE	0	0.26213934401159	1		477	1113	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143341	30143341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003206-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	56	266	0	ENST00000389048.3:c.185C>T	p.Ser62Leu	p.S62L	ENST00000389048	NM_004304.4	62	tCg/tTg	1/29	NA	2	FACETS	0.445	0.383	0.511			1	INDETERMINATE	1	TRUE	NA	0.756613609584314	2		266	333	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139614	202139614	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003206-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	96	370	0	ENST00000358485.4:c.775G>T	p.Glu259Ter	p.E259*	ENST00000358485	NM_001080125.1	259	Gag/Tag	6/9	1	2	FACETS	0.366	0.326	0.408	0.366	0.326	0.408	SUBCLONAL	1	TRUE	1	0.756613609584314	2		370	694	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342404	70342404	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003206-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	78	343	0	ENST00000374080.3:c.1295G>T	p.Gly432Val	p.G432V	ENST00000374080		432	gGa/gTa	9/45	0.756613609584314	3	FACETS	0.353	0.31	0.4	0.177	0.155	0.2	SUBCLONAL	1	TRUE	1	0.756613609584314	3		343	804	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182867	123182867	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003206-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	103	434	1	ENST00000218089.9:c.832C>G	p.Gln278Glu	p.Q278E	ENST00000218089	NM_001042749.1	278	Caa/Gaa	10/35	0.756613609584314	3	FACETS	0.407	0.363	0.453	0.204	0.181	0.227	SUBCLONAL	1	TRUE	1	0.756613609584314	3		435	922	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994137	21994178	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CCTGGTCTTCTAGGAAGCGGCTGCTGCCCTAGACGCTGGCTC	CCTGGTCTTCTAGGAAGCGGCTGCTGCCCTAGACGCTGGCTC	-	novel	NA	P-0003206-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	69	399	0	ENST00000579755.1:c.153_193+1del		p.X51_splice	ENST00000579755		51		1/3	1		FACETS		0.338	0.44				SUBCLONAL	1	TRUE	1	0.756613609584314	2		399	471	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575440	64575444	+	frameshift_variant	Frame_Shift_Del	DEL	TCTGC	TCTGC	-	novel	NA	P-0003206-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	88	337	0	ENST00000312049.6:c.573_577del	p.Glu191AspfsTer3	p.E191Dfs*3	ENST00000312049	NM_130799.2	191	gaGCAGAca/gaca	3/10	0.756613609584314	4	FACETS	0.598	0.53	0.671			1	SUBCLONAL	1	TRUE	NA	0.756613609584314	4		337	683	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	79	769	0				ENST00000310581	NM_198253.2	-/1132			0.269587447038931	4	FACETS	0.995	0.883	1	0.995	0.883	1	CLONAL	2	TRUE	2	0.33	4		769	320	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	16	515	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.245341448143496	5	FACETS	0.681	0.504	0.89	0.227	0.168	0.297	SUBCLONAL	1	TRUE	2	0.33	5		515	213	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760819	133760819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769953778	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	89	464	1	ENST00000318560.5:c.3142G>A	p.Glu1048Lys	p.E1048K	ENST00000318560	NM_005157.4	1048	Gag/Aag	11/11	0.3	3	FACETS	0.82	0.727	0.92	0.273	0.242	0.307	CLONAL	1	TRUE	0	0.33	3		465	766	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	203	687	0	ENST00000269305.4:c.853G>T	p.Glu285Ter	p.E285*	ENST00000269305	NM_001126112.2	285	Gag/Tag	8/11	0.189996266869084	3	FACETS	0.979	0.911	1	0.653	0.607	0.7	INDETERMINATE	2	TRUE	0	0.33	3		687	732	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259686	11259686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	101	337	0	ENST00000361445.4:c.4019G>A	p.Ser1340Asn	p.S1340N	ENST00000361445	NM_004958.3	1340	aGc/aAc	27/58	0.269587447038931	4	FACETS	1	0.978	1	0.682	0.611	0.757	CLONAL	1	TRUE	2	0.33	4		337	597	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797198	45797198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559963863	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	164	440	0	ENST00000450313.1:c.1217C>T	p.Ser406Phe	p.S406F	ENST00000450313	NM_012222.2	406	tCc/tTc	13/16	0.269587447038931	4	FACETS	0.8	0.735	0.868	0.8	0.735	0.868	SUBCLONAL	2	TRUE	2	0.33	4		440	826	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551879	150551879	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	75	168	0	ENST00000369026.2:c.128C>G	p.Ser43Trp	p.S43W	ENST00000369026	NM_021960.4	43	tCg/tGg	1/3	0.269587447038931	4	FACETS	1	0.973	1	0.701	0.617	0.791	CLONAL	1	TRUE	2	0.33	4		168	431	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165671	47165671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	79	399	0	ENST00000409792.3:c.455C>T	p.Thr152Ile	p.T152I	ENST00000409792	NM_014159.6	152	aCa/aTa	3/21	0.206315137614534	3	FACETS	0.841	0.74	0.95			1	CLONAL	1	TRUE	NA	0.33	3		399	663	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165752	47165752	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	68	420	0	ENST00000409792.3:c.374C>G	p.Ser125Cys	p.S125C	ENST00000409792	NM_014159.6	125	tCt/tGt	3/21	0.206315137614534	3	FACETS	0.743	0.646	0.848			1	SUBCLONAL	1	TRUE	NA	0.33	3		420	646	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165816	47165816	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	91	503	0	ENST00000409792.3:c.310C>G	p.Pro104Ala	p.P104A	ENST00000409792	NM_014159.6	104	Cca/Gca	3/21	0.206315137614534	3	FACETS	0.953	0.847	1			1	CLONAL	1	TRUE	NA	0.33	3		503	674	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390117	89390117	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	37	365	0	ENST00000336596.2:c.866A>T	p.Lys289Met	p.K289M	ENST00000336596	NM_005233.5	289	aAg/aTg	4/17	0.245341448143496	5	FACETS	1	0.905	1	0.381	0.315	0.454	CLONAL	1	TRUE	2	0.33	5		365	293	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242864	142242864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	38	429	0	ENST00000350721.4:c.4123G>A	p.Glu1375Lys	p.E1375K	ENST00000350721	NM_001184.3	1375	Gaa/Aaa	22/47	0.245341448143496	5	FACETS	0.824	0.681	0.982	0.275	0.227	0.328	CLONAL	1	TRUE	2	0.33	5		429	418	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752342	57752342	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	38	453	0	ENST00000274289.3:c.1231C>G	p.Pro411Ala	p.P411A	ENST00000274289	NM_006622.3	411	Ccc/Gcc	9/14	0.269587447038931	4	FACETS	0.823	0.682	0.981	0.412	0.341	0.491	CLONAL	1	TRUE	2	0.33	4		453	372	SUCCESS
APC	324	MSKCC	GRCh37	5	112174760	112174760	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1554085038	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	22	348	0	ENST00000257430.4:c.3469G>C	p.Glu1157Gln	p.E1157Q	ENST00000257430	NM_000038.5	1157	Gag/Cag	16/16	0.282075335203926	1	FACETS	0.415	0.322	0.523	0.415	0.322	0.523	SUBCLONAL	1	TRUE	0	0.33	1		348	268	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510123	149510123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1312583190	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	135	367	0	ENST00000261799.4:c.1346C>T	p.Ser449Phe	p.S449F	ENST00000261799	NM_002609.3	449	tCt/tTt	9/23	0.3	3	FACETS	1	0.981	1	0.653	0.594	0.714	CLONAL	1	TRUE	1	0.33	3		367	730	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402595	20402595	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	120	232	0	ENST00000346618.3:c.132C>A	p.Phe44Leu	p.F44L	ENST00000346618	NM_001949.4	44	ttC/ttA	1/7	0.245341448143496	5	FACETS	1	0.97	1	0.774	0.704	0.848	CLONAL	2	TRUE	2	0.33	5		232	468	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680503	30680503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	98	384	0	ENST00000376406.3:c.1216G>A	p.Asp406Asn	p.D406N	ENST00000376406	NM_014641.2	406	Gac/Aac	5/15	0.245341448143496	5	FACETS	1	0.906	1	0.339	0.302	0.379	CLONAL	1	TRUE	2	0.33	5		384	872	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677957	117677957	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	73	561	0	ENST00000368508.3:c.3976C>G	p.Gln1326Glu	p.Q1326E	ENST00000368508	NM_002944.2	1326	Caa/Gaa	25/43	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.33	2		561	364	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522156	157522156	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	69	309	0	ENST00000346085.5:c.4428G>C	p.Gln1476His	p.Q1476H	ENST00000346085	NM_020732.3	1476	caG/caC	18/20	0.3	4	FACETS	0.977	0.852	1	0.489	0.426	0.557	CLONAL	1	TRUE	2	0.33	4		309	569	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935537	13935537	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs980825182	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	52	274	0	ENST00000405192.2:c.1319G>A	p.Gly440Glu	p.G440E	ENST00000405192	NM_001163147.1	440	gGg/gAg	12/12	0.3	4	FACETS	0.835	0.711	0.97	0.417	0.355	0.485	CLONAL	1	TRUE	2	0.33	4		274	502	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484379	8484379	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	36	345	0	ENST00000356435.5:c.3154-1G>C		p.X1052_splice	ENST00000356435		1052			0.3	1	FACETS	0.68	0.562	0.811	0.68	0.562	0.811	SUBCLONAL	1	TRUE	0	0.33	1		345	268	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796766	135796766	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	110	408	0	ENST00000298552.3:c.721G>C	p.Glu241Gln	p.E241Q	ENST00000298552	NM_001162426.1	241	Gaa/Caa	8/23	0.3	3	FACETS	1	0.96	1	0.738	0.67	0.808	CLONAL	2	TRUE	0	0.33	3		408	351	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333543	70333543	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	51	520	0	ENST00000373644.4:c.1448C>G	p.Ser483Ter	p.S483*	ENST00000373644	NM_030625.2	483	tCa/tGa	2/12	0.269587447038931	4	FACETS	0.687	0.584	0.802	0.344	0.292	0.401	SUBCLONAL	1	TRUE	2	0.33	4		520	598	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446395	70446395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	136	414	0	ENST00000373644.4:c.5335C>T	p.Pro1779Ser	p.P1779S	ENST00000373644	NM_030625.2	1779	Ccc/Tcc	11/12	0.269587447038931	4	FACETS	1	0.986	1	0.749	0.682	0.819	CLONAL	1	TRUE	2	0.33	4		414	732	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274827	123274827	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	60	302	0	ENST00000358487.5:c.1091G>C	p.Gly364Ala	p.G364A	ENST00000358487	NM_000141.4	364	gGa/gCa	9/18	0.3	5	FACETS	0.877	0.755	1			1	CLONAL	1	TRUE	NA	0.33	5		302	620	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164202	108164202	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	rs876658587	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	59	231	0	ENST00000278616.4:c.4774G>T	p.Glu1592Ter	p.E1592*	ENST00000278616	NM_000051.3	1592	Gag/Tag	31/63	0.275465419666143	4	FACETS	1	0.967	1			1	CLONAL	1	TRUE	NA	0.33	4		231	333	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244110	46244110	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	33	372	0	ENST00000334344.6:c.2204G>C	p.Gly735Ala	p.G735A	ENST00000334344	NM_152641.2	735	gGa/gCa	15/21	0.281789918042109	4	FACETS	0.776	0.633	0.936	0.259	0.211	0.312	CLONAL	1	TRUE	1	0.33	4		372	343	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433958	49433958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749781307	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	158	206	0	ENST00000301067.7:c.7595C>T	p.Ser2532Phe	p.S2532F	ENST00000301067	NM_003482.3	2532	tCt/tTt	31/54	0.281789918042109	4	FACETS	1	0.983	1	0.821	0.758	0.887	CLONAL	2	TRUE	1	0.33	4		206	517	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433988	49433988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	147	221	0	ENST00000301067.7:c.7565C>T	p.Pro2522Leu	p.P2522L	ENST00000301067	NM_003482.3	2522	cCt/cTt	31/54	0.281789918042109	4	FACETS	1	0.975	1	0.768	0.706	0.833	CLONAL	2	TRUE	1	0.33	4		221	514	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434181	49434181	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	189	353	0	ENST00000301067.7:c.7372C>A	p.Gln2458Lys	p.Q2458K	ENST00000301067	NM_003482.3	2458	Cag/Aag	31/54	0.281789918042109	4	FACETS	0.988	0.915	1	0.659	0.61	0.709	CLONAL	2	TRUE	1	0.33	4		353	771	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133236076	133236076	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	83	324	0	ENST00000320574.5:c.3080C>G	p.Ser1027Cys	p.S1027C	ENST00000320574	NM_006231.2	1027	tCt/tGt	26/49	0.281789918042109	4	FACETS	0.883	0.778	0.995	0.294	0.259	0.332	CLONAL	1	TRUE	1	0.33	4		324	758	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240307	41240307	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1403000835	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	72	358	0	ENST00000379561.5:c.43G>C	p.Glu15Gln	p.E15Q	ENST00000379561	NM_002015.3	15	Gag/Cag	1/3	0.189996266869084	3	FACETS	0.786	0.686	0.893	0.262	0.228	0.298	INDETERMINATE	1	TRUE	0	0.33	3		358	647	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347917	73347917	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs202067860	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	81	319	0	ENST00000377767.4:c.1144C>G	p.Arg382Gly	p.R382G	ENST00000377767	NM_014953.3	382	Cga/Gga	8/21	0.189996266869084	3	FACETS	0.826	0.734	0.924	0.551	0.489	0.616	INDETERMINATE	2	TRUE	0	0.33	3		319	346	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046634	42046634	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	37	386	0	ENST00000219905.7:c.7009-1G>A		p.X2337_splice	ENST00000219905	NM_001164273.1	2337			NA	2	FACETS	0.526	0.434	0.63			1	INDETERMINATE	1	TRUE	NA	0.33	2		386	426	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052536	42052536	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	47	657	0	ENST00000219905.7:c.7207C>G	p.Leu2403Val	p.L2403V	ENST00000219905	NM_001164273.1	2403	Cta/Gta	20/24	NA	2	FACETS	0.454	0.383	0.534			1	INDETERMINATE	1	TRUE	NA	0.33	2		657	627	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052653	42052653	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	68	694	0	ENST00000219905.7:c.7324C>G	p.Leu2442Val	p.L2442V	ENST00000219905	NM_001164273.1	2442	Ctc/Gtc	20/24	NA	2	FACETS	0.544	0.473	0.622			1	INDETERMINATE	1	TRUE	NA	0.33	2		694	757	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732318	74732318	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	241	697	1	ENST00000359995.5:c.591G>C	p.Lys197Asn	p.K197N	ENST00000359995	NM_001195427.1	197	aaG/aaC	2/3	0.287959519394111	4	FACETS	0.854	0.797	0.912	0.427	0.398	0.456	CLONAL	2	TRUE	0	0.33	4		698	1138	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732409	74732409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326283685	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	243	727	0	ENST00000359995.5:c.500G>A	p.Arg167Gln	p.R167Q	ENST00000359995	NM_001195427.1	167	cGa/cAa	2/3	0.287959519394111	4	FACETS	0.777	0.724	0.831	0.388	0.362	0.416	SUBCLONAL	2	TRUE	0	0.33	4		727	1261	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794835	42794835	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	100	321	0	ENST00000575354.2:c.1915G>C	p.Glu639Gln	p.E639Q	ENST00000575354	NM_015125.3	639	Gag/Cag	10/20	0.245341448143496	5	FACETS	1	0.972	1	0.424	0.379	0.472	CLONAL	1	TRUE	2	0.33	5		321	712	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513240	44513240	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	214	178	0	ENST00000291552.4:c.695G>C	p.Arg232Thr	p.R232T	ENST00000291552	NM_006758.2	232	aGa/aCa	8/8	0.3	6	FACETS	1	0.98	1	0.882	0.829	0.936	CLONAL	4	TRUE	1	0.33	6		178	488	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000043	30000043	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	103	487	0	ENST00000338641.4:c.56C>G	p.Pro19Arg	p.P19R	ENST00000338641	NM_000268.3	19	cCc/cGc	1/16	0.269587447038931	4	FACETS	0.898	0.802	0.999	0.449	0.401	0.5	CLONAL	1	TRUE	2	0.33	4		487	925	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573610	41573610	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	200	483	1	ENST00000263253.7:c.5895G>T	p.Met1965Ile	p.M1965I	ENST00000263253	NM_001429.3	1965	atG/atT	31/31	0.269587447038931	4	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	2	0.33	4		484	804	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573708	41573708	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	224	415	0	ENST00000263253.7:c.5993G>C	p.Gly1998Ala	p.G1998A	ENST00000263253	NM_001429.3	1998	gGa/gCa	31/31	0.269587447038931	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.33	4		415	844	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942817	44942817	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	114	331	0	ENST00000377967.4:c.3397C>T	p.Gln1133Ter	p.Q1133*	ENST00000377967	NM_021140.2	1133	Caa/Taa	23/29	0.275465419666143	2	FACETS	1	0.967	1			1	CLONAL	2	TRUE	NA	0.33	2		331	307	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	96	174	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		174	207	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	80	515	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.25572137898813	4	FACETS	1	0.972	1	0.447	0.396	0.5	INDETERMINATE	1	TRUE	1	0.504750620712353	4		515	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0003320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	134	737	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	TRUE	1	0.504750620712353	2		737	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780071	NA	P-0003320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	200	516	0	ENST00000269305.4:c.580C>T	p.Leu194Phe	p.L194F	ENST00000269305	NM_001126112.2	194	Ctt/Ttt	6/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.504750620712353	2		516	749	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0003320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	86	197	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	1	2	FACETS	0.767	0.682	0.858	0.767	0.682	0.858	SUBCLONAL	1	TRUE	1	0.504750620712353	2		197	444	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143216	30143216	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs576431612	NA	P-0003320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	169	255	0	ENST00000389048.3:c.310C>T	p.Pro104Ser	p.P104S	ENST00000389048	NM_004304.4	104	Ccg/Tcg	1/29	0.320614995725446	5	FACETS	1	0.982	1	0.797	0.739	0.857	CLONAL	2	TRUE	2	0.504750620712353	5		255	492	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220432218	220432218	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0003320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	41	126	1				ENST00000243786	NM_002191.3	538/1896			0.504750620712353	1	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	0	0.504750620712353	1		127	118	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235375	235375	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	171	473	0	ENST00000264932.6:c.1181A>T	p.Asp394Val	p.D394V	ENST00000264932	NM_004168.2	394	gAc/gTc	9/15	1	2	FACETS	0.993	0.917	1	0.993	0.917	1	CLONAL	1	TRUE	1	0.504750620712353	2		473	682	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639023	176639023	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	126	287	0	ENST00000439151.2:c.3623C>G	p.Thr1208Ser	p.T1208S	ENST00000439151	NM_022455.4	1208	aCt/aGt	5/23	0.504750620712353	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.504750620712353	1		287	354	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403286	116403286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	338	459	0	ENST00000397752.3:c.2547G>A	p.Met849Ile	p.M849I	ENST00000397752	NM_000245.2	849	atG/atA	11/21	0.475527508756893	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.504750620712353	2		459	623	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152009018	152009018	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	193	336	0	ENST00000262189.6:c.604C>T	p.Gln202Ter	p.Q202*	ENST00000262189	NM_170606.2	202	Cag/Tag	5/59	NA	2	FACETS	0.893	0.837	0.95			1	INDETERMINATE	2	TRUE	NA	0.504750620712353	2		336	428	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90960050	90960050	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0003320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	192	400	0	ENST00000265433.3:c.1914+2T>A		p.X638_splice	ENST00000265433	NM_002485.4	638			0.224474070851481	3	FACETS	1	0.984	1	0.612	0.567	0.658	INDETERMINATE	1	TRUE	1	0.504750620712353	3		400	779	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400200	139400200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	102	333	0	ENST00000277541.6:c.4148G>A	p.Cys1383Tyr	p.C1383Y	ENST00000277541	NM_017617.3	1383	tGc/tAc	25/34	0.504750620712353	1	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	0	0.504750620712353	1		333	299	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436088	49436088	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	29	140	0	ENST00000301067.7:c.5893G>T	p.Glu1965Ter	p.E1965*	ENST00000301067	NM_003482.3	1965	Gaa/Taa	28/54	1	2	FACETS	0.809	0.659	0.975	0.809	0.659	0.975	CLONAL	1	TRUE	1	0.504750620712353	2		140	142	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438644	49438644	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	141	482	0	ENST00000301067.7:c.4846G>T	p.Gly1616Ter	p.G1616*	ENST00000301067	NM_003482.3	1616	Gga/Tga	19/54	1	2	FACETS	0.868	0.793	0.946	0.868	0.793	0.946	CLONAL	1	TRUE	1	0.504750620712353	2		482	644	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032238	10032238	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	141	348	0	ENST00000330684.3:c.585T>A	p.Phe195Leu	p.F195L	ENST00000330684	NM_001134407.1	195	ttT/ttA	3/13	0.504750620712353	1	FACETS	0.958	0.881	1	0.958	0.881	1	CLONAL	1	TRUE	0	0.504750620712353	1		348	436	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831635	72831635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	254	862	0	ENST00000268489.5:c.4946C>T	p.Ser1649Phe	p.S1649F	ENST00000268489	NM_006885.3	1649	tCc/tTc	9/10	0.504750620712353	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.504750620712353	1		862	749	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345262	70345262	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	176	283	0	ENST00000374080.3:c.2288A>T	p.Gln763Leu	p.Q763L	ENST00000374080		763	cAg/cTg	16/45	0.33635955098043	0	FACETS	0.892	0.834	0.952			1	CLONAL	1	TRUE	NA	0.504750620712353	0		283	387	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974713	21974713	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	115	443	0	ENST00000304494.5:c.114del	p.Asn39ThrfsTer14	p.N39Tfs*14	ENST00000304494	NM_000077.4	38	ccC/cc	1/3	0.504750620712353	1	FACETS	0.856	0.778	0.937	0.856	0.778	0.937	CLONAL	1	TRUE	0	0.504750620712353	1		443	398	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0003350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	58	769	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.839	0.731	0.952	0.839	0.731	0.952	CLONAL	1	TRUE	1	0.667999802347018	2		769	207	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220265	55220265	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	10757	353	3	ENST00000275493.2:c.655T>G	p.Cys219Gly	p.C219G	ENST00000275493	NM_005228.3	219	Tgc/Ggc	6/28	0.667999802347018	28	FACETS	1	0.998	1			1	CLONAL	27	TRUE	NA	0.667999802347018	28		356	11519	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272525	15272525	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	97	162	0	ENST00000263388.2:c.5914G>A	p.Glu1972Lys	p.E1972K	ENST00000263388	NM_000435.2	1972	Gag/Aag	33/33	0.667999802347018	3	FACETS	0.918	0.824	1	0.459	0.412	0.509	CLONAL	1	TRUE	1	0.667999802347018	3		162	422	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867149	45867149	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1322620921	NA	P-0003350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	85	150	0	ENST00000391945.4:c.970C>T	p.Arg324Cys	p.R324C	ENST00000391945	NM_000400.3	324	Cgc/Tgc	11/23	0.667999802347018	3	FACETS	0.862	0.766	0.962	0.431	0.383	0.481	CLONAL	1	TRUE	1	0.667999802347018	3		150	394	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	75	174	0				ENST00000310581	NM_198253.2	-/1132			0.799116292662109	3	FACETS	1	0.96	1	0.586	0.522	0.652	CLONAL	1	FALSE	1	0.830476575909376	3		174	218	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0003360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	22600	330	6	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.830476575909376	31	FACETS	0.995	0.994	0.997			1	CLONAL	31	FALSE	NA	0.830476575909376	31		336	23003	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464487	25464487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375399431	NA	P-0003360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	330	305	2	ENST00000264709.3:c.2026C>T	p.Arg676Trp	p.R676W	ENST00000264709	NM_175629.2	676	Cgg/Tgg	17/23	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	1	0.830476575909376	2		307	686	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755666	39755666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	275	298	0	ENST00000288319.7:c.1099C>T	p.Arg367Cys	p.R367C	ENST00000288319	NM_182918.3	367	Cgc/Tgc	10/10	0.18583847140823	1	FACETS	0.608	0.575	0.641	0.608	0.575	0.641	INDETERMINATE	1	FALSE	0	0.830476575909376	1		298	637	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0003438-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	112	455	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.97	0.892	1	1	0.99	1	CLONAL	2	TRUE	1	0.5	2		455	231	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0003438-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	234	764	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.945	0.905	0.984	1	0.996	1	CLONAL	3	TRUE	1	0.5	2		764	330	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102839	71102839	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003438-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	236	329	0	ENST00000318789.4:c.368C>T	p.Pro123Leu	p.P123L	ENST00000318789	NM_032682.5	123	cCt/cTt	8/21	1	2	FACETS	0.881	0.83	0.932	1	0.994	1	CLONAL	2	TRUE	1	0.5	2		329	536	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920378	114920378	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003438-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	371	642	0	ENST00000543371.1:c.1319A>T	p.Asp440Val	p.D440V	ENST00000543371	NM_001198531.1	440	gAt/gTt	13/14	1	2	FACETS	0.867	0.827	0.907	1	0.996	1	CLONAL	2	TRUE	1	0.5	2		642	856	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742921	17742921	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs769178698	NA	P-0003438-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	151	336	0	ENST00000250003.3:c.829G>C	p.Glu277Gln	p.E277Q	ENST00000250003	NM_002478.4	277	Gag/Cag	3/3	1	2	FACETS	0.827	0.767	0.889	1	0.991	1	CLONAL	2	TRUE	1	0.5	2		336	365	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444494	49444494	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0003438-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	210	296	0	ENST00000301067.7:c.2877C>G	p.Tyr959Ter	p.Y959*	ENST00000301067	NM_003482.3	959	taC/taG	11/54	1	2	FACETS	0.85	0.798	0.903	1	0.994	1	CLONAL	2	TRUE	1	0.5	2		296	494	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179197	123179197	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003438-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	360	221	0	ENST00000218089.9:c.646C>T	p.Arg216Ter	p.R216*	ENST00000218089	NM_001042749.1	216	Cga/Tga	8/35	1	1	FACETS	0.891	0.871	0.909	1	0.997	1	CLONAL	3	TRUE	0	0.5	1		221	404	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	38	174	0				ENST00000310581	NM_198253.2	-/1132			0.144035458310793	3	FACETS	0.9	0.781	1	0.9	0.781	1	INDETERMINATE	2	TRUE	1	0.813786701384958	3		174	73	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0003456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3011	5870	406	0	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.813786701384958	29	FACETS	1	0.998	1			1	CLONAL	19	TRUE	NA	0.813786701384958	29		406	8881	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221710	55221710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6493	644	364	0	ENST00000275493.2:c.754C>T	p.Arg252Cys	p.R252C	ENST00000275493	NM_005228.3	252	Cgc/Tgc	7/28	0.813786701384958	29	FACETS	0.886	0.847	0.926			1	CLONAL	3	TRUE	NA	0.813786701384958	29		364	7137	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167838	56167838	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	154	234	0	ENST00000399503.3:c.1403A>G	p.His468Arg	p.H468R	ENST00000399503	NM_005921.1	468	cAc/cGc	7/20	0.144035458310793	3	FACETS	1	0.983	1	0.618	0.571	0.666	INDETERMINATE	1	TRUE	1	0.813786701384958	3		234	431	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	128	174	0				ENST00000310581	NM_198253.2	-/1132			0.599070535258142	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.61170887643531	2		174	178	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225367748	225367748	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	298	277	0	ENST00000264414.4:c.1419G>A	p.Met473Ile	p.M473I	ENST00000264414	NM_003590.4	473	atG/atA	10/16	0.61170887643531	2	FACETS	1	0.987	1	0.574	0.542	0.606	CLONAL	1	TRUE	0	0.61170887643531	2		277	849	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851610	134851610	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	303	215	0	ENST00000398015.3:c.1016T>C	p.Ile339Thr	p.I339T	ENST00000398015	NM_004441.4	339	aTt/aCt	5/16	0.275344529631407	3	FACETS	0.958	0.91	1			1	INDETERMINATE	2	TRUE	NA	0.61170887643531	3		215	675	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178942545	178942545	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	195	217	0	ENST00000263967.3:c.2352G>C	p.Glu784Asp	p.E784D	ENST00000263967	NM_006218.2	784	gaG/gaC	16/21	0.61170887643531	3	FACETS	0.985	0.913	1	0.328	0.304	0.354	CLONAL	1	TRUE	0	0.61170887643531	3		217	845	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434256	49434256	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	457	341	0	ENST00000301067.7:c.7297G>T	p.Glu2433Ter	p.E2433*	ENST00000301067	NM_003482.3	2433	Gaa/Taa	31/54	0.61170887643531	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.61170887643531	3		341	956	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	39	174	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.915	1			1	INDETERMINATE	1	TRUE	NA	0.54194749022091	2		174	128	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780203	9780203	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	37	391	0	ENST00000377346.4:c.1373C>T	p.Thr458Ile	p.T458I	ENST00000377346	NM_005026.3	458	aCt/aTt	11/24	NA	2	FACETS	0.235	0.193	0.282			1	INDETERMINATE	1	TRUE	NA	0.54194749022091	2		391	581	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11177089	11177089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	68	495	0	ENST00000361445.4:c.6988G>A	p.Val2330Ile	p.V2330I	ENST00000361445	NM_004958.3	2330	Gtt/Att	50/58	1	2	FACETS	0.3	0.26	0.343	0.3	0.26	0.343	SUBCLONAL	1	TRUE	1	0.54194749022091	2		495	836	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294315	11294315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	23	301	0	ENST00000361445.4:c.2216C>T	p.Thr739Ile	p.T739I	ENST00000361445	NM_004958.3	739	aCa/aTa	14/58	1	2	FACETS	0.201	0.156	0.253	0.201	0.156	0.253	SUBCLONAL	1	TRUE	1	0.54194749022091	2		301	423	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255293	16255293	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775491800	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	153	438	0	ENST00000375759.3:c.2558G>A	p.Ser853Asn	p.S853N	ENST00000375759	NM_015001.2	853	aGt/aAt	11/15	1	2	FACETS	0.834	0.765	0.906	0.834	0.765	0.906	CLONAL	1	TRUE	1	0.54194749022091	2		438	677	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256108	16256108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	122	381	1	ENST00000375759.3:c.3373G>A	p.Glu1125Lys	p.E1125K	ENST00000375759	NM_015001.2	1125	Gag/Aag	11/15	1	2	FACETS	0.741	0.671	0.813	0.741	0.671	0.813	SUBCLONAL	1	TRUE	1	0.54194749022091	2		382	608	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256801	16256801	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	34	314	0	ENST00000375759.3:c.4066C>T	p.Pro1356Ser	p.P1356S	ENST00000375759	NM_015001.2	1356	Cca/Tca	11/15	1	2	FACETS	0.256	0.209	0.309	0.256	0.209	0.309	SUBCLONAL	1	TRUE	1	0.54194749022091	2		314	490	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258776	16258776	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	36	358	0	ENST00000375759.3:c.6041C>T	p.Thr2014Ile	p.T2014I	ENST00000375759	NM_015001.2	2014	aCc/aTc	11/15	1	2	FACETS	0.276	0.226	0.331	0.276	0.226	0.331	SUBCLONAL	1	TRUE	1	0.54194749022091	2		358	482	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262529	16262529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769505284	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	23	194	0	ENST00000375759.3:c.9794G>A	p.Gly3265Asp	p.G3265D	ENST00000375759	NM_015001.2	3265	gGt/gAt	11/15	1	2	FACETS	0.264	0.205	0.331	0.264	0.205	0.331	SUBCLONAL	1	TRUE	1	0.54194749022091	2		194	322	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092744	27092744	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	34	374	0	ENST00000324856.7:c.2765G>A	p.Gly922Asp	p.G922D	ENST00000324856	NM_006015.4	922	gGc/gAc	9/20	1	2	FACETS	0.264	0.215	0.318	0.264	0.215	0.318	SUBCLONAL	1	TRUE	1	0.54194749022091	2		374	476	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100819	27100819	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	40	407	0	ENST00000324856.7:c.4102-1G>A		p.X1368_splice	ENST00000324856	NM_006015.4	1368			1	2	FACETS	0.259	0.215	0.309	0.259	0.215	0.309	SUBCLONAL	1	TRUE	1	0.54194749022091	2		407	569	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363364	40363364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	47	277	0	ENST00000397332.2:c.865C>T	p.Pro289Ser	p.P289S	ENST00000397332	NM_001033082.2	289	Cct/Tct	3/3	1	2	FACETS	0.407	0.344	0.477	0.407	0.344	0.477	SUBCLONAL	1	TRUE	1	0.54194749022091	2		277	426	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803898	43803898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	31	271	0	ENST00000372470.3:c.208C>T	p.Pro70Ser	p.P70S	ENST00000372470	NM_005373.2	70	Ccg/Tcg	2/12	1	2	FACETS	0.296	0.239	0.36	0.296	0.239	0.36	SUBCLONAL	1	TRUE	1	0.54194749022091	2		271	387	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818250	43818250	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	55	472	0	ENST00000372470.3:c.1715C>T	p.Pro572Leu	p.P572L	ENST00000372470	NM_005373.2	572	cCc/cTc	12/12	1	2	FACETS	0.329	0.281	0.382	0.329	0.281	0.382	SUBCLONAL	1	TRUE	1	0.54194749022091	2		472	617	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509505	46509505	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1557545432	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	30	316	0	ENST00000262741.5:c.1226C>T	p.Thr409Ile	p.T409I	ENST00000262741	NM_003629.3	409	aCt/aTt	10/10	1	2	FACETS	0.226	0.182	0.277	0.226	0.182	0.277	SUBCLONAL	1	TRUE	1	0.54194749022091	2		316	489	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46714229	46714229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	24	312	0	ENST00000371975.4:c.49G>A	p.Gly17Ser	p.G17S	ENST00000371975	NM_003579.3	17	Ggc/Agc	2/18	1	2	FACETS	0.19	0.148	0.238	0.19	0.148	0.238	SUBCLONAL	1	TRUE	1	0.54194749022091	2		312	466	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303724	65303724	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	42	388	0	ENST00000342505.4:c.3031G>A	p.Val1011Ile	p.V1011I	ENST00000342505	NM_002227.2	1011	Gtt/Att	22/25	1	2	FACETS	0.223	0.186	0.265	0.223	0.186	0.265	SUBCLONAL	1	TRUE	1	0.54194749022091	2		388	694	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65316521	65316521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	31	347	1	ENST00000342505.4:c.1721G>A	p.Ser574Asn	p.S574N	ENST00000342505	NM_002227.2	574	aGt/aAt	12/25	1	2	FACETS	0.213	0.172	0.26	0.213	0.172	0.26	SUBCLONAL	1	TRUE	1	0.54194749022091	2		348	537	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330637	65330637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1378023815	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	141	319	0	ENST00000342505.4:c.1009G>A	p.Glu337Lys	p.E337K	ENST00000342505	NM_002227.2	337	Gaa/Aaa	8/25	1	2	FACETS	0.944	0.865	1	0.944	0.865	1	CLONAL	1	TRUE	1	0.54194749022091	2		319	551	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241914	72241914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	76	666	0	ENST00000357731.5:c.476C>T	p.Thr159Ile	p.T159I	ENST00000357731	NM_173808.2	159	aCt/aTt	3/7	1	2	FACETS	0.263	0.23	0.299	0.263	0.23	0.299	SUBCLONAL	1	TRUE	1	0.54194749022091	2		666	1066	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748047	72748047	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	55	609	0	ENST00000357731.5:c.131C>T	p.Ala44Val	p.A44V	ENST00000357731	NM_173808.2	44	gCc/gTc	1/7	1	2	FACETS	0.245	0.209	0.285	0.245	0.209	0.285	SUBCLONAL	1	TRUE	1	0.54194749022091	2		609	827	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699273	117699273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	39	458	0	ENST00000369458.3:c.368C>T	p.Thr123Ile	p.T123I	ENST00000369458	NM_024626.3	123	aCa/aTa	3/6	1	2	FACETS	0.213	0.176	0.255	0.213	0.176	0.255	SUBCLONAL	1	TRUE	1	0.54194749022091	2		458	675	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461970	120461970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	24	344	0	ENST00000256646.2:c.5746G>A	p.Ala1916Thr	p.A1916T	ENST00000256646	NM_024408.3	1916	Gct/Act	31/34	1	2	FACETS	0.185	0.144	0.231	0.185	0.144	0.231	SUBCLONAL	1	TRUE	1	0.54194749022091	2		344	480	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462908	120462908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144085962	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	52	288	0	ENST00000256646.2:c.5423C>T	p.Thr1808Ile	p.T1808I	ENST00000256646	NM_024408.3	1808	aCc/aTc	30/34	1	2	FACETS	0.401	0.341	0.466	0.401	0.341	0.466	SUBCLONAL	1	TRUE	1	0.54194749022091	2		288	479	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551481	150551481	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	51	496	0	ENST00000369026.2:c.526C>T	p.Arg176Trp	p.R176W	ENST00000369026	NM_021960.4	176	Cgg/Tgg	1/3	1	2	FACETS	0.218	0.184	0.255	0.218	0.184	0.255	SUBCLONAL	1	TRUE	1	0.54194749022091	2		496	864	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740198	162740198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	63	493	0	ENST00000367921.3:c.1400C>T	p.Ser467Phe	p.S467F	ENST00000367921	NM_006182.2	467	tCc/tTc	12/18	1	2	FACETS	0.32	0.276	0.368	0.32	0.276	0.368	SUBCLONAL	1	TRUE	1	0.54194749022091	2		493	726	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176176045	176176045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	23	290	0	ENST00000367669.3:c.70G>A	p.Val24Met	p.V24M	ENST00000367669	NM_022457.5	24	Gtg/Atg	1/20	1	2	FACETS	0.194	0.151	0.245	0.194	0.151	0.245	SUBCLONAL	1	TRUE	1	0.54194749022091	2		290	437	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967248	25967248	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	38	333	0	ENST00000435504.4:c.1958G>A	p.Gly653Glu	p.G653E	ENST00000435504		653	gGa/gAa	13/13	1	2	FACETS	0.287	0.237	0.343	0.287	0.237	0.343	SUBCLONAL	1	TRUE	1	0.54194749022091	2		333	489	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018133	48018133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659374	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	38	418	0	ENST00000234420.5:c.328G>A	p.Val110Ile	p.V110I	ENST00000234420	NM_000179.2	110	Gtt/Att	2/10	1	2	FACETS	0.21	0.173	0.252	0.21	0.173	0.252	SUBCLONAL	1	TRUE	1	0.54194749022091	2		418	668	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018146	48018146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	165	424	0	ENST00000234420.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000234420	NM_000179.2	114	cCc/cTc	2/10	1	2	FACETS	0.907	0.836	0.981	0.907	0.836	0.981	CLONAL	1	TRUE	1	0.54194749022091	2		424	671	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027322	48027322	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780671	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	76	403	2	ENST00000234420.5:c.2200G>A	p.Val734Met	p.V734M	ENST00000234420	NM_000179.2	734	Gtg/Atg	4/10	1	2	FACETS	0.463	0.406	0.524	0.463	0.406	0.524	SUBCLONAL	1	TRUE	1	0.54194749022091	2		405	606	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027422	48027422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781462	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	126	307	0	ENST00000234420.5:c.2300C>T	p.Thr767Ile	p.T767I	ENST00000234420	NM_000179.2	767	aCt/aTt	4/10	1	2	FACETS	0.985	0.898	1	0.985	0.898	1	CLONAL	1	TRUE	1	0.54194749022091	2		307	472	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919712	96919712	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	73	406	0	ENST00000258439.3:c.551G>A	p.Gly184Asp	p.G184D	ENST00000258439	NM_001193304.2	184	gGt/gAt	4/4	1	2	FACETS	0.466	0.408	0.529	0.466	0.408	0.529	SUBCLONAL	1	TRUE	1	0.54194749022091	2		406	578	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198260904	198260904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	42	408	0	ENST00000335508.6:c.3415C>T	p.Pro1139Ser	p.P1139S	ENST00000335508	NM_012433.2	1139	Cct/Tct	23/25	1	2	FACETS	0.215	0.179	0.256	0.215	0.179	0.256	SUBCLONAL	1	TRUE	1	0.54194749022091	2		408	720	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265576	198265576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	102	504	0	ENST00000335508.6:c.2581G>A	p.Ala861Thr	p.A861T	ENST00000335508	NM_012433.2	861	Gcc/Acc	18/25	1	2	FACETS	0.453	0.405	0.504	0.453	0.405	0.504	SUBCLONAL	1	TRUE	1	0.54194749022091	2		504	831	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659962	227659962	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	30	479	0	ENST00000305123.5:c.3493A>G	p.Lys1165Glu	p.K1165E	ENST00000305123	NM_005544.2	1165	Aaa/Gaa	1/2	1	2	FACETS	0.185	0.148	0.226	0.185	0.148	0.226	SUBCLONAL	1	TRUE	1	0.54194749022091	2		479	600	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050314	37050314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	118	308	0	ENST00000231790.2:c.463C>T	p.Leu155Phe	p.L155F	ENST00000231790	NM_000249.3	155	Ctt/Ttt	6/19	1	2	FACETS	0.726	0.657	0.798	0.726	0.657	0.798	SUBCLONAL	1	TRUE	1	0.54194749022091	2		308	600	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47061318	47061318	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	36	386	0	ENST00000409792.3:c.7363C>T	p.Pro2455Ser	p.P2455S	ENST00000409792	NM_014159.6	2455	Ccc/Tcc	19/21	1	2	FACETS	0.223	0.183	0.268	0.223	0.183	0.268	SUBCLONAL	1	TRUE	1	0.54194749022091	2		386	596	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098495	47098495	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759979231	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	42	375	1	ENST00000409792.3:c.6779C>T	p.Pro2260Leu	p.P2260L	ENST00000409792	NM_014159.6	2260	cCg/cTg	15/21	1	2	FACETS	0.292	0.244	0.347	0.292	0.244	0.347	SUBCLONAL	1	TRUE	1	0.54194749022091	2		376	530	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725078	49725078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	68	435	0	ENST00000449682.2:c.266G>A	p.Ser89Asn	p.S89N	ENST00000449682	NM_020998.3	89	aGc/aAc	3/18	1	2	FACETS	0.352	0.306	0.402	0.352	0.306	0.402	SUBCLONAL	1	TRUE	1	0.54194749022091	2		435	713	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799589	72799589	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1047731047	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	36	470	0	ENST00000325599.8:c.1580C>T	p.Ala527Val	p.A527V	ENST00000325599	NM_018130.2	527	gCc/gTc	11/11	1	2	FACETS	0.216	0.177	0.26	0.216	0.177	0.26	SUBCLONAL	1	TRUE	1	0.54194749022091	2		470	616	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259493	89259493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1293200426	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	39	408	0	ENST00000336596.2:c.637C>T	p.Pro213Ser	p.P213S	ENST00000336596	NM_005233.5	213	Cca/Tca	3/17	1	2	FACETS	0.211	0.174	0.252	0.211	0.174	0.252	SUBCLONAL	1	TRUE	1	0.54194749022091	2		408	683	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391199	89391199	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	23	262	0	ENST00000336596.2:c.1265C>T	p.Pro422Leu	p.P422L	ENST00000336596	NM_005233.5	422	cCa/cTa	5/17	1	2	FACETS	0.192	0.149	0.242	0.192	0.149	0.242	SUBCLONAL	1	TRUE	1	0.54194749022091	2		262	441	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461624	138461624	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	37	303	0	ENST00000289153.2:c.398-1G>A		p.X133_splice	ENST00000289153	NM_006219.2	133			1	2	FACETS	0.285	0.235	0.342	0.285	0.235	0.342	SUBCLONAL	1	TRUE	1	0.54194749022091	2		303	479	SUCCESS
ATR	545	MSKCC	GRCh37	3	142212090	142212090	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	44	435	0	ENST00000350721.4:c.5962G>A	p.Glu1988Lys	p.E1988K	ENST00000350721	NM_001184.3	1988	Gaa/Aaa	35/47	1	2	FACETS	0.223	0.186	0.264	0.223	0.186	0.264	SUBCLONAL	1	TRUE	1	0.54194749022091	2		435	728	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231122	142231122	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	157	341	1	ENST00000350721.4:c.4832G>A	p.Arg1611Lys	p.R1611K	ENST00000350721	NM_001184.3	1611	aGa/aAa	27/47	1	2	FACETS	0.972	0.895	1	0.972	0.895	1	CLONAL	1	TRUE	1	0.54194749022091	2		342	596	SUCCESS
ATR	545	MSKCC	GRCh37	3	142257418	142257418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	185	404	0	ENST00000350721.4:c.3631C>T	p.Leu1211Phe	p.L1211F	ENST00000350721	NM_001184.3	1211	Ctt/Ttt	19/47	1	2	FACETS	0.998	0.925	1	0.998	0.925	1	CLONAL	1	TRUE	1	0.54194749022091	2		404	684	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272169	142272169	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	81	442	0	ENST00000350721.4:c.2705C>T	p.Ser902Phe	p.S902F	ENST00000350721	NM_001184.3	902	tCt/tTt	13/47	1	2	FACETS	0.39	0.343	0.441	0.39	0.343	0.441	SUBCLONAL	1	TRUE	1	0.54194749022091	2		442	766	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952142	178952142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253171657	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	51	285	0	ENST00000263967.3:c.3197C>T	p.Ala1066Val	p.A1066V	ENST00000263967	NM_006218.2	1066	gCa/gTa	21/21	1	2	FACETS	0.352	0.299	0.41	0.352	0.299	0.41	SUBCLONAL	1	TRUE	1	0.54194749022091	2		285	535	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431055	181431055	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	41	223	0	ENST00000325404.1:c.907G>A	p.Val303Met	p.V303M	ENST00000325404	NM_003106.3	303	Gtg/Atg	1/1	1	2	FACETS	0.371	0.309	0.439	0.371	0.309	0.439	SUBCLONAL	1	TRUE	1	0.54194749022091	2		223	408	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665053	182665053	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	103	476	2	ENST00000292782.4:c.673G>A	p.Asp225Asn	p.D225N	ENST00000292782	NM_020640.2	225	Gat/Aat	6/7	1	2	FACETS	0.451	0.403	0.502	0.451	0.403	0.502	SUBCLONAL	1	TRUE	1	0.54194749022091	2		478	843	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161273	185161273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	41	485	0	ENST00000265026.3:c.700G>A	p.Glu234Lys	p.E234K	ENST00000265026	NM_004721.4	234	Gaa/Aaa	4/14	1	2	FACETS	0.204	0.169	0.243	0.204	0.169	0.243	SUBCLONAL	1	TRUE	1	0.54194749022091	2		485	743	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803753	1803753	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	38	285	0	ENST00000260795.2:c.930+1G>A		p.X310_splice	ENST00000260795		310			1	2	FACETS	0.281	0.232	0.336	0.281	0.232	0.336	SUBCLONAL	1	TRUE	1	0.54194749022091	2		285	499	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280028	66280028	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	53	419	0	ENST00000273854.3:c.1661G>A	p.Arg554Lys	p.R554K	ENST00000273854	NM_004439.5	554	aGa/aAa	7/18	1	2	FACETS	0.239	0.203	0.279	0.239	0.203	0.279	SUBCLONAL	1	TRUE	1	0.54194749022091	2		419	818	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143029297	143029297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757219824	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	184	344	0	ENST00000262992.4:c.2323G>A	p.Glu775Lys	p.E775K	ENST00000262992	NM_001101669.1	775	Gaa/Aaa	21/24	1	2	FACETS	0.999	0.925	1	0.999	0.925	1	CLONAL	1	TRUE	1	0.54194749022091	2		344	680	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143191833	143191833	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	50	511	0	ENST00000262992.4:c.598G>A	p.Asp200Asn	p.D200N	ENST00000262992	NM_001101669.1	200	Gat/Aat	8/24	1	2	FACETS	0.243	0.205	0.285	0.243	0.205	0.285	SUBCLONAL	1	TRUE	1	0.54194749022091	2		511	759	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143352393	143352393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1322547312	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	69	386	0	ENST00000262992.4:c.20G>A	p.Gly7Glu	p.G7E	ENST00000262992	NM_001101669.1	7	gGg/gAg	2/24	1	2	FACETS	0.367	0.319	0.419	0.367	0.319	0.419	SUBCLONAL	1	TRUE	1	0.54194749022091	2		386	693	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539014	187539014	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	51	578	0	ENST00000441802.2:c.8726C>T	p.Thr2909Ile	p.T2909I	ENST00000441802	NM_005245.3	2909	aCc/aTc	10/27	1	2	FACETS	0.233	0.197	0.272	0.233	0.197	0.272	SUBCLONAL	1	TRUE	1	0.54194749022091	2		578	808	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542435	187542435	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	44	415	0	ENST00000441802.2:c.5305G>A	p.Glu1769Lys	p.E1769K	ENST00000441802	NM_005245.3	1769	Gaa/Aaa	10/27	1	2	FACETS	0.244	0.204	0.288	0.244	0.204	0.288	SUBCLONAL	1	TRUE	1	0.54194749022091	2		415	666	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235450	235450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	58	296	0	ENST00000264932.6:c.1256G>A	p.Gly419Glu	p.G419E	ENST00000264932	NM_004168.2	419	gGg/gAg	9/15	NA	2	FACETS	0.516	0.444	0.593			1	INDETERMINATE	1	TRUE	NA	0.54194749022091	2		296	415	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35860962	35860962	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	49	292	0	ENST00000303115.3:c.91G>A	p.Glu31Lys	p.E31K	ENST00000303115	NM_002185.3	31	Gaa/Aaa	2/8	1	2	FACETS	0.338	0.286	0.395	0.338	0.286	0.395	SUBCLONAL	1	TRUE	1	0.54194749022091	2		292	535	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950205	38950205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	60	302	0	ENST00000357387.3:c.3745G>A	p.Asp1249Asn	p.D1249N	ENST00000357387	NM_152756.3	1249	Gac/Aac	31/38	1	2	FACETS	0.412	0.355	0.473	0.412	0.355	0.473	SUBCLONAL	1	TRUE	1	0.54194749022091	2		302	538	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168509	56168509	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	44	358	0	ENST00000399503.3:c.1465C>T	p.Pro489Ser	p.P489S	ENST00000399503	NM_005921.1	489	Ccc/Tcc	8/20	1	2	FACETS	0.238	0.199	0.281	0.238	0.199	0.281	SUBCLONAL	1	TRUE	1	0.54194749022091	2		358	683	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591303	67591303	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	76	286	0	ENST00000274335.5:c.1801G>A	p.Glu601Lys	p.E601K	ENST00000274335		601	Gaa/Aaa	13/15	1	2	FACETS	0.618	0.544	0.697	0.618	0.544	0.697	SUBCLONAL	1	TRUE	1	0.54194749022091	2		286	454	SUCCESS
APC	324	MSKCC	GRCh37	5	112137064	112137064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	72	325	0	ENST00000257430.4:c.818C>T	p.Thr273Ile	p.T273I	ENST00000257430	NM_000038.5	273	aCt/aTt	8/16	1	2	FACETS	0.426	0.372	0.485	0.426	0.372	0.485	SUBCLONAL	1	TRUE	1	0.54194749022091	2		325	623	SUCCESS
APC	324	MSKCC	GRCh37	5	112154663	112154663	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1060503285	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	106	238	0	ENST00000257430.4:c.934G>A	p.Val312Met	p.V312M	ENST00000257430	NM_000038.5	312	Gtg/Atg	10/16	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.54194749022091	2		238	382	SUCCESS
APC	324	MSKCC	GRCh37	5	112174650	112174650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28933379	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	205	435	0	ENST00000257430.4:c.3359G>A	p.Gly1120Glu	p.G1120E	ENST00000257430	NM_000038.5	1120	gGa/gAa	16/16	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.54194749022091	2		435	731	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449583	149449583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	126	431	0	ENST00000286301.3:c.1363C>T	p.Pro455Ser	p.P455S	ENST00000286301	NM_005211.3	455	Cct/Tct	10/22	1	2	FACETS	0.849	0.772	0.929	0.849	0.772	0.929	CLONAL	1	TRUE	1	0.54194749022091	2		431	548	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517817	176517817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	38	378	0	ENST00000292408.4:c.427C>T	p.Pro143Ser	p.P143S	ENST00000292408	NM_213647.1	143	Ccc/Tcc	4/18	NA	2	FACETS	0.28	0.231	0.335			1	INDETERMINATE	1	TRUE	NA	0.54194749022091	2		378	501	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721036	176721036	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	36	337	0	ENST00000439151.2:c.6667C>T	p.Pro2223Ser	p.P2223S	ENST00000439151	NM_022455.4	2223	Cct/Tct	23/23	NA	2	FACETS	0.263	0.215	0.316			1	INDETERMINATE	1	TRUE	NA	0.54194749022091	2		337	506	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402702	20402702	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	29	302	0	ENST00000346618.3:c.239C>A	p.Ala80Asp	p.A80D	ENST00000346618	NM_001949.4	80	gCc/gAc	1/7	1	2	FACETS	0.228	0.182	0.28	0.228	0.182	0.28	SUBCLONAL	1	TRUE	1	0.54194749022091	2		302	470	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056274	26056274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765547166	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	52	376	0	ENST00000343677.2:c.383C>T	p.Pro128Leu	p.P128L	ENST00000343677	NM_005319.3	128	cCt/cTt	1/1	1	2	FACETS	0.29	0.246	0.338	0.29	0.246	0.338	SUBCLONAL	1	TRUE	1	0.54194749022091	2		376	661	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250436	26250436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	65	808	1	ENST00000446824.2:c.398G>A	p.Gly133Glu	p.G133E	ENST00000446824	NM_021018.2	133	gGa/gAa	1/1	1	2	FACETS	0.251	0.217	0.289	0.251	0.217	0.289	SUBCLONAL	1	TRUE	1	0.54194749022091	2		809	955	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679972	30679972	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1021167504	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	54	377	1	ENST00000376406.3:c.1747G>A	p.Glu583Lys	p.E583K	ENST00000376406	NM_014641.2	583	Gag/Aag	5/15	1	2	FACETS	0.38	0.325	0.441	0.38	0.325	0.441	SUBCLONAL	1	TRUE	1	0.54194749022091	2		378	524	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188635	32188635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	31	404	0	ENST00000375023.3:c.820G>A	p.Glu274Lys	p.E274K	ENST00000375023	NM_004557.3	274	Gag/Aag	5/30	1	2	FACETS	0.195	0.157	0.238	0.195	0.157	0.238	SUBCLONAL	1	TRUE	1	0.54194749022091	2		404	587	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43745262	43745262	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755307045	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	227	544	0	ENST00000523873.1:c.175G>A	p.Val59Met	p.V59M	ENST00000523873		59	Gtg/Atg	3/8	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.54194749022091	2		544	818	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964405	93964405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	71	575	0	ENST00000369303.4:c.2492C>T	p.Ser831Phe	p.S831F	ENST00000369303	NM_004440.3	831	tCt/tTt	14/17	1	2	FACETS	0.267	0.232	0.304	0.267	0.232	0.304	SUBCLONAL	1	TRUE	1	0.54194749022091	2		575	983	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982138	93982138	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	165	488	0	ENST00000369303.4:c.1327C>T	p.Pro443Ser	p.P443S	ENST00000369303	NM_004440.3	443	Ccc/Tcc	6/17	1	2	FACETS	0.717	0.659	0.778	0.717	0.659	0.778	SUBCLONAL	1	TRUE	1	0.54194749022091	2		488	849	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536271	106536271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	52	254	0	ENST00000369096.4:c.238G>A	p.Glu80Lys	p.E80K	ENST00000369096	NM_001198.3	80	Gag/Aag	2/7	1	2	FACETS	0.36	0.306	0.419	0.36	0.306	0.419	SUBCLONAL	1	TRUE	1	0.54194749022091	2		254	533	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017602	112017602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	48	521	0	ENST00000368678.4:c.911C>T	p.Ser304Phe	p.S304F	ENST00000368678		304	tCc/tTc	9/13	NA	2	FACETS	0.208	0.175	0.245			1	INDETERMINATE	1	TRUE	NA	0.54194749022091	2		521	850	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678016	117678016	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	53	485	0	ENST00000368508.3:c.3917G>A	p.Ser1306Asn	p.S1306N	ENST00000368508	NM_002944.2	1306	aGt/aAt	25/43	NA	2	FACETS	0.244	0.207	0.285			1	INDETERMINATE	1	TRUE	NA	0.54194749022091	2		485	801	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405956	157405956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367698478	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	41	403	0	ENST00000346085.5:c.2198G>A	p.Gly733Glu	p.G733E	ENST00000346085	NM_020732.3	733	gGg/gAg	6/20	NA	2	FACETS	0.261	0.217	0.311			1	INDETERMINATE	1	TRUE	NA	0.54194749022091	2		403	579	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528915	157528915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	123	323	0	ENST00000346085.5:c.6640G>A	p.Glu2214Lys	p.E2214K	ENST00000346085	NM_020732.3	2214	Gaa/Aaa	20/20	NA	2	FACETS	0.906	0.824	0.992			1	INDETERMINATE	1	TRUE	NA	0.54194749022091	2		323	501	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956995	2956995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	28	241	0	ENST00000396946.4:c.2632C>T	p.Leu878Phe	p.L878F	ENST00000396946	NM_032415.4	878	Ctt/Ttt	20/25	0.527344401322474	3	FACETS	0.278	0.222	0.343	0.139	0.111	0.172	SUBCLONAL	1	TRUE	1	0.54194749022091	3		241	472	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467733	50467733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	74	391	0	ENST00000331340.3:c.968G>A	p.Gly323Glu	p.G323E	ENST00000331340	NM_006060.4	323	gGg/gAg	8/8	0.527344401322474	3	FACETS	0.547	0.478	0.62	0.273	0.239	0.31	SUBCLONAL	1	TRUE	1	0.54194749022091	3		391	635	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467951	50467951	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	50	323	0	ENST00000331340.3:c.1186G>A	p.Asp396Asn	p.D396N	ENST00000331340	NM_006060.4	396	Gac/Aac	8/8	0.527344401322474	3	FACETS	0.419	0.355	0.489	0.209	0.177	0.245	SUBCLONAL	1	TRUE	1	0.54194749022091	3		323	560	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273000	55273000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	56	385	0	ENST00000275493.2:c.3323C>T	p.Pro1108Leu	p.P1108L	ENST00000275493	NM_005228.3	1108	cCt/cTt	28/28	0.54194749022091	3	FACETS	0.338	0.289	0.392	0.169	0.144	0.196	SUBCLONAL	1	TRUE	1	0.54194749022091	3		385	777	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509417	106509417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	59	498	0	ENST00000359195.3:c.1411C>T	p.His471Tyr	p.H471Y	ENST00000359195	NM_002649.2	471	Cac/Tac	2/11	0.54194749022091	3	FACETS	0.3	0.257	0.348	0.15	0.128	0.174	SUBCLONAL	1	TRUE	1	0.54194749022091	3		498	921	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534551	140534551	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	54	318	0	ENST00000288602.6:c.362C>T	p.Thr121Ile	p.T121I	ENST00000288602	NM_004333.4	121	aCa/aTa	3/18	0.527344401322474	3	FACETS	0.352	0.3	0.409	0.176	0.15	0.205	SUBCLONAL	1	TRUE	1	0.54194749022091	3		318	720	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945421	151945421	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	32	231	0	ENST00000262189.6:c.2098G>A	p.Val700Met	p.V700M	ENST00000262189	NM_170606.2	700	Gtg/Atg	14/59	0.527344401322474	3	FACETS	0.277	0.224	0.337	0.139	0.112	0.169	SUBCLONAL	1	TRUE	1	0.54194749022091	3		231	541	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868486	117868486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	40	421	0	ENST00000297338.2:c.856C>T	p.Pro286Ser	p.P286S	ENST00000297338	NM_006265.2	286	Cca/Tca	8/14	1	2	FACETS	0.189	0.156	0.225	0.189	0.156	0.225	SUBCLONAL	1	TRUE	1	0.54194749022091	2		421	783	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752822	128752822	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	39	261	0	ENST00000377970.2:c.983C>T	p.Pro328Leu	p.P328L	ENST00000377970	NM_002467.4	328	cCc/cTc	3/3	1	2	FACETS	0.326	0.27	0.388	0.326	0.27	0.388	SUBCLONAL	1	TRUE	1	0.54194749022091	2		261	442	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457271	5457271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	42	303	0	ENST00000381577.3:c.245G>A	p.Arg82Lys	p.R82K	ENST00000381577	NM_014143.3	82	aGa/aAa	3/7	1	2	FACETS	0.306	0.255	0.362	0.306	0.255	0.362	SUBCLONAL	1	TRUE	1	0.54194749022091	2		303	507	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389329	8389329	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866195026	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	166	527	0	ENST00000356435.5:c.4289G>A	p.Gly1430Glu	p.G1430E	ENST00000356435		1430	gGa/gAa	26/35	1	2	FACETS	0.935	0.862	1	0.935	0.862	1	CLONAL	1	TRUE	1	0.54194749022091	2		527	655	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507366	8507366	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141604755	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	59	439	0	ENST00000356435.5:c.1612C>T	p.Pro538Ser	p.P538S	ENST00000356435		538	Cct/Tct	11/35	1	2	FACETS	0.281	0.241	0.325	0.281	0.241	0.325	SUBCLONAL	1	TRUE	1	0.54194749022091	2		439	774	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98244253	98244253	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	43	385	1	ENST00000331920.6:c.724C>T	p.Gln242Ter	p.Q242*	ENST00000331920	NM_000264.3	242	Cag/Tag	5/24	1	2	FACETS	0.287	0.24	0.34	0.287	0.24	0.34	SUBCLONAL	1	TRUE	1	0.54194749022091	2		386	553	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101909947	101909947	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	40	261	0	ENST00000374994.4:c.1267G>A	p.Asp423Asn	p.D423N	ENST00000374994	NM_004612.2	423	Gat/Aat	8/9	1	2	FACETS	0.334	0.277	0.397	0.334	0.277	0.397	SUBCLONAL	1	TRUE	1	0.54194749022091	2		261	442	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781037	135781037	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368016548	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	63	655	0	ENST00000298552.3:c.1928C>T	p.Thr643Ile	p.T643I	ENST00000298552	NM_001162426.1	643	aCc/aTc	15/23	1	2	FACETS	0.29	0.25	0.333	0.29	0.25	0.333	SUBCLONAL	1	TRUE	1	0.54194749022091	2		655	802	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417406	139417406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	58	333	0	ENST00000277541.6:c.638C>T	p.Pro213Leu	p.P213L	ENST00000277541	NM_017617.3	213	cCc/cTc	4/34	1	2	FACETS	0.414	0.356	0.477	0.414	0.356	0.477	SUBCLONAL	1	TRUE	1	0.54194749022091	2		333	517	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793206	139793206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	172	470	0	ENST00000247668.2:c.14G>A	p.Ser5Asn	p.S5N	ENST00000247668	NM_021138.3	5	aGc/aAc	2/11	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.54194749022091	2		470	633	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802543	139802543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1042886761	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	38	490	0	ENST00000247668.2:c.388C>T	p.Pro130Ser	p.P130S	ENST00000247668	NM_021138.3	130	Ccg/Tcg	5/11	1	2	FACETS	0.198	0.163	0.238	0.198	0.163	0.238	SUBCLONAL	1	TRUE	1	0.54194749022091	2		490	707	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820193	139820193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	44	571	0	ENST00000247668.2:c.1346C>T	p.Pro449Leu	p.P449L	ENST00000247668	NM_021138.3	449	cCc/cTc	11/11	1	2	FACETS	0.223	0.186	0.264	0.223	0.186	0.264	SUBCLONAL	1	TRUE	1	0.54194749022091	2		571	727	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100670	8100670	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1474106412	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	32	419	0	ENST00000346208.3:c.644C>T	p.Thr215Ile	p.T215I	ENST00000346208		215	aCc/aTc	3/6	0.50792616012607	1	FACETS	0.217	0.176	0.264	0.217	0.176	0.264	SUBCLONAL	1	TRUE	0	0.54194749022091	1		419	396	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332328	70332328	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1484377336	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	30	524	0	ENST00000373644.4:c.233G>A	p.Gly78Glu	p.G78E	ENST00000373644	NM_030625.2	78	gGa/gAa	2/12	0.54194749022091	1	FACETS	0.157	0.126	0.193	0.157	0.126	0.193	SUBCLONAL	1	TRUE	0	0.54194749022091	1		524	513	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910867	114910867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	46	603	1	ENST00000543371.1:c.986G>A	p.Gly329Asp	p.G329D	ENST00000543371	NM_001198531.1	329	gGc/gAc	9/14	0.54194749022091	1	FACETS	0.195	0.164	0.23	0.195	0.164	0.23	SUBCLONAL	1	TRUE	0	0.54194749022091	1		604	634	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243282	123243282	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375719482	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	31	453	0	ENST00000358487.5:c.2231C>T	p.Pro744Leu	p.P744L	ENST00000358487	NM_000141.4	744	cCc/cTc	17/18	0.54194749022091	1	FACETS	0.187	0.151	0.229	0.187	0.151	0.229	SUBCLONAL	1	TRUE	0	0.54194749022091	1		453	445	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076777	102076777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758360525	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	80	418	0	ENST00000282441.5:c.956G>A	p.Arg319Gln	p.R319Q	ENST00000282441	NM_001130145.2	319	cGg/cAg	5/9	1	2	FACETS	0.466	0.41	0.525	0.466	0.41	0.525	SUBCLONAL	1	TRUE	1	0.54194749022091	2		418	634	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123557	108123557	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	48	274	0	ENST00000278616.4:c.1816C>T	p.Leu606Phe	p.L606F	ENST00000278616	NM_000051.3	606	Ctt/Ttt	12/63	1	2	FACETS	0.321	0.271	0.377	0.321	0.271	0.377	SUBCLONAL	1	TRUE	1	0.54194749022091	2		274	551	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199959	108199959	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	100	246	0	ENST00000278616.4:c.7301C>T	p.Thr2434Ile	p.T2434I	ENST00000278616	NM_000051.3	2434	aCa/aTa	49/63	1	2	FACETS	0.909	0.818	1	0.909	0.818	1	CLONAL	1	TRUE	1	0.54194749022091	2		246	406	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376580	118376580	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	36	357	0	ENST00000534358.1:c.9973G>A	p.Asp3325Asn	p.D3325N	ENST00000534358	NM_005933.3	3325	Gat/Aat	27/36	1	2	FACETS	0.237	0.194	0.285	0.237	0.194	0.285	SUBCLONAL	1	TRUE	1	0.54194749022091	2		357	560	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125496685	125496685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	30	334	0	ENST00000428830.2:c.22G>A	p.Asp8Asn	p.D8N	ENST00000428830	NM_001114121.2	8	Gac/Aac	2/14	1	2	FACETS	0.204	0.164	0.25	0.204	0.164	0.25	SUBCLONAL	1	TRUE	1	0.54194749022091	2		334	542	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125513699	125513699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	32	459	0	ENST00000428830.2:c.827C>T	p.Pro276Leu	p.P276L	ENST00000428830	NM_001114121.2	276	cCc/cTc	9/14	1	2	FACETS	0.185	0.15	0.226	0.185	0.15	0.226	SUBCLONAL	1	TRUE	1	0.54194749022091	2		459	637	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416913	416913	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219688783	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	170	430	0	ENST00000399788.2:c.3637C>T	p.Pro1213Ser	p.P1213S	ENST00000399788	NM_001042603.1	1213	Cct/Tct	23/28	1	2	FACETS	0.909	0.839	0.982	0.909	0.839	0.982	CLONAL	1	TRUE	1	0.54194749022091	2		430	690	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385231	4385231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	56	385	0	ENST00000261254.3:c.256C>T	p.Arg86Cys	p.R86C	ENST00000261254	NM_001759.3	86	Cgt/Tgt	2/5	1	2	FACETS	0.306	0.261	0.354	0.306	0.261	0.354	SUBCLONAL	1	TRUE	1	0.54194749022091	2		385	676	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466909	18466909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	63	423	0	ENST00000266497.5:c.1048G>A	p.Gly350Arg	p.G350R	ENST00000266497		350	Ggg/Agg	5/31	1	2	FACETS	0.334	0.288	0.384	0.334	0.288	0.384	SUBCLONAL	1	TRUE	1	0.54194749022091	2		423	696	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544119	18544119	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	38	439	0	ENST00000266497.5:c.1936C>T	p.Leu646Phe	p.L646F	ENST00000266497		646	Ctt/Ttt	13/31	1	2	FACETS	0.207	0.17	0.248	0.207	0.17	0.248	SUBCLONAL	1	TRUE	1	0.54194749022091	2		439	679	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641492	18641492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	63	455	0	ENST00000266497.5:c.2491G>A	p.Glu831Lys	p.E831K	ENST00000266497		831	Gag/Aag	17/31	1	2	FACETS	0.282	0.243	0.325	0.282	0.243	0.325	SUBCLONAL	1	TRUE	1	0.54194749022091	2		455	823	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425688	49425688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778474	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	43	276	2	ENST00000301067.7:c.12800C>T	p.Pro4267Leu	p.P4267L	ENST00000301067	NM_003482.3	4267	cCt/cTt	39/54	1	2	FACETS	0.424	0.356	0.5	0.424	0.356	0.5	SUBCLONAL	1	TRUE	1	0.54194749022091	2		278	374	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431337	49431337	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	60	189	0	ENST00000301067.7:c.9802G>A	p.Ala3268Thr	p.A3268T	ENST00000301067	NM_003482.3	3268	Gca/Aca	34/54	1	2	FACETS	0.728	0.632	0.831	0.728	0.632	0.831	SUBCLONAL	1	TRUE	1	0.54194749022091	2		189	304	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443464	49443464	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	72	218	0	ENST00000301067.7:c.3906+1G>A		p.X1302_splice	ENST00000301067	NM_003482.3	1302			1	2	FACETS	0.736	0.647	0.831	0.736	0.647	0.831	SUBCLONAL	1	TRUE	1	0.54194749022091	2		218	361	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448741	49448741	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	119	363	0	ENST00000301067.7:c.118G>A	p.Glu40Lys	p.E40K	ENST00000301067	NM_003482.3	40	Gag/Aag	2/54	1	2	FACETS	0.686	0.621	0.755	0.686	0.621	0.755	SUBCLONAL	1	TRUE	1	0.54194749022091	2		363	640	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118760	115118760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	35	443	0	ENST00000257566.3:c.581G>A	p.Gly194Glu	p.G194E	ENST00000257566	NM_016569.3	194	gGg/gAg	2/8	NA	2	FACETS	0.205	0.168	0.248			1	INDETERMINATE	1	TRUE	NA	0.54194749022091	2		443	629	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219847	133219847	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500822	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	41	336	0	ENST00000320574.5:c.4514C>T	p.Pro1505Leu	p.P1505L	ENST00000320574	NM_006231.2	1505	cCc/cTc	35/49	NA	2	FACETS	0.326	0.271	0.387			1	INDETERMINATE	1	TRUE	NA	0.54194749022091	2		336	464	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26971321	26971321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	139	374	0	ENST00000381527.3:c.892G>A	p.Glu298Lys	p.E298K	ENST00000381527	NM_001260.1	298	Gaa/Aaa	9/13	1	2	FACETS	0.919	0.841	1	0.919	0.841	1	CLONAL	1	TRUE	1	0.54194749022091	2		374	558	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28644708	28644708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	72	394	0	ENST00000241453.7:c.85G>A	p.Asp29Asn	p.D29N	ENST00000241453	NM_004119.2	29	Gat/Aat	2/24	1	2	FACETS	0.403	0.351	0.458	0.403	0.351	0.458	SUBCLONAL	1	TRUE	1	0.54194749022091	2		394	660	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959087	28959087	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	45	384	0	ENST00000282397.4:c.2051C>T	p.Ala684Val	p.A684V	ENST00000282397	NM_002019.4	684	gCt/gTt	14/30	1	2	FACETS	0.256	0.215	0.302	0.256	0.215	0.302	SUBCLONAL	1	TRUE	1	0.54194749022091	2		384	648	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32899269	32899269	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	46	469	0	ENST00000380152.3:c.373G>A	p.Asp125Asn	p.D125N	ENST00000380152		125	Gat/Aat	4/27	1	2	FACETS	0.212	0.178	0.25	0.212	0.178	0.25	SUBCLONAL	1	TRUE	1	0.54194749022091	2		469	800	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134193	41134193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1325888640	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	192	568	1	ENST00000379561.5:c.1435C>T	p.Pro479Ser	p.P479S	ENST00000379561	NM_002015.3	479	Cca/Tca	2/3	1	2	FACETS	0.818	0.757	0.881	0.818	0.757	0.881	CLONAL	1	TRUE	1	0.54194749022091	2		569	866	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335635	73335635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	51	308	0	ENST00000377767.4:c.2536G>A	p.Val846Ile	p.V846I	ENST00000377767	NM_014953.3	846	Gta/Ata	19/21	1	2	FACETS	0.31	0.263	0.361	0.31	0.263	0.361	SUBCLONAL	1	TRUE	1	0.54194749022091	2		308	608	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527982	103527982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	35	261	0	ENST00000355739.4:c.3290C>T	p.Ser1097Phe	p.S1097F	ENST00000355739	NM_000123.3	1097	tCt/tTt	15/15	1	2	FACETS	0.307	0.251	0.369	0.307	0.251	0.369	SUBCLONAL	1	TRUE	1	0.54194749022091	2		261	421	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873631	35873631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	118	272	2	ENST00000216797.5:c.220G>A	p.Gly74Arg	p.G74R	ENST00000216797	NM_020529.2	74	Ggg/Agg	1/6	1	2	FACETS	0.793	0.718	0.872	0.793	0.718	0.872	SUBCLONAL	1	TRUE	1	0.54194749022091	2		274	549	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003506	42003506	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	45	647	0	ENST00000219905.7:c.3043G>A	p.Glu1015Lys	p.E1015K	ENST00000219905	NM_001164273.1	1015	Gag/Aag	8/24	NA	2	FACETS	0.197	0.165	0.234			1	INDETERMINATE	1	TRUE	NA	0.54194749022091	2		647	841	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66781575	66781575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	46	370	0	ENST00000307102.5:c.983G>A	p.Gly328Glu	p.G328E	ENST00000307102	NM_002755.3	328	gGa/gAa	9/11	1	2	FACETS	0.273	0.23	0.322	0.273	0.23	0.322	SUBCLONAL	1	TRUE	1	0.54194749022091	2		370	621	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479780	67479780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	87	436	0	ENST00000327367.4:c.1087G>A	p.Val363Ile	p.V363I	ENST00000327367	NM_005902.3	363	Gtc/Atc	8/9	1	2	FACETS	0.451	0.399	0.507	0.451	0.399	0.507	SUBCLONAL	1	TRUE	1	0.54194749022091	2		436	712	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99460060	99460060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs544049409	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	126	407	2	ENST00000268035.6:c.2156G>A	p.Arg719His	p.R719H	ENST00000268035	NM_000875.3	719	cGc/cAc	10/21	1	2	FACETS	0.923	0.84	1	0.923	0.84	1	CLONAL	1	TRUE	1	0.54194749022091	2		409	504	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341260	341260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374579262	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	136	298	0	ENST00000262320.3:c.2224G>A	p.Val742Ile	p.V742I	ENST00000262320	NM_003502.3	742	Gtc/Atc	9/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.54194749022091	2		298	463	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222201	2222201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	60	377	0	ENST00000326181.6:c.485C>T	p.Pro162Leu	p.P162L	ENST00000326181	NM_032271.2	162	cCc/cTc	8/21	1	2	FACETS	0.356	0.306	0.41	0.356	0.306	0.41	SUBCLONAL	1	TRUE	1	0.54194749022091	2		377	622	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225563	2225563	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	74	362	0	ENST00000326181.6:c.1566G>A	p.Trp522Ter	p.W522*	ENST00000326181	NM_032271.2	522	tgG/tgA	17/21	1	2	FACETS	0.507	0.444	0.574	0.507	0.444	0.574	SUBCLONAL	1	TRUE	1	0.54194749022091	2		362	539	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779596	3779596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	28	420	0	ENST00000262367.5:c.5452G>A	p.Val1818Met	p.V1818M	ENST00000262367	NM_004380.2	1818	Gtg/Atg	31/31	1	2	FACETS	0.205	0.163	0.252	0.205	0.163	0.252	SUBCLONAL	1	TRUE	1	0.54194749022091	2		420	505	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3842018	3842018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	35	397	0	ENST00000262367.5:c.1294C>T	p.Pro432Ser	p.P432S	ENST00000262367	NM_004380.2	432	Cct/Tct	5/31	1	2	FACETS	0.204	0.166	0.246	0.204	0.166	0.246	SUBCLONAL	1	TRUE	1	0.54194749022091	2		397	633	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274034	10274034	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	40	413	0	ENST00000330684.3:c.235C>T	p.Pro79Ser	p.P79S	ENST00000330684	NM_001134407.1	79	Ccc/Tcc	2/13	1	2	FACETS	0.263	0.218	0.313	0.263	0.218	0.313	SUBCLONAL	1	TRUE	1	0.54194749022091	2		413	562	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274085	10274085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	37	363	0	ENST00000330684.3:c.184G>A	p.Gly62Arg	p.G62R	ENST00000330684	NM_001134407.1	62	Ggg/Agg	2/13	1	2	FACETS	0.278	0.228	0.333	0.278	0.228	0.333	SUBCLONAL	1	TRUE	1	0.54194749022091	2		363	492	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23635391	23635391	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	48	462	0	ENST00000261584.4:c.2773G>A	p.Val925Met	p.V925M	ENST00000261584	NM_024675.3	925	Gtg/Atg	8/13	1	2	FACETS	0.268	0.226	0.315	0.268	0.226	0.315	SUBCLONAL	1	TRUE	1	0.54194749022091	2		462	660	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645163	67645163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	34	328	0	ENST00000264010.4:c.428C>T	p.Ser143Phe	p.S143F	ENST00000264010	NM_006565.3	143	tCt/tTt	3/12	1	2	FACETS	0.24	0.196	0.291	0.24	0.196	0.291	SUBCLONAL	1	TRUE	1	0.54194749022091	2		328	522	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845860	72845860	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	56	590	2	ENST00000268489.5:c.3607G>T	p.Glu1203Ter	p.E1203*	ENST00000268489	NM_006885.3	1203	Gag/Tag	6/10	1	2	FACETS	0.253	0.216	0.294	0.253	0.216	0.294	SUBCLONAL	1	TRUE	1	0.54194749022091	2		592	817	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993561	72993561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	59	496	0	ENST00000268489.5:c.484G>A	p.Gly162Ser	p.G162S	ENST00000268489	NM_006885.3	162	Ggc/Agc	2/10	1	2	FACETS	0.358	0.307	0.412	0.358	0.307	0.412	SUBCLONAL	1	TRUE	1	0.54194749022091	2		496	609	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81957097	81957097	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	39	490	1	ENST00000359376.3:c.2315G>A	p.Arg772Lys	p.R772K	ENST00000359376	NM_002661.3	772	aGa/aAa	22/33	0.54194749022091	1	FACETS	0.212	0.175	0.253	0.212	0.175	0.253	SUBCLONAL	1	TRUE	0	0.54194749022091	1		491	495	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81960727	81960727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866339098	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	53	569	0	ENST00000359376.3:c.2458C>T	p.Pro820Ser	p.P820S	ENST00000359376	NM_002661.3	820	Cca/Tca	23/33	0.54194749022091	1	FACETS	0.27	0.23	0.313	0.27	0.23	0.313	SUBCLONAL	1	TRUE	0	0.54194749022091	1		569	529	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990343	81990343	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	50	518	0	ENST00000359376.3:c.3614G>A	p.Arg1205Lys	p.R1205K	ENST00000359376	NM_002661.3	1205	aGg/aAg	32/33	0.54194749022091	1	FACETS	0.263	0.223	0.307	0.263	0.223	0.307	SUBCLONAL	1	TRUE	0	0.54194749022091	1		518	512	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350587	89350587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	39	558	0	ENST00000301030.4:c.2363C>T	p.Ser788Leu	p.S788L	ENST00000301030	NM_001256183.1	788	tCa/tTa	9/13	NA	2	FACETS	0.192	0.158	0.23			1	INDETERMINATE	1	TRUE	NA	0.54194749022091	2		558	750	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857817	89857817	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	30	319	0	ENST00000389301.3:c.1353G>A	p.Trp451Ter	p.W451*	ENST00000389301	NM_000135.2	451	tgG/tgA	14/43	NA	2	FACETS	0.241	0.193	0.294			1	INDETERMINATE	1	TRUE	NA	0.54194749022091	2		319	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691039	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	26	337	0	ENST00000269305.4:c.919+1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			1	2	FACETS	0.19	0.15	0.237	0.19	0.15	0.237	SUBCLONAL	1	TRUE	1	0.54194749022091	2		337	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577102	7577102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793881	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	25	741	1	ENST00000269305.4:c.836G>A	p.Gly279Glu	p.G279E	ENST00000269305	NM_001126112.2	279	gGg/gAg	8/11	1	2	FACETS	0.14	0.11	0.175	0.14	0.11	0.175	SUBCLONAL	1	TRUE	1	0.54194749022091	2		742	659	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028623	12028623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	47	413	0	ENST00000353533.5:c.826G>A	p.Asp276Asn	p.D276N	ENST00000353533	NM_003010.3	276	Gac/Aac	8/11	1	2	FACETS	0.251	0.211	0.295	0.251	0.211	0.295	SUBCLONAL	1	TRUE	1	0.54194749022091	2		413	692	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044471	12044471	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	32	243	0	ENST00000353533.5:c.1094C>T	p.Pro365Leu	p.P365L	ENST00000353533	NM_003010.3	365	cCc/cTc	11/11	1	2	FACETS	0.275	0.223	0.334	0.275	0.223	0.334	SUBCLONAL	1	TRUE	1	0.54194749022091	2		243	430	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961823	15961823	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	50	505	0	ENST00000268712.3:c.5972C>T	p.Thr1991Ile	p.T1991I	ENST00000268712	NM_006311.3	1991	aCc/aTc	38/46	1	2	FACETS	0.244	0.207	0.286	0.244	0.207	0.286	SUBCLONAL	1	TRUE	1	0.54194749022091	2		505	755	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973495	15973495	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	36	304	0	ENST00000268712.3:c.4497G>A	p.Met1499Ile	p.M1499I	ENST00000268712	NM_006311.3	1499	atG/atA	31/46	1	2	FACETS	0.235	0.192	0.282	0.235	0.192	0.282	SUBCLONAL	1	TRUE	1	0.54194749022091	2		304	566	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15978946	15978946	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	42	529	0	ENST00000268712.3:c.3572C>T	p.Pro1191Leu	p.P1191L	ENST00000268712	NM_006311.3	1191	cCc/cTc	27/46	1	2	FACETS	0.217	0.18	0.258	0.217	0.18	0.258	SUBCLONAL	1	TRUE	1	0.54194749022091	2		529	714	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989739	15989739	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	16	175	0	ENST00000268712.3:c.3034C>T	p.His1012Tyr	p.H1012Y	ENST00000268712	NM_006311.3	1012	Cat/Tat	23/46	1	2	FACETS	0.189	0.139	0.248	0.189	0.139	0.248	SUBCLONAL	1	TRUE	1	0.54194749022091	2		175	313	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528433	29528433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786201937	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	33	394	0	ENST00000356175.3:c.1190G>A	p.Cys397Tyr	p.C397Y	ENST00000356175	NM_000267.3	397	tGc/tAc	11/57	1	2	FACETS	0.186	0.15	0.226	0.186	0.15	0.226	SUBCLONAL	1	TRUE	1	0.54194749022091	2		394	656	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661945	29661945	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854552	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	168	421	0	ENST00000356175.3:c.5839C>T	p.Arg1947Ter	p.R1947*	ENST00000356175	NM_000267.3	1947	Cga/Tga	39/57	1	2	FACETS	0.973	0.898	1	0.973	0.898	1	CLONAL	1	TRUE	1	0.54194749022091	2		421	637	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687274	37687274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1217754901	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	31	392	0	ENST00000447079.4:c.4178G>A	p.Gly1393Glu	p.G1393E	ENST00000447079	NM_015083.1	1393	gGg/gAg	14/14	NA	2	FACETS	0.22	0.177	0.268			1	INDETERMINATE	1	TRUE	NA	0.54194749022091	2		392	521	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354407	40354407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167075556	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	59	703	0	ENST00000293328.3:c.2188C>T	p.Pro730Ser	p.P730S	ENST00000293328	NM_012448.3	730	Ccc/Tcc	18/19	NA	2	FACETS	0.26	0.223	0.3			1	INDETERMINATE	1	TRUE	NA	0.54194749022091	2		703	838	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234477	41234477	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	68	446	0	ENST00000357654.3:c.4301G>A	p.Ser1434Asn	p.S1434N	ENST00000357654	NM_007294.3	1434	aGt/aAt	12/23	NA	2	FACETS	0.357	0.31	0.408			1	INDETERMINATE	1	TRUE	NA	0.54194749022091	2		446	702	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885877	59885877	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148556781	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	67	479	0	ENST00000259008.2:c.869G>A	p.Gly290Asp	p.G290D	ENST00000259008	NM_032043.2	290	gGt/gAt	7/20	1	2	FACETS	0.325	0.282	0.372	0.325	0.282	0.372	SUBCLONAL	1	TRUE	1	0.54194749022091	2		479	760	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59934490	59934490	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	65	468	0	ENST00000259008.2:c.308G>A	p.Gly103Glu	p.G103E	ENST00000259008	NM_032043.2	103	gGa/gAa	4/20	1	2	FACETS	0.303	0.262	0.348	0.303	0.262	0.348	SUBCLONAL	1	TRUE	1	0.54194749022091	2		468	791	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533701	63533701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	80	294	0	ENST00000307078.5:c.1453G>A	p.Gly485Ser	p.G485S	ENST00000307078	NM_004655.3	485	Ggc/Agc	6/11	1	2	FACETS	0.846	0.75	0.947	0.846	0.75	0.947	CLONAL	1	TRUE	1	0.54194749022091	2		294	349	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221340	1221340	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	37	281	0	ENST00000326873.7:c.862+1G>A		p.X288_splice	ENST00000326873	NM_000455.4	288			0.527344401322474	3	FACETS	0.314	0.258	0.376	0.157	0.129	0.188	SUBCLONAL	1	TRUE	1	0.54194749022091	3		281	553	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2199901	2199901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	45	391	0	ENST00000398665.3:c.670C>T	p.Leu224Phe	p.L224F	ENST00000398665	NM_032482.2	224	Ctc/Ttc	8/28	0.527344401322474	3	FACETS	0.315	0.264	0.371	0.157	0.132	0.186	SUBCLONAL	1	TRUE	1	0.54194749022091	3		391	671	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211187	2211187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	37	341	1	ENST00000398665.3:c.1441C>T	p.Pro481Ser	p.P481S	ENST00000398665	NM_032482.2	481	Ccg/Tcg	15/28	0.527344401322474	3	FACETS	0.277	0.228	0.333	0.139	0.114	0.167	SUBCLONAL	1	TRUE	1	0.54194749022091	3		342	626	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222412	2222412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1394204460	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	18	157	0	ENST00000398665.3:c.3244G>A	p.Asp1082Asn	p.D1082N	ENST00000398665	NM_032482.2	1082	Gac/Aac	24/28	0.527344401322474	3	FACETS	0.245	0.184	0.317	0.122	0.092	0.159	SUBCLONAL	1	TRUE	1	0.54194749022091	3		157	345	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223328	2223328	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	181	437	1	ENST00000398665.3:c.3439G>T	p.Glu1147Ter	p.E1147*	ENST00000398665	NM_032482.2	1147	Gag/Tag	25/28	0.527344401322474	3	FACETS	0.983	0.907	1	0.491	0.453	0.531	CLONAL	1	TRUE	1	0.54194749022091	3		438	864	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226677	2226677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763271310	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	26	270	1	ENST00000398665.3:c.4157G>A	p.Gly1386Asp	p.G1386D	ENST00000398665	NM_032482.2	1386	gGc/gAc	27/28	0.527344401322474	3	FACETS	0.241	0.19	0.299	0.12	0.095	0.15	SUBCLONAL	1	TRUE	1	0.54194749022091	3		271	507	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210606	5210606	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	30	304	0	ENST00000357368.4:c.5362-1G>A		p.X1788_splice	ENST00000357368	NM_002850.3	1788			0.527344401322474	3	FACETS	0.252	0.202	0.309	0.126	0.101	0.155	SUBCLONAL	1	TRUE	1	0.54194749022091	3		304	558	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5225824	5225824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	32	331	0	ENST00000357368.4:c.2408C>T	p.Thr803Ile	p.T803I	ENST00000357368	NM_002850.3	803	aCc/aTc	17/38	0.527344401322474	3	FACETS	0.271	0.22	0.33	0.136	0.11	0.165	SUBCLONAL	1	TRUE	1	0.54194749022091	3		331	553	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123694	11123694	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	50	361	0	ENST00000358026.2:c.2344G>A	p.Gly782Ser	p.G782S	ENST00000358026	NM_001128849.1	782	Ggc/Agc	16/36	0.54194749022091	3	FACETS	0.344	0.291	0.403	0.172	0.145	0.202	SUBCLONAL	1	TRUE	1	0.54194749022091	3		361	681	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297734	15297734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	50	458	0	ENST00000263388.2:c.1906G>A	p.Asp636Asn	p.D636N	ENST00000263388	NM_000435.2	636	Gat/Aat	12/33	0.54194749022091	3	FACETS	0.327	0.276	0.382	0.163	0.138	0.191	SUBCLONAL	1	TRUE	1	0.54194749022091	3		458	718	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17940921	17940921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	33	341	0	ENST00000458235.1:c.3203C>T	p.Ala1068Val	p.A1068V	ENST00000458235	NM_000215.3	1068	gCt/gTt	23/24	0.54194749022091	3	FACETS	0.274	0.222	0.332	0.137	0.111	0.166	SUBCLONAL	1	TRUE	1	0.54194749022091	3		341	565	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40761137	40761137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765768303	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	116	389	1	ENST00000392038.2:c.215C>T	p.Thr72Ile	p.T72I	ENST00000392038	NM_001626.4	72	aCc/aTc	4/14	0.54194749022091	3	FACETS	0.857	0.774	0.944	0.428	0.387	0.472	CLONAL	1	TRUE	1	0.54194749022091	3		390	635	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745610	41745610	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	43	459	2	ENST00000301178.4:c.1297C>T	p.Pro433Ser	p.P433S	ENST00000301178	NM_021913.4	433	Cca/Tca	10/20	0.54194749022091	3	FACETS	0.235	0.195	0.279	0.117	0.097	0.14	SUBCLONAL	1	TRUE	1	0.54194749022091	3		461	859	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762388	41762388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	73	441	0	ENST00000301178.4:c.2068G>A	p.Asp690Asn	p.D690N	ENST00000301178	NM_021913.4	690	Gac/Aac	18/20	0.54194749022091	3	FACETS	0.447	0.39	0.508	0.223	0.195	0.254	SUBCLONAL	1	TRUE	1	0.54194749022091	3		441	766	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872231	45872231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	38	365	0	ENST00000391945.4:c.203C>T	p.Thr68Ile	p.T68I	ENST00000391945	NM_000400.3	68	aCc/aTc	4/23	0.50792616012607	1	FACETS	0.24	0.198	0.287	0.24	0.198	0.287	SUBCLONAL	1	TRUE	0	0.54194749022091	1		365	426	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714652	52714652	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	25	368	0	ENST00000322088.6:c.410G>A	p.Gly137Asp	p.G137D	ENST00000322088	NM_014225.5	137	gGc/gAc	4/15	NA	2	FACETS	0.202	0.159	0.252			1	INDETERMINATE	1	TRUE	NA	0.54194749022091	2		368	456	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546683	9546683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	52	368	0	ENST00000353224.5:c.1339G>A	p.Glu447Lys	p.E447K	ENST00000353224	NM_177990.2	447	Gaa/Aaa	5/10	0.527344401322474	3	FACETS	0.35	0.297	0.408	0.175	0.148	0.204	SUBCLONAL	1	TRUE	1	0.54194749022091	3		368	697	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560911	9560911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	37	441	0	ENST00000353224.5:c.871G>A	p.Gly291Arg	p.G291R	ENST00000353224	NM_177990.2	291	Gga/Aga	4/10	0.527344401322474	3	FACETS	0.236	0.193	0.283	0.118	0.096	0.142	SUBCLONAL	1	TRUE	1	0.54194749022091	3		441	736	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400191	41400191	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	102	331	0	ENST00000373198.4:c.569-1G>A		p.X190_splice	ENST00000373198	NM_133170.3	190			0.139003325542348	3	FACETS	0.8	0.717	0.888	0.267	0.239	0.296	INDETERMINATE	1	TRUE	0	0.54194749022091	3		331	598	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231824	36231824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	26	268	0	ENST00000300305.3:c.560C>T	p.Ala187Val	p.A187V	ENST00000300305		187	gCc/gTc	5/8	1	2	FACETS	0.217	0.171	0.269	0.217	0.171	0.269	SUBCLONAL	1	TRUE	1	0.54194749022091	2		268	443	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160210	22160210	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	34	364	1	ENST00000215832.6:c.421C>T	p.His141Tyr	p.H141Y	ENST00000215832	NM_002745.4	141	Cat/Tat	3/9	1	2	FACETS	0.2	0.163	0.243	0.2	0.163	0.243	SUBCLONAL	1	TRUE	1	0.54194749022091	2		365	626	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24135805	24135805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	44	410	0	ENST00000263121.7:c.292G>A	p.Glu98Lys	p.E98K	ENST00000263121	NM_003073.3	98	Gag/Aag	3/9	1	2	FACETS	0.263	0.22	0.311	0.263	0.22	0.311	SUBCLONAL	1	TRUE	1	0.54194749022091	2		410	618	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24158972	24158972	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769517643	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	72	368	0	ENST00000263121.7:c.644C>T	p.Pro215Leu	p.P215L	ENST00000263121	NM_003073.3	215	cCt/cTt	6/9	1	2	FACETS	0.536	0.469	0.607	0.536	0.469	0.607	SUBCLONAL	1	TRUE	1	0.54194749022091	2		368	496	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573611	41573611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369570698	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	29	432	0	ENST00000263253.7:c.5896G>A	p.Gly1966Ser	p.G1966S	ENST00000263253	NM_001429.3	1966	Ggt/Agt	31/31	1	2	FACETS	0.19	0.152	0.234	0.19	0.152	0.234	SUBCLONAL	1	TRUE	1	0.54194749022091	2		432	563	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357643	70357643	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	167	259	0	ENST00000374080.3:c.5894C>T	p.Pro1965Leu	p.P1965L	ENST00000374080		1965	cCc/cTc	41/45	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.54194749022091	1		259	345	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937293	76937293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	29	227	0	ENST00000373344.5:c.3455G>A	p.Gly1152Asp	p.G1152D	ENST00000373344	NM_000489.3	1152	gGc/gAc	9/35	1	1	FACETS	0.213	0.17	0.261	0.213	0.17	0.261	SUBCLONAL	1	TRUE	0	0.54194749022091	1		227	367	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952098	76952098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781803934	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	99	288	0	ENST00000373344.5:c.337G>A	p.Glu113Lys	p.E113K	ENST00000373344	NM_000489.3	113	Gaa/Aaa	5/35	1	1	FACETS	0.553	0.495	0.613	0.553	0.495	0.613	SUBCLONAL	1	TRUE	0	0.54194749022091	1		288	482	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196777	123196777	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	27	288	1	ENST00000218089.9:c.1664C>T	p.Thr555Ile	p.T555I	ENST00000218089	NM_001042749.1	555	aCa/aTa	18/35	1	1	FACETS	0.178	0.142	0.221	0.178	0.142	0.221	SUBCLONAL	1	TRUE	0	0.54194749022091	1		289	407	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0003529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	54	82	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.54194749022091	1	FACETS	0.891	0.777	1	0.891	0.777	1	CLONAL	1	TRUE	0	0.54194749022091	1		82	163	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	67	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.728502155741644	2		174	156	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	257	234	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.728502155741644	2		234	664	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468516	89468516	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1453560937	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	142	553	0	ENST00000336596.2:c.2050C>T	p.Arg684Ter	p.R684*	ENST00000336596	NM_005233.5	684	Cga/Tga	11/17	1	2	FACETS	0.994	0.916	1	0.994	0.916	1	CLONAL	1	TRUE	1	0.728502155741644	2		553	392	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770594	40770594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	278	536	0	ENST00000373198.4:c.2788G>A	p.Glu930Lys	p.E930K	ENST00000373198	NM_133170.3	930	Gaa/Aaa	19/32	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.728502155741644	2		536	523	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838347	156838347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1376334182	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	164	573	0	ENST00000524377.1:c.625G>A	p.Asp209Asn	p.D209N	ENST00000524377	NM_002529.3	209	Gac/Aac	6/17	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.728502155741644	2		573	431	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740215	162740215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771675675	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	209	778	0	ENST00000367921.3:c.1417C>T	p.Arg473Cys	p.R473C	ENST00000367921	NM_006182.2	473	Cgc/Tgc	12/18	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.728502155741644	2		778	501	SUCCESS
FH	2271	MSKCC	GRCh37	1	241661267	241661267	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	127	403	0	ENST00000366560.3:c.1394A>T	p.Tyr465Phe	p.Y465F	ENST00000366560	NM_000143.3	465	tAt/tTt	10/10	1	2	FACETS	0.971	0.89	1	0.971	0.89	1	CLONAL	1	TRUE	1	0.728502155741644	2		403	359	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086157	16086157	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	151	457	0	ENST00000281043.3:c.1333G>A	p.Glu445Lys	p.E445K	ENST00000281043	NM_005378.4	445	Gaa/Aaa	3/3	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.728502155741644	2		457	400	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606667	29606667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs4363989	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	219	708	2	ENST00000389048.3:c.1213G>A	p.Glu405Lys	p.E405K	ENST00000389048	NM_004304.4	405	Gaa/Aaa	5/29	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.728502155741644	2		710	583	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182187	99182187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	208	677	2	ENST00000074304.5:c.2252C>T	p.Ser751Phe	p.S751F	ENST00000074304	NM_001134224.1	751	tCc/tTc	21/26	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.728502155741644	2		679	545	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812293	212812293	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569995088	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	168	541	1	ENST00000342788.4:c.283C>T	p.Arg95Cys	p.R95C	ENST00000342788	NM_005235.2	95	Cgt/Tgt	3/28	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.728502155741644	2		542	392	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164784	47164784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1245212934	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	138	450	0	ENST00000409792.3:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000409792	NM_014159.6	448	Cgg/Tgg	3/21	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.728502155741644	2		450	353	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259262	89259262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770780950	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	118	531	0	ENST00000336596.2:c.406C>T	p.Arg136Ter	p.R136*	ENST00000336596	NM_005233.5	136	Cga/Tga	3/17	1	2	FACETS	0.855	0.779	0.933	0.855	0.779	0.933	CLONAL	1	TRUE	1	0.728502155741644	2		531	379	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55963855	55963855	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	183	793	0	ENST00000263923.4:c.2588G>A	p.Arg863Lys	p.R863K	ENST00000263923	NM_002253.2	863	aGg/aAg	18/30	1	2	FACETS	0.934	0.868	1	0.934	0.868	1	CLONAL	1	TRUE	1	0.728502155741644	2		793	538	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542252	187542252	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746692408	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	227	652	0	ENST00000441802.2:c.5488C>T	p.His1830Tyr	p.H1830Y	ENST00000441802	NM_005245.3	1830	Cat/Tat	10/27	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.728502155741644	2		652	540	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459725	149459725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	362	591	0	ENST00000286301.3:c.482G>A	p.Gly161Asp	p.G161D	ENST00000286301	NM_005211.3	161	gGc/gAc	4/22	0.728502155741644	3	FACETS	0.963	0.921	1	0.963	0.921	1	CLONAL	2	TRUE	1	0.728502155741644	3		591	704	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514528	149514528	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	150	569	1	ENST00000261799.4:c.416T>G	p.Leu139Arg	p.L139R	ENST00000261799	NM_002609.3	139	cTc/cGc	4/23	0.728502155741644	3	FACETS	0.846	0.775	0.92	0.423	0.387	0.46	CLONAL	1	TRUE	1	0.728502155741644	3		570	664	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043904	180043904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56082504	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	201	877	5	ENST00000261937.6:c.3092G>A	p.Arg1031Gln	p.R1031Q	ENST00000261937	NM_182925.4	1031	cGa/cAa	22/30	0.728502155741644	3	FACETS	1	0.95	1	0.514	0.477	0.551	CLONAL	1	TRUE	1	0.728502155741644	3		882	733	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185834	32185834	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	173	601	0	ENST00000375023.3:c.1562C>T	p.Pro521Leu	p.P521L	ENST00000375023	NM_004557.3	521	cCc/cTc	9/30	0.728502155741644	3	FACETS	0.998	0.923	1	0.499	0.461	0.539	CLONAL	1	TRUE	1	0.728502155741644	3		601	649	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715803	117715803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	185	774	0	ENST00000368508.3:c.955G>A	p.Asp319Asn	p.D319N	ENST00000368508	NM_002944.2	319	Gat/Aat	9/43	0.728502155741644	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.728502155741644	1		774	280	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729907	41729907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	240	1211	1	ENST00000242208.4:c.622G>A	p.Glu208Lys	p.E208K	ENST00000242208	NM_002192.2	208	Gaa/Aaa	3/3	0.728502155741644	3	FACETS	1	0.945	1	0.506	0.473	0.539	CLONAL	1	TRUE	1	0.728502155741644	3		1212	889	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	377	335	0	ENST00000288602.6:c.1742A>T	p.Asn581Ile	p.N581I	ENST00000288602	NM_004333.4	581	aAt/aTt	15/18	0.728502155741644	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	4	TRUE	0	0.728502155741644	4		335	433	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494220	140494220	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752186820	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	189	769	0	ENST00000288602.6:c.1028C>T	p.Pro343Leu	p.P343L	ENST00000288602	NM_004333.4	343	cCa/cTa	8/18	0.728502155741644	4	FACETS	1	0.974	1	0.278	0.257	0.3	CLONAL	1	TRUE	0	0.728502155741644	4		769	806	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880090	151880090	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	221	824	1	ENST00000262189.6:c.5234C>T	p.Ser1745Leu	p.S1745L	ENST00000262189	NM_170606.2	1745	tCa/tTa	35/59	0.728502155741644	4	FACETS	1	0.966	1	0.265	0.246	0.284	CLONAL	1	TRUE	0	0.728502155741644	4		825	990	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331594	8331594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1018594636	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	213	878	0	ENST00000356435.5:c.5522C>T	p.Ser1841Leu	p.S1841L	ENST00000356435		1841	tCa/tTa	33/35	0.728502155741644	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.728502155741644	1		878	358	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309776	104309776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202247756	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	186	423	0	ENST00000369902.3:c.367C>T	p.Arg123Cys	p.R123C	ENST00000369902	NM_016169.3	123	Cgt/Tgt	3/12	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.728502155741644	2		423	505	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894228	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	199	634	0	ENST00000451590.1:c.37G>T	p.Gly13Cys	p.G13C	ENST00000451590	NM_001130442.1	13	Ggt/Tgt	2/5	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.728502155741644	2		634	466	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203756	94203756	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	171	541	0	ENST00000323929.3:c.898C>T	p.Pro300Ser	p.P300S	ENST00000323929	NM_005591.3	300	Cct/Tct	9/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.728502155741644	2		541	433	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118361991	118361991	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1472952558	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	127	497	0	ENST00000534358.1:c.4777C>T	p.Arg1593Cys	p.R1593C	ENST00000534358	NM_005933.3	1593	Cgc/Tgc	14/36	1	2	FACETS	0.906	0.829	0.985	0.906	0.829	0.985	CLONAL	1	TRUE	1	0.728502155741644	2		497	385	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445683	49445683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	225	840	0	ENST00000301067.7:c.1783G>A	p.Glu595Lys	p.E595K	ENST00000301067	NM_003482.3	595	Gag/Aag	10/54	NA	2	FACETS	0.976	0.914	1			1	INDETERMINATE	1	TRUE	NA	0.728502155741644	2		840	633	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813370	102813370	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	193	655	0	ENST00000307046.8:c.319A>G	p.Met107Val	p.M107V	ENST00000307046	NM_001111285.1	107	Atg/Gtg	3/4	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.728502155741644	2		655	512	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112019	115112019	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	100	368	0	ENST00000257566.3:c.1721C>T	p.Ser574Phe	p.S574F	ENST00000257566	NM_016569.3	574	tCc/tTc	7/8	1	2	FACETS	0.97	0.879	1	0.97	0.879	1	CLONAL	1	TRUE	1	0.728502155741644	2		368	283	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574048	95574048	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	156	451	0	ENST00000393063.1:c.2701G>A	p.Glu901Lys	p.E901K	ENST00000393063	NM_030621.3	901	Gag/Aag	18/28	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.728502155741644	2		451	422	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239387	105239387	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	231	648	1	ENST00000349310.3:c.1000G>A	p.Gly334Arg	p.G334R	ENST00000349310	NM_001014432.1	334	Ggg/Agg	12/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.728502155741644	2		649	542	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456443	99456443	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	169	605	2	ENST00000268035.6:c.1760C>T	p.Thr587Ile	p.T587I	ENST00000268035	NM_000875.3	587	aCc/aTc	8/21	0.671991604285981	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.728502155741644	1		607	295	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	173	563	0	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.728502155741644	2		563	468	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245239	41245239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357063	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	201	727	0	ENST00000357654.3:c.2309C>T	p.Ser770Leu	p.S770L	ENST00000357654	NM_007294.3	770	tCa/tTa	10/23	NA	2	FACETS	0.994	0.928	1			1	INDETERMINATE	1	TRUE	NA	0.728502155741644	2		727	555	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117822	70117822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	156	635	2	ENST00000245479.2:c.290G>A	p.Gly97Asp	p.G97D	ENST00000245479	NM_000346.3	97	gGc/gAc	1/3	1	2	FACETS	0.991	0.917	1	0.991	0.917	1	CLONAL	1	TRUE	1	0.728502155741644	2		637	432	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525104	9525104	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	214	794	0	ENST00000353224.5:c.1781C>T	p.Ser594Phe	p.S594F	ENST00000353224	NM_177990.2	594	tCc/tTc	8/10	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.728502155741644	2		794	579	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561352	9561352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773981325	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	152	512	0	ENST00000353224.5:c.430G>A	p.Glu144Lys	p.E144K	ENST00000353224	NM_177990.2	144	Gaa/Aaa	4/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.728502155741644	2		512	354	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019234	31019234	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	384	769	0	ENST00000375687.4:c.829C>T	p.Pro277Ser	p.P277S	ENST00000375687	NM_015338.5	277	Cca/Tca	9/13	0.192668980665821	6	FACETS	0.911	0.873	0.948			1	INDETERMINATE	4	TRUE	NA	0.728502155741644	6		769	711	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790012	40790012	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759474238	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	299	503	0	ENST00000373198.4:c.2719G>A	p.Gly907Arg	p.G907R	ENST00000373198	NM_133170.3	907	Ggg/Agg	18/32	NA	2	FACETS	0.754	0.719	0.789			1	INDETERMINATE	2	TRUE	NA	0.728502155741644	2		503	544	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790087	40790087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	242	527	0	ENST00000373198.4:c.2644G>A	p.Asp882Asn	p.D882N	ENST00000373198	NM_133170.3	882	Gac/Aac	18/32	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.728502155741644	2		527	459	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344985	70344985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1365839691	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	200	388	0	ENST00000374080.3:c.2215C>T	p.Pro739Ser	p.P739S	ENST00000374080		739	Ccc/Tcc	15/45	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.728502155741644	1		388	281	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988782	41988782	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	235	1197	0	ENST00000219905.7:c.1575del	p.Glu525AspfsTer22	p.E525Dfs*22	ENST00000219905	NM_001164273.1	525	gAa/ga	3/24	NA	2	FACETS	0.963	0.903	1			1	INDETERMINATE	1	TRUE	NA	0.728502155741644	2		1197	670	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787673	135787676	+	frameshift_variant	Frame_Shift_Del	DEL	GCTA	GCTA	CTT	novel	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	159	722	0	ENST00000298552.3:c.906_909delinsAAG	p.Asn302LysfsTer16	p.N302Kfs*16	ENST00000298552	NM_001162426.1	302	aaTAGC/aaAAG	9/23	1	2	FACETS	0.896	0.828	0.966	0.896	0.828	0.966	CLONAL	1	TRUE	1	0.728502155741644	2		722	487	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244399	5244400	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0003560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	143	433	0	ENST00000357368.4:c.1082_1083delinsTT	p.Ser361Phe	p.S361F	ENST00000357368	NM_002850.3	361	tCC/tTT	11/38	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.728502155741644	2		433	330	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0003561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	65	769	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.991	0.885	1	0.991	0.885	1	CLONAL	1	TRUE	1	0.93	2		769	141	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	69	515	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.927	0.829	1	0.927	0.829	1	CLONAL	1	TRUE	1	0.93	2		515	160	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857524	9857524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778230379	NA	P-0003561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	112	241	0	ENST00000330684.3:c.3877G>A	p.Asp1293Asn	p.D1293N	ENST00000330684	NM_001134407.1	1293	Gat/Aat	13/13	0.0755732647133118	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		241	245	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551879	150551879	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	88	168	0	ENST00000369026.2:c.128C>G	p.Ser43Trp	p.S43W	ENST00000369026	NM_021960.4	43	tCg/tGg	1/3	1	2	FACETS	0.991	0.9	1	0.991	0.9	1	CLONAL	1	TRUE	1	0.93	2		168	191	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0003561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	80	764	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.165052910915011	3	FACETS	1	0.966	1	0.597	0.536	0.66	INDETERMINATE	1	TRUE	1	0.93	3		764	211	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566488	41566488	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	183	431	0	ENST00000263253.7:c.4365G>C	p.Gln1455His	p.Q1455H	ENST00000263253	NM_001429.3	1455	caG/caC	27/31	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.93	2		431	392	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690285	47690285	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	114	261	0	ENST00000233146.2:c.1502G>C	p.Arg501Thr	p.R501T	ENST00000233146	NM_000251.2	501	aGa/aCa	9/16	1	2	FACETS	0.977	0.897	1	0.977	0.897	1	CLONAL	1	TRUE	1	0.93	2		261	251	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231293	142231293	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780300351	NA	P-0003561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	22	369	1	ENST00000350721.4:c.4661C>T	p.Ala1554Val	p.A1554V	ENST00000350721	NM_001184.3	1554	gCa/gTa	27/47	1	2	FACETS	0.163	0.126	0.205	0.163	0.126	0.205	SUBCLONAL	1	TRUE	1	0.93	2		370	291	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84384762	84384762	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0003561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	98	221	0	ENST00000321945.7:c.682-1G>C		p.X228_splice	ENST00000321945	NM_139076.2	228			1	2	FACETS	0.912	0.83	0.996	0.912	0.83	0.996	CLONAL	1	TRUE	1	0.93	2		221	231	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638698	176638698	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	135	312	1	ENST00000439151.2:c.3298G>T	p.Glu1100Ter	p.E1100*	ENST00000439151	NM_022455.4	1100	Gaa/Taa	5/23	1	2	FACETS	0.919	0.848	0.99	0.919	0.848	0.99	CLONAL	1	TRUE	1	0.93	2		313	316	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710623	117710623	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763487146	NA	P-0003561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	121	331	0	ENST00000368508.3:c.1649C>T	p.Ser550Leu	p.S550L	ENST00000368508	NM_002944.2	550	tCa/tTa	12/43	0.3	1	FACETS	0.461	0.423	0.5	0.461	0.423	0.5	INDETERMINATE	1	TRUE	0	0.93	1		331	302	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951866	2951866	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1415600061	NA	P-0003561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	159	356	0	ENST00000396946.4:c.3084G>C	p.Glu1028Asp	p.E1028D	ENST00000396946	NM_032415.4	1028	gaG/gaC	23/25	1	2	FACETS	0.945	0.878	1	0.945	0.878	1	CLONAL	1	TRUE	1	0.93	2		356	362	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520043	106520043	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0003561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	170	306	0	ENST00000359195.3:c.2471C>G	p.Ser824Ter	p.S824*	ENST00000359195	NM_002649.2	824	tCa/tGa	6/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.93	2		306	352	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999663	100999663	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148270826	NA	P-0003561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	200	541	0	ENST00000325455.5:c.139G>A	p.Glu47Lys	p.E47K	ENST00000325455	NM_001202474.3	47	Gaa/Aaa	1/8	0.3	1	FACETS	0.557	0.523	0.591	0.557	0.523	0.591	INDETERMINATE	1	TRUE	0	0.93	1		541	413	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233613	69233613	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	74	155	0	ENST00000462284.1:c.1478T>G	p.Leu493Arg	p.L493R	ENST00000462284	NM_002392.5	493	cTa/cGa	11/11	1	2	FACETS	0.714	0.635	0.795	0.714	0.635	0.795	SUBCLONAL	1	TRUE	1	0.93	2		155	223	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114255	115114255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	202	342	0	ENST00000257566.3:c.962C>T	p.Ser321Phe	p.S321F	ENST00000257566	NM_016569.3	321	tCc/tTc	6/8	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.93	2		342	422	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632768	23632768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	136	370	0	ENST00000261584.4:c.3028G>A	p.Glu1010Lys	p.E1010K	ENST00000261584	NM_024675.3	1010	Gag/Aag	10/13	0.0755732647133118	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		370	304	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858941	45858941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	149	412	0	ENST00000391945.4:c.1525G>A	p.Glu509Lys	p.E509K	ENST00000391945	NM_000400.3	509	Gag/Aag	16/23	0.0755732647133118	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		412	323	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264403	46264403	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	190	660	1	ENST00000371998.3:c.1450C>G	p.Pro484Ala	p.P484A	ENST00000371998		484	Cct/Gct	11/23	0.3	1	FACETS	0.514	0.481	0.548	0.514	0.481	0.548	INDETERMINATE	1	TRUE	0	0.93	1		661	425	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044907	47044907	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	109	197	0	ENST00000377604.3:c.2237del	p.Gly746AlafsTer56	p.G746Afs*56	ENST00000377604	NM_001204468.1	745	Ggg/gg	20/24	1	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.93	1		197	124	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929438	81929438	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0003561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	187	590	0	ENST00000359376.3:c.1100del	p.Lys367SerfsTer35	p.K367Sfs*35	ENST00000359376	NM_002661.3	367	Aag/ag	13/33	0.165052910915011	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		590	466	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638591	176638592	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0003561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	124	308	0	ENST00000439151.2:c.3191_3192del	p.Leu1064ArgfsTer22	p.L1064Rfs*22	ENST00000439151	NM_022455.4	1064	cTT/c	5/23	1	2	FACETS	0.78	0.714	0.847	0.78	0.714	0.847	SUBCLONAL	1	TRUE	1	0.93	2		308	342	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781834	3781834	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	172	453	0	ENST00000262367.5:c.4833del	p.Asn1612ThrfsTer23	p.N1612Tfs*23	ENST00000262367	NM_004380.2	1611	ccC/cc	29/31	0.0755732647133118	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		453	340	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432320	49432320	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	144	373	0	ENST00000301067.7:c.8819del	p.Pro2940LeufsTer3	p.P2940Lfs*3	ENST00000301067	NM_003482.3	2940	cCt/ct	34/54	1	2	FACETS	0.968	0.897	1	0.968	0.897	1	CLONAL	1	TRUE	1	0.93	2		373	320	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	1282	919	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.725191946446933	3	FACETS	0.996	0.981	1	0.996	0.981	1	CLONAL	3	TRUE	0	0.730476770297308	3		919	1603	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	428	298	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	0.730476770297308	3	FACETS	1	0.975	1	0.519	0.493	0.545	CLONAL	1	TRUE	1	0.730476770297308	3		298	1542	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066446	94066446	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	905	892	0	ENST00000369303.4:c.1313C>A	p.Thr438Asn	p.T438N	ENST00000369303	NM_004440.3	438	aCt/aAt	5/17	0.730476770297308	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.730476770297308	2		892	1211	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166597	118166597	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	222	439	0	ENST00000369448.3:c.1107C>A	p.Ser369Arg	p.S369R	ENST00000369448	NM_017709.3	369	agC/agA	2/2	1	2	FACETS	0.995	0.932	1	0.995	0.932	1	CLONAL	1	TRUE	1	0.730476770297308	2		439	611	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226576371	226576371	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	411	841	2	ENST00000366794.5:c.703G>T	p.Glu235Ter	p.E235*	ENST00000366794	NM_001618.3	235	Gaa/Taa	5/23	1	2	FACETS	0.959	0.914	1	0.959	0.914	1	CLONAL	1	TRUE	1	0.730476770297308	2		843	1173	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727024	243727024	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	333	600	0	ENST00000263826.5:c.946G>T	p.Glu316Ter	p.E316*	ENST00000263826	NM_005465.4	316	Gag/Tag	9/13	1	2	FACETS	0.96	0.91	1	0.96	0.91	1	CLONAL	1	TRUE	1	0.730476770297308	2		600	950	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449859	29449859	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1376365612	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	426	880	0	ENST00000389048.3:c.2996C>A	p.Pro999His	p.P999H	ENST00000389048	NM_004304.4	999	cCt/cAt	18/29	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.730476770297308	2		880	1138	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519758	29519758	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	319	592	0	ENST00000389048.3:c.1813G>C	p.Asp605His	p.D605H	ENST00000389048	NM_004304.4	605	Gac/Cac	9/29	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.730476770297308	2		592	825	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578260	212578260	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs768893584	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	779	771	0	ENST00000342788.4:c.997G>T	p.Ala333Ser	p.A333S	ENST00000342788	NM_005235.2	333	Gct/Tct	8/28	0.730476770297308	2	FACETS	0.97	0.948	0.993	0.97	0.948	0.993	CLONAL	2	TRUE	0	0.730476770297308	2		771	1099	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795126	242795126	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	474	493	0	ENST00000334409.5:c.83C>A	p.Pro28Gln	p.P28Q	ENST00000334409	NM_005018.2	28	cCa/cAa	2/5	0.730476770297308	2	FACETS	0.986	0.957	1	0.986	0.957	1	CLONAL	2	TRUE	0	0.730476770297308	2		493	658	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231276	142231276	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	367	623	1	ENST00000350721.4:c.4678G>T	p.Asp1560Tyr	p.D1560Y	ENST00000350721	NM_001184.3	1560	Gat/Tat	27/47	1	2	FACETS	0.941	0.894	0.989	0.941	0.894	0.989	CLONAL	1	TRUE	1	0.730476770297308	2		624	1068	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447214	187447214	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1016920638	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	339	695	0	ENST00000232014.4:c.979G>T	p.Gly327Cys	p.G327C	ENST00000232014	NM_001130845.1	327	Ggt/Tgt	5/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.730476770297308	2		695	890	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604182	189604182	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	314	726	0	ENST00000264731.3:c.1350-1G>A		p.X450_splice	ENST00000264731	NM_003722.4	450			1	2	FACETS	0.857	0.81	0.905	0.857	0.81	0.905	CLONAL	1	TRUE	1	0.730476770297308	2		726	1003	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467476	66467476	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	714	667	0	ENST00000273854.3:c.793C>G	p.His265Asp	p.H265D	ENST00000273854	NM_004439.5	265	Cat/Gat	3/18	0.730476770297308	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.730476770297308	2		667	953	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510091	187510091	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	354	705	0	ENST00000441802.2:c.13422G>T	p.Leu4474Phe	p.L4474F	ENST00000441802	NM_005245.3	4474	ttG/ttT	27/27	0.730476770297308	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.730476770297308	1		705	569	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047936	180047936	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs774978737	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	463	704	1	ENST00000261937.6:c.2239C>A	p.Leu747Met	p.L747M	ENST00000261937	NM_182925.4	747	Ctg/Atg	15/30	0.700816600646801	2	FACETS	0.971	0.941	0.999	0.971	0.941	0.999	CLONAL	2	TRUE	0	0.730476770297308	2		705	653	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271309	26271309	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	1230	1655	3	ENST00000305910.3:c.304G>T	p.Val102Leu	p.V102L	ENST00000305910	NM_003534.2	102	Gtg/Ttg	1/1	0.730476770297308	3	FACETS	0.971	0.948	0.994	0.971	0.948	0.994	CLONAL	2	TRUE	1	0.730476770297308	3		1658	2367	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778179	27778179	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1885	577	1768	0	ENST00000369163.2:c.328C>G	p.Leu110Val	p.L110V	ENST00000369163	NM_003536.2	110	Ctg/Gtg	1/1	0.730476770297308	3	FACETS	0.876	0.838	0.914	0.438	0.419	0.457	CLONAL	1	TRUE	1	0.730476770297308	3		1768	2462	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004745	150004745	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1342174778	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	761	658	0	ENST00000253339.5:c.1480A>G	p.Ile494Val	p.I494V	ENST00000253339		494	Att/Gtt	3/7	0.730476770297308	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.730476770297308	2		658	995	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860435	151860435	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	519	810	0	ENST00000262189.6:c.10227G>C	p.Glu3409Asp	p.E3409D	ENST00000262189	NM_170606.2	3409	gaG/gaC	43/59	0.730476770297308	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.730476770297308	1		810	811	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759848	133759848	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	489	635	0	ENST00000318560.5:c.2171A>G	p.His724Arg	p.H724R	ENST00000318560	NM_005157.4	724	cAt/cGt	11/11	0.730476770297308	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.730476770297308	2		635	643	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998680	100998680	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	477	937	0	ENST00000325455.5:c.1122C>A	p.Tyr374Ter	p.Y374*	ENST00000325455	NM_001202474.3	374	taC/taA	1/8	0.413991435257654	3	FACETS	1	0.995	1	0.649	0.62	0.678	INDETERMINATE	1	TRUE	1	0.730476770297308	3		937	1374	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150312	108150312	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	413	499	0	ENST00000278616.4:c.3379G>T	p.Ala1127Ser	p.A1127S	ENST00000278616	NM_000051.3	1127	Gct/Tct	23/63	0.413991435257654	3	FACETS	0.861	0.823	0.898	0.861	0.823	0.898	INDETERMINATE	2	TRUE	1	0.730476770297308	3		499	897	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534713	18534713	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	439	546	0	ENST00000266497.5:c.1771G>T	p.Gly591Trp	p.G591W	ENST00000266497		591	Ggg/Tgg	12/31	0.413991435257654	3	FACETS	0.837	0.802	0.873	0.837	0.802	0.873	INDETERMINATE	2	TRUE	1	0.730476770297308	3		546	980	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246315	46246315	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	339	588	0	ENST00000334344.6:c.4409C>A	p.Ser1470Ter	p.S1470*	ENST00000334344	NM_152641.2	1470	tCa/tAa	15/21	0.730476770297308	1	FACETS	0.982	0.94	1	0.982	0.94	1	CLONAL	1	TRUE	0	0.730476770297308	1		588	600	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415848	49415848	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	619	875	0	ENST00000301067.7:c.16499G>T	p.Arg5500Leu	p.R5500L	ENST00000301067	NM_003482.3	5500	cGg/cTg	53/54	0.696041174351314	2	FACETS	0.921	0.895	0.946	0.921	0.895	0.946	CLONAL	2	TRUE	0	0.730476770297308	2		875	920	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861998	57861998	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	796	1005	0	ENST00000228682.2:c.1299G>T	p.Glu433Asp	p.E433D	ENST00000228682	NM_005269.2	433	gaG/gaT	10/12	0.696041174351314	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.730476770297308	2		1005	1080	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858348	9858348	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	471	585	0	ENST00000330684.3:c.3053T>A	p.Val1018Glu	p.V1018E	ENST00000330684	NM_001134407.1	1018	gTg/gAg	13/13	0.730476770297308	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.730476770297308	2		585	644	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556073	29556073	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	303	417	0	ENST00000356175.3:c.2440A>T	p.Lys814Ter	p.K814*	ENST00000356175	NM_000267.3	814	Aag/Tag	21/57	0.730476770297308	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.730476770297308	1		417	476	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39570424	39570424	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	416	441	1	ENST00000262039.4:c.620G>T	p.Ser207Ile	p.S207I	ENST00000262039	NM_002647.2	207	aGt/aTt	6/25	0.700816600646801	2	FACETS	0.951	0.92	0.981	0.951	0.92	0.981	CLONAL	2	TRUE	0	0.730476770297308	2		442	599	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191227	2191227	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	897	817	2	ENST00000398665.3:c.481G>T	p.Asp161Tyr	p.D161Y	ENST00000398665	NM_032482.2	161	Gac/Tac	5/28	0.157107227911432	3	FACETS	0.973	0.954	0.991			1	INDETERMINATE	3	TRUE	NA	0.730476770297308	3		819	1149	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026137	36026137	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	571	842	1	ENST00000358208.4:c.739G>T	p.Val247Leu	p.V247L	ENST00000358208		247	Gtg/Ttg	7/12	0.288727892014226	4	FACETS	0.921	0.886	0.958	0.921	0.886	0.958	INDETERMINATE	2	TRUE	2	0.730476770297308	4		843	1468	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40864893	40864893	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	532	676	0	ENST00000373198.4:c.2375A>T	p.Asn792Ile	p.N792I	ENST00000373198	NM_133170.3	792	aAt/aTt	16/32	0.288727892014226	4	FACETS	0.907	0.87	0.944	0.907	0.87	0.944	INDETERMINATE	2	TRUE	2	0.730476770297308	4		676	1390	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306757	41306757	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	343	521	0	ENST00000373198.4:c.902G>C	p.Gly301Ala	p.G301A	ENST00000373198	NM_133170.3	301	gGg/gCg	7/32	0.288727892014226	4	FACETS	0.93	0.883	0.977	0.93	0.883	0.977	INDETERMINATE	2	TRUE	2	0.730476770297308	4		521	874	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242903	142242904	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	420	737	1	ENST00000350721.4:c.4083_4084delinsTT	p.Leu1361_Gly1362delinsPheTrp	p.L1361_G1362delinsFW	ENST00000350721	NM_001184.3	1361	ttGGgg/ttTTgg	22/47	1	2	FACETS	0.974	0.929	1	0.974	0.929	1	CLONAL	1	TRUE	1	0.730476770297308	2		738	1181	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155365	47155365	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	115	660	3	ENST00000409792.3:c.4715+1G>A		p.X1572_splice	ENST00000409792	NM_014159.6	1572			1	2	FACETS	0.289	0.259	0.32	0.289	0.259	0.32	SUBCLONAL	1	TRUE	1	0.730476770297308	2		663	1090	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956509	93956509	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0003562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	850	866	0	ENST00000369303.4:c.2726+1G>T		p.X909_splice	ENST00000369303	NM_004440.3	909			0.730476770297308	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.730476770297308	2		866	1107	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	100	769	0				ENST00000310581	NM_198253.2	-/1132			0.252476265968505	4	FACETS	0.981	0.892	1	1	0.988	1	CLONAL	4	TRUE	2	0.26	4		769	247	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	26	638	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.957	0.763	1	0.957	0.763	1	CLONAL	1	TRUE	1	0.26	2		639	209	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	9	764	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.126597311207849	3	FACETS	0.317	0.209	0.455			1	INDETERMINATE	1	TRUE	NA	0.26	3		764	247	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650109	93650109	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	35	320	0	ENST00000375746.1:c.1660G>A	p.Asp554Asn	p.D554N	ENST00000375746	NM_001174167.1	554	Gat/Aat	12/14	1	2	FACETS	0.501	0.41	0.604	0.501	0.41	0.604	SUBCLONAL	1	TRUE	1	0.26	2		320	537	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480341	56480341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	37	288	0	ENST00000267101.3:c.448G>A	p.Glu150Lys	p.E150K	ENST00000267101	NM_001982.3	150	Gag/Aag	4/28	1	2	FACETS	0.737	0.609	0.881	0.737	0.609	0.881	SUBCLONAL	1	TRUE	1	0.26	2		288	386	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363243	40363243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	38	237	0	ENST00000397332.2:c.986C>T	p.Ser329Leu	p.S329L	ENST00000397332	NM_001033082.2	329	tCg/tTg	3/3	1	2	FACETS	0.883	0.732	1	0.883	0.732	1	CLONAL	1	TRUE	1	0.26	2		237	331	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567800	226567800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1389888337	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	26	284	0	ENST00000366794.5:c.1366G>A	p.Glu456Lys	p.E456K	ENST00000366794	NM_001618.3	456	Gag/Aag	10/23	0.137773833151517	3	FACETS	0.604	0.478	0.749	0.302	0.239	0.375	INDETERMINATE	1	TRUE	1	0.26	3		284	374	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645639	215645639	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	36	265	0	ENST00000260947.4:c.959G>A	p.Gly320Glu	p.G320E	ENST00000260947	NM_000465.2	320	gGa/gAa	4/11	1	2	FACETS	0.757	0.623	0.906	0.757	0.623	0.906	CLONAL	1	TRUE	1	0.26	2		265	366	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053566	37053566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	38	303	0	ENST00000231790.2:c.653C>T	p.Ser218Phe	p.S218F	ENST00000231790	NM_000249.3	218	tCc/tTc	8/19	1	2	FACETS	0.688	0.569	0.82	0.688	0.569	0.82	SUBCLONAL	1	TRUE	1	0.26	2		303	425	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125533	47125533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	43	372	0	ENST00000409792.3:c.5737G>A	p.Glu1913Lys	p.E1913K	ENST00000409792	NM_014159.6	1913	Gaa/Aaa	12/21	0.270539651690956	1	FACETS	0.607	0.508	0.717	0.607	0.508	0.717	SUBCLONAL	1	TRUE	0	0.26	1		372	474	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157491	106157491	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777279382	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	25	213	0	ENST00000380013.4:c.2392G>A	p.Glu798Lys	p.E798K	ENST00000380013	NM_001127208.2	798	Gag/Aag	3/11	1	2	FACETS	0.521	0.41	0.649	0.521	0.41	0.649	SUBCLONAL	1	TRUE	1	0.26	2		213	369	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876382	35876382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1283489708	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	46	236	0	ENST00000303115.3:c.1174G>A	p.Glu392Lys	p.E392K	ENST00000303115	NM_002185.3	392	Gag/Aag	8/8	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.26	2		236	344	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562804	176562804	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771968592	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	39	283	0	ENST00000439151.2:c.700G>A	p.Glu234Lys	p.E234K	ENST00000439151	NM_022455.4	234	Gaa/Aaa	2/23	1	2	FACETS	0.901	0.749	1	0.901	0.749	1	CLONAL	1	TRUE	1	0.26	2		283	333	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638668	176638668	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	31	227	0	ENST00000439151.2:c.3268C>A	p.Pro1090Thr	p.P1090T	ENST00000439151	NM_022455.4	1090	Ccc/Acc	5/23	1	2	FACETS	0.693	0.561	0.842	0.693	0.561	0.842	SUBCLONAL	1	TRUE	1	0.26	2		227	344	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502163	157502163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	49	236	0	ENST00000346085.5:c.3196G>A	p.Glu1066Lys	p.E1066K	ENST00000346085	NM_020732.3	1066	Gag/Aag	12/20	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.26	2		236	376	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750924	128750924	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	42	272	0	ENST00000377970.2:c.461C>T	p.Ser154Leu	p.S154L	ENST00000377970	NM_002467.4	154	tCg/tTg	2/3	0.3	3	FACETS	0.765	0.639	0.906			1	CLONAL	1	TRUE	NA	0.26	3		272	477	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430541	80430541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	32	131	0	ENST00000286548.4:c.467C>T	p.Ser156Phe	p.S156F	ENST00000286548	NM_002072.3	156	tCt/tTt	3/7	1	2	FACETS	0.898	0.732	1	0.898	0.732	1	CLONAL	1	TRUE	1	0.26	2		131	274	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904914	101904914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	30	245	0	ENST00000374994.4:c.902G>A	p.Gly301Glu	p.G301E	ENST00000374994	NM_004612.2	301	gGa/gAa	5/9	1	2	FACETS	0.514	0.414	0.628	0.514	0.414	0.628	SUBCLONAL	1	TRUE	1	0.26	2		245	449	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759700	133759700	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	28	198	0	ENST00000318560.5:c.2023G>A	p.Glu675Lys	p.E675K	ENST00000318560	NM_005157.4	675	Gag/Aag	11/11	0.150270855894261	0	FACETS	0.852	0.687	1			1	INDETERMINATE	1	TRUE	0	0.26	0		198	187	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623699	43623699	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	51	252	0	ENST00000355710.3:c.3327G>T	p.Met1109Ile	p.M1109I	ENST00000355710	NM_020975.4	1109	atG/atT	20/20	0.3	3	FACETS	1	0.91	1			1	CLONAL	1	TRUE	NA	0.26	3		252	404	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285666	46285666	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	50	242	1	ENST00000334344.6:c.5026C>T	p.Gln1676Ter	p.Q1676*	ENST00000334344	NM_152641.2	1676	Cag/Tag	17/21	1	2	FACETS	0.971	0.826	1	0.971	0.826	1	CLONAL	1	TRUE	1	0.26	2		243	396	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28611388	28611388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	52	386	0	ENST00000241453.7:c.1243G>A	p.Glu415Lys	p.E415K	ENST00000241453	NM_004119.2	415	Gaa/Aaa	10/24	NA	2	FACETS	0.805	0.686	0.935			1	INDETERMINATE	1	TRUE	NA	0.26	2		386	497	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988856	41988856	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	66	682	0	ENST00000219905.7:c.1648C>T	p.Gln550Ter	p.Q550*	ENST00000219905	NM_001164273.1	550	Cag/Tag	3/24	0.3	0	FACETS	0.667	0.58	0.762			1	SUBCLONAL	1	TRUE	0	0.26	0		682	563	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788674	3788674	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	29	226	0	ENST00000262367.5:c.4281-1G>A		p.X1427_splice	ENST00000262367	NM_004380.2	1427			0.214727294363302	1	FACETS	0.674	0.542	0.823	0.674	0.542	0.823	SUBCLONAL	1	TRUE	0	0.26	1		226	288	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619264	23619264	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs864622138	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	45	376	0	ENST00000261584.4:c.3271C>T	p.Gln1091Ter	p.Q1091*	ENST00000261584	NM_024675.3	1091	Cag/Tag	12/13	NA	2	FACETS	0.774	0.651	0.91			1	INDETERMINATE	1	TRUE	NA	0.26	2		376	447	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56792478	56792478	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	42	432	0	ENST00000308159.5:c.208G>A	p.Asp70Asn	p.D70N	ENST00000308159	NM_014669.4	70	Gac/Aac	3/22	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.26	NA		432	489	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828205	72828205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	58	549	1	ENST00000268489.5:c.8376G>A	p.Met2792Ile	p.M2792I	ENST00000268489	NM_006885.3	2792	atG/atA	9/10	0.150270855894261	0	FACETS	0.512	0.439	0.591			1	INDETERMINATE	1	TRUE	0	0.26	0		550	645	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993237	72993237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567606533	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	66	670	0	ENST00000268489.5:c.808G>A	p.Asp270Asn	p.D270N	ENST00000268489	NM_006885.3	270	Gat/Aat	2/10	0.150270855894261	0	FACETS	0.624	0.542	0.713			1	INDETERMINATE	1	TRUE	0	0.26	0		670	602	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619289	37619289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	37	124	0	ENST00000447079.4:c.965G>A	p.Arg322Gln	p.R322Q	ENST00000447079	NM_015083.1	322	cGa/cAa	1/14	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.26	2		124	274	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40478160	40478160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	62	447	0	ENST00000264657.5:c.1339C>T	p.His447Tyr	p.H447Y	ENST00000264657	NM_139276.2	447	Cac/Tac	15/24	0.3	1	FACETS	0.763	0.659	0.875	0.763	0.659	0.875	SUBCLONAL	1	TRUE	0	0.26	1		447	544	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677792	47677792	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	42	262	0	ENST00000347630.2:c.1073C>T	p.Ser358Leu	p.S358L	ENST00000347630	NM_001007230.1	358	tCa/tTa	11/11	1	2	FACETS	0.852	0.713	1	0.852	0.713	1	CLONAL	1	TRUE	1	0.26	2		262	379	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267597	7267597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	46	261	0	ENST00000302850.5:c.411G>A	p.Met137Ile	p.M137I	ENST00000302850	NM_000208.2	137	atG/atA	2/22	0.218448811738415	1	FACETS	0.749	0.632	0.878	0.749	0.632	0.878	SUBCLONAL	1	TRUE	0	0.26	1		261	411	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952217	17952217	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	32	207	0	ENST00000458235.1:c.1123C>T	p.Gln375Ter	p.Q375*	ENST00000458235	NM_000215.3	375	Cag/Tag	8/24	0.218448811738415	1	FACETS	0.843	0.688	1	0.843	0.688	1	CLONAL	1	TRUE	0	0.26	1		207	254	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953330	17953330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	40	237	0	ENST00000458235.1:c.656G>A	p.Arg219Lys	p.R219K	ENST00000458235	NM_000215.3	219	aGa/aAa	6/24	0.218448811738415	1	FACETS	0.804	0.67	0.952	0.804	0.67	0.952	CLONAL	1	TRUE	0	0.26	1		237	333	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871992	45871992	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	30	280	0	ENST00000391945.4:c.256G>C	p.Glu86Gln	p.E86Q	ENST00000391945	NM_000400.3	86	Gag/Cag	5/23	0.218448811738415	1	FACETS	0.749	0.606	0.91	0.749	0.606	0.91	CLONAL	1	TRUE	0	0.26	1		280	268	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206804	36206804	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	29	137	0	ENST00000300305.3:c.708G>A	p.Met236Ile	p.M236I	ENST00000300305		236	atG/atA	6/8	0.12541250541141	4	FACETS	1	0.876	1	0.56	0.451	0.682	INDETERMINATE	1	TRUE	2	0.26	4		137	251	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175881	24175881	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	42	208	0	ENST00000263121.7:c.1109G>C	p.Arg370Thr	p.R370T	ENST00000263121	NM_003073.3	370	aGg/aCg	8/9	1	2	FACETS	0.997	0.836	1	0.997	0.836	1	CLONAL	1	TRUE	1	0.26	2		208	324	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106297	27106303	+	frameshift_variant	Frame_Shift_Del	DEL	CTTCTGG	CTTCTGG	-	novel	NA	P-0003566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	40	252	0	ENST00000324856.7:c.5908_5914del	p.Leu1970ThrfsTer43	p.L1970Tfs*43	ENST00000324856	NM_006015.4	1970	CTTCTGGac/ac	20/20	1	2	FACETS	0.781	0.65	0.926	0.781	0.65	0.926	CLONAL	1	TRUE	1	0.26	2		252	394	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0003596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	33	769	0				ENST00000310581	NM_198253.2	-/1132			0.435271742903098	5	FACETS	1	0.893	1	0.733	0.61	0.864	CLONAL	2	FALSE	2	0.435271742903098	5		769	114	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0003596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	86	197	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	NA	2	FACETS	0.8	0.719	0.884			1	INDETERMINATE	2	FALSE	NA	0.435271742903098	2		197	247	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555525857	NA	P-0003596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	111	701	1	ENST00000269305.4:c.596G>A	p.Gly199Glu	p.G199E	ENST00000269305	NM_001126112.2	199	gGa/gAa	6/11	0.24487742803949	3	FACETS	0.95	0.864	1	0.633	0.576	0.692	INDETERMINATE	2	FALSE	0	0.435271742903098	3		702	327	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0003596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	60	404	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	0.325348123022316	5	FACETS	0.942	0.813	1	0.314	0.271	0.361	CLONAL	1	FALSE	2	0.435271742903098	5		404	484	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787846	135787846	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs118203440	NA	P-0003596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	98	201	0	ENST00000298552.3:c.738-2A>G		p.X246_splice	ENST00000298552	NM_001162426.1	246			0.272068237780173	3	FACETS	1	0.971	1	0.781	0.71	0.853	CLONAL	2	FALSE	0	0.435271742903098	3		201	234	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32905128	32905128	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	31	206	0	ENST00000380152.3:c.754G>C	p.Asp252His	p.D252H	ENST00000380152		252	Gac/Cac	9/27	0.255607100409331	2	FACETS	0.455	0.369	0.552	0.228	0.184	0.276	INDETERMINATE	1	FALSE	0	0.435271742903098	2		206	313	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910876	32910876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	92	496	0	ENST00000380152.3:c.2384C>T	p.Ser795Leu	p.S795L	ENST00000380152		795	tCa/tTa	11/27	0.255607100409331	2	FACETS	1	0.944	1	0.542	0.485	0.602	INDETERMINATE	1	FALSE	0	0.435271742903098	2		496	390	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105236697	105236697	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	95	334	0	ENST00000349310.3:c.1424C>T	p.Ser475Leu	p.S475L	ENST00000349310	NM_001014432.1	475	tCg/tTg	15/15	0.336419861894065	2	FACETS	0.814	0.736	0.895	0.814	0.736	0.895	CLONAL	2	FALSE	0	0.435271742903098	2		334	268	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	338239	338239	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	108	391	0	ENST00000262320.3:c.2472C>A	p.Phe824Leu	p.F824L	ENST00000262320	NM_003502.3	824	ttC/ttA	11/11	0.336419861894065	2	FACETS	0.909	0.829	0.99	0.909	0.829	0.99	CLONAL	2	FALSE	0	0.435271742903098	2		391	273	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916248	9916248	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	26	253	0	ENST00000330684.3:c.2041C>G	p.Arg681Gly	p.R681G	ENST00000330684	NM_001134407.1	681	Cga/Gga	10/13	0.336419861894065	2	FACETS	0.574	0.458	0.706	0.287	0.229	0.353	SUBCLONAL	1	FALSE	0	0.435271742903098	2		253	208	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913136	44913136	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	99	214	0	ENST00000377967.4:c.811C>T	p.Gln271Ter	p.Q271*	ENST00000377967	NM_021140.2	271	Cag/Tag	10/29	0.211591759950999	2	FACETS	1	0.917	1			1	INDETERMINATE	2	FALSE	NA	0.435271742903098	2		214	226	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225400316	225400319	+	frameshift_variant	Frame_Shift_Del	DEL	GAAG	GAAG	AAA	novel	NA	P-0003596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	93	311	1	ENST00000264414.4:c.304_307delinsTTT	p.Leu102PhefsTer4	p.L102Ffs*4	ENST00000264414	NM_003590.4	102	CTTCaa/TTTaa	3/16	0.316165466815697	4	FACETS	0.765	0.685	0.849	0.765	0.685	0.849	SUBCLONAL	2	FALSE	2	0.435271742903098	4		312	401	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578417	7578419	+	frameshift_variant	Frame_Shift_Del	DEL	CTC	CTC	TG	novel	NA	P-0003596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	63	221	0	ENST00000269305.4:c.511_513delinsCA	p.Glu171GlnfsTer3	p.E171Qfs*3	ENST00000269305	NM_001126112.2	171	GAG/CA	5/11	0.24487742803949	3	FACETS	0.932	0.822	1	0.622	0.548	0.699	INDETERMINATE	2	FALSE	0	0.435271742903098	3		221	189	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003607-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	50	174	0				ENST00000310581	NM_198253.2	-/1132			0.52880522155943	3	FACETS	1	0.923	1	0.372	0.32	0.429	CLONAL	1	TRUE	0	0.52880522155943	3		174	214	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003607-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	70	638	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.52880522155943	4	FACETS	0.987	0.865	1	0.329	0.288	0.373	CLONAL	1	TRUE	1	0.52880522155943	4		639	410	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257989	16257989	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003607-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	134	222	0	ENST00000375759.3:c.5254G>C	p.Glu1752Gln	p.E1752Q	ENST00000375759	NM_015001.2	1752	Gag/Cag	11/15	0.52880522155943	3	FACETS	0.942	0.858	1	0.471	0.429	0.516	CLONAL	1	TRUE	1	0.52880522155943	3		222	680	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001374	150001374	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003607-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	202	291	0	ENST00000253339.5:c.2230C>T	p.Arg744Ter	p.R744*	ENST00000253339		744	Cga/Tga	4/7	0.52880522155943	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.52880522155943	1		291	543	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285924	38285924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757823218	NA	P-0003607-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	94	210	0	ENST00000425967.3:c.487G>A	p.Asp163Asn	p.D163N	ENST00000425967	NM_001174067.1	163	Gat/Aat	5/19	1	2	FACETS	0.657	0.586	0.732	0.657	0.586	0.732	SUBCLONAL	1	TRUE	1	0.52880522155943	2		210	541	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867720	45867720	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150708456	NA	P-0003607-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	322	334	1	ENST00000391945.4:c.680G>A	p.Arg227His	p.R227H	ENST00000391945	NM_000400.3	227	cGc/cAc	8/23	0.52880522155943	4	FACETS	1	0.971	1	0.69	0.654	0.727	CLONAL	2	TRUE	1	0.52880522155943	4		335	899	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0003610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	45	586	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.607	0.511	0.713	0.607	0.511	0.713	SUBCLONAL	1	TRUE	1	0.36	2		586	412	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	20	174	0				ENST00000310581	NM_198253.2	-/1132			0.216554685561533	1	FACETS	1	0.836	1	1	0.836	1	CLONAL	1	TRUE	0	0.36	1		174	84	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0003610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	181	670	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.36	2		670	833	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0003610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	100	405	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	1	2	FACETS	0.943	0.844	1	0.943	0.844	1	CLONAL	1	TRUE	1	0.36	2		405	589	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539564	187539564	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	70	284	0	ENST00000441802.2:c.8176C>T	p.Arg2726Ter	p.R2726*	ENST00000441802	NM_005245.3	2726	Cga/Tga	10/27	0.281104824701478	0	FACETS	0.741	0.65	0.837			1	SUBCLONAL	1	TRUE	0	0.36	0		284	336	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0003610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	43	196	1	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.216554685561533	1	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	0	0.36	1		197	193	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413214	139413214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	60	350	0	ENST00000277541.6:c.928G>A	p.Gly310Arg	p.G310R	ENST00000277541	NM_017617.3	310	Ggg/Agg	6/34	1	2	FACETS	0.705	0.608	0.809	0.705	0.608	0.809	SUBCLONAL	1	TRUE	1	0.36	2		350	473	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797480	45797480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	29	326	0	ENST00000450313.1:c.1039G>A	p.Glu347Lys	p.E347K	ENST00000450313	NM_012222.2	347	Gag/Aag	12/16	0.166979401773563	2	FACETS	0.397	0.318	0.486	0.198	0.159	0.243	INDETERMINATE	1	TRUE	0	0.36	2		326	406	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29115390	29115390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	112	425	0	ENST00000328354.6:c.676C>T	p.Leu226Phe	p.L226F	ENST00000328354	NM_007194.3	226	Ctt/Ttt	5/15	1	2	FACETS	0.823	0.74	0.91	0.823	0.74	0.91	CLONAL	1	TRUE	1	0.36	2		425	756	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111048	193111048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	84	257	0	ENST00000367435.3:c.581G>A	p.Arg194Lys	p.R194K	ENST00000367435	NM_024529.4	194	aGa/aAa	7/17	0.166979401773563	2	FACETS	1	0.89	1	0.502	0.445	0.562	INDETERMINATE	1	TRUE	0	0.36	2		257	465	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172115	99172115	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	35	285	0	ENST00000074304.5:c.1681G>A	p.Asp561Asn	p.D561N	ENST00000074304	NM_001134224.1	561	Gat/Aat	17/26	0.185035939546548	1	FACETS	0.48	0.394	0.576	0.48	0.394	0.576	INDETERMINATE	1	TRUE	0	0.36	1		285	332	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027146	71027146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	78	215	0	ENST00000318789.4:c.1181C>T	p.Ser394Phe	p.S394F	ENST00000318789	NM_032682.5	394	tCc/tTc	15/21	0.3	3	FACETS	1	0.971	1			1	CLONAL	1	TRUE	NA	0.36	3		215	385	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149436923	149436923	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	85	298	0	ENST00000286301.3:c.2246C>T	p.Pro749Leu	p.P749L	ENST00000286301	NM_005211.3	749	cCc/cTc	17/22	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.36	2		298	400	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38283733	38283733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	97	348	0	ENST00000425967.3:c.745G>A	p.Asp249Asn	p.D249N	ENST00000425967	NM_001174067.1	249	Gac/Aac	7/19	0.25675424291022	3	FACETS	1	0.942	1	0.541	0.483	0.602	CLONAL	1	TRUE	1	0.36	3		348	588	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624597	93624597	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	95	344	0	ENST00000375746.1:c.688G>T	p.Glu230Ter	p.E230*	ENST00000375746	NM_001174167.1	230	Gag/Tag	4/14	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.36	2		344	430	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066830	77066830	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs150302040	NA	P-0003610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	78	353	0	ENST00000356341.3:c.655A>G	p.Thr219Ala	p.T219A	ENST00000356341	NM_002576.4	219	Aca/Gca	7/15	1	2	FACETS	0.816	0.719	0.92	0.816	0.719	0.92	CLONAL	1	TRUE	1	0.36	2		353	531	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244572	46244572	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	102	309	0	ENST00000334344.6:c.2666C>A	p.Ser889Ter	p.S889*	ENST00000334344	NM_152641.2	889	tCa/tAa	15/21	0.25675424291022	3	FACETS	1	0.968	1	0.602	0.54	0.668	CLONAL	1	TRUE	1	0.36	3		309	555	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245027	46245027	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	89	449	0	ENST00000334344.6:c.3121C>T	p.Gln1041Ter	p.Q1041*	ENST00000334344	NM_152641.2	1041	Caa/Taa	15/21	0.25675424291022	3	FACETS	0.96	0.852	1	0.48	0.426	0.537	CLONAL	1	TRUE	1	0.36	3		449	608	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3827656	3827656	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	67	295	0	ENST00000262367.5:c.2116G>A	p.Gly706Arg	p.G706R	ENST00000262367	NM_004380.2	706	Gga/Aga	11/31	0.166979401773563	2	FACETS	0.764	0.666	0.871	0.382	0.333	0.436	INDETERMINATE	1	TRUE	0	0.36	2		295	487	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681015	37681015	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	93	349	0	ENST00000447079.4:c.3184C>T	p.Pro1062Ser	p.P1062S	ENST00000447079	NM_015083.1	1062	Cca/Tca	12/14	1	2	FACETS	0.914	0.815	1	0.914	0.815	1	CLONAL	1	TRUE	1	0.36	2		349	565	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7174624	7174624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771406570	NA	P-0003610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	76	420	0	ENST00000302850.5:c.1093G>A	p.Gly365Arg	p.G365R	ENST00000302850	NM_000208.2	365	Ggg/Agg	4/22	0.3	1	FACETS	0.697	0.613	0.787	0.697	0.613	0.787	SUBCLONAL	1	TRUE	0	0.36	1		420	497	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745208	41745208	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	97	355	0	ENST00000301178.4:c.1274C>A	p.Ala425Asp	p.A425D	ENST00000301178	NM_021913.4	425	gCc/gAc	9/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.36	2		355	456	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027098	71027099	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0003610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	58	192	0	ENST00000318789.4:c.1228_1229delinsTT	p.Pro410Leu	p.P410L	ENST00000318789	NM_032682.5	410	CCa/TTa	15/21	0.3	3	FACETS	1	0.929	1			1	CLONAL	1	TRUE	NA	0.36	3		192	339	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177558	56177559	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0003610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	93	422	0	ENST00000399503.3:c.2531_2532delinsTT	p.Ser844Phe	p.S844F	ENST00000399503	NM_005921.1	844	tCC/tTT	14/20	1	2	FACETS	0.91	0.811	1	0.91	0.811	1	CLONAL	1	TRUE	1	0.36	2		422	568	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17380491	17380492	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0003610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	117	407	0	ENST00000375499.3:c.23_24delinsTT	p.Ser8Phe	p.S8F	ENST00000375499	NM_003000.2	8	tCC/tTT	1/8	0.166979401773563	2	FACETS	1	0.985	1	0.732	0.665	0.802	INDETERMINATE	1	TRUE	0	0.36	2		407	444	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	60	174	0				ENST00000310581	NM_198253.2	-/1132			0.701039393555194	3	FACETS	0.917	0.817	1	0.917	0.817	1	CLONAL	2	TRUE	1	0.701039393555194	3		174	126	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340444	8340444	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	144	350	0	ENST00000356435.5:c.5152C>T	p.Gln1718Ter	p.Q1718*	ENST00000356435		1718	Cag/Tag	31/35	0.701039393555194	4	FACETS	1	0.947	1	0.262	0.24	0.286	CLONAL	1	TRUE	0	0.701039393555194	4		350	666	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370786	225370786	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	311	286	1	ENST00000264414.4:c.1093C>G	p.Leu365Val	p.L365V	ENST00000264414	NM_003590.4	365	Ctc/Gtc	8/16	0.701039393555194	4	FACETS	0.932	0.883	0.981	0.932	0.883	0.981	CLONAL	2	TRUE	2	0.701039393555194	4		287	810	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047906	180047906	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	97	261	0	ENST00000261937.6:c.2269G>A	p.Val757Ile	p.V757I	ENST00000261937	NM_182925.4	757	Gtc/Atc	15/30	0.701039393555194	3	FACETS	0.925	0.831	1	0.463	0.415	0.512	CLONAL	1	TRUE	1	0.701039393555194	3		261	404	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273049	55273049	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	309	374	0	ENST00000275493.2:c.3372C>G	p.His1124Gln	p.H1124Q	ENST00000275493	NM_005228.3	1124	caC/caG	28/28	0.701039393555194	6	FACETS	1	0.968	1	0.518	0.489	0.548	CLONAL	2	TRUE	2	0.701039393555194	6		374	1022	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135800973	135800973	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs118203372	NA	P-0003693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	256	275	0	ENST00000298552.3:c.363+1G>A		p.X121_splice	ENST00000298552	NM_001162426.1	121			NA	2	FACETS	1	0.975	1			1	INDETERMINATE	2	TRUE	NA	0.701039393555194	2		275	357	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720650	89720650	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0003693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	69	61	0	ENST00000371953.3:c.802-1G>C		p.X268_splice	ENST00000371953	NM_000314.4	268			0.701039393555194	2	FACETS	0.834	0.757	0.91	0.834	0.757	0.91	CLONAL	2	TRUE	0	0.701039393555194	2		61	118	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0003694-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	36	769	0				ENST00000310581	NM_198253.2	-/1132			0.353546357857817	1	FACETS	0.735	0.63	0.84	0.735	0.63	0.84	INDETERMINATE	1	TRUE	0	0.77782597457461	1		769	77	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056132	26056132	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003694-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	208	254	0	ENST00000343677.2:c.525G>C	p.Lys175Asn	p.K175N	ENST00000343677	NM_005319.3	175	aaG/aaC	1/1	0.368275675902683	3	FACETS	0.813	0.763	0.862	0.813	0.763	0.862	INDETERMINATE	2	TRUE	1	0.77782597457461	3		254	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs985033810	NA	P-0003694-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	256	244	0	ENST00000269305.4:c.731G>T	p.Gly244Val	p.G244V	ENST00000269305	NM_001126112.2	244	gGc/gTc	7/11	0.77782597457461	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.77782597457461	2		244	323	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553703	29553703	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1555613843	NA	P-0003694-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	63	180	0	ENST00000356175.3:c.2251+1G>A		p.X751_splice	ENST00000356175	NM_000267.3	751			0.77782597457461	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.77782597457461	1		180	95	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0003700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	147	404	0	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	1	2	FACETS	0.927	0.844	1	0.927	0.844	1	CLONAL	1	TRUE	1	0.244944421723028	2		404	1295	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0003700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	42	349	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.244944421723028	2		351	305	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69230462	69230462	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	45	360	0	ENST00000462284.1:c.851T>A	p.Val284Asp	p.V284D	ENST00000462284	NM_002392.5	284	gTt/gAt	10/11	1	2	FACETS	0.888	0.747	1	0.888	0.747	1	CLONAL	1	TRUE	1	0.244944421723028	2		360	414	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774162	66774162	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1255	175	586	0	ENST00000307102.5:c.638G>T	p.Gly213Val	p.G213V	ENST00000307102	NM_002755.3	213	gGg/gTg	6/11	1	2	FACETS	0.999	0.917	1	0.999	0.917	1	CLONAL	1	TRUE	1	0.244944421723028	2		586	1430	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	26	174	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.748	0.598	0.915			1	INDETERMINATE	1	TRUE	NA	0.431927807719772	2		174	161	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	181	557	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.431927807719772	3	FACETS	0.756	0.7	0.814	0.756	0.7	0.814	SUBCLONAL	2	TRUE	1	0.431927807719772	3		557	674	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504401	8504401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757922864	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	50	252	0	ENST00000356435.5:c.1682G>A	p.Arg561Gln	p.R561Q	ENST00000356435		561	cGa/cAa	12/35	1	2	FACETS	0.665	0.567	0.773	0.665	0.567	0.773	SUBCLONAL	1	TRUE	1	0.431927807719772	2		252	348	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	91	306	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	1	2	FACETS	0.841	0.749	0.938	0.841	0.749	0.938	CLONAL	1	TRUE	1	0.431927807719772	2		306	501	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230571	46230571	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	192	374	0	ENST00000334344.6:c.820C>T	p.Arg274Ter	p.R274*	ENST00000334344	NM_152641.2	274	Cga/Tga	8/21	0.431927807719772	3	FACETS	0.911	0.848	0.976	0.911	0.848	0.976	CLONAL	2	TRUE	1	0.431927807719772	3		374	593	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741917	145741917	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	64	361	0	ENST00000428558.2:c.586A>G	p.Ser196Gly	p.S196G	ENST00000428558	NM_004260.3	196	Agt/Ggt	5/22	1	2	FACETS	0.879	0.766	1	0.879	0.766	1	CLONAL	1	TRUE	1	0.431927807719772	2		361	337	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599333	55599333	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913682	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	68	370	1	ENST00000288135.5:c.2459A>T	p.Asp820Val	p.D820V	ENST00000288135	NM_000222.2	820	gAt/gTt	17/21	1	2	FACETS	0.564	0.491	0.643	0.564	0.491	0.643	SUBCLONAL	1	TRUE	1	0.431927807719772	2		371	558	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088663	27088663	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	73	430	0	ENST00000324856.7:c.2272C>T	p.Gln758Ter	p.Q758*	ENST00000324856	NM_006015.4	758	Cag/Tag	7/20	1	2	FACETS	0.654	0.573	0.741	0.654	0.573	0.741	SUBCLONAL	1	TRUE	1	0.431927807719772	2		430	517	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363439	40363439	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	59	405	0	ENST00000397332.2:c.790C>T	p.Gln264Ter	p.Q264*	ENST00000397332	NM_001033082.2	264	Caa/Taa	3/3	1	2	FACETS	0.717	0.619	0.822	0.717	0.619	0.822	SUBCLONAL	1	TRUE	1	0.431927807719772	2		405	381	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076719	72076719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	88	529	0	ENST00000357731.5:c.778G>A	p.Gly260Arg	p.G260R	ENST00000357731	NM_173808.2	260	Gga/Aga	5/7	0.178298429602696	3	FACETS	0.773	0.685	0.867	0.386	0.342	0.434	INDETERMINATE	1	TRUE	1	0.431927807719772	3		529	641	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465277	120465277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587652462	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	81	357	0	ENST00000256646.2:c.4984C>T	p.Pro1662Ser	p.P1662S	ENST00000256646	NM_024408.3	1662	Cct/Tct	27/34	0.178298429602696	3	FACETS	1	0.95	1	0.566	0.501	0.634	INDETERMINATE	1	TRUE	1	0.431927807719772	3		357	403	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718991	190718991	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	80	322	0	ENST00000441310.2:c.993T>G	p.Asn331Lys	p.N331K	ENST00000441310	NM_000534.4	331	aaT/aaG	9/13	1	2	FACETS	0.641	0.565	0.722	0.641	0.565	0.722	SUBCLONAL	1	TRUE	1	0.431927807719772	2		322	578	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164342	47164342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	102	337	0	ENST00000409792.3:c.1784C>T	p.Ser595Leu	p.S595L	ENST00000409792	NM_014159.6	595	tCa/tTa	3/21	1	2	FACETS	0.819	0.734	0.908	0.819	0.734	0.908	CLONAL	1	TRUE	1	0.431927807719772	2		337	577	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447324	187447324	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	33	237	1	ENST00000232014.4:c.869A>T	p.Asn290Ile	p.N290I	ENST00000232014	NM_001130845.1	290	aAt/aTt	5/10	1	2	FACETS	0.56	0.458	0.674	0.56	0.458	0.674	SUBCLONAL	1	TRUE	1	0.431927807719772	2		238	273	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84388668	84388668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	87	447	0	ENST00000321945.7:c.620G>A	p.Gly207Glu	p.G207E	ENST00000321945	NM_139076.2	207	gGa/gAa	7/9	0.178298429602696	3	FACETS	0.796	0.706	0.893	0.398	0.353	0.447	INDETERMINATE	1	TRUE	1	0.431927807719772	3		447	615	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	256524	256524	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	53	254	0	ENST00000264932.6:c.1984C>T	p.Arg662Cys	p.R662C	ENST00000264932	NM_004168.2	662	Cgc/Tgc	15/15	NA	2	FACETS	0.733	0.628	0.846			1	INDETERMINATE	1	TRUE	NA	0.431927807719772	2		254	335	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871202	35871202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200772681	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	75	376	0	ENST00000303115.3:c.424G>A	p.Gly142Arg	p.G142R	ENST00000303115	NM_002185.3	142	Gga/Aga	4/8	0.178298429602696	3	FACETS	0.747	0.656	0.846	0.374	0.328	0.423	INDETERMINATE	1	TRUE	1	0.431927807719772	3		376	565	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873639	35873639	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1451953167	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	77	447	0	ENST00000303115.3:c.595G>A	p.Ala199Thr	p.A199T	ENST00000303115	NM_002185.3	199	Gca/Aca	5/8	0.178298429602696	3	FACETS	0.778	0.684	0.879	0.389	0.342	0.44	INDETERMINATE	1	TRUE	1	0.431927807719772	3		447	557	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721445	176721445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769699822	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	70	406	0	ENST00000439151.2:c.7076C>T	p.Pro2359Leu	p.P2359L	ENST00000439151	NM_022455.4	2359	cCa/cTa	23/23	1	2	FACETS	0.67	0.585	0.76	0.67	0.585	0.76	SUBCLONAL	1	TRUE	1	0.431927807719772	2		406	484	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665238	117665238	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	62	339	0	ENST00000368508.3:c.4509G>C	p.Leu1503Phe	p.L1503F	ENST00000368508	NM_002944.2	1503	ttG/ttC	27/43	NA	2	FACETS	0.61	0.527	0.698			1	INDETERMINATE	1	TRUE	NA	0.431927807719772	2		339	471	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528906	157528906	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	54	294	0	ENST00000346085.5:c.6631A>G	p.Asn2211Asp	p.N2211D	ENST00000346085	NM_020732.3	2211	Aac/Gac	20/20	1	2	FACETS	0.698	0.599	0.806	0.698	0.599	0.806	SUBCLONAL	1	TRUE	1	0.431927807719772	2		294	358	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983953	2983953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	94	654	0	ENST00000396946.4:c.577G>A	p.Glu193Lys	p.E193K	ENST00000396946	NM_032415.4	193	Gag/Aag	5/25	NA	2	FACETS	0.551	0.49	0.616			1	INDETERMINATE	1	TRUE	NA	0.431927807719772	2		654	790	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729679	41729679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1488698571	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	88	642	0	ENST00000242208.4:c.850G>A	p.Glu284Lys	p.E284K	ENST00000242208	NM_002192.2	284	Gaa/Aaa	3/3	0.431927807719772	3	FACETS	0.799	0.709	0.896	0.4	0.354	0.448	SUBCLONAL	1	TRUE	1	0.431927807719772	3		642	620	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444453	50444453	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	21	149	0	ENST00000331340.3:c.383G>A	p.Gly128Glu	p.G128E	ENST00000331340	NM_006060.4	128	gGg/gAg	4/8	0.431927807719772	3	FACETS	0.473	0.365	0.598	0.236	0.182	0.299	SUBCLONAL	1	TRUE	1	0.431927807719772	3		149	250	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450324	50450324	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	66	354	0	ENST00000331340.3:c.508G>A	p.Glu170Lys	p.E170K	ENST00000331340	NM_006060.4	170	Gag/Aag	5/8	0.431927807719772	3	FACETS	0.74	0.644	0.845	0.37	0.322	0.423	SUBCLONAL	1	TRUE	1	0.431927807719772	3		354	502	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508127	106508127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226250464	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	34	220	0	ENST00000359195.3:c.121G>A	p.Glu41Lys	p.E41K	ENST00000359195	NM_002649.2	41	Gag/Aag	2/11	NA	2	FACETS	0.661	0.544	0.792			1	INDETERMINATE	1	TRUE	NA	0.431927807719772	2		220	238	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878611	151878611	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	51	251	0	ENST00000262189.6:c.6334C>T	p.Pro2112Ser	p.P2112S	ENST00000262189	NM_170606.2	2112	Cct/Tct	36/59	1	2	FACETS	0.72	0.615	0.834	0.72	0.615	0.834	SUBCLONAL	1	TRUE	1	0.431927807719772	2		251	328	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331660	8331660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	79	493	0	ENST00000356435.5:c.5456G>A	p.Gly1819Glu	p.G1819E	ENST00000356435		1819	gGa/gAa	33/35	1	2	FACETS	0.604	0.531	0.681	0.604	0.531	0.681	SUBCLONAL	1	TRUE	1	0.431927807719772	2		493	606	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484287	8484287	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	80	500	0	ENST00000356435.5:c.3245C>T	p.Ser1082Leu	p.S1082L	ENST00000356435		1082	tCa/tTa	19/35	1	2	FACETS	0.669	0.59	0.753	0.669	0.59	0.753	SUBCLONAL	1	TRUE	1	0.431927807719772	2		500	554	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624601	93624601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	58	373	0	ENST00000375746.1:c.692G>A	p.Gly231Glu	p.G231E	ENST00000375746	NM_001174167.1	231	gGa/gAa	4/14	1	2	FACETS	0.712	0.615	0.818	0.712	0.615	0.818	SUBCLONAL	1	TRUE	1	0.431927807719772	2		373	377	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211547	98211547	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	45	300	0	ENST00000331920.6:c.3608G>A	p.Ser1203Asn	p.S1203N	ENST00000331920	NM_000264.3	1203	aGc/aAc	22/24	1	2	FACETS	0.692	0.585	0.81	0.692	0.585	0.81	SUBCLONAL	1	TRUE	1	0.431927807719772	2		300	301	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760960	133760960	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750196179	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	89	599	0	ENST00000318560.5:c.3283C>T	p.Arg1095Trp	p.R1095W	ENST00000318560	NM_005157.4	1095	Cgg/Tgg	11/11	1	2	FACETS	0.796	0.707	0.889	0.796	0.707	0.889	SUBCLONAL	1	TRUE	1	0.431927807719772	2		599	518	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779831	135779831	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	59	398	0	ENST00000298552.3:c.2008C>T	p.Pro670Ser	p.P670S	ENST00000298552	NM_001162426.1	670	Ccc/Tcc	16/23	1	2	FACETS	0.598	0.515	0.687	0.598	0.515	0.687	SUBCLONAL	1	TRUE	1	0.431927807719772	2		398	457	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421568	32421568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267602851	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	50	296	0	ENST00000332351.3:c.1024G>A	p.Asp342Asn	p.D342N	ENST00000332351	NM_024426.4	342	Gat/Aat	6/10	1	2	FACETS	0.706	0.602	0.819	0.706	0.602	0.819	SUBCLONAL	1	TRUE	1	0.431927807719772	2		296	328	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001438	29001438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1473309404	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	39	225	0	ENST00000282397.4:c.1294G>A	p.Glu432Lys	p.E432K	ENST00000282397	NM_002019.4	432	Gaa/Aaa	10/30	1	2	FACETS	0.592	0.493	0.702	0.592	0.493	0.702	SUBCLONAL	1	TRUE	1	0.431927807719772	2		225	305	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457396	67457396	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	107	376	0	ENST00000327367.4:c.370C>T	p.Pro124Ser	p.P124S	ENST00000327367	NM_005902.3	124	Ccc/Tcc	2/9	0.270895647313826	3	FACETS	1	0.978	1	0.655	0.591	0.722	CLONAL	1	TRUE	1	0.431927807719772	3		376	460	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678395	88678395	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	56	525	0	ENST00000360948.2:c.1141A>G	p.Lys381Glu	p.K381E	ENST00000360948	NM_001012338.2	381	Aaa/Gaa	9/19	0.270895647313826	3	FACETS	0.568	0.487	0.657	0.284	0.243	0.329	SUBCLONAL	1	TRUE	1	0.431927807719772	3		525	555	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857857	9857857	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375160358	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	67	448	0	ENST00000330684.3:c.3544G>A	p.Asp1182Asn	p.D1182N	ENST00000330684	NM_001134407.1	1182	Gac/Aac	13/13	1	2	FACETS	0.636	0.554	0.724	0.636	0.554	0.724	SUBCLONAL	1	TRUE	1	0.431927807719772	2		448	488	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508750	29508750	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs770339628	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	95	449	0	ENST00000356175.3:c.677A>C	p.Asn226Thr	p.N226T	ENST00000356175	NM_000267.3	226	aAt/aCt	7/57	1	2	FACETS	0.647	0.576	0.722	0.647	0.576	0.722	SUBCLONAL	1	TRUE	1	0.431927807719772	2		449	680	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763520	59763520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	53	285	0	ENST00000259008.2:c.2582C>T	p.Ser861Phe	p.S861F	ENST00000259008	NM_032043.2	861	tCt/tTt	19/20	1	2	FACETS	0.672	0.576	0.777	0.672	0.576	0.777	SUBCLONAL	1	TRUE	1	0.431927807719772	2		285	365	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78858939	78858939	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	23	346	0	ENST00000306801.3:c.1974G>A	p.Met658Ile	p.M658I	ENST00000306801	NM_020761.2	658	atG/atA	17/34	1	2	FACETS	0.37	0.288	0.464	0.37	0.288	0.464	SUBCLONAL	1	TRUE	1	0.431927807719772	2		346	288	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78882679	78882679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	70	416	0	ENST00000306801.3:c.2470C>T	p.Pro824Ser	p.P824S	ENST00000306801	NM_020761.2	824	Cca/Tca	21/34	1	2	FACETS	0.712	0.623	0.808	0.712	0.623	0.808	SUBCLONAL	1	TRUE	1	0.431927807719772	2		416	455	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210657	2210657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	51	401	0	ENST00000398665.3:c.1154C>T	p.Thr385Ile	p.T385I	ENST00000398665	NM_032482.2	385	aCc/aTc	14/28	1	2	FACETS	0.667	0.569	0.774	0.667	0.569	0.774	SUBCLONAL	1	TRUE	1	0.431927807719772	2		401	354	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247890	10247890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	40	373	0	ENST00000340748.4:c.4312G>A	p.Asp1438Asn	p.D1438N	ENST00000340748		1438	Gat/Aat	36/40	1	2	FACETS	0.522	0.434	0.618	0.522	0.434	0.618	SUBCLONAL	1	TRUE	1	0.431927807719772	2		373	355	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291770	15291770	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	50	299	0	ENST00000263388.2:c.2994+2T>G		p.X998_splice	ENST00000263388	NM_000435.2	998			0.381538119316569	1	FACETS	0.653	0.558	0.756	0.653	0.558	0.756	SUBCLONAL	1	TRUE	0	0.431927807719772	1		299	278	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920302	50920302	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	82	532	0	ENST00000440232.2:c.3068G>A	p.Gly1023Glu	p.G1023E	ENST00000440232	NM_002691.3	1023	gGa/gAa	25/27	1	2	FACETS	0.817	0.723	0.916	0.817	0.723	0.916	CLONAL	1	TRUE	1	0.431927807719772	2		532	465	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46252729	46252729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	121	617	0	ENST00000371998.3:c.158C>T	p.Ser53Phe	p.S53F	ENST00000371998		53	tCt/tTt	4/23	0.281581185662614	1	FACETS	0.603	0.545	0.663	0.603	0.545	0.663	SUBCLONAL	1	TRUE	0	0.431927807719772	1		617	729	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413139	63413139	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1373608390	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	55	170	0	ENST00000330258.3:c.28C>T	p.Gln10Ter	p.Q10*	ENST00000330258	NM_152424.3	10	Cag/Tag	2/2	1	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.431927807719772	1		170	186	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612205	189612206	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	76	420	0	ENST00000264731.3:c.1957_1958delinsTT	p.Pro653Leu	p.P653L	ENST00000264731	NM_003722.4	653	CCa/TTa	14/14	1	2	FACETS	0.763	0.672	0.861	0.763	0.672	0.861	SUBCLONAL	1	TRUE	1	0.431927807719772	2		420	461	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306712	41306713	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0003728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	46	356	0	ENST00000373198.4:c.946_947delinsAA	p.Gly316Lys	p.G316K	ENST00000373198	NM_133170.3	316	GGg/AAg	7/32	0.281581185662614	1	FACETS	0.456	0.385	0.534	0.456	0.385	0.534	SUBCLONAL	1	TRUE	0	0.431927807719772	1		356	366	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0003744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	287	691	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.643225169014881	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.643225169014881	1		691	579	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741879	145741879	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	79	238	0	ENST00000428558.2:c.624C>G	p.Cys208Trp	p.C208W	ENST00000428558	NM_004260.3	208	tgC/tgG	5/22	0.450719549456502	4	FACETS	0.379	0.332	0.429	0.189	0.166	0.215	SUBCLONAL	1	TRUE	2	0.643225169014881	4		238	1066	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865132	57865132	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	158	410	0	ENST00000228682.2:c.2609C>A	p.Pro870His	p.P870H	ENST00000228682	NM_005269.2	870	cCt/cAt	12/12	0.36471986435797	1	FACETS	0.455	0.418	0.494	0.455	0.418	0.494	INDETERMINATE	1	TRUE	0	0.643225169014881	1		410	732	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78617598	78617598	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	69	162	0	ENST00000306801.3:c.336C>G	p.Asn112Lys	p.N112K	ENST00000306801	NM_020761.2	112	aaC/aaG	3/34	0.643225169014881	2	FACETS	0.323	0.281	0.368	0.161	0.14	0.184	SUBCLONAL	1	TRUE	0	0.643225169014881	2		162	665	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252781	10252781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560179619	NA	P-0003744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	61	144	0	ENST00000340748.4:c.3184G>A	p.Val1062Met	p.V1062M	ENST00000340748		1062	Gtg/Atg	29/40	0.344765542746828	2	FACETS	0.386	0.333	0.443	0.193	0.166	0.222	INDETERMINATE	1	TRUE	0	0.643225169014881	2		144	492	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030556	47030722	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAAGGGGAGGAGGAGGAGGAGGAGGAGGATGAGGAGGAGGAGGAGAAGGCCAGTAACATCGTCATGCTGAGGATGCTGCCACAGGCAGCCACTGAGGATGACGTACGTGCCCCCCATGGCCCCGGGCAGGAGGCCAGGCTGGGTCTCCTCCAGGGCCCTCAACTTCT	CAAGGGGAGGAGGAGGAGGAGGAGGAGGATGAGGAGGAGGAGGAGAAGGCCAGTAACATCGTCATGCTGAGGATGCTGCCACAGGCAGCCACTGAGGATGACGTACGTGCCCCCCATGGCCCCGGGCAGGAGGCCAGGCTGGGTCTCCTCCAGGGCCCTCAACTTCT	-	novel	NA	P-0003744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	70	254	0	ENST00000377604.3:c.332_432+66del		p.X111_splice	ENST00000377604	NM_001204468.1	111		4/24	0.583143339166645	1	FACETS	0.32	0.28	0.364	0.32	0.28	0.364	SUBCLONAL	1	TRUE	0	0.643225169014881	1		254	461	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	81	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.809	0.722	0.899	1	0.982	1	CLONAL	2	TRUE	1	0.383746839067389	2		174	261	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0003757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	206	404	0	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	0.225128664610037	3	FACETS	1	0.991	1	0.731	0.679	0.785	INDETERMINATE	1	TRUE	1	0.383746839067389	3		404	875	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0003757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	204	270	1	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	0.225128664610037	3	FACETS	0.781	0.726	0.838	0.781	0.726	0.838	INDETERMINATE	2	TRUE	1	0.383746839067389	3		271	811	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643659	52643659	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	119	208	0	ENST00000394830.3:c.2237A>G	p.Tyr746Cys	p.Y746C	ENST00000394830	NM_018313.4	746	tAc/tGc	17/30	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.383746839067389	2		208	570	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557928	187557928	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	139	329	0	ENST00000441802.2:c.3783C>G	p.Asp1261Glu	p.D1261E	ENST00000441802	NM_005245.3	1261	gaC/gaG	5/27	1	2	FACETS	0.902	0.822	0.987	0.902	0.822	0.987	CLONAL	1	TRUE	1	0.383746839067389	2		329	803	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433667	49433667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	123	287	0	ENST00000301067.7:c.7886C>T	p.Ser2629Phe	p.S2629F	ENST00000301067	NM_003482.3	2629	tCc/tTc	31/54	1	2	FACETS	0.857	0.776	0.943	0.857	0.776	0.943	CLONAL	1	TRUE	1	0.383746839067389	2		287	748	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495044	56495044	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1334721954	NA	P-0003757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	160	338	0	ENST00000267101.3:c.3401C>T	p.Ser1134Phe	p.S1134F	ENST00000267101	NM_001982.3	1134	tCc/tTc	27/28	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.383746839067389	2		338	799	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112250	115112250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1345506334	NA	P-0003757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	68	91	0	ENST00000257566.3:c.1490C>T	p.Pro497Leu	p.P497L	ENST00000257566	NM_016569.3	497	cCc/cTc	7/8	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.383746839067389	2		91	269	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89815155	89815155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376089640	NA	P-0003757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	73	262	0	ENST00000389301.3:c.3260C>T	p.Ser1087Leu	p.S1087L	ENST00000389301	NM_000135.2	1087	tCg/tTg	33/43	0.362078684619009	1	FACETS	0.496	0.434	0.563	0.496	0.434	0.563	SUBCLONAL	1	TRUE	0	0.383746839067389	1		262	620	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047302	128047303	+	missense_variant	Missense_Mutation	DNP	GT	GT	AA	novel	NA	P-0003757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	124	305	0	ENST00000285398.2:c.619_620delinsTT	p.Thr207Phe	p.T207F	ENST00000285398	NM_000122.1	207	ACt/TTt	5/15	0.177408167220021	1	FACETS	0.775	0.702	0.851	0.775	0.702	0.851	INDETERMINATE	1	TRUE	0	0.383746839067389	1		305	674	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0003797-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	80	769	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.994	0.899	1	1	0.989	1	CLONAL	3	TRUE	1	0.31	2		769	173	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0003797-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	99	645	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.895	0.814	0.977	1	0.99	1	CLONAL	3	TRUE	1	0.31	2		645	238	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590927	95590927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003797-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	47	215	0	ENST00000393063.1:c.982G>A	p.Glu328Lys	p.E328K	ENST00000393063	NM_030621.3	328	Gaa/Aaa	9/28	0.134735045496092	3	FACETS	1	0.952	1	0.661	0.562	0.768	INDETERMINATE	1	TRUE	1	0.31	3		215	265	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934645	9934645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1360906241	NA	P-0003797-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	65	184	0	ENST00000330684.3:c.1510C>T	p.Arg504Trp	p.R504W	ENST00000330684	NM_001134407.1	504	Cgg/Tgg	7/13	1	2	FACETS	0.842	0.747	0.94	1	0.985	1	CLONAL	3	TRUE	1	0.31	2		184	166	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111995713	111995727	+	inframe_deletion	In_Frame_Del	DEL	ACTCTTCCTTTGGTG	ACTCTTCCTTTGGTG	-	novel	NA	P-0003797-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	47	338	0	ENST00000368678.4:c.1371_1385del	p.Thr458_Val462del	p.T458_V462del	ENST00000368678		457	gtCACCAAAGGAAGAGTg/gtg	12/13	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.31	NA		338	333	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	73	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.661534595162289	2		174	195	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220274	55220274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15072	8150	449	1	ENST00000275493.2:c.664C>T	p.Arg222Cys	p.R222C	ENST00000275493	NM_005228.3	222	Cgc/Tgc	6/28	0.661534595162289	33	FACETS	0.995	0.984	1			1	CLONAL	12	TRUE	NA	0.661534595162289	33		450	23222	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633888	86633888	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	203	273	0	ENST00000274376.6:c.997G>C	p.Glu333Gln	p.E333Q	ENST00000274376	NM_002890.2	333	Gaa/Caa	5/25	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.661534595162289	2		273	610	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571549	95571549	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	110	290	0	ENST00000393063.1:c.3128T>C	p.Ile1043Thr	p.I1043T	ENST00000393063	NM_030621.3	1043	aTt/aCt	21/28	1	2	FACETS	0.507	0.456	0.561	0.507	0.456	0.561	SUBCLONAL	1	TRUE	1	0.661534595162289	2		290	656	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0003857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	18	349	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.762	0.58	0.972	1	0.91	1	CLONAL	2	TRUE	1	0.190376520394444	2		351	124	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004922	150004922	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	63	531	0	ENST00000253339.5:c.1303C>T	p.Gln435Ter	p.Q435*	ENST00000253339		435	Cag/Tag	3/7	0.190376520394444	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.190376520394444	1		531	551	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695728	117695728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057433609	NA	P-0003857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	87	449	0	ENST00000369458.3:c.709G>A	p.Asp237Asn	p.D237N	ENST00000369458	NM_024626.3	237	Gat/Aat	4/6	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.190376520394444	2		449	636	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987151	69987151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	27	435	0	ENST00000394351.3:c.212C>T	p.Pro71Leu	p.P71L	ENST00000394351	NM_000248.3	71	cCc/cTc	2/9	1	2	FACETS	0.654	0.519	0.807	0.654	0.519	0.807	SUBCLONAL	1	TRUE	1	0.190376520394444	2		435	434	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180049775	180049775	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	37	698	0	ENST00000261937.6:c.1613A>G	p.Asn538Ser	p.N538S	ENST00000261937	NM_182925.4	538	aAc/aGc	12/30	1	2	FACETS	0.597	0.491	0.716	0.597	0.491	0.716	SUBCLONAL	1	TRUE	1	0.190376520394444	2		698	651	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704568	117704568	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1193257514	NA	P-0003857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	84	593	0	ENST00000368508.3:c.2408G>A	p.Trp803Ter	p.W803*	ENST00000368508	NM_002944.2	803	tGg/tAg	16/43	0.190376520394444	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.190376520394444	1		593	657	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864556	57864556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	110	836	0	ENST00000228682.2:c.2033C>T	p.Pro678Leu	p.P678L	ENST00000228682	NM_005269.2	678	cCt/cTt	12/12	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.190376520394444	2		836	867	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934208	48934208	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0003857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	61	483	0	ENST00000267163.4:c.663T>A	p.Cys221Ter	p.C221*	ENST00000267163	NM_000321.2	221	tgT/tgA	7/27	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.190376520394444	2		483	471	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543205	65543205	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	33	483	0	ENST00000358664.4:c.472G>C	p.Glu158Gln	p.E158Q	ENST00000358664	NM_002382.4	158	Gag/Cag	5/5	1	2	FACETS	0.676	0.55	0.819	0.676	0.55	0.819	SUBCLONAL	1	TRUE	1	0.190376520394444	2		483	513	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586089	29586089	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	84	540	0	ENST00000356175.3:c.4309G>C	p.Glu1437Gln	p.E1437Q	ENST00000356175	NM_000267.3	1437	Gaa/Caa	32/57	0.186699559875076	2	FACETS	0.844	0.747	0.947	0.844	0.747	0.947	CLONAL	2	TRUE	0	0.190376520394444	2		540	523	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023634	31023634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	61	579	0	ENST00000375687.4:c.3119C>T	p.Ser1040Phe	p.S1040F	ENST00000375687	NM_015338.5	1040	tCt/tTt	13/13	1	2	FACETS	0.968	0.834	1	0.968	0.834	1	CLONAL	1	TRUE	1	0.190376520394444	2		579	662	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038207	30038207	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0003857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	181	685	0	ENST00000338641.4:c.380T>G	p.Leu127Ter	p.L127*	ENST00000338641	NM_000268.3	127	tTa/tGa	4/16	0.158092540740023	2	FACETS	0.844	0.78	0.91	1	0.985	1	CLONAL	3	TRUE	0	0.190376520394444	2		685	751	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577548	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0003857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	59	433	0	ENST00000269305.4:c.733_734delinsAA	p.Gly245Asn	p.G245N	ENST00000269305	NM_001126112.2	245	GGc/AAc	7/11	0.186699559875076	2	FACETS	0.795	0.686	0.912	0.795	0.686	0.912	CLONAL	2	TRUE	0	0.190376520394444	2		433	390	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	68	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.85	0.754	0.949	0.85	0.754	0.949	CLONAL	1	TRUE	1	0.850881503847459	2		174	188	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	62	638	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.819	0.721	0.92	0.819	0.721	0.92	CLONAL	1	TRUE	1	0.850881503847459	2		639	178	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179197	123179197	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	160	221	0	ENST00000218089.9:c.646C>T	p.Arg216Ter	p.R216*	ENST00000218089	NM_001042749.1	216	Cga/Tga	8/35	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.850881503847459	1		221	200	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0003878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	284	825	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.986	0.933	1	0.986	0.933	1	CLONAL	1	TRUE	1	0.850881503847459	2		825	677	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100436	8100436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1220437638	NA	P-0003878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	315	459	0	ENST00000346208.3:c.410C>T	p.Ser137Leu	p.S137L	ENST00000346208		137	tCg/tTg	3/6	NA	2	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.850881503847459	2		459	725	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879604	37879604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196929947	NA	P-0003878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	255	285	0	ENST00000269571.5:c.1979G>A	p.Gly660Asp	p.G660D	ENST00000269571		660	gGc/gAc	17/27	1	2	FACETS	0.954	0.9	1	0.954	0.9	1	CLONAL	1	TRUE	1	0.850881503847459	2		285	628	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874261	155874261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352822	NA	P-0003878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	145	350	0	ENST00000368323.3:c.270G>A	p.Met90Ile	p.M90I	ENST00000368323	NM_006912.5	90	atG/atA	5/6	1	2	FACETS	0.944	0.873	1	0.944	0.873	1	CLONAL	1	TRUE	1	0.850881503847459	2		350	361	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209108293	209108293	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	162	406	0	ENST00000345146.2:c.556G>C	p.Asp186His	p.D186H	ENST00000345146	NM_005896.2	186	Gat/Cat	6/10	1	2	FACETS	0.909	0.843	0.976	0.909	0.843	0.976	CLONAL	1	TRUE	1	0.850881503847459	2		406	419	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645771	215645771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	113	373	0	ENST00000260947.4:c.827C>T	p.Thr276Ile	p.T276I	ENST00000260947	NM_000465.2	276	aCt/aTt	4/11	1	2	FACETS	0.882	0.806	0.961	0.882	0.806	0.961	CLONAL	1	TRUE	1	0.850881503847459	2		373	301	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562111	176562111	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	154	292	0	ENST00000439151.2:c.7C>G	p.Gln3Glu	p.Q3E	ENST00000439151	NM_022455.4	3	Cag/Gag	2/23	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.850881503847459	2		292	360	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245965	46245965	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	152	341	0	ENST00000334344.6:c.4059G>C	p.Leu1353Phe	p.L1353F	ENST00000334344	NM_152641.2	1353	ttG/ttC	15/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.850881503847459	2		341	337	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350561	89350561	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	166	672	0	ENST00000301030.4:c.2389G>C	p.Glu797Gln	p.E797Q	ENST00000301030	NM_001256183.1	797	Gaa/Caa	9/13	1	2	FACETS	0.893	0.829	0.958	0.893	0.829	0.958	CLONAL	1	TRUE	1	0.850881503847459	2		672	437	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657523	37657523	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	111	350	0	ENST00000447079.4:c.2440G>C	p.Glu814Gln	p.E814Q	ENST00000447079	NM_015083.1	814	Gag/Cag	6/14	1	2	FACETS	0.864	0.788	0.942	0.864	0.788	0.942	CLONAL	1	TRUE	1	0.850881503847459	2		350	302	SUCCESS
YES1	7525	MSKCC	GRCh37	18	747930	747930	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	140	383	0	ENST00000314574.4:c.460C>G	p.Gln154Glu	p.Q154E	ENST00000314574	NM_005433.3	154	Cag/Gag	4/12	0.850881503847459	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.850881503847459	1		383	187	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012660	36012660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	86	88	0	ENST00000358208.4:c.104C>T	p.Ser35Leu	p.S35L	ENST00000358208		35	tCg/tTg	2/12	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.850881503847459	2		88	196	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012765	36012765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	156	134	0	ENST00000358208.4:c.209C>T	p.Ser70Leu	p.S70L	ENST00000358208		70	tCg/tTg	2/12	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.850881503847459	2		134	350	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012780	36012780	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	145	127	0	ENST00000358208.4:c.224C>T	p.Ser75Phe	p.S75F	ENST00000358208		75	tCc/tTc	2/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.850881503847459	2		127	316	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29120997	29120997	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	160	417	1	ENST00000328354.6:c.560C>G	p.Ser187Cys	p.S187C	ENST00000328354	NM_007194.3	187	tCt/tGt	4/15	1	2	FACETS	0.931	0.864	0.999	0.931	0.864	0.999	CLONAL	1	TRUE	1	0.850881503847459	2		418	404	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295705	212295705	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	122	446	2	ENST00000342788.4:c.2608G>A	p.Gly870Arg	p.G870R	ENST00000342788	NM_005235.2	870	Gga/Aga	21/28	0.256045738384849	3	FACETS	1	0.976	1	0.627	0.567	0.69	CLONAL	1	TRUE	1	0.306478561731129	3		448	732	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	147	430	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.256045738384849	3	FACETS	0.758	0.693	0.825	0.758	0.693	0.825	SUBCLONAL	2	TRUE	1	0.306478561731129	3		431	730	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988856	41988856	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	120	682	0	ENST00000219905.7:c.1648C>T	p.Gln550Ter	p.Q550*	ENST00000219905	NM_001164273.1	550	Cag/Tag	3/24	0.241844568593652	1	FACETS	0.655	0.59	0.723	0.655	0.59	0.723	SUBCLONAL	1	TRUE	0	0.306478561731129	1		682	1013	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451914	29451914	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	117	308	0	ENST00000389048.3:c.2651A>T	p.Asn884Ile	p.N884I	ENST00000389048	NM_004304.4	884	aAt/aTt	16/29	0.256045738384849	3	FACETS	1	0.984	1	0.735	0.665	0.809	CLONAL	1	TRUE	1	0.306478561731129	3		308	599	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703632	47703632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138465383	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	149	373	0	ENST00000233146.2:c.2132G>A	p.Arg711Gln	p.R711Q	ENST00000233146	NM_000251.2	711	cGa/cAa	13/16	0.256045738384849	3	FACETS	0.803	0.735	0.874	0.803	0.735	0.874	CLONAL	2	TRUE	1	0.306478561731129	3		373	698	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136309	202136309	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	63	343	0	ENST00000358485.4:c.553G>T	p.Glu185Ter	p.E185*	ENST00000358485	NM_001080125.1	185	Gag/Tag	3/9	0.256045738384849	3	FACETS	0.667	0.576	0.766	0.333	0.288	0.383	SUBCLONAL	1	TRUE	1	0.306478561731129	3		343	711	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149778	202149778	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1242650624	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	149	400	1	ENST00000358485.4:c.1219C>T	p.Leu407Phe	p.L407F	ENST00000358485	NM_001080125.1	407	Ctt/Ttt	8/9	0.256045738384849	3	FACETS	1	0.987	1	0.742	0.678	0.808	CLONAL	1	TRUE	1	0.306478561731129	3		401	756	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652831	212652831	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	142	419	0	ENST00000342788.4:c.475G>T	p.Asp159Tyr	p.D159Y	ENST00000342788	NM_005235.2	159	Gac/Tac	4/28	0.256045738384849	3	FACETS	1	0.984	1	0.685	0.625	0.748	CLONAL	1	TRUE	1	0.306478561731129	3		419	780	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067486	37067486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	46	206	0	ENST00000231790.2:c.1397C>T	p.Ser466Phe	p.S466F	ENST00000231790	NM_000249.3	466	tCc/tTc	12/19	1	2	FACETS	0.78	0.658	0.913	0.78	0.658	0.913	CLONAL	1	TRUE	1	0.306478561731129	2		206	385	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919218	178919218	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	72	338	0	ENST00000263967.3:c.703T>A	p.Ser235Thr	p.S235T	ENST00000263967	NM_006218.2	235	Tcc/Acc	4/21	1	2	FACETS	0.765	0.669	0.869	0.765	0.669	0.869	SUBCLONAL	1	TRUE	1	0.306478561731129	2		338	614	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447214	187447214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	51	189	0	ENST00000232014.4:c.979G>A	p.Gly327Ser	p.G327S	ENST00000232014	NM_001130845.1	327	Ggt/Agt	5/10	1	2	FACETS	0.736	0.627	0.856	0.736	0.627	0.856	SUBCLONAL	1	TRUE	1	0.306478561731129	2		189	452	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806582	1806582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	58	316	0	ENST00000260795.2:c.1298C>T	p.Ser433Phe	p.S433F	ENST00000260795		433	tCc/tTc	9/17	1	2	FACETS	0.765	0.658	0.881	0.765	0.658	0.881	SUBCLONAL	1	TRUE	1	0.306478561731129	2		316	495	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518321	187518321	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	13	71	0	ENST00000441802.2:c.12373C>T	p.Gln4125Ter	p.Q4125*	ENST00000441802	NM_005245.3	4125	Cag/Tag	25/27	0.241844568593652	1	FACETS	0.671	0.484	0.895	0.671	0.484	0.895	SUBCLONAL	1	TRUE	0	0.306478561731129	1		71	107	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264640	1264640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	293	409	0	ENST00000310581.5:c.2722C>T	p.Pro908Ser	p.P908S	ENST00000310581	NM_198253.2	908	Cct/Tct	11/16	0.306478561731129	4	FACETS	0.955	0.901	1	0.955	0.901	1	CLONAL	3	TRUE	1	0.306478561731129	4		409	872	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295243	1295243	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs35550267	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	83	126	0				ENST00000310581	NM_198253.2	-/1132			0.306478561731129	4	FACETS	0.971	0.87	1	0.971	0.87	1	CLONAL	3	TRUE	1	0.306478561731129	4		126	243	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675792	30675793	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	110	625	0	ENST00000376406.3:c.2563_2564delinsAA	p.Gly855Lys	p.G855K	ENST00000376406	NM_014641.2	855	GGg/AAg	8/15	0.306478561731129	3	FACETS	0.795	0.713	0.883	0.398	0.356	0.442	SUBCLONAL	1	TRUE	1	0.306478561731129	3		625	1041	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138564	37138565	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	104	229	0	ENST00000373509.5:c.98_99delinsTT	p.Pro33Leu	p.P33L	ENST00000373509	NM_002648.3	33	cCC/cTT	2/6	0.306478561731129	3	FACETS	0.827	0.745	0.914	0.827	0.745	0.914	CLONAL	2	TRUE	1	0.306478561731129	3		229	473	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790782	89790782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772316901	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	54	380	0	ENST00000336032.3:c.169C>T	p.Leu57Phe	p.L57F	ENST00000336032	NM_006813.2	57	Ctc/Ttc	1/2	1	2	FACETS	0.552	0.471	0.641	0.552	0.471	0.641	SUBCLONAL	1	TRUE	1	0.306478561731129	2		380	638	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004628	150004628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	77	388	0	ENST00000253339.5:c.1597C>T	p.Pro533Ser	p.P533S	ENST00000253339		533	Cct/Tct	3/7	1	2	FACETS	0.714	0.626	0.808	0.714	0.626	0.808	SUBCLONAL	1	TRUE	1	0.306478561731129	2		388	704	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729393	41729393	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	107	601	0	ENST00000242208.4:c.1136G>C	p.Arg379Pro	p.R379P	ENST00000242208	NM_002192.2	379	cGg/cCg	3/3	0.256045738384849	3	FACETS	0.856	0.766	0.951	0.428	0.383	0.476	CLONAL	1	TRUE	1	0.306478561731129	3		601	941	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55087058	55087059	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	TA	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	16	137	0	ENST00000275493.2:c.88_88+1delinsTA		p.X30_splice	ENST00000275493	NM_005228.3	30		1/28	0.256045738384849	3	FACETS	0.519	0.384	0.68	0.26	0.192	0.34	SUBCLONAL	1	TRUE	1	0.306478561731129	3		137	232	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266482	55266482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	169	439	0	ENST00000275493.2:c.2774C>T	p.Ser925Phe	p.S925F	ENST00000275493	NM_005228.3	925	tCc/tTc	23/28	0.256045738384849	3	FACETS	0.787	0.724	0.852	0.787	0.724	0.852	SUBCLONAL	2	TRUE	1	0.306478561731129	3		439	808	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358969	81358969	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	89	383	1	ENST00000222390.5:c.992C>T	p.Ser331Phe	p.S331F	ENST00000222390	NM_000601.4	331	tCt/tTt	8/18	0.256045738384849	3	FACETS	0.857	0.759	0.961	0.428	0.379	0.481	CLONAL	1	TRUE	1	0.306478561731129	3		384	782	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850333	128850333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	50	333	0	ENST00000249373.3:c.1596G>A	p.Met532Ile	p.M532I	ENST00000249373	NM_005631.4	532	atG/atA	9/12	0.256045738384849	3	FACETS	0.639	0.541	0.746	0.319	0.27	0.373	SUBCLONAL	1	TRUE	1	0.306478561731129	3		333	589	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879231	151879231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	60	419	0	ENST00000262189.6:c.5714C>T	p.Pro1905Leu	p.P1905L	ENST00000262189	NM_170606.2	1905	cCt/cTt	36/59	0.256045738384849	3	FACETS	0.686	0.591	0.79	0.343	0.295	0.395	SUBCLONAL	1	TRUE	1	0.306478561731129	3		419	658	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285584	38285584	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs776567959	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	63	270	0	ENST00000425967.3:c.569A>G	p.Glu190Gly	p.E190G	ENST00000425967	NM_001174067.1	190	gAa/gGa	6/19	0.256045738384849	3	FACETS	0.854	0.739	0.979	0.427	0.369	0.49	CLONAL	1	TRUE	1	0.306478561731129	3		270	555	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319899	8319899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	254	384	0	ENST00000356435.5:c.5602G>A	p.Gly1868Arg	p.G1868R	ENST00000356435		1868	Gga/Aga	34/35	0.306478561731129	3	FACETS	1	0.983	1	0.754	0.708	0.802	CLONAL	2	TRUE	0	0.306478561731129	3		384	845	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8339020	8339020	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs760526678	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	199	330	0	ENST00000356435.5:c.5281G>C	p.Glu1761Gln	p.E1761Q	ENST00000356435		1761	Gaa/Caa	32/35	0.306478561731129	3	FACETS	1	0.966	1	0.708	0.658	0.759	CLONAL	2	TRUE	0	0.306478561731129	3		330	705	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971187	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	62	118	0	ENST00000304494.5:c.171_172delinsTT	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	57	gcCCga/gcTTga	2/3	0.306478561731129	3	FACETS	0.855	0.753	0.961	0.855	0.753	0.961	CLONAL	3	TRUE	0	0.306478561731129	3		118	182	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971187	21971187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658199	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	61	116	0	ENST00000579755.1:c.214C>T	p.Pro72Ser	p.P72S	ENST00000579755		72	Ccg/Tcg	2/3	0.306478561731129	3	FACETS	0.85	0.748	0.957	0.85	0.748	0.957	CLONAL	3	TRUE	0	0.306478561731129	3		116	180	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317335	87317336	+	splice_donor_variant	Splice_Site	DNP	GT	GT	AA	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	91	304	0	ENST00000277120.3:c.359+1_359+2delinsAA		p.X120_splice	ENST00000277120		120			0.181051112917844	2	FACETS	1	0.909	1	0.512	0.455	0.572	INDETERMINATE	1	TRUE	0	0.306478561731129	2		304	580	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209399	98209399	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777641179	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	74	258	0	ENST00000331920.6:c.4139C>T	p.Ala1380Val	p.A1380V	ENST00000331920	NM_000264.3	1380	gCc/gTc	23/24	0.181051112917844	2	FACETS	1	0.958	1	0.602	0.53	0.679	INDETERMINATE	1	TRUE	0	0.306478561731129	2		258	401	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412673	139412673	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762151552	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	128	338	0	ENST00000277541.6:c.1171C>T	p.Pro391Ser	p.P391S	ENST00000277541	NM_017617.3	391	Cct/Tct	7/34	0.181051112917844	2	FACETS	0.787	0.716	0.86	0.787	0.716	0.86	INDETERMINATE	2	TRUE	0	0.306478561731129	2		338	531	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417316	139417316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	72	162	0	ENST00000277541.6:c.728G>A	p.Cys243Tyr	p.C243Y	ENST00000277541	NM_017617.3	243	tGt/tAt	4/34	0.181051112917844	2	FACETS	0.918	0.812	1	0.918	0.812	1	INDETERMINATE	2	TRUE	0	0.306478561731129	2		162	256	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596152	43596152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1025290394	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	95	279	0	ENST00000355710.3:c.319G>A	p.Glu107Lys	p.E107K	ENST00000355710	NM_020975.4	107	Gag/Aag	2/20	0.256045738384849	3	FACETS	1	0.979	1	0.712	0.636	0.792	CLONAL	1	TRUE	1	0.306478561731129	3		279	502	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610162	43610162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	86	460	0	ENST00000355710.3:c.2114C>T	p.Ser705Phe	p.S705F	ENST00000355710	NM_020975.4	705	tCc/tTc	11/20	0.256045738384849	3	FACETS	0.804	0.71	0.904	0.402	0.355	0.452	CLONAL	1	TRUE	1	0.306478561731129	3		460	805	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239535	123239535	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	210	648	2	ENST00000358487.5:c.2302G>T	p.Glu768Ter	p.E768*	ENST00000358487	NM_000141.4	768	Gaa/Taa	18/18	0.256045738384849	3	FACETS	0.776	0.721	0.834	0.776	0.721	0.834	SUBCLONAL	2	TRUE	1	0.306478561731129	3		650	1018	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137301	64137301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	84	255	0	ENST00000334205.4:c.1733C>T	p.Pro578Leu	p.P578L	ENST00000334205	NM_003942.2	578	cCc/cTc	14/17	0.256045738384849	3	FACETS	1	0.976	1	0.701	0.622	0.785	CLONAL	1	TRUE	1	0.306478561731129	3		255	451	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137802	64137802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	63	410	0	ENST00000334205.4:c.1903C>T	p.Leu635Phe	p.L635F	ENST00000334205	NM_003942.2	635	Ctt/Ttt	15/17	0.256045738384849	3	FACETS	0.672	0.58	0.771	0.336	0.29	0.386	SUBCLONAL	1	TRUE	1	0.306478561731129	3		410	706	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102094420	102094420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	93	405	0	ENST00000282441.5:c.1100C>T	p.Ser367Phe	p.S367F	ENST00000282441	NM_001130145.2	367	tCt/tTt	7/9	0.256045738384849	3	FACETS	0.828	0.736	0.927	0.414	0.368	0.464	CLONAL	1	TRUE	1	0.306478561731129	3		405	845	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342400	118342400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	83	420	0	ENST00000534358.1:c.526C>T	p.Arg176Cys	p.R176C	ENST00000534358	NM_005933.3	176	Cgt/Tgt	3/36	0.256045738384849	3	FACETS	0.835	0.736	0.941	0.418	0.368	0.471	CLONAL	1	TRUE	1	0.306478561731129	3		420	748	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800900	18800900	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs372507637	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	54	407	0	ENST00000266497.5:c.4276C>T	p.Arg1426Ter	p.R1426*	ENST00000266497		1426	Cga/Tga	31/31	1	2	FACETS	0.53	0.452	0.616	0.53	0.452	0.616	SUBCLONAL	1	TRUE	1	0.306478561731129	2		407	665	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230641	46230642	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	78	458	0	ENST00000334344.6:c.890_891delinsTT	p.Ser297Phe	p.S297F	ENST00000334344	NM_152641.2	297	tCC/tTT	8/21	1	2	FACETS	0.694	0.61	0.786	0.694	0.61	0.786	SUBCLONAL	1	TRUE	1	0.306478561731129	2		458	733	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244361	46244361	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	86	394	0	ENST00000334344.6:c.2455C>T	p.Gln819Ter	p.Q819*	ENST00000334344	NM_152641.2	819	Caa/Taa	15/21	1	2	FACETS	0.779	0.689	0.876	0.779	0.689	0.876	SUBCLONAL	1	TRUE	1	0.306478561731129	2		394	720	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436527	49436527	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	51	389	0	ENST00000301067.7:c.5779C>T	p.Gln1927Ter	p.Q1927*	ENST00000301067	NM_003482.3	1927	Caa/Taa	26/54	1	2	FACETS	0.584	0.496	0.681	0.584	0.496	0.681	SUBCLONAL	1	TRUE	1	0.306478561731129	2		389	570	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434462	121434462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	75	357	0	ENST00000257555.6:c.1226C>T	p.Pro409Leu	p.P409L	ENST00000257555		409	cCt/cTt	6/10	1	2	FACETS	0.809	0.709	0.916	0.809	0.709	0.916	CLONAL	1	TRUE	1	0.306478561731129	2		357	605	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576148	88576148	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	44	312	0	ENST00000360948.2:c.1525C>T	p.Pro509Ser	p.P509S	ENST00000360948	NM_001012338.2	509	Cct/Tct	13/19	1	2	FACETS	0.56	0.469	0.66	0.56	0.469	0.66	SUBCLONAL	1	TRUE	1	0.306478561731129	2		312	513	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339519	339519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	68	390	0	ENST00000262320.3:c.2383C>T	p.Pro795Ser	p.P795S	ENST00000262320	NM_003502.3	795	Ccc/Tcc	10/11	1	2	FACETS	0.667	0.58	0.762	0.667	0.58	0.762	SUBCLONAL	1	TRUE	1	0.306478561731129	2		390	665	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778488	3778488	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760836018	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	55	386	2	ENST00000262367.5:c.6560C>T	p.Pro2187Leu	p.P2187L	ENST00000262367	NM_004380.2	2187	cCa/cTa	31/31	1	2	FACETS	0.617	0.527	0.715	0.617	0.527	0.715	SUBCLONAL	1	TRUE	1	0.306478561731129	2		388	582	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857500	9857500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	53	252	0	ENST00000330684.3:c.3901G>A	p.Glu1301Lys	p.E1301K	ENST00000330684	NM_001134407.1	1301	Gag/Aag	13/13	1	2	FACETS	0.749	0.639	0.868	0.749	0.639	0.868	SUBCLONAL	1	TRUE	1	0.306478561731129	2		252	462	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128002	30128002	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	68	449	2	ENST00000263025.4:c.1127T>G	p.Leu376Arg	p.L376R	ENST00000263025	NM_002746.2	376	cTg/cGg	8/9	1	2	FACETS	0.673	0.585	0.769	0.673	0.585	0.769	SUBCLONAL	1	TRUE	1	0.306478561731129	2		451	659	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351247	89351247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	108	555	1	ENST00000301030.4:c.1703C>T	p.Ser568Phe	p.S568F	ENST00000301030	NM_001256183.1	568	tCc/tTc	9/13	1	2	FACETS	0.82	0.735	0.909	0.82	0.735	0.909	CLONAL	1	TRUE	1	0.306478561731129	2		556	860	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836659	89836659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	50	299	0	ENST00000389301.3:c.2231C>T	p.Pro744Leu	p.P744L	ENST00000389301	NM_000135.2	744	cCc/cTc	25/43	1	2	FACETS	0.74	0.629	0.862	0.74	0.629	0.862	SUBCLONAL	1	TRUE	1	0.306478561731129	2		299	441	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29563033	29563033	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	69	394	0	ENST00000356175.3:c.3968C>T	p.Pro1323Leu	p.P1323L	ENST00000356175	NM_000267.3	1323	cCt/cTt	29/57	0.256045738384849	3	FACETS	0.717	0.624	0.818	0.359	0.312	0.409	SUBCLONAL	1	TRUE	1	0.306478561731129	3		394	724	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866371	37866371	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760895559	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	48	258	0	ENST00000269571.5:c.676C>T	p.Arg226Cys	p.R226C	ENST00000269571		226	Cgc/Tgc	6/27	0.256045738384849	3	FACETS	0.671	0.567	0.786	0.336	0.283	0.393	SUBCLONAL	1	TRUE	1	0.306478561731129	3		258	538	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37882013	37882013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	115	358	0	ENST00000269571.5:c.2779C>T	p.Pro927Ser	p.P927S	ENST00000269571		927	Cca/Tca	23/27	0.256045738384849	3	FACETS	1	0.979	1	0.665	0.6	0.733	CLONAL	1	TRUE	1	0.306478561731129	3		358	651	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883734	37883734	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1032811228	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	54	380	0	ENST00000269571.5:c.3346C>T	p.Pro1116Ser	p.P1116S	ENST00000269571		1116	Ccc/Tcc	26/27	0.256045738384849	3	FACETS	0.592	0.505	0.688	0.296	0.252	0.344	SUBCLONAL	1	TRUE	1	0.306478561731129	3		380	686	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375553	40375553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	195	561	0	ENST00000293328.3:c.397C>T	p.Leu133Phe	p.L133F	ENST00000293328	NM_012448.3	133	Ctt/Ttt	5/19	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.306478561731129	2		561	929	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696441	47696441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	139	376	0	ENST00000347630.2:c.382G>A	p.Gly128Ser	p.G128S	ENST00000347630	NM_001007230.1	128	Ggc/Agc	6/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.306478561731129	2		376	780	SUCCESS
YES1	7525	MSKCC	GRCh37	18	748017	748017	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	62	429	0	ENST00000314574.4:c.373G>A	p.Glu125Lys	p.E125K	ENST00000314574	NM_005433.3	125	Gaa/Aaa	4/12	1	2	FACETS	0.566	0.488	0.651	0.566	0.488	0.651	SUBCLONAL	1	TRUE	1	0.306478561731129	2		429	715	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791367	42791367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	43	256	0	ENST00000575354.2:c.427G>A	p.Glu143Lys	p.E143K	ENST00000575354	NM_015125.3	143	Gag/Aag	3/20	1	2	FACETS	0.635	0.532	0.749	0.635	0.532	0.749	SUBCLONAL	1	TRUE	1	0.306478561731129	2		256	442	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906847	50906848	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	74	437	0	ENST00000440232.2:c.1235_1236delinsTT	p.Thr412Ile	p.T412I	ENST00000440232	NM_002691.3	412	aCC/aTT	10/27	1	2	FACETS	0.794	0.696	0.9	0.794	0.696	0.9	SUBCLONAL	1	TRUE	1	0.306478561731129	2		437	608	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546650	9546650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	320	371	0	ENST00000353224.5:c.1372G>A	p.Gly458Ser	p.G458S	ENST00000353224	NM_177990.2	458	Ggc/Agc	5/10	0.306478561731129	4	FACETS	0.88	0.835	0.925	1	0.99	1	CLONAL	4	TRUE	1	0.306478561731129	4		371	775	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143262	24143262	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	81	467	0	ENST00000263121.7:c.494C>T	p.Pro165Leu	p.P165L	ENST00000263121	NM_003073.3	165	cCc/cTc	4/9	0.256045738384849	3	FACETS	0.726	0.638	0.82	0.363	0.319	0.41	SUBCLONAL	1	TRUE	1	0.306478561731129	3		467	840	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130412	29130412	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	117	298	0	ENST00000328354.6:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000328354	NM_007194.3	100	Cag/Tag	2/15	0.256045738384849	3	FACETS	1	0.983	1	0.718	0.649	0.791	CLONAL	1	TRUE	1	0.306478561731129	3		298	613	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564759	41564759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	82	415	0	ENST00000263253.7:c.4060C>T	p.Pro1354Ser	p.P1354S	ENST00000263253	NM_001429.3	1354	Cca/Tca	25/31	0.256045738384849	3	FACETS	0.749	0.659	0.845	0.374	0.329	0.423	SUBCLONAL	1	TRUE	1	0.306478561731129	3		415	824	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565507	41565507	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	154	360	2	ENST00000263253.7:c.4173G>C	p.Arg1391Ser	p.R1391S	ENST00000263253	NM_001429.3	1391	agG/agC	26/31	0.256045738384849	3	FACETS	0.85	0.78	0.922	0.85	0.78	0.922	CLONAL	2	TRUE	1	0.306478561731129	3		362	682	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039817	47039817	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	132	266	0	ENST00000377604.3:c.1161-1G>A		p.X387_splice	ENST00000377604	NM_001204468.1	387			0.279296420529309	2	FACETS	1	0.943	1			1	CLONAL	2	TRUE	NA	0.306478561731129	2		266	415	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0003933-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	215	300	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	0.652273936769642	2		300	625	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003933-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	205	415	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	0.652273936769642	2		416	585	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856020	68856020	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003933-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	287	672	0	ENST00000261769.5:c.1828C>T	p.Gln610Ter	p.Q610*	ENST00000261769	NM_004360.3	610	Cag/Tag	12/16	0.652273936769642	1	FACETS	0.952	0.903	1	0.952	0.903	1	CLONAL	1	TRUE	0	0.652273936769642	1		672	623	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851325	156851325	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201891311	NA	P-0003933-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	199	527	2	ENST00000524377.1:c.2282G>A	p.Arg761Gln	p.R761Q	ENST00000524377	NM_002529.3	761	cGg/cAg	17/17	0.652273936769642	4	FACETS	0.993	0.92	1	0.331	0.306	0.357	CLONAL	1	TRUE	1	0.652273936769642	4		529	1015	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945694	38945694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1175194099	NA	P-0003933-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	262	508	0	ENST00000357387.3:c.4532G>A	p.Gly1511Glu	p.G1511E	ENST00000357387	NM_152756.3	1511	gGa/gAa	34/38	1	2	FACETS	0.995	0.936	1	0.995	0.936	1	CLONAL	1	TRUE	1	0.652273936769642	2		508	807	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549137	21549137	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003933-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	48	756	0	ENST00000382592.4:c.3139G>C	p.Asp1047His	p.D1047H	ENST00000382592	NM_014572.2	1047	Gat/Cat	8/8	1	2	FACETS	0.175	0.147	0.206	0.175	0.147	0.206	SUBCLONAL	1	TRUE	1	0.652273936769642	2		756	839	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872987	136872987	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003933-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	349	884	0	ENST00000241393.3:c.511G>T	p.Asp171Tyr	p.D171Y	ENST00000241393	NM_003467.2	171	Gac/Tac	2/2	1	2	FACETS	0.984	0.933	1	0.984	0.933	1	CLONAL	1	TRUE	1	0.652273936769642	2		884	1087	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879620	151879620	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003933-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	22	155	0	ENST00000262189.6:c.5325G>C	p.Gln1775His	p.Q1775H	ENST00000262189	NM_170606.2	1775	caG/caC	36/59	1	2	FACETS	0.242	0.187	0.305	0.242	0.187	0.305	SUBCLONAL	1	TRUE	1	0.652273936769642	2		155	279	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003965-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	20	174	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		174	61	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	22	174	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.706371233118224	NA		174	64	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0003966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	737	318	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.706371233118224	5	FACETS	0.892	0.868	0.917	0.892	0.868	0.917	CLONAL	4	TRUE	1	0.706371233118224	5		318	1204	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462393	89462393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	213	155	0	ENST00000336596.2:c.1865C>T	p.Ser622Phe	p.S622F	ENST00000336596	NM_005233.5	622	tCc/tTc	10/17	0.137042348263294	6	FACETS	1	0.982	1	0.57	0.533	0.609	INDETERMINATE	2	TRUE	2	0.706371233118224	6		155	638	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047693	180047693	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	55	224	0	ENST00000261937.6:c.2322G>A	p.Met774Ile	p.M774I	ENST00000261937	NM_182925.4	774	atG/atA	16/30	0.667677978954516	1	FACETS	0.603	0.526	0.684	0.603	0.526	0.684	SUBCLONAL	1	TRUE	0	0.706371233118224	1		224	167	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778585	3778585	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755124235	NA	P-0003966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	117	198	0	ENST00000262367.5:c.6463C>T	p.Pro2155Ser	p.P2155S	ENST00000262367	NM_004380.2	2155	Cct/Tct	31/31	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.706371233118224	2		198	294	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830886	72830886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377177671	NA	P-0003966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	259	452	0	ENST00000268489.5:c.5695G>A	p.Gly1899Arg	p.G1899R	ENST00000268489	NM_006885.3	1899	Gga/Aga	9/10	1	2	FACETS	0.99	0.931	1	0.99	0.931	1	CLONAL	1	TRUE	1	0.706371233118224	2		452	741	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943680	17943680	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	90	210	0	ENST00000458235.1:c.2409G>A	p.Trp803Ter	p.W803*	ENST00000458235	NM_000215.3	803	tgG/tgA	18/24	1	2	FACETS	0.87	0.781	0.962	0.87	0.781	0.962	CLONAL	1	TRUE	1	0.706371233118224	2		210	293	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0003968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	135	769	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.904277578666916	2		769	281	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0003968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	231	379	2	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	0.904277578666916	2		381	469	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158626898	158626898	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs863224846	NA	P-0003968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	495	333	0	ENST00000263640.3:c.772A>G	p.Arg258Gly	p.R258G	ENST00000263640	NM_001105.4	258	Agg/Ggg	7/11	1	2	FACETS	0.946	0.908	0.985	0.946	0.908	0.985	CLONAL	1	TRUE	1	0.904277578666916	2		333	1157	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624616	93624616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201857010	NA	P-0003968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	37	179	0	ENST00000375746.1:c.707C>T	p.Thr236Met	p.T236M	ENST00000375746	NM_001174167.1	236	aCg/aTg	4/14	1	2	FACETS	0.144	0.118	0.173	0.144	0.118	0.173	SUBCLONAL	1	TRUE	1	0.904277578666916	2		179	568	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139411822	139411822	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	52	235	0	ENST00000277541.6:c.1457A>C	p.His486Pro	p.H486P	ENST00000277541	NM_017617.3	486	cAc/cCc	9/34	1	2	FACETS	0.195	0.165	0.227	0.195	0.165	0.227	SUBCLONAL	1	TRUE	1	0.904277578666916	2		235	590	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798160	42798161	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0003968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	259	259	0	ENST00000575354.2:c.4115_4116del	p.Pro1372LeufsTer68	p.P1372Lfs*68	ENST00000575354	NM_015125.3	1372	CCc/c	17/20	0.904277578666916	1	FACETS	0.934	0.9	0.966	0.934	0.9	0.966	CLONAL	1	TRUE	0	0.904277578666916	1		259	336	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432592	78432593	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0003968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	199	163	0	ENST00000370768.2:c.390_391del	p.Gly131MetfsTer8	p.G131Mfs*8	ENST00000370768	NM_003902.3	130	tcTGga/tcga	6/20	0.904277578666916	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.904277578666916	1		163	236	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	27	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.821	0.675	0.977	0.821	0.675	0.977	CLONAL	1	TRUE	1	0.832228505831139	2		174	79	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0004027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	100	379	2	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.907	0.823	0.993	0.907	0.823	0.993	CLONAL	1	TRUE	1	0.832228505831139	2		381	265	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791757	42791757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568504941	NA	P-0004027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	204	400	0	ENST00000575354.2:c.643C>T	p.Arg215Trp	p.R215W	ENST00000575354	NM_015125.3	215	Cgg/Tgg	5/20	0.832228505831139	1	FACETS	0.977	0.931	1	0.977	0.931	1	CLONAL	1	TRUE	0	0.832228505831139	1		400	293	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78420976	78420976	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	82	298	0	ENST00000370768.2:c.1744del	p.Tyr582IlefsTer83	p.Y582Ifs*83	ENST00000370768	NM_003902.3	582	Tat/at	18/20	0.832228505831139	1	FACETS	0.381	0.339	0.425	0.381	0.339	0.425	SUBCLONAL	1	TRUE	0	0.832228505831139	1		298	302	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0004060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	30	769	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.262500894783395	2		769	170	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0004060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	124	593	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.262500894783395	2		595	936	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0004060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	288	718	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.262500894783395	2		718	921	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0004060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	81	239	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.262500894783395	2		239	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578359	7578373	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCAGCTGCTCACCAT	CCAGCTGCTCACCAT	-	novel	NA	P-0004060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	45	142	0	ENST00000269305.4:c.557_559+12del		p.X186_splice	ENST00000269305	NM_001126112.2	186		5/11	1	2	FACETS	0.834	0.702	0.98	0.834	0.702	0.98	CLONAL	1	TRUE	1	0.262500894783395	2		142	411	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	237	174	0				ENST00000310581	NM_198253.2	-/1132			0.488075302842284	3	FACETS	0.916	0.868	0.964	0.916	0.868	0.964	CLONAL	3	TRUE	0	0.490375698627806	3		174	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0004091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	273	627	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.490375698627806	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.490375698627806	1		627	834	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459779	149459779	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	196	335	0	ENST00000286301.3:c.428T>A	p.Val143Glu	p.V143E	ENST00000286301	NM_005211.3	143	gTg/gAg	4/22	0.283473353512623	1	FACETS	0.84	0.781	0.902	0.84	0.781	0.902	INDETERMINATE	1	TRUE	0	0.490375698627806	1		335	718	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653210	29653210	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	167	278	0	ENST00000356175.3:c.5146del	p.Leu1716Ter	p.L1716*	ENST00000356175	NM_000267.3	1715	gaC/ga	36/57	1	2	FACETS	0.928	0.855	1	0.928	0.855	1	CLONAL	1	TRUE	1	0.490375698627806	2		278	734	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	48	174	0				ENST00000310581	NM_198253.2	-/1132			0.350552740896732	3	FACETS	0.852	0.732	0.98			1	CLONAL	2	TRUE	NA	0.375963512402094	3		174	178	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0004132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	2578	330	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.375963512402094	24	FACETS	1	0.993	1			1	CLONAL	23	TRUE	NA	0.375963512402094	24		330	3051	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92300791	92300791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	97	244	0	ENST00000265734.4:c.596C>T	p.Pro199Leu	p.P199L	ENST00000265734	NM_001259.6	199	cCc/cTc	5/8	0.375963512402094	4	FACETS	1	0.971	1			1	CLONAL	1	TRUE	NA	0.375963512402094	4		244	565	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857538	57857538	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	131	528	0	ENST00000228682.2:c.64C>T	p.Leu22Phe	p.L22F	ENST00000228682	NM_005269.2	22	Ctc/Ttc	2/12	0.177212922556683	1	FACETS	0.771	0.7	0.845	0.771	0.7	0.845	INDETERMINATE	1	TRUE	0	0.375963512402094	1		528	734	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679748	88679748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	103	414	0	ENST00000360948.2:c.715C>T	p.Pro239Ser	p.P239S	ENST00000360948	NM_001012338.2	239	Cct/Tct	7/19	0.375963512402094	3	FACETS	1	0.901	1	0.503	0.451	0.559	CLONAL	1	TRUE	1	0.375963512402094	3		414	647	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53241000	53241000	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	251	295	0	ENST00000375401.3:c.1211T>C	p.Phe404Ser	p.F404S	ENST00000375401	NM_004187.3	404	tTt/tCt	9/26	0.375963512402094	2	FACETS	0.978	0.929	1			1	CLONAL	3	TRUE	NA	0.375963512402094	2		295	455	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0004142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	341	670	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	1	2	FACETS	0.956	0.909	1	0.956	0.909	1	CLONAL	1	TRUE	1	0.859808414907141	2		670	830	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633380	8633380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768353460	NA	P-0004142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	358	561	0	ENST00000356435.5:c.289G>A	p.Glu97Lys	p.E97K	ENST00000356435		97	Gaa/Aaa	3/35	1	2	FACETS	0.987	0.94	1	0.987	0.94	1	CLONAL	1	TRUE	1	0.859808414907141	2		561	844	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0004142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	320	645	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.934	0.886	0.982	0.934	0.886	0.982	CLONAL	1	TRUE	1	0.859808414907141	2		645	797	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0004142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	91	349	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.912	0.825	1	0.912	0.825	1	CLONAL	1	TRUE	1	0.859808414907141	2		351	232	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414967	78414967	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1442633263	NA	P-0004142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	210	256	1	ENST00000370768.2:c.1799C>T	p.Pro600Leu	p.P600L	ENST00000370768	NM_003902.3	600	cCg/cTg	19/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.859808414907141	2		257	478	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459133	120459133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	241	371	0	ENST00000256646.2:c.6212C>T	p.Pro2071Leu	p.P2071L	ENST00000256646	NM_024408.3	2071	cCt/cTt	34/34	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.859808414907141	2		371	534	SUCCESS
REL	5966	MSKCC	GRCh37	2	61128167	61128168	+	missense_variant	Missense_Mutation	DNP	GT	GT	AA	novel	NA	P-0004142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	121	195	0	ENST00000295025.8:c.343_344delinsAA	p.Val115Lys	p.V115K	ENST00000295025	NM_002908.2	115	GTa/AAa	4/11	1	2	FACETS	0.823	0.753	0.895	0.823	0.753	0.895	CLONAL	1	TRUE	1	0.859808414907141	2		195	342	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913403	NA	P-0004142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	323	414	0	ENST00000349496.5:c.110C>A	p.Ser37Tyr	p.S37Y	ENST00000349496	NM_001904.3	37	tCt/tAt	3/15	1	2	FACETS	0.897	0.85	0.943	0.897	0.85	0.943	CLONAL	1	TRUE	1	0.859808414907141	2		414	838	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468489	89468490	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0004142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	217	393	1	ENST00000336596.2:c.2023_2024delinsAA	p.Gly675Lys	p.G675K	ENST00000336596	NM_005233.5	675	GGa/AAa	11/17	1	2	FACETS	0.864	0.81	0.92	0.864	0.81	0.92	CLONAL	1	TRUE	1	0.859808414907141	2		394	584	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630303	187630303	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774143174	NA	P-0004142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	267	385	0	ENST00000441802.2:c.679C>T	p.Arg227Cys	p.R227C	ENST00000441802	NM_005245.3	227	Cgt/Tgt	2/27	1	2	FACETS	0.981	0.927	1	0.981	0.927	1	CLONAL	1	TRUE	1	0.859808414907141	2		385	633	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715371	117715371	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	234	421	0	ENST00000368508.3:c.1118C>T	p.Ser373Phe	p.S373F	ENST00000368508	NM_002944.2	373	tCc/tTc	10/43	0.859808414907141	1	FACETS	0.967	0.927	1	0.967	0.927	1	CLONAL	1	TRUE	0	0.859808414907141	1		421	321	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467683	50467683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	239	381	0	ENST00000331340.3:c.918G>A	p.Met306Ile	p.M306I	ENST00000331340	NM_006060.4	306	atG/atA	8/8	1	2	FACETS	0.904	0.85	0.959	0.904	0.85	0.959	CLONAL	1	TRUE	1	0.859808414907141	2		381	615	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513006	106513006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	230	296	1	ENST00000359195.3:c.2020G>A	p.Asp674Asn	p.D674N	ENST00000359195	NM_002649.2	674	Gat/Aat	3/11	1	2	FACETS	0.987	0.929	1	0.987	0.929	1	CLONAL	1	TRUE	1	0.859808414907141	2		297	542	SUCCESS
MET	4233	MSKCC	GRCh37	7	116419003	116419003	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	176	215	0	ENST00000397752.3:c.3514G>A	p.Glu1172Lys	p.E1172K	ENST00000397752	NM_000245.2	1172	Gag/Aag	17/21	1	2	FACETS	0.952	0.887	1	0.952	0.887	1	CLONAL	1	TRUE	1	0.859808414907141	2		215	430	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625269	69625269	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	403	628	0	ENST00000334134.2:c.524C>T	p.Ser175Phe	p.S175F	ENST00000334134	NM_005247.2	175	tCc/tTc	3/3	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.859808414907141	2		628	914	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244787	46244787	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	432	608	0	ENST00000334344.6:c.2881C>T	p.Gln961Ter	p.Q961*	ENST00000334344	NM_152641.2	961	Cag/Tag	15/21	0.859808414907141	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.859808414907141	1		608	571	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426701	121426701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753998395	NA	P-0004142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	390	575	1	ENST00000257555.6:c.392G>A	p.Arg131Gln	p.R131Q	ENST00000257555		131	cGg/cAg	2/10	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.859808414907141	2		576	907	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7128942	7128942	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	223	342	0	ENST00000302850.5:c.2866A>C	p.Lys956Gln	p.K956Q	ENST00000302850	NM_000208.2	956	Aaa/Caa	15/22	1	2	FACETS	0.947	0.889	1	0.947	0.889	1	CLONAL	1	TRUE	1	0.859808414907141	2		342	548	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546785	9546785	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1225105907	NA	P-0004142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	149	222	0	ENST00000353224.5:c.1237C>G	p.Pro413Ala	p.P413A	ENST00000353224	NM_177990.2	413	Ccg/Gcg	5/10	1	2	FACETS	0.952	0.882	1	0.952	0.882	1	CLONAL	1	TRUE	1	0.859808414907141	2		222	364	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100942	41100942	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568909948	NA	P-0004142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	244	350	0	ENST00000373198.4:c.1414G>A	p.Glu472Lys	p.E472K	ENST00000373198	NM_133170.3	472	Gag/Aag	8/32	1	2	FACETS	0.894	0.841	0.948	0.894	0.841	0.948	CLONAL	1	TRUE	1	0.859808414907141	2		350	635	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420076	41420076	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	174	256	0	ENST00000373198.4:c.245G>C	p.Arg82Thr	p.R82T	ENST00000373198	NM_133170.3	82	aGa/aCa	3/32	1	2	FACETS	0.93	0.866	0.996	0.93	0.866	0.996	CLONAL	1	TRUE	1	0.859808414907141	2		256	435	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934406	39934406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	197	271	0	ENST00000378444.4:c.193G>A	p.Asp65Asn	p.D65N	ENST00000378444	NM_001123385.1	65	Gat/Aat	4/15	1	2	FACETS	0.981	0.919	1	0.981	0.919	1	CLONAL	1	TRUE	1	0.859808414907141	2		271	467	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239889	53239889	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	420	661	0	ENST00000375401.3:c.1552C>T	p.His518Tyr	p.H518Y	ENST00000375401	NM_004187.3	518	Cac/Tac	11/26	1	2	FACETS	0.972	0.929	1	0.972	0.929	1	CLONAL	1	TRUE	1	0.859808414907141	2		661	1005	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341598	70341598	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761157306	NA	P-0004142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	429	659	0	ENST00000374080.3:c.1033C>T	p.Pro345Ser	p.P345S	ENST00000374080		345	Ccc/Tcc	7/45	1	2	FACETS	0.914	0.873	0.955	0.914	0.873	0.955	CLONAL	1	TRUE	1	0.859808414907141	2		659	1092	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	46	174	0				ENST00000310581	NM_198253.2	-/1132			0.282917643916826	3	FACETS	1	0.915	1	1	0.915	1	CLONAL	2	TRUE	1	0.2	3		174	227	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0004176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	33	440	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	0.399	0.323	0.485	0.399	0.323	0.485	SUBCLONAL	1	TRUE	1	0.2	2		440	827	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576886	7576886	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	78	711	0	ENST00000269305.4:c.960G>C	p.Lys320Asn	p.K320N	ENST00000269305	NM_001126112.2	320	aaG/aaC	9/11	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.2	2		711	750	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0004176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	90	927	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	1	2	FACETS	0.913	0.808	1	0.913	0.808	1	CLONAL	1	TRUE	1	0.2	2		927	986	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859782	151859782	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	62	536	0	ENST00000262189.6:c.10880C>T	p.Ser3627Leu	p.S3627L	ENST00000262189	NM_170606.2	3627	tCa/tTa	43/59	1	2	FACETS	0.801	0.691	0.921	0.801	0.691	0.921	CLONAL	1	TRUE	1	0.2	2		536	774	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566488	41566488	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	102	915	0	ENST00000263253.7:c.4365G>T	p.Gln1455His	p.Q1455H	ENST00000263253	NM_001429.3	1455	caG/caT	27/31	1	2	FACETS	0.999	0.892	1	0.999	0.892	1	CLONAL	1	TRUE	1	0.2	2		915	1021	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15840881	15840881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780460054	NA	P-0004176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	84	753	0	ENST00000307771.7:c.965G>A	p.Arg322Lys	p.R322K	ENST00000307771	NM_005089.3	322	aGa/aAa	11/11	1	2	FACETS	0.837	0.738	0.945	0.837	0.738	0.945	CLONAL	1	TRUE	1	0.2	2		753	1003	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	110	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.906215156933592	2		174	216	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0004197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	334	476	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	0.991	0.943	1	0.991	0.943	1	CLONAL	1	TRUE	1	0.906215156933592	2		476	744	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663184	227663184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	316	439	0	ENST00000305123.5:c.271G>A	p.Glu91Lys	p.E91K	ENST00000305123	NM_005544.2	91	Gag/Aag	1/2	1	2	FACETS	0.864	0.819	0.91	0.864	0.819	0.91	CLONAL	1	TRUE	1	0.906215156933592	2		439	807	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418492	49418492	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0004197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	228	289	0	ENST00000301067.7:c.15922-1G>A		p.X5308_splice	ENST00000301067	NM_003482.3	5308			1	2	FACETS	0.955	0.899	1	0.955	0.899	1	CLONAL	1	TRUE	1	0.906215156933592	2		289	527	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252901	36252901	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	296	424	0	ENST00000300305.3:c.461A>C	p.Gln154Pro	p.Q154P	ENST00000300305		154	cAg/cCg	4/8	1	2	FACETS	0.89	0.843	0.938	0.89	0.843	0.938	CLONAL	1	TRUE	1	0.906215156933592	2		424	734	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184969	123184969	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0004197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	166	338	0	ENST00000218089.9:c.1018-2A>C		p.X340_splice	ENST00000218089	NM_001042749.1	340			1	2	FACETS	0.898	0.835	0.962	0.898	0.835	0.962	CLONAL	1	TRUE	1	0.906215156933592	2		338	408	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0004203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	35	769	0				ENST00000310581	NM_198253.2	-/1132			0.319284007089257	1	FACETS	0.378	0.312	0.45	0.378	0.312	0.45	INDETERMINATE	1	TRUE	0	0.616557984794127	1		769	208	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027345	48027345	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs769668640	NA	P-0004203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	38	305	0	ENST00000234420.5:c.2223C>G	p.Asn741Lys	p.N741K	ENST00000234420	NM_000179.2	741	aaC/aaG	4/10	0.616557984794127	1	FACETS	0.127	0.104	0.152	0.127	0.104	0.152	SUBCLONAL	1	TRUE	0	0.616557984794127	1		305	672	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404568	8404568	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	285	364	1	ENST00000356435.5:c.4179T>A	p.Asp1393Glu	p.D1393E	ENST00000356435		1393	gaT/gaA	25/35	1	2	FACETS	0.893	0.84	0.947	0.893	0.84	0.947	CLONAL	1	TRUE	1	0.616557984794127	2		365	1035	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390698	139390698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	33	268	0	ENST00000277541.6:c.7493C>T	p.Pro2498Leu	p.P2498L	ENST00000277541	NM_017617.3	2498	cCc/cTc	34/34	1	2	FACETS	0.223	0.181	0.27	0.223	0.181	0.27	SUBCLONAL	1	TRUE	1	0.616557984794127	2		268	481	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692848	89692848	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	82	68	0	ENST00000371953.3:c.332G>C	p.Trp111Ser	p.W111S	ENST00000371953	NM_000314.4	111	tGg/tCg	5/9	0.616557984794127	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.616557984794127	1		68	164	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385208	4385208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	189	285	0	ENST00000261254.3:c.233C>T	p.Pro78Leu	p.P78L	ENST00000261254	NM_001759.3	78	cCt/cTt	2/5	0.616557984794127	1	FACETS	0.9	0.841	0.961	0.9	0.841	0.961	CLONAL	1	TRUE	0	0.616557984794127	1		285	471	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145436	58145436	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	207	240	0	ENST00000257904.6:c.65A>T	p.Lys22Met	p.K22M	ENST00000257904	NM_000075.3	22	aAg/aTg	2/8	0.319284007089257	1	FACETS	0.816	0.763	0.871	0.816	0.763	0.871	INDETERMINATE	1	TRUE	0	0.616557984794127	1		240	569	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222151	2222151	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760542574	NA	P-0004203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	51	354	0	ENST00000398665.3:c.2983C>T	p.Arg995Trp	p.R995W	ENST00000398665	NM_032482.2	995	Cgg/Tgg	24/28	0.446235389875715	1	FACETS	0.221	0.187	0.258	0.221	0.187	0.258	SUBCLONAL	1	TRUE	0	0.616557984794127	1		354	518	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047001	128047002	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0004203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	213	366	1	ENST00000285398.2:c.733_734delinsTT	p.Pro245Phe	p.P245F	ENST00000285398	NM_000122.1	245	CCc/TTc	6/15	0.25095063325609	1	FACETS	0.624	0.581	0.668	0.624	0.581	0.668	INDETERMINATE	1	TRUE	0	0.616557984794127	1		367	766	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578450	+	protein_altering_variant	In_Frame_Del	DEL	TAGATGGCC	TAGATGGCC	CCG	novel	NA	P-0004203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	133	202	0	ENST00000269305.4:c.480_488delinsCGG	p.Met160_Tyr163delinsIleGly	p.M160_Y163delinsIG	ENST00000269305	NM_001126112.2	160	atGGCCATCTAc/atCGGc	5/11	0.616557984794127	1	FACETS	0.868	0.798	0.938	0.868	0.798	0.938	CLONAL	1	TRUE	0	0.616557984794127	1		202	344	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	62	174	0				ENST00000310581	NM_198253.2	-/1132			0.289141571516098	2	FACETS	1	0.978	1	0.703	0.635	0.77	INDETERMINATE	1	TRUE	0	0.839455055923255	2		174	105	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312725	91312725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	226	350	1	ENST00000355112.3:c.2464C>T	p.Pro822Ser	p.P822S	ENST00000355112	NM_000057.2	822	Cct/Tct	12/22	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.839455055923255	2		351	523	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	200	404	0	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	0.699570796998459	3	FACETS	0.827	0.777	0.877			1	CLONAL	2	TRUE	NA	0.839455055923255	3		404	409	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499823	8499823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1273962518	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	228	355	3	ENST00000356435.5:c.2146C>T	p.Arg716Cys	p.R716C	ENST00000356435		716	Cgc/Tgc	14/35	0.839455055923255	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.839455055923255	1		358	287	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	398	483	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.630499760149576	4	FACETS	1	0.988	1	1	0.997	1	CLONAL	3	TRUE	2	0.839455055923255	4		483	556	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129632	11129632	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	142	396	0	ENST00000358026.2:c.2439-1G>A		p.X813_splice	ENST00000358026	NM_001128849.1	813			1	2	FACETS	0.924	0.853	0.997	0.924	0.853	0.997	CLONAL	1	TRUE	1	0.839455055923255	2		396	366	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187093	11187093	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1386760919	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	85	390	0	ENST00000361445.4:c.6325C>T	p.Arg2109Ter	p.R2109*	ENST00000361445	NM_004958.3	2109	Cga/Tga	45/58	0.468111421903393	1	FACETS	0.378	0.337	0.42	0.378	0.337	0.42	INDETERMINATE	1	TRUE	0	0.839455055923255	1		390	311	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567683	226567683	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753253206	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	104	394	0	ENST00000366794.5:c.1483C>T	p.Pro495Ser	p.P495S	ENST00000366794	NM_001618.3	495	Cca/Tca	10/23	0.288543089549567	2	FACETS	0.702	0.635	0.772	0.351	0.317	0.386	INDETERMINATE	1	TRUE	0	0.839455055923255	2		394	353	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280711	41280711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	266	340	0	ENST00000349496.5:c.2224C>T	p.His742Tyr	p.H742Y	ENST00000349496	NM_001904.3	742	Cac/Tac	15/15	0.329497100759883	4	FACETS	1	0.972	1	1	0.972	1	INDETERMINATE	2	TRUE	2	0.839455055923255	4		340	561	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723500	49723500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	17	29	0	ENST00000449682.2:c.1142C>T	p.Pro381Leu	p.P381L	ENST00000449682	NM_020998.3	381	cCc/cTc	9/18	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.839455055923255	2		29	31	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678757	52678757	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	219	434	0	ENST00000394830.3:c.862G>A	p.Glu288Lys	p.E288K	ENST00000394830	NM_018313.4	288	Gaa/Aaa	9/30	0.272572591845269	4	FACETS	0.869	0.816	0.924	0.869	0.816	0.924	INDETERMINATE	2	TRUE	2	0.839455055923255	4		434	552	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955969	55955969	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs56302315	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	122	348	1	ENST00000263923.4:c.3193G>A	p.Ala1065Thr	p.A1065T	ENST00000263923	NM_002253.2	1065	Gct/Act	24/30	0.212741291093106	4	FACETS	0.854	0.783	0.926	0.854	0.783	0.926	INDETERMINATE	2	TRUE	2	0.839455055923255	4		349	313	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970851	55970851	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	162	426	0	ENST00000263923.4:c.1946C>T	p.Thr649Ile	p.T649I	ENST00000263923	NM_002253.2	649	aCc/aTc	13/30	0.212741291093106	4	FACETS	0.763	0.707	0.822	0.763	0.707	0.822	INDETERMINATE	2	TRUE	2	0.839455055923255	4		426	465	SUCCESS
APC	324	MSKCC	GRCh37	5	112177851	112177851	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146695342	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	220	337	1	ENST00000257430.4:c.6560G>A	p.Gly2187Glu	p.G2187E	ENST00000257430	NM_000038.5	2187	gGa/gAa	16/16	0.289141571516098	2	FACETS	1	0.993	1	0.681	0.645	0.716	INDETERMINATE	1	TRUE	0	0.839455055923255	2		338	385	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982036	93982036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1165179670	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	220	440	0	ENST00000369303.4:c.1429G>A	p.Glu477Lys	p.E477K	ENST00000369303	NM_004440.3	477	Gaa/Aaa	6/17	NA	2	FACETS	0.989	0.929	1			1	INDETERMINATE	1	TRUE	NA	0.839455055923255	2		440	530	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631251	117631251	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	174	468	0	ENST00000368508.3:c.6427G>A	p.Asp2143Asn	p.D2143N	ENST00000368508	NM_002944.2	2143	Gat/Aat	40/43	NA	2	FACETS	1	0.944	1			1	INDETERMINATE	1	TRUE	NA	0.839455055923255	2		468	409	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710558	117710558	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	167	275	1	ENST00000368508.3:c.1714C>T	p.Gln572Ter	p.Q572*	ENST00000368508	NM_002944.2	572	Cag/Tag	12/43	NA	2	FACETS	0.91	0.845	0.977			1	INDETERMINATE	1	TRUE	NA	0.839455055923255	2		276	437	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93627347	93627347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	162	381	0	ENST00000375746.1:c.814G>A	p.Gly272Ser	p.G272S	ENST00000375746	NM_001174167.1	272	Ggc/Agc	6/14	0.330383426973111	3	FACETS	0.776	0.723	0.83	0.776	0.723	0.83	INDETERMINATE	2	TRUE	1	0.839455055923255	3		381	353	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209379	98209379	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	163	315	0	ENST00000331920.6:c.4159C>T	p.Pro1387Ser	p.P1387S	ENST00000331920	NM_000264.3	1387	Cct/Tct	23/24	0.330383426973111	3	FACETS	1	0.99	1	0.727	0.677	0.779	INDETERMINATE	1	TRUE	1	0.839455055923255	3		315	379	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229629	98229629	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	165	316	0	ENST00000331920.6:c.2329C>A	p.Leu777Ile	p.L777I	ENST00000331920	NM_000264.3	777	Ctt/Att	15/24	0.330383426973111	3	FACETS	1	0.989	1	0.692	0.644	0.742	INDETERMINATE	1	TRUE	1	0.839455055923255	3		316	403	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110251295	110251295	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	134	311	2	ENST00000374672.4:c.42C>A	p.Asp14Glu	p.D14E	ENST00000374672	NM_004235.4	14	gaC/gaA	2/5	0.330383426973111	3	FACETS	1	0.988	1	0.729	0.673	0.785	INDETERMINATE	1	TRUE	1	0.839455055923255	3		313	311	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242662	46242662	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	158	287	0	ENST00000334344.6:c.1624C>T	p.Arg542Ter	p.R542*	ENST00000334344	NM_152641.2	542	Cga/Tga	13/21	0.330383426973111	3	FACETS	1	0.989	1	0.7	0.649	0.751	INDETERMINATE	1	TRUE	1	0.839455055923255	3		287	382	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244853	46244853	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	262	574	0	ENST00000334344.6:c.2947C>T	p.Gln983Ter	p.Q983*	ENST00000334344	NM_152641.2	983	Caa/Taa	15/21	0.330383426973111	3	FACETS	1	0.994	1	0.731	0.691	0.772	INDETERMINATE	1	TRUE	1	0.839455055923255	3		574	606	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913374	28913374	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	175	538	0	ENST00000282397.4:c.2419G>A	p.Asp807Asn	p.D807N	ENST00000282397	NM_002019.4	807	Gat/Aat	17/30	NA	2	FACETS	0.995	0.927	1			1	INDETERMINATE	1	TRUE	NA	0.839455055923255	2		538	419	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32918761	32918761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1239798218	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	174	512	0	ENST00000380152.3:c.6908C>T	p.Ser2303Phe	p.S2303F	ENST00000380152		2303	tCc/tTc	12/27	NA	2	FACETS	1	0.962	1			1	INDETERMINATE	1	TRUE	NA	0.839455055923255	2		512	397	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576115	88576115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	175	342	0	ENST00000360948.2:c.1558G>A	p.Gly520Arg	p.G520R	ENST00000360948	NM_001012338.2	520	Gga/Aga	13/19	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.839455055923255	2		342	408	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678446	88678446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779791807	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	185	499	0	ENST00000360948.2:c.1090C>T	p.Leu364Phe	p.L364F	ENST00000360948	NM_001012338.2	364	Ctc/Ttc	9/19	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.839455055923255	2		499	427	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679211	88679211	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	184	485	0	ENST00000360948.2:c.826G>A	p.Glu276Lys	p.E276K	ENST00000360948	NM_001012338.2	276	Gag/Aag	8/19	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.839455055923255	2		485	433	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858276	9858276	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	155	320	0	ENST00000330684.3:c.3125G>A	p.Arg1042Lys	p.R1042K	ENST00000330684	NM_001134407.1	1042	aGg/aAg	13/13	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.839455055923255	2		320	337	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56787259	56787259	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28363311	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	189	437	0	ENST00000337432.4:c.745C>T	p.Arg249Cys	p.R249C	ENST00000337432	NM_058216.2	249	Cgt/Tgt	5/9	0.405802925097549	4	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.839455055923255	4		437	619	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756577	756577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	170	305	0	ENST00000314574.4:c.251C>T	p.Ser84Leu	p.S84L	ENST00000314574	NM_005433.3	84	tCa/tTa	2/12	0.329497100759883	4	FACETS	0.985	0.919	1	0.985	0.919	1	INDETERMINATE	2	TRUE	2	0.839455055923255	4		305	378	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39644757	39644757	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	226	401	0	ENST00000262039.4:c.2486C>T	p.Pro829Leu	p.P829L	ENST00000262039	NM_002647.2	829	cCa/cTa	23/25	0.329497100759883	4	FACETS	1	0.972	1	1	0.972	1	INDETERMINATE	2	TRUE	2	0.839455055923255	4		401	472	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368303	45368303	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs79888759	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	172	386	0	ENST00000262160.6:c.1299T>A	p.Ser433Arg	p.S433R	ENST00000262160	NM_005901.5	433	agT/agA	11/11	0.329497100759883	4	FACETS	0.915	0.852	0.978	0.915	0.852	0.978	INDETERMINATE	2	TRUE	2	0.839455055923255	4		386	412	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272260	15272260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	105	201	0	ENST00000263388.2:c.6179C>T	p.Ser2060Phe	p.S2060F	ENST00000263388	NM_000435.2	2060	tCc/tTc	33/33	1	2	FACETS	0.973	0.888	1	0.973	0.888	1	CLONAL	1	TRUE	1	0.839455055923255	2		201	257	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400077	41400077	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs765578477	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	178	319	0	ENST00000373198.4:c.682C>T	p.Gln228Ter	p.Q228*	ENST00000373198	NM_133170.3	228	Cag/Tag	5/32	0.212741291093106	4	FACETS	0.899	0.838	0.961	0.899	0.838	0.961	INDETERMINATE	2	TRUE	2	0.839455055923255	4		319	434	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201817	152201818	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0004214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	204	400	0	ENST00000206249.3:c.671_672delinsTT	p.Thr224Ile	p.T224I	ENST00000206249	NM_000125.3	224	aCC/aTT	3/8	0.340776464513171	4	FACETS	0.91	0.853	0.969	0.91	0.853	0.969	INDETERMINATE	2	TRUE	2	0.839455055923255	4		400	491	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0004228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	34	769	0				ENST00000310581	NM_198253.2	-/1132			0.315231554251746	1	FACETS	0.903	0.759	1	0.903	0.759	1	INDETERMINATE	1	TRUE	0	0.547163824714563	1		769	100	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0004228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	53	340	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	0.547163824714563	2		340	145	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570767	226570767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs2230484	NA	P-0004228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	45	224	0	ENST00000366794.5:c.1129C>T	p.Pro377Ser	p.P377S	ENST00000366794	NM_001618.3	377	Cct/Tct	8/23	0.194672831000466	3	FACETS	0.77	0.662	0.884	0.77	0.662	0.884	INDETERMINATE	2	TRUE	1	0.547163824714563	3		224	136	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0004228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	53	498	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	1	2	FACETS	0.814	0.701	0.934	0.814	0.701	0.934	CLONAL	1	TRUE	1	0.547163824714563	2		498	238	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781853	9781853	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	67	451	0	ENST00000377346.4:c.1990T>G	p.Phe664Val	p.F664V	ENST00000377346	NM_005026.3	664	Ttc/Gtc	16/24	0.547163824714563	1	FACETS	0.946	0.839	1	0.946	0.839	1	CLONAL	1	TRUE	0	0.547163824714563	1		451	188	SUCCESS
FH	2271	MSKCC	GRCh37	1	241661153	241661153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	75	452	0	ENST00000366560.3:c.1508C>T	p.Pro503Leu	p.P503L	ENST00000366560	NM_000143.3	503	cCt/cTt	10/10	0.194672831000466	3	FACETS	0.808	0.721	0.899	0.808	0.721	0.899	INDETERMINATE	2	TRUE	1	0.547163824714563	3		452	216	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047803	128047803	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs775263112	NA	P-0004228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	51	479	0	ENST00000285398.2:c.518A>G	p.Asn173Ser	p.N173S	ENST00000285398	NM_000122.1	173	aAc/aGc	4/15	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.547163824714563	2		479	171	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158637104	158637104	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	42	649	0	ENST00000263640.3:c.76C>G	p.Pro26Ala	p.P26A	ENST00000263640	NM_001105.4	26	Ccc/Gcc	4/11	1	2	FACETS	0.486	0.407	0.572	0.486	0.407	0.572	SUBCLONAL	1	TRUE	1	0.547163824714563	2		649	316	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098803	178098803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	76	547	0	ENST00000397062.3:c.242G>A	p.Gly81Asp	p.G81D	ENST00000397062	NM_006164.4	81	gGt/gAt	2/5	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.547163824714563	2		547	239	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119562161	119562161	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs865826940	NA	P-0004228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	43	477	0	ENST00000316626.5:c.1175C>T	p.Pro392Leu	p.P392L	ENST00000316626		392	cCt/cTt	11/12	1	2	FACETS	0.898	0.763	1	0.898	0.763	1	CLONAL	1	TRUE	1	0.547163824714563	2		477	175	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433491	138433491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	42	437	2	ENST00000289153.2:c.1121C>T	p.Ser374Leu	p.S374L	ENST00000289153	NM_006219.2	374	tCa/tTa	7/22	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.547163824714563	2		439	134	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161420	185161420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	24	391	0	ENST00000265026.3:c.847C>T	p.Pro283Ser	p.P283S	ENST00000265026	NM_004721.4	283	Cct/Tct	4/14	1	2	FACETS	0.597	0.473	0.736	0.597	0.473	0.736	SUBCLONAL	1	TRUE	1	0.547163824714563	2		391	147	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356310	66356310	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	16	485	0	ENST00000273854.3:c.1187A>C	p.Lys396Thr	p.K396T	ENST00000273854	NM_004439.5	396	aAg/aCg	5/18	0.315231554251746	1	FACETS	0.345	0.258	0.448	0.345	0.258	0.448	INDETERMINATE	1	TRUE	0	0.547163824714563	1		485	123	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509768	187509768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766893768	NA	P-0004228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	27	219	0	ENST00000441802.2:c.13745C>T	p.Ser4582Phe	p.S4582F	ENST00000441802	NM_005245.3	4582	tCc/tTc	27/27	0.315231554251746	1	FACETS	0.864	0.708	1	0.864	0.708	1	INDETERMINATE	1	TRUE	0	0.547163824714563	1		219	83	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517724	187517724	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	22	210	0	ENST00000441802.2:c.12970C>T	p.Gln4324Ter	p.Q4324*	ENST00000441802	NM_005245.3	4324	Cag/Tag	25/27	0.315231554251746	1	FACETS	0.913	0.734	1	0.913	0.734	1	INDETERMINATE	1	TRUE	0	0.547163824714563	1		210	64	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38943017	38943017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	46	390	0	ENST00000357387.3:c.4970C>T	p.Ser1657Phe	p.S1657F	ENST00000357387	NM_152756.3	1657	tCc/tTc	37/38	0.315231554251746	1	FACETS	0.892	0.768	1	0.892	0.768	1	INDETERMINATE	1	TRUE	0	0.547163824714563	1		390	137	SUCCESS
APC	324	MSKCC	GRCh37	5	112178637	112178637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	45	472	0	ENST00000257430.4:c.7346G>A	p.Ser2449Asn	p.S2449N	ENST00000257430	NM_000038.5	2449	aGc/aAc	16/16	1	2	FACETS	0.94	0.802	1	0.94	0.802	1	CLONAL	1	TRUE	1	0.547163824714563	2		472	175	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418405	139418405	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1286309175	NA	P-0004228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	16	203	1	ENST00000277541.6:c.167G>A	p.Arg56Gln	p.R56Q	ENST00000277541	NM_017617.3	56	cGa/cAa	3/34	0.430958245872647	3	FACETS	0.637	0.476	0.824	0.212	0.158	0.275	SUBCLONAL	1	TRUE	0	0.547163824714563	3		204	117	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426000	49426000	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	81	520	0	ENST00000301067.7:c.12488C>T	p.Pro4163Leu	p.P4163L	ENST00000301067	NM_003482.3	4163	cCc/cTc	39/54	0.194672831000466	3	FACETS	0.786	0.703	0.871	0.786	0.703	0.871	INDETERMINATE	2	TRUE	1	0.547163824714563	3		520	240	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445179	49445179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	51	214	0	ENST00000301067.7:c.2287C>T	p.Pro763Ser	p.P763S	ENST00000301067	NM_003482.3	763	Ccg/Tcg	10/54	0.194672831000466	3	FACETS	1	0.965	1	0.711	0.615	0.811	INDETERMINATE	1	TRUE	1	0.547163824714563	3		214	167	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115111977	115111977	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	38	198	0	ENST00000257566.3:c.1763C>T	p.Ala588Val	p.A588V	ENST00000257566	NM_016569.3	588	gCc/gTc	7/8	1	2	FACETS	0.932	0.784	1	0.932	0.784	1	CLONAL	1	TRUE	1	0.547163824714563	2		198	149	SUCCESS
YES1	7525	MSKCC	GRCh37	18	751726	751726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	33	426	0	ENST00000314574.4:c.350G>A	p.Arg117Lys	p.R117K	ENST00000314574	NM_005433.3	117	aGa/aAa	3/12	0.547163824714563	1	FACETS	0.952	0.8	1	0.952	0.8	1	CLONAL	1	TRUE	0	0.547163824714563	1		426	92	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662151	227662152	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0004228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	58	460	1	ENST00000305123.5:c.1303_1304delinsTT	p.Pro435Phe	p.P435F	ENST00000305123	NM_005544.2	435	CCc/TTc	1/2	1	2	FACETS	0.794	0.689	0.907	0.794	0.689	0.907	CLONAL	1	TRUE	1	0.547163824714563	2		461	267	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551335	29551336	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0004228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	26	396	0	ENST00000389048.3:c.1294_1295delinsAA	p.Gly432Asn	p.G432N	ENST00000389048	NM_004304.4	432	GGc/AAc	6/29	1	2	FACETS	0.485	0.387	0.596	0.485	0.387	0.596	SUBCLONAL	1	TRUE	1	0.547163824714563	2		396	196	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0004233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	169	769	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.824976525036435	2		769	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0004233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	39	472	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	1	2	FACETS	0.137	0.113	0.164	0.137	0.113	0.164	SUBCLONAL	1	TRUE	1	0.824976525036435	2		472	689	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170522	11170522	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	55	422	0	ENST00000358026.2:c.4825G>C	p.Glu1609Gln	p.E1609Q	ENST00000358026	NM_001128849.1	1609	Gag/Cag	34/36	0.824976525036435	3	FACETS	0.211	0.179	0.245	0.105	0.089	0.123	SUBCLONAL	1	TRUE	1	0.824976525036435	3		422	894	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76764089	76764089	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1557034957	NA	P-0004233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	382	670	1	ENST00000373344.5:c.7219C>T	p.Arg2407Ter	p.R2407*	ENST00000373344	NM_000489.3	2407	Cga/Tga	35/35	NA	2	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.824976525036435	2		671	899	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0004253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	22	769	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.902	1			1	INDETERMINATE	1	TRUE	NA	0.425658846995061	2		769	82	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631341	117631341	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	144	352	0	ENST00000368508.3:c.6337G>A	p.Asp2113Asn	p.D2113N	ENST00000368508	NM_002944.2	2113	Gat/Aat	40/43	0.425658846995061	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.425658846995061	1		352	466	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0004253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	351	687	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.299034980608279	5	FACETS	1	0.99	1	0.88	0.843	0.917	CLONAL	4	TRUE	0	0.425658846995061	5		687	614	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480568	123480568	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	139	118	0	ENST00000371139.4:c.76G>A	p.Asp26Asn	p.D26N	ENST00000371139	NM_001114937.2	26	Gat/Aat	1/4	1	1	FACETS	1	0.956	1	1	0.992	1	CLONAL	2	TRUE	0	0.425658846995061	1		118	249	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547022	9547022	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs58486349	NA	P-0004253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	40	62	0	ENST00000353224.5:c.1000G>A	p.Asp334Asn	p.D334N	ENST00000353224	NM_177990.2	334	Gat/Aat	5/10	0.227428612449076	4	FACETS	0.985	0.836	1	0.985	0.836	1	INDETERMINATE	2	TRUE	2	0.425658846995061	4		62	136	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026984	71026984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763413735	NA	P-0004253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	106	140	0	ENST00000318789.4:c.1343C>T	p.Ser448Leu	p.S448L	ENST00000318789	NM_032682.5	448	tCg/tTg	15/21	0.425658846995061	4	FACETS	0.789	0.711	0.87			1	SUBCLONAL	2	TRUE	NA	0.425658846995061	4		140	450	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170367	119170367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1250041558	NA	P-0004253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	141	318	0	ENST00000264033.4:c.2597G>A	p.Ser866Asn	p.S866N	ENST00000264033	NM_005188.3	866	aGt/aAt	16/16	0.273502121253705	4	FACETS	0.786	0.719	0.856	0.786	0.719	0.856	SUBCLONAL	2	TRUE	2	0.425658846995061	4		318	601	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644811	67644811	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	105	202	0	ENST00000264010.4:c.76C>T	p.Gln26Ter	p.Q26*	ENST00000264010	NM_006565.3	26	Cag/Tag	3/12	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.425658846995061	2		202	483	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122350	17122350	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	108	196	0	ENST00000285071.4:c.1045C>T	p.Leu349Phe	p.L349F	ENST00000285071	NM_144997.5	349	Ctc/Ttc	9/14	0.38323267944385	3	FACETS	0.76	0.687	0.835	0.76	0.687	0.835	SUBCLONAL	2	TRUE	1	0.425658846995061	3		196	405	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306632	41306632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	126	302	0	ENST00000373198.4:c.1027C>T	p.Pro343Ser	p.P343S	ENST00000373198	NM_133170.3	343	Ccc/Tcc	7/32	0.227428612449076	4	FACETS	0.876	0.798	0.956	0.876	0.798	0.956	INDETERMINATE	2	TRUE	2	0.425658846995061	4		302	482	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	121	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.73	2		174	326	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0004274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	289	718	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	1	2	FACETS	0.937	0.884	0.991	0.937	0.884	0.991	CLONAL	1	TRUE	1	0.73	2		718	845	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685314	89685315	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TG	TG	-	rs1564826836	NA	P-0004274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	152	378	0	ENST00000371953.3:c.209+1_209+2del		p.X70_splice	ENST00000371953	NM_000314.4	70		3/9	1	2	FACETS	0.789	0.726	0.854	0.789	0.726	0.854	SUBCLONAL	1	TRUE	1	0.73	2		378	528	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624305	89624305	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	rs746128825	NA	P-0004274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	223	365	0	ENST00000371953.3:c.79T>A	p.Tyr27Asn	p.Y27N	ENST00000371953	NM_000314.4	27	Tat/Aat	1/9	1	2	FACETS	0.94	0.88	1	0.94	0.88	1	CLONAL	1	TRUE	1	0.73	2		365	650	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287446	46287446	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs774801990	NA	P-0004274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	298	724	1	ENST00000334344.6:c.5305C>T	p.Arg1769Ter	p.R1769*	ENST00000334344	NM_152641.2	1769	Cga/Tga	20/21	1	2	FACETS	0.85	0.802	0.9	0.85	0.802	0.9	CLONAL	1	TRUE	1	0.73	2		725	960	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041807	14041807	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	336	691	1	ENST00000311895.7:c.2354G>A	p.Ser785Asn	p.S785N	ENST00000311895	NM_005236.2	785	aGt/aAt	11/11	1	2	FACETS	0.996	0.945	1	0.996	0.945	1	CLONAL	1	TRUE	1	0.73	2		692	924	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004291-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	91	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.799619312784248	2		174	191	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0004291-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	427	300	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.759936343704412	2	FACETS	0.964	0.937	0.99	0.964	0.937	0.99	CLONAL	2	TRUE	0	0.799619312784248	2		300	554	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561911	55561911	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004291-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	83	249	0	ENST00000288135.5:c.301C>A	p.His101Asn	p.H101N	ENST00000288135	NM_000222.2	101	Cac/Aac	2/21	0.418090682812709	1	FACETS	0.222	0.196	0.25	0.222	0.196	0.25	INDETERMINATE	1	TRUE	0	0.799619312784248	1		249	562	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503842	149503842	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1554108211	NA	P-0004291-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	58	221	0	ENST00000261799.4:c.1994T>C	p.Val665Ala	p.V665A	ENST00000261799	NM_002609.3	665	gTc/gCc	14/23	1	2	FACETS	0.202	0.173	0.234	0.202	0.173	0.234	SUBCLONAL	1	TRUE	1	0.799619312784248	2		221	718	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004304-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	38	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.820786873047205	2		174	92	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0004304-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	137	379	2	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	0.820786873047205	2		381	306	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791757	42791757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568504941	NA	P-0004304-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	8	400	0	ENST00000575354.2:c.643C>T	p.Arg215Trp	p.R215W	ENST00000575354	NM_015125.3	215	Cgg/Tgg	5/20	0.820786873047205	1	FACETS	0.06	0.038	0.088	0.06	0.038	0.088	SUBCLONAL	1	TRUE	0	0.820786873047205	1		400	193	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444688	78444688	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0004304-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	70	207	0	ENST00000370768.2:c.1A>G	p.Met1?	p.M1?	ENST00000370768	NM_003902.3	1	Atg/Gtg	1/20	0.820786873047205	1	FACETS	0.845	0.768	0.921	0.845	0.768	0.921	CLONAL	1	TRUE	0	0.820786873047205	1		207	119	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39772528	39772528	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004304-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	153	507	0	ENST00000288319.7:c.713C>A	p.Pro238His	p.P238H	ENST00000288319	NM_182918.3	238	cCt/cAt	6/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.820786873047205	2		507	343	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0004306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	24	769	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		769	61	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	37	174	0				ENST00000310581	NM_198253.2	-/1132			0.282193841982225	4	FACETS	0.899	0.751	1	0.899	0.751	1	CLONAL	2	TRUE	2	0.307395828593839	4		174	175	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0004349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	303	318	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.307395828593839	4	FACETS	0.969	0.92	1	1	0.993	1	CLONAL	4	TRUE	1	0.307395828593839	4		318	665	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968251	2968251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377769236	NA	P-0004349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	214	226	0	ENST00000396946.4:c.1735G>A	p.Glu579Lys	p.E579K	ENST00000396946	NM_032415.4	579	Gag/Aag	13/25	0.253332889838839	4	FACETS	0.957	0.895	1	0.718	0.671	0.766	CLONAL	3	TRUE	0	0.307395828593839	4		226	634	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64126867	64126867	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749166781	NA	P-0004349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	59	166	0	ENST00000334205.4:c.73G>A	p.Glu25Lys	p.E25K	ENST00000334205	NM_003942.2	25	Gag/Aag	2/17	0.282444758519193	3	FACETS	1	0.897	1	0.523	0.452	0.601	CLONAL	1	TRUE	1	0.307395828593839	3		166	423	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933477	100933477	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	129	244	0	ENST00000325455.5:c.1913A>T	p.Lys638Ile	p.K638I	ENST00000325455	NM_001202474.3	638	aAa/aTa	4/8	0.299582221906052	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.307395828593839	2		244	383	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195370	102195370	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	214	370	0	ENST00000263464.3:c.130C>T	p.Pro44Ser	p.P44S	ENST00000263464	NM_001165.4	44	Cct/Tct	2/9	0.299582221906052	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.307395828593839	2		370	671	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687154	37687154	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1311838642	NA	P-0004349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	116	246	0	ENST00000447079.4:c.4058C>T	p.Thr1353Ile	p.T1353I	ENST00000447079	NM_015083.1	1353	aCt/aTt	14/14	0.282444758519193	3	FACETS	1	0.984	1	0.747	0.675	0.822	CLONAL	1	TRUE	1	0.307395828593839	3		246	583	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	12	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.628	0.442	0.858	0.628	0.442	0.858	SUBCLONAL	1	TRUE	1	0.177611230126262	2		174	215	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0004352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	65	780	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.872	0.755	1	0.872	0.755	1	CLONAL	1	TRUE	1	0.177611230126262	2		782	839	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713536	30713536	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	31	122	0	ENST00000295754.5:c.861G>A	p.Trp287Ter	p.W287*	ENST00000295754	NM_003242.5	287	tgG/tgA	4/7	1	2	FACETS	0.839	0.679	1	0.839	0.679	1	CLONAL	1	TRUE	1	0.177611230126262	2		122	416	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41276043	41276043	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	62	247	0	ENST00000357654.3:c.71G>T	p.Cys24Phe	p.C24F	ENST00000357654	NM_007294.3	24	tGt/tTt	2/23	1	2	FACETS	0.987	0.852	1	0.987	0.852	1	CLONAL	1	TRUE	1	0.177611230126262	2		247	707	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374317	31374317	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	54	194	0	ENST00000328111.2:c.316C>T	p.Arg106Ter	p.R106*	ENST00000328111	NM_006892.3	106	Cga/Tga	5/23	1	2	FACETS	0.753	0.641	0.875	0.753	0.641	0.875	SUBCLONAL	1	TRUE	1	0.177611230126262	2		194	808	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403382	139403424	+	frameshift_variant	Frame_Shift_Del	DEL	CTGACAGGTGCCGCCATGCAGGCAGGGCTGTGAGTCGCACTCA	CTGACAGGTGCCGCCATGCAGGCAGGGCTGTGAGTCGCACTCA	-	novel	NA	P-0004352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	113	179	0	ENST00000277541.6:c.3069_3111del	p.Asn1023LysfsTer142	p.N1023Kfs*142	ENST00000277541	NM_017617.3	1023	aaTGAGTGCGACTCACAGCCCTGCCTGCATGGCGGCACCTGTCAG/aa	19/34	0.177611230126262	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	0	0.177611230126262	2		179	607	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	41	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.370657853164536	2		174	169	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184613	11184613	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	138	334	0	ENST00000361445.4:c.6604T>C	p.Phe2202Leu	p.F2202L	ENST00000361445	NM_004958.3	2202	Ttc/Ctc	47/58	1	2	FACETS	0.872	0.793	0.954	0.872	0.793	0.954	CLONAL	1	TRUE	1	0.370657853164536	2		334	854	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089703	27089703	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	134	244	0	ENST00000324856.7:c.2659C>G	p.Pro887Ala	p.P887A	ENST00000324856	NM_006015.4	887	Cca/Gca	8/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.370657853164536	2		244	608	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346666	225346666	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	123	400	0	ENST00000264414.4:c.1972A>G	p.Ile658Val	p.I658V	ENST00000264414	NM_003590.4	658	Ata/Gta	14/16	1	2	FACETS	0.944	0.855	1	0.944	0.855	1	CLONAL	1	TRUE	1	0.370657853164536	2		400	703	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651513	52651513	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	123	371	0	ENST00000394830.3:c.1583A>T	p.Asn528Ile	p.N528I	ENST00000394830	NM_018313.4	528	aAt/aTt	15/30	0.370657853164536	1	FACETS	0.983	0.893	1	0.983	0.893	1	CLONAL	1	TRUE	0	0.370657853164536	1		371	550	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518221	8518221	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	188	319	0	ENST00000356435.5:c.1170A>C	p.Glu390Asp	p.E390D	ENST00000356435		390	gaA/gaC	10/35	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.370657853164536	2		319	872	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183752	10183752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs869025620	NA	P-0004376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	99	260	0	ENST00000256474.2:c.221del	p.Val74AlafsTer85	p.V74Afs*85	ENST00000256474	NM_000551.3	74	gTc/gc	1/3	0.370657853164536	1	FACETS	0.946	0.849	1	0.946	0.849	1	CLONAL	1	TRUE	0	0.370657853164536	1		260	460	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	106	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.77168881006217	2		174	258	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0004393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	121	764	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.786	0.716	0.858	0.786	0.716	0.858	SUBCLONAL	1	TRUE	1	0.77168881006217	2		764	399	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527680	157527680	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs751043203	NA	P-0004393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	214	301	0	ENST00000346085.5:c.5405G>T	p.Arg1802Leu	p.R1802L	ENST00000346085	NM_020732.3	1802	cGa/cTa	20/20	1	2	FACETS	0.873	0.816	0.932	0.873	0.816	0.932	CLONAL	1	TRUE	1	0.77168881006217	2		301	635	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044958	47044958	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	272	378	0	ENST00000377604.3:c.2284C>G	p.Leu762Val	p.L762V	ENST00000377604	NM_001204468.1	762	Ctg/Gtg	20/24	1	2	FACETS	0.968	0.914	1	0.968	0.914	1	CLONAL	1	TRUE	1	0.77168881006217	2		378	728	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797281	135797294	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGTACATTCCAT	AGGGTACATTCCAT	-	novel	NA	P-0004393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	212	354	0	ENST00000298552.3:c.575_588del	p.Tyr192LeufsTer21	p.Y192Lfs*21	ENST00000298552	NM_001162426.1	192	tATGGAATGTACCCT/t	7/23	0.77168881006217	1	FACETS	0.879	0.831	0.927	0.879	0.831	0.927	CLONAL	1	TRUE	0	0.77168881006217	1		354	384	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	39	769	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.951	0.811	1	0.951	0.811	1	CLONAL	1	TRUE	1	0.774123522325237	2		769	106	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188237	142188237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	57	281	0	ENST00000350721.4:c.6494C>T	p.Ala2165Val	p.A2165V	ENST00000350721	NM_001184.3	2165	gCc/gTc	38/47	1	2	FACETS	0.387	0.333	0.445	0.387	0.333	0.445	SUBCLONAL	1	TRUE	1	0.774123522325237	2		281	381	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220274	55220274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	103	449	1	ENST00000275493.2:c.664C>T	p.Arg222Cys	p.R222C	ENST00000275493	NM_005228.3	222	Cgc/Tgc	6/28	0.774123522325237	3	FACETS	0.529	0.473	0.588	0.264	0.236	0.294	SUBCLONAL	1	TRUE	1	0.774123522325237	3		450	698	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	81	845	2	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.774123522325237	3	FACETS	0.354	0.311	0.4	0.177	0.155	0.2	SUBCLONAL	1	TRUE	1	0.774123522325237	3		847	821	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204864	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	148	268	0	ENST00000371953.3:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000371953	NM_000314.4	171	Cag/Tag	6/9	0.774123522325237	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.774123522325237	1		268	221	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577085	+	missense_variant	Missense_Mutation	ONP	CCTC	CCTC	TCTT	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	184	418	0	ENST00000269305.4:c.853_856delinsAAGA	p.Glu285_Glu286delinsLysLys	p.E285_E286delinsKK	ENST00000269305	NM_001126112.2	285	GAGGaa/AAGAaa	8/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.774123522325237	2		418	447	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199469669	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	9	684	0	ENST00000374080.3:c.130G>T	p.Gly44Cys	p.G44C	ENST00000374080		44	Ggt/Tgt	2/45	1	1	FACETS	0.046	0.03	0.067	0.046	0.03	0.067	SUBCLONAL	1	TRUE	0	0.774123522325237	1		684	307	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731631	47731631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	16	46	0	ENST00000449228.1:c.161G>A	p.Arg54Gln	p.R54Q	ENST00000449228	NM_001127240.2	54	cGa/cAa	2/4	0.559078032822765	3	FACETS	0.869	0.659	1	0.434	0.329	0.552	CLONAL	1	TRUE	1	0.774123522325237	3		46	66	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503718	186503718	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	604	672	0	ENST00000323963.5:c.395G>A	p.Cys132Tyr	p.C132Y	ENST00000323963		132	tGt/tAt	5/11	0.633594778735999	4	FACETS	0.951	0.923	0.98	1	0.997	1	CLONAL	3	TRUE	2	0.774123522325237	4		672	970	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777146	9777146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	123	443	0	ENST00000377346.4:c.910C>T	p.Pro304Ser	p.P304S	ENST00000377346	NM_005026.3	304	Cct/Tct	7/24	1	2	FACETS	0.918	0.841	0.998	0.918	0.841	0.998	CLONAL	1	TRUE	1	0.774123522325237	2		443	346	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11269427	11269427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	47	514	0	ENST00000361445.4:c.3743G>A	p.Gly1248Glu	p.G1248E	ENST00000361445	NM_004958.3	1248	gGa/gAa	25/58	1	2	FACETS	0.243	0.205	0.285	0.243	0.205	0.285	SUBCLONAL	1	TRUE	1	0.774123522325237	2		514	500	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262730	16262730	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	72	215	1	ENST00000375759.3:c.9995G>A	p.Gly3332Asp	p.G3332D	ENST00000375759	NM_015001.2	3332	gGc/gAc	11/15	1	2	FACETS	0.865	0.769	0.965	0.865	0.769	0.965	CLONAL	1	TRUE	1	0.774123522325237	2		216	215	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106577	27106577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316245568	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	157	412	0	ENST00000324856.7:c.6188C>T	p.Thr2063Ile	p.T2063I	ENST00000324856	NM_006015.4	2063	aCa/aTa	20/20	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.774123522325237	2		412	401	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332642	65332642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772923219	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	192	412	0	ENST00000342505.4:c.897G>A	p.Met299Ile	p.M299I	ENST00000342505	NM_002227.2	299	atG/atA	7/25	1	2	FACETS	0.912	0.85	0.975	0.912	0.85	0.975	CLONAL	1	TRUE	1	0.774123522325237	2		412	544	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430773	78430773	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	38	395	0	ENST00000370768.2:c.616G>A	p.Glu206Lys	p.E206K	ENST00000370768	NM_003902.3	206	Gaa/Aaa	8/20	1	2	FACETS	0.213	0.176	0.255	0.213	0.176	0.255	SUBCLONAL	1	TRUE	1	0.774123522325237	2		395	461	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026507	48026507	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1558661506	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	157	480	0	ENST00000234420.5:c.1385C>T	p.Pro462Leu	p.P462L	ENST00000234420	NM_000179.2	462	cCt/cTt	4/10	1	2	FACETS	0.957	0.886	1	0.957	0.886	1	CLONAL	1	TRUE	1	0.774123522325237	2		480	424	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030787	48030787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	80	213	0	ENST00000234420.5:c.3401G>A	p.Gly1134Glu	p.G1134E	ENST00000234420	NM_000179.2	1134	gGa/gAa	5/10	1	2	FACETS	0.883	0.79	0.98	0.883	0.79	0.98	CLONAL	1	TRUE	1	0.774123522325237	2		213	234	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015303	128015303	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	106	270	0	ENST00000285398.2:c.2218G>A	p.Ala740Thr	p.A740T	ENST00000285398	NM_000122.1	740	Gca/Aca	15/15	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.774123522325237	2		270	261	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198283287	198283287	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768032201	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	49	397	0	ENST00000335508.6:c.441G>A	p.Met147Ile	p.M147I	ENST00000335508	NM_012433.2	147	atG/atA	5/25	1	2	FACETS	0.262	0.222	0.306	0.262	0.222	0.306	SUBCLONAL	1	TRUE	1	0.774123522325237	2		397	483	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660648	227660648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	111	324	1	ENST00000305123.5:c.2807C>T	p.Thr936Ile	p.T936I	ENST00000305123	NM_005544.2	936	aCt/aTt	1/2	1	2	FACETS	0.943	0.86	1	0.943	0.86	1	CLONAL	1	TRUE	1	0.774123522325237	2		325	304	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713147	30713147	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886058303	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	69	189	0	ENST00000295754.5:c.472C>T	p.Pro158Ser	p.P158S	ENST00000295754	NM_003242.5	158	Cct/Tct	4/7	1	2	FACETS	0.663	0.583	0.746	0.663	0.583	0.746	SUBCLONAL	1	TRUE	1	0.774123522325237	2		189	269	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275179	41275179	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771596917	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	24	333	0	ENST00000349496.5:c.1345C>T	p.Arg449Cys	p.R449C	ENST00000349496	NM_001904.3	449	Cgt/Tgt	9/15	1	2	FACETS	0.172	0.135	0.216	0.172	0.135	0.216	SUBCLONAL	1	TRUE	1	0.774123522325237	2		333	360	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52677322	52677322	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	64	401	0	ENST00000394830.3:c.937C>T	p.Pro313Ser	p.P313S	ENST00000394830	NM_018313.4	313	Cct/Tct	10/30	1	2	FACETS	0.342	0.296	0.391	0.342	0.296	0.391	SUBCLONAL	1	TRUE	1	0.774123522325237	2		401	484	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806638	1806638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	63	517	1	ENST00000260795.2:c.1354G>A	p.Ala452Thr	p.A452T	ENST00000260795		452	Gcc/Acc	9/17	1	2	FACETS	0.392	0.34	0.448	0.392	0.34	0.448	SUBCLONAL	1	TRUE	1	0.774123522325237	2		518	415	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964947	55964947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	115	334	0	ENST00000263923.4:c.2290G>A	p.Glu764Lys	p.E764K	ENST00000263923	NM_002253.2	764	Gaa/Aaa	16/30	1	2	FACETS	0.693	0.628	0.759	0.693	0.628	0.759	SUBCLONAL	1	TRUE	1	0.774123522325237	2		334	429	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213797	66213797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1195849754	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	48	393	0	ENST00000273854.3:c.2633C>T	p.Pro878Leu	p.P878L	ENST00000273854	NM_004439.5	878	cCc/cTc	15/18	1	2	FACETS	0.326	0.276	0.381	0.326	0.276	0.381	SUBCLONAL	1	TRUE	1	0.774123522325237	2		393	380	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158425	106158425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1441492512	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	24	341	0	ENST00000380013.4:c.3326C>T	p.Ser1109Phe	p.S1109F	ENST00000380013	NM_001127208.2	1109	tCc/tTc	3/11	1	2	FACETS	0.159	0.124	0.2	0.159	0.124	0.2	SUBCLONAL	1	TRUE	1	0.774123522325237	2		341	389	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629604	187629604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	20	336	0	ENST00000441802.2:c.1378C>T	p.Pro460Ser	p.P460S	ENST00000441802	NM_005245.3	460	Ccc/Tcc	2/27	1	2	FACETS	0.134	0.102	0.171	0.134	0.102	0.171	SUBCLONAL	1	TRUE	1	0.774123522325237	2		336	387	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294232	1294232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	52	195	0	ENST00000310581.5:c.769G>A	p.Ala257Thr	p.A257T	ENST00000310581	NM_198253.2	257	Gcc/Acc	2/16	1	2	FACETS	0.878	0.764	0.997	0.878	0.764	0.997	CLONAL	1	TRUE	1	0.774123522325237	2		195	153	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672738	86672738	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	140	324	0	ENST00000274376.6:c.2225C>T	p.Ser742Leu	p.S742L	ENST00000274376	NM_002890.2	742	tCa/tTa	17/25	1	2	FACETS	0.876	0.805	0.948	0.876	0.805	0.948	CLONAL	1	TRUE	1	0.774123522325237	2		324	413	SUCCESS
APC	324	MSKCC	GRCh37	5	112157676	112157676	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs781364007	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	42	284	0	ENST00000257430.4:c.1396A>G	p.Met466Val	p.M466V	ENST00000257430	NM_000038.5	466	Atg/Gtg	11/16	1	2	FACETS	0.278	0.232	0.329	0.278	0.232	0.329	SUBCLONAL	1	TRUE	1	0.774123522325237	2		284	390	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188784	32188784	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	97	305	0	ENST00000375023.3:c.770C>T	p.Ser257Phe	p.S257F	ENST00000375023	NM_004557.3	257	tCc/tTc	4/30	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.774123522325237	2		305	244	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651948	36651948	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1276639827	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	88	257	0	ENST00000244741.5:c.70C>T	p.Pro24Ser	p.P24S	ENST00000244741	NM_000389.4	24	Cca/Tca	2/3	1	2	FACETS	0.733	0.657	0.813	0.733	0.657	0.813	SUBCLONAL	1	TRUE	1	0.774123522325237	2		257	310	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681154	117681154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	18	300	0	ENST00000368508.3:c.3466C>T	p.Leu1156Phe	p.L1156F	ENST00000368508	NM_002944.2	1156	Ctc/Ttc	23/43	NA	2	FACETS	0.131	0.098	0.17			1	INDETERMINATE	1	TRUE	NA	0.774123522325237	2		300	354	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527940	157527940	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	104	187	0	ENST00000346085.5:c.5665C>T	p.Pro1889Ser	p.P1889S	ENST00000346085	NM_020732.3	1889	Cct/Tct	20/20	1	2	FACETS	0.981	0.892	1	0.981	0.892	1	CLONAL	1	TRUE	1	0.774123522325237	2		187	274	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398563	116398563	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	66	417	0	ENST00000397752.3:c.2153C>T	p.Thr718Ile	p.T718I	ENST00000397752	NM_000245.2	718	aCt/aTt	9/21	0.774123522325237	3	FACETS	0.357	0.309	0.408	0.178	0.154	0.204	SUBCLONAL	1	TRUE	1	0.774123522325237	3		417	663	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128848692	128848692	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	101	308	0	ENST00000249373.3:c.1357G>A	p.Gly453Ser	p.G453S	ENST00000249373	NM_005631.4	453	Ggc/Agc	7/12	0.774123522325237	3	FACETS	0.885	0.797	0.977	0.442	0.398	0.489	CLONAL	1	TRUE	1	0.774123522325237	3		308	409	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850338	128850338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	118	376	0	ENST00000249373.3:c.1601C>T	p.Thr534Ile	p.T534I	ENST00000249373	NM_005631.4	534	aCc/aTc	9/12	0.774123522325237	3	FACETS	0.786	0.712	0.863	0.393	0.356	0.432	SUBCLONAL	1	TRUE	1	0.774123522325237	3		376	538	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860613	151860613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200124578	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	172	434	0	ENST00000262189.6:c.10049G>A	p.Arg3350Lys	p.R3350K	ENST00000262189	NM_170606.2	3350	aGa/aAa	43/59	0.774123522325237	3	FACETS	0.971	0.897	1	0.485	0.448	0.524	CLONAL	1	TRUE	1	0.774123522325237	3		434	635	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868441	117868441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	216	617	0	ENST00000297338.2:c.901G>A	p.Glu301Lys	p.E301K	ENST00000297338	NM_006265.2	301	Gaa/Aaa	8/14	1	2	FACETS	0.936	0.877	0.997	0.936	0.877	0.997	CLONAL	1	TRUE	1	0.774123522325237	2		617	596	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232117	98232117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	53	311	0	ENST00000331920.6:c.1825G>A	p.Asp609Asn	p.D609N	ENST00000331920	NM_000264.3	609	Gat/Aat	13/24	1	2	FACETS	0.392	0.336	0.454	0.392	0.336	0.454	SUBCLONAL	1	TRUE	1	0.774123522325237	2		311	349	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390588	139390588	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	179	499	0	ENST00000277541.6:c.7603G>A	p.Gly2535Ser	p.G2535S	ENST00000277541	NM_017617.3	2535	Ggc/Agc	34/34	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.774123522325237	2		499	456	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100442	8100442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	174	511	0	ENST00000346208.3:c.416C>T	p.Ser139Phe	p.S139F	ENST00000346208		139	tCc/tTc	3/6	0.660709951470942	1	FACETS	0.928	0.874	0.981	0.928	0.874	0.981	CLONAL	1	TRUE	0	0.774123522325237	1		511	297	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63699993	63699993	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1455393290	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	40	229	0	ENST00000279873.7:c.328G>A	p.Val110Ile	p.V110I	ENST00000279873	NM_032199.2	110	Gtc/Atc	3/10	0.774123522325237	1	FACETS	0.342	0.288	0.401	0.342	0.288	0.401	SUBCLONAL	1	TRUE	0	0.774123522325237	1		229	185	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64126913	64126913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	22	315	0	ENST00000334205.4:c.119G>A	p.Gly40Asp	p.G40D	ENST00000334205	NM_003942.2	40	gGc/gAc	2/17	1	2	FACETS	0.219	0.169	0.275	0.219	0.169	0.275	SUBCLONAL	1	TRUE	1	0.774123522325237	2		315	260	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625120	69625120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782246758	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	90	261	0	ENST00000334134.2:c.673G>A	p.Val225Ile	p.V225I	ENST00000334134	NM_005247.2	225	Gtt/Att	3/3	1	2	FACETS	0.898	0.809	0.99	0.898	0.809	0.99	CLONAL	1	TRUE	1	0.774123522325237	2		261	259	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633587	69633587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	12	120	0	ENST00000334134.2:c.115C>T	p.Leu39Phe	p.L39F	ENST00000334134	NM_005247.2	39	Ctt/Ttt	1/3	1	2	FACETS	0.413	0.295	0.553	0.413	0.295	0.553	SUBCLONAL	1	TRUE	1	0.774123522325237	2		120	75	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981677	101981677	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	18	26	0	ENST00000282441.5:c.98C>T	p.Pro33Leu	p.P33L	ENST00000282441	NM_001130145.2	33	cCc/cTc	1/9	NA	2	FACETS	1	0.88	1			1	INDETERMINATE	1	TRUE	NA	0.774123522325237	2		26	40	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102056751	102056751	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	35	339	0	ENST00000282441.5:c.691C>T	p.Pro231Ser	p.P231S	ENST00000282441	NM_001130145.2	231	Cct/Tct	4/9	NA	2	FACETS	0.281	0.23	0.337			1	INDETERMINATE	1	TRUE	NA	0.774123522325237	2		339	322	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121493	108121493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	124	263	0	ENST00000278616.4:c.1301C>T	p.Pro434Leu	p.P434L	ENST00000278616	NM_000051.3	434	cCa/cTa	10/63	1	2	FACETS	0.921	0.843	1	0.921	0.843	1	CLONAL	1	TRUE	1	0.774123522325237	2		263	348	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344849	118344849	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	144	496	0	ENST00000534358.1:c.2975C>T	p.Ser992Phe	p.S992F	ENST00000534358	NM_005933.3	992	tCc/tTc	3/36	1	2	FACETS	0.752	0.69	0.815	0.752	0.69	0.815	SUBCLONAL	1	TRUE	1	0.774123522325237	2		496	495	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375321	118375321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	113	277	0	ENST00000534358.1:c.8714C>T	p.Pro2905Leu	p.P2905L	ENST00000534358	NM_005933.3	2905	cCt/cTt	27/36	1	2	FACETS	0.96	0.877	1	0.96	0.877	1	CLONAL	1	TRUE	1	0.774123522325237	2		277	304	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419103	419103	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	163	488	0	ENST00000399788.2:c.3244G>A	p.Val1082Ile	p.V1082I	ENST00000399788	NM_001042603.1	1082	Gta/Ata	22/28	NA	2	FACETS	0.948	0.879	1			1	INDETERMINATE	1	TRUE	NA	0.774123522325237	2		488	444	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432297	432297	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	51	373	0	ENST00000399788.2:c.2226G>A	p.Trp742Ter	p.W742*	ENST00000399788	NM_001042603.1	742	tgG/tgA	16/28	NA	2	FACETS	0.269	0.229	0.314			1	INDETERMINATE	1	TRUE	NA	0.774123522325237	2		373	489	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	495130	495130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	53	448	0	ENST00000399788.2:c.176C>T	p.Pro59Leu	p.P59L	ENST00000399788	NM_001042603.1	59	cCt/cTt	2/28	NA	2	FACETS	0.336	0.287	0.39			1	INDETERMINATE	1	TRUE	NA	0.774123522325237	2		448	407	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420739	49420739	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	82	304	0	ENST00000301067.7:c.15010G>A	p.Glu5004Lys	p.E5004K	ENST00000301067	NM_003482.3	5004	Gag/Aag	48/54	1	2	FACETS	0.738	0.658	0.821	0.738	0.658	0.821	SUBCLONAL	1	TRUE	1	0.774123522325237	2		304	287	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426147	49426147	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1342813038	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	94	225	0	ENST00000301067.7:c.12341G>A	p.Gly4114Glu	p.G4114E	ENST00000301067	NM_003482.3	4114	gGa/gAa	39/54	1	2	FACETS	0.995	0.901	1	0.995	0.901	1	CLONAL	1	TRUE	1	0.774123522325237	2		225	244	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440403	49440403	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	38	247	0	ENST00000301067.7:c.4407G>A	p.Trp1469Ter	p.W1469*	ENST00000301067	NM_003482.3	1469	tgG/tgA	15/54	1	2	FACETS	0.334	0.277	0.397	0.334	0.277	0.397	SUBCLONAL	1	TRUE	1	0.774123522325237	2		247	294	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222575	69222575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	173	329	0	ENST00000462284.1:c.548G>A	p.Gly183Asp	p.G183D	ENST00000462284	NM_002392.5	183	gGt/gAt	8/11	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.774123522325237	2		329	441	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112892428	112892428	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	156	313	0	ENST00000351677.2:c.586C>T	p.His196Tyr	p.H196Y	ENST00000351677	NM_002834.3	196	Cat/Tat	5/16	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.774123522325237	2		313	395	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959446	26959446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	163	390	0	ENST00000381527.3:c.613C>T	p.Leu205Phe	p.L205F	ENST00000381527	NM_001260.1	205	Ctt/Ttt	6/13	NA	2	FACETS	0.938	0.869	1			1	INDETERMINATE	1	TRUE	NA	0.774123522325237	2		390	449	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877491	28877491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765429388	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	83	217	0	ENST00000282397.4:c.3830G>A	p.Ser1277Asn	p.S1277N	ENST00000282397	NM_002019.4	1277	aGt/aAt	30/30	NA	2	FACETS	0.841	0.753	0.932			1	INDETERMINATE	1	TRUE	NA	0.774123522325237	2		217	255	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572036	95572036	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	45	390	0	ENST00000393063.1:c.3072G>A	p.Trp1024Ter	p.W1024*	ENST00000393063	NM_030621.3	1024	tgG/tgA	20/28	1	2	FACETS	0.224	0.188	0.264	0.224	0.188	0.264	SUBCLONAL	1	TRUE	1	0.774123522325237	2		390	519	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678455	88678455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	139	469	0	ENST00000360948.2:c.1081G>A	p.Gly361Ser	p.G361S	ENST00000360948	NM_001012338.2	361	Ggc/Agc	9/19	1	2	FACETS	0.916	0.843	0.991	0.916	0.843	0.991	CLONAL	1	TRUE	1	0.774123522325237	2		469	392	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99452053	99452053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	35	393	0	ENST00000268035.6:c.1387G>A	p.Glu463Lys	p.E463K	ENST00000268035	NM_000875.3	463	Gag/Aag	6/21	1	2	FACETS	0.253	0.207	0.304	0.253	0.207	0.304	SUBCLONAL	1	TRUE	1	0.774123522325237	2		393	358	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99473487	99473487	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	26	252	0	ENST00000268035.6:c.2909G>A	p.Gly970Glu	p.G970E	ENST00000268035	NM_000875.3	970	gGa/gAa	15/21	1	2	FACETS	0.204	0.161	0.252	0.204	0.161	0.252	SUBCLONAL	1	TRUE	1	0.774123522325237	2		252	330	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821730	72821730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202147244	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	49	621	0	ENST00000268489.5:c.10445G>A	p.Ser3482Asn	p.S3482N	ENST00000268489	NM_006885.3	3482	aGc/aAc	10/10	0.268165807102183	1	FACETS	0.165	0.14	0.194	0.165	0.14	0.194	INDETERMINATE	1	TRUE	0	0.774123522325237	1		621	469	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972412	81972412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779506592	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	53	665	0	ENST00000359376.3:c.3205G>A	p.Gly1069Ser	p.G1069S	ENST00000359376	NM_002661.3	1069	Ggt/Agt	29/33	0.268165807102183	1	FACETS	0.136	0.115	0.159	0.136	0.115	0.159	INDETERMINATE	1	TRUE	0	0.774123522325237	1		665	617	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989388	7989388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	107	340	0	ENST00000319144.4:c.298C>T	p.Pro100Ser	p.P100S	ENST00000319144	NM_001139.2	100	Ccc/Tcc	2/15	1	2	FACETS	0.861	0.782	0.943	0.861	0.782	0.943	CLONAL	1	TRUE	1	0.774123522325237	2		340	321	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881580	37881580	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	89	290	0	ENST00000269571.5:c.2650G>A	p.Val884Met	p.V884M	ENST00000269571		884	Gtg/Atg	22/27	1	2	FACETS	0.668	0.598	0.742	0.668	0.598	0.742	SUBCLONAL	1	TRUE	1	0.774123522325237	2		290	344	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40478201	40478201	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	208	538	0	ENST00000264657.5:c.1298C>T	p.Thr433Ile	p.T433I	ENST00000264657	NM_139276.2	433	aCt/aTt	15/24	NA	2	FACETS	0.96	0.898	1			1	INDETERMINATE	1	TRUE	NA	0.774123522325237	2		538	560	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696378	47696378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	37	318	0	ENST00000347630.2:c.445C>T	p.Leu149Phe	p.L149F	ENST00000347630	NM_001007230.1	149	Ctt/Ttt	6/11	1	2	FACETS	0.216	0.178	0.259	0.216	0.178	0.259	SUBCLONAL	1	TRUE	1	0.774123522325237	2		318	442	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59937156	59937156	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	30	335	0	ENST00000259008.2:c.205+1G>A		p.X69_splice	ENST00000259008	NM_032043.2	69			1	2	FACETS	0.171	0.137	0.209	0.171	0.137	0.209	SUBCLONAL	1	TRUE	1	0.774123522325237	2		335	454	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1646395	1646395	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1311327935	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	33	502	1	ENST00000344749.5:c.104G>A	p.Gly35Asp	p.G35D	ENST00000344749	NM_001136139.2	35	gGc/gAc	3/19	0.454839353875626	3	FACETS	0.224	0.182	0.272			1	INDETERMINATE	1	TRUE	NA	0.774123522325237	3		503	527	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7119586	7119586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555734564	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	71	284	0	ENST00000302850.5:c.3668G>A	p.Gly1223Asp	p.G1223D	ENST00000302850	NM_000208.2	1223	gGc/gAc	21/22	0.752079480194456	3	FACETS	0.569	0.498	0.645	0.285	0.249	0.323	SUBCLONAL	1	TRUE	1	0.774123522325237	3		284	447	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267799	7267799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	85	192	0	ENST00000302850.5:c.209C>T	p.Pro70Leu	p.P70L	ENST00000302850	NM_000208.2	70	cCc/cTc	2/22	0.752079480194456	3	FACETS	1	0.927	1	0.523	0.468	0.581	CLONAL	1	TRUE	1	0.774123522325237	3		192	291	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271816	15271816	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356235052	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	60	168	0	ENST00000263388.2:c.6623C>T	p.Pro2208Leu	p.P2208L	ENST00000263388	NM_000435.2	2208	cCc/cTc	33/33	0.752079480194456	3	FACETS	0.986	0.862	1	0.493	0.431	0.559	CLONAL	1	TRUE	1	0.774123522325237	3		168	218	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266729	18266729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	73	215	0	ENST00000222254.8:c.40C>T	p.Pro14Ser	p.P14S	ENST00000222254	NM_005027.3	14	Ccg/Tcg	2/16	0.752079480194456	3	FACETS	0.881	0.778	0.989	0.44	0.389	0.495	CLONAL	1	TRUE	1	0.774123522325237	3		215	297	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271374	18271374	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	28	371	0	ENST00000222254.8:c.415+1G>A		p.X139_splice	ENST00000222254	NM_005027.3	139			0.752079480194456	3	FACETS	0.197	0.157	0.243	0.099	0.078	0.122	SUBCLONAL	1	TRUE	1	0.774123522325237	3		371	509	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792082	42792082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1292046972	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	29	255	0	ENST00000575354.2:c.886C>T	p.Arg296Trp	p.R296W	ENST00000575354	NM_015125.3	296	Cgg/Tgg	6/20	0.559078032822765	3	FACETS	0.36	0.289	0.439	0.18	0.144	0.22	SUBCLONAL	1	TRUE	1	0.774123522325237	3		255	289	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855816	45855816	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755955616	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	100	335	0	ENST00000391945.4:c.1994G>A	p.Gly665Asp	p.G665D	ENST00000391945	NM_000400.3	665	gGt/gAt	21/23	0.559078032822765	3	FACETS	0.699	0.626	0.775	0.349	0.313	0.388	SUBCLONAL	1	TRUE	1	0.774123522325237	3		335	513	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167497	24167497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555880581	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	124	243	0	ENST00000263121.7:c.881C>T	p.Ala294Val	p.A294V	ENST00000263121	NM_003073.3	294	gCc/gTc	7/9	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.774123522325237	2		243	267	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573240	41573240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	84	364	0	ENST00000263253.7:c.5525G>A	p.Gly1842Glu	p.G1842E	ENST00000263253	NM_001429.3	1842	gGg/gAg	31/31	1	2	FACETS	0.764	0.683	0.849	0.764	0.683	0.849	SUBCLONAL	1	TRUE	1	0.774123522325237	2		364	284	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969474	44969474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	35	250	0	ENST00000377967.4:c.4156G>A	p.Val1386Ile	p.V1386I	ENST00000377967	NM_021140.2	1386	Gtc/Atc	28/29	1	1	FACETS	0.227	0.187	0.272	0.227	0.187	0.272	SUBCLONAL	1	TRUE	0	0.774123522325237	1		250	244	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	17	174	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		174	82	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004430-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	26	174	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.595	0.48	0.723			1	INDETERMINATE	1	FALSE	NA	0.752833223995377	2		174	116	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0004430-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	239	379	2	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.263830377989263	5	FACETS	0.877	0.821	0.933	0.584	0.547	0.622	INDETERMINATE	2	FALSE	2	0.752833223995377	5		381	771	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86686641	86686641	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs377550978	NA	P-0004430-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	309	447	0	ENST00000274376.6:c.3085A>G	p.Ile1029Val	p.I1029V	ENST00000274376	NM_002890.2	1029	Ata/Gta	25/25	0.752833223995377	4	FACETS	1	0.986	1	0.573	0.539	0.607	CLONAL	1	FALSE	2	0.752833223995377	4		447	1256	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798191	42798191	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004430-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	121	516	1	ENST00000575354.2:c.4145C>A	p.Ser1382Ter	p.S1382*	ENST00000575354	NM_015125.3	1382	tCa/tAa	17/20	0.181883137920415	5	FACETS	0.92	0.84	1			1	INDETERMINATE	2	FALSE	NA	0.752833223995377	5		517	372	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0004493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	56	769	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.933	1			1	INDETERMINATE	1	TRUE	NA	0.798484591644665	2		769	129	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0004493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	159	443	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.798484591644665	2		443	381	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953229	81953229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	263	704	0	ENST00000359376.3:c.2195G>A	p.Arg732His	p.R732H	ENST00000359376	NM_002661.3	732	cGc/cAc	20/33	NA	2	FACETS	1	0.956	1			1	INDETERMINATE	1	TRUE	NA	0.798484591644665	2		704	649	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796870	42796870	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	164	593	1	ENST00000575354.2:c.3328C>T	p.Gln1110Ter	p.Q1110*	ENST00000575354	NM_015125.3	1110	Cag/Tag	14/20	0.798484591644665	1	FACETS	0.878	0.825	0.93	0.878	0.825	0.93	CLONAL	1	TRUE	0	0.798484591644665	1		594	281	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	322	174	0				ENST00000310581	NM_198253.2	-/1132			0.698935252829647	7	FACETS	1	0.978	1	1	0.978	1	CLONAL	5	TRUE	2	0.698935252829647	7		174	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0004503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	428	410	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.698935252829647	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.698935252829647	2		410	586	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955419	48955419	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0004503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	34	460	0	ENST00000267163.4:c.1535T>A	p.Leu512Ter	p.L512*	ENST00000267163	NM_000321.2	512	tTg/tAg	17/27	0.648966210952619	2	FACETS	0.159	0.129	0.193	0.08	0.064	0.097	SUBCLONAL	1	TRUE	0	0.698935252829647	2		460	611	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602412	10602412	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	391	548	0	ENST00000171111.5:c.1166A>G	p.Asp389Gly	p.D389G	ENST00000171111	NM_203500.1	389	gAc/gGc	3/6	0.688502232881782	2	FACETS	0.975	0.941	1	0.975	0.941	1	CLONAL	2	TRUE	0	0.698935252829647	2		548	574	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	178	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.974	0.904	1	0.974	0.904	1	CLONAL	1	TRUE	1	0.668378636039685	2		174	547	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0004510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1652	474	406	0	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.668378636039685	3	FACETS	0.89	0.848	0.934	0.445	0.424	0.467	CLONAL	1	TRUE	1	0.668378636039685	3		406	2126	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888189	112888189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507511	NA	P-0004510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	281	663	1	ENST00000351677.2:c.205G>A	p.Glu69Lys	p.E69K	ENST00000351677	NM_002834.3	69	Gag/Aag	3/16	1	2	FACETS	0.762	0.716	0.809	0.762	0.716	0.809	SUBCLONAL	1	TRUE	1	0.668378636039685	2		664	1104	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624303	89624303	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs786204853	NA	P-0004510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	288	385	0	ENST00000371953.3:c.77C>T	p.Thr26Ile	p.T26I	ENST00000371953	NM_000314.4	26	aCc/aTc	1/9	0.668378636039685	1	FACETS	0.909	0.862	0.956	0.909	0.862	0.956	CLONAL	1	TRUE	0	0.668378636039685	1		385	631	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556889	29556889	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660444	NA	P-0004510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	183	261	0	ENST00000356175.3:c.2887C>T	p.Gln963Ter	p.Q963*	ENST00000356175	NM_000267.3	963	Caa/Taa	22/57	1	2	FACETS	0.966	0.897	1	0.966	0.897	1	CLONAL	1	TRUE	1	0.668378636039685	2		261	567	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	75	174	0				ENST00000310581	NM_198253.2	-/1132			0.70379056660781	1	FACETS	0.775	0.711	0.836	0.775	0.711	0.836	SUBCLONAL	1	TRUE	0	0.913946388226217	1		174	115	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0004531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	236	443	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	0.913946388226217	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.913946388226217	1		443	258	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0004531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	50	229	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.788775818675679	3	FACETS	0.291	0.247	0.34			1	SUBCLONAL	1	TRUE	NA	0.913946388226217	3		229	547	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0004531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	42	284	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	0.788775818675679	3	FACETS	0.313	0.261	0.37			1	SUBCLONAL	1	TRUE	NA	0.913946388226217	3		284	428	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415129	116415129	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	61	518	0	ENST00000397752.3:c.3223A>G	p.Ser1075Gly	p.S1075G	ENST00000397752	NM_000245.2	1075	Agc/Ggc	15/21	0.626287035414691	4	FACETS	0.235	0.202	0.271	0.078	0.067	0.091	SUBCLONAL	1	TRUE	1	0.913946388226217	4		518	1088	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006159	22006159	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	29	323	0	ENST00000276925.6:c.244C>G	p.Arg82Gly	p.R82G	ENST00000276925	NM_004936.3	82	Cga/Gga	2/2	0.913946388226217	2	FACETS	0.131	0.104	0.161	0.065	0.052	0.081	SUBCLONAL	1	TRUE	0	0.913946388226217	2		323	485	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226285	2226285	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	48	424	0	ENST00000326181.6:c.1898T>C	p.Met633Thr	p.M633T	ENST00000326181	NM_032271.2	633	aTg/aCg	20/21	1	2	FACETS	0.227	0.192	0.266	0.227	0.192	0.266	SUBCLONAL	1	TRUE	1	0.913946388226217	2		424	462	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211637	5211637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768527095	NA	P-0004531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	35	346	0	ENST00000357368.4:c.5198C>T	p.Ser1733Phe	p.S1733F	ENST00000357368	NM_002850.3	1733	tCt/tTt	33/38	1	2	FACETS	0.154	0.126	0.186	0.154	0.126	0.186	SUBCLONAL	1	TRUE	1	0.913946388226217	2		346	498	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795420	42795420	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	180	302	0	ENST00000575354.2:c.2500C>T	p.Gln834Ter	p.Q834*	ENST00000575354	NM_015125.3	834	Cag/Tag	10/20	0.913946388226217	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.913946388226217	1		302	197	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163503	32163505	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-	novel	NA	P-0004531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	83	438	0	ENST00000375023.3:c.5721_5723del	p.Gly1908del	p.G1908del	ENST00000375023	NM_004557.3	1907	ggAGGc/ggc	30/30	0.913946388226217	6	FACETS	0.408	0.359	0.462			1	SUBCLONAL	1	TRUE	NA	0.913946388226217	6		438	1258	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0004555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	98	327	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.225409583005426	4	FACETS	0.858	0.773	0.946	0.858	0.773	0.946	INDETERMINATE	2	TRUE	2	0.495123885863608	4		327	345	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0004555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	59	638	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.225409583005426	4	FACETS	0.852	0.744	0.966	0.852	0.744	0.966	INDETERMINATE	2	TRUE	2	0.495123885863608	4		639	209	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054984	176054984	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	108	673	0	ENST00000367669.3:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000367669	NM_022457.5	357	Cga/Tga	10/20	0.495123885863608	5	FACETS	1	0.975	1	0.319	0.287	0.353	CLONAL	1	TRUE	1	0.495123885863608	5		673	596	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226568877	226568877	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	85	401	0	ENST00000366794.5:c.1192C>T	p.Leu398Phe	p.L398F	ENST00000366794	NM_001618.3	398	Ctc/Ttc	9/23	0.495123885863608	5	FACETS	1	0.977	1	0.356	0.316	0.398	CLONAL	1	TRUE	1	0.495123885863608	5		401	420	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505393	25505393	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	68	413	0	ENST00000264709.3:c.365C>T	p.Ala122Val	p.A122V	ENST00000264709	NM_175629.2	122	gCt/gTt	4/23	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.495123885863608	2		413	214	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067329	37067329	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	91	430	0	ENST00000231790.2:c.1240G>T	p.Glu414Ter	p.E414*	ENST00000231790	NM_000249.3	414	Gag/Tag	12/19	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.495123885863608	2		430	292	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067404	37067404	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1302248679	NA	P-0004555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	83	371	0	ENST00000231790.2:c.1315G>T	p.Glu439Ter	p.E439*	ENST00000231790	NM_000249.3	439	Gaa/Taa	12/19	NA	2	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.495123885863608	2		371	272	SUCCESS
ATR	545	MSKCC	GRCh37	3	142259779	142259779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780802796	NA	P-0004555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	31	461	1	ENST00000350721.4:c.3548G>A	p.Arg1183Gln	p.R1183Q	ENST00000350721	NM_001184.3	1183	cGa/cAa	18/47	NA	2	FACETS	0.305	0.247	0.372			1	INDETERMINATE	1	TRUE	NA	0.495123885863608	2		462	410	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191253	185191253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56309231	NA	P-0004555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	60	245	0	ENST00000265026.3:c.2134G>A	p.Glu712Lys	p.E712K	ENST00000265026	NM_004721.4	712	Gag/Aag	11/14	0.225409583005426	4	FACETS	1	0.905	1	1	0.905	1	INDETERMINATE	2	TRUE	2	0.495123885863608	4		245	175	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593458	55593458	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1476093811	NA	P-0004555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	94	539	0	ENST00000288135.5:c.1615A>G	p.Ile539Val	p.I539V	ENST00000288135	NM_000222.2	539	Att/Gtt	10/21	0.196000536484189	4	FACETS	1	0.978	1	0.687	0.615	0.763	INDETERMINATE	1	TRUE	2	0.495123885863608	4		539	413	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962430	38962430	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	108	479	0	ENST00000357387.3:c.1702G>A	p.Glu568Lys	p.E568K	ENST00000357387	NM_152756.3	568	Gaa/Aaa	19/38	0.225409583005426	4	FACETS	1	0.984	1	0.748	0.676	0.824	INDETERMINATE	1	TRUE	2	0.495123885863608	4		479	436	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750453	57750453	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	25	522	0	ENST00000274289.3:c.2015G>C	p.Arg672Pro	p.R672P	ENST00000274289	NM_006622.3	672	cGa/cCa	14/14	0.225409583005426	4	FACETS	0.377	0.297	0.47	0.189	0.148	0.235	INDETERMINATE	1	TRUE	2	0.495123885863608	4		522	400	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131976454	131976454	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	82	487	0	ENST00000265335.6:c.3709C>G	p.Leu1237Val	p.L1237V	ENST00000265335		1237	Ctt/Gtt	24/25	0.214420586587536	3	FACETS	1	0.976	1	0.691	0.616	0.77	INDETERMINATE	1	TRUE	1	0.495123885863608	3		487	299	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287853	33287853	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	64	644	0	ENST00000374542.5:c.1400T>C	p.Leu467Pro	p.L467P	ENST00000374542	NM_001141970.1	467	cTg/cCg	5/8	0.225409583005426	4	FACETS	1	0.957	1	0.619	0.54	0.704	INDETERMINATE	1	TRUE	2	0.495123885863608	4		644	312	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041125	112041125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	17	730	0	ENST00000368678.4:c.130G>A	p.Val44Met	p.V44M	ENST00000368678		44	Gtg/Atg	3/13	0.495123885863608	1	FACETS	0.209	0.156	0.272	0.209	0.156	0.272	SUBCLONAL	1	TRUE	0	0.495123885863608	1		730	247	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846308	128846308	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1371471706	NA	P-0004555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	71	483	0	ENST00000249373.3:c.1144G>A	p.Asp382Asn	p.D382N	ENST00000249373	NM_005631.4	382	Gat/Aat	6/12	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.495123885863608	2		483	252	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949758	151949758	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	80	467	0	ENST00000262189.6:c.1342C>T	p.Gln448Ter	p.Q448*	ENST00000262189	NM_170606.2	448	Cag/Tag	10/59	1	2	FACETS	0.976	0.867	1	0.976	0.867	1	CLONAL	1	TRUE	1	0.495123885863608	2		467	331	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341772	8341772	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs773553807	NA	P-0004555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	103	552	0	ENST00000356435.5:c.4868G>C	p.Arg1623Thr	p.R1623T	ENST00000356435		1623	aGa/aCa	29/35	0.225409583005426	4	FACETS	0.798	0.719	0.879	0.798	0.719	0.879	INDETERMINATE	2	TRUE	2	0.495123885863608	4		552	390	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994327	21994327	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	44	303	0	ENST00000579755.1:c.4G>A	p.Val2Met	p.V2M	ENST00000579755		2	Gtg/Atg	1/3	0.225409583005426		FACETS		0.678	0.921				INDETERMINATE	2	TRUE	2	0.495123885863608	4		303	167	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127933401	127933401	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	97	774	2	ENST00000373547.4:c.134C>A	p.Ser45Ter	p.S45*	ENST00000373547	NM_002721.4	45	tCa/tAa	2/7	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.495123885863608	2		776	381	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63817025	63817025	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	75	334	0	ENST00000279873.7:c.996G>A	p.Met332Ile	p.M332I	ENST00000279873	NM_032199.2	332	atG/atA	6/10	0.469563762016149	4	FACETS	0.795	0.704	0.89			1	SUBCLONAL	2	TRUE	NA	0.495123885863608	4		334	285	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577161	64577161	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886039553	NA	P-0004555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	49	470	0	ENST00000312049.6:c.421C>T	p.Gln141Ter	p.Q141*	ENST00000312049	NM_130799.2	141	Cag/Tag	2/10	0.289488936891504	1	FACETS	0.856	0.737	0.982	0.856	0.737	0.982	INDETERMINATE	1	TRUE	0	0.495123885863608	1		470	174	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900831	3900831	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	59	356	0	ENST00000262367.5:c.265G>A	p.Val89Met	p.V89M	ENST00000262367	NM_004380.2	89	Gtg/Atg	2/31	0.210356957831164	5	FACETS	0.761	0.66	0.868	0.507	0.44	0.579	INDETERMINATE	2	TRUE	2	0.495123885863608	5		356	273	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	52	517	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.495123885863608	1	FACETS	0.97	0.842	1	0.97	0.842	1	CLONAL	1	TRUE	0	0.495123885863608	1		517	163	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346888	89346888	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	51	303	0	ENST00000301030.4:c.6062C>G	p.Ser2021Cys	p.S2021C	ENST00000301030	NM_001256183.1	2021	tCt/tGt	9/13	0.495123885863608	0	FACETS	0.542	0.48	0.603			1	SUBCLONAL	2	TRUE	0	0.495123885863608	0		303	96	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577069	7577069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55819519	NA	P-0004555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	61	449	1	ENST00000269305.4:c.869G>A	p.Arg290His	p.R290H	ENST00000269305	NM_001126112.2	290	cGc/cAc	8/11	0.495123885863608	1	FACETS	0.986	0.866	1	0.986	0.866	1	CLONAL	1	TRUE	0	0.495123885863608	1		450	188	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0004555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	83	577	2	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.495123885863608	2		579	269	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40379597	40379597	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	59	878	0	ENST00000293328.3:c.235G>C	p.Asp79His	p.D79H	ENST00000293328	NM_012448.3	79	Gat/Cat	3/19	0.400429585281957	1	FACETS	0.698	0.606	0.795	0.698	0.606	0.795	SUBCLONAL	1	TRUE	0	0.495123885863608	1		878	257	SUCCESS
YES1	7525	MSKCC	GRCh37	18	739782	739782	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	91	546	0	ENST00000314574.4:c.1090G>C	p.Asp364His	p.D364H	ENST00000314574	NM_005433.3	364	Gat/Cat	9/12	0.196000536484189	4	FACETS	0.799	0.716	0.886	0.799	0.716	0.886	INDETERMINATE	2	TRUE	2	0.495123885863608	4		546	344	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197011	123197011	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	116	656	0	ENST00000218089.9:c.1777C>G	p.Gln593Glu	p.Q593E	ENST00000218089	NM_001042749.1	593	Cag/Gag	19/35	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.495123885863608	2		656	452	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444659	78444659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs908264837	NA	P-0004555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	15	209	0	ENST00000370768.2:c.30del	p.Ser11LeufsTer43	p.S11Lfs*43	ENST00000370768	NM_003902.3	10	ccC/cc	1/20	0.225409583005426	4	FACETS	0.433	0.317	0.572	0.217	0.158	0.286	INDETERMINATE	1	TRUE	2	0.495123885863608	4		209	209	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	32	769	0				ENST00000310581	NM_198253.2	-/1132			0.267572925946145	0	FACETS	1	0.871	1			1	CLONAL	1	FALSE	0	0.267572925946145	0		769	163	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263850	133263850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	18	297	0	ENST00000320574.5:c.52G>A	p.Glu18Lys	p.E18K	ENST00000320574	NM_006231.2	18	Gag/Aag	1/49	0.150497238221539	1	FACETS	0.445	0.335	0.574	0.445	0.335	0.574	INDETERMINATE	1	FALSE	0	0.267572925946145	1		297	262	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127164	22127164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057519911	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	72	1023	0	ENST00000215832.6:c.964G>A	p.Glu322Lys	p.E322K	ENST00000215832	NM_002745.4	322	Gag/Aag	7/9	1	2	FACETS	0.733	0.64	0.834	0.733	0.64	0.834	SUBCLONAL	1	FALSE	1	0.267572925946145	2		1023	734	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142964	47142964	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	87	1051	0	ENST00000409792.3:c.4999C>T	p.Gln1667Ter	p.Q1667*	ENST00000409792	NM_014159.6	1667	Cag/Tag	8/21	1	2	FACETS	0.848	0.75	0.953	0.848	0.75	0.953	CLONAL	1	FALSE	1	0.267572925946145	2		1051	767	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872213	45872213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	96	983	1	ENST00000391945.4:c.221C>T	p.Ser74Leu	p.S74L	ENST00000391945	NM_000400.3	74	tCa/tTa	4/23	1	2	FACETS	0.89	0.793	0.994	0.89	0.793	0.994	CLONAL	1	FALSE	1	0.267572925946145	2		984	806	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099283	157099283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	66	329	0	ENST00000346085.5:c.220G>A	p.Glu74Lys	p.E74K	ENST00000346085	NM_020732.3	74	Gaa/Aaa	1/20	0.267572925946145	3	FACETS	1	0.962	1	0.65	0.566	0.741	CLONAL	1	FALSE	1	0.267572925946145	3		329	430	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797890	45797890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146044717	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	103	1156	1	ENST00000450313.1:c.881G>A	p.Arg294His	p.R294H	ENST00000450313	NM_012222.2	294	cGc/cAc	10/16	1	2	FACETS	0.93	0.832	1	0.93	0.832	1	CLONAL	1	FALSE	1	0.267572925946145	2		1157	828	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056277	27056277	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	91	746	0	ENST00000324856.7:c.1273C>T	p.Gln425Ter	p.Q425*	ENST00000324856	NM_006015.4	425	Cag/Tag	2/20	0.233919427845945	4	FACETS	0.999	0.886	1			1	CLONAL	1	FALSE	NA	0.267572925946145	4		746	863	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204494686	204494686	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	69	1197	0	ENST00000367182.3:c.40G>C	p.Asp14His	p.D14H	ENST00000367182	NM_001278516.1	14	Gac/Cac	2/11	1	2	FACETS	0.515	0.447	0.589	0.515	0.447	0.589	SUBCLONAL	1	FALSE	1	0.267572925946145	2		1197	1001	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881603	111881603	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	88	1134	1	ENST00000393256.3:c.281G>C	p.Ser94Thr	p.S94T	ENST00000393256	NM_006538.4	94	aGt/aCt	2/4	1	2	FACETS	0.677	0.599	0.762	0.677	0.599	0.762	SUBCLONAL	1	FALSE	1	0.267572925946145	2		1135	971	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368470	225368470	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	79	986	0	ENST00000264414.4:c.1276G>C	p.Asp426His	p.D426H	ENST00000264414	NM_003590.4	426	Gat/Cat	9/16	1	2	FACETS	0.657	0.576	0.744	0.657	0.576	0.744	SUBCLONAL	1	FALSE	1	0.267572925946145	2		986	899	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670325	134670325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	68	983	0	ENST00000398015.3:c.236G>A	p.Arg79Gln	p.R79Q	ENST00000398015	NM_004441.4	79	cGg/cAg	3/16	0.267572925946145	1	FACETS	0.762	0.663	0.868	0.762	0.663	0.868	SUBCLONAL	1	FALSE	0	0.267572925946145	1		983	578	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249441	153249441	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	63	964	1	ENST00000281708.4:c.1337G>T	p.Trp446Leu	p.W446L	ENST00000281708	NM_033632.3	446	tGg/tTg	9/12	1	2	FACETS	0.658	0.568	0.755	0.658	0.568	0.755	SUBCLONAL	1	FALSE	1	0.267572925946145	2		965	716	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977883	131977883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561655417	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	59	712	1	ENST00000265335.6:c.3766C>T	p.Arg1256Cys	p.R1256C	ENST00000265335		1256	Cgc/Tgc	25/25	0.159680319042979	1	FACETS	0.681	0.586	0.784	0.681	0.586	0.784	INDETERMINATE	1	FALSE	0	0.267572925946145	1		713	561	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271495	26271495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1546	183	1697	3	ENST00000305910.3:c.118C>T	p.His40Tyr	p.H40Y	ENST00000305910	NM_003534.2	40	Cat/Tat	1/1	0.267572925946145	6	FACETS	1	0.981	1			1	CLONAL	1	FALSE	NA	0.267572925946145	6		1700	1729	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502187	157502187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761227259	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	77	661	1	ENST00000346085.5:c.3220G>A	p.Asp1074Asn	p.D1074N	ENST00000346085	NM_020732.3	1074	Gac/Aac	12/20	0.267572925946145	3	FACETS	0.94	0.825	1	0.47	0.412	0.532	CLONAL	1	FALSE	1	0.267572925946145	3		662	694	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527328	157527328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	71	719	0	ENST00000346085.5:c.5053G>A	p.Glu1685Lys	p.E1685K	ENST00000346085	NM_020732.3	1685	Gag/Aag	20/20	0.267572925946145	3	FACETS	0.891	0.778	1	0.446	0.389	0.507	CLONAL	1	FALSE	1	0.267572925946145	3		719	675	SUCCESS
MET	4233	MSKCC	GRCh37	7	116417466	116417466	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	57	954	0	ENST00000397752.3:c.3283G>C	p.Gly1095Arg	p.G1095R	ENST00000397752	NM_000245.2	1095	Ggg/Cgg	16/21	1	2	FACETS	0.714	0.612	0.825	0.714	0.612	0.825	SUBCLONAL	1	FALSE	1	0.267572925946145	2		954	597	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524359	148524359	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	43	595	0	ENST00000320356.2:c.626-1G>A		p.X209_splice	ENST00000320356	NM_004456.4	209			1	2	FACETS	0.855	0.717	1	0.855	0.717	1	CLONAL	1	FALSE	1	0.267572925946145	2		595	376	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148526900	148526900	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	82	1087	0	ENST00000320356.2:c.404G>A	p.Gly135Glu	p.G135E	ENST00000320356	NM_004456.4	135	gGa/gAa	5/20	1	2	FACETS	0.758	0.667	0.855	0.758	0.667	0.855	SUBCLONAL	1	FALSE	1	0.267572925946145	2		1087	809	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835952	151835952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	80	1187	0	ENST00000262189.6:c.14572G>A	p.Glu4858Lys	p.E4858K	ENST00000262189	NM_170606.2	4858	Gaa/Aaa	58/59	1	2	FACETS	0.693	0.609	0.784	0.693	0.609	0.784	SUBCLONAL	1	FALSE	1	0.267572925946145	2		1187	863	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449764	8449764	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	44	814	0	ENST00000356435.5:c.3949G>C	p.Asp1317His	p.D1317H	ENST00000356435		1317	Gac/Cac	23/35	1	2	FACETS	0.614	0.514	0.724	0.614	0.514	0.724	SUBCLONAL	1	FALSE	1	0.267572925946145	2		814	536	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514272	69514272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1356578110	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	74	1106	0	ENST00000294312.3:c.409G>A	p.Glu137Lys	p.E137K	ENST00000294312	NM_005117.2	137	Gag/Aag	3/3	0.267572925946145	0	FACETS	0.603	0.527	0.684			1	SUBCLONAL	1	FALSE	0	0.267572925946145	0		1106	672	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394750	394750	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	89	1147	0	ENST00000399788.2:c.4945G>A	p.Glu1649Lys	p.E1649K	ENST00000399788	NM_001042603.1	1649	Gaa/Aaa	28/28	0.267572925946145	3	FACETS	0.901	0.798	1			1	CLONAL	1	FALSE	NA	0.267572925946145	3		1147	837	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442926	49442926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754797404	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	74	840	1	ENST00000301067.7:c.3982C>T	p.Arg1328Trp	p.R1328W	ENST00000301067	NM_003482.3	1328	Cgg/Tgg	12/54	0.208904711061786	3	FACETS	0.757	0.662	0.861	0.379	0.331	0.431	SUBCLONAL	1	FALSE	1	0.267572925946145	3		841	828	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004260	29004260	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	87	1148	0	ENST00000282397.4:c.1033G>C	p.Glu345Gln	p.E345Q	ENST00000282397	NM_002019.4	345	Gaa/Caa	8/30	0.267572925946145	1	FACETS	0.68	0.601	0.765	0.68	0.601	0.765	SUBCLONAL	1	FALSE	0	0.267572925946145	1		1148	828	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913783	32913783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	107	1874	0	ENST00000380152.3:c.5291C>T	p.Ser1764Leu	p.S1764L	ENST00000380152		1764	tCa/tTa	11/27	1	2	FACETS	0.747	0.668	0.83	0.747	0.668	0.83	SUBCLONAL	1	FALSE	1	0.267572925946145	2		1874	1071	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913801	32913801	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	115	1805	0	ENST00000380152.3:c.5309C>T	p.Ser1770Phe	p.S1770F	ENST00000380152		1770	tCt/tTt	11/27	1	2	FACETS	0.811	0.729	0.898	0.811	0.729	0.898	CLONAL	1	FALSE	1	0.267572925946145	2		1805	1060	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916220	9916220	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1445802934	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	66	1022	1	ENST00000330684.3:c.2069C>T	p.Thr690Met	p.T690M	ENST00000330684	NM_001134407.1	690	aCg/aTg	10/13	1	2	FACETS	0.851	0.739	0.972	0.851	0.739	0.972	CLONAL	1	FALSE	1	0.267572925946145	2		1023	580	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15976770	15976770	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	60	1237	0	ENST00000268712.3:c.3784G>T	p.Glu1262Ter	p.E1262*	ENST00000268712	NM_006311.3	1262	Gag/Tag	28/46	1	2	FACETS	0.561	0.482	0.647	0.561	0.482	0.647	SUBCLONAL	1	FALSE	1	0.267572925946145	2		1237	800	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995318	15995318	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	78	1028	0	ENST00000268712.3:c.2875C>G	p.Leu959Val	p.L959V	ENST00000268712	NM_006311.3	959	Ctc/Gtc	22/46	1	2	FACETS	0.62	0.544	0.703	0.62	0.544	0.703	SUBCLONAL	1	FALSE	1	0.267572925946145	2		1028	940	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320296	30320296	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	84	1025	0	ENST00000322652.5:c.1237A>T	p.Arg413Ter	p.R413*	ENST00000322652	NM_015355.2	413	Aga/Tga	11/16	1	2	FACETS	0.644	0.567	0.726	0.644	0.567	0.726	SUBCLONAL	1	FALSE	1	0.267572925946145	2		1025	975	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879888	37879888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	87	791	0	ENST00000269571.5:c.2183C>T	p.Ser728Phe	p.S728F	ENST00000269571		728	tCt/tTt	18/27	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	FALSE	1	0.267572925946145	2		791	619	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774768	73774768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	102	829	1	ENST00000254810.4:c.319G>A	p.Asp107Asn	p.D107N	ENST00000254810	NM_005324.3	107	Gat/Aat	4/4	0.208904711061786	3	FACETS	0.897	0.801	0.999	0.448	0.4	0.5	CLONAL	1	FALSE	1	0.267572925946145	3		830	964	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39595469	39595469	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	65	1191	1	ENST00000262039.4:c.1355C>A	p.Ser452Ter	p.S452*	ENST00000262039	NM_002647.2	452	tCa/tAa	12/25	1	2	FACETS	0.737	0.639	0.844	0.737	0.639	0.844	SUBCLONAL	1	FALSE	1	0.267572925946145	2		1192	659	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223350	2223350	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	105	1225	0	ENST00000398665.3:c.3461C>G	p.Pro1154Arg	p.P1154R	ENST00000398665	NM_032482.2	1154	cCt/cGt	25/28	NA	2	FACETS	0.926	0.829	1			1	INDETERMINATE	1	FALSE	NA	0.267572925946145	2		1225	848	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355142	15355142	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	43	534	0	ENST00000263377.2:c.2481C>G	p.Ile827Met	p.I827M	ENST00000263377	NM_058243.2	827	atC/atG	13/20	1	2	FACETS	0.873	0.733	1	0.873	0.733	1	CLONAL	1	FALSE	1	0.267572925946145	2		534	368	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52729001	52729001	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	77	998	0	ENST00000322088.6:c.1693G>C	p.Glu565Gln	p.E565Q	ENST00000322088	NM_014225.5	565	Gag/Cag	14/15	1	2	FACETS	0.754	0.661	0.854	0.754	0.661	0.854	SUBCLONAL	1	FALSE	1	0.267572925946145	2		998	763	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206722	36206722	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	96	488	0	ENST00000300305.3:c.790C>T	p.Gln264Ter	p.Q264*	ENST00000300305		264	Cag/Tag	6/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.267572925946145	2		488	489	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651264	45651264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772294235	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	126	1205	0	ENST00000407780.3:c.761C>T	p.Ala254Val	p.A254V	ENST00000407780	NM_001283052.1	254	gCg/gTg	5/7	1	2	FACETS	0.907	0.82	1	0.907	0.82	1	CLONAL	1	FALSE	1	0.267572925946145	2		1205	1038	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438545	49438549	+	frameshift_variant	Frame_Shift_Del	DEL	CATCG	CATCG	-	novel	NA	P-0004567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	77	1024	0	ENST00000301067.7:c.4941_4945del	p.Asp1648AlafsTer5	p.D1648Afs*5	ENST00000301067	NM_003482.3	1647	acCGATGag/acag	19/54	0.208904711061786	3	FACETS	0.822	0.721	0.931	0.411	0.36	0.466	CLONAL	1	FALSE	1	0.267572925946145	3		1024	794	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	50	174	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.929	0.805	1			1	INDETERMINATE	1	TRUE	NA	0.708525269097102	2		174	152	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944264	81944264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1009796025	NA	P-0004627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	202	358	0	ENST00000359376.3:c.1873G>A	p.Ala625Thr	p.A625T	ENST00000359376	NM_002661.3	625	Gcc/Acc	18/33	0.114728428984608	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.708525269097102	0		358	646	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509603	29509603	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	229	229	0	ENST00000356175.3:c.808C>T	p.Gln270Ter	p.Q270*	ENST00000356175	NM_000267.3	270	Caa/Taa	8/57	1	2	FACETS	0.895	0.838	0.954	0.895	0.838	0.954	CLONAL	1	TRUE	1	0.708525269097102	2		229	722	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939038	48939041	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	novel	NA	P-0004627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	245	292	0	ENST00000267163.4:c.871_874del	p.Val291IlefsTer9	p.V291Ifs*9	ENST00000267163	NM_000321.2	290	aaTGTT/aa	9/27	0.708525269097102	1	FACETS	0.904	0.855	0.953	0.904	0.855	0.953	CLONAL	1	TRUE	0	0.708525269097102	1		292	494	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933484	39933485	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0004627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	27	131	0	ENST00000378444.4:c.1114_1115del	p.Leu372ValfsTer8	p.L372Vfs*8	ENST00000378444	NM_001123385.1	372	CTg/g	4/15	1	1	FACETS	0.203	0.162	0.25	0.203	0.162	0.25	SUBCLONAL	1	TRUE	0	0.708525269097102	1		131	242	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586090	29586090	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	189	200	0	ENST00000356175.3:c.4311del	p.Glu1438AsnfsTer10	p.E1438Nfs*10	ENST00000356175	NM_000267.3	1437	gAa/ga	32/57	1	2	FACETS	0.739	0.685	0.795	0.739	0.685	0.795	SUBCLONAL	1	TRUE	1	0.708525269097102	2		200	722	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	55	174	0				ENST00000310581	NM_198253.2	-/1132			0.204360016872791	5	FACETS	1	0.894	1	0.692	0.599	0.791	INDETERMINATE	2	TRUE	2	0.366798989776658	5		174	224	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309776	104309776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202247756	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	159	423	0	ENST00000369902.3:c.367C>T	p.Arg123Cys	p.R123C	ENST00000369902	NM_016169.3	123	Cgt/Tgt	3/12	0.15262183346496	4	FACETS	1	0.987	1	0.699	0.641	0.759	INDETERMINATE	1	TRUE	2	0.366798989776658	4		423	848	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11210270	11210270	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	125	350	0	ENST00000361445.4:c.4483C>T	p.Gln1495Ter	p.Q1495*	ENST00000361445	NM_004958.3	1495	Cag/Tag	31/58	0.366798989776658	4	FACETS	0.959	0.867	1			1	CLONAL	1	TRUE	NA	0.366798989776658	4		350	971	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298606	11298606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199712134	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	107	321	0	ENST00000361445.4:c.1855C>T	p.Arg619Cys	p.R619C	ENST00000361445	NM_004958.3	619	Cgc/Tgc	12/58	0.366798989776658	4	FACETS	1	0.902	1			1	CLONAL	1	TRUE	NA	0.366798989776658	4		321	793	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484315	120484315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	192	426	0	ENST00000256646.2:c.2815C>T	p.Pro939Ser	p.P939S	ENST00000256646	NM_024408.3	939	Ccg/Tcg	18/34	0.316375298927466	5	FACETS	0.807	0.746	0.87	0.323	0.298	0.348	CLONAL	2	TRUE	0	0.366798989776658	5		426	1006	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518557	204518557	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	36	267	0	ENST00000367182.3:c.1220T>A	p.Ile407Asn	p.I407N	ENST00000367182	NM_001278516.1	407	aTc/aAc	11/11	0.304517495347497	4	FACETS	0.446	0.365	0.536	0.111	0.091	0.134	SUBCLONAL	1	TRUE	0	0.366798989776658	4		267	602	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158595059	158595059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	158	520	0	ENST00000263640.3:c.1288C>T	p.Pro430Ser	p.P430S	ENST00000263640	NM_001105.4	430	Ccg/Tcg	10/11	0.361606541932346	4	FACETS	1	0.969	1	0.56	0.512	0.61	CLONAL	1	TRUE	2	0.366798989776658	4		520	1051	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589809	212589809	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	91	285	0	ENST00000342788.4:c.733G>A	p.Asp245Asn	p.D245N	ENST00000342788	NM_005235.2	245	Gac/Aac	6/28	0.243863041362887	4	FACETS	1	0.922	1	0.523	0.465	0.586	CLONAL	1	TRUE	2	0.366798989776658	4		285	648	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651505	52651505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	204	519	0	ENST00000394830.3:c.1591C>T	p.Leu531Phe	p.L531F	ENST00000394830	NM_018313.4	531	Ctt/Ttt	15/30	0.194940419920985	4	FACETS	0.821	0.762	0.882	0.821	0.762	0.882	INDETERMINATE	2	TRUE	2	0.366798989776658	4		519	926	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946212	55946212	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	104	397	0	ENST00000263923.4:c.3967G>A	p.Glu1323Lys	p.E1323K	ENST00000263923	NM_002253.2	1323	Gaa/Aaa	30/30	1	2	FACETS	0.659	0.59	0.733	0.659	0.59	0.733	SUBCLONAL	1	TRUE	1	0.366798989776658	2		397	860	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948135	55948135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1001071878	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	74	388	0	ENST00000263923.4:c.3836C>T	p.Ser1279Phe	p.S1279F	ENST00000263923	NM_002253.2	1279	tCt/tTt	29/30	1	2	FACETS	0.581	0.508	0.659	0.581	0.508	0.659	SUBCLONAL	1	TRUE	1	0.366798989776658	2		388	695	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196994	106196994	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	151	369	0	ENST00000380013.4:c.5327C>T	p.Ser1776Phe	p.S1776F	ENST00000380013	NM_001127208.2	1776	tCt/tTt	11/11	0.366798989776658	3	FACETS	1	0.951	1	0.353	0.322	0.385	CLONAL	1	TRUE	0	0.366798989776658	3		369	921	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293472	1293472	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	139	303	0	ENST00000310581.5:c.1529G>A	p.Trp510Ter	p.W510*	ENST00000310581	NM_198253.2	510	tGg/tAg	2/16	0.204360016872791	5	FACETS	0.849	0.774	0.927	0.566	0.516	0.618	INDETERMINATE	2	TRUE	2	0.366798989776658	5		303	692	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497229	149497229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	131	302	0	ENST00000261799.4:c.3089C>T	p.Pro1030Leu	p.P1030L	ENST00000261799	NM_002609.3	1030	cCc/cTc	22/23	0.361606541932346	4	FACETS	1	0.978	1	0.626	0.568	0.686	CLONAL	1	TRUE	2	0.366798989776658	4		302	780	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514544	149514544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	116	310	0	ENST00000261799.4:c.400G>A	p.Glu134Lys	p.E134K	ENST00000261799	NM_002609.3	134	Gaa/Aaa	4/23	0.361606541932346	4	FACETS	1	0.972	1	0.607	0.548	0.67	CLONAL	1	TRUE	2	0.366798989776658	4		310	712	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665463	176665463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	114	274	0	ENST00000439151.2:c.4147C>T	p.Pro1383Ser	p.P1383S	ENST00000439151	NM_022455.4	1383	Cca/Tca	7/23	0.117939012403495	4	FACETS	1	0.973	1	0.615	0.554	0.679	INDETERMINATE	1	TRUE	2	0.366798989776658	4		274	691	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184992	32184992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	155	387	0	ENST00000375023.3:c.1676C>T	p.Pro559Leu	p.P559L	ENST00000375023	NM_004557.3	559	cCc/cTc	10/30	0.366798989776658	5	FACETS	0.777	0.712	0.845	0.518	0.474	0.564	SUBCLONAL	2	TRUE	2	0.366798989776658	5		387	843	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982080	93982080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	461	510	0	ENST00000369303.4:c.1385C>T	p.Ser462Phe	p.S462F	ENST00000369303	NM_004440.3	462	tCc/tTc	6/17	0.366798989776658	3	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.366798989776658	3		510	1192	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120885	94120885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	155	533	0	ENST00000369303.4:c.166G>A	p.Glu56Lys	p.E56K	ENST00000369303	NM_004440.3	56	Gaa/Aaa	3/17	0.366798989776658	3	FACETS	0.876	0.8	0.955			1	CLONAL	1	TRUE	NA	0.366798989776658	3		533	1142	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020775	112020775	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369151232	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1250	177	589	0	ENST00000368678.4:c.796C>T	p.Arg266Cys	p.R266C	ENST00000368678		266	Cgt/Tgt	8/13	0.117939012403495	4	FACETS	0.924	0.849	1	0.462	0.424	0.502	INDETERMINATE	1	TRUE	2	0.366798989776658	4		589	1427	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658356	117658356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	295	571	0	ENST00000368508.3:c.5227C>T	p.Pro1743Ser	p.P1743S	ENST00000368508	NM_002944.2	1743	Cca/Tca	31/43	0.117939012403495	4	FACETS	1	0.954	1	1	0.954	1	INDETERMINATE	2	TRUE	2	0.366798989776658	4		571	1083	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519298	137519298	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	60	340	0	ENST00000367739.4:c.1340C>T	p.Thr447Ile	p.T447I	ENST00000367739	NM_000416.2	447	aCc/aTc	7/7	0.366798989776658	4	FACETS	0.607	0.522	0.7	0.303	0.261	0.35	SUBCLONAL	1	TRUE	2	0.366798989776658	4		340	737	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023019	150023019	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	176	512	0	ENST00000253339.5:c.244C>T	p.Arg82Ter	p.R82*	ENST00000253339		82	Cga/Tga	1/7	0.366798989776658	4	FACETS	0.807	0.744	0.872	0.807	0.744	0.872	CLONAL	2	TRUE	2	0.366798989776658	4		512	813	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265409	152265409	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	65	280	0	ENST00000206249.3:c.862G>A	p.Ala288Thr	p.A288T	ENST00000206249	NM_000125.3	288	Gct/Act	4/8	0.366798989776658	4	FACETS	0.698	0.604	0.8	0.349	0.302	0.4	SUBCLONAL	1	TRUE	2	0.366798989776658	4		280	694	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976817	2976817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	139	501	0	ENST00000396946.4:c.1195G>A	p.Glu399Lys	p.E399K	ENST00000396946	NM_032415.4	399	Gaa/Aaa	9/25	0.366798989776658	5	FACETS	0.986	0.895	1	0.246	0.223	0.271	CLONAL	1	TRUE	1	0.366798989776658	5		501	1192	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268989	55268989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	149	355	0	ENST00000275493.2:c.3055C>T	p.Pro1019Ser	p.P1019S	ENST00000275493	NM_005228.3	1019	Cca/Tca	25/28	0.366798989776658	5	FACETS	1	0.979	1	0.31	0.283	0.339	CLONAL	1	TRUE	1	0.366798989776658	5		355	1015	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336630	81336630	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	129	406	0	ENST00000222390.5:c.1592C>G	p.Thr531Ser	p.T531S	ENST00000222390	NM_000601.4	531	aCt/aGt	14/18	0.366798989776658	5	FACETS	0.956	0.864	1	0.239	0.216	0.263	CLONAL	1	TRUE	1	0.366798989776658	5		406	1141	SUCCESS
MET	4233	MSKCC	GRCh37	7	116409831	116409831	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778115147	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	165	364	0	ENST00000397752.3:c.2716G>A	p.Glu906Lys	p.E906K	ENST00000397752	NM_000245.2	906	Gag/Aag	12/21	0.366798989776658	6	FACETS	1	0.984	1	0.264	0.242	0.288	CLONAL	1	TRUE	1	0.366798989776658	6		364	1181	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518336	8518336	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	129	236	1	ENST00000356435.5:c.1055C>T	p.Ser352Phe	p.S352F	ENST00000356435		352	tCt/tTt	10/35	0.330915042731612	4	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.366798989776658	4		237	657	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342839	87342839	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	128	233	0	ENST00000277120.3:c.1124C>T	p.Ser375Phe	p.S375F	ENST00000277120		375	tCt/tTt	9/19	0.366798989776658	4	FACETS	0.863	0.785	0.943	0.863	0.785	0.943	CLONAL	2	TRUE	2	0.366798989776658	4		233	553	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359975	87359975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752393508	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	103	281	0	ENST00000277120.3:c.1283G>A	p.Arg428Gln	p.R428Q	ENST00000277120		428	cGg/cAg	11/19	0.366798989776658	4	FACETS	0.969	0.867	1	0.485	0.433	0.539	CLONAL	1	TRUE	2	0.366798989776658	4		281	792	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218574	98218574	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1407852658	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	100	315	0	ENST00000331920.6:c.3290C>T	p.Thr1097Ile	p.T1097I	ENST00000331920	NM_000264.3	1097	aCc/aTc	19/24	0.366798989776658	4	FACETS	0.805	0.718	0.898	0.402	0.359	0.449	CLONAL	1	TRUE	2	0.366798989776658	4		315	926	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249626	110249626	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	112	291	1	ENST00000374672.4:c.1049C>T	p.Ser350Phe	p.S350F	ENST00000374672	NM_004235.4	350	tCc/tTc	3/5	0.366798989776658	4	FACETS	1	0.971	1	0.603	0.543	0.667	CLONAL	1	TRUE	2	0.366798989776658	4		292	692	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399895	139399895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	118	416	0	ENST00000277541.6:c.4453G>A	p.Asp1485Asn	p.D1485N	ENST00000277541	NM_017617.3	1485	Gac/Aac	25/34	0.204360016872791	5	FACETS	1	0.962	1	0.379	0.341	0.419	INDETERMINATE	1	TRUE	2	0.366798989776658	5		416	877	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100451	8100451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1266983268	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	138	410	0	ENST00000346208.3:c.425C>T	p.Ser142Leu	p.S142L	ENST00000346208		142	tCg/tTg	3/6	0.232313782945996	3	FACETS	1	0.964	1			1	CLONAL	1	TRUE	NA	0.366798989776658	3		410	801	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115924	8115924	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	94	251	0	ENST00000346208.3:c.1270C>T	p.Pro424Ser	p.P424S	ENST00000346208		424	Ccg/Tcg	6/6	0.232313782945996	3	FACETS	1	0.948	1			1	CLONAL	1	TRUE	NA	0.366798989776658	3		251	549	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63817033	63817033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	114	300	0	ENST00000279873.7:c.1004G>A	p.Arg335Lys	p.R335K	ENST00000279873	NM_032199.2	335	aGg/aAg	6/10	0.204360016872791	5	FACETS	0.767	0.692	0.846	0.511	0.461	0.564	INDETERMINATE	2	TRUE	2	0.366798989776658	5		300	628	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148875	119148875	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs397517076	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	200	212	0	ENST00000264033.4:c.1096-1G>C		p.X366_splice	ENST00000264033	NM_005188.3	366			0.304517495347497	4	FACETS	1	0.937	1	0.751	0.703	0.8	CLONAL	3	TRUE	0	0.366798989776658	4		212	496	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864141	57864141	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	182	494	0	ENST00000228682.2:c.1618G>A	p.Glu540Lys	p.E540K	ENST00000228682	NM_005269.2	540	Gaa/Aaa	12/12	0.15262183346496	4	FACETS	1	0.989	1	0.719	0.663	0.777	INDETERMINATE	1	TRUE	2	0.366798989776658	4		494	943	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864883	57864883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	189	575	0	ENST00000228682.2:c.2360C>T	p.Ser787Phe	p.S787F	ENST00000228682	NM_005269.2	787	tCt/tTt	12/12	0.15262183346496	4	FACETS	1	0.987	1	0.673	0.622	0.727	INDETERMINATE	1	TRUE	2	0.366798989776658	4		575	1046	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215766	133215766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	115	376	0	ENST00000320574.5:c.5497C>T	p.His1833Tyr	p.H1833Y	ENST00000320574	NM_006231.2	1833	Cat/Tat	40/49	0.15262183346496	4	FACETS	1	0.973	1	0.61	0.55	0.674	INDETERMINATE	1	TRUE	2	0.366798989776658	4		376	702	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68934917	68934917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	180	438	0	ENST00000487270.1:c.986C>T	p.Pro329Leu	p.P329L	ENST00000487270	NM_133509.3	329	cCc/cTc	10/11	0.194940419920985	4	FACETS	1	0.988	1	0.696	0.641	0.752	INDETERMINATE	1	TRUE	2	0.366798989776658	4		438	964	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961591	41961591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752397560	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	181	566	0	ENST00000219905.7:c.499C>T	p.His167Tyr	p.H167Y	ENST00000219905	NM_001164273.1	167	Cat/Tat	2/24	0.232313782945996	3	FACETS	1	0.962	1			1	CLONAL	1	TRUE	NA	0.366798989776658	3		566	1088	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483877	88483877	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	131	363	0	ENST00000360948.2:c.1693G>A	p.Asp565Asn	p.D565N	ENST00000360948	NM_001012338.2	565	Gac/Aac	14/19	0.361606541932346	4	FACETS	1	0.927	1	0.513	0.465	0.564	CLONAL	1	TRUE	2	0.366798989776658	4		363	951	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274210	10274211	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	65	163	1	ENST00000330684.3:c.58_59delinsAA	p.Gly20Asn	p.G20N	ENST00000330684	NM_001134407.1	20	GGt/AAt	2/13	0.366798989776658	3	FACETS	1	0.964	1			1	CLONAL	1	TRUE	NA	0.366798989776658	3		164	319	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637601	23637601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	186	460	0	ENST00000261584.4:c.2704G>A	p.Asp902Asn	p.D902N	ENST00000261584	NM_024675.3	902	Gat/Aat	7/13	0.366798989776658	3	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.366798989776658	3		460	1006	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845844	72845844	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760400785	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	211	615	0	ENST00000268489.5:c.3623C>T	p.Ser1208Leu	p.S1208L	ENST00000268489	NM_006885.3	1208	tCg/tTg	6/10	0.117939012403495	4	FACETS	1	0.989	1	0.683	0.633	0.734	INDETERMINATE	1	TRUE	2	0.366798989776658	4		615	1152	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81957171	81957171	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	155	421	0	ENST00000359376.3:c.2389C>T	p.His797Tyr	p.H797Y	ENST00000359376	NM_002661.3	797	Cac/Tac	22/33	0.117939012403495	4	FACETS	1	0.981	1	0.624	0.571	0.68	INDETERMINATE	1	TRUE	2	0.366798989776658	4		421	925	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578476	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	312	294	1	ENST00000269305.4:c.454_455delinsAA	p.Pro152Lys	p.P152K	ENST00000269305	NM_001126112.2	152	CCg/AAg	5/11	0.304517495347497	4	FACETS	1	0.983	1	0.81	0.769	0.851	CLONAL	3	TRUE	0	0.366798989776658	4		295	718	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548939	29548939	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs863224489	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	75	158	0	ENST00000356175.3:c.1713G>A	p.Trp571Ter	p.W571*	ENST00000356175	NM_000267.3	571	tgG/tgA	15/57	0.304517495347497	4	FACETS	1	0.897	1	0.506	0.449	0.567	CLONAL	2	TRUE	0	0.366798989776658	4		158	276	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884031	37884031	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	81	364	0	ENST00000269571.5:c.3502G>T	p.Glu1168Ter	p.E1168*	ENST00000269571		1168	Gaa/Taa	27/27	0.304517495347497	4	FACETS	0.79	0.695	0.892	0.198	0.173	0.223	SUBCLONAL	1	TRUE	0	0.366798989776658	4		364	764	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434906	56434906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	76	291	0	ENST00000407977.2:c.2231C>T	p.Pro744Leu	p.P744L	ENST00000407977		744	cCt/cTt	9/10	0.366798989776658	3	FACETS	0.65	0.57	0.737	0.217	0.19	0.246	SUBCLONAL	1	TRUE	0	0.366798989776658	3		291	754	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920433	50920433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	120	346	0	ENST00000440232.2:c.3125C>T	p.Ser1042Phe	p.S1042F	ENST00000440232	NM_002691.3	1042	tCc/tTc	26/27	0.286046168082994	3	FACETS	1	0.979	1	0.429	0.389	0.472	CLONAL	1	TRUE	0	0.366798989776658	3		346	601	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561250	9561250	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	157	326	0	ENST00000353224.5:c.532G>A	p.Gly178Arg	p.G178R	ENST00000353224	NM_177990.2	178	Ggg/Agg	4/10	0.316375298927466	5	FACETS	1	0.987	1	0.285	0.26	0.31	CLONAL	1	TRUE	0	0.366798989776658	5		326	932	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306689	41306689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868376470	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	139	310	0	ENST00000373198.4:c.970G>A	p.Glu324Lys	p.E324K	ENST00000373198	NM_133170.3	324	Gaa/Aaa	7/32	0.316375298927466	5	FACETS	1	0.984	1	0.275	0.25	0.302	CLONAL	1	TRUE	0	0.366798989776658	5		310	853	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41521892	41521892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	170	442	0	ENST00000263253.7:c.754C>T	p.Pro252Ser	p.P252S	ENST00000263253	NM_001429.3	252	Cct/Tct	3/31	0.366798989776658	5	FACETS	1	0.962	1	0.361	0.331	0.393	CLONAL	1	TRUE	2	0.366798989776658	5		442	1325	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545129	41545129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751005704	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	195	550	0	ENST00000263253.7:c.2329G>A	p.Val777Ile	p.V777I	ENST00000263253	NM_001429.3	777	Gta/Ata	13/31	0.366798989776658	5	FACETS	1	0.986	1	0.43	0.396	0.464	CLONAL	1	TRUE	2	0.366798989776658	5		550	1279	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15833876	15833876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	84	94	0	ENST00000307771.7:c.634G>A	p.Glu212Lys	p.E212K	ENST00000307771	NM_005089.3	212	Gag/Aag	8/11	0.352886336703064	2	FACETS	1	0.965	1			1	CLONAL	2	TRUE	NA	0.366798989776658	2		94	198	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410204	63410204	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	165	206	0	ENST00000330258.3:c.2963C>T	p.Pro988Leu	p.P988L	ENST00000330258	NM_152424.3	988	cCa/cTa	2/2	0.352886336703064	2	FACETS	0.857	0.792	0.923			1	CLONAL	2	TRUE	NA	0.366798989776658	2		206	525	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954211	48954242	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAAATTTTAGGTAAATTTTTTACTTTTAGTAA	AAAATTTTAGGTAAATTTTTTACTTTTAGTAA	-	novel	NA	P-0004650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	271	370	0	ENST00000267163.4:c.1420_1421+30del		p.X474_splice	ENST00000267163	NM_000321.2	474		15/27	0.366798989776658	3	FACETS	1	0.943	1	0.668	0.629	0.709	CLONAL	2	TRUE	0	0.366798989776658	3		370	872	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	56	174	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.915	1			1	INDETERMINATE	1	TRUE	NA	0.829460663405762	2		174	129	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921567	178921567	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553821144	NA	P-0004676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	272	409	0	ENST00000263967.3:c.1049A>G	p.Asp350Gly	p.D350G	ENST00000263967	NM_006218.2	350	gAc/gGc	5/21	0.272559058237748	4	FACETS	0.8	0.754	0.846	0.8	0.754	0.846	INDETERMINATE	2	TRUE	2	0.829460663405762	4		409	750	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690805	89690805	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1554897856	NA	P-0004676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	293	290	1	ENST00000371953.3:c.212G>T	p.Cys71Phe	p.C71F	ENST00000371953	NM_000314.4	71	tGt/tTt	4/9	0.829460663405762	1	FACETS	0.946	0.908	0.984	0.946	0.908	0.984	CLONAL	1	TRUE	0	0.829460663405762	1		291	437	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923055	39923055	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	725	472	0	ENST00000378444.4:c.3653G>A	p.Trp1218Ter	p.W1218*	ENST00000378444	NM_001123385.1	1218	tGg/tAg	8/15	0.539526513359243	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.829460663405762	2		472	810	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579703	7579703	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	512	591	0	ENST00000269305.4:c.93del	p.Leu32CysfsTer12	p.L32Cfs*12	ENST00000269305	NM_001126112.2	31	gtT/gt	3/11	NA	2	FACETS	0.96	0.936	0.983			1	INDETERMINATE	2	TRUE	NA	0.829460663405762	2		591	643	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	81	174	0				ENST00000310581	NM_198253.2	-/1132			0.275471505525291	3	FACETS	0.774	0.69	0.861	0.774	0.69	0.861	INDETERMINATE	2	TRUE	1	0.469983689302239	3		174	275	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0004679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	214	645	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.469983689302239	2		645	812	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0004679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	155	588	1	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.469983689302239	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.469983689302239	1		589	459	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0004679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	400	458	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.455349153998078	3	FACETS	0.904	0.867	0.942	0.904	0.867	0.942	CLONAL	3	TRUE	0	0.469983689302239	3		458	775	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247244	153247244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	258	764	0	ENST00000281708.4:c.1558G>A	p.Asp520Asn	p.D520N	ENST00000281708	NM_033632.3	520	Gat/Aat	10/12	0.469983689302239	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.469983689302239	1		764	726	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004694-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	117	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.922	0.844	1	0.922	0.844	1	CLONAL	1	TRUE	1	0.818451588136016	2		174	310	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197842	123197842	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004694-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	459	260	0	ENST00000218089.9:c.1966C>T	p.Gln656Ter	p.Q656*	ENST00000218089	NM_001042749.1	656	Caa/Taa	20/35	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.818451588136016	1		260	545	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516905	187516905	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377350329	NA	P-0004694-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	332	442	0	ENST00000441802.2:c.13076G>A	p.Arg4359Gln	p.R4359Q	ENST00000441802	NM_005245.3	4359	cGg/cAg	26/27	1	2	FACETS	0.892	0.845	0.938	0.892	0.845	0.938	CLONAL	1	TRUE	1	0.818451588136016	2		442	910	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393325	393325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004694-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	193	354	0	ENST00000380956.4:c.173G>A	p.Gly58Asp	p.G58D	ENST00000380956	NM_001195286.1	58	gGc/gAc	2/9	0.223070191078158	3	FACETS	0.707	0.654	0.762	0.354	0.327	0.381	INDETERMINATE	1	TRUE	1	0.818451588136016	3		354	940	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101884	11101884	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004694-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	272	353	0	ENST00000358026.2:c.1304A>C	p.Asn435Thr	p.N435T	ENST00000358026	NM_001128849.1	435	aAt/aCt	8/36	0.194764829563572	1	FACETS	0.471	0.444	0.5	0.471	0.444	0.5	INDETERMINATE	1	TRUE	0	0.818451588136016	1		353	833	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559748	29559751	+	frameshift_variant	Frame_Shift_Del	DEL	TGAC	TGAC	-	novel	NA	P-0004694-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	534	410	0	ENST00000356175.3:c.3347_3350del	p.Asp1116AlafsTer25	p.D1116Afs*25	ENST00000356175	NM_000267.3	1115	aaTGAC/aa	26/57	0.811184833513004	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.818451588136016	2		410	650	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044500	12044500	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367662793	NA	P-0121477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	124	678	1	ENST00000353533.5:c.1123G>A	p.Val375Ile	p.V375I	ENST00000353533	NM_003010.3	375	Gtt/Att	11/11	1	2	FACETS	0.722	0.657	0.791	0.722	0.657	0.791	SUBCLONAL	1	NA	1	0.655241776644082	2		679	524	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817803	3817803	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0121477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	241	986	0	ENST00000262367.5:c.3168del	p.Val1057Ter	p.V1057*	ENST00000262367	NM_004380.2	1056	aaA/aa	16/31	1	2	FACETS	0.925	0.867	0.985	0.925	0.867	0.985	CLONAL	1	NA	1	0.655241776644082	2		986	795	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980714	70980714	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0121477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	236	870	0	ENST00000276594.2:c.754G>A	p.Gly252Ser	p.G252S	ENST00000276594	NM_024504.3	252	Ggt/Agt	3/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	NA	1	0.655241776644082	2		870	637	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0005039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	83	769	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	FALSE	NA	0.759255614573804	2		769	190	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0005039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1184	183	670	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.759255614573804	7	FACETS	1	0.938	1	0.204	0.188	0.222	CLONAL	1	FALSE	2	0.759255614573804	7		670	1367	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0005039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	824	483	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.759255614573804	6	FACETS	1	0.986	1			1	CLONAL	6	FALSE	NA	0.759255614573804	6		483	911	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099332	193099332	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	460	527	0	ENST00000367435.3:c.266C>T	p.Pro89Leu	p.P89L	ENST00000367435	NM_024529.4	89	cCt/cTt	3/17	0.759255614573804	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	FALSE	1	0.759255614573804	4		527	707	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082958	16082958	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	65	211	0	ENST00000281043.3:c.772G>A	p.Asp258Asn	p.D258N	ENST00000281043	NM_005378.4	258	Gac/Aac	2/3	1	2	FACETS	0.946	0.837	1	0.946	0.837	1	CLONAL	1	FALSE	1	0.759255614573804	2		211	181	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047266	128047266	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	139	525	0	ENST00000285398.2:c.656C>T	p.Ala219Val	p.A219V	ENST00000285398	NM_000122.1	219	gCc/gTc	5/15	1	2	FACETS	0.946	0.871	1	0.946	0.871	1	CLONAL	1	FALSE	1	0.759255614573804	2		525	387	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191527	185191527	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754424536	NA	P-0005039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	125	319	1	ENST00000265026.3:c.2408G>A	p.Arg803Gln	p.R803Q	ENST00000265026	NM_004721.4	803	cGa/cAa	11/14	1	2	FACETS	0.974	0.893	1	0.974	0.893	1	CLONAL	1	FALSE	1	0.759255614573804	2		320	338	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456556	189456556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	121	524	0	ENST00000264731.3:c.317C>T	p.Pro106Leu	p.P106L	ENST00000264731	NM_003722.4	106	cCc/cTc	3/14	1	2	FACETS	0.949	0.868	1	0.949	0.868	1	CLONAL	1	FALSE	1	0.759255614573804	2		524	336	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356223	66356223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	136	535	1	ENST00000273854.3:c.1274C>T	p.Ser425Phe	p.S425F	ENST00000273854	NM_004439.5	425	tCt/tTt	5/18	1	2	FACETS	0.971	0.893	1	0.971	0.893	1	CLONAL	1	FALSE	1	0.759255614573804	2		536	369	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519753	176519753	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	112	612	0	ENST00000292408.4:c.1025C>T	p.Ser342Phe	p.S342F	ENST00000292408	NM_213647.1	342	tCc/tTc	8/18	1	2	FACETS	0.881	0.802	0.962	0.881	0.802	0.962	CLONAL	1	FALSE	1	0.759255614573804	2		612	335	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638483	176638483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	104	537	0	ENST00000439151.2:c.3083C>T	p.Ser1028Phe	p.S1028F	ENST00000439151	NM_022455.4	1028	tCc/tTc	5/23	1	2	FACETS	0.778	0.704	0.856	0.778	0.704	0.856	SUBCLONAL	1	FALSE	1	0.759255614573804	2		537	352	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066636	94066636	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	198	859	0	ENST00000369303.4:c.1123G>A	p.Glu375Lys	p.E375K	ENST00000369303	NM_004440.3	375	Gag/Aag	5/17	0.679014299875947	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	0	0.759255614573804	1		859	318	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389231	8389231	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0005039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	100	555	1	ENST00000356435.5:c.4386+1G>A		p.X1462_splice	ENST00000356435		1462			0.759255614573804	1	FACETS	0.961	0.888	1	0.961	0.888	1	CLONAL	1	FALSE	0	0.759255614573804	1		556	170	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376070	118376070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	158	532	0	ENST00000534358.1:c.9463G>A	p.Gly3155Arg	p.G3155R	ENST00000534358	NM_005933.3	3155	Gga/Aga	27/36	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.759255614573804	2		532	389	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142584	119142585	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0005039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	117	575	1	ENST00000264033.4:c.583_584delinsAT	p.Gly195Met	p.G195M	ENST00000264033	NM_005188.3	195	GGg/ATg	3/16	1	2	FACETS	0.784	0.713	0.857	0.784	0.713	0.857	SUBCLONAL	1	FALSE	1	0.759255614573804	2		576	393	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285793	46285793	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0005039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	139	499	0	ENST00000334344.6:c.5062-1G>A		p.X1688_splice	ENST00000334344	NM_152641.2	1688			1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	FALSE	1	0.759255614573804	2		499	354	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813334	102813334	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1430553116	NA	P-0005039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	200	613	1	ENST00000307046.8:c.355C>T	p.Arg119Cys	p.R119C	ENST00000307046	NM_001111285.1	119	Cgc/Tgc	3/4	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.759255614573804	2		614	511	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601310	28601310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	298	597	0	ENST00000241453.7:c.2122G>A	p.Glu708Lys	p.E708K	ENST00000241453	NM_004119.2	708	Gaa/Aaa	17/24	0.759255614573804	3	FACETS	0.986	0.94	1	0.986	0.94	1	CLONAL	2	FALSE	1	0.759255614573804	3		597	549	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622539	28622539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	235	507	0	ENST00000241453.7:c.1078G>A	p.Glu360Lys	p.E360K	ENST00000241453	NM_004119.2	360	Gaa/Aaa	9/24	0.759255614573804	3	FACETS	0.991	0.939	1	0.991	0.939	1	CLONAL	2	FALSE	1	0.759255614573804	3		507	431	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609381	81609381	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	205	779	0	ENST00000298171.2:c.979G>A	p.Glu327Lys	p.E327K	ENST00000298171	NM_000369.2	327	Gaa/Aaa	10/10	1	2	FACETS	0.959	0.896	1	0.959	0.896	1	CLONAL	1	FALSE	1	0.759255614573804	2		779	563	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292967	91292967	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	153	533	0	ENST00000355112.3:c.469A>G	p.Met157Val	p.M157V	ENST00000355112	NM_000057.2	157	Atg/Gtg	3/22	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.759255614573804	2		533	326	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129622	2129622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	170	638	0	ENST00000219476.3:c.3349G>A	p.Gly1117Arg	p.G1117R	ENST00000219476	NM_000548.3	1117	Ggg/Agg	29/42	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	FALSE	NA	0.759255614573804	2		638	366	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37871777	37871777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147382623	NA	P-0005039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	139	544	1	ENST00000269571.5:c.1301G>A	p.Arg434Gln	p.R434Q	ENST00000269571		434	cGa/cAa	11/27	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	FALSE	1	0.759255614573804	2		545	362	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508290	38508290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	199	556	0	ENST00000254066.5:c.598C>T	p.Pro200Ser	p.P200S	ENST00000254066	NM_000964.3	200	Cct/Tct	5/9	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.759255614573804	2		556	453	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41209118	41209118	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	163	654	2	ENST00000357654.3:c.5228G>T	p.Gly1743Val	p.G1743V	ENST00000357654	NM_007294.3	1743	gGa/gTa	19/23	0.109586509660665	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.759255614573804	0		656	425	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760695	59760695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1192747697	NA	P-0005039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	190	688	0	ENST00000259008.2:c.3712C>T	p.Pro1238Ser	p.P1238S	ENST00000259008	NM_032043.2	1238	Cct/Tct	20/20	1	2	FACETS	0.976	0.91	1	0.976	0.91	1	CLONAL	1	FALSE	1	0.759255614573804	2		688	513	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134239	11134239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	131	549	0	ENST00000358026.2:c.2905C>T	p.His969Tyr	p.H969Y	ENST00000358026	NM_001128849.1	969	Cac/Tac	20/36	0.759255614573804	3	FACETS	0.958	0.874	1	0.479	0.437	0.523	CLONAL	1	FALSE	1	0.759255614573804	3		549	497	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525065	9525065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1225133285	NA	P-0005039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	147	751	1	ENST00000353224.5:c.1820C>T	p.Pro607Leu	p.P607L	ENST00000353224	NM_177990.2	607	cCc/cTc	8/10	0.759255614573804	3	FACETS	0.805	0.737	0.875	0.402	0.368	0.438	CLONAL	1	FALSE	1	0.759255614573804	3		752	664	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747129	40747129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	155	504	0	ENST00000373198.4:c.2953G>A	p.Glu985Lys	p.E985K	ENST00000373198	NM_133170.3	985	Gag/Aag	22/32	0.759255614573804	3	FACETS	0.968	0.89	1	0.484	0.445	0.524	CLONAL	1	FALSE	1	0.759255614573804	3		504	582	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411014	63411014	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	189	786	0	ENST00000330258.3:c.2153T>G	p.Leu718Arg	p.L718R	ENST00000330258	NM_152424.3	718	cTg/cGg	2/2	0.759255614573804	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	0	0.759255614573804	1		786	276	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650386	48650386	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	93	338	0	ENST00000376670.3:c.356A>G	p.Gln119Arg	p.Q119R	ENST00000376670	NM_002049.3	119	cAg/cGg	3/6	0.238510357863993	0	FACETS	0.998	0.908	1			1	INDETERMINATE	1	TRUE	NA	0.47127463243713	0		338	209	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435297	110435302	+	inframe_deletion	In_Frame_Del	DEL	GGCGGT	GGCGGT	-	rs761851705	NA	P-0005180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	18	32	0	ENST00000375856.3:c.3099_3104del	p.Pro1035_Pro1036del	p.P1035_P1036del	ENST00000375856	NM_003749.2	1033	ccACCGCCg/ccg	1/2	0.359792512253989	3	FACETS	0.908	0.694	1	0.454	0.347	0.576	CLONAL	1	TRUE	1	0.47127463243713	3		32	104	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954198	48954198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123331	NA	P-0005266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	57	406	0	ENST00000267163.4:c.1399C>T	p.Arg467Ter	p.R467*	ENST00000267163	NM_000321.2	467	Cga/Tga	15/27	0.219466756786558	4	FACETS	0.711	0.609	0.824	0.356	0.304	0.412	SUBCLONAL	1	TRUE	2	0.24	4		406	828	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0005266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	45	398	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.938	0.789	1	0.938	0.789	1	CLONAL	1	TRUE	1	0.24	2		398	400	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187191	11187191	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	30	520	0	ENST00000361445.4:c.6227G>T	p.Arg2076Leu	p.R2076L	ENST00000361445	NM_004958.3	2076	cGa/cTa	45/58	NA	2	FACETS	0.562	0.452	0.686			1	INDETERMINATE	1	TRUE	NA	0.24	2		520	445	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377027	118377027	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs782405399	NA	P-0005266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	67	432	0	ENST00000534358.1:c.10420G>T	p.Asp3474Tyr	p.D3474Y	ENST00000534358	NM_005933.3	3474	Gat/Tat	27/36	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.24	2		432	556	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857647	9857647	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	62	411	0	ENST00000330684.3:c.3754C>A	p.Gln1252Lys	p.Q1252K	ENST00000330684	NM_001134407.1	1252	Cag/Aag	13/13	0.3	3	FACETS	1	0.922	1			1	CLONAL	1	TRUE	NA	0.24	3		411	528	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918622	44918622	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	111	293	0	ENST00000377967.4:c.1105C>T	p.Gln369Ter	p.Q369*	ENST00000377967	NM_021140.2	369	Cag/Tag	12/29	0.253038454880965	2	FACETS	1	0.958	1			1	CLONAL	2	TRUE	NA	0.24	2		293	419	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0005303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	30	769	0				ENST00000310581	NM_198253.2	-/1132			0.300813827643129	0	FACETS	0.827	0.678	0.99			1	CLONAL	1	TRUE	0	0.36	0		769	129	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0005303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	146	406	0	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.300813827643129	3	FACETS	0.943	0.86	1	0.471	0.43	0.516	CLONAL	1	TRUE	1	0.36	3		406	1015	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827934	72827934	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747060827	NA	P-0005303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1297	89	812	0	ENST00000268489.5:c.8647A>G	p.Met2883Val	p.M2883V	ENST00000268489	NM_006885.3	2883	Atg/Gtg	9/10	0.128768035833047	3	FACETS	0.421	0.372	0.474			1	INDETERMINATE	1	TRUE	NA	0.36	3		812	1386	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720679	89720680	+	missense_variant	Missense_Mutation	DNP	CA	CA	AT	novel	NA	P-0005303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	25	42	0	ENST00000371953.3:c.830_831delinsAT	p.Thr277Asn	p.T277N	ENST00000371953	NM_000314.4	277	aCA/aAT	8/9	0.300813827643129	1	FACETS	0.785	0.626	0.963	0.785	0.626	0.963	CLONAL	1	TRUE	0	0.36	1		42	145	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0005502-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	374	593	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.528486266720349	2		595	642	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939103	36939103	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005502-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	183	773	1	ENST00000361632.4:c.606G>A	p.Trp202Ter	p.W202*	ENST00000361632		202	tgG/tgA	5/16	0.530432427830857	2	FACETS	1	0.979	1	0.574	0.533	0.617	CLONAL	1	TRUE	0	0.528486266720349	2		774	603	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718114	117718114	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs759261834	NA	P-0005502-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	360	701	0	ENST00000368508.3:c.743T>A	p.Phe248Tyr	p.F248Y	ENST00000368508	NM_002944.2	248	tTc/tAc	7/43	0.530432427830857	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.528486266720349	4		701	981	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024570	14024570	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005502-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	150	347	0	ENST00000311895.7:c.796A>G	p.Ile266Val	p.I266V	ENST00000311895	NM_005236.2	266	Atc/Gtc	5/11	0.530432427830857	3	FACETS	0.939	0.869	1	0.939	0.869	1	CLONAL	2	TRUE	1	0.528486266720349	3		347	382	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044474	12044474	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005502-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	223	350	0	ENST00000353533.5:c.1097T>C	p.Phe366Ser	p.F366S	ENST00000353533	NM_003010.3	366	tTt/tCt	11/11	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.528486266720349	2		350	357	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324219	31324463	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTGGCCCCGGCCCCGCGGTCAGCCCAGTCCCCCGAGCCCCGCCCCGCCCCGACCAACCCGCGGGGATTTTGGCCTCAACTGAAAATGAAACCGGGTAAACGCGCCTGGGGCTCTCGCCGGTCGAGGGTCTGGGCGGGTCCCGCGGCCTCAGGGAGGCGGATCTCGGACCCGGAGACTCGGGGCGACCCGGGCCGTACGTGGGGGATGGGGAGTCGTGACCTGCGCCCCGGGCCGGGGTCACTCA	CCTGGCCCCGGCCCCGCGGTCAGCCCAGTCCCCCGAGCCCCGCCCCGCCCCGACCAACCCGCGGGGATTTTGGCCTCAACTGAAAATGAAACCGGGTAAACGCGCCTGGGGCTCTCGCCGGTCGAGGGTCTGGGCGGGTCCCGCGGCCTCAGGGAGGCGGATCTCGGACCCGGAGACTCGGGGCGACCCGGGCCGTACGTGGGGGATGGGGAGTCGTGACCTGCGCCCCGGGCCGGGGTCACTCA	-	novel	NA	P-0005502-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	46	686	0	ENST00000412585.2:c.343+2_344del		p.X115_splice	ENST00000412585	NM_005514.6	115		3/8	0.530432427830857	4	FACETS	0.31	0.26	0.365	0.155	0.13	0.183	SUBCLONAL	1	TRUE	2	0.528486266720349	4		686	859	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336636	81336636	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005502-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	110	470	0	ENST00000222390.5:c.1586T>G	p.Val529Gly	p.V529G	ENST00000222390	NM_000601.4	529	gTt/gGt	14/18	0.427114865819508	3	FACETS	1	0.975	1	0.412	0.372	0.453	CLONAL	1	TRUE	0	0.528486266720349	3		470	426	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323001	31323093	+	splice_acceptor_variant,splice_donor_variant,intron_variant	Splice_Site	DEL	CTGGGAAAGGAGGGGAAGATGAGGGGCCCTGACCCTGCTGAAGGGCTCCTGCTTTCCCTGAGAAGAGATATGACCCCTCATCCCCCTCCTTAC	CTGGGAAAGGAGGGGAAGATGAGGGGCCCTGACCCTGCTGAAGGGCTCCTGCTTTCCCTGAGAAGAGATATGACCCCTCATCCCCCTCCTTAC	-	novel	NA	P-0005502-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	157	894	0	ENST00000412585.2:c.895+1_896-1del		p.X299_splice	ENST00000412585	NM_005514.6	299			0.530432427830857	4	FACETS	0.776	0.71	0.846	0.388	0.355	0.423	SUBCLONAL	1	TRUE	2	0.528486266720349	4		894	1170	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005615-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	37	174	0				ENST00000310581	NM_198253.2	-/1132			0.242238643841995	1	FACETS	0.979	0.815	1	0.979	0.815	1	CLONAL	1	TRUE	0	0.315121565880201	1		174	202	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0005615-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	63	807	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.315121565880201	1	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	0	0.315121565880201	1		807	335	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0005615-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	59	82	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.302026562676775	2	FACETS	0.79	0.688	0.898	0.79	0.688	0.898	SUBCLONAL	2	TRUE	0	0.315121565880201	2		82	237	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0005615-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	188	233	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	0.209230906213583	3	FACETS	0.95	0.88	1	0.95	0.88	1	CLONAL	2	TRUE	1	0.315121565880201	3		233	727	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0005648-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	182	411	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	0.58044447540807	3	FACETS	0.985	0.912	1			1	CLONAL	1	TRUE	NA	0.754230146826429	3		411	675	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553402	41553402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005648-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	490	440	0	ENST00000263253.7:c.3491G>A	p.Cys1164Tyr	p.C1164Y	ENST00000263253	NM_001429.3	1164	tGt/tAt	18/31	0.747633785428728	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.754230146826429	2		440	645	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671558	30671558	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005648-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	372	677	1	ENST00000376406.3:c.5402C>A	p.Pro1801Gln	p.P1801Q	ENST00000376406	NM_014641.2	1801	cCg/cAg	10/15	0.747633785428728	2	FACETS	1	0.978	1	0.522	0.497	0.547	CLONAL	1	TRUE	0	0.754230146826429	2		678	945	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371806	55371806	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005648-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	143	58	0	ENST00000297316.4:c.496G>A	p.Ala166Thr	p.A166T	ENST00000297316	NM_022454.3	166	Gcg/Acg	2/2	0.754230146826429	7	FACETS	1	0.976	1			1	CLONAL	3	TRUE	NA	0.754230146826429	7		58	324	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	101	174	0				ENST00000310581	NM_198253.2	-/1132			0.412935089341546	5	FACETS	0.985	0.88	1	0.246	0.22	0.275	CLONAL	1	TRUE	1	0.412935089341546	5		174	804	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0005731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	390	430	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.412935089341546	3	FACETS	0.953	0.912	0.994	0.953	0.912	0.994	CLONAL	3	TRUE	0	0.412935089341546	3		431	797	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0005731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	534	367	2	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.412935089341546	5	FACETS	1	0.982	1			1	CLONAL	4	TRUE	NA	0.412935089341546	5		369	1019	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55524236	55524236	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1490714621	NA	P-0005731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	558	486	0	ENST00000288135.5:c.55C>T	p.Arg19Cys	p.R19C	ENST00000288135	NM_000222.2	19	Cgc/Tgc	1/21	0.412935089341546	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	1	0.412935089341546	4		486	1206	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200961	108200961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782310	NA	P-0005731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	208	252	0	ENST00000278616.4:c.7328G>A	p.Arg2443Gln	p.R2443Q	ENST00000278616	NM_000051.3	2443	cGa/cAa	50/63	0.412935089341546	4	FACETS	0.974	0.907	1			1	CLONAL	2	TRUE	NA	0.412935089341546	4		252	731	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059213	27059213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	254	418	0	ENST00000324856.7:c.1850C>T	p.Ser617Leu	p.S617L	ENST00000324856	NM_006015.4	617	tCa/tTa	4/20	0.364836565324223	5	FACETS	1	0.992	1			1	CLONAL	1	TRUE	NA	0.412935089341546	5		418	1334	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105796	27105796	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	610	448	0	ENST00000324856.7:c.5407G>T	p.Glu1803Ter	p.E1803*	ENST00000324856	NM_006015.4	1803	Gag/Tag	20/20	0.364836565324223	5	FACETS	0.949	0.916	0.982			1	CLONAL	4	TRUE	NA	0.412935089341546	5		448	1261	SUCCESS
REL	5966	MSKCC	GRCh37	2	61144146	61144146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	122	214	0	ENST00000295025.8:c.529G>A	p.Asp177Asn	p.D177N	ENST00000295025	NM_002908.2	177	Gac/Aac	5/11	0.412935089341546	4	FACETS	1	0.963	1	0.377	0.341	0.415	CLONAL	1	TRUE	1	0.412935089341546	4		214	738	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52677288	52677288	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	283	424	1	ENST00000394830.3:c.971G>A	p.Arg324Lys	p.R324K	ENST00000394830	NM_018313.4	324	aGa/aAa	10/30	0.387409535606457	4	FACETS	0.896	0.842	0.951	0.896	0.842	0.951	CLONAL	2	TRUE	2	0.412935089341546	4		425	1081	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186507037	186507037	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	246	595	0	ENST00000323963.5:c.1203G>C	p.Met401Ile	p.M401I	ENST00000323963		401	atG/atC	11/11	0.412935089341546	2	FACETS	1	0.972	1	0.537	0.501	0.573	CLONAL	1	TRUE	0	0.412935089341546	2		595	1110	SUCCESS
APC	324	MSKCC	GRCh37	5	112179006	112179006	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs876659280	NA	P-0005731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	84	215	0	ENST00000257430.4:c.7715C>G	p.Ser2572Ter	p.S2572*	ENST00000257430	NM_000038.5	2572	tCa/tGa	16/16	0.412935089341546	2	FACETS	0.806	0.714	0.904	0.403	0.357	0.452	CLONAL	1	TRUE	0	0.412935089341546	2		215	505	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286874	33286874	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	114	322	0	ENST00000374542.5:c.2063C>G	p.Ser688Cys	p.S688C	ENST00000374542	NM_001141970.1	688	tCt/tGt	7/8	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.412935089341546	2		322	543	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940403	13940403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1274578649	NA	P-0005731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	107	224	1	ENST00000405192.2:c.1103G>A	p.Arg368His	p.R368H	ENST00000405192	NM_001163147.1	368	cGt/cAt	11/12	0.412935089341546	3	FACETS	0.975	0.876	1	0.488	0.438	0.54	CLONAL	1	TRUE	1	0.412935089341546	3		225	641	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543643	148543643	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs199645805	NA	P-0005731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	70	238	1	ENST00000320356.2:c.165C>G	p.Ile55Met	p.I55M	ENST00000320356	NM_004456.4	55	atC/atG	3/20	0.297912212827803	5	FACETS	0.877	0.765	0.998	0.292	0.255	0.333	CLONAL	1	TRUE	2	0.412935089341546	5		239	626	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751185	128751185	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs186663828	NA	P-0005731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	92	236	0	ENST00000377970.2:c.722C>T	p.Ser241Leu	p.S241L	ENST00000377970	NM_002467.4	241	tCg/tTg	2/3	0.364275533115859	3	FACETS	1	0.97	1	0.625	0.558	0.695	CLONAL	1	TRUE	1	0.412935089341546	3		236	430	SUCCESS
ATM	472	MSKCC	GRCh37	11	108138018	108138018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	305	424	1	ENST00000278616.4:c.2587G>A	p.Asp863Asn	p.D863N	ENST00000278616	NM_000051.3	863	Gat/Aat	17/63	0.412935089341546	4	FACETS	0.86	0.81	0.911			1	CLONAL	2	TRUE	NA	0.412935089341546	4		425	1214	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858600	57858600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756282060	NA	P-0005731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	383	697	0	ENST00000228682.2:c.338G>A	p.Arg113Gln	p.R113Q	ENST00000228682	NM_005269.2	113	cGa/cAa	4/12	0.412935089341546	3	FACETS	0.898	0.853	0.944	0.898	0.853	0.944	CLONAL	2	TRUE	1	0.412935089341546	3		697	1246	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353904	68353904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	155	314	0	ENST00000487270.1:c.739G>A	p.Glu247Lys	p.E247K	ENST00000487270	NM_133509.3	247	Gag/Aag	7/11	0.412935089341546	3	FACETS	0.953	0.872	1	0.477	0.436	0.519	CLONAL	1	TRUE	1	0.412935089341546	3		314	950	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348810	11348810	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	35	116	0	ENST00000332029.2:c.526G>C	p.Glu176Gln	p.E176Q	ENST00000332029	NM_003745.1	176	Gag/Cag	2/2	1	2	FACETS	0.811	0.671	0.966	0.811	0.671	0.966	CLONAL	1	TRUE	1	0.412935089341546	2		116	209	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348912	11348912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765480579	NA	P-0005731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	65	221	0	ENST00000332029.2:c.424G>A	p.Glu142Lys	p.E142K	ENST00000332029	NM_003745.1	142	Gag/Aag	2/2	1	2	FACETS	0.943	0.823	1	0.943	0.823	1	CLONAL	1	TRUE	1	0.412935089341546	2		221	334	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348956	11348956	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	88	273	0	ENST00000332029.2:c.380G>A	p.Arg127His	p.R127H	ENST00000332029	NM_003745.1	127	cGc/cAc	2/2	1	2	FACETS	0.987	0.879	1	0.987	0.879	1	CLONAL	1	TRUE	1	0.412935089341546	2		273	432	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243508	41243508	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	143	372	0	ENST00000357654.3:c.4040G>C	p.Arg1347Thr	p.R1347T	ENST00000357654	NM_007294.3	1347	aGa/aCa	10/23	0.412935089341546	3	FACETS	0.831	0.757	0.91	0.416	0.378	0.455	CLONAL	1	TRUE	1	0.412935089341546	3		372	1005	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78865541	78865541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	121	267	0	ENST00000306801.3:c.2005C>T	p.His669Tyr	p.H669Y	ENST00000306801	NM_020761.2	669	Cat/Tat	18/34	0.412935089341546	3	FACETS	0.986	0.892	1	0.493	0.446	0.543	CLONAL	1	TRUE	1	0.412935089341546	3		267	717	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051624	30051624	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1325902176	NA	P-0005731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	252	383	0	ENST00000338641.4:c.558G>C	p.Glu186Asp	p.E186D	ENST00000338641	NM_000268.3	186	gaG/gaC	6/16	0.412935089341546	6	FACETS	0.889	0.83	0.949			1	CLONAL	2	TRUE	NA	0.412935089341546	6		383	1254	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53253979	53253979	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	228	306	0	ENST00000375401.3:c.93C>G	p.Ile31Met	p.I31M	ENST00000375401	NM_004187.3	31	atC/atG	1/26	0.383559132300024	2	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.412935089341546	2		306	777	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	125	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.895	0.82	0.973	0.895	0.82	0.973	CLONAL	1	TRUE	1	0.7799330102829	2		174	358	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0005912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	493	593	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.603516838888698	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.7799330102829	1		595	705	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685300	89685300	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs878853936	NA	P-0005912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	167	264	0	ENST00000371953.3:c.195C>G	p.Tyr65Ter	p.Y65*	ENST00000371953	NM_000314.4	65	taC/taG	3/9	0.7799330102829	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.7799330102829	1		264	260	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102199665	102199665	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	164	426	0	ENST00000263464.3:c.1070C>G	p.Ala357Gly	p.A357G	ENST00000263464	NM_001165.4	357	gCa/gGa	5/9	0.217511453088852	1	FACETS	0.429	0.395	0.464	0.429	0.395	0.464	INDETERMINATE	1	TRUE	0	0.7799330102829	1		426	598	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0005937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	64	497	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.704	0.611	0.805	0.704	0.611	0.805	SUBCLONAL	1	TRUE	1	0.364351950245781	2		497	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0005937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	100	586	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.31210180248465	1	FACETS	0.711	0.636	0.791	0.711	0.636	0.791	SUBCLONAL	1	TRUE	0	0.364351950245781	1		586	631	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603023	48603023	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555687378	NA	P-0005937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	69	258	2	ENST00000342988.3:c.1324C>T	p.Gln442Ter	p.Q442*	ENST00000342988	NM_005359.5	442	Cag/Tag	11/12	0.31210180248465	1	FACETS	0.772	0.676	0.876	0.772	0.676	0.876	SUBCLONAL	1	TRUE	0	0.364351950245781	1		260	401	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106364	27106364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	68	393	0	ENST00000324856.7:c.5975C>T	p.Ser1992Leu	p.S1992L	ENST00000324856	NM_006015.4	1992	tCa/tTa	20/20	1	2	FACETS	0.833	0.727	0.947	0.833	0.727	0.947	CLONAL	1	TRUE	1	0.364351950245781	2		393	448	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443940	18443940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866374517	NA	P-0005937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	41	279	0	ENST00000266497.5:c.913C>T	p.Pro305Ser	p.P305S	ENST00000266497		305	Cca/Tca	3/31	1	2	FACETS	0.697	0.582	0.823	0.697	0.582	0.823	SUBCLONAL	1	TRUE	1	0.364351950245781	2		279	323	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562270	95562270	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555367530	NA	P-0005937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	125	485	0	ENST00000393063.1:c.4987A>G	p.Ile1663Val	p.I1663V	ENST00000393063	NM_030621.3	1663	Ata/Gta	24/28	0.199956722240065	4	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.364351950245781	4		485	778	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20150381	20150381	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	36	301	0	ENST00000379607.5:c.256G>A	p.Asp86Asn	p.D86N	ENST00000379607	NM_001412.3	86	Gat/Aat	5/7	0.306401256030766	0	FACETS	0.362	0.298	0.433			1	SUBCLONAL	1	TRUE	0	0.364351950245781	0		301	347	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729821	47729856	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CCGCCGCTCGTACTGTGCGTTGAGGTCGTCCGCCAT	CCGCCGCTCGTACTGTGCGTTGAGGTCGTCCGCCAT	-	novel	NA	P-0005937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	63	456	0	ENST00000449228.1:c.533_568del	p.Asp178_Ala189del	p.D178_A189del	ENST00000449228	NM_001127240.2	178	gATGGCGGACGACCTCAACGCACAGTACGAGCGGCGGag/gag	3/4	0.216520831778236	3	FACETS	0.681	0.589	0.781	0.227	0.196	0.261	INDETERMINATE	1	TRUE	0	0.364351950245781	3		456	600	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006008-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	26	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.709	0.56	0.88	0.709	0.56	0.88	SUBCLONAL	1	TRUE	1	0.159142743304133	2		174	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0006008-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	83	691	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.861	0.757	0.973	0.861	0.757	0.973	CLONAL	1	TRUE	1	0.159142743304133	2		691	1212	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149917	202149917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006008-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	350	373	0	ENST00000358485.4:c.1358C>T	p.Pro453Leu	p.P453L	ENST00000358485	NM_001080125.1	453	cCg/cTg	8/9	0.159142743304133	6	FACETS	1	0.953	1			1	CLONAL	5	TRUE	NA	0.159142743304133	6		373	1153	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518842	187518842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773654248	NA	P-0006008-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	53	320	0	ENST00000441802.2:c.12362G>A	p.Gly4121Glu	p.G4121E	ENST00000441802	NM_005245.3	4121	gGa/gAa	24/27	1	2	FACETS	0.819	0.697	0.954	0.819	0.697	0.954	CLONAL	1	TRUE	1	0.159142743304133	2		320	813	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876995	151876995	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006008-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	142	493	0	ENST00000262189.6:c.7366G>T	p.Ala2456Ser	p.A2456S	ENST00000262189	NM_170606.2	2456	Gct/Tct	37/59	1	2	FACETS	0.844	0.768	0.924	1	0.989	1	CLONAL	2	TRUE	1	0.159142743304133	2		493	1057	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518091	8518091	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs970315764	NA	P-0006008-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	80	259	0	ENST00000356435.5:c.1300A>G	p.Ile434Val	p.I434V	ENST00000356435		434	Att/Gtt	10/35	0.159142743304133	2	FACETS	1	0.97	1	0.67	0.589	0.757	CLONAL	1	TRUE	0	0.159142743304133	2		259	750	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578262	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs483352697	NA	P-0006008-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	51	443	1	ENST00000269305.4:c.587G>T	p.Arg196Leu	p.R196L	ENST00000269305	NM_001126112.2	196	cGa/cTa	6/11	1	2	FACETS	0.6	0.508	0.702	0.6	0.508	0.702	SUBCLONAL	1	TRUE	1	0.159142743304133	2		444	1068	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246324	53246324	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0006008-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	68	256	0	ENST00000375401.3:c.657+1G>A		p.X219_splice	ENST00000375401	NM_004187.3	219			1	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.159142743304133	1		256	610	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243598	41243598	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006008-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	78	455	0	ENST00000357654.3:c.3950del	p.Leu1317Ter	p.L1317*	ENST00000357654	NM_007294.3	1317	tTg/tg	10/23	1	2	FACETS	0.909	0.797	1	0.909	0.797	1	CLONAL	1	TRUE	1	0.159142743304133	2		455	1078	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218908	193218908	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006008-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	130	388	0	ENST00000367435.3:c.1467del	p.Gln490ArgfsTer5	p.Q490Rfs*5	ENST00000367435	NM_024529.4	489	gTt/gt	16/17	1	2	FACETS	0.802	0.727	0.882	1	0.987	1	CLONAL	2	TRUE	1	0.159142743304133	2		388	1018	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162835	47162835	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0006036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	82	358	0	ENST00000409792.3:c.3291T>G	p.Tyr1097Ter	p.Y1097*	ENST00000409792	NM_014159.6	1097	taT/taG	3/21	NA	2	FACETS	0.923	0.83	1			1	INDETERMINATE	2	TRUE	NA	0.411110748756118	2		358	216	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436827	52436827	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0006036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	101	468	0	ENST00000460680.1:c.1951A>T	p.Lys651Ter	p.K651*	ENST00000460680	NM_004656.3	651	Aag/Tag	15/17	NA	2	FACETS	0.893	0.811	0.978			1	INDETERMINATE	2	TRUE	NA	0.411110748756118	2		468	275	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023120	1023120	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	48	409	0	ENST00000358495.3:c.1135C>A	p.Pro379Thr	p.P379T	ENST00000358495	NM_134424.2	379	Cca/Aca	11/12	0.305474286520386	4	FACETS	0.786	0.666	0.918			1	CLONAL	1	TRUE	NA	0.411110748756118	4		409	419	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259967	16259967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	266	646	3	ENST00000375759.3:c.7232C>T	p.Ser2411Leu	p.S2411L	ENST00000375759	NM_015001.2	2411	tCg/tTg	11/15	1	2	FACETS	0.961	0.899	1	0.961	0.899	1	CLONAL	1	TRUE	1	0.38724431747612	2		649	1429	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056191	27056191	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	277	593	0	ENST00000324856.7:c.1187G>A	p.Gly396Asp	p.G396D	ENST00000324856	NM_006015.4	396	gGc/gAc	2/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.38724431747612	2		593	1339	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932112	36932112	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1708	177	930	0	ENST00000361632.4:c.2357C>T	p.Ser786Phe	p.S786F	ENST00000361632		786	tCc/tTc	16/16	1	2	FACETS	0.485	0.445	0.527	0.485	0.445	0.527	SUBCLONAL	1	TRUE	1	0.38724431747612	2		930	1885	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944326	206944326	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1656	498	607	2	ENST00000423557.1:c.304G>A	p.Asp102Asn	p.D102N	ENST00000423557	NM_000572.2	102	Gac/Aac	3/5	0.334280391189328	5	FACETS	0.944	0.9	0.988	0.629	0.6	0.659	CLONAL	2	TRUE	2	0.38724431747612	5		609	2154	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143027	30143027	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	346	799	1	ENST00000389048.3:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000389048	NM_004304.4	167	Cag/Tag	1/29	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.38724431747612	2		800	1565	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172124	99172124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1255	145	627	2	ENST00000074304.5:c.1690C>T	p.Pro564Ser	p.P564S	ENST00000074304	NM_001134224.1	564	Ccc/Tcc	17/26	1	2	FACETS	0.535	0.486	0.586	0.535	0.486	0.586	SUBCLONAL	1	TRUE	1	0.38724431747612	2		629	1400	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873458	136873458	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1558837039	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2037	211	1015	0	ENST00000241393.3:c.40G>A	p.Glu14Lys	p.E14K	ENST00000241393	NM_003467.2	14	Gag/Aag	2/2	1	2	FACETS	0.485	0.448	0.524	0.485	0.448	0.524	SUBCLONAL	1	TRUE	1	0.38724431747612	2		1015	2248	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198260841	198260841	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	42	415	0	ENST00000335508.6:c.3478G>A	p.Glu1160Lys	p.E1160K	ENST00000335508	NM_012433.2	1160	Gaa/Aaa	23/25	1	2	FACETS	0.366	0.305	0.434	0.366	0.305	0.434	SUBCLONAL	1	TRUE	1	0.38724431747612	2		415	593	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295705	212295705	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	53	446	2	ENST00000342788.4:c.2608G>A	p.Gly870Arg	p.G870R	ENST00000342788	NM_005235.2	870	Gga/Aga	21/28	1	2	FACETS	0.41	0.349	0.478	0.41	0.349	0.478	SUBCLONAL	1	TRUE	1	0.38724431747612	2		448	667	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499483	89499483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1426641543	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	159	491	2	ENST00000336596.2:c.2653C>T	p.Pro885Ser	p.P885S	ENST00000336596	NM_005233.5	885	Ccc/Tcc	15/17	1	2	FACETS	0.761	0.697	0.829	0.761	0.697	0.829	SUBCLONAL	1	TRUE	1	0.38724431747612	2		493	1079	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803395	1803395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1349	330	784	2	ENST00000260795.2:c.664G>A	p.Asp222Asn	p.D222N	ENST00000260795		222	Gac/Aac	5/17	0.276590222133311	1	FACETS	0.819	0.771	0.867	0.819	0.771	0.867	CLONAL	1	TRUE	0	0.38724431747612	1		786	1679	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133889	55133889	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	55	451	0	ENST00000257290.5:c.1102G>A	p.Glu368Lys	p.E368K	ENST00000257290	NM_006206.4	368	Gaa/Aaa	7/23	0.276590222133311	1	FACETS	0.307	0.261	0.356	0.307	0.261	0.356	SUBCLONAL	1	TRUE	0	0.38724431747612	1		451	747	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	260	769	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.775	0.728	0.824	1	0.993	1	SUBCLONAL	2	TRUE	1	0.38724431747612	2		769	866	SUCCESS
APC	324	MSKCC	GRCh37	5	112175118	112175118	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	28	245	1	ENST00000257430.4:c.3827C>T	p.Ser1276Leu	p.S1276L	ENST00000257430	NM_000038.5	1276	tCa/tTa	16/16	0.38724431747612	1	FACETS	0.327	0.261	0.401	0.327	0.261	0.401	SUBCLONAL	1	TRUE	0	0.38724431747612	1		246	357	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170292	32170292	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	511	639	0	ENST00000375023.3:c.3316C>T	p.Pro1106Ser	p.P1106S	ENST00000375023	NM_004557.3	1106	Cct/Tct	21/30	0.366977419434086	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.38724431747612	3		639	1516	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288200	33288200	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	164	406	0	ENST00000374542.5:c.1208C>T	p.Ser403Phe	p.S403F	ENST00000374542	NM_001141970.1	403	tCc/tTc	4/8	0.366977419434086	3	FACETS	0.864	0.792	0.94	0.432	0.396	0.47	CLONAL	1	TRUE	1	0.38724431747612	3		406	1170	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120377	94120377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	190	895	0	ENST00000369303.4:c.674C>T	p.Ser225Phe	p.S225F	ENST00000369303	NM_004440.3	225	tCc/tTc	3/17	0.38724431747612	1	FACETS	0.768	0.71	0.829	0.768	0.71	0.829	SUBCLONAL	1	TRUE	0	0.38724431747612	1		895	1030	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631341	117631341	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	124	352	0	ENST00000368508.3:c.6337G>A	p.Asp2113Asn	p.D2113N	ENST00000368508	NM_002944.2	2113	Gat/Aat	40/43	0.38724431747612	1	FACETS	0.829	0.752	0.91	0.829	0.752	0.91	CLONAL	1	TRUE	0	0.38724431747612	1		352	623	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381451	81381451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	119	546	0	ENST00000222390.5:c.610C>T	p.Pro204Ser	p.P204S	ENST00000222390	NM_000601.4	204	Cct/Tct	5/18	1	2	FACETS	0.81	0.731	0.893	0.81	0.731	0.893	CLONAL	1	TRUE	1	0.38724431747612	2		546	759	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508406	106508406	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	35	228	0	ENST00000359195.3:c.400C>T	p.Gln134Ter	p.Q134*	ENST00000359195	NM_002649.2	134	Cag/Tag	2/11	1	2	FACETS	0.328	0.268	0.396	0.328	0.268	0.396	SUBCLONAL	1	TRUE	1	0.38724431747612	2		228	551	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271265	38271265	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377149398	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	179	513	1	ENST00000425967.3:c.2443C>T	p.Arg815Trp	p.R815W	ENST00000425967	NM_001174067.1	815	Cgg/Tgg	19/19	1	2	FACETS	0.797	0.733	0.863	0.797	0.733	0.863	SUBCLONAL	1	TRUE	1	0.38724431747612	2		514	1160	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371974	55371974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774048347	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	40	249	1	ENST00000297316.4:c.664C>T	p.Pro222Ser	p.P222S	ENST00000297316	NM_022454.3	222	Ccc/Tcc	2/2	1	2	FACETS	0.374	0.31	0.446	0.374	0.31	0.446	SUBCLONAL	1	TRUE	1	0.38724431747612	2		250	552	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317117	87317117	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	128	486	0	ENST00000277120.3:c.256G>A	p.Asp86Asn	p.D86N	ENST00000277120		86	Gat/Aat	3/19	1	2	FACETS	0.831	0.753	0.912	0.831	0.753	0.912	CLONAL	1	TRUE	1	0.38724431747612	2		486	796	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149241	119149241	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867564832	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	153	755	1	ENST00000264033.4:c.1249C>T	p.Pro417Ser	p.P417S	ENST00000264033	NM_005188.3	417	Cct/Tct	9/16	0.364221251542766	1	FACETS	0.706	0.646	0.77	0.706	0.646	0.77	SUBCLONAL	1	TRUE	0	0.38724431747612	1		756	902	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719887	18719887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146312199	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	56	432	0	ENST00000266497.5:c.3784C>T	p.Pro1262Ser	p.P1262S	ENST00000266497		1262	Cct/Tct	27/31	0.343087582783459	1	FACETS	0.519	0.446	0.6	0.519	0.446	0.6	SUBCLONAL	1	TRUE	0	0.38724431747612	1		432	449	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944947	31944947	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868835690	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	73	425	0	ENST00000340398.3:c.154C>T	p.Arg52Cys	p.R52C	ENST00000340398	NM_001013699.2	52	Cgt/Tgt	1/1	1	2	FACETS	0.363	0.316	0.413	0.363	0.316	0.413	SUBCLONAL	1	TRUE	1	0.38724431747612	2		425	1040	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856421	111856421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760318311	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	132	265	0	ENST00000341259.2:c.472C>T	p.His158Tyr	p.H158Y	ENST00000341259	NM_005475.2	158	Cac/Tac	2/8	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.38724431747612	2		265	666	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012362	29012362	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs762113174	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	118	506	2	ENST00000282397.4:c.509A>T	p.Lys170Ile	p.K170I	ENST00000282397	NM_002019.4	170	aAa/aTa	4/30	0.364221251542766	1	FACETS	0.74	0.669	0.815	0.74	0.669	0.815	SUBCLONAL	1	TRUE	0	0.38724431747612	1		508	664	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103391	2103391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1325855418	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1284	301	758	3	ENST00000219476.3:c.274G>A	p.Glu92Lys	p.E92K	ENST00000219476	NM_000548.3	92	Gag/Aag	4/42	1	2	FACETS	0.981	0.921	1	0.981	0.921	1	CLONAL	1	TRUE	1	0.38724431747612	2		761	1585	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2115592	2115592	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1433	141	696	0	ENST00000219476.3:c.1672G>A	p.Glu558Lys	p.E558K	ENST00000219476	NM_000548.3	558	Gag/Aag	16/42	1	2	FACETS	0.463	0.42	0.508	0.463	0.42	0.508	SUBCLONAL	1	TRUE	1	0.38724431747612	2		696	1574	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858735	9858735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	164	561	1	ENST00000330684.3:c.2666G>A	p.Gly889Glu	p.G889E	ENST00000330684	NM_001134407.1	889	gGa/gAa	13/13	1	2	FACETS	0.764	0.701	0.831	0.764	0.701	0.831	SUBCLONAL	1	TRUE	1	0.38724431747612	2		562	1108	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892177	9892177	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555488097	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1257	268	742	2	ENST00000330684.3:c.2313G>A	p.Trp771Ter	p.W771*	ENST00000330684	NM_001134407.1	771	tgG/tgA	11/13	1	2	FACETS	0.908	0.849	0.968	0.908	0.849	0.968	CLONAL	1	TRUE	1	0.38724431747612	2		744	1525	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934906	9934906	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866473134	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	81	570	0	ENST00000330684.3:c.1384G>A	p.Asp462Asn	p.D462N	ENST00000330684	NM_001134407.1	462	Gat/Aat	6/13	1	2	FACETS	0.451	0.397	0.51	0.451	0.397	0.51	SUBCLONAL	1	TRUE	1	0.38724431747612	2		570	927	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070581	67070581	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	132	655	0	ENST00000412916.2:c.205T>G	p.Phe69Val	p.F69V	ENST00000412916		69	Ttt/Gtt	3/6	0.228913486174667	1	FACETS	0.432	0.391	0.476	0.432	0.391	0.476	INDETERMINATE	1	TRUE	0	0.38724431747612	1		655	1272	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89865593	89865593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200220791	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	223	632	1	ENST00000389301.3:c.874C>T	p.His292Tyr	p.H292Y	ENST00000389301	NM_000135.2	292	Cac/Tac	10/43	0.228913486174667	1	FACETS	0.771	0.716	0.827	0.771	0.716	0.827	INDETERMINATE	1	TRUE	0	0.38724431747612	1		633	1205	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509639	29509639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	176	506	1	ENST00000356175.3:c.844C>T	p.Gln282Ter	p.Q282*	ENST00000356175	NM_000267.3	282	Cag/Tag	8/57	0.200157917969728	3	FACETS	1	0.985	1	0.644	0.593	0.696	INDETERMINATE	1	TRUE	1	0.38724431747612	3		507	843	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654559	29654559	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1131691103	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	202	552	0	ENST00000356175.3:c.5248A>G	p.Lys1750Glu	p.K1750E	ENST00000356175	NM_000267.3	1750	Aaa/Gaa	37/57	0.200157917969728	3	FACETS	0.984	0.911	1	0.492	0.455	0.531	INDETERMINATE	1	TRUE	1	0.38724431747612	3		552	1265	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223246	41223246	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357096	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	120	413	0	ENST00000357654.3:c.4685C>T	p.Pro1562Leu	p.P1562L	ENST00000357654	NM_007294.3	1562	cCt/cTt	15/23	0.200157917969728	3	FACETS	0.92	0.831	1	0.46	0.415	0.507	INDETERMINATE	1	TRUE	1	0.38724431747612	3		413	804	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117493	4117493	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	54	336	1	ENST00000262948.5:c.227C>T	p.Ser76Leu	p.S76L	ENST00000262948	NM_030662.3	76	tCa/tTa	2/11	0.228913486174667	1	FACETS	0.319	0.272	0.371	0.319	0.272	0.371	INDETERMINATE	1	TRUE	0	0.38724431747612	1		337	704	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262096	10262096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1247	305	744	0	ENST00000340748.4:c.2195C>T	p.Ser732Phe	p.S732F	ENST00000340748		732	tCt/tTt	23/40	0.228913486174667	1	FACETS	0.818	0.769	0.869	0.818	0.769	0.869	INDETERMINATE	1	TRUE	0	0.38724431747612	1		744	1552	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910609	50910609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1658	263	886	0	ENST00000440232.2:c.1712C>T	p.Pro571Leu	p.P571L	ENST00000440232	NM_002691.3	571	cCc/cTc	14/27	0.228913486174667	1	FACETS	0.57	0.532	0.61	0.57	0.532	0.61	INDETERMINATE	1	TRUE	0	0.38724431747612	1		886	1921	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538311	9538311	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	205	650	0	ENST00000353224.5:c.1687G>A	p.Gly563Arg	p.G563R	ENST00000353224	NM_177990.2	563	Gga/Aga	7/10	1	2	FACETS	0.875	0.81	0.942	0.875	0.81	0.942	CLONAL	1	TRUE	1	0.38724431747612	2		650	1210	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268747	46268747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1486	337	908	1	ENST00000371998.3:c.3032C>T	p.Pro1011Leu	p.P1011L	ENST00000371998		1011	cCc/cTc	16/23	1	2	FACETS	0.955	0.9	1	0.955	0.9	1	CLONAL	1	TRUE	1	0.38724431747612	2		909	1823	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321304	1321304	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	188	524	0	ENST00000400841.2:c.451C>T	p.Gln151Ter	p.Q151*	ENST00000400841		151	Cag/Tag	4/6	1	1	FACETS	0.671	0.619	0.726	0.671	0.619	0.726	SUBCLONAL	1	TRUE	0	0.38724431747612	1		524	1166	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006193-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	118	174	0				ENST00000310581	NM_198253.2	-/1132			0.288934079940513	4	FACETS	1	0.96	1			1	CLONAL	3	TRUE	NA	0.288934079940513	4		174	323	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0006193-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	282	318	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.288934079940513	5	FACETS	0.911	0.86	0.962	1	0.99	1	CLONAL	4	TRUE	2	0.288934079940513	5		318	768	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561263	9561263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769939031	NA	P-0006193-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	73	592	0	ENST00000353224.5:c.519G>A	p.Met173Ile	p.M173I	ENST00000353224	NM_177990.2	173	atG/atA	4/10	0.288934079940513	3	FACETS	1	0.965	1	0.644	0.565	0.728	CLONAL	1	TRUE	1	0.288934079940513	3		592	449	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248444	59248444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006193-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	88	471	0	ENST00000371222.2:c.299C>T	p.Pro100Leu	p.P100L	ENST00000371222	NM_002228.3	100	cCc/cTc	1/1	0.288934079940513	4	FACETS	1	0.972	1			1	CLONAL	1	TRUE	NA	0.288934079940513	4		471	593	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251620	212251620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006193-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	173	601	0	ENST00000342788.4:c.3439G>A	p.Glu1147Lys	p.E1147K	ENST00000342788	NM_005235.2	1147	Gag/Aag	27/28	0.288934079940513	5	FACETS	1	0.983	1	0.816	0.753	0.881	CLONAL	2	TRUE	2	0.288934079940513	5		601	701	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582106	189582106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006193-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	130	761	0	ENST00000264731.3:c.665G>A	p.Gly222Glu	p.G222E	ENST00000264731	NM_003722.4	222	gGa/gAa	5/14	0.234090582936372	4	FACETS	0.919	0.836	1	0.919	0.836	1	CLONAL	2	TRUE	2	0.288934079940513	4		761	631	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161465	2161465	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006193-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	81	734	0	ENST00000434045.2:c.62A>C	p.Gln21Pro	p.Q21P	ENST00000434045	NM_001127598.1	21	cAa/cCa	2/5	0.288934079940513	3	FACETS	1	0.95	1	0.573	0.505	0.645	CLONAL	1	TRUE	1	0.288934079940513	3		734	560	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888120	81888120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199638859	NA	P-0006193-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	111	901	1	ENST00000359376.3:c.265C>T	p.Arg89Cys	p.R89C	ENST00000359376	NM_002661.3	89	Cgc/Tgc	3/33	0.288934079940513	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.288934079940513	1		902	519	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222978	5222978	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293966082	NA	P-0006193-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	29	449	0	ENST00000357368.4:c.2825C>T	p.Ser942Leu	p.S942L	ENST00000357368	NM_002850.3	942	tCg/tTg	18/38	0.247927103318453	1	FACETS	0.565	0.454	0.69	0.565	0.454	0.69	SUBCLONAL	1	TRUE	0	0.288934079940513	1		449	304	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184326	7184326	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0006193-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	40	639	0	ENST00000302850.5:c.974+1G>T		p.X325_splice	ENST00000302850	NM_000208.2	325			1	2	FACETS	0.559	0.464	0.665	0.559	0.464	0.665	SUBCLONAL	1	TRUE	1	0.288934079940513	2		639	495	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040795	47040795	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006193-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	78	681	0	ENST00000377604.3:c.1430G>A	p.Gly477Glu	p.G477E	ENST00000377604	NM_001204468.1	477	gGa/gAa	13/24	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.288934079940513	2		681	425	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589557	67589598	+	inframe_deletion	In_Frame_Del	DEL	TAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACAC	TAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACAC	-	novel	NA	P-0121560-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	111	415	0	ENST00000274335.5:c.1321_1362del	p.Asn441_Thr454del	p.N441_T454del	ENST00000274335		440	gaTAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACACt/gat	10/15	1	2	FACETS	0.734	0.661	0.812	0.734	0.661	0.812	SUBCLONAL	1	NA	1	0.467974881991494	2		415	646	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120912	115120912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0121560-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	154	391	1	ENST00000257566.3:c.94G>A	p.Ala32Thr	p.A32T	ENST00000257566	NM_016569.3	32	Gcg/Acg	1/8	0.467974881991494	3	FACETS	1	0.984	1	0.649	0.596	0.704	CLONAL	1	NA	1	0.467974881991494	3		392	626	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0006239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	94	769	0				ENST00000310581	NM_198253.2	-/1132			0.215069912453014	5	FACETS	0.899	0.803	1	0.6	0.535	0.668	CLONAL	2	TRUE	2	0.28	5		769	530	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282564	1282564	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	75	379	0	ENST00000310581.5:c.1749G>T	p.Lys583Asn	p.K583N	ENST00000310581	NM_198253.2	583	aaG/aaT	3/16	0.215069912453014	5	FACETS	1	0.903	1	0.345	0.302	0.392	CLONAL	1	TRUE	2	0.28	5		379	734	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74858968	74858968	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	76	268	0	ENST00000284811.8:c.236A>G	p.Tyr79Cys	p.Y79C	ENST00000284811		79	tAc/tGc	4/4	0.281338414486071	2	FACETS	0.818	0.723	0.918	0.818	0.723	0.918	CLONAL	2	TRUE	0	0.28	2		268	332	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005617	42005617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567019933	NA	P-0006239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	156	797	1	ENST00000219905.7:c.3353C>T	p.Ala1118Val	p.A1118V	ENST00000219905	NM_001164273.1	1118	gCa/gTa	9/24	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.28	2		798	1108	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0006256-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	908	695	1	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.716406707851968	3	FACETS	1	0.995	1			1	CLONAL	3	TRUE	NA	0.716406707851968	3		696	1111	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255076	16255076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1283954838	NA	P-0006256-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	168	352	0	ENST00000375759.3:c.2341C>T	p.Arg781Cys	p.R781C	ENST00000375759	NM_015001.2	781	Cgt/Tgt	11/15	1	2	FACETS	0.949	0.88	1	0.949	0.88	1	CLONAL	1	TRUE	1	0.716406707851968	2		352	494	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034869	42034869	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006256-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	282	873	2	ENST00000219905.7:c.4711A>G	p.Arg1571Gly	p.R1571G	ENST00000219905	NM_001164273.1	1571	Aga/Gga	15/24	1	2	FACETS	0.763	0.717	0.81	0.763	0.717	0.81	SUBCLONAL	1	TRUE	1	0.716406707851968	2		875	1032	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198261014	198261014	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006256-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	222	475	1	ENST00000335508.6:c.3305A>T	p.Lys1102Ile	p.K1102I	ENST00000335508	NM_012433.2	1102	aAa/aTa	23/25	0.194698411813671	3	FACETS	1	0.988	1	0.618	0.578	0.659	INDETERMINATE	1	TRUE	1	0.716406707851968	3		476	681	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665280	138665280	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006256-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	287	739	0	ENST00000330315.3:c.285G>C	p.Lys95Asn	p.K95N	ENST00000330315	NM_023067.3	95	aaG/aaC	1/1	0.702767311903467	3	FACETS	0.977	0.919	1	0.488	0.459	0.519	CLONAL	1	TRUE	1	0.716406707851968	3		739	1114	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578226	7578226	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1464727668	NA	P-0006286-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	58	261	0	ENST00000269305.4:c.623A>T	p.Asp208Val	p.D208V	ENST00000269305	NM_001126112.2	208	gAc/gTc	6/11	0.154464822464501	2	FACETS	1	0.881	1	0.515	0.442	0.595	CLONAL	1	TRUE	0	0.154464822464501	2		261	729	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512029	148512029	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006286-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	24	137	0	ENST00000320356.2:c.1649A>C	p.Lys550Thr	p.K550T	ENST00000320356	NM_004456.4	550	aAg/aCg	14/20	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.154464822464501	2		137	256	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219401	1219401	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006286-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	49	229	0	ENST00000326873.7:c.454del	p.Gln152ArgfsTer9	p.Q152Rfs*9	ENST00000326873	NM_000455.4	151	tgC/tg	3/10	1	2	FACETS	0.948	0.802	1	0.948	0.802	1	CLONAL	1	TRUE	1	0.154464822464501	2		229	669	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0006304-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	129	769	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.917	0.835	1	0.917	0.835	1	CLONAL	1	TRUE	1	0.500671188705235	2		769	562	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0006304-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	134	300	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.913	0.833	0.997	0.913	0.833	0.997	CLONAL	1	TRUE	1	0.500671188705235	2		300	586	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027133	49027133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853292	NA	P-0006304-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	122	235	0	ENST00000267163.4:c.1700C>T	p.Ser567Leu	p.S567L	ENST00000267163	NM_000321.2	567	tCa/tTa	18/27	0.500671188705235	1	FACETS	0.882	0.804	0.963	0.882	0.804	0.963	CLONAL	1	TRUE	0	0.500671188705235	1		235	414	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608282	28608282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773466203	NA	P-0006304-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	159	430	0	ENST00000241453.7:c.1774G>A	p.Val592Ile	p.V592I	ENST00000241453	NM_004119.2	592	Gtt/Att	14/24	1	2	FACETS	0.907	0.834	0.984	0.907	0.834	0.984	CLONAL	1	TRUE	1	0.500671188705235	2		430	700	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572935	7572935	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006304-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	546	471	0	ENST00000269305.4:c.1174T>C	p.Ser392Pro	p.S392P	ENST00000269305	NM_001126112.2	392	Tca/Cca	11/11	0.500671188705235	2	FACETS	0.903	0.869	0.937	0.903	0.869	0.937	CLONAL	2	TRUE	0	0.500671188705235	2		471	1208	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577575	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587782289	NA	P-0006304-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	458	399	0	ENST00000269305.4:c.706T>A	p.Tyr236Asn	p.Y236N	ENST00000269305	NM_001126112.2	236	Tac/Aac	7/11	0.500671188705235	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.500671188705235	2		399	907	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600420	10600420	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006304-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	110	507	0	ENST00000171111.5:c.1435G>C	p.Asp479His	p.D479H	ENST00000171111	NM_203500.1	479	Gac/Cac	4/6	1	2	FACETS	0.426	0.382	0.473	0.426	0.382	0.473	SUBCLONAL	1	TRUE	1	0.500671188705235	2		507	1032	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577541	7577541	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201762	NA	P-0006340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	566	478	0	ENST00000269305.4:c.740A>T	p.Asn247Ile	p.N247I	ENST00000269305	NM_001126112.2	247	aAc/aTc	7/11	0.804555962946629	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	FALSE	0	0.804919243133835	2		478	691	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106162585	106162585	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1356919272	NA	P-0006340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	120	315	0	ENST00000380013.4:c.3499A>G	p.Arg1167Gly	p.R1167G	ENST00000380013	NM_001127208.2	1167	Agg/Ggg	4/11	0.804919243133835	2	FACETS	0.852	0.778	0.928	0.426	0.389	0.464	CLONAL	1	FALSE	0	0.804919243133835	2		315	350	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278073	18278073	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1276	72	464	0	ENST00000222254.8:c.1693C>A	p.Pro565Thr	p.P565T	ENST00000222254	NM_005027.3	565	Ccg/Acg	13/16	0.75661164841492	4	FACETS	0.24	0.208	0.274	0.08	0.069	0.092	SUBCLONAL	1	FALSE	1	0.804919243133835	4		464	1348	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087503	27087503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006376-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	360	1011	4	ENST00000324856.7:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000324856	NM_006015.4	693	Cga/Tga	5/20	0.552257182257317	1	FACETS	0.962	0.914	1	0.962	0.914	1	CLONAL	1	TRUE	0	0.552257182257317	1		1015	981	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881002	37881003	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCTCCCCA	rs397516982	NA	P-0006376-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	306	1123	0	ENST00000269571.5:c.2332_2340dup	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	-/GGCTCCCCA	20/27	1	2	FACETS	0.807	0.759	0.856	0.807	0.759	0.856	CLONAL	1	TRUE	1	0.552257182257317	2		1123	1373	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562734	29562734	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006376-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	307	874	0	ENST00000356175.3:c.3814C>T	p.Gln1272Ter	p.Q1272*	ENST00000356175	NM_000267.3	1272	Cag/Tag	28/57	1	2	FACETS	0.984	0.928	1	0.984	0.928	1	CLONAL	1	TRUE	1	0.552257182257317	2		874	1130	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508508	29508509	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0006376-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	375	1094	0	ENST00000356175.3:c.654+2dup		p.X218_splice	ENST00000356175	NM_000267.3	218			1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.552257182257317	2		1094	1355	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88677065	88677065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765530074	NA	P-0006376-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	218	745	0	ENST00000372037.3:c.850C>T	p.Arg284Cys	p.R284C	ENST00000372037	NM_004329.2	284	Cgc/Tgc	9/13	1	2	FACETS	0.844	0.786	0.905	0.844	0.786	0.905	CLONAL	1	TRUE	1	0.552257182257317	2		745	935	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0006468-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	401	472	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.7351653132463	2	FACETS	0.97	0.939	1	0.97	0.939	1	CLONAL	2	TRUE	0	0.740686189505189	2		472	558	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687471	37687472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs760014508	NA	P-0006468-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	343	509	0	ENST00000447079.4:c.4382dup	p.Thr1463AsnfsTer50	p.T1463Nfs*50	ENST00000447079	NM_015083.1	1459	tgg/tGgg	14/14	0.740686189505189	5	FACETS	1	0.982	1			1	CLONAL	2	TRUE	NA	0.740686189505189	5		509	911	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647631	23647631	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs766710382	NA	P-0006468-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	381	525	0	ENST00000261584.4:c.236A>T	p.Tyr79Phe	p.Y79F	ENST00000261584	NM_024675.3	79	tAt/tTt	4/13	0.740686189505189	3	FACETS	0.924	0.884	0.964	0.924	0.884	0.964	CLONAL	2	TRUE	1	0.740686189505189	3		525	763	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687665	29687665	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006468-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	583	859	0	ENST00000356175.3:c.8258C>G	p.Ala2753Gly	p.A2753G	ENST00000356175	NM_000267.3	2753	gCc/gGc	56/57	0.691245901291284	4	FACETS	0.914	0.879	0.95	0.914	0.879	0.95	CLONAL	2	TRUE	2	0.740686189505189	4		859	1499	SUCCESS
APC	324	MSKCC	GRCh37	5	112175345	112175346	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006468-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	390	518	0	ENST00000257430.4:c.4056dup	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1352	gtt/gTtt	16/16	0.729107197918075	2	FACETS	0.93	0.898	0.961	0.93	0.898	0.961	CLONAL	2	TRUE	0	0.740686189505189	2		518	566	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	83	174	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.873	0.784	0.964			1	INDETERMINATE	1	TRUE	NA	0.852928416001067	2		174	223	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692818	89692818	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1339631701	NA	P-0006500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	81	168	0	ENST00000371953.3:c.302T>C	p.Ile101Thr	p.I101T	ENST00000371953	NM_000314.4	101	aTc/aCc	5/9	0.852928416001067	1	FACETS	0.908	0.838	0.974	0.908	0.838	0.974	CLONAL	1	TRUE	0	0.852928416001067	1		168	120	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056274	180056274	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770915197	NA	P-0006500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	234	544	1	ENST00000261937.6:c.970G>A	p.Glu324Lys	p.E324K	ENST00000261937	NM_182925.4	324	Gag/Aag	7/30	1	2	FACETS	0.99	0.932	1	0.99	0.932	1	CLONAL	1	TRUE	1	0.852928416001067	2		545	554	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055919	180055919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1368679940	NA	P-0006500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	177	467	0	ENST00000261937.6:c.1066G>A	p.Val356Met	p.V356M	ENST00000261937	NM_182925.4	356	Gtg/Atg	8/30	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.852928416001067	2		467	407	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414223	32414223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	124	572	0	ENST00000332351.3:c.1328G>A	p.Arg443Lys	p.R443K	ENST00000332351	NM_024426.4	443	aGg/aAg	8/10	1	2	FACETS	0.383	0.347	0.422	0.383	0.347	0.422	SUBCLONAL	1	TRUE	1	0.852928416001067	2		572	759	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895685	28895687	+	inframe_deletion	In_Frame_Del	DEL	AAA	AAA	-	novel	NA	P-0006500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	224	477	0	ENST00000282397.4:c.3087_3089del	p.Leu1030del	p.L1030del	ENST00000282397	NM_002019.4	1029	ctTTTa/cta	23/30	0.276323202710463	1	FACETS	0.563	0.529	0.598	0.563	0.529	0.598	INDETERMINATE	1	TRUE	0	0.852928416001067	1		477	535	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	103	174	0				ENST00000310581	NM_198253.2	-/1132			0.159967805434542	2	FACETS	0.814	0.741	0.888	0.814	0.741	0.888	INDETERMINATE	2	TRUE	0	0.494198397061275	2		174	256	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0006515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	391	386	0	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	0.494198397061275	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.494198397061275	3		386	607	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663281	227663281	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs942929290	NA	P-0006515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	126	385	0	ENST00000305123.5:c.174C>A	p.Ser58Arg	p.S58R	ENST00000305123	NM_005544.2	58	agC/agA	1/2	NA	2	FACETS	1	0.947	1			1	INDETERMINATE	1	TRUE	NA	0.494198397061275	2		385	483	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037213	71037213	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	112	427	0	ENST00000318789.4:c.1078G>T	p.Glu360Ter	p.E360*	ENST00000318789	NM_032682.5	360	Gaa/Taa	14/21	1	2	FACETS	0.905	0.818	0.996	0.905	0.818	0.996	CLONAL	1	TRUE	1	0.494198397061275	2		427	501	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416516	49416516	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	161	463	0	ENST00000301067.7:c.16195G>T	p.Val5399Leu	p.V5399L	ENST00000301067	NM_003482.3	5399	Gtg/Ttg	51/54	0.494198397061275	3	FACETS	1	0.942	1	0.516	0.473	0.56	CLONAL	1	TRUE	1	0.494198397061275	3		463	788	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652038	36652135	+	frameshift_variant	Frame_Shift_Del	DEL	GTCACCGAGACACCACTGGAGGGTGACTTCGCCTGGGAGCGTGTGCGGGGCCTTGGCCTGCCCAAGCTCTACCTTCCCACGGGGCCCCGGCGAGGCCG	GTCACCGAGACACCACTGGAGGGTGACTTCGCCTGGGAGCGTGTGCGGGGCCTTGGCCTGCCCAAGCTCTACCTTCCCACGGGGCCCCGGCGAGGCCG	-	novel	NA	P-0006515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	282	511	0	ENST00000244741.5:c.161_258del	p.Val54GlyfsTer2	p.V54Gfs*2	ENST00000244741	NM_000389.4	54	GTCACCGAGACACCACTGGAGGGTGACTTCGCCTGGGAGCGTGTGCGGGGCCTTGGCCTGCCCAAGCTCTACCTTCCCACGGGGCCCCGGCGAGGCCGg/g	2/3	0.494198397061275	4	FACETS	0.899	0.847	0.953	0.899	0.847	0.953	CLONAL	2	TRUE	2	0.494198397061275	4		511	948	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	114	769	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.271557941880459	2		769	640	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015054	71015054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	128	329	0	ENST00000318789.4:c.1876C>T	p.Pro626Ser	p.P626S	ENST00000318789	NM_032682.5	626	Cct/Tct	20/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.271557941880459	2		329	827	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146527	185146527	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35961174	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	118	377	1	ENST00000265026.3:c.158G>A	p.Arg53Gln	p.R53Q	ENST00000265026	NM_004721.4	53	cGa/cAa	2/14	1	2	FACETS	0.944	0.85	1	0.944	0.85	1	CLONAL	1	TRUE	1	0.271557941880459	2		378	921	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981554	55981554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	99	271	0	ENST00000263923.4:c.383C>T	p.Ser128Phe	p.S128F	ENST00000263923	NM_002253.2	128	tCt/tTt	4/30	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.271557941880459	2		271	690	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242749	66242749	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	60	480	1	ENST00000273854.3:c.1823C>T	p.Ser608Phe	p.S608F	ENST00000273854	NM_004439.5	608	tCc/tTc	9/18	1	2	FACETS	0.396	0.34	0.458	0.396	0.34	0.458	SUBCLONAL	1	TRUE	1	0.271557941880459	2		481	1115	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467388	66467388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	55	243	1	ENST00000273854.3:c.881G>A	p.Gly294Glu	p.G294E	ENST00000273854	NM_004439.5	294	gGa/gAa	3/18	1	2	FACETS	0.735	0.629	0.851	0.735	0.629	0.851	SUBCLONAL	1	TRUE	1	0.271557941880459	2		244	551	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467550	66467550	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	80	510	0	ENST00000273854.3:c.719T>G	p.Leu240Trp	p.L240W	ENST00000273854	NM_004439.5	240	tTg/tGg	3/18	1	2	FACETS	0.527	0.463	0.597	0.527	0.463	0.597	SUBCLONAL	1	TRUE	1	0.271557941880459	2		510	1117	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156595	106156595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	44	354	0	ENST00000380013.4:c.1496C>T	p.Pro499Leu	p.P499L	ENST00000380013	NM_001127208.2	499	cCa/cTa	3/11	1	2	FACETS	0.376	0.314	0.446	0.376	0.314	0.446	SUBCLONAL	1	TRUE	1	0.271557941880459	2		354	861	SUCCESS
APC	324	MSKCC	GRCh37	5	112173476	112173476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	196	422	0	ENST00000257430.4:c.2185C>T	p.Leu729Phe	p.L729F	ENST00000257430	NM_000038.5	729	Ctc/Ttc	16/16	0.226312673417273	2	FACETS	0.855	0.793	0.92	0.855	0.793	0.92	CLONAL	2	TRUE	0	0.271557941880459	2		422	844	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170827844	170827844	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs544573727	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	82	410	0	ENST00000296930.5:c.584C>T	p.Ser195Phe	p.S195F	ENST00000296930	NM_002520.6	195	tCt/tTt	8/11	0.226312673417273	2	FACETS	0.603	0.53	0.682	0.302	0.265	0.341	SUBCLONAL	1	TRUE	0	0.271557941880459	2		410	1001	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662475	117662475	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	221	330	0	ENST00000368508.3:c.4903-1G>A		p.X1635_splice	ENST00000368508	NM_002944.2	1635			0.221414481862534	3	FACETS	0.971	0.904	1	0.971	0.904	1	CLONAL	2	TRUE	1	0.271557941880459	3		330	952	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714415	117714415	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	124	395	0	ENST00000368508.3:c.1234C>T	p.Gln412Ter	p.Q412*	ENST00000368508	NM_002944.2	412	Caa/Taa	11/43	0.221414481862534	3	FACETS	0.981	0.886	1	0.491	0.443	0.541	CLONAL	1	TRUE	1	0.271557941880459	3		395	1057	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508791	106508791	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	126	384	0	ENST00000359195.3:c.785C>T	p.Pro262Leu	p.P262L	ENST00000359195	NM_002649.2	262	cCc/cTc	2/11	1	2	FACETS	0.965	0.872	1	0.965	0.872	1	CLONAL	1	TRUE	1	0.271557941880459	2		384	962	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545695	106545695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1258726641	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	187	378	0	ENST00000359195.3:c.3172G>A	p.Gly1058Arg	p.G1058R	ENST00000359195	NM_002649.2	1058	Ggg/Agg	11/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.271557941880459	2		378	1145	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500859	8500859	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329398246	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	135	303	0	ENST00000356435.5:c.2023G>A	p.Glu675Lys	p.E675K	ENST00000356435		675	Gaa/Aaa	13/35	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.271557941880459	2		303	748	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521296	8521296	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	43	214	0	ENST00000356435.5:c.942A>G	p.Ile314Met	p.I314M	ENST00000356435		314	atA/atG	9/35	1	2	FACETS	0.573	0.479	0.677	0.573	0.479	0.677	SUBCLONAL	1	TRUE	1	0.271557941880459	2		214	553	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220550	98220550	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	40	255	0	ENST00000331920.6:c.2913T>G	p.Tyr971Ter	p.Y971*	ENST00000331920	NM_000264.3	971	taT/taG	18/24	1	2	FACETS	0.498	0.413	0.593	0.498	0.413	0.593	SUBCLONAL	1	TRUE	1	0.271557941880459	2		255	592	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98244415	98244415	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	123	350	1	ENST00000331920.6:c.654+1G>A		p.X218_splice	ENST00000331920	NM_000264.3	218			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.271557941880459	2		351	798	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412306	139412306	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	161	416	0	ENST00000277541.6:c.1339C>T	p.Pro447Ser	p.P447S	ENST00000277541	NM_017617.3	447	Ccc/Tcc	8/34	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.271557941880459	2		416	990	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413983	139413983	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	146	366	0	ENST00000277541.6:c.777C>G	p.Asp259Glu	p.D259E	ENST00000277541	NM_017617.3	259	gaC/gaG	5/34	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.271557941880459	2		366	997	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405122	70405122	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771580099	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	104	386	0	ENST00000373644.4:c.2636C>T	p.Ser879Leu	p.S879L	ENST00000373644	NM_030625.2	879	tCg/tTg	4/12	1	2	FACETS	0.787	0.704	0.876	0.787	0.704	0.876	SUBCLONAL	1	TRUE	1	0.271557941880459	2		386	973	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115600	108115600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772821016	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	103	361	0	ENST00000278616.4:c.748C>T	p.Arg250Ter	p.R250*	ENST00000278616	NM_000051.3	250	Cga/Tga	7/63	0.271557941880459	1	FACETS	0.918	0.822	1	0.918	0.822	1	CLONAL	1	TRUE	0	0.271557941880459	1		361	714	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134796	41134796	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1281	173	625	0	ENST00000379561.5:c.832C>T	p.Gln278Ter	p.Q278*	ENST00000379561	NM_002015.3	278	Cag/Tag	2/3	1	2	FACETS	0.876	0.804	0.952	0.876	0.804	0.952	CLONAL	1	TRUE	1	0.271557941880459	2		625	1454	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95597863	95597863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	77	344	0	ENST00000393063.1:c.421G>A	p.Glu141Lys	p.E141K	ENST00000393063	NM_030621.3	141	Gag/Aag	5/28	1	2	FACETS	0.736	0.645	0.833	0.736	0.645	0.833	SUBCLONAL	1	TRUE	1	0.271557941880459	2		344	771	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021428	42021428	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	237	651	0	ENST00000219905.7:c.3724C>T	p.Arg1242Ter	p.R1242*	ENST00000219905	NM_001164273.1	1242	Cga/Tga	11/24	0.271557941880459	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.271557941880459	1		651	1437	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108768	2108768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	156	429	0	ENST00000219476.3:c.869C>T	p.Pro290Leu	p.P290L	ENST00000219476	NM_000548.3	290	cCc/cTc	10/42	1	2	FACETS	0.962	0.879	1	0.962	0.879	1	CLONAL	1	TRUE	1	0.271557941880459	2		429	1194	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992054	72992054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	171	588	0	ENST00000268489.5:c.1991C>T	p.Ser664Phe	p.S664F	ENST00000268489	NM_006885.3	664	tCt/tTt	2/10	1	2	FACETS	0.985	0.904	1	0.985	0.904	1	CLONAL	1	TRUE	1	0.271557941880459	2		588	1278	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348880	89348880	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1336866100	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1420	240	728	2	ENST00000301030.4:c.4070C>T	p.Ser1357Phe	p.S1357F	ENST00000301030	NM_001256183.1	1357	tCc/tTc	9/13	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.271557941880459	2		730	1660	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805594	89805594	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1302438780	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	152	436	0	ENST00000389301.3:c.4114G>A	p.Asp1372Asn	p.D1372N	ENST00000389301	NM_000135.2	1372	Gat/Aat	41/43	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.271557941880459	2		436	1027	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579361	7579361	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1064796722	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	119	435	0	ENST00000269305.4:c.326T>C	p.Phe109Ser	p.F109S	ENST00000269305	NM_001126112.2	109	tTc/tCc	4/11	1	2	FACETS	0.891	0.803	0.984	0.891	0.803	0.984	CLONAL	1	TRUE	1	0.271557941880459	2		435	984	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627787	37627787	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	131	382	0	ENST00000447079.4:c.1702C>T	p.Pro568Ser	p.P568S	ENST00000447079	NM_015083.1	568	Cct/Tct	2/14	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.271557941880459	2		382	953	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243979	41243979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755209182	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	123	309	2	ENST00000357654.3:c.3569C>T	p.Pro1190Leu	p.P1190L	ENST00000357654	NM_007294.3	1190	cCt/cTt	10/23	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.271557941880459	2		311	763	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371725	45371725	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	105	369	0	ENST00000262160.6:c.1266G>A	p.Trp422Ter	p.W422*	ENST00000262160	NM_005901.5	422	tgG/tgA	10/11	1	2	FACETS	0.897	0.803	0.997	0.897	0.803	0.997	CLONAL	1	TRUE	1	0.271557941880459	2		369	862	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222040	2222040	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	114	320	0	ENST00000398665.3:c.2872C>T	p.Pro958Ser	p.P958S	ENST00000398665	NM_032482.2	958	Cct/Tct	24/28	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.271557941880459	2		320	817	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2225430	2225430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1302008529	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	136	364	0	ENST00000398665.3:c.3640C>T	p.Pro1214Ser	p.P1214S	ENST00000398665	NM_032482.2	1214	Ccc/Tcc	26/28	1	2	FACETS	0.904	0.82	0.992	0.904	0.82	0.992	CLONAL	1	TRUE	1	0.271557941880459	2		364	1108	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117180	7117180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	149	403	2	ENST00000302850.5:c.4036G>A	p.Gly1346Arg	p.G1346R	ENST00000302850	NM_000208.2	1346	Ggg/Agg	22/22	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.271557941880459	2		405	1039	SUCCESS
CALR	811	MSKCC	GRCh37	19	13049960	13049960	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	175	528	0	ENST00000316448.5:c.104C>T	p.Ser35Phe	p.S35F	ENST00000316448	NM_004343.3	35	tCc/tTc	2/9	1	2	FACETS	0.988	0.908	1	0.988	0.908	1	CLONAL	1	TRUE	1	0.271557941880459	2		528	1304	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355249	15355250	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	47	202	0	ENST00000263377.2:c.2373_2374delinsAA	p.Ala792Thr	p.A792T	ENST00000263377	NM_058243.2	791	ccGGcg/ccAAcg	13/20	1	2	FACETS	0.853	0.721	0.997	0.853	0.721	0.997	CLONAL	1	TRUE	1	0.271557941880459	2		202	406	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024302	31024302	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	144	355	0	ENST00000375687.4:c.3787C>T	p.Pro1263Ser	p.P1263S	ENST00000375687	NM_015338.5	1263	Cca/Tca	13/13	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.271557941880459	2		355	974	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265432	46265432	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1461	210	691	0	ENST00000371998.3:c.2302C>T	p.Gln768Ter	p.Q768*	ENST00000371998		768	Cag/Tag	12/23	1	2	FACETS	0.926	0.856	0.998	0.926	0.856	0.998	CLONAL	1	TRUE	1	0.271557941880459	2		691	1671	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914741	39914741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757308049	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1215	86	520	2	ENST00000378444.4:c.4621G>A	p.Asp1541Asn	p.D1541N	ENST00000378444	NM_001123385.1	1541	Gat/Aat	12/15	1	2	FACETS	0.487	0.429	0.549	0.487	0.429	0.549	SUBCLONAL	1	TRUE	1	0.271557941880459	2		522	1301	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344928	70344928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1333	80	562	1	ENST00000374080.3:c.2158G>A	p.Gly720Arg	p.G720R	ENST00000374080		720	Ggg/Agg	15/45	1	2	FACETS	0.417	0.365	0.473	0.417	0.365	0.473	SUBCLONAL	1	TRUE	1	0.271557941880459	2		563	1413	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	350	769	0				ENST00000310581	NM_198253.2	-/1132			0.741269506630281	1	FACETS	0.532	0.506	0.558	0.532	0.506	0.558	SUBCLONAL	1	TRUE	0	0.882905293810089	1		769	832	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	546	687	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.965	0.928	1	0.965	0.928	1	CLONAL	1	TRUE	1	0.882905293810089	2		687	1282	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943694	17943694	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201241352	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	445	666	0	ENST00000458235.1:c.2395C>T	p.Arg799Cys	p.R799C	ENST00000458235	NM_000215.3	799	Cgt/Tgt	18/24	1	2	FACETS	0.922	0.882	0.963	0.922	0.882	0.963	CLONAL	1	TRUE	1	0.882905293810089	2		666	1093	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569702	95569702	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	322	529	0	ENST00000393063.1:c.4031C>T	p.Ser1344Leu	p.S1344L	ENST00000393063	NM_030621.3	1344	tCa/tTa	22/28	1	2	FACETS	0.836	0.793	0.881	0.836	0.793	0.881	CLONAL	1	TRUE	1	0.882905293810089	2		529	872	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243859016	243859016	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs397514606	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	320	393	0	ENST00000263826.5:c.49G>A	p.Glu17Lys	p.E17K	ENST00000263826	NM_005465.4	17	Gaa/Aaa	2/13	0.882905293810089	3	FACETS	1	0.979	1	0.534	0.505	0.564	CLONAL	1	TRUE	1	0.882905293810089	3		393	978	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254987	16254987	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	306	514	0	ENST00000375759.3:c.2252C>T	p.Ser751Phe	p.S751F	ENST00000375759	NM_015001.2	751	tCt/tTt	11/15	1	2	FACETS	0.924	0.876	0.973	0.924	0.876	0.973	CLONAL	1	TRUE	1	0.882905293810089	2		514	750	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451917	29451917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	548	619	2	ENST00000389048.3:c.2648G>A	p.Trp883Ter	p.W883*	ENST00000389048	NM_004304.4	883	tGg/tAg	16/29	1	2	FACETS	0.945	0.909	0.982	0.945	0.909	0.982	CLONAL	1	TRUE	1	0.882905293810089	2		621	1313	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530198	212530198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	276	458	0	ENST00000342788.4:c.1721C>T	p.Pro574Leu	p.P574L	ENST00000342788	NM_005235.2	574	cCt/cTt	15/28	1	2	FACETS	0.906	0.856	0.957	0.906	0.856	0.957	CLONAL	1	TRUE	1	0.882905293810089	2		458	690	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480345	89480345	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	467	737	0	ENST00000336596.2:c.2182C>G	p.Arg728Gly	p.R728G	ENST00000336596	NM_005233.5	728	Cga/Gga	13/17	1	2	FACETS	0.949	0.909	0.989	0.949	0.909	0.989	CLONAL	1	TRUE	1	0.882905293810089	2		737	1115	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524737	187524737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs944996340	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	458	780	0	ENST00000441802.2:c.10943C>T	p.Ala3648Val	p.A3648V	ENST00000441802	NM_005245.3	3648	gCc/gTc	19/27	1	2	FACETS	0.879	0.841	0.918	0.879	0.841	0.918	CLONAL	1	TRUE	1	0.882905293810089	2		780	1180	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707725	176707725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1165008451	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	405	614	1	ENST00000439151.2:c.5782G>A	p.Gly1928Arg	p.G1928R	ENST00000439151	NM_022455.4	1928	Gga/Aga	18/23	1	2	FACETS	0.875	0.835	0.916	0.875	0.835	0.916	CLONAL	1	TRUE	1	0.882905293810089	2		615	1048	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945021	151945021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756918375	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	39	46	0	ENST00000262189.6:c.2498G>A	p.Arg833Lys	p.R833K	ENST00000262189	NM_170606.2	833	aGa/aAa	14/59	1	2	FACETS	0.505	0.424	0.592	0.505	0.424	0.592	SUBCLONAL	1	TRUE	1	0.882905293810089	2		46	175	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372379	55372379	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	347	659	1	ENST00000297316.4:c.1069G>A	p.Glu357Lys	p.E357K	ENST00000297316	NM_022454.3	357	Gag/Aag	2/2	1	2	FACETS	0.881	0.837	0.925	0.881	0.837	0.925	CLONAL	1	TRUE	1	0.882905293810089	2		660	892	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63662131	63662131	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	341	401	0	ENST00000279873.7:c.235C>T	p.Pro79Ser	p.P79S	ENST00000279873	NM_032199.2	79	Cca/Tca	2/10	1	2	FACETS	0.966	0.919	1	0.966	0.919	1	CLONAL	1	TRUE	1	0.882905293810089	2		401	800	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450891	70450891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	274	468	1	ENST00000373644.4:c.5731C>T	p.Pro1911Ser	p.P1911S	ENST00000373644	NM_030625.2	1911	Ccc/Tcc	12/12	1	2	FACETS	0.987	0.934	1	0.987	0.934	1	CLONAL	1	TRUE	1	0.882905293810089	2		469	629	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413577	32413577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1037084691	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	516	601	0	ENST00000332351.3:c.1373G>A	p.Arg458Gln	p.R458Q	ENST00000332351	NM_024426.4	458	cGa/cAa	9/10	1	2	FACETS	0.951	0.913	0.989	0.951	0.913	0.989	CLONAL	1	TRUE	1	0.882905293810089	2		601	1229	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344087	118344087	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1555036415	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	301	452	0	ENST00000534358.1:c.2213G>T	p.Arg738Ile	p.R738I	ENST00000534358	NM_005933.3	738	aGa/aTa	3/36	0.882905293810089	1	FACETS	0.841	0.807	0.874	0.841	0.807	0.874	CLONAL	1	TRUE	0	0.882905293810089	1		452	453	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149003	119149003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	362	585	0	ENST00000264033.4:c.1223G>A	p.Trp408Ter	p.W408*	ENST00000264033	NM_005188.3	408	tGg/tAg	8/16	0.882905293810089	1	FACETS	0.877	0.846	0.908	0.877	0.846	0.908	CLONAL	1	TRUE	0	0.882905293810089	1		585	522	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433634	49433634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1019336916	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	548	772	0	ENST00000301067.7:c.7919C>T	p.Ser2640Phe	p.S2640F	ENST00000301067	NM_003482.3	2640	tCt/tTt	31/54	1	2	FACETS	0.929	0.893	0.966	0.929	0.893	0.966	CLONAL	1	TRUE	1	0.882905293810089	2		772	1336	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865581	57865581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	674	974	1	ENST00000228682.2:c.3058G>A	p.Gly1020Arg	p.G1020R	ENST00000228682	NM_005269.2	1020	Gga/Aga	12/12	1	2	FACETS	0.883	0.851	0.915	0.883	0.851	0.915	CLONAL	1	TRUE	1	0.882905293810089	2		975	1729	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914220	32914220	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1197	843	1091	0	ENST00000380152.3:c.5728A>G	p.Asn1910Asp	p.N1910D	ENST00000380152		1910	Aat/Gat	11/27	1	2	FACETS	0.936	0.907	0.966	0.936	0.907	0.966	CLONAL	1	TRUE	1	0.882905293810089	2		1091	2040	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945216	32945216	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	496	675	0	ENST00000380152.3:c.8611G>A	p.Glu2871Lys	p.E2871K	ENST00000380152		2871	Gag/Aag	20/27	1	2	FACETS	0.889	0.852	0.926	0.889	0.852	0.926	CLONAL	1	TRUE	1	0.882905293810089	2		675	1264	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436671	110436671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	430	682	0	ENST00000375856.3:c.1730C>T	p.Ser577Phe	p.S577F	ENST00000375856	NM_003749.2	577	tCc/tTc	1/2	1	2	FACETS	0.894	0.855	0.935	0.894	0.855	0.935	CLONAL	1	TRUE	1	0.882905293810089	2		682	1089	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331729	68331729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	354	387	1	ENST00000487270.1:c.325C>T	p.Pro109Ser	p.P109S	ENST00000487270	NM_133509.3	109	Cca/Tca	5/11	1	2	FACETS	0.958	0.912	1	0.958	0.912	1	CLONAL	1	TRUE	1	0.882905293810089	2		388	837	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845475	72845475	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1456563586	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	563	814	0	ENST00000268489.5:c.3864+1G>A		p.X1288_splice	ENST00000268489	NM_006885.3	1288			1	2	FACETS	0.919	0.884	0.955	0.919	0.884	0.955	CLONAL	1	TRUE	1	0.882905293810089	2		814	1387	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41209086	41209086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80357432	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1195	806	996	0	ENST00000357654.3:c.5260G>A	p.Glu1754Lys	p.E1754K	ENST00000357654	NM_007294.3	1754	Gaa/Aaa	19/23	1	2	FACETS	0.912	0.883	0.942	0.912	0.883	0.942	CLONAL	1	TRUE	1	0.882905293810089	2		996	2001	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7163202	7163202	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	446	624	0	ENST00000302850.5:c.1870G>A	p.Val624Met	p.V624M	ENST00000302850	NM_000208.2	624	Gtg/Atg	9/22	1	2	FACETS	0.884	0.845	0.923	0.884	0.845	0.923	CLONAL	1	TRUE	1	0.882905293810089	2		624	1143	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290078	15290078	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	365	626	0	ENST00000263388.2:c.3476T>A	p.Ile1159Asn	p.I1159N	ENST00000263388	NM_000435.2	1159	aTt/aAt	22/33	1	2	FACETS	0.973	0.927	1	0.973	0.927	1	CLONAL	1	TRUE	1	0.882905293810089	2		626	850	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39690066	39690066	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	436	577	0	ENST00000361337.2:c.91C>T	p.Arg31Ter	p.R31*	ENST00000361337	NM_003286.2	31	Cga/Tga	3/21	1	2	FACETS	0.775	0.74	0.811	0.775	0.74	0.811	SUBCLONAL	1	TRUE	1	0.882905293810089	2		577	1274	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206767	36206767	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	331	515	2	ENST00000300305.3:c.745C>T	p.Pro249Ser	p.P249S	ENST00000300305		249	Cct/Tct	6/8	1	2	FACETS	0.937	0.891	0.984	0.937	0.891	0.984	CLONAL	1	TRUE	1	0.882905293810089	2		517	800	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933179	39933179	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1174	732	1006	0	ENST00000378444.4:c.1420G>A	p.Gly474Ser	p.G474S	ENST00000378444	NM_001123385.1	474	Ggc/Agc	4/15	1	2	FACETS	0.87	0.84	0.9	0.87	0.84	0.9	CLONAL	1	TRUE	1	0.882905293810089	2		1006	1906	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345969	70345969	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	645	939	2	ENST00000374080.3:c.2506C>T	p.Leu836Phe	p.L836F	ENST00000374080		836	Ctt/Ttt	18/45	1	2	FACETS	0.841	0.81	0.873	0.841	0.81	0.873	CLONAL	1	TRUE	1	0.882905293810089	2		941	1737	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351957	70351957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771349148	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	729	1050	1	ENST00000374080.3:c.4154C>T	p.Ala1385Val	p.A1385V	ENST00000374080		1385	gCc/gTc	30/45	1	2	FACETS	0.988	0.955	1	0.988	0.955	1	CLONAL	1	TRUE	1	0.882905293810089	2		1051	1672	SUCCESS
BTK	695	MSKCC	GRCh37	X	100625033	100625033	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	571	817	0	ENST00000308731.7:c.344C>A	p.Ser115Tyr	p.S115Y	ENST00000308731	NM_000061.2	115	tCc/tAc	5/19	1	2	FACETS	0.823	0.79	0.856	0.823	0.79	0.856	CLONAL	1	TRUE	1	0.882905293810089	2		817	1572	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590574	95590574	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	569	746	0	ENST00000393063.1:c.1335del	p.Ile446PhefsTer12	p.I446Ffs*12	ENST00000393063	NM_030621.3	445	atT/at	9/28	1	2	FACETS	0.882	0.847	0.916	0.882	0.847	0.916	CLONAL	1	TRUE	1	0.882905293810089	2		746	1462	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524334	187524334	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	259	471	0	ENST00000441802.2:c.11346C>A	p.Cys3782Ter	p.C3782*	ENST00000441802	NM_005245.3	3782	tgC/tgA	19/27	1	2	FACETS	0.9	0.849	0.952	0.9	0.849	0.952	CLONAL	1	TRUE	1	0.882905293810089	2		471	652	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348837	89348838	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0006796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1324	957	1261	2	ENST00000301030.4:c.4112_4113delinsTT	p.Ala1371Val	p.A1371V	ENST00000301030	NM_001256183.1	1371	gCC/gTT	9/13	1	2	FACETS	0.95	0.922	0.979	0.95	0.922	0.979	CLONAL	1	TRUE	1	0.882905293810089	2		1263	2281	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0006819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	127	611	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.468241374438455	1	FACETS	0.905	0.826	0.987	0.905	0.826	0.987	CLONAL	1	TRUE	0	0.468241374438455	1		611	459	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0006819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	88	435	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	0.18730239205036	2	FACETS	0.862	0.779	0.947	0.862	0.779	0.947	INDETERMINATE	2	TRUE	0	0.468241374438455	2		435	218	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861838	57861838	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381253752	NA	P-0006819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	182	849	5	ENST00000228682.2:c.1139G>A	p.Arg380Gln	p.R380Q	ENST00000228682	NM_005269.2	380	cGa/cAa	10/12	0.129464142109774	4	FACETS	0.84	0.778	0.905	0.84	0.778	0.905	INDETERMINATE	2	TRUE	2	0.468241374438455	4		854	679	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852264	128852264	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	101	525	0	ENST00000249373.3:c.2336A>T	p.Glu779Val	p.E779V	ENST00000249373	NM_005631.4	779	gAa/gTa	12/12	0.273057594789793	3	FACETS	1	0.981	1	0.704	0.635	0.777	INDETERMINATE	1	TRUE	1	0.468241374438455	3		525	378	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710706	114710706	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0006819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	208	607	0	ENST00000543371.1:c.189+2T>C		p.X63_splice	ENST00000543371	NM_001198531.1	63			0.312419718692779	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.468241374438455	1		607	579	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117368	115117368	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775378442	NA	P-0006819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	73	694	0	ENST00000257566.3:c.806G>A	p.Arg269Gln	p.R269Q	ENST00000257566	NM_016569.3	269	cGg/cAg	4/8	0.468241374438455	1	FACETS	0.667	0.587	0.752	0.667	0.587	0.752	SUBCLONAL	1	TRUE	0	0.468241374438455	1		694	358	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629021	14629021	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	298	626	0	ENST00000254322.2:c.141G>C	p.Glu47Asp	p.E47D	ENST00000254322	NM_006145.1	47	gaG/gaC	1/3	0.204420610261998	2	FACETS	1	0.994	1	0.724	0.684	0.765	INDETERMINATE	1	TRUE	0	0.468241374438455	2		626	879	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006848-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	107	174	0				ENST00000310581	NM_198253.2	-/1132			0.208858331117121	5	FACETS	0.926	0.837	1	0.617	0.558	0.679	INDETERMINATE	2	TRUE	2	0.501250075914329	5		174	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0006848-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	470	791	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.427103305601133	3	FACETS	0.975	0.94	1	0.975	0.94	1	CLONAL	3	TRUE	0	0.501250075914329	3		791	802	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684326	29684326	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201367	NA	P-0006848-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	36	798	3	ENST00000356175.3:c.7846C>T	p.Arg2616Ter	p.R2616*	ENST00000356175	NM_000267.3	2616	Cga/Tga	53/57	0.501250075914329	1	FACETS	0.206	0.169	0.248	0.206	0.169	0.248	SUBCLONAL	1	TRUE	0	0.501250075914329	1		801	522	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717663	89717663	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554825186	NA	P-0006848-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	285	673	0	ENST00000371953.3:c.688G>T	p.Gly230Ter	p.G230*	ENST00000371953	NM_000314.4	230	Gga/Tga	7/9	0.498854258074714	2	FACETS	0.982	0.933	1	0.982	0.933	1	CLONAL	2	TRUE	0	0.501250075914329	2		673	579	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456495	189456498	+	frameshift_variant	Frame_Shift_Del	DEL	ACAA	ACAA	-	novel	NA	P-0006848-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	287	749	0	ENST00000264731.3:c.260_263del	p.Asn87ArgfsTer16	p.N87Rfs*16	ENST00000264731	NM_003722.4	86	ACAAac/ac	3/14	0.270298930347798	4	FACETS	1	0.959	1	1	0.959	1	INDETERMINATE	2	TRUE	2	0.501250075914329	4		749	843	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128071	30128071	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs773193659	NA	P-0006848-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	67	1241	0	ENST00000263025.4:c.1058A>G	p.Asp353Gly	p.D353G	ENST00000263025	NM_002746.2	353	gAt/gGt	8/9	0.501250075914329	3	FACETS	0.266	0.23	0.306	0.133	0.115	0.153	SUBCLONAL	1	TRUE	1	0.501250075914329	3		1241	1256	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368200	45368204	+	frameshift_variant,stop_lost	Frame_Shift_Del	DEL	ATGAC	ATGAC	-	novel	NA	P-0006848-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	48	641	0	ENST00000262160.6:c.1398_1402del	p.Met466IlefsTer20	p.M466Ifs*20	ENST00000262160	NM_005901.5	466	atGTCATaa/ataa	11/11	0.487731495793134	2	FACETS	0.325	0.274	0.381	0.163	0.137	0.191	SUBCLONAL	1	TRUE	0	0.501250075914329	2		641	589	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0006866-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	105	515	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.475102780871771	4	FACETS	0.992	0.89	1	0.496	0.445	0.55	CLONAL	1	TRUE	2	0.475102780871771	4		515	657	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0006866-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	184	362	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	0.443266460427744	3	FACETS	1	0.937	1			1	CLONAL	1	TRUE	NA	0.475102780871771	3		362	943	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006866-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	166	415	1	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.475102780871771	2	FACETS	1	0.964	1	0.539	0.497	0.583	CLONAL	1	TRUE	0	0.475102780871771	2		416	648	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99163051	99163051	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006866-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	238	283	0	ENST00000074304.5:c.1057C>A	p.Gln353Lys	p.Q353K	ENST00000074304	NM_001134224.1	353	Cag/Aag	13/26	0.475102780871771	3	FACETS	0.978	0.919	1	0.978	0.919	1	CLONAL	2	TRUE	1	0.475102780871771	3		283	634	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828538	72828538	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006866-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	250	630	0	ENST00000268489.5:c.8043G>C	p.Lys2681Asn	p.K2681N	ENST00000268489	NM_006885.3	2681	aaG/aaC	9/10	0.475102780871771	2	FACETS	0.946	0.884	1	0.473	0.442	0.505	CLONAL	1	TRUE	0	0.475102780871771	2		630	1113	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007210-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	74	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.783	0.692	0.879	1	0.978	1	SUBCLONAL	2	TRUE	1	0.310936599686742	2		174	304	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191488	10191488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs5030818	NA	P-0007210-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	96	278	0	ENST00000256474.2:c.481C>T	p.Arg161Ter	p.R161*	ENST00000256474	NM_000551.3	161	Cga/Tga	3/3	0.310936599686742	1	FACETS	0.982	0.878	1	0.982	0.878	1	CLONAL	1	TRUE	0	0.310936599686742	1		278	531	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286907	33286907	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753556048	NA	P-0007210-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	175	320	0	ENST00000374542.5:c.2030C>T	p.Ala677Val	p.A677V	ENST00000374542	NM_001141970.1	677	gCc/gTc	7/8	0.103940569927871	4	FACETS	0.824	0.759	0.892	0.824	0.759	0.892	INDETERMINATE	2	TRUE	2	0.310936599686742	4		320	895	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817532	39817532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1302693098	NA	P-0007210-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	156	341	0	ENST00000288319.7:c.31G>A	p.Val11Ile	p.V11I	ENST00000288319	NM_182918.3	11	Gtt/Att	2/10	0.310936599686742	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.310936599686742	1		341	653	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	131	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.815	0.742	0.891	0.815	0.742	0.891	CLONAL	1	TRUE	1	0.544859405730881	2		174	590	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926248	112926248	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs121918468	NA	P-0007503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	221	408	0	ENST00000351677.2:c.1381G>A	p.Ala461Thr	p.A461T	ENST00000351677	NM_002834.3	461	Gct/Act	12/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.544859405730881	2		408	797	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650283	12650283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755681685	NA	P-0007503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	187	464	0	ENST00000251849.4:c.563G>A	p.Ser188Asn	p.S188N	ENST00000251849	NM_002880.3	188	aGt/aAt	5/17	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.544859405730881	2		464	655	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552179	29552179	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1555613567	NA	P-0007503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	136	457	0	ENST00000356175.3:c.1912G>T	p.Gly638Ter	p.G638*	ENST00000356175	NM_000267.3	638	Gga/Tga	17/57	0.528852686112564	1	FACETS	0.825	0.757	0.896	0.825	0.757	0.896	CLONAL	1	TRUE	0	0.544859405730881	1		457	440	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589213	67589233	+	inframe_deletion	In_Frame_Del	DEL	GTGGTTGAATTAATAAACCAC	GTGGTTGAATTAATAAACCAC	-	novel	NA	P-0007503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	138	370	0	ENST00000274335.5:c.1201_1221del	p.Val401_His407del	p.V401_H407del	ENST00000274335		401	GTGGTTGAATTAATAAACCAC/-	9/15	1	2	FACETS	0.938	0.858	1	0.938	0.858	1	CLONAL	1	TRUE	1	0.544859405730881	2		370	540	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295368	1295368	+	upstream_gene_variant	5'Flank	SNP	T	T	C	novel	NA	P-0007505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	35	161	0				ENST00000310581	NM_198253.2	-/1132			0.229191685026023	3	FACETS	0.878	0.72	1	0.439	0.36	0.527	CLONAL	1	TRUE	1	0.235081957298872	3		161	379	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235813	108235813	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	64	374	0	ENST00000278616.4:c.8855T>C	p.Leu2952Pro	p.L2952P	ENST00000278616	NM_000051.3	2952	cTt/cCt	62/63	1	2	FACETS	0.615	0.531	0.707	0.615	0.531	0.707	SUBCLONAL	1	TRUE	1	0.235081957298872	2		374	885	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547004	9547004	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	52	130	0	ENST00000353224.5:c.1018C>T	p.Leu340Phe	p.L340F	ENST00000353224	NM_177990.2	340	Ctc/Ttc	5/10	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.235081957298872	2		130	360	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357453	70357453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	128	248	0	ENST00000374080.3:c.5794C>T	p.Pro1932Ser	p.P1932S	ENST00000374080		1932	Ccc/Tcc	40/45	1	1	FACETS	0.755	0.686	0.828	1	0.986	1	SUBCLONAL	2	TRUE	0	0.235081957298872	1		248	636	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs967461896	NA	P-0007637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	17	278	0	ENST00000269305.4:c.526T>G	p.Cys176Gly	p.C176G	ENST00000269305	NM_001126112.2	176	Tgc/Ggc	5/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		278	519	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	89	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.42138622164943	2		174	418	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888198	112888198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121918453	NA	P-0007833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	190	551	0	ENST00000351677.2:c.214G>A	p.Ala72Thr	p.A72T	ENST00000351677	NM_002834.3	72	Gcc/Acc	3/16	1	2	FACETS	0.858	0.793	0.926	0.858	0.793	0.926	CLONAL	1	TRUE	1	0.42138622164943	2		551	1051	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0007833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	133	280	0	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.42138622164943	2		280	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578541	7578541	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	157	366	0	ENST00000269305.4:c.389T>A	p.Leu130His	p.L130H	ENST00000269305	NM_001126112.2	130	cTc/cAc	5/11	1	2	FACETS	0.923	0.847	1	0.923	0.847	1	CLONAL	1	TRUE	1	0.42138622164943	2		366	807	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654553	29654553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876657714	NA	P-0007833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	199	472	0	ENST00000356175.3:c.5242C>T	p.Arg1748Ter	p.R1748*	ENST00000356175	NM_000267.3	1748	Cga/Tga	37/57	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.42138622164943	2		472	936	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	55	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.96	0.835	1	0.96	0.835	1	CLONAL	1	TRUE	1	0.596567109052089	2		174	192	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	195	687	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.596567109052089	2		687	650	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	255	234	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.596567109052089	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.596567109052089	1		234	585	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976861	55976861	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	188	390	0	ENST00000263923.4:c.1051C>T	p.Pro351Ser	p.P351S	ENST00000263923	NM_002253.2	351	Cct/Tct	8/30	1	2	FACETS	0.878	0.814	0.944	0.878	0.814	0.944	CLONAL	1	TRUE	1	0.596567109052089	2		390	718	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17380510	17380510	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199948437	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	116	320	4	ENST00000375499.3:c.5C>T	p.Ala2Val	p.A2V	ENST00000375499	NM_003000.2	2	gCg/gTg	1/8	1	2	FACETS	0.831	0.753	0.912	0.831	0.753	0.912	CLONAL	1	TRUE	1	0.596567109052089	2		324	468	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739098	46739098	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	229	468	4	ENST00000371975.4:c.1447C>T	p.Pro483Ser	p.P483S	ENST00000371975	NM_003579.3	483	Cct/Tct	13/18	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.596567109052089	2		472	730	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973239	25973239	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	117	260	2	ENST00000435504.4:c.1186C>T	p.Pro396Ser	p.P396S	ENST00000435504		396	Ccc/Tcc	12/13	1	2	FACETS	0.783	0.71	0.86	0.783	0.71	0.86	SUBCLONAL	1	TRUE	1	0.596567109052089	2		262	501	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268463	198268463	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs748320317	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	174	384	0	ENST00000335508.6:c.1565A>G	p.Lys522Arg	p.K522R	ENST00000335508	NM_012433.2	522	aAa/aGa	12/25	1	2	FACETS	0.971	0.898	1	0.971	0.898	1	CLONAL	1	TRUE	1	0.596567109052089	2		384	601	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713871	30713871	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	161	307	1	ENST00000295754.5:c.1196G>A	p.Gly399Glu	p.G399E	ENST00000295754	NM_003242.5	399	gGg/gAg	4/7	1	2	FACETS	0.994	0.917	1	0.994	0.917	1	CLONAL	1	TRUE	1	0.596567109052089	2		308	543	SUCCESS
ATR	545	MSKCC	GRCh37	3	142180893	142180893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	168	372	1	ENST00000350721.4:c.7081C>T	p.His2361Tyr	p.H2361Y	ENST00000350721	NM_001184.3	2361	Cat/Tat	42/47	1	2	FACETS	0.913	0.843	0.985	0.913	0.843	0.985	CLONAL	1	TRUE	1	0.596567109052089	2		373	617	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587118	189587118	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	185	348	0	ENST00000264731.3:c.1135C>A	p.Arg379Ser	p.R379S	ENST00000264731	NM_003722.4	379	Cgt/Agt	9/14	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.596567109052089	2		348	612	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747900	41747900	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	98	312	0	ENST00000226382.2:c.869C>T	p.Pro290Leu	p.P290L	ENST00000226382	NM_003924.3	290	cCc/cTc	3/3	1	2	FACETS	0.867	0.78	0.958	0.867	0.78	0.958	CLONAL	1	TRUE	1	0.596567109052089	2		312	379	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658412	117658412	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	167	461	1	ENST00000368508.3:c.5171C>T	p.Ser1724Leu	p.S1724L	ENST00000368508	NM_002944.2	1724	tCa/tTa	31/43	0.596567109052089	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.596567109052089	1		462	388	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522394	157522394	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	140	304	0	ENST00000346085.5:c.4666C>T	p.Pro1556Ser	p.P1556S	ENST00000346085	NM_020732.3	1556	Cca/Tca	18/20	0.596567109052089	1	FACETS	0.995	0.92	1	0.995	0.92	1	CLONAL	1	TRUE	0	0.596567109052089	1		304	331	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979544	2979544	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	139	381	0	ENST00000396946.4:c.703C>G	p.Arg235Gly	p.R235G	ENST00000396946	NM_032415.4	235	Cgg/Ggg	6/25	1	2	FACETS	0.838	0.767	0.912	0.838	0.767	0.912	CLONAL	1	TRUE	1	0.596567109052089	2		381	556	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563491	87563491	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201553907	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	120	246	1	ENST00000277120.3:c.1879G>A	p.Asp627Asn	p.D627N	ENST00000277120		627	Gac/Aac	16/19	0.596567109052089	1	FACETS	0.874	0.8	0.95	0.874	0.8	0.95	CLONAL	1	TRUE	0	0.596567109052089	1		247	323	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793298	139793298	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	176	426	1	ENST00000247668.2:c.106G>T	p.Ala36Ser	p.A36S	ENST00000247668	NM_021138.3	36	Gcc/Tcc	2/11	0.596567109052089	1	FACETS	0.937	0.872	1	0.937	0.872	1	CLONAL	1	TRUE	0	0.596567109052089	1		427	442	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344609	118344609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	262	613	0	ENST00000534358.1:c.2735C>T	p.Ser912Phe	p.S912F	ENST00000534358	NM_005933.3	912	tCc/tTc	3/36	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.596567109052089	2		613	855	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372543	118372543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	212	477	1	ENST00000534358.1:c.6476C>T	p.Ser2159Phe	p.S2159F	ENST00000534358	NM_005933.3	2159	tCc/tTc	26/36	1	2	FACETS	0.945	0.881	1	0.945	0.881	1	CLONAL	1	TRUE	1	0.596567109052089	2		478	752	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022504	12022504	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	201	401	0	ENST00000396373.4:c.610C>T	p.Pro204Ser	p.P204S	ENST00000396373	NM_001987.4	204	Ccc/Tcc	5/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.596567109052089	2		401	627	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230704	46230704	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	202	519	1	ENST00000334344.6:c.953T>A	p.Leu318His	p.L318H	ENST00000334344	NM_152641.2	318	cTt/cAt	8/21	1	2	FACETS	0.925	0.86	0.992	0.925	0.86	0.992	CLONAL	1	TRUE	1	0.596567109052089	2		520	732	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426447	49426447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	187	467	1	ENST00000301067.7:c.12041C>T	p.Ala4014Val	p.A4014V	ENST00000301067	NM_003482.3	4014	gCc/gTc	39/54	1	2	FACETS	0.907	0.841	0.975	0.907	0.841	0.975	CLONAL	1	TRUE	1	0.596567109052089	2		468	691	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589322	28589322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	206	474	1	ENST00000241453.7:c.2725G>A	p.Asp909Asn	p.D909N	ENST00000241453	NM_004119.2	909	Gat/Aat	22/24	0.544551617808781	3	FACETS	1	0.933	1	0.503	0.467	0.54	CLONAL	1	TRUE	1	0.596567109052089	3		475	892	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28979974	28979974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	149	495	1	ENST00000282397.4:c.1494G>A	p.Met498Ile	p.M498I	ENST00000282397	NM_002019.4	498	atG/atA	11/30	0.544551617808781	3	FACETS	0.835	0.763	0.909	0.417	0.381	0.455	CLONAL	1	TRUE	1	0.596567109052089	3		496	777	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574717	95574717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060503620	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	209	432	0	ENST00000393063.1:c.2380C>T	p.Pro794Ser	p.P794S	ENST00000393063	NM_030621.3	794	Cct/Tct	16/28	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.596567109052089	2		432	677	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857873	9857873	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	201	419	0	ENST00000330684.3:c.3528G>C	p.Glu1176Asp	p.E1176D	ENST00000330684	NM_001134407.1	1176	gaG/gaC	13/13	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.596567109052089	2		419	610	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992025	72992025	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	229	529	0	ENST00000268489.5:c.2020C>T	p.Pro674Ser	p.P674S	ENST00000268489	NM_006885.3	674	Ccc/Tcc	2/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.596567109052089	2		529	670	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78921067	78921067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	190	438	0	ENST00000306801.3:c.3181C>T	p.His1061Tyr	p.H1061Y	ENST00000306801	NM_020761.2	1061	Cac/Tac	27/34	1	2	FACETS	0.967	0.897	1	0.967	0.897	1	CLONAL	1	TRUE	1	0.596567109052089	2		438	659	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222173	2222173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	126	308	0	ENST00000398665.3:c.3005C>T	p.Pro1002Leu	p.P1002L	ENST00000398665	NM_032482.2	1002	cCc/cTc	24/28	1	2	FACETS	0.994	0.908	1	0.994	0.908	1	CLONAL	1	TRUE	1	0.596567109052089	2		308	425	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827990	40827990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	112	227	1	ENST00000373198.4:c.2438C>T	p.Ala813Val	p.A813V	ENST00000373198	NM_133170.3	813	gCc/gTc	17/32	1	2	FACETS	0.888	0.804	0.975	0.888	0.804	0.975	CLONAL	1	TRUE	1	0.596567109052089	2		228	423	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100951	41100951	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	129	269	0	ENST00000373198.4:c.1405G>A	p.Gly469Ser	p.G469S	ENST00000373198	NM_133170.3	469	Ggc/Agc	8/32	1	2	FACETS	0.92	0.84	1	0.92	0.84	1	CLONAL	1	TRUE	1	0.596567109052089	2		269	470	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428415	47428415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1183909266	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	185	541	1	ENST00000377045.4:c.1283G>A	p.Arg428Gln	p.R428Q	ENST00000377045	NM_001654.4	428	cGa/cAa	12/16	0.183875820500011	1	FACETS	0.576	0.533	0.621	0.576	0.533	0.621	INDETERMINATE	1	TRUE	0	0.596567109052089	1		542	755	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412488	63412488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	207	507	0	ENST00000330258.3:c.679G>A	p.Glu227Lys	p.E227K	ENST00000330258	NM_152424.3	227	Gaa/Aaa	2/2	0.183875820500011	1	FACETS	0.747	0.697	0.798	0.747	0.697	0.798	INDETERMINATE	1	TRUE	0	0.596567109052089	1		507	652	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339226	70339226	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	198	486	0	ENST00000374080.3:c.103G>A	p.Glu35Lys	p.E35K	ENST00000374080		35	Gaa/Aaa	2/45	0.183875820500011	1	FACETS	0.576	0.534	0.619	0.576	0.534	0.619	INDETERMINATE	1	TRUE	0	0.596567109052089	1		486	809	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344126	70344126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519381	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	206	517	2	ENST00000374080.3:c.1862G>A	p.Arg621Gln	p.R621Q	ENST00000374080		621	cGa/cAa	13/45	0.183875820500011	1	FACETS	0.648	0.603	0.694	0.648	0.603	0.694	INDETERMINATE	1	TRUE	0	0.596567109052089	1		519	748	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357109	70357109	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	195	529	0	ENST00000374080.3:c.5624C>T	p.Pro1875Leu	p.P1875L	ENST00000374080		1875	cCt/cTt	39/45	0.183875820500011	1	FACETS	0.627	0.582	0.673	0.627	0.582	0.673	INDETERMINATE	1	TRUE	0	0.596567109052089	1		529	732	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179020	123179020	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	168	476	0	ENST00000218089.9:c.469G>A	p.Gly157Arg	p.G157R	ENST00000218089	NM_001042749.1	157	Gga/Aga	8/35	0.183875820500011	1	FACETS	0.685	0.633	0.739	0.685	0.633	0.739	INDETERMINATE	1	TRUE	0	0.596567109052089	1		476	577	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166317	7166318	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0007876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	138	404	0	ENST00000302850.5:c.1708_1709delinsTT	p.Pro570Phe	p.P570F	ENST00000302850	NM_000208.2	570	CCc/TTc	8/22	1	2	FACETS	0.81	0.74	0.883	0.81	0.74	0.883	CLONAL	1	TRUE	1	0.596567109052089	2		404	571	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	106	174	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.945	1			1	INDETERMINATE	1	TRUE	NA	0.563736772325747	2		174	354	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914811	32914811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	357	723	2	ENST00000380152.3:c.6319C>T	p.Pro2107Ser	p.P2107S	ENST00000380152		2107	Cct/Tct	11/27	1	2	FACETS	0.962	0.911	1	0.962	0.911	1	CLONAL	1	TRUE	1	0.563736772325747	2		725	1317	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14017058	14017058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1435454184	NA	P-0007980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	502	315	1	ENST00000405192.2:c.229G>A	p.Glu77Lys	p.E77K	ENST00000405192	NM_001163147.1	77	Gaa/Aaa	5/12	0.563736772325747	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.563736772325747	3		316	1096	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165547	118165547	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	200	331	0	ENST00000369448.3:c.57G>A	p.Trp19Ter	p.W19*	ENST00000369448	NM_017709.3	19	tgG/tgA	2/2	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.563736772325747	2		331	675	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177933	56177933	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750940532	NA	P-0007980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	280	435	0	ENST00000399503.3:c.2906C>T	p.Ser969Phe	p.S969F	ENST00000399503	NM_005921.1	969	tCc/tTc	14/20	1	2	FACETS	0.995	0.936	1	0.995	0.936	1	CLONAL	1	TRUE	1	0.563736772325747	2		435	998	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967883	93967883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	424	530	0	ENST00000369303.4:c.2044G>A	p.Glu682Lys	p.E682K	ENST00000369303	NM_004440.3	682	Gaa/Aaa	11/17	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.563736772325747	2		530	1461	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524329	148524329	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	562	443	1	ENST00000320356.2:c.655C>T	p.Pro219Ser	p.P219S	ENST00000320356	NM_004456.4	219	Cct/Tct	7/20	0.563736772325747	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.563736772325747	3		444	1231	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797282	135797282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	244	446	0	ENST00000298552.3:c.587C>T	p.Pro196Leu	p.P196L	ENST00000298552	NM_001162426.1	196	cCt/cTt	7/23	1	2	FACETS	0.954	0.893	1	0.954	0.893	1	CLONAL	1	TRUE	1	0.563736772325747	2		446	907	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920761	100920761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	292	603	0	ENST00000325455.5:c.2387C>T	p.Ser796Leu	p.S796L	ENST00000325455	NM_001202474.3	796	tCa/tTa	6/8	1	2	FACETS	0.854	0.803	0.906	0.854	0.803	0.906	CLONAL	1	TRUE	1	0.563736772325747	2		603	1213	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245634	41245634	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	272	422	1	ENST00000357654.3:c.1914A>T	p.Glu638Asp	p.E638D	ENST00000357654	NM_007294.3	638	gaA/gaT	10/23	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.563736772325747	2		423	940	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980895	40980895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	314	254	0	ENST00000373198.4:c.1591C>T	p.Pro531Ser	p.P531S	ENST00000373198	NM_133170.3	531	Cca/Tca	10/32	0.563736772325747	3	FACETS	0.943	0.895	0.992	0.943	0.895	0.992	CLONAL	2	TRUE	1	0.563736772325747	3		254	757	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843595	156843595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139875058	NA	P-0007987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	125	439	0	ENST00000524377.1:c.1021G>A	p.Val341Met	p.V341M	ENST00000524377	NM_002529.3	341	Gtg/Atg	8/17	0.296191633093028	4	FACETS	1	0.959	1			1	CLONAL	1	TRUE	NA	0.31	4		439	950	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057520000	NA	P-0007987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	155	384	0	ENST00000269305.4:c.452C>G	p.Pro151Arg	p.P151R	ENST00000269305	NM_001126112.2	151	cCc/cGc	5/11	0.204277520194658	2	FACETS	0.779	0.715	0.845	0.779	0.715	0.845	SUBCLONAL	2	TRUE	0	0.31	2		384	642	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118365075	118365075	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs886041896	NA	P-0007987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	58	432	0	ENST00000534358.1:c.5251A>T	p.Lys1751Ter	p.K1751*	ENST00000534358	NM_005933.3	1751	Aaa/Taa	17/36	0.132562935835777	3	FACETS	0.479	0.41	0.555	0.24	0.205	0.278	INDETERMINATE	1	TRUE	1	0.31	3		432	902	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972585	25972585	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	60	399	0	ENST00000435504.4:c.1840C>T	p.Arg614Ter	p.R614*	ENST00000435504		614	Cga/Tga	12/13	0.18506999831245	3	FACETS	0.442	0.379	0.51			1	INDETERMINATE	1	TRUE	NA	0.31	3		399	1012	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457934	69457934	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	136	476	0	ENST00000227507.2:c.335del	p.Lys112ArgfsTer2	p.K112Rfs*2	ENST00000227507	NM_053056.2	112	Aag/ag	2/5	0.132562935835777	3	FACETS	1	0.964	1	0.56	0.509	0.614	INDETERMINATE	1	TRUE	1	0.31	3		476	905	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099408	4099408	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	117	444	0	ENST00000262948.5:c.710A>T	p.Glu237Val	p.E237V	ENST00000262948	NM_030662.3	237	gAg/gTg	7/11	0.506673385916781	2	FACETS	1	0.975	1	0.6	0.546	0.656	CLONAL	1	TRUE	0	0.506673385916781	2		444	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578395	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0008269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	309	313	0	ENST00000269305.4:c.535_536del	p.His179Ter	p.H179*	ENST00000269305	NM_001126112.2	179	CAt/t	5/11	0.506673385916781	3	FACETS	1	0.983	1			1	CLONAL	3	TRUE	NA	0.506673385916781	3		313	487	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0008313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	303	542	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.768560523736101	2		543	745	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0008313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	270	517	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.768560523736101	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.768560523736101	1		517	402	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120530	2120530	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137854322	NA	P-0008313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	68	558	0	ENST00000219476.3:c.1790A>G	p.His597Arg	p.H597R	ENST00000219476	NM_000548.3	597	cAc/cGc	17/42	0.768560523736101	1	FACETS	0.241	0.21	0.274	0.241	0.21	0.274	SUBCLONAL	1	TRUE	0	0.768560523736101	1		558	452	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0008326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	32	1347	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		1347	549	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260675	1260675	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	50	1016	0	ENST00000310581.5:c.2884C>G	p.Arg962Gly	p.R962G	ENST00000310581	NM_198253.2	962	Cgc/Ggc	12/16	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		1016	640	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	25	174	0				ENST00000310581	NM_198253.2	-/1132			0.267208567138341	3	FACETS	1	0.924	1	0.711	0.563	0.878	CLONAL	1	TRUE	1	0.18	3		174	213	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0008453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	103	772	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.213739118618083	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.18	3		772	508	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521253	187521253	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	88	448	0	ENST00000441802.2:c.11902C>T	p.Gln3968Ter	p.Q3968*	ENST00000441802	NM_005245.3	3968	Caa/Taa	22/27	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.18	2		448	765	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426076	49426089	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGCTGAGCCAGC	AGGGCTGAGCCAGC	-	novel	NA	P-0008453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	18	181	0	ENST00000301067.7:c.12399_12412del	p.Leu4134CysfsTer29	p.L4134Cfs*29	ENST00000301067	NM_003482.3	4133	ctGCTGGCTCAGCCCTct/ctct	39/54	1	2	FACETS	0.667	0.502	0.862	0.667	0.502	0.862	SUBCLONAL	1	TRUE	1	0.18	2		181	300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121912651	NA	P-0008562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	259	359	0	ENST00000269305.4:c.742C>G	p.Arg248Gly	p.R248G	ENST00000269305	NM_001126112.2	248	Cgg/Ggg	7/11	0.414754864977527	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.578206779582487	1		359	560	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204513670	204513670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	270	217	0	ENST00000367182.3:c.680G>A	p.Gly227Asp	p.G227D	ENST00000367182	NM_001278516.1	227	gGt/gAt	9/11	0.212297501867743	5	FACETS	1	0.988	1	0.786	0.741	0.831	INDETERMINATE	2	TRUE	2	0.578206779582487	5		217	740	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812314	212812314	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	278	318	0	ENST00000342788.4:c.262T>A	p.Leu88Ile	p.L88I	ENST00000342788	NM_005235.2	88	Tta/Ata	3/28	0.24965963345559	3	FACETS	0.818	0.772	0.864	0.818	0.772	0.864	INDETERMINATE	2	TRUE	1	0.578206779582487	3		318	758	SUCCESS
ATR	545	MSKCC	GRCh37	3	142183982	142183982	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	352	425	0	ENST00000350721.4:c.6998G>T	p.Arg2333Ile	p.R2333I	ENST00000350721	NM_001184.3	2333	aGa/aTa	41/47	0.130499241366274	3	FACETS	1	0.993	1	0.663	0.628	0.699	INDETERMINATE	1	TRUE	1	0.578206779582487	3		425	1183	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020931	26020931	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1905	632	1278	0	ENST00000357647.3:c.214G>T	p.Val72Leu	p.V72L	ENST00000357647	NM_003529.2	72	Gtg/Ttg	1/1	0.190406590048132	4	FACETS	1	0.996	1	0.68	0.652	0.708	INDETERMINATE	1	TRUE	2	0.578206779582487	4		1278	2537	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845187	151845187	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	314	414	0	ENST00000262189.6:c.13825C>T	p.Pro4609Ser	p.P4609S	ENST00000262189	NM_170606.2	4609	Cca/Tca	52/59	0.24965963345559	3	FACETS	0.775	0.734	0.818	0.775	0.734	0.818	INDETERMINATE	2	TRUE	1	0.578206779582487	3		414	903	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960212	151960212	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	28	142	0	ENST00000262189.6:c.1188A>T	p.Gln396His	p.Q396H	ENST00000262189	NM_170606.2	396	caA/caT	9/59	0.24965963345559	3	FACETS	0.375	0.3	0.46	0.187	0.15	0.23	INDETERMINATE	1	TRUE	1	0.578206779582487	3		142	333	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943717	17943717	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	379	271	0	ENST00000458235.1:c.2372C>G	p.Pro791Arg	p.P791R	ENST00000458235	NM_000215.3	791	cCc/cGc	18/24	0.375077052270229	4	FACETS	0.933	0.893	0.973	0.933	0.893	0.973	CLONAL	3	TRUE	1	0.578206779582487	4		271	739	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39725893	39725893	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	287	297	0	ENST00000361337.2:c.764A>C	p.Glu255Ala	p.E255A	ENST00000361337	NM_003286.2	255	gAa/gCa	10/21	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.578206779582487	2		297	799	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535453	66535453	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	70	135	0	ENST00000273854.3:c.8del	p.Gly3AlafsTer59	p.G3Afs*59	ENST00000273854	NM_004439.5	3	gGc/gc	1/18	NA	2	FACETS	1	0.916	1			1	INDETERMINATE	1	TRUE	NA	0.578206779582487	2		135	232	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0008583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	302	691	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.28229029315725	2	FACETS	0.864	0.814	0.914	0.864	0.814	0.914	CLONAL	2	TRUE	0	0.334589895253599	2		691	1045	SUCCESS
APC	324	MSKCC	GRCh37	5	112170788	112170788	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs863224817	NA	P-0008583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	137	460	1	ENST00000257430.4:c.1886del	p.Leu629Ter	p.L629*	ENST00000257430	NM_000038.5	628	acT/ac	15/16	0.334589895253599	1	FACETS	0.828	0.753	0.906	0.828	0.753	0.906	CLONAL	1	TRUE	0	0.334589895253599	1		461	824	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587782272	NA	P-0008970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	403	420	0	ENST00000269305.4:c.994-1G>C		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.698712814790776	2	FACETS	0.876	0.848	0.904	0.876	0.848	0.904	CLONAL	2	TRUE	0	0.812474250924498	2		420	566	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797301	135797301	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	173	383	0	ENST00000298552.3:c.568del	p.Arg190AlafsTer20	p.R190Afs*20	ENST00000298552	NM_001162426.1	190	Cgc/gc	7/23	NA	2	FACETS	0.848	0.787	0.911			1	INDETERMINATE	1	TRUE	NA	0.812474250924498	2		383	502	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035095	37035095	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	119	310	0	ENST00000231790.2:c.57C>G	p.Ile19Met	p.I19M	ENST00000231790	NM_000249.3	19	atC/atG	1/19	0.740344857457004	5	FACETS	0.868	0.784	0.956	0.217	0.196	0.239	CLONAL	1	TRUE	1	0.812474250924498	5		310	749	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100697	67100697	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	370	400	0	ENST00000412916.2:c.395C>T	p.Ala132Val	p.A132V	ENST00000412916		132	gCc/gTc	4/6	0.717412047573189	2	FACETS	0.918	0.889	0.946	0.918	0.889	0.946	CLONAL	2	TRUE	0	0.812474250924498	2		400	496	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961825	15961826	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	471	551	0	ENST00000268712.3:c.5969dup	p.Thr1991AspfsTer8	p.T1991Dfs*8	ENST00000268712	NM_006311.3	1990	cag/caAg	38/46	0.698712814790776	2	FACETS	0.843	0.816	0.868	0.843	0.816	0.868	CLONAL	2	TRUE	0	0.812474250924498	2		551	688	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847346	68847365	+	protein_altering_variant	In_Frame_Del	DEL	TTGTCGTCACCACAAATCCA	TTGTCGTCACCACAAATCCA	CG	novel	NA	P-0008970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	388	513	0	ENST00000261769.5:c.1268_1287delinsCG	p.Phe423_Pro429delinsSer	p.F423_P429delinsS	ENST00000261769	NM_004360.3	423	tTTGTCGTCACCACAAATCCA/tCG	9/16	0.717412047573189	2	FACETS	0.822	0.793	0.85	0.822	0.793	0.85	CLONAL	2	TRUE	0	0.812474250924498	2		513	581	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	192	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.758235105284009	2		174	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691022	NA	P-0009113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	651	498	0	ENST00000269305.4:c.1024del	p.Arg342GlufsTer3	p.R342Efs*3	ENST00000269305	NM_001126112.2	342	Cga/ga	10/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.758235105284009	2		498	1619	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114126	115114126	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	514	388	2	ENST00000257566.3:c.1091A>G	p.Asn364Ser	p.N364S	ENST00000257566	NM_016569.3	364	aAc/aGc	6/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.758235105284009	2		390	1290	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937334	32937334	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	146	377	0	ENST00000380152.3:c.7995T>A	p.Asp2665Glu	p.D2665E	ENST00000380152		2665	gaT/gaA	18/27	1	2	FACETS	0.473	0.431	0.516	0.473	0.431	0.516	SUBCLONAL	1	TRUE	1	0.758235105284009	2		377	815	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs864622237	NA	P-0009113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	379	357	2	ENST00000269305.4:c.700T>G	p.Tyr234Asp	p.Y234D	ENST00000269305	NM_001126112.2	234	Tac/Gac	7/11	1	2	FACETS	0.919	0.874	0.965	0.919	0.874	0.965	CLONAL	1	TRUE	1	0.758235105284009	2		359	1088	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791857	42791857	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	349	303	0	ENST00000575354.2:c.743A>G	p.Lys248Arg	p.K248R	ENST00000575354	NM_015125.3	248	aAg/aGg	5/20	1	2	FACETS	0.915	0.868	0.963	0.915	0.868	0.963	CLONAL	1	TRUE	1	0.758235105284009	2		303	1006	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352743	70352743	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0009113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1936	119	755	0	ENST00000374080.3:c.4464T>A	p.Cys1488Ter	p.C1488*	ENST00000374080		1488	tgT/tgA	32/45	1	2	FACETS	0.153	0.137	0.17	0.153	0.137	0.17	SUBCLONAL	1	TRUE	1	0.758235105284009	2		755	2055	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039419	49039419	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	622	614	4	ENST00000267163.4:c.2406del	p.Asn803ThrfsTer7	p.N803Tfs*7	ENST00000267163	NM_000321.2	802	Ggg/gg	23/27	0.758235105284009	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.758235105284009	1		618	991	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343536	70343536	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1378	285	626	0	ENST00000374080.3:c.1711del	p.Leu571CysfsTer11	p.L571Cfs*11	ENST00000374080		570	ctC/ct	12/45	1	2	FACETS	0.452	0.423	0.482	0.452	0.423	0.482	SUBCLONAL	1	TRUE	1	0.758235105284009	2		626	1663	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653819	89653819	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs786204895	NA	P-0009113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	211	437	0	ENST00000371953.3:c.117del	p.Glu40LysfsTer14	p.E40Kfs*14	ENST00000371953	NM_000314.4	39	gcA/gc	2/9	0.758235105284009	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.758235105284009	1		437	304	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	60	174	0				ENST00000310581	NM_198253.2	-/1132			0.235812742941976	3	FACETS	0.951	0.826	1	0.951	0.826	1	CLONAL	2	TRUE	1	0.235812742941976	3		174	299	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0009486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	101	318	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	0.235812742941976	2		318	712	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0009486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	22	670	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	1	2	FACETS	0.204	0.157	0.259	0.204	0.157	0.259	SUBCLONAL	1	TRUE	1	0.235812742941976	2		670	914	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65349005	65349005	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	45	228	0	ENST00000342505.4:c.160G>C	p.Glu54Gln	p.E54Q	ENST00000342505	NM_002227.2	54	Gag/Cag	3/25	1	2	FACETS	0.716	0.601	0.843	0.716	0.601	0.843	SUBCLONAL	1	TRUE	1	0.235812742941976	2		228	533	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907161	101907161	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	119	235	0	ENST00000374994.4:c.1121G>C	p.Gly374Ala	p.G374A	ENST00000374994	NM_004612.2	374	gGa/gCa	6/9	0.235812742941976	2	FACETS	0.982	0.89	1	0.982	0.89	1	CLONAL	2	TRUE	0	0.235812742941976	2		235	514	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245552	41245552	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1368	167	693	0	ENST00000357654.3:c.1996C>A	p.Leu666Ile	p.L666I	ENST00000357654	NM_007294.3	666	Cta/Ata	10/23	1	2	FACETS	0.923	0.845	1	0.923	0.845	1	CLONAL	1	TRUE	1	0.235812742941976	2		693	1535	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44515599	44515599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	123	392	0	ENST00000291552.4:c.297G>A	p.Met99Ile	p.M99I	ENST00000291552	NM_006758.2	99	atG/atA	5/8	1	2	FACETS	0.976	0.881	1	0.976	0.881	1	CLONAL	1	TRUE	1	0.235812742941976	2		392	1069	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	109	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.912227542729167	2		174	228	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953760	48953760	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913302	NA	P-0009599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	409	304	0	ENST00000267163.4:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000267163	NM_000321.2	455	Cga/Tga	14/27	0.912227542729167	1	FACETS	0.964	0.938	0.988	0.964	0.938	0.988	CLONAL	1	TRUE	0	0.912227542729167	1		304	506	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720876	89720876	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs786201041	NA	P-0009599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	216	194	0	ENST00000371953.3:c.1026+1G>A		p.X342_splice	ENST00000371953	NM_000314.4	342			0.912227542729167	1	FACETS	0.998	0.964	1	0.998	0.964	1	CLONAL	1	TRUE	0	0.912227542729167	1		194	258	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579584	7579601	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGGGGACTGTAGATGGG	AGGGGGACTGTAGATGGG	-	novel	NA	P-0009599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	251	211	0	ENST00000269305.4:c.97-11_103del		p.X33_splice	ENST00000269305	NM_001126112.2	33		4/11	0.896709757398075	1	FACETS	0.985	0.952	1	0.985	0.952	1	CLONAL	1	TRUE	0	0.912227542729167	1		211	304	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0009616-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	588	627	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.510256643048478	3	FACETS	0.838	0.811	0.865	0.838	0.811	0.865	CLONAL	3	TRUE	0	0.612086199955319	3		627	998	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829850	72829850	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs776161171	NA	P-0009616-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	847	1124	0	ENST00000268489.5:c.6731C>G	p.Ser2244Cys	p.S2244C	ENST00000268489	NM_006885.3	2244	tCt/tGt	9/10	0.576071328224938	2	FACETS	0.971	0.945	0.996	0.971	0.945	0.996	CLONAL	2	TRUE	0	0.612086199955319	2		1124	1425	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	97	174	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.57693557389936	2		174	264	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0009664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	262	352	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.57693557389936	2		352	865	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504417	186504417	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	377	644	0	ENST00000323963.5:c.754A>G	p.Ile252Val	p.I252V	ENST00000323963		252	Att/Gtt	7/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.57693557389936	2		644	1128	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590506	67590506	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs756643064	NA	P-0009664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	289	477	0	ENST00000274335.5:c.1568G>A	p.Arg523Lys	p.R523K	ENST00000274335		523	aGg/aAg	11/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.57693557389936	2		477	888	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163362	32163362	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1476443176	NA	P-0009664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1846	534	719	1	ENST00000375023.3:c.5864C>T	p.Ala1955Val	p.A1955V	ENST00000375023	NM_004557.3	1955	gCc/gTc	30/30	0.57693557389936	4	FACETS	1	0.994	1	0.409	0.39	0.428	CLONAL	1	TRUE	1	0.57693557389936	4		720	2380	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007080	152007080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	113	536	2	ENST00000262189.6:c.820G>A	p.Asp274Asn	p.D274N	ENST00000262189	NM_170606.2	274	Gac/Aac	6/59	NA	2	FACETS	0.43	0.386	0.476			1	INDETERMINATE	1	TRUE	NA	0.57693557389936	2		538	912	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307239	118307239	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	26	57	0	ENST00000534358.1:c.12C>G	p.Ser4Arg	p.S4R	ENST00000534358	NM_005933.3	4	agC/agG	1/36	1	2	FACETS	0.487	0.389	0.598	0.487	0.389	0.598	SUBCLONAL	1	TRUE	1	0.57693557389936	2		57	185	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244919	46244919	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	327	519	0	ENST00000334344.6:c.3013C>T	p.Gln1005Ter	p.Q1005*	ENST00000334344	NM_152641.2	1005	Caa/Taa	15/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.57693557389936	2		519	1092	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821323	72821323	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	376	669	0	ENST00000268489.5:c.10852C>A	p.Pro3618Thr	p.P3618T	ENST00000268489	NM_006885.3	3618	Ccg/Acg	10/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.57693557389936	2		669	1220	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873633	35873633	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	146	373	0	ENST00000303115.3:c.590del	p.Pro197ArgfsTer47	p.P197Rfs*47	ENST00000303115	NM_002185.3	197	Ccg/cg	5/8	1	2	FACETS	0.977	0.897	1	0.977	0.897	1	CLONAL	1	TRUE	1	0.57693557389936	2		373	518	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231161	46231167	+	frameshift_variant	Frame_Shift_Del	DEL	AAATGTC	AAATGTC	-	novel	NA	P-0009664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	230	461	0	ENST00000334344.6:c.1081_1087del	p.Lys361Ter	p.K361*	ENST00000334344	NM_152641.2	361	AAATGTCta/ta	9/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.57693557389936	2		461	779	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0009913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	126	514	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.527787547736395	1	FACETS	0.849	0.775	0.925	0.849	0.775	0.925	CLONAL	1	TRUE	0	0.527787547736395	1		514	414	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874261	155874261	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs483352822	NA	P-0009913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	181	380	0	ENST00000368323.3:c.270G>C	p.Met90Ile	p.M90I	ENST00000368323	NM_006912.5	90	atG/atC	5/6	0.527787547736395	4	FACETS	0.965	0.889	1	0.322	0.296	0.348	CLONAL	1	TRUE	1	0.527787547736395	4		380	1086	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199839	108199839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779861	NA	P-0009913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	152	186	0	ENST00000278616.4:c.7181C>T	p.Ser2394Leu	p.S2394L	ENST00000278616	NM_000051.3	2394	tCa/tTa	49/63	0.525794512285841	5	FACETS	0.863	0.793	0.936			1	CLONAL	2	TRUE	NA	0.527787547736395	5		186	598	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11206779	11206779	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	138	452	0	ENST00000361445.4:c.4640G>C	p.Arg1547Thr	p.R1547T	ENST00000361445	NM_004958.3	1547	aGa/aCa	32/58	0.434032311982766	0	FACETS	0.555	0.509	0.602			1	SUBCLONAL	1	TRUE	0	0.527787547736395	0		452	445	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087548	27087548	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	238	429	0	ENST00000324856.7:c.2122C>T	p.Gln708Ter	p.Q708*	ENST00000324856	NM_006015.4	708	Cag/Tag	5/20	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.527787547736395	2		429	604	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665360	138665360	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906920	NA	P-0009913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	132	337	0	ENST00000330315.3:c.205G>A	p.Glu69Lys	p.E69K	ENST00000330315	NM_023067.3	69	Gag/Aag	1/1	0.191047668632085	1	FACETS	0.788	0.721	0.859	0.788	0.721	0.859	INDETERMINATE	1	TRUE	0	0.527787547736395	1		337	467	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176461	142176461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	154	322	1	ENST00000350721.4:c.7640G>A	p.Arg2547Gln	p.R2547Q	ENST00000350721	NM_001184.3	2547	cGa/cAa	45/47	0.191047668632085	1	FACETS	0.747	0.687	0.809	0.747	0.687	0.809	INDETERMINATE	1	TRUE	0	0.527787547736395	1		323	575	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672233	86672233	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554049394	NA	P-0009913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	85	265	0	ENST00000274376.6:c.2035C>T	p.Arg679Ter	p.R679*	ENST00000274376	NM_002890.2	679	Cga/Tga	16/25	1	2	FACETS	0.763	0.678	0.853	0.763	0.678	0.853	SUBCLONAL	1	TRUE	1	0.527787547736395	2		265	422	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502190	157502190	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs387907144	NA	P-0009913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	38	228	0	ENST00000346085.5:c.3223C>T	p.Arg1075Ter	p.R1075*	ENST00000346085	NM_020732.3	1075	Cga/Tga	12/20	0.364135820262708	4	FACETS	0.361	0.298	0.432			1	SUBCLONAL	1	TRUE	NA	0.527787547736395	4		228	609	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874923	151874923	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	160	390	0	ENST00000262189.6:c.7615C>T	p.Gln2539Ter	p.Q2539*	ENST00000262189	NM_170606.2	2539	Cag/Tag	38/59	NA	2	FACETS	0.908	0.835	0.983			1	INDETERMINATE	1	TRUE	NA	0.527787547736395	2		390	668	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994138	21994138	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	187	420	0	ENST00000579755.1:c.193G>C	p.Gly65Arg	p.G65R	ENST00000579755		65	Ggt/Cgt	1/3	1		FACETS		0.906	1				CLONAL	1	TRUE	1	0.527787547736395	2		420	725	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138158	64138158	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747011048	NA	P-0009913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	96	233	0	ENST00000334205.4:c.2081C>T	p.Ser694Phe	p.S694F	ENST00000334205	NM_003942.2	694	tCt/tTt	16/17	0.126422070238033	0	FACETS	0.51	0.459	0.563			1	INDETERMINATE	1	TRUE	0	0.527787547736395	0		233	337	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416720	416720	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	158	349	0	ENST00000399788.2:c.3830C>G	p.Ser1277Cys	p.S1277C	ENST00000399788	NM_001042603.1	1277	tCt/tGt	23/28	1	2	FACETS	0.966	0.889	1	0.966	0.889	1	CLONAL	1	TRUE	1	0.527787547736395	2		349	620	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482607	56482607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs993665271	NA	P-0009913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	264	397	0	ENST00000267101.3:c.1064C>T	p.Thr355Ile	p.T355I	ENST00000267101	NM_001982.3	355	aCc/aTc	9/28	0.204720518903417	4	FACETS	0.785	0.737	0.835	0.785	0.737	0.835	INDETERMINATE	2	TRUE	2	0.527787547736395	4		397	973	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354339	354339	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	306	348	0	ENST00000262320.3:c.1219G>T	p.Glu407Ter	p.E407*	ENST00000262320	NM_003502.3	407	Gag/Tag	5/11	0.527787547736395	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.527787547736395	2		348	481	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604754	48604754	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	158	393	0	ENST00000342988.3:c.1576G>C	p.Glu526Gln	p.E526Q	ENST00000342988	NM_005359.5	526	Gaa/Caa	12/12	0.527787547736395	1	FACETS	0.916	0.846	0.988	0.916	0.846	0.988	CLONAL	1	TRUE	0	0.527787547736395	1		393	481	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412755	63412755	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	119	204	0	ENST00000330258.3:c.412G>T	p.Glu138Ter	p.E138*	ENST00000330258	NM_152424.3	138	Gag/Tag	2/2	0.427855874953693	0	FACETS	0.887	0.819	0.956			1	CLONAL	1	TRUE	NA	0.527787547736395	0		204	240	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0010035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	164	515	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.667743888060976	3	FACETS	1	0.965	1	0.541	0.498	0.584	CLONAL	1	TRUE	1	0.663495480614254	3		515	609	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244816	41244816	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	1181	635	0	ENST00000357654.3:c.2732del	p.Gly911GlufsTer89	p.G911Efs*89	ENST00000357654	NM_007294.3	911	gGa/ga	10/23	0.667743888060976	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	4	TRUE	0	0.663495480614254	4		635	1453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579359	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0010035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	652	671	0	ENST00000269305.4:c.327_328dup	p.Arg110ProfsTer14	p.R110Pfs*14	ENST00000269305	NM_001126112.2	110	cgt/cCCgt	4/11	0.667743888060976	2	FACETS	0.988	0.96	1	0.988	0.96	1	CLONAL	2	TRUE	0	0.663495480614254	2		671	995	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43700281	43700281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	258	577	2	ENST00000382044.4:c.5606C>T	p.Pro1869Leu	p.P1869L	ENST00000382044	NM_001141980.1	1869	cCc/cTc	27/28	0.374326603289926	5	FACETS	1	0.989	1	0.421	0.394	0.45	INDETERMINATE	1	TRUE	2	0.663495480614254	5		579	1228	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612827	228612827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	245	585	2	ENST00000366696.1:c.200C>A	p.Pro67His	p.P67H	ENST00000366696	NM_003493.2	67	cCc/cAc	1/1	0.326451351431773	6	FACETS	1	0.989	1	0.425	0.396	0.455	INDETERMINATE	1	TRUE	3	0.663495480614254	6		587	1347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0010537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	416	670	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.486659842220827	2	FACETS	0.948	0.907	0.988	0.948	0.907	0.988	CLONAL	2	TRUE	0	0.486659842220827	2		670	902	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11297992	11297992	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	446	456	0	ENST00000361445.4:c.2116G>C	p.Glu706Gln	p.E706Q	ENST00000361445	NM_004958.3	706	Gag/Cag	13/58	0.116250993008488	3	FACETS	0.839	0.806	0.873			1	INDETERMINATE	3	TRUE	NA	0.486659842220827	3		456	905	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919328	48919444	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTGGAAAGGTAAAGTAAACATTTTATTAGGTTTACACTCTGATTTTTTATGTCATTGTTCACAATTAGATTCTGGGAATTATTTAACACATTTAGTAAAGTTAGTAAGTATTAATTC	TTGGAAAGGTAAAGTAAACATTTTATTAGGTTTACACTCTGATTTTTTATGTCATTGTTCACAATTAGATTCTGGGAATTATTTAACACATTTAGTAAAGTTAGTAAGTATTAATTC	-	novel	NA	P-0010537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	84	404	0	ENST00000267163.4:c.495_500+111del		p.X165_splice	ENST00000267163	NM_000321.2	165		4/27	0.380069196257616	3	FACETS	0.769	0.688	0.854	0.513	0.458	0.569	SUBCLONAL	2	TRUE	0	0.486659842220827	3		404	279	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0010660-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	207	352	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.752654332271917	2		352	529	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21565435	21565435	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1217575272	NA	P-0010660-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	61	642	1	ENST00000382592.4:c.451C>T	p.Arg151Trp	p.R151W	ENST00000382592	NM_014572.2	151	Cgg/Tgg	3/8	1	2	FACETS	0.158	0.135	0.182	0.158	0.135	0.182	SUBCLONAL	1	TRUE	1	0.752654332271917	2		643	1029	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589579	67589593	+	inframe_deletion	In_Frame_Del	DEL	AAATTACATGAATAT	AAATTACATGAATAT	-	novel	NA	P-0010660-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	41	282	0	ENST00000274335.5:c.1344_1358del	p.Lys448_Tyr452del	p.K448_Y452del	ENST00000274335		448	AAATTACATGAATAT/-	10/15	0.752654332271917	3	FACETS	0.652	0.548	0.766	0.326	0.274	0.383	SUBCLONAL	1	TRUE	1	0.752654332271917	3		282	230	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097654	27097655	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0010660-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	726	735	2	ENST00000324856.7:c.3245_3246del	p.Val1082GlyfsTer22	p.V1082Gfs*22	ENST00000324856	NM_006015.4	1081	aaTGtg/aatg	12/20	0.741863512038594	2	FACETS	0.974	0.952	0.997	0.974	0.952	0.997	CLONAL	2	TRUE	0	0.752654332271917	2		737	990	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711941	89711964	+	frameshift_variant	Frame_Shift_Del	DEL	GATTATAGACCAGTGGCACTGTTG	GATTATAGACCAGTGGCACTGTTG	C	novel	NA	P-0010660-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	191	539	0	ENST00000371953.3:c.559_582delinsC	p.Asp187LeufsTer7	p.D187Lfs*7	ENST00000371953	NM_000314.4	187	GATTATAGACCAGTGGCACTGTTG/C	6/9	0.752654332271917	3	FACETS	1	0.988	1	0.768	0.728	0.808	CLONAL	2	TRUE	0	0.752654332271917	3		539	303	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873802	35873802	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	115	357	0	ENST00000216797.5:c.49C>G	p.Arg17Gly	p.R17G	ENST00000216797	NM_020529.2	17	Cgc/Ggc	1/6	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.322275522794725	2		357	645	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441182	52441239	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTGCCTACCATGGTCAATGGGGTAGACCTTCAGCCCATCCAGCTCAAAGAGCCGGCCT	GTGCCTACCATGGTCAATGGGGTAGACCTTCAGCCCATCCAGCTCAAAGAGCCGGCCT	-	novel	NA	P-0010679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	43	125	0	ENST00000460680.1:c.531_580+8del		p.X177_splice	ENST00000460680	NM_004656.3	177		7/17	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.322275522794725	2		125	260	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439286	52439286	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	48	174	0	ENST00000460680.1:c.956del	p.Ser319TyrfsTer16	p.S319Yfs*16	ENST00000460680	NM_004656.3	319	tCa/ta	11/17	1	2	FACETS	0.821	0.696	0.957	0.821	0.696	0.957	CLONAL	1	TRUE	1	0.322275522794725	2		174	363	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219127	94219127	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	113	226	0	ENST00000323929.3:c.277del	p.Ile93PhefsTer17	p.I93Ffs*17	ENST00000323929	NM_005591.3	93	Att/tt	4/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.322275522794725	2		226	637	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057231	30057231	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	79	271	0	ENST00000338641.4:c.715del	p.Leu239TrpfsTer12	p.L239Wfs*12	ENST00000338641	NM_000268.3	238	gCc/gc	8/16	0.313554610695824	1	FACETS	0.78	0.688	0.879	0.78	0.688	0.879	SUBCLONAL	1	TRUE	0	0.322275522794725	1		271	527	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0011108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	772	492	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.87432763977242	3	FACETS	0.974	0.959	0.987			1	CLONAL	3	TRUE	NA	0.87432763977242	3		492	869	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0011108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	722	670	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.809161122907599	2	FACETS	0.952	0.934	0.97	0.952	0.934	0.97	CLONAL	2	TRUE	0	0.87432763977242	2		670	867	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371683	55371683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753693798	NA	P-0011108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	96	463	0	ENST00000297316.4:c.373C>T	p.Arg125Cys	p.R125C	ENST00000297316	NM_022454.3	125	Cgc/Tgc	2/2	0.822789985995634	4	FACETS	0.345	0.306	0.386	0.172	0.153	0.193	SUBCLONAL	1	TRUE	2	0.87432763977242	4		463	1194	SUCCESS
APC	324	MSKCC	GRCh37	5	112116494	112116494	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0011108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	270	311	0	ENST00000257430.4:c.539T>G	p.Leu180Ter	p.L180*	ENST00000257430	NM_000038.5	180	tTa/tGa	6/16	0.814138130518092	2	FACETS	0.9	0.869	0.93	0.9	0.869	0.93	CLONAL	2	TRUE	0	0.87432763977242	2		311	343	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459462	50459462	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	568	364	0	ENST00000331340.3:c.751G>T	p.Glu251Ter	p.E251*	ENST00000331340	NM_006060.4	251	Gaa/Taa	7/8	0.87432763977242	5	FACETS	0.896	0.865	0.928	0.896	0.865	0.928	CLONAL	3	TRUE	2	0.87432763977242	5		364	1117	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342789	87342789	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	473	452	0	ENST00000277120.3:c.1074C>G	p.Asp358Glu	p.D358E	ENST00000277120		358	gaC/gaG	9/19	0.384657974285574	5	FACETS	0.912	0.877	0.947	0.912	0.877	0.947	INDETERMINATE	3	TRUE	2	0.87432763977242	5		452	914	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	532715	532715	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753977266	NA	P-0011108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	775	683	0	ENST00000451590.1:c.491G>A	p.Arg164Gln	p.R164Q	ENST00000451590	NM_001130442.1	164	cGg/cAg	5/5	0.83177293634003	3	FACETS	0.932	0.905	0.958	0.932	0.905	0.958	CLONAL	2	TRUE	1	0.87432763977242	3		683	1367	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143448	108143448	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1555085973	NA	P-0011108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	303	624	0	ENST00000278616.4:c.3154-1G>A		p.X1052_splice	ENST00000278616	NM_000051.3	1052			1	2	FACETS	0.9	0.853	0.948	0.9	0.853	0.948	CLONAL	1	TRUE	1	0.87432763977242	2		624	770	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163500	108163500	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	230	483	0	ENST00000278616.4:c.4591C>T	p.Gln1531Ter	p.Q1531*	ENST00000278616	NM_000051.3	1531	Cag/Tag	30/63	1	2	FACETS	0.969	0.912	1	0.969	0.912	1	CLONAL	1	TRUE	1	0.87432763977242	2		483	543	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0011400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	119	769	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.314334715371376	2		769	605	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0011400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	295	593	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.314334715371376	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.314334715371376	1		595	1421	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	189	356	0	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.314334715371376	2		356	1200	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0011400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	197	540	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.944	0.872	1	0.944	0.872	1	CLONAL	1	TRUE	1	0.314334715371376	2		540	1328	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120668	115120668	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1483	272	556	3	ENST00000257566.3:c.338G>A	p.Trp113Ter	p.W113*	ENST00000257566	NM_016569.3	113	tGg/tAg	1/8	NA	2	FACETS	0.986	0.922	1			1	INDETERMINATE	1	TRUE	NA	0.314334715371376	2		559	1755	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215674175	215674175	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs71579841	NA	P-0011400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	181	393	1	ENST00000260947.4:c.119C>T	p.Ala40Val	p.A40V	ENST00000260947	NM_000465.2	40	gCg/gTg	1/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.314334715371376	2		394	1072	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940889	49940889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144338909	NA	P-0011400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1412	222	657	0	ENST00000296474.3:c.154G>A	p.Gly52Arg	p.G52R	ENST00000296474	NM_002447.2	52	Gga/Aga	1/20	1	2	FACETS	0.864	0.802	0.93	0.864	0.802	0.93	CLONAL	1	TRUE	1	0.314334715371376	2		657	1634	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878785	151878785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	174	405	1	ENST00000262189.6:c.6160C>T	p.Gln2054Ter	p.Q2054*	ENST00000262189	NM_170606.2	2054	Cag/Tag	36/59	1	2	FACETS	0.846	0.777	0.918	0.846	0.777	0.918	CLONAL	1	TRUE	1	0.314334715371376	2		406	1309	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717741	89717741	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121909228	NA	P-0011400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	128	215	2	ENST00000371953.3:c.766G>T	p.Glu256Ter	p.E256*	ENST00000371953	NM_000314.4	256	Gag/Tag	7/9	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.314334715371376	2		217	687	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416554	49416554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	181	360	0	ENST00000301067.7:c.16157C>T	p.Ser5386Phe	p.S5386F	ENST00000301067	NM_003482.3	5386	tCt/tTt	51/54	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.314334715371376	2		360	1080	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832025	72832025	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0011400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1341	301	658	0	ENST00000268489.5:c.4556C>G	p.Ser1519Ter	p.S1519*	ENST00000268489	NM_006885.3	1519	tCa/tGa	9/10	0.314334715371376	1	FACETS	0.983	0.923	1	0.983	0.923	1	CLONAL	1	TRUE	0	0.314334715371376	1		658	1642	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650881	93650881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200438123	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	147	230	0	ENST00000375746.1:c.1807G>A	p.Asp603Asn	p.D603N	ENST00000375746	NM_001174167.1	603	Gat/Aat	13/14	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.463958517583754	2		230	586	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146616	55146616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs34392012	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	192	376	0	ENST00000257290.5:c.2290C>T	p.Arg764Cys	p.R764C	ENST00000257290	NM_006206.4	764	Cgt/Tgt	16/23	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.463958517583754	2		376	794	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857524	9857524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778230379	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	147	241	0	ENST00000330684.3:c.3877G>A	p.Asp1293Asn	p.D1293N	ENST00000330684	NM_001134407.1	1293	Gat/Aat	13/13	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.463958517583754	2		241	536	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912815	100912815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1000609240	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	226	607	2	ENST00000325455.5:c.2507G>A	p.Arg836Gln	p.R836Q	ENST00000325455	NM_001202474.3	836	cGa/cAa	7/8	1	2	FACETS	0.931	0.867	0.998	0.931	0.867	0.998	CLONAL	1	TRUE	1	0.463958517583754	2		609	1046	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144880	47144880	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	192	414	1	ENST00000409792.3:c.4873C>T	p.Arg1625Cys	p.R1625C	ENST00000409792	NM_014159.6	1625	Cgt/Tgt	7/21	1	2	FACETS	0.998	0.925	1	0.998	0.925	1	CLONAL	1	TRUE	1	0.463958517583754	2		415	829	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633380	8633380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768353460	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	232	561	0	ENST00000356435.5:c.289G>A	p.Glu97Lys	p.E97K	ENST00000356435		97	Gaa/Aaa	3/35	0.28916764910736	1	FACETS	0.93	0.869	0.992	0.93	0.869	0.992	CLONAL	1	TRUE	0	0.463958517583754	1		561	826	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312725	91312725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	226	350	1	ENST00000355112.3:c.2464C>T	p.Pro822Ser	p.P822S	ENST00000355112	NM_000057.2	822	Cct/Tct	12/22	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.463958517583754	2		351	945	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938229	76938229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	202	537	0	ENST00000373344.5:c.2519G>A	p.Arg840Lys	p.R840K	ENST00000373344	NM_000489.3	840	aGa/aAa	9/35	1	2	FACETS	0.878	0.814	0.944	0.878	0.814	0.944	CLONAL	1	TRUE	1	0.463958517583754	2		537	992	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188237	142188237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	126	281	0	ENST00000350721.4:c.6494C>T	p.Ala2165Val	p.A2165V	ENST00000350721	NM_001184.3	2165	gCc/gTc	38/47	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.463958517583754	2		281	543	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203492	108203492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs138941496	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	100	192	0	ENST00000278616.4:c.7792C>T	p.Arg2598Ter	p.R2598*	ENST00000278616	NM_000051.3	2598	Cga/Tga	53/63	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.463958517583754	2		192	342	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420005	41420005	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	385	545	1	ENST00000373198.4:c.316C>T	p.His106Tyr	p.H106Y	ENST00000373198	NM_133170.3	106	Cat/Tat	3/32	0.463958517583754	3	FACETS	0.917	0.872	0.962	0.917	0.872	0.962	CLONAL	2	TRUE	1	0.463958517583754	3		546	1115	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633430	8633430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	180	410	1	ENST00000356435.5:c.239C>T	p.Ser80Leu	p.S80L	ENST00000356435		80	tCa/tTa	3/35	0.28916764910736	1	FACETS	0.833	0.771	0.898	0.833	0.771	0.898	CLONAL	1	TRUE	0	0.463958517583754	1		411	715	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562641	29562641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854562	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	239	592	2	ENST00000356175.3:c.3721C>T	p.Arg1241Ter	p.R1241*	ENST00000356175	NM_000267.3	1241	Cga/Tga	28/57	0.463958517583754	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.463958517583754	1		594	788	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288993	212288993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867944951	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	211	441	0	ENST00000342788.4:c.2753G>A	p.Gly918Glu	p.G918E	ENST00000342788	NM_005235.2	918	gGa/gAa	23/28	0.463958517583754	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.463958517583754	1		441	622	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945627	206945627	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	194	510	0	ENST00000423557.1:c.154A>C	p.Lys52Gln	p.K52Q	ENST00000423557	NM_000572.2	52	Aag/Cag	1/5	1	2	FACETS	0.948	0.878	1	0.948	0.878	1	CLONAL	1	TRUE	1	0.463958517583754	2		510	882	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455248	29455248	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs371441614	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	184	539	0	ENST00000389048.3:c.2554A>G	p.Lys852Glu	p.K852E	ENST00000389048	NM_004304.4	852	Aag/Gag	15/29	1	2	FACETS	0.928	0.857	1	0.928	0.857	1	CLONAL	1	TRUE	1	0.463958517583754	2		539	855	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033346	48033346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63749898	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	138	346	0	ENST00000234420.5:c.3650G>A	p.Arg1217Lys	p.R1217K	ENST00000234420	NM_000179.2	1217	aGa/aAa	8/10	1	2	FACETS	0.94	0.858	1	0.94	0.858	1	CLONAL	1	TRUE	1	0.463958517583754	2		346	633	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713850	30713850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	143	435	0	ENST00000295754.5:c.1175C>T	p.Thr392Ile	p.T392I	ENST00000295754	NM_003242.5	392	aCc/aTc	4/7	1	2	FACETS	0.871	0.795	0.949	0.871	0.795	0.949	CLONAL	1	TRUE	1	0.463958517583754	2		435	708	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526242	189526242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	195	559	0	ENST00000264731.3:c.506C>T	p.Thr169Ile	p.T169I	ENST00000264731	NM_003722.4	169	aCc/aTc	4/14	1	2	FACETS	0.929	0.86	1	0.929	0.86	1	CLONAL	1	TRUE	1	0.463958517583754	2		559	905	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612281	189612281	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	92	226	0	ENST00000264731.3:c.2033A>T	p.Glu678Val	p.E678V	ENST00000264731	NM_003722.4	678	gAg/gTg	14/14	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.463958517583754	2		226	348	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946259	55946259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	183	418	0	ENST00000263923.4:c.3920C>T	p.Ser1307Phe	p.S1307F	ENST00000263923	NM_002253.2	1307	tCc/tTc	30/30	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.463958517583754	2		418	744	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976644	55976644	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	224	539	0	ENST00000263923.4:c.1181G>A	p.Gly394Glu	p.G394E	ENST00000263923	NM_002253.2	394	gGa/gAa	9/30	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.463958517583754	2		539	955	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155943	106155943	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	108	255	1	ENST00000380013.4:c.844T>A	p.Ser282Thr	p.S282T	ENST00000380013	NM_001127208.2	282	Tct/Act	3/11	1	2	FACETS	0.931	0.84	1	0.931	0.84	1	CLONAL	1	TRUE	1	0.463958517583754	2		256	500	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56171012	56171012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	66	295	0	ENST00000399503.3:c.1840C>T	p.Pro614Ser	p.P614S	ENST00000399503	NM_005921.1	614	Ccg/Tcg	10/20	0.28916764910736	1	FACETS	0.505	0.439	0.575	0.505	0.439	0.575	SUBCLONAL	1	TRUE	0	0.463958517583754	1		295	433	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751143	57751143	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	113	292	0	ENST00000274289.3:c.1724T>A	p.Phe575Tyr	p.F575Y	ENST00000274289	NM_006622.3	575	tTt/tAt	12/14	0.28916764910736	1	FACETS	0.645	0.582	0.711	0.645	0.582	0.711	SUBCLONAL	1	TRUE	0	0.463958517583754	1		292	580	SUCCESS
APC	324	MSKCC	GRCh37	5	112162829	112162829	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	111	336	0	ENST00000257430.4:c.1433T>C	p.Leu478Ser	p.L478S	ENST00000257430	NM_000038.5	478	tTa/tCa	12/16	0.28916764910736	1	FACETS	0.705	0.637	0.777	0.705	0.637	0.777	SUBCLONAL	1	TRUE	0	0.463958517583754	1		336	521	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057594	180057594	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371804364	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	203	707	0	ENST00000261937.6:c.361G>A	p.Glu121Lys	p.E121K	ENST00000261937	NM_182925.4	121	Gag/Aag	3/30	0.28916764910736	1	FACETS	0.73	0.677	0.784	0.73	0.677	0.784	SUBCLONAL	1	TRUE	0	0.463958517583754	1		707	921	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536095	106536095	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	157	396	0	ENST00000369096.4:c.62C>T	p.Ser21Phe	p.S21F	ENST00000369096	NM_001198.3	21	tCc/tTc	2/7	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.463958517583754	2		396	630	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552990	106552990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	176	472	1	ENST00000369096.4:c.955G>A	p.Glu319Lys	p.E319K	ENST00000369096	NM_001198.3	319	Gag/Aag	5/7	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.463958517583754	2		473	712	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554847	106554847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	105	317	0	ENST00000369096.4:c.1964G>A	p.Gly655Glu	p.G655E	ENST00000369096	NM_001198.3	655	gGa/gAa	7/7	1	2	FACETS	0.843	0.758	0.932	0.843	0.758	0.932	CLONAL	1	TRUE	1	0.463958517583754	2		317	537	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638350	117638350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	183	503	1	ENST00000368508.3:c.6091G>A	p.Gly2031Arg	p.G2031R	ENST00000368508	NM_002944.2	2031	Gga/Aga	38/43	1	2	FACETS	0.96	0.887	1	0.96	0.887	1	CLONAL	1	TRUE	1	0.463958517583754	2		504	822	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163826	152163826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	183	404	1	ENST00000206249.3:c.547C>T	p.Arg183Cys	p.R183C	ENST00000206249	NM_000125.3	183	Cgc/Tgc	2/8	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.463958517583754	2		405	777	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405920	157405920	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	145	401	0	ENST00000346085.5:c.2162C>T	p.Ser721Phe	p.S721F	ENST00000346085	NM_020732.3	721	tCc/tTc	6/20	1	2	FACETS	0.954	0.873	1	0.954	0.873	1	CLONAL	1	TRUE	1	0.463958517583754	2		401	655	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987418	2987418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	195	416	0	ENST00000396946.4:c.11G>A	p.Gly4Glu	p.G4E	ENST00000396946	NM_032415.4	4	gGa/gAa	3/25	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.463958517583754	2		416	807	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151919124	151919124	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	114	341	0	ENST00000262189.6:c.3461C>T	p.Ser1154Leu	p.S1154L	ENST00000262189	NM_170606.2	1154	tCa/tTa	22/59	1	2	FACETS	0.881	0.796	0.97	0.881	0.796	0.97	CLONAL	1	TRUE	1	0.463958517583754	2		341	558	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949141	151949141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758799285	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	168	406	0	ENST00000262189.6:c.1504C>T	p.His502Tyr	p.H502Y	ENST00000262189	NM_170606.2	502	Cat/Tat	11/59	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.463958517583754	2		406	699	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5078391	5078391	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	150	401	0	ENST00000381652.3:c.2078C>T	p.Pro693Leu	p.P693L	ENST00000381652	NM_004972.3	693	cCt/cTt	16/25	0.28916764910736	1	FACETS	0.932	0.857	1	0.932	0.857	1	CLONAL	1	TRUE	0	0.463958517583754	1		401	533	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521397	8521397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	203	520	0	ENST00000356435.5:c.841G>A	p.Asp281Asn	p.D281N	ENST00000356435		281	Gat/Aat	9/35	0.28916764910736	1	FACETS	0.919	0.855	0.985	0.919	0.855	0.985	CLONAL	1	TRUE	0	0.463958517583754	1		520	731	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87338515	87338515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139913267	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	192	483	1	ENST00000277120.3:c.611C>T	p.Pro204Leu	p.P204L	ENST00000277120		204	cCt/cTt	7/19	1	2	FACETS	0.955	0.884	1	0.955	0.884	1	CLONAL	1	TRUE	1	0.463958517583754	2		484	867	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606271	93606271	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	188	563	1	ENST00000375746.1:c.91C>T	p.Gln31Ter	p.Q31*	ENST00000375746	NM_001174167.1	31	Cag/Tag	2/14	1	2	FACETS	0.922	0.853	0.994	0.922	0.853	0.994	CLONAL	1	TRUE	1	0.463958517583754	2		564	879	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604515	43604515	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs763759702	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	204	674	0	ENST00000355710.3:c.1100A>G	p.Asn367Ser	p.N367S	ENST00000355710	NM_020975.4	367	aAc/aGc	6/20	1	2	FACETS	0.96	0.891	1	0.96	0.891	1	CLONAL	1	TRUE	1	0.463958517583754	2		674	916	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852437	63852437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1362687523	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	221	438	0	ENST00000279873.7:c.3215C>T	p.Pro1072Leu	p.P1072L	ENST00000279873	NM_032199.2	1072	cCc/cTc	10/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.463958517583754	2		438	799	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104377094	104377094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	167	500	0	ENST00000369902.3:c.1205G>A	p.Gly402Asp	p.G402D	ENST00000369902	NM_016169.3	402	gGt/gAt	10/12	1	2	FACETS	0.869	0.8	0.942	0.869	0.8	0.942	CLONAL	1	TRUE	1	0.463958517583754	2		500	828	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514329	69514329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	160	368	0	ENST00000294312.3:c.352G>A	p.Glu118Lys	p.E118K	ENST00000294312	NM_005117.2	118	Gaa/Aaa	3/3	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.463958517583754	2		368	588	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588107	69588107	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	219	560	0	ENST00000168712.1:c.591G>A	p.Met197Ile	p.M197I	ENST00000168712	NM_002007.2	197	atG/atA	3/3	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.463958517583754	2		560	851	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920729	100920729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	286	707	0	ENST00000325455.5:c.2419G>A	p.Glu807Lys	p.E807K	ENST00000325455	NM_001202474.3	807	Gag/Aag	6/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.463958517583754	2		707	1110	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118354977	118354977	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555040236	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	133	399	0	ENST00000534358.1:c.4166C>T	p.Ser1389Phe	p.S1389F	ENST00000534358	NM_005933.3	1389	tCt/tTt	9/36	1	2	FACETS	0.791	0.719	0.866	0.791	0.719	0.866	SUBCLONAL	1	TRUE	1	0.463958517583754	2		399	725	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443490	49443490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	125	372	0	ENST00000301067.7:c.3881C>T	p.Ser1294Phe	p.S1294F	ENST00000301067	NM_003482.3	1294	tCc/tTc	11/54	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.463958517583754	2		372	532	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445406	49445406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	127	419	0	ENST00000301067.7:c.2060C>T	p.Ser687Leu	p.S687L	ENST00000301067	NM_003482.3	687	tCa/tTa	10/54	1	2	FACETS	0.89	0.809	0.975	0.89	0.809	0.975	CLONAL	1	TRUE	1	0.463958517583754	2		419	615	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858649	57858649	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	203	533	0	ENST00000228682.2:c.387G>A	p.Met129Ile	p.M129I	ENST00000228682	NM_005269.2	129	atG/atA	4/12	1	2	FACETS	0.999	0.927	1	0.999	0.927	1	CLONAL	1	TRUE	1	0.463958517583754	2		533	876	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416662	121416662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	150	513	0	ENST00000257555.6:c.91G>A	p.Gly31Ser	p.G31S	ENST00000257555		31	Ggt/Agt	1/10	1	2	FACETS	0.94	0.861	1	0.94	0.861	1	CLONAL	1	TRUE	1	0.463958517583754	2		513	688	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052602	42052602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	321	728	2	ENST00000219905.7:c.7273C>T	p.Arg2425Cys	p.R2425C	ENST00000219905	NM_001164273.1	2425	Cgc/Tgc	20/24	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.463958517583754	2		730	1372	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857452	9857452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	124	437	0	ENST00000330684.3:c.3949G>A	p.Glu1317Lys	p.E1317K	ENST00000330684	NM_001134407.1	1317	Gaa/Aaa	13/13	1	2	FACETS	0.755	0.684	0.83	0.755	0.684	0.83	SUBCLONAL	1	TRUE	1	0.463958517583754	2		437	708	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934864	9934864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766162952	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	267	581	0	ENST00000330684.3:c.1426G>A	p.Asp476Asn	p.D476N	ENST00000330684	NM_001134407.1	476	Gac/Aac	6/13	1	2	FACETS	0.984	0.922	1	0.984	0.922	1	CLONAL	1	TRUE	1	0.463958517583754	2		581	1170	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024649	14024649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202243691	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	195	463	0	ENST00000311895.7:c.875G>A	p.Arg292Gln	p.R292Q	ENST00000311895	NM_005236.2	292	cGa/cAa	5/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.463958517583754	2		463	811	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677330	29677330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1215473858	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	105	318	0	ENST00000356175.3:c.7388C>T	p.Ser2463Phe	p.S2463F	ENST00000356175	NM_000267.3	2463	tCc/tTc	49/57	0.463958517583754	1	FACETS	0.882	0.797	0.971	0.882	0.797	0.971	CLONAL	1	TRUE	0	0.463958517583754	1		318	394	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30293176	30293176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764786746	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	144	258	1	ENST00000322652.5:c.466C>T	p.His156Tyr	p.H156Y	ENST00000322652	NM_015355.2	156	Cat/Tat	5/16	0.463958517583754	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.463958517583754	1		259	461	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292531	15292531	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs572814447	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	190	563	0	ENST00000263388.2:c.2648G>A	p.Arg883Gln	p.R883Q	ENST00000263388	NM_000435.2	883	cGa/cAa	17/33	1	2	FACETS	0.974	0.902	1	0.974	0.902	1	CLONAL	1	TRUE	1	0.463958517583754	2		563	841	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15378278	15378278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1228	320	799	0	ENST00000263377.2:c.508G>A	p.Glu170Lys	p.E170K	ENST00000263377	NM_058243.2	170	Gag/Aag	4/20	1	2	FACETS	0.891	0.839	0.945	0.891	0.839	0.945	CLONAL	1	TRUE	1	0.463958517583754	2		799	1548	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278025	18278025	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	150	404	2	ENST00000222254.8:c.1645C>T	p.Gln549Ter	p.Q549*	ENST00000222254	NM_005027.3	549	Cag/Tag	13/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.463958517583754	2		406	600	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257121	19257121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1368664931	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	82	289	0	ENST00000162023.5:c.842C>T	p.Ser281Leu	p.S281L	ENST00000162023		281	tCg/tTg	12/13	1	2	FACETS	0.935	0.83	1	0.935	0.83	1	CLONAL	1	TRUE	1	0.463958517583754	2		289	378	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523368	9523368	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs6118639	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	150	440	0	ENST00000353224.5:c.1870-1G>A		p.X624_splice	ENST00000353224	NM_177990.2	624			1	2	FACETS	0.922	0.845	1	0.922	0.845	1	CLONAL	1	TRUE	1	0.463958517583754	2		440	701	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561097	9561097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	117	308	0	ENST00000353224.5:c.685G>A	p.Asp229Asn	p.D229N	ENST00000353224	NM_177990.2	229	Gat/Aat	4/10	1	2	FACETS	0.937	0.849	1	0.937	0.849	1	CLONAL	1	TRUE	1	0.463958517583754	2		308	538	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739023	40739023	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	313	412	0	ENST00000373198.4:c.3261G>C	p.Gln1087His	p.Q1087H	ENST00000373198	NM_133170.3	1087	caG/caC	24/32	0.463958517583754	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.463958517583754	3		412	811	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875904	76875904	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	250	565	1	ENST00000373344.5:c.5231T>A	p.Ile1744Asn	p.I1744N	ENST00000373344	NM_000489.3	1744	aTt/aAt	20/35	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.463958517583754	2		566	973	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939409	76939409	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	239	594	0	ENST00000373344.5:c.1339G>A	p.Glu447Lys	p.E447K	ENST00000373344	NM_000489.3	447	Gaa/Aaa	9/35	1	2	FACETS	0.913	0.851	0.976	0.913	0.851	0.976	CLONAL	1	TRUE	1	0.463958517583754	2		594	1129	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185169	123185169	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	141	403	0	ENST00000218089.9:c.1121G>A	p.Arg374Lys	p.R374K	ENST00000218089	NM_001042749.1	374	aGa/aAa	13/35	1	2	FACETS	0.861	0.786	0.939	0.861	0.786	0.939	CLONAL	1	TRUE	1	0.463958517583754	2		403	706	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577501	7577501	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	rs1427471466	NA	P-0011467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	163	459	0	ENST00000269305.4:c.780del	p.Ser261ValfsTer84	p.S261Vfs*84	ENST00000269305	NM_001126112.2	260	tcC/tc	7/11	0.463958517583754	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.463958517583754	1		459	522	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393216	393216	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	99	498	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	0.323367045903244	NA		498	791	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0011537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	469	764	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	0.869950509308507	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.869950509308507	2		764	507	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174379	11174379	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1200645333	NA	P-0011537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	511	315	0	ENST00000361445.4:c.7296G>A	p.Met2432Ile	p.M2432I	ENST00000361445	NM_004958.3	2432	atG/atA	53/58	0.194065424559821	6	FACETS	0.97	0.938	1			1	INDETERMINATE	4	TRUE	NA	0.869950509308507	6		315	830	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412187	63412187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	750	322	1	ENST00000330258.3:c.980G>A	p.Gly327Asp	p.G327D	ENST00000330258	NM_152424.3	327	gGt/gAt	2/2	0.528239579810047	2	FACETS	1	0.998	1			1	CLONAL	2	TRUE	NA	0.869950509308507	2		323	797	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039133	49039134	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GA	GA	CC	novel	NA	P-0011537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	168	178	0	ENST00000267163.4:c.2212-1_2212delinsCC		p.X738_splice	ENST00000267163	NM_000321.2	738		22/27	0.869950509308507	2	FACETS	0.99	0.954	1	0.99	0.954	1	CLONAL	2	TRUE	0	0.869950509308507	2		178	195	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0011555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	117	492	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.401472494702766	4	FACETS	1	0.941	1			1	CLONAL	2	TRUE	NA	0.528734890939252	4		492	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0011555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	61	807	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.492135035613284	2	FACETS	0.764	0.676	0.854	0.764	0.676	0.854	SUBCLONAL	2	TRUE	0	0.528734890939252	2		807	151	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836312	89836312	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	260	497	0	ENST00000389301.3:c.2437C>T	p.Pro813Ser	p.P813S	ENST00000389301	NM_000135.2	813	Cct/Tct	26/43	0.529406823665002	5	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	2	0.528734890939252	5		497	521	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956233	175956233	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	59	307	0	ENST00000367669.3:c.1979A>C	p.Glu660Ala	p.E660A	ENST00000367669	NM_022457.5	660	gAa/gCa	18/20	0.233116186945077	3	FACETS	0.904	0.797	1	0.603	0.531	0.677	INDETERMINATE	2	TRUE	0	0.528734890939252	3		307	156	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879559	151879559	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	95	304	0	ENST00000262189.6:c.5386C>T	p.Gln1796Ter	p.Q1796*	ENST00000262189	NM_170606.2	1796	Cag/Tag	36/59	0.371983334638035	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.528734890939252	4		304	229	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645884	215645921	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTTGCTTAGATTCCTCTTTGGAGTCAAATTCACCAT	CTTTTGCTTAGATTCCTCTTTGGAGTCAAATTCACCAT	-	novel	NA	P-0011555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	22	687	0	ENST00000260947.4:c.677_714del	p.Asp226AlafsTer6	p.D226Afs*6	ENST00000260947	NM_000465.2	226	gATGGTGAATTTGACTCCAAAGAGGAATCTAAGCAAAAG/g	4/11	0.466341778159509	4	FACETS	0.31	0.24	0.392	0.155	0.12	0.196	SUBCLONAL	1	TRUE	2	0.528734890939252	4		687	410	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057796	27057796	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012048-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	112	1192	1	ENST00000324856.7:c.1504C>T	p.Gln502Ter	p.Q502*	ENST00000324856	NM_006015.4	502	Cag/Tag	3/20	0.61900580987206	1	FACETS	0.175	0.156	0.194	0.175	0.156	0.194	SUBCLONAL	1	TRUE	0	0.711237111677637	1		1193	1162	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857968	9857968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779746293	NA	P-0012048-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	366	716	2	ENST00000330684.3:c.3433G>A	p.Val1145Met	p.V1145M	ENST00000330684	NM_001134407.1	1145	Gtg/Atg	13/13	1	2	FACETS	0.915	0.869	0.962	0.915	0.869	0.962	CLONAL	1	TRUE	1	0.711237111677637	2		718	1125	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984837	72984837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761672999	NA	P-0012048-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	176	825	0	ENST00000268489.5:c.2747G>A	p.Arg916Gln	p.R916Q	ENST00000268489	NM_006885.3	916	cGg/cAg	3/10	0.711237111677637	1	FACETS	0.437	0.404	0.472	0.437	0.404	0.472	SUBCLONAL	1	TRUE	0	0.711237111677637	1		825	729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577111	7577111	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs786202082	NA	P-0012443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	730	568	0	ENST00000269305.4:c.827C>G	p.Ala276Gly	p.A276G	ENST00000269305	NM_001126112.2	276	gCc/gGc	8/11	0.740381047210247	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.740381047210247	1		568	1211	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559779	29559779	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555614947	NA	P-0012443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	595	473	0	ENST00000356175.3:c.3376C>T	p.Gln1126Ter	p.Q1126*	ENST00000356175	NM_000267.3	1126	Caa/Taa	26/57	0.740381047210247	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.740381047210247	1		473	995	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538378	9538378	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	322	378	0	ENST00000353224.5:c.1620G>C	p.Met540Ile	p.M540I	ENST00000353224	NM_177990.2	540	atG/atC	7/10	0.425362080679624	1	FACETS	0.704	0.668	0.74	0.704	0.668	0.74	INDETERMINATE	1	TRUE	0	0.740381047210247	1		378	778	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0012599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	320	489	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.261948273259784	5	FACETS	0.998	0.943	1	0.665	0.629	0.703	INDETERMINATE	2	TRUE	2	0.552858120358389	5		489	1061	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203436	NA	P-0012599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	155	327	0	ENST00000269305.4:c.487T>C	p.Tyr163His	p.Y163H	ENST00000269305	NM_001126112.2	163	Tac/Cac	5/11	0.421006247322234	3	FACETS	0.921	0.844	1	0.461	0.422	0.501	CLONAL	1	TRUE	1	0.552858120358389	3		327	777	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867518	35867518	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs548638151	NA	P-0012599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	187	254	0	ENST00000303115.3:c.332T>C	p.Val111Ala	p.V111A	ENST00000303115	NM_002185.3	111	gTt/gCt	3/8	0.217487802563849	6	FACETS	1	0.986	1	0.832	0.773	0.891	INDETERMINATE	2	TRUE	3	0.552858120358389	6		254	571	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	238	279	0	ENST00000269305.4:c.542del	p.Arg181ProfsTer66	p.R181Pfs*66	ENST00000269305	NM_001126112.2	181	cGc/cc	5/11	0.421006247322234	3	FACETS	0.878	0.825	0.931	0.878	0.825	0.931	CLONAL	2	TRUE	1	0.552858120358389	3		279	626	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910976	32910977	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1579	87	741	1	ENST00000380152.3:c.2489dup	p.Asn830LysfsTer3	p.N830Kfs*3	ENST00000380152		828	-/A	11/27	0.437006927747439	4	FACETS	0.293	0.258	0.331	0.147	0.129	0.166	SUBCLONAL	1	TRUE	2	0.552858120358389	4		742	1666	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0012653-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	570	730	2	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.57190776744615	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.57190776744615	2		732	975	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0012653-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	440	607	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.57190776744615	3	FACETS	0.961	0.919	1	0.961	0.919	1	CLONAL	2	TRUE	1	0.57190776744615	3		607	1030	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0012653-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	476	327	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.57190776744615	2	FACETS	0.924	0.889	0.958	0.924	0.889	0.958	CLONAL	2	TRUE	0	0.57190776744615	2		327	901	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076870	41076870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751972373	NA	P-0012653-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	539	819	2	ENST00000373198.4:c.1550C>T	p.Thr517Met	p.T517M	ENST00000373198	NM_133170.3	517	aCg/aTg	9/32	0.226514010116795	3	FACETS	0.979	0.941	1			1	INDETERMINATE	2	TRUE	NA	0.57190776744615	3		821	1238	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0012730-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	455	399	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.482888727056897	4	FACETS	1	0.985	1			1	CLONAL	2	TRUE	NA	0.760746027570971	4		399	998	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0012730-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	11	443	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	0.760746027570971	1	FACETS	0.037	0.025	0.052	0.037	0.025	0.052	SUBCLONAL	1	TRUE	0	0.760746027570971	1		443	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0012730-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	322	386	0	ENST00000269305.4:c.920-2A>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.718794487890419	2	FACETS	0.987	0.953	1	0.987	0.953	1	CLONAL	2	TRUE	0	0.760746027570971	2		386	429	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405541	70405541	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs72799515	NA	P-0012730-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	331	342	0	ENST00000373644.4:c.3055A>G	p.Lys1019Glu	p.K1019E	ENST00000373644	NM_030625.2	1019	Aaa/Gaa	4/12	0.760746027570971	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.760746027570971	2		342	418	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862850	9862850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751455326	NA	P-0012730-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	328	584	0	ENST00000330684.3:c.2453C>T	p.Ala818Val	p.A818V	ENST00000330684	NM_001134407.1	818	gCg/gTg	12/13	0.760746027570971	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.760746027570971	1		584	472	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248487	59248487	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012730-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	321	518	0	ENST00000371222.2:c.256G>T	p.Gly86Trp	p.G86W	ENST00000371222	NM_002228.3	86	Ggg/Tgg	1/1	0.155853165342886	3	FACETS	1	0.995	1	0.495	0.469	0.52	INDETERMINATE	1	TRUE	0	0.760746027570971	3		518	785	SUCCESS
APC	324	MSKCC	GRCh37	5	112154972	112154972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756336949	NA	P-0012730-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	563	527	0	ENST00000257430.4:c.1243G>A	p.Ala415Thr	p.A415T	ENST00000257430	NM_000038.5	415	Gct/Act	10/16	0.369135158545001	3	FACETS	1	0.996	1	0.782	0.758	0.805	INDETERMINATE	2	TRUE	0	0.760746027570971	3		527	871	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120658	94120658	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012730-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	864	1126	0	ENST00000369303.4:c.393C>G	p.Asp131Glu	p.D131E	ENST00000369303	NM_004440.3	131	gaC/gaG	3/17	0.760746027570971	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.760746027570971	2		1126	1105	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55229241	55229241	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012730-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	201	471	0	ENST00000275493.2:c.1548G>A	p.Trp516Ter	p.W516*	ENST00000275493	NM_005228.3	516	tgG/tgA	13/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.760746027570971	2		471	484	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331600	8331600	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012730-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	338	712	0	ENST00000356435.5:c.5516C>A	p.Pro1839His	p.P1839H	ENST00000356435		1839	cCc/cAc	33/35	0.760746027570971	1	FACETS	0.684	0.65	0.718	0.684	0.65	0.718	SUBCLONAL	1	TRUE	0	0.760746027570971	1		712	805	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815652	139815652	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767258846	NA	P-0012730-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	298	868	2	ENST00000247668.2:c.1123G>A	p.Ala375Thr	p.A375T	ENST00000247668	NM_021138.3	375	Gcc/Acc	9/11	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.760746027570971	2		870	782	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576277	88576277	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0012730-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	126	207	0	ENST00000360948.2:c.1397-1G>T		p.X466_splice	ENST00000360948	NM_001012338.2	466			0.760746027570971	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.760746027570971	1		207	177	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141493	11141493	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs11537675	NA	P-0012730-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	367	571	2	ENST00000358026.2:c.3470G>T	p.Arg1157Leu	p.R1157L	ENST00000358026	NM_001128849.1	1157	cGg/cTg	25/36	0.760746027570971	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.760746027570971	1		573	500	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537177	80537177	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012730-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	116	268	0	ENST00000286548.4:c.221del	p.Gly74AlafsTer17	p.G74Afs*17	ENST00000286548	NM_002072.3	74	gGc/gc	2/7	1	2	FACETS	0.842	0.767	0.92	0.842	0.767	0.92	CLONAL	1	TRUE	1	0.760746027570971	2		268	362	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0012736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	405	539	0	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.511166874756829	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.511166874756829	2		539	745	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023055	33023055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	169	669	0	ENST00000300177.4:c.164C>T	p.Ser55Phe	p.S55F	ENST00000300177	NM_001191322.1	55	tCc/tTc	2/2	1	2	FACETS	0.873	0.805	0.945	0.873	0.805	0.945	CLONAL	1	TRUE	1	0.511166874756829	2		669	757	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600324	10600324	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	377	561	0	ENST00000171111.5:c.1531G>T	p.Gly511Cys	p.G511C	ENST00000171111	NM_203500.1	511	Ggc/Tgc	4/6	0.511166874756829	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.511166874756829	2		561	679	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092801	27092801	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	166	579	0	ENST00000324856.7:c.2822T>C	p.Ile941Thr	p.I941T	ENST00000324856	NM_006015.4	941	aTc/aCc	9/20	0.509707349078762	3	FACETS	1	0.931	1	0.507	0.466	0.549	CLONAL	1	TRUE	1	0.511166874756829	3		579	805	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834576	156834576	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	168	653	1	ENST00000524377.1:c.344C>A	p.Pro115His	p.P115H	ENST00000524377	NM_002529.3	115	cCt/cAt	3/17	0.511166874756829	3	FACETS	0.696	0.638	0.756	0.348	0.319	0.378	SUBCLONAL	1	TRUE	1	0.511166874756829	3		654	1186	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724530	162724530	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	131	508	0	ENST00000367921.3:c.302G>T	p.Gly101Val	p.G101V	ENST00000367921	NM_006182.2	101	gGg/gTg	5/18	0.511166874756829	3	FACETS	0.652	0.591	0.717	0.326	0.295	0.359	SUBCLONAL	1	TRUE	1	0.511166874756829	3		508	987	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158637113	158637113	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0012736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	428	681	0	ENST00000263640.3:c.68-1G>C		p.X23_splice	ENST00000263640	NM_001105.4	23			0.509707349078762	3	FACETS	0.956	0.913	0.999	0.956	0.913	0.999	CLONAL	2	TRUE	1	0.511166874756829	3		681	1100	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265576	198265576	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	192	686	1	ENST00000335508.6:c.2581G>T	p.Ala861Ser	p.A861S	ENST00000335508	NM_012433.2	861	Gcc/Tcc	18/25	0.509707349078762	3	FACETS	0.853	0.788	0.921	0.426	0.394	0.461	CLONAL	1	TRUE	1	0.511166874756829	3		687	1106	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940103	49940103	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1334727093	NA	P-0012736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	547	802	0	ENST00000296474.3:c.940G>T	p.Gly314Cys	p.G314C	ENST00000296474	NM_002447.2	314	Ggc/Tgc	1/20	0.508109038697353	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.511166874756829	2		802	1034	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	163148700	163148700	+	start_lost	Translation_Start_Site	SNP	T	T	C	rs772786691	NA	P-0012736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	373	618	0	ENST00000366898.1:c.1A>G	p.Met1?	p.M1?	ENST00000366898	NM_004562.2	1	Atg/Gtg	1/12	0.509707349078762	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.511166874756829	3		618	879	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509208	106509208	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	188	596	1	ENST00000359195.3:c.1202C>A	p.Pro401His	p.P401H	ENST00000359195	NM_002649.2	401	cCc/cAc	2/11	0.509707349078762	3	FACETS	0.907	0.838	0.979	0.454	0.419	0.49	CLONAL	1	TRUE	1	0.511166874756829	3		597	1018	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044488	5044488	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	354	536	3	ENST00000381652.3:c.436G>T	p.Asp146Tyr	p.D146Y	ENST00000381652	NM_004972.3	146	Gat/Tat	5/25	0.511166874756829	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.511166874756829	2		539	683	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126786	5126786	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	236	393	0	ENST00000381652.3:c.3394G>T	p.Gly1132Ter	p.G1132*	ENST00000381652	NM_004972.3	1132	Gga/Tga	25/25	0.511166874756829	2	FACETS	0.92	0.868	0.972	0.92	0.868	0.972	CLONAL	2	TRUE	0	0.511166874756829	2		393	502	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5463076	5463076	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0012736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	197	320	0	ENST00000381577.3:c.637A>T	p.Arg213Ter	p.R213*	ENST00000381577	NM_014143.3	213	Aga/Tga	4/7	0.511166874756829	2	FACETS	0.913	0.857	0.97	0.913	0.857	0.97	CLONAL	2	TRUE	0	0.511166874756829	2		320	422	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331695	8331695	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	479	572	0	ENST00000356435.5:c.5421C>A	p.Asp1807Glu	p.D1807E	ENST00000356435		1807	gaC/gaA	33/35	0.511166874756829	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.511166874756829	2		572	863	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912159	114912159	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	304	927	0	ENST00000543371.1:c.1229A>T	p.His410Leu	p.H410L	ENST00000543371	NM_001198531.1	410	cAt/cTt	11/14	1	2	FACETS	0.934	0.88	0.991	0.934	0.88	0.991	CLONAL	1	TRUE	1	0.511166874756829	2		927	1273	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414301	32414301	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs869025561	NA	P-0012736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	100	449	1	ENST00000332351.3:c.1250G>T	p.Gly417Val	p.G417V	ENST00000332351	NM_024426.4	417	gGt/gTt	8/10	0.509707349078762	3	FACETS	0.834	0.747	0.927	0.417	0.373	0.464	CLONAL	1	TRUE	1	0.511166874756829	3		450	589	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610261	81610261	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	147	478	0	ENST00000298171.2:c.1859C>A	p.Thr620Asn	p.T620N	ENST00000298171	NM_000369.2	620	aCc/aAc	10/10	1	2	FACETS	0.993	0.911	1	0.993	0.911	1	CLONAL	1	TRUE	1	0.511166874756829	2		478	579	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66679734	66679734	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	218	635	0	ENST00000307102.5:c.49G>T	p.Gly17Cys	p.G17C	ENST00000307102	NM_002755.3	17	Ggc/Tgc	1/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.511166874756829	2		635	825	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370277	40370277	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	813	945	3	ENST00000293328.3:c.1061T>C	p.Leu354Pro	p.L354P	ENST00000293328	NM_012448.3	354	cTg/cCg	9/19	0.136194044432043	4	FACETS	0.912	0.889	0.936			1	INDETERMINATE	4	TRUE	NA	0.511166874756829	4		948	1317	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288499	15288499	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	64	267	0	ENST00000263388.2:c.4240G>T	p.Gly1414Cys	p.G1414C	ENST00000263388	NM_000435.2	1414	Ggc/Tgc	24/33	0.511166874756829	2	FACETS	1	0.885	1	0.505	0.442	0.571	CLONAL	1	TRUE	0	0.511166874756829	2		267	248	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024416	31024416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	395	579	0	ENST00000375687.4:c.3901G>A	p.Gly1301Arg	p.G1301R	ENST00000375687	NM_015338.5	1301	Ggg/Agg	13/13	0.332969989210163	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.511166874756829	4		579	1113	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714442	40714442	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	230	492	0	ENST00000373198.4:c.3955C>A	p.Gln1319Lys	p.Q1319K	ENST00000373198	NM_133170.3	1319	Cag/Aag	29/32	0.332969989210163	4	FACETS	0.832	0.778	0.888	0.832	0.778	0.888	CLONAL	2	TRUE	2	0.511166874756829	4		492	817	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675375	241675376	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0012736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1359	153	553	0	ENST00000366560.3:c.446_447del	p.Thr149LysfsTer6	p.T149Kfs*6	ENST00000366560	NM_000143.3	149	aCA/a	4/10	0.486998263369379	6	FACETS	0.801	0.73	0.875	0.16	0.146	0.175	CLONAL	1	TRUE	1	0.511166874756829	6		553	1512	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494633	2494633	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	161	590	0	ENST00000355716.4:c.773del	p.Leu258ArgfsTer44	p.L258Rfs*44	ENST00000355716	NM_003820.2	258	cTg/cg	8/8	0.509707349078762	3	FACETS	0.912	0.837	0.991	0.456	0.418	0.496	CLONAL	1	TRUE	1	0.511166874756829	3		590	867	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624488	93624489	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0012736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	206	412	0	ENST00000375746.1:c.579_580delinsTT	p.Ile194Phe	p.I194F	ENST00000375746	NM_001174167.1	193	ctGAtc/ctTTtc	4/14	0.511166874756829	2	FACETS	0.92	0.865	0.976	0.92	0.865	0.976	CLONAL	2	TRUE	0	0.511166874756829	2		412	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0012808-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	665	586	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.777154637483286	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.777154637483286	2		586	830	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435843	149435843	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs281860274	NA	P-0012808-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	361	553	0	ENST00000286301.3:c.2381T>C	p.Ile794Thr	p.I794T	ENST00000286301	NM_005211.3	794	aTt/aCt	18/22	1	2	FACETS	0.94	0.894	0.988	0.94	0.894	0.988	CLONAL	1	TRUE	1	0.777154637483286	2		553	988	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975450	13975450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012808-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	247	372	0	ENST00000405192.2:c.437C>T	p.Ser146Phe	p.S146F	ENST00000405192	NM_001163147.1	146	tCc/tTc	7/12	0.777154637483286	2	FACETS	0.943	0.887	1	0.472	0.443	0.5	CLONAL	1	TRUE	0	0.777154637483286	2		372	674	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41276094	41276094	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144792613	NA	P-0012808-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	568	387	0	ENST00000357654.3:c.20G>A	p.Arg7His	p.R7H	ENST00000357654	NM_007294.3	7	cGc/cAc	2/23	NA	2	FACETS	0.993	0.969	1			1	INDETERMINATE	2	TRUE	NA	0.777154637483286	2		387	736	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260129	19260129	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012808-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	412	539	0	ENST00000162023.5:c.164T>C	p.Phe55Ser	p.F55S	ENST00000162023		55	tTc/tCc	7/13	0.691839093018492	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.777154637483286	1		539	620	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385045	31385045	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012808-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	113	536	0	ENST00000328111.2:c.1430A>G	p.Tyr477Cys	p.Y477C	ENST00000328111	NM_006892.3	477	tAc/tGc	14/23	0.777154637483286	3	FACETS	0.34	0.305	0.377	0.17	0.152	0.189	SUBCLONAL	1	TRUE	1	0.777154637483286	3		536	1188	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1327723	1327723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012808-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	362	579	1	ENST00000400841.2:c.158G>A	p.Arg53Lys	p.R53K	ENST00000400841		53	aGg/aAg	2/6	0.777154637483286	3	FACETS	1	0.966	1	0.513	0.486	0.54	CLONAL	1	TRUE	1	0.777154637483286	3		580	1262	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410566	63410566	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012808-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1878	502	930	1	ENST00000330258.3:c.2601C>G	p.Ser867Arg	p.S867R	ENST00000330258	NM_152424.3	867	agC/agG	2/2	0.68410031311849	4	FACETS	0.965	0.92	1			1	CLONAL	1	TRUE	NA	0.777154637483286	4		931	2380	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185195	123185195	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012808-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	333	561	0	ENST00000218089.9:c.1147G>A	p.Glu383Lys	p.E383K	ENST00000218089	NM_001042749.1	383	Gaa/Aaa	13/35	0.329257361656946	3	FACETS	0.989	0.935	1			1	INDETERMINATE	1	TRUE	NA	0.777154637483286	3		561	1203	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722232	176722233	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	TT	novel	NA	P-0012808-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	363	641	1	ENST00000439151.2:c.7863_7864delinsTT	p.Glu2621_Gln2622delinsAspTer	p.E2621_Q2622delinsD*	ENST00000439151	NM_022455.4	2621	gaGCaa/gaTTaa	23/23	1	2	FACETS	0.972	0.925	1	0.972	0.925	1	CLONAL	1	TRUE	1	0.777154637483286	2		642	961	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0012832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	187	542	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.244936711887525	2	FACETS	0.979	0.907	1	0.979	0.907	1	CLONAL	2	TRUE	0	0.26	2		542	735	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0012832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	44	166	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.244936711887525	2	FACETS	0.975	0.821	1	0.488	0.41	0.573	CLONAL	1	TRUE	0	0.26	2		166	347	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	119	403	0	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	1	2	FACETS	0.957	0.862	1	0.957	0.862	1	CLONAL	1	TRUE	1	0.26	2		403	957	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937219	36937219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140159756	NA	P-0012832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1302	429	736	1	ENST00000361632.4:c.1100G>A	p.Arg367Gln	p.R367Q	ENST00000361632		367	cGg/cAg	9/16	0.244936711887525	2	FACETS	0.953	0.906	1	0.953	0.906	1	CLONAL	2	TRUE	0	0.26	2		737	1731	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630626	158630626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912678	NA	P-0012832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1556	224	660	1	ENST00000263640.3:c.617G>A	p.Arg206His	p.R206H	ENST00000263640	NM_001105.4	206	cGc/cAc	6/11	1	2	FACETS	0.968	0.898	1	0.968	0.898	1	CLONAL	1	TRUE	1	0.26	2		661	1780	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030463	47030463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781862400	NA	P-0012832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1246	193	640	1	ENST00000377604.3:c.238C>T	p.Arg80Cys	p.R80C	ENST00000377604	NM_001204468.1	80	Cgt/Tgt	4/24	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.26	2		641	1439	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259598	89259598	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	61	252	0	ENST00000336596.2:c.742G>C	p.Gly248Arg	p.G248R	ENST00000336596	NM_005233.5	248	Ggc/Cgc	3/17	1	2	FACETS	0.938	0.811	1	0.938	0.811	1	CLONAL	1	TRUE	1	0.26	2		252	500	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674230	117674230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1406	215	674	2	ENST00000368508.3:c.4244G>A	p.Gly1415Glu	p.G1415E	ENST00000368508	NM_002944.2	1415	gGg/gAg	26/43	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.26	2		676	1621	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645326	67645326	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0012832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	121	468	1	ENST00000264010.4:c.591T>A	p.Tyr197Ter	p.Y197*	ENST00000264010	NM_006565.3	197	taT/taA	3/12	1	2	FACETS	0.89	0.802	0.983	0.89	0.802	0.983	CLONAL	1	TRUE	1	0.26	2		469	1046	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374882	45374882	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs776149698	NA	P-0012832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	133	538	0	ENST00000262160.6:c.961C>T	p.Arg321Ter	p.R321*	ENST00000262160	NM_005901.5	321	Cga/Tga	8/11	1	2	FACETS	0.873	0.791	0.96	0.873	0.791	0.96	CLONAL	1	TRUE	1	0.26	2		538	1172	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727174	40727174	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200157212	NA	P-0012832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	121	428	0	ENST00000373198.4:c.3790G>A	p.Ala1264Thr	p.A1264T	ENST00000373198	NM_133170.3	1264	Gcc/Acc	28/32	1	2	FACETS	0.997	0.899	1	0.997	0.899	1	CLONAL	1	TRUE	1	0.26	2		428	934	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591312	67591323	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAAGAGTAAGTA	GAAGAGTAAGTA	-	novel	NA	P-0012832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	64	322	0	ENST00000274335.5:c.1811_1814+8del		p.X604_splice	ENST00000274335		604		13/15	1	2	FACETS	0.536	0.463	0.616	0.536	0.463	0.616	SUBCLONAL	1	TRUE	1	0.26	2		322	918	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087395	27087396	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	332	583	0	ENST00000324856.7:c.1970dup	p.Ser658GlufsTer18	p.S658Efs*18	ENST00000324856	NM_006015.4	657	ctg/cTtg	5/20	0.244936711887525	2	FACETS	0.918	0.866	0.971	0.918	0.866	0.971	CLONAL	2	TRUE	0	0.26	2		583	1391	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218151	69218151	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20603	1658	365	0	ENST00000462284.1:c.367G>C	p.Asp123His	p.D123H	ENST00000462284	NM_002392.5	123	Gac/Cac	6/11	0.711594504107676	35	FACETS	0.889	0.864	0.915			1	CLONAL	3	TRUE	NA	0.711594504107676	35		365	22261	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218427	69218427	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs778784299	NA	P-0012838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18391	1472	374	0	ENST00000462284.1:c.519G>C	p.Glu173Asp	p.E173D	ENST00000462284	NM_002392.5	173	gaG/gaC	7/11	0.711594504107676	35	FACETS	0.885	0.858	0.911			1	CLONAL	3	TRUE	NA	0.711594504107676	35		374	19863	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889088	76889088	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	539	751	1	ENST00000373344.5:c.4922G>A	p.Trp1641Ter	p.W1641*	ENST00000373344	NM_000489.3	1641	tGg/tAg	18/35	0.340214366835836	1	FACETS	0.74	0.711	0.769	0.74	0.711	0.769	INDETERMINATE	1	TRUE	0	0.711594504107676	1		752	1319	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45377691	45377692	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0012838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	29	263	0	ENST00000262160.6:c.737dup	p.Ala247SerfsTer12	p.A247Sfs*12	ENST00000262160	NM_005901.5	246	cca/ccCa	7/11	1	2	FACETS	0.158	0.126	0.195	0.158	0.126	0.195	SUBCLONAL	1	TRUE	1	0.711594504107676	2		263	515	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781181	135781181	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	502	977	2	ENST00000298552.3:c.1784G>T	p.Gly595Val	p.G595V	ENST00000298552	NM_001162426.1	595	gGc/gTc	15/23	0.713645819508639	2	FACETS	1	0.959	1	0.501	0.479	0.522	CLONAL	1	TRUE	0	0.731011871928205	2		979	1372	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30954260	30954260	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	358	530	0	ENST00000375687.4:c.131A>G	p.Lys44Arg	p.K44R	ENST00000375687	NM_015338.5	44	aAg/aGg	2/13	0.705763376759791	3	FACETS	0.921	0.871	0.972	0.461	0.435	0.486	CLONAL	1	TRUE	1	0.731011871928205	3		530	1452	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1365	291	174	0				ENST00000310581	NM_198253.2	-/1132			0.700894435565275	7	FACETS	1	0.992	1	0.276	0.259	0.294	CLONAL	1	TRUE	2	0.700894435565275	7		174	1656	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	272	515	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.616184638823199	5	FACETS	0.949	0.9	0.998	0.949	0.9	0.998	CLONAL	3	TRUE	2	0.700894435565275	5		515	559	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604515	43604515	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs763759702	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	238	674	0	ENST00000355710.3:c.1100A>G	p.Asn367Ser	p.N367S	ENST00000355710	NM_020975.4	367	aAc/aGc	6/20	0.614219466555983	3	FACETS	0.805	0.751	0.861	0.403	0.375	0.431	CLONAL	1	TRUE	1	0.700894435565275	3		674	1139	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012253	152012253	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1563831738	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	617	733	0	ENST00000262189.6:c.560C>G	p.Ser187Ter	p.S187*	ENST00000262189	NM_170606.2	187	tCa/tGa	4/59	0.614219466555983	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.700894435565275	3		733	1127	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	769	430	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.547815899982881	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.700894435565275	4		431	1852	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	608	440	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.547815899982881	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.700894435565275	4		440	1445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576886	7576886	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	456	711	0	ENST00000269305.4:c.960G>C	p.Lys320Asn	p.K320N	ENST00000269305	NM_001126112.2	320	aaG/aaC	9/11	0.547815899982881	4	FACETS	0.955	0.914	0.996	0.955	0.914	0.996	CLONAL	2	TRUE	2	0.700894435565275	4		711	1159	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778535	3778535	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1301	109	1043	0	ENST00000262367.5:c.6513G>C	p.Leu2171Phe	p.L2171F	ENST00000262367	NM_004380.2	2171	ttG/ttC	31/31	0.606414985090541	2	FACETS	0.221	0.197	0.246	0.11	0.098	0.123	SUBCLONAL	1	TRUE	0	0.700894435565275	2		1043	1410	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257653	16257653	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	286	627	0	ENST00000375759.3:c.4918C>G	p.Pro1640Ala	p.P1640A	ENST00000375759	NM_015001.2	1640	Cca/Gca	11/15	1	2	FACETS	0.939	0.886	0.994	0.939	0.886	0.994	CLONAL	1	TRUE	1	0.700894435565275	2		627	869	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919590	96919590	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	832	783	0	ENST00000258439.3:c.673G>A	p.Glu225Lys	p.E225K	ENST00000258439	NM_001193304.2	225	Gag/Aag	4/4	0.700894435565275	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.700894435565275	2		783	1037	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919617	96919617	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	745	725	0	ENST00000258439.3:c.646G>C	p.Glu216Gln	p.E216Q	ENST00000258439	NM_001193304.2	216	Gag/Cag	4/4	0.700894435565275	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.700894435565275	2		725	933	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72897461	72897461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	417	418	0	ENST00000325599.8:c.31G>A	p.Asp11Asn	p.D11N	ENST00000325599	NM_018130.2	11	Gat/Aat	1/11	0.700894435565275	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.700894435565275	2		418	527	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119642324	119642324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	141	311	0	ENST00000316626.5:c.373G>A	p.Glu125Lys	p.E125K	ENST00000316626		125	Gag/Aag	4/12	0.179372942954992	5	FACETS	0.869	0.797	0.943			1	INDETERMINATE	2	TRUE	NA	0.700894435565275	5		311	475	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612166	189612166	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	782	621	0	ENST00000264731.3:c.1918G>A	p.Asp640Asn	p.D640N	ENST00000264731	NM_003722.4	640	Gat/Aat	14/14	0.406435259538043	4	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.700894435565275	4		621	1716	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55962434	55962434	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1190176904	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	468	690	0	ENST00000263923.4:c.2690A>G	p.Asn897Ser	p.N897S	ENST00000263923	NM_002253.2	897	aAt/aGt	19/30	0.262036286705773	5	FACETS	1	0.994	1	0.822	0.788	0.857	INDETERMINATE	2	TRUE	2	0.700894435565275	5		690	1111	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197571	106197571	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	387	628	0	ENST00000380013.4:c.5904C>G	p.Ile1968Met	p.I1968M	ENST00000380013	NM_001127208.2	1968	atC/atG	11/11	0.262036286705773	5	FACETS	0.935	0.889	0.982	0.624	0.593	0.655	INDETERMINATE	2	TRUE	2	0.700894435565275	5		628	1211	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032099	26032099	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1807	734	1319	0	ENST00000244661.2:c.190C>G	p.Arg64Gly	p.R64G	ENST00000244661	NM_003537.3	64	Cgg/Ggg	1/1	0.633699244464718	3	FACETS	1	0.993	1	0.557	0.536	0.578	CLONAL	1	TRUE	1	0.700894435565275	3		1319	2541	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912169	29912169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41545513	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	105	124	0	ENST00000376809.5:c.890G>A	p.Arg297Lys	p.R297K	ENST00000376809	NM_002116.7	297	aGa/aAa	4/8	0.633699244464718	3	FACETS	0.819	0.748	0.891	0.819	0.748	0.891	CLONAL	2	TRUE	1	0.700894435565275	3		124	247	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790830	89790830	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	359	577	0	ENST00000336032.3:c.217C>G	p.Arg73Gly	p.R73G	ENST00000336032	NM_006813.2	73	Cgc/Ggc	1/2	0.633699244464718	3	FACETS	1	0.991	1	0.594	0.563	0.625	CLONAL	1	TRUE	1	0.700894435565275	3		577	1165	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554962	106554962	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	236	489	0	ENST00000369096.4:c.2079C>A	p.His693Gln	p.H693Q	ENST00000369096	NM_001198.3	693	caC/caA	7/7	0.633699244464718	3	FACETS	1	0.954	1	0.513	0.479	0.547	CLONAL	1	TRUE	1	0.700894435565275	3		489	887	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609696	117609696	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	400	489	0	ENST00000368508.3:c.7003G>C	p.Ala2335Pro	p.A2335P	ENST00000368508	NM_002944.2	2335	Gcc/Ccc	43/43	0.339177967845608	3	FACETS	1	0.981	1			1	INDETERMINATE	2	TRUE	NA	0.700894435565275	3		489	743	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8339044	8339044	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2446	145	393	0	ENST00000356435.5:c.5257A>G	p.Lys1753Glu	p.K1753E	ENST00000356435		1753	Aaa/Gaa	32/35	0.700894435565275	16	FACETS	0.943	0.856	1	0.067	0.061	0.074	CLONAL	1	TRUE	2	0.700894435565275	16		393	2591	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396938	139396938	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	158	196	0	ENST00000277541.6:c.5170G>T	p.Glu1724Ter	p.E1724*	ENST00000277541	NM_017617.3	1724	Gag/Tag	28/34	0.700894435565275	3	FACETS	1	0.988	1	0.69	0.639	0.743	CLONAL	1	TRUE	1	0.700894435565275	3		196	441	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852428	63852428	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	286	578	0	ENST00000279873.7:c.3206A>G	p.His1069Arg	p.H1069R	ENST00000279873	NM_032199.2	1069	cAc/cGc	10/10	0.614219466555983	3	FACETS	0.846	0.794	0.899	0.423	0.397	0.45	CLONAL	1	TRUE	1	0.700894435565275	3		578	1303	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77054959	77054959	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	241	584	0	ENST00000356341.3:c.903G>A	p.Met301Ile	p.M301I	ENST00000356341	NM_002576.4	301	atG/atA	10/15	0.633699244464718	3	FACETS	1	0.974	1	0.537	0.503	0.573	CLONAL	1	TRUE	1	0.700894435565275	3		584	864	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912771	100912771	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	899	1136	0	ENST00000325455.5:c.2551G>C	p.Glu851Gln	p.E851Q	ENST00000325455	NM_001202474.3	851	Gag/Cag	7/8	0.633699244464718	3	FACETS	0.978	0.95	1	0.978	0.95	1	CLONAL	2	TRUE	1	0.700894435565275	3		1136	1772	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118339557	118339557	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	484	542	0	ENST00000534358.1:c.500C>T	p.Ser167Leu	p.S167L	ENST00000534358	NM_005933.3	167	tCa/tTa	2/36	0.633699244464718	3	FACETS	0.994	0.957	1	0.994	0.957	1	CLONAL	2	TRUE	1	0.700894435565275	3		542	938	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342821	118342821	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	253	563	1	ENST00000534358.1:c.947C>A	p.Ser316Ter	p.S316*	ENST00000534358	NM_005933.3	316	tCg/tAg	3/36	0.633699244464718	3	FACETS	0.975	0.913	1	0.487	0.456	0.52	CLONAL	1	TRUE	1	0.700894435565275	3		564	1000	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374945	118374945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	280	620	1	ENST00000534358.1:c.8338G>A	p.Glu2780Lys	p.E2780K	ENST00000534358	NM_005933.3	2780	Gag/Aag	27/36	0.633699244464718	3	FACETS	1	0.969	1	0.523	0.492	0.556	CLONAL	1	TRUE	1	0.700894435565275	3		621	1031	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404837	404837	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	442	647	0	ENST00000399788.2:c.4357G>A	p.Asp1453Asn	p.D1453N	ENST00000399788	NM_001042603.1	1453	Gat/Aat	26/28	0.20954733125929	5	FACETS	1	0.989	1	0.731	0.699	0.765	INDETERMINATE	2	TRUE	2	0.700894435565275	5		647	1179	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478878	56478878	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1462065910	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	581	982	1	ENST00000267101.3:c.334G>A	p.Asp112Asn	p.D112N	ENST00000267101	NM_001982.3	112	Gat/Aat	3/28	0.20954733125929	5	FACETS	1	0.991	1	0.729	0.7	0.758	INDETERMINATE	2	TRUE	2	0.700894435565275	5		983	1555	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495789	56495789	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	212	297	0	ENST00000267101.3:c.3979G>C	p.Asp1327His	p.D1327H	ENST00000267101	NM_001982.3	1327	Gat/Cat	28/28	0.20954733125929	5	FACETS	1	0.984	1	0.769	0.72	0.818	INDETERMINATE	2	TRUE	2	0.700894435565275	5		297	538	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26978177	26978177	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	532	556	0	ENST00000381527.3:c.1354C>T	p.Gln452Ter	p.Q452*	ENST00000381527	NM_001260.1	452	Cag/Tag	13/13	0.496027622276256	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.700894435565275	4		556	1239	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396717	396717	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	641	647	0	ENST00000262320.3:c.309G>C	p.Arg103Ser	p.R103S	ENST00000262320	NM_003502.3	103	agG/agC	2/11	0.339177967845608	3	FACETS	0.913	0.889	0.936			1	INDETERMINATE	3	TRUE	NA	0.700894435565275	3		647	902	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820936	3820936	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	29	253	1	ENST00000262367.5:c.2515C>T	p.Gln839Ter	p.Q839*	ENST00000262367	NM_004380.2	839	Cag/Tag	14/31	0.606414985090541	2	FACETS	0.218	0.175	0.268	0.109	0.087	0.134	SUBCLONAL	1	TRUE	0	0.700894435565275	2		254	379	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845679	68845679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	965	572	0	ENST00000261769.5:c.925C>T	p.Pro309Ser	p.P309S	ENST00000261769	NM_004360.3	309	Cct/Tct	7/16	0.406435259538043	4	FACETS	0.91	0.892	0.927			1	INDETERMINATE	4	TRUE	NA	0.700894435565275	4		572	1287	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830649	72830649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1863	288	1442	2	ENST00000268489.5:c.5932G>A	p.Glu1978Lys	p.E1978K	ENST00000268489	NM_006885.3	1978	Gag/Aag	9/10	0.47985817603804	3	FACETS	0.516	0.483	0.55	0.172	0.161	0.184	SUBCLONAL	1	TRUE	0	0.700894435565275	3		1444	2151	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89871690	89871690	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	89	486	0	ENST00000389301.3:c.707C>T	p.Ser236Phe	p.S236F	ENST00000389301	NM_000135.2	236	tCt/tTt	7/43	0.404957752520639	5	FACETS	0.534	0.473	0.601	0.107	0.094	0.121	INDETERMINATE	1	TRUE	0	0.700894435565275	5		486	975	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16052790	16052790	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	273	505	0	ENST00000268712.3:c.884G>C	p.Arg295Thr	p.R295T	ENST00000268712	NM_006311.3	295	aGa/aCa	9/46	0.547815899982881	4	FACETS	0.892	0.841	0.943	0.892	0.841	0.943	CLONAL	2	TRUE	2	0.700894435565275	4		505	743	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526131	66526131	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	346	427	0	ENST00000358598.2:c.962C>G	p.Ser321Cys	p.S321C	ENST00000358598	NM_212471.2	321	tCt/tGt	10/11	0.547815899982881	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.700894435565275	4		427	812	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841349	15841349	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	781	456	0	ENST00000307771.7:c.1433G>A	p.Ser478Asn	p.S478N	ENST00000307771	NM_005089.3	478	aGt/aAt	11/11	0.572108006956125	2	FACETS	1	0.998	1			1	CLONAL	2	TRUE	NA	0.700894435565275	2		456	925	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224604	123224604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	531	459	0	ENST00000218089.9:c.3457C>T	p.Leu1153Phe	p.L1153F	ENST00000218089	NM_001042749.1	1153	Ctt/Ttt	31/35	0.572108006956125	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.700894435565275	2		459	657	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922728	44922744	+	frameshift_variant	Frame_Shift_Del	DEL	ACTCATCACTGCCTACA	ACTCATCACTGCCTACA	-	novel	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	611	387	0	ENST00000377967.4:c.1590_1606del	p.Asp530GlufsTer17	p.D530Efs*17	ENST00000377967	NM_021140.2	530	gACTCATCACTGCCTACA/g	16/29	0.572108006956125	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.700894435565275	2		387	764	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979356	93979357	+	missense_variant	Missense_Mutation	DNP	GA	GA	AG	novel	NA	P-0012901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	352	1148	2	ENST00000369303.4:c.1471_1472delinsCT	p.Ser491Leu	p.S491L	ENST00000369303	NM_004440.3	491	TCa/CTa	7/17	0.633699244464718	3	FACETS	1	0.951	1	0.503	0.475	0.531	CLONAL	1	TRUE	1	0.700894435565275	3		1150	1349	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961103	55961103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140041720	NA	P-0012918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	245	585	2	ENST00000263923.4:c.2837G>A	p.Arg946His	p.R946H	ENST00000263923	NM_002253.2	946	cGt/cAt	21/30	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.429396964896165	2		587	1135	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0012945-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	49	399	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.959	0.812	1	0.959	0.812	1	CLONAL	1	TRUE	1	0.17	2		399	601	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0012945-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	35	300	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.65	0.532	0.785	0.65	0.532	0.785	SUBCLONAL	1	TRUE	1	0.17	2		300	633	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900171	101900171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564161322	NA	P-0012945-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	59	606	1	ENST00000374994.4:c.605C>T	p.Ala202Val	p.A202V	ENST00000374994	NM_004612.2	202	gCg/gTg	4/9	1	2	FACETS	0.985	0.846	1	0.985	0.846	1	CLONAL	1	TRUE	1	0.17	2		607	705	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626629	12626629	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012945-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1248	72	815	0	ENST00000251849.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000251849	NM_002880.3	554	Cga/Tga	15/17	1	2	FACETS	0.642	0.558	0.732	0.642	0.558	0.732	SUBCLONAL	1	TRUE	1	0.17	2		815	1320	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442624	52442624	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0012945-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	30	239	0	ENST00000460680.1:c.123-2A>T		p.X41_splice	ENST00000460680	NM_004656.3	41			1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.17	2		239	321	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0012995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	173	540	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	0.569589959418538	4	FACETS	0.897	0.825	0.973	0.449	0.412	0.487	CLONAL	1	TRUE	2	0.595768718923379	4		540	1033	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061147	38061203	+	inframe_deletion	In_Frame_Del	DEL	CCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTGG	CCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTGG	-	novel	NA	P-0012995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	360	213	0	ENST00000250448.2:c.786_842del	p.Gln263_Gly281del	p.Q263_G281del	ENST00000250448	NM_004496.3	262	cgCCAGAAGCGCTTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGa/cga	2/2	0.569589959418538	4	FACETS	1	0.992	1	1	0.997	1	CLONAL	3	TRUE	2	0.595768718923379	4		213	572	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923408	36923408	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	193	652	0	ENST00000358127.4:c.854C>A	p.Thr285Asn	p.T285N	ENST00000358127	NM_001280556.1	285	aCc/aAc	7/10	0.178305949572727	5	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.595768718923379	5		652	937	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785971	135785971	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs77464996	NA	P-0013000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	259	578	1	ENST00000298552.3:c.1250C>T	p.Thr417Ile	p.T417I	ENST00000298552	NM_001162426.1	417	aCa/aTa	12/23	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.561835534702187	2		579	816	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	247	695	0	ENST00000347630.2:c.399C>A	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttA	6/11	1	2	FACETS	0.955	0.894	1	0.955	0.894	1	CLONAL	1	TRUE	1	0.561835534702187	2		695	921	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199604	11199604	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	283	767	0	ENST00000361445.4:c.4984A>C	p.Lys1662Gln	p.K1662Q	ENST00000361445	NM_004958.3	1662	Aag/Cag	35/58	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.561835534702187	2		767	997	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808940	3808940	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	259	740	0	ENST00000262367.5:c.3284T>C	p.Met1095Thr	p.M1095T	ENST00000262367	NM_004380.2	1095	aTg/aCg	17/31	1	2	FACETS	0.855	0.801	0.911	0.855	0.801	0.911	CLONAL	1	TRUE	1	0.561835534702187	2		740	1078	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958378	90958379	+	missense_variant	Missense_Mutation	DNP	TT	TT	AA	novel	NA	P-0013000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	450	508	0	ENST00000265433.3:c.2059_2060inv	p.Lys687Leu	p.K687L	ENST00000265433	NM_002485.4	687	AAa/TTa	13/16	0.550692502560499	4	FACETS	0.923	0.886	0.959	0.923	0.886	0.959	CLONAL	3	TRUE	1	0.561835534702187	4		508	904	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	209	174	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.985	0.926	1			1	INDETERMINATE	1	TRUE	NA	0.920457545865305	2		174	461	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033844	49033844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853294	NA	P-0013005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	344	586	1	ENST00000267163.4:c.1981C>T	p.Arg661Trp	p.R661W	ENST00000267163	NM_000321.2	661	Cgg/Tgg	20/27	0.920457545865305	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.920457545865305	1		587	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0013005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	574	732	0	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.912940253006406	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.920457545865305	1		732	627	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837948	156837948	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755045059	NA	P-0013005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	472	556	2	ENST00000524377.1:c.481C>T	p.Arg161Cys	p.R161C	ENST00000524377	NM_002529.3	161	Cgc/Tgc	5/17	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.920457545865305	2		558	952	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097802	8097802	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1320708723	NA	P-0013005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	548	727	1	ENST00000346208.3:c.184C>A	p.Pro62Thr	p.P62T	ENST00000346208		62	Ccc/Acc	2/6	0.920457545865305	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.920457545865305	1		728	632	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0013007-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	271	482	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	1	2	FACETS	0.91	0.86	0.962	0.91	0.86	0.962	CLONAL	1	TRUE	1	0.880597163934497	2		482	676	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149144	119149285	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAAATGTATTTTCTAGTAGATTAATATTTTAAGTATTTTCAGATGCATCTGTTACTATCTTTTGCTTCTTCTGCAGGAATCAGAAGGTCAGGGCTGTCCTTTCTGCCGATGTGAAATTAAAGGTACTGAACCCATCGTGGTA	GAAATGTATTTTCTAGTAGATTAATATTTTAAGTATTTTCAGATGCATCTGTTACTATCTTTTGCTTCTTCTGCAGGAATCAGAAGGTCAGGGCTGTCCTTTCTGCCGATGTGAAATTAAAGGTACTGAACCCATCGTGGTA	-	novel	NA	P-0013007-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	68	247	0	ENST00000264033.4:c.1228-74_1295del		p.X410_splice	ENST00000264033	NM_005188.3	410		9/16	1	2	FACETS	0.743	0.657	0.832	0.743	0.657	0.832	SUBCLONAL	1	TRUE	1	0.880597163934497	2		247	208	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0013088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	222	327	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	0.57013974566969	2		327	758	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0013088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	127	737	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.57013974566969	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.57013974566969	1		737	312	SUCCESS
APC	324	MSKCC	GRCh37	5	112174784	112174784	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0013088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	147	318	0	ENST00000257430.4:c.3493A>T	p.Lys1165Ter	p.K1165*	ENST00000257430	NM_000038.5	1165	Aaa/Taa	16/16	0.569970569123678	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.57013974566969	1		318	352	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448468	89448468	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	145	322	0	ENST00000336596.2:c.1432C>A	p.Gln478Lys	p.Q478K	ENST00000336596	NM_005233.5	478	Cag/Aag	7/17	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.57013974566969	2		322	474	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253787	153253787	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	171	422	1	ENST00000281708.4:c.946G>T	p.Glu316Ter	p.E316*	ENST00000281708	NM_033632.3	316	Gaa/Taa	6/12	0.57013974566969	1	FACETS	0.893	0.829	0.959	0.893	0.829	0.959	CLONAL	1	TRUE	0	0.57013974566969	1		423	480	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671613	67671624	+	inframe_deletion	In_Frame_Del	DEL	AGACCAGAATAC	AGACCAGAATAC	-	novel	NA	P-0013088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	64	413	0	ENST00000264010.4:c.2024_2035del	p.Asp675_Thr678del	p.D675_T678del	ENST00000264010	NM_006565.3	674	gaAGACCAGAATACa/gaa	12/12	0.57013974566969	1	FACETS	0.315	0.273	0.36	0.315	0.273	0.36	SUBCLONAL	1	TRUE	0	0.57013974566969	1		413	510	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913517	NA	P-0013114-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	275	396	0	ENST00000288135.5:c.1676T>A	p.Val559Asp	p.V559D	ENST00000288135	NM_000222.2	559	gTt/gAt	11/21	1	2	FACETS	0.996	0.939	1	0.996	0.939	1	CLONAL	1	TRUE	1	0.745578782784115	2		396	741	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594258	55594258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913523	NA	P-0013114-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	297	443	0	ENST00000288135.5:c.1961T>C	p.Val654Ala	p.V654A	ENST00000288135	NM_000222.2	654	gTg/gCg	13/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.745578782784115	2		443	758	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	213	336	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.53808223589846	4	FACETS	1	0.982	1	0.742	0.698	0.786	CLONAL	2	TRUE	1	0.749221249530692	4		336	447	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0013144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	397	530	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.749221249530692	3	FACETS	0.945	0.905	0.984	0.945	0.905	0.984	CLONAL	2	TRUE	1	0.749221249530692	3		530	771	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519985	NA	P-0013144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	614	728	0	ENST00000269305.4:c.857A>T	p.Glu286Val	p.E286V	ENST00000269305	NM_001126112.2	286	gAa/gTa	8/11	0.749221249530692	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.749221249530692	2		728	796	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411366	63411366	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	589	421	2	ENST00000330258.3:c.1801C>T	p.Arg601Ter	p.R601*	ENST00000330258	NM_152424.3	601	Cga/Tga	2/2	0.696590469583882	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.749221249530692	2		423	671	SUCCESS
APC	324	MSKCC	GRCh37	5	112173429	112173429	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	161	669	0	ENST00000257430.4:c.2138C>A	p.Ser713Ter	p.S713*	ENST00000257430	NM_000038.5	713	tCa/tAa	16/16	0.749221249530692	3	FACETS	0.967	0.891	1	0.483	0.445	0.523	CLONAL	1	TRUE	1	0.749221249530692	3		669	611	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518014	176518014	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1326935512	NA	P-0013144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	322	794	0	ENST00000292408.4:c.512G>A	p.Arg171His	p.R171H	ENST00000292408	NM_213647.1	171	cGc/cAc	5/18	0.749221249530692	3	FACETS	1	0.965	1	0.514	0.485	0.544	CLONAL	1	TRUE	1	0.749221249530692	3		794	1149	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0013173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	99	515	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.5867005582444	3	FACETS	0.9	0.807	0.998	0.45	0.403	0.499	CLONAL	1	TRUE	1	0.5867005582444	3		515	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0013173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	299	405	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.5867005582444	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.5867005582444	1		405	654	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466522	120466522	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	312	671	0	ENST00000256646.2:c.4597G>T	p.Asp1533Tyr	p.D1533Y	ENST00000256646	NM_024408.3	1533	Gac/Tac	26/34	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.5867005582444	2		671	1026	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460545	149460545	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	198	416	0	ENST00000286301.3:c.92T>G	p.Val31Gly	p.V31G	ENST00000286301	NM_005211.3	31	gTc/gGc	3/22	0.5867005582444	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.5867005582444	1		416	427	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846122	151846122	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	210	477	0	ENST00000262189.6:c.12890A>T	p.Glu4297Val	p.E4297V	ENST00000262189	NM_170606.2	4297	gAg/gTg	52/59	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.5867005582444	2		477	658	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650659	18650659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	143	289	0	ENST00000266497.5:c.2870G>A	p.Cys957Tyr	p.C957Y	ENST00000266497		957	tGt/tAt	20/31	1	2	FACETS	0.995	0.913	1	0.995	0.913	1	CLONAL	1	TRUE	1	0.5867005582444	2		289	490	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426510	49426510	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	311	752	0	ENST00000301067.7:c.11978A>T	p.Gln3993Leu	p.Q3993L	ENST00000301067	NM_003482.3	3993	cAg/cTg	39/54	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.5867005582444	2		752	1043	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432165	49432165	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	228	607	0	ENST00000301067.7:c.8974G>T	p.Glu2992Ter	p.E2992*	ENST00000301067	NM_003482.3	2992	Gag/Tag	34/54	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.5867005582444	2		607	772	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28971147	28971147	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	158	425	0	ENST00000282397.4:c.1610C>A	p.Ala537Asp	p.A537D	ENST00000282397	NM_002019.4	537	gCt/gAt	12/30	0.5867005582444	1	FACETS	0.838	0.775	0.903	0.838	0.775	0.903	CLONAL	1	TRUE	0	0.5867005582444	1		425	454	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831324	72831324	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	258	704	1	ENST00000268489.5:c.5257C>T	p.Gln1753Ter	p.Q1753*	ENST00000268489	NM_006885.3	1753	Caa/Taa	9/10	0.5867005582444	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.5867005582444	1		705	595	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855822	45855822	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	257	535	0	ENST00000391945.4:c.1988G>A	p.Cys663Tyr	p.C663Y	ENST00000391945	NM_000400.3	663	tGt/tAt	21/23	1	2	FACETS	0.997	0.935	1	0.997	0.935	1	CLONAL	1	TRUE	1	0.5867005582444	2		535	879	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36028676	36028676	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	220	499	0	ENST00000358208.4:c.1018G>T	p.Val340Phe	p.V340F	ENST00000358208		340	Gtc/Ttc	8/12	1	2	FACETS	0.92	0.858	0.984	0.92	0.858	0.984	CLONAL	1	TRUE	1	0.5867005582444	2		499	815	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0013258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	228	318	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.996	0.93	1	0.996	0.93	1	CLONAL	1	TRUE	1	0.533736709525274	2		318	858	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0013258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	157	807	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.533736709525274	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.533736709525274	1		807	399	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870214	155870214	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	376	884	0	ENST00000368323.3:c.625T>C	p.Ser209Pro	p.S209P	ENST00000368323	NM_006912.5	209	Tca/Cca	6/6	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.533736709525274	2		884	1390	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166755	32166755	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	226	533	0	ENST00000375023.3:c.4483T>C	p.Ser1495Pro	p.S1495P	ENST00000375023	NM_004557.3	1495	Tca/Cca	24/30	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.533736709525274	2		533	841	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771189	161771189	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	235	648	1	ENST00000366898.1:c.1340G>A	p.Trp447Ter	p.W447*	ENST00000366898	NM_004562.2	447	tGg/tAg	12/12	0.533736709525274	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.533736709525274	1		649	628	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845518	128845518	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748004767	NA	P-0013258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	284	809	0	ENST00000249373.3:c.815C>T	p.Ala272Val	p.A272V	ENST00000249373	NM_005631.4	272	gCg/gTg	4/12	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.533736709525274	2		809	1056	SUCCESS
BLM	641	MSKCC	GRCh37	15	91308526	91308526	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1200392081	NA	P-0013258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	312	651	0	ENST00000355112.3:c.2075G>T	p.Gly692Val	p.G692V	ENST00000355112	NM_000057.2	692	gGa/gTa	9/22	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.533736709525274	2		651	1167	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354511	91354511	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	195	548	0	ENST00000355112.3:c.3951G>C	p.Glu1317Asp	p.E1317D	ENST00000355112	NM_000057.2	1317	gaG/gaC	21/22	1	2	FACETS	0.951	0.883	1	0.951	0.883	1	CLONAL	1	TRUE	1	0.533736709525274	2		548	768	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42840450	42840450	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013503-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	340	718	0	ENST00000398585.3:c.1298T>A	p.Val433Glu	p.V433E	ENST00000398585	NM_001135099.1	433	gTg/gAg	12/14	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.739001024085753	2		718	848	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852447	42852447	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013503-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	385	776	0	ENST00000398585.3:c.639G>C	p.Trp213Cys	p.W213C	ENST00000398585	NM_001135099.1	213	tgG/tgC	6/14	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.739001024085753	2		776	1010	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79974767	79974767	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013503-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	326	825	0	ENST00000265081.6:c.1195G>T	p.Glu399Ter	p.E399*	ENST00000265081	NM_002439.4	399	Gag/Tag	8/24	0.566553010282748	1	FACETS	0.848	0.808	0.888	0.848	0.808	0.888	CLONAL	1	TRUE	0	0.739001024085753	1		825	656	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37034007	37034007	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013503-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	297	620	0	ENST00000358127.4:c.22C>A	p.Pro8Thr	p.P8T	ENST00000358127	NM_001280556.1	8	Ccg/Acg	1/10	0.566553010282748	1	FACETS	0.895	0.853	0.938	0.895	0.853	0.938	CLONAL	1	TRUE	0	0.739001024085753	1		620	566	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0013533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	298	645	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.947	0.896	0.999	0.947	0.896	0.999	CLONAL	1	TRUE	1	0.811804463042124	2		645	775	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921464	39921465	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCCGG	novel	NA	P-0013533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	409	354	0	ENST00000378444.4:c.4351_4355dup	p.Glu1452AspfsTer34	p.E1452Dfs*34	ENST00000378444	NM_001123385.1	1452	gaa/gaCCGGAa	10/15	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.811804463042124	1		354	556	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0013570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	352	984	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.878890807461477	2		984	789	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881001	37881002	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGCTCCCC	rs397516981	NA	P-0013572-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	394	1176	0	ENST00000269571.5:c.2331_2339dup	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	gtg/gtGGGCTCCCCg	20/27	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.650645848359682	2		1176	994	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61711081	61711081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs996736538	NA	P-0013572-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	165	678	1	ENST00000401558.2:c.2668G>A	p.Ala890Thr	p.A890T	ENST00000401558	NM_003400.3	890	Gca/Aca	21/25	1	2	FACETS	0.89	0.822	0.96	0.89	0.822	0.96	CLONAL	1	TRUE	1	0.650645848359682	2		679	570	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259178	36259178	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013572-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	200	742	1	ENST00000300305.3:c.313C>T	p.His105Tyr	p.H105Y	ENST00000300305		105	Cac/Tac	3/8	1	2	FACETS	0.881	0.819	0.944	0.881	0.819	0.944	CLONAL	1	TRUE	1	0.650645848359682	2		743	698	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857532	68857532	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	C	novel	NA	P-0013572-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	70	465	0	ENST00000261769.5:c.2164+3A>C		p.X722_splice	ENST00000261769	NM_004360.3	722			0.650645848359682	1	FACETS	0.654	0.579	0.732	0.654	0.579	0.732	SUBCLONAL	1	TRUE	0	0.650645848359682	1		465	222	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593391	48593391	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	rs863224507	NA	P-0013572-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	145	505	0	ENST00000342988.3:c.1142T>A	p.Leu381Ter	p.L381*	ENST00000342988	NM_005359.5	381	tTg/tAg	10/12	0.626944766966582	1	FACETS	0.914	0.847	0.982	0.914	0.847	0.982	CLONAL	1	TRUE	0	0.650645848359682	1		505	329	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0013625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	496	689	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.87122505523469	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.87122505523469	1		689	626	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164237	47164247	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTTTTTTAA	AGCTTTTTTAA	-	novel	NA	P-0013625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	116	468	0	ENST00000409792.3:c.1879_1889del	p.Leu627ArgfsTer2	p.L627Rfs*2	ENST00000409792	NM_014159.6	627	TTAAAAAAGCTa/a	3/21	0.635670265508596	3	FACETS	0.562	0.507	0.62	0.281	0.253	0.31	SUBCLONAL	1	TRUE	1	0.87122505523469	3		468	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0013709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	344	691	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.71268919199181	2	FACETS	0.956	0.925	0.985	0.956	0.925	0.985	CLONAL	2	TRUE	0	0.799610980487455	2		691	450	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0013709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	2253	556	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.799610980487455	7	FACETS	0.97	0.962	0.977			1	CLONAL	7	TRUE	NA	0.799610980487455	7		556	2490	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135246	2135246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1051502900	NA	P-0013709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	255	643	4	ENST00000219476.3:c.4585C>T	p.Arg1529Trp	p.R1529W	ENST00000219476	NM_000548.3	1529	Cgg/Tgg	36/42	0.799610980487455	3	FACETS	0.867	0.821	0.913	0.867	0.821	0.913	CLONAL	2	TRUE	1	0.799610980487455	3		647	515	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	53	174	0				ENST00000310581	NM_198253.2	-/1132			0.114363399486882	0	FACETS	0.446	0.388	0.506			1	INDETERMINATE	1	TRUE	0	0.610036512025591	0		174	152	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0013711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	234	318	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.607652906462969	3	FACETS	1	0.966	1	0.527	0.492	0.563	CLONAL	1	TRUE	1	0.610036512025591	3		318	950	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463275	25463275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	196	450	0	ENST00000264709.3:c.2218G>A	p.Asp740Asn	p.D740N	ENST00000264709	NM_175629.2	740	Gat/Aat	19/23	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.610036512025591	2		450	623	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486335	8486338	+	frameshift_variant	Frame_Shift_Del	DEL	GAGG	GAGG	-	novel	NA	P-0013711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	32	166	0	ENST00000356435.5:c.2479_2482del	p.Pro827GlyfsTer3	p.P827Gfs*3	ENST00000356435		827	CCTCgg/gg	17/35	1	2	FACETS	0.413	0.337	0.498	0.413	0.337	0.498	SUBCLONAL	1	TRUE	1	0.610036512025591	2		166	254	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	182	174	0				ENST00000310581	NM_198253.2	-/1132			0.765425909185528	4	FACETS	0.996	0.943	1	1	0.993	1	CLONAL	3	TRUE	2	0.765425909185528	4		174	281	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0013712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	202	515	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.765425909185528	3	FACETS	0.931	0.877	0.985	0.931	0.877	0.985	CLONAL	2	TRUE	1	0.765425909185528	3		515	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0013712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	503	780	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.740786824816465	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.765425909185528	3		782	887	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0013712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	252	927	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.740786824816465	3	FACETS	0.926	0.867	0.987	0.463	0.433	0.494	CLONAL	1	TRUE	1	0.765425909185528	3		927	983	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983911	2983911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237589286	NA	P-0013712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	311	848	1	ENST00000396946.4:c.619C>T	p.Arg207Cys	p.R207C	ENST00000396946	NM_032415.4	207	Cgc/Tgc	5/25	0.765425909185528	3	FACETS	0.898	0.846	0.951	0.449	0.423	0.476	CLONAL	1	TRUE	1	0.765425909185528	3		849	1251	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092947	27092947	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0013712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	433	422	0	ENST00000324856.7:c.2879-1G>A		p.X960_splice	ENST00000324856	NM_006015.4	960			0.562419294529712	4	FACETS	0.895	0.862	0.928	0.895	0.862	0.928	CLONAL	3	TRUE	1	0.765425909185528	4		422	744	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935371	36935371	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1420858282	NA	P-0013712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	297	826	2	ENST00000361632.4:c.1356del	p.Asn453IlefsTer8	p.N453Ifs*8	ENST00000361632		452	ccC/cc	10/16	0.562419294529712	4	FACETS	1	0.962	1	0.344	0.323	0.365	CLONAL	1	TRUE	1	0.765425909185528	4		828	1328	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405138	70405138	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	169	383	0	ENST00000373644.4:c.2652G>C	p.Arg884Ser	p.R884S	ENST00000373644	NM_030625.2	884	agG/agC	4/12	1	2	FACETS	0.95	0.881	1	0.95	0.881	1	CLONAL	1	TRUE	1	0.765425909185528	2		383	465	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741912	17741912	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs997869046	NA	P-0013712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	20	40	0	ENST00000250003.3:c.583G>T	p.Gly195Cys	p.G195C	ENST00000250003	NM_002478.4	195	Ggc/Tgc	1/3	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.765425909185528	2		40	44	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242647	46242647	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	150	317	0	ENST00000334344.6:c.1609G>C	p.Asp537His	p.D537H	ENST00000334344	NM_152641.2	537	Gat/Cat	13/21	1	2	FACETS	0.924	0.853	0.997	0.924	0.853	0.997	CLONAL	1	TRUE	1	0.765425909185528	2		317	424	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865236	57865236	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	385	924	0	ENST00000228682.2:c.2713C>T	p.Gln905Ter	p.Q905*	ENST00000228682	NM_005269.2	905	Caa/Taa	12/12	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.765425909185528	2		924	1000	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130201	2130201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	264	622	0	ENST00000219476.3:c.3433C>T	p.Pro1145Ser	p.P1145S	ENST00000219476	NM_000548.3	1145	Ccg/Tcg	30/42	0.765425909185528	2	FACETS	1	0.976	1	0.531	0.501	0.562	CLONAL	1	TRUE	0	0.765425909185528	2		622	649	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832577	72832577	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	309	703	0	ENST00000268489.5:c.4004C>G	p.Ser1335Cys	p.S1335C	ENST00000268489	NM_006885.3	1335	tCc/tGc	9/10	0.765425909185528	2	FACETS	0.916	0.867	0.967	0.458	0.433	0.484	CLONAL	1	TRUE	0	0.765425909185528	2		703	881	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883998	37883998	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	195	467	0	ENST00000269571.5:c.3469C>G	p.Leu1157Val	p.L1157V	ENST00000269571		1157	Ctg/Gtg	27/27	0.740786824816465	3	FACETS	0.999	0.928	1	0.5	0.464	0.537	CLONAL	1	TRUE	1	0.765425909185528	3		467	705	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136182	11136182	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs267605281	NA	P-0013712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	358	527	0	ENST00000358026.2:c.3166G>A	p.Glu1056Lys	p.E1056K	ENST00000358026	NM_001128849.1	1056	Gag/Aag	22/36	0.527147891422007	2	FACETS	0.941	0.909	0.972	0.941	0.909	0.972	CLONAL	2	TRUE	0	0.765425909185528	2		527	497	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023070	31023070	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371542005	NA	P-0013712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	608	630	0	ENST00000375687.4:c.2555C>T	p.Ser852Leu	p.S852L	ENST00000375687	NM_015338.5	852	tCa/tTa	13/13	0.689615334508586	4	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.765425909185528	4		630	1326	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217475	142217475	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	565	464	0	ENST00000350721.4:c.5522G>C	p.Arg1841Thr	p.R1841T	ENST00000350721	NM_001184.3	1841	aGa/aCa	32/47	0.715457153105469	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	2	0.765425909185528	4		464	1221	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190830	185190830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs961866050	NA	P-0013712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	288	599	1	ENST00000265026.3:c.1711G>A	p.Gly571Arg	p.G571R	ENST00000265026	NM_004721.4	571	Gga/Aga	11/14	0.765425909185528	3	FACETS	1	0.965	1	0.517	0.486	0.548	CLONAL	1	TRUE	1	0.765425909185528	3		600	1007	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0013783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	90	807	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.179840031569875	3	FACETS	0.794	0.724	0.864	0.794	0.724	0.864	INDETERMINATE	2	TRUE	1	0.904579355592345	3		807	182	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0013783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	56	379	2	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	NA	2	FACETS	1	0.937	1			1	INDETERMINATE	1	TRUE	NA	0.904579355592345	2		381	114	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023718	27023718	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	15	534	1	ENST00000324856.7:c.824G>A	p.Gly275Glu	p.G275E	ENST00000324856	NM_006015.4	275	gGg/gAg	1/20	0.194134256149658	4	FACETS	0.25	0.182	0.331	0.125	0.091	0.166	INDETERMINATE	1	TRUE	2	0.904579355592345	4		535	253	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937095	48937095	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0013783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3	47	204	0	ENST00000267163.4:c.861+2T>G		p.X287_splice	ENST00000267163	NM_000321.2	287			NA	2	FACETS	1	0.969	1			1	INDETERMINATE	2	TRUE	NA	0.904579355592345	2		204	50	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579328	7579328	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	126	427	0	ENST00000269305.4:c.359del	p.Lys120SerfsTer3	p.K120Sfs*3	ENST00000269305	NM_001126112.2	120	aAg/ag	4/11	0.179840031569875	3	FACETS	1	0.988	1	0.741	0.684	0.799	INDETERMINATE	1	TRUE	1	0.904579355592345	3		427	273	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138564	55138564	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1231	508	357	0	ENST00000257290.5:c.1241C>T	p.Pro414Leu	p.P414L	ENST00000257290	NM_006206.4	414	cCt/cTt	9/23	0.904579355592345	17	FACETS	1	0.961	1			1	CLONAL	5	TRUE	NA	0.904579355592345	17		357	1739	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141081	55141081	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	1458	483	0	ENST00000257290.5:c.1727A>G	p.Asp576Gly	p.D576G	ENST00000257290	NM_006206.4	576	gAc/gGc	12/23	0.904579355592345	17	FACETS	0.972	0.962	0.982			1	CLONAL	16	TRUE	NA	0.904579355592345	17		483	1613	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152094	55152096	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	novel	NA	P-0013783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2109	119	493	0	ENST00000257290.5:c.2529_2531del	p.Ile843del	p.I843del	ENST00000257290	NM_006206.4	842	gaCATc/gac	18/23	0.904579355592345	17	FACETS	0.919	0.825	1			1	CLONAL	1	TRUE	NA	0.904579355592345	17		493	2228	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340357	8340357	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324340491	NA	P-0013783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	133	498	0	ENST00000356435.5:c.5239C>T	p.Arg1747Cys	p.R1747C	ENST00000356435		1747	Cgt/Tgt	31/35	0.313373166394211	3	FACETS	1	0.977	1	0.588	0.541	0.637	INDETERMINATE	1	TRUE	1	0.904579355592345	3		498	363	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	495	611	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.638766649845352	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.638766649845352	1		611	823	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143341	30143341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	242	266	0	ENST00000389048.3:c.185C>T	p.Ser62Leu	p.S62L	ENST00000389048	NM_004304.4	62	tCg/tTg	1/29	0.319364519031919	2	FACETS	1	0.992	1	0.685	0.646	0.725	INDETERMINATE	1	TRUE	0	0.638766649845352	2		266	553	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727920	41727920	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138094666	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	257	603	2	ENST00000301178.4:c.545C>T	p.Thr182Met	p.T182M	ENST00000301178	NM_021913.4	182	aCg/aTg	4/20	0.638766649845352	2	FACETS	1	0.976	1	0.536	0.504	0.569	CLONAL	1	TRUE	0	0.638766649845352	2		605	750	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919979	50919979	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	359	414	0	ENST00000440232.2:c.3066G>T	p.Gln1022His	p.Q1022H	ENST00000440232	NM_002691.3	1022	caG/caT	24/27	0.638766649845352	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.638766649845352	2		414	533	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257887	16257887	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	70	246	0	ENST00000375759.3:c.5152G>T	p.Gly1718Cys	p.G1718C	ENST00000375759	NM_015001.2	1718	Ggt/Tgt	11/15	0.276495500972986	3	FACETS	0.656	0.574	0.744	0.328	0.287	0.372	INDETERMINATE	1	TRUE	1	0.638766649845352	3		246	441	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716239	243716239	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	127	379	0	ENST00000263826.5:c.955G>C	p.Glu319Gln	p.E319Q	ENST00000263826	NM_005465.4	319	Gaa/Caa	10/13	0.370841243676369	1	FACETS	0.357	0.323	0.392	0.357	0.323	0.392	INDETERMINATE	1	TRUE	0	0.638766649845352	1		379	759	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121513	108121513	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1565382267	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	87	282	2	ENST00000278616.4:c.1321C>T	p.Gln441Ter	p.Q441*	ENST00000278616	NM_000051.3	441	Cag/Tag	10/63	1	2	FACETS	0.394	0.348	0.442	0.394	0.348	0.442	SUBCLONAL	1	TRUE	1	0.638766649845352	2		284	692	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498251	498251	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	162	256	0	ENST00000399788.2:c.7G>T	p.Gly3Cys	p.G3C	ENST00000399788	NM_001042603.1	3	Ggc/Tgc	1/28	0.424574876593276	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.638766649845352	1		256	300	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466979	18466979	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	432	469	0	ENST00000266497.5:c.1118C>A	p.Pro373Gln	p.P373Q	ENST00000266497		373	cCa/cAa	5/31	0.155302042176479	1	FACETS	0.888	0.849	0.927	0.888	0.849	0.927	INDETERMINATE	1	TRUE	0	0.638766649845352	1		469	1037	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112611	115112611	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs780968472	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	246	286	0	ENST00000257566.3:c.1129G>T	p.Ala377Ser	p.A377S	ENST00000257566	NM_016569.3	377	Gcc/Tcc	7/8	0.350323558701467	3	FACETS	0.932	0.88	0.985	0.932	0.88	0.985	INDETERMINATE	2	TRUE	1	0.638766649845352	3		286	545	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037865	49037865	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	299	369	1	ENST00000267163.4:c.2107-2A>T		p.X703_splice	ENST00000267163	NM_000321.2	703			0.638766649845352	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.638766649845352	1		370	607	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251282	99251282	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	109	487	1	ENST00000268035.6:c.586A>T	p.Thr196Ser	p.T196S	ENST00000268035	NM_000875.3	196	Acc/Tcc	2/21	0.638766649845352	1	FACETS	0.329	0.296	0.365	0.329	0.296	0.365	SUBCLONAL	1	TRUE	0	0.638766649845352	1		488	705	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029446	14029446	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs376216413	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	204	365	0	ENST00000311895.7:c.1657A>G	p.Ile553Val	p.I553V	ENST00000311895	NM_005236.2	553	Atc/Gtc	8/11	1	2	FACETS	0.916	0.853	0.981	0.916	0.853	0.981	CLONAL	1	TRUE	1	0.638766649845352	2		365	697	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100669	67100669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	814	581	1	ENST00000412916.2:c.367G>T	p.Gly123Cys	p.G123C	ENST00000412916		123	Ggc/Tgc	4/6	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.638766649845352	2		582	1211	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829757	72829757	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	1101	872	0	ENST00000268489.5:c.6824T>A	p.Leu2275His	p.L2275H	ENST00000268489	NM_006885.3	2275	cTc/cAc	9/10	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	2	TRUE	NA	0.638766649845352	2		872	1622	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510683	38510683	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	175	512	0	ENST00000254066.5:c.937G>T	p.Ala313Ser	p.A313S	ENST00000254066	NM_000964.3	313	Gcc/Tcc	7/9	0.428868378239608	3	FACETS	0.765	0.704	0.828			1	SUBCLONAL	1	TRUE	NA	0.638766649845352	3		512	945	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677924	58677924	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	214	290	0	ENST00000305921.3:c.149C>T	p.Pro50Leu	p.P50L	ENST00000305921	NM_003620.3	50	cCt/cTt	1/6	0.638766649845352	3	FACETS	1	0.976	1	0.552	0.514	0.591	CLONAL	1	TRUE	1	0.638766649845352	3		290	801	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584351	39584351	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	326	369	2	ENST00000262039.4:c.1016G>T	p.Trp339Leu	p.W339L	ENST00000262039	NM_002647.2	339	tGg/tTg	10/25	0.319326781064389	3	FACETS	0.796	0.755	0.837	0.796	0.755	0.837	INDETERMINATE	2	TRUE	1	0.638766649845352	3		371	846	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602329	10602329	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	579	487	0	ENST00000171111.5:c.1249G>T	p.Gly417Trp	p.G417W	ENST00000171111	NM_203500.1	417	Ggg/Tgg	3/6	0.638766649845352	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.638766649845352	2		487	840	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383080	42383080	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	547	604	1	ENST00000221972.3:c.100T>A	p.Trp34Arg	p.W34R	ENST00000221972	NM_021601.3	34	Tgg/Agg	2/5	0.638766649845352	2	FACETS	0.983	0.952	1	0.983	0.952	1	CLONAL	2	TRUE	0	0.638766649845352	2		605	871	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659952	227659952	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	276	700	1	ENST00000305123.5:c.3503G>T	p.Gly1168Val	p.G1168V	ENST00000305123	NM_005544.2	1168	gGg/gTg	1/2	NA	2	FACETS	0.727	0.682	0.774			1	INDETERMINATE	1	TRUE	NA	0.638766649845352	2		701	1188	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770585	40770585	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	394	479	0	ENST00000373198.4:c.2797A>C	p.Asn933His	p.N933H	ENST00000373198	NM_133170.3	933	Aat/Cat	19/32	0.638766649845352	3	FACETS	1	0.994	1	0.67	0.637	0.703	CLONAL	1	TRUE	1	0.638766649845352	3		479	1215	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944469	40944470	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	489	632	1	ENST00000373198.4:c.2032_2033delinsAT	p.Pro678Ile	p.P678I	ENST00000373198	NM_133170.3	678	CCa/ATa	12/32	0.638766649845352	3	FACETS	1	0.993	1	0.594	0.567	0.622	CLONAL	1	TRUE	1	0.638766649845352	3		633	1700	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264792	46264792	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1630	720	893	1	ENST00000371998.3:c.1662G>A	p.Met554Ile	p.M554I	ENST00000371998		554	atG/atA	12/23	0.638766649845352	3	FACETS	1	0.996	1	0.633	0.609	0.657	CLONAL	1	TRUE	1	0.638766649845352	3		894	2350	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163617	47163617	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	311	311	0	ENST00000409792.3:c.2509G>C	p.Asp837His	p.D837H	ENST00000409792	NM_014159.6	837	Gat/Cat	3/21	0.581677482551555	2	FACETS	0.887	0.847	0.926	0.887	0.847	0.926	CLONAL	2	TRUE	0	0.638766649845352	2		311	549	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153655	55153655	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	385	661	0	ENST00000257290.5:c.2621C>T	p.Thr874Ile	p.T874I	ENST00000257290	NM_006206.4	874	aCa/aTa	19/23	0.408658532587993	1	FACETS	0.775	0.737	0.813	0.775	0.737	0.813	SUBCLONAL	1	TRUE	0	0.638766649845352	1		661	1059	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155207	55155207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	132	501	0	ENST00000257290.5:c.2806G>T	p.Glu936Ter	p.E936*	ENST00000257290	NM_006206.4	936	Gag/Tag	21/23	0.408658532587993	1	FACETS	0.406	0.369	0.445	0.406	0.369	0.445	SUBCLONAL	1	TRUE	0	0.638766649845352	1		501	692	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249427	153249427	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	194	577	1	ENST00000281708.4:c.1351G>T	p.Gly451Ter	p.G451*	ENST00000281708	NM_033632.3	451	Gga/Tga	9/12	0.408658532587993	1	FACETS	0.428	0.395	0.461	0.428	0.395	0.461	SUBCLONAL	1	TRUE	0	0.638766649845352	1		578	967	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35860999	35860999	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs373694709	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	280	392	0	ENST00000303115.3:c.128A>G	p.Tyr43Cys	p.Y43C	ENST00000303115	NM_002185.3	43	tAt/tGt	2/8	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.638766649845352	2		392	860	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441079	149441079	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	163	761	0	ENST00000286301.3:c.1833del	p.Lys612ArgfsTer4	p.K612Rfs*4	ENST00000286301	NM_005211.3	611	ctG/ct	13/22	0.582391793820819	1	FACETS	0.406	0.373	0.441	0.406	0.373	0.441	SUBCLONAL	1	TRUE	0	0.638766649845352	1		761	855	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449484	149449484	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	136	529	0	ENST00000286301.3:c.1462C>A	p.His488Asn	p.H488N	ENST00000286301	NM_005211.3	488	Cac/Aac	10/22	0.582391793820819	1	FACETS	0.424	0.386	0.464	0.424	0.386	0.464	SUBCLONAL	1	TRUE	0	0.638766649845352	1		529	683	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520274	176520275	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	83	413	1	ENST00000292408.4:c.1193_1194delinsTT	p.Arg398Leu	p.R398L	ENST00000292408	NM_213647.1	398	cGG/cTT	9/18	0.408658532587993	1	FACETS	0.431	0.383	0.483	0.431	0.383	0.483	SUBCLONAL	1	TRUE	0	0.638766649845352	1		414	410	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201868	152201868	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	316	357	0	ENST00000206249.3:c.722G>T	p.Arg241Leu	p.R241L	ENST00000206249	NM_000125.3	241	cGg/cTg	3/8	0.539687459532633	2	FACETS	0.883	0.844	0.922	0.883	0.844	0.922	CLONAL	2	TRUE	0	0.638766649845352	2		357	560	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382244	152382244	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	406	404	0	ENST00000206249.3:c.1354A>G	p.Ile452Val	p.I452V	ENST00000206249	NM_000125.3	452	Att/Gtt	6/8	0.539687459532633	2	FACETS	0.864	0.829	0.898	0.864	0.829	0.898	CLONAL	2	TRUE	0	0.638766649845352	2		404	736	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683682	162683682	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	243	535	0	ENST00000366898.1:c.287A>T	p.Glu96Val	p.E96V	ENST00000366898	NM_004562.2	96	gAg/gTg	3/12	0.406887289058907	0	FACETS	0.443	0.416	0.469			1	SUBCLONAL	1	TRUE	0	0.638766649845352	0		535	621	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346629	81346629	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	517	493	1	ENST00000222390.5:c.1324A>T	p.Asn442Tyr	p.N442Y	ENST00000222390	NM_000601.4	442	Aat/Tat	11/18	0.276495500972986	3	FACETS	0.867	0.832	0.902	0.867	0.832	0.902	INDETERMINATE	2	TRUE	1	0.638766649845352	3		494	1232	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515195	106515195	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	300	436	1	ENST00000359195.3:c.2338C>A	p.Pro780Thr	p.P780T	ENST00000359195	NM_002649.2	780	Ccc/Acc	5/11	0.504561245226073	4	FACETS	1	0.988	1	0.398	0.374	0.423	CLONAL	1	TRUE	1	0.638766649845352	4		437	1289	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523498	106523498	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	223	341	0	ENST00000359195.3:c.2650G>C	p.Asp884His	p.D884H	ENST00000359195	NM_002649.2	884	Gac/Cac	8/11	0.504561245226073	4	FACETS	1	0.988	1	0.423	0.394	0.453	CLONAL	1	TRUE	1	0.638766649845352	4		341	902	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282168	38282168	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1415	79	442	0	ENST00000425967.3:c.888A>T	p.Lys296Asn	p.K296N	ENST00000425967	NM_001174067.1	296	aaA/aaT	8/19	0.508200870702555	5	FACETS	0.324	0.284	0.368			1	SUBCLONAL	1	TRUE	NA	0.638766649845352	5		442	1494	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341122	8341122	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	133	464	0	ENST00000356435.5:c.5094T>A	p.Asp1698Glu	p.D1698E	ENST00000356435		1698	gaT/gaA	30/35	0.373230962343863	1	FACETS	0.317	0.288	0.349	0.317	0.288	0.349	INDETERMINATE	1	TRUE	0	0.638766649845352	1		464	893	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517846	8517846	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	179	562	0	ENST00000356435.5:c.1543+2T>A		p.X515_splice	ENST00000356435		515			0.373230962343863	1	FACETS	0.343	0.316	0.372	0.343	0.316	0.372	INDETERMINATE	1	TRUE	0	0.638766649845352	1		562	1111	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934060	39934060	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	315	671	0	ENST00000378444.4:c.539A>G	p.Asn180Ser	p.N180S	ENST00000378444	NM_001123385.1	180	aAc/aGc	4/15	0.283449044483366	1	FACETS	0.641	0.605	0.677	0.641	0.605	0.677	INDETERMINATE	1	TRUE	0	0.638766649845352	1		671	1048	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934290	39934290	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	370	750	0	ENST00000378444.4:c.309G>T	p.Glu103Asp	p.E103D	ENST00000378444	NM_001123385.1	103	gaG/gaT	4/15	0.283449044483366	1	FACETS	0.683	0.649	0.719	0.683	0.649	0.719	INDETERMINATE	1	TRUE	0	0.638766649845352	1		750	1154	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879967	44879967	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	350	528	0	ENST00000377967.4:c.556A>T	p.Ser186Cys	p.S186C	ENST00000377967	NM_021140.2	186	Agt/Tgt	6/29	0.283449044483366	1	FACETS	0.629	0.596	0.663	0.629	0.596	0.663	INDETERMINATE	1	TRUE	0	0.638766649845352	1		528	1186	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422634	47422634	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1283082877	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	351	797	1	ENST00000377045.4:c.106C>G	p.Arg36Gly	p.R36G	ENST00000377045	NM_001654.4	36	Cgg/Ggg	3/16	0.283449044483366	1	FACETS	0.627	0.594	0.661	0.627	0.594	0.661	INDETERMINATE	1	TRUE	0	0.638766649845352	1		798	1193	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430351	47430351	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	291	758	2	ENST00000377045.4:c.1626G>T	p.Met542Ile	p.M542I	ENST00000377045	NM_001654.4	542	atG/atT	15/16	0.283449044483366	1	FACETS	0.564	0.53	0.598	0.564	0.53	0.598	INDETERMINATE	1	TRUE	0	0.638766649845352	1		760	1100	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250099	53250099	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	362	610	0	ENST00000375401.3:c.151-1G>T		p.X51_splice	ENST00000375401	NM_004187.3	51			0.283449044483366	1	FACETS	0.667	0.632	0.702	0.667	0.632	0.702	INDETERMINATE	1	TRUE	0	0.638766649845352	1		610	1157	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410342	63410342	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	345	830	0	ENST00000330258.3:c.2825G>C	p.Arg942Pro	p.R942P	ENST00000330258	NM_152424.3	942	cGa/cCa	2/2	0.638766649845352	1	FACETS	0.905	0.862	0.95	0.905	0.862	0.95	CLONAL	1	TRUE	0	0.638766649845352	1		830	812	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013852-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	28	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.9	0.735	1	1	0.954	1	CLONAL	2	TRUE	1	0.293659117605774	2		174	106	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333105	70333105	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755974529	NA	P-0013852-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	235	908	0	ENST00000373644.4:c.1010C>T	p.Ala337Val	p.A337V	ENST00000373644	NM_030625.2	337	gCg/gTg	2/12	0.263839053555218	0	FACETS	0.824	0.787	0.859			1	CLONAL	4	TRUE	0	0.293659117605774	0		908	343	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29662034	29662034	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs876660696	NA	P-0013852-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	93	388	0	ENST00000356175.3:c.5928G>A	p.Trp1976Ter	p.W1976*	ENST00000356175	NM_000267.3	1976	tgG/tgA	39/57	0.293659117605774	0	FACETS	0.742	0.675	0.809			1	SUBCLONAL	3	TRUE	0	0.293659117605774	0		388	201	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383272	31383272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1268577906	NA	P-0013852-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	118	937	0	ENST00000328111.2:c.1184C>T	p.Ala395Val	p.A395V	ENST00000328111	NM_006892.3	395	gCa/gTa	11/23	0.293659117605774	5	FACETS	1	0.927	1	0.514	0.465	0.565	CLONAL	2	TRUE	1	0.293659117605774	5		937	563	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599321	55599321	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913507	NA	P-0013857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	163	488	2	ENST00000288135.5:c.2447A>T	p.Asp816Val	p.D816V	ENST00000288135	NM_000222.2	816	gAc/gTc	17/21	0.215854036048253	5	FACETS	1	0.987	1	0.467	0.429	0.507	INDETERMINATE	1	TRUE	2	0.443191793065534	5		490	874	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631837	90631837	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519736	NA	P-0013857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	190	488	0	ENST00000330062.3:c.516G>C	p.Arg172Ser	p.R172S	ENST00000330062	NM_002168.2	172	agG/agC	4/11	0.389641246859754	3	FACETS	1	0.983	1	0.605	0.559	0.652	CLONAL	1	TRUE	1	0.443191793065534	3		488	866	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245082	46245087	+	inframe_deletion	In_Frame_Del	DEL	TGATTA	TGATTA	-	novel	NA	P-0013857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	145	538	0	ENST00000334344.6:c.3176_3181del	p.Leu1059_Lys1061delinsGln	p.L1059_K1061delinsQ	ENST00000334344	NM_152641.2	1059	cTGATTAaa/caa	15/21	0.372330711775906	4	FACETS	0.973	0.887	1	0.486	0.443	0.532	CLONAL	1	TRUE	2	0.443191793065534	4		538	971	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434694	49434694	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	159	610	0	ENST00000301067.7:c.6859G>A	p.Val2287Met	p.V2287M	ENST00000301067	NM_003482.3	2287	Gtg/Atg	31/54	0.372330711775906	4	FACETS	0.994	0.91	1	0.497	0.455	0.541	CLONAL	1	TRUE	2	0.443191793065534	4		610	1042	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991354	41991354	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	171	765	0	ENST00000219905.7:c.2185G>T	p.Glu729Ter	p.E729*	ENST00000219905	NM_001164273.1	729	Gaa/Taa	5/24	1	2	FACETS	0.862	0.793	0.934	0.862	0.793	0.934	CLONAL	1	TRUE	1	0.443191793065534	2		765	895	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0013857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	568	590	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.443191793065534	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	4	TRUE	0	0.443191793065534	4		590	889	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559128	29559128	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	156	230	0	ENST00000356175.3:c.3235C>G	p.Leu1079Val	p.L1079V	ENST00000356175	NM_000267.3	1079	Ctt/Gtt	25/57	0.443191793065534	5	FACETS	1	0.974	1	0.754	0.695	0.815	CLONAL	2	TRUE	2	0.443191793065534	5		230	518	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456439	29456439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756963896	NA	P-0013857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1399	213	812	2	ENST00000389048.3:c.2479G>A	p.Val827Ile	p.V827I	ENST00000389048	NM_004304.4	827	Gta/Ata	14/29	0.325373929402108	5	FACETS	0.993	0.919	1	0.331	0.306	0.357	CLONAL	1	TRUE	2	0.443191793065534	5		814	1612	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446949	187446949	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs774320115	NA	P-0013857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	180	580	0	ENST00000232014.4:c.1244A>G	p.Gln415Arg	p.Q415R	ENST00000232014	NM_001130845.1	415	cAg/cGg	5/10	0.42863527135434	4	FACETS	0.97	0.892	1	0.485	0.446	0.525	CLONAL	1	TRUE	2	0.443191793065534	4		580	1209	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382235	152382235	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	88	419	0	ENST00000206249.3:c.1345A>C	p.Lys449Gln	p.K449Q	ENST00000206249	NM_000125.3	449	Aaa/Caa	6/8	0.42863527135434	4	FACETS	0.682	0.604	0.767	0.341	0.302	0.384	SUBCLONAL	1	TRUE	2	0.443191793065534	4		419	840	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946273	2946273	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	novel	NA	P-0013857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	57	530	0	ENST00000396946.4:c.3464G>C	p.Ter1155SerextTer16	p.*1155Sext*16	ENST00000396946	NM_032415.4	1155	tGa/tCa	25/25	0.443191793065534	3	FACETS	0.409	0.35	0.474	0.205	0.175	0.237	SUBCLONAL	1	TRUE	1	0.443191793065534	3		530	768	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508609	106508609	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	29	312	1	ENST00000359195.3:c.603G>T	p.Trp201Cys	p.W201C	ENST00000359195	NM_002649.2	201	tgG/tgT	2/11	0.443191793065534	3	FACETS	0.313	0.251	0.385	0.157	0.125	0.193	SUBCLONAL	1	TRUE	1	0.443191793065534	3		313	510	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0013877-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	651	585	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	0.693114606877356	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.693114606877356	3		585	809	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347124	89347128	+	frameshift_variant	Frame_Shift_Del	DEL	GACGG	GACGG	-	novel	NA	P-0013877-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	147	899	0	ENST00000301030.4:c.5822_5826del	p.Ala1941AspfsTer7	p.A1941Dfs*7	ENST00000301030	NM_001256183.1	1941	gCCGTC/g	9/13	0.693114606877356	1	FACETS	0.428	0.392	0.466	0.428	0.392	0.466	SUBCLONAL	1	TRUE	0	0.693114606877356	1		899	647	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0013881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	352	670	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.677152779708875	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.677152779708875	1		670	647	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916836	178916836	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1227	618	1545	0	ENST00000263967.3:c.223C>G	p.Gln75Glu	p.Q75E	ENST00000263967	NM_006218.2	75	Caa/Gaa	2/21	1	2	FACETS	0.989	0.951	1	0.989	0.951	1	CLONAL	1	TRUE	1	0.677152779708875	2		1545	1845	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0013881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	382	457	1	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.677152779708875	2		458	969	SUCCESS
APC	324	MSKCC	GRCh37	5	112175636	112175636	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	390	837	0	ENST00000257430.4:c.4346del	p.Lys1449SerfsTer24	p.K1449Sfs*24	ENST00000257430	NM_000038.5	1449	Aag/ag	16/16	1	2	FACETS	0.956	0.909	1	0.956	0.909	1	CLONAL	1	TRUE	1	0.677152779708875	2		837	1205	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593504	48593504	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	217	481	0	ENST00000342988.3:c.1255G>A	p.Gly419Arg	p.G419R	ENST00000342988	NM_005359.5	419	Ggg/Agg	10/12	0.677152779708875	1	FACETS	0.93	0.875	0.984	0.93	0.875	0.984	CLONAL	1	TRUE	0	0.677152779708875	1		481	456	SUCCESS
APC	324	MSKCC	GRCh37	5	112164585	112164585	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398123116	NA	P-0013881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	160	268	0	ENST00000257430.4:c.1659G>A	p.Trp553Ter	p.W553*	ENST00000257430	NM_000038.5	553	tgG/tgA	14/16	1	2	FACETS	0.893	0.824	0.964	0.893	0.824	0.964	CLONAL	1	TRUE	1	0.677152779708875	2		268	529	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992076	72992076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772258894	NA	P-0013881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	392	1031	1	ENST00000268489.5:c.1969G>A	p.Gly657Ser	p.G657S	ENST00000268489	NM_006885.3	657	Ggc/Agc	2/10	1	2	FACETS	0.958	0.911	1	0.958	0.911	1	CLONAL	1	TRUE	1	0.677152779708875	2		1032	1209	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931925	39931925	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	TTT	novel	NA	P-0013881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	320	792	0	ENST00000378444.4:c.2674delinsAAA	p.Leu892LysfsTer2	p.L892Kfs*2	ENST00000378444	NM_001123385.1	892	Cta/AAAta	4/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.677152779708875	2		792	926	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6414400	6414400	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	326	267	0	ENST00000356142.4:c.34G>A	p.Gly12Arg	p.G12R	ENST00000356142	NM_018890.3	12	Gga/Aga	1/7	0.538746875748396	5	FACETS	1	0.992	1	0.435	0.41	0.461	CLONAL	1	TRUE	2	0.698061292963345	5		267	1466	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625640	1625640	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773698137	NA	P-0013960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	447	825	0	ENST00000344749.5:c.434G>A	p.Gly145Glu	p.G145E	ENST00000344749	NM_001136139.2	145	gGg/gAg	7/19	0.698061292963345	3	FACETS	1	0.983	1	0.532	0.507	0.558	CLONAL	1	TRUE	1	0.698061292963345	3		825	1623	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104359205	104359205	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	314	669	0	ENST00000369902.3:c.926G>C	p.Arg309Pro	p.R309P	ENST00000369902	NM_016169.3	309	cGg/cCg	8/12	0.524293638680045	3	FACETS	0.949	0.894	1			1	CLONAL	1	TRUE	NA	0.698061292963345	3		669	1279	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0013980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	259	807	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.746047545395122	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.757338414376619	2		807	315	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430600	181430600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1372564199	NA	P-0013980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	35	337	0	ENST00000325404.1:c.452C>T	p.Ala151Val	p.A151V	ENST00000325404	NM_003106.3	151	gCg/gTg	1/1	0.72848287658474	4	FACETS	0.324	0.265	0.39	0.162	0.132	0.195	SUBCLONAL	1	TRUE	2	0.757338414376619	4		337	502	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41276092	41276092	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528902306	NA	P-0013980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	189	469	0	ENST00000357654.3:c.22G>A	p.Val8Ile	p.V8I	ENST00000357654	NM_007294.3	8	Gtt/Att	2/23	0.757338414376619	4	FACETS	0.792	0.737	0.848	0.792	0.737	0.848	SUBCLONAL	2	TRUE	2	0.757338414376619	4		469	554	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42840333	42840333	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	210	489	0	ENST00000398585.3:c.1415A>T	p.Asp472Val	p.D472V	ENST00000398585	NM_001135099.1	472	gAt/gTt	12/14	0.309288995116709	6	FACETS	1	0.99	1	0.471	0.437	0.506	INDETERMINATE	1	TRUE	3	0.757338414376619	6		489	987	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849203	76849203	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	387	801	0	ENST00000373344.5:c.6073G>T	p.Glu2025Ter	p.E2025*	ENST00000373344	NM_000489.3	2025	Gaa/Taa	26/35	0.715109076445173	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	2	0.757338414376619	4		801	868	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0014012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	869	611	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.865041346802712	2	FACETS	0.993	0.978	1	0.993	0.978	1	CLONAL	2	TRUE	0	0.880427445964474	2		611	994	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0014012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	373	530	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.880427445964474	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.880427445964474	1		530	465	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218953	193218953	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759222387	NA	P-0014012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	330	559	1	ENST00000367435.3:c.1511G>A	p.Arg504His	p.R504H	ENST00000367435	NM_024529.4	504	cGt/cAt	16/17	1	2	FACETS	0.915	0.869	0.962	0.915	0.869	0.962	CLONAL	1	TRUE	1	0.880427445964474	2		560	819	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	55	995	1	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	0.415	0.356	0.479	0.415	0.356	0.479	SUBCLONAL	1	TRUE	1	0.69755796910967	2		996	380	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031973	26031973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	85	1064	0	ENST00000244661.2:c.316G>C	p.Glu106Gln	p.E106Q	ENST00000244661	NM_003537.3	106	Gag/Cag	1/1	0.24168865293412	3	FACETS	0.552	0.488	0.619	0.276	0.244	0.31	INDETERMINATE	1	TRUE	1	0.69755796910967	3		1064	596	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572904	41572904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	82	498	1	ENST00000263253.7:c.5189C>T	p.Ser1730Phe	p.S1730F	ENST00000263253	NM_001429.3	1730	tCt/tTt	31/31	1	2	FACETS	0.532	0.471	0.597	0.532	0.471	0.597	SUBCLONAL	1	TRUE	1	0.69755796910967	2		499	442	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2202742	2202742	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	168	717	0	ENST00000398665.3:c.751C>T	p.His251Tyr	p.H251Y	ENST00000398665	NM_032482.2	251	Cac/Tac	9/28	0.191075698951008	2	FACETS	1	0.974	1	0.552	0.513	0.593	INDETERMINATE	1	TRUE	0	0.69755796910967	2		717	436	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276266	15276266	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	88	531	0	ENST00000263388.2:c.5728C>G	p.Leu1910Val	p.L1910V	ENST00000263388	NM_000435.2	1910	Ctg/Gtg	31/33	0.191075698951008	2	FACETS	0.632	0.564	0.705	0.316	0.282	0.353	INDETERMINATE	1	TRUE	0	0.69755796910967	2		531	399	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37141805	37141805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	58	467	0	ENST00000373509.5:c.880C>T	p.Leu294Phe	p.L294F	ENST00000373509	NM_002648.3	294	Ctc/Ttc	6/6	0.24168865293412	3	FACETS	0.568	0.489	0.653	0.284	0.244	0.327	INDETERMINATE	1	TRUE	1	0.69755796910967	3		467	395	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287871	33287872	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATGA	novel	NA	P-0014073-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	415	903	0	ENST00000374542.5:c.1381_1382insTCAT	p.Ser461PhefsTer3	p.S461Ffs*3	ENST00000374542	NM_001141970.1	461	tct/tTCATct	5/8	0.760938030429469	2	FACETS	0.917	0.887	0.946	0.917	0.887	0.946	CLONAL	2	TRUE	0	0.760938030429469	2		903	595	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0014128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	478	503	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	2	TRUE	NA	0.766530832830607	2		503	616	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380282	25380282	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	445	498	0	ENST00000311936.3:c.176C>G	p.Ala59Gly	p.A59G	ENST00000311936	NM_004985.3	59	gCa/gGa	3/5	0.757447464417102	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	2	0.766530832830607	4		498	868	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514046	125514046	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	403	730	0	ENST00000428830.2:c.984G>T	p.Trp328Cys	p.W328C	ENST00000428830	NM_001114121.2	328	tgG/tgT	10/14	0.766530832830607	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.766530832830607	1		730	572	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222389	2222389	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	112	252	0	ENST00000398665.3:c.3221del	p.Asp1074AlafsTer26	p.D1074Afs*26	ENST00000398665	NM_032482.2	1074	gAc/gc	24/28	0.766530832830607	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.766530832830607	1		252	172	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446364	29446364	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	467	826	2	ENST00000389048.3:c.3203C>A	p.Ala1068Asp	p.A1068D	ENST00000389048	NM_004304.4	1068	gCc/gAc	20/29	0.766530832830607	3	FACETS	1	0.995	1	0.646	0.618	0.675	CLONAL	1	TRUE	1	0.766530832830607	3		828	1304	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400110	41400110	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	353	450	0	ENST00000373198.4:c.649G>T	p.Gly217Trp	p.G217W	ENST00000373198	NM_133170.3	217	Ggg/Tgg	5/32	0.358467786582241	6	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.766530832830607	6		450	999	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662909	52662910	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0014128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	396	408	1	ENST00000394830.3:c.1443_1443+1delinsTT		p.X481_splice	ENST00000394830	NM_018313.4	481		13/30	0.748980363663551	2	FACETS	0.988	0.958	1	0.988	0.958	1	CLONAL	2	TRUE	0	0.766530832830607	2		409	523	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752826	57752826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	382	373	0	ENST00000274289.3:c.1102G>A	p.Ala368Thr	p.A368T	ENST00000274289	NM_006622.3	368	Gct/Act	8/14	0.766530832830607	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.766530832830607	2		373	475	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509174	106509174	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	138	527	2	ENST00000359195.3:c.1168G>T	p.Gly390Trp	p.G390W	ENST00000359195	NM_002649.2	390	Ggg/Tgg	2/11	NA	2	FACETS	0.707	0.647	0.769			1	INDETERMINATE	1	TRUE	NA	0.766530832830607	2		529	509	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653788	89654114	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATCCAAACATTATTGCTATGGGATTTCCTGCAGAAAGACTTGAAGGCGTATACAGGAACAATATTGATGATGTAGTAAGGTAAGAATGCTTTGATTTTCTATTTCAAATATTGATGTTTATATTCATGTTGTGTTTTCATTTAGAAAAGATTTCTAAGCCACAGAAAAAGATACTTTGTGATGTAAACTATTATTGTAGTGCTCTATAATCATTTTTTGGCTTACCGTACCTAATGGACTTCAGGGGGATACAGTTCATTTGATAAGAACTGACCTTATACATTACATAATCAGGTACTTATGTGATATCATTTCCTGGACTCCATA	ATCCAAACATTATTGCTATGGGATTTCCTGCAGAAAGACTTGAAGGCGTATACAGGAACAATATTGATGATGTAGTAAGGTAAGAATGCTTTGATTTTCTATTTCAAATATTGATGTTTATATTCATGTTGTGTTTTCATTTAGAAAAGATTTCTAAGCCACAGAAAAAGATACTTTGTGATGTAAACTATTATTGTAGTGCTCTATAATCATTTTTTGGCTTACCGTACCTAATGGACTTCAGGGGGATACAGTTCATTTGATAAGAACTGACCTTATACATTACATAATCAGGTACTTATGTGATATCATTTCCTGGACTCCATA	-	novel	NA	P-0014134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	50	512	0	ENST00000371953.3:c.87_164+249del		p.X29_splice	ENST00000371953	NM_000314.4	29		2/9	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		512	73	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435254	49435254	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199761931	NA	P-0014244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	438	723	1	ENST00000301067.7:c.6299C>A	p.Pro2100Gln	p.P2100Q	ENST00000301067	NM_003482.3	2100	cCg/cAg	31/54	0.812404012319821	3	FACETS	1	0.955	1	0.501	0.477	0.526	CLONAL	1	TRUE	1	0.812404012319821	3		724	1513	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347935	89347935	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0014244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	428	751	0	ENST00000301030.4:c.5015C>G	p.Ser1672Ter	p.S1672*	ENST00000301030	NM_001256183.1	1672	tCa/tGa	9/13	0.800880406387461	1	FACETS	0.935	0.903	0.967	0.935	0.903	0.967	CLONAL	1	TRUE	0	0.812404012319821	1		751	669	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750824	57750824	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	260	366	0	ENST00000274289.3:c.1780G>T	p.Asp594Tyr	p.D594Y	ENST00000274289	NM_006622.3	594	Gat/Tat	13/14	1	2	FACETS	0.89	0.838	0.943	0.89	0.838	0.943	CLONAL	1	TRUE	1	0.812404012319821	2		366	719	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577530	7577530	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs730882007	NA	P-0014261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	341	459	0	ENST00000269305.4:c.751A>C	p.Ile251Leu	p.I251L	ENST00000269305	NM_001126112.2	251	Atc/Ctc	7/11	0.377116262590896	2	FACETS	1	0.995	1	0.736	0.698	0.774	CLONAL	1	TRUE	0	0.492470712539558	2		459	941	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86648997	86648997	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	144	331	0	ENST00000274376.6:c.1277A>G	p.Tyr426Cys	p.Y426C	ENST00000274376	NM_002890.2	426	tAt/tGt	9/25	0.492470712539558	1	FACETS	0.771	0.717	0.824	1	0.99	1	SUBCLONAL	2	TRUE	0	0.492470712539558	1		331	286	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562346	176562346	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1342105953	NA	P-0014261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	300	517	0	ENST00000439151.2:c.242T>A	p.Met81Lys	p.M81K	ENST00000439151	NM_022455.4	81	aTg/aAg	2/23	0.492470712539558	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.492470712539558	1		517	697	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509685	106509685	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	269	467	0	ENST00000359195.3:c.1679C>T	p.Ala560Val	p.A560V	ENST00000359195	NM_002649.2	560	gCc/gTc	2/11	0.492470712539558	3	FACETS	1	0.992	1	0.678	0.636	0.721	CLONAL	1	TRUE	1	0.492470712539558	3		467	1004	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692919	89692919	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782360	NA	P-0014279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	275	660	0	ENST00000371953.3:c.403A>G	p.Ile135Val	p.I135V	ENST00000371953	NM_000314.4	135	Ata/Gta	5/9	1	2	FACETS	0.906	0.857	0.955	0.906	0.857	0.955	CLONAL	1	TRUE	1	0.942826269360307	2		660	644	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937055	48937055	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	153	325	1	ENST00000267163.4:c.823G>T	p.Glu275Ter	p.E275*	ENST00000267163	NM_000321.2	275	Gaa/Taa	8/27	0.930800443352118	1	FACETS	0.953	0.915	0.987	0.953	0.915	0.987	CLONAL	1	TRUE	0	0.942826269360307	1		326	180	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245716	41245716	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	368	518	0	ENST00000357654.3:c.1832T>A	p.Leu611Gln	p.L611Q	ENST00000357654	NM_007294.3	611	cTg/cAg	10/23	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.903660181740909	2		518	802	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921404	178921404	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	373	473	0	ENST00000263967.3:c.886C>T	p.Gln296Ter	p.Q296*	ENST00000263967	NM_006218.2	296	Caa/Taa	5/21	1	2	FACETS	0.928	0.884	0.971	0.928	0.884	0.971	CLONAL	1	TRUE	1	0.903660181740909	2		473	890	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	231	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.77642871968293	2		174	577	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0014501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	163	318	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.77642871968293	3	FACETS	0.919	0.847	0.994	0.46	0.423	0.497	CLONAL	1	TRUE	1	0.77642871968293	3		318	634	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692847	89692847	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123321	NA	P-0014501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	47	179	0	ENST00000371953.3:c.331T>C	p.Trp111Arg	p.W111R	ENST00000371953	NM_000314.4	111	Tgg/Cgg	5/9	0.741354321370148	1	FACETS	0.764	0.669	0.858	0.764	0.669	0.858	SUBCLONAL	1	TRUE	0	0.77642871968293	1		179	97	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0014554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	105	497	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.164236333752036	3	FACETS	1	0.942	1	0.539	0.482	0.6	CLONAL	1	TRUE	1	0.22	3		497	982	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	236	399	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	0.3	4	FACETS	0.89	0.831	0.951	0.89	0.831	0.951	CLONAL	3	TRUE	1	0.22	4		399	980	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220650	1220650	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	115	683	0	ENST00000326873.7:c.668A>T	p.Glu223Val	p.E223V	ENST00000326873	NM_000455.4	223	gAg/gTg	5/10	0.231163254966568	1	FACETS	0.866	0.778	0.959	0.866	0.778	0.959	CLONAL	1	TRUE	0	0.22	1		683	1075	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115048	3115048	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769982397	NA	P-0014554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	67	663	1	ENST00000078429.4:c.583G>A	p.Asp195Asn	p.D195N	ENST00000078429	NM_002067.2	195	Gac/Aac	4/7	0.231163254966568	1	FACETS	0.526	0.455	0.603	0.526	0.455	0.603	SUBCLONAL	1	TRUE	0	0.22	1		664	1031	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163307855	163307855	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	157	371	0	ENST00000271452.3:c.481G>A	p.Glu161Lys	p.E161K	ENST00000271452	NM_145697.2	161	Gag/Aag	7/14	0.3	5	FACETS	1	0.987	1	0.489	0.446	0.533	CLONAL	1	TRUE	2	0.22	5		371	1295	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682997	241682997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	141	406	0	ENST00000366560.3:c.26C>T	p.Ala9Val	p.A9V	ENST00000366560	NM_000143.3	9	gCg/gTg	1/10	0.3	5	FACETS	0.781	0.71	0.856	0.521	0.473	0.571	SUBCLONAL	2	TRUE	2	0.22	5		406	1091	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998283	100998283	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	53	157	0	ENST00000325455.5:c.1519del	p.Ala507ArgfsTer39	p.A507Rfs*39	ENST00000325455	NM_001202474.3	507	Gcg/cg	1/8	0.164236333752036	3	FACETS	0.9	0.773	1	0.9	0.773	1	CLONAL	2	TRUE	1	0.22	3		157	297	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139175	108139175	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555083131	NA	P-0014554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	149	508	0	ENST00000278616.4:c.2677C>T	p.Gln893Ter	p.Q893*	ENST00000278616	NM_000051.3	893	Caa/Taa	18/63	0.164236333752036	3	FACETS	1	0.985	1	0.707	0.644	0.772	CLONAL	1	TRUE	1	0.22	3		508	1064	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914126	32914126	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs80358784	NA	P-0014554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	54	307	0	ENST00000380152.3:c.5634C>A	p.Asn1878Lys	p.N1878K	ENST00000380152		1878	aaC/aaA	11/27	0.164236333752036	3	FACETS	0.655	0.558	0.762	0.327	0.279	0.381	SUBCLONAL	1	TRUE	1	0.22	3		307	832	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219323	1219336	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GTATATGGTGATGG	GTATATGGTGATGG	-	novel	NA	P-0014554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	44	520	0	ENST00000326873.7:c.375_388del	p.Met125IlefsTer33	p.M125Ifs*33	ENST00000326873	NM_000455.4	125	atGTATATGGTGATGGag/atag	3/10	0.231163254966568	1	FACETS	0.438	0.366	0.518	0.438	0.366	0.518	SUBCLONAL	1	TRUE	0	0.22	1		520	813	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410063	139410063	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs544117297	NA	P-0014554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	81	779	1	ENST00000277541.6:c.1775G>T	p.Arg592Leu	p.R592L	ENST00000277541	NM_017617.3	592	cGc/cTc	11/34	0.174124205974873	0	FACETS	0.566	0.497	0.64			1	SUBCLONAL	1	TRUE	0	0.22	0		780	1015	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913517	NA	P-0014592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	224	396	0	ENST00000288135.5:c.1676T>A	p.Val559Asp	p.V559D	ENST00000288135	NM_000222.2	559	gTt/gAt	11/21	1	2	FACETS	0.995	0.936	1	0.995	0.936	1	CLONAL	1	TRUE	1	0.839642518588542	2		396	536	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320279	30320279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	28	486	0	ENST00000322652.5:c.1220C>T	p.Thr407Ile	p.T407I	ENST00000322652	NM_015355.2	407	aCt/aTt	11/16	1	2	FACETS	0.131	0.104	0.161	0.131	0.104	0.161	SUBCLONAL	1	TRUE	1	0.839642518588542	2		486	510	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0014599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	552	739	1	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	0.550002894179847	3	FACETS	0.961	0.93	0.991	0.961	0.93	0.991	CLONAL	3	TRUE	0	0.550002894179847	3		740	888	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540230	23540235	+	inframe_deletion	In_Frame_Del	DEL	GGCTCC	GGCTCC	-	rs753037741	NA	P-0014599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	58	533	3	ENST00000380871.4:c.168_173del	p.Pro62_Glu63del	p.P62_E63del	ENST00000380871	NM_006167.3	56	ccGGAGCCa/cca	1/2	0.550002894179847	1	FACETS	0.662	0.576	0.754	0.662	0.576	0.754	SUBCLONAL	1	TRUE	0	0.550002894179847	1		536	231	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725463	117725463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	94	655	0	ENST00000368508.3:c.418G>A	p.Gly140Arg	p.G140R	ENST00000368508	NM_002944.2	140	Gga/Aga	5/43	0.448738010361708	3	FACETS	0.977	0.874	1	0.489	0.437	0.543	CLONAL	1	TRUE	1	0.550002894179847	3		655	446	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64126867	64126867	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	164	796	0	ENST00000334205.4:c.73G>T	p.Glu25Ter	p.E25*	ENST00000334205	NM_003942.2	25	Gag/Tag	2/17	0.550002894179847	3	FACETS	1	0.966	1	0.544	0.5	0.589	CLONAL	1	TRUE	1	0.550002894179847	3		796	699	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610137	28610138	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0014599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	180	635	0	ENST00000241453.7:c.1352_1353delinsAA	p.Ser451Ter	p.S451*	ENST00000241453	NM_004119.2	451	tCC/tAA	11/24	0.535127822388028	2	FACETS	0.829	0.775	0.883	0.829	0.775	0.883	CLONAL	2	TRUE	0	0.550002894179847	2		635	395	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644516	3644516	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1367749586	NA	P-0014599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	456	1125	0	ENST00000294008.3:c.2098G>A	p.Gly700Arg	p.G700R	ENST00000294008	NM_032444.2	700	Ggg/Agg	10/15	0.550002894179847	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.550002894179847	3		1125	1022	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615765	1615767	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs756376945	NA	P-0014599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	160	904	0	ENST00000344749.5:c.1504_1506del	p.Lys502del	p.K502del	ENST00000344749	NM_001136139.2	502	AAG/-	17/19	0.533776010437828	2	FACETS	0.934	0.86	1	0.467	0.43	0.506	CLONAL	1	TRUE	0	0.550002894179847	2		904	623	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610227	10610227	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	344	945	0	ENST00000171111.5:c.483G>C	p.Met161Ile	p.M161I	ENST00000171111	NM_203500.1	161	atG/atC	2/6	0.533776010437828	2	FACETS	0.928	0.886	0.97	0.928	0.886	0.97	CLONAL	2	TRUE	0	0.550002894179847	2		945	674	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076868	41076868	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	173	579	0	ENST00000373198.4:c.1552C>A	p.Leu518Ile	p.L518I	ENST00000373198	NM_133170.3	518	Ctc/Atc	9/32	0.503281741364151	4	FACETS	0.898	0.832	0.966	0.898	0.832	0.966	CLONAL	2	TRUE	2	0.550002894179847	4		579	543	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970826	55970826	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	616	547	0	ENST00000263923.4:c.1971del	p.Arg657SerfsTer6	p.R657Sfs*6	ENST00000263923	NM_002253.2	657	agG/ag	13/30	0.550002894179847	9	FACETS	0.993	0.961	1	0.993	0.961	1	CLONAL	6	TRUE	3	0.550002894179847	9		547	1100	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293849	1293849	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	168	1101	0	ENST00000310581.5:c.1152G>C	p.Gln384His	p.Q384H	ENST00000310581	NM_198253.2	384	caG/caC	2/16	0.550002894179847	4	FACETS	0.83	0.761	0.902	0.277	0.253	0.301	CLONAL	1	TRUE	1	0.550002894179847	4		1101	1141	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80074652	80074652	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	137	408	0	ENST00000265081.6:c.2432T>C	p.Leu811Pro	p.L811P	ENST00000265081	NM_002439.4	811	cTa/cCa	17/24	0.535127822388028	2	FACETS	0.89	0.825	0.954	0.89	0.825	0.954	CLONAL	2	TRUE	0	0.550002894179847	2		408	280	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670416	30670416	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	312	692	0	ENST00000376406.3:c.6016G>C	p.Gly2006Arg	p.G2006R	ENST00000376406	NM_014641.2	2006	Gga/Cga	14/15	0.535127822388028	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.550002894179847	2		692	552	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139054	37139054	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs760353228	NA	P-0014599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	128	584	0	ENST00000373509.5:c.394T>C	p.Phe132Leu	p.F132L	ENST00000373509	NM_002648.3	132	Ttc/Ctc	4/6	0.535127822388028	2	FACETS	1	0.919	1	0.504	0.46	0.55	CLONAL	1	TRUE	0	0.550002894179847	2		584	462	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509826	106509826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	239	707	0	ENST00000359195.3:c.1820C>T	p.Thr607Ile	p.T607I	ENST00000359195	NM_002649.2	607	aCa/aTa	2/11	0.489794986739916	4	FACETS	0.92	0.863	0.979	0.92	0.863	0.979	CLONAL	2	TRUE	2	0.550002894179847	4		707	732	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403492	139403492	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	230	988	0	ENST00000277541.6:c.3001G>T	p.Gly1001Cys	p.G1001C	ENST00000277541	NM_017617.3	1001	Ggc/Tgc	19/34	0.550002894179847	3	FACETS	1	0.988	1	0.629	0.587	0.671	CLONAL	1	TRUE	1	0.550002894179847	3		988	848	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841231	15841236	+	inframe_deletion	In_Frame_Del	DEL	AGCCGG	AGCCGG	-	rs752736259	NA	P-0014599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	81	422	0	ENST00000307771.7:c.1338_1343del	p.Ser447_Arg448del	p.S447_R448del	ENST00000307771	NM_005089.3	439	AGCCGG/-	11/11	1	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.550002894179847	1		422	198	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0014634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	217	670	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.311961732160858	2	FACETS	0.923	0.863	0.985	0.923	0.863	0.985	CLONAL	2	TRUE	0	0.351299586694635	2		670	669	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660481	67660482	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0014634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	182	451	0	ENST00000264010.4:c.1383dup	p.Tyr462LeufsTer3	p.Y462Lfs*3	ENST00000264010	NM_006565.3	461	tcc/tCcc	8/12	0.197719533471536	5	FACETS	1	0.976	1	0.75	0.694	0.808	INDETERMINATE	2	TRUE	2	0.351299586694635	5		451	703	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171475	123171475	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0014634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	88	464	1	ENST00000218089.9:c.385+2T>A		p.X129_splice	ENST00000218089	NM_001042749.1	129			0.351299586694635	5	FACETS	1	0.975	1	0.457	0.406	0.512	CLONAL	1	TRUE	2	0.351299586694635	5		465	558	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	213	300	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.307164400649034	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	1	0.307164400649034	3		300	778	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0014643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	109	668	2	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	0.307164400649034	1	FACETS	0.791	0.711	0.877	0.791	0.711	0.877	SUBCLONAL	1	TRUE	0	0.307164400649034	1		670	759	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271460	26271460	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	37	373	0	ENST00000305910.3:c.153G>C	p.Glu51Asp	p.E51D	ENST00000305910	NM_003534.2	51	gaG/gaC	1/1	0.307164400649034	1	FACETS	0.487	0.401	0.582	0.487	0.401	0.582	SUBCLONAL	1	TRUE	0	0.307164400649034	1		373	419	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916747	48916747	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690915	NA	P-0014643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	73	430	0	ENST00000267163.4:c.277C>T	p.Gln93Ter	p.Q93*	ENST00000267163	NM_000321.2	93	Caa/Taa	3/27	0.307164400649034	1	FACETS	0.861	0.756	0.975	0.861	0.756	0.975	CLONAL	1	TRUE	0	0.307164400649034	1		430	467	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606131	81606131	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	123	668	0	ENST00000298171.2:c.801G>C	p.Leu267Phe	p.L267F	ENST00000298171	NM_000369.2	267	ttG/ttC	9/10	1	2	FACETS	0.908	0.821	1	0.908	0.821	1	CLONAL	1	TRUE	1	0.307164400649034	2		668	882	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202851	16202851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777745414	NA	P-0014643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	92	592	1	ENST00000375759.3:c.559C>T	p.Arg187Trp	p.R187W	ENST00000375759	NM_015001.2	187	Cgg/Tgg	3/15	NA	2	FACETS	0.8	0.71	0.895			1	INDETERMINATE	1	TRUE	NA	0.307164400649034	2		593	749	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218793	133218793	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1368719601	NA	P-0014643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	73	589	2	ENST00000320574.5:c.5143G>A	p.Glu1715Lys	p.E1715K	ENST00000320574	NM_006231.2	1715	Gag/Aag	38/49	1	2	FACETS	0.584	0.51	0.664	0.584	0.51	0.664	SUBCLONAL	1	TRUE	1	0.307164400649034	2		591	814	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250731	10250731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	130	806	0	ENST00000340748.4:c.3749C>T	p.Ser1250Phe	p.S1250F	ENST00000340748		1250	tCc/tTc	32/40	1	2	FACETS	0.912	0.827	1	0.912	0.827	1	CLONAL	1	TRUE	1	0.307164400649034	2		806	928	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026303	48026303	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1410933611	NA	P-0014643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	90	420	0	ENST00000234420.5:c.1181C>G	p.Ser394Cys	p.S394C	ENST00000234420	NM_000179.2	394	tCt/tGt	4/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.307164400649034	2		420	535	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793242	242793242	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	186	807	0	ENST00000334409.5:c.835C>G	p.Pro279Ala	p.P279A	ENST00000334409	NM_005018.2	279	Cct/Gct	5/5	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.307164400649034	2		807	1001	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628694	187628694	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	128	724	0	ENST00000441802.2:c.2288G>T	p.Ser763Ile	p.S763I	ENST00000441802	NM_005245.3	763	aGt/aTt	2/27	0.307164400649034	1	FACETS	0.931	0.844	1	0.931	0.844	1	CLONAL	1	TRUE	0	0.307164400649034	1		724	758	SUCCESS
APC	324	MSKCC	GRCh37	5	112090627	112090627	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	51	426	0	ENST00000257430.4:c.40G>C	p.Glu14Gln	p.E14Q	ENST00000257430	NM_000038.5	14	Gag/Cag	2/16	1	2	FACETS	0.603	0.512	0.702	0.603	0.512	0.702	SUBCLONAL	1	TRUE	1	0.307164400649034	2		426	551	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148526856	148526856	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	102	541	0	ENST00000320356.2:c.448A>G	p.Ile150Val	p.I150V	ENST00000320356	NM_004456.4	150	Ata/Gta	5/20	1	2	FACETS	0.921	0.824	1	0.921	0.824	1	CLONAL	1	TRUE	1	0.307164400649034	2		541	721	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202866	27202866	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	77	656	0	ENST00000380036.4:c.1958C>T	p.Ser653Phe	p.S653F	ENST00000380036	NM_000459.3	653	tCc/tTc	13/23	1	2	FACETS	0.677	0.593	0.766	0.677	0.593	0.766	SUBCLONAL	1	TRUE	1	0.307164400649034	2		656	741	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640983	3640983	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	260	839	2	ENST00000294008.3:c.2656G>A	p.Val886Ile	p.V886I	ENST00000294008	NM_032444.2	886	Gtt/Att	12/15	1	2	FACETS	0.953	0.893	1	0.953	0.893	1	CLONAL	1	TRUE	1	0.527788800200964	2		841	1034	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556397	29556397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1135402831	NA	P-0014845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	213	569	0	ENST00000356175.3:c.2764G>A	p.Gly922Ser	p.G922S	ENST00000356175	NM_000267.3	922	Ggt/Agt	21/57	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.527788800200964	2		569	739	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39721111	39721111	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0014845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	130	408	0	ENST00000361337.2:c.615-1G>A		p.X205_splice	ENST00000361337	NM_003286.2	205			1	2	FACETS	0.928	0.846	1	0.928	0.846	1	CLONAL	1	TRUE	1	0.527788800200964	2		408	531	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9928021	9928021	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	295	622	0	ENST00000330684.3:c.1718T>A	p.Val573Asp	p.V573D	ENST00000330684	NM_001134407.1	573	gTt/gAt	8/13	1	2	FACETS	0.888	0.838	0.939	0.888	0.838	0.939	CLONAL	1	TRUE	1	0.733245624508241	2		622	906	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577017	7577017	+	splice_donor_variant	Splice_Site	SNP	A	A	C	rs1131691016	NA	P-0014903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	445	812	0	ENST00000269305.4:c.919+2T>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.733245624508241	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.733245624508241	1		812	756	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249378	110249379	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CA	CA	-	novel	NA	P-0014903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	1351	1496	1	ENST00000374672.4:c.1194_1195del	p.Cys398Ter	p.C398*	ENST00000374672	NM_004235.4	398	tgTGat/tgat	4/5	NA	2	FACETS	0.957	0.939	0.974			1	INDETERMINATE	2	TRUE	NA	0.733245624508241	2		1497	1926	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0014957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	627	732	0	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.831158704338162	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.831158704338162	2		732	737	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942067	71942067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	292	801	1	ENST00000298229.2:c.1331C>T	p.Ser444Phe	p.S444F	ENST00000298229	NM_001567.3	444	tCc/tTc	12/28	0.78430638090041	4	FACETS	0.945	0.888	1			1	CLONAL	1	TRUE	NA	0.831158704338162	4		802	1361	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828716	3828716	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	238	613	0	ENST00000262367.5:c.1926G>C	p.Glu642Asp	p.E642D	ENST00000262367	NM_004380.2	642	gaG/gaC	9/31	1	2	FACETS	0.885	0.831	0.94	0.885	0.831	0.94	CLONAL	1	TRUE	1	0.831158704338162	2		613	647	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532501	63532501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755519590	NA	P-0014957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	722	745	2	ENST00000307078.5:c.2078C>T	p.Thr693Met	p.T693M	ENST00000307078	NM_004655.3	693	aCg/aTg	8/11	0.831158704338162	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.831158704338162	3		747	794	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265400	10265400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	246	721	0	ENST00000340748.4:c.1646C>T	p.Ser549Phe	p.S549F	ENST00000340748		549	tCc/tTc	20/40	0.761680373235127	3	FACETS	0.938	0.879	1	0.469	0.439	0.5	CLONAL	1	TRUE	1	0.831158704338162	3		721	893	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953244	17953244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	213	868	2	ENST00000458235.1:c.742G>A	p.Ala248Thr	p.A248T	ENST00000458235	NM_000215.3	248	Gcc/Acc	6/24	0.761680373235127	3	FACETS	0.913	0.85	0.977	0.456	0.425	0.489	CLONAL	1	TRUE	1	0.831158704338162	3		870	795	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971744	18971744	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339813676	NA	P-0014957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	227	677	0	ENST00000262803.5:c.2410G>A	p.Val804Met	p.V804M	ENST00000262803	NM_002911.3	804	Gtg/Atg	17/24	0.761680373235127	3	FACETS	0.928	0.867	0.991	0.464	0.433	0.496	CLONAL	1	TRUE	1	0.831158704338162	3		677	833	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309867	30309867	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1187252281	NA	P-0014957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1363	218	522	0	ENST00000307677.4:c.155A>G	p.Asn52Ser	p.N52S	ENST00000307677	NM_138578.1	52	aAt/aGt	2/3	0.831158704338162	6	FACETS	0.883	0.819	0.951	0.221	0.204	0.238	CLONAL	1	TRUE	2	0.831158704338162	6		522	1581	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132856	152132856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	107	508	0	ENST00000262189.6:c.16G>A	p.Asp6Asn	p.D6N	ENST00000262189	NM_170606.2	6	Gac/Aac	1/59	0.726044413457562	3	FACETS	0.592	0.532	0.655			1	SUBCLONAL	1	TRUE	NA	0.831158704338162	3		508	616	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27229067	27229188	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTAAGAAAACCAAGGTATTGCTGTAACTGCCGCTGGCAGAGGTGGAATCAAAGCAGCCTATGTCTCTGAACCATTTTCATTCTTCCAGACCTACGTGAATACCACGCTTTATGAGAAGTTT	ACTAAGAAAACCAAGGTATTGCTGTAACTGCCGCTGGCAGAGGTGGAATCAAAGCAGCCTATGTCTCTGAACCATTTTCATTCTTCCAGACCTACGTGAATACCACGCTTTATGAGAAGTTT	-	novel	NA	P-0014957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	127	193	0	ENST00000380036.4:c.3301-86_3336del		p.X1101_splice	ENST00000380036	NM_000459.3	1101		23/23	0.831158704338162	3	FACETS	0.764	0.705	0.824	0.51	0.47	0.55	SUBCLONAL	2	TRUE	0	0.831158704338162	3		193	283	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877183	89877183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	506	671	1	ENST00000389301.3:c.454G>A	p.Ala152Thr	p.A152T	ENST00000389301	NM_000135.2	152	Gct/Act	5/43	0.90271838264755	1	FACETS	0.973	0.949	0.996	0.973	0.949	0.996	CLONAL	1	TRUE	0	0.90271838264755	1		672	632	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653160	29653160	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	312	383	0	ENST00000356175.3:c.5095G>T	p.Glu1699Ter	p.E1699*	ENST00000356175	NM_000267.3	1699	Gag/Tag	36/57	0.90271838264755	1	FACETS	0.967	0.937	0.996	0.967	0.937	0.996	CLONAL	1	TRUE	0	0.90271838264755	1		383	392	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281574	15281574	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	894	1082	0	ENST00000263388.2:c.4799G>A	p.Cys1600Tyr	p.C1600Y	ENST00000263388	NM_000435.2	1600	tGc/tAc	26/33	0.90271838264755	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.90271838264755	1		1082	1059	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659262	86659262	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	277	351	0	ENST00000274376.6:c.1551A>T	p.Lys517Asn	p.K517N	ENST00000274376	NM_002890.2	517	aaA/aaT	11/25	0.90271838264755	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.90271838264755	1		351	325	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974682	21974695	+	frameshift_variant	Frame_Shift_Del	DEL	TCGGCCTCCGACCG	TCGGCCTCCGACCG	-	novel	NA	P-0015013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	333	490	0	ENST00000304494.5:c.132_145del	p.Gly45ProfsTer70	p.G45Pfs*70	ENST00000304494	NM_000077.4	44	taCGGTCGGAGGCCGAtc/tatc	1/3	0.90271838264755	1	FACETS	0.944	0.914	0.972	0.944	0.914	0.972	CLONAL	1	TRUE	0	0.90271838264755	1		490	429	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0015064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	76	515	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.260566595372281	3	FACETS	0.477	0.418	0.542	0.239	0.209	0.271	INDETERMINATE	1	TRUE	1	0.517748093359417	3		515	774	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0015064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	266	585	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.517748093359417	2		585	779	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040972	42040972	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	177	570	0	ENST00000219905.7:c.5350G>T	p.Gly1784Ter	p.G1784*	ENST00000219905	NM_001164273.1	1784	Gga/Tga	16/24	1	2	FACETS	0.864	0.798	0.934	0.864	0.798	0.934	CLONAL	1	TRUE	1	0.517748093359417	2		570	791	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506164	148506164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	75	441	0	ENST00000320356.2:c.2194A>G	p.Arg732Gly	p.R732G	ENST00000320356	NM_004456.4	732	Aga/Gga	19/20	0.517748093359417	3	FACETS	0.474	0.415	0.538	0.237	0.207	0.269	SUBCLONAL	1	TRUE	1	0.517748093359417	3		441	769	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115955	8115956	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0016627-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	111	408	0	ENST00000346208.3:c.1305dup	p.Ser436LeufsTer71	p.S436Lfs*71	ENST00000346208		434	cac/caCc	6/6	0.277305318989925	5	FACETS	1	0.962	1	0.227	0.204	0.251	INDETERMINATE	1	TRUE	0	0.712179738161837	5		408	568	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530077	63530077	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016627-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4975	994	587	0	ENST00000307078.5:c.2358G>C	p.Leu786Phe	p.L786F	ENST00000307078	NM_004655.3	786	ttG/ttC	10/11	0.712179738161837	24	FACETS	1	0.985	1			1	CLONAL	4	TRUE	NA	0.712179738161837	24		587	5969	SUCCESS
BTK	695	MSKCC	GRCh37	X	100612524	100612524	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016627-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	129	426	1	ENST00000308731.7:c.1150G>A	p.Ala384Thr	p.A384T	ENST00000308731	NM_000061.2	384	Gca/Aca	13/19	NA	2	FACETS	1	0.958	1			1	INDETERMINATE	1	TRUE	NA	0.712179738161837	2		427	339	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521306	8521306	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs776820755	NA	P-0016627-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	70	308	0	ENST00000356435.5:c.932T>C	p.Ile311Thr	p.I311T	ENST00000356435		311	aTt/aCt	9/35	0.712523151596255	3	FACETS	0.791	0.695	0.894	0.264	0.231	0.298	SUBCLONAL	1	TRUE	0	0.712179738161837	3		308	337	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212002	94212002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016627-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	22	403	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	0.712179738161837	NA		403	362	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720649	89720649	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs587782455	NA	P-0016983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	180	256	0	ENST00000371953.3:c.802-2A>T		p.X268_splice	ENST00000371953	NM_000314.4	268			NA	2	FACETS	0.814	0.768	0.859			1	INDETERMINATE	2	TRUE	NA	0.742434659242827	2		256	298	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057520005	NA	P-0016983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	616	755	0	ENST00000269305.4:c.820G>T	p.Val274Phe	p.V274F	ENST00000269305	NM_001126112.2	274	Gtt/Ttt	8/11	1	2	FACETS	1	0.994	1	1	0.998	1	CLONAL	2	TRUE	1	0.742434659242827	2		755	788	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790908	89790910	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs746966684	NA	P-0016983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	110	571	2	ENST00000336032.3:c.301_303del	p.Lys101del	p.K101del	ENST00000336032	NM_006813.2	99	AAG/-	1/2	0.481227199732752	1	FACETS	0.344	0.31	0.38	0.344	0.31	0.38	SUBCLONAL	1	TRUE	0	0.742434659242827	1		573	542	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375135	118375145	+	frameshift_variant	Frame_Shift_Del	DEL	ACTGTGGGAAT	ACTGTGGGAAT	-	novel	NA	P-0016983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	133	473	0	ENST00000534358.1:c.8529_8539del	p.Cys2844ProfsTer21	p.C2844Pfs*21	ENST00000534358	NM_005933.3	2843	gACTGTGGGAAT/g	27/36	0.457832143197299	3	FACETS	0.871	0.794	0.951	0.436	0.397	0.476	CLONAL	1	TRUE	1	0.742434659242827	3		473	564	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965128	25965132	+	frameshift_variant	Frame_Shift_Del	DEL	ATGAC	ATGAC	-	novel	NA	P-0016983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	465	622	0	ENST00000435504.4:c.4074_4078del	p.Met1358IlefsTer11	p.M1358Ifs*11	ENST00000435504		1358	atGTCATtt/attt	13/13	0.742434659242827	3	FACETS	0.93	0.894	0.967	0.93	0.894	0.967	CLONAL	2	TRUE	1	0.742434659242827	3		622	923	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405911	157405911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779271100	NA	P-0016983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	218	530	1	ENST00000346085.5:c.2153C>T	p.Ser718Leu	p.S718L	ENST00000346085	NM_020732.3	718	tCg/tTg	6/20	0.481227199732752	1	FACETS	0.763	0.718	0.809	0.763	0.718	0.809	SUBCLONAL	1	TRUE	0	0.742434659242827	1		531	484	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0019042-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	248	482	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	1	2	FACETS	0.879	0.825	0.935	0.879	0.825	0.935	CLONAL	1	TRUE	1	0.721479337919313	2		482	782	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339568	70339568	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019042-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	45	502	1	ENST00000374080.3:c.237G>T	p.Glu79Asp	p.E79D	ENST00000374080		79	gaG/gaT	3/45	1	2	FACETS	0.146	0.122	0.172	0.146	0.122	0.172	SUBCLONAL	1	TRUE	1	0.721479337919313	2		503	856	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125222	47125222	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019042-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	192	312	0	ENST00000409792.3:c.6048G>A	p.Trp2016Ter	p.W2016*	ENST00000409792	NM_014159.6	2016	tgG/tgA	12/21	1	2	FACETS	0.939	0.874	1	0.939	0.874	1	CLONAL	1	TRUE	1	0.721479337919313	2		312	567	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261234	115261234	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019042-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	33	442	0	ENST00000438362.2:c.2487G>A	p.Met829Ile	p.M829I	ENST00000438362	NM_001242891.1	829	atG/atA	19/20	0.721479337919313	1	FACETS	0.124	0.1	0.15	0.124	0.1	0.15	SUBCLONAL	1	TRUE	0	0.721479337919313	1		442	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0019465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	766	976	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.453156587290019	6	FACETS	0.974	0.943	1	0.974	0.943	1	CLONAL	4	TRUE	2	0.453156587290019	6		976	1655	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0019465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	315	833	3	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.453156587290019	6	FACETS	0.934	0.879	0.99	0.467	0.439	0.495	CLONAL	2	TRUE	2	0.453156587290019	6		836	1419	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	304	579	2	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.216915207321633	6	FACETS	0.885	0.836	0.936			1	INDETERMINATE	3	TRUE	NA	0.453156587290019	6		581	963	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630529	47630529	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs768824654	NA	P-0019465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	204	484	0	ENST00000233146.2:c.199A>G	p.Met67Val	p.M67V	ENST00000233146	NM_000251.2	67	Atg/Gtg	1/16	0.341590663937608	5	FACETS	1	0.956	1	0.692	0.643	0.741	CLONAL	2	TRUE	2	0.453156587290019	5		484	729	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140151	50140151	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	352	637	2	ENST00000246792.3:c.274G>T	p.Ala92Ser	p.A92S	ENST00000246792	NM_006270.3	92	Gcc/Tcc	3/6	0.216915207321633	6	FACETS	0.85	0.805	0.895			1	INDETERMINATE	3	TRUE	NA	0.453156587290019	6		639	1162	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0020476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	245	300	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.251407014458189	3	FACETS	0.786	0.737	0.837	0.786	0.737	0.837	INDETERMINATE	2	TRUE	1	0.470521731916092	3		300	818	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911005	94911007	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0020476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	277	1239	1	ENST00000536441.1:c.1123_1125del	p.Leu375del	p.L375del	ENST00000536441	NM_144665.3	375	CTT/-	8/10	0.470521731916092	1	FACETS	0.77	0.723	0.819	0.77	0.723	0.819	SUBCLONAL	1	TRUE	0	0.470521731916092	1		1240	1169	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348962	11348962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	471	1191	0	ENST00000332029.2:c.374G>A	p.Ser125Asn	p.S125N	ENST00000332029	NM_003745.1	125	aGc/aAc	2/2	0.179814083965353	3	FACETS	0.794	0.758	0.83	0.794	0.758	0.83	INDETERMINATE	2	TRUE	1	0.470521731916092	3		1191	1558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577061	7577062	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0020476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	392	1186	0	ENST00000269305.4:c.876_877del	p.Glu294AlafsTer11	p.E294Afs*11	ENST00000269305	NM_001126112.2	292	aaAGgg/aagg	8/11	0.470521731916092	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.470521731916092	1		1186	1221	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026832	71026832	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	215	614	0	ENST00000318789.4:c.1390G>C	p.Val464Leu	p.V464L	ENST00000318789	NM_032682.5	464	Gtt/Ctt	16/21	0.251407014458189	3	FACETS	1	0.991	1	0.707	0.659	0.757	INDETERMINATE	1	TRUE	1	0.470521731916092	3		614	798	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0020549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	73	271	2	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	0.918306026354522	1	FACETS	0.735	0.671	0.796	0.735	0.671	0.796	SUBCLONAL	1	TRUE	0	0.918306026354522	1		273	117	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0020549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	727	961	3	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	NA	2	FACETS	0.993	0.979	1			1	INDETERMINATE	2	TRUE	NA	0.918306026354522	2		964	797	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114255	73114266	+	inframe_deletion	In_Frame_Del	DEL	AGAAGAGGATGA	AGAAGAGGATGA	-	rs754988583	NA	P-0020549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	20	327	0	ENST00000356692.5:c.906_917del	p.Asp304_Glu307del	p.D304_E307del	ENST00000356692		297	acAGAAGAGGATGAa/aca	8/9	1	2	FACETS	0.199	0.152	0.253	0.199	0.152	0.253	SUBCLONAL	1	TRUE	1	0.918306026354522	2		327	219	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47679234	47679234	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs890324763	NA	P-0020549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	234	516	0	ENST00000347630.2:c.973A>G	p.Ile325Val	p.I325V	ENST00000347630	NM_001007230.1	325	Atc/Gtc	10/11	0.918306026354522	2	FACETS	1	0.951	1	0.505	0.476	0.534	CLONAL	1	TRUE	0	0.918306026354522	2		516	505	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38955805	38955805	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	121	409	0	ENST00000357387.3:c.2501A>T	p.Glu834Val	p.E834V	ENST00000357387	NM_152756.3	834	gAa/gTa	26/38	0.879047043252068	3	FACETS	0.896	0.816	0.98	0.448	0.408	0.49	CLONAL	1	TRUE	1	0.918306026354522	3		409	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0020562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	323	917	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.649620423654692	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.649620423654692	1		917	651	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0020562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	262	957	4	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	0.4632814486346	1	FACETS	0.884	0.835	0.934	0.884	0.835	0.934	CLONAL	1	TRUE	0	0.649620423654692	1		961	616	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134988	41134988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	95	406	0	ENST00000379561.5:c.640C>T	p.Arg214Cys	p.R214C	ENST00000379561	NM_002015.3	214	Cgt/Tgt	2/3	1	2	FACETS	0.908	0.818	1	0.908	0.818	1	CLONAL	1	TRUE	1	0.649620423654692	2		406	322	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920669	100920670	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0020562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	156	798	2	ENST00000325455.5:c.2478_2479delinsAA	p.Leu827Ile	p.L827I	ENST00000325455	NM_001202474.3	826	ctTCtt/ctAAtt	6/8	1	2	FACETS	0.858	0.79	0.928	0.858	0.79	0.928	CLONAL	1	TRUE	1	0.649620423654692	2		800	560	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128601	30128601	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	151	645	0	ENST00000263025.4:c.781C>G	p.Leu261Val	p.L261V	ENST00000263025	NM_002746.2	261	Ctg/Gtg	6/9	1	2	FACETS	0.975	0.898	1	0.975	0.898	1	CLONAL	1	TRUE	1	0.649620423654692	2		645	477	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324922	31324922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	301	870	0	ENST00000412585.2:c.14C>T	p.Ala5Val	p.A5V	ENST00000412585	NM_005514.6	5	gCg/gTg	1/8	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.649620423654692	2		870	727	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238417	98238417	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs137903539	NA	P-0020562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	176	714	1	ENST00000331920.6:c.1627C>A	p.Arg543Ser	p.R543S	ENST00000331920	NM_000264.3	543	Cgc/Agc	12/24	0.649620423654692	1	FACETS	0.941	0.879	1	0.941	0.879	1	CLONAL	1	TRUE	0	0.649620423654692	1		715	389	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0020577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	81	958	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.196195567696046	5	FACETS	1	0.972	1	0.456	0.401	0.514	CLONAL	1	TRUE	2	0.257504349616297	5		958	638	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	109	336	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.256107334866884	2	FACETS	0.966	0.874	1	0.966	0.874	1	CLONAL	2	TRUE	0	0.257504349616297	2		336	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs786202525	NA	P-0020577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	224	900	1	ENST00000269305.4:c.532del	p.His178ThrfsTer69	p.H178Tfs*69	ENST00000269305	NM_001126112.2	178	Cac/ac	5/11	0.255068798606236	2	FACETS	0.97	0.904	1	0.97	0.904	1	CLONAL	2	TRUE	0	0.257504349616297	2		901	897	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0020577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	247	588	1	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.255068798606236	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.257504349616297	2		589	923	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857910	9857910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	171	754	9	ENST00000330684.3:c.3491C>T	p.Thr1164Met	p.T1164M	ENST00000330684	NM_001134407.1	1164	aCg/aTg	13/13	0.144446648461869	5	FACETS	0.956	0.879	1	0.637	0.586	0.691	INDETERMINATE	2	TRUE	2	0.257504349616297	5		763	963	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100117	157100119	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs797045268	NA	P-0020577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	10	70	0	ENST00000346085.5:c.1069_1071del	p.Gly357del	p.G357del	ENST00000346085	NM_020732.3	352	GGC/-	1/20	0.257504349616297	3	FACETS	0.985	0.675	1	0.493	0.337	0.683	CLONAL	1	TRUE	1	0.257504349616297	3		70	89	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40367512	40367512	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1334492695	NA	P-0020577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	11	56	0	ENST00000397332.2:c.49G>T	p.Gly17Cys	p.G17C	ENST00000397332	NM_001033082.2	17	Ggt/Tgt	1/3	0.213831830616852	3	FACETS	1	0.801	1	0.603	0.422	0.82	CLONAL	1	TRUE	1	0.257504349616297	3		56	80	SUCCESS
ATM	472	MSKCC	GRCh37	11	108183136	108183137	+	splice_acceptor_variant	Splice_Site	DEL	AG	AG	-	novel	NA	P-0020577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	67	540	0	ENST00000278616.4:c.5919-1_5919del		p.X1973_splice	ENST00000278616	NM_000051.3	1973			0.196195567696046	5	FACETS	1	0.883	1	0.674	0.589	0.764	CLONAL	2	TRUE	2	0.257504349616297	5		540	357	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202630	108202630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	79	580	1	ENST00000278616.4:c.7654C>T	p.His2552Tyr	p.H2552Y	ENST00000278616	NM_000051.3	2552	Cac/Tac	52/63	0.196195567696046	5	FACETS	1	0.919	1	0.7	0.619	0.786	CLONAL	2	TRUE	2	0.257504349616297	5		581	405	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929175	44929176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	215	912	0	ENST00000377967.4:c.2278dup	p.Cys760LeufsTer4	p.C760Lfs*4	ENST00000377967	NM_021140.2	759	gtt/gTtt	17/29	0.213831830616852	3	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	1	0.257504349616297	3		912	932	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410733	63410733	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374879781	NA	P-0020577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	189	976	3	ENST00000330258.3:c.2434G>A	p.Ala812Thr	p.A812T	ENST00000330258	NM_152424.3	812	Gct/Act	2/2	0.213831830616852	3	FACETS	0.827	0.764	0.892	0.827	0.764	0.892	CLONAL	2	TRUE	1	0.257504349616297	3		979	1002	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0020589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	223	479	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	0.991	1	CLONAL	1	TRUE	1	0.464834080979564	2		479	703	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426955	49426955	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	53	654	0	ENST00000301067.7:c.11533C>T	p.Gln3845Ter	p.Q3845*	ENST00000301067	NM_003482.3	3845	Cag/Tag	39/54	1	2	FACETS	0.315	0.267	0.366	0.315	0.267	0.366	SUBCLONAL	1	TRUE	1	0.464834080979564	2		654	725	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432741	49432741	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1315374796	NA	P-0020589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	57	868	0	ENST00000301067.7:c.8398C>T	p.Gln2800Ter	p.Q2800*	ENST00000301067	NM_003482.3	2800	Cag/Tag	34/54	1	2	FACETS	0.252	0.215	0.292	0.252	0.215	0.292	SUBCLONAL	1	TRUE	1	0.464834080979564	2		868	974	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023196	48023196	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	47	686	0	ENST00000234420.5:c.621G>C	p.Glu207Asp	p.E207D	ENST00000234420	NM_000179.2	207	gaG/gaC	3/10	1	2	FACETS	0.226	0.189	0.266	0.226	0.189	0.266	SUBCLONAL	1	TRUE	1	0.464834080979564	2		686	896	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016336	150016336	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	60	597	0	ENST00000253339.5:c.370C>T	p.Gln124Ter	p.Q124*	ENST00000253339		124	Cag/Tag	2/7	0.464834080979564	1	FACETS	0.334	0.287	0.384	0.334	0.287	0.384	SUBCLONAL	1	TRUE	0	0.464834080979564	1		597	594	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	503	174	0				ENST00000310581	NM_198253.2	-/1132			0.581647167776092	4	FACETS	0.963	0.928	0.998	0.963	0.928	0.998	CLONAL	3	TRUE	1	0.581647167776092	4		174	947	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243708901	243708901	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0020592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	115	689	1	ENST00000263826.5:c.1164-2A>G		p.X388_splice	ENST00000263826	NM_005465.4	388			NA	2	FACETS	0.777	0.703	0.854			1	INDETERMINATE	1	TRUE	NA	0.581647167776092	2		690	509	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440142	49440145	+	frameshift_variant	Frame_Shift_Del	DEL	TAAC	TAAC	-	novel	NA	P-0020592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	95	976	0	ENST00000301067.7:c.4481_4484del	p.Ser1494ThrfsTer11	p.S1494Tfs*11	ENST00000301067	NM_003482.3	1494	aGTTAc/ac	16/54	0.290120278631254	2	FACETS	0.374	0.332	0.419	0.187	0.166	0.21	INDETERMINATE	1	TRUE	0	0.581647167776092	2		976	873	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579503	7579503	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567556752	NA	P-0020592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	367	1163	0	ENST00000269305.4:c.184G>T	p.Glu62Ter	p.E62*	ENST00000269305	NM_001126112.2	62	Gaa/Taa	4/11	0.100810840271738	3	FACETS	0.984	0.938	1			1	INDETERMINATE	2	TRUE	NA	0.581647167776092	3		1163	828	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651959	36651959	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	788	826	0	ENST00000244741.5:c.81del	p.Ser27ArgfsTer4	p.S27Rfs*4	ENST00000244741	NM_000389.4	27	agC/ag	2/3	0.581647167776092	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	TRUE	0	0.581647167776092	3		826	1166	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522588	157522588	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1385677376	NA	P-0020592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	99	1051	0	ENST00000346085.5:c.4860G>C	p.Leu1620Phe	p.L1620F	ENST00000346085	NM_020732.3	1620	ttG/ttC	18/20	1	2	FACETS	0.387	0.345	0.432	0.387	0.345	0.432	SUBCLONAL	1	TRUE	1	0.581647167776092	2		1051	880	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974105	2974105	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1286226733	NA	P-0020592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	202	640	1	ENST00000396946.4:c.1500G>A	p.Met500Ile	p.M500I	ENST00000396946	NM_032415.4	500	atG/atA	10/25	0.323969249016792	3	FACETS	1	0.991	1	0.731	0.682	0.782	INDETERMINATE	1	TRUE	1	0.581647167776092	3		641	613	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938916	76938918	+	missense_variant	Missense_Mutation	TNP	TCT	TCT	ATC	novel	NA	P-0020592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	110	578	0	ENST00000373344.5:c.1830_1832delinsGAT	p.Asp611Ile	p.D611I	ENST00000373344	NM_000489.3	610	caAGAt/caGATt	9/35	0.373275316349466	2	FACETS	0.743	0.671	0.819			1	SUBCLONAL	1	TRUE	NA	0.581647167776092	2		578	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0020608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	271	670	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.553318129604783	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.646179198183335	1		670	541	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242454	55242454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778250	NA	P-0020608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	177	745	1	ENST00000275493.2:c.2224G>A	p.Val742Ile	p.V742I	ENST00000275493	NM_005228.3	742	Gtc/Atc	19/28	0.56529872493383	4	FACETS	0.857	0.789	0.928	0.429	0.394	0.464	CLONAL	1	TRUE	2	0.646179198183335	4		746	1052	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206648	108206648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881321	NA	P-0020608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	373	620	2	ENST00000278616.4:c.8228C>T	p.Thr2743Met	p.T2743M	ENST00000278616	NM_000051.3	2743	aCg/aTg	56/63	0.646749272212046	3	FACETS	0.927	0.885	0.969	0.927	0.885	0.969	CLONAL	2	TRUE	1	0.646179198183335	3		622	824	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106830	27106831	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	433	700	0	ENST00000324856.7:c.6442dup	p.Tyr2148LeufsTer2	p.Y2148Lfs*2	ENST00000324856	NM_006015.4	2147	-/T	20/20	NA	2	FACETS	0.967	0.933	1			1	INDETERMINATE	2	TRUE	NA	0.646179198183335	2		700	693	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627506	37627506	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	165	720	1	ENST00000447079.4:c.1421A>G	p.Asn474Ser	p.N474S	ENST00000447079	NM_015083.1	474	aAt/aGt	2/14	1	2	FACETS	0.802	0.739	0.866	0.802	0.739	0.866	CLONAL	1	TRUE	1	0.661727085666773	2		721	622	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144645	55144645	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1318827602	NA	P-0020671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	167	634	0	ENST00000257290.5:c.2119A>G	p.Ile707Val	p.I707V	ENST00000257290	NM_006206.4	707	Atc/Gtc	15/23	1	2	FACETS	0.988	0.914	1	0.988	0.914	1	CLONAL	1	TRUE	1	0.661727085666773	2		634	511	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649640	48649640	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	119	972	0	ENST00000376670.3:c.124G>C	p.Asp42His	p.D42H	ENST00000376670	NM_002049.3	42	Gat/Cat	2/6	1	2	FACETS	0.478	0.431	0.527	0.478	0.431	0.527	SUBCLONAL	1	TRUE	1	0.661727085666773	2		972	753	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0020685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	487	844	1	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.710082806021984	2	FACETS	0.891	0.863	0.918	0.891	0.863	0.918	CLONAL	2	TRUE	0	0.755049869627154	2		845	724	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598246	28598246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	178	897	1	ENST00000253063.3:c.218C>T	p.Ser73Phe	p.S73F	ENST00000253063	NM_031459.4	73	tCt/tTt	3/10	1	2	FACETS	0.455	0.418	0.492	0.455	0.418	0.492	SUBCLONAL	1	TRUE	1	0.755049869627154	2		898	1037	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747109	40747109	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	133	700	2	ENST00000373198.4:c.2973G>T	p.Trp991Cys	p.W991C	ENST00000373198	NM_133170.3	991	tgG/tgT	22/32	0.362362697791068	4	FACETS	0.604	0.548	0.664	0.302	0.274	0.332	INDETERMINATE	1	TRUE	2	0.755049869627154	4		702	1023	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242482	55242506	+	protein_altering_variant	In_Frame_Del	DEL	CATCTCCGAAAGCCAACAAGGAAAT	CATCTCCGAAAGCCAACAAGGAAAT	A	novel	NA	P-0020685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	2437	656	0	ENST00000275493.2:c.2252_2276delinsA	p.Thr751_Ile759delinsAsn	p.T751_I759delinsN	ENST00000275493	NM_005228.3	751	aCATCTCCGAAAGCCAACAAGGAAATc/aAc	19/28	0.755049869627154	17	FACETS	0.994	0.981	1			1	CLONAL	13	TRUE	NA	0.755049869627154	17		656	3328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579355	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519997	NA	P-0020699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	485	1173	0	ENST00000269305.4:c.332T>C	p.Leu111Pro	p.L111P	ENST00000269305	NM_001126112.2	111	cTg/cCg	4/11	0.56014174821609	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.56014174821609	1		1173	1130	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165869	118165869	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	115	525	0	ENST00000369448.3:c.379C>G	p.Leu127Val	p.L127V	ENST00000369448	NM_017709.3	127	Ctc/Gtc	2/2	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.838671115314884	2		525	242	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166016	118166016	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	208	590	1	ENST00000369448.3:c.526C>G	p.Gln176Glu	p.Q176E	ENST00000369448	NM_017709.3	176	Cag/Gag	2/2	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.838671115314884	2		591	372	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166315	118166315	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	54	396	0	ENST00000369448.3:c.825C>G	p.Phe275Leu	p.F275L	ENST00000369448	NM_017709.3	275	ttC/ttG	2/2	1	2	FACETS	0.776	0.676	0.88	0.776	0.676	0.88	SUBCLONAL	1	TRUE	1	0.838671115314884	2		396	166	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166528	118166528	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	105	565	0	ENST00000369448.3:c.1038C>G	p.Ile346Met	p.I346M	ENST00000369448	NM_017709.3	346	atC/atG	2/2	1	2	FACETS	0.697	0.631	0.767	0.697	0.631	0.767	SUBCLONAL	1	TRUE	1	0.838671115314884	2		565	359	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840078	27840095	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	GCTTTGTTCGTGCCATGG	GCTTTGTTCGTGCCATGG	-	novel	NA	P-0020700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	126	561	0	ENST00000328488.2:c.-2_16del		p.*1*	ENST00000328488	NM_003533.2	?-6/136		1/1	0.760897777098076	2	FACETS	0.799	0.75	0.847	0.799	0.75	0.847	SUBCLONAL	2	TRUE	0	0.838671115314884	2		561	188	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38134009	38134009	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	116	695	0	ENST00000317025.8:c.3877G>A	p.Ala1293Thr	p.A1293T	ENST00000317025	NM_023034.1	1293	Gcg/Acg	23/24	1	2	FACETS	0.957	0.877	1	0.957	0.877	1	CLONAL	1	TRUE	1	0.838671115314884	2		695	289	SUCCESS
EED	8726	MSKCC	GRCh37	11	85961452	85961452	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0020752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	209	397	0	ENST00000263360.6:c.229A>T	p.Lys77Ter	p.K77*	ENST00000263360	NM_003797.3	77	Aaa/Taa	2/12	0.622716026181365	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.622716026181365	2		397	310	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585494	29585494	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	113	413	0	ENST00000356175.3:c.4243del	p.Glu1415LysfsTer4	p.E1415Kfs*4	ENST00000356175	NM_000267.3	1415	Gaa/aa	31/57	0.270208438848097	4	FACETS	1	0.985	1	0.742	0.673	0.813	INDETERMINATE	1	TRUE	2	0.622716026181365	4		413	397	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	199	174	0				ENST00000310581	NM_198253.2	-/1132			0.157291330088905	5	FACETS	1	0.934	1	0.668	0.622	0.714	INDETERMINATE	2	TRUE	2	0.702561186580446	5		174	581	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0020772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1601	390	406	0	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.702561186580446	7	FACETS	0.769	0.727	0.811			1	SUBCLONAL	2	TRUE	NA	0.702561186580446	7		406	1991	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711958	89711958	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	118	702	0	ENST00000371953.3:c.576del	p.Leu193CysfsTer6	p.L193Cfs*6	ENST00000371953	NM_000314.4	192	gcA/gc	6/9	0.702561186580446	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.702561186580446	2		702	161	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770554	40770554	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0020772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	191	677	0	ENST00000373198.4:c.2827+1G>T		p.X943_splice	ENST00000373198	NM_133170.3	943			0.157291330088905	5	FACETS	0.968	0.901	1	0.645	0.6	0.691	INDETERMINATE	2	TRUE	2	0.702561186580446	5		677	577	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210077	55210077	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	377	849	0	ENST00000275493.2:c.187G>C	p.Gly63Arg	p.G63R	ENST00000275493	NM_005228.3	63	Ggg/Cgg	2/28	0.702561186580446	7	FACETS	0.86	0.818	0.904			1	CLONAL	3	TRUE	NA	0.702561186580446	7		849	1146	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442567	52442567	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1253151209	NA	P-0020843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	40	805	5	ENST00000460680.1:c.178C>T	p.Arg60Ter	p.R60*	ENST00000460680	NM_004656.3	60	Cga/Tga	4/17	0.283077256744527	3	FACETS	0.497	0.412	0.592	0.249	0.206	0.296	SUBCLONAL	1	TRUE	1	0.283077256744527	3		810	649	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	60	174	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.963	1			1	INDETERMINATE	1	TRUE	NA	0.762027950786985	2		174	129	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220274	55220274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4908	375	449	1	ENST00000275493.2:c.664C>T	p.Arg222Cys	p.R222C	ENST00000275493	NM_005228.3	222	Cgc/Tgc	6/28	0.762027950786985	63	FACETS	0.903	0.851	0.958			1	CLONAL	5	TRUE	NA	0.762027950786985	63		450	5283	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0020872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4549	591	845	2	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.762027950786985	63	FACETS	1	0.98	1			1	CLONAL	7	TRUE	NA	0.762027950786985	63		847	5140	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439882	51439882	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	72	425	0	ENST00000262662.1:c.447G>C	p.Arg149Ser	p.R149S	ENST00000262662		149	agG/agC	4/4	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.762027950786985	2		425	172	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0020928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	78	435	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.120201740843096	4	FACETS	0.775	0.687	0.869	0.775	0.687	0.869	INDETERMINATE	2	TRUE	2	0.436548128956741	4		435	331	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835632	68835633	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0020928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	332	1100	0	ENST00000261769.5:c.223_224del	p.Phe75GlnfsTer18	p.F75Qfs*18	ENST00000261769	NM_004360.3	75	TTc/c	3/16	0.436548128956741	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.436548128956741	1		1100	885	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189423	56189431	+	inframe_deletion	In_Frame_Del	DEL	TCTTCGTTG	TCTTCGTTG	-	novel	NA	P-0020928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	249	1049	0	ENST00000399503.3:c.4456_4464del	p.Arg1487_Leu1489del	p.R1487_L1489del	ENST00000399503	NM_005921.1	1485	gcTCTTCGTTGt/gct	20/20	0.120201740843096	4	FACETS	0.801	0.749	0.854	0.801	0.749	0.854	INDETERMINATE	2	TRUE	2	0.436548128956741	4		1049	1023	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752831	128752831	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772772048	NA	P-0020928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	61	534	0	ENST00000377970.2:c.992G>A	p.Arg331Gln	p.R331Q	ENST00000377970	NM_002467.4	331	cGg/cAg	3/3	0.436548128956741	3	FACETS	0.411	0.353	0.473	0.205	0.176	0.237	SUBCLONAL	1	TRUE	1	0.436548128956741	3		534	829	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480447	89480447	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	56	530	1	ENST00000336596.2:c.2284G>T	p.Val762Phe	p.V762F	ENST00000336596	NM_005233.5	762	Gtt/Ttt	13/17	0.362203766754451	2	FACETS	0.875	0.754	1	0.437	0.377	0.502	CLONAL	1	TRUE	0	0.413031745604858	2		531	310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0020950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	284	927	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.667500872320169	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.666652112754713	2		927	388	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0020950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	393	932	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	0.667500872320169	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	1	0.666652112754713	4		932	637	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204864	NA	P-0020950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	301	268	0	ENST00000371953.3:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000371953	NM_000314.4	171	Cag/Tag	6/9	0.667500872320169	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.666652112754713	2		268	390	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625652	1625652	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs533848977	NA	P-0020950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	304	1204	1	ENST00000344749.5:c.422C>T	p.Ser141Leu	p.S141L	ENST00000344749	NM_001136139.2	141	tCg/tTg	7/19	0.667500872320169	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.666652112754713	2		1205	386	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039404	47039404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556778215	NA	P-0020950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	217	498	1	ENST00000377604.3:c.1027C>T	p.Arg343Cys	p.R343C	ENST00000377604	NM_001204468.1	343	Cgc/Tgc	10/24	0.547834366062706	2	FACETS	0.844	0.816	0.87			1	CLONAL	3	TRUE	NA	0.666652112754713	2		499	257	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2964000	2964000	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0020950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	136	869	0	ENST00000396946.4:c.1808-1G>A		p.X603_splice	ENST00000396946	NM_032415.4	603			0.667500872320169	4	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.666652112754713	4		869	524	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846312	156846312	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	235	1131	1	ENST00000524377.1:c.1753C>A	p.Leu585Met	p.L585M	ENST00000524377	NM_002529.3	585	Ctg/Atg	14/17	NA	2	FACETS	0.801	0.759	0.844			1	INDETERMINATE	2	TRUE	NA	0.666652112754713	2		1132	440	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934627	9934627	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	13	587	0	ENST00000330684.3:c.1528G>T	p.Gly510Cys	p.G510C	ENST00000330684	NM_001134407.1	510	Ggc/Tgc	7/13	0.488658877960244	3	FACETS	0.2	0.142	0.271			1	SUBCLONAL	1	TRUE	NA	0.666652112754713	3		587	260	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101134	41101134	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs769639671	NA	P-0020950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	138	905	0	ENST00000373198.4:c.1222G>C	p.Glu408Gln	p.E408Q	ENST00000373198	NM_133170.3	408	Gag/Cag	8/32	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.666652112754713	2		905	372	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556714	41556714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1176732027	NA	P-0020950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	196	701	0	ENST00000263253.7:c.3659C>T	p.Ser1220Phe	p.S1220F	ENST00000263253	NM_001429.3	1220	tCc/tTc	20/31	0.667500872320169	3	FACETS	0.99	0.93	1	0.99	0.93	1	CLONAL	2	TRUE	1	0.666652112754713	3		701	396	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411871	116411920	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTAACAAGCTCTTTCTTTCTCTCTGTTTTAAGATCTGGGCAGTGAATTAG	TTAACAAGCTCTTTCTTTCTCTCTGTTTTAAGATCTGGGCAGTGAATTAG	-	novel	NA	P-0020950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	382	1340	0	ENST00000397752.3:c.2888-30_2907del		p.X963_splice	ENST00000397752	NM_000245.2	963		14/21	0.667500872320169	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.666652112754713	2		1340	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578541	7578541	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	416	1226	0	ENST00000269305.4:c.389T>G	p.Leu130Arg	p.L130R	ENST00000269305	NM_001126112.2	130	cTc/cGc	5/11	0.702636463921475	1	FACETS	0.972	0.933	1	0.972	0.933	1	CLONAL	1	TRUE	0	0.703138063518563	1		1226	789	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073271	8073271	+	stop_lost	Nonstop_Mutation	SNP	T	T	C	novel	NA	P-0020984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	59	487	0	ENST00000377482.5:c.1388A>G	p.Ter463TrpextTer30	p.*463Wext*30	ENST00000377482	NM_018948.3	463	tAg/tGg	4/4	1	2	FACETS	0.293	0.252	0.338	0.293	0.252	0.338	SUBCLONAL	1	TRUE	1	0.703138063518563	2		487	573	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644700	134644700	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	235	836	0	ENST00000398015.3:c.102del	p.Trp34Ter	p.W34*	ENST00000398015	NM_004441.4	34	tGg/tg	2/16	0.405156121264132	1	FACETS	0.564	0.528	0.601	0.564	0.528	0.601	INDETERMINATE	1	TRUE	0	0.703138063518563	1		836	769	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	131	379	2	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.111013238531637	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.96194274042651	0		381	285	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	422	795	2	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	0.866613215400225	3	FACETS	0.907	0.873	0.941	0.907	0.873	0.941	CLONAL	2	FALSE	1	0.96194274042651	3		797	716	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520017	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	498	903	0	ENST00000326873.7:c.647C>T	p.Ser216Phe	p.S216F	ENST00000326873	NM_000455.4	216	tCc/tTc	5/10	1	2	FACETS	0.914	0.877	0.951	0.914	0.877	0.951	CLONAL	1	FALSE	1	0.96194274042651	2		903	1133	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435372	56435372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	552	872	2	ENST00000407977.2:c.1765C>T	p.Pro589Ser	p.P589S	ENST00000407977		589	Cca/Tca	9/10	0.607137662012745	4	FACETS	1	0.996	1	0.669	0.642	0.698	CLONAL	1	FALSE	2	0.96194274042651	4		874	1682	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729175	66729175	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908596	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	485	1012	0	ENST00000307102.5:c.383G>A	p.Gly128Asp	p.G128D	ENST00000307102	NM_002755.3	128	gGc/gAc	3/11	1	2	FACETS	0.892	0.856	0.929	0.892	0.856	0.929	CLONAL	1	FALSE	1	0.96194274042651	2		1012	1130	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577586	7577586	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587781589	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	631	834	0	ENST00000269305.4:c.695T>G	p.Ile232Ser	p.I232S	ENST00000269305	NM_001126112.2	232	aTc/aGc	7/11	0.922609491574668	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	FALSE	0	0.96194274042651	1		834	671	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233090	69233090	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746910913	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	302	542	1	ENST00000462284.1:c.961del	p.Leu321PhefsTer52	p.L321Ffs*52	ENST00000462284	NM_002392.5	319	Ccc/cc	11/11	0.371549464734651	3	FACETS	0.947	0.906	0.987	0.631	0.604	0.658	INDETERMINATE	2	FALSE	0	0.96194274042651	3		543	491	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711891	89711891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	183	683	0	ENST00000371953.3:c.509G>A	p.Ser170Asn	p.S170N	ENST00000371953	NM_000314.4	170	aGt/aAt	6/9	0.892578117974066	1	FACETS	0.862	0.827	0.895	0.862	0.827	0.895	CLONAL	1	FALSE	0	0.96194274042651	1		683	229	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167590	24167590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1244451002	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	420	671	1	ENST00000263121.7:c.974C>T	p.Thr325Ile	p.T325I	ENST00000263121	NM_003073.3	325	aCc/aTc	7/9	1	2	FACETS	0.964	0.923	1	0.964	0.923	1	CLONAL	1	FALSE	1	0.96194274042651	2		672	906	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877384	89877384	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	507	831	0	ENST00000389301.3:c.379G>A	p.Ala127Thr	p.A127T	ENST00000389301	NM_000135.2	127	Gct/Act	4/43	1	2	FACETS	0.946	0.909	0.983	0.946	0.909	0.983	CLONAL	1	FALSE	1	0.96194274042651	2		831	1114	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247806	10247806	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147984942	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	580	970	0	ENST00000340748.4:c.4396C>T	p.Arg1466Cys	p.R1466C	ENST00000340748		1466	Cgc/Tgc	36/40	1	2	FACETS	0.984	0.948	1	0.984	0.948	1	CLONAL	1	FALSE	1	0.96194274042651	2		970	1226	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508733	106508733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1207051578	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	67	687	0	ENST00000359195.3:c.727G>A	p.Ala243Thr	p.A243T	ENST00000359195	NM_002649.2	243	Gcc/Acc	2/11	1	2	FACETS	0.186	0.161	0.213	0.186	0.161	0.213	SUBCLONAL	1	FALSE	1	0.96194274042651	2		687	749	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592708	28592708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	317	775	0	ENST00000241453.7:c.2437G>A	p.Ala813Thr	p.A813T	ENST00000241453	NM_004119.2	813	Gcc/Acc	20/24	1	2	FACETS	0.865	0.821	0.909	0.865	0.821	0.909	CLONAL	1	FALSE	1	0.96194274042651	2		775	762	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492900	56492900	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	278	402	0	ENST00000407977.2:c.39G>A	p.Trp13Ter	p.W13*	ENST00000407977		13	tgG/tgA	2/10	0.607137662012745	4	FACETS	1	0.994	1	0.734	0.693	0.777	CLONAL	1	FALSE	2	0.96194274042651	4		402	772	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932479	39932479	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	489	920	3	ENST00000378444.4:c.2120C>T	p.Pro707Leu	p.P707L	ENST00000378444	NM_001123385.1	707	cCc/cTc	4/15	0.616872719902953	1	FACETS	0.68	0.657	0.702	0.68	0.657	0.702	SUBCLONAL	1	FALSE	0	0.96194274042651	1		923	776	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498082	29498082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	316	892	0	ENST00000389048.3:c.1924G>A	p.Asp642Asn	p.D642N	ENST00000389048	NM_004304.4	642	Gac/Aac	11/29	0.96194274042651	3	FACETS	0.812	0.766	0.859	0.406	0.383	0.43	CLONAL	1	FALSE	1	0.96194274042651	3		892	1198	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298723	46298724	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	126	520	0	ENST00000334344.6:c.5371_5372del	p.Lys1791GlufsTer3	p.K1791Efs*3	ENST00000334344	NM_152641.2	1790	ttAAag/ttag	21/21	0.556985737185698	4	FACETS	1	0.981	1	0.424	0.387	0.462	INDETERMINATE	1	FALSE	1	0.96194274042651	4		520	404	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923406	36923406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1393968437	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	432	965	0	ENST00000358127.4:c.856C>T	p.Pro286Ser	p.P286S	ENST00000358127	NM_001280556.1	286	Cct/Tct	7/10	1	2	FACETS	0.862	0.824	0.9	0.862	0.824	0.9	CLONAL	1	FALSE	1	0.96194274042651	2		965	1042	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255538	16255538	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	275	623	0	ENST00000375759.3:c.2803G>A	p.Val935Ile	p.V935I	ENST00000375759	NM_015001.2	935	Gtt/Att	11/15	0.142601313093496	4	FACETS	0.881	0.833	0.928	0.881	0.833	0.928	INDETERMINATE	2	FALSE	2	0.96194274042651	4		623	637	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115277095	115277095	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	184	754	2	ENST00000438362.2:c.688G>A	p.Ala230Thr	p.A230T	ENST00000438362	NM_001242891.1	230	Gcc/Acc	7/20	1	2	FACETS	0.959	0.897	1	0.959	0.897	1	CLONAL	1	FALSE	1	0.96194274042651	2		756	399	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165749	118165749	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	238	590	0	ENST00000369448.3:c.259G>A	p.Gly87Ser	p.G87S	ENST00000369448	NM_017709.3	87	Ggc/Agc	2/2	1	2	FACETS	0.873	0.822	0.924	0.873	0.822	0.924	CLONAL	1	FALSE	1	0.96194274042651	2		590	567	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120611957	120611957	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868921483	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	17	111	0	ENST00000256646.2:c.64C>T	p.Pro22Ser	p.P22S	ENST00000256646	NM_024408.3	22	Ccc/Tcc	1/34	1	2	FACETS	0.302	0.228	0.388	0.302	0.228	0.388	SUBCLONAL	1	FALSE	1	0.96194274042651	2		111	117	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849095	156849095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	568	1045	1	ENST00000524377.1:c.1987G>A	p.Val663Met	p.V663M	ENST00000524377	NM_002529.3	663	Gtg/Atg	15/17	1	2	FACETS	0.933	0.898	0.968	0.933	0.898	0.968	CLONAL	1	FALSE	1	0.96194274042651	2		1046	1266	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204499887	204499887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	299	899	0	ENST00000367182.3:c.229G>A	p.Gly77Ser	p.G77S	ENST00000367182	NM_001278516.1	77	Ggt/Agt	4/11	1	2	FACETS	0.909	0.862	0.956	0.909	0.862	0.956	CLONAL	1	FALSE	1	0.96194274042651	2		899	684	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333197	70333197	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	30	864	0	ENST00000373644.4:c.1102G>A	p.Ala368Thr	p.A368T	ENST00000373644	NM_030625.2	368	Gcc/Acc	2/12	0.892578117974066	1	FACETS	0.055	0.044	0.068	0.055	0.044	0.068	SUBCLONAL	1	FALSE	0	0.96194274042651	1		864	589	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533887	533887	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	516	909	1	ENST00000451590.1:c.169G>A	p.Asp57Asn	p.D57N	ENST00000451590	NM_001130442.1	57	Gat/Aat	3/5	1	2	FACETS	0.864	0.829	0.899	0.864	0.829	0.899	CLONAL	1	FALSE	1	0.96194274042651	2		910	1242	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533940	533940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	367	605	2	ENST00000451590.1:c.116C>T	p.Ser39Phe	p.S39F	ENST00000451590	NM_001130442.1	39	tCc/tTc	3/5	1	2	FACETS	0.977	0.933	1	0.977	0.933	1	CLONAL	1	FALSE	1	0.96194274042651	2		607	781	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450154	32450154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	389	760	0	ENST00000332351.3:c.658G>A	p.Val220Ile	p.V220I	ENST00000332351	NM_024426.4	220	Gtc/Atc	2/10	1	2	FACETS	0.944	0.902	0.986	0.944	0.902	0.986	CLONAL	1	FALSE	1	0.96194274042651	2		760	857	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128030	64128030	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	585	889	1	ENST00000334205.4:c.428G>A	p.Gly143Asp	p.G143D	ENST00000334205	NM_003942.2	143	gGt/gAt	4/17	1	2	FACETS	0.974	0.939	1	0.974	0.939	1	CLONAL	1	FALSE	1	0.96194274042651	2		890	1249	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457874	69457874	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	545	870	0	ENST00000227507.2:c.274G>A	p.Glu92Lys	p.E92K	ENST00000227507	NM_053056.2	92	Gag/Aag	2/5	1	2	FACETS	0.933	0.898	0.969	0.933	0.898	0.969	CLONAL	1	FALSE	1	0.96194274042651	2		870	1214	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195410	102195410	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	182	582	0	ENST00000263464.3:c.170A>G	p.Tyr57Cys	p.Y57C	ENST00000263464	NM_001165.4	57	tAc/tGc	2/9	0.96194274042651	3	FACETS	0.948	0.88	1	0.474	0.44	0.509	CLONAL	1	FALSE	1	0.96194274042651	3		582	591	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435167	18435167	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1203841141	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	236	622	0	ENST00000266497.5:c.152T>C	p.Ile51Thr	p.I51T	ENST00000266497		51	aTt/aCt	1/31	0.74111609236804	6	FACETS	1	0.982	1	0.447	0.419	0.475	CLONAL	2	FALSE	1	0.96194274042651	6		622	642	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112893799	112893799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239878972	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	394	584	0	ENST00000351677.2:c.688G>A	p.Val230Ile	p.V230I	ENST00000351677	NM_002834.3	230	Gtt/Att	6/16	0.371549464734651	3	FACETS	0.977	0.963	0.989	0.977	0.963	0.989	INDETERMINATE	3	FALSE	0	0.96194274042651	3		584	414	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784080	120784080	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1314404635	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	799	989	2	ENST00000257552.2:c.905G>A	p.Ser302Asn	p.S302N	ENST00000257552	NM_002442.3	302	aGc/aAc	13/15	0.371549464734651	3	FACETS	1	0.998	1	0.498	0.482	0.513	INDETERMINATE	1	FALSE	0	0.96194274042651	3		991	1648	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32971114	32971114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	175	827	0	ENST00000380152.3:c.9581C>T	p.Pro3194Leu	p.P3194L	ENST00000380152		3194	cCa/cTa	26/27	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.96194274042651	2		827	349	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436362	110436362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	446	756	1	ENST00000375856.3:c.2039C>T	p.Pro680Leu	p.P680L	ENST00000375856	NM_003749.2	680	cCc/cTc	1/2	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.96194274042651	2		757	923	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436677	110436677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	533	1017	0	ENST00000375856.3:c.1724C>T	p.Thr575Ile	p.T575I	ENST00000375856	NM_003749.2	575	aCc/aTc	1/2	1	2	FACETS	0.979	0.942	1	0.979	0.942	1	CLONAL	1	FALSE	1	0.96194274042651	2		1017	1132	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310146	91310146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	168	497	0	ENST00000355112.3:c.2200G>A	p.Ala734Thr	p.A734T	ENST00000355112	NM_000057.2	734	Gct/Act	10/22	1	2	FACETS	0.858	0.798	0.919	0.858	0.798	0.919	CLONAL	1	FALSE	1	0.96194274042651	2		497	407	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858283	9858283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778490114	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	205	622	1	ENST00000330684.3:c.3118G>A	p.Glu1040Lys	p.E1040K	ENST00000330684	NM_001134407.1	1040	Gag/Aag	13/13	1	2	FACETS	0.954	0.896	1	0.954	0.896	1	CLONAL	1	FALSE	1	0.96194274042651	2		623	447	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645381	67645381	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	200	598	0	ENST00000264010.4:c.646G>A	p.Glu216Lys	p.E216K	ENST00000264010	NM_006565.3	216	Gag/Aag	3/12	1	2	FACETS	0.96	0.901	1	0.96	0.901	1	CLONAL	1	FALSE	1	0.96194274042651	2		598	433	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772290	68772290	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	512	838	0	ENST00000261769.5:c.139G>A	p.Glu47Lys	p.E47K	ENST00000261769	NM_004360.3	47	Gag/Aag	2/16	1	2	FACETS	0.938	0.901	0.975	0.938	0.901	0.975	CLONAL	1	FALSE	1	0.96194274042651	2		838	1135	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827417	72827417	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	339	936	1	ENST00000268489.5:c.9164C>T	p.Thr3055Ile	p.T3055I	ENST00000268489	NM_006885.3	3055	aCc/aTc	9/10	1	2	FACETS	0.832	0.791	0.874	0.832	0.791	0.874	CLONAL	1	FALSE	1	0.96194274042651	2		937	847	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553480	29553480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	572	799	2	ENST00000356175.3:c.2029C>T	p.Pro677Ser	p.P677S	ENST00000356175	NM_000267.3	677	Ccc/Tcc	18/57	0.607137662012745	4	FACETS	1	0.997	1	0.731	0.702	0.76	CLONAL	1	FALSE	2	0.96194274042651	4		801	1596	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619031	37619031	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	558	802	0	ENST00000447079.4:c.707G>A	p.Ser236Asn	p.S236N	ENST00000447079	NM_015083.1	236	aGc/aAc	1/14	0.607137662012745	4	FACETS	1	0.996	1	0.664	0.637	0.692	CLONAL	1	FALSE	2	0.96194274042651	4		802	1714	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40864479	40864479	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	580	910	0	ENST00000428826.2:c.1229C>T	p.Pro410Leu	p.P410L	ENST00000428826		410	cCc/cTc	12/21	0.607137662012745	4	FACETS	1	0.996	1	0.669	0.642	0.696	CLONAL	1	FALSE	2	0.96194274042651	4		910	1769	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805699	46805699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	396	897	0	ENST00000290295.7:c.257G>A	p.Gly86Glu	p.G86E	ENST00000290295	NM_006361.5	86	gGg/gAg	1/2	0.607137662012745	4	FACETS	1	0.986	1	0.551	0.523	0.58	CLONAL	1	FALSE	2	0.96194274042651	4		897	1466	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763384	59763384	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	406	1062	0	ENST00000259008.2:c.2718G>C	p.Glu906Asp	p.E906D	ENST00000259008	NM_032043.2	906	gaG/gaC	19/20	0.607137662012745	4	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	FALSE	2	0.96194274042651	4		1062	683	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622184	1622184	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	480	824	4	ENST00000344749.5:c.691C>T	p.Pro231Ser	p.P231S	ENST00000344749	NM_001136139.2	231	Ccg/Tcg	10/19	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.96194274042651	2		828	974	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954605	17954605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	487	1025	1	ENST00000458235.1:c.289G>A	p.Val97Ile	p.V97I	ENST00000458235	NM_000215.3	97	Gtc/Atc	3/24	1	2	FACETS	0.95	0.912	0.988	0.95	0.912	0.988	CLONAL	1	FALSE	1	0.96194274042651	2		1026	1066	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272236	18272236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	54	24	0	ENST00000222254.8:c.746C>T	p.Thr249Ile	p.T249I	ENST00000222254	NM_005027.3	249	aCc/aTc	6/16	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.96194274042651	2		24	82	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968196	18968196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	421	740	0	ENST00000262803.5:c.2036G>A	p.Gly679Glu	p.G679E	ENST00000262803	NM_002911.3	679	gGg/gAg	15/24	1	2	FACETS	0.906	0.867	0.946	0.906	0.867	0.946	CLONAL	1	FALSE	1	0.96194274042651	2		740	966	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622708	158622708	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	114	425	0	ENST00000263640.3:c.791G>A	p.Gly264Asp	p.G264D	ENST00000263640	NM_001105.4	264	gGt/gAt	8/11	0.111013238531637	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.96194274042651	0		425	222	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190717442	190717442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	190	784	0	ENST00000441310.2:c.761C>T	p.Thr254Ile	p.T254I	ENST00000441310	NM_000534.4	254	aCa/aTa	7/13	0.111013238531637	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.96194274042651	0		784	433	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718738	190718738	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	182	696	2	ENST00000441310.2:c.896T>A	p.Ile299Asn	p.I299N	ENST00000441310	NM_000534.4	299	aTc/aAc	8/13	0.111013238531637	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.96194274042651	0		698	449	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661303	227661303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	489	873	0	ENST00000305123.5:c.2152G>A	p.Val718Met	p.V718M	ENST00000305123	NM_005544.2	718	Gtg/Atg	1/2	0.111013238531637	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.96194274042651	0		873	997	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319053	62319053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	901	915	3	ENST00000360203.5:c.1411G>A	p.Gly471Ser	p.G471S	ENST00000360203	NM_001283009.1	471	Ggc/Agc	17/35	0.545892053534559	3	FACETS	0.9	0.877	0.923	0.9	0.877	0.923	INDETERMINATE	2	FALSE	1	0.96194274042651	3		918	1541	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722210	49722210	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1288496355	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	301	526	3	ENST00000449682.2:c.1730G>A	p.Gly577Glu	p.G577E	ENST00000449682	NM_020998.3	577	gGg/gAg	15/18	1	2	FACETS	0.948	0.9	0.996	0.948	0.9	0.996	CLONAL	1	FALSE	1	0.96194274042651	2		529	660	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940102	49940102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1473729899	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	451	806	1	ENST00000296474.3:c.941G>A	p.Gly314Asp	p.G314D	ENST00000296474	NM_002447.2	314	gGc/gAc	1/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.96194274042651	2		807	905	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541855	187541855	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	96	731	0	ENST00000441802.2:c.5885T>G	p.Leu1962Arg	p.L1962R	ENST00000441802	NM_005245.3	1962	cTt/cGt	10/27	1	2	FACETS	0.279	0.248	0.311	0.279	0.248	0.311	SUBCLONAL	1	FALSE	1	0.96194274042651	2		731	716	SUCCESS
APC	324	MSKCC	GRCh37	5	112174278	112174278	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1561581181	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	166	587	2	ENST00000257430.4:c.2987G>A	p.Ser996Asn	p.S996N	ENST00000257430	NM_000038.5	996	aGt/aAt	16/16	1	2	FACETS	0.98	0.915	1	0.98	0.915	1	CLONAL	1	FALSE	1	0.96194274042651	2		589	352	SUCCESS
APC	324	MSKCC	GRCh37	5	112174416	112174416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	80	402	2	ENST00000257430.4:c.3125G>A	p.Ser1042Asn	p.S1042N	ENST00000257430	NM_000038.5	1042	aGt/aAt	16/16	1	2	FACETS	0.819	0.736	0.905	0.819	0.736	0.905	CLONAL	1	FALSE	1	0.96194274042651	2		404	203	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170814992	170814992	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	48	477	0	ENST00000296930.5:c.43del	p.Gln15ArgfsTer9	p.Q15Rfs*9	ENST00000296930	NM_002520.6	14	Ccc/cc	1/11	1	2	FACETS	0.139	0.117	0.164	0.139	0.117	0.164	SUBCLONAL	1	FALSE	1	0.96194274042651	2		477	717	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271362	26271362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781608741	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	55	741	0	ENST00000305910.3:c.251G>A	p.Arg84His	p.R84H	ENST00000305910	NM_003534.2	84	cGc/cAc	1/1	0.939283880294282	2	FACETS	0.149	0.127	0.173	0.074	0.063	0.087	SUBCLONAL	1	FALSE	0	0.96194274042651	2		741	768	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675175	30675175	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	847	878	0	ENST00000376406.3:c.3070G>A	p.Glu1024Lys	p.E1024K	ENST00000376406	NM_014641.2	1024	Gag/Aag	9/15	0.556985737185698	4	FACETS	1	0.997	1	0.833	0.811	0.854	INDETERMINATE	2	FALSE	1	0.96194274042651	4		878	1383	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168922	32168922	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs8192572	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	1133	982	0	ENST00000375023.3:c.4111G>A	p.Gly1371Ser	p.G1371S	ENST00000375023	NM_004557.3	1371	Ggc/Agc	22/30	0.556985737185698	4	FACETS	0.852	0.833	0.871	0.852	0.833	0.871	INDETERMINATE	3	FALSE	1	0.96194274042651	4		982	1808	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803115	32803115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	883	779	0	ENST00000374899.4:c.761G>A	p.Ser254Asn	p.S254N	ENST00000374899	NM_018833.2	254	aGc/aAc	5/12	0.556985737185698	4	FACETS	0.85	0.829	0.871	0.85	0.829	0.871	INDETERMINATE	3	FALSE	1	0.96194274042651	4		779	1412	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015896	112015896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	255	609	0	ENST00000368678.4:c.1045G>A	p.Asp349Asn	p.D349N	ENST00000368678		349	Gat/Aat	10/13	0.96194274042651	1	FACETS	0.905	0.877	0.931	0.905	0.877	0.931	CLONAL	1	FALSE	0	0.96194274042651	1		609	304	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042083	6042083	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs863224450	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2	26	62	0	ENST00000265849.7:c.537+1G>A		p.X179_splice	ENST00000265849	NM_000535.5	179			0.96194274042651	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	FALSE	0	0.96194274042651	1		62	28	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877013	151877013	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1193738624	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	246	596	1	ENST00000262189.6:c.7348C>T	p.Pro2450Ser	p.P2450S	ENST00000262189	NM_170606.2	2450	Cct/Tct	37/59	0.892578117974066	1	FACETS	0.906	0.877	0.933	0.906	0.877	0.933	CLONAL	1	FALSE	0	0.96194274042651	1		597	293	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90976694	90976694	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881862	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	45	822	0	ENST00000265433.3:c.938C>T	p.Ala313Val	p.A313V	ENST00000265433	NM_002485.4	313	gCg/gTg	8/16	0.1663502423842	1	FACETS	0.118	0.099	0.139	0.118	0.099	0.139	INDETERMINATE	1	FALSE	0	0.96194274042651	1		822	412	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5465550	5465550	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	243	617	0	ENST00000381577.3:c.734G>A	p.Gly245Glu	p.G245E	ENST00000381577	NM_014143.3	245	gGa/gAa	5/7	0.96194274042651	1	FACETS	0.982	0.958	1	0.982	0.958	1	CLONAL	1	FALSE	0	0.96194274042651	1		617	267	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002761	37002761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1208415118	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	263	621	0	ENST00000358127.4:c.488C>T	p.Ser163Phe	p.S163F	ENST00000358127	NM_001280556.1	163	tCc/tTc	5/10	1	2	FACETS	0.882	0.833	0.931	0.882	0.833	0.931	CLONAL	1	FALSE	1	0.96194274042651	2		621	620	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864129	97864129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	329	734	0	ENST00000289081.3:c.1537G>A	p.Ala513Thr	p.A513T	ENST00000289081	NM_000136.2	513	Gct/Act	15/15	1	2	FACETS	0.902	0.858	0.947	0.902	0.858	0.947	CLONAL	1	FALSE	1	0.96194274042651	2		734	758	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300052	137300052	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	629	895	0	ENST00000481739.1:c.337C>T	p.Leu113Phe	p.L113F	ENST00000481739	NM_002957.4	113	Ctc/Ttc	3/10	1	2	FACETS	0.95	0.917	0.984	0.95	0.917	0.984	CLONAL	1	FALSE	1	0.96194274042651	2		895	1376	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137320990	137320990	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1220410660	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	608	1041	2	ENST00000481739.1:c.947G>A	p.Arg316His	p.R316H	ENST00000481739	NM_002957.4	316	cGc/cAc	7/10	1	2	FACETS	0.981	0.946	1	0.981	0.946	1	CLONAL	1	FALSE	1	0.96194274042651	2		1043	1289	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399477	139399477	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	563	865	0	ENST00000277541.6:c.4666T>C	p.Trp1556Arg	p.W1556R	ENST00000277541	NM_017617.3	1556	Tgg/Cgg	26/34	1	2	FACETS	0.96	0.925	0.996	0.96	0.925	0.996	CLONAL	1	FALSE	1	0.96194274042651	2		865	1219	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407900	139407900	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	672	1008	3	ENST00000277541.6:c.2297G>A	p.Gly766Asp	p.G766D	ENST00000277541	NM_017617.3	766	gGc/gAc	14/34	1	2	FACETS	0.947	0.915	0.98	0.947	0.915	0.98	CLONAL	1	FALSE	1	0.96194274042651	2		1011	1475	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347846	70347846	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	487	827	1	ENST00000374080.3:c.3085C>T	p.Pro1029Ser	p.P1029S	ENST00000374080		1029	Cct/Tct	22/45	0.616872719902953	1	FACETS	0.728	0.705	0.75	0.728	0.705	0.75	SUBCLONAL	1	FALSE	0	0.96194274042651	1		828	722	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347880	70347880	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	182	815	2	ENST00000374080.3:c.3119G>A	p.Gly1040Asp	p.G1040D	ENST00000374080		1040	gGc/gAc	22/45	0.616872719902953	1	FACETS	0.245	0.226	0.264	0.245	0.226	0.264	SUBCLONAL	1	FALSE	0	0.96194274042651	1		817	803	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220300	5220300	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753240051	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	541	792	0	ENST00000357368.4:c.3520G>A	p.Gly1174Ser	p.G1174S	ENST00000357368	NM_002850.3	1174	Ggt/Agt	21/38	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	1	0.96194274042651	2		792	1038	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724322	112724322	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs781645815	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	83	809	0	ENST00000369452.4:c.206A>G	p.Asp69Gly	p.D69G	ENST00000369452	NM_007373.3	69	gAc/gGc	2/9	0.892578117974066	1	FACETS	0.207	0.183	0.232	0.207	0.183	0.232	SUBCLONAL	1	FALSE	0	0.96194274042651	1		809	433	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197808	66197808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	175	652	0	ENST00000273854.3:c.2891C>T	p.Ser964Phe	p.S964F	ENST00000273854	NM_004439.5	964	tCt/tTt	17/18	1	2	FACETS	0.973	0.909	1	0.973	0.909	1	CLONAL	1	FALSE	1	0.96194274042651	2		652	374	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643953	52643953	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	211	655	0	ENST00000394830.3:c.1943C>T	p.Ser648Phe	p.S648F	ENST00000394830	NM_018313.4	648	tCt/tTt	17/30	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	1	0.96194274042651	2		655	433	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231825	36231825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1429953108	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	471	919	1	ENST00000300305.3:c.559G>A	p.Ala187Thr	p.A187T	ENST00000300305		187	Gcc/Acc	5/8	0.892578117974066	1	FACETS	0.934	0.915	0.953	0.934	0.915	0.953	CLONAL	1	FALSE	0	0.96194274042651	1		920	544	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176710822	176710822	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1327806844	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	166	632	0	ENST00000439151.2:c.6044A>G	p.Tyr2015Cys	p.Y2015C	ENST00000439151	NM_022455.4	2015	tAt/tGt	20/23	1	2	FACETS	0.546	0.503	0.59	0.546	0.503	0.59	SUBCLONAL	1	FALSE	1	0.96194274042651	2		632	632	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609695	28609695	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748392919	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	278	907	3	ENST00000241453.7:c.1534G>A	p.Val512Ile	p.V512I	ENST00000241453	NM_004119.2	512	Gtc/Atc	12/24	1	2	FACETS	0.9	0.852	0.949	0.9	0.852	0.949	CLONAL	1	FALSE	1	0.96194274042651	2		910	642	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643219	38643219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	138	547	0	ENST00000299084.4:c.689C>T	p.Pro230Leu	p.P230L	ENST00000299084	NM_152594.2	230	cCt/cTt	7/7	1	2	FACETS	0.856	0.791	0.923	0.856	0.791	0.923	CLONAL	1	FALSE	1	0.96194274042651	2		547	335	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428615	78428615	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	109	593	0	ENST00000370768.2:c.1184G>A	p.Gly395Glu	p.G395E	ENST00000370768	NM_003902.3	395	gGa/gAa	14/20	1	2	FACETS	0.855	0.781	0.93	0.855	0.781	0.93	CLONAL	1	FALSE	1	0.96194274042651	2		593	265	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5286111	5286111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	521	896	0	ENST00000357368.4:c.41G>A	p.Gly14Asp	p.G14D	ENST00000357368	NM_002850.3	14	gGt/gAt	2/38	1	2	FACETS	0.883	0.848	0.918	0.883	0.848	0.918	CLONAL	1	FALSE	1	0.96194274042651	2		896	1227	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923358	36923358	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	327	755	2	ENST00000358127.4:c.904G>A	p.Val302Met	p.V302M	ENST00000358127	NM_001280556.1	302	Gtg/Atg	7/10	1	2	FACETS	0.851	0.808	0.894	0.851	0.808	0.894	CLONAL	1	FALSE	1	0.96194274042651	2		757	799	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268128	153268128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	308	590	0	ENST00000281708.4:c.680C>T	p.Ser227Phe	p.S227F	ENST00000281708	NM_033632.3	227	tCt/tTt	4/12	1	2	FACETS	0.776	0.735	0.818	0.776	0.735	0.818	SUBCLONAL	1	FALSE	1	0.96194274042651	2		590	825	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562418	21562418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1390515980	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	311	660	2	ENST00000382592.4:c.1501C>T	p.Pro501Ser	p.P501S	ENST00000382592	NM_014572.2	501	Ccg/Tcg	4/8	1	2	FACETS	0.972	0.925	1	0.972	0.925	1	CLONAL	1	FALSE	1	0.96194274042651	2		662	665	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2115527	2115527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45517187	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	475	798	0	ENST00000219476.3:c.1607C>T	p.Ala536Val	p.A536V	ENST00000219476	NM_000548.3	536	gCc/gTc	16/42	1	2	FACETS	0.97	0.931	1	0.97	0.931	1	CLONAL	1	FALSE	1	0.96194274042651	2		798	1018	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262462	10262462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	538	889	1	ENST00000340748.4:c.2033G>A	p.Gly678Asp	p.G678D	ENST00000340748		678	gGc/gAc	22/40	1	2	FACETS	0.916	0.881	0.951	0.916	0.881	0.951	CLONAL	1	FALSE	1	0.96194274042651	2		890	1221	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165450	47165450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780963440	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	260	702	0	ENST00000409792.3:c.676C>T	p.Pro226Ser	p.P226S	ENST00000409792	NM_014159.6	226	Cca/Tca	3/21	1	2	FACETS	0.938	0.887	0.99	0.938	0.887	0.99	CLONAL	1	FALSE	1	0.96194274042651	2		702	576	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518622	204518622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	136	568	0	ENST00000367182.3:c.1285G>A	p.Asp429Asn	p.D429N	ENST00000367182	NM_001278516.1	429	Gat/Aat	11/11	1	2	FACETS	0.775	0.713	0.838	0.775	0.713	0.838	SUBCLONAL	1	FALSE	1	0.96194274042651	2		568	365	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772902	135772902	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	66	878	0	ENST00000298552.3:c.2721del	p.Lys907AsnfsTer24	p.K907Nfs*24	ENST00000298552	NM_001162426.1	907	aaA/aa	21/23	1	2	FACETS	0.165	0.143	0.19	0.165	0.143	0.19	SUBCLONAL	1	FALSE	1	0.96194274042651	2		878	830	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609362	81609362	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	117	593	0	ENST00000298171.2:c.964del	p.Leu322SerfsTer90	p.L322Sfs*90	ENST00000298171	NM_000369.2	320	agC/ag	10/10	0.545892053534559	3	FACETS	0.392	0.353	0.434	0.196	0.176	0.217	INDETERMINATE	1	FALSE	1	0.96194274042651	3		593	919	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578281	7578281	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660254	NA	P-0021108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	264	844	0	ENST00000269305.4:c.568C>A	p.Pro190Thr	p.P190T	ENST00000269305	NM_001126112.2	190	Cct/Act	6/11	0.689127996994514	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.689127996994514	1		844	493	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942183	81942183	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	208	756	0	ENST00000359376.3:c.1720A>G	p.Thr574Ala	p.T574A	ENST00000359376	NM_002661.3	574	Acc/Gcc	17/33	1	2	FACETS	0.923	0.861	0.986	0.923	0.861	0.986	CLONAL	1	TRUE	1	0.689127996994514	2		756	654	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091722	29091722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555913662	NA	P-0021108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	42	137	2	ENST00000328354.6:c.1235G>A	p.Ser412Asn	p.S412N	ENST00000328354	NM_007194.3	412	aGt/aAt	11/15	1	2	FACETS	0.952	0.814	1	0.952	0.814	1	CLONAL	1	TRUE	1	0.689127996994514	2		139	128	SUCCESS
APC	324	MSKCC	GRCh37	5	112175271	112175271	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1554085429	NA	P-0021108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	213	398	0	ENST00000257430.4:c.3980C>G	p.Ser1327Ter	p.S1327*	ENST00000257430	NM_000038.5	1327	tCa/tGa	16/16	0.684148139286226	2	FACETS	0.912	0.866	0.957	0.912	0.866	0.957	CLONAL	2	TRUE	0	0.689127996994514	2		398	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579530	7579537	+	frameshift_variant	Frame_Shift_Del	DEL	ATTGTTCA	ATTGTTCA	-	novel	NA	P-0021175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	454	1056	1	ENST00000269305.4:c.150_157del	p.Ile50MetfsTer4	p.I50Mfs*4	ENST00000269305	NM_001126112.2	50	atTGAACAATgg/atgg	4/11	0.89215516481919	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.89215516481919	1		1057	553	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137360	202137360	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0021175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	909	363	0	ENST00000358485.4:c.589-1G>C		p.X197_splice	ENST00000358485	NM_001080125.1	197			0.89215516481919	10	FACETS	1	0.995	1			1	CLONAL	6	TRUE	NA	0.89215516481919	10		363	1449	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137393	202137393	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	1262	473	0	ENST00000358485.4:c.621G>T	p.Lys207Asn	p.K207N	ENST00000358485	NM_001080125.1	207	aaG/aaT	4/9	0.89215516481919	10	FACETS	0.941	0.921	0.96			1	CLONAL	7	TRUE	NA	0.89215516481919	10		473	1963	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137653	202137653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	1402	612	0	ENST00000358485.4:c.760G>A	p.Glu254Lys	p.E254K	ENST00000358485	NM_001080125.1	254	Gaa/Aaa	5/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.89215516481919	NA		612	2277	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163580	47163580	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs776511280	NA	P-0021175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	181	515	0	ENST00000409792.3:c.2546G>T	p.Cys849Phe	p.C849F	ENST00000409792	NM_014159.6	849	tGt/tTt	3/21	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.89215516481919	2		515	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0021179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	554	725	0	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	0.92632161435634	2	FACETS	0.997	0.984	1	0.997	0.984	1	CLONAL	2	TRUE	0	0.941532081949978	2		725	590	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850777	63850777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374377066	NA	P-0021179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	140	627	1	ENST00000279873.7:c.1555G>A	p.Glu519Lys	p.E519K	ENST00000279873	NM_032199.2	519	Gaa/Aaa	10/10	1	2	FACETS	0.985	0.913	1	0.985	0.913	1	CLONAL	1	TRUE	1	0.941532081949978	2		628	302	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047147	77047147	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	207	892	0	ENST00000356341.3:c.1397A>G	p.Asn466Ser	p.N466S	ENST00000356341	NM_002576.4	466	aAt/aGt	13/15	1	2	FACETS	0.841	0.787	0.895	0.841	0.787	0.895	CLONAL	1	TRUE	1	0.941532081949978	2		892	523	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628536	90628536	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745389409	NA	P-0021179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	505	972	4	ENST00000330062.3:c.1051G>A	p.Val351Ile	p.V351I	ENST00000330062	NM_002168.2	351	Gtc/Atc	8/11	0.932607215652694	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.941532081949978	2		976	535	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745076	41745076	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs555871583	NA	P-0021179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	170	992	4	ENST00000301178.4:c.1142T>C	p.Met381Thr	p.M381T	ENST00000301178	NM_021913.4	381	aTg/aCg	9/20	0.941532081949978	1	FACETS	0.975	0.941	1	0.975	0.941	1	CLONAL	1	TRUE	0	0.941532081949978	1		996	196	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408882	41408882	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	173	696	2	ENST00000373198.4:c.544G>T	p.Val182Phe	p.V182F	ENST00000373198	NM_133170.3	182	Gtc/Ttc	4/32	0.933082245664161	4	FACETS	1	0.965	1	0.269	0.249	0.291	CLONAL	1	TRUE	0	0.941532081949978	4		698	662	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272847	142272847	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	122	692	0	ENST00000350721.4:c.2352del	p.Asp784GlufsTer19	p.D784Efs*19	ENST00000350721	NM_001184.3	784	gaT/ga	11/47	0.896145679369183	3	FACETS	0.82	0.746	0.897	0.41	0.373	0.449	CLONAL	1	TRUE	1	0.941532081949978	3		692	465	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589625	67589627	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	novel	NA	P-0021179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	276	554	0	ENST00000274335.5:c.1390_1392del	p.Asp464del	p.D464del	ENST00000274335		463	tATGat/tat	10/15	0.934575516535931	2	FACETS	0.961	0.938	0.981	0.961	0.938	0.981	CLONAL	2	TRUE	0	0.941532081949978	2		554	305	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0021206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	596	737	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.895848472316095	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.895848472316095	2		737	632	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685307	89685307	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123317	NA	P-0021206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	156	566	0	ENST00000371953.3:c.202T>C	p.Tyr68His	p.Y68H	ENST00000371953	NM_000314.4	68	Tac/Cac	3/9	0.895848472316095	2	FACETS	0.995	0.961	1	0.995	0.961	1	CLONAL	2	TRUE	0	0.895848472316095	2		566	175	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127755	64127755	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	277	548	0	ENST00000334205.4:c.248G>C	p.Arg83Pro	p.R83P	ENST00000334205	NM_003942.2	83	cGc/cCc	3/17	0.886428472289703	3	FACETS	0.902	0.848	0.957	0.451	0.424	0.479	CLONAL	1	TRUE	1	0.895848472316095	3		548	993	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652237	3652237	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141597706	NA	P-0021206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	292	612	2	ENST00000294008.3:c.832C>T	p.Arg278Trp	p.R278W	ENST00000294008	NM_032444.2	278	Cgg/Tgg	4/15	0.895848472316095	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.895848472316095	1		614	312	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573138	41573138	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	389	722	0	ENST00000263253.7:c.5423A>C	p.Asn1808Thr	p.N1808T	ENST00000263253	NM_001429.3	1808	aAc/aCc	31/31	0.895848472316095	2	FACETS	1	0.987	1	0.539	0.516	0.563	CLONAL	1	TRUE	0	0.895848472316095	2		722	805	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259384	89259384	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	327	588	0	ENST00000336596.2:c.528G>T	p.Lys176Asn	p.K176N	ENST00000336596	NM_005233.5	176	aaG/aaT	3/17	0.895848472316095	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.895848472316095	2		588	349	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447371	187447371	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	537	665	0	ENST00000232014.4:c.822C>G	p.His274Gln	p.H274Q	ENST00000232014	NM_001130845.1	274	caC/caG	5/10	0.856180135424455	5	FACETS	0.968	0.928	1	0.645	0.619	0.672	CLONAL	2	TRUE	2	0.895848472316095	5		665	1452	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542873	187542873	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	133	522	0	ENST00000441802.2:c.4867A>G	p.Lys1623Glu	p.K1623E	ENST00000441802	NM_005245.3	1623	Aaa/Gaa	10/27	0.895848472316095	3	FACETS	1	0.951	1	0.527	0.483	0.572	CLONAL	1	TRUE	1	0.895848472316095	3		522	408	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028134	69028134	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	299	663	0	ENST00000288368.4:c.3293G>T	p.Gly1098Val	p.G1098V	ENST00000288368	NM_024870.2	1098	gGt/gTt	26/40	0.886428472289703	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.895848472316095	3		663	481	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752917	128752917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	160	379	0	ENST00000377970.2:c.1078C>T	p.Pro360Ser	p.P360S	ENST00000377970	NM_002467.4	360	Ccc/Tcc	3/3	0.886428472289703	3	FACETS	1	0.958	1	0.527	0.486	0.568	CLONAL	1	TRUE	1	0.895848472316095	3		379	491	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482205	87482205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	507	666	0	ENST00000277120.3:c.1492C>T	p.His498Tyr	p.H498Y	ENST00000277120		498	Cat/Tat	14/19	0.863550905810736	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.895848472316095	4		666	1066	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0021297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	221	841	1	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	2	TRUE	NA	0.516625472476032	2		842	406	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81891937	81891937	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777990663	NA	P-0021297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	41	810	1	ENST00000359376.3:c.407C>T	p.Ala136Val	p.A136V	ENST00000359376	NM_002661.3	136	gCg/gTg	4/33	0.516625472476032	2	FACETS	0.42	0.35	0.497	0.21	0.175	0.249	SUBCLONAL	1	TRUE	0	0.516625472476032	2		811	378	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400023	139400023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766146375	NA	P-0021297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	243	879	0	ENST00000277541.6:c.4325C>T	p.Pro1442Leu	p.P1442L	ENST00000277541	NM_017617.3	1442	cCg/cTg	25/34	0.106300959219613	3	FACETS	1	0.987	1			1	INDETERMINATE	2	TRUE	NA	0.516625472476032	3		879	516	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511119	148511119	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	174	645	0	ENST00000320356.2:c.1783del	p.Ala595ProfsTer80	p.A595Pfs*80	ENST00000320356	NM_004456.4	595	Gcc/cc	15/20	0.445188329118062	4	FACETS	0.857	0.793	0.923	0.857	0.793	0.923	CLONAL	2	TRUE	2	0.516625472476032	4		645	596	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0021310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	431	737	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.903818521228284	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.903818521228284	1		737	513	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	440	782	0	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	0.903818521228284	1	FACETS	0.92	0.894	0.945	0.92	0.894	0.945	CLONAL	1	TRUE	0	0.903818521228284	1		782	580	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624242	89624242	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0021310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	145	322	0	ENST00000371953.3:c.16A>T	p.Lys6Ter	p.K6*	ENST00000371953	NM_000314.4	6	Aaa/Taa	1/9	0.903818521228284	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.903818521228284	1		322	168	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763509	59763509	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs578022079	NA	P-0021310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	296	707	2	ENST00000259008.2:c.2593C>T	p.Arg865Trp	p.R865W	ENST00000259008	NM_032043.2	865	Cgg/Tgg	19/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.903818521228284	2		709	646	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917753	29917753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	457	1078	0	ENST00000389048.3:c.915del	p.Asp305GlufsTer30	p.D305Efs*30	ENST00000389048	NM_004304.4	305	gaT/ga	3/29	0.133639098456605	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.903818521228284	0		1078	1049	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624451	140624451	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	121	246	0	ENST00000288602.6:c.53T>A	p.Leu18Gln	p.L18Q	ENST00000288602	NM_004333.4	18	cTg/cAg	1/18	1	2	FACETS	0.902	0.827	0.977	0.902	0.827	0.977	CLONAL	1	TRUE	1	0.903818521228284	2		246	297	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0021323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	438	677	12	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	0.833388097617475	1	FACETS	0.842	0.812	0.872	0.842	0.812	0.872	CLONAL	1	TRUE	0	0.833388097617475	1		689	728	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0021323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	789	1210	13	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	0.833388097617475	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.833388097617475	1		1223	1051	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207153	1207155	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs587782056	NA	P-0021323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	88	1249	2	ENST00000326873.7:c.250_252del	p.Lys84del	p.K84del	ENST00000326873	NM_000455.4	81	AAG/-	1/10	0.833388097617475	1	FACETS	0.106	0.093	0.119	0.106	0.093	0.119	SUBCLONAL	1	TRUE	0	0.833388097617475	1		1251	1167	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666384	206666384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367815847	NA	P-0021323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	301	974	1	ENST00000367120.3:c.1864C>T	p.Arg622Cys	p.R622C	ENST00000367120	NM_014002.3	622	Cgc/Tgc	19/22	0.833388097617475	1	FACETS	0.471	0.445	0.498	0.471	0.445	0.498	SUBCLONAL	1	TRUE	0	0.833388097617475	1		975	895	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557725	21557725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs915063122	NA	P-0021323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	694	903	2	ENST00000382592.4:c.2120G>A	p.Arg707Gln	p.R707Q	ENST00000382592	NM_014572.2	707	cGg/cAg	5/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.833388097617475	2		905	1650	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600425	10600425	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	798	1202	17	ENST00000171111.5:c.1430del	p.Gly477AlafsTer23	p.G477Afs*23	ENST00000171111	NM_203500.1	477	gGc/gc	4/6	0.833388097617475	1	FACETS	0.96	0.937	0.982	0.96	0.937	0.982	CLONAL	1	TRUE	0	0.833388097617475	1		1219	1164	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652976	29652979	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	rs1085307459	NA	P-0021323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	536	770	11	ENST00000356175.3:c.4914_4917del	p.Lys1640GlyfsTer36	p.K1640Gfs*36	ENST00000356175	NM_000267.3	1637	ttTCTC/tt	36/57	0.833388097617475	1	FACETS	0.98	0.951	1	0.98	0.951	1	CLONAL	1	TRUE	0	0.833388097617475	1		781	766	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351811	89351811	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	794	1277	18	ENST00000301030.4:c.1139T>C	p.Phe380Ser	p.F380S	ENST00000301030	NM_001256183.1	380	tTt/tCt	9/13	0.833388097617475	1	FACETS	0.992	0.968	1	0.992	0.968	1	CLONAL	1	TRUE	0	0.833388097617475	1		1295	1121	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053590	37053590	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs63751711	NA	P-0021323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	445	708	13	ENST00000231790.2:c.677G>A	p.Arg226Gln	p.R226Q	ENST00000231790	NM_000249.3	226	cGa/cAa	8/19	0.833388097617475	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.833388097617475	1		721	616	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421002	49421002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529656123	NA	P-0021323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	173	606	0	ENST00000301067.7:c.14747C>T	p.Pro4916Leu	p.P4916L	ENST00000301067	NM_003482.3	4916	cCg/cTg	48/54	0.833388097617475	1	FACETS	0.432	0.4	0.466	0.432	0.4	0.466	SUBCLONAL	1	TRUE	0	0.833388097617475	1		606	560	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037866	49037866	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0021323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	408	550	0	ENST00000267163.4:c.2107-1G>T		p.X703_splice	ENST00000267163	NM_000321.2	703			0.833388097617475	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.833388097617475	1		550	551	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779046	3779046	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	57	788	0	ENST00000262367.5:c.6002A>G	p.Asn2001Ser	p.N2001S	ENST00000262367	NM_004380.2	2001	aAt/aGt	31/31	0.833388097617475	1	FACETS	0.104	0.088	0.12	0.104	0.088	0.12	SUBCLONAL	1	TRUE	0	0.833388097617475	1		788	770	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346406	89346406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762590968	NA	P-0021323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	571	793	14	ENST00000301030.4:c.6544G>A	p.Val2182Ile	p.V2182I	ENST00000301030	NM_001256183.1	2182	Gta/Ata	9/13	0.833388097617475	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.833388097617475	1		807	779	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221711	36221711	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	109	1202	2	ENST00000222270.7:c.5380C>A	p.His1794Asn	p.H1794N	ENST00000222270	NM_014727.1	1794	Cac/Aac	26/37	0.833388097617475	1	FACETS	0.133	0.119	0.148	0.133	0.119	0.148	SUBCLONAL	1	TRUE	0	0.833388097617475	1		1204	1147	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257062	198257062	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	534	742	2	ENST00000335508.6:c.3880A>G	p.Thr1294Ala	p.T1294A	ENST00000335508	NM_012433.2	1294	Acc/Gcc	25/25	0.833388097617475	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.833388097617475	1		744	745	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961396	54961396	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	261	354	6	ENST00000312783.6:c.236T>C	p.Leu79Ser	p.L79S	ENST00000312783	NM_198436.1	79	tTg/tCg	4/10	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.833388097617475	2		360	624	SUCCESS
ATR	545	MSKCC	GRCh37	3	142204039	142204039	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	662	883	15	ENST00000350721.4:c.6164A>G	p.Asp2055Gly	p.D2055G	ENST00000350721	NM_001184.3	2055	gAc/gGc	36/47	0.833388097617475	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.833388097617475	1		898	891	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287155	33287155	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0021323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	428	661	9	ENST00000374542.5:c.1940+2T>C		p.X647_splice	ENST00000374542	NM_001141970.1	647			0.833388097617475	1	FACETS	0.913	0.882	0.944	0.913	0.882	0.944	CLONAL	1	TRUE	0	0.833388097617475	1		670	656	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339167	116339167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs919828654	NA	P-0021323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	354	415	8	ENST00000397752.3:c.29G>A	p.Gly10Asp	p.G10D	ENST00000397752	NM_000245.2	10	gGc/gAc	2/21	0.833388097617475	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.833388097617475	1		423	482	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829074	128829075	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	85	83	0	ENST00000249373.3:c.82_83insT	p.Arg28LeufsTer108	p.R28Lfs*108	ENST00000249373	NM_005631.4	28	cgg/cTgg	1/12	0.833388097617475	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.833388097617475	1		83	114	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139804432	139804432	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	637	905	1	ENST00000247668.2:c.589A>G	p.Ile197Val	p.I197V	ENST00000247668	NM_021138.3	197	Atc/Gtc	6/11	0.833388097617475	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.833388097617475	1		906	858	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	190	958	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.430330503785927	2		958	847	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11181367	11181367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	178	944	2	ENST00000361445.4:c.6869C>T	p.Ala2290Val	p.A2290V	ENST00000361445	NM_004958.3	2290	gCc/gTc	49/58	1	2	FACETS	0.945	0.872	1	0.945	0.872	1	CLONAL	1	TRUE	1	0.430330503785927	2		946	875	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190585	11190585	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	143	604	1	ENST00000361445.4:c.5613+1G>T		p.X1871_splice	ENST00000361445	NM_004958.3	1871			1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.430330503785927	2		605	651	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100175	27100176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	103	629	0	ENST00000324856.7:c.3977dup	p.Gln1327AlafsTer11	p.Q1327Afs*11	ENST00000324856	NM_006015.4	1324	tac/taCc	16/20	1	2	FACETS	0.877	0.787	0.971	0.877	0.787	0.971	CLONAL	1	TRUE	1	0.430330503785927	2		629	546	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46733219	46733219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	174	850	1	ENST00000371975.4:c.980C>T	p.Pro327Leu	p.P327L	ENST00000371975	NM_003579.3	327	cCc/cTc	9/18	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.430330503785927	2		851	797	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	73	506	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.581	0.508	0.659	0.581	0.508	0.659	SUBCLONAL	1	TRUE	1	0.430330503785927	2		507	584	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	61	623	2	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.476	0.411	0.548	0.476	0.411	0.548	SUBCLONAL	1	TRUE	1	0.430330503785927	2		625	595	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	60	612	0	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	1	2	FACETS	0.433	0.373	0.499	0.433	0.373	0.499	SUBCLONAL	1	TRUE	1	0.430330503785927	2		612	644	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339110	65339111	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	92	649	3	ENST00000342505.4:c.425dup	p.Ile143AspfsTer9	p.I143Dfs*9	ENST00000342505	NM_002227.2	142	aag/aaAg	5/25	1	2	FACETS	0.596	0.53	0.667	0.596	0.53	0.667	SUBCLONAL	1	TRUE	1	0.430330503785927	2		652	717	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506250	120506250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553199293	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	101	528	1	ENST00000256646.2:c.1862G>A	p.Arg621His	p.R621H	ENST00000256646	NM_024408.3	621	cGc/cAc	11/34	1	2	FACETS	0.876	0.785	0.971	0.876	0.785	0.971	CLONAL	1	TRUE	1	0.430330503785927	2		529	536	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175759	176175760	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1373807885	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	65	846	0	ENST00000367669.3:c.355dup	p.Leu119ProfsTer23	p.L119Pfs*23	ENST00000367669	NM_022457.5	119	ctc/cCtc	1/20	1	2	FACETS	0.357	0.309	0.41	0.357	0.309	0.41	SUBCLONAL	1	TRUE	1	0.430330503785927	2		846	846	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100462	8100462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752779081	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	55	938	0	ENST00000346208.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000346208		146	Gcc/Acc	3/6	1	2	FACETS	0.326	0.278	0.379	0.326	0.278	0.379	SUBCLONAL	1	TRUE	1	0.430330503785927	2		938	784	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693002	89693003	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	77	434	1	ENST00000371953.3:c.491dup	p.Val166SerfsTer14	p.V166Sfs*14	ENST00000371953	NM_000314.4	162	-/A	5/9	1	2	FACETS	0.84	0.741	0.946	0.84	0.741	0.946	CLONAL	1	TRUE	1	0.430330503785927	2		435	426	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	139	455	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.927	0.845	1	0.927	0.845	1	CLONAL	1	TRUE	1	0.430330503785927	2		455	697	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104359213	104359213	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	50	568	0	ENST00000369902.3:c.934C>A	p.Leu312Met	p.L312M	ENST00000369902	NM_016169.3	312	Ctg/Atg	8/12	1	2	FACETS	0.363	0.307	0.424	0.363	0.307	0.424	SUBCLONAL	1	TRUE	1	0.430330503785927	2		568	641	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	241	339	0	ENST00000256196.4:c.68G>T	p.Gly23Val	p.G23V	ENST00000256196		23	gGc/gTc	1/6	0.430330503785927	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.430330503785927	2		339	526	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373618	118373618	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	38	688	0	ENST00000534358.1:c.7011G>T	p.Gln2337His	p.Q2337H	ENST00000534358	NM_005933.3	2337	caG/caT	27/36	1	2	FACETS	0.296	0.244	0.355	0.296	0.244	0.355	SUBCLONAL	1	TRUE	1	0.430330503785927	2		688	596	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427743	49427743	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	188	888	2	ENST00000301067.7:c.10745G>A	p.Arg3582Gln	p.R3582Q	ENST00000301067	NM_003482.3	3582	cGg/cAg	39/54	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.430330503785927	2		890	822	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	258	1051	2	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	0.430330503785927	2		1053	1048	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117342	115117342	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	77	655	0	ENST00000257566.3:c.832T>C	p.Phe278Leu	p.F278L	ENST00000257566	NM_016569.3	278	Ttc/Ctc	4/8	1	2	FACETS	0.559	0.491	0.633	0.559	0.491	0.633	SUBCLONAL	1	TRUE	1	0.430330503785927	2		655	640	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953633	32953633	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359732	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	82	558	0	ENST00000380152.3:c.8940del	p.Glu2981LysfsTer7	p.E2981Kfs*7	ENST00000380152		2978	tcA/tc	22/27	1	2	FACETS	0.676	0.597	0.76	0.676	0.597	0.76	SUBCLONAL	1	TRUE	1	0.430330503785927	2		558	564	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73348134	73348134	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	124	722	0	ENST00000377767.4:c.1051del	p.Arg351GlyfsTer35	p.R351Gfs*35	ENST00000377767	NM_014953.3	351	Agg/gg	7/21	1	2	FACETS	0.913	0.828	1	0.913	0.828	1	CLONAL	1	TRUE	1	0.430330503785927	2		722	631	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762249	43762249	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763084380	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	138	852	1	ENST00000382044.4:c.1196C>T	p.Thr399Met	p.T399M	ENST00000382044	NM_001141980.1	399	aCg/aTg	11/28	1	2	FACETS	0.8	0.728	0.875	0.8	0.728	0.875	SUBCLONAL	1	TRUE	1	0.430330503785927	2		853	802	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900741	3900741	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	56	635	0	ENST00000262367.5:c.355G>T	p.Gly119Cys	p.G119C	ENST00000262367	NM_004380.2	119	Ggc/Tgc	2/31	1	2	FACETS	0.426	0.364	0.493	0.426	0.364	0.493	SUBCLONAL	1	TRUE	1	0.430330503785927	2		635	611	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	113	577	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.827	0.746	0.913	0.827	0.746	0.913	CLONAL	1	TRUE	1	0.430330503785927	2		577	635	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821918	72821918	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	60	436	1	ENST00000268489.5:c.10257del	p.Lys3420AsnfsTer65	p.K3420Nfs*65	ENST00000268489	NM_006885.3	3419	ccC/cc	10/10	1	2	FACETS	0.538	0.464	0.619	0.538	0.464	0.619	SUBCLONAL	1	TRUE	1	0.430330503785927	2		437	518	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993551	72993551	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	59	750	0	ENST00000268489.5:c.494C>T	p.Pro165Leu	p.P165L	ENST00000268489	NM_006885.3	165	cCt/cTt	2/10	1	2	FACETS	0.393	0.337	0.454	0.393	0.337	0.454	SUBCLONAL	1	TRUE	1	0.430330503785927	2		750	698	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	208	871	0	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.430330503785927	2		871	933	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604809	48604809	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	42	468	0	ENST00000342988.3:c.1631C>A	p.Pro544Gln	p.P544Q	ENST00000342988	NM_005359.5	544	cCg/cAg	12/12	1	2	FACETS	0.372	0.31	0.441	0.372	0.31	0.441	SUBCLONAL	1	TRUE	1	0.430330503785927	2		468	525	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611771	1611771	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	177	995	0	ENST00000344749.5:c.1891del	p.Gln631ArgfsTer11	p.Q631Rfs*11	ENST00000344749	NM_001136139.2	631	Cag/ag	19/19	1	2	FACETS	0.892	0.822	0.965	0.892	0.822	0.965	CLONAL	1	TRUE	1	0.430330503785927	2		995	922	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216397	2216400	+	missense_variant	Missense_Mutation	ONP	CGCG	CGCG	TGCA	novel	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	143	852	0	ENST00000398665.3:c.2041_2044delinsTGCA	p.Arg681_Glu682delinsCysLys	p.R681_E682delinsCK	ENST00000398665	NM_032482.2	681	CGCGag/TGCAag	20/28	1	2	FACETS	0.928	0.848	1	0.928	0.848	1	CLONAL	1	TRUE	1	0.430330503785927	2		852	716	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145605	11145605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	144	655	0	ENST00000358026.2:c.3967C>T	p.Arg1323Cys	p.R1323C	ENST00000358026	NM_001128849.1	1323	Cgc/Tgc	29/36	1	2	FACETS	0.991	0.907	1	0.991	0.907	1	CLONAL	1	TRUE	1	0.430330503785927	2		655	675	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271730	15271730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749189648	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	100	1179	2	ENST00000263388.2:c.6709C>T	p.Arg2237Trp	p.R2237W	ENST00000263388	NM_000435.2	2237	Cgg/Tgg	33/33	1	2	FACETS	0.478	0.426	0.533	0.478	0.426	0.533	SUBCLONAL	1	TRUE	1	0.430330503785927	2		1181	973	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300155	15300155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768208563	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	217	976	1	ENST00000263388.2:c.1121G>A	p.Arg374Gln	p.R374Q	ENST00000263388	NM_000435.2	374	cGg/cAg	7/33	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.430330503785927	2		977	909	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279937	18279937	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867192525	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	225	907	0	ENST00000222254.8:c.2020G>A	p.Ala674Thr	p.A674T	ENST00000222254	NM_005027.3	674	Gcc/Acc	16/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.430330503785927	2		907	934	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250275	39250275	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs267607080	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	242	1210	0	ENST00000402219.2:c.1294T>C	p.Trp432Arg	p.W432R	ENST00000402219	NM_005633.3	432	Tgg/Cgg	10/23	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.430330503785927	2		1210	1093	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030691	48030692	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs267608092	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	128	527	1	ENST00000234420.5:c.3312dup	p.Gly1105TrpfsTer3	p.G1105Wfs*3	ENST00000234420	NM_000179.2	1102	act/acTt	5/10	1	2	FACETS	0.932	0.847	1	0.932	0.847	1	CLONAL	1	TRUE	1	0.430330503785927	2		528	638	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033352	48033352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750949	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	134	691	0	ENST00000234420.5:c.3656C>T	p.Thr1219Ile	p.T1219I	ENST00000234420	NM_000179.2	1219	aCt/aTt	8/10	1	2	FACETS	0.941	0.857	1	0.941	0.857	1	CLONAL	1	TRUE	1	0.430330503785927	2		691	662	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659859	227659859	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372040825	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	153	634	1	ENST00000305123.5:c.3596C>T	p.Pro1199Leu	p.P1199L	ENST00000305123	NM_005544.2	1199	cCg/cTg	1/2	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.430330503785927	2		635	597	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375249	31375249	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	77	929	0	ENST00000328111.2:c.646del	p.Glu216SerfsTer10	p.E216Sfs*10	ENST00000328111	NM_006892.3	216	Gag/ag	6/23	1	2	FACETS	0.45	0.394	0.51	0.45	0.394	0.51	SUBCLONAL	1	TRUE	1	0.430330503785927	2		929	796	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747065	40747065	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	149	744	0	ENST00000373198.4:c.3017C>T	p.Thr1006Ile	p.T1006I	ENST00000373198	NM_133170.3	1006	aCa/aTa	22/32	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.430330503785927	2		744	685	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21272266	21272266	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	59	632	0	ENST00000354336.3:c.44A>G	p.Tyr15Cys	p.Y15C	ENST00000354336	NM_005207.3	15	tAt/tGt	1/3	1	2	FACETS	0.586	0.505	0.674	0.586	0.505	0.674	SUBCLONAL	1	TRUE	1	0.430330503785927	2		632	468	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620542	52620542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	204	810	1	ENST00000394830.3:c.3211C>T	p.Arg1071Cys	p.R1071C	ENST00000394830	NM_018313.4	1071	Cgc/Tgc	21/30	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.430330503785927	2		811	934	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176551	142176551	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	166	728	0	ENST00000350721.4:c.7550A>G	p.His2517Arg	p.H2517R	ENST00000350721	NM_001184.3	2517	cAt/cGt	45/47	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.430330503785927	2		728	724	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31431766	31431766	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	150	679	1	ENST00000344624.3:c.3062T>G	p.Phe1021Cys	p.F1021C	ENST00000344624		1021	tTt/tGt	23/33	1	2	FACETS	0.945	0.865	1	0.945	0.865	1	CLONAL	1	TRUE	1	0.430330503785927	2		680	738	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675571	86675571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1561325048	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	107	482	0	ENST00000274376.6:c.2513del	p.Asn838MetfsTer4	p.N838Mfs*4	ENST00000274376	NM_002890.2	836	gAa/ga	19/25	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.430330503785927	2		482	463	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322269	31322270	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	52	503	0	ENST00000412585.2:c.1079_1080del	p.Leu360HisfsTer39	p.L360Hfs*39	ENST00000412585	NM_005514.6	360	cTC/c	7/8	1	2	FACETS	0.465	0.396	0.541	0.465	0.396	0.541	SUBCLONAL	1	TRUE	1	0.430330503785927	2		503	520	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004525	150004525	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	173	954	0	ENST00000253339.5:c.1700A>G	p.Asn567Ser	p.N567S	ENST00000253339		567	aAc/aGc	3/7	1	2	FACETS	0.883	0.812	0.956	0.883	0.812	0.956	CLONAL	1	TRUE	1	0.430330503785927	2		954	911	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150551	157150551	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	114	547	0	ENST00000346085.5:c.1733A>C	p.Gln578Pro	p.Q578P	ENST00000346085	NM_020732.3	578	cAg/cCg	2/20	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.430330503785927	2		547	530	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528830	157528831	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	147	689	0	ENST00000346085.5:c.6559dup	p.Leu2187ProfsTer5	p.L2187Pfs*5	ENST00000346085	NM_020732.3	2185	-/C	20/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.430330503785927	2		689	641	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	102	728	2	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.643	0.575	0.715	0.643	0.575	0.715	SUBCLONAL	1	TRUE	1	0.430330503785927	2		730	737	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5078388	5078388	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	117	775	0	ENST00000381652.3:c.2075C>A	p.Pro692His	p.P692H	ENST00000381652	NM_004972.3	692	cCt/cAt	16/25	1	2	FACETS	0.874	0.79	0.963	0.874	0.79	0.963	CLONAL	1	TRUE	1	0.430330503785927	2		775	622	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180334	27180334	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	83	592	0	ENST00000380036.4:c.998C>T	p.Pro333Leu	p.P333L	ENST00000380036	NM_000459.3	333	cCa/cTa	7/23	1	2	FACETS	0.645	0.57	0.726	0.645	0.57	0.726	SUBCLONAL	1	TRUE	1	0.430330503785927	2		592	598	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801080	135801080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	124	599	0	ENST00000298552.3:c.257G>A	p.Arg86His	p.R86H	ENST00000298552	NM_001162426.1	86	cGt/cAt	5/23	1	2	FACETS	0.977	0.887	1	0.977	0.887	1	CLONAL	1	TRUE	1	0.430330503785927	2		599	590	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309024	137309024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1348109062	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	170	941	3	ENST00000481739.1:c.631C>T	p.Arg211Cys	p.R211C	ENST00000481739	NM_002957.4	211	Cgt/Tgt	5/10	1	2	FACETS	0.966	0.889	1	0.966	0.889	1	CLONAL	1	TRUE	1	0.430330503785927	2		944	818	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564123	139564123	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	91	898	0	ENST00000308874.7:c.263G>A	p.Cys88Tyr	p.C88Y	ENST00000308874		88	tGc/tAc	5/10	1	2	FACETS	0.5	0.443	0.561	0.5	0.443	0.561	SUBCLONAL	1	TRUE	1	0.430330503785927	2		898	846	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0021518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	152	497	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.956	0.881	1	0.956	0.881	1	CLONAL	1	TRUE	1	0.658403269017552	2		497	483	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692919	89692919	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782360	NA	P-0021518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	152	660	0	ENST00000371953.3:c.403A>G	p.Ile135Val	p.I135V	ENST00000371953	NM_000314.4	135	Ata/Gta	5/9	0.658403269017552	1	FACETS	0.98	0.912	1	0.98	0.912	1	CLONAL	1	TRUE	0	0.658403269017552	1		660	316	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058569	72058569	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	53	735	2	ENST00000357731.5:c.871C>T	p.His291Tyr	p.H291Y	ENST00000357731	NM_173808.2	291	Cac/Tac	6/7	1	2	FACETS	0.201	0.171	0.235	0.201	0.171	0.235	SUBCLONAL	1	TRUE	1	0.658403269017552	2		737	800	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258744	115258744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434596	NA	P-0021518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	246	621	0	ENST00000369535.4:c.38G>A	p.Gly13Asp	p.G13D	ENST00000369535	NM_002524.4	13	gGt/gAt	2/7	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.658403269017552	2		621	724	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858337	9858337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs560057284	NA	P-0021518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	223	541	2	ENST00000330684.3:c.3064C>T	p.Arg1022Cys	p.R1022C	ENST00000330684	NM_001134407.1	1022	Cgc/Tgc	13/13	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.658403269017552	2		543	666	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0021518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	467	857	0	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.658403269017552	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.658403269017552	1		857	865	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821817	59821817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780235	NA	P-0021518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	145	796	0	ENST00000259008.2:c.2233G>A	p.Ala745Thr	p.A745T	ENST00000259008	NM_032043.2	745	Gca/Aca	15/20	0.425438506716216	1	FACETS	0.517	0.474	0.562	0.517	0.474	0.562	SUBCLONAL	1	TRUE	0	0.658403269017552	1		796	571	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155411	185155411	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140970208	NA	P-0021518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	33	499	2	ENST00000265026.3:c.652G>A	p.Ala218Thr	p.A218T	ENST00000265026	NM_004721.4	218	Gca/Aca	3/14	0.284615557151545	3	FACETS	0.242	0.197	0.294	0.121	0.098	0.147	INDETERMINATE	1	TRUE	1	0.658403269017552	3		501	550	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957873	1957873	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs943974282	NA	P-0021518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	327	734	1	ENST00000382891.5:c.2839C>T	p.Arg947Cys	p.R947C	ENST00000382891	NM_133335.3	947	Cgc/Tgc	15/22	0.407911885061695	1	FACETS	0.717	0.679	0.756	0.717	0.679	0.756	SUBCLONAL	1	TRUE	0	0.658403269017552	1		735	929	SUCCESS
APC	324	MSKCC	GRCh37	5	112174310	112174310	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	88	496	0	ENST00000257430.4:c.3022del	p.Ile1008TyrfsTer14	p.I1008Yfs*14	ENST00000257430	NM_000038.5	1007	Aaa/aa	16/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.658403269017552	2		496	246	SUCCESS
APC	324	MSKCC	GRCh37	5	112175802	112175802	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	114	439	0	ENST00000257430.4:c.4512del	p.Ser1505AlafsTer2	p.S1505Afs*2	ENST00000257430	NM_000038.5	1504	tCc/tc	16/16	1	2	FACETS	0.962	0.875	1	0.962	0.875	1	CLONAL	1	TRUE	1	0.658403269017552	2		439	360	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039570	180039570	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1185976621	NA	P-0021518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	467	985	2	ENST00000261937.6:c.3473C>T	p.Ala1158Val	p.A1158V	ENST00000261937	NM_182925.4	1158	gCg/gTg	26/30	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.658403269017552	2		987	1390	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158411	26158411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1050932839	NA	P-0021518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	366	973	2	ENST00000289316.2:c.14C>T	p.Thr5Ile	p.T5I	ENST00000289316	NM_138720.2	5	aCc/aTc	1/2	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.658403269017552	2		975	1083	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900200	101900200	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	118	590	0	ENST00000374994.4:c.634G>A	p.Gly212Ser	p.G212S	ENST00000374994	NM_004612.2	212	Ggc/Agc	4/9	1	2	FACETS	0.892	0.811	0.975	0.892	0.811	0.975	CLONAL	1	TRUE	1	0.658403269017552	2		590	402	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412391	63412392	+	stop_gained	Nonsense_Mutation	DNP	TC	TC	CA	novel	NA	P-0021518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	389	994	1	ENST00000330258.3:c.775_776delinsTG	p.Glu259Ter	p.E259*	ENST00000330258	NM_152424.3	259	GAa/TGa	2/2	0.658403269017552	1	FACETS	0.971	0.929	1	0.971	0.929	1	CLONAL	1	TRUE	0	0.658403269017552	1		995	816	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	224	576	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.805	0.755	0.855	1	0.993	1	CLONAL	2	TRUE	1	0.48	2		580	580	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	130	611	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.824	0.75	0.903	0.824	0.75	0.903	CLONAL	1	TRUE	1	0.48	2		611	657	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	107	673	3	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	0.174054330826643	3	FACETS	1	0.945	1	0.537	0.483	0.593	INDETERMINATE	1	TRUE	1	0.48	3		676	515	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261554	142261555	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1043355995	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	434	624	1	ENST00000350721.4:c.3402dup	p.Asn1135Ter	p.N1135*	ENST00000350721	NM_001184.3	1134	-/T	17/47	0.3	5	FACETS	0.992	0.949	1	0.744	0.712	0.777	CLONAL	3	TRUE	1	0.48	5		625	1045	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915779	112915779	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507534	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	88	485	0	ENST00000351677.2:c.1052G>A	p.Arg351Gln	p.R351Q	ENST00000351677	NM_002834.3	351	cGa/cAa	9/16	1	2	FACETS	0.865	0.77	0.964	0.865	0.77	0.964	CLONAL	1	TRUE	1	0.48	2		485	424	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796883	42796883	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	143	999	2	ENST00000575354.2:c.3347del	p.Pro1116GlnfsTer45	p.P1116Qfs*45	ENST00000575354	NM_015125.3	1114	gCc/gc	14/20	1	2	FACETS	0.919	0.841	1	0.919	0.841	1	CLONAL	1	TRUE	1	0.48	2		1001	648	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	160	692	1	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	1	2	FACETS	0.827	0.759	0.898	0.827	0.759	0.898	CLONAL	1	TRUE	1	0.48	2		693	806	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	113	569	5	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	0.81	0.731	0.893	0.81	0.731	0.893	CLONAL	1	TRUE	1	0.48	2		574	581	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	85	344	0	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	0.3	0	FACETS	0.731	0.656	0.808			1	SUBCLONAL	1	TRUE	NA	0.48	0		344	252	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	151	329	0	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	0.781	0.714	0.85	0.781	0.714	0.85	SUBCLONAL	1	TRUE	1	0.48	2		329	806	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375990	8375990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142960593	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	69	476	0	ENST00000356435.5:c.4607G>A	p.Arg1536His	p.R1536H	ENST00000356435		1536	cGt/cAt	28/35	0.162936335874719	0	FACETS	0.352	0.307	0.399			1	INDETERMINATE	1	TRUE	0	0.48	0		476	425	SUCCESS
APC	324	MSKCC	GRCh37	5	112178033	112178033	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs773874693	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	80	523	0	ENST00000257430.4:c.6747del	p.Gly2250AlafsTer29	p.G2250Afs*29	ENST00000257430	NM_000038.5	2248	Aaa/aa	16/16	0.174054330826643	3	FACETS	0.78	0.688	0.878	0.39	0.344	0.439	INDETERMINATE	1	TRUE	1	0.48	3		523	530	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822586	72822586	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	43	538	6	ENST00000268489.5:c.9589del	p.Gln3197SerfsTer44	p.Q3197Sfs*44	ENST00000268489	NM_006885.3	3197	Cag/ag	10/10	0.3	1	FACETS	0.463	0.389	0.544	0.463	0.389	0.544	SUBCLONAL	1	TRUE	0	0.48	1		544	294	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724361	52724361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	45	543	1	ENST00000322088.6:c.1493G>A	p.Arg498His	p.R498H	ENST00000322088	NM_014225.5	498	cGc/cAc	12/15	0.283351300484298	0	FACETS	0.348	0.294	0.407			1	INDETERMINATE	1	TRUE	0	0.48	0		544	280	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240271	5240271	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	28	837	2	ENST00000357368.4:c.1643del	p.Pro548ArgfsTer37	p.P548Rfs*37	ENST00000357368	NM_002850.3	548	cCg/cg	12/38	0.3	1	FACETS	0.208	0.165	0.256	0.208	0.165	0.256	SUBCLONAL	1	TRUE	0	0.48	1		839	427	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098609	108098609	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	70	406	0	ENST00000278616.4:c.183del	p.Phe61LeufsTer15	p.F61Lfs*15	ENST00000278616	NM_000051.3	60	gTt/gt	3/63	0.127553224520552	3	FACETS	0.735	0.642	0.835			1	INDETERMINATE	1	TRUE	NA	0.48	3		406	492	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752651	128752653	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs761021550	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	60	358	0	ENST00000377970.2:c.816_818del	p.Glu272del	p.E272del	ENST00000377970	NM_002467.4	271	cAAGaa/caa	3/3	0.3	5	FACETS	0.841	0.726	0.967	0.28	0.242	0.323	CLONAL	1	TRUE	2	0.48	5		358	511	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214728	36214728	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	61	529	1	ENST00000222270.7:c.3159del	p.Arg1055GlyfsTer127	p.R1055Gfs*127	ENST00000222270	NM_014727.1	1052	Ggg/gg	8/37	1	2	FACETS	0.82	0.712	0.935	0.82	0.712	0.935	CLONAL	1	TRUE	1	0.48	2		530	310	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899254	78899254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542518961	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	128	582	0	ENST00000306801.3:c.2893C>T	p.Arg965Cys	p.R965C	ENST00000306801	NM_020761.2	965	Cgc/Tgc	24/34	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.48	2		582	533	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944413	40944414	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	73	783	0	ENST00000373198.4:c.2088_2089del	p.Leu698GlufsTer54	p.L698Efs*54	ENST00000373198	NM_133170.3	696	tcTCcc/tccc	12/32	0.3	0	FACETS	0.319	0.279	0.361			1	SUBCLONAL	1	TRUE	0	0.48	0		783	496	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262022	16262022	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	99	536	0	ENST00000375759.3:c.9287G>C	p.Gly3096Ala	p.G3096A	ENST00000375759	NM_015001.2	3096	gGc/gCc	11/15	0.174054330826643	3	FACETS	1	0.953	1	0.554	0.497	0.614	INDETERMINATE	1	TRUE	1	0.48	3		536	462	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416371	49416371	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1555184777	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	117	544	0	ENST00000301067.7:c.16338+2T>C		p.X5446_splice	ENST00000301067	NM_003482.3	5446			0.132260571501113	4	FACETS	1	0.981	1	0.673	0.609	0.74	INDETERMINATE	1	TRUE	2	0.48	4		544	536	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106691	2106691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760100924	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	177	886	1	ENST00000219476.3:c.695C>T	p.Pro232Leu	p.P232L	ENST00000219476	NM_000548.3	232	cCg/cTg	8/42	NA	2	FACETS	1	0.955	1			1	INDETERMINATE	1	TRUE	NA	0.48	2		887	704	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783992	50783992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	62	817	1	ENST00000398568.2:c.383G>A	p.Gly128Asp	p.G128D	ENST00000398568	NM_001042412.1	128	gGc/gAc	3/18	NA	2	FACETS	0.4	0.345	0.46			1	INDETERMINATE	1	TRUE	NA	0.48	2		818	646	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622369	1622369	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143406385	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	143	830	0	ENST00000344749.5:c.595G>A	p.Ala199Thr	p.A199T	ENST00000344749	NM_001136139.2	199	Gcc/Acc	9/19	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.48	2		830	576	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218851	36218851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773513850	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	112	788	0	ENST00000222270.7:c.4462C>T	p.Arg1488Trp	p.R1488W	ENST00000222270	NM_014727.1	1488	Cgg/Tgg	18/37	1	2	FACETS	0.945	0.854	1	0.945	0.854	1	CLONAL	1	TRUE	1	0.48	2		788	494	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839764	42839764	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	150	793	0	ENST00000398585.3:c.1475T>C	p.Leu492Pro	p.L492P	ENST00000398585	NM_001135099.1	492	cTg/cCg	13/14	1	2	FACETS	0.975	0.894	1	0.975	0.894	1	CLONAL	1	TRUE	1	0.48	2		793	641	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884869	134884869	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1261079719	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	80	652	1	ENST00000398015.3:c.1645G>A	p.Gly549Arg	p.G549R	ENST00000398015	NM_004441.4	549	Ggg/Agg	8/16	0.127553224520552	3	FACETS	0.657	0.579	0.741			1	INDETERMINATE	1	TRUE	NA	0.48	3		653	629	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664793	138664793	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs28937885	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	21	494	0	ENST00000330315.3:c.772T>A	p.Tyr258Asn	p.Y258N	ENST00000330315	NM_023067.3	258	Tac/Aac	1/1	0.3	5	FACETS	0.39	0.3	0.496	0.097	0.075	0.124	SUBCLONAL	1	TRUE	1	0.48	5		494	386	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902677	1902677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751138696	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	153	800	0	ENST00000382891.5:c.296G>A	p.Arg99His	p.R99H	ENST00000382891	NM_133335.3	99	cGt/cAt	2/22	1	2	FACETS	0.889	0.815	0.966	0.889	0.815	0.966	CLONAL	1	TRUE	1	0.48	2		800	717	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631295	176631295	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	57	307	0	ENST00000439151.2:c.1236+2T>C		p.X412_splice	ENST00000439151	NM_022455.4	412			0.127553224520552	3	FACETS	1	0.928	1			1	INDETERMINATE	1	TRUE	NA	0.48	3		307	265	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652119	36652119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	101	670	1	ENST00000244741.5:c.241G>A	p.Gly81Arg	p.G81R	ENST00000244741	NM_000389.4	81	Ggg/Agg	2/3	0.132260571501113	4	FACETS	1	0.966	1	0.593	0.532	0.658	INDETERMINATE	1	TRUE	2	0.48	4		671	525	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536256	106536256	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	123	635	0	ENST00000369096.4:c.223A>G	p.Thr75Ala	p.T75A	ENST00000369096	NM_001198.3	75	Act/Gct	2/7	0.3	3	FACETS	0.891	0.807	0.98			1	CLONAL	1	TRUE	NA	0.48	3		635	713	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539062	23539062	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	34	625	1	ENST00000380871.4:c.377G>A	p.Arg126His	p.R126H	ENST00000380871	NM_006167.3	126	cGc/cAc	2/2	0.3	3	FACETS	0.39	0.318	0.47	0.195	0.159	0.235	SUBCLONAL	1	TRUE	1	0.48	3		626	451	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606506	93606506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756646754	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	123	800	2	ENST00000375746.1:c.326G>A	p.Arg109Gln	p.R109Q	ENST00000375746	NM_001174167.1	109	cGg/cAg	2/14	1	2	FACETS	0.999	0.908	1	0.999	0.908	1	CLONAL	1	TRUE	1	0.48	2		802	513	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276798	15276798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763602970	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	88	802	0	ENST00000263388.2:c.5467G>A	p.Asp1823Asn	p.D1823N	ENST00000263388	NM_000435.2	1823	Gac/Aac	30/33	0.3	1	FACETS	0.607	0.54	0.678	0.607	0.54	0.678	SUBCLONAL	1	TRUE	0	0.48	1		802	459	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007898	45007898	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	110	483	0	ENST00000558401.1:c.345G>A	p.Trp115Ter	p.W115*	ENST00000558401	NM_004048.2	115	tgG/tgA	2/4	1	2	FACETS	0.77	0.694	0.851	0.77	0.694	0.851	SUBCLONAL	1	TRUE	1	0.48	2		483	595	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941429	71941429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754156985	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	158	791	4	ENST00000298229.2:c.1114C>T	p.Arg372Cys	p.R372C	ENST00000298229	NM_001567.3	372	Cgt/Tgt	10/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.48	2		795	594	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187350	38187350	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	133	758	0	ENST00000317025.8:c.1127A>C	p.Glu376Ala	p.E376A	ENST00000317025	NM_023034.1	376	gAg/gCg	6/24	0.3	3	FACETS	0.753	0.683	0.826	0.376	0.341	0.413	SUBCLONAL	1	TRUE	1	0.48	3		758	913	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804397	46804397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1014715541	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	81	494	1	ENST00000290295.7:c.610G>A	p.Gly204Arg	p.G204R	ENST00000290295	NM_006361.5	204	Ggg/Agg	2/2	1	2	FACETS	0.902	0.8	1	0.902	0.8	1	CLONAL	1	TRUE	1	0.48	2		495	374	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187222	38187222	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs759901656	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	217	1011	0	ENST00000317025.8:c.1255A>C	p.Thr419Pro	p.T419P	ENST00000317025	NM_023034.1	419	Acc/Ccc	6/24	0.3	3	FACETS	0.908	0.843	0.975	0.454	0.421	0.488	CLONAL	1	TRUE	1	0.48	3		1011	1235	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397709	139397709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1417478070	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	115	761	2	ENST00000277541.6:c.5092G>A	p.Asp1698Asn	p.D1698N	ENST00000277541	NM_017617.3	1698	Gac/Aac	27/34	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.48	2		763	462	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137313618	137313618	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	112	810	1	ENST00000481739.1:c.880del	p.Leu294TrpfsTer27	p.L294Wfs*27	ENST00000481739	NM_002957.4	293	Ccc/cc	6/10	1	2	FACETS	0.933	0.844	1	0.933	0.844	1	CLONAL	1	TRUE	1	0.48	2		811	500	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793676	89793677	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	93	443	1	ENST00000336032.3:c.752dup	p.Pro252AlafsTer3	p.P252Afs*3	ENST00000336032	NM_006813.2	249	gaa/gAaa	2/2	0.132260571501113	4	FACETS	1	0.921	1	0.52	0.464	0.581	INDETERMINATE	1	TRUE	2	0.48	4		444	551	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0021520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	184	336	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.874	0.808	0.943	0.874	0.808	0.943	CLONAL	1	TRUE	1	0.49	2		336	859	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0021520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	156	601	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.962	0.884	1	0.962	0.884	1	CLONAL	1	TRUE	1	0.49	2		602	662	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249348	110249348	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	267	557	0	ENST00000374672.4:c.1225A>C	p.Lys409Gln	p.K409Q	ENST00000374672	NM_004235.4	409	Aag/Cag	4/5	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.49	2		557	1003	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610164	43610164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137855422	NA	P-0021520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	154	826	2	ENST00000355710.3:c.2116G>A	p.Val706Met	p.V706M	ENST00000355710	NM_020975.4	706	Gtg/Atg	11/20	1	2	FACETS	0.866	0.794	0.941	0.866	0.794	0.941	CLONAL	1	TRUE	1	0.49	2		828	726	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221243	1221243	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1057520606	NA	P-0021521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	203	872	5	ENST00000326873.7:c.766G>T	p.Glu256Ter	p.E256*	ENST00000326873	NM_000455.4	256	Gaa/Taa	6/10	0.22036045905191	2	FACETS	1	0.988	1	0.668	0.619	0.719	CLONAL	1	TRUE	0	0.292602637514055	2		877	1038	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849872	156849872	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	330	868	1	ENST00000524377.1:c.2128G>T	p.Val710Leu	p.V710L	ENST00000524377	NM_002529.3	710	Gtg/Ttg	16/17	0.292602637514055	4	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.292602637514055	4		869	1188	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214725	133214726	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0021521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	162	654	0	ENST00000320574.5:c.5553-1_5553delinsTT		p.X1851_splice	ENST00000320574	NM_006231.2	1851		41/49	0.133448943904446	3	FACETS	0.788	0.724	0.855	0.788	0.724	0.855	INDETERMINATE	2	TRUE	1	0.292602637514055	3		654	805	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514650	103514650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	42	520	0	ENST00000355739.4:c.1151C>T	p.Ser384Leu	p.S384L	ENST00000355739	NM_000123.3	384	tCa/tTa	8/15	0.218517545150787	4	FACETS	0.574	0.478	0.68	0.287	0.239	0.34	SUBCLONAL	1	TRUE	2	0.292602637514055	4		520	647	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55229197	55229197	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	95	410	1	ENST00000275493.2:c.1504A>G	p.Thr502Ala	p.T502A	ENST00000275493	NM_005228.3	502	Aca/Gca	13/28	0.258405862262316	3	FACETS	0.928	0.832	1	0.928	0.832	1	CLONAL	2	TRUE	1	0.292602637514055	3		411	401	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245151	53245151	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	107	427	2	ENST00000375401.3:c.789G>T	p.Glu263Asp	p.E263D	ENST00000375401	NM_004187.3	263	gaG/gaT	7/26	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.292602637514055	1		429	425	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88679204	88679204	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	44	400	0	ENST00000372037.3:c.1144G>T	p.Gly382Cys	p.G382C	ENST00000372037	NM_004329.2	382	Ggc/Tgc	10/13	1	2	FACETS	0.785	0.66	0.923	0.785	0.66	0.923	CLONAL	1	TRUE	1	0.292602637514055	2		400	383	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262553	16262553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	79	594	0	ENST00000375759.3:c.9818C>T	p.Thr3273Ile	p.T3273I	ENST00000375759	NM_015001.2	3273	aCc/aTc	11/15	1	2	FACETS	0.881	0.775	0.994	0.881	0.775	0.994	CLONAL	1	TRUE	1	0.292602637514055	2		594	613	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591964	48591964	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	42	504	0	ENST00000342988.3:c.1127T>A	p.Ile376Asn	p.I376N	ENST00000342988	NM_005359.5	376	aTt/aAt	9/12	1	2	FACETS	0.627	0.523	0.741	0.627	0.523	0.741	SUBCLONAL	1	TRUE	1	0.292602637514055	2		504	458	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47710066	47710066	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0021521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	51	421	0	ENST00000233146.2:c.2783C>G	p.Ser928Ter	p.S928*	ENST00000233146	NM_000251.2	928	tCa/tGa	16/16	0.121723421887366	3	FACETS	0.94	0.801	1	0.47	0.4	0.547	INDETERMINATE	1	TRUE	1	0.292602637514055	3		421	425	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69050686	69050686	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	124	862	0	ENST00000288368.4:c.4021del	p.Ala1341HisfsTer37	p.A1341Hfs*37	ENST00000288368	NM_024870.2	1341	Gca/ca	33/40	0.121723421887366	3	FACETS	1	0.977	1	0.627	0.567	0.69	INDETERMINATE	1	TRUE	1	0.292602637514055	3		862	775	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597475	10597490	+	frameshift_variant	Frame_Shift_Del	DEL	CGTGTGACCATCATAG	CGTGTGACCATCATAG	-	novel	NA	P-0021521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	130	921	0	ENST00000171111.5:c.1713_1728del	p.Tyr572SerfsTer18	p.Y572Sfs*18	ENST00000171111	NM_203500.1	571	ggCTATGATGGTCACACG/gg	6/6	0.22036045905191	2	FACETS	0.956	0.867	1	0.478	0.433	0.526	CLONAL	1	TRUE	0	0.292602637514055	2		921	929	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0021522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	133	515	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.888	0.808	0.972	0.888	0.808	0.972	CLONAL	1	FALSE	1	0.426057363158331	2		515	703	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	203	644	5	ENST00000269305.4:c.166G>T	p.Glu56Ter	p.E56*	ENST00000269305	NM_001126112.2	56	Gaa/Taa	4/11	0.426057363158331	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	0	0.426057363158331	1		649	717	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0021522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	100	455	0				ENST00000310581	NM_198253.2	-/1132			0.253592515074617	1	FACETS	0.842	0.756	0.931	0.842	0.756	0.931	INDETERMINATE	1	FALSE	0	0.426057363158331	1		455	439	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579545	7579545	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	233	1161	1	ENST00000269305.4:c.142G>A	p.Asp48Asn	p.D48N	ENST00000269305	NM_001126112.2	48	Gac/Aac	4/11	0.426057363158331	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	0	0.426057363158331	1		1162	729	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420664	49420664	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	101	1008	0	ENST00000301067.7:c.15085del	p.Met5029CysfsTer22	p.M5029Cfs*22	ENST00000301067	NM_003482.3	5029	Atg/tg	48/54	1	2	FACETS	0.677	0.606	0.753	0.677	0.606	0.753	SUBCLONAL	1	FALSE	1	0.426057363158331	2		1008	700	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439847	49439847	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs886041406	NA	P-0021522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	149	962	0	ENST00000301067.7:c.4693+1G>T		p.X1565_splice	ENST00000301067	NM_003482.3	1565			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.426057363158331	2		962	631	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671635	67671635	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	135	915	0	ENST00000264010.4:c.2044G>C	p.Glu682Gln	p.E682Q	ENST00000264010	NM_006565.3	682	Gag/Cag	12/12	1	2	FACETS	0.903	0.822	0.987	0.903	0.822	0.987	CLONAL	1	FALSE	1	0.426057363158331	2		915	702	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579566	7579566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555526789	NA	P-0021522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	224	1107	0	ENST00000269305.4:c.121G>A	p.Asp41Asn	p.D41N	ENST00000269305	NM_001126112.2	41	Gat/Aat	4/11	0.426057363158331	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	0	0.426057363158331	1		1107	688	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687561	37687561	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	99	561	0	ENST00000447079.4:c.4465C>G	p.Pro1489Ala	p.P1489A	ENST00000447079	NM_015083.1	1489	Cct/Gct	14/14	1	2	FACETS	0.968	0.868	1	0.968	0.868	1	CLONAL	1	FALSE	1	0.426057363158331	2		561	480	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686913	37686913	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	164	915	0	ENST00000447079.4:c.3817C>G	p.Pro1273Ala	p.P1273A	ENST00000447079	NM_015083.1	1273	Cca/Gca	14/14	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.426057363158331	2		915	731	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578496	7578496	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782197	NA	P-0021523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1599	54	1149	0	ENST00000269305.4:c.434T>C	p.Leu145Pro	p.L145P	ENST00000269305	NM_001126112.2	145	cTg/cCg	5/11	1	2	FACETS	0.344	0.292	0.401	0.344	0.292	0.401	SUBCLONAL	1	TRUE	1	0.19	2		1149	1653	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907522	32907522	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	37	409	0	ENST00000380152.3:c.1907C>A	p.Ser636Ter	p.S636*	ENST00000380152		636	tCa/tAa	10/27	1	2	FACETS	0.679	0.558	0.813	0.679	0.558	0.813	SUBCLONAL	1	TRUE	1	0.19	2		409	574	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829058	128829071	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGGGGGACCCGG	GCTGGGGGACCCGG	-	novel	NA	P-0021523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	10	100	0	ENST00000249373.3:c.68_81del	p.Leu23ProfsTer108	p.L23Pfs*108	ENST00000249373	NM_005631.4	22	ctGCTGGGGGACCCGGgc/ctgc	1/12	1	2	FACETS	0.757	0.515	1	0.757	0.515	1	CLONAL	1	TRUE	1	0.19	2		100	139	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0021525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	46	638	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.13	2		639	690	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0021525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	50	748	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	0.685	0.579	0.803	0.685	0.579	0.803	SUBCLONAL	1	TRUE	1	0.13	2		748	1123	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405078	70405078	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	71	772	0	ENST00000373644.4:c.2592T>A	p.Ser864Arg	p.S864R	ENST00000373644	NM_030625.2	864	agT/agA	4/12	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.13	2		772	1086	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841892	151841892	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	117	615	0	ENST00000262189.6:c.14249A>C	p.Tyr4750Ser	p.Y4750S	ENST00000262189	NM_170606.2	4750	tAt/tCt	55/59	1	2	FACETS	0.976	0.879	1	1	0.988	1	CLONAL	2	TRUE	1	0.13	2		615	922	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573639	41573639	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1273051199	NA	P-0021525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	73	779	0	ENST00000263253.7:c.5924G>T	p.Gly1975Val	p.G1975V	ENST00000263253	NM_001429.3	1975	gGt/gTt	31/31	1	2	FACETS	0.976	0.85	1	0.976	0.85	1	CLONAL	1	TRUE	1	0.13	2		779	1151	SUCCESS
APC	324	MSKCC	GRCh37	5	112175884	112175884	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	30	371	0	ENST00000257430.4:c.4593del	p.Asn1531LysfsTer34	p.N1531Kfs*34	ENST00000257430	NM_000038.5	1531	aaT/aa	16/16	1	2	FACETS	0.799	0.642	0.977	0.799	0.642	0.977	CLONAL	1	TRUE	1	0.13	2		371	578	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063717	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0021555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	174	383	1	ENST00000412916.2:c.165+1G>T		p.X55_splice	ENST00000412916		55			0.38334529884275	2	FACETS	1	0.949	1	1	0.992	1	CLONAL	3	TRUE	0	0.38334529884275	2		384	300	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115712	8115715	+	frameshift_variant	Frame_Shift_Del	DEL	CCCT	CCCT	-	novel	NA	P-0021555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	120	453	0	ENST00000346208.3:c.1058_1061del	p.Pro353ArgfsTer3	p.P353Rfs*3	ENST00000346208		353	cCCCTg/cg	6/6	0.336486974358384	3	FACETS	0.944	0.861	1	0.944	0.861	1	CLONAL	2	TRUE	1	0.38334529884275	3		453	395	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151164299	151164299	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0021555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	247	659	1	ENST00000262187.5:c.463-2A>G		p.X155_splice	ENST00000262187	NM_005614.3	155			0.366455299232141	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.38334529884275	4		660	773	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199469669	NA	P-0021556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	190	684	0	ENST00000374080.3:c.130G>T	p.Gly44Cys	p.G44C	ENST00000374080		44	Ggt/Tgt	2/45	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	FALSE	NA	0.412204443924778	2		684	744	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0021556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	153	439	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	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.412204443924778	2		439	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577109	7577109	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1064795369	NA	P-0021559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	110	792	0	ENST00000269305.4:c.829T>G	p.Cys277Gly	p.C277G	ENST00000269305	NM_001126112.2	277	Tgt/Ggt	8/11	0.178396285741265	2	FACETS	1	0.963	1	0.577	0.518	0.639	CLONAL	1	TRUE	0	0.24519898533634	2		792	778	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876449	35876449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2229232	NA	P-0021561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	199	768	1	ENST00000303115.3:c.1241C>T	p.Thr414Met	p.T414M	ENST00000303115	NM_002185.3	414	aCg/aTg	8/8	0.424128266728593	1	FACETS	0.922	0.856	0.99	0.922	0.856	0.99	CLONAL	1	FALSE	0	0.424128266728593	1		769	802	SUCCESS
AR	367	MSKCC	GRCh37	X	66937371	66937371	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	220	401	0	ENST00000374690.3:c.2225G>T	p.Trp742Leu	p.W742L	ENST00000374690	NM_000044.3	742	tGg/tTg	5/8	1	1	FACETS	0.781	0.734	0.829	1	0.993	1	SUBCLONAL	2	FALSE	0	0.424128266728593	1		401	523	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061288	38061288	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	493	769	0	ENST00000250448.2:c.701C>T	p.Ser234Phe	p.S234F	ENST00000250448	NM_004496.3	234	tCc/tTc	2/2	1	2	FACETS	0.838	0.802	0.874	1	0.997	1	CLONAL	2	FALSE	1	0.424128266728593	2		769	1387	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	528	174	0				ENST00000310581	NM_198253.2	-/1132			0.586568921831238	4	FACETS	0.964	0.93	0.997	0.964	0.93	0.997	CLONAL	3	TRUE	1	0.613095579664645	4		174	961	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727451	66727451	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519729	NA	P-0021563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	172	497	0	ENST00000307102.5:c.167A>C	p.Gln56Pro	p.Q56P	ENST00000307102	NM_002755.3	56	cAg/cCg	2/11	1	2	FACETS	0.941	0.871	1	0.941	0.871	1	CLONAL	1	TRUE	1	0.613095579664645	2		497	596	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604787	48604787	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519741	NA	P-0021563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	191	499	1	ENST00000342988.3:c.1609G>T	p.Asp537Tyr	p.D537Y	ENST00000342988	NM_005359.5	537	Gac/Tac	12/12	0.613095579664645	1	FACETS	0.982	0.919	1	0.982	0.919	1	CLONAL	1	TRUE	0	0.613095579664645	1		500	440	SUCCESS
APC	324	MSKCC	GRCh37	5	112174119	112174119	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1554084512	NA	P-0021563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	183	401	0	ENST00000257430.4:c.2828C>A	p.Ser943Ter	p.S943*	ENST00000257430	NM_000038.5	943	tCa/tAa	16/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.613095579664645	2		401	553	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794941	42794941	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs773111863	NA	P-0021563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	283	753	0	ENST00000575354.2:c.2021A>G	p.Asn674Ser	p.N674S	ENST00000575354	NM_015125.3	674	aAt/aGt	10/20	1	2	FACETS	0.994	0.936	1	0.994	0.936	1	CLONAL	1	TRUE	1	0.613095579664645	2		753	929	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937461	178937461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776503460	NA	P-0021563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	222	551	0	ENST00000263967.3:c.1849C>T	p.Arg617Trp	p.R617W	ENST00000263967	NM_006218.2	617	Cgg/Tgg	12/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.613095579664645	2		551	703	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910882	114910882	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	170	485	0	ENST00000543371.1:c.1001C>A	p.Ser334Ter	p.S334*	ENST00000543371	NM_001198531.1	334	tCa/tAa	9/14	1	2	FACETS	0.842	0.777	0.909	0.842	0.777	0.909	CLONAL	1	TRUE	1	0.613095579664645	2		485	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578543	7578556	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GGCAGGGGAGTACT	GGCAGGGGAGTACT	-	novel	NA	P-0021563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	260	884	0	ENST00000269305.4:c.376-2_387del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	0.613095579664645	1	FACETS	0.861	0.812	0.911	0.861	0.812	0.911	CLONAL	1	TRUE	0	0.613095579664645	1		884	683	SUCCESS
APC	324	MSKCC	GRCh37	5	112175609	112175609	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1131691145	NA	P-0021563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	149	383	0	ENST00000257430.4:c.4319del	p.Pro1440HisfsTer33	p.P1440Hfs*33	ENST00000257430	NM_000038.5	1440	Cca/ca	16/16	1	2	FACETS	0.915	0.841	0.992	0.915	0.841	0.992	CLONAL	1	TRUE	1	0.613095579664645	2		383	531	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106534450	106534450	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	151	377	0	ENST00000369096.4:c.22A>C	p.Lys8Gln	p.K8Q	ENST00000369096	NM_001198.3	8	Aaa/Caa	1/7	1	2	FACETS	0.933	0.858	1	0.933	0.858	1	CLONAL	1	TRUE	1	0.613095579664645	2		377	528	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043414	6043414	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1340959686	NA	P-0021563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	22	66	0	ENST00000265849.7:c.260A>G	p.His87Arg	p.H87R	ENST00000265849	NM_000535.5	87	cAt/cGt	4/15	0.613095579664645	2	FACETS	0.854	0.706	1	0.854	0.706	1	CLONAL	2	TRUE	0	0.613095579664645	2		66	42	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816231	89816231	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	274	787	0	ENST00000389301.3:c.3146T>C	p.Phe1049Ser	p.F1049S	ENST00000389301	NM_000135.2	1049	tTt/tCt	32/43	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.784368941857919	2		787	666	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352340	70352343	+	missense_variant	Missense_Mutation	ONP	ACCT	ACCT	GCCG	novel	NA	P-0021564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	29	316	0	ENST00000374080.3:c.4367_4370delinsGCCG	p.His1456_Leu1457delinsArgArg	p.H1456_L1457delinsRR	ENST00000374080		1456	cACCTg/cGCCGg	31/45	1	1	FACETS	0.132	0.105	0.162	0.132	0.105	0.162	SUBCLONAL	1	TRUE	0	0.784368941857919	1		316	341	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042349	42042349	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	300	713	0	ENST00000219905.7:c.6544T>G	p.Leu2182Val	p.L2182V	ENST00000219905	NM_001164273.1	2182	Tta/Gta	17/24	1	2	FACETS	0.959	0.908	1	0.959	0.908	1	CLONAL	1	TRUE	1	0.82030495319918	2		713	763	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226309	2226309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	46	786	1	ENST00000326181.6:c.1922G>A	p.Arg641His	p.R641H	ENST00000326181	NM_032271.2	641	cGt/cAt	20/21	1	2	FACETS	0.225	0.188	0.265	0.225	0.188	0.265	SUBCLONAL	1	TRUE	1	0.449213001764124	2		787	912	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969969	161969969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199657839	NA	P-0021566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	57	665	1	ENST00000366898.1:c.1000C>T	p.Arg334Cys	p.R334C	ENST00000366898	NM_004562.2	334	Cgc/Tgc	9/12	1	2	FACETS	0.331	0.283	0.384	0.331	0.283	0.384	SUBCLONAL	1	TRUE	1	0.449213001764124	2		666	766	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6439806	6439806	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	46	559	0	ENST00000356142.4:c.332A>C	p.Asn111Thr	p.N111T	ENST00000356142	NM_018890.3	111	aAt/aCt	5/7	1	2	FACETS	0.536	0.452	0.628	0.536	0.452	0.628	SUBCLONAL	1	TRUE	1	0.449213001764124	2		559	382	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357573	89357573	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779534634	NA	P-0021566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	136	614	0	ENST00000301030.4:c.245G>A	p.Arg82Gln	p.R82Q	ENST00000301030	NM_001256183.1	82	cGg/cAg	5/13	1	2	FACETS	0.86	0.783	0.94	0.86	0.783	0.94	CLONAL	1	TRUE	1	0.449213001764124	2		614	704	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940351	49940351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	54	719	0	ENST00000296474.3:c.692G>A	p.Gly231Asp	p.G231D	ENST00000296474	NM_002447.2	231	gGc/gAc	1/20	0.449213001764124	1	FACETS	0.264	0.225	0.308	0.264	0.225	0.308	SUBCLONAL	1	TRUE	0	0.449213001764124	1		719	705	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144582	55144582	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	60	558	0	ENST00000257290.5:c.2056T>G	p.Leu686Val	p.L686V	ENST00000257290	NM_006206.4	686	Ttg/Gtg	15/23	1	2	FACETS	0.655	0.566	0.751	0.655	0.566	0.751	SUBCLONAL	1	TRUE	1	0.449213001764124	2		558	408	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	269	695	0	ENST00000347630.2:c.399C>A	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttA	6/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.788004058050819	2		695	671	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	305	782	0	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	0.788004058050819	1	FACETS	0.986	0.945	1	0.986	0.945	1	CLONAL	1	TRUE	0	0.788004058050819	1		782	476	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060896	38061003	+	inframe_deletion	In_Frame_Del	DEL	CGGGCCCGGAGCTTATGGGGGGCGCAGTTGAGGAGGCTGGAGTCTTCAACTCCGAGGCGCCCCCTGTCGCCGTCGCCCCACTGTGGTCCAGAGTCTGGGGGCTGGCGG	CGGGCCCGGAGCTTATGGGGGGCGCAGTTGAGGAGGCTGGAGTCTTCAACTCCGAGGCGCCCCCTGTCGCCGTCGCCCCACTGTGGTCCAGAGTCTGGGGGCTGGCGG	-	novel	NA	P-0021603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	39	669	0	ENST00000250448.2:c.986_1093del	p.Ala329_Pro364del	p.A329_P364del	ENST00000250448	NM_004496.3	329	gCCGCCAGCCCCCAGACTCTGGACCACAGTGGGGCGACGGCGACAGGGGGCGCCTCGGAGTTGAAGACTCCAGCCTCCTCAACTGCGCCCCCCATAAGCTCCGGGCCCGgg/ggg	2/2	1	2	FACETS	0.165	0.136	0.197	0.165	0.136	0.197	SUBCLONAL	1	TRUE	1	0.788004058050819	2		669	600	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712892	43712893	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	280	713	0	ENST00000382044.4:c.4291dup	p.Ser1431PhefsTer3	p.S1431Ffs*3	ENST00000382044	NM_001141980.1	1431	tca/tTca	21/28	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.788004058050819	2		713	684	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753292	42753292	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	381	1136	2	ENST00000222329.4:c.972C>A	p.Tyr324Ter	p.Y324*	ENST00000222329	NM_006494.2	324	taC/taA	4/4	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.788004058050819	2		1138	960	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288636	33288636	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs776342399	NA	P-0021604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	211	423	3	ENST00000374542.5:c.916C>T	p.Arg306Ter	p.R306*	ENST00000374542	NM_001141970.1	306	Cga/Tga	3/8	0.818544802672006	1	FACETS	0.909	0.863	0.954	0.909	0.863	0.954	CLONAL	1	TRUE	0	0.818544802672006	1		426	335	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415652	49415652	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	152	423	0	ENST00000301067.7:c.16525A>C	p.Thr5509Pro	p.T5509P	ENST00000301067	NM_003482.3	5509	Acc/Ccc	54/54	1	2	FACETS	0.85	0.785	0.917	0.85	0.785	0.917	CLONAL	1	TRUE	1	0.818544802672006	2		423	437	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651882	36651883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGAACCGGCTGGGGATGTCCGTCAGAACCCTTGCGG	novel	NA	P-0021604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	191	579	0	ENST00000244741.5:c.35_36insTTGCGGCAGAACCGGCTGGGGATGTCCGTCAGAACCC	p.Ser15ArgfsTer33	p.S15Rfs*33	ENST00000244741	NM_000389.4	2	tca/tCAGAACCGGCTGGGGATGTCCGTCAGAACCCTTGCGGca	2/3	0.818544802672006	1	FACETS	0.467	0.434	0.501	0.467	0.434	0.501	SUBCLONAL	1	TRUE	0	0.818544802672006	1		579	590	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0021606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	187	755	1	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.906	0.837	0.978	1	0.995	1	CLONAL	4	TRUE	1	0.11	2		756	938	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0021606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	19	824	1	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	1	2	FACETS	0.391	0.295	0.506	0.391	0.295	0.506	SUBCLONAL	1	TRUE	1	0.11	2		825	883	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50488224	50488224	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	43	719	0	ENST00000394963.4:c.1138G>A	p.Asp380Asn	p.D380N	ENST00000394963	NM_003076.4	380	Gac/Aac	10/13	1	2	FACETS	0.942	0.786	1	0.942	0.786	1	CLONAL	1	TRUE	1	0.11	2		719	830	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50488269	50488269	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	49	806	0	ENST00000394963.4:c.1183G>T	p.Glu395Ter	p.E395*	ENST00000394963	NM_003076.4	395	Gaa/Taa	10/13	1	2	FACETS	0.974	0.822	1	0.974	0.822	1	CLONAL	1	TRUE	1	0.11	2		806	915	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50488278	50488278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	49	784	0	ENST00000394963.4:c.1192G>A	p.Asp398Asn	p.D398N	ENST00000394963	NM_003076.4	398	Gac/Aac	10/13	1	2	FACETS	0.97	0.819	1	0.97	0.819	1	CLONAL	1	TRUE	1	0.11	2		784	918	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575085	48575086	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	27	511	0	ENST00000342988.3:c.279_280insT	p.Ile94TyrfsTer10	p.I94Yfs*10	ENST00000342988	NM_005359.5	93	-/T	3/12	1	2	FACETS	0.937	0.744	1	0.937	0.744	1	CLONAL	1	TRUE	1	0.11	2		511	524	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0021607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	45	515	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.741	0.621	0.874	0.741	0.621	0.874	SUBCLONAL	1	TRUE	1	0.15	2		515	810	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216125	7216125	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	43	484	0	ENST00000380728.2:c.934C>T	p.Arg312Trp	p.R312W	ENST00000380728		312	Cgg/Tgg	11/11	1	2	FACETS	0.847	0.707	1	0.847	0.707	1	CLONAL	1	TRUE	1	0.15	2		484	677	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813029	76813029	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	37	454	0	ENST00000373344.5:c.6592C>T	p.His2198Tyr	p.H2198Y	ENST00000373344	NM_000489.3	2198	Cat/Tat	30/35	1	1	FACETS	0.922	0.76	1	0.922	0.76	1	CLONAL	1	TRUE	0	0.15	1		454	495	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0021609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	147	549	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.6	2		549	486	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061225	38061225	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	154	692	0	ENST00000250448.2:c.764A>G	p.Glu255Gly	p.E255G	ENST00000250448	NM_004496.3	255	gAg/gGg	2/2	1	2	FACETS	0.7	0.642	0.761	0.7	0.642	0.761	SUBCLONAL	1	TRUE	1	0.6	2		692	733	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0021611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	681	492	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.451867862472852	5	FACETS	0.976	0.95	1	0.976	0.95	1	CLONAL	5	FALSE	0	0.451867862472852	5		492	1036	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0021611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	221	769	0				ENST00000310581	NM_198253.2	-/1132			0.398897436828453	5	FACETS	1	0.964	1	0.699	0.652	0.747	CLONAL	2	FALSE	2	0.451867862472852	5		769	783	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0021611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	172	366	1	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.451867862472852	4	FACETS	0.985	0.912	1	0.985	0.912	1	CLONAL	2	FALSE	2	0.451867862472852	4		367	561	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0021611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	1313	825	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.451867862472852	13	FACETS	0.989	0.968	1			1	CLONAL	9	FALSE	NA	0.451867862472852	13		825	2275	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844184	156844184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199646180	NA	P-0021611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	142	1052	1	ENST00000524377.1:c.1187C>T	p.Ser396Leu	p.S396L	ENST00000524377	NM_002529.3	396	tCg/tTg	9/17	0.451867862472852	5	FACETS	0.903	0.821	0.989	0.181	0.164	0.198	CLONAL	1	FALSE	0	0.451867862472852	5		1053	1168	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106330	27106330	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	417	757	0	ENST00000324856.7:c.5941T>C	p.Cys1981Arg	p.C1981R	ENST00000324856	NM_006015.4	1981	Tgc/Cgc	20/20	0.394056628396502	4	FACETS	1	0.987	1			1	CLONAL	3	FALSE	NA	0.451867862472852	4		757	833	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192663	94192663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	281	756	1	ENST00000323929.3:c.1411G>A	p.Glu471Lys	p.E471K	ENST00000323929	NM_005591.3	471	Gag/Aag	13/20	0.451867862472852	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	FALSE	1	0.451867862472852	3		757	748	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156020	119156020	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	333	950	0	ENST00000264033.4:c.1685G>C	p.Arg562Thr	p.R562T	ENST00000264033	NM_005188.3	562	aGa/aCa	11/16	0.451867862472852	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	FALSE	1	0.451867862472852	3		950	875	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865042	57865042	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	506	1032	4	ENST00000228682.2:c.2519G>T	p.Gly840Val	p.G840V	ENST00000228682	NM_005269.2	840	gGg/gTg	12/12	0.451867862472852	5	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	FALSE	2	0.451867862472852	5		1036	1205	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225989	133225989	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	254	877	0	ENST00000320574.5:c.3908G>T	p.Arg1303Met	p.R1303M	ENST00000320574	NM_006231.2	1303	aGg/aTg	31/49	0.451867862472852	5	FACETS	0.919	0.861	0.979	0.613	0.574	0.653	CLONAL	2	FALSE	2	0.451867862472852	5		877	1026	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618337	37618337	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	376	376	0	ENST00000447079.4:c.13G>A	p.Glu5Lys	p.E5K	ENST00000447079	NM_015083.1	5	Gag/Aag	1/14	0.451867862472852	13	FACETS	0.999	0.956	1			1	CLONAL	8	FALSE	NA	0.451867862472852	13		376	726	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618380	37618380	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1293588243	NA	P-0021611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	511	483	1	ENST00000447079.4:c.56G>C	p.Gly19Ala	p.G19A	ENST00000447079	NM_015083.1	19	gGa/gCa	1/14	0.451867862472852	13	FACETS	0.949	0.915	0.982			1	CLONAL	9	FALSE	NA	0.451867862472852	13		484	923	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866080	37866080	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2221	129	855	0	ENST00000269571.5:c.589C>G	p.Pro197Ala	p.P197A	ENST00000269571		197	Ccg/Gcg	5/27	0.451867862472852	13	FACETS	0.847	0.764	0.935			1	CLONAL	1	FALSE	NA	0.451867862472852	13		855	2350	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547966	41547966	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	291	774	2	ENST00000263253.7:c.2947G>T	p.Glu983Ter	p.E983*	ENST00000263253	NM_001429.3	983	Gaa/Taa	15/31	0.451867862472852	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	FALSE	2	0.451867862472852	4		776	855	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38949911	38949911	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	223	490	0	ENST00000357387.3:c.4039C>T	p.His1347Tyr	p.H1347Y	ENST00000357387	NM_152756.3	1347	Cac/Tac	31/38	0.451867862472852	6	FACETS	0.916	0.857	0.976	0.687	0.642	0.732	CLONAL	3	FALSE	2	0.451867862472852	6		490	684	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945148	44945148	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	443	771	0	ENST00000377967.4:c.3472A>T	p.Asn1158Tyr	p.N1158Y	ENST00000377967	NM_021140.2	1158	Aat/Tat	24/29	0.451867862472852	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	FALSE	1	0.451867862472852	4		771	916	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0021623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	49	704	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	0.244408794591623	2	FACETS	0.689	0.584	0.804	0.344	0.292	0.402	SUBCLONAL	1	TRUE	0	0.311930191900773	2		704	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0021623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	89	945	1	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	0.309569664870645	1	FACETS	0.904	0.803	1	0.904	0.803	1	CLONAL	1	TRUE	0	0.311930191900773	1		946	533	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040746	42041483	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTGTCTTAAAAAATATTATGAATACTTTTTTTTCCTACGTGTGTTAAAGGGGAATTTGGGTACCATGTTTCCATTTCCTGTTTTTCAGAAAATGCTGCTCAAATTCCAGTGGCTACTCCACAGGTCTCTCCTAACACAGTGAAACGTGCTGGACCTCGATTGTTGTTGATTCCAGTGCAGCAGGGTTCTCCTACTCTTAGACCTGTCTCAAACACACAACTTCAGGGACATCGGATGGTCTTGCAGCCTGTTAGGAGTCCAAGTGGAATGAACTTATTCAGGCACCCTAATGGGCAGATTGTCCAGCTTCTACCTTTGCATCAGCTTCGAGGCTCTAATACCCAGCCCAACTTACAGCCTGTCATGTTTCGGAACCCAGGTATAAAGTTCTTTTTTATGAACTTTTCTTTTGTTGAATCACTTGGCCATATGGTATGTTAATACACCAAGATTGTTTTTCTTCATCTCTTAAGAGTTACTTTTCCAAAAAGAAAAGCAAACATTGGAAGTCTTGATATGGGCAGTCATGATTTAAAAATTTCTCTCTTATTTTTTAAACCAGGGTCTGTGATGGGAATCCGGTTACCTGCTCCTTCCAAACCCTCTGAGACTCCGCCATCTTCCACTTCGTCCTCTGCTTTCTCTGTCATGAATCCTGTAATTCAAGCTGTTGGGTCTTCTTCAGCAGTGAATGTTATCACTCAGGCACCATCATTGCTTTCCTCTGGAGCTAGTTT	TGTGTCTTAAAAAATATTATGAATACTTTTTTTTCCTACGTGTGTTAAAGGGGAATTTGGGTACCATGTTTCCATTTCCTGTTTTTCAGAAAATGCTGCTCAAATTCCAGTGGCTACTCCACAGGTCTCTCCTAACACAGTGAAACGTGCTGGACCTCGATTGTTGTTGATTCCAGTGCAGCAGGGTTCTCCTACTCTTAGACCTGTCTCAAACACACAACTTCAGGGACATCGGATGGTCTTGCAGCCTGTTAGGAGTCCAAGTGGAATGAACTTATTCAGGCACCCTAATGGGCAGATTGTCCAGCTTCTACCTTTGCATCAGCTTCGAGGCTCTAATACCCAGCCCAACTTACAGCCTGTCATGTTTCGGAACCCAGGTATAAAGTTCTTTTTTATGAACTTTTCTTTTGTTGAATCACTTGGCCATATGGTATGTTAATACACCAAGATTGTTTTTCTTCATCTCTTAAGAGTTACTTTTCCAAAAAGAAAAGCAAACATTGGAAGTCTTGATATGGGCAGTCATGATTTAAAAATTTCTCTCTTATTTTTTAAACCAGGGTCTGTGATGGGAATCCGGTTACCTGCTCCTTCCAAACCCTCTGAGACTCCGCCATCTTCCACTTCGTCCTCTGCTTTCTCTGTCATGAATCCTGTAATTCAAGCTGTTGGGTCTTCTTCAGCAGTGAATGTTATCACTCAGGCACCATCATTGCTTTCCTCTGGAGCTAGTTT	-	novel	NA	P-0021623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	18	109	0	ENST00000219905.7:c.5213-82_5685del		p.X1738_splice	ENST00000219905	NM_001164273.1	1738		16-17/24	1	2	FACETS	0.769	0.594	0.966	1	0.916	1	CLONAL	2	TRUE	1	0.311930191900773	2		109	75	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641323	23641323	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	53	1008	0	ENST00000261584.4:c.2152A>T	p.Arg718Trp	p.R718W	ENST00000261584	NM_024675.3	718	Agg/Tgg	5/13	0.244408794591623	2	FACETS	0.567	0.483	0.659	0.284	0.241	0.33	SUBCLONAL	1	TRUE	0	0.311930191900773	2		1008	599	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496990	29496990	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0021623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	212	546	0	ENST00000356175.3:c.561T>A	p.Cys187Ter	p.C187*	ENST00000356175	NM_000267.3	187	tgT/tgA	5/57	NA	2	FACETS	0.95	0.892	1			1	INDETERMINATE	3	TRUE	NA	0.311930191900773	2		546	477	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868180	37868180	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0021623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	31	885	0	ENST00000269571.5:c.902-1G>C		p.X301_splice	ENST00000269571		301			0.311930191900773	2	FACETS	0.372	0.3	0.454	0.186	0.15	0.227	SUBCLONAL	1	TRUE	0	0.311930191900773	2		885	534	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105628	11105628	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	26	1028	0	ENST00000358026.2:c.1544A>C	p.Gln515Pro	p.Q515P	ENST00000358026	NM_001128849.1	515	cAg/cCg	9/36	0.311930191900773	1	FACETS	0.283	0.223	0.351	0.283	0.223	0.351	SUBCLONAL	1	TRUE	0	0.311930191900773	1		1028	498	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965411	25965411	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	90	972	1	ENST00000435504.4:c.3795A>T	p.Leu1265Phe	p.L1265F	ENST00000435504		1265	ttA/ttT	13/13	1	2	FACETS	0.976	0.868	1	0.976	0.868	1	CLONAL	1	TRUE	1	0.311930191900773	2		973	591	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198260818	198260818	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0021623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	53	832	0	ENST00000335508.6:c.3501T>A	p.Tyr1167Ter	p.Y1167*	ENST00000335508	NM_012433.2	1167	taT/taA	23/25	1	2	FACETS	0.685	0.585	0.795	0.685	0.585	0.795	SUBCLONAL	1	TRUE	1	0.311930191900773	2		832	496	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62320850	62320866	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTAGGCCAGCGAGGGG	CCTAGGCCAGCGAGGGG	AGGGAGGGA	novel	NA	P-0021623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	44	1139	3	ENST00000360203.5:c.1879-5_1890delinsAGGGAGGGA		p.X627_splice	ENST00000360203	NM_001283009.1	627		23/35	0.26939289508987	3	FACETS	0.451	0.377	0.533	0.15	0.125	0.178	SUBCLONAL	1	TRUE	0	0.311930191900773	3		1142	723	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084162	47084162	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	51	738	0	ENST00000409792.3:c.7127T>C	p.Leu2376Ser	p.L2376S	ENST00000409792	NM_014159.6	2376	tTg/tCg	17/21	0.129014395864543	0	FACETS	0.534	0.455	0.621			1	INDETERMINATE	1	TRUE	0	0.311930191900773	0		738	421	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505033	186505033	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	22	455	0	ENST00000323963.5:c.889G>C	p.Asp297His	p.D297H	ENST00000323963		297	Gac/Cac	8/11	0.311930191900773	3	FACETS	0.402	0.311	0.508	0.201	0.155	0.254	SUBCLONAL	1	TRUE	1	0.311930191900773	3		455	406	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289203	33289203	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1160519056	NA	P-0021623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	35	674	0	ENST00000374542.5:c.349C>T	p.Arg117Trp	p.R117W	ENST00000374542	NM_001141970.1	117	Cgg/Tgg	3/8	1	2	FACETS	0.483	0.395	0.581	0.483	0.395	0.581	SUBCLONAL	1	TRUE	1	0.311930191900773	2		674	465	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145472	58145474	+	missense_variant	Missense_Mutation	TNP	GCC	GCC	CCA	novel	NA	P-0021623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	75	670	0	ENST00000257904.6:c.27_29delinsTGG	p.Ala10Gly	p.A10G	ENST00000257904	NM_000075.3	9	gtGGCt/gtTGGt	2/8	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.311930191900773	2		670	407	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780684	9780684	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022075-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	644	570	0	ENST00000377346.4:c.1486C>T	p.Arg496Ter	p.R496*	ENST00000377346	NM_005026.3	496	Cga/Tga	12/24	0.575686904182214	4	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.575686904182214	4		570	1669	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322590	30322590	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022075-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	247	380	0	ENST00000322652.5:c.1603C>T	p.Arg535Ter	p.R535*	ENST00000322652	NM_015355.2	535	Cga/Tga	14/16	0.456241373043223	3	FACETS	1	0.992	1	0.824	0.782	0.866	CLONAL	2	TRUE	0	0.575686904182214	3		380	447	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152093	55152093	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121908585	NA	P-0023543-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	414	664	0	ENST00000257290.5:c.2525A>T	p.Asp842Val	p.D842V	ENST00000257290	NM_006206.4	842	gAc/gTc	18/23	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.671613979943114	2		664	1229	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0024991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	599	670	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.708656498792325	2		670	830	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031919	26031919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	61	369	0	ENST00000244661.2:c.370G>A	p.Asp124Asn	p.D124N	ENST00000244661	NM_003537.3	124	Gac/Aac	1/1	0.659932054808201	3	FACETS	0.401	0.345	0.461	0.2	0.172	0.231	SUBCLONAL	1	TRUE	1	0.708656498792325	3		369	582	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937893	36937893	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1431	250	1011	0	ENST00000361632.4:c.943C>A	p.Pro315Thr	p.P315T	ENST00000361632		315	Cct/Act	7/16	0.159749435855433	5	FACETS	0.866	0.807	0.927			1	INDETERMINATE	1	TRUE	NA	0.708656498792325	5		1011	1681	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677924	117677924	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	99	436	0	ENST00000368508.3:c.4009A>C	p.Ser1337Arg	p.S1337R	ENST00000368508	NM_002944.2	1337	Agt/Cgt	25/43	0.659932054808201	3	FACETS	0.545	0.487	0.607	0.273	0.243	0.304	SUBCLONAL	1	TRUE	1	0.708656498792325	3		436	694	SUCCESS
MET	4233	MSKCC	GRCh37	7	116422120	116422120	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	99	443	0	ENST00000397752.3:c.3601G>C	p.Val1201Leu	p.V1201L	ENST00000397752	NM_000245.2	1201	Gtc/Ctc	18/21	0.604744224736938	2	FACETS	0.443	0.396	0.494	0.222	0.198	0.247	SUBCLONAL	1	TRUE	0	0.708656498792325	2		443	630	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0025691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	177	541	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.381069762530951	3	FACETS	0.927	0.859	0.997	0.927	0.859	0.997	CLONAL	2	TRUE	1	0.394817573675295	3		541	579	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0025691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	145	460	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.381069762530951	3	FACETS	0.986	0.907	1	0.986	0.907	1	CLONAL	2	TRUE	1	0.394817573675295	3		460	446	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578217	7578217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	105	558	0	ENST00000269305.4:c.632C>T	p.Thr211Ile	p.T211I	ENST00000269305	NM_001126112.2	211	aCt/aTt	6/11	0.394817573675295	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.394817573675295	1		558	392	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012845	176012845	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0025691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	85	325	0	ENST00000367669.3:c.1530+1del		p.X510_splice	ENST00000367669	NM_022457.5	510			1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.394817573675295	2		325	356	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201739	66201739	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	79	455	2	ENST00000273854.3:c.2763C>A	p.Ser921Arg	p.S921R	ENST00000273854	NM_004439.5	921	agC/agA	16/18	1	2	FACETS	0.804	0.709	0.905	0.804	0.709	0.905	CLONAL	1	TRUE	1	0.394817573675295	2		457	498	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293461	1293461	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	164	582	0	ENST00000310581.5:c.1540G>T	p.Val514Leu	p.V514L	ENST00000310581	NM_198253.2	514	Gtg/Ttg	2/16	0.394817573675295	3	FACETS	0.906	0.837	0.977	0.906	0.837	0.977	CLONAL	2	TRUE	1	0.394817573675295	3		582	549	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671655	30671655	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	103	635	0	ENST00000376406.3:c.5305G>A	p.Ala1769Thr	p.A1769T	ENST00000376406	NM_014641.2	1769	Gcc/Acc	10/15	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.394817573675295	2		635	507	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850885	128850885	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	77	538	0	ENST00000249373.3:c.1732G>T	p.Glu578Ter	p.E578*	ENST00000249373	NM_005631.4	578	Gag/Tag	10/12	NA	2	FACETS	0.785	0.691	0.885			1	INDETERMINATE	1	TRUE	NA	0.394817573675295	2		538	497	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670570	30670570	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	81	488	1	ENST00000376406.3:c.5950C>T	p.Gln1984Ter	p.Q1984*	ENST00000376406	NM_014641.2	1984	Caa/Taa	13/15	1	2	FACETS	0.857	0.757	0.962	0.857	0.757	0.962	CLONAL	1	TRUE	1	0.394817573675295	2		489	479	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936058	44936058	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs752439298	NA	P-0025691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	57	191	0	ENST00000377967.4:c.2819C>A	p.Thr940Lys	p.T940K	ENST00000377967	NM_021140.2	940	aCa/aAa	18/29	0.366354842620756	2	FACETS	0.8	0.689	0.919			1	CLONAL	1	TRUE	NA	0.394817573675295	2		191	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0029115-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	289	670	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.430190620323239	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.476374051505323	1		670	861	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029115-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	179	336	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.216394598981307	3	FACETS	0.818	0.758	0.878			1	INDETERMINATE	2	TRUE	NA	0.476374051505323	3		336	569	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603147	48603147	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs377767387	NA	P-0029115-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	127	413	1	ENST00000342988.3:c.1447+1G>A		p.X483_splice	ENST00000342988	NM_005359.5	483			0.476374051505323	1	FACETS	0.85	0.775	0.928	0.85	0.775	0.928	CLONAL	1	TRUE	0	0.476374051505323	1		414	478	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223751	36223751	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs780362707	NA	P-0029115-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	402	959	0	ENST00000222270.7:c.6301G>C	p.Asp2101His	p.D2101H	ENST00000222270	NM_014727.1	2101	Gac/Cac	28/37	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.476374051505323	2		959	1523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0029362-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	134	772	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.258675868963312	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.258675868963312	1		772	807	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720681	89720681	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029362-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	40	221	0	ENST00000371953.3:c.833del	p.Phe278SerfsTer13	p.F278Sfs*13	ENST00000371953	NM_000314.4	278	Ttc/tc	8/9	1	2	FACETS	0.923	0.77	1	0.923	0.77	1	CLONAL	1	TRUE	1	0.258675868963312	2		221	335	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591136	67591144	+	inframe_deletion	In_Frame_Del	DEL	AGAGACCAA	AGAGACCAA	-	novel	NA	P-0029362-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	49	282	0	ENST00000274335.5:c.1729_1737del	p.Arg577_Gln579del	p.R577_Q579del	ENST00000274335		577	AGAGACCAA/-	12/15	1	2	FACETS	0.772	0.654	0.901	0.772	0.654	0.901	CLONAL	1	TRUE	1	0.258675868963312	2		282	491	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457255	5457255	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029362-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	26	307	0	ENST00000381577.3:c.229C>T	p.Gln77Ter	p.Q77*	ENST00000381577	NM_014143.3	77	Cag/Tag	3/7	0.258675868963312	2	FACETS	0.482	0.381	0.598	0.241	0.19	0.299	SUBCLONAL	1	TRUE	0	0.258675868963312	2		307	417	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387692	17387692	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029362-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	83	596	0	ENST00000359435.4:c.760G>T	p.Glu254Ter	p.E254*	ENST00000359435	NM_001033549.1	254	Gag/Tag	8/9	1	2	FACETS	0.841	0.742	0.948	0.841	0.742	0.948	CLONAL	1	TRUE	1	0.258675868963312	2		596	763	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790463	3790463	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	361	542	0	ENST00000262367.5:c.4070T>G	p.Val1357Gly	p.V1357G	ENST00000262367	NM_004380.2	1357	gTt/gGt	24/31	0.768809489372168	1	FACETS	0.875	0.838	0.911	0.875	0.838	0.911	CLONAL	1	TRUE	0	0.768809489372168	1		542	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0029537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	929	598	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	NA	2	FACETS	0.991	0.972	1			1	INDETERMINATE	2	TRUE	NA	0.768809489372168	2		598	1219	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631323	117631323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	109	342	0	ENST00000368508.3:c.6355G>A	p.Gly2119Arg	p.G2119R	ENST00000368508	NM_002944.2	2119	Ggg/Agg	40/43	0.768809489372168	1	FACETS	0.335	0.302	0.37	0.335	0.302	0.37	SUBCLONAL	1	TRUE	0	0.768809489372168	1		342	521	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0029685-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	446	515	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.712565531203814	5	FACETS	1	0.979	1	0.521	0.497	0.545	CLONAL	2	TRUE	1	0.712565531203814	5		515	1243	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519922	NA	P-0029685-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	279	585	0	ENST00000397062.3:c.235G>A	p.Glu79Lys	p.E79K	ENST00000397062	NM_006164.4	79	Gag/Aag	2/5	NA	2	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.712565531203814	2		585	776	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258619	16258619	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029685-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	280	527	1	ENST00000375759.3:c.5884G>A	p.Glu1962Lys	p.E1962K	ENST00000375759	NM_015001.2	1962	Gaa/Aaa	11/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.712565531203814	2		528	763	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259525	16259525	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029685-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	191	518	0	ENST00000375759.3:c.6790G>T	p.Glu2264Ter	p.E2264*	ENST00000375759	NM_015001.2	2264	Gag/Tag	11/15	1	2	FACETS	0.944	0.879	1	0.944	0.879	1	CLONAL	1	TRUE	1	0.712565531203814	2		518	568	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259531	16259531	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138783204	NA	P-0029685-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	181	518	0	ENST00000375759.3:c.6796G>A	p.Asp2266Asn	p.D2266N	ENST00000375759	NM_015001.2	2266	Gat/Aat	11/15	1	2	FACETS	0.93	0.864	0.998	0.93	0.864	0.998	CLONAL	1	TRUE	1	0.712565531203814	2		518	546	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115267844	115267844	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029685-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	199	506	0	ENST00000438362.2:c.1889C>T	p.Ser630Leu	p.S630L	ENST00000438362	NM_001242891.1	630	tCa/tTa	15/20	1	2	FACETS	0.975	0.909	1	0.975	0.909	1	CLONAL	1	TRUE	1	0.712565531203814	2		506	573	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457304	67457304	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029685-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	338	592	0	ENST00000327367.4:c.278G>C	p.Arg93Pro	p.R93P	ENST00000327367	NM_005902.3	93	cGa/cCa	2/9	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.712565531203814	2		592	871	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752972	42752972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029685-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	366	665	0	ENST00000222329.4:c.1292C>T	p.Ser431Leu	p.S431L	ENST00000222329	NM_006494.2	431	tCg/tTg	4/4	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.712565531203814	2		665	867	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097218	178097218	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029685-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	258	492	0	ENST00000397062.3:c.496G>A	p.Glu166Lys	p.E166K	ENST00000397062	NM_006164.4	166	Gaa/Aaa	4/5	NA	2	FACETS	0.913	0.858	0.969			1	INDETERMINATE	1	TRUE	NA	0.712565531203814	2		492	793	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775433	39775433	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1168532464	NA	P-0029685-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	179	428	0	ENST00000288319.7:c.587G>A	p.Arg196Lys	p.R196K	ENST00000288319	NM_182918.3	196	aGa/aAa	4/10	1	2	FACETS	0.936	0.869	1	0.936	0.869	1	CLONAL	1	TRUE	1	0.712565531203814	2		428	537	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933409	39933409	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776961342	NA	P-0029685-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	452	310	1	ENST00000378444.4:c.1190C>T	p.Pro397Leu	p.P397L	ENST00000378444	NM_001123385.1	397	cCg/cTg	4/15	0.712565531203814	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.712565531203814	2		311	534	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456687	138456687	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs757001098	NA	P-0029685-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	165	460	0	ENST00000289153.2:c.663C>G	p.Ile221Met	p.I221M	ENST00000289153	NM_006219.2	221	atC/atG	4/22	0.712565531203814	3	FACETS	0.94	0.866	1	0.47	0.433	0.509	CLONAL	1	TRUE	1	0.712565531203814	3		460	668	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0031258-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	195	639	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.370328472473414	3	FACETS	1	0.972	1	0.554	0.512	0.598	CLONAL	1	TRUE	1	0.370328472473414	3		639	1127	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259439	55259439	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs397517126	NA	P-0031258-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	160	481	0	ENST00000275493.2:c.2497T>G	p.Leu833Val	p.L833V	ENST00000275493	NM_005228.3	833	Ttg/Gtg	21/28	0.370328472473414	3	FACETS	1	0.976	1	0.584	0.535	0.635	CLONAL	1	TRUE	1	0.370328472473414	3		481	877	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913396	NA	P-0031258-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	80	379	0	ENST00000349496.5:c.95A>G	p.Asp32Gly	p.D32G	ENST00000349496	NM_001904.3	32	gAc/gGc	3/15	0.369612931140962	1	FACETS	0.838	0.741	0.941	0.838	0.741	0.941	CLONAL	1	TRUE	0	0.370328472473414	1		379	420	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905560	50905568	+	inframe_deletion	In_Frame_Del	DEL	GGCATCCGT	GGCATCCGT	-	novel	NA	P-0031258-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	227	968	0	ENST00000440232.2:c.689_697del	p.Gly230_Arg232del	p.G230_R232del	ENST00000440232	NM_002691.3	230	GGCATCCGT/-	6/27	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.370328472473414	2		968	1205	SUCCESS
AR	367	MSKCC	GRCh37	X	66943552	66943552	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137852578	NA	P-0031808-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	292	229	0	ENST00000374690.3:c.2632A>G	p.Thr878Ala	p.T878A	ENST00000374690	NM_000044.3	878	Act/Gct	8/8	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.726858871653376	1		229	387	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79974778	79974778	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031808-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	393	608	0	ENST00000265081.6:c.1206T>G	p.Phe402Leu	p.F402L	ENST00000265081	NM_002439.4	402	ttT/ttG	8/24	0.682366036809859	1	FACETS	0.931	0.893	0.97	0.931	0.893	0.97	CLONAL	1	TRUE	0	0.726858871653376	1		608	739	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878689	151878689	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031808-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	280	409	0	ENST00000262189.6:c.6256del	p.Ser2086LeufsTer20	p.S2086Lfs*20	ENST00000262189	NM_170606.2	2086	Tct/ct	36/59	0.682366036809859	1	FACETS	0.999	0.952	1	0.999	0.952	1	CLONAL	1	TRUE	0	0.726858871653376	1		409	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0033283-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	299	807	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.113558107243707	3	FACETS	0.87	0.826	0.914			1	INDETERMINATE	3	TRUE	NA	0.426227448823344	3		807	652	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61729431	61729431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033283-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	83	376	0	ENST00000401558.2:c.316G>A	p.Val106Ile	p.V106I	ENST00000401558	NM_003400.3	106	Gtt/Att	5/25	0.125912602102902	6	FACETS	1	0.973	1	0.457	0.404	0.514	INDETERMINATE	1	TRUE	3	0.426227448823344	6		376	526	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033758-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	130	492	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.364204950265116	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	0	0.364204950265116	2		492	343	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692911	89692911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909241	NA	P-0033758-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	148	504	0	ENST00000371953.3:c.395G>A	p.Gly132Asp	p.G132D	ENST00000371953	NM_000314.4	132	gGt/gAt	5/9	0.364204950265116	2	FACETS	0.899	0.828	0.972	0.899	0.828	0.972	CLONAL	2	TRUE	0	0.364204950265116	2		504	452	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939263	71939264	+	missense_variant	Missense_Mutation	DNP	TT	TT	AC	novel	NA	P-0033758-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	103	712	0	ENST00000298229.2:c.212_213delinsAC	p.Ile71Asn	p.I71N	ENST00000298229	NM_001567.3	71	aTT/aAC	2/28	0.364204950265116	1	FACETS	0.865	0.776	0.958	0.865	0.776	0.958	CLONAL	1	TRUE	0	0.364204950265116	1		712	535	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348771	11348771	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033758-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	78	376	0	ENST00000332029.2:c.565G>T	p.Glu189Ter	p.E189*	ENST00000332029	NM_003745.1	189	Gag/Tag	2/2	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.364204950265116	2		376	407	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250211	133250211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115047349	NA	P-0033819-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	10	683	1	ENST00000320574.5:c.1309G>A	p.Val437Met	p.V437M	ENST00000320574	NM_006231.2	437	Gtg/Atg	13/49	1	2	FACETS	1	0.687	1	1	0.687	1	CLONAL	1	TRUE	1	0.13	2		684	152	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752935	128752935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756666851	NA	P-0033819-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	10	360	0	ENST00000377970.2:c.1096G>A	p.Glu366Lys	p.E366K	ENST00000377970	NM_002467.4	366	Gag/Aag	3/3	1	2	FACETS	1	0.696	1	1	0.696	1	CLONAL	1	TRUE	1	0.13	2		360	150	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794418	42794418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267605512	NA	P-0033819-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	10	1052	1	ENST00000575354.2:c.1498C>T	p.Arg500Cys	p.R500C	ENST00000575354	NM_015125.3	500	Cgt/Tgt	10/20	1	2	FACETS	0.823	0.558	1	0.823	0.558	1	CLONAL	1	TRUE	1	0.13	2		1053	187	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300039	137300040	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755912201	NA	P-0033819-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	10	837	4	ENST00000481739.1:c.331dup	p.Leu111ProfsTer70	p.L111Pfs*70	ENST00000481739	NM_002957.4	108	-/C	3/10	0.0784867496456898	0	FACETS	0.769	0.522	1			1	CLONAL	1	TRUE	0	0.13	0		841	174	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034026-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	49	492	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.231104518709743	3	FACETS	1	0.96	1	0.717	0.61	0.833	CLONAL	1	TRUE	1	0.231104518709743	3		492	330	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710540	114710540	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034026-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	70	435	0	ENST00000543371.1:c.28del	p.Asp10MetfsTer3	p.D10Mfs*3	ENST00000543371	NM_001198531.1	9	Ggg/gg	1/14	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.231104518709743	2		435	583	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577529	7577529	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs730882027	NA	P-0034026-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	182	572	0	ENST00000269305.4:c.752T>C	p.Ile251Thr	p.I251T	ENST00000269305	NM_001126112.2	251	aTc/aCc	7/11	0.221809747885871	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.231104518709743	3		572	791	SUCCESS
APC	324	MSKCC	GRCh37	5	112174389	112174389	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034026-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	26	248	0	ENST00000257430.4:c.3098del	p.Asp1033ValfsTer4	p.D1033Vfs*4	ENST00000257430	NM_000038.5	1033	gAt/gt	16/16	0.135810362686665	4	FACETS	1	0.903	1	0.624	0.497	0.768	INDETERMINATE	1	TRUE	2	0.231104518709743	4		248	222	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78426078	78426078	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034026-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	64	535	0	ENST00000370768.2:c.1447C>G	p.Pro483Ala	p.P483A	ENST00000370768	NM_003902.3	483	Cca/Gca	15/20	1	2	FACETS	0.822	0.711	0.942	0.822	0.711	0.942	CLONAL	1	TRUE	1	0.231104518709743	2		535	674	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916932	178916943	+	inframe_deletion	In_Frame_Del	DEL	AACCGTGAAGAA	AACCGTGAAGAA	-	novel	NA	P-0034026-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	27	395	0	ENST00000263967.3:c.321_332del	p.Asn107_Glu110del	p.N107_E110del	ENST00000263967	NM_006218.2	107	AACCGTGAAGAA/-	2/21	0.221809747885871	3	FACETS	0.652	0.518	0.804	0.326	0.259	0.402	SUBCLONAL	1	TRUE	1	0.231104518709743	3		395	400	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401284	139401284	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034026-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	137	788	0	ENST00000277541.6:c.3785A>T	p.Glu1262Val	p.E1262V	ENST00000277541	NM_017617.3	1262	gAg/gTg	23/34	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.231104518709743	2		788	1154	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0034395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	105	515	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.321584091598532	3	FACETS	0.9	0.813	0.991	0.6	0.542	0.661	CLONAL	2	TRUE	0	0.350771166561794	3		515	391	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974792	21974792	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs141798398	NA	P-0034395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	58	158	0	ENST00000304494.5:c.35C>A	p.Ser12Ter	p.S12*	ENST00000304494	NM_000077.4	12	tCg/tAg	1/3	0.294386786797126	2	FACETS	0.852	0.744	0.966	0.852	0.744	0.966	CLONAL	2	TRUE	0	0.350771166561794	2		158	194	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099981	27099981	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	194	596	0	ENST00000324856.7:c.3860G>C	p.Arg1287Thr	p.R1287T	ENST00000324856	NM_006015.4	1287	aGa/aCa	15/20	0.204582415227237	4	FACETS	0.819	0.758	0.882	0.819	0.758	0.882	INDETERMINATE	2	TRUE	2	0.350771166561794	4		596	912	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253911	NA	P-0034395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	242	605	0	ENST00000269305.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000269305	NM_001126112.2	180	Gag/Aag	5/11	0.283888184234875	2	FACETS	0.884	0.829	0.941	0.884	0.829	0.941	CLONAL	2	TRUE	0	0.350771166561794	2		605	780	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247367	153247367	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747241612	NA	P-0034395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	73	247	0	ENST00000281708.4:c.1435C>G	p.Arg479Gly	p.R479G	ENST00000281708	NM_033632.3	479	Cga/Gga	10/12	0.350771166561794	3	FACETS	1	0.962	1	0.624	0.548	0.705	CLONAL	1	TRUE	1	0.350771166561794	3		247	392	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972719	76972719	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	49	342	0	ENST00000373344.5:c.22G>A	p.Glu8Lys	p.E8K	ENST00000373344	NM_000489.3	8	Gaa/Aaa	2/35	0.302346666577685	4	FACETS	0.828	0.702	0.966	0.207	0.175	0.242	CLONAL	1	TRUE	0	0.350771166561794	4		342	456	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80024675	80024675	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	88	427	0	ENST00000265081.6:c.1459C>G	p.Gln487Glu	p.Q487E	ENST00000265081	NM_002439.4	487	Caa/Gaa	10/24	0.350771166561794	2	FACETS	1	0.973	1	0.653	0.583	0.728	CLONAL	1	TRUE	0	0.350771166561794	2		427	384	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693856	47693856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755818010	NA	P-0034395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	92	435	2	ENST00000233146.2:c.1570C>T	p.Arg524Cys	p.R524C	ENST00000233146	NM_000251.2	524	Cgt/Tgt	10/16	0.350771166561794	3	FACETS	0.991	0.891	1	0.991	0.891	1	CLONAL	2	TRUE	1	0.350771166561794	3		437	311	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681443	30681443	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	106	504	0	ENST00000376406.3:c.569C>T	p.Ser190Phe	p.S190F	ENST00000376406	NM_014641.2	190	tCt/tTt	4/15	0.350771166561794	3	FACETS	1	0.932	1	0.35	0.314	0.388	CLONAL	1	TRUE	0	0.350771166561794	3		504	677	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405181	70405181	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	114	473	0	ENST00000373644.4:c.2695C>G	p.Gln899Glu	p.Q899E	ENST00000373644	NM_030625.2	899	Caa/Gaa	4/12	0.315808957176067	3	FACETS	1	0.98	1	0.675	0.61	0.744	CLONAL	1	TRUE	1	0.350771166561794	3		473	566	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226595586	226595586	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	65	468	0	ENST00000366794.5:c.45G>C	p.Lys15Asn	p.K15N	ENST00000366794	NM_001618.3	15	aaG/aaC	1/23	0.350771166561794	5	FACETS	0.589	0.509	0.676	0.196	0.169	0.226	SUBCLONAL	1	TRUE	2	0.350771166561794	5		468	960	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667398	241667398	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1060500896	NA	P-0034395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	155	497	0	ENST00000366560.3:c.1052C>G	p.Ser351Ter	p.S351*	ENST00000366560	NM_000143.3	351	tCa/tGa	7/10	0.350771166561794	5	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.350771166561794	5		497	943	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344360	118344360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	93	352	0	ENST00000534358.1:c.2486C>T	p.Ser829Leu	p.S829L	ENST00000534358	NM_005933.3	829	tCa/tTa	3/36	0.242289472611139	3	FACETS	0.793	0.71	0.88	0.793	0.71	0.88	SUBCLONAL	2	TRUE	1	0.350771166561794	3		352	393	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344377	118344377	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	92	322	0	ENST00000534358.1:c.2503C>G	p.Leu835Val	p.L835V	ENST00000534358	NM_005933.3	835	Ctc/Gtc	3/36	0.242289472611139	3	FACETS	0.799	0.715	0.887	0.799	0.715	0.887	SUBCLONAL	2	TRUE	1	0.350771166561794	3		322	386	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445487	49445487	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	377	675	0	ENST00000301067.7:c.1979C>A	p.Ser660Ter	p.S660*	ENST00000301067	NM_003482.3	660	tCa/tAa	10/54	0.350771166561794	3	FACETS	0.923	0.88	0.967	0.923	0.88	0.967	CLONAL	3	TRUE	0	0.350771166561794	3		675	912	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650779	67650779	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	184	492	0	ENST00000264010.4:c.1084G>A	p.Glu362Lys	p.E362K	ENST00000264010	NM_006565.3	362	Gaa/Aaa	5/12	0.204582415227237	4	FACETS	0.816	0.754	0.881	0.816	0.754	0.881	INDETERMINATE	2	TRUE	2	0.350771166561794	4		492	868	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829758	72829758	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	225	744	0	ENST00000268489.5:c.6823C>G	p.Leu2275Val	p.L2275V	ENST00000268489	NM_006885.3	2275	Ctc/Gtc	9/10	0.204582415227237	4	FACETS	0.873	0.814	0.935	0.873	0.814	0.935	INDETERMINATE	2	TRUE	2	0.350771166561794	4		744	992	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991481	72991481	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	271	758	0	ENST00000268489.5:c.2564C>A	p.Ser855Ter	p.S855*	ENST00000268489	NM_006885.3	855	tCa/tAa	2/10	0.204582415227237	4	FACETS	0.853	0.799	0.908	0.853	0.799	0.908	INDETERMINATE	2	TRUE	2	0.350771166561794	4		758	1224	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562740	29562740	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	130	534	0	ENST00000356175.3:c.3820C>G	p.Leu1274Val	p.L1274V	ENST00000356175	NM_000267.3	1274	Ctc/Gtc	28/57	0.350771166561794	3	FACETS	1	0.985	1	0.475	0.432	0.52	CLONAL	1	TRUE	0	0.350771166561794	3		534	611	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243920	41243920	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	187	641	0	ENST00000357654.3:c.3628G>C	p.Glu1210Gln	p.E1210Q	ENST00000357654	NM_007294.3	1210	Gag/Cag	10/23	0.350771166561794	3	FACETS	1	0.988	1	0.459	0.424	0.495	CLONAL	1	TRUE	0	0.350771166561794	3		641	910	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435938	56435938	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1289374449	NA	P-0034395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	166	465	0	ENST00000407977.2:c.1199G>A	p.Gly400Glu	p.G400E	ENST00000407977		400	gGa/gAa	9/10	0.350771166561794	3	FACETS	1	0.988	1	0.477	0.439	0.517	CLONAL	1	TRUE	0	0.350771166561794	3		465	777	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27016028	27016028	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	109	540	0	ENST00000335756.4:c.304C>G	p.Leu102Val	p.L102V	ENST00000335756	NM_001809.3	102	Cta/Gta	4/5	0.350771166561794	3	FACETS	0.801	0.718	0.889	0.4	0.359	0.445	CLONAL	1	TRUE	1	0.350771166561794	3		540	912	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379395	225379395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	58	646	0	ENST00000264414.4:c.473G>A	p.Arg158Lys	p.R158K	ENST00000264414	NM_003590.4	158	aGg/aAg	4/16	0.321584091598532	3	FACETS	0.818	0.704	0.942	0.273	0.234	0.314	CLONAL	1	TRUE	0	0.350771166561794	3		646	475	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944498	40944498	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	170	579	0	ENST00000373198.4:c.2004G>T	p.Leu668Phe	p.L668F	ENST00000373198	NM_133170.3	668	ttG/ttT	12/32	0.184416873621367	5	FACETS	0.851	0.783	0.922	0.567	0.522	0.615	INDETERMINATE	2	TRUE	2	0.350771166561794	5		579	869	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52685796	52685796	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	87	491	0	ENST00000394830.3:c.676G>T	p.Glu226Ter	p.E226*	ENST00000394830	NM_018313.4	226	Gag/Tag	7/30	0.283888184234875	2	FACETS	1	0.973	1	0.658	0.586	0.733	CLONAL	1	TRUE	0	0.350771166561794	2		491	377	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84384707	84384707	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	65	461	0	ENST00000321945.7:c.736G>T	p.Asp246Tyr	p.D246Y	ENST00000321945	NM_139076.2	246	Gat/Tat	8/9	NA	2	FACETS	0.638	0.553	0.73			1	INDETERMINATE	1	TRUE	NA	0.350771166561794	2		461	581	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161714	56161714	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	124	520	0	ENST00000399503.3:c.1211C>G	p.Ser404Cys	p.S404C	ENST00000399503	NM_005921.1	404	tCt/tGt	6/20	0.350771166561794	3	FACETS	0.769	0.699	0.843	0.513	0.466	0.562	SUBCLONAL	2	TRUE	0	0.350771166561794	3		520	540	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225466	26225466	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	60	251	0	ENST00000360408.1:c.84G>C	p.Lys28Asn	p.K28N	ENST00000360408	NM_003532.2	28	aaG/aaC	1/1	0.350771166561794	3	FACETS	1	0.927	1	0.369	0.319	0.423	CLONAL	1	TRUE	0	0.350771166561794	3		251	363	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028157	69028157	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	74	487	1	ENST00000288368.4:c.3316G>C	p.Asp1106His	p.D1106H	ENST00000288368	NM_024870.2	1106	Gac/Cac	26/40	0.204582415227237	4	FACETS	1	0.973	1	0.707	0.622	0.798	INDETERMINATE	1	TRUE	2	0.350771166561794	4		488	403	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938585	44938585	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	101	451	1	ENST00000377967.4:c.3133G>A	p.Glu1045Lys	p.E1045K	ENST00000377967	NM_021140.2	1045	Gaa/Aaa	20/29	0.297335556815609	3	FACETS	1	0.915	1	0.676	0.61	0.743	CLONAL	2	TRUE	0	0.350771166561794	3		452	334	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890120	76890120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	158	570	0	ENST00000373344.5:c.4774C>T	p.Leu1592Phe	p.L1592F	ENST00000373344	NM_000489.3	1592	Ctt/Ttt	17/35	0.302346666577685	4	FACETS	0.946	0.87	1	0.473	0.435	0.513	CLONAL	2	TRUE	0	0.350771166561794	4		570	643	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220429	123220429	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	226	496	0	ENST00000218089.9:c.3086A>G	p.Gln1029Arg	p.Q1029R	ENST00000218089	NM_001042749.1	1029	cAg/cGg	30/35	0.302346666577685	4	FACETS	0.957	0.893	1	0.479	0.446	0.512	CLONAL	2	TRUE	0	0.350771166561794	4		496	909	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0034880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	223	300	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.80750545389737	2		300	514	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653796	89653798	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs1554893765	NA	P-0034880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	142	332	0	ENST00000371953.3:c.97_99del	p.Ile33del	p.I33del	ENST00000371953	NM_000314.4	32	ATT/-	2/9	1	2	FACETS	0.909	0.838	0.981	0.909	0.838	0.981	CLONAL	1	TRUE	1	0.80750545389737	2		332	387	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0034880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	202	295	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	0.80750545389737	2		295	480	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106336	27106337	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0034880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	570	525	0	ENST00000324856.7:c.5952_5953del	p.Ser1985GlnfsTer13	p.S1985Qfs*13	ENST00000324856	NM_006015.4	1983	TGt/t	20/20	0.80750545389737	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.80750545389737	2		525	690	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022288	31022288	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs371369583	NA	P-0034880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	180	380	0	ENST00000375687.4:c.1773C>A	p.Tyr591Ter	p.Y591*	ENST00000375687	NM_015338.5	591	taC/taA	13/13	1	2	FACETS	0.947	0.881	1	0.947	0.881	1	CLONAL	1	TRUE	1	0.80750545389737	2		380	471	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466023	69466052	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	CACCGACGTGCGGGACGTGGACATCTGAGG	CACCGACGTGCGGGACGTGGACATCTGAGG	-	novel	NA	P-0034880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	158	573	0	ENST00000227507.2:c.861_*2del		p.*287*	ENST00000227507	NM_053056.2	287		5/5	1	2	FACETS	0.721	0.664	0.779	0.721	0.664	0.779	SUBCLONAL	1	TRUE	1	0.80750545389737	2		573	543	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67646003	67646003	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	197	413	0	ENST00000264010.4:c.932del	p.Asn311IlefsTer22	p.N311Ifs*22	ENST00000264010	NM_006565.3	311	Aat/at	4/12	1	2	FACETS	0.876	0.817	0.936	0.876	0.817	0.936	CLONAL	1	TRUE	1	0.80750545389737	2		413	557	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0036891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	45	541	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.731	0.614	0.862	0.731	0.614	0.862	SUBCLONAL	1	TRUE	1	0.21	2		541	586	SUCCESS
FH	2271	MSKCC	GRCh37	1	241671965	241671965	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	96	579	0	ENST00000366560.3:c.676G>T	p.Ala226Ser	p.A226S	ENST00000366560	NM_000143.3	226	Gca/Tca	5/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.21	2		579	814	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005312	29005312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774536767	NA	P-0036891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	44	568	0	ENST00000282397.4:c.949C>T	p.Pro317Ser	p.P317S	ENST00000282397	NM_002019.4	317	Cca/Tca	7/30	1	2	FACETS	0.68	0.57	0.803	0.68	0.57	0.803	SUBCLONAL	1	TRUE	1	0.21	2		568	616	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96931064	96931064	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1331019402	NA	P-0036891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	15	125	0	ENST00000258439.3:c.56G>T	p.Gly19Val	p.G19V	ENST00000258439	NM_001193304.2	19	gGa/gTa	2/4	1	2	FACETS	1	0.805	1	1	0.805	1	CLONAL	1	TRUE	1	0.21	2		125	128	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793288	242793289	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0036891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	66	881	2	ENST00000334409.5:c.788_789delinsAA	p.Ala263Glu	p.A263E	ENST00000334409	NM_005018.2	263	gCC/gAA	5/5	1	2	FACETS	0.816	0.707	0.935	0.816	0.707	0.935	CLONAL	1	TRUE	1	0.21	2		883	770	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127261	55127261	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0036891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	46	491	0	ENST00000257290.5:c.50-1G>T		p.X17_splice	ENST00000257290	NM_006206.4	17			1	2	FACETS	0.885	0.745	1	0.885	0.745	1	CLONAL	1	TRUE	1	0.21	2		491	495	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271347	26271347	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	29	494	0	ENST00000305910.3:c.266C>A	p.Ala89Glu	p.A89E	ENST00000305910	NM_003534.2	89	gCg/gAg	1/1	1	2	FACETS	0.504	0.403	0.619	0.504	0.403	0.619	SUBCLONAL	1	TRUE	1	0.21	2		494	548	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040761	47040762	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	A	novel	NA	P-0036891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	72	807	0	ENST00000377604.3:c.1396_1397delinsA	p.Pro466MetfsTer19	p.P466Mfs*19	ENST00000377604	NM_001204468.1	466	CCt/At	13/24	1	2	FACETS	0.96	0.838	1	0.96	0.838	1	CLONAL	1	TRUE	1	0.21	2		807	714	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0037279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	97	336	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.456616576382536	1	FACETS	0.929	0.836	1	0.929	0.836	1	CLONAL	1	TRUE	0	0.456616576382536	1		336	353	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740365	58740365	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs780886952	NA	P-0037279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	124	379	0	ENST00000305921.3:c.1270G>T	p.Glu424Ter	p.E424*	ENST00000305921	NM_003620.3	424	Gag/Tag	6/6	0.456616576382536	3	FACETS	1	0.937	1	0.521	0.472	0.572	CLONAL	1	TRUE	1	0.456616576382536	3		379	640	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675399	241675399	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	70	352	0	ENST00000366560.3:c.423G>T	p.Trp141Cys	p.W141C	ENST00000366560	NM_000143.3	141	tgG/tgT	4/10	0.443924682447387	3	FACETS	0.912	0.798	1	0.456	0.399	0.517	CLONAL	1	TRUE	1	0.456616576382536	3		352	413	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579722	7579722	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0037279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	60	616	0	ENST00000269305.4:c.75-1G>A		p.X25_splice	ENST00000269305	NM_001126112.2	25			0.456616576382536	1	FACETS	0.331	0.285	0.381	0.331	0.285	0.381	SUBCLONAL	1	TRUE	0	0.456616576382536	1		616	613	SUCCESS
FH	2271	MSKCC	GRCh37	1	241665833	241665833	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	144	407	0	ENST00000366560.3:c.1146G>T	p.Met382Ile	p.M382I	ENST00000366560	NM_000143.3	382	atG/atT	8/10	0.443924682447387	3	FACETS	0.915	0.834	0.999	0.457	0.417	0.5	CLONAL	1	TRUE	1	0.456616576382536	3		407	847	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048797	180048797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	236	812	1	ENST00000261937.6:c.1765C>T	p.Arg589Cys	p.R589C	ENST00000261937	NM_182925.4	589	Cgc/Tgc	13/30	1	2	FACETS	0.918	0.856	0.982	0.918	0.856	0.982	CLONAL	1	TRUE	1	0.456616576382536	2		813	1126	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973743	15973743	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	44	391	0	ENST00000268712.3:c.4249A>T	p.Met1417Leu	p.M1417L	ENST00000268712	NM_006311.3	1417	Atg/Ttg	31/46	1	2	FACETS	0.403	0.338	0.474	0.403	0.338	0.474	SUBCLONAL	1	TRUE	1	0.5	2		391	437	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0037773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	303	497	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.530259780732643	3	FACETS	0.917	0.869	0.967	0.917	0.869	0.967	CLONAL	2	TRUE	1	0.530259780732643	3		497	788	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008057	29008057	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	128	403	0	ENST00000282397.4:c.712C>A	p.Arg238Ser	p.R238S	ENST00000282397	NM_002019.4	238	Cgc/Agc	6/30	1	2	FACETS	0.936	0.852	1	0.936	0.852	1	CLONAL	1	TRUE	1	0.530259780732643	2		403	516	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207105	1207105	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	336	838	1	ENST00000326873.7:c.193G>T	p.Glu65Ter	p.E65*	ENST00000326873	NM_000455.4	65	Gag/Tag	1/10	0.530259780732643	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.530259780732643	1		839	837	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602746	10602746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	271	894	0	ENST00000171111.5:c.832C>T	p.Pro278Ser	p.P278S	ENST00000171111	NM_203500.1	278	Ccg/Tcg	3/6	0.530259780732643	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.530259780732643	1		894	720	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096891	11096891	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	294	959	0	ENST00000358026.2:c.382G>T	p.Glu128Ter	p.E128*	ENST00000358026	NM_001128849.1	128	Gag/Tag	4/36	0.530259780732643	1	FACETS	0.975	0.921	1	0.975	0.921	1	CLONAL	1	TRUE	0	0.530259780732643	1		959	836	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142943	30142943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	297	843	0	ENST00000389048.3:c.583G>A	p.Ala195Thr	p.A195T	ENST00000389048	NM_004304.4	195	Gcg/Acg	1/29	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.530259780732643	2		843	946	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46525072	46525072	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	226	674	0	ENST00000263734.3:c.22A>C	p.Lys8Gln	p.K8Q	ENST00000263734	NM_001430.4	8	Aaa/Caa	1/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.530259780732643	2		674	789	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188379	32188379	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	231	667	0	ENST00000375023.3:c.962A>T	p.Gln321Leu	p.Q321L	ENST00000375023	NM_004557.3	321	cAg/cTg	6/30	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.530259780732643	2		667	814	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164884	123164884	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	129	393	0	ENST00000218089.9:c.197G>T	p.Gly66Val	p.G66V	ENST00000218089	NM_001042749.1	66	gGt/gTt	5/35	1	2	FACETS	0.977	0.891	1	0.977	0.891	1	CLONAL	1	TRUE	1	0.530259780732643	2		393	498	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0038208-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	38	497	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.84	1	1	0.84	1	CLONAL	1	TRUE	1	0.15	2		497	498	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519989	NA	P-0038208-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	23	458	0	ENST00000269305.4:c.730G>C	p.Gly244Arg	p.G244R	ENST00000269305	NM_001126112.2	244	Ggc/Cgc	7/11	1	2	FACETS	0.443	0.344	0.559	0.443	0.344	0.559	SUBCLONAL	1	TRUE	1	0.15	2		458	692	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	251	174	0				ENST00000310581	NM_198253.2	-/1132			0.313978265641386	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.390479740457297	3		174	673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	273	841	1	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.390479740457297	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.390479740457297	1		842	828	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992136	11992136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	31	507	1	ENST00000396373.4:c.226G>A	p.Glu76Lys	p.E76K	ENST00000396373	NM_001987.4	76	Gag/Aag	3/8	1	2	FACETS	0.271	0.219	0.331	0.271	0.219	0.331	SUBCLONAL	1	TRUE	1	0.390479740457297	2		508	585	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793700	89793700	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370470988	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	18	388	0	ENST00000336032.3:c.769G>A	p.Glu257Lys	p.E257K	ENST00000336032	NM_006813.2	257	Gag/Aag	2/2	0.390479740457297	1	FACETS	0.291	0.219	0.376	0.291	0.219	0.376	SUBCLONAL	1	TRUE	0	0.390479740457297	1		388	255	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164509	36164509	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	214	666	3	ENST00000300305.3:c.1366G>A	p.Glu456Lys	p.E456K	ENST00000300305		456	Gag/Aag	8/8	0.127548661980362	4	FACETS	0.895	0.834	0.959	0.448	0.417	0.48	INDETERMINATE	2	TRUE	0	0.390479740457297	4		669	851	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239915	53239915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	120	395	0	ENST00000375401.3:c.1526C>T	p.Ser509Leu	p.S509L	ENST00000375401	NM_004187.3	509	tCa/tTa	11/26	1	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.390479740457297	1		395	417	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500838	8500838	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	157	516	0	ENST00000356435.5:c.2044G>A	p.Glu682Lys	p.E682K	ENST00000356435		682	Gaa/Aaa	13/35	0.390479740457297	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.390479740457297	1		516	436	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856356	45856356	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	241	995	0	ENST00000391945.4:c.1816G>C	p.Glu606Gln	p.E606Q	ENST00000391945	NM_000400.3	606	Gag/Cag	19/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.390479740457297	2		995	1096	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100532	157100532	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	27	340	0	ENST00000346085.5:c.1469G>A	p.Trp490Ter	p.W490*	ENST00000346085	NM_020732.3	490	tGg/tAg	1/20	0.390479740457297	1	FACETS	0.285	0.226	0.352	0.285	0.226	0.352	SUBCLONAL	1	TRUE	0	0.390479740457297	1		340	391	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556049	29556049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	40	297	0	ENST00000356175.3:c.2416G>A	p.Glu806Lys	p.E806K	ENST00000356175	NM_000267.3	806	Gaa/Aaa	21/57	1	2	FACETS	0.699	0.584	0.826	0.699	0.584	0.826	SUBCLONAL	1	TRUE	1	0.390479740457297	2		297	293	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29701088	29701088	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	130	472	0	ENST00000356175.3:c.8372G>A	p.Arg2791Gln	p.R2791Q	ENST00000356175	NM_000267.3	2791	cGa/cAa	57/57	1	2	FACETS	0.986	0.897	1	0.986	0.897	1	CLONAL	1	TRUE	1	0.390479740457297	2		472	675	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245288	46245288	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	171	565	0	ENST00000334344.6:c.3382C>T	p.Gln1128Ter	p.Q1128*	ENST00000334344	NM_152641.2	1128	Cag/Tag	15/21	0.390479740457297	5	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.390479740457297	5		565	1006	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936978	48936978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	24	449	0	ENST00000267163.4:c.746C>T	p.Ser249Leu	p.S249L	ENST00000267163	NM_000321.2	249	tCa/tTa	8/27	1	2	FACETS	0.314	0.246	0.393	0.314	0.246	0.393	SUBCLONAL	1	TRUE	1	0.390479740457297	2		449	391	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258970	153258970	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	25	262	0	ENST00000281708.4:c.845C>G	p.Ser282Ter	p.S282*	ENST00000281708	NM_033632.3	282	tCa/tGa	5/12	1	2	FACETS	0.848	0.676	1	0.848	0.676	1	CLONAL	1	TRUE	1	0.390479740457297	2		262	151	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738189	133738189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150134901	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	145	651	2	ENST00000318560.5:c.589G>A	p.Glu197Lys	p.E197K	ENST00000318560	NM_005157.4	197	Gag/Aag	4/11	0.390479740457297	1	FACETS	0.854	0.781	0.93	0.854	0.781	0.93	CLONAL	1	TRUE	0	0.390479740457297	1		653	700	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223469	2223469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1462122341	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	73	423	1	ENST00000398665.3:c.3580G>A	p.Glu1194Lys	p.E1194K	ENST00000398665	NM_032482.2	1194	Gag/Aag	25/28	1	2	FACETS	0.836	0.734	0.946	0.836	0.734	0.946	CLONAL	1	TRUE	1	0.390479740457297	2		424	447	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287395	33287395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	86	634	0	ENST00000374542.5:c.1702G>A	p.Glu568Lys	p.E568K	ENST00000374542	NM_001141970.1	568	Gag/Aag	6/8	1	2	FACETS	0.77	0.682	0.864	0.77	0.682	0.864	SUBCLONAL	1	TRUE	1	0.390479740457297	2		634	572	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268865	98268865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	78	387	0	ENST00000331920.6:c.218G>A	p.Arg73Gln	p.R73Q	ENST00000331920	NM_000264.3	73	cGg/cAg	2/24	0.390479740457297	1	FACETS	0.741	0.654	0.834	0.741	0.654	0.834	SUBCLONAL	1	TRUE	0	0.390479740457297	1		387	434	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106498	27106498	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	275	769	0	ENST00000324856.7:c.6109C>T	p.Gln2037Ter	p.Q2037*	ENST00000324856	NM_006015.4	2037	Cag/Tag	20/20	1	2	FACETS	0.762	0.717	0.809	1	0.994	1	SUBCLONAL	2	TRUE	1	0.390479740457297	2		769	924	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073515	8073515	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	69	455	0	ENST00000377482.5:c.1144A>G	p.Ile382Val	p.I382V	ENST00000377482	NM_018948.3	382	Att/Gtt	4/4	1	2	FACETS	0.682	0.595	0.776	0.682	0.595	0.776	SUBCLONAL	1	TRUE	1	0.390479740457297	2		455	518	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63662161	63662161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	175	430	0	ENST00000279873.7:c.265G>A	p.Asp89Asn	p.D89N	ENST00000279873	NM_032199.2	89	Gac/Aac	2/10	0.324031650714065	3	FACETS	0.943	0.874	1	0.943	0.874	1	CLONAL	2	TRUE	1	0.390479740457297	3		430	568	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	532660	532660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748639813	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	164	958	0	ENST00000451590.1:c.546G>A	p.Met182Ile	p.M182I	ENST00000451590	NM_001130442.1	182	atG/atA	5/5	0.35925492825496	0	FACETS	0.762	0.702	0.824			1	SUBCLONAL	1	TRUE	0	0.390479740457297	0		958	672	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450042	32450042	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	139	599	0	ENST00000332351.3:c.769+1G>T		p.X257_splice	ENST00000332351	NM_024426.4	257			0.229315991408549	2	FACETS	1	0.982	1	0.639	0.584	0.696	INDETERMINATE	1	TRUE	0	0.390479740457297	2		599	557	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211525	46211525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	180	368	0	ENST00000334344.6:c.491C>T	p.Ser164Leu	p.S164L	ENST00000334344	NM_152641.2	164	tCa/tTa	5/21	0.390479740457297	5	FACETS	1	0.977	1			1	CLONAL	4	TRUE	NA	0.390479740457297	5		368	338	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448526	49448526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371342351	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	64	592	1	ENST00000301067.7:c.185C>T	p.Pro62Leu	p.P62L	ENST00000301067	NM_003482.3	62	cCg/cTg	3/54	0.324031650714065	3	FACETS	0.534	0.461	0.613	0.267	0.23	0.307	SUBCLONAL	1	TRUE	1	0.390479740457297	3		593	734	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606025	81606025	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	68	423	0	ENST00000298171.2:c.695A>G	p.Asp232Gly	p.D232G	ENST00000298171	NM_000369.2	232	gAc/gGc	9/10	0.390479740457297	1	FACETS	0.671	0.586	0.762	0.671	0.586	0.762	SUBCLONAL	1	TRUE	0	0.390479740457297	1		423	418	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641130	3641130	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	168	1297	0	ENST00000294008.3:c.2509A>G	p.Lys837Glu	p.K837E	ENST00000294008	NM_032444.2	837	Aag/Gag	12/15	0.390479740457297	1	FACETS	0.659	0.605	0.715	0.659	0.605	0.715	SUBCLONAL	1	TRUE	0	0.390479740457297	1		1297	1051	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40462653	40462653	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	218	663	0	ENST00000345506.4:c.2351G>T	p.Gly784Val	p.G784V	ENST00000345506	NM_003152.3	784	gGt/gTt	20/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.390479740457297	2		663	824	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437558	56437558	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	313	844	0	ENST00000407977.2:c.904T>G	p.Trp302Gly	p.W302G	ENST00000407977		302	Tgg/Ggg	8/10	1	2	FACETS	0.835	0.789	0.882	1	0.995	1	CLONAL	2	TRUE	1	0.390479740457297	2		844	960	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677778	58677778	+	start_lost	Translation_Start_Site	SNP	G	G	C	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	174	663	0	ENST00000305921.3:c.3G>C	p.Met1?	p.M1?	ENST00000305921	NM_003620.3	1	atG/atC	1/6	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.390479740457297	2		663	730	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367038	15367038	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	44	344	0	ENST00000263377.2:c.1588C>T	p.Gln530Ter	p.Q530*	ENST00000263377	NM_058243.2	530	Cag/Tag	9/20	1	2	FACETS	0.571	0.479	0.671	0.571	0.479	0.671	SUBCLONAL	1	TRUE	1	0.390479740457297	2		344	395	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428439	72428439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	237	669	0	ENST00000477973.2:c.565C>T	p.Pro189Ser	p.P189S	ENST00000477973	NM_012234.5	189	Cct/Tct	2/4	0.238095921205195	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.390479740457297	3		669	635	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443325	187443325	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	149	440	0	ENST00000232014.4:c.1801C>G	p.Pro601Ala	p.P601A	ENST00000232014	NM_001130845.1	601	Ccc/Gcc	8/10	0.238095921205195	3	FACETS	0.789	0.724	0.856	0.789	0.724	0.856	SUBCLONAL	2	TRUE	1	0.390479740457297	3		440	578	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516891	187516891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	66	580	0	ENST00000441802.2:c.13090G>A	p.Glu4364Lys	p.E4364K	ENST00000441802	NM_005245.3	4364	Gaa/Aaa	26/27	1	2	FACETS	0.545	0.473	0.623	0.545	0.473	0.623	SUBCLONAL	1	TRUE	1	0.390479740457297	2		580	620	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158433	26158477	+	inframe_deletion	In_Frame_Del	DEL	GAAGGGCTCCAAGAAGGCGGTGACTAAGGCTCAGAAGAAGGACGG	GAAGGGCTCCAAGAAGGCGGTGACTAAGGCTCAGAAGAAGGACGG	-	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	122	1010	0	ENST00000289316.2:c.40_84del	p.Gly14_Lys28del	p.G14_K28del	ENST00000289316	NM_138720.2	12	aaGAAGGGCTCCAAGAAGGCGGTGACTAAGGCTCAGAAGAAGGACGGg/aag	1/2	1	2	FACETS	0.512	0.461	0.566	0.512	0.461	0.566	SUBCLONAL	1	TRUE	1	0.390479740457297	2		1010	1221	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839986	27839994	+	inframe_deletion	In_Frame_Del	DEL	GACGCCACC	GACGCCACC	-	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	92	634	0	ENST00000328488.2:c.100_108del	p.Gly34_Val36del	p.G34_V36del	ENST00000328488	NM_003533.2	34	GGTGGCGTC/-	1/1	1	2	FACETS	0.681	0.605	0.762	0.681	0.605	0.762	SUBCLONAL	1	TRUE	1	0.390479740457297	2		634	692	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793518	89793518	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs940509117	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	82	316	0	ENST00000336032.3:c.587A>G	p.His196Arg	p.H196R	ENST00000336032	NM_006813.2	196	cAt/cGt	2/2	0.390479740457297	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.390479740457297	1		316	226	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001017	150001017	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	48	367	0	ENST00000253339.5:c.2587C>T	p.Gln863Ter	p.Q863*	ENST00000253339		863	Cag/Tag	4/7	0.390479740457297	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.390479740457297	1		367	148	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508547	106508547	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	24	385	0	ENST00000359195.3:c.541G>C	p.Val181Leu	p.V181L	ENST00000359195	NM_002649.2	181	Gtg/Ctg	2/11	1	2	FACETS	0.348	0.273	0.435	0.348	0.273	0.435	SUBCLONAL	1	TRUE	1	0.390479740457297	2		385	353	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859678	151859678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	150	410	1	ENST00000262189.6:c.10984G>A	p.Glu3662Lys	p.E3662K	ENST00000262189	NM_170606.2	3662	Gaa/Aaa	43/59	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.390479740457297	2		411	526	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194818	29194818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	56	1109	1	ENST00000240100.2:c.910G>A	p.Glu304Lys	p.E304K	ENST00000240100	NM_001394.6	304	Gag/Aag	4/4	1	2	FACETS	0.28	0.239	0.326	0.28	0.239	0.326	SUBCLONAL	1	TRUE	1	0.390479740457297	2		1110	1023	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220423	98220423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	123	760	0	ENST00000331920.6:c.3040C>T	p.Pro1014Ser	p.P1014S	ENST00000331920	NM_000264.3	1014	Ccc/Tcc	18/24	0.390479740457297	1	FACETS	0.776	0.703	0.853	0.776	0.703	0.853	SUBCLONAL	1	TRUE	0	0.390479740457297	1		760	653	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483351	120483351	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	44	438	0	ENST00000256646.2:c.3010G>C	p.Asp1004His	p.D1004H	ENST00000256646	NM_024408.3	1004	Gat/Cat	19/34	1	2	FACETS	0.425	0.356	0.502	0.425	0.356	0.502	SUBCLONAL	1	TRUE	1	0.390479740457297	2		438	530	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481346	56481379	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCCTTCCCAACCAGGTCCCCCCTGTCATGAGGT	TTCCTTCCCAACCAGGTCCCCCCTGTCATGAGGT	-	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	90	727	0	ENST00000267101.3:c.548-13_568del		p.X183_splice	ENST00000267101	NM_001982.3	183		5/28	0.324031650714065	3	FACETS	0.614	0.543	0.689	0.307	0.271	0.345	SUBCLONAL	1	TRUE	1	0.390479740457297	3		727	898	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347892	73347892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	20	337	0	ENST00000377767.4:c.1169C>T	p.Ala390Val	p.A390V	ENST00000377767	NM_014953.3	390	gCt/gTt	8/21	1	2	FACETS	0.523	0.401	0.663	0.523	0.401	0.663	SUBCLONAL	1	TRUE	1	0.390479740457297	2		337	196	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627415	37627415	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs139661788	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	52	686	0	ENST00000447079.4:c.1330T>C	p.Ser444Pro	p.S444P	ENST00000447079	NM_015083.1	444	Tct/Cct	2/14	1	2	FACETS	0.454	0.386	0.528	0.454	0.386	0.528	SUBCLONAL	1	TRUE	1	0.390479740457297	2		686	587	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732993	74732993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	56	573	0	ENST00000359995.5:c.250G>A	p.Glu84Lys	p.E84K	ENST00000359995	NM_001195427.1	84	Gag/Aag	1/3	1	2	FACETS	0.421	0.36	0.487	0.421	0.36	0.487	SUBCLONAL	1	TRUE	1	0.390479740457297	2		573	682	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187558020	187558020	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	32	309	0	ENST00000441802.2:c.3691G>A	p.Val1231Ile	p.V1231I	ENST00000441802	NM_005245.3	1231	Gtc/Atc	5/27	1	2	FACETS	0.532	0.433	0.644	0.532	0.433	0.644	SUBCLONAL	1	TRUE	1	0.390479740457297	2		309	308	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672015	30672015	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	50	838	0	ENST00000376406.3:c.4945A>G	p.Thr1649Ala	p.T1649A	ENST00000376406	NM_014641.2	1649	Act/Gct	10/15	1	2	FACETS	0.271	0.229	0.318	0.271	0.229	0.318	SUBCLONAL	1	TRUE	1	0.390479740457297	2		838	944	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324551	31324551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs12721803	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	59	946	0	ENST00000412585.2:c.257G>A	p.Arg86Gln	p.R86Q	ENST00000412585	NM_005514.6	86	cGg/cAg	2/8	1	2	FACETS	0.36	0.309	0.416	0.36	0.309	0.416	SUBCLONAL	1	TRUE	1	0.390479740457297	2		946	839	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100098	157100116	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCGGCAGCAGCAGGA	GGCGGCGGCAGCAGCAGGA	-	rs943407609	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	11	45	0	ENST00000346085.5:c.1044_1062del	p.Gly351AlafsTer12	p.G351Afs*12	ENST00000346085	NM_020732.3	345	gcGGCGGCGGCAGCAGCAGGA/gc	1/20	0.390479740457297	1	FACETS	0.855	0.607	1	0.855	0.607	1	CLONAL	1	TRUE	0	0.390479740457297	1		45	53	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958383	90958383	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	22	376	0	ENST00000265433.3:c.2055C>G	p.Phe685Leu	p.F685L	ENST00000265433	NM_002485.4	685	ttC/ttG	13/16	1	2	FACETS	0.609	0.475	0.763	0.609	0.475	0.763	SUBCLONAL	1	TRUE	1	0.390479740457297	2		376	185	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833956	44833957	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0038352-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	17	262	1	ENST00000377967.4:c.380_381delinsAA	p.Trp127Ter	p.W127*	ENST00000377967	NM_021140.2	127	tGG/tAA	4/29	1	1	FACETS	0.361	0.27	0.468	0.361	0.27	0.468	SUBCLONAL	1	TRUE	0	0.390479740457297	1		263	194	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	343	644	5	ENST00000269305.4:c.166G>T	p.Glu56Ter	p.E56*	ENST00000269305	NM_001126112.2	56	Gaa/Taa	4/11	NA	2	FACETS	0.751	0.714	0.788			1	INDETERMINATE	2	TRUE	NA	0.566847447542501	2		649	806	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0038440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	185	363	4	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.315231428470329	4	FACETS	1	0.987	1	0.656	0.607	0.707	INDETERMINATE	1	TRUE	2	0.566847447542501	4		367	779	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106532	27106532	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	322	647	3	ENST00000324856.7:c.6143G>A	p.Trp2048Ter	p.W2048*	ENST00000324856	NM_006015.4	2048	tGg/tAg	20/20	0.395622074423007	2	FACETS	1	0.995	1	0.737	0.7	0.774	CLONAL	1	TRUE	0	0.566847447542501	2		650	771	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956084	175956084	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	72	257	0	ENST00000367669.3:c.2128G>A	p.Asp710Asn	p.D710N	ENST00000367669	NM_022457.5	710	Gat/Aat	18/20	0.315231428470329	4	FACETS	1	0.928	1	0.539	0.474	0.609	INDETERMINATE	1	TRUE	2	0.566847447542501	4		257	369	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416499	29416499	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	272	596	7	ENST00000389048.3:c.4454C>A	p.Pro1485His	p.P1485H	ENST00000389048	NM_004304.4	1485	cCt/cAt	29/29	0.315231428470329	4	FACETS	0.774	0.727	0.821	0.774	0.727	0.821	INDETERMINATE	2	TRUE	2	0.566847447542501	4		603	972	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733444	85733444	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs556621354	NA	P-0038440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	174	359	4	ENST00000370580.1:c.568A>T	p.Thr190Ser	p.T190S	ENST00000370580	NM_003921.4	190	Act/Tct	3/3	0.315231428470329	4	FACETS	0.796	0.737	0.858	0.796	0.737	0.858	INDETERMINATE	2	TRUE	2	0.566847447542501	4		363	604	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506209	120506209	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	108	269	4	ENST00000256646.2:c.1903C>G	p.Pro635Ala	p.P635A	ENST00000256646	NM_024408.3	635	Cca/Gca	11/34	0.315231428470329	4	FACETS	1	0.984	1	0.741	0.67	0.814	INDETERMINATE	1	TRUE	2	0.566847447542501	4		273	403	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911052	94911052	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	167	408	1	ENST00000536441.1:c.1078G>T	p.Gly360Trp	p.G360W	ENST00000536441	NM_144665.3	360	Ggg/Tgg	8/10	0.395622074423007	2	FACETS	1	0.969	1	0.546	0.504	0.588	CLONAL	1	TRUE	0	0.566847447542501	2		409	540	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610498	10610498	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1443914847	NA	P-0038440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	357	564	6	ENST00000171111.5:c.212G>A	p.Arg71Gln	p.R71Q	ENST00000171111	NM_203500.1	71	cGg/cAg	2/6	0.395622074423007	2	FACETS	1	0.995	1	0.743	0.707	0.779	CLONAL	1	TRUE	0	0.566847447542501	2		570	848	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11019846	11019846	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	289	472	9	ENST00000327064.4:c.521G>T	p.Arg174Leu	p.R174L	ENST00000327064	NM_199141.1	174	cGc/cTc	4/16	0.395622074423007	2	FACETS	1	0.994	1	0.748	0.708	0.788	CLONAL	1	TRUE	0	0.566847447542501	2		481	682	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61722744	61722744	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	121	273	5	ENST00000401558.2:c.893T>C	p.Leu298Pro	p.L298P	ENST00000401558	NM_003400.3	298	cTt/cCt	11/25	0.315231428470329	4	FACETS	1	0.982	1	0.676	0.614	0.74	INDETERMINATE	1	TRUE	2	0.566847447542501	4		278	495	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388054	31388054	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	164	260	0	ENST00000328111.2:c.1855G>T	p.Glu619Ter	p.E619*	ENST00000328111	NM_006892.3	619	Gag/Tag	17/23	0.395622074423007	2	FACETS	1	0.99	1	0.742	0.69	0.795	CLONAL	1	TRUE	0	0.566847447542501	2		260	390	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021826	71021826	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	109	150	3	ENST00000318789.4:c.1532A>C	p.Asn511Thr	p.N511T	ENST00000318789	NM_032682.5	511	aAt/aCt	18/21	0.436336331070372	2	FACETS	0.808	0.741	0.876	0.808	0.741	0.876	CLONAL	2	TRUE	0	0.566847447542501	2		153	238	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401495	401495	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	347	291	7	ENST00000380956.4:c.817G>T	p.Gly273Cys	p.G273C	ENST00000380956	NM_001195286.1	273	Ggc/Tgc	7/9	0.566847447542501	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.566847447542501	3		298	667	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6045544	6045544	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	153	229	5	ENST00000265849.7:c.142G>T	p.Asp48Tyr	p.D48Y	ENST00000265849	NM_000535.5	48	Gat/Tat	2/15	0.566847447542501	3	FACETS	0.875	0.81	0.941	0.875	0.81	0.941	CLONAL	2	TRUE	1	0.566847447542501	3		234	396	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971035	21971035	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1339792331	NA	P-0038440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	144	367	3	ENST00000304494.5:c.323A>T	p.Asp108Val	p.D108V	ENST00000304494	NM_000077.4	108	gAt/gTt	2/3	0.449345161630951	1	FACETS	0.871	0.802	0.941	0.871	0.802	0.941	CLONAL	1	TRUE	0	0.566847447542501	1		370	418	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061139	38061168	+	inframe_deletion	In_Frame_Del	DEL	CCCCGCTTCCGCTCCCGCCCCCGCCGCCGG	CCCCGCTTCCGCTCCCGCCCCCGCCGCCGG	-	novel	NA	P-0038440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	17	196	0	ENST00000250448.2:c.821_850del	p.Ala274_Gly283del	p.A274_G283del	ENST00000250448	NM_004496.3	274	gCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGgc/ggc	2/2	0.395622074423007	2	FACETS	0.254	0.19	0.33	0.127	0.095	0.165	SUBCLONAL	1	TRUE	0	0.566847447542501	2		196	236	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339492	81339496	+	missense_variant	Missense_Mutation	ONP	GTTTG	GTTTG	TTTTT	novel	NA	P-0038440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	79	332	3	ENST00000222390.5:c.1508_1512delinsAAAAA	p.Thr503_Asn504delinsLysLys	p.T503_N504delinsKK	ENST00000222390	NM_000601.4	503	aCAAAC/aAAAAA	13/18	0.566847447542501	3	FACETS	0.671	0.591	0.756	0.336	0.295	0.378	SUBCLONAL	1	TRUE	1	0.566847447542501	3		335	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs863224499	NA	P-0038619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	312	736	2	ENST00000269305.4:c.672+1G>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.446545549474736	2	FACETS	0.78	0.738	0.823	0.78	0.738	0.823	SUBCLONAL	2	TRUE	0	0.460730334783492	2		738	868	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599250	55599250	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	61	405	0	ENST00000288135.5:c.2376C>A	p.Asp792Glu	p.D792E	ENST00000288135	NM_000222.2	792	gaC/gaA	17/21	0.243299906769029	1	FACETS	0.429	0.371	0.492	0.429	0.371	0.492	INDETERMINATE	1	TRUE	0	0.460730334783492	1		405	475	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285105	15285105	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038698-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	309	1043	0	ENST00000263388.2:c.4510G>C	p.Val1504Leu	p.V1504L	ENST00000263388	NM_000435.2	1504	Gtg/Ctg	25/33	1	2	FACETS	0.953	0.901	1	0.953	0.901	1	CLONAL	1	TRUE	1	0.672406045497729	2		1043	964	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0038727-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	27	517	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.086	0.068	0.107	0.086	0.068	0.107	SUBCLONAL	1	TRUE	1	0.776942236286897	2		517	805	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858228	59858229	+	missense_variant	Missense_Mutation	DNP	TA	TA	AG	novel	NA	P-0038727-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	185	377	0	ENST00000259008.2:c.1766_1767delinsCT	p.Leu589Pro	p.L589P	ENST00000259008	NM_032043.2	589	cTA/cCT	12/20	1	2	FACETS	0.925	0.861	0.99	0.925	0.861	0.99	CLONAL	1	TRUE	1	0.776942236286897	2		377	515	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24133981	24133981	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038727-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	190	335	0	ENST00000263121.7:c.132del	p.Tyr44Ter	p.Y44*	ENST00000263121	NM_003073.3	44	taC/ta	2/9	1	2	FACETS	0.955	0.891	1	0.955	0.891	1	CLONAL	1	TRUE	1	0.776942236286897	2		335	512	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167532	24167532	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038727-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	321	590	0	ENST00000263121.7:c.916G>T	p.Glu306Ter	p.E306*	ENST00000263121	NM_003073.3	306	Gag/Tag	7/9	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.776942236286897	2		590	797	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119812213	119812213	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs769312285	NA	P-0038727-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	167	297	0	ENST00000316626.5:c.69T>A	p.Phe23Leu	p.F23L	ENST00000316626		23	ttT/ttA	1/12	1	2	FACETS	0.96	0.891	1	0.96	0.891	1	CLONAL	1	TRUE	1	0.776942236286897	2		297	448	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952352	38952352	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038727-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	104	262	0	ENST00000357387.3:c.3073A>C	p.Asn1025His	p.N1025H	ENST00000357387	NM_152756.3	1025	Aac/Cac	30/38	1	2	FACETS	0.869	0.788	0.953	0.869	0.788	0.953	CLONAL	1	TRUE	1	0.776942236286897	2		262	308	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0038851-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	373	833	3	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.169620106369899	3	FACETS	0.846	0.807	0.887	0.846	0.807	0.887	INDETERMINATE	3	TRUE	0	0.38852808311716	3		836	903	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654646	67654646	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038851-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	203	506	1	ENST00000264010.4:c.1133C>A	p.Pro378Gln	p.P378Q	ENST00000264010	NM_006565.3	378	cCg/cAg	6/12	0.339816806484284	2	FACETS	0.878	0.819	0.938	0.878	0.819	0.938	CLONAL	2	TRUE	0	0.38852808311716	2		507	595	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922202	39922202	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038851-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	85	514	0	ENST00000378444.4:c.3970A>G	p.Ile1324Val	p.I1324V	ENST00000378444	NM_001123385.1	1324	Att/Gtt	9/15	0.326418807221812	2	FACETS	0.688	0.608	0.773	0.344	0.304	0.387	SUBCLONAL	1	TRUE	0	0.38852808311716	2		514	636	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202843	128202843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	207	538	0	ENST00000341105.2:c.877C>T	p.Arg293Trp	p.R293W	ENST00000341105	NM_032638.4	293	Cgg/Tgg	4/6	0.357293764632696	4	FACETS	1	0.99	1	0.485	0.45	0.522	CLONAL	1	TRUE	1	0.413027957152942	4		538	973	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665419	117665419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376021394	NA	P-0038857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	19	206	1	ENST00000368508.3:c.4328C>T	p.Ala1443Val	p.A1443V	ENST00000368508	NM_002944.2	1443	gCg/gTg	27/43	0.341595494883686	3	FACETS	0.358	0.271	0.46	0.119	0.09	0.154	SUBCLONAL	1	TRUE	0	0.413027957152942	3		207	310	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426042	47426042	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138292173	NA	P-0038857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	31	349	2	ENST00000377045.4:c.562C>T	p.Arg188Cys	p.R188C	ENST00000377045	NM_001654.4	188	Cgc/Tgc	7/16	0.27234508230362	2	FACETS	0.254	0.204	0.31			1	SUBCLONAL	1	TRUE	NA	0.413027957152942	2		351	592	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403235	213403235	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	174	395	0	ENST00000342788.4:c.20T>G	p.Leu7Arg	p.L7R	ENST00000342788	NM_005235.2	7	cTt/cGt	1/28	0.375884008182621	4	FACETS	0.819	0.756	0.884	0.819	0.756	0.884	CLONAL	2	TRUE	2	0.413027957152942	4		395	727	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256541	115256541	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	112	498	0	ENST00000369535.4:c.170del	p.Asp57ValfsTer11	p.D57Vfs*11	ENST00000369535	NM_002524.4	57	gAt/gt	3/7	0.414378460941079	3	FACETS	0.72	0.647	0.798	0.36	0.323	0.399	SUBCLONAL	1	TRUE	1	0.413027957152942	3		498	909	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510802	120510802	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1273608383	NA	P-0038857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	83	385	1	ENST00000256646.2:c.1162G>A	p.Ala388Thr	p.A388T	ENST00000256646	NM_024408.3	388	Gca/Aca	7/34	0.414378460941079	3	FACETS	0.676	0.597	0.762	0.338	0.298	0.381	SUBCLONAL	1	TRUE	1	0.413027957152942	3		386	717	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32918727	32918727	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	75	217	0	ENST00000380152.3:c.6874G>A	p.Glu2292Lys	p.E2292K	ENST00000380152		2292	Gaa/Aaa	12/27	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.413027957152942	2		217	284	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578365	7578398	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTCACCATCGCTATCTGAGCAGCGCTCATGGTG	GCTCACCATCGCTATCTGAGCAGCGCTCATGGTG	-	novel	NA	P-0038857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	378	446	0	ENST00000269305.4:c.532_559+6del		p.X178_splice	ENST00000269305	NM_001126112.2	178		5/11	0.291950413064959	3	FACETS	0.879	0.84	0.92	0.879	0.84	0.92	CLONAL	3	TRUE	0	0.413027957152942	3		446	837	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245963	5245963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1490066505	NA	P-0038857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	323	623	0	ENST00000357368.4:c.812C>T	p.Ser271Leu	p.S271L	ENST00000357368	NM_002850.3	271	tCg/tTg	10/38	0.352512047403244	2	FACETS	0.898	0.851	0.945	0.898	0.851	0.945	CLONAL	2	TRUE	0	0.413027957152942	2		623	871	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483976	212483976	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	143	365	0	ENST00000342788.4:c.2227A>C	p.Thr743Pro	p.T743P	ENST00000342788	NM_005235.2	743	Act/Cct	19/28	0.375884008182621	4	FACETS	1	0.985	1	0.696	0.636	0.759	CLONAL	1	TRUE	2	0.413027957152942	4		365	703	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419992	41419992	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	113	431	0	ENST00000373198.4:c.329C>A	p.Ser110Tyr	p.S110Y	ENST00000373198	NM_133170.3	110	tCc/tAc	3/32	0.414378460941079	4	FACETS	0.743	0.668	0.824	0.372	0.334	0.412	SUBCLONAL	1	TRUE	2	0.413027957152942	4		431	1040	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249348	110249348	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	154	557	0	ENST00000374672.4:c.1225A>C	p.Lys409Gln	p.K409Q	ENST00000374672	NM_004235.4	409	Aag/Cag	4/5	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.316574500232246	2		557	886	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453136	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	rs397516897	NA	P-0038951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	50	228	0	ENST00000288602.6:c.1799_1801del	p.Val600_Lys601delinsGlu	p.V600_K601delinsE	ENST00000288602	NM_004333.4	600	gTGAaa/gaa	15/18	1	2	FACETS	0.908	0.773	1	0.908	0.773	1	CLONAL	1	TRUE	1	0.316574500232246	2		228	348	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933442	39933455	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGCGGGGAACTC	GCCGCGGGGAACTC	-	novel	NA	P-0038951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	37	494	0	ENST00000378444.4:c.1144_1157del	p.Glu382GlnfsTer53	p.E382Qfs*53	ENST00000378444	NM_001123385.1	382	GAGTTCCCCGCGGCc/c	4/15	1	2	FACETS	0.364	0.299	0.437	0.364	0.299	0.437	SUBCLONAL	1	TRUE	1	0.316574500232246	2		494	642	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118354974	118354974	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1002595965	NA	P-0039006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	44	316	0	ENST00000534358.1:c.4163G>T	p.Ser1388Ile	p.S1388I	ENST00000534358	NM_005933.3	1388	aGt/aTt	9/36	1	2	FACETS	0.457	0.382	0.539	0.457	0.382	0.539	SUBCLONAL	1	TRUE	1	0.35552884266458	2		316	542	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0039023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	65	230	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.395400950142106	2		230	270	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0039023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	101	437	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.395400950142106	2		437	471	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135800978	135800978	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	54	223	0	ENST00000298552.3:c.359T>A	p.Leu120His	p.L120H	ENST00000298552	NM_001162426.1	120	cTc/cAc	5/23	0.395400950142106	3	FACETS	1	0.937	1	0.582	0.501	0.669	CLONAL	1	TRUE	1	0.395400950142106	3		223	281	SUCCESS
APC	324	MSKCC	GRCh37	5	112175908	112175908	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	71	165	0	ENST00000257430.4:c.4617del	p.Glu1540SerfsTer25	p.E1540Sfs*25	ENST00000257430	NM_000038.5	1539	tcA/tc	16/16	0.3	0	FACETS	0.64	0.575	0.705			1	INDETERMINATE	1	TRUE	0	0.6	0		165	148	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913255	NA	P-0039041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	251	478	0	ENST00000369535.4:c.183A>T	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caT	3/7	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.78233358323835	2		478	629	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144049	11144051	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0039041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	348	702	0	ENST00000358026.2:c.3634_3636del	p.Glu1212del	p.E1212del	ENST00000358026	NM_001128849.1	1210	gtGGAg/gtg	26/36	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.78233358323835	2		702	833	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225684	26225686	+	inframe_deletion	In_Frame_Del	DEL	TGG	TGG	-	rs764871937	NA	P-0039041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	218	580	0	ENST00000360408.1:c.305_307del	p.Val102del	p.V102del	ENST00000360408	NM_003532.2	101	tTGGtg/ttg	1/1	0.78233358323835	2	FACETS	0.895	0.837	0.953	0.447	0.418	0.477	CLONAL	1	TRUE	0	0.78233358323835	2		580	623	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851482	151851482	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	172	360	0	ENST00000262189.6:c.12009del	p.Ser4004HisfsTer10	p.S4004Hfs*10	ENST00000262189	NM_170606.2	4003	ccC/cc	47/59	0.776217887057158	3	FACETS	0.902	0.833	0.974	0.301	0.277	0.325	CLONAL	1	TRUE	0	0.78233358323835	3		360	678	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	142	174	0				ENST00000310581	NM_198253.2	-/1132			0.758509333880584	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.758509333880584	3		174	250	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266110	41266110	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	108	281	0	ENST00000349496.5:c.107A>C	p.His36Pro	p.H36P	ENST00000349496	NM_001904.3	36	cAt/cCt	3/15	0.103370409549595	4	FACETS	0.879	0.801	0.958	0.879	0.801	0.958	INDETERMINATE	2	TRUE	2	0.758509333880584	4		281	285	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098959	178098959	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519921	NA	P-0039043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	69	244	0	ENST00000397062.3:c.86A>G	p.Asp29Gly	p.D29G	ENST00000397062	NM_006164.4	29	gAt/gGt	2/5	1	2	FACETS	0.896	0.795	1	0.896	0.795	1	CLONAL	1	TRUE	1	0.758509333880584	2		244	203	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162201	47162201	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0039043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	95	372	0	ENST00000409792.3:c.3925A>T	p.Arg1309Ter	p.R1309*	ENST00000409792	NM_014159.6	1309	Aga/Tga	3/21	0.103370409549595	4	FACETS	1	0.98	1	0.706	0.636	0.779	INDETERMINATE	1	TRUE	2	0.758509333880584	4		372	312	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390066	89390066	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs559831321	NA	P-0039043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	47	217	1	ENST00000336596.2:c.815C>T	p.Ala272Val	p.A272V	ENST00000336596	NM_005233.5	272	gCt/gTt	4/17	1	2	FACETS	0.843	0.726	0.966	0.843	0.726	0.966	CLONAL	1	TRUE	1	0.758509333880584	2		218	147	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0039046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	50	541	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.175925641668454	3	FACETS	0.291	0.246	0.341	0.146	0.123	0.171	INDETERMINATE	1	TRUE	1	0.62	3		541	725	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0039046-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	193	541	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.95	0.88	1	0.95	0.88	1	CLONAL	1	TRUE	1	0.508047556387158	2		541	800	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971177	21971177	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913382	NA	P-0039048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	159	302	0	ENST00000304494.5:c.181G>T	p.Glu61Ter	p.E61*	ENST00000304494	NM_000077.4	61	Gag/Tag	2/3	0.559754719698009	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.559754719698009	1		302	353	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094455	27094456	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0039048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	141	460	0	ENST00000324856.7:c.3164_3165del	p.Tyr1055CysfsTer49	p.Y1055Cfs*49	ENST00000324856	NM_006015.4	1055	TAt/t	11/20	0.559754719698009	1	FACETS	0.981	0.904	1	0.981	0.904	1	CLONAL	1	TRUE	0	0.559754719698009	1		460	370	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944864	31944864	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs768711923	NA	P-0039048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	89	564	0	ENST00000340398.3:c.237C>A	p.Asn79Lys	p.N79K	ENST00000340398	NM_001013699.2	79	aaC/aaA	1/1	0.120220069424022	5	FACETS	0.622	0.55	0.699			1	INDETERMINATE	1	TRUE	NA	0.559754719698009	5		564	941	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0039048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	359	496	0	ENST00000269305.4:c.375+1del		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.552727055225375	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.559754719698009	2		496	609	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944836	31944836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148314204	NA	P-0039048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1217	134	763	0	ENST00000340398.3:c.265G>A	p.Val89Ile	p.V89I	ENST00000340398	NM_001013699.2	89	Gtc/Atc	1/1	0.120220069424022	5	FACETS	0.652	0.59	0.717			1	INDETERMINATE	1	TRUE	NA	0.559754719698009	5		763	1351	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944789	31944789	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs765335762	NA	P-0039048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	119	517	0	ENST00000340398.3:c.312G>C	p.Leu104Phe	p.L104F	ENST00000340398	NM_001013699.2	104	ttG/ttC	1/1	0.120220069424022	5	FACETS	0.847	0.763	0.935			1	INDETERMINATE	1	TRUE	NA	0.559754719698009	5		517	924	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944989	31944990	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTT	rs879122881	NA	P-0039048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	127	766	0	ENST00000340398.3:c.109_111dup	p.Lys37dup	p.K37dup	ENST00000340398	NM_001013699.2	37	-/AAG	1/1	0.120220069424022	5	FACETS	0.646	0.583	0.713			1	INDETERMINATE	1	TRUE	NA	0.559754719698009	5		766	1292	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945001	31945001	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs878902492	NA	P-0039048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1154	125	772	0	ENST00000340398.3:c.100T>G	p.Cys34Gly	p.C34G	ENST00000340398	NM_001013699.2	34	Tgc/Ggc	1/1	0.120220069424022	5	FACETS	0.642	0.58	0.709			1	INDETERMINATE	1	TRUE	NA	0.559754719698009	5		772	1279	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945013	31945013	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs879142499	NA	P-0039048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	107	753	0	ENST00000340398.3:c.88A>G	p.Thr30Ala	p.T30A	ENST00000340398	NM_001013699.2	30	Acc/Gcc	1/1	0.120220069424022	5	FACETS	0.548	0.49	0.61			1	INDETERMINATE	1	TRUE	NA	0.559754719698009	5		753	1284	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443860	49443861	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0039048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	210	735	0	ENST00000301067.7:c.3509_3510dup	p.Glu1171ProfsTer42	p.E1171Pfs*42	ENST00000301067	NM_003482.3	1170	-/CC	11/54	0.559754719698009	1	FACETS	0.92	0.861	0.981	0.92	0.861	0.981	CLONAL	1	TRUE	0	0.559754719698009	1		735	587	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249853	133249853	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854842	NA	P-0039048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	127	442	0	ENST00000320574.5:c.1370C>T	p.Thr457Met	p.T457M	ENST00000320574	NM_006231.2	457	aCg/aTg	14/49	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.559754719698009	2		442	447	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829102	72829102	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	240	557	0	ENST00000268489.5:c.7479del	p.Leu2494TyrfsTer34	p.L2494Yfs*34	ENST00000268489	NM_006885.3	2493	ccC/cc	9/10	0.559754719698009	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.559754719698009	1		557	547	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610364	10610364	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	283	686	0	ENST00000171111.5:c.346C>G	p.Arg116Gly	p.R116G	ENST00000171111	NM_203500.1	116	Cgg/Ggg	2/6	1	2	FACETS	0.994	0.935	1	0.994	0.935	1	CLONAL	1	TRUE	1	0.559754719698009	2		686	1017	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561333	9561333	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	134	387	0	ENST00000353224.5:c.449G>T	p.Ser150Ile	p.S150I	ENST00000353224	NM_177990.2	150	aGt/aTt	4/10	1	2	FACETS	0.923	0.843	1	0.923	0.843	1	CLONAL	1	TRUE	1	0.559754719698009	2		387	519	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564521	55564521	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	146	495	0	ENST00000288135.5:c.409C>G	p.Pro137Ala	p.P137A	ENST00000288135	NM_000222.2	137	Cct/Gct	3/21	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.559754719698009	2		495	507	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876452	35876452	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	378	550	0	ENST00000303115.3:c.1244T>A	p.Leu415Gln	p.L415Q	ENST00000303115	NM_002185.3	415	cTg/cAg	8/8	0.559754719698009	3	FACETS	0.99	0.945	1	0.99	0.945	1	CLONAL	2	TRUE	1	0.559754719698009	3		550	873	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0039050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	399	490	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.783589723566037	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.783589723566037	1		490	600	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030485	49030485	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs483352690	NA	P-0039050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	200	260	0	ENST00000267163.4:c.1960G>A	p.Val654Met	p.V654M	ENST00000267163	NM_000321.2	654	Gtg/Atg	19/27	0.756944518092089	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.783589723566037	1		260	289	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170102	32170102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748069011	NA	P-0039050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1293	478	805	2	ENST00000375023.3:c.3506G>A	p.Arg1169Gln	p.R1169Q	ENST00000375023	NM_004557.3	1169	cGg/cAg	21/30	0.752972378450212	3	FACETS	0.959	0.915	1	0.479	0.457	0.502	CLONAL	1	TRUE	1	0.783589723566037	3		807	1771	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242484	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAGCAACAT	TTAAGAGAAGCAACAT	CAAC	novel	NA	P-0039050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	5730	342	1	ENST00000275493.2:c.2239_2254delinsCAAC	p.Leu747_Ser752delinsGlnPro	p.L747_S752delinsQP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGCAACATct/CAACct	19/28	0.783589723566037	24	FACETS	1	0.998	1	0.923	0.916	0.929	CLONAL	20	TRUE	2	0.783589723566037	24		343	6929	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53241009	53241009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	390	297	0	ENST00000375401.3:c.1202C>T	p.Ala401Val	p.A401V	ENST00000375401	NM_004187.3	401	gCc/gTc	9/26	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.783589723566037	1		297	474	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696432	47696432	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519968	NA	P-0039053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	150	482	0	ENST00000347630.2:c.391T>G	p.Trp131Gly	p.W131G	ENST00000347630	NM_001007230.1	131	Tgg/Ggg	6/11	1	2	FACETS	0.884	0.809	0.961	0.884	0.809	0.961	CLONAL	1	TRUE	1	0.477426477238804	2		482	711	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63817028	63817028	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	86	280	0	ENST00000279873.7:c.999A>C	p.Lys333Asn	p.K333N	ENST00000279873	NM_032199.2	333	aaA/aaC	6/10	1	2	FACETS	0.905	0.806	1	0.905	0.806	1	CLONAL	1	TRUE	1	0.477426477238804	2		280	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	358	772	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	0.972	0.923	1	0.972	0.923	1	CLONAL	1	TRUE	1	0.76130320175478	2		772	968	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220274	55220274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	387	449	1	ENST00000275493.2:c.664C>T	p.Arg222Cys	p.R222C	ENST00000275493	NM_005228.3	222	Cgc/Tgc	6/28	1	2	FACETS	0.996	0.949	1	0.996	0.949	1	CLONAL	1	TRUE	1	0.76130320175478	2		450	1021	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489164	2489164	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	135	567	2	ENST00000355716.4:c.70-1G>T		p.X24_splice	ENST00000355716	NM_003820.2	24			1	2	FACETS	0.513	0.466	0.561	0.513	0.466	0.561	SUBCLONAL	1	TRUE	1	0.76130320175478	2		569	692	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784861	9784861	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	283	590	0	ENST00000377346.4:c.2865-1G>T		p.X955_splice	ENST00000377346	NM_005026.3	955			1	2	FACETS	0.952	0.899	1	0.952	0.899	1	CLONAL	1	TRUE	1	0.76130320175478	2		590	781	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174501	11174501	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	289	498	0	ENST00000361445.4:c.7174C>A	p.Leu2392Met	p.L2392M	ENST00000361445	NM_004958.3	2392	Ctg/Atg	53/58	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.76130320175478	2		498	740	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255320	16255320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	261	467	0	ENST00000375759.3:c.2585C>T	p.Ala862Val	p.A862V	ENST00000375759	NM_015001.2	862	gCt/gTt	11/15	1	2	FACETS	0.973	0.916	1	0.973	0.916	1	CLONAL	1	TRUE	1	0.76130320175478	2		467	705	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100871	27100871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761500441	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	290	467	0	ENST00000324856.7:c.4153G>A	p.Glu1385Lys	p.E1385K	ENST00000324856	NM_006015.4	1385	Gaa/Aaa	18/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.76130320175478	2		467	724	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938156	36938156	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	360	750	0	ENST00000361632.4:c.805C>T	p.Arg269Cys	p.R269C	ENST00000361632		269	Cgc/Tgc	6/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.76130320175478	2		750	916	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805058	43805058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1339501124	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	61	627	1	ENST00000372470.3:c.508C>T	p.Arg170Cys	p.R170C	ENST00000372470	NM_005373.2	170	Cgc/Tgc	4/12	1	2	FACETS	0.183	0.157	0.212	0.183	0.157	0.212	SUBCLONAL	1	TRUE	1	0.76130320175478	2		628	874	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814955	43814955	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	53	382	0	ENST00000372470.3:c.1490C>A	p.Ala497Asp	p.A497D	ENST00000372470	NM_005373.2	497	gCt/gAt	10/12	1	2	FACETS	0.209	0.178	0.244	0.209	0.178	0.244	SUBCLONAL	1	TRUE	1	0.76130320175478	2		382	666	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818232	43818232	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	275	604	1	ENST00000372470.3:c.1697G>A	p.Ser566Asn	p.S566N	ENST00000372470	NM_005373.2	566	aGc/aAc	12/12	1	2	FACETS	0.984	0.929	1	0.984	0.929	1	CLONAL	1	TRUE	1	0.76130320175478	2		605	734	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46543206	46543206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	195	460	0	ENST00000262741.5:c.295G>A	p.Asp99Asn	p.D99N	ENST00000262741	NM_003629.3	99	Gat/Aat	3/10	1	2	FACETS	0.926	0.864	0.99	0.926	0.864	0.99	CLONAL	1	TRUE	1	0.76130320175478	2		460	553	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743605	46743605	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	350	656	0	ENST00000371975.4:c.1986G>T	p.Lys662Asn	p.K662N	ENST00000371975	NM_003579.3	662	aaG/aaT	17/18	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.76130320175478	2		656	896	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65304233	65304233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1163790865	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	143	373	0	ENST00000342505.4:c.2882C>T	p.Ser961Leu	p.S961L	ENST00000342505	NM_002227.2	961	tCg/tTg	21/25	1	2	FACETS	0.848	0.78	0.918	0.848	0.78	0.918	CLONAL	1	TRUE	1	0.76130320175478	2		373	443	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834214	156834214	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	93	758	0	ENST00000524377.1:c.281G>T	p.Arg94Ile	p.R94I	ENST00000524377	NM_002529.3	94	aGa/aTa	2/17	1	2	FACETS	0.201	0.178	0.226	0.201	0.178	0.226	SUBCLONAL	1	TRUE	1	0.76130320175478	2		758	1216	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837999	156837999	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	403	816	1	ENST00000524377.1:c.532C>A	p.His178Asn	p.H178N	ENST00000524377	NM_002529.3	178	Cat/Aat	5/17	1	2	FACETS	0.982	0.936	1	0.982	0.936	1	CLONAL	1	TRUE	1	0.76130320175478	2		817	1078	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162722915	162722915	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	64	520	0	ENST00000367921.3:c.113G>T	p.Gly38Val	p.G38V	ENST00000367921	NM_006182.2	38	gGa/gTa	4/18	1	2	FACETS	0.245	0.211	0.281	0.245	0.211	0.281	SUBCLONAL	1	TRUE	1	0.76130320175478	2		520	687	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740231	162740231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773598662	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	214	413	2	ENST00000367921.3:c.1433G>A	p.Arg478His	p.R478H	ENST00000367921	NM_006182.2	478	cGc/cAc	12/18	1	2	FACETS	0.878	0.821	0.937	0.878	0.821	0.937	CLONAL	1	TRUE	1	0.76130320175478	2		415	640	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740279	162740279	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	161	315	0	ENST00000367921.3:c.1481T>C	p.Phe494Ser	p.F494S	ENST00000367921	NM_006182.2	494	tTt/tCt	12/18	1	2	FACETS	0.833	0.769	0.898	0.833	0.769	0.898	CLONAL	1	TRUE	1	0.76130320175478	2		315	508	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306559	163306559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781627921	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	118	430	0	ENST00000271452.3:c.356G>A	p.Arg119Gln	p.R119Q	ENST00000271452	NM_145697.2	119	cGg/cAg	6/14	1	2	FACETS	0.868	0.792	0.947	0.868	0.792	0.947	CLONAL	1	TRUE	1	0.76130320175478	2		430	357	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050315	176050315	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	91	377	0	ENST00000367669.3:c.1250T>C	p.Leu417Pro	p.L417P	ENST00000367669	NM_022457.5	417	cTc/cCc	11/20	1	2	FACETS	0.833	0.749	0.92	0.833	0.749	0.92	CLONAL	1	TRUE	1	0.76130320175478	2		377	287	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107231	193107231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	69	233	0	ENST00000367435.3:c.440G>A	p.Arg147His	p.R147H	ENST00000367435	NM_024529.4	147	cGc/cAc	6/17	1	2	FACETS	0.781	0.69	0.877	0.781	0.69	0.877	SUBCLONAL	1	TRUE	1	0.76130320175478	2		233	232	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653395	206653395	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374485120	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	367	598	1	ENST00000367120.3:c.1279C>T	p.Arg427Trp	p.R427W	ENST00000367120	NM_014002.3	427	Cgg/Tgg	12/22	1	2	FACETS	0.989	0.941	1	0.989	0.941	1	CLONAL	1	TRUE	1	0.76130320175478	2		599	975	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666648	206666648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	336	645	0	ENST00000367120.3:c.1982C>T	p.Ala661Val	p.A661V	ENST00000367120	NM_014002.3	661	gCt/gTt	20/22	1	2	FACETS	0.964	0.914	1	0.964	0.914	1	CLONAL	1	TRUE	1	0.76130320175478	2		645	916	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567276	226567276	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	180	408	0	ENST00000366794.5:c.1610C>T	p.Ser537Phe	p.S537F	ENST00000366794	NM_001618.3	537	tCt/tTt	11/23	1	2	FACETS	0.892	0.829	0.957	0.892	0.829	0.957	CLONAL	1	TRUE	1	0.76130320175478	2		408	530	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226574088	226574088	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	225	475	1	ENST00000366794.5:c.773C>A	p.Thr258Asn	p.T258N	ENST00000366794	NM_001618.3	258	aCt/aAt	6/23	1	2	FACETS	0.921	0.863	0.98	0.921	0.863	0.98	CLONAL	1	TRUE	1	0.76130320175478	2		476	642	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578195	226578195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202057244	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	284	470	2	ENST00000366794.5:c.533C>T	p.Ala178Val	p.A178V	ENST00000366794	NM_001618.3	178	gCg/gTg	4/23	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.76130320175478	2		472	738	SUCCESS
FH	2271	MSKCC	GRCh37	1	241669371	241669371	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	163	363	0	ENST00000366560.3:c.836T>C	p.Val279Ala	p.V279A	ENST00000366560	NM_000143.3	279	gTt/gCt	6/10	1	2	FACETS	0.786	0.725	0.848	0.786	0.725	0.848	SUBCLONAL	1	TRUE	1	0.76130320175478	2		363	545	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675266	241675266	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1375252870	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	26	339	0	ENST00000366560.3:c.555+1G>A		p.X185_splice	ENST00000366560	NM_000143.3	185			1	2	FACETS	0.236	0.187	0.291	0.236	0.187	0.291	SUBCLONAL	1	TRUE	1	0.76130320175478	2		339	290	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736334	243736334	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771134997	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	188	362	0	ENST00000263826.5:c.713C>T	p.Ser238Leu	p.S238L	ENST00000263826	NM_005465.4	238	tCg/tTg	8/13	1	2	FACETS	0.946	0.881	1	0.946	0.881	1	CLONAL	1	TRUE	1	0.76130320175478	2		362	522	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800950	243800950	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	115	399	0	ENST00000263826.5:c.524C>A	p.Ala175Asp	p.A175D	ENST00000263826	NM_005465.4	175	gCt/gAt	5/13	1	2	FACETS	0.835	0.76	0.912	0.835	0.76	0.912	CLONAL	1	TRUE	1	0.76130320175478	2		399	362	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097667	8097667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	170	308	0	ENST00000346208.3:c.49G>A	p.Ala17Thr	p.A17T	ENST00000346208		17	Gcc/Acc	2/6	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.76130320175478	2		308	419	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851756	63851756	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	281	623	0	ENST00000279873.7:c.2534A>G	p.Glu845Gly	p.E845G	ENST00000279873	NM_032199.2	845	gAg/gGg	10/10	1	2	FACETS	0.889	0.839	0.941	0.889	0.839	0.941	CLONAL	1	TRUE	1	0.76130320175478	2		623	830	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406694	70406694	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	220	483	0	ENST00000373644.4:c.4208T>G	p.Phe1403Cys	p.F1403C	ENST00000373644	NM_030625.2	1403	tTt/tGt	4/12	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.76130320175478	2		483	554	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450724	70450724	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	58	497	0	ENST00000373644.4:c.5564C>T	p.Ala1855Val	p.A1855V	ENST00000373644	NM_030625.2	1855	gCt/gTt	12/12	1	2	FACETS	0.209	0.179	0.242	0.209	0.179	0.242	SUBCLONAL	1	TRUE	1	0.76130320175478	2		497	728	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450795	70450795	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	49	468	0	ENST00000373644.4:c.5635C>T	p.Pro1879Ser	p.P1879S	ENST00000373644	NM_030625.2	1879	Ccc/Tcc	12/12	1	2	FACETS	0.201	0.169	0.235	0.201	0.169	0.235	SUBCLONAL	1	TRUE	1	0.76130320175478	2		468	641	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88672038	88672038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746231785	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	122	346	1	ENST00000372037.3:c.572G>A	p.Arg191His	p.R191H	ENST00000372037	NM_004329.2	191	cGt/cAt	8/13	1	2	FACETS	0.96	0.879	1	0.96	0.879	1	CLONAL	1	TRUE	1	0.76130320175478	2		347	334	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692770	89692770	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs1114167658	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	128	389	0	ENST00000371953.3:c.254T>G	p.Val85Gly	p.V85G	ENST00000371953	NM_000314.4	85	gTt/gGt	5/9	1	2	FACETS	0.88	0.806	0.956	0.88	0.806	0.956	CLONAL	1	TRUE	1	0.76130320175478	2		389	382	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692940	89692940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746152219	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	184	510	0	ENST00000371953.3:c.424C>T	p.Arg142Trp	p.R142W	ENST00000371953	NM_000314.4	142	Cgg/Tgg	5/9	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.76130320175478	2		510	477	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720744	89720744	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167674	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	16	216	1	ENST00000371953.3:c.895G>T	p.Glu299Ter	p.E299*	ENST00000371953	NM_000314.4	299	Gaa/Taa	8/9	1	2	FACETS	0.331	0.247	0.43	0.331	0.247	0.43	SUBCLONAL	1	TRUE	1	0.76130320175478	2		217	127	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720870	89720870	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1554825652	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	151	361	0	ENST00000371953.3:c.1021T>G	p.Phe341Val	p.F341V	ENST00000371953	NM_000314.4	341	Ttt/Gtt	8/9	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.76130320175478	2		361	372	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161441	2161441	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	100	505	0	ENST00000434045.2:c.86T>C	p.Val29Ala	p.V29A	ENST00000434045	NM_001127598.1	29	gTa/gCa	2/5	1	2	FACETS	0.302	0.269	0.337	0.302	0.269	0.337	SUBCLONAL	1	TRUE	1	0.76130320175478	2		505	869	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248592	8248592	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	325	656	0	ENST00000335790.3:c.295G>A	p.Glu99Lys	p.E99K	ENST00000335790	NM_002315.2	99	Gag/Aag	3/4	1	2	FACETS	0.979	0.928	1	0.979	0.928	1	CLONAL	1	TRUE	1	0.76130320175478	2		656	872	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251991	8251991	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760736132	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	362	689	1	ENST00000335790.3:c.86G>A	p.Arg29His	p.R29H	ENST00000335790	NM_002315.2	29	cGc/cAc	2/4	1	2	FACETS	0.979	0.931	1	0.979	0.931	1	CLONAL	1	TRUE	1	0.76130320175478	2		690	971	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14303203	14303203	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	107	531	1	ENST00000256196.4:c.472G>T	p.Ala158Ser	p.A158S	ENST00000256196		158	Gca/Tca	5/6	1	2	FACETS	0.523	0.471	0.579	0.523	0.471	0.579	SUBCLONAL	1	TRUE	1	0.76130320175478	2		532	537	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741378	17741378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	371	706	1	ENST00000250003.3:c.49G>A	p.Asp17Asn	p.D17N	ENST00000250003	NM_002478.4	17	Gac/Aac	1/3	1	2	FACETS	0.949	0.902	0.996	0.949	0.902	0.996	CLONAL	1	TRUE	1	0.76130320175478	2		707	1027	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456743	32456743	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	250	445	1	ENST00000332351.3:c.149C>A	p.Ala50Asp	p.A50D	ENST00000332351	NM_024426.4	50	gCt/gAt	1/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.76130320175478	2		446	621	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128948	64128948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143154193	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	291	607	0	ENST00000334205.4:c.578G>A	p.Arg193Gln	p.R193Q	ENST00000334205	NM_003942.2	193	cGg/cAg	6/17	1	2	FACETS	0.878	0.828	0.928	0.878	0.828	0.928	CLONAL	1	TRUE	1	0.76130320175478	2		607	871	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138755	64138755	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	277	484	2	ENST00000334205.4:c.2122G>T	p.Ala708Ser	p.A708S	ENST00000334205	NM_003942.2	708	Gca/Tca	17/17	1	2	FACETS	0.964	0.91	1	0.964	0.91	1	CLONAL	1	TRUE	1	0.76130320175478	2		486	755	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572200	64572200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1450318836	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	191	271	0	ENST00000312049.6:c.1439G>A	p.Arg480Gln	p.R480Q	ENST00000312049	NM_130799.2	480	cGg/cAg	10/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.76130320175478	2		271	396	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457911	69457911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	319	451	0	ENST00000227507.2:c.311C>T	p.Ala104Val	p.A104V	ENST00000227507	NM_053056.2	104	gCc/gTc	2/5	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.76130320175478	2		451	743	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941313	71941313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs927834612	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	315	623	1	ENST00000298229.2:c.1088G>A	p.Arg363His	p.R363H	ENST00000298229	NM_001567.3	363	cGc/cAc	9/28	1	2	FACETS	0.926	0.876	0.976	0.926	0.876	0.976	CLONAL	1	TRUE	1	0.76130320175478	2		624	894	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77043912	77043912	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	217	517	0	ENST00000356341.3:c.1414G>A	p.Ala472Thr	p.A472T	ENST00000356341	NM_002576.4	472	Gcc/Acc	14/15	1	2	FACETS	0.821	0.767	0.877	0.821	0.767	0.877	CLONAL	1	TRUE	1	0.76130320175478	2		517	694	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94170371	94170371	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745614941	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	92	316	0	ENST00000323929.3:c.1898G>A	p.Arg633Gln	p.R633Q	ENST00000323929	NM_005591.3	633	cGa/cAa	17/20	1	2	FACETS	0.866	0.78	0.955	0.866	0.78	0.955	CLONAL	1	TRUE	1	0.76130320175478	2		316	279	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098413	108098413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1442769051	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	85	357	0	ENST00000278616.4:c.62C>T	p.Thr21Ile	p.T21I	ENST00000278616	NM_000051.3	21	aCa/aTa	2/63	1	2	FACETS	0.83	0.744	0.92	0.83	0.744	0.92	CLONAL	1	TRUE	1	0.76130320175478	2		357	269	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121727	108121727	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	209	523	0	ENST00000278616.4:c.1535T>G	p.Ile512Ser	p.I512S	ENST00000278616	NM_000051.3	512	aTt/aGt	10/63	1	2	FACETS	0.947	0.885	1	0.947	0.885	1	CLONAL	1	TRUE	1	0.76130320175478	2		523	580	SUCCESS
ATM	472	MSKCC	GRCh37	11	108128207	108128207	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	75	262	0	ENST00000278616.4:c.2251-1G>T		p.X751_splice	ENST00000278616	NM_000051.3	751			1	2	FACETS	0.758	0.672	0.847	0.758	0.672	0.847	SUBCLONAL	1	TRUE	1	0.76130320175478	2		262	260	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139166	108139166	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	135	476	0	ENST00000278616.4:c.2668C>A	p.Leu890Met	p.L890M	ENST00000278616	NM_000051.3	890	Ctg/Atg	18/63	1	2	FACETS	0.867	0.796	0.94	0.867	0.796	0.94	CLONAL	1	TRUE	1	0.76130320175478	2		476	409	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343982	118343982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	41	373	0	ENST00000534358.1:c.2108C>T	p.Thr703Ile	p.T703I	ENST00000534358	NM_005933.3	703	aCt/aTt	3/36	1	2	FACETS	0.234	0.195	0.278	0.234	0.195	0.278	SUBCLONAL	1	TRUE	1	0.76130320175478	2		373	460	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360843	118360843	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	123	224	0	ENST00000534358.1:c.4576-1G>T		p.X1526_splice	ENST00000534358	NM_005933.3	1526			1	2	FACETS	0.895	0.819	0.974	0.895	0.819	0.974	CLONAL	1	TRUE	1	0.76130320175478	2		224	361	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375159	118375159	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	168	343	0	ENST00000534358.1:c.8552A>G	p.Asp2851Gly	p.D2851G	ENST00000534358	NM_005933.3	2851	gAc/gGc	27/36	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.76130320175478	2		343	428	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375513	118375513	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	144	309	0	ENST00000534358.1:c.8906C>T	p.Ser2969Phe	p.S2969F	ENST00000534358	NM_005933.3	2969	tCt/tTt	27/36	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.76130320175478	2		309	355	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375933	118375933	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	194	462	0	ENST00000534358.1:c.9326C>A	p.Ser3109Tyr	p.S3109Y	ENST00000534358	NM_005933.3	3109	tCt/tAt	27/36	1	2	FACETS	0.894	0.833	0.957	0.894	0.833	0.957	CLONAL	1	TRUE	1	0.76130320175478	2		462	570	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156097	119156097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs747357424	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	356	648	0	ENST00000264033.4:c.1762G>T	p.Asp588Tyr	p.D588Y	ENST00000264033	NM_005188.3	588	Gac/Tac	11/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.76130320175478	2		648	913	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125496693	125496693	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	159	295	0	ENST00000428830.2:c.30C>A	p.Asp10Glu	p.D10E	ENST00000428830	NM_001114121.2	10	gaC/gaA	2/14	1	2	FACETS	0.893	0.825	0.962	0.893	0.825	0.962	CLONAL	1	TRUE	1	0.76130320175478	2		295	468	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497679	125497679	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	138	374	0	ENST00000428830.2:c.243T>G	p.Tyr81Ter	p.Y81*	ENST00000428830	NM_001114121.2	81	taT/taG	3/14	1	2	FACETS	0.977	0.9	1	0.977	0.9	1	CLONAL	1	TRUE	1	0.76130320175478	2		374	371	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475146	475146	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	196	546	0	ENST00000399788.2:c.491G>T	p.Arg164Ile	p.R164I	ENST00000399788	NM_001042603.1	164	aGa/aTa	4/28	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.76130320175478	2		546	515	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446936	18446936	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs377755015	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	15	284	0	ENST00000266497.5:c.1021G>T	p.Glu341Ter	p.E341*	ENST00000266497		341	Gaa/Taa	4/31	1	2	FACETS	0.147	0.107	0.195	0.147	0.107	0.195	SUBCLONAL	1	TRUE	1	0.76130320175478	2		284	268	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793432	18793432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs187869576	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	131	419	0	ENST00000266497.5:c.4129C>T	p.Arg1377Cys	p.R1377C	ENST00000266497		1377	Cgt/Tgt	30/31	1	2	FACETS	0.806	0.738	0.877	0.806	0.738	0.877	CLONAL	1	TRUE	1	0.76130320175478	2		419	427	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380283	25380283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913528	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	178	467	0	ENST00000311936.3:c.175G>A	p.Ala59Thr	p.A59T	ENST00000311936	NM_004985.3	59	Gca/Aca	3/5	1	2	FACETS	0.844	0.783	0.907	0.844	0.783	0.907	CLONAL	1	TRUE	1	0.76130320175478	2		467	554	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233172	46233172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376273452	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	35	316	0	ENST00000334344.6:c.1391C>T	p.Ala464Val	p.A464V	ENST00000334344	NM_152641.2	464	gCg/gTg	11/21	1	2	FACETS	0.213	0.174	0.256	0.213	0.174	0.256	SUBCLONAL	1	TRUE	1	0.76130320175478	2		316	432	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244164	46244164	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	183	401	0	ENST00000334344.6:c.2258C>A	p.Pro753His	p.P753H	ENST00000334344	NM_152641.2	753	cCt/cAt	15/21	1	2	FACETS	0.926	0.862	0.992	0.926	0.862	0.992	CLONAL	1	TRUE	1	0.76130320175478	2		401	519	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420090	49420090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746471452	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	272	541	1	ENST00000301067.7:c.15659G>A	p.Arg5220His	p.R5220H	ENST00000301067	NM_003482.3	5220	cGc/cAc	48/54	1	2	FACETS	0.982	0.926	1	0.982	0.926	1	CLONAL	1	TRUE	1	0.76130320175478	2		542	728	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420253	49420253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758730277	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	330	577	0	ENST00000301067.7:c.15496G>A	p.Ala5166Thr	p.A5166T	ENST00000301067	NM_003482.3	5166	Gct/Act	48/54	1	2	FACETS	0.906	0.858	0.954	0.906	0.858	0.954	CLONAL	1	TRUE	1	0.76130320175478	2		577	957	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436954	49436954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778359468	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	282	544	1	ENST00000301067.7:c.5549G>A	p.Gly1850Asp	p.G1850D	ENST00000301067	NM_003482.3	1850	gGc/gAc	25/54	1	2	FACETS	0.906	0.854	0.958	0.906	0.854	0.958	CLONAL	1	TRUE	1	0.76130320175478	2		545	818	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445330	49445330	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	110	902	1	ENST00000301067.7:c.2136G>T	p.Glu712Asp	p.E712D	ENST00000301067	NM_003482.3	712	gaG/gaT	10/54	1	2	FACETS	0.244	0.218	0.271	0.244	0.218	0.271	SUBCLONAL	1	TRUE	1	0.76130320175478	2		903	1186	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858918	57858918	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1019239130	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	345	611	0	ENST00000228682.2:c.414G>T	p.Gln138His	p.Q138H	ENST00000228682	NM_005269.2	138	caG/caT	5/12	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.76130320175478	2		611	881	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864237	57864237	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	279	499	0	ENST00000228682.2:c.1714G>T	p.Glu572Ter	p.E572*	ENST00000228682	NM_005269.2	572	Gag/Tag	12/12	1	2	FACETS	0.997	0.942	1	0.997	0.942	1	CLONAL	1	TRUE	1	0.76130320175478	2		499	735	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865509	57865509	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	326	696	1	ENST00000228682.2:c.2986C>T	p.Pro996Ser	p.P996S	ENST00000228682	NM_005269.2	996	Ccc/Tcc	12/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.76130320175478	2		697	834	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145356	58145356	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	336	582	0	ENST00000257904.6:c.145C>A	p.Leu49Ile	p.L49I	ENST00000257904	NM_000075.3	49	Ctt/Att	2/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.76130320175478	2		582	840	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811711	102811711	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	306	615	0	ENST00000307046.8:c.473G>T	p.Gly158Val	p.G158V	ENST00000307046	NM_001111285.1	158	gGa/gTa	4/4	1	2	FACETS	0.934	0.883	0.985	0.934	0.883	0.985	CLONAL	1	TRUE	1	0.76130320175478	2		615	861	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811775	102811775	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	227	447	0	ENST00000307046.8:c.409C>A	p.Pro137Thr	p.P137T	ENST00000307046	NM_001111285.1	137	Ccc/Acc	4/4	1	2	FACETS	0.976	0.916	1	0.976	0.916	1	CLONAL	1	TRUE	1	0.76130320175478	2		447	611	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813316	102813316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1404671399	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	46	450	0	ENST00000307046.8:c.373C>T	p.Arg125Cys	p.R125C	ENST00000307046	NM_001111285.1	125	Cgc/Tgc	3/4	1	2	FACETS	0.171	0.143	0.202	0.171	0.143	0.202	SUBCLONAL	1	TRUE	1	0.76130320175478	2		450	706	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856154	111856154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	205	237	1	ENST00000341259.2:c.205G>A	p.Asp69Asn	p.D69N	ENST00000341259	NM_005475.2	69	Gac/Aac	2/8	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.76130320175478	2		238	518	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112893803	112893803	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1223522089	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	160	378	1	ENST00000351677.2:c.692G>A	p.Arg231Gln	p.R231Q	ENST00000351677	NM_002834.3	231	cGa/cAa	6/16	1	2	FACETS	0.96	0.889	1	0.96	0.889	1	CLONAL	1	TRUE	1	0.76130320175478	2		379	438	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112034	115112034	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	365	664	0	ENST00000257566.3:c.1706G>T	p.Gly569Val	p.G569V	ENST00000257566	NM_016569.3	569	gGa/gTa	7/8	1	2	FACETS	0.985	0.937	1	0.985	0.937	1	CLONAL	1	TRUE	1	0.76130320175478	2		664	973	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120783945	120783945	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	251	530	0	ENST00000257552.2:c.1040G>T	p.Ser347Ile	p.S347I	ENST00000257552	NM_002442.3	347	aGt/aTt	13/15	1	2	FACETS	0.933	0.877	0.989	0.933	0.877	0.989	CLONAL	1	TRUE	1	0.76130320175478	2		530	707	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202740	133202740	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs5745068	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	279	542	0	ENST00000320574.5:c.6494G>A	p.Arg2165His	p.R2165H	ENST00000320574	NM_006231.2	2165	cGc/cAc	46/49	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.76130320175478	2		542	702	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219522	133219522	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	191	684	1	ENST00000320574.5:c.4612C>A	p.Leu1538Met	p.L1538M	ENST00000320574	NM_006231.2	1538	Ctg/Atg	36/49	1	2	FACETS	0.551	0.509	0.594	0.551	0.509	0.594	SUBCLONAL	1	TRUE	1	0.76130320175478	2		685	911	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249784	133249784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs951851739	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	67	460	0	ENST00000320574.5:c.1439C>T	p.Ala480Val	p.A480V	ENST00000320574	NM_006231.2	480	gCt/gTt	14/49	1	2	FACETS	0.254	0.22	0.291	0.254	0.22	0.291	SUBCLONAL	1	TRUE	1	0.76130320175478	2		460	693	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249847	133249847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	219	402	0	ENST00000320574.5:c.1376C>T	p.Ser459Phe	p.S459F	ENST00000320574	NM_006231.2	459	tCt/tTt	14/49	1	2	FACETS	0.977	0.915	1	0.977	0.915	1	CLONAL	1	TRUE	1	0.76130320175478	2		402	589	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253235	133253235	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	156	477	1	ENST00000320574.5:c.806C>T	p.Pro269Leu	p.P269L	ENST00000320574	NM_006231.2	269	cCt/cTt	9/49	1	2	FACETS	0.592	0.544	0.643	0.592	0.544	0.643	SUBCLONAL	1	TRUE	1	0.76130320175478	2		478	692	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257789	133257789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143626223	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	314	551	1	ENST00000320574.5:c.139C>T	p.Arg47Trp	p.R47W	ENST00000320574	NM_006231.2	47	Cgg/Tgg	2/49	1	2	FACETS	0.941	0.89	0.992	0.941	0.89	0.992	CLONAL	1	TRUE	1	0.76130320175478	2		552	877	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549320	21549320	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	358	655	1	ENST00000382592.4:c.2956C>A	p.Pro986Thr	p.P986T	ENST00000382592	NM_014572.2	986	Cca/Aca	8/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.76130320175478	2		656	908	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562610	21562610	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	140	176	0	ENST00000382592.4:c.1309G>A	p.Ala437Thr	p.A437T	ENST00000382592	NM_014572.2	437	Gcc/Acc	4/8	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.76130320175478	2		176	354	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622457	28622457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751562024	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	191	512	0	ENST00000241453.7:c.1160G>A	p.Arg387Gln	p.R387Q	ENST00000241453	NM_004119.2	387	cGa/cAa	9/24	1	2	FACETS	0.994	0.927	1	0.994	0.927	1	CLONAL	1	TRUE	1	0.76130320175478	2		512	505	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28880897	28880897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372046832	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	213	380	0	ENST00000282397.4:c.3733G>A	p.Asp1245Asn	p.D1245N	ENST00000282397	NM_002019.4	1245	Gac/Aac	29/30	1	2	FACETS	0.922	0.862	0.983	0.922	0.862	0.983	CLONAL	1	TRUE	1	0.76130320175478	2		380	607	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28885772	28885772	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	127	451	0	ENST00000282397.4:c.3590G>T	p.Ser1197Ile	p.S1197I	ENST00000282397	NM_002019.4	1197	aGt/aTt	27/30	1	2	FACETS	0.883	0.808	0.959	0.883	0.808	0.959	CLONAL	1	TRUE	1	0.76130320175478	2		451	378	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28886174	28886174	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	55	506	2	ENST00000282397.4:c.3448C>A	p.Leu1150Ile	p.L1150I	ENST00000282397	NM_002019.4	1150	Ctt/Att	26/30	1	2	FACETS	0.242	0.207	0.281	0.242	0.207	0.281	SUBCLONAL	1	TRUE	1	0.76130320175478	2		508	597	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28903769	28903769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	242	493	0	ENST00000282397.4:c.2690C>T	p.Ala897Val	p.A897V	ENST00000282397	NM_002019.4	897	gCc/gTc	19/30	1	2	FACETS	0.977	0.918	1	0.977	0.918	1	CLONAL	1	TRUE	1	0.76130320175478	2		493	651	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005329	29005329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	117	428	0	ENST00000282397.4:c.932G>A	p.Cys311Tyr	p.C311Y	ENST00000282397	NM_002019.4	311	tGt/tAt	7/30	1	2	FACETS	0.891	0.813	0.971	0.891	0.813	0.971	CLONAL	1	TRUE	1	0.76130320175478	2		428	345	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32890650	32890650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358762	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	65	274	0	ENST00000380152.3:c.53G>A	p.Arg18His	p.R18H	ENST00000380152		18	cGc/cAc	2/27	1	2	FACETS	0.589	0.515	0.667	0.589	0.515	0.667	SUBCLONAL	1	TRUE	1	0.76130320175478	2		274	290	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912948	32912948	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	192	488	1	ENST00000380152.3:c.4456G>T	p.Val1486Phe	p.V1486F	ENST00000380152		1486	Gtt/Ttt	11/27	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.76130320175478	2		489	471	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913044	32913044	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs397507727	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	187	581	2	ENST00000380152.3:c.4552G>T	p.Glu1518Ter	p.E1518*	ENST00000380152		1518	Gaa/Taa	11/27	1	2	FACETS	0.908	0.845	0.972	0.908	0.845	0.972	CLONAL	1	TRUE	1	0.76130320175478	2		583	541	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914947	32914947	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs80358881	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	109	425	0	ENST00000380152.3:c.6455C>A	p.Ser2152Tyr	p.S2152Y	ENST00000380152		2152	tCt/tAt	11/27	1	2	FACETS	0.93	0.846	1	0.93	0.846	1	CLONAL	1	TRUE	1	0.76130320175478	2		425	308	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240222	41240222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	51	77	0	ENST00000379561.5:c.128C>T	p.Ala43Val	p.A43V	ENST00000379561	NM_002015.3	43	gCg/gTg	1/3	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.76130320175478	2		77	118	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916850	48916850	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1131690843	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	89	259	0	ENST00000267163.4:c.380G>A	p.Ser127Asn	p.S127N	ENST00000267163	NM_000321.2	127	aGt/aAt	3/27	1	2	FACETS	0.943	0.85	1	0.943	0.85	1	CLONAL	1	TRUE	1	0.76130320175478	2		259	248	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48921968	48921968	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs587778826	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	101	274	1	ENST00000267163.4:c.508G>T	p.Glu170Ter	p.E170*	ENST00000267163	NM_000321.2	170	Gaa/Taa	5/27	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.76130320175478	2		275	264	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939055	48939055	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	109	311	0	ENST00000267163.4:c.887T>G	p.Phe296Cys	p.F296C	ENST00000267163	NM_000321.2	296	tTt/tGt	9/27	1	2	FACETS	0.984	0.897	1	0.984	0.897	1	CLONAL	1	TRUE	1	0.76130320175478	2		311	291	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050942	49050942	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143105337	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	155	378	0	ENST00000267163.4:c.2626C>T	p.Arg876Cys	p.R876C	ENST00000267163	NM_000321.2	876	Cgc/Tgc	25/27	1	2	FACETS	0.915	0.846	0.986	0.915	0.846	0.986	CLONAL	1	TRUE	1	0.76130320175478	2		378	445	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49054137	49054137	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	107	234	0	ENST00000267163.4:c.2717C>A	p.Ser906Tyr	p.S906Y	ENST00000267163	NM_000321.2	906	tCt/tAt	27/27	1	2	FACETS	0.89	0.808	0.974	0.89	0.808	0.974	CLONAL	1	TRUE	1	0.76130320175478	2		234	316	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281680	49281680	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	363	752	0	ENST00000282018.3:c.727A>G	p.Arg243Gly	p.R243G	ENST00000282018	NM_020377.2	243	Agg/Ggg	1/1	1	2	FACETS	0.943	0.896	0.991	0.943	0.896	0.991	CLONAL	1	TRUE	1	0.76130320175478	2		752	1011	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347875	73347875	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs917054849	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	45	315	0	ENST00000377767.4:c.1186C>T	p.Arg396Trp	p.R396W	ENST00000377767	NM_014953.3	396	Cgg/Tgg	8/21	1	2	FACETS	0.507	0.43	0.591	0.507	0.43	0.591	SUBCLONAL	1	TRUE	1	0.76130320175478	2		315	233	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436246	110436246	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	93	252	0	ENST00000375856.3:c.2155A>C	p.Thr719Pro	p.T719P	ENST00000375856	NM_003749.2	719	Aca/Cca	1/2	1	2	FACETS	0.756	0.68	0.836	0.756	0.68	0.836	SUBCLONAL	1	TRUE	1	0.76130320175478	2		252	323	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066913	30066913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	248	475	0	ENST00000331968.5:c.2218C>T	p.Arg740Trp	p.R740W	ENST00000331968	NM_002742.2	740	Cgg/Tgg	16/18	1	2	FACETS	0.957	0.9	1	0.957	0.9	1	CLONAL	1	TRUE	1	0.76130320175478	2		475	681	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987012	36987012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	237	454	0	ENST00000354822.5:c.677G>A	p.Ser226Asn	p.S226N	ENST00000354822	NM_001079668.2	226	aGc/aAc	3/3	1	2	FACETS	0.973	0.914	1	0.973	0.914	1	CLONAL	1	TRUE	1	0.76130320175478	2		454	640	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68301819	68301819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	186	365	0	ENST00000487270.1:c.221G>A	p.Arg74Lys	p.R74K	ENST00000487270	NM_133509.3	74	aGg/aAg	4/11	1	2	FACETS	0.9	0.837	0.964	0.9	0.837	0.964	CLONAL	1	TRUE	1	0.76130320175478	2		365	543	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105240263	105240263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1367895795	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	353	636	1	ENST00000349310.3:c.688G>A	p.Ala230Thr	p.A230T	ENST00000349310	NM_001014432.1	230	Gcc/Acc	9/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.76130320175478	2		637	875	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38617006	38617006	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	132	343	0	ENST00000299084.4:c.419T>C	p.Leu140Ser	p.L140S	ENST00000299084	NM_152594.2	140	tTa/tCa	4/7	1	2	FACETS	0.999	0.919	1	0.999	0.919	1	CLONAL	1	TRUE	1	0.76130320175478	2		343	347	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41023362	41023362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	182	397	0	ENST00000267868.3:c.1006G>A	p.Asp336Asn	p.D336N	ENST00000267868	NM_002875.4	336	Gat/Aat	10/10	1	2	FACETS	0.897	0.834	0.962	0.897	0.834	0.962	CLONAL	1	TRUE	1	0.76130320175478	2		397	533	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41962145	41962145	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	106	259	0	ENST00000219905.7:c.1053G>T	p.Glu351Asp	p.E351D	ENST00000219905	NM_001164273.1	351	gaG/gaT	2/24	1	2	FACETS	0.957	0.87	1	0.957	0.87	1	CLONAL	1	TRUE	1	0.76130320175478	2		259	291	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005460	42005460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	56	592	0	ENST00000219905.7:c.3196C>T	p.Arg1066Cys	p.R1066C	ENST00000219905	NM_001164273.1	1066	Cgc/Tgc	9/24	1	2	FACETS	0.154	0.131	0.179	0.154	0.131	0.179	SUBCLONAL	1	TRUE	1	0.76130320175478	2		592	956	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019407	42019407	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	200	459	0	ENST00000219905.7:c.3460G>A	p.Val1154Ile	p.V1154I	ENST00000219905	NM_001164273.1	1154	Gtt/Att	10/24	1	2	FACETS	0.98	0.916	1	0.98	0.916	1	CLONAL	1	TRUE	1	0.76130320175478	2		459	536	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707795	43707795	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	349	613	0	ENST00000382044.4:c.5086C>T	p.Pro1696Ser	p.P1696S	ENST00000382044	NM_001141980.1	1696	Cct/Tct	23/28	1	2	FACETS	0.994	0.945	1	0.994	0.945	1	CLONAL	1	TRUE	1	0.76130320175478	2		613	922	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727483	66727483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504317	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	231	484	0	ENST00000307102.5:c.199G>A	p.Asp67Asn	p.D67N	ENST00000307102	NM_002755.3	67	Gac/Aac	2/11	1	2	FACETS	0.902	0.845	0.959	0.902	0.845	0.959	CLONAL	1	TRUE	1	0.76130320175478	2		484	673	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994595	73994595	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	95	765	0	ENST00000318443.5:c.80-1G>T		p.X27_splice	ENST00000318443	NM_001024736.1	27			1	2	FACETS	0.25	0.222	0.281	0.25	0.222	0.281	SUBCLONAL	1	TRUE	1	0.76130320175478	2		765	997	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74000731	74000731	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	329	633	0	ENST00000318443.5:c.1421C>A	p.Ser474Tyr	p.S474Y	ENST00000318443	NM_001024736.1	474	tCt/tAt	7/10	1	2	FACETS	0.969	0.919	1	0.969	0.919	1	CLONAL	1	TRUE	1	0.76130320175478	2		633	892	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472559	88472559	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	239	472	1	ENST00000360948.2:c.1996G>A	p.Gly666Ser	p.G666S	ENST00000360948	NM_001012338.2	666	Ggt/Agt	16/19	1	2	FACETS	0.872	0.818	0.927	0.872	0.818	0.927	CLONAL	1	TRUE	1	0.76130320175478	2		473	720	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631671	90631671	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	328	611	0	ENST00000330062.3:c.598G>T	p.Asp200Tyr	p.D200Y	ENST00000330062	NM_002168.2	200	Gat/Tat	5/11	1	2	FACETS	0.992	0.941	1	0.992	0.941	1	CLONAL	1	TRUE	1	0.76130320175478	2		611	869	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292947	91292947	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	219	538	0	ENST00000355112.3:c.449C>A	p.Thr150Asn	p.T150N	ENST00000355112	NM_000057.2	150	aCc/aAc	3/22	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.76130320175478	2		538	575	SUCCESS
BLM	641	MSKCC	GRCh37	15	91352442	91352442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760554566	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	141	338	0	ENST00000355112.3:c.3827C>T	p.Ala1276Val	p.A1276V	ENST00000355112	NM_000057.2	1276	gCg/gTg	20/22	1	2	FACETS	0.82	0.753	0.888	0.82	0.753	0.888	CLONAL	1	TRUE	1	0.76130320175478	2		338	452	SUCCESS
BLM	641	MSKCC	GRCh37	15	91352490	91352490	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	37	238	1	ENST00000355112.3:c.3874+1G>A		p.X1292_splice	ENST00000355112	NM_000057.2	1292			1	2	FACETS	0.273	0.225	0.326	0.273	0.225	0.326	SUBCLONAL	1	TRUE	1	0.76130320175478	2		239	356	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	360049	360049	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	299	575	0	ENST00000262320.3:c.1040G>T	p.Arg347Met	p.R347M	ENST00000262320	NM_003502.3	347	aGg/aTg	4/11	1	2	FACETS	0.9	0.85	0.95	0.9	0.85	0.95	CLONAL	1	TRUE	1	0.76130320175478	2		575	873	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124246	2124246	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	189	703	0	ENST00000219476.3:c.2401G>A	p.Ala801Thr	p.A801T	ENST00000219476	NM_000548.3	801	Gcc/Acc	22/42	1	2	FACETS	0.484	0.447	0.523	0.484	0.447	0.523	SUBCLONAL	1	TRUE	1	0.76130320175478	2		703	1026	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213953	2213953	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759408599	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	368	640	1	ENST00000326181.6:c.32G>A	p.Arg11His	p.R11H	ENST00000326181	NM_032271.2	11	cGc/cAc	2/21	1	2	FACETS	0.968	0.92	1	0.968	0.92	1	CLONAL	1	TRUE	1	0.76130320175478	2		641	999	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778558	3778558	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	360	796	0	ENST00000262367.5:c.6490C>A	p.Leu2164Met	p.L2164M	ENST00000262367	NM_004380.2	2164	Ctg/Atg	31/31	1	2	FACETS	0.962	0.914	1	0.962	0.914	1	CLONAL	1	TRUE	1	0.76130320175478	2		796	983	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779676	3779676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1214172132	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	308	718	0	ENST00000262367.5:c.5372C>T	p.Ser1791Leu	p.S1791L	ENST00000262367	NM_004380.2	1791	tCg/tTg	31/31	1	2	FACETS	0.898	0.849	0.948	0.898	0.849	0.948	CLONAL	1	TRUE	1	0.76130320175478	2		718	901	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786130	3786130	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	322	650	0	ENST00000262367.5:c.4635G>A	p.Trp1545Ter	p.W1545*	ENST00000262367	NM_004380.2	1545	tgG/tgA	28/31	1	2	FACETS	0.994	0.942	1	0.994	0.942	1	CLONAL	1	TRUE	1	0.76130320175478	2		650	851	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900540	3900540	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	381	703	1	ENST00000262367.5:c.556C>T	p.Pro186Ser	p.P186S	ENST00000262367	NM_004380.2	186	Cca/Tca	2/31	1	2	FACETS	0.998	0.95	1	0.998	0.95	1	CLONAL	1	TRUE	1	0.76130320175478	2		704	1003	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858613	9858613	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	199	428	4	ENST00000330684.3:c.2788C>A	p.Leu930Ile	p.L930I	ENST00000330684	NM_001134407.1	930	Ctc/Atc	13/13	1	2	FACETS	0.935	0.873	0.999	0.935	0.873	0.999	CLONAL	1	TRUE	1	0.76130320175478	2		432	559	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934569	9934569	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	120	456	0	ENST00000330684.3:c.1586T>G	p.Val529Gly	p.V529G	ENST00000330684	NM_001134407.1	529	gTg/gGg	7/13	1	2	FACETS	0.514	0.465	0.566	0.514	0.465	0.566	SUBCLONAL	1	TRUE	1	0.76130320175478	2		456	613	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031919	10031919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs901717931	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	314	574	3	ENST00000330684.3:c.904G>A	p.Ala302Thr	p.A302T	ENST00000330684	NM_001134407.1	302	Gct/Act	3/13	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.76130320175478	2		577	729	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032083	10032083	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	296	575	0	ENST00000330684.3:c.740G>A	p.Gly247Asp	p.G247D	ENST00000330684	NM_001134407.1	247	gGc/gAc	3/13	1	2	FACETS	0.974	0.921	1	0.974	0.921	1	CLONAL	1	TRUE	1	0.76130320175478	2		575	798	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041657	14041657	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	212	423	0	ENST00000311895.7:c.2204C>A	p.Ser735Tyr	p.S735Y	ENST00000311895	NM_005236.2	735	tCt/tAt	11/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.76130320175478	2		423	557	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641274	23641274	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	307	648	0	ENST00000261584.4:c.2201C>T	p.Thr734Ile	p.T734I	ENST00000261584	NM_024675.3	734	aCt/aTt	5/13	1	2	FACETS	0.991	0.938	1	0.991	0.938	1	CLONAL	1	TRUE	1	0.76130320175478	2		648	814	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646440	23646440	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	265	575	0	ENST00000261584.4:c.1427G>T	p.Arg476Ile	p.R476I	ENST00000261584	NM_024675.3	476	aGa/aTa	4/13	1	2	FACETS	0.923	0.87	0.978	0.923	0.87	0.978	CLONAL	1	TRUE	1	0.76130320175478	2		575	754	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56878487	56878487	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752264053	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	222	353	0	ENST00000308159.5:c.2426C>T	p.Ala809Val	p.A809V	ENST00000308159	NM_014669.4	809	gCg/gTg	22/22	1	2	FACETS	0.921	0.863	0.981	0.921	0.863	0.981	CLONAL	1	TRUE	1	0.76130320175478	2		353	633	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063703	67063703	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	155	185	0	ENST00000412916.2:c.152G>T	p.Gly51Val	p.G51V	ENST00000412916		51	gGc/gTc	2/6	1	2	FACETS	0.899	0.83	0.969	0.899	0.83	0.969	CLONAL	1	TRUE	1	0.76130320175478	2		185	453	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655380	67655380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	199	461	1	ENST00000264010.4:c.1243C>T	p.Arg415Trp	p.R415W	ENST00000264010	NM_006565.3	415	Cgg/Tgg	7/12	1	2	FACETS	0.979	0.914	1	0.979	0.914	1	CLONAL	1	TRUE	1	0.76130320175478	2		462	534	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655431	67655431	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	244	513	0	ENST00000264010.4:c.1294G>T	p.Glu432Ter	p.E432*	ENST00000264010	NM_006565.3	432	Gaa/Taa	7/12	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.76130320175478	2		513	617	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829283	72829283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773115759	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	327	619	0	ENST00000268489.5:c.7298C>T	p.Ala2433Val	p.A2433V	ENST00000268489	NM_006885.3	2433	gCg/gTg	9/10	1	2	FACETS	0.901	0.854	0.95	0.901	0.854	0.95	CLONAL	1	TRUE	1	0.76130320175478	2		619	953	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830100	72830100	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs549883293	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	278	521	0	ENST00000268489.5:c.6481C>T	p.Arg2161Trp	p.R2161W	ENST00000268489	NM_006885.3	2161	Cgg/Tgg	9/10	1	2	FACETS	0.975	0.92	1	0.975	0.92	1	CLONAL	1	TRUE	1	0.76130320175478	2		521	749	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830895	72830895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770650936	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	62	510	0	ENST00000268489.5:c.5686G>A	p.Ala1896Thr	p.A1896T	ENST00000268489	NM_006885.3	1896	Gcc/Acc	9/10	1	2	FACETS	0.229	0.197	0.263	0.229	0.197	0.263	SUBCLONAL	1	TRUE	1	0.76130320175478	2		510	712	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992422	72992422	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs570223860	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	418	795	0	ENST00000268489.5:c.1623G>T	p.Gln541His	p.Q541H	ENST00000268489	NM_006885.3	541	caG/caT	2/10	1	2	FACETS	0.974	0.929	1	0.974	0.929	1	CLONAL	1	TRUE	1	0.76130320175478	2		795	1128	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81973535	81973535	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	201	484	0	ENST00000359376.3:c.3352G>T	p.Glu1118Ter	p.E1118*	ENST00000359376	NM_002661.3	1118	Gag/Tag	30/33	1	2	FACETS	0.886	0.826	0.947	0.886	0.826	0.947	CLONAL	1	TRUE	1	0.76130320175478	2		484	596	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351541	89351541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	347	734	0	ENST00000301030.4:c.1409G>A	p.Gly470Glu	p.G470E	ENST00000301030	NM_001256183.1	470	gGa/gAa	9/13	1	2	FACETS	0.964	0.915	1	0.964	0.915	1	CLONAL	1	TRUE	1	0.76130320175478	2		734	946	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805351	89805351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149851163	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	269	507	1	ENST00000389301.3:c.4199G>A	p.Arg1400His	p.R1400H	ENST00000389301	NM_000135.2	1400	cGt/cAt	42/43	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.76130320175478	2		508	702	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805355	89805355	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	257	496	1	ENST00000389301.3:c.4195G>T	p.Ala1399Ser	p.A1399S	ENST00000389301	NM_000135.2	1399	Gct/Tct	42/43	1	2	FACETS	0.963	0.907	1	0.963	0.907	1	CLONAL	1	TRUE	1	0.76130320175478	2		497	701	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831335	89831335	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	63	531	0	ENST00000389301.3:c.2741G>A	p.Arg914Lys	p.R914K	ENST00000389301	NM_000135.2	914	aGa/aAa	28/43	1	2	FACETS	0.221	0.19	0.254	0.221	0.19	0.254	SUBCLONAL	1	TRUE	1	0.76130320175478	2		531	749	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89837020	89837020	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	356	642	1	ENST00000389301.3:c.2174C>A	p.Ser725Tyr	p.S725Y	ENST00000389301	NM_000135.2	725	tCt/tAt	24/43	1	2	FACETS	0.969	0.921	1	0.969	0.921	1	CLONAL	1	TRUE	1	0.76130320175478	2		643	965	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89874709	89874709	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	266	514	0	ENST00000389301.3:c.589C>A	p.Leu197Met	p.L197M	ENST00000389301	NM_000135.2	197	Ctg/Atg	6/43	1	2	FACETS	0.885	0.833	0.938	0.885	0.833	0.938	CLONAL	1	TRUE	1	0.76130320175478	2		514	790	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216433	7216433	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774633910	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	341	694	0	ENST00000380728.2:c.815G>A	p.Arg272His	p.R272H	ENST00000380728		272	cGc/cAc	10/11	1	2	FACETS	0.978	0.928	1	0.978	0.928	1	CLONAL	1	TRUE	1	0.76130320175478	2		694	916	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216782	7216782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324992597	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	198	452	0	ENST00000380728.2:c.641C>T	p.Ser214Leu	p.S214L	ENST00000380728		214	tCg/tTg	8/11	1	2	FACETS	0.995	0.929	1	0.995	0.929	1	CLONAL	1	TRUE	1	0.76130320175478	2		452	523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	282	546	0	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	1	2	FACETS	0.945	0.892	0.999	0.945	0.892	0.999	CLONAL	1	TRUE	1	0.76130320175478	2		546	784	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138729528	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	346	630	0	ENST00000269305.4:c.523C>T	p.Arg175Cys	p.R175C	ENST00000269305	NM_001126112.2	175	Cgc/Tgc	5/11	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.76130320175478	2		630	909	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983766	15983766	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	64	427	1	ENST00000268712.3:c.3356C>A	p.Pro1119His	p.P1119H	ENST00000268712	NM_006311.3	1119	cCt/cAt	25/46	1	2	FACETS	0.243	0.21	0.279	0.243	0.21	0.279	SUBCLONAL	1	TRUE	1	0.76130320175478	2		428	692	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16062109	16062109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1373145988	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	226	425	0	ENST00000268712.3:c.697C>T	p.Arg233Cys	p.R233C	ENST00000268712	NM_006311.3	233	Cgc/Tgc	6/46	1	2	FACETS	0.848	0.794	0.904	0.848	0.794	0.904	CLONAL	1	TRUE	1	0.76130320175478	2		425	700	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131207	17131207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	398	722	1	ENST00000285071.4:c.245G>A	p.Cys82Tyr	p.C82Y	ENST00000285071	NM_144997.5	82	tGc/tAc	4/14	1	2	FACETS	0.978	0.932	1	0.978	0.932	1	CLONAL	1	TRUE	1	0.76130320175478	2		723	1069	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496916	29496916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	87	229	0	ENST00000356175.3:c.487G>A	p.Glu163Lys	p.E163K	ENST00000356175	NM_000267.3	163	Gaa/Aaa	5/57	1	2	FACETS	0.876	0.787	0.968	0.876	0.787	0.968	CLONAL	1	TRUE	1	0.76130320175478	2		229	261	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653100	29653100	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	199	328	0	ENST00000356175.3:c.5035C>A	p.Leu1679Ile	p.L1679I	ENST00000356175	NM_000267.3	1679	Ctc/Atc	36/57	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.76130320175478	2		328	488	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667643	29667643	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	172	372	0	ENST00000356175.3:c.6979C>A	p.Leu2327Ile	p.L2327I	ENST00000356175	NM_000267.3	2327	Ctc/Atc	46/57	1	2	FACETS	0.909	0.843	0.976	0.909	0.843	0.976	CLONAL	1	TRUE	1	0.76130320175478	2		372	497	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670081	29670081	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555535417	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	164	411	0	ENST00000356175.3:c.7054C>T	p.Gln2352Ter	p.Q2352*	ENST00000356175	NM_000267.3	2352	Caa/Taa	47/57	1	2	FACETS	0.997	0.925	1	0.997	0.925	1	CLONAL	1	TRUE	1	0.76130320175478	2		411	432	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676266	29676266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1484172751	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	96	283	1	ENST00000356175.3:c.7255G>A	p.Ala2419Thr	p.A2419T	ENST00000356175	NM_000267.3	2419	Gca/Aca	48/57	1	2	FACETS	0.879	0.794	0.967	0.879	0.794	0.967	CLONAL	1	TRUE	1	0.76130320175478	2		284	287	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	90	355	1	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.906	0.816	0.999	0.906	0.816	0.999	CLONAL	1	TRUE	1	0.76130320175478	2		356	261	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684332	29684332	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	169	451	2	ENST00000356175.3:c.7852C>A	p.Leu2618Ile	p.L2618I	ENST00000356175	NM_000267.3	2618	Ctt/Att	53/57	1	2	FACETS	0.967	0.898	1	0.967	0.898	1	CLONAL	1	TRUE	1	0.76130320175478	2		453	459	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428326	33428326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779808083	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	309	536	3	ENST00000345365.6:c.797G>A	p.Arg266His	p.R266H	ENST00000345365	NM_002878.3	266	cGc/cAc	9/10	1	2	FACETS	0.956	0.905	1	0.956	0.905	1	CLONAL	1	TRUE	1	0.76130320175478	2		539	849	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353848	40353848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1489641088	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	325	497	1	ENST00000293328.3:c.2272G>A	p.Asp758Asn	p.D758N	ENST00000293328	NM_012448.3	758	Gat/Aat	19/19	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.76130320175478	2		498	797	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375442	40375442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	80	536	0	ENST00000293328.3:c.508G>A	p.Glu170Lys	p.E170K	ENST00000293328	NM_012448.3	170	Gag/Aag	5/19	1	2	FACETS	0.239	0.21	0.271	0.239	0.21	0.271	SUBCLONAL	1	TRUE	1	0.76130320175478	2		536	878	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40478169	40478169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1288968449	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	49	544	0	ENST00000264657.5:c.1330G>A	p.Glu444Lys	p.E444K	ENST00000264657	NM_139276.2	444	Gag/Aag	15/24	1	2	FACETS	0.155	0.131	0.183	0.155	0.131	0.183	SUBCLONAL	1	TRUE	1	0.76130320175478	2		544	828	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485784	40485784	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	213	439	0	ENST00000264657.5:c.957-1G>T		p.X319_splice	ENST00000264657	NM_139276.2	319			1	2	FACETS	0.9	0.841	0.96	0.9	0.841	0.96	CLONAL	1	TRUE	1	0.76130320175478	2		439	622	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870552	40870552	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	377	635	0	ENST00000428826.2:c.851C>A	p.Ser284Tyr	p.S284Y	ENST00000428826		284	tCt/tAt	9/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.76130320175478	2		635	967	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234531	41234531	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	246	527	1	ENST00000357654.3:c.4247C>A	p.Ala1416Asp	p.A1416D	ENST00000357654	NM_007294.3	1416	gCt/gAt	12/23	1	2	FACETS	0.979	0.921	1	0.979	0.921	1	CLONAL	1	TRUE	1	0.76130320175478	2		528	660	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246374	41246374	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	209	580	2	ENST00000357654.3:c.1174C>A	p.Leu392Met	p.L392M	ENST00000357654	NM_007294.3	392	Ctg/Atg	10/23	1	2	FACETS	0.915	0.855	0.976	0.915	0.855	0.976	CLONAL	1	TRUE	1	0.76130320175478	2		582	600	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41251898	41251898	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	32	336	0	ENST00000357654.3:c.442-1G>A		p.X148_splice	ENST00000357654	NM_007294.3	148			1	2	FACETS	0.189	0.153	0.23	0.189	0.153	0.23	SUBCLONAL	1	TRUE	1	0.76130320175478	2		336	445	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256222	41256222	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	195	430	0	ENST00000357654.3:c.358G>T	p.Asp120Tyr	p.D120Y	ENST00000357654	NM_007294.3	120	Gat/Tat	6/23	1	2	FACETS	0.98	0.914	1	0.98	0.914	1	CLONAL	1	TRUE	1	0.76130320175478	2		430	523	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440951	56440951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777370273	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	72	525	1	ENST00000407977.2:c.386C>T	p.Ala129Val	p.A129V	ENST00000407977		129	gCg/gTg	4/10	1	2	FACETS	0.24	0.209	0.273	0.24	0.209	0.273	SUBCLONAL	1	TRUE	1	0.76130320175478	2		526	789	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774184	56774184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	152	353	0	ENST00000337432.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000337432	NM_058216.2	179	Cac/Tac	3/9	1	2	FACETS	0.92	0.85	0.992	0.92	0.85	0.992	CLONAL	1	TRUE	1	0.76130320175478	2		353	434	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761340	59761340	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	234	581	2	ENST00000259008.2:c.3067C>T	p.Leu1023Phe	p.L1023F	ENST00000259008	NM_032043.2	1023	Ctc/Ttc	20/20	1	2	FACETS	0.936	0.878	0.994	0.936	0.878	0.994	CLONAL	1	TRUE	1	0.76130320175478	2		583	657	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533860	63533860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751843834	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	258	552	0	ENST00000307078.5:c.1294G>A	p.Glu432Lys	p.E432K	ENST00000307078	NM_004655.3	432	Gag/Aag	6/11	1	2	FACETS	0.951	0.895	1	0.951	0.895	1	CLONAL	1	TRUE	1	0.76130320175478	2		552	713	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775251	73775251	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	42	382	0	ENST00000254810.4:c.5C>T	p.Ala2Val	p.A2V	ENST00000254810	NM_005324.3	2	gCc/gTc	2/4	1	2	FACETS	0.197	0.164	0.234	0.197	0.164	0.234	SUBCLONAL	1	TRUE	1	0.76130320175478	2		382	560	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867576	78867576	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1163896758	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	314	636	0	ENST00000306801.3:c.2312G>T	p.Ser771Ile	p.S771I	ENST00000306801	NM_020761.2	771	aGc/aTc	20/34	1	2	FACETS	0.933	0.883	0.984	0.933	0.883	0.984	CLONAL	1	TRUE	1	0.76130320175478	2		636	884	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756556	756556	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	160	328	0	ENST00000314574.4:c.271+1G>T		p.X91_splice	ENST00000314574	NM_005433.3	91			1	2	FACETS	0.973	0.901	1	0.973	0.901	1	CLONAL	1	TRUE	1	0.76130320175478	2		328	432	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375016	45375016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226662382	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	154	385	0	ENST00000262160.6:c.827C>T	p.Ser276Leu	p.S276L	ENST00000262160	NM_005901.5	276	tCg/tTg	8/11	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.76130320175478	2		385	402	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348505	56348505	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	162	289	0	ENST00000348428.3:c.313G>T	p.Glu105Ter	p.E105*	ENST00000348428	NM_006785.3	105	Gaa/Taa	2/17	1	2	FACETS	0.959	0.888	1	0.959	0.888	1	CLONAL	1	TRUE	1	0.76130320175478	2		289	444	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348545	56348545	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	147	271	0	ENST00000348428.3:c.353T>C	p.Val118Ala	p.V118A	ENST00000348428	NM_006785.3	118	gTt/gCt	2/17	1	2	FACETS	0.973	0.898	1	0.973	0.898	1	CLONAL	1	TRUE	1	0.76130320175478	2		271	397	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56377265	56377265	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	79	248	0	ENST00000348428.3:c.886C>T	p.Arg296Ter	p.R296*	ENST00000348428	NM_006785.3	296	Cga/Tga	6/17	1	2	FACETS	0.844	0.753	0.938	0.844	0.753	0.938	CLONAL	1	TRUE	1	0.76130320175478	2		248	246	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56383182	56383182	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	53	179	0	ENST00000348428.3:c.1001C>T	p.Thr334Ile	p.T334I	ENST00000348428	NM_006785.3	334	aCa/aTa	9/17	1	2	FACETS	0.564	0.485	0.648	0.564	0.485	0.648	SUBCLONAL	1	TRUE	1	0.76130320175478	2		179	247	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400688	56400688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140664950	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	111	295	2	ENST00000348428.3:c.1282G>A	p.Val428Ile	p.V428I	ENST00000348428	NM_006785.3	428	Gtt/Att	11/17	1	2	FACETS	0.886	0.806	0.969	0.886	0.806	0.969	CLONAL	1	TRUE	1	0.76130320175478	2		297	329	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220679	1220679	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781638	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	58	622	0	ENST00000326873.7:c.697G>A	p.Gly233Ser	p.G233S	ENST00000326873	NM_000455.4	233	Ggc/Agc	5/10	1	2	FACETS	0.175	0.15	0.203	0.175	0.15	0.203	SUBCLONAL	1	TRUE	1	0.76130320175478	2		622	869	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619347	1619347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	284	378	0	ENST00000344749.5:c.1294C>T	p.Pro432Ser	p.P432S	ENST00000344749	NM_001136139.2	432	Ccc/Tcc	15/19	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.76130320175478	2		378	715	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2193750	2193750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	52	607	0	ENST00000398665.3:c.556G>A	p.Glu186Lys	p.E186K	ENST00000398665	NM_032482.2	186	Gag/Aag	6/28	1	2	FACETS	0.148	0.125	0.173	0.148	0.125	0.173	SUBCLONAL	1	TRUE	1	0.76130320175478	2		607	923	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2206739	2206739	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	258	472	0	ENST00000398665.3:c.799G>A	p.Val267Met	p.V267M	ENST00000398665	NM_032482.2	267	Gtg/Atg	10/28	1	2	FACETS	0.905	0.851	0.96	0.905	0.851	0.96	CLONAL	1	TRUE	1	0.76130320175478	2		472	749	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222467	2222467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	256	437	0	ENST00000398665.3:c.3299G>A	p.Ser1100Asn	p.S1100N	ENST00000398665	NM_032482.2	1100	aGc/aAc	24/28	1	2	FACETS	0.979	0.922	1	0.979	0.922	1	CLONAL	1	TRUE	1	0.76130320175478	2		437	687	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210541	5210541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1440460687	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	335	608	0	ENST00000357368.4:c.5426C>T	p.Pro1809Leu	p.P1809L	ENST00000357368	NM_002850.3	1809	cCg/cTg	35/38	1	2	FACETS	0.997	0.946	1	0.997	0.946	1	CLONAL	1	TRUE	1	0.76130320175478	2		608	883	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221065	5221065	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	322	611	0	ENST00000357368.4:c.3401C>A	p.Ala1134Asp	p.A1134D	ENST00000357368	NM_002850.3	1134	gCt/gAt	20/38	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.76130320175478	2		611	817	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244070	5244070	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs945169302	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	384	668	3	ENST00000357368.4:c.1412C>A	p.Pro471His	p.P471H	ENST00000357368	NM_002850.3	471	cCc/cAc	11/38	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.76130320175478	2		671	992	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244185	5244185	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774952239	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	304	590	1	ENST00000357368.4:c.1297G>A	p.Val433Met	p.V433M	ENST00000357368	NM_002850.3	433	Gtg/Atg	11/38	1	2	FACETS	0.995	0.942	1	0.995	0.942	1	CLONAL	1	TRUE	1	0.76130320175478	2		591	803	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244359	5244359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	410	682	0	ENST00000357368.4:c.1123C>T	p.Pro375Ser	p.P375S	ENST00000357368	NM_002850.3	375	Ccg/Tcg	11/38	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.76130320175478	2		682	1042	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142844	7142844	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1135401738	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	237	502	0	ENST00000302850.5:c.2525C>T	p.Ala842Val	p.A842V	ENST00000302850	NM_000208.2	842	gCg/gTg	12/22	1	2	FACETS	0.871	0.816	0.926	0.871	0.816	0.926	CLONAL	1	TRUE	1	0.76130320175478	2		502	715	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267839	7267839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886044001	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	240	485	0	ENST00000302850.5:c.169G>A	p.Glu57Lys	p.E57K	ENST00000302850	NM_000208.2	57	Gaa/Aaa	2/22	1	2	FACETS	0.92	0.864	0.978	0.92	0.864	0.978	CLONAL	1	TRUE	1	0.76130320175478	2		485	685	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10284548	10284548	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	91	390	0	ENST00000340748.4:c.634C>T	p.Arg212Ter	p.R212*	ENST00000340748		212	Cga/Tga	7/40	1	2	FACETS	0.43	0.382	0.48	0.43	0.382	0.48	SUBCLONAL	1	TRUE	1	0.76130320175478	2		390	556	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597441	10597441	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	340	735	0	ENST00000171111.5:c.1762A>G	p.Thr588Ala	p.T588A	ENST00000171111	NM_203500.1	588	Aca/Gca	6/6	1	2	FACETS	0.877	0.832	0.924	0.877	0.832	0.924	CLONAL	1	TRUE	1	0.76130320175478	2		735	1018	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600385	10600385	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	371	748	0	ENST00000171111.5:c.1470C>A	p.Tyr490Ter	p.Y490*	ENST00000171111	NM_203500.1	490	taC/taA	4/6	1	2	FACETS	0.962	0.915	1	0.962	0.915	1	CLONAL	1	TRUE	1	0.76130320175478	2		748	1013	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602797	10602797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	432	745	1	ENST00000171111.5:c.781C>T	p.Arg261Trp	p.R261W	ENST00000171111	NM_203500.1	261	Cgg/Tgg	3/6	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.76130320175478	2		746	1118	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610463	10610463	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	61	714	1	ENST00000171111.5:c.247G>T	p.Val83Phe	p.V83F	ENST00000171111	NM_203500.1	83	Gtc/Ttc	2/6	1	2	FACETS	0.184	0.158	0.212	0.184	0.158	0.212	SUBCLONAL	1	TRUE	1	0.76130320175478	2		715	871	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11015752	11015752	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	219	387	0	ENST00000327064.4:c.346G>A	p.Asp116Asn	p.D116N	ENST00000327064	NM_199141.1	116	Gat/Aat	2/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.76130320175478	2		387	518	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135016	11135016	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	271	607	0	ENST00000358026.2:c.2983G>A	p.Val995Ile	p.V995I	ENST00000358026	NM_001128849.1	995	Gtc/Atc	21/36	1	2	FACETS	0.949	0.895	1	0.949	0.895	1	CLONAL	1	TRUE	1	0.76130320175478	2		607	750	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144798	11144798	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	229	397	1	ENST00000358026.2:c.3874-1G>T		p.X1292_splice	ENST00000358026	NM_001128849.1	1292			1	2	FACETS	0.883	0.828	0.94	0.883	0.828	0.94	CLONAL	1	TRUE	1	0.76130320175478	2		398	681	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271741	15271741	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1478958013	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	73	894	2	ENST00000263388.2:c.6698C>T	p.Ala2233Val	p.A2233V	ENST00000263388	NM_000435.2	2233	gCc/gTc	33/33	1	2	FACETS	0.161	0.14	0.184	0.161	0.14	0.184	SUBCLONAL	1	TRUE	1	0.76130320175478	2		896	1193	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288720	15288720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	31	29	0	ENST00000263388.2:c.4019C>T	p.Ala1340Val	p.A1340V	ENST00000263388	NM_000435.2	1340	gCg/gTg	24/33	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.76130320175478	2		29	69	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15378284	15378284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	47	449	0	ENST00000263377.2:c.502G>A	p.Glu168Lys	p.E168K	ENST00000263377	NM_058243.2	168	Gaa/Aaa	4/20	1	2	FACETS	0.185	0.155	0.217	0.185	0.155	0.217	SUBCLONAL	1	TRUE	1	0.76130320175478	2		449	669	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15379802	15379802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	207	420	0	ENST00000263377.2:c.337C>T	p.Arg113Cys	p.R113C	ENST00000263377	NM_058243.2	113	Cgc/Tgc	3/20	1	2	FACETS	0.951	0.889	1	0.951	0.889	1	CLONAL	1	TRUE	1	0.76130320175478	2		420	572	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383764	15383764	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	251	561	0	ENST00000263377.2:c.147G>T	p.Glu49Asp	p.E49D	ENST00000263377	NM_058243.2	49	gaG/gaT	2/20	1	2	FACETS	0.863	0.811	0.917	0.863	0.811	0.917	CLONAL	1	TRUE	1	0.76130320175478	2		561	764	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384996	17384996	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	305	665	0	ENST00000359435.4:c.544+2T>C		p.X182_splice	ENST00000359435	NM_001033549.1	182			1	2	FACETS	0.926	0.876	0.977	0.926	0.876	0.977	CLONAL	1	TRUE	1	0.76130320175478	2		665	865	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954701	17954701	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	379	651	0	ENST00000458235.1:c.193C>T	p.Pro65Ser	p.P65S	ENST00000458235	NM_000215.3	65	Cct/Tct	3/24	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.76130320175478	2		651	993	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266810	18266810	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	224	244	0	ENST00000222254.8:c.121C>A	p.Leu41Met	p.L41M	ENST00000222254	NM_005027.3	41	Ctg/Atg	2/16	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.76130320175478	2		244	476	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273060	18273060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	370	657	0	ENST00000222254.8:c.950C>T	p.Ala317Val	p.A317V	ENST00000222254	NM_005027.3	317	gCc/gTc	8/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.76130320175478	2		657	953	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279606	18279606	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	313	669	0	ENST00000222254.8:c.1879A>C	p.Ile627Leu	p.I627L	ENST00000222254	NM_005027.3	627	Atc/Ctc	15/16	1	2	FACETS	0.873	0.825	0.921	0.873	0.825	0.921	CLONAL	1	TRUE	1	0.76130320175478	2		669	942	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18956885	18956885	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	270	540	0	ENST00000262803.5:c.328G>T	p.Glu110Ter	p.E110*	ENST00000262803	NM_002911.3	110	Gaa/Taa	2/24	1	2	FACETS	0.909	0.857	0.963	0.909	0.857	0.963	CLONAL	1	TRUE	1	0.76130320175478	2		540	780	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961586	18961586	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	84	596	0	ENST00000262803.5:c.719C>A	p.Ser240Tyr	p.S240Y	ENST00000262803	NM_002911.3	240	tCc/tAc	5/24	1	2	FACETS	0.28	0.247	0.316	0.28	0.247	0.316	SUBCLONAL	1	TRUE	1	0.76130320175478	2		596	787	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974273	18974273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1053729454	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	271	506	2	ENST00000262803.5:c.2627C>T	p.Pro876Leu	p.P876L	ENST00000262803	NM_002911.3	876	cCg/cTg	19/24	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.76130320175478	2		508	711	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976403	18976403	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	99	819	0	ENST00000262803.5:c.3053G>A	p.Gly1018Glu	p.G1018E	ENST00000262803	NM_002911.3	1018	gGg/gAg	22/24	1	2	FACETS	0.233	0.207	0.261	0.233	0.207	0.261	SUBCLONAL	1	TRUE	1	0.76130320175478	2		819	1116	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256767	19256767	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	249	491	0	ENST00000162023.5:c.946G>T	p.Val316Phe	p.V316F	ENST00000162023		316	Gtc/Ttc	13/13	1	2	FACETS	0.972	0.914	1	0.972	0.914	1	CLONAL	1	TRUE	1	0.76130320175478	2		491	673	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256818	19256818	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs780254315	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	241	473	0	ENST00000162023.5:c.895C>A	p.Leu299Met	p.L299M	ENST00000162023		299	Ctg/Atg	13/13	1	2	FACETS	0.939	0.882	0.997	0.939	0.882	0.997	CLONAL	1	TRUE	1	0.76130320175478	2		473	674	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210901	36210901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1449929699	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	331	744	1	ENST00000222270.7:c.652C>T	p.Arg218Trp	p.R218W	ENST00000222270	NM_014727.1	218	Cgg/Tgg	3/37	1	2	FACETS	0.998	0.947	1	0.998	0.947	1	CLONAL	1	TRUE	1	0.76130320175478	2		745	871	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212258	36212258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762157346	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	351	628	0	ENST00000222270.7:c.2009C>T	p.Pro670Leu	p.P670L	ENST00000222270	NM_014727.1	670	cCt/cTt	3/37	1	2	FACETS	0.997	0.947	1	0.997	0.947	1	CLONAL	1	TRUE	1	0.76130320175478	2		628	925	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222925	36222925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746346674	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	460	837	0	ENST00000222270.7:c.5554G>A	p.Ala1852Thr	p.A1852T	ENST00000222270	NM_014727.1	1852	Gcc/Acc	27/37	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.76130320175478	2		837	1118	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224199	36224199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775887663	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	258	441	0	ENST00000222270.7:c.6749G>A	p.Arg2250His	p.R2250H	ENST00000222270	NM_014727.1	2250	cGc/cAc	28/37	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.76130320175478	2		441	634	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224406	36224406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226855044	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	413	744	0	ENST00000222270.7:c.6956G>A	p.Gly2319Asp	p.G2319D	ENST00000222270	NM_014727.1	2319	gGc/gAc	28/37	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.76130320175478	2		744	1079	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229435	36229435	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	260	491	0	ENST00000222270.7:c.8125C>T	p.Arg2709Cys	p.R2709C	ENST00000222270	NM_014727.1	2709	Cgc/Tgc	37/37	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.76130320175478	2		491	660	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40744850	40744850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1322643388	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	347	653	0	ENST00000392038.2:c.670C>T	p.Arg224Cys	p.R224C	ENST00000392038	NM_001626.4	224	Cgc/Tgc	8/14	1	2	FACETS	0.97	0.921	1	0.97	0.921	1	CLONAL	1	TRUE	1	0.76130320175478	2		653	940	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762394	41762394	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1347040167	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	47	638	0	ENST00000301178.4:c.2074G>A	p.Gly692Arg	p.G692R	ENST00000301178	NM_021913.4	692	Ggg/Agg	18/20	1	2	FACETS	0.14	0.118	0.166	0.14	0.118	0.166	SUBCLONAL	1	TRUE	1	0.76130320175478	2		638	879	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753319	42753319	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	454	858	0	ENST00000222329.4:c.945G>T	p.Gln315His	p.Q315H	ENST00000222329	NM_006494.2	315	caG/caT	4/4	1	2	FACETS	0.989	0.946	1	0.989	0.946	1	CLONAL	1	TRUE	1	0.76130320175478	2		858	1206	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42788897	42788897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs970360488	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	281	454	0	ENST00000575354.2:c.41C>T	p.Ala14Val	p.A14V	ENST00000575354	NM_015125.3	14	gCg/gTg	1/20	1	2	FACETS	0.998	0.942	1	0.998	0.942	1	CLONAL	1	TRUE	1	0.76130320175478	2		454	740	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793356	42793356	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	103	671	0	ENST00000575354.2:c.1158C>A	p.Tyr386Ter	p.Y386*	ENST00000575354	NM_015125.3	386	taC/taA	8/20	1	2	FACETS	0.36	0.322	0.401	0.36	0.322	0.401	SUBCLONAL	1	TRUE	1	0.76130320175478	2		671	751	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856394	45856394	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	372	664	0	ENST00000391945.4:c.1778G>A	p.Gly593Glu	p.G593E	ENST00000391945	NM_000400.3	593	gGg/gAg	19/23	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.76130320175478	2		664	955	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902267	50902267	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	404	850	1	ENST00000440232.2:c.159G>T	p.Gln53His	p.Q53H	ENST00000440232	NM_002691.3	53	caG/caT	2/27	1	2	FACETS	0.922	0.878	0.966	0.922	0.878	0.966	CLONAL	1	TRUE	1	0.76130320175478	2		851	1151	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905106	50905106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	356	716	0	ENST00000440232.2:c.388G>A	p.Val130Ile	p.V130I	ENST00000440232	NM_002691.3	130	Gtc/Atc	4/27	1	2	FACETS	0.934	0.887	0.982	0.934	0.887	0.982	CLONAL	1	TRUE	1	0.76130320175478	2		716	1001	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910328	50910328	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	334	779	0	ENST00000440232.2:c.1583T>C	p.Val528Ala	p.V528A	ENST00000440232	NM_002691.3	528	gTg/gCg	13/27	1	2	FACETS	0.922	0.874	0.97	0.922	0.874	0.97	CLONAL	1	TRUE	1	0.76130320175478	2		779	952	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919079	50919079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064795958	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	228	525	0	ENST00000440232.2:c.2816C>T	p.Ser939Leu	p.S939L	ENST00000440232	NM_002691.3	939	tCg/tTg	22/27	1	2	FACETS	0.987	0.926	1	0.987	0.926	1	CLONAL	1	TRUE	1	0.76130320175478	2		525	607	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921136	50921136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs963136799	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	327	620	1	ENST00000440232.2:c.3256C>T	p.Arg1086Trp	p.R1086W	ENST00000440232	NM_002691.3	1086	Cgg/Tgg	27/27	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.76130320175478	2		621	851	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723453	52723453	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	232	458	0	ENST00000322088.6:c.1314C>A	p.Phe438Leu	p.F438L	ENST00000322088	NM_014225.5	438	ttC/ttA	11/15	1	2	FACETS	0.964	0.905	1	0.964	0.905	1	CLONAL	1	TRUE	1	0.76130320175478	2		458	632	SUCCESS
ALK	238	MSKCC	GRCh37	2	29419652	29419652	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	204	422	0	ENST00000389048.3:c.4148T>G	p.Ile1383Ser	p.I1383S	ENST00000389048	NM_004304.4	1383	aTt/aGt	28/29	1	2	FACETS	0.954	0.891	1	0.954	0.891	1	CLONAL	1	TRUE	1	0.76130320175478	2		422	562	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213098	39213098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	416	738	2	ENST00000402219.2:c.3869C>T	p.Pro1290Leu	p.P1290L	ENST00000402219	NM_005633.3	1290	cCg/cTg	23/23	1	2	FACETS	0.957	0.913	1	0.957	0.913	1	CLONAL	1	TRUE	1	0.76130320175478	2		740	1142	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39237762	39237762	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	144	344	0	ENST00000402219.2:c.2473A>G	p.Ile825Val	p.I825V	ENST00000402219	NM_005633.3	825	Att/Gtt	15/23	1	2	FACETS	0.88	0.81	0.952	0.88	0.81	0.952	CLONAL	1	TRUE	1	0.76130320175478	2		344	430	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249900	39249900	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	194	543	0	ENST00000402219.2:c.1669A>G	p.Thr557Ala	p.T557A	ENST00000402219	NM_005633.3	557	Aca/Gca	10/23	1	2	FACETS	0.852	0.793	0.913	0.852	0.793	0.913	CLONAL	1	TRUE	1	0.76130320175478	2		543	598	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47607082	47607082	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	245	501	0	ENST00000263735.4:c.832G>T	p.Ala278Ser	p.A278S	ENST00000263735	NM_002354.2	278	Gca/Tca	7/9	1	2	FACETS	0.98	0.921	1	0.98	0.921	1	CLONAL	1	TRUE	1	0.76130320175478	2		501	657	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630414	47630414	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	300	658	0	ENST00000233146.2:c.84G>T	p.Glu28Asp	p.E28D	ENST00000233146	NM_000251.2	28	gaG/gaT	1/16	1	2	FACETS	0.953	0.901	1	0.953	0.901	1	CLONAL	1	TRUE	1	0.76130320175478	2		658	827	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703661	47703661	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1060502032	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	213	406	0	ENST00000233146.2:c.2161G>T	p.Gly721Ter	p.G721*	ENST00000233146	NM_000251.2	721	Gga/Tga	13/16	1	2	FACETS	0.968	0.906	1	0.968	0.906	1	CLONAL	1	TRUE	1	0.76130320175478	2		406	578	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023176	48023176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	203	426	0	ENST00000234420.5:c.601G>A	p.Glu201Lys	p.E201K	ENST00000234420	NM_000179.2	201	Gag/Aag	3/10	1	2	FACETS	0.915	0.854	0.977	0.915	0.854	0.977	CLONAL	1	TRUE	1	0.76130320175478	2		426	583	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027680	48027680	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	119	271	0	ENST00000234420.5:c.2558A>C	p.Lys853Thr	p.K853T	ENST00000234420	NM_000179.2	853	aAg/aCg	4/10	1	2	FACETS	0.974	0.891	1	0.974	0.891	1	CLONAL	1	TRUE	1	0.76130320175478	2		271	321	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033421	48033421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750119	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	137	446	1	ENST00000234420.5:c.3725G>A	p.Arg1242His	p.R1242H	ENST00000234420	NM_000179.2	1242	cGt/cAt	8/10	1	2	FACETS	0.863	0.793	0.936	0.863	0.793	0.936	CLONAL	1	TRUE	1	0.76130320175478	2		447	417	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033753	48033753	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1553333707	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	193	330	0	ENST00000234420.5:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000234420	NM_000179.2	1322	Gaa/Taa	9/10	1	2	FACETS	0.975	0.932	1	1	0.995	1	CLONAL	2	TRUE	1	0.76130320175478	2		330	260	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99169368	99169368	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	69	456	0	ENST00000074304.5:c.1298C>T	p.Ser433Leu	p.S433L	ENST00000074304	NM_001134224.1	433	tCa/tTa	15/26	1	2	FACETS	0.269	0.234	0.307	0.269	0.234	0.307	SUBCLONAL	1	TRUE	1	0.76130320175478	2		456	674	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182177	99182177	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	301	533	0	ENST00000074304.5:c.2242C>T	p.Gln748Ter	p.Q748*	ENST00000074304	NM_001134224.1	748	Cag/Tag	21/26	1	2	FACETS	0.98	0.927	1	0.98	0.927	1	CLONAL	1	TRUE	1	0.76130320175478	2		533	807	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182607	99182607	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	194	378	0	ENST00000074304.5:c.2410A>G	p.Asn804Asp	p.N804D	ENST00000074304	NM_001134224.1	804	Aat/Gat	22/26	1	2	FACETS	0.965	0.901	1	0.965	0.901	1	CLONAL	1	TRUE	1	0.76130320175478	2		378	528	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907686	111907686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370016302	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	220	360	0	ENST00000393256.3:c.460C>T	p.Arg154Cys	p.R154C	ENST00000393256	NM_006538.4	154	Cgt/Tgt	3/4	1	2	FACETS	0.897	0.84	0.956	0.897	0.84	0.956	CLONAL	1	TRUE	1	0.76130320175478	2		360	644	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873059	136873059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	195	398	2	ENST00000241393.3:c.439C>T	p.Pro147Ser	p.P147S	ENST00000241393	NM_003467.2	147	Cca/Tca	2/2	1	2	FACETS	0.991	0.925	1	0.991	0.925	1	CLONAL	1	TRUE	1	0.76130320175478	2		400	517	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098816	178098816	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	263	576	0	ENST00000397062.3:c.229G>T	p.Asp77Tyr	p.D77Y	ENST00000397062	NM_006164.4	77	Gat/Tat	2/5	1	2	FACETS	0.869	0.818	0.922	0.869	0.818	0.922	CLONAL	1	TRUE	1	0.76130320175478	2		576	795	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265533	198265533	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	136	505	0	ENST00000335508.6:c.2624T>G	p.Ile875Ser	p.I875S	ENST00000335508	NM_012433.2	875	aTt/aGt	18/25	1	2	FACETS	0.867	0.796	0.94	0.867	0.796	0.94	CLONAL	1	TRUE	1	0.76130320175478	2		505	412	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266767	198266767	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	218	490	0	ENST00000335508.6:c.2165A>C	p.Glu722Ala	p.E722A	ENST00000335508	NM_012433.2	722	gAa/gCa	15/25	1	2	FACETS	0.868	0.811	0.925	0.868	0.811	0.925	CLONAL	1	TRUE	1	0.76130320175478	2		490	660	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273245	198273245	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	248	498	0	ENST00000335508.6:c.965C>A	p.Ser322Tyr	p.S322Y	ENST00000335508	NM_012433.2	322	tCt/tAt	8/25	1	2	FACETS	0.951	0.894	1	0.951	0.894	1	CLONAL	1	TRUE	1	0.76130320175478	2		498	685	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735518	204735518	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	242	444	0	ENST00000302823.3:c.319T>C	p.Ser107Pro	p.S107P	ENST00000302823	NM_005214.4	107	Tcc/Ccc	2/4	1	2	FACETS	0.99	0.931	1	0.99	0.931	1	CLONAL	1	TRUE	1	0.76130320175478	2		444	642	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248588	212248588	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	225	444	0	ENST00000342788.4:c.3679C>A	p.Leu1227Met	p.L1227M	ENST00000342788	NM_005235.2	1227	Ctg/Atg	28/28	1	2	FACETS	0.858	0.803	0.914	0.858	0.803	0.914	CLONAL	1	TRUE	1	0.76130320175478	2		444	689	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285173	212285173	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754420079	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	121	416	0	ENST00000342788.4:c.3128C>T	p.Ser1043Leu	p.S1043L	ENST00000342788	NM_005235.2	1043	tCg/tTg	25/28	1	2	FACETS	0.99	0.907	1	0.99	0.907	1	CLONAL	1	TRUE	1	0.76130320175478	2		416	321	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215617254	215617254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757281184	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	70	313	0	ENST00000260947.4:c.1594G>A	p.Asp532Asn	p.D532N	ENST00000260947	NM_000465.2	532	Gat/Aat	7/11	1	2	FACETS	0.821	0.727	0.919	0.821	0.727	0.919	CLONAL	1	TRUE	1	0.76130320175478	2		313	224	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657143	215657143	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	94	306	0	ENST00000260947.4:c.242C>A	p.Thr81Asn	p.T81N	ENST00000260947	NM_000465.2	81	aCt/aAt	3/11	1	2	FACETS	0.939	0.848	1	0.939	0.848	1	CLONAL	1	TRUE	1	0.76130320175478	2		306	263	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379426	225379426	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	139	502	0	ENST00000264414.4:c.442C>T	p.Arg148Ter	p.R148*	ENST00000264414	NM_003590.4	148	Cga/Tga	4/16	1	2	FACETS	0.815	0.748	0.884	0.815	0.748	0.884	CLONAL	1	TRUE	1	0.76130320175478	2		502	448	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793427	242793427	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	52	649	0	ENST00000334409.5:c.650C>A	p.Pro217His	p.P217H	ENST00000334409	NM_005018.2	217	cCt/cAt	5/5	1	2	FACETS	0.16	0.135	0.187	0.16	0.135	0.187	SUBCLONAL	1	TRUE	1	0.76130320175478	2		649	855	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520265	9520265	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	166	352	0	ENST00000353224.5:c.2005-1G>A		p.X669_splice	ENST00000353224	NM_177990.2	669			1	2	FACETS	0.818	0.757	0.882	0.818	0.757	0.882	CLONAL	1	TRUE	1	0.76130320175478	2		352	533	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021439	31021439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs545224250	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	226	477	1	ENST00000375687.4:c.1438G>A	p.Glu480Lys	p.E480K	ENST00000375687	NM_015338.5	480	Gaa/Aaa	12/13	1	2	FACETS	0.922	0.864	0.981	0.922	0.864	0.981	CLONAL	1	TRUE	1	0.76130320175478	2		478	644	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022296	31022296	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	206	421	1	ENST00000375687.4:c.1781G>A	p.Cys594Tyr	p.C594Y	ENST00000375687	NM_015338.5	594	tGc/tAc	13/13	1	2	FACETS	0.965	0.902	1	0.965	0.902	1	CLONAL	1	TRUE	1	0.76130320175478	2		422	561	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024619	31024619	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	265	549	0	ENST00000375687.4:c.4104G>T	p.Lys1368Asn	p.K1368N	ENST00000375687	NM_015338.5	1368	aaG/aaT	13/13	1	2	FACETS	0.947	0.892	1	0.947	0.892	1	CLONAL	1	TRUE	1	0.76130320175478	2		549	735	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31390266	31390266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769823434	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	233	466	1	ENST00000328111.2:c.2221G>A	p.Gly741Arg	p.G741R	ENST00000328111	NM_006892.3	741	Ggg/Agg	20/23	1	2	FACETS	0.885	0.829	0.941	0.885	0.829	0.941	CLONAL	1	TRUE	1	0.76130320175478	2		467	692	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39726933	39726933	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	64	262	1	ENST00000361337.2:c.931G>T	p.Ala311Ser	p.A311S	ENST00000361337	NM_003286.2	311	Gcc/Tcc	11/21	1	2	FACETS	0.712	0.625	0.805	0.712	0.625	0.805	SUBCLONAL	1	TRUE	1	0.76130320175478	2		263	236	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750345	39750345	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	177	294	0	ENST00000361337.2:c.1960A>G	p.Lys654Glu	p.K654E	ENST00000361337	NM_003286.2	654	Aag/Gag	19/21	1	2	FACETS	0.989	0.92	1	0.989	0.92	1	CLONAL	1	TRUE	1	0.76130320175478	2		294	470	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980910	40980910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	46	425	0	ENST00000373198.4:c.1576G>A	p.Val526Ile	p.V526I	ENST00000373198	NM_133170.3	526	Gtc/Atc	10/32	1	2	FACETS	0.21	0.176	0.247	0.21	0.176	0.247	SUBCLONAL	1	TRUE	1	0.76130320175478	2		425	575	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46250994	46250994	+	start_lost	Translation_Start_Site	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	149	292	0	ENST00000371998.3:c.3G>T	p.Met1?	p.M1?	ENST00000371998		1	atG/atT	3/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.76130320175478	2		292	356	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262791	46262791	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	130	350	2	ENST00000371998.3:c.965-1G>T		p.X322_splice	ENST00000371998		322			1	2	FACETS	0.817	0.748	0.889	0.817	0.748	0.889	CLONAL	1	TRUE	1	0.76130320175478	2		352	418	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54948603	54948603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	124	300	0	ENST00000312783.6:c.715G>A	p.Glu239Lys	p.E239K	ENST00000312783	NM_198436.1	239	Gaa/Aaa	8/10	1	2	FACETS	0.931	0.852	1	0.931	0.852	1	CLONAL	1	TRUE	1	0.76130320175478	2		300	350	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485125	57485125	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	159	348	0	ENST00000371085.3:c.959C>A	p.Thr320Asn	p.T320N	ENST00000371085	NM_000516.4	320	aCt/aAt	11/13	1	2	FACETS	0.908	0.84	0.978	0.908	0.84	0.978	CLONAL	1	TRUE	1	0.76130320175478	2		348	460	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755543	39755543	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	198	478	0	ENST00000288319.7:c.1222C>A	p.Leu408Met	p.L408M	ENST00000288319	NM_182918.3	408	Ctg/Atg	10/10	1	2	FACETS	0.849	0.79	0.908	0.849	0.79	0.908	CLONAL	1	TRUE	1	0.76130320175478	2		478	613	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39772559	39772559	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	172	350	0	ENST00000288319.7:c.682G>T	p.Ala228Ser	p.A228S	ENST00000288319	NM_182918.3	228	Gct/Tct	6/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.76130320175478	2		350	439	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092931	29092931	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782268	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	190	494	0	ENST00000328354.6:c.1053G>T	p.Glu351Asp	p.E351D	ENST00000328354	NM_007194.3	351	gaG/gaT	10/15	1	2	FACETS	0.998	0.931	1	0.998	0.931	1	CLONAL	1	TRUE	1	0.76130320175478	2		494	500	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513352	41513352	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	272	504	1	ENST00000263253.7:c.256C>T	p.Arg86Ter	p.R86*	ENST00000263253	NM_001429.3	86	Cga/Tga	2/31	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.76130320175478	2		505	708	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513481	41513481	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	81	577	0	ENST00000263253.7:c.385G>A	p.Ala129Thr	p.A129T	ENST00000263253	NM_001429.3	129	Gca/Aca	2/31	1	2	FACETS	0.271	0.238	0.306	0.271	0.238	0.306	SUBCLONAL	1	TRUE	1	0.76130320175478	2		577	786	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556655	41556655	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	50	407	0	ENST00000263253.7:c.3600C>A	p.Phe1200Leu	p.F1200L	ENST00000263253	NM_001429.3	1200	ttC/ttA	20/31	1	2	FACETS	0.212	0.179	0.248	0.212	0.179	0.248	SUBCLONAL	1	TRUE	1	0.76130320175478	2		407	620	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12647733	12647733	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761703202	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	156	333	0	ENST00000251849.4:c.647G>A	p.Arg216His	p.R216H	ENST00000251849	NM_002880.3	216	cGt/cAt	6/17	1	2	FACETS	0.907	0.838	0.977	0.907	0.838	0.977	CLONAL	1	TRUE	1	0.76130320175478	2		333	452	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713436	30713436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751948498	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	307	474	1	ENST00000295754.5:c.761G>A	p.Arg254His	p.R254H	ENST00000295754	NM_003242.5	254	cGc/cAc	4/7	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.76130320175478	2		475	732	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158131	47158131	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	76	431	2	ENST00000409792.3:c.4568G>A	p.Arg1523His	p.R1523H	ENST00000409792	NM_014159.6	1523	cGt/cAt	4/21	1	2	FACETS	0.442	0.389	0.498	0.442	0.389	0.498	SUBCLONAL	1	TRUE	1	0.76130320175478	2		433	452	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721866	49721866	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	87	216	1	ENST00000449682.2:c.1897C>A	p.Leu633Ile	p.L633I	ENST00000449682	NM_020998.3	633	Cta/Ata	17/18	1	2	FACETS	0.925	0.832	1	0.925	0.832	1	CLONAL	1	TRUE	1	0.76130320175478	2		217	247	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723617	49723617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	107	161	0	ENST00000449682.2:c.1025G>A	p.Arg342Gln	p.R342Q	ENST00000449682	NM_020998.3	342	cGg/cAg	9/18	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.76130320175478	2		161	221	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934984	49934984	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	80	631	0	ENST00000296474.3:c.2015G>T	p.Gly672Val	p.G672V	ENST00000296474	NM_002447.2	672	gGc/gTc	6/20	1	2	FACETS	0.238	0.209	0.27	0.238	0.209	0.27	SUBCLONAL	1	TRUE	1	0.76130320175478	2		631	882	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940127	49940127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs553617101	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	327	629	1	ENST00000296474.3:c.916C>T	p.Arg306Cys	p.R306C	ENST00000296474	NM_002447.2	306	Cgc/Tgc	1/20	1	2	FACETS	0.894	0.847	0.942	0.894	0.847	0.942	CLONAL	1	TRUE	1	0.76130320175478	2		630	961	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637735	52637735	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	127	341	0	ENST00000394830.3:c.2581A>G	p.Ile861Val	p.I861V	ENST00000394830	NM_018313.4	861	Ata/Gta	18/30	1	2	FACETS	0.996	0.914	1	0.996	0.914	1	CLONAL	1	TRUE	1	0.76130320175478	2		341	335	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682413	52682413	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	111	327	0	ENST00000394830.3:c.760C>A	p.Leu254Ile	p.L254I	ENST00000394830	NM_018313.4	254	Ctc/Atc	8/30	1	2	FACETS	0.884	0.804	0.966	0.884	0.804	0.966	CLONAL	1	TRUE	1	0.76130320175478	2		327	330	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987054	69987054	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	285	528	0	ENST00000394351.3:c.115A>G	p.Thr39Ala	p.T39A	ENST00000394351	NM_000248.3	39	Act/Gct	2/9	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.76130320175478	2		528	745	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008542	70008542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202020443	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	219	346	0	ENST00000394351.3:c.829G>A	p.Ala277Thr	p.A277T	ENST00000394351	NM_000248.3	277	Gcc/Acc	8/9	1	2	FACETS	0.9	0.842	0.96	0.9	0.842	0.96	CLONAL	1	TRUE	1	0.76130320175478	2		346	639	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259607	89259607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	119	336	0	ENST00000336596.2:c.751C>T	p.Leu251Phe	p.L251F	ENST00000336596	NM_005233.5	251	Ctt/Ttt	3/17	1	2	FACETS	0.859	0.784	0.936	0.859	0.784	0.936	CLONAL	1	TRUE	1	0.76130320175478	2		336	364	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391030	89391030	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1188537096	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	264	517	0	ENST00000336596.2:c.1096T>C	p.Cys366Arg	p.C366R	ENST00000336596	NM_005233.5	366	Tgt/Cgt	5/17	1	2	FACETS	0.961	0.905	1	0.961	0.905	1	CLONAL	1	TRUE	1	0.76130320175478	2		517	722	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468516	89468516	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1453560937	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	117	553	0	ENST00000336596.2:c.2050C>T	p.Arg684Ter	p.R684*	ENST00000336596	NM_005233.5	684	Cga/Tga	11/17	1	2	FACETS	0.831	0.757	0.907	0.831	0.757	0.907	CLONAL	1	TRUE	1	0.76130320175478	2		553	370	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582302	119582302	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	197	275	0	ENST00000316626.5:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000316626		367	Cga/Tga	10/12	1	2	FACETS	0.99	0.924	1	0.99	0.924	1	CLONAL	1	TRUE	1	0.76130320175478	2		275	523	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670282	134670282	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748807854	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	243	499	0	ENST00000398015.3:c.193G>A	p.Glu65Lys	p.E65K	ENST00000398015	NM_004441.4	65	Gag/Aag	3/16	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.76130320175478	2		499	638	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911638	134911638	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	152	320	0	ENST00000398015.3:c.2103G>T	p.Glu701Asp	p.E701D	ENST00000398015	NM_004441.4	701	gaG/gaT	11/16	1	2	FACETS	0.83	0.765	0.897	0.83	0.765	0.897	CLONAL	1	TRUE	1	0.76130320175478	2		320	481	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272858	142272858	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	91	321	0	ENST00000350721.4:c.2342-1G>A		p.X781_splice	ENST00000350721	NM_001184.3	781			1	2	FACETS	0.952	0.86	1	0.952	0.86	1	CLONAL	1	TRUE	1	0.76130320175478	2		321	251	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	178	566	0	ENST00000263967.3:c.241G>T	p.Glu81Ter	p.E81*	ENST00000263967	NM_006218.2	81	Gaa/Taa	2/21	1	2	FACETS	0.843	0.782	0.905	0.843	0.782	0.905	CLONAL	1	TRUE	1	0.76130320175478	2		566	555	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936067	178936067	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	120	356	0	ENST00000263967.3:c.1609C>T	p.Arg537Ter	p.R537*	ENST00000263967	NM_006218.2	537	Cga/Tga	10/21	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.76130320175478	2		356	303	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937027	178937027	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	98	383	0	ENST00000263967.3:c.1708C>A	p.Leu570Met	p.L570M	ENST00000263967	NM_006218.2	570	Ctg/Atg	11/21	1	2	FACETS	0.83	0.75	0.914	0.83	0.75	0.914	CLONAL	1	TRUE	1	0.76130320175478	2		383	310	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947796	178947796	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	53	225	0	ENST00000263967.3:c.2671G>T	p.Asp891Tyr	p.D891Y	ENST00000263967	NM_006218.2	891	Gat/Tat	19/21	1	2	FACETS	0.834	0.725	0.948	0.834	0.725	0.948	CLONAL	1	TRUE	1	0.76130320175478	2		225	167	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430444	181430444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	357	518	0	ENST00000325404.1:c.296C>T	p.Ala99Val	p.A99V	ENST00000325404	NM_003106.3	99	gCg/gTg	1/1	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.76130320175478	2		518	855	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155301	185155301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140999720	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	157	431	0	ENST00000265026.3:c.542C>T	p.Ala181Val	p.A181V	ENST00000265026	NM_004721.4	181	gCg/gTg	3/14	1	2	FACETS	0.639	0.588	0.693	0.639	0.588	0.693	SUBCLONAL	1	TRUE	1	0.76130320175478	2		431	645	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184733	185184733	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	178	341	0	ENST00000265026.3:c.1625C>A	p.Ser542Tyr	p.S542Y	ENST00000265026	NM_004721.4	542	tCt/tAt	10/14	1	2	FACETS	0.97	0.902	1	0.97	0.902	1	CLONAL	1	TRUE	1	0.76130320175478	2		341	482	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506990	186506990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	113	223	0	ENST00000323963.5:c.1156C>T	p.Arg386Cys	p.R386C	ENST00000323963		386	Cgt/Tgt	11/11	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.76130320175478	2		223	292	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447660	187447660	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	332	637	0	ENST00000232014.4:c.533G>T	p.Arg178Ile	p.R178I	ENST00000232014	NM_001130845.1	178	aGa/aTa	5/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.76130320175478	2		637	870	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526092	189526092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	274	588	0	ENST00000264731.3:c.356G>A	p.Ser119Asn	p.S119N	ENST00000264731	NM_003722.4	119	aGc/aAc	4/14	1	2	FACETS	0.896	0.845	0.949	0.896	0.845	0.949	CLONAL	1	TRUE	1	0.76130320175478	2		588	803	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586455	189586455	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	237	465	0	ENST00000264731.3:c.1079G>T	p.Arg360Ile	p.R360I	ENST00000264731	NM_003722.4	360	aGa/aTa	8/14	1	2	FACETS	0.959	0.901	1	0.959	0.901	1	CLONAL	1	TRUE	1	0.76130320175478	2		465	649	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902586	1902586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1401743505	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	330	645	1	ENST00000382891.5:c.205G>A	p.Asp69Asn	p.D69N	ENST00000382891	NM_133335.3	69	Gac/Aac	2/22	1	2	FACETS	0.916	0.868	0.965	0.916	0.868	0.965	CLONAL	1	TRUE	1	0.76130320175478	2		646	946	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902589	1902589	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753748334	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	319	644	1	ENST00000382891.5:c.208G>A	p.Ala70Thr	p.A70T	ENST00000382891	NM_133335.3	70	Gcc/Acc	2/22	1	2	FACETS	0.883	0.836	0.931	0.883	0.836	0.931	CLONAL	1	TRUE	1	0.76130320175478	2		645	949	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747984	41747984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	49	69	0	ENST00000226382.2:c.785G>A	p.Gly262Asp	p.G262D	ENST00000226382	NM_003924.3	262	gGc/gAc	3/3	1	2	FACETS	0.947	0.821	1	0.947	0.821	1	CLONAL	1	TRUE	1	0.76130320175478	2		69	136	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138645	55138645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1031763557	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	244	411	0	ENST00000257290.5:c.1322C>T	p.Pro441Leu	p.P441L	ENST00000257290	NM_006206.4	441	cCg/cTg	9/23	1	2	FACETS	0.974	0.916	1	0.974	0.916	1	CLONAL	1	TRUE	1	0.76130320175478	2		411	658	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564641	55564641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	272	494	4	ENST00000288135.5:c.529C>T	p.Arg177Cys	p.R177C	ENST00000288135	NM_000222.2	177	Cgc/Tgc	3/21	1	2	FACETS	0.958	0.903	1	0.958	0.903	1	CLONAL	1	TRUE	1	0.76130320175478	2		498	746	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598161	55598161	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs202144208	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	157	314	0	ENST00000288135.5:c.2358G>T	p.Lys786Asn	p.K786N	ENST00000288135	NM_000222.2	786	aaG/aaT	16/21	1	2	FACETS	0.946	0.875	1	0.946	0.875	1	CLONAL	1	TRUE	1	0.76130320175478	2		314	436	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602667	55602667	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1330182390	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	28	248	1	ENST00000288135.5:c.2488C>T	p.Arg830Ter	p.R830*	ENST00000288135	NM_000222.2	830	Cga/Tga	18/21	1	2	FACETS	0.226	0.18	0.277	0.226	0.18	0.277	SUBCLONAL	1	TRUE	1	0.76130320175478	2		249	326	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946156	55946156	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	164	286	0	ENST00000263923.4:c.4023G>T	p.Gln1341His	p.Q1341H	ENST00000263923	NM_002253.2	1341	caG/caT	30/30	1	2	FACETS	0.881	0.815	0.948	0.881	0.815	0.948	CLONAL	1	TRUE	1	0.76130320175478	2		286	489	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981210	55981210	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	102	333	0	ENST00000263923.4:c.490-1G>T		p.X164_splice	ENST00000263923	NM_002253.2	164			1	2	FACETS	0.996	0.905	1	0.996	0.905	1	CLONAL	1	TRUE	1	0.76130320175478	2		333	269	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280112	66280112	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	111	281	0	ENST00000273854.3:c.1577C>T	p.Thr526Ile	p.T526I	ENST00000273854	NM_004439.5	526	aCt/aTt	7/18	1	2	FACETS	0.769	0.698	0.843	0.769	0.698	0.843	SUBCLONAL	1	TRUE	1	0.76130320175478	2		281	379	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356355	66356355	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	39	393	1	ENST00000273854.3:c.1142C>T	p.Ala381Val	p.A381V	ENST00000273854	NM_004439.5	381	gCt/gTt	5/18	1	2	FACETS	0.197	0.163	0.236	0.197	0.163	0.236	SUBCLONAL	1	TRUE	1	0.76130320175478	2		394	519	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99806158	99806158	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	69	252	0	ENST00000280892.6:c.514G>A	p.Ala172Thr	p.A172T	ENST00000280892	NM_001130678.1	172	Gct/Act	6/7	1	2	FACETS	0.809	0.716	0.907	0.809	0.716	0.907	CLONAL	1	TRUE	1	0.76130320175478	2		252	224	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003277	143003277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369778611	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	214	459	0	ENST00000262992.4:c.2549C>T	p.Ser850Leu	p.S850L	ENST00000262992	NM_001101669.1	850	tCg/tTg	23/24	1	2	FACETS	0.865	0.808	0.923	0.865	0.808	0.923	CLONAL	1	TRUE	1	0.76130320175478	2		459	650	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159105	143159105	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs763155133	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	112	353	3	ENST00000262992.4:c.748C>T	p.Arg250Ter	p.R250*	ENST00000262992	NM_001101669.1	250	Cga/Tga	10/24	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.76130320175478	2		356	284	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143181669	143181669	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	145	431	0	ENST00000262992.4:c.664G>T	p.Asp222Tyr	p.D222Y	ENST00000262992	NM_001101669.1	222	Gat/Tat	9/24	1	2	FACETS	0.967	0.892	1	0.967	0.892	1	CLONAL	1	TRUE	1	0.76130320175478	2		431	394	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143226689	143226689	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs149208667	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	145	303	0	ENST00000262992.4:c.425G>A	p.Arg142Gln	p.R142Q	ENST00000262992	NM_001101669.1	142	cGa/cAa	7/24	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.76130320175478	2		303	374	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258965	153258965	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	43	218	0	ENST00000281708.4:c.850C>T	p.Leu284Phe	p.L284F	ENST00000281708	NM_033632.3	284	Ctc/Ttc	5/12	1	2	FACETS	0.71	0.605	0.823	0.71	0.605	0.823	SUBCLONAL	1	TRUE	1	0.76130320175478	2		218	159	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527368	187527368	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	337	325	0	ENST00000441802.2:c.10207-1G>T		p.X3403_splice	ENST00000441802	NM_005245.3	3403			0.651404322563186	3	FACETS	0.984	0.941	1	0.984	0.941	1	CLONAL	2	TRUE	1	0.76130320175478	3		325	621	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539443	187539443	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	111	375	0	ENST00000441802.2:c.8297T>G	p.Leu2766Arg	p.L2766R	ENST00000441802	NM_005245.3	2766	cTt/cGt	10/27	0.651404322563186	3	FACETS	0.621	0.559	0.687	0.311	0.279	0.344	SUBCLONAL	1	TRUE	1	0.76130320175478	3		375	648	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539969	187539969	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	196	386	1	ENST00000441802.2:c.7771G>T	p.Asp2591Tyr	p.D2591Y	ENST00000441802	NM_005245.3	2591	Gac/Tac	10/27	0.651404322563186	3	FACETS	1	0.947	1	0.511	0.475	0.549	CLONAL	1	TRUE	1	0.76130320175478	3		387	695	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542246	187542246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	212	369	0	ENST00000441802.2:c.5494G>A	p.Val1832Ile	p.V1832I	ENST00000441802	NM_005245.3	1832	Gta/Ata	10/27	0.651404322563186	3	FACETS	0.834	0.784	0.884	0.834	0.784	0.884	CLONAL	2	TRUE	1	0.76130320175478	3		369	461	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224587	224587	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	297	522	0	ENST00000264932.6:c.263C>T	p.Ala88Val	p.A88V	ENST00000264932	NM_004168.2	88	gCa/gTa	3/15	1	2	FACETS	0.941	0.89	0.994	0.941	0.89	0.994	CLONAL	1	TRUE	1	0.76130320175478	2		522	829	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224599	224599	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	242	445	0	ENST00000264932.6:c.275A>T	p.Lys92Met	p.K92M	ENST00000264932	NM_004168.2	92	aAg/aTg	3/15	1	2	FACETS	0.945	0.887	1	0.945	0.887	1	CLONAL	1	TRUE	1	0.76130320175478	2		445	673	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224636	224636	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	92	186	0	ENST00000264932.6:c.312G>T	p.Gln104His	p.Q104H	ENST00000264932	NM_004168.2	104	caG/caT	3/15	1	2	FACETS	0.967	0.873	1	0.967	0.873	1	CLONAL	1	TRUE	1	0.76130320175478	2		186	250	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225634	225634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1342456775	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	266	456	0	ENST00000264932.6:c.413C>T	p.Ala138Val	p.A138V	ENST00000264932	NM_004168.2	138	gCc/gTc	4/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.76130320175478	2		456	683	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233697	233697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765180271	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	306	470	0	ENST00000264932.6:c.1001C>T	p.Ala334Val	p.A334V	ENST00000264932	NM_004168.2	334	gCg/gTg	8/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.76130320175478	2		470	731	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31424539	31424539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	305	638	0	ENST00000344624.3:c.3256C>T	p.Leu1086Phe	p.L1086F	ENST00000344624		1086	Ctc/Ttc	25/33	1	2	FACETS	0.939	0.889	0.991	0.939	0.889	0.991	CLONAL	1	TRUE	1	0.76130320175478	2		638	853	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950727	38950727	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1364147652	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	69	253	0	ENST00000357387.3:c.3223C>T	p.Arg1075Ter	p.R1075*	ENST00000357387	NM_152756.3	1075	Cga/Tga	31/38	1	2	FACETS	0.813	0.719	0.911	0.813	0.719	0.911	CLONAL	1	TRUE	1	0.76130320175478	2		253	223	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168704	56168704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	40	354	0	ENST00000399503.3:c.1558C>T	p.Gln520Ter	p.Q520*	ENST00000399503	NM_005921.1	520	Cag/Tag	9/20	1	2	FACETS	0.181	0.15	0.216	0.181	0.15	0.216	SUBCLONAL	1	TRUE	1	0.76130320175478	2		354	581	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176614	56176614	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	160	340	0	ENST00000399503.3:c.2164G>T	p.Glu722Ter	p.E722*	ENST00000399503	NM_005921.1	722	Gaa/Taa	12/20	1	2	FACETS	0.847	0.783	0.914	0.847	0.783	0.914	CLONAL	1	TRUE	1	0.76130320175478	2		340	496	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177447	56177447	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	141	312	0	ENST00000399503.3:c.2420A>C	p.Asn807Thr	p.N807T	ENST00000399503	NM_005921.1	807	aAt/aCt	14/20	1	2	FACETS	0.915	0.842	0.989	0.915	0.842	0.989	CLONAL	1	TRUE	1	0.76130320175478	2		312	405	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754564	57754564	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	116	371	0	ENST00000274289.3:c.483C>A	p.Tyr161Ter	p.Y161*	ENST00000274289	NM_006622.3	161	taC/taA	3/14	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.76130320175478	2		371	300	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522532	67522532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767837787	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	61	177	0	ENST00000274335.5:c.29C>T	p.Ala10Val	p.A10V	ENST00000274335		10	gCg/gTg	1/15	1	2	FACETS	0.7	0.612	0.793	0.7	0.612	0.793	SUBCLONAL	1	TRUE	1	0.76130320175478	2		177	229	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589609	67589609	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	81	235	0	ENST00000274335.5:c.1372G>T	p.Glu458Ter	p.E458*	ENST00000274335		458	Gaa/Taa	10/15	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.76130320175478	2		235	211	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589618	67589618	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519838	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	70	232	0	ENST00000274335.5:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000274335		461	Cga/Tga	10/15	1	2	FACETS	0.863	0.765	0.965	0.863	0.765	0.965	CLONAL	1	TRUE	1	0.76130320175478	2		232	213	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593382	67593382	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	68	212	0	ENST00000274335.5:c.2128C>A	p.Leu710Ile	p.L710I	ENST00000274335		710	Ctc/Atc	15/15	1	2	FACETS	0.503	0.44	0.57	0.503	0.44	0.57	SUBCLONAL	1	TRUE	1	0.76130320175478	2		212	355	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564335	86564335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	224	378	1	ENST00000274376.6:c.67G>A	p.Ala23Thr	p.A23T	ENST00000274376	NM_002890.2	23	Gcg/Acg	1/25	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.76130320175478	2		379	514	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564734	86564734	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	204	665	1	ENST00000274376.6:c.466G>T	p.Gly156Cys	p.G156C	ENST00000274376	NM_002890.2	156	Ggt/Tgt	1/25	1	2	FACETS	0.618	0.574	0.664	0.618	0.574	0.664	SUBCLONAL	1	TRUE	1	0.76130320175478	2		666	867	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628362	86628362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	81	280	0	ENST00000274376.6:c.731G>A	p.Arg244Lys	p.R244K	ENST00000274376	NM_002890.2	244	aGa/aAa	3/25	1	2	FACETS	0.872	0.78	0.967	0.872	0.78	0.967	CLONAL	1	TRUE	1	0.76130320175478	2		280	244	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629147	86629147	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	94	279	0	ENST00000274376.6:c.892G>T	p.Glu298Ter	p.E298*	ENST00000274376	NM_002890.2	298	Gaa/Taa	4/25	1	2	FACETS	0.915	0.826	1	0.915	0.826	1	CLONAL	1	TRUE	1	0.76130320175478	2		279	270	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86686620	86686620	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373643445	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	93	233	1	ENST00000274376.6:c.3064G>A	p.Val1022Ile	p.V1022I	ENST00000274376	NM_002890.2	1022	Gta/Ata	25/25	1	2	FACETS	0.817	0.735	0.902	0.817	0.735	0.902	CLONAL	1	TRUE	1	0.76130320175478	2		234	299	SUCCESS
APC	324	MSKCC	GRCh37	5	112154923	112154923	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	66	605	0	ENST00000257430.4:c.1194G>T	p.Lys398Asn	p.K398N	ENST00000257430	NM_000038.5	398	aaG/aaT	10/16	1	2	FACETS	0.205	0.177	0.235	0.205	0.177	0.235	SUBCLONAL	1	TRUE	1	0.76130320175478	2		605	847	SUCCESS
APC	324	MSKCC	GRCh37	5	112162851	112162851	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747739964	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	102	411	0	ENST00000257430.4:c.1455G>A	p.Met485Ile	p.M485I	ENST00000257430	NM_000038.5	485	atG/atA	12/16	1	2	FACETS	0.896	0.812	0.983	0.896	0.812	0.983	CLONAL	1	TRUE	1	0.76130320175478	2		411	299	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	25	309	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.137	0.107	0.171	0.137	0.107	0.171	SUBCLONAL	1	TRUE	1	0.76130320175478	2		310	480	SUCCESS
APC	324	MSKCC	GRCh37	5	112176234	112176234	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	229	460	0	ENST00000257430.4:c.4943C>A	p.Pro1648His	p.P1648H	ENST00000257430	NM_000038.5	1648	cCt/cAt	16/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.76130320175478	2		460	580	SUCCESS
APC	324	MSKCC	GRCh37	5	112178025	112178025	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	216	414	0	ENST00000257430.4:c.6734C>A	p.Pro2245His	p.P2245H	ENST00000257430	NM_000038.5	2245	cCt/cAt	16/16	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.76130320175478	2		414	559	SUCCESS
APC	324	MSKCC	GRCh37	5	112179635	112179635	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	52	384	0	ENST00000257430.4:c.8344A>G	p.Thr2782Ala	p.T2782A	ENST00000257430	NM_000038.5	2782	Act/Gct	16/16	1	2	FACETS	0.269	0.229	0.313	0.269	0.229	0.313	SUBCLONAL	1	TRUE	1	0.76130320175478	2		384	508	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915032	131915032	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	112	339	0	ENST00000265335.6:c.389G>A	p.Ser130Asn	p.S130N	ENST00000265335		130	aGc/aAc	4/25	1	2	FACETS	0.873	0.795	0.954	0.873	0.795	0.954	CLONAL	1	TRUE	1	0.76130320175478	2		339	337	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503914	149503914	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56339845	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	58	521	0	ENST00000261799.4:c.1922G>A	p.Arg641His	p.R641H	ENST00000261799	NM_002609.3	641	cGc/cAc	14/23	1	2	FACETS	0.23	0.197	0.266	0.23	0.197	0.266	SUBCLONAL	1	TRUE	1	0.76130320175478	2		521	662	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505007	149505007	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	149	322	0	ENST00000261799.4:c.1807+1G>A		p.X603_splice	ENST00000261799	NM_002609.3	603			1	2	FACETS	0.955	0.882	1	0.955	0.882	1	CLONAL	1	TRUE	1	0.76130320175478	2		322	410	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514342	149514342	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	199	459	0	ENST00000261799.4:c.602C>A	p.Ser201Tyr	p.S201Y	ENST00000261799	NM_002609.3	201	tCt/tAt	4/23	1	2	FACETS	0.942	0.879	1	0.942	0.879	1	CLONAL	1	TRUE	1	0.76130320175478	2		459	555	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514472	149514472	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	299	571	0	ENST00000261799.4:c.472G>A	p.Val158Met	p.V158M	ENST00000261799	NM_002609.3	158	Gtg/Atg	4/23	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.76130320175478	2		571	752	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818375	170818375	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	161	239	0	ENST00000296930.5:c.205G>T	p.Gly69Cys	p.G69C	ENST00000296930	NM_002520.6	69	Ggc/Tgc	3/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.76130320175478	2		239	357	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819785	170819785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	167	323	0	ENST00000296930.5:c.424C>T	p.Arg142Trp	p.R142W	ENST00000296930	NM_002520.6	142	Cgg/Tgg	5/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.76130320175478	2		323	420	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523708	176523708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	342	736	0	ENST00000292408.4:c.2119C>T	p.Arg707Trp	p.R707W	ENST00000292408	NM_213647.1	707	Cgg/Tgg	16/18	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.76130320175478	2		736	876	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562130	176562130	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	222	472	0	ENST00000439151.2:c.26G>T	p.Arg9Ile	p.R9I	ENST00000439151	NM_022455.4	9	aGa/aTa	2/23	1	2	FACETS	0.935	0.875	0.995	0.935	0.875	0.995	CLONAL	1	TRUE	1	0.76130320175478	2		472	624	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639098	176639098	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774868314	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	145	494	0	ENST00000439151.2:c.3698G>A	p.Arg1233Gln	p.R1233Q	ENST00000439151	NM_022455.4	1233	cGg/cAg	5/23	1	2	FACETS	0.507	0.463	0.553	0.507	0.463	0.553	SUBCLONAL	1	TRUE	1	0.76130320175478	2		494	752	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639128	176639128	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1383897418	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	272	511	1	ENST00000439151.2:c.3728G>T	p.Ser1243Ile	p.S1243I	ENST00000439151	NM_022455.4	1243	aGc/aTc	5/23	1	2	FACETS	0.932	0.878	0.986	0.932	0.878	0.986	CLONAL	1	TRUE	1	0.76130320175478	2		512	767	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180050997	180050997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	396	737	0	ENST00000261937.6:c.1486G>A	p.Asp496Asn	p.D496N	ENST00000261937	NM_182925.4	496	Gat/Aat	11/30	1	2	FACETS	0.989	0.942	1	0.989	0.942	1	CLONAL	1	TRUE	1	0.76130320175478	2		737	1052	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393304	393304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	325	401	0	ENST00000380956.4:c.152G>A	p.Arg51His	p.R51H	ENST00000380956	NM_001195286.1	51	cGc/cAc	2/9	0.76130320175478	2	FACETS	1	0.981	1	0.533	0.506	0.56	CLONAL	1	TRUE	0	0.76130320175478	2		401	801	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045864	26045864	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	81	545	2	ENST00000540144.1:c.226G>A	p.Ala76Thr	p.A76T	ENST00000540144	NM_003531.2	76	Gcc/Acc	1/1	0.76130320175478	2	FACETS	0.286	0.252	0.324	0.143	0.126	0.162	SUBCLONAL	1	TRUE	0	0.76130320175478	2		547	743	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197183	26197183	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	267	526	0	ENST00000356476.2:c.296C>T	p.Ala99Val	p.A99V	ENST00000356476		99	gCc/gTc	1/1	0.76130320175478	2	FACETS	1	0.984	1	0.552	0.522	0.583	CLONAL	1	TRUE	0	0.76130320175478	2		526	635	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671841	30671841	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	64	710	0	ENST00000376406.3:c.5119G>T	p.Asp1707Tyr	p.D1707Y	ENST00000376406	NM_014641.2	1707	Gac/Tac	10/15	0.76130320175478	2	FACETS	0.178	0.153	0.205	0.089	0.076	0.103	SUBCLONAL	1	TRUE	0	0.76130320175478	2		710	946	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679915	30679915	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	200	410	1	ENST00000376406.3:c.1804G>A	p.Ala602Thr	p.A602T	ENST00000376406	NM_014641.2	602	Gca/Aca	5/15	0.76130320175478	2	FACETS	1	0.955	1	0.513	0.48	0.547	CLONAL	1	TRUE	0	0.76130320175478	2		411	512	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324540	31324540	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs151341192	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	501	699	0	ENST00000412585.2:c.268A>C	p.Ile90Leu	p.I90L	ENST00000412585	NM_005514.6	90	Atc/Ctc	2/8	0.76130320175478	2	FACETS	1	0.986	1	0.529	0.508	0.552	CLONAL	1	TRUE	0	0.76130320175478	2		699	1243	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184977	32184977	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	648	626	0	ENST00000375023.3:c.1691G>T	p.Gly564Val	p.G564V	ENST00000375023	NM_004557.3	564	gGg/gTg	10/30	0.76130320175478	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.76130320175478	2		626	845	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805548	32805548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763454543	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	444	723	0	ENST00000374899.4:c.463G>A	p.Ala155Thr	p.A155T	ENST00000374899	NM_018833.2	155	Gcc/Acc	2/12	0.76130320175478	2	FACETS	1	0.987	1	0.538	0.515	0.562	CLONAL	1	TRUE	0	0.76130320175478	2		723	1084	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821568	32821568	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	52	743	1	ENST00000354258.4:c.26G>T	p.Gly9Val	p.G9V	ENST00000354258	NM_000593.5	9	gGa/gTa	1/11	0.76130320175478	2	FACETS	0.15	0.127	0.175	0.075	0.063	0.088	SUBCLONAL	1	TRUE	0	0.76130320175478	2		744	913	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288743	33288743	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs533137350	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	219	449	0	ENST00000374542.5:c.809G>A	p.Arg270His	p.R270H	ENST00000374542	NM_001141970.1	270	cGc/cAc	3/8	0.76130320175478	2	FACETS	0.948	0.888	1	0.474	0.444	0.505	CLONAL	1	TRUE	0	0.76130320175478	2		449	607	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138924	37138924	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1561983108	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	289	580	0	ENST00000373509.5:c.264G>T	p.Met88Ile	p.M88I	ENST00000373509	NM_002648.3	88	atG/atT	4/6	0.76130320175478	2	FACETS	0.967	0.914	1	0.484	0.457	0.511	CLONAL	1	TRUE	0	0.76130320175478	2		580	785	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41905026	41905026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374294883	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	265	425	0	ENST00000372991.4:c.521G>A	p.Arg174Gln	p.R174Q	ENST00000372991	NM_001760.3	174	cGa/cAa	3/5	0.76130320175478	2	FACETS	0.975	0.919	1	0.488	0.459	0.516	CLONAL	1	TRUE	0	0.76130320175478	2		425	714	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974387	93974387	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	137	378	0	ENST00000369303.4:c.1667T>C	p.Ile556Thr	p.I556T	ENST00000369303	NM_004440.3	556	aTt/aCt	8/17	1	2	FACETS	0.935	0.86	1	0.935	0.86	1	CLONAL	1	TRUE	1	0.76130320175478	2		378	385	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638326	117638326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752085591	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	159	362	2	ENST00000368508.3:c.6115C>T	p.Arg2039Cys	p.R2039C	ENST00000368508	NM_002944.2	2039	Cgt/Tgt	38/43	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.76130320175478	2		364	408	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658421	117658421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	150	536	0	ENST00000368508.3:c.5162C>T	p.Pro1721Leu	p.P1721L	ENST00000368508	NM_002944.2	1721	cCt/cTt	31/43	1	2	FACETS	0.934	0.862	1	0.934	0.862	1	CLONAL	1	TRUE	1	0.76130320175478	2		536	422	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674333	117674333	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	134	322	0	ENST00000368508.3:c.4142-1G>A		p.X1381_splice	ENST00000368508	NM_002944.2	1381			1	2	FACETS	0.981	0.902	1	0.981	0.902	1	CLONAL	1	TRUE	1	0.76130320175478	2		322	359	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001583	150001583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	99	360	0	ENST00000253339.5:c.2021C>T	p.Ser674Phe	p.S674F	ENST00000253339		674	tCt/tTt	4/7	1	2	FACETS	0.932	0.844	1	0.932	0.844	1	CLONAL	1	TRUE	1	0.76130320175478	2		360	279	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004302	150004302	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs35163691	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	95	387	0	ENST00000253339.5:c.1923C>A	p.Phe641Leu	p.F641L	ENST00000253339		641	ttC/ttA	3/7	1	2	FACETS	0.901	0.814	0.991	0.901	0.814	0.991	CLONAL	1	TRUE	1	0.76130320175478	2		387	277	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005204	150005204	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	205	396	0	ENST00000253339.5:c.1021C>T	p.Pro341Ser	p.P341S	ENST00000253339		341	Cca/Tca	3/7	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.76130320175478	2		396	519	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129413	152129413	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs939987866	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	215	362	0	ENST00000206249.3:c.366G>T	p.Gln122His	p.Q122H	ENST00000206249	NM_000125.3	122	caG/caT	1/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.76130320175478	2		362	507	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265535	152265535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571716552	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	301	463	0	ENST00000206249.3:c.988G>A	p.Glu330Lys	p.E330K	ENST00000206249	NM_000125.3	330	Gag/Aag	4/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.76130320175478	2		463	741	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394441	162394441	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	133	337	0	ENST00000366898.1:c.627C>A	p.Phe209Leu	p.F209L	ENST00000366898	NM_004562.2	209	ttC/ttA	6/12	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.76130320175478	2		337	340	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394447	162394447	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	129	322	0	ENST00000366898.1:c.621A>T	p.Glu207Asp	p.E207D	ENST00000366898	NM_004562.2	207	gaA/gaT	6/12	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.76130320175478	2		322	321	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959225	2959225	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	335	654	0	ENST00000396946.4:c.2291A>G	p.Asp764Gly	p.D764G	ENST00000396946	NM_032415.4	764	gAc/gGc	18/25	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.76130320175478	2		654	876	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2972174	2972174	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	314	598	0	ENST00000396946.4:c.1565T>G	p.Phe522Cys	p.F522C	ENST00000396946	NM_032415.4	522	tTt/tGt	11/25	1	2	FACETS	0.902	0.853	0.951	0.902	0.853	0.951	CLONAL	1	TRUE	1	0.76130320175478	2		598	915	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729566	41729566	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	248	555	1	ENST00000242208.4:c.963C>A	p.Cys321Ter	p.C321*	ENST00000242208	NM_002192.2	321	tgC/tgA	3/3	1	2	FACETS	0.884	0.83	0.939	0.884	0.83	0.939	CLONAL	1	TRUE	1	0.76130320175478	2		556	737	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55229238	55229238	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	236	393	0	ENST00000275493.2:c.1545C>A	p.Cys515Ter	p.C515*	ENST00000275493	NM_005228.3	515	tgC/tgA	13/28	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.76130320175478	2		393	597	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241704	55241704	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	303	602	0	ENST00000275493.2:c.2152C>A	p.Leu718Met	p.L718M	ENST00000275493	NM_005228.3	718	Ctg/Atg	18/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.76130320175478	2		602	728	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241726	55241726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767505234	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	220	516	0	ENST00000275493.2:c.2174C>T	p.Thr725Met	p.T725M	ENST00000275493	NM_005228.3	725	aCg/aTg	18/28	1	2	FACETS	0.913	0.855	0.973	0.913	0.855	0.973	CLONAL	1	TRUE	1	0.76130320175478	2		516	633	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513165	106513165	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs778461029	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	117	262	2	ENST00000359195.3:c.2069G>T	p.Arg690Ile	p.R690I	ENST00000359195	NM_002649.2	690	aGa/aTa	4/11	1	2	FACETS	0.985	0.901	1	0.985	0.901	1	CLONAL	1	TRUE	1	0.76130320175478	2		264	312	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397696	116397696	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	35	453	0	ENST00000397752.3:c.1970C>T	p.Pro657Leu	p.P657L	ENST00000397752	NM_000245.2	657	cCt/cTt	8/21	1	2	FACETS	0.252	0.206	0.303	0.252	0.206	0.303	SUBCLONAL	1	TRUE	1	0.76130320175478	2		453	365	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418907	116418907	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1333930330	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	193	377	1	ENST00000397752.3:c.3418C>T	p.Leu1140Phe	p.L1140F	ENST00000397752	NM_000245.2	1140	Ctc/Ttc	17/21	1	2	FACETS	0.951	0.887	1	0.951	0.887	1	CLONAL	1	TRUE	1	0.76130320175478	2		378	533	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436021	116436021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1453842331	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	74	603	0	ENST00000397752.3:c.4016C>T	p.Ala1339Val	p.A1339V	ENST00000397752	NM_000245.2	1339	gCg/gTg	21/21	1	2	FACETS	0.233	0.204	0.266	0.233	0.204	0.266	SUBCLONAL	1	TRUE	1	0.76130320175478	2		603	833	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851930	128851930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779777438	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	323	656	0	ENST00000249373.3:c.2002C>T	p.Arg668Cys	p.R668C	ENST00000249373	NM_005631.4	668	Cgc/Tgc	12/12	1	2	FACETS	0.922	0.874	0.972	0.922	0.874	0.972	CLONAL	1	TRUE	1	0.76130320175478	2		656	920	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434546	140434546	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	106	215	0	ENST00000288602.6:c.2152G>A	p.Ala718Thr	p.A718T	ENST00000288602	NM_004333.4	718	Gcc/Acc	18/18	1	2	FACETS	0.91	0.827	0.996	0.91	0.827	0.996	CLONAL	1	TRUE	1	0.76130320175478	2		215	306	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477867	140477867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	106	399	0	ENST00000288602.6:c.1441G>A	p.Ala481Thr	p.A481T	ENST00000288602	NM_004333.4	481	Gca/Aca	12/18	1	2	FACETS	0.819	0.742	0.899	0.819	0.742	0.899	CLONAL	1	TRUE	1	0.76130320175478	2		399	340	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494206	140494206	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	363	709	0	ENST00000288602.6:c.1042C>A	p.Pro348Thr	p.P348T	ENST00000288602	NM_004333.4	348	Cca/Aca	8/18	1	2	FACETS	0.938	0.891	0.985	0.938	0.891	0.985	CLONAL	1	TRUE	1	0.76130320175478	2		709	1017	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148504761	148504761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397515548	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	249	448	0	ENST00000320356.2:c.2233G>A	p.Glu745Lys	p.E745K	ENST00000320356	NM_004456.4	745	Gaa/Aaa	20/20	1	2	FACETS	0.928	0.872	0.985	0.928	0.872	0.985	CLONAL	1	TRUE	1	0.76130320175478	2		448	705	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512042	148512042	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	203	328	0	ENST00000320356.2:c.1636A>C	p.Asn546His	p.N546H	ENST00000320356	NM_004456.4	546	Aat/Cat	14/20	1	2	FACETS	0.979	0.915	1	0.979	0.915	1	CLONAL	1	TRUE	1	0.76130320175478	2		328	545	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148544273	148544273	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	47	313	0	ENST00000320356.2:c.117+1G>T		p.X39_splice	ENST00000320356	NM_004456.4	39			1	2	FACETS	0.291	0.246	0.341	0.291	0.246	0.341	SUBCLONAL	1	TRUE	1	0.76130320175478	2		313	424	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859311	151859311	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	133	300	0	ENST00000262189.6:c.11351A>C	p.Lys3784Thr	p.K3784T	ENST00000262189	NM_170606.2	3784	aAa/aCa	43/59	1	2	FACETS	0.922	0.847	0.999	0.922	0.847	0.999	CLONAL	1	TRUE	1	0.76130320175478	2		300	379	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864304	151864304	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	224	436	0	ENST00000262189.6:c.9677T>G	p.Phe3226Cys	p.F3226C	ENST00000262189	NM_170606.2	3226	tTt/tGt	42/59	1	2	FACETS	0.927	0.868	0.986	0.927	0.868	0.986	CLONAL	1	TRUE	1	0.76130320175478	2		436	635	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874476	151874476	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	33	352	0	ENST00000262189.6:c.8062A>C	p.Lys2688Gln	p.K2688Q	ENST00000262189	NM_170606.2	2688	Aaa/Caa	38/59	1	2	FACETS	0.22	0.179	0.266	0.22	0.179	0.266	SUBCLONAL	1	TRUE	1	0.76130320175478	2		352	394	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538882	23538882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1254712780	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	210	449	0	ENST00000380871.4:c.557C>T	p.Ser186Leu	p.S186L	ENST00000380871	NM_006167.3	186	tCg/tTg	2/2	1	2	FACETS	0.887	0.828	0.947	0.887	0.828	0.947	CLONAL	1	TRUE	1	0.76130320175478	2		449	622	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538920	23538920	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	287	560	1	ENST00000380871.4:c.519G>T	p.Gln173His	p.Q173H	ENST00000380871	NM_006167.3	173	caG/caT	2/2	1	2	FACETS	0.983	0.929	1	0.983	0.929	1	CLONAL	1	TRUE	1	0.76130320175478	2		561	767	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38135879	38135879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375135970	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	269	490	0	ENST00000317025.8:c.3812C>T	p.Thr1271Met	p.T1271M	ENST00000317025	NM_023034.1	1271	aCg/aTg	22/24	1	2	FACETS	0.937	0.883	0.992	0.937	0.883	0.992	CLONAL	1	TRUE	1	0.76130320175478	2		490	754	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205524	38205524	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	298	700	0	ENST00000317025.8:c.166G>T	p.Gly56Cys	p.G56C	ENST00000317025	NM_023034.1	56	Ggc/Tgc	2/24	1	2	FACETS	0.849	0.801	0.898	0.849	0.801	0.898	CLONAL	1	TRUE	1	0.76130320175478	2		700	922	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287386	38287386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1162148796	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	275	540	0	ENST00000425967.3:c.271C>T	p.Arg91Trp	p.R91W	ENST00000425967	NM_001174067.1	91	Cgg/Tgg	4/19	1	2	FACETS	0.962	0.908	1	0.962	0.908	1	CLONAL	1	TRUE	1	0.76130320175478	2		540	751	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983401	90983401	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	79	274	0	ENST00000265433.3:c.702G>T	p.Gln234His	p.Q234H	ENST00000265433	NM_002485.4	234	caG/caT	6/16	1	2	FACETS	0.922	0.825	1	0.922	0.825	1	CLONAL	1	TRUE	1	0.76130320175478	2		274	225	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752819	128752819	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	93	293	0	ENST00000377970.2:c.980C>T	p.Pro327Leu	p.P327L	ENST00000377970	NM_002467.4	327	cCt/cTt	3/3	1	2	FACETS	0.524	0.468	0.584	0.524	0.468	0.584	SUBCLONAL	1	TRUE	1	0.76130320175478	2		293	466	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551447	141551447	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	238	455	0	ENST00000220592.5:c.1850G>T	p.Ser617Ile	p.S617I	ENST00000220592	NM_012154.3	617	aGc/aTc	15/19	1	2	FACETS	0.907	0.852	0.965	0.907	0.852	0.965	CLONAL	1	TRUE	1	0.76130320175478	2		455	689	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141568583	141568583	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	328	503	0	ENST00000220592.5:c.878+1G>A		p.X293_splice	ENST00000220592	NM_012154.3	293			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.76130320175478	2		503	833	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742015	145742015	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	371	635	0	ENST00000428558.2:c.488C>A	p.Pro163His	p.P163H	ENST00000428558	NM_004260.3	163	cCt/cAt	5/22	1	2	FACETS	0.985	0.938	1	0.985	0.938	1	CLONAL	1	TRUE	1	0.76130320175478	2		635	989	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054750	5054750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	98	319	0	ENST00000381652.3:c.802G>A	p.Glu268Lys	p.E268K	ENST00000381652	NM_004972.3	268	Gag/Aag	7/25	1	2	FACETS	0.873	0.789	0.959	0.873	0.789	0.959	CLONAL	1	TRUE	1	0.76130320175478	2		319	295	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072541	5072541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368927897	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	100	352	0	ENST00000381652.3:c.1691G>A	p.Arg564Gln	p.R564Q	ENST00000381652	NM_004972.3	564	cGa/cAa	13/25	1	2	FACETS	0.847	0.766	0.931	0.847	0.766	0.931	CLONAL	1	TRUE	1	0.76130320175478	2		352	310	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080656	5080656	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs769318116	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	117	363	0	ENST00000381652.3:c.2407C>T	p.Arg803Ter	p.R803*	ENST00000381652	NM_004972.3	803	Cga/Tga	18/25	1	2	FACETS	0.859	0.783	0.937	0.859	0.783	0.937	CLONAL	1	TRUE	1	0.76130320175478	2		363	358	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341925	8341925	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	122	368	1	ENST00000356435.5:c.4715G>T	p.Arg1572Ile	p.R1572I	ENST00000356435		1572	aGa/aTa	29/35	1	2	FACETS	0.965	0.884	1	0.965	0.884	1	CLONAL	1	TRUE	1	0.76130320175478	2		369	332	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471048	8471048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	129	366	0	ENST00000356435.5:c.3451C>T	p.Arg1151Cys	p.R1151C	ENST00000356435		1151	Cgc/Tgc	20/35	1	2	FACETS	0.823	0.753	0.895	0.823	0.753	0.895	CLONAL	1	TRUE	1	0.76130320175478	2		366	412	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486004	8486004	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	237	511	0	ENST00000356435.5:c.2813C>A	p.Ser938Tyr	p.S938Y	ENST00000356435		938	tCt/tAt	17/35	1	2	FACETS	0.958	0.9	1	0.958	0.9	1	CLONAL	1	TRUE	1	0.76130320175478	2		511	650	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500947	8500947	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	178	376	0	ENST00000356435.5:c.1935C>A	p.Tyr645Ter	p.Y645*	ENST00000356435		645	taC/taA	13/35	1	2	FACETS	0.976	0.908	1	0.976	0.908	1	CLONAL	1	TRUE	1	0.76130320175478	2		376	479	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521481	8521481	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760428875	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	261	514	0	ENST00000356435.5:c.757G>A	p.Val253Ile	p.V253I	ENST00000356435		253	Gtt/Att	9/35	1	2	FACETS	0.909	0.856	0.964	0.909	0.856	0.964	CLONAL	1	TRUE	1	0.76130320175478	2		514	754	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157948	27157948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	40	541	0	ENST00000380036.4:c.172G>A	p.Gly58Arg	p.G58R	ENST00000380036	NM_000459.3	58	Gga/Aga	2/23	1	2	FACETS	0.148	0.122	0.176	0.148	0.122	0.176	SUBCLONAL	1	TRUE	1	0.76130320175478	2		541	712	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197484	27197484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756064806	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	325	649	0	ENST00000380036.4:c.1796C>T	p.Ser599Leu	p.S599L	ENST00000380036	NM_000459.3	599	tCg/tTg	12/23	1	2	FACETS	0.94	0.891	0.99	0.94	0.891	0.99	CLONAL	1	TRUE	1	0.76130320175478	2		649	908	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206739	27206739	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147231791	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	253	490	0	ENST00000380036.4:c.2524C>T	p.Arg842Cys	p.R842C	ENST00000380036	NM_000459.3	842	Cgc/Tgc	15/23	1	2	FACETS	0.976	0.919	1	0.976	0.919	1	CLONAL	1	TRUE	1	0.76130320175478	2		490	681	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209415	98209415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769022340	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	288	618	1	ENST00000331920.6:c.4123G>A	p.Ala1375Thr	p.A1375T	ENST00000331920	NM_000264.3	1375	Gcc/Acc	23/24	1	2	FACETS	0.905	0.854	0.957	0.905	0.854	0.957	CLONAL	1	TRUE	1	0.76130320175478	2		619	836	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894949	101894949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519144	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	118	275	0	ENST00000374994.4:c.502C>T	p.Arg168Cys	p.R168C	ENST00000374994	NM_004612.2	168	Cgc/Tgc	3/9	1	2	FACETS	0.803	0.731	0.877	0.803	0.731	0.877	CLONAL	1	TRUE	1	0.76130320175478	2		275	386	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128347905	128347905	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	213	644	0	ENST00000265960.3:c.600C>A	p.Ser200Arg	p.S200R	ENST00000265960	NM_001006617.1	200	agC/agA	5/12	1	2	FACETS	0.568	0.528	0.61	0.568	0.528	0.61	SUBCLONAL	1	TRUE	1	0.76130320175478	2		644	985	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755968	133755968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752060211	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	300	574	0	ENST00000318560.5:c.1595C>T	p.Thr532Met	p.T532M	ENST00000318560	NM_005157.4	532	aCg/aTg	10/11	1	2	FACETS	0.932	0.881	0.983	0.932	0.881	0.983	CLONAL	1	TRUE	1	0.76130320175478	2		574	846	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759698	133759698	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs971577563	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	299	670	0	ENST00000318560.5:c.2021G>A	p.Arg674Gln	p.R674Q	ENST00000318560	NM_005157.4	674	cGg/cAg	11/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.76130320175478	2		670	756	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293477	137293477	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	438	860	1	ENST00000481739.1:c.29-1G>A		p.X10_splice	ENST00000481739	NM_002957.4	10			1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.76130320175478	2		861	1075	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399191	139399191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1243453790	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	72	512	0	ENST00000277541.6:c.4952C>T	p.Ser1651Leu	p.S1651L	ENST00000277541	NM_017617.3	1651	tCg/tTg	26/34	1	2	FACETS	0.26	0.227	0.296	0.26	0.227	0.296	SUBCLONAL	1	TRUE	1	0.76130320175478	2		512	727	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399286	139399286	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	79	647	1	ENST00000277541.6:c.4857C>A	p.Tyr1619Ter	p.Y1619*	ENST00000277541	NM_017617.3	1619	taC/taA	26/34	1	2	FACETS	0.21	0.184	0.238	0.21	0.184	0.238	SUBCLONAL	1	TRUE	1	0.76130320175478	2		648	989	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399387	139399387	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1418474023	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	102	609	0	ENST00000277541.6:c.4756C>T	p.Arg1586Cys	p.R1586C	ENST00000277541	NM_017617.3	1586	Cgc/Tgc	26/34	1	2	FACETS	0.286	0.255	0.319	0.286	0.255	0.319	SUBCLONAL	1	TRUE	1	0.76130320175478	2		609	936	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399766	139399766	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	300	505	0	ENST00000277541.6:c.4582T>C	p.Cys1528Arg	p.C1528R	ENST00000277541	NM_017617.3	1528	Tgc/Cgc	25/34	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.76130320175478	2		505	745	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399777	139399777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774374213	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	265	553	1	ENST00000277541.6:c.4571C>T	p.Ala1524Val	p.A1524V	ENST00000277541	NM_017617.3	1524	gCg/gTg	25/34	1	2	FACETS	0.88	0.828	0.933	0.88	0.828	0.933	CLONAL	1	TRUE	1	0.76130320175478	2		554	791	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399834	139399834	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	98	763	0	ENST00000277541.6:c.4514G>A	p.Cys1505Tyr	p.C1505Y	ENST00000277541	NM_017617.3	1505	tGt/tAt	25/34	1	2	FACETS	0.237	0.21	0.265	0.237	0.21	0.265	SUBCLONAL	1	TRUE	1	0.76130320175478	2		763	1087	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403409	139403409	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	401	704	0	ENST00000277541.6:c.3084G>T	p.Gln1028His	p.Q1028H	ENST00000277541	NM_017617.3	1028	caG/caT	19/34	1	2	FACETS	0.985	0.939	1	0.985	0.939	1	CLONAL	1	TRUE	1	0.76130320175478	2		704	1070	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139562805	139562805	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs755134733	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	340	737	0	ENST00000308874.7:c.71A>G	p.Tyr24Cys	p.Y24C	ENST00000308874		24	tAc/tGc	3/10	1	2	FACETS	0.937	0.889	0.986	0.937	0.889	0.986	CLONAL	1	TRUE	1	0.76130320175478	2		737	953	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314987	1314987	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	297	801	0	ENST00000400841.2:c.674C>A	p.Pro225His	p.P225H	ENST00000400841		225	cCc/cAc	6/6	1	2	FACETS	0.622	0.585	0.66	0.622	0.585	0.66	SUBCLONAL	1	TRUE	1	0.76130320175478	2		801	1254	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15827393	15827393	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	186	462	0	ENST00000307771.7:c.509C>A	p.Ala170Asp	p.A170D	ENST00000307771	NM_005089.3	170	gCt/gAt	7/11	1	2	FACETS	0.874	0.813	0.937	0.874	0.813	0.937	CLONAL	1	TRUE	1	0.76130320175478	2		462	559	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841229	15841229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	114	193	0	ENST00000307771.7:c.1313G>A	p.Gly438Asp	p.G438D	ENST00000307771	NM_005089.3	438	gGc/gAc	11/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.76130320175478	2		193	253	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914723	39914723	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	230	471	0	ENST00000378444.4:c.4639C>T	p.Arg1547Ter	p.R1547*	ENST00000378444	NM_001123385.1	1547	Cga/Tga	12/15	1	2	FACETS	0.934	0.876	0.993	0.934	0.876	0.993	CLONAL	1	TRUE	1	0.76130320175478	2		471	647	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922009	39922009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	260	543	2	ENST00000378444.4:c.4163C>T	p.Ala1388Val	p.A1388V	ENST00000378444	NM_001123385.1	1388	gCc/gTc	9/15	1	2	FACETS	0.873	0.821	0.927	0.873	0.821	0.927	CLONAL	1	TRUE	1	0.76130320175478	2		545	782	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931931	39931931	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	86	706	0	ENST00000378444.4:c.2668G>T	p.Glu890Ter	p.E890*	ENST00000378444	NM_001123385.1	890	Gag/Tag	4/15	1	2	FACETS	0.215	0.189	0.242	0.215	0.189	0.242	SUBCLONAL	1	TRUE	1	0.76130320175478	2		706	1052	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040789	47040789	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	71	724	1	ENST00000377604.3:c.1424C>A	p.Pro475His	p.P475H	ENST00000377604	NM_001204468.1	475	cCc/cAc	13/24	1	2	FACETS	0.208	0.181	0.238	0.208	0.181	0.238	SUBCLONAL	1	TRUE	1	0.76130320175478	2		725	896	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044595	47044595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	365	803	0	ENST00000377604.3:c.2092G>A	p.Glu698Lys	p.E698K	ENST00000377604	NM_001204468.1	698	Gag/Aag	18/24	1	2	FACETS	0.935	0.889	0.983	0.935	0.889	0.983	CLONAL	1	TRUE	1	0.76130320175478	2		803	1025	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429332	47429332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1277297558	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	373	723	0	ENST00000377045.4:c.1460G>A	p.Ser487Asn	p.S487N	ENST00000377045	NM_001654.4	487	aGc/aAc	14/16	1	2	FACETS	0.915	0.87	0.961	0.915	0.87	0.961	CLONAL	1	TRUE	1	0.76130320175478	2		723	1071	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224470	53224470	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	196	635	0	ENST00000375401.3:c.3243G>A	p.Trp1081Ter	p.W1081*	ENST00000375401	NM_004187.3	1081	tgG/tgA	21/26	1	2	FACETS	0.521	0.482	0.561	0.521	0.482	0.561	SUBCLONAL	1	TRUE	1	0.76130320175478	2		635	989	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227993	53227993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	366	705	1	ENST00000375401.3:c.2321C>T	p.Ala774Val	p.A774V	ENST00000375401	NM_004187.3	774	gCc/gTc	16/26	1	2	FACETS	0.946	0.9	0.994	0.946	0.9	0.994	CLONAL	1	TRUE	1	0.76130320175478	2		706	1016	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247064	53247064	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	282	597	0	ENST00000375401.3:c.436G>T	p.Gly146Cys	p.G146C	ENST00000375401	NM_004187.3	146	Ggc/Tgc	4/26	1	2	FACETS	0.884	0.834	0.935	0.884	0.834	0.935	CLONAL	1	TRUE	1	0.76130320175478	2		597	838	SUCCESS
AR	367	MSKCC	GRCh37	X	66766085	66766085	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	279	592	0	ENST00000374690.3:c.1097A>C	p.Asn366Thr	p.N366T	ENST00000374690	NM_000044.3	366	aAc/aCc	1/8	1	2	FACETS	0.866	0.816	0.917	0.866	0.816	0.917	CLONAL	1	TRUE	1	0.76130320175478	2		592	846	SUCCESS
AR	367	MSKCC	GRCh37	X	66766097	66766097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	341	572	0	ENST00000374690.3:c.1109C>T	p.Ala370Val	p.A370V	ENST00000374690	NM_000044.3	370	gCt/gTt	1/8	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.76130320175478	2		572	782	SUCCESS
AR	367	MSKCC	GRCh37	X	66766144	66766144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	217	412	0	ENST00000374690.3:c.1156C>T	p.Arg386Cys	p.R386C	ENST00000374690	NM_000044.3	386	Cgc/Tgc	1/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.76130320175478	2		412	532	SUCCESS
AR	367	MSKCC	GRCh37	X	66766207	66766207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	154	265	0	ENST00000374690.3:c.1219C>T	p.Arg407Cys	p.R407C	ENST00000374690	NM_000044.3	407	Cgc/Tgc	1/8	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.76130320175478	2		265	359	SUCCESS
AR	367	MSKCC	GRCh37	X	66766468	66766468	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	210	464	0	ENST00000374690.3:c.1480G>A	p.Glu494Lys	p.E494K	ENST00000374690	NM_000044.3	494	Gaa/Aaa	1/8	1	2	FACETS	0.886	0.827	0.945	0.886	0.827	0.945	CLONAL	1	TRUE	1	0.76130320175478	2		464	623	SUCCESS
AR	367	MSKCC	GRCh37	X	66937379	66937379	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	300	592	0	ENST00000374690.3:c.2233C>A	p.Leu745Ile	p.L745I	ENST00000374690	NM_000044.3	745	Ctc/Atc	5/8	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.76130320175478	2		592	778	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344137	70344137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318670088	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	56	641	0	ENST00000374080.3:c.1873G>A	p.Ala625Thr	p.A625T	ENST00000374080		625	Gcc/Acc	13/45	1	2	FACETS	0.176	0.15	0.204	0.176	0.15	0.204	SUBCLONAL	1	TRUE	1	0.76130320175478	2		641	838	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345909	70345909	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	259	490	1	ENST00000374080.3:c.2446C>T	p.Arg816Ter	p.R816*	ENST00000374080		816	Cga/Tga	18/45	1	2	FACETS	0.893	0.84	0.947	0.893	0.84	0.947	CLONAL	1	TRUE	1	0.76130320175478	2		491	762	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347853	70347853	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	302	544	0	ENST00000374080.3:c.3092C>T	p.Ala1031Val	p.A1031V	ENST00000374080		1031	gCt/gTt	22/45	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.76130320175478	2		544	738	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349186	70349186	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1304464082	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	251	600	0	ENST00000374080.3:c.3598C>T	p.Arg1200Cys	p.R1200C	ENST00000374080		1200	Cgc/Tgc	26/45	1	2	FACETS	0.877	0.824	0.931	0.877	0.824	0.931	CLONAL	1	TRUE	1	0.76130320175478	2		600	752	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845384	76845384	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	84	334	1	ENST00000373344.5:c.6137C>A	p.Ser2046Tyr	p.S2046Y	ENST00000373344	NM_000489.3	2046	tCt/tAt	27/35	1	2	FACETS	0.698	0.623	0.777	0.698	0.623	0.777	SUBCLONAL	1	TRUE	1	0.76130320175478	2		335	316	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854949	76854949	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	158	566	0	ENST00000373344.5:c.5887C>T	p.Arg1963Trp	p.R1963W	ENST00000373344	NM_000489.3	1963	Cgg/Tgg	25/35	1	2	FACETS	0.863	0.797	0.931	0.863	0.797	0.931	CLONAL	1	TRUE	1	0.76130320175478	2		566	481	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874365	76874365	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	131	493	0	ENST00000373344.5:c.5357A>G	p.Asn1786Ser	p.N1786S	ENST00000373344	NM_000489.3	1786	aAt/aGt	21/35	1	2	FACETS	0.896	0.822	0.972	0.896	0.822	0.972	CLONAL	1	TRUE	1	0.76130320175478	2		493	384	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891519	76891519	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	145	494	0	ENST00000373344.5:c.4586C>A	p.Thr1529Asn	p.T1529N	ENST00000373344	NM_000489.3	1529	aCc/aAc	16/35	1	2	FACETS	0.745	0.684	0.809	0.745	0.684	0.809	SUBCLONAL	1	TRUE	1	0.76130320175478	2		494	511	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920205	76920205	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	142	398	0	ENST00000373344.5:c.3872C>A	p.Ser1291Tyr	p.S1291Y	ENST00000373344	NM_000489.3	1291	tCt/tAt	11/35	1	2	FACETS	0.795	0.73	0.863	0.795	0.73	0.863	SUBCLONAL	1	TRUE	1	0.76130320175478	2		398	469	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920255	76920255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	89	304	0	ENST00000373344.5:c.3822G>T	p.Lys1274Asn	p.K1274N	ENST00000373344	NM_000489.3	1274	aaG/aaT	11/35	1	2	FACETS	0.728	0.652	0.808	0.728	0.652	0.808	SUBCLONAL	1	TRUE	1	0.76130320175478	2		304	321	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937587	76937587	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	80	325	0	ENST00000373344.5:c.3161C>A	p.Ser1054Tyr	p.S1054Y	ENST00000373344	NM_000489.3	1054	tCt/tAt	9/35	1	2	FACETS	0.887	0.793	0.984	0.887	0.793	0.984	CLONAL	1	TRUE	1	0.76130320175478	2		325	237	SUCCESS
BTK	695	MSKCC	GRCh37	X	100609640	100609640	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	38	430	0	ENST00000308731.7:c.1609G>A	p.Val537Ile	p.V537I	ENST00000308731	NM_000061.2	537	Gta/Ata	16/19	1	2	FACETS	0.149	0.122	0.178	0.149	0.122	0.178	SUBCLONAL	1	TRUE	1	0.76130320175478	2		430	671	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611061	100611061	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	315	673	0	ENST00000308731.7:c.1545G>T	p.Lys515Asn	p.K515N	ENST00000308731	NM_000061.2	515	aaG/aaT	15/19	1	2	FACETS	0.959	0.908	1	0.959	0.908	1	CLONAL	1	TRUE	1	0.76130320175478	2		673	863	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630236	100630236	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs128620187	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	200	399	1	ENST00000308731.7:c.37C>T	p.Arg13Ter	p.R13*	ENST00000308731	NM_000061.2	13	Cga/Tga	2/19	1	2	FACETS	0.984	0.919	1	0.984	0.919	1	CLONAL	1	TRUE	1	0.76130320175478	2		400	534	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164933	123164933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	118	319	0	ENST00000218089.9:c.246G>A	p.Met82Ile	p.M82I	ENST00000218089	NM_001042749.1	82	atG/atA	5/35	1	2	FACETS	0.785	0.714	0.858	0.785	0.714	0.858	SUBCLONAL	1	TRUE	1	0.76130320175478	2		319	395	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191804	123191804	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	128	332	0	ENST00000218089.9:c.1393G>T	p.Val465Phe	p.V465F	ENST00000218089	NM_001042749.1	465	Gtt/Ttt	15/35	1	2	FACETS	0.883	0.808	0.959	0.883	0.808	0.959	CLONAL	1	TRUE	1	0.76130320175478	2		332	381	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195182	123195182	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	91	380	0	ENST00000218089.9:c.1525G>T	p.Gly509Ter	p.G509*	ENST00000218089	NM_001042749.1	509	Gga/Tga	16/35	1	2	FACETS	0.701	0.628	0.777	0.701	0.628	0.777	SUBCLONAL	1	TRUE	1	0.76130320175478	2		380	341	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197899	123197899	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	79	293	0	ENST00000218089.9:c.2023G>A	p.Glu675Lys	p.E675K	ENST00000218089	NM_001042749.1	675	Gag/Aag	20/35	1	2	FACETS	0.783	0.698	0.872	0.783	0.698	0.872	SUBCLONAL	1	TRUE	1	0.76130320175478	2		293	265	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205151	123205151	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	74	334	1	ENST00000218089.9:c.2511G>T	p.Gln837His	p.Q837H	ENST00000218089	NM_001042749.1	837	caG/caT	25/35	1	2	FACETS	0.948	0.846	1	0.948	0.846	1	CLONAL	1	TRUE	1	0.76130320175478	2		335	205	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224425	123224425	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1364566054	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	135	417	0	ENST00000218089.9:c.3278C>T	p.Thr1093Ile	p.T1093I	ENST00000218089	NM_001042749.1	1093	aCt/aTt	31/35	1	2	FACETS	0.714	0.653	0.777	0.714	0.653	0.777	SUBCLONAL	1	TRUE	1	0.76130320175478	2		417	497	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161392	55161392	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767697835	NA	P-0039054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	188	427	0	ENST00000257290.5:c.3223G>A	p.Asp1075Asn	p.D1075N	ENST00000257290	NM_006206.4	1075	Gac/Aac	23/23	1	2	FACETS	0.839	0.779	0.899	0.839	0.779	0.899	CLONAL	1	TRUE	1	0.76130320175478	2		427	589	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0039055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	195	721	0	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.115554959453923	3	FACETS	1	0.985	1			1	INDETERMINATE	2	TRUE	NA	0.223281928445092	3		721	789	SUCCESS
APC	324	MSKCC	GRCh37	5	112175248	112175249	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0039055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	33	232	0	ENST00000257430.4:c.3959_3960del	p.Val1320GlufsTer11	p.V1320Efs*11	ENST00000257430	NM_000038.5	1319	ccTGtg/cctg	16/16	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.223281928445092	2		232	276	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0039055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	36	344	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	1	2	FACETS	0.713	0.586	0.856	0.713	0.586	0.856	SUBCLONAL	1	TRUE	1	0.223281928445092	2		344	452	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434953	110434953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	51	604	0	ENST00000375856.3:c.3448G>A	p.Glu1150Lys	p.E1150K	ENST00000375856	NM_003749.2	1150	Gag/Aag	1/2	0.223281928445092	6	FACETS	0.669	0.566	0.782	0.134	0.113	0.157	SUBCLONAL	1	TRUE	1	0.223281928445092	6		604	988	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212450	5212450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196839847	NA	P-0039055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	202	651	0	ENST00000357368.4:c.4667C>T	p.Pro1556Leu	p.P1556L	ENST00000357368	NM_002850.3	1556	cCg/cTg	31/38	0.131556366091035	3	FACETS	1	0.984	1	1	0.984	1	INDETERMINATE	2	TRUE	1	0.223281928445092	3		651	837	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031939	26031939	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	99	334	0	ENST00000244661.2:c.350G>A	p.Arg117Gln	p.R117Q	ENST00000244661	NM_003537.3	117	cGa/cAa	1/1	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.493802422305036	2		334	373	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118947	70118947	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	253	684	0	ENST00000245479.2:c.519G>T	p.Lys173Asn	p.K173N	ENST00000245479	NM_000346.3	173	aaG/aaT	2/3	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.493802422305036	2		684	749	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968154	18968154	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	164	643	0	ENST00000262803.5:c.1994A>C	p.Gln665Pro	p.Q665P	ENST00000262803	NM_002911.3	665	cAg/cCg	15/24	NA	2	FACETS	1	0.932	1			1	INDETERMINATE	1	TRUE	NA	0.493802422305036	2		643	656	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799327	42799347	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	CTGCCACAGGCAGGTGAGGGA	CTGCCACAGGCAGGTGAGGGA	-	novel	NA	P-0039066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	48	357	0	ENST00000575354.2:c.4812_*5del		p.*1604*	ENST00000575354	NM_015125.3	1604		20/20	0.44219536322009	1	FACETS	0.583	0.497	0.676	0.583	0.497	0.676	SUBCLONAL	1	TRUE	0	0.493802422305036	1		357	251	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860191	151860191	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	112	399	0	ENST00000262189.6:c.10471G>A	p.Gly3491Arg	p.G3491R	ENST00000262189	NM_170606.2	3491	Gga/Aga	43/59	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.493802422305036	2		399	440	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0039068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	79	233	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	1	2	FACETS	0.897	0.803	0.993	0.897	0.803	0.993	CLONAL	1	TRUE	1	0.815634367648737	2		233	216	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	800	620	0	ENST00000269305.4:c.472C>G	p.Arg158Gly	p.R158G	ENST00000269305	NM_001126112.2	158	Cgc/Ggc	5/11	0.799799332009161	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.815634367648737	2		620	975	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280061	66280061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1254027522	NA	P-0039068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	84	222	0	ENST00000273854.3:c.1628G>A	p.Arg543His	p.R543H	ENST00000273854	NM_004439.5	543	cGt/cAt	7/18	1	2	FACETS	0.656	0.585	0.73	0.656	0.585	0.73	SUBCLONAL	1	TRUE	1	0.815634367648737	2		222	314	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933965	39933993	+	frameshift_variant	Frame_Shift_Del	DEL	TATTTGGCGAGTCGAGGAAAGGGTAGATG	TATTTGGCGAGTCGAGGAAAGGGTAGATG	-	novel	NA	P-0039068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	307	318	0	ENST00000378444.4:c.606_634del	p.Ile203ValfsTer88	p.I203Vfs*88	ENST00000378444	NM_001123385.1	202	gcCATCTACCCTTTCCTCGACTCGCCAAATAag/gcag	4/15	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.815634367648737	1		318	384	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	155	649	5	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	0.27	2		654	873	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	94	318	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.767	0.686	0.852	1	0.982	1	SUBCLONAL	2	TRUE	1	0.27	2		318	454	SUCCESS
APC	324	MSKCC	GRCh37	5	112164585	112164585	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398123116	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	88	268	0	ENST00000257430.4:c.1659G>A	p.Trp553Ter	p.W553*	ENST00000257430	NM_000038.5	553	tgG/tgA	14/16	1	2	FACETS	0.762	0.678	0.849	1	0.98	1	SUBCLONAL	2	TRUE	1	0.27	2		268	428	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99440129	99440129	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	75	356	1	ENST00000268035.6:c.1101del	p.Asn368IlefsTer17	p.N368Ifs*17	ENST00000268035	NM_000875.3	366	cGg/cg	4/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.27	2		357	462	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532653	63532654	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1301294410	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	165	672	0	ENST00000307078.5:c.1925dup	p.Ala643GlyfsTer64	p.A643Gfs*64	ENST00000307078	NM_004655.3	642	aag/aaAg	8/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.27	2		672	870	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	164	335	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	1	0.983	1	1	0.993	1	CLONAL	2	TRUE	1	0.27	2		335	495	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451784	29451784	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs772809305	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	117	705	0	ENST00000389048.3:c.2781del	p.Cys928AlafsTer11	p.C928Afs*11	ENST00000389048	NM_004304.4	927	ggG/gg	16/29	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.27	2		705	708	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518024	187518024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147405100	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	106	480	0	ENST00000441802.2:c.12670G>A	p.Ala4224Thr	p.A4224T	ENST00000441802	NM_005245.3	4224	Gct/Act	25/27	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.27	2		480	628	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	93	418	2	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.27	2		420	587	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026852	48026852	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376220212	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	95	380	0	ENST00000234420.5:c.1730G>A	p.Arg577His	p.R577H	ENST00000234420	NM_000179.2	577	cGc/cAc	4/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.27	2		380	501	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519505	137519506	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs780346130	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	83	304	3	ENST00000367739.4:c.1132_1133del	p.Ser378PhefsTer6	p.S378Ffs*6	ENST00000367739	NM_000416.2	378	AGt/t	7/7	1	2	FACETS	0.907	0.807	1	1	0.984	1	CLONAL	2	TRUE	1	0.27	2		307	339	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173696	108173696	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	79	343	0	ENST00000278616.4:c.5441del	p.Leu1814TrpfsTer14	p.L1814Wfs*14	ENST00000278616	NM_000051.3	1812	gcT/gc	36/63	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.27	2		343	456	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755470	39755470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	113	461	1	ENST00000288319.7:c.1295C>T	p.Ala432Val	p.A432V	ENST00000288319	NM_182918.3	432	gCg/gTg	10/10	1	2	FACETS	0.754	0.681	0.831	1	0.984	1	SUBCLONAL	2	TRUE	1	0.27	2		462	555	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	148	838	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	0.27	2		842	784	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	182	862	1	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.27	2		863	961	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231610	5231611	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	21	180	0	ENST00000357368.4:c.1865dup	p.Gln623SerfsTer4	p.Q623Sfs*4	ENST00000357368	NM_002850.3	622	cct/ccCt	14/38	1	2	FACETS	0.794	0.614	1	0.794	0.614	1	CLONAL	1	TRUE	1	0.27	2		180	196	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135314	30135314	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	53	454	0	ENST00000331968.5:c.504G>T	p.Trp168Cys	p.W168C	ENST00000331968	NM_002742.2	168	tgG/tgT	3/18	1	2	FACETS	0.684	0.583	0.795	0.684	0.583	0.795	SUBCLONAL	1	TRUE	1	0.27	2		454	574	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84393376	84393376	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	69	243	0	ENST00000321945.7:c.281del	p.Lys94ArgfsTer4	p.K94Rfs*4	ENST00000321945	NM_139076.2	94	aAg/ag	4/9	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.27	2		243	394	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444808	49444809	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	190	851	0	ENST00000301067.7:c.2657dup	p.Gly887TrpfsTer16	p.G887Wfs*16	ENST00000301067	NM_003482.3	886	cct/ccCt	10/54	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.27	2		851	1021	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243809	41243809	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80357191	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	146	543	0	ENST00000357654.3:c.3739G>A	p.Val1247Ile	p.V1247I	ENST00000357654	NM_007294.3	1247	Gtt/Att	10/23	1	2	FACETS	0.904	0.829	0.983	1	0.99	1	CLONAL	2	TRUE	1	0.27	2		543	598	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779742	3779742	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	143	674	0	ENST00000262367.5:c.5306G>A	p.Arg1769Gln	p.R1769Q	ENST00000262367	NM_004380.2	1769	cGg/cAg	31/31	1	2	FACETS	0.798	0.729	0.869	1	0.988	1	SUBCLONAL	2	TRUE	1	0.27	2		674	664	SUCCESS
APC	324	MSKCC	GRCh37	5	112176017	112176017	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554086134	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	78	247	0	ENST00000257430.4:c.4726G>T	p.Glu1576Ter	p.E1576*	ENST00000257430	NM_000038.5	1576	Gaa/Taa	16/16	1	2	FACETS	0.787	0.696	0.883	1	0.979	1	SUBCLONAL	2	TRUE	1	0.27	2		247	367	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749989	162749989	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	131	409	0	ENST00000367921.3:c.2521T>G	p.Ser841Ala	p.S841A	ENST00000367921	NM_006182.2	841	Tca/Gca	18/18	1	2	FACETS	0.813	0.74	0.889	1	0.988	1	CLONAL	2	TRUE	1	0.27	2		409	597	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982349	201982349	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	240	866	0	ENST00000359651.3:c.728G>T	p.Gly243Val	p.G243V	ENST00000359651		243	gGg/gTg	6/8	1	2	FACETS	0.847	0.79	0.904	1	0.993	1	CLONAL	2	TRUE	1	0.27	2		866	1050	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097655	8097655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751464240	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	97	322	0	ENST00000346208.3:c.37C>T	p.His13Tyr	p.H13Y	ENST00000346208		13	Cac/Tac	2/6	1	2	FACETS	0.916	0.823	1	1	0.986	1	CLONAL	2	TRUE	1	0.27	2		322	392	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742823	17742823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	201	853	2	ENST00000250003.3:c.731C>T	p.Ala244Val	p.A244V	ENST00000250003	NM_002478.4	244	gCg/gTg	3/3	1	2	FACETS	0.81	0.751	0.871	1	0.992	1	CLONAL	2	TRUE	1	0.27	2		855	919	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112893850	112893850	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	121	427	0	ENST00000351677.2:c.739T>G	p.Phe247Val	p.F247V	ENST00000351677	NM_002834.3	247	Ttt/Gtt	6/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.27	2		427	735	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992834	72992834	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	132	675	1	ENST00000268489.5:c.1211G>A	p.Gly404Asp	p.G404D	ENST00000268489	NM_006885.3	404	gGc/gAc	2/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.27	2		676	739	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942084	81942084	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	102	605	2	ENST00000359376.3:c.1621A>T	p.Thr541Ser	p.T541S	ENST00000359376	NM_002661.3	541	Acg/Tcg	17/33	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.27	2		607	694	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40461064	40461064	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	53	708	0	ENST00000345506.4:c.2063-1G>A		p.X688_splice	ENST00000345506	NM_003152.3	688			1	2	FACETS	0.453	0.385	0.528	0.453	0.385	0.528	SUBCLONAL	1	TRUE	1	0.27	2		708	867	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727931	78727931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	125	551	0	ENST00000306801.3:c.776C>T	p.Pro259Leu	p.P259L	ENST00000306801	NM_020761.2	259	cCg/cTg	6/34	1	2	FACETS	0.759	0.689	0.832	1	0.986	1	SUBCLONAL	2	TRUE	1	0.27	2		551	610	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117608	4117608	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	143	554	0	ENST00000262948.5:c.112C>T	p.Gln38Ter	p.Q38*	ENST00000262948	NM_030662.3	38	Cag/Tag	2/11	1	2	FACETS	0.795	0.727	0.867	1	0.988	1	SUBCLONAL	2	TRUE	1	0.27	2		554	666	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149668	202149668	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	105	438	0	ENST00000358485.4:c.1109T>G	p.Ile370Ser	p.I370S	ENST00000358485	NM_001080125.1	370	aTc/aGc	8/9	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.27	2		438	575	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509804	187509804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770939534	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	52	273	0	ENST00000441802.2:c.13709G>A	p.Gly4570Asp	p.G4570D	ENST00000441802	NM_005245.3	4570	gGc/gAc	27/27	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.27	2		273	353	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295394	1295394	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	45	191	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.975	0.832	1	1	0.973	1	CLONAL	2	TRUE	1	0.27	2		191	171	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576801	67576801	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	78	313	0	ENST00000274335.5:c.883T>C	p.Ser295Pro	p.S295P	ENST00000274335		295	Tca/Cca	6/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.27	2		313	435	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527599	157527599	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	154	509	0	ENST00000346085.5:c.5324A>C	p.Lys1775Thr	p.K1775T	ENST00000346085	NM_020732.3	1775	aAg/aCg	20/20	1	2	FACETS	0.92	0.845	0.997	1	0.991	1	CLONAL	2	TRUE	1	0.27	2		509	620	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187274	38187274	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	134	530	0	ENST00000317025.8:c.1203G>T	p.Glu401Asp	p.E401D	ENST00000317025	NM_023034.1	401	gaG/gaT	6/24	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.27	2		530	812	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759821	133759821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571264328	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	116	613	1	ENST00000318560.5:c.2144G>A	p.Arg715His	p.R715H	ENST00000318560	NM_005157.4	715	cGc/cAc	11/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.27	2		614	622	SUCCESS
AR	367	MSKCC	GRCh37	X	66766079	66766079	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	180	414	0	ENST00000374690.3:c.1091A>G	p.Tyr364Cys	p.Y364C	ENST00000374690	NM_000044.3	364	tAc/tGc	1/8	1	1	FACETS	0.858	0.8	0.917	1	0.994	1	CLONAL	3	TRUE	0	0.27	1		414	448	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557476	21557476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	95	534	0	ENST00000382592.4:c.2369G>A	p.Arg790Gln	p.R790Q	ENST00000382592	NM_014572.2	790	cGa/cAa	5/8	0.266561219845566	1	FACETS	0.981	0.877	1	0.981	0.877	1	CLONAL	1	TRUE	0	0.34056346451187	1		534	472	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051652	30051652	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555993336	NA	P-0039074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	80	320	0	ENST00000338641.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000338641	NM_000268.3	196	Cga/Tga	6/16	0.34056346451187	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.34056346451187	1		320	304	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130310	2130310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373481458	NA	P-0039074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	250	909	3	ENST00000219476.3:c.3542C>T	p.Thr1181Met	p.T1181M	ENST00000219476	NM_000548.3	1181	aCg/aTg	30/42	0.306332770387268	3	FACETS	0.828	0.774	0.883	0.828	0.774	0.883	CLONAL	2	TRUE	1	0.34056346451187	3		912	1038	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40864342	40864344	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	novel	NA	P-0039074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	126	724	1	ENST00000428826.2:c.1364_1366del	p.Ser455_Ile456delinsLeu	p.S455_I456delinsL	ENST00000428826		455	tCAAta/tta	12/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.34056346451187	2		725	684	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937605	17937605	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754575891	NA	P-0039075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	97	861	0	ENST00000458235.1:c.3322C>T	p.His1108Tyr	p.H1108Y	ENST00000458235	NM_000215.3	1108	Cat/Tat	24/24	1	2	FACETS	0.902	0.803	1	0.902	0.803	1	CLONAL	1	TRUE	1	0.274114790194487	2		861	785	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068269	30068269	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	54	378	0	ENST00000331968.5:c.2130A>C	p.Glu710Asp	p.E710D	ENST00000331968	NM_002742.2	710	gaA/gaC	15/18	1	2	FACETS	0.931	0.798	1	0.931	0.798	1	CLONAL	1	TRUE	1	0.274114790194487	2		378	423	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087417	27087426	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGGATTTC	CAGGGATTTC	-	novel	NA	P-0039087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	86	629	0	ENST00000324856.7:c.1994_2003del	p.Gly665AlafsTer74	p.G665Afs*74	ENST00000324856	NM_006015.4	664	tCAGGGATTTCc/tc	5/20	1	2	FACETS	0.761	0.672	0.856	0.761	0.672	0.856	SUBCLONAL	1	TRUE	1	0.292466443402811	2		629	773	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143181696	143181696	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	46	334	0	ENST00000262992.4:c.637A>T	p.Thr213Ser	p.T213S	ENST00000262992	NM_001101669.1	213	Aca/Tca	9/24	1	2	FACETS	0.725	0.611	0.85	0.725	0.611	0.85	SUBCLONAL	1	TRUE	1	0.292466443402811	2		334	434	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0039088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	40	316	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		316	479	SUCCESS
APC	324	MSKCC	GRCh37	5	112175324	112175324	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1211642532	NA	P-0039088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	62	180	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		180	313	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210796	5210796	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758652323	NA	P-0039088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	88	543	2	ENST00000357368.4:c.5255C>T	p.Ala1752Val	p.A1752V	ENST00000357368	NM_002850.3	1752	gCg/gTg	34/38	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		545	754	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265544	152265544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	66	429	1	ENST00000206249.3:c.997C>T	p.Pro333Ser	p.P333S	ENST00000206249	NM_000125.3	333	Cct/Tct	4/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		430	641	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	122	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.74965882593005	2		174	267	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0039090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	371	611	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.74965882593005	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.74965882593005	1		611	605	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683977	29683977	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0039090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	407	414	0	ENST00000356175.3:c.7676-1G>C		p.X2559_splice	ENST00000356175	NM_000267.3	2559			0.733335560501555	2	FACETS	0.987	0.957	1	0.987	0.957	1	CLONAL	2	TRUE	0	0.74965882593005	2		414	550	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857196	9857196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs74935155	NA	P-0039090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	172	416	0	ENST00000330684.3:c.4205G>A	p.Arg1402Gln	p.R1402Q	ENST00000330684	NM_001134407.1	1402	cGg/cAg	13/13	1	2	FACETS	0.912	0.846	0.98	0.912	0.846	0.98	CLONAL	1	TRUE	1	0.74965882593005	2		416	503	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653831	89653832	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1564814541	NA	P-0039090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	325	366	0	ENST00000371953.3:c.131dup	p.Val45ArgfsTer7	p.V45Rfs*7	ENST00000371953	NM_000314.4	43	-/G	2/9	0.74965882593005	2	FACETS	0.926	0.892	0.96	0.926	0.892	0.96	CLONAL	2	TRUE	0	0.74965882593005	2		366	468	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523725	148523725	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0039090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	59	199	0	ENST00000320356.2:c.729-1G>C		p.X243_splice	ENST00000320356	NM_004456.4	243			0.74965882593005	3	FACETS	0.625	0.541	0.716	0.313	0.27	0.358	SUBCLONAL	1	TRUE	1	0.74965882593005	3		199	346	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0039092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	83	318	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA	2	FACETS	0.899	0.797	1			1	INDETERMINATE	1	TRUE	NA	0.441891541471625	2		318	418	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448310	56448310	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567880628	NA	P-0039092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	214	569	0	ENST00000407977.2:c.337C>T	p.Arg113Ter	p.R113*	ENST00000407977		113	Cga/Tga	3/10	0.441891541471625	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.441891541471625	1		569	661	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105561	11105561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372078902	NA	P-0039092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	202	550	1	ENST00000358026.2:c.1477G>A	p.Val493Ile	p.V493I	ENST00000358026	NM_001128849.1	493	Gtc/Atc	9/36	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.441891541471625	2		551	892	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831345	89831346	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs878853663	NA	P-0039092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	178	519	2	ENST00000389301.3:c.2730_2731del	p.Trp911AspfsTer31	p.W911Dfs*31	ENST00000389301	NM_000135.2	910	ctCTgg/ctgg	28/43	1	2	FACETS	0.981	0.906	1	0.981	0.906	1	CLONAL	1	TRUE	1	0.441891541471625	2		521	821	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873120	151873280	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCGTCTCAAAACAAAACAAACAAACTCCTCAAGGAGGAATAGAAAAACTCAGTGCTTTATTCCAACTGTAATTCTAATAATAAAATCTTATAAGCATATCGCATGCCACTCTAATACCCATAGTAATATACGTTGAGACTCAAGAAAACTCCTACCAATA	TCCGTCTCAAAACAAAACAAACAAACTCCTCAAGGAGGAATAGAAAAACTCAGTGCTTTATTCCAACTGTAATTCTAATAATAAAATCTTATAAGCATATCGCATGCCACTCTAATACCCATAGTAATATACGTTGAGACTCAAGAAAACTCCTACCAATA	-	novel	NA	P-0039092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	32	38	0	ENST00000262189.6:c.9258_9262+156del		p.X3086_splice	ENST00000262189	NM_170606.2	3086		38/59	0.441891541471625	1	FACETS	1	0.939	1	1	0.973	1	CLONAL	2	TRUE	0	0.441891541471625	1		38	49	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560257	95560257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	100	318	0	ENST00000393063.1:c.5332G>C	p.Glu1778Gln	p.E1778Q	ENST00000393063	NM_030621.3	1778	Gag/Cag	25/28	0.513149849221169	5	FACETS	1	0.941	1			1	CLONAL	1	TRUE	NA	0.51541311479507	5		318	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577095	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519984	NA	P-0039094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	383	729	0	ENST00000269305.4:c.843C>G	p.Asp281Glu	p.D281E	ENST00000269305	NM_001126112.2	281	gaC/gaG	8/11	0.506825633222032	2	FACETS	0.971	0.93	1	0.971	0.93	1	CLONAL	2	TRUE	0	0.51541311479507	2		729	765	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260165	16260165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751562088	NA	P-0039094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	194	524	0	ENST00000375759.3:c.7430C>T	p.Ala2477Val	p.A2477V	ENST00000375759	NM_015001.2	2477	gCa/gTa	11/15	0.51541311479507	4	FACETS	1	0.985	1	0.417	0.385	0.449	CLONAL	1	TRUE	1	0.51541311479507	4		524	913	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536741	120536741	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0039094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	143	629	0	ENST00000229340.5:c.353-2A>T		p.X118_splice	ENST00000229340	NM_006861.6	118			0.421973907476599	3	FACETS	0.921	0.84	1			1	CLONAL	1	TRUE	NA	0.51541311479507	3		629	758	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912648	32912660	+	frameshift_variant	Frame_Shift_Del	DEL	GATTTAACTTTTT	GATTTAACTTTTT	-	novel	NA	P-0039094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	296	417	0	ENST00000380152.3:c.4156_4168del	p.Asp1386TrpfsTer20	p.D1386Wfs*20	ENST00000380152		1386	GATTTAACTTTTTtg/tg	11/27	0.51541311479507	3	FACETS	0.914	0.872	0.955	0.914	0.872	0.955	CLONAL	3	TRUE	0	0.51541311479507	3		417	527	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117550	70117551	+	missense_variant	Missense_Mutation	DNP	CT	CT	TG	novel	NA	P-0039094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	125	570	1	ENST00000245479.2:c.18_19delinsTG	p.Phe7Val	p.F7V	ENST00000245479	NM_000346.3	6	ccCTtc/ccTGtc	1/3	0.506825633222032	2	FACETS	0.847	0.769	0.928	0.423	0.384	0.464	CLONAL	1	TRUE	0	0.51541311479507	2		571	573	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212173	5212173	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	175	782	0	ENST00000357368.4:c.4858C>T	p.His1620Tyr	p.H1620Y	ENST00000357368	NM_002850.3	1620	Cac/Tac	32/38	1	2	FACETS	0.923	0.852	0.996	0.923	0.852	0.996	CLONAL	1	TRUE	1	0.51541311479507	2		782	736	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130507	29130507	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	164	551	0	ENST00000328354.6:c.203C>G	p.Thr68Ser	p.T68S	ENST00000328354	NM_007194.3	68	aCt/aGt	2/15	0.51541311479507	3	FACETS	0.965	0.887	1	0.483	0.443	0.524	CLONAL	1	TRUE	1	0.51541311479507	3		551	829	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226049	226049	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	40	90	0	ENST00000264932.6:c.508C>A	p.Gln170Lys	p.Q170K	ENST00000264932	NM_004168.2	170	Cag/Aag	5/15	0.51541311479507	6	FACETS	1	0.943	1			1	CLONAL	1	TRUE	NA	0.51541311479507	6		90	240	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637666	176637666	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs142657029	NA	P-0039094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	154	579	0	ENST00000439151.2:c.2266A>G	p.Asn756Asp	p.N756D	ENST00000439151	NM_022455.4	756	Aac/Gac	5/23	0.506825633222032	2	FACETS	1	0.965	1	0.544	0.501	0.589	CLONAL	1	TRUE	0	0.51541311479507	2		579	549	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023262	150023262	+	start_lost	Translation_Start_Site	SNP	T	T	G	novel	NA	P-0039094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	78	306	0	ENST00000253339.5:c.1A>C	p.Met1?	p.M1?	ENST00000253339		1	Atg/Ctg	1/7	1	2	FACETS	0.86	0.761	0.964	0.86	0.761	0.964	CLONAL	1	TRUE	1	0.51541311479507	2		306	352	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117551	70117551	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	122	571	0	ENST00000245479.2:c.19T>G	p.Phe7Val	p.F7V	ENST00000245479	NM_000346.3	7	Ttc/Gtc	1/3	0.506825633222032	2	FACETS	0.826	0.749	0.907	0.413	0.374	0.454	CLONAL	1	TRUE	0	0.51541311479507	2		571	573	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0039096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	80	248	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.291840240305259	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.291840240305259	1		248	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0039096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	252	709	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.291840240305259	1	FACETS	0.861	0.807	0.915	1	0.994	1	CLONAL	2	TRUE	0	0.291840240305259	1		709	857	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753132	42753132	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0039096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	102	553	0	ENST00000222329.4:c.1132A>T	p.Lys378Ter	p.K378*	ENST00000222329	NM_006494.2	378	Aag/Tag	4/4	1	2	FACETS	0.892	0.797	0.992	0.892	0.797	0.992	CLONAL	1	TRUE	1	0.291840240305259	2		553	784	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	84	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.45618271794016	2		174	329	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313265	65313265	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	161	466	0	ENST00000342505.4:c.1849A>G	p.Ile617Val	p.I617V	ENST00000342505	NM_002227.2	617	Ata/Gta	13/25	1	2	FACETS	0.978	0.899	1	0.978	0.899	1	CLONAL	1	TRUE	1	0.45618271794016	2		466	722	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548866	29548866	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0039097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	139	558	0	ENST00000356175.3:c.1642-2A>C		p.X548_splice	ENST00000356175	NM_000267.3	548			1	2	FACETS	0.811	0.74	0.887	0.811	0.74	0.887	CLONAL	1	TRUE	1	0.45618271794016	2		558	751	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711913	89711918	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	TTATAG	TTATAG	A	novel	NA	P-0039097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	54	426	0	ENST00000371953.3:c.531_536delinsA	p.Tyr177Ter	p.Y177*	ENST00000371953	NM_000314.4	177	taTTATAGc/taAc	6/9	0.45618271794016	1	FACETS	0.483	0.414	0.559	0.483	0.414	0.559	SUBCLONAL	1	TRUE	0	0.45618271794016	1		426	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0039104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	935	732	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.604128589086869	3	FACETS	1	0.981	1			1	CLONAL	3	TRUE	NA	0.606288540793001	3		732	1336	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119721044	119721044	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	220	511	0	ENST00000316626.5:c.131C>G	p.Pro44Arg	p.P44R	ENST00000316626		44	cCt/cGt	2/12	0.606288540793001	5	FACETS	1	0.929	1	0.334	0.309	0.359	CLONAL	1	TRUE	2	0.606288540793001	5		511	1385	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045986	26045986	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	96	414	0	ENST00000540144.1:c.348A>T	p.Lys116Asn	p.K116N	ENST00000540144	NM_003531.2	116	aaA/aaT	1/1	0.579684614984167	4	FACETS	0.529	0.471	0.592	0.265	0.235	0.296	SUBCLONAL	1	TRUE	2	0.606288540793001	4		414	961	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100553	157100553	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764716697	NA	P-0039104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	89	398	0	ENST00000346085.5:c.1490G>A	p.Ser497Asn	p.S497N	ENST00000346085	NM_020732.3	497	aGt/aAt	1/20	0.606288540793001	1	FACETS	0.546	0.487	0.607	0.546	0.487	0.607	SUBCLONAL	1	TRUE	0	0.606288540793001	1		398	375	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864015	97864015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	51	509	0	ENST00000289081.3:c.1651C>T	p.Leu551Phe	p.L551F	ENST00000289081	NM_000136.2	551	Ctt/Ttt	15/15	0.606288540793001	2	FACETS	0.223	0.189	0.261	0.111	0.094	0.131	SUBCLONAL	1	TRUE	0	0.606288540793001	2		509	755	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	19	174	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	TRUE	0	0.14	1		174	213	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652198	36652199	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	38	526	0	ENST00000244741.5:c.322dup	p.Glu108GlyfsTer21	p.E108Gfs*21	ENST00000244741	NM_000389.4	107	gag/gaGg	2/3	1	2	FACETS	0.917	0.757	1	0.917	0.757	1	CLONAL	1	TRUE	1	0.14	2		526	592	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539091	187539092	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0039109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	38	378	0	ENST00000441802.2:c.8648dup	p.Tyr2883Ter	p.Y2883*	ENST00000441802	NM_005245.3	2883	tac/taAc	10/27	1	2	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	TRUE	1	0.14	2		378	529	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224447	123224448	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CATG	novel	NA	P-0039109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	34	213	0	ENST00000218089.9:c.3300_3301insCATG	p.Ser1101HisfsTer36	p.S1101Hfs*36	ENST00000218089	NM_001042749.1	1100	-/CATG	31/35	1	1	FACETS	0.886	0.728	1	1	0.958	1	CLONAL	2	TRUE	0	0.14	1		213	255	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912656	NA	P-0039112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	212	551	0	ENST00000269305.4:c.734G>C	p.Gly245Ala	p.G245A	ENST00000269305	NM_001126112.2	245	gGc/gCc	7/11	0.150452648061372	2	FACETS	1	0.979	1	1	0.994	1	CLONAL	4	TRUE	0	0.150452648061372	2		551	633	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578433	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	289	705	0	ENST00000269305.4:c.497C>A	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	166	tCa/tAa	5/11	0.655050941418497	1	FACETS	0.992	0.942	1	0.992	0.942	1	CLONAL	1	TRUE	0	0.655050941418497	1		705	598	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451092	70451092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	221	547	0	ENST00000373644.4:c.5932G>A	p.Asp1978Asn	p.D1978N	ENST00000373644	NM_030625.2	1978	Gac/Aac	12/12	0.655050941418497	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.655050941418497	1		547	418	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456665	32456665	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	75	222	0	ENST00000332351.3:c.227T>A	p.Leu76Gln	p.L76Q	ENST00000332351	NM_024426.4	76	cTg/cAg	1/10	0.655050941418497	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.655050941418497	1		222	137	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620451	52620451	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	93	357	0	ENST00000394830.3:c.3302A>G	p.Asn1101Ser	p.N1101S	ENST00000394830	NM_018313.4	1101	aAc/aGc	21/30	0.655050941418497	1	FACETS	0.86	0.78	0.941	0.86	0.78	0.941	CLONAL	1	TRUE	0	0.655050941418497	1		357	222	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443348	187443348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	155	342	0	ENST00000232014.4:c.1778C>T	p.Thr593Ile	p.T593I	ENST00000232014	NM_001130845.1	593	aCt/aTt	8/10	0.183214331842093	5	FACETS	0.795	0.731	0.861	0.53	0.487	0.574	INDETERMINATE	2	TRUE	2	0.655050941418497	5		342	590	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520262	176520262	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	188	610	0	ENST00000292408.4:c.1181C>G	p.Ala394Gly	p.A394G	ENST00000292408	NM_213647.1	394	gCg/gGg	9/18	1	2	FACETS	0.762	0.706	0.82	0.762	0.706	0.82	SUBCLONAL	1	TRUE	1	0.655050941418497	2		610	753	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240748	55240748	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	168	711	0	ENST00000275493.2:c.1992C>G	p.Ile664Met	p.I664M	ENST00000275493	NM_005228.3	664	atC/atG	17/28	0.208151863041542	1	FACETS	0.505	0.465	0.546	0.505	0.465	0.546	INDETERMINATE	1	TRUE	0	0.655050941418497	1		711	683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0039118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	489	670	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.940294525288074	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.940294525288074	1		670	527	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425358	49425358	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	516	622	2	ENST00000301067.7:c.13130G>A	p.Trp4377Ter	p.W4377*	ENST00000301067	NM_003482.3	4377	tGg/tAg	39/54	0.940294525288074	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.940294525288074	1		624	564	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511574	66511574	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	264	234	0	ENST00000358598.2:c.34G>T	p.Ala12Ser	p.A12S	ENST00000358598	NM_212471.2	12	Gca/Tca	2/11	0.940294525288074	2	FACETS	1	0.97	1	0.517	0.49	0.544	CLONAL	1	TRUE	0	0.940294525288074	2		234	543	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38148037	38148038	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	A	novel	NA	P-0039118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	390	480	0	ENST00000317025.8:c.3073_3074delinsT	p.Phe1026LeufsTer26	p.F1026Lfs*26	ENST00000317025	NM_023034.1	1025	AGc/Tc	17/24	1	2	FACETS	0.905	0.863	0.946	0.905	0.863	0.946	CLONAL	1	TRUE	1	0.940294525288074	2		480	917	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0039120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	365	559	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.8286855861113	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.8286855861113	1		559	466	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039093	49039241	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTTTTTTTTTTTTTTTTTTTTTTTTACTGTTCTTCCTCAGACATTCAAACGTGTTTTGATCAAAGAAGAGGAGTATGATTCTATTATAGTATTCTATAACTCGGTCTTCATGCAGAGACTGAAAACAAATATTTTGCAGTATGCTTCC	ACTTTTTTTTTTTTTTTTTTTTTTTTACTGTTCTTCCTCAGACATTCAAACGTGTTTTGATCAAAGAAGAGGAGTATGATTCTATTATAGTATTCTATAACTCGGTCTTCATGCAGAGACTGAAAACAAATATTTTGCAGTATGCTTCC	-	novel	NA	P-0039120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	45	75	0	ENST00000267163.4:c.2212-39_2321del		p.X738_splice	ENST00000267163	NM_000321.2	738		22/27	0.758821131354224	1	FACETS	0.86	0.763	0.952	0.86	0.763	0.952	CLONAL	1	TRUE	0	0.8286855861113	1		75	74	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49280972	49280972	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	156	416	0	ENST00000282018.3:c.19T>C	p.Ser7Pro	p.S7P	ENST00000282018	NM_020377.2	7	Tcc/Ccc	1/1	0.8286855861113	1	FACETS	0.984	0.932	1	0.984	0.932	1	CLONAL	1	TRUE	0	0.8286855861113	1		416	224	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528053	29528053	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1060500358	NA	P-0039120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	32	51	0	ENST00000356175.3:c.1063-2A>G		p.X355_splice	ENST00000356175	NM_000267.3	355			0.8286855861113	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.8286855861113	1		51	40	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016321	150016321	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0039120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	156	364	0	ENST00000253339.5:c.385A>T	p.Arg129Ter	p.R129*	ENST00000253339		129	Aga/Tga	2/7	0.8286855861113	1	FACETS	0.971	0.919	1	0.971	0.919	1	CLONAL	1	TRUE	0	0.8286855861113	1		364	227	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436162	116436162	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	116	258	0	ENST00000397752.3:c.4157T>A	p.Phe1386Tyr	p.F1386Y	ENST00000397752	NM_000245.2	1386	tTc/tAc	21/21	1	2	FACETS	0.921	0.842	1	0.921	0.842	1	CLONAL	1	TRUE	1	0.8286855861113	2		258	304	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798755	135798755	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	69	246	0	ENST00000298552.3:c.488C>A	p.Ser163Ter	p.S163*	ENST00000298552	NM_001162426.1	163	tCa/tAa	6/23	0.8286855861113	1	FACETS	0.646	0.578	0.714	0.646	0.578	0.714	SUBCLONAL	1	TRUE	0	0.8286855861113	1		246	151	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0039124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	106	833	3	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.327007374291521	1	FACETS	0.878	0.788	0.972	0.878	0.788	0.972	CLONAL	1	TRUE	0	0.327007374291521	1		836	618	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0039124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	146	557	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.276940028564287	3	FACETS	0.827	0.758	0.9	0.827	0.758	0.9	CLONAL	2	TRUE	1	0.327007374291521	3		557	628	SUCCESS
APC	324	MSKCC	GRCh37	5	112175466	112175466	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786204170	NA	P-0039124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	78	391	0	ENST00000257430.4:c.4175C>A	p.Ser1392Ter	p.S1392*	ENST00000257430	NM_000038.5	1392	tCa/tAa	16/16	0.270451180348303	2	FACETS	0.755	0.669	0.845	0.755	0.669	0.845	SUBCLONAL	2	TRUE	0	0.327007374291521	2		391	316	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983127	149983127	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	50	722	0	ENST00000253339.5:c.3131del	p.Pro1044LeufsTer14	p.P1044Lfs*14	ENST00000253339		1044	cCt/ct	7/7	1	2	FACETS	0.433	0.366	0.506	0.433	0.366	0.506	SUBCLONAL	1	TRUE	1	0.327007374291521	2		722	707	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	169	174	0				ENST00000310581	NM_198253.2	-/1132			0.155284520233115	4	FACETS	1	0.928	1	1	0.928	1	INDETERMINATE	2	TRUE	2	0.29	4		174	746	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527264	187527264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754008095	NA	P-0039126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	228	507	3	ENST00000441802.2:c.10310C>T	p.Ala3437Val	p.A3437V	ENST00000441802	NM_005245.3	3437	gCg/gTg	17/27	0.283083163819046	2	FACETS	0.96	0.897	1	0.96	0.897	1	CLONAL	2	TRUE	0	0.29	2		510	819	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47079197	47079197	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	250	572	0	ENST00000409792.3:c.7309A>G	p.Met2437Val	p.M2437V	ENST00000409792	NM_014159.6	2437	Atg/Gtg	18/21	0.155284520233115	4	FACETS	1	0.97	1	1	0.97	1	INDETERMINATE	2	TRUE	2	0.29	4		572	1048	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0039127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	529	515	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.276850646483257	11	FACETS	0.939	0.904	0.975			1	CLONAL	8	TRUE	NA	0.276850646483257	11		515	1142	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	24	339	0	ENST00000256196.4:c.68G>T	p.Gly23Val	p.G23V	ENST00000256196		23	gGc/gTc	1/6	1	2	FACETS	0.375	0.293	0.47	0.375	0.293	0.47	SUBCLONAL	1	TRUE	1	0.276850646483257	2		339	462	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760700	59760700	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265133595	NA	P-0039127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	63	737	0	ENST00000259008.2:c.3707C>T	p.Pro1236Leu	p.P1236L	ENST00000259008	NM_032043.2	1236	cCa/cTa	20/20	0.275642138642413	3	FACETS	0.651	0.562	0.748	0.325	0.281	0.374	SUBCLONAL	1	TRUE	1	0.276850646483257	3		737	796	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0039128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	123	638	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.52669762119761	4	FACETS	0.869	0.786	0.956	0.29	0.262	0.319	CLONAL	1	TRUE	1	0.536486589149999	4		639	811	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024488	31024488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs6057581	NA	P-0039128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	486	729	0	ENST00000375687.4:c.3973C>T	p.Leu1325Phe	p.L1325F	ENST00000375687	NM_015338.5	1325	Ctt/Ttt	13/13	0.40043430991062	3	FACETS	0.999	0.958	1	0.999	0.958	1	CLONAL	2	TRUE	1	0.536486589149999	3		729	1150	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207064	1207065	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1131690917	NA	P-0039128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	566	926	0	ENST00000326873.7:c.157dup	p.Asp53GlyfsTer110	p.D53Gfs*110	ENST00000326873	NM_000455.4	51	atg/atGg	1/10	0.536486589149999	2	FACETS	0.962	0.928	0.995	0.962	0.928	0.995	CLONAL	2	TRUE	0	0.536486589149999	2		926	1097	SUCCESS
APC	324	MSKCC	GRCh37	5	112177434	112177435	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	107	412	0	ENST00000257430.4:c.6149dup	p.Lys2051GlufsTer9	p.K2051Efs*9	ENST00000257430	NM_000038.5	2048	cca/ccAa	16/16	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.536486589149999	2		412	385	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883131	37883131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774520188	NA	P-0039128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	301	897	2	ENST00000269571.5:c.3034G>A	p.Asp1012Asn	p.D1012N	ENST00000269571		1012	Gat/Aat	25/27	1	2	FACETS	0.994	0.936	1	0.994	0.936	1	CLONAL	1	TRUE	1	0.536486589149999	2		899	1129	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422898	49422898	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	279	819	0	ENST00000301067.7:c.14197G>C	p.Glu4733Gln	p.E4733Q	ENST00000301067	NM_003482.3	4733	Gag/Cag	44/54	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.536486589149999	2		819	922	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134206	11134206	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	228	682	0	ENST00000358026.2:c.2872G>C	p.Glu958Gln	p.E958Q	ENST00000358026	NM_001128849.1	958	Gag/Cag	20/36	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.536486589149999	2		682	822	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395571	31395571	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	176	668	0	ENST00000328111.2:c.2424C>G	p.Ile808Met	p.I808M	ENST00000328111	NM_006892.3	808	atC/atG	23/23	0.40043430991062	3	FACETS	0.878	0.808	0.95	0.439	0.404	0.475	CLONAL	1	TRUE	1	0.536486589149999	3		668	948	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444625	187444625	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1333525198	NA	P-0039128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	212	566	0	ENST00000232014.4:c.1602G>C	p.Lys534Asn	p.K534N	ENST00000232014	NM_001130845.1	534	aaG/aaC	7/10	0.52669762119761	4	FACETS	1	0.932	1	0.335	0.31	0.361	CLONAL	1	TRUE	1	0.536486589149999	4		566	1208	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339285	70339285	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	43	332	0	ENST00000374080.3:c.162T>G	p.Asp54Glu	p.D54E	ENST00000374080		54	gaT/gaG	2/45	1	1	FACETS	0.261	0.218	0.309	0.261	0.218	0.309	SUBCLONAL	1	TRUE	0	0.536486589149999	1		332	449	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0039129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	219	541	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.268111071954584	5	FACETS	1	0.987	1	0.828	0.771	0.887	CLONAL	2	TRUE	2	0.268111071954584	5		541	922	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426830	121426830	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201934320	NA	P-0039129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	36	500	0	ENST00000257555.6:c.521C>T	p.Ala174Val	p.A174V	ENST00000257555		174	gCg/gTg	2/10	1	2	FACETS	0.575	0.472	0.69	0.575	0.472	0.69	SUBCLONAL	1	TRUE	1	0.268111071954584	2		500	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576885	7576885	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0039129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	124	692	0	ENST00000269305.4:c.961A>T	p.Lys321Ter	p.K321*	ENST00000269305	NM_001126112.2	321	Aaa/Taa	9/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.268111071954584	2		692	764	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	33	315	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	0.714	0.582	0.861	0.714	0.582	0.861	SUBCLONAL	1	TRUE	1	0.268111071954584	2		315	345	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0039130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	28	455	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.729	0.582	0.898	0.729	0.582	0.898	SUBCLONAL	1	TRUE	1	0.16	2		455	480	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260550	10260550	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0039130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	52	673	0	ENST00000340748.4:c.2312C>G	p.Ser771Ter	p.S771*	ENST00000340748		771	tCa/tGa	24/40	1	2	FACETS	0.831	0.706	0.969	0.831	0.706	0.969	CLONAL	1	TRUE	1	0.16	2		673	782	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442041	52442041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	62	593	0	ENST00000460680.1:c.308G>A	p.Cys103Tyr	p.C103Y	ENST00000460680	NM_004656.3	103	tGc/tAc	5/17	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.16	2		593	744	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0039131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	36	725	0	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	0.382542445368285	1	FACETS	0.24	0.197	0.289	0.24	0.197	0.289	SUBCLONAL	1	FALSE	0	0.382542445368285	1		725	634	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021817	71021817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs797045586	NA	P-0039131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	11	212	0	ENST00000318789.4:c.1541G>A	p.Arg514His	p.R514H	ENST00000318789	NM_032682.5	514	cGt/cAt	18/21	1	2	FACETS	0.479	0.333	0.658	0.479	0.333	0.658	SUBCLONAL	1	FALSE	1	0.382542445368285	2		212	120	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285570	46285570	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs78222561	NA	P-0039131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	20	289	0	ENST00000334344.6:c.4930C>T	p.Gln1644Ter	p.Q1644*	ENST00000334344	NM_152641.2	1644	Cag/Tag	17/21	0.175999737048053	4	FACETS	1	0.801	1	0.52	0.402	0.656	INDETERMINATE	1	FALSE	2	0.382542445368285	4		289	139	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679299	29679299	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs863224493	NA	P-0039131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	38	378	0	ENST00000356175.3:c.7419G>A	p.Trp2473Ter	p.W2473*	ENST00000356175	NM_000267.3	2473	tgG/tgA	50/57	0.382542445368285	1	FACETS	0.69	0.574	0.816	0.69	0.574	0.816	SUBCLONAL	1	FALSE	0	0.382542445368285	1		378	233	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831999	72831999	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0039131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	13	687	0	ENST00000268489.5:c.4582A>T	p.Arg1528Ter	p.R1528*	ENST00000268489	NM_006885.3	1528	Aga/Tga	9/10	0.382542445368285	1	FACETS	0.224	0.16	0.303	0.224	0.16	0.303	SUBCLONAL	1	FALSE	0	0.382542445368285	1		687	245	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679315	29679315	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	40	419	0	ENST00000356175.3:c.7435T>G	p.Ser2479Ala	p.S2479A	ENST00000356175	NM_000267.3	2479	Tct/Gct	50/57	0.382542445368285	1	FACETS	0.636	0.531	0.75	0.636	0.531	0.75	SUBCLONAL	1	FALSE	0	0.382542445368285	1		419	266	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0039132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	572	851	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.537854701314229	2	FACETS	0.838	0.808	0.867	0.838	0.808	0.867	CLONAL	2	TRUE	0	0.594864764046697	2		851	1148	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52693345	52693372	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	CCAAGATGGCGGCGGCCGACGGCGACGA	CCAAGATGGCGGCGGCCGACGGCGACGA	-	novel	NA	P-0039132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	392	479	0	ENST00000322088.6:c.-4_24del		p.*2*	ENST00000322088	NM_014225.5	?-8/589		1/15	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.594864764046697	NA		479	1103	SUCCESS
ATR	545	MSKCC	GRCh37	3	142212150	142212151	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0039132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	50	343	1	ENST00000350721.4:c.5901_5902delinsCT	p.Asp1968Tyr	p.D1968Y	ENST00000350721	NM_001184.3	1967	ggTGat/ggCTat	35/47	0.320289440714115	4	FACETS	0.395	0.335	0.462	0.198	0.167	0.231	INDETERMINATE	1	TRUE	2	0.594864764046697	4		344	678	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0039133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	216	318	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.44351382161174	4	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	2	0.44351382161174	4		318	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520006	NA	P-0039133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	389	841	0	ENST00000269305.4:c.821T>C	p.Val274Ala	p.V274A	ENST00000269305	NM_001126112.2	274	gTt/gCt	8/11	0.44351382161174	1	FACETS	0.886	0.849	0.924	1	0.997	1	CLONAL	2	TRUE	0	0.44351382161174	1		841	770	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370945	55370945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	202	725	1	ENST00000297316.4:c.247C>T	p.Arg83Cys	p.R83C	ENST00000297316	NM_022454.3	83	Cgc/Tgc	1/2	0.44351382161174	4	FACETS	1	0.982	1	0.397	0.368	0.428	CLONAL	1	TRUE	1	0.44351382161174	4		726	1103	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213843	66213843	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	79	491	0	ENST00000273854.3:c.2587A>T	p.Ser863Cys	p.S863C	ENST00000273854	NM_004439.5	863	Agt/Tgt	15/18	NA	2	FACETS	0.968	0.857	1			1	INDETERMINATE	1	TRUE	NA	0.44351382161174	2		491	368	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636409	21636409	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	194	597	0	ENST00000421138.2:c.601A>G	p.Met201Val	p.M201V	ENST00000421138		201	Atg/Gtg	7/16	0.44351382161174	3	FACETS	0.953	0.888	1	0.953	0.888	1	CLONAL	2	TRUE	1	0.44351382161174	3		597	561	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292411	15292411	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	290	831	0	ENST00000263388.2:c.2768A>C	p.Gln923Pro	p.Q923P	ENST00000263388	NM_000435.2	923	cAg/cCg	17/33	0.103044213828804	6	FACETS	0.857	0.807	0.907	0.857	0.807	0.907	INDETERMINATE	3	TRUE	3	0.44351382161174	6		831	960	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264671	46264671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	172	376	0	ENST00000371998.3:c.1541G>T	p.Gly514Val	p.G514V	ENST00000371998		514	gGg/gTg	12/23	0.359680308963175	5	FACETS	1	0.973	1	0.74	0.684	0.797	CLONAL	2	TRUE	2	0.44351382161174	5		376	582	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251974	153251974	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	92	560	0	ENST00000281708.4:c.1032del	p.Gly345ValfsTer32	p.G345Vfs*32	ENST00000281708	NM_033632.3	344	ccA/cc	7/12	NA	2	FACETS	0.932	0.833	1			1	INDETERMINATE	1	TRUE	NA	0.44351382161174	2		560	445	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576459	67576459	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	112	351	0	ENST00000274335.5:c.740del	p.Phe247SerfsTer13	p.F247Sfs*13	ENST00000274335		246	caT/ca	5/15	0.44351382161174	2	FACETS	0.868	0.792	0.945	0.868	0.792	0.945	CLONAL	2	TRUE	0	0.44351382161174	2		351	291	SUCCESS
APC	324	MSKCC	GRCh37	5	112137018	112137019	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	220	487	0	ENST00000257430.4:c.773dup	p.Arg259AlafsTer4	p.R259Afs*4	ENST00000257430	NM_000038.5	258	gag/gAag	8/16	0.44351382161174	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.44351382161174	2		487	482	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056399	26056399	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	67	377	0	ENST00000343677.2:c.258C>A	p.Ser86Arg	p.S86R	ENST00000343677	NM_005319.3	86	agC/agA	1/1	0.44351382161174	5	FACETS	1	0.918	1	0.358	0.311	0.407	CLONAL	1	TRUE	2	0.44351382161174	5		377	469	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68984737	68984737	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs951212628	NA	P-0039133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	74	338	1	ENST00000288368.4:c.1501G>T	p.Asp501Tyr	p.D501Y	ENST00000288368	NM_024870.2	501	Gat/Tat	14/40	0.44351382161174	4	FACETS	1	0.975	1	0.487	0.429	0.547	CLONAL	1	TRUE	1	0.44351382161174	4		339	330	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939030	76939030	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	193	664	0	ENST00000373344.5:c.1718G>A	p.Gly573Asp	p.G573D	ENST00000373344	NM_000489.3	573	gGt/gAt	9/35	0.44351382161174	5	FACETS	0.882	0.817	0.949	0.588	0.544	0.633	CLONAL	2	TRUE	2	0.44351382161174	5		664	822	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0039138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	131	515	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	TRUE	1	0.498743505135631	2		515	515	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0039138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	274	764	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	0.498743505135631	2		764	1074	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0039138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	215	561	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.498743505135631	2		561	811	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924238	11924238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	11	21	0	ENST00000353533.5:c.35C>T	p.Ser12Phe	p.S12F	ENST00000353533	NM_003010.3	12	tCc/tTc	1/11	1	2	FACETS	1	0.749	1	1	0.749	1	CLONAL	1	TRUE	1	0.498743505135631	2		21	42	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436054	49436054	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0039138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	215	632	0	ENST00000301067.7:c.5927C>G	p.Ser1976Ter	p.S1976*	ENST00000301067	NM_003482.3	1976	tCa/tGa	28/54	1	2	FACETS	0.9	0.837	0.965	0.9	0.837	0.965	CLONAL	1	TRUE	1	0.498743505135631	2		632	958	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982373	201982373	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	387	846	0	ENST00000359651.3:c.752G>T	p.Arg251Leu	p.R251L	ENST00000359651		251	cGa/cTa	6/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.498743505135631	2		846	1377	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983035	201983035	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	350	856	0	ENST00000359651.3:c.884G>C	p.Trp295Ser	p.W295S	ENST00000359651		295	tGg/tCg	7/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.498743505135631	2		856	1379	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432069	49432069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	345	880	0	ENST00000301067.7:c.9070G>A	p.Glu3024Lys	p.E3024K	ENST00000301067	NM_003482.3	3024	Gaa/Aaa	34/54	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.498743505135631	2		880	1337	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562736	29562736	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs756780735	NA	P-0039138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	201	476	0	ENST00000356175.3:c.3816G>C	p.Gln1272His	p.Q1272H	ENST00000356175	NM_000267.3	1272	caG/caC	28/57	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.498743505135631	2		476	658	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524129	187524129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375766862	NA	P-0039139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	114	651	0	ENST00000441802.2:c.11410G>A	p.Glu3804Lys	p.E3804K	ENST00000441802	NM_005245.3	3804	Gaa/Aaa	20/27	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.31	2		651	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579321	7579322	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs587780067	NA	P-0039142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	127	684	0	ENST00000269305.4:c.365_366del	p.Val122AspfsTer26	p.V122Dfs*26	ENST00000269305	NM_001126112.2	122	gTG/g	4/11	0.470203059257323	1	FACETS	0.866	0.791	0.944	0.866	0.791	0.944	CLONAL	1	TRUE	0	0.506978252870426	1		684	432	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	63	492	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.332603764894522	1	FACETS	0.836	0.728	0.952	0.836	0.728	0.952	CLONAL	1	TRUE	0	0.370925460302298	1		492	331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0039143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	174	976	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.355451898052668	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.370925460302298	1		976	742	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0039143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	71	514	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.370925460302298	1	FACETS	0.945	0.831	1	0.945	0.831	1	CLONAL	1	TRUE	0	0.370925460302298	1		514	330	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770587	40770587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776338672	NA	P-0039143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	49	579	0	ENST00000373198.4:c.2795G>A	p.Arg932His	p.R932H	ENST00000373198	NM_133170.3	932	cGc/cAc	19/32	0.214871877211698	0	FACETS	0.422	0.358	0.492			1	INDETERMINATE	1	TRUE	0	0.370925460302298	0		579	394	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121008	3121008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762218250	NA	P-0039143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	68	924	1	ENST00000078429.4:c.911C>T	p.Ala304Val	p.A304V	ENST00000078429	NM_002067.2	304	gCg/gTg	7/7	0.370925460302298	1	FACETS	0.408	0.354	0.466	0.408	0.354	0.466	SUBCLONAL	1	TRUE	0	0.370925460302298	1		925	732	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	116	775	0	ENST00000304494.5:c.247del	p.His83ThrfsTer63	p.H83Tfs*63	ENST00000304494	NM_000077.4	83	Cac/ac	2/3	0.370925460302298	1	FACETS	0.838	0.757	0.923	0.838	0.757	0.923	CLONAL	1	TRUE	0	0.370925460302298	1		775	608	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0039144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	135	399	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.138802887036973	3	FACETS	0.827	0.756	0.901			1	INDETERMINATE	2	TRUE	NA	0.379280958709514	3		399	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577123	7577124	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0039144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	133	759	0	ENST00000269305.4:c.814dup	p.Val272GlyfsTer34	p.V272Gfs*34	ENST00000269305	NM_001126112.2	272	gtg/gGtg	8/11	0.379280958709514	1	FACETS	0.985	0.898	1	0.985	0.898	1	CLONAL	1	TRUE	0	0.379280958709514	1		759	577	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907035	101907035	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	48	298	0	ENST00000374994.4:c.995G>C	p.Arg332Thr	p.R332T	ENST00000374994	NM_004612.2	332	aGa/aCa	6/9	0.379280958709514	1	FACETS	0.851	0.726	0.986	0.851	0.726	0.986	CLONAL	1	TRUE	0	0.379280958709514	1		298	241	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0039145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	234	601	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.786637204398835	3	FACETS	0.939	0.877	1	0.469	0.438	0.501	CLONAL	1	TRUE	1	0.786637204398835	3		602	883	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0039145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	34	365	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	0.145	0.118	0.176	0.145	0.118	0.176	SUBCLONAL	1	TRUE	1	0.786637204398835	2		365	595	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0039145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	335	638	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.775244824381176	4	FACETS	1	0.953	1	0.667	0.635	0.7	CLONAL	2	TRUE	1	0.786637204398835	4		639	760	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439727	140439727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507485	NA	P-0039145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	174	550	0	ENST00000288602.6:c.2012G>A	p.Arg671Gln	p.R671Q	ENST00000288602	NM_004333.4	671	cGa/cAa	17/18	1	2	FACETS	0.866	0.803	0.93	0.866	0.803	0.93	CLONAL	1	TRUE	1	0.786637204398835	2		550	511	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952093	178952093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs2108429932	NA	P-0039145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	392	372	0	ENST00000263967.3:c.3148G>A	p.Gly1050Ser	p.G1050S	ENST00000263967	NM_006218.2	1050	Ggc/Agc	21/21	0.775244824381176	4	FACETS	0.877	0.842	0.911	0.877	0.842	0.911	CLONAL	3	TRUE	1	0.786637204398835	4		372	677	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978947	25978947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	212	427	0	ENST00000435504.4:c.976G>A	p.Ala326Thr	p.A326T	ENST00000435504		326	Gcc/Acc	10/13	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.786637204398835	2		427	539	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134885801	134885801	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	283	638	0	ENST00000398015.3:c.1712A>G	p.Lys571Arg	p.K571R	ENST00000398015	NM_004441.4	571	aAa/aGa	9/16	1	2	FACETS	0.98	0.926	1	0.98	0.926	1	CLONAL	1	TRUE	1	0.786637204398835	2		638	734	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0039146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	300	541	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.460369403633345	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.460369403633345	3		541	735	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241672	55241672	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	367	848	0	ENST00000275493.2:c.2120T>G	p.Leu707Trp	p.L707W	ENST00000275493	NM_005228.3	707	tTg/tGg	18/28	0.460369403633345	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.460369403633345	3		848	844	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919239	48919239	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	43	181	0	ENST00000267163.4:c.404T>C	p.Leu135Pro	p.L135P	ENST00000267163	NM_000321.2	135	cTa/cCa	4/27	0.374758625356328	1	FACETS	0.846	0.719	0.982	0.846	0.719	0.982	CLONAL	1	TRUE	0	0.460369403633345	1		181	170	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164484	47164484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	76	390	0	ENST00000409792.3:c.1642C>T	p.His548Tyr	p.H548Y	ENST00000409792	NM_014159.6	548	Cat/Tat	3/21	1	2	FACETS	0.892	0.788	1	0.892	0.788	1	CLONAL	1	TRUE	1	0.460369403633345	2		390	370	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209319	98209319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56161606	NA	P-0039146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	55	883	0	ENST00000331920.6:c.4219G>A	p.Gly1407Ser	p.G1407S	ENST00000331920	NM_000264.3	1407	Ggc/Agc	23/24	0.362571007495205	1	FACETS	0.377	0.323	0.436	0.377	0.323	0.436	SUBCLONAL	1	TRUE	0	0.460369403633345	1		883	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0039147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	38	691	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.590193188809691	1	FACETS	0.16	0.131	0.191	0.16	0.131	0.191	SUBCLONAL	1	TRUE	0	0.590193188809691	1		691	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0039147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	308	764	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	0.590193188809691	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.590193188809691	1		764	517	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	139	336	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.590193188809691	2		336	350	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0039147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	20	638	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.168	0.128	0.215	0.168	0.128	0.215	SUBCLONAL	1	TRUE	1	0.590193188809691	2		639	404	SUCCESS
APC	324	MSKCC	GRCh37	5	112174241	112174241	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1254176854	NA	P-0039147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	94	392	1	ENST00000257430.4:c.2950G>T	p.Glu984Ter	p.E984*	ENST00000257430	NM_000038.5	984	Gaa/Taa	16/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.590193188809691	2		393	289	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440716	56440716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	30	590	0	ENST00000407977.2:c.502G>A	p.Asp168Asn	p.D168N	ENST00000407977		168	Gac/Aac	5/10	0.159396358069245	1	FACETS	0.125	0.1	0.153	0.125	0.1	0.153	INDETERMINATE	1	TRUE	0	0.590193188809691	1		590	575	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724277	112724277	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	167	528	0	ENST00000369452.4:c.161A>T	p.Lys54Met	p.K54M	ENST00000369452	NM_007373.3	54	aAg/aTg	2/9	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.590193188809691	2		528	487	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867155	45867155	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	283	777	0	ENST00000391945.4:c.964T>C	p.Ser322Pro	p.S322P	ENST00000391945	NM_000400.3	322	Tcc/Ccc	11/23	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.590193188809691	2		777	729	SUCCESS
APC	324	MSKCC	GRCh37	5	112175572	112175573	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGACAAACCATGCCACCAAGCA	novel	NA	P-0039147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	73	370	0	ENST00000257430.4:c.4283_4304dup	p.Ser1436ThrfsTer9	p.S1436Tfs*9	ENST00000257430	NM_000038.5	1427	-/GGACAAACCATGCCACCAAGCA	16/16	1	2	FACETS	0.732	0.645	0.824	0.732	0.645	0.824	SUBCLONAL	1	TRUE	1	0.590193188809691	2		370	338	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879610	151879610	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	111	296	0	ENST00000262189.6:c.5335G>T	p.Glu1779Ter	p.E1779*	ENST00000262189	NM_170606.2	1779	Gag/Tag	36/59	0.590193188809691	3	FACETS	1	0.973	1	0.603	0.546	0.662	CLONAL	1	TRUE	1	0.590193188809691	3		296	404	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896362	151896362	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0039147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	171	381	0	ENST00000262189.6:c.4273+2T>G		p.X1425_splice	ENST00000262189	NM_170606.2	1425			0.590193188809691	3	FACETS	0.975	0.909	1	0.975	0.909	1	CLONAL	2	TRUE	1	0.590193188809691	3		381	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0039159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	240	670	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.475038975581613	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.500425402112337	1		670	708	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251007	99251007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1335469497	NA	P-0039159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	119	580	0	ENST00000268035.6:c.311C>T	p.Thr104Met	p.T104M	ENST00000268035	NM_000875.3	104	aCg/aTg	2/21	1	2	FACETS	0.5	0.45	0.552	0.5	0.45	0.552	SUBCLONAL	1	TRUE	1	0.500425402112337	2		580	952	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5064997	5065001	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGT	GCCGT	-	novel	NA	P-0039159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	55	324	0	ENST00000381652.3:c.1173_1177del	p.Val392Ter	p.V392*	ENST00000381652	NM_004972.3	391	GCCGTg/g	9/25	0.500425402112337	1	FACETS	0.495	0.425	0.57	0.495	0.425	0.57	SUBCLONAL	1	TRUE	0	0.500425402112337	1		324	333	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	346	492	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.741409037845401	4	FACETS	0.889	0.851	0.926	0.889	0.851	0.926	CLONAL	3	TRUE	1	0.751424366450631	4		492	605	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0039163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	523	780	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.735080392901329	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.751424366450631	2		782	694	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0039163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	342	361	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	0.634403327151041	4	FACETS	0.915	0.877	0.952	0.915	0.877	0.952	CLONAL	3	TRUE	1	0.751424366450631	4		361	581	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81957157	81957157	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202210217	NA	P-0039163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	148	606	1	ENST00000359376.3:c.2375G>A	p.Arg792His	p.R792H	ENST00000359376	NM_002661.3	792	cGt/cAt	22/33	0.707052238310855	5	FACETS	0.64	0.583	0.701	0.213	0.194	0.234	SUBCLONAL	1	TRUE	2	0.751424366450631	5		607	1309	SUCCESS
APC	324	MSKCC	GRCh37	5	112137078	112137078	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1554076217	NA	P-0039163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	117	357	0	ENST00000257430.4:c.832C>T	p.Gln278Ter	p.Q278*	ENST00000257430	NM_000038.5	278	Cag/Tag	8/16	0.634403327151041	4	FACETS	1	0.921	1	0.34	0.307	0.374	CLONAL	1	TRUE	1	0.751424366450631	4		357	535	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412602	63412602	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	644	327	0	ENST00000330258.3:c.565C>T	p.Gln189Ter	p.Q189*	ENST00000330258	NM_152424.3	189	Caa/Taa	2/2	0.751424366450631	3	FACETS	1	0.997	1			1	CLONAL	3	TRUE	NA	0.751424366450631	3		327	717	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786733	3786734	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	465	668	0	ENST00000262367.5:c.4477dup	p.Ile1493AsnfsTer26	p.I1493Nfs*26	ENST00000262367	NM_004380.2	1493	ata/aAta	27/31	0.707052238310855	5	FACETS	0.931	0.889	0.973	0.621	0.593	0.649	CLONAL	2	TRUE	2	0.751424366450631	5		668	1414	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118954	70118954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555629169	NA	P-0039163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	587	783	2	ENST00000245479.2:c.526C>T	p.Pro176Ser	p.P176S	ENST00000245479	NM_000346.3	176	Ccg/Tcg	2/3	0.727322635123269	4	FACETS	0.978	0.941	1	0.978	0.941	1	CLONAL	2	TRUE	2	0.751424366450631	4		785	1399	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231708	66231708	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	24	438	0	ENST00000273854.3:c.1992C>G	p.His664Gln	p.H664Q	ENST00000273854	NM_004439.5	664	caC/caG	11/18	0.630717591915662	3	FACETS	0.278	0.218	0.347	0.139	0.109	0.174	SUBCLONAL	1	TRUE	1	0.751424366450631	3		438	316	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0039164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	267	728	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.166750271641265	5	FACETS	1	0.988	1	0.798	0.749	0.849	INDETERMINATE	2	TRUE	2	0.323455945530619	5		728	1024	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221313	1221314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs121913321	NA	P-0039164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	287	668	0	ENST00000326873.7:c.842dup	p.Leu282AlafsTer3	p.L282Afs*3	ENST00000326873	NM_000455.4	279	ggc/ggCc	6/10	0.271331546342971	3	FACETS	1	0.974	1	0.706	0.665	0.748	CLONAL	2	TRUE	0	0.323455945530619	3		668	973	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123353315	123353315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3750819	NA	P-0039164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	76	697	1	ENST00000358487.5:c.17G>A	p.Arg6His	p.R6H	ENST00000358487	NM_000141.4	6	cGt/cAt	2/18	0.295238399731122	3	FACETS	0.532	0.465	0.604	0.266	0.232	0.302	SUBCLONAL	1	TRUE	1	0.323455945530619	3		698	1027	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729968	41729968	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	180	659	0	ENST00000242208.4:c.561C>A	p.Asp187Glu	p.D187E	ENST00000242208	NM_002192.2	187	gaC/gaA	3/3	0.232428049292324	5	FACETS	0.829	0.764	0.897	0.553	0.509	0.598	CLONAL	2	TRUE	2	0.323455945530619	5		659	997	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400033	139400033	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200232299	NA	P-0039164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	88	797	1	ENST00000277541.6:c.4315G>A	p.Asp1439Asn	p.D1439N	ENST00000277541	NM_017617.3	1439	Gac/Aac	25/34	0.310936382417996	2	FACETS	0.526	0.464	0.592	0.263	0.232	0.296	SUBCLONAL	1	TRUE	0	0.323455945530619	2		798	1035	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600005	10600005	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	357	783	0	ENST00000171111.5:c.1571G>T	p.Gly524Val	p.G524V	ENST00000171111	NM_203500.1	524	gGc/gTc	5/6	0.271331546342971	3	FACETS	1	0.992	1	0.818	0.776	0.86	CLONAL	2	TRUE	0	0.323455945530619	3		783	1045	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25990467	25990467	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	83	396	0	ENST00000435504.4:c.760G>C	p.Glu254Gln	p.E254Q	ENST00000435504		254	Gag/Cag	8/13	0.295238399731122	3	FACETS	1	0.976	1	0.706	0.627	0.791	CLONAL	1	TRUE	1	0.323455945530619	3		396	422	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246498674	246498674	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	147	419	0	ENST00000388985.4:c.331A>C	p.Lys111Gln	p.K111Q	ENST00000388985		111	Aaa/Caa	3/12	0.323455945530619	5	FACETS	0.928	0.849	1	0.619	0.566	0.674	CLONAL	2	TRUE	2	0.323455945530619	5		419	727	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578525	7578526	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0039164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	205	870	3	ENST00000269305.4:c.404_405delinsTT	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGC/tTT	5/11	0.166750271641265	5	FACETS	1	0.988	1	0.446	0.412	0.481	INDETERMINATE	1	TRUE	2	0.323455945530619	5		873	1408	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945459	17945459	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	335	737	0	ENST00000458235.1:c.2271A>T	p.Gln757His	p.Q757H	ENST00000458235	NM_000215.3	757	caA/caT	17/24	0.271331546342971	3	FACETS	1	0.991	1	0.814	0.772	0.858	CLONAL	2	TRUE	0	0.323455945530619	3		737	985	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416182	29416196	+	inframe_deletion	In_Frame_Del	DEL	AGCCCTGTTGCTGGT	AGCCCTGTTGCTGGT	-	novel	NA	P-0039164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	47	565	0	ENST00000389048.3:c.4757_4771del	p.Tyr1586_Gly1590del	p.Y1586_G1590del	ENST00000389048	NM_004304.4	1586	tACCAGCAACAGGGCTtg/ttg	29/29	0.295238399731122	3	FACETS	0.433	0.364	0.51	0.217	0.182	0.255	SUBCLONAL	1	TRUE	1	0.323455945530619	3		565	779	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190742109	190742109	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	93	382	0	ENST00000441310.2:c.2746G>C	p.Val916Leu	p.V916L	ENST00000441310	NM_000534.4	916	Gtt/Ctt	13/13	0.201019460280536	5	FACETS	1	0.905	1	0.675	0.603	0.75	CLONAL	2	TRUE	2	0.323455945530619	5		382	422	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164751	36164751	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	464	772	0	ENST00000300305.3:c.1124C>A	p.Thr375Lys	p.T375K	ENST00000300305		375	aCg/aAg	8/8	0.284910937281876	5	FACETS	0.953	0.913	0.993			1	CLONAL	4	TRUE	NA	0.323455945530619	5		772	1118	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069411	30069411	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs926406926	NA	P-0039164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	236	627	1	ENST00000338641.4:c.1276A>T	p.Met426Leu	p.M426L	ENST00000338641	NM_000268.3	426	Atg/Ttg	12/16	0.277333222784887	3	FACETS	1	0.983	1	0.76	0.711	0.809	CLONAL	2	TRUE	0	0.323455945530619	3		628	744	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428191	72428191	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	76	414	0	ENST00000477973.2:c.701G>T	p.Arg234Met	p.R234M	ENST00000477973	NM_012234.5	234	aGg/aTg	3/4	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.323455945530619	2		414	441	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876094	35876094	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	128	313	0	ENST00000303115.3:c.886G>T	p.Val296Leu	p.V296L	ENST00000303115	NM_002185.3	296	Gtg/Ttg	8/8	0.241776070652634	4	FACETS	1	0.973	1			1	CLONAL	2	TRUE	NA	0.323455945530619	4		313	449	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242458	55242458	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	44	415	0	ENST00000275493.2:c.2228C>G	p.Ala743Gly	p.A743G	ENST00000275493	NM_005228.3	743	gCt/gGt	19/28	0.323455945530619	3	FACETS	0.432	0.361	0.511			1	SUBCLONAL	1	TRUE	NA	0.323455945530619	3		415	731	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577540	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	156	582	0	ENST00000269305.4:c.741_742insA	p.Arg248ThrfsTer16	p.R248Tfs*16	ENST00000269305	NM_001126112.2	247	-/A	7/11	0.21596055582178	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.217319876265167	2		582	688	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233092	66233092	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1208501614	NA	P-0039165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	39	362	0	ENST00000273854.3:c.1907A>G	p.His636Arg	p.H636R	ENST00000273854	NM_004439.5	636	cAt/cGt	10/18	0.21596055582178	2	FACETS	0.873	0.725	1	0.437	0.362	0.52	CLONAL	1	TRUE	0	0.217319876265167	2		362	411	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787758	135787758	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1554817636	NA	P-0039165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	67	438	0	ENST00000298552.3:c.824A>G	p.Tyr275Cys	p.Y275C	ENST00000298552	NM_001162426.1	275	tAt/tGt	9/23	0.21596055582178	2	FACETS	1	0.905	1	0.525	0.456	0.6	CLONAL	1	TRUE	0	0.217319876265167	2		438	587	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0039167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	942	515	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.204321118307817	12	FACETS	1	0.991	1			1	CLONAL	10	TRUE	NA	0.204321118307817	12		515	1789	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0039167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	120	627	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.204321118307817	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.204321118307817	1		627	895	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196213	106196213	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs370735654	NA	P-0039167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	51	161	0	ENST00000380013.4:c.4546C>T	p.Arg1516Ter	p.R1516*	ENST00000380013	NM_001127208.2	1516	Cga/Tga	11/11	0.159353018805269	2	FACETS	0.84	0.719	0.972	0.84	0.719	0.972	CLONAL	2	TRUE	0	0.204321118307817	2		161	297	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0039170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	194	234	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.832182661507472	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.832182661507472	1		234	265	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312725	91312725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	217	350	1	ENST00000355112.3:c.2464C>T	p.Pro822Ser	p.P822S	ENST00000355112	NM_000057.2	822	Cct/Tct	12/22	1	2	FACETS	0.891	0.835	0.949	0.891	0.835	0.949	CLONAL	1	TRUE	1	0.832182661507472	2		351	585	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0039170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	309	483	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	0.94	0.891	0.99	0.94	0.891	0.99	CLONAL	1	TRUE	1	0.832182661507472	2		483	790	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143551	108143551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201780199	NA	P-0039170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	205	316	1	ENST00000278616.4:c.3256C>T	p.Arg1086Cys	p.R1086C	ENST00000278616	NM_000051.3	1086	Cgc/Tgc	22/63	1	2	FACETS	0.976	0.914	1	0.976	0.914	1	CLONAL	1	TRUE	1	0.832182661507472	2		317	505	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526134	189526134	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	291	476	0	ENST00000264731.3:c.398C>T	p.Pro133Leu	p.P133L	ENST00000264731	NM_003722.4	133	cCc/cTc	4/14	1	2	FACETS	0.931	0.881	0.982	0.931	0.881	0.982	CLONAL	1	TRUE	1	0.832182661507472	2		476	751	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11015734	11015734	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	219	405	0	ENST00000327064.4:c.328C>T	p.Gln110Ter	p.Q110*	ENST00000327064	NM_199141.1	110	Cag/Tag	2/16	1	2	FACETS	0.925	0.867	0.984	0.925	0.867	0.984	CLONAL	1	TRUE	1	0.832182661507472	2		405	569	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390935	89390935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	201	291	0	ENST00000336596.2:c.1001C>T	p.Ser334Phe	p.S334F	ENST00000336596	NM_005233.5	334	tCt/tTt	5/17	1	2	FACETS	0.978	0.915	1	0.978	0.915	1	CLONAL	1	TRUE	1	0.832182661507472	2		291	494	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589298	28589298	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	181	243	0	ENST00000241453.7:c.2749G>A	p.Glu917Lys	p.E917K	ENST00000241453	NM_004119.2	917	Gaa/Aaa	22/24	1	2	FACETS	0.982	0.916	1	0.982	0.916	1	CLONAL	1	TRUE	1	0.832182661507472	2		243	443	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156836758	156836758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	1032	569	0	ENST00000524377.1:c.416C>T	p.Ser139Phe	p.S139F	ENST00000524377	NM_002529.3	139	tCc/tTc	4/17	0.828829331857756	3	FACETS	0.994	0.98	1	0.994	0.98	1	CLONAL	3	TRUE	0	0.832182661507472	3		569	1178	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629152	14629152	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs891936896	NA	P-0039170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	187	319	0	ENST00000254322.2:c.10G>A	p.Asp4Asn	p.D4N	ENST00000254322	NM_006145.1	4	Gac/Aac	1/3	1	2	FACETS	0.956	0.892	1	0.956	0.892	1	CLONAL	1	TRUE	1	0.832182661507472	2		319	470	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263712	16263712	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	39	387	1	ENST00000375759.3:c.10081C>A	p.Gln3361Lys	p.Q3361K	ENST00000375759	NM_015001.2	3361	Cag/Aag	12/15	1	2	FACETS	0.141	0.116	0.169	0.141	0.116	0.169	SUBCLONAL	1	TRUE	1	0.832182661507472	2		388	665	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772376	56772376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	219	436	1	ENST00000337432.4:c.230G>A	p.Gly77Asp	p.G77D	ENST00000337432	NM_058216.2	77	gGt/gAt	2/9	1	2	FACETS	0.795	0.743	0.848	0.795	0.743	0.848	SUBCLONAL	1	TRUE	1	0.832182661507472	2		437	662	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097066	11097066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs942370486	NA	P-0039170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	362	653	0	ENST00000358026.2:c.557C>T	p.Ala186Val	p.A186V	ENST00000358026	NM_001128849.1	186	gCc/gTc	4/36	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.832182661507472	2		653	870	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286772	212286772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	230	312	0	ENST00000342788.4:c.2924C>T	p.Ser975Leu	p.S975L	ENST00000342788	NM_005235.2	975	tCa/tTa	24/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.832182661507472	2		312	521	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461488	138461488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	293	451	1	ENST00000289153.2:c.533C>T	p.Pro178Leu	p.P178L	ENST00000289153	NM_006219.2	178	cCa/cTa	3/22	1	2	FACETS	0.953	0.902	1	0.953	0.902	1	CLONAL	1	TRUE	1	0.832182661507472	2		452	739	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803160	1803160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	359	632	0	ENST00000260795.2:c.512C>T	p.Thr171Ile	p.T171I	ENST00000260795		171	aCc/aTc	4/17	1	2	FACETS	0.969	0.923	1	0.969	0.923	1	CLONAL	1	TRUE	1	0.832182661507472	2		632	890	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157315	106157315	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	234	308	0	ENST00000380013.4:c.2216C>T	p.Pro739Leu	p.P739L	ENST00000380013	NM_001127208.2	739	cCt/cTt	3/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.832182661507472	2		308	537	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540271	187540271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	209	329	0	ENST00000441802.2:c.7469C>T	p.Pro2490Leu	p.P2490L	ENST00000441802	NM_005245.3	2490	cCt/cTt	10/27	1	2	FACETS	0.88	0.823	0.938	0.88	0.823	0.938	CLONAL	1	TRUE	1	0.832182661507472	2		329	571	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628644	187628644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781755435	NA	P-0039170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	366	582	0	ENST00000441802.2:c.2338C>T	p.Leu780Phe	p.L780F	ENST00000441802	NM_005245.3	780	Ctt/Ttt	2/27	1	2	FACETS	0.922	0.877	0.967	0.922	0.877	0.967	CLONAL	1	TRUE	1	0.832182661507472	2		582	954	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80021339	80021339	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	306	385	0	ENST00000265081.6:c.1408C>T	p.Gln470Ter	p.Q470*	ENST00000265081	NM_002439.4	470	Cag/Tag	9/24	1	2	FACETS	0.981	0.93	1	0.981	0.93	1	CLONAL	1	TRUE	1	0.832182661507472	2		385	750	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608917	100608996	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GACCACCGGACTGGAAATTTGGAGCCTACTGAGCTTGTGTATTCATCATCCAGGACATACCTGCAAGGGATTCAGGACTT	GACCACCGGACTGGAAATTTGGAGCCTACTGAGCTTGTGTATTCATCATCCAGGACATACCTGCAAGGGATTCAGGACTT	-	novel	NA	P-0039170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	42	387	0	ENST00000308731.7:c.1632-20_1691del		p.X544_splice	ENST00000308731	NM_000061.2	544		17/19	1	2	FACETS	0.152	0.126	0.18	0.152	0.126	0.18	SUBCLONAL	1	TRUE	1	0.832182661507472	2		387	666	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81574753	81574753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	23	311	0	ENST00000298171.2:c.649G>A	p.Asp217Asn	p.D217N	ENST00000298171	NM_000369.2	217	Gac/Aac	8/10	0.110349635775093	5	FACETS	0.691	0.54	0.864	0.173	0.135	0.216	INDETERMINATE	1	TRUE	1	0.475142691252997	5		311	240	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578509	7578509	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	240	945	0	ENST00000269305.4:c.421del	p.Cys141AlafsTer29	p.C141Afs*29	ENST00000269305	NM_001126112.2	141	Tgc/gc	5/11	0.110349635775093	5	FACETS	0.921	0.866	0.977	0.691	0.65	0.733	INDETERMINATE	3	TRUE	1	0.475142691252997	5		945	626	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244421	5244421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	43	857	2	ENST00000357368.4:c.1061C>T	p.Ser354Leu	p.S354L	ENST00000357368	NM_002850.3	354	tCg/tTg	11/38	1	2	FACETS	0.458	0.384	0.54	0.458	0.384	0.54	SUBCLONAL	1	TRUE	1	0.475142691252997	2		859	395	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713398	40713398	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	33	753	1	ENST00000373198.4:c.4117C>A	p.Leu1373Ile	p.L1373I	ENST00000373198	NM_133170.3	1373	Ctc/Atc	30/32	0.315453347920559	4	FACETS	0.508	0.414	0.615	0.254	0.207	0.308	SUBCLONAL	1	TRUE	2	0.475142691252997	4		754	403	SUCCESS
APC	324	MSKCC	GRCh37	5	112137041	112137042	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0039175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	73	495	0	ENST00000257430.4:c.797_798dup	p.Gly267TrpfsTer27	p.G267Wfs*27	ENST00000257430	NM_000038.5	265	-/GT	8/16	0.293364096043521	3	FACETS	1	0.917	1	0.527	0.463	0.594	CLONAL	1	TRUE	1	0.475142691252997	3		495	361	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401203	139401203	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1281437674	NA	P-0039175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	142	830	1	ENST00000277541.6:c.3866A>G	p.Asn1289Ser	p.N1289S	ENST00000277541	NM_017617.3	1289	aAt/aGt	23/34	0.45839817611474	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.475142691252997	1		831	402	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200089	123200089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1477970164	NA	P-0039175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	90	284	1	ENST00000218089.9:c.2161G>A	p.Glu721Lys	p.E721K	ENST00000218089	NM_001042749.1	721	Gaa/Aaa	22/35	0.475142691252997	2	FACETS	1	0.962	1			1	CLONAL	1	TRUE	NA	0.475142691252997	2		285	327	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0039177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	54	327	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.27023344949456	0	FACETS	0.596	0.51	0.689			1	SUBCLONAL	1	FALSE	0	0.310193231995828	0		327	403	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0039177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	35	219	0	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	0.26340241840232	3	FACETS	1	0.858	1	0.523	0.431	0.625	CLONAL	1	FALSE	1	0.310193231995828	3		219	249	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579355	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519997	NA	P-0039177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	100	626	0	ENST00000269305.4:c.332T>A	p.Leu111Gln	p.L111Q	ENST00000269305	NM_001126112.2	111	cTg/cAg	4/11	0.224414796366188	1	FACETS	0.87	0.779	0.967	0.87	0.779	0.967	CLONAL	1	FALSE	0	0.310193231995828	1		626	626	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741443	145741443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs551940973	NA	P-0039177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	64	750	1	ENST00000428558.2:c.1060G>A	p.Val354Ile	p.V354I	ENST00000428558	NM_004260.3	354	Gta/Ata	5/22	0.165851190087401	2	FACETS	0.548	0.474	0.629	0.274	0.237	0.315	INDETERMINATE	1	FALSE	0	0.310193231995828	2		751	753	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524363	187524363	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774876308	NA	P-0039177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	29	366	0	ENST00000441802.2:c.11317C>T	p.Arg3773Cys	p.R3773C	ENST00000441802	NM_005245.3	3773	Cgc/Tgc	19/27	1	2	FACETS	0.464	0.372	0.569	0.464	0.372	0.569	SUBCLONAL	1	FALSE	1	0.310193231995828	2		366	403	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	125	561	0				ENST00000310581	NM_198253.2	-/1132			0.183644095813161	4	FACETS	1	0.983	1	0.458	0.417	0.5	INDETERMINATE	1	TRUE	1	0.628390940060452	4		561	472	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777894	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	229	613	0	ENST00000361445.4:c.6644C>T	p.Ser2215Phe	p.S2215F	ENST00000361445	NM_004958.3	2215	tCt/tTt	47/58	0.628390940060452	5	FACETS	1	0.989	1			1	CLONAL	1	TRUE	NA	0.628390940060452	5		613	1076	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262301	16262301	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	54	320	2	ENST00000375759.3:c.9566A>T	p.Tyr3189Phe	p.Y3189F	ENST00000375759	NM_015001.2	3189	tAt/tTt	11/15	0.628390940060452	5	FACETS	1	0.919	1			1	CLONAL	1	TRUE	NA	0.628390940060452	5		322	303	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420049	49420049	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1159189200	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	259	634	0	ENST00000301067.7:c.15700G>T	p.Glu5234Ter	p.E5234*	ENST00000301067	NM_003482.3	5234	Gag/Tag	48/54	0.575006107165908	3	FACETS	0.909	0.859	0.96	0.909	0.859	0.96	CLONAL	2	TRUE	1	0.628390940060452	3		634	596	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420362	49420362	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	243	715	0	ENST00000301067.7:c.15387G>C	p.Lys5129Asn	p.K5129N	ENST00000301067	NM_003482.3	5129	aaG/aaC	48/54	0.575006107165908	3	FACETS	0.964	0.911	1	0.964	0.911	1	CLONAL	2	TRUE	1	0.628390940060452	3		715	527	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626729	28626729	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	83	478	1	ENST00000241453.7:c.567del	p.Pro190GlnfsTer40	p.P190Qfs*40	ENST00000241453	NM_004119.2	189	gtT/gt	5/24	0.619290526450778	3	FACETS	0.663	0.586	0.744	0.221	0.195	0.248	SUBCLONAL	1	TRUE	0	0.628390940060452	3		479	524	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068926	30068926	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	105	590	0	ENST00000331968.5:c.2003A>T	p.Glu668Val	p.E668V	ENST00000331968	NM_002742.2	668	gAa/gTa	14/18	0.575006107165908	3	FACETS	0.991	0.894	1	0.496	0.447	0.547	CLONAL	1	TRUE	1	0.628390940060452	3		590	443	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639366	3639366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766448056	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	159	864	0	ENST00000294008.3:c.4273G>A	p.Asp1425Asn	p.D1425N	ENST00000294008	NM_032444.2	1425	Gac/Aac	12/15	0.115614250093795	5	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.628390940060452	5		864	700	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032220	10032220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	114	677	0	ENST00000330684.3:c.603G>T	p.Gln201His	p.Q201H	ENST00000330684	NM_001134407.1	201	caG/caT	3/13	1	2	FACETS	0.761	0.689	0.836	0.761	0.689	0.836	SUBCLONAL	1	TRUE	1	0.628390940060452	2		677	477	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	429	796	0	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	0.619290526450778	3	FACETS	0.962	0.93	0.992	0.962	0.93	0.992	CLONAL	3	TRUE	0	0.628390940060452	3		796	622	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029445	16029445	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	178	410	0	ENST00000268712.3:c.1585del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	529	Gaa/aa	15/46	0.259153689121598	5	FACETS	1	0.982	1			1	INDETERMINATE	3	TRUE	NA	0.628390940060452	5		410	328	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40461115	40461115	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	242	393	0	ENST00000345506.4:c.2113G>C	p.Glu705Gln	p.E705Q	ENST00000345506	NM_003152.3	705	Gag/Cag	18/20	0.47824176115007	5	FACETS	0.955	0.902	1	0.955	0.902	1	CLONAL	3	TRUE	2	0.628390940060452	5		393	522	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41201212	41201212	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs80358126	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	112	537	0	ENST00000357654.3:c.5333-1G>C		p.X1778_splice	ENST00000357654	NM_007294.3	1778			0.47824176115007	5	FACETS	1	0.965	1	0.385	0.347	0.425	CLONAL	1	TRUE	2	0.628390940060452	5		537	600	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55607061	55607061	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	75	501	0	ENST00000284073.2:c.430G>C	p.Asp144His	p.D144H	ENST00000284073	NM_138962.2	144	Gat/Cat	7/14	0.47824176115007	5	FACETS	0.821	0.72	0.929	0.274	0.24	0.31	CLONAL	1	TRUE	2	0.628390940060452	5		501	565	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55754356	55754356	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	123	640	0	ENST00000284073.2:c.954G>C	p.Leu318Phe	p.L318F	ENST00000284073	NM_138962.2	318	ttG/ttC	13/14	0.47824176115007	5	FACETS	0.912	0.824	1	0.304	0.274	0.335	CLONAL	1	TRUE	2	0.628390940060452	5		640	834	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117569	70117569	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1478425968	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	407	736	2	ENST00000245479.2:c.37G>A	p.Glu13Lys	p.E13K	ENST00000245479	NM_000346.3	13	Gag/Aag	1/3	0.47824176115007	5	FACETS	0.928	0.887	0.969	0.928	0.887	0.969	CLONAL	3	TRUE	2	0.628390940060452	5		738	904	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78865623	78865623	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	234	427	0	ENST00000306801.3:c.2087C>G	p.Ser696Cys	p.S696C	ENST00000306801	NM_020761.2	696	tCt/tGt	18/34	0.47824176115007	5	FACETS	1	0.987	1	0.785	0.738	0.834	CLONAL	2	TRUE	2	0.628390940060452	5		427	614	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265047	10265047	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	89	588	0	ENST00000340748.4:c.1893C>G	p.Phe631Leu	p.F631L	ENST00000340748		631	ttC/ttG	21/40	0.412464195295171	5	FACETS	0.735	0.651	0.824	0.245	0.217	0.275	SUBCLONAL	1	TRUE	2	0.628390940060452	5		588	749	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113708	11113708	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	114	591	0	ENST00000358026.2:c.1816C>G	p.Leu606Val	p.L606V	ENST00000358026	NM_001128849.1	606	Ctg/Gtg	12/36	0.412464195295171	5	FACETS	0.902	0.813	0.998	0.301	0.271	0.333	CLONAL	1	TRUE	2	0.628390940060452	5		591	781	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144143	11144143	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555784586	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	425	721	0	ENST00000358026.2:c.3724G>A	p.Glu1242Lys	p.E1242K	ENST00000358026	NM_001128849.1	1242	Gag/Aag	26/36	0.412464195295171	5	FACETS	0.882	0.844	0.921	0.882	0.844	0.921	CLONAL	3	TRUE	2	0.628390940060452	5		721	993	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281224	15281224	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	197	944	0	ENST00000263388.2:c.5032G>A	p.Glu1678Lys	p.E1678K	ENST00000263388	NM_000435.2	1678	Gag/Aag	27/33	0.412464195295171	5	FACETS	1	0.939	1	0.339	0.313	0.366	CLONAL	1	TRUE	2	0.628390940060452	5		944	1197	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228592	36228592	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	325	883	1	ENST00000222270.7:c.7606G>A	p.Glu2536Lys	p.E2536K	ENST00000222270	NM_014727.1	2536	Gag/Aag	34/37	0.226111996052387	6	FACETS	0.902	0.855	0.949			1	INDETERMINATE	3	TRUE	NA	0.628390940060452	6		884	863	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753329	42753329	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	388	1018	0	ENST00000222329.4:c.935G>T	p.Arg312Leu	p.R312L	ENST00000222329	NM_006494.2	312	cGg/cTg	4/4	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	1	TRUE	NA	0.628390940060452	2		1018	884	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753334	42753334	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	206	1015	1	ENST00000222329.4:c.930G>A	p.Met310Ile	p.M310I	ENST00000222329	NM_006494.2	310	atG/atA	4/4	NA	2	FACETS	0.744	0.691	0.799			1	INDETERMINATE	1	TRUE	NA	0.628390940060452	2		1016	881	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432730	29432730	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	69	528	0	ENST00000389048.3:c.3758G>A	p.Arg1253Lys	p.R1253K	ENST00000389048	NM_004304.4	1253	aGa/aAa	25/29	0.628390940060452	4	FACETS	0.788	0.688	0.895	0.263	0.229	0.299	SUBCLONAL	1	TRUE	1	0.628390940060452	4		528	454	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033615	48033615	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	65	419	0	ENST00000234420.5:c.3826G>T	p.Glu1276Ter	p.E1276*	ENST00000234420	NM_000179.2	1276	Gaa/Taa	9/10	0.628390940060452	4	FACETS	0.826	0.719	0.941	0.275	0.239	0.314	CLONAL	1	TRUE	1	0.628390940060452	4		419	408	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561492	9561492	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs776084037	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	89	509	0	ENST00000353224.5:c.290C>G	p.Ser97Cys	p.S97C	ENST00000353224	NM_177990.2	97	tCc/tGc	4/10	0.628390940060452	6	FACETS	0.73	0.646	0.82	0.182	0.161	0.205	SUBCLONAL	1	TRUE	2	0.628390940060452	6		509	876	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513766	41513766	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	110	617	0	ENST00000263253.7:c.670C>T	p.Gln224Ter	p.Q224*	ENST00000263253	NM_001429.3	224	Cag/Tag	2/31	0.628390940060452	3	FACETS	0.727	0.654	0.803	0.242	0.218	0.268	SUBCLONAL	1	TRUE	0	0.628390940060452	3		617	633	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461492	138461492	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	99	566	0	ENST00000289153.2:c.529C>G	p.Pro177Ala	p.P177A	ENST00000289153	NM_006219.2	177	Cca/Gca	3/22	0.628390940060452	4	FACETS	0.907	0.811	1	0.302	0.27	0.336	CLONAL	1	TRUE	1	0.628390940060452	4		566	566	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665358	138665358	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	337	836	0	ENST00000330315.3:c.207G>C	p.Glu69Asp	p.E69D	ENST00000330315	NM_023067.3	69	gaG/gaC	1/1	0.628390940060452	4	FACETS	0.814	0.771	0.858	0.543	0.514	0.572	CLONAL	2	TRUE	1	0.628390940060452	4		836	1073	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594055	55594055	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	97	449	0	ENST00000288135.5:c.1841C>G	p.Ser614Ter	p.S614*	ENST00000288135	NM_000222.2	614	tCa/tGa	12/21	1	2	FACETS	0.9	0.81	0.993	0.9	0.81	0.993	CLONAL	1	TRUE	1	0.628390940060452	2		449	343	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001124	150001124	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	58	474	0	ENST00000253339.5:c.2480G>C	p.Arg827Thr	p.R827T	ENST00000253339		827	aGa/aCa	4/7	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.628390940060452	2		474	183	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099496	157099496	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	79	361	0	ENST00000346085.5:c.434del	p.Gly145AlafsTer35	p.G145Afs*35	ENST00000346085	NM_020732.3	145	Ggc/gc	1/20	1	2	FACETS	0.796	0.706	0.89	0.796	0.706	0.89	SUBCLONAL	1	TRUE	1	0.628390940060452	2		361	316	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951926	2951926	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	116	483	0	ENST00000396946.4:c.3024C>G	p.Ile1008Met	p.I1008M	ENST00000396946	NM_032415.4	1008	atC/atG	23/25	0.115614250093795	5	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.628390940060452	5		483	524	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140449173	140449173	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	15	284	0	ENST00000288602.6:c.1906C>T	p.Gln636Ter	p.Q636*	ENST00000288602	NM_004333.4	636	Cag/Tag	16/18	0.603913001310854	4	FACETS	0.37	0.271	0.489	0.185	0.135	0.245	SUBCLONAL	1	TRUE	2	0.628390940060452	4		284	210	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205403	38205403	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	122	748	0	ENST00000317025.8:c.287C>G	p.Ser96Ter	p.S96*	ENST00000317025	NM_023034.1	96	tCa/tGa	2/24	0.628390940060452	2	FACETS	0.873	0.794	0.954	0.436	0.397	0.477	CLONAL	1	TRUE	0	0.628390940060452	2		748	445	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069114	5069220	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTTAAAGATCTTTTGAATTGTTACCAGATGGAAACTGTTCGCTCAGACAATATAATTTTCCAGTTTACTAAATGCTGTCCCCCAAAGCCAAAAGGTAAGATAATTT	TCTTAAAGATCTTTTGAATTGTTACCAGATGGAAACTGTTCGCTCAGACAATATAATTTTCCAGTTTACTAAATGCTGTCCCCCAAAGCCAAAAGGTAAGATAATTT	-	novel	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	53	458	0	ENST00000381652.3:c.1422_1513+15del		p.X474_splice	ENST00000381652	NM_004972.3	474		11/25	0.601599910604437	2	FACETS	1	0.967	1	0.68	0.598	0.765	CLONAL	1	TRUE	0	0.628390940060452	2		458	124	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169511	27169511	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	465	519	0	ENST00000380036.4:c.512C>A	p.Pro171His	p.P171H	ENST00000380036	NM_000459.3	171	cCt/cAt	4/23	0.628390940060452	4	FACETS	0.98	0.952	1	0.98	0.952	1	CLONAL	4	TRUE	0	0.628390940060452	4		519	615	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617172	100617172	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555978783	NA	P-0039178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	119	334	0	ENST00000308731.7:c.577G>C	p.Glu193Gln	p.E193Q	ENST00000308731	NM_000061.2	193	Gag/Cag	7/19	1	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.628390940060452	1		334	219	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	169	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.965	1	1	0.993	1	CLONAL	2	TRUE	1	0.279745236145159	2		174	563	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0039181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	337	764	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.279745236145159	2	FACETS	0.979	0.937	1	1	0.996	1	CLONAL	4	TRUE	0	0.279745236145159	2		764	615	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196791	108196791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039471	NA	P-0039181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	92	277	0	ENST00000278616.4:c.6814G>A	p.Glu2272Lys	p.E2272K	ENST00000278616	NM_000051.3	2272	Gaa/Aaa	47/63	1	2	FACETS	1	0.928	1	1	0.987	1	CLONAL	2	TRUE	1	0.279745236145159	2		277	316	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180936	108180936	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786203668	NA	P-0039181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	87	337	0	ENST00000278616.4:c.5812T>A	p.Tyr1938Asn	p.Y1938N	ENST00000278616	NM_000051.3	1938	Tat/Aat	39/63	1	2	FACETS	0.836	0.746	0.931	1	0.983	1	CLONAL	2	TRUE	1	0.279745236145159	2		337	372	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347562	118347562	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	204	496	0	ENST00000534358.1:c.3199C>T	p.Arg1067Trp	p.R1067W	ENST00000534358	NM_005933.3	1067	Cgg/Tgg	4/36	1	2	FACETS	1	0.969	1	1	0.994	1	CLONAL	2	TRUE	1	0.279745236145159	2		496	682	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641055	3641055	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs200715208	NA	P-0039181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	70	1072	2	ENST00000294008.3:c.2584C>T	p.Arg862Ter	p.R862*	ENST00000294008	NM_032444.2	862	Cga/Tga	12/15	1	2	FACETS	0.421	0.366	0.482	0.421	0.366	0.482	SUBCLONAL	1	TRUE	1	0.279745236145159	2		1074	1188	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892133	9892133	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0039181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	164	568	0	ENST00000330684.3:c.2356+1G>C		p.X786_splice	ENST00000330684	NM_001134407.1	786			1	2	FACETS	1	0.952	1	1	0.993	1	CLONAL	2	TRUE	1	0.279745236145159	2		568	563	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502381	186502381	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	140	419	0	ENST00000323963.5:c.104T>C	p.Phe35Ser	p.F35S	ENST00000323963		35	tTt/tCt	3/11	1	2	FACETS	0.993	0.91	1	1	0.991	1	CLONAL	2	TRUE	1	0.279745236145159	2		419	504	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163372	32163372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	317	1011	0	ENST00000375023.3:c.5854G>A	p.Asp1952Asn	p.D1952N	ENST00000375023	NM_004557.3	1952	Gat/Aat	30/30	1	2	FACETS	0.957	0.903	1	1	0.996	1	CLONAL	2	TRUE	1	0.279745236145159	2		1011	1184	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814798	139814798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201857326	NA	P-0039181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	150	817	0	ENST00000247668.2:c.791C>T	p.Ala264Val	p.A264V	ENST00000247668	NM_021138.3	264	gCg/gTg	8/11	0.279745236145159	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.279745236145159	1		817	803	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44894227	44894228	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	157	230	0	ENST00000377967.4:c.619dup	p.Ile207AsnfsTer10	p.I207Nfs*10	ENST00000377967	NM_021140.2	206	gaa/gAaa	7/29	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	4	TRUE	NA	0.279745236145159	2		230	257	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196804	123196805	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	133	314	0	ENST00000218089.9:c.1692dup	p.Glu565Ter	p.E565*	ENST00000218089	NM_001042749.1	564	act/acTt	18/35	NA	2	FACETS	0.897	0.832	0.962			1	INDETERMINATE	4	TRUE	NA	0.279745236145159	2		314	265	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191570	10191570	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1559429824	NA	P-0039182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	86	544	0	ENST00000256474.2:c.563T>C	p.Leu188Pro	p.L188P	ENST00000256474	NM_000551.3	188	cTg/cCg	3/3	0.398730676024705	1	FACETS	0.834	0.742	0.932	0.834	0.742	0.932	CLONAL	1	TRUE	0	0.398730676024705	1		544	414	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518445	69518445	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	41	315	0	ENST00000294312.3:c.200T>C	p.Val67Ala	p.V67A	ENST00000294312	NM_005117.2	67	gTc/gCc	1/3	1	2	FACETS	0.833	0.699	0.979	0.833	0.699	0.979	CLONAL	1	TRUE	1	0.398730676024705	2		315	247	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0039183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	135	318	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	0.993	1	CLONAL	3	TRUE	1	0.13	2		318	618	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422928	12422928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765206131	NA	P-0039183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	53	583	1	ENST00000287820.6:c.418C>T	p.Arg140Cys	p.R140C	ENST00000287820	NM_015869.4	140	Cgt/Tgt	3/7	1	2	FACETS	0.931	0.791	1	0.931	0.791	1	CLONAL	1	TRUE	1	0.13	2		584	876	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0039184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	150	542	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.233319700748954	3	FACETS	1	0.966	1	0.551	0.506	0.599	INDETERMINATE	1	TRUE	1	0.556432161488071	3		542	625	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0039184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	362	838	4	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	0.556432161488071	2		842	1201	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	109	531	1	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	0.484	0.434	0.537	0.484	0.434	0.537	SUBCLONAL	1	TRUE	1	0.556432161488071	2		532	809	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	114	570	1	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.537	0.483	0.594	0.537	0.483	0.594	SUBCLONAL	1	TRUE	1	0.556432161488071	2		571	763	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515036	103515036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775996769	NA	P-0039184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	68	335	0	ENST00000355739.4:c.1537G>A	p.Ala513Thr	p.A513T	ENST00000355739	NM_000123.3	513	Gca/Aca	8/15	1	2	FACETS	0.541	0.472	0.615	0.541	0.472	0.615	SUBCLONAL	1	TRUE	1	0.556432161488071	2		335	452	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308383	15308383	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	153	826	3	ENST00000263388.2:c.125del	p.Pro42LeufsTer194	p.P42Lfs*194	ENST00000263388	NM_000435.2	42	cCt/ct	2/33	1	2	FACETS	0.452	0.412	0.494	0.452	0.412	0.494	SUBCLONAL	1	TRUE	1	0.556432161488071	2		829	1217	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528621	89528621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780470195	NA	P-0039184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	38	302	0	ENST00000336596.2:c.2921C>T	p.Thr974Met	p.T974M	ENST00000336596	NM_005233.5	974	aCg/aTg	17/17	1	2	FACETS	0.405	0.336	0.482	0.405	0.336	0.482	SUBCLONAL	1	TRUE	1	0.556432161488071	2		302	337	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	124	610	2	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.537	0.486	0.591	0.537	0.486	0.591	SUBCLONAL	1	TRUE	1	0.556432161488071	2		612	830	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030612	48030612	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750617	NA	P-0039184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	91	459	0	ENST00000234420.5:c.3226C>T	p.Arg1076Cys	p.R1076C	ENST00000234420	NM_000179.2	1076	Cgc/Tgc	5/10	1	2	FACETS	0.481	0.427	0.539	0.481	0.427	0.539	SUBCLONAL	1	TRUE	1	0.556432161488071	2		459	680	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274777	123274777	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs387906678	NA	P-0039184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	198	597	0	ENST00000358487.5:c.1141T>G	p.Tyr381Asp	p.Y381D	ENST00000358487	NM_000141.4	381	Tac/Gac	9/18	0.233319700748954	3	FACETS	1	0.939	1	0.507	0.47	0.546	INDETERMINATE	1	TRUE	1	0.556432161488071	3		597	897	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281070	49281070	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs754945976	NA	P-0039184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	119	670	0	ENST00000282018.3:c.117A>T	p.Glu39Asp	p.E39D	ENST00000282018	NM_020377.2	39	gaA/gaT	1/1	1	2	FACETS	0.519	0.468	0.573	0.519	0.468	0.573	SUBCLONAL	1	TRUE	1	0.556432161488071	2		670	824	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222938	36222938	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1247	194	1059	1	ENST00000222270.7:c.5572del	p.Arg1858ValfsTer37	p.R1858Vfs*37	ENST00000222270	NM_014727.1	1856	gCc/gc	27/37	1	2	FACETS	0.484	0.446	0.523	0.484	0.446	0.523	SUBCLONAL	1	TRUE	1	0.556432161488071	2		1060	1441	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357108	89357108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs900210533	NA	P-0039184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	131	763	1	ENST00000301030.4:c.526G>A	p.Ala176Thr	p.A176T	ENST00000301030	NM_001256183.1	176	Gcc/Acc	6/13	1	2	FACETS	0.458	0.415	0.504	0.458	0.415	0.504	SUBCLONAL	1	TRUE	1	0.556432161488071	2		764	1028	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712824	43712824	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1201648831	NA	P-0039184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	127	861	0	ENST00000382044.4:c.4360C>T	p.Arg1454Ter	p.R1454*	ENST00000382044	NM_001141980.1	1454	Cga/Tga	21/28	1	2	FACETS	0.425	0.384	0.468	0.425	0.384	0.468	SUBCLONAL	1	TRUE	1	0.556432161488071	2		861	1075	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467922	50467922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	87	537	0	ENST00000331340.3:c.1157G>A	p.Arg386His	p.R386H	ENST00000331340	NM_006060.4	386	cGc/cAc	8/8	1	2	FACETS	0.444	0.392	0.498	0.444	0.392	0.498	SUBCLONAL	1	TRUE	1	0.556432161488071	2		537	705	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089560	27089561	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	152	717	0	ENST00000324856.7:c.2517dup	p.Gln840SerfsTer32	p.Q840Sfs*32	ENST00000324856	NM_006015.4	839	ggt/ggTt	8/20	1	2	FACETS	0.556	0.508	0.607	0.556	0.508	0.607	SUBCLONAL	1	TRUE	1	0.556432161488071	2		717	982	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119829	108119829	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	40	246	0	ENST00000278616.4:c.1235G>T	p.Trp412Leu	p.W412L	ENST00000278616	NM_000051.3	412	tGg/tTg	9/63	1	2	FACETS	0.408	0.34	0.484	0.408	0.34	0.484	SUBCLONAL	1	TRUE	1	0.556432161488071	2		246	352	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129759	30129759	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	126	664	3	ENST00000263025.4:c.454C>T	p.Arg152Trp	p.R152W	ENST00000263025	NM_002746.2	152	Cgg/Tgg	3/9	1	2	FACETS	0.462	0.417	0.509	0.462	0.417	0.509	SUBCLONAL	1	TRUE	1	0.556432161488071	2		667	981	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609400	39609400	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	63	366	0	ENST00000262039.4:c.1706del	p.Lys569ArgfsTer15	p.K569Rfs*15	ENST00000262039	NM_002647.2	568	Aaa/aa	15/25	1	2	FACETS	0.417	0.361	0.478	0.417	0.361	0.478	SUBCLONAL	1	TRUE	1	0.556432161488071	2		366	543	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376188	15376188	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772107398	NA	P-0039184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	120	577	1	ENST00000263377.2:c.826G>A	p.Ala276Thr	p.A276T	ENST00000263377	NM_058243.2	276	Gcg/Acg	5/20	1	2	FACETS	0.486	0.439	0.537	0.486	0.439	0.537	SUBCLONAL	1	TRUE	1	0.556432161488071	2		578	887	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224134	36224135	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0039184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	124	839	0	ENST00000222270.7:c.6687dup	p.Thr2230HisfsTer73	p.T2230Hfs*73	ENST00000222270	NM_014727.1	2228	-/C	28/37	1	2	FACETS	0.371	0.335	0.41	0.371	0.335	0.41	SUBCLONAL	1	TRUE	1	0.556432161488071	2		839	1201	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47596650	47596651	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0039184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	80	338	0	ENST00000263735.4:c.11dup	p.Gln5AlafsTer26	p.Q5Afs*26	ENST00000263735	NM_002354.2	2	-/C	1/9	1	2	FACETS	0.533	0.47	0.601	0.533	0.47	0.601	SUBCLONAL	1	TRUE	1	0.556432161488071	2		338	539	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456659	138456659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777549389	NA	P-0039184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	38	542	0	ENST00000289153.2:c.691C>T	p.Arg231Cys	p.R231C	ENST00000289153	NM_006219.2	231	Cgt/Tgt	4/22	1	2	FACETS	0.208	0.171	0.249	0.208	0.171	0.249	SUBCLONAL	1	TRUE	1	0.556432161488071	2		542	658	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629387	187629387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1006561183	NA	P-0039184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	149	736	2	ENST00000441802.2:c.1595G>A	p.Arg532Gln	p.R532Q	ENST00000441802	NM_005245.3	532	cGg/cAg	2/27	1	2	FACETS	0.558	0.509	0.609	0.558	0.509	0.609	SUBCLONAL	1	TRUE	1	0.556432161488071	2		738	960	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26021091	26021091	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	91	451	0	ENST00000357647.3:c.374T>A	p.Ile125Asn	p.I125N	ENST00000357647	NM_003529.2	125	aTc/aAc	1/1	1	2	FACETS	0.482	0.428	0.539	0.482	0.428	0.539	SUBCLONAL	1	TRUE	1	0.556432161488071	2		451	679	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172167	32172167	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0039184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	111	637	0	ENST00000375023.3:c.2866-1G>C		p.X956_splice	ENST00000375023	NM_004557.3	956			1	2	FACETS	0.434	0.39	0.481	0.434	0.39	0.481	SUBCLONAL	1	TRUE	1	0.556432161488071	2		637	919	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100138	157100138	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1289468231	NA	P-0039184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	12	46	0	ENST00000346085.5:c.1079del	p.Gly360AlafsTer9	p.G360Afs*9	ENST00000346085	NM_020732.3	359	Ggg/gg	1/20	1	2	FACETS	0.324	0.229	0.44	0.324	0.229	0.44	SUBCLONAL	1	TRUE	1	0.556432161488071	2		46	133	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755470	133755470	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	125	653	0	ENST00000318560.5:c.1439C>A	p.Pro480His	p.P480H	ENST00000318560	NM_005157.4	480	cCc/cAc	9/11	1	2	FACETS	0.519	0.469	0.571	0.519	0.469	0.571	SUBCLONAL	1	TRUE	1	0.556432161488071	2		653	866	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15836735	15836735	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs956963587	NA	P-0039184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	35	483	0	ENST00000307771.7:c.797T>C	p.Leu266Pro	p.L266P	ENST00000307771	NM_005089.3	266	cTg/cCg	9/11	1	2	FACETS	0.2	0.163	0.242	0.2	0.163	0.242	SUBCLONAL	1	TRUE	1	0.556432161488071	2		483	629	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923021	44923025	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGA	GCAGA	-	novel	NA	P-0039184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	120	681	0	ENST00000377967.4:c.1883_1887del	p.Ala628GlyfsTer9	p.A628Gfs*9	ENST00000377967	NM_021140.2	628	GCAGAg/g	16/29	1	2	FACETS	0.462	0.417	0.51	0.462	0.417	0.51	SUBCLONAL	1	TRUE	1	0.556432161488071	2		681	933	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360623	70360624	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAG	rs754533796	NA	P-0039184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	67	420	0	ENST00000374080.3:c.6198_6200dup	p.Gln2076dup	p.Q2076dup	ENST00000374080		2076	-/CAG	42/45	1	2	FACETS	0.432	0.376	0.493	0.432	0.376	0.493	SUBCLONAL	1	TRUE	1	0.556432161488071	2		420	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0039185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	75	780	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.859	0.753	0.972	0.859	0.753	0.972	CLONAL	1	TRUE	1	0.28	2		782	624	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672323	86672323	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554049422	NA	P-0039185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	38	464	0	ENST00000274376.6:c.2125C>T	p.Arg709Ter	p.R709*	ENST00000274376	NM_002890.2	709	Cga/Tga	16/25	0.02044825365182	3	FACETS	0.614	0.507	0.734	0.307	0.253	0.367	INDETERMINATE	1	TRUE	1	0.28	3		464	504	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974714	21974714	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	44	427	0	ENST00000304494.5:c.113C>A	p.Pro38His	p.P38H	ENST00000304494	NM_000077.4	38	cCc/cAc	1/3	1	2	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	TRUE	1	0.28	2		427	309	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603044	48603044	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781359	NA	P-0039185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	40	385	0	ENST00000342988.3:c.1345C>T	p.Gln449Ter	p.Q449*	ENST00000342988	NM_005359.5	449	Cag/Tag	11/12	1	2	FACETS	0.772	0.643	0.915	0.772	0.643	0.915	CLONAL	1	TRUE	1	0.28	2		385	370	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031759	36031759	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	63	643	0	ENST00000358208.4:c.1588T>C	p.Tyr530His	p.Y530H	ENST00000358208		530	Tac/Cac	12/12	1	2	FACETS	0.736	0.637	0.845	0.736	0.637	0.845	SUBCLONAL	1	TRUE	1	0.28	2		643	611	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691874	+	inframe_deletion	In_Frame_Del	DEL	AAA	AAA	-	novel	NA	P-0039185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	23	399	0	ENST00000295754.5:c.381_383del	p.Lys128del	p.K128del	ENST00000295754	NM_003242.5	125	gAAAaa/gaa	3/7	1	2	FACETS	0.421	0.328	0.53	0.421	0.328	0.53	SUBCLONAL	1	TRUE	1	0.28	2		399	390	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032230	26032233	+	frameshift_variant	Frame_Shift_Del	DEL	TGCT	TGCT	-	novel	NA	P-0039185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	24	388	0	ENST00000244661.2:c.56_59del	p.Lys19SerfsTer17	p.K19Sfs*17	ENST00000244661	NM_003537.3	19	aAGCAg/ag	1/1	0.3	5	FACETS	0.669	0.524	0.836			1	SUBCLONAL	1	TRUE	NA	0.28	5		388	364	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974723	21974723	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs746834149	NA	P-0039185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	41	411	0	ENST00000304494.5:c.104G>C	p.Gly35Ala	p.G35A	ENST00000304494	NM_000077.4	35	gGg/gCg	1/3	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.28	2		411	276	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0039187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	75	365	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	0.816	0.716	0.924	0.816	0.716	0.924	CLONAL	1	TRUE	1	0.310327028738471	2		365	592	SUCCESS
APC	324	MSKCC	GRCh37	5	112175411	112175411	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	102	255	0	ENST00000257430.4:c.4120G>T	p.Glu1374Ter	p.E1374*	ENST00000257430	NM_000038.5	1374	Gaa/Taa	16/16	0.268994416269151	2	FACETS	0.921	0.831	1	0.921	0.831	1	CLONAL	2	TRUE	0	0.310327028738471	2		255	357	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120151	70120152	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0039187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	135	303	1	ENST00000245479.2:c.1154_1155dup	p.Ser386Ter	p.S386*	ENST00000245479	NM_000346.3	385	ctg/cTGtg	3/3	0.268994416269151	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	2	TRUE	0	0.310327028738471	2		304	431	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955186	17955186	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780084832	NA	P-0039187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	178	775	2	ENST00000458235.1:c.41G>A	p.Arg14His	p.R14H	ENST00000458235	NM_000215.3	14	cGt/cAt	2/24	1	2	FACETS	0.91	0.837	0.987	0.91	0.837	0.987	CLONAL	1	TRUE	1	0.310327028738471	2		777	1260	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714731	52714731	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	119	557	0	ENST00000322088.6:c.489G>C	p.Lys163Asn	p.K163N	ENST00000322088	NM_014225.5	163	aaG/aaC	4/15	1	2	FACETS	0.902	0.814	0.996	0.902	0.814	0.996	CLONAL	1	TRUE	1	0.310327028738471	2		557	850	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070400	37070400	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	53	305	0	ENST00000231790.2:c.1535A>C	p.Glu512Ala	p.E512A	ENST00000231790	NM_000249.3	512	gAa/gCa	13/19	1	2	FACETS	0.756	0.645	0.876	0.756	0.645	0.876	SUBCLONAL	1	TRUE	1	0.310327028738471	2		305	452	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49399935	49399935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	87	392	1	ENST00000418115.1:c.402G>A	p.Met134Ile	p.M134I	ENST00000418115	NM_001664.2	134	atG/atA	4/5	1	2	FACETS	0.82	0.726	0.92	0.82	0.726	0.92	CLONAL	1	TRUE	1	0.310327028738471	2		393	684	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015209	71015210	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TG	TG	-	novel	NA	P-0039187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	25	192	0	ENST00000318789.4:c.1723-3_1723-2del		p.X575_splice	ENST00000318789	NM_032682.5	575			1	2	FACETS	0.577	0.456	0.716	0.577	0.456	0.716	SUBCLONAL	1	TRUE	1	0.310327028738471	2		192	279	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	290	492	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.246464178525623	7	FACETS	0.993	0.939	1			1	CLONAL	5	TRUE	NA	0.246464178525623	7		492	766	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578426	7578435	+	frameshift_variant	Frame_Shift_Del	DEL	GTGCTGTGAC	GTGCTGTGAC	-	novel	NA	P-0039193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	185	743	0	ENST00000269305.4:c.495_504del	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	165	caGTCACAGCAC/ca	5/11	0.225883461994655	2	FACETS	0.847	0.783	0.914	0.847	0.783	0.914	CLONAL	2	TRUE	0	0.246464178525623	2		743	886	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0039194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	323	687	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	0.665504713684314	2		687	907	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913338	NA	P-0039194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	185	372	0	ENST00000288602.6:c.1781A>C	p.Asp594Ala	p.D594A	ENST00000288602	NM_004333.4	594	gAt/gCt	15/18	0.665504713684314	3	FACETS	1	0.965	1	0.534	0.494	0.575	CLONAL	1	TRUE	1	0.665504713684314	3		372	694	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594258	55594258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913523	NA	P-0039196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	364	443	0	ENST00000288135.5:c.1961T>C	p.Val654Ala	p.V654A	ENST00000288135	NM_000222.2	654	gTg/gCg	13/21	0.595858581026772	4	FACETS	0.894	0.856	0.933	0.894	0.856	0.933	CLONAL	3	TRUE	1	0.654369552769618	4		443	686	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572248	64572248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778728934	NA	P-0039196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	101	721	0	ENST00000312049.6:c.1391C>T	p.Ala464Val	p.A464V	ENST00000312049	NM_130799.2	464	gCg/gTg	10/10	0.518135116194587	3	FACETS	0.546	0.487	0.607	0.273	0.243	0.304	SUBCLONAL	1	TRUE	1	0.654369552769618	3		721	751	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593586	55593615	+	protein_altering_variant	In_Frame_Del	DEL	CCATGTATGAAGTACAGTGGAAGGTTGTTG	CCATGTATGAAGTACAGTGGAAGGTTGTTG	TCA	novel	NA	P-0039196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	257	477	1	ENST00000288135.5:c.1652_1681delinsTCA	p.Pro551_Glu561delinsLeuLys	p.P551_E561delinsLK	ENST00000288135	NM_000222.2	551	cCCATGTATGAAGTACAGTGGAAGGTTGTTGag/cTCAag	11/21	0.595858581026772	4	FACETS	1	0.947	1	0.669	0.631	0.708	CLONAL	2	TRUE	1	0.654369552769618	4		478	647	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115744	8115744	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	209	564	0	ENST00000346208.3:c.1090A>G	p.Arg364Gly	p.R364G	ENST00000346208		364	Aga/Gga	6/6	1	2	FACETS	0.928	0.863	0.994	0.928	0.863	0.994	CLONAL	1	TRUE	1	0.566840234579702	2		564	795	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470596	25470601	+	inframe_deletion	In_Frame_Del	DEL	CCAATG	CCAATG	-	novel	NA	P-0039197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	136	985	0	ENST00000264709.3:c.873_878del	p.Ile292_Gly293del	p.I292_G293del	ENST00000264709	NM_175629.2	291	ggCATTGGg/ggg	8/23	0.280466161356375	1	FACETS	0.364	0.331	0.4	0.364	0.331	0.4	INDETERMINATE	1	TRUE	0	0.566840234579702	1		985	944	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260110	16260110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	199	583	0	ENST00000375759.3:c.7375G>A	p.Val2459Met	p.V2459M	ENST00000375759	NM_015001.2	2459	Gtg/Atg	11/15	0.879666184603233	5	FACETS	0.781	0.726	0.837	0.521	0.484	0.558	SUBCLONAL	2	TRUE	2	0.879666184603233	5		583	672	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264040	16264040	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	432	857	0	ENST00000375759.3:c.10409G>A	p.Gly3470Glu	p.G3470E	ENST00000375759	NM_015001.2	3470	gGa/gAa	12/15	0.879666184603233	5	FACETS	0.853	0.813	0.894	0.569	0.542	0.596	CLONAL	2	TRUE	2	0.879666184603233	5		857	1335	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092753	27092753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	189	493	0	ENST00000324856.7:c.2774G>A	p.Gly925Glu	p.G925E	ENST00000324856	NM_006015.4	925	gGa/gAa	9/20	0.879666184603233	3	FACETS	1	0.977	1	0.556	0.518	0.596	CLONAL	1	TRUE	1	0.879666184603233	3		493	556	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248474	59248474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	228	622	0	ENST00000371222.2:c.269C>T	p.Thr90Ile	p.T90I	ENST00000371222	NM_002228.3	90	aCc/aTc	1/1	0.879666184603233	3	FACETS	0.973	0.91	1	0.487	0.455	0.519	CLONAL	1	TRUE	1	0.879666184603233	3		622	767	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483194	120483194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	130	449	1	ENST00000256646.2:c.3167C>T	p.Thr1056Ile	p.T1056I	ENST00000256646	NM_024408.3	1056	aCt/aTt	19/34	0.843050392480271	3	FACETS	0.858	0.783	0.936	0.429	0.391	0.468	CLONAL	1	TRUE	1	0.879666184603233	3		450	496	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206667312	206667312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781860835	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	208	571	2	ENST00000367120.3:c.2105G>A	p.Arg702His	p.R702H	ENST00000367120	NM_014002.3	702	cGc/cAc	21/22	0.879666184603233	3	FACETS	0.864	0.804	0.926	0.432	0.402	0.463	CLONAL	1	TRUE	1	0.879666184603233	3		573	788	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287480	46287480	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	95	387	0	ENST00000334344.6:c.5339G>A	p.Gly1780Asp	p.G1780D	ENST00000334344	NM_152641.2	1780	gGt/gAt	20/21	NA	2	FACETS	0.85	0.77	0.933			1	INDETERMINATE	1	TRUE	NA	0.879666184603233	2		387	254	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446476	49446476	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	177	480	1	ENST00000301067.7:c.1129C>T	p.Pro377Ser	p.P377S	ENST00000301067	NM_003482.3	377	Cct/Tct	9/54	0.727910619111229	4	FACETS	1	0.936	1			1	CLONAL	1	TRUE	NA	0.879666184603233	4		481	745	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446828	49446828	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	205	491	0	ENST00000301067.7:c.982G>A	p.Ala328Thr	p.A328T	ENST00000301067	NM_003482.3	328	Gcg/Acg	8/54	0.727910619111229	4	FACETS	0.914	0.849	0.983			1	CLONAL	1	TRUE	NA	0.879666184603233	4		491	958	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557503	21557503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	237	611	1	ENST00000382592.4:c.2342G>A	p.Ser781Asn	p.S781N	ENST00000382592	NM_014572.2	781	aGt/aAt	5/8	0.879666184603233	2	FACETS	0.966	0.909	1	0.483	0.454	0.511	CLONAL	1	TRUE	0	0.879666184603233	2		612	558	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001359	29001359	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	154	347	0	ENST00000282397.4:c.1373G>A	p.Gly458Asp	p.G458D	ENST00000282397	NM_002019.4	458	gGt/gAt	10/30	0.879666184603233	2	FACETS	1	0.965	1	0.531	0.493	0.568	CLONAL	1	TRUE	0	0.879666184603233	2		347	330	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95556890	95556890	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	200	399	0	ENST00000393063.1:c.5714C>T	p.Ala1905Val	p.A1905V	ENST00000393063	NM_030621.3	1905	gCa/gTa	28/28	0.876825208612688	3	FACETS	1	0.982	1	0.383	0.357	0.409	CLONAL	1	TRUE	0	0.879666184603233	3		399	570	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571571	95571571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749392411	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	106	319	0	ENST00000393063.1:c.3106G>A	p.Glu1036Lys	p.E1036K	ENST00000393063	NM_030621.3	1036	Gaa/Aaa	21/28	0.876825208612688	3	FACETS	0.933	0.844	1	0.311	0.281	0.342	CLONAL	1	TRUE	0	0.879666184603233	3		319	372	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40678566	40678566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	193	546	1	ENST00000249776.8:c.308C>T	p.Thr103Ile	p.T103I	ENST00000249776	NM_033286.3	103	aCa/aTa	3/9	0.843050392480271	3	FACETS	0.89	0.826	0.956	0.445	0.413	0.478	CLONAL	1	TRUE	1	0.879666184603233	3		547	710	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988923	41988923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	147	526	0	ENST00000219905.7:c.1715C>T	p.Ser572Leu	p.S572L	ENST00000219905	NM_001164273.1	572	tCa/tTa	3/24	0.843050392480271	3	FACETS	0.94	0.864	1	0.47	0.432	0.51	CLONAL	1	TRUE	1	0.879666184603233	3		526	512	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42026793	42026793	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	164	270	0	ENST00000219905.7:c.3916+1G>C		p.X1306_splice	ENST00000219905	NM_001164273.1	1306			0.843050392480271	3	FACETS	0.952	0.894	1	0.952	0.894	1	CLONAL	2	TRUE	1	0.879666184603233	3		270	282	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748285	43748285	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	237	796	0	ENST00000382044.4:c.2521C>T	p.Pro841Ser	p.P841S	ENST00000382044	NM_001141980.1	841	Cct/Tct	12/28	0.843050392480271	3	FACETS	0.946	0.885	1	0.473	0.442	0.504	CLONAL	1	TRUE	1	0.879666184603233	3		796	820	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457307	67457307	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	221	690	0	ENST00000327367.4:c.281G>A	p.Trp94Ter	p.W94*	ENST00000327367	NM_005902.3	94	tGg/tAg	2/9	0.689364617426727	4	FACETS	0.956	0.89	1	0.478	0.445	0.512	CLONAL	1	TRUE	2	0.879666184603233	4		690	988	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996309	73996309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	39	99	0	ENST00000318443.5:c.1043G>A	p.Gly348Asp	p.G348D	ENST00000318443	NM_001024736.1	348	gGc/gAc	5/10	0.689364617426727	4	FACETS	1	0.917	1	0.571	0.481	0.666	CLONAL	1	TRUE	2	0.879666184603233	4		99	146	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348208	348208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	291	760	0	ENST00000262320.3:c.1298G>A	p.Gly433Glu	p.G433E	ENST00000262320	NM_003502.3	433	gGg/gAg	6/11	0.879666184603233	4	FACETS	1	0.961	1	0.343	0.322	0.365	CLONAL	1	TRUE	1	0.879666184603233	4		760	1208	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778605	3778605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1293915714	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	231	645	1	ENST00000262367.5:c.6443G>A	p.Gly2148Asp	p.G2148D	ENST00000262367	NM_004380.2	2148	gGc/gAc	31/31	0.727910619111229	4	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.879666184603233	4		646	886	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779440	3779440	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1411086593	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	352	873	0	ENST00000262367.5:c.5608G>A	p.Ala1870Thr	p.A1870T	ENST00000262367	NM_004380.2	1870	Gcc/Acc	31/31	0.727910619111229	4	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.879666184603233	4		873	1368	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843479	3843479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	237	476	0	ENST00000262367.5:c.1124G>A	p.Gly375Glu	p.G375E	ENST00000262367	NM_004380.2	375	gGa/gAa	4/31	0.727910619111229	4	FACETS	1	0.962	1			1	CLONAL	1	TRUE	NA	0.879666184603233	4		476	972	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029395	16029395	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	85	374	0	ENST00000268712.3:c.1634+1G>A		p.X545_splice	ENST00000268712	NM_006311.3	545			0.879666184603233	2	FACETS	0.695	0.622	0.771	0.348	0.311	0.386	SUBCLONAL	1	TRUE	0	0.879666184603233	2		374	278	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588817	29588817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	134	347	0	ENST00000356175.3:c.4603G>A	p.Asp1535Asn	p.D1535N	ENST00000356175	NM_000267.3	1535	Gat/Aat	34/57	0.879666184603233	2	FACETS	0.964	0.89	1	0.482	0.445	0.52	CLONAL	1	TRUE	0	0.879666184603233	2		347	316	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884005	37884005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	286	731	0	ENST00000269571.5:c.3476C>T	p.Ala1159Val	p.A1159V	ENST00000269571		1159	gCt/gTt	27/27	0.879666184603233	3	FACETS	1	0.982	1	0.365	0.344	0.387	CLONAL	1	TRUE	0	0.879666184603233	3		731	854	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696668	47696668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	173	491	1	ENST00000347630.2:c.280C>T	p.Pro94Ser	p.P94S	ENST00000347630	NM_001007230.1	94	Cca/Tca	5/11	0.879666184603233	3	FACETS	0.93	0.86	1	0.31	0.286	0.334	CLONAL	1	TRUE	0	0.879666184603233	3		492	609	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435594	56435594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	282	716	0	ENST00000407977.2:c.1543G>A	p.Gly515Arg	p.G515R	ENST00000407977		515	Ggg/Agg	9/10	0.879666184603233	3	FACETS	1	0.969	1	0.347	0.327	0.368	CLONAL	1	TRUE	0	0.879666184603233	3		716	886	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511557	66511557	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	106	280	0	ENST00000358598.2:c.17C>T	p.Thr6Ile	p.T6I	ENST00000358598	NM_212471.2	6	aCc/aTc	2/11	0.879666184603233	3	FACETS	0.89	0.804	0.979	0.297	0.268	0.327	CLONAL	1	TRUE	0	0.879666184603233	3		280	390	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66522054	66522054	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	84	202	0	ENST00000358598.2:c.708+1G>A		p.X236_splice	ENST00000358598	NM_212471.2	236			0.879666184603233	3	FACETS	0.844	0.752	0.94	0.281	0.25	0.314	CLONAL	1	TRUE	0	0.879666184603233	3		202	326	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796005	78796005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	218	543	0	ENST00000306801.3:c.895C>T	p.Pro299Ser	p.P299S	ENST00000306801	NM_020761.2	299	Cct/Tct	8/34	0.879666184603233	3	FACETS	0.657	0.61	0.705	0.219	0.203	0.235	SUBCLONAL	1	TRUE	0	0.879666184603233	3		543	1087	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213861	2213861	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1204733528	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	277	734	0	ENST00000398665.3:c.1673C>T	p.Ala558Val	p.A558V	ENST00000398665	NM_032482.2	558	gCg/gTg	18/28	0.689364617426727	4	FACETS	0.963	0.904	1	0.482	0.452	0.513	CLONAL	1	TRUE	2	0.879666184603233	4		734	1229	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229660	5229660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	33	48	0	ENST00000357368.4:c.2191G>A	p.Ala731Thr	p.A731T	ENST00000357368	NM_002850.3	731	Gcg/Acg	15/38	0.689364617426727	4	FACETS	1	0.934	1	0.635	0.53	0.748	CLONAL	1	TRUE	2	0.879666184603233	4		48	111	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170517	11170517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854229	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	300	781	0	ENST00000358026.2:c.4820G>A	p.Ser1607Asn	p.S1607N	ENST00000358026	NM_001128849.1	1607	aGt/aAt	34/36	0.689364617426727	4	FACETS	1	0.977	1	0.535	0.504	0.567	CLONAL	1	TRUE	2	0.879666184603233	4		781	1198	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271723	15271723	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	320	1030	1	ENST00000263388.2:c.6716C>T	p.Pro2239Leu	p.P2239L	ENST00000263388	NM_000435.2	2239	cCc/cTc	33/33	0.689364617426727	4	FACETS	1	0.961	1	0.512	0.483	0.542	CLONAL	1	TRUE	2	0.879666184603233	4		1031	1335	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291830	15291830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1222604193	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	263	879	2	ENST00000263388.2:c.2936C>T	p.Ala979Val	p.A979V	ENST00000263388	NM_000435.2	979	gCc/gTc	18/33	0.689364617426727	4	FACETS	1	0.938	1	0.5	0.469	0.533	CLONAL	1	TRUE	2	0.879666184603233	4		881	1123	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375315	15375315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	270	671	0	ENST00000263377.2:c.1112C>T	p.Ala371Val	p.A371V	ENST00000263377	NM_058243.2	371	gCc/gTc	6/20	0.689364617426727	4	FACETS	1	0.945	1	0.504	0.473	0.537	CLONAL	1	TRUE	2	0.879666184603233	4		671	1144	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273291	18273291	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	148	428	0	ENST00000222254.8:c.1084C>T	p.Gln362Ter	p.Q362*	ENST00000222254	NM_005027.3	362	Cag/Tag	9/16	0.689364617426727	4	FACETS	0.812	0.742	0.885	0.406	0.371	0.443	CLONAL	1	TRUE	2	0.879666184603233	4		428	779	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968337	18968337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1305929623	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	272	637	0	ENST00000262803.5:c.2177C>T	p.Thr726Ile	p.T726I	ENST00000262803	NM_002911.3	726	aCt/aTt	15/24	0.689364617426727	4	FACETS	1	0.976	1	0.538	0.505	0.572	CLONAL	1	TRUE	2	0.879666184603233	4		637	1080	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257405	19257405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	334	860	1	ENST00000162023.5:c.728C>T	p.Pro243Leu	p.P243L	ENST00000162023		243	cCc/cTc	11/13	0.689364617426727	4	FACETS	0.996	0.94	1	0.498	0.47	0.527	CLONAL	1	TRUE	2	0.879666184603233	4		861	1433	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257429	19257429	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	354	885	0	ENST00000162023.5:c.704C>T	p.Pro235Leu	p.P235L	ENST00000162023		235	cCc/cTc	11/13	0.689364617426727	4	FACETS	1	0.957	1	0.507	0.479	0.536	CLONAL	1	TRUE	2	0.879666184603233	4		885	1492	SUCCESS
AXL	558	MSKCC	GRCh37	19	41725356	41725356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	266	829	1	ENST00000301178.4:c.59G>A	p.Cys20Tyr	p.C20Y	ENST00000301178	NM_021913.4	20	tGc/tAc	1/20	0.689364617426727	4	FACETS	1	0.97	1	0.527	0.494	0.561	CLONAL	1	TRUE	2	0.879666184603233	4		830	1078	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743885	41743885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780282463	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	285	813	1	ENST00000301178.4:c.820G>A	p.Gly274Arg	p.G274R	ENST00000301178	NM_021913.4	274	Gga/Aga	7/20	0.689364617426727	4	FACETS	1	0.939	1	0.5	0.469	0.531	CLONAL	1	TRUE	2	0.879666184603233	4		814	1218	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799332	42799332	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	131	329	0	ENST00000575354.2:c.4816A>G	p.Thr1606Ala	p.T1606A	ENST00000575354	NM_015125.3	1606	Aca/Gca	20/20	0.689364617426727	4	FACETS	1	0.979	1	0.613	0.56	0.667	CLONAL	1	TRUE	2	0.879666184603233	4		329	457	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856036	45856036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	320	702	0	ENST00000391945.4:c.1870C>T	p.Pro624Ser	p.P624S	ENST00000391945	NM_000400.3	624	Ccc/Tcc	20/23	0.689364617426727	4	FACETS	1	0.977	1	0.533	0.502	0.564	CLONAL	1	TRUE	2	0.879666184603233	4		702	1283	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624933	9624933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	142	404	0	ENST00000353224.5:c.44C>T	p.Ser15Phe	p.S15F	ENST00000353224	NM_177990.2	15	tCc/tTc	3/10	0.861756404746423	5	FACETS	1	0.925	1			1	CLONAL	1	TRUE	NA	0.879666184603233	5		404	738	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253820	30253820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs577055474	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	250	550	0	ENST00000307677.4:c.634C>T	p.Arg212Cys	p.R212C	ENST00000307677	NM_138578.1	212	Cgc/Tgc	3/3	0.689364617426727	4	FACETS	0.945	0.884	1	0.473	0.442	0.505	CLONAL	1	TRUE	2	0.879666184603233	4		550	1130	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911147	40911147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	103	377	0	ENST00000373198.4:c.2158G>A	p.Val720Ile	p.V720I	ENST00000373198	NM_133170.3	720	Gtt/Att	13/32	0.689364617426727	4	FACETS	0.945	0.85	1	0.472	0.425	0.522	CLONAL	1	TRUE	2	0.879666184603233	4		377	466	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306665	41306665	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	238	671	0	ENST00000373198.4:c.994G>A	p.Gly332Ser	p.G332S	ENST00000373198	NM_133170.3	332	Ggc/Agc	7/32	0.689364617426727	4	FACETS	1	0.935	1	0.501	0.467	0.535	CLONAL	1	TRUE	2	0.879666184603233	4		671	1016	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46275829	46275829	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	146	435	0	ENST00000371998.3:c.3265G>A	p.Glu1089Lys	p.E1089K	ENST00000371998		1089	Gag/Aag	18/23	0.689364617426727	4	FACETS	0.96	0.879	1	0.48	0.439	0.522	CLONAL	1	TRUE	2	0.879666184603233	4		435	650	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326482	62326482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150686112	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1721	328	855	2	ENST00000360203.5:c.3407C>T	p.Thr1136Ile	p.T1136I	ENST00000360203	NM_001283009.1	1136	aCc/aTc	33/35	0.879666184603233	6	FACETS	1	0.945	1	0.251	0.236	0.267	CLONAL	1	TRUE	2	0.879666184603233	6		857	2049	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36265248	36265248	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	71	309	0	ENST00000300305.3:c.71G>A	p.Gly24Glu	p.G24E	ENST00000300305		24	gGa/gAa	2/8	0.689364617426727	4	FACETS	0.89	0.782	1	0.445	0.391	0.502	CLONAL	1	TRUE	2	0.879666184603233	4		309	341	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495753	72495753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	182	392	0	ENST00000477973.2:c.319C>T	p.Pro107Ser	p.P107S	ENST00000477973	NM_012234.5	107	Cct/Tct	1/4	0.879666184603233	3	FACETS	0.866	0.802	0.932	0.433	0.401	0.466	CLONAL	1	TRUE	1	0.879666184603233	3		392	688	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165588	185165588	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	17	310	0	ENST00000265026.3:c.863C>T	p.Thr288Ile	p.T288I	ENST00000265026	NM_004721.4	288	aCc/aTc	5/14	1	2	FACETS	0.16	0.119	0.208	0.16	0.119	0.208	SUBCLONAL	1	TRUE	1	0.879666184603233	2		310	242	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807494	1807494	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1474187970	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	239	828	1	ENST00000260795.2:c.1663G>A	p.Val555Met	p.V555M	ENST00000260795		555	Gtg/Atg	12/17	0.843050392480271	3	FACETS	1	0.94	1	0.502	0.47	0.534	CLONAL	1	TRUE	1	0.879666184603233	3		829	780	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189835	66189835	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs55784741	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	136	388	0	ENST00000273854.3:c.3111G>T	p.Leu1037Phe	p.L1037F	ENST00000273854	NM_004439.5	1037	ttG/ttT	18/18	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.879666184603233	2		388	309	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554962	187554962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	117	326	0	ENST00000441802.2:c.4199G>A	p.Ser1400Asn	p.S1400N	ENST00000441802	NM_005245.3	1400	aGt/aAt	7/27	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.879666184603233	2		326	260	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584702	187584702	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	166	460	0	ENST00000441802.2:c.3331G>A	p.Ala1111Thr	p.A1111T	ENST00000441802	NM_005245.3	1111	Gca/Aca	3/27	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.879666184603233	2		460	346	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630750	187630750	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1202383911	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	182	571	0	ENST00000441802.2:c.232G>A	p.Asp78Asn	p.D78N	ENST00000441802	NM_005245.3	78	Gac/Aac	2/27	1	2	FACETS	0.943	0.88	1	0.943	0.88	1	CLONAL	1	TRUE	1	0.879666184603233	2		571	439	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294589	1294589	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	209	616	0	ENST00000310581.5:c.412G>A	p.Gly138Arg	p.G138R	ENST00000310581	NM_198253.2	138	Ggg/Agg	2/16	0.879666184603233	2	FACETS	0.978	0.917	1	0.489	0.458	0.52	CLONAL	1	TRUE	0	0.879666184603233	2		616	486	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633909	86633909	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	55	313	0	ENST00000274376.6:c.1017+1G>A		p.X339_splice	ENST00000274376	NM_002890.2	339			0.863684835599667	2	FACETS	0.736	0.641	0.834	0.368	0.32	0.417	SUBCLONAL	1	TRUE	0	0.879666184603233	2		313	170	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149436864	149436864	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	162	586	0	ENST00000286301.3:c.2305C>T	p.Leu769Phe	p.L769F	ENST00000286301	NM_005211.3	769	Ctc/Ttc	17/22	0.879666184603233	2	FACETS	0.721	0.666	0.777	0.36	0.333	0.389	SUBCLONAL	1	TRUE	0	0.879666184603233	2		586	511	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045714	26045714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	204	255	0	ENST00000540144.1:c.76G>A	p.Ala26Thr	p.A26T	ENST00000540144	NM_003531.2	26	Gcc/Acc	1/1	0.689364617426727	4	FACETS	0.991	0.931	1	0.991	0.931	1	CLONAL	2	TRUE	2	0.879666184603233	4		255	440	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777945	27777945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	128	344	0	ENST00000369163.2:c.94G>A	p.Ala32Thr	p.A32T	ENST00000369163	NM_003536.2	32	Gcc/Acc	1/1	0.689364617426727	4	FACETS	1	0.943	1	0.523	0.476	0.572	CLONAL	1	TRUE	2	0.879666184603233	4		344	523	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680494	30680494	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	188	525	0	ENST00000376406.3:c.1225G>A	p.Glu409Lys	p.E409K	ENST00000376406	NM_014641.2	409	Gaa/Aaa	5/15	0.689364617426727	4	FACETS	0.961	0.889	1	0.481	0.444	0.518	CLONAL	1	TRUE	2	0.879666184603233	4		525	836	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120341	94120341	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	80	304	0	ENST00000369303.4:c.710G>A	p.Ser237Asn	p.S237N	ENST00000369303	NM_004440.3	237	aGt/aAt	3/17	0.689364617426727	4	FACETS	0.768	0.679	0.863	0.384	0.339	0.432	SUBCLONAL	1	TRUE	2	0.879666184603233	4		304	445	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710726	117710726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	114	353	0	ENST00000368508.3:c.1546G>A	p.Val516Ile	p.V516I	ENST00000368508	NM_002944.2	516	Gtc/Atc	12/43	0.689364617426727	4	FACETS	0.97	0.878	1	0.485	0.439	0.534	CLONAL	1	TRUE	2	0.879666184603233	4		353	502	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520076	106520076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	65	207	0	ENST00000359195.3:c.2504G>A	p.Gly835Asp	p.G835D	ENST00000359195	NM_002649.2	835	gGt/gAt	6/11	NA	2	FACETS	1	0.908	1			1	INDETERMINATE	1	TRUE	NA	0.879666184603233	2		207	145	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68982073	68982073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	103	567	0	ENST00000288368.4:c.1447G>A	p.Val483Ile	p.V483I	ENST00000288368	NM_024870.2	483	Gta/Ata	13/40	0.879666184603233	3	FACETS	0.716	0.644	0.792	0.358	0.322	0.396	SUBCLONAL	1	TRUE	1	0.879666184603233	3		567	471	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045755	47045755	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs782214369	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	275	810	1	ENST00000377604.3:c.2636G>T	p.Arg879Leu	p.R879L	ENST00000377604	NM_001204468.1	879	cGc/cTc	23/24	0.879666184603233	3	FACETS	0.929	0.873	0.986	0.31	0.291	0.329	CLONAL	1	TRUE	0	0.879666184603233	3		811	969	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228207	53228207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	284	641	0	ENST00000375401.3:c.2195C>T	p.Ser732Phe	p.S732F	ENST00000375401	NM_004187.3	732	tCc/tTc	15/26	0.879666184603233	3	FACETS	1	0.97	1	0.348	0.328	0.369	CLONAL	1	TRUE	0	0.879666184603233	3		641	890	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352345	70352345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	231	605	0	ENST00000374080.3:c.4372G>A	p.Gly1458Ser	p.G1458S	ENST00000374080		1458	Ggt/Agt	31/45	0.879666184603233	3	FACETS	0.958	0.896	1	0.319	0.298	0.341	CLONAL	1	TRUE	0	0.879666184603233	3		605	789	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257530	16257530	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747290184	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	125	406	0	ENST00000375759.3:c.4795G>A	p.Glu1599Lys	p.E1599K	ENST00000375759	NM_015001.2	1599	Gaa/Aaa	11/15	0.879666184603233	5	FACETS	0.789	0.72	0.86	0.526	0.48	0.573	SUBCLONAL	2	TRUE	2	0.879666184603233	5		406	418	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525707	187525708	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	C	novel	NA	P-0039208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	138	351	0	ENST00000441802.2:c.10371_10372delinsG	p.Phe3457LeufsTer7	p.F3457Lfs*7	ENST00000441802	NM_005245.3	3457	ttCAgc/ttGgc	18/27	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.879666184603233	2		351	310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0039209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	561	517	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.769	0.744	0.794	1	0.997	1	SUBCLONAL	2	TRUE	1	0.765106456741336	2		517	953	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0039209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	321	457	1	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.474274778535699	3	FACETS	0.856	0.814	0.897	0.856	0.814	0.897	CLONAL	2	TRUE	1	0.765106456741336	3		458	678	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	53	317	0	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	0.398498361245821	1	FACETS	0.281	0.241	0.325	0.281	0.241	0.325	INDETERMINATE	1	TRUE	0	0.765106456741336	1		317	304	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223023	5223023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759129843	NA	P-0039209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	238	744	2	ENST00000357368.4:c.2780C>T	p.Thr927Met	p.T927M	ENST00000357368	NM_002850.3	927	aCg/aTg	18/38	1	2	FACETS	0.508	0.473	0.544	0.508	0.473	0.544	SUBCLONAL	1	TRUE	1	0.765106456741336	2		746	1225	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509966	106509966	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	254	485	0	ENST00000359195.3:c.1960G>A	p.Asp654Asn	p.D654N	ENST00000359195	NM_002649.2	654	Gat/Aat	2/11	0.472509871856932	4	FACETS	0.875	0.824	0.926	0.875	0.824	0.926	CLONAL	2	TRUE	2	0.765106456741336	4		485	670	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627710	37627710	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	135	678	0	ENST00000447079.4:c.1625C>A	p.Thr542Asn	p.T542N	ENST00000447079	NM_015083.1	542	aCt/aAt	2/14	0.131820492242947	6	FACETS	0.698	0.633	0.767	0.233	0.211	0.256	INDETERMINATE	1	TRUE	3	0.765106456741336	6		678	1279	SUCCESS
APC	324	MSKCC	GRCh37	5	112170863	112170863	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0039209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	144	350	1	ENST00000257430.4:c.1958+1G>T		p.X653_splice	ENST00000257430	NM_000038.5	653			0.398498361245821	1	FACETS	0.651	0.602	0.701	0.651	0.602	0.701	INDETERMINATE	1	TRUE	0	0.765106456741336	1		351	357	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099423	157099424	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	TT	novel	NA	P-0039209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	325	261	0	ENST00000346085.5:c.360_361delinsTT	p.Gln120_Gln121delinsHisTer	p.Q120_Q121delinsH*	ENST00000346085	NM_020732.3	120	caGCaa/caTTaa	1/20	0.765106456741336	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.765106456741336	1		261	419	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0039211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	18	365	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	0.4	0.299	0.519	0.4	0.299	0.519	SUBCLONAL	1	TRUE	1	0.16	2		365	563	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519896	NA	P-0039211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	23	234	1	ENST00000281708.4:c.1514G>A	p.Arg505His	p.R505H	ENST00000281708	NM_033632.3	505	cGc/cAc	10/12	1	2	FACETS	0.549	0.426	0.691	0.549	0.426	0.691	SUBCLONAL	1	TRUE	1	0.16	2		235	524	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858403	9858403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	33	322	0	ENST00000330684.3:c.2998G>A	p.Val1000Met	p.V1000M	ENST00000330684	NM_001134407.1	1000	Gtg/Atg	13/13	1	2	FACETS	0.644	0.523	0.781	0.644	0.523	0.781	SUBCLONAL	1	TRUE	1	0.16	2		322	641	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs878854073	NA	P-0039211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	36	315	0	ENST00000269305.4:c.673-1G>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			1	2	FACETS	0.672	0.551	0.808	0.672	0.551	0.808	SUBCLONAL	1	TRUE	1	0.16	2		315	670	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102861	71102861	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	27	223	0	ENST00000318789.4:c.346del	p.Leu116SerfsTer6	p.L116Sfs*6	ENST00000318789	NM_032682.5	116	Ctc/tc	8/21	1	2	FACETS	0.66	0.524	0.817	0.66	0.524	0.817	SUBCLONAL	1	TRUE	1	0.16	2		223	511	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0039212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	49	414	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		414	505	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	247	576	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.935	0.875	0.996	0.935	0.875	0.996	CLONAL	1	TRUE	1	0.55	2		580	961	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	74	327	2	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.661	0.581	0.746	0.661	0.581	0.746	SUBCLONAL	1	TRUE	1	0.55	2		329	407	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	163	525	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.947	0.873	1	0.947	0.873	1	CLONAL	1	TRUE	1	0.55	2		528	626	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	220	649	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.947	0.883	1	0.947	0.883	1	CLONAL	1	TRUE	1	0.55	2		654	845	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	231	912	0	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	1	2	FACETS	0.643	0.598	0.69	0.643	0.598	0.69	SUBCLONAL	1	TRUE	1	0.55	2		912	1306	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	238	691	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.964	0.901	1	0.964	0.901	1	CLONAL	1	TRUE	1	0.55	2		691	898	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	117	300	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	0.55	2		300	413	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	51	271	2	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	1	FACETS	0.805	0.697	0.919	0.805	0.697	0.919	CLONAL	1	TRUE	0	0.55	1		273	167	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796883	42796883	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	273	999	2	ENST00000575354.2:c.3347del	p.Pro1116GlnfsTer45	p.P1116Qfs*45	ENST00000575354	NM_015125.3	1114	gCc/gc	14/20	1	2	FACETS	0.983	0.923	1	0.983	0.923	1	CLONAL	1	TRUE	1	0.55	2		1001	1010	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	67	233	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	1	2	FACETS	0.818	0.717	0.925	0.818	0.717	0.925	CLONAL	1	TRUE	1	0.55	2		233	298	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199383	11199383	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	135	534	1	ENST00000361445.4:c.5108del	p.Asn1703ThrfsTer50	p.N1703Tfs*50	ENST00000361445	NM_004958.3	1703	aAc/ac	36/58	0.3	1	FACETS	0.625	0.571	0.682	0.625	0.571	0.682	INDETERMINATE	1	TRUE	0	0.55	1		535	569	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	153	531	1	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	0.843	0.774	0.915	0.843	0.774	0.915	CLONAL	1	TRUE	1	0.55	2		532	660	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097647	27097647	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs372945891	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	185	633	0	ENST00000324856.7:c.3236A>G	p.Asn1079Ser	p.N1079S	ENST00000324856	NM_006015.4	1079	aAc/aGc	12/20	1	2	FACETS	0.932	0.863	1	0.932	0.863	1	CLONAL	1	TRUE	1	0.55	2		633	722	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509521	46509521	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	44	425	0	ENST00000262741.5:c.1210T>G	p.Cys404Gly	p.C404G	ENST00000262741	NM_003629.3	404	Tgt/Ggt	10/10	1	2	FACETS	0.3	0.251	0.354	0.3	0.251	0.354	SUBCLONAL	1	TRUE	1	0.55	2		425	533	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46736426	46736426	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150138364	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	184	609	0	ENST00000371975.4:c.1138C>T	p.Arg380Trp	p.R380W	ENST00000371975	NM_003579.3	380	Cgg/Tgg	10/18	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.55	2		609	669	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115267956	115267956	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	141	409	0	ENST00000438362.2:c.1779-2A>G		p.X593_splice	ENST00000438362	NM_001242891.1	593			1	2	FACETS	0.999	0.916	1	0.999	0.916	1	CLONAL	1	TRUE	1	0.55	2		409	513	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601836	43601836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	40	625	0	ENST00000355710.3:c.880G>A	p.Ala294Thr	p.A294T	ENST00000355710	NM_020975.4	294	Gcc/Acc	5/20	1	2	FACETS	0.214	0.177	0.256	0.214	0.177	0.256	SUBCLONAL	1	TRUE	1	0.55	2		625	679	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88671991	88671992	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	A	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	147	598	0	ENST00000372037.3:c.531-2dup		p.X177_splice	ENST00000372037	NM_004329.2	177			1	2	FACETS	0.871	0.798	0.946	0.871	0.798	0.946	CLONAL	1	TRUE	1	0.55	2		598	614	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456329	32456329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572926487	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	225	873	0	ENST00000332351.3:c.563C>T	p.Ala188Val	p.A188V	ENST00000332351	NM_024426.4	188	gCg/gTg	1/10	1	2	FACETS	0.859	0.8	0.919	0.859	0.8	0.919	CLONAL	1	TRUE	1	0.55	2		873	953	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572277	64572278	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	233	823	1	ENST00000312049.6:c.1361dup	p.Val455GlyfsTer76	p.V455Gfs*76	ENST00000312049	NM_130799.2	454	aag/aaAg	10/10	1	2	FACETS	0.916	0.855	0.978	0.916	0.855	0.978	CLONAL	1	TRUE	1	0.55	2		824	925	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118370583	118370583	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	73	317	0	ENST00000534358.1:c.6113A>C	p.Asn2038Thr	p.N2038T	ENST00000534358	NM_005933.3	2038	aAt/aCt	24/36	1	2	FACETS	0.785	0.692	0.884	0.785	0.692	0.884	SUBCLONAL	1	TRUE	1	0.55	2		317	338	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	464374	464374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1225548195	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	185	538	0	ENST00000399788.2:c.820G>A	p.Ala274Thr	p.A274T	ENST00000399788	NM_001042603.1	274	Gca/Aca	7/28	1	2	FACETS	0.972	0.901	1	0.972	0.901	1	CLONAL	1	TRUE	1	0.55	2		538	692	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443804	18443804	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	71	291	0	ENST00000266497.5:c.777T>G	p.Tyr259Ter	p.Y259*	ENST00000266497		259	taT/taG	3/31	1	2	FACETS	0.906	0.799	1	0.906	0.799	1	CLONAL	1	TRUE	1	0.55	2		291	285	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524201	18524201	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	152	585	0	ENST00000266497.5:c.1713T>G	p.Asn571Lys	p.N571K	ENST00000266497		571	aaT/aaG	11/31	1	2	FACETS	0.948	0.871	1	0.948	0.871	1	CLONAL	1	TRUE	1	0.55	2		585	583	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46215217	46215217	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	60	278	1	ENST00000334344.6:c.652T>C	p.Ser218Pro	p.S218P	ENST00000334344	NM_152641.2	218	Tcc/Ccc	6/21	1	2	FACETS	0.905	0.789	1	0.905	0.789	1	CLONAL	1	TRUE	1	0.55	2		279	241	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432030	49432030	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	275	963	2	ENST00000301067.7:c.9109del	p.His3037ThrfsTer34	p.H3037Tfs*34	ENST00000301067	NM_003482.3	3037	Cac/ac	34/54	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.55	2		965	973	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885145	111885145	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs892433462	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	192	646	1	ENST00000341259.2:c.1038del	p.Leu347CysfsTer26	p.L347Cfs*26	ENST00000341259	NM_005475.2	345	Ggg/gg	6/8	1	2	FACETS	0.919	0.852	0.988	0.919	0.852	0.988	CLONAL	1	TRUE	1	0.55	2		647	760	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123880944	123880944	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	148	399	0	ENST00000330479.4:c.562C>T	p.Arg188Ter	p.R188*	ENST00000330479	NM_020382.3	188	Cga/Tga	5/9	1	2	FACETS	0.979	0.899	1	0.979	0.899	1	CLONAL	1	TRUE	1	0.55	2		399	550	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602329	28602329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372303125	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	76	503	4	ENST00000241453.7:c.2039C>T	p.Ala680Val	p.A680V	ENST00000241453	NM_004119.2	680	gCg/gTg	16/24	1	2	FACETS	0.445	0.39	0.504	0.445	0.39	0.504	SUBCLONAL	1	TRUE	1	0.55	2		507	621	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964002	28964002	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	106	430	0	ENST00000282397.4:c.1900T>C	p.Tyr634His	p.Y634H	ENST00000282397	NM_002019.4	634	Tat/Cat	13/30	1	2	FACETS	0.8	0.72	0.883	0.8	0.72	0.883	SUBCLONAL	1	TRUE	1	0.55	2		430	482	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913559	32913559	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359479	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	140	431	1	ENST00000380152.3:c.5073del	p.Lys1691AsnfsTer15	p.K1691Nfs*15	ENST00000380152		1689	gcA/gc	11/27	1	2	FACETS	0.992	0.909	1	0.992	0.909	1	CLONAL	1	TRUE	1	0.55	2		432	513	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878105	48878106	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	49	209	0	ENST00000267163.4:c.62dup	p.Ala22GlyfsTer9	p.A22Gfs*9	ENST00000267163	NM_000321.2	19	-/C	1/27	1	2	FACETS	0.803	0.687	0.926	0.803	0.687	0.926	CLONAL	1	TRUE	1	0.55	2		209	222	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614463	38614463	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	127	443	0	ENST00000299084.4:c.234del	p.Asp79ThrfsTer42	p.D79Tfs*42	ENST00000299084	NM_152594.2	77	Aaa/aa	3/7	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.55	2		443	442	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032293	42032293	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1040107611	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	186	638	0	ENST00000219905.7:c.4477A>G	p.Thr1493Ala	p.T1493A	ENST00000219905	NM_001164273.1	1493	Acc/Gcc	14/24	1	2	FACETS	0.881	0.815	0.948	0.881	0.815	0.948	CLONAL	1	TRUE	1	0.55	2		638	768	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	190	571	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.805	0.745	0.868	0.805	0.745	0.868	CLONAL	1	TRUE	1	0.55	2		571	858	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007824	45007825	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	112	419	0	ENST00000558401.1:c.276dup	p.Thr93HisfsTer2	p.T93Hfs*2	ENST00000558401	NM_004048.2	91	acc/aCcc	2/4	1	2	FACETS	0.779	0.703	0.858	0.779	0.703	0.858	SUBCLONAL	1	TRUE	1	0.55	2		419	523	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614824	23614824	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	162	562	0	ENST00000261584.4:c.3517G>C	p.Ala1173Pro	p.A1173P	ENST00000261584	NM_024675.3	1173	Gct/Cct	13/13	1	2	FACETS	0.926	0.853	1	0.926	0.853	1	CLONAL	1	TRUE	1	0.55	2		562	636	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835728	68835728	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	238	656	0	ENST00000261769.5:c.319T>C	p.Tyr107His	p.Y107H	ENST00000261769	NM_004360.3	107	Tac/Cac	3/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.55	2		656	839	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	353	645	5	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.972	0.93	1	1	0.997	1	CLONAL	2	TRUE	1	0.55	2		650	660	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481781	40481781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781724933	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	106	385	0	ENST00000264657.5:c.1123G>A	p.Val375Ile	p.V375I	ENST00000264657	NM_139276.2	375	Gtt/Att	12/24	1	2	FACETS	0.774	0.697	0.855	0.774	0.697	0.855	SUBCLONAL	1	TRUE	1	0.55	2		385	498	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41219709	41219709	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	110	294	0	ENST00000357654.3:c.4990C>G	p.Leu1664Val	p.L1664V	ENST00000357654	NM_007294.3	1664	Ctc/Gtc	16/23	1	2	FACETS	0.959	0.868	1	0.959	0.868	1	CLONAL	1	TRUE	1	0.55	2		294	417	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435068	56435068	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	241	772	0	ENST00000407977.2:c.2069A>G	p.Tyr690Cys	p.Y690C	ENST00000407977		690	tAt/tGt	9/10	1	2	FACETS	0.94	0.879	1	0.94	0.879	1	CLONAL	1	TRUE	1	0.55	2		772	932	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760966	59760967	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs753683450	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	138	564	2	ENST00000259008.2:c.3440dup	p.Asn1147LysfsTer2	p.N1147Kfs*2	ENST00000259008	NM_032043.2	1147	aat/aaAt	20/20	1	2	FACETS	0.815	0.744	0.889	0.815	0.744	0.889	CLONAL	1	TRUE	1	0.55	2		566	616	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120031	70120031	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	37	96	0	ENST00000245479.2:c.1037del	p.Pro346ArgfsTer37	p.P346Rfs*37	ENST00000245479	NM_000346.3	345	Ccc/cc	3/3	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.55	2		96	106	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745738	745738	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	127	531	0	ENST00000314574.4:c.694A>G	p.Thr232Ala	p.T232A	ENST00000314574	NM_005433.3	232	Act/Gct	6/12	1	2	FACETS	0.97	0.885	1	0.97	0.885	1	CLONAL	1	TRUE	1	0.55	2		531	476	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1620979	1620979	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1329397192	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	256	995	3	ENST00000344749.5:c.1081del	p.Gln361ArgfsTer33	p.Q361Rfs*33	ENST00000344749	NM_001136139.2	361	Cag/ag	13/19	1	2	FACETS	0.827	0.774	0.882	0.827	0.774	0.882	CLONAL	1	TRUE	1	0.55	2		998	1125	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184534	7184534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775222338	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	220	577	2	ENST00000302850.5:c.767G>A	p.Arg256His	p.R256H	ENST00000302850	NM_000208.2	256	cGc/cAc	3/22	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.55	2		579	792	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272336	15272337	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGG	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	126	1012	0	ENST00000263388.2:c.6100_6102dup	p.Pro2034dup	p.P2034dup	ENST00000263388	NM_000435.2	2034	-/CCC	33/33	1	2	FACETS	0.501	0.453	0.551	0.501	0.453	0.551	SUBCLONAL	1	TRUE	1	0.55	2		1012	915	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792890	33792890	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	43	149	0	ENST00000498907.2:c.431A>G	p.Glu144Gly	p.E144G	ENST00000498907	NM_004364.3	144	gAg/gGg	1/1	1	2	FACETS	0.755	0.639	0.881	0.755	0.639	0.881	SUBCLONAL	1	TRUE	1	0.55	2		149	207	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218081	36218081	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774047474	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	110	419	1	ENST00000222270.7:c.4028G>A	p.Arg1343His	p.R1343H	ENST00000222270	NM_014727.1	1343	cGc/cAc	15/37	1	2	FACETS	0.926	0.838	1	0.926	0.838	1	CLONAL	1	TRUE	1	0.55	2		420	432	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744384	41744385	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1450387909	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	174	727	1	ENST00000301178.4:c.1010dup	p.Glu338Ter	p.E338*	ENST00000301178	NM_021913.4	335	ggc/ggCc	8/20	1	2	FACETS	0.799	0.737	0.864	0.799	0.737	0.864	SUBCLONAL	1	TRUE	1	0.55	2		728	792	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222520	39222520	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	51	494	2	ENST00000402219.2:c.3090del	p.Lys1030AsnfsTer6	p.K1030Nfs*6	ENST00000402219	NM_005633.3	1030	aaA/aa	20/23	1	2	FACETS	0.29	0.246	0.338	0.29	0.246	0.338	SUBCLONAL	1	TRUE	1	0.55	2		496	640	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249753	39249753	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	116	457	0	ENST00000402219.2:c.1816G>A	p.Val606Ile	p.V606I	ENST00000402219	NM_005633.3	606	Gtt/Att	10/23	1	2	FACETS	0.791	0.716	0.87	0.791	0.716	0.87	SUBCLONAL	1	TRUE	1	0.55	2		457	533	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641480	47641480	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060502003	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	182	519	0	ENST00000233146.2:c.865T>C	p.Phe289Leu	p.F289L	ENST00000233146	NM_000251.2	289	Ttt/Ctt	5/16	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.55	2		519	655	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702411	47702411	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs267607987	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	56	157	0	ENST00000233146.2:c.2005+2T>C		p.X669_splice	ENST00000233146	NM_000251.2	669			1	2	FACETS	0.901	0.781	1	0.901	0.781	1	CLONAL	1	TRUE	1	0.55	2		157	226	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	126	490	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.743	0.674	0.814	0.743	0.674	0.814	SUBCLONAL	1	TRUE	1	0.55	2		492	617	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038189	128038189	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	43	473	0	ENST00000285398.2:c.1361T>C	p.Val454Ala	p.V454A	ENST00000285398	NM_000122.1	454	gTg/gCg	9/15	1	2	FACETS	0.244	0.203	0.289	0.244	0.203	0.289	SUBCLONAL	1	TRUE	1	0.55	2		473	642	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713414	40713414	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	52	762	0	ENST00000373198.4:c.4101del	p.Ser1368ProfsTer31	p.S1368Pfs*31	ENST00000373198	NM_133170.3	1367	ccC/cc	30/32	1	2	FACETS	0.237	0.201	0.276	0.237	0.201	0.276	SUBCLONAL	1	TRUE	1	0.55	2		762	799	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385120	41385120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	205	774	2	ENST00000373198.4:c.841G>A	p.Ala281Thr	p.A281T	ENST00000373198	NM_133170.3	281	Gcg/Acg	6/32	1	2	FACETS	0.915	0.85	0.981	0.915	0.85	0.981	CLONAL	1	TRUE	1	0.55	2		776	815	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485116	57485116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1369025856	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	130	399	0	ENST00000371085.3:c.950G>A	p.Arg317His	p.R317H	ENST00000371085	NM_000516.4	317	cGc/cAc	11/13	1	2	FACETS	0.989	0.903	1	0.989	0.903	1	CLONAL	1	TRUE	1	0.55	2		399	478	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206769	36206769	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	203	697	0	ENST00000300305.3:c.743A>G	p.Asn248Ser	p.N248S	ENST00000300305		248	aAc/aGc	6/8	1	2	FACETS	0.926	0.861	0.994	0.926	0.861	0.994	CLONAL	1	TRUE	1	0.55	2		697	797	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183862	10183862	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1559426203	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	216	637	0	ENST00000256474.2:c.331A>G	p.Ser111Gly	p.S111G	ENST00000256474	NM_000551.3	111	Agc/Ggc	1/3	1	2	FACETS	0.94	0.875	1	0.94	0.875	1	CLONAL	1	TRUE	1	0.55	2		637	836	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268766	41268766	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	130	417	0	ENST00000349496.5:c.1004A>T	p.Lys335Ile	p.K335I	ENST00000349496	NM_001904.3	335	aAa/aTa	7/15	1	2	FACETS	0.977	0.892	1	0.977	0.892	1	CLONAL	1	TRUE	1	0.55	2		417	484	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143009	47143010	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	201	619	0	ENST00000409792.3:c.4953dup	p.Thr1652TyrfsTer14	p.T1652Yfs*14	ENST00000409792	NM_014159.6	1651	-/T	8/21	1	2	FACETS	0.986	0.917	1	0.986	0.917	1	CLONAL	1	TRUE	1	0.55	2		619	741	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936519	49936519	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757151241	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	247	873	1	ENST00000296474.3:c.1408C>T	p.Arg470Cys	p.R470C	ENST00000296474	NM_002447.2	470	Cgt/Tgt	2/20	1	2	FACETS	0.965	0.903	1	0.965	0.903	1	CLONAL	1	TRUE	1	0.55	2		874	931	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665116	138665116	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1282298232	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	147	565	0	ENST00000330315.3:c.449A>G	p.Lys150Arg	p.K150R	ENST00000330315	NM_023067.3	150	aAg/aGg	1/1	1	2	FACETS	0.871	0.798	0.946	0.871	0.798	0.946	CLONAL	1	TRUE	1	0.55	2		565	614	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188337	142188337	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	112	463	0	ENST00000350721.4:c.6394T>C	p.Tyr2132His	p.Y2132H	ENST00000350721	NM_001184.3	2132	Tat/Cat	38/47	1	2	FACETS	0.882	0.798	0.969	0.882	0.798	0.969	CLONAL	1	TRUE	1	0.55	2		463	462	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593646	55593646	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	94	476	0	ENST00000288135.5:c.1712T>C	p.Ile571Thr	p.I571T	ENST00000288135	NM_000222.2	571	aTa/aCa	11/21	1	2	FACETS	0.566	0.504	0.631	0.566	0.504	0.631	SUBCLONAL	1	TRUE	1	0.55	2		476	604	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	120	371	2	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.828	0.751	0.908	0.828	0.751	0.908	CLONAL	1	TRUE	1	0.55	2		373	527	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588996	67588996	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	77	291	0	ENST00000274335.5:c.1090del	p.Met364CysfsTer9	p.M364Cfs*9	ENST00000274335		363	Aaa/aa	8/15	1	2	FACETS	0.883	0.782	0.99	0.883	0.782	0.99	CLONAL	1	TRUE	1	0.55	2		291	317	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674345	86674345	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	67	273	0	ENST00000274376.6:c.2477A>C	p.Gln826Pro	p.Q826P	ENST00000274376	NM_002890.2	826	cAg/cCg	18/25	1	2	FACETS	0.867	0.761	0.979	0.867	0.761	0.979	CLONAL	1	TRUE	1	0.55	2		273	281	SUCCESS
APC	324	MSKCC	GRCh37	5	112164565	112164566	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1554082091	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	56	211	0	ENST00000257430.4:c.1643dup	p.Leu548PhefsTer12	p.L548Ffs*12	ENST00000257430	NM_000038.5	547	gtt/gTtt	14/16	1	2	FACETS	0.642	0.554	0.738	0.642	0.554	0.738	SUBCLONAL	1	TRUE	1	0.55	2		211	317	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	97	245	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.862	0.774	0.955	0.862	0.774	0.955	CLONAL	1	TRUE	1	0.55	2		245	409	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048713	180048713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1176988485	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	231	835	0	ENST00000261937.6:c.1849G>A	p.Ala617Thr	p.A617T	ENST00000261937	NM_182925.4	617	Gcc/Acc	13/30	1	2	FACETS	0.916	0.855	0.979	0.916	0.855	0.979	CLONAL	1	TRUE	1	0.55	2		835	917	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166430	32166430	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	232	700	0	ENST00000375023.3:c.4613G>T	p.Gly1538Val	p.G1538V	ENST00000375023	NM_004557.3	1538	gGc/gTc	25/30	1	2	FACETS	0.938	0.876	1	0.938	0.876	1	CLONAL	1	TRUE	1	0.55	2		700	899	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180398	32180398	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	205	663	0	ENST00000375023.3:c.2533A>G	p.Met845Val	p.M845V	ENST00000375023	NM_004557.3	845	Atg/Gtg	17/30	1	2	FACETS	0.993	0.924	1	0.993	0.924	1	CLONAL	1	TRUE	1	0.55	2		663	751	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068034	94068034	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	87	346	0	ENST00000369303.4:c.928T>C	p.Cys310Arg	p.C310R	ENST00000369303	NM_004440.3	310	Tgt/Cgt	4/17	1	2	FACETS	0.759	0.675	0.847	0.759	0.675	0.847	SUBCLONAL	1	TRUE	1	0.55	2		346	417	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679149	117679149	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	73	351	0	ENST00000368508.3:c.3672del	p.Phe1224LeufsTer19	p.F1224Lfs*19	ENST00000368508	NM_002944.2	1224	ttT/tt	24/43	1	2	FACETS	0.731	0.644	0.825	0.731	0.644	0.825	SUBCLONAL	1	TRUE	1	0.55	2		351	363	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528594	157528594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	243	708	3	ENST00000346085.5:c.6319C>T	p.Arg2107Cys	p.R2107C	ENST00000346085	NM_020732.3	2107	Cgt/Tgt	20/20	1	2	FACETS	0.99	0.926	1	0.99	0.926	1	CLONAL	1	TRUE	1	0.55	2		711	893	SUCCESS
MET	4233	MSKCC	GRCh37	7	116399473	116399473	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1554395889	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	148	482	0	ENST00000397752.3:c.2293A>G	p.Lys765Glu	p.K765E	ENST00000397752	NM_000245.2	765	Aaa/Gaa	10/21	1	2	FACETS	0.943	0.865	1	0.943	0.865	1	CLONAL	1	TRUE	1	0.55	2		482	571	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436138	116436138	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	137	404	0	ENST00000397752.3:c.4133A>G	p.Glu1378Gly	p.E1378G	ENST00000397752	NM_000245.2	1378	gAg/gGg	21/21	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.55	2		404	486	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850915	128850915	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	216	723	0	ENST00000249373.3:c.1762T>C	p.Ser588Pro	p.S588P	ENST00000249373	NM_005631.4	588	Tcc/Ccc	10/12	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.55	2		723	765	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851863	128851863	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	rs752417456	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	214	750	0	ENST00000249373.3:c.1937-2A>C		p.X646_splice	ENST00000249373	NM_005631.4	646			1	2	FACETS	0.935	0.871	1	0.935	0.871	1	CLONAL	1	TRUE	1	0.55	2		750	832	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140454003	140454003	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	20	280	0	ENST00000288602.6:c.1725A>C	p.Arg575Ser	p.R575S	ENST00000288602	NM_004333.4	575	agA/agC	14/18	1	2	FACETS	0.25	0.191	0.319	0.25	0.191	0.319	SUBCLONAL	1	TRUE	1	0.55	2		280	291	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188058	151188058	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	142	430	0	ENST00000262187.5:c.95T>C	p.Val32Ala	p.V32A	ENST00000262187	NM_005614.3	32	gTg/gCg	2/8	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.55	2		430	486	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152009008	152009008	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	103	353	0	ENST00000262189.6:c.614T>A	p.Ile205Lys	p.I205K	ENST00000262189	NM_170606.2	205	aTa/aAa	5/59	1	2	FACETS	0.975	0.88	1	0.975	0.88	1	CLONAL	1	TRUE	1	0.55	2		353	384	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189038	38189039	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	221	733	0	ENST00000317025.8:c.975dup	p.Arg326ThrfsTer6	p.R326Tfs*6	ENST00000317025	NM_023034.1	325	-/A	5/24	1	2	FACETS	0.957	0.892	1	0.957	0.892	1	CLONAL	1	TRUE	1	0.55	2		733	840	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542143	141542143	+	stop_lost	Nonstop_Mutation	SNP	T	T	C	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	146	594	0	ENST00000220592.5:c.2580A>G	p.Ter860TrpextTer29	p.*860Wext*29	ENST00000220592	NM_012154.3	860	tgA/tgG	19/19	1	2	FACETS	0.872	0.799	0.948	0.872	0.799	0.948	CLONAL	1	TRUE	1	0.55	2		594	609	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342827	87342827	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	135	491	0	ENST00000277120.3:c.1112A>C	p.Glu371Ala	p.E371A	ENST00000277120		371	gAg/gCg	9/19	1	2	FACETS	0.986	0.902	1	0.986	0.902	1	CLONAL	1	TRUE	1	0.55	2		491	498	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	189	570	1	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.886	0.82	0.953	0.886	0.82	0.953	CLONAL	1	TRUE	1	0.55	2		571	776	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930915	39930915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	138	249	0	ENST00000378444.4:c.3026del	p.Leu1009TyrfsTer12	p.L1009Yfs*12	ENST00000378444	NM_001123385.1	1009	tTa/ta	5/15	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.55	1		249	244	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617162	100617162	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	157	301	0	ENST00000308731.7:c.587A>C	p.Gln196Pro	p.Q196P	ENST00000308731	NM_000061.2	196	cAg/cCg	7/19	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.55	1		301	313	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020768	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs926053251	NA	P-0039214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	177	518	1	ENST00000358127.4:c.77T>G	p.Val26Gly	p.V26G	ENST00000358127	NM_001280556.1	26	gTt/gGt	2/10	1	2	FACETS	0.955	0.883	1	0.955	0.883	1	CLONAL	1	TRUE	1	0.55	2		519	674	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717777	89717777	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0039218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	173	270	0	ENST00000371953.3:c.801+1G>T		p.X267_splice	ENST00000371953	NM_000314.4	267			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.808698663291689	2		270	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577544	7577544	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587780074	NA	P-0039218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	321	621	2	ENST00000269305.4:c.737T>G	p.Met246Arg	p.M246R	ENST00000269305	NM_001126112.2	246	aTg/aGg	7/11	0.80342582821949	1	FACETS	0.983	0.945	1	0.983	0.945	1	CLONAL	1	FALSE	0	0.808698663291689	1		623	481	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791339	42791339	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	84	726	0	ENST00000575354.2:c.404del	p.Pro135GlnfsTer70	p.P135Qfs*70	ENST00000575354	NM_015125.3	133	ggC/gg	3/20	0.666299040264271	1	FACETS	0.184	0.162	0.207	0.184	0.162	0.207	SUBCLONAL	1	FALSE	0	0.808698663291689	1		726	674	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692805	89692809	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCT	CAGCT	-	novel	NA	P-0039218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	149	261	0	ENST00000371953.3:c.289_293del	p.Gln97ArgfsTer8	p.Q97Rfs*8	ENST00000371953	NM_000314.4	97	CAGCTa/a	5/9	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.808698663291689	2		261	334	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0039220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	164	583	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.492516630583678	4	FACETS	0.907	0.831	0.986	0.302	0.277	0.329	CLONAL	1	TRUE	1	0.492516630583678	4		583	1096	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183755	10183757	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs5030648	NA	P-0039220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	250	743	0	ENST00000256474.2:c.227_229del	p.Phe76del	p.F76del	ENST00000256474	NM_000551.3	75	aTCTtc/atc	1/3	0.369092491874236	2	FACETS	1	0.993	1	0.71	0.667	0.753	CLONAL	1	TRUE	0	0.492516630583678	2		743	715	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158239	47158242	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TTCT	TTCT	-	rs1553699115	NA	P-0039220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	49	266	0	ENST00000409792.3:c.4457_4460del	p.Lys1486ArgfsTer28	p.K1486Rfs*28	ENST00000409792	NM_014159.6	1486	aAGAAg/ag	4/21	0.369092491874236	2	FACETS	1	0.932	1	0.572	0.492	0.656	CLONAL	1	TRUE	0	0.492516630583678	2		266	174	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195738	102195738	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	21	333	0	ENST00000263464.3:c.498G>A	p.Met166Ile	p.M166I	ENST00000263464	NM_001165.4	166	atG/atA	2/9	1	2	FACETS	0.36	0.278	0.455	0.36	0.278	0.455	SUBCLONAL	1	TRUE	1	0.492516630583678	2		333	237	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702566	52702566	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	72	423	0	ENST00000394830.3:c.332del	p.Leu111CysfsTer2	p.L111Cfs*2	ENST00000394830	NM_018313.4	111	tTg/tg	4/30	0.369092491874236	2	FACETS	1	0.956	1	0.585	0.517	0.655	CLONAL	1	TRUE	0	0.492516630583678	2		423	250	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287287	33287287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	199	501	0	ENST00000374542.5:c.1810G>A	p.Gly604Arg	p.G604R	ENST00000374542	NM_001141970.1	604	Gga/Aga	6/8	0.375199555589605	3	FACETS	1	0.985	1	0.772	0.724	0.82	CLONAL	2	TRUE	0	0.492516630583678	3		501	435	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151868401	151868401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	110	487	0	ENST00000262189.6:c.9401C>T	p.Thr3134Ile	p.T3134I	ENST00000262189	NM_170606.2	3134	aCt/aTt	40/59	0.492516630583678	4	FACETS	0.966	0.869	1	0.322	0.289	0.357	CLONAL	1	TRUE	1	0.492516630583678	4		487	690	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574030	7574030	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	290	587	1	ENST00000269305.4:c.997del	p.Arg333ValfsTer12	p.R333Vfs*12	ENST00000269305	NM_001126112.2	333	Cgt/gt	10/11	0.311707346096657	3	FACETS	1	0.99	1	0.795	0.754	0.837	CLONAL	2	TRUE	0	0.459140797928019	3		588	651	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152428	56152428	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs778331321	NA	P-0039222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	40	161	0	ENST00000399503.3:c.484C>T	p.Arg162Cys	p.R162C	ENST00000399503	NM_005921.1	162	Cgt/Tgt	2/20	0.355433598640702	2	FACETS	1	0.883	1	0.528	0.445	0.617	CLONAL	1	TRUE	0	0.459140797928019	2		161	165	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929412	44929415	+	frameshift_variant	Frame_Shift_Del	DEL	ACAA	ACAA	-	rs786205676	NA	P-0039222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	69	609	0	ENST00000377967.4:c.2515_2518del	p.Asn839ValfsTer27	p.N839Vfs*27	ENST00000377967	NM_021140.2	838	ACAAac/ac	17/29	0.456556835738311	3	FACETS	0.46	0.399	0.525	0.23	0.199	0.263	SUBCLONAL	1	TRUE	1	0.459140797928019	3		609	804	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45864887	45864887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs186220206	NA	P-0039222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	197	799	2	ENST00000391945.4:c.1132C>T	p.Arg378Cys	p.R378C	ENST00000391945	NM_000400.3	378	Cgc/Tgc	12/23	0.459140797928019	3	FACETS	1	0.94	1	0.509	0.471	0.548	CLONAL	1	TRUE	1	0.459140797928019	3		801	1037	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0039223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	43	477	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	1	2	FACETS	0.674	0.564	0.796	0.674	0.564	0.796	SUBCLONAL	1	TRUE	1	0.278499237323199	2		477	458	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933432	100933432	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	37	375	1	ENST00000325455.5:c.1958C>A	p.Ala653Asp	p.A653D	ENST00000325455	NM_001202474.3	653	gCt/gAt	4/8	1	2	FACETS	0.616	0.508	0.737	0.616	0.508	0.737	SUBCLONAL	1	TRUE	1	0.278499237323199	2		376	431	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163913	152163913	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	28	442	0	ENST00000206249.3:c.634A>T	p.Ser212Cys	p.S212C	ENST00000206249	NM_000125.3	212	Agt/Tgt	2/8	1	2	FACETS	0.438	0.349	0.539	0.438	0.349	0.539	SUBCLONAL	1	TRUE	1	0.278499237323199	2		442	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0039224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	158	670	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.291625780765393	2	FACETS	0.948	0.874	1	0.948	0.874	1	CLONAL	2	TRUE	0	0.298587985288456	2		670	558	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952120	178952120	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	95	319	0	ENST00000263967.3:c.3175T>C	p.Phe1059Leu	p.F1059L	ENST00000263967	NM_006218.2	1059	Ttc/Ctc	21/21	0.298587985288456	5	FACETS	0.978	0.881	1	0.978	0.881	1	CLONAL	3	TRUE	2	0.298587985288456	5		319	314	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111509	8111510	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAATGGGGACCCTGTCTGCAATGCCTGTGGGCTCTACTACAAGCTT	novel	NA	P-0039225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	97	572	0	ENST00000346208.3:c.998_1043dup	p.His348GlnfsTer19	p.H348Qfs*19	ENST00000346208		332	gcc/gcCAATGGGGACCCTGTCTGCAATGCCTGTGGGCTCTACTACAAGCTTc	5/6	1	2	FACETS	0.361	0.321	0.404	0.361	0.321	0.404	SUBCLONAL	1	TRUE	1	0.598212361114281	2		572	898	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26046034	26046035	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	41	267	0	ENST00000540144.1:c.400dup	p.Glu134GlyfsTer?	p.E134Gfs*?	ENST00000540144	NM_003531.2	132	-/G	1/1	1	2	FACETS	0.473	0.396	0.557	0.473	0.396	0.557	SUBCLONAL	1	TRUE	1	0.598212361114281	2		267	290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0039226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	235	807	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.378149825022624	2	FACETS	0.958	0.9	1	0.958	0.9	1	CLONAL	2	TRUE	0	0.383186651844718	2		807	640	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073680	8073680	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	64	431	0	ENST00000377482.5:c.979C>G	p.Pro327Ala	p.P327A	ENST00000377482	NM_018948.3	327	Ccg/Gcg	4/4	0.302809434734497	3	FACETS	0.819	0.711	0.936			1	CLONAL	1	TRUE	NA	0.383186651844718	3		431	486	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937863	36937868	+	inframe_deletion	In_Frame_Del	DEL	GGCTGG	GGCTGG	-	novel	NA	P-0039226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	283	1064	0	ENST00000361632.4:c.968_973del	p.Pro323_Ser324del	p.P323_S324del	ENST00000361632		323	cCCAGCCtg/ctg	7/16	0.361280208485555	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.383186651844718	2		1064	723	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061186	38061186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	137	396	1	ENST00000250448.2:c.803G>A	p.Cys268Tyr	p.C268Y	ENST00000250448	NM_004496.3	268	tGc/tAc	2/2	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	2	TRUE	NA	0.383186651844718	2		397	325	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705430	43705430	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	113	855	0	ENST00000382044.4:c.5192A>G	p.Lys1731Arg	p.K1731R	ENST00000382044	NM_001141980.1	1731	aAg/aGg	24/28	NA	2	FACETS	0.856	0.771	0.946			1	INDETERMINATE	1	TRUE	NA	0.383186651844718	2		855	689	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246559	41246559	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	206	658	0	ENST00000357654.3:c.989del	p.Asp330ValfsTer11	p.D330Vfs*11	ENST00000357654	NM_007294.3	330	gAt/gt	10/23	NA	2	FACETS	0.933	0.872	0.996			1	INDETERMINATE	2	TRUE	NA	0.383186651844718	2		658	576	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	281	492	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.560730624607771	3	FACETS	0.944	0.893	0.995	0.944	0.893	0.995	CLONAL	2	TRUE	1	0.560730624607771	3		492	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520006	NA	P-0039229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	297	841	0	ENST00000269305.4:c.821T>C	p.Val274Ala	p.V274A	ENST00000269305	NM_001126112.2	274	gTt/gCt	8/11	0.560730624607771	1	FACETS	0.934	0.883	0.986	0.934	0.883	0.986	CLONAL	1	TRUE	0	0.560730624607771	1		841	816	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288799	15288799	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764992581	NA	P-0039229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	138	201	0	ENST00000263388.2:c.3940G>A	p.Ala1314Thr	p.A1314T	ENST00000263388	NM_000435.2	1314	Gcc/Acc	24/33	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.560730624607771	2		201	433	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713829	30713829	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	271	618	2	ENST00000295754.5:c.1154T>A	p.Ile385Asn	p.I385N	ENST00000295754	NM_003242.5	385	aTc/aAc	4/7	0.560730624607771	2	FACETS	0.953	0.895	1	0.477	0.447	0.507	CLONAL	1	TRUE	0	0.560730624607771	2		620	1014	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90992975	90992975	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	137	362	0	ENST00000265433.3:c.467A>T	p.Lys156Ile	p.K156I	ENST00000265433	NM_002485.4	156	aAa/aTa	4/16	1	2	FACETS	0.879	0.803	0.958	0.879	0.803	0.958	CLONAL	1	TRUE	1	0.560730624607771	2		362	556	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855977	76855977	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	171	495	0	ENST00000373344.5:c.5623G>T	p.Asp1875Tyr	p.D1875Y	ENST00000373344	NM_000489.3	1875	Gat/Tat	23/35	0.338529199900535	6	FACETS	1	0.96	1	0.268	0.246	0.292	CLONAL	1	TRUE	2	0.560730624607771	6		495	1205	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	166	508	2	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.287948943279757	5	FACETS	1	0.961	1	0.708	0.654	0.763	INDETERMINATE	2	TRUE	2	0.490889199542249	5		510	553	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0039230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	204	407	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	0.324016327592381	6	FACETS	1	0.982	1			1	CLONAL	3	TRUE	NA	0.490889199542249	6		407	487	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643297	38643297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1348585688	NA	P-0039230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	28	353	0	ENST00000299084.4:c.767G>A	p.Arg256His	p.R256H	ENST00000299084	NM_152594.2	256	cGt/cAt	7/7	0.394794664543926	3	FACETS	0.368	0.294	0.453	0.123	0.098	0.151	SUBCLONAL	1	TRUE	0	0.490889199542249	3		353	386	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0039231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	92	576	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.727	0.644	0.815	0.727	0.644	0.815	SUBCLONAL	1	FALSE	1	0.262326107018021	2		580	965	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974899	15974899	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	59	378	0	ENST00000268712.3:c.3976C>T	p.Arg1326Ter	p.R1326*	ENST00000268712	NM_006311.3	1326	Cga/Tga	30/46	1	2	FACETS	0.697	0.599	0.804	0.697	0.599	0.804	SUBCLONAL	1	FALSE	1	0.262326107018021	2		378	645	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841231	15841236	+	inframe_deletion	In_Frame_Del	DEL	AGCCGG	AGCCGG	-	rs752736259	NA	P-0039231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	54	422	0	ENST00000307771.7:c.1338_1343del	p.Ser447_Arg448del	p.S447_R448del	ENST00000307771	NM_005089.3	439	AGCCGG/-	11/11	0.262326107018021	1	FACETS	0.582	0.496	0.675	0.582	0.496	0.675	SUBCLONAL	1	FALSE	0	0.262326107018021	1		422	615	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0039231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	19	271	2	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	0.262326107018021	1	FACETS	0.36	0.272	0.462	0.36	0.272	0.462	SUBCLONAL	1	FALSE	0	0.262326107018021	1		273	350	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561423	9561423	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201131316	NA	P-0039231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	66	479	0	ENST00000353224.5:c.359C>T	p.Ala120Val	p.A120V	ENST00000353224	NM_177990.2	120	gCg/gTg	4/10	1	2	FACETS	0.699	0.606	0.8	0.699	0.606	0.8	SUBCLONAL	1	FALSE	1	0.262326107018021	2		479	720	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0039231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	74	473	0	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	0.746	0.653	0.848	0.746	0.653	0.848	SUBCLONAL	1	FALSE	1	0.262326107018021	2		473	756	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	69	521	1	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.73	0.635	0.832	0.73	0.635	0.832	SUBCLONAL	1	FALSE	1	0.262326107018021	2		522	721	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951964	178951964	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	59	384	0	ENST00000263967.3:c.3019G>C	p.Gly1007Arg	p.G1007R	ENST00000263967	NM_006218.2	1007	Ggc/Cgc	21/21	1	2	FACETS	0.808	0.695	0.93	0.808	0.695	0.93	CLONAL	1	FALSE	1	0.262326107018021	2		384	557	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	49	288	0	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.678	0.574	0.793	0.678	0.574	0.793	SUBCLONAL	1	FALSE	1	0.262326107018021	2		288	551	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0039231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	114	637	0	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	0.846	0.76	0.937	0.846	0.76	0.937	CLONAL	1	FALSE	1	0.262326107018021	2		637	1027	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508374	106508374	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200423506	NA	P-0039231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	38	290	0	ENST00000359195.3:c.368G>A	p.Arg123His	p.R123H	ENST00000359195	NM_002649.2	123	cGc/cAc	2/11	1	2	FACETS	0.615	0.508	0.735	0.615	0.508	0.735	SUBCLONAL	1	FALSE	1	0.262326107018021	2		290	471	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693003	89693003	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs786204900	NA	P-0039231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	43	392	0	ENST00000371953.3:c.491del	p.Lys164ArgfsTer3	p.K164Rfs*3	ENST00000371953	NM_000314.4	163	Aaa/aa	5/9	1	2	FACETS	0.534	0.446	0.632	0.534	0.446	0.632	SUBCLONAL	1	FALSE	1	0.262326107018021	2		392	614	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437606	56437606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886926322	NA	P-0039231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	72	429	3	ENST00000407977.2:c.856C>T	p.Arg286Trp	p.R286W	ENST00000407977		286	Cgg/Tgg	8/10	1	2	FACETS	0.881	0.77	1	0.881	0.77	1	CLONAL	1	FALSE	1	0.262326107018021	2		432	623	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993013	72993014	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	119	822	1	ENST00000268489.5:c.1031dup	p.Asn344LysfsTer13	p.N344Kfs*13	ENST00000268489	NM_006885.3	344	aac/aaAc	2/10	1	2	FACETS	0.713	0.642	0.789	0.713	0.642	0.789	SUBCLONAL	1	FALSE	1	0.262326107018021	2		823	1272	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249468	153249468	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	68	422	0	ENST00000281708.4:c.1310G>T	p.Gly437Val	p.G437V	ENST00000281708	NM_033632.3	437	gGa/gTa	9/12	1	2	FACETS	0.778	0.677	0.888	0.778	0.677	0.888	SUBCLONAL	1	FALSE	1	0.262326107018021	2		422	666	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120460319	120460319	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1446995271	NA	P-0039231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	61	439	1	ENST00000256646.2:c.5996del	p.Asn1999MetfsTer32	p.N1999Mfs*32	ENST00000256646	NM_024408.3	1999	aAt/at	33/34	1	2	FACETS	0.556	0.479	0.641	0.556	0.479	0.641	SUBCLONAL	1	FALSE	1	0.262326107018021	2		440	836	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624306	89624306	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0039231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	62	510	0	ENST00000371953.3:c.79+1G>A		p.X27_splice	ENST00000371953	NM_000314.4	27			1	2	FACETS	0.572	0.493	0.659	0.572	0.493	0.659	SUBCLONAL	1	FALSE	1	0.262326107018021	2		510	826	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106100	27106100	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	79	488	1	ENST00000324856.7:c.5715del	p.Lys1905AsnfsTer18	p.K1905Nfs*18	ENST00000324856	NM_006015.4	1904	gAa/ga	20/20	1	2	FACETS	0.79	0.694	0.894	0.79	0.694	0.894	SUBCLONAL	1	FALSE	1	0.262326107018021	2		489	762	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605204	46605204	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1459319402	NA	P-0039231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	44	312	3	ENST00000263734.3:c.1421G>C	p.Ser474Thr	p.S474T	ENST00000263734	NM_001430.4	474	aGc/aCc	10/16	1	2	FACETS	0.766	0.643	0.902	0.766	0.643	0.902	CLONAL	1	FALSE	1	0.262326107018021	2		315	438	SUCCESS
APC	324	MSKCC	GRCh37	5	112176192	112176192	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370433763	NA	P-0039231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	52	365	0	ENST00000257430.4:c.4901C>T	p.Pro1634Leu	p.P1634L	ENST00000257430	NM_000038.5	1634	cCg/cTg	16/16	1	2	FACETS	0.553	0.47	0.645	0.553	0.47	0.645	SUBCLONAL	1	FALSE	1	0.262326107018021	2		365	717	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099405	4099405	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1348137830	NA	P-0039231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	99	599	1	ENST00000262948.5:c.713G>A	p.Arg238Gln	p.R238Q	ENST00000262948	NM_030662.3	238	cGg/cAg	7/11	1	2	FACETS	0.744	0.663	0.831	0.744	0.663	0.831	SUBCLONAL	1	FALSE	1	0.262326107018021	2		600	1014	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353767	40353767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760771231	NA	P-0039231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	58	582	0	ENST00000293328.3:c.2353G>A	p.Ala785Thr	p.A785T	ENST00000293328	NM_012448.3	785	Gca/Aca	19/19	1	2	FACETS	0.481	0.412	0.556	0.481	0.412	0.556	SUBCLONAL	1	FALSE	1	0.262326107018021	2		582	920	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073878	8073878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	50	291	0	ENST00000377482.5:c.781G>A	p.Ala261Thr	p.A261T	ENST00000377482	NM_018948.3	261	Gcc/Acc	4/4	1	2	FACETS	0.775	0.658	0.903	0.775	0.658	0.903	CLONAL	1	FALSE	1	0.262326107018021	2		291	492	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624294	89624294	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	53	472	0	ENST00000371953.3:c.68T>C	p.Leu23Ser	p.L23S	ENST00000371953	NM_000314.4	23	tTa/tCa	1/9	1	2	FACETS	0.53	0.451	0.617	0.53	0.451	0.617	SUBCLONAL	1	FALSE	1	0.262326107018021	2		472	762	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4387968	4387968	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	59	516	0	ENST00000261254.3:c.454G>A	p.Ala152Thr	p.A152T	ENST00000261254	NM_001759.3	152	Gca/Aca	3/5	NA	2	FACETS	0.543	0.466	0.627			1	INDETERMINATE	1	FALSE	NA	0.262326107018021	2		516	829	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281669	49281669	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199903030	NA	P-0039231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	94	690	1	ENST00000282018.3:c.716G>A	p.Arg239Gln	p.R239Q	ENST00000282018	NM_020377.2	239	cGg/cAg	1/1	1	2	FACETS	0.648	0.575	0.726	0.648	0.575	0.726	SUBCLONAL	1	FALSE	1	0.262326107018021	2		691	1106	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512297	38512297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762998209	NA	P-0039231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	97	667	1	ENST00000254066.5:c.1208C>T	p.Pro403Leu	p.P403L	ENST00000254066	NM_000964.3	403	cCg/cTg	9/9	1	2	FACETS	0.724	0.644	0.809	0.724	0.644	0.809	SUBCLONAL	1	FALSE	1	0.262326107018021	2		668	1022	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267618	7267618	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	99	683	0	ENST00000302850.5:c.390A>T	p.Glu130Asp	p.E130D	ENST00000302850	NM_000208.2	130	gaA/gaT	2/22	1	2	FACETS	0.631	0.562	0.706	0.631	0.562	0.706	SUBCLONAL	1	FALSE	1	0.262326107018021	2		683	1196	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098952	47098952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	63	461	0	ENST00000409792.3:c.6322G>A	p.Val2108Ile	p.V2108I	ENST00000409792	NM_014159.6	2108	Gta/Ata	15/21	1	2	FACETS	0.624	0.538	0.717	0.624	0.538	0.717	SUBCLONAL	1	FALSE	1	0.262326107018021	2		461	770	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597385	52597386	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0039231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	46	443	0	ENST00000394830.3:c.3924_3925del	p.Asp1308GlufsTer2	p.D1308Efs*2	ENST00000394830	NM_018313.4	1308	gaTAgt/gagt	25/30	1	2	FACETS	0.525	0.441	0.618	0.525	0.441	0.618	SUBCLONAL	1	FALSE	1	0.262326107018021	2		443	668	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413665	138413665	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762171492	NA	P-0039231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	69	390	1	ENST00000289153.2:c.1855G>A	p.Val619Ile	p.V619I	ENST00000289153	NM_006219.2	619	Gtt/Att	12/22	1	2	FACETS	0.745	0.648	0.85	0.745	0.648	0.85	SUBCLONAL	1	FALSE	1	0.262326107018021	2		391	706	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938775	178938775	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	76	381	0	ENST00000263967.3:c.2017T>A	p.Ser673Thr	p.S673T	ENST00000263967	NM_006218.2	673	Tct/Act	14/21	1	2	FACETS	0.796	0.698	0.902	0.796	0.698	0.902	CLONAL	1	FALSE	1	0.262326107018021	2		381	728	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156570	55156570	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1184746473	NA	P-0039231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	65	440	0	ENST00000257290.5:c.2971G>A	p.Val991Ile	p.V991I	ENST00000257290	NM_006206.4	991	Gtc/Atc	22/23	1	2	FACETS	0.635	0.549	0.728	0.635	0.549	0.728	SUBCLONAL	1	FALSE	1	0.262326107018021	2		440	781	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56171015	56171016	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0039231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	40	250	0	ENST00000399503.3:c.1845_1846dup	p.Gly616ValfsTer41	p.G616Vfs*41	ENST00000399503	NM_005921.1	615	agt/aGTgt	10/20	1	2	FACETS	0.718	0.597	0.852	0.718	0.597	0.852	SUBCLONAL	1	FALSE	1	0.262326107018021	2		250	425	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177000	56177000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs553060905	NA	P-0039231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	38	294	0	ENST00000399503.3:c.2270G>A	p.Arg757His	p.R757H	ENST00000399503	NM_005921.1	757	cGc/cAc	13/20	1	2	FACETS	0.661	0.547	0.789	0.661	0.547	0.789	SUBCLONAL	1	FALSE	1	0.262326107018021	2		294	438	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0039232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	111	300	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	0.896726232299556	2		300	238	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496924	29496927	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs786201874	NA	P-0039232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	103	234	0	ENST00000356175.3:c.499_502del	p.Cys167GlnfsTer10	p.C167Qfs*10	ENST00000356175	NM_000267.3	165	acTGTT/ac	5/57	0.896726232299556	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.896726232299556	1		234	124	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11297973	11297985	+	frameshift_variant	Frame_Shift_Del	DEL	ATGGCCAGCTCCC	ATGGCCAGCTCCC	-	novel	NA	P-0039232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	231	557	0	ENST00000361445.4:c.2123_2135del	p.Arg708ProfsTer10	p.R708Pfs*10	ENST00000361445	NM_004958.3	708	cGGGAGCTGGCCATc/cc	13/58	0.780957433521176	3	FACETS	1	0.977	1	0.545	0.511	0.581	CLONAL	1	TRUE	1	0.896726232299556	3		557	684	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107167	27107167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	128	426	0	ENST00000324856.7:c.6778G>A	p.Asp2260Asn	p.D2260N	ENST00000324856	NM_006015.4	2260	Gac/Aac	20/20	1	2	FACETS	0.751	0.688	0.816	0.751	0.688	0.816	SUBCLONAL	1	TRUE	1	0.896726232299556	2		426	380	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41905096	41905096	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	146	360	0	ENST00000372991.4:c.451G>A	p.Asp151Asn	p.D151N	ENST00000372991	NM_001760.3	151	Gac/Aac	3/5	0.783712154033569	3	FACETS	0.897	0.823	0.973			1	CLONAL	1	TRUE	NA	0.896726232299556	3		360	526	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145337	58145337	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	4302	435	0	ENST00000257904.6:c.164G>C	p.Arg55Pro	p.R55P	ENST00000257904	NM_000075.3	55	cGt/cCt	2/8	0.3	49	FACETS	1	0.994	1			1	CLONAL	46	TRUE	NA	0.3	49		435	5010	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796161	42796246	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CACTTGAGGTCTTGGTCTTCCCCTGCCCCAGTCTGGGGCCACAGCTCACCCTGGCCTATGGGTGCCCTTCTCCACAGATCATCCAG	CACTTGAGGTCTTGGTCTTCCCCTGCCCCAGTCTGGGGCCACAGCTCACCCTGGCCTATGGGTGCCCTTCTCCACAGATCATCCAG	-	novel	NA	P-0039236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	116	250	0	ENST00000575354.2:c.2887-76_2896del		p.X963_splice	ENST00000575354	NM_015125.3	963		12/20	1	2	FACETS	0.848	0.775	0.922	1	0.991	1	CLONAL	3	TRUE	1	0.3	2		250	304	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057000	180057000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762995809	NA	P-0039238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	97	805	0	ENST00000261937.6:c.619G>A	p.Glu207Lys	p.E207K	ENST00000261937	NM_182925.4	207	Gag/Aag	5/30	0.218225661516987	3	FACETS	0.633	0.563	0.708	0.316	0.281	0.354	SUBCLONAL	1	TRUE	1	0.307484040801728	3		805	1150	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0039241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	222	501	0	ENST00000269305.4:c.97-1G>A		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.599104027232998	2	FACETS	0.95	0.9	1	0.95	0.9	1	CLONAL	2	TRUE	0	0.599104027232998	2		501	390	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228288	53228288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1569264240	NA	P-0039241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	94	617	1	ENST00000375401.3:c.2114G>A	p.Arg705His	p.R705H	ENST00000375401	NM_004187.3	705	cGc/cAc	15/26	0.599104027232998	1	FACETS	0.556	0.498	0.617	0.556	0.498	0.617	SUBCLONAL	1	TRUE	0	0.599104027232998	1		618	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0039245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	14	593	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.334788355927053	1	FACETS	0.1	0.072	0.135	0.1	0.072	0.135	SUBCLONAL	1	TRUE	0	0.334788355927053	1		595	694	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	111	657	1	ENST00000269305.4:c.273del	p.Trp91CysfsTer32	p.W91Cfs*32	ENST00000269305	NM_001126112.2	91	tgG/tg	4/11	0.334788355927053	1	FACETS	0.786	0.708	0.87	0.786	0.708	0.87	SUBCLONAL	1	TRUE	0	0.334788355927053	1		658	702	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470611	25470611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749572719	NA	P-0039245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	201	548	0	ENST00000264709.3:c.863G>A	p.Arg288Gln	p.R288Q	ENST00000264709	NM_175629.2	288	cGg/cAg	8/23	NA	2	FACETS	0.794	0.738	0.852			1	INDETERMINATE	2	TRUE	NA	0.334788355927053	2		548	756	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895635	28895635	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	27	440	0	ENST00000282397.4:c.3139A>T	p.Ile1047Phe	p.I1047F	ENST00000282397	NM_002019.4	1047	Att/Ttt	23/30	1	2	FACETS	0.367	0.292	0.454	0.367	0.292	0.454	SUBCLONAL	1	TRUE	1	0.334788355927053	2		440	439	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618805	37618806	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0039245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	94	549	0	ENST00000447079.4:c.482dup	p.Tyr161Ter	p.Y161*	ENST00000447079	NM_015083.1	161	tat/tAat	1/14	0.334788355927053	1	FACETS	0.869	0.775	0.968	0.869	0.775	0.968	CLONAL	1	TRUE	0	0.334788355927053	1		549	538	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222941	36222941	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1569	89	835	0	ENST00000222270.7:c.5570C>A	p.Pro1857His	p.P1857H	ENST00000222270	NM_014727.1	1857	cCc/cAc	27/37	0.334788355927053	6	FACETS	0.535	0.472	0.603			1	SUBCLONAL	1	TRUE	NA	0.334788355927053	6		835	1658	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0039246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	255	618	0	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	0.518990109234776	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.519422119725045	2		618	483	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380329	14380329	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	48	181	0	ENST00000256196.4:c.88C>G	p.Leu30Val	p.L30V	ENST00000256196		30	Ctc/Gtc	1/6	0.518990109234776	2	FACETS	1	0.891	1	0.522	0.448	0.601	CLONAL	1	TRUE	0	0.519422119725045	2		181	177	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566136	95566168	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	TTATCTGTGTTGCTTTTGTCTTGATTTACTACA	TTATCTGTGTTGCTTTTGTCTTGATTTACTACA	-	novel	NA	P-0039246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	53	300	0	ENST00000393063.1:c.4155_4187del	p.Tyr1385_Lys1396delinsTer	p.Y1385_K1396delins*	ENST00000393063	NM_030621.3	1385	taTGTAGTAAATCAAGACAAAAGCAACACAGATAAa/taa	23/28	1	2	FACETS	0.761	0.655	0.876	0.761	0.655	0.876	SUBCLONAL	1	TRUE	1	0.519422119725045	2		300	268	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966413	25966433	+	inframe_deletion	In_Frame_Del	DEL	AGTTCCTGGGGTTTTAAGGCT	AGTTCCTGGGGTTTTAAGGCT	-	novel	NA	P-0039246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	317	626	0	ENST00000435504.4:c.2773_2793del	p.Lys927_Leu933del	p.K927_L933del	ENST00000435504		925	AGCCTTAAAACCCCAGGAACT/-	13/13	0.518990109234776	4	FACETS	0.945	0.9	0.991	0.709	0.675	0.743	CLONAL	3	TRUE	0	0.519422119725045	4		626	654	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46597055	46597055	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1189570289	NA	P-0039246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	83	419	0	ENST00000263734.3:c.869C>T	p.Thr290Ile	p.T290I	ENST00000263734	NM_001430.4	290	aCc/aTc	7/16	0.518990109234776	3	FACETS	1	0.9	1	0.507	0.45	0.567	CLONAL	1	TRUE	1	0.519422119725045	3		419	397	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180049745	180049745	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	390	539	0	ENST00000261937.6:c.1643A>T	p.Tyr548Phe	p.Y548F	ENST00000261937	NM_182925.4	548	tAc/tTc	12/30	0.518990109234776	4	FACETS	1	0.973	1	0.765	0.733	0.797	CLONAL	3	TRUE	0	0.519422119725045	4		539	746	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482220	87482220	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	101	531	0	ENST00000277120.3:c.1507G>T	p.Gly503Trp	p.G503W	ENST00000277120		503	Ggg/Tgg	14/19	0.518990109234776	2	FACETS	1	0.92	1	0.512	0.461	0.565	CLONAL	1	TRUE	0	0.519422119725045	2		531	380	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417478	139417478	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	157	695	0	ENST00000277541.6:c.566G>T	p.Cys189Phe	p.C189F	ENST00000277541	NM_017617.3	189	tGc/tTc	4/34	0.518990109234776	2	FACETS	1	0.953	1	0.525	0.483	0.568	CLONAL	1	TRUE	0	0.519422119725045	2		695	576	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0039247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	130	455	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.907676299432502	1	FACETS	0.937	0.889	0.981	0.937	0.889	0.981	CLONAL	1	TRUE	0	0.907676299432502	1		455	167	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0039247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	448	483	0	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	1	2	FACETS	0.952	0.912	0.992	0.952	0.912	0.992	CLONAL	1	TRUE	1	0.907676299432502	2		483	1037	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913514	NA	P-0039247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	99	321	0	ENST00000288135.5:c.2466T>G	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaG	17/21	1	2	FACETS	0.924	0.841	1	0.924	0.841	1	CLONAL	1	TRUE	1	0.907676299432502	2		321	236	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593612	55593647	+	inframe_deletion	In_Frame_Del	DEL	GTTGAGGAGATAAATGGAAACAATTATGTTTACATA	GTTGAGGAGATAAATGGAAACAATTATGTTTACATA	-	novel	NA	P-0039247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	125	341	0	ENST00000288135.5:c.1679_1714del	p.Val560_Ile571del	p.V560_I571del	ENST00000288135	NM_000222.2	560	GTTGAGGAGATAAATGGAAACAATTATGTTTACATA/-	11/21	1	2	FACETS	0.874	0.803	0.947	0.874	0.803	0.947	CLONAL	1	TRUE	1	0.907676299432502	2		341	315	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870996	12870996	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	125	343	0	ENST00000228872.4:c.223G>T	p.Glu75Ter	p.E75*	ENST00000228872	NM_004064.3	75	Gag/Tag	1/3	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.628819156520162	2		343	396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0039248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	219	611	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.61253456850487	1	FACETS	0.984	0.925	1	0.984	0.925	1	CLONAL	1	TRUE	0	0.61253456850487	1		611	504	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0039248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	62	557	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.196755489846628	4	FACETS	0.837	0.736	0.943	0.837	0.736	0.943	INDETERMINATE	2	TRUE	2	0.61253456850487	4		557	195	SUCCESS
APC	324	MSKCC	GRCh37	5	112175174	112175174	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	28	166	0	ENST00000257430.4:c.3883G>T	p.Glu1295Ter	p.E1295*	ENST00000257430	NM_000038.5	1295	Gaa/Taa	16/16	0.595886652383212	1	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	0	0.61253456850487	1		166	58	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763832	76763832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	39	400	1	ENST00000373344.5:c.7476G>A	p.Met2492Ile	p.M2492I	ENST00000373344	NM_000489.3	2492	atG/atA	35/35	0.374530102404358	1	FACETS	0.29	0.241	0.344	0.29	0.241	0.344	SUBCLONAL	1	TRUE	0	0.61253456850487	1		401	305	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0039258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	111	586	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	0.258808877456863	2		586	722	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	377	336	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.258808877456863	5	FACETS	1	0.986	1			1	CLONAL	5	TRUE	NA	0.258808877456863	5		336	756	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602646	10602646	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	130	687	0	ENST00000171111.5:c.932A>G	p.His311Arg	p.H311R	ENST00000171111	NM_203500.1	311	cAc/cGc	3/6	0.180893161377725	2	FACETS	1	0.976	1	0.611	0.554	0.671	CLONAL	1	TRUE	0	0.258808877456863	2		687	822	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221996	1221996	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs376280361	NA	P-0039258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	117	604	0	ENST00000326873.7:c.911G>C	p.Arg304Pro	p.R304P	ENST00000326873	NM_000455.4	304	cGg/cCg	7/10	0.180893161377725	2	FACETS	1	0.982	1	0.699	0.631	0.77	CLONAL	1	TRUE	0	0.258808877456863	2		604	647	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69012034	69012034	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	42	499	0	ENST00000288368.4:c.2671G>C	p.Glu891Gln	p.E891Q	ENST00000288368	NM_024870.2	891	Gaa/Caa	23/40	1	2	FACETS	0.522	0.435	0.619	0.522	0.435	0.619	SUBCLONAL	1	TRUE	1	0.258808877456863	2		499	622	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360684	70360684	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	13	140	0	ENST00000374080.3:c.6244C>A	p.Gln2082Lys	p.Q2082K	ENST00000374080		2082	Cag/Aag	42/45	1	2	FACETS	0.546	0.39	0.735	0.546	0.39	0.735	SUBCLONAL	1	TRUE	1	0.258808877456863	2		140	184	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384968	17384968	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	97	625	0	ENST00000359435.4:c.518T>A	p.Leu173Gln	p.L173Q	ENST00000359435	NM_001033549.1	173	cTg/cAg	5/9	1	2	FACETS	0.836	0.755	0.92	0.836	0.755	0.92	CLONAL	1	TRUE	1	0.776436242664219	2		625	299	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	99	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.560456729478205	2		174	310	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974752	15974752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1276291276	NA	P-0039262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	120	397	0	ENST00000268712.3:c.4123C>T	p.Arg1375Trp	p.R1375W	ENST00000268712	NM_006311.3	1375	Cgg/Tgg	30/46	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.560456729478205	2		397	419	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158213	47158213	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	103	322	0	ENST00000409792.3:c.4486C>T	p.Arg1496Ter	p.R1496*	ENST00000409792	NM_014159.6	1496	Cga/Tga	4/21	1	2	FACETS	0.983	0.887	1	0.983	0.887	1	CLONAL	1	TRUE	1	0.560456729478205	2		322	374	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101294	27101294	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773815689	NA	P-0039267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	36	587	0	ENST00000324856.7:c.4576G>A	p.Val1526Met	p.V1526M	ENST00000324856	NM_006015.4	1526	Gtg/Atg	18/20	1	2	FACETS	0.338	0.279	0.404	0.338	0.279	0.404	SUBCLONAL	1	TRUE	1	0.793838745843626	2		587	268	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023481	27023481	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	110	426	0	ENST00000324856.7:c.587del	p.Ala196GlyfsTer36	p.A196Gfs*36	ENST00000324856	NM_006015.4	196	gCg/gg	1/20	1	2	FACETS	0.668	0.604	0.734	0.668	0.604	0.734	SUBCLONAL	1	TRUE	1	0.793838745843626	2		426	415	SUCCESS
FH	2271	MSKCC	GRCh37	1	241672064	241672064	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	19	287	0	ENST00000366560.3:c.577A>T	p.Thr193Ser	p.T193S	ENST00000366560	NM_000143.3	193	Aca/Tca	5/10	0.582248845000871	3	FACETS	0.488	0.374	0.619	0.244	0.187	0.31	SUBCLONAL	1	TRUE	1	0.793838745843626	3		287	137	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188048	32188048	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	51	647	0	ENST00000375023.3:c.1173C>A	p.His391Gln	p.H391Q	ENST00000375023	NM_004557.3	391	caC/caA	7/30	0.162292307496246	5	FACETS	0.828	0.707	0.959	0.276	0.235	0.32	INDETERMINATE	1	TRUE	2	0.793838745843626	5		647	340	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0039268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	145	638	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.630245171636806	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	TRUE	1	0.630245171636806	4		639	232	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862107	68862107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501244	NA	P-0039268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	278	333	4	ENST00000261769.5:c.2195G>A	p.Arg732Gln	p.R732Q	ENST00000261769	NM_004360.3	732	cGg/cAg	14/16	0.630245171636806	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.630245171636806	2		337	413	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976766	2976766	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1562490836	NA	P-0039268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	163	448	4	ENST00000396946.4:c.1246G>A	p.Glu416Lys	p.E416K	ENST00000396946	NM_032415.4	416	Gag/Aag	9/25	0.577667736843283	4	FACETS	1	0.92	1	0.501	0.46	0.544	CLONAL	1	TRUE	2	0.630245171636806	4		452	842	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138897	64138897	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	136	352	0	ENST00000334205.4:c.2264C>A	p.Pro755His	p.P755H	ENST00000334205	NM_003942.2	755	cCc/cAc	17/17	0.536906592268567	3	FACETS	1	0.987	1	0.708	0.65	0.767	CLONAL	1	TRUE	1	0.630245171636806	3		352	401	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577573	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	TACACATG	TACACATG	-	novel	NA	P-0039268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	316	364	0	ENST00000269305.4:c.708_715del	p.Tyr236Ter	p.Y236*	ENST00000269305	NM_001126112.2	236	taCATGTGTAac/taac	7/11	0.630245171636806	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.630245171636806	2		364	496	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054849	5054849	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	106	276	1	ENST00000381652.3:c.903del	p.Lys302AsnfsTer8	p.K302Nfs*8	ENST00000381652	NM_004972.3	301	Ggg/gg	7/25	0.630245171636806	5	FACETS	0.804	0.726	0.885	0.536	0.484	0.59	CLONAL	2	TRUE	2	0.630245171636806	5		277	407	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0039270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	372	542	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.740112944016514	2	FACETS	0.999	0.967	1	0.999	0.967	1	CLONAL	2	TRUE	0	0.740112944016514	2		542	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0039270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	255	517	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.740112944016514	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.740112944016514	1		517	418	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0039270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	253	489	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.740112944016514	2		489	665	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494587	2494587	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs556584527	NA	P-0039270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	181	470	0	ENST00000355716.4:c.727C>T	p.Arg243Trp	p.R243W	ENST00000355716	NM_003820.2	243	Cgg/Tgg	8/8	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.740112944016514	2		470	486	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99160343	99160343	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	264	291	0	ENST00000074304.5:c.822del	p.Cys275ValfsTer35	p.C275Vfs*35	ENST00000074304	NM_001134224.1	274	gtG/gt	11/26	0.72077334961271	2	FACETS	0.972	0.933	1	0.972	0.933	1	CLONAL	2	TRUE	0	0.740112944016514	2		291	367	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321555	62321555	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	216	567	0	ENST00000360203.5:c.2257G>C	p.Glu753Gln	p.E753Q	ENST00000360203	NM_001283009.1	753	Gag/Cag	25/35	0.740112944016514	3	FACETS	0.905	0.842	0.969	0.452	0.421	0.485	CLONAL	1	TRUE	1	0.740112944016514	3		567	884	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0039272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	55	542	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.421682010144989	3	FACETS	0.863	0.762	0.965	1	0.966	1	CLONAL	3	FALSE	1	0.421682010144989	3		543	122	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0039272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	32	278	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.421682010144989	3	FACETS	1	0.902	1	0.738	0.62	0.861	CLONAL	2	FALSE	0	0.421682010144989	3		278	83	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0039272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	83	559	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.259026962270846	4	FACETS	0.821	0.73	0.916	0.821	0.73	0.916	CLONAL	2	FALSE	2	0.421682010144989	4		559	341	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577579	7577579	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0039272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	54	630	0	ENST00000269305.4:c.702C>G	p.Tyr234Ter	p.Y234*	ENST00000269305	NM_001126112.2	234	taC/taG	7/11	0.259026962270846	4	FACETS	1	0.954	1	0.641	0.552	0.737	CLONAL	1	FALSE	2	0.421682010144989	4		630	284	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41489040	41489040	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765627133	NA	P-0039272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	80	566	0	ENST00000263253.7:c.32C>T	p.Pro11Leu	p.P11L	ENST00000263253	NM_001429.3	11	cCt/cTt	1/31	0.421682010144989	3	FACETS	0.753	0.67	0.841	0.753	0.67	0.841	SUBCLONAL	2	FALSE	1	0.421682010144989	3		566	305	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0039274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	201	300	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.387902981099372	2	FACETS	0.816	0.762	0.872	0.816	0.762	0.872	CLONAL	2	TRUE	0	0.437316299228369	2		300	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0039274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	189	670	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.433674256661341	1	FACETS	0.887	0.822	0.955	0.887	0.822	0.955	CLONAL	1	TRUE	0	0.437316299228369	1		670	761	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952088	178952088	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553826184	NA	P-0039274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	201	433	1	ENST00000263967.3:c.3143A>G	p.His1048Arg	p.H1048R	ENST00000263967	NM_006218.2	1048	cAt/cGt	21/21	0.387902981099372	2	FACETS	0.815	0.761	0.87	0.815	0.761	0.87	CLONAL	2	TRUE	0	0.437316299228369	2		434	564	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732943	44732943	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	106	492	0	ENST00000377967.4:c.146T>G	p.Leu49Arg	p.L49R	ENST00000377967	NM_021140.2	49	cTc/cGc	1/29	0.318453474496641	1	FACETS	0.694	0.624	0.767	0.694	0.624	0.767	SUBCLONAL	1	TRUE	0	0.437316299228369	1		492	546	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907693	111907697	+	frameshift_variant	Frame_Shift_Del	DEL	GAGAC	GAGAC	-	novel	NA	P-0039274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	100	447	0	ENST00000393256.3:c.470_474del	p.Asp157ValfsTer2	p.D157Vfs*2	ENST00000393256	NM_006538.4	156	gGAGAC/g	3/4	0.17869308959283	4	FACETS	0.849	0.758	0.946	0.425	0.379	0.473	INDETERMINATE	1	TRUE	2	0.437316299228369	4		447	774	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560476	95560476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	127	492	1	ENST00000393063.1:c.5113G>A	p.Glu1705Lys	p.E1705K	ENST00000393063	NM_030621.3	1705	Gaa/Aaa	25/28	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		493	522	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569888	95569888	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	117	368	1	ENST00000393063.1:c.3845del	p.Ser1282LeufsTer20	p.S1282Lfs*20	ENST00000393063	NM_030621.3	1282	tCt/tt	22/28	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		369	470	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	202	508	2	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.515961653013517	1	FACETS	0.866	0.806	0.927	0.866	0.806	0.927	CLONAL	1	TRUE	0	0.515961653013517	1		510	671	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794583	42794583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	259	752	2	ENST00000575354.2:c.1663G>A	p.Gly555Arg	p.G555R	ENST00000575354	NM_015125.3	555	Gga/Aga	10/20	1	2	FACETS	0.917	0.859	0.977	0.917	0.859	0.977	CLONAL	1	TRUE	1	0.515961653013517	2		754	1095	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248124	59248124	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	74	198	0	ENST00000371222.2:c.619C>T	p.Pro207Ser	p.P207S	ENST00000371222	NM_002228.3	207	Ccg/Tcg	1/1	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.515961653013517	2		198	280	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246093197	246093197	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	343	565	0	ENST00000388985.4:c.574G>T	p.Glu192Ter	p.E192*	ENST00000388985		192	Gaa/Taa	6/12	0.515961653013517	3	FACETS	0.887	0.842	0.933	0.887	0.842	0.933	CLONAL	2	TRUE	1	0.515961653013517	3		565	943	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111459	8111496	+	frameshift_variant	Frame_Shift_Del	DEL	GTCCTGTGCGAACTGTCAGACCACCACAACCACACTCT	GTCCTGTGCGAACTGTCAGACCACCACAACCACACTCT	-	novel	NA	P-0039276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	169	572	0	ENST00000346208.3:c.946_983del	p.Ser316GlufsTer23	p.S316Efs*23	ENST00000346208		315	acGTCCTGTGCGAACTGTCAGACCACCACAACCACACTCTgg/acgg	5/6	1	2	FACETS	0.806	0.742	0.872	0.806	0.742	0.872	CLONAL	1	TRUE	1	0.515961653013517	2		572	813	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913879	32914629	+	frameshift_variant	Frame_Shift_Del	DEL	ATGCAAATGCATACCCACAAACTGTAAATGAAGATATTTGCGTTGAGGAACTTGTGACTAGCTCTTCACCCTGCAAAAATAAAAATGCAGCCATTAAATTGTCCATATCTAATAGTAATAATTTTGAGGTAGGGCCACCTGCATTTAGGATAGCCAGTGGTAAAATCGTTTGTGTTTCACATGAAACAATTAAAAAAGTGAAAGACATATTTACAGACAGTTTCAGTAAAGTAATTAAGGAAAACAACGAGAATAAATCAAAAATTTGCCAAACGAAAATTATGGCAGGTTGTTACGAGGCATTGGATGATTCAGAGGATATTCTTCATAACTCTCTAGATAATGATGAATGTAGCACGCATTCACATAAGGTTTTTGCTGACATTCAGAGTGAAGAAATTTTACAACATAACCAAAATATGTCTGGATTGGAGAAAGTTTCTAAAATATCACCTTGTGATGTTAGTTTGGAAACTTCAGATATATGTAAATGTAGTATAGGGAAGCTTCATAAGTCAGTCTCATCTGCAAATACTTGTGGGATTTTTAGCACAGCAAGTGGAAAATCTGTCCAGGTATCAGATGCTTCATTACAAAACGCAAGACAAGTGTTTTCTGAAATAGAAGATAGTACCAAGCAAGTCTTTTCCAAAGTATTGTTTAAAAGTAACGAACATTCAGACCAGCTCACAAGAGAAGAAAATACTGCTATACGTACTCCAGAACATTTAATATCCCAAAAAGGCTTTTC	ATGCAAATGCATACCCACAAACTGTAAATGAAGATATTTGCGTTGAGGAACTTGTGACTAGCTCTTCACCCTGCAAAAATAAAAATGCAGCCATTAAATTGTCCATATCTAATAGTAATAATTTTGAGGTAGGGCCACCTGCATTTAGGATAGCCAGTGGTAAAATCGTTTGTGTTTCACATGAAACAATTAAAAAAGTGAAAGACATATTTACAGACAGTTTCAGTAAAGTAATTAAGGAAAACAACGAGAATAAATCAAAAATTTGCCAAACGAAAATTATGGCAGGTTGTTACGAGGCATTGGATGATTCAGAGGATATTCTTCATAACTCTCTAGATAATGATGAATGTAGCACGCATTCACATAAGGTTTTTGCTGACATTCAGAGTGAAGAAATTTTACAACATAACCAAAATATGTCTGGATTGGAGAAAGTTTCTAAAATATCACCTTGTGATGTTAGTTTGGAAACTTCAGATATATGTAAATGTAGTATAGGGAAGCTTCATAAGTCAGTCTCATCTGCAAATACTTGTGGGATTTTTAGCACAGCAAGTGGAAAATCTGTCCAGGTATCAGATGCTTCATTACAAAACGCAAGACAAGTGTTTTCTGAAATAGAAGATAGTACCAAGCAAGTCTTTTCCAAAGTATTGTTTAAAAGTAACGAACATTCAGACCAGCTCACAAGAGAAGAAAATACTGCTATACGTACTCCAGAACATTTAATATCCCAAAAAGGCTTTTC	-	novel	NA	P-0039276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	84	489	0	ENST00000380152.3:c.5389_6139del	p.Ala1797IlefsTer4	p.A1797Ifs*4	ENST00000380152		1796	gATGCAAATGCATACCCACAAACTGTAAATGAAGATATTTGCGTTGAGGAACTTGTGACTAGCTCTTCACCCTGCAAAAATAAAAATGCAGCCATTAAATTGTCCATATCTAATAGTAATAATTTTGAGGTAGGGCCACCTGCATTTAGGATAGCCAGTGGTAAAATCGTTTGTGTTTCACATGAAACAATTAAAAAAGTGAAAGACATATTTACAGACAGTTTCAGTAAAGTAATTAAGGAAAACAACGAGAATAAATCAAAAATTTGCCAAACGAAAATTATGGCAGGTTGTTACGAGGCATTGGATGATTCAGAGGATATTCTTCATAACTCTCTAGATAATGATGAATGTAGCACGCATTCACATAAGGTTTTTGCTGACATTCAGAGTGAAGAAATTTTACAACATAACCAAAATATGTCTGGATTGGAGAAAGTTTCTAAAATATCACCTTGTGATGTTAGTTTGGAAACTTCAGATATATGTAAATGTAGTATAGGGAAGCTTCATAAGTCAGTCTCATCTGCAAATACTTGTGGGATTTTTAGCACAGCAAGTGGAAAATCTGTCCAGGTATCAGATGCTTCATTACAAAACGCAAGACAAGTGTTTTCTGAAATAGAAGATAGTACCAAGCAAGTCTTTTCCAAAGTATTGTTTAAAAGTAACGAACATTCAGACCAGCTCACAAGAGAAGAAAATACTGCTATACGTACTCCAGAACATTTAATATCCCAAAAAGGCTTTTCa/ga	11/27	0.515961653013517	1	FACETS	0.929	0.832	1	0.929	0.832	1	CLONAL	1	TRUE	0	0.515961653013517	1		489	260	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915017	32915018	+	inframe_insertion	In_Frame_Ins	INS	-	-	AACAAA	novel	NA	P-0039276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	96	541	0	ENST00000380152.3:c.6529_6530insAAAACA	p.Asn2176_Ile2177insLysAsn	p.N2176_I2177insKN	ENST00000380152		2175	-/AACAAA	11/27	0.515961653013517	1	FACETS	0.868	0.782	0.958	0.868	0.782	0.958	CLONAL	1	TRUE	0	0.515961653013517	1		541	318	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066936	30066936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749621467	NA	P-0039276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	134	454	0	ENST00000331968.5:c.2195G>A	p.Arg732Gln	p.R732Q	ENST00000331968	NM_002742.2	732	cGg/cAg	16/18	1	2	FACETS	0.87	0.793	0.95	0.87	0.793	0.95	CLONAL	1	TRUE	1	0.515961653013517	2		454	597	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603132	48603549	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAGCTCCAGCTATCAGTAAGTATGCTTTTCATTCTTTTTTAAAGGTATAATAGTTGATATTTTTATCTTGATTTACTCAGTTGATTAGTTTCTTTGAGCAGTAATAGAAATTAAAGTTTTTTTTTACTGGGATGATGACATTTTTGAATTGGTAAAATCTGTTCTTCTGTAATAGTTGCTTTTTGCCTATGACCCTGTTTGCATTCTTTTTGTATCAAAAATGGAGTATGGGATGAAGGAGAAAGGGGATGATTATTATATTATACTGTTCTATCTCCTCCTTTTTTGTTGATGCTTATTATAATTCTGCCTCACCAGCCAGGGTGGGTTGTAATCACTGAAGTGCTTGGCTTTATTCTAGTAAGGAAAGCATATTTCAATTTCAGAATTGGACACTTTTCCAATTTTTTTTTTAAAG	TAGCTCCAGCTATCAGTAAGTATGCTTTTCATTCTTTTTTAAAGGTATAATAGTTGATATTTTTATCTTGATTTACTCAGTTGATTAGTTTCTTTGAGCAGTAATAGAAATTAAAGTTTTTTTTTACTGGGATGATGACATTTTTGAATTGGTAAAATCTGTTCTTCTGTAATAGTTGCTTTTTGCCTATGACCCTGTTTGCATTCTTTTTGTATCAAAAATGGAGTATGGGATGAAGGAGAAAGGGGATGATTATTATATTATACTGTTCTATCTCCTCCTTTTTTGTTGATGCTTATTATAATTCTGCCTCACCAGCCAGGGTGGGTTGTAATCACTGAAGTGCTTGGCTTTATTCTAGTAAGGAAAGCATATTTCAATTTCAGAATTGGACACTTTTCCAATTTTTTTTTTAAAG	-	novel	NA	P-0039276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	111	532	0	ENST00000342988.3:c.1435_1447+405del		p.X479_splice	ENST00000342988	NM_005359.5	479		11/12	0.493096628875632	1	FACETS	0.675	0.61	0.743	0.675	0.61	0.743	SUBCLONAL	1	TRUE	0	0.515961653013517	1		532	473	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321646	62321646	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0039276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	243	650	0	ENST00000360203.5:c.2266-1G>C		p.X756_splice	ENST00000360203	NM_001283009.1	756			0.515961653013517	3	FACETS	1	0.963	1	0.523	0.488	0.559	CLONAL	1	TRUE	1	0.515961653013517	3		650	1133	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0039277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	355	588	1	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.316658402237187	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.470124073190979	1		589	884	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076812	72076812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	113	404	0	ENST00000357731.5:c.685G>A	p.Glu229Lys	p.E229K	ENST00000357731	NM_173808.2	229	Gaa/Aaa	5/7	0.343501958062117	1	FACETS	0.803	0.727	0.882	0.803	0.727	0.882	CLONAL	1	TRUE	0	0.470124073190979	1		404	458	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919214	48919214	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0039277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	53	84	0	ENST00000267163.4:c.381-2A>T		p.X127_splice	ENST00000267163	NM_000321.2	127			0.460362046125978	3	FACETS	0.901	0.799	1	0.901	0.799	1	CLONAL	3	TRUE	0	0.470124073190979	3		84	103	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242701	98242701	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	321	433	0	ENST00000331920.6:c.916G>T	p.Ala306Ser	p.A306S	ENST00000331920	NM_000264.3	306	Gcc/Tcc	6/24	0.470124073190979	3	FACETS	0.977	0.926	1	0.977	0.926	1	CLONAL	2	TRUE	1	0.470124073190979	3		433	863	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508424	106508424	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	94	319	0	ENST00000359195.3:c.418C>G	p.Arg140Gly	p.R140G	ENST00000359195	NM_002649.2	140	Cgg/Ggg	2/11	1	2	FACETS	0.93	0.832	1	0.93	0.832	1	CLONAL	1	TRUE	1	0.470124073190979	2		319	430	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156790	106156790	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1180357765	NA	P-0039277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	173	467	0	ENST00000380013.4:c.1691G>A	p.Trp564Ter	p.W564*	ENST00000380013	NM_001127208.2	564	tGg/tAg	3/11	1	2	FACETS	0.992	0.915	1	0.992	0.915	1	CLONAL	1	TRUE	1	0.470124073190979	2		467	742	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996746	100996746	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	76	428	0	ENST00000325455.5:c.1781C>A	p.Ala594Glu	p.A594E	ENST00000325455	NM_001202474.3	594	gCa/gAa	2/8	1	2	FACETS	0.75	0.661	0.846	0.75	0.661	0.846	SUBCLONAL	1	TRUE	1	0.470124073190979	2		428	431	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36989309	36989309	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	165	475	0	ENST00000354822.5:c.26C>A	p.Ala9Glu	p.A9E	ENST00000354822	NM_001079668.2	9	gCg/gAg	1/3	0.470124073190979	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.470124073190979	1		475	516	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304171	91304171	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	155	468	0	ENST00000355112.3:c.1568A>G	p.Asn523Ser	p.N523S	ENST00000355112	NM_000057.2	523	aAt/aGt	7/22	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.470124073190979	2		468	585	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032222	10032222	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	197	654	0	ENST00000330684.3:c.601C>A	p.Gln201Lys	p.Q201K	ENST00000330684	NM_001134407.1	201	Cag/Aag	3/13	1	2	FACETS	0.904	0.838	0.973	0.904	0.838	0.973	CLONAL	1	TRUE	1	0.470124073190979	2		654	927	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99160440	99160440	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	213	478	0	ENST00000074304.5:c.919G>C	p.Glu307Gln	p.E307Q	ENST00000074304	NM_001134224.1	307	Gag/Cag	11/26	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.470124073190979	2		478	837	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098973	178098973	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	74	243	0	ENST00000397062.3:c.72G>T	p.Trp24Cys	p.W24C	ENST00000397062	NM_006164.4	24	tgG/tgT	2/5	1	2	FACETS	0.879	0.775	0.99	0.879	0.775	0.99	CLONAL	1	TRUE	1	0.470124073190979	2		243	358	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12647738	12647738	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	124	417	0	ENST00000251849.4:c.642G>T	p.Met214Ile	p.M214I	ENST00000251849	NM_002880.3	214	atG/atT	6/17	1	2	FACETS	0.992	0.901	1	0.992	0.901	1	CLONAL	1	TRUE	1	0.470124073190979	2		417	532	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164788	106164788	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	182	551	0	ENST00000380013.4:c.3656A>T	p.His1219Leu	p.H1219L	ENST00000380013	NM_001127208.2	1219	cAc/cTc	6/11	1	2	FACETS	0.932	0.861	1	0.932	0.861	1	CLONAL	1	TRUE	1	0.470124073190979	2		551	831	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982054	38982054	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	124	454	0	ENST00000357387.3:c.668T>C	p.Ile223Thr	p.I223T	ENST00000357387	NM_152756.3	223	aTa/aCa	8/38	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.470124073190979	2		454	408	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879335	151879335	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	153	455	0	ENST00000262189.6:c.5610G>T	p.Gln1870His	p.Q1870H	ENST00000262189	NM_170606.2	1870	caG/caT	36/59	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.470124073190979	2		455	646	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	51	336	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.20022913634103	2		336	371	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845356	89845356	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs753980264	NA	P-0039278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	166	811	0	ENST00000389301.3:c.1771C>G	p.Arg591Gly	p.R591G	ENST00000389301	NM_000135.2	591	Cga/Gga	19/43	1	2	FACETS	0.947	0.871	1	1	0.992	1	CLONAL	2	TRUE	1	0.20022913634103	2		811	875	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960140	134960140	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0039278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	86	571	0	ENST00000398015.3:c.2496+1G>T		p.X832_splice	ENST00000398015	NM_004441.4	832			1	2	FACETS	0.862	0.765	0.966	1	0.983	1	CLONAL	2	TRUE	1	0.20022913634103	2		571	498	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31437397	31437397	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	111	659	0	ENST00000344624.3:c.2891A>G	p.His964Arg	p.H964R	ENST00000344624		964	cAc/cGc	21/33	0.137032585871452	3	FACETS	0.854	0.772	0.94	1	0.977	1	CLONAL	3	TRUE	1	0.20022913634103	3		659	476	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039906	47039906	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0039278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	136	729	0	ENST00000377604.3:c.1248+1G>A		p.X416_splice	ENST00000377604	NM_001204468.1	416			1	2	FACETS	0.889	0.809	0.973	1	0.989	1	CLONAL	2	TRUE	1	0.20022913634103	2		729	764	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412046	116412046	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	G	novel	NA	P-0039279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	77	645	0	ENST00000397752.3:c.3028+3A>G		p.X1010_splice	ENST00000397752	NM_000245.2	1010			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		645	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	182	583	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.356082674841792	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.368258239402184	2		583	479	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589586	67589591	+	inframe_deletion	In_Frame_Del	DEL	ATGAAT	ATGAAT	-	novel	NA	P-0039282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	40	260	0	ENST00000274335.5:c.1351_1356del	p.Glu451_Tyr452del	p.E451_Y452del	ENST00000274335		450	cATGAATat/cat	10/15	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.368258239402184	2		260	195	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692886	89692886	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	43	347	0	ENST00000371953.3:c.370T>A	p.Cys124Ser	p.C124S	ENST00000371953	NM_000314.4	124	Tgt/Agt	5/9	0.348739464954885	3	FACETS	1	0.864	1	0.514	0.433	0.603	CLONAL	1	TRUE	1	0.368258239402184	3		347	269	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685314	89685314	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	75	278	0	ENST00000371953.3:c.209T>G	p.Leu70Arg	p.L70R	ENST00000371953	NM_000314.4	70	cTt/cGt	3/9	0.348739464954885	3	FACETS	0.928	0.823	1	0.928	0.823	1	CLONAL	2	TRUE	1	0.368258239402184	3		278	260	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281875	49281875	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	192	589	0	ENST00000282018.3:c.922G>A	p.Ala308Thr	p.A308T	ENST00000282018	NM_020377.2	308	Gct/Act	1/1	0.368258239402184	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.368258239402184	2		589	498	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574033	7574033	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	194	565	0	ENST00000269305.4:c.994A>T	p.Ile332Phe	p.I332F	ENST00000269305	NM_001126112.2	332	Atc/Ttc	10/11	0.356082674841792	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.368258239402184	2		565	474	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591860	48591861	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCTTCAAGCTGCCCTATTGTTACTGTTGATGGATACGTGGAC	novel	NA	P-0039282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	94	458	0	ENST00000342988.3:c.1029_1070dup	p.Ser344_Ser357dup	p.S344_S357dup	ENST00000342988	NM_005359.5	344	-/CCTTCAAGCTGCCCTATTGTTACTGTTGATGGATACGTGGAC	9/12	0.356082674841792	2	FACETS	1	0.922	1	0.52	0.464	0.579	CLONAL	1	TRUE	0	0.368258239402184	2		458	491	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197267	26197267	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	51	471	0	ENST00000356476.2:c.212T>A	p.Leu71Gln	p.L71Q	ENST00000356476		71	cTa/cAa	1/1	0.304228085201483	3	FACETS	0.722	0.615	0.84	0.361	0.307	0.42	SUBCLONAL	1	TRUE	1	0.368258239402184	3		471	454	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230783	53230783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	193	723	0	ENST00000375401.3:c.2010G>A	p.Met670Ile	p.M670I	ENST00000375401	NM_004187.3	670	atG/atA	14/26	0.252610672295177	3	FACETS	0.845	0.784	0.908	0.845	0.784	0.908	CLONAL	2	TRUE	1	0.368258239402184	3		723	734	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020324	123020325	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	89	500	0	ENST00000355640.3:c.816dup	p.Gly273TrpfsTer8	p.G273Wfs*8	ENST00000355640		271	act/acTt	2/7	0.285064508499052	4	FACETS	1	0.945	1			1	CLONAL	1	TRUE	NA	0.368258239402184	4		500	598	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860076	152860076	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	63	713	0	ENST00000406277.2:c.352A>T	p.Ser118Cys	p.S118C	ENST00000406277	NM_152274.4	118	Agc/Tgc	5/7	0.285064508499052		FACETS		0.445	0.593				SUBCLONAL	1	TRUE	NA	0.368258239402184	4		713	908	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACAACCCCC	rs397517115	NA	P-0039286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	131	498	0	ENST00000275493.2:c.2311_2319dup	p.Asn771_His773dup	p.N771_H773dup	ENST00000275493	NM_005228.3	771	gac/gACAACCCCCac	20/28	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		498	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0039291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	324	590	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.508379900831173	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.508379900831173	2		590	621	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622419	28622419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776699712	NA	P-0039291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	23	475	1	ENST00000241453.7:c.1198G>A	p.Gly400Arg	p.G400R	ENST00000241453	NM_004119.2	400	Gga/Aga	9/24	1	2	FACETS	0.203	0.158	0.256	0.203	0.158	0.256	SUBCLONAL	1	TRUE	1	0.508379900831173	2		476	445	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943673	9943673	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	195	670	0	ENST00000330684.3:c.1268A>G	p.Asp423Gly	p.D423G	ENST00000330684	NM_001134407.1	423	gAc/gGc	5/13	1	2	FACETS	0.975	0.904	1	0.975	0.904	1	CLONAL	1	TRUE	1	0.508379900831173	2		670	787	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604748	48604748	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	172	477	0	ENST00000342988.3:c.1570T>A	p.Trp524Arg	p.W524R	ENST00000342988	NM_005359.5	524	Tgg/Agg	12/12	0.503282890475217	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.508379900831173	1		477	454	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230632	46230632	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	145	539	0	ENST00000334344.6:c.881G>C	p.Arg294Thr	p.R294T	ENST00000334344	NM_152641.2	294	aGa/aCa	8/21	0.508379900831173	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.508379900831173	1		539	408	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0039295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	279	515	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.453355481525833	6	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	3	0.453355481525833	6		515	719	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264586	1264586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs547377569	NA	P-0039295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	192	528	0	ENST00000310581.5:c.2776G>A	p.Gly926Ser	p.G926S	ENST00000310581	NM_198253.2	926	Ggc/Agc	11/16	0.404347771453007	4	FACETS	1	0.951	1			1	CLONAL	2	TRUE	NA	0.453355481525833	4		528	599	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226595555	226595555	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	75	354	0	ENST00000366794.5:c.76G>C	p.Glu26Gln	p.E26Q	ENST00000366794	NM_001618.3	26	Gag/Cag	1/23	0.453355481525833	5	FACETS	1	0.933	1	0.365	0.32	0.413	CLONAL	1	TRUE	2	0.453355481525833	5		354	508	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919595	28919595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs553261958	NA	P-0039297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	176	471	0	ENST00000282397.4:c.2342G>A	p.Arg781Gln	p.R781Q	ENST00000282397	NM_002019.4	781	cGa/cAa	16/30	NA	2	FACETS	0.759	0.704	0.814			1	INDETERMINATE	1	TRUE	NA	0.897541036841539	2		471	517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579707	7579707	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	270	474	0	ENST00000269305.4:c.89del	p.Asn30ThrfsTer14	p.N30Tfs*14	ENST00000269305	NM_001126112.2	30	aAc/ac	3/11	0.897541036841539	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.897541036841539	1		474	329	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554567	29554567	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs199474778	NA	P-0039297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	103	222	0	ENST00000356175.3:c.2352G>A	p.Trp784Ter	p.W784*	ENST00000356175	NM_000267.3	784	tgG/tgA	20/57	0.897541036841539	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.897541036841539	1		222	119	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0039299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	284	307	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.868627371151187	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.868627371151187	2		307	314	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165212	47165213	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	102	212	0	ENST00000409792.3:c.913dup	p.Thr305AsnfsTer4	p.T305Nfs*4	ENST00000409792	NM_014159.6	305	aca/aAca	3/21	0.868627371151187	2	FACETS	1	0.967	1	0.557	0.51	0.604	CLONAL	1	TRUE	0	0.868627371151187	2		212	211	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998020	169998020	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	22	380	2	ENST00000295797.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000295797	NM_002740.5	237	atG/atT	9/18	0.868627371151187	2	FACETS	0.123	0.095	0.156	0.061	0.047	0.078	SUBCLONAL	1	TRUE	0	0.868627371151187	2		382	412	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870997	12870998	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	266	313	0	ENST00000228872.4:c.225dup	p.Trp76ValfsTer49	p.W76Vfs*49	ENST00000228872	NM_004064.3	75	gag/gaGg	1/3	0.535954720442653	6	FACETS	1	0.99	1	0.825	0.779	0.873	CLONAL	2	TRUE	3	0.868627371151187	6		313	677	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38139004	38139004	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	226	286	0	ENST00000317025.8:c.3599A>G	p.Tyr1200Cys	p.Y1200C	ENST00000317025	NM_023034.1	1200	tAt/tGt	20/24	0.868627371151187	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.868627371151187	2		286	242	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578485	7578487	+	inframe_deletion	In_Frame_Del	DEL	AAT	AAT	-	novel	NA	P-0039300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	325	599	0	ENST00000269305.4:c.443_445del	p.Asp148_Ser149delinsAla	p.D148_S149delinsA	ENST00000269305	NM_001126112.2	148	gATTcc/gcc	5/11	0.785613073720994	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.785613073720994	1		599	489	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0039303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	256	576	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.904	0.852	0.958	1	0.995	1	CLONAL	2	TRUE	1	0.42	2		580	674	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0039303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	84	515	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.998	0.886	1	0.998	0.886	1	CLONAL	1	TRUE	1	0.42	2		515	401	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0039303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	109	838	4	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.805	0.724	0.89	0.805	0.724	0.89	CLONAL	1	TRUE	1	0.42	2		842	645	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0039303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	60	254	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.42	2		255	256	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100172	27100172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775802127	NA	P-0039303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	98	392	0	ENST00000324856.7:c.3968G>A	p.Arg1323His	p.R1323H	ENST00000324856	NM_006015.4	1323	cGc/cAc	16/20	1	2	FACETS	0.935	0.838	1	0.935	0.838	1	CLONAL	1	TRUE	1	0.42	2		392	499	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	116	508	1	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.869	0.784	0.957	0.869	0.784	0.957	CLONAL	1	TRUE	1	0.42	2		509	636	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692893	89692893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1114167656	NA	P-0039303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	36	270	0	ENST00000371953.3:c.377C>T	p.Ala126Val	p.A126V	ENST00000371953	NM_000314.4	126	gCt/gTt	5/9	1	2	FACETS	0.708	0.586	0.843	0.708	0.586	0.843	SUBCLONAL	1	TRUE	1	0.42	2		270	242	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497512	125497512	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	37	200	0	ENST00000428830.2:c.76G>A	p.Ala26Thr	p.A26T	ENST00000428830	NM_001114121.2	26	Gct/Act	3/14	1	2	FACETS	0.927	0.773	1	0.927	0.773	1	CLONAL	1	TRUE	1	0.42	2		200	190	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560464	95560464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	109	456	0	ENST00000393063.1:c.5125G>A	p.Asp1709Asn	p.D1709N	ENST00000393063	NM_030621.3	1709	Gat/Aat	25/28	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.42	2		456	517	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572555	95572555	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	52	173	0	ENST00000393063.1:c.2810G>T	p.Arg937Leu	p.R937L	ENST00000393063	NM_030621.3	937	cGc/cTc	19/28	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.42	2		173	214	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645174	67645175	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	75	540	0	ENST00000264010.4:c.441dup	p.Ala148CysfsTer4	p.A148Cfs*4	ENST00000264010	NM_006565.3	147	ctt/cTtt	3/12	1	2	FACETS	0.546	0.478	0.619	0.546	0.478	0.619	SUBCLONAL	1	TRUE	1	0.42	2		540	654	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821642	72821643	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCGCCG	rs762513291	NA	P-0039303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	11	81	0	ENST00000268489.5:c.10527_10532dup	p.Gly3511_Gly3512dup	p.G3511_G3512dup	ENST00000268489	NM_006885.3	3511	ggt/ggCGGCGGt	10/10	1	2	FACETS	0.509	0.354	0.696	0.509	0.354	0.696	SUBCLONAL	1	TRUE	1	0.42	2		81	103	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829164	72829164	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	126	469	0	ENST00000268489.5:c.7417C>T	p.Gln2473Ter	p.Q2473*	ENST00000268489	NM_006885.3	2473	Cag/Tag	9/10	1	2	FACETS	0.801	0.726	0.88	0.801	0.726	0.88	CLONAL	1	TRUE	1	0.42	2		469	749	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992474	72992474	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	168	651	0	ENST00000268489.5:c.1571del	p.Ala524ValfsTer12	p.A524Vfs*12	ENST00000268489	NM_006885.3	524	gCt/gt	2/10	1	2	FACETS	0.892	0.82	0.967	0.892	0.82	0.967	CLONAL	1	TRUE	1	0.42	2		651	897	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226373	2226373	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs369642113	NA	P-0039303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	170	617	1	ENST00000398665.3:c.3853G>T	p.Asp1285Tyr	p.D1285Y	ENST00000398665	NM_032482.2	1285	Gat/Tat	27/28	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.42	2		618	770	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274317	5274317	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	129	522	0	ENST00000357368.4:c.130G>A	p.Gly44Ser	p.G44S	ENST00000357368	NM_002850.3	44	Ggc/Agc	3/38	1	2	FACETS	0.905	0.822	0.992	0.905	0.822	0.992	CLONAL	1	TRUE	1	0.42	2		522	679	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651306	45651307	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0039303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	122	514	0	ENST00000407780.3:c.718_719del	p.Asp240GlnfsTer81	p.D240Qfs*81	ENST00000407780	NM_001283052.1	240	GAc/c	5/7	1	2	FACETS	0.925	0.838	1	0.925	0.838	1	CLONAL	1	TRUE	1	0.42	2		514	628	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650827	12650827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	49	288	0	ENST00000251849.4:c.328G>A	p.Ala110Thr	p.A110T	ENST00000251849	NM_002880.3	110	Gca/Aca	4/17	1	2	FACETS	0.887	0.757	1	0.887	0.757	1	CLONAL	1	TRUE	1	0.42	2		288	263	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155721	56155722	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0039303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	50	317	0	ENST00000399503.3:c.816_817del	p.Arg273SerfsTer27	p.R273Sfs*27	ENST00000399503	NM_005921.1	271	agAAaa/agaa	3/20	1	2	FACETS	0.623	0.53	0.725	0.623	0.53	0.725	SUBCLONAL	1	TRUE	1	0.42	2		317	382	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179449	56179451	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	novel	NA	P-0039303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	34	245	0	ENST00000399503.3:c.3767_3769del	p.Ser1256del	p.S1256del	ENST00000399503	NM_005921.1	1254	ttTTCt/ttt	15/20	1	2	FACETS	0.604	0.496	0.725	0.604	0.496	0.725	SUBCLONAL	1	TRUE	1	0.42	2		245	268	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515198	149515198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1272810440	NA	P-0039303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	165	582	1	ENST00000261799.4:c.284C>T	p.Thr95Met	p.T95M	ENST00000261799	NM_002609.3	95	aCg/aTg	3/23	1	2	FACETS	0.997	0.917	1	0.997	0.917	1	CLONAL	1	TRUE	1	0.42	2		583	788	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0039304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	25	371	2	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.435	0.342	0.541	0.435	0.342	0.541	SUBCLONAL	1	TRUE	1	0.28760096854682	2		373	400	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0039304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	55	230	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.194311573088578	3	FACETS	1	0.925	1	0.374	0.321	0.432	CLONAL	1	TRUE	0	0.28760096854682	3		230	390	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110584	4110584	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519807	NA	P-0039304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	142	637	0	ENST00000262948.5:c.373T>A	p.Cys125Ser	p.C125S	ENST00000262948	NM_030662.3	125	Tgc/Agc	3/11	0.28760096854682	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.28760096854682	1		637	843	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	34	457	1	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	1	2	FACETS	0.441	0.36	0.533	0.441	0.36	0.533	SUBCLONAL	1	TRUE	1	0.28760096854682	2		458	536	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97869536	97869536	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1800367	NA	P-0039304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	30	461	0	ENST00000289081.3:c.1345G>A	p.Val449Met	p.V449M	ENST00000289081	NM_000136.2	449	Gtg/Atg	14/15	1	2	FACETS	0.422	0.34	0.517	0.422	0.34	0.517	SUBCLONAL	1	TRUE	1	0.28760096854682	2		461	494	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406146	70406146	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	49	561	0	ENST00000373644.4:c.3660G>A	p.Trp1220Ter	p.W1220*	ENST00000373644	NM_030625.2	1220	tgG/tgA	4/12	1	2	FACETS	0.693	0.587	0.809	0.693	0.587	0.809	SUBCLONAL	1	TRUE	1	0.28760096854682	2		561	492	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117531	4117575	+	inframe_deletion	In_Frame_Del	DEL	CTTGGCTTTCTGGGTGAGAAAGGCTTCCAGCCGCTTCTTCTGCTG	CTTGGCTTTCTGGGTGAGAAAGGCTTCCAGCCGCTTCTTCTGCTG	-	novel	NA	P-0039304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	36	242	0	ENST00000262948.5:c.145_189del	p.Gln49_Lys63del	p.Q49_K63del	ENST00000262948	NM_030662.3	49	CAGCAGAAGAAGCGGCTGGAAGCCTTTCTCACCCAGAAAGCCAAG/-	2/11	0.28760096854682	1	FACETS	0.763	0.63	0.91	0.763	0.63	0.91	CLONAL	1	TRUE	0	0.28760096854682	1		242	281	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266060	41266114	+	protein_altering_variant	In_Frame_Del	DEL	AGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCT	AGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCT	TTCC	novel	NA	P-0039304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	30	324	2	ENST00000349496.5:c.57_111delinsTTCC	p.Lys19_His36delinsAsn	p.K19_H36delinsN	ENST00000349496	NM_001904.3	19	aaAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCT/aaTTCC	3/15	1	2	FACETS	0.54	0.435	0.66	0.54	0.435	0.66	SUBCLONAL	1	TRUE	1	0.28760096854682	2		326	386	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952003	178952003	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	40	343	0	ENST00000263967.3:c.3058G>T	p.Ala1020Ser	p.A1020S	ENST00000263967	NM_006218.2	1020	Gca/Tca	21/21	0.194311573088578	3	FACETS	0.759	0.631	0.901	0.253	0.21	0.301	CLONAL	1	TRUE	0	0.28760096854682	3		343	419	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0039306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	133	497	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.275301550783749	3	FACETS	0.786	0.721	0.853	0.786	0.721	0.853	INDETERMINATE	2	TRUE	1	0.531114914917775	3		497	403	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0039306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	183	309	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.520139348233397	2	FACETS	0.914	0.857	0.972	0.914	0.857	0.972	CLONAL	2	TRUE	0	0.531114914917775	2		309	377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576851	7576851	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0039306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	168	360	0	ENST00000269305.4:c.993+2T>C		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.531114914917775	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.531114914917775	1		360	422	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118370116	118370116	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	137	249	0	ENST00000534358.1:c.6060A>C	p.Glu2020Asp	p.E2020D	ENST00000534358	NM_005933.3	2020	gaA/gaC	23/36	0.519567113702365	2	FACETS	0.941	0.874	1	0.941	0.874	1	CLONAL	2	TRUE	0	0.531114914917775	2		249	274	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636799	176636799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	125	379	0	ENST00000439151.2:c.1399G>A	p.Glu467Lys	p.E467K	ENST00000439151	NM_022455.4	467	Gaa/Aaa	5/23	0.520139348233397	2	FACETS	0.903	0.822	0.989	0.452	0.411	0.495	CLONAL	1	TRUE	0	0.531114914917775	2		379	521	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0039307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	82	272	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	0.808	0.716	0.905	1	0.981	1	CLONAL	2	TRUE	1	0.247524232575302	2		272	410	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918582	44918582	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	23	179	0	ENST00000377967.4:c.1065G>A	p.Trp355Ter	p.W355*	ENST00000377967	NM_021140.2	355	tgG/tgA	12/29	1	1	FACETS	0.571	0.446	0.716	0.571	0.446	0.716	SUBCLONAL	1	TRUE	0	0.247524232575302	1		179	285	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913471	NA	P-0039307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	139	519	0	ENST00000269571.5:c.2329G>C	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ctg	20/27	1	2	FACETS	0.791	0.721	0.864	1	0.988	1	SUBCLONAL	2	TRUE	1	0.247524232575302	2		519	710	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022535	12022535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159947	NA	P-0039307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	132	469	1	ENST00000396373.4:c.641C>T	p.Pro214Leu	p.P214L	ENST00000396373	NM_001987.4	214	cCg/cTg	5/8	0.247524232575302	1	FACETS	0.848	0.773	0.926	1	0.989	1	CLONAL	2	TRUE	0	0.247524232575302	1		470	551	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285754	87285754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370304899	NA	P-0039307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	107	398	2	ENST00000277120.3:c.91G>A	p.Ala31Thr	p.A31T	ENST00000277120		31	Gcc/Acc	2/19	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.247524232575302	2		400	579	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215595140	215595140	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730881422	NA	P-0039307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	51	240	0	ENST00000260947.4:c.1996C>T	p.Gln666Ter	p.Q666*	ENST00000260947	NM_000465.2	666	Cag/Tag	10/11	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.247524232575302	2		240	367	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715688	30715688	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893807	NA	P-0039307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	32	269	0	ENST00000295754.5:c.1346C>T	p.Ser449Phe	p.S449F	ENST00000295754	NM_003242.5	449	tCc/tTc	5/7	1	2	FACETS	0.724	0.589	0.877	0.724	0.589	0.877	SUBCLONAL	1	TRUE	1	0.247524232575302	2		269	357	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324203	31324203	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs41560712	NA	P-0039307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	59	271	0	ENST00000412585.2:c.360G>C	p.Gln120His	p.Q120H	ENST00000412585	NM_005514.6	120	caG/caC	3/8	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.247524232575302	2		271	321	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341742	8341742	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	96	372	0	ENST00000356435.5:c.4898C>A	p.Thr1633Lys	p.T1633K	ENST00000356435		1633	aCa/aAa	29/35	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.247524232575302	2		372	622	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578463	7578463	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371524413	NA	P-0039308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	296	551	0	ENST00000269305.4:c.467G>C	p.Arg156Pro	p.R156P	ENST00000269305	NM_001126112.2	156	cGc/cCc	5/11	NA	2	FACETS	0.866	0.821	0.912			1	INDETERMINATE	2	TRUE	NA	0.49311708381804	2		551	693	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896954	28896954	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	60	339	0	ENST00000282397.4:c.2926A>G	p.Ser976Gly	p.S976G	ENST00000282397	NM_002019.4	976	Agt/Ggt	21/30	0.481008410333327	2	FACETS	0.661	0.572	0.757	0.331	0.286	0.379	SUBCLONAL	1	TRUE	0	0.49311708381804	2		339	368	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124202	2124202	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	90	421	0	ENST00000219476.3:c.2357G>C	p.Arg786Pro	p.R786P	ENST00000219476	NM_000548.3	786	cGc/cCc	22/42	0.493483035456619	1	FACETS	0.854	0.766	0.946	0.854	0.766	0.946	CLONAL	1	TRUE	0	0.49311708381804	1		421	322	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475080	40475080	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	243	454	1	ENST00000264657.5:c.1830del	p.Phe610LeufsTer36	p.F610Lfs*36	ENST00000264657	NM_139276.2	610	ttC/tt	20/24	0.474892071692375	2	FACETS	0.85	0.8	0.899	0.85	0.8	0.899	CLONAL	2	TRUE	0	0.49311708381804	2		455	580	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17949113	17949113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs763628238	NA	P-0039308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	131	553	0	ENST00000458235.1:c.1528C>G	p.Gln510Glu	p.Q510E	ENST00000458235	NM_000215.3	510	Cag/Gag	11/24	0.468925101928041	4	FACETS	0.842	0.763	0.925	0.281	0.254	0.309	CLONAL	1	TRUE	1	0.49311708381804	4		553	942	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17949123	17949123	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0039308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	127	575	0	ENST00000458235.1:c.1518C>G	p.Tyr506Ter	p.Y506*	ENST00000458235	NM_000215.3	506	taC/taG	11/24	0.468925101928041	4	FACETS	0.79	0.715	0.87	0.263	0.238	0.29	SUBCLONAL	1	TRUE	1	0.49311708381804	4		575	973	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326695	62326695	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	130	542	0	ENST00000360203.5:c.3514G>C	p.Glu1172Gln	p.E1172Q	ENST00000360203	NM_001283009.1	1172	Gag/Cag	34/35	0.327646320534272	4	FACETS	0.823	0.746	0.905	0.412	0.373	0.453	CLONAL	1	TRUE	2	0.49311708381804	4		542	956	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495653	72495653	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	59	225	0	ENST00000477973.2:c.419C>A	p.Ser140Tyr	p.S140Y	ENST00000477973	NM_012234.5	140	tCc/tAc	1/4	0.316127383175215	5	FACETS	0.89	0.767	1			1	CLONAL	1	TRUE	NA	0.49311708381804	5		225	468	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245442	153245442	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	234	421	0	ENST00000281708.4:c.1749A>T	p.Leu583Phe	p.L583F	ENST00000281708	NM_033632.3	583	ttA/ttT	11/12	0.481008410333327	2	FACETS	0.968	0.914	1	0.968	0.914	1	CLONAL	2	TRUE	0	0.49311708381804	2		421	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0039319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	279	611	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.387278124961815	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.387278124961815	2		611	680	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167577	NA	P-0039319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	44	314	0	ENST00000257430.4:c.4463del	p.Leu1488TyrfsTer19	p.L1488Yfs*19	ENST00000257430	NM_000038.5	1487	acT/ac	16/16	1	2	FACETS	0.792	0.668	0.927	0.792	0.668	0.927	CLONAL	1	TRUE	1	0.387278124961815	2		314	287	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615035	43615035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142318626	NA	P-0039319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	97	598	0	ENST00000355710.3:c.2449C>T	p.Arg817Cys	p.R817C	ENST00000355710	NM_020975.4	817	Cgc/Tgc	14/20	0.368803491800122	3	FACETS	1	0.95	1	0.553	0.494	0.615	CLONAL	1	TRUE	1	0.387278124961815	3		598	541	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984024	2984024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	172	532	0	ENST00000396946.4:c.506C>T	p.Thr169Met	p.T169M	ENST00000396946	NM_032415.4	169	aCg/aTg	5/25	0.368803491800122	3	FACETS	0.932	0.862	1	0.932	0.862	1	CLONAL	2	TRUE	1	0.387278124961815	3		532	569	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419957	41419957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369230837	NA	P-0039319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	115	524	0	ENST00000373198.4:c.364G>A	p.Val122Ile	p.V122I	ENST00000373198	NM_133170.3	122	Gtc/Atc	3/32	0.387278124961815	7	FACETS	1	0.963	1	0.287	0.258	0.318	CLONAL	1	TRUE	3	0.387278124961815	7		524	1018	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564615	55564615	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149092990	NA	P-0039319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	106	532	0	ENST00000288135.5:c.503C>T	p.Ala168Val	p.A168V	ENST00000288135	NM_000222.2	168	gCg/gTg	3/21	0.368803491800122	3	FACETS	1	0.949	1	0.545	0.489	0.603	CLONAL	1	TRUE	1	0.387278124961815	3		532	600	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085824	16085824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763830786	NA	P-0039319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	195	499	0	ENST00000281043.3:c.1000G>A	p.Ala334Thr	p.A334T	ENST00000281043	NM_005378.4	334	Gcc/Acc	3/3	0.368803491800122	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.387278124961815	3		499	552	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3799677	3799677	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	25	263	0	ENST00000262367.5:c.3787T>G	p.Ser1263Ala	p.S1263A	ENST00000262367	NM_004380.2	1263	Tca/Gca	21/31	0.387278124961815	4	FACETS	0.74	0.585	0.916	0.247	0.195	0.306	CLONAL	1	TRUE	1	0.387278124961815	4		263	242	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828584	72828584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763156400	NA	P-0039319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	62	572	1	ENST00000268489.5:c.7997C>T	p.Pro2666Leu	p.P2666L	ENST00000268489	NM_006885.3	2666	cCg/cTg	9/10	0.387278124961815	4	FACETS	0.526	0.453	0.606	0.175	0.151	0.202	SUBCLONAL	1	TRUE	1	0.387278124961815	4		573	844	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543634	29543634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776351932	NA	P-0039319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	98	533	0	ENST00000389048.3:c.1529G>A	p.Arg510Gln	p.R510Q	ENST00000389048	NM_004304.4	510	cGg/cAg	7/29	0.368803491800122	3	FACETS	0.932	0.833	1	0.466	0.416	0.519	CLONAL	1	TRUE	1	0.387278124961815	3		533	648	SUCCESS
APC	324	MSKCC	GRCh37	5	112174555	112174556	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0039319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	61	420	0	ENST00000257430.4:c.3265_3266insAT	p.Phe1089TyrfsTer38	p.F1089Yfs*38	ENST00000257430	NM_000038.5	1088	-/TA	16/16	1	2	FACETS	0.972	0.844	1	0.972	0.844	1	CLONAL	1	TRUE	1	0.387278124961815	2		420	324	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575204	48575206	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	ACG	ACG	-	novel	NA	P-0039320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	71	273	0	ENST00000342988.3:c.399_401del	p.Tyr133_Glu134delinsTer	p.Y133_E134delins*	ENST00000342988	NM_005359.5	133	tACGaa/taa	3/12	0.448026980503134	1	FACETS	0.908	0.801	1	0.908	0.801	1	CLONAL	1	TRUE	0	0.448026980503134	1		273	271	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867348	45867348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs948547865	NA	P-0039320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	125	599	0	ENST00000391945.4:c.845G>A	p.Arg282Gln	p.R282Q	ENST00000391945	NM_000400.3	282	cGg/cAg	10/23	1	2	FACETS	0.995	0.904	1	0.995	0.904	1	CLONAL	1	TRUE	1	0.448026980503134	2		599	561	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0039322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	155	399	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.36	2		399	646	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971124	21971125	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0039322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	72	370	0	ENST00000304494.5:c.233_234del	p.Leu78HisfsTer41	p.L78Hfs*41	ENST00000304494	NM_000077.4	78	cTC/c	2/3	0.3	1	FACETS	0.587	0.513	0.666	0.587	0.513	0.666	SUBCLONAL	1	TRUE	0	0.36	1		370	559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579538	7579539	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1567556956	NA	P-0039322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	127	552	0	ENST00000269305.4:c.148dup	p.Ile50AsnfsTer2	p.I50Nfs*2	ENST00000269305	NM_001126112.2	50	att/aAtt	4/11	1	2	FACETS	0.894	0.81	0.983	0.894	0.81	0.983	CLONAL	1	TRUE	1	0.36	2		552	789	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101153	27101153	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	100	520	0	ENST00000324856.7:c.4435C>T	p.Gln1479Ter	p.Q1479*	ENST00000324856	NM_006015.4	1479	Caa/Taa	18/20	1	2	FACETS	0.737	0.658	0.821	0.737	0.658	0.821	SUBCLONAL	1	TRUE	1	0.36	2		520	754	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436892	49436893	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CATCCCTTCA	novel	NA	P-0039322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	62	554	0	ENST00000301067.7:c.5601_5610dup	p.Leu1871Ter	p.L1871*	ENST00000301067	NM_003482.3	1870	-/TGAAGGGATG	25/54	1	2	FACETS	0.436	0.376	0.502	0.436	0.376	0.502	SUBCLONAL	1	TRUE	1	0.36	2		554	790	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604762	48604763	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	rs876660150	NA	P-0039322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	79	354	0	ENST00000342988.3:c.1585_1586dup	p.Leu529PhefsTer9	p.L529Ffs*9	ENST00000342988	NM_005359.5	528	-/TT	12/12	0.156849356463149	2	FACETS	0.873	0.769	0.983	0.436	0.384	0.492	INDETERMINATE	1	TRUE	0	0.36	2		354	503	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225600	225600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777600956	NA	P-0039324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	23	172	1	ENST00000264932.6:c.379G>A	p.Val127Met	p.V127M	ENST00000264932	NM_004168.2	127	Gtg/Atg	4/15	1	2	FACETS	0.403	0.316	0.502	0.403	0.316	0.502	SUBCLONAL	1	TRUE	1	0.63765846891057	2		173	179	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0039325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	66	515	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.501889086680742	2		515	247	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578266	7578266	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs942158624	NA	P-0039325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	93	554	0	ENST00000269305.4:c.583A>T	p.Ile195Phe	p.I195F	ENST00000269305	NM_001126112.2	195	Atc/Ttc	6/11	0.501889086680742	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.501889086680742	1		554	273	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874286	155874286	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs868208063	NA	P-0039325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	90	444	0	ENST00000368323.3:c.245T>G	p.Phe82Cys	p.F82C	ENST00000368323	NM_006912.5	82	tTt/tGt	5/6	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.501889086680742	2		444	345	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797330	135797337	+	frameshift_variant	Frame_Shift_Del	DEL	AGATGGAC	AGATGGAC	-	novel	NA	P-0039325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	18	348	0	ENST00000298552.3:c.532_539del	p.Val178ProfsTer37	p.V178Pfs*37	ENST00000298552	NM_001162426.1	178	GTCCATCTc/c	7/23	1	2	FACETS	0.203	0.152	0.263	0.203	0.152	0.263	SUBCLONAL	1	TRUE	1	0.501889086680742	2		348	353	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938323	76938323	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	24	490	0	ENST00000373344.5:c.2425C>G	p.Gln809Glu	p.Q809E	ENST00000373344	NM_000489.3	809	Caa/Gaa	9/35	1	2	FACETS	0.364	0.286	0.453	0.364	0.286	0.453	SUBCLONAL	1	TRUE	1	0.501889086680742	2		490	263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578181	7578192	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCTCATAG	GGCGGCTCATAG	-	rs876660749	NA	P-0039326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	241	536	1	ENST00000269305.4:c.657_668del	p.Tyr220_Pro223del	p.Y220_P223del	ENST00000269305	NM_001126112.2	219	ccCTATGAGCCGCCt/cct	6/11	0.486416695582241	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.486416695582241	2		537	485	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092938	27093460	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTTTTACAGGGATGGCAGCCAGCCCAGAGATGATGGGCCTTGGGGATGTAAAGTTAACTCCAGCCACCAAAATGAACAACAAGGCAGATGGGACACCCAAGACAGAATCCAAATCCAAGGTAGTGATTTTTGTCTTGACTCCTTTCAACTTTGTGTCCTATCTTTTTCAGTGATAGGAAGGAAAAAGAAAAGAGAGTGACAAGATCCCAGCCTTTTATGACACCGGACTAGATAGTCTCTGAAAAAGCTGCTGTTGCCTCCTCTTATCATGAAAGGTCCCAGAATAATAGCTCAGTGAGTTGGGTCTGGGTTGGTCTAAGGGATCCTGGTAAATAACATAATATTCTCACAGCTGTTTGTTATGGGGGAAATGCCAGACACTGCAGCATCAAACTCTCTGTACTGTTTGGCTGGTGCCCTCTGTGAAACCGTGCCTCCTATACTCAAGCATTGATAGATGGGGTGTGCCATGGGCAACTAGTTGCTCTTCTCTTCCTGAACCTTACTCATAGCAGCAGGAAT	TCTTTTACAGGGATGGCAGCCAGCCCAGAGATGATGGGCCTTGGGGATGTAAAGTTAACTCCAGCCACCAAAATGAACAACAAGGCAGATGGGACACCCAAGACAGAATCCAAATCCAAGGTAGTGATTTTTGTCTTGACTCCTTTCAACTTTGTGTCCTATCTTTTTCAGTGATAGGAAGGAAAAAGAAAAGAGAGTGACAAGATCCCAGCCTTTTATGACACCGGACTAGATAGTCTCTGAAAAAGCTGCTGTTGCCTCCTCTTATCATGAAAGGTCCCAGAATAATAGCTCAGTGAGTTGGGTCTGGGTTGGTCTAAGGGATCCTGGTAAATAACATAATATTCTCACAGCTGTTTGTTATGGGGGAAATGCCAGACACTGCAGCATCAAACTCTCTGTACTGTTTGGCTGGTGCCCTCTGTGAAACCGTGCCTCCTATACTCAAGCATTGATAGATGGGGTGTGCCATGGGCAACTAGTTGCTCTTCTCTTCCTGAACCTTACTCATAGCAGCAGGAAT	-	novel	NA	P-0039326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	60	290	0	ENST00000324856.7:c.2879-10_2988+403del		p.X960_splice	ENST00000324856	NM_006015.4	960		10/20	NA	2	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.486416695582241	2		290	187	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711882	89711883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0039326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	99	398	0	ENST00000371953.3:c.501_502insTT	p.Ile168LeufsTer16	p.I168Lfs*16	ENST00000371953	NM_000314.4	167	act/acTTt	6/9	0.486416695582241	2	FACETS	0.845	0.768	0.922	0.845	0.768	0.922	CLONAL	2	TRUE	0	0.486416695582241	2		398	241	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952554	17952554	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	163	490	0	ENST00000458235.1:c.879C>A	p.Cys293Ter	p.C293*	ENST00000458235	NM_000215.3	293	tgC/tgA	7/24	0.174567365038028	6	FACETS	0.838	0.774	0.903	0.838	0.774	0.903	INDETERMINATE	3	TRUE	3	0.486416695582241	6		490	526	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791189	42791190	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGGC	novel	NA	P-0039326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	195	614	0	ENST00000575354.2:c.251_254dup	p.Pro86AlafsTer9	p.P86Afs*9	ENST00000575354	NM_015125.3	83	-/CGGC	3/20	0.486416695582241	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.486416695582241	2		614	399	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176715908	176715929	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTGGGTGTAAGGCCAAAGGTA	CTTGGGTGTAAGGCCAAAGGTA	-	novel	NA	P-0039326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	45	462	0	ENST00000439151.2:c.6241_6258+4del		p.X2081_splice	ENST00000439151	NM_022455.4	2081		21/23	0.348413126366885	4	FACETS	0.433	0.363	0.511			1	SUBCLONAL	1	TRUE	NA	0.486416695582241	4		462	635	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816523	32816524	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	276	621	0	ENST00000354258.4:c.1651dup	p.Ser551LysfsTer83	p.S551Kfs*83	ENST00000354258	NM_000593.5	551	agt/aAgt	7/11	0.454137648996915	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.486416695582241	2		621	542	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380936	116380962	+	inframe_deletion	In_Frame_Del	DEL	TGCAGACATTTCCAGTCCTGCAGTCAA	TGCAGACATTTCCAGTCCTGCAGTCAA	-	novel	NA	P-0039326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	170	487	0	ENST00000397752.3:c.1561_1587del	p.Arg521_Cys529del	p.R521_C529del	ENST00000397752	NM_000245.2	520	TGCAGACATTTCCAGTCCTGCAGTCAA/-	5/21	NA	2	FACETS	0.876	0.816	0.937			1	INDETERMINATE	2	TRUE	NA	0.486416695582241	2		487	399	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969466	44969468	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0039326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	136	223	0	ENST00000377967.4:c.4150_4152del	p.Met1384del	p.M1384del	ENST00000377967	NM_021140.2	1383	cTGAtg/ctg	28/29	0.482691078264401	2	FACETS	0.892	0.837	0.945			1	CLONAL	3	TRUE	NA	0.486416695582241	2		223	209	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603119	48603120	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	A	novel	NA	P-0039326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	125	429	0	ENST00000342988.3:c.1420_1421delinsA	p.Ser474LysfsTer2	p.S474Kfs*2	ENST00000342988	NM_005359.5	474	TCa/Aa	11/12	0.486416695582241	2	FACETS	0.911	0.84	0.984	0.911	0.84	0.984	CLONAL	2	TRUE	0	0.486416695582241	2		429	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0039328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	771	477	18	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.929425488275673	2	FACETS	0.99	0.977	1	0.99	0.977	1	CLONAL	2	TRUE	0	0.93505725264085	2		495	833	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0039329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	102	254	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.301615401637241	3	FACETS	1	0.93	1	0.52	0.469	0.574	INDETERMINATE	1	TRUE	1	0.6581050918564	3		254	396	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073751	8073756	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	GCTGAC	GCTGAC	-	novel	NA	P-0039329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	165	331	0	ENST00000377482.5:c.903_908del	p.Trp301_Ala303delinsTer	p.W301_A303delins*	ENST00000377482	NM_018948.3	301	tgGTCAGCa/tga	4/4	0.6581050918564	1	FACETS	0.998	0.933	1	0.998	0.933	1	CLONAL	1	TRUE	0	0.6581050918564	1		331	337	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488233	56488233	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	268	454	0	ENST00000267101.3:c.1752C>A	p.His584Gln	p.H584Q	ENST00000267101	NM_001982.3	584	caC/caA	15/28	0.6581050918564	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.6581050918564	1		454	535	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577035	7577036	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	342	580	0	ENST00000269305.4:c.902dup	p.Gly302ArgfsTer4	p.G302Rfs*4	ENST00000269305	NM_001126112.2	301	cca/ccCa	8/11	0.6581050918564	1	FACETS	0.848	0.807	0.89	0.848	0.807	0.89	CLONAL	1	TRUE	0	0.6581050918564	1		580	822	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993052	90993052	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	254	386	0	ENST00000265433.3:c.390del	p.Ala131LeufsTer10	p.A131Lfs*10	ENST00000265433	NM_002485.4	130	caA/ca	4/16	0.526298763583884	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.6581050918564	3		386	500	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	167	576	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.904	0.83	0.982	0.904	0.83	0.982	CLONAL	1	TRUE	1	0.376862138735004	2		580	980	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	75	327	2	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.921	0.811	1	0.921	0.811	1	CLONAL	1	TRUE	1	0.376862138735004	2		329	432	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350862	89350862	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	170	833	0	ENST00000301030.4:c.2088del	p.Glu697LysfsTer7	p.E697Kfs*7	ENST00000301030	NM_001256183.1	696	aaA/aa	9/13	1	2	FACETS	0.804	0.738	0.873	0.804	0.738	0.873	CLONAL	1	TRUE	1	0.376862138735004	2		833	1122	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	209	771	10	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	0.903	0.837	0.972	0.903	0.837	0.972	CLONAL	1	TRUE	1	0.376862138735004	2		781	1228	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258485	16258485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780910569	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	138	617	0	ENST00000375759.3:c.5750G>A	p.Arg1917His	p.R1917H	ENST00000375759	NM_015001.2	1917	cGc/cAc	11/15	1	2	FACETS	0.814	0.74	0.891	0.814	0.74	0.891	CLONAL	1	TRUE	1	0.376862138735004	2		617	900	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	233	525	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.854	0.8	0.909	1	0.994	1	CLONAL	2	TRUE	1	0.376862138735004	2		528	724	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780711	9780711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs545136223	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	51	609	0	ENST00000377346.4:c.1513G>A	p.Glu505Lys	p.E505K	ENST00000377346	NM_005026.3	505	Gag/Aag	12/24	1	2	FACETS	0.299	0.253	0.35	0.299	0.253	0.35	SUBCLONAL	1	TRUE	1	0.376862138735004	2		609	904	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435128	110435129	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs772322568	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	146	622	0	ENST00000375856.3:c.3272dup	p.Lys1092GlufsTer233	p.K1092Efs*233	ENST00000375856	NM_003749.2	1091	ccg/ccCg	1/2	1	2	FACETS	0.749	0.683	0.819	0.749	0.683	0.819	SUBCLONAL	1	TRUE	1	0.376862138735004	2		622	1034	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	113	423	1	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	0.995	0.897	1	0.995	0.897	1	CLONAL	1	TRUE	1	0.376862138735004	2		424	603	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846336	156846336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781209572	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	185	592	1	ENST00000524377.1:c.1777C>T	p.Arg593Trp	p.R593W	ENST00000524377	NM_002529.3	593	Cgg/Tgg	14/17	1	2	FACETS	0.976	0.901	1	0.976	0.901	1	CLONAL	1	TRUE	1	0.376862138735004	2		593	1006	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224538	53224538	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556835963	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	194	337	1	ENST00000375401.3:c.3175C>T	p.Arg1059Trp	p.R1059W	ENST00000375401	NM_004187.3	1059	Cgg/Tgg	21/26	1	1	FACETS	0.778	0.725	0.832	1	0.992	1	SUBCLONAL	2	TRUE	0	0.376862138735004	1		338	537	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974899	15974899	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	102	378	0	ENST00000268712.3:c.3976C>T	p.Arg1326Ter	p.R1326*	ENST00000268712	NM_006311.3	1326	Cga/Tga	30/46	1	2	FACETS	0.785	0.702	0.872	0.785	0.702	0.872	SUBCLONAL	1	TRUE	1	0.376862138735004	2		378	690	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	130	600	0	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	0.819	0.743	0.9	0.819	0.743	0.9	CLONAL	1	TRUE	1	0.376862138735004	2		600	842	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76812945	76812947	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs1557059596	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	89	275	2	ENST00000373344.5:c.6674_6676del	p.Lys2225del	p.K2225del	ENST00000373344	NM_000489.3	2225	aAGAgg/agg	30/35	1	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.376862138735004	1		277	299	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155325	185155325	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746379057	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	171	557	0	ENST00000265026.3:c.566C>T	p.Ala189Val	p.A189V	ENST00000265026	NM_004721.4	189	gCg/gTg	3/14	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.376862138735004	2		557	849	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384650	31384651	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs756395138	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	156	637	1	ENST00000328111.2:c.1359dup	p.Leu454AlafsTer11	p.L454Afs*11	ENST00000328111	NM_006892.3	451	gag/gaGg	13/23	1	2	FACETS	0.884	0.809	0.962	0.884	0.809	0.962	CLONAL	1	TRUE	1	0.376862138735004	2		638	937	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622516	158622516	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs387906589	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	115	517	0	ENST00000263640.3:c.983G>T	p.Gly328Val	p.G328V	ENST00000263640	NM_001105.4	328	gGg/gTg	8/11	1	2	FACETS	0.852	0.768	0.941	0.852	0.768	0.941	CLONAL	1	TRUE	1	0.376862138735004	2		517	716	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494324	2494324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143033733	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	170	645	0	ENST00000355716.4:c.715G>A	p.Val239Ile	p.V239I	ENST00000355716	NM_003820.2	239	Gtc/Atc	7/8	1	2	FACETS	0.862	0.792	0.935	0.862	0.792	0.935	CLONAL	1	TRUE	1	0.376862138735004	2		645	1047	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347446	91347446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757088548	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	133	412	0	ENST00000355112.3:c.3608C>T	p.Ala1203Val	p.A1203V	ENST00000355112	NM_000057.2	1203	gCg/gTg	19/22	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.376862138735004	2		412	667	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	130	649	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.804	0.729	0.883	0.804	0.729	0.883	CLONAL	1	TRUE	1	0.376862138735004	2		654	858	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	73	912	0	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	1	2	FACETS	0.338	0.295	0.386	0.338	0.295	0.386	SUBCLONAL	1	TRUE	1	0.376862138735004	2		912	1145	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255141	16255142	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	124	544	1	ENST00000375759.3:c.2417_2418dup	p.Arg807AspfsTer3	p.R807Dfs*3	ENST00000375759	NM_015001.2	802	-/GA	11/15	1	2	FACETS	0.866	0.784	0.952	0.866	0.784	0.952	CLONAL	1	TRUE	1	0.376862138735004	2		545	760	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420204	49420204	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	194	648	0	ENST00000301067.7:c.15545del	p.Gly5182AlafsTer61	p.G5182Afs*61	ENST00000301067	NM_003482.3	5182	gGc/gc	48/54	1	2	FACETS	0.997	0.922	1	0.997	0.922	1	CLONAL	1	TRUE	1	0.376862138735004	2		648	1033	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261291	16261292	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	156	583	0	ENST00000375759.3:c.8558dup	p.Ser2854ValfsTer6	p.S2854Vfs*6	ENST00000375759	NM_015001.2	2852	-/A	11/15	1	2	FACETS	0.962	0.881	1	0.962	0.881	1	CLONAL	1	TRUE	1	0.376862138735004	2		583	861	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834203	156834203	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	173	713	0	ENST00000524377.1:c.274del	p.Glu92SerfsTer2	p.E92Sfs*2	ENST00000524377	NM_002529.3	90	ctG/ct	2/17	1	2	FACETS	0.824	0.757	0.894	0.824	0.757	0.894	CLONAL	1	TRUE	1	0.376862138735004	2		713	1114	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8105983	8105983	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	132	455	0	ENST00000346208.3:c.803C>A	p.Ala268Glu	p.A268E	ENST00000346208		268	gCa/gAa	4/6	1	2	FACETS	0.918	0.834	1	0.918	0.834	1	CLONAL	1	TRUE	1	0.376862138735004	2		455	763	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497657	125497657	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	96	441	0	ENST00000428830.2:c.221G>T	p.Arg74Met	p.R74M	ENST00000428830	NM_001114121.2	74	aGg/aTg	3/14	1	2	FACETS	0.965	0.863	1	0.965	0.863	1	CLONAL	1	TRUE	1	0.376862138735004	2		441	528	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606151	81606151	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367893332	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	135	539	0	ENST00000298171.2:c.821G>A	p.Arg274Gln	p.R274Q	ENST00000298171	NM_000369.2	274	cGg/cAg	9/10	1	2	FACETS	0.872	0.792	0.955	0.872	0.792	0.955	CLONAL	1	TRUE	1	0.376862138735004	2		539	822	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813705	50813705	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	83	646	0	ENST00000398568.2:c.1259T>C	p.Leu420Pro	p.L420P	ENST00000398568	NM_001042412.1	420	cTc/cCc	8/18	1	2	FACETS	0.432	0.38	0.488	0.432	0.38	0.488	SUBCLONAL	1	TRUE	1	0.376862138735004	2		646	1020	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829272	72829272	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	189	717	0	ENST00000268489.5:c.7309del	p.Ser2437ValfsTer91	p.S2437Vfs*91	ENST00000268489	NM_006885.3	2437	Agt/gt	9/10	1	2	FACETS	0.859	0.792	0.928	0.859	0.792	0.928	CLONAL	1	TRUE	1	0.376862138735004	2		717	1168	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10286250	10286250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781646588	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	185	750	2	ENST00000340748.4:c.566C>T	p.Ser189Leu	p.S189L	ENST00000340748		189	tCg/tTg	6/40	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.376862138735004	2		752	941	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224692	36224692	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568382897	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	203	763	0	ENST00000222270.7:c.7078C>T	p.Pro2360Ser	p.P2360S	ENST00000222270	NM_014727.1	2360	Cca/Tca	30/37	1	2	FACETS	0.944	0.874	1	0.944	0.874	1	CLONAL	1	TRUE	1	0.376862138735004	2		763	1141	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170011257	170011257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1341309666	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	126	540	1	ENST00000295797.4:c.1378G>A	p.Asp460Asn	p.D460N	ENST00000295797	NM_002740.5	460	Gat/Aat	14/18	1	2	FACETS	0.819	0.742	0.901	0.819	0.742	0.901	CLONAL	1	TRUE	1	0.376862138735004	2		541	816	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130126	143130126	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769344936	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	108	507	0	ENST00000262992.4:c.890G>A	p.Arg297Gln	p.R297Q	ENST00000262992	NM_001101669.1	297	cGa/cAa	11/24	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.376862138735004	2		507	561	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286937	33286937	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	216	746	1	ENST00000374542.5:c.2000C>A	p.Pro667His	p.P667H	ENST00000374542	NM_001141970.1	667	cCc/cAc	7/8	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.376862138735004	2		747	1070	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64290026	64290026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	114	470	1	ENST00000370651.3:c.469C>T	p.Arg157Trp	p.R157W	ENST00000370651	NM_003463.4	157	Cgg/Tgg	6/6	1	2	FACETS	0.838	0.755	0.926	0.838	0.755	0.926	CLONAL	1	TRUE	1	0.376862138735004	2		471	722	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309085	137309085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777558913	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	214	777	2	ENST00000481739.1:c.692C>T	p.Pro231Leu	p.P231L	ENST00000481739	NM_002957.4	231	cCg/cTg	5/10	1	2	FACETS	0.976	0.906	1	0.976	0.906	1	CLONAL	1	TRUE	1	0.376862138735004	2		779	1164	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357413	70357413	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	140	339	0	ENST00000374080.3:c.5754T>G	p.Ser1918Arg	p.S1918R	ENST00000374080		1918	agT/agG	40/45	1	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.376862138735004	1		339	476	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0039352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	292	497	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.760172358617545	3	FACETS	0.998	0.952	1	0.998	0.952	1	CLONAL	2	TRUE	1	0.760172358617545	3		497	531	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435125	18435125	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	144	498	0	ENST00000266497.5:c.110G>T	p.Ser37Ile	p.S37I	ENST00000266497		37	aGt/aTt	1/31	0.760172358617545	3	FACETS	0.956	0.876	1	0.478	0.438	0.519	CLONAL	1	TRUE	1	0.760172358617545	3		498	547	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180981	108180981	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	202	399	0	ENST00000278616.4:c.5857A>G	p.Thr1953Ala	p.T1953A	ENST00000278616	NM_000051.3	1953	Aca/Gca	39/63	0.759208284800634	2	FACETS	0.939	0.896	0.98	0.939	0.896	0.98	CLONAL	2	TRUE	0	0.760172358617545	2		399	283	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988873	41988882	+	frameshift_variant	Frame_Shift_Del	DEL	TATATCTGAC	TATATCTGAC	-	novel	NA	P-0039352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	194	594	0	ENST00000219905.7:c.1665_1674del	p.Asp555GlufsTer42	p.D555Efs*42	ENST00000219905	NM_001164273.1	555	gaTATATCTGAC/ga	3/24	1	2	FACETS	0.969	0.904	1	0.969	0.904	1	CLONAL	1	TRUE	1	0.760172358617545	2		594	527	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122357	2122357	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	494	614	1	ENST00000219476.3:c.2213G>T	p.Cys738Phe	p.C738F	ENST00000219476	NM_000548.3	738	tGc/tTc	20/42	0.760172358617545	3	FACETS	0.998	0.962	1	0.998	0.962	1	CLONAL	2	TRUE	1	0.760172358617545	3		615	899	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143235875	143235875	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	161	398	0	ENST00000262992.4:c.413C>T	p.Pro138Leu	p.P138L	ENST00000262992	NM_001101669.1	138	cCa/cTa	6/24	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.760172358617545	2		398	420	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341776	8341776	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	589	664	1	ENST00000356435.5:c.4864G>T	p.Ala1622Ser	p.A1622S	ENST00000356435		1622	Gct/Tct	29/35	0.722102590944152	4	FACETS	0.931	0.902	0.959	0.931	0.902	0.959	CLONAL	3	TRUE	1	0.760172358617545	4		665	977	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028875	47028875	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0039352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	425	551	0	ENST00000377604.3:c.179C>G	p.Ser60Ter	p.S60*	ENST00000377604	NM_001204468.1	60	tCa/tGa	3/24	0.285496210043529	5	FACETS	1	0.993	1	0.788	0.754	0.823	INDETERMINATE	2	TRUE	2	0.760172358617545	5		551	1012	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944337	76944337	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	267	572	1	ENST00000373344.5:c.568C>A	p.Pro190Thr	p.P190T	ENST00000373344	NM_000489.3	190	Cct/Act	7/35	0.285496210043529	5	FACETS	1	0.985	1	0.748	0.706	0.791	INDETERMINATE	2	TRUE	2	0.760172358617545	5		573	670	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	17	492	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.773	0.575	1	0.773	0.575	1	CLONAL	1	TRUE	1	0.11	2		492	400	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0039353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	32	542	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.11	2		542	444	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0039353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	13	958	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.444	0.315	0.603	0.444	0.315	0.603	SUBCLONAL	1	TRUE	1	0.11	2		958	532	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857977	9857977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1163517430	NA	P-0039354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	103	676	0	ENST00000330684.3:c.3424C>T	p.Pro1142Ser	p.P1142S	ENST00000330684	NM_001134407.1	1142	Ccc/Tcc	13/13	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.415871017350792	2		676	438	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65323383	65323384	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0039354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	74	599	0	ENST00000342505.4:c.1413_1414del	p.Phe472Ter	p.F472*	ENST00000342505	NM_002227.2	471	gaCTtt/gatt	10/25	1	2	FACETS	0.757	0.665	0.856	0.757	0.665	0.856	SUBCLONAL	1	FALSE	1	0.415871017350792	2		599	470	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468263	50468263	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	93	640	0	ENST00000331340.3:c.1498C>T	p.Gln500Ter	p.Q500*	ENST00000331340	NM_006060.4	500	Cag/Tag	8/8	0.215927173319584	4	FACETS	1	0.979	1	0.715	0.639	0.795	INDETERMINATE	1	FALSE	2	0.415871017350792	4		640	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0039355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1458	95	841	1	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	1	2	FACETS	0.51	0.452	0.572	0.51	0.452	0.572	SUBCLONAL	1	FALSE	1	0.239924770910984	2		842	1553	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347265	70347265	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	67	629	0	ENST00000374080.3:c.2929G>C	p.Asp977His	p.D977H	ENST00000374080		977	Gat/Cat	21/45	1	2	FACETS	0.488	0.422	0.559	0.488	0.422	0.559	SUBCLONAL	1	FALSE	1	0.239924770910984	2		629	1145	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551681	150551681	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	64	471	0	ENST00000369026.2:c.326A>T	p.Glu109Val	p.E109V	ENST00000369026	NM_021960.4	109	gAg/gTg	1/3	1	2	FACETS	0.605	0.522	0.695	0.605	0.522	0.695	SUBCLONAL	1	FALSE	1	0.239924770910984	2		471	882	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333573	70333573	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	43	539	0	ENST00000373644.4:c.1478C>T	p.Ala493Val	p.A493V	ENST00000373644	NM_030625.2	493	gCt/gTt	2/12	1	2	FACETS	0.449	0.374	0.532	0.449	0.374	0.532	SUBCLONAL	1	FALSE	1	0.239924770910984	2		539	799	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872514	35872514	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	75	456	0	ENST00000216797.5:c.389T>A	p.Leu130His	p.L130H	ENST00000216797	NM_020529.2	130	cTt/cAt	3/6	1	2	FACETS	0.573	0.5	0.651	0.573	0.5	0.651	SUBCLONAL	1	FALSE	1	0.239924770910984	2		456	1092	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982773	7982773	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	77	676	0	ENST00000319144.4:c.1012G>C	p.Ala338Pro	p.A338P	ENST00000319144	NM_001139.2	338	Gcc/Ccc	8/15	1	2	FACETS	0.532	0.465	0.604	0.532	0.465	0.604	SUBCLONAL	1	FALSE	1	0.239924770910984	2		676	1207	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133851	55133851	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	50	429	1	ENST00000257290.5:c.1064C>T	p.Thr355Ile	p.T355I	ENST00000257290	NM_006206.4	355	aCt/aTt	7/23	1	2	FACETS	0.454	0.384	0.532	0.454	0.384	0.532	SUBCLONAL	1	FALSE	1	0.239924770910984	2		430	918	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874559	35874559	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1187307876	NA	P-0039355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	48	497	2	ENST00000303115.3:c.715G>T	p.Asp239Tyr	p.D239Y	ENST00000303115	NM_002185.3	239	Gat/Tat	6/8	1	2	FACETS	0.476	0.401	0.559	0.476	0.401	0.559	SUBCLONAL	1	FALSE	1	0.239924770910984	2		499	841	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188395	32188395	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	78	529	0	ENST00000375023.3:c.946G>T	p.Asp316Tyr	p.D316Y	ENST00000375023	NM_004557.3	316	Gat/Tat	6/30	1	2	FACETS	0.595	0.521	0.675	0.595	0.521	0.675	SUBCLONAL	1	FALSE	1	0.239924770910984	2		529	1092	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	252	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.678615964802759	2		174	704	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0039357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	209	254	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.678615964802759	2		254	558	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068105	94068105	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	207	393	0	ENST00000369303.4:c.857C>T	p.Ser286Phe	p.S286F	ENST00000369303	NM_004440.3	286	tCt/tTt	4/17	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.678615964802759	2		393	562	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578446	7578466	+	inframe_deletion	In_Frame_Del	DEL	TGGCCATGGCGCGGACGCGGG	TGGCCATGGCGCGGACGCGGG	-	novel	NA	P-0039357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	99	877	0	ENST00000269305.4:c.464_484del	p.Thr155_Ala161del	p.T155_A161del	ENST00000269305	NM_001126112.2	155	aCCCGCGTCCGCGCCATGGCCAtc/atc	5/11	1	2	FACETS	0.225	0.2	0.252	0.225	0.2	0.252	SUBCLONAL	1	TRUE	1	0.678615964802759	2		877	1298	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30302522	30302522	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	36	167	0	ENST00000322652.5:c.613C>T	p.Gln205Ter	p.Q205*	ENST00000322652	NM_015355.2	205	Caa/Taa	7/16	0.66887497388897	1	FACETS	0.674	0.57	0.784	0.674	0.57	0.784	SUBCLONAL	1	TRUE	0	0.678615964802759	1		167	104	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342989	70342989	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	108	389	0	ENST00000374080.3:c.1530G>A	p.Trp510Ter	p.W510*	ENST00000374080		510	tgG/tgA	11/45	1	1	FACETS	0.397	0.357	0.438	0.397	0.357	0.438	SUBCLONAL	1	TRUE	0	0.678615964802759	1		389	530	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352389	70352389	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0039357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	38	275	0	ENST00000374080.3:c.4415+1G>A		p.X1472_splice	ENST00000374080		1472			1	1	FACETS	0.186	0.153	0.222	0.186	0.153	0.222	SUBCLONAL	1	TRUE	0	0.678615964802759	1		275	398	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352989	70352989	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	86	323	0	ENST00000374080.3:c.4544del	p.Arg1515GlnfsTer6	p.R1515Qfs*6	ENST00000374080		1515	cGa/ca	33/45	1	1	FACETS	0.354	0.314	0.396	0.354	0.314	0.396	SUBCLONAL	1	TRUE	0	0.678615964802759	1		323	473	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	46	995	1	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	0.282	0.237	0.333	0.282	0.237	0.333	SUBCLONAL	1	TRUE	1	0.458296666833149	2		996	711	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0039358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	17	389	0	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS	0.19	0.141	0.248	0.19	0.141	0.248	SUBCLONAL	1	TRUE	1	0.458296666833149	2		389	391	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156731	20156731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	142	411	0	ENST00000379607.5:c.26G>A	p.Gly9Asp	p.G9D	ENST00000379607	NM_001412.3	9	gGt/gAt	2/7	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.458296666833149	2		411	541	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639842	3639842	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	195	655	0	ENST00000294008.3:c.3797G>C	p.Ser1266Thr	p.S1266T	ENST00000294008	NM_032444.2	1266	aGc/aCc	12/15	1	2	FACETS	0.993	0.92	1	0.993	0.92	1	CLONAL	1	TRUE	1	0.458296666833149	2		655	857	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916571	39916574	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CTTC	CTTC	-	novel	NA	P-0039358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	138	473	0	ENST00000378444.4:c.4429_4432del	p.Glu1477TrpfsTer6	p.E1477Wfs*6	ENST00000378444	NM_001123385.1	1477	GAAGtg/tg	11/15	NA	2	FACETS	0.974	0.89	1			1	INDETERMINATE	1	TRUE	NA	0.458296666833149	2		473	618	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303634	65303634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1180745512	NA	P-0039365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	78	710	0	ENST00000342505.4:c.3121C>T	p.Arg1041Trp	p.R1041W	ENST00000342505	NM_002227.2	1041	Cgg/Tgg	22/25	1	2	FACETS	0.757	0.664	0.858	0.757	0.664	0.858	SUBCLONAL	1	FALSE	1	0.234124470038171	2		710	880	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553477	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	56	673	0	ENST00000356175.3:c.2026A>C	p.Thr676Pro	p.T676P	ENST00000356175	NM_000267.3	676	Acc/Ccc	18/57	1	2	FACETS	0.5	0.427	0.581	0.5	0.427	0.581	SUBCLONAL	1	FALSE	1	0.234124470038171	2		673	956	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279574	18279574	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	184	815	0	ENST00000222254.8:c.1847A>G	p.His616Arg	p.H616R	ENST00000222254	NM_005027.3	616	cAc/cGc	15/16	1	2	FACETS	0.789	0.728	0.853	1	0.991	1	SUBCLONAL	2	FALSE	1	0.234124470038171	2		815	996	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0039366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	111	515	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.132976097438544	3	FACETS	1	0.981	1	0.703	0.633	0.776	INDETERMINATE	1	TRUE	1	0.290808775016054	3		515	622	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0039366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	90	525	1	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.290808775016054	2		526	574	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589875	212589875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758827443	NA	P-0039366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	38	587	0	ENST00000342788.4:c.667G>A	p.Gly223Arg	p.G223R	ENST00000342788	NM_005235.2	223	Gga/Aga	6/28	1	2	FACETS	0.398	0.328	0.476	0.398	0.328	0.476	SUBCLONAL	1	TRUE	1	0.290808775016054	2		587	657	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577555	7577555	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	94	618	1	ENST00000269305.4:c.726C>A	p.Cys242Ter	p.C242*	ENST00000269305	NM_001126112.2	242	tgC/tgA	7/11	0.277870812267915	1	FACETS	0.907	0.808	1	0.907	0.808	1	CLONAL	1	TRUE	0	0.290808775016054	1		619	609	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100389	27100389	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	72	526	1	ENST00000324856.7:c.4101G>T	p.Gln1367His	p.Q1367H	ENST00000324856	NM_006015.4	1367	caG/caT	17/20	1	2	FACETS	0.909	0.795	1	0.909	0.795	1	CLONAL	1	TRUE	1	0.290808775016054	2		527	545	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874164	155874164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1213963509	NA	P-0039366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	60	699	2	ENST00000368323.3:c.367C>T	p.Arg123Cys	p.R123C	ENST00000368323	NM_006912.5	123	Cgt/Tgt	5/6	1	2	FACETS	0.481	0.413	0.555	0.481	0.413	0.555	SUBCLONAL	1	TRUE	1	0.290808775016054	2		701	858	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581273	48581273	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	99	545	0	ENST00000342988.3:c.577del	p.Glu193ArgfsTer9	p.E193Rfs*9	ENST00000342988	NM_005359.5	193	Gag/ag	5/12	0.277870812267915	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.290808775016054	1		545	566	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115885	8115886	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	170	623	0	ENST00000346208.3:c.1232dup	p.His411GlnfsTer96	p.H411Qfs*96	ENST00000346208		411	cac/cAac	6/6	1	2	FACETS	0.924	0.851	0.999	0.924	0.851	0.999	CLONAL	1	TRUE	1	0.471908371291676	2		623	780	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060868	38060869	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGAG	novel	NA	P-0039367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	204	719	0	ENST00000250448.2:c.1116_1120dup	p.His374ProfsTer17	p.H374Pfs*17	ENST00000250448	NM_004496.3	374	cac/cCTCTCac	2/2	1	2	FACETS	0.962	0.893	1	0.962	0.893	1	CLONAL	1	TRUE	1	0.471908371291676	2		719	899	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0039369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	194	691	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.281381895650272	2		691	1197	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	152	713	0	ENST00000322088.6:c.767C>A	p.Ser256Tyr	p.S256Y	ENST00000322088	NM_014225.5	256	tCc/tAc	6/15	0.0655487703965449	3	FACETS	1	0.95	1	0.529	0.483	0.578	INDETERMINATE	1	TRUE	1	0.281381895650272	3		713	1165	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419951	41419951	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	148	677	0	ENST00000373198.4:c.370G>A	p.Val124Met	p.V124M	ENST00000373198	NM_133170.3	124	Gtg/Atg	3/32	1	2	FACETS	0.984	0.897	1	0.984	0.897	1	CLONAL	1	TRUE	1	0.281381895650272	2		677	1069	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577096	+	protein_altering_variant	In_Frame_Ins	INS	-	-	TTT	novel	NA	P-0039369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1209	99	840	0	ENST00000269305.4:c.842_843insAAA	p.Asp281delinsGluAsn	p.D281delinsEN	ENST00000269305	NM_001126112.2	281	gac/gaAAAc	8/11	1	2	FACETS	0.538	0.478	0.602	0.538	0.478	0.602	SUBCLONAL	1	TRUE	1	0.281381895650272	2		840	1308	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507414	8507414	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	39	375	0	ENST00000356435.5:c.1564T>A	p.Phe522Ile	p.F522I	ENST00000356435		522	Ttc/Atc	11/35	1	2	FACETS	0.562	0.466	0.67	0.562	0.466	0.67	SUBCLONAL	1	TRUE	1	0.281381895650272	2		375	493	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440925	52440925	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1430317959	NA	P-0039370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	321	562	0	ENST00000460680.1:c.581-2A>G		p.X194_splice	ENST00000460680	NM_004656.3	194			0.786876776173433	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.786876776173433	1		562	481	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105554	30105554	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	195	651	0	ENST00000331968.5:c.1132G>T	p.Asp378Tyr	p.D378Y	ENST00000331968	NM_002742.2	378	Gac/Tac	7/18	1	2	FACETS	0.45	0.416	0.485	0.45	0.416	0.485	SUBCLONAL	1	TRUE	1	0.786876776173433	2		651	1102	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	62	174	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.825	0.715	0.944			1	INDETERMINATE	1	TRUE	NA	0.366446245903563	2		174	410	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0039372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	3467	845	2	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.366446245903563	23	FACETS	1	0.996	1	0.963	0.954	0.972	CLONAL	21	TRUE	1	0.366446245903563	23		847	4330	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0039372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	91	383	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	1	2	FACETS	0.976	0.869	1	0.976	0.869	1	CLONAL	1	TRUE	1	0.366446245903563	2		383	509	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775625	39775625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140222241	NA	P-0039372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	75	388	1	ENST00000288319.7:c.395C>T	p.Thr132Met	p.T132M	ENST00000288319	NM_182918.3	132	aCg/aTg	4/10	0.174717308607117	1	FACETS	0.998	0.881	1	0.998	0.881	1	INDETERMINATE	1	TRUE	0	0.366446245903563	1		389	335	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752870	57752870	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1338885665	NA	P-0039372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	66	492	0	ENST00000274289.3:c.1058A>G	p.Asp353Gly	p.D353G	ENST00000274289	NM_006622.3	353	gAt/gGt	8/14	1	2	FACETS	0.677	0.588	0.773	0.677	0.588	0.773	SUBCLONAL	1	TRUE	1	0.366446245903563	2		492	532	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0039374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	113	316	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.475536941394809	3	FACETS	0.789	0.716	0.863	0.789	0.716	0.863	SUBCLONAL	2	TRUE	1	0.475536941394809	3		316	373	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0039374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	117	338	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	0.475536941394809	3	FACETS	0.926	0.845	1	0.926	0.845	1	CLONAL	2	TRUE	1	0.475536941394809	3		338	329	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0039374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	59	309	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.475536941394809	3	FACETS	0.856	0.74	0.98	0.428	0.37	0.49	CLONAL	1	TRUE	1	0.475536941394809	3		309	359	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577520	7577520	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	251	679	0	ENST00000269305.4:c.761T>A	p.Ile254Asn	p.I254N	ENST00000269305	NM_001126112.2	254	aTc/aAc	7/11	0.471360853313071	2	FACETS	0.886	0.835	0.936	0.886	0.835	0.936	CLONAL	2	TRUE	0	0.475536941394809	2		679	596	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180838	106180838	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1382453941	NA	P-0039374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	65	426	0	ENST00000380013.4:c.3866G>A	p.Cys1289Tyr	p.C1289Y	ENST00000380013	NM_001127208.2	1289	tGt/tAt	7/11	0.475536941394809	3	FACETS	0.893	0.778	1	0.446	0.389	0.508	CLONAL	1	TRUE	1	0.475536941394809	3		426	379	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212439	5212439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150241840	NA	P-0039374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	264	853	1	ENST00000357368.4:c.4678G>A	p.Val1560Met	p.V1560M	ENST00000357368	NM_002850.3	1560	Gtg/Atg	31/38	0.298548249786742	4	FACETS	0.887	0.833	0.943	0.887	0.833	0.943	CLONAL	2	TRUE	2	0.475536941394809	4		854	923	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56787260	56787260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881925	NA	P-0039374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	89	684	0	ENST00000337432.4:c.746G>A	p.Arg249His	p.R249H	ENST00000337432	NM_058216.2	249	cGt/cAt	5/9	0.475536941394809	3	FACETS	0.93	0.828	1	0.465	0.414	0.52	CLONAL	1	TRUE	1	0.475536941394809	3		684	498	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939133	36939133	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs761312181	NA	P-0039374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	51	903	0	ENST00000361632.4:c.576C>A	p.His192Gln	p.H192Q	ENST00000361632		192	caC/caA	5/16	1	2	FACETS	0.303	0.257	0.354	0.303	0.257	0.354	SUBCLONAL	1	TRUE	1	0.475536941394809	2		903	707	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128016984	128016984	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	119	760	0	ENST00000285398.2:c.2105C>G	p.Ala702Gly	p.A702G	ENST00000285398	NM_000122.1	702	gCg/gGg	14/15	0.475536941394809	3	FACETS	0.833	0.752	0.918	0.416	0.376	0.459	CLONAL	1	TRUE	1	0.475536941394809	3		760	744	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120573	94120573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	70	454	0	ENST00000369303.4:c.478C>T	p.Leu160Phe	p.L160F	ENST00000369303	NM_004440.3	160	Ctt/Ttt	3/17	0.475536941394809	3	FACETS	0.925	0.81	1	0.462	0.405	0.524	CLONAL	1	TRUE	1	0.475536941394809	3		454	394	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412308	139412308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223043989	NA	P-0039374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	130	837	1	ENST00000277541.6:c.1337G>A	p.Gly446Asp	p.G446D	ENST00000277541	NM_017617.3	446	gGc/gAc	8/34	0.16070296017045	2	FACETS	0.724	0.657	0.794	0.362	0.328	0.397	INDETERMINATE	1	TRUE	0	0.475536941394809	2		838	755	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0039377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	293	813	2	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	0.547240130544895	1	FACETS	0.918	0.867	0.97	0.918	0.867	0.97	CLONAL	1	TRUE	0	0.547240130544895	1		815	847	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155903	119155903	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	249	686	0	ENST00000264033.4:c.1568C>A	p.Ala523Asp	p.A523D	ENST00000264033	NM_005188.3	523	gCt/gAt	11/16	1	2	FACETS	0.929	0.869	0.99	0.929	0.869	0.99	CLONAL	1	TRUE	1	0.547240130544895	2		686	980	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653271	29653271	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0039377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	91	283	1	ENST00000356175.3:c.5205+1G>C		p.X1735_splice	ENST00000356175	NM_000267.3	1735			0.547240130544895	1	FACETS	0.933	0.841	1	0.933	0.841	1	CLONAL	1	TRUE	0	0.547240130544895	1		284	259	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0039384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	457	755	1	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.841356347273399	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.841356347273399	1		756	629	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825539	50825539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762650238	NA	P-0039384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	344	457	0	ENST00000398568.2:c.2170G>A	p.Val724Ile	p.V724I	ENST00000398568	NM_001042412.1	724	Gtt/Att	14/18	0.841356347273399	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.841356347273399	1		457	466	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939048	48939048	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0039384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	226	341	0	ENST00000267163.4:c.880A>T	p.Lys294Ter	p.K294*	ENST00000267163	NM_000321.2	294	Aaa/Taa	9/27	0.841356347273399	1	FACETS	0.952	0.909	0.993	0.952	0.909	0.993	CLONAL	1	TRUE	0	0.841356347273399	1		341	327	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155008	55155008	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	273	540	0	ENST00000257290.5:c.2717A>G	p.Tyr906Cys	p.Y906C	ENST00000257290	NM_006206.4	906	tAc/tGc	20/23	0.168172838531794	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.841356347273399	0		540	679	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685313	86685328	+	frameshift_variant	Frame_Shift_Del	DEL	GAACGCTCAGTAATGA	GAACGCTCAGTAATGA	TGT	novel	NA	P-0039384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	159	234	1	ENST00000274376.6:c.3029_3044delinsTGT	p.Arg1010LeufsTer10	p.R1010Lfs*10	ENST00000274376	NM_002890.2	1010	cGAACGCTCAGTAATGAg/cTGTg	24/25	0.792347831342446	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.841356347273399	1		235	216	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440912	52440912	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1553645720	NA	P-0039385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	433	529	0	ENST00000460680.1:c.592G>T	p.Glu198Ter	p.E198*	ENST00000460680	NM_004656.3	198	Gag/Tag	8/17	0.568604051627046	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.568604051627046	2		529	622	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003206	143003206	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	144	450	0	ENST00000262992.4:c.2620C>T	p.Arg874Ter	p.R874*	ENST00000262992	NM_001101669.1	874	Cga/Tga	23/24	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.568604051627046	2		450	491	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	475	492	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.628600569262268	2	FACETS	0.975	0.942	1	0.975	0.942	1	CLONAL	2	TRUE	0	0.629283491642609	2		492	774	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	298	399	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	0.629283491642609	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.629283491642609	1		399	615	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577102	7577102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793881	NA	P-0039387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	413	741	1	ENST00000269305.4:c.836G>A	p.Gly279Glu	p.G279E	ENST00000269305	NM_001126112.2	279	gGg/gAg	8/11	0.629283491642609	1	FACETS	0.998	0.955	1	0.998	0.955	1	CLONAL	1	TRUE	0	0.629283491642609	1		742	901	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361743	70361744	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	426	410	1	ENST00000374080.3:c.6423dup	p.Leu2142AlafsTer23	p.L2142Afs*23	ENST00000374080		2140	cag/caGg	44/45	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.629283491642609	1		411	700	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	208	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.989	0.923	1	0.989	0.923	1	CLONAL	1	TRUE	1	0.621969301330801	2		174	676	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	197	453	0	ENST00000263967.3:c.3132T>G	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaG	21/21	1	2	FACETS	0.969	0.901	1	0.969	0.901	1	CLONAL	1	TRUE	1	0.621969301330801	2		453	654	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422845	12422845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	189	475	0	ENST00000287820.6:c.335C>T	p.Ser112Phe	p.S112F	ENST00000287820	NM_015869.4	112	tCt/tTt	3/7	1	2	FACETS	0.892	0.828	0.959	0.892	0.828	0.959	CLONAL	1	TRUE	1	0.621969301330801	2		475	681	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499642	18499642	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	263	625	0	ENST00000266497.5:c.1497C>G	p.Asn499Lys	p.N499K	ENST00000266497		499	aaC/aaG	10/31	1	2	FACETS	0.979	0.92	1	0.979	0.92	1	CLONAL	1	TRUE	1	0.621969301330801	2		625	864	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005420	29005420	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	32	408	0	ENST00000282397.4:c.841C>T	p.Arg281Ter	p.R281*	ENST00000282397	NM_002019.4	281	Cga/Tga	7/30	1	2	FACETS	0.177	0.143	0.215	0.177	0.143	0.215	SUBCLONAL	1	TRUE	1	0.621969301330801	2		408	582	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106519977	106519977	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	97	290	0	ENST00000359195.3:c.2405A>C	p.Lys802Thr	p.K802T	ENST00000359195	NM_002649.2	802	aAa/aCa	6/11	0.621969301330801	3	FACETS	0.805	0.72	0.894	0.402	0.36	0.447	CLONAL	1	TRUE	1	0.621969301330801	3		290	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0039389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	657	807	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.791365944522227	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.791365944522227	2		807	815	SUCCESS
APC	324	MSKCC	GRCh37	5	112175211	112175212	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	222	251	0	ENST00000257430.4:c.3924dup	p.Glu1309ArgfsTer6	p.E1309Rfs*6	ENST00000257430	NM_000038.5	1307	ata/atAa	16/16	0.753502250634987	2	FACETS	0.938	0.899	0.975	0.938	0.899	0.975	CLONAL	2	TRUE	0	0.791365944522227	2		251	299	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099397	27099397	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	162	590	0	ENST00000324856.7:c.3634C>T	p.Gln1212Ter	p.Q1212*	ENST00000324856	NM_006015.4	1212	Cag/Tag	14/20	0.584469401588848	1	FACETS	0.394	0.363	0.426	0.394	0.363	0.426	SUBCLONAL	1	TRUE	0	0.791365944522227	1		590	628	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120016	70120016	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1339655148	NA	P-0039389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	183	152	0	ENST00000245479.2:c.1018C>T	p.Gln340Ter	p.Q340*	ENST00000245479	NM_000346.3	340	Cag/Tag	3/3	0.78127698333814	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	3	TRUE	0	0.791365944522227	3		152	215	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115269668	115269668	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	137	597	0	ENST00000438362.2:c.1538A>T	p.Lys513Ile	p.K513I	ENST00000438362	NM_001242891.1	513	aAa/aTa	13/20	1	2	FACETS	0.476	0.434	0.521	0.476	0.434	0.521	SUBCLONAL	1	TRUE	1	0.791365944522227	2		597	727	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972683	25972683	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	495	480	0	ENST00000435504.4:c.1742G>T	p.Trp581Leu	p.W581L	ENST00000435504		581	tGg/tTg	12/13	0.413625699497031	3	FACETS	1	0.995	1	0.781	0.757	0.805	INDETERMINATE	2	TRUE	0	0.791365944522227	3		480	745	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0039390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	180	497	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.407291026826374	4	FACETS	0.981	0.926	1	0.981	0.926	1	CLONAL	4	TRUE	0	0.4340341832731	4		497	303	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs587781702	NA	P-0039390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	170	819	0	ENST00000269305.4:c.920-1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.394666015661631	2	FACETS	0.909	0.845	0.974	0.909	0.845	0.974	CLONAL	2	TRUE	0	0.4340341832731	2		819	431	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36823932	36823932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs945529881	NA	P-0039390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	94	822	2	ENST00000373129.3:c.250C>T	p.Arg84Trp	p.R84W	ENST00000373129	NM_032017.1	84	Cgg/Tgg	5/12	1	2	FACETS	0.866	0.774	0.964	0.866	0.774	0.964	CLONAL	1	TRUE	1	0.4340341832731	2		824	500	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964944	25964944	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	153	617	0	ENST00000435504.4:c.4262G>T	p.Cys1421Phe	p.C1421F	ENST00000435504		1421	tGc/tTc	13/13	0.4340341832731	3	FACETS	0.964	0.89	1	0.964	0.89	1	CLONAL	2	TRUE	1	0.4340341832731	3		617	445	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393175	393175	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139884486	NA	P-0039390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	140	581	0	ENST00000380956.4:c.23G>A	p.Arg8Gln	p.R8Q	ENST00000380956	NM_001195286.1	8	cGa/cAa	2/9	0.286756023296093	3	FACETS	0.833	0.765	0.905			1	CLONAL	2	TRUE	NA	0.4340341832731	3		581	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0039392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	157	517	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.238780523973439	2	FACETS	1	0.982	1	0.632	0.579	0.686	CLONAL	1	TRUE	0	0.329231174523069	2		517	755	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246436	105246436	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	307	626	0	ENST00000349310.3:c.164T>A	p.Phe55Tyr	p.F55Y	ENST00000349310	NM_001014432.1	55	tTc/tAc	4/15	0.238780523973439	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.329231174523069	2		626	804	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481403	140481403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913357	NA	P-0039392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	48	466	0	ENST00000288602.6:c.1405G>A	p.Gly469Arg	p.G469R	ENST00000288602	NM_004333.4	469	Gga/Aga	11/18	0.193828126319971	3	FACETS	0.803	0.68	0.938	0.401	0.34	0.469	INDETERMINATE	1	TRUE	1	0.329231174523069	3		466	423	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246445	105246445	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	321	654	0	ENST00000349310.3:c.155T>G	p.Leu52Arg	p.L52R	ENST00000349310	NM_001014432.1	52	cTc/cGc	4/15	0.238780523973439	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.329231174523069	2		654	847	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375266	15375275	+	frameshift_variant	Frame_Shift_Del	DEL	TAGGCCCAGT	TAGGCCCAGT	GAG	novel	NA	P-0039392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	95	684	3	ENST00000263377.2:c.1152_1161delinsCTC	p.Leu385SerfsTer14	p.L385Sfs*14	ENST00000263377	NM_058243.2	384	gcACTGGGCCTA/gcCTC	6/20	1	2	FACETS	0.768	0.684	0.858	0.768	0.684	0.858	SUBCLONAL	1	TRUE	1	0.329231174523069	2		687	751	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0039398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	415	436	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	0.799780768451939	5	FACETS	0.937	0.893	0.981			1	CLONAL	2	TRUE	NA	0.874006220262416	5		436	1171	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426274	49426274	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772102499	NA	P-0039398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	298	927	2	ENST00000301067.7:c.12214G>A	p.Asp4072Asn	p.D4072N	ENST00000301067	NM_003482.3	4072	Gac/Aac	39/54	0.6164118888785	3	FACETS	0.767	0.722	0.814	0.384	0.361	0.407	SUBCLONAL	1	TRUE	1	0.874006220262416	3		929	1277	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241964	133241964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	342	711	1	ENST00000320574.5:c.2392G>A	p.Glu798Lys	p.E798K	ENST00000320574	NM_006231.2	798	Gag/Aag	21/49	0.6164118888785	3	FACETS	1	0.956	1	0.505	0.478	0.533	CLONAL	1	TRUE	1	0.874006220262416	3		712	1113	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606174	81606174	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	259	539	0	ENST00000298171.2:c.844C>G	p.His282Asp	p.H282D	ENST00000298171	NM_000369.2	282	Cac/Gac	9/10	0.874006220262416	2	FACETS	1	0.961	1	0.51	0.482	0.538	CLONAL	1	TRUE	0	0.874006220262416	2		539	581	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576774	67576774	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	83	384	0	ENST00000274335.5:c.856C>T	p.Leu286Phe	p.L286F	ENST00000274335		286	Ctc/Ttc	6/15	0.389512169355106	3	FACETS	0.525	0.464	0.59	0.262	0.232	0.295	INDETERMINATE	1	TRUE	1	0.874006220262416	3		384	520	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199979	138199980	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0039398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	520	575	1	ENST00000237289.4:c.1397_1398delinsAA	p.Ser466Lys	p.S466K	ENST00000237289	NM_001270507.1	466	aGC/aAA	7/9	0.874006220262416	3	FACETS	0.95	0.917	0.982	0.95	0.917	0.982	CLONAL	2	TRUE	1	0.874006220262416	3		576	900	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942845	68942845	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	1953	614	1	ENST00000288368.4:c.657G>T	p.Glu219Asp	p.E219D	ENST00000288368	NM_024870.2	219	gaG/gaT	6/40	0.874006220262416	8	FACETS	1	0.987	1	1	0.987	1	CLONAL	6	TRUE	2	0.874006220262416	8		615	2693	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94226074	94226079	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TAAAAA	TAAAAA	-	novel	NA	P-0039398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	164	138	0	ENST00000323929.3:c.-105-7_-105-2del		p.X35_splice	ENST00000323929	NM_005591.3	35			0.874006220262416	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.874006220262416	2		138	185	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0039399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	78	638	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.765	0.673	0.863	0.765	0.673	0.863	SUBCLONAL	1	TRUE	1	0.372760689555782	2		639	547	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120668	115120668	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	149	745	0	ENST00000257566.3:c.338G>C	p.Trp113Ser	p.W113S	ENST00000257566	NM_016569.3	113	tGg/tCg	1/8	1	2	FACETS	0.85	0.776	0.927	0.85	0.776	0.927	CLONAL	1	TRUE	1	0.372760689555782	2		745	941	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0039400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	49	523	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.23	NA		523	525	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0039400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	93	596	0	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	1	2	FACETS	0.907	0.805	1	0.907	0.805	1	CLONAL	1	TRUE	1	0.23	2		596	892	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581275	48581306	+	frameshift_variant	Frame_Shift_Del	DEL	GACATACAGCACCCCAGCTCTGTTAGCCCCAT	GACATACAGCACCCCAGCTCTGTTAGCCCCAT	TTA	novel	NA	P-0039400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	50	505	2	ENST00000342988.3:c.579_610delinsTTA	p.Glu193AspfsTer3	p.E193Dfs*3	ENST00000342988	NM_005359.5	193	gaGACATACAGCACCCCAGCTCTGTTAGCCCCATct/gaTTAct	5/12	1	2	FACETS	0.637	0.539	0.744	0.637	0.539	0.744	SUBCLONAL	1	TRUE	1	0.23	2		507	683	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140507764	140507764	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	11	333	0	ENST00000288602.6:c.707A>C	p.Asn236Thr	p.N236T	ENST00000288602	NM_004333.4	236	aAc/aCc	5/18	1	2	FACETS	0.669	0.464	0.921	0.669	0.464	0.921	SUBCLONAL	1	TRUE	1	0.23	2		333	143	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	201	687	0	ENST00000269305.4:c.853G>T	p.Glu285Ter	p.E285*	ENST00000269305	NM_001126112.2	285	Gag/Tag	8/11	0.321473321317653	1	FACETS	0.897	0.83	0.966	0.897	0.83	0.966	CLONAL	1	TRUE	0	0.341665059601754	1		687	1088	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092829	27092829	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	75	585	0	ENST00000324856.7:c.2850G>T	p.Met950Ile	p.M950I	ENST00000324856	NM_006015.4	950	atG/atT	9/20	1	2	FACETS	0.433	0.378	0.492	0.433	0.378	0.492	SUBCLONAL	1	TRUE	1	0.341665059601754	2		585	1015	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830815	156830815	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	142	425	0	ENST00000524377.1:c.89C>A	p.Ser30Tyr	p.S30Y	ENST00000524377	NM_002529.3	30	tCt/tAt	1/17	0.108875315834553	4	FACETS	1	0.987	1	0.749	0.684	0.818	INDETERMINATE	1	TRUE	2	0.341665059601754	4		425	744	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927414	245927414	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	83	577	1	ENST00000388985.4:c.1114C>G	p.Gln372Glu	p.Q372E	ENST00000388985		372	Caa/Gaa	11/12	0.108875315834553	4	FACETS	0.613	0.539	0.692	0.306	0.269	0.346	INDETERMINATE	1	TRUE	2	0.341665059601754	4		578	1064	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219232	94219232	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	104	453	0	ENST00000323929.3:c.172G>T	p.Gly58Cys	p.G58C	ENST00000323929	NM_005591.3	58	Ggt/Tgt	4/20	1	2	FACETS	0.971	0.871	1	0.971	0.871	1	CLONAL	1	TRUE	1	0.341665059601754	2		453	627	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121799	108121799	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	95	380	0	ENST00000278616.4:c.1607G>T	p.Cys536Phe	p.C536F	ENST00000278616	NM_000051.3	536	tGt/tTt	10/63	1	2	FACETS	0.884	0.788	0.986	0.884	0.788	0.986	CLONAL	1	TRUE	1	0.341665059601754	2		380	629	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396689	396689	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	145	637	0	ENST00000262320.3:c.337G>T	p.Asp113Tyr	p.D113Y	ENST00000262320	NM_003502.3	113	Gac/Tac	2/11	1	2	FACETS	0.912	0.831	0.996	0.912	0.831	0.996	CLONAL	1	TRUE	1	0.341665059601754	2		637	931	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777819	3777819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1279	131	843	0	ENST00000262367.5:c.7229C>T	p.Pro2410Leu	p.P2410L	ENST00000262367	NM_004380.2	2410	cCc/cTc	31/31	1	2	FACETS	0.544	0.492	0.599	0.544	0.492	0.599	SUBCLONAL	1	TRUE	1	0.341665059601754	2		843	1410	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063702	67063702	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	95	344	0	ENST00000412916.2:c.151G>A	p.Gly51Ser	p.G51S	ENST00000412916		51	Ggc/Agc	2/6	0.317452768170594	1	FACETS	0.878	0.785	0.977	0.878	0.785	0.977	CLONAL	1	TRUE	0	0.341665059601754	1		344	525	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024476	16024476	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	76	464	0	ENST00000268712.3:c.1742G>T	p.Arg581Leu	p.R581L	ENST00000268712	NM_006311.3	581	cGt/cTt	16/46	1	2	FACETS	0.543	0.475	0.616	0.543	0.475	0.616	SUBCLONAL	1	TRUE	1	0.341665059601754	2		464	820	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585401	29585401	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1256219174	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	145	540	0	ENST00000356175.3:c.4150G>A	p.Val1384Ile	p.V1384I	ENST00000356175	NM_000267.3	1384	Gta/Ata	31/57	1	2	FACETS	0.82	0.747	0.897	0.82	0.747	0.897	CLONAL	1	TRUE	1	0.341665059601754	2		540	1035	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41251813	41251813	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	98	597	0	ENST00000357654.3:c.526A>G	p.Thr176Ala	p.T176A	ENST00000357654	NM_007294.3	176	Acg/Gcg	7/23	1	2	FACETS	0.538	0.479	0.602	0.538	0.479	0.602	SUBCLONAL	1	TRUE	1	0.341665059601754	2		597	1066	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222807	5222807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	263	727	0	ENST00000357368.4:c.2996G>A	p.Gly999Asp	p.G999D	ENST00000357368	NM_002850.3	999	gGc/gAc	18/38	0.253026217871854	2	FACETS	0.792	0.743	0.842	0.792	0.743	0.842	SUBCLONAL	2	TRUE	0	0.341665059601754	2		727	972	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703630	47703631	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	132	542	2	ENST00000233146.2:c.2130_2131delinsTT	p.Arg711Ter	p.R711*	ENST00000233146	NM_000251.2	710	gcCCga/gcTTga	13/16	1	2	FACETS	0.924	0.839	1	0.924	0.839	1	CLONAL	1	TRUE	1	0.341665059601754	2		544	836	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617406	158617406	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	260	430	0	ENST00000263640.3:c.1250G>T	p.Arg417Leu	p.R417L	ENST00000263640	NM_001105.4	417	cGg/cTg	9/11	0.341665059601754	2	FACETS	0.927	0.871	0.984	0.927	0.871	0.984	CLONAL	2	TRUE	0	0.341665059601754	2		430	821	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794402	242794402	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	357	725	0	ENST00000334409.5:c.540C>A	p.Ser180Arg	p.S180R	ENST00000334409	NM_005018.2	180	agC/agA	3/5	0.341665059601754	2	FACETS	0.914	0.867	0.962	0.914	0.867	0.962	CLONAL	2	TRUE	0	0.341665059601754	2		725	1143	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543648	9543648	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	126	513	0	ENST00000353224.5:c.1506C>A	p.His502Gln	p.H502Q	ENST00000353224	NM_177990.2	502	caC/caA	6/10	1	2	FACETS	0.88	0.797	0.968	0.88	0.797	0.968	CLONAL	1	TRUE	1	0.341665059601754	2		513	838	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735473	40735473	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	151	645	0	ENST00000373198.4:c.3400T>G	p.Cys1134Gly	p.C1134G	ENST00000373198	NM_133170.3	1134	Tgc/Ggc	25/32	1	2	FACETS	0.818	0.747	0.893	0.818	0.747	0.893	CLONAL	1	TRUE	1	0.341665059601754	2		645	1080	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747141	40747141	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	132	466	0	ENST00000373198.4:c.2942-1G>T		p.X981_splice	ENST00000373198	NM_133170.3	981			1	2	FACETS	0.963	0.875	1	0.963	0.875	1	CLONAL	1	TRUE	1	0.341665059601754	2		466	802	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770575	40770575	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	118	506	0	ENST00000373198.4:c.2807G>T	p.Arg936Leu	p.R936L	ENST00000373198	NM_133170.3	936	cGa/cTa	19/32	1	2	FACETS	0.839	0.757	0.926	0.839	0.757	0.926	CLONAL	1	TRUE	1	0.341665059601754	2		506	823	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514555	41514555	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	118	497	1	ENST00000373198.4:c.106G>T	p.Glu36Ter	p.E36*	ENST00000373198	NM_133170.3	36	Gag/Tag	2/32	1	2	FACETS	0.797	0.718	0.88	0.797	0.718	0.88	SUBCLONAL	1	TRUE	1	0.341665059601754	2		498	867	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57474040	57474040	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	86	359	0	ENST00000371085.3:c.257G>T	p.Gly86Val	p.G86V	ENST00000371085	NM_000516.4	86	gGt/gTt	3/13	1	2	FACETS	0.724	0.641	0.814	0.724	0.641	0.814	SUBCLONAL	1	TRUE	1	0.341665059601754	2		359	695	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221705	22221705	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	36	95	1	ENST00000215832.6:c.26C>T	p.Ala9Val	p.A9V	ENST00000215832	NM_002745.4	9	gCg/gTg	1/9	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.341665059601754	2		96	165	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458608	12458608	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	231	555	0	ENST00000287820.6:c.1225G>T	p.Asp409Tyr	p.D409Y	ENST00000287820	NM_015869.4	409	Gac/Tac	6/7	0.253026217871854	2	FACETS	0.754	0.704	0.805	0.754	0.704	0.805	SUBCLONAL	2	TRUE	0	0.341665059601754	2		555	897	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936639	49936639	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	271	663	0	ENST00000296474.3:c.1288A>T	p.Ser430Cys	p.S430C	ENST00000296474	NM_002447.2	430	Agt/Tgt	2/20	0.253026217871854	2	FACETS	0.776	0.729	0.825	0.776	0.729	0.825	SUBCLONAL	2	TRUE	0	0.341665059601754	2		663	1022	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169993046	169993046	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	107	371	0	ENST00000295797.4:c.676A>T	p.Ser226Cys	p.S226C	ENST00000295797	NM_002740.5	226	Agt/Tgt	8/18	0.253026217871854	2	FACETS	1	0.982	1	0.709	0.639	0.781	CLONAL	1	TRUE	0	0.341665059601754	2		371	442	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356240	66356240	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs753971619	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	156	575	1	ENST00000273854.3:c.1257C>A	p.Ser419Arg	p.S419R	ENST00000273854	NM_004439.5	419	agC/agA	5/18	1	2	FACETS	0.887	0.812	0.967	0.887	0.812	0.967	CLONAL	1	TRUE	1	0.341665059601754	2		576	1029	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081512	143081512	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	119	390	0	ENST00000262992.4:c.1562G>A	p.Trp521Ter	p.W521*	ENST00000262992	NM_001101669.1	521	tGg/tAg	15/24	0.321473321317653	1	FACETS	0.971	0.879	1	0.971	0.879	1	CLONAL	1	TRUE	0	0.341665059601754	1		390	595	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628395	187628395	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	224	742	0	ENST00000441802.2:c.2587A>G	p.Thr863Ala	p.T863A	ENST00000441802	NM_005245.3	863	Aca/Gca	2/27	0.321473321317653	1	FACETS	0.982	0.914	1	0.982	0.914	1	CLONAL	1	TRUE	0	0.341665059601754	1		742	1107	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294268	1294268	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	214	733	0	ENST00000310581.5:c.733G>C	p.Glu245Gln	p.E245Q	ENST00000310581	NM_198253.2	245	Gag/Cag	2/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.341665059601754	2		733	1086	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675783	30675783	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1268	297	790	2	ENST00000376406.3:c.2573A>G	p.Asp858Gly	p.D858G	ENST00000376406	NM_014641.2	858	gAc/gGc	8/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.341665059601754	2		792	1565	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180997	32180997	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	181	698	0	ENST00000375023.3:c.2353A>T	p.Arg785Trp	p.R785W	ENST00000375023	NM_004557.3	785	Agg/Tgg	15/30	1	2	FACETS	0.89	0.82	0.964	0.89	0.82	0.964	CLONAL	1	TRUE	1	0.341665059601754	2		698	1190	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184760	32184760	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	177	601	1	ENST00000375023.3:c.1823C>A	p.Pro608Gln	p.P608Q	ENST00000375023	NM_004557.3	608	cCa/cAa	11/30	1	2	FACETS	0.896	0.824	0.971	0.896	0.824	0.971	CLONAL	1	TRUE	1	0.341665059601754	2		602	1157	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286881	33286881	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	162	607	0	ENST00000374542.5:c.2056G>T	p.Val686Leu	p.V686L	ENST00000374542	NM_001141970.1	686	Gtg/Ttg	7/8	1	2	FACETS	0.854	0.782	0.929	0.854	0.782	0.929	CLONAL	1	TRUE	1	0.341665059601754	2		607	1111	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444362	50444362	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1443120422	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	170	447	0	ENST00000331340.3:c.292G>C	p.Asp98His	p.D98H	ENST00000331340	NM_006060.4	98	Gac/Cac	4/8	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.341665059601754	2		447	859	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151174431	151174431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	70	396	0	ENST00000262187.5:c.263C>T	p.Thr88Ile	p.T88I	ENST00000262187	NM_005614.3	88	aCa/aTa	4/8	1	2	FACETS	0.584	0.508	0.665	0.584	0.508	0.665	SUBCLONAL	1	TRUE	1	0.341665059601754	2		396	702	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540164	23540164	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	92	378	0	ENST00000380871.4:c.239C>A	p.Pro80His	p.P80H	ENST00000380871	NM_006167.3	80	cCc/cAc	1/2	1	2	FACETS	0.948	0.844	1	0.948	0.844	1	CLONAL	1	TRUE	1	0.341665059601754	2		378	568	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965473	68965473	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	102	634	0	ENST00000288368.4:c.1085G>T	p.Arg362Leu	p.R362L	ENST00000288368	NM_024870.2	362	cGg/cTg	9/40	1	2	FACETS	0.678	0.606	0.756	0.678	0.606	0.756	SUBCLONAL	1	TRUE	1	0.341665059601754	2		634	880	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981465	70981465	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	195	871	1	ENST00000276594.2:c.631C>A	p.Pro211Thr	p.P211T	ENST00000276594	NM_024504.3	211	Ccc/Acc	2/8	1	2	FACETS	0.915	0.845	0.988	0.915	0.845	0.988	CLONAL	1	TRUE	1	0.341665059601754	2		872	1247	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981627	70981627	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1152	100	851	1	ENST00000276594.2:c.469G>T	p.Ala157Ser	p.A157S	ENST00000276594	NM_024504.3	157	Gct/Tct	2/8	1	2	FACETS	0.468	0.416	0.523	0.468	0.416	0.523	SUBCLONAL	1	TRUE	1	0.341665059601754	2		852	1252	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389369	8389369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	42	459	1	ENST00000356435.5:c.4249G>A	p.Asp1417Asn	p.D1417N	ENST00000356435		1417	Gat/Aat	26/35	0.203361587156935	1	FACETS	0.295	0.245	0.35	0.295	0.245	0.35	INDETERMINATE	1	TRUE	0	0.341665059601754	1		460	691	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	87	562	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.203361587156935	1	FACETS	0.494	0.437	0.556	0.494	0.437	0.556	INDETERMINATE	1	TRUE	0	0.341665059601754	1		562	854	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972614	76972614	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	155	414	0	ENST00000373344.5:c.127A>T	p.Asn43Tyr	p.N43Y	ENST00000373344	NM_000489.3	43	Aac/Tac	2/35	0.321473321317653	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.341665059601754	1		414	743	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627234	86627238	+	frameshift_variant	Frame_Shift_Del	DEL	TTATC	TTATC	-	rs1060503441	NA	P-0039402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	87	398	0	ENST00000274376.6:c.613_617del	p.Leu205LysfsTer4	p.L205Kfs*4	ENST00000274376	NM_002890.2	203	agTTATCtt/agtt	2/25	1	2	FACETS	0.739	0.657	0.827	0.739	0.657	0.827	SUBCLONAL	1	TRUE	1	0.467876600927968	2		398	503	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438067	49438067	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886043414	NA	P-0039402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	104	685	1	ENST00000301067.7:c.5104C>T	p.Arg1702Ter	p.R1702*	ENST00000301067	NM_003482.3	1702	Cga/Tga	21/54	0.0801544476563669	4	FACETS	0.791	0.708	0.879	0.395	0.354	0.44	INDETERMINATE	1	TRUE	2	0.467876600927968	4		686	825	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720869	89720869	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1564568689	NA	P-0039402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	116	373	0	ENST00000371953.3:c.1023del	p.Phe341LeufsTer3	p.F341Lfs*3	ENST00000371953	NM_000314.4	340	aaT/aa	8/9	0.467876600927968	1	FACETS	0.954	0.868	1	0.954	0.868	1	CLONAL	1	TRUE	0	0.467876600927968	1		373	398	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372252	55372252	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	119	633	0	ENST00000297316.4:c.942G>C	p.Gln314His	p.Q314H	ENST00000297316	NM_022454.3	314	caG/caC	2/2	0.467876600927968	1	FACETS	0.738	0.669	0.81	0.738	0.669	0.81	SUBCLONAL	1	TRUE	0	0.467876600927968	1		633	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0039403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	539	691	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.606141411677683	2	FACETS	0.916	0.886	0.946	0.916	0.886	0.946	CLONAL	2	TRUE	0	0.657452189797681	2		691	895	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120502116	120502116	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	212	488	1	ENST00000256646.2:c.1925G>T	p.Cys642Phe	p.C642F	ENST00000256646	NM_024408.3	642	tGt/tTt	12/34	0.335775065784744	1	FACETS	0.745	0.697	0.794	0.745	0.697	0.794	INDETERMINATE	1	TRUE	0	0.657452189797681	1		489	581	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870249	155870249	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1359	179	613	0	ENST00000368323.3:c.590C>G	p.Ser197Cys	p.S197C	ENST00000368323	NM_006912.5	197	tCt/tGt	6/6	0.253237546076888	5	FACETS	0.703	0.646	0.763	0.141	0.129	0.153	INDETERMINATE	1	TRUE	0	0.657452189797681	5		613	1538	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263956	104263956	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	136	268	1	ENST00000369902.3:c.47C>T	p.Pro16Leu	p.P16L	ENST00000369902	NM_016169.3	16	cCg/cTg	1/12	0.335775065784744	1	FACETS	0.586	0.536	0.637	0.586	0.536	0.637	INDETERMINATE	1	TRUE	0	0.657452189797681	1		269	474	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790038	40790038	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	143	608	0	ENST00000373198.4:c.2693C>G	p.Thr898Arg	p.T898R	ENST00000373198	NM_133170.3	898	aCg/aGg	18/32	1	2	FACETS	0.509	0.464	0.556	0.509	0.464	0.556	SUBCLONAL	1	TRUE	1	0.657452189797681	2		608	855	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55597497	55597497	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	265	434	3	ENST00000288135.5:c.2145C>G	p.Ser715Arg	p.S715R	ENST00000288135	NM_000222.2	715	agC/agG	15/21	0.657452189797681	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.657452189797681	1		437	466	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0039404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	117	755	1	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	1	0.957	1	1	0.99	1	CLONAL	2	FALSE	1	0.205312322753318	2		756	519	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555525857	NA	P-0039404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	109	701	1	ENST00000269305.4:c.596G>A	p.Gly199Glu	p.G199E	ENST00000269305	NM_001126112.2	199	gGa/gAa	6/11	0.125655866242272	3	FACETS	1	0.977	1	0.664	0.595	0.736	CLONAL	1	FALSE	1	0.205312322753318	3		702	882	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198384	108198384	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs148432863	NA	P-0039404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	32	426	1	ENST00000278616.4:c.6988C>G	p.Leu2330Val	p.L2330V	ENST00000278616	NM_000051.3	2330	Cta/Gta	48/63	0.117129709834343	3	FACETS	0.718	0.582	0.871	0.359	0.291	0.436	INDETERMINATE	1	FALSE	1	0.205312322753318	3		427	479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	175	762	0	ENST00000269305.4:c.880del	p.Glu294SerfsTer51	p.E294Sfs*51	ENST00000269305	NM_001126112.2	294	Gag/ag	8/11	0.125655866242272	3	FACETS	0.842	0.774	0.913	0.842	0.774	0.913	CLONAL	2	FALSE	1	0.205312322753318	3		762	1116	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678476	88678476	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	47	643	1	ENST00000360948.2:c.1060C>A	p.Gln354Lys	p.Q354K	ENST00000360948	NM_001012338.2	354	Caa/Aaa	9/19	1	2	FACETS	0.641	0.54	0.754	0.641	0.54	0.754	SUBCLONAL	1	FALSE	1	0.205312322753318	2		644	714	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422910	49422910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123719	NA	P-0039404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	77	674	3	ENST00000301067.7:c.14185C>T	p.Arg4729Trp	p.R4729W	ENST00000301067	NM_003482.3	4729	Cgg/Tgg	44/54	1	2	FACETS	0.87	0.763	0.986	0.87	0.763	0.986	CLONAL	1	FALSE	1	0.205312322753318	2		677	862	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33446619	33446619	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	39	601	0	ENST00000345365.6:c.14G>T	p.Arg5Met	p.R5M	ENST00000345365	NM_002878.3	5	aGg/aTg	1/10	0.125655866242272	3	FACETS	0.556	0.459	0.664	0.278	0.229	0.332	SUBCLONAL	1	FALSE	1	0.205312322753318	3		601	754	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749455	41749455	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	173	536	0	ENST00000226382.2:c.340G>T	p.Glu114Ter	p.E114*	ENST00000226382	NM_003924.3	114	Gaa/Taa	2/3	0.117129709834343	3	FACETS	1	0.976	1	1	0.976	1	INDETERMINATE	2	FALSE	1	0.205312322753318	3		536	810	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133901	55133901	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	28	339	0	ENST00000257290.5:c.1114G>T	p.Glu372Ter	p.E372*	ENST00000257290	NM_006206.4	372	Gaa/Taa	7/23	0.117129709834343	3	FACETS	0.67	0.535	0.824	0.335	0.267	0.412	INDETERMINATE	1	FALSE	1	0.205312322753318	3		339	449	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547398	106547398	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	54	378	0	ENST00000369096.4:c.635A>T	p.Tyr212Phe	p.Y212F	ENST00000369096	NM_001198.3	212	tAt/tTt	4/7	1	2	FACETS	0.985	0.842	1	0.985	0.842	1	CLONAL	1	FALSE	1	0.205312322753318	2		378	534	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163909	152163909	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	41	481	1	ENST00000206249.3:c.630G>T	p.Lys210Asn	p.K210N	ENST00000206249	NM_000125.3	210	aaG/aaT	2/8	1	2	FACETS	0.827	0.689	0.981	0.827	0.689	0.981	CLONAL	1	FALSE	1	0.205312322753318	2		482	483	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92244602	92244602	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0039404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	38	286	0	ENST00000265734.4:c.835-2A>C		p.X279_splice	ENST00000265734	NM_001259.6	279			0.205312322753318	3	FACETS	1	0.914	1	0.588	0.487	0.7	CLONAL	1	FALSE	1	0.205312322753318	3		286	347	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8526641	8526641	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	60	403	0	ENST00000356435.5:c.554G>T	p.Gly185Val	p.G185V	ENST00000356435		185	gGt/gTt	6/35	0.125655866242272	3	FACETS	1	0.901	1	1	0.901	1	CLONAL	2	FALSE	1	0.205312322753318	3		403	308	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615121	100615121	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	84	533	0	ENST00000308731.7:c.794C>A	p.Pro265His	p.P265H	ENST00000308731	NM_000061.2	265	cCt/cAt	9/19	0.205312322753318	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	0	0.205312322753318	1		533	548	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242482	+	protein_altering_variant	In_Frame_Del	DEL	GAATTAAGAGAAGCAAC	GAATTAAGAGAAGCAAC	AT	rs727504402	NA	P-0039405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	134	486	2	ENST00000275493.2:c.2236_2252delinsAT	p.Glu746_Thr751delinsIle	p.E746_T751delinsI	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCAACa/ATa	19/28	0.364850504415232	3	FACETS	1	0.935	1	0.517	0.47	0.567	CLONAL	1	TRUE	1	0.377335515332317	3		488	816	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249505	153249505	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	151	499	0	ENST00000281708.4:c.1273T>C	p.Trp425Arg	p.W425R	ENST00000281708	NM_033632.3	425	Tgg/Cgg	9/12	0.354240089660864	4	FACETS	1	0.933	1	1	0.933	1	CLONAL	2	TRUE	2	0.377550481666853	4		499	542	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443760	52443760	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1553646367	NA	P-0039411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	159	580	0	ENST00000460680.1:c.38-1G>A		p.X13_splice	ENST00000460680	NM_004656.3	13			0.191988836877865	6	FACETS	0.837	0.771	0.905	0.837	0.771	0.905	INDETERMINATE	3	TRUE	3	0.377550481666853	6		580	589	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439269	52439269	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	GCTGGGGC	novel	NA	P-0039411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	188	653	0	ENST00000460680.1:c.973delinsGCCCCAGC	p.Ser325AlafsTer75	p.S325Afs*75	ENST00000460680	NM_004656.3	325	Tcc/GCCCCAGCcc	11/17	0.191988836877865	6	FACETS	0.87	0.807	0.934	0.87	0.807	0.934	INDETERMINATE	3	TRUE	3	0.377550481666853	6		653	670	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0039412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	679	595	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.816739511154088	2	FACETS	0.961	0.94	0.981	0.961	0.94	0.981	CLONAL	2	TRUE	0	0.816739511154088	2		595	865	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252155	226252155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553260624	NA	P-0039412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	139	168	0	ENST00000366813.1:c.103G>A	p.Gly35Arg	p.G35R	ENST00000366813		35	Ggg/Agg	1/3	0.803524705953114	3	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	1	0.816739511154088	3		168	239	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131161	55131161	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	237	509	0	ENST00000257290.5:c.704G>T	p.Cys235Phe	p.C235F	ENST00000257290	NM_006206.4	235	tGt/tTt	5/23	0.131036075289867	3	FACETS	0.771	0.727	0.816	0.771	0.727	0.816	INDETERMINATE	2	TRUE	1	0.816739511154088	3		509	530	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907706	76907707	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0039412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	176	263	0	ENST00000373344.5:c.4454_4455del	p.Lys1485ArgfsTer2	p.K1485Rfs*2	ENST00000373344	NM_000489.3	1485	aAA/a	15/35	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.816739511154088	1		263	220	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551647	150551647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	31	538	0	ENST00000369026.2:c.360G>A	p.Met120Ile	p.M120I	ENST00000369026	NM_021960.4	120	atG/atA	1/3	0.364872948458241	3	FACETS	0.273	0.22	0.334	0.137	0.11	0.167	SUBCLONAL	1	TRUE	1	0.486377363506143	3		538	580	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577151	7577156	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	TACCAC	TACCAC	-	novel	NA	P-0039416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	332	670	1	ENST00000269305.4:c.783-1_787del		p.X261_splice	ENST00000269305	NM_001126112.2	261		8/11	0.480731592321428	2	FACETS	0.855	0.813	0.898	0.855	0.813	0.898	CLONAL	2	TRUE	0	0.506756802438022	2		671	766	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	protein_altering_variant	In_Frame_Ins	INS	-	-	GTT	rs1554350347	NA	P-0039416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	537	612	0	ENST00000275493.2:c.2308_2309insGTT	p.Asp770delinsGlyTyr	p.D770delinsGY	ENST00000275493	NM_005228.3	770	gac/gGTTac	20/28	0.506756802438022	5	FACETS	0.957	0.92	0.995	0.957	0.92	0.995	CLONAL	3	TRUE	2	0.506756802438022	5		612	1299	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246490567	246490567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	127	554	1	ENST00000388985.4:c.467G>A	p.Arg156Lys	p.R156K	ENST00000388985		156	aGa/aAa	5/12	0.489256708719148	3	FACETS	0.855	0.775	0.938	0.427	0.387	0.469	CLONAL	1	TRUE	1	0.506756802438022	3		555	735	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0039418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	90	497	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.191083765935112	2	FACETS	1	0.957	1	0.578	0.514	0.647	CLONAL	1	TRUE	0	0.264612052301499	2		497	588	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0039418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	31	254	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.0687884182084673	3	FACETS	0.758	0.614	0.921	0.379	0.307	0.461	INDETERMINATE	1	TRUE	1	0.264612052301499	3		254	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0039418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	91	675	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	0.264612052301499	1	FACETS	0.836	0.742	0.936	0.836	0.742	0.936	CLONAL	1	TRUE	0	0.264612052301499	1		675	714	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806180	1806181	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760502257	NA	P-0039418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	85	734	1	ENST00000260795.2:c.1206dup	p.Lys403GlnfsTer93	p.K403Qfs*93	ENST00000260795		400	agc/agCc	8/17	1	2	FACETS	0.728	0.642	0.82	0.728	0.642	0.82	SUBCLONAL	1	TRUE	1	0.264612052301499	2		735	883	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517532	176517532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200146267	NA	P-0039418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	130	865	4	ENST00000292408.4:c.233G>A	p.Arg78His	p.R78H	ENST00000292408	NM_213647.1	78	cGt/cAt	3/18	NA	2	FACETS	1	0.922	1			1	INDETERMINATE	1	TRUE	NA	0.264612052301499	2		869	964	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	134	492	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.928	0.849	1	0.928	0.849	1	CLONAL	1	TRUE	1	0.584364485691694	2		492	494	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415622	49415622	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	98	343	0	ENST00000301067.7:c.16555G>T	p.Asp5519Tyr	p.D5519Y	ENST00000301067	NM_003482.3	5519	Gat/Tat	54/54	1	2	FACETS	0.814	0.731	0.901	0.814	0.731	0.901	CLONAL	1	TRUE	1	0.584364485691694	2		343	412	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560489	65560490	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0039420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	126	467	0	ENST00000358664.4:c.107_108delinsCT	p.Arg36Thr	p.R36T	ENST00000358664	NM_002382.4	36	aGG/aCT	3/5	0.584364485691694	1	FACETS	0.834	0.764	0.906	0.834	0.764	0.906	CLONAL	1	TRUE	0	0.584364485691694	1		467	366	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041420	42041420	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	170	491	0	ENST00000219905.7:c.5615G>C	p.Gly1872Ala	p.G1872A	ENST00000219905	NM_001164273.1	1872	gGg/gCg	17/24	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.584364485691694	2		491	543	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131267	17131267	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	267	818	0	ENST00000285071.4:c.185G>T	p.Ser62Ile	p.S62I	ENST00000285071	NM_144997.5	62	aGc/aTc	4/14	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.584364485691694	2		818	863	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989580	212989580	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	112	328	0	ENST00000342788.4:c.131A>T	p.Gln44Leu	p.Q44L	ENST00000342788	NM_005235.2	44	cAg/cTg	2/28	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.584364485691694	2		328	359	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162111	47162111	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	116	344	0	ENST00000409792.3:c.4015G>T	p.Glu1339Ter	p.E1339*	ENST00000409792	NM_014159.6	1339	Gag/Tag	3/21	1	2	FACETS	0.964	0.876	1	0.964	0.876	1	CLONAL	1	TRUE	1	0.584364485691694	2		344	412	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204836	128204836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	249	878	3	ENST00000341105.2:c.605C>T	p.Ala202Val	p.A202V	ENST00000341105	NM_032638.4	202	gCa/gTa	3/6	1	2	FACETS	0.936	0.877	0.997	0.936	0.877	0.997	CLONAL	1	TRUE	1	0.584364485691694	2		881	910	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566480	139566480	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	232	829	0	ENST00000308874.7:c.739C>G	p.Leu247Val	p.L247V	ENST00000308874		247	Ctc/Gtc	9/10	1	2	FACETS	0.968	0.905	1	0.968	0.905	1	CLONAL	1	TRUE	1	0.584364485691694	2		829	820	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152853826	152853826	+	synonymous_variant	Silent	SNP	G	G	T	novel	NA	P-0039420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	51	55	0	ENST00000406277.2:c.738C>A	p.Pro246=	p.P246=	ENST00000406277	NM_152274.4	246	ccC/ccA	7/7	1	1	FACETS	0.772	0.693	0.847	1	0.977	1	SUBCLONAL	2	TRUE	0	0.584364485691694	1		55	80	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0039421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	35	638	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.986	0.811	1	0.986	0.811	1	CLONAL	1	TRUE	1	0.227512259800301	2		639	312	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098944	178098944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	46	330	0	ENST00000397062.3:c.101G>A	p.Arg34Gln	p.R34Q	ENST00000397062	NM_006164.4	34	cGa/cAa	2/5	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.227512259800301	2		330	370	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760106	133760106	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2229071	NA	P-0039421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	138	727	1	ENST00000318560.5:c.2429C>T	p.Pro810Leu	p.P810L	ENST00000318560	NM_005157.4	810	cCg/cTg	11/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.227512259800301	2		728	934	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443703	49443703	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0039421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	95	686	0	ENST00000301067.7:c.3668C>G	p.Ser1223Ter	p.S1223*	ENST00000301067	NM_003482.3	1223	tCa/tGa	11/54	0.211001314806746	1	FACETS	0.849	0.755	0.949	0.849	0.755	0.949	CLONAL	1	TRUE	0	0.227512259800301	1		686	872	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552921	106552921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	107	810	0	ENST00000369096.4:c.886C>T	p.Arg296Trp	p.R296W	ENST00000369096	NM_001198.3	296	Cgg/Tgg	5/7	1	2	FACETS	0.807	0.722	0.898	0.807	0.722	0.898	CLONAL	1	TRUE	1	0.227512259800301	2		810	1165	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890189	76890189	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	23	402	0	ENST00000373344.5:c.4705C>T	p.Gln1569Ter	p.Q1569*	ENST00000373344	NM_000489.3	1569	Cag/Tag	17/35	0.211001314806746	1	FACETS	0.512	0.399	0.643	0.512	0.399	0.643	SUBCLONAL	1	TRUE	0	0.227512259800301	1		402	350	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218934	193218934	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	25	294	0	ENST00000367435.3:c.1492G>C	p.Glu498Gln	p.E498Q	ENST00000367435	NM_024529.4	498	Gaa/Caa	16/17	1	2	FACETS	0.939	0.743	1	0.939	0.743	1	CLONAL	1	TRUE	1	0.227512259800301	2		294	234	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139193	108139193	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	53	549	0	ENST00000278616.4:c.2695G>C	p.Asp899His	p.D899H	ENST00000278616	NM_000051.3	899	Gac/Cac	18/63	1	2	FACETS	0.801	0.682	0.93	0.801	0.682	0.93	CLONAL	1	TRUE	1	0.227512259800301	2		549	582	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434079	49434079	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	83	699	0	ENST00000301067.7:c.7474G>C	p.Gly2492Arg	p.G2492R	ENST00000301067	NM_003482.3	2492	Ggg/Cgg	31/54	0.211001314806746	1	FACETS	0.815	0.719	0.919	0.815	0.719	0.919	CLONAL	1	TRUE	0	0.227512259800301	1		699	793	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916767	48916780	+	frameshift_variant	Frame_Shift_Del	DEL	GGGAATCTGTATCT	GGGAATCTGTATCT	-	novel	NA	P-0039421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	16	381	0	ENST00000267163.4:c.297_310del	p.Trp99CysfsTer6	p.W99Cfs*6	ENST00000267163	NM_000321.2	99	tgGGGAATCTGTATCTtt/tgtt	3/27	0.227512259800301	1	FACETS	0.66	0.489	0.862	0.66	0.489	0.862	SUBCLONAL	1	TRUE	0	0.227512259800301	1		381	189	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285176	198285176	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	50	388	0	ENST00000335508.6:c.391G>C	p.Glu131Gln	p.E131Q	ENST00000335508	NM_012433.2	131	Gag/Cag	4/25	1	2	FACETS	0.901	0.765	1	0.901	0.765	1	CLONAL	1	TRUE	1	0.227512259800301	2		388	488	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41554426	41554426	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	46	424	0	ENST00000263253.7:c.3512C>G	p.Ser1171Cys	p.S1171C	ENST00000263253	NM_001429.3	1171	tCt/tGt	19/31	1	2	FACETS	0.627	0.527	0.738	0.627	0.527	0.738	SUBCLONAL	1	TRUE	1	0.227512259800301	2		424	645	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197395	26197395	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	39	333	0	ENST00000356476.2:c.84G>C	p.Lys28Asn	p.K28N	ENST00000356476		28	aaG/aaC	1/1	0.227512259800301	3	FACETS	0.768	0.636	0.916	0.256	0.212	0.306	CLONAL	1	TRUE	0	0.227512259800301	3		333	497	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41276095	41276098	+	missense_variant	Missense_Mutation	ONP	GAAG	GAAG	AAAA	novel	NA	P-0039421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	39	451	2	ENST00000357654.3:c.16_19delinsTTTT	p.Leu6_Arg7delinsPheCys	p.L6_R7delinsFC	ENST00000357654	NM_007294.3	6	CTTCgc/TTTTgc	2/23	0.227512259800301	1	FACETS	0.741	0.615	0.882	0.741	0.615	0.882	SUBCLONAL	1	TRUE	0	0.227512259800301	1		453	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555526097	NA	P-0039427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	344	773	3	ENST00000269305.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000269305	NM_001126112.2	167	Cag/Tag	5/11	0.624793229407951	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.624793229407951	1		776	709	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0039427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	80	278	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	0.797	0.998	0.895	0.797	0.998	CLONAL	1	TRUE	1	0.624793229407951	2		278	286	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0039427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	243	529	7	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	0.624793229407951	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.624793229407951	1		536	490	SUCCESS
APC	324	MSKCC	GRCh37	5	112162834	112162834	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	148	370	0	ENST00000257430.4:c.1438C>T	p.Gln480Ter	p.Q480*	ENST00000257430	NM_000038.5	480	Caa/Taa	12/16	1	2	FACETS	0.911	0.837	0.987	0.911	0.837	0.987	CLONAL	1	TRUE	1	0.624793229407951	2		370	520	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248608	10248608	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375225009	NA	P-0039427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	290	688	10	ENST00000340748.4:c.4145C>T	p.Ser1382Leu	p.S1382L	ENST00000340748		1382	tCg/tTg	35/40	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.624793229407951	2		698	862	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573544	48573544	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	132	268	0	ENST00000342988.3:c.128T>G	p.Leu43Trp	p.L43W	ENST00000342988	NM_005359.5	43	tTg/tGg	2/12	0.624793229407951	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.624793229407951	1		268	285	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	145	492	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.398745682808706	3	FACETS	0.752	0.689	0.817	0.752	0.689	0.817	SUBCLONAL	2	TRUE	1	0.398745682808706	3		492	580	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0039428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	46	861	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	1	2	FACETS	0.311	0.261	0.366	0.311	0.261	0.366	SUBCLONAL	1	TRUE	1	0.398745682808706	2		861	742	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077427	30077427	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0039428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	25	203	0	ENST00000338641.4:c.1575-1G>C		p.X525_splice	ENST00000338641	NM_000268.3	525			1	2	FACETS	0.54	0.428	0.669	0.54	0.428	0.669	SUBCLONAL	1	TRUE	1	0.398745682808706	2		203	232	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264625	1264625	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	39	805	0	ENST00000310581.5:c.2737G>T	p.Ala913Ser	p.A913S	ENST00000310581	NM_198253.2	913	Gcc/Tcc	11/16	1	2	FACETS	0.297	0.246	0.355	0.297	0.246	0.355	SUBCLONAL	1	TRUE	1	0.398745682808706	2		805	658	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152857997	152857997	+	synonymous_variant	Silent	SNP	G	G	A	rs201983563	NA	P-0039428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	11	156	0	ENST00000406277.2:c.618C>T	p.Pro206=	p.P206=	ENST00000406277	NM_152274.4	206	ccC/ccT	6/7	1	1	FACETS	0.421	0.293	0.576	0.421	0.293	0.576	SUBCLONAL	1	TRUE	0	0.398745682808706	1		156	105	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945669	206945669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	34	475	0	ENST00000423557.1:c.112C>A	p.Pro38Thr	p.P38T	ENST00000423557	NM_000572.2	38	Cct/Act	1/5	1	2	FACETS	0.317	0.258	0.383	0.317	0.258	0.383	SUBCLONAL	1	TRUE	1	0.398745682808706	2		475	538	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785677	50785677	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	40	609	0	ENST00000398568.2:c.667A>G	p.Met223Val	p.M223V	ENST00000398568	NM_001042412.1	223	Atg/Gtg	4/18	1	2	FACETS	0.332	0.275	0.396	0.332	0.275	0.396	SUBCLONAL	1	TRUE	1	0.398745682808706	2		609	604	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610247	10610247	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	34	728	0	ENST00000171111.5:c.463G>T	p.Val155Phe	p.V155F	ENST00000171111	NM_203500.1	155	Gtc/Ttc	2/6	0.215816565943019	0	FACETS	1	0.856	1			1	CLONAL	1	FALSE	0	0.215816565943019	0		728	236	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562628	29562628	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1555615431	NA	P-0039430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	10	327	0	ENST00000356175.3:c.3709-1G>A		p.X1237_splice	ENST00000356175	NM_000267.3	1237			0.215816565943019	3	FACETS	1	0.79	1	1	0.881	1	CLONAL	3	FALSE	1	0.215816565943019	3		327	30	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221976	1221976	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs730881984	NA	P-0039430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1259	250	595	0	ENST00000326873.7:c.891G>T	p.Arg297Ser	p.R297S	ENST00000326873	NM_000455.4	297	agG/agT	7/10	0.215816565943019	8	FACETS	0.843	0.786	0.902	0.506	0.472	0.541	CLONAL	3	FALSE	3	0.215816565943019	8		595	1509	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752723	42752724	+	missense_variant	Missense_Mutation	DNP	CG	CG	AT	novel	NA	P-0039430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	156	621	0	ENST00000222329.4:c.1540_1541delinsAT	p.Arg514Ile	p.R514I	ENST00000222329	NM_006494.2	514	CGt/ATt	4/4	0.215816565943019	5	FACETS	1	0.987	1	0.364	0.332	0.397	CLONAL	1	FALSE	1	0.215816565943019	5		621	1315	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665329	138665329	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	65	696	0	ENST00000330315.3:c.236G>T	p.Gly79Val	p.G79V	ENST00000330315	NM_023067.3	79	gGc/gTc	1/1	0.215816565943019	3	FACETS	0.62	0.536	0.712	0.31	0.268	0.356	SUBCLONAL	1	FALSE	1	0.215816565943019	3		696	1076	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	58	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.4	2		174	257	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0039438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	47	318	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.521	0.44	0.61	0.521	0.44	0.61	SUBCLONAL	1	TRUE	1	0.4	2		318	451	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987107	36987115	+	inframe_deletion	In_Frame_Del	DEL	GCGCTTCCT	GCGCTTCCT	-	novel	NA	P-0039438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	68	484	0	ENST00000354822.5:c.574_582del	p.Lys193_Arg195del	p.K193_R195del	ENST00000354822	NM_001079668.2	192	AGGAAGCGC/-	3/3	1	2	FACETS	0.609	0.53	0.694	0.609	0.53	0.694	SUBCLONAL	1	TRUE	1	0.4	2		484	558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0039439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	138	440	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	0.901	0.82	0.985	0.901	0.82	0.985	CLONAL	1	TRUE	1	0.38016265836517	2		440	806	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0039439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	191	559	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.975	0.901	1	0.975	0.901	1	CLONAL	1	TRUE	1	0.38016265836517	2		559	1031	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716327	52716327	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	173	442	2	ENST00000322088.6:c.771G>C	p.Trp257Cys	p.W257C	ENST00000322088	NM_014225.5	257	tgG/tgC	6/15	0.168600520511841	0	FACETS	0.698	0.643	0.755			1	INDETERMINATE	1	TRUE	0	0.38016265836517	0		444	808	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952073	178952073	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519937	NA	P-0039439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	19	273	1	ENST00000263967.3:c.3128T>C	p.Met1043Thr	p.M1043T	ENST00000263967	NM_006218.2	1043	aTg/aCg	21/21	1	2	FACETS	0.223	0.168	0.287	0.223	0.168	0.287	SUBCLONAL	1	TRUE	1	0.38016265836517	2		274	449	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31424569	31424585	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGCGCAGGTCCTGGAAA	CGCGCAGGTCCTGGAAA	-	novel	NA	P-0039439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	102	497	0	ENST00000344624.3:c.3217-7_3226del		p.X1073_splice	ENST00000344624		1073		25/33	0.131782906705123	3	FACETS	0.664	0.593	0.74	0.332	0.296	0.37	INDETERMINATE	1	TRUE	1	0.38016265836517	3		497	962	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	188	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.717581755542806	2		174	511	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0039440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	282	687	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.997	0.941	1	0.997	0.941	1	CLONAL	1	TRUE	1	0.717581755542806	2		687	788	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713568	30713568	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs751587466	NA	P-0039440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	194	551	0	ENST00000295754.5:c.893A>G	p.Asn298Ser	p.N298S	ENST00000295754	NM_003242.5	298	aAt/aGt	4/7	1	2	FACETS	0.872	0.811	0.934	0.872	0.811	0.934	CLONAL	1	TRUE	1	0.717581755542806	2		551	620	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	49	525	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.968	0.835	1	0.968	0.835	1	CLONAL	1	TRUE	1	0.61	2		528	166	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	23	300	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.61	2		300	55	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	89	673	3	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.871	0.78	0.967	0.871	0.78	0.967	CLONAL	1	TRUE	1	0.61	2		676	335	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	32	329	0	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	0.833	0.689	0.988	0.833	0.689	0.988	CLONAL	1	TRUE	1	0.61	2		329	126	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	14	254	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	1	0.783	1	1	0.783	1	CLONAL	1	TRUE	1	0.61	2		255	44	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	18	314	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.757	0.583	0.951	0.757	0.583	0.951	CLONAL	1	TRUE	1	0.61	2		314	78	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	97	763	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	1	2	FACETS	0.828	0.744	0.916	0.828	0.744	0.916	CLONAL	1	TRUE	1	0.61	2		763	384	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165213	47165213	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	15	255	0	ENST00000409792.3:c.913del	p.Thr305GlnfsTer35	p.T305Qfs*35	ENST00000409792	NM_014159.6	305	Aca/ca	3/21	1	2	FACETS	1	0.82	1	1	0.82	1	CLONAL	1	TRUE	1	0.61	2		255	45	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354008	15354008	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	26	365	1	ENST00000263377.2:c.2872del	p.Leu958CysfsTer110	p.L958Cfs*110	ENST00000263377	NM_058243.2	958	Ctg/tg	14/20	1	2	FACETS	0.661	0.531	0.804	0.661	0.531	0.804	SUBCLONAL	1	TRUE	1	0.61	2		366	129	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755554	39755554	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	25	675	3	ENST00000288319.7:c.1211del	p.Pro404ArgfsTer25	p.P404Rfs*25	ENST00000288319	NM_182918.3	404	cCg/cg	10/10	0.108286252219463	3	FACETS	0.392	0.309	0.486	0.196	0.154	0.243	INDETERMINATE	1	TRUE	1	0.61	3		678	273	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	58	392	13	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.61	2		405	162	SUCCESS
APC	324	MSKCC	GRCh37	5	112173830	112173831	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	23	316	0	ENST00000257430.4:c.2544dup	p.Asp849ArgfsTer2	p.D849Rfs*2	ENST00000257430	NM_000038.5	847	gaa/gAaa	16/16	1	2	FACETS	1	0.808	1	1	0.808	1	CLONAL	1	TRUE	1	0.61	2		316	75	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422384	47422384	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	113	760	1	ENST00000377045.4:c.23del	p.Pro8LeufsTer26	p.P8Lfs*26	ENST00000377045	NM_001654.4	6	ggC/gg	2/16	1	2	FACETS	0.972	0.883	1	0.972	0.883	1	CLONAL	1	TRUE	1	0.61	2		761	381	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390666	139390667	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	150	1438	0	ENST00000277541.6:c.7524dup	p.Phe2509LeufsTer7	p.F2509Lfs*7	ENST00000277541	NM_017617.3	2508	-/C	34/34	1	2	FACETS	0.796	0.73	0.864	0.796	0.73	0.864	SUBCLONAL	1	TRUE	1	0.61	2		1438	618	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274211	10274211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779149309	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	109	626	0	ENST00000330684.3:c.58G>A	p.Gly20Ser	p.G20S	ENST00000330684	NM_001134407.1	20	Ggt/Agt	2/13	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.61	2		626	341	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795407	39795407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371043321	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	144	1061	3	ENST00000288319.7:c.313G>A	p.Gly105Ser	p.G105S	ENST00000288319	NM_182918.3	105	Ggc/Agc	3/10	0.108286252219463	3	FACETS	1	0.985	1	0.664	0.61	0.719	INDETERMINATE	1	TRUE	1	0.61	3		1064	464	SUCCESS
APC	324	MSKCC	GRCh37	5	112151245	112151246	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs1114167567	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	29	446	0	ENST00000257430.4:c.893_894del	p.His298LeufsTer28	p.H298Lfs*28	ENST00000257430	NM_000038.5	296	agCAca/agca	9/16	1	2	FACETS	0.834	0.683	0.998	0.834	0.683	0.998	CLONAL	1	TRUE	1	0.61	2		446	114	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37056036	37056036	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs267607789	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	18	326	1	ENST00000231790.2:c.790+1G>A		p.X264_splice	ENST00000231790	NM_000249.3	264			1	2	FACETS	0.984	0.766	1	0.984	0.766	1	CLONAL	1	TRUE	1	0.61	2		327	60	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003812	45003812	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	115	689	0	ENST00000558401.1:c.67+1G>A		p.X23_splice	ENST00000558401	NM_004048.2	23			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.61	2		689	335	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276958	123276958	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	20	363	1	ENST00000358487.5:c.959C>T	p.Thr320Met	p.T320M	ENST00000358487	NM_000141.4	320	aCg/aTg	8/18	1	2	FACETS	0.596	0.463	0.747	0.596	0.463	0.747	SUBCLONAL	1	TRUE	1	0.61	2		364	110	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162945	38162945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs185811622	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	11	547	0	ENST00000317025.8:c.2261C>T	p.Ser754Leu	p.S754L	ENST00000317025	NM_023034.1	754	tCg/tTg	13/24	1	2	FACETS	0.221	0.153	0.306	0.221	0.153	0.306	SUBCLONAL	1	TRUE	1	0.61	2		547	163	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424466	47424466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	85	955	0	ENST00000377045.4:c.386G>A	p.Gly129Asp	p.G129D	ENST00000377045	NM_001654.4	129	gGc/gAc	5/16	1	2	FACETS	0.954	0.854	1	0.954	0.854	1	CLONAL	1	TRUE	1	0.61	2		955	292	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831295	72831295	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113529778	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	74	580	0	ENST00000268489.5:c.5286A>T	p.Gln1762His	p.Q1762H	ENST00000268489	NM_006885.3	1762	caA/caT	9/10	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.61	2		580	227	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921637	39921637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1288166926	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	100	713	0	ENST00000378444.4:c.4183C>T	p.Arg1395Trp	p.R1395W	ENST00000378444	NM_001123385.1	1395	Cgg/Tgg	10/15	1	2	FACETS	0.997	0.9	1	0.997	0.9	1	CLONAL	1	TRUE	1	0.61	2		713	329	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164466	36164466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	91	608	0	ENST00000300305.3:c.1409C>T	p.Ala470Val	p.A470V	ENST00000300305		470	gCg/gTg	8/8	0.108286252219463	3	FACETS	1	0.956	1	0.563	0.504	0.624	INDETERMINATE	1	TRUE	1	0.61	3		608	346	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348283	89348283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781186923	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	171	1297	0	ENST00000301030.4:c.4667C>T	p.Ala1556Val	p.A1556V	ENST00000301030	NM_001256183.1	1556	gCg/gTg	9/13	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.61	2		1297	552	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219552	133219552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373468985	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	114	938	1	ENST00000320574.5:c.4582G>A	p.Ala1528Thr	p.A1528T	ENST00000320574	NM_006231.2	1528	Gcc/Acc	36/49	0.108286252219463	3	FACETS	1	0.98	1	0.65	0.591	0.712	INDETERMINATE	1	TRUE	1	0.61	3		939	375	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047135	77047135	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	46	580	0	ENST00000356341.3:c.1409T>C	p.Leu470Pro	p.L470P	ENST00000356341	NM_002576.4	470	cTg/cCg	13/15	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.61	2		580	150	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49419977	49419977	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762350923	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	73	665	2	ENST00000301067.7:c.15772G>A	p.Ala5258Thr	p.A5258T	ENST00000301067	NM_003482.3	5258	Gcc/Acc	48/54	0.108286252219463	3	FACETS	1	0.956	1	0.585	0.517	0.656	INDETERMINATE	1	TRUE	1	0.61	3		667	267	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366670	40366670	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	55	779	0	ENST00000397332.2:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000397332	NM_001033082.2	176	tGt/tAt	2/3	1	2	FACETS	0.435	0.372	0.502	0.435	0.372	0.502	SUBCLONAL	1	TRUE	1	0.61	2		779	415	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206733	102206733	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	22	335	0	ENST00000263464.3:c.1365del	p.Gln456AsnfsTer3	p.Q456Nfs*3	ENST00000263464	NM_001165.4	454	cTt/ct	7/9	1	2	FACETS	0.744	0.588	0.916	0.744	0.588	0.916	CLONAL	1	TRUE	1	0.61	2		335	97	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438025	49438025	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	166	1158	2	ENST00000301067.7:c.5146G>A	p.Ala1716Thr	p.A1716T	ENST00000301067	NM_003482.3	1716	Gca/Aca	21/54	0.108286252219463	3	FACETS	1	0.987	1	0.66	0.61	0.711	INDETERMINATE	1	TRUE	1	0.61	3		1160	538	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061867	38061867	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs571158363	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	150	1377	2	ENST00000250448.2:c.122T>C	p.Met41Thr	p.M41T	ENST00000250448	NM_004496.3	41	aTg/aCg	2/2	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.61	2		1379	455	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763458	59763458	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	15	536	1	ENST00000259008.2:c.2644G>A	p.Ala882Thr	p.A882T	ENST00000259008	NM_032043.2	882	Gct/Act	19/20	1	2	FACETS	0.546	0.406	0.709	0.546	0.406	0.709	SUBCLONAL	1	TRUE	1	0.61	2		537	90	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222155	2222155	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	111	1402	0	ENST00000398665.3:c.2987A>G	p.Asn996Ser	p.N996S	ENST00000398665	NM_032482.2	996	aAc/aGc	24/28	1	2	FACETS	0.509	0.458	0.563	0.509	0.458	0.563	SUBCLONAL	1	TRUE	1	0.61	2		1402	715	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602934	10602934	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	144	1147	0	ENST00000171111.5:c.644C>A	p.Ala215Asp	p.A215D	ENST00000171111	NM_203500.1	215	gCc/gAc	3/6	1	2	FACETS	0.86	0.788	0.934	0.86	0.788	0.934	CLONAL	1	TRUE	1	0.61	2		1147	549	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271565	15271565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	180	1652	0	ENST00000263388.2:c.6874C>T	p.Leu2292Phe	p.L2292F	ENST00000263388	NM_000435.2	2292	Ctt/Ttt	33/33	1	2	FACETS	0.852	0.788	0.917	0.852	0.788	0.917	CLONAL	1	TRUE	1	0.61	2		1652	693	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211367	36211367	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	66	911	0	ENST00000222270.7:c.1122del	p.Asp375ThrfsTer12	p.D375Tfs*12	ENST00000222270	NM_014727.1	373	gAa/ga	3/37	1	2	FACETS	0.807	0.708	0.912	0.807	0.708	0.912	CLONAL	1	TRUE	1	0.61	2		911	268	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795220	42795220	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	135	1230	0	ENST00000575354.2:c.2303del	p.Pro768ArgfsTer156	p.P768Rfs*156	ENST00000575354	NM_015125.3	767	aCc/ac	10/20	1	2	FACETS	0.986	0.903	1	0.986	0.903	1	CLONAL	1	TRUE	1	0.61	2		1230	449	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735448	40735448	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	112	1015	0	ENST00000373198.4:c.3425G>T	p.Arg1142Met	p.R1142M	ENST00000373198	NM_133170.3	1142	aGg/aTg	25/32	1	2	FACETS	0.925	0.839	1	0.925	0.839	1	CLONAL	1	TRUE	1	0.61	2		1015	397	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090099	37090099	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	22	504	0	ENST00000231790.2:c.1988A>T	p.Glu663Val	p.E663V	ENST00000231790	NM_000249.3	663	gAg/gTg	17/19	1	2	FACETS	0.65	0.512	0.804	0.65	0.512	0.804	SUBCLONAL	1	TRUE	1	0.61	2		504	111	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205043	128205043	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	151	1110	3	ENST00000341105.2:c.398G>A	p.Gly133Asp	p.G133D	ENST00000341105	NM_032638.4	133	gGc/gAc	3/6	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.61	2		1113	412	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575441	67575441	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs112487959	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	23	254	0	ENST00000274335.5:c.514G>A	p.Val172Met	p.V172M	ENST00000274335		172	Gtg/Atg	4/15	1	2	FACETS	0.725	0.576	0.89	0.725	0.576	0.89	SUBCLONAL	1	TRUE	1	0.61	2		254	104	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502242	157502242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	100	767	0	ENST00000346085.5:c.3275C>T	p.Ala1092Val	p.A1092V	ENST00000346085	NM_020732.3	1092	gCc/gTc	12/20	0.108286252219463	3	FACETS	0.871	0.782	0.966	0.436	0.391	0.483	INDETERMINATE	1	TRUE	1	0.61	3		767	491	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859569	151859569	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138747124	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	26	504	1	ENST00000262189.6:c.11093C>T	p.Thr3698Met	p.T3698M	ENST00000262189	NM_170606.2	3698	aCg/aTg	43/59	0.108286252219463	3	FACETS	0.818	0.657	0.997	0.409	0.328	0.499	INDETERMINATE	1	TRUE	1	0.61	3		505	136	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635156	87635156	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	84	726	0	ENST00000277120.3:c.2208G>A	p.Met736Ile	p.M736I	ENST00000277120		736	atG/atA	18/19	1	2	FACETS	0.886	0.79	0.985	0.886	0.79	0.985	CLONAL	1	TRUE	1	0.61	2		726	311	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396205	139396205	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	162	1140	0	ENST00000277541.6:c.5633G>T	p.Gly1878Val	p.G1878V	ENST00000277541	NM_017617.3	1878	gGg/gTg	30/34	1	2	FACETS	0.906	0.836	0.979	0.906	0.836	0.979	CLONAL	1	TRUE	1	0.61	2		1140	586	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932047	39932047	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	27	1080	0	ENST00000378444.4:c.2552A>G	p.Asp851Gly	p.D851G	ENST00000378444	NM_001123385.1	851	gAt/gGt	4/15	1	2	FACETS	0.171	0.135	0.211	0.171	0.135	0.211	SUBCLONAL	1	TRUE	1	0.61	2		1080	519	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0039442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	30	497	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.843	0.678	1	0.843	0.678	1	CLONAL	1	TRUE	1	0.16	2		497	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0039442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	38	611	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.796	0.656	0.952	0.796	0.656	0.952	CLONAL	1	TRUE	1	0.16	2		611	597	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0039442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	31	530	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.16	2		530	357	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851646	134851646	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757558701	NA	P-0039442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	28	594	1	ENST00000398015.3:c.1052G>A	p.Arg351Gln	p.R351Q	ENST00000398015	NM_004441.4	351	cGg/cAg	5/16	1	2	FACETS	0.778	0.621	0.957	0.778	0.621	0.957	CLONAL	1	TRUE	1	0.16	2		595	450	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624290	89624290	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660420	NA	P-0039442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	36	554	2	ENST00000371953.3:c.64G>T	p.Asp22Tyr	p.D22Y	ENST00000371953	NM_000314.4	22	Gac/Tac	1/9	1	2	FACETS	0.821	0.674	0.987	0.821	0.674	0.987	CLONAL	1	TRUE	1	0.16	2		556	548	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604658	55604658	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778433	NA	P-0039442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	45	550	2	ENST00000288135.5:c.2866C>T	p.Arg956Trp	p.R956W	ENST00000288135	NM_000222.2	956	Cgg/Tgg	21/21	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.16	2		552	525	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273297	18273297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1470167636	NA	P-0039442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	30	524	1	ENST00000222254.8:c.1090G>A	p.Glu364Lys	p.E364K	ENST00000222254	NM_005027.3	364	Gag/Aag	9/16	1	2	FACETS	0.876	0.706	1	0.876	0.706	1	CLONAL	1	TRUE	1	0.16	2		525	428	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530159	212530159	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs769719990	NA	P-0039442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	20	339	0	ENST00000342788.4:c.1760C>G	p.Pro587Arg	p.P587R	ENST00000342788	NM_005235.2	587	cCa/cGa	15/28	1	2	FACETS	0.646	0.493	0.826	0.646	0.493	0.826	SUBCLONAL	1	TRUE	1	0.16	2		339	387	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891313	151891313	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0039442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	51	416	0	ENST00000262189.6:c.4540+1G>C		p.X1514_splice	ENST00000262189	NM_170606.2	1514			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.16	2		416	487	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130342	11130342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	398	823	1	ENST00000358026.2:c.2581G>A	p.Glu861Lys	p.E861K	ENST00000358026	NM_001128849.1	861	Gag/Aag	18/36	0.546458225613808	3	FACETS	0.832	0.795	0.869	0.832	0.795	0.869	CLONAL	2	TRUE	1	0.716389470200705	3		824	907	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191547	10191547	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	303	556	0	ENST00000256474.2:c.540del	p.Ile180MetfsTer22	p.I180Mfs*22	ENST00000256474	NM_000551.3	180	atC/at	3/3	0.464938739865184	3	FACETS	1	0.972	1	0.685	0.653	0.717	CLONAL	2	TRUE	0	0.716389470200705	3		556	559	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098625	47098625	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	354	721	0	ENST00000409792.3:c.6649del	p.Leu2217PhefsTer31	p.L2217Ffs*31	ENST00000409792	NM_014159.6	2217	Ctt/tt	15/21	0.464938739865184	3	FACETS	0.97	0.927	1	0.647	0.618	0.675	CLONAL	2	TRUE	0	0.716389470200705	3		721	692	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651405	52651405	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	285	611	0	ENST00000394830.3:c.1691del	p.Glu564GlyfsTer5	p.E564Gfs*5	ENST00000394830	NM_018313.4	564	gAg/gg	15/30	NA	2	FACETS	0.759	0.723	0.795			1	INDETERMINATE	2	TRUE	NA	0.716389470200705	2		611	524	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151935881	151935881	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	23	11	0	ENST00000262189.6:c.2563C>A	p.Pro855Thr	p.P855T	ENST00000262189	NM_170606.2	855	Cca/Aca	15/59	0.677885004614945	3	FACETS	0.938	0.812	1	1	0.953	1	CLONAL	3	TRUE	1	0.716389470200705	3		11	31	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	58	492	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.137532829693347	3	FACETS	0.942	0.809	1	0.471	0.404	0.544	INDETERMINATE	1	TRUE	1	0.23	3		492	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0039445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	100	833	3	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.23	2		836	857	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938468	44938468	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1556341546	NA	P-0039445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	40	476	0	ENST00000377967.4:c.3016C>T	p.Gln1006Ter	p.Q1006*	ENST00000377967	NM_021140.2	1006	Cag/Tag	20/29	0.262679983462097	1	FACETS	0.46	0.381	0.548	0.46	0.381	0.548	SUBCLONAL	1	TRUE	0	0.23	1		476	669	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519988	NA	P-0039446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	382	750	0	ENST00000269305.4:c.808T>C	p.Phe270Leu	p.F270L	ENST00000269305	NM_001126112.2	270	Ttt/Ctt	8/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.832038009545784	2		750	884	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579718	7579718	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	260	657	0	ENST00000269305.4:c.78del	p.Pro27LeufsTer17	p.P27Lfs*17	ENST00000269305	NM_001126112.2	26	ctT/ct	3/11	1	2	FACETS	0.819	0.771	0.869	0.819	0.771	0.869	CLONAL	1	TRUE	1	0.832038009545784	2		657	763	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524238	18524238	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	347	528	0	ENST00000266497.5:c.1751del	p.Pro584GlnfsTer14	p.P584Qfs*14	ENST00000266497		584	Cca/ca	11/31	0.160702011171795	2	FACETS	1	0.989	1	0.563	0.536	0.589	INDETERMINATE	1	TRUE	0	0.832038009545784	2		528	741	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061206	38061235	+	inframe_deletion	In_Frame_Del	DEL	GCGCAAGTAGCAGCCGTTCTCGAACATGTT	GCGCAAGTAGCAGCCGTTCTCGAACATGTT	-	novel	NA	P-0039446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	247	543	0	ENST00000250448.2:c.754_783del	p.Asn252_Arg261del	p.N252_R261del	ENST00000250448	NM_004496.3	252	AACATGTTCGAGAACGGCTGCTACTTGCGC/-	2/2	1	2	FACETS	0.856	0.804	0.908	0.856	0.804	0.908	CLONAL	1	TRUE	1	0.832038009545784	2		543	694	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059169	42059170	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0039446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	223	462	0	ENST00000219905.7:c.8895dup	p.Thr2966HisfsTer33	p.T2966Hfs*33	ENST00000219905	NM_001164273.1	2963	-/C	24/24	1	2	FACETS	0.91	0.853	0.968	0.91	0.853	0.968	CLONAL	1	TRUE	1	0.832038009545784	2		462	589	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0039447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	164	318	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.826	0.765	0.889	0.826	0.765	0.889	CLONAL	1	TRUE	1	0.810122749928965	2		318	490	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0039447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	209	349	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.810122749928965	2		351	464	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266769	18266769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778478327	NA	P-0039447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	322	696	0	ENST00000222254.8:c.80C>T	p.Pro27Leu	p.P27L	ENST00000222254	NM_005027.3	27	cCc/cTc	2/16	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.810122749928965	2		696	703	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169935	32169935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142477287	NA	P-0039447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	307	952	2	ENST00000375023.3:c.3673C>T	p.Arg1225Trp	p.R1225W	ENST00000375023	NM_004557.3	1225	Cgg/Tgg	21/30	1	2	FACETS	0.914	0.865	0.964	0.914	0.865	0.964	CLONAL	1	TRUE	1	0.810122749928965	2		954	829	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763500	41763500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	257	553	0	ENST00000301178.4:c.2299C>T	p.Arg767Cys	p.R767C	ENST00000301178	NM_021913.4	767	Cgc/Tgc	19/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.810122749928965	2		553	625	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123246934	123246934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554907364	NA	P-0039447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	205	471	0	ENST00000358487.5:c.1991G>A	p.Arg664Gln	p.R664Q	ENST00000358487	NM_000141.4	664	cGg/cAg	15/18	0.810122749928965	1	FACETS	0.938	0.891	0.984	0.938	0.891	0.984	CLONAL	1	TRUE	0	0.810122749928965	1		471	321	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262528	16262528	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1369676611	NA	P-0039447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	161	374	0	ENST00000375759.3:c.9793G>A	p.Gly3265Ser	p.G3265S	ENST00000375759	NM_015001.2	3265	Ggt/Agt	11/15	0.674537942474584	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.810122749928965	1		374	226	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248495	59248495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	263	633	0	ENST00000371222.2:c.248C>T	p.Ser83Phe	p.S83F	ENST00000371222	NM_002228.3	83	tCc/tTc	1/1	1	2	FACETS	0.918	0.865	0.972	0.918	0.865	0.972	CLONAL	1	TRUE	1	0.810122749928965	2		633	707	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105240317	105240317	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	36	724	0	ENST00000349310.3:c.634G>A	p.Ala212Thr	p.A212T	ENST00000349310	NM_001014432.1	212	Gcc/Acc	9/15	1	2	FACETS	0.131	0.107	0.159	0.131	0.107	0.159	SUBCLONAL	1	TRUE	1	0.810122749928965	2		724	676	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632476	3632476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560381786	NA	P-0039447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	365	966	1	ENST00000294008.3:c.5372G>A	p.Arg1791His	p.R1791H	ENST00000294008	NM_032444.2	1791	cGt/cAt	15/15	1	2	FACETS	0.942	0.896	0.988	0.942	0.896	0.988	CLONAL	1	TRUE	1	0.810122749928965	2		967	957	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857259	9857259	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	290	612	0	ENST00000330684.3:c.4142G>A	p.Arg1381Lys	p.R1381K	ENST00000330684	NM_001134407.1	1381	aGa/aAa	13/13	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.810122749928965	2		612	695	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106975	11106975	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0039447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	373	835	0	ENST00000358026.2:c.1680C>G	p.Tyr560Ter	p.Y560*	ENST00000358026	NM_001128849.1	560	taC/taG	10/36	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.810122749928965	2		835	909	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213940	36213941	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0039447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	342	1022	0	ENST00000222270.7:c.2766_2767delinsTT	p.Arg923Trp	p.R923W	ENST00000222270	NM_014727.1	922	tcCCgg/tcTTgg	6/37	1	2	FACETS	0.912	0.866	0.959	0.912	0.866	0.959	CLONAL	1	TRUE	1	0.810122749928965	2		1022	926	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437308	220437308	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1236786282	NA	P-0039447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	402	1102	0	ENST00000243786.2:c.212G>A	p.Gly71Asp	p.G71D	ENST00000243786	NM_002191.3	71	gGc/gAc	1/2	0.441443048134692	3	FACETS	1	0.989	1	0.56	0.533	0.588	INDETERMINATE	1	TRUE	1	0.810122749928965	3		1102	1244	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524426	187524426	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1331553677	NA	P-0039447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	280	592	0	ENST00000441802.2:c.11254G>T	p.Val3752Leu	p.V3752L	ENST00000441802	NM_005245.3	3752	Gtg/Ttg	19/27	0.46659441137952	1	FACETS	0.752	0.714	0.789	0.752	0.714	0.789	INDETERMINATE	1	TRUE	0	0.810122749928965	1		592	547	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674231	117674231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	321	636	0	ENST00000368508.3:c.4243G>A	p.Gly1415Arg	p.G1415R	ENST00000368508	NM_002944.2	1415	Ggg/Agg	26/43	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.810122749928965	2		636	762	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872162	76872162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	135	516	0	ENST00000373344.5:c.5485C>T	p.Pro1829Ser	p.P1829S	ENST00000373344	NM_000489.3	1829	Cca/Tca	22/35	0.523522470659302	1	FACETS	0.409	0.374	0.445	0.409	0.374	0.445	SUBCLONAL	1	TRUE	0	0.810122749928965	1		516	485	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0039451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	48	515	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.699	0.591	0.819	0.699	0.591	0.819	SUBCLONAL	1	TRUE	1	0.26	2		515	528	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	58	336	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.989	0.852	1	0.989	0.852	1	CLONAL	1	TRUE	1	0.26	2		336	451	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0039451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	74	577	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.809	0.707	0.918	0.809	0.707	0.918	CLONAL	1	TRUE	1	0.26	2		577	704	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0039451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	50	254	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.986	0.839	1	0.986	0.839	1	CLONAL	1	TRUE	1	0.26	2		255	390	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	63	478	0	ENST00000263967.3:c.3012G>A	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atA	21/21	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.26	2		478	475	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0039451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	60	422	1	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.962	0.83	1	0.962	0.83	1	CLONAL	1	TRUE	1	0.26	2		423	480	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370985	55370985	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	119	645	0	ENST00000297316.4:c.287C>G	p.Ala96Gly	p.A96G	ENST00000297316	NM_022454.3	96	gCc/gGc	1/2	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.26	2		645	779	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0039451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	120	772	4	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	1	2	FACETS	0.971	0.875	1	0.971	0.875	1	CLONAL	1	TRUE	1	0.26	2		776	951	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199953	108199953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	33	190	0	ENST00000278616.4:c.7296del	p.Gln2433ArgfsTer7	p.Q2433Rfs*7	ENST00000278616	NM_000051.3	2432	aTt/at	49/63	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.26	2		190	235	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717712	89717712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782350	NA	P-0039451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	59	464	0	ENST00000371953.3:c.737C>T	p.Pro246Leu	p.P246L	ENST00000371953	NM_000314.4	246	cCg/cTg	7/9	1	2	FACETS	0.855	0.736	0.984	0.855	0.736	0.984	CLONAL	1	TRUE	1	0.26	2		464	531	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058045	27058045	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	82	543	0	ENST00000324856.7:c.1753C>T	p.Gln585Ter	p.Q585*	ENST00000324856	NM_006015.4	585	Cag/Tag	3/20	1	2	FACETS	0.992	0.875	1	0.992	0.875	1	CLONAL	1	TRUE	1	0.26	2		543	636	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701889	43701889	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	45	282	0	ENST00000382044.4:c.5356C>T	p.Arg1786Ter	p.R1786*	ENST00000382044	NM_001141980.1	1786	Cga/Tga	25/28	1	2	FACETS	0.931	0.784	1	0.931	0.784	1	CLONAL	1	TRUE	1	0.26	2		282	372	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220916	36220918	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	rs1568378410	NA	P-0039451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	55	361	0	ENST00000222270.7:c.4970_4972del	p.Ser1657del	p.S1657del	ENST00000222270	NM_014727.1	1656	TCC/-	23/37	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.26	2		361	401	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52709249	52709249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	107	649	0	ENST00000322088.6:c.203C>T	p.Ala68Val	p.A68V	ENST00000322088	NM_014225.5	68	gCc/gTc	3/15	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.26	2		649	767	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519281	187519281	+	splice_acceptor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0039451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	62	461	0	ENST00000441802.2:c.12104-2del		p.X4035_splice	ENST00000441802	NM_005245.3	4035			1	2	FACETS	0.907	0.784	1	0.907	0.784	1	CLONAL	1	TRUE	1	0.26	2		461	526	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178653	32178653	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	78	896	0	ENST00000375023.3:c.2741A>G	p.Tyr914Cys	p.Y914C	ENST00000375023	NM_004557.3	914	tAt/tGt	18/30	1	2	FACETS	0.569	0.499	0.646	0.569	0.499	0.646	SUBCLONAL	1	TRUE	1	0.26	2		896	1054	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457336	67457336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1360614387	NA	P-0039451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	109	754	1	ENST00000327367.4:c.310C>T	p.Arg104Trp	p.R104W	ENST00000327367	NM_005902.3	104	Cgg/Tgg	2/9	1	2	FACETS	0.986	0.885	1	0.986	0.885	1	CLONAL	1	TRUE	1	0.26	2		755	850	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0039459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	38	542	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.842	0.695	1	0.842	0.695	1	CLONAL	1	TRUE	1	0.16	2		542	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0039459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	73	976	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	1	2	FACETS	0.85	0.741	0.969	0.85	0.741	0.969	CLONAL	1	TRUE	1	0.16	2		976	1073	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0039459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	89	755	1	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.268961799418784	3	FACETS	1	0.922	1	1	0.922	1	CLONAL	2	TRUE	1	0.16	3		756	573	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	39	356	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	0.867	0.718	1	0.867	0.718	1	CLONAL	1	TRUE	1	0.16	2		356	562	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247175	153247175	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	30	210	0	ENST00000281708.4:c.1627A>G	p.Arg543Gly	p.R543G	ENST00000281708	NM_033632.3	543	Aga/Gga	10/12	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.16	2		210	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0039460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	258	721	0	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.460634496352665	1	FACETS	0.724	0.681	0.768	0.724	0.681	0.768	SUBCLONAL	1	TRUE	0	0.635940941761242	1		721	764	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577115	7577115	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519983	NA	P-0039460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	161	710	0	ENST00000269305.4:c.823T>C	p.Cys275Arg	p.C275R	ENST00000269305	NM_001126112.2	275	Tgt/Cgt	8/11	0.460634496352665	1	FACETS	0.432	0.397	0.469	0.432	0.397	0.469	SUBCLONAL	1	TRUE	0	0.635940941761242	1		710	799	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0039460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	43	273	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.46867365502327	1	FACETS	0.373	0.315	0.437	0.373	0.315	0.437	SUBCLONAL	1	TRUE	0	0.635940941761242	1		273	247	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0039461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	56	399	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	TRUE	1	0.324401141997272	2		399	292	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs760043106	NA	P-0039461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	76	609	0	ENST00000269305.4:c.584T>A	p.Ile195Asn	p.I195N	ENST00000269305	NM_001126112.2	195	aTc/aAc	6/11	1	2	FACETS	0.787	0.691	0.891	0.787	0.691	0.891	SUBCLONAL	1	TRUE	1	0.324401141997272	2		609	595	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970900	21970900	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0039461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	99	778	0	ENST00000304494.5:c.457+1G>A		p.X153_splice	ENST00000304494	NM_000077.4	153			0.324401141997272	1	FACETS	0.658	0.587	0.734	0.658	0.587	0.734	SUBCLONAL	1	TRUE	0	0.324401141997272	1		778	777	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855469	45855469	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs767253793	NA	P-0039461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	87	613	0	ENST00000391945.4:c.2188C>T	p.Arg730Trp	p.R730W	ENST00000391945	NM_000400.3	730	Cgg/Tgg	22/23	0.0695039073147004	3	FACETS	0.77	0.681	0.865			1	INDETERMINATE	1	TRUE	NA	0.324401141997272	3		613	810	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706985	117706985	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372637439	NA	P-0039461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	54	495	0	ENST00000368508.3:c.2165C>T	p.Thr722Met	p.T722M	ENST00000368508	NM_002944.2	722	aCg/aTg	15/43	0.145582766885862	0	FACETS	0.476	0.406	0.551			1	INDETERMINATE	1	TRUE	0	0.324401141997272	0		495	473	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650753	48650753	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776454	NA	P-0039464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	48	679	0	ENST00000376670.3:c.622G>A	p.Gly208Arg	p.G208R	ENST00000376670	NM_002049.3	208	Gga/Aga	4/6	1	2	FACETS	0.262	0.221	0.307	0.262	0.221	0.307	SUBCLONAL	1	TRUE	1	0.603693430025909	2		679	607	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864884	117864884	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	40	367	0	ENST00000297338.2:c.1225G>T	p.Glu409Ter	p.E409*	ENST00000297338	NM_006265.2	409	Gag/Tag	10/14	0.591493946700572	4	FACETS	0.325	0.269	0.387	0.162	0.134	0.194	SUBCLONAL	1	TRUE	2	0.603693430025909	4		367	654	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0039473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	174	585	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	1	0.984	1	1	0.994	1	CLONAL	2	FALSE	1	0.32128415795892	2		585	450	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0039473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	39	245	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.299356729653043	0	FACETS	1	0.929	1			1	CLONAL	1	FALSE	0	0.32128415795892	0		245	139	SUCCESS
APC	324	MSKCC	GRCh37	5	112178000	112178000	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768922431	NA	P-0039473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	19	423	0	ENST00000257430.4:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000257430	NM_000038.5	2237	Cga/Tga	16/16	0.299356729653043	0	FACETS	0.403	0.307	0.515			1	SUBCLONAL	1	FALSE	0	0.32128415795892	0		423	199	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589663	67589663	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587777709	NA	P-0039473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	34	272	0	ENST00000274335.5:c.1425+1G>T		p.X475_splice	ENST00000274335		475			0.299356729653043	0	FACETS	0.977	0.811	1			1	CLONAL	1	FALSE	0	0.32128415795892	0		272	147	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061593	38061622	+	inframe_deletion	In_Frame_Del	DEL	GGCCGCGTAGGGGCCCAGGCCATTCATGGA	GGCCGCGTAGGGGCCCAGGCCATTCATGGA	-	novel	NA	P-0039473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	126	387	0	ENST00000250448.2:c.367_396del	p.Ser123_Ala132del	p.S123_A132del	ENST00000250448	NM_004496.3	123	TCCATGAATGGCCTGGGCCCCTACGCGGCC/-	2/2	0.32128415795892	6	FACETS	1	0.972	1	0.586	0.532	0.641	CLONAL	2	FALSE	2	0.32128415795892	6		387	550	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	278	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.80433715451128	2		174	644	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0039476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	371	687	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	0.80433715451128	2		687	762	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	355	576	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.858	0.822	0.895	1	0.996	1	CLONAL	2	TRUE	1	0.647194267123519	2		580	639	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	136	399	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.868	0.795	0.944	0.868	0.795	0.944	CLONAL	1	TRUE	1	0.647194267123519	2		399	484	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	175	455	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.86	0.795	0.926	0.86	0.795	0.926	CLONAL	1	TRUE	1	0.647194267123519	2		455	629	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	171	673	3	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.945	0.875	1	0.945	0.875	1	CLONAL	1	TRUE	1	0.647194267123519	2		676	559	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	213	692	1	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	1	2	FACETS	0.792	0.737	0.849	0.792	0.737	0.849	SUBCLONAL	1	TRUE	1	0.647194267123519	2		693	831	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	95	838	4	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.405	0.361	0.453	0.405	0.361	0.453	SUBCLONAL	1	TRUE	1	0.647194267123519	2		842	724	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	90	298	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	1	2	FACETS	0.76	0.68	0.844	0.76	0.68	0.844	SUBCLONAL	1	TRUE	1	0.647194267123519	2		298	366	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217297	11217297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs955557159	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	206	712	0	ENST00000361445.4:c.4381G>A	p.Val1461Met	p.V1461M	ENST00000361445	NM_004958.3	1461	Gtg/Atg	30/58	1	2	FACETS	0.842	0.784	0.902	0.842	0.784	0.902	CLONAL	1	TRUE	1	0.647194267123519	2		712	756	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	199	574	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.923	0.859	0.989	0.923	0.859	0.989	CLONAL	1	TRUE	1	0.647194267123519	2		574	666	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428516	78428516	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	170	409	0	ENST00000370768.2:c.1283C>T	p.Thr428Ile	p.T428I	ENST00000370768	NM_003902.3	428	aCa/aTa	14/20	1	2	FACETS	0.947	0.876	1	0.947	0.876	1	CLONAL	1	TRUE	1	0.647194267123519	2		409	555	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982360	201982360	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1359638271	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	267	782	1	ENST00000359651.3:c.739C>T	p.Arg247Ter	p.R247*	ENST00000359651		247	Cga/Tga	6/8	1	2	FACETS	0.896	0.842	0.951	0.896	0.842	0.951	CLONAL	1	TRUE	1	0.647194267123519	2		783	921	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	97	254	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.793	0.713	0.877	0.793	0.713	0.877	SUBCLONAL	1	TRUE	1	0.647194267123519	2		255	378	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316397	14316397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782457908	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	198	442	0	ENST00000256196.4:c.208G>A	p.Ala70Thr	p.A70T	ENST00000256196		70	Gca/Aca	3/6	1	2	FACETS	0.985	0.918	1	0.985	0.918	1	CLONAL	1	TRUE	1	0.647194267123519	2		442	621	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	220	729	0	ENST00000227507.2:c.859C>T	p.Pro287Ser	p.P287S	ENST00000227507	NM_053056.2	287	Ccc/Tcc	5/5	1	2	FACETS	0.885	0.826	0.946	0.885	0.826	0.946	CLONAL	1	TRUE	1	0.647194267123519	2		729	768	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939413	71939413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148394356	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	285	749	1	ENST00000298229.2:c.268C>T	p.Arg90Cys	p.R90C	ENST00000298229	NM_001567.3	90	Cgc/Tgc	3/28	1	2	FACETS	0.986	0.93	1	0.986	0.93	1	CLONAL	1	TRUE	1	0.647194267123519	2		750	893	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	292	932	2	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.925	0.871	0.979	0.925	0.871	0.979	CLONAL	1	TRUE	1	0.647194267123519	2		934	976	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948527	71948527	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749369759	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	218	816	1	ENST00000298229.2:c.3239G>A	p.Arg1080His	p.R1080H	ENST00000298229	NM_001567.3	1080	cGt/cAt	26/28	1	2	FACETS	0.883	0.824	0.944	0.883	0.824	0.944	CLONAL	1	TRUE	1	0.647194267123519	2		817	763	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1039231	1039231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144832155	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	169	437	0	ENST00000358495.3:c.266C>T	p.Thr89Met	p.T89M	ENST00000358495	NM_134424.2	89	aCg/aTg	4/12	1	2	FACETS	0.95	0.879	1	0.95	0.879	1	CLONAL	1	TRUE	1	0.647194267123519	2		437	550	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491390	18491390	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1377942847	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	103	261	1	ENST00000266497.5:c.1309del	p.Ile437TyrfsTer5	p.I437Yfs*5	ENST00000266497		435	Aaa/aa	8/31	1	2	FACETS	0.798	0.719	0.88	0.798	0.719	0.88	SUBCLONAL	1	TRUE	1	0.647194267123519	2		262	399	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244595	46244595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	179	523	0	ENST00000334344.6:c.2689G>A	p.Ala897Thr	p.A897T	ENST00000334344	NM_152641.2	897	Gca/Aca	15/21	1	2	FACETS	0.885	0.82	0.952	0.885	0.82	0.952	CLONAL	1	TRUE	1	0.647194267123519	2		523	625	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	212	842	2	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.885	0.825	0.947	0.885	0.825	0.947	CLONAL	1	TRUE	1	0.647194267123519	2		844	740	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99192851	99192851	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	139	363	1	ENST00000268035.6:c.45del	p.Leu16SerfsTer31	p.L16Sfs*31	ENST00000268035	NM_000875.3	14	tGg/tg	1/21	1	2	FACETS	0.863	0.79	0.937	0.863	0.79	0.937	CLONAL	1	TRUE	1	0.647194267123519	2		364	498	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246037	41246037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56272539	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	192	564	0	ENST00000357654.3:c.1511G>A	p.Arg504His	p.R504H	ENST00000357654	NM_007294.3	504	cGt/cAt	10/23	1	2	FACETS	0.916	0.851	0.982	0.916	0.851	0.982	CLONAL	1	TRUE	1	0.647194267123519	2		564	648	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448297	56448297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2257205	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	261	621	0	ENST00000407977.2:c.350G>A	p.Arg117His	p.R117H	ENST00000407977		117	cGc/cAc	3/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.647194267123519	2		621	789	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774681	73774682	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	26	113	0	ENST00000254810.4:c.405_406del	p.Arg135SerfsTer12	p.R135Sfs*12	ENST00000254810	NM_005324.3	135	agAGct/agct	4/4	1	2	FACETS	0.487	0.389	0.596	0.487	0.389	0.596	SUBCLONAL	1	TRUE	1	0.647194267123519	2		113	165	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756622	756622	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749885349	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	188	446	0	ENST00000314574.4:c.206C>T	p.Thr69Met	p.T69M	ENST00000314574	NM_005433.3	69	aCg/aTg	2/12	1	2	FACETS	0.928	0.862	0.996	0.928	0.862	0.996	CLONAL	1	TRUE	1	0.647194267123519	2		446	626	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272336	15272337	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs771517374	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	219	831	6	ENST00000263388.2:c.6102dup	p.Gly2035ArgfsTer60	p.G2035Rfs*60	ENST00000263388	NM_000435.2	2034	-/C	33/33	1	2	FACETS	0.899	0.839	0.96	0.899	0.839	0.96	CLONAL	1	TRUE	1	0.647194267123519	2		837	753	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276310	15276310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369768722	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	240	681	1	ENST00000263388.2:c.5684G>A	p.Arg1895His	p.R1895H	ENST00000263388	NM_000435.2	1895	cGc/cAc	31/33	1	2	FACETS	0.99	0.928	1	0.99	0.928	1	CLONAL	1	TRUE	1	0.647194267123519	2		682	749	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350824	15350824	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148664288	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	213	556	1	ENST00000263377.2:c.3179G>A	p.Arg1060His	p.R1060H	ENST00000263377	NM_058243.2	1060	cGc/cAc	15/20	1	2	FACETS	0.93	0.867	0.994	0.93	0.867	0.994	CLONAL	1	TRUE	1	0.647194267123519	2		557	708	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752695	42752695	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1366176199	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	206	691	9	ENST00000222329.4:c.1569del	p.Leu525SerfsTer6	p.L525Sfs*6	ENST00000222329	NM_006494.2	523	ggG/gg	4/4	1	2	FACETS	0.966	0.901	1	0.966	0.901	1	CLONAL	1	TRUE	1	0.647194267123519	2		700	659	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752781	42752781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772231752	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	216	800	0	ENST00000222329.4:c.1483G>A	p.Glu495Lys	p.E495K	ENST00000222329	NM_006494.2	495	Gaa/Aaa	4/4	1	2	FACETS	0.822	0.766	0.88	0.822	0.766	0.88	CLONAL	1	TRUE	1	0.647194267123519	2		800	812	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753650	42753650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1053655	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	251	807	0	ENST00000222329.4:c.614G>A	p.Arg205His	p.R205H	ENST00000222329	NM_006494.2	205	cGc/cAc	4/4	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.647194267123519	2		807	768	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798218	42798218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568528562	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	184	685	0	ENST00000575354.2:c.4172G>A	p.Arg1391His	p.R1391H	ENST00000575354	NM_015125.3	1391	cGc/cAc	17/20	1	2	FACETS	0.796	0.737	0.857	0.796	0.737	0.857	SUBCLONAL	1	TRUE	1	0.647194267123519	2		685	714	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867058	45867058	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	199	657	0	ENST00000391945.4:c.1061C>T	p.Pro354Leu	p.P354L	ENST00000391945	NM_000400.3	354	cCg/cTg	11/23	1	2	FACETS	0.949	0.883	1	0.949	0.883	1	CLONAL	1	TRUE	1	0.647194267123519	2		657	648	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905173	50905173	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41563714	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	286	857	0	ENST00000440232.2:c.455C>T	p.Ala152Val	p.A152V	ENST00000440232	NM_002691.3	152	gCg/gTg	4/27	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.647194267123519	2		857	834	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906393	50906393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762330164	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	229	843	0	ENST00000440232.2:c.1054C>T	p.Arg352Cys	p.R352C	ENST00000440232	NM_002691.3	352	Cgc/Tgc	9/27	1	2	FACETS	0.911	0.852	0.972	0.911	0.852	0.972	CLONAL	1	TRUE	1	0.647194267123519	2		843	777	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630541	47630541	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	131	592	0	ENST00000233146.2:c.211G>T	p.Gly71Ter	p.G71*	ENST00000233146	NM_000251.2	71	Gga/Tga	1/16	1	2	FACETS	0.842	0.769	0.917	0.842	0.769	0.917	CLONAL	1	TRUE	1	0.647194267123519	2		592	481	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637455	47637468	+	frameshift_variant	Frame_Shift_Del	DEL	AAGGAATGTGTTTT	AAGGAATGTGTTTT	-	novel	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	159	455	0	ENST00000233146.2:c.590_603del	p.Lys197ThrfsTer30	p.K197Tfs*30	ENST00000233146	NM_000251.2	197	AAGGAATGTGTTTTa/a	3/16	1	2	FACETS	0.822	0.757	0.889	0.822	0.757	0.889	CLONAL	1	TRUE	1	0.647194267123519	2		455	598	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877391	40877391	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372713520	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	145	536	1	ENST00000373198.4:c.2305G>A	p.Val769Met	p.V769M	ENST00000373198	NM_133170.3	769	Gtg/Atg	15/32	1	2	FACETS	0.884	0.812	0.958	0.884	0.812	0.958	CLONAL	1	TRUE	1	0.647194267123519	2		537	507	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084146	47084146	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	197	465	0	ENST00000409792.3:c.7143del	p.Ser2382LeufsTer29	p.S2382Lfs*29	ENST00000409792	NM_014159.6	2381	ccC/cc	17/21	1	2	FACETS	0.928	0.863	0.994	0.928	0.863	0.994	CLONAL	1	TRUE	1	0.647194267123519	2		465	656	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591132	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	rs1057519842	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	135	284	0	ENST00000274335.5:c.1727_1729del	p.Thr576del	p.T576del	ENST00000274335		575	aaGACg/aag	12/15	1	2	FACETS	0.991	0.909	1	0.991	0.909	1	CLONAL	1	TRUE	1	0.647194267123519	2		284	421	SUCCESS
APC	324	MSKCC	GRCh37	5	112170666	112170666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372416031	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	110	319	0	ENST00000257430.4:c.1762G>A	p.Val588Ile	p.V588I	ENST00000257430	NM_000038.5	588	Gta/Ata	15/16	1	2	FACETS	0.966	0.877	1	0.966	0.877	1	CLONAL	1	TRUE	1	0.647194267123519	2		319	352	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053022	180053023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750808726	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	161	838	2	ENST00000261937.6:c.1267dup	p.Gln423ProfsTer4	p.Q423Pfs*4	ENST00000261937	NM_182925.4	423	cag/cCag	10/30	1	2	FACETS	0.676	0.621	0.733	0.676	0.621	0.733	SUBCLONAL	1	TRUE	1	0.647194267123519	2		840	736	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055897	180055897	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	38	669	2	ENST00000261937.6:c.1088del	p.Pro363ArgfsTer27	p.P363Rfs*27	ENST00000261937	NM_182925.4	363	cCg/cg	8/30	1	2	FACETS	0.216	0.178	0.259	0.216	0.178	0.259	SUBCLONAL	1	TRUE	1	0.647194267123519	2		671	543	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	212	827	0	ENST00000220592.5:c.1805_1806dup	p.Ala603ProfsTer93	p.A603Pfs*93	ENST00000220592	NM_012154.3	602	-/CC	14/19	1	2	FACETS	0.739	0.688	0.793	0.739	0.688	0.793	SUBCLONAL	1	TRUE	1	0.647194267123519	2		827	886	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797231	135797231	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	21	217	0	ENST00000298552.3:c.638T>C	p.Leu213Pro	p.L213P	ENST00000298552	NM_001162426.1	213	cTg/cCg	7/23	1	2	FACETS	0.221	0.17	0.28	0.221	0.17	0.28	SUBCLONAL	1	TRUE	1	0.647194267123519	2		217	294	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105609	11105609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1263541939	NA	P-0039477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	225	635	1	ENST00000358026.2:c.1525G>A	p.Ala509Thr	p.A509T	ENST00000358026	NM_001128849.1	509	Gcc/Acc	9/36	1	2	FACETS	0.885	0.826	0.945	0.885	0.826	0.945	CLONAL	1	TRUE	1	0.647194267123519	2		636	786	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0039478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	264	737	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.596462927533166	1	FACETS	0.983	0.928	1	0.983	0.928	1	CLONAL	1	TRUE	0	0.596462927533166	1		737	632	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0039478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	542	595	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	0.596462927533166	4	FACETS	0.953	0.919	0.986	0.953	0.919	0.986	CLONAL	3	TRUE	1	0.596462927533166	4		595	1015	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781388	3781388	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	53	793	0	ENST00000262367.5:c.4977C>A	p.Asp1659Glu	p.D1659E	ENST00000262367	NM_004380.2	1659	gaC/gaA	30/31	1	2	FACETS	0.169	0.143	0.197	0.169	0.143	0.197	SUBCLONAL	1	TRUE	1	0.596462927533166	2		793	1052	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610163	10610163	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	118	744	0	ENST00000171111.5:c.547A>G	p.Asn183Asp	p.N183D	ENST00000171111	NM_203500.1	183	Aat/Gat	2/6	1	2	FACETS	0.415	0.373	0.459	0.415	0.373	0.459	SUBCLONAL	1	TRUE	1	0.596462927533166	2		744	954	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	17	492	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.565	0.42	0.738	0.565	0.42	0.738	SUBCLONAL	1	TRUE	1	0.13	2		492	463	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711875	89711875	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	rs587782603	NA	P-0039479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	27	376	0	ENST00000371953.3:c.493G>T	p.Gly165Ter	p.G165*	ENST00000371953	NM_000314.4	165	Gga/Tga	6/9	1	2	FACETS	0.987	0.785	1	0.987	0.785	1	CLONAL	1	TRUE	1	0.13	2		376	421	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27098980	27099001	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTGTCCACAGCGGGATCAGGA	TCTGTCCACAGCGGGATCAGGA	-	novel	NA	P-0039479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	27	445	0	ENST00000324856.7:c.3407-8_3420del		p.X1136_splice	ENST00000324856	NM_006015.4	1136		13/20	1	2	FACETS	0.819	0.651	1	0.819	0.651	1	CLONAL	1	TRUE	1	0.13	2		445	507	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0039498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	69	300	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.399294347604314	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.581967328948141	4		300	153	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0039498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	154	917	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.35998665656869	2	FACETS	0.76	0.706	0.815	0.76	0.706	0.815	SUBCLONAL	2	TRUE	0	0.581967328948141	2		917	348	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274045	10274045	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	56	1129	0	ENST00000330684.3:c.224A>T	p.Asn75Ile	p.N75I	ENST00000330684	NM_001134407.1	75	aAc/aTc	2/13	0.220704959792112	2	FACETS	0.607	0.523	0.697	0.304	0.261	0.349	INDETERMINATE	1	TRUE	0	0.581967328948141	2		1129	317	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183298	56183298	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	16	573	0	ENST00000399503.3:c.4208G>C	p.Gly1403Ala	p.G1403A	ENST00000399503	NM_005921.1	1403	gGa/gCa	18/20	0.225604927387721	3	FACETS	0.3	0.221	0.393	0.1	0.073	0.131	INDETERMINATE	1	TRUE	0	0.581967328948141	3		573	237	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0039500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	770	490	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.9090779207168	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.9090779207168	2		490	826	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937504	32937504	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	314	817	0	ENST00000380152.3:c.8165del	p.Thr2722LysfsTer11	p.T2722Kfs*11	ENST00000380152		2722	aCa/aa	18/27	0.9090779207168	1	FACETS	0.999	0.971	1	0.999	0.971	1	CLONAL	1	TRUE	0	0.9090779207168	1		817	377	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858423	27858423	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	286	655	0	ENST00000359303.2:c.148C>G	p.Arg50Gly	p.R50G	ENST00000359303	NM_003535.2	50	Cgt/Ggt	1/1	0.9090779207168	3	FACETS	0.907	0.854	0.962	0.454	0.427	0.481	CLONAL	1	TRUE	1	0.9090779207168	3		655	1009	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672884	30672884	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	405	986	0	ENST00000376406.3:c.4076C>G	p.Ser1359Cys	p.S1359C	ENST00000376406	NM_014641.2	1359	tCt/tGt	10/15	0.9090779207168	3	FACETS	0.91	0.865	0.956	0.455	0.432	0.478	CLONAL	1	TRUE	1	0.9090779207168	3		986	1424	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426955	49426955	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	52	654	0	ENST00000301067.7:c.11533C>T	p.Gln3845Ter	p.Q3845*	ENST00000301067	NM_003482.3	3845	Cag/Tag	39/54	1	2	FACETS	0.397	0.337	0.463	0.397	0.337	0.463	SUBCLONAL	1	TRUE	1	0.386267808889059	2		654	678	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0039502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	753	764	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.386267808889059	6	FACETS	0.942	0.916	0.967			1	CLONAL	6	TRUE	NA	0.386267808889059	6		764	1223	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100913	27100913	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	74	540	0	ENST00000324856.7:c.4195C>T	p.Gln1399Ter	p.Q1399*	ENST00000324856	NM_006015.4	1399	Cag/Tag	18/20	1	2	FACETS	0.645	0.565	0.731	0.645	0.565	0.731	SUBCLONAL	1	TRUE	1	0.386267808889059	2		540	594	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106570	27106571	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0039502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	110	727	0	ENST00000324856.7:c.6182_6183dup	p.Val2062TrpfsTer74	p.V2062Wfs*74	ENST00000324856	NM_006015.4	2061	ttg/tTGtg	20/20	1	2	FACETS	0.634	0.569	0.703	0.634	0.569	0.703	SUBCLONAL	1	TRUE	1	0.386267808889059	2		727	898	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43700189	43700189	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	70	468	0	ENST00000382044.4:c.5698G>A	p.Gly1900Ser	p.G1900S	ENST00000382044	NM_001141980.1	1900	Ggt/Agt	27/28	1	2	FACETS	0.57	0.497	0.649	0.57	0.497	0.649	SUBCLONAL	1	TRUE	1	0.386267808889059	2		468	636	SUCCESS
BLM	641	MSKCC	GRCh37	15	91337508	91337508	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs747571272	NA	P-0039502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	83	399	0	ENST00000355112.3:c.3131A>G	p.Tyr1044Cys	p.Y1044C	ENST00000355112	NM_000057.2	1044	tAc/tGc	16/22	1	2	FACETS	0.541	0.477	0.61	0.541	0.477	0.61	SUBCLONAL	1	TRUE	1	0.386267808889059	2		399	794	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640008	3640008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202032197	NA	P-0039502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	206	831	0	ENST00000294008.3:c.3631G>A	p.Glu1211Lys	p.E1211K	ENST00000294008	NM_032444.2	1211	Gaa/Aaa	12/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.386267808889059	2		831	946	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641097	3641097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	251	874	0	ENST00000294008.3:c.2542G>A	p.Glu848Lys	p.E848K	ENST00000294008	NM_032444.2	848	Gaa/Aaa	12/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.386267808889059	2		874	1202	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923384	9923384	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	132	540	0	ENST00000330684.3:c.1903G>A	p.Ala635Thr	p.A635T	ENST00000330684	NM_001134407.1	635	Gcc/Acc	9/13	1	2	FACETS	0.943	0.857	1	0.943	0.857	1	CLONAL	1	TRUE	1	0.386267808889059	2		540	725	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641043	23641043	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	89	606	0	ENST00000261584.4:c.2432C>T	p.Pro811Leu	p.P811L	ENST00000261584	NM_024675.3	811	cCa/cTa	5/13	1	2	FACETS	0.563	0.498	0.632	0.563	0.498	0.632	SUBCLONAL	1	TRUE	1	0.386267808889059	2		606	819	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880926	134880926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371083718	NA	P-0039502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	59	553	1	ENST00000398015.3:c.1489C>T	p.Arg497Trp	p.R497W	ENST00000398015	NM_004441.4	497	Cgg/Tgg	7/16	1	2	FACETS	0.415	0.356	0.479	0.415	0.356	0.479	SUBCLONAL	1	TRUE	1	0.386267808889059	2		554	737	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0039502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	92	561	0				ENST00000310581	NM_198253.2	-/1132			0.0450491667507618	3	FACETS	1	0.915	1	0.516	0.459	0.576	INDETERMINATE	1	TRUE	1	0.386267808889059	3		561	551	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038858	47038858	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1556777925	NA	P-0039502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	28	417	0	ENST00000377604.3:c.865C>T	p.Gln289Ter	p.Q289*	ENST00000377604	NM_001204468.1	289	Cag/Tag	9/24	0.170948781687781	2	FACETS	0.28	0.223	0.345			1	INDETERMINATE	1	TRUE	NA	0.386267808889059	2		417	518	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10286250	10286250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781646588	NA	P-0039507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1290	224	750	2	ENST00000340748.4:c.566C>T	p.Ser189Leu	p.S189L	ENST00000340748		189	tCg/tTg	6/40	0.219859710974765	4	FACETS	0.821	0.762	0.882	0.41	0.381	0.441	CLONAL	2	TRUE	0	0.219859710974765	4		752	1514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0039507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	86	517	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.219859710974765	1	FACETS	0.843	0.745	0.948	0.843	0.745	0.948	CLONAL	1	TRUE	0	0.219859710974765	1		517	826	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023008	27023010	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs587779737	NA	P-0039507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	10	60	0	ENST00000324856.7:c.126_128del	p.Ala45del	p.A45del	ENST00000324856	NM_006015.4	38	gaGGCg/gag	1/20	0.219859710974765	3	FACETS	0.926	0.632	1	0.463	0.316	0.645	CLONAL	1	TRUE	1	0.219859710974765	3		60	109	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067192	37067192	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201673334	NA	P-0039507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	121	407	1	ENST00000231790.2:c.1103C>T	p.Ser368Leu	p.S368L	ENST00000231790	NM_000249.3	368	tCg/tTg	12/19	0.197619667216493	3	FACETS	0.928	0.84	1	0.619	0.56	0.681	CLONAL	2	TRUE	0	0.219859710974765	3		408	658	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100133	30100133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370296777	NA	P-0039507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	159	823	0	ENST00000331968.5:c.1487C>T	p.Thr496Met	p.T496M	ENST00000331968	NM_002742.2	496	aCg/aTg	10/18	0.18382154213189	3	FACETS	1	0.988	1	0.74	0.677	0.806	CLONAL	1	TRUE	1	0.219859710974765	3		823	1085	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141559	11141559	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	507	802	0	ENST00000358026.2:c.3536A>T	p.Asn1179Ile	p.N1179I	ENST00000358026	NM_001128849.1	1179	aAt/aTt	25/36	0.219859710974765	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	4	TRUE	0	0.219859710974765	4		802	1313	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805422	46805422	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	129	940	0	ENST00000290295.7:c.534G>A	p.Trp178Ter	p.W178*	ENST00000290295	NM_006361.5	178	tgG/tgA	1/2	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.219859710974765	2		940	1088	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427054	49427054	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	158	644	0	ENST00000301067.7:c.11434C>T	p.Gln3812Ter	p.Q3812*	ENST00000301067	NM_003482.3	3812	Cag/Tag	39/54	0.219859710974765	3	FACETS	0.992	0.91	1	0.992	0.91	1	CLONAL	2	TRUE	1	0.219859710974765	3		644	804	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839778	27839778	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	171	672	0	ENST00000328488.2:c.316G>C	p.Glu106Gln	p.E106Q	ENST00000328488	NM_003533.2	106	Gag/Cag	1/1	0.219859710974765	3	FACETS	0.854	0.785	0.926	0.854	0.785	0.926	CLONAL	2	TRUE	1	0.219859710974765	3		672	1011	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075574	8075574	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	70	446	1	ENST00000377482.5:c.106A>T	p.Ser36Cys	p.S36C	ENST00000377482	NM_018948.3	36	Agt/Tgt	2/4	0.18382154213189	3	FACETS	0.883	0.769	1	0.442	0.384	0.504	CLONAL	1	TRUE	1	0.219859710974765	3		447	800	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426616	49426616	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	113	710	0	ENST00000301067.7:c.11872C>T	p.Gln3958Ter	p.Q3958*	ENST00000301067	NM_003482.3	3958	Caa/Taa	39/54	0.219859710974765	3	FACETS	1	0.942	1	0.536	0.481	0.594	CLONAL	1	TRUE	1	0.219859710974765	3		710	1065	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444478	49444478	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	97	850	0	ENST00000301067.7:c.2893G>T	p.Gly965Trp	p.G965W	ENST00000301067	NM_003482.3	965	Ggg/Tgg	11/54	0.219859710974765	3	FACETS	0.844	0.75	0.944	0.422	0.375	0.472	CLONAL	1	TRUE	1	0.219859710974765	3		850	1161	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490378	56490378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	84	515	0	ENST00000267101.3:c.2147G>A	p.Gly716Asp	p.G716D	ENST00000267101	NM_001982.3	716	gGc/gAc	18/28	0.219859710974765	3	FACETS	0.931	0.821	1	0.465	0.41	0.525	CLONAL	1	TRUE	1	0.219859710974765	3		515	911	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805580	46805580	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	120	1088	0	ENST00000290295.7:c.376G>C	p.Glu126Gln	p.E126Q	ENST00000290295	NM_006361.5	126	Gag/Cag	1/2	1	2	FACETS	0.959	0.864	1	0.959	0.864	1	CLONAL	1	TRUE	1	0.219859710974765	2		1088	1138	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39576644	39576644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370435146	NA	P-0039507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	39	383	0	ENST00000262039.4:c.934G>A	p.Glu312Lys	p.E312K	ENST00000262039	NM_002647.2	312	Gaa/Aaa	9/25	1	2	FACETS	0.672	0.556	0.801	0.672	0.556	0.801	SUBCLONAL	1	TRUE	1	0.219859710974765	2		383	528	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10257145	10257145	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	103	645	0	ENST00000340748.4:c.2728G>T	p.Val910Phe	p.V910F	ENST00000340748		910	Gtc/Ttc	27/40	0.219859710974765	2	FACETS	0.963	0.86	1	0.481	0.43	0.536	CLONAL	1	TRUE	0	0.219859710974765	2		645	973	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71008437	71008437	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	89	385	0	ENST00000318789.4:c.1995A>T	p.Arg665Ser	p.R665S	ENST00000318789	NM_032682.5	665	agA/agT	21/21	0.197619667216493	3	FACETS	0.801	0.712	0.896	0.534	0.474	0.597	CLONAL	2	TRUE	0	0.219859710974765	3		385	561	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445019	89445019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780126700	NA	P-0039507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	206	496	0	ENST00000336596.2:c.1339C>T	p.Arg447Trp	p.R447W	ENST00000336596	NM_005233.5	447	Cgg/Tgg	6/17	0.195888053748623	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.219859710974765	4		496	931	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486188	8486188	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	100	499	0	ENST00000356435.5:c.2629G>T	p.Glu877Ter	p.E877*	ENST00000356435		877	Gaa/Taa	17/35	0.219859710974765	2	FACETS	1	0.976	1	0.671	0.6	0.746	CLONAL	1	TRUE	0	0.219859710974765	2		499	678	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867546	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGC	GGCGGCGGC	-	rs11466445	NA	P-0039508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	17	28	1	ENST00000374994.4:c.70_78del	p.Ala24_Ala26del	p.A24_A26del	ENST00000374994	NM_004612.2	17	ctGGCGGCGGCg/ctg	1/9	1	2	FACETS	0.859	0.659	1	1	0.923	1	CLONAL	2	FALSE	1	0.3	2		29	66	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0039509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	208	865	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	1	2	FACETS	0.913	0.85	0.977	0.913	0.85	0.977	CLONAL	1	TRUE	1	0.608603403538502	2		865	749	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	G	rs1131691039	NA	P-0039509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	194	806	0	ENST00000269305.4:c.919+1G>C		p.X307_splice	ENST00000269305	NM_001126112.2	307			1	2	FACETS	0.944	0.878	1	0.944	0.878	1	CLONAL	1	TRUE	1	0.608603403538502	2		806	675	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0039510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	117	399	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.862	0.777	0.952	0.862	0.777	0.952	CLONAL	1	TRUE	1	0.326804219448235	2		399	831	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974769	21974770	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCCGT	rs1563892769	NA	P-0039510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	33	294	0	ENST00000304494.5:c.52_57dup	p.Thr18_Ala19dup	p.T18_A19dup	ENST00000304494	NM_000077.4	18	-/ACGGCC	1/3	0.326804219448235	1	FACETS	0.55	0.449	0.663	0.55	0.449	0.663	SUBCLONAL	1	TRUE	0	0.326804219448235	1		294	307	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435311	56435311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759694077	NA	P-0039510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	138	658	1	ENST00000407977.2:c.1826G>A	p.Arg609Gln	p.R609Q	ENST00000407977		609	cGg/cAg	9/10	0.326804219448235	1	FACETS	0.862	0.784	0.943	0.862	0.784	0.943	CLONAL	1	TRUE	0	0.326804219448235	1		659	820	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064794618	NA	P-0039510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	169	886	0	ENST00000269305.4:c.159G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgG/tgA	4/11	0.326804219448235	1	FACETS	0.861	0.791	0.934	0.861	0.791	0.934	CLONAL	1	TRUE	0	0.326804219448235	1		886	1005	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713702	30713721	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTGGGAGGACCTGCGCAA	AGCTGGGAGGACCTGCGCAA	-	novel	NA	P-0039510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	105	601	0	ENST00000295754.5:c.1027_1046del	p.Ser343AlafsTer15	p.S343Afs*15	ENST00000295754	NM_003242.5	343	AGCTGGGAGGACCTGCGCAAg/g	4/7	0.326804219448235	1	FACETS	0.837	0.751	0.928	0.837	0.751	0.928	CLONAL	1	TRUE	0	0.326804219448235	1		601	642	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	113	492	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.893	0.814	0.973	1	0.992	1	CLONAL	4	FALSE	1	0.202176900928853	2		492	313	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	161	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.922	0.854	0.991	1	0.994	1	CLONAL	4	FALSE	1	0.202176900928853	2		174	432	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44935940	44935940	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0039512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	38	267	0	ENST00000377967.4:c.2703-2A>G		p.X901_splice	ENST00000377967	NM_021140.2	901			1	2	FACETS	1	0.867	1	1	0.976	1	CLONAL	3	FALSE	1	0.202176900928853	2		267	122	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0039512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	160	879	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	0.994	1	CLONAL	3	FALSE	1	0.202176900928853	2		879	492	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233687	233687	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200526913	NA	P-0039512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	20	356	0	ENST00000264932.6:c.991G>A	p.Ala331Thr	p.A331T	ENST00000264932	NM_004168.2	331	Gcc/Acc	8/15	1	2	FACETS	0.653	0.499	0.833	0.653	0.499	0.833	SUBCLONAL	1	FALSE	1	0.202176900928853	2		356	303	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196796	123196796	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	114	540	0	ENST00000218089.9:c.1687del	p.Ile563SerfsTer13	p.I563Sfs*13	ENST00000218089	NM_001042749.1	561	acA/ac	18/35	1	2	FACETS	1	0.95	1	1	0.992	1	CLONAL	3	FALSE	1	0.202176900928853	2		540	353	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807895	3807895	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs28937315	NA	P-0039512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	110	535	0	ENST00000262367.5:c.3524A>G	p.Tyr1175Cys	p.Y1175C	ENST00000262367	NM_004380.2	1175	tAt/tGt	18/31	1	2	FACETS	0.923	0.836	1	1	0.991	1	CLONAL	3	FALSE	1	0.202176900928853	2		535	393	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934525	9934525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	21	472	0	ENST00000330684.3:c.1630G>A	p.Val544Ile	p.V544I	ENST00000330684	NM_001134407.1	544	Gtc/Atc	7/13	1	2	FACETS	0.571	0.439	0.725	0.571	0.439	0.725	SUBCLONAL	1	FALSE	1	0.202176900928853	2		472	364	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	216	174	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.747500695290634	2		174	559	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0039515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	226	582	5	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	1	2	FACETS	0.879	0.823	0.936	0.879	0.823	0.936	CLONAL	1	TRUE	1	0.747500695290634	2		587	688	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032805	30032805	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs780872661	NA	P-0039515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	274	420	1	ENST00000338641.4:c.180G>A	p.Trp60Ter	p.W60*	ENST00000338641	NM_000268.3	60	tgG/tgA	2/16	0.747500695290634	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.747500695290634	1		421	446	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	133	492	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.832	0.758	0.91	0.832	0.758	0.91	CLONAL	1	TRUE	1	0.498796551185564	2		492	641	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336068	73336068	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	59	232	0	ENST00000377767.4:c.2335A>T	p.Ile779Phe	p.I779F	ENST00000377767	NM_014953.3	779	Att/Ttt	17/21	1	2	FACETS	0.839	0.728	0.957	0.839	0.728	0.957	CLONAL	1	TRUE	1	0.498796551185564	2		232	282	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106162529	106162529	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	111	308	0	ENST00000380013.4:c.3443A>G	p.Tyr1148Cys	p.Y1148C	ENST00000380013	NM_001127208.2	1148	tAt/tGt	4/11	1	2	FACETS	0.993	0.899	1	0.993	0.899	1	CLONAL	1	TRUE	1	0.498796551185564	2		308	448	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097763	8097763	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1409408969	NA	P-0039647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	332	802	0	ENST00000346208.3:c.145G>A	p.Val49Met	p.V49M	ENST00000346208		49	Gtg/Atg	2/6	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.498796551185564	2		802	1315	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543382	65543382	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0039647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	218	590	0	ENST00000358664.4:c.296-1G>C		p.X99_splice	ENST00000358664	NM_002382.4	99			0.498796551185564	1	FACETS	0.978	0.914	1	0.978	0.914	1	CLONAL	1	TRUE	0	0.498796551185564	1		590	671	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100526	157100526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769085274	NA	P-0039692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	23	162	0	ENST00000346085.5:c.1463C>T	p.Pro488Leu	p.P488L	ENST00000346085	NM_020732.3	488	cCg/cTg	1/20	0.180858056395015	6	FACETS	1	0.91	1			1	CLONAL	1	TRUE	NA	0.180858056395015	6		162	253	SUCCESS
RET	5979	MSKCC	GRCh37	10	43598069	43598069	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	49	427	0	ENST00000355710.3:c.617T>A	p.Leu206His	p.L206H	ENST00000355710	NM_020975.4	206	cTc/cAc	3/20	0.180858056395015	3	FACETS	0.986	0.835	1	0.493	0.417	0.577	CLONAL	1	TRUE	1	0.180858056395015	3		427	599	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149452934	149452934	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	48	449	0	ENST00000286301.3:c.1012T>C	p.Tyr338His	p.Y338H	ENST00000286301	NM_005211.3	338	Tac/Cac	7/22	0.180858056395015	3	FACETS	0.825	0.696	0.967	0.412	0.348	0.484	CLONAL	1	TRUE	1	0.180858056395015	3		449	702	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707605	176707605	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	58	407	0	ENST00000439151.2:c.5662G>C	p.Asp1888His	p.D1888H	ENST00000439151	NM_022455.4	1888	Gac/Cac	18/23	1	2	FACETS	0.916	0.786	1	0.916	0.786	1	CLONAL	1	TRUE	1	0.180858056395015	2		407	700	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181030	32181030	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0039692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	52	393	0	ENST00000375023.3:c.2321-1G>A		p.X774_splice	ENST00000375023	NM_004557.3	774			0.165266812396289	4	FACETS	1	0.85	1	0.5	0.425	0.583	CLONAL	1	TRUE	2	0.180858056395015	4		393	679	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967595	90967595	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786203131	NA	P-0039692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	48	289	0	ENST00000265433.3:c.1313G>T	p.Ser438Ile	p.S438I	ENST00000265433	NM_002485.4	438	aGt/aTt	10/16	0.177216940573665	4	FACETS	1	0.867	1			1	CLONAL	1	TRUE	NA	0.180858056395015	4		289	609	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578484	7578487	+	protein_altering_variant	In_Frame_Del	DEL	GAAT	GAAT	A	novel	NA	P-0039692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	178	589	0	ENST00000269305.4:c.443_446delinsT	p.Asp148_Ser149delinsVal	p.D148_S149delinsV	ENST00000269305	NM_001126112.2	148	gATTCc/gTc	5/11	0.163424294591889	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.180858056395015	2		589	796	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0001550-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	311	1131	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.312688951502705	3	FACETS	1	0.991	1	0.829	0.784	0.875	CLONAL	2	TRUE	0	0.312688951502705	3		1132	925	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273269	115273269	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001550-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	73	405	0	ENST00000438362.2:c.1189G>T	p.Gly397Cys	p.G397C	ENST00000438362	NM_001242891.1	397	Ggt/Tgt	11/20	0.312688951502705	3	FACETS	0.971	0.85	1	0.486	0.425	0.551	CLONAL	1	TRUE	1	0.312688951502705	3		405	556	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844175	156844175	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001550-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	685	795	0	ENST00000524377.1:c.1178T>A	p.Val393Asp	p.V393D	ENST00000524377	NM_002529.3	393	gTc/gAc	9/17	0.312688951502705	5	FACETS	0.971	0.94	1	0.971	0.94	1	CLONAL	5	TRUE	0	0.312688951502705	5		795	1326	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426112	49426112	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001550-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	64	714	0	ENST00000301067.7:c.12376G>C	p.Glu4126Gln	p.E4126Q	ENST00000301067	NM_003482.3	4126	Gag/Cag	39/54	0.312688951502705	3	FACETS	0.518	0.448	0.596			1	SUBCLONAL	1	TRUE	NA	0.312688951502705	3		714	913	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431492	49431492	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001550-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	156	679	0	ENST00000301067.7:c.9647A>T	p.Glu3216Val	p.E3216V	ENST00000301067	NM_003482.3	3216	gAg/gTg	34/54	0.312688951502705	3	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.312688951502705	3		679	957	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28631586	28631587	+	missense_variant	Missense_Mutation	DNP	TG	TG	AT	novel	NA	P-0001550-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	78	396	2	ENST00000241453.7:c.381_382delinsAT	p.Met128Leu	p.M128L	ENST00000241453	NM_004119.2	127	tcCAtg/tcATtg	4/24	0.268365106365635	2	FACETS	1	0.969	1	0.651	0.576	0.732	CLONAL	1	TRUE	0	0.312688951502705	2		398	383	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955391	48955391	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001550-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	63	257	0	ENST00000267163.4:c.1507del	p.Ser503LeufsTer16	p.S503Lfs*16	ENST00000267163	NM_000321.2	503	Tct/ct	17/27	0.268365106365635	2	FACETS	0.796	0.697	0.902	0.796	0.697	0.902	CLONAL	2	TRUE	0	0.312688951502705	2		257	253	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041452	42041452	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370050031	NA	P-0001550-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	184	560	0	ENST00000219905.7:c.5647G>A	p.Ala1883Thr	p.A1883T	ENST00000219905	NM_001164273.1	1883	Gca/Aca	17/24	0.26860240279724	2	FACETS	0.911	0.845	0.979	0.911	0.845	0.979	CLONAL	2	TRUE	0	0.312688951502705	2		560	646	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556178	29556178	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1064794275	NA	P-0001550-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	58	126	0	ENST00000356175.3:c.2545G>T	p.Gly849Ter	p.G849*	ENST00000356175	NM_000267.3	849	Gga/Tga	21/57	0.312688951502705	5	FACETS	0.913	0.797	1	0.913	0.797	1	CLONAL	3	TRUE	2	0.312688951502705	5		126	199	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661861	29661861	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1376900184	NA	P-0001550-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	109	323	0	ENST00000356175.3:c.5755G>T	p.Glu1919Ter	p.E1919*	ENST00000356175	NM_000267.3	1919	Gaa/Taa	39/57	0.312688951502705	5	FACETS	0.821	0.738	0.907	0.547	0.492	0.605	CLONAL	2	TRUE	2	0.312688951502705	5		323	624	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860924	45860924	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001550-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	486	769	0	ENST00000391945.4:c.1271G>C	p.Arg424Thr	p.R424T	ENST00000391945	NM_000400.3	424	aGa/aCa	13/23	0.280077343161764	4	FACETS	0.932	0.895	0.97	0.932	0.895	0.97	CLONAL	4	TRUE	0	0.312688951502705	4		769	1094	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032801	48032801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182024561	NA	P-0001550-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	86	339	0	ENST00000234420.5:c.3601C>T	p.Leu1201Phe	p.L1201F	ENST00000234420	NM_000179.2	1201	Ctc/Ttc	7/10	0.272082554985012	4	FACETS	0.797	0.708	0.891	0.797	0.708	0.891	SUBCLONAL	2	TRUE	2	0.312688951502705	4		339	453	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248389	212248389	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001550-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	90	322	0	ENST00000342788.4:c.3878G>T	p.Gly1293Val	p.G1293V	ENST00000342788	NM_005235.2	1293	gGc/gTc	28/28	0.272082554985012	4	FACETS	1	0.915	1	1	0.915	1	CLONAL	2	TRUE	2	0.312688951502705	4		322	368	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514522	41514522	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001550-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	137	492	1	ENST00000373198.4:c.139C>A	p.Leu47Ile	p.L47I	ENST00000373198	NM_133170.3	47	Cta/Ata	2/32	0.202780636109027	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.312688951502705	1		493	589	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62294226	62294226	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001550-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	105	599	0	ENST00000360203.5:c.522C>A	p.Phe174Leu	p.F174L	ENST00000360203	NM_001283009.1	174	ttC/ttA	6/35	0.20647425003054	4	FACETS	0.915	0.819	1	0.458	0.409	0.509	CLONAL	1	TRUE	2	0.312688951502705	4		599	963	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590666	189590666	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001550-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	77	425	0	ENST00000264731.3:c.1231T>C	p.Tyr411His	p.Y411H	ENST00000264731	NM_003722.4	411	Tat/Cat	10/14	0.312688951502705	5	FACETS	1	0.894	1	0.255	0.223	0.289	CLONAL	1	TRUE	1	0.312688951502705	5		425	709	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637926	176637926	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001550-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	81	594	0	ENST00000439151.2:c.2526G>T	p.Met842Ile	p.M842I	ENST00000439151	NM_022455.4	842	atG/atT	5/23	0.242116577927203	3	FACETS	0.731	0.643	0.825	0.365	0.321	0.413	SUBCLONAL	1	TRUE	1	0.312688951502705	3		594	820	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652546	48652546	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001550-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	330	500	0	ENST00000376670.3:c.1217C>A	p.Thr406Asn	p.T406N	ENST00000376670	NM_002049.3	406	aCt/aAt	6/6	0.312688951502705	4	FACETS	1	0.99	1			1	CLONAL	3	TRUE	NA	0.312688951502705	4		500	803	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880997	37880998	+	protein_altering_variant	In_Frame_Ins	INS	-	-	CTGTGGGCT	novel	NA	P-0001758-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	351	396	0	ENST00000269571.5:c.2326_2327insCTGTGGGCT	p.Gly776delinsAlaValGlyCys	p.G776delinsAVGC	ENST00000269571		776	ggt/gCTGTGGGCTgt	20/27	0.301950957627193	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	FALSE	2	0.326743918791543	4		396	1171	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880997	37880998	+	protein_altering_variant	In_Frame_Ins	INS	-	-	TGT	rs397516979	NA	P-0002320-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1217	1254	369	0	ENST00000269571.5:c.2326_2327insTGT	p.Gly776delinsValCys	p.G776delinsVC	ENST00000269571		776	ggt/gTGTgt	20/27	0.255219685533415	9	FACETS	0.941	0.919	0.964			1	CLONAL	8	TRUE	NA	0.255219685533415	9		369	2471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201059	NA	P-0002320-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1201	170	382	0	ENST00000269305.4:c.856G>T	p.Glu286Ter	p.E286*	ENST00000269305	NM_001126112.2	286	Gaa/Taa	8/11	0.238845960097938	1	FACETS	0.848	0.777	0.922	0.848	0.777	0.922	CLONAL	1	TRUE	0	0.255219685533415	1		382	1371	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543896	212543896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002320-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1343	105	361	0	ENST00000342788.4:c.1503G>A	p.Met501Ile	p.M501I	ENST00000342788	NM_005235.2	501	atG/atA	13/28	0.168297260428935	3	FACETS	0.641	0.572	0.715	0.32	0.286	0.358	SUBCLONAL	1	TRUE	1	0.255219685533415	3		361	1448	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950694	38950694	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002320-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1759	146	480	0	ENST00000357387.3:c.3256C>G	p.Pro1086Ala	p.P1086A	ENST00000357387	NM_152756.3	1086	Cct/Gct	31/38	0.168297260428935	3	FACETS	0.677	0.615	0.743	0.339	0.307	0.372	SUBCLONAL	1	TRUE	1	0.255219685533415	3		480	1905	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103412	77103412	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002320-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1747	177	467	0	ENST00000356341.3:c.154G>A	p.Asp52Asn	p.D52N	ENST00000356341	NM_002576.4	52	Gac/Aac	2/15	1	2	FACETS	0.721	0.661	0.784	0.721	0.661	0.784	SUBCLONAL	1	TRUE	1	0.255219685533415	2		467	1924	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649132	37649132	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002320-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1345	91	248	0	ENST00000447079.4:c.2237A>G	p.Asp746Gly	p.D746G	ENST00000447079	NM_015083.1	746	gAc/gGc	4/14	0.255219685533415	5	FACETS	0.687	0.607	0.772			1	SUBCLONAL	1	TRUE	NA	0.255219685533415	5		248	1436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0003198-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	182	630	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.412097844698979	2		630	678	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468158	50468158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003198-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	105	492	1	ENST00000331340.3:c.1393G>A	p.Glu465Lys	p.E465K	ENST00000331340	NM_006060.4	465	Gaa/Aaa	8/8	0.412097844698979	5	FACETS	0.857	0.767	0.954	0.286	0.255	0.318	CLONAL	1	TRUE	2	0.412097844698979	5		493	962	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426988	70426988	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003198-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	73	290	0	ENST00000373644.4:c.4648G>T	p.Asp1550Tyr	p.D1550Y	ENST00000373644	NM_030625.2	1550	Gac/Tac	7/12	1	2	FACETS	0.587	0.513	0.666	0.587	0.513	0.666	SUBCLONAL	1	TRUE	1	0.412097844698979	2		290	604	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756758	756758	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003198-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	107	415	0	ENST00000314574.4:c.70C>A	p.Pro24Thr	p.P24T	ENST00000314574	NM_005433.3	24	Cct/Act	2/12	0.192782730080119	5	FACETS	0.887	0.795	0.986			1	INDETERMINATE	1	TRUE	NA	0.412097844698979	5		415	947	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0004883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	404	360	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.498923733043844	4	FACETS	0.968	0.927	1	0.968	0.927	1	CLONAL	3	TRUE	1	0.498923733043844	4		360	836	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577587	7577587	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	203	698	2	ENST00000269305.4:c.694A>T	p.Ile232Phe	p.I232F	ENST00000269305	NM_001126112.2	232	Atc/Ttc	7/11	0.498923733043844	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.498923733043844	1		700	597	SUCCESS
APC	324	MSKCC	GRCh37	5	112175772	112175772	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	96	356	0	ENST00000257430.4:c.4483del	p.Ser1495ValfsTer12	p.S1495Vfs*12	ENST00000257430	NM_000038.5	1494	gAa/ga	16/16	0.498923733043844	1	FACETS	0.891	0.803	0.983	0.891	0.803	0.983	CLONAL	1	TRUE	0	0.498923733043844	1		356	324	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005445	42005445	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	236	748	0	ENST00000219905.7:c.3181C>G	p.Leu1061Val	p.L1061V	ENST00000219905	NM_001164273.1	1061	Cta/Gta	9/24	1	2	FACETS	0.952	0.889	1	0.952	0.889	1	CLONAL	1	TRUE	1	0.498923733043844	2		748	994	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777868	27777868	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	131	428	0	ENST00000369163.2:c.17A>C	p.Gln6Pro	p.Q6P	ENST00000369163	NM_003536.2	6	cAg/cCg	1/1	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.498923733043844	2		428	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0005858-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	147	625	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.477104072724569	3	FACETS	1	0.972	1	0.567	0.52	0.616	CLONAL	1	TRUE	1	0.616637316143234	3		627	550	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0005858-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	324	630	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.477104072724569	3	FACETS	0.955	0.908	1	0.955	0.908	1	CLONAL	2	TRUE	1	0.616637316143234	3		631	720	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0005858-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	153	343	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	0.616637316143234	4	FACETS	0.841	0.775	0.908	0.561	0.517	0.606	CLONAL	2	TRUE	1	0.616637316143234	4		343	477	SUCCESS
APC	324	MSKCC	GRCh37	5	112163677	112163677	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0005858-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	49	255	0	ENST00000257430.4:c.1600A>T	p.Lys534Ter	p.K534*	ENST00000257430	NM_000038.5	534	Aaa/Taa	13/16	0.326171786824781	3	FACETS	0.782	0.667	0.905	0.391	0.333	0.453	INDETERMINATE	1	TRUE	1	0.616637316143234	3		255	266	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857925	9857925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs534440095	NA	P-0005858-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	132	508	1	ENST00000330684.3:c.3476G>A	p.Arg1159His	p.R1159H	ENST00000330684	NM_001134407.1	1159	cGc/cAc	13/13	0.616637316143234	3	FACETS	0.815	0.742	0.893	0.408	0.371	0.447	CLONAL	1	TRUE	1	0.616637316143234	3		509	687	SUCCESS
APC	324	MSKCC	GRCh37	5	112173378	112173378	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005858-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	57	331	0	ENST00000257430.4:c.2087A>T	p.Glu696Val	p.E696V	ENST00000257430	NM_000038.5	696	gAa/gTa	16/16	0.326171786824781	3	FACETS	1	0.888	1	0.512	0.445	0.585	INDETERMINATE	1	TRUE	1	0.616637316143234	3		331	236	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005858-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	146	313	0	ENST00000257430.4:c.4199del	p.Ser1400Ter	p.S1400*	ENST00000257430	NM_000038.5	1400	tCg/tg	16/16	0.326171786824781	3	FACETS	0.903	0.836	0.971	0.903	0.836	0.971	INDETERMINATE	2	TRUE	1	0.616637316143234	3		313	343	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94963966	94963966	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005858-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	46	395	0	ENST00000536441.1:c.59G>T	p.Cys20Phe	p.C20F	ENST00000536441	NM_144665.3	20	tGc/tTc	1/10	0.616637316143234	3	FACETS	0.394	0.331	0.462	0.197	0.165	0.231	SUBCLONAL	1	TRUE	1	0.616637316143234	3		395	496	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443878	18443878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005858-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	32	311	0	ENST00000266497.5:c.851C>T	p.Ser284Phe	p.S284F	ENST00000266497		284	tCt/tTt	3/31	0.226782208103838	5	FACETS	0.571	0.464	0.691	0.114	0.092	0.139	INDETERMINATE	1	TRUE	0	0.616637316143234	5		311	350	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0006162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	166	523	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.972	0.902	1	0.972	0.902	1	CLONAL	1	TRUE	1	0.760566673476989	2		523	449	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0006162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	345	492	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	1	2	FACETS	0.889	0.843	0.935	0.889	0.843	0.935	CLONAL	1	TRUE	1	0.760566673476989	2		492	1021	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	270	322	1	ENST00000206249.3:c.1610A>G	p.Tyr537Cys	p.Y537C	ENST00000206249	NM_000125.3	537	tAt/tGt	8/8	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.760566673476989	2		323	690	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417865	138417865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	52	450	1	ENST00000289153.2:c.1654G>A	p.Glu552Lys	p.E552K	ENST00000289153	NM_006219.2	552	Gaa/Aaa	11/22	1	2	FACETS	0.157	0.133	0.184	0.157	0.133	0.184	SUBCLONAL	1	TRUE	1	0.760566673476989	2		451	869	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001539	150001539	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	197	255	0	ENST00000253339.5:c.2065G>C	p.Glu689Gln	p.E689Q	ENST00000253339		689	Gaa/Caa	4/7	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.760566673476989	2		255	513	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265533	152265533	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	191	334	0	ENST00000206249.3:c.986C>A	p.Ser329Tyr	p.S329Y	ENST00000206249	NM_000125.3	329	tCc/tAc	4/8	1	2	FACETS	0.86	0.8	0.921	0.86	0.8	0.921	CLONAL	1	TRUE	1	0.760566673476989	2		334	584	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611806	100611806	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	388	559	1	ENST00000308731.7:c.1315G>A	p.Glu439Lys	p.E439K	ENST00000308731	NM_000061.2	439	Gaa/Aaa	14/19	1	2	FACETS	0.975	0.929	1	0.975	0.929	1	CLONAL	1	TRUE	1	0.760566673476989	2		560	1046	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463300	25463301	+	protein_altering_variant	In_Frame_Ins	INS	-	-	TTT	novel	NA	P-0006162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	206	346	0	ENST00000264709.3:c.2192_2193insAAA	p.Phe731delinsLeuAsn	p.F731delinsLN	ENST00000264709	NM_175629.2	731	ttc/ttAAAc	19/23	1	2	FACETS	0.959	0.896	1	0.959	0.896	1	CLONAL	1	TRUE	1	0.760566673476989	2		346	565	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508823	106508823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	13	430	0	ENST00000359195.3:c.817C>T	p.Arg273Cys	p.R273C	ENST00000359195	NM_002649.2	273	Cgc/Tgc	2/11	0.499344951401222	3	FACETS	0.372	0.266	0.499	0.186	0.133	0.25	SUBCLONAL	1	TRUE	1	0.578240127022535	3		430	156	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127715	64127715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	60	449	0	ENST00000334205.4:c.208G>A	p.Ala70Thr	p.A70T	ENST00000334205	NM_003942.2	70	Gcg/Acg	3/17	0.589471228350995	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.578240127022535	1		449	100	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888178	81888178	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs535715020	NA	P-0006490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	17	625	0	ENST00000359376.3:c.323C>T	p.Thr108Met	p.T108M	ENST00000359376	NM_002661.3	108	aCg/aTg	3/33	0.589471228350995	1	FACETS	0.498	0.379	0.633	0.498	0.379	0.633	SUBCLONAL	1	TRUE	0	0.578240127022535	1		625	84	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035197	30035197	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0006490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	30	459	0	ENST00000338641.4:c.359T>A	p.Leu120Ter	p.L120*	ENST00000338641	NM_000268.3	120	tTa/tAa	3/16	0.503710696502436	1	FACETS	0.934	0.779	1	0.934	0.779	1	CLONAL	1	TRUE	0	0.578240127022535	1		459	79	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55524241	55524241	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	34	511	0	ENST00000288135.5:c.61del	p.Gln21ArgfsTer9	p.Q21Rfs*9	ENST00000288135	NM_000222.2	20	gtC/gt	1/21	0.318164765426302	2	FACETS	1	0.935	1	0.619	0.521	0.722	INDETERMINATE	1	TRUE	0	0.578240127022535	2		511	95	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593603	55593603	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913235	NA	P-0006501-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	219	459	0	ENST00000288135.5:c.1669T>G	p.Trp557Gly	p.W557G	ENST00000288135	NM_000222.2	557	Tgg/Ggg	11/21	1	2	FACETS	0.894	0.837	0.952	0.894	0.837	0.952	CLONAL	1	TRUE	1	0.813886507551181	2		459	602	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955080	93955080	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006501-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	343	513	0	ENST00000369303.4:c.2818T>C	p.Tyr940His	p.Y940H	ENST00000369303	NM_004440.3	940	Tat/Cat	16/17	1	2	FACETS	0.97	0.922	1	0.97	0.922	1	CLONAL	1	TRUE	1	0.813886507551181	2		513	869	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005421	150005421	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006501-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	311	468	0	ENST00000253339.5:c.804G>A	p.Trp268Ter	p.W268*	ENST00000253339		268	tgG/tgA	3/7	1	2	FACETS	0.979	0.928	1	0.979	0.928	1	CLONAL	1	TRUE	1	0.813886507551181	2		468	781	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6439806	6439806	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006501-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	337	359	0	ENST00000356142.4:c.332A>G	p.Asn111Ser	p.N111S	ENST00000356142	NM_018890.3	111	aAt/aGt	5/7	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.813886507551181	2		359	757	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010535	48010547	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGGGCCCAGGC	CCTGGGCCCAGGC	-	novel	NA	P-0006501-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	161	191	0	ENST00000234420.5:c.166_178del	p.Gly56TrpfsTer21	p.G56Wfs*21	ENST00000234420	NM_000179.2	55	CCTGGGCCCAGGCcc/cc	1/10	1	2	FACETS	0.938	0.869	1	0.938	0.869	1	CLONAL	1	TRUE	1	0.813886507551181	2		191	422	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592203	55592205	+	frameshift_variant	Frame_Shift_Del	DEL	AGG	AGG	T	novel	NA	P-0006501-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	32	333	0	ENST00000288135.5:c.1527_1529delinsT	p.Lys509AsnfsTer2	p.K509Nfs*2	ENST00000288135	NM_000222.2	509	aaAGGt/aaTt	9/21	1	2	FACETS	0.147	0.119	0.179	0.147	0.119	0.179	SUBCLONAL	1	TRUE	1	0.813886507551181	2		333	535	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579406	7579406	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006601-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	69	674	2	ENST00000269305.4:c.281C>A	p.Ser94Ter	p.S94*	ENST00000269305	NM_001126112.2	94	tCa/tAa	4/11	1	2	FACETS	0.843	0.732	0.963	0.843	0.732	0.963	CLONAL	1	FALSE	1	0.180773036978553	2		676	906	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115457	115115458	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006601-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	60	402	0	ENST00000257566.3:c.868dup	p.Thr290AsnfsTer37	p.T290Nfs*37	ENST00000257566	NM_016569.3	290	acc/aAcc	5/8	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	FALSE	1	0.180773036978553	2		402	654	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720701	89720701	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006601-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	14	129	0	ENST00000371953.3:c.853del	p.Glu285LysfsTer6	p.E285Kfs*6	ENST00000371953	NM_000314.4	284	gaG/ga	8/9	1	2	FACETS	0.815	0.591	1	0.815	0.591	1	CLONAL	1	FALSE	1	0.180773036978553	2		129	190	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943810	71943810	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0006601-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	63	552	0	ENST00000298229.2:c.1851+2T>G		p.X617_splice	ENST00000298229	NM_001567.3	617			NA	2	FACETS	0.89	0.769	1			1	INDETERMINATE	1	FALSE	NA	0.180773036978553	2		552	783	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947601	48947605	+	frameshift_variant	Frame_Shift_Del	DEL	TTCAG	TTCAG	CAAA	novel	NA	P-0006601-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	47	294	0	ENST00000267163.4:c.1188_1192delinsCAAA	p.Ser397LysfsTer4	p.S397Kfs*4	ENST00000267163	NM_000321.2	396	ccTTCAGaa/ccCAAAaa	12/27	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	FALSE	1	0.180773036978553	2		294	430	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006741-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	149	614	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.434162642292811	2		614	636	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983930	2983930	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006741-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	159	979	0	ENST00000396946.4:c.600C>A	p.Asp200Glu	p.D200E	ENST00000396946	NM_032415.4	200	gaC/gaA	5/25	1	2	FACETS	0.944	0.866	1	0.944	0.866	1	CLONAL	1	TRUE	1	0.434162642292811	2		979	776	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576397	7576978	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCGCCACTGCACTCCAGCCTGGGTGACAGAGTGAGACTCTGTCTCCAAAAAAAAAAAAAAAAAAAGCAGGCTAGGCTAAGCTATGATGTTCCTTAGATTAGGTGTATTAAATCCATTTTCAACTTACAATATTTTCAACTTACGACGAGTTTATCAGGAAGTAACACCATCGTAAGTCAAGTAGCATCTGTATCAGGCAAAGTCATAGAACCATTTTCATGCTCTCTTTAACAATTTTCTTTTTGAAAGCTGGTCTGGTCCTTTAAAATATATATTATGGTATAAGTTGGTGTTCTGAAGTTAGTTAGCTACAACCAGGAGCCATTGTCTTTGAGGCATCACTGCCCCCTGATGGCAAATGCCCCAATTGCAGGTAAAACAGTCAAGAAGAAAACGGCATTTTGAGTGTTAGACTGGAAACTTTCCACTTGATAAGAGGTCCCAAGACTTAGTACCTGAAGGGTGAAATATTCTCCATCCAGTGGTTTCTTCTTTGGCTGGGGAGAGGAGCTGGTGTTGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAAAGTGAATCTGAGGCATAACTGCA	CCCGCCACTGCACTCCAGCCTGGGTGACAGAGTGAGACTCTGTCTCCAAAAAAAAAAAAAAAAAAAGCAGGCTAGGCTAAGCTATGATGTTCCTTAGATTAGGTGTATTAAATCCATTTTCAACTTACAATATTTTCAACTTACGACGAGTTTATCAGGAAGTAACACCATCGTAAGTCAAGTAGCATCTGTATCAGGCAAAGTCATAGAACCATTTTCATGCTCTCTTTAACAATTTTCTTTTTGAAAGCTGGTCTGGTCCTTTAAAATATATATTATGGTATAAGTTGGTGTTCTGAAGTTAGTTAGCTACAACCAGGAGCCATTGTCTTTGAGGCATCACTGCCCCCTGATGGCAAATGCCCCAATTGCAGGTAAAACAGTCAAGAAGAAAACGGCATTTTGAGTGTTAGACTGGAAACTTTCCACTTGATAAGAGGTCCCAAGACTTAGTACCTGAAGGGTGAAATATTCTCCATCCAGTGGTTTCTTCTTTGGCTGGGGAGAGGAGCTGGTGTTGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAAAGTGAATCTGAGGCATAACTGCA	-	novel	NA	P-0006741-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	71	33	0	ENST00000269305.4:c.919+41_993+456del		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	0.434162642292811	1	FACETS	0.845	0.778	0.908	1	0.988	1	CLONAL	3	TRUE	0	0.434162642292811	1		33	101	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115861	8115862	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGAG	novel	NA	P-0006741-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	150	777	0	ENST00000346208.3:c.1208_1211dup	p.His405GlufsTer103	p.H405Efs*103	ENST00000346208		403	ctg/cTGAGtg	6/6	0.434162642292811	4	FACETS	0.987	0.901	1			1	CLONAL	1	TRUE	NA	0.434162642292811	4		777	1004	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319090	62319090	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006741-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	161	897	0	ENST00000360203.5:c.1448C>A	p.Ala483Asp	p.A483D	ENST00000360203	NM_001283009.1	483	gCc/gAc	17/35	0.431385510931443	5	FACETS	1	0.974	1	0.384	0.351	0.418	CLONAL	1	TRUE	2	0.434162642292811	5		897	1064	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143226687	143226687	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006741-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	91	419	0	ENST00000262992.4:c.427A>C	p.Ser143Arg	p.S143R	ENST00000262992	NM_001101669.1	143	Agt/Cgt	7/24	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.434162642292811	2		419	344	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445007	49445007	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006741-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	194	1139	0	ENST00000301067.7:c.2459A>C	p.Glu820Ala	p.E820A	ENST00000301067	NM_003482.3	820	gAg/gCg	10/54	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.434162642292811	2		1139	839	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	213	647	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.803	0.754	0.853	1	0.993	1	CLONAL	2	TRUE	1	0.52	2		647	510	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489217	2489217	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	287	642	0	ENST00000355716.4:c.122C>A	p.Ser41Tyr	p.S41Y	ENST00000355716	NM_003820.2	41	tCc/tAc	2/8	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		642	815	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073341	8073341	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs867572106	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	480	893	0	ENST00000377482.5:c.1318G>T	p.Asp440Tyr	p.D440Y	ENST00000377482	NM_018948.3	440	Gac/Tac	4/4	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.52	2		893	1477	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073460	8073460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770845999	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	497	1119	1	ENST00000377482.5:c.1199G>A	p.Arg400Gln	p.R400Q	ENST00000377482	NM_018948.3	400	cGa/cAa	4/4	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.52	2		1120	1577	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16246013	16246013	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	320	535	0	ENST00000375759.3:c.1635+1G>A		p.X545_splice	ENST00000375759	NM_015001.2	545			1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		535	915	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255346	16255346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151043425	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	431	732	1	ENST00000375759.3:c.2611C>T	p.Arg871Cys	p.R871C	ENST00000375759	NM_015001.2	871	Cgc/Tgc	11/15	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.52	2		733	1252	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256547	16256547	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	277	590	0	ENST00000375759.3:c.3812A>G	p.Glu1271Gly	p.E1271G	ENST00000375759	NM_015001.2	1271	gAa/gGa	11/15	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.52	2		590	829	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257770	16257770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779103344	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	197	385	0	ENST00000375759.3:c.5035G>A	p.Val1679Ile	p.V1679I	ENST00000375759	NM_015001.2	1679	Gtc/Atc	11/15	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.52	2		385	550	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260257	16260257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	117	238	1	ENST00000375759.3:c.7522C>T	p.Pro2508Ser	p.P2508S	ENST00000375759	NM_015001.2	2508	Cca/Tca	11/15	1	2	FACETS	0.771	0.706	0.837	1	0.987	1	SUBCLONAL	2	TRUE	1	0.52	2		239	292	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056224	27056224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780917379	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	297	527	0	ENST00000324856.7:c.1220C>T	p.Pro407Leu	p.P407L	ENST00000324856	NM_006015.4	407	cCt/cTt	2/20	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		527	848	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248451	59248451	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1467696555	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	51	462	0	ENST00000371222.2:c.292C>A	p.Leu98Met	p.L98M	ENST00000371222	NM_002228.3	98	Ctg/Atg	1/1	1	2	FACETS	0.253	0.215	0.296	0.253	0.215	0.296	SUBCLONAL	1	TRUE	1	0.52	2		462	774	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458467	120458467	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	131	371	0	ENST00000256646.2:c.6878A>G	p.His2293Arg	p.H2293R	ENST00000256646	NM_024408.3	2293	cAc/cGc	34/34	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.52	2		371	373	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466432	120466432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194257253	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	313	588	1	ENST00000256646.2:c.4687C>T	p.Arg1563Cys	p.R1563C	ENST00000256646	NM_024408.3	1563	Cgc/Tgc	26/34	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		589	889	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162735790	162735790	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	257	489	1	ENST00000367921.3:c.1100-1G>T		p.X367_splice	ENST00000367921	NM_006182.2	367			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.52	2		490	902	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162742026	162742026	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	306	548	0	ENST00000367921.3:c.1717C>T	p.Gln573Ter	p.Q573*	ENST00000367921	NM_006182.2	573	Cag/Tag	13/18	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		548	890	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204513673	204513673	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	39	378	0	ENST00000367182.3:c.683C>A	p.Thr228Asn	p.T228N	ENST00000367182	NM_001278516.1	228	aCt/aAt	9/11	1	2	FACETS	0.247	0.204	0.295	0.247	0.204	0.295	SUBCLONAL	1	TRUE	1	0.52	2		378	608	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658404	206658404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781938435	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	242	501	0	ENST00000367120.3:c.1498C>T	p.Arg500Trp	p.R500W	ENST00000367120	NM_014002.3	500	Cgg/Tgg	14/22	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.52	2		501	703	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206665012	206665012	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	335	514	0	ENST00000367120.3:c.1765C>A	p.Leu589Met	p.L589M	ENST00000367120	NM_014002.3	589	Ctg/Atg	18/22	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.52	2		514	862	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470027	25470027	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	180	370	0	ENST00000264709.3:c.1015G>A	p.Val339Met	p.V339M	ENST00000264709	NM_175629.2	339	Gtg/Atg	9/23	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.52	2		370	484	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965935	25965935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749408482	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	284	580	2	ENST00000435504.4:c.3271G>A	p.Ala1091Thr	p.A1091T	ENST00000435504		1091	Gct/Act	13/13	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.52	2		582	878	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978956	25978956	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	333	536	0	ENST00000435504.4:c.967A>C	p.Asn323His	p.N323H	ENST00000435504		323	Aat/Cat	10/13	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		536	967	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991736	25991736	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs530632623	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	199	388	0	ENST00000435504.4:c.506C>T	p.Ala169Val	p.A169V	ENST00000435504		169	gCg/gTg	7/13	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.52	2		388	609	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026852	48026852	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376220212	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	266	563	0	ENST00000234420.5:c.1730G>A	p.Arg577His	p.R577H	ENST00000234420	NM_000179.2	577	cGc/cAc	4/10	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.52	2		563	814	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027043	48027043	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1553413305	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	252	508	0	ENST00000234420.5:c.1921G>T	p.Glu641Ter	p.E641*	ENST00000234420	NM_000179.2	641	Gaa/Taa	4/10	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.52	2		508	767	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028265	48028265	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	147	487	1	ENST00000234420.5:c.3143A>G	p.Gln1048Arg	p.Q1048R	ENST00000234420	NM_000179.2	1048	cAg/cGg	4/10	1	2	FACETS	0.607	0.553	0.662	0.607	0.553	0.662	SUBCLONAL	1	TRUE	1	0.52	2		488	932	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033753	48033753	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1553333707	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	234	506	0	ENST00000234420.5:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000234420	NM_000179.2	1322	Gaa/Taa	9/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.52	2		506	764	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715401	61715401	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	115	423	0	ENST00000401558.2:c.2212A>C	p.Met738Leu	p.M738L	ENST00000401558	NM_003400.3	738	Atg/Ctg	19/25	1	2	FACETS	0.788	0.713	0.868	0.788	0.713	0.868	SUBCLONAL	1	TRUE	1	0.52	2		423	561	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172215	99172215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867982356	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	271	544	0	ENST00000074304.5:c.1781C>T	p.Ser594Phe	p.S594F	ENST00000074304	NM_001134224.1	594	tCc/tTc	17/26	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.52	2		544	829	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189362	99189362	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	244	488	0	ENST00000074304.5:c.2618A>C	p.Asn873Thr	p.N873T	ENST00000074304	NM_001134224.1	873	aAc/aCc	24/26	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.52	2		488	731	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047800	128047800	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	301	579	0	ENST00000285398.2:c.521G>T	p.Arg174Ile	p.R174I	ENST00000285398	NM_000122.1	174	aGa/aTa	4/15	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.52	2		579	831	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095520	178095520	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	221	423	0	ENST00000397062.3:c.1811A>C	p.Lys604Thr	p.K604T	ENST00000397062	NM_006164.4	604	aAa/aCa	5/5	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.52	2		423	661	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268346	198268346	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	279	504	0	ENST00000335508.6:c.1682A>T	p.Tyr561Phe	p.Y561F	ENST00000335508	NM_012433.2	561	tAc/tTc	12/25	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.52	2		504	726	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136238	202136238	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	253	515	0	ENST00000358485.4:c.483-1G>T		p.X161_splice	ENST00000358485	NM_001080125.1	161			1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.52	2		515	757	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735458	204735458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1270679463	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	279	519	0	ENST00000302823.3:c.259G>A	p.Ala87Thr	p.A87T	ENST00000302823	NM_005214.4	87	Gca/Aca	2/4	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		519	792	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543829	212543829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771154734	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	273	460	0	ENST00000342788.4:c.1570C>T	p.Arg524Cys	p.R524C	ENST00000342788	NM_005235.2	524	Cgc/Tgc	13/28	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.52	2		460	819	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578349	212578349	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	179	375	1	ENST00000342788.4:c.908C>A	p.Ser303Tyr	p.S303Y	ENST00000342788	NM_005235.2	303	tCt/tAt	8/28	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.52	2		376	574	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812251	212812251	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	72	506	0	ENST00000342788.4:c.325A>C	p.Lys109Gln	p.K109Q	ENST00000342788	NM_005235.2	109	Aaa/Caa	3/28	1	2	FACETS	0.36	0.314	0.41	0.36	0.314	0.41	SUBCLONAL	1	TRUE	1	0.52	2		506	769	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593434	215593434	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	39	457	0	ENST00000260947.4:c.2300T>C	p.Val767Ala	p.V767A	ENST00000260947	NM_000465.2	767	gTg/gCg	11/11	1	2	FACETS	0.195	0.161	0.234	0.195	0.161	0.234	SUBCLONAL	1	TRUE	1	0.52	2		457	768	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659832	227659832	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	95	163	0	ENST00000305123.5:c.3623A>G	p.His1208Arg	p.H1208R	ENST00000305123	NM_005544.2	1208	cAt/cGt	1/2	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.52	2		163	281	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662924	227662924	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	338	628	1	ENST00000305123.5:c.531G>T	p.Lys177Asn	p.K177N	ENST00000305123	NM_005544.2	177	aaG/aaT	1/2	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		629	989	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633244	12633244	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	127	570	1	ENST00000251849.4:c.1156C>T	p.Gln386Ter	p.Q386*	ENST00000251849	NM_002880.3	386	Caa/Taa	11/17	1	2	FACETS	0.547	0.495	0.602	0.547	0.495	0.602	SUBCLONAL	1	TRUE	1	0.52	2		571	893	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650355	12650355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	338	569	1	ENST00000251849.4:c.491G>A	p.Arg164Gln	p.R164Q	ENST00000251849	NM_002880.3	164	cGa/cAa	5/17	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.52	2		570	929	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274877	41274877	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	238	490	1	ENST00000349496.5:c.1127G>A	p.Arg376His	p.R376H	ENST00000349496	NM_001904.3	376	cGt/cAt	8/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.52	2		491	828	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162449	47162449	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	285	521	0	ENST00000409792.3:c.3677C>A	p.Pro1226Gln	p.P1226Q	ENST00000409792	NM_014159.6	1226	cCa/cAa	3/21	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.52	2		521	830	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162783	47162783	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	127	381	1	ENST00000409792.3:c.3343G>T	p.Glu1115Ter	p.E1115*	ENST00000409792	NM_014159.6	1115	Gaa/Taa	3/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.52	2		382	426	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934752	49934752	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777611015	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	369	719	1	ENST00000296474.3:c.2144G>A	p.Arg715Gln	p.R715Q	ENST00000296474	NM_002447.2	715	cGg/cAg	7/20	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.52	2		720	1045	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436399	52436399	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372987719	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	240	457	3	ENST00000460680.1:c.2095C>T	p.Arg699Trp	p.R699W	ENST00000460680	NM_004656.3	699	Cgg/Tgg	17/17	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.52	2		460	660	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610695	52610695	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	206	402	0	ENST00000394830.3:c.3478C>T	p.Arg1160Ter	p.R1160*	ENST00000394830	NM_018313.4	1160	Cga/Tga	23/30	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.52	2		402	592	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643540	52643540	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	310	580	0	ENST00000394830.3:c.2356T>G	p.Phe786Val	p.F786V	ENST00000394830	NM_018313.4	786	Ttt/Gtt	17/30	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.52	2		580	863	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643768	52643768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	249	581	0	ENST00000394830.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000394830	NM_018313.4	710	Cga/Tga	17/30	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.52	2		581	760	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987148	69987148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	235	462	0	ENST00000394351.3:c.209C>T	p.Ala70Val	p.A70V	ENST00000394351	NM_000248.3	70	gCa/gTa	2/9	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.52	2		462	626	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71008489	71008489	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	172	592	0	ENST00000318789.4:c.1943C>T	p.Pro648Leu	p.P648L	ENST00000318789	NM_032682.5	648	cCc/cTc	21/21	1	2	FACETS	0.641	0.589	0.695	0.641	0.589	0.695	SUBCLONAL	1	TRUE	1	0.52	2		592	1032	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247463	71247463	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	292	479	0	ENST00000318789.4:c.70A>G	p.Asn24Asp	p.N24D	ENST00000318789	NM_032682.5	24	Aac/Gac	6/21	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		479	827	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890203	72890203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758931723	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	264	570	0	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	0.52	2		570	867	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72891469	72891469	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	76	444	0	ENST00000325599.8:c.293G>T	p.Arg98Ile	p.R98I	ENST00000325599	NM_018130.2	98	aGa/aTa	3/11	1	2	FACETS	0.403	0.353	0.457	0.403	0.353	0.457	SUBCLONAL	1	TRUE	1	0.52	2		444	725	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72891538	72891538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs529764235	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	210	443	2	ENST00000325599.8:c.224G>A	p.Arg75His	p.R75H	ENST00000325599	NM_018130.2	75	cGc/cAc	3/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.52	2		445	700	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448624	89448624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	247	527	2	ENST00000336596.2:c.1588C>T	p.Pro530Ser	p.P530S	ENST00000336596	NM_005233.5	530	Cca/Tca	7/17	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.52	2		529	734	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119562107	119562107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139402886	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	251	493	0	ENST00000316626.5:c.1229C>T	p.Ala410Val	p.A410V	ENST00000316626		410	gCg/gTg	11/12	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.52	2		493	793	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911523	134911523	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749562219	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	67	601	0	ENST00000398015.3:c.1988G>A	p.Arg663Gln	p.R663Q	ENST00000398015	NM_004441.4	663	cGg/cAg	11/16	1	2	FACETS	0.301	0.26	0.344	0.301	0.26	0.344	SUBCLONAL	1	TRUE	1	0.52	2		601	857	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138409931	138409931	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	300	454	1	ENST00000289153.2:c.1947G>T	p.Glu649Asp	p.E649D	ENST00000289153	NM_006219.2	649	gaG/gaT	13/22	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.52	2		455	824	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478146	138478146	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	307	516	0	ENST00000289153.2:c.40A>C	p.Ile14Leu	p.I14L	ENST00000289153	NM_006219.2	14	Atc/Ctc	1/22	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.52	2		516	908	SUCCESS
ATR	545	MSKCC	GRCh37	3	142185236	142185236	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs777219248	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	165	598	0	ENST00000350721.4:c.6827C>A	p.Thr2276Asn	p.T2276N	ENST00000350721	NM_001184.3	2276	aCc/aAc	40/47	1	2	FACETS	0.637	0.584	0.692	0.637	0.584	0.692	SUBCLONAL	1	TRUE	1	0.52	2		598	997	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278201	142278201	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	173	382	0	ENST00000350721.4:c.1624A>C	p.Lys542Gln	p.K542Q	ENST00000350721	NM_001184.3	542	Aaa/Caa	7/47	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.52	2		382	521	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948056	178948056	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	237	439	0	ENST00000263967.3:c.2828A>C	p.Lys943Thr	p.K943T	ENST00000263967	NM_006218.2	943	aAa/aCa	20/21	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.52	2		439	756	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526194	189526194	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	320	580	2	ENST00000264731.3:c.458G>T	p.Ser153Ile	p.S153I	ENST00000264731	NM_003722.4	153	aGc/aTc	4/14	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		582	936	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808862	1808862	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140211846	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	147	623	1	ENST00000260795.2:c.2294C>T	p.Ala765Val	p.A765V	ENST00000260795		765	gCg/gTg	17/17	1	2	FACETS	0.63	0.575	0.687	0.63	0.575	0.687	SUBCLONAL	1	TRUE	1	0.52	2		624	898	SUCCESS
FIP1L1	81608	MSKCC	GRCh37	4	54280854	54280854	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1470714975	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	362	592	0	ENST00000358575.5:c.843G>T	p.Gln281His	p.Q281H	ENST00000358575	NM_001134937.1	281	caG/caT	10/18	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.52	2		592	955	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55962398	55962398	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	293	646	0	ENST00000263923.4:c.2726G>A	p.Gly909Glu	p.G909E	ENST00000263923	NM_002253.2	909	gGa/gAa	19/30	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.52	2		646	900	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55991433	55991433	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375186728	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	220	555	1	ENST00000263923.4:c.28G>A	p.Ala10Thr	p.A10T	ENST00000263923	NM_002253.2	10	Gcc/Acc	1/30	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.52	2		556	669	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231680	66231680	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	264	555	0	ENST00000273854.3:c.2020T>C	p.Cys674Arg	p.C674R	ENST00000273854	NM_004439.5	674	Tgt/Cgt	11/18	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		555	723	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270122	66270122	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140536477	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	330	633	0	ENST00000273854.3:c.1760C>T	p.Ala587Val	p.A587V	ENST00000273854	NM_004439.5	587	gCa/gTa	8/18	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.52	2		633	1007	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467697	66467697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779449792	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	39	474	0	ENST00000273854.3:c.572G>A	p.Arg191His	p.R191H	ENST00000273854	NM_004439.5	191	cGt/cAt	3/18	1	2	FACETS	0.201	0.166	0.241	0.201	0.166	0.241	SUBCLONAL	1	TRUE	1	0.52	2		474	745	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143350344	143350344	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	111	324	0	ENST00000262992.4:c.118C>T	p.Gln40Ter	p.Q40*	ENST00000262992	NM_001101669.1	40	Cag/Tag	3/24	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.52	2		324	373	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143350355	143350355	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	22	307	0	ENST00000262992.4:c.107C>A	p.Pro36Gln	p.P36Q	ENST00000262992	NM_001101669.1	36	cCa/cAa	3/24	1	2	FACETS	0.246	0.19	0.311	0.246	0.19	0.311	SUBCLONAL	1	TRUE	1	0.52	2		307	344	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	273	427	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		427	739	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247174	153247174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	219	497	0	ENST00000281708.4:c.1628G>A	p.Arg543Lys	p.R543K	ENST00000281708	NM_033632.3	543	aGa/aAa	10/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.52	2		497	734	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534377	187534377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	259	574	1	ENST00000441802.2:c.9349G>A	p.Asp3117Asn	p.D3117N	ENST00000441802	NM_005245.3	3117	Gat/Aat	13/27	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.52	2		575	898	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538862	187538862	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	37	362	0	ENST00000441802.2:c.8878G>T	p.Gly2960Ter	p.G2960*	ENST00000441802	NM_005245.3	2960	Gga/Tga	10/27	1	2	FACETS	0.259	0.213	0.31	0.259	0.213	0.31	SUBCLONAL	1	TRUE	1	0.52	2		362	550	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540027	187540027	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	124	557	0	ENST00000441802.2:c.7713G>T	p.Lys2571Asn	p.K2571N	ENST00000441802	NM_005245.3	2571	aaG/aaT	10/27	1	2	FACETS	0.547	0.494	0.602	0.547	0.494	0.602	SUBCLONAL	1	TRUE	1	0.52	2		557	872	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549707	187549707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377067763	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	82	545	1	ENST00000441802.2:c.4534G>A	p.Gly1512Ser	p.G1512S	ENST00000441802	NM_005245.3	1512	Ggc/Agc	8/27	1	2	FACETS	0.385	0.338	0.434	0.385	0.338	0.434	SUBCLONAL	1	TRUE	1	0.52	2		546	820	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557302	187557302	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	339	580	1	ENST00000441802.2:c.4060G>A	p.Glu1354Lys	p.E1354K	ENST00000441802	NM_005245.3	1354	Gag/Aag	6/27	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		581	996	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629619	187629619	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	50	476	1	ENST00000441802.2:c.1363G>T	p.Gly455Cys	p.G455C	ENST00000441802	NM_005245.3	455	Ggt/Tgt	2/27	1	2	FACETS	0.23	0.194	0.27	0.23	0.194	0.27	SUBCLONAL	1	TRUE	1	0.52	2		477	836	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251567	251567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	58	514	0	ENST00000264932.6:c.1778C>T	p.Ala593Val	p.A593V	ENST00000264932	NM_004168.2	593	gCc/gTc	13/15	1	2	FACETS	0.333	0.285	0.385	0.333	0.285	0.385	SUBCLONAL	1	TRUE	1	0.52	2		514	670	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278854	1278854	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761116773	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	54	503	3	ENST00000310581.5:c.2188G>A	p.Ala730Thr	p.A730T	ENST00000310581	NM_198253.2	730	Gcc/Acc	6/16	1	2	FACETS	0.286	0.244	0.333	0.286	0.244	0.333	SUBCLONAL	1	TRUE	1	0.52	2		506	725	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944623	38944623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	211	485	0	ENST00000357387.3:c.4838G>A	p.Arg1613His	p.R1613H	ENST00000357387	NM_152756.3	1613	cGc/cAc	36/38	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.52	2		485	597	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39002730	39002730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs926090441	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	321	444	0	ENST00000357387.3:c.299G>A	p.Arg100Gln	p.R100Q	ENST00000357387	NM_152756.3	100	cGa/cAa	5/38	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.52	2		444	865	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181765	56181765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1287268127	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	189	368	4	ENST00000399503.3:c.3989C>T	p.Ser1330Leu	p.S1330L	ENST00000399503	NM_005921.1	1330	tCg/tTg	17/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.52	2		372	546	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659288	86659288	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	77	544	1	ENST00000274376.6:c.1577C>A	p.Ser526Tyr	p.S526Y	ENST00000274376	NM_002890.2	526	tCt/tAt	11/25	1	2	FACETS	0.351	0.307	0.398	0.351	0.307	0.398	SUBCLONAL	1	TRUE	1	0.52	2		545	844	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665672	86665672	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	167	376	0	ENST00000274376.6:c.1653A>C	p.Glu551Asp	p.E551D	ENST00000274376	NM_002890.2	551	gaA/gaC	12/25	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.52	2		376	599	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672844	86672844	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	184	289	0	ENST00000274376.6:c.2331A>C	p.Glu777Asp	p.E777D	ENST00000274376	NM_002890.2	777	gaA/gaC	17/25	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.52	2		289	561	SUCCESS
APC	324	MSKCC	GRCh37	5	112173647	112173647	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1165139414	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	226	479	0	ENST00000257430.4:c.2356C>T	p.Arg786Cys	p.R786C	ENST00000257430	NM_000038.5	786	Cgt/Tgt	16/16	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.52	2		479	642	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	337	539	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		539	1010	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	191	429	0	ENST00000257430.4:c.4199C>A	p.Ser1400Ter	p.S1400*	ENST00000257430	NM_000038.5	1400	tCg/tAg	16/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.52	2		429	625	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505025	149505025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1222946958	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	244	453	0	ENST00000261799.4:c.1790G>A	p.Arg597Gln	p.R597Q	ENST00000261799	NM_002609.3	597	cGg/cAg	12/23	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		453	648	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518782	176518782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752817668	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	272	488	0	ENST00000292408.4:c.700C>T	p.Arg234Cys	p.R234C	ENST00000292408	NM_213647.1	234	Cgc/Tgc	6/18	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		488	759	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523357	176523357	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs775373903	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	221	532	0	ENST00000292408.4:c.2014G>A	p.Val672Met	p.V672M	ENST00000292408	NM_213647.1	672	Gtg/Atg	15/18	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.52	2		532	664	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047965	180047965	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370847176	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	230	549	0	ENST00000261937.6:c.2210G>A	p.Arg737His	p.R737H	ENST00000261937	NM_182925.4	737	cGc/cAc	15/30	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.52	2		549	649	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394896	394896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	113	442	1	ENST00000380956.4:c.292C>T	p.Arg98Trp	p.R98W	ENST00000380956	NM_001195286.1	98	Cgg/Tgg	3/9	1	2	FACETS	0.656	0.591	0.724	0.656	0.591	0.724	SUBCLONAL	1	TRUE	1	0.52	2		443	663	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225539	26225539	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377708081	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	605	1148	0	ENST00000360408.1:c.157C>T	p.Arg53Cys	p.R53C	ENST00000360408	NM_003532.2	53	Cgt/Tgt	1/1	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.52	2		1148	1785	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912857	29912857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	38	296	0	ENST00000376809.5:c.1034C>T	p.Thr345Ile	p.T345I	ENST00000376809	NM_002116.7	345	aCt/aTt	6/8	1	2	FACETS	0.262	0.216	0.314	0.262	0.216	0.314	SUBCLONAL	1	TRUE	1	0.52	2		296	557	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670344	30670344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	432	680	0	ENST00000376406.3:c.6088C>T	p.Pro2030Ser	p.P2030S	ENST00000376406	NM_014641.2	2030	Cct/Tct	14/15	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.52	2		680	1194	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673724	30673724	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61733207	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	300	575	1	ENST00000376406.3:c.3236G>A	p.Arg1079His	p.R1079H	ENST00000376406	NM_014641.2	1079	cGt/cAt	10/15	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.52	2		576	929	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681476	30681476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756890775	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	314	561	2	ENST00000376406.3:c.536G>A	p.Arg179His	p.R179H	ENST00000376406	NM_014641.2	179	cGt/cAt	4/15	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.52	2		563	982	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93968000	93968000	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	307	550	1	ENST00000369303.4:c.1927G>T	p.Glu643Ter	p.E643*	ENST00000369303	NM_004440.3	643	Gaa/Taa	11/17	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.52	2		551	943	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969189	93969189	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	345	658	0	ENST00000369303.4:c.1807C>A	p.Pro603Thr	p.P603T	ENST00000369303	NM_004440.3	603	Cca/Aca	10/17	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		658	1035	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979215	93979215	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	365	712	1	ENST00000369303.4:c.1613C>T	p.Ala538Val	p.A538V	ENST00000369303	NM_004440.3	538	gCt/gTt	7/17	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		713	1122	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553011	106553011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs955184509	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	220	463	1	ENST00000369096.4:c.976C>T	p.Arg326Cys	p.R326C	ENST00000369096	NM_001198.3	326	Cgc/Tgc	5/7	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.52	2		464	635	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112029156	112029156	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1251	116	777	1	ENST00000368678.4:c.412G>A	p.Val138Met	p.V138M	ENST00000368678		138	Gtg/Atg	5/13	1	2	FACETS	0.326	0.293	0.362	0.326	0.293	0.362	SUBCLONAL	1	TRUE	1	0.52	2		778	1367	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117629975	117629975	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	209	498	0	ENST00000368508.3:c.6551G>T	p.Arg2184Ile	p.R2184I	ENST00000368508	NM_002944.2	2184	aGa/aTa	41/43	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.52	2		498	599	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708052	117708052	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	235	517	0	ENST00000368508.3:c.2125G>T	p.Asp709Tyr	p.D709Y	ENST00000368508	NM_002944.2	709	Gac/Tac	14/43	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.52	2		517	668	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519291	137519291	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	125	489	0	ENST00000367739.4:c.1347A>G	p.Ile449Met	p.I449M	ENST00000367739	NM_000416.2	449	atA/atG	7/7	1	2	FACETS	0.6	0.543	0.66	0.6	0.543	0.66	SUBCLONAL	1	TRUE	1	0.52	2		489	801	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997697	149997697	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs145871963	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	213	422	0	ENST00000253339.5:c.2770C>T	p.Arg924Ter	p.R924*	ENST00000253339		924	Cga/Tga	5/7	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.52	2		422	603	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001176	150001176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1396310382	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	346	667	0	ENST00000253339.5:c.2428G>A	p.Ala810Thr	p.A810T	ENST00000253339		810	Gca/Aca	4/7	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		667	1010	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005300	150005300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753329720	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	346	597	0	ENST00000253339.5:c.925C>T	p.Pro309Ser	p.P309S	ENST00000253339		309	Ccc/Tcc	3/7	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.52	2		597	960	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023019	150023019	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	362	648	1	ENST00000253339.5:c.244C>T	p.Arg82Ter	p.R82*	ENST00000253339		82	Cga/Tga	1/7	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.52	2		649	1038	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023160	150023160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	311	584	2	ENST00000253339.5:c.103C>T	p.Arg35Trp	p.R35W	ENST00000253339		35	Cgg/Tgg	1/7	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.52	2		586	993	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265353	152265353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188957694	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	289	592	0	ENST00000206249.3:c.806G>A	p.Arg269His	p.R269H	ENST00000206249	NM_000125.3	269	cGc/cAc	4/8	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.52	2		592	843	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100605	157100605	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	193	412	0	ENST00000346085.5:c.1542G>T	p.Gln514His	p.Q514H	ENST00000346085	NM_020732.3	514	caG/caT	1/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.52	2		412	582	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517397	157517397	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	377	581	0	ENST00000346085.5:c.3961C>A	p.Leu1321Met	p.L1321M	ENST00000346085	NM_020732.3	1321	Ctg/Atg	16/20	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.52	2		581	1045	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527797	157527797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	225	395	1	ENST00000346085.5:c.5522C>T	p.Pro1841Leu	p.P1841L	ENST00000346085	NM_020732.3	1841	cCt/cTt	20/20	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		396	586	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161807903	161807903	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	232	434	0	ENST00000366898.1:c.1090T>G	p.Phe364Val	p.F364V	ENST00000366898	NM_004562.2	364	Ttc/Gtc	10/12	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.52	2		434	666	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976831	2976831	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753594488	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	283	568	0	ENST00000396946.4:c.1181C>T	p.Ser394Leu	p.S394L	ENST00000396946	NM_032415.4	394	tCg/tTg	9/25	0.178966475121966	3	FACETS	0.779	0.734	0.825	0.779	0.734	0.825	INDETERMINATE	2	TRUE	1	0.52	3		568	880	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935661	13935661	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	45	516	0	ENST00000405192.2:c.1195T>C	p.Phe399Leu	p.F399L	ENST00000405192	NM_001163147.1	399	Ttc/Ctc	12/12	0.178966475121966	3	FACETS	0.25	0.209	0.295	0.125	0.104	0.148	INDETERMINATE	1	TRUE	1	0.52	3		516	874	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946171	13946171	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	210	474	0	ENST00000405192.2:c.925C>T	p.Arg309Ter	p.R309*	ENST00000405192	NM_001163147.1	309	Cga/Tga	10/12	0.178966475121966	3	FACETS	1	0.99	1	0.679	0.633	0.727	INDETERMINATE	1	TRUE	1	0.52	3		474	749	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946222	13946222	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	97	273	1	ENST00000405192.2:c.874G>T	p.Asp292Tyr	p.D292Y	ENST00000405192	NM_001163147.1	292	Gac/Tac	10/12	0.178966475121966	3	FACETS	1	0.978	1	0.675	0.608	0.746	INDETERMINATE	1	TRUE	1	0.52	3		274	348	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242511	55242511	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs121913418	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	281	394	0	ENST00000275493.2:c.2281G>A	p.Asp761Asn	p.D761N	ENST00000275493	NM_005228.3	761	Gat/Aat	19/28	0.178966475121966	3	FACETS	1	0.97	1	1	0.97	1	INDETERMINATE	2	TRUE	1	0.52	3		394	657	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259469	55259469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146795390	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	48	554	2	ENST00000275493.2:c.2527G>A	p.Val843Ile	p.V843I	ENST00000275493	NM_005228.3	843	Gta/Ata	21/28	0.178966475121966	3	FACETS	0.268	0.226	0.315	0.134	0.113	0.158	INDETERMINATE	1	TRUE	1	0.52	3		556	867	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372746	81372746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	294	568	2	ENST00000222390.5:c.788C>T	p.Pro263Leu	p.P263L	ENST00000222390	NM_000601.4	263	cCc/cTc	7/18	0.178966475121966	3	FACETS	0.759	0.715	0.803	0.759	0.715	0.803	INDETERMINATE	2	TRUE	1	0.52	3		570	939	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374361	81374361	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1476385169	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	371	506	2	ENST00000222390.5:c.701G>A	p.Arg234His	p.R234H	ENST00000222390	NM_000601.4	234	cGc/cAc	6/18	0.178966475121966	3	FACETS	0.952	0.907	0.998	0.952	0.907	0.998	INDETERMINATE	2	TRUE	1	0.52	3		508	944	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836323	151836323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759486790	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	277	398	1	ENST00000262189.6:c.14482C>T	p.Arg4828Cys	p.R4828C	ENST00000262189	NM_170606.2	4828	Cgc/Tgc	57/59	0.178966475121966	3	FACETS	0.908	0.857	0.96	0.908	0.857	0.96	INDETERMINATE	2	TRUE	1	0.52	3		399	739	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845244	151845244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	98	527	0	ENST00000262189.6:c.13768C>T	p.Arg4590Cys	p.R4590C	ENST00000262189	NM_170606.2	4590	Cgc/Tgc	52/59	0.178966475121966	3	FACETS	0.688	0.614	0.767	0.344	0.307	0.384	INDETERMINATE	1	TRUE	1	0.52	3		527	690	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845763	151845763	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	425	565	2	ENST00000262189.6:c.13249G>A	p.Ala4417Thr	p.A4417T	ENST00000262189	NM_170606.2	4417	Gca/Aca	52/59	0.178966475121966	3	FACETS	1	0.982	1	1	0.982	1	INDETERMINATE	2	TRUE	1	0.52	3		567	981	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874052	151874052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	348	563	0	ENST00000262189.6:c.8486C>T	p.Pro2829Leu	p.P2829L	ENST00000262189	NM_170606.2	2829	cCa/cTa	38/59	0.178966475121966	3	FACETS	0.889	0.844	0.934	0.889	0.844	0.934	INDETERMINATE	2	TRUE	1	0.52	3		563	949	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874626	151874626	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	288	530	0	ENST00000262189.6:c.7912T>G	p.Ser2638Ala	p.S2638A	ENST00000262189	NM_170606.2	2638	Tct/Gct	38/59	0.178966475121966	3	FACETS	0.775	0.73	0.82	0.775	0.73	0.82	INDETERMINATE	2	TRUE	1	0.52	3		530	901	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055755	152055755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1403418496	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	186	390	0	ENST00000262189.6:c.167G>A	p.Arg56Gln	p.R56Q	ENST00000262189	NM_170606.2	56	cGa/cAa	2/59	0.178966475121966	3	FACETS	1	0.988	1	0.666	0.617	0.716	INDETERMINATE	1	TRUE	1	0.52	3		390	677	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271174	38271174	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	139	339	0	ENST00000425967.3:c.2534T>G	p.Leu845Arg	p.L845R	ENST00000425967	NM_001174067.1	845	cTt/cGt	19/19	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.52	2		339	420	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287397	38287397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145315779	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	252	515	0	ENST00000425967.3:c.260G>A	p.Arg87His	p.R87H	ENST00000425967	NM_001174067.1	87	cGc/cAc	4/19	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.52	2		515	696	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117870684	117870684	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	69	813	0	ENST00000297338.2:c.388G>A	p.Ala130Thr	p.A130T	ENST00000297338	NM_006265.2	130	Gcc/Acc	5/14	1	2	FACETS	0.245	0.213	0.281	0.245	0.213	0.281	SUBCLONAL	1	TRUE	1	0.52	2		813	1081	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738064	145738064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370549048	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	52	690	1	ENST00000428558.2:c.2846G>A	p.Cys949Tyr	p.C949Y	ENST00000428558	NM_004260.3	949	tGc/tAc	17/22	1	2	FACETS	0.233	0.198	0.272	0.233	0.198	0.272	SUBCLONAL	1	TRUE	1	0.52	2		691	858	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072504	5072504	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	158	307	0	ENST00000381652.3:c.1654G>A	p.Gly552Ser	p.G552S	ENST00000381652	NM_004972.3	552	Ggc/Agc	13/25	0.3	3	FACETS	1	0.989	1	0.742	0.684	0.801	INDETERMINATE	1	TRUE	1	0.52	3		307	516	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319950	8319950	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	308	398	0	ENST00000356435.5:c.5551A>G	p.Thr1851Ala	p.T1851A	ENST00000356435		1851	Act/Gct	34/35	0.3	3	FACETS	1	0.965	1	1	0.965	1	INDETERMINATE	2	TRUE	1	0.52	3		398	731	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404576	8404576	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146844299	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	363	558	1	ENST00000356435.5:c.4171G>A	p.Ala1391Thr	p.A1391T	ENST00000356435		1391	Gca/Aca	25/35	0.3	3	FACETS	1	0.973	1	1	0.973	1	INDETERMINATE	2	TRUE	1	0.52	3		559	854	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8733794	8733794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs949202374	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	386	520	1	ENST00000356435.5:c.50G>A	p.Arg17His	p.R17H	ENST00000356435		17	cGc/cAc	1/35	0.3	3	FACETS	1	0.986	1	1	0.986	1	INDETERMINATE	2	TRUE	1	0.52	3		521	869	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974798	21974798	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	35	150	0	ENST00000304494.5:c.29A>T	p.Glu10Val	p.E10V	ENST00000304494	NM_000077.4	10	gAg/gTg	1/3	0.3	3	FACETS	0.645	0.531	0.771	0.322	0.265	0.386	INDETERMINATE	1	TRUE	1	0.52	3		150	263	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80343580	80343580	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	320	274	0	ENST00000286548.4:c.739C>T	p.Arg247Ter	p.R247*	ENST00000286548	NM_002072.3	247	Cga/Tga	6/7	0.3	4	FACETS	1	0.96	1	1	0.96	1	INDETERMINATE	3	TRUE	1	0.52	4		274	619	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80646130	80646130	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	18	42	0	ENST00000286548.4:c.22G>T	p.Ala8Ser	p.A8S	ENST00000286548	NM_002072.3	8	Gcg/Tcg	1/7	0.3	4	FACETS	1	0.891	1	0.438	0.337	0.552	INDETERMINATE	1	TRUE	1	0.52	4		42	80	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482158	87482158	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs149694868	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	210	444	0	ENST00000277120.3:c.1445G>A	p.Gly482Asp	p.G482D	ENST00000277120		482	gGc/gAc	14/19	0.3	4	FACETS	1	0.991	1	0.477	0.443	0.512	INDETERMINATE	1	TRUE	1	0.52	4		444	858	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635252	87635252	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	332	399	0	ENST00000277120.3:c.2304G>T	p.Gln768His	p.Q768H	ENST00000277120		768	caG/caT	18/19	0.3	4	FACETS	0.914	0.87	0.957	0.914	0.87	0.957	INDETERMINATE	3	TRUE	1	0.52	4		399	708	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637049	93637049	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	321	563	1	ENST00000375746.1:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000375746	NM_001174167.1	367	Cga/Tga	9/14	0.3	4	FACETS	0.799	0.755	0.845	0.533	0.503	0.564	INDETERMINATE	2	TRUE	1	0.52	4		564	1174	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639903	93639903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs551292916	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	91	461	0	ENST00000375746.1:c.1232C>T	p.Pro411Leu	p.P411L	ENST00000375746	NM_001174167.1	411	cCc/cTc	10/14	0.3	4	FACETS	0.588	0.521	0.66	0.196	0.173	0.22	INDETERMINATE	1	TRUE	1	0.52	4		461	905	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650128	93650128	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	78	577	0	ENST00000375746.1:c.1679T>C	p.Val560Ala	p.V560A	ENST00000375746	NM_001174167.1	560	gTg/gCg	12/14	0.3	4	FACETS	0.367	0.321	0.417	0.122	0.107	0.139	INDETERMINATE	1	TRUE	1	0.52	4		577	1242	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239912	98239912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766898310	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	261	477	0	ENST00000331920.6:c.1420G>A	p.Val474Ile	p.V474I	ENST00000331920	NM_000264.3	474	Gtc/Atc	10/24	0.3	4	FACETS	0.811	0.761	0.862	0.541	0.507	0.575	INDETERMINATE	2	TRUE	1	0.52	4		477	941	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248055	98248055	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	652	638	0	ENST00000331920.6:c.496G>T	p.Gly166Cys	p.G166C	ENST00000331920	NM_000264.3	166	Ggt/Tgt	3/24	0.3	4	FACETS	0.932	0.901	0.964	0.932	0.901	0.964	INDETERMINATE	3	TRUE	1	0.52	4		638	1363	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270571	98270571	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	79	86	0	ENST00000331920.6:c.73G>A	p.Gly25Arg	p.G25R	ENST00000331920	NM_000264.3	25	Gga/Aga	1/24	0.3	4	FACETS	1	0.924	1	1	0.924	1	INDETERMINATE	3	TRUE	1	0.52	4		86	151	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891287	101891287	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757374917	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	550	537	1	ENST00000374994.4:c.248C>T	p.Pro83Leu	p.P83L	ENST00000374994	NM_004612.2	83	cCg/cTg	2/9	0.3	4	FACETS	0.925	0.891	0.959	0.925	0.891	0.959	INDETERMINATE	3	TRUE	1	0.52	4		538	1159	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900171	101900171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564161322	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	241	449	0	ENST00000374994.4:c.605C>T	p.Ala202Val	p.A202V	ENST00000374994	NM_004612.2	202	gCg/gTg	4/9	0.3	4	FACETS	1	0.991	1	0.456	0.426	0.488	INDETERMINATE	1	TRUE	1	0.52	4		449	1029	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907074	101907074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	256	471	0	ENST00000374994.4:c.1034G>A	p.Gly345Glu	p.G345E	ENST00000374994	NM_004612.2	345	gGa/gAa	6/9	0.3	4	FACETS	1	0.992	1	0.487	0.456	0.519	INDETERMINATE	1	TRUE	1	0.52	4		471	1024	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730245	133730245	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	278	543	2	ENST00000318560.5:c.311C>T	p.Thr104Ile	p.T104I	ENST00000318560	NM_005157.4	104	aCc/aTc	3/11	0.3	4	FACETS	0.761	0.715	0.808	0.507	0.476	0.539	INDETERMINATE	2	TRUE	1	0.52	4		545	1068	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396512	139396512	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	238	528	0	ENST00000277541.6:c.5413C>A	p.Leu1805Ile	p.L1805I	ENST00000277541	NM_017617.3	1805	Ctc/Atc	29/34	0.3	4	FACETS	1	0.992	1	0.497	0.464	0.531	INDETERMINATE	1	TRUE	1	0.52	4		528	933	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412717	139412717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	288	623	2	ENST00000277541.6:c.1127G>A	p.Cys376Tyr	p.C376Y	ENST00000277541	NM_017617.3	376	tGc/tAc	7/34	0.3	4	FACETS	1	0.993	1	0.485	0.456	0.516	INDETERMINATE	1	TRUE	1	0.52	4		625	1156	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417436	139417436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182763411	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	165	604	1	ENST00000277541.6:c.608G>A	p.Arg203His	p.R203H	ENST00000277541	NM_017617.3	203	cGc/cAc	4/34	0.3	4	FACETS	0.789	0.723	0.859	0.263	0.241	0.287	INDETERMINATE	1	TRUE	1	0.52	4		605	1222	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610186	43610186	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	296	801	0	ENST00000355710.3:c.2136+2T>C		p.X712_splice	ENST00000355710	NM_020975.4	712			1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		801	814	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70412277	70412277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	270	635	0	ENST00000373644.4:c.4387G>A	p.Ala1463Thr	p.A1463T	ENST00000373644	NM_030625.2	1463	Gca/Aca	6/12	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.52	2		635	816	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446203	70446203	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	45	530	0	ENST00000373644.4:c.5143G>T	p.Asp1715Tyr	p.D1715Y	ENST00000373644	NM_030625.2	1715	Gac/Tac	11/12	1	2	FACETS	0.221	0.185	0.261	0.221	0.185	0.261	SUBCLONAL	1	TRUE	1	0.52	2		530	784	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446272	70446272	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	233	394	0	ENST00000373644.4:c.5212G>T	p.Ala1738Ser	p.A1738S	ENST00000373644	NM_030625.2	1738	Gca/Tca	11/12	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.52	2		394	691	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693000	89693000	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	144	274	0	ENST00000371953.3:c.484G>T	p.Asp162Tyr	p.D162Y	ENST00000371953	NM_000314.4	162	Gac/Tac	5/9	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.52	2		274	377	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123246935	123246935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113014479	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	240	528	2	ENST00000358487.5:c.1990C>T	p.Arg664Trp	p.R664W	ENST00000358487	NM_000141.4	664	Cgg/Tgg	15/18	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.52	2		530	752	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156668	2156668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	52	663	0	ENST00000434045.2:c.254G>A	p.Ser85Asn	p.S85N	ENST00000434045	NM_001127598.1	85	aGt/aAt	3/5	1	2	FACETS	0.209	0.177	0.244	0.209	0.177	0.244	SUBCLONAL	1	TRUE	1	0.52	2		663	957	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251961	8251961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	267	671	2	ENST00000335790.3:c.116C>T	p.Ala39Val	p.A39V	ENST00000335790	NM_002315.2	39	gCa/gTa	2/4	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		673	744	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741493	17741493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	243	436	0	ENST00000250003.3:c.164C>T	p.Ala55Val	p.A55V	ENST00000250003	NM_002478.4	55	gCg/gTg	1/3	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		436	641	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137020	64137020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1174133485	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	274	479	0	ENST00000334205.4:c.1531C>T	p.Arg511Cys	p.R511C	ENST00000334205	NM_003942.2	511	Cgc/Tgc	13/17	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		479	734	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202630	67202630	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	33	330	1	ENST00000312629.5:c.1439C>A	p.Pro480Gln	p.P480Q	ENST00000312629	NM_003952.2	480	cCa/cAa	15/15	1	2	FACETS	0.243	0.197	0.294	0.243	0.197	0.294	SUBCLONAL	1	TRUE	1	0.52	2		331	523	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090300	77090300	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	335	589	0	ENST00000356341.3:c.425A>G	p.Tyr142Cys	p.Y142C	ENST00000356341	NM_002576.4	142	tAc/tGc	4/15	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.52	2		589	935	SUCCESS
EED	8726	MSKCC	GRCh37	11	85975226	85975226	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	211	417	0	ENST00000263360.6:c.647G>A	p.Arg216Gln	p.R216Q	ENST00000263360	NM_003797.3	216	cGa/cAa	7/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.52	2		417	706	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988124	85988124	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	45	555	0	ENST00000263360.6:c.1069G>A	p.Asp357Asn	p.D357N	ENST00000263360	NM_003797.3	357	Gat/Aat	10/12	1	2	FACETS	0.21	0.175	0.248	0.21	0.175	0.248	SUBCLONAL	1	TRUE	1	0.52	2		555	826	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933432	100933432	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	360	666	0	ENST00000325455.5:c.1958C>A	p.Ala653Asp	p.A653D	ENST00000325455	NM_001202474.3	653	gCt/gAt	4/8	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.52	2		666	1053	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196243	108196243	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	100	406	0	ENST00000278616.4:c.6779T>C	p.Ile2260Thr	p.I2260T	ENST00000278616	NM_000051.3	2260	aTa/aCa	46/63	1	2	FACETS	0.597	0.534	0.664	0.597	0.534	0.664	SUBCLONAL	1	TRUE	1	0.52	2		406	644	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344723	118344723	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	109	523	0	ENST00000534358.1:c.2849T>C	p.Leu950Pro	p.L950P	ENST00000534358	NM_005933.3	950	cTt/cCt	3/36	1	2	FACETS	0.525	0.471	0.583	0.525	0.471	0.583	SUBCLONAL	1	TRUE	1	0.52	2		523	798	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376306	118376306	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	445	785	2	ENST00000534358.1:c.9699G>T	p.Lys3233Asn	p.K3233N	ENST00000534358	NM_005933.3	3233	aaG/aaT	27/36	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.52	2		787	1262	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	441088	441088	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	370	593	0	ENST00000399788.2:c.1670A>T	p.Gln557Leu	p.Q557L	ENST00000399788	NM_001042603.1	557	cAg/cTg	13/28	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.52	2		593	1068	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023137	1023137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	299	590	4	ENST00000358495.3:c.1118G>A	p.Ser373Asn	p.S373N	ENST00000358495	NM_134424.2	373	aGc/aAc	11/12	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.52	2		594	939	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18439865	18439865	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	65	357	0	ENST00000266497.5:c.761+2T>C		p.X254_splice	ENST00000266497		254			NA	2	FACETS	0.459	0.398	0.525			1	INDETERMINATE	1	TRUE	NA	0.52	2		357	545	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446850	18446850	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	159	342	0	ENST00000266497.5:c.935A>G	p.Lys312Arg	p.K312R	ENST00000266497		312	aAa/aGa	4/31	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.52	2		342	459	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641499	18641499	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	328	558	0	ENST00000266497.5:c.2498A>C	p.Lys833Thr	p.K833T	ENST00000266497		833	aAa/aCa	17/31	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.52	2		558	927	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	147	491	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.52	2		491	476	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398253	25398253	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	294	503	0	ENST00000311936.3:c.66G>T	p.Gln22His	p.Q22H	ENST00000311936	NM_004985.3	22	caG/caT	2/5	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.52	2		503	826	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246324	46246324	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	249	415	1	ENST00000334344.6:c.4418C>A	p.Ser1473Tyr	p.S1473Y	ENST00000334344	NM_152641.2	1473	tCt/tAt	15/21	0.178966475121966	3	FACETS	0.921	0.867	0.976	0.921	0.867	0.976	INDETERMINATE	2	TRUE	1	0.52	3		416	655	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246470	46246470	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	329	632	0	ENST00000334344.6:c.4564A>G	p.Thr1522Ala	p.T1522A	ENST00000334344	NM_152641.2	1522	Act/Gct	15/21	0.178966475121966	3	FACETS	0.837	0.792	0.881	0.837	0.792	0.881	INDETERMINATE	2	TRUE	1	0.52	3		632	953	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427014	49427014	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	34	417	1	ENST00000301067.7:c.11474G>T	p.Arg3825Ile	p.R3825I	ENST00000301067	NM_003482.3	3825	aGa/aTa	39/54	0.178966475121966	3	FACETS	0.31	0.253	0.375	0.155	0.126	0.188	INDETERMINATE	1	TRUE	1	0.52	3		418	531	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434244	49434244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	445	849	3	ENST00000301067.7:c.7309C>T	p.Pro2437Ser	p.P2437S	ENST00000301067	NM_003482.3	2437	Cca/Tca	31/54	0.178966475121966	3	FACETS	0.867	0.828	0.907	0.867	0.828	0.907	INDETERMINATE	2	TRUE	1	0.52	3		852	1243	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434664	49434664	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748334191	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	248	465	0	ENST00000301067.7:c.6889C>T	p.Pro2297Ser	p.P2297S	ENST00000301067	NM_003482.3	2297	Cct/Tct	31/54	0.178966475121966	3	FACETS	0.922	0.867	0.977	0.922	0.867	0.977	INDETERMINATE	2	TRUE	1	0.52	3		465	652	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440420	49440420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1474346582	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	48	430	1	ENST00000301067.7:c.4390G>A	p.Val1464Ile	p.V1464I	ENST00000301067	NM_003482.3	1464	Gtc/Atc	15/54	0.178966475121966	3	FACETS	0.312	0.263	0.367	0.156	0.131	0.184	INDETERMINATE	1	TRUE	1	0.52	3		431	745	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446350	49446350	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	278	450	0	ENST00000301067.7:c.1255C>A	p.Leu419Ile	p.L419I	ENST00000301067	NM_003482.3	419	Cta/Ata	9/54	0.178966475121966	3	FACETS	0.912	0.861	0.963	0.912	0.861	0.963	INDETERMINATE	2	TRUE	1	0.52	3		450	739	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857520	57857520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	60	714	1	ENST00000228682.2:c.46C>T	p.Pro16Ser	p.P16S	ENST00000228682	NM_005269.2	16	Ccc/Tcc	2/12	0.178966475121966	3	FACETS	0.261	0.224	0.302	0.131	0.112	0.151	INDETERMINATE	1	TRUE	1	0.52	3		715	1114	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856365	111856365	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750857643	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	67	127	0	ENST00000341259.2:c.416G>A	p.Arg139His	p.R139H	ENST00000341259	NM_005475.2	139	cGc/cAc	2/8	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.52	2		127	218	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856529	111856529	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	47	305	2	ENST00000341259.2:c.580G>A	p.Glu194Lys	p.E194K	ENST00000341259	NM_005475.2	194	Gag/Aag	2/8	1	2	FACETS	0.302	0.254	0.355	0.302	0.254	0.355	SUBCLONAL	1	TRUE	1	0.52	2		307	598	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885484	111885484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs925290350	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	408	632	1	ENST00000341259.2:c.1261C>T	p.Arg421Trp	p.R421W	ENST00000341259	NM_005475.2	421	Cgg/Tgg	7/8	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.52	2		633	1062	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891154	112891154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	268	532	1	ENST00000351677.2:c.488G>A	p.Gly163Asp	p.G163D	ENST00000351677	NM_002834.3	163	gGc/gAc	4/16	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.52	2		533	791	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112893854	112893854	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	216	463	0	ENST00000351677.2:c.743G>A	p.Trp248Ter	p.W248*	ENST00000351677	NM_002834.3	248	tGg/tAg	6/16	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.52	2		463	654	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220026	133220026	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528264567	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	218	563	0	ENST00000320574.5:c.4411C>T	p.Arg1471Cys	p.R1471C	ENST00000320574	NM_006231.2	1471	Cgc/Tgc	34/49	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.52	2		563	656	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244105	133244105	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	117	462	0	ENST00000320574.5:c.2303T>C	p.Phe768Ser	p.F768S	ENST00000320574	NM_006231.2	768	tTc/tCc	20/49	1	2	FACETS	0.558	0.503	0.616	0.558	0.503	0.616	SUBCLONAL	1	TRUE	1	0.52	2		462	807	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252340	133252340	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	258	544	0	ENST00000320574.5:c.1087A>G	p.Asn363Asp	p.N363D	ENST00000320574	NM_006231.2	363	Aac/Gac	11/49	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.52	2		544	792	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257725	133257725	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	86	414	0	ENST00000320574.5:c.203C>A	p.Pro68His	p.P68H	ENST00000320574	NM_006231.2	68	cCt/cAt	2/49	1	2	FACETS	0.524	0.464	0.589	0.524	0.464	0.589	SUBCLONAL	1	TRUE	1	0.52	2		414	631	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623788	28623788	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	291	541	0	ENST00000241453.7:c.866A>G	p.Asn289Ser	p.N289S	ENST00000241453	NM_004119.2	289	aAc/aGc	7/24	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		541	811	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28963948	28963948	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	305	579	0	ENST00000282397.4:c.1954G>A	p.Glu652Lys	p.E652K	ENST00000282397	NM_002019.4	652	Gaa/Aaa	13/30	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.52	2		579	831	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32905116	32905116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55854959	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	203	415	0	ENST00000380152.3:c.742G>A	p.Ala248Thr	p.A248T	ENST00000380152		248	Gct/Act	9/27	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.52	2		415	663	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912807	32912807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358666	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	536	857	5	ENST00000380152.3:c.4315G>A	p.Ala1439Thr	p.A1439T	ENST00000380152		1439	Gcc/Acc	11/27	1	2	FACETS	0.897	0.863	0.931	1	0.997	1	CLONAL	2	TRUE	1	0.52	2		862	1149	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913182	32913182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	472	945	0	ENST00000380152.3:c.4690G>A	p.Ala1564Thr	p.A1564T	ENST00000380152		1564	Gca/Aca	11/27	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.52	2		945	1352	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913215	32913215	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587782013	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	425	970	1	ENST00000380152.3:c.4723G>T	p.Asp1575Tyr	p.D1575Y	ENST00000380152		1575	Gac/Tac	11/27	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.52	2		971	1408	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915232	32915232	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	447	895	2	ENST00000380152.3:c.6740G>T	p.Ser2247Ile	p.S2247I	ENST00000380152		2247	aGt/aTt	11/27	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.52	2		897	1268	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929375	32929375	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	393	849	0	ENST00000380152.3:c.7385C>A	p.Ser2462Tyr	p.S2462Y	ENST00000380152		2462	tCc/tAc	14/27	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		849	1193	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239736	41239736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	331	637	2	ENST00000379561.5:c.614G>A	p.Ser205Asn	p.S205N	ENST00000379561	NM_002015.3	205	aGc/aAc	1/3	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.52	2		639	938	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239785	41239785	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	313	640	0	ENST00000379561.5:c.565T>C	p.Trp189Arg	p.W189R	ENST00000379561	NM_002015.3	189	Tgg/Cgg	1/3	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.52	2		640	990	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881516	48881516	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	211	492	0	ENST00000267163.4:c.238A>T	p.Lys80Ter	p.K80*	ENST00000267163	NM_000321.2	80	Aaa/Taa	2/27	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.52	2		492	610	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941657	48941657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1060503077	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	187	390	1	ENST00000267163.4:c.967G>T	p.Glu323Ter	p.E323*	ENST00000267163	NM_000321.2	323	Gaa/Taa	10/27	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.52	2		391	533	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954342	48954342	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780248969	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	174	337	0	ENST00000267163.4:c.1463C>T	p.Ala488Val	p.A488V	ENST00000267163	NM_000321.2	488	gCg/gTg	16/27	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.52	2		337	520	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515220	103515220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	279	538	0	ENST00000355739.4:c.1721C>A	p.Ala574Asp	p.A574D	ENST00000355739	NM_000123.3	574	gCt/gAt	8/15	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.52	2		538	907	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435130	110435130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	204	382	0	ENST00000375856.3:c.3271C>T	p.Pro1091Ser	p.P1091S	ENST00000375856	NM_003749.2	1091	Ccg/Tcg	1/2	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.52	2		382	545	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435522	110435522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1387644128	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	107	209	1	ENST00000375856.3:c.2879C>T	p.Ser960Leu	p.S960L	ENST00000375856	NM_003749.2	960	tCa/tTa	1/2	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.52	2		210	288	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437478	110437478	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	224	438	0	ENST00000375856.3:c.923C>T	p.Ser308Leu	p.S308L	ENST00000375856	NM_003749.2	308	tCg/tTg	1/2	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.52	2		438	642	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560364	95560364	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	246	504	0	ENST00000393063.1:c.5225A>G	p.Asn1742Ser	p.N1742S	ENST00000393063	NM_030621.3	1742	aAc/aGc	25/28	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.52	2		504	712	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105240286	105240286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369698909	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	187	564	2	ENST00000349310.3:c.665G>A	p.Arg222His	p.R222H	ENST00000349310	NM_001014432.1	222	cGc/cAc	9/15	1	2	FACETS	0.87	0.805	0.937	0.87	0.805	0.937	CLONAL	1	TRUE	1	0.52	2		566	827	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246530	105246530	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	103	511	0	ENST00000349310.3:c.70C>T	p.Pro24Ser	p.P24S	ENST00000349310	NM_001014432.1	24	Cca/Tca	4/15	1	2	FACETS	0.594	0.532	0.66	0.594	0.532	0.66	SUBCLONAL	1	TRUE	1	0.52	2		511	667	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023446	33023446	+	stop_lost	Nonstop_Mutation	SNP	A	A	C	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	498	900	0	ENST00000300177.4:c.555A>C	p.Ter185TyrextTer29	p.*185Yext*29	ENST00000300177	NM_001191322.1	185	taA/taC	2/2	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.52	2		900	1385	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003414	42003414	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269317379	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	409	845	2	ENST00000219905.7:c.2951G>A	p.Arg984His	p.R984H	ENST00000219905	NM_001164273.1	984	cGc/cAc	8/24	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.52	2		847	1318	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003779	45003779	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	115	508	0	ENST00000558401.1:c.35T>C	p.Leu12Pro	p.L12P	ENST00000558401	NM_004048.2	12	cTa/cCa	1/4	1	2	FACETS	0.619	0.558	0.684	0.619	0.558	0.684	SUBCLONAL	1	TRUE	1	0.52	2		508	714	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003799	45003799	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	83	459	0	ENST00000558401.1:c.55G>T	p.Glu19Ter	p.E19*	ENST00000558401	NM_004048.2	19	Gag/Tag	1/4	1	2	FACETS	0.496	0.437	0.558	0.496	0.437	0.558	SUBCLONAL	1	TRUE	1	0.52	2		459	644	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457244	67457244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	48	368	0	ENST00000327367.4:c.218G>A	p.Gly73Asp	p.G73D	ENST00000327367	NM_005902.3	73	gGc/gAc	2/9	1	2	FACETS	0.335	0.283	0.393	0.335	0.283	0.393	SUBCLONAL	1	TRUE	1	0.52	2		368	551	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347908	347908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146189916	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	316	784	1	ENST00000262320.3:c.1598G>A	p.Arg533Gln	p.R533Q	ENST00000262320	NM_003502.3	533	cGa/cAa	6/11	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		785	890	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2221577	2221577	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	308	545	2	ENST00000326181.6:c.446C>T	p.Thr149Met	p.T149M	ENST00000326181	NM_032271.2	149	aCg/aTg	7/21	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.52	2		547	819	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225320	2225320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	40	596	0	ENST00000326181.6:c.1405C>A	p.Leu469Met	p.L469M	ENST00000326181	NM_032271.2	469	Ctg/Atg	16/21	1	2	FACETS	0.203	0.168	0.242	0.203	0.168	0.242	SUBCLONAL	1	TRUE	1	0.52	2		596	759	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779019	3779019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766553839	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	20	344	0	ENST00000262367.5:c.6029G>A	p.Gly2010Glu	p.G2010E	ENST00000262367	NM_004380.2	2010	gGg/gAg	31/31	1	2	FACETS	0.21	0.16	0.268	0.21	0.16	0.268	SUBCLONAL	1	TRUE	1	0.52	2		344	367	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786682	3786682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780939128	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	432	704	6	ENST00000262367.5:c.4529C>T	p.Ala1510Val	p.A1510V	ENST00000262367	NM_004380.2	1510	gCg/gTg	27/31	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.52	2		710	1160	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820732	3820732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	343	610	1	ENST00000262367.5:c.2719C>T	p.Pro907Ser	p.P907S	ENST00000262367	NM_004380.2	907	Ccc/Tcc	14/31	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.52	2		611	971	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857200	9857200	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	400	781	0	ENST00000330684.3:c.4201C>A	p.Leu1401Ile	p.L1401I	ENST00000330684	NM_001134407.1	1401	Ctt/Att	13/13	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.52	2		781	1091	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641750	23641750	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	193	479	0	ENST00000261584.4:c.1725G>A	p.Trp575Ter	p.W575*	ENST00000261584	NM_024675.3	575	tgG/tgA	5/13	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.52	2		479	589	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646683	23646683	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	209	473	0	ENST00000261584.4:c.1184C>A	p.Ser395Tyr	p.S395Y	ENST00000261584	NM_024675.3	395	tCt/tAt	4/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.52	2		473	690	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865888	56865888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755863852	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	454	786	2	ENST00000308159.5:c.1220C>T	p.Ala407Val	p.A407V	ENST00000308159	NM_014669.4	407	gCg/gTg	11/22	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.52	2		788	1242	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56875638	56875638	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239777742	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	73	635	0	ENST00000308159.5:c.2242G>A	p.Val748Met	p.V748M	ENST00000308159	NM_014669.4	748	Gtg/Atg	21/22	1	2	FACETS	0.288	0.251	0.329	0.288	0.251	0.329	SUBCLONAL	1	TRUE	1	0.52	2		635	974	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645489	67645489	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	208	396	2	ENST00000264010.4:c.754C>A	p.Pro252Thr	p.P252T	ENST00000264010	NM_006565.3	252	Cca/Aca	3/12	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.52	2		398	568	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828777	72828777	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	453	890	0	ENST00000268489.5:c.7804A>G	p.Thr2602Ala	p.T2602A	ENST00000268489	NM_006885.3	2602	Act/Gct	9/10	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.52	2		890	1204	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828915	72828915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1178647450	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	487	896	2	ENST00000268489.5:c.7666G>A	p.Ala2556Thr	p.A2556T	ENST00000268489	NM_006885.3	2556	Gcg/Acg	9/10	1	2	FACETS	0.807	0.774	0.841	1	0.997	1	CLONAL	2	TRUE	1	0.52	2		898	1160	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829200	72829200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779491169	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	333	919	2	ENST00000268489.5:c.7381G>A	p.Glu2461Lys	p.E2461K	ENST00000268489	NM_006885.3	2461	Gag/Aag	9/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.52	2		921	1192	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819752	81819752	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253716514	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	412	716	0	ENST00000359376.3:c.158C>T	p.Ala53Val	p.A53V	ENST00000359376	NM_002661.3	53	gCc/gTc	2/33	1	2	FACETS	0.788	0.753	0.824	1	0.996	1	SUBCLONAL	2	TRUE	1	0.52	2		716	1005	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81991597	81991597	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1284	76	834	0	ENST00000359376.3:c.3792C>A	p.Tyr1264Ter	p.Y1264*	ENST00000359376	NM_002661.3	1264	taC/taA	33/33	1	2	FACETS	0.215	0.187	0.245	0.215	0.187	0.245	SUBCLONAL	1	TRUE	1	0.52	2		834	1360	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347863	89347863	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	293	725	0	ENST00000301030.4:c.5087A>G	p.Asp1696Gly	p.D1696G	ENST00000301030	NM_001256183.1	1696	gAc/gGc	9/13	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.52	2		725	888	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348610	89348610	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	297	973	2	ENST00000301030.4:c.4340C>A	p.Pro1447His	p.P1447H	ENST00000301030	NM_001256183.1	1447	cCt/cAt	9/13	1	2	FACETS	0.779	0.731	0.827	0.779	0.731	0.827	SUBCLONAL	1	TRUE	1	0.52	2		975	1467	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357447	89357447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1312503091	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	292	708	2	ENST00000301030.4:c.371C>T	p.Thr124Met	p.T124M	ENST00000301030	NM_001256183.1	124	aCg/aTg	5/13	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.52	2		710	929	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89807231	89807231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752800577	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	376	653	0	ENST00000389301.3:c.3809C>T	p.Ser1270Leu	p.S1270L	ENST00000389301	NM_000135.2	1270	tCg/tTg	38/43	1	2	FACETS	0.76	0.723	0.796	1	0.996	1	SUBCLONAL	2	TRUE	1	0.52	2		653	952	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89809275	89809275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs545742908	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	351	621	3	ENST00000389301.3:c.3698C>T	p.Ala1233Val	p.A1233V	ENST00000389301	NM_000135.2	1233	gCg/gTg	37/43	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.52	2		624	994	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836633	89836633	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs757797015	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	271	540	0	ENST00000389301.3:c.2257A>G	p.Met753Val	p.M753V	ENST00000389301	NM_000135.2	753	Atg/Gtg	25/43	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.52	2		540	799	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89839685	89839685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778312	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	277	594	1	ENST00000389301.3:c.2008C>T	p.Arg670Cys	p.R670C	ENST00000389301	NM_000135.2	670	Cgt/Tgt	22/43	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		595	775	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89851371	89851371	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	117	430	0	ENST00000389301.3:c.1361C>T	p.Ala454Val	p.A454V	ENST00000389301	NM_000135.2	454	gCc/gTc	15/43	1	2	FACETS	0.697	0.629	0.767	0.697	0.629	0.767	SUBCLONAL	1	TRUE	1	0.52	2		430	646	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	212	496	0	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.52	2		496	636	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579400	7579400	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	109	476	0	ENST00000269305.4:c.287C>A	p.Ser96Tyr	p.S96Y	ENST00000269305	NM_001126112.2	96	tCt/tAt	4/11	1	2	FACETS	0.556	0.499	0.616	0.556	0.499	0.616	SUBCLONAL	1	TRUE	1	0.52	2		476	754	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980034	7980034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369807670	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	306	527	0	ENST00000319144.4:c.1303G>A	p.Val435Ile	p.V435I	ENST00000319144	NM_001139.2	435	Gtc/Atc	10/15	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.52	2		527	810	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964969	15964969	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	276	618	0	ENST00000268712.3:c.5627G>T	p.Arg1876Ile	p.R1876I	ENST00000268712	NM_006311.3	1876	aGa/aTa	37/46	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.52	2		618	887	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968823	15968823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	163	506	0	ENST00000268712.3:c.4927G>A	p.Gly1643Ser	p.G1643S	ENST00000268712	NM_006311.3	1643	Ggt/Agt	33/46	1	2	FACETS	0.668	0.612	0.725	0.668	0.612	0.725	SUBCLONAL	1	TRUE	1	0.52	2		506	939	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974781	15974781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1454297938	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	50	525	0	ENST00000268712.3:c.4094G>A	p.Arg1365Gln	p.R1365Q	ENST00000268712	NM_006311.3	1365	cGg/cAg	30/46	1	2	FACETS	0.201	0.17	0.236	0.201	0.17	0.236	SUBCLONAL	1	TRUE	1	0.52	2		525	956	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004727	16004727	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	303	648	0	ENST00000268712.3:c.2527G>T	p.Glu843Ter	p.E843*	ENST00000268712	NM_006311.3	843	Gaa/Taa	20/46	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.52	2		648	1013	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131282	17131282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749770193	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	316	592	0	ENST00000285071.4:c.170G>A	p.Arg57Gln	p.R57Q	ENST00000285071	NM_144997.5	57	cGg/cAg	4/14	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.52	2		592	867	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541468	29541468	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1131691131	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	16	131	0	ENST00000356175.3:c.1393-1G>A		p.X465_splice	ENST00000356175	NM_000267.3	465			1	2	FACETS	0.387	0.287	0.504	0.387	0.287	0.504	SUBCLONAL	1	TRUE	1	0.52	2		131	159	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653140	29653140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	261	415	0	ENST00000356175.3:c.5075G>A	p.Gly1692Glu	p.G1692E	ENST00000356175	NM_000267.3	1692	gGg/gAg	36/57	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		415	692	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511667	38511667	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773956341	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	220	478	2	ENST00000254066.5:c.1165G>A	p.Ala389Thr	p.A389T	ENST00000254066	NM_000964.3	389	Gcc/Acc	8/9	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.52	2		480	670	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245300	41245300	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	266	486	1	ENST00000357654.3:c.2248C>A	p.Leu750Ile	p.L750I	ENST00000357654	NM_007294.3	750	Ctc/Atc	10/23	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		487	736	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696419	47696419	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1006096444	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	45	511	0	ENST00000347630.2:c.404A>C	p.Lys135Thr	p.K135T	ENST00000347630	NM_001007230.1	135	aAa/aCa	6/11	1	2	FACETS	0.195	0.163	0.231	0.195	0.163	0.231	SUBCLONAL	1	TRUE	1	0.52	2		511	888	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437609	56437609	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	41	431	0	ENST00000407977.2:c.853C>A	p.Leu285Ile	p.L285I	ENST00000407977		285	Cta/Ata	8/10	1	2	FACETS	0.244	0.203	0.29	0.244	0.203	0.29	SUBCLONAL	1	TRUE	1	0.52	2		431	646	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58711228	58711228	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	376	639	0	ENST00000305921.3:c.716C>A	p.Ser239Tyr	p.S239Y	ENST00000305921	NM_003620.3	239	tCt/tAt	3/6	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		639	1132	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59924463	59924463	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs748912293	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	221	508	0	ENST00000259008.2:c.626A>G	p.Lys209Arg	p.K209R	ENST00000259008	NM_032043.2	209	aAa/aGa	6/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.52	2		508	762	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59934512	59934512	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	387	656	0	ENST00000259008.2:c.286A>G	p.Thr96Ala	p.T96A	ENST00000259008	NM_032043.2	96	Aca/Gca	4/20	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.52	2		656	1045	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59937169	59937169	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	277	506	0	ENST00000259008.2:c.193C>G	p.Gln65Glu	p.Q65E	ENST00000259008	NM_032043.2	65	Caa/Gaa	3/20	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.52	2		506	828	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006627	62006627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1063625	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	259	581	0	ENST00000392795.3:c.652G>A	p.Glu218Lys	p.E218K	ENST00000392795	NM_001039933.1	218	Gaa/Aaa	6/6	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		581	711	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533760	63533760	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764640447	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	230	470	1	ENST00000307078.5:c.1394G>A	p.Arg465His	p.R465H	ENST00000307078	NM_004655.3	465	cGc/cAc	6/11	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.52	2		471	608	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511551	66511551	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	154	248	0	ENST00000358598.2:c.11G>A	p.Gly4Asp	p.G4D	ENST00000358598	NM_212471.2	4	gGc/gAc	2/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.52	2		248	470	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724456	724456	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	213	520	0	ENST00000314574.4:c.1600G>T	p.Glu534Ter	p.E534*	ENST00000314574	NM_005433.3	534	Gag/Tag	12/12	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.52	2		520	657	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400748	56400748	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	399	802	1	ENST00000348428.3:c.1342T>G	p.Leu448Val	p.L448V	ENST00000348428	NM_006785.3	448	Ttg/Gtg	11/17	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.52	2		803	1142	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216994	2216994	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	310	557	1	ENST00000398665.3:c.2449C>T	p.Pro817Ser	p.P817S	ENST00000398665	NM_032482.2	817	Ccc/Tcc	21/28	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.52	2		558	803	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223431	2223431	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1038361699	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	253	469	0	ENST00000398665.3:c.3542C>T	p.Ser1181Phe	p.S1181F	ENST00000398665	NM_032482.2	1181	tCc/tTc	25/28	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		469	670	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110203	3110203	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147528229	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	276	595	0	ENST00000078429.4:c.193G>A	p.Ala65Thr	p.A65T	ENST00000078429	NM_002067.2	65	Gcc/Acc	2/7	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.52	2		595	794	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117445	4117445	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	65	293	0	ENST00000262948.5:c.275G>T	p.Arg92Ile	p.R92I	ENST00000262948	NM_030662.3	92	aGa/aTa	2/11	1	2	FACETS	0.54	0.469	0.616	0.54	0.469	0.616	SUBCLONAL	1	TRUE	1	0.52	2		293	463	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4123817	4123817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	269	406	2	ENST00000262948.5:c.56C>T	p.Ala19Val	p.A19V	ENST00000262948	NM_030662.3	19	gCc/gTc	1/11	1	2	FACETS	0.791	0.747	0.835	1	0.994	1	SUBCLONAL	2	TRUE	1	0.52	2		408	654	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215601	5215601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1285393473	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	87	417	0	ENST00000357368.4:c.4102C>T	p.Leu1368Phe	p.L1368F	ENST00000357368	NM_002850.3	1368	Ctt/Ttt	27/38	1	2	FACETS	0.7	0.622	0.783	0.7	0.622	0.783	SUBCLONAL	1	TRUE	1	0.52	2		417	478	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221131	5221131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201447856	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	34	586	1	ENST00000357368.4:c.3335C>T	p.Thr1112Met	p.T1112M	ENST00000357368	NM_002850.3	1112	aCg/aTg	20/38	1	2	FACETS	0.198	0.161	0.24	0.198	0.161	0.24	SUBCLONAL	1	TRUE	1	0.52	2		587	661	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7141827	7141827	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs781081662	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	123	473	2	ENST00000302850.5:c.2543C>T	p.Ala848Val	p.A848V	ENST00000302850	NM_000208.2	848	gCc/gTc	13/22	1	2	FACETS	0.635	0.575	0.699	0.635	0.575	0.699	SUBCLONAL	1	TRUE	1	0.52	2		475	745	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249230	10249230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779967013	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	209	538	0	ENST00000340748.4:c.3952G>A	p.Ala1318Thr	p.A1318T	ENST00000340748		1318	Gcg/Acg	34/40	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.52	2		538	614	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10259684	10259684	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	213	393	0	ENST00000340748.4:c.2548G>T	p.Asp850Tyr	p.D850Y	ENST00000340748		850	Gat/Tat	26/40	1	2	FACETS	0.769	0.72	0.817	1	0.993	1	SUBCLONAL	2	TRUE	1	0.52	2		393	533	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260191	10260191	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	48	531	0	ENST00000340748.4:c.2476T>C	p.Ser826Pro	p.S826P	ENST00000340748		826	Tca/Cca	25/40	1	2	FACETS	0.234	0.197	0.275	0.234	0.197	0.275	SUBCLONAL	1	TRUE	1	0.52	2		531	790	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094867	11094867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	149	607	0	ENST00000358026.2:c.40C>T	p.Pro14Ser	p.P14S	ENST00000358026	NM_001128849.1	14	Cca/Tca	2/36	1	2	FACETS	0.694	0.634	0.756	0.694	0.634	0.756	SUBCLONAL	1	TRUE	1	0.52	2		607	826	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098566	11098566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776534924	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	284	571	3	ENST00000358026.2:c.1084G>A	p.Asp362Asn	p.D362N	ENST00000358026	NM_001128849.1	362	Gac/Aac	6/36	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		574	800	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101970	11101970	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	248	520	1	ENST00000358026.2:c.1390C>T	p.Gln464Ter	p.Q464*	ENST00000358026	NM_001128849.1	464	Cag/Tag	8/36	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.52	2		521	767	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121068	11121068	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	57	732	0	ENST00000358026.2:c.2135A>G	p.Gln712Arg	p.Q712R	ENST00000358026	NM_001128849.1	712	cAa/cGa	15/36	1	2	FACETS	0.209	0.178	0.242	0.209	0.178	0.242	SUBCLONAL	1	TRUE	1	0.52	2		732	1050	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168978	11168978	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1388483526	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	259	598	0	ENST00000358026.2:c.4568G>A	p.Arg1523Gln	p.R1523Q	ENST00000358026	NM_001128849.1	1523	cGa/cAa	32/36	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.52	2		598	812	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15273295	15273295	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	244	558	0	ENST00000263388.2:c.5894A>C	p.Lys1965Thr	p.K1965T	ENST00000263388	NM_000435.2	1965	aAg/aCg	32/33	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.52	2		558	820	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276687	15276687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	249	601	2	ENST00000263388.2:c.5578G>A	p.Asp1860Asn	p.D1860N	ENST00000263388	NM_000435.2	1860	Gat/Aat	30/33	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.52	2		603	711	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299969	15299969	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	43	560	0	ENST00000263388.2:c.1209G>T	p.Glu403Asp	p.E403D	ENST00000263388	NM_000435.2	403	gaG/gaT	8/33	1	2	FACETS	0.244	0.204	0.29	0.244	0.204	0.29	SUBCLONAL	1	TRUE	1	0.52	2		560	677	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366309	15366309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	196	516	1	ENST00000263377.2:c.1846C>T	p.Arg616Trp	p.R616W	ENST00000263377	NM_058243.2	616	Cgg/Tgg	10/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.52	2		517	693	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952321	17952321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	238	494	1	ENST00000458235.1:c.1019C>T	p.Ser340Leu	p.S340L	ENST00000458235	NM_000215.3	340	tCg/tTg	8/24	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.52	2		495	664	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955187	17955187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs896064879	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	294	620	2	ENST00000458235.1:c.40C>T	p.Arg14Cys	p.R14C	ENST00000458235	NM_000215.3	14	Cgt/Tgt	2/24	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		622	838	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273283	18273283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	56	602	2	ENST00000222254.8:c.1076G>A	p.Ser359Asn	p.S359N	ENST00000222254	NM_005027.3	359	aGc/aAc	9/16	1	2	FACETS	0.221	0.188	0.257	0.221	0.188	0.257	SUBCLONAL	1	TRUE	1	0.52	2		604	975	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257967	19257967	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	48	572	0	ENST00000162023.5:c.419C>A	p.Pro140Gln	p.P140Q	ENST00000162023		140	cCa/cAa	9/13	1	2	FACETS	0.271	0.228	0.318	0.271	0.228	0.318	SUBCLONAL	1	TRUE	1	0.52	2		572	682	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308069	30308069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs998966219	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	301	470	1	ENST00000262643.3:c.206C>T	p.Ala69Val	p.A69V	ENST00000262643	NM_001238.2	69	gCa/gTa	5/12	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.52	2		471	819	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727935	41727935	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	258	526	0	ENST00000301178.4:c.560G>A	p.Gly187Asp	p.G187D	ENST00000301178	NM_021913.4	187	gGc/gAc	4/20	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.52	2		526	760	SUCCESS
AXL	558	MSKCC	GRCh37	19	41737100	41737100	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	301	601	0	ENST00000301178.4:c.680A>C	p.Gln227Pro	p.Q227P	ENST00000301178	NM_021913.4	227	cAg/cCg	6/20	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		601	865	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793393	42793393	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	77	351	1	ENST00000575354.2:c.1195G>T	p.Gly399Ter	p.G399*	ENST00000575354	NM_015125.3	399	Gga/Tga	8/20	1	2	FACETS	0.666	0.586	0.75	0.666	0.586	0.75	SUBCLONAL	1	TRUE	1	0.52	2		352	445	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795033	42795033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	295	529	0	ENST00000575354.2:c.2113G>A	p.Ala705Thr	p.A705T	ENST00000575354	NM_015125.3	705	Gca/Aca	10/20	1	2	FACETS	0.753	0.713	0.794	1	0.994	1	SUBCLONAL	2	TRUE	1	0.52	2		529	753	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797266	42797266	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	183	443	0	ENST00000575354.2:c.3628C>A	p.Pro1210Thr	p.P1210T	ENST00000575354	NM_015125.3	1210	Cct/Act	15/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.52	2		443	552	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798364	42798364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	266	539	1	ENST00000575354.2:c.4235G>A	p.Arg1412His	p.R1412H	ENST00000575354	NM_015125.3	1412	cGc/cAc	18/20	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		540	740	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798990	42798990	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368086483	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	60	506	0	ENST00000575354.2:c.4474G>A	p.Ala1492Thr	p.A1492T	ENST00000575354	NM_015125.3	1492	Gcc/Acc	20/20	1	2	FACETS	0.266	0.228	0.307	0.266	0.228	0.307	SUBCLONAL	1	TRUE	1	0.52	2		506	867	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872188	45872188	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	293	524	0	ENST00000391945.4:c.246G>T	p.Lys82Asn	p.K82N	ENST00000391945	NM_000400.3	82	aaG/aaT	4/23	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.52	2		524	874	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906383	50906383	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs867385484	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	440	641	0	ENST00000440232.2:c.1044G>T	p.Glu348Asp	p.E348D	ENST00000440232	NM_002691.3	348	gaG/gaT	9/27	1	2	FACETS	0.92	0.882	0.958	1	0.997	1	CLONAL	2	TRUE	1	0.52	2		641	920	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918105	50918105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	142	693	2	ENST00000440232.2:c.2422C>T	p.Arg808Cys	p.R808C	ENST00000440232	NM_002691.3	808	Cgc/Tgc	20/27	1	2	FACETS	0.621	0.566	0.679	0.621	0.566	0.679	SUBCLONAL	1	TRUE	1	0.52	2		695	879	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714597	52714597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	226	635	0	ENST00000322088.6:c.355C>T	p.His119Tyr	p.H119Y	ENST00000322088	NM_014225.5	119	Cac/Tac	4/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.52	2		635	822	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520162	9520162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	308	520	0	ENST00000353224.5:c.2107G>A	p.Ala703Thr	p.A703T	ENST00000353224	NM_177990.2	703	Gca/Aca	10/10	0.3	1	FACETS	1	0.97	1	1	0.97	1	INDETERMINATE	1	TRUE	0	0.52	1		520	846	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30954254	30954254	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	54	576	1	ENST00000375687.4:c.125G>A	p.Gly42Glu	p.G42E	ENST00000375687	NM_015338.5	42	gGa/gAa	2/13	0.3	1	FACETS	0.174	0.148	0.203	0.174	0.148	0.203	INDETERMINATE	1	TRUE	0	0.52	1		577	881	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023949	31023949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777670355	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	257	575	0	ENST00000375687.4:c.3434G>A	p.Gly1145Asp	p.G1145D	ENST00000375687	NM_015338.5	1145	gGc/gAc	13/13	0.3	1	FACETS	0.955	0.898	1	0.955	0.898	1	INDETERMINATE	1	TRUE	0	0.52	1		575	766	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030050	36030050	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	253	553	2	ENST00000358208.4:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000358208		362	cGg/cAg	9/12	0.3	1	FACETS	0.976	0.917	1	0.976	0.917	1	INDETERMINATE	1	TRUE	0	0.52	1		555	738	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39746809	39746809	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	149	349	1	ENST00000361337.2:c.1823C>T	p.Pro608Leu	p.P608L	ENST00000361337	NM_003286.2	608	cCg/cTg	18/21	0.3	1	FACETS	0.908	0.836	0.982	0.908	0.836	0.982	INDETERMINATE	1	TRUE	0	0.52	1		350	467	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419951	41419951	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	59	620	1	ENST00000373198.4:c.370G>A	p.Val124Met	p.V124M	ENST00000373198	NM_133170.3	124	Gtg/Atg	3/32	0.3	1	FACETS	0.207	0.177	0.239	0.207	0.177	0.239	INDETERMINATE	1	TRUE	0	0.52	1		621	812	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420025	41420025	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	270	623	0	ENST00000373198.4:c.296A>G	p.Asp99Gly	p.D99G	ENST00000373198	NM_133170.3	99	gAc/gGc	3/32	0.3	1	FACETS	0.936	0.881	0.992	0.936	0.881	0.992	INDETERMINATE	1	TRUE	0	0.52	1		623	821	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264640	46264640	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	101	579	2	ENST00000371998.3:c.1510C>T	p.His504Tyr	p.H504Y	ENST00000371998		504	Cac/Tac	12/23	0.3	1	FACETS	0.398	0.356	0.443	0.398	0.356	0.443	INDETERMINATE	1	TRUE	0	0.52	1		581	722	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46266528	46266528	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	37	592	1	ENST00000371998.3:c.2512+1G>A		p.X838_splice	ENST00000371998		838			0.3	1	FACETS	0.156	0.128	0.188	0.156	0.128	0.188	INDETERMINATE	1	TRUE	0	0.52	1		593	674	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268465	46268465	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	353	811	0	ENST00000371998.3:c.2852G>T	p.Arg951Ile	p.R951I	ENST00000371998		951	aGa/aTa	15/23	0.3	1	FACETS	0.889	0.843	0.936	0.889	0.843	0.936	INDETERMINATE	1	TRUE	0	0.52	1		811	1130	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54948603	54948603	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	178	367	0	ENST00000312783.6:c.715G>T	p.Glu239Ter	p.E239*	ENST00000312783	NM_198436.1	239	Gaa/Taa	8/10	0.3	1	FACETS	0.913	0.847	0.981	0.913	0.847	0.981	INDETERMINATE	1	TRUE	0	0.52	1		367	555	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958084	54958084	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	101	421	0	ENST00000312783.6:c.523G>A	p.Glu175Lys	p.E175K	ENST00000312783	NM_198436.1	175	Gag/Aag	6/10	0.3	1	FACETS	0.458	0.41	0.51	0.458	0.41	0.51	INDETERMINATE	1	TRUE	0	0.52	1		421	627	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480483	57480483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	258	434	0	ENST00000371085.3:c.478C>T	p.Arg160Cys	p.R160C	ENST00000371085	NM_000516.4	160	Cgt/Tgt	6/13	0.3	1	FACETS	1	0.973	1	1	0.973	1	INDETERMINATE	1	TRUE	0	0.52	1		434	696	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164781	36164781	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1225645057	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	44	630	0	ENST00000300305.3:c.1094G>T	p.Gly365Val	p.G365V	ENST00000300305		365	gGc/gTc	8/8	1	2	FACETS	0.198	0.165	0.234	0.198	0.165	0.234	SUBCLONAL	1	TRUE	1	0.52	2		630	856	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839812	42839812	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	188	334	0	ENST00000398585.3:c.1427G>A	p.Gly476Asp	p.G476D	ENST00000398585	NM_001135099.1	476	gGt/gAt	13/14	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.52	2		334	524	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866328	42866328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150389990	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	32	367	2	ENST00000398585.3:c.304G>A	p.Val102Ile	p.V102I	ENST00000398585	NM_001135099.1	102	Gtc/Atc	3/14	1	2	FACETS	0.227	0.184	0.277	0.227	0.184	0.277	SUBCLONAL	1	TRUE	1	0.52	2		369	541	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44520566	44520566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	308	445	1	ENST00000291552.4:c.196C>T	p.Arg66Cys	p.R66C	ENST00000291552	NM_006758.2	66	Cgc/Tgc	3/8	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		446	892	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064376	30064376	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1365006505	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	345	668	0	ENST00000338641.4:c.940G>A	p.Asp314Asn	p.D314N	ENST00000338641	NM_000268.3	314	Gat/Aat	10/16	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		668	1009	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547987	41547987	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs987040002	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	167	659	1	ENST00000263253.7:c.2968G>A	p.Ala990Thr	p.A990T	ENST00000263253	NM_001429.3	990	Gca/Aca	15/31	1	2	FACETS	0.64	0.588	0.695	0.64	0.588	0.695	SUBCLONAL	1	TRUE	1	0.52	2		660	1003	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572256	41572256	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	237	376	0	ENST00000263253.7:c.4785C>A	p.Phe1595Leu	p.F1595L	ENST00000263253	NM_001429.3	1595	ttC/ttA	30/31	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.52	2		376	638	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574502	41574502	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	231	546	1	ENST00000263253.7:c.6787C>T	p.Arg2263Ter	p.R2263*	ENST00000263253	NM_001429.3	2263	Cga/Tga	31/31	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.52	2		547	652	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1331455	1331455	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	179	660	0	ENST00000400841.2:c.73G>T	p.Gly25Ter	p.G25*	ENST00000400841		25	Gga/Tga	1/6	0.3	4	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.52	4		660	963	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938543	44938543	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	57	285	0	ENST00000377967.4:c.3091A>G	p.Thr1031Ala	p.T1031A	ENST00000377967	NM_021140.2	1031	Aca/Gca	20/29	0.3	4	FACETS	0.453	0.388	0.524			1	INDETERMINATE	1	TRUE	NA	0.52	4		285	736	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045463	47045463	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	91	274	1	ENST00000377604.3:c.2431-1G>T		p.X811_splice	ENST00000377604	NM_001204468.1	811			0.3	4	FACETS	0.693	0.615	0.776			1	INDETERMINATE	1	TRUE	NA	0.52	4		275	768	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424197	47424197	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	287	285	0	ENST00000377045.4:c.202C>T	p.Arg68Ter	p.R68*	ENST00000377045	NM_001654.4	68	Cga/Tga	4/16	0.3	4	FACETS	1	0.977	1			1	INDETERMINATE	2	TRUE	NA	0.52	4		285	789	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430276	47430276	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	51	383	0	ENST00000377045.4:c.1552-1G>T		p.X518_splice	ENST00000377045	NM_001654.4	518			0.3	4	FACETS	0.307	0.26	0.36			1	INDETERMINATE	1	TRUE	NA	0.52	4		383	970	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651642	48651642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	343	379	1	ENST00000376670.3:c.808C>T	p.Arg270Trp	p.R270W	ENST00000376670	NM_002049.3	270	Cgg/Tgg	5/6	0.3	4	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.52	4		380	868	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245265	53245265	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1569278482	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	61	360	1	ENST00000375401.3:c.772C>T	p.Arg258Trp	p.R258W	ENST00000375401	NM_004187.3	258	Cgg/Tgg	6/26	0.3	4	FACETS	0.341	0.293	0.394			1	INDETERMINATE	1	TRUE	NA	0.52	4		361	1046	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246450	53246450	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1393694550	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	48	312	0	ENST00000375401.3:c.532A>G	p.Thr178Ala	p.T178A	ENST00000375401	NM_004187.3	178	Aca/Gca	5/26	0.3	4	FACETS	0.384	0.324	0.451			1	INDETERMINATE	1	TRUE	NA	0.52	4		312	730	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409822	63409822	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	102	356	0	ENST00000330258.3:c.3345G>T	p.Glu1115Asp	p.E1115D	ENST00000330258	NM_152424.3	1115	gaG/gaT	2/2	0.3	4	FACETS	0.776	0.694	0.864			1	INDETERMINATE	1	TRUE	NA	0.52	4		356	768	SUCCESS
AR	367	MSKCC	GRCh37	X	66765579	66765579	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	103	397	0	ENST00000374690.3:c.591G>T	p.Gln197His	p.Q197H	ENST00000374690	NM_000044.3	197	caG/caT	1/8	0.3	4	FACETS	0.859	0.769	0.954			1	INDETERMINATE	1	TRUE	NA	0.52	4		397	701	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356811	70356811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	89	379	0	ENST00000374080.3:c.5483C>T	p.Ser1828Phe	p.S1828F	ENST00000374080		1828	tCt/tTt	38/45	0.3	4	FACETS	0.554	0.49	0.622			1	INDETERMINATE	1	TRUE	NA	0.52	4		379	940	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181221	123181221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	183	347	0	ENST00000218089.9:c.685G>A	p.Ala229Thr	p.A229T	ENST00000218089	NM_001042749.1	229	Gct/Act	9/35	0.3	4	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.52	4		347	921	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197867	123197867	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	656	335	0	ENST00000218089.9:c.1991A>C	p.Lys664Thr	p.K664T	ENST00000218089	NM_001042749.1	664	aAa/aCa	20/35	0.3	4	FACETS	0.938	0.918	0.957			1	INDETERMINATE	5	TRUE	NA	0.52	4		335	818	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211868	123211868	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	638	390	1	ENST00000218089.9:c.2735A>C	p.Lys912Thr	p.K912T	ENST00000218089	NM_001042749.1	912	aAa/aCa	27/35	0.3	4	FACETS	0.932	0.912	0.952			1	INDETERMINATE	5	TRUE	NA	0.52	4		391	800	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39647436	39647437	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	247	563	0	ENST00000262039.4:c.2613dup	p.Ala872CysfsTer77	p.A872Cfs*77	ENST00000262039	NM_002647.2	870	ctt/cTtt	24/25	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.52	2		563	877	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55603379	55603380	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	282	640	0	ENST00000288135.5:c.2740dup	p.Arg914LysfsTer12	p.R914Kfs*12	ENST00000288135	NM_000222.2	912	cta/ctAa	20/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.52	2		640	953	SUCCESS
ATR	545	MSKCC	GRCh37	3	142185232	142185232	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	341	607	0	ENST00000350721.4:c.6831del	p.His2277GlnfsTer38	p.H2277Qfs*38	ENST00000350721	NM_001184.3	2277	caT/ca	40/47	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.52	2		607	1005	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965660	90965660	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	264	537	0	ENST00000265433.3:c.1657del	p.Met553TrpfsTer6	p.M553Wfs*6	ENST00000265433	NM_002485.4	553	Atg/tg	11/16	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.52	2		537	844	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0007051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	59	461	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.525887239719226	4	FACETS	1	0.93	1	0.558	0.483	0.638	CLONAL	1	TRUE	2	0.525887239719226	4		461	307	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0007051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	252	463	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.525887239719226	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.525887239719226	4		463	705	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584560	48584560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	278	420	0	ENST00000342988.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000342988	NM_005359.5	245	Cag/Tag	6/12	0.525887239719226	2	FACETS	0.921	0.874	0.968	0.921	0.874	0.968	CLONAL	2	TRUE	0	0.525887239719226	2		420	574	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520017	NA	P-0007051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	316	580	2	ENST00000326873.7:c.647C>T	p.Ser216Phe	p.S216F	ENST00000326873	NM_000455.4	216	tCc/tTc	5/10	0.525887239719226	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.525887239719226	2		582	573	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610380	10610380	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	339	509	1	ENST00000171111.5:c.330G>T	p.Met110Ile	p.M110I	ENST00000171111	NM_203500.1	110	atG/atT	2/6	0.525887239719226	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.525887239719226	2		510	598	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458746	120458746	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	96	463	0	ENST00000256646.2:c.6599C>G	p.Ser2200Cys	p.S2200C	ENST00000256646	NM_024408.3	2200	tCt/tGt	34/34	0.525887239719226	4	FACETS	0.643	0.572	0.719	0.322	0.286	0.36	SUBCLONAL	1	TRUE	2	0.525887239719226	4		463	866	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436887	52436887	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	48	377	0	ENST00000460680.1:c.1891G>C	p.Glu631Gln	p.E631Q	ENST00000460680	NM_004656.3	631	Gag/Cag	15/17	0.497424923446885	3	FACETS	0.459	0.388	0.538	0.153	0.129	0.18	SUBCLONAL	1	TRUE	0	0.525887239719226	3		377	502	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670760	134670760	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	115	407	0	ENST00000398015.3:c.671C>A	p.Thr224Lys	p.T224K	ENST00000398015	NM_004441.4	224	aCa/aAa	3/16	0.525887239719226	4	FACETS	0.952	0.859	1	0.476	0.429	0.526	CLONAL	1	TRUE	2	0.525887239719226	4		407	701	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612221	189612221	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	286	407	0	ENST00000264731.3:c.1973G>A	p.Trp658Ter	p.W658*	ENST00000264731	NM_003722.4	658	tGg/tAg	14/14	0.490575313983012	5	FACETS	1	0.989	1	0.799	0.754	0.844	CLONAL	2	TRUE	2	0.525887239719226	5		407	812	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953574	38953574	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	165	354	0	ENST00000357387.3:c.2779C>G	p.Leu927Val	p.L927V	ENST00000357387	NM_152756.3	927	Ctt/Gtt	28/38	0.525887239719226	6	FACETS	0.89	0.82	0.964	0.297	0.273	0.322	CLONAL	2	TRUE	0	0.525887239719226	6		354	723	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917617	151917617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	40	290	0	ENST00000262189.6:c.3703G>A	p.Asp1235Asn	p.D1235N	ENST00000262189	NM_170606.2	1235	Gat/Aat	23/59	0.525887239719226	4	FACETS	0.573	0.477	0.68	0.287	0.238	0.34	SUBCLONAL	1	TRUE	2	0.525887239719226	4		290	405	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752935	128752935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756666851	NA	P-0007051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	94	409	0	ENST00000377970.2:c.1096G>A	p.Glu366Lys	p.E366K	ENST00000377970	NM_002467.4	366	Gag/Aag	3/3	0.525887239719226	4	FACETS	0.563	0.5	0.631	0.281	0.25	0.316	SUBCLONAL	1	TRUE	2	0.525887239719226	4		409	969	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114159	115114159	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	173	633	0	ENST00000257566.3:c.1058C>T	p.Ser353Phe	p.S353F	ENST00000257566	NM_016569.3	353	tCt/tTt	6/8	0.525887239719226	4	FACETS	0.897	0.824	0.973	0.449	0.412	0.487	CLONAL	1	TRUE	2	0.525887239719226	4		633	1119	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578456	7578482	+	inframe_deletion	In_Frame_Del	DEL	GCGGACGCGGGTGCCGGGCGGGGGTGT	GCGGACGCGGGTGCCGGGCGGGGGTGT	-	novel	NA	P-0007051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	312	491	0	ENST00000269305.4:c.448_474del	p.Thr150_Arg158del	p.T150_R158del	ENST00000269305	NM_001126112.2	150	ACACCCCCGCCCGGCACCCGCGTCCGC/-	5/11	0.525887239719226	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.525887239719226	2		491	567	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0008865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	142	557	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	0.451494071044654	1	FACETS	0.6	0.55	0.65	0.6	0.55	0.65	SUBCLONAL	1	TRUE	0	0.674950455865245	1		557	465	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298725	46298725	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	42	391	0	ENST00000334344.6:c.5372A>G	p.Lys1791Arg	p.K1791R	ENST00000334344	NM_152641.2	1791	aAg/aGg	21/21	1	2	FACETS	0.249	0.207	0.295	0.249	0.207	0.295	SUBCLONAL	1	TRUE	1	0.674950455865245	2		391	500	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604632	55604633	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0008865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	424	426	0	ENST00000288135.5:c.2841_2842del	p.Lys948AlafsTer100	p.K948Afs*100	ENST00000288135	NM_000222.2	947	cAG/c	21/21	0.451494071044654	1	FACETS	0.676	0.644	0.708	0.676	0.644	0.708	SUBCLONAL	1	TRUE	0	0.674950455865245	1		426	1232	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0011283-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	160	875	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.338480101115398	1	FACETS	0.963	0.883	1	0.963	0.883	1	CLONAL	1	TRUE	0	0.338480101115398	1		876	816	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0011283-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	138	283	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	0.33039591707722	3	FACETS	0.999	0.924	1	0.999	0.924	1	CLONAL	3	TRUE	0	0.338480101115398	3		283	318	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114917779	114917779	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0011283-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	167	482	0	ENST00000543371.1:c.1270-1G>A		p.X424_splice	ENST00000543371	NM_001198531.1	424			0.338480101115398	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.338480101115398	3		482	481	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537975	212537975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267599192	NA	P-0011283-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	156	423	1	ENST00000342788.4:c.1630C>T	p.Arg544Trp	p.R544W	ENST00000342788	NM_005235.2	544	Cgg/Tgg	14/28	0.117305782995677	4	FACETS	0.86	0.79	0.934	0.86	0.79	0.934	INDETERMINATE	2	TRUE	2	0.338480101115398	4		424	717	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0011308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	1523	493	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.3	11	FACETS	0.961	0.942	0.98			1	CLONAL	12	TRUE	NA	0.19	11		493	2579	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495360	149495360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs114435947	NA	P-0011308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	58	283	0	ENST00000261799.4:c.3287C>T	p.Ala1096Val	p.A1096V	ENST00000261799	NM_002609.3	1096	gCg/gTg	23/23	1	2	FACETS	0.78	0.669	0.902	0.78	0.669	0.902	CLONAL	1	TRUE	1	0.19	2		283	783	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347943	73347943	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	53	247	0	ENST00000377767.4:c.1118T>C	p.Phe373Ser	p.F373S	ENST00000377767	NM_014953.3	373	tTt/tCt	8/21	1	2	FACETS	0.888	0.757	1	0.888	0.757	1	CLONAL	1	TRUE	1	0.19	2		247	628	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578470	+	protein_altering_variant	In_Frame_Ins	INS	-	-	GGG	novel	NA	P-0011308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	128	347	0	ENST00000269305.4:c.460_461insCCC	p.Gly154delinsAlaArg	p.G154delinsAR	ENST00000269305	NM_001126112.2	154	ggc/gCCCgc	5/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.19	2		347	1017	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0011454-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	259	787	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.49364049907812	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.49364049907812	2		787	520	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122682	7122682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs111993466	NA	P-0011454-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	92	730	3	ENST00000302850.5:c.3472C>T	p.Arg1158Trp	p.R1158W	ENST00000302850	NM_000208.2	1158	Cgg/Tgg	19/22	1	2	FACETS	0.807	0.72	0.898	0.807	0.72	0.898	CLONAL	1	TRUE	1	0.49364049907812	2		733	462	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	protein_altering_variant	In_Frame_Ins	INS	-	-	GCACAC	novel	NA	P-0012196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	23	513	0	ENST00000275493.2:c.2308_2309insGCACAC	p.Asp770delinsGlyThrHis	p.D770delinsGTH	ENST00000275493	NM_005228.3	770	gac/gGCACACac	20/28	1	2	FACETS	0.579	0.451	0.728	0.579	0.451	0.728	SUBCLONAL	1	TRUE	1	0.2	2		513	397	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	187	404	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.893	0.829	0.957	1	0.993	1	CLONAL	2	TRUE	1	0.352715792778256	2		405	594	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294665	1294665	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	32	102	0	ENST00000310581.5:c.336del	p.Glu113ArgfsTer15	p.E113Rfs*15	ENST00000310581	NM_198253.2	112	ccC/cc	2/16	1	2	FACETS	0.965	0.791	1	0.965	0.791	1	CLONAL	1	TRUE	1	0.352715792778256	2		102	188	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	170	859	1	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	1	2	FACETS	0.89	0.817	0.966	0.89	0.817	0.966	CLONAL	1	TRUE	1	0.352715792778256	2		860	1083	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742463	17742463	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	145	624	1	ENST00000250003.3:c.650del	p.Pro217ArgfsTer33	p.P217Rfs*33	ENST00000250003	NM_002478.4	215	ggC/gg	2/3	1	2	FACETS	0.923	0.842	1	0.923	0.842	1	CLONAL	1	TRUE	1	0.352715792778256	2		625	891	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964077	28964077	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1565998842	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	150	550	0	ENST00000282397.4:c.1825del	p.Met609TrpfsTer16	p.M609Wfs*16	ENST00000282397	NM_002019.4	609	Atg/tg	13/30	1	2	FACETS	0.825	0.753	0.901	0.825	0.753	0.901	CLONAL	1	TRUE	1	0.352715792778256	2		550	1031	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	152	422	2	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.352715792778256	2		424	778	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100998	41100998	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772057709	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	142	417	1	ENST00000373198.4:c.1358G>A	p.Arg453His	p.R453H	ENST00000373198	NM_133170.3	453	cGc/cAc	8/32	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.352715792778256	2		418	708	SUCCESS
APC	324	MSKCC	GRCh37	5	112176206	112176206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	134	502	1	ENST00000257430.4:c.4915C>T	p.Pro1639Ser	p.P1639S	ENST00000257430	NM_000038.5	1639	Cca/Tca	16/16	1	2	FACETS	0.813	0.738	0.892	0.813	0.738	0.892	CLONAL	1	TRUE	1	0.352715792778256	2		503	935	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149516594	149516594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150173975	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	203	546	1	ENST00000261799.4:c.17C>T	p.Ala6Val	p.A6V	ENST00000261799	NM_002609.3	6	gCg/gTg	2/23	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.352715792778256	2		547	1026	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101690	27101690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1442666063	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	133	446	2	ENST00000324856.7:c.4972C>T	p.Arg1658Trp	p.R1658W	ENST00000324856	NM_006015.4	1658	Cgg/Tgg	18/20	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.352715792778256	2		448	711	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99203983	99203983	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	107	406	0	ENST00000074304.5:c.2846G>A	p.Arg949His	p.R949H	ENST00000074304	NM_001134224.1	949	cGc/cAc	26/26	1	2	FACETS	0.799	0.717	0.887	0.799	0.717	0.887	SUBCLONAL	1	TRUE	1	0.352715792778256	2		406	759	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587119	189587119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765502786	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	163	400	1	ENST00000264731.3:c.1136G>A	p.Arg379His	p.R379H	ENST00000264731	NM_003722.4	379	cGt/cAt	9/14	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.352715792778256	2		401	808	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332496	153332496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138477494	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	176	608	0	ENST00000281708.4:c.460G>A	p.Val154Ile	p.V154I	ENST00000281708	NM_033632.3	154	Gtt/Att	2/12	1	2	FACETS	0.924	0.85	1	0.924	0.85	1	CLONAL	1	TRUE	1	0.352715792778256	2		608	1080	SUCCESS
APC	324	MSKCC	GRCh37	5	112179453	112179453	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780606	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	198	659	0	ENST00000257430.4:c.8162G>A	p.Arg2721His	p.R2721H	ENST00000257430	NM_000038.5	2721	cGc/cAc	16/16	1	2	FACETS	0.926	0.856	0.998	0.926	0.856	0.998	CLONAL	1	TRUE	1	0.352715792778256	2		659	1213	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240806	55240806	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	80	332	0	ENST00000275493.2:c.2050C>T	p.Gln684Ter	p.Q684*	ENST00000275493	NM_005228.3	684	Cag/Tag	17/28	1	2	FACETS	0.904	0.798	1	0.904	0.798	1	CLONAL	1	TRUE	1	0.352715792778256	2		332	502	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287297	38287297	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	178	630	0	ENST00000425967.3:c.360G>T	p.Glu120Asp	p.E120D	ENST00000425967	NM_001174067.1	120	gaG/gaT	4/19	1	2	FACETS	0.99	0.911	1	0.99	0.911	1	CLONAL	1	TRUE	1	0.352715792778256	2		630	1020	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123324952	123324952	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	152	556	0	ENST00000358487.5:c.376G>T	p.Asp126Tyr	p.D126Y	ENST00000358487	NM_000141.4	126	Gat/Tat	3/18	1	2	FACETS	0.881	0.805	0.961	0.881	0.805	0.961	CLONAL	1	TRUE	1	0.352715792778256	2		556	978	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94211942	94211942	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	129	435	0	ENST00000323929.3:c.503T>C	p.Leu168Ser	p.L168S	ENST00000323929	NM_005591.3	168	tTg/tCg	6/20	1	2	FACETS	0.992	0.901	1	0.992	0.901	1	CLONAL	1	TRUE	1	0.352715792778256	2		435	737	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224507	108224507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	116	371	0	ENST00000278616.4:c.8686C>T	p.Gln2896Ter	p.Q2896*	ENST00000278616	NM_000051.3	2896	Cag/Tag	60/63	1	2	FACETS	0.923	0.832	1	0.923	0.832	1	CLONAL	1	TRUE	1	0.352715792778256	2		371	713	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570038	95570038	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	56	498	0	ENST00000393063.1:c.3695G>C	p.Ser1232Thr	p.S1232T	ENST00000393063	NM_030621.3	1232	aGc/aCc	22/28	1	2	FACETS	0.323	0.276	0.375	0.323	0.276	0.375	SUBCLONAL	1	TRUE	1	0.352715792778256	2		498	983	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040904	42040904	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764392749	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	211	711	0	ENST00000219905.7:c.5282G>A	p.Arg1761Gln	p.R1761Q	ENST00000219905	NM_001164273.1	1761	cGa/cAa	16/24	1	2	FACETS	0.903	0.837	0.972	0.903	0.837	0.972	CLONAL	1	TRUE	1	0.352715792778256	2		711	1325	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126085	2126085	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs999523698	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	199	709	1	ENST00000219476.3:c.2656G>A	p.Val886Met	p.V886M	ENST00000219476	NM_000548.3	886	Gtg/Atg	24/42	1	2	FACETS	0.978	0.905	1	0.978	0.905	1	CLONAL	1	TRUE	1	0.352715792778256	2		710	1154	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816139	89816139	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs760392231	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	159	580	0	ENST00000389301.3:c.3238C>T	p.Arg1080Trp	p.R1080W	ENST00000389301	NM_000135.2	1080	Cgg/Tgg	32/43	1	2	FACETS	0.989	0.906	1	0.989	0.906	1	CLONAL	1	TRUE	1	0.352715792778256	2		580	912	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857923	89857923	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	134	405	2	ENST00000389301.3:c.1247C>T	p.Ala416Val	p.A416V	ENST00000389301	NM_000135.2	416	gCc/gTc	14/43	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.352715792778256	2		407	728	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984839	11984839	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	105	258	0	ENST00000353533.5:c.385G>A	p.Ala129Thr	p.A129T	ENST00000353533	NM_003010.3	129	Gca/Aca	3/11	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.352715792778256	2		258	575	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298797	15298797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1208817958	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	144	417	0	ENST00000263388.2:c.1501G>A	p.Gly501Ser	p.G501S	ENST00000263388	NM_000435.2	501	Ggc/Agc	10/33	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.352715792778256	2		417	761	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299827	15299827	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	175	489	0	ENST00000263388.2:c.1351G>T	p.Gly451Cys	p.G451C	ENST00000263388	NM_000435.2	451	Ggc/Tgc	8/33	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.352715792778256	2		489	965	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942128	17942128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	143	481	1	ENST00000458235.1:c.2887G>A	p.Val963Ile	p.V963I	ENST00000458235	NM_000215.3	963	Gtc/Atc	21/24	1	2	FACETS	0.903	0.823	0.987	0.903	0.823	0.987	CLONAL	1	TRUE	1	0.352715792778256	2		482	898	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762385	41762385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	61	596	1	ENST00000301178.4:c.2065G>A	p.Ala689Thr	p.A689T	ENST00000301178	NM_021913.4	689	Gcg/Acg	18/20	1	2	FACETS	0.303	0.26	0.35	0.303	0.26	0.35	SUBCLONAL	1	TRUE	1	0.352715792778256	2		597	1142	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918548	44918548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	204	616	0	ENST00000377967.4:c.1031C>T	p.Ala344Val	p.A344V	ENST00000377967	NM_021140.2	344	gCt/gTt	12/29	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.352715792778256	2		616	1084	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428212	47428212	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	211	680	0	ENST00000377045.4:c.1172A>G	p.Tyr391Cys	p.Y391C	ENST00000377045	NM_001654.4	391	tAc/tGc	11/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.352715792778256	2		680	1086	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403254	213403254	+	frameshift_variant,start_lost,start_retained_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	145	405	1	ENST00000342788.4:c.1del	p.Met1?	p.M1?	ENST00000342788	NM_005235.2	1	Atg/tg	1/28	1	2	FACETS	0.951	0.867	1	0.951	0.867	1	CLONAL	1	TRUE	1	0.352715792778256	2		406	865	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686961	37686962	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	158	516	0	ENST00000447079.4:c.3871dup	p.Gln1291ProfsTer19	p.Q1291Pfs*19	ENST00000447079	NM_015083.1	1289	gcc/gCcc	14/14	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.352715792778256	2		516	872	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907261	32907263	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	121	431	0	ENST00000380152.3:c.1650_1652del	p.Glu550del	p.E550del	ENST00000380152		549	aAGGag/aag	10/27	1	2	FACETS	0.914	0.826	1	0.914	0.826	1	CLONAL	1	TRUE	1	0.352715792778256	2		431	751	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524589	187524589	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	144	372	0	ENST00000441802.2:c.11091del	p.Phe3697LeufsTer2	p.F3697Lfs*2	ENST00000441802	NM_005245.3	3697	ttT/tt	19/27	1	2	FACETS	0.941	0.858	1	0.941	0.858	1	CLONAL	1	TRUE	1	0.352715792778256	2		372	868	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924269	11924269	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	28	92	0	ENST00000353533.5:c.69del	p.Val24Ter	p.V24*	ENST00000353533	NM_003010.3	22	ggC/gg	1/11	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.352715792778256	2		92	147	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561901	55561901	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	113	381	0	ENST00000288135.5:c.291del	p.Cys97Ter	p.C97*	ENST00000288135	NM_000222.2	97	tgC/tg	2/21	1	2	FACETS	0.769	0.692	0.851	0.769	0.692	0.851	SUBCLONAL	1	TRUE	1	0.352715792778256	2		381	833	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265339	16265341	+	inframe_deletion	In_Frame_Del	DEL	ATC	ATC	-	novel	NA	P-0012249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	147	577	0	ENST00000375759.3:c.10835_10837del	p.Ile3612del	p.I3612del	ENST00000375759	NM_015001.2	3611	ATC/-	14/15	1	2	FACETS	0.78	0.711	0.853	0.78	0.711	0.853	SUBCLONAL	1	TRUE	1	0.352715792778256	2		577	1068	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0012406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	24	377	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	NA	2	FACETS	0.658	0.519	0.816			1	INDETERMINATE	1	TRUE	NA	0.377775115927434	2		377	193	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376124	118376124	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	74	510	0	ENST00000534358.1:c.9517C>T	p.Gln3173Ter	p.Q3173*	ENST00000534358	NM_005933.3	3173	Caa/Taa	27/36	0.289175419244861	3	FACETS	0.863	0.764	0.966			1	CLONAL	2	TRUE	NA	0.377775115927434	3		510	270	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579359	+	protein_altering_variant	In_Frame_Ins	INS	-	-	TTT	novel	NA	P-0012406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	77	566	0	ENST00000269305.4:c.328_329insAAA	p.Arg110delinsGlnSer	p.R110delinsQS	ENST00000269305	NM_001126112.2	110	cgt/cAAAgt	4/11	0.16040512494865	3	FACETS	0.985	0.877	1	0.657	0.585	0.732	INDETERMINATE	2	TRUE	0	0.377775115927434	3		566	246	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743841	46743841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	139	744	0	ENST00000371975.4:c.2131G>A	p.Asp711Asn	p.D711N	ENST00000371975	NM_003579.3	711	Gat/Aat	18/18	0.316024388818506	3	FACETS	0.955	0.868	1	0.477	0.434	0.523	CLONAL	1	TRUE	1	0.316024388818506	3		744	1067	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	119	655	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.316024388818506	5	FACETS	0.88	0.792	0.974	0.293	0.264	0.325	CLONAL	1	TRUE	2	0.316024388818506	5		655	1261	SUCCESS
CBL	867	MSKCC	GRCh37	11	119167702	119167702	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	110	583	0	ENST00000264033.4:c.2111C>G	p.Ser704Cys	p.S704C	ENST00000264033	NM_005188.3	704	tCt/tGt	13/16	0.316024388818506	3	FACETS	0.851	0.764	0.944	0.426	0.382	0.472	CLONAL	1	TRUE	1	0.316024388818506	3		583	947	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858769	9858769	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	55	321	0	ENST00000330684.3:c.2632G>A	p.Glu878Lys	p.E878K	ENST00000330684	NM_001134407.1	878	Gaa/Aaa	13/13	0.316024388818506	3	FACETS	0.84	0.719	0.971	0.42	0.359	0.486	CLONAL	1	TRUE	1	0.316024388818506	3		321	480	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095593	178095593	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	89	422	0	ENST00000397062.3:c.1738G>A	p.Glu580Lys	p.E580K	ENST00000397062	NM_006164.4	580	Gaa/Aaa	5/5	0.316024388818506	4	FACETS	0.978	0.867	1	0.489	0.433	0.549	CLONAL	1	TRUE	2	0.316024388818506	4		422	758	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490318	29490318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775191883	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	203	442	0	ENST00000356175.3:c.403C>T	p.Arg135Trp	p.R135W	ENST00000356175	NM_000267.3	135	Cgg/Tgg	4/57	0.316024388818506	5	FACETS	0.969	0.899	1	0.646	0.599	0.695	CLONAL	2	TRUE	2	0.316024388818506	5		442	977	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729940	30729940	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752444160	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	84	489	0	ENST00000295754.5:c.1461G>A	p.Met487Ile	p.M487I	ENST00000295754	NM_003242.5	487	atG/atA	6/7	0.316024388818506	4	FACETS	0.875	0.772	0.985	0.437	0.386	0.493	CLONAL	1	TRUE	2	0.316024388818506	4		489	800	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866686	37866686	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1319	156	742	1	ENST00000269571.5:c.853C>G	p.Pro285Ala	p.P285A	ENST00000269571		285	Ccc/Gcc	7/27	0.316024388818506	5	FACETS	0.987	0.9	1	0.329	0.3	0.359	CLONAL	1	TRUE	2	0.316024388818506	5		743	1475	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456514	29456514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	141	686	0	ENST00000389048.3:c.2404G>A	p.Glu802Lys	p.E802K	ENST00000389048	NM_004304.4	802	Gaa/Aaa	14/29	0.316024388818506	4	FACETS	1	0.915	1	0.504	0.458	0.552	CLONAL	1	TRUE	2	0.316024388818506	4		686	1166	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645841	215645841	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	124	605	0	ENST00000260947.4:c.757C>T	p.Gln253Ter	p.Q253*	ENST00000260947	NM_000465.2	253	Cag/Tag	4/11	1	2	FACETS	0.911	0.824	1	0.911	0.824	1	CLONAL	1	TRUE	1	0.316024388818506	2		605	861	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442712	442712	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs754959640	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	109	568	0	ENST00000399788.2:c.1594C>A	p.Leu532Ile	p.L532I	ENST00000399788	NM_001042603.1	532	Ctt/Att	12/28	0.316024388818506	3	FACETS	0.903	0.81	1	0.451	0.405	0.501	CLONAL	1	TRUE	1	0.316024388818506	3		568	885	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279184	142279184	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	103	565	0	ENST00000350721.4:c.1462G>C	p.Glu488Gln	p.E488Q	ENST00000350721	NM_001184.3	488	Gag/Cag	6/47	0.316024388818506	4	FACETS	0.877	0.784	0.977	0.439	0.392	0.489	CLONAL	1	TRUE	2	0.316024388818506	4		565	978	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026015	48026015	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765237563	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	96	506	0	ENST00000234420.5:c.893G>A	p.Arg298Gln	p.R298Q	ENST00000234420	NM_000179.2	298	cGa/cAa	4/10	0.316024388818506	4	FACETS	0.993	0.884	1	0.497	0.442	0.555	CLONAL	1	TRUE	2	0.316024388818506	4		506	805	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367315	50367315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751092583	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	92	517	0	ENST00000331340.3:c.122C>T	p.Ser41Leu	p.S41L	ENST00000331340	NM_006060.4	41	tCg/tTg	3/8	0.316024388818506	3	FACETS	0.837	0.743	0.937	0.418	0.371	0.469	CLONAL	1	TRUE	1	0.316024388818506	3		517	806	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099349	27099350	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	131	632	0	ENST00000324856.7:c.3587dup	p.Asp1196GlufsTer24	p.D1196Efs*24	ENST00000324856	NM_006015.4	1196	gac/gAac	14/20	0.316024388818506	3	FACETS	1	0.912	1	0.503	0.456	0.553	CLONAL	1	TRUE	1	0.316024388818506	3		632	954	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123635	108123635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	62	306	0	ENST00000278616.4:c.1894G>A	p.Glu632Lys	p.E632K	ENST00000278616	NM_000051.3	632	Gaa/Aaa	12/63	0.316024388818506	3	FACETS	0.929	0.804	1	0.465	0.402	0.533	CLONAL	1	TRUE	1	0.316024388818506	3		306	489	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21565525	21565525	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	122	620	0	ENST00000382592.4:c.361C>G	p.Leu121Val	p.L121V	ENST00000382592	NM_014572.2	121	Ctc/Gtc	3/8	0.316024388818506	3	FACETS	0.891	0.804	0.984	0.446	0.402	0.492	CLONAL	1	TRUE	1	0.316024388818506	3		620	1003	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	360015	360015	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs752268532	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	121	765	0	ENST00000262320.3:c.1074G>C	p.Glu358Asp	p.E358D	ENST00000262320	NM_003502.3	358	gaG/gaC	4/11	0.316024388818506	3	FACETS	0.845	0.762	0.933	0.423	0.381	0.467	CLONAL	1	TRUE	1	0.316024388818506	3		765	1049	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37680989	37680989	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	101	589	0	ENST00000447079.4:c.3158G>C	p.Ser1053Thr	p.S1053T	ENST00000447079	NM_015083.1	1053	aGt/aCt	12/14	0.316024388818506	5	FACETS	0.862	0.769	0.962	0.287	0.256	0.321	CLONAL	1	TRUE	2	0.316024388818506	5		589	1093	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56811519	56811519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773843495	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1421	113	554	0	ENST00000337432.4:c.1067C>T	p.Ser356Leu	p.S356L	ENST00000337432	NM_058216.2	356	tCa/tTa	9/9	0.316024388818506	9	FACETS	0.982	0.88	1			1	CLONAL	1	TRUE	NA	0.316024388818506	9		554	1534	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63531815	63531815	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1263	127	612	0	ENST00000307078.5:c.2166G>T	p.Arg722Ser	p.R722S	ENST00000307078	NM_004655.3	722	agG/agT	9/11	0.316024388818506	6	FACETS	0.944	0.852	1	0.236	0.213	0.261	CLONAL	1	TRUE	2	0.316024388818506	6		612	1390	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139083	50139083	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	139	658	0	ENST00000246792.3:c.480C>A	p.Phe160Leu	p.F160L	ENST00000246792	NM_006270.3	160	ttC/ttA	5/6	0.316024388818506	5	FACETS	1	0.929	1	0.342	0.311	0.376	CLONAL	1	TRUE	2	0.316024388818506	5		658	1262	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416230	29416230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148351049	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	137	643	0	ENST00000389048.3:c.4723C>T	p.Arg1575Cys	p.R1575C	ENST00000389048	NM_004304.4	1575	Cgt/Tgt	29/29	0.316024388818506	4	FACETS	0.99	0.898	1	0.495	0.449	0.543	CLONAL	1	TRUE	2	0.316024388818506	4		643	1153	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026221	48026221	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	68	448	0	ENST00000234420.5:c.1099C>T	p.His367Tyr	p.H367Y	ENST00000234420	NM_000179.2	367	Cat/Tat	4/10	0.316024388818506	4	FACETS	0.749	0.651	0.856	0.375	0.325	0.428	SUBCLONAL	1	TRUE	2	0.316024388818506	4		448	756	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026971	48026971	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	60	469	0	ENST00000234420.5:c.1849C>G	p.Leu617Val	p.L617V	ENST00000234420	NM_000179.2	617	Ctt/Gtt	4/10	0.316024388818506	4	FACETS	0.664	0.571	0.765	0.332	0.285	0.383	SUBCLONAL	1	TRUE	2	0.316024388818506	4		469	753	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198263198	198263198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	64	417	0	ENST00000335508.6:c.3121C>T	p.Arg1041Cys	p.R1041C	ENST00000335508	NM_012433.2	1041	Cgt/Tgt	21/25	0.316024388818506	4	FACETS	0.75	0.648	0.86	0.375	0.324	0.43	SUBCLONAL	1	TRUE	2	0.316024388818506	4		417	711	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265573	198265573	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	102	509	1	ENST00000335508.6:c.2584G>A	p.Glu862Lys	p.E862K	ENST00000335508	NM_012433.2	862	Gaa/Aaa	18/25	0.316024388818506	4	FACETS	0.925	0.826	1	0.463	0.413	0.516	CLONAL	1	TRUE	2	0.316024388818506	4		510	918	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022656	31022656	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	300	727	0	ENST00000375687.4:c.2141C>G	p.Ser714Cys	p.S714C	ENST00000375687	NM_015338.5	714	tCc/tGc	13/13	0.316024388818506	4	FACETS	1	0.979	1			1	CLONAL	2	TRUE	NA	0.316024388818506	4		727	1154	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633234	12633234	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs941801765	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	117	608	2	ENST00000251849.4:c.1166C>A	p.Ala389Asp	p.A389D	ENST00000251849	NM_002880.3	389	gCc/gAc	11/17	0.316024388818506	4	FACETS	0.933	0.84	1	0.467	0.42	0.516	CLONAL	1	TRUE	2	0.316024388818506	4		610	1044	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437315	52437315	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	113	676	0	ENST00000460680.1:c.1730-1G>C		p.X577_splice	ENST00000460680	NM_004656.3	577			0.316024388818506	4	FACETS	0.87	0.781	0.964	0.435	0.39	0.482	CLONAL	1	TRUE	2	0.316024388818506	4		676	1082	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281160	142281160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	90	430	0	ENST00000350721.4:c.1084G>A	p.Glu362Lys	p.E362K	ENST00000350721	NM_001184.3	362	Gaa/Aaa	4/47	0.316024388818506	4	FACETS	0.962	0.853	1	0.481	0.426	0.54	CLONAL	1	TRUE	2	0.316024388818506	4		430	779	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281576	142281576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	99	649	0	ENST00000350721.4:c.668G>A	p.Arg223Lys	p.R223K	ENST00000350721	NM_001184.3	223	aGa/aAa	4/47	0.316024388818506	4	FACETS	0.8	0.712	0.893	0.4	0.356	0.447	SUBCLONAL	1	TRUE	2	0.316024388818506	4		649	1031	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807540	1807540	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1012768863	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1905	146	800	0	ENST00000260795.2:c.1709G>A	p.Arg570Gln	p.R570Q	ENST00000260795		570	cGg/cAg	12/17	0.316024388818506	8	FACETS	0.878	0.797	0.963			1	CLONAL	1	TRUE	NA	0.316024388818506	8		800	2051	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592115	55592115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	100	544	0	ENST00000288135.5:c.1439C>T	p.Ser480Phe	p.S480F	ENST00000288135	NM_000222.2	480	tCt/tTt	9/21	0.316024388818506	3	FACETS	0.858	0.766	0.957	0.429	0.383	0.479	CLONAL	1	TRUE	1	0.316024388818506	3		544	854	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55974043	55974043	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	101	561	0	ENST00000263923.4:c.1273G>A	p.Glu425Lys	p.E425K	ENST00000263923	NM_002253.2	425	Gag/Aag	10/30	0.316024388818506	3	FACETS	0.938	0.838	1	0.469	0.419	0.522	CLONAL	1	TRUE	1	0.316024388818506	3		561	789	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976903	55976903	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	102	540	0	ENST00000263923.4:c.1009G>T	p.Glu337Ter	p.E337*	ENST00000263923	NM_002253.2	337	Gaa/Taa	8/30	0.316024388818506	3	FACETS	1	0.906	1	0.507	0.453	0.564	CLONAL	1	TRUE	1	0.316024388818506	3		540	737	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590496	67590496	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	53	234	0	ENST00000274335.5:c.1558G>A	p.Glu520Lys	p.E520K	ENST00000274335		520	Gaa/Aaa	11/15	0.316024388818506	3	FACETS	1	0.865	1	0.506	0.433	0.585	CLONAL	1	TRUE	1	0.316024388818506	3		234	384	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517620	176517620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	160	854	0	ENST00000292408.4:c.321G>A	p.Met107Ile	p.M107I	ENST00000292408	NM_213647.1	107	atG/atA	3/18	0.316024388818506	3	FACETS	0.954	0.873	1	0.477	0.436	0.52	CLONAL	1	TRUE	1	0.316024388818506	3		854	1229	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197129	26197129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	196	454	0	ENST00000356476.2:c.350G>A	p.Arg117Gln	p.R117Q	ENST00000356476		117	cGa/cAa	1/1	0.316024388818506	5	FACETS	0.978	0.906	1	0.652	0.604	0.702	CLONAL	2	TRUE	2	0.316024388818506	5		454	935	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197235	26197235	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	98	419	0	ENST00000356476.2:c.244G>A	p.Asp82Asn	p.D82N	ENST00000356476		82	Gat/Aat	1/1	0.316024388818506	5	FACETS	1	0.922	1	0.347	0.309	0.388	CLONAL	1	TRUE	2	0.316024388818506	5		419	877	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163832	32163832	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1230115030	NA	P-0012706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	260	663	0	ENST00000375023.3:c.5394G>C	p.Gln1798His	p.Q1798H	ENST00000375023	NM_004557.3	1798	caG/caC	30/30	0.316024388818506	5	FACETS	0.997	0.933	1	0.665	0.622	0.709	CLONAL	2	TRUE	2	0.316024388818506	5		663	1216	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0013110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1967	68	580	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.800928209643422	3	FACETS	0.117	0.101	0.135	0.058	0.05	0.068	SUBCLONAL	1	TRUE	1	0.799926617566886	3		580	2035	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594258	55594258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913523	NA	P-0013110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	274	466	0	ENST00000288135.5:c.1961T>C	p.Val654Ala	p.V654A	ENST00000288135	NM_000222.2	654	gTg/gCg	13/21	0.69906602912086	4	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.799926617566886	4		466	1104	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593607	55593608	+	protein_altering_variant	In_Frame_Ins	INS	-	-	TCC	novel	NA	P-0013110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	812	679	0	ENST00000288135.5:c.1673_1674insTCC	p.Lys558delinsAsnPro	p.K558delinsNP	ENST00000288135	NM_000222.2	558	aag/aaTCCg	11/21	0.69906602912086	4	FACETS	0.874	0.851	0.898			1	CLONAL	3	TRUE	NA	0.799926617566886	4		679	1393	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595539	55595539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752221484	NA	P-0013110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1302	75	668	1	ENST00000288135.5:c.2029G>A	p.Asp677Asn	p.D677N	ENST00000288135	NM_000222.2	677	Gat/Aat	14/21	0.69906602912086	4	FACETS	0.245	0.214	0.279			1	SUBCLONAL	1	TRUE	NA	0.799926617566886	4		669	1377	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599299	55599299	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1202	117	549	0	ENST00000288135.5:c.2425T>G	p.Cys809Gly	p.C809G	ENST00000288135	NM_000222.2	809	Tgt/Ggt	17/21	0.69906602912086	4	FACETS	0.399	0.359	0.442			1	SUBCLONAL	1	TRUE	NA	0.799926617566886	4		549	1319	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599334	55599337	+	protein_altering_variant	In_Frame_Del	DEL	TTCT	TTCT	G	novel	NA	P-0013110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	141	505	0	ENST00000288135.5:c.2460_2463delinsG	p.Asp820_Ser821delinsGlu	p.D820_S821delinsE	ENST00000288135	NM_000222.2	820	gaTTCT/gaG	17/21	0.69906602912086	4	FACETS	0.547	0.497	0.6			1	SUBCLONAL	1	TRUE	NA	0.799926617566886	4		505	1159	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0013342-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	137	493	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.17022055125839	3	FACETS	0.895	0.813	0.982	0.448	0.406	0.491	INDETERMINATE	1	TRUE	1	0.330907115535172	3		493	1078	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259442	55259442	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397517127	NA	P-0013342-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	99	421	1	ENST00000275493.2:c.2500G>T	p.Val834Leu	p.V834L	ENST00000275493	NM_005228.3	834	Gtg/Ttg	21/28	0.17022055125839	3	FACETS	0.813	0.725	0.907	0.406	0.362	0.454	INDETERMINATE	1	TRUE	1	0.330907115535172	3		422	858	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575597	55575606	+	frameshift_variant	Frame_Shift_Del	DEL	AGTGAACTTC	AGTGAACTTC	-	novel	NA	P-0013342-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	100	567	0	ENST00000288135.5:c.1124_1133del	p.Ser375IlefsTer2	p.S375Ifs*2	ENST00000288135	NM_000222.2	375	AGTGAACTTCat/at	7/21	1	2	FACETS	0.744	0.664	0.829	0.744	0.664	0.829	SUBCLONAL	1	TRUE	1	0.330907115535172	2		567	812	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	189	578	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.392339588352777	5	FACETS	1	0.971	1	0.726	0.673	0.779	CLONAL	2	TRUE	2	0.429297408423259	5		578	665	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	300	1179	0	ENST00000269305.4:c.166del	p.Glu56LysfsTer67	p.E56Kfs*67	ENST00000269305	NM_001126112.2	56	Gaa/aa	4/11	NA	2	FACETS	0.867	0.82	0.915			1	INDETERMINATE	2	TRUE	NA	0.429297408423259	2		1179	806	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0015121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	125	283	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	0.429297408423259	3	FACETS	0.864	0.797	0.931	0.864	0.797	0.931	CLONAL	3	TRUE	0	0.429297408423259	3		283	273	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455082	50455082	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs869312883	NA	P-0015121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	61	470	0	ENST00000331340.3:c.629A>G	p.Tyr210Cys	p.Y210C	ENST00000331340	NM_006060.4	210	tAt/tGt	6/8	0.429297408423259	3	FACETS	0.786	0.68	0.901	0.393	0.34	0.451	CLONAL	1	TRUE	1	0.429297408423259	3		470	439	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	66	526	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.712	0.618	0.814	0.712	0.618	0.814	SUBCLONAL	1	TRUE	1	0.31	2		526	598	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	56	578	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.67	0.574	0.775	0.67	0.574	0.775	SUBCLONAL	1	TRUE	1	0.31	2		578	539	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	50	319	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.638	0.541	0.743	0.638	0.541	0.743	SUBCLONAL	1	TRUE	1	0.31	2		320	506	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0017086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	94	794	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.81	0.72	0.905	0.81	0.72	0.905	CLONAL	1	TRUE	1	0.31	2		794	749	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0017086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	42	681	5	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.333	0.277	0.396	0.333	0.277	0.396	SUBCLONAL	1	TRUE	1	0.31	2		686	813	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245024	133245024	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs752846614	NA	P-0017086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	52	931	8	ENST00000320574.5:c.2091del	p.Leu698CysfsTer94	p.L698Cfs*94	ENST00000320574	NM_006231.2	697	ccC/cc	19/49	1	2	FACETS	0.367	0.311	0.429	0.367	0.311	0.429	SUBCLONAL	1	TRUE	1	0.31	2		939	914	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514495	NA	P-0017086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	91	805	1	ENST00000269305.4:c.542G>A	p.Arg181His	p.R181H	ENST00000269305	NM_001126112.2	181	cGc/cAc	5/11	1	2	FACETS	0.786	0.698	0.88	0.786	0.698	0.88	SUBCLONAL	1	TRUE	1	0.31	2		806	747	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193507	99193507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1471383993	NA	P-0017086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	125	885	1	ENST00000074304.5:c.2702G>A	p.Arg901His	p.R901H	ENST00000074304	NM_001134224.1	901	cGt/cAt	25/26	1	2	FACETS	0.925	0.837	1	0.925	0.837	1	CLONAL	1	TRUE	1	0.31	2		886	872	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	29	364	2	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.33	0.264	0.406	0.33	0.264	0.406	SUBCLONAL	1	TRUE	1	0.31	2		366	567	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	107	1007	0	ENST00000227507.2:c.859C>G	p.Pro287Ala	p.P287A	ENST00000227507	NM_053056.2	287	Ccc/Gcc	5/5	1	2	FACETS	0.759	0.679	0.843	0.759	0.679	0.843	SUBCLONAL	1	TRUE	1	0.31	2		1007	910	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591259	67591259	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	76	422	3	ENST00000274335.5:c.1761del	p.Gly588ValfsTer7	p.G588Vfs*7	ENST00000274335		586	cAa/ca	13/15	1	2	FACETS	0.856	0.751	0.968	0.856	0.751	0.968	CLONAL	1	TRUE	1	0.31	2		425	573	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944400	76944400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	28	520	0	ENST00000373344.5:c.505G>A	p.Val169Met	p.V169M	ENST00000373344	NM_000489.3	169	Gtg/Atg	7/35	1	2	FACETS	0.332	0.264	0.409	0.332	0.264	0.409	SUBCLONAL	1	TRUE	1	0.31	2		520	544	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188098	11188098	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	33	520	0	ENST00000361445.4:c.5996G>A	p.Cys1999Tyr	p.C1999Y	ENST00000361445	NM_004958.3	1999	tGt/tAt	43/58	1	2	FACETS	0.351	0.285	0.426	0.351	0.285	0.426	SUBCLONAL	1	TRUE	1	0.31	2		520	607	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059243	27059244	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	107	658	0	ENST00000324856.7:c.1881dup	p.Met628TyrfsTer14	p.M628Yfs*14	ENST00000324856	NM_006015.4	627	gat/gaTt	4/20	1	2	FACETS	0.955	0.857	1	0.955	0.857	1	CLONAL	1	TRUE	1	0.31	2		658	723	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720745	89720745	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	15	247	0	ENST00000371953.3:c.898del	p.Ile300SerfsTer7	p.I300Sfs*7	ENST00000371953	NM_000314.4	299	gAa/ga	8/9	0.252408814459843	2	FACETS	0.461	0.337	0.609	0.23	0.168	0.305	SUBCLONAL	1	TRUE	0	0.31	2		247	210	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221962	1221962	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123405	NA	P-0017086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	60	1002	1	ENST00000326873.7:c.877G>A	p.Glu293Lys	p.E293K	ENST00000326873	NM_000455.4	293	Gaa/Aaa	7/10	1	2	FACETS	0.329	0.282	0.381	0.329	0.282	0.381	SUBCLONAL	1	TRUE	1	0.31	2		1003	1175	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918991	50918991	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1228707178	NA	P-0017086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	56	829	1	ENST00000440232.2:c.2728C>T	p.Arg910Trp	p.R910W	ENST00000440232	NM_002691.3	910	Cgg/Tgg	22/27	1	2	FACETS	0.431	0.368	0.5	0.431	0.368	0.5	SUBCLONAL	1	TRUE	1	0.31	2		830	838	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182593	99182593	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	39	529	0	ENST00000074304.5:c.2396T>C	p.Phe799Ser	p.F799S	ENST00000074304	NM_001134224.1	799	tTc/tCc	22/26	1	2	FACETS	0.477	0.395	0.569	0.477	0.395	0.569	SUBCLONAL	1	TRUE	1	0.31	2		529	527	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128018877	128018877	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	88	632	0	ENST00000285398.2:c.1991C>A	p.Ser664Tyr	p.S664Y	ENST00000285398	NM_000122.1	664	tCc/tAc	13/15	1	2	FACETS	0.805	0.713	0.904	0.805	0.713	0.904	CLONAL	1	TRUE	1	0.31	2		632	705	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098804	178098804	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	36	627	0	ENST00000397062.3:c.241G>T	p.Gly81Cys	p.G81C	ENST00000397062	NM_006164.4	81	Ggt/Tgt	2/5	1	2	FACETS	0.269	0.22	0.325	0.269	0.22	0.325	SUBCLONAL	1	TRUE	1	0.31	2		627	862	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513246	44513246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	84	563	0	ENST00000291552.4:c.689G>A	p.Arg230Gln	p.R230Q	ENST00000291552	NM_006758.2	230	cGg/cAg	8/8	1	2	FACETS	0.768	0.678	0.864	0.768	0.678	0.864	SUBCLONAL	1	TRUE	1	0.31	2		563	706	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127163	22127163	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	23	429	0	ENST00000215832.6:c.965A>G	p.Glu322Gly	p.E322G	ENST00000215832	NM_002745.4	322	gAg/gGg	7/9	1	2	FACETS	0.254	0.197	0.32	0.254	0.197	0.32	SUBCLONAL	1	TRUE	1	0.31	2		429	585	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231182	142231182	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	78	523	0	ENST00000350721.4:c.4772G>T	p.Trp1591Leu	p.W1591L	ENST00000350721	NM_001184.3	1591	tGg/tTg	27/47	1	2	FACETS	0.691	0.607	0.782	0.691	0.607	0.782	SUBCLONAL	1	TRUE	1	0.31	2		523	728	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0017812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	304	647	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.490443264970118	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.490443264970118	2		647	603	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029437	16029439	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	rs774778469	NA	P-0017812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	93	493	1	ENST00000268712.3:c.1591_1593del	p.Glu531del	p.E531del	ENST00000268712	NM_006311.3	531	GAA/-	15/46	0.490443264970118	2	FACETS	0.415	0.368	0.466	0.208	0.184	0.233	SUBCLONAL	1	TRUE	0	0.490443264970118	2		494	913	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964333	70964333	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	89	357	0	ENST00000276594.2:c.1695G>A	p.Met565Ile	p.M565I	ENST00000276594	NM_024504.3	565	atG/atA	8/8	0.277559620568038	5	FACETS	1	0.928	1			1	INDETERMINATE	1	TRUE	NA	0.490443264970118	5		357	594	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598812	28598812	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	162	663	0	ENST00000253063.3:c.372G>C	p.Gln124His	p.Q124H	ENST00000253063	NM_031459.4	124	caG/caC	4/10	0.490443264970118	1	FACETS	0.811	0.747	0.877	0.811	0.747	0.877	CLONAL	1	TRUE	0	0.490443264970118	1		663	615	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644561	3644561	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	115	846	0	ENST00000294008.3:c.2053G>C	p.Val685Leu	p.V685L	ENST00000294008	NM_032444.2	685	Gtc/Ctc	10/15	0.352565602345373	1	FACETS	0.414	0.372	0.457	0.414	0.372	0.457	SUBCLONAL	1	TRUE	0	0.490443264970118	1		846	856	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589840	55589841	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0017812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	69	436	0	ENST00000288135.5:c.1326_1327dup	p.Cys443PhefsTer21	p.C443Ffs*21	ENST00000288135	NM_000222.2	441	tat/taTTt	8/21	0.243753582869158	3	FACETS	0.449	0.39	0.513	0.15	0.13	0.171	INDETERMINATE	1	TRUE	0	0.490443264970118	3		436	780	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947596	48947596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1566196458	NA	P-0017973-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	193	345	0	ENST00000267163.4:c.1183C>T	p.Gln395Ter	p.Q395*	ENST00000267163	NM_000321.2	395	Caa/Taa	12/27	0.499989436443158	2	FACETS	1	0.99	1	0.679	0.636	0.723	CLONAL	1	TRUE	0	0.64012019459062	2		345	444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587781525	NA	P-0017973-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	790	784	0	ENST00000269305.4:c.842A>T	p.Asp281Val	p.D281V	ENST00000269305	NM_001126112.2	281	gAc/gTc	8/11	NA	2	FACETS	0.971	0.945	0.996			1	INDETERMINATE	2	TRUE	NA	0.64012019459062	2		784	1271	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221211	1221211	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0017973-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	555	671	0	ENST00000326873.7:c.735-1G>T		p.X245_splice	ENST00000326873	NM_000455.4	245			0.533083656712434	3	FACETS	1	0.996	1	0.805	0.778	0.831	CLONAL	2	TRUE	0	0.64012019459062	3		671	948	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465025	120465025	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017973-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	288	418	0	ENST00000256646.2:c.5047G>T	p.Ala1683Ser	p.A1683S	ENST00000256646	NM_024408.3	1683	Gct/Tct	28/34	0.282171684789171	5	FACETS	1	0.983	1	0.734	0.693	0.776	INDETERMINATE	2	TRUE	2	0.64012019459062	5		418	801	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636140	28636140	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769807030	NA	P-0017973-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	405	599	0	ENST00000241453.7:c.232G>A	p.Ala78Thr	p.A78T	ENST00000241453	NM_004119.2	78	Gct/Act	3/24	0.499989436443158	2	FACETS	0.759	0.726	0.791	0.759	0.726	0.791	SUBCLONAL	2	TRUE	0	0.64012019459062	2		599	834	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264426	46264426	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017973-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1260	139	457	0	ENST00000371998.3:c.1473G>T	p.Lys491Asn	p.K491N	ENST00000371998		491	aaG/aaT	11/23	0.64012019459062	6	FACETS	0.708	0.642	0.777	0.142	0.128	0.156	SUBCLONAL	1	TRUE	1	0.64012019459062	6		457	1399	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295237	1295237	+	upstream_gene_variant	5'Flank	SNP	G	G	C	novel	NA	P-0017973-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	272	425	0				ENST00000310581	NM_198253.2	-/1132			0.298894460425592	5	FACETS	1	0.96	1	1	0.96	1	INDETERMINATE	3	TRUE	2	0.64012019459062	5		425	548	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517530	176517530	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017973-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	459	828	0	ENST00000292408.4:c.232del	p.Arg78ValfsTer9	p.R78Vfs*9	ENST00000292408	NM_213647.1	77	ggC/gg	3/18	0.526597220288747	2	FACETS	0.854	0.821	0.886	0.854	0.821	0.886	CLONAL	2	TRUE	0	0.64012019459062	2		828	840	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70971001	70971001	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017973-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	437	758	0	ENST00000276594.2:c.1260G>T	p.Lys420Asn	p.K420N	ENST00000276594	NM_024504.3	420	aaG/aaT	6/8	0.499281469210465	4	FACETS	0.882	0.842	0.923	0.882	0.842	0.923	CLONAL	2	TRUE	2	0.64012019459062	4		758	1269	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090788	5090788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1443056014	NA	P-0017973-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	165	409	0	ENST00000381652.3:c.2936C>T	p.Thr979Met	p.T979M	ENST00000381652	NM_004972.3	979	aCg/aTg	22/25	0.549560117754044	4	FACETS	0.818	0.756	0.881	0.818	0.756	0.881	CLONAL	2	TRUE	2	0.64012019459062	4		409	517	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229249	123229249	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017973-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	216	364	0	ENST00000218089.9:c.3733A>G	p.Thr1245Ala	p.T1245A	ENST00000218089	NM_001042749.1	1245	Aca/Gca	34/35	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.64012019459062	NA		364	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578376	7578379	+	frameshift_variant	Frame_Shift_Del	DEL	CTAT	CTAT	-	novel	NA	P-0018288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	149	545	0	ENST00000269305.4:c.551_554del	p.Asp184AlafsTer62	p.D184Afs*62	ENST00000269305	NM_001126112.2	184	gATAGc/gc	5/11	0.369927688436187	1	FACETS	0.919	0.843	0.999	0.919	0.843	0.999	CLONAL	1	TRUE	0	0.403635416992663	1		545	641	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754574	42754574	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768322408	NA	P-0018288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	190	723	0	ENST00000222329.4:c.166G>A	p.Val56Ile	p.V56I	ENST00000222329	NM_006494.2	56	Gtc/Atc	2/4	1	2	FACETS	0.953	0.881	1	0.953	0.881	1	CLONAL	1	TRUE	1	0.403635416992663	2		723	988	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149506162	149506162	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	344	608	1	ENST00000261799.4:c.1595T>C	p.Val532Ala	p.V532A	ENST00000261799	NM_002609.3	532	gTg/gCg	11/23	NA	2	FACETS	0.95	0.903	0.998			1	INDETERMINATE	2	TRUE	NA	0.403635416992663	2		609	897	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68982089	68982089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376775544	NA	P-0018288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	89	565	0	ENST00000288368.4:c.1463G>A	p.Arg488His	p.R488H	ENST00000288368	NM_024870.2	488	cGt/cAt	13/40	0.403635416992663	3	FACETS	0.616	0.545	0.691	0.308	0.272	0.346	SUBCLONAL	1	TRUE	1	0.403635416992663	3		565	861	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40490783	40490784	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0018288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	100	353	0	ENST00000264657.5:c.515_516del	p.Phe172Ter	p.F172*	ENST00000264657	NM_139276.2	172	tTT/t	6/24	0.369927688436187	1	FACETS	0.783	0.702	0.868	0.783	0.702	0.868	SUBCLONAL	1	TRUE	0	0.403635416992663	1		353	505	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242430	55242430	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	116	420	0	ENST00000275493.2:c.2200G>T	p.Glu734Ter	p.E734*	ENST00000275493	NM_005228.3	734	Gaa/Taa	19/28	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.403635416992663	2		420	569	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534545	140534545	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	130	427	0	ENST00000288602.6:c.368C>G	p.Ser123Cys	p.S123C	ENST00000288602	NM_004333.4	123	tCt/tGt	3/18	1	2	FACETS	0.936	0.851	1	0.936	0.851	1	CLONAL	1	TRUE	1	0.403635416992663	2		427	688	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285954	38285954	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0018288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	108	464	0	ENST00000425967.3:c.458-1G>C		p.X153_splice	ENST00000425967	NM_001174067.1	153			0.37424845178513	1	FACETS	0.872	0.786	0.961	0.872	0.786	0.961	CLONAL	1	TRUE	0	0.403635416992663	1		464	490	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492952	8492952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	107	453	0	ENST00000356435.5:c.2377G>A	p.Glu793Lys	p.E793K	ENST00000356435		793	Gaa/Aaa	16/35	1	2	FACETS	0.716	0.643	0.795	0.716	0.643	0.795	SUBCLONAL	1	TRUE	1	0.403635416992663	2		453	740	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018366-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	198	859	1	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	1	2	FACETS	0.952	0.88	1	0.952	0.88	1	CLONAL	1	FALSE	1	0.353055300095034	2		860	1178	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727455	66727455	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs869025608	NA	P-0018366-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	317	653	0	ENST00000307102.5:c.171G>T	p.Lys57Asn	p.K57N	ENST00000307102	NM_002755.3	57	aaG/aaT	2/11	0.353055300095034	3	FACETS	1	0.988	1	0.762	0.721	0.804	CLONAL	2	FALSE	0	0.353055300095034	3		653	924	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610227	10610227	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018366-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	435	950	0	ENST00000171111.5:c.483G>T	p.Met161Ile	p.M161I	ENST00000171111	NM_203500.1	161	atG/atT	2/6	0.217208467217089	3	FACETS	0.982	0.935	1	0.655	0.623	0.687	CLONAL	2	FALSE	0	0.353055300095034	3		950	1476	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076932	41076932	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018366-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	92	703	0	ENST00000373198.4:c.1488del	p.Phe498LeufsTer103	p.F498Lfs*103	ENST00000373198	NM_133170.3	496	ggG/gg	9/32	0.353055300095034	3	FACETS	0.645	0.572	0.723	0.322	0.286	0.362	SUBCLONAL	1	FALSE	1	0.353055300095034	3		703	951	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0018366-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	349	760	0	ENST00000269305.4:c.560-1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.217208467217089	3	FACETS	1	0.988	1	0.753	0.715	0.793	CLONAL	2	FALSE	0	0.353055300095034	3		760	1029	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120457936	120457936	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018366-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	119	616	0	ENST00000256646.2:c.7409A>T	p.Tyr2470Phe	p.Y2470F	ENST00000256646	NM_024408.3	2470	tAt/tTt	34/34	1	2	FACETS	0.77	0.694	0.849	0.77	0.694	0.849	SUBCLONAL	1	FALSE	1	0.353055300095034	2		616	876	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742846	17742846	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018366-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	333	892	0	ENST00000250003.3:c.754C>A	p.Leu252Met	p.L252M	ENST00000250003	NM_002478.4	252	Ctg/Atg	3/3	0.294148274191596	2	FACETS	0.766	0.723	0.809	0.766	0.723	0.809	SUBCLONAL	2	FALSE	0	0.353055300095034	2		892	1232	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835678	68835678	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018366-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	164	731	0	ENST00000261769.5:c.269G>T	p.Arg90Leu	p.R90L	ENST00000261769	NM_004360.3	90	cGg/cTg	3/16	0.353055300095034	3	FACETS	0.879	0.805	0.957	0.44	0.402	0.479	CLONAL	1	FALSE	1	0.353055300095034	3		731	1243	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985802	60985802	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018366-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	246	458	1	ENST00000333681.4:c.98del	p.Gly33GlufsTer63	p.G33Efs*63	ENST00000333681		33	gGa/ga	2/3	0.282542728907628	3	FACETS	1	0.961	1	0.689	0.646	0.733	CLONAL	2	FALSE	0	0.353055300095034	3		459	793	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7168056	7168056	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018366-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	155	730	0	ENST00000302850.5:c.1533G>C	p.Lys511Asn	p.K511N	ENST00000302850	NM_000208.2	511	aaG/aaC	7/22	0.217208467217089	3	FACETS	0.976	0.893	1	0.325	0.297	0.355	CLONAL	1	FALSE	0	0.353055300095034	3		730	1058	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31422927	31422927	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018366-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	124	710	0	ENST00000344624.3:c.3386C>T	p.Thr1129Ile	p.T1129I	ENST00000344624		1129	aCa/aTa	26/33	0.353055300095034	3	FACETS	0.769	0.695	0.849	0.385	0.347	0.425	SUBCLONAL	1	FALSE	1	0.353055300095034	3		710	1074	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367323	50367323	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018366-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	235	606	0	ENST00000331340.3:c.130C>T	p.Gln44Ter	p.Q44*	ENST00000331340	NM_006060.4	44	Cag/Tag	3/8	0.297586548436566	2	FACETS	0.782	0.731	0.834	0.782	0.731	0.834	SUBCLONAL	2	FALSE	0	0.353055300095034	2		606	851	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80343543	80343543	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018366-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	112	513	0	ENST00000286548.4:c.776T>C	p.Ile259Thr	p.I259T	ENST00000286548	NM_002072.3	259	aTc/aCc	6/7	0.217208467217089	3	FACETS	0.998	0.898	1	0.333	0.299	0.368	CLONAL	1	FALSE	0	0.353055300095034	3		513	748	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937724	76937724	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018366-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	96	257	1	ENST00000373344.5:c.3024G>T	p.Gln1008His	p.Q1008H	ENST00000373344	NM_000489.3	1008	caG/caT	9/35	1	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	0	0.353055300095034	1		258	326	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198970	67198970	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018366-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	114	474	0	ENST00000312629.5:c.442del	p.Glu149SerfsTer62	p.E149Sfs*62	ENST00000312629	NM_003952.2	147	atC/at	5/15	0.353055300095034	5	FACETS	0.837	0.752	0.928	0.279	0.25	0.31	CLONAL	1	FALSE	2	0.353055300095034	5		474	1180	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497601	125497601	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018366-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	139	404	0	ENST00000428830.2:c.165G>C	p.Glu55Asp	p.E55D	ENST00000428830	NM_001114121.2	55	gaG/gaC	3/14	0.353055300095034	3	FACETS	1	0.985	1			1	CLONAL	1	FALSE	NA	0.353055300095034	3		404	653	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0018583-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	398	531	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	1	2	FACETS	0.835	0.795	0.876	0.835	0.795	0.876	CLONAL	1	TRUE	1	0.803060705089083	2		531	1187	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0018645-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	82	333	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.361176505229854	3	FACETS	1	0.946	1	0.56	0.495	0.628	CLONAL	1	TRUE	1	0.361176505229854	3		333	479	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619232	43619232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1384605415	NA	P-0018645-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	240	407	0	ENST00000355710.3:c.2915G>A	p.Arg972Lys	p.R972K	ENST00000355710	NM_020975.4	972	aGg/aAg	17/20	0.361176505229854	3	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.361176505229854	3		407	631	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446287	70446291	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	novel	NA	P-0018645-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	159	380	0	ENST00000373644.4:c.5229_5233del	p.Lys1743AsnfsTer25	p.K1743Nfs*25	ENST00000373644	NM_030625.2	1743	AAAAGa/a	11/12	0.361176505229854	4	FACETS	0.905	0.832	0.981	0.453	0.416	0.491	CLONAL	2	TRUE	0	0.361176505229854	4		380	662	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426832	47426833	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0018645-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	68	309	0	ENST00000377045.4:c.1076+2dup		p.X359_splice	ENST00000377045	NM_001654.4	359			0.361176505229854	3	FACETS	0.932	0.813	1	0.466	0.406	0.53	CLONAL	1	TRUE	1	0.361176505229854	3		309	477	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346319	89346319	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167046199	NA	P-0018948-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	117	560	0	ENST00000301030.4:c.6631C>T	p.Pro2211Ser	p.P2211S	ENST00000301030	NM_001256183.1	2211	Cca/Tca	9/13	0.380319805023433	3	FACETS	1	0.981	1	0.677	0.613	0.744	CLONAL	1	TRUE	1	0.380319805023433	3		560	541	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46733199	46733220	+	frameshift_variant	Frame_Shift_Del	DEL	GGTGCTCATCTCCGGAACTCCC	GGTGCTCATCTCCGGAACTCCC	-	novel	NA	P-0018948-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	87	666	0	ENST00000371975.4:c.960_981del	p.Val321SerfsTer20	p.V321Sfs*20	ENST00000371975	NM_003579.3	320	cgGGTGCTCATCTCCGGAACTCCC/cg	9/18	0.380319805023433	3	FACETS	0.706	0.625	0.794	0.353	0.312	0.397	SUBCLONAL	1	TRUE	1	0.380319805023433	3		666	771	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593529	48593529	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555686619	NA	P-0018948-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	49	315	0	ENST00000342988.3:c.1280A>G	p.His427Arg	p.H427R	ENST00000342988	NM_005359.5	427	cAt/cGt	10/12	0.380319805023433	3	FACETS	0.871	0.741	1	0.436	0.37	0.507	CLONAL	1	TRUE	1	0.380319805023433	3		315	352	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936092	+	missense_variant	Missense_Mutation	DNP	GA	GA	AG	novel	NA	P-0018948-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	241	704	4	ENST00000263967.3:c.1633_1634delinsAG	p.Glu545Arg	p.E545R	ENST00000263967	NM_006218.2	545	GAg/AGg	10/21	0.380319805023433	3	FACETS	0.964	0.904	1	0.643	0.602	0.684	CLONAL	2	TRUE	0	0.380319805023433	3		708	782	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876659675	NA	P-0020057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	59	824	0	ENST00000269305.4:c.764T>G	p.Ile255Ser	p.I255S	ENST00000269305	NM_001126112.2	255	aTc/aGc	7/11	0.227530412589694	2	FACETS	0.858	0.742	0.983	0.429	0.371	0.492	INDETERMINATE	1	FALSE	0	0.387571052085951	2		824	355	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847312	68847313	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	12	704	0	ENST00000261769.5:c.1235dup	p.Tyr413IlefsTer6	p.Y413Ifs*6	ENST00000261769	NM_004360.3	412	gta/gTta	9/16	0.387571052085951	1	FACETS	0.212	0.148	0.289	0.212	0.148	0.289	SUBCLONAL	1	FALSE	0	0.387571052085951	1		704	236	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844115	68844116	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTT	novel	NA	P-0020057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	45	620	0	ENST00000261769.5:c.706_707insTTGT	p.Ser236PhefsTer9	p.S236Ffs*9	ENST00000261769	NM_004360.3	235	gtg/gTGTTtg	6/16	0.387571052085951	1	FACETS	0.847	0.719	0.985	0.847	0.719	0.985	CLONAL	1	FALSE	0	0.387571052085951	1		620	221	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0020707-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	257	492	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.625844299044509	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.63506329834955	2		492	381	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665213	138665213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020707-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	187	684	0	ENST00000330315.3:c.352G>A	p.Glu118Lys	p.E118K	ENST00000330315	NM_023067.3	118	Gag/Aag	1/1	0.591367196366489	4	FACETS	1	0.966	1	0.54	0.499	0.582	CLONAL	1	TRUE	2	0.63506329834955	4		684	892	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106537	108106537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020707-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	71	261	0	ENST00000278616.4:c.472G>A	p.Glu158Lys	p.E158K	ENST00000278616	NM_000051.3	158	Gaa/Aaa	5/63	0.63506329834955	3	FACETS	0.904	0.795	1	0.301	0.265	0.34	CLONAL	1	TRUE	0	0.63506329834955	3		261	326	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114724	108114724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020707-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	86	314	0	ENST00000278616.4:c.541G>A	p.Asp181Asn	p.D181N	ENST00000278616	NM_000051.3	181	Gat/Aat	6/63	0.63506329834955	3	FACETS	1	0.927	1	0.35	0.312	0.39	CLONAL	1	TRUE	0	0.63506329834955	3		314	340	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117816	108117816	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020707-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	80	290	0	ENST00000278616.4:c.1027G>T	p.Glu343Ter	p.E343*	ENST00000278616	NM_000051.3	343	Gaa/Taa	8/63	0.63506329834955	3	FACETS	0.9	0.797	1	0.3	0.265	0.336	CLONAL	1	TRUE	0	0.63506329834955	3		290	369	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641082	3641082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020707-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	165	822	0	ENST00000294008.3:c.2557G>A	p.Glu853Lys	p.E853K	ENST00000294008	NM_032444.2	853	Gaa/Aaa	12/15	0.436147457574775	4	FACETS	0.892	0.818	0.968	0.446	0.409	0.484	CLONAL	1	TRUE	2	0.63506329834955	4		822	953	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641688	23641688	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs187191947	NA	P-0020707-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	82	409	0	ENST00000261584.4:c.1787G>A	p.Gly596Glu	p.G596E	ENST00000261584	NM_024675.3	596	gGa/gAa	5/13	0.436147457574775	4	FACETS	0.828	0.732	0.93	0.414	0.366	0.465	CLONAL	1	TRUE	2	0.63506329834955	4		409	510	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864531	56864531	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758920885	NA	P-0020707-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	120	467	0	ENST00000308159.5:c.1019G>A	p.Arg340Gln	p.R340Q	ENST00000308159	NM_014669.4	340	cGa/cAa	10/22	0.610490205962849	2	FACETS	1	0.942	1	0.521	0.475	0.567	CLONAL	1	TRUE	0	0.63506329834955	2		467	363	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003236	143003236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020707-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	106	399	0	ENST00000262992.4:c.2590G>A	p.Glu864Lys	p.E864K	ENST00000262992	NM_001101669.1	864	Gag/Aag	23/24	0.632255710833126	3	FACETS	0.944	0.851	1	0.472	0.425	0.521	CLONAL	1	TRUE	1	0.63506329834955	3		399	466	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031982	26031982	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020707-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	80	391	0	ENST00000244661.2:c.307G>C	p.Gly103Arg	p.G103R	ENST00000244661	NM_003537.3	103	Ggg/Cgg	1/1	0.62980615737342	4	FACETS	0.884	0.781	0.994	0.221	0.195	0.249	CLONAL	1	TRUE	0	0.63506329834955	4		391	466	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864656	37864656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs950730453	NA	P-0021574-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	264	779	1	ENST00000269571.5:c.308G>A	p.Arg103Gln	p.R103Q	ENST00000269571		103	cGa/cAa	3/27	0.658193548595023	4	FACETS	0.956	0.894	1	0.319	0.298	0.34	CLONAL	1	TRUE	1	0.658193548595023	4		780	1392	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0021574-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	265	472	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.658193548595023	4	FACETS	1	0.973	1			1	CLONAL	3	TRUE	NA	0.658193548595023	4		472	433	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690306	117690306	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021574-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	132	420	0	ENST00000369458.3:c.823C>G	p.Leu275Val	p.L275V	ENST00000369458	NM_024626.3	275	Ctc/Gtc	5/6	0.633973042198947	2	FACETS	0.916	0.838	0.996	0.458	0.419	0.498	CLONAL	1	TRUE	0	0.658193548595023	2		420	438	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112035575	112035575	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1159797492	NA	P-0021574-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	122	320	0	ENST00000368678.4:c.319G>C	p.Glu107Gln	p.E107Q	ENST00000368678		107	Gaa/Caa	4/13	0.658193548595023	3	FACETS	1	0.935	1	0.518	0.47	0.567	CLONAL	1	TRUE	1	0.658193548595023	3		320	476	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137830	64137830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021574-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1501	368	1156	1	ENST00000334205.4:c.1931C>T	p.Ser644Phe	p.S644F	ENST00000334205	NM_003942.2	644	tCc/tTc	15/17	0.658193548595023	4	FACETS	0.992	0.938	1	0.496	0.469	0.524	CLONAL	1	TRUE	2	0.658193548595023	4		1157	1869	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425644	49425644	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057517992	NA	P-0021574-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	242	765	1	ENST00000301067.7:c.12844C>T	p.Arg4282Ter	p.R4282*	ENST00000301067	NM_003482.3	4282	Cga/Tga	39/54	0.658193548595023	3	FACETS	0.96	0.897	1	0.48	0.448	0.513	CLONAL	1	TRUE	1	0.658193548595023	3		766	1018	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199864	138199864	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021574-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	141	436	0	ENST00000237289.4:c.1282G>C	p.Glu428Gln	p.E428Q	ENST00000237289	NM_001270507.1	428	Gag/Cag	7/9	0.658193548595023	3	FACETS	0.833	0.76	0.908	0.416	0.38	0.454	CLONAL	1	TRUE	1	0.658193548595023	3		436	684	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448173	49448173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021574-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	182	652	0	ENST00000301067.7:c.427G>A	p.Ala143Thr	p.A143T	ENST00000301067	NM_003482.3	143	Gct/Act	4/54	0.658193548595023	3	FACETS	0.92	0.85	0.992	0.46	0.425	0.496	CLONAL	1	TRUE	1	0.658193548595023	3		652	799	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211836	2211836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021574-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	469	742	0	ENST00000398665.3:c.1552G>A	p.Glu518Lys	p.E518K	ENST00000398665	NM_032482.2	518	Gag/Aag	16/28	0.658193548595023	3	FACETS	0.977	0.939	1	0.977	0.939	1	CLONAL	2	TRUE	1	0.658193548595023	3		742	969	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243262	123243262	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021574-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	245	882	0	ENST00000358487.5:c.2251A>G	p.Lys751Glu	p.K751E	ENST00000358487	NM_000141.4	751	Aag/Gag	17/18	0.619996509395491	2	FACETS	0.862	0.807	0.918	0.431	0.403	0.459	CLONAL	1	TRUE	0	0.658193548595023	2		882	864	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404558	8404558	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021574-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	47	235	0	ENST00000356435.5:c.4189G>T	p.Val1397Phe	p.V1397F	ENST00000356435		1397	Gtt/Ttt	25/35	0.641608340613121	5	FACETS	0.847	0.718	0.989	0.169	0.143	0.198	CLONAL	1	TRUE	0	0.658193548595023	5		235	335	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260193	149260194	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTGCTG	rs748784098	NA	P-0022440-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	258	492	0	ENST00000360632.3:c.694_699dup	p.Gln232_Gln233dup	p.Q232_Q233dup	ENST00000360632	NM_015472.4	232	-/CAGCAG	4/7	0.901036782893468	1	FACETS	0.734	0.699	0.768	0.734	0.699	0.768	SUBCLONAL	1	TRUE	0	0.901036782893468	1		492	429	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260789	16260789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022440-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	153	460	0	ENST00000375759.3:c.8054C>T	p.Thr2685Ile	p.T2685I	ENST00000375759	NM_015001.2	2685	aCc/aTc	11/15	0.901036782893468	1	FACETS	0.4	0.368	0.432	0.4	0.368	0.432	SUBCLONAL	1	TRUE	0	0.901036782893468	1		460	467	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254623	46254623	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs547684429	NA	P-0022440-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	132	381	0	ENST00000334344.6:c.4813G>A	p.Gly1605Ser	p.G1605S	ENST00000334344	NM_152641.2	1605	Ggc/Agc	16/21	1	2	FACETS	0.473	0.43	0.517	0.473	0.43	0.517	SUBCLONAL	1	TRUE	1	0.901036782893468	2		381	620	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42843871	42843871	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022440-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	99	379	1	ENST00000398585.3:c.1048G>A	p.Gly350Arg	p.G350R	ENST00000398585	NM_001135099.1	350	Ggg/Agg	10/14	0.901036782893468	1	FACETS	0.392	0.354	0.431	0.392	0.354	0.431	SUBCLONAL	1	TRUE	0	0.901036782893468	1		380	308	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0023465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	321	647	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.276554528687598	3	FACETS	1	0.991	1	0.813	0.769	0.858	CLONAL	2	TRUE	0	0.307441544291759	3		647	988	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725053	89725058	+	inframe_deletion	In_Frame_Del	DEL	TACTTC	TACTTC	-	novel	NA	P-0023465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	82	168	0	ENST00000371953.3:c.1036_1041del	p.Tyr346_Phe347del	p.Y346_F347del	ENST00000371953	NM_000314.4	346	TACTTC/-	9/9	0.288593895256036	3	FACETS	0.858	0.769	0.951	0.858	0.769	0.951	CLONAL	3	TRUE	0	0.307441544291759	3		168	239	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944019	71944019	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0023465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	169	517	0	ENST00000298229.2:c.1951+1G>C		p.X651_splice	ENST00000298229	NM_001567.3	651			NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.307441544291759	2		517	816	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888809	76888809	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	80	370	0	ENST00000373344.5:c.5020G>C	p.Glu1674Gln	p.E1674Q	ENST00000373344	NM_000489.3	1674	Gaa/Caa	19/35	0.158504666663082	4	FACETS	1	0.959	1	0.601	0.53	0.677	INDETERMINATE	1	TRUE	2	0.307441544291759	4		370	566	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0023614-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	385	622	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.329916662103052	3	FACETS	1	0.968	1			1	CLONAL	4	TRUE	NA	0.329916662103052	3		622	673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0023614-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	251	647	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	0.329916662103052	2	FACETS	0.94	0.883	1	0.94	0.883	1	CLONAL	2	TRUE	0	0.329916662103052	2		647	809	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145430	58145430	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894340	NA	P-0023614-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	296	489	0	ENST00000257904.6:c.71G>T	p.Arg24Leu	p.R24L	ENST00000257904	NM_000075.3	24	cGt/cTt	2/8	0.329916662103052	4	FACETS	0.95	0.902	0.998	0.95	0.902	0.998	CLONAL	4	TRUE	0	0.329916662103052	4		489	628	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183766	10183766	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs200885420	NA	P-0023614-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	40	641	0	ENST00000256474.2:c.235C>G	p.Arg79Gly	p.R79G	ENST00000256474	NM_000551.3	79	Cgc/Ggc	1/3	1	2	FACETS	0.329	0.272	0.392	0.329	0.272	0.392	SUBCLONAL	1	TRUE	1	0.329916662103052	2		641	738	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171462	123171462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023614-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	150	367	0	ENST00000218089.9:c.374C>T	p.Ser125Leu	p.S125L	ENST00000218089	NM_001042749.1	125	tCa/tTa	6/35	0.313263661146113	4	FACETS	0.925	0.848	1	0.616	0.565	0.67	CLONAL	2	TRUE	1	0.329916662103052	4		367	654	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524486	44524486	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023614-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	56	284	0	ENST00000291552.4:c.71T>C	p.Ile24Thr	p.I24T	ENST00000291552	NM_006758.2	24	aTt/aCt	2/8	0.329916662103052	3	FACETS	1	0.887	1	0.518	0.445	0.596	CLONAL	1	TRUE	1	0.329916662103052	3		284	382	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190685	108190685	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023614-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	70	313	0	ENST00000278616.4:c.6352G>C	p.Glu2118Gln	p.E2118Q	ENST00000278616	NM_000051.3	2118	Gaa/Caa	44/63	0.329916662103052	4	FACETS	0.941	0.82	1	0.47	0.41	0.535	CLONAL	1	TRUE	2	0.329916662103052	4		313	600	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348758	118348758	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023614-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	167	274	0	ENST00000534358.1:c.3411A>T	p.Arg1137Ser	p.R1137S	ENST00000534358	NM_005933.3	1137	agA/agT	5/36	0.329916662103052	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.329916662103052	4		274	540	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253966	133253966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023614-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	62	517	0	ENST00000320574.5:c.784G>A	p.Asp262Asn	p.D262N	ENST00000320574	NM_006231.2	262	Gac/Aac	8/49	0.329916662103052	3	FACETS	0.562	0.484	0.647	0.187	0.161	0.216	SUBCLONAL	1	TRUE	0	0.329916662103052	3		517	779	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554403	63554403	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023614-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	173	613	0	ENST00000307078.5:c.336T>A	p.Phe112Leu	p.F112L	ENST00000307078	NM_004655.3	112	ttT/ttA	2/11	0.329916662103052	6	FACETS	0.827	0.761	0.897	0.414	0.38	0.449	CLONAL	2	TRUE	2	0.329916662103052	6		613	1052	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142933	30142933	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1275464904	NA	P-0023614-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	247	814	1	ENST00000389048.3:c.593T>A	p.Val198Glu	p.V198E	ENST00000389048	NM_004304.4	198	gTg/gAg	1/29	0.329916662103052	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	2	0.329916662103052	4		815	920	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309458	30309458	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023614-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	176	515	0	ENST00000307677.4:c.564G>T	p.Trp188Cys	p.W188C	ENST00000307677	NM_138578.1	188	tgG/tgT	2/3	0.329916662103052	5	FACETS	0.77	0.708	0.834	0.513	0.472	0.556	SUBCLONAL	2	TRUE	2	0.329916662103052	5		515	1036	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022666	31022666	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1337715441	NA	P-0023614-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	96	573	0	ENST00000375687.4:c.2151G>C	p.Arg717Ser	p.R717S	ENST00000375687	NM_015338.5	717	agG/agC	13/13	0.329916662103052	5	FACETS	1	0.936	1	0.358	0.318	0.4	CLONAL	1	TRUE	2	0.329916662103052	5		573	810	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306532	41306532	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023614-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	187	479	0	ENST00000373198.4:c.1127C>A	p.Pro376His	p.P376H	ENST00000373198	NM_133170.3	376	cCc/cAc	7/32	0.329916662103052	3	FACETS	1	0.968	1			1	CLONAL	2	TRUE	NA	0.329916662103052	3		479	615	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947866	178947866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023614-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	30	301	0	ENST00000263967.3:c.2741G>A	p.Gly914Glu	p.G914E	ENST00000263967	NM_006218.2	914	gGa/gAa	19/21	0.197519250848943	5	FACETS	0.582	0.468	0.712	0.194	0.156	0.238	INDETERMINATE	1	TRUE	2	0.329916662103052	5		301	467	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176678829	176678832	+	frameshift_variant	Frame_Shift_Del	DEL	ATTT	ATTT	TGA	novel	NA	P-0023614-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	123	315	1	ENST00000439151.2:c.4740_4743delinsTGA	p.Lys1580AsnfsTer62	p.K1580Nfs*62	ENST00000439151	NM_022455.4	1580	aaATTT/aaTGA	12/23	0.329916662103052	5	FACETS	0.836	0.757	0.918	0.557	0.504	0.612	CLONAL	2	TRUE	2	0.329916662103052	5		316	667	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212174	98212174	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023614-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	139	351	0	ENST00000331920.6:c.3498T>A	p.Asn1166Lys	p.N1166K	ENST00000331920	NM_000264.3	1166	aaT/aaA	21/24	0.329916662103052	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.329916662103052	2		351	405	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179102	123179102	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023614-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	86	510	0	ENST00000218089.9:c.552del	p.Gln185AsnfsTer12	p.Q185Nfs*12	ENST00000218089	NM_001042749.1	184	cGg/cg	8/35	0.313263661146113	4	FACETS	0.822	0.727	0.925	0.274	0.242	0.309	CLONAL	1	TRUE	1	0.329916662103052	4		510	843	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504033	123504033	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023614-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	82	293	2	ENST00000371139.4:c.209C>A	p.Pro70His	p.P70H	ENST00000371139	NM_001114937.2	70	cCt/cAt	3/4	0.313263661146113	4	FACETS	0.812	0.72	0.91	0.541	0.48	0.607	CLONAL	2	TRUE	1	0.329916662103052	4		295	407	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0024319-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	750	543	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.416659753764721	16	FACETS	1	0.981	1			1	CLONAL	14	TRUE	NA	0.416659753764721	16		543	1003	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597378	10597378	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024319-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	45	702	1	ENST00000171111.5:c.1825A>T	p.Thr609Ser	p.T609S	ENST00000171111	NM_203500.1	609	Acc/Tcc	6/6	0.416659753764721	1	FACETS	0.95	0.81	1	0.95	0.81	1	CLONAL	1	TRUE	0	0.416659753764721	1		703	180	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61708412	61708412	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024319-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	31	272	0	ENST00000401558.2:c.2977C>T	p.Gln993Ter	p.Q993*	ENST00000401558	NM_003400.3	993	Caa/Taa	24/25	0.416659753764721	3	FACETS	1	0.872	1	0.361	0.295	0.434	CLONAL	1	TRUE	0	0.416659753764721	3		272	166	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212522506	212522506	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748501593	NA	P-0024319-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	66	346	0	ENST00000342788.4:c.1919G>A	p.Gly640Asp	p.G640D	ENST00000342788	NM_005235.2	640	gGc/gAc	16/28	0.416659753764721	3	FACETS	1	0.974	1	0.493	0.432	0.556	CLONAL	1	TRUE	0	0.416659753764721	3		346	259	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646891	37646891	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024325-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	335	708	0	ENST00000447079.4:c.2015del	p.Pro672LeufsTer81	p.P672Lfs*81	ENST00000447079	NM_015083.1	671	ctC/ct	3/14	0.744495457049796	4	FACETS	0.901	0.856	0.948	0.901	0.856	0.948	CLONAL	2	FALSE	2	0.745783802107898	4		708	870	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618691	37618691	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024325-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	310	575	0	ENST00000447079.4:c.367del	p.Leu123Ter	p.L123*	ENST00000447079	NM_015083.1	123	Cta/ta	1/14	0.744495457049796	4	FACETS	0.991	0.941	1	0.991	0.941	1	CLONAL	2	FALSE	2	0.745783802107898	4		575	732	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0024735-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	122	630	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.617	0.557	0.681	0.617	0.557	0.681	SUBCLONAL	1	TRUE	1	0.424010051299038	2		631	932	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842633	68842633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024735-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	52	676	0	ENST00000261769.5:c.569A>G	p.Tyr190Cys	p.Y190C	ENST00000261769	NM_004360.3	190	tAc/tGc	5/16	1	2	FACETS	0.34	0.289	0.397	0.34	0.289	0.397	SUBCLONAL	1	TRUE	1	0.424010051299038	2		676	721	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286746	212286746	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024735-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	23	294	0	ENST00000342788.4:c.2950T>C	p.Tyr984His	p.Y984H	ENST00000342788	NM_005235.2	984	Tac/Cac	24/28	1	2	FACETS	0.377	0.294	0.472	0.377	0.294	0.472	SUBCLONAL	1	TRUE	1	0.424010051299038	2		294	288	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	193	578	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.629401312552475	3	FACETS	0.851	0.795	0.907	0.851	0.795	0.907	CLONAL	2	TRUE	1	0.638196573236816	3		578	469	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971177	21971177	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913382	NA	P-0024793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	160	460	0	ENST00000304494.5:c.181G>T	p.Glu61Ter	p.E61*	ENST00000304494	NM_000077.4	61	Gag/Tag	2/3	0.606013940040419	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.638196573236816	1		460	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579384	7579387	+	frameshift_variant	Frame_Shift_Del	DEL	TTTC	TTTC	-	novel	NA	P-0024793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	121	806	0	ENST00000269305.4:c.300_303del	p.Lys101ProfsTer21	p.K101Pfs*21	ENST00000269305	NM_001126112.2	100	caGAAA/ca	4/11	0.600599215343515	1	FACETS	0.764	0.699	0.831	0.764	0.699	0.831	SUBCLONAL	1	TRUE	0	0.638196573236816	1		806	338	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281940	39281940	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	75	377	0	ENST00000402219.2:c.535G>C	p.Asp179His	p.D179H	ENST00000402219	NM_005633.3	179	Gat/Cat	5/23	1	2	FACETS	0.955	0.849	1	0.955	0.849	1	CLONAL	1	TRUE	1	0.638196573236816	2		377	246	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561789	55561793	+	frameshift_variant	Frame_Shift_Del	DEL	ATCCG	ATCCG	TTA	novel	NA	P-0024793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	88	441	1	ENST00000288135.5:c.179_183delinsTTA	p.Asp60ValfsTer9	p.D60Vfs*9	ENST00000288135	NM_000222.2	60	gATCCG/gTTA	2/21	1	2	FACETS	0.77	0.688	0.857	0.77	0.688	0.857	SUBCLONAL	1	TRUE	1	0.638196573236816	2		442	358	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	180	404	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.917	0.852	0.983	0.917	0.852	0.983	CLONAL	1	TRUE	1	0.763685227223414	2		405	514	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	79	339	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.494	0.436	0.555	0.494	0.436	0.555	SUBCLONAL	1	TRUE	1	0.763685227223414	2		339	419	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	106	454	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.581	0.523	0.641	0.581	0.523	0.641	SUBCLONAL	1	TRUE	1	0.763685227223414	2		454	478	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	75	319	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.474	0.417	0.535	0.474	0.417	0.535	SUBCLONAL	1	TRUE	1	0.763685227223414	2		320	414	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785964	135785964	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs118203506	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	80	369	1	ENST00000298552.3:c.1257del	p.Arg420GlyfsTer20	p.R420Gfs*20	ENST00000298552	NM_001162426.1	419	ccC/cc	12/23	1	2	FACETS	0.46	0.407	0.518	0.46	0.407	0.518	SUBCLONAL	1	TRUE	1	0.763685227223414	2		370	455	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591115	67591116	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1561299903	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	71	282	0	ENST00000274335.5:c.1710dup	p.Ile571TyrfsTer31	p.I571Yfs*31	ENST00000274335		570	ctt/cTtt	12/15	1	2	FACETS	0.525	0.461	0.593	0.525	0.461	0.593	SUBCLONAL	1	TRUE	1	0.763685227223414	2		282	354	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692791	89692791	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	149	316	0	ENST00000371953.3:c.275A>T	p.Asp92Val	p.D92V	ENST00000371953	NM_000314.4	92	gAc/gTc	5/9	0.39935583925156	2	FACETS	1	0.973	1	0.553	0.512	0.594	INDETERMINATE	1	TRUE	0	0.763685227223414	2		316	353	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156070	119156070	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	37	447	0	ENST00000264033.4:c.1739del	p.Pro580LeufsTer35	p.P580Lfs*35	ENST00000264033	NM_005188.3	579	Ccc/cc	11/16	1	2	FACETS	0.166	0.136	0.199	0.166	0.136	0.199	SUBCLONAL	1	TRUE	1	0.763685227223414	2		447	585	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19261495	19261495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775651286	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	111	449	1	ENST00000162023.5:c.50G>A	p.Arg17Gln	p.R17Q	ENST00000162023		17	cGg/cAg	6/13	1	2	FACETS	0.512	0.461	0.565	0.512	0.461	0.565	SUBCLONAL	1	TRUE	1	0.763685227223414	2		450	568	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217557	142217557	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1268253442	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	88	501	3	ENST00000350721.4:c.5440del	p.Arg1814GlufsTer10	p.R1814Efs*10	ENST00000350721	NM_001184.3	1814	Aga/ga	32/47	0.459074571680539	1	FACETS	0.325	0.289	0.363	0.325	0.289	0.363	SUBCLONAL	1	TRUE	0	0.763685227223414	1		504	438	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919915	50919915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	101	368	0	ENST00000440232.2:c.3002G>A	p.Gly1001Asp	p.G1001D	ENST00000440232	NM_002691.3	1001	gGc/gAc	24/27	1	2	FACETS	0.501	0.449	0.556	0.501	0.449	0.556	SUBCLONAL	1	TRUE	1	0.763685227223414	2		368	528	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259480	16259480	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	78	422	0	ENST00000375759.3:c.6750del	p.Ala2251GlnfsTer102	p.A2251Qfs*102	ENST00000375759	NM_015001.2	2249	Ccc/cc	11/15	1	2	FACETS	0.484	0.427	0.545	0.484	0.427	0.545	SUBCLONAL	1	TRUE	1	0.763685227223414	2		422	422	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435289	121435289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371544082	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	91	362	0	ENST00000257555.6:c.1322C>T	p.Thr441Met	p.T441M	ENST00000257555		441	aCg/aTg	7/10	1	2	FACETS	0.542	0.483	0.603	0.542	0.483	0.603	SUBCLONAL	1	TRUE	1	0.763685227223414	2		362	440	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	26	261	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	0.195	0.154	0.241	0.195	0.154	0.241	SUBCLONAL	1	TRUE	1	0.763685227223414	2		261	350	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096313	2096313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774831009	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	107	481	0	ENST00000219066.1:c.194G>A	p.Arg65His	p.R65H	ENST00000219066	NM_002528.5	65	cGt/cAt	2/6	1	2	FACETS	0.42	0.377	0.466	0.42	0.377	0.466	SUBCLONAL	1	TRUE	1	0.763685227223414	2		481	667	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491381	2491381	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs551576039	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	38	440	2	ENST00000355716.4:c.424G>A	p.Ala142Thr	p.A142T	ENST00000355716	NM_003820.2	142	Gcc/Acc	4/8	1	2	FACETS	0.171	0.14	0.205	0.171	0.14	0.205	SUBCLONAL	1	TRUE	1	0.763685227223414	2		442	583	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268950	115268950	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs750855257	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	52	440	3	ENST00000438362.2:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000438362	NM_001242891.1	554	Cga/Tga	14/20	1	2	FACETS	0.28	0.238	0.325	0.28	0.238	0.325	SUBCLONAL	1	TRUE	1	0.763685227223414	2		443	487	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119452	193119452	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	82	347	0	ENST00000367435.3:c.847A>C	p.Lys283Gln	p.K283Q	ENST00000367435	NM_024529.4	283	Aaa/Caa	9/17	0.719027760163998	3	FACETS	0.484	0.427	0.545	0.242	0.213	0.273	SUBCLONAL	1	TRUE	1	0.763685227223414	3		347	613	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392125	118392125	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	63	304	0	ENST00000534358.1:c.11636A>G	p.Asp3879Gly	p.D3879G	ENST00000534358	NM_005933.3	3879	gAc/gGc	35/36	1	2	FACETS	0.441	0.383	0.503	0.441	0.383	0.503	SUBCLONAL	1	TRUE	1	0.763685227223414	2		304	374	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426832	49426832	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	88	331	0	ENST00000301067.7:c.11656C>T	p.Gln3886Ter	p.Q3886*	ENST00000301067	NM_003482.3	3886	Cag/Tag	39/54	1	2	FACETS	0.572	0.51	0.637	0.572	0.51	0.637	SUBCLONAL	1	TRUE	1	0.763685227223414	2		331	403	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337737	73337737	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	24	215	0	ENST00000377767.4:c.1979A>C	p.Asn660Thr	p.N660T	ENST00000377767	NM_014953.3	660	aAt/aCt	16/21	1	2	FACETS	0.248	0.195	0.31	0.248	0.195	0.31	SUBCLONAL	1	TRUE	1	0.763685227223414	2		215	253	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129130	2129130	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	141	486	0	ENST00000219476.3:c.3064C>T	p.Leu1022Phe	p.L1022F	ENST00000219476	NM_000548.3	1022	Ctc/Ttc	27/42	1	2	FACETS	0.545	0.498	0.595	0.545	0.498	0.595	SUBCLONAL	1	TRUE	1	0.763685227223414	2		486	677	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81922819	81922819	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	87	425	0	ENST00000359376.3:c.808A>C	p.Thr270Pro	p.T270P	ENST00000359376	NM_002661.3	270	Aca/Cca	10/33	1	2	FACETS	0.456	0.405	0.51	0.456	0.405	0.51	SUBCLONAL	1	TRUE	1	0.763685227223414	2		425	500	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838120	89838120	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	34	437	0	ENST00000389301.3:c.2117T>C	p.Ile706Thr	p.I706T	ENST00000389301	NM_000135.2	706	aTc/aCc	23/43	1	2	FACETS	0.159	0.13	0.193	0.159	0.13	0.193	SUBCLONAL	1	TRUE	1	0.763685227223414	2		437	559	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983748	15983748	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	37	427	0	ENST00000268712.3:c.3374G>T	p.Arg1125Met	p.R1125M	ENST00000268712	NM_006311.3	1125	aGg/aTg	25/46	1	2	FACETS	0.18	0.148	0.216	0.18	0.148	0.216	SUBCLONAL	1	TRUE	1	0.763685227223414	2		427	539	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211700	36211700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	91	332	0	ENST00000222270.7:c.1451C>T	p.Ala484Val	p.A484V	ENST00000222270	NM_014727.1	484	gCt/gTt	3/37	1	2	FACETS	0.61	0.545	0.678	0.61	0.545	0.678	SUBCLONAL	1	TRUE	1	0.763685227223414	2		332	391	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026774	48026774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587779917	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	72	389	0	ENST00000234420.5:c.1652G>A	p.Gly551Asp	p.G551D	ENST00000234420	NM_000179.2	551	gGc/gAc	4/10	1	2	FACETS	0.495	0.435	0.559	0.495	0.435	0.559	SUBCLONAL	1	TRUE	1	0.763685227223414	2		389	381	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61720123	61720123	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	39	502	0	ENST00000401558.2:c.1311A>C	p.Gln437His	p.Q437H	ENST00000401558	NM_003400.3	437	caA/caC	13/25	1	2	FACETS	0.181	0.149	0.216	0.181	0.149	0.216	SUBCLONAL	1	TRUE	1	0.763685227223414	2		502	564	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527458	41527458	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	92	467	0	ENST00000263253.7:c.1353del	p.Asn452ThrfsTer2	p.N452Tfs*2	ENST00000263253	NM_001429.3	450	gCc/gc	6/31	1	2	FACETS	0.385	0.343	0.431	0.385	0.343	0.431	SUBCLONAL	1	TRUE	1	0.763685227223414	2		467	625	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55603380	55603380	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	74	369	1	ENST00000288135.5:c.2740del	p.Arg914AspfsTer10	p.R914Dfs*10	ENST00000288135	NM_000222.2	912	ctA/ct	20/21	1	2	FACETS	0.54	0.476	0.608	0.54	0.476	0.608	SUBCLONAL	1	TRUE	1	0.763685227223414	2		370	359	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332757	153332757	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	26	444	0	ENST00000281708.4:c.199G>T	p.Gly67Ter	p.G67*	ENST00000281708	NM_033632.3	67	Gga/Tga	2/12	1	2	FACETS	0.153	0.121	0.191	0.153	0.121	0.191	SUBCLONAL	1	TRUE	1	0.763685227223414	2		444	444	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592007	67592007	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	28	212	0	ENST00000274335.5:c.1823C>G	p.Ser608Ter	p.S608*	ENST00000274335		608	tCa/tGa	14/15	1	2	FACETS	0.374	0.301	0.456	0.374	0.301	0.456	SUBCLONAL	1	TRUE	1	0.763685227223414	2		212	196	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089864	5089864	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	42	195	0	ENST00000381652.3:c.2761+1G>T		p.X921_splice	ENST00000381652	NM_004972.3	921			1	2	FACETS	0.588	0.497	0.686	0.588	0.497	0.686	SUBCLONAL	1	TRUE	1	0.763685227223414	2		195	187	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389319	8389319	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	117	538	0	ENST00000356435.5:c.4299del	p.Glu1434LysfsTer9	p.E1434Kfs*9	ENST00000356435		1433	ccC/cc	26/35	1	2	FACETS	0.562	0.509	0.618	0.562	0.509	0.618	SUBCLONAL	1	TRUE	1	0.763685227223414	2		538	545	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779157	135779801	+	splice_acceptor_variant,splice_donor_variant,frameshift_variant,stop_lost,intron_variant	Splice_Site	DEL	AAAGCAACTGGTCTCGGAGGGTGCGGATCTCATCTGAAGGAGGAGAGCCTGATTGTAAAGCAGAGGGAGGGTGGCAGAAATGCCTTTTACAGATGGTTCAATCAAGCCCCCTTCCCATGTGTTGTTAGCTTAACAAACACAATTCTTTAAAAACAAATCACCACTCTCTTTGCAAATGACCACTTGACTCCCAGCAACAGCAGGGGGGAAAGTATGGACTATGTGTCTCCCCCGTGAAGGAATGCAAAAGGTCATATCATGTGGGATGACTCTTTGAGAGCCTGCTTTCCTTTCCCCACAAATCTAGATCACGCATTTCAGATGCCCTGTTTCTCAAGACACTTCCTTCGCTGTGTGTTCTCCCCCAGGAAGATGCTTCACTCTGGTCTTCTCCAGGGAAGCCTGGCAGGAAGTCTGTATTTTGCACTTATACTCTCAAGCGCATAGTACTTGCCACTTTTCAAAAATAAGAAATGCTGACTTGGCAACACTTGAGATCCTTTAGCCAAGCAGATAGCCTGGCCGGAGCAATAGCCAAGGGGAGATCTGTTTCCCAGAGGGCACCTCCTTCAAGGACAGAAAGGGCAACAAGCAAGCAGGAACCATGTGGGCTGGATTTGGAGCTAAAGTAACAACTTTACCTCC	AAAGCAACTGGTCTCGGAGGGTGCGGATCTCATCTGAAGGAGGAGAGCCTGATTGTAAAGCAGAGGGAGGGTGGCAGAAATGCCTTTTACAGATGGTTCAATCAAGCCCCCTTCCCATGTGTTGTTAGCTTAACAAACACAATTCTTTAAAAACAAATCACCACTCTCTTTGCAAATGACCACTTGACTCCCAGCAACAGCAGGGGGGAAAGTATGGACTATGTGTCTCCCCCGTGAAGGAATGCAAAAGGTCATATCATGTGGGATGACTCTTTGAGAGCCTGCTTTCCTTTCCCCACAAATCTAGATCACGCATTTCAGATGCCCTGTTTCTCAAGACACTTCCTTCGCTGTGTGTTCTCCCCCAGGAAGATGCTTCACTCTGGTCTTCTCCAGGGAAGCCTGGCAGGAAGTCTGTATTTTGCACTTATACTCTCAAGCGCATAGTACTTGCCACTTTTCAAAAATAAGAAATGCTGACTTGGCAACACTTGAGATCCTTTAGCCAAGCAGATAGCCTGGCCGGAGCAATAGCCAAGGGGAGATCTGTTTCCCAGAGGGCACCTCCTTCAAGGACAGAAAGGGCAACAAGCAAGCAGGAACCATGTGGGCTGGATTTGGAGCTAAAGTAACAACTTTACCTCC	-	novel	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	82	404	0	ENST00000298552.3:c.2038_2089del		p.X680_splice	ENST00000298552	NM_001162426.1	680	GGAGGTAAAGTTGTTACTTTAGCTCCAAATCCAGCCCACATGGTTCCTGCTTGCTTGTTGCCCTTTCTGTCCTTGAAGGAGGTGCCCTCTGGGAAACAGATCTCCCCTTGGCTATTGCTCCGGCCAGGCTATCTGCTTGGCTAAAGGATCTCAAGTGTTGCCAAGTCAGCATTTCTTATTTTTGAAAAGTGGCAAGTACTATGCGCTTGAGAGTATAAGTGCAAAATACAGACTTCCTGCCAGGCTTCCCTGGAGAAGACCAGAGTGAAGCATCTTCCTGGGGGAGAACACACAGCGAAGGAAGTGTCTTGAGAAACAGGGCATCTGAAATGCGTGATCTAGATTTGTGGGGAAAGGAAAGCAGGCTCTCAAAGAGTCATCCCACATGATATGACCTTTTGCATTCCTTCACGGGGGAGACACATAGTCCATACTTTCCCCCCTGCTGTTGCTGGGAGTCAAGTGGTCATTTGCAAAGAGAGTGGTGATTTGTTTTTAAAGAATTGTGTTTGTTAAGCTAACAACACATGGGAAGGGGGCTTGATTGAACCATCTGTAAAAGGCATTTCTGCCACCCTCCCTCTGCTTTACAATCAGGCTCTCCTCCTTCAGATGAGATCCGCACCCTCCGAGACCAGTTGCTTTta/ta	16-17/23	1	2	FACETS	0.478	0.423	0.537	0.478	0.423	0.537	SUBCLONAL	1	TRUE	1	0.763685227223414	2		404	449	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652207	48652207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	82	367	0	ENST00000376670.3:c.878G>A	p.Arg293Gln	p.R293Q	ENST00000376670	NM_002049.3	293	cGg/cAg	6/6	1	2	FACETS	0.508	0.45	0.569	0.508	0.45	0.569	SUBCLONAL	1	TRUE	1	0.763685227223414	2		367	423	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0026050-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	190	480	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.199966687673593	21	FACETS	1	0.962	1			1	CLONAL	22	TRUE	NA	0.199966687673593	21		480	249	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579585	7579585	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026050-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	10	550	0	ENST00000269305.4:c.102del	p.Leu35CysfsTer9	p.L35Cfs*9	ENST00000269305	NM_001126112.2	34	ccC/cc	4/11	1	2	FACETS	0.769	0.531	1	1	0.854	1	CLONAL	2	TRUE	1	0.199966687673593	2		550	65	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265138	5265138	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026050-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	14	610	0	ENST00000357368.4:c.449G>T	p.Arg150Leu	p.R150L	ENST00000357368	NM_002850.3	150	cGg/cTg	5/38	0.199966687673593	1	FACETS	0.778	0.572	1	1	0.893	1	CLONAL	2	TRUE	0	0.199966687673593	1		610	81	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0026288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	251	505	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.512732572968201	2	FACETS	0.828	0.782	0.875	0.828	0.782	0.875	CLONAL	2	TRUE	0	0.536486161145885	2		505	565	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820570	3820570	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0026288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	314	530	1	ENST00000262367.5:c.2880+1G>T		p.X960_splice	ENST00000262367	NM_004380.2	960			0.346856967797021	2	FACETS	0.851	0.809	0.893	0.851	0.809	0.893	CLONAL	2	TRUE	0	0.536486161145885	2		531	688	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120798	94120798	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	49	394	1	ENST00000369303.4:c.253C>A	p.Leu85Met	p.L85M	ENST00000369303	NM_004440.3	85	Ctg/Atg	3/17	0.246393701827121	2	FACETS	0.408	0.346	0.476	0.204	0.173	0.238	INDETERMINATE	1	TRUE	0	0.536486161145885	2		395	448	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099359	157099359	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1188660877	NA	P-0026288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	30	242	0	ENST00000346085.5:c.296A>T	p.His99Leu	p.H99L	ENST00000346085	NM_020732.3	99	cAc/cTc	1/20	0.329329329755546	2	FACETS	0.387	0.312	0.471	0.193	0.156	0.236	SUBCLONAL	1	TRUE	0	0.536486161145885	2		242	289	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928070	178928085	+	protein_altering_variant	In_Frame_Del	DEL	CATGGATTAGAAGATT	CATGGATTAGAAGATT	G	novel	NA	P-0026288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	102	387	0	ENST00000263967.3:c.1348_1363delinsG	p.His450_Leu455delinsVal	p.H450_L455delinsV	ENST00000263967	NM_006218.2	450	CATGGATTAGAAGATTtg/Gtg	8/21	1	2	FACETS	0.711	0.638	0.788	0.711	0.638	0.788	SUBCLONAL	1	TRUE	1	0.536486161145885	2		387	535	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76936810	76937170	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TACTAGCAATGTTCAAAATATCTTCCAATGGCAGCATAAAAATAAATAGGGAAACTTTTTTTAATAAACTCCTAAATAATTTTTAAGTGGTATTCTCCTAAGTAGTAACCCTAAATTTGATTAGCTTCAGAGGAAATTAAACAATGTAGTAACTCAAGAGGGGGAAGTACAAATTATGAATTTTTTATTTATTTTTGCATACCTGAAGATTGGCAAAATCCAGTATGTGAAGACAGCACTAAATTTTCAGTCACAGGCTTAATTTTCTGTTCATCGCTGCTTCCCTCACCTATAGAATTCTGATCATCATCTTCTATATCAGAAGAAGATGAGGATGTAATGTCAGCTTGCTTCCTTTTAG	TACTAGCAATGTTCAAAATATCTTCCAATGGCAGCATAAAAATAAATAGGGAAACTTTTTTTAATAAACTCCTAAATAATTTTTAAGTGGTATTCTCCTAAGTAGTAACCCTAAATTTGATTAGCTTCAGAGGAAATTAAACAATGTAGTAACTCAAGAGGGGGAAGTACAAATTATGAATTTTTTATTTATTTTTGCATACCTGAAGATTGGCAAAATCCAGTATGTGAAGACAGCACTAAATTTTCAGTCACAGGCTTAATTTTCTGTTCATCGCTGCTTCCCTCACCTATAGAATTCTGATCATCATCTTCTATATCAGAAGAAGATGAGGATGTAATGTCAGCTTGCTTCCTTTTAG	-	novel	NA	P-0026288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	32	20	0	ENST00000373344.5:c.3578_3736+202del		p.X1193_splice	ENST00000373344	NM_000489.3	1193		9/35	0.246393701827121	2	FACETS	1	0.952	1	1	0.952	1	INDETERMINATE	2	TRUE	0	0.536486161145885	2		20	48	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0026540-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	267	523	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.437584389872387	3	FACETS	0.931	0.876	0.986	0.931	0.876	0.986	CLONAL	2	TRUE	1	0.437584389872387	3		523	799	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026540-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	119	538	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.529	0.476	0.585	0.529	0.476	0.585	SUBCLONAL	1	TRUE	1	0.437584389872387	2		538	1028	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610171	10610171	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026540-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	210	840	0	ENST00000171111.5:c.539A>T	p.Asp180Val	p.D180V	ENST00000171111	NM_203500.1	180	gAc/gTc	2/6	0.298050580920788	1	FACETS	0.662	0.614	0.712	0.662	0.614	0.712	SUBCLONAL	1	TRUE	0	0.437584389872387	1		840	1133	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174909	56174909	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026540-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	173	440	0	ENST00000399503.3:c.2070del	p.Lys690AsnfsTer35	p.K690Nfs*35	ENST00000399503	NM_005921.1	690	Aaa/aa	11/20	0.355566149168155	4	FACETS	0.775	0.715	0.838	0.517	0.477	0.559	SUBCLONAL	2	TRUE	1	0.437584389872387	4		440	733	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178245	56178246	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026540-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	349	447	0	ENST00000399503.3:c.3221dup	p.Asp1075ArgfsTer6	p.D1075Rfs*6	ENST00000399503	NM_005921.1	1073	cag/caGg	14/20	0.355566149168155	4	FACETS	0.957	0.911	1	0.957	0.911	1	CLONAL	3	TRUE	1	0.437584389872387	4		447	799	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878175	151878175	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026540-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	380	725	0	ENST00000262189.6:c.6770del	p.Arg2257GlnfsTer10	p.R2257Qfs*10	ENST00000262189	NM_170606.2	2257	cGa/ca	36/59	0.437584389872387	3	FACETS	0.944	0.898	0.991			1	CLONAL	2	TRUE	NA	0.437584389872387	3		725	1121	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0026936-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	133	347	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.320193785217845	3	FACETS	0.871	0.8	0.943	1	0.984	1	CLONAL	3	TRUE	1	0.320193785217845	3		347	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0026936-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	238	578	1	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.320193785217845	1	FACETS	0.952	0.894	1	1	0.995	1	CLONAL	2	TRUE	0	0.320193785217845	1		579	656	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0026936-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	135	518	0	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	0.320193785217845	2	FACETS	0.958	0.878	1	0.958	0.878	1	CLONAL	2	TRUE	0	0.320193785217845	2		518	440	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120783979	120783979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112244011	NA	P-0027089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	240	672	1	ENST00000257552.2:c.1006G>A	p.Ala336Thr	p.A336T	ENST00000257552	NM_002442.3	336	Gcc/Acc	13/15	0.728404094680741	3	FACETS	0.993	0.929	1	0.497	0.464	0.53	CLONAL	1	TRUE	1	0.728404094680741	3		673	905	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592280	29592280	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	58	258	0	ENST00000356175.3:c.4697del	p.Leu1566Ter	p.L1566*	ENST00000356175	NM_000267.3	1565	gcT/gc	35/57	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.728404094680741	2		258	144	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652936	29652936	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	111	376	0	ENST00000356175.3:c.4872del	p.Thr1625ProfsTer52	p.T1625Pfs*52	ENST00000356175	NM_000267.3	1624	cTt/ct	36/57	1	2	FACETS	0.968	0.881	1	0.968	0.881	1	CLONAL	1	TRUE	1	0.728404094680741	2		376	315	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0027336-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	38	283	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.913	0.755	1	0.913	0.755	1	CLONAL	1	TRUE	1	0.198775932292305	2		283	419	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027336-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	38	399	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.881	0.729	1	0.881	0.729	1	CLONAL	1	TRUE	1	0.198775932292305	2		399	434	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174873	11174873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027336-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	60	416	0	ENST00000361445.4:c.7161G>A	p.Met2387Ile	p.M2387I	ENST00000361445	NM_004958.3	2387	atG/atA	52/58	1	2	FACETS	0.99	0.852	1	0.99	0.852	1	CLONAL	1	TRUE	1	0.198775932292305	2		416	610	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972418	32972418	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027336-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	66	511	0	ENST00000380152.3:c.9768G>C	p.Glu3256Asp	p.E3256D	ENST00000380152		3256	gaG/gaC	27/27	1	2	FACETS	0.971	0.842	1	0.971	0.842	1	CLONAL	1	TRUE	1	0.198775932292305	2		511	684	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196580	106196580	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1372410810	NA	P-0027336-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	61	374	0	ENST00000380013.4:c.4913C>G	p.Ser1638Ter	p.S1638*	ENST00000380013	NM_001127208.2	1638	tCa/tGa	11/11	1	2	FACETS	0.976	0.841	1	0.976	0.841	1	CLONAL	1	TRUE	1	0.198775932292305	2		374	629	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518143	187518143	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027336-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	60	402	0	ENST00000441802.2:c.12551G>C	p.Gly4184Ala	p.G4184A	ENST00000441802	NM_005245.3	4184	gGa/gCa	25/27	1	2	FACETS	0.999	0.861	1	0.999	0.861	1	CLONAL	1	TRUE	1	0.198775932292305	2		402	604	SUCCESS
BTK	695	MSKCC	GRCh37	X	100609625	100609625	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027336-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	51	170	0	ENST00000308731.7:c.1624C>A	p.Leu542Met	p.L542M	ENST00000308731	NM_000061.2	542	Ctg/Atg	16/19	1	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.198775932292305	1		170	312	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200063	123200064	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027336-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	12	179	0	ENST00000218089.9:c.2137dup	p.Tyr713LeufsTer15	p.Y713Lfs*15	ENST00000218089	NM_001042749.1	712	aat/aaTt	22/35	1	1	FACETS	1	0.739	1	1	0.739	1	CLONAL	1	TRUE	0	0.198775932292305	1		179	104	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645163	86645163	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027336-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	16	222	0	ENST00000274376.6:c.1235G>C	p.Gly412Ala	p.G412A	ENST00000274376	NM_002890.2	412	gGa/gCa	8/25	1	2	FACETS	0.763	0.565	0.998	0.763	0.565	0.998	CLONAL	1	TRUE	1	0.198775932292305	2		222	211	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622168	43622168	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	198	534	1	ENST00000355710.3:c.3185A>T	p.Tyr1062Phe	p.Y1062F	ENST00000355710	NM_020975.4	1062	tAt/tTt	19/20	0.604125882677669	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.595517122690718	1		535	440	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346360	89346383	+	inframe_deletion	In_Frame_Del	DEL	GTGGAGGCCTGGTCAGGAGGCAGT	GTGGAGGCCTGGTCAGGAGGCAGT	-	novel	NA	P-0029069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	220	511	0	ENST00000301030.4:c.6567_6590del	p.Leu2190_Thr2197del	p.L2190_T2197del	ENST00000301030	NM_001256183.1	2189	gcACTGCCTCCTGACCAGGCCTCCACc/gcc	9/13	0.422138889643245	3	FACETS	1	0.986	1	0.401	0.374	0.429	CLONAL	1	TRUE	0	0.595517122690718	3		511	797	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	488	711	0	ENST00000269305.4:c.517G>C	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ctg	5/11	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.595517122690718	2		711	791	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40742178	40742178	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	60	698	0	ENST00000392038.2:c.946T>C	p.Tyr316His	p.Y316H	ENST00000392038	NM_001626.4	316	Tac/Cac	10/14	0.141747035990092	4	FACETS	0.284	0.244	0.329	0.142	0.122	0.165	INDETERMINATE	1	TRUE	2	0.595517122690718	4		698	1131	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0029069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	265	283	1	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.255857439717489	5	FACETS	0.876	0.833	0.919			1	INDETERMINATE	4	TRUE	NA	0.595517122690718	5		284	481	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803537	32803537	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	199	575	0	ENST00000374899.4:c.622G>A	p.Gly208Ser	p.G208S	ENST00000374899	NM_018833.2	208	Ggc/Agc	4/12	0.226481378505078	4	FACETS	0.919	0.85	0.991	0.46	0.425	0.496	INDETERMINATE	1	TRUE	2	0.595517122690718	4		575	1160	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874188	151874188	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0029069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	389	394	0	ENST00000262189.6:c.8350A>T	p.Lys2784Ter	p.K2784*	ENST00000262189	NM_170606.2	2784	Aag/Tag	38/59	0.604125882677669	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.595517122690718	2		394	528	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750924	128750924	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029272-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	421	648	0	ENST00000377970.2:c.461C>T	p.Ser154Leu	p.S154L	ENST00000377970	NM_002467.4	154	tCg/tTg	2/3	0.648694643298399	1	FACETS	0.989	0.947	1	0.989	0.947	1	CLONAL	1	TRUE	0	0.648694643298399	1		648	887	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786705	3786705	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029272-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	472	751	0	ENST00000262367.5:c.4506G>C	p.Trp1502Cys	p.W1502C	ENST00000262367	NM_004380.2	1502	tgG/tgC	27/31	0.648694643298399	1	FACETS	0.979	0.94	1	0.979	0.94	1	CLONAL	1	TRUE	0	0.648694643298399	1		751	1004	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104325	2104327	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs1342475885	NA	P-0029272-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	411	624	0	ENST00000219476.3:c.369_371del	p.Phe124del	p.F124del	ENST00000219476	NM_000548.3	122	cTCTtc/ctc	5/42	0.648694643298399	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.648694643298399	1		624	833	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779826	3779826	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029272-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	517	791	0	ENST00000262367.5:c.5222A>T	p.Lys1741Met	p.K1741M	ENST00000262367	NM_004380.2	1741	aAg/aTg	31/31	0.648694643298399	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.648694643298399	1		791	1042	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575147	64575147	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029272-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	383	531	0	ENST00000312049.6:c.660G>C	p.Trp220Cys	p.W220C	ENST00000312049	NM_130799.2	220	tgG/tgC	4/10	0.648694643298399	1	FACETS	0.983	0.939	1	0.983	0.939	1	CLONAL	1	TRUE	0	0.648694643298399	1		531	812	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514385	103514385	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029272-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	193	264	0	ENST00000355739.4:c.886C>G	p.Gln296Glu	p.Q296E	ENST00000355739	NM_000123.3	296	Caa/Gaa	8/15	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.648694643298399	2		264	582	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046477	30046477	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029272-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	364	595	0	ENST00000331968.5:c.2706G>C	p.Met902Ile	p.M902I	ENST00000331968	NM_002742.2	902	atG/atC	18/18	1	2	FACETS	0.925	0.877	0.974	0.925	0.877	0.974	CLONAL	1	TRUE	1	0.648694643298399	2		595	1213	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713480	40713480	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029272-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	448	703	0	ENST00000373198.4:c.4035G>C	p.Gln1345His	p.Q1345H	ENST00000373198	NM_133170.3	1345	caG/caC	30/32	1	2	FACETS	0.999	0.954	1	0.999	0.954	1	CLONAL	1	TRUE	1	0.648694643298399	2		703	1382	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729885	30729886	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029272-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	229	408	0	ENST00000295754.5:c.1408dup	p.Tyr470LeufsTer2	p.Y470Lfs*2	ENST00000295754	NM_003242.5	469	gat/gaTt	6/7	0.648694643298399	1	FACETS	0.888	0.836	0.941	0.888	0.836	0.941	CLONAL	1	TRUE	0	0.648694643298399	1		408	537	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289211	33289211	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029272-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	384	598	0	ENST00000374542.5:c.341del	p.Ser114PhefsTer30	p.S114Ffs*30	ENST00000374542	NM_001141970.1	114	tCt/tt	3/8	0.648694643298399	1	FACETS	0.953	0.911	0.996	0.953	0.911	0.996	CLONAL	1	TRUE	0	0.648694643298399	1		598	839	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0031102-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	233	614	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.247526140617773	3	FACETS	1	0.978	1	0.724	0.68	0.768	INDETERMINATE	2	TRUE	0	0.452203496867661	3		614	582	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0031102-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	113	444	1	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.397475186936342	3	FACETS	0.856	0.778	0.936	0.856	0.778	0.936	CLONAL	2	TRUE	1	0.452203496867661	3		445	358	SUCCESS
APC	324	MSKCC	GRCh37	5	112175141	112175141	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031102-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	25	183	0	ENST00000257430.4:c.3850G>T	p.Glu1284Ter	p.E1284*	ENST00000257430	NM_000038.5	1284	Gaa/Taa	16/16	0.397475186936342	3	FACETS	0.929	0.741	1	0.464	0.37	0.57	CLONAL	1	TRUE	1	0.452203496867661	3		183	146	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201068	108201068	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031102-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	57	306	0	ENST00000278616.4:c.7435G>T	p.Glu2479Ter	p.E2479*	ENST00000278616	NM_000051.3	2479	Gaa/Taa	50/63	0.376434630857327	5	FACETS	0.804	0.697	0.919	0.536	0.464	0.613	CLONAL	2	TRUE	2	0.452203496867661	5		306	263	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	79	345	3	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.868	0.769	0.973	0.868	0.769	0.973	CLONAL	1	TRUE	1	0.50422772046901	2		348	361	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255310	16255311	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	150	504	0	ENST00000375759.3:c.2580_2581del	p.Lys861SerfsTer2	p.K861Sfs*2	ENST00000375759	NM_015001.2	859	AGa/a	11/15	0.50422772046901	1	FACETS	0.856	0.787	0.927	0.856	0.787	0.927	CLONAL	1	TRUE	0	0.50422772046901	1		504	520	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261673	16261673	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	229	563	0	ENST00000375759.3:c.8938T>C	p.Ser2980Pro	p.S2980P	ENST00000375759	NM_015001.2	2980	Tcc/Ccc	11/15	0.50422772046901	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.50422772046901	1		563	653	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	188	602	0	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	NA	2	FACETS	0.873	0.808	0.941			1	INDETERMINATE	1	TRUE	NA	0.50422772046901	2		602	854	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1485978447	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	179	571	2	ENST00000324856.7:c.5164C>T	p.Arg1722Ter	p.R1722*	ENST00000324856	NM_006015.4	1722	Cga/Tga	20/20	NA	2	FACETS	0.881	0.813	0.951			1	INDETERMINATE	1	TRUE	NA	0.50422772046901	2		573	806	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803533	43803533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	265	669	0	ENST00000372470.3:c.14C>T	p.Ala5Val	p.A5V	ENST00000372470	NM_005373.2	5	gCc/gTc	1/12	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.50422772046901	2		669	922	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748150	72748150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	134	360	0	ENST00000357731.5:c.28G>A	p.Ala10Thr	p.A10T	ENST00000357731	NM_173808.2	10	Gct/Act	1/7	1	2	FACETS	0.993	0.907	1	0.993	0.907	1	CLONAL	1	TRUE	1	0.50422772046901	2		360	535	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458694	120458695	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	185	550	0	ENST00000256646.2:c.6650_6651del	p.Val2217AlafsTer26	p.V2217Afs*26	ENST00000256646	NM_024408.3	2217	gTG/g	34/34	1	2	FACETS	0.908	0.84	0.979	0.908	0.84	0.979	CLONAL	1	TRUE	1	0.50422772046901	2		550	808	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426908	70426908	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	199	494	0	ENST00000373644.4:c.4568A>G	p.Asp1523Gly	p.D1523G	ENST00000373644	NM_030625.2	1523	gAt/gGt	7/12	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.50422772046901	2		494	759	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692889	89692889	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	165	446	1	ENST00000371953.3:c.375del	p.Ala126LeufsTer8	p.A126Lfs*8	ENST00000371953	NM_000314.4	125	Aaa/aa	5/9	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.50422772046901	2		447	643	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692901	89692901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786204929	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	203	542	0	ENST00000371953.3:c.385G>A	p.Gly129Arg	p.G129R	ENST00000371953	NM_000314.4	129	Gga/Aga	5/9	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.50422772046901	2		542	794	SUCCESS
ATM	472	MSKCC	GRCh37	11	108137926	108137926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199875915	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	134	401	0	ENST00000278616.4:c.2495G>A	p.Arg832His	p.R832H	ENST00000278616	NM_000051.3	832	cGt/cAt	17/63	1	2	FACETS	0.954	0.871	1	0.954	0.871	1	CLONAL	1	TRUE	1	0.50422772046901	2		401	557	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151775	108151776	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	173	480	0	ENST00000278616.4:c.3457_3458del	p.Val1153PhefsTer12	p.V1153Ffs*12	ENST00000278616	NM_000051.3	1152	tcTGtt/tctt	24/63	1	2	FACETS	0.986	0.91	1	0.986	0.91	1	CLONAL	1	TRUE	1	0.50422772046901	2		480	696	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118370597	118370597	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	165	429	0	ENST00000534358.1:c.6127T>C	p.Cys2043Arg	p.C2043R	ENST00000534358	NM_005933.3	2043	Tgt/Cgt	24/36	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.50422772046901	2		429	618	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373789	118373790	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	106	382	0	ENST00000534358.1:c.7185_7186del	p.Pro2396ArgfsTer2	p.P2396Rfs*2	ENST00000534358	NM_005933.3	2394	tcCTct/tcct	27/36	1	2	FACETS	0.756	0.68	0.836	0.756	0.68	0.836	SUBCLONAL	1	TRUE	1	0.50422772046901	2		382	556	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871758	12871758	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	57	122	0	ENST00000228872.4:c.476-1G>T		p.X159_splice	ENST00000228872	NM_004064.3	159			0.473079918125157	1	FACETS	0.989	0.865	1	0.989	0.865	1	CLONAL	1	TRUE	0	0.50422772046901	1		122	171	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220519	133220520	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs1323151304	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	249	687	0	ENST00000320574.5:c.4193_4194del	p.Tyr1398Ter	p.Y1398*	ENST00000320574	NM_006231.2	1398	tAT/t	33/49	0.50422772046901	3	FACETS	0.978	0.914	1	0.326	0.304	0.349	CLONAL	1	TRUE	0	0.50422772046901	3		687	1264	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562303	21562303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	290	843	0	ENST00000382592.4:c.1616G>A	p.Gly539Asp	p.G539D	ENST00000382592	NM_014572.2	539	gGc/gAc	4/8	NA	2	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.50422772046901	2		843	1086	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934251	48934251	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	176	558	0	ENST00000267163.4:c.706A>T	p.Lys236Ter	p.K236*	ENST00000267163	NM_000321.2	236	Aaa/Taa	7/27	0.50422772046901	1	FACETS	0.932	0.864	1	0.932	0.864	1	CLONAL	1	TRUE	0	0.50422772046901	1		558	560	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436437	110436437	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	267	836	1	ENST00000375856.3:c.1964C>A	p.Pro655His	p.P655H	ENST00000375856	NM_003749.2	655	cCc/cAc	1/2	0.50422772046901	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.50422772046901	1		837	754	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988520	41988520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	179	568	0	ENST00000219905.7:c.1312G>A	p.Ala438Thr	p.A438T	ENST00000219905	NM_001164273.1	438	Gct/Act	3/24	1	2	FACETS	0.792	0.731	0.856	0.792	0.731	0.856	SUBCLONAL	1	TRUE	1	0.50422772046901	2		568	896	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713351	43713354	+	frameshift_variant	Frame_Shift_Del	DEL	CTGA	CTGA	-	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	332	1037	0	ENST00000382044.4:c.4119_4122del	p.Ser1373ArgfsTer54	p.S1373Rfs*54	ENST00000382044	NM_001141980.1	1373	agTCAG/ag	20/28	1	2	FACETS	0.972	0.917	1	0.972	0.917	1	CLONAL	1	TRUE	1	0.50422772046901	2		1037	1355	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251196	99251196	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	198	670	0	ENST00000268035.6:c.500A>G	p.Asn167Ser	p.N167S	ENST00000268035	NM_000875.3	167	aAc/aGc	2/21	1	2	FACETS	0.914	0.848	0.983	0.914	0.848	0.983	CLONAL	1	TRUE	1	0.50422772046901	2		670	859	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830049	72830050	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	260	791	0	ENST00000268489.5:c.6531_6532del	p.Glu2177AspfsTer27	p.E2177Dfs*27	ENST00000268489	NM_006885.3	2177	gaGAtg/gatg	9/10	1	2	FACETS	0.936	0.876	0.997	0.936	0.876	0.997	CLONAL	1	TRUE	1	0.50422772046901	2		791	1102	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830767	72830768	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	265	681	1	ENST00000268489.5:c.5813_5814del	p.Ser1938Ter	p.S1938*	ENST00000268489	NM_006885.3	1938	tCA/t	9/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.50422772046901	2		682	999	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993641	72993641	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	238	650	0	ENST00000268489.5:c.404A>T	p.Tyr135Phe	p.Y135F	ENST00000268489	NM_006885.3	135	tAc/tTc	2/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.50422772046901	2		650	866	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	204	508	2	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	1	2	FACETS	0.881	0.818	0.947	0.881	0.818	0.947	CLONAL	1	TRUE	1	0.50422772046901	2		510	918	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119796	17119796	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148257120	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	202	679	1	ENST00000285071.4:c.1198G>A	p.Val400Ile	p.V400I	ENST00000285071	NM_144997.5	400	Gtc/Atc	11/14	1	2	FACETS	0.865	0.803	0.93	0.865	0.803	0.93	CLONAL	1	TRUE	1	0.50422772046901	2		680	926	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322602	30322602	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	140	449	0	ENST00000322652.5:c.1615A>G	p.Ser539Gly	p.S539G	ENST00000322652	NM_015355.2	539	Agc/Ggc	14/16	1	2	FACETS	0.823	0.751	0.898	0.823	0.751	0.898	CLONAL	1	TRUE	1	0.50422772046901	2		449	675	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40461451	40461451	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	332	717	0	ENST00000345506.4:c.2175del	p.Ser726ProfsTer90	p.S726Pfs*90	ENST00000345506	NM_003152.3	724	gCc/gc	19/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.50422772046901	2		717	1227	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436067	56436067	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	220	506	0	ENST00000407977.2:c.1070A>G	p.Tyr357Cys	p.Y357C	ENST00000407977		357	tAc/tGc	9/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.50422772046901	2		506	830	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56787338	56787338	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	179	492	0	ENST00000337432.4:c.824A>G	p.Asn275Ser	p.N275S	ENST00000337432	NM_058216.2	275	aAt/aGt	5/9	1	2	FACETS	0.885	0.817	0.956	0.885	0.817	0.956	CLONAL	1	TRUE	1	0.50422772046901	2		492	802	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533673	63533673	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881396	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	219	599	0	ENST00000307078.5:c.1481C>T	p.Pro494Leu	p.P494L	ENST00000307078	NM_004655.3	494	cCg/cTg	6/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.50422772046901	2		599	857	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796954	78796954	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	210	706	0	ENST00000306801.3:c.1067T>A	p.Ile356Asn	p.I356N	ENST00000306801	NM_020761.2	356	aTt/aAt	9/34	1	2	FACETS	0.827	0.768	0.889	0.827	0.768	0.889	CLONAL	1	TRUE	1	0.50422772046901	2		706	1007	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226453	1226453	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	294	787	0	ENST00000326873.7:c.1109G>T	p.Gly370Val	p.G370V	ENST00000326873	NM_000455.4	370	gGa/gTa	9/10	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.50422772046901	2		787	1157	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2185898	2185898	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	264	646	0	ENST00000398665.3:c.170A>T	p.Asn57Ile	p.N57I	ENST00000398665	NM_032482.2	57	aAt/aTt	3/28	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.50422772046901	2		646	1047	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222973	5222973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1014796224	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	241	656	2	ENST00000357368.4:c.2830G>A	p.Gly944Arg	p.G944R	ENST00000357368	NM_002850.3	944	Ggg/Agg	18/38	1	2	FACETS	0.974	0.911	1	0.974	0.911	1	CLONAL	1	TRUE	1	0.50422772046901	2		658	981	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223279	5223279	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	263	701	2	ENST00000357368.4:c.2524C>T	p.Gln842Ter	p.Q842*	ENST00000357368	NM_002850.3	842	Cag/Tag	18/38	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.50422772046901	2		703	996	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796508	42796508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770714432	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	346	958	0	ENST00000575354.2:c.3065C>T	p.Ala1022Val	p.A1022V	ENST00000575354	NM_015125.3	1022	gCg/gTg	13/20	1	2	FACETS	0.994	0.94	1	0.994	0.94	1	CLONAL	1	TRUE	1	0.50422772046901	2		958	1380	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797333	42797333	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	278	854	0	ENST00000575354.2:c.3695C>A	p.Pro1232His	p.P1232H	ENST00000575354	NM_015125.3	1232	cCt/cAt	15/20	1	2	FACETS	0.924	0.867	0.982	0.924	0.867	0.982	CLONAL	1	TRUE	1	0.50422772046901	2		854	1194	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919678	50919678	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	296	920	0	ENST00000440232.2:c.2846G>T	p.Ser949Ile	p.S949I	ENST00000440232	NM_002691.3	949	aGc/aTc	23/27	1	2	FACETS	0.897	0.843	0.952	0.897	0.843	0.952	CLONAL	1	TRUE	1	0.50422772046901	2		920	1309	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46588066	46588066	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	253	733	0	ENST00000263734.3:c.616C>A	p.Pro206Thr	p.P206T	ENST00000263734	NM_001430.4	206	Cct/Act	6/16	0.50422772046901	1	FACETS	0.946	0.889	1	0.946	0.889	1	CLONAL	1	TRUE	0	0.50422772046901	1		733	793	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96930957	96930957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	266	638	0	ENST00000258439.3:c.163C>T	p.His55Tyr	p.H55Y	ENST00000258439	NM_001193304.2	55	Cac/Tac	2/4	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.50422772046901	2		638	954	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39704905	39704906	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	57	186	0	ENST00000361337.2:c.253_254del	p.Asp85GlnfsTer27	p.D85Qfs*27	ENST00000361337	NM_003286.2	84	AGa/a	4/21	1	2	FACETS	0.772	0.667	0.884	0.772	0.667	0.884	SUBCLONAL	1	TRUE	1	0.50422772046901	2		186	293	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702569	52702569	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	204	585	0	ENST00000394830.3:c.329A>T	p.Asn110Ile	p.N110I	ENST00000394830	NM_018313.4	110	aAt/aTt	4/30	0.489666339285237	1	FACETS	0.796	0.74	0.854	0.796	0.74	0.854	SUBCLONAL	1	TRUE	0	0.50422772046901	1		585	760	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431092	181431093	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	192	490	0	ENST00000325404.1:c.948_949del	p.Met317ValfsTer120	p.M317Vfs*120	ENST00000325404	NM_003106.3	315	tCA/t	1/1	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.50422772046901	2		490	702	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190885	185190885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746928773	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	292	770	0	ENST00000265026.3:c.1766G>A	p.Arg589His	p.R589H	ENST00000265026	NM_004721.4	589	cGc/cAc	11/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.50422772046901	2		770	1062	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589841	55589841	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	174	582	0	ENST00000288135.5:c.1327del	p.Cys443ValfsTer20	p.C443Vfs*20	ENST00000288135	NM_000222.2	441	taT/ta	8/21	1	2	FACETS	0.896	0.827	0.968	0.896	0.827	0.968	CLONAL	1	TRUE	1	0.50422772046901	2		582	770	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155784	106155785	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	158	469	0	ENST00000380013.4:c.687_688del	p.Leu230ValfsTer23	p.L230Vfs*23	ENST00000380013	NM_001127208.2	229	ACa/a	3/11	1	2	FACETS	0.875	0.804	0.95	0.875	0.804	0.95	CLONAL	1	TRUE	1	0.50422772046901	2		469	716	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410922	31410922	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1396439517	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	256	820	2	ENST00000344624.3:c.3598G>A	p.Ala1200Thr	p.A1200T	ENST00000344624		1200	Gcc/Acc	28/33	1	2	FACETS	0.881	0.824	0.939	0.881	0.824	0.939	CLONAL	1	TRUE	1	0.50422772046901	2		822	1153	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176618895	176618896	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	197	498	0	ENST00000439151.2:c.939_940del	p.Lys315ValfsTer7	p.K315Vfs*7	ENST00000439151	NM_022455.4	313	aAG/a	3/23	1	2	FACETS	0.91	0.843	0.978	0.91	0.843	0.978	CLONAL	1	TRUE	1	0.50422772046901	2		498	859	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522353	157522353	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs570186838	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	270	742	0	ENST00000346085.5:c.4625C>T	p.Thr1542Met	p.T1542M	ENST00000346085	NM_020732.3	1542	aCg/aTg	18/20	1	2	FACETS	0.998	0.937	1	0.998	0.937	1	CLONAL	1	TRUE	1	0.50422772046901	2		742	1073	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859484	151859485	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	227	649	0	ENST00000262189.6:c.11177_11178del	p.Glu3726ValfsTer9	p.E3726Vfs*9	ENST00000262189	NM_170606.2	3726	gAG/g	43/59	0.488393261997753	3	FACETS	0.977	0.909	1	0.488	0.454	0.524	CLONAL	1	TRUE	1	0.50422772046901	3		649	1154	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146223	38146224	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	247	764	0	ENST00000317025.8:c.3282_3283del	p.Glu1094AspfsTer5	p.E1094Dfs*5	ENST00000317025	NM_023034.1	1094	gaGAtt/gatt	19/24	NA	2	FACETS	0.848	0.792	0.905			1	INDETERMINATE	1	TRUE	NA	0.50422772046901	2		764	1156	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117875375	117875375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057522888	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	121	469	0	ENST00000297338.2:c.268C>T	p.Arg90Trp	p.R90W	ENST00000297338	NM_006265.2	90	Cgg/Tgg	3/14	1	2	FACETS	0.835	0.757	0.916	0.835	0.757	0.916	CLONAL	1	TRUE	1	0.50422772046901	2		469	575	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8525018	8525018	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1329822805	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	127	418	1	ENST00000356435.5:c.586C>T	p.Gln196Ter	p.Q196*	ENST00000356435		196	Cag/Tag	7/35	1	2	FACETS	0.893	0.812	0.978	0.893	0.812	0.978	CLONAL	1	TRUE	1	0.50422772046901	2		419	564	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80646066	80646066	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	73	185	0	ENST00000286548.4:c.86T>A	p.Leu29His	p.L29H	ENST00000286548	NM_002072.3	29	cTc/cAc	1/7	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.50422772046901	2		185	279	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300040	137300040	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	248	797	1	ENST00000481739.1:c.331del	p.Leu111TrpfsTer57	p.L111Wfs*57	ENST00000481739	NM_002957.4	109	Ccc/cc	3/10	1	2	FACETS	0.84	0.785	0.897	0.84	0.785	0.897	CLONAL	1	TRUE	1	0.50422772046901	2		798	1171	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15840943	15840943	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	146	185	0	ENST00000307771.7:c.1027A>T	p.Asn343Tyr	p.N343Y	ENST00000307771	NM_005089.3	343	Aat/Tat	11/11	1	1	FACETS	0.808	0.754	0.861	1	0.991	1	CLONAL	2	TRUE	0	0.50422772046901	1		185	268	SUCCESS
AR	367	MSKCC	GRCh37	X	66943552	66943552	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137852578	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	166	253	0	ENST00000374690.3:c.2632A>G	p.Thr878Ala	p.T878A	ENST00000374690	NM_000044.3	878	Act/Gct	8/8	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.50422772046901	1		253	339	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6027112	6027112	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	16	14	0	ENST00000265849.7:c.1284C>A	p.His428Gln	p.H428Q	ENST00000265849	NM_000535.5	428	caC/caA	11/15	0.488393261997753	3	FACETS	1	0.88	1	1	0.938	1	CLONAL	3	TRUE	1	0.50422772046901	3		14	24	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	394	399	0				ENST00000310581	NM_198253.2	-/1132			0.887658448480873	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	2	0.887658448480873	4		399	825	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0032097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	722	616	1	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.549098795293171	5	FACETS	1	0.994	1	0.754	0.729	0.779	CLONAL	2	TRUE	2	0.887658448480873	5		617	1677	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149982897	149982897	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	105	503	0	ENST00000253339.5:c.3361G>A	p.Glu1121Lys	p.E1121K	ENST00000253339		1121	Gag/Aag	7/7	0.467418856140457	2	FACETS	0.55	0.496	0.607	0.275	0.248	0.304	INDETERMINATE	1	TRUE	0	0.887658448480873	2		503	430	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944872	31944872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	314	577	0	ENST00000340398.3:c.229G>A	p.Asp77Asn	p.D77N	ENST00000340398	NM_001013699.2	77	Gat/Aat	1/1	0.354350548316051	3	FACETS	1	0.989	1	0.584	0.552	0.615	INDETERMINATE	1	TRUE	1	0.887658448480873	3		577	875	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95592977	95592977	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	339	513	1	ENST00000393063.1:c.843C>G	p.Ile281Met	p.I281M	ENST00000393063	NM_030621.3	281	atC/atG	8/28	0.521113909244919	5	FACETS	1	0.968	1			1	INDETERMINATE	2	TRUE	NA	0.887658448480873	5		514	869	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858621	9858621	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs752992319	NA	P-0032097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	128	611	0	ENST00000330684.3:c.2780G>C	p.Arg927Thr	p.R927T	ENST00000330684	NM_001134407.1	927	aGa/aCa	13/13	0.469804730812797	2	FACETS	0.479	0.435	0.525	0.24	0.217	0.263	INDETERMINATE	1	TRUE	0	0.887658448480873	2		611	602	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108203	8108203	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs267605101	NA	P-0032097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1350	222	812	3	ENST00000585124.1:c.1021C>T	p.Gln341Ter	p.Q341*	ENST00000585124	NM_004217.3	341	Caa/Taa	9/9	0.549098795293171	5	FACETS	0.742	0.688	0.798	0.247	0.229	0.266	SUBCLONAL	1	TRUE	2	0.887658448480873	5		815	1572	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117755	70117755	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	225	783	0	ENST00000245479.2:c.223G>C	p.Glu75Gln	p.E75Q	ENST00000245479	NM_000346.3	75	Gag/Cag	1/3	0.448441094128407	3	FACETS	0.673	0.627	0.722	0.337	0.313	0.361	INDETERMINATE	1	TRUE	1	0.887658448480873	3		783	1087	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252766	10252766	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1355	218	850	0	ENST00000340748.4:c.3199G>T	p.Asp1067Tyr	p.D1067Y	ENST00000340748		1067	Gac/Tac	29/40	0.654518537272771	4	FACETS	0.589	0.546	0.634	0.196	0.182	0.212	SUBCLONAL	1	TRUE	1	0.887658448480873	4		850	1573	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105636	11105636	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1541	185	807	0	ENST00000358026.2:c.1552G>C	p.Glu518Gln	p.E518Q	ENST00000358026	NM_001128849.1	518	Gag/Cag	9/36	0.654518537272771	4	FACETS	0.456	0.419	0.495	0.152	0.139	0.165	SUBCLONAL	1	TRUE	1	0.887658448480873	4		807	1726	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319512	62319512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs909417142	NA	P-0032097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	240	911	1	ENST00000360203.5:c.1616C>T	p.Ser539Phe	p.S539F	ENST00000360203	NM_001283009.1	539	tCc/tTc	19/35	0.448441094128407	3	FACETS	0.633	0.59	0.677	0.316	0.295	0.339	INDETERMINATE	1	TRUE	1	0.887658448480873	3		912	1234	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037213	71037213	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	134	429	0	ENST00000318789.4:c.1078G>C	p.Glu360Gln	p.E360Q	ENST00000318789	NM_032682.5	360	Gaa/Caa	14/21	0.293881983640236	4	FACETS	0.812	0.739	0.888	0.203	0.184	0.222	INDETERMINATE	1	TRUE	0	0.887658448480873	4		429	702	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202937	27202937	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	146	616	0	ENST00000380036.4:c.2029C>T	p.Gln677Ter	p.Q677*	ENST00000380036	NM_000459.3	677	Caa/Taa	13/23	0.448441094128407	3	FACETS	0.609	0.556	0.664	0.304	0.278	0.332	INDETERMINATE	1	TRUE	1	0.887658448480873	3		616	780	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578459	+	missense_variant	Missense_Mutation	TNP	CGG	CGG	GGA	novel	NA	P-0032097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	891	866	1	ENST00000269305.4:c.471_473delinsTCC	p.Arg158Pro	p.R158P	ENST00000269305	NM_001126112.2	157	gtCCGc/gtTCCc	5/11	0.549098795293171	5	FACETS	0.93	0.905	0.956	0.93	0.905	0.956	CLONAL	3	TRUE	2	0.887658448480873	5		867	1677	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026513	6026513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780044	NA	P-0032097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	86	716	1	ENST00000265849.7:c.1883G>A	p.Arg628Gln	p.R628Q	ENST00000265849	NM_000535.5	628	cGa/cAa	11/15	0.354658781410084	3	FACETS	0.262	0.231	0.296	0.131	0.115	0.148	INDETERMINATE	1	TRUE	1	0.887658448480873	3		717	1066	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435317	56435317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200066146	NA	P-0033436-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	208	718	1	ENST00000407977.2:c.1820C>T	p.Ser607Leu	p.S607L	ENST00000407977		607	tCg/tTg	9/10	0.268781794465069	5	FACETS	1	0.986	1	0.806	0.752	0.861	INDETERMINATE	2	TRUE	2	0.456682641786279	5		719	635	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0033436-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	283	768	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.456682641786279	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.456682641786279	2		768	497	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444987	49444987	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033436-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	301	654	0	ENST00000301067.7:c.2479del	p.Gln827AsnfsTer103	p.Q827Nfs*103	ENST00000301067	NM_003482.3	827	Caa/aa	10/54	0.456682641786279	3	FACETS	0.949	0.904	0.993	0.949	0.904	0.993	CLONAL	3	TRUE	0	0.456682641786279	3		654	569	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982529	10982529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1163340108	NA	P-0033436-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	70	188	1	ENST00000327064.4:c.151G>A	p.Ala51Thr	p.A51T	ENST00000327064	NM_199141.1	51	Gcg/Acg	1/16	0.304553698568	4	FACETS	1	0.898	1	1	0.898	1	CLONAL	2	TRUE	2	0.456682641786279	4		189	220	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638273	176638273	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0033436-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	166	722	0	ENST00000439151.2:c.2873C>G	p.Ser958Ter	p.S958*	ENST00000439151	NM_022455.4	958	tCa/tGa	5/23	NA	2	FACETS	1	0.963	1			1	INDETERMINATE	1	TRUE	NA	0.456682641786279	2		722	675	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880071	151880071	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033436-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	136	364	0	ENST00000262189.6:c.5253G>A	p.Trp1751Ter	p.W1751*	ENST00000262189	NM_170606.2	1751	tgG/tgA	35/59	0.268781794465069	5	FACETS	0.992	0.907	1	0.661	0.605	0.72	INDETERMINATE	2	TRUE	2	0.456682641786279	5		364	506	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0033490-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	112	347	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.261450438313001	5	FACETS	1	0.957	1	0.729	0.662	0.798	INDETERMINATE	2	TRUE	2	0.471364567156223	5		347	371	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033490-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	71	614	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.336744838976214	3	FACETS	0.969	0.851	1	0.323	0.283	0.366	CLONAL	1	TRUE	0	0.471364567156223	3		614	384	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948385	71948385	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138023922	NA	P-0033490-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	129	1003	1	ENST00000298229.2:c.3097C>T	p.Arg1033Cys	p.R1033C	ENST00000298229	NM_001567.3	1033	Cgt/Tgt	26/28	0.418468309750014	4	FACETS	0.832	0.759	0.908			1	CLONAL	2	TRUE	NA	0.471364567156223	4		1004	484	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254718	16254718	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033490-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	166	812	0	ENST00000375759.3:c.1983G>A	p.Trp661Ter	p.W661*	ENST00000375759	NM_015001.2	661	tgG/tgA	11/15	0.471364567156223	6	FACETS	1	0.974	1			1	CLONAL	2	TRUE	NA	0.471364567156223	6		812	606	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874981	151874982	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0033490-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	90	325	0	ENST00000262189.6:c.7556_7557del	p.Ser2519CysfsTer5	p.S2519Cfs*5	ENST00000262189	NM_170606.2	2519	tCT/t	38/59	0.261450438313001	5	FACETS	1	0.944	1	0.72	0.646	0.796	INDETERMINATE	2	TRUE	2	0.471364567156223	5		325	302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0033527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	262	773	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.500418782457026	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.500418782457026	1		774	784	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484338	120484338	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	80	476	0	ENST00000256646.2:c.2792A>T	p.Asn931Ile	p.N931I	ENST00000256646	NM_024408.3	931	aAt/aTt	18/34	1	2	FACETS	0.791	0.7	0.888	0.791	0.7	0.888	SUBCLONAL	1	TRUE	1	0.500418782457026	2		476	404	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397643	49397643	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	novel	NA	P-0033527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	172	657	0	ENST00000418115.1:c.581G>C	p.Ter194SerextTer54	p.*194Sext*54	ENST00000418115	NM_001664.2	194	tGa/tCa	5/5	0.500418782457026	1	FACETS	0.976	0.905	1	0.976	0.905	1	CLONAL	1	TRUE	0	0.500418782457026	1		657	528	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253817	153253817	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	134	487	0	ENST00000281708.4:c.916C>G	p.Gln306Glu	p.Q306E	ENST00000281708	NM_033632.3	306	Cag/Gag	6/12	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.500418782457026	2		487	521	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322886	31322886	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	46	598	0	ENST00000412585.2:c.1010C>T	p.Ser337Leu	p.S337L	ENST00000412585	NM_005514.6	337	tCa/tTa	5/8	0.485579662812928	2	FACETS	0.286	0.24	0.337	0.143	0.12	0.169	SUBCLONAL	1	TRUE	0	0.500418782457026	2		598	643	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949146	151949147	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	130	698	0	ENST00000262189.6:c.1498dup	p.Thr500AsnfsTer4	p.T500Nfs*4	ENST00000262189	NM_170606.2	500	aca/aAca	11/59	0.500418782457026	1	FACETS	0.856	0.782	0.933	0.856	0.782	0.933	CLONAL	1	TRUE	0	0.500418782457026	1		698	455	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0033914-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	159	283	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.69	2		283	453	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033914-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	153	399	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.96	0.886	1	0.96	0.886	1	CLONAL	1	TRUE	1	0.69	2		399	462	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299106	15299106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033914-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	273	744	0	ENST00000263388.2:c.1432T>C	p.Cys478Arg	p.C478R	ENST00000263388	NM_000435.2	478	Tgt/Cgt	9/33	1	2	FACETS	0.878	0.826	0.932	0.878	0.826	0.932	CLONAL	1	TRUE	1	0.69	2		744	901	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874419	151874419	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033914-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	144	328	0	ENST00000262189.6:c.8119G>T	p.Val2707Phe	p.V2707F	ENST00000262189	NM_170606.2	2707	Gtt/Ttt	38/59	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.69	2		328	405	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033948-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	189	565	5	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.883	0.815	0.953	0.883	0.815	0.953	CLONAL	1	TRUE	1	0.385485475240478	2		570	1111	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0033948-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	128	408	1	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.31403739468407	2	FACETS	0.841	0.769	0.914	0.841	0.769	0.914	CLONAL	2	TRUE	0	0.385485475240478	2		409	395	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0033948-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1266	287	803	21	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.959	0.899	1	0.959	0.899	1	CLONAL	1	TRUE	1	0.385485475240478	2		824	1553	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0033948-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	564	396	0	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.379946258389628	2	FACETS	0.951	0.913	0.99	0.951	0.913	0.99	CLONAL	2	TRUE	0	0.385485475240478	2		396	1538	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0033948-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	42	451	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.385485475240478	1	FACETS	0.363	0.303	0.429	0.363	0.303	0.429	SUBCLONAL	1	TRUE	0	0.385485475240478	1		451	485	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37081727	37081727	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63751277	NA	P-0033948-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	142	570	1	ENST00000231790.2:c.1609C>T	p.Gln537Ter	p.Q537*	ENST00000231790	NM_000249.3	537	Cag/Tag	14/19	0.345143619819268	1	FACETS	0.877	0.801	0.956	0.877	0.801	0.956	CLONAL	1	TRUE	0	0.385485475240478	1		571	678	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572092	64572093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs767319284	NA	P-0033948-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	580	703	1	ENST00000312049.6:c.1546dup	p.Arg516ProfsTer15	p.R516Pfs*15	ENST00000312049	NM_130799.2	516	cgg/cCgg	10/10	1	2	FACETS	0.905	0.869	0.942	1	0.997	1	CLONAL	2	TRUE	1	0.385485475240478	2		704	1662	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164163	108164164	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs864622164	NA	P-0033948-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	34	242	0	ENST00000278616.4:c.4741dup	p.Ile1581AsnfsTer5	p.I1581Nfs*5	ENST00000278616	NM_000051.3	1579	caa/cAaa	31/63	1	2	FACETS	0.658	0.54	0.789	0.658	0.54	0.789	SUBCLONAL	1	TRUE	1	0.385485475240478	2		242	268	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609084	43609086	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs377767399	NA	P-0033948-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1412	346	913	2	ENST00000355710.3:c.1846_1848del	p.Glu616del	p.E616del	ENST00000355710	NM_020975.4	614	GAG/-	10/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.385485475240478	2		915	1758	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788609	3788609	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs945398646	NA	P-0033948-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	97	512	1	ENST00000262367.5:c.4345G>A	p.Val1449Ile	p.V1449I	ENST00000262367	NM_004380.2	1449	Gtt/Att	26/31	1	2	FACETS	0.738	0.658	0.823	0.738	0.658	0.823	SUBCLONAL	1	TRUE	1	0.385485475240478	2		513	682	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90633831	90633831	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316240101	NA	P-0033948-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1552	310	687	0	ENST00000330062.3:c.253G>A	p.Gly85Arg	p.G85R	ENST00000330062	NM_002168.2	85	Ggg/Agg	3/11	0.291158142935136	3	FACETS	1	0.961	1	0.515	0.484	0.548	CLONAL	1	TRUE	1	0.385485475240478	3		687	1862	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245139	41245142	+	frameshift_variant	Frame_Shift_Del	DEL	ACTC	ACTC	-	rs80357674	NA	P-0033948-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	66	782	0	ENST00000357654.3:c.2406_2409del	p.Gln804ValfsTer10	p.Q804Vfs*10	ENST00000357654	NM_007294.3	802	gtGAGT/gt	10/23	1	2	FACETS	0.497	0.431	0.569	0.497	0.431	0.569	SUBCLONAL	1	TRUE	1	0.385485475240478	2		782	689	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271813	15271813	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033948-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1557	384	879	0	ENST00000263388.2:c.6626del	p.Pro2209ArgfsTer37	p.P2209Rfs*37	ENST00000263388	NM_000435.2	2209	cCg/cg	33/33	0.379946258389628	2	FACETS	1	0.966	1	0.513	0.485	0.542	CLONAL	1	TRUE	0	0.385485475240478	2		879	1941	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546719	9546719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033948-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	83	417	0	ENST00000353224.5:c.1303G>A	p.Ala435Thr	p.A435T	ENST00000353224	NM_177990.2	435	Gcc/Acc	5/10	0.385485475240478	3	FACETS	0.724	0.639	0.816	0.362	0.319	0.408	SUBCLONAL	1	TRUE	1	0.385485475240478	3		417	709	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662973	52662973	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033948-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	83	404	0	ENST00000394830.3:c.1380del	p.Lys460AsnfsTer15	p.K460Nfs*15	ENST00000394830	NM_018313.4	460	aaA/aa	13/30	0.345143619819268	1	FACETS	0.867	0.77	0.97	0.867	0.77	0.97	CLONAL	1	TRUE	0	0.385485475240478	1		404	401	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0034011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	255	578	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.7220435614226	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	0	0.7220435614226	1		578	397	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	331	775	0	ENST00000269571.5:c.829G>T	p.Asp277Tyr	p.D277Y	ENST00000269571		277	Gac/Tac	7/27	0.7220435614226	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	FALSE	0	0.7220435614226	1		775	462	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491272	2491273	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0034350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	54	733	0	ENST00000355716.4:c.316dup	p.Arg106ProfsTer128	p.R106Pfs*128	ENST00000355716	NM_003820.2	105	-/C	4/8	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.714126942141437	2		733	117	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579361	7579364	+	frameshift_variant	Frame_Shift_Del	DEL	AAAC	AAAC	-	novel	NA	P-0034350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	78	761	0	ENST00000269305.4:c.323_326del	p.Gly108AlafsTer14	p.G108Afs*14	ENST00000269305	NM_001126112.2	108	gGTTTc/gc	4/11	0.672488628661077	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.714126942141437	1		761	140	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095869	178095869	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	84	606	0	ENST00000397062.3:c.1462G>C	p.Glu488Gln	p.E488Q	ENST00000397062	NM_006164.4	488	Gag/Cag	5/5	0.296452877675696	4	FACETS	1	0.902	1	0.508	0.451	0.568	INDETERMINATE	1	TRUE	2	0.714126942141437	4		606	397	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561754	55561754	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	39	417	0	ENST00000288135.5:c.145del	p.Arg49AlafsTer55	p.R49Afs*55	ENST00000288135	NM_000222.2	48	gtC/gt	2/21	0.23344467190951	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.714126942141437	0		417	112	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963019	38963019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	20	439	1	ENST00000357387.3:c.1525G>A	p.Asp509Asn	p.D509N	ENST00000357387	NM_152756.3	509	Gat/Aat	17/38	0.522694542202429	2	FACETS	0.56	0.436	0.7	0.28	0.218	0.35	SUBCLONAL	1	TRUE	0	0.714126942141437	2		440	100	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004865	150004865	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	123	626	0	ENST00000253339.5:c.1360T>G	p.Trp454Gly	p.W454G	ENST00000253339		454	Tgg/Ggg	3/7	0.273491677998458	5	FACETS	0.944	0.883	1	0.755	0.706	0.802	INDETERMINATE	4	TRUE	0	0.714126942141437	5		626	189	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	92	399	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.335678381425075	2		399	442	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0034354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	881	622	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.335678381425075	10	FACETS	0.982	0.958	1	0.982	0.958	1	CLONAL	9	TRUE	1	0.335678381425075	10		622	1391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0034354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	296	840	2	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.249637059015477	2	FACETS	0.846	0.797	0.896	0.846	0.797	0.896	CLONAL	2	TRUE	0	0.335678381425075	2		842	1042	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346365	73346365	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	39	567	0	ENST00000377767.4:c.1435G>T	p.Asp479Tyr	p.D479Y	ENST00000377767	NM_014953.3	479	Gac/Tac	10/21	1	2	FACETS	0.687	0.571	0.816	0.687	0.571	0.816	SUBCLONAL	1	TRUE	1	0.335678381425075	2		567	338	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725043	89725043	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1057517809	NA	P-0034354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	62	204	0	ENST00000371953.3:c.1027-1G>A		p.X343_splice	ENST00000371953	NM_000314.4	343			0.249637059015477	2	FACETS	0.855	0.749	0.966	0.855	0.749	0.966	CLONAL	2	TRUE	0	0.335678381425075	2		204	216	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745576	162745576	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	100	582	0	ENST00000367921.3:c.1991A>C	p.Gln664Pro	p.Q664P	ENST00000367921	NM_006182.2	664	cAg/cCg	15/18	0.326821031394481	4	FACETS	0.721	0.642	0.805	0.24	0.214	0.269	SUBCLONAL	1	TRUE	1	0.335678381425075	4		582	1104	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962505	100962505	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	125	583	0	ENST00000325455.5:c.1892G>T	p.Gly631Val	p.G631V	ENST00000325455	NM_001202474.3	631	gGc/gTc	3/8	1	2	FACETS	0.729	0.659	0.804	0.729	0.659	0.804	SUBCLONAL	1	TRUE	1	0.335678381425075	2		583	1021	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190591	11190591	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	78	609	0	ENST00000361445.4:c.5608A>T	p.Thr1870Ser	p.T1870S	ENST00000361445	NM_004958.3	1870	Act/Tct	39/58	1	2	FACETS	0.531	0.465	0.601	0.531	0.465	0.601	SUBCLONAL	1	TRUE	1	0.335678381425075	2		609	876	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101402	27101403	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0034354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	122	525	0	ENST00000324856.7:c.4688_4689del	p.Pro1563HisfsTer8	p.P1563Hfs*8	ENST00000324856	NM_006015.4	1562	CCc/c	18/20	1	2	FACETS	0.993	0.898	1	0.993	0.898	1	CLONAL	1	TRUE	1	0.335678381425075	2		525	732	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106361	27106361	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	190	645	0	ENST00000324856.7:c.5972T>A	p.Leu1991Gln	p.L1991Q	ENST00000324856	NM_006015.4	1991	cTg/cAg	20/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.335678381425075	2		645	1090	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404833	70404833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	210	498	0	ENST00000373644.4:c.2348del	p.Gly783AlafsTer12	p.G783Afs*12	ENST00000373644	NM_030625.2	783	Ggc/gc	4/12	0.335678381425075	4	FACETS	1	0.986	1			1	CLONAL	3	TRUE	NA	0.335678381425075	4		498	478	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242702	46242702	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	40	565	0	ENST00000334344.6:c.1664A>T	p.Lys555Ile	p.K555I	ENST00000334344	NM_152641.2	555	aAa/aTa	13/21	1	2	FACETS	0.845	0.706	0.998	0.845	0.706	0.998	CLONAL	1	TRUE	1	0.335678381425075	2		565	282	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120494	2120494	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	333	993	0	ENST00000219476.3:c.1754G>T	p.Arg585Leu	p.R585L	ENST00000219476	NM_000548.3	585	cGt/cTt	17/42	0.335678381425075	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.335678381425075	1		993	1169	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39613788	39613788	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0034354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	22	404	0	ENST00000262039.4:c.1708-2A>G		p.X570_splice	ENST00000262039	NM_002647.2	570			1	2	FACETS	0.563	0.437	0.707	0.563	0.437	0.707	SUBCLONAL	1	TRUE	1	0.335678381425075	2		404	233	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314604	30314604	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	236	723	0	ENST00000262643.3:c.1153A>T	p.Arg385Trp	p.R385W	ENST00000262643	NM_001238.2	385	Agg/Tgg	12/12	0.335678381425075	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.335678381425075	1		723	931	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139835	55139835	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	117	480	0	ENST00000257290.5:c.1496T>A	p.Val499Glu	p.V499E	ENST00000257290	NM_006206.4	499	gTg/gAg	10/23	1	2	FACETS	0.887	0.8	0.979	0.887	0.8	0.979	CLONAL	1	TRUE	1	0.335678381425075	2		480	786	SUCCESS
APC	324	MSKCC	GRCh37	5	112175384	112175384	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	126	340	0	ENST00000257430.4:c.4093G>T	p.Gly1365Cys	p.G1365C	ENST00000257430	NM_000038.5	1365	Ggt/Tgt	16/16	0.335678381425075	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.335678381425075	1		340	472	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271456	26271456	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	270	493	0	ENST00000305910.3:c.157C>A	p.Arg53Ser	p.R53S	ENST00000305910	NM_003534.2	53	Cgc/Agc	1/1	0.335678381425075	5	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.335678381425075	5		493	1002	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275848	38275848	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs756375285	NA	P-0034354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	261	667	0	ENST00000425967.3:c.1421T>C	p.Leu474Pro	p.L474P	ENST00000425967	NM_001174067.1	474	cTg/cCg	11/19	0.249637059015477	2	FACETS	0.893	0.838	0.948	0.893	0.838	0.948	CLONAL	2	TRUE	0	0.335678381425075	2		667	871	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222259	53222283	+	frameshift_variant	Frame_Shift_Del	DEL	CATTCTGGTTCTCCTGGGTGCTGGG	CATTCTGGTTCTCCTGGGTGCTGGG	-	novel	NA	P-0034354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	254	529	0	ENST00000375401.3:c.4549_4573del	p.Pro1517AlafsTer19	p.P1517Afs*19	ENST00000375401	NM_004187.3	1517	CCCAGCACCCAGGAGAACCAGAATGgc/gc	26/26	0.226572011776191	2	FACETS	0.932	0.875	0.99			1	CLONAL	2	TRUE	NA	0.335678381425075	2		529	812	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034911-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	270	399	0				ENST00000310581	NM_198253.2	-/1132			0.299986623962147	4	FACETS	0.852	0.802	0.902	0.852	0.802	0.902	CLONAL	3	TRUE	1	0.364653100410819	4		399	791	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0034911-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	247	578	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.295598695027916	2	FACETS	0.823	0.772	0.876	0.823	0.772	0.876	CLONAL	2	TRUE	0	0.364653100410819	2		578	823	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937055	48937055	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034911-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	60	279	0	ENST00000267163.4:c.823G>T	p.Glu275Ter	p.E275*	ENST00000267163	NM_000321.2	275	Gaa/Taa	8/27	0.198122266765509	0	FACETS	0.531	0.459	0.608			1	INDETERMINATE	1	TRUE	0	0.364653100410819	0		279	394	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641019	3641019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113420526	NA	P-0034911-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1157	175	951	1	ENST00000294008.3:c.2620G>A	p.Gly874Ser	p.G874S	ENST00000294008	NM_032444.2	874	Ggc/Agc	12/15	1	2	FACETS	0.721	0.662	0.782	0.721	0.662	0.782	SUBCLONAL	1	TRUE	1	0.364653100410819	2		952	1332	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	101	399	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.972	0.872	1	0.972	0.872	1	CLONAL	1	TRUE	1	0.40919712189454	2		399	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0035247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	259	685	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.40919712189454	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.40919712189454	1		685	934	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438673	49438673	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0035247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	167	554	0	ENST00000301067.7:c.4817C>G	p.Ser1606Ter	p.S1606*	ENST00000301067	NM_003482.3	1606	tCa/tGa	19/54	1	2	FACETS	0.912	0.838	0.989	0.912	0.838	0.989	CLONAL	1	TRUE	1	0.40919712189454	2		554	895	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440042	49440042	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0035247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	166	531	0	ENST00000301067.7:c.4583+1G>A		p.X1528_splice	ENST00000301067	NM_003482.3	1528			1	2	FACETS	0.999	0.919	1	0.999	0.919	1	CLONAL	1	TRUE	1	0.40919712189454	2		531	812	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0035289-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	353	647	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.831905906305183	2	FACETS	0.984	0.958	1	0.984	0.958	1	CLONAL	2	TRUE	0	0.854204076863105	2		647	420	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567782	226567782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763508057	NA	P-0035289-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	770	544	0	ENST00000366794.5:c.1384G>A	p.Val462Ile	p.V462I	ENST00000366794	NM_001618.3	462	Gtc/Atc	10/23	0.854204076863105	7	FACETS	1	0.995	1	0.837	0.811	0.864	CLONAL	3	TRUE	3	0.854204076863105	7		544	1688	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29701075	29701075	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035289-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	614	331	1	ENST00000356175.3:c.8359T>C	p.Cys2787Arg	p.C2787R	ENST00000356175	NM_000267.3	2787	Tgt/Cgt	57/57	0.854204076863105	4	FACETS	0.989	0.974	1	0.989	0.974	1	CLONAL	4	TRUE	0	0.854204076863105	4		332	674	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170015131	170015131	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035289-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	606	468	1	ENST00000295797.4:c.1537T>A	p.Phe513Ile	p.F513I	ENST00000295797	NM_002740.5	513	Ttt/Att	16/18	0.854204076863105	6	FACETS	0.969	0.94	0.999	0.646	0.626	0.666	CLONAL	4	TRUE	0	0.854204076863105	6		469	991	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798806	135798806	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035289-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	343	187	0	ENST00000298552.3:c.437C>G	p.Ser146Cys	p.S146C	ENST00000298552	NM_001162426.1	146	tCt/tGt	6/23	0.854204076863105	6	FACETS	1	0.96	1			1	CLONAL	4	TRUE	NA	0.854204076863105	6		187	544	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137323775	137323775	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035289-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	6603	622	9	ENST00000481739.1:c.1068G>C	p.Lys356Asn	p.K356N	ENST00000481739	NM_002957.4	356	aaG/aaC	8/10	0.854204076863105	22	FACETS	1	0.998	1			1	CLONAL	21	TRUE	NA	0.854204076863105	22		631	7006	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831330	72831330	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1332657698	NA	P-0035289-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	169	316	0	ENST00000268489.5:c.5251C>G	p.Gln1751Glu	p.Q1751E	ENST00000268489	NM_006885.3	1751	Caa/Gaa	9/10	0.809160933970637	5	FACETS	1	0.984	1	0.478	0.445	0.51	CLONAL	2	TRUE	0	0.854204076863105	5		316	378	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0035641-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	120	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.523479164122677	2		457	457	SUCCESS
APC	324	MSKCC	GRCh37	5	112178000	112178000	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768922431	NA	P-0035641-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	112	347	0	ENST00000257430.4:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000257430	NM_000038.5	2237	Cga/Tga	16/16	0.523479164122677	1	FACETS	0.921	0.838	1	0.921	0.838	1	CLONAL	1	TRUE	0	0.523479164122677	1		347	343	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980527	1980527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760185069	NA	P-0035641-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	280	668	1	ENST00000382891.5:c.3989C>T	p.Ala1330Val	p.A1330V	ENST00000382891	NM_133335.3	1330	gCg/gTg	22/22	0.523479164122677	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.523479164122677	1		669	752	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844191	68844191	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035808-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	144	743	1	ENST00000261769.5:c.779C>G	p.Pro260Arg	p.P260R	ENST00000261769	NM_004360.3	260	cCc/cGc	6/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.21	2		744	1126	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764356	39764356	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0035808-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	55	517	0	ENST00000288319.7:c.756T>G	p.Tyr252Ter	p.Y252*	ENST00000288319	NM_182918.3	252	taT/taG	7/10	1	2	FACETS	0.545	0.465	0.634	0.545	0.465	0.634	SUBCLONAL	1	TRUE	1	0.21	2		517	961	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747342068	NA	P-0036253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	594	848	0	ENST00000269305.4:c.394A>G	p.Lys132Glu	p.K132E	ENST00000269305	NM_001126112.2	132	Aag/Gag	5/11	0.715854350095719	4	FACETS	1	0.995	1	1	0.995	1	CLONAL	4	TRUE	0	0.711187297898493	4		848	684	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347852	347852	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	68	762	0	ENST00000262320.3:c.1654G>C	p.Ala552Pro	p.A552P	ENST00000262320	NM_003502.3	552	Gcc/Ccc	6/11	0.715854350095719	2	FACETS	0.368	0.32	0.419	0.184	0.16	0.21	SUBCLONAL	1	TRUE	0	0.711187297898493	2		762	520	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582849	95582849	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	50	357	0	ENST00000393063.1:c.1693G>T	p.Asp565Tyr	p.D565Y	ENST00000393063	NM_030621.3	565	Gat/Tat	11/28	0.715854350095719	4	FACETS	1	0.944	1	0.301	0.258	0.346	CLONAL	1	TRUE	0	0.711187297898493	4		357	200	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786069	3786069	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	365	573	0	ENST00000262367.5:c.4696G>T	p.Glu1566Ter	p.E1566*	ENST00000262367	NM_004380.2	1566	Gaa/Taa	28/31	0.715854350095719	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.711187297898493	2		573	434	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350181	89350181	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	74	834	0	ENST00000301030.4:c.2769G>C	p.Gln923His	p.Q923H	ENST00000301030	NM_001256183.1	923	caG/caC	9/13	0.715854350095719	4	FACETS	0.456	0.398	0.518	0.114	0.099	0.13	SUBCLONAL	1	TRUE	0	0.711187297898493	4		834	781	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727938	78727948	+	frameshift_variant	Frame_Shift_Del	DEL	CCTATTCACCT	CCTATTCACCT	-	novel	NA	P-0036253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	45	444	0	ENST00000306801.3:c.786_796del	p.Phe263ProfsTer45	p.F263Pfs*45	ENST00000306801	NM_020761.2	261	gaCCTATTCACCTcc/gacc	6/34	0.715854350095719	4	FACETS	0.389	0.327	0.459	0.097	0.081	0.115	SUBCLONAL	1	TRUE	0	0.711187297898493	4		444	556	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599903	10599903	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	502	578	0	ENST00000171111.5:c.1673G>T	p.Gly558Val	p.G558V	ENST00000171111	NM_203500.1	558	gGg/gTg	5/6	0.715854350095719	5	FACETS	1	0.982	1			1	CLONAL	3	TRUE	NA	0.711187297898493	5		578	943	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113822	11113822	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	124	475	0	ENST00000358026.2:c.1930G>C	p.Glu644Gln	p.E644Q	ENST00000358026	NM_001128849.1	644	Gag/Cag	12/36	0.715854350095719	5	FACETS	0.908	0.821	0.999			1	CLONAL	1	TRUE	NA	0.711187297898493	5		475	794	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247382	71247382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781486254	NA	P-0036253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	218	454	0	ENST00000318789.4:c.151C>T	p.Leu51Phe	p.L51F	ENST00000318789	NM_032682.5	51	Ctc/Ttc	6/21	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.711187297898493	2		454	287	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417913	138417913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	96	368	0	ENST00000289153.2:c.1606C>T	p.Pro536Ser	p.P536S	ENST00000289153	NM_006219.2	536	Cct/Tct	11/22	0.711187297898493	6	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.711187297898493	6		368	448	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561796	55561809	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTGTCAAATGGA	CTTTGTCAAATGGA	-	novel	NA	P-0036253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	154	355	0	ENST00000288135.5:c.190_203del	p.Val64Ter	p.V64*	ENST00000288135	NM_000222.2	62	ggCTTTGTCAAATGGAct/ggct	2/21	0.697958649753594	4	FACETS	1	0.988	1	0.727	0.669	0.785	CLONAL	1	TRUE	2	0.711187297898493	4		355	510	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27229161	27229161	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	290	491	0	ENST00000380036.4:c.3306C>A	p.Tyr1102Ter	p.Y1102*	ENST00000380036	NM_000459.3	1102	taC/taA	23/23	0.565670442293069	5	FACETS	1	0.964	1	1	0.964	1	CLONAL	3	TRUE	2	0.711187297898493	5		491	553	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417343	139417352	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCAGGTGC	CGGCAGGTGC	-	novel	NA	P-0036253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	24	389	0	ENST00000277541.6:c.692_701del	p.Gly231AlafsTer43	p.G231Afs*43	ENST00000277541	NM_017617.3	231	gGCACCTGCCGc/gc	4/34	0.715854350095719	3	FACETS	0.206	0.161	0.258	0.069	0.053	0.086	SUBCLONAL	1	TRUE	0	0.711187297898493	3		389	444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	419	661	2	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.659598134812514	2	FACETS	0.919	0.885	0.952	0.919	0.885	0.952	CLONAL	2	TRUE	0	0.66586962988941	2		663	685	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750639	128750639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775522201	NA	P-0036257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	388	660	0	ENST00000377970.2:c.176C>T	p.Ala59Val	p.A59V	ENST00000377970	NM_002467.4	59	gCg/gTg	2/3	0.537886332325416	4	FACETS	0.879	0.843	0.916	0.879	0.843	0.916	CLONAL	3	TRUE	1	0.66586962988941	4		660	736	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445813	49445813	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	602	1115	0	ENST00000301067.7:c.1653del	p.Glu551AspfsTer379	p.E551Dfs*379	ENST00000301067	NM_003482.3	551	gaA/ga	10/54	0.66586962988941	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.66586962988941	3		1115	1201	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0036669-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	212	347	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.987	0.941	1	1	0.996	1	CLONAL	3	FALSE	1	0.463226755065211	2		347	309	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036669-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	113	526	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.917	0.84	0.995	1	0.989	1	CLONAL	2	FALSE	1	0.463226755065211	2		526	266	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792755	33792757	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs746430067	NA	P-0036669-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	10	37	0	ENST00000498907.2:c.564_566del	p.Pro189del	p.P189del	ENST00000498907	NM_004364.3	188	ccGCCc/ccc	1/1	0.167894668160393	4	FACETS	0.81	0.556	1	0.405	0.278	0.56	INDETERMINATE	1	FALSE	2	0.463226755065211	4		37	78	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333123	70333123	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036669-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	232	677	1	ENST00000373644.4:c.1028C>G	p.Pro343Arg	p.P343R	ENST00000373644	NM_030625.2	343	cCa/cGa	2/12	1	2	FACETS	0.921	0.867	0.975	1	0.994	1	CLONAL	2	FALSE	1	0.463226755065211	2		678	544	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608503	28608503	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036669-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	104	592	0	ENST00000241453.7:c.1639A>G	p.Thr547Ala	p.T547A	ENST00000241453	NM_004119.2	547	Aca/Gca	13/24	0.139382780195512	0	FACETS	0.543	0.497	0.589			1	INDETERMINATE	2	FALSE	0	0.463226755065211	0		592	222	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042341	16042341	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0036669-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	77	444	0	ENST00000268712.3:c.1333A>T	p.Lys445Ter	p.K445*	ENST00000268712	NM_006311.3	445	Aag/Tag	12/46	1	2	FACETS	0.792	0.708	0.878	1	0.981	1	SUBCLONAL	2	FALSE	1	0.463226755065211	2		444	210	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417487	139417487	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036669-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	372	782	1	ENST00000277541.6:c.557C>A	p.Pro186His	p.P186H	ENST00000277541	NM_017617.3	186	cCc/cAc	4/34	0.379293887061857	4	FACETS	0.936	0.893	0.979	1	0.995	1	CLONAL	3	FALSE	2	0.463226755065211	4		783	837	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	332	538	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.667155403812581	2	FACETS	0.908	0.859	0.957	0.454	0.429	0.479	CLONAL	1	TRUE	0	0.712379744203906	2		538	1027	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482592	56482592	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	419	655	1	ENST00000267101.3:c.1049G>T	p.Gly350Val	p.G350V	ENST00000267101	NM_001982.3	350	gGa/gTa	9/28	1	2	FACETS	0.971	0.926	1	0.971	0.926	1	CLONAL	1	TRUE	1	0.712379744203906	2		656	1211	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112458	115112478	+	inframe_deletion	In_Frame_Del	DEL	GCCGCCCGCTGTCCCGGGGCC	GCCGCCCGCTGTCCCGGGGCC	-	novel	NA	P-0036694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	354	575	0	ENST00000257566.3:c.1262_1282del	p.Arg421_Arg427del	p.R421_R427del	ENST00000257566	NM_016569.3	421	cGGCCCCGGGACAGCGGGCGGCtg/ctg	7/8	0.699434442193911	1	FACETS	0.921	0.88	0.961	0.921	0.88	0.961	CLONAL	1	TRUE	0	0.712379744203906	1		575	695	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90645622	90645622	+	start_lost	Translation_Start_Site	SNP	T	T	A	novel	NA	P-0036694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	87	129	0	ENST00000330062.3:c.1A>T	p.Met1?	p.M1?	ENST00000330062	NM_002168.2	1	Atg/Ttg	1/11	0.693486970401393	3	FACETS	0.845	0.753	0.942	0.423	0.376	0.471	CLONAL	1	TRUE	1	0.712379744203906	3		129	392	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403629	138403629	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1032389846	NA	P-0036694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	271	402	0	ENST00000289153.2:c.2153A>G	p.Lys718Arg	p.K718R	ENST00000289153	NM_006219.2	718	aAg/aGg	15/22	1	2	FACETS	0.94	0.886	0.996	0.94	0.886	0.996	CLONAL	1	TRUE	1	0.712379744203906	2		402	809	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915615	131915615	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	177	281	0	ENST00000265335.6:c.613G>T	p.Glu205Ter	p.E205*	ENST00000265335		205	Gaa/Taa	5/25	1	2	FACETS	0.824	0.763	0.887	0.824	0.763	0.887	CLONAL	1	TRUE	1	0.712379744203906	2		281	603	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0036804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	129	401	1	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	0.413931359490323	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.413931359490323	1		402	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579419	7579420	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs587783062	NA	P-0036804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	241	602	0	ENST00000269305.4:c.267dup	p.Ser90LeufsTer59	p.S90Lfs*59	ENST00000269305	NM_001126112.2	89	-/C	4/11	0.413931359490323	1	FACETS	0.925	0.865	0.988	0.925	0.865	0.988	CLONAL	1	TRUE	0	0.413931359490323	1		602	998	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0036976-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	67	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.345331970246545	1	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	0	0.345331970246545	1		457	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0036976-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	63	536	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.345331970246545	1	FACETS	0.749	0.65	0.855	0.749	0.65	0.855	SUBCLONAL	1	TRUE	0	0.345331970246545	1		537	403	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492817	56492817	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036976-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	94	436	0	ENST00000407977.2:c.122C>A	p.Ser41Ter	p.S41*	ENST00000407977		41	tCa/tAa	2/10	0.345331970246545	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.345331970246545	1		436	358	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851593	128851593	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036976-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	35	591	0	ENST00000249373.3:c.1918A>T	p.Thr640Ser	p.T640S	ENST00000249373	NM_005631.4	640	Acc/Tcc	11/12	1	2	FACETS	0.422	0.346	0.508	0.422	0.346	0.508	SUBCLONAL	1	TRUE	1	0.345331970246545	2		591	480	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263850	133263850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	13	149	0	ENST00000320574.5:c.52G>A	p.Glu18Lys	p.E18K	ENST00000320574	NM_006231.2	18	Gag/Aag	1/49	1	2	FACETS	0.845	0.604	1	0.845	0.604	1	CLONAL	1	TRUE	1	0.17	2		149	181	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971138	21971138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760640852	NA	P-0037092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	30	333	0	ENST00000304494.5:c.220G>A	p.Asp74Asn	p.D74N	ENST00000304494	NM_000077.4	74	Gac/Aac	2/3	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.17	2		333	323	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46603829	46603829	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	30	682	0	ENST00000263734.3:c.1186G>A	p.Glu396Lys	p.E396K	ENST00000263734	NM_001430.4	396	Gag/Aag	9/16	1	2	FACETS	0.605	0.486	0.741	0.605	0.486	0.741	SUBCLONAL	1	TRUE	1	0.17	2		682	583	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578393	7578396	+	protein_altering_variant	In_Frame_Del	DEL	ATGG	ATGG	T	novel	NA	P-0037162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	92	557	0	ENST00000269305.4:c.534_537delinsA	p.His178_His179delinsGln	p.H178_H179delinsQ	ENST00000269305	NM_001126112.2	178	caCCAT/caA	5/11	0.174622361074035	2	FACETS	0.948	0.844	1	0.948	0.844	1	CLONAL	2	TRUE	0	0.174622361074035	2		557	556	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578528	7578528	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037389-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	382	894	0	ENST00000269305.4:c.402T>G	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	ttT/ttG	5/11	0.296530472509475	2	FACETS	0.954	0.905	1	0.954	0.905	1	CLONAL	2	TRUE	0	0.299782374328446	2		894	1336	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10283800	10283800	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143598088	NA	P-0037389-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	229	610	0	ENST00000340748.4:c.686C>T	p.Thr229Met	p.T229M	ENST00000340748		229	aCg/aTg	8/40	0.299782374328446	7	FACETS	0.93	0.864	0.998			1	CLONAL	2	TRUE	NA	0.299782374328446	7		610	1437	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564525	41564526	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0037389-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	141	454	0	ENST00000263253.7:c.3947_3948del	p.Pro1316ArgfsTer8	p.P1316Rfs*8	ENST00000263253	NM_001429.3	1316	cCT/c	24/31	0.289465442098388	2	FACETS	1	0.971	1	0.577	0.526	0.631	CLONAL	1	TRUE	0	0.299782374328446	2		454	815	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs79184941	NA	P-0037528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	130	381	0	ENST00000358487.5:c.755C>T	p.Ser252Leu	p.S252L	ENST00000358487	NM_000141.4	252	tCg/tTg	7/18	0.663082717879632	3	FACETS	0.947	0.864	1	0.474	0.432	0.517	CLONAL	1	TRUE	1	0.752322790365801	3		381	502	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979257	93979257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	263	453	0	ENST00000369303.4:c.1571G>A	p.Gly524Glu	p.G524E	ENST00000369303	NM_004440.3	524	gGa/gAa	7/17	0.535391693098443	4	FACETS	0.959	0.905	1	0.959	0.905	1	CLONAL	2	TRUE	2	0.752322790365801	4		453	639	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149242	119149242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779039234	NA	P-0037528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	437	647	0	ENST00000264033.4:c.1250C>T	p.Pro417Leu	p.P417L	ENST00000264033	NM_005188.3	417	cCt/cTt	9/16	0.738665751006334	2	FACETS	0.957	0.927	0.986	0.957	0.927	0.986	CLONAL	2	TRUE	0	0.752322790365801	2		647	607	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961812	55961812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	320	448	0	ENST00000263923.4:c.2749G>A	p.Glu917Lys	p.E917K	ENST00000263923	NM_002253.2	917	Gaa/Aaa	20/30	0.485186261324542	4	FACETS	0.986	0.936	1	0.986	0.936	1	CLONAL	2	TRUE	2	0.752322790365801	4		448	756	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18576896	18576896	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs753453484	NA	P-0037528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	369	584	0	ENST00000266497.5:c.2304G>A	p.Trp768Ter	p.W768*	ENST00000266497		768	tgG/tgA	16/31	0.663082717879632	3	FACETS	0.881	0.842	0.921	0.881	0.842	0.921	CLONAL	2	TRUE	1	0.752322790365801	3		584	766	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858064	9858064	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	460	596	0	ENST00000330684.3:c.3337C>T	p.Pro1113Ser	p.P1113S	ENST00000330684	NM_001134407.1	1113	Cct/Tct	13/13	0.740508303582985	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.752322790365801	2		596	607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579519	7579520	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0037528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	1005	817	0	ENST00000269305.4:c.167_168del	p.Glu56GlyfsTer6	p.E56Gfs*6	ENST00000269305	NM_001126112.2	56	gAA/g	4/11	0.752322790365801	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.752322790365801	3		817	1215	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995359	15995359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	521	410	0	ENST00000268712.3:c.2834C>T	p.Pro945Leu	p.P945L	ENST00000268712	NM_006311.3	945	cCa/cTa	22/46	0.752322790365801	3	FACETS	0.988	0.965	1	0.988	0.965	1	CLONAL	3	TRUE	0	0.752322790365801	3		410	643	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93953224	93953224	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	283	489	0	ENST00000369303.4:c.2917C>T	p.His973Tyr	p.H973Y	ENST00000369303	NM_004440.3	973	Cat/Tat	17/17	0.535391693098443	4	FACETS	0.899	0.85	0.949	0.899	0.85	0.949	CLONAL	2	TRUE	2	0.752322790365801	4		489	733	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938866	76938866	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	522	772	0	ENST00000373344.5:c.1882G>T	p.Gly628Ter	p.G628*	ENST00000373344	NM_000489.3	628	Gga/Tga	9/35	0.738665751006334	2	FACETS	0.968	0.941	0.994	0.968	0.941	0.994	CLONAL	2	TRUE	0	0.752322790365801	2		772	717	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226573335	226573335	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138017860	NA	P-0037528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	302	571	0	ENST00000366794.5:c.881C>T	p.Pro294Leu	p.P294L	ENST00000366794	NM_001618.3	294	cCc/cTc	7/23	0.184401689645544	2	FACETS	1	0.992	1	0.618	0.587	0.649	INDETERMINATE	1	TRUE	0	0.752322790365801	2		571	650	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022405	12022405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	624	909	0	ENST00000396373.4:c.511C>T	p.His171Tyr	p.H171Y	ENST00000396373	NM_001987.4	171	Cat/Tat	5/8	0.292907549735923	5	FACETS	0.92	0.889	0.952			1	INDETERMINATE	3	TRUE	NA	0.752322790365801	5		909	1279	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478073	99478073	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	317	464	0	ENST00000268035.6:c.2977G>C	p.Glu993Gln	p.E993Q	ENST00000268035	NM_000875.3	993	Gag/Cag	16/21	0.485186261324542	4	FACETS	0.969	0.92	1	0.969	0.92	1	CLONAL	2	TRUE	2	0.752322790365801	4		464	762	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663792	29663793	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0037528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	283	633	0	ENST00000356175.3:c.6226dup	p.Ala2076GlyfsTer23	p.A2076Gfs*23	ENST00000356175	NM_000267.3	2075	gtg/gtGg	41/57	0.752322790365801	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.752322790365801	1		633	446	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082811	16082811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	65	85	0	ENST00000281043.3:c.625C>T	p.Pro209Ser	p.P209S	ENST00000281043	NM_005378.4	209	Ccg/Tcg	2/3	0.740508303582985	2	FACETS	0.96	0.883	1	0.96	0.883	1	CLONAL	2	TRUE	0	0.752322790365801	2		85	90	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29197672	29197672	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	463	720	0	ENST00000240100.2:c.522T>G	p.Ser174Arg	p.S174R	ENST00000240100	NM_001394.6	174	agT/agG	2/4	0.354852052960424	4	FACETS	0.975	0.934	1	0.975	0.934	1	INDETERMINATE	2	TRUE	2	0.752322790365801	4		720	1106	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577571	7577571	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs765848205	NA	P-0037734-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	201	646	0	ENST00000269305.4:c.710T>A	p.Met237Lys	p.M237K	ENST00000269305	NM_001126112.2	237	aTg/aAg	7/11	0.340970458972244	2	FACETS	0.763	0.714	0.814	0.763	0.714	0.814	SUBCLONAL	2	FALSE	0	0.509328589256286	2		646	517	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604765	48604766	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0037734-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	58	412	1	ENST00000342988.3:c.1589_1590del	p.His530ProfsTer46	p.H530Pfs*46	ENST00000342988	NM_005359.5	529	ttACac/ttac	12/12	0.39383210589387	1	FACETS	0.537	0.464	0.615	0.537	0.464	0.615	SUBCLONAL	1	FALSE	0	0.509328589256286	1		413	316	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TG	novel	NA	P-0037734-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	163	480	0	ENST00000311936.3:c.180_181delinsCA	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggCAaa	3/5	0.249696928268598	4	FACETS	1	0.989	1	0.742	0.683	0.803	INDETERMINATE	1	FALSE	2	0.509328589256286	4		480	651	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356230	66356230	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037734-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	154	559	2	ENST00000273854.3:c.1267A>C	p.Asn423His	p.N423H	ENST00000273854	NM_004439.5	423	Aac/Cac	5/18	0.36860591528881	2	FACETS	1	0.984	1	0.63	0.581	0.68	CLONAL	1	FALSE	0	0.509328589256286	2		561	480	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562256	176562256	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037734-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	212	675	0	ENST00000439151.2:c.152C>T	p.Ser51Leu	p.S51L	ENST00000439151	NM_022455.4	51	tCg/tTg	2/23	0.351519451152059	3	FACETS	1	0.99	1	0.682	0.635	0.73	CLONAL	1	FALSE	1	0.509328589256286	3		675	766	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0037761-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	46	523	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	FALSE	1	0.23115632534324	2		523	372	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0037761-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	22	377	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.146043586619838	0	FACETS	0.319	0.246	0.404			1	SUBCLONAL	1	FALSE	0	0.23115632534324	0		377	459	SUCCESS
APC	324	MSKCC	GRCh37	5	112173572	112173572	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037761-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	20	273	0	ENST00000257430.4:c.2281G>T	p.Glu761Ter	p.E761*	ENST00000257430	NM_000038.5	761	Gaa/Taa	16/16	0.23115632534324	1	FACETS	0.517	0.395	0.659	0.517	0.395	0.659	SUBCLONAL	1	FALSE	0	0.23115632534324	1		273	296	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0037761-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	74	569	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	1	2	FACETS	0.73	0.638	0.83	0.73	0.638	0.83	SUBCLONAL	1	FALSE	1	0.23115632534324	2		569	877	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986533	36986534	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGAG	novel	NA	P-0037761-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	66	623	0	ENST00000354822.5:c.1152_1155dup	p.Asp386LeufsTer54	p.D386Lfs*54	ENST00000354822	NM_001079668.2	385	-/CTCG	3/3	0.23115632534324	1	FACETS	0.575	0.498	0.659	0.575	0.498	0.659	SUBCLONAL	1	FALSE	0	0.23115632534324	1		623	878	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	132	526	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	0.613008656798807	3	FACETS	0.975	0.889	1	0.488	0.444	0.533	CLONAL	1	TRUE	1	0.613008656798807	3		526	577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0037865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	398	630	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.613008656798807	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.613008656798807	2		631	638	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0037865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	409	879	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	0.613008656798807	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.613008656798807	2		879	609	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748309	41748309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs894529129	NA	P-0037865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	214	844	0	ENST00000226382.2:c.460C>T	p.Arg154Cys	p.R154C	ENST00000226382	NM_003924.3	154	Cgc/Tgc	3/3	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.613008656798807	2		844	641	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468275	50468275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	285	638	0	ENST00000331340.3:c.1510G>A	p.Glu504Lys	p.E504K	ENST00000331340	NM_006060.4	504	Gag/Aag	8/8	0.613008656798807	4	FACETS	0.976	0.922	1	0.976	0.922	1	CLONAL	2	TRUE	2	0.613008656798807	4		638	768	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522551	176522551	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774571806	NA	P-0037865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	374	821	0	ENST00000292408.4:c.1648G>A	p.Val550Met	p.V550M	ENST00000292408	NM_213647.1	550	Gtg/Atg	13/18	0.613008656798807	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.613008656798807	2		821	583	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888166	112888166	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121918461	NA	P-0037865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	215	623	0	ENST00000351677.2:c.182A>T	p.Asp61Val	p.D61V	ENST00000351677	NM_002834.3	61	gAt/gTt	3/16	0.147881460855715	3	FACETS	0.88	0.825	0.934	0.586	0.55	0.623	INDETERMINATE	2	TRUE	0	0.613008656798807	3		623	521	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523142	176523142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778323767	NA	P-0037865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	339	787	0	ENST00000292408.4:c.1906G>A	p.Gly636Ser	p.G636S	ENST00000292408	NM_213647.1	636	Ggc/Agc	14/18	0.613008656798807	2	FACETS	0.982	0.942	1	0.982	0.942	1	CLONAL	2	TRUE	0	0.613008656798807	2		787	563	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252745	133252745	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs116162724	NA	P-0037865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	83	516	0	ENST00000320574.5:c.955G>A	p.Asp319Asn	p.D319N	ENST00000320574	NM_006231.2	319	Gat/Aat	10/49	0.147881460855715	3	FACETS	0.746	0.661	0.837	0.249	0.22	0.279	INDETERMINATE	1	TRUE	0	0.613008656798807	3		516	474	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952094	76952104	+	frameshift_variant	Frame_Shift_Del	DEL	TTTTCTGAATT	TTTTCTGAATT	-	novel	NA	P-0037866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	13	98	0	ENST00000373344.5:c.331_341del	p.Asn111Ter	p.N111*	ENST00000373344	NM_000489.3	111	AATTCAGAAAAt/t	5/35	1	1	FACETS	0.153	0.109	0.208	0.153	0.109	0.208	SUBCLONAL	1	TRUE	0	0.54	1		98	229	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0037866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	40	297	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.362	0.3	0.431	0.362	0.3	0.431	SUBCLONAL	1	TRUE	1	0.45	2		297	491	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022007	5022007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770579392	NA	P-0037866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	66	304	0	ENST00000381652.3:c.20C>T	p.Thr7Met	p.T7M	ENST00000381652	NM_004972.3	7	aCg/aTg	3/25	1	2	FACETS	0.478	0.414	0.546	0.478	0.414	0.546	SUBCLONAL	1	TRUE	1	0.45	2		304	614	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024703	31024703	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	153	504	1	ENST00000375687.4:c.4190del	p.Gly1397ValfsTer53	p.G1397Vfs*53	ENST00000375687	NM_015338.5	1396	gtG/gt	13/13	1	2	FACETS	0.883	0.809	0.96	0.883	0.809	0.96	CLONAL	1	TRUE	1	0.45	2		505	770	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444455	50444455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	95	279	0	ENST00000331340.3:c.385C>T	p.Pro129Ser	p.P129S	ENST00000331340	NM_006060.4	129	Ccc/Tcc	4/8	1	2	FACETS	0.908	0.812	1	0.908	0.812	1	CLONAL	1	TRUE	1	0.45	2		279	465	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006098	22006098	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	100	435	0	ENST00000276925.6:c.305C>G	p.Ala102Gly	p.A102G	ENST00000276925	NM_004936.3	102	gCc/gGc	2/2	1	2	FACETS	0.583	0.521	0.65	0.583	0.521	0.65	SUBCLONAL	1	TRUE	1	0.45	2		435	762	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44733211	44733211	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	23	194	0	ENST00000377967.4:c.204del	p.Thr69ArgfsTer15	p.T69Rfs*15	ENST00000377967	NM_021140.2	68	aGg/ag	2/29	1	1	FACETS	0.211	0.164	0.265	0.211	0.164	0.265	SUBCLONAL	1	TRUE	0	0.45	1		194	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0037887-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	50	553	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	1	2	FACETS	0.656	0.557	0.766	0.656	0.557	0.766	SUBCLONAL	1	FALSE	1	0.277533606319633	2		553	549	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0037984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	96	523	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.899143336153152	3	FACETS	0.408	0.363	0.456	0.204	0.181	0.228	SUBCLONAL	1	TRUE	1	0.899143336153152	3		523	759	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0037984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	128	461	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.899143336153152	3	FACETS	0.629	0.571	0.69	0.315	0.285	0.345	SUBCLONAL	1	TRUE	1	0.899143336153152	3		461	656	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714370	40714370	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs956451753	NA	P-0037984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	211	440	0	ENST00000373198.4:c.4027C>T	p.Arg1343Trp	p.R1343W	ENST00000373198	NM_133170.3	1343	Cgg/Tgg	29/32	0.201620825218578	3	FACETS	1	0.992	1	0.47	0.442	0.5	INDETERMINATE	1	TRUE	0	0.899143336153152	3		440	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519991	NA	P-0037984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	312	639	0	ENST00000269305.4:c.536A>C	p.His179Pro	p.H179P	ENST00000269305	NM_001126112.2	179	cAt/cCt	5/11	0.82552200837709	1	FACETS	0.901	0.869	0.932	0.901	0.869	0.932	CLONAL	1	TRUE	0	0.899143336153152	1		639	424	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743841	46743841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	205	744	0	ENST00000371975.4:c.2131G>A	p.Asp711Asn	p.D711N	ENST00000371975	NM_003579.3	711	Gat/Aat	18/18	1	2	FACETS	0.536	0.498	0.576	0.536	0.498	0.576	SUBCLONAL	1	TRUE	1	0.899143336153152	2		744	850	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627506	37627506	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	285	551	3	ENST00000447079.4:c.1421A>T	p.Asn474Ile	p.N474I	ENST00000447079	NM_015083.1	474	aAt/aTt	2/14	0.234808729730382	1	FACETS	0.959	0.926	0.989	0.959	0.926	0.989	INDETERMINATE	1	TRUE	0	0.899143336153152	1		554	364	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518004	176518004	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150920445	NA	P-0037984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	147	744	2	ENST00000292408.4:c.502G>A	p.Val168Ile	p.V168I	ENST00000292408	NM_213647.1	168	Gtc/Atc	5/18	1	2	FACETS	0.425	0.388	0.464	0.425	0.388	0.464	SUBCLONAL	1	TRUE	1	0.899143336153152	2		746	769	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0037985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	117	220	0				ENST00000310581	NM_198253.2	-/1132			0.224712232346926	1	FACETS	0.805	0.729	0.884	0.805	0.729	0.884	INDETERMINATE	1	FALSE	0	0.439503123972127	1		220	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0037985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	227	669	1	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	0.363703503883149	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	0	0.439503123972127	1		670	738	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0037985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	210	598	0	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	0.282397449503458	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	0	0.439503123972127	1		598	664	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724537	112724537	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	155	468	0	ENST00000369452.4:c.421G>C	p.Glu141Gln	p.E141Q	ENST00000369452	NM_007373.3	141	Gag/Cag	2/9	0.3126418815722	0	FACETS	0.701	0.645	0.759			1	SUBCLONAL	1	FALSE	0	0.439503123972127	0		468	564	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564831	41564832	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTC	novel	NA	P-0037985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	338	436	0	ENST00000263253.7:c.4133_4135dup	p.Val1378_Gln1379insLeu	p.V1378_Q1379insL	ENST00000263253	NM_001429.3	1378	gtt/gTTCtt	25/31	0.427782454845027	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	FALSE	1	0.439503123972127	3		436	921	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157431648	157431648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	179	466	0	ENST00000346085.5:c.2324C>T	p.Ser775Phe	p.S775F	ENST00000346085	NM_020732.3	775	tCc/tTc	7/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.439503123972127	2		466	760	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750587	128750587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	207	577	0	ENST00000377970.2:c.124G>A	p.Glu42Lys	p.E42K	ENST00000377970	NM_002467.4	42	Gag/Aag	2/3	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.439503123972127	2		577	783	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112767305	112767305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	70	391	0	ENST00000369452.4:c.1178C>T	p.Ser393Leu	p.S393L	ENST00000369452	NM_007373.3	393	tCa/tTa	6/9	0.3126418815722	0	FACETS	0.428	0.375	0.485			1	SUBCLONAL	1	FALSE	0	0.439503123972127	0		391	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0037987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	194	625	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.27139762512269	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	2	TRUE	0	0.278326099222247	2		627	694	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0037987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	170	483	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.147175269555657	4	FACETS	1	0.965	1	0.722	0.666	0.78	INDETERMINATE	2	TRUE	1	0.278326099222247	4		483	721	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868325	56868325	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	58	407	0	ENST00000308159.5:c.1708G>T	p.Val570Leu	p.V570L	ENST00000308159	NM_014669.4	570	Gtg/Ttg	15/22	0.278326099222247	5	FACETS	1	0.964	1	0.467	0.402	0.537	CLONAL	1	TRUE	2	0.278326099222247	5		407	422	SUCCESS
APC	324	MSKCC	GRCh37	5	112175617	112175617	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	113	409	0	ENST00000257430.4:c.4326del	p.Pro1443LeufsTer30	p.P1443Lfs*30	ENST00000257430	NM_000038.5	1442	ccT/cc	16/16	0.258879627428117	4	FACETS	0.872	0.791	0.955	0.872	0.791	0.955	CLONAL	3	TRUE	1	0.278326099222247	4		409	397	SUCCESS
APC	324	MSKCC	GRCh37	5	112175658	112175658	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	109	399	0	ENST00000257430.4:c.4367A>T	p.Lys1456Ile	p.K1456I	ENST00000257430	NM_000038.5	1456	aAa/aTa	16/16	0.258879627428117	4	FACETS	0.89	0.807	0.977	0.89	0.807	0.977	CLONAL	3	TRUE	1	0.278326099222247	4		399	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520006	NA	P-0037990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	98	641	0	ENST00000269305.4:c.821T>C	p.Val274Ala	p.V274A	ENST00000269305	NM_001126112.2	274	gTt/gCt	8/11	0.210417694158717	3	FACETS	0.944	0.841	1	0.472	0.42	0.527	CLONAL	1	FALSE	1	0.268770442996233	3		641	876	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180300	27180300	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	31	468	1	ENST00000380036.4:c.964A>T	p.Met322Leu	p.M322L	ENST00000380036	NM_000459.3	322	Atg/Ttg	7/23	1	2	FACETS	0.414	0.334	0.505	0.414	0.334	0.505	SUBCLONAL	1	FALSE	1	0.268770442996233	2		469	557	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981921	70981921	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	41	733	0	ENST00000276594.2:c.175G>C	p.Ala59Pro	p.A59P	ENST00000276594	NM_024504.3	59	Gca/Cca	2/8	0.210417694158717	3	FACETS	0.521	0.433	0.62	0.261	0.216	0.31	SUBCLONAL	1	FALSE	1	0.268770442996233	3		733	664	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037994-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	187	578	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.271004957618614	3	FACETS	0.839	0.78	0.9	0.839	0.78	0.9	CLONAL	3	FALSE	0	0.285828695371925	3		578	594	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114835	108114835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555066551	NA	P-0037994-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	91	352	0	ENST00000278616.4:c.652C>T	p.Gln218Ter	p.Q218*	ENST00000278616	NM_000051.3	218	Cag/Tag	6/63	0.285828695371925	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	FALSE	0	0.285828695371925	1		352	526	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915901	127915901	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037994-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	109	335	0	ENST00000373547.4:c.580C>A	p.Leu194Met	p.L194M	ENST00000373547	NM_002721.4	194	Ctg/Atg	6/7	0.285828695371925	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	0	0.285828695371925	1		335	607	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484315	50484315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037994-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	185	628	0	ENST00000394963.4:c.1075C>T	p.Gln359Ter	p.Q359*	ENST00000394963	NM_003076.4	359	Cag/Tag	9/13	0.285828695371925	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	0	0.285828695371925	1		628	748	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136124	11136124	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037994-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	214	542	0	ENST00000358026.2:c.3108G>A	p.Met1036Ile	p.M1036I	ENST00000358026	NM_001128849.1	1036	atG/atA	22/36	0.285828695371925	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	0	0.285828695371925	1		542	942	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064407	30064642	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGCCAGGGAGGAGAAGGCTAGAAAGCAGGTGAGCACAACCTTGTTTTAACTGATGATGTCACTGTGTGGTCAGTCCTGGCCTGGGAGGCGAGGAGTGGTCATGGGCTGGCAGGAGTCTTTTGGCCGTGGACATACCTGCTCTTGTTTTATACCTTTTGGATCTTCATTTGCCGATGCCTACCTGGTGGGATGTCATCTCTGGAAATGAGGAATAAACCCTAATAGCATATCTAAA	AGGCCAGGGAGGAGAAGGCTAGAAAGCAGGTGAGCACAACCTTGTTTTAACTGATGATGTCACTGTGTGGTCAGTCCTGGCCTGGGAGGCGAGGAGTGGTCATGGGCTGGCAGGAGTCTTTTGGCCGTGGACATACCTGCTCTTGTTTTATACCTTTTGGATCTTCATTTGCCGATGCCTACCTGGTGGGATGTCATCTCTGGAAATGAGGAATAAACCCTAATAGCATATCTAAA	-	novel	NA	P-0037994-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	44	372	0	ENST00000338641.4:c.973_999+209del		p.X325_splice	ENST00000338641	NM_000268.3	325		10/16	0.285828695371925	1	FACETS	0.486	0.407	0.573	0.486	0.407	0.573	SUBCLONAL	1	FALSE	0	0.285828695371925	1		372	543	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915971	127915971	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037994-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	104	331	0	ENST00000373547.4:c.510C>G	p.Ile170Met	p.I170M	ENST00000373547	NM_002721.4	170	atC/atG	6/7	0.285828695371925	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	0	0.285828695371925	1		331	531	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0038161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	325	879	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	0.488893621539903	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.488893621539903	1		879	859	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0038161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	163	454	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	NA	2	FACETS	1	0.925	1			1	INDETERMINATE	1	TRUE	NA	0.488893621539903	2		454	664	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650044	93650044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	206	506	0	ENST00000375746.1:c.1595G>A	p.Gly532Glu	p.G532E	ENST00000375746	NM_001174167.1	532	gGa/gAa	12/14	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.488893621539903	2		506	715	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104673	193104673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	170	385	0	ENST00000367435.3:c.377G>A	p.Arg126Gln	p.R126Q	ENST00000367435	NM_024529.4	126	cGa/cAa	5/17	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.488893621539903	2		385	653	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492599	56492829	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCGTGTATGGTATTTCATTTGGGAGACAAAAGAAGAAAGACATATTTCAAACAGATGGAAAGTGAAATATAATAAAGTTATACTTGCCTGCATTAATTTTCCTTCTGCTGGAGTTATTTCAGCAACACCAGCAAACACACCTTCCAAAGTGAGATTCAGTTTTCCTGTGGGGTCCATTTTCAAGGGGATCACTCTGATAATAGCTTTCTGTTCTGCTGATCTTTCAGACT	CCCGTGTATGGTATTTCATTTGGGAGACAAAAGAAGAAAGACATATTTCAAACAGATGGAAAGTGAAATATAATAAAGTTATACTTGCCTGCATTAATTTTCCTTCTGCTGGAGTTATTTCAGCAACACCAGCAAACACACCTTCCAAAGTGAGATTCAGTTTTCCTGTGGGGTCCATTTTCAAGGGGATCACTCTGATAATAGCTTTCTGTTCTGCTGATCTTTCAGACT	-	novel	NA	P-0038161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	38	158	0	ENST00000407977.2:c.110_252+88del		p.X37_splice	ENST00000407977		37		2/10	0.488893621539903	1	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	0	0.488893621539903	1		158	116	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240269	5240269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758563821	NA	P-0038161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	250	983	1	ENST00000357368.4:c.1645C>T	p.Arg549Trp	p.R549W	ENST00000357368	NM_002850.3	549	Cgg/Tgg	12/38	1	2	FACETS	0.996	0.932	1	0.996	0.932	1	CLONAL	1	TRUE	1	0.488893621539903	2		984	1027	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221276	36221276	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	287	874	1	ENST00000222270.7:c.5110C>T	p.Arg1704Cys	p.R1704C	ENST00000222270	NM_014727.1	1704	Cgc/Tgc	24/37	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.488893621539903	2		875	1121	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253860	153253860	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0038161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	154	333	0	ENST00000281708.4:c.873T>A	p.Tyr291Ter	p.Y291*	ENST00000281708	NM_033632.3	291	taT/taA	6/12	0.488893621539903	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.488893621539903	1		333	461	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845679	151845679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	189	570	0	ENST00000262189.6:c.13333G>A	p.Gly4445Ser	p.G4445S	ENST00000262189	NM_170606.2	4445	Ggt/Agt	52/59	1	2	FACETS	0.975	0.903	1	0.975	0.903	1	CLONAL	1	TRUE	1	0.488893621539903	2		570	793	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0038162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	263	283	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.664809241087829	4	FACETS	0.907	0.855	0.959	0.907	0.855	0.959	CLONAL	2	TRUE	2	0.745959487121466	4		283	679	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735458	40735458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1243407933	NA	P-0038162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1201	581	655	1	ENST00000373198.4:c.3415C>T	p.Arg1139Trp	p.R1139W	ENST00000373198	NM_133170.3	1139	Cgg/Tgg	25/32	0.745959487121466	5	FACETS	0.926	0.889	0.964	0.617	0.592	0.643	CLONAL	2	TRUE	2	0.745959487121466	5		656	1782	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578476	7578477	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGTGT	novel	NA	P-0038162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	652	827	0	ENST00000269305.4:c.448_453dup	p.Thr150_Pro151dup	p.T150_P151dup	ENST00000269305	NM_001126112.2	150	-/ACACCC	5/11	0.720893585284487	2	FACETS	0.812	0.787	0.835	0.812	0.787	0.835	CLONAL	2	TRUE	0	0.745959487121466	2		827	1077	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961701	41961701	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	137	457	1	ENST00000219905.7:c.609G>T	p.Arg203Ser	p.R203S	ENST00000219905	NM_001164273.1	203	agG/agT	2/24	0.814560649909626	3	FACETS	0.857	0.784	0.932	0.428	0.392	0.466	CLONAL	1	TRUE	1	0.893090179609514	3		458	518	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165655	185165655	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	124	412	0	ENST00000265026.3:c.930G>C	p.Lys310Asn	p.K310N	ENST00000265026	NM_004721.4	310	aaG/aaC	5/14	0.83769284247357	4	FACETS	0.647	0.585	0.712	0.323	0.292	0.356	SUBCLONAL	1	TRUE	2	0.893090179609514	4		412	813	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578464	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	241	937	0	ENST00000269305.4:c.466del	p.Arg156AlafsTer14	p.R156Afs*14	ENST00000269305	NM_001126112.2	156	Cgc/gc	5/11	0.463459001425117	1	FACETS	0.914	0.855	0.974	0.914	0.855	0.974	CLONAL	1	TRUE	0	0.463459001425117	1		937	874	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278779	1278779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576633619	NA	P-0038166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	171	728	0	ENST00000310581.5:c.2263G>A	p.Val755Ile	p.V755I	ENST00000310581	NM_198253.2	755	Gtc/Atc	6/16	0.455088559539176	3	FACETS	0.857	0.788	0.93	0.429	0.394	0.465	CLONAL	1	TRUE	1	0.463459001425117	3		728	1060	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914234	32914234	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	64	522	0	ENST00000380152.3:c.5742C>A	p.Ser1914Arg	p.S1914R	ENST00000380152		1914	agC/agA	11/27	1	2	FACETS	0.43	0.372	0.492	0.43	0.372	0.492	SUBCLONAL	1	TRUE	1	0.463459001425117	2		522	643	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991508	72991508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755878058	NA	P-0038166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	194	827	0	ENST00000268489.5:c.2537G>A	p.Arg846His	p.R846H	ENST00000268489	NM_006885.3	846	cGc/cAc	2/10	1	2	FACETS	0.809	0.748	0.872	0.809	0.748	0.872	CLONAL	1	TRUE	1	0.463459001425117	2		827	1035	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999693	100999693	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	271	1079	0	ENST00000325455.5:c.109C>A	p.Pro37Thr	p.P37T	ENST00000325455	NM_001202474.3	37	Ccg/Acg	1/8	0.463459001425117	1	FACETS	0.843	0.791	0.896	0.843	0.791	0.896	CLONAL	1	TRUE	0	0.463459001425117	1		1079	1066	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760962	59760962	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	218	691	0	ENST00000259008.2:c.3445C>G	p.Leu1149Val	p.L1149V	ENST00000259008	NM_032043.2	1149	Cta/Gta	20/20	1	2	FACETS	0.947	0.881	1	0.947	0.881	1	CLONAL	1	TRUE	1	0.463459001425117	2		691	993	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980411	55980411	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	105	326	0	ENST00000263923.4:c.680T>G	p.Val227Gly	p.V227G	ENST00000263923	NM_002253.2	227	gTt/gGt	6/30	0.463459001425117	1	FACETS	0.811	0.732	0.895	0.811	0.732	0.895	CLONAL	1	TRUE	0	0.463459001425117	1		326	429	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683801	117683801	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	146	458	0	ENST00000368508.3:c.3346G>A	p.Glu1116Lys	p.E1116K	ENST00000368508	NM_002944.2	1116	Gaa/Aaa	21/43	1	2	FACETS	0.899	0.822	0.979	0.899	0.822	0.979	CLONAL	1	TRUE	1	0.463459001425117	2		458	701	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983305	149983305	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs937398843	NA	P-0038166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	191	591	0	ENST00000253339.5:c.2953A>T	p.Ile985Phe	p.I985F	ENST00000253339		985	Att/Ttt	7/7	1	2	FACETS	0.942	0.872	1	0.942	0.872	1	CLONAL	1	TRUE	1	0.463459001425117	2		591	875	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309769	30309769	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	34	580	0	ENST00000307677.4:c.253G>T	p.Ala85Ser	p.A85S	ENST00000307677	NM_138578.1	85	Gca/Tca	2/3	1	2	FACETS	0.218	0.177	0.264	0.218	0.177	0.264	SUBCLONAL	1	TRUE	1	0.463459001425117	2		580	673	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939244	76939244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	37	418	0	ENST00000373344.5:c.1504C>T	p.Pro502Ser	p.P502S	ENST00000373344	NM_000489.3	502	Cct/Tct	9/35	1	1	FACETS	0.228	0.187	0.274	0.228	0.187	0.274	SUBCLONAL	1	TRUE	0	0.463459001425117	1		418	538	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0038172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	901	622	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.490433850591792	6	FACETS	0.946	0.922	0.971			1	CLONAL	5	TRUE	NA	0.490433850591792	6		622	1538	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0038172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	271	647	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.455771163097644	1	FACETS	0.908	0.853	0.963	0.908	0.853	0.963	CLONAL	1	TRUE	0	0.490433850591792	1		647	919	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586470	189586470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147148566	NA	P-0038172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	72	419	0	ENST00000264731.3:c.1094C>T	p.Ser365Leu	p.S365L	ENST00000264731	NM_003722.4	365	tCg/tTg	8/14	1	2	FACETS	0.373	0.325	0.425	0.373	0.325	0.425	SUBCLONAL	1	TRUE	1	0.490433850591792	2		419	787	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038874	12038874	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	150	327	0	ENST00000396373.4:c.1167G>T	p.Met389Ile	p.M389I	ENST00000396373	NM_001987.4	389	atG/atT	7/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.490433850591792	2		327	539	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986531	36986532	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	254	668	0	ENST00000354822.5:c.1157dup	p.Asp386GlufsTer53	p.D386Efs*53	ENST00000354822	NM_001079668.2	386	gac/gaAc	3/3	1	2	FACETS	0.983	0.92	1	0.983	0.92	1	CLONAL	1	TRUE	1	0.490433850591792	2		668	1054	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0038180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	228	491	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.638116895404517	3	FACETS	0.97	0.914	1	0.97	0.914	1	CLONAL	2	TRUE	1	0.638116895404517	3		491	486	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221243	1221243	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1057520606	NA	P-0038180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	638	919	1	ENST00000326873.7:c.766G>T	p.Glu256Ter	p.E256*	ENST00000326873	NM_000455.4	256	Gaa/Taa	6/10	0.638116895404517	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.638116895404517	3		920	844	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477861	140477861	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs397507474	NA	P-0038180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	134	654	0	ENST00000288602.6:c.1447A>G	p.Lys483Glu	p.K483E	ENST00000288602	NM_004333.4	483	Aaa/Gaa	12/18	0.540914999174175	4	FACETS	0.893	0.812	0.979	0.447	0.406	0.49	CLONAL	1	TRUE	2	0.638116895404517	4		654	770	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828186	243828186	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0038180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	195	413	0	ENST00000263826.5:c.173-1G>A		p.X58_splice	ENST00000263826	NM_005465.4	58			0.622216788271905	5	FACETS	0.955	0.889	1	0.637	0.592	0.683	CLONAL	2	TRUE	2	0.638116895404517	5		413	626	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948299	71948299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868794416	NA	P-0038180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	446	1063	0	ENST00000298229.2:c.3011C>T	p.Pro1004Leu	p.P1004L	ENST00000298229	NM_001567.3	1004	cCt/cTt	26/28	0.638116895404517	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.638116895404517	3		1063	896	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135282	30135283	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0038180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	187	517	0	ENST00000331968.5:c.535_535+1delinsTT		p.X179_splice	ENST00000331968	NM_002742.2	179		3/18	0.638116895404517	3	FACETS	0.903	0.845	0.962	0.903	0.845	0.962	CLONAL	2	TRUE	1	0.638116895404517	3		517	428	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211109	36211109	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	689	1060	0	ENST00000222270.7:c.860G>T	p.Arg287Leu	p.R287L	ENST00000222270	NM_014727.1	287	cGt/cTt	3/37	0.563490180058882	5	FACETS	0.951	0.919	0.982	0.951	0.919	0.982	CLONAL	3	TRUE	2	0.638116895404517	5		1060	1482	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661810	227661810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	351	1044	0	ENST00000305123.5:c.1645G>A	p.Glu549Lys	p.E549K	ENST00000305123	NM_005544.2	549	Gag/Aag	1/2	0.540914999174175	4	FACETS	0.951	0.904	1	0.951	0.904	1	CLONAL	2	TRUE	2	0.638116895404517	4		1044	947	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280128	66280128	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	89	407	0	ENST00000273854.3:c.1561A>G	p.Lys521Glu	p.K521E	ENST00000273854	NM_004439.5	521	Aaa/Gaa	7/18	1	2	FACETS	0.933	0.837	1	0.933	0.837	1	CLONAL	1	TRUE	1	0.638116895404517	2		407	299	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579314	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	494	547	0	ENST00000269305.4:c.373dup	p.Thr125AsnfsTer24	p.T125Nfs*24	ENST00000269305	NM_001126112.2	125	acg/aAcg	4/11	0.639205328964605	2	FACETS	0.919	0.888	0.948	0.919	0.888	0.948	CLONAL	2	TRUE	0	0.691230779789113	2		547	778	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202332	138202332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1016313423	NA	P-0038182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	104	637	0	ENST00000237289.4:c.2249G>A	p.Gly750Asp	p.G750D	ENST00000237289	NM_001270507.1	750	gGt/gAt	9/9	0.691230779789113	3	FACETS	0.399	0.356	0.444	0.199	0.178	0.222	SUBCLONAL	1	TRUE	1	0.691230779789113	3		637	1015	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	114	578	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.223867276467	2	FACETS	0.981	0.887	1	0.981	0.887	1	CLONAL	2	TRUE	0	0.223867276467	2		578	519	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555687605	NA	P-0038184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	39	570	0	ENST00000342988.3:c.1610A>G	p.Asp537Gly	p.D537G	ENST00000342988	NM_005359.5	537	gAc/gGc	12/12	0.223867276467	2	FACETS	0.652	0.54	0.778	0.326	0.27	0.389	SUBCLONAL	1	TRUE	0	0.223867276467	2		570	534	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226017	226017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759827541	NA	P-0038184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	27	179	1	ENST00000264932.6:c.476C>T	p.Pro159Leu	p.P159L	ENST00000264932	NM_004168.2	159	cCg/cTg	5/15	0.180948962416727	4	FACETS	1	0.911	1	0.426	0.34	0.523	CLONAL	1	TRUE	1	0.223867276467	4		180	231	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570793	226570793	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749502012	NA	P-0038184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	83	655	0	ENST00000366794.5:c.1103C>T	p.Thr368Met	p.T368M	ENST00000366794	NM_001618.3	368	aCg/aTg	8/23	0.223867276467	3	FACETS	1	0.899	1	0.511	0.45	0.576	CLONAL	1	TRUE	1	0.223867276467	3		655	807	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090575	71090575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	35	588	1	ENST00000318789.4:c.773G>A	p.Cys258Tyr	p.C258Y	ENST00000318789	NM_032682.5	258	tGt/tAt	11/21	0.223867276467	2	FACETS	0.538	0.44	0.649	0.269	0.22	0.325	SUBCLONAL	1	TRUE	0	0.223867276467	2		589	581	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129157	152129157	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	67	859	0	ENST00000206249.3:c.110G>C	p.Arg37Pro	p.R37P	ENST00000206249	NM_000125.3	37	cGg/cCg	1/8	1	2	FACETS	0.758	0.657	0.867	0.758	0.657	0.867	SUBCLONAL	1	TRUE	1	0.223867276467	2		859	790	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0038187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	262	701	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.163608657869586	2	FACETS	0.989	0.93	1	0.989	0.93	1	INDETERMINATE	2	TRUE	0	0.320288780550277	2		701	827	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678036	117678036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764738348	NA	P-0038187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	57	609	0	ENST00000368508.3:c.3897G>A	p.Met1299Ile	p.M1299I	ENST00000368508	NM_002944.2	1299	atG/atA	25/43	0.163608657869586	2	FACETS	0.584	0.501	0.676	0.292	0.25	0.338	INDETERMINATE	1	TRUE	0	0.320288780550277	2		609	609	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248409	59248409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184098204	NA	P-0038187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	105	527	0	ENST00000371222.2:c.334G>A	p.Glu112Lys	p.E112K	ENST00000371222	NM_002228.3	112	Gag/Aag	1/1	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.320288780550277	2		527	580	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874959	151874959	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs942085097	NA	P-0038187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	70	405	0	ENST00000262189.6:c.7579A>C	p.Asn2527His	p.N2527H	ENST00000262189	NM_170606.2	2527	Aat/Cat	38/59	0.28128768737679	1	FACETS	0.829	0.725	0.94	0.829	0.725	0.94	CLONAL	1	TRUE	0	0.320288780550277	1		405	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577499	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0038187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	72	710	0	ENST00000269305.4:c.782_782+1delinsAA		p.X261_splice	ENST00000269305	NM_001126112.2	261		7/11	0.320288780550277	1	FACETS	0.586	0.512	0.666	0.586	0.512	0.666	SUBCLONAL	1	TRUE	0	0.320288780550277	1		710	644	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458114	120458114	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1251821430	NA	P-0038187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	116	865	0	ENST00000256646.2:c.7231G>C	p.Glu2411Gln	p.E2411Q	ENST00000256646	NM_024408.3	2411	Gag/Cag	34/34	1	2	FACETS	0.958	0.864	1	0.958	0.864	1	CLONAL	1	TRUE	1	0.320288780550277	2		865	756	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120496167	120496167	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	77	614	0	ENST00000256646.2:c.2364A>C	p.Lys788Asn	p.K788N	ENST00000256646	NM_024408.3	788	aaA/aaC	14/34	1	2	FACETS	0.668	0.586	0.756	0.668	0.586	0.756	SUBCLONAL	1	TRUE	1	0.320288780550277	2		614	720	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156848940	156848940	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	106	901	0	ENST00000524377.1:c.1832T>C	p.Leu611Pro	p.L611P	ENST00000524377	NM_002529.3	611	cTg/cCg	15/17	1	2	FACETS	0.827	0.741	0.919	0.827	0.741	0.919	CLONAL	1	TRUE	1	0.320288780550277	2		901	800	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32968864	32968864	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	52	388	0	ENST00000380152.3:c.9295A>C	p.Asn3099His	p.N3099H	ENST00000380152		3099	Aat/Cat	25/27	1	2	FACETS	0.731	0.624	0.849	0.731	0.624	0.849	SUBCLONAL	1	TRUE	1	0.320288780550277	2		388	444	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32968925	32968925	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs80359207	NA	P-0038187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	80	427	0	ENST00000380152.3:c.9356T>A	p.Leu3119Ter	p.L3119*	ENST00000380152		3119	tTa/tAa	25/27	1	2	FACETS	0.944	0.833	1	0.944	0.833	1	CLONAL	1	TRUE	1	0.320288780550277	2		427	529	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550522	29550523	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs786204059	NA	P-0038187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	95	440	0	ENST00000356175.3:c.1783_1784del	p.Glu595AsnfsTer14	p.E595Nfs*14	ENST00000356175	NM_000267.3	594	acAGaa/acaa	16/57	0.320288780550277	1	FACETS	0.99	0.885	1	0.99	0.885	1	CLONAL	1	TRUE	0	0.320288780550277	1		440	503	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361105	66361105	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs746890888	NA	P-0038187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	63	384	0	ENST00000273854.3:c.1066+1G>A		p.X356_splice	ENST00000273854	NM_004439.5	356			1	2	FACETS	0.793	0.687	0.908	0.793	0.687	0.908	CLONAL	1	TRUE	1	0.320288780550277	2		384	496	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157519965	157519966	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0038187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	84	780	0	ENST00000346085.5:c.4034_4035del	p.Gln1345LeufsTer113	p.Q1345Lfs*113	ENST00000346085	NM_020732.3	1345	cAG/c	17/20	0.163608657869586	2	FACETS	0.598	0.527	0.674	0.299	0.263	0.337	INDETERMINATE	1	TRUE	0	0.320288780550277	2		780	877	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0038191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	72	794	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.747	0.651	0.85	0.747	0.651	0.85	SUBCLONAL	1	TRUE	1	0.23046088626324	2		794	837	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398280	25398281	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCA	novel	NA	P-0038191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	54	600	0	ENST00000311936.3:c.36_38dup	p.Gly13dup	p.G13dup	ENST00000311936	NM_004985.3	13	ggc/ggTGGc	2/5	1	2	FACETS	0.894	0.764	1	0.894	0.764	1	CLONAL	1	TRUE	1	0.23046088626324	2		600	524	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099988	27099988	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0038191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	72	854	0	ENST00000324856.7:c.3866+1G>T		p.X1289_splice	ENST00000324856	NM_006015.4	1289			1	2	FACETS	0.686	0.598	0.781	0.686	0.598	0.781	SUBCLONAL	1	TRUE	1	0.23046088626324	2		854	911	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591135	67591136	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0038191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	46	456	0	ENST00000274335.5:c.1732_1733del	p.Asp578ProfsTer23	p.D578Pfs*23	ENST00000274335		576	acGAga/acga	12/15	1	2	FACETS	0.784	0.66	0.921	0.784	0.66	0.921	CLONAL	1	TRUE	1	0.23046088626324	2		456	509	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466018	69466018	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	58	771	0	ENST00000227507.2:c.856A>G	p.Thr286Ala	p.T286A	ENST00000227507	NM_053056.2	286	Aca/Gca	5/5	1	2	FACETS	0.644	0.552	0.745	0.644	0.552	0.745	SUBCLONAL	1	TRUE	1	0.23046088626324	2		771	781	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023377	27023387	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCGCCGCCG	CGCCGCCGCCG	-	novel	NA	P-0038191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	53	144	0	ENST00000324856.7:c.485_495del	p.Ala162GlyfsTer234	p.A162Gfs*234	ENST00000324856	NM_006015.4	161	gtCGCCGCCGCCGcg/gtcg	1/20	1	2	FACETS	0.807	0.693	0.929	1	0.97	1	CLONAL	2	TRUE	1	0.23046088626324	2		144	285	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933221	100933222	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	74	593	0	ENST00000325455.5:c.2168dup	p.Arg724GlufsTer11	p.R724Efs*11	ENST00000325455	NM_001202474.3	723	gag/gaAg	4/8	1	2	FACETS	0.841	0.735	0.955	0.841	0.735	0.955	CLONAL	1	TRUE	1	0.23046088626324	2		593	764	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627242	12627242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	74	721	0	ENST00000251849.4:c.1474G>A	p.Val492Ile	p.V492I	ENST00000251849	NM_002880.3	492	Gta/Ata	14/17	1	2	FACETS	0.75	0.655	0.853	0.75	0.655	0.853	SUBCLONAL	1	TRUE	1	0.23046088626324	2		721	856	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591140	67591153	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ACCAATACTTGATG	ACCAATACTTGATG	TCTT	novel	NA	P-0038191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	29	476	1	ENST00000274335.5:c.1733_1745+1delinsTCTT		p.X578_splice	ENST00000274335		578		12/15	1	2	FACETS	0.496	0.397	0.609	0.496	0.397	0.609	SUBCLONAL	1	TRUE	1	0.23046088626324	2		477	507	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371716	55371716	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	51	643	0	ENST00000297316.4:c.406A>G	p.Lys136Glu	p.K136E	ENST00000297316	NM_022454.3	136	Aag/Gag	2/2	1	2	FACETS	0.665	0.564	0.775	0.665	0.564	0.775	SUBCLONAL	1	TRUE	1	0.23046088626324	2		643	666	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405848	157405848	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	156	378	0	ENST00000346085.5:c.2090G>A	p.Ser697Asn	p.S697N	ENST00000346085	NM_020732.3	697	aGc/aAc	6/20	1	2	FACETS	0.784	0.722	0.847	0.784	0.722	0.847	SUBCLONAL	1	TRUE	1	0.77	2		378	517	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	181	399	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.849616383917507	2		399	413	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740665	58740665	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	293	456	0	ENST00000305921.3:c.1570C>T	p.Gln524Ter	p.Q524*	ENST00000305921	NM_003620.3	524	Caa/Taa	6/6	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.849616383917507	2		456	648	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11269472	11269472	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1000321853	NA	P-0038218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	247	462	0	ENST00000361445.4:c.3698A>G	p.Gln1233Arg	p.Q1233R	ENST00000361445	NM_004958.3	1233	cAg/cGg	25/58	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.849616383917507	2		462	532	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031678	36031678	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564099857	NA	P-0038218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	294	728	2	ENST00000358208.4:c.1507C>T	p.Arg503Trp	p.R503W	ENST00000358208		503	Cgg/Tgg	12/12	1	2	FACETS	0.885	0.837	0.934	0.885	0.837	0.934	CLONAL	1	TRUE	1	0.849616383917507	2		730	782	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952138	178952160	+	stop_retained_variant,3_prime_UTR_variant	Silent	DEL	CATGCATTGAACTGAAAAGATAA	CATGCATTGAACTGAAAAGATAA	TTG	novel	NA	P-0038218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	62	184	1	ENST00000263967.3:c.3193_*8delinsTTG		p.*1065*	ENST00000263967	NM_006218.2	1065		21/21	1	2	FACETS	0.591	0.516	0.67	0.591	0.516	0.67	SUBCLONAL	1	TRUE	1	0.849616383917507	2		185	247	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933822	39933838	+	frameshift_variant	Frame_Shift_Del	DEL	CGATGGGATGTGGGGAC	CGATGGGATGTGGGGAC	-	novel	NA	P-0038218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	321	719	0	ENST00000378444.4:c.761_777del	p.Gly254ValfsTer41	p.G254Vfs*41	ENST00000378444	NM_001123385.1	254	gGTCCCCACATCCCATCG/g	4/15	1	2	FACETS	0.997	0.947	1	0.997	0.947	1	CLONAL	1	TRUE	1	0.849616383917507	2		719	758	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0038219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	68	283	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.754	0.663	0.849	1	0.975	1	SUBCLONAL	2	TRUE	1	0.346923582289228	2		283	260	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28611336	28611336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201905189	NA	P-0038219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	64	319	0	ENST00000241453.7:c.1295C>T	p.Thr432Met	p.T432M	ENST00000241453	NM_004119.2	432	aCg/aTg	10/24	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.346923582289228	2		319	280	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216476	108216477	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587782558	NA	P-0038219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	24	166	0	ENST00000278616.4:c.8432dup	p.Ser2812ValfsTer3	p.S2812Vfs*3	ENST00000278616	NM_000051.3	2809	caa/cAaa	58/63	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.346923582289228	2		166	104	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588981	67588981	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	32	214	0	ENST00000274335.5:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000274335		358	Cga/Tga	8/15	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.346923582289228	2		214	134	SUCCESS
ATM	472	MSKCC	GRCh37	11	108183190	108183191	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	26	202	0	ENST00000278616.4:c.5977dup	p.Ser1993LysfsTer2	p.S1993Kfs*2	ENST00000278616	NM_000051.3	1991	gaa/gAaa	40/63	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.346923582289228	2		202	131	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962543	100962544	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	115	362	0	ENST00000325455.5:c.1853dup	p.Asn618LysfsTer8	p.N618Kfs*8	ENST00000325455	NM_001202474.3	618	aac/aaAc	3/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.346923582289228	2		362	507	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156540	55156540	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775205485	NA	P-0038219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	138	437	1	ENST00000257290.5:c.2941C>T	p.Arg981Cys	p.R981C	ENST00000257290	NM_006206.4	981	Cgt/Tgt	22/23	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.346923582289228	2		438	580	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106036	27106037	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0038219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	116	448	0	ENST00000324856.7:c.5648dup	p.Thr1884AsnfsTer17	p.T1884Nfs*17	ENST00000324856	NM_006015.4	1883	aca/aCca	20/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.346923582289228	2		448	555	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106746	27106746	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	196	541	0	ENST00000324856.7:c.6358del	p.Glu2120LysfsTer15	p.E2120Kfs*15	ENST00000324856	NM_006015.4	2119	ttG/tt	20/20	1	2	FACETS	0.75	0.696	0.806	1	0.991	1	SUBCLONAL	2	TRUE	1	0.346923582289228	2		541	753	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11018787	11018787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	265	691	0	ENST00000327064.4:c.419G>A	p.Arg140Gln	p.R140Q	ENST00000327064	NM_199141.1	140	cGg/cAg	3/16	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.346923582289228	2		691	1196	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211853	36211853	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs527331134	NA	P-0038219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	276	768	1	ENST00000222270.7:c.1604G>A	p.Arg535His	p.R535H	ENST00000222270	NM_014727.1	535	cGc/cAc	3/37	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.346923582289228	2		769	1196	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665078	138665078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776277339	NA	P-0038219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	98	192	0	ENST00000330315.3:c.487G>A	p.Gly163Ser	p.G163S	ENST00000330315	NM_023067.3	163	Ggc/Agc	1/1	1	2	FACETS	0.812	0.731	0.896	1	0.985	1	CLONAL	2	TRUE	1	0.346923582289228	2		192	348	SUCCESS
ATR	545	MSKCC	GRCh37	3	142185363	142185363	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	34	213	0	ENST00000350721.4:c.6700A>T	p.Ser2234Cys	p.S2234C	ENST00000350721	NM_001184.3	2234	Agt/Tgt	40/47	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.346923582289228	2		213	161	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430434	181430434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	254	635	1	ENST00000325404.1:c.286C>T	p.Arg96Trp	p.R96W	ENST00000325404	NM_003106.3	96	Cgg/Tgg	1/1	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.346923582289228	2		636	1080	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0038220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	149	220	0				ENST00000310581	NM_198253.2	-/1132			0.413531479946516	0	FACETS	0.703	0.645	0.764			1	SUBCLONAL	1	FALSE	0	0.413531479946516	0		220	601	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0038220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1182	329	805	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	0.205672049117266	3	FACETS	1	0.991	1	0.635	0.599	0.673	INDETERMINATE	1	FALSE	1	0.413531479946516	3		805	1511	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0038220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	139	482	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.413531479946516	0	FACETS	0.499	0.454	0.546			1	SUBCLONAL	1	FALSE	0	0.413531479946516	0		482	790	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872219	45872219	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	118	758	0	ENST00000391945.4:c.215A>G	p.Tyr72Cys	p.Y72C	ENST00000391945	NM_000400.3	72	tAc/tGc	4/23	0.413531479946516	1	FACETS	0.461	0.415	0.51	0.461	0.415	0.51	SUBCLONAL	1	FALSE	0	0.413531479946516	1		758	981	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843447	3843447	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783461	NA	P-0038220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	138	484	1	ENST00000262367.5:c.1156C>T	p.Arg386Ter	p.R386*	ENST00000262367	NM_004380.2	386	Cga/Tga	4/31	0.413531479946516	0	FACETS	0.491	0.446	0.537			1	SUBCLONAL	1	FALSE	0	0.413531479946516	0		485	798	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974679	21974679	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs864622636	NA	P-0038220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	119	501	0	ENST00000304494.5:c.148C>T	p.Gln50Ter	p.Q50*	ENST00000304494	NM_000077.4	50	Cag/Tag	1/3	0.413531479946516	1	FACETS	0.878	0.796	0.963	0.878	0.796	0.963	CLONAL	1	FALSE	0	0.413531479946516	1		501	520	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023796	27023796	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	120	426	0	ENST00000324856.7:c.902C>A	p.Ser301Ter	p.S301*	ENST00000324856	NM_006015.4	301	tCg/tAg	1/20	0.413531479946516	0	FACETS	0.506	0.457	0.557			1	SUBCLONAL	1	FALSE	0	0.413531479946516	0		426	673	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690312	117690312	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	111	495	0	ENST00000369458.3:c.817C>G	p.Leu273Val	p.L273V	ENST00000369458	NM_024626.3	273	Ctg/Gtg	5/6	0.413531479946516	0	FACETS	0.477	0.429	0.527			1	SUBCLONAL	1	FALSE	0	0.413531479946516	0		495	660	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204901	94204901	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	63	382	0	ENST00000323929.3:c.684C>G	p.Phe228Leu	p.F228L	ENST00000323929	NM_005591.3	228	ttC/ttG	8/20	0.205672049117266	3	FACETS	0.973	0.845	1	0.486	0.422	0.555	INDETERMINATE	1	FALSE	1	0.413531479946516	3		382	378	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006384	12006384	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	37	442	0	ENST00000396373.4:c.352C>G	p.Gln118Glu	p.Q118E	ENST00000396373	NM_001987.4	118	Cag/Gag	4/8	0.413531479946516	0	FACETS	0.241	0.199	0.289			1	SUBCLONAL	1	FALSE	0	0.413531479946516	0		442	435	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480590	50480590	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	107	515	0	ENST00000394963.4:c.460G>A	p.Glu154Lys	p.E154K	ENST00000394963	NM_003076.4	154	Gaa/Aaa	4/13	0.413531479946516	0	FACETS	0.492	0.442	0.545			1	SUBCLONAL	1	FALSE	0	0.413531479946516	0		515	617	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943626	9943626	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	78	594	0	ENST00000330684.3:c.1315T>G	p.Phe439Val	p.F439V	ENST00000330684	NM_001134407.1	439	Ttc/Gtc	5/13	0.413531479946516	0	FACETS	0.248	0.217	0.281			1	SUBCLONAL	1	FALSE	0	0.413531479946516	0		594	892	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991398	72991398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761279495	NA	P-0038220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	228	807	1	ENST00000268489.5:c.2647G>A	p.Asp883Asn	p.D883N	ENST00000268489	NM_006885.3	883	Gac/Aac	2/10	0.413531479946516	0	FACETS	0.557	0.519	0.598			1	SUBCLONAL	1	FALSE	0	0.413531479946516	0		808	1160	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578218	7578218	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1060501198	NA	P-0038220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	198	776	0	ENST00000269305.4:c.631A>C	p.Thr211Pro	p.T211P	ENST00000269305	NM_001126112.2	211	Act/Cct	6/11	0.413531479946516	1	FACETS	0.934	0.867	1	0.934	0.867	1	CLONAL	1	FALSE	0	0.413531479946516	1		776	813	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678001	58678001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	63	186	0	ENST00000305921.3:c.226C>T	p.Arg76Cys	p.R76C	ENST00000305921	NM_003620.3	76	Cgc/Tgc	1/6	0.413531479946516	0	FACETS	0.667	0.582	0.756			1	SUBCLONAL	1	FALSE	0	0.413531479946516	0		186	268	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129635	11129635	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	211	642	0	ENST00000358026.2:c.2441C>A	p.Thr814Lys	p.T814K	ENST00000358026	NM_001128849.1	814	aCg/aAg	17/36	0.413531479946516	0	FACETS	0.588	0.546	0.632			1	SUBCLONAL	1	FALSE	0	0.413531479946516	0		642	1017	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719823	61719823	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	157	571	0	ENST00000401558.2:c.1445A>G	p.Asn482Ser	p.N482S	ENST00000401558	NM_003400.3	482	aAt/aGt	14/25	0.189795380963373	2	FACETS	1	0.988	1	0.714	0.658	0.771	INDETERMINATE	1	FALSE	0	0.413531479946516	2		571	532	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21304089	21304089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	155	665	0	ENST00000354336.3:c.868C>T	p.His290Tyr	p.H290Y	ENST00000354336	NM_005207.3	290	Cac/Tac	3/3	0.413531479946516	1	FACETS	0.553	0.505	0.603	0.553	0.505	0.603	SUBCLONAL	1	FALSE	0	0.413531479946516	1		665	1075	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221673	22221673	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	57	143	0	ENST00000215832.6:c.58G>A	p.Asp20Asn	p.D20N	ENST00000215832	NM_002745.4	20	Gac/Aac	1/9	0.413531479946516	1	FACETS	0.503	0.432	0.579	0.503	0.432	0.579	SUBCLONAL	1	FALSE	0	0.413531479946516	1		143	435	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643777	52643777	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	106	577	0	ENST00000394830.3:c.2119G>A	p.Glu707Lys	p.E707K	ENST00000394830	NM_018313.4	707	Gaa/Aaa	17/30	0.413531479946516	0	FACETS	0.549	0.493	0.607			1	SUBCLONAL	1	FALSE	0	0.413531479946516	0		577	548	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55524186	55524186	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	148	516	0	ENST00000288135.5:c.5G>A	p.Arg2Lys	p.R2K	ENST00000288135	NM_000222.2	2	aGa/aAa	1/21	0.413531479946516	1	FACETS	0.887	0.813	0.964	0.887	0.813	0.964	CLONAL	1	FALSE	0	0.413531479946516	1		516	640	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527514	157527514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1322306509	NA	P-0038220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	57	525	0	ENST00000346085.5:c.5239G>A	p.Asp1747Asn	p.D1747N	ENST00000346085	NM_020732.3	1747	Gat/Aat	20/20	0.413531479946516	1	FACETS	0.329	0.282	0.381	0.329	0.282	0.381	SUBCLONAL	1	FALSE	0	0.413531479946516	1		525	664	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519958	NA	P-0038220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	204	788	0	ENST00000481739.1:c.1280C>A	p.Ser427Tyr	p.S427Y	ENST00000481739	NM_002957.4	427	tCc/tAc	10/10	0.413531479946516	0	FACETS	0.547	0.507	0.589			1	SUBCLONAL	1	FALSE	0	0.413531479946516	0		788	1058	SUCCESS
AR	367	MSKCC	GRCh37	X	66905872	66905872	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137852569	NA	P-0038223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	11	270	0	ENST00000374690.3:c.1789G>A	p.Ala597Thr	p.A597T	ENST00000374690	NM_000044.3	597	Gcc/Acc	3/8	0.306881574849919	1	FACETS	0.114	0.078	0.158	0.114	0.078	0.158	INDETERMINATE	1	TRUE	0	0.667516602222614	1		270	193	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082901	16082901	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1270397686	NA	P-0038223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	43	189	0	ENST00000281043.3:c.715C>A	p.Pro239Thr	p.P239T	ENST00000281043	NM_005378.4	239	Cca/Aca	2/3	1	2	FACETS	0.563	0.475	0.658	0.563	0.475	0.658	SUBCLONAL	1	TRUE	1	0.667516602222614	2		189	229	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981492	70981492	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	54	841	1	ENST00000276594.2:c.604C>A	p.Leu202Met	p.L202M	ENST00000276594	NM_024504.3	202	Ctg/Atg	2/8	1	2	FACETS	0.172	0.146	0.2	0.172	0.146	0.2	SUBCLONAL	1	TRUE	1	0.667516602222614	2		842	942	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0038224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	203	647	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.498688030659654	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.498688030659654	1		647	489	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0038224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	57	258	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.39068332184258	1	FACETS	0.784	0.681	0.892	0.784	0.681	0.892	SUBCLONAL	1	TRUE	0	0.498688030659654	1		258	219	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517201	NA	P-0038224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	10	555	0	ENST00000263967.3:c.1637A>C	p.Gln546Pro	p.Q546P	ENST00000263967	NM_006218.2	546	cAg/cCg	10/21	1	2	FACETS	0.082	0.055	0.117	0.082	0.055	0.117	SUBCLONAL	1	TRUE	1	0.498688030659654	2		555	488	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940222	49940222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	58	738	2	ENST00000296474.3:c.821G>A	p.Ser274Asn	p.S274N	ENST00000296474	NM_002447.2	274	aGt/aAt	1/20	1	2	FACETS	0.356	0.305	0.412	0.356	0.305	0.412	SUBCLONAL	1	TRUE	1	0.498688030659654	2		740	653	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0038225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	617	523	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.478152244702181	6	FACETS	0.949	0.923	0.974	1	0.996	1	CLONAL	6	TRUE	1	0.478152244702181	6		523	887	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0038225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	52	659	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.474	0.404	0.55	0.474	0.404	0.55	SUBCLONAL	1	TRUE	1	0.478152244702181	2		659	459	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934194	48934194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	254	339	0	ENST00000267163.4:c.649C>T	p.Gln217Ter	p.Q217*	ENST00000267163	NM_000321.2	217	Cag/Tag	7/27	0.478152244702181	2	FACETS	0.91	0.87	0.95	1	0.994	1	CLONAL	3	TRUE	0	0.478152244702181	2		339	389	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348978	70348978	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	175	541	1	ENST00000374080.3:c.3490G>T	p.Asp1164Tyr	p.D1164Y	ENST00000374080		1164	Gac/Tac	25/45	0.415286848859764	0	FACETS	0.55	0.515	0.585			1	SUBCLONAL	2	TRUE	0	0.478152244702181	0		542	347	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50481248	50481248	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	44	380	0	ENST00000394963.4:c.634G>C	p.Glu212Gln	p.E212Q	ENST00000394963	NM_003076.4	212	Gaa/Caa	5/13	0.11069019510869	6	FACETS	0.822	0.69	0.968	0.274	0.23	0.323	INDETERMINATE	1	TRUE	3	0.478152244702181	6		380	438	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029327	14029327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1475291650	NA	P-0038225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	111	286	0	ENST00000311895.7:c.1538G>A	p.Gly513Glu	p.G513E	ENST00000311895	NM_005236.2	513	gGa/gAa	8/11	1	2	FACETS	0.838	0.766	0.912	1	0.988	1	CLONAL	2	TRUE	1	0.478152244702181	2		286	277	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627298	37627298	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	209	387	0	ENST00000447079.4:c.1213G>A	p.Glu405Lys	p.E405K	ENST00000447079	NM_015083.1	405	Gaa/Aaa	2/14	0.124089041526069	4	FACETS	0.911	0.855	0.967	1	0.991	1	INDETERMINATE	3	TRUE	2	0.478152244702181	4		387	473	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137409	202137409	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	106	292	0	ENST00000358485.4:c.637G>A	p.Glu213Lys	p.E213K	ENST00000358485	NM_001080125.1	213	Gaa/Aaa	4/9	0.124089041526069	4	FACETS	1	0.917	1	1	0.917	1	INDETERMINATE	2	TRUE	2	0.478152244702181	4		292	324	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36014517	36014517	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	236	498	0	ENST00000358208.4:c.290C>G	p.Ser97Cys	p.S97C	ENST00000358208		97	tCt/tGt	3/12	1	2	FACETS	0.975	0.92	1	1	0.995	1	CLONAL	2	TRUE	1	0.478152244702181	2		498	506	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873000	134873000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	27	418	0	ENST00000398015.3:c.1304C>T	p.Ser435Phe	p.S435F	ENST00000398015	NM_004441.4	435	tCc/tTc	6/16	NA	2	FACETS	0.235	0.186	0.291			1	INDETERMINATE	1	TRUE	NA	0.478152244702181	2		418	481	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509199	106509199	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	149	566	0	ENST00000359195.3:c.1193G>T	p.Arg398Ile	p.R398I	ENST00000359195	NM_002649.2	398	aGa/aTa	2/11	1	2	FACETS	0.783	0.723	0.844	1	0.99	1	SUBCLONAL	2	TRUE	1	0.478152244702181	2		566	398	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339953	70339953	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	20	422	0	ENST00000374080.3:c.486G>A	p.Met162Ile	p.M162I	ENST00000374080		162	atG/atA	4/45	0.415286848859764	0	FACETS	0.134	0.102	0.171			1	SUBCLONAL	1	TRUE	0	0.478152244702181	0		422	327	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038269-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	111	578	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.479383648130375	3	FACETS	0.944	0.861	1	0.944	0.861	1	CLONAL	2	TRUE	1	0.479383648130375	3		578	304	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499619	18499619	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038269-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	67	368	0	ENST00000266497.5:c.1474C>A	p.Gln492Lys	p.Q492K	ENST00000266497		492	Cag/Aag	10/31	0.46041190408831	2	FACETS	0.868	0.76	0.983	0.434	0.38	0.492	CLONAL	1	TRUE	0	0.479383648130375	2		368	322	SUCCESS
APC	324	MSKCC	GRCh37	5	112175147	112175147	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038269-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	42	156	0	ENST00000257430.4:c.3856G>A	p.Glu1286Lys	p.E1286K	ENST00000257430	NM_000038.5	1286	Gaa/Aaa	16/16	0.479383648130375	4	FACETS	1	0.877	1	0.525	0.441	0.616	CLONAL	1	TRUE	2	0.479383648130375	4		156	247	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335624	81335624	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038269-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	71	319	0	ENST00000222390.5:c.1736T>A	p.Leu579Gln	p.L579Q	ENST00000222390	NM_000601.4	579	cTg/cAg	15/18	0.479383648130375	3	FACETS	1	0.955	1			1	CLONAL	1	TRUE	NA	0.479383648130375	3		319	310	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941696	48941696	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	18	125	0	ENST00000267163.4:c.1010del	p.Leu337TrpfsTer12	p.L337Wfs*12	ENST00000267163	NM_000321.2	336	Ttt/tt	10/27	0.171706640088513	3	FACETS	1	0.841	1	0.574	0.436	0.735	CLONAL	1	TRUE	1	0.25	3		125	141	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257210	16257210	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	20	300	0	ENST00000375759.3:c.4475C>G	p.Ser1492Cys	p.S1492C	ENST00000375759	NM_015001.2	1492	tCc/tGc	11/15	0.171706640088513	3	FACETS	0.552	0.422	0.705	0.276	0.211	0.353	SUBCLONAL	1	TRUE	1	0.25	3		300	326	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797278	42797278	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs968289754	NA	P-0038277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	66	498	0	ENST00000575354.2:c.3640C>T	p.Arg1214Ter	p.R1214*	ENST00000575354	NM_015125.3	1214	Cga/Tga	15/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.28	2		498	396	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874012	151874013	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	39	248	0	ENST00000262189.6:c.8525dup	p.Asn2842LysfsTer2	p.N2842Kfs*2	ENST00000262189	NM_170606.2	2842	aat/aaAt	38/59	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.28	2		248	195	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451459	70451459	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	85	333	0	ENST00000373644.4:c.6299A>T	p.Glu2100Val	p.E2100V	ENST00000373644	NM_030625.2	2100	gAa/gTa	12/12	1	2	FACETS	0.903	0.806	1	1	0.984	1	CLONAL	2	TRUE	1	0.28	2		333	336	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871112	12871112	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	35	180	0	ENST00000228872.4:c.341del	p.Pro114ArgfsTer5	p.P114Rfs*5	ENST00000228872	NM_004064.3	113	cgC/cg	1/3	0.0558116250833827	4	FACETS	1	0.939	1	0.675	0.557	0.806	INDETERMINATE	1	TRUE	2	0.28	4		180	237	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845361	151845361	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	77	361	0	ENST00000262189.6:c.13651G>C	p.Gly4551Arg	p.G4551R	ENST00000262189	NM_170606.2	4551	Ggt/Cgt	52/59	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.28	2		361	386	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696644	47696644	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519964	NA	P-0038278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	32	244	0	ENST00000347630.2:c.304T>G	p.Phe102Val	p.F102V	ENST00000347630	NM_001007230.1	102	Ttc/Gtc	5/11	1	2	FACETS	0.782	0.634	0.948	0.782	0.634	0.948	CLONAL	1	TRUE	1	0.19	2		244	431	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	164	270	0	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	0.95	0.884	1	0.95	0.884	1	CLONAL	1	TRUE	1	0.921073659481109	2		270	375	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0038280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	260	396	0	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	1	2	FACETS	0.865	0.815	0.914	0.865	0.815	0.914	CLONAL	1	TRUE	1	0.921073659481109	2		396	653	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308382	15308383	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs749829137	NA	P-0038280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	213	450	0	ENST00000263388.2:c.125dup	p.Cys43LeufsTer32	p.C43Lfs*32	ENST00000263388	NM_000435.2	42	cct/ccCt	2/33	1	2	FACETS	0.727	0.679	0.776	0.727	0.679	0.776	SUBCLONAL	1	TRUE	1	0.921073659481109	2		450	636	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532555	63532555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881401	NA	P-0038280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	311	466	0	ENST00000307078.5:c.2024G>A	p.Arg675His	p.R675H	ENST00000307078	NM_004655.3	675	cGt/cAt	8/11	1	2	FACETS	0.977	0.929	1	0.977	0.929	1	CLONAL	1	TRUE	1	0.921073659481109	2		466	691	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467855	99467856	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0038280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	144	199	0	ENST00000268035.6:c.2732_2733dup	p.Gly912LeufsTer26	p.G912Lfs*26	ENST00000268035	NM_000875.3	908	-/TC	13/21	1	2	FACETS	0.917	0.849	0.986	0.917	0.849	0.986	CLONAL	1	TRUE	1	0.921073659481109	2		199	341	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870921	12870922	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0038280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	131	189	0	ENST00000228872.4:c.151_152del	p.Asp51HisfsTer73	p.D51Hfs*73	ENST00000228872	NM_004064.3	50	AGa/a	1/3	0.921073659481109	1	FACETS	0.941	0.896	0.983	0.941	0.896	0.983	CLONAL	1	TRUE	0	0.921073659481109	1		189	163	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78820340	78820340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1284870590	NA	P-0038280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	300	473	0	ENST00000306801.3:c.1280G>A	p.Arg427Gln	p.R427Q	ENST00000306801	NM_020761.2	427	cGa/cAa	11/34	1	2	FACETS	0.948	0.9	0.997	0.948	0.9	0.997	CLONAL	1	TRUE	1	0.921073659481109	2		473	687	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433482	138433482	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	150	285	0	ENST00000289153.2:c.1130del	p.Asn377MetfsTer35	p.N377Mfs*35	ENST00000289153	NM_006219.2	377	aAt/at	7/22	1	2	FACETS	0.873	0.808	0.939	0.873	0.808	0.939	CLONAL	1	TRUE	1	0.921073659481109	2		285	373	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107136	27107137	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0038280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	436	319	0	ENST00000324856.7:c.6749_6750del	p.Glu2250ValfsTer27	p.E2250Vfs*27	ENST00000324856	NM_006015.4	2249	tcAGag/tcag	20/20	NA	2	FACETS	0.986	0.968	1			1	INDETERMINATE	2	TRUE	NA	0.921073659481109	2		319	480	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439770	51439772	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0038280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	354	219	0	ENST00000262662.1:c.338_340del	p.Glu113del	p.E113del	ENST00000262662		112	aAAGaa/aaa	4/4	0.921073659481109	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.921073659481109	2		219	382	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570833	226570833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753458085	NA	P-0038280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	199	275	0	ENST00000366794.5:c.1063C>T	p.Arg355Cys	p.R355C	ENST00000366794	NM_001618.3	355	Cgt/Tgt	8/23	1	2	FACETS	0.898	0.841	0.957	0.898	0.841	0.957	CLONAL	1	TRUE	1	0.921073659481109	2		275	481	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878068	48878069	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	148	175	0	ENST00000267163.4:c.25dup	p.Thr9AsnfsTer22	p.T9Nfs*22	ENST00000267163	NM_000321.2	7	cga/cgAa	1/27	0.908810649923795	1	FACETS	0.958	0.916	0.996	0.958	0.916	0.996	CLONAL	1	TRUE	0	0.921073659481109	1		175	181	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434588	49434589	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0038280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	285	472	0	ENST00000301067.7:c.6964_6965del	p.Lys2322AspfsTer3	p.K2322Dfs*3	ENST00000301067	NM_003482.3	2322	AAg/g	31/54	1	2	FACETS	0.959	0.909	1	0.959	0.909	1	CLONAL	1	TRUE	1	0.921073659481109	2		472	645	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353842	68353842	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	137	235	0	ENST00000487270.1:c.677G>A	p.Gly226Asp	p.G226D	ENST00000487270	NM_133509.3	226	gGc/gAc	7/11	0.565651696089247	4	FACETS	1	0.974	1	0.386	0.353	0.42	CLONAL	1	TRUE	1	0.921073659481109	4		235	493	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570149	95570150	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0038280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	120	210	0	ENST00000393063.1:c.3583_3584del	p.Asp1195LeufsTer39	p.D1195Lfs*39	ENST00000393063	NM_030621.3	1195	GAc/c	22/28	0.565651696089247	4	FACETS	1	0.976	1	0.406	0.369	0.444	CLONAL	1	TRUE	1	0.921073659481109	4		210	411	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655477	67655477	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	141	283	0	ENST00000264010.4:c.1340C>T	p.Ala447Val	p.A447V	ENST00000264010	NM_006565.3	447	gCc/gTc	7/12	1	2	FACETS	0.762	0.701	0.824	0.762	0.701	0.824	SUBCLONAL	1	TRUE	1	0.921073659481109	2		283	402	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585422	29585422	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555618515	NA	P-0038280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	54	291	0	ENST00000356175.3:c.4171A>G	p.Arg1391Gly	p.R1391G	ENST00000356175	NM_000267.3	1391	Aga/Gga	31/57	1	2	FACETS	0.208	0.177	0.241	0.208	0.177	0.241	SUBCLONAL	1	TRUE	1	0.921073659481109	2		291	565	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40879755	40879755	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	207	316	0	ENST00000428826.2:c.144G>T	p.Lys48Asn	p.K48N	ENST00000428826		48	aaG/aaT	4/21	1	2	FACETS	0.958	0.9	1	0.958	0.9	1	CLONAL	1	TRUE	1	0.921073659481109	2		316	469	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371844	45371844	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	138	194	0	ENST00000262160.6:c.1147A>G	p.Lys383Glu	p.K383E	ENST00000262160	NM_005901.5	383	Aag/Gag	10/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.921073659481109	2		194	286	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226611	1226611	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555740268	NA	P-0038280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	183	331	0	ENST00000326873.7:c.1267A>G	p.Lys423Glu	p.K423E	ENST00000326873	NM_000455.4	423	Aag/Gag	9/10	1	2	FACETS	0.969	0.906	1	0.969	0.906	1	CLONAL	1	TRUE	1	0.921073659481109	2		331	410	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276648	15276648	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	61	476	0	ENST00000263388.2:c.5617C>A	p.Arg1873Ser	p.R1873S	ENST00000263388	NM_000435.2	1873	Cgc/Agc	30/33	1	2	FACETS	0.215	0.185	0.248	0.215	0.185	0.248	SUBCLONAL	1	TRUE	1	0.921073659481109	2		476	615	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30733051	30733053	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0038280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	177	262	0	ENST00000295754.5:c.1667_1669del	p.Lys556del	p.K556del	ENST00000295754	NM_003242.5	555	gAGAag/gag	7/7	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.921073659481109	2		262	383	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99812440	99812440	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	45	266	0	ENST00000280892.6:c.229C>T	p.Gln77Ter	p.Q77*	ENST00000280892	NM_001130678.1	77	Caa/Taa	3/7	1	2	FACETS	0.31	0.262	0.363	0.31	0.262	0.363	SUBCLONAL	1	TRUE	1	0.921073659481109	2		266	315	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681031	117681031	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	161	254	0	ENST00000368508.3:c.3589T>C	p.Tyr1197His	p.Y1197H	ENST00000368508	NM_002944.2	1197	Tat/Cat	23/43	0.921073659481109	3	FACETS	1	0.965	1	0.536	0.496	0.578	CLONAL	1	TRUE	1	0.921073659481109	3		254	476	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911423	39911424	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0038280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	230	355	0	ENST00000378444.4:c.5206_5207del	p.Leu1736AlafsTer12	p.L1736Afs*12	ENST00000378444	NM_001123385.1	1736	CTg/g	15/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.921073659481109	2		355	464	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0038280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	38	339	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.325	0.269	0.388	0.325	0.269	0.388	SUBCLONAL	1	TRUE	1	0.624369638172119	2		339	374	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0038280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	127	396	0	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	1	2	FACETS	0.997	0.912	1	0.997	0.912	1	CLONAL	1	TRUE	1	0.624369638172119	2		396	408	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308382	15308383	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs749829137	NA	P-0038280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	100	450	0	ENST00000263388.2:c.125dup	p.Cys43LeufsTer32	p.C43Lfs*32	ENST00000263388	NM_000435.2	42	cct/ccCt	2/33	1	2	FACETS	0.735	0.66	0.813	0.735	0.66	0.813	SUBCLONAL	1	TRUE	1	0.624369638172119	2		450	436	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532555	63532555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881401	NA	P-0038280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	136	466	0	ENST00000307078.5:c.2024G>A	p.Arg675His	p.R675H	ENST00000307078	NM_004655.3	675	cGt/cAt	8/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.624369638172119	2		466	410	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870921	12870922	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0038280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	58	189	0	ENST00000228872.4:c.151_152del	p.Asp51HisfsTer73	p.D51Hfs*73	ENST00000228872	NM_004064.3	50	AGa/a	1/3	NA	2	FACETS	1	0.952	1			1	INDETERMINATE	1	TRUE	NA	0.624369638172119	2		189	158	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78820340	78820340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1284870590	NA	P-0038280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	172	473	0	ENST00000306801.3:c.1280G>A	p.Arg427Gln	p.R427Q	ENST00000306801	NM_020761.2	427	cGa/cAa	11/34	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.624369638172119	2		473	506	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433482	138433482	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	98	285	0	ENST00000289153.2:c.1130del	p.Asn377MetfsTer35	p.N377Mfs*35	ENST00000289153	NM_006219.2	377	aAt/at	7/22	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.624369638172119	2		285	303	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107136	27107137	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0038280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	248	319	0	ENST00000324856.7:c.6749_6750del	p.Glu2250ValfsTer27	p.E2250Vfs*27	ENST00000324856	NM_006015.4	2249	tcAGag/tcag	20/20	0.624369638172119	2	FACETS	0.948	0.902	0.993	0.948	0.902	0.993	CLONAL	2	TRUE	0	0.624369638172119	2		319	419	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439770	51439772	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0038280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	227	219	0	ENST00000262662.1:c.338_340del	p.Glu113del	p.E113del	ENST00000262662		112	aAAGaa/aaa	4/4	0.624369638172119	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.624369638172119	2		219	328	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570833	226570833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753458085	NA	P-0038280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	84	275	0	ENST00000366794.5:c.1063C>T	p.Arg355Cys	p.R355C	ENST00000366794	NM_001618.3	355	Cgt/Tgt	8/23	1	2	FACETS	0.758	0.675	0.846	0.758	0.675	0.846	SUBCLONAL	1	TRUE	1	0.624369638172119	2		275	355	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878068	48878069	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	75	175	0	ENST00000267163.4:c.25dup	p.Thr9AsnfsTer22	p.T9Nfs*22	ENST00000267163	NM_000321.2	7	cga/cgAa	1/27	0.624369638172119	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	0	0.624369638172119	1		175	164	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434588	49434589	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0038280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	130	472	0	ENST00000301067.7:c.6964_6965del	p.Lys2322AspfsTer3	p.K2322Dfs*3	ENST00000301067	NM_003482.3	2322	AAg/g	31/54	1	2	FACETS	0.894	0.816	0.974	0.894	0.816	0.974	CLONAL	1	TRUE	1	0.624369638172119	2		472	466	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353842	68353842	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	79	235	0	ENST00000487270.1:c.677G>A	p.Gly226Asp	p.G226D	ENST00000487270	NM_133509.3	226	gGc/gAc	7/11	0.624369638172119	3	FACETS	0.933	0.826	1	0.466	0.413	0.523	CLONAL	1	TRUE	1	0.624369638172119	3		235	356	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570149	95570150	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0038280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	51	210	0	ENST00000393063.1:c.3583_3584del	p.Asp1195LeufsTer39	p.D1195Lfs*39	ENST00000393063	NM_030621.3	1195	GAc/c	22/28	0.624369638172119	3	FACETS	0.777	0.665	0.897	0.388	0.332	0.449	SUBCLONAL	1	TRUE	1	0.624369638172119	3		210	276	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40879755	40879755	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	126	316	0	ENST00000428826.2:c.144G>T	p.Lys48Asn	p.K48N	ENST00000428826		48	aaG/aaT	4/21	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.624369638172119	2		316	398	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371844	45371844	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	76	194	0	ENST00000262160.6:c.1147A>G	p.Lys383Glu	p.K383E	ENST00000262160	NM_005901.5	383	Aag/Gag	10/11	1	2	FACETS	0.986	0.877	1	0.986	0.877	1	CLONAL	1	TRUE	1	0.624369638172119	2		194	247	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226611	1226611	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555740268	NA	P-0038280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	78	331	0	ENST00000326873.7:c.1267A>G	p.Lys423Glu	p.K423E	ENST00000326873	NM_000455.4	423	Aag/Gag	9/10	1	2	FACETS	0.874	0.776	0.976	0.874	0.776	0.976	CLONAL	1	TRUE	1	0.624369638172119	2		331	286	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30733051	30733053	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0038280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	83	262	0	ENST00000295754.5:c.1667_1669del	p.Lys556del	p.K556del	ENST00000295754	NM_003242.5	555	gAGAag/gag	7/7	1	2	FACETS	0.883	0.788	0.983	0.883	0.788	0.983	CLONAL	1	TRUE	1	0.624369638172119	2		262	301	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681031	117681031	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	96	254	0	ENST00000368508.3:c.3589T>C	p.Tyr1197His	p.Y1197H	ENST00000368508	NM_002944.2	1197	Tat/Cat	23/43	0.624369638172119	3	FACETS	1	0.94	1	0.534	0.479	0.591	CLONAL	1	TRUE	1	0.624369638172119	3		254	378	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911423	39911424	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0038280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	132	355	0	ENST00000378444.4:c.5206_5207del	p.Leu1736AlafsTer12	p.L1736Afs*12	ENST00000378444	NM_001123385.1	1736	CTg/g	15/15	0.341620998607214	1	FACETS	0.78	0.716	0.845	0.78	0.716	0.845	INDETERMINATE	1	TRUE	0	0.624369638172119	1		355	373	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736320	243736320	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	24	282	0	ENST00000263826.5:c.727T>C	p.Phe243Leu	p.F243L	ENST00000263826	NM_005465.4	243	Ttc/Ctc	8/13	1	2	FACETS	0.2	0.156	0.25	0.2	0.156	0.25	SUBCLONAL	1	TRUE	1	0.624369638172119	2		282	385	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954698	17954698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs992942163	NA	P-0038280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	107	449	0	ENST00000458235.1:c.196G>A	p.Val66Met	p.V66M	ENST00000458235	NM_000215.3	66	Gtg/Atg	3/24	1	2	FACETS	0.683	0.615	0.754	0.683	0.615	0.754	SUBCLONAL	1	TRUE	1	0.624369638172119	2		449	502	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	128	578	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.706523051735844	3	FACETS	0.872	0.805	0.94	0.872	0.805	0.94	CLONAL	2	TRUE	1	0.706523051735844	3		578	281	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	110	276	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.706523051735844	2		276	300	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466027	69466035	+	inframe_deletion	In_Frame_Del	DEL	GACGTGCGG	GACGTGCGG	-	novel	NA	P-0038281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	45	522	0	ENST00000227507.2:c.871_879del	p.Arg291_Val293del	p.R291_V293del	ENST00000227507	NM_053056.2	289	GACGTGCGG/-	5/5	1	2	FACETS	0.236	0.198	0.279	0.236	0.198	0.279	SUBCLONAL	1	TRUE	1	0.706523051735844	2		522	539	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286283	66286283	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	42	172	0	ENST00000273854.3:c.1403C>G	p.Ala468Gly	p.A468G	ENST00000273854	NM_004439.5	468	gCt/gGt	6/18	1	2	FACETS	0.826	0.703	0.956	0.826	0.703	0.956	CLONAL	1	TRUE	1	0.706523051735844	2		172	144	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084144	47084144	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	48	279	0	ENST00000409792.3:c.7145C>G	p.Ser2382Cys	p.S2382C	ENST00000409792	NM_014159.6	2382	tCt/tGt	17/21	0.168370289306009	2	FACETS	1	0.953	1	0.675	0.572	0.788	CLONAL	1	TRUE	0	0.179957481307411	2		279	395	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799737	72799737	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	34	355	0	ENST00000325599.8:c.1432G>C	p.Asp478His	p.D478H	ENST00000325599	NM_018130.2	478	Gat/Cat	11/11	0.168370289306009	2	FACETS	0.926	0.757	1	0.463	0.378	0.558	CLONAL	1	TRUE	0	0.179957481307411	2		355	408	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221820	55221822	+	missense_variant	Missense_Mutation	TNP	TGC	TGC	GTA	novel	NA	P-0038283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	144	482	1	ENST00000275493.2:c.864_866delinsGTA	p.Ala289Tyr	p.A289Y	ENST00000275493	NM_005228.3	288	ggTGCc/ggGTAc	7/28	0.179957481307411	6	FACETS	1	0.957	1	0.805	0.736	0.877	CLONAL	3	TRUE	2	0.179957481307411	6		483	676	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224209	98224209	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	53	224	0	ENST00000331920.6:c.2632G>T	p.Asp878Tyr	p.D878Y	ENST00000331920	NM_000264.3	878	Gac/Tac	16/24	0.179957481307411	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	TRUE	0	0.179957481307411	2		224	261	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0038288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	85	1107	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	1	2	FACETS	0.564	0.496	0.636	0.564	0.496	0.636	SUBCLONAL	1	TRUE	1	0.259545886393339	2		1107	1162	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125094	46125095	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1251963733	NA	P-0038288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	32	201	0	ENST00000334344.6:c.282dup	p.Arg95AlafsTer16	p.R95Afs*16	ENST00000334344	NM_152641.2	94	ttg/ttGg	3/21	0.160225264132617	2	FACETS	0.986	0.805	1	0.493	0.402	0.595	CLONAL	1	TRUE	0	0.259545886393339	2		201	250	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514236	69514236	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1367835916	NA	P-0038288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	85	968	0	ENST00000294312.3:c.445A>G	p.Lys149Glu	p.K149E	ENST00000294312	NM_005117.2	149	Aaa/Gaa	3/3	1	2	FACETS	0.667	0.588	0.752	0.667	0.588	0.752	SUBCLONAL	1	TRUE	1	0.259545886393339	2		968	982	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197196	26197196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	94	522	0	ENST00000356476.2:c.283G>A	p.Glu95Lys	p.E95K	ENST00000356476		95	Gag/Aag	1/1	0.259545886393339	3	FACETS	1	0.973	1	0.653	0.581	0.728	CLONAL	1	TRUE	1	0.259545886393339	3		522	627	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0038289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	396	805	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.602064634608455	4	FACETS	1	0.989	1			1	CLONAL	3	FALSE	NA	0.666682326936331	4		805	619	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060939	38060940	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1421	163	568	0	ENST00000250448.2:c.1049dup	p.Thr351AspfsTer64	p.T351Dfs*64	ENST00000250448	NM_004496.3	350	aag/aaAg	2/2	0.666682326936331	14	FACETS	0.772	0.706	0.841			1	SUBCLONAL	2	FALSE	NA	0.666682326936331	14		568	1584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573977	7574014	+	frameshift_variant	Frame_Shift_Del	DEL	GAGTTCCAAGGCCTCATTCAGCTCTCGGAACATCTCGA	GAGTTCCAAGGCCTCATTCAGCTCTCGGAACATCTCGA	CAGT	novel	NA	P-0038289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	308	929	2	ENST00000269305.4:c.1013_1050delinsACTG	p.Phe338TyrfsTer2	p.F338Yfs*2	ENST00000269305	NM_001126112.2	338	tTCGAGATGTTCCGAGAGCTGAATGAGGCCTTGGAACTC/tACTG	10/11	0.670818170457448	4	FACETS	0.908	0.875	0.94	0.908	0.875	0.94	CLONAL	4	FALSE	0	0.666682326936331	4		931	424	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166298	32166298	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	101	880	3	ENST00000375023.3:c.4656G>A	p.Trp1552Ter	p.W1552*	ENST00000375023	NM_004557.3	1552	tgG/tgA	26/30	0.670818170457448	5	FACETS	0.622	0.555	0.694	0.124	0.111	0.139	SUBCLONAL	1	FALSE	0	0.666682326936331	5		883	974	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005944	69005944	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	35	545	0	ENST00000288368.4:c.2355C>A	p.Asp785Glu	p.D785E	ENST00000288368	NM_024870.2	785	gaC/gaA	21/40	0.670818170457448	1	FACETS	0.56	0.468	0.658	0.56	0.468	0.658	SUBCLONAL	1	FALSE	0	0.666682326936331	1		545	125	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630203	100630203	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	95	251	0	ENST00000308731.7:c.70A>C	p.Asn24His	p.N24H	ENST00000308731	NM_000061.2	24	Aac/Cac	2/19	0.356223815094408	2	FACETS	0.819	0.752	0.886			1	INDETERMINATE	2	FALSE	NA	0.666682326936331	2		251	174	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0038290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	22	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.339	0.262	0.429	0.339	0.262	0.429	SUBCLONAL	1	TRUE	1	0.25	2		457	519	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0038290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	16	622	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.25	0.184	0.33	0.25	0.184	0.33	SUBCLONAL	1	TRUE	1	0.25	2		622	512	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0038290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	32	226	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.813	0.661	0.983	0.813	0.661	0.983	CLONAL	1	TRUE	1	0.25	2		226	315	SUCCESS
AR	367	MSKCC	GRCh37	X	66765403	66765403	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1264061748	NA	P-0038290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	62	432	2	ENST00000374690.3:c.415G>A	p.Val139Met	p.V139M	ENST00000374690	NM_000044.3	139	Gtg/Atg	1/8	1	1	FACETS	0.962	0.833	1	0.962	0.833	1	CLONAL	1	TRUE	0	0.25	1		434	451	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86668007	86668007	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	27	267	0	ENST00000274376.6:c.1771C>T	p.Arg591Cys	p.R591C	ENST00000274376	NM_002890.2	591	Cgt/Tgt	13/25	1	2	FACETS	0.564	0.449	0.696	0.564	0.449	0.696	SUBCLONAL	1	TRUE	1	0.25	2		267	383	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139818391	139818393	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs1004692565	NA	P-0038290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	70	897	0	ENST00000247668.2:c.1230_1232del	p.Phe411del	p.F411del	ENST00000247668	NM_021138.3	409	cTCTtc/ctc	10/11	1	2	FACETS	0.525	0.456	0.6	0.525	0.456	0.6	SUBCLONAL	1	TRUE	1	0.25	2		897	1066	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393419	139393419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	260	886	3	ENST00000277541.6:c.6112G>A	p.Val2038Met	p.V2038M	ENST00000277541	NM_017617.3	2038	Gtg/Atg	33/34	0.492502653609135	3	FACETS	1	0.986	1	0.587	0.55	0.626	CLONAL	1	TRUE	1	0.49	3		889	1125	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937487	76937487	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0038291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	112	384	0	ENST00000373344.5:c.3261T>A	p.Tyr1087Ter	p.Y1087*	ENST00000373344	NM_000489.3	1087	taT/taA	9/35	0.492502653609135	3	FACETS	1	0.973	1	0.605	0.548	0.666	CLONAL	1	TRUE	1	0.49	3		384	470	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0038292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	45	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.352636017492042	2		457	226	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0038292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	68	875	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.352636017492042	1	FACETS	0.859	0.751	0.973	0.859	0.751	0.973	CLONAL	1	TRUE	0	0.352636017492042	1		876	370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0038293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	571	630	1	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	0.667475232706138	2		631	835	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0038293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	193	332	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.340058752970286	3	FACETS	1	0.986	1	0.763	0.72	0.805	INDETERMINATE	2	TRUE	0	0.667475232706138	3		332	337	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0038293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	196	517	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.65149963660957	3	FACETS	1	0.933	1	0.503	0.466	0.54	CLONAL	1	TRUE	1	0.667475232706138	3		518	779	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920422	114920422	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	431	570	0	ENST00000543371.1:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000543371	NM_001198531.1	455	Cga/Tga	13/14	0.65149963660957	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.667475232706138	3		570	843	SUCCESS
APC	324	MSKCC	GRCh37	5	112174152	112174152	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0038293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	45	360	0	ENST00000257430.4:c.2861T>A	p.Leu954Ter	p.L954*	ENST00000257430	NM_000038.5	954	tTa/tAa	16/16	0.340058752970286	3	FACETS	0.552	0.465	0.646	0.184	0.155	0.216	INDETERMINATE	1	TRUE	0	0.667475232706138	3		360	326	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220467	133220467	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146711942	NA	P-0038293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	45	669	0	ENST00000320574.5:c.4246G>A	p.Ala1416Thr	p.A1416T	ENST00000320574	NM_006231.2	1416	Gct/Act	33/49	1	2	FACETS	0.222	0.186	0.262	0.222	0.186	0.262	SUBCLONAL	1	TRUE	1	0.667475232706138	2		669	607	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139642	202139642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1351320412	NA	P-0038293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	85	353	0	ENST00000358485.4:c.803C>T	p.Ser268Leu	p.S268L	ENST00000358485	NM_001080125.1	268	tCg/tTg	6/9	1	2	FACETS	0.793	0.708	0.883	0.793	0.708	0.883	SUBCLONAL	1	TRUE	1	0.667475232706138	2		353	321	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906393	50906393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762330164	NA	P-0038293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	307	1016	0	ENST00000440232.2:c.1054C>T	p.Arg352Cys	p.R352C	ENST00000440232	NM_002691.3	352	Cgc/Tgc	9/27	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.667475232706138	2		1016	888	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727077	40727077	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	60	468	0	ENST00000373198.4:c.3887A>C	p.Glu1296Ala	p.E1296A	ENST00000373198	NM_133170.3	1296	gAg/gCg	28/32	0.223730718049805	3	FACETS	0.767	0.659	0.884	0.383	0.329	0.442	SUBCLONAL	1	TRUE	1	0.223730718049805	3		468	778	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106607	27106608	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0038294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	261	649	0	ENST00000324856.7:c.6219_6220insAA	p.Ser2074AsnfsTer62	p.S2074Nfs*62	ENST00000324856	NM_006015.4	2073	cta/ctAAa	20/20	0.223730718049805	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.223730718049805	2		649	1015	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505403	25505403	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	87	666	1	ENST00000264709.3:c.355G>T	p.Glu119Ter	p.E119*	ENST00000264709	NM_175629.2	119	Gag/Tag	4/23	1	2	FACETS	0.89	0.787	1	0.89	0.787	1	CLONAL	1	TRUE	1	0.223730718049805	2		667	874	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213812	66213812	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	46	400	0	ENST00000273854.3:c.2618C>A	p.Ser873Tyr	p.S873Y	ENST00000273854	NM_004439.5	873	tCt/tAt	15/18	0.193838157085798	1	FACETS	0.744	0.626	0.873	0.744	0.626	0.873	SUBCLONAL	1	TRUE	0	0.223730718049805	1		400	491	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670734	86670735	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0038294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	14	118	0	ENST00000274376.6:c.2011+2dup		p.X671_splice	ENST00000274376	NM_002890.2	671			1	2	FACETS	0.602	0.435	0.802	0.602	0.435	0.802	SUBCLONAL	1	TRUE	1	0.223730718049805	2		118	208	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69012080	69012080	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0038294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	50	361	0	ENST00000288368.4:c.2715+2T>G		p.X905_splice	ENST00000288368	NM_024870.2	905			1	2	FACETS	0.758	0.642	0.885	0.758	0.642	0.885	SUBCLONAL	1	TRUE	1	0.223730718049805	2		361	590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520008	NA	P-0038295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	342	754	2	ENST00000269305.4:c.613T>C	p.Tyr205His	p.Y205H	ENST00000269305	NM_001126112.2	205	Tat/Cat	6/11	0.642392402244737	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.715691490132463	2		756	477	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	154	399	0				ENST00000310581	NM_198253.2	-/1132			0.291934631906527	1	FACETS	0.716	0.662	0.771	0.716	0.662	0.771	INDETERMINATE	1	TRUE	0	0.67	1		399	427	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346338	73346338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	119	299	0	ENST00000377767.4:c.1462G>A	p.Asp488Asn	p.D488N	ENST00000377767	NM_014953.3	488	Gat/Aat	10/21	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.67	2		299	353	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0038296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	53	99	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.67	2		99	145	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141081	55141081	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	145	374	0	ENST00000257290.5:c.1727A>G	p.Asp576Gly	p.D576G	ENST00000257290	NM_006206.4	576	gAc/gGc	12/23	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.67	2		374	431	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139825	55139826	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCATCG	novel	NA	P-0038296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	185	550	0	ENST00000257290.5:c.1489_1494dup	p.Ile497_Ala498dup	p.I497_A498dup	ENST00000257290	NM_006206.4	497	acc/aCCATCGcc	10/23	1	2	FACETS	0.83	0.77	0.893	0.83	0.77	0.893	CLONAL	1	TRUE	1	0.67	2		550	665	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0038297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	160	704	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.316895473753726	1	FACETS	0.967	0.887	1	0.967	0.887	1	CLONAL	1	TRUE	0	0.316895473753726	1		705	879	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610608	52610608	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	96	410	1	ENST00000394830.3:c.3565G>T	p.Glu1189Ter	p.E1189*	ENST00000394830	NM_018313.4	1189	Gaa/Taa	23/30	0.316895473753726	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.316895473753726	1		411	496	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154869	2154869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	168	868	0	ENST00000434045.2:c.352C>T	p.Arg118Cys	p.R118C	ENST00000434045	NM_001127598.1	118	Cgc/Tgc	4/5	1	2	FACETS	0.913	0.838	0.992	0.913	0.838	0.992	CLONAL	1	TRUE	1	0.316895473753726	2		868	1161	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244436	5244436	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	172	877	0	ENST00000357368.4:c.1046C>T	p.Thr349Ile	p.T349I	ENST00000357368	NM_002850.3	349	aCc/aTc	11/38	1	2	FACETS	0.913	0.838	0.991	0.913	0.838	0.991	CLONAL	1	TRUE	1	0.316895473753726	2		877	1189	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172048	32172060	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCAGGCACAGT	GGGCAGGCACAGT	-	novel	NA	P-0038297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	148	802	0	ENST00000375023.3:c.2972_2984del	p.His991LeufsTer53	p.H991Lfs*53	ENST00000375023	NM_004557.3	991	cACTGTGCCTGCCCt/ct	19/30	1	2	FACETS	0.852	0.777	0.931	0.852	0.777	0.931	CLONAL	1	TRUE	1	0.316895473753726	2		802	1096	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101229	4101229	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs530342723	NA	P-0038298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	169	839	2	ENST00000262948.5:c.578G>A	p.Arg193Gln	p.R193Q	ENST00000262948	NM_030662.3	193	cGa/cAa	5/11	0.350405340886748	4	FACETS	0.834	0.767	0.904	0.209	0.191	0.226	INDETERMINATE	1	TRUE	0	0.89914156161572	4		841	856	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0038299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	13	489	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.599	0.427	0.809	0.599	0.427	0.809	SUBCLONAL	1	TRUE	1	0.172918040556179	2		489	251	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0038299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	11	512	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.482	0.332	0.669	0.482	0.332	0.669	SUBCLONAL	1	TRUE	1	0.172918040556179	2		512	264	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260150	149260150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761556137	NA	P-0038299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	64	395	1	ENST00000360632.3:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000360632	NM_015472.4	248	cGa/cAa	4/7	1	2	FACETS	1	0.905	1	1	0.985	1	CLONAL	3	TRUE	1	0.172918040556179	2		396	238	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350471	89350471	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	217	950	0	ENST00000301030.4:c.2479G>A	p.Glu827Lys	p.E827K	ENST00000301030	NM_001256183.1	827	Gaa/Aaa	9/13	0.578922404559173	3	FACETS	1	0.933	1	0.501	0.466	0.538	CLONAL	1	TRUE	1	0.578922404559173	3		950	964	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240337	5240337	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	451	742	1	ENST00000357368.4:c.1577G>T	p.Gly526Val	p.G526V	ENST00000357368	NM_002850.3	526	gGc/gTc	12/38	0.578922404559173	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.578922404559173	2		743	734	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188034	32188034	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	201	813	0	ENST00000375023.3:c.1187G>C	p.Cys396Ser	p.C396S	ENST00000375023	NM_004557.3	396	tGt/tCt	7/30	0.578244662001481	2	FACETS	0.912	0.848	0.979	0.456	0.424	0.49	CLONAL	1	TRUE	0	0.578922404559173	2		813	761	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	22	630	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.104	0.08	0.132	0.104	0.08	0.132	SUBCLONAL	1	TRUE	1	0.637554916509948	2		631	663	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	74	833	4	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.377	0.33	0.428	0.377	0.33	0.428	SUBCLONAL	1	TRUE	1	0.637554916509948	2		837	615	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	73	360	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.996	0.884	1	0.996	0.884	1	CLONAL	1	TRUE	1	0.637554916509948	2		360	230	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	229	679	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.637554916509948	2		679	582	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	55	319	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	0.637554916509948	2	FACETS	0.923	0.802	1	0.461	0.401	0.525	CLONAL	1	TRUE	0	0.637554916509948	2		320	187	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	158	794	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.366207891319198	1	FACETS	0.785	0.727	0.845	0.785	0.727	0.845	INDETERMINATE	1	TRUE	0	0.637554916509948	1		794	430	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	42	364	2	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.591	0.498	0.692	0.591	0.498	0.692	SUBCLONAL	1	TRUE	1	0.637554916509948	2		366	223	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	20	536	0	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	0.366207891319198	1	FACETS	0.125	0.095	0.16	0.125	0.095	0.16	INDETERMINATE	1	TRUE	0	0.637554916509948	1		536	343	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	197	517	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.637554916509948	2	FACETS	0.934	0.883	0.983	0.934	0.883	0.983	CLONAL	2	TRUE	0	0.637554916509948	2		518	331	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	129	482	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.637554916509948	2	FACETS	0.987	0.903	1	0.494	0.451	0.537	CLONAL	1	TRUE	0	0.637554916509948	2		482	410	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846308	156846308	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	46	771	0	ENST00000524377.1:c.1753del	p.Leu585CysfsTer73	p.L585Cfs*73	ENST00000524377	NM_002529.3	583	cgC/cg	14/17	1	2	FACETS	0.27	0.227	0.317	0.27	0.227	0.317	SUBCLONAL	1	TRUE	1	0.637554916509948	2		771	535	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685315	89685315	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1554897280	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	26	238	0	ENST00000371953.3:c.209+1G>A		p.X70_splice	ENST00000371953	NM_000314.4	70			1	2	FACETS	0.816	0.661	0.985	0.816	0.661	0.985	CLONAL	1	TRUE	1	0.637554916509948	2		238	100	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434367	121434367	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	47	691	3	ENST00000257555.6:c.1136del	p.Pro379LeufsTer5	p.P379Lfs*5	ENST00000257555		377	ctC/ct	6/10	1	2	FACETS	0.33	0.278	0.386	0.33	0.278	0.386	SUBCLONAL	1	TRUE	1	0.637554916509948	2		694	447	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101268	27101268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	161	564	0	ENST00000324856.7:c.4555del	p.Gln1519ArgfsTer8	p.Q1519Rfs*8	ENST00000324856	NM_006015.4	1517	gCc/gc	18/20	0.637554916509948	2	FACETS	1	0.979	1	0.577	0.534	0.62	CLONAL	1	TRUE	0	0.637554916509948	2		564	438	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	174	697	0	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	1	2	FACETS	0.966	0.895	1	0.966	0.895	1	CLONAL	1	TRUE	1	0.637554916509948	2		697	565	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	56	321	0	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.616	0.532	0.707	0.616	0.532	0.707	SUBCLONAL	1	TRUE	1	0.637554916509948	2		321	285	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	58	295	1	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.722	0.627	0.823	0.722	0.627	0.823	SUBCLONAL	1	TRUE	1	0.637554916509948	2		296	252	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484049	50484049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	34	569	0	ENST00000394963.4:c.899G>A	p.Arg300His	p.R300H	ENST00000394963	NM_003076.4	300	cGc/cAc	8/13	1	2	FACETS	0.22	0.179	0.266	0.22	0.179	0.266	SUBCLONAL	1	TRUE	1	0.637554916509948	2		569	485	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245841	5245841	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532977374	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	218	838	0	ENST00000357368.4:c.934G>A	p.Val312Met	p.V312M	ENST00000357368	NM_002850.3	312	Gtg/Atg	10/38	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.637554916509948	2		838	673	SUCCESS
BTK	695	MSKCC	GRCh37	X	100609618	100609618	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	24	391	0	ENST00000308731.7:c.1631G>T	p.Arg544Met	p.R544M	ENST00000308731	NM_000061.2	544	aGg/aTg	16/19	0.366207891319198	1	FACETS	0.203	0.159	0.253	0.203	0.159	0.253	INDETERMINATE	1	TRUE	0	0.637554916509948	1		391	253	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257144	19257144	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	55	544	0	ENST00000162023.5:c.819del	p.Thr274ProfsTer?	p.T274Pfs*?	ENST00000162023		273	ccC/cc	12/13	1	2	FACETS	0.482	0.414	0.556	0.482	0.414	0.556	SUBCLONAL	1	TRUE	1	0.637554916509948	2		544	358	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458724	120458724	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	16	489	0	ENST00000256646.2:c.6621G>A	p.Met2207Ile	p.M2207I	ENST00000256646	NM_024408.3	2207	atG/atA	34/34	1	2	FACETS	0.159	0.117	0.21	0.159	0.117	0.21	SUBCLONAL	1	TRUE	1	0.637554916509948	2		489	315	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163866	152163866	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	100	479	0	ENST00000206249.3:c.587A>G	p.His196Arg	p.H196R	ENST00000206249	NM_000125.3	196	cAt/cGt	2/8	0.182945870980717	3	FACETS	1	0.967	1	0.584	0.527	0.644	INDETERMINATE	1	TRUE	1	0.637554916509948	3		479	354	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991949	72991949	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs753977275	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	122	486	0	ENST00000268489.5:c.2096del	p.Gly699AlafsTer125	p.G699Afs*125	ENST00000268489	NM_006885.3	699	gGc/gc	2/10	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.637554916509948	2		486	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577111	7577111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	219	633	1	ENST00000269305.4:c.827C>T	p.Ala276Val	p.A276V	ENST00000269305	NM_001126112.2	276	gCc/gTc	8/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.637554916509948	2		634	627	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692832	89692832	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1085308039	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	14	162	0	ENST00000371953.3:c.316G>T	p.Glu106Ter	p.E106*	ENST00000371953	NM_000314.4	106	Gaa/Taa	5/9	1	2	FACETS	0.549	0.404	0.718	0.549	0.404	0.718	SUBCLONAL	1	TRUE	1	0.637554916509948	2		162	80	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213358	36213359	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	103	798	0	ENST00000222270.7:c.2561_2562del	p.Glu854AlafsTer34	p.E854Afs*34	ENST00000222270	NM_014727.1	852	aAG/a	4/37	1	2	FACETS	0.509	0.456	0.565	0.509	0.456	0.565	SUBCLONAL	1	TRUE	1	0.637554916509948	2		798	635	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223858	36223858	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	239	871	4	ENST00000222270.7:c.6413del	p.Pro2138ArgfsTer15	p.P2138Rfs*15	ENST00000222270	NM_014727.1	2136	ctC/ct	28/37	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.637554916509948	2		875	582	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911107	29911107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45542135	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	20	381	0	ENST00000376809.5:c.406G>A	p.Gly136Arg	p.G136R	ENST00000376809	NM_002116.7	136	Ggg/Agg	3/8	0.182945870980717	3	FACETS	0.215	0.164	0.276	0.108	0.082	0.138	INDETERMINATE	1	TRUE	1	0.637554916509948	3		381	384	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910774	29910774	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs9260139	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	51	723	0	ENST00000376809.5:c.314T>C	p.Leu105Pro	p.L105P	ENST00000376809	NM_002116.7	105	cTg/cCg	2/8	0.182945870980717	3	FACETS	0.343	0.291	0.4	0.172	0.145	0.2	INDETERMINATE	1	TRUE	1	0.637554916509948	3		723	615	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980293	201980293	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	32	591	0	ENST00000359651.3:c.33del	p.Phe11LeufsTer32	p.F11Lfs*32	ENST00000359651		10	aTt/at	1/8	1	2	FACETS	0.166	0.134	0.203	0.166	0.134	0.203	SUBCLONAL	1	TRUE	1	0.637554916509948	2		591	604	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015264	128015264	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	42	420	1	ENST00000285398.2:c.2257G>A	p.Ala753Thr	p.A753T	ENST00000285398	NM_000122.1	753	Gcc/Acc	15/15	1	2	FACETS	0.287	0.239	0.34	0.287	0.239	0.34	SUBCLONAL	1	TRUE	1	0.637554916509948	2		421	459	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307276	65307279	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	novel	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	94	313	0	ENST00000342505.4:c.2409_2412del	p.Glu803AspfsTer10	p.E803Dfs*10	ENST00000342505	NM_002227.2	803	gaGAGA/ga	18/25	0.637554916509948	2	FACETS	1	0.941	1	0.53	0.478	0.584	CLONAL	1	TRUE	0	0.637554916509948	2		313	278	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600522	43600522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1299878945	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	56	597	0	ENST00000355710.3:c.748C>T	p.Arg250Cys	p.R250C	ENST00000355710	NM_020975.4	250	Cgc/Tgc	4/20	1	2	FACETS	0.325	0.278	0.376	0.325	0.278	0.376	SUBCLONAL	1	TRUE	1	0.637554916509948	2		597	540	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77069983	77069983	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	44	424	0	ENST00000356341.3:c.557del	p.Pro186HisfsTer4	p.P186Hfs*4	ENST00000356341	NM_002576.4	186	cCa/ca	6/15	1	2	FACETS	0.364	0.306	0.428	0.364	0.306	0.428	SUBCLONAL	1	TRUE	1	0.637554916509948	2		424	379	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394624	394624	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	novel	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	98	376	0	ENST00000399788.2:c.5071T>C	p.Ter1691GlnextTer5	p.*1691Qext*5	ENST00000399788	NM_001042603.1	1691	Tag/Cag	28/28	NA	2	FACETS	1	0.96	1			1	INDETERMINATE	1	TRUE	NA	0.637554916509948	2		376	276	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118878	115118878	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1296731331	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	13	317	0	ENST00000257566.3:c.463A>G	p.Ile155Val	p.I155V	ENST00000257566	NM_016569.3	155	Att/Gtt	2/8	1	2	FACETS	0.192	0.137	0.26	0.192	0.137	0.26	SUBCLONAL	1	TRUE	1	0.637554916509948	2		317	212	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519945	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	15	517	0	ENST00000320574.5:c.1231G>A	p.Val411Met	p.V411M	ENST00000320574	NM_006231.2	411	Gtg/Atg	13/49	1	2	FACETS	0.15	0.109	0.199	0.15	0.109	0.199	SUBCLONAL	1	TRUE	1	0.637554916509948	2		517	314	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3795282	3795282	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	26	354	0	ENST00000262367.5:c.3910T>C	p.Ser1304Pro	p.S1304P	ENST00000262367	NM_004380.2	1304	Tca/Cca	22/31	1	2	FACETS	0.258	0.204	0.32	0.258	0.204	0.32	SUBCLONAL	1	TRUE	1	0.637554916509948	2		354	316	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821210	72821210	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	141	630	0	ENST00000268489.5:c.10965G>A	p.Met3655Ile	p.M3655I	ENST00000268489	NM_006885.3	3655	atG/atA	10/10	1	2	FACETS	0.862	0.79	0.937	0.862	0.79	0.937	CLONAL	1	TRUE	1	0.637554916509948	2		630	513	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350267	89350267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781323579	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	223	776	1	ENST00000301030.4:c.2683C>T	p.Arg895Trp	p.R895W	ENST00000301030	NM_001256183.1	895	Cgg/Tgg	9/13	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.637554916509948	2		777	636	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980019	7980019	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs150272126	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	147	684	0	ENST00000319144.4:c.1318A>G	p.Ile440Val	p.I440V	ENST00000319144	NM_001139.2	440	Att/Gtt	10/15	1	2	FACETS	0.798	0.732	0.866	0.798	0.732	0.866	SUBCLONAL	1	TRUE	1	0.637554916509948	2		684	578	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511608	38511608	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771371291	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	59	629	1	ENST00000254066.5:c.1106G>A	p.Ser369Asn	p.S369N	ENST00000254066	NM_000964.3	369	aGc/aAc	8/9	0.637554916509948	2	FACETS	0.336	0.289	0.387	0.168	0.144	0.194	SUBCLONAL	1	TRUE	0	0.637554916509948	2		630	551	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118905	70118906	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCTC	novel	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	445	718	0	ENST00000245479.2:c.478_479insCTCC	p.Arg160ProfsTer93	p.R160Pfs*93	ENST00000245479	NM_000346.3	159	-/CCTC	2/3	0.637554916509948	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.637554916509948	2		718	654	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727808	78727808	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	45	565	1	ENST00000306801.3:c.655-2A>G		p.X219_splice	ENST00000306801	NM_020761.2	219			0.637554916509948	2	FACETS	0.331	0.279	0.39	0.166	0.139	0.195	SUBCLONAL	1	TRUE	0	0.637554916509948	2		566	426	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223279	2223279	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	29	683	0	ENST00000398665.3:c.3391-1G>T		p.X1131_splice	ENST00000398665	NM_032482.2	1131			1	2	FACETS	0.17	0.136	0.21	0.17	0.136	0.21	SUBCLONAL	1	TRUE	1	0.637554916509948	2		683	534	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251656	212251656	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	43	406	0	ENST00000342788.4:c.3403T>C	p.Phe1135Leu	p.F1135L	ENST00000342788	NM_005235.2	1135	Ttt/Ctt	27/28	1	2	FACETS	0.323	0.27	0.381	0.323	0.27	0.381	SUBCLONAL	1	TRUE	1	0.637554916509948	2		406	418	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593690	215593690	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs749485640	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	65	270	0	ENST00000260947.4:c.2044A>G	p.Thr682Ala	p.T682A	ENST00000260947	NM_000465.2	682	Acc/Gcc	11/11	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.637554916509948	2		270	202	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660151	227660151	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748578334	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	38	642	0	ENST00000305123.5:c.3304G>A	p.Glu1102Lys	p.E1102K	ENST00000305123	NM_005544.2	1102	Gag/Aag	1/2	1	2	FACETS	0.259	0.214	0.31	0.259	0.214	0.31	SUBCLONAL	1	TRUE	1	0.637554916509948	2		642	460	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030986	36030986	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759567556	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	37	536	0	ENST00000358208.4:c.1265G>A	p.Arg422Gln	p.R422Q	ENST00000358208		422	cGg/cAg	10/12	0.366207891319198	1	FACETS	0.187	0.154	0.224	0.187	0.154	0.224	INDETERMINATE	1	TRUE	0	0.637554916509948	1		536	422	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626479	12626479	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	15	313	0	ENST00000251849.4:c.1670T>A	p.Ile557Asn	p.I557N	ENST00000251849	NM_002880.3	557	aTc/aAc	16/17	1	2	FACETS	0.282	0.207	0.371	0.282	0.207	0.371	SUBCLONAL	1	TRUE	1	0.637554916509948	2		313	167	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71050169	71050169	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	10	266	0	ENST00000318789.4:c.1016C>T	p.Ala339Val	p.A339V	ENST00000318789	NM_032682.5	339	gCc/gTc	13/21	1	2	FACETS	0.165	0.111	0.232	0.165	0.111	0.232	SUBCLONAL	1	TRUE	1	0.637554916509948	2		266	190	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217577	142217577	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	11	358	0	ENST00000350721.4:c.5420T>C	p.Leu1807Pro	p.L1807P	ENST00000350721	NM_001184.3	1807	cTa/cCa	32/47	1	2	FACETS	0.209	0.144	0.289	0.209	0.144	0.289	SUBCLONAL	1	TRUE	1	0.637554916509948	2		358	165	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928057	178928083	+	inframe_deletion	In_Frame_Del	DEL	TTGGCCAGTACCTCATGGATTAGAAGA	TTGGCCAGTACCTCATGGATTAGAAGA	-	novel	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	18	449	0	ENST00000263967.3:c.1337_1363del	p.Trp446_Asp454del	p.W446_D454del	ENST00000263967	NM_006218.2	445	ctTTGGCCAGTACCTCATGGATTAGAAGAt/ctt	8/21	1	2	FACETS	0.364	0.276	0.467	0.364	0.276	0.467	SUBCLONAL	1	TRUE	1	0.637554916509948	2		449	155	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808053	1808053	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1426369141	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	32	814	3	ENST00000260795.2:c.2029G>A	p.Val677Ile	p.V677I	ENST00000260795		677	Gtc/Atc	14/17	1	2	FACETS	0.179	0.145	0.218	0.179	0.145	0.218	SUBCLONAL	1	TRUE	1	0.637554916509948	2		817	560	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056463	26056463	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	64	214	0	ENST00000343677.2:c.194C>G	p.Ala65Gly	p.A65G	ENST00000343677	NM_005319.3	65	gCg/gGg	1/1	0.507088356551758	4	FACETS	1	0.973	1	0.727	0.639	0.821	CLONAL	1	TRUE	2	0.637554916509948	4		214	226	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6442036	6442036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs16063	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	20	40	0	ENST00000356142.4:c.595C>T	p.Pro199Ser	p.P199S	ENST00000356142	NM_018890.3	199	Cct/Tct	7/7	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.637554916509948	2		40	43	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981866	70981866	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	190	737	0	ENST00000276594.2:c.230T>C	p.Leu77Ser	p.L77S	ENST00000276594	NM_024504.3	77	tTg/tCg	2/8	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.637554916509948	2		737	451	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426421	47426421	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs771213170	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	36	693	0	ENST00000377045.4:c.768del	p.Ser257AlafsTer35	p.S257Afs*35	ENST00000377045	NM_001654.4	255	cGg/cg	9/16	0.366207891319198	1	FACETS	0.137	0.112	0.165	0.137	0.112	0.165	INDETERMINATE	1	TRUE	0	0.637554916509948	1		693	561	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410115	63410115	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	108	703	1	ENST00000330258.3:c.3052C>T	p.Pro1018Ser	p.P1018S	ENST00000330258	NM_152424.3	1018	Cct/Tct	2/2	0.366207891319198	1	FACETS	0.617	0.559	0.678	0.617	0.559	0.678	INDETERMINATE	1	TRUE	0	0.637554916509948	1		704	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs967461896	NA	P-0038306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	123	638	0	ENST00000269305.4:c.526T>G	p.Cys176Gly	p.C176G	ENST00000269305	NM_001126112.2	176	Tgc/Ggc	5/11	0.500386576272965	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.500386576272965	1		638	357	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165741	118165741	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	132	323	0	ENST00000369448.3:c.251A>G	p.Asn84Ser	p.N84S	ENST00000369448	NM_017709.3	84	aAt/aGt	2/2	0.500386576272965	4	FACETS	0.772	0.704	0.841	0.772	0.704	0.841	SUBCLONAL	2	TRUE	2	0.500386576272965	4		323	513	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28624234	28624234	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	166	374	0	ENST00000241453.7:c.740T>C	p.Ile247Thr	p.I247T	ENST00000241453	NM_004119.2	247	aTa/aCa	6/24	0.500386576272965	2	FACETS	0.981	0.917	1	0.981	0.917	1	CLONAL	2	TRUE	0	0.500386576272965	2		374	338	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243630	41243630	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	263	439	1	ENST00000357654.3:c.3918del	p.Thr1307LeufsTer11	p.T1307Lfs*11	ENST00000357654	NM_007294.3	1306	ttG/tt	10/23	0.488786489773427	3	FACETS	0.901	0.856	0.946	0.901	0.856	0.946	CLONAL	3	TRUE	0	0.500386576272965	3		440	486	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291858	15291858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	293	781	0	ENST00000263388.2:c.2908C>T	p.Pro970Ser	p.P970S	ENST00000263388	NM_000435.2	970	Ccc/Tcc	18/33	0.500386576272965	5	FACETS	0.939	0.884	0.995	0.626	0.589	0.664	CLONAL	2	TRUE	2	0.500386576272965	5		781	1092	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979249	93979249	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	41	326	0	ENST00000369303.4:c.1579A>G	p.Ser527Gly	p.S527G	ENST00000369303	NM_004440.3	527	Agt/Ggt	7/17	0.493486868871146	2	FACETS	0.537	0.449	0.634	0.269	0.224	0.317	SUBCLONAL	1	TRUE	0	0.500386576272965	2		326	305	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983846	2983846	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	204	523	0	ENST00000396946.4:c.684G>C	p.Glu228Asp	p.E228D	ENST00000396946	NM_032415.4	228	gaG/gaC	5/25	0.495614500840275	3	FACETS	0.94	0.879	1	0.94	0.879	1	CLONAL	2	TRUE	1	0.500386576272965	3		523	542	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205145	123205156	+	inframe_deletion	In_Frame_Del	DEL	TGAACAGGATGA	TGAACAGGATGA	-	novel	NA	P-0038306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	24	310	0	ENST00000218089.9:c.2508_2519del	p.Glu836_Asp839del	p.E836_D839del	ENST00000218089	NM_001042749.1	835	atTGAACAGGATGAt/att	25/35	0.365533138086085	4	FACETS	0.439	0.344	0.548			1	SUBCLONAL	1	TRUE	NA	0.500386576272965	4		310	328	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060776	38060793	+	inframe_deletion	In_Frame_Del	DEL	GGTTGTTGATGGAGAACG	GGTTGTTGATGGAGAACG	-	novel	NA	P-0038307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	347	893	0	ENST00000250448.2:c.1196_1213del	p.Pro399_Asn404del	p.P399_N404del	ENST00000250448	NM_004496.3	399	cCGTTCTCCATCAACAACCtc/ctc	2/2	1	2	FACETS	0.99	0.942	1	0.99	0.942	1	CLONAL	1	TRUE	1	0.807357957406157	2		893	868	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061277	38061291	+	inframe_deletion	In_Frame_Del	DEL	GCTTGTCCGGGGAGC	GCTTGTCCGGGGAGC	-	novel	NA	P-0038307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	246	687	0	ENST00000250448.2:c.698_712del	p.Arg233_Lys237del	p.R233_K237del	ENST00000250448	NM_004496.3	233	cGCTCCCCGGACAAGCcg/ccg	2/2	1	2	FACETS	0.843	0.792	0.895	0.843	0.792	0.895	CLONAL	1	TRUE	1	0.807357957406157	2		687	723	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253780	153253780	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	124	341	0	ENST00000281708.4:c.953A>G	p.Asn318Ser	p.N318S	ENST00000281708	NM_033632.3	318	aAc/aGc	6/12	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.807357957406157	2		341	294	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332903	153332903	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs778748560	NA	P-0038307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	124	361	0	ENST00000281708.4:c.53C>G	p.Ser18Cys	p.S18C	ENST00000281708	NM_033632.3	18	tCt/tGt	2/12	1	2	FACETS	0.878	0.804	0.954	0.878	0.804	0.954	CLONAL	1	TRUE	1	0.807357957406157	2		361	350	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858476	57858476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199685332	NA	P-0038312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	121	538	1	ENST00000228682.2:c.214C>T	p.Arg72Trp	p.R72W	ENST00000228682	NM_005269.2	72	Cgg/Tgg	4/12	1	2	FACETS	0.743	0.672	0.818	0.743	0.672	0.818	SUBCLONAL	1	TRUE	1	0.44026521088086	2		539	740	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0038312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	98	467	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	0.743	0.664	0.827	0.743	0.664	0.827	SUBCLONAL	1	TRUE	1	0.44026521088086	2		467	599	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967146	25967146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	79	363	0	ENST00000435504.4:c.2060G>A	p.Gly687Glu	p.G687E	ENST00000435504		687	gGa/gAa	13/13	1	2	FACETS	0.691	0.609	0.779	0.691	0.609	0.779	SUBCLONAL	1	TRUE	1	0.44026521088086	2		363	519	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199873	108199873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879254179	NA	P-0038312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	43	166	0	ENST00000278616.4:c.7215G>A	p.Met2405Ile	p.M2405I	ENST00000278616	NM_000051.3	2405	atG/atA	49/63	1	2	FACETS	0.828	0.699	0.968	0.828	0.699	0.968	CLONAL	1	TRUE	1	0.44026521088086	2		166	236	SUCCESS
APC	324	MSKCC	GRCh37	5	112178747	112178747	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	106	370	0	ENST00000257430.4:c.7457del	p.Pro2486LeufsTer30	p.P2486Lfs*30	ENST00000257430	NM_000038.5	2486	Cct/ct	16/16	0.329244185984619	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.44026521088086	1		370	367	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672594	30672596	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0038312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	118	597	0	ENST00000376406.3:c.4364_4366del	p.Leu1455del	p.L1455del	ENST00000376406	NM_014641.2	1455	cTCCag/cag	10/15	1	2	FACETS	0.758	0.685	0.836	0.758	0.685	0.836	SUBCLONAL	1	TRUE	1	0.44026521088086	2		597	707	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0038317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	16	347	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.505	0.372	0.666	0.505	0.372	0.666	SUBCLONAL	1	TRUE	1	0.13	2		347	487	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4097279	4097279	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	25	526	1	ENST00000262948.5:c.982G>A	p.Glu328Lys	p.E328K	ENST00000262948	NM_030662.3	328	Gag/Aag	8/11	0.109403999003959	0	FACETS	0.68	0.535	0.848			1	SUBCLONAL	1	TRUE	0	0.13	0		527	492	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112377	115112401	+	frameshift_variant	Frame_Shift_Del	DEL	TGCGCTCCTCCGCGCCCAGGCCGCG	TGCGCTCCTCCGCGCCCAGGCCGCG	-	novel	NA	P-0038317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	17	202	1	ENST00000257566.3:c.1339_1363del	p.Arg447GlyfsTer177	p.R447Gfs*177	ENST00000257566	NM_016569.3	447	CGCGGCCTGGGCGCGGAGGAGCGCAgg/gg	7/8	1	2	FACETS	1	0.812	1	1	0.812	1	CLONAL	1	TRUE	1	0.13	2		203	236	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938617	76938617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	167	497	0	ENST00000373344.5:c.2131C>T	p.Pro711Ser	p.P711S	ENST00000373344	NM_000489.3	711	Cct/Tct	9/35	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.478876644044957	2		497	647	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026810	6026810	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658794	NA	P-0038319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	70	342	0	ENST00000265849.7:c.1586C>T	p.Ser529Leu	p.S529L	ENST00000265849	NM_000535.5	529	tCg/tTg	11/15	0.389536610143923	1	FACETS	0.465	0.406	0.528	0.465	0.406	0.528	SUBCLONAL	1	TRUE	0	0.478876644044957	1		342	478	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444204	49444204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	140	901	2	ENST00000301067.7:c.3167G>A	p.Ser1056Asn	p.S1056N	ENST00000301067	NM_003482.3	1056	aGt/aAt	11/54	1	2	FACETS	0.463	0.42	0.508	0.463	0.42	0.508	SUBCLONAL	1	TRUE	1	0.478876644044957	2		903	1263	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098024	178098024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217896899	NA	P-0038319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	62	349	0	ENST00000397062.3:c.356G>A	p.Cys119Tyr	p.C119Y	ENST00000397062	NM_006164.4	119	tGc/tAc	3/5	0.389536610143923	1	FACETS	0.404	0.349	0.463	0.404	0.349	0.463	SUBCLONAL	1	TRUE	0	0.478876644044957	1		349	488	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249445	153249445	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	155	535	0	ENST00000281708.4:c.1333G>C	p.Val445Leu	p.V445L	ENST00000281708	NM_033632.3	445	Gtg/Ctg	9/12	1	2	FACETS	0.89	0.817	0.967	0.89	0.817	0.967	CLONAL	1	TRUE	1	0.478876644044957	2		535	727	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	96	399	0				ENST00000310581	NM_198253.2	-/1132			0.429028550987633	3	FACETS	0.923	0.835	1	0.923	0.835	1	CLONAL	2	TRUE	1	0.474892260501458	3		399	271	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0038321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	146	127	0	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	0.459005314204903	2	FACETS	0.842	0.779	0.907	0.842	0.779	0.907	CLONAL	2	TRUE	0	0.474892260501458	2		127	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0038321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	261	714	0	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	0.2608377180996	3	FACETS	1	0.949	1	0.509	0.475	0.543	INDETERMINATE	1	TRUE	1	0.474892260501458	3		714	1337	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	218	571	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	0.417727162623395	2	FACETS	1	0.985	1	0.593	0.553	0.634	CLONAL	1	TRUE	0	0.474892260501458	2		571	774	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871053	12871053	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	114	345	0	ENST00000228872.4:c.285del	p.Gly97ValfsTer22	p.G97Vfs*22	ENST00000228872	NM_004064.3	94	Ccc/cc	1/3	0.2608377180996	3	FACETS	0.934	0.843	1	0.467	0.421	0.515	INDETERMINATE	1	TRUE	1	0.474892260501458	3		345	636	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879549	151879549	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	117	350	1	ENST00000262189.6:c.5396C>A	p.Ser1799Ter	p.S1799*	ENST00000262189	NM_170606.2	1799	tCa/tAa	36/59	0.2608377180996	3	FACETS	1	0.911	1	0.504	0.455	0.555	INDETERMINATE	1	TRUE	1	0.474892260501458	3		351	605	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487884	56487884	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	188	523	0	ENST00000267101.3:c.1615G>C	p.Glu539Gln	p.E539Q	ENST00000267101	NM_001982.3	539	Gag/Cag	14/28	0.417727162623395	2	FACETS	1	0.949	1	0.515	0.477	0.555	CLONAL	1	TRUE	0	0.474892260501458	2		523	768	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71019925	71019926	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0038321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	74	202	0	ENST00000318789.4:c.1683dup	p.Ser562GlnfsTer18	p.S562Qfs*18	ENST00000318789	NM_032682.5	561	-/C	19/21	0.474892260501458	3	FACETS	0.831	0.73	0.939	0.416	0.365	0.47	CLONAL	1	TRUE	1	0.474892260501458	3		202	464	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199904	128199904	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	365	497	0	ENST00000341105.2:c.1401C>A	p.Phe467Leu	p.F467L	ENST00000341105	NM_032638.4	467	ttC/ttA	6/6	0.2608377180996	3	FACETS	0.943	0.896	0.99	0.943	0.896	0.99	INDETERMINATE	2	TRUE	1	0.474892260501458	3		497	1009	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	158	881	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.334956510622778	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.334956510622778	1		881	734	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109987	115109987	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs769814877	NA	P-0038322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	157	772	0	ENST00000257566.3:c.1891C>G	p.Leu631Val	p.L631V	ENST00000257566	NM_016569.3	631	Ctg/Gtg	8/8	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.334956510622778	2		772	900	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12043894	12043894	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	92	486	0	ENST00000396373.4:c.1273G>A	p.Glu425Lys	p.E425K	ENST00000396373	NM_001987.4	425	Gaa/Aaa	8/8	1	2	FACETS	0.88	0.783	0.984	0.88	0.783	0.984	CLONAL	1	TRUE	1	0.334956510622778	2		486	624	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176700745	176700745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745582394	NA	P-0038322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	79	487	1	ENST00000439151.2:c.5582G>A	p.Arg1861Gln	p.R1861Q	ENST00000439151	NM_022455.4	1861	cGa/cAa	17/23	0.334956510622778	3	FACETS	0.919	0.809	1	0.46	0.404	0.519	CLONAL	1	TRUE	1	0.334956510622778	3		488	599	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051594	30051595	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	182	371	0	ENST00000338641.4:c.529dup	p.Tyr177LeufsTer26	p.Y177Lfs*26	ENST00000338641	NM_000268.3	176	-/T	6/16	0.289118980998437	3	FACETS	0.859	0.802	0.918	0.859	0.802	0.918	CLONAL	3	TRUE	0	0.381252089823263	3		371	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579592	7579592	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0038325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	395	554	0	ENST00000269305.4:c.97-2A>C		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.314294171811929	4	FACETS	1	0.992	1	0.866	0.829	0.904	CLONAL	3	TRUE	0	0.381252089823263	4		554	826	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0038326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	87	283	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.942	0.842	1	0.942	0.842	1	CLONAL	1	TRUE	1	0.564955642238907	2		283	327	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	100	399	0				ENST00000310581	NM_198253.2	-/1132			0.222158968583081	0	FACETS	0.723	0.655	0.792			1	SUBCLONAL	3	FALSE	0	0.249871608662456	0		399	277	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682342	37682342	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6499	345	600	0	ENST00000447079.4:c.3533C>G	p.Ser1178Cys	p.S1178C	ENST00000447079	NM_015083.1	1178	tCt/tGt	13/14	0.249871608662456	47	FACETS	0.891	0.836	0.947			1	CLONAL	3	FALSE	NA	0.249871608662456	47		600	6844	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352324	70352324	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	277	677	0	ENST00000374080.3:c.4351T>A	p.Leu1451Met	p.L1451M	ENST00000374080		1451	Ttg/Atg	31/45	0.249871608662456	1	FACETS	1	0.983	1	1	0.996	1	CLONAL	2	FALSE	0	0.249871608662456	1		677	871	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692911	89692911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909241	NA	P-0038328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	108	569	0	ENST00000371953.3:c.395G>A	p.Gly132Asp	p.G132D	ENST00000371953	NM_000314.4	132	gGt/gAt	5/9	0.558851319464876	1	FACETS	0.676	0.611	0.744	0.676	0.611	0.744	SUBCLONAL	1	TRUE	0	0.558851319464876	1		569	412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578532	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28934873	NA	P-0038328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	319	914	0	ENST00000269305.4:c.398T>C	p.Met133Thr	p.M133T	ENST00000269305	NM_001126112.2	133	aTg/aCg	5/11	0.554843248314246	1	FACETS	0.899	0.851	0.948	0.899	0.851	0.948	CLONAL	1	TRUE	0	0.558851319464876	1		914	915	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207621	2207621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1208115143	NA	P-0038328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	265	750	0	ENST00000398665.3:c.905C>T	p.Ser302Leu	p.S302L	ENST00000398665	NM_032482.2	302	tCg/tTg	11/28	0.171415975325278	0	FACETS	0.448	0.42	0.476			1	INDETERMINATE	1	TRUE	0	0.558851319464876	0		750	934	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267491	198267491	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763149798	NA	P-0038328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	92	361	0	ENST00000335508.6:c.1866G>T	p.Glu622Asp	p.E622D	ENST00000335508	NM_012433.2	622	gaG/gaT	14/25	0.558851319464876	3	FACETS	0.704	0.627	0.787	0.352	0.313	0.394	SUBCLONAL	1	TRUE	1	0.558851319464876	3		361	598	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30323896	30323896	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	72	271	0	ENST00000322652.5:c.1874G>C	p.Gly625Ala	p.G625A	ENST00000322652	NM_015355.2	625	gGg/gCg	15/16	1	2	FACETS	0.676	0.594	0.764	0.676	0.594	0.764	SUBCLONAL	1	TRUE	1	0.558851319464876	2		271	381	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	209	399	0				ENST00000310581	NM_198253.2	-/1132			0.31119773372105	2	FACETS	1	0.985	1	0.583	0.547	0.619	INDETERMINATE	1	TRUE	0	0.745609309068006	2		399	481	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206593	108206593	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587782049	NA	P-0038329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	88	348	0	ENST00000278616.4:c.8173G>C	p.Asp2725His	p.D2725H	ENST00000278616	NM_000051.3	2725	Gat/Cat	56/63	0.568604864737333	2	FACETS	1	0.984	1	0.724	0.662	0.786	CLONAL	1	TRUE	0	0.745609309068006	2		348	163	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47685245	47685245	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	119	415	0	ENST00000347630.2:c.705G>C	p.Glu235Asp	p.E235D	ENST00000347630	NM_001007230.1	235	gaG/gaC	8/11	0.587061825460834	3	FACETS	1	0.986	1	0.735	0.674	0.798	CLONAL	1	TRUE	1	0.745609309068006	3		415	298	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612212	189612212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764601563	NA	P-0038329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	471	529	0	ENST00000264731.3:c.1964G>A	p.Arg655Gln	p.R655Q	ENST00000264731	NM_003722.4	655	cGa/cAa	14/14	0.657459184129367	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.745609309068006	3		529	830	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878910	117878910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	75	408	1	ENST00000297338.2:c.59C>T	p.Ala20Val	p.A20V	ENST00000297338	NM_006265.2	20	gCg/gTg	2/14	0.238739167959488	2	FACETS	0.538	0.474	0.606	0.269	0.237	0.303	INDETERMINATE	1	TRUE	0	0.745609309068006	2		409	374	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937723	44937723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	69	565	1	ENST00000377967.4:c.2911C>T	p.Arg971Cys	p.R971C	ENST00000377967	NM_021140.2	971	Cgt/Tgt	19/29	0.687146539928444	2	FACETS	0.663	0.584	0.748	0.332	0.292	0.374	SUBCLONAL	1	TRUE	0	0.745609309068006	2		566	279	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248525	59248525	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	644	663	1	ENST00000371222.2:c.218C>T	p.Ser73Leu	p.S73L	ENST00000371222	NM_002228.3	73	tCg/tTg	1/1	0.587061825460834	3	FACETS	0.901	0.871	0.931	0.901	0.871	0.931	CLONAL	2	TRUE	1	0.745609309068006	3		664	1316	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514038	69514038	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1629	446	588	0	ENST00000294312.3:c.643G>C	p.Glu215Gln	p.E215Q	ENST00000294312	NM_005117.2	215	Gag/Cag	3/3	0.745609309068006	5	FACETS	1	0.993	1	0.407	0.387	0.428	CLONAL	1	TRUE	2	0.745609309068006	5		588	2075	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106194	27106194	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	528	553	0	ENST00000324856.7:c.5805del	p.Ser1936AlafsTer20	p.S1936Afs*20	ENST00000324856	NM_006015.4	1935	gaG/ga	20/20	0.384622700890034	4	FACETS	0.858	0.827	0.887			1	INDETERMINATE	3	TRUE	NA	0.745609309068006	4		553	961	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946749	71946749	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1289	263	707	0	ENST00000298229.2:c.2690G>C	p.Gly897Ala	p.G897A	ENST00000298229	NM_001567.3	897	gGa/gCa	24/28	0.745609309068006	5	FACETS	0.963	0.9	1	0.321	0.3	0.343	CLONAL	1	TRUE	2	0.745609309068006	5		707	1552	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864994	57864994	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs993256018	NA	P-0038329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	308	745	0	ENST00000228682.2:c.2471C>G	p.Ser824Cys	p.S824C	ENST00000228682	NM_005269.2	824	tCt/tGt	12/12	0.521941377464028	4	FACETS	1	0.975	1	0.355	0.334	0.376	CLONAL	1	TRUE	1	0.745609309068006	4		745	1355	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915295	32915295	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	73	696	0	ENST00000380152.3:c.6803G>C	p.Arg2268Thr	p.R2268T	ENST00000380152		2268	aGa/aCa	11/27	0.294051593154912	3	FACETS	0.766	0.674	0.863	0.255	0.224	0.288	INDETERMINATE	1	TRUE	0	0.745609309068006	3		696	351	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304079	91304079	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	96	579	0	ENST00000355112.3:c.1476C>G	p.Phe492Leu	p.F492L	ENST00000355112	NM_000057.2	492	ttC/ttG	7/22	1	2	FACETS	0.817	0.737	0.901	0.817	0.737	0.901	CLONAL	1	TRUE	1	0.745609309068006	2		579	315	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867331	68867734	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	GACTACTTGAACGAATGGGGCAATCGCTTCAAGAAGCTGGCTGACATGTACGGAGGCGGCGAGGACGACTAGGGGACTCGAGAGAGGCGGGCCCCAGACCCATGTGCTGGGAAATGCAGAAATCACGTTGCTGGTGGTTTTTCAGCTCCCTTCCCTTGAGATGAGTTTCTGGGGAAAAAAAAGAGACTGGTTAGTGATGCAGTTAGTATAGCTTTATACTCTCTCCACTTTATAGCTCTAATAAGTTTGTGTTAGAAAAGTTTCGACTTATTTCTTAAAGCTTTTTTTTTTTTCCCATCACTCTTTACATGGTGGTGATGTCCAAAAGATACCCAAATTTTAATATTCCAGAAGAACAACTTTAGCATCAGAAGGTTCACCCAGCACCTTGCAGATTTTCTTAA	GACTACTTGAACGAATGGGGCAATCGCTTCAAGAAGCTGGCTGACATGTACGGAGGCGGCGAGGACGACTAGGGGACTCGAGAGAGGCGGGCCCCAGACCCATGTGCTGGGAAATGCAGAAATCACGTTGCTGGTGGTTTTTCAGCTCCCTTCCCTTGAGATGAGTTTCTGGGGAAAAAAAAGAGACTGGTTAGTGATGCAGTTAGTATAGCTTTATACTCTCTCCACTTTATAGCTCTAATAAGTTTGTGTTAGAAAAGTTTCGACTTATTTCTTAAAGCTTTTTTTTTTTTCCCATCACTCTTTACATGGTGGTGATGTCCAAAAGATACCCAAATTTTAATATTCCAGAAGAACAACTTTAGCATCAGAAGGTTCACCCAGCACCTTGCAGATTTTCTTAA	-	novel	NA	P-0038329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	97	537	0	ENST00000261769.5:c.2579_*333del		p.*860*	ENST00000261769	NM_004360.3	860		16/16	0.657459184129367	3	FACETS	0.386	0.343	0.431	0.193	0.171	0.216	SUBCLONAL	1	TRUE	1	0.745609309068006	3		537	926	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740472	58740472	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	245	586	0	ENST00000305921.3:c.1377del	p.Asn460MetfsTer5	p.N460Mfs*5	ENST00000305921	NM_003620.3	459	gaG/ga	6/6	0.587061825460834	3	FACETS	0.864	0.816	0.912	0.864	0.816	0.912	CLONAL	2	TRUE	1	0.745609309068006	3		586	522	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252940	36252940	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	208	429	1	ENST00000300305.3:c.422del	p.Ser141TrpfsTer4	p.S141Wfs*4	ENST00000300305		141	tCg/tg	4/8	0.745609309068006	3	FACETS	1	0.97	1			1	CLONAL	1	TRUE	NA	0.745609309068006	3		430	713	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38153395	38153395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	25	613	2	ENST00000317025.8:c.2834G>A	p.Gly945Asp	p.G945D	ENST00000317025	NM_023034.1	945	gGc/gAc	16/24	0.687182606606034	1	FACETS	0.098	0.077	0.123	0.098	0.077	0.123	SUBCLONAL	1	TRUE	0	0.745609309068006	1		615	429	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	363	578	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.376803308772753	6	FACETS	0.994	0.947	1	0.994	0.947	1	CLONAL	4	TRUE	2	0.376803308772753	6		578	850	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920413	114920413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767830105	NA	P-0038331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	96	435	0	ENST00000543371.1:c.1354G>A	p.Gly452Arg	p.G452R	ENST00000543371	NM_001198531.1	452	Ggg/Agg	13/14	1	2	FACETS	0.712	0.634	0.794	0.712	0.634	0.794	SUBCLONAL	1	TRUE	1	0.376803308772753	2		435	716	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856098	111856098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	76	266	0	ENST00000341259.2:c.149G>A	p.Arg50Gln	p.R50Q	ENST00000341259	NM_005475.2	50	cGg/cAg	2/8	0.361312943505473	3	FACETS	1	0.884	1	0.503	0.442	0.567	CLONAL	1	TRUE	1	0.376803308772753	3		266	477	SUCCESS
APC	324	MSKCC	GRCh37	5	112175248	112175249	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTGA	novel	NA	P-0038331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	96	206	0	ENST00000257430.4:c.3959_3962dup	p.Val1323ArgfsTer10	p.V1323Rfs*10	ENST00000257430	NM_000038.5	1319	-/GTGA	16/16	0.376803308772753	2	FACETS	0.855	0.771	0.941	0.855	0.771	0.941	CLONAL	2	TRUE	0	0.376803308772753	2		206	298	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577574	+	protein_altering_variant	In_Frame_Del	DEL	CACATGT	CACATGT	A	novel	NA	P-0038331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	224	497	1	ENST00000269305.4:c.707_713delinsT	p.Tyr236_Cys238delinsPhe	p.Y236_C238delinsF	ENST00000269305	NM_001126112.2	236	tACATGTGt/tTt	7/11	NA	2	FACETS	0.864	0.808	0.921			1	INDETERMINATE	2	TRUE	NA	0.376803308772753	2		498	688	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0038334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	205	283	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		283	540	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	39	399	0				ENST00000310581	NM_198253.2	-/1132			0.161791574551144	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		399	137	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217380	123217380	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	133	179	0	ENST00000218089.9:c.3034C>T	p.Arg1012Ter	p.R1012*	ENST00000218089	NM_001042749.1	1012	Cga/Tga	29/35	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	0	NA	2		179	205	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993874	72993874	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	59	433	0	ENST00000268489.5:c.171C>A	p.Phe57Leu	p.F57L	ENST00000268489	NM_006885.3	57	ttC/ttA	2/10	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		433	349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0038335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	238	625	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.47824304527831	1	FACETS	0.922	0.863	0.982	0.922	0.863	0.982	CLONAL	1	TRUE	0	0.492616484841133	1		627	790	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0038335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	123	413	0	ENST00000311936.3:c.34_35delinsCT	p.Gly12Leu	p.G12L	ENST00000311936	NM_004985.3	12	GGt/CTt	2/5	1	2	FACETS	0.788	0.714	0.865	0.788	0.714	0.865	SUBCLONAL	1	TRUE	1	0.492616484841133	2		413	634	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226398	41226398	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs41293457	NA	P-0038336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	60	620	0	ENST00000357654.3:c.4625C>G	p.Ser1542Cys	p.S1542C	ENST00000357654	NM_007294.3	1542	tCt/tGt	14/23	1	2	FACETS	0.51	0.438	0.589	0.51	0.438	0.589	SUBCLONAL	1	TRUE	1	0.29	2		620	811	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192140	108192141	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0038336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	69	506	0	ENST00000278616.4:c.6568_6569dup	p.Arg2191GlnfsTer45	p.R2191Qfs*45	ENST00000278616	NM_000051.3	2189	ttc/tTCtc	45/63	1	2	FACETS	0.784	0.683	0.893	0.784	0.683	0.893	SUBCLONAL	1	TRUE	1	0.29	2		506	607	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562112	21562113	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	187	1074	0	ENST00000382592.4:c.1806dup	p.Lys603Ter	p.K603*	ENST00000382592	NM_014572.2	602	-/T	4/8	0.262970328620008	1	FACETS	0.892	0.822	0.965	0.892	0.822	0.965	CLONAL	1	TRUE	0	0.29	1		1074	1236	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005009	150006016	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAATACTTCCATTTGTATATGACGAAGGAGCAGCAGATCCCCCTGTTTGTAAAGCAGAAGGGCTTTGTCCATTAGCTGCTGTCAGAGGATATGGAGGTGGTGGCTGCCGATTCACAGTGCCAGCAGGGACAACATTTTGGTGTATCATGAAATCAGTTTGTCCAGTACCATTCTGCATTCCAGGTCTCCCTGATGGAAAGTTAAATTTGCTAGAACTCTGCATGATGATTGGTTGTCTGCCAACAGGAACAGAACTAATGCCTCTCTGTCCTTGATTAGGAGGATTCATGGGGGAAGTGTTGAGAGGTGGTGGAGGATAGCCCTCTTGCCATGCCCCAGGTGGGACAGGAGAGATTCGGGAGATTACGTATTCCATGTTTCCAGAATAGCGCTTTGTTTGAGAGTTTGGTTCCCATGAAGGGGGAGGTGGAGTTGTACCTCTTGGAGGGGGAGTCTGGCCTCTTGGAGGTGGTGGAGGAGTAACACTCCTTACTTGAGGTGGTGGTGGGGGGTTCACTCTCTGTCCGTTGCTAGGGTGAGCTTGAACAAATGCTGATATACCAGATCCAGACAAAGGTCTTCCTACATCTGTCTGTGAGTTGGGACTCTCAGAATGATAGGCCACACTTTCTCCTAGTGGCGGGCCATGCCTCTGAGGAACTAAGGATTCTTTAGAACCTTTCCAGCTCTGTTTGCGGTTAACTGATTGCTGCACATTCCCTATGGTTATAAGAGAGATAAAGAGAAAAAAGAATCATGTTTTTAACCTCTAATTTTTGAAAACCTTAGCTTGCAATTCTGATATTACAAATGATACTCAATTCTCTTTCAAGAATTATAAAAATATAAAAAAGTTCAAGTGATCTCTTGTACAAAATGGTGACTGTAGTTAATAACAACGTATTGTACTCCTGAAAATTGCCGAGAGTAAATTTGAAGTATTCTCACTACAAAAAAATGATATGTGAGGTAATAATACATGTTATTTGGCTCAATTTAGCAAAAAAA	GAATACTTCCATTTGTATATGACGAAGGAGCAGCAGATCCCCCTGTTTGTAAAGCAGAAGGGCTTTGTCCATTAGCTGCTGTCAGAGGATATGGAGGTGGTGGCTGCCGATTCACAGTGCCAGCAGGGACAACATTTTGGTGTATCATGAAATCAGTTTGTCCAGTACCATTCTGCATTCCAGGTCTCCCTGATGGAAAGTTAAATTTGCTAGAACTCTGCATGATGATTGGTTGTCTGCCAACAGGAACAGAACTAATGCCTCTCTGTCCTTGATTAGGAGGATTCATGGGGGAAGTGTTGAGAGGTGGTGGAGGATAGCCCTCTTGCCATGCCCCAGGTGGGACAGGAGAGATTCGGGAGATTACGTATTCCATGTTTCCAGAATAGCGCTTTGTTTGAGAGTTTGGTTCCCATGAAGGGGGAGGTGGAGTTGTACCTCTTGGAGGGGGAGTCTGGCCTCTTGGAGGTGGTGGAGGAGTAACACTCCTTACTTGAGGTGGTGGTGGGGGGTTCACTCTCTGTCCGTTGCTAGGGTGAGCTTGAACAAATGCTGATATACCAGATCCAGACAAAGGTCTTCCTACATCTGTCTGTGAGTTGGGACTCTCAGAATGATAGGCCACACTTTCTCCTAGTGGCGGGCCATGCCTCTGAGGAACTAAGGATTCTTTAGAACCTTTCCAGCTCTGTTTGCGGTTAACTGATTGCTGCACATTCCCTATGGTTATAAGAGAGATAAAGAGAAAAAAGAATCATGTTTTTAACCTCTAATTTTTGAAAACCTTAGCTTGCAATTCTGATATTACAAATGATACTCAATTCTCTTTCAAGAATTATAAAAATATAAAAAAGTTCAAGTGATCTCTTGTACAAAATGGTGACTGTAGTTAATAACAACGTATTGTACTCCTGAAAATTGCCGAGAGTAAATTTGAAGTATTCTCACTACAAAAAAATGATATGTGAGGTAATAATACATGTTATTTGGCTCAATTTAGCAAAAAAA	-	novel	NA	P-0038336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	44	389	0	ENST00000253339.5:c.497-288_1216del		p.X166_splice	ENST00000253339		166		3/7	0.204885082532764	2	FACETS	0.712	0.598	0.838	0.356	0.299	0.419	SUBCLONAL	1	TRUE	0	0.29	2		389	426	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346281	152346281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	51	558	0	ENST00000359321.1:c.289G>A	p.Glu97Lys	p.E97K	ENST00000359321	NM_005431.1	97	Gag/Aag	3/3	1	2	FACETS	0.52	0.441	0.607	0.52	0.441	0.607	SUBCLONAL	1	TRUE	1	0.29	2		558	676	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436833	52436840	+	frameshift_variant	Frame_Shift_Del	DEL	ACGCCTCA	ACGCCTCA	G	novel	NA	P-0038336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	62	650	0	ENST00000460680.1:c.1938_1945delinsC	p.Glu647AlafsTer6	p.E647Afs*6	ENST00000460680	NM_004656.3	646	taTGAGGCGTgc/taCgc	15/17	1	2	FACETS	0.622	0.537	0.715	0.622	0.537	0.715	SUBCLONAL	1	TRUE	1	0.29	2		650	687	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0038337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	199	283	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		283	553	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0038338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	65	483	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.85	0.738	0.971	0.85	0.738	0.971	CLONAL	1	TRUE	1	0.3	2		483	510	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591896	48591896	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	55	447	0	ENST00000342988.3:c.1059C>A	p.Tyr353Ter	p.Y353*	ENST00000342988	NM_005359.5	353	taC/taA	9/12	1	2	FACETS	0.849	0.728	0.98	0.849	0.728	0.98	CLONAL	1	TRUE	1	0.3	2		447	432	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528069	103528069	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	86	412	0	ENST00000355739.4:c.3377C>A	p.Ala1126Asp	p.A1126D	ENST00000355739	NM_000123.3	1126	gCt/gAt	15/15	1	2	FACETS	0.94	0.832	1	0.94	0.832	1	CLONAL	1	TRUE	1	0.3	2		412	610	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929083	32929083	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	AG	novel	NA	P-0038338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	36	520	0	ENST00000380152.3:c.7093delinsAG	p.His2365ArgfsTer27	p.H2365Rfs*27	ENST00000380152		2365	Cat/AGat	14/27	1	2	FACETS	1	0.831	1	1	0.831	1	CLONAL	1	TRUE	1	0.3	2		520	239	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0038339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	76	701	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.233725099898354	1	FACETS	0.923	0.81	1	0.923	0.81	1	CLONAL	1	TRUE	0	0.233725099898354	1		701	622	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577140	7577140	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	369	641	0	ENST00000269305.4:c.798del	p.Arg267GlyfsTer78	p.R267Gfs*78	ENST00000269305	NM_001126112.2	266	ggA/gg	8/11	0.233725099898354	1	FACETS	0.897	0.857	0.938	1	0.997	1	CLONAL	4	TRUE	0	0.233725099898354	1		641	777	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383608	42383608	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782307227	NA	P-0038339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	154	441	2	ENST00000221972.3:c.383C>T	p.Pro128Leu	p.P128L	ENST00000221972	NM_021601.3	128	cCg/cTg	3/5	0.233725099898354	1	FACETS	1	0.976	1	1	0.993	1	CLONAL	2	TRUE	0	0.233725099898354	1		443	505	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398280	25398281	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCA	novel	NA	P-0038339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	233	600	0	ENST00000311936.3:c.36_38dup	p.Gly13dup	p.G13dup	ENST00000311936	NM_004985.3	13	ggc/ggTGGc	2/5	0.233725099898354	2	FACETS	1	0.971	1	1	0.993	1	CLONAL	3	TRUE	0	0.233725099898354	2		600	628	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0038340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	91	614	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.271356633277333	1	FACETS	0.92	0.818	1	0.92	0.818	1	CLONAL	1	TRUE	0	0.271356633277333	1		614	630	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845511	128845511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs111694017	NA	P-0038340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	41	736	0	ENST00000249373.3:c.808G>A	p.Val270Ile	p.V270I	ENST00000249373	NM_005631.4	270	Gtc/Atc	4/12	1	2	FACETS	0.477	0.397	0.567	0.477	0.397	0.567	SUBCLONAL	1	TRUE	1	0.271356633277333	2		736	633	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176504	142176504	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1196005889	NA	P-0038340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	37	372	1	ENST00000350721.4:c.7597C>T	p.Arg2533Ter	p.R2533*	ENST00000350721	NM_001184.3	2533	Cga/Tga	45/47	1	2	FACETS	0.557	0.458	0.667	0.557	0.458	0.667	SUBCLONAL	1	TRUE	1	0.271356633277333	2		373	490	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300134	15300204	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGGACAGGTGCAAATGGCCCGGCCGTTCACCGGATTTGTGTCACAGATAGCATCCTCGTGGCAGGGGTT	GGAGGACAGGTGCAAATGGCCCGGCCGTTCACCGGATTTGTGTCACAGATAGCATCCTCGTGGCAGGGGTT	-	novel	NA	P-0038340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	39	737	0	ENST00000263388.2:c.1072_1142del	p.Asn358ArgfsTer8	p.N358Rfs*8	ENST00000263388	NM_000435.2	358	AACCCCTGCCACGAGGATGCTATCTGTGACACAAATCCGGTGAACGGCCGGGCCATTTGCACCTGTCCTCCc/c	7/33	0.247098748752926	1	FACETS	0.386	0.319	0.462	0.386	0.319	0.462	SUBCLONAL	1	TRUE	0	0.271356633277333	1		737	643	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0038341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	358	426	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	0.550693397896471	4	FACETS	0.968	0.922	1			1	CLONAL	2	TRUE	NA	0.807528040800606	4		426	828	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595518	55595520	+	missense_variant	Missense_Mutation	TNP	ACA	ACA	TTT	novel	NA	P-0038341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	289	320	0	ENST00000288135.5:c.2008_2010delinsTTT	p.Thr670Phe	p.T670F	ENST00000288135	NM_000222.2	670	ACA/TTT	14/21	0.550693397896471	4	FACETS	0.906	0.857	0.955			1	CLONAL	2	TRUE	NA	0.807528040800606	4		320	714	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0038342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	297	428	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	0.630380083076302	4	FACETS	0.967	0.915	1	0.967	0.915	1	CLONAL	2	TRUE	2	0.630380083076302	4		428	794	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579346	7579346	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs781724995	NA	P-0038342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	345	936	0	ENST00000269305.4:c.341T>A	p.Leu114Ter	p.L114*	ENST00000269305	NM_001126112.2	114	tTg/tAg	4/11	0.571826998706377	1	FACETS	0.984	0.937	1	0.984	0.937	1	CLONAL	1	TRUE	0	0.630380083076302	1		936	762	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137243	64137243	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs565756385	NA	P-0038342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	203	788	3	ENST00000334205.4:c.1675C>T	p.Pro559Ser	p.P559S	ENST00000334205	NM_003942.2	559	Ccg/Tcg	14/17	1	2	FACETS	0.668	0.619	0.719	0.668	0.619	0.719	SUBCLONAL	1	TRUE	1	0.630380083076302	2		791	964	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431652	431652	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	417	695	0	ENST00000399788.2:c.2357A>G	p.Asp786Gly	p.D786G	ENST00000399788	NM_001042603.1	786	gAt/gGt	17/28	NA	2	FACETS	0.986	0.95	1			1	INDETERMINATE	2	TRUE	NA	0.630380083076302	2		695	671	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743919	41743919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201003955	NA	P-0038342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1206	762	1066	0	ENST00000301178.4:c.854C>T	p.Ser285Leu	p.S285L	ENST00000301178	NM_021913.4	285	tCg/tTg	7/20	0.459575154976008	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.630380083076302	4		1066	1968	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39713177	39713177	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	29	337	0	ENST00000361337.2:c.583C>A	p.Pro195Thr	p.P195T	ENST00000361337	NM_003286.2	195	Ccg/Acg	8/21	0.611750722550513	3	FACETS	0.328	0.263	0.402	0.164	0.131	0.201	SUBCLONAL	1	TRUE	1	0.630380083076302	3		337	369	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520543	176520543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	478	888	0	ENST00000292408.4:c.1388C>T	p.Pro463Leu	p.P463L	ENST00000292408	NM_213647.1	463	cCc/cTc	10/18	0.19537341730062	2	FACETS	1	0.995	1	0.647	0.62	0.674	INDETERMINATE	1	TRUE	0	0.630380083076302	2		888	1172	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012254	152012254	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	101	595	0	ENST00000262189.6:c.559T>G	p.Ser187Ala	p.S187A	ENST00000262189	NM_170606.2	187	Tca/Gca	4/59	0.549206640862188	3	FACETS	0.623	0.558	0.693			1	SUBCLONAL	1	TRUE	NA	0.630380083076302	3		595	676	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061006	38061017	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCCGGGGGCC	GGCCCGGGGGCC	CGCCGGCCCCG	novel	NA	P-0038342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	26	111	0	ENST00000250448.2:c.972_983delinsCGGGGCCGGCG	p.Ala325GlyfsTer25	p.A325Gfs*25	ENST00000250448	NM_004496.3	324	ccGGCCCCCGGGCCc/ccCGGGGCCGGCGc	2/2	1	2	FACETS	0.737	0.594	0.893	0.737	0.594	0.893	SUBCLONAL	1	TRUE	1	0.630380083076302	2		111	112	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0038343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	54	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	0.671	0.912	0.786	0.671	0.912	CLONAL	1	TRUE	1	0.239292734390816	2		457	574	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215224	142215224	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1473705248	NA	P-0038343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	70	386	0	ENST00000350721.4:c.5877G>T	p.Arg1959Ser	p.R1959S	ENST00000350721	NM_001184.3	1959	agG/agT	34/47	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.239292734390816	2		386	449	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184119	123184119	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	46	361	0	ENST00000218089.9:c.977A>G	p.Asp326Gly	p.D326G	ENST00000218089	NM_001042749.1	326	gAc/gGc	11/35	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.345224510044196	2		361	225	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	51	399	0				ENST00000310581	NM_198253.2	-/1132			0.132187911294936	6	FACETS	1	0.923	1	0.733	0.634	0.837	INDETERMINATE	2	TRUE	3	0.601306307627641	6		399	170	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0038346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	457	940	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	0.601306307627641	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.601306307627641	2		940	680	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	56	578	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.393541500601485	1	FACETS	0.387	0.332	0.446	0.387	0.332	0.446	SUBCLONAL	1	TRUE	0	0.482193412724274	1		578	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0038347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	230	855	0	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.420474422941573	0	FACETS	0.815	0.765	0.866			1	CLONAL	1	TRUE	0	0.482193412724274	0		855	606	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589584	67589589	+	inframe_deletion	In_Frame_Del	DEL	ACATGA	ACATGA	-	novel	NA	P-0038347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	34	275	0	ENST00000274335.5:c.1348_1353del	p.His450_Glu451del	p.H450_E451del	ENST00000274335		449	ttACATGAa/tta	10/15	0.482193412724274	1	FACETS	0.369	0.302	0.443	0.369	0.302	0.443	SUBCLONAL	1	TRUE	0	0.482193412724274	1		275	290	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95598956	95598956	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	88	416	0	ENST00000393063.1:c.203C>A	p.Ser68Ter	p.S68*	ENST00000393063	NM_030621.3	68	tCa/tAa	4/28	0.482193412724274	1	FACETS	0.791	0.707	0.88	0.791	0.707	0.88	SUBCLONAL	1	TRUE	0	0.482193412724274	1		416	350	SUCCESS
APC	324	MSKCC	GRCh37	5	112173728	112173728	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0038347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	135	354	0	ENST00000257430.4:c.2438del	p.Asn813IlefsTer7	p.N813Ifs*7	ENST00000257430	NM_000038.5	813	Aat/at	16/16	0.482193412724274	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.482193412724274	1		354	309	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411492	63411493	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	226	449	0	ENST00000330258.3:c.1674dup	p.Glu559ArgfsTer21	p.E559Rfs*21	ENST00000330258	NM_152424.3	558	-/A	2/2	0.109307683791813	2	FACETS	1	0.947	1			1	INDETERMINATE	2	TRUE	NA	0.482193412724274	2		449	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0038349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	160	799	1	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.748149526366628	1	FACETS	0.988	0.928	1	0.988	0.928	1	CLONAL	1	TRUE	0	0.748149526366628	1		800	271	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521543	8521543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868728165	NA	P-0038349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	101	503	0	ENST00000356435.5:c.695G>A	p.Arg232His	p.R232H	ENST00000356435		232	cGc/cAc	9/35	0.411737728346067	3	FACETS	1	0.952	1	0.544	0.491	0.599	INDETERMINATE	1	TRUE	1	0.748149526366628	3		503	341	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455090	50455090	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	87	423	1	ENST00000331340.3:c.637C>T	p.Arg213Ter	p.R213*	ENST00000331340	NM_006060.4	213	Cga/Tga	6/8	0.748149526366628	3	FACETS	0.852	0.76	0.949	0.426	0.38	0.475	CLONAL	1	TRUE	1	0.748149526366628	3		424	375	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	103	399	0				ENST00000310581	NM_198253.2	-/1132			0.244226849524374	3	FACETS	0.962	0.871	1	1	0.983	1	CLONAL	3	FALSE	1	0.244226849524374	3		399	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	253	578	1	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.244226849524374	1	FACETS	0.92	0.861	0.98	1	0.994	1	CLONAL	2	FALSE	0	0.244226849524374	1		579	989	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992136	11992136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	78	317	0	ENST00000396373.4:c.226G>A	p.Glu76Lys	p.E76K	ENST00000396373	NM_001987.4	76	Gag/Aag	3/8	0.244226849524374	1	FACETS	0.876	0.77	0.99	0.876	0.77	0.99	CLONAL	1	FALSE	0	0.244226849524374	1		317	640	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164509	36164509	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	117	198	1	ENST00000300305.3:c.1366G>A	p.Glu456Lys	p.E456K	ENST00000300305		456	Gag/Aag	8/8	1	2	FACETS	0.776	0.702	0.855	1	0.985	1	SUBCLONAL	2	FALSE	1	0.244226849524374	2		199	617	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239915	53239915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	118	278	0	ENST00000375401.3:c.1526C>T	p.Ser509Leu	p.S509L	ENST00000375401	NM_004187.3	509	tCa/tTa	11/26	0.215868164583656	2	FACETS	1	0.929	1			1	CLONAL	2	FALSE	NA	0.244226849524374	2		278	470	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500838	8500838	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	130	401	0	ENST00000356435.5:c.2044G>A	p.Glu682Lys	p.E682K	ENST00000356435		682	Gaa/Aaa	13/35	0.244226849524374	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	0	0.244226849524374	1		401	667	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856356	45856356	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	118	626	0	ENST00000391945.4:c.1816G>C	p.Glu606Gln	p.E606Q	ENST00000391945	NM_000400.3	606	Gag/Cag	19/23	0.244226849524374	1	FACETS	0.812	0.731	0.898	0.812	0.731	0.898	CLONAL	1	FALSE	0	0.244226849524374	1		626	1045	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556049	29556049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	35	217	0	ENST00000356175.3:c.2416G>A	p.Glu806Lys	p.E806K	ENST00000356175	NM_000267.3	806	Gaa/Aaa	21/57	0.244226849524374	1	FACETS	0.987	0.813	1	0.987	0.813	1	CLONAL	1	FALSE	0	0.244226849524374	1		217	255	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29701088	29701088	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	77	371	0	ENST00000356175.3:c.8372G>A	p.Arg2791Gln	p.R2791Q	ENST00000356175	NM_000267.3	2791	cGa/cAa	57/57	0.244226849524374	1	FACETS	0.813	0.713	0.92	0.813	0.713	0.92	CLONAL	1	FALSE	0	0.244226849524374	1		371	681	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245288	46245288	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	146	424	0	ENST00000334344.6:c.3382C>T	p.Gln1128Ter	p.Q1128*	ENST00000334344	NM_152641.2	1128	Cag/Tag	15/21	0.244226849524374	4	FACETS	0.868	0.792	0.947			1	CLONAL	2	FALSE	NA	0.244226849524374	4		424	857	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115889	8115889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	130	556	0	ENST00000346208.3:c.1235C>T	p.Ser412Phe	p.S412F	ENST00000346208		412	tCc/tTc	6/6	0.244226849524374	3	FACETS	1	0.929	1	0.516	0.467	0.568	CLONAL	1	FALSE	1	0.244226849524374	3		556	1158	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983095	149983095	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	21	441	0	ENST00000253339.5:c.3163G>C	p.Glu1055Gln	p.E1055Q	ENST00000253339		1055	Gaa/Caa	7/7	1	2	FACETS	0.454	0.349	0.576	0.454	0.349	0.576	SUBCLONAL	1	FALSE	1	0.244226849524374	2		441	379	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738189	133738189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150134901	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	69	441	1	ENST00000318560.5:c.589G>A	p.Glu197Lys	p.E197K	ENST00000318560	NM_005157.4	197	Gag/Aag	4/11	0.244226849524374	1	FACETS	0.588	0.511	0.672	0.588	0.511	0.672	SUBCLONAL	1	FALSE	0	0.244226849524374	1		442	843	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223469	2223469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1462122341	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	52	286	0	ENST00000398665.3:c.3580G>A	p.Glu1194Lys	p.E1194K	ENST00000398665	NM_032482.2	1194	Gag/Aag	25/28	0.244226849524374	1	FACETS	0.831	0.708	0.964	0.831	0.708	0.964	CLONAL	1	FALSE	0	0.244226849524374	1		286	450	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287395	33287395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	58	448	0	ENST00000374542.5:c.1702G>A	p.Glu568Lys	p.E568K	ENST00000374542	NM_001141970.1	568	Gag/Aag	6/8	1	2	FACETS	0.793	0.681	0.915	0.793	0.681	0.915	CLONAL	1	FALSE	1	0.244226849524374	2		448	599	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268865	98268865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	106	194	0	ENST00000331920.6:c.218G>A	p.Arg73Gln	p.R73Q	ENST00000331920	NM_000264.3	73	cGg/cAg	2/24	0.244226849524374	1	FACETS	0.85	0.767	0.938	1	0.986	1	CLONAL	2	FALSE	0	0.244226849524374	1		194	448	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106498	27106498	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	212	639	0	ENST00000324856.7:c.6109C>T	p.Gln2037Ter	p.Q2037*	ENST00000324856	NM_006015.4	2037	Cag/Tag	20/20	1	2	FACETS	0.811	0.752	0.871	1	0.992	1	CLONAL	2	FALSE	1	0.244226849524374	2		639	1071	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073515	8073515	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	63	342	0	ENST00000377482.5:c.1144A>G	p.Ile382Val	p.I382V	ENST00000377482	NM_018948.3	382	Att/Gtt	4/4	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	FALSE	1	0.244226849524374	2		342	512	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63662161	63662161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	93	306	0	ENST00000279873.7:c.265G>A	p.Asp89Asn	p.D89N	ENST00000279873	NM_032199.2	89	Gac/Aac	2/10	0.244226849524374	3	FACETS	0.805	0.718	0.897	0.805	0.718	0.897	CLONAL	2	FALSE	1	0.244226849524374	3		306	531	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	532660	532660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748639813	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	114	629	1	ENST00000451590.1:c.546G>A	p.Met182Ile	p.M182I	ENST00000451590	NM_001130442.1	182	atG/atA	5/5	0.244226849524374	1	FACETS	0.968	0.871	1	0.968	0.871	1	CLONAL	1	FALSE	0	0.244226849524374	1		630	847	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450042	32450042	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	90	450	0	ENST00000332351.3:c.769+1G>T		p.X257_splice	ENST00000332351	NM_024426.4	257			0.244226849524374	1	FACETS	0.837	0.742	0.938	0.837	0.742	0.938	CLONAL	1	FALSE	0	0.244226849524374	1		450	773	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211525	46211525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	59	251	0	ENST00000334344.6:c.491C>T	p.Ser164Leu	p.S164L	ENST00000334344	NM_152641.2	164	tCa/tTa	5/21	0.244226849524374	4	FACETS	1	0.952	1			1	CLONAL	2	FALSE	NA	0.244226849524374	4		251	248	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448526	49448526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371342351	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	51	432	0	ENST00000301067.7:c.185C>T	p.Pro62Leu	p.P62L	ENST00000301067	NM_003482.3	62	cCg/cTg	3/54	1	2	FACETS	0.653	0.554	0.761	0.653	0.554	0.761	SUBCLONAL	1	FALSE	1	0.244226849524374	2		432	640	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606025	81606025	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	40	341	0	ENST00000298171.2:c.695A>G	p.Asp232Gly	p.D232G	ENST00000298171	NM_000369.2	232	gAc/gGc	9/10	0.244226849524374	1	FACETS	0.499	0.414	0.594	0.499	0.414	0.594	SUBCLONAL	1	FALSE	0	0.244226849524374	1		341	576	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641130	3641130	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	86	969	0	ENST00000294008.3:c.2509A>G	p.Lys837Glu	p.K837E	ENST00000294008	NM_032444.2	837	Aag/Gag	12/15	0.244226849524374	1	FACETS	0.544	0.48	0.614	0.544	0.48	0.614	SUBCLONAL	1	FALSE	0	0.244226849524374	1		969	1136	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40462653	40462653	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	147	469	0	ENST00000345506.4:c.2351G>T	p.Gly784Val	p.G784V	ENST00000345506	NM_003152.3	784	gGt/gTt	20/20	0.244226849524374	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	0	0.244226849524374	1		469	732	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437558	56437558	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	187	572	0	ENST00000407977.2:c.904T>G	p.Trp302Gly	p.W302G	ENST00000407977		302	Tgg/Ggg	8/10	0.244226849524374	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	0	0.244226849524374	1		572	1077	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677778	58677778	+	start_lost	Translation_Start_Site	SNP	G	G	C	novel	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	138	332	0	ENST00000305921.3:c.3G>C	p.Met1?	p.M1?	ENST00000305921	NM_003620.3	1	atG/atC	1/6	0.244226849524374	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	0	0.244226849524374	1		332	742	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367038	15367038	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	44	251	0	ENST00000263377.2:c.1588C>T	p.Gln530Ter	p.Q530*	ENST00000263377	NM_058243.2	530	Cag/Tag	9/20	0.244226849524374	1	FACETS	0.703	0.59	0.828	0.703	0.59	0.828	SUBCLONAL	1	FALSE	0	0.244226849524374	1		251	450	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428439	72428439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	176	521	0	ENST00000477973.2:c.565C>T	p.Pro189Ser	p.P189S	ENST00000477973	NM_012234.5	189	Cct/Tct	2/4	1	2	FACETS	0.954	0.881	1	1	0.992	1	CLONAL	2	FALSE	1	0.244226849524374	2		521	755	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443325	187443325	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	157	314	0	ENST00000232014.4:c.1801C>G	p.Pro601Ala	p.P601A	ENST00000232014	NM_001130845.1	601	Ccc/Gcc	8/10	1	2	FACETS	0.899	0.825	0.976	1	0.991	1	CLONAL	2	FALSE	1	0.244226849524374	2		314	715	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516891	187516891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	64	438	0	ENST00000441802.2:c.13090G>A	p.Glu4364Lys	p.E4364K	ENST00000441802	NM_005245.3	4364	Gaa/Aaa	26/27	1	2	FACETS	0.648	0.56	0.744	0.648	0.56	0.744	SUBCLONAL	1	FALSE	1	0.244226849524374	2		438	809	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158433	26158477	+	inframe_deletion	In_Frame_Del	DEL	GAAGGGCTCCAAGAAGGCGGTGACTAAGGCTCAGAAGAAGGACGG	GAAGGGCTCCAAGAAGGCGGTGACTAAGGCTCAGAAGAAGGACGG	-	novel	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1275	104	751	0	ENST00000289316.2:c.40_84del	p.Gly14_Lys28del	p.G14_K28del	ENST00000289316	NM_138720.2	12	aaGAAGGGCTCCAAGAAGGCGGTGACTAAGGCTCAGAAGAAGGACGGg/aag	1/2	1	2	FACETS	0.618	0.551	0.689	0.618	0.551	0.689	SUBCLONAL	1	FALSE	1	0.244226849524374	2		751	1379	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839986	27839994	+	inframe_deletion	In_Frame_Del	DEL	GACGCCACC	GACGCCACC	-	novel	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	65	257	0	ENST00000328488.2:c.100_108del	p.Gly34_Val36del	p.G34_V36del	ENST00000328488	NM_003533.2	34	GGTGGCGTC/-	1/1	1	2	FACETS	0.895	0.776	1	0.895	0.776	1	CLONAL	1	FALSE	1	0.244226849524374	2		257	595	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793518	89793518	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs940509117	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	52	295	0	ENST00000336032.3:c.587A>G	p.His196Arg	p.H196R	ENST00000336032	NM_006813.2	196	cAt/cGt	2/2	1	2	FACETS	0.852	0.732	0.98	1	0.972	1	CLONAL	2	FALSE	1	0.244226849524374	2		295	250	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001017	150001017	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	51	272	0	ENST00000253339.5:c.2587C>T	p.Gln863Ter	p.Q863*	ENST00000253339		863	Cag/Tag	4/7	1	2	FACETS	0.976	0.84	1	1	0.976	1	CLONAL	2	FALSE	1	0.244226849524374	2		272	214	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508547	106508547	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	30	292	0	ENST00000359195.3:c.541G>C	p.Val181Leu	p.V181L	ENST00000359195	NM_002649.2	181	Gtg/Ctg	2/11	1	2	FACETS	0.578	0.465	0.706	0.578	0.465	0.706	SUBCLONAL	1	FALSE	1	0.244226849524374	2		292	425	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859678	151859678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	102	331	0	ENST00000262189.6:c.10984G>A	p.Glu3662Lys	p.E3662K	ENST00000262189	NM_170606.2	3662	Gaa/Aaa	43/59	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.244226849524374	2		331	651	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194818	29194818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1224	94	902	0	ENST00000240100.2:c.910G>A	p.Glu304Lys	p.E304K	ENST00000240100	NM_001394.6	304	Gag/Aag	4/4	1	2	FACETS	0.584	0.518	0.655	0.584	0.518	0.655	SUBCLONAL	1	FALSE	1	0.244226849524374	2		902	1318	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220423	98220423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	195	555	0	ENST00000331920.6:c.3040C>T	p.Pro1014Ser	p.P1014S	ENST00000331920	NM_000264.3	1014	Ccc/Tcc	18/24	0.244226849524374	1	FACETS	0.802	0.743	0.863	1	0.991	1	CLONAL	2	FALSE	0	0.244226849524374	1		555	874	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0038353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	132	556	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	0.253714688079944	2		556	742	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0038353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	21	698	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	1	2	FACETS	0.189	0.144	0.241	0.189	0.144	0.241	SUBCLONAL	1	TRUE	1	0.253714688079944	2		698	876	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0038369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	265	755	0	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.434482800319253	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.434482800319253	1		755	866	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682384	37682384	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	327	645	0	ENST00000447079.4:c.3575del	p.Ala1192GlufsTer23	p.A1192Efs*23	ENST00000447079	NM_015083.1	1192	gCa/ga	13/14	0.362556684236667	1	FACETS	0.76	0.722	0.798	1	0.995	1	SUBCLONAL	2	TRUE	0	0.434482800319253	1		645	775	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216504	36216504	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	201	791	0	ENST00000222270.7:c.3767G>A	p.Gly1256Glu	p.G1256E	ENST00000222270	NM_014727.1	1256	gGa/gAa	12/37	0.108507816452658	6	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.434482800319253	6		791	1301	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	415	399	0				ENST00000310581	NM_198253.2	-/1132			0.449002434881052	4	FACETS	1	0.991	1	1	0.991	1	INDETERMINATE	3	TRUE	1	0.839365301910658	4		399	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0038370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	329	630	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	0.839365301910658	2		630	755	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0038370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	90	618	0	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	1	2	FACETS	0.293	0.26	0.329	0.293	0.26	0.329	SUBCLONAL	1	TRUE	1	0.839365301910658	2		618	732	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373136	118373136	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	254	376	1	ENST00000534358.1:c.6529G>T	p.Glu2177Ter	p.E2177*	ENST00000534358	NM_005933.3	2177	Gaa/Taa	27/36	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.839365301910658	2		377	551	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221679	36221679	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	433	850	2	ENST00000222270.7:c.5348A>G	p.Tyr1783Cys	p.Y1783C	ENST00000222270	NM_014727.1	1783	tAt/tGt	26/37	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.839365301910658	2		852	1004	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	162	578	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.379938274916737	5	FACETS	1	0.985	1			1	INDETERMINATE	3	TRUE	NA	0.683606606917054	5		578	276	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0038371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	234	481	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	1	2	FACETS	0.697	0.651	0.745	0.697	0.651	0.745	SUBCLONAL	1	TRUE	1	0.683606606917054	2		481	982	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876660825	NA	P-0038371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	249	674	0	ENST00000269305.4:c.569C>G	p.Pro190Arg	p.P190R	ENST00000269305	NM_001126112.2	190	cCt/cGt	6/11	0.653316465307257	1	FACETS	0.794	0.748	0.84	0.794	0.748	0.84	SUBCLONAL	1	TRUE	0	0.683606606917054	1		674	604	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257170	16257170	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	63	551	0	ENST00000375759.3:c.4435G>A	p.Asp1479Asn	p.D1479N	ENST00000375759	NM_015001.2	1479	Gat/Aat	11/15	1	2	FACETS	0.547	0.476	0.623	0.547	0.476	0.623	SUBCLONAL	1	TRUE	1	0.683606606917054	2		551	337	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584543	48584544	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0038371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	259	506	0	ENST00000342988.3:c.717_718del	p.Gln239HisfsTer24	p.Q239Hfs*24	ENST00000342988	NM_005359.5	239	cAG/c	6/12	0.581851897623512	2	FACETS	0.767	0.728	0.806	0.767	0.728	0.806	SUBCLONAL	2	TRUE	0	0.683606606917054	2		506	494	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566300	141566300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	175	483	0	ENST00000220592.5:c.1112C>T	p.Ser371Leu	p.S371L	ENST00000220592	NM_012154.3	371	tCg/tTg	9/19	1	2	FACETS	0.817	0.755	0.88	0.817	0.755	0.88	CLONAL	1	TRUE	1	0.683606606917054	2		483	627	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971192	21971193	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	GCCCATCATC	novel	NA	P-0038371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	189	499	0	ENST00000579755.1:c.199_208dup	p.Gln70ArgfsTer2	p.Q70Rfs*2	ENST00000579755		70	cag/cGATGATGGGCag	2/3	1	2	FACETS	0.615	0.569	0.663	0.615	0.569	0.663	SUBCLONAL	1	TRUE	1	0.683606606917054	2		499	899	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519975	NA	P-0038374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	299	729	0	ENST00000269305.4:c.403T>C	p.Cys135Arg	p.C135R	ENST00000269305	NM_001126112.2	135	Tgc/Cgc	5/11	0.214497446780252	2	FACETS	0.82	0.773	0.868	0.82	0.773	0.868	INDETERMINATE	2	TRUE	0	0.358393420012582	2		729	1017	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938932	178938932	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	99	394	0	ENST00000263967.3:c.2174A>G	p.Asp725Gly	p.D725G	ENST00000263967	NM_006218.2	725	gAt/gGt	14/21	0.171075213498884	5	FACETS	0.902	0.809	0.999	0.601	0.539	0.666	INDETERMINATE	2	TRUE	2	0.358393420012582	5		394	471	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056455	26056455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61751205	NA	P-0038374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	47	286	1	ENST00000343677.2:c.202G>A	p.Ala68Thr	p.A68T	ENST00000343677	NM_005319.3	68	Gcc/Acc	1/1	0.278763071044573	3	FACETS	0.907	0.768	1	0.453	0.384	0.529	CLONAL	1	TRUE	1	0.358393420012582	3		287	341	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020138	123020138	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	359	702	0	ENST00000355640.3:c.626A>T	p.Asn209Ile	p.N209I	ENST00000355640		209	aAt/aTt	2/7	0.208417763753569	4	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.358393420012582	4		702	1227	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0038375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	139	347	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.316033508778433	2	FACETS	0.843	0.774	0.914	0.843	0.774	0.914	CLONAL	2	TRUE	0	0.368061188075591	2		347	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578206	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs886039484	NA	P-0038375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	177	663	0	ENST00000269305.4:c.643A>C	p.Ser215Arg	p.S215R	ENST00000269305	NM_001126112.2	215	Agt/Cgt	6/11	0.368061188075591	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.368061188075591	1		663	773	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923144	48923144	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	51	287	0	ENST00000267163.4:c.596del	p.Leu199TyrfsTer2	p.L199Yfs*2	ENST00000267163	NM_000321.2	198	Ttt/tt	6/27	0.368061188075591	1	FACETS	0.983	0.845	1	0.983	0.845	1	CLONAL	1	TRUE	0	0.368061188075591	1		287	230	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800998	243800998	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	33	533	0	ENST00000263826.5:c.476T>A	p.Phe159Tyr	p.F159Y	ENST00000263826	NM_005465.4	159	tTt/tAt	5/13	0.295244904731568	4	FACETS	0.385	0.312	0.467	0.128	0.104	0.156	SUBCLONAL	1	TRUE	1	0.368061188075591	4		533	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579323	7579324	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	390	698	0	ENST00000269305.4:c.363dup	p.Val122CysfsTer27	p.V122Cfs*27	ENST00000269305	NM_001126112.2	121	-/T	4/11	0.42166878276984	5	FACETS	1	0.991	1	0.889	0.854	0.924	CLONAL	4	TRUE	0	0.42166878276984	5		698	679	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395569	116395569	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs375951814	NA	P-0038377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	48	474	0	ENST00000397752.3:c.1862C>T	p.Thr621Ile	p.T621I	ENST00000397752	NM_000245.2	621	aCa/aTa	6/21	0.397338771489856	4	FACETS	1	0.963	1	0.739	0.632	0.854	CLONAL	1	TRUE	2	0.42166878276984	4		474	219	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122894	7122894	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	64	700	0	ENST00000302850.5:c.3365C>G	p.Ala1122Gly	p.A1122G	ENST00000302850	NM_000208.2	1122	gCt/gGt	18/22	0.42166878276984	4	FACETS	0.78	0.676	0.893	0.39	0.338	0.447	SUBCLONAL	1	TRUE	2	0.42166878276984	4		700	553	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960089	134960089	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	278	698	0	ENST00000398015.3:c.2446G>T	p.Glu816Ter	p.E816*	ENST00000398015	NM_004441.4	816	Gaa/Taa	13/16	0.42166878276984	3	FACETS	0.987	0.938	1	0.987	0.938	1	CLONAL	3	TRUE	0	0.42166878276984	3		698	539	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	114	536	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.884	0.796	0.976	0.884	0.796	0.976	CLONAL	1	TRUE	1	0.34539046526204	2		542	747	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	82	283	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.34539046526204	2		283	462	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	90	444	1	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.944	0.84	1	0.944	0.84	1	CLONAL	1	TRUE	1	0.34539046526204	2		445	552	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244269	5244269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568465790	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	118	619	0	ENST00000357368.4:c.1213G>A	p.Val405Ile	p.V405I	ENST00000357368	NM_002850.3	405	Gtc/Atc	11/38	1	2	FACETS	0.909	0.82	1	0.909	0.82	1	CLONAL	1	TRUE	1	0.34539046526204	2		619	752	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	105	681	5	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.811	0.726	0.9	0.811	0.726	0.9	CLONAL	1	TRUE	1	0.34539046526204	2		686	750	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	96	638	0	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.733	0.653	0.819	0.733	0.653	0.819	SUBCLONAL	1	TRUE	1	0.34539046526204	2		638	758	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	68	344	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.86	0.75	0.978	0.86	0.75	0.978	CLONAL	1	TRUE	1	0.34539046526204	2		344	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	134	616	1	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	1	2	FACETS	0.982	0.893	1	0.982	0.893	1	CLONAL	1	TRUE	1	0.34539046526204	2		617	790	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	58	270	0	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	0.767	0.66	0.882	0.767	0.66	0.882	SUBCLONAL	1	TRUE	1	0.34539046526204	2		270	438	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913558	32913559	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359479	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	70	455	0	ENST00000380152.3:c.5073dup	p.Trp1692MetfsTer3	p.W1692Mfs*3	ENST00000380152		1689	gca/gcAa	11/27	1	2	FACETS	0.774	0.675	0.879	0.774	0.675	0.879	SUBCLONAL	1	TRUE	1	0.34539046526204	2		455	524	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391024	89391024	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	111	551	0	ENST00000336596.2:c.1095del	p.Lys365AsnfsTer6	p.K365Nfs*6	ENST00000336596	NM_005233.5	364	Aaa/aa	5/17	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.34539046526204	2		551	592	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042434	16042434	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1568277803	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	91	458	0	ENST00000268712.3:c.1240C>T	p.Arg414Ter	p.R414*	ENST00000268712	NM_006311.3	414	Cga/Tga	12/46	1	2	FACETS	0.916	0.815	1	0.916	0.815	1	CLONAL	1	TRUE	1	0.34539046526204	2		458	575	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114817	108114817	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786204543	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	87	495	1	ENST00000278616.4:c.640del	p.Ser214ProfsTer16	p.S214Pfs*16	ENST00000278616	NM_000051.3	212	Ttt/tt	6/63	1	2	FACETS	0.9	0.798	1	0.9	0.798	1	CLONAL	1	TRUE	1	0.34539046526204	2		496	560	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509085	66509085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	54	268	0	ENST00000273854.3:c.242del	p.Asn81MetfsTer24	p.N81Mfs*24	ENST00000273854	NM_004439.5	81	aAt/at	2/18	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.34539046526204	2		268	284	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	277	662	2	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	0.342915491871757	3	FACETS	0.978	0.919	1	0.978	0.919	1	CLONAL	2	TRUE	1	0.34539046526204	3		664	962	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890149	76890150	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	88	427	0	ENST00000373344.5:c.4744dup	p.Thr1582AsnfsTer19	p.T1582Nfs*19	ENST00000373344	NM_000489.3	1582	aca/aAca	17/35	NA	2	FACETS	0.865	0.768	0.969			1	INDETERMINATE	1	TRUE	NA	0.34539046526204	2		427	589	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007824	45007825	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	77	418	0	ENST00000558401.1:c.276dup	p.Thr93HisfsTer2	p.T93Hfs*2	ENST00000558401	NM_004048.2	91	acc/aCcc	2/4	1	2	FACETS	0.83	0.73	0.937	0.83	0.73	0.937	CLONAL	1	TRUE	1	0.34539046526204	2		418	537	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007619	45007619	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs111482205	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	32	268	0	ENST00000558401.1:c.68-2A>G		p.X23_splice	ENST00000558401	NM_004048.2	23			1	2	FACETS	0.648	0.528	0.783	0.648	0.528	0.783	SUBCLONAL	1	TRUE	1	0.34539046526204	2		268	286	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097624	11097625	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1165714406	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	134	726	0	ENST00000358026.2:c.810dup	p.Gly271ArgfsTer16	p.G271Rfs*16	ENST00000358026	NM_001128849.1	268	-/C	5/36	1	2	FACETS	0.96	0.873	1	0.96	0.873	1	CLONAL	1	TRUE	1	0.34539046526204	2		726	808	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125379	7125379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778982272	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	125	668	1	ENST00000302850.5:c.3173C>T	p.Thr1058Met	p.T1058M	ENST00000302850	NM_000208.2	1058	aCg/aTg	17/22	1	2	FACETS	0.888	0.804	0.977	0.888	0.804	0.977	CLONAL	1	TRUE	1	0.34539046526204	2		669	815	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39772564	39772564	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	71	360	0	ENST00000288319.7:c.677del	p.Gly226ValfsTer65	p.G226Vfs*65	ENST00000288319	NM_182918.3	226	gGt/gt	6/10	0.34539046526204	2	FACETS	0.862	0.754	0.977	0.431	0.377	0.489	CLONAL	1	TRUE	0	0.34539046526204	2		360	477	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412898	49412898	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519954	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	110	671	0	ENST00000418115.1:c.125A>G	p.Tyr42Cys	p.Y42C	ENST00000418115	NM_001664.2	42	tAt/tGt	2/5	1	2	FACETS	0.841	0.756	0.932	0.841	0.756	0.932	CLONAL	1	TRUE	1	0.34539046526204	2		671	757	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346391	73346391	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	49	279	0	ENST00000377767.4:c.1409T>C	p.Leu470Pro	p.L470P	ENST00000377767	NM_014953.3	470	cTg/cCg	10/21	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.34539046526204	2		279	266	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524120	18524120	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	49	338	0	ENST00000266497.5:c.1635del	p.Glu548LysfsTer2	p.E548Kfs*2	ENST00000266497		544	aaT/aa	11/31	0.342915491871757	3	FACETS	0.99	0.843	1	0.495	0.421	0.576	CLONAL	1	TRUE	1	0.34539046526204	3		338	336	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120031	70120031	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	12	93	0	ENST00000245479.2:c.1037del	p.Pro346ArgfsTer37	p.P346Rfs*37	ENST00000245479	NM_000346.3	345	Ccc/cc	3/3	1	2	FACETS	0.817	0.583	1	0.817	0.583	1	CLONAL	1	TRUE	1	0.34539046526204	2		93	85	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957465	175957465	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	85	415	0	ENST00000367669.3:c.1931del	p.Asn644ThrfsTer3	p.N644Tfs*3	ENST00000367669	NM_022457.5	644	aAc/ac	17/20	1	2	FACETS	0.87	0.77	0.976	0.87	0.77	0.976	CLONAL	1	TRUE	1	0.34539046526204	2		415	566	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332699	153332699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780061054	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	89	402	0	ENST00000281708.4:c.257C>T	p.Ser86Leu	p.S86L	ENST00000281708	NM_033632.3	86	tCg/tTg	2/12	1	2	FACETS	0.958	0.852	1	0.958	0.852	1	CLONAL	1	TRUE	1	0.34539046526204	2		402	538	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143181675	143181675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377427325	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	104	418	0	ENST00000262992.4:c.658G>A	p.Gly220Arg	p.G220R	ENST00000262992	NM_001101669.1	220	Gga/Aga	9/24	1	2	FACETS	0.987	0.886	1	0.987	0.886	1	CLONAL	1	TRUE	1	0.34539046526204	2		418	610	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271193	153271193	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	37	222	0	ENST00000281708.4:c.584+1G>A		p.X195_splice	ENST00000281708	NM_033632.3	195			1	2	FACETS	0.944	0.784	1	0.944	0.784	1	CLONAL	1	TRUE	1	0.34539046526204	2		222	227	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431874	49431874	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	217	618	1	ENST00000301067.7:c.9265del	p.Val3089TrpfsTer30	p.V3089Wfs*30	ENST00000301067	NM_003482.3	3089	Gtg/tg	34/54	0.342915491871757	3	FACETS	0.872	0.812	0.933	0.872	0.812	0.933	CLONAL	2	TRUE	1	0.34539046526204	3		619	845	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39709868	39709870	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs748165145	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	48	277	0	ENST00000361337.2:c.504_506del	p.Glu169del	p.E169del	ENST00000361337	NM_003286.2	165	ctAGAa/cta	7/21	1	2	FACETS	0.933	0.793	1	0.933	0.793	1	CLONAL	1	TRUE	1	0.34539046526204	2		277	298	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31405819	31405819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	64	240	1	ENST00000344624.3:c.3959C>T	p.Ala1320Val	p.A1320V	ENST00000344624		1320	gCg/gTg	32/33	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.34539046526204	2		241	361	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81973526	81973526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372606303	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	89	487	0	ENST00000359376.3:c.3343C>T	p.Pro1115Ser	p.P1115S	ENST00000359376	NM_002661.3	1115	Cca/Tca	30/33	1	2	FACETS	0.991	0.881	1	0.991	0.881	1	CLONAL	1	TRUE	1	0.34539046526204	2		487	520	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25536847	25536847	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745380962	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	91	562	0	ENST00000264709.3:c.7G>A	p.Ala3Thr	p.A3T	ENST00000264709	NM_175629.2	3	Gcc/Acc	2/23	1	2	FACETS	0.875	0.778	0.978	0.875	0.778	0.978	CLONAL	1	TRUE	1	0.34539046526204	2		562	602	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345760	152345760	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	65	241	1	ENST00000359321.1:c.810del	p.Phe270LeufsTer27	p.F270Lfs*27	ENST00000359321	NM_005431.1	270	ttT/tt	3/3	1	2	FACETS	0.941	0.819	1	0.941	0.819	1	CLONAL	1	TRUE	1	0.34539046526204	2		242	400	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792437	33792437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	115	537	1	ENST00000498907.2:c.884C>T	p.Ala295Val	p.A295V	ENST00000498907	NM_004364.3	295	gCg/gTg	1/1	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.34539046526204	2		538	633	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420327	88420327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs548727485	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	60	405	1	ENST00000360948.2:c.2359C>T	p.Arg787Cys	p.R787C	ENST00000360948	NM_001012338.2	787	Cgt/Tgt	19/19	1	2	FACETS	0.705	0.608	0.81	0.705	0.608	0.81	SUBCLONAL	1	TRUE	1	0.34539046526204	2		406	493	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1620979	1620979	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1329397192	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	91	675	5	ENST00000344749.5:c.1081del	p.Gln361ArgfsTer33	p.Q361Rfs*33	ENST00000344749	NM_001136139.2	361	Cag/ag	13/19	1	2	FACETS	0.695	0.617	0.779	0.695	0.617	0.779	SUBCLONAL	1	TRUE	1	0.34539046526204	2		680	758	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197307	94197308	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	67	426	0	ENST00000323929.3:c.1196dup	p.Arg400GlnfsTer3	p.R400Qfs*3	ENST00000323929	NM_005591.3	399	ttc/ttTc	11/20	1	2	FACETS	0.753	0.656	0.859	0.753	0.656	0.859	SUBCLONAL	1	TRUE	1	0.34539046526204	2		426	515	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163315547	163315547	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	65	432	0	ENST00000271452.3:c.887A>G	p.Tyr296Cys	p.Y296C	ENST00000271452	NM_145697.2	296	tAt/tGt	11/14	1	2	FACETS	0.831	0.722	0.948	0.831	0.722	0.948	CLONAL	1	TRUE	1	0.34539046526204	2		432	453	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243675627	243675627	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	62	211	0	ENST00000263826.5:c.1353del	p.Lys451AsnfsTer55	p.K451Nfs*55	ENST00000263826	NM_005465.4	451	aaA/aa	12/13	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.34539046526204	2		211	315	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205580	61205580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	86	396	0	ENST00000301761.2:c.365C>T	p.Ala122Val	p.A122V	ENST00000301761	NM_017841.2	122	gCc/gTc	3/4	1	2	FACETS	0.975	0.865	1	0.975	0.865	1	CLONAL	1	TRUE	1	0.34539046526204	2		396	511	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224603	108224603	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	59	331	0	ENST00000278616.4:c.8782A>G	p.Arg2928Gly	p.R2928G	ENST00000278616	NM_000051.3	2928	Aga/Gga	60/63	1	2	FACETS	0.869	0.751	0.997	0.869	0.751	0.997	CLONAL	1	TRUE	1	0.34539046526204	2		331	393	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2113013	2113013	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1158055650	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	139	624	2	ENST00000219476.3:c.1402G>A	p.Val468Met	p.V468M	ENST00000219476	NM_000548.3	468	Gtg/Atg	14/42	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.34539046526204	2		626	736	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858561	9858561	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	114	493	0	ENST00000330684.3:c.2840G>T	p.Arg947Met	p.R947M	ENST00000330684	NM_001134407.1	947	aGg/aTg	13/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.34539046526204	2		493	576	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348494	89348494	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs189656772	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	130	661	0	ENST00000301030.4:c.4456C>T	p.Arg1486Trp	p.R1486W	ENST00000301030	NM_001256183.1	1486	Cgg/Tgg	9/13	1	2	FACETS	0.971	0.882	1	0.971	0.882	1	CLONAL	1	TRUE	1	0.34539046526204	2		661	775	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117882	70117882	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	102	501	1	ENST00000245479.2:c.350A>G	p.Gln117Arg	p.Q117R	ENST00000245479	NM_000346.3	117	cAg/cGg	1/3	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.34539046526204	2		502	543	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216587	2216587	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	153	643	0	ENST00000398665.3:c.2231A>G	p.Asp744Gly	p.D744G	ENST00000398665	NM_032482.2	744	gAc/gGc	20/28	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.34539046526204	2		643	789	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600036	10600036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371976438	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	137	579	0	ENST00000171111.5:c.1540G>A	p.Val514Ile	p.V514I	ENST00000171111	NM_203500.1	514	Gtc/Atc	5/6	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.34539046526204	2		579	772	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123724	11123724	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	122	568	0	ENST00000358026.2:c.2374C>T	p.Leu792Phe	p.L792F	ENST00000358026	NM_001128849.1	792	Ctc/Ttc	16/36	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.34539046526204	2		568	678	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627645	14627645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	125	538	0	ENST00000254322.2:c.425C>T	p.Thr142Ile	p.T142I	ENST00000254322	NM_006145.1	142	aCc/aTc	2/3	1	2	FACETS	0.997	0.903	1	0.997	0.903	1	CLONAL	1	TRUE	1	0.34539046526204	2		538	726	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026891	48026891	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	88	407	1	ENST00000234420.5:c.1769C>A	p.Pro590His	p.P590H	ENST00000234420	NM_000179.2	590	cCc/cAc	4/10	1	2	FACETS	0.999	0.888	1	0.999	0.888	1	CLONAL	1	TRUE	1	0.34539046526204	2		408	510	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545790	41545790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749702423	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	134	558	0	ENST00000263253.7:c.2405C>T	p.Pro802Leu	p.P802L	ENST00000263253	NM_001429.3	802	cCg/cTg	14/31	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.34539046526204	2		558	681	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	231052	231052	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	74	346	0	ENST00000264932.6:c.832G>T	p.Ala278Ser	p.A278S	ENST00000264932	NM_004168.2	278	Gcc/Tcc	7/15	1	2	FACETS	0.936	0.822	1	0.936	0.822	1	CLONAL	1	TRUE	1	0.34539046526204	2		346	458	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181757	56181758	+	splice_acceptor_variant	Splice_Site	INS	-	-	G	novel	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	45	272	0	ENST00000399503.3:c.3986dup		p.X1329_splice	ENST00000399503	NM_005921.1	1329			1	2	FACETS	0.769	0.648	0.901	0.769	0.648	0.901	CLONAL	1	TRUE	1	0.34539046526204	2		272	339	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588186	67588186	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	53	285	1	ENST00000274335.5:c.1016C>A	p.Ser339Ter	p.S339*	ENST00000274335		339	tCg/tAg	7/15	1	2	FACETS	0.86	0.736	0.994	0.86	0.736	0.994	CLONAL	1	TRUE	1	0.34539046526204	2		286	357	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048241	180048241	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	128	591	0	ENST00000261937.6:c.2032C>T	p.Pro678Ser	p.P678S	ENST00000261937	NM_182925.4	678	Cct/Tct	14/30	0.221491782097941	1	FACETS	0.783	0.71	0.86	0.783	0.71	0.86	SUBCLONAL	1	TRUE	0	0.34539046526204	1		591	783	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730017	41730017	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	86	561	0	ENST00000242208.4:c.512T>C	p.Val171Ala	p.V171A	ENST00000242208	NM_002192.2	171	gTc/gCc	3/3	1	2	FACETS	0.857	0.759	0.961	0.857	0.759	0.961	CLONAL	1	TRUE	1	0.34539046526204	2		561	581	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741961	145741961	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1001801628	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	102	609	0	ENST00000428558.2:c.542A>G	p.Gln181Arg	p.Q181R	ENST00000428558	NM_004260.3	181	cAg/cGg	5/22	1	2	FACETS	0.823	0.736	0.915	0.823	0.736	0.915	CLONAL	1	TRUE	1	0.34539046526204	2		609	718	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409841	63409841	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	62	481	0	ENST00000330258.3:c.3326T>C	p.Leu1109Pro	p.L1109P	ENST00000330258	NM_152424.3	1109	cTg/cCg	2/2	NA	2	FACETS	0.68	0.588	0.78			1	INDETERMINATE	1	TRUE	NA	0.34539046526204	2		481	528	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0038379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	169	220	0				ENST00000310581	NM_198253.2	-/1132			0.259014001069164	5	FACETS	1	0.978	1	0.746	0.695	0.798	INDETERMINATE	2	FALSE	2	0.923118445503336	5		220	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0038379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	713	606	0	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	0.643170575363172	4	FACETS	1	0.997	1	1	0.999	1	CLONAL	4	FALSE	2	0.923118445503336	4		606	732	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624296	89624296	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1554890405	NA	P-0038379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	299	468	0	ENST00000371953.3:c.70del	p.Asp24ThrfsTer2	p.D24Tfs*2	ENST00000371953	NM_000314.4	24	Gac/ac	1/9	0.913236455284759	2	FACETS	0.961	0.938	0.982	0.961	0.938	0.982	CLONAL	2	FALSE	0	0.923118445503336	2		468	337	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200134	138200134	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	360	509	0	ENST00000237289.4:c.1552C>A	p.Pro518Thr	p.P518T	ENST00000237289	NM_001270507.1	518	Ccc/Acc	7/9	0.832131044608673	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	FALSE	2	0.923118445503336	4		509	739	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	96	678	0	ENST00000269305.4:c.527G>C	p.Cys176Ser	p.C176S	ENST00000269305	NM_001126112.2	176	tGc/tCc	5/11	0.371122000795997	1	FACETS	0.934	0.837	1	0.934	0.837	1	CLONAL	1	FALSE	0	0.371122000795997	1		678	451	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063640	67063640	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	69	393	1	ENST00000412916.2:c.89C>A	p.Thr30Lys	p.T30K	ENST00000412916		30	aCg/aAg	2/6	0.371122000795997	1	FACETS	0.803	0.703	0.91	0.803	0.703	0.91	CLONAL	1	FALSE	0	0.371122000795997	1		394	377	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857526	68857526	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1567513504	NA	P-0038380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	68	436	0	ENST00000261769.5:c.2161C>G	p.Leu721Val	p.L721V	ENST00000261769	NM_004360.3	721	Cta/Gta	13/16	0.371122000795997	1	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	FALSE	0	0.371122000795997	1		436	287	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0038381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	31	534	0	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	1	2	FACETS	0.776	0.627	0.944	0.776	0.627	0.944	CLONAL	1	TRUE	1	0.199328849640269	2		534	401	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813361	102813361	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1280732914	NA	P-0038381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	65	597	0	ENST00000307046.8:c.328G>A	p.Ala110Thr	p.A110T	ENST00000307046	NM_001111285.1	110	Gca/Aca	3/4	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.199328849640269	2		597	516	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0038383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	60	283	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.213801391740611	2		283	549	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0038383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	105	587	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.213801391740611	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.213801391740611	1		588	822	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0038383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	50	401	1	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.832	0.706	0.971	0.832	0.706	0.971	CLONAL	1	TRUE	1	0.213801391740611	2		402	562	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521481	8521481	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760428875	NA	P-0038383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	113	544	0	ENST00000356435.5:c.757G>A	p.Val253Ile	p.V253I	ENST00000356435		253	Gtt/Att	9/35	0.195154529209174	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.213801391740611	1		544	835	SUCCESS
APC	324	MSKCC	GRCh37	5	112175879	112175880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	40	269	0	ENST00000257430.4:c.4592dup	p.Asn1531LysfsTer2	p.N1531Kfs*2	ENST00000257430	NM_000038.5	1530	gaa/gAaa	16/16	1	2	FACETS	0.94	0.782	1	0.94	0.782	1	CLONAL	1	TRUE	1	0.213801391740611	2		269	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0038387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	429	779	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	0.772193773673051	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.772193773673051	1		779	674	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920422	114920422	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	243	570	0	ENST00000543371.1:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000543371	NM_001198531.1	455	Cga/Tga	13/14	1	2	FACETS	0.872	0.817	0.928	0.872	0.817	0.928	CLONAL	1	TRUE	1	0.715510819352626	2		570	779	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954933	2954933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755425231	NA	P-0038388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	310	610	0	ENST00000396946.4:c.2777C>T	p.Pro926Leu	p.P926L	ENST00000396946	NM_032415.4	926	cCg/cTg	21/25	0.655178640681862	4	FACETS	1	0.969	1	0.348	0.328	0.37	CLONAL	1	TRUE	1	0.715510819352626	4		610	1422	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787720	135787720	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770653972	NA	P-0038388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	417	572	0	ENST00000298552.3:c.862C>T	p.Arg288Cys	p.R288C	ENST00000298552	NM_001162426.1	288	Cgt/Tgt	9/23	0.654924048805074	2	FACETS	0.858	0.827	0.889	0.858	0.827	0.889	CLONAL	2	TRUE	0	0.715510819352626	2		572	679	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72893564	72893564	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	187	466	2	ENST00000325599.8:c.154C>T	p.Pro52Ser	p.P52S	ENST00000325599	NM_018130.2	52	Cct/Tct	2/11	0.129537624179578	5	FACETS	0.931	0.865	0.998	0.621	0.577	0.666	INDETERMINATE	2	TRUE	2	0.715510819352626	5		468	582	SUCCESS
APC	324	MSKCC	GRCh37	5	112175450	112175451	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0038388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	213	390	0	ENST00000257430.4:c.4159_4160insA	p.Cys1387Ter	p.C1387*	ENST00000257430	NM_000038.5	1387	tgt/tAgt	16/16	0.575833082325454	2	FACETS	0.858	0.814	0.901	0.858	0.814	0.901	CLONAL	2	TRUE	0	0.715510819352626	2		390	347	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	200	399	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.852809855870798	2		399	418	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653815	206653815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782278442	NA	P-0038389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	458	772	1	ENST00000367120.3:c.1366C>T	p.Arg456Trp	p.R456W	ENST00000367120	NM_014002.3	456	Cgg/Tgg	13/22	0.271884748333107	3	FACETS	0.795	0.763	0.828	0.795	0.763	0.828	INDETERMINATE	2	TRUE	1	0.852809855870798	3		773	963	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223565	55223565	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26086	4490	801	0	ENST00000275493.2:c.932G>T	p.Cys311Phe	p.C311F	ENST00000275493	NM_005228.3	311	tGt/tTt	8/28	0.852809855870798	31	FACETS	0.921	0.905	0.936	0.148	0.146	0.151	CLONAL	5	TRUE	0	0.852809855870798	31		801	30576	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0038391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	133	622	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.909	0.829	0.994	0.909	0.829	0.994	CLONAL	1	TRUE	1	0.474804617920265	2		622	616	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81916879	81916879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	173	806	0	ENST00000359376.3:c.698C>T	p.Thr233Ile	p.T233I	ENST00000359376	NM_002661.3	233	aCt/aTt	9/33	1	2	FACETS	0.875	0.806	0.946	0.875	0.806	0.946	CLONAL	1	TRUE	1	0.474804617920265	2		806	833	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556484	29556484	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1131691122	NA	P-0038391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	90	333	0	ENST00000356175.3:c.2850+1G>T		p.X950_splice	ENST00000356175	NM_000267.3	950			1	2	FACETS	0.985	0.88	1	0.985	0.88	1	CLONAL	1	TRUE	1	0.474804617920265	2		333	385	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912175	29912175	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs41547331	NA	P-0038391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	44	328	0	ENST00000376809.5:c.895+1G>T		p.X299_splice	ENST00000376809	NM_002116.7	299			1	2	FACETS	0.614	0.517	0.719	0.614	0.517	0.719	SUBCLONAL	1	TRUE	1	0.474804617920265	2		328	302	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658560	206658560	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	142	567	0	ENST00000367120.3:c.1533A>T	p.Gln511His	p.Q511H	ENST00000367120	NM_014002.3	511	caA/caT	15/22	0.474804617920265	4	FACETS	0.991	0.903	1	0.33	0.301	0.362	CLONAL	1	TRUE	1	0.474804617920265	4		567	890	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228613002	228613002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147766330	NA	P-0038391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	221	506	0	ENST00000366696.1:c.25C>T	p.Arg9Cys	p.R9C	ENST00000366696	NM_003493.2	9	Cgc/Tgc	1/1	0.474804617920265	4	FACETS	0.919	0.858	0.981	0.613	0.572	0.654	CLONAL	2	TRUE	1	0.474804617920265	4		506	747	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633616	69633616	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781998314	NA	P-0038391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	29	54	2	ENST00000334134.2:c.86C>T	p.Ala29Val	p.A29V	ENST00000334134	NM_005247.2	29	gCg/gTg	1/3	0.474804617920265	3	FACETS	1	0.942	1	0.72	0.591	0.859	CLONAL	1	TRUE	1	0.474804617920265	3		56	105	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856655	111856655	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	88	359	0	ENST00000341259.2:c.706G>T	p.Val236Leu	p.V236L	ENST00000341259	NM_005475.2	236	Gtg/Ttg	2/8	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.474804617920265	2		359	367	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916193	9916193	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	162	647	0	ENST00000330684.3:c.2096C>A	p.Pro699His	p.P699H	ENST00000330684	NM_001134407.1	699	cCc/cAc	10/13	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.474804617920265	2		647	666	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657356	29657356	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1567613616	NA	P-0038391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	174	653	0	ENST00000356175.3:c.5589T>A	p.Phe1863Leu	p.F1863L	ENST00000356175	NM_000267.3	1863	ttT/ttA	38/57	1	2	FACETS	0.899	0.829	0.972	0.899	0.829	0.972	CLONAL	1	TRUE	1	0.474804617920265	2		653	815	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485873	57485873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397514456	NA	P-0038391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	124	422	0	ENST00000371085.3:c.1174G>A	p.Glu392Lys	p.E392K	ENST00000371085	NM_000516.4	392	Gag/Aag	13/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.474804617920265	2		422	483	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39772567	39772567	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	85	457	0	ENST00000288319.7:c.674G>T	p.Gly225Val	p.G225V	ENST00000288319	NM_182918.3	225	gGg/gTg	6/10	1	2	FACETS	0.754	0.669	0.844	0.754	0.669	0.844	SUBCLONAL	1	TRUE	1	0.474804617920265	2		457	475	SUCCESS
ATR	545	MSKCC	GRCh37	3	142238524	142238524	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	68	338	0	ENST00000350721.4:c.4369C>A	p.His1457Asn	p.H1457N	ENST00000350721	NM_001184.3	1457	Cat/Aat	24/47	1	2	FACETS	0.74	0.647	0.84	0.74	0.647	0.84	SUBCLONAL	1	TRUE	1	0.474804617920265	2		338	387	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374707	149374708	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0038391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	159	662	0	ENST00000360632.3:c.386dup	p.Trp130LeufsTer27	p.W130Lfs*27	ENST00000360632	NM_015472.4	129	ggc/ggGc	2/7	1	2	FACETS	0.997	0.916	1	0.997	0.916	1	CLONAL	1	TRUE	1	0.474804617920265	2		662	672	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584471	189584471	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	123	382	0	ENST00000264731.3:c.767G>T	p.Gly256Val	p.G256V	ENST00000264731	NM_003722.4	256	gGa/gTa	6/14	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.474804617920265	2		382	393	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142950058	142950058	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	104	407	0	ENST00000262992.4:c.2652C>A	p.Cys884Ter	p.C884*	ENST00000262992	NM_001101669.1	884	tgC/tgA	24/24	1	2	FACETS	0.94	0.846	1	0.94	0.846	1	CLONAL	1	TRUE	1	0.474804617920265	2		407	466	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729375	41729375	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	179	707	0	ENST00000242208.4:c.1154C>T	p.Ala385Val	p.A385V	ENST00000242208	NM_002192.2	385	gCc/gTc	3/3	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.474804617920265	2		707	722	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0038392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	497	767	1	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.196216523448905	8	FACETS	1	0.98	1			1	CLONAL	6	FALSE	NA	0.196216523448905	8		768	1293	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0038392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	81	605	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.196216523448905	2		605	706	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325252	39325252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	39	541	0	ENST00000373001.3:c.67C>T	p.Pro23Ser	p.P23S	ENST00000373001	NM_022157.3	23	Cca/Tca	1/7	1	2	FACETS	0.781	0.647	0.931	0.781	0.647	0.931	CLONAL	1	FALSE	1	0.196216523448905	2		541	509	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246134	46246134	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	51	511	0	ENST00000334344.6:c.4228G>A	p.Asp1410Asn	p.D1410N	ENST00000334344	NM_152641.2	1410	Gat/Aat	15/21	0.192566374370796	2	FACETS	0.966	0.821	1	0.483	0.41	0.563	CLONAL	1	FALSE	0	0.196216523448905	2		511	538	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149516606	149516606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372399976	NA	P-0038392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	43	709	0	ENST00000261799.4:c.5G>A	p.Arg2Gln	p.R2Q	ENST00000261799	NM_002609.3	2	cGg/cAg	2/23	0.196216523448905	0	FACETS	0.473	0.394	0.56			1	SUBCLONAL	1	FALSE	0	0.196216523448905	0		709	745	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251243	99251243	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	160	771	1	ENST00000268035.6:c.547C>T	p.Pro183Ser	p.P183S	ENST00000268035	NM_000875.3	183	Cca/Tca	2/21	0.410831242918391	1	FACETS	0.952	0.876	1	0.952	0.876	1	CLONAL	1	TRUE	0	0.410831242918391	1		772	650	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170827925	170827925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	57	681	1	ENST00000296930.5:c.665C>T	p.Ser222Leu	p.S222L	ENST00000296930	NM_002520.6	222	tCa/tTa	8/11	0.324755710544339	3	FACETS	0.316	0.27	0.367	0.158	0.135	0.184	SUBCLONAL	1	TRUE	1	0.410831242918391	3		682	1059	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168997	32168997	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs911402506	NA	P-0038394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	130	894	2	ENST00000375023.3:c.4036C>T	p.Arg1346Trp	p.R1346W	ENST00000375023	NM_004557.3	1346	Cgg/Tgg	22/30	0.343450403381254	2	FACETS	0.836	0.759	0.917	0.418	0.379	0.459	CLONAL	1	TRUE	0	0.410831242918391	2		896	757	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932515	39932515	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	145	455	1	ENST00000378444.4:c.2084A>T	p.His695Leu	p.H695L	ENST00000378444	NM_001123385.1	695	cAc/cTc	4/15	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.410831242918391	1		456	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0038401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	162	1131	1	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	0.262179739800063	2		1132	961	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604667	43604667	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	139	704	0	ENST00000355710.3:c.1252C>T	p.Arg418Ter	p.R418*	ENST00000355710	NM_020975.4	418	Cga/Tga	6/20	0.262179739800063	4	FACETS	0.776	0.707	0.85	0.518	0.471	0.567	SUBCLONAL	2	TRUE	1	0.262179739800063	4		704	862	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107000	11107000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141090393	NA	P-0038401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	41	796	2	ENST00000358026.2:c.1705C>T	p.Arg569Trp	p.R569W	ENST00000358026	NM_001128849.1	569	Cgg/Tgg	10/36	1	2	FACETS	0.383	0.318	0.456	0.383	0.318	0.456	SUBCLONAL	1	TRUE	1	0.262179739800063	2		798	817	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0038401-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	107	1131	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.164669601626412	3	FACETS	0.886	0.798	0.979	1	0.978	1	CLONAL	3	FALSE	1	0.164669601626412	3		1132	529	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604667	43604667	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038401-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	40	704	0	ENST00000355710.3:c.1252C>T	p.Arg418Ter	p.R418*	ENST00000355710	NM_020975.4	418	Cga/Tga	6/20	0.164669601626412	6	FACETS	1	0.851	1	0.511	0.426	0.605	CLONAL	2	FALSE	2	0.164669601626412	6		704	316	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	59	578	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.918	0.791	1	0.918	0.791	1	CLONAL	1	TRUE	1	0.259699571112048	2		578	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	147	740	2	ENST00000269305.4:c.569del	p.Pro190LeufsTer57	p.P190Lfs*57	ENST00000269305	NM_001126112.2	190	cCt/ct	6/11	0.226911155718837	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.259699571112048	1		742	852	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028656	12028656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	80	426	0	ENST00000353533.5:c.859C>T	p.Arg287Cys	p.R287C	ENST00000353533	NM_003010.3	287	Cgc/Tgc	8/11	0.226911155718837	1	FACETS	0.966	0.852	1	0.966	0.852	1	CLONAL	1	TRUE	0	0.259699571112048	1		426	555	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089603	27089603	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	291	883	2	ENST00000324856.7:c.2561del	p.Pro854LeufsTer5	p.P854Lfs*5	ENST00000324856	NM_006015.4	853	ctC/ct	8/20	1	2	FACETS	0.992	0.938	1	1	0.997	1	CLONAL	5	FALSE	1	0.154217017238277	2		885	761	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615568	43615569	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	rs377767429	NA	P-0038403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	228	694	1	ENST00000355710.3:c.2647_2648delinsTT	p.Ala883Phe	p.A883F	ENST00000355710	NM_020975.4	883	GCt/TTt	15/20	1	2	FACETS	0.917	0.859	0.975	1	0.996	1	CLONAL	5	FALSE	1	0.154217017238277	2		695	645	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096179	2096179	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	239	1053	0	ENST00000219066.1:c.328G>C	p.Val110Leu	p.V110L	ENST00000219066	NM_002528.5	110	Gtg/Ctg	2/6	1	2	FACETS	0.905	0.844	0.967	1	0.995	1	CLONAL	3	FALSE	1	0.154217017238277	2		1053	1142	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061208	38061208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	649	457	3	ENST00000250448.2:c.781C>T	p.Arg261Cys	p.R261C	ENST00000250448	NM_004496.3	261	Cgc/Tgc	2/2	0.56433321550524	5	FACETS	0.978	0.946	1			1	CLONAL	3	FALSE	NA	0.737647661729619	5		460	1263	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026308	48026308	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs2020908	NA	P-0038404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	210	453	0	ENST00000234420.5:c.1186C>G	p.Leu396Val	p.L396V	ENST00000234420	NM_000179.2	396	Ctc/Gtc	4/10	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	FALSE	1	0.737647661729619	2		453	565	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426656	121426656	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752886203	NA	P-0038404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	279	754	0	ENST00000257555.6:c.347C>T	p.Ala116Val	p.A116V	ENST00000257555		116	gCg/gTg	2/10	0.737647661729619	2	FACETS	0.672	0.631	0.715	0.336	0.315	0.358	SUBCLONAL	1	FALSE	0	0.737647661729619	2		754	1125	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646847	37646847	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	286	632	1	ENST00000447079.4:c.1969G>T	p.Glu657Ter	p.E657*	ENST00000447079	NM_015083.1	657	Gag/Tag	3/14	0.729118948159688	3	FACETS	0.902	0.847	0.958			1	CLONAL	1	FALSE	NA	0.737647661729619	3		633	1177	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657663	37657671	+	inframe_deletion	In_Frame_Del	DEL	TAAGTGTTC	TAAGTGTTC	-	novel	NA	P-0038404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	410	531	0	ENST00000447079.4:c.2583_2591del	p.Lys861_Ser863del	p.K861_S863del	ENST00000447079	NM_015083.1	860	atTAAGTGTTCt/att	6/14	0.729118948159688	3	FACETS	0.837	0.801	0.874			1	CLONAL	2	FALSE	NA	0.737647661729619	3		531	909	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002738	37002738	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs762775984	NA	P-0038404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	264	578	7	ENST00000358127.4:c.511A>G	p.Ser171Gly	p.S171G	ENST00000358127	NM_001280556.1	171	Agc/Ggc	5/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.737647661729619	2		585	700	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0038405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	125	220	0				ENST00000310581	NM_198253.2	-/1132			0.302999040446395	3	FACETS	1	0.984	1	0.675	0.619	0.733	INDETERMINATE	1	TRUE	1	0.733306586453751	3		220	345	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0038405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	485	324	1	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.628643166444572	4	FACETS	1	0.985	1			1	CLONAL	3	TRUE	NA	0.733306586453751	4		325	743	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0038405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	356	517	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.733306586453751	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.733306586453751	1		518	530	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663360	67663360	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	280	354	0	ENST00000264010.4:c.1761T>A	p.Asn587Lys	p.N587K	ENST00000264010	NM_006565.3	587	aaT/aaA	10/12	0.733306586453751	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.733306586453751	1		354	415	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546133	29546133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	254	363	0	ENST00000356175.3:c.1638G>A	p.Met546Ile	p.M546I	ENST00000356175	NM_000267.3	546	atG/atA	14/57	0.3044047405241	4	FACETS	0.941	0.887	0.996	0.941	0.887	0.996	INDETERMINATE	2	TRUE	2	0.733306586453751	4		363	638	SUCCESS
AXL	558	MSKCC	GRCh37	19	41737171	41737171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1051415960	NA	P-0038405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	338	742	3	ENST00000301178.4:c.751G>A	p.Gly251Ser	p.G251S	ENST00000301178	NM_021913.4	251	Ggc/Agc	6/20	0.302999040446395	3	FACETS	1	0.992	1	0.62	0.587	0.653	INDETERMINATE	1	TRUE	1	0.733306586453751	3		745	1016	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252865	36252865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060499616	NA	P-0038405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	168	345	0	ENST00000300305.3:c.497G>A	p.Arg166Gln	p.R166Q	ENST00000300305		166	cGa/cAa	4/8	0.302999040446395	3	FACETS	1	0.984	1	0.62	0.574	0.667	INDETERMINATE	1	TRUE	1	0.733306586453751	3		345	505	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1800999	1801000	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0038405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	521	835	3	ENST00000260795.2:c.128_129delinsTT	p.Pro43Leu	p.P43L	ENST00000260795		43	cCC/cTT	2/17	0.302999040446395	3	FACETS	0.815	0.783	0.847	0.815	0.783	0.847	INDETERMINATE	2	TRUE	1	0.733306586453751	3		838	1191	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80021291	80021291	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs539295465	NA	P-0038405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	264	363	1	ENST00000265081.6:c.1360C>T	p.Arg454Ter	p.R454*	ENST00000265081	NM_002439.4	454	Cga/Tga	9/24	0.302999040446395	3	FACETS	0.821	0.777	0.867	0.821	0.777	0.867	INDETERMINATE	2	TRUE	1	0.733306586453751	3		364	599	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976682	2976682	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	313	492	0	ENST00000396946.4:c.1330A>G	p.Asn444Asp	p.N444D	ENST00000396946	NM_032415.4	444	Aac/Gac	9/25	0.3044047405241	4	FACETS	0.958	0.909	1	0.958	0.909	1	INDETERMINATE	2	TRUE	2	0.733306586453751	4		492	772	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194733	29194733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	647	837	0	ENST00000240100.2:c.995C>T	p.Ser332Phe	p.S332F	ENST00000240100	NM_001394.6	332	tCc/tTc	4/4	0.302999040446395	3	FACETS	0.944	0.912	0.975	0.944	0.912	0.975	INDETERMINATE	2	TRUE	1	0.733306586453751	3		837	1278	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20153872	20153872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1235062718	NA	P-0038405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	295	455	0	ENST00000379607.5:c.188G>A	p.Gly63Glu	p.G63E	ENST00000379607	NM_001412.3	63	gGa/gAa	3/7	0.733306586453751	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.733306586453751	1		455	429	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	26	399	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.803	1	1	0.803	1	CLONAL	1	TRUE	1	0.24	2		399	215	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0038406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	61	461	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.24	2		461	483	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510606	38510606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	61	981	1	ENST00000254066.5:c.860C>T	p.Ser287Leu	p.S287L	ENST00000254066	NM_000964.3	287	tCg/tTg	7/9	0.262918998245818	3	FACETS	0.675	0.58	0.777	0.337	0.29	0.389	SUBCLONAL	1	TRUE	1	0.24	3		982	844	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004735	16004735	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	89	902	1	ENST00000268712.3:c.2519del	p.Asn840IlefsTer23	p.N840Ifs*23	ENST00000268712	NM_006311.3	840	aAt/at	20/46	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.24	2		903	672	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676339	37676339	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	62	649	0	ENST00000447079.4:c.3094G>C	p.Asp1032His	p.D1032H	ENST00000447079	NM_015083.1	1032	Gac/Cac	11/14	0.262918998245818	3	FACETS	0.86	0.742	0.988	0.43	0.371	0.494	CLONAL	1	TRUE	1	0.24	3		649	673	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5563181	5563183	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0038406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	48	505	0	ENST00000397747.3:c.789_791del	p.Thr265del	p.T265del	ENST00000397747	NM_025239.3	262	gtCACc/gtc	6/7	1	2	FACETS	0.818	0.692	0.957	0.818	0.692	0.957	CLONAL	1	TRUE	1	0.24	2		505	489	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918502	44918502	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	103	416	0	ENST00000377967.4:c.985C>T	p.Gln329Ter	p.Q329*	ENST00000377967	NM_021140.2	329	Cag/Tag	12/29	0.723570786071191	3	FACETS	0.697	0.626	0.773	0.349	0.313	0.387	SUBCLONAL	1	TRUE	1	0.723570786071191	3		416	556	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692818	89692818	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1339631701	NA	P-0038407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	212	304	0	ENST00000371953.3:c.302T>C	p.Ile101Thr	p.I101T	ENST00000371953	NM_000314.4	101	aTc/aCc	5/9	0.634567532408175	3	FACETS	0.855	0.815	0.894	0.855	0.815	0.894	CLONAL	3	TRUE	0	0.723570786071191	3		304	311	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	469	708	1	ENST00000322088.6:c.767C>A	p.Ser256Tyr	p.S256Y	ENST00000322088	NM_014225.5	256	tCc/tAc	6/15	0.723570786071191	3	FACETS	0.992	0.954	1	0.992	0.954	1	CLONAL	2	TRUE	1	0.723570786071191	3		709	890	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579485	7579485	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs869312782	NA	P-0038407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	1078	878	2	ENST00000269305.4:c.202G>T	p.Glu68Ter	p.E68*	ENST00000269305	NM_001126112.2	68	Gag/Tag	4/11	0.723570786071191	4	FACETS	0.947	0.931	0.962	0.947	0.931	0.962	CLONAL	4	TRUE	0	0.723570786071191	4		880	1356	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588197	69588197	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	172	799	0	ENST00000168712.1:c.501C>A	p.Asn167Lys	p.N167K	ENST00000168712	NM_002007.2	167	aaC/aaA	3/3	0.627557949904909	3	FACETS	0.794	0.732	0.859	0.397	0.366	0.43	SUBCLONAL	1	TRUE	1	0.723570786071191	3		799	815	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591227	67591289	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTTTCAAAACTGTTTTTCAGGTGGTTGACTCAAAAAGGTGTTCGGCAAAAGAAGTTGAACGA	CTTTTCAAAACTGTTTTTCAGGTGGTTGACTCAAAAAGGTGTTCGGCAAAAGAAGTTGAACGA	-	novel	NA	P-0038407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	66	390	0	ENST00000274335.5:c.1746-21_1787del		p.X582_splice	ENST00000274335		582		13/15	0.646557530097397	3	FACETS	0.696	0.607	0.79	0.348	0.303	0.395	SUBCLONAL	1	TRUE	1	0.723570786071191	3		390	357	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045687	26045687	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	54	308	0	ENST00000540144.1:c.49C>G	p.Pro17Ala	p.P17A	ENST00000540144	NM_003531.2	17	Ccg/Gcg	1/1	0.723570786071191	4	FACETS	0.484	0.414	0.562	0.161	0.138	0.188	SUBCLONAL	1	TRUE	1	0.723570786071191	4		308	531	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0038408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	196	220	0				ENST00000310581	NM_198253.2	-/1132			0.379604279057191	0	FACETS	0.794	0.758	0.828			1	SUBCLONAL	3	TRUE	0	0.379604279057191	0		220	269	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0038408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	423	395	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.379604279057191	4	FACETS	0.983	0.944	1	1	0.995	1	CLONAL	4	TRUE	1	0.379604279057191	4		395	782	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462051	120462051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750477480	NA	P-0038408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	326	568	0	ENST00000256646.2:c.5665C>T	p.Arg1889Trp	p.R1889W	ENST00000256646	NM_024408.3	1889	Cgg/Tgg	31/34	0.379604279057191	1	FACETS	1	0.974	1	1	0.996	1	CLONAL	2	TRUE	0	0.379604279057191	1		568	674	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857692	9857692	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1389208302	NA	P-0038408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	214	501	1	ENST00000330684.3:c.3709G>A	p.Asp1237Asn	p.D1237N	ENST00000330684	NM_001134407.1	1237	Gat/Aat	13/13	1	2	FACETS	1	0.979	1	1	0.995	1	CLONAL	2	TRUE	1	0.379604279057191	2		502	515	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032739	30032739	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0038408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	179	309	0	ENST00000338641.4:c.115-1G>C		p.X39_splice	ENST00000338641	NM_000268.3	39			0.379604279057191	0	FACETS	0.722	0.684	0.759			1	SUBCLONAL	3	TRUE	0	0.379604279057191	0		309	270	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875648	35875648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	149	356	0	ENST00000303115.3:c.835C>T	p.His279Tyr	p.H279Y	ENST00000303115	NM_002185.3	279	Cat/Tat	7/8	0.379604279057191	4	FACETS	0.823	0.754	0.895	0.549	0.503	0.597	CLONAL	2	TRUE	1	0.379604279057191	4		356	658	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485897	8485897	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765439647	NA	P-0038408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	206	439	0	ENST00000356435.5:c.2920C>T	p.Pro974Ser	p.P974S	ENST00000356435		974	Cca/Tca	17/35	1	2	FACETS	0.996	0.931	1	1	0.994	1	CLONAL	2	TRUE	1	0.379604279057191	2		439	545	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866441	42866441	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770444484	NA	P-0038408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	505	960	1	ENST00000398585.3:c.191C>T	p.Pro64Leu	p.P64L	ENST00000398585	NM_001135099.1	64	cCc/cTc	3/14	1	2	FACETS	1	0.991	1	1	0.997	1	CLONAL	2	TRUE	1	0.379604279057191	2		961	1208	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939259	71939259	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771645618	NA	P-0038408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	320	758	0	ENST00000298229.2:c.208C>T	p.Arg70Cys	p.R70C	ENST00000298229	NM_001567.3	70	Cgc/Tgc	2/28	1	2	FACETS	0.961	0.911	1	1	0.996	1	CLONAL	2	TRUE	1	0.379604279057191	2		758	877	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644561	21644561	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	268	433	0	ENST00000421138.2:c.106A>T	p.Ile36Phe	p.I36F	ENST00000421138		36	Att/Ttt	4/16	1	2	FACETS	1	0.983	1	1	0.996	1	CLONAL	2	TRUE	1	0.379604279057191	2		433	645	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110644	4110644	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	285	553	1	ENST00000262948.5:c.313C>T	p.Leu105Phe	p.L105F	ENST00000262948	NM_030662.3	105	Ctt/Ttt	3/11	1	2	FACETS	0.993	0.938	1	1	0.996	1	CLONAL	2	TRUE	1	0.379604279057191	2		554	756	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586434	189586434	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	242	460	0	ENST00000264731.3:c.1058A>G	p.Lys353Arg	p.K353R	ENST00000264731	NM_003722.4	353	aAg/aGg	8/14	1	2	FACETS	1	0.963	1	1	0.995	1	CLONAL	2	TRUE	1	0.379604279057191	2		460	618	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170832349	170832349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	517	439	0	ENST00000296930.5:c.713C>T	p.Pro238Leu	p.P238L	ENST00000296930	NM_002520.6	238	cCa/cTa	9/11	0.379604279057191	4	FACETS	1	0.977	1	1	0.997	1	CLONAL	4	TRUE	1	0.379604279057191	4		439	924	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805731	32805731	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	374	759	0	ENST00000374899.4:c.280G>C	p.Val94Leu	p.V94L	ENST00000374899	NM_018833.2	94	Gtc/Ctc	2/12	0.379604279057191	4	FACETS	1	0.976	1	0.698	0.662	0.734	CLONAL	2	TRUE	1	0.379604279057191	4		759	1299	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151932981	151932981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1402089231	NA	P-0038408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	61	50	0	ENST00000262189.6:c.2690G>A	p.Arg897Gln	p.R897Q	ENST00000262189	NM_170606.2	897	cGa/cAa	16/59	0.379604279057191	4	FACETS	0.99	0.888	1	1	0.973	1	CLONAL	4	TRUE	1	0.379604279057191	4		50	112	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894815	101894815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878854713	NA	P-0038408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	173	315	0	ENST00000374994.4:c.368C>T	p.Pro123Leu	p.P123L	ENST00000374994	NM_004612.2	123	cCt/cTt	3/9	1	2	FACETS	1	0.931	1	1	0.993	1	CLONAL	2	TRUE	1	0.379604279057191	2		315	455	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426073	47426073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	477	426	0	ENST00000377045.4:c.593C>T	p.Pro198Leu	p.P198L	ENST00000377045	NM_001654.4	198	cCc/cTc	7/16	1	1	FACETS	1	0.996	1	1	0.998	1	CLONAL	3	TRUE	0	0.379604279057191	1		426	585	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	81	399	0				ENST00000310581	NM_198253.2	-/1132			0.3	3	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	1	0.2	3		399	413	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0038410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	130	625	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.2	2		627	974	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576871	212576871	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	28	555	0	ENST00000342788.4:c.1028T>A	p.Met343Lys	p.M343K	ENST00000342788	NM_005235.2	343	aTg/aAg	9/28	NA	2	FACETS	0.512	0.408	0.631			1	INDETERMINATE	1	TRUE	NA	0.2	2		555	547	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62325742	62325742	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	56	765	0	ENST00000360203.5:c.3010C>T	p.Pro1004Ser	p.P1004S	ENST00000360203	NM_001283009.1	1004	Ccc/Tcc	31/35	0.112132282048025	4	FACETS	0.646	0.551	0.75	0.323	0.275	0.375	INDETERMINATE	1	TRUE	2	0.2	4		765	1041	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109309771	109309771	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	52	619	0	ENST00000436639.2:c.1544G>A	p.Trp515Ter	p.W515*	ENST00000436639	NM_014454.2	515	tGg/tAg	9/10	NA	2	FACETS	0.596	0.505	0.695			1	INDETERMINATE	1	TRUE	NA	0.2	2		619	873	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942673	48942673	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	42	353	0	ENST00000267163.4:c.1060del	p.Gln354ArgfsTer13	p.Q354Rfs*13	ENST00000267163	NM_000321.2	354	Cag/ag	11/27	1	2	FACETS	0.85	0.71	1	0.85	0.71	1	CLONAL	1	TRUE	1	0.2	2		353	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0038412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	410	875	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.749040900560648	1	FACETS	0.973	0.935	1	0.973	0.935	1	CLONAL	1	TRUE	0	0.749040900560648	1		876	704	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913558	32913559	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359479	NA	P-0038412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	182	455	0	ENST00000380152.3:c.5073dup	p.Trp1692MetfsTer3	p.W1692Mfs*3	ENST00000380152		1689	gca/gcAa	11/27	0.749040900560648	1	FACETS	0.947	0.892	1	0.947	0.892	1	CLONAL	1	TRUE	0	0.749040900560648	1		455	321	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858503	57858523	+	inframe_deletion	In_Frame_Del	DEL	CGGGCACTGTCCATCTCACCT	CGGGCACTGTCCATCTCACCT	-	novel	NA	P-0038412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	51	897	0	ENST00000228682.2:c.242_262del	p.Arg81_Pro87del	p.R81_P87del	ENST00000228682	NM_005269.2	81	CGGGCACTGTCCATCTCACCT/-	4/12	0.0960830573882749	4	FACETS	0.237	0.2	0.277	0.118	0.1	0.139	INDETERMINATE	1	TRUE	2	0.749040900560648	4		897	1005	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643216	38643216	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	137	385	0	ENST00000299084.4:c.686T>C	p.Val229Ala	p.V229A	ENST00000299084	NM_152594.2	229	gTc/gCc	7/7	1	2	FACETS	0.933	0.858	1	0.933	0.858	1	CLONAL	1	TRUE	1	0.749040900560648	2		385	392	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141456	11141456	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	362	979	0	ENST00000358026.2:c.3433C>A	p.Pro1145Thr	p.P1145T	ENST00000358026	NM_001128849.1	1145	Ccc/Acc	25/36	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.749040900560648	2		979	961	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381555	81381555	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1228314400	NA	P-0038412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	44	365	0	ENST00000222390.5:c.506G>T	p.Gly169Val	p.G169V	ENST00000222390	NM_000601.4	169	gGt/gTt	5/18	1	2	FACETS	0.284	0.238	0.334	0.284	0.238	0.334	SUBCLONAL	1	TRUE	1	0.749040900560648	2		365	414	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	257	399	0				ENST00000310581	NM_198253.2	-/1132			0.384777156993766	1	FACETS	0.93	0.884	0.975	0.93	0.884	0.975	INDETERMINATE	1	TRUE	0	0.755692984765479	1		399	455	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371972	55371972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	67	323	0	ENST00000297316.4:c.662C>T	p.Thr221Met	p.T221M	ENST00000297316	NM_022454.3	221	aCg/aTg	2/2	1	2	FACETS	0.263	0.228	0.301	0.263	0.228	0.301	SUBCLONAL	1	TRUE	1	0.755692984765479	2		323	673	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781811	3781818	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGACAG	TGGGACAG	-	novel	NA	P-0038414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	65	767	0	ENST00000262367.5:c.4849_4856del	p.Leu1617GlufsTer40	p.L1617Efs*40	ENST00000262367	NM_004380.2	1617	CTGTCCCAg/g	29/31	0.153980857516473	2	FACETS	0.15	0.129	0.173	0.075	0.064	0.087	INDETERMINATE	1	TRUE	0	0.755692984765479	2		767	1146	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3799676	3799676	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0038414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	177	418	0	ENST00000262367.5:c.3788C>G	p.Ser1263Ter	p.S1263*	ENST00000262367	NM_004380.2	1263	tCa/tGa	21/31	0.153980857516473	2	FACETS	1	0.989	1	0.64	0.599	0.681	INDETERMINATE	1	TRUE	0	0.755692984765479	2		418	366	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215606	5215606	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	96	731	0	ENST00000357368.4:c.4097G>T	p.Ser1366Ile	p.S1366I	ENST00000357368	NM_002850.3	1366	aGc/aTc	27/38	1	2	FACETS	0.268	0.238	0.3	0.268	0.238	0.3	SUBCLONAL	1	TRUE	1	0.755692984765479	2		731	949	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271230	26271230	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs150252598	NA	P-0038414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	68	618	0	ENST00000305910.3:c.383C>G	p.Ala128Gly	p.A128G	ENST00000305910	NM_003534.2	128	gCt/gGt	1/1	0.191293348112408	2	FACETS	0.23	0.199	0.263	0.115	0.099	0.132	INDETERMINATE	1	TRUE	0	0.755692984765479	2		618	783	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964370	93964370	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1342659278	NA	P-0038414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	126	540	0	ENST00000369303.4:c.2527C>G	p.Gln843Glu	p.Q843E	ENST00000369303	NM_004440.3	843	Caa/Gaa	14/17	0.191293348112408	2	FACETS	0.857	0.784	0.933	0.429	0.392	0.467	INDETERMINATE	1	TRUE	0	0.755692984765479	2		540	389	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889085	76889085	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	33	273	0	ENST00000373344.5:c.4925A>C	p.Gln1642Pro	p.Q1642P	ENST00000373344	NM_000489.3	1642	cAa/cCa	18/35	1	1	FACETS	0.27	0.222	0.324	0.27	0.222	0.324	SUBCLONAL	1	TRUE	0	0.755692984765479	1		273	201	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215380	123215380	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0038414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	187	236	0	ENST00000218089.9:c.2924+2T>C		p.X975_splice	ENST00000218089	NM_001042749.1	975			1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.755692984765479	1		236	210	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155196	55155196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	66	721	1	ENST00000257290.5:c.2795G>A	p.Cys932Tyr	p.C932Y	ENST00000257290	NM_006206.4	932	tGc/tAc	21/23	1	2	FACETS	0.642	0.559	0.732	0.642	0.559	0.732	SUBCLONAL	1	TRUE	1	0.43	2		722	478	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78704450	78704450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	65	679	0	ENST00000306801.3:c.598G>A	p.Gly200Ser	p.G200S	ENST00000306801	NM_020761.2	200	Ggc/Agc	5/34	0.155363615536641	0	FACETS	0.387	0.336	0.442			1	INDETERMINATE	1	TRUE	0	0.43	0		679	445	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978404	2978404	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	66	1022	0	ENST00000396946.4:c.926G>C	p.Arg309Pro	p.R309P	ENST00000396946	NM_032415.4	309	cGc/cCc	7/25	0.3	1	FACETS	0.558	0.486	0.635	0.558	0.486	0.635	SUBCLONAL	1	TRUE	0	0.43	1		1022	432	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319853	8319853	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	67	471	0	ENST00000356435.5:c.5648G>C	p.Arg1883Pro	p.R1883P	ENST00000356435		1883	cGa/cCa	34/35	0.197583531898301	1	FACETS	0.601	0.524	0.683	0.601	0.524	0.683	INDETERMINATE	1	TRUE	0	0.43	1		471	407	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366905	40366905	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	108	758	1	ENST00000397332.2:c.292T>C	p.Cys98Arg	p.C98R	ENST00000397332	NM_001033082.2	98	Tgc/Cgc	2/3	0.161043277294947	6	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.687338979093025	6		759	620	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916821	48916849	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TACTGAGCTACAGAAAAACATAGAAATCA	TACTGAGCTACAGAAAAACATAGAAATCA	ACCTGATTTC	novel	NA	P-0038416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	101	504	1	ENST00000267163.4:c.351_379delinsACCTGATTTC	p.Phe117LeufsTer13	p.F117Lfs*13	ENST00000267163	NM_000321.2	117	ttTACTGAGCTACAGAAAAACATAGAAATCAgt/ttACCTGATTTCgt	3/27	0.694736102138921	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.687338979093025	2		505	142	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133799	55133799	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	47	756	0	ENST00000257290.5:c.1012G>C	p.Glu338Gln	p.E338Q	ENST00000257290	NM_006206.4	338	Gag/Cag	7/23	0.534962223669742	5	FACETS	0.382	0.321	0.449	0.127	0.107	0.15	SUBCLONAL	1	TRUE	2	0.687338979093025	5		756	727	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578204	7578204	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520001	NA	P-0038418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	100	933	0	ENST00000269305.4:c.645T>G	p.Ser215Arg	p.S215R	ENST00000269305	NM_001126112.2	215	agT/agG	6/11	0.252295836810073	1	FACETS	0.906	0.809	1	0.906	0.809	1	CLONAL	1	TRUE	0	0.252295836810073	1		933	765	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798483	32798483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200271380	NA	P-0038418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	52	955	2	ENST00000374899.4:c.1373C>T	p.Thr458Met	p.T458M	ENST00000374899	NM_018833.2	458	aCg/aTg	8/12	1	2	FACETS	0.437	0.371	0.51	0.437	0.371	0.51	SUBCLONAL	1	TRUE	1	0.252295836810073	2		957	943	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0038420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	135	347	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.891	0.818	0.966	1	0.992	1	CLONAL	3	FALSE	1	0.250690252089095	2		347	403	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984663	11984678	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTTTAACAGAGAGAG	ATTTTAACAGAGAGAG	-	novel	NA	P-0038420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	63	396	0	ENST00000353533.5:c.219-9_225del		p.X73_splice	ENST00000353533	NM_003010.3	73		3/11	0.250690252089095	0	FACETS	0.826	0.733	0.921			1	CLONAL	3	FALSE	0	0.250690252089095	0		396	152	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0038422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	563	777	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.776102607928826	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.776102607928826	2		777	706	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0038423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	130	539	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.495670506654681	2		539	496	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258744	115258744	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121434596	NA	P-0038423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	203	555	0	ENST00000369535.4:c.38G>T	p.Gly13Val	p.G13V	ENST00000369535	NM_002524.4	13	gGt/gTt	2/7	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.495670506654681	2		555	678	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913237	NA	P-0038423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	178	555	0	ENST00000369535.4:c.35G>T	p.Gly12Val	p.G12V	ENST00000369535	NM_002524.4	12	gGt/gTt	2/7	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.495670506654681	2		555	685	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720735	89720736	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0038423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	38	226	0	ENST00000371953.3:c.887dup	p.Cys296TrpfsTer2	p.C296Wfs*2	ENST00000371953	NM_000314.4	296	tgt/tGgt	8/9	0.489668762765331	2	FACETS	1	0.877	1	0.525	0.442	0.615	CLONAL	1	TRUE	0	0.495670506654681	2		226	146	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741897	17741897	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752898631	NA	P-0038423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	76	155	0	ENST00000250003.3:c.568G>A	p.Gly190Ser	p.G190S	ENST00000250003	NM_002478.4	190	Ggc/Agc	1/3	1	2	FACETS	0.767	0.686	0.85	1	0.98	1	SUBCLONAL	2	TRUE	1	0.495670506654681	2		155	200	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117833	108117833	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	87	448	0	ENST00000278616.4:c.1044G>C	p.Leu348Phe	p.L348F	ENST00000278616	NM_000051.3	348	ttG/ttC	8/63	1	2	FACETS	0.875	0.78	0.976	0.875	0.78	0.976	CLONAL	1	TRUE	1	0.495670506654681	2		448	401	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967567	26967567	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	119	550	0	ENST00000381527.3:c.710G>A	p.Arg237Gln	p.R237Q	ENST00000381527	NM_001260.1	237	cGa/cAa	7/13	1	2	FACETS	0.884	0.801	0.971	0.884	0.801	0.971	CLONAL	1	TRUE	1	0.495670506654681	2		550	543	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068433	26068433	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0038423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	105	421	0	ENST00000435504.4:c.58-1G>C		p.X20_splice	ENST00000435504		20			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.495670506654681	2		421	354	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591145	67591145	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	88	461	0	ENST00000274335.5:c.1738T>G	p.Tyr580Asp	p.Y580D	ENST00000274335		580	Tac/Gac	12/15	1	2	FACETS	0.805	0.717	0.899	0.805	0.717	0.899	CLONAL	1	TRUE	1	0.495670506654681	2		461	441	SUCCESS
APC	324	MSKCC	GRCh37	5	112175780	112175780	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	111	390	0	ENST00000257430.4:c.4490del	p.Pro1497GlnfsTer10	p.P1497Qfs*10	ENST00000257430	NM_000038.5	1497	Cca/ca	16/16	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.495670506654681	2		390	445	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76764088	76764088	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	110	643	0	ENST00000373344.5:c.7220G>C	p.Arg2407Pro	p.R2407P	ENST00000373344	NM_000489.3	2407	cGa/cCa	35/35	1	2	FACETS	0.801	0.722	0.884	0.801	0.722	0.884	CLONAL	1	TRUE	1	0.495670506654681	2		643	554	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	32	399	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.24	2		399	206	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0038426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	24	249	1	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	1	2	FACETS	0.597	0.468	0.746	0.597	0.468	0.746	SUBCLONAL	1	TRUE	1	0.24	2		250	335	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	57	578	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.947	0.811	1	0.947	0.811	1	CLONAL	1	TRUE	1	0.18	2		578	669	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044541	47044548	+	frameshift_variant	Frame_Shift_Del	DEL	CGAGATGA	CGAGATGA	-	novel	NA	P-0038428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	57	892	0	ENST00000377604.3:c.2043_2050del	p.Asp681GlufsTer36	p.D681Efs*36	ENST00000377604	NM_001204468.1	680	CGAGATGAc/c	18/24	1	2	FACETS	0.716	0.613	0.83	0.716	0.613	0.83	SUBCLONAL	1	TRUE	1	0.18	2		892	884	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048168	180048168	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	71	900	1	ENST00000261937.6:c.2105C>A	p.Ala702Asp	p.A702D	ENST00000261937	NM_182925.4	702	gCc/gAc	14/30	1	2	FACETS	0.77	0.67	0.878	0.77	0.67	0.878	SUBCLONAL	1	TRUE	1	0.18	2		901	1025	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120753	115120753	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	58	715	0	ENST00000257566.3:c.253G>A	p.Ala85Thr	p.A85T	ENST00000257566	NM_016569.3	85	Gcg/Acg	1/8	1	2	FACETS	0.817	0.7	0.944	0.817	0.7	0.944	CLONAL	1	TRUE	1	0.18	2		715	789	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198421	108198422	+	missense_variant	Missense_Mutation	DNP	GC	GC	AG	novel	NA	P-0038428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	49	541	2	ENST00000278616.4:c.7025_7026delinsAG	p.Gly2342Glu	p.G2342E	ENST00000278616	NM_000051.3	2342	gGC/gAG	48/63	1	2	FACETS	0.67	0.566	0.786	0.67	0.566	0.786	SUBCLONAL	1	TRUE	1	0.18	2		543	812	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112892378	112892378	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	47	568	0	ENST00000351677.2:c.536A>T	p.Tyr179Phe	p.Y179F	ENST00000351677	NM_002834.3	179	tAc/tTc	5/16	1	2	FACETS	0.684	0.575	0.804	0.684	0.575	0.804	SUBCLONAL	1	TRUE	1	0.18	2		568	764	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134326	41134326	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	43	642	0	ENST00000379561.5:c.1302G>T	p.Leu434Phe	p.L434F	ENST00000379561	NM_002015.3	434	ttG/ttT	2/3	1	2	FACETS	0.672	0.561	0.796	0.672	0.561	0.796	SUBCLONAL	1	TRUE	1	0.18	2		642	711	SUCCESS
ALK	238	MSKCC	GRCh37	2	29448372	29448372	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs761736018	NA	P-0038428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	93	984	0	ENST00000389048.3:c.3127G>T	p.Ala1043Ser	p.A1043S	ENST00000389048	NM_004304.4	1043	Gcc/Tcc	19/29	1	2	FACETS	0.98	0.87	1	0.98	0.87	1	CLONAL	1	TRUE	1	0.18	2		984	1054	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561170	9561170	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	41	535	0	ENST00000353224.5:c.612C>A	p.Asp204Glu	p.D204E	ENST00000353224	NM_177990.2	204	gaC/gaA	4/10	1	2	FACETS	0.749	0.623	0.89	0.749	0.623	0.89	SUBCLONAL	1	TRUE	1	0.18	2		535	608	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421279	12421279	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	94	808	0	ENST00000287820.6:c.159G>T	p.Met53Ile	p.M53I	ENST00000287820	NM_015869.4	53	atG/atT	2/7	1	2	FACETS	0.968	0.859	1	0.968	0.859	1	CLONAL	1	TRUE	1	0.18	2		808	1079	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946287	55946287	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	51	432	0	ENST00000263923.4:c.3892G>T	p.Gly1298Cys	p.G1298C	ENST00000263923	NM_002253.2	1298	Ggc/Tgc	30/30	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.18	2		432	560	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157972	106157972	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1394175048	NA	P-0038428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	46	439	1	ENST00000380013.4:c.2873A>T	p.Gln958Leu	p.Q958L	ENST00000380013	NM_001127208.2	958	cAg/cTg	3/11	1	2	FACETS	0.832	0.7	0.979	0.832	0.7	0.979	CLONAL	1	TRUE	1	0.18	2		440	614	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638653	176638653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	86	840	0	ENST00000439151.2:c.3253C>T	p.Pro1085Ser	p.P1085S	ENST00000439151	NM_022455.4	1085	Cct/Tct	5/23	1	2	FACETS	0.854	0.753	0.962	0.854	0.753	0.962	CLONAL	1	TRUE	1	0.18	2		840	1119	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652238	48652238	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	53	827	1	ENST00000376670.3:c.909G>T	p.Gln303His	p.Q303H	ENST00000376670	NM_002049.3	303	caG/caT	6/6	1	2	FACETS	0.656	0.557	0.764	0.656	0.557	0.764	SUBCLONAL	1	TRUE	1	0.18	2		828	898	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0038428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	124	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.410746722804702	1	FACETS	0.788	0.716	0.863	0.788	0.716	0.863	SUBCLONAL	1	TRUE	0	0.463944516567889	1		457	521	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63700138	63700138	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs775723099	NA	P-0038428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	86	315	0	ENST00000279873.7:c.473A>G	p.Lys158Arg	p.K158R	ENST00000279873	NM_032199.2	158	aAa/aGa	3/10	1	2	FACETS	0.858	0.763	0.959	0.858	0.763	0.959	CLONAL	1	TRUE	1	0.463944516567889	2		315	432	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344469	118344469	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	56	411	0	ENST00000534358.1:c.2595C>A	p.Asp865Glu	p.D865E	ENST00000534358	NM_005933.3	865	gaC/gaA	3/36	1	2	FACETS	0.462	0.396	0.535	0.462	0.396	0.535	SUBCLONAL	1	TRUE	1	0.463944516567889	2		411	522	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677880	47677880	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	192	661	0	ENST00000347630.2:c.985G>T	p.Ala329Ser	p.A329S	ENST00000347630	NM_001007230.1	329	Gct/Tct	11/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.463944516567889	2		661	788	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677894	58677894	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	78	576	0	ENST00000305921.3:c.119C>T	p.Ser40Leu	p.S40L	ENST00000305921	NM_003620.3	40	tCg/tTg	1/6	1	2	FACETS	0.55	0.484	0.622	0.55	0.484	0.622	SUBCLONAL	1	TRUE	1	0.463944516567889	2		576	611	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	180	578	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.986	0.915	1	0.986	0.915	1	CLONAL	1	TRUE	1	0.624876782199396	2		578	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0038429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	89	587	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.504058651885686	1	FACETS	0.311	0.276	0.348	0.311	0.276	0.348	SUBCLONAL	1	TRUE	0	0.624876782199396	1		588	630	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0038429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	77	805	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.504058651885686	1	FACETS	0.281	0.247	0.318	0.281	0.247	0.318	SUBCLONAL	1	TRUE	0	0.624876782199396	1		805	602	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0038429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	310	909	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.624876782199396	2		909	972	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952152	178952152	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	novel	NA	P-0038429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	107	306	0	ENST00000263967.3:c.3207A>G	p.Ter1069TrpextTer4	p.*1069Wext*4	ENST00000263967	NM_006218.2	1069	tgA/tgG	21/21	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.624876782199396	2		306	338	SUCCESS
APC	324	MSKCC	GRCh37	5	112175818	112175893	+	frameshift_variant	Frame_Shift_Del	DEL	GAGCCTCGATGAGCCATTTATACAGAAAGATGTGGAATTAAGAATAATGCCTCCAGTTCAGGAAAATGACAATGGG	GAGCCTCGATGAGCCATTTATACAGAAAGATGTGGAATTAAGAATAATGCCTCCAGTTCAGGAAAATGACAATGGG	-	novel	NA	P-0038429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	220	363	0	ENST00000257430.4:c.4527_4602del	p.Ser1510MetfsTer30	p.S1510Mfs*30	ENST00000257430	NM_000038.5	1509	ctGAGCCTCGATGAGCCATTTATACAGAAAGATGTGGAATTAAGAATAATGCCTCCAGTTCAGGAAAATGACAATGGG/ct	16/16	0.624876782199396	2	FACETS	0.959	0.91	1	0.959	0.91	1	CLONAL	2	TRUE	0	0.624876782199396	2		363	367	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183725	10183725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs5030826	NA	P-0038430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	38	700	0	ENST00000256474.2:c.194C>T	p.Ser65Leu	p.S65L	ENST00000256474	NM_000551.3	65	tCg/tTg	1/3	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		700	233	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347954	347954	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867582108	NA	P-0038430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	11	991	0	ENST00000262320.3:c.1552C>T	p.Pro518Ser	p.P518S	ENST00000262320	NM_003502.3	518	Ccc/Tcc	6/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		991	192	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0038431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	63	283	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	FALSE	1	0.36926450860295	2		283	257	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	201	399	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.864	0.805	0.924	1	0.993	1	CLONAL	2	FALSE	1	0.36926450860295	2		399	630	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610258	81610258	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121908859	NA	P-0038431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	123	611	0	ENST00000298171.2:c.1856A>G	p.Asp619Gly	p.D619G	ENST00000298171	NM_000369.2	619	gAt/gGt	10/10	0.156885882168047	4	FACETS	1	0.975	1	1	0.975	1	INDETERMINATE	2	FALSE	2	0.36926450860295	4		611	386	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386613	81386613	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	64	482	0	ENST00000222390.5:c.374T>G	p.Ile125Ser	p.I125S	ENST00000222390	NM_000601.4	125	aTt/aGt	4/18	1	2	FACETS	0.88	0.775	0.989	1	0.979	1	CLONAL	2	FALSE	1	0.36926450860295	2		482	197	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197002	123197002	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	56	364	0	ENST00000218089.9:c.1768C>T	p.Gln590Ter	p.Q590*	ENST00000218089	NM_001042749.1	590	Cag/Tag	19/35	0.323066156056515	2	FACETS	0.982	0.876	1			1	CLONAL	3	FALSE	NA	0.36926450860295	2		364	103	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0038432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	136	606	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.218808429776664	2	FACETS	0.965	0.881	1	0.965	0.881	1	CLONAL	2	TRUE	0	0.238823125495838	2		606	590	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0038432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	51	347	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.933	0.794	1	0.933	0.794	1	CLONAL	1	TRUE	1	0.238823125495838	2		347	458	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215787	98215787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376844749	NA	P-0038432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	90	763	0	ENST00000331920.6:c.3422C>T	p.Ala1141Val	p.A1141V	ENST00000331920	NM_000264.3	1141	gCg/gTg	20/24	1	2	FACETS	0.793	0.702	0.89	0.793	0.702	0.89	SUBCLONAL	1	TRUE	1	0.238823125495838	2		763	951	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650654	67650654	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	72	594	0	ENST00000264010.4:c.959G>A	p.Arg320His	p.R320H	ENST00000264010	NM_006565.3	320	cGt/cAt	5/12	1	2	FACETS	0.765	0.667	0.871	0.765	0.667	0.871	SUBCLONAL	1	TRUE	1	0.238823125495838	2		594	788	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074115	8074115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	86	537	0	ENST00000377482.5:c.544del	p.Leu182PhefsTer2	p.L182Ffs*2	ENST00000377482	NM_018948.3	182	Ctt/tt	4/4	0.238823125495838	3	FACETS	1	0.976	1	0.712	0.631	0.799	CLONAL	1	TRUE	1	0.238823125495838	3		537	566	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0038434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	332	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.874291068806381	4	FACETS	0.894	0.857	0.929	0.894	0.857	0.929	CLONAL	3	TRUE	1	0.874291068806381	4		457	531	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225560	26225560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375842011	NA	P-0038434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	92	677	0	ENST00000360408.1:c.178G>A	p.Glu60Lys	p.E60K	ENST00000360408	NM_003532.2	60	Gag/Aag	1/1	0.874291068806381	6	FACETS	0.636	0.564	0.713	0.212	0.188	0.238	SUBCLONAL	1	TRUE	3	0.874291068806381	6		677	909	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0038436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	122	455	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.37420935730659	2		455	633	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934573	NA	P-0038436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	212	674	0	ENST00000269305.4:c.722C>A	p.Ser241Tyr	p.S241Y	ENST00000269305	NM_001126112.2	241	tCc/tAc	7/11	0.37420935730659	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.37420935730659	1		674	650	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130268	11130268	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	127	586	0	ENST00000358026.2:c.2507G>A	p.Gly836Glu	p.G836E	ENST00000358026	NM_001128849.1	836	gGa/gAa	18/36	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.37420935730659	2		586	667	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37871562	37871562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748700504	NA	P-0038436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	137	845	2	ENST00000269571.5:c.1172C>T	p.Pro391Leu	p.P391L	ENST00000269571		391	cCg/cTg	10/27	0.358617346231252	2	FACETS	0.828	0.753	0.907	0.414	0.376	0.454	CLONAL	1	TRUE	0	0.37420935730659	2		847	884	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120496288	120496288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782151048	NA	P-0038436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	104	528	0	ENST00000256646.2:c.2243G>A	p.Gly748Asp	p.G748D	ENST00000256646	NM_024408.3	748	gGc/gAc	14/34	0.334659212772686	3	FACETS	0.899	0.805	0.998			1	CLONAL	1	TRUE	NA	0.37420935730659	3		528	734	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107284	193107284	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	79	413	0	ENST00000367435.3:c.493G>A	p.Val165Ile	p.V165I	ENST00000367435	NM_024529.4	165	Gta/Ata	6/17	0.37420935730659	3	FACETS	0.944	0.832	1	0.472	0.416	0.532	CLONAL	1	TRUE	1	0.37420935730659	3		413	531	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439852	49439889	+	frameshift_variant	Frame_Shift_Del	DEL	AGGCTTTACCACGTAGGGCTGGCAGGAGACACAGTCAA	AGGCTTTACCACGTAGGGCTGGCAGGAGACACAGTCAA	-	novel	NA	P-0038437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	356	858	0	ENST00000301067.7:c.4652_4689del	p.Phe1551CysfsTer39	p.F1551Cfs*39	ENST00000301067	NM_003482.3	1551	tTTGACTGTGTCTCCTGCCAGCCCTACGTGGTAAAGCCT/t	17/54	1	2	FACETS	0.856	0.812	0.9	0.856	0.812	0.9	CLONAL	1	TRUE	1	0.768477959958292	2		858	1083	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950922	32950922	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0038437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	362	684	0	ENST00000380152.3:c.8748C>G	p.Tyr2916Ter	p.Y2916*	ENST00000380152		2916	taC/taG	21/27	0.768477959958292	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.768477959958292	1		684	555	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579484	7579491	+	frameshift_variant	Frame_Shift_Del	DEL	TCTGGCAT	TCTGGCAT	-	novel	NA	P-0038437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	231	873	0	ENST00000269305.4:c.196_203del	p.Met66GlyfsTer80	p.M66Gfs*80	ENST00000269305	NM_001126112.2	66	ATGCCAGAg/g	4/11	0.768477959958292	1	FACETS	0.442	0.413	0.472	0.442	0.413	0.472	SUBCLONAL	1	TRUE	0	0.768477959958292	1		873	838	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136172	11136172	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	410	822	0	ENST00000358026.2:c.3156C>G	p.Phe1052Leu	p.F1052L	ENST00000358026	NM_001128849.1	1052	ttC/ttG	22/36	0.768477959958292	1	FACETS	0.982	0.946	1	0.982	0.946	1	CLONAL	1	TRUE	0	0.768477959958292	1		822	669	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288653	15288864	+	frameshift_variant	Frame_Shift_Del	DEL	AGCGCAGCGGAAGAAGGGCGCGAGCGGCGCGGGGCGGCAGGAGCCCCCGTGGAGACAGGGGGCGGCCGCGCAGCTGGCGTTGCTGGCCCCCGGCGGCGACCCCGGGAAGCTGCGGCAGGAGGGTCCCGACAACCCTGGGGGGCAGGCGCAGCGCGGCCCGCGGGGCGTCTGCTGGCATGGGACGCCCACCGGGCACTGCAGCTCCCGGCAGG	AGCGCAGCGGAAGAAGGGCGCGAGCGGCGCGGGGCGGCAGGAGCCCCCGTGGAGACAGGGGGCGGCCGCGCAGCTGGCGTTGCTGGCCCCCGGCGGCGACCCCGGGAAGCTGCGGCAGGAGGGTCCCGACAACCCTGGGGGGCAGGCGCAGCGCGGCCCGCGGGGCGTCTGCTGGCATGGGACGCCCACCGGGCACTGCAGCTCCCGGCAGG	-	novel	NA	P-0038437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	0	57	20	0	ENST00000263388.2:c.3875_4086del	p.Ser1292LeufsTer200	p.S1292Lfs*200	ENST00000263388	NM_000435.2	1292	tCCTGCCGGGAGCTGCAGTGCCCGGTGGGCGTCCCATGCCAGCAGACGCCCCGCGGGCCGCGCTGCGCCTGCCCCCCAGGGTTGTCGGGACCCTCCTGCCGCAGCTTCCCGGGGTCGCCGCCGGGGGCCAGCAACGCCAGCTGCGCGGCCGCCCCCTGTCTCCACGGGGGCTCCTGCCGCCCCGCGCCGCTCGCGCCCTTCTTCCGCTGCGCT/t	24/33	0.768477959958292	1	FACETS		NA	1	1	0.987	1	NA	2	TRUE	0	0.768477959958292	1		20	57	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138376596	138376596	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	342	752	0	ENST00000289153.2:c.2878C>G	p.Leu960Val	p.L960V	ENST00000289153	NM_006219.2	960	Ctt/Gtt	20/22	0.768477959958292	1	FACETS	0.991	0.951	1	0.991	0.951	1	CLONAL	1	TRUE	0	0.768477959958292	1		752	553	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0038438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	26	523	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.302452064719356	5	FACETS	0.293	0.231	0.365	0.098	0.077	0.122	SUBCLONAL	1	TRUE	2	0.412410960126566	5		523	696	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0038438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	366	557	0	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	0.353895889130885	3	FACETS	0.97	0.927	1	0.97	0.927	1	CLONAL	3	TRUE	0	0.412410960126566	3		557	736	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130243	2130243	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45517295	NA	P-0038438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	299	728	2	ENST00000219476.3:c.3475C>T	p.Arg1159Trp	p.R1159W	ENST00000219476	NM_000548.3	1159	Cgg/Tgg	30/42	0.412410960126566	3	FACETS	0.945	0.892	0.999	0.945	0.892	0.999	CLONAL	2	TRUE	1	0.412410960126566	3		730	925	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915589	131915589	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764784659	NA	P-0038438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	81	212	2	ENST00000265335.6:c.587G>A	p.Arg196His	p.R196H	ENST00000265335		196	cGt/cAt	5/25	NA	2	FACETS	0.944	0.849	1			1	INDETERMINATE	2	TRUE	NA	0.412410960126566	2		214	208	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38949832	38949832	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	164	189	0	ENST00000357387.3:c.4118C>G	p.Ser1373Cys	p.S1373C	ENST00000357387	NM_152756.3	1373	tCc/tGc	31/38	0.412410960126566	13	FACETS	0.925	0.849	1			1	CLONAL	3	TRUE	NA	0.412410960126566	13		189	937	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41258552	41258558	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TATAAAT	TATAAAT	-	rs1555597329	NA	P-0038438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	37	274	0	ENST00000357654.3:c.135-8_135-2del		p.X45_splice	ENST00000357654	NM_007294.3	45			0.36124501203567	5	FACETS	0.519	0.427	0.622	0.173	0.142	0.208	SUBCLONAL	1	TRUE	2	0.412410960126566	5		274	560	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	109	399	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.913	0.823	1	0.913	0.823	1	CLONAL	1	TRUE	1	0.462696762696486	2		399	516	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685289	89685289	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0038439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	57	184	0	ENST00000371953.3:c.184A>T	p.Lys62Ter	p.K62*	ENST00000371953	NM_000314.4	62	Aaa/Taa	3/9	0.462696762696486	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.462696762696486	1		184	175	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17355150	17355150	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	139	360	0	ENST00000375499.3:c.368A>T	p.Lys123Met	p.K123M	ENST00000375499	NM_003000.2	123	aAg/aTg	4/8	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.462696762696486	2		360	589	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557929	29557929	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0038439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	46	130	0	ENST00000356175.3:c.3186del	p.Lys1062AsnfsTer15	p.K1062Nfs*15	ENST00000356175	NM_000267.3	1061	gtA/gt	24/57	0.462696762696486	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.462696762696486	1		130	124	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786795	3786795	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	106	316	1	ENST00000262367.5:c.4416G>T	p.Trp1472Cys	p.W1472C	ENST00000262367	NM_004380.2	1472	tgG/tgT	27/31	0.139198995039635	5	FACETS	0.963	0.862	1	0.481	0.431	0.535	CLONAL	2	TRUE	1	0.139198995039635	5		317	956	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1912	91	691	0	ENST00000269305.4:c.811G>C	p.Glu271Gln	p.E271Q	ENST00000269305	NM_001126112.2	271	Gag/Cag	8/11	0.139198995039635	3	FACETS	0.698	0.617	0.786	0.349	0.308	0.393	SUBCLONAL	1	TRUE	1	0.139198995039635	3		691	2003	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0038441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1474	269	534	0	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	0.139198995039635	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.139198995039635	3		534	1743	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627330	37627330	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	40	435	0	ENST00000447079.4:c.1245G>T	p.Met415Ile	p.M415I	ENST00000447079	NM_015083.1	415	atG/atT	2/14	0.139198995039635	3	FACETS	1	0.952	1	0.728	0.606	0.865	CLONAL	1	TRUE	1	0.139198995039635	3		435	422	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141499	11141499	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1733	412	586	2	ENST00000358026.2:c.3476G>T	p.Gly1159Val	p.G1159V	ENST00000358026	NM_001128849.1	1159	gGg/gTg	25/36	0.139198995039635	3	FACETS	0.984	0.933	1	1	0.995	1	CLONAL	3	TRUE	1	0.139198995039635	3		588	2145	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629038	14629038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1490195444	NA	P-0038441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2105	177	370	0	ENST00000254322.2:c.124G>A	p.Glu42Lys	p.E42K	ENST00000254322	NM_006145.1	42	Gag/Aag	1/3	0.139198995039635	3	FACETS	1	0.978	1	0.596	0.546	0.648	CLONAL	1	TRUE	1	0.139198995039635	3		370	2282	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629122	14629122	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2263	219	320	2	ENST00000254322.2:c.40G>A	p.Gly14Ser	p.G14S	ENST00000254322	NM_006145.1	14	Ggc/Agc	1/3	0.139198995039635	3	FACETS	1	0.988	1	0.678	0.627	0.731	CLONAL	1	TRUE	1	0.139198995039635	3		322	2482	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209110081	209110081	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	10	444	0	ENST00000345146.2:c.482G>A	p.Gly161Glu	p.G161E	ENST00000345146	NM_005896.2	161	gGa/gAa	5/10	1	2	FACETS	1	0.711	1	1	0.711	1	CLONAL	1	TRUE	1	0.139198995039635	2		444	137	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748111	41748111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	160	104	0	ENST00000226382.2:c.658C>A	p.Pro220Thr	p.P220T	ENST00000226382	NM_003924.3	220	Ccg/Acg	3/3	0.139198995039635	3	FACETS	1	0.923	1	1	0.992	1	CLONAL	4	TRUE	1	0.139198995039635	3		104	613	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155576	56155576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	97	279	0	ENST00000399503.3:c.668C>T	p.Ser223Phe	p.S223F	ENST00000399503	NM_005921.1	223	tCt/tTt	3/20	0.139198995039635	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	0	0.139198995039635	2		279	645	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188963	32188963	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2131	303	609	0	ENST00000375023.3:c.591G>T	p.Glu197Asp	p.E197D	ENST00000375023	NM_004557.3	197	gaG/gaT	4/30	0.139198995039635	7	FACETS	1	0.988	1	0.603	0.565	0.642	CLONAL	2	TRUE	3	0.139198995039635	7		609	2434	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528930	157528930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1371496107	NA	P-0038441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1398	223	425	0	ENST00000346085.5:c.6655G>A	p.Glu2219Lys	p.E2219K	ENST00000346085	NM_020732.3	2219	Gag/Aag	20/20	0.139198995039635	6	FACETS	0.842	0.781	0.906	0.632	0.586	0.679	CLONAL	3	TRUE	2	0.139198995039635	6		425	1621	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349167	70349167	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	256	442	1	ENST00000374080.3:c.3579C>A	p.Asn1193Lys	p.N1193K	ENST00000374080		1193	aaC/aaA	26/45	0.139198995039635	5	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	2	0.139198995039635	5		443	1376	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938752	76938752	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	19	535	0	ENST00000373344.5:c.1996C>G	p.Arg666Gly	p.R666G	ENST00000373344	NM_000489.3	666	Cga/Gga	9/35	0.139198995039635	1	FACETS	0.914	0.7	1	1	0.93	1	CLONAL	2	TRUE	0	0.139198995039635	1		535	139	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939036	76939036	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	23	422	0	ENST00000373344.5:c.1712G>C	p.Arg571Thr	p.R571T	ENST00000373344	NM_000489.3	571	aGa/aCa	9/35	0.139198995039635	1	FACETS	1	0.889	1	1	0.954	1	CLONAL	2	TRUE	0	0.139198995039635	1		422	127	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0038443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	224	622	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.481508354747307	2	FACETS	0.889	0.837	0.942	0.889	0.837	0.942	CLONAL	2	TRUE	0	0.500937211695024	2		622	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0038443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	474	545	0	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.500937211695024	2	FACETS	0.996	0.957	1	0.996	0.957	1	CLONAL	2	TRUE	0	0.500937211695024	2		545	950	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913315	NA	P-0038443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	464	586	0	ENST00000326873.7:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000326873	NM_000455.4	194	Gac/Tac	4/10	0.500937211695024	2	FACETS	0.995	0.956	1	0.995	0.956	1	CLONAL	2	TRUE	0	0.500937211695024	2		586	931	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906958	32906958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358423	NA	P-0038443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	115	309	0	ENST00000380152.3:c.1343G>A	p.Arg448His	p.R448H	ENST00000380152		448	cGt/cAt	10/27	1	2	FACETS	0.897	0.812	0.986	0.897	0.812	0.986	CLONAL	1	TRUE	1	0.500937211695024	2		309	512	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655391	67655391	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	391	416	0	ENST00000264010.4:c.1254A>T	p.Gln418His	p.Q418H	ENST00000264010	NM_006565.3	418	caA/caT	7/12	0.500937211695024	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.500937211695024	3		416	907	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610078	10610078	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	399	452	0	ENST00000171111.5:c.632T>A	p.Phe211Tyr	p.F211Y	ENST00000171111	NM_203500.1	211	tTt/tAt	2/6	0.500937211695024	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.500937211695024	2		452	784	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917703	151917703	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0038443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	185	232	0	ENST00000262189.6:c.3617T>A	p.Leu1206Ter	p.L1206*	ENST00000262189	NM_170606.2	1206	tTg/tAg	23/59	0.500937211695024	5	FACETS	0.889	0.829	0.951	0.889	0.829	0.951	CLONAL	3	TRUE	2	0.500937211695024	5		232	485	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38157097	38157097	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	153	439	0	ENST00000317025.8:c.2623C>A	p.Gln875Lys	p.Q875K	ENST00000317025	NM_023034.1	875	Cag/Aag	15/24	0.500937211695024	1	FACETS	0.846	0.779	0.916	0.846	0.779	0.916	CLONAL	1	TRUE	0	0.500937211695024	1		439	541	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138729528	NA	P-0038444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	906	419	0	ENST00000269305.4:c.523C>G	p.Arg175Gly	p.R175G	ENST00000269305	NM_001126112.2	175	Cgc/Ggc	5/11	0.929160849156539	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.929160849156539	2		419	964	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951164	48951165	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0038444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	122	238	0	ENST00000267163.4:c.1326_1327del	p.Ser443ThrfsTer19	p.S443Tfs*19	ENST00000267163	NM_000321.2	442	ggATca/ggca	13/27	0.929160849156539	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.929160849156539	1		238	138	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339257	70339271	+	inframe_deletion	In_Frame_Del	DEL	TCAATAACCAGCCTG	TCAATAACCAGCCTG	-	novel	NA	P-0038444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	372	370	0	ENST00000374080.3:c.134_148del	p.Phe45_Ala50delinsSer	p.F45_A50delinsS	ENST00000374080		45	tTCAATAACCAGCCTGct/tct	2/45	0.929160849156539	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.929160849156539	1		370	417	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920268	76920268	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0038444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	103	178	0	ENST00000373344.5:c.3810-1G>T		p.X1270_splice	ENST00000373344	NM_000489.3	1270			0.929160849156539	1	FACETS	0.973	0.925	1	0.973	0.925	1	CLONAL	1	TRUE	0	0.929160849156539	1		178	122	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881001	37881002	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGCTCCCC	rs397516981	NA	P-0038445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	117	543	0	ENST00000269571.5:c.2331_2339dup	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	gtg/gtGGGCTCCCCg	20/27	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		543	835	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0038446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	362	647	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	0.96	0.915	1	0.96	0.915	1	CLONAL	1	TRUE	1	0.891523434740653	2		647	846	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0038447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	83	625	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.338	0.297	0.381	0.338	0.297	0.381	SUBCLONAL	1	TRUE	1	0.57	2		627	862	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372133	55372133	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	45	350	0	ENST00000297316.4:c.823G>T	p.Gly275Cys	p.G275C	ENST00000297316	NM_022454.3	275	Ggc/Tgc	2/2	1	2	FACETS	0.246	0.206	0.291	0.246	0.206	0.291	SUBCLONAL	1	TRUE	1	0.57	2		350	641	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0038448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	35	655	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.725	0.592	0.875	0.725	0.592	0.875	SUBCLONAL	1	TRUE	1	0.13	2		655	743	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0038449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	265	661	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.566833994446689	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.582120275197182	1		661	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0038449-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	176	661	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.211657977692854	2	FACETS	0.823	0.759	0.889	0.823	0.759	0.889	CLONAL	2	TRUE	0	0.259556507715023	2		661	824	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242668	46242668	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038449-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	39	364	0	ENST00000334344.6:c.1630G>C	p.Glu544Gln	p.E544Q	ENST00000334344	NM_152641.2	544	Gaa/Caa	13/21	0.234287088274953	3	FACETS	0.786	0.652	0.935	0.262	0.217	0.312	CLONAL	1	TRUE	0	0.259556507715023	3		364	432	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56839443	56839443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778313837	NA	P-0038449-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	140	449	1	ENST00000308159.5:c.388C>T	p.Arg130Trp	p.R130W	ENST00000308159	NM_014669.4	130	Cgg/Tgg	5/22	0.149948244773898	2	FACETS	0.798	0.728	0.871	0.798	0.728	0.871	INDETERMINATE	2	TRUE	0	0.259556507715023	2		450	676	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165719	185165719	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038449-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	63	404	0	ENST00000265026.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000265026	NM_004721.4	332	Gaa/Aaa	5/14	0.248512529340858	2	FACETS	0.691	0.596	0.793	0.345	0.298	0.397	SUBCLONAL	1	TRUE	0	0.259556507715023	2		404	703	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845562	151845562	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038449-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	175	622	0	ENST00000262189.6:c.13450C>A	p.His4484Asn	p.H4484N	ENST00000262189	NM_170606.2	4484	Cac/Aac	52/59	0.259556507715023	3	FACETS	1	0.974	1	0.748	0.691	0.807	CLONAL	2	TRUE	0	0.259556507715023	3		622	679	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845685	151845685	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038449-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	221	538	0	ENST00000262189.6:c.13327C>T	p.Gln4443Ter	p.Q4443*	ENST00000262189	NM_170606.2	4443	Cag/Tag	52/59	0.259556507715023	3	FACETS	0.899	0.841	0.96	0.899	0.841	0.96	CLONAL	3	TRUE	0	0.259556507715023	3		538	713	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0038450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	180	523	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.594712112404451	2		523	508	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	197	399	0				ENST00000310581	NM_198253.2	-/1132			0.310423228570084	3	FACETS	0.82	0.766	0.875	0.82	0.766	0.875	INDETERMINATE	2	TRUE	1	0.594712112404451	3		399	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	24	691	0	ENST00000269305.4:c.811G>C	p.Glu271Gln	p.E271Q	ENST00000269305	NM_001126112.2	271	Gag/Cag	8/11	1	2	FACETS	0.097	0.075	0.122	0.097	0.075	0.122	SUBCLONAL	1	TRUE	1	0.594712112404451	2		691	832	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36823935	36823935	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	253	533	0	ENST00000373129.3:c.247G>C	p.Glu83Gln	p.E83Q	ENST00000373129	NM_032017.1	83	Gag/Cag	5/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.594712112404451	2		533	802	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099358	193099358	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	110	269	0	ENST00000367435.3:c.292C>G	p.Leu98Val	p.L98V	ENST00000367435	NM_024529.4	98	Ctc/Gtc	3/17	0.594712112404451	3	FACETS	0.897	0.809	0.989	0.449	0.404	0.495	CLONAL	1	TRUE	1	0.594712112404451	3		269	535	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710670	114710670	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	162	397	0	ENST00000543371.1:c.155C>A	p.Ser52Ter	p.S52*	ENST00000543371	NM_001198531.1	52	tCa/tAa	1/14	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.594712112404451	2		397	492	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139170	108139170	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs876660780	NA	P-0038450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	54	405	0	ENST00000278616.4:c.2672C>G	p.Ser891Ter	p.S891*	ENST00000278616	NM_000051.3	891	tCa/tGa	18/63	1	2	FACETS	0.329	0.281	0.382	0.329	0.281	0.382	SUBCLONAL	1	TRUE	1	0.594712112404451	2		405	552	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376967	118376967	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	125	329	0	ENST00000534358.1:c.10360C>T	p.Gln3454Ter	p.Q3454*	ENST00000534358	NM_005933.3	3454	Cag/Tag	27/36	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.594712112404451	2		329	409	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390389	118390389	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	228	457	1	ENST00000534358.1:c.11203G>T	p.Glu3735Ter	p.E3735*	ENST00000534358	NM_005933.3	3735	Gag/Tag	32/36	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.594712112404451	2		458	689	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431733	49431733	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	258	654	0	ENST00000301067.7:c.9406del	p.Ile3136LeufsTer6	p.I3136Lfs*6	ENST00000301067	NM_003482.3	3136	Att/tt	34/54	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.594712112404451	2		654	829	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934234	48934234	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0038450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	106	369	0	ENST00000267163.4:c.689C>G	p.Ser230Ter	p.S230*	ENST00000267163	NM_000321.2	230	tCa/tGa	7/27	0.594712112404451	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.594712112404451	1		369	246	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436135	110436135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	334	595	1	ENST00000375856.3:c.2266G>A	p.Ala756Thr	p.A756T	ENST00000375856	NM_003749.2	756	Gca/Aca	1/2	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.594712112404451	2		596	894	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061193	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0038450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	141	349	0	ENST00000250448.2:c.796_798del	p.Phe266del	p.F266del	ENST00000250448	NM_004496.3	266	TTC/-	2/2	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.594712112404451	2		349	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0038450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	54	651	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	0.192	0.163	0.224	0.192	0.163	0.224	SUBCLONAL	1	TRUE	1	0.594712112404451	2		651	945	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519990	NA	P-0038450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	53	502	0	ENST00000269305.4:c.796G>C	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Cga	8/11	1	2	FACETS	0.24	0.204	0.28	0.24	0.204	0.28	SUBCLONAL	1	TRUE	1	0.594712112404451	2		502	743	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864656	37864656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs950730453	NA	P-0038450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	298	779	1	ENST00000269571.5:c.308G>A	p.Arg103Gln	p.R103Q	ENST00000269571		103	cGa/cAa	3/27	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.594712112404451	2		780	879	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879854	37879854	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	89	738	0	ENST00000269571.5:c.2149G>A	p.Glu717Lys	p.E717K	ENST00000269571		717	Gag/Aag	18/27	1	2	FACETS	0.402	0.356	0.451	0.402	0.356	0.451	SUBCLONAL	1	TRUE	1	0.594712112404451	2		738	744	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs121913468	NA	P-0038450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	37	425	0	ENST00000269571.5:c.2305G>C	p.Asp769His	p.D769H	ENST00000269571		769	Gac/Cac	19/27	1	2	FACETS	0.238	0.196	0.285	0.238	0.196	0.285	SUBCLONAL	1	TRUE	1	0.594712112404451	2		425	523	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0038450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	240	767	1	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.594712112404451	2		768	766	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170591	7170591	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	223	413	0	ENST00000302850.5:c.1440G>C	p.Glu480Asp	p.E480D	ENST00000302850	NM_000208.2	480	gaG/gaC	6/22	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.594712112404451	2		413	671	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682844	190682844	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1372328007	NA	P-0038450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	157	346	0	ENST00000441310.2:c.520G>A	p.Asp174Asn	p.D174N	ENST00000441310	NM_000534.4	174	Gat/Aat	5/13	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.594712112404451	2		346	513	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092951	29092951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs864622537	NA	P-0038450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	161	338	0	ENST00000328354.6:c.1033C>T	p.His345Tyr	p.H345Y	ENST00000328354	NM_007194.3	345	Cac/Tac	10/15	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.594712112404451	2		338	527	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170913	56170913	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	23	226	0	ENST00000399503.3:c.1741G>C	p.Glu581Gln	p.E581Q	ENST00000399503	NM_005921.1	581	Gag/Cag	10/20	0.191068302718023	1	FACETS	0.161	0.125	0.203	0.161	0.125	0.203	INDETERMINATE	1	TRUE	0	0.594712112404451	1		226	337	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679573	86679573	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	120	322	0	ENST00000274376.6:c.2734C>T	p.Pro912Ser	p.P912S	ENST00000274376	NM_002890.2	912	Cca/Tca	21/25	0.191068302718023	1	FACETS	0.752	0.686	0.82	0.752	0.686	0.82	INDETERMINATE	1	TRUE	0	0.594712112404451	1		322	377	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31939790	31939790	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	103	645	0	ENST00000375333.2:c.17C>T	p.Ser6Phe	p.S6F	ENST00000375333	NM_032454.1	6	tCt/tTt	1/8	1	2	FACETS	0.369	0.329	0.411	0.369	0.329	0.411	SUBCLONAL	1	TRUE	1	0.594712112404451	2		645	939	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793550	89793550	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1333507341	NA	P-0038450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	21	249	0	ENST00000336032.3:c.619G>C	p.Glu207Gln	p.E207Q	ENST00000336032	NM_006813.2	207	Gag/Cag	2/2	1	2	FACETS	0.176	0.135	0.224	0.176	0.135	0.224	SUBCLONAL	1	TRUE	1	0.594712112404451	2		249	402	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	163148698	163148698	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0038450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	29	325	0	ENST00000366898.1:c.3G>A	p.Met1?	p.M1?	ENST00000366898	NM_004562.2	1	atG/atA	1/12	1	2	FACETS	0.176	0.141	0.217	0.176	0.141	0.217	SUBCLONAL	1	TRUE	1	0.594712112404451	2		325	554	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982713	90982713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201559159	NA	P-0038450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	38	327	0	ENST00000265433.3:c.775G>A	p.Glu259Lys	p.E259K	ENST00000265433	NM_002485.4	259	Gaa/Aaa	7/16	0.594712112404451	3	FACETS	0.332	0.274	0.397	0.166	0.137	0.199	SUBCLONAL	1	TRUE	1	0.594712112404451	3		327	499	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27173286	27173286	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	208	517	2	ENST00000380036.4:c.827C>G	p.Ser276Cys	p.S276C	ENST00000380036	NM_000459.3	276	tCt/tGt	6/23	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.594712112404451	2		519	658	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221930	98221930	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs768039033	NA	P-0038450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	207	469	0	ENST00000331920.6:c.2839G>C	p.Glu947Gln	p.E947Q	ENST00000331920	NM_000264.3	947	Gaa/Caa	17/24	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.594712112404451	2		469	602	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328382	137328382	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	297	637	2	ENST00000481739.1:c.1311C>A	p.Phe437Leu	p.F437L	ENST00000481739	NM_002957.4	437	ttC/ttA	10/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.594712112404451	2		639	842	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0038457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	25	461	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.285489737143783	5	FACETS	0.233	0.183	0.292	0.078	0.061	0.098	INDETERMINATE	1	TRUE	2	0.62448831090063	5		461	665	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0038457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	134	418	1	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.874	0.799	0.952	0.874	0.799	0.952	CLONAL	1	TRUE	1	0.62448831090063	2		419	491	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936097	178936097	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	35	564	0	ENST00000263967.3:c.1639G>C	p.Glu547Gln	p.E547Q	ENST00000263967	NM_006218.2	547	Gag/Cag	10/21	0.285489737143783	5	FACETS	0.264	0.216	0.32	0.088	0.072	0.107	INDETERMINATE	1	TRUE	2	0.62448831090063	5		564	821	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440330	52440333	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	novel	NA	P-0038457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	199	531	0	ENST00000460680.1:c.719_722del	p.Lys240MetfsTer8	p.K240Mfs*8	ENST00000460680	NM_004656.3	240	aAGTAt/at	9/17	0.62448831090063	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.62448831090063	1		531	417	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916636	178916636	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	149	287	0	ENST00000263967.3:c.23G>C	p.Gly8Ala	p.G8A	ENST00000263967	NM_006218.2	8	gGt/gCt	2/21	0.285489737143783	5	FACETS	1	0.975	1	0.753	0.695	0.812	INDETERMINATE	2	TRUE	2	0.62448831090063	5		287	409	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484269	8484269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	72	356	1	ENST00000356435.5:c.3263G>A	p.Arg1088His	p.R1088H	ENST00000356435		1088	cGt/cAt	19/35	0.485439787192433	1	FACETS	0.374	0.328	0.423	0.374	0.328	0.423	SUBCLONAL	1	TRUE	0	0.62448831090063	1		357	424	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006228	22006228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	226	523	1	ENST00000276925.6:c.175G>A	p.Ala59Thr	p.A59T	ENST00000276925	NM_004936.3	59	Gcc/Acc	2/2	0.485439787192433	1	FACETS	0.858	0.806	0.912	0.858	0.806	0.912	CLONAL	1	TRUE	0	0.62448831090063	1		524	580	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770575	40770575	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	69	362	0	ENST00000373198.4:c.2807G>C	p.Arg936Pro	p.R936P	ENST00000373198	NM_133170.3	936	cGa/cCa	19/32	0.259588839747602	0	FACETS	0.173	0.15	0.196			1	INDETERMINATE	1	TRUE	0	0.62448831090063	0		362	481	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0038457-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	30	461	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.387401940729223	3	FACETS	0.554	0.446	0.675	0.277	0.223	0.338	SUBCLONAL	1	TRUE	1	0.387401940729223	3		461	334	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0038457-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	29	418	1	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.832	0.674	1	0.832	0.674	1	CLONAL	1	TRUE	1	0.387401940729223	2		419	180	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936097	178936097	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038457-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	43	564	0	ENST00000263967.3:c.1639G>C	p.Glu547Gln	p.E547Q	ENST00000263967	NM_006218.2	547	Gag/Cag	10/21	0.387401940729223	3	FACETS	0.621	0.52	0.732	0.31	0.26	0.366	SUBCLONAL	1	TRUE	1	0.387401940729223	3		564	427	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440330	52440333	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	novel	NA	P-0038457-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	87	531	0	ENST00000460680.1:c.719_722del	p.Lys240MetfsTer8	p.K240Mfs*8	ENST00000460680	NM_004656.3	240	aAGTAt/at	9/17	0.387401940729223	1	FACETS	0.908	0.809	1	0.908	0.809	1	CLONAL	1	TRUE	0	0.387401940729223	1		531	399	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916636	178916636	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038457-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	40	287	0	ENST00000263967.3:c.23G>C	p.Gly8Ala	p.G8A	ENST00000263967	NM_006218.2	8	gGt/gCt	2/21	0.387401940729223	3	FACETS	1	0.956	1	0.725	0.611	0.848	CLONAL	1	TRUE	1	0.387401940729223	3		287	170	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484269	8484269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038457-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	69	356	1	ENST00000356435.5:c.3263G>A	p.Arg1088His	p.R1088H	ENST00000356435		1088	cGt/cAt	19/35	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.387401940729223	2		357	332	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006228	22006228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038457-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	102	523	1	ENST00000276925.6:c.175G>A	p.Ala59Thr	p.A59T	ENST00000276925	NM_004936.3	59	Gcc/Acc	2/2	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.387401940729223	2		524	471	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0038458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	191	577	2	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.668067048196769	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.668067048196769	3		579	370	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0038458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	376	681	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.668067048196769	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.668067048196769	3		681	722	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0038458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	621	1009	1	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.668067048196769	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.668067048196769	2		1010	890	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030329	180030329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142322370	NA	P-0038458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	135	903	0	ENST00000261937.6:c.3955C>T	p.Arg1319Trp	p.R1319W	ENST00000261937	NM_182925.4	1319	Cgg/Tgg	30/30	0.61062951283936	4	FACETS	0.573	0.52	0.63	0.287	0.26	0.315	SUBCLONAL	1	TRUE	2	0.668067048196769	4		903	1176	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244269	5244269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568465790	NA	P-0038458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	304	619	0	ENST00000357368.4:c.1213G>A	p.Val405Ile	p.V405I	ENST00000357368	NM_002850.3	405	Gtc/Atc	11/38	0.668067048196769	2	FACETS	1	0.991	1	0.599	0.567	0.631	CLONAL	1	TRUE	0	0.668067048196769	2		619	760	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054013	42054013	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	101	424	0	ENST00000219905.7:c.7475G>C	p.Arg2492Pro	p.R2492P	ENST00000219905	NM_001164273.1	2492	cGg/cCg	21/24	0.668067048196769	3	FACETS	0.913	0.834	0.992	0.913	0.834	0.992	CLONAL	2	TRUE	1	0.668067048196769	3		424	221	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40490804	40490804	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	276	464	0	ENST00000264657.5:c.495del	p.Glu166ArgfsTer23	p.E166Rfs*23	ENST00000264657	NM_139276.2	165	gtA/gt	6/24	0.668067048196769	5	FACETS	0.979	0.929	1	0.979	0.929	1	CLONAL	3	TRUE	2	0.668067048196769	5		464	563	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922340	178922340	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	96	485	1	ENST00000263967.3:c.1109A>T	p.Asn370Ile	p.N370I	ENST00000263967	NM_006218.2	370	aAt/aTt	6/21	0.668067048196769	3	FACETS	1	0.901	1	0.502	0.45	0.556	CLONAL	1	TRUE	1	0.668067048196769	3		486	382	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507395	8507395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	37	376	2	ENST00000356435.5:c.1583C>T	p.Ser528Phe	p.S528F	ENST00000356435		528	tCt/tTt	11/35	0.668067048196769	3	FACETS	0.412	0.34	0.492	0.206	0.17	0.246	SUBCLONAL	1	TRUE	1	0.668067048196769	3		378	359	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039901	47039901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	91	914	1	ENST00000377604.3:c.1244C>T	p.Ser415Leu	p.S415L	ENST00000377604	NM_001204468.1	415	tCa/tTa	12/24	1	2	FACETS	0.386	0.343	0.433	0.386	0.343	0.433	SUBCLONAL	1	TRUE	1	0.668067048196769	2		915	705	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259654	16259654	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	36	561	1	ENST00000375759.3:c.6919G>A	p.Glu2307Lys	p.E2307K	ENST00000375759	NM_015001.2	2307	Gaa/Aaa	11/15	1	2	FACETS	0.567	0.465	0.682	0.567	0.465	0.682	SUBCLONAL	1	TRUE	1	0.227147602478766	2		562	559	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260557	16260557	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	43	597	0	ENST00000375759.3:c.7822G>T	p.Glu2608Ter	p.E2608*	ENST00000375759	NM_015001.2	2608	Gaa/Taa	11/15	1	2	FACETS	0.593	0.495	0.701	0.593	0.495	0.701	SUBCLONAL	1	TRUE	1	0.227147602478766	2		597	639	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799177	45799177	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs781163298	NA	P-0038459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	39	631	0	ENST00000450313.1:c.256C>G	p.Leu86Val	p.L86V	ENST00000450313	NM_012222.2	86	Cta/Gta	3/16	1	2	FACETS	0.495	0.409	0.591	0.495	0.409	0.591	SUBCLONAL	1	TRUE	1	0.227147602478766	2		631	694	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220291	5220291	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	57	692	0	ENST00000357368.4:c.3529G>C	p.Glu1177Gln	p.E1177Q	ENST00000357368	NM_002850.3	1177	Gag/Cag	21/38	1	2	FACETS	0.677	0.58	0.784	0.677	0.58	0.784	SUBCLONAL	1	TRUE	1	0.227147602478766	2		692	741	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796535	42796535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs539384322	NA	P-0038459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	76	965	1	ENST00000575354.2:c.3092C>T	p.Ser1031Leu	p.S1031L	ENST00000575354	NM_015125.3	1031	tCg/tTg	13/20	1	2	FACETS	0.679	0.594	0.771	0.679	0.594	0.771	SUBCLONAL	1	TRUE	1	0.227147602478766	2		966	985	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519922	NA	P-0038459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	16	631	0	ENST00000397062.3:c.235G>A	p.Glu79Lys	p.E79K	ENST00000397062	NM_006164.4	79	Gag/Aag	2/5	1	2	FACETS	0.237	0.174	0.313	0.237	0.174	0.313	SUBCLONAL	1	TRUE	1	0.227147602478766	2		631	594	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572298	41572298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	56	765	0	ENST00000263253.7:c.4827del	p.Pro1610LeufsTer14	p.P1610Lfs*14	ENST00000263253	NM_001429.3	1609	ctG/ct	30/31	1	2	FACETS	0.587	0.501	0.681	0.587	0.501	0.681	SUBCLONAL	1	TRUE	1	0.227147602478766	2		765	840	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0038459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	25	375	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	1	2	FACETS	0.636	0.501	0.791	0.636	0.501	0.791	SUBCLONAL	1	TRUE	1	0.227147602478766	2		375	346	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058707	180058707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs918215332	NA	P-0038459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	195	921	0	ENST00000261937.6:c.130G>A	p.Gly44Ser	p.G44S	ENST00000261937	NM_182925.4	44	Ggt/Agt	2/30	1	2	FACETS	0.822	0.761	0.887	1	0.992	1	CLONAL	2	TRUE	1	0.227147602478766	2		921	1044	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858279	27858279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	78	550	1	ENST00000359303.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000359303	NM_003535.2	98	Gag/Aag	1/1	0.162269740222646	2	FACETS	1	0.959	1	0.605	0.532	0.682	CLONAL	1	TRUE	0	0.227147602478766	2		551	568	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150430	157150430	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057518951	NA	P-0038459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	39	540	0	ENST00000346085.5:c.1612C>T	p.Gln538Ter	p.Q538*	ENST00000346085	NM_020732.3	538	Cag/Tag	2/20	0.162269740222646	2	FACETS	0.592	0.49	0.706	0.296	0.245	0.353	SUBCLONAL	1	TRUE	0	0.227147602478766	2		540	580	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945673	151945673	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	26	677	0	ENST00000262189.6:c.1846G>A	p.Glu616Lys	p.E616K	ENST00000262189	NM_170606.2	616	Gaa/Aaa	14/59	1	2	FACETS	0.465	0.368	0.578	0.465	0.368	0.578	SUBCLONAL	1	TRUE	1	0.227147602478766	2		677	492	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376036	8376036	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	20	293	0	ENST00000356435.5:c.4561G>A	p.Asp1521Asn	p.D1521N	ENST00000356435		1521	Gat/Aat	28/35	0.227147602478766	3	FACETS	0.562	0.429	0.718	0.281	0.214	0.359	SUBCLONAL	1	TRUE	1	0.227147602478766	3		293	349	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023045	31023046	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs750170870	NA	P-0038464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	152	637	0	ENST00000375687.4:c.2535dup	p.Ser846GlnfsTer5	p.S846Qfs*5	ENST00000375687	NM_015338.5	844	acc/aCcc	13/13	1	2	FACETS	0.986	0.914	1	0.986	0.914	1	CLONAL	1	TRUE	1	0.813233815269622	2		637	379	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	30	578	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.0741418367579569	4	FACETS	0.782	0.629	0.955	0.391	0.314	0.478	INDETERMINATE	1	TRUE	2	0.20893506682351	4		578	444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0038465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	43	643	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.20893506682351	1	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	0	0.20893506682351	1		643	349	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0038466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	376	672	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	0.368608769893863	6	FACETS	1	0.962	1	0.807	0.77	0.845	CLONAL	4	TRUE	1	0.368608769893863	6		672	878	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578177	7578177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs267605076	NA	P-0038466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	241	677	0	ENST00000269305.4:c.672G>T	p.Glu224Asp	p.E224D	ENST00000269305	NM_001126112.2	224	gaG/gaT	6/11	0.350947991209629	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.368608769893863	1		677	833	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098962	178098962	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	47	282	0	ENST00000397062.3:c.83T>C	p.Ile28Thr	p.I28T	ENST00000397062	NM_006164.4	28	aTa/aCa	2/5	1	2	FACETS	0.78	0.661	0.91	0.78	0.661	0.91	CLONAL	1	TRUE	1	0.368608769893863	2		282	327	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420490	49420490	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	174	715	0	ENST00000301067.7:c.15259G>A	p.Gly5087Arg	p.G5087R	ENST00000301067	NM_003482.3	5087	Gga/Aga	48/54	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.368608769893863	2		715	866	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813325	102813325	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	137	602	0	ENST00000307046.8:c.364C>A	p.Arg122Ser	p.R122S	ENST00000307046	NM_001111285.1	122	Cgt/Agt	3/4	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.368608769893863	2		602	662	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134329	2134329	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	180	957	0	ENST00000219476.3:c.4106G>T	p.Arg1369Leu	p.R1369L	ENST00000219476	NM_000548.3	1369	cGg/cTg	34/42	1	2	FACETS	0.875	0.806	0.947	0.875	0.806	0.947	CLONAL	1	TRUE	1	0.368608769893863	2		957	1116	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279597	18279597	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	179	786	0	ENST00000222254.8:c.1870G>T	p.Val624Leu	p.V624L	ENST00000222254	NM_005027.3	624	Gtg/Ttg	15/16	1	2	FACETS	0.966	0.89	1	0.966	0.89	1	CLONAL	1	TRUE	1	0.368608769893863	2		786	1005	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31372645	31372645	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	125	630	0	ENST00000328111.2:c.286A>T	p.Thr96Ser	p.T96S	ENST00000328111	NM_006892.3	96	Act/Tct	4/23	1	2	FACETS	0.898	0.814	0.987	0.898	0.814	0.987	CLONAL	1	TRUE	1	0.368608769893863	2		630	755	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162021	47162021	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	71	371	0	ENST00000409792.3:c.4105G>T	p.Ala1369Ser	p.A1369S	ENST00000409792	NM_014159.6	1369	Gca/Tca	3/21	0.368608769893863	1	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	0	0.368608769893863	1		371	308	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155270	55155270	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	85	432	0	ENST00000257290.5:c.2869C>A	p.Gln957Lys	p.Q957K	ENST00000257290	NM_006206.4	957	Caa/Aaa	21/23	1	2	FACETS	0.906	0.803	1	0.906	0.803	1	CLONAL	1	TRUE	1	0.368608769893863	2		432	509	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294382	1294382	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	171	822	2	ENST00000310581.5:c.619G>T	p.Val207Phe	p.V207F	ENST00000310581	NM_198253.2	207	Gtc/Ttc	2/16	0.245189941082952	3	FACETS	1	0.966	1	0.547	0.502	0.593	CLONAL	1	TRUE	1	0.368608769893863	3		824	1005	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971146	21971146	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	118	519	0	ENST00000304494.5:c.212A>T	p.Asn71Ile	p.N71I	ENST00000304494	NM_000077.4	71	aAc/aTc	2/3	0.368608769893863	1	FACETS	0.911	0.825	1	0.911	0.825	1	CLONAL	1	TRUE	0	0.368608769893863	1		519	573	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412259	63412259	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	190	472	0	ENST00000330258.3:c.908G>T	p.Gly303Val	p.G303V	ENST00000330258	NM_152424.3	303	gGc/gTc	2/2	1	1	FACETS	0.831	0.775	0.888	1	0.992	1	CLONAL	2	TRUE	0	0.368608769893863	1		472	506	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068872	30068872	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	111	596	0	ENST00000331968.5:c.2057T>C	p.Leu686Ser	p.L686S	ENST00000331968	NM_002742.2	686	tTa/tCa	14/18	0.618331476570441	3	FACETS	0.824	0.743	0.909	0.275	0.247	0.303	CLONAL	1	TRUE	0	0.645930427176238	3		596	552	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958598	175958598	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1352053056	NA	P-0038479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	114	393	0	ENST00000367669.3:c.1747T>C	p.Tyr583His	p.Y583H	ENST00000367669	NM_022457.5	583	Tat/Cat	16/20	0.206861771993728	3	FACETS	0.932	0.843	1	0.311	0.281	0.342	INDETERMINATE	1	TRUE	0	0.645930427176238	3		393	501	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	312	399	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		399	764	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112769470	112769470	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0038480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	189	375	0	ENST00000369452.4:c.1423-1del		p.X475_splice	ENST00000369452	NM_007373.3	475			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		375	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0038481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	564	614	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.725886676876246	2	FACETS	0.991	0.964	1	0.991	0.964	1	CLONAL	2	TRUE	0	0.723811357157399	2		614	786	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300492	11300492	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	277	805	0	ENST00000361445.4:c.1654C>G	p.Leu552Val	p.L552V	ENST00000361445	NM_004958.3	552	Ctt/Gtt	11/58	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.723811357157399	2		805	749	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023364	27023463	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCGTCTGCCGTCGCCGCCGCCGCGGCCGCCGTCTTCCACCAACAACATGGCGGACAACAAAGCCCTGGCCTGGCAGCGCTGCAGAGCGGCGGCGGCGG	GCCCGTCTGCCGTCGCCGCCGCCGCGGCCGCCGTCTTCCACCAACAACATGGCGGACAACAAAGCCCTGGCCTGGCAGCGCTGCAGAGCGGCGGCGGCGG	-	novel	NA	P-0038481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	113	231	0	ENST00000324856.7:c.471_570del	p.Ser157ArgfsTer42	p.S157Rfs*42	ENST00000324856	NM_006015.4	157	aGCCCGTCTGCCGTCGCCGCCGCCGCGGCCGCCGTCTTCCACCAACAACATGGCGGACAACAAAGCCCTGGCCTGGCAGCGCTGCAGAGCGGCGGCGGCGGg/ag	1/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.723811357157399	2		231	274	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777923	27777950	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCTCGGAAGAGCGCTCCGGCCACC	GGCGGCTCGGAAGAGCGCTCCGGCCACC	-	novel	NA	P-0038481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	275	422	0	ENST00000369163.2:c.77_104del	p.Ala26ValfsTer28	p.A26Vfs*28	ENST00000369163	NM_003536.2	24	aaGGCGGCTCGGAAGAGCGCTCCGGCCACC/aa	1/1	0.725886676876246	6	FACETS	0.887	0.833	0.943	0.296	0.277	0.315	CLONAL	2	TRUE	0	0.723811357157399	6		422	1048	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781266	135781344	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGGCTTTCATCAGCACTGCCGCAGGGCAGGTCTATGGGAGTAAAGGCTTGCTTTGGTGTGTCAGGCCCAAGCTTGTC	CAGGGCTTTCATCAGCACTGCCGCAGGGCAGGTCTATGGGAGTAAAGGCTTGCTTTGGTGTGTCAGGCCCAAGCTTGTC	-	novel	NA	P-0038481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	209	593	0	ENST00000298552.3:c.1621_1699del	p.Asp541ArgfsTer62	p.D541Rfs*62	ENST00000298552	NM_001162426.1	541	GACAAGCTTGGGCCTGACACACCAAAGCAAGCCTTTACTCCCATAGACCTGCCCTGCGGCAGTGCTGATGAAAGCCCTGcg/cg	15/23	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.723811357157399	2		593	573	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220514	123220514	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	249	616	2	ENST00000218089.9:c.3171G>C	p.Met1057Ile	p.M1057I	ENST00000218089	NM_001042749.1	1057	atG/atC	30/35	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.723811357157399	2		618	663	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	157	399	0				ENST00000310581	NM_198253.2	-/1132			0.2821572567604	2	FACETS	0.897	0.825	0.971	0.897	0.825	0.971	CLONAL	2	TRUE	0	0.287479409541158	2		399	609	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0038482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	62	376	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.946	0.819	1	0.946	0.819	1	CLONAL	1	TRUE	1	0.287479409541158	2		376	456	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641144	117641144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866970127	NA	P-0038482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	124	783	0	ENST00000368508.3:c.5827G>A	p.Glu1943Lys	p.E1943K	ENST00000368508	NM_002944.2	1943	Gaa/Aaa	36/43	0.287479409541158	1	FACETS	0.819	0.74	0.902	0.819	0.74	0.902	CLONAL	1	TRUE	0	0.287479409541158	1		783	902	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777894	NA	P-0038482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	186	744	0	ENST00000361445.4:c.6644C>T	p.Ser2215Phe	p.S2215F	ENST00000361445	NM_004958.3	2215	tCt/tTt	47/58	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.287479409541158	2		744	1153	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0038482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	143	395	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.253717820392644	3	FACETS	0.943	0.863	1	0.943	0.863	1	CLONAL	2	TRUE	1	0.287479409541158	3		395	603	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495044	56495044	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1334721954	NA	P-0038482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	156	735	0	ENST00000267101.3:c.3401C>T	p.Ser1134Phe	p.S1134F	ENST00000267101	NM_001982.3	1134	tCc/tTc	27/28	1	2	FACETS	0.853	0.779	0.93	0.853	0.779	0.93	CLONAL	1	TRUE	1	0.287479409541158	2		735	1273	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120885	94120885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	59	483	0	ENST00000369303.4:c.166G>A	p.Glu56Lys	p.E56K	ENST00000369303	NM_004440.3	56	Gaa/Aaa	3/17	0.287479409541158	1	FACETS	0.717	0.618	0.825	0.717	0.618	0.825	SUBCLONAL	1	TRUE	0	0.287479409541158	1		483	490	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219243	133219243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147467247	NA	P-0038482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	174	827	0	ENST00000320574.5:c.4801C>T	p.Pro1601Ser	p.P1601S	ENST00000320574	NM_006231.2	1601	Cct/Tct	37/49	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.287479409541158	2		827	1118	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40376841	40376841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	182	770	0	ENST00000293328.3:c.331C>T	p.His111Tyr	p.H111Y	ENST00000293328	NM_012448.3	111	Cat/Tat	4/19	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.287479409541158	2		770	1252	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058471	69058471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	53	542	0	ENST00000288368.4:c.4115G>A	p.Gly1372Glu	p.G1372E	ENST00000288368	NM_024870.2	1372	gGa/gAa	34/40	1	2	FACETS	0.743	0.634	0.863	0.743	0.634	0.863	SUBCLONAL	1	TRUE	1	0.287479409541158	2		542	496	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675059	40675059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	149	844	0	ENST00000249776.8:c.23C>T	p.Pro8Leu	p.P8L	ENST00000249776	NM_033286.3	8	cCc/cTc	1/9	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.287479409541158	2		844	988	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138942	64138942	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	95	449	0	ENST00000334205.4:c.2309C>T	p.Pro770Leu	p.P770L	ENST00000334205	NM_003942.2	770	cCc/cTc	17/17	1	2	FACETS	0.898	0.8	1	0.898	0.8	1	CLONAL	1	TRUE	1	0.287479409541158	2		449	736	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427387	49427387	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	173	857	0	ENST00000301067.7:c.11101C>T	p.Pro3701Ser	p.P3701S	ENST00000301067	NM_003482.3	3701	Cct/Tct	39/54	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.287479409541158	2		857	1190	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042464	16042464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	61	601	0	ENST00000268712.3:c.1210C>T	p.Pro404Ser	p.P404S	ENST00000268712	NM_006311.3	404	Cca/Tca	12/46	1	2	FACETS	0.762	0.658	0.875	0.762	0.658	0.875	SUBCLONAL	1	TRUE	1	0.287479409541158	2		601	557	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220161	5220161	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	143	713	0	ENST00000357368.4:c.3554T>C	p.Ile1185Thr	p.I1185T	ENST00000357368	NM_002850.3	1185	aTc/aCc	22/38	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.287479409541158	2		713	952	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220937	36220937	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	102	467	1	ENST00000222270.7:c.4987C>T	p.His1663Tyr	p.H1663Y	ENST00000222270	NM_014727.1	1663	Cac/Tac	23/37	1	2	FACETS	0.987	0.883	1	0.987	0.883	1	CLONAL	1	TRUE	1	0.287479409541158	2		468	719	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436105	116436105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	214	511	0	ENST00000397752.3:c.4100C>T	p.Ser1367Phe	p.S1367F	ENST00000397752	NM_000245.2	1367	tCt/tTt	21/21	0.253717820392644	3	FACETS	0.895	0.832	0.96	0.895	0.832	0.96	CLONAL	2	TRUE	1	0.287479409541158	3		511	951	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93636535	93636535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs903194537	NA	P-0038482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	108	581	0	ENST00000375746.1:c.965C>T	p.Pro322Leu	p.P322L	ENST00000375746	NM_001174167.1	322	cCg/cTg	8/14	1	2	FACETS	0.91	0.816	1	0.91	0.816	1	CLONAL	1	TRUE	1	0.287479409541158	2		581	826	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0038483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	843	875	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.693386120743796	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.693386120743796	3		876	1039	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0038484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	112	347	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.951	0.858	1	0.951	0.858	1	CLONAL	1	TRUE	1	0.433842942765633	2		347	543	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120469187	120469187	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	159	514	0	ENST00000256646.2:c.3940C>G	p.Leu1314Val	p.L1314V	ENST00000256646	NM_024408.3	1314	Ctg/Gtg	24/34	1	2	FACETS	0.899	0.825	0.977	0.899	0.825	0.977	CLONAL	1	TRUE	1	0.433842942765633	2		514	815	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717733	89717733	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	46	426	0	ENST00000371953.3:c.758T>C	p.Ile253Thr	p.I253T	ENST00000371953	NM_000314.4	253	aTc/aCc	7/9	1	2	FACETS	0.351	0.294	0.412	0.351	0.294	0.412	SUBCLONAL	1	TRUE	1	0.433842942765633	2		426	605	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167533	24167533	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	190	574	0	ENST00000263121.7:c.917A>G	p.Glu306Gly	p.E306G	ENST00000263121	NM_003073.3	306	gAg/gGg	7/9	1	2	FACETS	0.97	0.897	1	0.97	0.897	1	CLONAL	1	TRUE	1	0.433842942765633	2		574	903	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	58	220	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.694	0.597	0.8	0.694	0.597	0.8	SUBCLONAL	1	TRUE	1	0.317633214251804	2		220	526	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	138	635	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.271101556313343	3	FACETS	0.964	0.875	1	0.482	0.437	0.528	CLONAL	1	TRUE	1	0.317633214251804	3		635	1045	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230641	46230641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	102	503	1	ENST00000334344.6:c.890C>T	p.Ser297Phe	p.S297F	ENST00000334344	NM_152641.2	297	tCc/tTc	8/21	0.317633214251804	1	FACETS	0.851	0.762	0.945	0.851	0.762	0.945	CLONAL	1	TRUE	0	0.317633214251804	1		504	635	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979619	7979619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140306846	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	118	550	0	ENST00000319144.4:c.1406G>A	p.Arg469Gln	p.R469Q	ENST00000319144	NM_001139.2	469	cGg/cAg	11/15	1	2	FACETS	0.892	0.804	0.985	0.892	0.804	0.985	CLONAL	1	TRUE	1	0.317633214251804	2		550	833	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104619	69104619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61753704	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	119	677	1	ENST00000288368.4:c.4463C>T	p.Ser1488Leu	p.S1488L	ENST00000288368	NM_024870.2	1488	tCg/tTg	37/40	1	2	FACETS	0.772	0.696	0.853	0.772	0.696	0.853	SUBCLONAL	1	TRUE	1	0.317633214251804	2		678	970	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012419	29012419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867762505	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	99	594	0	ENST00000282397.4:c.452G>A	p.Gly151Glu	p.G151E	ENST00000282397	NM_002019.4	151	gGa/gAa	4/30	1	2	FACETS	0.681	0.607	0.76	0.681	0.607	0.76	SUBCLONAL	1	TRUE	1	0.317633214251804	2		594	915	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031979	10031979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	112	688	1	ENST00000330684.3:c.844G>A	p.Asp282Asn	p.D282N	ENST00000330684	NM_001134407.1	282	Gat/Aat	3/13	1	2	FACETS	0.803	0.722	0.89	0.803	0.722	0.89	CLONAL	1	TRUE	1	0.317633214251804	2		689	878	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584476	52584476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	121	538	1	ENST00000394830.3:c.4537G>A	p.Glu1513Lys	p.E1513K	ENST00000394830	NM_018313.4	1513	Gag/Aag	29/30	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.317633214251804	2		539	744	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101132	4101132	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	128	565	0	ENST00000262948.5:c.590C>T	p.Pro197Leu	p.P197L	ENST00000262948	NM_030662.3	197	cCc/cTc	6/11	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.317633214251804	2		565	795	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435460	110435460	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	107	513	1	ENST00000375856.3:c.2941C>T	p.Leu981Phe	p.L981F	ENST00000375856	NM_003749.2	981	Ctc/Ttc	1/2	1	2	FACETS	0.821	0.736	0.911	0.821	0.736	0.911	CLONAL	1	TRUE	1	0.317633214251804	2		514	821	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152864447	152864447	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	24	74	0	ENST00000406277.2:c.79C>T	p.Arg27Ter	p.R27*	ENST00000406277	NM_152274.4	27	Cga/Tga	3/7	1		FACETS		0.935	1				CLONAL	1	TRUE	0	0.317633214251804	1		74	85	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860908	151860908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	59	317	1	ENST00000262189.6:c.9754C>T	p.Arg3252Cys	p.R3252C	ENST00000262189	NM_170606.2	3252	Cgt/Tgt	43/59	1	2	FACETS	0.86	0.742	0.988	0.86	0.742	0.988	CLONAL	1	TRUE	1	0.317633214251804	2		318	432	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18649003	18649003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	53	435	0	ENST00000266497.5:c.2678C>T	p.Ser893Leu	p.S893L	ENST00000266497		893	tCa/tTa	19/31	1	2	FACETS	0.638	0.544	0.741	0.638	0.544	0.741	SUBCLONAL	1	TRUE	1	0.317633214251804	2		435	523	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246754	41246754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	122	514	0	ENST00000357654.3:c.794C>T	p.Ser265Phe	p.S265F	ENST00000357654	NM_007294.3	265	tCt/tTt	10/23	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.317633214251804	2		514	756	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521663	89521663	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs549868478	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	124	547	0	ENST00000336596.2:c.2740C>T	p.Arg914Cys	p.R914C	ENST00000336596	NM_005233.5	914	Cgc/Tgc	16/17	1	2	FACETS	0.993	0.899	1	0.993	0.899	1	CLONAL	1	TRUE	1	0.317633214251804	2		547	786	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608060	28608060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	112	634	1	ENST00000241453.7:c.1906G>A	p.Gly636Arg	p.G636R	ENST00000241453	NM_004119.2	636	Gga/Aga	15/24	1	2	FACETS	0.871	0.783	0.964	0.871	0.783	0.964	CLONAL	1	TRUE	1	0.317633214251804	2		635	810	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420107	41420107	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	51	336	0	ENST00000373198.4:c.215-1G>A		p.X72_splice	ENST00000373198	NM_133170.3	72			1	2	FACETS	0.847	0.723	0.983	0.847	0.723	0.983	CLONAL	1	TRUE	1	0.317633214251804	2		336	379	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489857	2489857	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1026422880	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	131	615	2	ENST00000355716.4:c.254C>T	p.Ala85Val	p.A85V	ENST00000355716	NM_003820.2	85	gCc/gTc	3/8	NA	2	FACETS	0.895	0.811	0.983			1	INDETERMINATE	1	TRUE	NA	0.317633214251804	2		617	922	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288849	11288849	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	128	576	1	ENST00000361445.4:c.2906C>T	p.Thr969Ile	p.T969I	ENST00000361445	NM_004958.3	969	aCc/aTc	19/58	1	2	FACETS	0.961	0.871	1	0.961	0.871	1	CLONAL	1	TRUE	1	0.317633214251804	2		577	839	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400866	72400866	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557442866	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	178	344	0	ENST00000357731.5:c.305G>A	p.Ser102Asn	p.S102N	ENST00000357731	NM_173808.2	102	aGc/aAc	2/7	0.271101556313343	3	FACETS	0.991	0.917	1	0.991	0.917	1	CLONAL	2	TRUE	1	0.317633214251804	3		344	655	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851287	63851287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	126	616	0	ENST00000279873.7:c.2065C>T	p.Pro689Ser	p.P689S	ENST00000279873	NM_032199.2	689	Cca/Tca	10/10	1	2	FACETS	0.849	0.768	0.935	0.849	0.768	0.935	CLONAL	1	TRUE	1	0.317633214251804	2		616	934	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442652	442652	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	131	523	0	ENST00000399788.2:c.1653+1G>C		p.X551_splice	ENST00000399788	NM_001042603.1	551			0.149704307448883	3	FACETS	0.997	0.904	1			1	INDETERMINATE	1	TRUE	NA	0.317633214251804	3		523	959	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800945	18800945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	127	395	0	ENST00000266497.5:c.4321G>A	p.Gly1441Arg	p.G1441R	ENST00000266497		1441	Gga/Aga	31/31	1	2	FACETS	0.775	0.706	0.847	1	0.987	1	SUBCLONAL	2	TRUE	1	0.317633214251804	2		395	516	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557770	21557770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	128	739	1	ENST00000382592.4:c.2075C>T	p.Ala692Val	p.A692V	ENST00000382592	NM_014572.2	692	gCc/gTc	5/8	1	2	FACETS	0.833	0.754	0.917	0.833	0.754	0.917	CLONAL	1	TRUE	1	0.317633214251804	2		740	967	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28624307	28624307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754816108	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	93	545	1	ENST00000241453.7:c.667G>A	p.Glu223Lys	p.E223K	ENST00000241453	NM_004119.2	223	Gaa/Aaa	6/24	1	2	FACETS	0.762	0.678	0.853	0.762	0.678	0.853	SUBCLONAL	1	TRUE	1	0.317633214251804	2		546	768	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28908239	28908239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	68	519	0	ENST00000282397.4:c.2516G>A	p.Gly839Glu	p.G839E	ENST00000282397	NM_002019.4	839	gGa/gAa	18/30	1	2	FACETS	0.576	0.501	0.658	0.576	0.501	0.658	SUBCLONAL	1	TRUE	1	0.317633214251804	2		519	743	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781425	3781425	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760145292	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	120	534	0	ENST00000262367.5:c.4940C>T	p.Pro1647Leu	p.P1647L	ENST00000262367	NM_004380.2	1647	cCc/cTc	30/31	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.317633214251804	2		534	747	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619306	23619306	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	117	514	0	ENST00000261584.4:c.3229C>T	p.Pro1077Ser	p.P1077S	ENST00000261584	NM_024675.3	1077	Ccc/Tcc	12/13	1	2	FACETS	0.934	0.842	1	0.934	0.842	1	CLONAL	1	TRUE	1	0.317633214251804	2		514	789	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857692	59857692	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	100	466	1	ENST00000259008.2:c.1865C>T	p.Ser622Phe	p.S622F	ENST00000259008	NM_032043.2	622	tCc/tTc	13/20	1	2	FACETS	0.948	0.848	1	0.948	0.848	1	CLONAL	1	TRUE	1	0.317633214251804	2		467	664	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276224	15276224	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	137	609	0	ENST00000263388.2:c.5770G>T	p.Glu1924Ter	p.E1924*	ENST00000263388	NM_000435.2	1924	Gag/Tag	31/33	1	2	FACETS	0.979	0.89	1	0.979	0.89	1	CLONAL	1	TRUE	1	0.317633214251804	2		609	881	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296418	15296418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758980434	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	161	832	0	ENST00000263388.2:c.2024G>A	p.Gly675Glu	p.G675E	ENST00000263388	NM_000435.2	675	gGg/gAg	13/33	1	2	FACETS	0.987	0.904	1	0.987	0.904	1	CLONAL	1	TRUE	1	0.317633214251804	2		832	1027	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52728993	52728993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	101	546	0	ENST00000322088.6:c.1685C>T	p.Pro562Leu	p.P562L	ENST00000322088	NM_014225.5	562	cCc/cTc	14/15	1	2	FACETS	0.806	0.72	0.897	0.806	0.72	0.897	CLONAL	1	TRUE	1	0.317633214251804	2		546	789	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169977829	169977829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	97	520	0	ENST00000295797.4:c.296C>T	p.Ser99Phe	p.S99F	ENST00000295797	NM_002740.5	99	tCt/tTt	3/18	1	2	FACETS	0.822	0.733	0.917	0.822	0.733	0.917	CLONAL	1	TRUE	1	0.317633214251804	2		520	743	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149452994	149452994	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1196040337	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	79	583	1	ENST00000286301.3:c.952G>A	p.Gly318Arg	p.G318R	ENST00000286301	NM_005211.3	318	Ggg/Agg	7/22	1	2	FACETS	0.68	0.597	0.768	0.68	0.597	0.768	SUBCLONAL	1	TRUE	1	0.317633214251804	2		584	732	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171914	32171914	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	84	444	1	ENST00000375023.3:c.3118G>A	p.Gly1040Ser	p.G1040S	ENST00000375023	NM_004557.3	1040	Ggc/Agc	19/30	0.271101556313343	3	FACETS	1	0.884	1	0.5	0.442	0.562	CLONAL	1	TRUE	1	0.317633214251804	3		445	613	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184757	32184757	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	126	641	0	ENST00000375023.3:c.1826G>A	p.Gly609Glu	p.G609E	ENST00000375023	NM_004557.3	609	gGa/gAa	11/30	0.271101556313343	3	FACETS	0.914	0.826	1	0.457	0.413	0.504	CLONAL	1	TRUE	1	0.317633214251804	3		641	1006	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700278	117700278	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	113	528	0	ENST00000368508.3:c.2541G>A	p.Trp847Ter	p.W847*	ENST00000368508	NM_002944.2	847	tgG/tgA	17/43	0.317633214251804	1	FACETS	0.964	0.869	1	0.964	0.869	1	CLONAL	1	TRUE	0	0.317633214251804	1		528	621	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852147	128852147	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	151	812	0	ENST00000249373.3:c.2219A>C	p.Glu740Ala	p.E740A	ENST00000249373	NM_005631.4	740	gAg/gCg	12/12	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.317633214251804	2		812	938	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521563	46521563	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	56	580	0	ENST00000262741.5:c.845A>G	p.Lys282Arg	p.K282R	ENST00000262741	NM_003629.3	282	aAg/aGg	7/10	0.44465994735976	4	FACETS	0.39	0.332	0.452	0.195	0.166	0.226	SUBCLONAL	1	TRUE	2	0.44465994735976	4		580	934	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157533	106157533	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	103	363	0	ENST00000380013.4:c.2434A>T	p.Ile812Leu	p.I812L	ENST00000380013	NM_001127208.2	812	Ata/Tta	3/11	0.43439003755789	2	FACETS	1	0.979	1	0.666	0.602	0.732	CLONAL	1	TRUE	0	0.44465994735976	2		363	348	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	31	399	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.825	0.669	1	0.825	0.669	1	CLONAL	1	TRUE	1	0.24	2		399	313	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806119	1806119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931614	NA	P-0038500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	104	753	1	ENST00000260795.2:c.1138G>A	p.Gly380Arg	p.G380R	ENST00000260795		380	Ggg/Agg	8/17	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.24	2		754	637	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397742	49397742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552757	NA	P-0038500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	107	658	0	ENST00000418115.1:c.482C>T	p.Ala161Val	p.A161V	ENST00000418115	NM_001664.2	161	gCa/gTa	5/5	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.24	2		658	841	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465510	99465510	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	64	608	0	ENST00000268035.6:c.2335G>A	p.Glu779Lys	p.E779K	ENST00000268035	NM_000875.3	779	Gag/Aag	11/21	1	2	FACETS	0.874	0.757	1	0.874	0.757	1	CLONAL	1	TRUE	1	0.24	2		608	610	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984875	9984875	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	38	570	0	ENST00000330684.3:c.1090A>T	p.Ile364Phe	p.I364F	ENST00000330684	NM_001134407.1	364	Att/Ttt	4/13	1	2	FACETS	0.519	0.428	0.621	0.519	0.428	0.621	SUBCLONAL	1	TRUE	1	0.24	2		570	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0038502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	332	614	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.583505030775033	2	FACETS	0.875	0.836	0.913	0.875	0.836	0.913	CLONAL	2	TRUE	0	0.634633622734002	2		614	598	SUCCESS
APC	324	MSKCC	GRCh37	5	112175766	112175766	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	77	370	0	ENST00000257430.4:c.4476del	p.Thr1493ArgfsTer14	p.T1493Rfs*14	ENST00000257430	NM_000038.5	1492	gCc/gc	16/16	1	2	FACETS	0.886	0.787	0.989	0.886	0.787	0.989	CLONAL	1	TRUE	1	0.634633622734002	2		370	274	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481397	140481397	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913376	NA	P-0038502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	93	401	0	ENST00000288602.6:c.1411G>T	p.Val471Phe	p.V471F	ENST00000288602	NM_004333.4	471	Gtc/Ttc	11/18	0.609072488830577	4	FACETS	0.954	0.852	1	0.477	0.426	0.532	CLONAL	1	TRUE	2	0.634633622734002	4		401	502	SUCCESS
APC	324	MSKCC	GRCh37	5	112175944	112175945	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0038502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	38	288	0	ENST00000257430.4:c.4655_4656del	p.Glu1552GlyfsTer6	p.E1552Gfs*6	ENST00000257430	NM_000038.5	1551	aaAGag/aaag	16/16	1	2	FACETS	0.528	0.439	0.624	0.528	0.439	0.624	SUBCLONAL	1	TRUE	1	0.634633622734002	2		288	227	SUCCESS
APC	324	MSKCC	GRCh37	5	112116529	112116529	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	79	393	1	ENST00000257430.4:c.574G>T	p.Glu192Ter	p.E192*	ENST00000257430	NM_000038.5	192	Gaa/Taa	6/16	1	2	FACETS	0.722	0.64	0.808	0.722	0.64	0.808	SUBCLONAL	1	TRUE	1	0.634633622734002	2		394	345	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622235	162622235	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0038502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	193	520	0	ENST00000366898.1:c.462T>A	p.Cys154Ter	p.C154*	ENST00000366898	NM_004562.2	154	tgT/tgA	4/12	0.521808332639718	3	FACETS	0.816	0.762	0.871	0.816	0.762	0.871	CLONAL	2	TRUE	1	0.634633622734002	3		520	491	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5078325	5078325	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	19	403	0	ENST00000381652.3:c.2012A>C	p.His671Pro	p.H671P	ENST00000381652	NM_004972.3	671	cAt/cCt	16/25	0.600609593597694	2	FACETS	0.204	0.155	0.263	0.102	0.077	0.132	SUBCLONAL	1	TRUE	0	0.634633622734002	2		403	293	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	405	540	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.752053232603066	2		540	1070	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0038504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	621	625	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.84083062186889	2		627	733	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631837	90631837	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	320	598	0	ENST00000330062.3:c.516G>T	p.Arg172Ser	p.R172S	ENST00000330062	NM_002168.2	172	agG/agT	4/11	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.84083062186889	2		598	692	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609925	81609925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772490052	NA	P-0038504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	233	372	1	ENST00000298171.2:c.1523C>T	p.Ser508Leu	p.S508L	ENST00000298171	NM_000369.2	508	tCg/tTg	10/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.84083062186889	2		373	538	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189066	38189066	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	41	520	0	ENST00000317025.8:c.948G>C	p.Gln316His	p.Q316H	ENST00000317025	NM_023034.1	316	caG/caC	5/24	1	2	FACETS	0.131	0.109	0.157	0.131	0.109	0.157	SUBCLONAL	1	TRUE	1	0.84083062186889	2		520	743	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858975	57858975	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	303	734	0	ENST00000228682.2:c.471T>G	p.His157Gln	p.H157Q	ENST00000228682	NM_005269.2	157	caT/caG	5/12	1	2	FACETS	0.975	0.924	1	0.975	0.924	1	CLONAL	1	TRUE	1	0.84083062186889	2		734	739	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781303	135781303	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs118203554	NA	P-0038504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	731	645	0	ENST00000298552.3:c.1662del	p.Ile555Ter	p.I555*	ENST00000298552	NM_001162426.1	554	ccC/cc	15/23	0.834640171331805	3	FACETS	0.966	0.949	0.982	0.966	0.949	0.982	CLONAL	3	TRUE	0	0.84083062186889	3		645	852	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625386	69625386	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	112	690	0	ENST00000334134.2:c.407C>G	p.Thr136Arg	p.T136R	ENST00000334134	NM_005247.2	136	aCg/aGg	3/3	1	2	FACETS	0.369	0.332	0.408	0.369	0.332	0.408	SUBCLONAL	1	TRUE	1	0.84083062186889	2		690	722	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0038505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	477	612	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.836433502291494	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.857024239783896	1		612	593	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0038505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	12	399	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	0.857024239783896	1	FACETS	0.043	0.03	0.06	0.043	0.03	0.06	SUBCLONAL	1	TRUE	0	0.857024239783896	1		399	371	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554093	63554093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555583315	NA	P-0038505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	53	713	1	ENST00000307078.5:c.646G>A	p.Gly216Arg	p.G216R	ENST00000307078	NM_004655.3	216	Ggg/Agg	2/11	1	2	FACETS	0.118	0.1	0.138	0.118	0.1	0.138	SUBCLONAL	1	TRUE	1	0.857024239783896	2		714	1045	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218143	69218143	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	260	391	0	ENST00000462284.1:c.359A>G	p.Glu120Gly	p.E120G	ENST00000462284	NM_002392.5	120	gAa/gGa	6/11	1	2	FACETS	0.985	0.93	1	0.985	0.93	1	CLONAL	1	TRUE	1	0.857024239783896	2		391	616	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916733	48916733	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0038505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	213	386	0	ENST00000267163.4:c.265-2A>T		p.X89_splice	ENST00000267163	NM_000321.2	89			0.857024239783896	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.857024239783896	1		386	253	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3824689	3824689	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	375	551	0	ENST00000262367.5:c.2164A>T	p.Asn722Tyr	p.N722Y	ENST00000262367	NM_004380.2	722	Aat/Tat	12/31	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.857024239783896	2		551	860	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	61	399	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.607	0.527	0.694	0.607	0.527	0.694	SUBCLONAL	1	TRUE	1	0.579001922571135	2		399	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863224683	NA	P-0038506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	417	778	2	ENST00000269305.4:c.388C>T	p.Leu130Phe	p.L130F	ENST00000269305	NM_001126112.2	130	Ctc/Ttc	5/11	0.534190712032032	2	FACETS	0.916	0.88	0.953	0.916	0.88	0.953	CLONAL	2	TRUE	0	0.579001922571135	2		780	786	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367350	50367350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369417059	NA	P-0038506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	126	487	4	ENST00000331340.3:c.157G>A	p.Val53Met	p.V53M	ENST00000331340	NM_006060.4	53	Gtg/Atg	3/8	1	2	FACETS	0.837	0.762	0.915	0.837	0.762	0.915	CLONAL	1	TRUE	1	0.579001922571135	2		491	520	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941944	71941944	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0038506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	146	720	0	ENST00000298229.2:c.1300+2T>G		p.X434_splice	ENST00000298229	NM_001567.3	434			1	2	FACETS	0.886	0.813	0.963	0.886	0.813	0.963	CLONAL	1	TRUE	1	0.579001922571135	2		720	569	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692971	89692971	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	124	586	0	ENST00000371953.3:c.455T>A	p.Leu152Gln	p.L152Q	ENST00000371953	NM_000314.4	152	cTa/cAa	5/9	0.579001922571135	1	FACETS	0.812	0.742	0.883	0.812	0.742	0.883	CLONAL	1	TRUE	0	0.579001922571135	1		586	375	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0038507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	100	772	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	1	2	FACETS	0.658	0.586	0.736	0.658	0.586	0.736	SUBCLONAL	1	TRUE	1	0.241100086854917	2		773	1260	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0038507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	70	333	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	1	2	FACETS	0.712	0.62	0.813	0.712	0.62	0.813	SUBCLONAL	1	TRUE	1	0.241100086854917	2		333	815	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	175	810	0	ENST00000269305.4:c.596del	p.Gly199GlufsTer48	p.G199Efs*48	ENST00000269305	NM_001126112.2	199	gGa/ga	6/11	0.241876403251934	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.241100086854917	1		810	1182	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695884	117695884	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	67	870	0	ENST00000369458.3:c.553G>T	p.Val185Phe	p.V185F	ENST00000369458	NM_024626.3	185	Gtt/Ttt	4/6	0.169342329309427	1	FACETS	0.404	0.349	0.463	0.404	0.349	0.463	SUBCLONAL	1	TRUE	0	0.241100086854917	1		870	1210	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353827	40353827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780699949	NA	P-0038507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1197	104	805	0	ENST00000293328.3:c.2293G>A	p.Val765Ile	p.V765I	ENST00000293328	NM_012448.3	765	Gta/Ata	19/19	1	2	FACETS	0.663	0.592	0.74	0.663	0.592	0.74	SUBCLONAL	1	TRUE	1	0.241100086854917	2		805	1301	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213005	39213005	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1054147959	NA	P-0038507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1344	116	905	0	ENST00000402219.2:c.3962G>C	p.Arg1321Thr	p.R1321T	ENST00000402219	NM_005633.3	1321	aGa/aCa	23/23	1	2	FACETS	0.659	0.592	0.731	0.659	0.592	0.731	SUBCLONAL	1	TRUE	1	0.241100086854917	2		905	1460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0038508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1403	201	755	0	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.223656543972466	2		755	1604	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426795	212426795	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	79	608	0	ENST00000342788.4:c.2320A>C	p.Ser774Arg	p.S774R	ENST00000342788	NM_005235.2	774	Agt/Cgt	20/28	1	2	FACETS	0.815	0.715	0.922	0.815	0.715	0.922	CLONAL	1	TRUE	1	0.223656543972466	2		608	867	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727077	40727077	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	89	468	0	ENST00000373198.4:c.3887A>C	p.Glu1296Ala	p.E1296A	ENST00000373198	NM_133170.3	1296	gAg/gCg	28/32	1	2	FACETS	0.826	0.73	0.928	0.826	0.73	0.928	CLONAL	1	TRUE	1	0.223656543972466	2		468	964	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681341	88681341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786202611	NA	P-0038508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	52	344	1	ENST00000372037.3:c.1231G>A	p.Glu411Lys	p.E411K	ENST00000372037	NM_004329.2	411	Gaa/Aaa	11/13	1	2	FACETS	0.998	0.851	1	0.998	0.851	1	CLONAL	1	TRUE	1	0.223656543972466	2		345	466	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132546	11132546	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1384	140	1045	0	ENST00000358026.2:c.2762T>A	p.Leu921His	p.L921H	ENST00000358026	NM_001128849.1	921	cTc/cAc	19/36	0.0810151007722459	3	FACETS	0.913	0.829	1	0.457	0.414	0.502	INDETERMINATE	1	TRUE	1	0.223656543972466	3		1045	1524	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710563	40710563	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	108	929	0	ENST00000373198.4:c.4288A>G	p.Lys1430Glu	p.K1430E	ENST00000373198	NM_133170.3	1430	Aaa/Gaa	31/32	1	2	FACETS	0.751	0.672	0.836	0.751	0.672	0.836	SUBCLONAL	1	TRUE	1	0.223656543972466	2		929	1286	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0038510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	121	347	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	0.31294980618566	2		347	658	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921551	178921551	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519939	NA	P-0038510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	82	466	0	ENST00000263967.3:c.1033A>C	p.Asn345His	p.N345H	ENST00000263967	NM_006218.2	345	Aat/Cat	5/21	1	2	FACETS	0.863	0.762	0.972	0.863	0.762	0.972	CLONAL	1	TRUE	1	0.31294980618566	2		466	607	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088715	27088716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCT	novel	NA	P-0038510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	176	810	0	ENST00000324856.7:c.2325_2328dup	p.Ser777AlafsTer41	p.S777Afs*41	ENST00000324856	NM_006015.4	775	cag/caGCCTg	7/20	0.31294980618566	1	FACETS	0.852	0.784	0.924	0.852	0.784	0.924	CLONAL	1	TRUE	0	0.31294980618566	1		810	1113	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271250	1271250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1046621943	NA	P-0038510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	95	455	1	ENST00000310581.5:c.2452G>A	p.Val818Met	p.V818M	ENST00000310581	NM_198253.2	818	Gtg/Atg	8/16	1	2	FACETS	0.938	0.836	1	0.938	0.836	1	CLONAL	1	TRUE	1	0.31294980618566	2		456	647	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43749818	43749818	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	70	503	0	ENST00000523873.1:c.671C>A	p.Thr224Asn	p.T224N	ENST00000523873		224	aCt/aAt	7/8	0.31294980618566	2	FACETS	0.571	0.497	0.652	0.286	0.248	0.326	SUBCLONAL	1	TRUE	0	0.31294980618566	2		503	783	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0038510-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	142	347	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	0.422234144603856	2		347	622	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0038510-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	156	610	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.904	0.829	0.983	0.904	0.829	0.983	CLONAL	1	TRUE	1	0.422234144603856	2		610	817	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070565	67070566	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0038510-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	103	363	0	ENST00000412916.2:c.190_191del	p.Leu64ValfsTer18	p.L64Vfs*18	ENST00000412916		63	aaTCtg/aatg	3/6	0.422234144603856	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.422234144603856	1		363	376	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524485	44524485	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038510-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	81	404	0	ENST00000291552.4:c.72T>G	p.Ile24Met	p.I24M	ENST00000291552	NM_006758.2	24	atT/atG	2/8	1	2	FACETS	0.718	0.634	0.808	0.718	0.634	0.808	SUBCLONAL	1	TRUE	1	0.422234144603856	2		404	534	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	51	578	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.829	0.712	0.953	0.829	0.712	0.953	CLONAL	1	FALSE	1	0.547085064103094	2		578	225	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057947	27057948	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	378	688	0	ENST00000324856.7:c.1656dup	p.Gln553ThrfsTer70	p.Q553Tfs*70	ENST00000324856	NM_006015.4	552	tca/tcAa	3/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.547085064103094	2		688	1340	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573537	48573537	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	22	391	0	ENST00000342988.3:c.121G>T	p.Glu41Ter	p.E41*	ENST00000342988	NM_005359.5	41	Gaa/Taa	2/12	0.559266526017162	1	FACETS	0.847	0.678	1	0.847	0.678	1	CLONAL	1	FALSE	0	0.547085064103094	1		391	69	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022983	27022984	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0038511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	40	28	0	ENST00000324856.7:c.90dup	p.Gln31AlafsTer80	p.Q31Afs*80	ENST00000324856	NM_006015.4	30	cag/caGg	1/20	1	2	FACETS	0.831	0.717	0.946	1	0.969	1	CLONAL	2	FALSE	1	0.547085064103094	2		28	88	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446409	49446409	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	224	820	0	ENST00000301067.7:c.1196G>A	p.Gly399Glu	p.G399E	ENST00000301067	NM_003482.3	399	gGg/gAg	9/54	0.185424008869801	1	FACETS	0.768	0.717	0.82	0.768	0.717	0.82	INDETERMINATE	1	FALSE	0	0.547085064103094	1		820	775	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381528	81381528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776090604	NA	P-0038511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	31	438	0	ENST00000222390.5:c.533G>A	p.Arg178Gln	p.R178Q	ENST00000222390	NM_000601.4	178	cGa/cAa	5/18	NA	2	FACETS	1	0.856	1			1	INDETERMINATE	1	FALSE	NA	0.547085064103094	2		438	109	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	28	578	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.190395125332691	3	FACETS	0.719	0.573	0.885	0.359	0.286	0.443	SUBCLONAL	1	TRUE	1	0.16	3		578	526	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0038512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	36	677	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.62	0.508	0.746	0.62	0.508	0.746	SUBCLONAL	1	TRUE	1	0.16	2		677	726	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368223	45368223	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	31	563	1	ENST00000262160.6:c.1379C>A	p.Ser460Ter	p.S460*	ENST00000262160	NM_005901.5	460	tCa/tAa	11/11	1	2	FACETS	0.885	0.715	1	0.885	0.715	1	CLONAL	1	TRUE	1	0.16	2		564	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578529	7578529	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	651	1003	0	ENST00000269305.4:c.401T>C	p.Phe134Ser	p.F134S	ENST00000269305	NM_001126112.2	134	tTt/tCt	5/11	0.65939263271957	2	FACETS	0.993	0.965	1	0.993	0.965	1	CLONAL	2	TRUE	0	0.658153003424421	2		1003	996	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268890	115268890	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	278	741	0	ENST00000438362.2:c.1720G>T	p.Asp574Tyr	p.D574Y	ENST00000438362	NM_001242891.1	574	Gat/Tat	14/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.658153003424421	2		741	818	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945719	206945719	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	485	724	1	ENST00000423557.1:c.62G>T	p.Gly21Val	p.G21V	ENST00000423557	NM_000572.2	21	gGc/gTc	1/5	0.65939263271957	5	FACETS	1	0.985	1	0.707	0.676	0.738	CLONAL	2	TRUE	2	0.658153003424421	5		725	1381	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514016	125514016	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	306	604	0	ENST00000428830.2:c.954G>C	p.Gln318His	p.Q318H	ENST00000428830	NM_001114121.2	318	caG/caC	10/14	0.427945551806481	4	FACETS	0.825	0.779	0.871	0.825	0.779	0.871	CLONAL	2	TRUE	2	0.658153003424421	4		604	935	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856344	111856344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1235787724	NA	P-0038513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	33	118	0	ENST00000341259.2:c.395C>T	p.Pro132Leu	p.P132L	ENST00000341259	NM_005475.2	132	cCc/cTc	2/8	0.65939263271957	2	FACETS	0.664	0.549	0.79	0.332	0.274	0.395	SUBCLONAL	1	TRUE	0	0.658153003424421	2		118	151	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557441	21557441	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1200842582	NA	P-0038513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	220	723	0	ENST00000382592.4:c.2404G>C	p.Asp802His	p.D802H	ENST00000382592	NM_014572.2	802	Gat/Cat	5/8	NA	2	FACETS	1	0.946	1			1	INDETERMINATE	1	TRUE	NA	0.658153003424421	2		723	660	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40679408	40679408	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0038513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	206	713	0	ENST00000249776.8:c.485+1G>T		p.X162_splice	ENST00000249776	NM_033286.3	162			0.596318942379451	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.658153003424421	1		713	393	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857860	89857860	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	322	884	1	ENST00000389301.3:c.1310C>T	p.Ala437Val	p.A437V	ENST00000389301	NM_000135.2	437	gCa/gTa	14/43	0.65939263271957	3	FACETS	1	0.975	1	0.529	0.499	0.559	CLONAL	1	TRUE	1	0.658153003424421	3		885	1230	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220152	5220152	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	210	809	0	ENST00000357368.4:c.3563T>C	p.Ile1188Thr	p.I1188T	ENST00000357368	NM_002850.3	1188	aTc/aCc	22/38	0.65939263271957	2	FACETS	0.964	0.9	1	0.482	0.45	0.515	CLONAL	1	TRUE	0	0.658153003424421	2		809	662	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484583	57484583	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	537	724	0	ENST00000371085.3:c.667G>C	p.Asp223His	p.D223H	ENST00000371085	NM_000516.4	223	Gac/Cac	9/13	0.65939263271957	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.658153003424421	2		724	751	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912072	76912072	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	232	559	0	ENST00000373344.5:c.4192G>C	p.Asp1398His	p.D1398H	ENST00000373344	NM_000489.3	1398	Gat/Cat	13/35	0.14587043792469	5	FACETS	0.864	0.808	0.921			1	INDETERMINATE	2	TRUE	NA	0.658153003424421	5		559	811	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0038514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	285	552	2	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	0.430310290717862	3	FACETS	0.903	0.857	0.949	0.903	0.857	0.949	CLONAL	3	TRUE	0	0.430310290717862	3		554	594	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0038514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	354	881	1	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.0900680854750052	5	FACETS	1	0.99	1			1	INDETERMINATE	3	TRUE	NA	0.430310290717862	5		882	792	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801080	135801080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	116	710	0	ENST00000298552.3:c.257G>A	p.Arg86His	p.R86H	ENST00000298552	NM_001162426.1	86	cGt/cAt	5/23	0.423014904713273	2	FACETS	0.732	0.66	0.807	0.366	0.33	0.404	SUBCLONAL	1	TRUE	0	0.430310290717862	2		710	737	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615117	43615117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55947360	NA	P-0038514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	123	1085	0	ENST00000355710.3:c.2531G>A	p.Arg844Gln	p.R844Q	ENST00000355710	NM_020975.4	844	cGg/cAg	14/20	1	2	FACETS	0.723	0.654	0.796	0.723	0.654	0.796	SUBCLONAL	1	TRUE	1	0.430310290717862	2		1085	791	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279449	1279449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756152343	NA	P-0038514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	81	1169	1	ENST00000310581.5:c.2087G>A	p.Arg696His	p.R696H	ENST00000310581	NM_198253.2	696	cGt/cAt	5/16	0.139066258728206	5	FACETS	0.681	0.598	0.769	0.17	0.149	0.193	INDETERMINATE	1	TRUE	1	0.430310290717862	5		1170	910	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675668	86675669	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0038514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	213	431	0	ENST00000274376.6:c.2603+2dup		p.X868_splice	ENST00000274376	NM_002890.2	868			0.430310290717862	3	FACETS	1	0.988	1	0.805	0.756	0.855	CLONAL	2	TRUE	0	0.430310290717862	3		431	498	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922682	44922682	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	101	253	0	ENST00000377967.4:c.1543G>C	p.Val515Leu	p.V515L	ENST00000377967	NM_021140.2	515	Gtt/Ctt	16/29	0.430310290717862	6	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.430310290717862	6		253	663	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451272	70451272	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	502	914	2	ENST00000373644.4:c.6112C>T	p.Arg2038Cys	p.R2038C	ENST00000373644	NM_030625.2	2038	Cgt/Tgt	12/12	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.826080850142907	2		916	1206	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0038516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	111	518	0	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.16	2		518	1018	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974770	21974770	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	26	262	0	ENST00000304494.5:c.57del	p.Ala20ArgfsTer6	p.A20Rfs*6	ENST00000304494	NM_000077.4	19	gcC/gc	1/3	1	2	FACETS	0.915	0.725	1	0.915	0.725	1	CLONAL	1	TRUE	1	0.16	2		262	355	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057644	27057644	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	47	429	0	ENST00000324856.7:c.1353del	p.Pro452LeufsTer167	p.P452Lfs*167	ENST00000324856	NM_006015.4	451	aTt/at	3/20	1	2	FACETS	0.944	0.795	1	0.944	0.795	1	CLONAL	1	TRUE	1	0.15	2		429	664	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344006	118344007	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	30	334	0	ENST00000534358.1:c.2133dup	p.Phe712IlefsTer2	p.F712Ifs*2	ENST00000534358	NM_005933.3	711	ata/atAa	3/36	1	2	FACETS	0.791	0.636	0.967	0.791	0.636	0.967	CLONAL	1	TRUE	1	0.15	2		334	506	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177009	56177009	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	21	305	0	ENST00000399503.3:c.2279T>G	p.Leu760Arg	p.L760R	ENST00000399503	NM_005921.1	760	cTt/cGt	13/20	1	2	FACETS	0.737	0.567	0.936	0.737	0.567	0.936	CLONAL	1	TRUE	1	0.15	2		305	380	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	80	339	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.244719393663341	2		339	501	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	63	565	5	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.244719393663341	2		570	495	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	29	454	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.644	0.517	0.788	0.644	0.517	0.788	SUBCLONAL	1	TRUE	1	0.244719393663341	2		454	368	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259480	16259480	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	45	422	0	ENST00000375759.3:c.6750del	p.Ala2251GlnfsTer102	p.A2251Qfs*102	ENST00000375759	NM_015001.2	2249	Ccc/cc	11/15	1	2	FACETS	0.765	0.643	0.899	0.765	0.643	0.899	SUBCLONAL	1	TRUE	1	0.244719393663341	2		422	481	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	85	447	3	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.244719393663341	2		450	504	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	23	410	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.466	0.363	0.586	0.466	0.363	0.586	SUBCLONAL	1	TRUE	1	0.244719393663341	2		410	403	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	131	592	2	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.847	0.771	0.927	1	0.988	1	CLONAL	2	TRUE	1	0.244719393663341	2		594	632	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	36	335	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.838	0.69	1	0.838	0.69	1	CLONAL	1	TRUE	1	0.244719393663341	2		335	351	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	59	536	0	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	1	2	FACETS	0.931	0.802	1	0.931	0.802	1	CLONAL	1	TRUE	1	0.244719393663341	2		536	518	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243045	105243045	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	70	798	0	ENST00000349310.3:c.238T>C	p.Trp80Arg	p.W80R	ENST00000349310	NM_001014432.1	80	Tgg/Cgg	5/15	0.224011098128368	3	FACETS	0.725	0.63	0.827	0.362	0.315	0.414	SUBCLONAL	1	TRUE	1	0.244719393663341	3		798	886	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094340	193094340	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	37	273	1	ENST00000367435.3:c.230G>A	p.Arg77His	p.R77H	ENST00000367435	NM_024529.4	77	cGt/cAt	2/17	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.244719393663341	2		274	285	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482927	140482927	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	44	492	2	ENST00000288602.6:c.1208del	p.Pro403LeufsTer8	p.P403Lfs*8	ENST00000288602	NM_004333.4	403	cCt/ct	10/18	1	2	FACETS	0.621	0.52	0.733	0.621	0.52	0.733	SUBCLONAL	1	TRUE	1	0.244719393663341	2		494	579	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934190	39934190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146403660	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	86	649	0	ENST00000378444.4:c.409G>A	p.Val137Ile	p.V137I	ENST00000378444	NM_001123385.1	137	Gtc/Atc	4/15	1	2	FACETS	0.946	0.836	1	0.946	0.836	1	CLONAL	1	TRUE	1	0.244719393663341	2		649	743	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983228	149983228	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	34	512	0	ENST00000253339.5:c.3030del	p.Phe1010LeufsTer10	p.F1010Lfs*10	ENST00000253339		1010	ttT/tt	7/7	1	2	FACETS	0.501	0.408	0.605	0.501	0.408	0.605	SUBCLONAL	1	TRUE	1	0.244719393663341	2		512	555	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	57	416	0	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	1	2	FACETS	0.983	0.845	1	0.983	0.845	1	CLONAL	1	TRUE	1	0.244719393663341	2		416	474	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245587	41245587	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357522	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	78	552	4	ENST00000357654.3:c.1961del	p.Lys654SerfsTer47	p.K654Sfs*47	ENST00000357654	NM_007294.3	654	aAg/ag	10/23	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.244719393663341	2		556	630	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468185	120468185	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	65	606	1	ENST00000256646.2:c.4254del	p.Ser1419AlafsTer8	p.S1419Afs*8	ENST00000256646	NM_024408.3	1418	ccC/cc	25/34	1	2	FACETS	0.784	0.679	0.897	0.784	0.679	0.897	SUBCLONAL	1	TRUE	1	0.244719393663341	2		607	678	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505462	157505462	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	68	410	0	ENST00000346085.5:c.3443A>G	p.Tyr1148Cys	p.Y1148C	ENST00000346085	NM_020732.3	1148	tAc/tGc	13/20	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.244719393663341	2		410	504	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131412	202131412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339962485	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	50	464	0	ENST00000358485.4:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000358485	NM_001080125.1	127	cGa/cAa	2/9	1	2	FACETS	0.826	0.701	0.962	0.826	0.701	0.962	CLONAL	1	TRUE	1	0.244719393663341	2		464	495	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	46	270	0	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	0.917	0.774	1	0.917	0.774	1	CLONAL	1	TRUE	1	0.244719393663341	2		270	410	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2488147	2488147	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	85	600	0	ENST00000355716.4:c.48del	p.Thr18ProfsTer4	p.T18Pfs*4	ENST00000355716	NM_003820.2	15	aCc/ac	1/8	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.244719393663341	2		600	666	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33433413	33433413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80116829	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	89	519	0	ENST00000345365.6:c.568G>A	p.Ala190Thr	p.A190T	ENST00000345365	NM_002878.3	190	Gcc/Acc	6/10	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.244719393663341	2		519	673	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264985	46264985	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	25	395	1	ENST00000371998.3:c.1860del	p.Lys620AsnfsTer18	p.K620Nfs*18	ENST00000371998		619	Aaa/aa	12/23	1	2	FACETS	0.469	0.369	0.584	0.469	0.369	0.584	SUBCLONAL	1	TRUE	1	0.244719393663341	2		396	436	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216380	7216380	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	40	623	1	ENST00000380728.2:c.868del	p.Gln290SerfsTer55	p.Q290Sfs*55	ENST00000380728		290	Cag/ag	10/11	1	2	FACETS	0.541	0.449	0.645	0.541	0.449	0.645	SUBCLONAL	1	TRUE	1	0.244719393663341	2		624	604	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981721	101981721	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555075353	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	13	237	0	ENST00000282441.5:c.147del	p.Ala50ProfsTer24	p.A50Pfs*24	ENST00000282441	NM_001130145.2	48	Ccc/cc	1/9	0.188344452033038	2	FACETS	0.506	0.361	0.682	0.253	0.18	0.341	SUBCLONAL	1	TRUE	0	0.244719393663341	2		237	210	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278343	39278343	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	79	583	0	ENST00000402219.2:c.806T>A	p.Met269Lys	p.M269K	ENST00000402219	NM_005633.3	269	aTg/aAg	6/23	0.244719393663341	2	FACETS	1	0.976	1	0.727	0.642	0.818	CLONAL	1	TRUE	0	0.244719393663341	2		583	444	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	83	640	2	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.244719393663341	2		642	628	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376683	118376683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149340870	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	26	440	2	ENST00000534358.1:c.10076C>T	p.Ala3359Val	p.A3359V	ENST00000534358	NM_005933.3	3359	gCg/gTg	27/36	0.188344452033038	2	FACETS	0.458	0.362	0.568	0.229	0.181	0.284	SUBCLONAL	1	TRUE	0	0.244719393663341	2		442	464	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792404	33792404	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	38	693	2	ENST00000498907.2:c.917G>A	p.Arg306His	p.R306H	ENST00000498907	NM_004364.3	306	cGc/cAc	1/1	1	2	FACETS	0.496	0.409	0.594	0.496	0.409	0.594	SUBCLONAL	1	TRUE	1	0.244719393663341	2		695	626	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	364669	364669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	129	588	0	ENST00000262320.3:c.893G>A	p.Arg298Gln	p.R298Q	ENST00000262320	NM_003502.3	298	cGg/cAg	3/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.244719393663341	2		588	733	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197245	106197245	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	32	302	0	ENST00000380013.4:c.5582del	p.Gly1861GlufsTer26	p.G1861Efs*26	ENST00000380013	NM_001127208.2	1860	Ggg/gg	11/11	1	2	FACETS	0.776	0.631	0.939	0.776	0.631	0.939	CLONAL	1	TRUE	1	0.244719393663341	2		302	337	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991602	72991602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs926058661	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	50	603	1	ENST00000268489.5:c.2443G>A	p.Val815Met	p.V815M	ENST00000268489	NM_006885.3	815	Gtg/Atg	2/10	1	2	FACETS	0.521	0.441	0.61	0.521	0.441	0.61	SUBCLONAL	1	TRUE	1	0.244719393663341	2		604	784	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860074	57860075	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs759448855	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	86	805	0	ENST00000228682.2:c.821dup	p.Cys275LeufsTer32	p.C275Lfs*32	ENST00000228682	NM_005269.2	272	tgg/tGgg	8/12	1	2	FACETS	0.843	0.745	0.948	0.843	0.745	0.948	CLONAL	1	TRUE	1	0.244719393663341	2		805	834	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149819	202149819	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	58	540	0	ENST00000358485.4:c.1264del	p.Asp422IlefsTer19	p.D422Ifs*19	ENST00000358485	NM_001080125.1	420	caG/ca	8/9	1	2	FACETS	0.822	0.706	0.948	0.822	0.706	0.948	CLONAL	1	TRUE	1	0.244719393663341	2		540	577	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932050	39932050	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs923387791	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	92	594	2	ENST00000378444.4:c.2549G>A	p.Arg850His	p.R850H	ENST00000378444	NM_001123385.1	850	cGt/cAt	4/15	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.244719393663341	2		596	739	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041137	180041137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1376446971	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	92	815	0	ENST00000261937.6:c.3262G>A	p.Asp1088Asn	p.D1088N	ENST00000261937	NM_182925.4	1088	Gac/Aac	24/30	1	2	FACETS	0.908	0.806	1	0.908	0.806	1	CLONAL	1	TRUE	1	0.244719393663341	2		815	828	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166146	118166146	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	25	360	0	ENST00000369448.3:c.656T>C	p.Phe219Ser	p.F219S	ENST00000369448	NM_017709.3	219	tTt/tCt	2/2	1	2	FACETS	0.533	0.42	0.664	0.533	0.42	0.664	SUBCLONAL	1	TRUE	1	0.244719393663341	2		360	383	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120496261	120496261	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1553198082	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	32	396	0	ENST00000256646.2:c.2270A>G	p.Asp757Gly	p.D757G	ENST00000256646	NM_024408.3	757	gAc/gGc	14/34	1	2	FACETS	0.556	0.451	0.676	0.556	0.451	0.676	SUBCLONAL	1	TRUE	1	0.244719393663341	2		396	470	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551483	150551483	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	57	777	0	ENST00000369026.2:c.524A>G	p.Tyr175Cys	p.Y175C	ENST00000369026	NM_021960.4	175	tAc/tGc	1/3	1	2	FACETS	0.515	0.44	0.597	0.515	0.44	0.597	SUBCLONAL	1	TRUE	1	0.244719393663341	2		777	905	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731028	162731028	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	48	308	0	ENST00000367921.3:c.883G>A	p.Gly295Ser	p.G295S	ENST00000367921	NM_006182.2	295	Ggt/Agt	9/18	1	2	FACETS	0.941	0.797	1	0.941	0.797	1	CLONAL	1	TRUE	1	0.244719393663341	2		308	417	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620404	43620404	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	53	483	0	ENST00000355710.3:c.3013C>A	p.Leu1005Met	p.L1005M	ENST00000355710	NM_020975.4	1005	Ctg/Atg	18/20	1	2	FACETS	0.81	0.691	0.94	0.81	0.691	0.94	CLONAL	1	TRUE	1	0.244719393663341	2		483	535	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310932	123310932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	27	373	0	ENST00000358487.5:c.496C>T	p.Leu166Phe	p.L166F	ENST00000358487	NM_000141.4	166	Ctc/Ttc	5/18	1	2	FACETS	0.457	0.363	0.565	0.457	0.363	0.565	SUBCLONAL	1	TRUE	1	0.244719393663341	2		373	483	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424177	49424177	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	20	417	2	ENST00000301067.7:c.13885A>C	p.Thr4629Pro	p.T4629P	ENST00000301067	NM_003482.3	4629	Acc/Ccc	42/54	1	2	FACETS	0.41	0.312	0.524	0.41	0.312	0.524	SUBCLONAL	1	TRUE	1	0.244719393663341	2		419	399	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858986	57858986	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	48	617	0	ENST00000228682.2:c.485del	p.Gly162ValfsTer3	p.G162Vfs*3	ENST00000228682	NM_005269.2	161	cGg/cg	5/12	1	2	FACETS	0.533	0.449	0.626	0.533	0.449	0.626	SUBCLONAL	1	TRUE	1	0.244719393663341	2		617	736	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134040	41134040	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	44	423	1	ENST00000379561.5:c.1588C>T	p.Gln530Ter	p.Q530*	ENST00000379561	NM_002015.3	530	Cag/Tag	2/3	1	2	FACETS	0.743	0.623	0.876	0.743	0.623	0.876	SUBCLONAL	1	TRUE	1	0.244719393663341	2		424	484	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569829	95569829	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	17	287	0	ENST00000393063.1:c.3904A>G	p.Thr1302Ala	p.T1302A	ENST00000393063	NM_030621.3	1302	Act/Gct	22/28	0.224011098128368	3	FACETS	0.474	0.353	0.618	0.237	0.176	0.309	SUBCLONAL	1	TRUE	1	0.244719393663341	3		287	329	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807822	3807822	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	78	395	1	ENST00000262367.5:c.3597C>A	p.Cys1199Ter	p.C1199*	ENST00000262367	NM_004380.2	1199	tgC/tgA	18/31	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.244719393663341	2		396	456	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56862947	56862947	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	68	424	0	ENST00000308159.5:c.856del	p.Val286CysfsTer12	p.V286Cfs*12	ENST00000308159	NM_014669.4	285	Ggg/gg	9/22	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.244719393663341	2		424	519	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56871568	56871568	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750817566	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	89	508	0	ENST00000308159.5:c.1948G>A	p.Val650Ile	p.V650I	ENST00000308159	NM_014669.4	650	Gtc/Atc	18/22	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.244719393663341	2		508	598	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829320	72829320	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	32	582	0	ENST00000268489.5:c.7261T>C	p.Ser2421Pro	p.S2421P	ENST00000268489	NM_006885.3	2421	Tca/Cca	9/10	1	2	FACETS	0.416	0.336	0.506	0.416	0.336	0.506	SUBCLONAL	1	TRUE	1	0.244719393663341	2		582	629	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830884	72830885	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	63	507	1	ENST00000268489.5:c.5696dup	p.Glu1900ArgfsTer29	p.E1900Rfs*29	ENST00000268489	NM_006885.3	1899	gga/ggGa	9/10	1	2	FACETS	0.844	0.73	0.968	0.844	0.73	0.968	CLONAL	1	TRUE	1	0.244719393663341	2		508	610	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991671	72991671	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	97	437	0	ENST00000268489.5:c.2374del	p.Ala792ProfsTer32	p.A792Pfs*32	ENST00000268489	NM_006885.3	792	Gcc/cc	2/10	1	2	FACETS	0.847	0.759	0.94	1	0.984	1	CLONAL	2	TRUE	1	0.244719393663341	2		437	468	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974887	15974887	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	58	400	0	ENST00000268712.3:c.3988G>T	p.Gly1330Cys	p.G1330C	ENST00000268712	NM_006311.3	1330	Ggt/Tgt	30/46	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.244719393663341	2		400	432	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049809	16049809	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	23	350	0	ENST00000268712.3:c.963del	p.Val322TrpfsTer4	p.V322Wfs*4	ENST00000268712	NM_006311.3	321	aaA/aa	10/46	1	2	FACETS	0.54	0.421	0.678	0.54	0.421	0.678	SUBCLONAL	1	TRUE	1	0.244719393663341	2		350	348	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534382	63534382	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	86	651	0	ENST00000307078.5:c.1139del	p.Lys380SerfsTer2	p.K380Sfs*2	ENST00000307078	NM_004655.3	380	aAg/ag	5/11	1	2	FACETS	0.905	0.8	1	0.905	0.8	1	CLONAL	1	TRUE	1	0.244719393663341	2		651	777	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11032344	11032344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	115	674	1	ENST00000327064.4:c.1738G>A	p.Val580Ile	p.V580I	ENST00000327064	NM_199141.1	580	Gtc/Atc	16/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.244719393663341	2		675	679	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629004	14629004	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	32	586	0	ENST00000254322.2:c.158A>G	p.Asp53Gly	p.D53G	ENST00000254322	NM_006145.1	53	gAc/gGc	1/3	1	2	FACETS	0.47	0.38	0.571	0.47	0.38	0.571	SUBCLONAL	1	TRUE	1	0.244719393663341	2		586	557	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905088	50905088	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	79	743	0	ENST00000440232.2:c.370del	p.Val124CysfsTer45	p.V124Cfs*45	ENST00000440232	NM_002691.3	124	Gtg/tg	4/27	1	2	FACETS	0.853	0.749	0.964	0.853	0.749	0.964	CLONAL	1	TRUE	1	0.244719393663341	2		743	757	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463547	25463547	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	67	568	1	ENST00000264709.3:c.2135A>T	p.Asp712Val	p.D712V	ENST00000264709	NM_175629.2	712	gAc/gTc	18/23	0.244719393663341	2	FACETS	0.905	0.787	1	0.453	0.393	0.517	CLONAL	1	TRUE	0	0.244719393663341	2		569	605	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698162	47698162	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63751298	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	69	314	0	ENST00000233146.2:c.1720C>T	p.Gln574Ter	p.Q574*	ENST00000233146	NM_000251.2	574	Cag/Tag	11/16	0.244719393663341	2	FACETS	0.895	0.786	1	0.895	0.786	1	CLONAL	2	TRUE	0	0.244719393663341	2		314	315	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032130	48032130	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	23	275	0	ENST00000234420.5:c.3520T>C	p.Phe1174Leu	p.F1174L	ENST00000234420	NM_000179.2	1174	Ttt/Ctt	6/10	0.244719393663341	2	FACETS	0.518	0.403	0.65	0.259	0.201	0.325	SUBCLONAL	1	TRUE	0	0.244719393663341	2		275	363	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660270	227660270	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	33	574	2	ENST00000305123.5:c.3185del	p.Gly1062AlafsTer8	p.G1062Afs*8	ENST00000305123	NM_005544.2	1062	gGc/gc	1/2	1	2	FACETS	0.512	0.416	0.62	0.512	0.416	0.62	SUBCLONAL	1	TRUE	1	0.244719393663341	2		576	527	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661112	227661112	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	95	675	1	ENST00000305123.5:c.2343G>T	p.Glu781Asp	p.E781D	ENST00000305123	NM_005544.2	781	gaG/gaT	1/2	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.244719393663341	2		676	720	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662845	227662845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1305808839	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	49	602	1	ENST00000305123.5:c.610G>A	p.Val204Met	p.V204M	ENST00000305123	NM_005544.2	204	Gtg/Atg	1/2	1	2	FACETS	0.588	0.497	0.689	0.588	0.497	0.689	SUBCLONAL	1	TRUE	1	0.244719393663341	2		603	681	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39726854	39726854	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	24	145	0	ENST00000361337.2:c.853-1G>T		p.X285_splice	ENST00000361337	NM_003286.2	285			1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.244719393663341	2		145	146	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630678	187630678	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	61	564	0	ENST00000441802.2:c.304G>T	p.Gly102Ter	p.G102*	ENST00000441802	NM_005245.3	102	Gga/Tga	2/27	1	2	FACETS	0.92	0.794	1	0.92	0.794	1	CLONAL	1	TRUE	1	0.244719393663341	2		564	542	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294231	1294231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	37	630	0	ENST00000310581.5:c.770C>T	p.Ala257Val	p.A257V	ENST00000310581	NM_198253.2	257	gCc/gTc	2/16	1	2	FACETS	0.487	0.4	0.584	0.487	0.4	0.584	SUBCLONAL	1	TRUE	1	0.244719393663341	2		630	621	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750546	57750546	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	26	363	0	ENST00000274289.3:c.1922A>T	p.Tyr641Phe	p.Y641F	ENST00000274289	NM_006622.3	641	tAc/tTc	14/14	1	2	FACETS	0.517	0.409	0.641	0.517	0.409	0.641	SUBCLONAL	1	TRUE	1	0.244719393663341	2		363	411	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672970	30672971	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	78	739	0	ENST00000376406.3:c.3989dup	p.Glu1331Ter	p.E1331*	ENST00000376406	NM_014641.2	1330	cct/ccCt	10/15	1	2	FACETS	0.865	0.759	0.979	0.865	0.759	0.979	CLONAL	1	TRUE	1	0.244719393663341	2		739	737	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163791	32163791	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	71	551	0	ENST00000375023.3:c.5435A>G	p.His1812Arg	p.H1812R	ENST00000375023	NM_004557.3	1812	cAc/cGc	30/30	1	2	FACETS	0.987	0.862	1	0.987	0.862	1	CLONAL	1	TRUE	1	0.244719393663341	2		551	588	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289244	33289244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200370559	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	35	506	1	ENST00000374542.5:c.308C>T	p.Ala103Val	p.A103V	ENST00000374542	NM_001141970.1	103	gCg/gTg	3/8	1	2	FACETS	0.514	0.42	0.619	0.514	0.42	0.619	SUBCLONAL	1	TRUE	1	0.244719393663341	2		507	557	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099301	157099301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	26	374	0	ENST00000346085.5:c.238C>T	p.Pro80Ser	p.P80S	ENST00000346085	NM_020732.3	80	Ccc/Tcc	1/20	1	2	FACETS	0.496	0.393	0.616	0.496	0.393	0.616	SUBCLONAL	1	TRUE	1	0.244719393663341	2		374	428	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15821891	15821891	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	32	390	0	ENST00000307771.7:c.284C>A	p.Ala95Glu	p.A95E	ENST00000307771	NM_005089.3	95	gCg/gAg	4/11	1	2	FACETS	0.795	0.646	0.962	0.795	0.646	0.962	CLONAL	1	TRUE	1	0.244719393663341	2		390	329	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424502	47424502	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	47	558	0	ENST00000377045.4:c.422C>A	p.Pro141His	p.P141H	ENST00000377045	NM_001654.4	141	cCc/cAc	5/16	1	2	FACETS	0.676	0.57	0.794	0.676	0.57	0.794	SUBCLONAL	1	TRUE	1	0.244719393663341	2		558	568	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344989	70344989	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	53	511	2	ENST00000374080.3:c.2219T>C	p.Ile740Thr	p.I740T	ENST00000374080		740	aTc/aCc	15/45	1	2	FACETS	0.904	0.772	1	0.904	0.772	1	CLONAL	1	TRUE	1	0.244719393663341	2		513	479	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347244	70347244	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	69	506	0	ENST00000374080.3:c.2908T>C	p.Cys970Arg	p.C970R	ENST00000374080		970	Tgt/Cgt	21/45	1	2	FACETS	0.882	0.768	1	0.882	0.768	1	CLONAL	1	TRUE	1	0.244719393663341	2		506	639	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0038521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	42	580	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.795	0.665	0.94	0.795	0.665	0.94	CLONAL	1	TRUE	1	0.254448678870168	2		580	415	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370985	55370985	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	56	561	0	ENST00000297316.4:c.287C>G	p.Ala96Gly	p.A96G	ENST00000297316	NM_022454.3	96	gCc/gGc	1/2	1	2	FACETS	0.682	0.584	0.79	0.682	0.584	0.79	SUBCLONAL	1	TRUE	1	0.254448678870168	2		561	645	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0038521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	18	292	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.427	0.321	0.553	0.427	0.321	0.553	SUBCLONAL	1	TRUE	1	0.254448678870168	2		292	331	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259397	11259397	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	86	519	0	ENST00000361445.4:c.4171C>G	p.Arg1391Gly	p.R1391G	ENST00000361445	NM_004958.3	1391	Cga/Gga	28/58	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.254448678870168	2		519	613	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685269	89685269	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs786203847	NA	P-0038521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	14	157	0	ENST00000371953.3:c.165-1G>A		p.X55_splice	ENST00000371953	NM_000314.4	55			1	2	FACETS	1	0.769	1	1	0.769	1	CLONAL	1	TRUE	1	0.254448678870168	2		157	104	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482552	56482552	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1439217874	NA	P-0038521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	42	551	0	ENST00000267101.3:c.1009G>C	p.Gly337Arg	p.G337R	ENST00000267101	NM_001982.3	337	Ggg/Cgg	9/28	1	2	FACETS	0.551	0.459	0.653	0.551	0.459	0.653	SUBCLONAL	1	TRUE	1	0.254448678870168	2		551	599	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692792	89692792	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	61	315	0	ENST00000371953.3:c.276C>G	p.Asp92Glu	p.D92E	ENST00000371953	NM_000314.4	92	gaC/gaG	5/9	1	2	FACETS	0.827	0.719	0.941	1	0.975	1	CLONAL	2	TRUE	1	0.254448678870168	2		315	290	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105546	27105547	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0038521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	86	416	0	ENST00000324856.7:c.5158_5159del	p.Phe1720ProfsTer6	p.F1720Pfs*6	ENST00000324856	NM_006015.4	1719	taTTtc/tatc	20/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.254448678870168	2		416	456	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163584	47163584	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	12	251	0	ENST00000409792.3:c.2542G>T	p.Ala848Ser	p.A848S	ENST00000409792	NM_014159.6	848	Gca/Tca	3/21	1	2	FACETS	0.484	0.34	0.66	0.484	0.34	0.66	SUBCLONAL	1	TRUE	1	0.254448678870168	2		251	195	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591147	67591147	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0038521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	45	280	0	ENST00000274335.5:c.1740C>G	p.Tyr580Ter	p.Y580*	ENST00000274335		580	taC/taG	12/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.254448678870168	2		280	236	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0038522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	46	840	2	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		842	729	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139562793	139562793	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	50	616	0	ENST00000308874.7:c.59C>G	p.Thr20Arg	p.T20R	ENST00000308874		20	aCa/aGa	3/10	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		616	674	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	356	538	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.573464629927204	2	FACETS	0.917	0.878	0.955	0.917	0.878	0.955	CLONAL	2	TRUE	0	0.61940200161935	2		538	627	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063672	67063672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	133	258	0	ENST00000412916.2:c.121C>T	p.Gln41Ter	p.Q41*	ENST00000412916		41	Cag/Tag	2/6	0.61940200161935	1	FACETS	0.808	0.742	0.875	0.808	0.742	0.875	CLONAL	1	TRUE	0	0.61940200161935	1		258	367	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115711	8115711	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	210	283	1	ENST00000346208.3:c.1060del	p.Leu354Ter	p.L354*	ENST00000346208		353	Ccc/cc	6/6	0.578115449761053	3	FACETS	0.872	0.818	0.927	0.872	0.818	0.927	CLONAL	2	TRUE	1	0.61940200161935	3		284	509	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	130	399	0				ENST00000310581	NM_198253.2	-/1132			0.421312145502573	3	FACETS	0.874	0.807	0.941	1	0.985	1	CLONAL	3	TRUE	1	0.421312145502573	3		399	285	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652121	36652122	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0038527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	160	599	0	ENST00000244741.5:c.247dup	p.Arg83ProfsTer6	p.R83Pfs*6	ENST00000244741	NM_000389.4	81	-/C	2/3	1	2	FACETS	0.811	0.75	0.874	1	0.991	1	CLONAL	2	TRUE	1	0.421312145502573	2		599	468	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101401	27101402	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0038527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	36	446	0	ENST00000324856.7:c.4689dup	p.Met1564HisfsTer8	p.M1564Hfs*8	ENST00000324856	NM_006015.4	1561	-/C	18/20	1	2	FACETS	0.521	0.429	0.623	0.521	0.429	0.623	SUBCLONAL	1	TRUE	1	0.421312145502573	2		446	328	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868316	56868317	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	78	234	0	ENST00000308159.5:c.1699_1700insA	p.Leu567HisfsTer6	p.L567Hfs*6	ENST00000308159	NM_014669.4	567	ctg/cAtg	15/22	1	2	FACETS	0.857	0.767	0.95	1	0.983	1	CLONAL	2	TRUE	1	0.421312145502573	2		234	216	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940913	49940913	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	126	646	0	ENST00000296474.3:c.130T>C	p.Tyr44His	p.Y44H	ENST00000296474	NM_002447.2	44	Tac/Cac	1/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.421312145502573	2		646	420	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259350	89259350	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	98	365	0	ENST00000336596.2:c.494A>G	p.Asn165Ser	p.N165S	ENST00000336596	NM_005233.5	165	aAc/aGc	3/17	1	2	FACETS	0.858	0.777	0.941	1	0.986	1	CLONAL	2	TRUE	1	0.421312145502573	2		365	271	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274739	142274739	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1313136034	NA	P-0038527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	65	245	0	ENST00000350721.4:c.2321T>A	p.Ile774Lys	p.I774K	ENST00000350721	NM_001184.3	774	aTa/aAa	10/47	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.421312145502573	2		245	209	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0038528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	178	630	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.219010644916126	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.219010644916126	1		631	1049	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039374	49039374	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853293	NA	P-0038528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	84	546	1	ENST00000267163.4:c.2359C>T	p.Arg787Ter	p.R787*	ENST00000267163	NM_000321.2	787	Cga/Tga	23/27	0.219010644916126	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.219010644916126	1		547	579	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024029	27024029	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	14	92	0	ENST00000324856.7:c.1135C>T	p.Gln379Ter	p.Q379*	ENST00000324856	NM_006015.4	379	Cag/Tag	1/20	0.210897261087194	1	FACETS	0.918	0.669	1	0.918	0.669	1	CLONAL	1	TRUE	0	0.219010644916126	1		92	124	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs371769427	NA	P-0038528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	16	244	0	ENST00000291552.4:c.101C>A	p.Ser34Tyr	p.S34Y	ENST00000291552	NM_006758.2	34	tCt/tAt	2/8	0.210897261087194	1	FACETS	0.453	0.335	0.595	0.453	0.335	0.595	SUBCLONAL	1	TRUE	0	0.219010644916126	1		244	287	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245949	5245949	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	177	749	0	ENST00000357368.4:c.826G>A	p.Val276Met	p.V276M	ENST00000357368	NM_002850.3	276	Gtg/Atg	10/38	0.210897261087194	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.219010644916126	1		749	1225	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932068	39932068	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140780988	NA	P-0038528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	97	631	1	ENST00000378444.4:c.2531C>T	p.Pro844Leu	p.P844L	ENST00000378444	NM_001123385.1	844	cCg/cTg	4/15	1	2	FACETS	0.81	0.721	0.907	0.81	0.721	0.907	CLONAL	1	TRUE	1	0.219010644916126	2		632	1093	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713867	30713867	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	49	599	0	ENST00000295754.5:c.1194del	p.Phe398LeufsTer33	p.F398Lfs*33	ENST00000295754	NM_003242.5	398	Ttt/tt	4/7	0.219010644916126	1	FACETS	0.524	0.443	0.614	0.524	0.443	0.614	SUBCLONAL	1	TRUE	0	0.219010644916126	1		599	760	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645687	12645687	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397516828	NA	P-0038529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	30	253	0	ENST00000251849.4:c.782C>G	p.Pro261Arg	p.P261R	ENST00000251849	NM_002880.3	261	cCt/cGt	7/17	0.884354648438247	1	FACETS	0.462	0.384	0.543	0.462	0.384	0.543	SUBCLONAL	1	TRUE	0	0.884354648438247	1		253	82	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856283	111856283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1420086510	NA	P-0038529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	15	25	0	ENST00000341259.2:c.334G>A	p.Ala112Thr	p.A112T	ENST00000341259	NM_005475.2	112	Gcc/Acc	2/8	1	2	FACETS	1	0.822	1	1	0.822	1	CLONAL	1	TRUE	1	0.884354648438247	2		25	32	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464904	120464904	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1437895792	NA	P-0038529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	109	328	0	ENST00000256646.2:c.5168A>G	p.Asn1723Ser	p.N1723S	ENST00000256646	NM_024408.3	1723	aAt/aGt	28/34	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.884354648438247	2		328	226	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416659	29416659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	37	343	0	ENST00000389048.3:c.4294C>T	p.Arg1432Trp	p.R1432W	ENST00000389048	NM_004304.4	1432	Cgg/Tgg	29/29	0.159824777789052	3	FACETS	0.81	0.667	0.97	0.405	0.333	0.485	CLONAL	1	TRUE	1	0.198588536440896	3		343	506	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692844	89692844	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1114167629	NA	P-0038530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	26	142	0	ENST00000371953.3:c.328C>T	p.Gln110Ter	p.Q110*	ENST00000371953	NM_000314.4	110	Caa/Taa	5/9	0.159824777789052	3	FACETS	0.9	0.72	1	0.9	0.72	1	CLONAL	2	TRUE	1	0.198588536440896	3		142	160	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	63	276	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	0.169127048494038	2	FACETS	1	0.949	1	0.604	0.523	0.692	CLONAL	1	TRUE	0	0.198588536440896	2		276	525	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0038530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	37	434	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.159824777789052	3	FACETS	0.962	0.793	1	0.481	0.396	0.575	CLONAL	1	TRUE	1	0.198588536440896	3		434	426	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428052	49428052	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	54	508	0	ENST00000301067.7:c.10538G>A	p.Trp3513Ter	p.W3513*	ENST00000301067	NM_003482.3	3513	tGg/tAg	38/54	1	2	FACETS	0.792	0.675	0.92	0.792	0.675	0.92	CLONAL	1	TRUE	1	0.198588536440896	2		508	687	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560134	29560134	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	29	262	0	ENST00000356175.3:c.3611G>A	p.Arg1204Gln	p.R1204Q	ENST00000356175	NM_000267.3	1204	cGg/cAg	27/57	1	2	FACETS	0.91	0.731	1	0.91	0.731	1	CLONAL	1	TRUE	1	0.198588536440896	2		262	321	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0038532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	78	324	1	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.315447037585967	2		325	454	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560464	95560464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	84	349	0	ENST00000393063.1:c.5125G>A	p.Asp1709Asn	p.D1709N	ENST00000393063	NM_030621.3	1709	Gat/Aat	25/28	1	2	FACETS	0.807	0.713	0.908	0.807	0.713	0.908	CLONAL	1	TRUE	1	0.315447037585967	2		349	660	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572555	95572555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	36	148	0	ENST00000393063.1:c.2810G>A	p.Arg937His	p.R937H	ENST00000393063	NM_030621.3	937	cGc/cAc	19/28	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.315447037585967	2		148	207	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711873	89711873	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs587781784	NA	P-0038532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	35	316	0	ENST00000371953.3:c.493-2A>G		p.X165_splice	ENST00000371953	NM_000314.4	165			1	2	FACETS	0.844	0.695	1	0.844	0.695	1	CLONAL	1	TRUE	1	0.315447037585967	2		316	263	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107135	27107136	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0038532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	106	389	0	ENST00000324856.7:c.6746_6747del	p.Ser2249Ter	p.S2249*	ENST00000324856	NM_006015.4	2249	tCA/t	20/20	1	2	FACETS	0.943	0.846	1	0.943	0.846	1	CLONAL	1	TRUE	1	0.315447037585967	2		389	713	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711957	89711957	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	52	356	0	ENST00000371953.3:c.575del	p.Ala192AspfsTer7	p.A192Dfs*7	ENST00000371953	NM_000314.4	192	gCa/ga	6/9	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.315447037585967	2		356	318	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593246	67593247	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCGA	novel	NA	P-0038532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	43	182	0	ENST00000274335.5:c.1993_1997dup	p.Val667AlafsTer3	p.V667Afs*3	ENST00000274335		664	-/GGCGA	15/15	1	2	FACETS	0.93	0.783	1	0.93	0.783	1	CLONAL	1	TRUE	1	0.315447037585967	2		182	293	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642845	3642845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776707468	NA	P-0038535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	284	634	1	ENST00000294008.3:c.2182G>A	p.Ala728Thr	p.A728T	ENST00000294008	NM_032444.2	728	Gct/Act	11/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.921101391327372	2		635	592	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41962117	41962117	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	111	305	0	ENST00000219905.7:c.1025T>G	p.Leu342Arg	p.L342R	ENST00000219905	NM_001164273.1	342	cTt/cGt	2/24	1	2	FACETS	0.949	0.869	1	0.949	0.869	1	CLONAL	1	TRUE	1	0.921101391327372	2		305	254	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876659802	NA	P-0038536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	43	778	0	ENST00000269305.4:c.833C>A	p.Pro278His	p.P278H	ENST00000269305	NM_001126112.2	278	cCt/cAt	8/11	1	2	FACETS	0.489	0.409	0.579	0.489	0.409	0.579	SUBCLONAL	1	FALSE	1	0.3	2		778	586	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489556	40489569	+	frameshift_variant	Frame_Shift_Del	DEL	GCACGTACTCCATC	GCACGTACTCCATC	-	novel	NA	P-0038536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	28	592	0	ENST00000264657.5:c.681_694del	p.Met228GlufsTer10	p.M228Efs*10	ENST00000264657	NM_139276.2	227	gcGATGGAGTACGTGCag/gcag	8/24	1	2	FACETS	0.341	0.272	0.421	0.341	0.272	0.421	SUBCLONAL	1	FALSE	1	0.3	2		592	547	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679649	30679649	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0038536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	42	610	0	ENST00000376406.3:c.2068+2T>C		p.X690_splice	ENST00000376406	NM_014641.2	690			0.212374488050853	3	FACETS	0.577	0.481	0.684	0.289	0.24	0.342	SUBCLONAL	1	FALSE	1	0.3	3		610	558	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	235	565	5	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	0.685362885472176	1	FACETS	0.866	0.817	0.915	0.866	0.817	0.915	CLONAL	1	TRUE	0	0.703742286695218	1		570	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0038537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	291	825	4	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	1	2	FACETS	0.917	0.865	0.97	0.917	0.865	0.97	CLONAL	1	TRUE	1	0.703742286695218	2		829	902	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577138	7577138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780075	NA	P-0038537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	307	718	3	ENST00000269305.4:c.800G>A	p.Arg267Gln	p.R267Q	ENST00000269305	NM_001126112.2	267	cGg/cAg	8/11	1	2	FACETS	0.998	0.944	1	0.998	0.944	1	CLONAL	1	TRUE	1	0.703742286695218	2		721	874	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354008	15354008	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	77	313	1	ENST00000263377.2:c.2872del	p.Leu958CysfsTer110	p.L958Cfs*110	ENST00000263377	NM_058243.2	958	Ctg/tg	14/20	0.676665442957312	4	FACETS	0.565	0.496	0.639			1	SUBCLONAL	1	TRUE	NA	0.703742286695218	4		314	660	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057788	27057788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748935625	NA	P-0038537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	408	818	7	ENST00000324856.7:c.1496C>T	p.Ser499Leu	p.S499L	ENST00000324856	NM_006015.4	499	tCg/tTg	3/20	0.685362885472176	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.703742286695218	1		825	672	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720712	89720712	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0038537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	105	162	5	ENST00000371953.3:c.867del	p.Val290Ter	p.V290*	ENST00000371953	NM_000314.4	288	gAa/ga	8/9	0.664532261281119	2	FACETS	1	0.982	1	0.654	0.599	0.71	CLONAL	1	TRUE	0	0.703742286695218	2		167	228	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845883	72845883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756387925	NA	P-0038537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	215	568	8	ENST00000268489.5:c.3584G>A	p.Arg1195His	p.R1195H	ENST00000268489	NM_006885.3	1195	cGc/cAc	6/10	1	2	FACETS	0.912	0.852	0.973	0.912	0.852	0.973	CLONAL	1	TRUE	1	0.703742286695218	2		576	670	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435652	110435652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753831518	NA	P-0038537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	150	494	2	ENST00000375856.3:c.2749G>A	p.Gly917Ser	p.G917S	ENST00000375856	NM_003749.2	917	Ggc/Agc	1/2	1	2	FACETS	0.897	0.827	0.97	0.897	0.827	0.97	CLONAL	1	TRUE	1	0.703742286695218	2		496	475	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	714	876	0	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.867	0.843	0.891	1	0.998	1	CLONAL	2	TRUE	1	0.703742286695218	2		876	1170	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0038537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	379	407	17	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	0.704280200174406	3	FACETS	0.875	0.836	0.915	0.875	0.836	0.915	CLONAL	2	TRUE	1	0.703742286695218	3		424	832	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169985715	169985715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567380681	NA	P-0038537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	217	436	7	ENST00000295797.4:c.377G>A	p.Arg126His	p.R126H	ENST00000295797	NM_002740.5	126	cGt/cAt	5/18	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.703742286695218	2		443	578	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989484	7989484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772959657	NA	P-0038537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	307	735	2	ENST00000319144.4:c.202C>T	p.Arg68Cys	p.R68C	ENST00000319144	NM_001139.2	68	Cgc/Tgc	2/15	1	2	FACETS	0.994	0.94	1	0.994	0.94	1	CLONAL	1	TRUE	1	0.703742286695218	2		737	878	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500576	99500576	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141802822	NA	P-0038537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	250	663	4	ENST00000268035.6:c.4009C>T	p.Arg1337Cys	p.R1337C	ENST00000268035	NM_000875.3	1337	Cgc/Tgc	21/21	1	2	FACETS	0.981	0.922	1	0.981	0.922	1	CLONAL	1	TRUE	1	0.703742286695218	2		667	724	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868134	45868134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143960980	NA	P-0038537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	72	895	2	ENST00000391945.4:c.556C>T	p.Arg186Cys	p.R186C	ENST00000391945	NM_000400.3	186	Cgc/Tgc	7/23	1	2	FACETS	0.203	0.177	0.232	0.203	0.177	0.232	SUBCLONAL	1	TRUE	1	0.703742286695218	2		897	1006	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444809	49444809	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	402	978	10	ENST00000301067.7:c.2657del	p.Pro886LeufsTer44	p.P886Lfs*44	ENST00000301067	NM_003482.3	886	cCt/ct	10/54	1	2	FACETS	0.976	0.929	1	0.976	0.929	1	CLONAL	1	TRUE	1	0.703742286695218	2		988	1171	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533176	63533176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1165490589	NA	P-0038537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	323	778	3	ENST00000307078.5:c.1718G>A	p.Ser573Asn	p.S573N	ENST00000307078	NM_004655.3	573	aGc/aAc	7/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.703742286695218	2		781	896	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435558	18435560	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0038537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	123	256	0	ENST00000266497.5:c.545_547del	p.Phe182del	p.F182del	ENST00000266497		181	tcCTTc/tcc	1/31	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.703742286695218	2		256	349	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416891	121416891	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	363	910	3	ENST00000257555.6:c.320T>G	p.Leu107Arg	p.L107R	ENST00000257555		107	cTt/cGt	1/10	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.703742286695218	2		913	1025	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355077	73355077	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	209	400	0	ENST00000377767.4:c.293T>C	p.Val98Ala	p.V98A	ENST00000377767	NM_014953.3	98	gTg/gCg	2/21	1	2	FACETS	0.956	0.893	1	0.956	0.893	1	CLONAL	1	TRUE	1	0.703742286695218	2		400	621	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577551	+	protein_altering_variant	In_Frame_Del	DEL	GGTTCATGCCGCC	GGTTCATGCCGCC	AGTT	novel	NA	P-0038537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	254	687	6	ENST00000269305.4:c.730_742delinsAACT	p.Gly244_Arg248delinsAsnTrp	p.G244_R248delinsNW	ENST00000269305	NM_001126112.2	244	GGCGGCATGAACCgg/AACTgg	7/11	1	2	FACETS	0.882	0.828	0.938	0.882	0.828	0.938	CLONAL	1	TRUE	1	0.703742286695218	2		693	818	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66525134	66525134	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0038537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	134	250	3	ENST00000358598.2:c.891+2T>C		p.X297_splice	ENST00000358598	NM_212471.2	297			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.703742286695218	2		253	327	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855813	45855813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	52	811	1	ENST00000391945.4:c.1997G>A	p.Arg666Gln	p.R666Q	ENST00000391945	NM_000400.3	666	cGg/cAg	21/23	1	2	FACETS	0.145	0.122	0.169	0.145	0.122	0.169	SUBCLONAL	1	TRUE	1	0.703742286695218	2		812	1022	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46276048	46276048	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746518804	NA	P-0038537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	233	577	0	ENST00000371998.3:c.3487del	p.Arg1163GlyfsTer22	p.R1163Gfs*22	ENST00000371998		1162	Ccc/cc	18/23	1	2	FACETS	0.901	0.844	0.959	0.901	0.844	0.959	CLONAL	1	TRUE	1	0.703742286695218	2		577	735	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967218	134967218	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	206	590	0	ENST00000398015.3:c.2557C>A	p.Leu853Ile	p.L853I	ENST00000398015	NM_004441.4	853	Cta/Ata	14/16	1	2	FACETS	0.839	0.781	0.898	0.839	0.781	0.898	CLONAL	1	TRUE	1	0.703742286695218	2		590	698	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26021013	26021013	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	184	445	1	ENST00000357647.3:c.296C>G	p.Ala99Gly	p.A99G	ENST00000357647	NM_003529.2	99	gCc/gGc	1/1	1	2	FACETS	0.831	0.771	0.893	0.831	0.771	0.893	CLONAL	1	TRUE	1	0.703742286695218	2		446	629	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519612	137519612	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	175	376	1	ENST00000367739.4:c.1026del	p.Val343TrpfsTer10	p.V343Wfs*10	ENST00000367739	NM_000416.2	342	aaA/aa	7/7	0.703742286695218	1	FACETS	0.918	0.86	0.977	0.918	0.86	0.977	CLONAL	1	TRUE	0	0.703742286695218	1		377	351	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525018	157525018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs544895806	NA	P-0038537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	134	333	0	ENST00000346085.5:c.4913G>A	p.Arg1638His	p.R1638H	ENST00000346085	NM_020732.3	1638	cGt/cAt	19/20	0.703742286695218	1	FACETS	0.979	0.911	1	0.979	0.911	1	CLONAL	1	TRUE	0	0.703742286695218	1		333	252	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128420055	128420058	+	frameshift_variant	Frame_Shift_Del	DEL	CAAA	CAAA	-	novel	NA	P-0038537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	187	585	3	ENST00000265960.3:c.370_373del	p.Phe124LysfsTer22	p.F124Kfs*22	ENST00000265960	NM_001006617.1	124	TTTGaa/aa	4/12	0.704280200174406	3	FACETS	0.739	0.683	0.798	0.37	0.341	0.399	SUBCLONAL	1	TRUE	1	0.703742286695218	3		588	972	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391902	139391902	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	385	948	6	ENST00000277541.6:c.6289C>T	p.Pro2097Ser	p.P2097S	ENST00000277541	NM_017617.3	2097	Ccg/Tcg	34/34	0.698619115842797	3	FACETS	0.985	0.934	1	0.492	0.467	0.519	CLONAL	1	TRUE	1	0.703742286695218	3		954	1502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0038538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	1426	647	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.772777735374151	6	FACETS	1	0.99	1	1	0.99	1	CLONAL	6	TRUE	0	0.772777735374151	6		647	1566	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180783	106180784	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755283040	NA	P-0038538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	178	198	0	ENST00000380013.4:c.3812dup	p.Cys1271TrpfsTer29	p.C1271Wfs*29	ENST00000380013	NM_001127208.2	1271	tgc/tGgc	7/11	0.686309963691043	4	FACETS	0.975	0.909	1	0.975	0.909	1	CLONAL	2	TRUE	2	0.772777735374151	4		198	419	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247157	153247157	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0038538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	139	191	0	ENST00000281708.4:c.1644+1G>A		p.X548_splice	ENST00000281708	NM_033632.3	548			0.686309963691043	4	FACETS	0.891	0.821	0.961	0.891	0.821	0.961	CLONAL	2	TRUE	2	0.772777735374151	4		191	358	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243898	41243898	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs398122676	NA	P-0038538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	536	429	0	ENST00000357654.3:c.3650C>G	p.Ser1217Cys	p.S1217C	ENST00000357654	NM_007294.3	1217	tCt/tGt	10/23	0.772777735374151	3	FACETS	0.94	0.917	0.962	0.94	0.917	0.962	CLONAL	3	TRUE	0	0.772777735374151	3		429	682	SUCCESS
APC	324	MSKCC	GRCh37	5	112175907	112175907	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1554086008	NA	P-0038538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	160	206	0	ENST00000257430.4:c.4616C>A	p.Ser1539Ter	p.S1539*	ENST00000257430	NM_000038.5	1539	tCa/tAa	16/16	0.754696097161768	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.772777735374151	2		206	205	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0038541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	536	630	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.64299788112316	2	FACETS	0.974	0.943	1	0.974	0.943	1	CLONAL	2	TRUE	0	0.64299788112316	2		631	856	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	275	578	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.64299788112316	4	FACETS	0.983	0.928	1	0.983	0.928	1	CLONAL	2	TRUE	2	0.64299788112316	4		578	715	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0038541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	374	580	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.64299788112316	2	FACETS	0.913	0.877	0.949	0.913	0.877	0.949	CLONAL	2	TRUE	0	0.64299788112316	2		580	637	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793211	139793212	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs748531430	NA	P-0038541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	206	724	1	ENST00000247668.2:c.26dup	p.Gly10TrpfsTer70	p.G10Wfs*70	ENST00000247668	NM_021138.3	7	acc/aCcc	2/11	0.64299788112316	2	FACETS	0.718	0.667	0.771	0.359	0.333	0.386	SUBCLONAL	1	TRUE	0	0.64299788112316	2		725	892	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913711	32913714	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	TAAG	TAAG	AAA	novel	NA	P-0038541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	314	368	0	ENST00000380152.3:c.5219_5222delinsAAA	p.Leu1740Ter	p.L1740*	ENST00000380152		1740	tTAAGt/tAAAt	11/27	0.38138188272135	5	FACETS	0.886	0.841	0.931	0.886	0.841	0.931	INDETERMINATE	3	TRUE	2	0.64299788112316	5		368	722	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0038542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	50	339	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.194	0.164	0.227	0.194	0.164	0.227	SUBCLONAL	1	TRUE	1	0.946868449590588	2		339	544	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	113	876	0	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.256	0.23	0.284	0.256	0.23	0.284	SUBCLONAL	1	TRUE	1	0.946868449590588	2		876	933	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0038542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	130	794	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.483	0.44	0.529	0.483	0.44	0.529	SUBCLONAL	1	TRUE	1	0.946868449590588	2		794	568	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0038542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	108	489	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.4	0.36	0.443	0.4	0.36	0.443	SUBCLONAL	1	TRUE	1	0.946868449590588	2		489	570	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922321	178922321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	77	337	1	ENST00000263967.3:c.1090G>A	p.Gly364Arg	p.G364R	ENST00000263967	NM_006218.2	364	Gga/Aga	6/21	1	2	FACETS	0.484	0.428	0.543	0.484	0.428	0.543	SUBCLONAL	1	TRUE	1	0.946868449590588	2		338	336	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363243	40363243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	35	523	1	ENST00000397332.2:c.986C>T	p.Ser329Leu	p.S329L	ENST00000397332	NM_001033082.2	329	tCg/tTg	3/3	1	2	FACETS	0.133	0.109	0.161	0.133	0.109	0.161	SUBCLONAL	1	TRUE	1	0.946868449590588	2		524	554	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692794	89692794	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121909238	NA	P-0038542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	76	327	0	ENST00000371953.3:c.278A>G	p.His93Arg	p.H93R	ENST00000371953	NM_000314.4	93	cAt/cGt	5/9	1	2	FACETS	0.513	0.454	0.575	0.513	0.454	0.575	SUBCLONAL	1	TRUE	1	0.946868449590588	2		327	313	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0038542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	222	681	5	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.708	0.663	0.755	0.708	0.663	0.755	SUBCLONAL	1	TRUE	1	0.946868449590588	2		686	662	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564852	41564852	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	136	429	0	ENST00000263253.7:c.4153T>C	p.Cys1385Arg	p.C1385R	ENST00000263253	NM_001429.3	1385	Tgc/Cgc	25/31	1	2	FACETS	0.494	0.45	0.539	0.494	0.45	0.539	SUBCLONAL	1	TRUE	1	0.946868449590588	2		429	582	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981599	101981599	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	20	126	0	ENST00000282441.5:c.20C>A	p.Pro7Gln	p.P7Q	ENST00000282441	NM_001130145.2	7	cCg/cAg	1/9	1	2	FACETS	0.285	0.22	0.361	0.285	0.22	0.361	SUBCLONAL	1	TRUE	1	0.946868449590588	2		126	148	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633171	3633171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1218491919	NA	P-0038542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	105	872	2	ENST00000294008.3:c.5080G>A	p.Ala1694Thr	p.A1694T	ENST00000294008	NM_032444.2	1694	Gcc/Acc	14/15	1	2	FACETS	0.232	0.207	0.258	0.232	0.207	0.258	SUBCLONAL	1	TRUE	1	0.946868449590588	2		874	958	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956206	175956206	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	21	288	1	ENST00000367669.3:c.2006A>T	p.Lys669Ile	p.K669I	ENST00000367669	NM_022457.5	669	aAa/aTa	18/20	0.946868449590588	3	FACETS	0.189	0.145	0.241	0.095	0.072	0.121	SUBCLONAL	1	TRUE	1	0.946868449590588	3		289	345	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957498	175957498	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	74	396	1	ENST00000367669.3:c.1898T>A	p.Leu633Gln	p.L633Q	ENST00000367669	NM_022457.5	633	cTa/cAa	17/20	0.946868449590588	3	FACETS	0.325	0.284	0.369	0.162	0.142	0.185	SUBCLONAL	1	TRUE	1	0.946868449590588	3		397	709	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650020	206650020	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0038542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	106	453	1	ENST00000367120.3:c.541-1G>A		p.X181_splice	ENST00000367120	NM_014002.3	181			0.946868449590588	3	FACETS	0.476	0.427	0.528	0.238	0.213	0.264	SUBCLONAL	1	TRUE	1	0.946868449590588	3		454	693	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43766906	43766906	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	19	180	0	ENST00000382044.4:c.1145T>C	p.Val382Ala	p.V382A	ENST00000382044	NM_001141980.1	382	gTt/gCt	10/28	1	2	FACETS	0.143	0.108	0.184	0.143	0.108	0.184	SUBCLONAL	1	TRUE	1	0.946868449590588	2		180	280	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991764	72991764	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	45	405	0	ENST00000268489.5:c.2281G>T	p.Gly761Trp	p.G761W	ENST00000268489	NM_006885.3	761	Ggg/Tgg	2/10	1	2	FACETS	0.244	0.205	0.287	0.244	0.205	0.287	SUBCLONAL	1	TRUE	1	0.946868449590588	2		405	389	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992696	72992696	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	113	544	0	ENST00000268489.5:c.1349del	p.Asp450ValfsTer7	p.D450Vfs*7	ENST00000268489	NM_006885.3	450	gAt/gt	2/10	1	2	FACETS	0.456	0.412	0.503	0.456	0.412	0.503	SUBCLONAL	1	TRUE	1	0.946868449590588	2		544	523	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56367785	56367785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1320720757	NA	P-0038542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	21	337	0	ENST00000348428.3:c.611C>T	p.Ser204Leu	p.S204L	ENST00000348428	NM_006785.3	204	tCa/tTa	4/17	1	2	FACETS	0.108	0.083	0.138	0.108	0.083	0.138	SUBCLONAL	1	TRUE	1	0.946868449590588	2		337	409	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57569972	57569972	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	70	232	0	ENST00000316660.6:c.152G>T	p.Cys51Phe	p.C51F	ENST00000316660	NM_021127.2	51	tGc/tTc	2/2	1	2	FACETS	0.5	0.439	0.563	0.5	0.439	0.563	SUBCLONAL	1	TRUE	1	0.946868449590588	2		232	296	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621170	1621170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	158	767	0	ENST00000344749.5:c.976G>A	p.Gly326Ser	p.G326S	ENST00000344749	NM_001136139.2	326	Ggc/Agc	12/19	1	2	FACETS	0.48	0.441	0.521	0.48	0.441	0.521	SUBCLONAL	1	TRUE	1	0.946868449590588	2		767	695	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208398	5208398	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	142	479	1	ENST00000357368.4:c.5492G>A	p.Gly1831Asp	p.G1831D	ENST00000357368	NM_002850.3	1831	gGc/gAc	36/38	1	2	FACETS	0.568	0.52	0.617	0.568	0.52	0.617	SUBCLONAL	1	TRUE	1	0.946868449590588	2		480	528	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599965	10599965	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	195	651	0	ENST00000171111.5:c.1611C>A	p.Tyr537Ter	p.Y537*	ENST00000171111	NM_203500.1	537	taC/taA	5/6	1	2	FACETS	0.512	0.474	0.55	0.512	0.474	0.55	SUBCLONAL	1	TRUE	1	0.946868449590588	2		651	805	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610385	10610385	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	170	719	0	ENST00000171111.5:c.325G>A	p.Ala109Thr	p.A109T	ENST00000171111	NM_203500.1	109	Gcc/Acc	2/6	1	2	FACETS	0.472	0.435	0.511	0.472	0.435	0.511	SUBCLONAL	1	TRUE	1	0.946868449590588	2		719	761	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270168	198270168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	61	292	0	ENST00000335508.6:c.1268C>T	p.Pro423Leu	p.P423L	ENST00000335508	NM_012433.2	423	cCt/cTt	10/25	1	2	FACETS	0.386	0.335	0.441	0.386	0.335	0.441	SUBCLONAL	1	TRUE	1	0.946868449590588	2		292	334	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31015943	31015943	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs752178487	NA	P-0038542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	40	334	0	ENST00000375687.4:c.265C>A	p.Gln89Lys	p.Q89K	ENST00000375687	NM_015338.5	89	Cag/Aag	5/13	1	2	FACETS	0.21	0.174	0.25	0.21	0.174	0.25	SUBCLONAL	1	TRUE	1	0.946868449590588	2		334	402	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161250	185161250	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	43	495	0	ENST00000265026.3:c.677C>T	p.Ala226Val	p.A226V	ENST00000265026	NM_004721.4	226	gCc/gTc	4/14	1	2	FACETS	0.172	0.144	0.204	0.172	0.144	0.204	SUBCLONAL	1	TRUE	1	0.946868449590588	2		495	527	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163226	32163226	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	201	767	0	ENST00000375023.3:c.6000G>T	p.Glu2000Asp	p.E2000D	ENST00000375023	NM_004557.3	2000	gaG/gaT	30/30	1	2	FACETS	0.533	0.495	0.573	0.533	0.495	0.573	SUBCLONAL	1	TRUE	1	0.946868449590588	2		767	796	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199882	138199882	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	89	403	0	ENST00000237289.4:c.1300G>T	p.Ala434Ser	p.A434S	ENST00000237289	NM_001270507.1	434	Gcg/Tcg	7/9	1	2	FACETS	0.452	0.403	0.504	0.452	0.403	0.504	SUBCLONAL	1	TRUE	1	0.946868449590588	2		403	416	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879167	151879168	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0038542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	102	450	0	ENST00000262189.6:c.5777_5778del	p.Cys1926TyrfsTer8	p.C1926Yfs*8	ENST00000262189	NM_170606.2	1926	tGT/t	36/59	1	2	FACETS	0.402	0.36	0.446	0.402	0.36	0.446	SUBCLONAL	1	TRUE	1	0.946868449590588	2		450	536	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390549	139390549	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761156723	NA	P-0038542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	200	745	0	ENST00000277541.6:c.7642G>A	p.Ala2548Thr	p.A2548T	ENST00000277541	NM_017617.3	2548	Gcc/Acc	34/34	1	2	FACETS	0.46	0.426	0.495	0.46	0.426	0.495	SUBCLONAL	1	TRUE	1	0.946868449590588	2		745	918	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410006	63410006	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	108	558	1	ENST00000330258.3:c.3161C>A	p.Pro1054His	p.P1054H	ENST00000330258	NM_152424.3	1054	cCt/cAt	2/2	1	2	FACETS	0.448	0.404	0.495	0.448	0.404	0.495	SUBCLONAL	1	TRUE	1	0.946868449590588	2		559	509	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937065	76937065	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	25	310	0	ENST00000373344.5:c.3683C>A	p.Pro1228His	p.P1228H	ENST00000373344	NM_000489.3	1228	cCt/cAt	9/35	1	2	FACETS	0.192	0.151	0.239	0.192	0.151	0.239	SUBCLONAL	1	TRUE	1	0.946868449590588	2		310	275	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0038543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	274	875	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.363606609625295	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.444835379649087	2		876	578	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270531	98270531	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs143494325	NA	P-0038543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	86	301	0	ENST00000331920.6:c.113G>T	p.Gly38Val	p.G38V	ENST00000331920	NM_000264.3	38	gGg/gTg	1/24	0.145145573257703	6	FACETS	1	0.97	1	0.828	0.741	0.919	INDETERMINATE	2	TRUE	3	0.444835379649087	6		301	294	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882301	89882301	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	149	455	0	ENST00000389301.3:c.173A>G	p.Asn58Ser	p.N58S	ENST00000389301	NM_000135.2	58	aAt/aGt	2/43	0.424522094462366	2	FACETS	0.908	0.84	0.976	0.908	0.84	0.976	CLONAL	2	TRUE	0	0.444835379649087	2		455	369	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244247	41244248	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0038543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	307	504	0	ENST00000357654.3:c.3300_3301del	p.Ser1101Ter	p.S1101*	ENST00000357654	NM_007294.3	1100	ggAAgt/gggt	10/23	0.432522260292822	4	FACETS	0.959	0.917	1	0.959	0.917	1	CLONAL	4	TRUE	0	0.444835379649087	4		504	520	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86669980	86669980	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	46	188	0	ENST00000274376.6:c.1777G>T	p.Val593Phe	p.V593F	ENST00000274376	NM_002890.2	593	Gtc/Ttc	14/25	0.424522094462366	2	FACETS	0.766	0.66	0.877	0.766	0.66	0.877	SUBCLONAL	2	TRUE	0	0.444835379649087	2		188	135	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0038545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	274	601	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	1.01	2		601	523	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514780	44514780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769567889	NA	P-0038545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	238	467	0	ENST00000291552.4:c.467G>A	p.Arg156His	p.R156H	ENST00000291552	NM_006758.2	156	cGt/cAt	6/8	1	2	FACETS	0.803	0.755	0.851	0.803	0.755	0.851	CLONAL	1	TRUE	1	1.01	2		467	587	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432409	49432412	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	novel	NA	P-0038545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	324	712	0	ENST00000301067.7:c.8727_8730del	p.Ser2910ArgfsTer32	p.S2910Rfs*32	ENST00000301067	NM_003482.3	2909	gtAAGT/gt	34/54	1	2	FACETS	0.899	0.855	0.943	0.899	0.855	0.943	CLONAL	1	TRUE	1	1.01	2		712	714	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470908	25470908	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	rs201882909	NA	P-0038545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	256	635	0	ENST00000264709.3:c.853G>T	p.Glu285Ter	p.E285*	ENST00000264709	NM_175629.2	285	Gag/Tag	7/23	1	2	FACETS	0.826	0.779	0.873	0.826	0.779	0.873	CLONAL	1	TRUE	1	1.01	2		635	614	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0038547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	40	376	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.936	0.782	1	0.936	0.782	1	CLONAL	1	TRUE	1	0.320262054913555	2		376	267	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797375	42797376	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0038547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	103	679	0	ENST00000575354.2:c.3743dup	p.Leu1249ThrfsTer6	p.L1249Tfs*6	ENST00000575354	NM_015125.3	1246	agc/agCc	15/20	1	2	FACETS	0.961	0.861	1	0.961	0.861	1	CLONAL	1	TRUE	1	0.320262054913555	2		679	669	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088669	27088673	+	frameshift_variant	Frame_Shift_Ins	INS	CCCCA	CCCCA	TCCCCG	novel	NA	P-0038547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	109	610	1	ENST00000324856.7:c.2278_2282delinsTCCCCG	p.Pro760SerfsTer57	p.P760Sfs*57	ENST00000324856	NM_006015.4	760	CCCCAg/TCCCCGg	7/20	0.301739921771793	1	FACETS	0.969	0.872	1	0.969	0.872	1	CLONAL	1	TRUE	0	0.320262054913555	1		611	590	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803598	1803598	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	155	565	0	ENST00000260795.2:c.776T>G	p.Leu259Arg	p.L259R	ENST00000260795		259	cTg/cGg	6/17	0.280506755755627	3	FACETS	0.963	0.886	1	0.963	0.886	1	CLONAL	2	TRUE	1	0.320262054913555	3		565	583	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0038548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	267	630	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.19501030376634	3	FACETS	0.879	0.826	0.933	0.879	0.826	0.933	CLONAL	3	TRUE	0	0.249854368685564	3		631	912	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	44	578	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.249854368685564	3	FACETS	0.804	0.674	0.947	0.402	0.337	0.474	CLONAL	1	TRUE	1	0.249854368685564	3		578	493	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0038548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	127	444	1	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.249854368685564	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.249854368685564	3		445	505	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0038548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	93	454	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.249854368685564	3	FACETS	0.851	0.76	0.948	0.851	0.76	0.948	CLONAL	2	TRUE	1	0.249854368685564	3		454	492	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0038548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	25	238	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.249854368685564	3	FACETS	0.849	0.671	1	0.425	0.335	0.527	CLONAL	1	TRUE	1	0.249854368685564	3		238	265	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0038548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	47	377	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.249854368685564	3	FACETS	0.98	0.828	1	0.49	0.414	0.573	CLONAL	1	TRUE	1	0.249854368685564	3		377	432	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508083	106508083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339698935	NA	P-0038548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	14	239	0	ENST00000359195.3:c.77G>A	p.Arg26His	p.R26H	ENST00000359195	NM_002649.2	26	cGc/cAc	2/11	0.249854368685564	6	FACETS	0.67	0.484	0.895	0.223	0.161	0.299	SUBCLONAL	1	TRUE	3	0.249854368685564	6		239	251	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830925	72830925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	48	481	0	ENST00000268489.5:c.5656G>A	p.Glu1886Lys	p.E1886K	ENST00000268489	NM_006885.3	1886	Gaa/Aaa	9/10	0.137718006778771	4	FACETS	0.842	0.712	0.987	0.421	0.356	0.494	INDETERMINATE	1	TRUE	2	0.249854368685564	4		481	570	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419897	41419897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs577588058	NA	P-0038548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	67	532	1	ENST00000373198.4:c.424G>A	p.Val142Ile	p.V142I	ENST00000373198	NM_133170.3	142	Gtc/Atc	3/32	0.249854368685564	6	FACETS	1	0.873	1	0.252	0.218	0.288	CLONAL	1	TRUE	2	0.249854368685564	6		533	799	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372254	55372254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1358462345	NA	P-0038548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	40	476	0	ENST00000297316.4:c.944C>T	p.Pro315Leu	p.P315L	ENST00000297316	NM_022454.3	315	cCg/cTg	2/2	0.249854368685564	3	FACETS	0.71	0.59	0.845	0.355	0.295	0.423	SUBCLONAL	1	TRUE	1	0.249854368685564	3		476	507	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088795	27088795	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	71	562	0	ENST00000324856.7:c.2404C>T	p.Gln802Ter	p.Q802*	ENST00000324856	NM_006015.4	802	Cag/Tag	7/20	1	2	FACETS	0.97	0.847	1	0.97	0.847	1	CLONAL	1	TRUE	1	0.249854368685564	2		562	586	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644703	134644703	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536029159	NA	P-0038548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	64	446	0	ENST00000398015.3:c.104C>T	p.Thr35Met	p.T35M	ENST00000398015	NM_004441.4	35	aCg/aTg	2/16	0.0436876101485111	4	FACETS	1	0.922	1	0.547	0.474	0.627	INDETERMINATE	1	TRUE	2	0.249854368685564	4		446	585	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528243	157528243	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs797045283	NA	P-0038548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	111	553	0	ENST00000346085.5:c.5968C>T	p.Arg1990Ter	p.R1990*	ENST00000346085	NM_020732.3	1990	Cga/Tga	20/20	0.137718006778771	4	FACETS	0.762	0.685	0.843	0.762	0.685	0.843	INDETERMINATE	2	TRUE	2	0.249854368685564	4		553	729	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903709	114903712	+	frameshift_variant	Frame_Shift_Del	DEL	ATAT	ATAT	-	novel	NA	P-0038548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	151	553	0	ENST00000543371.1:c.715_718del	p.Ile239ProfsTer11	p.I239Pfs*11	ENST00000543371	NM_001198531.1	238	gATATa/ga	7/14	0.249854368685564	3	FACETS	0.95	0.87	1	0.95	0.87	1	CLONAL	2	TRUE	1	0.249854368685564	3		553	716	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119706	17119706	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs911287169	NA	P-0038548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	53	519	0	ENST00000285071.4:c.1288G>A	p.Val430Met	p.V430M	ENST00000285071	NM_144997.5	430	Gtg/Atg	11/14	0.19501030376634	3	FACETS	0.916	0.781	1	0.305	0.26	0.355	CLONAL	1	TRUE	0	0.249854368685564	3		519	521	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278106	41278106	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	42	380	0	ENST00000349496.5:c.1982G>C	p.Arg661Pro	p.R661P	ENST00000349496	NM_001904.3	661	cGa/cCa	13/15	0.0436876101485111	4	FACETS	0.989	0.826	1	0.494	0.413	0.584	INDETERMINATE	1	TRUE	2	0.249854368685564	4		380	425	SUCCESS
APC	324	MSKCC	GRCh37	5	112175460	112175464	+	frameshift_variant	Frame_Shift_Del	DEL	TCAGT	TCAGT	-	novel	NA	P-0038548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	28	293	0	ENST00000257430.4:c.4172_4176del	p.Ser1391ThrfsTer2	p.S1391Tfs*2	ENST00000257430	NM_000038.5	1390	gTCAGT/g	16/16	0.249854368685564	3	FACETS	0.781	0.625	0.958	0.39	0.312	0.479	CLONAL	1	TRUE	1	0.249854368685564	3		293	323	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109415113	109415113	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	138	751	0	ENST00000436639.2:c.164del	p.Asn55IlefsTer8	p.N55Ifs*8	ENST00000436639	NM_014454.2	55	aAt/at	1/10	0.137718006778771	4	FACETS	1	0.982	1	0.662	0.602	0.726	INDETERMINATE	1	TRUE	2	0.249854368685564	4		751	1042	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228268	53228268	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	154	309	0	ENST00000375401.3:c.2134A>T	p.Thr712Ser	p.T712S	ENST00000375401	NM_004187.3	712	Act/Tct	15/26	1	1	FACETS		NA	1			1	NA	NA	TRUE	0	NA	1		309	261	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554261	106554261	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	27	300	0	ENST00000369096.4:c.1789C>A	p.His597Asn	p.H597N	ENST00000369096	NM_001198.3	597	Cac/Aac	6/7	1	2	FACETS	0.777	0.629	0.94	0.777	0.629	0.94	CLONAL	1	NA	1	0.569442929006608	2		300	122	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	130	523	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	0.530877570395422	2		523	483	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	108	399	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.530877570395422	2		399	336	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	29	659	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.189	0.151	0.232	0.189	0.151	0.232	SUBCLONAL	1	TRUE	1	0.530877570395422	2		659	579	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023702	31023702	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1311033207	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	51	661	0	ENST00000375687.4:c.3187C>T	p.Gln1063Ter	p.Q1063*	ENST00000375687	NM_015338.5	1063	Cag/Tag	13/13	0.305039652530307	3	FACETS	0.255	0.215	0.298			1	INDETERMINATE	1	TRUE	NA	0.530877570395422	3		661	955	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879854	37879854	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	60	738	0	ENST00000269571.5:c.2149G>A	p.Glu717Lys	p.E717K	ENST00000269571		717	Gag/Aag	18/27	1	2	FACETS	0.293	0.251	0.338	0.293	0.251	0.338	SUBCLONAL	1	TRUE	1	0.530877570395422	2		738	772	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775801	9775801	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	103	826	0	ENST00000377346.4:c.344C>G	p.Ser115Ter	p.S115*	ENST00000377346	NM_005026.3	115	tCa/tGa	4/24	1	2	FACETS	0.475	0.425	0.529	0.475	0.425	0.529	SUBCLONAL	1	TRUE	1	0.530877570395422	2		826	817	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100375	27100375	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	183	610	1	ENST00000324856.7:c.4087C>T	p.Gln1363Ter	p.Q1363*	ENST00000324856	NM_006015.4	1363	Caa/Taa	17/20	1	2	FACETS	0.971	0.899	1	0.971	0.899	1	CLONAL	1	TRUE	1	0.530877570395422	2		611	710	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106255	27106255	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	47	678	0	ENST00000324856.7:c.5866G>C	p.Glu1956Gln	p.E1956Q	ENST00000324856	NM_006015.4	1956	Gag/Cag	20/20	1	2	FACETS	0.229	0.192	0.27	0.229	0.192	0.27	SUBCLONAL	1	TRUE	1	0.530877570395422	2		678	773	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932259	36932259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	204	809	0	ENST00000361632.4:c.2210C>T	p.Ser737Phe	p.S737F	ENST00000361632		737	tCc/tTc	16/16	1	2	FACETS	0.973	0.904	1	0.973	0.904	1	CLONAL	1	TRUE	1	0.530877570395422	2		809	790	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120478113	120478113	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	41	500	0	ENST00000256646.2:c.3637T>C	p.Cys1213Arg	p.C1213R	ENST00000256646	NM_024408.3	1213	Tgc/Cgc	22/34	1	2	FACETS	0.29	0.241	0.344	0.29	0.241	0.344	SUBCLONAL	1	TRUE	1	0.530877570395422	2		500	533	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162750023	162750023	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	44	406	0	ENST00000367921.3:c.2555A>G	p.Gln852Arg	p.Q852R	ENST00000367921	NM_006182.2	852	cAa/cGa	18/18	1	2	FACETS	0.355	0.298	0.418	0.355	0.298	0.418	SUBCLONAL	1	TRUE	1	0.530877570395422	2		406	467	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982105	201982105	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	57	873	1	ENST00000359651.3:c.629C>G	p.Ser210Ter	p.S210*	ENST00000359651		210	tCa/tGa	5/8	1	2	FACETS	0.231	0.197	0.268	0.231	0.197	0.268	SUBCLONAL	1	TRUE	1	0.530877570395422	2		874	931	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692900	89692900	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1114167645	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	18	448	0	ENST00000371953.3:c.384G>C	p.Lys128Asn	p.K128N	ENST00000371953	NM_000314.4	128	aaG/aaC	5/9	1	2	FACETS	0.131	0.098	0.171	0.131	0.098	0.171	SUBCLONAL	1	TRUE	1	0.530877570395422	2		448	517	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205238	61205238	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	159	568	0	ENST00000301761.2:c.178G>C	p.Asp60His	p.D60H	ENST00000301761	NM_017841.2	60	Gat/Cat	2/4	1	2	FACETS	0.988	0.91	1	0.988	0.91	1	CLONAL	1	TRUE	1	0.530877570395422	2		568	606	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998438	100998438	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	103	420	0	ENST00000325455.5:c.1364G>C	p.Gly455Ala	p.G455A	ENST00000325455	NM_001202474.3	455	gGg/gCg	1/8	1	2	FACETS	0.878	0.79	0.97	0.878	0.79	0.97	CLONAL	1	TRUE	1	0.530877570395422	2		420	442	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114734	108114734	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	93	349	0	ENST00000278616.4:c.551G>C	p.Arg184Thr	p.R184T	ENST00000278616	NM_000051.3	184	aGa/aCa	6/63	1	2	FACETS	0.876	0.784	0.972	0.876	0.784	0.972	CLONAL	1	TRUE	1	0.530877570395422	2		349	400	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118355667	118355668	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	38	529	0	ENST00000534358.1:c.4311_4312del	p.Ala1438GlnfsTer2	p.A1438Qfs*2	ENST00000534358	NM_005933.3	1437	TGt/t	10/36	1	2	FACETS	0.234	0.193	0.281	0.234	0.193	0.281	SUBCLONAL	1	TRUE	1	0.530877570395422	2		529	611	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375770	118375770	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	44	490	0	ENST00000534358.1:c.9163G>T	p.Asp3055Tyr	p.D3055Y	ENST00000534358	NM_005933.3	3055	Gat/Tat	27/36	1	2	FACETS	0.305	0.255	0.36	0.305	0.255	0.36	SUBCLONAL	1	TRUE	1	0.530877570395422	2		490	544	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416523	49416523	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	84	671	0	ENST00000301067.7:c.16188G>C	p.Lys5396Asn	p.K5396N	ENST00000301067	NM_003482.3	5396	aaG/aaC	51/54	1	2	FACETS	0.435	0.384	0.49	0.435	0.384	0.49	SUBCLONAL	1	TRUE	1	0.530877570395422	2		671	727	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480320	56480320	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	32	389	0	ENST00000267101.3:c.427C>G	p.Leu143Val	p.L143V	ENST00000267101	NM_001982.3	143	Ctg/Gtg	4/28	1	2	FACETS	0.279	0.226	0.339	0.279	0.226	0.339	SUBCLONAL	1	TRUE	1	0.530877570395422	2		389	432	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549161	21549161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1301579203	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	49	726	1	ENST00000382592.4:c.3115G>A	p.Glu1039Lys	p.E1039K	ENST00000382592	NM_014572.2	1039	Gaa/Aaa	8/8	1	2	FACETS	0.227	0.191	0.266	0.227	0.191	0.266	SUBCLONAL	1	TRUE	1	0.530877570395422	2		727	815	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877384	28877384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768225561	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	38	459	1	ENST00000282397.4:c.3937G>A	p.Glu1313Lys	p.E1313K	ENST00000282397	NM_002019.4	1313	Gag/Aag	30/30	1	2	FACETS	0.211	0.173	0.253	0.211	0.173	0.253	SUBCLONAL	1	TRUE	1	0.530877570395422	2		460	679	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950806	32950806	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	95	306	0	ENST00000380152.3:c.8633-1G>C		p.X2878_splice	ENST00000380152		2878			1	2	FACETS	0.944	0.847	1	0.944	0.847	1	CLONAL	1	TRUE	1	0.530877570395422	2		306	379	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041731	42041731	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	27	394	0	ENST00000219905.7:c.5926G>C	p.Asp1976His	p.D1976H	ENST00000219905	NM_001164273.1	1976	Gac/Cac	17/24	1	2	FACETS	0.23	0.182	0.284	0.23	0.182	0.284	SUBCLONAL	1	TRUE	1	0.530877570395422	2		394	443	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701095	43701095	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	140	380	0	ENST00000382044.4:c.5600G>C	p.Trp1867Ser	p.W1867S	ENST00000382044	NM_001141980.1	1867	tGg/tCg	26/28	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.530877570395422	2		380	479	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799166	88799166	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	35	526	0	ENST00000360948.2:c.219C>G	p.Ile73Met	p.I73M	ENST00000360948	NM_001012338.2	73	atC/atG	2/19	1	2	FACETS	0.223	0.182	0.269	0.223	0.182	0.269	SUBCLONAL	1	TRUE	1	0.530877570395422	2		526	592	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857250	9857250	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	124	556	0	ENST00000330684.3:c.4151C>G	p.Ser1384Trp	p.S1384W	ENST00000330684	NM_001134407.1	1384	tCg/tGg	13/13	1	2	FACETS	0.867	0.788	0.949	0.867	0.788	0.949	CLONAL	1	TRUE	1	0.530877570395422	2		556	539	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842603	68842603	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	195	561	0	ENST00000261769.5:c.539C>A	p.Ser180Tyr	p.S180Y	ENST00000261769	NM_004360.3	180	tCc/tAc	5/16	0.530877570395422	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.530877570395422	1		561	510	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348889	89348889	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	53	953	0	ENST00000301030.4:c.4061C>T	p.Ser1354Leu	p.S1354L	ENST00000301030	NM_001256183.1	1354	tCa/tTa	9/13	0.530877570395422	1	FACETS	0.201	0.17	0.234	0.201	0.17	0.234	SUBCLONAL	1	TRUE	0	0.530877570395422	1		953	731	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	80	773	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.465512947913049	1	FACETS	0.314	0.276	0.354	0.314	0.276	0.354	SUBCLONAL	1	TRUE	0	0.530877570395422	1		773	706	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57569902	57569902	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	24	267	0	ENST00000316660.6:c.82C>T	p.Gln28Ter	p.Q28*	ENST00000316660	NM_021127.2	28	Caa/Taa	2/2	1	2	FACETS	0.267	0.209	0.333	0.267	0.209	0.333	SUBCLONAL	1	TRUE	1	0.530877570395422	2		267	339	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211158	2211158	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	53	950	0	ENST00000398665.3:c.1412C>T	p.Ser471Phe	p.S471F	ENST00000398665	NM_032482.2	471	tCc/tTc	15/28	1	2	FACETS	0.259	0.22	0.301	0.259	0.22	0.301	SUBCLONAL	1	TRUE	1	0.530877570395422	2		950	772	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758823	41758823	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	89	770	0	ENST00000301178.4:c.1877G>C	p.Gly626Ala	p.G626A	ENST00000301178	NM_021913.4	626	gGa/gCa	16/20	0.520898422755017	3	FACETS	0.416	0.367	0.467	0.208	0.183	0.234	SUBCLONAL	1	TRUE	1	0.530877570395422	3		770	1021	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976456	25976456	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	62	369	0	ENST00000435504.4:c.1089G>C	p.Glu363Asp	p.E363D	ENST00000435504		363	gaG/gaC	11/13	1	2	FACETS	0.496	0.429	0.568	0.496	0.429	0.568	SUBCLONAL	1	TRUE	1	0.530877570395422	2		369	471	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022280	26022280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	154	554	0	ENST00000435504.4:c.377G>A	p.Gly126Glu	p.G126E	ENST00000435504		126	gGa/gAa	5/13	1	2	FACETS	0.857	0.786	0.93	0.857	0.786	0.93	CLONAL	1	TRUE	1	0.530877570395422	2		554	677	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249906	39249906	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	35	579	0	ENST00000402219.2:c.1663G>C	p.Asp555His	p.D555H	ENST00000402219	NM_005633.3	555	Gat/Cat	10/23	1	2	FACETS	0.214	0.175	0.259	0.214	0.175	0.259	SUBCLONAL	1	TRUE	1	0.530877570395422	2		579	615	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026263	48026263	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142111387	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	117	369	0	ENST00000234420.5:c.1141G>A	p.Glu381Lys	p.E381K	ENST00000234420	NM_000179.2	381	Gag/Aag	4/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.530877570395422	2		369	409	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026377	48026377	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs762814792	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	30	479	0	ENST00000234420.5:c.1255C>G	p.Gln419Glu	p.Q419E	ENST00000234420	NM_000179.2	419	Cag/Gag	4/10	1	2	FACETS	0.21	0.169	0.258	0.21	0.169	0.258	SUBCLONAL	1	TRUE	1	0.530877570395422	2		479	537	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026927	48026927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	26	386	0	ENST00000234420.5:c.1805C>T	p.Ser602Leu	p.S602L	ENST00000234420	NM_000179.2	602	tCa/tTa	4/10	1	2	FACETS	0.263	0.208	0.326	0.263	0.208	0.326	SUBCLONAL	1	TRUE	1	0.530877570395422	2		386	373	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096642	178096642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	19	308	0	ENST00000397062.3:c.689C>T	p.Ser230Leu	p.S230L	ENST00000397062	NM_006164.4	230	tCa/tTa	5/5	1	2	FACETS	0.202	0.152	0.26	0.202	0.152	0.26	SUBCLONAL	1	TRUE	1	0.530877570395422	2		308	355	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732639	190732639	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1172503363	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	25	387	0	ENST00000441310.2:c.2457G>C	p.Lys819Asn	p.K819N	ENST00000441310	NM_000534.4	819	aaG/aaC	11/13	1	2	FACETS	0.299	0.236	0.372	0.299	0.236	0.372	SUBCLONAL	1	TRUE	1	0.530877570395422	2		387	315	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368470	225368470	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	44	435	0	ENST00000264414.4:c.1276G>C	p.Asp426His	p.D426H	ENST00000264414	NM_003590.4	426	Gat/Cat	9/16	1	2	FACETS	0.372	0.312	0.438	0.372	0.312	0.438	SUBCLONAL	1	TRUE	1	0.530877570395422	2		435	446	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62309528	62309529	+	missense_variant	Missense_Mutation	DNP	AG	AG	CA	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	62	825	1	ENST00000360203.5:c.950_951delinsCA	p.Lys317Thr	p.K317T	ENST00000360203	NM_001283009.1	317	aAG/aCA	11/35	1	2	FACETS	0.263	0.226	0.303	0.263	0.226	0.303	SUBCLONAL	1	TRUE	1	0.530877570395422	2		826	888	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514662	44514662	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	36	568	0	ENST00000291552.4:c.494G>A	p.Arg165Gln	p.R165Q	ENST00000291552	NM_006758.2	165	cGa/cAa	7/8	1	2	FACETS	0.202	0.165	0.244	0.202	0.165	0.244	SUBCLONAL	1	TRUE	1	0.530877570395422	2		568	671	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533795	41533795	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	50	405	0	ENST00000263253.7:c.1760+1G>A		p.X587_splice	ENST00000263253	NM_001429.3	587			0.530877570395422	1	FACETS	0.434	0.37	0.503	0.434	0.37	0.503	SUBCLONAL	1	TRUE	0	0.530877570395422	1		405	319	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536169	41536169	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	49	534	0	ENST00000263253.7:c.1786G>C	p.Asp596His	p.D596H	ENST00000263253	NM_001429.3	596	Gat/Cat	9/31	0.530877570395422	1	FACETS	0.31	0.263	0.362	0.31	0.263	0.362	SUBCLONAL	1	TRUE	0	0.530877570395422	1		534	437	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536244	41536244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	64	446	1	ENST00000263253.7:c.1861G>A	p.Glu621Lys	p.E621K	ENST00000263253	NM_001429.3	621	Gaa/Aaa	9/31	0.530877570395422	1	FACETS	0.384	0.333	0.439	0.384	0.333	0.439	SUBCLONAL	1	TRUE	0	0.530877570395422	1		447	461	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573560	41573560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	39	776	0	ENST00000263253.7:c.5845C>T	p.Gln1949Ter	p.Q1949*	ENST00000263253	NM_001429.3	1949	Caa/Taa	31/31	0.530877570395422	1	FACETS	0.19	0.157	0.227	0.19	0.157	0.227	SUBCLONAL	1	TRUE	0	0.530877570395422	1		776	567	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	25	325	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	1	2	FACETS	0.247	0.194	0.307	0.247	0.194	0.307	SUBCLONAL	1	TRUE	1	0.530877570395422	2		325	382	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	56	940	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	0.244	0.208	0.283	0.244	0.208	0.283	SUBCLONAL	1	TRUE	1	0.530877570395422	2		940	866	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573323	55573323	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	38	429	0	ENST00000288135.5:c.985G>A	p.Glu329Lys	p.E329K	ENST00000288135	NM_000222.2	329	Gaa/Aaa	6/21	1	2	FACETS	0.342	0.283	0.409	0.342	0.283	0.409	SUBCLONAL	1	TRUE	1	0.530877570395422	2		429	418	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535346	66535346	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1180540482	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	176	627	0	ENST00000273854.3:c.115C>G	p.Pro39Ala	p.P39A	ENST00000273854	NM_004439.5	39	Ccc/Gcc	1/18	1	2	FACETS	0.945	0.873	1	0.945	0.873	1	CLONAL	1	TRUE	1	0.530877570395422	2		627	702	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534494	187534494	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs779324710	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	85	333	0	ENST00000441802.2:c.9232G>A	p.Glu3078Lys	p.E3078K	ENST00000441802	NM_005245.3	3078	Gaa/Aaa	13/27	0.157662526553499	3	FACETS	1	0.91	1	0.513	0.456	0.573	INDETERMINATE	1	TRUE	1	0.530877570395422	3		333	395	SUCCESS
APC	324	MSKCC	GRCh37	5	112174929	112174929	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554085199	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	27	227	0	ENST00000257430.4:c.3638C>T	p.Ser1213Leu	p.S1213L	ENST00000257430	NM_000038.5	1213	tCa/tTa	16/16	1	2	FACETS	0.402	0.321	0.494	0.402	0.321	0.494	SUBCLONAL	1	TRUE	1	0.530877570395422	2		227	253	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046349	180046349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	178	644	0	ENST00000261937.6:c.2665G>A	p.Glu889Lys	p.E889K	ENST00000261937	NM_182925.4	889	Gag/Aag	19/30	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.530877570395422	2		644	624	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032045	26032045	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	36	469	0	ENST00000244661.2:c.244G>C	p.Asp82His	p.D82H	ENST00000244661	NM_003537.3	82	Gat/Cat	1/1	1	2	FACETS	0.27	0.222	0.325	0.27	0.222	0.325	SUBCLONAL	1	TRUE	1	0.530877570395422	2		469	502	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631415	117631415	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	107	327	0	ENST00000368508.3:c.6263C>T	p.Ser2088Phe	p.S2088F	ENST00000368508	NM_002944.2	2088	tCc/tTc	40/43	0.530877570395422	1	FACETS	0.848	0.769	0.931	0.848	0.769	0.931	CLONAL	1	TRUE	0	0.530877570395422	1		327	349	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527318	137527318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	32	564	0	ENST00000367739.4:c.328G>A	p.Glu110Lys	p.E110K	ENST00000367739	NM_000416.2	110	Gaa/Aaa	3/7	0.530877570395422	1	FACETS	0.176	0.142	0.214	0.176	0.142	0.214	SUBCLONAL	1	TRUE	0	0.530877570395422	1		564	503	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004355	150004355	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	25	431	0	ENST00000253339.5:c.1870G>T	p.Glu624Ter	p.E624*	ENST00000253339		624	Gaa/Taa	3/7	0.530877570395422	1	FACETS	0.208	0.163	0.259	0.208	0.163	0.259	SUBCLONAL	1	TRUE	0	0.530877570395422	1		431	333	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963963	2963963	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	188	693	0	ENST00000396946.4:c.1844C>G	p.Ser615Cys	p.S615C	ENST00000396946	NM_032415.4	615	tCc/tGc	15/25	1	2	FACETS	0.958	0.888	1	0.958	0.888	1	CLONAL	1	TRUE	1	0.530877570395422	2		693	739	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92244544	92244544	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	91	375	0	ENST00000265734.4:c.891C>G	p.His297Gln	p.H297Q	ENST00000265734	NM_001259.6	297	caC/caG	8/8	1	2	FACETS	0.963	0.862	1	0.963	0.862	1	CLONAL	1	TRUE	1	0.530877570395422	2		375	356	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439637	140439637	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	37	444	0	ENST00000288602.6:c.2102G>C	p.Arg701Thr	p.R701T	ENST00000288602	NM_004333.4	701	aGa/aCa	17/18	1	2	FACETS	0.261	0.215	0.313	0.261	0.215	0.313	SUBCLONAL	1	TRUE	1	0.530877570395422	2		444	534	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873492	151873492	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	73	545	0	ENST00000262189.6:c.9046C>T	p.Gln3016Ter	p.Q3016*	ENST00000262189	NM_170606.2	3016	Caa/Taa	38/59	1	2	FACETS	0.453	0.396	0.514	0.453	0.396	0.514	SUBCLONAL	1	TRUE	1	0.530877570395422	2		545	607	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968147	68968147	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	61	582	0	ENST00000288368.4:c.1176A>C	p.Gln392His	p.Q392H	ENST00000288368	NM_024870.2	392	caA/caC	10/40	1	2	FACETS	0.347	0.299	0.4	0.347	0.299	0.4	SUBCLONAL	1	TRUE	1	0.530877570395422	2		582	662	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5064982	5064982	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	30	320	0	ENST00000381652.3:c.1156G>C	p.Glu386Gln	p.E386Q	ENST00000381652	NM_004972.3	386	Gaa/Caa	9/25	1	2	FACETS	0.329	0.265	0.401	0.329	0.265	0.401	SUBCLONAL	1	TRUE	1	0.530877570395422	2		320	344	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5066705	5066705	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	20	373	0	ENST00000381652.3:c.1242G>C	p.Lys414Asn	p.K414N	ENST00000381652	NM_004972.3	414	aaG/aaC	10/25	1	2	FACETS	0.231	0.176	0.295	0.231	0.176	0.295	SUBCLONAL	1	TRUE	1	0.530877570395422	2		373	326	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518342	8518342	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	26	272	0	ENST00000356435.5:c.1049C>A	p.Pro350His	p.P350H	ENST00000356435		350	cCt/cAt	10/35	1	2	FACETS	0.331	0.262	0.409	0.331	0.262	0.409	SUBCLONAL	1	TRUE	1	0.530877570395422	2		272	296	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229611	98229611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502293	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	40	367	0	ENST00000331920.6:c.2347C>T	p.Arg783Trp	p.R783W	ENST00000331920	NM_000264.3	783	Cgg/Tgg	15/24	1	2	FACETS	0.342	0.284	0.407	0.342	0.284	0.407	SUBCLONAL	1	TRUE	1	0.530877570395422	2		367	440	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325403	1325403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1398846596	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	157	577	0	ENST00000400841.2:c.272G>A	p.Arg91Gln	p.R91Q	ENST00000400841		91	cGa/cAa	3/6	1	1	FACETS	0.626	0.575	0.679	0.626	0.575	0.679	SUBCLONAL	1	TRUE	0	0.530877570395422	1		577	694	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928872	44928872	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs755440519	NA	P-0038551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	29	185	0	ENST00000377967.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000377967	NM_021140.2	658	Cga/Tga	17/29	1	1	FACETS	0.324	0.261	0.394	0.324	0.261	0.394	SUBCLONAL	1	TRUE	0	0.530877570395422	1		185	248	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0038552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	110	701	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.348706977761643	2	FACETS	0.946	0.86	1	0.946	0.86	1	CLONAL	2	TRUE	0	0.350344175866423	2		701	332	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063718	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0038552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	61	237	0	ENST00000412916.2:c.165+2dup		p.X55_splice	ENST00000412916		55			0.350344175866423	2	FACETS	0.973	0.856	1	0.973	0.856	1	CLONAL	2	TRUE	0	0.350344175866423	2		237	179	SUCCESS
ATR	545	MSKCC	GRCh37	3	142218544	142218544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	132	343	0	ENST00000350721.4:c.5305G>A	p.Glu1769Lys	p.E1769K	ENST00000350721	NM_001184.3	1769	Gaa/Aaa	31/47	0.348706977761643	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.350344175866423	2		343	357	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95583975	95583975	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	114	257	0	ENST00000393063.1:c.1493T>G	p.Phe498Cys	p.F498C	ENST00000393063	NM_030621.3	498	tTc/tGc	10/28	0.348706977761643	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.350344175866423	2		257	297	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874923	151874923	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	128	274	0	ENST00000262189.6:c.7615C>T	p.Gln2539Ter	p.Q2539*	ENST00000262189	NM_170606.2	2539	Cag/Tag	38/59	0.350344175866423	5	FACETS	0.953	0.872	1	0.953	0.872	1	CLONAL	3	TRUE	2	0.350344175866423	5		274	390	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878118	151878118	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	133	479	0	ENST00000262189.6:c.6827del	p.Pro2276LeufsTer29	p.P2276Lfs*29	ENST00000262189	NM_170606.2	2276	cCt/ct	36/59	0.350344175866423	5	FACETS	1	0.95	1	0.707	0.645	0.772	CLONAL	2	TRUE	2	0.350344175866423	5		479	546	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552144	29552144	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	59	213	1	ENST00000356175.3:c.1882del	p.Tyr628ThrfsTer3	p.Y628Tfs*3	ENST00000356175	NM_000267.3	626	cTt/ct	17/57	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.5	2		214	234	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	129	563	4	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.863	0.785	0.944	0.863	0.785	0.944	CLONAL	1	TRUE	1	0.5	2		567	598	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	58	345	3	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.768	0.665	0.879	0.768	0.665	0.879	SUBCLONAL	1	TRUE	1	0.5	2		348	302	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	85	454	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.831	0.739	0.929	0.831	0.739	0.929	CLONAL	1	TRUE	1	0.5	2		454	409	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934752	49934752	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777611015	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	154	719	1	ENST00000296474.3:c.2144G>A	p.Arg715Gln	p.R715Q	ENST00000296474	NM_002447.2	715	cGg/cAg	7/20	1	2	FACETS	0.932	0.856	1	0.932	0.856	1	CLONAL	1	TRUE	1	0.5	2		720	661	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403254	213403254	+	frameshift_variant,start_lost,start_retained_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	66	405	1	ENST00000342788.4:c.1del	p.Met1?	p.M1?	ENST00000342788	NM_005235.2	1	Atg/tg	1/28	1	2	FACETS	0.731	0.638	0.831	0.731	0.638	0.831	SUBCLONAL	1	TRUE	1	0.5	2		406	361	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	96	377	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.5	2		377	376	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188513	11188513	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	92	428	0	ENST00000361445.4:c.5908del	p.Gln1970ArgfsTer7	p.Q1970Rfs*7	ENST00000361445	NM_004958.3	1970	Cag/ag	42/58	1	2	FACETS	0.856	0.765	0.952	0.856	0.765	0.952	CLONAL	1	TRUE	1	0.5	2		428	430	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190747	11190747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759603938	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	148	711	0	ENST00000361445.4:c.5452C>T	p.Arg1818Cys	p.R1818C	ENST00000361445	NM_004958.3	1818	Cgt/Tgt	39/58	1	2	FACETS	0.885	0.81	0.962	0.885	0.81	0.962	CLONAL	1	TRUE	1	0.5	2		711	669	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259654	11259654	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1205998733	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	123	504	0	ENST00000361445.4:c.4051G>A	p.Ala1351Thr	p.A1351T	ENST00000361445	NM_004958.3	1351	Gct/Act	27/58	1	2	FACETS	0.928	0.843	1	0.928	0.843	1	CLONAL	1	TRUE	1	0.5	2		504	530	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256367	16256367	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	125	525	0	ENST00000375759.3:c.3632T>C	p.Val1211Ala	p.V1211A	ENST00000375759	NM_015001.2	1211	gTa/gCa	11/15	1	2	FACETS	0.898	0.816	0.983	0.898	0.816	0.983	CLONAL	1	TRUE	1	0.5	2		525	557	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023498	27023498	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	116	473	0	ENST00000324856.7:c.604T>A	p.Ser202Thr	p.S202T	ENST00000324856	NM_006015.4	202	Tct/Act	1/20	1	2	FACETS	0.928	0.841	1	0.928	0.841	1	CLONAL	1	TRUE	1	0.5	2		473	500	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101057	27101057	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	172	707	0	ENST00000324856.7:c.4339C>T	p.Pro1447Ser	p.P1447S	ENST00000324856	NM_006015.4	1447	Cca/Tca	18/20	1	2	FACETS	0.966	0.892	1	0.966	0.892	1	CLONAL	1	TRUE	1	0.5	2		707	712	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598846	28598846	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	182	793	0	ENST00000253063.3:c.406T>C	p.Phe136Leu	p.F136L	ENST00000253063	NM_031459.4	136	Ttt/Ctt	4/10	1	2	FACETS	0.953	0.881	1	0.953	0.881	1	CLONAL	1	TRUE	1	0.5	2		793	764	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261305	115261305	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	128	443	0	ENST00000438362.2:c.2416A>G	p.Ile806Val	p.I806V	ENST00000438362	NM_001242891.1	806	Atc/Gtc	19/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.5	2		443	496	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843709	156843709	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	202	946	0	ENST00000524377.1:c.1135A>C	p.Met379Leu	p.M379L	ENST00000524377	NM_002529.3	379	Atg/Ctg	8/17	1	2	FACETS	0.92	0.854	0.989	0.92	0.854	0.989	CLONAL	1	TRUE	1	0.5	2		946	878	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982424	201982424	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	74	764	0	ENST00000359651.3:c.803A>G	p.His268Arg	p.H268R	ENST00000359651		268	cAc/cGc	6/8	1	2	FACETS	0.408	0.357	0.464	0.408	0.357	0.464	SUBCLONAL	1	TRUE	1	0.5	2		764	725	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226568891	226568891	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs757155449	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	33	386	0	ENST00000366794.5:c.1178T>C	p.Met393Thr	p.M393T	ENST00000366794	NM_001618.3	393	aTg/aCg	9/23	1	2	FACETS	0.32	0.261	0.388	0.32	0.261	0.388	SUBCLONAL	1	TRUE	1	0.5	2		386	412	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243778402	243778402	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	50	316	0	ENST00000263826.5:c.623del	p.Leu208Ter	p.L208*	ENST00000263826	NM_005465.4	208	tTa/ta	6/13	1	2	FACETS	0.948	0.814	1	0.948	0.814	1	CLONAL	1	TRUE	1	0.5	2		316	211	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850705	63850705	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs201178069	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	76	377	0	ENST00000279873.7:c.1489del	p.Ile497Ter	p.I497*	ENST00000279873	NM_032199.2	495	Aaa/aa	10/10	1	2	FACETS	0.77	0.679	0.866	0.77	0.679	0.866	SUBCLONAL	1	TRUE	1	0.5	2		377	395	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404669	70404669	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564988139	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	32	550	0	ENST00000373644.4:c.2183C>T	p.Ala728Val	p.A728V	ENST00000373644	NM_030625.2	728	gCt/gTt	4/12	1	2	FACETS	0.201	0.162	0.245	0.201	0.162	0.245	SUBCLONAL	1	TRUE	1	0.5	2		550	637	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925318	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	97	427	0	ENST00000543371.1:c.1402_1403del	p.Lys468ValfsTer8	p.K468Vfs*8	ENST00000543371	NM_001198531.1	465	agAAaa/agaa	14/14	1	2	FACETS	0.87	0.78	0.965	0.87	0.78	0.965	CLONAL	1	TRUE	1	0.5	2		427	446	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138915	64138915	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	109	511	0	ENST00000334205.4:c.2287del	p.Arg763AlafsTer21	p.R763Afs*21	ENST00000334205	NM_003942.2	761	gCc/gc	17/17	1	2	FACETS	0.768	0.691	0.848	0.768	0.691	0.848	SUBCLONAL	1	TRUE	1	0.5	2		511	568	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	70	686	6	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	1	2	FACETS	0.437	0.381	0.498	0.437	0.381	0.498	SUBCLONAL	1	TRUE	1	0.5	2		692	641	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945661	71945661	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	121	409	0	ENST00000298229.2:c.2415+2T>C		p.X805_splice	ENST00000298229	NM_001567.3	805			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.5	2		409	449	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988074	85988074	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747972868	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	54	243	0	ENST00000263360.6:c.1019T>C	p.Ile340Thr	p.I340T	ENST00000263360	NM_003797.3	340	aTa/aCa	10/12	1	2	FACETS	0.878	0.758	1	0.878	0.758	1	CLONAL	1	TRUE	1	0.5	2		243	246	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343597	118343597	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	108	399	0	ENST00000534358.1:c.1723G>A	p.Ala575Thr	p.A575T	ENST00000534358	NM_005933.3	575	Gcc/Acc	3/36	1	2	FACETS	0.96	0.867	1	0.96	0.867	1	CLONAL	1	TRUE	1	0.5	2		399	450	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	117	447	3	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.862	0.78	0.947	0.862	0.78	0.947	CLONAL	1	TRUE	1	0.5	2		450	543	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427234	49427234	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	166	768	0	ENST00000301067.7:c.11254G>A	p.Ala3752Thr	p.A3752T	ENST00000301067	NM_003482.3	3752	Gca/Aca	39/54	1	2	FACETS	0.957	0.881	1	0.957	0.881	1	CLONAL	1	TRUE	1	0.5	2		768	694	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445512	49445512	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301516107	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	188	857	0	ENST00000301067.7:c.1954C>T	p.Arg652Cys	p.R652C	ENST00000301067	NM_003482.3	652	Cgc/Tgc	10/54	1	2	FACETS	0.936	0.867	1	0.936	0.867	1	CLONAL	1	TRUE	1	0.5	2		857	803	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784098	120784098	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	192	907	2	ENST00000257552.2:c.887del	p.Pro296LeufsTer57	p.P296Lfs*57	ENST00000257552	NM_002442.3	296	cCt/ct	13/15	1	2	FACETS	0.949	0.88	1	0.949	0.88	1	CLONAL	1	TRUE	1	0.5	2		909	809	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	150	803	21	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.783	0.717	0.853	0.783	0.717	0.853	SUBCLONAL	1	TRUE	1	0.5	2		824	766	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201368	133201368	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	147	763	0	ENST00000320574.5:c.6776G>T	p.Arg2259Leu	p.R2259L	ENST00000320574	NM_006231.2	2259	cGg/cTg	49/49	1	2	FACETS	0.862	0.789	0.938	0.862	0.789	0.938	CLONAL	1	TRUE	1	0.5	2		763	682	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245024	133245024	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs752846614	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	179	931	8	ENST00000320574.5:c.2091del	p.Leu698CysfsTer94	p.L698Cfs*94	ENST00000320574	NM_006231.2	697	ccC/cc	19/49	1	2	FACETS	0.94	0.868	1	0.94	0.868	1	CLONAL	1	TRUE	1	0.5	2		939	762	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012432	29012432	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	106	499	0	ENST00000282397.4:c.439C>T	p.His147Tyr	p.H147Y	ENST00000282397	NM_002019.4	147	Cac/Tac	4/30	1	2	FACETS	0.869	0.783	0.959	0.869	0.783	0.959	CLONAL	1	TRUE	1	0.5	2		499	488	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041262	29041262	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	82	348	0	ENST00000282397.4:c.166del	p.Glu56LysfsTer12	p.E56Kfs*12	ENST00000282397	NM_002019.4	56	Gaa/aa	3/30	1	2	FACETS	0.865	0.768	0.968	0.865	0.768	0.968	CLONAL	1	TRUE	1	0.5	2		348	379	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915089	32915090	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	rs80359607	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	90	496	0	ENST00000380152.3:c.6600_6601del	p.Ser2201Ter	p.S2201*	ENST00000380152		2199	acTTtt/actt	11/27	1	2	FACETS	0.874	0.78	0.973	0.874	0.78	0.973	CLONAL	1	TRUE	1	0.5	2		496	412	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	80	261	7	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	1	2	FACETS	0.988	0.877	1	0.988	0.877	1	CLONAL	1	TRUE	1	0.5	2		268	324	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066844	30066844	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	109	514	0	ENST00000331968.5:c.2287T>C	p.Ser763Pro	p.S763P	ENST00000331968	NM_002742.2	763	Tct/Cct	16/18	1	2	FACETS	0.832	0.75	0.918	0.832	0.75	0.918	CLONAL	1	TRUE	1	0.5	2		514	524	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066865	30066865	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	111	542	0	ENST00000331968.5:c.2266A>T	p.Arg756Trp	p.R756W	ENST00000331968	NM_002742.2	756	Agg/Tgg	16/18	1	2	FACETS	0.833	0.752	0.918	0.833	0.752	0.918	CLONAL	1	TRUE	1	0.5	2		542	533	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560242	95560242	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	15	289	0	ENST00000393063.1:c.5347C>T	p.Gln1783Ter	p.Q1783*	ENST00000393063	NM_030621.3	1783	Caa/Taa	25/28	1	2	FACETS	0.207	0.151	0.274	0.207	0.151	0.274	SUBCLONAL	1	TRUE	1	0.5	2		289	290	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714075	43714075	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs773155828	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	177	686	2	ENST00000382044.4:c.4078C>T	p.Arg1360Ter	p.R1360*	ENST00000382044	NM_001141980.1	1360	Cga/Tga	19/28	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.5	2		688	673	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003747	45003747	+	start_lost	Translation_Start_Site	SNP	G	G	T	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	106	434	0	ENST00000558401.1:c.3G>T	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	atG/atT	1/4	1	2	FACETS	0.893	0.804	0.985	0.893	0.804	0.985	CLONAL	1	TRUE	1	0.5	2		434	475	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	117	410	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.878	0.795	0.965	0.878	0.795	0.965	CLONAL	1	TRUE	1	0.5	2		410	533	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007896	45007897	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	88	299	0	ENST00000558401.1:c.346+1dup		p.W115fs	ENST00000558401	NM_004048.2	115	tgg/tGgg	2/4	1	2	FACETS	0.929	0.829	1	0.929	0.829	1	CLONAL	1	TRUE	1	0.5	2		299	379	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347983	347983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760961378	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	177	772	3	ENST00000262320.3:c.1523del	p.Gly508ValfsTer197	p.G508Vfs*197	ENST00000262320	NM_003502.3	508	gGt/gt	6/11	1	2	FACETS	0.925	0.855	0.999	0.925	0.855	0.999	CLONAL	1	TRUE	1	0.5	2		775	765	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104393	2104393	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	164	700	0	ENST00000219476.3:c.433G>C	p.Ala145Pro	p.A145P	ENST00000219476	NM_000548.3	145	Gcc/Ccc	5/42	1	2	FACETS	0.936	0.861	1	0.936	0.861	1	CLONAL	1	TRUE	1	0.5	2		700	701	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351327	89351327	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	197	914	0	ENST00000301030.4:c.1623G>T	p.Gln541His	p.Q541H	ENST00000301030	NM_001256183.1	541	caG/caT	9/13	1	2	FACETS	0.927	0.86	0.997	0.927	0.86	0.997	CLONAL	1	TRUE	1	0.5	2		914	850	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965000	15965002	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	48	507	1	ENST00000268712.3:c.5594_5596del	p.Gln1865del	p.Q1865del	ENST00000268712	NM_006311.3	1865	cAGCta/cta	37/46	1	2	FACETS	0.364	0.307	0.426	0.364	0.307	0.426	SUBCLONAL	1	TRUE	1	0.5	2		508	528	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	29	507	2	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	0.21	0.168	0.258	0.21	0.168	0.258	SUBCLONAL	1	TRUE	1	0.5	2		509	552	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885980	59885980	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	113	420	0	ENST00000259008.2:c.766A>T	p.Ile256Phe	p.I256F	ENST00000259008	NM_032043.2	256	Att/Ttt	7/20	1	2	FACETS	0.906	0.819	0.997	0.906	0.819	0.997	CLONAL	1	TRUE	1	0.5	2		420	499	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936338	78936338	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1212387005	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	134	717	0	ENST00000306801.3:c.3770C>T	p.Thr1257Met	p.T1257M	ENST00000306801	NM_020761.2	1257	aCg/aTg	32/34	1	2	FACETS	0.848	0.773	0.927	0.848	0.773	0.927	CLONAL	1	TRUE	1	0.5	2		717	632	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348561	56348561	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	66	252	0	ENST00000348428.3:c.374del	p.Pro125GlnfsTer3	p.P125Qfs*3	ENST00000348428	NM_006785.3	123	agC/ag	2/17	1	2	FACETS	0.91	0.797	1	0.91	0.797	1	CLONAL	1	TRUE	1	0.5	2		252	290	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222058	2222058	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	165	798	0	ENST00000398665.3:c.2890A>G	p.Thr964Ala	p.T964A	ENST00000398665	NM_032482.2	964	Acc/Gcc	24/28	1	2	FACETS	0.865	0.796	0.937	0.865	0.796	0.937	CLONAL	1	TRUE	1	0.5	2		798	763	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210754	5210754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768674983	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	158	693	0	ENST00000357368.4:c.5297G>A	p.Arg1766His	p.R1766H	ENST00000357368	NM_002850.3	1766	cGc/cAc	34/38	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.5	2		693	616	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	17	171	1	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	0.378	0.283	0.489	0.378	0.283	0.489	SUBCLONAL	1	TRUE	1	0.5	2		172	180	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095029	11095029	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	193	847	0	ENST00000358026.2:c.202A>G	p.Asn68Asp	p.N68D	ENST00000358026	NM_001128849.1	68	Aac/Gac	2/36	1	2	FACETS	0.891	0.826	0.96	0.891	0.826	0.96	CLONAL	1	TRUE	1	0.5	2		847	866	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627694	14627694	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	147	680	0	ENST00000254322.2:c.376G>A	p.Asp126Asn	p.D126N	ENST00000254322	NM_006145.1	126	Gac/Aac	2/3	1	2	FACETS	0.913	0.836	0.993	0.913	0.836	0.993	CLONAL	1	TRUE	1	0.5	2		680	644	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296358	15296358	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	91	821	0	ENST00000263388.2:c.2084del	p.Pro695ArgfsTer165	p.P695Rfs*165	ENST00000263388	NM_000435.2	695	cCg/cg	13/33	1	2	FACETS	0.467	0.414	0.523	0.467	0.414	0.523	SUBCLONAL	1	TRUE	1	0.5	2		821	780	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	181	638	0	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.792	0.731	0.856	0.792	0.731	0.856	SUBCLONAL	1	TRUE	1	0.5	2		638	914	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	184	777	2	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	1	2	FACETS	0.85	0.785	0.917	0.85	0.785	0.917	CLONAL	1	TRUE	1	0.5	2		779	866	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868346	45868346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776313922	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	187	850	0	ENST00000391945.4:c.431C>T	p.Ala144Val	p.A144V	ENST00000391945	NM_000400.3	144	gCg/gTg	6/23	1	2	FACETS	0.948	0.877	1	0.948	0.877	1	CLONAL	1	TRUE	1	0.5	2		850	789	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47735772	47735772	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	143	613	0	ENST00000449228.1:c.88G>A	p.Gly30Ser	p.G30S	ENST00000449228	NM_001127240.2	30	Ggc/Agc	1/4	1	2	FACETS	0.85	0.777	0.926	0.85	0.777	0.926	CLONAL	1	TRUE	1	0.5	2		613	673	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716302	52716302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	142	630	0	ENST00000322088.6:c.746G>A	p.Arg249His	p.R249H	ENST00000322088	NM_014225.5	249	cGc/cAc	6/15	1	2	FACETS	0.936	0.856	1	0.936	0.856	1	CLONAL	1	TRUE	1	0.5	2		630	607	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022301	26022301	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs578025365	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	124	497	0	ENST00000435504.4:c.356A>G	p.Asp119Gly	p.D119G	ENST00000435504		119	gAt/gGt	5/13	1	2	FACETS	0.804	0.729	0.882	0.804	0.729	0.882	CLONAL	1	TRUE	1	0.5	2		497	617	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143336	30143336	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	149	650	0	ENST00000389048.3:c.190T>C	p.Phe64Leu	p.F64L	ENST00000389048	NM_004304.4	64	Ttc/Ctc	1/29	1	2	FACETS	0.939	0.86	1	0.939	0.86	1	CLONAL	1	TRUE	1	0.5	2		650	635	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606178	47606181	+	frameshift_variant	Frame_Shift_Del	DEL	TTAT	TTAT	-	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	67	316	0	ENST00000263735.4:c.644_647del	p.Tyr215LeufsTer18	p.Y215Lfs*18	ENST00000263735	NM_002354.2	214	taTTAT/ta	6/9	1	2	FACETS	0.838	0.733	0.948	0.838	0.733	0.948	CLONAL	1	TRUE	1	0.5	2		316	320	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99179993	99179993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	155	701	0	ENST00000074304.5:c.1936G>A	p.Asp646Asn	p.D646N	ENST00000074304	NM_001134224.1	646	Gac/Aac	19/26	1	2	FACETS	0.96	0.882	1	0.96	0.882	1	CLONAL	1	TRUE	1	0.5	2		701	646	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131193	202131193	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	64	296	0	ENST00000358485.4:c.161T>G	p.Leu54Arg	p.L54R	ENST00000358485	NM_001080125.1	54	cTc/cGc	2/9	1	2	FACETS	0.839	0.733	0.953	0.839	0.733	0.953	CLONAL	1	TRUE	1	0.5	2		296	305	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812292	212812292	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778048381	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	95	268	0	ENST00000342788.4:c.284G>A	p.Arg95His	p.R95H	ENST00000342788	NM_005235.2	95	cGt/cAt	3/28	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.5	2		268	328	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437223	220437223	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	171	901	0	ENST00000243786.2:c.132del	p.Ala45ArgfsTer2	p.A45Rfs*2	ENST00000243786	NM_002191.3	43	Ccc/cc	1/2	1	2	FACETS	0.861	0.794	0.932	0.861	0.794	0.932	CLONAL	1	TRUE	1	0.5	2		901	794	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775998497	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	111	528	0	ENST00000373198.4:c.3281C>T	p.Pro1094Leu	p.P1094L	ENST00000373198	NM_133170.3	1094	cCg/cTg	24/32	1	2	FACETS	0.912	0.824	1	0.912	0.824	1	CLONAL	1	TRUE	1	0.5	2		528	487	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42842590	42842590	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs771443342	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	151	644	1	ENST00000398585.3:c.1267del	p.Ala423ProfsTer12	p.A423Pfs*12	ENST00000398585	NM_001135099.1	423	Gcc/cc	11/14	1	2	FACETS	0.904	0.829	0.982	0.904	0.829	0.982	CLONAL	1	TRUE	1	0.5	2		645	668	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573608	41573608	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	179	853	0	ENST00000263253.7:c.5893A>G	p.Met1965Val	p.M1965V	ENST00000263253	NM_001429.3	1965	Atg/Gtg	31/31	1	2	FACETS	0.988	0.913	1	0.988	0.913	1	CLONAL	1	TRUE	1	0.5	2		853	725	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	185	332	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.892	0.834	0.95	1	0.993	1	CLONAL	2	TRUE	1	0.5	2		332	415	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090432	37090432	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	84	505	0	ENST00000231790.2:c.2027T>A	p.Leu676His	p.L676H	ENST00000231790	NM_000249.3	676	cTc/cAc	18/19	1	2	FACETS	0.683	0.605	0.766	0.683	0.605	0.766	SUBCLONAL	1	TRUE	1	0.5	2		505	492	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180365	38180365	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	52	818	0	ENST00000396334.3:c.213C>G	p.Tyr71Ter	p.Y71*	ENST00000396334	NM_002468.4	71	taC/taG	1/5	1	2	FACETS	0.261	0.221	0.304	0.261	0.221	0.304	SUBCLONAL	1	TRUE	1	0.5	2		818	798	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597387	52597389	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	113	541	0	ENST00000394830.3:c.3921_3923del	p.Glu1307del	p.E1307del	ENST00000394830	NM_018313.4	1307	gaAGAt/gat	25/30	1	2	FACETS	0.921	0.833	1	0.921	0.833	1	CLONAL	1	TRUE	1	0.5	2		541	491	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52649393	52649393	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	129	543	0	ENST00000394830.3:c.1898A>G	p.Asp633Gly	p.D633G	ENST00000394830	NM_018313.4	633	gAc/gGc	16/30	1	2	FACETS	0.828	0.753	0.907	0.828	0.753	0.907	CLONAL	1	TRUE	1	0.5	2		543	623	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52663007	52663007	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs758971781	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	55	268	0	ENST00000394830.3:c.1346A>G	p.Glu449Gly	p.E449G	ENST00000394830	NM_018313.4	449	gAg/gGg	13/30	1	2	FACETS	0.821	0.708	0.942	0.821	0.708	0.942	CLONAL	1	TRUE	1	0.5	2		268	268	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682400	52682400	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	64	266	0	ENST00000394830.3:c.773del	p.Asn258MetfsTer25	p.N258Mfs*25	ENST00000394830	NM_018313.4	258	aAt/at	8/30	1	2	FACETS	0.828	0.723	0.941	0.828	0.723	0.941	CLONAL	1	TRUE	1	0.5	2		266	309	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502404	186502405	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	80	355	0	ENST00000323963.5:c.131_132del	p.Leu44ProfsTer10	p.L44Pfs*10	ENST00000323963		43	TCt/t	3/11	1	2	FACETS	0.81	0.717	0.909	0.81	0.717	0.909	CLONAL	1	TRUE	1	0.5	2		355	395	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1962801	1962801	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772470710	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	108	481	0	ENST00000382891.5:c.3295G>A	p.Glu1099Lys	p.E1099K	ENST00000382891	NM_133335.3	1099	Gag/Aag	18/22	1	2	FACETS	0.828	0.746	0.914	0.828	0.746	0.914	CLONAL	1	TRUE	1	0.5	2		481	522	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	105	418	1	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.961	0.867	1	0.961	0.867	1	CLONAL	1	TRUE	1	0.5	2		419	437	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521091	187521091	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	107	435	0	ENST00000441802.2:c.12064T>G	p.Cys4022Gly	p.C4022G	ENST00000441802	NM_005245.3	4022	Tgc/Ggc	22/27	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.5	2		435	415	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630605	187630605	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	128	560	0	ENST00000441802.2:c.377del	p.Asn126IlefsTer20	p.N126Ifs*20	ENST00000441802	NM_005245.3	126	aAt/at	2/27	1	2	FACETS	0.798	0.725	0.874	0.798	0.725	0.874	SUBCLONAL	1	TRUE	1	0.5	2		560	642	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264618	1264618	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	137	757	0	ENST00000310581.5:c.2744del	p.Gly915ValfsTer66	p.G915Vfs*66	ENST00000310581	NM_198253.2	915	gGt/gt	11/16	0.3	2	FACETS	0.764	0.696	0.836			1	SUBCLONAL	1	TRUE	NA	0.5	2		757	717	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161240	56161240	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	73	371	1	ENST00000399503.3:c.1109C>A	p.Pro370His	p.P370H	ENST00000399503	NM_005921.1	370	cCt/cAt	5/20	1	2	FACETS	0.766	0.674	0.865	0.766	0.674	0.865	SUBCLONAL	1	TRUE	1	0.5	2		372	381	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176582	56176582	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1337909159	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	109	346	0	ENST00000399503.3:c.2132A>G	p.Lys711Arg	p.K711R	ENST00000399503	NM_005921.1	711	aAa/aGa	12/20	1	2	FACETS	0.954	0.862	1	0.954	0.862	1	CLONAL	1	TRUE	1	0.5	2		346	457	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79966113	79966114	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	83	357	0	ENST00000265081.6:c.781dup	p.Glu261GlyfsTer43	p.E261Gfs*43	ENST00000265081	NM_002439.4	259	-/G	4/24	1	2	FACETS	0.843	0.748	0.943	0.843	0.748	0.943	CLONAL	1	TRUE	1	0.5	2		357	394	SUCCESS
APC	324	MSKCC	GRCh37	5	112175969	112175970	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1114167552	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	41	259	0	ENST00000257430.4:c.4682dup	p.Asp1562GlyfsTer5	p.D1562Gfs*5	ENST00000257430	NM_000038.5	1560	gaa/gAaa	16/16	1	2	FACETS	0.638	0.535	0.751	0.638	0.535	0.751	SUBCLONAL	1	TRUE	1	0.5	2		259	257	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	151	768	6	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	1	2	FACETS	0.845	0.774	0.919	0.845	0.774	0.919	CLONAL	1	TRUE	1	0.5	2		774	715	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681766	30681766	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	149	604	0	ENST00000376406.3:c.331del	p.Val111Ter	p.V111*	ENST00000376406	NM_014641.2	111	Gtg/tg	3/15	1	2	FACETS	0.979	0.898	1	0.979	0.898	1	CLONAL	1	TRUE	1	0.5	2		604	609	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166275	32166275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs967436228	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	150	682	0	ENST00000375023.3:c.4679C>T	p.Ala1560Val	p.A1560V	ENST00000375023	NM_004557.3	1560	gCg/gTg	26/30	1	2	FACETS	0.882	0.809	0.959	0.882	0.809	0.959	CLONAL	1	TRUE	1	0.5	2		682	680	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	168	821	2	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	1	2	FACETS	0.842	0.775	0.912	0.842	0.775	0.912	CLONAL	1	TRUE	1	0.5	2		823	798	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109415236	109415236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	171	620	0	ENST00000436639.2:c.41G>A	p.Cys14Tyr	p.C14Y	ENST00000436639	NM_014454.2	14	tGc/tAc	1/10	1	2	FACETS	0.911	0.84	0.985	0.911	0.84	0.985	CLONAL	1	TRUE	1	0.5	2		620	751	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706922	117706922	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	105	440	0	ENST00000368508.3:c.2228C>A	p.Pro743His	p.P743H	ENST00000368508	NM_002944.2	743	cCc/cAc	15/43	1	2	FACETS	0.87	0.783	0.961	0.87	0.783	0.961	CLONAL	1	TRUE	1	0.5	2		440	483	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	133	693	4	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.801	0.729	0.876	0.801	0.729	0.876	CLONAL	1	TRUE	1	0.5	2		697	664	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13949264	13949264	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	61	244	0	ENST00000405192.2:c.864del	p.Lys288AsnfsTer32	p.K288Nfs*32	ENST00000405192	NM_001163147.1	288	aaA/aa	9/12	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.5	2		244	243	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467637	50467637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1262982300	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	86	406	2	ENST00000331340.3:c.872C>T	p.Thr291Met	p.T291M	ENST00000331340	NM_006060.4	291	aCg/aTg	8/8	1	2	FACETS	0.835	0.743	0.932	0.835	0.743	0.932	CLONAL	1	TRUE	1	0.5	2		408	412	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482926	140482927	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs777474487	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	88	520	0	ENST00000288602.6:c.1208dup	p.Ala404CysfsTer9	p.A404Cfs*9	ENST00000288602	NM_004333.4	403	cct/ccCt	10/18	1	2	FACETS	0.605	0.537	0.677	0.605	0.537	0.677	SUBCLONAL	1	TRUE	1	0.5	2		520	582	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851177	151851177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141966811	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	75	306	0	ENST00000262189.6:c.12194C>T	p.Ala4065Val	p.A4065V	ENST00000262189	NM_170606.2	4065	gCg/gTg	48/59	1	2	FACETS	0.89	0.786	1	0.89	0.786	1	CLONAL	1	TRUE	1	0.5	2		306	337	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370885	55370885	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	126	639	0	ENST00000297316.4:c.187A>G	p.Lys63Glu	p.K63E	ENST00000297316	NM_022454.3	63	Aag/Gag	1/2	1	2	FACETS	0.939	0.854	1	0.939	0.854	1	CLONAL	1	TRUE	1	0.5	2		639	537	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	67	258	3	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	1	2	FACETS	0.835	0.731	0.945	0.835	0.731	0.945	CLONAL	1	TRUE	1	0.5	2		261	321	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971196	21971198	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	89	357	0	ENST00000304494.5:c.160_162del	p.Met54del	p.M54del	ENST00000304494	NM_000077.4	54	ATG/-	2/3	1	2	FACETS	0.811	0.723	0.904	0.811	0.723	0.904	CLONAL	1	TRUE	1	0.5	2		357	439	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231257	98231257	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1270892737	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	169	657	0	ENST00000331920.6:c.2026T>C	p.Tyr676His	p.Y676H	ENST00000331920	NM_000264.3	676	Tac/Cac	14/24	1	2	FACETS	0.944	0.87	1	0.944	0.87	1	CLONAL	1	TRUE	1	0.5	2		657	716	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912128	127912128	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	70	309	0	ENST00000373547.4:c.742T>C	p.Phe248Leu	p.F248L	ENST00000373547	NM_002721.4	248	Ttt/Ctt	7/7	1	2	FACETS	0.946	0.833	1	0.946	0.833	1	CLONAL	1	TRUE	1	0.5	2		309	296	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028857	47028857	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	124	682	1	ENST00000377604.3:c.161A>G	p.Lys54Arg	p.K54R	ENST00000377604	NM_001204468.1	54	aAg/aGg	3/24	1	2	FACETS	0.768	0.696	0.843	0.768	0.696	0.843	SUBCLONAL	1	TRUE	1	0.5	2		683	646	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554344	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	180	843	0	ENST00000220592.5:c.1807G>C	p.Ala603Pro	p.A603P	ENST00000220592	NM_012154.3	603	Gcc/Ccc	14/19	1	2	FACETS	0.839	0.774	0.906	0.839	0.774	0.906	CLONAL	1	TRUE	1	0.5	2		843	858	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026450	6026450	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	21	78	0	ENST00000265849.7:c.1946G>T	p.Arg649Met	p.R649M	ENST00000265849	NM_000535.5	649	aGg/aTg	11/15	1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	1	0.5	2		78	77	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15833927	15833927	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	10	40	0	ENST00000307771.7:c.685G>A	p.Glu229Lys	p.E229K	ENST00000307771	NM_005089.3	229	Gag/Aag	8/11	1	2	FACETS	1	0.842	1	1	0.842	1	CLONAL	1	TRUE	1	0.5	2		40	30	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554343	141554344	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	169	843	0	ENST00000220592.5:c.1807_1808insA	p.Ala603AspfsTer71	p.A603Dfs*71	ENST00000220592	NM_012154.3	603	gcc/gAcc	14/19	1	2	FACETS	0.788	0.725	0.854	0.788	0.725	0.854	SUBCLONAL	1	TRUE	1	0.5	2		843	858	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0038555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	38	426	1	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	1	2	FACETS	0.957	0.79	1	0.957	0.79	1	CLONAL	1	TRUE	1	0.14	2		427	567	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578204	7578204	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520001	NA	P-0038555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	24	933	0	ENST00000269305.4:c.645T>G	p.Ser215Arg	p.S215R	ENST00000269305	NM_001126112.2	215	agT/agG	6/11	1	2	FACETS	0.491	0.383	0.617	0.491	0.383	0.617	SUBCLONAL	1	TRUE	1	0.14	2		933	698	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380262	25380262	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	39	439	0	ENST00000311936.3:c.196G>T	p.Ala66Ser	p.A66S	ENST00000311936	NM_004985.3	66	Gca/Tca	3/5	1	2	FACETS	0.977	0.809	1	0.977	0.809	1	CLONAL	1	TRUE	1	0.14	2		439	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0038556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	284	647	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.306509124159008	2	FACETS	0.835	0.789	0.883	0.835	0.789	0.883	CLONAL	2	TRUE	0	0.440896437471614	2		647	771	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279573	123279573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1461081253	NA	P-0038556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	201	630	0	ENST00000358487.5:c.859C>T	p.His287Tyr	p.H287Y	ENST00000358487	NM_000141.4	287	Cac/Tac	7/18	0.328478717527138	3	FACETS	1	0.988	1	0.65	0.603	0.698	CLONAL	1	TRUE	1	0.440896437471614	3		630	856	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343547	118343547	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	83	343	0	ENST00000534358.1:c.1673C>A	p.Ser558Tyr	p.S558Y	ENST00000534358	NM_005933.3	558	tCc/tAc	3/36	1	2	FACETS	0.827	0.733	0.928	0.827	0.733	0.928	CLONAL	1	TRUE	1	0.440896437471614	2		343	455	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219414	133219414	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	435	697	0	ENST00000320574.5:c.4720G>T	p.Ala1574Ser	p.A1574S	ENST00000320574	NM_006231.2	1574	Gcc/Tcc	36/49	0.351231253996188	5	FACETS	1	0.993	1	0.806	0.768	0.844	CLONAL	2	TRUE	2	0.440896437471614	5		697	1356	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984532	72984532	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	178	666	1	ENST00000268489.5:c.3052A>G	p.Ile1018Val	p.I1018V	ENST00000268489	NM_006885.3	1018	Atc/Gtc	3/10	0.328478717527138	3	FACETS	0.896	0.825	0.97	0.448	0.412	0.485	CLONAL	1	TRUE	1	0.440896437471614	3		667	1100	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119034	3119034	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	114	651	0	ENST00000078429.4:c.718G>C	p.Val240Leu	p.V240L	ENST00000078429	NM_002067.2	240	Gtg/Ctg	5/7	0.317835314228645	4	FACETS	0.751	0.675	0.832	0.376	0.337	0.416	SUBCLONAL	1	TRUE	2	0.440896437471614	4		651	992	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599884	10599884	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	338	735	0	ENST00000171111.5:c.1692del	p.Arg565GlufsTer30	p.R565Efs*30	ENST00000171111	NM_203500.1	564	ggG/gg	5/6	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	1	TRUE	NA	0.440896437471614	2		735	1035	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035203	30035203	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0038556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	55	414	0	ENST00000338641.4:c.363+2T>C		p.X121_splice	ENST00000338641	NM_000268.3	121			0.127742224501841	3	FACETS	0.625	0.535	0.723	0.208	0.178	0.241	INDETERMINATE	1	TRUE	0	0.440896437471614	3		414	487	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928010	178928010	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	27	332	1	ENST00000263967.3:c.1288T>C	p.Phe430Leu	p.F430L	ENST00000263967	NM_006218.2	430	Ttt/Ctt	8/21	0.440896437471614	6	FACETS	0.6	0.477	0.741	0.12	0.095	0.149	SUBCLONAL	1	TRUE	1	0.440896437471614	6		333	384	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332838	153332838	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	277	360	0	ENST00000281708.4:c.118G>T	p.Glu40Ter	p.E40*	ENST00000281708	NM_033632.3	40	Gaa/Taa	2/12	0.277575930926745	3	FACETS	0.844	0.799	0.888	0.844	0.799	0.888	CLONAL	3	TRUE	0	0.440896437471614	3		360	606	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679879	30679879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	294	447	0	ENST00000376406.3:c.1840G>A	p.Val614Ile	p.V614I	ENST00000376406	NM_014641.2	614	Gtt/Att	5/15	0.434499504319267	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.440896437471614	2		447	549	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969906	161969906	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1166764231	NA	P-0038556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	283	516	0	ENST00000366898.1:c.1063G>T	p.Gly355Cys	p.G355C	ENST00000366898	NM_004562.2	355	Ggc/Tgc	9/12	0.351231253996188	5	FACETS	1	0.97	1	0.698	0.657	0.741	CLONAL	2	TRUE	2	0.440896437471614	5		516	1018	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578549	7578550	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0038559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	21	747	2	ENST00000269305.4:c.380_381delinsTT	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCC/tTT	5/11	1	2	FACETS	0.694	0.533	0.884	0.694	0.533	0.884	SUBCLONAL	1	TRUE	1	0.11	2		749	550	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47061239	47061251	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCAAACCTTACCT	CCAAACCTTACCT	-	novel	NA	P-0038559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	18	277	0	ENST00000409792.3:c.7430_7431+11del		p.X2477_splice	ENST00000409792	NM_014159.6	2477		19/21	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.11	2		277	239	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720833	89720836	+	frameshift_variant	Frame_Shift_Del	DEL	AAAT	AAAT	-	rs587782304	NA	P-0038560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	154	263	0	ENST00000371953.3:c.987_990del	p.Asn329LysfsTer14	p.N329Kfs*14	ENST00000371953	NM_000314.4	328	gcAAAT/gc	8/9	0.320521268181187	1	FACETS	0.83	0.766	0.897	1	0.99	1	CLONAL	2	TRUE	0	0.320521268181187	1		263	486	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940237	71940238	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCGTAC	novel	NA	P-0038560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	85	704	0	ENST00000298229.2:c.625_631dup	p.Leu211ProfsTer13	p.L211Pfs*13	ENST00000298229	NM_001567.3	208	acc/aCCCGTACcc	5/28	0.309092234276964	2	FACETS	1	0.973	1	0.66	0.586	0.737	CLONAL	1	TRUE	0	0.320521268181187	2		704	402	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790093	40790093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1481819261	NA	P-0038562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	86	576	0	ENST00000373198.4:c.2638C>T	p.Pro880Ser	p.P880S	ENST00000373198	NM_133170.3	880	Ccc/Tcc	18/32	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.37150379134642	2		576	386	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115678	108115678	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782902	NA	P-0038562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	30	240	0	ENST00000278616.4:c.826A>G	p.Lys276Glu	p.K276E	ENST00000278616	NM_000051.3	276	Aaa/Gaa	7/63	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.37150379134642	2		240	138	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735461	40735461	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	26	615	0	ENST00000373198.4:c.3412C>G	p.Leu1138Val	p.L1138V	ENST00000373198	NM_133170.3	1138	Ctc/Gtc	25/32	1	2	FACETS	0.363	0.287	0.45	0.363	0.287	0.45	SUBCLONAL	1	TRUE	1	0.37150379134642	2		615	386	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188260	10188260	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	109	587	0	ENST00000256474.2:c.404del	p.Leu135TyrfsTer24	p.L135Yfs*24	ENST00000256474	NM_000551.3	135	Tta/ta	2/3	0.37150379134642	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.37150379134642	1		587	357	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47205253	47205359	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCGGCCCGCGCCGCCACCCGTCAGGACGCGCCGCCCTCGGCTGGGGATAAGGCGGCCGACAGCAGCGGGGGGCCGCGGAGCTGATACTTACTCAGGGGTCGGGTGCT	CCGGCCCGCGCCGCCACCCGTCAGGACGCGCCGCCCTCGGCTGGGGATAAGGCGGCCGACAGCAGCGGGGGGCCGCGGAGCTGATACTTACTCAGGGGTCGGGTGCT	-	novel	NA	P-0038562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	27	108	0	ENST00000409792.3:c.56_71+91del		p.X19_splice	ENST00000409792	NM_014159.6	19		1/21	0.37150379134642	1	FACETS	0.858	0.709	1	1	0.954	1	CLONAL	2	TRUE	0	0.37150379134642	1		108	69	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227922	53227973	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCTCCATCCCCCCCATCACTCACTGCGCTTCCGCCCATCCTCCACCTCCAG	CCCTCCATCCCCCCCATCACTCACTGCGCTTCCGCCCATCCTCCACCTCCAG	-	novel	NA	P-0038562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	68	304	0	ENST00000375401.3:c.2341_2368+24del		p.X781_splice	ENST00000375401	NM_004187.3	781		16/26	0.213174938379983	2	FACETS	1	0.893	1			1	INDETERMINATE	2	TRUE	NA	0.37150379134642	2		304	182	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	147	703	0	ENST00000397752.3:c.3028G>A	p.Asp1010Asn	p.D1010N	ENST00000397752	NM_000245.2	1010	Gat/Aat	14/21	1	2	FACETS	0.383	0.349	0.418	0.383	0.349	0.418	SUBCLONAL	1	TRUE	1	0.91	2		703	844	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559149	29559149	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	30	281	0	ENST00000356175.3:c.3256C>T	p.Gln1086Ter	p.Q1086*	ENST00000356175	NM_000267.3	1086	Cag/Tag	25/57	1	2	FACETS	0.133	0.107	0.163	0.133	0.107	0.163	SUBCLONAL	1	TRUE	1	0.91	2		281	495	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850786	63850786	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	53	439	0	ENST00000279873.7:c.1564C>T	p.Gln522Ter	p.Q522*	ENST00000279873	NM_032199.2	522	Caa/Taa	10/10	1	2	FACETS	0.215	0.183	0.25	0.215	0.183	0.25	SUBCLONAL	1	TRUE	1	0.91	2		439	541	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041351	42041352	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0038563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	47	559	0	ENST00000219905.7:c.5547_5548insTT	p.Glu1850LeufsTer16	p.E1850Lfs*16	ENST00000219905	NM_001164273.1	1849	tct/tcTTt	17/24	1	2	FACETS	0.168	0.141	0.197	0.168	0.141	0.197	SUBCLONAL	1	TRUE	1	0.91	2		559	616	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559860	29559860	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	21	264	0	ENST00000356175.3:c.3457C>A	p.Leu1153Ile	p.L1153I	ENST00000356175	NM_000267.3	1153	Ctc/Atc	26/57	1	2	FACETS	0.132	0.101	0.168	0.132	0.101	0.168	SUBCLONAL	1	TRUE	1	0.91	2		264	350	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46602902	46602902	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	56	749	0	ENST00000263734.3:c.960G>T	p.Glu320Asp	p.E320D	ENST00000263734	NM_001430.4	320	gaG/gaT	8/16	1	2	FACETS	0.148	0.126	0.172	0.148	0.126	0.172	SUBCLONAL	1	TRUE	1	0.91	2		749	833	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539012	187539012	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753412687	NA	P-0038563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	47	439	0	ENST00000441802.2:c.8728G>A	p.Asp2910Asn	p.D2910N	ENST00000441802	NM_005245.3	2910	Gat/Aat	10/27	1	2	FACETS	0.202	0.17	0.237	0.202	0.17	0.237	SUBCLONAL	1	TRUE	1	0.91	2		439	512	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	123	399	0				ENST00000310581	NM_198253.2	-/1132			0.292274164937566	3	FACETS	1	0.933	1	1	0.933	1	CLONAL	2	TRUE	1	0.292262168034923	3		399	468	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0038565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	128	518	0	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	0.178068264216556	3	FACETS	0.887	0.807	0.97	0.591	0.538	0.647	CLONAL	2	TRUE	0	0.292262168034923	3		518	566	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023393	27023394	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCGTCTTCCA	novel	NA	P-0038565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	56	345	0	ENST00000324856.7:c.502_511dup	p.Gln171ArgfsTer232	p.Q171Rfs*232	ENST00000324856	NM_006015.4	167	gcc/gCCGTCTTCCAcc	1/20	1	2	FACETS	0.904	0.776	1	0.904	0.776	1	CLONAL	1	TRUE	1	0.292262168034923	2		345	424	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981298	201981298	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	46	676	0	ENST00000359651.3:c.377G>C	p.Arg126Pro	p.R126P	ENST00000359651		126	cGa/cCa	2/8	1	2	FACETS	0.518	0.435	0.609	0.518	0.435	0.609	SUBCLONAL	1	TRUE	1	0.292262168034923	2		676	608	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948477	71948477	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	48	962	0	ENST00000298229.2:c.3189C>G	p.Ile1063Met	p.I1063M	ENST00000298229	NM_001567.3	1063	atC/atG	26/28	1	2	FACETS	0.347	0.292	0.408	0.347	0.292	0.408	SUBCLONAL	1	TRUE	1	0.292262168034923	2		962	947	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872049	37872049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	63	824	0	ENST00000269571.5:c.1370C>T	p.Ser457Leu	p.S457L	ENST00000269571		457	tCa/tTa	12/27	0.178068264216556	3	FACETS	0.527	0.455	0.607	0.176	0.151	0.203	SUBCLONAL	1	TRUE	0	0.292262168034923	3		824	937	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047034	128047034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1249110579	NA	P-0038565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	32	567	0	ENST00000285398.2:c.701G>A	p.Arg234Gln	p.R234Q	ENST00000285398	NM_000122.1	234	cGa/cAa	6/15	1	2	FACETS	0.375	0.303	0.456	0.375	0.303	0.456	SUBCLONAL	1	TRUE	1	0.292262168034923	2		567	584	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608277	100608277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	23	316	0	ENST00000308731.7:c.1813G>A	p.Glu605Lys	p.E605K	ENST00000308731	NM_000061.2	605	Gag/Aag	18/19	0.216202500414024	2	FACETS	0.359	0.279	0.452			1	SUBCLONAL	1	TRUE	NA	0.292262168034923	2		316	438	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0038566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	119	493	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.234415350347039	4	FACETS	0.821	0.742	0.905	0.548	0.494	0.604	CLONAL	2	TRUE	1	0.234415350347039	4		493	763	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0038566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	40	312	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.88	0.732	1	0.88	0.732	1	CLONAL	1	TRUE	1	0.234415350347039	2		312	388	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221743	55221743	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519829	NA	P-0038566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	75	503	0	ENST00000275493.2:c.787A>C	p.Thr263Pro	p.T263P	ENST00000275493	NM_005228.3	263	Acc/Ccc	7/28	0.234415350347039	4	FACETS	1	0.959	1	0.408	0.357	0.463	CLONAL	1	TRUE	1	0.234415350347039	4		503	645	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510609	38510609	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	35	597	1	ENST00000254066.5:c.863A>G	p.Asp288Gly	p.D288G	ENST00000254066	NM_000964.3	288	gAc/gGc	7/9	1	2	FACETS	0.476	0.389	0.574	0.476	0.389	0.574	SUBCLONAL	1	TRUE	1	0.234415350347039	2		598	628	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59793426	59793460	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TAATAATTTTAAAATATATTTAAAAAATTAGTAGA	TAATAATTTTAAAATATATTTAAAAAATTAGTAGA	-	novel	NA	P-0038566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	29	279	0	ENST00000259008.2:c.2380-36_2380-2del		p.X794_splice	ENST00000259008	NM_032043.2	794			1	2	FACETS	0.822	0.661	1	0.822	0.661	1	CLONAL	1	TRUE	1	0.234415350347039	2		279	301	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561231	9561231	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	27	397	0	ENST00000353224.5:c.551A>T	p.Glu184Val	p.E184V	ENST00000353224	NM_177990.2	184	gAg/gTg	4/10	0.234415350347039	3	FACETS	0.528	0.42	0.653	0.264	0.21	0.327	SUBCLONAL	1	TRUE	1	0.234415350347039	3		397	487	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739858	145739858	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	239	742	0	ENST00000428558.2:c.1672A>G	p.Thr558Ala	p.T558A	ENST00000428558	NM_004260.3	558	Acc/Gcc	10/22	0.234415350347039	3	FACETS	0.96	0.899	1	1	0.992	1	CLONAL	3	TRUE	1	0.234415350347039	3		742	791	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0038567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	528	679	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.797408737024168	2	FACETS	0.981	0.957	1	0.981	0.957	1	CLONAL	2	TRUE	0	0.797408737024168	2		679	675	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212456	5212456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1191088838	NA	P-0038567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	131	745	3	ENST00000357368.4:c.4661C>T	p.Ala1554Val	p.A1554V	ENST00000357368	NM_002850.3	1554	gCg/gTg	31/38	0.267888540878318	2	FACETS	0.676	0.617	0.737	0.338	0.308	0.369	INDETERMINATE	1	TRUE	0	0.797408737024168	2		748	486	SUCCESS
APC	324	MSKCC	GRCh37	5	112175193	112175193	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1064794042	NA	P-0038567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	58	233	0	ENST00000257430.4:c.3904del	p.Leu1302CysfsTer3	p.L1302Cfs*3	ENST00000257430	NM_000038.5	1301	aCc/ac	16/16	0.797408737024168	1	FACETS	0.921	0.83	1	0.921	0.83	1	CLONAL	1	TRUE	0	0.797408737024168	1		233	95	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061439	38061439	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	214	561	0	ENST00000250448.2:c.550del	p.Gln184SerfsTer10	p.Q184Sfs*10	ENST00000250448	NM_004496.3	184	Cag/ag	2/2	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.585146520178897	2		561	632	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024679	11024679	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	129	524	0	ENST00000327064.4:c.796G>A	p.Glu266Lys	p.E266K	ENST00000327064	NM_199141.1	266	Gag/Aag	6/16	0.33032362274484	1	FACETS	0.704	0.643	0.767	0.704	0.643	0.767	INDETERMINATE	1	TRUE	0	0.585146520178897	1		524	443	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965728	93965728	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038570-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	125	270	0	ENST00000369303.4:c.2200C>T	p.Gln734Ter	p.Q734*	ENST00000369303	NM_004440.3	734	Cag/Tag	13/17	1	2	FACETS	0.864	0.792	0.938	0.864	0.792	0.938	CLONAL	1	TRUE	1	0.84342614586284	2		270	343	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866674	117866675	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCTTCC	novel	NA	P-0038570-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	401	456	0	ENST00000297338.2:c.965_970dup	p.Arg322_Lys323dup	p.R322_K323dup	ENST00000297338	NM_006265.2	322	cta/cGGAAGCta	9/14	0.84342614586284	3	FACETS	0.783	0.749	0.817	0.783	0.749	0.817	SUBCLONAL	2	TRUE	1	0.84342614586284	3		456	863	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499834	8499834	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038570-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	199	391	0	ENST00000356435.5:c.2135G>C	p.Ser712Thr	p.S712T	ENST00000356435		712	aGt/aCt	14/35	1	2	FACETS	0.897	0.838	0.957	0.897	0.838	0.957	CLONAL	1	TRUE	1	0.84342614586284	2		391	526	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087545	27087554	+	frameshift_variant	Frame_Shift_Del	DEL	GCTCAGTCTC	GCTCAGTCTC	-	novel	NA	P-0038581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	246	566	0	ENST00000324856.7:c.2125_2134del	p.Ser709AspfsTer30	p.S709Dfs*30	ENST00000324856	NM_006015.4	707	GCTCAGTCTCgc/gc	5/20	0.77761065989302	1	FACETS	0.952	0.907	0.997	0.952	0.907	0.997	CLONAL	1	TRUE	0	0.77761065989302	1		566	406	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433722	49433722	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	331	781	0	ENST00000301067.7:c.7831C>G	p.Arg2611Gly	p.R2611G	ENST00000301067	NM_003482.3	2611	Cgc/Ggc	31/54	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.77761065989302	2		781	844	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442490	52442490	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	67	373	0	ENST00000460680.1:c.255G>C	p.Gln85His	p.Q85H	ENST00000460680	NM_004656.3	85	caG/caC	4/17	0.77761065989302	1	FACETS	0.359	0.315	0.407	0.359	0.315	0.407	SUBCLONAL	1	TRUE	0	0.77761065989302	1		373	293	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117531	4117531	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	49	265	0	ENST00000262948.5:c.189G>T	p.Lys63Asn	p.K63N	ENST00000262948	NM_030662.3	63	aaG/aaT	2/11	0.192305467310706	2	FACETS	0.722	0.612	0.843	0.361	0.306	0.422	SUBCLONAL	1	TRUE	0	0.280298538451434	2		265	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1555525429	NA	P-0038582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	258	621	0	ENST00000269305.4:c.782+1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.253848194554299	2	FACETS	0.841	0.787	0.896	0.841	0.787	0.896	CLONAL	2	TRUE	0	0.280298538451434	2		621	1095	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610299	81610299	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28937584	NA	P-0038582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	76	487	1	ENST00000298171.2:c.1897G>A	p.Asp633Asn	p.D633N	ENST00000298171	NM_000369.2	633	Gac/Aac	10/10	1	2	FACETS	0.77	0.675	0.873	0.77	0.675	0.873	SUBCLONAL	1	TRUE	1	0.280298538451434	2		488	704	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736393	85736393	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	36	394	0	ENST00000370580.1:c.254C>A	p.Ser85Tyr	p.S85Y	ENST00000370580	NM_003921.4	85	tCt/tAt	2/3	1	2	FACETS	0.527	0.433	0.633	0.527	0.433	0.633	SUBCLONAL	1	TRUE	1	0.280298538451434	2		394	487	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567642	226567642	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	88	562	0	ENST00000366794.5:c.1524G>T	p.Lys508Asn	p.K508N	ENST00000366794	NM_001618.3	508	aaG/aaT	10/23	0.280298538451434	3	FACETS	0.656	0.579	0.738	0.328	0.289	0.369	SUBCLONAL	1	TRUE	1	0.280298538451434	3		562	1092	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352564	118352564	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	60	558	0	ENST00000534358.1:c.3769A>C	p.Ser1257Arg	p.S1257R	ENST00000534358	NM_005933.3	1257	Agc/Cgc	7/36	0.192305467310706	2	FACETS	0.459	0.394	0.53	0.23	0.197	0.265	SUBCLONAL	1	TRUE	0	0.280298538451434	2		558	932	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947573	48947573	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs767908749	NA	P-0038582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	13	386	0	ENST00000267163.4:c.1160T>C	p.Met387Thr	p.M387T	ENST00000267163	NM_000321.2	387	aTg/aCg	12/27	0.215224227226456	1	FACETS	0.418	0.298	0.563	0.418	0.298	0.563	SUBCLONAL	1	TRUE	0	0.280298538451434	1		386	191	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74003509	74003509	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	61	634	0	ENST00000318443.5:c.1580A>G	p.Glu527Gly	p.E527G	ENST00000318443	NM_001024736.1	527	gAa/gGa	9/10	0.215224227226456	1	FACETS	0.358	0.308	0.414	0.358	0.308	0.414	SUBCLONAL	1	TRUE	0	0.280298538451434	1		634	1044	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983979	15983979	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	75	364	0	ENST00000268712.3:c.3240G>T	p.Lys1080Asn	p.K1080N	ENST00000268712	NM_006311.3	1080	aaG/aaT	24/46	0.253848194554299	2	FACETS	0.753	0.659	0.854	0.376	0.329	0.427	SUBCLONAL	1	TRUE	0	0.280298538451434	2		364	711	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48586278	48586278	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs377119288	NA	P-0038582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	20	396	0	ENST00000342988.3:c.947A>G	p.Asn316Ser	p.N316S	ENST00000342988	NM_005359.5	316	aAt/aGt	8/12	0.229505162045892	3	FACETS	0.695	0.533	0.884	0.348	0.266	0.442	SUBCLONAL	1	TRUE	1	0.280298538451434	3		396	234	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144162	11144162	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	62	712	0	ENST00000358026.2:c.3743A>C	p.Gln1248Pro	p.Q1248P	ENST00000358026	NM_001128849.1	1248	cAg/cCg	26/36	0.192305467310706	2	FACETS	0.374	0.321	0.431	0.187	0.16	0.216	SUBCLONAL	1	TRUE	0	0.280298538451434	2		712	1184	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054387	13054387	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	93	643	0	ENST00000316448.5:c.997A>G	p.Thr333Ala	p.T333A	ENST00000316448	NM_004343.3	333	Acc/Gcc	8/9	0.192305467310706	2	FACETS	0.585	0.518	0.656	0.292	0.259	0.328	SUBCLONAL	1	TRUE	0	0.280298538451434	2		643	1135	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910289	50910289	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1420	175	770	0	ENST00000440232.2:c.1544A>G	p.Asp515Gly	p.D515G	ENST00000440232	NM_002691.3	515	gAt/gGt	13/27	0.152389203637166	5	FACETS	1	0.969	1	0.371	0.34	0.403	INDETERMINATE	1	TRUE	2	0.280298538451434	5		770	1595	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750543	57750543	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	38	454	0	ENST00000274289.3:c.1925T>G	p.Leu642Arg	p.L642R	ENST00000274289	NM_006622.3	642	cTt/cGt	14/14	0.192305467310706	2	FACETS	0.497	0.41	0.594	0.248	0.205	0.297	SUBCLONAL	1	TRUE	0	0.280298538451434	2		454	546	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967934	93967934	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	112	473	0	ENST00000369303.4:c.1993A>C	p.Lys665Gln	p.K665Q	ENST00000369303	NM_004440.3	665	Aaa/Caa	11/17	0.229505162045892	3	FACETS	1	0.978	1	0.659	0.594	0.729	CLONAL	1	TRUE	1	0.280298538451434	3		473	691	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371935	55371935	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	61	405	0	ENST00000297316.4:c.625C>A	p.Leu209Met	p.L209M	ENST00000297316	NM_022454.3	209	Ctg/Atg	2/2	0.280298538451434	2	FACETS	0.616	0.53	0.709	0.308	0.265	0.355	SUBCLONAL	1	TRUE	0	0.280298538451434	2		405	707	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98009765	98009765	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	65	296	0	ENST00000289081.3:c.199A>C	p.Ile67Leu	p.I67L	ENST00000289081	NM_000136.2	67	Att/Ctt	3/15	0.192305467310706	2	FACETS	0.783	0.685	0.888	0.783	0.685	0.888	SUBCLONAL	2	TRUE	0	0.280298538451434	2		296	296	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98241407	98241407	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	44	432	0	ENST00000331920.6:c.1090T>C	p.Phe364Leu	p.F364L	ENST00000331920	NM_000264.3	364	Ttc/Ctc	8/24	0.192305467310706	2	FACETS	0.415	0.347	0.491	0.208	0.173	0.246	SUBCLONAL	1	TRUE	0	0.280298538451434	2		432	756	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410580	63410580	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	47	410	0	ENST00000330258.3:c.2587C>T	p.Pro863Ser	p.P863S	ENST00000330258	NM_152424.3	863	Ccc/Tcc	2/2	0.0858144821730935	2	FACETS	0.495	0.416	0.581			1	INDETERMINATE	1	TRUE	NA	0.280298538451434	2		410	678	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691022	NA	P-0038583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	786	719	1	ENST00000269305.4:c.1024del	p.Arg342GlufsTer3	p.R342Efs*3	ENST00000269305	NM_001126112.2	342	Cga/ga	10/11	0.562456783890498	5	FACETS	0.981	0.959	1	0.981	0.959	1	CLONAL	5	TRUE	0	0.562456783890498	5		720	1051	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28607302	28607302	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	97	534	0	ENST00000253063.3:c.1432T>A	p.Tyr478Asn	p.Y478N	ENST00000253063	NM_031459.4	478	Tac/Aac	10/10	0.441292444458907	4	FACETS	0.882	0.788	0.982	0.441	0.394	0.491	CLONAL	1	TRUE	2	0.562456783890498	4		534	611	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226347	41226347	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs80358044	NA	P-0038583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	136	426	0	ENST00000357654.3:c.4675+1G>A		p.X1559_splice	ENST00000357654	NM_007294.3	1559			0.562456783890498	2	FACETS	0.96	0.893	1	0.96	0.893	1	CLONAL	2	TRUE	0	0.562456783890498	2		426	252	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965228	25965228	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	86	607	0	ENST00000435504.4:c.3978C>G	p.Ser1326Arg	p.S1326R	ENST00000435504		1326	agC/agG	13/13	0.343660107999636	4	FACETS	0.75	0.664	0.842	0.375	0.332	0.421	SUBCLONAL	1	TRUE	2	0.562456783890498	4		607	637	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50358679	50358679	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	66	252	0	ENST00000331340.3:c.22G>C	p.Asp8His	p.D8H	ENST00000331340	NM_006060.4	8	Gac/Cac	2/8	0.145213458074478	6	FACETS	1	0.96	1	0.811	0.716	0.91	INDETERMINATE	2	TRUE	3	0.562456783890498	6		252	205	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578281	7578281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	98	628	0	ENST00000269305.4:c.568C>T	p.Pro190Ser	p.P190S	ENST00000269305	NM_001126112.2	190	Cct/Tct	6/11	1	2	FACETS	0.958	0.857	1	0.958	0.857	1	CLONAL	1	TRUE	1	0.37	2		628	553	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702552	52702552	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	72	421	0	ENST00000394830.3:c.346T>C	p.Phe116Leu	p.F116L	ENST00000394830	NM_018313.4	116	Ttc/Ctc	4/30	1	2	FACETS	0.729	0.638	0.827	0.729	0.638	0.827	SUBCLONAL	1	TRUE	1	0.37	2		421	534	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710650	117710650	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	71	347	0	ENST00000368508.3:c.1622G>T	p.Gly541Val	p.G541V	ENST00000368508	NM_002944.2	541	gGg/gTg	12/43	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.37	2		347	356	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922749	44922750	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	90	213	0	ENST00000377967.4:c.1611dup	p.Val538SerfsTer15	p.V538Sfs*15	ENST00000377967	NM_021140.2	537	tca/tcAa	16/29	0.0739548349329984	2	FACETS	0.973	0.877	1			1	INDETERMINATE	2	TRUE	NA	0.37	2		213	250	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0038586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	162	523	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.629984219982779	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.629984219982779	2		523	253	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	143	614	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.629984219982779	2	FACETS	0.95	0.872	1	0.475	0.436	0.515	CLONAL	1	TRUE	0	0.629984219982779	2		614	478	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	424	881	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.629984219982779	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.629984219982779	2		881	633	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691039	NA	P-0038587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	680	671	0	ENST00000269305.4:c.919+1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		671	857	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0038588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	154	569	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.357519113317702	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.357519113317702	1		569	581	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0038588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	30	324	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.271010187723983	3	FACETS	0.419	0.337	0.512	0.14	0.112	0.171	SUBCLONAL	1	TRUE	0	0.357519113317702	3		324	472	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948136	178948136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	27	182	0	ENST00000263967.3:c.2908G>A	p.Glu970Lys	p.E970K	ENST00000263967	NM_006218.2	970	Gaa/Aaa	20/21	0.150999165903541	3	FACETS	0.927	0.744	1	0.309	0.248	0.378	INDETERMINATE	1	TRUE	0	0.357519113317702	3		182	192	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589555	67589557	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	novel	NA	P-0038588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	37	187	0	ENST00000274335.5:c.1318_1320del	p.Asp440del	p.D440del	ENST00000274335		440	GAT/-	10/15	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.357519113317702	2		187	182	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222796	5222796	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756049037	NA	P-0038588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	76	506	0	ENST00000357368.4:c.3007G>A	p.Asp1003Asn	p.D1003N	ENST00000357368	NM_002850.3	1003	Gac/Aac	18/38	1	2	FACETS	0.65	0.57	0.736	0.65	0.57	0.736	SUBCLONAL	1	TRUE	1	0.357519113317702	2		506	654	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048166	180048166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1369049878	NA	P-0038588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	91	659	0	ENST00000261937.6:c.2107G>A	p.Gly703Arg	p.G703R	ENST00000261937	NM_182925.4	703	Gga/Aga	14/30	1	2	FACETS	0.651	0.577	0.73	0.651	0.577	0.73	SUBCLONAL	1	TRUE	1	0.357519113317702	2		659	782	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717679	89717679	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554825202	NA	P-0038588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	94	440	0	ENST00000371953.3:c.705del	p.Asp236ThrfsTer20	p.D236Tfs*20	ENST00000371953	NM_000314.4	235	gAa/ga	7/9	NA	2	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.357519113317702	2		440	408	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156083	119156083	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	154	560	0	ENST00000264033.4:c.1748C>G	p.Ser583Cys	p.S583C	ENST00000264033	NM_005188.3	583	tCt/tGt	11/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.357519113317702	2		560	696	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217236	7217236	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	155	585	0	ENST00000380728.2:c.469C>T	p.Gln157Ter	p.Q157*	ENST00000380728		157	Caa/Taa	6/11	0.357519113317702	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.357519113317702	1		585	577	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513512	149513512	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	72	506	0	ENST00000261799.4:c.691del	p.Ile231SerfsTer7	p.I231Sfs*7	ENST00000261799	NM_002609.3	231	Atc/tc	5/23	1	2	FACETS	0.575	0.502	0.654	0.575	0.502	0.654	SUBCLONAL	1	TRUE	1	0.357519113317702	2		506	700	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912656	NA	P-0038589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	62	594	1	ENST00000269305.4:c.734G>C	p.Gly245Ala	p.G245A	ENST00000269305	NM_001126112.2	245	gGc/gCc	7/11	0.141397082426814	3	FACETS	1	0.915	1	0.541	0.467	0.622	CLONAL	1	TRUE	1	0.2	3		595	630	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221162	5221162	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	44	684	0	ENST00000357368.4:c.3304C>G	p.Arg1102Gly	p.R1102G	ENST00000357368	NM_002850.3	1102	Cgc/Ggc	20/38	1	2	FACETS	0.503	0.421	0.596	0.503	0.421	0.596	SUBCLONAL	1	TRUE	1	0.2	2		684	874	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274087	18274087	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	45	555	0	ENST00000222254.8:c.1305G>T	p.Lys435Asn	p.K435N	ENST00000222254	NM_005027.3	435	aaG/aaT	11/16	1	2	FACETS	0.792	0.665	0.933	0.792	0.665	0.933	CLONAL	1	TRUE	1	0.2	2		555	568	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111695	56111695	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	25	137	0	ENST00000399503.3:c.295G>C	p.Ala99Pro	p.A99P	ENST00000399503	NM_005921.1	99	Gcg/Ccg	1/20	1	2	FACETS	0.996	0.788	1	0.996	0.788	1	CLONAL	1	TRUE	1	0.2	2		137	251	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179209	123179209	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	17	349	0	ENST00000218089.9:c.658A>T	p.Thr220Ser	p.T220S	ENST00000218089	NM_001042749.1	220	Acc/Tcc	8/35	1	2	FACETS	0.899	0.674	1	0.899	0.674	1	CLONAL	1	TRUE	1	0.2	2		349	189	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0038590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	124	220	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.963	0.878	1	0.963	0.878	1	CLONAL	1	TRUE	1	0.607580864296537	2		220	424	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0038590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	400	556	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.606924253584954	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.607580864296537	2		556	651	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578202	7578202	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520004	NA	P-0038590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	242	643	0	ENST00000269305.4:c.647T>G	p.Val216Gly	p.V216G	ENST00000269305	NM_001126112.2	216	gTg/gGg	6/11	0.607580864296537	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.607580864296537	1		643	546	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790165	40790165	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	423	427	0	ENST00000373198.4:c.2566G>A	p.Glu856Lys	p.E856K	ENST00000373198	NM_133170.3	856	Gag/Aag	18/32	0.607580864296537	3	FACETS	0.84	0.809	0.872	1	0.995	1	CLONAL	3	TRUE	1	0.607580864296537	3		427	720	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508169	106508169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381484125	NA	P-0038590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	78	233	0	ENST00000359195.3:c.163G>A	p.Glu55Lys	p.E55K	ENST00000359195	NM_002649.2	55	Gaa/Aaa	2/11	1	2	FACETS	0.904	0.803	1	0.904	0.803	1	CLONAL	1	TRUE	1	0.607580864296537	2		233	284	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70971044	70971044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	165	541	0	ENST00000276594.2:c.1217G>A	p.Gly406Glu	p.G406E	ENST00000276594	NM_024504.3	406	gGg/gAg	6/8	1	2	FACETS	0.824	0.759	0.891	0.824	0.759	0.891	CLONAL	1	TRUE	1	0.607580864296537	2		541	659	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518223	8518223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	109	345	0	ENST00000356435.5:c.1168G>A	p.Glu390Lys	p.E390K	ENST00000356435		390	Gaa/Aaa	10/35	0.607580864296537	1	FACETS	0.908	0.829	0.989	0.908	0.829	0.989	CLONAL	1	TRUE	0	0.607580864296537	1		345	275	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812299	212812299	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	88	246	0	ENST00000342788.4:c.277C>T	p.Gln93Ter	p.Q93*	ENST00000342788	NM_005235.2	93	Cag/Tag	3/28	1	2	FACETS	0.84	0.75	0.933	0.84	0.75	0.933	CLONAL	1	TRUE	1	0.607580864296537	2		246	345	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39774533	39774533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	136	372	0	ENST00000288319.7:c.619G>A	p.Asp207Asn	p.D207N	ENST00000288319	NM_182918.3	207	Gat/Aat	5/10	0.525663379896931	3	FACETS	1	0.934	1	0.514	0.469	0.56	CLONAL	1	TRUE	1	0.607580864296537	3		372	568	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716122	243716122	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	284	479	0	ENST00000263826.5:c.1072A>T	p.Ile358Leu	p.I358L	ENST00000263826	NM_005465.4	358	Ata/Tta	10/13	0.593371004720465	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.607580864296537	2		479	465	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032012	10032012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	189	601	0	ENST00000330684.3:c.811G>A	p.Glu271Lys	p.E271K	ENST00000330684	NM_001134407.1	271	Gag/Aag	3/13	NA	2	FACETS	0.884	0.82	0.95			1	INDETERMINATE	1	TRUE	NA	0.607580864296537	2		601	704	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530048	212530048	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	74	197	0	ENST00000342788.4:c.1871G>A	p.Gly624Glu	p.G624E	ENST00000342788	NM_005235.2	624	gGg/gAg	15/28	1	2	FACETS	0.982	0.872	1	0.982	0.872	1	CLONAL	1	TRUE	1	0.607580864296537	2		197	248	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27220079	27220079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748239410	NA	P-0038590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	208	491	0	ENST00000380036.4:c.3136G>A	p.Glu1046Lys	p.E1046K	ENST00000380036	NM_000459.3	1046	Gaa/Aaa	21/23	0.607580864296537	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.607580864296537	1		491	471	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250125	110250125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1020085505	NA	P-0038590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	262	682	0	ENST00000374672.4:c.550C>T	p.Pro184Ser	p.P184S	ENST00000374672	NM_004235.4	184	Ccc/Tcc	3/5	0.292353797682445	1	FACETS	0.809	0.762	0.857	0.809	0.762	0.857	INDETERMINATE	1	TRUE	0	0.607580864296537	1		682	742	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	131	399	0				ENST00000310581	NM_198253.2	-/1132			0.742069797992905	3	FACETS	1	0.921	1	0.504	0.46	0.549	CLONAL	1	TRUE	1	0.783239965903466	3		399	462	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944965	31944965	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	391	494	1	ENST00000340398.3:c.136G>A	p.Val46Met	p.V46M	ENST00000340398	NM_001013699.2	46	Gtg/Atg	1/1	0.783239965903466	3	FACETS	0.888	0.85	0.926	0.888	0.85	0.926	CLONAL	2	TRUE	1	0.783239965903466	3		495	782	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0038593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	94	220	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.769	0.686	0.856	1	0.981	1	SUBCLONAL	2	TRUE	1	0.24169059020458	2		220	506	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874261	155874261	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs483352822	NA	P-0038593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	65	557	0	ENST00000368323.3:c.270G>C	p.Met90Ile	p.M90I	ENST00000368323	NM_006912.5	90	atG/atC	5/6	0.24169059020458	3	FACETS	0.6	0.518	0.689	0.3	0.259	0.345	SUBCLONAL	1	TRUE	1	0.24169059020458	3		557	1005	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645156	67645156	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	81	686	0	ENST00000264010.4:c.421G>T	p.Glu141Ter	p.E141*	ENST00000264010	NM_006565.3	141	Gaa/Taa	3/12	1	2	FACETS	0.628	0.552	0.711	0.628	0.552	0.711	SUBCLONAL	1	TRUE	1	0.24169059020458	2		686	1067	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257464	16257464	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	37	475	1	ENST00000375759.3:c.4729C>T	p.Gln1577Ter	p.Q1577*	ENST00000375759	NM_015001.2	1577	Caa/Taa	11/15	1	2	FACETS	0.506	0.416	0.607	0.506	0.416	0.607	SUBCLONAL	1	TRUE	1	0.24169059020458	2		476	605	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942160	71942160	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1237	87	858	0	ENST00000298229.2:c.1424C>A	p.Ser475Ter	p.S475*	ENST00000298229	NM_001567.3	475	tCa/tAa	12/28	1	2	FACETS	0.544	0.479	0.613	0.544	0.479	0.613	SUBCLONAL	1	TRUE	1	0.24169059020458	2		858	1324	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431031	49431031	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	64	637	1	ENST00000301067.7:c.10108C>A	p.Gln3370Lys	p.Q3370K	ENST00000301067	NM_003482.3	3370	Cag/Aag	34/54	1	2	FACETS	0.588	0.508	0.676	0.588	0.508	0.676	SUBCLONAL	1	TRUE	1	0.24169059020458	2		638	900	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440063	49440063	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	79	746	0	ENST00000301067.7:c.4563C>G	p.Ile1521Met	p.I1521M	ENST00000301067	NM_003482.3	1521	atC/atG	16/54	1	2	FACETS	0.592	0.519	0.671	0.592	0.519	0.671	SUBCLONAL	1	TRUE	1	0.24169059020458	2		746	1104	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658644	3658644	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1345	88	813	0	ENST00000294008.3:c.322G>C	p.Glu108Gln	p.E108Q	ENST00000294008	NM_032444.2	108	Gag/Cag	2/15	1	2	FACETS	0.508	0.448	0.573	0.508	0.448	0.573	SUBCLONAL	1	TRUE	1	0.24169059020458	2		813	1433	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653151	29653151	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	72	331	0	ENST00000356175.3:c.5086G>C	p.Glu1696Gln	p.E1696Q	ENST00000356175	NM_000267.3	1696	Gag/Cag	36/57	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.24169059020458	2		331	575	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37083790	37083790	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	34	316	0	ENST00000231790.2:c.1699G>C	p.Asp567His	p.D567H	ENST00000231790	NM_000249.3	567	Gat/Cat	15/19	0.24169059020458	3	FACETS	0.512	0.417	0.619	0.256	0.208	0.31	SUBCLONAL	1	TRUE	1	0.24169059020458	3		316	616	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412945	49412950	+	inframe_deletion	In_Frame_Del	DEL	GCTGAA	GCTGAA	-	novel	NA	P-0038593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	79	690	0	ENST00000418115.1:c.73_78del	p.Phe25_Ser26del	p.F25_S26del	ENST00000418115	NM_001664.2	25	TTCAGC/-	2/5	1	2	FACETS	0.601	0.527	0.681	0.601	0.527	0.681	SUBCLONAL	1	TRUE	1	0.24169059020458	2		690	1088	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281484	142281484	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	79	561	1	ENST00000350721.4:c.760G>C	p.Glu254Gln	p.E254Q	ENST00000350721	NM_001184.3	254	Gaa/Caa	4/47	0.24169059020458	1	FACETS	0.757	0.665	0.856	0.757	0.665	0.856	SUBCLONAL	1	TRUE	0	0.24169059020458	1		562	759	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0038594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	94	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.264040024250678	1	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	0	0.264040024250678	1		457	611	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579312	7579313	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0038594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	91	644	0	ENST00000269305.4:c.373_374dup	p.Tyr126ArgfsTer45	p.Y126Rfs*45	ENST00000269305	NM_001126112.2	125	acg/acACg	4/11	0.264040024250678	1	FACETS	0.872	0.775	0.976	0.872	0.775	0.976	CLONAL	1	TRUE	0	0.264040024250678	1		644	686	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332838	153332841	+	frameshift_variant	Frame_Shift_Del	DEL	CCTC	CCTC	-	novel	NA	P-0038594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	73	405	0	ENST00000281708.4:c.115_118del	p.Glu39AsnfsTer23	p.E39Nfs*23	ENST00000281708	NM_033632.3	39	GAGGaa/aa	2/12	1	2	FACETS	0.752	0.657	0.855	0.752	0.657	0.855	SUBCLONAL	1	TRUE	1	0.264040024250678	2		405	735	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593603	55593603	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913235	NA	P-0038595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	242	481	0	ENST00000288135.5:c.1669T>A	p.Trp557Arg	p.W557R	ENST00000288135	NM_000222.2	557	Tgg/Agg	11/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.841115243115291	2		481	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578496	7578496	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587782197	NA	P-0038596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	133	966	0	ENST00000269305.4:c.434T>A	p.Leu145Gln	p.L145Q	ENST00000269305	NM_001126112.2	145	cTg/cAg	5/11	0.242750510813649	1	FACETS	0.859	0.779	0.944	0.859	0.779	0.944	CLONAL	1	TRUE	0	0.248065808455408	1		966	1093	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591923	48591925	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs377767349	NA	P-0038596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	76	435	0	ENST00000342988.3:c.1088_1090del	p.Cys363del	p.C363del	ENST00000342988	NM_005359.5	362	ttTTGt/ttt	9/12	0.242750510813649	1	FACETS	0.916	0.804	1	0.916	0.804	1	CLONAL	1	TRUE	0	0.248065808455408	1		435	586	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760203	133760203	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0038596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	73	594	0	ENST00000318560.5:c.2526del	p.Thr844ProfsTer8	p.T844Pfs*8	ENST00000318560	NM_005157.4	842	ttA/tt	11/11	1	2	FACETS	0.981	0.858	1	0.981	0.858	1	CLONAL	1	TRUE	1	0.248065808455408	2		594	600	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36823982	36823982	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	73	541	0	ENST00000373129.3:c.200T>A	p.Ile67Asn	p.I67N	ENST00000373129	NM_032017.1	67	aTc/aAc	5/12	0.143092682957791	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		541	779	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	92	399	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.551666851480666	2		399	277	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0038602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	304	249	1	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	0.509642506639726	4	FACETS	0.922	0.878	0.967			1	CLONAL	3	TRUE	NA	0.551666851480666	4		250	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	252	518	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.551666851480666	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.551666851480666	1		518	577	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0038602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	269	578	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.551666851480666	2		578	955	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243801005	243801005	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	133	355	0	ENST00000263826.5:c.469G>T	p.Gly157Cys	p.G157C	ENST00000263826	NM_005465.4	157	Ggc/Tgc	5/13	1	2	FACETS	0.893	0.815	0.974	0.893	0.815	0.974	CLONAL	1	TRUE	1	0.551666851480666	2		355	540	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375445	118375445	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	136	287	0	ENST00000534358.1:c.8839del	p.Gln2947ArgfsTer6	p.Q2947Rfs*6	ENST00000534358	NM_005933.3	2946	agC/ag	27/36	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.551666851480666	2		287	432	SUCCESS
CBL	867	MSKCC	GRCh37	11	119077194	119077194	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	212	452	0	ENST00000264033.4:c.67G>C	p.Gly23Arg	p.G23R	ENST00000264033	NM_005188.3	23	Ggt/Cgt	1/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.551666851480666	2		452	676	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008287	29008287	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	121	286	0	ENST00000282397.4:c.584C>A	p.Ser195Ter	p.S195*	ENST00000282397	NM_002019.4	195	tCa/tAa	5/30	NA	2	FACETS	0.925	0.841	1			1	INDETERMINATE	1	TRUE	NA	0.551666851480666	2		286	474	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939044	48939044	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0038602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	87	163	0	ENST00000267163.4:c.876T>A	p.Tyr292Ter	p.Y292*	ENST00000267163	NM_000321.2	292	taT/taA	9/27	0.42968623593238	1	FACETS	0.928	0.835	1	0.928	0.835	1	CLONAL	1	TRUE	0	0.551666851480666	1		163	246	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56866282	56866282	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	44	271	0	ENST00000308159.5:c.1327C>G	p.Gln443Glu	p.Q443E	ENST00000308159	NM_014669.4	443	Cag/Gag	12/22	0.441488453464334	1	FACETS	0.267	0.224	0.315	0.267	0.224	0.315	SUBCLONAL	1	TRUE	0	0.551666851480666	1		271	432	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216153	36216153	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	247	614	1	ENST00000222270.7:c.3561G>T	p.Met1187Ile	p.M1187I	ENST00000222270	NM_014727.1	1187	atG/atT	11/37	0.543763458045404	3	FACETS	1	0.979	1	0.554	0.518	0.591	CLONAL	1	TRUE	1	0.551666851480666	3		615	1031	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917742	29917742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748017801	NA	P-0038602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	270	636	0	ENST00000389048.3:c.926C>T	p.Ala309Val	p.A309V	ENST00000389048	NM_004304.4	309	gCa/gTa	3/29	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.551666851480666	2		636	937	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39751890	39751890	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	42	447	0	ENST00000361337.2:c.2251A>C	p.Lys751Gln	p.K751Q	ENST00000361337	NM_003286.2	751	Aag/Cag	21/21	1	2	FACETS	0.203	0.169	0.241	0.203	0.169	0.241	SUBCLONAL	1	TRUE	1	0.551666851480666	2		447	750	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306647	41306647	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	253	727	0	ENST00000373198.4:c.1012C>G	p.His338Asp	p.H338D	ENST00000373198	NM_133170.3	338	Cac/Gac	7/32	1	2	FACETS	0.924	0.865	0.984	0.924	0.865	0.984	CLONAL	1	TRUE	1	0.551666851480666	2		727	993	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971098	55971098	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	247	485	0	ENST00000263923.4:c.1699G>C	p.Val567Leu	p.V567L	ENST00000263923	NM_002253.2	567	Gtg/Ctg	13/30	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.551666851480666	2		485	802	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27173259	27173259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	268	658	0	ENST00000380036.4:c.800G>A	p.Arg267Lys	p.R267K	ENST00000380036	NM_000459.3	267	aGg/aAg	6/23	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.551666851480666	2		658	966	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044507	47044508	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0038602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	296	350	0	ENST00000377604.3:c.2004_2005del	p.Phe669GlnfsTer3	p.F669Qfs*3	ENST00000377604	NM_001204468.1	668	aaCTtc/aatc	18/24	1	1	FACETS	0.827	0.791	0.861	1	0.996	1	CLONAL	2	TRUE	0	0.551666851480666	1		350	470	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	34	399	0				ENST00000310581	NM_198253.2	-/1132			0.286876835985425	1	FACETS	0.338	0.277	0.406	0.338	0.277	0.406	INDETERMINATE	1	TRUE	0	0.524253700379416	1		399	283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0038614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	270	773	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.508424931287625	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.524253700379416	1		773	752	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983142	201983143	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0038614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	278	589	1	ENST00000359651.3:c.994dup	p.Ala332GlyfsTer139	p.A332Gfs*139	ENST00000359651		331	cgg/cGgg	7/8	0.231435098200624	2	FACETS	0.885	0.839	0.932	0.885	0.839	0.932	INDETERMINATE	2	TRUE	0	0.524253700379416	2		590	599	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477152	67477152	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	96	597	0	ENST00000327367.4:c.959G>C	p.Cys320Ser	p.C320S	ENST00000327367	NM_005902.3	320	tGt/tCt	7/9	1	2	FACETS	0.518	0.461	0.578	0.518	0.461	0.578	SUBCLONAL	1	TRUE	1	0.524253700379416	2		597	707	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339919	70339919	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	176	272	0	ENST00000374080.3:c.452T>C	p.Val151Ala	p.V151A	ENST00000374080		151	gTg/gCg	4/45	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.524253700379416	1		272	353	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438210	49438211	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1555194303	NA	P-0038615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	361	942	0	ENST00000301067.7:c.5058dup	p.Arg1687ThrfsTer4	p.R1687Tfs*4	ENST00000301067	NM_003482.3	1686	-/A	20/54	1	2	FACETS	0.916	0.871	0.962	0.916	0.871	0.962	CLONAL	1	TRUE	1	0.803239534109403	2		942	981	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101093	27101093	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	344	887	1	ENST00000324856.7:c.4377del	p.Phe1459LeufsTer22	p.F1459Lfs*22	ENST00000324856	NM_006015.4	1459	Ttt/tt	18/20	0.803239534109403	1	FACETS	0.946	0.909	0.982	0.946	0.909	0.982	CLONAL	1	TRUE	0	0.803239534109403	1		888	542	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17940942	17940942	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	339	939	0	ENST00000458235.1:c.3182C>A	p.Pro1061Gln	p.P1061Q	ENST00000458235	NM_000215.3	1061	cCg/cAg	23/24	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.803239534109403	2		939	810	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057201	30057202	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0038615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	248	461	0	ENST00000338641.4:c.683_684del	p.Lys228ArgfsTer17	p.K228Rfs*17	ENST00000338641	NM_000268.3	228	aAG/a	8/16	0.803239534109403	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.803239534109403	1		461	367	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438210	49438211	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1555194303	NA	P-0038615-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	30	942	0	ENST00000301067.7:c.5058dup	p.Arg1687ThrfsTer4	p.R1687Tfs*4	ENST00000301067	NM_003482.3	1686	-/A	20/54	0.0890481898460347	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		942	552	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0038616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	76	239	1	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	0.372019404873068	2	FACETS	0.783	0.698	0.872	0.783	0.698	0.872	SUBCLONAL	2	TRUE	0	0.423584333929968	2		240	229	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553668	106553668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1261004652	NA	P-0038616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	69	427	1	ENST00000369096.4:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000369096	NM_001198.3	545	Gaa/Aaa	5/7	1	2	FACETS	0.573	0.499	0.652	0.573	0.499	0.652	SUBCLONAL	1	TRUE	1	0.423584333929968	2		428	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577520	7577520	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	119	638	0	ENST00000269305.4:c.761T>C	p.Ile254Thr	p.I254T	ENST00000269305	NM_001126112.2	254	aTc/aCc	7/11	0.397498643423115	1	FACETS	0.898	0.815	0.985	0.898	0.815	0.985	CLONAL	1	TRUE	0	0.423584333929968	1		638	493	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912046	127912046	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs764840021	NA	P-0038616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	60	367	0	ENST00000373547.4:c.824A>G	p.Lys275Arg	p.K275R	ENST00000373547	NM_002721.4	275	aAa/aGa	7/7	1	2	FACETS	0.778	0.674	0.891	0.778	0.674	0.891	SUBCLONAL	1	TRUE	1	0.423584333929968	2		367	364	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0038625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	65	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.919	0.799	1	0.919	0.799	1	CLONAL	1	TRUE	1	0.324479623575592	2		457	436	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782645	9782645	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	149	787	0	ENST00000377346.4:c.2407C>A	p.Gln803Lys	p.Q803K	ENST00000377346	NM_005026.3	803	Cag/Aag	19/24	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.324479623575592	2		787	722	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579573	7579585	+	frameshift_variant	Frame_Shift_Del	DEL	TTGGGACGGCAAG	TTGGGACGGCAAG	-	novel	NA	P-0038625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	90	694	0	ENST00000269305.4:c.102_114del	p.Leu35GlnfsTer5	p.L35Qfs*5	ENST00000269305	NM_001126112.2	34	ccCTTGCCGTCCCAA/cc	4/11	0.316275080280931	1	FACETS	0.991	0.883	1	0.991	0.883	1	CLONAL	1	TRUE	0	0.324479623575592	1		694	469	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0038627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	492	523	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.681752549342765	3	FACETS	1	0.969	1			1	CLONAL	2	TRUE	NA	0.833132030657033	3		523	833	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	335	578	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.833132030657033	3	FACETS	0.815	0.777	0.853	0.815	0.777	0.853	CLONAL	2	TRUE	1	0.833132030657033	3		578	699	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	304	538	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.833132030657033	2		538	706	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871145	12871146	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs786201011	NA	P-0038627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	132	319	0	ENST00000228872.4:c.374_375del	p.Ser125Ter	p.S125*	ENST00000228872	NM_004064.3	124	aaCTct/aact	1/3	0.833132030657033	3	FACETS	0.947	0.866	1	0.473	0.433	0.516	CLONAL	1	TRUE	1	0.833132030657033	3		319	474	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799734	72799734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	274	660	0	ENST00000325599.8:c.1435G>A	p.Glu479Lys	p.E479K	ENST00000325599	NM_018130.2	479	Gaa/Aaa	11/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.833132030657033	2		660	623	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727880	41727880	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756018335	NA	P-0038627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	94	929	1	ENST00000301178.4:c.505G>A	p.Val169Met	p.V169M	ENST00000301178	NM_021913.4	169	Gtg/Atg	4/20	1	2	FACETS	0.25	0.221	0.28	0.25	0.221	0.28	SUBCLONAL	1	TRUE	1	0.833132030657033	2		930	904	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650768	67650768	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	292	542	0	ENST00000264010.4:c.1073A>G	p.Tyr358Cys	p.Y358C	ENST00000264010	NM_006565.3	358	tAc/tGc	5/12	0.833132030657033	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.833132030657033	1		542	400	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873077	136873077	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	109	487	0	ENST00000241393.3:c.421G>T	p.Ala141Ser	p.A141S	ENST00000241393	NM_003467.2	141	Gcc/Tcc	2/2	0.39502685158159	1	FACETS	0.373	0.337	0.411	0.373	0.337	0.411	INDETERMINATE	1	TRUE	0	0.833132030657033	1		487	409	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255631	16255631	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	124	479	0	ENST00000375759.3:c.2896C>G	p.Pro966Ala	p.P966A	ENST00000375759	NM_015001.2	966	Cct/Gct	11/15	0.627060587912292	3	FACETS	0.919	0.835	1	0.46	0.417	0.504	CLONAL	1	TRUE	1	0.667619054186489	3		479	539	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248157	59248157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	37	145	0	ENST00000371222.2:c.586G>A	p.Ala196Thr	p.A196T	ENST00000371222	NM_002228.3	196	Gcc/Acc	1/1	1	2	FACETS	0.924	0.779	1	0.924	0.779	1	CLONAL	1	TRUE	1	0.667619054186489	2		145	120	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892154	9892154	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	173	584	0	ENST00000330684.3:c.2336T>G	p.Leu779Trp	p.L779W	ENST00000330684	NM_001134407.1	779	tTg/tGg	11/13	1	2	FACETS	0.929	0.86	0.999	0.929	0.86	0.999	CLONAL	1	TRUE	1	0.667619054186489	2		584	558	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319052	62319052	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	270	925	2	ENST00000360203.5:c.1410G>C	p.Gln470His	p.Q470H	ENST00000360203	NM_001283009.1	470	caG/caC	17/35	0.101586830722634	5	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.667619054186489	5		927	1202	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44515807	44515807	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	193	558	0	ENST00000291552.4:c.246T>G	p.Phe82Leu	p.F82L	ENST00000291552	NM_006758.2	82	ttT/ttG	4/8	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.667619054186489	2		558	575	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98244479	98244479	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	116	421	0	ENST00000331920.6:c.591G>C	p.Trp197Cys	p.W197C	ENST00000331920	NM_000264.3	197	tgG/tgC	4/24	1	2	FACETS	0.856	0.778	0.937	0.856	0.778	0.937	CLONAL	1	TRUE	1	0.667619054186489	2		421	406	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0038629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	95	339	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.976	0.873	1	0.976	0.873	1	CLONAL	1	TRUE	1	0.37781543538051	2		339	515	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089705	27089706	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1286891446	NA	P-0038629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	108	692	0	ENST00000324856.7:c.2666dup	p.Met890HisfsTer46	p.M890Hfs*46	ENST00000324856	NM_006015.4	887	-/G	8/20	1	2	FACETS	0.781	0.701	0.866	0.781	0.701	0.866	SUBCLONAL	1	TRUE	1	0.37781543538051	2		692	732	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101367	27101406	+	frameshift_variant	Frame_Shift_Del	DEL	CACGCCAGCCCCCATATGGTCCCTCTGCCCCTGTGCCCCC	CACGCCAGCCCCCATATGGTCCCTCTGCCCCTGTGCCCCC	-	novel	NA	P-0038629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	85	680	0	ENST00000324856.7:c.4651_4690del	p.Arg1551Ter	p.R1551*	ENST00000324856	NM_006015.4	1550	aCACGCCAGCCCCCATATGGTCCCTCTGCCCCTGTGCCCCCc/ac	18/20	1	2	FACETS	0.706	0.625	0.794	0.706	0.625	0.794	SUBCLONAL	1	TRUE	1	0.37781543538051	2		680	637	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107017	27107017	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	91	502	1	ENST00000324856.7:c.6628C>T	p.Gln2210Ter	p.Q2210*	ENST00000324856	NM_006015.4	2210	Cag/Tag	20/20	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.37781543538051	2		503	463	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330629	65330630	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	51	290	0	ENST00000342505.4:c.1016dup	p.Asn339LysfsTer2	p.N339Kfs*2	ENST00000342505	NM_002227.2	339	aat/aaAt	8/25	1	2	FACETS	0.651	0.554	0.756	0.651	0.554	0.756	SUBCLONAL	1	TRUE	1	0.37781543538051	2		290	415	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850704	63850705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	51	374	0	ENST00000279873.7:c.1489dup	p.Ile497AsnfsTer31	p.I497Nfs*31	ENST00000279873	NM_032199.2	494	-/A	10/10	1	2	FACETS	0.678	0.578	0.788	0.678	0.578	0.788	SUBCLONAL	1	TRUE	1	0.37781543538051	2		374	398	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720711	89720712	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	17	155	0	ENST00000371953.3:c.867dup	p.Val290SerfsTer8	p.V290Sfs*8	ENST00000371953	NM_000314.4	288	gaa/gAaa	8/9	1	2	FACETS	0.448	0.335	0.581	0.448	0.335	0.581	SUBCLONAL	1	TRUE	1	0.37781543538051	2		155	201	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720876	89720876	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0038629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	90	338	0	ENST00000371953.3:c.1026+1G>T		p.X342_splice	ENST00000371953	NM_000314.4	342			1	2	FACETS	0.904	0.804	1	0.904	0.804	1	CLONAL	1	TRUE	1	0.37781543538051	2		338	527	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0038629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	122	533	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.37781543538051	2		533	637	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373313	118373313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1335499500	NA	P-0038629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	115	432	2	ENST00000534358.1:c.6706G>A	p.Ala2236Thr	p.A2236T	ENST00000534358	NM_005933.3	2236	Gct/Act	27/36	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.37781543538051	2		434	503	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906610	32906610	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1555281682	NA	P-0038629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	69	383	0	ENST00000380152.3:c.995T>A	p.Ile332Asn	p.I332N	ENST00000380152		332	aTt/aAt	10/27	1	2	FACETS	0.853	0.746	0.969	0.853	0.746	0.969	CLONAL	1	TRUE	1	0.37781543538051	2		383	428	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050932	49050933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	74	358	0	ENST00000267163.4:c.2622dup	p.Leu875ThrfsTer4	p.L875Tfs*4	ENST00000267163	NM_000321.2	872	-/A	25/27	1	2	FACETS	0.796	0.699	0.901	0.796	0.699	0.901	CLONAL	1	TRUE	1	0.37781543538051	2		358	492	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138124	2138141	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TGGCCCTGCACGCAAATG	TGGCCCTGCACGCAAATG	-	novel	NA	P-0038629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	250	808	1	ENST00000219476.3:c.5146_5160+3del		p.X1716_splice	ENST00000219476	NM_000548.3	1716		40/42	0.37781543538051	2	FACETS	0.952	0.895	1	0.952	0.895	1	CLONAL	2	TRUE	0	0.37781543538051	2		809	695	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3794922	3794922	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555475250	NA	P-0038629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	69	394	0	ENST00000262367.5:c.3955C>T	p.Arg1319Ter	p.R1319*	ENST00000262367	NM_004380.2	1319	Cga/Tga	23/31	0.37781543538051	2	FACETS	0.683	0.595	0.777	0.341	0.297	0.389	SUBCLONAL	1	TRUE	0	0.37781543538051	2		394	535	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965124	81965124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691537	NA	P-0038629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	71	535	0	ENST00000359376.3:c.2604C>A	p.Asn868Lys	p.N868K	ENST00000359376	NM_002661.3	868	aaC/aaA	25/33	1	2	FACETS	0.828	0.725	0.938	0.828	0.725	0.938	CLONAL	1	TRUE	1	0.37781543538051	2		535	454	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134267	11134267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1180804356	NA	P-0038629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	138	655	0	ENST00000358026.2:c.2933G>A	p.Arg978Gln	p.R978Q	ENST00000358026	NM_001128849.1	978	cGa/cAa	20/36	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.37781543538051	2		655	674	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952540	17952540	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	80	615	0	ENST00000458235.1:c.893T>G	p.Ile298Ser	p.I298S	ENST00000458235	NM_000215.3	298	aTc/aGc	7/24	1	2	FACETS	0.767	0.676	0.864	0.767	0.676	0.864	SUBCLONAL	1	TRUE	1	0.37781543538051	2		615	552	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918760	50918760	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	122	807	0	ENST00000440232.2:c.2630A>C	p.Asp877Ala	p.D877A	ENST00000440232	NM_002691.3	877	gAt/gCt	21/27	1	2	FACETS	0.917	0.83	1	0.917	0.83	1	CLONAL	1	TRUE	1	0.37781543538051	2		807	704	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0038629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	128	677	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	0.856	0.776	0.94	0.856	0.776	0.94	CLONAL	1	TRUE	1	0.37781543538051	2		677	792	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519941	NA	P-0038629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	14	306	1	ENST00000263967.3:c.1031T>C	p.Val344Ala	p.V344A	ENST00000263967	NM_006218.2	344	gTg/gCg	5/21	1	2	FACETS	0.17	0.122	0.228	0.17	0.122	0.228	SUBCLONAL	1	TRUE	1	0.37781543538051	2		307	437	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155582	56155582	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs770879992	NA	P-0038629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	52	337	0	ENST00000399503.3:c.674T>C	p.Met225Thr	p.M225T	ENST00000399503	NM_005921.1	225	aTg/aCg	3/20	1	2	FACETS	0.626	0.533	0.726	0.626	0.533	0.726	SUBCLONAL	1	TRUE	1	0.37781543538051	2		337	440	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14027758	14027758	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	51	316	0	ENST00000405192.2:c.86T>C	p.Val29Ala	p.V29A	ENST00000405192	NM_001163147.1	29	gTc/gCc	3/12	1	2	FACETS	0.652	0.555	0.758	0.652	0.555	0.758	SUBCLONAL	1	TRUE	1	0.37781543538051	2		316	414	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0038629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	62	404	0	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	1	2	FACETS	0.776	0.672	0.888	0.776	0.672	0.888	SUBCLONAL	1	TRUE	1	0.37781543538051	2		404	423	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010560	48010560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	119	645	0	ENST00000234420.5:c.188C>T	p.Ser63Phe	p.S63F	ENST00000234420	NM_000179.2	63	tCc/tTc	1/10	0.248158791074503	5	FACETS	1	0.97	1	0.397	0.358	0.438	CLONAL	1	TRUE	2	0.389737441617559	5		645	813	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343132	118343132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	52	347	0	ENST00000534358.1:c.1258C>T	p.Arg420Trp	p.R420W	ENST00000534358	NM_005933.3	420	Cgg/Tgg	3/36	0.389737441617559	2	FACETS	0.778	0.665	0.9	0.389	0.332	0.45	SUBCLONAL	1	TRUE	0	0.389737441617559	2		347	343	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166026	118166026	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	93	453	0	ENST00000369448.3:c.536T>A	p.Phe179Tyr	p.F179Y	ENST00000369448	NM_017709.3	179	tTc/tAc	2/2	0.248158791074503	5	FACETS	1	0.972	1	0.43	0.383	0.48	CLONAL	1	TRUE	2	0.389737441617559	5		453	586	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466934	18466934	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1284974002	NA	P-0038630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	161	413	0	ENST00000266497.5:c.1073A>G	p.Asp358Gly	p.D358G	ENST00000266497		358	gAt/gGt	5/31	0.378337365627283	3	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	1	0.389737441617559	3		413	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579565	7579583	+	frameshift_variant	Frame_Shift_Del	DEL	TCCATTGCTTGGGACGGCA	TCCATTGCTTGGGACGGCA	CCC	novel	NA	P-0038630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	192	759	3	ENST00000269305.4:c.104_122delinsGGG	p.Leu35TrpfsTer4	p.L35Wfs*4	ENST00000269305	NM_001126112.2	35	tTGCCGTCCCAAGCAATGGAt/tGGGt	4/11	0.389737441617559	2	FACETS	0.771	0.716	0.827	0.771	0.716	0.827	SUBCLONAL	2	TRUE	0	0.389737441617559	2		762	639	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46597047	46597047	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	91	496	0	ENST00000263734.3:c.861G>C	p.Glu287Asp	p.E287D	ENST00000263734	NM_001430.4	287	gaG/gaC	7/16	0.389737441617559	3	FACETS	0.981	0.873	1	0.49	0.436	0.548	CLONAL	1	TRUE	1	0.389737441617559	3		496	569	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860221	151860221	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	179	483	1	ENST00000262189.6:c.10441C>T	p.Gln3481Ter	p.Q3481*	ENST00000262189	NM_170606.2	3481	Cag/Tag	43/59	0.248158791074503	5	FACETS	1	0.967	1	0.72	0.666	0.776	CLONAL	2	TRUE	2	0.389737441617559	5		484	674	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0038631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	289	1107	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.372315906485824	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.372315906485824	2		1107	754	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280007	66280007	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	10	194	0	ENST00000273854.3:c.1682C>A	p.Pro561Gln	p.P561Q	ENST00000273854	NM_004439.5	561	cCa/cAa	7/18	1	2	FACETS	0.298	0.202	0.419	0.298	0.202	0.419	SUBCLONAL	1	TRUE	1	0.372315906485824	2		194	180	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876392	35876392	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	29	588	0	ENST00000303115.3:c.1184A>G	p.Lys395Arg	p.K395R	ENST00000303115	NM_002185.3	395	aAg/aGg	8/8	0.254705907315871	5	FACETS	0.3	0.24	0.37	0.1	0.08	0.124	SUBCLONAL	1	TRUE	2	0.372315906485824	5		588	809	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864658	68864658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1418006656	NA	P-0038631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	90	270	0	ENST00000288368.4:c.29G>A	p.Arg10His	p.R10H	ENST00000288368	NM_024870.2	10	cGc/cAc	1/40	0.310907061588564	4	FACETS	0.878	0.784	0.975	0.878	0.784	0.975	CLONAL	2	TRUE	2	0.372315906485824	4		270	378	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29002038	29002038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757020625	NA	P-0038631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	56	366	0	ENST00000282397.4:c.1127C>T	p.Ala376Val	p.A376V	ENST00000282397	NM_002019.4	376	gCg/gTg	9/30	0.323531134423761	3	FACETS	0.802	0.688	0.925	0.401	0.344	0.463	CLONAL	1	TRUE	1	0.372315906485824	3		366	445	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243675669	243675669	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	27	233	0	ENST00000263826.5:c.1311A>C	p.Glu437Asp	p.E437D	ENST00000263826	NM_005465.4	437	gaA/gaC	12/13	0.372315906485824	5	FACETS	0.564	0.448	0.696			1	SUBCLONAL	1	TRUE	NA	0.372315906485824	5		233	401	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857066	9857066	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	50	307	0	ENST00000330684.3:c.4335A>C	p.Leu1445Phe	p.L1445F	ENST00000330684	NM_001134407.1	1445	ttA/ttC	13/13	0.372315906485824	5	FACETS	0.842	0.715	0.982			1	CLONAL	1	TRUE	NA	0.372315906485824	5		307	497	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713724	30713724	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	58	480	0	ENST00000295754.5:c.1049T>C	p.Leu350Pro	p.L350P	ENST00000295754	NM_003242.5	350	cTg/cCg	4/7	1	2	FACETS	0.642	0.553	0.74	0.642	0.553	0.74	SUBCLONAL	1	TRUE	1	0.372315906485824	2		480	485	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721984	49721984	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	27	207	0	ENST00000449682.2:c.1875A>C	p.Lys625Asn	p.K625N	ENST00000449682	NM_020998.3	625	aaA/aaC	16/18	1	2	FACETS	0.901	0.725	1	0.901	0.725	1	CLONAL	1	TRUE	1	0.372315906485824	2		207	161	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971246	13971246	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	84	462	0	ENST00000405192.2:c.683A>C	p.Lys228Thr	p.K228T	ENST00000405192	NM_001163147.1	228	aAg/aCg	8/12	0.238590113120643	4	FACETS	1	0.889	1	0.503	0.444	0.565	CLONAL	1	TRUE	2	0.372315906485824	4		462	616	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0038632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	197	325	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.779281476195688	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.779281476195688	1		325	231	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0038632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	154	304	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	0.948	0.877	1	0.948	0.877	1	CLONAL	1	TRUE	1	0.779281476195688	2		304	417	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466022	69466022	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	304	949	0	ENST00000227507.2:c.860C>G	p.Pro287Arg	p.P287R	ENST00000227507	NM_053056.2	287	cCc/cGc	5/5	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.779281476195688	2		949	772	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100291	27100291	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0038632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	498	596	1	ENST00000324856.7:c.4005-2A>T		p.X1335_splice	ENST00000324856	NM_006015.4	1335			0.779281476195688	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.779281476195688	1		597	581	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100351	157100352	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	149	332	0	ENST00000346085.5:c.1289dup	p.Met430IlefsTer105	p.M430Ifs*105	ENST00000346085	NM_020732.3	430	atg/aTtg	1/20	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.779281476195688	2		332	368	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833954	44833954	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0038632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	228	467	0	ENST00000377967.4:c.378C>G	p.Tyr126Ter	p.Y126*	ENST00000377967	NM_021140.2	126	taC/taG	4/29	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.779281476195688	2		467	536	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0038633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	83	324	1	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.919	0.816	1	0.919	0.816	1	CLONAL	1	TRUE	1	0.455054833669316	2		325	397	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101195	27101195	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	399	739	0	ENST00000324856.7:c.4477C>T	p.Gln1493Ter	p.Q1493*	ENST00000324856	NM_006015.4	1493	Cag/Tag	18/20	0.442290591063954	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.455054833669316	2		739	818	SUCCESS
APC	324	MSKCC	GRCh37	5	112177133	112177133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	63	352	0	ENST00000257430.4:c.5842G>A	p.Asp1948Asn	p.D1948N	ENST00000257430	NM_000038.5	1948	Gat/Aat	16/16	1	2	FACETS	0.641	0.556	0.733	0.641	0.556	0.733	SUBCLONAL	1	TRUE	1	0.455054833669316	2		352	432	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864739	37864739	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	143	597	1	ENST00000269571.5:c.391G>A	p.Gly131Arg	p.G131R	ENST00000269571		131	Ggg/Agg	3/27	1	2	FACETS	0.869	0.794	0.948	0.869	0.794	0.948	CLONAL	1	TRUE	1	0.455054833669316	2		598	723	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245334	153245334	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0038633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	208	423	0	ENST00000281708.4:c.1855+2T>G		p.X619_splice	ENST00000281708	NM_033632.3	619			0.455054833669316	2	FACETS	0.911	0.854	0.968	0.911	0.854	0.968	CLONAL	2	TRUE	0	0.455054833669316	2		423	502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0038634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	1390	1131	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.722148163347203	3	FACETS	1	0.99	1			1	CLONAL	3	TRUE	NA	0.774619724243642	3		1132	1652	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39321417	39321417	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	284	402	0	ENST00000373001.3:c.604G>C	p.Asp202His	p.D202H	ENST00000373001	NM_022157.3	202	Gac/Cac	3/7	0.774619724243642	3	FACETS	1	0.957	1	0.51	0.48	0.541	CLONAL	1	TRUE	1	0.774619724243642	3		402	997	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562999	21562999	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1482	593	844	0	ENST00000382592.4:c.920C>T	p.Pro307Leu	p.P307L	ENST00000382592	NM_014572.2	307	cCt/cTt	4/8	0.600313147279181	3	FACETS	1	0.976	1			1	CLONAL	1	TRUE	NA	0.774619724243642	3		844	2075	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682152	37682152	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	263	402	1	ENST00000447079.4:c.3343G>A	p.Glu1115Lys	p.E1115K	ENST00000447079	NM_015083.1	1115	Gaa/Aaa	13/14	0.774619724243642	2	FACETS	0.886	0.834	0.94	0.443	0.417	0.47	CLONAL	1	TRUE	0	0.774619724243642	2		403	766	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058712	180058712	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	168	829	0	ENST00000261937.6:c.125A>G	p.Asp42Gly	p.D42G	ENST00000261937	NM_182925.4	42	gAc/gGc	2/30	0.774619724243642	1	FACETS	0.274	0.251	0.298	0.274	0.251	0.298	SUBCLONAL	1	TRUE	0	0.774619724243642	1		829	970	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0038636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	242	704	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.197446599717046	4	FACETS	1	0.958	1	1	0.958	1	CLONAL	3	TRUE	1	0.197446599717046	4		705	948	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs869320707	NA	P-0038636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	212	826	2	ENST00000397752.3:c.3028+1G>T		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.197446599717046	3	FACETS	0.943	0.878	1	0.943	0.878	1	CLONAL	3	TRUE	0	0.197446599717046	3		828	834	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012701	36012701	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	48	177	1	ENST00000358208.4:c.145G>T	p.Gly49Cys	p.G49C	ENST00000358208		49	Ggc/Tgc	2/12	0.175604086245037	4	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	2	0.197446599717046	4		178	238	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876566	35876566	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs767469485	NA	P-0038636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	92	540	0	ENST00000303115.3:c.1358C>A	p.Ser453Tyr	p.S453Y	ENST00000303115	NM_002185.3	453	tCc/tAc	8/8	0.197446599717046	3	FACETS	0.815	0.725	0.911	0.815	0.725	0.911	CLONAL	2	TRUE	1	0.197446599717046	3		540	628	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902221	151902221	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1378676586	NA	P-0038636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	62	593	0	ENST00000262189.6:c.3931A>G	p.Ile1311Val	p.I1311V	ENST00000262189	NM_170606.2	1311	Att/Gtt	25/59	0.197446599717046	6	FACETS	1	0.958	1	0.216	0.186	0.249	CLONAL	1	TRUE	0	0.197446599717046	6		593	676	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	294	404	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.991	1	1	0.996	1	CLONAL	2	TRUE	1	0.402398430562543	2		405	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882019	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	233	754	1	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	0.402398430562543	2		755	920	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	161	795	1	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.402398430562543	2		796	737	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741915	17741915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	75	255	0	ENST00000250003.3:c.586G>A	p.Asp196Asn	p.D196N	ENST00000250003	NM_002478.4	196	Gac/Aac	1/3	1	2	FACETS	0.836	0.745	0.93	1	0.981	1	CLONAL	2	TRUE	1	0.402398430562543	2		255	223	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	47	895	3	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.345	0.29	0.405	0.345	0.29	0.405	SUBCLONAL	1	TRUE	1	0.402398430562543	2		898	678	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772951	135772951	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs118203724	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	93	380	0	ENST00000298552.3:c.2672del	p.Asn891ThrfsTer40	p.N891Tfs*40	ENST00000298552	NM_001162426.1	891	aAc/ac	21/23	1	2	FACETS	0.996	0.89	1	0.996	0.89	1	CLONAL	1	TRUE	1	0.402398430562543	2		380	464	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107096	27107096	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	26	543	0	ENST00000324856.7:c.6707G>C	p.Arg2236Pro	p.R2236P	ENST00000324856	NM_006015.4	2236	cGc/cCc	20/20	1	2	FACETS	0.27	0.213	0.335	0.27	0.213	0.335	SUBCLONAL	1	TRUE	1	0.402398430562543	2		543	479	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	126	563	4	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.402398430562543	2		567	484	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903745	41903746	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	161	817	0	ENST00000372991.4:c.811dup	p.Arg271ProfsTer53	p.R271Pfs*53	ENST00000372991	NM_001760.3	271	cgg/cCgg	5/5	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.402398430562543	2		817	636	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759905	133759905	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369171735	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	44	885	1	ENST00000318560.5:c.2228C>T	p.Thr743Met	p.T743M	ENST00000318560	NM_005157.4	743	aCg/aTg	11/11	1	2	FACETS	0.283	0.236	0.334	0.283	0.236	0.334	SUBCLONAL	1	TRUE	1	0.402398430562543	2		886	774	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416659	29416659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	105	343	0	ENST00000389048.3:c.4294C>T	p.Arg1432Trp	p.R1432W	ENST00000389048	NM_004304.4	1432	Cgg/Tgg	29/29	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.402398430562543	2		343	357	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992721	68992721	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs764112302	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	32	641	1	ENST00000288368.4:c.1693del	p.Ser565ArgfsTer10	p.S565Rfs*10	ENST00000288368	NM_024870.2	562	cgT/cg	16/40	1	2	FACETS	0.305	0.247	0.371	0.305	0.247	0.371	SUBCLONAL	1	TRUE	1	0.402398430562543	2		642	521	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210697	36210697	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	173	864	1	ENST00000222270.7:c.448C>T	p.Arg150Ter	p.R150*	ENST00000222270	NM_014727.1	150	Cga/Tga	3/37	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.402398430562543	2		865	689	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129400	2129400	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs137854302	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	148	882	2	ENST00000219476.3:c.3259del	p.Glu1087SerfsTer16	p.E1087Sfs*16	ENST00000219476	NM_000548.3	1085	tcG/tc	28/42	1	2	FACETS	0.99	0.906	1	0.99	0.906	1	CLONAL	1	TRUE	1	0.402398430562543	2		884	743	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739012	145739012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373292946	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	47	747	0	ENST00000428558.2:c.2143C>T	p.Arg715Trp	p.R715W	ENST00000428558	NM_004260.3	715	Cgg/Tgg	13/22	1	2	FACETS	0.32	0.269	0.376	0.32	0.269	0.376	SUBCLONAL	1	TRUE	1	0.402398430562543	2		747	730	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921541	39921541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	177	805	0	ENST00000378444.4:c.4279C>T	p.Pro1427Ser	p.P1427S	ENST00000378444	NM_001123385.1	1427	Cca/Tca	10/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.402398430562543	2		805	770	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858503	27858503	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	58	367	0	ENST00000359303.2:c.68C>T	p.Thr23Ile	p.T23I	ENST00000359303	NM_003535.2	23	aCc/aTc	1/1	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.402398430562543	2		367	265	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912186	114912186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	42	602	0	ENST00000543371.1:c.1256C>T	p.Ala419Val	p.A419V	ENST00000543371	NM_001198531.1	419	gCg/gTg	11/14	1	2	FACETS	0.382	0.318	0.452	0.382	0.318	0.452	SUBCLONAL	1	TRUE	1	0.402398430562543	2		602	547	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850965	63850965	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	118	628	0	ENST00000279873.7:c.1746del	p.Phe582LeufsTer47	p.F582Lfs*47	ENST00000279873	NM_032199.2	581	tgT/tg	10/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.402398430562543	2		628	543	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112767332	112767332	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	57	468	0	ENST00000369452.4:c.1205C>T	p.Thr402Ile	p.T402I	ENST00000369452	NM_007373.3	402	aCc/aTc	6/9	1	2	FACETS	0.812	0.7	0.932	0.812	0.7	0.932	CLONAL	1	TRUE	1	0.402398430562543	2		468	349	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219486	133219487	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs754220952	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	193	880	0	ENST00000320574.5:c.4647dup	p.Lys1550GlnfsTer11	p.K1550Qfs*11	ENST00000320574	NM_006231.2	1549	-/C	36/49	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.402398430562543	2		880	768	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312717	91312717	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1265964518	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	93	406	0	ENST00000355112.3:c.2456A>G	p.Gln819Arg	p.Q819R	ENST00000355112	NM_000057.2	819	cAg/cGg	12/22	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.402398430562543	2		406	408	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347755	347755	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	146	994	2	ENST00000262320.3:c.1751C>A	p.Ala584Asp	p.A584D	ENST00000262320	NM_003502.3	584	gCt/gAt	6/11	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.402398430562543	2		996	692	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646713	23646713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	26	612	0	ENST00000261584.4:c.1154C>T	p.Ala385Val	p.A385V	ENST00000261584	NM_024675.3	385	gCa/gTa	4/13	1	2	FACETS	0.253	0.2	0.315	0.253	0.2	0.315	SUBCLONAL	1	TRUE	1	0.402398430562543	2		612	510	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134381	30134381	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	43	826	0	ENST00000263025.4:c.150G>T	p.Glu50Asp	p.E50D	ENST00000263025	NM_002746.2	50	gaG/gaT	1/9	1	2	FACETS	0.307	0.256	0.364	0.307	0.256	0.364	SUBCLONAL	1	TRUE	1	0.402398430562543	2		826	696	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863665	68863665	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	119	603	0	ENST00000261769.5:c.2404G>A	p.Ala802Thr	p.A802T	ENST00000261769	NM_004360.3	802	Gcc/Acc	15/16	1	2	FACETS	0.974	0.882	1	0.974	0.882	1	CLONAL	1	TRUE	1	0.402398430562543	2		603	607	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56412983	56412983	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	90	381	1	ENST00000348428.3:c.1997A>G	p.His666Arg	p.H666R	ENST00000348428	NM_006785.3	666	cAt/cGt	16/17	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.402398430562543	2		382	371	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223673	36223673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	50	1111	0	ENST00000222270.7:c.6223G>A	p.Val2075Met	p.V2075M	ENST00000222270	NM_014727.1	2075	Gtg/Atg	28/37	1	2	FACETS	0.317	0.268	0.372	0.317	0.268	0.372	SUBCLONAL	1	TRUE	1	0.402398430562543	2		1111	783	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855577	45855577	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764868582	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	234	890	0	ENST00000391945.4:c.2080C>T	p.Pro694Ser	p.P694S	ENST00000391945	NM_000400.3	694	Ccc/Tcc	22/23	1	2	FACETS	0.81	0.759	0.862	1	0.993	1	CLONAL	2	TRUE	1	0.402398430562543	2		890	718	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149570	202149570	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	61	469	0	ENST00000358485.4:c.1014del	p.Phe338LeufsTer11	p.F338Lfs*11	ENST00000358485	NM_001080125.1	337	caT/ca	8/9	1	2	FACETS	0.811	0.703	0.927	0.811	0.703	0.927	CLONAL	1	TRUE	1	0.402398430562543	2		469	374	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164877	36164877	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200104203	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	187	1011	0	ENST00000300305.3:c.998C>T	p.Pro333Leu	p.P333L	ENST00000300305		333	cCg/cTg	8/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.402398430562543	2		1011	745	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42861448	42861448	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	108	579	0	ENST00000398585.3:c.422T>G	p.Leu141Arg	p.L141R	ENST00000398585	NM_001135099.1	141	cTa/cGa	4/14	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.402398430562543	2		579	491	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21304083	21304083	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	39	676	0	ENST00000354336.3:c.862T>C	p.Phe288Leu	p.F288L	ENST00000354336	NM_005207.3	288	Ttt/Ctt	3/3	1	2	FACETS	0.279	0.231	0.334	0.279	0.231	0.334	SUBCLONAL	1	TRUE	1	0.402398430562543	2		676	694	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439387	149439387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1392968737	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	120	730	3	ENST00000286301.3:c.2008G>A	p.Asp670Asn	p.D670N	ENST00000286301	NM_005211.3	670	Gac/Aac	15/22	0.380394727000186	1	FACETS	0.781	0.707	0.859	0.781	0.707	0.859	SUBCLONAL	1	TRUE	0	0.402398430562543	1		733	610	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520286	176520286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764568046	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	66	783	0	ENST00000292408.4:c.1205C>T	p.Pro402Leu	p.P402L	ENST00000292408	NM_213647.1	402	cCg/cTg	9/18	1	2	FACETS	0.585	0.508	0.668	0.585	0.508	0.668	SUBCLONAL	1	TRUE	1	0.402398430562543	2		783	561	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323308	31323308	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	59	149	0	ENST00000412585.2:c.681C>A	p.Cys227Ter	p.C227*	ENST00000412585	NM_005514.6	227	tgC/tgA	4/8	1	2	FACETS	0.971	0.856	1	1	0.98	1	CLONAL	2	TRUE	1	0.402398430562543	2		149	151	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38194848	38194848	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	41	604	0	ENST00000317025.8:c.885G>T	p.Glu295Asp	p.E295D	ENST00000317025	NM_023034.1	295	gaG/gaT	4/24	1	2	FACETS	0.298	0.248	0.355	0.298	0.248	0.355	SUBCLONAL	1	TRUE	1	0.402398430562543	2		604	683	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104654	69104654	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	121	660	0	ENST00000288368.4:c.4498A>G	p.Asn1500Asp	p.N1500D	ENST00000288368	NM_024870.2	1500	Aac/Gac	37/40	1	2	FACETS	0.968	0.877	1	0.968	0.877	1	CLONAL	1	TRUE	1	0.402398430562543	2		660	621	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864898	117864898	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1357605618	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	116	406	0	ENST00000297338.2:c.1211G>A	p.Arg404Lys	p.R404K	ENST00000297338	NM_006265.2	404	aGg/aAg	10/14	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.402398430562543	2		406	419	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409816	139409816	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	56	1036	1	ENST00000277541.6:c.1940G>A	p.Ser647Asn	p.S647N	ENST00000277541	NM_017617.3	647	aGc/aAc	12/34	1	2	FACETS	0.329	0.281	0.382	0.329	0.281	0.382	SUBCLONAL	1	TRUE	1	0.402398430562543	2		1037	845	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937221	76937221	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	71	521	1	ENST00000373344.5:c.3527del	p.Lys1176ArgfsTer14	p.K1176Rfs*14	ENST00000373344	NM_000489.3	1176	aAg/ag	9/35	1	2	FACETS	0.941	0.826	1	0.941	0.826	1	CLONAL	1	TRUE	1	0.402398430562543	2		522	375	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0038641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	37	523	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.94	0.775	1	0.94	0.775	1	CLONAL	1	TRUE	1	0.17	2		523	463	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0038641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	31	386	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.737	0.595	0.898	0.737	0.595	0.898	SUBCLONAL	1	TRUE	1	0.17	2		387	495	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0038641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	30	503	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.618	0.497	0.757	0.618	0.497	0.757	SUBCLONAL	1	TRUE	1	0.17	2		503	571	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844172	68844172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	89	703	0	ENST00000261769.5:c.760G>A	p.Asp254Asn	p.D254N	ENST00000261769	NM_004360.3	254	Gat/Aat	6/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.17	2		703	807	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118924	70118926	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0038641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	61	774	0	ENST00000245479.2:c.499_501del	p.Lys167del	p.K167del	ENST00000245479	NM_000346.3	166	AAG/-	2/3	1	2	FACETS	0.795	0.684	0.916	0.795	0.684	0.916	CLONAL	1	TRUE	1	0.17	2		774	903	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117935	70117935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	24	408	0	ENST00000245479.2:c.403C>T	p.Leu135Phe	p.L135F	ENST00000245479	NM_000346.3	135	Ctc/Ttc	1/3	1	2	FACETS	0.614	0.48	0.769	0.614	0.48	0.769	SUBCLONAL	1	TRUE	1	0.17	2		408	460	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732958	30732958	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	33	365	0	ENST00000295754.5:c.1571A>G	p.Asp524Gly	p.D524G	ENST00000295754	NM_003242.5	524	gAc/gGc	7/7	1	2	FACETS	0.878	0.715	1	0.878	0.715	1	CLONAL	1	TRUE	1	0.17	2		365	442	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443864	52443864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	91	747	0	ENST00000460680.1:c.31G>A	p.Asp11Asn	p.D11N	ENST00000460680	NM_004656.3	11	Gac/Aac	1/17	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.17	2		747	893	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	160	578	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.138005294695602	5	FACETS	1	0.983	1			1	INDETERMINATE	2	FALSE	NA	0.409699752152009	5		578	515	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440943	56440943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786205215	NA	P-0038642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	126	512	1	ENST00000407977.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000407977		132	Cga/Tga	4/10	0.174021327519662	2	FACETS	0.64	0.579	0.705	0.32	0.289	0.353	INDETERMINATE	1	FALSE	0	0.409699752152009	2		513	961	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578496	7578496	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	414	873	0	ENST00000269305.4:c.434T>G	p.Leu145Arg	p.L145R	ENST00000269305	NM_001126112.2	145	cTg/cGg	5/11	0.327984074129077	2	FACETS	0.83	0.791	0.87	0.83	0.791	0.87	CLONAL	2	FALSE	0	0.409699752152009	2		873	1217	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425125	49425125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530054198	NA	P-0038642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	434	837	0	ENST00000301067.7:c.13363C>T	p.Arg4455Cys	p.R4455C	ENST00000301067	NM_003482.3	4455	Cgc/Tgc	39/54	0.388304350597175	2	FACETS	0.895	0.854	0.936	0.895	0.854	0.936	CLONAL	2	FALSE	0	0.409699752152009	2		837	1184	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759930	63759930	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	51	287	0	ENST00000279873.7:c.583C>A	p.Gln195Lys	p.Q195K	ENST00000279873	NM_032199.2	195	Cag/Aag	4/10	1	2	FACETS	0.77	0.657	0.893	0.77	0.657	0.893	SUBCLONAL	1	TRUE	1	0.372072946048725	2		287	356	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617734	39617734	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	41	386	0	ENST00000262039.4:c.1918G>A	p.Asp640Asn	p.D640N	ENST00000262039	NM_002647.2	640	Gat/Aat	17/25	1	2	FACETS	0.505	0.421	0.599	0.505	0.421	0.599	SUBCLONAL	1	TRUE	1	0.372072946048725	2		386	436	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323978	31323978	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	22	146	0	ENST00000412585.2:c.585C>A	p.Tyr195Ter	p.Y195*	ENST00000412585	NM_005514.6	195	taC/taA	3/8	1	2	FACETS	0.816	0.639	1	0.816	0.639	1	CLONAL	1	TRUE	1	0.372072946048725	2		146	145	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249426	110249426	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs752741545	NA	P-0038644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	118	987	0	ENST00000374672.4:c.1147A>G	p.Arg383Gly	p.R383G	ENST00000374672	NM_004235.4	383	Agg/Ggg	4/5	1	2	FACETS	0.609	0.548	0.673	0.609	0.548	0.673	SUBCLONAL	1	TRUE	1	0.372072946048725	2		987	1042	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0038645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	290	625	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.46985164359602	2	FACETS	0.795	0.755	0.836	0.795	0.755	0.836	SUBCLONAL	2	TRUE	0	0.587299756083413	2		627	621	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	125	578	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.472953696280292	4	FACETS	1	0.985	1	0.711	0.648	0.777	CLONAL	1	TRUE	2	0.587299756083413	4		578	475	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104712	193104712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	104	262	0	ENST00000367435.3:c.416G>A	p.Arg139Gln	p.R139Q	ENST00000367435	NM_024529.4	139	cGa/cAa	5/17	0.587299756083413	5	FACETS	1	0.979	1	0.455	0.409	0.503	CLONAL	1	TRUE	2	0.587299756083413	5		262	488	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50483727	50483727	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200921207	NA	P-0038645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	154	478	0	ENST00000394963.4:c.832G>A	p.Val278Met	p.V278M	ENST00000394963	NM_003076.4	278	Gtg/Atg	7/13	0.472953696280292	4	FACETS	1	0.922	1	0.503	0.461	0.548	CLONAL	1	TRUE	2	0.587299756083413	4		478	827	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262259	16262259	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	53	199	1	ENST00000375759.3:c.9524C>T	p.Ser3175Leu	p.S3175L	ENST00000375759	NM_015001.2	3175	tCa/tTa	11/15	0.472953696280292	4	FACETS	0.85	0.729	0.982	0.425	0.364	0.491	CLONAL	1	TRUE	2	0.587299756083413	4		200	337	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355078	73355078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	61	351	0	ENST00000377767.4:c.292G>A	p.Val98Met	p.V98M	ENST00000377767	NM_014953.3	98	Gtg/Atg	2/21	0.465488018229817	3	FACETS	0.551	0.476	0.632	0.275	0.238	0.316	SUBCLONAL	1	TRUE	1	0.587299756083413	3		351	488	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0038647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	78	622	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.780624943890002	2	FACETS	0.898	0.803	0.996	0.449	0.401	0.498	CLONAL	1	TRUE	0	0.793295579472165	2		622	219	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0038647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	247	332	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.779394840450505	2	FACETS	0.908	0.871	0.943	0.908	0.871	0.943	CLONAL	2	TRUE	0	0.793295579472165	2		332	343	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0038647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	751	875	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	2	TRUE	NA	0.793295579472165	2		876	938	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748596	40748596	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754546663	NA	P-0038647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	172	513	1	ENST00000373198.4:c.2920C>T	p.Arg974Trp	p.R974W	ENST00000373198	NM_133170.3	974	Cgg/Tgg	21/32	0.764015201510855	4	FACETS	0.854	0.786	0.925	0.285	0.262	0.309	CLONAL	1	TRUE	1	0.793295579472165	4		514	911	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575150	48575150	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	85	396	1	ENST00000342988.3:c.344G>C	p.Cys115Ser	p.C115S	ENST00000342988	NM_005359.5	115	tGt/tCt	3/12	0.793295579472165	1	FACETS	0.995	0.918	1	0.995	0.918	1	CLONAL	1	TRUE	0	0.793295579472165	1		397	130	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225060	NA	P-0038647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	91	565	4	ENST00000263967.3:c.311C>T	p.Pro104Leu	p.P104L	ENST00000263967	NM_006218.2	104	cCa/cTa	2/21	0.780624943890002	2	FACETS	0.91	0.821	1	0.455	0.41	0.501	CLONAL	1	TRUE	0	0.793295579472165	2		569	252	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411441	63411441	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	732	446	4	ENST00000330258.3:c.1726G>T	p.Glu576Ter	p.E576*	ENST00000330258	NM_152424.3	576	Gag/Tag	2/2	0.721044284234009	2	FACETS	1	0.998	1			1	CLONAL	2	TRUE	NA	0.793295579472165	2		450	833	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0038656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	64	451	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.735	0.637	0.841	0.735	0.637	0.841	SUBCLONAL	1	TRUE	1	0.332187757020279	2		451	524	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584513	48584514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs377767334	NA	P-0038656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	74	444	0	ENST00000342988.3:c.692dup	p.Ser232GlnfsTer3	p.S232Qfs*3	ENST00000342988	NM_005359.5	229	ctg/ctGg	6/12	0.332187757020279	1	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	0	0.332187757020279	1		444	364	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0038656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	105	855	0	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.332187757020279	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.332187757020279	1		855	475	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198986	67198986	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	60	393	1	ENST00000312629.5:c.457G>A	p.Gly153Ser	p.G153S	ENST00000312629	NM_003952.2	153	Ggt/Agt	5/15	1	2	FACETS	0.888	0.767	1	0.888	0.767	1	CLONAL	1	TRUE	1	0.332187757020279	2		394	407	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974762	21974768	+	frameshift_variant	Frame_Shift_Del	DEL	CGGGCCG	CGGGCCG	-	novel	NA	P-0038656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	61	278	0	ENST00000304494.5:c.59_65del	p.Ala20GlyfsTer4	p.A20Gfs*4	ENST00000304494	NM_000077.4	20	gCGGCCCGg/gg	1/3	0.332187757020279	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.332187757020279	1		278	260	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0038658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	98	772	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.496262359808431	7	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.496262359808431	7		773	639	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0038658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	401	472	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.496262359808431	7	FACETS	0.965	0.942	0.986			1	CLONAL	8	TRUE	NA	0.496262359808431	7		472	469	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374390	31374390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773207465	NA	P-0038658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	48	211	0	ENST00000328111.2:c.389G>A	p.Arg130His	p.R130H	ENST00000328111	NM_006892.3	130	cGc/cAc	5/23	0.45102152642329	2	FACETS	0.676	0.575	0.786	0.338	0.287	0.393	SUBCLONAL	1	TRUE	0	0.496262359808431	2		211	286	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523285	9523285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767541766	NA	P-0038658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	87	247	0	ENST00000353224.5:c.1952C>T	p.Ala651Val	p.A651V	ENST00000353224	NM_177990.2	651	gCg/gTg	9/10	0.45102152642329	2	FACETS	1	0.971	1	0.619	0.555	0.686	CLONAL	1	TRUE	0	0.496262359808431	2		247	283	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63819026	63819026	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	34	174	0	ENST00000279873.7:c.1073C>G	p.Ala358Gly	p.A358G	ENST00000279873	NM_032199.2	358	gCt/gGt	7/10	0.496262359808431	7	FACETS	0.793	0.649	0.956			1	CLONAL	1	TRUE	NA	0.496262359808431	7		174	387	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608225	28608225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	75	250	0	ENST00000241453.7:c.1831G>A	p.Glu611Lys	p.E611K	ENST00000241453	NM_004119.2	611	Gag/Aag	14/24	0.50504900128727	1	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	0	0.496262359808431	1		250	227	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004489	150004489	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	131	252	0	ENST00000253339.5:c.1736C>T	p.Pro579Leu	p.P579L	ENST00000253339		579	cCt/cTt	3/7	NA	2	FACETS	0.795	0.732	0.86			1	INDETERMINATE	2	TRUE	NA	0.496262359808431	2		252	332	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0038659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	110	220	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.776684074646401	2		220	279	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578226	7578226	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1464727668	NA	P-0038659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	224	815	0	ENST00000269305.4:c.623A>T	p.Asp208Val	p.D208V	ENST00000269305	NM_001126112.2	208	gAc/gTc	6/11	1	2	FACETS	0.92	0.862	0.979	0.92	0.862	0.979	CLONAL	1	TRUE	1	0.776684074646401	2		815	627	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653814	89653814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780004	NA	P-0038659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	51	496	0	ENST00000371953.3:c.112C>T	p.Pro38Ser	p.P38S	ENST00000371953	NM_000314.4	38	Cct/Tct	2/9	0.776684074646401	1	FACETS	0.359	0.308	0.413	0.359	0.308	0.413	SUBCLONAL	1	TRUE	0	0.776684074646401	1		496	224	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653814	89653814	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587780004	NA	P-0038659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	87	496	0	ENST00000371953.3:c.112C>A	p.Pro38Thr	p.P38T	ENST00000371953	NM_000314.4	38	Cct/Act	2/9	0.776684074646401	1	FACETS	0.612	0.552	0.673	0.612	0.552	0.673	SUBCLONAL	1	TRUE	0	0.776684074646401	1		496	224	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919309	48919309	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1319691084	NA	P-0038659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	21	238	0	ENST00000267163.4:c.474G>C	p.Leu158Phe	p.L158F	ENST00000267163	NM_000321.2	158	ttG/ttC	4/27	1	2	FACETS	0.233	0.18	0.295	0.233	0.18	0.295	SUBCLONAL	1	TRUE	1	0.776684074646401	2		238	232	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577499	7577499	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs786203396	NA	P-0038659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	180	658	0	ENST00000269305.4:c.782G>C	p.Ser261Thr	p.S261T	ENST00000269305	NM_001126112.2	261	aGt/aCt	7/11	1	2	FACETS	0.911	0.847	0.976	0.911	0.847	0.976	CLONAL	1	TRUE	1	0.776684074646401	2		658	509	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352334	70352334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	54	605	0	ENST00000374080.3:c.4361G>A	p.Gly1454Asp	p.G1454D	ENST00000374080		1454	gGt/gAt	31/45	0.521809442667609	2	FACETS	0.329	0.282	0.381	0.165	0.141	0.191	SUBCLONAL	1	TRUE	0	0.757268384842789	2		605	433	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0038661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	69	455	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.923	0.807	1	1	0.98	1	CLONAL	2	TRUE	1	0.178905366579502	2		455	418	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732533	74732533	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	19	251	0	ENST00000359995.5:c.376C>T	p.Arg126Cys	p.R126C	ENST00000359995	NM_001195427.1	126	Cgc/Tgc	2/3	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.178905366579502	2		251	160	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061621	38061621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	53	400	0	ENST00000250448.2:c.368C>T	p.Ser123Phe	p.S123F	ENST00000250448	NM_004496.3	123	tCc/tTc	2/2	1	2	FACETS	1	0.92	1	1	0.978	1	CLONAL	2	TRUE	1	0.178905366579502	2		400	268	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160643	56160658	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGTGTTAACAAAGT	GCCGTGTTAACAAAGT	-	novel	NA	P-0038661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	50	481	0	ENST00000399503.3:c.918_933del	p.Arg307CysfsTer11	p.R307Cfs*11	ENST00000399503	NM_005921.1	306	cGCCGTGTTAACAAAGTg/cg	4/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.178905366579502	2		481	398	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184057	56184057	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	64	344	0	ENST00000399503.3:c.4262T>G	p.Leu1421Arg	p.L1421R	ENST00000399503	NM_005921.1	1421	cTa/cGa	19/20	1	2	FACETS	0.994	0.865	1	1	0.98	1	CLONAL	2	TRUE	1	0.178905366579502	2		344	360	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944982	31944982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	87	857	3	ENST00000340398.3:c.119G>A	p.Arg40His	p.R40H	ENST00000340398	NM_001013699.2	40	cGc/cAc	1/1	1	2	FACETS	0.502	0.443	0.565	0.502	0.443	0.565	SUBCLONAL	1	TRUE	1	0.347259686568573	2		860	999	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726656	88726656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1222707412	NA	P-0038662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	130	566	0	ENST00000360948.2:c.388C>T	p.Arg130Cys	p.R130C	ENST00000360948	NM_001012338.2	130	Cgt/Tgt	4/19	0.347259686568573	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.347259686568573	1		566	595	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825400	134825400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749679220	NA	P-0038662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	184	638	2	ENST00000398015.3:c.916G>A	p.Gly306Ser	p.G306S	ENST00000398015	NM_004441.4	306	Ggt/Agt	4/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.347259686568573	2		640	862	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	104	399	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.862	0.781	0.946	0.862	0.781	0.946	CLONAL	1	TRUE	1	0.739860912006122	2		399	326	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0038666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	81	382	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.739860912006122	2		382	209	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799059	42799059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	166	1029	5	ENST00000575354.2:c.4543C>T	p.Arg1515Cys	p.R1515C	ENST00000575354	NM_015125.3	1515	Cgc/Tgc	20/20	0.739860912006122	1	FACETS	0.615	0.57	0.66	0.615	0.57	0.66	SUBCLONAL	1	TRUE	0	0.739860912006122	1		1034	460	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793462	42793462	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	42	765	1	ENST00000575354.2:c.1264C>T	p.Arg422Ter	p.R422*	ENST00000575354	NM_015125.3	422	Cga/Tga	8/20	0.739860912006122	1	FACETS	0.189	0.158	0.223	0.189	0.158	0.223	SUBCLONAL	1	TRUE	0	0.739860912006122	1		766	379	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791836	42791836	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	29	727	0	ENST00000575354.2:c.722T>G	p.Leu241Arg	p.L241R	ENST00000575354	NM_015125.3	241	cTg/cGg	5/20	0.739860912006122	1	FACETS	0.111	0.089	0.137	0.111	0.089	0.137	SUBCLONAL	1	TRUE	0	0.739860912006122	1		727	443	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	132	142	0	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	1	2	FACETS	0.87	0.793	0.95	0.87	0.793	0.95	CLONAL	1	TRUE	1	0.538782813948205	2		142	563	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780650	56780662	+	frameshift_variant	Frame_Shift_Del	DEL	AAGTTTATCTTCT	AAGTTTATCTTCT	-	novel	NA	P-0038668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	108	120	0	ENST00000337432.4:c.665_677del	p.Gln222LeufsTer13	p.Q222Lfs*13	ENST00000337432	NM_058216.2	222	cAAGTTTATCTTCTt/ct	4/9	1	2	FACETS	0.741	0.667	0.819	0.741	0.667	0.819	SUBCLONAL	1	TRUE	1	0.538782813948205	2		120	541	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593640	55593660	+	inframe_deletion	In_Frame_Del	DEL	TTTACATAGACCCAACACAAC	TTTACATAGACCCAACACAAC	-	novel	NA	P-0038669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	112	475	0	ENST00000288135.5:c.1708_1728del	p.Tyr570_Leu576del	p.Y570_L576del	ENST00000288135	NM_000222.2	569	gTTTACATAGACCCAACACAACtt/gtt	11/21	1	2	FACETS	0.917	0.834	1	0.917	0.834	1	CLONAL	1	TRUE	1	0.703952228837926	2		475	347	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090383	77090383	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	221	473	0	ENST00000356341.3:c.342G>C	p.Lys114Asn	p.K114N	ENST00000356341	NM_002576.4	114	aaG/aaC	4/15	1	2	FACETS	0.964	0.903	1	0.964	0.903	1	CLONAL	1	TRUE	1	0.703952228837926	2		473	651	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224493	108224493	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs748192003	NA	P-0038670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	27	296	2	ENST00000278616.4:c.8672G>A	p.Gly2891Asp	p.G2891D	ENST00000278616	NM_000051.3	2891	gGt/gAt	60/63	0.496678735117111	1	FACETS	0.434	0.349	0.528	0.434	0.349	0.528	SUBCLONAL	1	TRUE	0	0.560321672909411	1		298	160	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249086	55249086	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	505	725	3	ENST00000275493.2:c.2384T>G	p.Phe795Cys	p.F795C	ENST00000275493	NM_005228.3	795	tTc/tGc	20/28	0.498492503169614	3	FACETS	0.868	0.832	0.905	0.868	0.832	0.905	CLONAL	2	TRUE	1	0.560321672909411	3		728	1329	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443697	29443697	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs281864719	NA	P-0121454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	217	535	0	ENST00000389048.3:c.3520T>C	p.Phe1174Leu	p.F1174L	ENST00000389048	NM_004304.4	1174	Ttc/Ctc	23/29	0.728460675359788	3	FACETS	1	0.986	1	0.599	0.559	0.639	CLONAL	1	NA	1	0.728460675359788	3		535	679	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954180	32954180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45580035	NA	P-0121454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	129	471	0	ENST00000380152.3:c.9154C>T	p.Arg3052Trp	p.R3052W	ENST00000380152		3052	Cgg/Tgg	24/27	0.705766807536773	4	FACETS	0.824	0.748	0.904	0.412	0.374	0.452	CLONAL	1	NA	2	0.728460675359788	4		471	743	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170015135	170015135	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	210	726	0	ENST00000295797.4:c.1541C>A	p.Ala514Asp	p.A514D	ENST00000295797	NM_002740.5	514	gCt/gAt	16/18	0.723425176280969	2	FACETS	0.959	0.897	1	0.48	0.448	0.512	CLONAL	1	NA	0	0.728460675359788	2		726	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519975	NA	P-0038673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	171	729	0	ENST00000269305.4:c.403T>C	p.Cys135Arg	p.C135R	ENST00000269305	NM_001126112.2	135	Tgc/Cgc	5/11	0.267128393812354	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.284315067097723	1		729	1010	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595638	55595638	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1268795324	NA	P-0038673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	41	221	0	ENST00000288135.5:c.2128A>G	p.Lys710Glu	p.K710E	ENST00000288135	NM_000222.2	710	Aag/Gag	14/21	0.267128393812354	1	FACETS	0.913	0.765	1	0.913	0.765	1	CLONAL	1	TRUE	0	0.284315067097723	1		221	271	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588678	28588678	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	42	313	0	ENST00000241453.7:c.2770T>A	p.Ser924Thr	p.S924T	ENST00000241453	NM_004119.2	924	Tcc/Acc	23/24	1	2	FACETS	0.695	0.581	0.822	0.695	0.581	0.822	SUBCLONAL	1	TRUE	1	0.284315067097723	2		313	425	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629152	14629152	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs891936896	NA	P-0038673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	75	430	0	ENST00000254322.2:c.10G>A	p.Asp4Asn	p.D4N	ENST00000254322	NM_006145.1	4	Gac/Aac	1/3	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.284315067097723	2		430	507	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508343	106508343	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	45	350	0	ENST00000359195.3:c.337T>A	p.Tyr113Asn	p.Y113N	ENST00000359195	NM_002649.2	113	Tac/Aac	2/11	1	2	FACETS	0.824	0.694	0.967	0.824	0.694	0.967	CLONAL	1	TRUE	1	0.284315067097723	2		350	384	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0038675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	50	347	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.296259768941007	4	FACETS	1	0.956	1	0.678	0.578	0.786	CLONAL	1	TRUE	2	0.312309524883706	4		347	310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0038675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	79	796	1	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.201224135509657	3	FACETS	1	0.889	1	0.337	0.296	0.38	CLONAL	1	TRUE	0	0.312309524883706	3		797	579	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0038677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	128	768	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	1	2	FACETS	1	0.972	1	1	0.993	1	CLONAL	3	TRUE	1	0.15	2		768	490	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057682	27057682	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520585	NA	P-0038678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	138	662	1	ENST00000324856.7:c.1390C>T	p.Gln464Ter	p.Q464*	ENST00000324856	NM_006015.4	464	Caa/Taa	3/20	0.837350191316277	2	FACETS	0.787	0.723	0.853	0.393	0.361	0.427	SUBCLONAL	1	TRUE	0	0.837350191316277	2		663	419	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289247	33289247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1455644209	NA	P-0038678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	301	591	0	ENST00000374542.5:c.305C>T	p.Ser102Leu	p.S102L	ENST00000374542	NM_001141970.1	102	tCg/tTg	3/8	0.837350191316277	2	FACETS	0.974	0.944	1	0.974	0.944	1	CLONAL	2	TRUE	0	0.837350191316277	2		591	369	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438640	49438640	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1374905609	NA	P-0038678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	443	737	2	ENST00000301067.7:c.4850G>A	p.Arg1617Gln	p.R1617Q	ENST00000301067	NM_003482.3	1617	cGg/cAg	19/54	0.507283562637179	6	FACETS	0.985	0.944	1	0.985	0.944	1	CLONAL	3	TRUE	3	0.837350191316277	6		739	958	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033964	49033964	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778859	NA	P-0038678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	209	392	1	ENST00000267163.4:c.2101G>A	p.Asp701Asn	p.D701N	ENST00000267163	NM_000321.2	701	Gac/Aac	20/27	0.837350191316277	2	FACETS	0.956	0.92	0.99	0.956	0.92	0.99	CLONAL	2	TRUE	0	0.837350191316277	2		393	261	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057649	27057649	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	100	572	0	ENST00000324856.7:c.1357C>A	p.Pro453Thr	p.P453T	ENST00000324856	NM_006015.4	453	Cct/Act	3/20	0.837350191316277	2	FACETS	0.796	0.72	0.874	0.398	0.36	0.437	SUBCLONAL	1	TRUE	0	0.837350191316277	2		572	300	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057719	27057719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	186	730	0	ENST00000324856.7:c.1427C>T	p.Pro476Leu	p.P476L	ENST00000324856	NM_006015.4	476	cCt/cTt	3/20	0.837350191316277	2	FACETS	0.824	0.767	0.883	0.412	0.383	0.442	CLONAL	1	TRUE	0	0.837350191316277	2		730	539	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956084	175956084	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs751253552	NA	P-0038678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	141	336	0	ENST00000367669.3:c.2128G>C	p.Asp710His	p.D710H	ENST00000367669	NM_022457.5	710	Gat/Cat	18/20	0.33800617378769	6	FACETS	0.858	0.792	0.925	0.858	0.792	0.925	INDETERMINATE	3	TRUE	3	0.837350191316277	6		336	350	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431242	49431243	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0038678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	309	678	0	ENST00000301067.7:c.9896_9897del	p.His3299ArgfsTer123	p.H3299Rfs*123	ENST00000301067	NM_003482.3	3299	cAT/c	34/54	0.507283562637179	6	FACETS	1	0.966	1	1	0.966	1	CLONAL	3	TRUE	3	0.837350191316277	6		678	646	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369226	40369226	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	335	576	2	ENST00000293328.3:c.1332T>A	p.Phe444Leu	p.F444L	ENST00000293328	NM_012448.3	444	ttT/ttA	11/19	0.750337388703935	4	FACETS	0.933	0.887	0.979	0.933	0.887	0.979	CLONAL	2	TRUE	2	0.837350191316277	4		578	788	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747342068	NA	P-0038679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	524	848	0	ENST00000269305.4:c.394A>G	p.Lys132Glu	p.K132E	ENST00000269305	NM_001126112.2	132	Aag/Gag	5/11	0.806358562733577	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.806358562733577	1		848	740	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32439124	32439124	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	247	488	0	ENST00000332351.3:c.949G>A	p.Gly317Arg	p.G317R	ENST00000332351	NM_024426.4	317	Gga/Aga	4/10	0.806358562733577	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.806358562733577	1		488	348	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254807	16254807	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1474120500	NA	P-0038679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	339	565	0	ENST00000375759.3:c.2072A>G	p.Asp691Gly	p.D691G	ENST00000375759	NM_015001.2	691	gAt/gGt	11/15	0.111679856650503	3	FACETS	1	0.995	1			1	INDETERMINATE	1	TRUE	NA	0.806358562733577	3		565	835	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210505	5210505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764990671	NA	P-0038679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	45	625	0	ENST00000357368.4:c.5462G>A	p.Arg1821Gln	p.R1821Q	ENST00000357368	NM_002850.3	1821	cGa/cAa	35/38	1	2	FACETS	0.139	0.116	0.164	0.139	0.116	0.164	SUBCLONAL	1	TRUE	1	0.806358562733577	2		625	804	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259229	89259229	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	141	420	0	ENST00000336596.2:c.373A>G	p.Met125Val	p.M125V	ENST00000336596	NM_005233.5	125	Atg/Gtg	3/17	0.806358562733577	1	FACETS	0.892	0.835	0.948	0.892	0.835	0.948	CLONAL	1	TRUE	0	0.806358562733577	1		420	234	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0038680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	94	622	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.929	0.835	1	0.929	0.835	1	CLONAL	1	TRUE	1	0.614891560996032	2		622	329	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0038680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	246	647	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.590992107553472	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.614891560996032	1		647	475	SUCCESS
APC	324	MSKCC	GRCh37	5	112175235	112175235	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	49	252	0	ENST00000257430.4:c.3944C>A	p.Ser1315Ter	p.S1315*	ENST00000257430	NM_000038.5	1315	tCa/tAa	16/16	1	2	FACETS	0.943	0.813	1	0.943	0.813	1	CLONAL	1	TRUE	1	0.614891560996032	2		252	169	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976745	2976745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748839211	NA	P-0038680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	406	789	2	ENST00000396946.4:c.1267C>T	p.Arg423Trp	p.R423W	ENST00000396946	NM_032415.4	423	Cgg/Tgg	9/25	0.557418176424608	3	FACETS	0.989	0.946	1	0.989	0.946	1	CLONAL	2	TRUE	1	0.614891560996032	3		791	873	SUCCESS
APC	324	MSKCC	GRCh37	5	112174998	112174999	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs1554085246	NA	P-0038680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	20	208	0	ENST00000257430.4:c.3709_3710del	p.Gln1237GlufsTer2	p.Q1237Efs*2	ENST00000257430	NM_000038.5	1236	gCA/g	16/16	1	2	FACETS	0.478	0.369	0.603	0.478	0.369	0.603	SUBCLONAL	1	TRUE	1	0.614891560996032	2		208	136	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210796	5210796	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758652323	NA	P-0038680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	172	658	2	ENST00000357368.4:c.5255C>T	p.Ala1752Val	p.A1752V	ENST00000357368	NM_002850.3	1752	gCg/gTg	34/38	1	2	FACETS	0.963	0.891	1	0.963	0.891	1	CLONAL	1	TRUE	1	0.614891560996032	2		660	581	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099403	157099426	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAGCAGCAA	CAGCAGCAGCAGCAGCAGCAGCAA	-	rs770869529	NA	P-0038680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	18	289	0	ENST00000346085.5:c.369_392del	p.Gln124_Gln131del	p.Q124_Q131del	ENST00000346085	NM_020732.3	114	CAGCAGCAGCAGCAGCAGCAGCAA/-	1/20	1	2	FACETS	0.252	0.19	0.326	0.252	0.19	0.326	SUBCLONAL	1	TRUE	1	0.614891560996032	2		289	232	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390816	139390816	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	299	898	0	ENST00000277541.6:c.7375del	p.Gln2459ArgfsTer18	p.Q2459Rfs*18	ENST00000277541	NM_017617.3	2459	Cag/ag	34/34	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.614891560996032	2		898	881	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139804435	139804437	+	missense_variant	Missense_Mutation	TNP	CCC	CCC	TCT	novel	NA	P-0038680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	88	737	0	ENST00000247668.2:c.592_594delinsTCT	p.Pro198Ser	p.P198S	ENST00000247668	NM_021138.3	198	CCC/TCT	6/11	1	2	FACETS	0.379	0.335	0.426	0.379	0.335	0.426	SUBCLONAL	1	TRUE	1	0.614891560996032	2		737	755	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0038681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	48	347	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.872	0.74	1	0.872	0.74	1	CLONAL	1	TRUE	1	0.321029056626754	2		347	343	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	90	538	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.321029056626754	2		538	478	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519938	NA	P-0038681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	44	409	0	ENST00000263967.3:c.1034A>C	p.Asn345Thr	p.N345T	ENST00000263967	NM_006218.2	345	aAt/aCt	5/21	1	2	FACETS	0.917	0.773	1	0.917	0.773	1	CLONAL	1	TRUE	1	0.321029056626754	2		409	299	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119741	70119741	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	35	872	0	ENST00000245479.2:c.743G>C	p.Gly248Ala	p.G248A	ENST00000245479	NM_000346.3	248	gGc/gCc	3/3	1	2	FACETS	0.341	0.279	0.412	0.341	0.279	0.412	SUBCLONAL	1	TRUE	1	0.321029056626754	2		872	639	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0038682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	50	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.115775538453105	0	FACETS	0.819	0.705	0.941			1	CLONAL	3	FALSE	0	0.172653751235519	0		457	195	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0038682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	45	461	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.139425158382321	3	FACETS	1	0.868	1	1	0.964	1	CLONAL	3	FALSE	1	0.172653751235519	3		461	185	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0038682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	42	610	2	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	0.172653751235519	5	FACETS	0.869	0.732	1	0.652	0.549	0.764	CLONAL	3	FALSE	1	0.172653751235519	5		612	235	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383144	42383144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764758292	NA	P-0038682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	30	699	1	ENST00000221972.3:c.164C>T	p.Pro55Leu	p.P55L	ENST00000221972	NM_021601.3	55	cCg/cTg	2/5	0.172653751235519	5	FACETS	1	0.893	1	0.292	0.235	0.357	CLONAL	1	FALSE	1	0.172653751235519	5		700	374	SUCCESS
APC	324	MSKCC	GRCh37	5	112175749	112175756	+	frameshift_variant	Frame_Shift_Del	DEL	TACTTTAT	TACTTTAT	-	novel	NA	P-0038682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	22	287	0	ENST00000257430.4:c.4461_4468del	p.Leu1488PhefsTer23	p.L1488Ffs*23	ENST00000257430	NM_000038.5	1486	gaTACTTTATta/gata	16/16	0.172653751235519	5	FACETS	0.955	0.759	1	0.955	0.759	1	CLONAL	4	FALSE	1	0.172653751235519	5		287	84	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201873	152201873	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779180038	NA	P-0038682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	21	354	0	ENST00000206249.3:c.727C>T	p.Arg243Cys	p.R243C	ENST00000206249	NM_000125.3	243	Cgt/Tgt	3/8	0.139425158382321	3	FACETS	0.864	0.671	1	0.864	0.671	1	CLONAL	2	FALSE	1	0.172653751235519	3		354	153	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910854	114910854	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	48	483	0	ENST00000543371.1:c.973C>T	p.Gln325Ter	p.Q325*	ENST00000543371	NM_001198531.1	325	Cag/Tag	9/14	1	2	FACETS	1	0.94	1	1	0.977	1	CLONAL	2	FALSE	1	0.172653751235519	2		483	230	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119406	70119725	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCACCCCAAAAGCACACACAGGGCTCTTACACAAGTAGCAATTAGGTCTTCCGGACCCTCCGGGCCCCAGACCCTCCCCTGATAAAAGGGGGCTGTCCAGTGTGTACCGGCGGGTTAATCATTGGGCGACTTATCTCCGGTGCAGCGCGCCTCTTGCGCGGGTGCGGGCCCTTATTACACTTTAGCAGCGAGGGAGGGTCCCCGGAGGGTGCCTAAGACTAGGGCGTCTGCACAGCCCTTGTTGATTTTCTCGTGCTTGTTCTTTTATTGTCCACAGGGCAATCCCAGGGCCCACCGACCCCACCCACCACCCCCAAAA	CCCACCCCAAAAGCACACACAGGGCTCTTACACAAGTAGCAATTAGGTCTTCCGGACCCTCCGGGCCCCAGACCCTCCCCTGATAAAAGGGGGCTGTCCAGTGTGTACCGGCGGGTTAATCATTGGGCGACTTATCTCCGGTGCAGCGCGCCTCTTGCGCGGGTGCGGGCCCTTATTACACTTTAGCAGCGAGGGAGGGTCCCCGGAGGGTGCCTAAGACTAGGGCGTCTGCACAGCCCTTGTTGATTTTCTCGTGCTTGTTCTTTTATTGTCCACAGGGCAATCCCAGGGCCCACCGACCCCACCCACCACCCCCAAAA	-	novel	NA	P-0038682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	133	44	0	ENST00000245479.2:c.686-276_729del		p.X229_splice	ENST00000245479	NM_000346.3	229		3/3	0.172653751235519	1	FACETS	1	0.987	1	1	0.994	1	CLONAL	10	FALSE	0	0.172653751235519	1		44	138	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715656	30715656	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	21	272	0	ENST00000295754.5:c.1314T>A	p.Asn438Lys	p.N438K	ENST00000295754	NM_003242.5	438	aaT/aaA	5/7	0.139425158382321	3	FACETS	1	0.819	1	1	0.819	1	CLONAL	2	FALSE	1	0.172653751235519	3		272	125	SUCCESS
APC	324	MSKCC	GRCh37	5	112174263	112174263	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0038682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	20	298	0	ENST00000257430.4:c.2974del	p.Ser992ValfsTer13	p.S992Vfs*13	ENST00000257430	NM_000038.5	991	gAa/ga	16/16	0.172653751235519	5	FACETS	1	0.819	1	0.793	0.618	0.987	CLONAL	3	FALSE	1	0.172653751235519	5		298	92	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199963	138199963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	54	479	0	ENST00000237289.4:c.1381C>T	p.Pro461Ser	p.P461S	ENST00000237289	NM_001270507.1	461	Cca/Tca	7/9	0.139425158382321	3	FACETS	1	0.927	1	1	0.973	1	CLONAL	3	FALSE	1	0.172653751235519	3		479	204	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0038683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	83	373	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	0.471322416491981	1	FACETS	0.364	0.322	0.407	0.364	0.322	0.407	SUBCLONAL	1	TRUE	0	0.696797979883896	1		373	427	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592144	55592145	+	inframe_insertion	In_Frame_Ins	INS	-	-	AATGTA	novel	NA	P-0038683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1316	2292	568	0	ENST00000288135.5:c.1470_1475dup	p.Cys491_Lys492dup	p.C491_K492dup	ENST00000288135	NM_000222.2	491	gaa/gAATGTAaa	9/21	0.696797979883896	13	FACETS	0.979	0.964	0.994			1	CLONAL	9	TRUE	NA	0.696797979883896	13		568	3608	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	78	578	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	1	0.402357684000758	2		578	362	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	17	301	0	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	0.212574150064391	0	FACETS	0.214	0.16	0.278			1	INDETERMINATE	1	FALSE	0	0.402357684000758	0		301	236	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0038684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	13	560	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.402357684000758	1	FACETS	0.139	0.099	0.189	0.139	0.099	0.189	SUBCLONAL	1	FALSE	0	0.402357684000758	1		560	371	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395776	45395776	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	28	365	0	ENST00000262160.6:c.358C>T	p.Arg120Ter	p.R120*	ENST00000262160	NM_005901.5	120	Cga/Tga	4/11	0.212574150064391	0	FACETS	0.347	0.278	0.424			1	INDETERMINATE	1	FALSE	0	0.402357684000758	0		365	240	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981167	201981168	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	148	841	0	ENST00000359651.3:c.248dup	p.Asn83LysfsTer9	p.N83Kfs*9	ENST00000359651		82	-/A	2/8	1	2	FACETS	0.986	0.902	1	0.986	0.902	1	CLONAL	1	FALSE	1	0.402357684000758	2		841	746	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562621	21562621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	202	394	0	ENST00000382592.4:c.1298C>T	p.Thr433Met	p.T433M	ENST00000382592	NM_014572.2	433	aCg/aTg	4/8	0.359111179260333	3	FACETS	0.846	0.793	0.9	0.846	0.793	0.9	CLONAL	3	FALSE	0	0.402357684000758	3		394	475	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119871	70119872	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	131	743	0	ENST00000245479.2:c.875dup	p.Asn292LysfsTer4	p.N292Kfs*4	ENST00000245479	NM_000346.3	291	-/A	3/3	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	FALSE	1	0.402357684000758	2		743	638	SUCCESS
APC	324	MSKCC	GRCh37	5	112173597	112173597	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0038684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	64	271	0	ENST00000257430.4:c.2306T>G	p.Leu769Ter	p.L769*	ENST00000257430	NM_000038.5	769	tTa/tGa	16/16	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.402357684000758	2		271	256	SUCCESS
APC	324	MSKCC	GRCh37	5	112175763	112175764	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	G	novel	NA	P-0038684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	40	340	0	ENST00000257430.4:c.4472_4473delinsG	p.Phe1491TrpfsTer16	p.F1491Wfs*16	ENST00000257430	NM_000038.5	1491	tTT/tG	16/16	1	2	FACETS	0.777	0.65	0.916	0.777	0.65	0.916	CLONAL	1	FALSE	1	0.402357684000758	2		340	256	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0038688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	125	523	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.835	0.758	0.915	0.835	0.758	0.915	CLONAL	1	TRUE	1	0.52077362078616	2		523	575	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0038688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	147	569	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	1	2	FACETS	0.844	0.772	0.918	0.844	0.772	0.918	CLONAL	1	TRUE	1	0.52077362078616	2		569	669	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016559	12016559	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	87	252	0	ENST00000353533.5:c.695C>T	p.Pro232Leu	p.P232L	ENST00000353533	NM_003010.3	232	cCt/cTt	7/11	0.458829629912163	1	FACETS	0.94	0.844	1	0.94	0.844	1	CLONAL	1	TRUE	0	0.52077362078616	1		252	263	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0038690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	51	283	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.0982604441935474	3	FACETS	1	0.924	1	0.575	0.488	0.671	CLONAL	1	TRUE	1	0.14	3		283	678	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920325	134920325	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1166499752	NA	P-0038690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	26	311	0	ENST00000398015.3:c.2140G>A	p.Gly714Arg	p.G714R	ENST00000398015	NM_004441.4	714	Ggg/Agg	12/16	0.3	0	FACETS	0.704	0.556	0.873			1	SUBCLONAL	1	TRUE	0	0.14	0		311	454	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612879	228612879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767647652	NA	P-0038690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	37	597	0	ENST00000366696.1:c.148C>T	p.Arg50Cys	p.R50C	ENST00000366696	NM_003493.2	50	Cgc/Tgc	1/1	1	2	FACETS	0.809	0.666	0.971	0.809	0.666	0.971	CLONAL	1	TRUE	1	0.14	2		597	653	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961295	15961295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	59	454	0	ENST00000268712.3:c.6094C>T	p.Pro2032Ser	p.P2032S	ENST00000268712	NM_006311.3	2032	Cct/Tct	39/46	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.14	2		454	731	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440698	56440698	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	58	538	1	ENST00000407977.2:c.520del	p.Glu174SerfsTer11	p.E174Sfs*11	ENST00000407977		174	Gag/ag	5/10	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.14	2		539	743	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753539	42753539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	56	650	0	ENST00000222329.4:c.725C>A	p.Pro242His	p.P242H	ENST00000222329	NM_006494.2	242	cCt/cAt	4/4	0.0982604441935474	0	FACETS	0.894	0.764	1			1	CLONAL	1	TRUE	0	0.14	0		650	770	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250928	153250928	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	24	204	0	ENST00000281708.4:c.1132G>T	p.Gly378Ter	p.G378*	ENST00000281708	NM_033632.3	378	Gga/Tga	8/12	0.0982604441935474	3	FACETS	0.838	0.656	1	0.419	0.328	0.524	CLONAL	1	TRUE	1	0.14	3		204	438	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743924	40743924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199514226	NA	P-0038691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	169	426	1	ENST00000373198.4:c.3071C>T	p.Thr1024Met	p.T1024M	ENST00000373198	NM_133170.3	1024	aCg/aTg	23/32	0.559090486628843	3	FACETS	0.913	0.84	0.989	0.457	0.42	0.495	CLONAL	1	TRUE	1	0.559090486628843	3		427	847	SUCCESS
APC	324	MSKCC	GRCh37	5	112151245	112151246	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs1114167567	NA	P-0038691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	111	375	0	ENST00000257430.4:c.893_894del	p.His298LeufsTer28	p.H298Lfs*28	ENST00000257430	NM_000038.5	296	agCAca/agca	9/16	1	2	FACETS	0.771	0.696	0.85	0.771	0.696	0.85	SUBCLONAL	1	TRUE	1	0.559090486628843	2		375	515	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925328	114925328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	135	463	0	ENST00000543371.1:c.1406G>A	p.Cys469Tyr	p.C469Y	ENST00000543371	NM_001198531.1	469	tGc/tAc	14/14	1	2	FACETS	0.889	0.812	0.969	0.889	0.812	0.969	CLONAL	1	TRUE	1	0.559090486628843	2		463	543	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202221	108202221	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs775621333	NA	P-0038691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	104	397	0	ENST00000278616.4:c.7566A>T	p.Gln2522His	p.Q2522H	ENST00000278616	NM_000051.3	2522	caA/caT	51/63	1	2	FACETS	0.966	0.873	1	0.966	0.873	1	CLONAL	1	TRUE	1	0.559090486628843	2		397	385	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121634	108121634	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs1555070980	NA	P-0038691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	151	408	0	ENST00000278616.4:c.1442T>G	p.Leu481Ter	p.L481*	ENST00000278616	NM_000051.3	481	tTa/tGa	10/63	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.559090486628843	2		408	509	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913791	32913791	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0038691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	146	373	0	ENST00000380152.3:c.5299A>T	p.Lys1767Ter	p.K1767*	ENST00000380152		1767	Aaa/Taa	11/27	0.178403758636801	4	FACETS	0.891	0.82	0.964	0.891	0.82	0.964	INDETERMINATE	2	TRUE	2	0.559090486628843	4		373	457	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11114074	11114075	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0038691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	177	422	0	ENST00000358026.2:c.2001+2dup		p.X667_splice	ENST00000358026	NM_001128849.1	667			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.559090486628843	2		422	545	SUCCESS
APC	324	MSKCC	GRCh37	5	112174370	112174371	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0038691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	70	223	0	ENST00000257430.4:c.3081_3082del	p.Tyr1027Ter	p.Y1027*	ENST00000257430	NM_000038.5	1027	TAt/t	16/16	1	2	FACETS	0.931	0.821	1	0.931	0.821	1	CLONAL	1	TRUE	1	0.559090486628843	2		223	269	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243472	46243472	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	111	378	0	ENST00000334344.6:c.1825C>T	p.Gln609Ter	p.Q609*	ENST00000334344	NM_152641.2	609	Cag/Tag	14/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.328056652309885	2		378	569	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653815	89653815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	30	367	0	ENST00000371953.3:c.113C>T	p.Pro38Leu	p.P38L	ENST00000371953	NM_000314.4	38	cCt/cTt	2/9	1	2	FACETS	0.339	0.273	0.415	0.339	0.273	0.415	SUBCLONAL	1	TRUE	1	0.328056652309885	2		367	539	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100208	27100208	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	100	433	0	ENST00000324856.7:c.4004+1del		p.R1335fs	ENST00000324856	NM_006015.4	1335	cGa/ca	16/20	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.328056652309885	2		433	602	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100383	27100395	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACAGCAGGTGAGG	ACAGCAGGTGAGG	-	novel	NA	P-0038692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	61	486	0	ENST00000324856.7:c.4096_4101+7del		p.X1366_splice	ENST00000324856	NM_006015.4	1366		17/20	1	2	FACETS	0.534	0.46	0.614	0.534	0.46	0.614	SUBCLONAL	1	TRUE	1	0.328056652309885	2		486	697	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111496	8111497	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGAG	novel	NA	P-0038692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	153	638	0	ENST00000346208.3:c.984_987dup	p.Arg330GlufsTer23	p.R330Efs*23	ENST00000346208		328	tgg/tGGAGgg	5/6	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.328056652309885	2		638	883	SUCCESS
ATR	545	MSKCC	GRCh37	3	142185210	142185210	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	102	522	0	ENST00000350721.4:c.6853C>T	p.Pro2285Ser	p.P2285S	ENST00000350721	NM_001184.3	2285	Cca/Tca	40/47	1	2	FACETS	0.946	0.848	1	0.946	0.848	1	CLONAL	1	TRUE	1	0.328056652309885	2		522	657	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0121524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	214	283	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.882	0.826	0.938	0.882	0.826	0.938	CLONAL	1	NA	1	0.871594833999479	2		283	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0038694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	169	630	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.257771269758731	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.257771269758731	2		630	621	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924378	112924378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	81	548	0	ENST00000351677.2:c.1324G>A	p.Val442Met	p.V442M	ENST00000351677	NM_002834.3	442	Gtg/Atg	11/16	0.257771269758731	4	FACETS	1	0.893	1	0.508	0.447	0.574	CLONAL	1	TRUE	2	0.257771269758731	4		548	778	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994794	73994794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747338278	NA	P-0038694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	97	702	2	ENST00000318443.5:c.278C>T	p.Thr93Met	p.T93M	ENST00000318443	NM_001024736.1	93	aCg/aTg	3/10	0.257771269758731	3	FACETS	1	0.953	1	0.563	0.502	0.629	CLONAL	1	TRUE	1	0.257771269758731	3		704	754	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898705	134898705	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	41	253	0	ENST00000398015.3:c.1766del	p.Pro589GlnfsTer3	p.P589Qfs*3	ENST00000398015	NM_004441.4	588	tCc/tc	10/16	0.227032800088588	5	FACETS	1	0.927	1	0.403	0.336	0.477	CLONAL	1	TRUE	2	0.257771269758731	5		253	365	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143181683	143181683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	55	423	0	ENST00000262992.4:c.650G>A	p.Ser217Asn	p.S217N	ENST00000262992	NM_001101669.1	217	aGt/aAt	9/24	0.257771269758731	3	FACETS	0.989	0.847	1	0.495	0.423	0.572	CLONAL	1	TRUE	1	0.257771269758731	3		423	487	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0038697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	288	805	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.724806106960769	2		805	778	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816153	89816153	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	208	630	0	ENST00000389301.3:c.3224T>A	p.Leu1075Gln	p.L1075Q	ENST00000389301	NM_000135.2	1075	cTg/cAg	32/43	1	2	FACETS	0.991	0.927	1	0.991	0.927	1	CLONAL	1	TRUE	1	0.724806106960769	2		630	579	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0038721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	212	493	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.225321427122201	4	FACETS	0.855	0.795	0.916	0.855	0.795	0.916	CLONAL	3	TRUE	1	0.232746722512645	4		493	876	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032566	47032566	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	88	731	1	ENST00000377604.3:c.472G>T	p.Glu158Ter	p.E158*	ENST00000377604	NM_001204468.1	158	Gag/Tag	5/24	0.232746722512645	1	FACETS	0.925	0.82	1	0.925	0.82	1	CLONAL	1	TRUE	0	0.232746722512645	1		732	722	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562785	95562785	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	57	483	0	ENST00000393063.1:c.4472G>C	p.Ser1491Thr	p.S1491T	ENST00000393063	NM_030621.3	1491	aGt/aCt	24/28	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.232746722512645	2		483	471	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38545389	38545389	+	start_lost	Translation_Start_Site	SNP	G	G	C	novel	NA	P-0038721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	48	531	0	ENST00000299084.4:c.3G>C	p.Met1?	p.M1?	ENST00000299084	NM_152594.2	1	atG/atC	1/7	1	2	FACETS	0.616	0.519	0.722	0.616	0.519	0.722	SUBCLONAL	1	TRUE	1	0.232746722512645	2		531	670	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943716	9943716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1351978664	NA	P-0038721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	92	766	0	ENST00000330684.3:c.1225G>A	p.Val409Ile	p.V409I	ENST00000330684	NM_001134407.1	409	Gtc/Atc	5/13	0.225321427122201	4	FACETS	0.951	0.843	1	0.317	0.281	0.356	CLONAL	1	TRUE	1	0.232746722512645	4		766	1025	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349185	11349226	+	inframe_deletion	In_Frame_Del	DEL	CGGGGGCCGGGGCCGGGACCGCGGGGCACGGCCGCGGGCGCG	CGGGGGCCGGGGCCGGGACCGCGGGGCACGGCCGCGGGCGCG	-	rs1567455544	NA	P-0038721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	28	110	0	ENST00000332029.2:c.110_151del	p.Ala37_Pro50del	p.A37_P50del	ENST00000332029	NM_003745.1	37	gCGCGCCCGCGGCCGTGCCCCGCGGTCCCGGCCCCGGCCCCCGgc/ggc	2/2	0.225321427122201	4	FACETS	0.81	0.653	0.986	0.54	0.435	0.657	CLONAL	2	TRUE	1	0.232746722512645	4		110	183	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245506	153245506	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	43	596	0	ENST00000281708.4:c.1685C>T	p.Ser562Leu	p.S562L	ENST00000281708	NM_033632.3	562	tCa/tTa	11/12	1	2	FACETS	0.625	0.522	0.74	0.625	0.522	0.74	SUBCLONAL	1	TRUE	1	0.232746722512645	2		596	591	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	202	399	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.708262628068242	2		399	453	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643768	52643768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	339	581	0	ENST00000394830.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000394830	NM_018313.4	710	Cga/Tga	17/30	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.708262628068242	2		581	888	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561263	9561263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769939031	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	224	476	0	ENST00000353224.5:c.519G>A	p.Met173Ile	p.M173I	ENST00000353224	NM_177990.2	173	atG/atA	4/10	1	2	FACETS	0.932	0.872	0.993	0.932	0.872	0.993	CLONAL	1	TRUE	1	0.708262628068242	2		476	679	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956220	55956220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190050670	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	271	423	0	ENST00000263923.4:c.3095G>A	p.Arg1032Gln	p.R1032Q	ENST00000263923	NM_002253.2	1032	cGa/cAa	23/30	1	2	FACETS	0.986	0.929	1	0.986	0.929	1	CLONAL	1	TRUE	1	0.708262628068242	2		423	776	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980832	40980832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465279954	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	297	554	0	ENST00000373198.4:c.1654C>T	p.Leu552Phe	p.L552F	ENST00000373198	NM_133170.3	552	Ctc/Ttc	10/32	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.708262628068242	2		554	793	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641144	117641144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866970127	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	391	783	0	ENST00000368508.3:c.5827G>A	p.Glu1943Lys	p.E1943K	ENST00000368508	NM_002944.2	1943	Gaa/Aaa	36/43	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.708262628068242	2		783	1032	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401556	401556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	264	494	0	ENST00000380956.4:c.878C>T	p.Pro293Leu	p.P293L	ENST00000380956	NM_001195286.1	293	cCc/cTc	7/9	0.708262628068242	3	FACETS	0.969	0.908	1	0.484	0.454	0.516	CLONAL	1	TRUE	1	0.708262628068242	3		494	1042	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862964	117862964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	259	485	0	ENST00000297338.2:c.1513C>T	p.Pro505Ser	p.P505S	ENST00000297338	NM_006265.2	505	Ccc/Tcc	12/14	0.697377907258913	4	FACETS	1	0.959	1	0.344	0.322	0.368	CLONAL	1	TRUE	1	0.708262628068242	4		485	1209	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913255	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	311	720	0	ENST00000369535.4:c.183A>C	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caC	3/7	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.708262628068242	2		720	877	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332741	153332741	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	279	517	0	ENST00000281708.4:c.215C>T	p.Ser72Phe	p.S72F	ENST00000281708	NM_033632.3	72	tCc/tTc	2/12	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.708262628068242	2		517	739	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656259	18656259	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201569993	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	208	383	1	ENST00000266497.5:c.2938C>T	p.His980Tyr	p.H980Y	ENST00000266497		980	Cat/Tat	21/31	1	2	FACETS	0.94	0.877	1	0.94	0.877	1	CLONAL	1	TRUE	1	0.708262628068242	2		384	625	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440680	56440680	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs759809905	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	324	607	0	ENST00000407977.2:c.538C>T	p.Gln180Ter	p.Q180*	ENST00000407977		180	Caa/Taa	5/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.708262628068242	2		607	911	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942153	81942153	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	287	496	0	ENST00000359376.3:c.1690C>T	p.Arg564Trp	p.R564W	ENST00000359376	NM_002661.3	564	Cgg/Tgg	17/33	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.708262628068242	2		496	810	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604760	48604760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	231	429	0	ENST00000342988.3:c.1582C>T	p.His528Tyr	p.H528Y	ENST00000342988	NM_005359.5	528	Cac/Tac	12/12	1	2	FACETS	0.891	0.834	0.949	0.891	0.834	0.949	CLONAL	1	TRUE	1	0.708262628068242	2		429	732	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1863	689	678	0	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	0.708262628068242	3	FACETS	1	0.981	1	0.516	0.496	0.537	CLONAL	1	TRUE	1	0.708262628068242	3		678	2552	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6414397	6414397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	132	117	0	ENST00000356142.4:c.31G>A	p.Asp11Asn	p.D11N	ENST00000356142	NM_018890.3	11	Gac/Aac	1/7	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.708262628068242	2		117	351	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966462	25966462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	379	733	0	ENST00000435504.4:c.2744C>T	p.Pro915Leu	p.P915L	ENST00000435504		915	cCa/cTa	13/13	1	2	FACETS	0.996	0.947	1	0.996	0.947	1	CLONAL	1	TRUE	1	0.708262628068242	2		733	1075	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726698	88726698	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375475747	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	677	460	2	ENST00000360948.2:c.346C>T	p.Arg116Trp	p.R116W	ENST00000360948	NM_001012338.2	116	Cgg/Tgg	4/19	0.414772103516334	4	FACETS	0.967	0.939	0.995			1	INDETERMINATE	3	TRUE	NA	0.708262628068242	4		462	1126	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349229	11349229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	47	125	0	ENST00000332029.2:c.107C>T	p.Pro36Leu	p.P36L	ENST00000332029	NM_003745.1	36	cCc/cTc	2/2	1	2	FACETS	0.829	0.713	0.953	0.829	0.713	0.953	CLONAL	1	TRUE	1	0.708262628068242	2		125	160	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992756	72992756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1178788473	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	278	614	0	ENST00000268489.5:c.1289C>T	p.Ser430Phe	p.S430F	ENST00000268489	NM_006885.3	430	tCc/tTc	2/10	1	2	FACETS	0.99	0.934	1	0.99	0.934	1	CLONAL	1	TRUE	1	0.708262628068242	2		614	793	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879672	123879672	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776298564	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	41	175	0	ENST00000330479.4:c.368C>T	p.Pro123Leu	p.P123L	ENST00000330479	NM_020382.3	123	cCc/cTc	4/9	1	2	FACETS	0.546	0.459	0.64	0.546	0.459	0.64	SUBCLONAL	1	TRUE	1	0.708262628068242	2		175	212	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797859	32797859	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	200	392	0	ENST00000374899.4:c.1643C>T	p.Ser548Leu	p.S548L	ENST00000374899	NM_018833.2	548	tCa/tTa	10/12	0.708262628068242	3	FACETS	0.93	0.864	0.999	0.465	0.432	0.5	CLONAL	1	TRUE	1	0.708262628068242	3		392	822	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458492	120458492	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1553193507	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	275	594	1	ENST00000256646.2:c.6853C>T	p.Gln2285Ter	p.Q2285*	ENST00000256646	NM_024408.3	2285	Cag/Tag	34/34	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.708262628068242	2		595	735	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858913	243858913	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs866698621	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	224	406	0	ENST00000263826.5:c.152T>G	p.Leu51Arg	p.L51R	ENST00000263826	NM_005465.4	51	cTc/cGc	2/13	0.6907187744182	3	FACETS	1	0.965	1	0.525	0.49	0.562	CLONAL	1	TRUE	1	0.708262628068242	3		406	815	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518153	187518153	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	269	441	0	ENST00000441802.2:c.12541G>A	p.Glu4181Lys	p.E4181K	ENST00000441802	NM_005245.3	4181	Gaa/Aaa	25/27	1	2	FACETS	0.989	0.932	1	0.989	0.932	1	CLONAL	1	TRUE	1	0.708262628068242	2		441	768	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436006	110436006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	389	615	0	ENST00000375856.3:c.2395C>T	p.Pro799Ser	p.P799S	ENST00000375856	NM_003749.2	799	Ccc/Tcc	1/2	1	2	FACETS	0.977	0.93	1	0.977	0.93	1	CLONAL	1	TRUE	1	0.708262628068242	2		615	1124	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050388	13050388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	391	527	0	ENST00000316448.5:c.340C>T	p.Pro114Ser	p.P114S	ENST00000316448	NM_004343.3	114	Cct/Tct	3/9	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.708262628068242	2		527	1087	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199360	16199360	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	237	439	0	ENST00000375759.3:c.133G>A	p.Gly45Arg	p.G45R	ENST00000375759	NM_015001.2	45	Gga/Aga	2/15	1	2	FACETS	0.945	0.886	1	0.945	0.886	1	CLONAL	1	TRUE	1	0.708262628068242	2		439	708	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255554	16255554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	263	482	0	ENST00000375759.3:c.2819C>T	p.Pro940Leu	p.P940L	ENST00000375759	NM_015001.2	940	cCa/cTa	11/15	1	2	FACETS	0.917	0.862	0.973	0.917	0.862	0.973	CLONAL	1	TRUE	1	0.708262628068242	2		482	810	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65304230	65304231	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	193	405	1	ENST00000342505.4:c.2884_2885delinsAA	p.Gly962Lys	p.G962K	ENST00000342505	NM_002227.2	962	GGa/AAa	21/25	1	2	FACETS	0.845	0.785	0.906	0.845	0.785	0.906	CLONAL	1	TRUE	1	0.708262628068242	2		406	645	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459052	120459053	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	278	614	0	ENST00000256646.2:c.6292_6293delinsTT	p.Pro2098Leu	p.P2098L	ENST00000256646	NM_024408.3	2098	CCa/TTa	34/34	1	2	FACETS	0.95	0.896	1	0.95	0.896	1	CLONAL	1	TRUE	1	0.708262628068242	2		614	826	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206661284	206661284	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	241	553	0	ENST00000367120.3:c.1650G>A	p.Met550Ile	p.M550I	ENST00000367120	NM_014002.3	550	atG/atA	16/22	0.6907187744182	3	FACETS	0.852	0.795	0.91	0.426	0.397	0.455	CLONAL	1	TRUE	1	0.708262628068242	3		553	1082	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555267	226555268	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	193	506	1	ENST00000366794.5:c.2319_2320delinsAA	p.Ala774Thr	p.A774T	ENST00000366794	NM_001618.3	773	gtGGcc/gtAAcc	17/23	0.6907187744182	3	FACETS	0.774	0.716	0.834	0.387	0.358	0.417	SUBCLONAL	1	TRUE	1	0.708262628068242	3		507	954	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137199	64137199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1422279060	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	309	464	1	ENST00000334205.4:c.1631G>A	p.Gly544Glu	p.G544E	ENST00000334205	NM_003942.2	544	gGg/gAg	14/17	0.708262628068242	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.708262628068242	1		465	519	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465960	69465961	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1903	267	601	0	ENST00000227507.2:c.798_799delinsAA	p.Met266_Asp267delinsIleAsn	p.M266_D267delinsIN	ENST00000227507	NM_053056.2	266	atGGac/atAAac	5/5	0.708262628068242	7	FACETS	0.963	0.898	1	0.16	0.149	0.172	CLONAL	1	TRUE	1	0.708262628068242	7		601	2170	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195527	102195527	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2429	249	485	0	ENST00000263464.3:c.287T>C	p.Val96Ala	p.V96A	ENST00000263464	NM_001165.4	96	gTt/gCt	2/9	0.708262628068242	9	FACETS	0.913	0.849	0.98			1	CLONAL	1	TRUE	NA	0.708262628068242	9		485	2678	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207494	102207494	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs998326954	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2059	214	421	0	ENST00000263464.3:c.1583A>G	p.Gln528Arg	p.Q528R	ENST00000263464	NM_001165.4	528	cAa/cGa	8/9	0.708262628068242	9	FACETS	0.925	0.855	0.998			1	CLONAL	1	TRUE	NA	0.708262628068242	9		421	2273	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377289	118377290	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	254	444	1	ENST00000534358.1:c.10682_10683delinsTT	p.Ser3561Phe	p.S3561F	ENST00000534358	NM_005933.3	3561	tCC/tTT	27/36	0.708262628068242	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.708262628068242	1		445	447	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431162	49431163	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	280	573	2	ENST00000301067.7:c.9976_9977delinsTT	p.Pro3326Phe	p.P3326F	ENST00000301067	NM_003482.3	3326	CCc/TTc	34/54	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.708262628068242	2		575	766	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431645	49431645	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	288	677	0	ENST00000301067.7:c.9494A>G	p.Asp3165Gly	p.D3165G	ENST00000301067	NM_003482.3	3165	gAt/gGt	34/54	1	2	FACETS	0.994	0.939	1	0.994	0.939	1	CLONAL	1	TRUE	1	0.708262628068242	2		677	818	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440432	49440432	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	299	683	0	ENST00000301067.7:c.4378C>A	p.Pro1460Thr	p.P1460T	ENST00000301067	NM_003482.3	1460	Cca/Aca	15/54	1	2	FACETS	0.958	0.905	1	0.958	0.905	1	CLONAL	1	TRUE	1	0.708262628068242	2		683	881	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859435	57859435	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779506563	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	278	605	0	ENST00000228682.2:c.580C>T	p.Pro194Ser	p.P194S	ENST00000228682	NM_005269.2	194	Ccc/Tcc	6/12	1	2	FACETS	0.99	0.934	1	0.99	0.934	1	CLONAL	1	TRUE	1	0.708262628068242	2		605	793	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30095744	30095744	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	258	415	0	ENST00000331968.5:c.1744C>G	p.Gln582Glu	p.Q582E	ENST00000331968	NM_002742.2	582	Cag/Gag	12/18	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.708262628068242	2		415	717	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562614	95562615	+	missense_variant	Missense_Mutation	DNP	AA	AA	GT	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	226	416	0	ENST00000393063.1:c.4642_4643delinsAC	p.Leu1548Thr	p.L1548T	ENST00000393063	NM_030621.3	1548	TTg/ACg	24/28	NA	2	FACETS	1	0.949	1			1	INDETERMINATE	1	TRUE	NA	0.708262628068242	2		416	629	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38545389	38545389	+	start_lost	Translation_Start_Site	SNP	G	G	T	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	393	416	0	ENST00000299084.4:c.3G>T	p.Met1?	p.M1?	ENST00000299084	NM_152594.2	1	atG/atT	1/7	0.708262628068242	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.708262628068242	1		416	611	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007647	45007648	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	176	288	0	ENST00000558401.1:c.95dup	p.His33SerfsTer24	p.H33Sfs*24	ENST00000558401	NM_004048.2	32	cgt/cGgt	2/4	0.708262628068242	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.708262628068242	1		288	311	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9927964	9927964	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	178	357	0	ENST00000330684.3:c.1775A>T	p.Lys592Ile	p.K592I	ENST00000330684	NM_001134407.1	592	aAa/aTa	8/13	1	2	FACETS	0.947	0.879	1	0.947	0.879	1	CLONAL	1	TRUE	1	0.708262628068242	2		357	531	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984772	72984772	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	289	583	0	ENST00000268489.5:c.2812A>C	p.Asn938His	p.N938H	ENST00000268489	NM_006885.3	938	Aac/Cac	3/10	1	2	FACETS	0.961	0.907	1	0.961	0.907	1	CLONAL	1	TRUE	1	0.708262628068242	2		583	849	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984794	11984795	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	226	461	0	ENST00000353533.5:c.340_341delinsAA	p.Gly114Asn	p.G114N	ENST00000353533	NM_003010.3	114	GGt/AAt	3/11	1	2	FACETS	0.862	0.806	0.92	0.862	0.806	0.92	CLONAL	1	TRUE	1	0.708262628068242	2		461	740	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474367	40474368	+	missense_variant	Missense_Mutation	DNP	GG	GG	AC	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	347	505	1	ENST00000264657.5:c.2033_2034delinsGT	p.Pro678Arg	p.P678R	ENST00000264657	NM_139276.2	678	cCC/cGT	21/24	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.708262628068242	2		506	912	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096936	11096937	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	322	699	0	ENST00000358026.2:c.427_428delinsTT	p.Pro143Phe	p.P143F	ENST00000358026	NM_001128849.1	143	CCc/TTc	4/36	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.708262628068242	2		699	901	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106982	11106982	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	334	687	0	ENST00000358026.2:c.1687A>T	p.Asn563Tyr	p.N563Y	ENST00000358026	NM_001128849.1	563	Aac/Tac	10/36	1	2	FACETS	0.995	0.943	1	0.995	0.943	1	CLONAL	1	TRUE	1	0.708262628068242	2		687	948	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18960979	18960979	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	250	580	0	ENST00000262803.5:c.557G>T	p.Cys186Phe	p.C186F	ENST00000262803	NM_002911.3	186	tGc/tTc	4/24	1	2	FACETS	0.761	0.712	0.81	0.761	0.712	0.81	SUBCLONAL	1	TRUE	1	0.708262628068242	2		580	928	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211694	36211695	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	251	559	1	ENST00000222270.7:c.1445_1446delinsAA	p.Arg482Gln	p.R482Q	ENST00000222270	NM_014727.1	482	cGG/cAA	3/37	1	2	FACETS	0.989	0.929	1	0.989	0.929	1	CLONAL	1	TRUE	1	0.708262628068242	2		560	717	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763495	41763495	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868015563	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	278	510	0	ENST00000301178.4:c.2294G>A	p.Gly765Glu	p.G765E	ENST00000301178	NM_021913.4	765	gGa/gAa	19/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.708262628068242	2		510	727	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190708793	190708793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	244	371	0	ENST00000441310.2:c.686C>T	p.Ser229Phe	p.S229F	ENST00000441310	NM_000534.4	229	tCt/tTt	6/13	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.708262628068242	2		371	592	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561399	9561399	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	306	569	0	ENST00000353224.5:c.383T>A	p.Phe128Tyr	p.F128Y	ENST00000353224	NM_177990.2	128	tTc/tAc	4/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.708262628068242	2		569	787	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024239	31024256	+	inframe_deletion	In_Frame_Del	DEL	GATCAGAAGGAAGTCCGT	GATCAGAAGGAAGTCCGT	-	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	248	491	0	ENST00000375687.4:c.3725_3742del	p.Asp1242_Arg1247del	p.D1242_R1247del	ENST00000375687	NM_015338.5	1242	GATCAGAAGGAAGTCCGT/-	13/13	1	2	FACETS	0.963	0.905	1	0.963	0.905	1	CLONAL	1	TRUE	1	0.708262628068242	2		491	727	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375066	31375066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	271	486	0	ENST00000328111.2:c.463G>A	p.Gly155Arg	p.G155R	ENST00000328111	NM_006892.3	155	Gga/Aga	6/23	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.708262628068242	2		486	751	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747109	40747109	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	235	552	0	ENST00000373198.4:c.2973G>A	p.Trp991Ter	p.W991*	ENST00000373198	NM_133170.3	991	tgG/tgA	22/32	1	2	FACETS	0.905	0.848	0.964	0.905	0.848	0.964	CLONAL	1	TRUE	1	0.708262628068242	2		552	733	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944412	40944412	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	282	569	0	ENST00000373198.4:c.2090C>T	p.Pro697Leu	p.P697L	ENST00000373198	NM_133170.3	697	cCc/cTc	12/32	1	2	FACETS	0.963	0.908	1	0.963	0.908	1	CLONAL	1	TRUE	1	0.708262628068242	2		569	827	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54948513	54948513	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	296	460	0	ENST00000312783.6:c.805G>A	p.Glu269Lys	p.E269K	ENST00000312783	NM_198436.1	269	Gag/Aag	8/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.708262628068242	2		460	749	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434227	12434227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	257	411	0	ENST00000287820.6:c.595C>T	p.Leu199Phe	p.L199F	ENST00000287820	NM_015869.4	199	Ctt/Ttt	4/7	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.708262628068242	2		411	722	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37091980	37091980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747727493	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	195	403	0	ENST00000231790.2:c.2107G>A	p.Glu703Lys	p.E703K	ENST00000231790	NM_000249.3	703	Gaa/Aaa	19/19	1	2	FACETS	0.892	0.831	0.956	0.892	0.831	0.956	CLONAL	1	TRUE	1	0.708262628068242	2		403	617	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620674	52620675	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	189	305	1	ENST00000394830.3:c.3078_3079delinsTT	p.Arg1027Ter	p.R1027*	ENST00000394830	NM_018313.4	1026	ttCCga/ttTTga	21/30	1	2	FACETS	0.953	0.887	1	0.953	0.887	1	CLONAL	1	TRUE	1	0.708262628068242	2		306	560	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205146	128205147	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	306	647	0	ENST00000341105.2:c.294_295delinsAA	p.Asp99Asn	p.D99N	ENST00000341105	NM_032638.4	98	ctGGac/ctAAac	3/6	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.708262628068242	2		647	844	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185169088	185169088	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	247	405	0	ENST00000265026.3:c.1183C>T	p.Arg395Ter	p.R395*	ENST00000265026	NM_004721.4	395	Cga/Tga	7/14	1	2	FACETS	0.87	0.816	0.925	0.87	0.816	0.925	CLONAL	1	TRUE	1	0.708262628068242	2		405	802	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873703	35873703	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	167	343	0	ENST00000303115.3:c.659G>A	p.Trp220Ter	p.W220*	ENST00000303115	NM_002185.3	220	tGg/tAg	5/8	1	2	FACETS	0.888	0.822	0.956	0.888	0.822	0.956	CLONAL	1	TRUE	1	0.708262628068242	2		343	531	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167766	56167766	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	254	369	0	ENST00000399503.3:c.1331C>T	p.Pro444Leu	p.P444L	ENST00000399503	NM_005921.1	444	cCt/cTt	7/20	NA	2	FACETS	0.959	0.901	1			1	INDETERMINATE	1	TRUE	NA	0.708262628068242	2		369	748	SUCCESS
APC	324	MSKCC	GRCh37	5	112174167	112174167	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757526267	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	229	368	0	ENST00000257430.4:c.2876C>T	p.Ser959Phe	p.S959F	ENST00000257430	NM_000038.5	959	tCt/tTt	16/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.708262628068242	2		368	574	SUCCESS
APC	324	MSKCC	GRCh37	5	112176705	112176705	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	173	310	0	ENST00000257430.4:c.5414T>A	p.Phe1805Tyr	p.F1805Y	ENST00000257430	NM_000038.5	1805	tTc/tAc	16/16	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.708262628068242	2		310	486	SUCCESS
APC	324	MSKCC	GRCh37	5	112178193	112178193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	262	370	0	ENST00000257430.4:c.6902G>A	p.Arg2301Lys	p.R2301K	ENST00000257430	NM_000038.5	2301	aGa/aAa	16/16	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.708262628068242	2		370	645	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124428	94124428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	189	345	0	ENST00000369303.4:c.155C>T	p.Pro52Leu	p.P52L	ENST00000369303	NM_004440.3	52	cCc/cTc	2/17	1	2	FACETS	0.875	0.813	0.938	0.875	0.813	0.938	CLONAL	1	TRUE	1	0.708262628068242	2		345	610	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124447	94124447	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140813099	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	212	380	0	ENST00000369303.4:c.136G>A	p.Glu46Lys	p.E46K	ENST00000369303	NM_004440.3	46	Gag/Aag	2/17	1	2	FACETS	0.861	0.804	0.921	0.861	0.804	0.921	CLONAL	1	TRUE	1	0.708262628068242	2		380	695	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554343	106554343	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	214	424	0	ENST00000369096.4:c.1871T>C	p.Val624Ala	p.V624A	ENST00000369096	NM_001198.3	624	gTa/gCa	6/7	0.610879336637844	1	FACETS	0.881	0.83	0.933	0.881	0.83	0.933	CLONAL	1	TRUE	0	0.708262628068242	1		424	443	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678991	117678991	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	203	352	0	ENST00000368508.3:c.3830C>T	p.Ser1277Phe	p.S1277F	ENST00000368508	NM_002944.2	1277	tCt/tTt	24/43	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.708262628068242	2		352	506	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971184	13971184	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	209	425	0	ENST00000405192.2:c.745A>T	p.Ser249Cys	p.S249C	ENST00000405192	NM_001163147.1	249	Agc/Tgc	8/12	1	2	FACETS	0.972	0.908	1	0.972	0.908	1	CLONAL	1	TRUE	1	0.708262628068242	2		425	607	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843399	128843399	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	216	595	0	ENST00000249373.3:c.506del	p.Cys169SerfsTer133	p.C169Sfs*133	ENST00000249373	NM_005631.4	169	tGc/tc	2/12	1	2	FACETS	0.926	0.865	0.988	0.926	0.865	0.988	CLONAL	1	TRUE	1	0.708262628068242	2		595	659	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027719	152027719	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	359	628	0	ENST00000262189.6:c.356C>A	p.Ser119Tyr	p.S119Y	ENST00000262189	NM_170606.2	119	tCc/tAc	3/59	1	2	FACETS	0.923	0.876	0.971	0.923	0.876	0.971	CLONAL	1	TRUE	1	0.708262628068242	2		628	1098	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939456	68939456	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	543	357	0	ENST00000288368.4:c.442-1G>A		p.X148_splice	ENST00000288368	NM_024870.2	148			0.697377907258913	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	1	0.708262628068242	4		357	844	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020350	69020350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367863793	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	647	383	0	ENST00000288368.4:c.2722C>T	p.Arg908Cys	p.R908C	ENST00000288368	NM_024870.2	908	Cgt/Tgt	24/40	0.697377907258913	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	1	0.708262628068242	4		383	1023	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500993	8500993	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	203	385	0	ENST00000356435.5:c.1889G>A	p.Trp630Ter	p.W630*	ENST00000356435		630	tGg/tAg	13/35	1	2	FACETS	0.94	0.877	1	0.94	0.877	1	CLONAL	1	TRUE	1	0.708262628068242	2		385	610	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27168535	27168535	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	247	543	0	ENST00000380036.4:c.407G>T	p.Gly136Val	p.G136V	ENST00000380036	NM_000459.3	136	gGa/gTa	3/23	1	2	FACETS	0.946	0.889	1	0.946	0.889	1	CLONAL	1	TRUE	1	0.708262628068242	2		543	737	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248075	110248075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	297	488	2	ENST00000374672.4:c.1397C>T	p.Ser466Phe	p.S466F	ENST00000374672	NM_004235.4	466	tCc/tTc	5/5	1	2	FACETS	0.947	0.894	1	0.947	0.894	1	CLONAL	1	TRUE	1	0.708262628068242	2		490	886	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753879	133753879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	309	575	0	ENST00000318560.5:c.1348G>A	p.Glu450Lys	p.E450K	ENST00000318560	NM_005157.4	450	Gag/Aag	8/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.708262628068242	2		575	820	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	183	538	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.877	0.81	0.948	0.877	0.81	0.948	CLONAL	1	TRUE	1	0.429125560558755	2		538	972	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578254	28578254	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs191501493	NA	P-0038724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	198	636	1	ENST00000241453.7:c.2917C>T	p.Arg973Ter	p.R973*	ENST00000241453	NM_004119.2	973	Cga/Tga	24/24	0.429125560558755	2	FACETS	0.963	0.892	1	0.482	0.446	0.519	CLONAL	1	TRUE	0	0.429125560558755	2		637	958	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061208	38061208	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1292426539	NA	P-0038724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	144	420	0	ENST00000250448.2:c.781C>G	p.Arg261Gly	p.R261G	ENST00000250448	NM_004496.3	261	Cgc/Ggc	2/2	1	2	FACETS	0.981	0.897	1	0.981	0.897	1	CLONAL	1	TRUE	1	0.429125560558755	2		420	684	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867222	68867223	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0038724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	193	623	0	ENST00000261769.5:c.2470dup	p.Ala824GlyfsTer5	p.A824Gfs*5	ENST00000261769	NM_004360.3	823	-/G	16/16	0.429261141738403	1	FACETS	0.984	0.913	1	0.984	0.913	1	CLONAL	1	TRUE	0	0.429125560558755	1		623	718	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743029	743029	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	220	694	0	ENST00000314574.4:c.949T>G	p.Phe317Val	p.F317V	ENST00000314574	NM_005433.3	317	Ttc/Gtc	8/12	1	2	FACETS	0.907	0.843	0.974	0.907	0.843	0.974	CLONAL	1	TRUE	1	0.429125560558755	2		694	1130	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928219	178928219	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	315	518	0	ENST00000263967.3:c.1405G>A	p.Glu469Lys	p.E469K	ENST00000263967	NM_006218.2	469	Gaa/Aaa	9/21	0.418455661929755	3	FACETS	0.907	0.857	0.958	0.907	0.857	0.958	CLONAL	2	TRUE	1	0.429125560558755	3		518	983	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636777	8636777	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	203	693	0	ENST00000356435.5:c.132C>G	p.Ile44Met	p.I44M	ENST00000356435		44	atC/atG	2/35	0.418455661929755	3	FACETS	0.991	0.918	1	0.496	0.459	0.534	CLONAL	1	TRUE	1	0.429125560558755	3		693	1159	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061208	38061208	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1292426539	NA	P-0038724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	96	420	0	ENST00000250448.2:c.781C>G	p.Arg261Gly	p.R261G	ENST00000250448	NM_004496.3	261	Cgc/Ggc	2/2	0.480044441405879	3	FACETS	0.792	0.707	0.883	0.396	0.353	0.442	SUBCLONAL	1	TRUE	1	0.49182364218008	3		420	614	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867222	68867223	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0038724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	197	623	0	ENST00000261769.5:c.2470dup	p.Ala824GlyfsTer5	p.A824Gfs*5	ENST00000261769	NM_004360.3	823	-/G	16/16	0.483562709618096	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.49182364218008	1		623	573	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743029	743029	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	128	694	0	ENST00000314574.4:c.949T>G	p.Phe317Val	p.F317V	ENST00000314574	NM_005433.3	317	Ttc/Gtc	8/12	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.49182364218008	2		694	506	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928219	178928219	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	150	518	0	ENST00000263967.3:c.1405G>A	p.Glu469Lys	p.E469K	ENST00000263967	NM_006218.2	469	Gaa/Aaa	9/21	0.491766839742827	3	FACETS	0.795	0.732	0.86	0.795	0.732	0.86	SUBCLONAL	2	TRUE	1	0.49182364218008	3		518	478	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0038725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	138	283	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.941	0.86	1	0.941	0.86	1	CLONAL	1	TRUE	1	0.51	2		283	575	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913255	NA	P-0038726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	159	720	0	ENST00000369535.4:c.183A>C	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caC	3/7	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.34	2		720	852	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0038726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	43	374	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	1	2	FACETS	0.662	0.555	0.78	0.662	0.555	0.78	SUBCLONAL	1	TRUE	1	0.34	2		374	382	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	G	rs1131691039	NA	P-0038726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	157	822	0	ENST00000269305.4:c.919+1G>C		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.167799932073953	2	FACETS	0.989	0.905	1	0.494	0.452	0.538	INDETERMINATE	1	TRUE	0	0.34	2		822	934	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120100	70120100	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	13	76	0	ENST00000245479.2:c.1102C>T	p.Gln368Ter	p.Q368*	ENST00000245479	NM_000346.3	368	Cag/Tag	3/3	0.167799932073953	2	FACETS	0.921	0.668	1	0.461	0.334	0.61	INDETERMINATE	1	TRUE	0	0.34	2		76	83	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636257	87636257	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	125	644	1	ENST00000277120.3:c.2422C>T	p.Arg808Ter	p.R808*	ENST00000277120		808	Cga/Tga	19/19	1	2	FACETS	0.926	0.838	1	0.926	0.838	1	CLONAL	1	TRUE	1	0.34	2		645	794	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371633	55371633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs931390946	NA	P-0038739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	345	704	1	ENST00000297316.4:c.323C>T	p.Ala108Val	p.A108V	ENST00000297316	NM_022454.3	108	gCg/gTg	2/2	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.75209546014348	2		705	909	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874011	123874013	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs780061449	NA	P-0038739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	12	61	0	ENST00000330479.4:c.62_64del	p.Ala21del	p.A21del	ENST00000330479	NM_020382.3	14	gaGGCg/gag	2/9	1	2	FACETS	0.205	0.144	0.279	0.205	0.144	0.279	SUBCLONAL	1	TRUE	1	0.75209546014348	2		61	156	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77085388	77085389	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	150	517	0	ENST00000356341.3:c.461dup	p.Asn154LysfsTer4	p.N154Kfs*4	ENST00000356341	NM_002576.4	154	aat/aaAt	5/15	1	2	FACETS	0.936	0.864	1	0.936	0.864	1	CLONAL	1	TRUE	1	0.75209546014348	2		517	426	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976154	18976154	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375690310	NA	P-0038739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	429	1022	1	ENST00000262803.5:c.2914G>A	p.Gly972Ser	p.G972S	ENST00000262803	NM_002911.3	972	Ggc/Agc	21/24	1	2	FACETS	0.978	0.933	1	0.978	0.933	1	CLONAL	1	TRUE	1	0.75209546014348	2		1023	1167	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591246	67591246	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0038740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	28	412	1	ENST00000274335.5:c.1746-2A>G		p.X582_splice	ENST00000274335		582			0.154801766201369	2	FACETS	0.288	0.23	0.355	0.144	0.115	0.178	INDETERMINATE	1	TRUE	0	0.370742586663636	2		413	524	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984340	201984340	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	214	635	0	ENST00000359651.3:c.1005C>A	p.Tyr335Ter	p.Y335*	ENST00000359651		335	taC/taA	8/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.370742586663636	2		635	1021	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860349	151860349	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs778718870	NA	P-0038740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	101	573	0	ENST00000262189.6:c.10313G>C	p.Gly3438Ala	p.G3438A	ENST00000262189	NM_170606.2	3438	gGc/gCc	43/59	0.283275141886751	1	FACETS	0.817	0.733	0.907	0.817	0.733	0.907	CLONAL	1	TRUE	0	0.370742586663636	1		573	543	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5068999	5069071	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTTTATAATTAAACTTATACAGCGAGAAAATGTCATTGAATATAAACACTGTTTGATTACAAAAAATGAGAA	TCTTTATAATTAAACTTATACAGCGAGAAAATGTCATTGAATATAAACACTGTTTGATTACAAAAAATGAGAA	-	novel	NA	P-0038740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	34	213	0	ENST00000381652.3:c.1327-22_1377del		p.X443_splice	ENST00000381652	NM_004972.3	443		11/25	0.272018263938713	1	FACETS	0.808	0.667	0.962	0.808	0.667	0.962	CLONAL	1	TRUE	0	0.370742586663636	1		213	185	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579309	7579320	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GACCGTGCAAGT	GACCGTGCAAGT	-	novel	NA	P-0038740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	222	604	0	ENST00000269305.4:c.368_375+4del		p.X123_splice	ENST00000269305	NM_001126112.2	123		4/11	NA	2	FACETS	0.763	0.712	0.815			1	INDETERMINATE	2	TRUE	NA	0.370742586663636	2		604	785	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104356969	104356969	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	84	734	0	ENST00000369902.3:c.829G>A	p.Asp277Asn	p.D277N	ENST00000369902	NM_016169.3	277	Gac/Aac	7/12	0.395518621576571	5	FACETS	1	0.892	1	0.335	0.297	0.376	INDETERMINATE	1	TRUE	2	0.850851640045624	5		734	447	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912453	32912453	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750055488	NA	P-0038741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	61	416	0	ENST00000380152.3:c.3961G>A	p.Asp1321Asn	p.D1321N	ENST00000380152		1321	Gat/Aat	11/27	0.789702778483828	2	FACETS	0.874	0.771	0.981	0.437	0.385	0.491	CLONAL	1	TRUE	0	0.850851640045624	2		416	164	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30133048	30133048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	71	501	1	ENST00000331968.5:c.553C>T	p.His185Tyr	p.H185Y	ENST00000331968	NM_002742.2	185	Cat/Tat	4/18	0.850851640045624	4	FACETS	1	0.939	1	0.552	0.486	0.62	CLONAL	1	TRUE	2	0.850851640045624	4		502	280	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574002	7574002	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs375338359	NA	P-0038741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	243	932	0	ENST00000269305.4:c.1025G>C	p.Arg342Pro	p.R342P	ENST00000269305	NM_001126112.2	342	cGa/cCa	10/11	0.8093099028988	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.850851640045624	2		932	279	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578438	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0038743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	94	885	1	ENST00000269305.4:c.492_493del	p.Gln165ValfsTer15	p.Q165Vfs*15	ENST00000269305	NM_001126112.2	164	aaGCag/aaag	5/11	1	2	FACETS	0.705	0.625	0.79	0.705	0.625	0.79	SUBCLONAL	1	FALSE	1	0.220610919765981	2		886	1209	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0038744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	33	523	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.708	0.576	0.858	0.708	0.576	0.858	SUBCLONAL	1	TRUE	1	0.17	2		523	548	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0038744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	59	606	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.17	2		606	673	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0038744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	33	454	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.6	0.487	0.728	0.6	0.487	0.728	SUBCLONAL	1	TRUE	1	0.17	2		454	647	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370985	55370985	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	37	561	0	ENST00000297316.4:c.287C>G	p.Ala96Gly	p.A96G	ENST00000297316	NM_022454.3	96	gCc/gGc	1/2	1	2	FACETS	0.789	0.649	0.945	0.789	0.649	0.945	CLONAL	1	TRUE	1	0.17	2		561	552	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622369	1622369	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143406385	NA	P-0038744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	48	1038	1	ENST00000344749.5:c.595G>A	p.Ala199Thr	p.A199T	ENST00000344749	NM_001136139.2	199	Gcc/Acc	9/19	1	2	FACETS	0.85	0.718	0.997	0.85	0.718	0.997	CLONAL	1	TRUE	1	0.17	2		1039	664	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089603	27089603	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	117	883	2	ENST00000324856.7:c.2561del	p.Pro854LeufsTer5	p.P854Lfs*5	ENST00000324856	NM_006015.4	853	ctC/ct	8/20	0.233876824406583	4	FACETS	1	0.915	1			1	CLONAL	2	TRUE	NA	0.17	4		885	793	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0038746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	92	647	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.169259314739719	2		647	1059	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0038746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	82	587	1	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.169259314739719	2		588	914	SUCCESS
APC	324	MSKCC	GRCh37	5	112175358	112175358	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	70	376	0	ENST00000257430.4:c.4067C>A	p.Ser1356Ter	p.S1356*	ENST00000257430	NM_000038.5	1356	tCa/tAa	16/16	0.169259314739719	2	FACETS	0.824	0.72	0.936	0.824	0.72	0.936	CLONAL	2	TRUE	0	0.169259314739719	2		376	502	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651153	206651153	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553385836	NA	P-0038746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	71	845	1	ENST00000367120.3:c.763G>A	p.Gly255Arg	p.G255R	ENST00000367120	NM_014002.3	255	Ggg/Agg	8/22	1	2	FACETS	0.748	0.65	0.854	0.748	0.65	0.854	SUBCLONAL	1	TRUE	1	0.169259314739719	2		846	1122	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918159	50918159	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	81	850	0	ENST00000440232.2:c.2476T>A	p.Cys826Ser	p.C826S	ENST00000440232	NM_002691.3	826	Tgc/Agc	20/27	1	2	FACETS	0.834	0.732	0.943	0.834	0.732	0.943	CLONAL	1	TRUE	1	0.169259314739719	2		850	1148	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346592	81346592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764869064	NA	P-0038747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	168	485	0	ENST00000222390.5:c.1361C>T	p.Thr454Met	p.T454M	ENST00000222390	NM_000601.4	454	aCg/aTg	11/18	1	2	FACETS	0.995	0.916	1	0.995	0.916	1	CLONAL	1	TRUE	1	0.405755602560802	2		485	832	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578448	7578448	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1064795691	NA	P-0038747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	345	963	0	ENST00000269305.4:c.482C>A	p.Ala161Asp	p.A161D	ENST00000269305	NM_001126112.2	161	gCc/gAc	5/11	0.405755602560802	1	FACETS	0.977	0.923	1	0.977	0.923	1	CLONAL	1	TRUE	0	0.405755602560802	1		963	1388	SUCCESS
APC	324	MSKCC	GRCh37	5	112175351	112175351	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	104	379	0	ENST00000257430.4:c.4063del	p.Ser1355LeufsTer60	p.S1355Lfs*60	ENST00000257430	NM_000038.5	1354	Ttt/tt	16/16	0.405755602560802	1	FACETS	0.831	0.747	0.918	0.831	0.747	0.918	CLONAL	1	TRUE	0	0.405755602560802	1		379	492	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489802	2489802	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	338	830	0	ENST00000355716.4:c.199T>A	p.Cys67Ser	p.C67S	ENST00000355716	NM_003820.2	67	Tgc/Agc	3/8	0.405755602560802	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.405755602560802	1		830	1268	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640323	3640323	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200057338	NA	P-0038747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1487	185	1018	0	ENST00000294008.3:c.3316G>A	p.Val1106Met	p.V1106M	ENST00000294008	NM_032444.2	1106	Gtg/Atg	12/15	0.368998413948876	1	FACETS	0.435	0.4	0.472	0.435	0.4	0.472	SUBCLONAL	1	TRUE	0	0.405755602560802	1		1018	1672	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0038748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	148	283	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.624963928920358	4	FACETS	0.987	0.938	1	0.987	0.938	1	CLONAL	4	TRUE	0	0.624963928920358	4		283	195	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372025	55372025	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	111	460	1	ENST00000297316.4:c.715G>A	p.Ala239Thr	p.A239T	ENST00000297316	NM_022454.3	239	Gcc/Acc	2/2	0.38759372664052	2	FACETS	1	0.987	1	0.746	0.685	0.808	CLONAL	1	TRUE	0	0.624963928920358	2		461	238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577115	7577115	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	146	786	0	ENST00000269305.4:c.823T>G	p.Cys275Gly	p.C275G	ENST00000269305	NM_001126112.2	275	Tgt/Ggt	8/11	0.624963928920358	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.624963928920358	1		786	274	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430231	181430231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	161	465	3	ENST00000325404.1:c.83C>T	p.Ala28Val	p.A28V	ENST00000325404	NM_003106.3	28	gCg/gTg	1/1	0.38759372664052	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.624963928920358	2		468	244	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383356	42383356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782043875	NA	P-0038748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	69	633	1	ENST00000221972.3:c.376C>T	p.Arg126Cys	p.R126C	ENST00000221972	NM_021601.3	126	Cgc/Tgc	2/5	0.186115864943398	4	FACETS	1	0.968	1	0.657	0.578	0.74	INDETERMINATE	1	TRUE	2	0.624963928920358	4		634	273	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849078	156849078	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	136	1009	0	ENST00000524377.1:c.1970T>C	p.Leu657Pro	p.L657P	ENST00000524377	NM_002529.3	657	cTa/cCa	15/17	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.624963928920358	2		1009	321	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913123	32913123	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	29	632	0	ENST00000380152.3:c.4631A>C	p.Asn1544Thr	p.N1544T	ENST00000380152		1544	aAc/aCc	11/27	0.291398172491065	3	FACETS	0.47	0.379	0.573	0.235	0.189	0.287	INDETERMINATE	1	TRUE	1	0.624963928920358	3		632	259	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685569	29685569	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	33	602	0	ENST00000356175.3:c.7979T>C	p.Ile2660Thr	p.I2660T	ENST00000356175	NM_000267.3	2660	aTc/aCc	54/57	0.624963928920358	1	FACETS	0.522	0.432	0.62	0.522	0.432	0.62	SUBCLONAL	1	TRUE	0	0.624963928920358	1		602	139	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11019804	11019804	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	138	598	0	ENST00000327064.4:c.479A>G	p.Gln160Arg	p.Q160R	ENST00000327064	NM_199141.1	160	cAg/cGg	4/16	0.186115864943398	4	FACETS	0.962	0.886	1	0.962	0.886	1	INDETERMINATE	2	TRUE	2	0.624963928920358	4		598	373	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0038753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	190	325	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.570301715678492	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	1	0.583294087845832	4		325	317	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0038753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	217	543	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.583294087845832	2		543	729	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778488	3778488	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760836018	NA	P-0038753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	122	864	0	ENST00000262367.5:c.6560C>T	p.Pro2187Leu	p.P2187L	ENST00000262367	NM_004380.2	2187	cCa/cTa	31/31	1	2	FACETS	0.408	0.368	0.45	0.408	0.368	0.45	SUBCLONAL	1	TRUE	1	0.583294087845832	2		864	1026	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577125	7577126	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	295	693	0	ENST00000269305.4:c.812dup	p.Val272GlyfsTer34	p.V272Gfs*34	ENST00000269305	NM_001126112.2	271	gag/gaAg	8/11	0.583294087845832	1	FACETS	0.952	0.9	1	0.952	0.9	1	CLONAL	1	TRUE	0	0.583294087845832	1		693	753	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711259	114711259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	71	361	1	ENST00000543371.1:c.274G>A	p.Gly92Arg	p.G92R	ENST00000543371	NM_001198531.1	92	Gga/Aga	3/14	1	2	FACETS	0.367	0.32	0.417	0.367	0.32	0.417	SUBCLONAL	1	TRUE	1	0.583294087845832	2		362	664	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484315	50484315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	147	628	0	ENST00000394963.4:c.1075C>T	p.Gln359Ter	p.Q359*	ENST00000394963	NM_003076.4	359	Cag/Tag	9/13	0.203430809000456	2	FACETS	0.856	0.782	0.933	0.856	0.782	0.933	CLONAL	2	TRUE	0	0.21985619652481	2		628	781	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	155	691	0	ENST00000269305.4:c.811G>C	p.Glu271Gln	p.E271Q	ENST00000269305	NM_001126112.2	271	Gag/Cag	8/11	0.203430809000456	2	FACETS	0.82	0.751	0.892	0.82	0.751	0.892	CLONAL	2	TRUE	0	0.21985619652481	2		691	860	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729180	66729180	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs397516793	NA	P-0038754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	104	640	0	ENST00000307102.5:c.388T>C	p.Tyr130His	p.Y130H	ENST00000307102	NM_002755.3	130	Tat/Cat	3/11	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.21985619652481	2		640	861	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	172	732	0	ENST00000269305.4:c.853G>C	p.Glu285Gln	p.E285Q	ENST00000269305	NM_001126112.2	285	Gag/Cag	8/11	0.203430809000456	2	FACETS	0.859	0.79	0.93	0.859	0.79	0.93	CLONAL	2	TRUE	0	0.21985619652481	2		732	911	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968280	2968280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	220	761	0	ENST00000396946.4:c.1706G>A	p.Gly569Glu	p.G569E	ENST00000396946	NM_032415.4	569	gGa/gAa	13/25	0.21985619652481	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.21985619652481	3		761	944	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753175	57753175	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	57	352	0	ENST00000274289.3:c.841G>A	p.Glu281Lys	p.E281K	ENST00000274289	NM_006622.3	281	Gaa/Aaa	7/14	0.125739961383941	3	FACETS	1	0.939	1	0.587	0.504	0.677	INDETERMINATE	1	TRUE	1	0.21985619652481	3		352	490	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096931	11096931	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060502073	NA	P-0038754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	173	813	1	ENST00000358026.2:c.422C>T	p.Ser141Leu	p.S141L	ENST00000358026	NM_001128849.1	141	tCg/tTg	4/36	0.137522554099696	4	FACETS	0.942	0.866	1	0.942	0.866	1	CLONAL	2	TRUE	2	0.21985619652481	4		814	1019	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902197	50902197	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs765969481	NA	P-0038754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	167	799	0	ENST00000440232.2:c.89G>T	p.Arg30Leu	p.R30L	ENST00000440232	NM_002691.3	30	cGg/cTg	2/27	0.137522554099696	4	FACETS	0.969	0.89	1	0.969	0.89	1	CLONAL	2	TRUE	2	0.21985619652481	4		799	956	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39704817	39704818	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	62	188	0	ENST00000361337.2:c.165dup	p.Asp56ArgfsTer3	p.D56Rfs*3	ENST00000361337	NM_003286.2	54	-/A	4/21	0.125739961383941	3	FACETS	1	0.916	1	1	0.916	1	INDETERMINATE	2	TRUE	1	0.21985619652481	3		188	293	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971190	13971190	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	58	459	0	ENST00000405192.2:c.739A>T	p.Ser247Cys	p.S247C	ENST00000405192	NM_001163147.1	247	Agc/Tgc	8/12	0.21985619652481	3	FACETS	0.96	0.825	1	0.48	0.412	0.554	CLONAL	1	TRUE	1	0.21985619652481	3		459	610	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860095	152860095	+	synonymous_variant	Silent	SNP	G	G	T	novel	NA	P-0038754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	76	727	0	ENST00000406277.2:c.333C>A	p.Arg111=	p.R111=	ENST00000406277	NM_152274.4	111	cgC/cgA	5/7	1		FACETS		0.65	0.843				SUBCLONAL	1	TRUE	1	0.21985619652481	2		727	931	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919230	48919235	+	frameshift_variant	Frame_Shift_Del	DEL	TTAACT	TTAACT	A	novel	NA	P-0038754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	32	225	0	ENST00000267163.4:c.395_400delinsA	p.Phe132TyrfsTer6	p.F132Yfs*6	ENST00000267163	NM_000321.2	132	tTTAACTta/tAta	4/27	0.203430809000456	2	FACETS	1	0.921	1	0.63	0.515	0.759	CLONAL	1	TRUE	0	0.21985619652481	2		225	231	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207090	1207096	+	protein_altering_variant	In_Frame_Del	DEL	TACGGCA	TACGGCA	G	novel	NA	P-0038754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	357	850	0	ENST00000326873.7:c.178_184delinsG	p.Tyr60_Lys62delinsGlu	p.Y60_K62delinsE	ENST00000326873	NM_000455.4	60	TACGGCAag/Gag	1/10	0.150141172478639	4	FACETS	0.876	0.83	0.922			1	CLONAL	4	TRUE	NA	0.21985619652481	4		850	1131	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0038756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	117	283	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.446341788294118	3	FACETS	1	0.958	1	0.552	0.499	0.607	CLONAL	1	TRUE	1	0.459669751406845	3		283	567	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0038756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	161	1107	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.44857032722637	1	FACETS	0.919	0.847	0.993	0.919	0.847	0.993	CLONAL	1	TRUE	0	0.459669751406845	1		1107	587	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0038756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	190	344	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.459669751406845	2	FACETS	0.906	0.847	0.966	0.906	0.847	0.966	CLONAL	2	TRUE	0	0.459669751406845	2		344	456	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143209	30143209	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1037485859	NA	P-0038756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	125	619	0	ENST00000389048.3:c.317C>T	p.Pro106Leu	p.P106L	ENST00000389048	NM_004304.4	106	cCg/cTg	1/29	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.459669751406845	2		619	524	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500473	149500473	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1292468244	NA	P-0038756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	156	745	0	ENST00000261799.4:c.2564C>T	p.Ser855Leu	p.S855L	ENST00000261799	NM_002609.3	855	tCg/tTg	18/23	0.459669751406845	2	FACETS	1	0.932	1	0.508	0.466	0.551	CLONAL	1	TRUE	0	0.459669751406845	2		745	668	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006834	47006834	+	5_prime_UTR_variant	5'UTR	SNP	A	A	G	novel	NA	P-0038756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	166	836	0	ENST00000377604.3:c.-47A>G		p.*16*	ENST00000377604	NM_001204468.1	-/852		2/24	0.459669751406845	3	FACETS	0.961	0.883	1	0.481	0.441	0.522	CLONAL	1	TRUE	1	0.459669751406845	3		836	924	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456481	89456481	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	52	414	0	ENST00000336596.2:c.1657A>C	p.Ile553Leu	p.I553L	ENST00000336596	NM_005233.5	553	Att/Ctt	8/17	1	2	FACETS	0.758	0.644	0.883	0.758	0.644	0.883	SUBCLONAL	1	TRUE	1	0.193783602610761	2		414	708	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412033	116412046	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTCCAGAAGGTA	TTTTCCAGAAGGTA	CTT	novel	NA	P-0038759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	126	810	1	ENST00000397752.3:c.3018_3028+3delinsCTT		p.X1006_splice	ENST00000397752	NM_000245.2	1006		14/21	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.193783602610761	2		811	1249	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0038762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	245	557	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	0.664585703043683	2		557	715	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139198	37139198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	206	561	0	ENST00000373509.5:c.538G>A	p.Gly180Ser	p.G180S	ENST00000373509	NM_002648.3	180	Ggc/Agc	4/6	1	2	FACETS	0.992	0.926	1	0.992	0.926	1	CLONAL	1	TRUE	1	0.664585703043683	2		561	625	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249002	55249003	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCGTGGA	rs397517109	NA	P-0038763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	151	665	0	ENST00000275493.2:c.2303_2311dup	p.Ser768_Asp770dup	p.S768_D770dup	ENST00000275493	NM_005228.3	768	gcc/gcCAGCGTGGAc	20/28	0.329929988039364	3	FACETS	0.788	0.723	0.855	0.788	0.723	0.855	SUBCLONAL	2	TRUE	1	0.369825430317381	3		665	614	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032092	10032092	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201674066	NA	P-0038763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	118	744	0	ENST00000330684.3:c.731G>A	p.Arg244His	p.R244H	ENST00000330684	NM_001134407.1	244	cGc/cAc	3/13	1	2	FACETS	0.971	0.878	1	0.971	0.878	1	CLONAL	1	TRUE	1	0.369825430317381	2		744	657	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196051	108196051	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	68	436	0	ENST00000278616.4:c.6587G>C	p.Arg2196Thr	p.R2196T	ENST00000278616	NM_000051.3	2196	aGa/aCa	46/63	1	2	FACETS	0.812	0.708	0.923	0.812	0.708	0.923	CLONAL	1	TRUE	1	0.369825430317381	2		436	453	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891296	101891296	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	156	748	0	ENST00000374994.4:c.257G>A	p.Cys86Tyr	p.C86Y	ENST00000374994	NM_004612.2	86	tGt/tAt	2/9	0.369825430317381	1	FACETS	0.919	0.843	0.998	0.919	0.843	0.998	CLONAL	1	TRUE	0	0.369825430317381	1		748	748	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827414	72827414	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs374608671	NA	P-0038769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	242	536	0	ENST00000268489.5:c.9167T>C	p.Ile3056Thr	p.I3056T	ENST00000268489	NM_006885.3	3056	aTt/aCt	9/10	0.335957394906167	3	FACETS	0.878	0.828	0.929	0.878	0.828	0.929	CLONAL	3	FALSE	0	0.394923556597333	3		536	557	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205316	46205316	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	159	284	0	ENST00000334344.6:c.400C>T	p.Gln134Ter	p.Q134*	ENST00000334344	NM_152641.2	134	Cag/Tag	4/21	0.394923556597333	5	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	FALSE	2	0.394923556597333	5		284	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577056	7577057	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	304	604	0	ENST00000269305.4:c.881dup	p.Pro295AlafsTer11	p.P295Afs*11	ENST00000269305	NM_001126112.2	294	gag/gaAg	8/11	0.394923556597333	3	FACETS	0.866	0.821	0.91	1	0.993	1	CLONAL	3	FALSE	1	0.394923556597333	3		604	710	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430227	181430227	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	62	315	0	ENST00000325404.1:c.79G>A	p.Ala27Thr	p.A27T	ENST00000325404	NM_003106.3	27	Gcg/Acg	1/1	0.292627315266419	3	FACETS	1	0.901	1	0.522	0.453	0.596	CLONAL	1	FALSE	1	0.394923556597333	3		315	360	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737930	145737930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	203	619	0	ENST00000428558.2:c.2900C>T	p.Ala967Val	p.A967V	ENST00000428558	NM_004260.3	967	gCt/gTt	18/22	0.394923556597333	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	FALSE	1	0.394923556597333	3		619	582	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	168	399	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	1	0.978	1	1	0.993	1	CLONAL	2	TRUE	0	0.27	1		399	471	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0038770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	374	601	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	0.997	1	CLONAL	3	TRUE	1	0.27	2		601	820	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118955	70118955	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	197	703	0	ENST00000245479.2:c.527C>T	p.Pro176Leu	p.P176L	ENST00000245479	NM_000346.3	176	cCg/cTg	2/3	0.685213967686004	4	FACETS	1	0.984	1	0.602	0.558	0.647	CLONAL	1	TRUE	2	0.685213967686004	4		703	805	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944554	40944554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775796300	NA	P-0038771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	93	440	0	ENST00000373198.4:c.1948G>A	p.Val650Met	p.V650M	ENST00000373198	NM_133170.3	650	Gtg/Atg	12/32	0.0702479440902199	4	FACETS	1	0.934	1			1	INDETERMINATE	1	TRUE	NA	0.685213967686004	4		440	431	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855025	76855026	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0038771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	225	445	0	ENST00000373344.5:c.5810_5811del	p.Gly1937GlufsTer4	p.G1937Efs*4	ENST00000373344	NM_000489.3	1937	gGG/g	25/35	0.182843275108617	3	FACETS	0.883	0.842	0.922			1	INDETERMINATE	3	TRUE	NA	0.685213967686004	3		445	333	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443631	29443631	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519784	NA	P-0038772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	178	657	1	ENST00000389048.3:c.3586C>A	p.Leu1196Met	p.L1196M	ENST00000389048	NM_004304.4	1196	Ctg/Atg	23/29	0.186469327737092	2	FACETS	1	0.989	1	0.741	0.683	0.801	CLONAL	1	TRUE	0	0.269273701864657	2		658	892	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794598	42794598	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	72	748	0	ENST00000575354.2:c.1678C>T	p.Gln560Ter	p.Q560*	ENST00000575354	NM_015125.3	560	Cag/Tag	10/20	0.223311419917023	3	FACETS	0.544	0.473	0.62	0.272	0.236	0.31	SUBCLONAL	1	TRUE	1	0.269273701864657	3		748	1116	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352625	118352625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782070742	NA	P-0038772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	66	477	1	ENST00000534358.1:c.3830C>T	p.Ser1277Leu	p.S1277L	ENST00000534358	NM_005933.3	1277	tCg/tTg	7/36	1	2	FACETS	0.719	0.623	0.822	0.719	0.623	0.822	SUBCLONAL	1	TRUE	1	0.269273701864657	2		478	682	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665410	138665410	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	102	721	0	ENST00000330315.3:c.155C>A	p.Ala52Glu	p.A52E	ENST00000330315	NM_023067.3	52	gCg/gAg	1/1	1	2	FACETS	0.84	0.75	0.936	0.84	0.75	0.936	CLONAL	1	TRUE	1	0.269273701864657	2		721	902	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057641	27057641	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0038773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	116	458	0	ENST00000324856.7:c.1351-2A>G		p.X451_splice	ENST00000324856	NM_006015.4	451			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		458	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0038774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	415	695	1	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.559526493027502	2	FACETS	0.982	0.944	1	0.982	0.944	1	CLONAL	2	TRUE	0	0.559526493027502	2		696	755	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947585	48947585	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0038774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	75	386	0	ENST00000267163.4:c.1172C>G	p.Ser391Ter	p.S391*	ENST00000267163	NM_000321.2	391	tCa/tGa	12/27	0.559526493027502	1	FACETS	0.866	0.771	0.964	0.866	0.771	0.964	CLONAL	1	TRUE	0	0.559526493027502	1		386	223	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221785	55221787	+	missense_variant	Missense_Mutation	TNP	ATG	ATG	GAA	novel	NA	P-0038774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	2421	696	0	ENST00000275493.2:c.829_831delinsGAA	p.Met277Glu	p.M277E	ENST00000275493	NM_005228.3	277	ATG/GAA	7/28	0.559526493027502	15	FACETS	0.975	0.964	0.985	0.975	0.964	0.985	CLONAL	14	TRUE	1	0.559526493027502	15		696	2941	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	55	578	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	0.21	2		578	402	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343603	118343603	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs782733922	NA	P-0038776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	49	385	0	ENST00000534358.1:c.1729A>G	p.Ser577Gly	p.S577G	ENST00000534358	NM_005933.3	577	Agt/Ggt	3/36	1	2	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	1	0.21	2		385	466	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752336	55752336	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	86	674	0	ENST00000284073.2:c.794C>G	p.Ser265Cys	p.S265C	ENST00000284073	NM_138962.2	265	tCc/tGc	12/14	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.21	2		674	793	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78599573	78599573	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	47	392	0	ENST00000306801.3:c.245C>T	p.Ala82Val	p.A82V	ENST00000306801	NM_020761.2	82	gCa/gTa	2/34	1	2	FACETS	0.933	0.787	1	0.933	0.787	1	CLONAL	1	TRUE	1	0.21	2		392	480	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593510	48593511	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0038776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	31	278	0	ENST00000342988.3:c.1261_1262del	p.Ala421ThrfsTer7	p.A421Tfs*7	ENST00000342988	NM_005359.5	421	GCa/a	10/12	1	2	FACETS	1	0.845	1	1	0.845	1	CLONAL	1	TRUE	1	0.21	2		278	282	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266606	198266606	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	45	368	0	ENST00000335508.6:c.2230G>C	p.Ala744Pro	p.A744P	ENST00000335508	NM_012433.2	744	Gct/Cct	16/25	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.21	2		368	344	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058633	47058633	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	73	606	0	ENST00000409792.3:c.7645C>G	p.Gln2549Glu	p.Q2549E	ENST00000409792	NM_014159.6	2549	Cag/Gag	21/21	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.21	2		606	678	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045539	47045542	+	frameshift_variant	Frame_Shift_Del	DEL	AGGA	AGGA	-	novel	NA	P-0038776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	57	640	0	ENST00000377604.3:c.2508_2511del	p.Arg836SerfsTer10	p.R836Sfs*10	ENST00000377604	NM_001204468.1	836	AGGAag/ag	22/24	1	2	FACETS	0.871	0.747	1	0.871	0.747	1	CLONAL	1	TRUE	1	0.21	2		640	623	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0038778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	57	526	0	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	1	2	FACETS	0.304	0.26	0.351	0.304	0.26	0.351	SUBCLONAL	1	TRUE	1	0.60849853394747	2		526	617	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223620	36223620	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374062006	NA	P-0038778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	286	977	1	ENST00000222270.7:c.6170G>A	p.Arg2057His	p.R2057H	ENST00000222270	NM_014727.1	2057	cGc/cAc	28/37	1	2	FACETS	0.879	0.826	0.932	0.879	0.826	0.932	CLONAL	1	TRUE	1	0.60849853394747	2		978	1070	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026605	48026605	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779212	NA	P-0038778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	151	324	0	ENST00000234420.5:c.1483C>T	p.Arg495Ter	p.R495*	ENST00000234420	NM_000179.2	495	Cga/Tga	4/10	1	2	FACETS	0.989	0.91	1	0.989	0.91	1	CLONAL	1	TRUE	1	0.60849853394747	2		324	502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	329	735	0	ENST00000269305.4:c.329del	p.Arg110LeufsTer13	p.R110Lfs*13	ENST00000269305	NM_001126112.2	110	cGt/ct	4/11	0.485212406861055	2	FACETS	0.924	0.88	0.969	0.924	0.88	0.969	CLONAL	2	TRUE	0	0.501250719811437	2		735	710	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23635370	23635370	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45624036	NA	P-0038779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	127	592	0	ENST00000261584.4:c.2794G>A	p.Val932Met	p.V932M	ENST00000261584	NM_024675.3	932	Gtg/Atg	8/13	0.231746711576561	5	FACETS	1	0.959	1	0.369	0.334	0.406	INDETERMINATE	1	TRUE	2	0.501250719811437	5		592	802	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809796	36809796	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780348168	NA	P-0038779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	147	744	1	ENST00000373129.3:c.809G>A	p.Gly270Asp	p.G270D	ENST00000373129	NM_032017.1	270	gGc/gAc	9/12	0.503971764467714	3	FACETS	0.7	0.638	0.765	0.35	0.319	0.383	SUBCLONAL	1	TRUE	1	0.501250719811437	3		745	1048	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027225	49027255	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AATAATCACACTGCAGCAGATATGTAAGCAA	AATAATCACACTGCAGCAGATATGTAAGCAA	-	novel	NA	P-0038779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	150	385	0	ENST00000267163.4:c.1796_1814+12del		p.X599_splice	ENST00000267163	NM_000321.2	599		18/27	0.503971764467714	2	FACETS	0.924	0.858	0.989	0.924	0.858	0.989	CLONAL	2	TRUE	0	0.501250719811437	2		385	324	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245594	41245595	+	stop_gained	Nonsense_Mutation	DNP	TC	TC	AA	novel	NA	P-0038779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	416	622	0	ENST00000357654.3:c.1953_1954delinsTT	p.Lys651_Lys652delinsAsnTer	p.K651_K652delinsN*	ENST00000357654	NM_007294.3	651	aaGAaa/aaTTaa	10/23	0.503971764467714	3	FACETS	0.958	0.922	0.995	0.958	0.922	0.995	CLONAL	3	TRUE	0	0.501250719811437	3		622	722	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933271	49933271	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	280	794	0	ENST00000296474.3:c.2839C>G	p.Arg947Gly	p.R947G	ENST00000296474	NM_002447.2	947	Cgg/Ggg	12/20	0.503971764467714	3	FACETS	1	0.992	1	0.681	0.64	0.723	CLONAL	1	TRUE	1	0.501250719811437	3		794	1026	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79952340	79952358	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGCAACTCTGGTGAGTTG	TGGCAACTCTGGTGAGTTG	-	novel	NA	P-0038779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	177	411	0	ENST00000265081.6:c.351_358+11del		p.X117_splice	ENST00000265081	NM_002439.4	117		2/24	0.485212406861055	2	FACETS	0.87	0.812	0.928	0.87	0.812	0.928	CLONAL	2	TRUE	0	0.501250719811437	2		411	406	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671238	30671238	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	553	657	0	ENST00000376406.3:c.5639G>T	p.Ser1880Ile	p.S1880I	ENST00000376406	NM_014641.2	1880	aGc/aTc	11/15	0.503971764467714	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	0	0.501250719811437	3		657	907	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729566	41729566	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	278	595	0	ENST00000242208.4:c.963C>G	p.Cys321Trp	p.C321W	ENST00000242208	NM_002192.2	321	tgC/tgG	3/3	0.359532403269468	5	FACETS	1	0.979	1	0.723	0.68	0.766	CLONAL	2	TRUE	2	0.501250719811437	5		595	896	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224213	53224213	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	252	728	0	ENST00000375401.3:c.3338C>A	p.Thr1113Asn	p.T1113N	ENST00000375401	NM_004187.3	1113	aCc/aAc	22/26	0.503971764467714	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.501250719811437	1		728	608	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0038790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	197	622	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.728974655595685	2	FACETS	0.99	0.945	1	0.99	0.945	1	CLONAL	2	TRUE	0	0.728974655595685	2		622	273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0038790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	489	589	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.728974655595685	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.728974655595685	2		589	627	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045024	47045024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	180	293	0	ENST00000377604.3:c.2350C>T	p.His784Tyr	p.H784Y	ENST00000377604	NM_001204468.1	784	Cac/Tac	20/24	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.728974655595685	1		293	245	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27098999	27098999	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	139	409	0	ENST00000324856.7:c.3415G>T	p.Gly1139Ter	p.G1139*	ENST00000324856	NM_006015.4	1139	Gga/Tga	13/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.728974655595685	2		409	360	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246387	46246387	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	198	280	0	ENST00000334344.6:c.4483del	p.His1495IlefsTer21	p.H1495Ifs*21	ENST00000334344	NM_152641.2	1494	tCc/tc	15/21	0.728974655595685	2	FACETS	0.96	0.914	1	0.96	0.914	1	CLONAL	2	TRUE	0	0.728974655595685	2		280	283	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610560	81610560	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	218	313	0	ENST00000298171.2:c.2158C>A	p.Gln720Lys	p.Q720K	ENST00000298171	NM_000369.2	720	Cag/Aag	10/10	0.728974655595685	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.728974655595685	3		313	398	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817493	39817493	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	144	457	0	ENST00000288319.7:c.70G>T	p.Gly24Ter	p.G24*	ENST00000288319	NM_182918.3	24	Gga/Tga	2/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.728974655595685	2		457	379	SUCCESS
ATR	545	MSKCC	GRCh37	3	142177816	142177816	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs373093280	NA	P-0038790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	155	227	0	ENST00000350721.4:c.7487A>G	p.Asn2496Ser	p.N2496S	ENST00000350721	NM_001184.3	2496	aAt/aGt	44/47	0.728974655595685	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.728974655595685	3		227	272	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6036983	6036983	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0038790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	279	416	0	ENST00000265849.7:c.777T>A	p.Cys259Ter	p.C259*	ENST00000265849	NM_000535.5	259	tgT/tgA	7/15	0.697934882617786	4	FACETS	0.871	0.822	0.92	0.871	0.822	0.92	CLONAL	2	TRUE	2	0.728974655595685	4		416	760	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508617	106508617	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	236	373	0	ENST00000359195.3:c.611C>G	p.Ser204Cys	p.S204C	ENST00000359195	NM_002649.2	204	tCc/tGc	2/11	0.697934882617786	4	FACETS	0.957	0.9	1	0.957	0.9	1	CLONAL	2	TRUE	2	0.728974655595685	4		373	585	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340351	8340351	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	248	361	0	ENST00000356435.5:c.5245A>C	p.Met1749Leu	p.M1749L	ENST00000356435		1749	Atg/Ctg	31/35	0.728974655595685	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.728974655595685	2		361	338	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738186	133738186	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	252	364	0	ENST00000318560.5:c.586G>T	p.Ala196Ser	p.A196S	ENST00000318560	NM_005157.4	196	Gcc/Tcc	4/11	0.691561484696809	3	FACETS	0.957	0.907	1	0.957	0.907	1	CLONAL	2	TRUE	1	0.728974655595685	3		364	493	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18943113	18943113	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	102	310	2	ENST00000262803.5:c.95A>T	p.Glu32Val	p.E32V	ENST00000262803	NM_002911.3	32	gAg/gTg	1/24	1	2	FACETS	0.879	0.792	0.97	0.879	0.792	0.97	CLONAL	1	TRUE	1	0.57455988119415	2		312	404	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593611	55593667	+	inframe_deletion	In_Frame_Del	DEL	TGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTTCCTTA	TGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTTCCTTA	-	novel	NA	P-0038792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	176	397	1	ENST00000288135.5:c.1679_1735del	p.Val560_Tyr578del	p.V560_Y578del	ENST00000288135	NM_000222.2	559	gtTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTTCCTTAt/gtt	11/21	0.543230251147822	3	FACETS	0.888	0.827	0.95	0.888	0.827	0.95	CLONAL	2	TRUE	1	0.57455988119415	3		398	444	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0038794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	58	347	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	0.305464029455823	2		347	331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0038794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	104	630	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.305464029455823	1	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	0	0.305464029455823	1		630	569	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246027143	246027143	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	88	489	0	ENST00000388985.4:c.859C>T	p.Gln287Ter	p.Q287*	ENST00000388985		287	Caa/Taa	9/12	1	2	FACETS	0.962	0.853	1	0.962	0.853	1	CLONAL	1	TRUE	1	0.305464029455823	2		489	599	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443518	49443518	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	71	417	0	ENST00000301067.7:c.3853G>C	p.Glu1285Gln	p.E1285Q	ENST00000301067	NM_003482.3	1285	Gag/Cag	11/54	1	2	FACETS	0.912	0.797	1	0.912	0.797	1	CLONAL	1	TRUE	1	0.305464029455823	2		417	510	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910723	32910723	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs397507282	NA	P-0038794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	57	386	0	ENST00000380152.3:c.2231C>G	p.Ser744Ter	p.S744*	ENST00000380152		744	tCa/tGa	11/27	0.305464029455823	1	FACETS	0.961	0.829	1	0.961	0.829	1	CLONAL	1	TRUE	0	0.305464029455823	1		386	329	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911143	32911143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777421358	NA	P-0038794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	69	383	0	ENST00000380152.3:c.2651C>T	p.Ser884Leu	p.S884L	ENST00000380152		884	tCa/tTa	11/27	0.305464029455823	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.305464029455823	1		383	345	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	91	578	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.224823995835695	2	FACETS	0.88	0.785	0.98	0.88	0.785	0.98	CLONAL	2	TRUE	0	0.224823995835695	2		578	460	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971035	21971035	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	72	445	0	ENST00000304494.5:c.323A>G	p.Asp108Gly	p.D108G	ENST00000304494	NM_000077.4	108	gAt/gGt	2/3	0.224823995835695	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.224823995835695	1		445	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577504	7577524	+	inframe_deletion	In_Frame_Del	DEL	GTCTTCCAGTGTGATGATGGT	GTCTTCCAGTGTGATGATGGT	-	novel	NA	P-0038795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	114	561	0	ENST00000269305.4:c.757_777del	p.Thr253_Asp259del	p.T253_D259del	ENST00000269305	NM_001126112.2	253	ACCATCATCACACTGGAAGAC/-	7/11	0.224823995835695	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.224823995835695	1		561	653	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435739	56435740	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0038795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	90	464	0	ENST00000407977.2:c.1397_1398del	p.Ser466Ter	p.S466*	ENST00000407977		466	tCC/t	9/10	0.224823995835695	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.224823995835695	1		464	497	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0038796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	91	461	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.891	0.793	0.994	0.891	0.793	0.994	CLONAL	1	TRUE	1	0.389252558769225	2		461	525	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063248	67063336	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	CAGCCAGCGGGTGCCCGCGCAAGCCCCGAGCGCGGCCGGCCGGCGCGGCCTCAGGGCGGGAAGATGCCGCGCGTCGTGCCCGACCAGAG	CAGCCAGCGGGTGCCCGCGCAAGCCCCGAGCGCGGCCGGCCGGCGCGGCCTCAGGGCGGGAAGATGCCGCGCGTCGTGCCCGACCAGAG	-	novel	NA	P-0038796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	60	5	0	ENST00000412916.2:c.-63_26del		p.*21*	ENST00000412916		?-9/187		1/6	0.350147046696479	1	FACETS	0.877	0.762	1	0.877	0.762	1	CLONAL	1	TRUE	0	0.389252558769225	1		5	283	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014035	70014035	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	77	323	0	ENST00000394351.3:c.896T>G	p.Leu299Arg	p.L299R	ENST00000394351	NM_000248.3	299	cTt/cGt	9/9	1	2	FACETS	0.92	0.811	1	0.92	0.811	1	CLONAL	1	TRUE	1	0.389252558769225	2		323	430	SUCCESS
AR	367	MSKCC	GRCh37	X	66765146	66765158	+	frameshift_variant	Frame_Shift_Del	DEL	GTTTGCTGCTGCT	GTTTGCTGCTGCT	-	novel	NA	P-0038796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	33	331	0	ENST00000374690.3:c.159_171del	p.Leu54SerfsTer117	p.L54Sfs*117	ENST00000374690	NM_000044.3	53	aGTTTGCTGCTGCTg/ag	1/8	0.389252558769225	1	FACETS	0.61	0.5	0.731	0.61	0.5	0.731	SUBCLONAL	1	TRUE	0	0.389252558769225	1		331	224	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0038800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	171	283	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.276545572512202	4	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	2	0.444625950998872	4		283	541	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578464	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	456	682	0	ENST00000269305.4:c.466C>G	p.Arg156Gly	p.R156G	ENST00000269305	NM_001126112.2	156	Cgc/Ggc	5/11	0.444625950998872	2	FACETS	0.998	0.956	1	0.998	0.956	1	CLONAL	2	TRUE	0	0.444625950998872	2		682	1028	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653820	89653821	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	25	307	0	ENST00000371953.3:c.121dup	p.Arg41LysfsTer3	p.R41Kfs*3	ENST00000371953	NM_000314.4	40	gaa/gAaa	2/9	0.15938823250075	4	FACETS	1	0.901	1	0.616	0.492	0.754	INDETERMINATE	1	FALSE	2	0.43444800566471	4		307	134	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711993	89711999	+	frameshift_variant	Frame_Shift_Del	DEL	CAATGTT	CAATGTT	-	novel	NA	P-0038806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	25	241	0	ENST00000371953.3:c.613_619del	p.Met205ValfsTer14	p.M205Vfs*14	ENST00000371953	NM_000314.4	204	cCAATGTTc/cc	6/9	0.15938823250075	4	FACETS	0.794	0.638	0.964	0.794	0.638	0.964	INDETERMINATE	2	FALSE	2	0.43444800566471	4		241	104	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591134	67591135	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAATCCAGCTGA	novel	NA	P-0038806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	26	264	0	ENST00000274335.5:c.1727_1728insCAATCCAGCTGA	p.Thr576_Arg577insAsnProAlaGlu	p.T576_R577insNPAE	ENST00000274335		576	acg/acCAATCCAGCTGAg	12/15	1	2	FACETS	0.843	0.676	1	0.843	0.676	1	CLONAL	1	FALSE	1	0.43444800566471	2		264	142	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578374	7578374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501206	NA	P-0038806-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	8	491	2	ENST00000269305.4:c.556G>A	p.Asp186Asn	p.D186N	ENST00000269305	NM_001126112.2	186	Gat/Aat	5/11	1	2	FACETS	0.316	0.203	0.464	0.316	0.203	0.464	SUBCLONAL	1	TRUE	1	0.18	2		493	281	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38139043	38139043	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038806-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	10	381	0	ENST00000317025.8:c.3560G>A	p.Arg1187Gln	p.R1187Q	ENST00000317025	NM_023034.1	1187	cGa/cAa	20/24	1	2	FACETS	0.601	0.407	0.844	0.601	0.407	0.844	SUBCLONAL	1	TRUE	1	0.18	2		381	185	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782144	NA	P-0038808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	166	70	0	ENST00000269305.4:c.473G>C	p.Arg158Pro	p.R158P	ENST00000269305	NM_001126112.2	158	cGc/cCc	5/11	0.187107758020069	2	FACETS	0.876	0.808	0.946	0.876	0.808	0.946	CLONAL	2	FALSE	0	0.3	2		70	632	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624242	89624272	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGAGATCGTTAGCAGAAACAAAAGGAGAT	AAAGAGATCGTTAGCAGAAACAAAAGGAGAT	-	novel	NA	P-0038808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	23	21	0	ENST00000371953.3:c.17_47del	p.Lys6IlefsTer8	p.K6Ifs*8	ENST00000371953	NM_000314.4	6	AAAGAGATCGTTAGCAGAAACAAAAGGAGATat/at	1/9	1	2	FACETS	0.767	0.601	0.956	0.767	0.601	0.956	CLONAL	1	FALSE	1	0.3	2		21	200	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980744	40980744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199751250	NA	P-0038808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	82	49	0	ENST00000373198.4:c.1742G>A	p.Arg581Gln	p.R581Q	ENST00000373198	NM_133170.3	581	cGg/cAg	10/32	NA	2	FACETS	0.816	0.726	0.911			1	INDETERMINATE	2	FALSE	NA	0.3	2		49	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577043	7577044	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0038809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	161	693	0	ENST00000269305.4:c.894dup	p.Leu299AlafsTer7	p.L299Afs*7	ENST00000269305	NM_001126112.2	298	-/G	8/11	0.186989842109565	2	FACETS	1	0.983	1	0.635	0.583	0.689	INDETERMINATE	1	TRUE	0	0.331887584756288	2		693	764	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246760	41246760	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs397509319	NA	P-0038809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	41	432	0	ENST00000357654.3:c.788G>T	p.Gly263Val	p.G263V	ENST00000357654	NM_007294.3	263	gGt/gTt	10/23	0.331887584756288	1	FACETS	0.56	0.467	0.662	0.56	0.467	0.662	SUBCLONAL	1	TRUE	0	0.331887584756288	1		432	368	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554364	141554364	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	106	797	0	ENST00000220592.5:c.1787C>G	p.Ala596Gly	p.A596G	ENST00000220592	NM_012154.3	596	gCa/gGa	14/19	0.331887584756288	3	FACETS	0.788	0.705	0.876	0.394	0.352	0.438	SUBCLONAL	1	TRUE	1	0.331887584756288	3		797	945	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	289	399	0				ENST00000310581	NM_198253.2	-/1132			0.579564738499307	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.627310301371418	4		399	699	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0038810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	72	297	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.8	0.706	0.899	0.8	0.706	0.899	SUBCLONAL	1	TRUE	1	0.627310301371418	2		297	287	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474482	40474482	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs769031989	NA	P-0038810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	228	418	0	ENST00000264657.5:c.1919A>T	p.Tyr640Phe	p.Y640F	ENST00000264657	NM_139276.2	640	tAc/tTc	21/24	0.627310301371418	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.627310301371418	3		418	461	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858168	9858168	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	134	544	0	ENST00000330684.3:c.3233A>C	p.Lys1078Thr	p.K1078T	ENST00000330684	NM_001134407.1	1078	aAg/aCg	13/13	0.623632781541156	2	FACETS	0.907	0.83	0.987	0.454	0.415	0.494	CLONAL	1	TRUE	0	0.627310301371418	2		544	471	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164809	32164809	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs900740951	NA	P-0038810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	180	508	0	ENST00000375023.3:c.5093C>T	p.Thr1698Ile	p.T1698I	ENST00000375023	NM_004557.3	1698	aCa/aTa	28/30	0.627310301371418	3	FACETS	1	0.935	1	0.506	0.467	0.546	CLONAL	1	TRUE	1	0.627310301371418	3		508	745	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	452	769	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.799176339176736	1	FACETS	0.991	0.959	1	0.991	0.959	1	CLONAL	1	TRUE	0	0.81214247998443	1		769	667	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	238	578	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.997	0.938	1	0.997	0.938	1	CLONAL	1	TRUE	1	0.81214247998443	2		578	588	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0038811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	285	433	2	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.81214247998443	2		435	699	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039430	49039430	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0038811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	297	505	0	ENST00000267163.4:c.2415T>G	p.Tyr805Ter	p.Y805*	ENST00000267163	NM_000321.2	805	taT/taG	23/27	0.81214247998443	1	FACETS	0.97	0.93	1	0.97	0.93	1	CLONAL	1	TRUE	0	0.81214247998443	1		505	448	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846152	151846152	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0038811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	268	469	0	ENST00000262189.6:c.12860T>A	p.Leu4287Ter	p.L4287*	ENST00000262189	NM_170606.2	4287	tTg/tAg	52/59	1	2	FACETS	0.922	0.869	0.975	0.922	0.869	0.975	CLONAL	1	TRUE	1	0.81214247998443	2		469	716	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633425	8633425	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776040231	NA	P-0038811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	176	391	0	ENST00000356435.5:c.244C>T	p.Leu82Phe	p.L82F	ENST00000356435		82	Ctc/Ttc	3/35	0.401915494233267	1	FACETS	0.586	0.546	0.627	0.586	0.546	0.627	INDETERMINATE	1	TRUE	0	0.81214247998443	1		391	439	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0038814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	390	578	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	1	2	FACETS	0.884	0.859	0.908	1	0.997	1	CLONAL	2	TRUE	1	0.896455724798013	2		578	492	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248736	59248736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767611605	NA	P-0038814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	309	698	1	ENST00000371222.2:c.7G>A	p.Ala3Thr	p.A3T	ENST00000371222	NM_002228.3	3	Gca/Aca	1/1	1	2	FACETS	0.884	0.856	0.911	1	0.997	1	CLONAL	2	TRUE	1	0.896455724798013	2		699	390	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785683	50785683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	522	510	0	ENST00000398568.2:c.673G>A	p.Val225Ile	p.V225I	ENST00000398568	NM_001042412.1	225	Gtc/Atc	4/18	0.326838844857025	6	FACETS	0.94	0.915	0.964			1	INDETERMINATE	5	TRUE	NA	0.896455724798013	6		510	692	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603134	48603154	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTCCAGCTATCAGTAAGTAT	GCTCCAGCTATCAGTAAGTAT	-	novel	NA	P-0038814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	137	401	0	ENST00000342988.3:c.1438_1447+11del		p.X480_splice	ENST00000342988	NM_005359.5	480		11/12	0.896526680946867	1	FACETS	0.947	0.9	0.992	0.947	0.9	0.992	CLONAL	1	TRUE	0	0.896455724798013	1		401	178	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0038818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	171	483	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.518873833703637	2		483	592	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115559	108115559	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	135	337	0	ENST00000278616.4:c.707T>G	p.Leu236Arg	p.L236R	ENST00000278616	NM_000051.3	236	cTt/cGt	7/63	0.518873833703637	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.518873833703637	1		337	369	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1034666	1034666	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	142	421	0	ENST00000358495.3:c.493T>A	p.Cys165Ser	p.C165S	ENST00000358495	NM_134424.2	165	Tgt/Agt	7/12	0.476733491874246	0	FACETS	0.514	0.471	0.559			1	SUBCLONAL	1	TRUE	0	0.518873833703637	0		421	512	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0038819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	294	451	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.179148834457854	6	FACETS	1	0.986	1	0.757	0.714	0.801	INDETERMINATE	2	TRUE	3	0.617214126127863	6		451	937	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572002	64572002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779413959	NA	P-0038819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	323	726	7	ENST00000312049.6:c.1637C>T	p.Pro546Leu	p.P546L	ENST00000312049	NM_130799.2	546	cCg/cTg	10/10	1	2	FACETS	0.998	0.943	1	0.998	0.943	1	CLONAL	1	TRUE	1	0.617214126127863	2		733	1049	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971029	21971029	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519852	NA	P-0038819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	245	468	1	ENST00000304494.5:c.329G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tGg/tAg	2/3	0.617214126127863	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.617214126127863	1		469	460	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894916	101894916	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060502040	NA	P-0038819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	121	291	0	ENST00000374994.4:c.469C>T	p.Arg157Ter	p.R157*	ENST00000374994	NM_004612.2	157	Cga/Tga	3/9	0.617214126127863	1	FACETS	0.922	0.847	0.999	0.922	0.847	0.999	CLONAL	1	TRUE	0	0.617214126127863	1		291	294	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0038821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	220	622	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.979	0.918	1	0.979	0.918	1	CLONAL	1	TRUE	1	0.75264482164013	2		622	597	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207021	1207021	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913324	NA	P-0038821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	325	719	1	ENST00000326873.7:c.109C>T	p.Gln37Ter	p.Q37*	ENST00000326873	NM_000455.4	37	Cag/Tag	1/10	0.75264482164013	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.75264482164013	1		720	519	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602493	10602493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	279	555	0	ENST00000171111.5:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000171111	NM_203500.1	362	cGg/cAg	3/6	0.75264482164013	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.75264482164013	1		555	426	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180037025	180037025	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	173	556	0	ENST00000261937.6:c.3687G>T	p.Arg1229Ser	p.R1229S	ENST00000261937	NM_182925.4	1229	agG/agT	28/30	NA	2	FACETS	0.896	0.831	0.963			1	INDETERMINATE	1	TRUE	NA	0.75264482164013	2		556	513	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210101	55210101	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	44	363	0	ENST00000275493.2:c.211C>G	p.Gln71Glu	p.Q71E	ENST00000275493	NM_005228.3	71	Cag/Gag	2/28	1	2	FACETS	0.186	0.155	0.22	0.186	0.155	0.22	SUBCLONAL	1	TRUE	1	0.75264482164013	2		363	629	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009287	69009287	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	320	401	0	ENST00000288368.4:c.2404G>C	p.Asp802His	p.D802H	ENST00000288368	NM_024870.2	802	Gat/Cat	22/40	0.415078872628774	3	FACETS	0.917	0.874	0.96	0.917	0.874	0.96	INDETERMINATE	2	TRUE	1	0.75264482164013	3		401	638	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486014	8486014	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs375803455	NA	P-0038821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	173	506	0	ENST00000356435.5:c.2803G>T	p.Val935Phe	p.V935F	ENST00000356435		935	Gtc/Ttc	17/35	1	2	FACETS	0.912	0.846	0.98	0.912	0.846	0.98	CLONAL	1	TRUE	1	0.75264482164013	2		506	504	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044848	47044848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375052241	NA	P-0038822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	298	844	1	ENST00000377604.3:c.2174C>T	p.Pro725Leu	p.P725L	ENST00000377604	NM_001204468.1	725	cCg/cTg	20/24	0.580879123644168	4	FACETS	0.907	0.86	0.955	0.907	0.86	0.955	CLONAL	2	TRUE	2	0.886380621585884	4		845	699	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0038822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	352	619	0	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	0.881004796879378	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.886380621585884	2		619	385	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999272	100999272	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	386	719	0	ENST00000325455.5:c.530G>T	p.Gly177Val	p.G177V	ENST00000325455	NM_001202474.3	177	gGg/gTg	1/8	0.799685840269355	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	2	0.886380621585884	4		719	747	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509733	106509733	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	359	555	0	ENST00000359195.3:c.1728del	p.Trp576CysfsTer21	p.W576Cfs*21	ENST00000359195	NM_002649.2	576	tGg/tg	2/11	0.886380621585884	5	FACETS	0.975	0.934	1	0.975	0.934	1	CLONAL	3	TRUE	2	0.886380621585884	5		555	645	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410128	139410128	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	756	614	1	ENST00000277541.6:c.1710C>A	p.Cys570Ter	p.C570*	ENST00000277541	NM_017617.3	570	tgC/tgA	11/34	0.881479332806037	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	4	TRUE	0	0.886380621585884	4		615	802	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412250	63412250	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	340	819	1	ENST00000330258.3:c.917G>A	p.Gly306Glu	p.G306E	ENST00000330258	NM_152424.3	306	gGg/gAg	2/2	0.580879123644168	4	FACETS	0.91	0.866	0.955	0.91	0.866	0.955	CLONAL	2	TRUE	2	0.886380621585884	4		820	795	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456470	89456470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147450955	NA	P-0038823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	134	342	3	ENST00000336596.2:c.1646C>T	p.Ala549Val	p.A549V	ENST00000336596	NM_005233.5	549	gCg/gTg	8/17	1	2	FACETS	0.88	0.807	0.956	0.88	0.807	0.956	CLONAL	1	TRUE	1	0.721304432666669	2		345	422	SUCCESS
AR	367	MSKCC	GRCh37	X	66931247	66931247	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs868669253	NA	P-0038823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	131	424	1	ENST00000374690.3:c.1889G>T	p.Arg630Leu	p.R630L	ENST00000374690	NM_000044.3	630	cGg/cTg	4/8	1	2	FACETS	0.859	0.786	0.934	0.859	0.786	0.934	CLONAL	1	TRUE	1	0.721304432666669	2		425	423	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0038824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	120	382	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	0.805837050982979	2		382	293	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0038824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	824	856	1	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.805837050982979	2	FACETS	0.995	0.976	1	0.995	0.976	1	CLONAL	2	TRUE	0	0.805837050982979	2		857	1028	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918922	76918922	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0038824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	258	297	0	ENST00000373344.5:c.4069A>T	p.Lys1357Ter	p.K1357*	ENST00000373344	NM_000489.3	1357	Aag/Tag	12/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.805837050982979	1		297	326	SUCCESS
APC	324	MSKCC	GRCh37	5	112174784	112174784	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0038825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	54	290	0	ENST00000257430.4:c.3493A>T	p.Lys1165Ter	p.K1165*	ENST00000257430	NM_000038.5	1165	Aaa/Taa	16/16	0.3	1	FACETS	0.851	0.73	0.983	0.851	0.73	0.983	CLONAL	1	TRUE	0	0.29	1		290	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0038825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	129	457	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.3	1	FACETS	0.96	0.871	1	0.96	0.871	1	CLONAL	1	TRUE	0	0.29	1		457	792	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0038825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	150	524	2	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.29	2		526	904	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646279	3646279	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749277750	NA	P-0038825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	95	803	1	ENST00000294008.3:c.1799C>T	p.Pro600Leu	p.P600L	ENST00000294008	NM_032444.2	600	cCg/cTg	8/15	1	2	FACETS	0.532	0.472	0.597	0.532	0.472	0.597	SUBCLONAL	1	TRUE	1	0.29	2		804	1231	SUCCESS
APC	324	MSKCC	GRCh37	5	112174533	112174533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374380039	NA	P-0038825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	67	339	0	ENST00000257430.4:c.3242G>A	p.Ser1081Asn	p.S1081N	ENST00000257430	NM_000038.5	1081	aGc/aAc	16/16	0.3	1	FACETS	0.773	0.673	0.881	0.773	0.673	0.881	SUBCLONAL	1	TRUE	0	0.29	1		339	511	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145736819	145736819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41555416	NA	P-0038826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	95	509	0	ENST00000428558.2:c.3622C>T	p.Arg1208Cys	p.R1208C	ENST00000428558	NM_004260.3	1208	Cgc/Tgc	22/22	1	2	FACETS	0.696	0.622	0.774	0.696	0.622	0.774	SUBCLONAL	1	TRUE	1	0.555896217678983	2		509	491	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923343	131923343	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	17	240	0	ENST00000265335.6:c.846G>A	p.Met282Ile	p.M282I	ENST00000265335		282	atG/atA	6/25	0.555896217678983	1	FACETS	0.247	0.185	0.32	0.247	0.185	0.32	SUBCLONAL	1	TRUE	0	0.555896217678983	1		240	179	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11181390	11181390	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	32	600	0	ENST00000361445.4:c.6846G>C	p.Gln2282His	p.Q2282H	ENST00000361445	NM_004958.3	2282	caG/caC	49/58	0.449128144134614	0	FACETS	0.103	0.083	0.125			1	SUBCLONAL	1	TRUE	0	0.555896217678983	0		600	498	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36824355	36824355	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	31	515	0	ENST00000373129.3:c.181G>C	p.Asp61His	p.D61H	ENST00000373129	NM_032017.1	61	Gac/Cac	4/12	0.1022740644716	4	FACETS	0.401	0.324	0.488	0.1	0.081	0.122	INDETERMINATE	1	TRUE	0	0.555896217678983	4		515	433	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724472	162724472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	29	475	0	ENST00000367921.3:c.244G>A	p.Asp82Asn	p.D82N	ENST00000367921	NM_006182.2	82	Gac/Aac	5/18	0.1022740644716	4	FACETS	0.457	0.367	0.56	0.114	0.091	0.14	INDETERMINATE	1	TRUE	0	0.555896217678983	4		475	355	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725544	162725544	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	22	320	0	ENST00000367921.3:c.656G>C	p.Gly219Ala	p.G219A	ENST00000367921	NM_006182.2	219	gGa/gCa	7/18	0.1022740644716	4	FACETS	0.419	0.325	0.528	0.105	0.081	0.132	INDETERMINATE	1	TRUE	0	0.555896217678983	4		320	294	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433287	49433287	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	313	710	0	ENST00000301067.7:c.8160G>A	p.Trp2720Ter	p.W2720*	ENST00000301067	NM_003482.3	2720	tgG/tgA	32/54	0.451525262421883	3	FACETS	0.935	0.895	0.974	0.935	0.895	0.974	CLONAL	3	TRUE	0	0.555896217678983	3		710	513	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589353	28589353	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	22	415	0	ENST00000241453.7:c.2694C>G	p.Phe898Leu	p.F898L	ENST00000241453	NM_004119.2	898	ttC/ttG	22/24	0.450957811668677	1	FACETS	0.187	0.145	0.237	0.187	0.145	0.237	SUBCLONAL	1	TRUE	0	0.555896217678983	1		415	305	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777855	3777855	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	88	881	0	ENST00000262367.5:c.7193G>A	p.Gly2398Glu	p.G2398E	ENST00000262367	NM_004380.2	2398	gGa/gAa	31/31	1	2	FACETS	0.441	0.39	0.495	0.441	0.39	0.495	SUBCLONAL	1	TRUE	1	0.555896217678983	2		881	718	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31406964	31406964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	140	513	0	ENST00000344624.3:c.3943C>T	p.Pro1315Ser	p.P1315S	ENST00000344624		1315	Cca/Tca	31/33	0.359896253586197	3	FACETS	1	0.961	1	0.545	0.498	0.593	CLONAL	1	TRUE	1	0.555896217678983	3		513	591	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0038827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	90	332	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.882	0.786	0.982	0.882	0.786	0.982	CLONAL	1	TRUE	1	0.466178764087455	2		332	438	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398287	25398288	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTC	novel	NA	P-0038827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	104	369	0	ENST00000311936.3:c.29_31dup	p.Gly10dup	p.G10dup	ENST00000311936	NM_004985.3	10	gct/gGAGct	2/5	1	2	FACETS	0.836	0.751	0.925	0.836	0.751	0.925	CLONAL	1	TRUE	1	0.466178764087455	2		369	534	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274899	41274899	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	120	348	0	ENST00000349496.5:c.1149G>T	p.Trp383Cys	p.W383C	ENST00000349496	NM_001904.3	383	tgG/tgT	8/15	1	2	FACETS	0.902	0.817	0.99	0.902	0.817	0.99	CLONAL	1	TRUE	1	0.466178764087455	2		348	571	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215595191	215595191	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	51	300	0	ENST00000260947.4:c.1945G>A	p.Glu649Lys	p.E649K	ENST00000260947	NM_000465.2	649	Gaa/Aaa	10/11	1	2	FACETS	0.521	0.444	0.606	0.521	0.444	0.606	SUBCLONAL	1	TRUE	1	0.466178764087455	2		300	420	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797721	45797721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs558173961	NA	P-0038827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	247	706	0	ENST00000450313.1:c.971C>T	p.Ser324Leu	p.S324L	ENST00000450313	NM_012222.2	324	tCg/tTg	11/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.466178764087455	2		706	990	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193219805	193219805	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0038827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	45	204	0	ENST00000367435.3:c.1560-1G>T		p.X520_splice	ENST00000367435	NM_024529.4	520			1	2	FACETS	0.801	0.679	0.933	0.801	0.679	0.933	CLONAL	1	TRUE	1	0.466178764087455	2		204	241	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119952	70119953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	100	431	0	ENST00000245479.2:c.955dup	p.Tyr319LeufsTer259	p.Y319Lfs*259	ENST00000245479	NM_000346.3	318	-/T	3/3	1	2	FACETS	0.751	0.673	0.834	0.751	0.673	0.834	SUBCLONAL	1	TRUE	1	0.466178764087455	2		431	571	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593388	48593408	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GGTTGCACATAGGCAAAGGTG	GGTTGCACATAGGCAAAGGTG	-	novel	NA	P-0038827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	68	258	0	ENST00000342988.3:c.1140-1_1159del		p.X380_splice	ENST00000342988	NM_005359.5	380		10/12	0.466178764087455	1	FACETS	0.796	0.7	0.898	0.796	0.7	0.898	SUBCLONAL	1	TRUE	0	0.466178764087455	1		258	281	SUCCESS
APC	324	MSKCC	GRCh37	5	112174607	112174607	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554084921	NA	P-0038827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	133	356	0	ENST00000257430.4:c.3316G>T	p.Gly1106Ter	p.G1106*	ENST00000257430	NM_000038.5	1106	Gga/Tga	16/16	1	2	FACETS	0.999	0.911	1	0.999	0.911	1	CLONAL	1	TRUE	1	0.466178764087455	2		356	571	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339207	65339207	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0038833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	22	303	0	ENST00000342505.4:c.330-1G>C		p.X110_splice	ENST00000342505	NM_002227.2	110			0.364102235669716	1	FACETS	0.376	0.292	0.473	0.376	0.292	0.473	SUBCLONAL	1	TRUE	0	0.364102235669716	1		303	263	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-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	90	616	0	ENST00000326873.7:c.989_1108+466del		p.X330_splice	ENST00000326873	NM_000455.4	330		8/10	0.364102235669716	1	FACETS	0.759	0.675	0.848	0.759	0.675	0.848	SUBCLONAL	1	TRUE	0	0.364102235669716	1		616	533	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611829	1611829	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	74	548	0	ENST00000344749.5:c.1833A>T	p.Lys611Asn	p.K611N	ENST00000344749	NM_001136139.2	611	aaA/aaT	19/19	0.364102235669716	1	FACETS	0.534	0.467	0.605	0.534	0.467	0.605	SUBCLONAL	1	TRUE	0	0.364102235669716	1		548	623	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-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	182	570	0	ENST00000171111.5:c.1532-22_1538del		p.X511_splice	ENST00000171111	NM_203500.1	511		5/6	0.364102235669716	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.364102235669716	1		570	601	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266826	18266826	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	62	490	0	ENST00000222254.8:c.137G>T	p.Gly46Val	p.G46V	ENST00000222254	NM_005027.3	46	gGt/gTt	2/16	0.364102235669716	1	FACETS	0.606	0.524	0.694	0.606	0.524	0.694	SUBCLONAL	1	TRUE	0	0.364102235669716	1		490	460	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733240	40733240	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	61	529	0	ENST00000373198.4:c.3566C>A	p.Thr1189Lys	p.T1189K	ENST00000373198	NM_133170.3	1189	aCa/aAa	26/32	1	2	FACETS	0.579	0.499	0.665	0.579	0.499	0.665	SUBCLONAL	1	TRUE	1	0.364102235669716	2		529	579	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72897431	72897431	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	49	362	0	ENST00000325599.8:c.61G>C	p.Val21Leu	p.V21L	ENST00000325599	NM_018130.2	21	Gtg/Ctg	1/11	0.28663191288335	1	FACETS	0.587	0.499	0.684	0.587	0.499	0.684	SUBCLONAL	1	TRUE	0	0.364102235669716	1		362	375	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31495424	31495424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561252258	NA	P-0038833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	43	527	0	ENST00000344624.3:c.1724G>A	p.Arg575Gln	p.R575Q	ENST00000344624		575	cGg/cAg	9/33	0.0817196709286757	5	FACETS	0.465	0.388	0.551	0.155	0.129	0.184	INDETERMINATE	1	TRUE	2	0.364102235669716	5		527	785	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867505	35867505	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs764440449	NA	P-0038833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	22	292	0	ENST00000303115.3:c.319A>G	p.Ile107Val	p.I107V	ENST00000303115	NM_002185.3	107	Ata/Gta	3/8	0.0817196709286757	5	FACETS	0.548	0.424	0.692	0.183	0.141	0.231	INDETERMINATE	1	TRUE	2	0.364102235669716	5		292	341	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6037056	6037056	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	rs745487791	NA	P-0038833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	25	285	0	ENST00000265849.7:c.706-2A>C		p.X236_splice	ENST00000265849	NM_000535.5	236			0.364102235669716	3	FACETS	0.457	0.36	0.569	0.229	0.18	0.285	SUBCLONAL	1	TRUE	1	0.364102235669716	3		285	355	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0038834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	109	493	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.328260707017609	2		493	504	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627438	37627447	+	frameshift_variant	Frame_Shift_Del	DEL	AAAATTGGAA	AAAATTGGAA	-	novel	NA	P-0038834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	74	464	0	ENST00000447079.4:c.1356_1365del	p.Lys452AsnfsTer9	p.K452Nfs*9	ENST00000447079	NM_015083.1	451	gtAAAATTGGAA/gt	2/14	0.294686692706357	3	FACETS	0.934	0.819	1	0.467	0.409	0.529	CLONAL	1	TRUE	1	0.328260707017609	3		464	562	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267260	41267260	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	42	325	0	ENST00000349496.5:c.844A>T	p.Met282Leu	p.M282L	ENST00000349496	NM_001904.3	282	Atg/Ttg	6/15	1	2	FACETS	0.873	0.733	1	0.873	0.733	1	CLONAL	1	TRUE	1	0.328260707017609	2		325	293	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44920597	44920597	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	72	308	0	ENST00000377967.4:c.1358A>T	p.His453Leu	p.H453L	ENST00000377967	NM_021140.2	453	cAt/cTt	14/29	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.328260707017609	2		308	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0038835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	26	457	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.450047161872855	1	FACETS	0.163	0.129	0.203	0.163	0.129	0.203	SUBCLONAL	1	TRUE	0	0.450047161872855	1		457	548	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0038835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	169	875	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.450047161872855	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.450047161872855	1		876	553	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790866	89790866	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1243623521	NA	P-0038835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	182	554	1	ENST00000336032.3:c.253G>A	p.Val85Met	p.V85M	ENST00000336032	NM_006813.2	85	Gtg/Atg	1/2	0.450047161872855	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.450047161872855	1		555	568	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	109	399	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.889	0.808	0.973	0.889	0.808	0.973	CLONAL	1	TRUE	1	0.754180114980683	2		399	325	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0038836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	125	297	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.961	0.881	1	0.961	0.881	1	CLONAL	1	TRUE	1	0.754180114980683	2		297	345	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073929	8073929	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	150	334	0	ENST00000377482.5:c.730C>T	p.Arg244Ter	p.R244*	ENST00000377482	NM_018948.3	244	Cga/Tga	4/4	1	2	FACETS	0.987	0.912	1	0.987	0.912	1	CLONAL	1	TRUE	1	0.754180114980683	2		334	403	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074057	8074105	+	frameshift_variant	Frame_Shift_Del	DEL	AAGCTTCGCCTGCCAGGAACATCATATTTGAAATCAGAAAGTGTAGAGT	AAGCTTCGCCTGCCAGGAACATCATATTTGAAATCAGAAAGTGTAGAGT	-	novel	NA	P-0038836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	110	301	0	ENST00000377482.5:c.554_602del	p.Asp185AlafsTer46	p.D185Afs*46	ENST00000377482	NM_018948.3	185	gACTCTACACTTTCTGATTTCAAATATGATGTTCCTGGCAGGCGAAGCTTc/gc	4/4	1	2	FACETS	0.941	0.857	1	0.941	0.857	1	CLONAL	1	TRUE	1	0.754180114980683	2		301	310	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430711	181430711	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	242	541	0	ENST00000325404.1:c.563C>G	p.Ala188Gly	p.A188G	ENST00000325404	NM_003106.3	188	gCg/gGg	1/1	1	2	FACETS	0.99	0.931	1	0.99	0.931	1	CLONAL	1	TRUE	1	0.754180114980683	2		541	648	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120365	94120365	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	113	212	0	ENST00000369303.4:c.686A>C	p.Glu229Ala	p.E229A	ENST00000369303	NM_004440.3	229	gAg/gCg	3/17	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.754180114980683	2		212	260	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0038837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	113	456	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.203285487226642	2	FACETS	0.928	0.838	1	0.928	0.838	1	CLONAL	2	TRUE	0	0.217894574527276	2		456	559	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0038837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	19	187	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.768	0.585	0.983	0.768	0.585	0.983	CLONAL	1	TRUE	1	0.217894574527276	2		187	227	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741528	17741528	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	29	313	1	ENST00000250003.3:c.199G>A	p.Ala67Thr	p.A67T	ENST00000250003	NM_002478.4	67	Gcg/Acg	1/3	0.217894574527276	3	FACETS	0.757	0.607	0.927	0.378	0.303	0.464	CLONAL	1	TRUE	1	0.217894574527276	3		314	390	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777936	3777940	+	protein_altering_variant	In_Frame_Del	DEL	GGCTG	GGCTG	CT	novel	NA	P-0038837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	60	707	3	ENST00000262367.5:c.7108_7112delinsAG	p.Gln2370_Pro2371delinsSer	p.Q2370_P2371delinsS	ENST00000262367	NM_004380.2	2370	CAGCCt/AGt	31/31	0.186196035115048	3	FACETS	0.762	0.655	0.879			1	SUBCLONAL	1	TRUE	NA	0.217894574527276	3		710	801	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577129	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519986	NA	P-0038838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	98	537	0	ENST00000269305.4:c.809T>C	p.Phe270Ser	p.F270S	ENST00000269305	NM_001126112.2	270	tTt/tCt	8/11	0.170266898006739	2	FACETS	1	0.967	1	0.605	0.54	0.675	CLONAL	1	TRUE	0	0.229991541548873	2		537	704	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425038	49425038	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783690	NA	P-0038838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	98	697	0	ENST00000301067.7:c.13450C>T	p.Arg4484Ter	p.R4484*	ENST00000301067	NM_003482.3	4484	Cga/Tga	39/54	0.229991541548873	5	FACETS	1	0.977	1	0.688	0.613	0.768	CLONAL	1	TRUE	3	0.229991541548873	5		697	833	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197182	106197182	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	16	289	0	ENST00000380013.4:c.5515G>T	p.Gly1839Cys	p.G1839C	ENST00000380013	NM_001127208.2	1839	Ggt/Tgt	11/11	1	2	FACETS	0.669	0.496	0.875	0.669	0.496	0.875	SUBCLONAL	1	TRUE	1	0.229991541548873	2		289	208	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0038839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	20	454	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.404	0.309	0.515	0.404	0.309	0.515	SUBCLONAL	1	TRUE	1	0.352519036925776	2		454	281	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087961	27087961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	22	379	0	ENST00000324856.7:c.2248C>T	p.Arg750Ter	p.R750*	ENST00000324856	NM_006015.4	750	Cga/Tga	6/20	1	2	FACETS	0.328	0.253	0.414	0.328	0.253	0.414	SUBCLONAL	1	TRUE	1	0.352519036925776	2		379	381	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624271	89624272	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs786204883	NA	P-0038839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	93	281	0	ENST00000371953.3:c.46dup	p.Tyr16LeufsTer28	p.Y16Lfs*28	ENST00000371953	NM_000314.4	15	-/T	1/9	0.125882541537578	5	FACETS	1	0.964	1	0.585	0.524	0.647	INDETERMINATE	2	TRUE	1	0.352519036925776	5		281	345	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220066	36220066	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	48	579	2	ENST00000222270.7:c.4786G>T	p.Gly1596Trp	p.G1596W	ENST00000222270	NM_014727.1	1596	Ggg/Tgg	22/37	1	2	FACETS	0.552	0.467	0.646	0.552	0.467	0.646	SUBCLONAL	1	TRUE	1	0.352519036925776	2		581	493	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589283	67589284	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	19	228	0	ENST00000274335.5:c.1272dup	p.Leu425ThrfsTer17	p.L425Tfs*17	ENST00000274335		424	tta/ttAa	9/15	1	2	FACETS	0.455	0.346	0.582	0.455	0.346	0.582	SUBCLONAL	1	TRUE	1	0.352519036925776	2		228	237	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0038840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	145	588	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		588	713	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829245	72829245	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0038840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	44	609	0	ENST00000268489.5:c.7336A>T	p.Lys2446Ter	p.K2446*	ENST00000268489	NM_006885.3	2446	Aag/Tag	9/10	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		609	682	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0038847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	131	622	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.43508246650714	1	FACETS	0.855	0.783	0.929	0.855	0.783	0.929	CLONAL	1	TRUE	0	0.548895850447067	1		622	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0038847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	266	607	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.548895850447067	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.548895850447067	1		607	677	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0038847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	173	454	7	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	0.548895850447067	1	FACETS	0.957	0.889	1	0.957	0.889	1	CLONAL	1	TRUE	0	0.548895850447067	1		461	478	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39570433	39570433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747825815	NA	P-0038847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	110	136	0	ENST00000262039.4:c.629G>A	p.Arg210Gln	p.R210Q	ENST00000262039	NM_002647.2	210	cGa/cAa	6/25	0.543837281689356	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.548895850447067	2		136	193	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247810	59247811	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0038847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	335	621	0	ENST00000371222.2:c.932_933del	p.Lys311SerfsTer6	p.K311Sfs*6	ENST00000371222	NM_002228.3	311	aAA/a	1/1	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.548895850447067	2		621	1175	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798348	45798348	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	73	590	0	ENST00000450313.1:c.588G>T	p.Glu196Asp	p.E196D	ENST00000450313	NM_012222.2	196	gaG/gaT	8/16	1	2	FACETS	0.282	0.246	0.322	0.282	0.246	0.322	SUBCLONAL	1	TRUE	1	0.548895850447067	2		590	942	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939444	71939444	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	321	718	2	ENST00000298229.2:c.299G>T	p.Gly100Val	p.G100V	ENST00000298229	NM_001567.3	100	gGc/gTc	3/28	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.548895850447067	2		720	1121	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245455	133245456	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0038847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	206	583	0	ENST00000320574.5:c.1864_1865del	p.Ile622LeufsTer33	p.I622Lfs*33	ENST00000320574	NM_006231.2	622	ATc/c	17/49	1	2	FACETS	0.879	0.817	0.943	0.879	0.817	0.943	CLONAL	1	TRUE	1	0.548895850447067	2		583	854	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279907	18279907	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	48	565	0	ENST00000222254.8:c.1990G>A	p.Asp664Asn	p.D664N	ENST00000222254	NM_005027.3	664	Gac/Aac	16/16	0.473301698138561	2	FACETS	0.198	0.166	0.233	0.099	0.083	0.117	SUBCLONAL	1	TRUE	0	0.548895850447067	2		565	884	SUCCESS
APC	324	MSKCC	GRCh37	5	112174171	112174175	+	frameshift_variant	Frame_Shift_Del	DEL	AAATG	AAATG	-	novel	NA	P-0038847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	231	318	0	ENST00000257430.4:c.2881_2885del	p.Asn961Ter	p.N961*	ENST00000257430	NM_000038.5	960	tcAAATGat/tcat	16/16	0.548895850447067	2	FACETS	0.882	0.833	0.932	0.882	0.833	0.932	CLONAL	2	TRUE	0	0.548895850447067	2		318	477	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0038848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	527	695	1	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.584488974000099	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.584488974000099	2		696	853	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0038848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	142	428	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	0.584488974000099	2	FACETS	0.996	0.914	1	0.498	0.457	0.54	CLONAL	1	TRUE	0	0.584488974000099	2		428	488	SUCCESS
AR	367	MSKCC	GRCh37	X	66766187	66766187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	22	213	0	ENST00000374690.3:c.1199C>T	p.Ala400Val	p.A400V	ENST00000374690	NM_000044.3	400	gCg/gTg	1/8	0.56449630929073	2	FACETS	0.19	0.147	0.241			1	SUBCLONAL	1	TRUE	NA	0.584488974000099	2		213	396	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988193	36988193	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1009176098	NA	P-0038848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	232	433	0	ENST00000354822.5:c.460G>A	p.Ala154Thr	p.A154T	ENST00000354822	NM_001079668.2	154	Gcc/Acc	2/3	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.584488974000099	2		433	719	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814810	139814810	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1382	241	638	0	ENST00000247668.2:c.803T>C	p.Leu268Pro	p.L268P	ENST00000247668	NM_021138.3	268	cTc/cCc	8/11	0.387118214891169	5	FACETS	0.954	0.888	1			1	CLONAL	1	TRUE	NA	0.584488974000099	5		638	1623	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	251	578	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.319933357034637	3	FACETS	1	0.99	1			1	CLONAL	2	TRUE	NA	0.47140972731186	3		578	543	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0038850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	138	455	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.47140972731186	4	FACETS	1	0.981	1	0.428	0.39	0.468	CLONAL	1	TRUE	1	0.47140972731186	4		455	671	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628323	86628323	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0038850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	68	242	0	ENST00000274376.6:c.693-1G>A		p.X231_splice	ENST00000274376	NM_002890.2	231			1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.47140972731186	2		242	288	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442838	187442863	+	frameshift_variant	Frame_Shift_Del	DEL	ATAAGCACATGGGCACGGAGGTGGGC	ATAAGCACATGGGCACGGAGGTGGGC	-	novel	NA	P-0038850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	224	395	0	ENST00000232014.4:c.1843_1868del	p.Ala615ProfsTer4	p.A615Pfs*4	ENST00000232014	NM_001130845.1	615	GCCCACCTCCGTGCCCATGTGCTTATc/c	9/10	0.47140972731186	4	FACETS	1	0.986	1	0.789	0.74	0.838	CLONAL	2	TRUE	1	0.47140972731186	4		395	591	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5456118	5456118	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	33	228	0	ENST00000381577.3:c.5G>A	p.Arg2Lys	p.R2K	ENST00000381577	NM_014143.3	2	aGg/aAg	2/7	1	2	FACETS	0.458	0.374	0.552	0.458	0.374	0.552	SUBCLONAL	1	TRUE	1	0.47140972731186	2		228	306	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889181	76889181	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	120	366	0	ENST00000373344.5:c.4829C>G	p.Thr1610Arg	p.T1610R	ENST00000373344	NM_000489.3	1610	aCa/aGa	18/35	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.47140972731186	2		366	429	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0038852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	75	283	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.28	2		283	476	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0038852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	11	577	2	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.181	0.124	0.253	0.181	0.124	0.253	SUBCLONAL	1	TRUE	1	0.28	2		579	433	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602869	10602869	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	99	815	0	ENST00000171111.5:c.709C>G	p.Leu237Val	p.L237V	ENST00000171111	NM_203500.1	237	Ctg/Gtg	3/6	1	2	FACETS	0.737	0.657	0.823	0.737	0.657	0.823	SUBCLONAL	1	TRUE	1	0.28	2		815	959	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47088006	47088007	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	72	447	0	ENST00000409792.3:c.7068dup	p.Ala2357CysfsTer12	p.A2357Cfs*12	ENST00000409792	NM_014159.6	2356	-/T	16/21	1	2	FACETS	0.796	0.695	0.905	0.796	0.695	0.905	CLONAL	1	TRUE	1	0.28	2		447	646	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0038856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	59	494	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.665557423704274	1	FACETS	0.545	0.475	0.619	0.545	0.475	0.619	SUBCLONAL	1	TRUE	0	0.665557423704274	1		494	217	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0038856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	74	465	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	0.22551854297195	1	FACETS	0.623	0.554	0.696	0.623	0.554	0.696	INDETERMINATE	1	TRUE	0	0.665557423704274	1		465	238	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690801	89690801	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0038856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	47	242	1	ENST00000371953.3:c.210-2A>T		p.X70_splice	ENST00000371953	NM_000314.4	70			0.665557423704274	1	FACETS	0.865	0.754	0.978	0.865	0.754	0.978	CLONAL	1	TRUE	0	0.665557423704274	1		243	109	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041565	42041566	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	80	470	1	ENST00000219905.7:c.5764dup	p.Ile1922AsnfsTer4	p.I1922Nfs*4	ENST00000219905	NM_001164273.1	1920	-/A	17/24	0.22551854297195	1	FACETS	0.637	0.568	0.707	0.637	0.568	0.707	INDETERMINATE	1	TRUE	0	0.665557423704274	1		471	252	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830775	72830778	+	frameshift_variant	Frame_Shift_Del	DEL	TGCG	TGCG	-	novel	NA	P-0038856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	84	495	0	ENST00000268489.5:c.5803_5806del	p.Arg1935LeufsTer61	p.R1935Lfs*61	ENST00000268489	NM_006885.3	1935	CGCAtt/tt	9/10	0.162929087297878	1	FACETS	0.619	0.554	0.687	0.619	0.554	0.687	INDETERMINATE	1	TRUE	0	0.665557423704274	1		495	272	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15975464	15975464	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	76	387	0	ENST00000268712.3:c.3890T>C	p.Met1297Thr	p.M1297T	ENST00000268712	NM_006311.3	1297	aTg/aCg	29/46	0.665557423704274	1	FACETS	0.989	0.894	1	0.989	0.894	1	CLONAL	1	TRUE	0	0.665557423704274	1		387	154	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110315	3110315	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	89	520	0	ENST00000078429.4:c.305A>T	p.Lys102Met	p.K102M	ENST00000078429	NM_002067.2	102	aAg/aTg	2/7	0.162929087297878	1	FACETS	0.686	0.618	0.757	0.686	0.618	0.757	INDETERMINATE	1	TRUE	0	0.665557423704274	1		520	260	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55269429	55269429	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	104	703	1	ENST00000275493.2:c.3116G>A	p.Ser1039Asn	p.S1039N	ENST00000275493	NM_005228.3	1039	aGt/aAt	26/28	0.292125167584736	6	FACETS	0.954	0.861	1	0.477	0.43	0.525	INDETERMINATE	2	TRUE	2	0.665557423704274	6		704	382	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38137058	38137058	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	40	416	1	ENST00000317025.8:c.3760G>A	p.Gly1254Arg	p.G1254R	ENST00000317025	NM_023034.1	1254	Ggg/Agg	21/24	0.665557423704274	3	FACETS	0.566	0.473	0.669	0.283	0.236	0.335	SUBCLONAL	1	TRUE	1	0.665557423704274	3		417	283	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0038858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	25	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.392	0.308	0.49	0.392	0.308	0.49	SUBCLONAL	1	TRUE	1	0.26	2		457	490	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218439	1218439	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0038858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	43	463	0	ENST00000326873.7:c.314T>A	p.Leu105Ter	p.L105*	ENST00000326873	NM_000455.4	105	tTa/tAa	2/10	1	2	FACETS	0.486	0.405	0.575	0.486	0.405	0.575	SUBCLONAL	1	TRUE	1	0.26	2		463	681	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096881	11096881	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	66	691	0	ENST00000358026.2:c.374del	p.Gly125ValfsTer178	p.G125Vfs*178	ENST00000358026	NM_001128849.1	124	ctG/ct	4/36	1	2	FACETS	0.525	0.454	0.602	0.525	0.454	0.602	SUBCLONAL	1	TRUE	1	0.26	2		691	967	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467531	66467532	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0038858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	26	232	1	ENST00000273854.3:c.737_738delinsAA	p.Thr246Lys	p.T246K	ENST00000273854	NM_004439.5	246	aCC/aAA	3/18	1	2	FACETS	0.505	0.4	0.626	0.505	0.4	0.626	SUBCLONAL	1	TRUE	1	0.26	2		233	396	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056221	27056222	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACCTCCGTCAGGAC	novel	NA	P-0038859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	62	441	0	ENST00000324856.7:c.1218_1231dup	p.Pro411HisfsTer27	p.P411Hfs*27	ENST00000324856	NM_006015.4	406	gga/ggACCTCCGTCAGGACa	2/20	1	2	FACETS	0.617	0.532	0.709	0.617	0.532	0.709	SUBCLONAL	1	TRUE	1	0.3	2		441	670	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089488	27089489	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	100	505	0	ENST00000324856.7:c.2445dup	p.Asn816Ter	p.N816*	ENST00000324856	NM_006015.4	815	tat/taTt	8/20	1	2	FACETS	0.932	0.833	1	0.932	0.833	1	CLONAL	1	TRUE	1	0.3	2		505	715	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685271	89685271	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	45	149	1	ENST00000371953.3:c.170del	p.Leu57TrpfsTer42	p.L57Wfs*42	ENST00000371953	NM_000314.4	56	Ttt/tt	3/9	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.3	2		150	282	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717777	89717777	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0038859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	56	256	0	ENST00000371953.3:c.801+1G>T		p.X267_splice	ENST00000371953	NM_000314.4	267			1	2	FACETS	0.962	0.827	1	0.962	0.827	1	CLONAL	1	TRUE	1	0.3	2		256	388	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0038859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	43	256	1	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.697	0.584	0.822	0.697	0.584	0.822	SUBCLONAL	1	TRUE	1	0.3	2		257	411	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0038859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	13	701	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.152	0.107	0.207	0.152	0.107	0.207	SUBCLONAL	1	TRUE	1	0.3	2		701	571	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654625	67654625	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	96	313	0	ENST00000264010.4:c.1112G>A	p.Arg371His	p.R371H	ENST00000264010	NM_006565.3	371	cGc/cAc	6/12	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.3	2		313	634	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210848	36210848	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	126	632	0	ENST00000222270.7:c.601del	p.Gln201ArgfsTer38	p.Q201Rfs*38	ENST00000222270	NM_014727.1	200	gCc/gc	3/37	1	2	FACETS	0.978	0.885	1	0.978	0.885	1	CLONAL	1	TRUE	1	0.3	2		632	859	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927451	178927451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	136	314	0	ENST00000263967.3:c.1214C>T	p.Ser405Phe	p.S405F	ENST00000263967	NM_006218.2	405	tCc/tTc	7/21	0.296195681859357	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.3	2		314	420	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0038859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	137	241	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	0.296195681859357	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.3	2		241	405	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125006	46125006	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	51	227	0	ENST00000334344.6:c.193G>T	p.Glu65Ter	p.E65*	ENST00000334344	NM_152641.2	65	Gag/Tag	3/21	0.487819299900587	6	FACETS	0.924	0.787	1	0.231	0.196	0.269	CLONAL	1	FALSE	2	0.487819299900587	6		227	447	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217299	11217299	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519779	NA	P-0038860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	127	656	0	ENST00000361445.4:c.4379T>C	p.Leu1460Pro	p.L1460P	ENST00000361445	NM_004958.3	1460	cTt/cCt	30/58	0.479086165193565	2	FACETS	0.692	0.628	0.76	0.346	0.314	0.38	SUBCLONAL	1	FALSE	0	0.487819299900587	2		656	752	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125036	46125036	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	55	231	0	ENST00000334344.6:c.223G>C	p.Glu75Gln	p.E75Q	ENST00000334344	NM_152641.2	75	Gag/Cag	3/21	0.487819299900587	6	FACETS	0.902	0.772	1	0.225	0.193	0.261	CLONAL	1	FALSE	2	0.487819299900587	6		231	494	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812170	212812170	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	74	269	0	ENST00000342788.4:c.406T>G	p.Leu136Val	p.L136V	ENST00000342788	NM_005235.2	136	Tta/Gta	3/28	0.194062276075181	3	FACETS	1	0.972	1	0.679	0.601	0.761	INDETERMINATE	1	FALSE	1	0.487819299900587	3		269	278	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594078	55594078	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	158	335	1	ENST00000288135.5:c.1864G>T	p.Val622Leu	p.V622L	ENST00000288135	NM_000222.2	622	Gta/Tta	12/21	0.488143737995327	4	FACETS	0.868	0.8	0.939	0.868	0.8	0.939	CLONAL	2	FALSE	2	0.487819299900587	4		336	555	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444308	50444308	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	133	313	3	ENST00000331340.3:c.238G>A	p.Glu80Lys	p.E80K	ENST00000331340	NM_006060.4	80	Gag/Aag	4/8	0.488143737995327	4	FACETS	0.768	0.701	0.838	0.768	0.701	0.838	SUBCLONAL	2	FALSE	2	0.487819299900587	4		316	528	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0038882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	97	503	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.252109005304502	2		503	712	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982157	201982158	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	G	novel	NA	P-0038882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	265	668	0	ENST00000359651.3:c.681_682delinsG	p.Phe227LeufsTer27	p.F227Lfs*27	ENST00000359651		227	ttCCcc/ttGcc	5/8	0.252106013893206	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.252109005304502	2		668	1017	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0038902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	198	347	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.978	0.91	1	0.978	0.91	1	CLONAL	1	TRUE	1	0.628663152284783	2		347	644	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0038902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	443	647	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.576578225635341	2	FACETS	0.854	0.821	0.887	0.854	0.821	0.887	CLONAL	2	TRUE	0	0.628663152284783	2		647	825	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184781	32184781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762081312	NA	P-0038902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	154	676	0	ENST00000375023.3:c.1802G>A	p.Gly601Glu	p.G601E	ENST00000375023	NM_004557.3	601	gGa/gAa	11/30	0.3147656140675	1	FACETS	0.417	0.382	0.454	0.417	0.382	0.454	INDETERMINATE	1	TRUE	0	0.628663152284783	1		676	806	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903779	41903779	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	149	633	0	ENST00000372991.4:c.778C>T	p.Gln260Ter	p.Q260*	ENST00000372991	NM_001760.3	260	Cag/Tag	5/5	NA	2	FACETS	0.489	0.446	0.534			1	INDETERMINATE	1	TRUE	NA	0.628663152284783	2		633	970	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497952	25497952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	226	485	0	ENST00000264709.3:c.497C>T	p.Ser166Phe	p.S166F	ENST00000264709	NM_175629.2	166	tCc/tTc	6/23	1	2	FACETS	0.904	0.845	0.966	0.904	0.845	0.966	CLONAL	1	TRUE	1	0.628663152284783	2		485	795	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021828	71021828	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0038902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	101	204	0	ENST00000318789.4:c.1531-1G>A		p.X511_splice	ENST00000318789	NM_032682.5	511			0.421335511726602	1	FACETS	0.838	0.761	0.916	0.838	0.761	0.916	CLONAL	1	TRUE	0	0.628663152284783	1		204	263	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960039	134960039	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs533462328	NA	P-0038902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	261	534	0	ENST00000398015.3:c.2396G>A	p.Arg799His	p.R799H	ENST00000398015	NM_004441.4	799	cGc/cAc	13/16	0.421335511726602	1	FACETS	0.799	0.752	0.846	0.799	0.752	0.846	SUBCLONAL	1	TRUE	0	0.628663152284783	1		534	713	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073892	8073892	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	203	383	0	ENST00000377482.5:c.767C>G	p.Ser256Cys	p.S256C	ENST00000377482	NM_018948.3	256	tCc/tGc	4/4	0.628663152284783	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.628663152284783	1		383	442	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456436	32456436	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	126	510	0	ENST00000332351.3:c.456C>G	p.His152Gln	p.H152Q	ENST00000332351	NM_024426.4	152	caC/caG	1/10	0.421335511726602	1	FACETS	0.485	0.44	0.531	0.485	0.44	0.531	SUBCLONAL	1	TRUE	0	0.628663152284783	1		510	567	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988112	85988112	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1460129527	NA	P-0038902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	83	372	0	ENST00000263360.6:c.1057C>G	p.Leu353Val	p.L353V	ENST00000263360	NM_003797.3	353	Ctt/Gtt	10/12	0.370144637659451	1	FACETS	0.375	0.332	0.421	0.375	0.332	0.421	INDETERMINATE	1	TRUE	0	0.628663152284783	1		372	483	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285606	46285606	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	208	407	0	ENST00000334344.6:c.4966G>T	p.Glu1656Ter	p.E1656*	ENST00000334344	NM_152641.2	1656	Gaa/Taa	17/21	1	2	FACETS	0.992	0.925	1	0.992	0.925	1	CLONAL	1	TRUE	1	0.628663152284783	2		407	667	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426279	49426279	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	362	832	0	ENST00000301067.7:c.12209C>G	p.Ser4070Cys	p.S4070C	ENST00000301067	NM_003482.3	4070	tCt/tGt	39/54	1	2	FACETS	0.941	0.892	0.991	0.941	0.892	0.991	CLONAL	1	TRUE	1	0.628663152284783	2		832	1224	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435146	49435146	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs748118345	NA	P-0038902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	243	555	0	ENST00000301067.7:c.6407C>G	p.Ser2136Cys	p.S2136C	ENST00000301067	NM_003482.3	2136	tCt/tGt	31/54	1	2	FACETS	0.939	0.88	1	0.939	0.88	1	CLONAL	1	TRUE	1	0.628663152284783	2		555	823	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28908221	28908221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	89	482	0	ENST00000282397.4:c.2534C>T	p.Ser845Leu	p.S845L	ENST00000282397	NM_002019.4	845	tCa/tTa	18/30	1	2	FACETS	0.327	0.289	0.368	0.327	0.289	0.368	SUBCLONAL	1	TRUE	1	0.628663152284783	2		482	865	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345970	73345970	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	155	395	0	ENST00000377767.4:c.1568C>T	p.Ser523Leu	p.S523L	ENST00000377767	NM_014953.3	523	tCa/tTa	11/21	0.370144637659451	1	FACETS	0.699	0.644	0.754	0.699	0.644	0.754	INDETERMINATE	1	TRUE	0	0.628663152284783	1		395	484	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292979	91292979	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	150	516	0	ENST00000355112.3:c.481G>C	p.Asp161His	p.D161H	ENST00000355112	NM_000057.2	161	Gat/Cat	3/22	NA	2	FACETS	0.501	0.457	0.546			1	INDETERMINATE	1	TRUE	NA	0.628663152284783	2		516	953	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55693435	55693435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	134	608	2	ENST00000284073.2:c.642G>A	p.Met214Ile	p.M214I	ENST00000284073	NM_138962.2	214	atG/atA	9/14	0.628663152284783	1	FACETS	0.457	0.416	0.499	0.457	0.416	0.499	SUBCLONAL	1	TRUE	0	0.628663152284783	1		610	640	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602728	10602728	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	436	749	0	ENST00000171111.5:c.850C>T	p.Gln284Ter	p.Q284*	ENST00000171111	NM_203500.1	284	Cag/Tag	3/6	0.628663152284783	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.628663152284783	1		749	916	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376135	225376135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	130	622	0	ENST00000264414.4:c.819G>A	p.Met273Ile	p.M273I	ENST00000264414	NM_003590.4	273	atG/atA	6/16	0.370144637659451	1	FACETS	0.396	0.359	0.434	0.396	0.359	0.434	INDETERMINATE	1	TRUE	0	0.628663152284783	1		622	716	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987171	69987171	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	67	464	0	ENST00000394351.3:c.232C>T	p.Leu78Phe	p.L78F	ENST00000394351	NM_000248.3	78	Ctt/Ttt	2/9	0.421335511726602	1	FACETS	0.247	0.215	0.283	0.247	0.215	0.283	SUBCLONAL	1	TRUE	0	0.628663152284783	1		464	591	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008540	70008540	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	172	405	0	ENST00000394351.3:c.827A>T	p.His276Leu	p.H276L	ENST00000394351	NM_000248.3	276	cAc/cTc	8/9	0.421335511726602	1	FACETS	0.746	0.692	0.801	0.746	0.692	0.801	SUBCLONAL	1	TRUE	0	0.628663152284783	1		405	503	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947139	178947139	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	56	324	1	ENST00000263967.3:c.2575C>A	p.Gln859Lys	p.Q859K	ENST00000263967	NM_006218.2	859	Caa/Aaa	18/21	1	2	FACETS	0.311	0.266	0.361	0.311	0.266	0.361	SUBCLONAL	1	TRUE	1	0.628663152284783	2		325	572	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	231105	231105	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	158	642	0	ENST00000264932.6:c.885C>A	p.Phe295Leu	p.F295L	ENST00000264932	NM_004168.2	295	ttC/ttA	7/15	0.370144637659451	1	FACETS	0.397	0.363	0.431	0.397	0.363	0.431	INDETERMINATE	1	TRUE	0	0.628663152284783	1		642	869	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468291	50468291	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	116	631	0	ENST00000331340.3:c.1526T>A	p.Ile509Lys	p.I509K	ENST00000331340	NM_006060.4	509	aTa/aAa	8/8	1	2	FACETS	0.436	0.392	0.482	0.436	0.392	0.482	SUBCLONAL	1	TRUE	1	0.628663152284783	2		631	847	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371947	55371947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	206	417	0	ENST00000297316.4:c.637C>T	p.Pro213Ser	p.P213S	ENST00000297316	NM_022454.3	213	Ccg/Tcg	2/2	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.628663152284783	2		417	626	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0038904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	73	347	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	0.267531073627736	2		347	476	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846398	128846398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879255280	NA	P-0038905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	258	736	0	ENST00000249373.3:c.1234C>T	p.Leu412Phe	p.L412F	ENST00000249373	NM_005631.4	412	Ctc/Ttc	6/12	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		736	746	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0038907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	347	553	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.352144621715103	3	FACETS	0.916	0.871	0.96	0.916	0.871	0.96	CLONAL	3	TRUE	0	0.364741845688497	3		553	819	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	211	525	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.300656030845737	3	FACETS	0.973	0.907	1	0.973	0.907	1	CLONAL	2	TRUE	1	0.364741845688497	3		525	703	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249510	153249510	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1157879635	NA	P-0038907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	1884	443	0	ENST00000281708.4:c.1268G>T	p.Gly423Val	p.G423V	ENST00000281708	NM_033632.3	423	gGa/gTa	9/12	0.364741845688497	13	FACETS	1	0.997	1			1	CLONAL	13	TRUE	NA	0.364741845688497	13		443	2302	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952049	178952049	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1242945375	NA	P-0038907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	62	300	0	ENST00000263967.3:c.3104C>T	p.Ala1035Val	p.A1035V	ENST00000263967	NM_006218.2	1035	gCt/gTt	21/21	0.329885166289	3	FACETS	0.814	0.704	0.932	0.407	0.352	0.466	CLONAL	1	TRUE	1	0.364741845688497	3		300	494	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737650	145737650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374254271	NA	P-0038907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	216	672	0	ENST00000428558.2:c.3113G>A	p.Arg1038His	p.R1038H	ENST00000428558	NM_004260.3	1038	cGc/cAc	19/22	0.364741845688497	5	FACETS	0.875	0.813	0.939	0.583	0.542	0.626	CLONAL	2	TRUE	2	0.364741845688497	5		672	1047	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0038908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	85	283	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.246564175937584	3	FACETS	0.874	0.776	0.978	0.874	0.776	0.978	CLONAL	2	TRUE	1	0.246564175937584	3		283	443	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263973	104263974	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776579	NA	P-0038908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	40	231	3	ENST00000369902.3:c.71dup	p.Ala25GlyfsTer23	p.A25Gfs*23	ENST00000369902	NM_016169.3	22	gcc/gCcc	1/12	1	2	FACETS	0.729	0.606	0.866	0.729	0.606	0.866	SUBCLONAL	1	TRUE	1	0.246564175937584	2		234	445	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	100	565	5	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.913	0.815	1	0.913	0.815	1	CLONAL	1	TRUE	1	0.246564175937584	2		570	888	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0038908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	61	408	1	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.906	0.782	1	0.906	0.782	1	CLONAL	1	TRUE	1	0.246564175937584	2		409	546	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0038908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	70	345	3	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	0.246564175937584	3	FACETS	1	0.969	1	0.689	0.602	0.782	CLONAL	1	TRUE	1	0.246564175937584	3		348	463	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70005681	70005681	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs756923654	NA	P-0038908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	48	316	0	ENST00000394351.3:c.710C>T	p.Pro237Leu	p.P237L	ENST00000394351	NM_000248.3	237	cCa/cTa	7/9	1	2	FACETS	0.883	0.747	1	0.883	0.747	1	CLONAL	1	TRUE	1	0.246564175937584	2		316	441	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584513	48584514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs377767334	NA	P-0038908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	61	444	0	ENST00000342988.3:c.692dup	p.Ser232GlnfsTer3	p.S232Qfs*3	ENST00000342988	NM_005359.5	229	ctg/ctGg	6/12	1	2	FACETS	0.953	0.823	1	0.953	0.823	1	CLONAL	1	TRUE	1	0.246564175937584	2		444	519	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	158	833	4	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	0.246564175937584	2	FACETS	1	0.955	1	0.534	0.488	0.582	CLONAL	1	TRUE	0	0.246564175937584	2		837	1201	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161718	47161718	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	48	287	0	ENST00000409792.3:c.4408C>T	p.Pro1470Ser	p.P1470S	ENST00000409792	NM_014159.6	1470	Cca/Tca	3/21	1	2	FACETS	0.798	0.675	0.933	0.798	0.675	0.933	CLONAL	1	TRUE	1	0.246564175937584	2		287	488	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916845	178916845	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	59	522	0	ENST00000263967.3:c.232G>A	p.Glu78Lys	p.E78K	ENST00000263967	NM_006218.2	78	Gaa/Aaa	2/21	1	2	FACETS	0.736	0.633	0.849	0.736	0.633	0.849	SUBCLONAL	1	TRUE	1	0.246564175937584	2		522	650	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150022	202150022	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	133	473	0	ENST00000358485.4:c.1463T>C	p.Leu488Pro	p.L488P	ENST00000358485	NM_001080125.1	488	cTg/cCg	8/9	0.246564175937584	2	FACETS	1	0.973	1	0.595	0.54	0.653	CLONAL	1	TRUE	0	0.246564175937584	2		473	906	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007825	45007825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	52	339	0	ENST00000558401.1:c.276del	p.Thr93LeufsTer10	p.T93Lfs*10	ENST00000558401	NM_004048.2	91	aCc/ac	2/4	1	2	FACETS	0.844	0.719	0.98	0.844	0.719	0.98	CLONAL	1	TRUE	1	0.246564175937584	2		339	500	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026147	36026147	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767829559	NA	P-0038908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	131	659	0	ENST00000358208.4:c.749C>T	p.Thr250Met	p.T250M	ENST00000358208		250	aCg/aTg	7/12	0.246564175937584	3	FACETS	0.95	0.86	1	0.475	0.43	0.523	CLONAL	1	TRUE	1	0.246564175937584	3		659	1256	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265049	46265049	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	155	407	0	ENST00000371998.3:c.1924del	p.Leu642Ter	p.L642*	ENST00000371998		640	tCc/tc	12/23	0.246564175937584	3	FACETS	0.9	0.824	0.978	0.9	0.824	0.978	CLONAL	2	TRUE	1	0.246564175937584	3		407	785	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998128	169998128	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs753143066	NA	P-0038908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	79	564	5	ENST00000295797.4:c.826del	p.Thr276GlnfsTer7	p.T276Qfs*7	ENST00000295797	NM_002740.5	273	ttA/tt	9/18	1	2	FACETS	0.775	0.68	0.877	0.775	0.68	0.877	SUBCLONAL	1	TRUE	1	0.246564175937584	2		569	827	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830807	72830807	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	100	550	0	ENST00000268489.5:c.5774del	p.Gly1925ValfsTer72	p.G1925Vfs*72	ENST00000268489	NM_006885.3	1925	gGt/gt	9/10	1	2	FACETS	0.808	0.72	0.902	0.808	0.72	0.902	CLONAL	1	TRUE	1	0.246564175937584	2		550	1004	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216189	36216189	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	229	592	7	ENST00000222270.7:c.3602del	p.Pro1201ArgfsTer154	p.P1201Rfs*154	ENST00000222270	NM_014727.1	1199	ggC/gg	11/37	0.246564175937584	3	FACETS	0.834	0.776	0.894	0.834	0.776	0.894	CLONAL	2	TRUE	1	0.246564175937584	3		599	1251	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8111056	8111056	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs548042738	NA	P-0038908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	150	601	0	ENST00000585124.1:c.151G>T	p.Ala51Ser	p.A51S	ENST00000585124	NM_004217.3	51	Gct/Tct	3/9	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.246564175937584	2		601	1093	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520704	176520704	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs574060950	NA	P-0038908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	124	590	0	ENST00000292408.4:c.1447C>T	p.Arg483Cys	p.R483C	ENST00000292408	NM_213647.1	483	Cgt/Tgt	11/18	1	2	FACETS	0.903	0.815	0.996	0.903	0.815	0.996	CLONAL	1	TRUE	1	0.246564175937584	2		590	1114	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435162	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0038908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	113	594	0	ENST00000407977.2:c.1975_1976del	p.Gly659SerfsTer87	p.G659Sfs*87	ENST00000407977		659	GGt/t	9/10	1	2	FACETS	0.846	0.76	0.938	0.846	0.76	0.938	CLONAL	1	TRUE	1	0.246564175937584	2		594	1083	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880271	155880271	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	62	353	0	ENST00000368323.3:c.133C>T	p.Arg45Ter	p.R45*	ENST00000368323	NM_006912.5	45	Cga/Tga	3/6	1	2	FACETS	0.963	0.833	1	0.963	0.833	1	CLONAL	1	TRUE	1	0.246564175937584	2		353	522	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426730	49426735	+	inframe_deletion	In_Frame_Del	DEL	GCTGCT	GCTGCT	-	rs576788910	NA	P-0038908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	40	288	0	ENST00000301067.7:c.11753_11758del	p.Gln3918_Gln3919del	p.Q3918_Q3919del	ENST00000301067	NM_003482.3	3918	cAGCAGCta/cta	39/54	1	2	FACETS	0.861	0.717	1	0.861	0.717	1	CLONAL	1	TRUE	1	0.246564175937584	2		288	377	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937249	36937249	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0038908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	86	581	0	ENST00000361632.4:c.1072-2A>G		p.X358_splice	ENST00000361632		358			1	2	FACETS	0.7	0.617	0.788	0.7	0.617	0.788	SUBCLONAL	1	TRUE	1	0.246564175937584	2		581	997	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433994	49433994	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369965791	NA	P-0038908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	115	594	1	ENST00000301067.7:c.7559G>A	p.Arg2520Gln	p.R2520Q	ENST00000301067	NM_003482.3	2520	cGg/cAg	31/54	1	2	FACETS	0.873	0.784	0.966	0.873	0.784	0.966	CLONAL	1	TRUE	1	0.246564175937584	2		595	1069	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678458	88678458	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747624231	NA	P-0038908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	103	586	0	ENST00000360948.2:c.1078G>A	p.Glu360Lys	p.E360K	ENST00000360948	NM_001012338.2	360	Gag/Aag	9/19	1	2	FACETS	0.918	0.821	1	0.918	0.821	1	CLONAL	1	TRUE	1	0.246564175937584	2		586	910	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615692	1615692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767665186	NA	P-0038908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	297	701	1	ENST00000344749.5:c.1579C>T	p.Arg527Trp	p.R527W	ENST00000344749	NM_001136139.2	527	Cgg/Tgg	17/19	0.246564175937584	3	FACETS	0.95	0.892	1	0.95	0.892	1	CLONAL	2	TRUE	1	0.246564175937584	3		702	1425	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871985	45871985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777095373	NA	P-0038908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	104	464	0	ENST00000391945.4:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000391945	NM_000400.3	88	cGa/cAa	5/23	0.246564175937584	3	FACETS	0.969	0.866	1	0.484	0.433	0.54	CLONAL	1	TRUE	1	0.246564175937584	3		464	978	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803187	1803187	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	115	601	2	ENST00000260795.2:c.539G>A	p.Gly180Asp	p.G180D	ENST00000260795		180	gGc/gAc	4/17	1	2	FACETS	0.836	0.751	0.926	0.836	0.751	0.926	CLONAL	1	TRUE	1	0.246564175937584	2		603	1116	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535457	66535457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	104	376	0	ENST00000273854.3:c.4C>T	p.Arg2Trp	p.R2W	ENST00000273854	NM_004439.5	2	Cgg/Tgg	1/18	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.246564175937584	2		376	677	SUCCESS
APC	324	MSKCC	GRCh37	5	112177620	112177620	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	27	335	0	ENST00000257430.4:c.6329C>A	p.Ser2110Tyr	p.S2110Y	ENST00000257430	NM_000038.5	2110	tCc/tAc	16/16	1	2	FACETS	0.608	0.484	0.75	0.608	0.484	0.75	SUBCLONAL	1	TRUE	1	0.246564175937584	2		335	360	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505058	149505058	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	85	524	0	ENST00000261799.4:c.1757A>G	p.Gln586Arg	p.Q586R	ENST00000261799	NM_002609.3	586	cAg/cGg	12/23	1	2	FACETS	0.765	0.675	0.862	0.765	0.675	0.862	SUBCLONAL	1	TRUE	1	0.246564175937584	2		524	901	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138197301	138197301	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	80	253	0	ENST00000237289.4:c.803C>T	p.Pro268Leu	p.P268L	ENST00000237289	NM_001270507.1	268	cCt/cTt	5/9	0.246564175937584	3	FACETS	0.84	0.743	0.943	0.84	0.743	0.943	CLONAL	2	TRUE	1	0.246564175937584	3		253	434	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843732	151843732	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs758584381	NA	P-0038908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	73	355	0	ENST00000262189.6:c.13983G>T	p.Glu4661Asp	p.E4661D	ENST00000262189	NM_170606.2	4661	gaG/gaT	53/59	0.246564175937584	3	FACETS	0.727	0.634	0.827	0.363	0.317	0.414	SUBCLONAL	1	TRUE	1	0.246564175937584	3		355	915	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0038909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	242	347	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.427571326597734	4	FACETS	0.978	0.917	1	0.978	0.917	1	CLONAL	2	TRUE	2	0.481820257849074	4		347	761	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039374	49039374	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853293	NA	P-0038909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	60	546	1	ENST00000267163.4:c.2359C>T	p.Arg787Ter	p.R787*	ENST00000267163	NM_000321.2	787	Cga/Tga	23/27	0.421815740199491	1	FACETS	0.305	0.262	0.351	0.305	0.262	0.351	SUBCLONAL	1	TRUE	0	0.481820257849074	1		547	620	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635601	47635603	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs267607919	NA	P-0038909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	127	441	0	ENST00000233146.2:c.279_281del	p.Leu94del	p.L94del	ENST00000233146	NM_000251.2	91	gaTCTt/gat	2/16	1	2	FACETS	0.8	0.726	0.877	0.8	0.726	0.877	SUBCLONAL	1	TRUE	1	0.481820257849074	2		441	659	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410700	32410702	+	inframe_deletion	In_Frame_Del	DEL	CCA	CCA	-	novel	NA	P-0038909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	213	413	0	ENST00000332351.3:c.1456_1458del	p.Trp486del	p.W486del	ENST00000332351	NM_024426.4	486	TGG/-	10/10	0.372365288497799	4	FACETS	0.873	0.814	0.934	0.873	0.814	0.934	CLONAL	2	TRUE	2	0.481820257849074	4		413	750	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008278	29008286	+	inframe_deletion	In_Frame_Del	DEL	GTTGCATTT	GTTGCATTT	-	novel	NA	P-0038909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	81	351	2	ENST00000282397.4:c.585_593del	p.Asn196_Thr198del	p.N196_T198del	ENST00000282397	NM_002019.4	195	tcAAATGCAACg/tcg	5/30	0.372365288497799	4	FACETS	0.757	0.667	0.854	0.379	0.333	0.427	SUBCLONAL	1	TRUE	2	0.481820257849074	4		353	658	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579482	+	frameshift_variant	Frame_Shift_Del	DEL	CGGGGGGAGCAGC	CGGGGGGAGCAGC	-	novel	NA	P-0038909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	589	741	0	ENST00000269305.4:c.205_217del	p.Ala69TrpfsTer50	p.A69Wfs*50	ENST00000269305	NM_001126112.2	69	GCTGCTCCCCCCGtg/tg	4/11	0.413622983386356	3	FACETS	0.915	0.884	0.946			1	CLONAL	3	TRUE	NA	0.481820257849074	3		741	1105	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966850	18966850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1231	93	769	0	ENST00000262803.5:c.1661C>T	p.Ser554Phe	p.S554F	ENST00000262803	NM_002911.3	554	tCc/tTc	12/24	0.413622983386356	3	FACETS	0.362	0.32	0.406			1	SUBCLONAL	1	TRUE	NA	0.481820257849074	3		769	1324	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913517	NA	P-0038910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	209	430	0	ENST00000288135.5:c.1676T>A	p.Val559Asp	p.V559D	ENST00000288135	NM_000222.2	559	gTt/gAt	11/21	1	2	FACETS	0.96	0.898	1	1	0.994	1	CLONAL	2	TRUE	1	0.382481117593903	2		430	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0038937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	190	647	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.334459503996027	2	FACETS	0.963	0.897	1	0.963	0.897	1	CLONAL	2	TRUE	0	0.36545666690864	2		647	540	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588624	28588624	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	172	358	0	ENST00000241453.7:c.2824T>C	p.Phe942Leu	p.F942L	ENST00000241453	NM_004119.2	942	Ttt/Ctt	23/24	0.36545666690864	3	FACETS	0.978	0.906	1	0.978	0.906	1	CLONAL	2	TRUE	1	0.36545666690864	3		358	569	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713251	43713251	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	85	570	0	ENST00000382044.4:c.4222C>T	p.Arg1408Cys	p.R1408C	ENST00000382044	NM_001141980.1	1408	Cgc/Tgc	20/28	1	2	FACETS	0.673	0.595	0.757	0.673	0.595	0.757	SUBCLONAL	1	TRUE	1	0.36545666690864	2		570	691	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0038938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	225	701	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.481163815869056	3	FACETS	0.959	0.899	1	0.959	0.899	1	CLONAL	2	TRUE	1	0.481163815869056	3		701	605	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161326470	161326470	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	152	435	0	ENST00000367975.2:c.245T>C	p.Val82Ala	p.V82A	ENST00000367975	NM_003001.3	82	gTc/gCc	5/6	0.481163815869056	4	FACETS	1	0.922	1	0.336	0.307	0.367	CLONAL	1	TRUE	1	0.481163815869056	4		435	928	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274746	123274746	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs387906677	NA	P-0038938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	157	371	0	ENST00000358487.5:c.1172T>G	p.Met391Arg	p.M391R	ENST00000358487	NM_000141.4	391	aTg/aGg	9/18	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.481163815869056	2		371	570	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0038942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	140	347	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.878	0.807	0.952	0.878	0.807	0.952	CLONAL	1	TRUE	1	0.71797489263301	2		347	444	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28600565	28600565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	223	380	0	ENST00000253063.3:c.916C>T	p.Pro306Ser	p.P306S	ENST00000253063	NM_031459.4	306	Ccc/Tcc	7/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.71797489263301	2		380	593	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0038943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	241	523	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.790232082989084	7	FACETS	0.894	0.835	0.955	0.298	0.278	0.319	CLONAL	2	TRUE	1	0.790232082989084	7		523	1015	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320963	30320963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371166327	NA	P-0038943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	50	318	1	ENST00000322652.5:c.1373G>A	p.Arg458His	p.R458H	ENST00000322652	NM_015355.2	458	cGc/cAc	12/16	1	2	FACETS	0.214	0.181	0.25	0.214	0.181	0.25	SUBCLONAL	1	TRUE	1	0.790232082989084	2		319	591	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612127	189612128	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0038943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	1085	434	0	ENST00000264731.3:c.1879_1880del	p.Ser627CysfsTer5	p.S627Cfs*5	ENST00000264731	NM_003722.4	627	AGt/t	14/14	0.790232082989084	7	FACETS	1	0.991	1	0.688	0.671	0.706	CLONAL	4	TRUE	1	0.790232082989084	7		434	1978	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	54	606	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.716	0.614	0.827	0.716	0.614	0.827	SUBCLONAL	1	TRUE	1	0.4	2		606	377	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	65	347	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.994	0.868	1	0.994	0.868	1	CLONAL	1	TRUE	1	0.4	2		347	327	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	32	404	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.253	0.205	0.308	0.253	0.205	0.308	SUBCLONAL	1	TRUE	1	0.4	2		405	632	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552144	29552144	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	41	213	1	ENST00000356175.3:c.1882del	p.Tyr628ThrfsTer3	p.Y628Tfs*3	ENST00000356175	NM_000267.3	626	cTt/ct	17/57	1	2	FACETS	0.928	0.78	1	0.928	0.78	1	CLONAL	1	TRUE	1	0.4	2		214	221	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	72	192	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.994	0.874	1	0.994	0.874	1	CLONAL	1	TRUE	1	0.4	2		192	362	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	58	339	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.503	0.432	0.581	0.503	0.432	0.581	SUBCLONAL	1	TRUE	1	0.4	2		339	576	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812260	212812260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751175543	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	58	228	0	ENST00000342788.4:c.316C>T	p.Arg106Cys	p.R106C	ENST00000342788	NM_005235.2	106	Cgt/Tgt	3/28	1	2	FACETS	0.876	0.757	1	0.876	0.757	1	CLONAL	1	TRUE	1	0.4	2		228	331	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	105	340	1	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	0.874	0.784	0.968	0.874	0.784	0.968	CLONAL	1	TRUE	1	0.4	2		341	601	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	89	526	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.4	2		526	439	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426701	121426701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753998395	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	114	443	1	ENST00000257555.6:c.392G>A	p.Arg131Gln	p.R131Q	ENST00000257555		131	cGg/cAg	2/10	1	2	FACETS	0.911	0.822	1	0.911	0.822	1	CLONAL	1	TRUE	1	0.4	2		444	626	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538269	187538269	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs748652484	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	96	349	1	ENST00000441802.2:c.8965del	p.Arg2989GlyfsTer20	p.R2989Gfs*20	ENST00000441802	NM_005245.3	2989	Agg/gg	11/27	1	2	FACETS	0.879	0.785	0.978	0.879	0.785	0.978	CLONAL	1	TRUE	1	0.4	2		350	546	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512402	38512402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	118	372	0	ENST00000254066.5:c.1319del	p.Pro440ArgfsTer203	p.P440Rfs*203	ENST00000254066	NM_000964.3	438	gCc/gc	9/9	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.4	2		372	572	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745962	745963	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	44	309	0	ENST00000314574.4:c.559_560del	p.Ser187Ter	p.S187*	ENST00000314574	NM_005433.3	187	AGt/t	5/12	1	2	FACETS	0.62	0.521	0.728	0.62	0.521	0.728	SUBCLONAL	1	TRUE	1	0.4	2		309	355	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339002	225339002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	70	286	1	ENST00000264414.4:c.2267G>A	p.Arg756Gln	p.R756Q	ENST00000264414	NM_003590.4	756	cGa/cAa	16/16	1	2	FACETS	0.879	0.77	0.996	0.879	0.77	0.996	CLONAL	1	TRUE	1	0.4	2		287	398	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176719045	176719045	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784190	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	82	236	0	ENST00000439151.2:c.6349C>T	p.Arg2117Ter	p.R2117*	ENST00000439151	NM_022455.4	2117	Cga/Tga	22/23	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.4	2		236	407	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	189	536	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.761	0.707	0.816	1	0.991	1	SUBCLONAL	2	TRUE	1	0.4	2		542	621	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223328	36223328	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	41	545	0	ENST00000222270.7:c.5882del	p.Pro1961LeufsTer26	p.P1961Lfs*26	ENST00000222270	NM_014727.1	1960	Ccc/cc	28/37	1	2	FACETS	0.273	0.226	0.325	0.273	0.226	0.325	SUBCLONAL	1	TRUE	1	0.4	2		545	751	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827231	72827231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375039347	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	99	396	0	ENST00000268489.5:c.9350C>T	p.Ala3117Val	p.A3117V	ENST00000268489	NM_006885.3	3117	gCg/gTg	9/10	1	2	FACETS	0.801	0.716	0.891	0.801	0.716	0.891	CLONAL	1	TRUE	1	0.4	2		396	618	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845391	151845391	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	64	401	0	ENST00000262189.6:c.13621C>T	p.Arg4541Ter	p.R4541*	ENST00000262189	NM_170606.2	4541	Cga/Tga	52/59	1	2	FACETS	0.466	0.403	0.535	0.466	0.403	0.535	SUBCLONAL	1	TRUE	1	0.4	2		401	686	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101109	27101110	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	110	447	0	ENST00000324856.7:c.4394_4395del	p.Ser1465CysfsTer25	p.S1465Cfs*25	ENST00000324856	NM_006015.4	1464	gTC/g	18/20	1	2	FACETS	0.796	0.716	0.881	0.796	0.716	0.881	SUBCLONAL	1	TRUE	1	0.4	2		447	691	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690801	89690801	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1564828914	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	51	190	0	ENST00000371953.3:c.210-2A>G		p.X70_splice	ENST00000371953	NM_000314.4	70			1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.4	2		190	229	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633500	3633500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199969428	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	35	436	1	ENST00000294008.3:c.4751G>A	p.Arg1584His	p.R1584H	ENST00000294008	NM_032444.2	1584	cGc/cAc	14/15	1	2	FACETS	0.254	0.208	0.307	0.254	0.208	0.307	SUBCLONAL	1	TRUE	1	0.4	2		437	688	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662453	67662453	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs879255516	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	51	441	0	ENST00000264010.4:c.1699C>T	p.Arg567Trp	p.R567W	ENST00000264010	NM_006565.3	567	Cgg/Tgg	9/12	1	2	FACETS	0.376	0.318	0.438	0.376	0.318	0.438	SUBCLONAL	1	TRUE	1	0.4	2		441	679	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120796847	120796847	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769968859	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	155	444	0	ENST00000257552.2:c.412G>A	p.Ala138Thr	p.A138T	ENST00000257552	NM_002442.3	138	Gcc/Acc	7/15	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.4	2		444	734	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451273	70451273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	144	363	0	ENST00000373644.4:c.6113G>A	p.Arg2038His	p.R2038H	ENST00000373644	NM_030625.2	2038	cGt/cAt	12/12	1	2	FACETS	0.959	0.876	1	0.959	0.876	1	CLONAL	1	TRUE	1	0.4	2		363	751	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106019	27106019	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	56	340	0	ENST00000324856.7:c.5633del	p.Pro1878LeufsTer5	p.P1878Lfs*5	ENST00000324856	NM_006015.4	1877	gCc/gc	20/20	1	2	FACETS	0.536	0.46	0.62	0.536	0.46	0.62	SUBCLONAL	1	TRUE	1	0.4	2		340	522	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176085774	176085774	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	89	243	0	ENST00000367669.3:c.1012A>C	p.Ser338Arg	p.S338R	ENST00000367669	NM_022457.5	338	Agt/Cgt	9/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.4	2		243	368	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348866	89348866	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748428674	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	54	526	1	ENST00000301030.4:c.4084G>A	p.Asp1362Asn	p.D1362N	ENST00000301030	NM_001256183.1	1362	Gac/Aac	9/13	1	2	FACETS	0.277	0.236	0.323	0.277	0.236	0.323	SUBCLONAL	1	TRUE	1	0.4	2		527	974	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117404	7117404	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs771104206	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	108	409	1	ENST00000302850.5:c.3812T>C	p.Met1271Thr	p.M1271T	ENST00000302850	NM_000208.2	1271	aTg/aCg	22/22	1	2	FACETS	0.952	0.857	1	0.952	0.857	1	CLONAL	1	TRUE	1	0.4	2		410	567	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656933	47656933	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750267	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	94	203	0	ENST00000233146.2:c.1129C>T	p.Gln377Ter	p.Q377*	ENST00000233146	NM_000251.2	377	Caa/Taa	7/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.4	2		203	361	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698199	47698199	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	42	169	0	ENST00000233146.2:c.1757C>A	p.Ser586Ter	p.S586*	ENST00000233146	NM_000251.2	586	tCa/tAa	11/16	1	2	FACETS	0.875	0.736	1	0.875	0.736	1	CLONAL	1	TRUE	1	0.4	2		169	240	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89444996	89444996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	48	277	0	ENST00000336596.2:c.1316C>T	p.Pro439Leu	p.P439L	ENST00000336596	NM_005233.5	439	cCt/cTt	6/17	1	2	FACETS	0.569	0.481	0.664	0.569	0.481	0.664	SUBCLONAL	1	TRUE	1	0.4	2		277	422	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808898	1808898	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775451126	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	60	488	0	ENST00000260795.2:c.2330C>T	p.Thr777Ile	p.T777I	ENST00000260795		777	aCc/aTc	17/17	1	2	FACETS	0.458	0.394	0.528	0.458	0.394	0.528	SUBCLONAL	1	TRUE	1	0.4	2		488	655	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627738	187627738	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	79	300	0	ENST00000441802.2:c.3244T>A	p.Phe1082Ile	p.F1082I	ENST00000441802	NM_005245.3	1082	Ttc/Atc	2/27	1	2	FACETS	0.83	0.732	0.934	0.83	0.732	0.934	CLONAL	1	TRUE	1	0.4	2		300	476	SUCCESS
APC	324	MSKCC	GRCh37	5	112128204	112128204	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1433658799	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	77	231	0	ENST00000257430.4:c.707A>G	p.Gln236Arg	p.Q236R	ENST00000257430	NM_000038.5	236	cAg/cGg	7/16	1	2	FACETS	0.948	0.837	1	0.948	0.837	1	CLONAL	1	TRUE	1	0.4	2		231	406	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730364	133730364	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1314838108	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	115	343	0	ENST00000318560.5:c.430G>A	p.Gly144Arg	p.G144R	ENST00000318560	NM_005157.4	144	Ggg/Agg	3/11	1	2	FACETS	0.998	0.902	1	0.998	0.902	1	CLONAL	1	TRUE	1	0.4	2		343	576	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344217	70344218	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0038944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	79	211	0	ENST00000374080.3:c.1953_1954del	p.Ser652GlnfsTer17	p.S652Qfs*17	ENST00000374080		651	ggCAgc/gggc	13/45	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.4	2		211	371	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0038945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	44	622	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.679	0.57	0.799	0.679	0.57	0.799	SUBCLONAL	1	TRUE	1	0.31	2		622	418	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266512	198266512	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	38	211	0	ENST00000335508.6:c.2324G>T	p.Arg775Leu	p.R775L	ENST00000335508	NM_012433.2	775	cGa/cTa	16/25	1	2	FACETS	0.608	0.503	0.725	0.608	0.503	0.725	SUBCLONAL	1	TRUE	1	0.31	2		211	403	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0038945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	17	212	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	0.26	0.193	0.34	0.26	0.193	0.34	SUBCLONAL	1	TRUE	1	0.31	2		212	422	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045533	47045533	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0038945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	62	198	0	ENST00000377604.3:c.2500A>T	p.Lys834Ter	p.K834*	ENST00000377604	NM_001204468.1	834	Aag/Tag	22/24	1	1	FACETS	0.98	0.851	1	0.98	0.851	1	CLONAL	1	TRUE	0	0.31	1		198	345	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322619	39322619	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	57	360	0	ENST00000373001.3:c.373G>T	p.Asp125Tyr	p.D125Y	ENST00000373001	NM_022157.3	125	Gac/Tac	2/7	1	2	FACETS	0.674	0.578	0.778	0.674	0.578	0.778	SUBCLONAL	1	TRUE	1	0.31	2		360	546	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933246	49933246	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	63	482	1	ENST00000296474.3:c.2864A>G	p.Gln955Arg	p.Q955R	ENST00000296474	NM_002447.2	955	cAg/cGg	12/20	1	2	FACETS	0.548	0.473	0.629	0.548	0.473	0.629	SUBCLONAL	1	TRUE	1	0.31	2		483	742	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325493	1325493	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0038945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	49	301	0	ENST00000400841.2:c.183-1G>T		p.X61_splice	ENST00000400841		61			1	1	FACETS	0.552	0.468	0.645	0.552	0.468	0.645	SUBCLONAL	1	TRUE	0	0.31	1		301	484	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0038946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	64	283	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	0.988	1	CLONAL	6	TRUE	1	0.156768655192596	2		283	132	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	157	399	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.971	1	1	0.995	1	CLONAL	5	TRUE	1	0.156768655192596	2		399	368	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25458627	25458627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	97	352	0	ENST00000264709.3:c.2546C>T	p.Pro849Leu	p.P849L	ENST00000264709	NM_175629.2	849	cCt/cTt	22/23	1	2	FACETS	0.907	0.817	1	1	0.99	1	CLONAL	4	TRUE	1	0.156768655192596	2		352	341	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	rs786202799	NA	P-0038948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	260	486	0	ENST00000269305.4:c.376-2A>C		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.267349233207084	3	FACETS	1	0.991	1	0.424	0.4	0.449	INDETERMINATE	1	TRUE	0	0.873331134814848	3		486	672	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921431	39921431	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	187	311	0	ENST00000378444.4:c.4389del	p.Glu1464ArgfsTer20	p.E1464Rfs*20	ENST00000378444	NM_001123385.1	1463	ggC/gg	10/15	NA	2	FACETS	0.858	0.8	0.918			1	INDETERMINATE	1	TRUE	NA	0.873331134814848	2		311	499	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0038949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	101	523	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.496490295353085	5	FACETS	1	0.953	1	0.279	0.249	0.31	CLONAL	1	TRUE	1	0.496490295353085	5		523	636	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099030	27099030	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0038949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	98	352	0	ENST00000324856.7:c.3446C>G	p.Ser1149Ter	p.S1149*	ENST00000324856	NM_006015.4	1149	tCa/tGa	13/20	1	2	FACETS	0.903	0.811	1	0.903	0.811	1	CLONAL	1	TRUE	1	0.496490295353085	2		352	437	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36217194	36217194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	149	528	0	ENST00000222270.7:c.3943G>A	p.Asp1315Asn	p.D1315N	ENST00000222270	NM_014727.1	1315	Gac/Aac	14/37	1	2	FACETS	0.896	0.821	0.974	0.896	0.821	0.974	CLONAL	1	TRUE	1	0.496490295353085	2		528	670	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170016826	170016826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	107	338	0	ENST00000295797.4:c.1631C>T	p.Ser544Phe	p.S544F	ENST00000295797	NM_002740.5	544	tCt/tTt	17/18	0.496490295353085	5	FACETS	0.867	0.777	0.963	0.217	0.194	0.241	CLONAL	1	TRUE	1	0.496490295353085	5		338	867	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151850040	151850040	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0038949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	52	190	0	ENST00000262189.6:c.12277-1G>T		p.X4093_splice	ENST00000262189	NM_170606.2	4093			0.47384642120499	1	FACETS	0.709	0.611	0.814	0.709	0.611	0.814	SUBCLONAL	1	TRUE	0	0.496490295353085	1		190	222	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578490	7578490	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	124	518	1	ENST00000269305.4:c.440T>A	p.Val147Asp	p.V147D	ENST00000269305	NM_001126112.2	147	gTt/gAt	5/11	0.162075051519026	3	FACETS	1	0.957	1	0.729	0.661	0.8	CLONAL	2	TRUE	0	0.203489044226246	3		519	614	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588835	29588836	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0038950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	43	238	0	ENST00000356175.3:c.4622_4623dup	p.Asn1542LeufsTer12	p.N1542Lfs*12	ENST00000356175	NM_000267.3	1541	ctt/cTTtt	34/57	0.162075051519026	3	FACETS	1	0.914	1	0.75	0.634	0.875	CLONAL	2	TRUE	0	0.203489044226246	3		238	207	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345986	70345986	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	19	219	0	ENST00000374080.3:c.2523A>C	p.Gln841His	p.Q841H	ENST00000374080		841	caA/caC	18/45	0.203489044226246	2	FACETS	0.841	0.64	1			1	CLONAL	1	TRUE	NA	0.203489044226246	2		219	222	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436685	52436707	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATCAATCTGTAGGAGAGAAGAAG	ATCAATCTGTAGGAGAGAAGAAG	-	novel	NA	P-0038952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	124	551	0	ENST00000460680.1:c.1984-17_1989del		p.X662_splice	ENST00000460680	NM_004656.3	662		16/17	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		551	546	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0038956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	313	523	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.530306153765052	5	FACETS	1	0.947	1	0.501	0.473	0.53	CLONAL	2	TRUE	1	0.530306153765052	5		523	1057	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061406	38061406	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	166	670	0	ENST00000250448.2:c.583G>C	p.Glu195Gln	p.E195Q	ENST00000250448	NM_004496.3	195	Gag/Cag	2/2	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.530306153765052	2		670	600	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588864	29588864	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	74	293	0	ENST00000356175.3:c.4650A>T	p.Glu1550Asp	p.E1550D	ENST00000356175	NM_000267.3	1550	gaA/gaT	34/57	0.530306153765052	2	FACETS	0.807	0.711	0.908	0.403	0.355	0.454	CLONAL	1	TRUE	0	0.530306153765052	2		293	346	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72861930	72861930	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	105	441	0	ENST00000325599.8:c.952C>G	p.His318Asp	p.H318D	ENST00000325599	NM_018130.2	318	Cat/Gat	9/11	1	2	FACETS	0.959	0.865	1	0.959	0.865	1	CLONAL	1	TRUE	1	0.530306153765052	2		441	413	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586425	189586425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	134	444	0	ENST00000264731.3:c.1049G>A	p.Arg350Lys	p.R350K	ENST00000264731	NM_003722.4	350	aGa/aAa	8/14	0.530306153765052	5	FACETS	0.856	0.776	0.94	0.214	0.194	0.235	CLONAL	1	TRUE	1	0.530306153765052	5		444	1060	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675242	176675242	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1361796691	NA	P-0038957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	34	292	0	ENST00000439151.2:c.4558G>A	p.Glu1520Lys	p.E1520K	ENST00000439151	NM_022455.4	1520	Gaa/Aaa	11/23	0.539634298967398	4	FACETS	0.349	0.284	0.422	0.116	0.094	0.141	SUBCLONAL	1	TRUE	1	0.558528367016888	4		292	544	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0038958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	203	360	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.379216772237046	3	FACETS	1	0.964	1			1	CLONAL	2	TRUE	NA	0.379216772237046	3		360	606	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772299	68772299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	153	943	0	ENST00000261769.5:c.148C>T	p.Arg50Cys	p.R50C	ENST00000261769	NM_004360.3	50	Cgc/Tgc	2/16	1	2	FACETS	0.977	0.894	1	0.977	0.894	1	CLONAL	1	TRUE	1	0.379216772237046	2		943	826	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175762	176175762	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	218	886	0	ENST00000367669.3:c.353C>T	p.Pro118Leu	p.P118L	ENST00000367669	NM_022457.5	118	cCc/cTc	1/20	0.379216772237046	3	FACETS	1	0.988	1	0.642	0.596	0.688	CLONAL	1	TRUE	1	0.379216772237046	3		886	1066	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845553	63845553	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	71	306	0	ENST00000279873.7:c.1292A>G	p.Glu431Gly	p.E431G	ENST00000279873	NM_032199.2	431	gAa/gGa	9/10	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.379216772237046	2		306	344	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518783	176518783	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199935139	NA	P-0038959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	415	799	2	ENST00000292408.4:c.701G>A	p.Arg234His	p.R234H	ENST00000292408	NM_213647.1	234	cGc/cAc	6/18	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.858719826399944	2		801	950	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520260	9520260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	189	410	2	ENST00000353224.5:c.2009C>T	p.Ser670Phe	p.S670F	ENST00000353224	NM_177990.2	670	tCt/tTt	10/10	1	2	FACETS	0.923	0.861	0.985	0.923	0.861	0.985	CLONAL	1	TRUE	1	0.858719826399944	2		412	477	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129303	152129303	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	340	708	1	ENST00000206249.3:c.256G>A	p.Ala86Thr	p.A86T	ENST00000206249	NM_000125.3	86	Gct/Act	1/8	0.858719826399944	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.858719826399944	1		709	445	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495396	149495396	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1160163328	NA	P-0038962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	489	883	0	ENST00000261799.4:c.3251C>T	p.Pro1084Leu	p.P1084L	ENST00000261799	NM_002609.3	1084	cCa/cTa	23/23	0.614366412642415	3	FACETS	0.953	0.915	0.991	0.953	0.915	0.991	CLONAL	2	TRUE	1	0.614366412642415	3		883	1092	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0038964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	38	523	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.0717528271472696	3	FACETS	0.54	0.445	0.646	0.27	0.222	0.323	INDETERMINATE	1	FALSE	1	0.226840414545174	3		523	691	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0038964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	31	386	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.731	0.591	0.888	0.731	0.591	0.888	SUBCLONAL	1	FALSE	1	0.226840414545174	2		387	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0038964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	78	662	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	1	2	FACETS	0.627	0.549	0.711	0.627	0.549	0.711	SUBCLONAL	1	FALSE	1	0.226840414545174	2		662	1097	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77064592	77064592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	29	373	0	ENST00000356341.3:c.825G>T	p.Lys275Asn	p.K275N	ENST00000356341	NM_002576.4	275	aaG/aaT	8/15	1	2	FACETS	0.61	0.489	0.748	0.61	0.489	0.748	SUBCLONAL	1	FALSE	1	0.226840414545174	2		373	419	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878464	151878464	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	65	600	1	ENST00000262189.6:c.6481C>T	p.Gln2161Ter	p.Q2161*	ENST00000262189	NM_170606.2	2161	Caa/Taa	36/59	1	2	FACETS	0.742	0.642	0.851	0.742	0.642	0.851	SUBCLONAL	1	FALSE	1	0.226840414545174	2		601	772	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321707	62321707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746677388	NA	P-0038964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	55	686	0	ENST00000360203.5:c.2326G>A	p.Glu776Lys	p.E776K	ENST00000360203	NM_001283009.1	776	Gag/Aag	26/35	1	2	FACETS	0.564	0.481	0.655	0.564	0.481	0.655	SUBCLONAL	1	FALSE	1	0.226840414545174	2		686	860	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980413	201980413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	63	678	0	ENST00000359651.3:c.149C>T	p.Ser50Leu	p.S50L	ENST00000359651		50	tCa/tTa	1/8	1	2	FACETS	0.526	0.454	0.606	0.526	0.454	0.606	SUBCLONAL	1	FALSE	1	0.226840414545174	2		678	1055	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123324046	123324046	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	55	462	0	ENST00000358487.5:c.424G>A	p.Asp142Asn	p.D142N	ENST00000358487	NM_000141.4	142	Gat/Aat	4/18	1	2	FACETS	0.729	0.623	0.846	0.729	0.623	0.846	SUBCLONAL	1	FALSE	1	0.226840414545174	2		462	665	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420789	49420789	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	90	499	0	ENST00000301067.7:c.14960G>A	p.Trp4987Ter	p.W4987*	ENST00000301067	NM_003482.3	4987	tGg/tAg	48/54	0.149410683319893	2	FACETS	1	0.964	1	0.608	0.539	0.68	CLONAL	1	FALSE	0	0.226840414545174	2		499	653	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420809	49420809	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	90	475	0	ENST00000301067.7:c.14940G>C	p.Lys4980Asn	p.K4980N	ENST00000301067	NM_003482.3	4980	aaG/aaC	48/54	0.149410683319893	2	FACETS	1	0.962	1	0.598	0.531	0.67	CLONAL	1	FALSE	0	0.226840414545174	2		475	663	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437355	220437355	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	71	755	0	ENST00000243786.2:c.259C>G	p.Pro87Ala	p.P87A	ENST00000243786	NM_002191.3	87	Cca/Gca	1/2	1	2	FACETS	0.629	0.547	0.717	0.629	0.547	0.717	SUBCLONAL	1	FALSE	1	0.226840414545174	2		755	996	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145513	24145513	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	69	584	0	ENST00000263121.7:c.532G>C	p.Glu178Gln	p.E178Q	ENST00000263121	NM_003073.3	178	Gag/Cag	5/9	1	2	FACETS	0.727	0.632	0.83	0.727	0.632	0.83	SUBCLONAL	1	FALSE	1	0.226840414545174	2		584	837	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534481	187534481	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0038964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	24	333	0	ENST00000441802.2:c.9245C>G	p.Ser3082Ter	p.S3082*	ENST00000441802	NM_005245.3	3082	tCa/tGa	13/27	1	2	FACETS	0.507	0.397	0.635	0.507	0.397	0.635	SUBCLONAL	1	FALSE	1	0.226840414545174	2		333	417	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909369	41909369	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	48	444	0	ENST00000372991.4:c.19G>T	p.Glu7Ter	p.E7*	ENST00000372991	NM_001760.3	7	Gaa/Taa	1/5	1	2	FACETS	0.744	0.628	0.871	0.744	0.628	0.871	SUBCLONAL	1	FALSE	1	0.226840414545174	2		444	569	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226217	53226217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868976198	NA	P-0038964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	94	653	0	ENST00000375401.3:c.2632G>A	p.Glu878Lys	p.E878K	ENST00000375401	NM_004187.3	878	Gaa/Aaa	19/26	1	2	FACETS	0.921	0.818	1	0.921	0.818	1	CLONAL	1	FALSE	1	0.226840414545174	2		653	900	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874386	76874386	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	22	442	0	ENST00000373344.5:c.5336G>A	p.Arg1779Lys	p.R1779K	ENST00000373344	NM_000489.3	1779	aGa/aAa	21/35	1	2	FACETS	0.47	0.363	0.594	0.47	0.363	0.594	SUBCLONAL	1	FALSE	1	0.226840414545174	2		442	413	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196788	123196788	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	22	384	0	ENST00000218089.9:c.1675G>A	p.Asp559Asn	p.D559N	ENST00000218089	NM_001042749.1	559	Gat/Aat	18/35	1	2	FACETS	0.549	0.425	0.694	0.549	0.425	0.694	SUBCLONAL	1	FALSE	1	0.226840414545174	2		384	353	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0038965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	172	879	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	0.39	2		879	827	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229510	5229510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1303613614	NA	P-0038965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	58	161	0	ENST00000357368.4:c.2341G>A	p.Asp781Asn	p.D781N	ENST00000357368	NM_002850.3	781	Gat/Aat	15/38	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.39	2		161	244	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536842	120536842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751790181	NA	P-0038965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	153	506	0	ENST00000229340.5:c.344G>A	p.Arg115Gln	p.R115Q	ENST00000229340	NM_006861.6	115	cGa/cAa	4/6	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.39	2		506	719	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105678	27105678	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	187	324	0	ENST00000324856.7:c.5289A>C	p.Glu1763Asp	p.E1763D	ENST00000324856	NM_006015.4	1763	gaA/gaC	20/20	0.3	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.39	2		324	430	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105682	27105682	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	185	309	0	ENST00000324856.7:c.5293G>T	p.Glu1765Ter	p.E1765*	ENST00000324856	NM_006015.4	1765	Gaa/Taa	20/20	0.3	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.39	2		309	419	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591136	67591137	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTC	novel	NA	P-0038965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	62	259	0	ENST00000274335.5:c.1730_1731insTCG	p.Thr576_Arg577insSer	p.T576_R577insS	ENST00000274335		577	aga/aGTCga	12/15	1	2	FACETS	0.828	0.718	0.946	0.828	0.718	0.946	CLONAL	1	TRUE	1	0.39	2		259	384	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	548	399	0				ENST00000310581	NM_198253.2	-/1132			0.413165702167964	3	FACETS	1	0.996	1	0.78	0.757	0.803	INDETERMINATE	2	TRUE	0	0.827411332862634	3		399	800	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0038966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	449	659	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	NA	2	FACETS	0.931	0.89	0.972			1	INDETERMINATE	1	TRUE	NA	0.827411332862634	2		659	1166	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0038966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	247	461	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.827411332862634	2		461	533	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0038966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	315	463	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	0.984	0.933	1	0.984	0.933	1	CLONAL	1	TRUE	1	0.827411332862634	2		463	774	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910849	32910849	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs80358501	NA	P-0038966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	159	439	0	ENST00000380152.3:c.2357C>G	p.Ser786Cys	p.S786C	ENST00000380152		786	tCt/tGt	11/27	1	2	FACETS	0.468	0.429	0.508	0.468	0.429	0.508	SUBCLONAL	1	TRUE	1	0.827411332862634	2		439	822	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55335635	55335635	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	379	583	0	ENST00000284073.2:c.190T>G	p.Phe64Val	p.F64V	ENST00000284073	NM_138962.2	64	Ttc/Gtc	4/14	1	2	FACETS	0.818	0.778	0.859	0.818	0.778	0.859	CLONAL	1	TRUE	1	0.827411332862634	2		583	1120	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149599	202149599	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	582	513	0	ENST00000358485.4:c.1040C>A	p.Thr347Lys	p.T347K	ENST00000358485	NM_001080125.1	347	aCa/aAa	8/9	0.784709877931382	2	FACETS	0.934	0.912	0.956	0.934	0.912	0.956	CLONAL	2	TRUE	0	0.827411332862634	2		513	753	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326773	62326773	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771457769	NA	P-0038966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1338	667	835	0	ENST00000360203.5:c.3592G>A	p.Glu1198Lys	p.E1198K	ENST00000360203	NM_001283009.1	1198	Gag/Aag	34/35	0.437676033407538	3	FACETS	1	0.994	1	0.568	0.547	0.59	INDETERMINATE	1	TRUE	1	0.827411332862634	3		835	2005	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398560	116398560	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0038966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	167	526	0	ENST00000397752.3:c.2150C>G	p.Ser717Ter	p.S717*	ENST00000397752	NM_000245.2	717	tCa/tGa	9/21	1	2	FACETS	0.496	0.456	0.537	0.496	0.456	0.537	SUBCLONAL	1	TRUE	1	0.827411332862634	2		526	814	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205652	38205652	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	565	723	0	ENST00000317025.8:c.38G>C	p.Gly13Ala	p.G13A	ENST00000317025	NM_023034.1	13	gGa/gCa	2/24	0.437676033407538	3	FACETS	1	0.993	1	0.571	0.547	0.595	INDETERMINATE	1	TRUE	1	0.827411332862634	3		723	1691	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2107145	2107145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373818076	NA	P-0038968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	113	910	2	ENST00000219476.3:c.814G>A	p.Ala272Thr	p.A272T	ENST00000219476	NM_000548.3	272	Gcc/Acc	9/42	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.249148756385804	2		912	625	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245912888	245912888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767335863	NA	P-0038969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	21	412	1	ENST00000388985.4:c.1264G>A	p.Asp422Asn	p.D422N	ENST00000388985		422	Gac/Aac	12/12	1	2	FACETS	0.512	0.394	0.651	0.512	0.394	0.651	SUBCLONAL	1	FALSE	1	0.218117789777025	2		413	376	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515195	31515195	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	95	801	0	ENST00000344624.3:c.1190C>G	p.Pro397Arg	p.P397R	ENST00000344624		397	cCt/cGt	5/33	0.149251295418926	3	FACETS	1	0.975	1	0.67	0.596	0.748	CLONAL	1	FALSE	1	0.218117789777025	3		801	721	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44919335	44919335	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	49	264	0	ENST00000377967.4:c.1264del	p.Ala422ArgfsTer17	p.A422Rfs*17	ENST00000377967	NM_021140.2	421	gaG/ga	13/29	0.218117789777025	2	FACETS	0.908	0.783	1			1	CLONAL	3	FALSE	NA	0.218117789777025	2		264	165	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0038970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	108	701	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.343903274614902	2		701	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0038970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	119	930	0	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	0.343903274614902	1	FACETS	0.845	0.764	0.931	0.845	0.764	0.931	CLONAL	1	TRUE	0	0.343903274614902	1		930	678	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153609	55153609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501520	NA	P-0038970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	97	623	0	ENST00000257290.5:c.2575G>A	p.Val859Met	p.V859M	ENST00000257290	NM_006206.4	859	Gtg/Atg	19/23	1	2	FACETS	0.984	0.88	1	0.984	0.88	1	CLONAL	1	TRUE	1	0.343903274614902	2		623	573	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129782	108129783	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0038970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	37	515	1	ENST00000278616.4:c.2446_2447delinsTT	p.Ala816Leu	p.A816L	ENST00000278616	NM_000051.3	816	GCa/TTa	16/63	1	2	FACETS	0.433	0.356	0.519	0.433	0.356	0.519	SUBCLONAL	1	TRUE	1	0.343903274614902	2		516	497	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932459	39932459	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs140858321	NA	P-0038970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	99	945	0	ENST00000378444.4:c.2140G>C	p.Val714Leu	p.V714L	ENST00000378444	NM_001123385.1	714	Gtg/Ctg	4/15	1	2	FACETS	0.754	0.673	0.84	0.754	0.673	0.84	SUBCLONAL	1	TRUE	1	0.343903274614902	2		945	764	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	127	399	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.720980925896787	2		399	330	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984826	72984826	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376414532	NA	P-0038976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	206	476	2	ENST00000268489.5:c.2758G>A	p.Gly920Arg	p.G920R	ENST00000268489	NM_006885.3	920	Ggg/Agg	3/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.720980925896787	2		478	527	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439807	51439808	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCTT	novel	NA	P-0038976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	269	307	0	ENST00000262662.1:c.373_374insCTTC	p.His125ProfsTer13	p.H125Pfs*13	ENST00000262662		124	-/CCTT	4/4	0.720980925896787	2	FACETS	0.908	0.869	0.946	0.908	0.869	0.946	CLONAL	2	TRUE	0	0.720980925896787	2		307	411	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133671	55133872	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GATCCATATGTGGTAATCATTATTTAATGGAAACTCTTCCCTGTACAGAGAAAGGTTTCATTGAAATCAAACCCACCTTCAGCCAGTTGGAAGCTGTCAACCTGCATGAAGTCAAACATTTTGTTGTAGAGGTGCGGGCCTACCCACCTCCCAGGATATCCTGGCTGAAAAACAATCTGACTCTGATTGAAAATCTCACTGA	GATCCATATGTGGTAATCATTATTTAATGGAAACTCTTCCCTGTACAGAGAAAGGTTTCATTGAAATCAAACCCACCTTCAGCCAGTTGGAAGCTGTCAACCTGCATGAAGTCAAACATTTTGTTGTAGAGGTGCGGGCCTACCCACCTCCCAGGATATCCTGGCTGAAAAACAATCTGACTCTGATTGAAAATCTCACTGA	-	novel	NA	P-0038976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	2032	344	0	ENST00000257290.5:c.932-44_1089del		p.X311_splice	ENST00000257290	NM_006206.4	311		7/23	0.720980925896787	20	FACETS	0.983	0.969	0.998			1	CLONAL	15	TRUE	NA	0.720980925896787	20		344	2862	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980892	40980892	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	45	436	0	ENST00000373198.4:c.1594A>C	p.Ser532Arg	p.S532R	ENST00000373198	NM_133170.3	532	Agt/Cgt	10/32	0.187984368598772	3	FACETS	0.631	0.528	0.744	0.315	0.264	0.372	SUBCLONAL	1	TRUE	1	0.208790679179528	3		436	755	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927018	131927018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753680691	NA	P-0038977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	38	284	0	ENST00000265335.6:c.1555C>T	p.Arg519Cys	p.R519C	ENST00000265335		519	Cgt/Tgt	10/25	1	2	FACETS	0.79	0.653	0.943	0.79	0.653	0.943	CLONAL	1	TRUE	1	0.208790679179528	2		284	461	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223252	5223252	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763535247	NA	P-0038977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	110	631	0	ENST00000357368.4:c.2551C>T	p.Arg851Cys	p.R851C	ENST00000357368	NM_002850.3	851	Cgc/Tgc	18/38	0.208790679179528	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.208790679179528	1		631	914	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281727	49281727	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1484341813	NA	P-0038977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	296	698	0	ENST00000282018.3:c.774G>C	p.Leu258Phe	p.L258F	ENST00000282018	NM_020377.2	258	ttG/ttC	1/1	0.160379775820689	3	FACETS	0.873	0.821	0.926	0.873	0.821	0.926	CLONAL	3	TRUE	0	0.208790679179528	3		698	1196	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840001	27840005	+	frameshift_variant	Frame_Shift_Del	DEL	CGGAG	CGGAG	-	novel	NA	P-0038977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	64	409	0	ENST00000328488.2:c.89_93del	p.Ala30GlyfsTer49	p.A30Gfs*49	ENST00000328488	NM_003533.2	30	gCTCCG/g	1/1	1	2	FACETS	0.899	0.778	1	0.899	0.778	1	CLONAL	1	TRUE	1	0.208790679179528	2		409	682	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120576	94120576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	49	348	0	ENST00000369303.4:c.475G>A	p.Asp159Asn	p.D159N	ENST00000369303	NM_004440.3	159	Gac/Aac	3/17	1	2	FACETS	0.886	0.75	1	0.886	0.75	1	CLONAL	1	TRUE	1	0.208790679179528	2		348	530	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0038978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	154	523	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.267391334329071	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.281514806329078	3		523	583	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0038978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	326	622	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.266144415471881	4	FACETS	1	0.989	1	1	0.996	1	CLONAL	3	TRUE	2	0.281514806329078	4		622	857	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0038978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	202	535	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.275235912864573	2	FACETS	0.897	0.833	0.963	0.897	0.833	0.963	CLONAL	2	TRUE	0	0.281514806329078	2		535	800	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245939	46245939	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	126	371	0	ENST00000334344.6:c.4033G>A	p.Asp1345Asn	p.D1345N	ENST00000334344	NM_152641.2	1345	Gac/Aac	15/21	0.267391334329071	3	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	1	0.281514806329078	3		371	487	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023702	31023702	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1311033207	NA	P-0038978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	242	661	0	ENST00000375687.4:c.3187C>T	p.Gln1063Ter	p.Q1063*	ENST00000375687	NM_015338.5	1063	Cag/Tag	13/13	0.281514806329078	5	FACETS	1	0.965	1	0.701	0.655	0.75	CLONAL	2	TRUE	2	0.281514806329078	5		661	1162	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246352	41246352	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780794	NA	P-0038978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	113	546	0	ENST00000357654.3:c.1196A>G	p.His399Arg	p.H399R	ENST00000357654	NM_007294.3	399	cAt/cGt	10/23	0.267391334329071	3	FACETS	1	0.904	1	0.503	0.452	0.557	CLONAL	1	TRUE	1	0.281514806329078	3		546	910	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73340135	73340135	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs377447325	NA	P-0038978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	99	297	0	ENST00000377767.4:c.1945A>G	p.Ile649Val	p.I649V	ENST00000377767	NM_014953.3	649	Ata/Gta	15/21	0.278296602885936	2	FACETS	0.858	0.771	0.949	0.858	0.771	0.949	CLONAL	2	TRUE	0	0.281514806329078	2		297	410	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288333	33288333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200104639	NA	P-0038978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	88	505	0	ENST00000374542.5:c.1075C>T	p.Arg359Trp	p.R359W	ENST00000374542	NM_001141970.1	359	Cgg/Tgg	4/8	0.267391334329071	3	FACETS	0.98	0.868	1	0.49	0.434	0.55	CLONAL	1	TRUE	1	0.281514806329078	3		505	728	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313292	65313292	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750622516	NA	P-0038978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	164	561	0	ENST00000342505.4:c.1822G>A	p.Asp608Asn	p.D608N	ENST00000342505	NM_002227.2	608	Gac/Aac	13/25	0.278296602885936	2	FACETS	0.896	0.826	0.969	0.896	0.826	0.969	CLONAL	2	TRUE	0	0.281514806329078	2		561	650	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612890	228612890	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	285	604	0	ENST00000366696.1:c.137C>A	p.Thr46Lys	p.T46K	ENST00000366696	NM_003493.2	46	aCg/aAg	1/1	0.281514806329078	3	FACETS	0.896	0.845	0.948	0.896	0.845	0.948	CLONAL	3	TRUE	0	0.281514806329078	3		604	859	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683460	88683460	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	15	28	0	ENST00000372037.3:c.1583A>T	p.Gln528Leu	p.Q528L	ENST00000372037	NM_004329.2	528	cAa/cTa	13/13	0.281514806329078	3	FACETS	1	0.786	1	0.699	0.527	0.891	CLONAL	2	TRUE	0	0.281514806329078	3		28	58	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447773	49447773	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	168	435	0	ENST00000301067.7:c.661G>A	p.Ala221Thr	p.A221T	ENST00000301067	NM_003482.3	221	Gct/Act	5/54	0.267391334329071	3	FACETS	0.96	0.885	1	0.96	0.885	1	CLONAL	2	TRUE	1	0.281514806329078	3		435	709	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437507	110437507	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	222	587	0	ENST00000375856.3:c.894C>G	p.Phe298Leu	p.F298L	ENST00000375856	NM_003749.2	298	ttC/ttG	1/2	0.278296602885936	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.281514806329078	2		587	722	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858094	9858094	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	78	539	0	ENST00000330684.3:c.3307C>G	p.Arg1103Gly	p.R1103G	ENST00000330684	NM_001134407.1	1103	Cgc/Ggc	13/13	0.267391334329071	3	FACETS	0.81	0.711	0.917	0.405	0.355	0.459	CLONAL	1	TRUE	1	0.281514806329078	3		539	780	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520235	9520235	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	144	426	0	ENST00000353224.5:c.2034C>G	p.Asp678Glu	p.D678E	ENST00000353224	NM_177990.2	678	gaC/gaG	10/10	0.201987142640378	4	FACETS	0.946	0.865	1	0.946	0.865	1	CLONAL	2	TRUE	2	0.281514806329078	4		426	693	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390074	89390075	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	86	256	0	ENST00000336596.2:c.823_824insA	p.Pro275HisfsTer10	p.P275Hfs*10	ENST00000336596	NM_005233.5	275	cca/cAca	4/17	0.267391334329071	3	FACETS	0.896	0.798	0.999	0.896	0.798	0.999	CLONAL	2	TRUE	1	0.281514806329078	3		256	389	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390979	89390980	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	156	480	0	ENST00000336596.2:c.1046dup	p.Asp350GlyfsTer15	p.D350Gfs*15	ENST00000336596	NM_005233.5	349	ctg/cTtg	5/17	0.267391334329071	3	FACETS	0.939	0.863	1	0.939	0.863	1	CLONAL	2	TRUE	1	0.281514806329078	3		480	673	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390981	89390982	+	frameshift_variant	Frame_Shift_Ins	INS	GG	GG	TAT	novel	NA	P-0038978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	156	482	2	ENST00000336596.2:c.1047_1048delinsTAT	p.Asp350IlefsTer15	p.D350Ifs*15	ENST00000336596	NM_005233.5	349	ctGGac/ctTATac	5/17	0.267391334329071	3	FACETS	0.924	0.849	1	0.924	0.849	1	CLONAL	2	TRUE	1	0.281514806329078	3		484	684	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508834	31508834	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	197	539	0	ENST00000344624.3:c.1481C>G	p.Ser494Cys	p.S494C	ENST00000344624		494	tCt/tGt	7/33	0.267391334329071	3	FACETS	0.981	0.91	1	0.981	0.91	1	CLONAL	2	TRUE	1	0.281514806329078	3		539	814	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509561	106509561	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	88	581	1	ENST00000359195.3:c.1555C>A	p.Leu519Ile	p.L519I	ENST00000359195	NM_002649.2	519	Ctt/Att	2/11	1	2	FACETS	0.876	0.776	0.982	0.876	0.776	0.982	CLONAL	1	TRUE	1	0.281514806329078	2		582	714	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275872	38275872	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	187	547	0	ENST00000425967.3:c.1397C>A	p.Ala466Glu	p.A466E	ENST00000425967	NM_001174067.1	466	gCa/gAa	11/19	0.281514806329078	3	FACETS	0.917	0.849	0.989	0.917	0.849	0.989	CLONAL	2	TRUE	1	0.281514806329078	3		547	826	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815592	139815592	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs777030483	NA	P-0038978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	132	656	0	ENST00000247668.2:c.1063A>C	p.Ile355Leu	p.I355L	ENST00000247668	NM_021138.3	355	Atc/Ctc	9/11	0.278296602885936	2	FACETS	1	0.958	1	0.548	0.498	0.602	CLONAL	1	TRUE	0	0.281514806329078	2		656	855	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039328	47039329	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	T	novel	NA	P-0038978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	250	390	0	ENST00000377604.3:c.951_952delinsT	p.Ala319ProfsTer16	p.A319Pfs*16	ENST00000377604	NM_001204468.1	317	ctGGgg/ctTgg	10/24	0.260386738525761	2	FACETS	1	0.952	1			1	CLONAL	3	TRUE	NA	0.281514806329078	2		390	586	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024584	11024584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757525257	NA	P-0038979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	119	525	0	ENST00000327064.4:c.701G>A	p.Arg234His	p.R234H	ENST00000327064	NM_199141.1	234	cGc/cAc	6/16	1	2	FACETS	0.99	0.894	1	0.99	0.894	1	CLONAL	1	TRUE	1	0.32	2		525	751	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593578	55593606	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	In_Frame_Del	DEL	ACAGAAACCCATGTATGAAGTACAGTGGA	ACAGAAACCCATGTATGAAGTACAGTGGA	-	novel	NA	P-0038980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	97	396	0	ENST00000288135.5:c.1648-3_1673del		p.K550_K558del	ENST00000288135	NM_000222.2	550		11/21	1	2	FACETS	0.855	0.765	0.949	0.855	0.765	0.949	CLONAL	1	TRUE	1	0.467962072108694	2		396	485	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69456188	69456188	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	105	591	0	ENST00000227507.2:c.107A>G	p.Glu36Gly	p.E36G	ENST00000227507	NM_053056.2	36	gAg/gGg	1/5	0.215775763460512	2	FACETS	0.498	0.445	0.553	0.249	0.222	0.277	INDETERMINATE	1	TRUE	0	0.467962072108694	2		591	902	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0038981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	160	563	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.432105071898409	1	FACETS	0.924	0.851	1	0.924	0.851	1	CLONAL	1	TRUE	0	0.432105071898409	1		563	628	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27204924	27204924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	116	428	0	ENST00000380036.4:c.2225G>A	p.Gly742Glu	p.G742E	ENST00000380036	NM_000459.3	742	gGa/gAa	14/23	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.432105071898409	2		428	530	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914995	32914995	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	76	441	0	ENST00000380152.3:c.6503G>T	p.Gly2168Val	p.G2168V	ENST00000380152		2168	gGa/gTa	11/27	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.432105071898409	2		441	345	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540853	187540853	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1336474278	NA	P-0038981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	98	319	0	ENST00000441802.2:c.6887C>G	p.Ser2296Cys	p.S2296C	ENST00000441802	NM_005245.3	2296	tCt/tGt	10/27	0.432105071898409	1	FACETS	0.972	0.874	1	0.972	0.874	1	CLONAL	1	TRUE	0	0.432105071898409	1		319	366	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0038982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	21	343	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	0.109024506451433	3	FACETS	0.667	0.512	0.849	0.333	0.256	0.425	SUBCLONAL	1	TRUE	1	0.13	3		343	516	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0038982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	11	312	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.413	0.284	0.575	0.413	0.284	0.575	SUBCLONAL	1	TRUE	1	0.13	2		312	410	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094445	27094446	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	38	505	0	ENST00000324856.7:c.3154dup	p.Tyr1052LeufsTer53	p.Y1052Lfs*53	ENST00000324856	NM_006015.4	1051	-/T	11/20	1	2	FACETS	0.966	0.797	1	0.966	0.797	1	CLONAL	1	TRUE	1	0.13	2		505	605	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534285	534285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894226	NA	P-0038982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	28	630	0	ENST00000451590.1:c.38G>T	p.Gly13Val	p.G13V	ENST00000451590	NM_001130442.1	13	gGt/gTt	2/5	1	2	FACETS	0.786	0.627	0.969	0.786	0.627	0.969	CLONAL	1	TRUE	1	0.13	2		630	548	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023676	27023676	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs867647567	NA	P-0038982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	41	477	1	ENST00000324856.7:c.782C>A	p.Ser261Ter	p.S261*	ENST00000324856	NM_006015.4	261	tCg/tAg	1/20	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.13	2		478	589	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296299	15296300	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	39	650	0	ENST00000263388.2:c.2142_2143insT	p.Gly715TrpfsTer7	p.G715Wfs*7	ENST00000263388	NM_000435.2	714	-/T	13/33	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.13	2		650	524	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936083	178936083	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519927	NA	P-0038983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	123	427	1	ENST00000263967.3:c.1625A>T	p.Glu542Val	p.E542V	ENST00000263967	NM_006218.2	542	gAa/gTa	10/21	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.553840526782987	2		428	438	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115956	8115957	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCT	novel	NA	P-0038983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	131	301	0	ENST00000346208.3:c.1305_1308dup	p.Ser437LeufsTer71	p.S437Lfs*71	ENST00000346208		434	-/CCCT	6/6	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.553840526782987	2		301	471	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0038984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	120	187	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.931	0.843	1	1	0.989	1	CLONAL	2	TRUE	1	0.223033989365918	2		187	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912660	NA	P-0038984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	125	718	0	ENST00000269305.4:c.839G>T	p.Arg280Ile	p.R280I	ENST00000269305	NM_001126112.2	280	aGa/aTa	8/11	0.223033989365918	1	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	0	0.223033989365918	1		718	986	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0038984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	67	454	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.223033989365918	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.223033989365918	1		454	474	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939457	76939457	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	90	619	0	ENST00000373344.5:c.1291G>T	p.Glu431Ter	p.E431*	ENST00000373344	NM_000489.3	431	Gag/Tag	9/35	1	2	FACETS	0.953	0.844	1	0.953	0.844	1	CLONAL	1	TRUE	1	0.223033989365918	2		619	847	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948302	31948302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	78	619	0	ENST00000375333.2:c.890G>T	p.Arg297Ile	p.R297I	ENST00000375333	NM_032454.1	297	aGa/aTa	6/8	1	2	FACETS	0.894	0.785	1	0.894	0.785	1	CLONAL	1	TRUE	1	0.223033989365918	2		619	782	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182156	11182156	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	104	651	0	ENST00000361445.4:c.6690A>T	p.Leu2230Phe	p.L2230F	ENST00000361445	NM_004958.3	2230	ttA/ttT	48/58	1	2	FACETS	0.929	0.83	1	0.929	0.83	1	CLONAL	1	TRUE	1	0.223033989365918	2		651	1004	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352428	118352428	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0038984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	42	201	0	ENST00000534358.1:c.3635-2A>T		p.X1212_splice	ENST00000534358	NM_005933.3	1212			1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.223033989365918	2		201	309	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135320	30135320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	102	407	0	ENST00000331968.5:c.498G>T	p.Met166Ile	p.M166I	ENST00000331968	NM_002742.2	166	atG/atT	3/18	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.223033989365918	2		407	696	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685544	29685544	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1567627751	NA	P-0038984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	61	457	0	ENST00000356175.3:c.7954C>T	p.Gln2652Ter	p.Q2652*	ENST00000356175	NM_000267.3	2652	Caa/Taa	54/57	1	2	FACETS	0.929	0.801	1	0.929	0.801	1	CLONAL	1	TRUE	1	0.223033989365918	2		457	589	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584409	39584409	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	52	377	0	ENST00000262039.4:c.1074G>T	p.Met358Ile	p.M358I	ENST00000262039	NM_002647.2	358	atG/atT	10/25	0.219268495768532	1	FACETS	0.865	0.737	1	0.865	0.737	1	CLONAL	1	TRUE	0	0.223033989365918	1		377	479	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615740	1615740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	109	742	2	ENST00000344749.5:c.1531G>A	p.Ala511Thr	p.A511T	ENST00000344749	NM_001136139.2	511	Gct/Act	17/19	0.223033989365918	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.223033989365918	1		744	791	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033768	48033768	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs756216566	NA	P-0038984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	58	319	0	ENST00000234420.5:c.3979A>T	p.Asn1327Tyr	p.N1327Y	ENST00000234420	NM_000179.2	1327	Aat/Tat	9/10	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.223033989365918	2		319	477	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156032	99156032	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	93	598	1	ENST00000074304.5:c.712A>T	p.Thr238Ser	p.T238S	ENST00000074304	NM_001134224.1	238	Act/Tct	10/26	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.223033989365918	2		599	781	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495264	212495264	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	65	423	0	ENST00000342788.4:c.2002G>T	p.Gly668Cys	p.G668C	ENST00000342788	NM_005235.2	668	Ggt/Tgt	17/28	1	2	FACETS	0.846	0.733	0.969	0.846	0.733	0.969	CLONAL	1	TRUE	1	0.223033989365918	2		423	689	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023778	31023778	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	102	598	0	ENST00000375687.4:c.3263A>T	p.Gln1088Leu	p.Q1088L	ENST00000375687	NM_015338.5	1088	cAg/cTg	13/13	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.223033989365918	2		598	776	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827970	40827970	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	81	447	0	ENST00000373198.4:c.2458G>T	p.Val820Leu	p.V820L	ENST00000373198	NM_133170.3	820	Gtg/Ttg	17/32	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.223033989365918	2		447	589	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445085	89445085	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	57	325	0	ENST00000336596.2:c.1405G>C	p.Asp469His	p.D469H	ENST00000336596	NM_005233.5	469	Gac/Cac	6/17	1	2	FACETS	0.952	0.817	1	0.952	0.817	1	CLONAL	1	TRUE	1	0.223033989365918	2		325	537	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670340	134670340	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	78	406	0	ENST00000398015.3:c.251G>T	p.Arg84Leu	p.R84L	ENST00000398015	NM_004441.4	84	cGc/cTc	3/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.223033989365918	2		406	527	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030346	180030346	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs185808242	NA	P-0038984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	125	703	0	ENST00000261937.6:c.3938C>G	p.Pro1313Arg	p.P1313R	ENST00000261937	NM_182925.4	1313	cCt/cGt	30/30	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.223033989365918	2		703	872	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686791	117686791	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs771176235	NA	P-0038984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	43	431	0	ENST00000368508.3:c.2926G>T	p.Asp976Tyr	p.D976Y	ENST00000368508	NM_002944.2	976	Gac/Tac	19/43	1	2	FACETS	0.691	0.578	0.817	0.691	0.578	0.817	SUBCLONAL	1	TRUE	1	0.223033989365918	2		431	558	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739969	41739969	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	67	389	0	ENST00000242208.4:c.4C>A	p.Pro2Thr	p.P2T	ENST00000242208	NM_002192.2	2	Ccc/Acc	2/3	1	2	FACETS	0.949	0.825	1	0.949	0.825	1	CLONAL	1	TRUE	1	0.223033989365918	2		389	633	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0038985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	189	347	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.719466793993548	2	FACETS	0.94	0.897	0.98	0.94	0.897	0.98	CLONAL	2	TRUE	0	0.782609389259289	2		347	257	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	154	578	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.35813671153926	1	FACETS	0.73	0.68	0.781	0.73	0.68	0.781	INDETERMINATE	1	TRUE	0	0.782609389259289	1		578	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0038985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	217	647	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.745564278671079	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.782609389259289	1		647	296	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0038985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	49	238	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.782609389259289	1	FACETS	0.794	0.7	0.887	0.794	0.7	0.887	SUBCLONAL	1	TRUE	0	0.782609389259289	1		238	96	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	70	230	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	0.241591018909907	2	FACETS	0.864	0.767	0.965	0.432	0.383	0.483	INDETERMINATE	1	TRUE	0	0.782609389259289	2		230	207	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42790944	42790944	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367972487	NA	P-0038985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	255	670	1	ENST00000575354.2:c.89G>A	p.Arg30His	p.R30H	ENST00000575354	NM_015125.3	30	cGc/cAc	2/20	0.340461605241008	1	FACETS	0.792	0.75	0.833	0.792	0.75	0.833	INDETERMINATE	1	TRUE	0	0.782609389259289	1		671	501	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323991	31323991	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1050692	NA	P-0038985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	18	434	2	ENST00000412585.2:c.572G>C	p.Trp191Ser	p.W191S	ENST00000412585	NM_005514.6	191	tGg/tCg	3/8	0.241591018909907	2	FACETS	0.188	0.141	0.243	0.094	0.07	0.122	INDETERMINATE	1	TRUE	0	0.782609389259289	2		436	245	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324049	31324049	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137854752	NA	P-0038985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	18	543	0	ENST00000412585.2:c.514G>A	p.Glu172Lys	p.E172K	ENST00000412585	NM_005514.6	172	Gag/Aag	3/8	0.241591018909907	2	FACETS	0.139	0.104	0.18	0.069	0.052	0.09	INDETERMINATE	1	TRUE	0	0.782609389259289	2		543	331	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729841	41729841	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1489240461	NA	P-0038985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	95	417	0	ENST00000242208.4:c.688T>A	p.Leu230Met	p.L230M	ENST00000242208	NM_002192.2	230	Ttg/Atg	3/3	1	2	FACETS	0.971	0.879	1	0.971	0.879	1	CLONAL	1	TRUE	1	0.782609389259289	2		417	250	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	406	660	0	ENST00000269305.4:c.469G>C	p.Val157Leu	p.V157L	ENST00000269305	NM_001126112.2	157	Gtc/Ctc	5/11	0.715611946294243	1	FACETS	0.902	0.866	0.938	0.902	0.866	0.938	CLONAL	1	TRUE	0	0.7536398293937	1		660	744	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30133059	30133059	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	189	281	0	ENST00000331968.5:c.542G>T	p.Gly181Val	p.G181V	ENST00000331968	NM_002742.2	181	gGt/gTt	4/18	1	2	FACETS	0.932	0.868	0.998	0.932	0.868	0.998	CLONAL	1	TRUE	1	0.7536398293937	2		281	538	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130228	2130228	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	310	667	0	ENST00000219476.3:c.3460A>T	p.Thr1154Ser	p.T1154S	ENST00000219476	NM_000548.3	1154	Act/Tct	30/42	1	2	FACETS	0.976	0.924	1	0.976	0.924	1	CLONAL	1	TRUE	1	0.7536398293937	2		667	843	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188194	10188196	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	ATA	ATA	TT	novel	NA	P-0038989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	230	360	1	ENST00000256474.2:c.341-4_341-2delinsTT		p.X114_splice	ENST00000256474	NM_000551.3	114			0.715611946294243	1	FACETS	0.764	0.72	0.808	0.764	0.72	0.808	SUBCLONAL	1	TRUE	0	0.7536398293937	1		361	498	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623107	52623107	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	254	372	0	ENST00000394830.3:c.2944del	p.Arg982AspfsTer26	p.R982Dfs*26	ENST00000394830	NM_018313.4	982	Aga/ga	19/30	0.715611946294243	1	FACETS	0.87	0.825	0.914	0.87	0.825	0.914	CLONAL	1	TRUE	0	0.7536398293937	1		372	483	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246378	53246379	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	AA	novel	NA	P-0038989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	312	292	2	ENST00000375401.3:c.603_604delinsTT	p.Gln202Ter	p.Q202*	ENST00000375401	NM_004187.3	201	gtGCag/gtTTag	5/26	0.118607174753858	2	FACETS	0.922	0.887	0.956			1	INDETERMINATE	2	TRUE	NA	0.7536398293937	2		294	449	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	66	399	0				ENST00000310581	NM_198253.2	-/1132			0.382968156713522	8	FACETS	1	0.918	1	0.18	0.156	0.207	CLONAL	1	TRUE	2	0.382968156713522	8		399	685	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882019	NA	P-0038991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	321	754	1	ENST00000269305.4:c.455del	p.Pro152ArgfsTer18	p.P152Rfs*18	ENST00000269305	NM_001126112.2	152	cCg/cg	5/11	0.382968156713522	2	FACETS	0.961	0.911	1	0.961	0.911	1	CLONAL	2	TRUE	0	0.382968156713522	2		755	872	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81528563	81528563	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	82	221	0	ENST00000298171.2:c.242T>C	p.Ile81Thr	p.I81T	ENST00000298171	NM_000369.2	81	aTc/aCc	2/10	0.382968156713522	6	FACETS	0.9	0.798	1	0.45	0.399	0.505	CLONAL	2	TRUE	2	0.382968156713522	6		221	420	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553475	29553475	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	294	585	0	ENST00000356175.3:c.2024G>T	p.Gly675Val	p.G675V	ENST00000356175	NM_000267.3	675	gGa/gTa	18/57	0.382968156713522	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.382968156713522	2		585	699	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264332	46264332	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	72	393	0	ENST00000371998.3:c.1379G>C	p.Gly460Ala	p.G460A	ENST00000371998		460	gGg/gCg	11/23	0.316275626717739	4	FACETS	0.809	0.707	0.919	0.404	0.353	0.46	CLONAL	1	TRUE	2	0.382968156713522	4		393	643	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0038992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	70	622	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	0.200298528902323	2		622	604	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948644	71948644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572965433	NA	P-0038992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	59	791	2	ENST00000298229.2:c.3356G>A	p.Arg1119Gln	p.R1119Q	ENST00000298229	NM_001567.3	1119	cGg/cAg	26/28	1	2	FACETS	0.623	0.535	0.721	0.623	0.535	0.721	SUBCLONAL	1	TRUE	1	0.200298528902323	2		793	945	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644588	21644588	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	69	439	0	ENST00000421138.2:c.79G>C	p.Glu27Gln	p.E27Q	ENST00000421138		27	Gaa/Caa	4/16	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.200298528902323	2		439	666	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41258501	41258501	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	34	448	0	ENST00000357654.3:c.184C>G	p.Pro62Ala	p.P62A	ENST00000357654	NM_007294.3	62	Cct/Gct	4/23	1	2	FACETS	0.552	0.45	0.668	0.552	0.45	0.668	SUBCLONAL	1	TRUE	1	0.200298528902323	2		448	615	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260214	19260214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751538422	NA	P-0038992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	110	731	0	ENST00000162023.5:c.79G>A	p.Gly27Arg	p.G27R	ENST00000162023		27	Ggg/Agg	7/13	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.200298528902323	2		731	933	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436395	52436395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	87	638	0	ENST00000460680.1:c.2099G>A	p.Arg700Gln	p.R700Q	ENST00000460680	NM_004656.3	700	cGg/cAg	17/17	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.200298528902323	2		638	818	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502659	149502659	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	60	558	1	ENST00000261799.4:c.2129C>A	p.Pro710Gln	p.P710Q	ENST00000261799	NM_002609.3	710	cCg/cAg	15/23	0.200298528902323	1	FACETS	0.902	0.777	1	0.902	0.777	1	CLONAL	1	TRUE	0	0.200298528902323	1		559	598	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679225	30679225	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	59	606	0	ENST00000376406.3:c.2185G>C	p.Glu729Gln	p.E729Q	ENST00000376406	NM_014641.2	729	Gag/Cag	7/15	0.130366369427503	3	FACETS	0.771	0.661	0.89			1	SUBCLONAL	1	TRUE	NA	0.200298528902323	3		606	841	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335696	81335696	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	52	380	0	ENST00000222390.5:c.1664G>C	p.Gly555Ala	p.G555A	ENST00000222390	NM_000601.4	555	gGa/gCa	15/18	1	2	FACETS	0.873	0.742	1	0.873	0.742	1	CLONAL	1	TRUE	1	0.200298528902323	2		380	595	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960181	151960181	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	22	270	0	ENST00000262189.6:c.1219G>A	p.Asp407Asn	p.D407N	ENST00000262189	NM_170606.2	407	Gat/Aat	9/59	0.136380173750417	4	FACETS	0.643	0.497	0.813	0.322	0.248	0.407	SUBCLONAL	1	TRUE	2	0.200298528902323	4		270	410	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347962	70347962	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	60	557	0	ENST00000374080.3:c.3201T>G	p.Asp1067Glu	p.D1067E	ENST00000374080		1067	gaT/gaG	22/45	0.200298528902323	1	FACETS	0.845	0.728	0.973	0.845	0.728	0.973	CLONAL	1	TRUE	0	0.200298528902323	1		557	638	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611806	100611806	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	37	512	0	ENST00000308731.7:c.1315G>C	p.Glu439Gln	p.E439Q	ENST00000308731	NM_000061.2	439	Gaa/Caa	14/19	0.200298528902323	1	FACETS	0.532	0.437	0.638	0.532	0.437	0.638	SUBCLONAL	1	TRUE	0	0.200298528902323	1		512	625	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0038993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	435	523	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.666008497260094	2	FACETS	0.963	0.93	0.996	0.963	0.93	0.996	CLONAL	2	TRUE	0	0.666008497260094	2		523	678	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0038993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	179	492	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.335134546849682	1	FACETS	0.517	0.478	0.557	0.517	0.478	0.557	INDETERMINATE	1	TRUE	0	0.666008497260094	1		492	694	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511337	157511337	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	39	324	0	ENST00000346085.5:c.3855G>A	p.Met1285Ile	p.M1285I	ENST00000346085	NM_020732.3	1285	atG/atA	15/20	0.335134546849682	1	FACETS	0.17	0.141	0.203	0.17	0.141	0.203	INDETERMINATE	1	TRUE	0	0.666008497260094	1		324	459	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71008496	71008496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756987886	NA	P-0038993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	77	289	0	ENST00000318789.4:c.1936G>A	p.Glu646Lys	p.E646K	ENST00000318789	NM_032682.5	646	Gaa/Aaa	21/21	0.666008497260094	1	FACETS	0.424	0.374	0.476	0.424	0.374	0.476	SUBCLONAL	1	TRUE	0	0.666008497260094	1		289	364	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878287	151878287	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	37	551	0	ENST00000262189.6:c.6658C>T	p.Gln2220Ter	p.Q2220*	ENST00000262189	NM_170606.2	2220	Cag/Tag	36/59	0.666008497260094	1	FACETS	0.107	0.088	0.129	0.107	0.088	0.129	SUBCLONAL	1	TRUE	0	0.666008497260094	1		551	690	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541457	187541457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	53	364	0	ENST00000441802.2:c.6283G>A	p.Glu2095Lys	p.E2095K	ENST00000441802	NM_005245.3	2095	Gag/Aag	10/27	1	2	FACETS	0.235	0.2	0.273	0.235	0.2	0.273	SUBCLONAL	1	TRUE	1	0.666008497260094	2		364	678	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911491	114911491	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	55	150	0	ENST00000543371.1:c.1009C>T	p.Gln337Ter	p.Q337*	ENST00000543371	NM_001198531.1	337	Cag/Tag	10/14	0.495280523316094	1	FACETS	0.471	0.407	0.539	0.471	0.407	0.539	SUBCLONAL	1	TRUE	0	0.666008497260094	1		150	234	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370847	55370847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	320	452	0	ENST00000297316.4:c.149C>T	p.Ala50Val	p.A50V	ENST00000297316	NM_022454.3	50	gCg/gTg	1/2	0.41613788840957	3	FACETS	1	0.993	1	0.66	0.624	0.696	CLONAL	1	TRUE	1	0.666008497260094	3		452	971	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589534	69589534	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	48	125	0	ENST00000168712.1:c.319G>A	p.Ala107Thr	p.A107T	ENST00000168712	NM_002007.2	107	Gcg/Acg	1/3	0.666008497260094	6	FACETS	0.646	0.546	0.757			1	SUBCLONAL	1	TRUE	NA	0.666008497260094	6		125	520	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557583	21557583	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	440	633	0	ENST00000382592.4:c.2262G>A	p.Met754Ile	p.M754I	ENST00000382592	NM_014572.2	754	atG/atA	5/8	0.210482187704036	3	FACETS	0.751	0.718	0.785	0.751	0.718	0.785	INDETERMINATE	2	TRUE	1	0.666008497260094	3		633	1172	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027213	49027213	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	98	371	0	ENST00000267163.4:c.1780C>G	p.Leu594Val	p.L594V	ENST00000267163	NM_000321.2	594	Ctt/Gtt	18/27	NA	2	FACETS	0.486	0.434	0.541			1	INDETERMINATE	1	TRUE	NA	0.666008497260094	2		371	606	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857055	9857055	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	32	253	0	ENST00000330684.3:c.4346G>T	p.Ser1449Ile	p.S1449I	ENST00000330684	NM_001134407.1	1449	aGc/aTc	13/13	1	2	FACETS	0.199	0.161	0.242	0.199	0.161	0.242	SUBCLONAL	1	TRUE	1	0.666008497260094	2		253	482	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31015985	31015985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	332	357	0	ENST00000375687.4:c.307G>A	p.Glu103Lys	p.E103K	ENST00000375687	NM_015338.5	103	Gag/Aag	5/13	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.666008497260094	2		357	856	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928082	178928082	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	446	473	0	ENST00000263967.3:c.1360G>C	p.Asp454His	p.D454H	ENST00000263967	NM_006218.2	454	Gat/Cat	8/21	0.666008497260094	2	FACETS	0.954	0.921	0.986	0.954	0.921	0.986	CLONAL	2	TRUE	0	0.666008497260094	2		473	702	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	99	677	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	0.328417443008515	3	FACETS	1	0.908	1	0.511	0.455	0.57	CLONAL	1	TRUE	1	0.22	3		677	978	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	89	461	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.328417443008515	3	FACETS	1	0.962	1	0.602	0.533	0.675	CLONAL	1	TRUE	1	0.22	3		461	746	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257828	133257828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771051323	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	50	528	2	ENST00000320574.5:c.100C>T	p.Arg34Cys	p.R34C	ENST00000320574	NM_006231.2	34	Cgc/Tgc	2/49	1	2	FACETS	0.669	0.567	0.783	0.669	0.567	0.783	SUBCLONAL	1	TRUE	1	0.22	2		530	679	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	70	504	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.328417443008515	3	FACETS	1	0.908	1	0.526	0.458	0.599	CLONAL	1	TRUE	1	0.22	3		504	672	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160227	22160227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	34	348	0	ENST00000215832.6:c.404G>A	p.Arg135Lys	p.R135K	ENST00000215832	NM_002745.4	135	aGa/aAa	3/9	0.0783336551336039	0	FACETS	0.628	0.513	0.756			1	INDETERMINATE	1	TRUE	0	0.22	0		348	384	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916747	48916747	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690915	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	42	430	0	ENST00000267163.4:c.277C>T	p.Gln93Ter	p.Q93*	ENST00000267163	NM_000321.2	93	Caa/Taa	3/27	0.219154630748798	1	FACETS	0.755	0.631	0.893	0.755	0.631	0.893	SUBCLONAL	1	TRUE	0	0.22	1		430	450	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840041	27840041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	45	380	0	ENST00000328488.2:c.53G>A	p.Arg18His	p.R18H	ENST00000328488	NM_003533.2	18	cGc/cAc	1/1	1	2	FACETS	0.878	0.738	1	0.878	0.738	1	CLONAL	1	TRUE	1	0.22	2		380	466	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790830	89790830	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	81	764	0	ENST00000336032.3:c.217C>G	p.Arg73Gly	p.R73G	ENST00000336032	NM_006813.2	73	Cgc/Ggc	1/2	1	2	FACETS	0.776	0.682	0.877	0.776	0.682	0.877	SUBCLONAL	1	TRUE	1	0.22	2		764	949	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539071	187539071	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	56	573	0	ENST00000441802.2:c.8669C>G	p.Ser2890Ter	p.S2890*	ENST00000441802	NM_005245.3	2890	tCa/tGa	10/27	0.0783336551336039	0	FACETS	0.622	0.533	0.721			1	INDETERMINATE	1	TRUE	0	0.22	0		573	638	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665015	138665015	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	20	142	0	ENST00000330315.3:c.550G>A	p.Asp184Asn	p.D184N	ENST00000330315	NM_023067.3	184	Gac/Aac	1/1	0.3	2	FACETS	0.937	0.72	1			1	CLONAL	1	TRUE	NA	0.22	2		142	194	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575071	48575071	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	34	412	0	ENST00000342988.3:c.265G>C	p.Gly89Arg	p.G89R	ENST00000342988	NM_005359.5	89	Gga/Cga	3/12	1	2	FACETS	0.726	0.593	0.875	0.726	0.593	0.875	SUBCLONAL	1	TRUE	1	0.22	2		412	426	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982109	38982109	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	43	441	0	ENST00000357387.3:c.613C>T	p.Arg205Ter	p.R205*	ENST00000357387	NM_152756.3	205	Cga/Tga	8/38	0.219154630748798	1	FACETS	0.689	0.576	0.814	0.689	0.576	0.814	SUBCLONAL	1	TRUE	0	0.22	1		441	505	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444286	49444286	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	101	1066	0	ENST00000301067.7:c.3085C>T	p.Gln1029Ter	p.Q1029*	ENST00000301067	NM_003482.3	1029	Cag/Tag	11/54	1	2	FACETS	0.726	0.647	0.811	0.726	0.647	0.811	SUBCLONAL	1	TRUE	1	0.22	2		1066	1265	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	47	220	0				ENST00000310581	NM_198253.2	-/1132			0.219154630748798	1	FACETS	0.828	0.7	0.97	0.828	0.7	0.97	CLONAL	1	TRUE	0	0.22	1		220	459	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519709	137519709	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	29	364	0	ENST00000367739.4:c.929C>G	p.Ser310Ter	p.S310*	ENST00000367739	NM_000416.2	310	tCa/tGa	7/7	0.0783336551336039	0	FACETS	0.536	0.43	0.656			1	INDETERMINATE	1	TRUE	0	0.22	0		364	384	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028498	42028498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	93	499	0	ENST00000219905.7:c.4036G>A	p.Glu1346Lys	p.E1346K	ENST00000219905	NM_001164273.1	1346	Gaa/Aaa	13/24	0.219154630748798	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.22	1		499	576	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319364	11319364	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	54	626	0	ENST00000361445.4:c.103G>C	p.Glu35Gln	p.E35Q	ENST00000361445	NM_004958.3	35	Gaa/Caa	2/58	1	2	FACETS	0.649	0.553	0.755	0.649	0.553	0.755	SUBCLONAL	1	TRUE	1	0.22	2		626	756	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265231	16265231	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	39	473	0	ENST00000375759.3:c.10723C>G	p.Leu3575Val	p.L3575V	ENST00000375759	NM_015001.2	3575	Ctg/Gtg	14/15	1	2	FACETS	0.605	0.501	0.722	0.605	0.501	0.722	SUBCLONAL	1	TRUE	1	0.22	2		473	586	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481411	56481411	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	63	717	0	ENST00000267101.3:c.598G>C	p.Glu200Gln	p.E200Q	ENST00000267101	NM_001982.3	200	Gaa/Caa	5/28	1	2	FACETS	0.653	0.563	0.751	0.653	0.563	0.751	SUBCLONAL	1	TRUE	1	0.22	2		717	877	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112884087	112884087	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	51	553	0	ENST00000351677.2:c.22C>A	p.His8Asn	p.H8N	ENST00000351677	NM_002834.3	8	Cac/Aac	2/16	1	2	FACETS	0.697	0.592	0.814	0.697	0.592	0.814	SUBCLONAL	1	TRUE	1	0.22	2		553	665	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220511	133220511	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	55	674	0	ENST00000320574.5:c.4202C>T	p.Ser1401Leu	p.S1401L	ENST00000320574	NM_006231.2	1401	tCa/tTa	33/49	1	2	FACETS	0.611	0.521	0.709	0.611	0.521	0.709	SUBCLONAL	1	TRUE	1	0.22	2		674	819	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007798	45007801	+	frameshift_variant	Frame_Shift_Del	DEL	TCTA	TCTA	-	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	65	407	1	ENST00000558401.1:c.248_251del	p.Tyr83SerfsTer19	p.Y83Sfs*19	ENST00000558401	NM_004048.2	82	tTCTAt/tt	2/4	0.219154630748798	1	FACETS	0.99	0.86	1	0.99	0.86	1	CLONAL	1	TRUE	0	0.22	1		408	531	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900469	3900469	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	85	913	0	ENST00000262367.5:c.627G>A	p.Met209Ile	p.M209I	ENST00000262367	NM_004380.2	209	atG/atA	2/31	1	2	FACETS	0.732	0.645	0.825	0.732	0.645	0.825	SUBCLONAL	1	TRUE	1	0.22	2		913	1056	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14031643	14031643	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	56	464	0	ENST00000311895.7:c.1832G>A	p.Gly611Glu	p.G611E	ENST00000311895	NM_005236.2	611	gGa/gAa	9/11	1	2	FACETS	0.822	0.704	0.952	0.822	0.704	0.952	CLONAL	1	TRUE	1	0.22	2		464	619	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038581	14038581	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	35	407	0	ENST00000311895.7:c.1906G>C	p.Glu636Gln	p.E636Q	ENST00000311895	NM_005236.2	636	Gaa/Caa	10/11	1	2	FACETS	0.645	0.528	0.777	0.645	0.528	0.777	SUBCLONAL	1	TRUE	1	0.22	2		407	493	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645450	67645450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	31	451	0	ENST00000264010.4:c.715G>A	p.Glu239Lys	p.E239K	ENST00000264010	NM_006565.3	239	Gag/Aag	3/12	1	2	FACETS	0.513	0.414	0.626	0.513	0.414	0.626	SUBCLONAL	1	TRUE	1	0.22	2		451	549	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16046940	16046940	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	33	426	0	ENST00000268712.3:c.1153G>C	p.Asp385His	p.D385H	ENST00000268712	NM_006311.3	385	Gat/Cat	11/46	0.219154630748798	1	FACETS	0.548	0.446	0.664	0.548	0.446	0.664	SUBCLONAL	1	TRUE	0	0.22	1		426	487	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559770	29559770	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	21	317	0	ENST00000356175.3:c.3367G>C	p.Glu1123Gln	p.E1123Q	ENST00000356175	NM_000267.3	1123	Gaa/Caa	26/57	0.219154630748798	1	FACETS	0.48	0.369	0.609	0.48	0.369	0.609	SUBCLONAL	1	TRUE	0	0.22	1		317	354	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743416	743416	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	37	353	0	ENST00000314574.4:c.725-1G>A		p.X242_splice	ENST00000314574	NM_005433.3	242			1	2	FACETS	0.708	0.583	0.848	0.708	0.583	0.848	SUBCLONAL	1	TRUE	1	0.22	2		353	475	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122754	7122754	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	63	770	0	ENST00000302850.5:c.3400C>G	p.Gln1134Glu	p.Q1134E	ENST00000302850	NM_000208.2	1134	Caa/Gaa	19/22	0.0783336551336039	0	FACETS	0.548	0.473	0.63			1	INDETERMINATE	1	TRUE	0	0.22	0		770	815	SUCCESS
ALK	238	MSKCC	GRCh37	2	29450515	29450515	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	77	817	0	ENST00000389048.3:c.2839G>C	p.Asp947His	p.D947H	ENST00000389048	NM_004304.4	947	Gac/Cac	17/29	0.0783336551336039	0	FACETS	0.617	0.54	0.7			1	INDETERMINATE	1	TRUE	0	0.22	0		817	885	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026084	48026084	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	38	480	0	ENST00000234420.5:c.962C>A	p.Ser321Ter	p.S321*	ENST00000234420	NM_000179.2	321	tCa/tAa	4/10	0.0783336551336039	0	FACETS	0.531	0.439	0.635			1	INDETERMINATE	1	TRUE	0	0.22	0		480	507	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44515806	44515806	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	62	520	0	ENST00000291552.4:c.247G>C	p.Glu83Gln	p.E83Q	ENST00000291552	NM_006758.2	83	Gag/Cag	4/8	1	2	FACETS	0.762	0.657	0.876	0.762	0.657	0.876	SUBCLONAL	1	TRUE	1	0.22	2		520	740	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182631	38182631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	24	348	0	ENST00000396334.3:c.784C>T	p.Gln262Ter	p.Q262*	ENST00000396334	NM_002468.4	262	Cag/Tag	5/5	1	2	FACETS	0.558	0.437	0.698	0.558	0.437	0.698	SUBCLONAL	1	TRUE	1	0.22	2		348	391	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474767	138474767	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	99	590	0	ENST00000289153.2:c.226G>C	p.Asp76His	p.D76H	ENST00000289153	NM_006219.2	76	Gac/Cac	2/22	0.3	2	FACETS	1	0.974	1			1	CLONAL	1	TRUE	NA	0.22	2		590	688	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170009705	170009705	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	75	363	0	ENST00000295797.4:c.1267G>A	p.Glu423Lys	p.E423K	ENST00000295797	NM_002740.5	423	Gaa/Aaa	13/18	0.328417443008515	3	FACETS	1	0.973	1	0.721	0.633	0.815	CLONAL	1	TRUE	1	0.22	3		363	525	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1952827	1952827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201252361	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	49	619	1	ENST00000382891.5:c.1910C>T	p.Ser637Leu	p.S637L	ENST00000382891	NM_133335.3	637	tCg/tTg	10/22	0.0783336551336039	0	FACETS	0.506	0.428	0.593			1	INDETERMINATE	1	TRUE	0	0.22	0		620	686	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519266	137519266	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	38	493	0	ENST00000367739.4:c.1372G>C	p.Asp458His	p.D458H	ENST00000367739	NM_000416.2	458	Gat/Cat	7/7	0.0783336551336039	0	FACETS	0.504	0.416	0.602			1	INDETERMINATE	1	TRUE	0	0.22	0		493	535	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519428	137519428	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	41	299	0	ENST00000367739.4:c.1210G>A	p.Glu404Lys	p.E404K	ENST00000367739	NM_000416.2	404	Gag/Aag	7/7	0.0783336551336039	0	FACETS	0.742	0.619	0.878			1	INDETERMINATE	1	TRUE	0	0.22	0		299	392	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004455	150004455	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	42	612	0	ENST00000253339.5:c.1770A>T	p.Glu590Asp	p.E590D	ENST00000253339		590	gaA/gaT	3/7	0.0783336551336039	0	FACETS	0.465	0.388	0.552			1	INDETERMINATE	1	TRUE	0	0.22	0		612	640	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2952931	2952931	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1460089226	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	62	681	0	ENST00000396946.4:c.3009C>G	p.Ile1003Met	p.I1003M	ENST00000396946	NM_032415.4	1003	atC/atG	22/25	0.0783336551336039	0	FACETS	0.583	0.503	0.671			1	INDETERMINATE	1	TRUE	0	0.22	0		681	754	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374434	81374434	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	27	394	0	ENST00000222390.5:c.628G>C	p.Glu210Gln	p.E210Q	ENST00000222390	NM_000601.4	210	Gaa/Caa	6/18	0.0783336551336039	0	FACETS	0.525	0.417	0.647			1	INDETERMINATE	1	TRUE	0	0.22	0		394	365	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509444	106509444	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	74	669	0	ENST00000359195.3:c.1438T>A	p.Tyr480Asn	p.Y480N	ENST00000359195	NM_002649.2	480	Tac/Aac	2/11	0.0783336551336039	0	FACETS	0.719	0.629	0.816			1	INDETERMINATE	1	TRUE	0	0.22	0		669	730	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341979	8341980	+	splice_acceptor_variant	Splice_Site	DNP	CT	CT	AA	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	26	351	1	ENST00000356435.5:c.4662-2_4662-1delinsTT		p.X1554_splice	ENST00000356435		1554			1	2	FACETS	0.634	0.502	0.785	0.634	0.502	0.785	SUBCLONAL	1	TRUE	1	0.22	2		352	373	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441562	6441562	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	16	154	0	ENST00000356142.4:c.409G>C	p.Asp137His	p.D137H	ENST00000356142	NM_018890.3	137	Gat/Cat	6/7	0.0783336551336039	0	FACETS	0.834	0.622	1			1	INDETERMINATE	1	TRUE	0	0.22	0		154	136	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0038995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	137	523	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.393088064611904	3	FACETS	1	0.947	1	0.528	0.481	0.577	CLONAL	1	TRUE	1	0.458584167983048	3		523	696	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602493	10602493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	142	555	0	ENST00000171111.5:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000171111	NM_203500.1	362	cGg/cAg	3/6	0.458584167983048	5	FACETS	1	0.921	1	0.253	0.23	0.278	CLONAL	1	TRUE	1	0.458584167983048	5		555	1032	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240765	53240765	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	132	365	0	ENST00000375401.3:c.1315G>C	p.Glu439Gln	p.E439Q	ENST00000375401	NM_004187.3	439	Gag/Cag	10/26	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.458584167983048	1		365	316	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256061	16256061	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0038995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	39	525	0	ENST00000375759.3:c.3326C>G	p.Ser1109Ter	p.S1109*	ENST00000375759	NM_015001.2	1109	tCa/tGa	11/15	1	2	FACETS	0.288	0.238	0.344	0.288	0.238	0.344	SUBCLONAL	1	TRUE	1	0.458584167983048	2		525	590	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260843	16260843	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	123	541	0	ENST00000375759.3:c.8108C>A	p.Pro2703Gln	p.P2703Q	ENST00000375759	NM_015001.2	2703	cCa/cAa	11/15	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.458584167983048	2		541	517	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912815	100912815	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	78	362	0	ENST00000325455.5:c.2507G>T	p.Arg836Leu	p.R836L	ENST00000325455	NM_001202474.3	836	cGa/cTa	7/8	1	2	FACETS	0.87	0.769	0.977	0.87	0.769	0.977	CLONAL	1	TRUE	1	0.458584167983048	2		362	391	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416641	121416641	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	177	683	0	ENST00000257555.6:c.70G>C	p.Glu24Gln	p.E24Q	ENST00000257555		24	Gag/Cag	1/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.458584167983048	2		683	659	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416769	121416769	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	217	874	0	ENST00000257555.6:c.198G>C	p.Glu66Asp	p.E66D	ENST00000257555		66	gaG/gaC	1/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.458584167983048	2		874	809	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528205	103528205	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	93	365	0	ENST00000355739.4:c.3513G>C	p.Lys1171Asn	p.K1171N	ENST00000355739	NM_000123.3	1171	aaG/aaC	15/15	0.198640233876875	4	FACETS	1	0.938	1	0.359	0.319	0.4	INDETERMINATE	1	TRUE	1	0.458584167983048	4		365	550	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654731	29654731	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660298	NA	P-0038995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	22	322	0	ENST00000356175.3:c.5420G>A	p.Arg1807Gln	p.R1807Q	ENST00000356175	NM_000267.3	1807	cGg/cAg	37/57	1	2	FACETS	0.231	0.179	0.293	0.231	0.179	0.293	SUBCLONAL	1	TRUE	1	0.458584167983048	2		322	415	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207134	1207134	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	188	809	0	ENST00000326873.7:c.222G>C	p.Arg74Ser	p.R74S	ENST00000326873	NM_000455.4	74	agG/agC	1/10	0.458584167983048	1	FACETS	0.942	0.874	1	0.942	0.874	1	CLONAL	1	TRUE	0	0.458584167983048	1		809	671	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15280929	15280930	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0038995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	125	719	0	ENST00000263388.2:c.5166_5167delinsTT	p.Met1722_Asp1723delinsIleTyr	p.M1722_D1723delinsIY	ENST00000263388	NM_000435.2	1722	atGGac/atTTac	28/33	1	2	FACETS	0.733	0.664	0.805	0.733	0.664	0.805	SUBCLONAL	1	TRUE	1	0.458584167983048	2		719	744	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31372652	31372652	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0038995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	123	523	0	ENST00000328111.2:c.293C>G	p.Ser98Ter	p.S98*	ENST00000328111	NM_006892.3	98	tCa/tGa	4/23	0.458584167983048	3	FACETS	0.924	0.836	1	0.462	0.418	0.508	CLONAL	1	TRUE	1	0.458584167983048	3		523	714	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931445	131931445	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0038995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	97	356	0	ENST00000265335.6:c.2150C>G	p.Ser717Ter	p.S717*	ENST00000265335		717	tCa/tGa	13/25	1	2	FACETS	0.961	0.862	1	0.961	0.862	1	CLONAL	1	TRUE	1	0.458584167983048	2		356	440	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339469	81339469	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	22	320	0	ENST00000222390.5:c.1535G>C	p.Arg512Thr	p.R512T	ENST00000222390	NM_000601.4	512	aGa/aCa	13/18	1	2	FACETS	0.242	0.187	0.306	0.242	0.187	0.306	SUBCLONAL	1	TRUE	1	0.458584167983048	2		320	396	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513354	106513354	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	67	307	0	ENST00000359195.3:c.2258C>G	p.Ser753Cys	p.S753C	ENST00000359195	NM_002649.2	753	tCt/tGt	4/11	1	2	FACETS	0.812	0.709	0.921	0.812	0.709	0.921	CLONAL	1	TRUE	1	0.458584167983048	2		307	360	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965564	90965564	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	66	316	0	ENST00000265433.3:c.1753G>A	p.Glu585Lys	p.E585K	ENST00000265433	NM_002485.4	585	Gaa/Aaa	11/16	0.403638579222954	4	FACETS	0.743	0.645	0.849	0.372	0.322	0.425	SUBCLONAL	1	TRUE	2	0.458584167983048	4		316	565	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907037	101907037	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	44	261	0	ENST00000374994.4:c.997G>C	p.Asp333His	p.D333H	ENST00000374994	NM_004612.2	333	Gat/Cat	6/9	0.393088064611904	3	FACETS	0.776	0.654	0.91	0.388	0.327	0.455	CLONAL	1	TRUE	1	0.458584167983048	3		261	304	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0038996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	603	875	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.838436251142588	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.840101089645572	2		876	705	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374245	138374245	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	117	307	0	ENST00000289153.2:c.3199G>T	p.Asp1067Tyr	p.D1067Y	ENST00000289153	NM_006219.2	1067	Gac/Tac	22/22	0.840101089645572	5	FACETS	0.703	0.633	0.776	0.234	0.211	0.259	SUBCLONAL	1	TRUE	2	0.840101089645572	5		307	896	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873760	35873760	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	243	278	0	ENST00000216797.5:c.91G>C	p.Asp31His	p.D31H	ENST00000216797	NM_020529.2	31	Gac/Cac	1/6	0.722906689203127	4	FACETS	0.843	0.786	0.902	0.281	0.262	0.301	CLONAL	1	TRUE	1	0.840101089645572	4		278	1263	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554368	81554368	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	67	232	0	ENST00000298171.2:c.388T>G	p.Phe130Val	p.F130V	ENST00000298171	NM_000369.2	130	Ttc/Gtc	4/10	1	2	FACETS	0.822	0.728	0.92	0.822	0.728	0.92	CLONAL	1	TRUE	1	0.840101089645572	2		232	194	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923416	9923468	+	frameshift_variant	Frame_Shift_Del	DEL	CCTTTAGGATTCTGGACAGGCACGGAGTTATTGAACACCAGGCCCCAAAGAAG	CCTTTAGGATTCTGGACAGGCACGGAGTTATTGAACACCAGGCCCCAAAGAAG	-	novel	NA	P-0038996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	108	378	0	ENST00000330684.3:c.1819_1871del	p.Leu607AspfsTer20	p.L607Dfs*20	ENST00000330684	NM_001134407.1	607	CTTCTTTGGGGCCTGGTGTTCAATAACTCCGTGCCTGTCCAGAATCCTAAAGGg/g	9/13	1	2	FACETS	0.656	0.593	0.721	0.656	0.593	0.721	SUBCLONAL	1	TRUE	1	0.840101089645572	2		378	392	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228128	36228128	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	295	453	0	ENST00000222270.7:c.7514A>G	p.Asn2505Ser	p.N2505S	ENST00000222270	NM_014727.1	2505	aAt/aGt	33/37	0.457914640953921	6	FACETS	1	0.993	1	0.486	0.456	0.516	INDETERMINATE	1	TRUE	3	0.840101089645572	6		453	1292	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374308	138374308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	121	336	0	ENST00000289153.2:c.3136G>A	p.Asp1046Asn	p.D1046N	ENST00000289153	NM_006219.2	1046	Gat/Aat	22/22	0.840101089645572	5	FACETS	0.702	0.634	0.775	0.234	0.211	0.259	SUBCLONAL	1	TRUE	2	0.840101089645572	5		336	927	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557913	187557914	+	missense_variant	Missense_Mutation	DNP	GG	GG	TC	novel	NA	P-0038996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	162	229	0	ENST00000441802.2:c.3797_3798delinsGA	p.Ala1266Gly	p.A1266G	ENST00000441802	NM_005245.3	1266	gCC/gGA	5/27	0.840101089645572	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.840101089645572	1		229	217	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950802	38950817	+	frameshift_variant	Frame_Shift_Del	DEL	CATCCTCCAATATGAA	CATCCTCCAATATGAA	-	novel	NA	P-0038996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	20	109	0	ENST00000357387.3:c.3133_3148del	p.Phe1045ThrfsTer30	p.F1045Tfs*30	ENST00000357387	NM_152756.3	1045	TTCATATTGGAGGATGac/ac	31/38	0.836094408731781	3	FACETS	0.512	0.396	0.645	0.256	0.198	0.323	SUBCLONAL	1	TRUE	1	0.840101089645572	3		109	132	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608454	28608454	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	AA	novel	NA	P-0038996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	53	293	0	ENST00000241453.7:c.1688delinsTT	p.Cys563PhefsTer9	p.C563Ffs*9	ENST00000241453	NM_004119.2	563	tGt/tTTt	13/24	1	2	FACETS	0.804	0.7	0.912	0.804	0.7	0.912	CLONAL	1	TRUE	1	0.840101089645572	2		293	157	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	274	399	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.817954145899057	2		399	624	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919214	48919214	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0039001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	23	95	0	ENST00000267163.4:c.381-2A>T		p.X127_splice	ENST00000267163	NM_000321.2	127			0.454194178198957	1	FACETS	0.212	0.166	0.263	0.212	0.166	0.263	INDETERMINATE	1	TRUE	0	0.817954145899057	1		95	157	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941180	36941180	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	378	650	1	ENST00000361632.4:c.159C>A	p.Ser53Arg	p.S53R	ENST00000361632		53	agC/agA	3/16	1	2	FACETS	0.939	0.894	0.985	0.939	0.894	0.985	CLONAL	1	TRUE	1	0.817954145899057	2		651	984	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863557	68863557	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs1471460728	NA	P-0039001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	326	411	0	ENST00000261769.5:c.2296G>C	p.Asp766His	p.D766H	ENST00000261769	NM_004360.3	766	Gac/Cac	15/16	0.345171338565298	1	FACETS	0.748	0.713	0.782	0.748	0.713	0.782	INDETERMINATE	1	TRUE	0	0.817954145899057	1		411	630	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801119	135801122	+	frameshift_variant	Frame_Shift_Del	DEL	AAGA	AAGA	-	novel	NA	P-0039001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	180	253	0	ENST00000298552.3:c.215_218del	p.Leu72ArgfsTer25	p.L72Rfs*25	ENST00000298552	NM_001162426.1	72	cTCTTg/cg	5/23	0.817954145899057	1	FACETS	0.993	0.943	1	0.993	0.943	1	CLONAL	1	TRUE	0	0.817954145899057	1		253	262	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574005	7574009	+	frameshift_variant	Frame_Shift_Del	DEL	AACAT	AACAT	-	novel	NA	P-0039001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	349	586	1	ENST00000269305.4:c.1018_1022del	p.Met340ProfsTer5	p.M340Pfs*5	ENST00000269305	NM_001126112.2	340	ATGTTc/c	10/11	0.813766324918255	1	FACETS	0.932	0.896	0.967	0.932	0.896	0.967	CLONAL	1	TRUE	0	0.817954145899057	1		587	541	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	179	703	0	ENST00000397752.3:c.3028G>A	p.Asp1010Asn	p.D1010N	ENST00000397752	NM_000245.2	1010	Gat/Aat	14/21	0.166298276333944	2	FACETS	1	0.987	1	0.673	0.62	0.727	INDETERMINATE	1	TRUE	0	0.287396434484363	2		703	926	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513451	149513451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754451292	NA	P-0039002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	54	474	0	ENST00000261799.4:c.752G>A	p.Arg251His	p.R251H	ENST00000261799	NM_002609.3	251	cGc/cAc	5/23	1	2	FACETS	0.597	0.51	0.694	0.597	0.51	0.694	SUBCLONAL	1	TRUE	1	0.287396434484363	2		474	629	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874713	151874713	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	54	344	2	ENST00000262189.6:c.7825C>T	p.Arg2609Ter	p.R2609*	ENST00000262189	NM_170606.2	2609	Cga/Tga	38/59	0.166298276333944	2	FACETS	0.641	0.547	0.744	0.321	0.273	0.372	INDETERMINATE	1	TRUE	0	0.287396434484363	2		346	586	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741556	17741556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	44	367	1	ENST00000250003.3:c.227G>A	p.Arg76His	p.R76H	ENST00000250003	NM_002478.4	76	cGt/cAt	1/3	1	2	FACETS	0.642	0.538	0.756	0.642	0.538	0.756	SUBCLONAL	1	TRUE	1	0.287396434484363	2		368	477	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468409	89468409	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	50	229	0	ENST00000336596.2:c.1943T>G	p.Ile648Ser	p.I648S	ENST00000336596	NM_005233.5	648	aTt/aGt	11/17	0.287396434484363	7	FACETS	0.811	0.687	0.949			1	CLONAL	1	TRUE	NA	0.287396434484363	7		229	737	SUCCESS
APC	324	MSKCC	GRCh37	5	112174784	112174784	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0039003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	86	290	0	ENST00000257430.4:c.3493A>T	p.Lys1165Ter	p.K1165*	ENST00000257430	NM_000038.5	1165	Aaa/Taa	16/16	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.514493176724003	2		290	311	SUCCESS
APC	324	MSKCC	GRCh37	5	112175789	112175789	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	89	271	0	ENST00000257430.4:c.4501del	p.Ser1501LeufsTer6	p.S1501Lfs*6	ENST00000257430	NM_000038.5	1500	Ttt/tt	16/16	1	2	FACETS	0.848	0.756	0.944	0.848	0.756	0.944	CLONAL	1	TRUE	1	0.514493176724003	2		271	408	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003775	45003775	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs104894481	NA	P-0039003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	235	347	0	ENST00000558401.1:c.31G>C	p.Ala11Pro	p.A11P	ENST00000558401	NM_004048.2	11	Gcg/Ccg	1/4	0.514493176724003	1	FACETS	0.819	0.766	0.874	0.819	0.766	0.874	CLONAL	1	TRUE	0	0.514493176724003	1		347	828	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727456	66727470	+	inframe_deletion	In_Frame_Del	DEL	CAGAAGGTGGGAGAA	CAGAAGGTGGGAGAA	-	novel	NA	P-0039003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	138	354	0	ENST00000307102.5:c.173_187del	p.Gln58_Glu62del	p.Q58_E62del	ENST00000307102	NM_002755.3	58	CAGAAGGTGGGAGAA/-	2/11	0.514493176724003	1	FACETS	0.723	0.661	0.788	0.723	0.661	0.788	SUBCLONAL	1	TRUE	0	0.514493176724003	1		354	551	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282445	115282445	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	162	447	0	ENST00000438362.2:c.205G>T	p.Ala69Ser	p.A69S	ENST00000438362	NM_001242891.1	69	Gca/Tca	3/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.514493176724003	2		447	566	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482820	67482820	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	206	441	0	ENST00000327367.4:c.1224C>A	p.Asp408Glu	p.D408E	ENST00000327367	NM_005902.3	408	gaC/gaA	9/9	0.514493176724003	1	FACETS	0.802	0.746	0.859	0.802	0.746	0.859	CLONAL	1	TRUE	0	0.514493176724003	1		441	742	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39294883	39294883	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	101	355	0	ENST00000402219.2:c.99A>C	p.Gln33His	p.Q33H	ENST00000402219	NM_005633.3	33	caA/caC	2/23	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.514493176724003	2		355	389	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225367723	225367726	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	novel	NA	P-0039003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	126	304	0	ENST00000264414.4:c.1441_1444del	p.Asn481GlnfsTer17	p.N481Qfs*17	ENST00000264414	NM_003590.4	481	AACAca/ca	10/16	1	2	FACETS	0.859	0.781	0.941	0.859	0.781	0.941	CLONAL	1	TRUE	1	0.514493176724003	2		304	570	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959958	38959962	+	frameshift_variant	Frame_Shift_Del	DEL	GTGTT	GTGTT	-	novel	NA	P-0039003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	89	229	0	ENST00000357387.3:c.1970_1974del	p.Gln657LeufsTer16	p.Q657Lfs*16	ENST00000357387	NM_152756.3	657	cAACAC/c	21/38	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.514493176724003	2		229	271	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589213	67589236	+	inframe_deletion	In_Frame_Del	DEL	GTGGTTGAATTAATAAACCACTAC	GTGGTTGAATTAATAAACCACTAC	-	novel	NA	P-0039003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	67	314	0	ENST00000274335.5:c.1201_1224del	p.Val401_Tyr408del	p.V401_Y408del	ENST00000274335		401	GTGGTTGAATTAATAAACCACTAC/-	9/15	0.514493176724003	1	FACETS	0.783	0.689	0.882	0.783	0.689	0.882	SUBCLONAL	1	TRUE	0	0.514493176724003	1		314	247	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20483101	20483101	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	76	283	0	ENST00000346618.3:c.834A>T	p.Gln278His	p.Q278H	ENST00000346618	NM_001949.4	278	caA/caT	4/7	1	2	FACETS	0.433	0.38	0.491	0.433	0.38	0.491	SUBCLONAL	1	TRUE	1	0.514493176724003	2		283	682	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205680	38205680	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	185	486	0	ENST00000317025.8:c.10T>C	p.Ser4Pro	p.S4P	ENST00000317025	NM_023034.1	4	Tct/Cct	2/24	1	2	FACETS	0.929	0.86	1	0.929	0.86	1	CLONAL	1	TRUE	1	0.514493176724003	2		486	774	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549535	5549535	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	197	570	0	ENST00000397747.3:c.562A>G	p.Arg188Gly	p.R188G	ENST00000397747	NM_025239.3	188	Aga/Gga	4/7	1	2	FACETS	0.767	0.71	0.827	0.767	0.71	0.827	SUBCLONAL	1	TRUE	1	0.514493176724003	2		570	998	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257510	16257510	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370305920	NA	P-0039009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	153	426	1	ENST00000375759.3:c.4775G>A	p.Arg1592Gln	p.R1592Q	ENST00000375759	NM_015001.2	1592	cGg/cAg	11/15	1	2	FACETS	0.786	0.723	0.852	1	0.989	1	SUBCLONAL	2	TRUE	1	0.337168931178755	2		427	577	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193121546	193121546	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	61	287	0	ENST00000367435.3:c.944A>G	p.Tyr315Cys	p.Y315C	ENST00000367435	NM_024529.4	315	tAc/tGc	10/17	0.337168931178755	4	FACETS	0.788	0.68	0.906	0.263	0.226	0.302	CLONAL	1	TRUE	1	0.337168931178755	4		287	614	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922201	100922201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1186005749	NA	P-0039009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	70	450	0	ENST00000325455.5:c.2311G>A	p.Val771Ile	p.V771I	ENST00000325455	NM_001202474.3	771	Gtc/Atc	5/8	0.337168931178755	2	FACETS	0.731	0.638	0.831	0.366	0.319	0.416	SUBCLONAL	1	TRUE	0	0.337168931178755	2		450	568	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449508	187449509	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	81	304	0	ENST00000232014.4:c.371_372insA	p.Phe124LeufsTer3	p.F124Lfs*3	ENST00000232014	NM_001130845.1	124	ttt/ttAt	4/10	0.337168931178755	2	FACETS	1	0.951	1	0.569	0.504	0.639	CLONAL	1	TRUE	0	0.337168931178755	2		304	422	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985488	2985488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	43	479	0	ENST00000396946.4:c.323G>A	p.Gly108Glu	p.G108E	ENST00000396946	NM_032415.4	108	gGg/gAg	4/25	0.337168931178755	3	FACETS	0.38	0.317	0.45	0.19	0.158	0.225	SUBCLONAL	1	TRUE	1	0.337168931178755	3		479	785	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38314904	38314904	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	78	535	0	ENST00000425967.3:c.160G>T	p.Ala54Ser	p.A54S	ENST00000425967	NM_001174067.1	54	Gct/Tct	3/19	0.279420398526488	4	FACETS	0.771	0.677	0.873	0.257	0.225	0.291	SUBCLONAL	1	TRUE	1	0.337168931178755	4		535	802	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562606	176562606	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	106	566	0	ENST00000439151.2:c.502A>G	p.Met168Val	p.M168V	ENST00000439151	NM_022455.4	168	Atg/Gtg	2/23	0.783768209987761	3	FACETS	0.379	0.339	0.422	0.19	0.169	0.211	SUBCLONAL	1	TRUE	1	0.783768209987761	3		566	993	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	114	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.318385444843976	4	FACETS	0.874	0.792	0.96	0.874	0.792	0.96	CLONAL	2	TRUE	2	0.401625416959725	4		457	455	SUCCESS
EED	8726	MSKCC	GRCh37	11	85967458	85967458	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	89	309	0	ENST00000263360.6:c.456G>T	p.Trp152Cys	p.W152C	ENST00000263360	NM_003797.3	152	tgG/tgT	5/12	0.284556811750249	4	FACETS	0.922	0.825	1	0.922	0.825	1	CLONAL	2	TRUE	2	0.401625416959725	4		309	337	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602926	10602926	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	287	658	1	ENST00000171111.5:c.652G>T	p.Glu218Ter	p.E218*	ENST00000171111	NM_203500.1	218	Gag/Tag	3/6	0.401625416959725	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.401625416959725	2		659	656	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881686	111881686	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	110	508	0	ENST00000393256.3:c.364C>T	p.Gln122Ter	p.Q122*	ENST00000393256	NM_006538.4	122	Cag/Tag	2/4	0.390307798463264	3	FACETS	0.94	0.845	1	0.47	0.422	0.52	CLONAL	1	TRUE	1	0.401625416959725	3		508	700	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675666	30675666	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	260	630	1	ENST00000376406.3:c.2690C>A	p.Ser897Tyr	p.S897Y	ENST00000376406	NM_014641.2	897	tCt/tAt	8/15	0.390307798463264	3	FACETS	0.98	0.922	1	0.98	0.922	1	CLONAL	2	TRUE	1	0.401625416959725	3		631	793	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611146	100611146	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	198	265	1	ENST00000308731.7:c.1460G>C	p.Arg487Thr	p.R487T	ENST00000308731	NM_000061.2	487	aGg/aCg	15/19	0.347859667020592	2	FACETS	0.95	0.897	1			1	CLONAL	3	TRUE	NA	0.401625416959725	2		266	346	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	27	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.761	0.607	0.935	0.761	0.607	0.935	CLONAL	1	TRUE	1	0.25	2		457	284	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779451	3779451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886043017	NA	P-0039020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	93	962	1	ENST00000262367.5:c.5597G>A	p.Arg1866His	p.R1866H	ENST00000262367	NM_004380.2	1866	cGc/cAc	31/31	1	2	FACETS	0.862	0.766	0.965	0.862	0.766	0.965	CLONAL	1	TRUE	1	0.25	2		963	863	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0039022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	49	325	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.470367850491949	4	FACETS	1	0.928	1	1	0.928	1	CLONAL	3	TRUE	1	0.470367850491949	4		325	95	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	97	292	0	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	0.470367850491949	4	FACETS	1	0.949	1	1	0.949	1	CLONAL	3	TRUE	1	0.470367850491949	4		292	192	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991337	72991337	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs138667148	NA	P-0039022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	107	515	0	ENST00000268489.5:c.2708C>A	p.Thr903Lys	p.T903K	ENST00000268489	NM_006885.3	903	aCg/aAg	2/10	0.470367850491949	3	FACETS	1	0.92	1	0.513	0.461	0.567	CLONAL	1	TRUE	1	0.470367850491949	3		515	548	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139920	50139920	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757080959	NA	P-0039022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	221	980	1	ENST00000246792.3:c.409G>A	p.Val137Ile	p.V137I	ENST00000246792	NM_006270.3	137	Gtt/Att	4/6	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.470367850491949	2		981	893	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541702	187541702	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	44	305	0	ENST00000441802.2:c.6038T>C	p.Phe2013Ser	p.F2013S	ENST00000441802	NM_005245.3	2013	tTt/tCt	10/27	0.470367850491949	3	FACETS	0.811	0.684	0.949	0.405	0.342	0.475	CLONAL	1	TRUE	1	0.470367850491949	3		305	285	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243053	105243054	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGCGGATGATGAAGGTGTTGGGCCGGGGCCGCTCCGTCTTCA	novel	NA	P-0039024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	234	893	1	ENST00000349310.3:c.188_229dup	p.Arg76_Cys77insLeuLysThrGluArgProArgProAsnThrPheIleIleArg	p.R76_C77insLKTERPRPNTFIIR	ENST00000349310	NM_001014432.1	77	tgc/tTGAAGACGGAGCGGCCCCGGCCCAACACCTTCATCATCCGCTgc	5/15	1	2	FACETS	0.53	0.493	0.568	0.53	0.493	0.568	SUBCLONAL	1	TRUE	1	0.688796965421712	2		894	1283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577010	7577060	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTGCTTACCTCGCTTAGTGCTCCCTGGGGGCAGCTCGTGGTGAGGCTCCC	CTTGCTTACCTCGCTTAGTGCTCCCTGGGGGCAGCTCGTGGTGAGGCTCCC	-	novel	NA	P-0039024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	208	631	0	ENST00000269305.4:c.878_919+9del		p.X293_splice	ENST00000269305	NM_001126112.2	293		8/11	0.688796965421712	1	FACETS	0.902	0.848	0.956	0.902	0.848	0.956	CLONAL	1	TRUE	0	0.688796965421712	1		631	439	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	152	399	0				ENST00000310581	NM_198253.2	-/1132			0.737942024317233	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.737942024317233	1		399	242	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0039025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	991	789	8	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.737942024317233	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.737942024317233	2		797	1246	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0039025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	356	297	2	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	0.737942024317233	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.737942024317233	2		299	472	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044468	128044468	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	180	521	1	ENST00000285398.2:c.1153G>A	p.Asp385Asn	p.D385N	ENST00000285398	NM_000122.1	385	Gac/Aac	8/15	1	2	FACETS	0.887	0.823	0.952	0.887	0.823	0.952	CLONAL	1	TRUE	1	0.737942024317233	2		522	550	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	9	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.274	0.18	0.394	0.274	0.18	0.394	SUBCLONAL	1	TRUE	1	0.184104263770505	2		457	357	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101342	27101342	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	54	713	1	ENST00000324856.7:c.4624G>T	p.Glu1542Ter	p.E1542*	ENST00000324856	NM_006015.4	1542	Gaa/Taa	18/20	1	2	FACETS	0.798	0.68	0.928	0.798	0.68	0.928	CLONAL	1	TRUE	1	0.184104263770505	2		714	735	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284969	15284969	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	75	1025	2	ENST00000263388.2:c.4646C>T	p.Ala1549Val	p.A1549V	ENST00000263388	NM_000435.2	1549	gCg/gTg	25/33	1	2	FACETS	0.845	0.739	0.96	0.845	0.739	0.96	CLONAL	1	TRUE	1	0.184104263770505	2		1027	964	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747086	40747086	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	38	564	0	ENST00000373198.4:c.2996C>A	p.Ser999Tyr	p.S999Y	ENST00000373198	NM_133170.3	999	tCc/tAc	22/32	1	2	FACETS	0.685	0.565	0.819	0.685	0.565	0.819	SUBCLONAL	1	TRUE	1	0.184104263770505	2		564	603	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654633	67654633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	35	379	0	ENST00000264010.4:c.1120A>G	p.Thr374Ala	p.T374A	ENST00000264010	NM_006565.3	374	Act/Gct	6/12	1	2	FACETS	0.767	0.628	0.923	0.767	0.628	0.923	CLONAL	1	TRUE	1	0.184104263770505	2		379	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578254	7578259	+	inframe_deletion	In_Frame_Del	DEL	CTTCCA	CTTCCA	-	novel	NA	P-0039027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	48	647	0	ENST00000269305.4:c.590_595del	p.Val197_Glu198del	p.V197_E198del	ENST00000269305	NM_001126112.2	197	gTGGAAGga/gga	6/11	1	2	FACETS	0.795	0.671	0.932	0.795	0.671	0.932	CLONAL	1	TRUE	1	0.184104263770505	2		647	656	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446232	29446232	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	37	525	1	ENST00000389048.3:c.3335C>A	p.Pro1112Gln	p.P1112Q	ENST00000389048	NM_004304.4	1112	cCg/cAg	20/29	1	2	FACETS	0.708	0.582	0.848	0.708	0.582	0.848	SUBCLONAL	1	TRUE	1	0.184104263770505	2		526	568	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940519	29940519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	27	376	0	ENST00000389048.3:c.712C>T	p.Pro238Ser	p.P238S	ENST00000389048	NM_004304.4	238	Cct/Tct	2/29	1	2	FACETS	0.752	0.598	0.928	0.752	0.598	0.928	CLONAL	1	TRUE	1	0.184104263770505	2		376	390	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46602941	46602941	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	56	695	1	ENST00000263734.3:c.999G>T	p.Gln333His	p.Q333H	ENST00000263734	NM_001430.4	333	caG/caT	8/16	1	2	FACETS	0.803	0.686	0.93	0.803	0.686	0.93	CLONAL	1	TRUE	1	0.184104263770505	2		696	758	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382259	152382259	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	18	239	0	ENST00000206249.3:c.1369G>T	p.Gly457Ter	p.G457*	ENST00000206249	NM_000125.3	457	Gga/Tga	6/8	1	2	FACETS	0.732	0.552	0.945	0.732	0.552	0.945	CLONAL	1	TRUE	1	0.184104263770505	2		239	267	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390704	139390704	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	89	972	0	ENST00000277541.6:c.7487A>G	p.Asn2496Ser	p.N2496S	ENST00000277541	NM_017617.3	2496	aAc/aGc	34/34	1	2	FACETS	0.949	0.839	1	0.949	0.839	1	CLONAL	1	TRUE	1	0.184104263770505	2		972	1019	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0039029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	137	493	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.180499946206709	6	FACETS	1	0.951	1	0.535	0.486	0.586	CLONAL	2	TRUE	2	0.180499946206709	6		493	966	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241678	55241678	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517085	NA	P-0039029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	165	653	0	ENST00000275493.2:c.2126A>C	p.Glu709Ala	p.E709A	ENST00000275493	NM_005228.3	709	gAa/gCa	18/28	0.180499946206709	6	FACETS	1	0.972	1	0.568	0.52	0.617	CLONAL	2	TRUE	2	0.180499946206709	6		653	1096	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872909	35872909	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	39	324	0	ENST00000216797.5:c.323A>G	p.Asn108Ser	p.N108S	ENST00000216797	NM_020529.2	108	aAc/aGc	2/6	1	2	FACETS	0.677	0.56	0.809	0.677	0.56	0.809	SUBCLONAL	1	TRUE	1	0.180499946206709	2		324	638	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030557	48030557	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs1553331242	NA	P-0039029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	21	222	0	ENST00000234420.5:c.3173-2A>T		p.X1058_splice	ENST00000234420	NM_000179.2	1058			0.180499946206709	5	FACETS	0.831	0.639	1	0.277	0.213	0.352	CLONAL	1	TRUE	2	0.180499946206709	5		222	356	SUCCESS
APC	324	MSKCC	GRCh37	5	112175746	112175746	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	19	192	2	ENST00000257430.4:c.4455del	p.Asp1486IlefsTer21	p.D1486Ifs*21	ENST00000257430	NM_000038.5	1485	gcT/gc	16/16	1	2	FACETS	0.902	0.685	1	0.902	0.685	1	CLONAL	1	TRUE	1	0.15	2		194	281	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	90	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.912	0.816	1	0.912	0.816	1	CLONAL	1	TRUE	1	0.538995362492813	2		457	366	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0039042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	265	752	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.538995362492813	3	FACETS	0.921	0.861	0.982	0.46	0.43	0.491	CLONAL	1	TRUE	1	0.538995362492813	3		752	1356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0039042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	270	471	2	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.538995362492813	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.538995362492813	1		473	684	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	190	228	0	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	0.538995362492813	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.538995362492813	2		228	348	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783347	9783347	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148984508	NA	P-0039042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	229	433	1	ENST00000377346.4:c.2591C>T	p.Pro864Leu	p.P864L	ENST00000377346	NM_005026.3	864	cCg/cTg	20/24	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.538995362492813	2		434	827	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561571	9561571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758518559	NA	P-0039042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	246	351	2	ENST00000353224.5:c.211G>A	p.Val71Ile	p.V71I	ENST00000353224	NM_177990.2	71	Gtt/Att	4/10	0.157384791848004	6	FACETS	1	0.989	1	0.823	0.772	0.875	INDETERMINATE	2	TRUE	3	0.538995362492813	6		353	768	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252097	226252099	+	missense_variant	Missense_Mutation	TNP	AGC	AGC	CGT	novel	NA	P-0039042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	35	76	0	ENST00000366813.1:c.45_47delinsCGT	p.Lys15_Ala16delinsAsnVal	p.K15_A16delinsNV	ENST00000366813		15	aaAGCa/aaCGTa	1/3	1	2	FACETS	0.746	0.619	0.885	0.746	0.619	0.885	SUBCLONAL	1	TRUE	1	0.538995362492813	2		76	174	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0039058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	102	283	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.944	0.852	1	0.944	0.852	1	CLONAL	1	TRUE	1	0.612362980394386	2		283	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	457	769	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.612362980394386	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.612362980394386	2		769	698	SUCCESS
APC	324	MSKCC	GRCh37	5	112175536	112175536	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	83	291	0	ENST00000257430.4:c.4245del	p.Ser1415ArgfsTer4	p.S1415Rfs*4	ENST00000257430	NM_000038.5	1415	agT/ag	16/16	1	2	FACETS	0.821	0.731	0.916	0.821	0.731	0.916	CLONAL	1	TRUE	1	0.612362980394386	2		291	330	SUCCESS
APC	324	MSKCC	GRCh37	5	112173730	112173730	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	64	279	0	ENST00000257430.4:c.2442del	p.Phe814LeufsTer6	p.F814Lfs*6	ENST00000257430	NM_000038.5	813	aaT/aa	16/16	1	2	FACETS	0.813	0.712	0.92	0.813	0.712	0.92	CLONAL	1	TRUE	1	0.612362980394386	2		279	257	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114546	73114547	+	splice_acceptor_variant	Splice_Site	DEL	AG	AG	-	novel	NA	P-0039058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	41	201	0	ENST00000356692.5:c.929_930del		p.X310_splice	ENST00000356692		310			1	2	FACETS	0.93	0.79	1	0.93	0.79	1	CLONAL	1	TRUE	1	0.612362980394386	2		201	144	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675097	40675097	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	193	673	1	ENST00000249776.8:c.61G>T	p.Glu21Ter	p.E21*	ENST00000249776	NM_033286.3	21	Gag/Tag	1/9	0.443751059113259	1	FACETS	0.516	0.478	0.556	0.516	0.478	0.556	SUBCLONAL	1	TRUE	0	0.612362980394386	1		674	847	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473726	67473726	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	223	531	0	ENST00000327367.4:c.806T>C	p.Phe269Ser	p.F269S	ENST00000327367	NM_005902.3	269	tTc/tCc	6/9	0.443751059113259	1	FACETS	0.943	0.886	1	0.943	0.886	1	CLONAL	1	TRUE	0	0.612362980394386	1		531	536	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251986	153251986	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	115	391	0	ENST00000281708.4:c.1020del	p.Val341Ter	p.V341*	ENST00000281708	NM_033632.3	340	aaA/aa	7/12	1	2	FACETS	0.914	0.83	1	0.914	0.83	1	CLONAL	1	TRUE	1	0.612362980394386	2		391	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0039059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	23	456	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.471	0.365	0.594	0.471	0.365	0.594	SUBCLONAL	1	TRUE	1	0.13	2		456	752	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413049	139413049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064795070	NA	P-0039059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	30	479	0	ENST00000277541.6:c.1093C>T	p.Arg365Cys	p.R365C	ENST00000277541	NM_017617.3	365	Cgc/Tgc	6/34	1	2	FACETS	0.94	0.756	1	0.94	0.756	1	CLONAL	1	TRUE	1	0.13	2		479	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578204	7578204	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	17	692	1	ENST00000269305.4:c.645T>A	p.Ser215Arg	p.S215R	ENST00000269305	NM_001126112.2	215	agT/agA	6/11	1	2	FACETS	0.339	0.252	0.444	0.339	0.252	0.444	SUBCLONAL	1	TRUE	1	0.13	2		693	771	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	459813	459813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779410726	NA	P-0039059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	44	668	1	ENST00000399788.2:c.1282C>T	p.Arg428Trp	p.R428W	ENST00000399788	NM_001042603.1	428	Cgg/Tgg	10/28	1	2	FACETS	0.995	0.833	1	0.995	0.833	1	CLONAL	1	TRUE	1	0.13	2		669	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782082	NA	P-0039059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	30	586	0	ENST00000269305.4:c.745A>T	p.Arg249Trp	p.R249W	ENST00000269305	NM_001126112.2	249	Agg/Tgg	7/11	1	2	FACETS	0.696	0.559	0.853	0.696	0.559	0.853	SUBCLONAL	1	TRUE	1	0.13	2		586	663	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412663	139412663	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1368532867	NA	P-0039059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	108	720	0	ENST00000277541.6:c.1181G>T	p.Gly394Val	p.G394V	ENST00000277541	NM_017617.3	394	gGc/gTc	7/34	1	2	FACETS	1	0.963	1	1	0.989	1	CLONAL	2	TRUE	1	0.13	2		720	719	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243975	46243975	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	28	452	0	ENST00000334344.6:c.2069C>G	p.Pro690Arg	p.P690R	ENST00000334344	NM_152641.2	690	cCt/cGt	15/21	1	2	FACETS	0.87	0.694	1	0.87	0.694	1	CLONAL	1	TRUE	1	0.13	2		452	495	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482369	56482369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	38	613	0	ENST00000267101.3:c.917C>T	p.Pro306Leu	p.P306L	ENST00000267101	NM_001982.3	306	cCt/cTt	8/28	1	2	FACETS	0.984	0.812	1	0.984	0.812	1	CLONAL	1	TRUE	1	0.13	2		613	594	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412359	139412359	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	37	667	0	ENST00000277541.6:c.1286G>T	p.Cys429Phe	p.C429F	ENST00000277541	NM_017617.3	429	tGc/tTc	8/34	1	2	FACETS	0.837	0.688	1	0.837	0.688	1	CLONAL	1	TRUE	1	0.13	2		667	680	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412690	139412690	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	36	693	1	ENST00000277541.6:c.1154C>A	p.Ser385Tyr	p.S385Y	ENST00000277541	NM_017617.3	385	tCc/tAc	7/34	1	2	FACETS	0.772	0.633	0.93	0.772	0.633	0.93	CLONAL	1	TRUE	1	0.13	2		694	717	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0039061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	210	523	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.382591937555703	3	FACETS	1	0.942	1	1	0.942	1	CLONAL	3	TRUE	0	0.395172817428239	3		523	424	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032155	26032155	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	77	367	0	ENST00000244661.2:c.134G>T	p.Gly45Val	p.G45V	ENST00000244661	NM_003537.3	45	gGc/gTc	1/1	0.38982549672592	3	FACETS	0.886	0.779	1	0.443	0.389	0.5	CLONAL	1	TRUE	1	0.395172817428239	3		367	527	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436624	52436624	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs387906848	NA	P-0039062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	93	535	1	ENST00000460680.1:c.2050C>T	p.Gln684Ter	p.Q684*	ENST00000460680	NM_004656.3	684	Cag/Tag	16/17	0.477269669582323	1	FACETS	0.943	0.848	1	0.943	0.848	1	CLONAL	1	TRUE	0	0.480415696281301	1		536	312	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701248	43701248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773338141	NA	P-0039062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	44	541	0	ENST00000382044.4:c.5447G>A	p.Arg1816Gln	p.R1816Q	ENST00000382044	NM_001141980.1	1816	cGa/cAa	26/28	1	2	FACETS	0.394	0.33	0.464	0.394	0.33	0.464	SUBCLONAL	1	TRUE	1	0.480415696281301	2		541	465	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101427	27101427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	92	552	0	ENST00000324856.7:c.4709C>T	p.Ser1570Phe	p.S1570F	ENST00000324856	NM_006015.4	1570	tCt/tTt	18/20	1	2	FACETS	0.918	0.821	1	0.918	0.821	1	CLONAL	1	TRUE	1	0.480415696281301	2		552	417	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487568	56487568	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	195	533	1	ENST00000267101.3:c.1501G>T	p.Asp501Tyr	p.D501Y	ENST00000267101	NM_001982.3	501	Gac/Tac	13/28	0.475945322861419	3	FACETS	0.991	0.925	1	0.991	0.925	1	CLONAL	2	TRUE	1	0.480415696281301	3		534	508	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434819	128434819	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	104	564	0	ENST00000265960.3:c.35C>A	p.Ala12Asp	p.A12D	ENST00000265960	NM_001006617.1	12	gCt/gAt	2/12	0.480415696281301	2	FACETS	0.854	0.768	0.945	0.427	0.384	0.473	CLONAL	1	TRUE	0	0.480415696281301	2		564	507	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426253	49426253	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	139	799	0	ENST00000301067.7:c.12235C>T	p.Gln4079Ter	p.Q4079*	ENST00000301067	NM_003482.3	4079	Caa/Taa	39/54	0.0843019426102869	4	FACETS	0.879	0.799	0.962	0.879	0.799	0.962	INDETERMINATE	2	TRUE	2	0.20151197978035	4		799	943	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664433	29664433	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	127	428	0	ENST00000356175.3:c.6414del	p.Lys2139AsnfsTer40	p.K2139Nfs*40	ENST00000356175	NM_000267.3	2138	Ccc/cc	42/57	0.20151197978035	3	FACETS	0.948	0.864	1	0.948	0.864	1	CLONAL	3	TRUE	0	0.20151197978035	3		428	488	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897417	78897417	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	227	614	0	ENST00000306801.3:c.2752C>G	p.Pro918Ala	p.P918A	ENST00000306801	NM_020761.2	918	Cct/Gct	23/34	0.20151197978035	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	0	0.20151197978035	3		614	768	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584615	48584615	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1568206107	NA	P-0039063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	27	339	0	ENST00000342988.3:c.787+1G>A		p.X263_splice	ENST00000342988	NM_005359.5	263			0.0944724448759131	3	FACETS	0.843	0.671	1	0.421	0.335	0.52	INDETERMINATE	1	TRUE	1	0.20151197978035	3		339	350	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80024718	80024718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770367587	NA	P-0039063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	19	378	0	ENST00000265081.6:c.1502G>A	p.Cys501Tyr	p.C501Y	ENST00000265081	NM_002439.4	501	tGc/tAc	10/24	0.150417023684532	2	FACETS	0.587	0.446	0.755	0.294	0.223	0.378	SUBCLONAL	1	TRUE	0	0.20151197978035	2		378	321	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265551	152265551	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	93	441	1	ENST00000206249.3:c.1004G>T	p.Arg335Ile	p.R335I	ENST00000206249	NM_000125.3	335	aGa/aTa	4/8	0.12621567358105	3	FACETS	1	0.906	1	0.677	0.604	0.755	CLONAL	2	TRUE	0	0.20151197978035	3		442	500	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739896	41739896	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	41	402	0	ENST00000242208.4:c.77C>A	p.Ser26Tyr	p.S26Y	ENST00000242208	NM_002192.2	26	tCc/tAc	2/3	0.0811685772529047	4	FACETS	1	0.934	1	0.627	0.523	0.742	INDETERMINATE	1	TRUE	2	0.20151197978035	4		402	390	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359076	81359076	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs141751290	NA	P-0039063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	35	327	0	ENST00000222390.5:c.885C>A	p.Asp295Glu	p.D295E	ENST00000222390	NM_000601.4	295	gaC/gaA	8/18	0.0811685772529047	4	FACETS	1	0.917	1	0.607	0.498	0.728	INDETERMINATE	1	TRUE	2	0.20151197978035	4		327	344	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030485	49030485	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	67	243	0	ENST00000267163.4:c.1960G>T	p.Val654Leu	p.V654L	ENST00000267163	NM_000321.2	654	Gtg/Ttg	19/27	0.429336046487003	2	FACETS	1	0.97	1	0.669	0.591	0.75	CLONAL	1	TRUE	0	0.486201967794607	2		243	206	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939373	76939373	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0039064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	218	304	1	ENST00000373344.5:c.1375A>T	p.Lys459Ter	p.K459*	ENST00000373344	NM_000489.3	459	Aag/Tag	9/35	0.370824573641314	2	FACETS	1	0.987	1			1	CLONAL	2	TRUE	NA	0.486201967794607	2		305	390	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0039065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	125	493	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.292617913894947	2		493	844	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0039065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	129	630	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.996	0.903	1	0.996	0.903	1	CLONAL	1	TRUE	1	0.292617913894947	2		630	885	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578218	7578218	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060501198	NA	P-0039065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	77	650	0	ENST00000269305.4:c.631A>G	p.Thr211Ala	p.T211A	ENST00000269305	NM_001126112.2	211	Act/Gct	6/11	1	2	FACETS	0.567	0.497	0.643	0.567	0.497	0.643	SUBCLONAL	1	TRUE	1	0.292617913894947	2		650	928	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47612304	47612304	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0039065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	29	315	0	ENST00000263735.4:c.859-1G>T		p.X287_splice	ENST00000263735	NM_002354.2	287			1	2	FACETS	0.698	0.562	0.852	0.698	0.562	0.852	SUBCLONAL	1	TRUE	1	0.292617913894947	2		315	284	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459501	50459501	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	47	280	0	ENST00000331340.3:c.790C>A	p.Leu264Met	p.L264M	ENST00000331340	NM_006060.4	264	Ctg/Atg	7/8	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		280	355	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0039070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	236	570	0	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	0.562400294172546	2	FACETS	0.999	0.948	1	0.999	0.948	1	CLONAL	2	TRUE	0	0.562400294172546	2		570	420	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858477	57858477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760192848	NA	P-0039070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	156	495	0	ENST00000228682.2:c.215G>A	p.Arg72Gln	p.R72Q	ENST00000228682	NM_005269.2	72	cGg/cAg	4/12	0.562400294172546	4	FACETS	0.824	0.759	0.891	0.824	0.759	0.891	CLONAL	2	TRUE	2	0.562400294172546	4		495	526	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435417	49435475	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCCAGCCCAGCCCCACTCACCTTCTGCACCTTGTTGATGCGGTGAGCTGCCCGGTTAT	CCCCAGCCCAGCCCCACTCACCTTCTGCACCTTGTTGATGCGGTGAGCTGCCCGGTTAT	-	novel	NA	P-0039070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	80	541	0	ENST00000301067.7:c.6197_6234+21del		p.X2066_splice	ENST00000301067	NM_003482.3	2066		30/54	0.562400294172546	4	FACETS	0.994	0.879	1	0.497	0.439	0.559	CLONAL	1	TRUE	2	0.562400294172546	4		541	447	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598101	55598101	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	258	388	0	ENST00000288135.5:c.2298A>T	p.Leu766Phe	p.L766F	ENST00000288135	NM_000222.2	766	ttA/ttT	16/21	0.562400294172546	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	2	0.562400294172546	4		388	699	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533812	533812	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	91	758	0	ENST00000451590.1:c.244T>G	p.Phe82Val	p.F82V	ENST00000451590	NM_001130442.1	82	Ttt/Gtt	3/5	0.169830478550404	1	FACETS	1	0.944	1	1	0.987	1	CLONAL	2	FALSE	0	0.214336395060215	1		758	350	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061140	38061146	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGCTT	CCCGCTT	-	novel	NA	P-0039071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	32	326	0	ENST00000250448.2:c.843_849del	p.Ser282AlafsTer37	p.S282Afs*37	ENST00000250448	NM_004496.3	281	ggAAGCGGG/gg	2/2	0.128076003212612	4	FACETS	1	0.923	1	1	0.923	1	INDETERMINATE	2	FALSE	2	0.214336395060215	4		326	146	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296400	15296400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	72	960	2	ENST00000263388.2:c.2042G>A	p.Cys681Tyr	p.C681Y	ENST00000263388	NM_000435.2	681	tGc/tAc	13/33	0.169830478550404	1	FACETS	0.854	0.752	0.964	1	0.98	1	CLONAL	2	FALSE	0	0.214336395060215	1		962	351	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754809	29754830	+	frameshift_variant	Frame_Shift_Del	DEL	GGATCTCTCTTGCAGCCTCGTT	GGATCTCTCTTGCAGCCTCGTT	-	novel	NA	P-0039071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	27	441	0	ENST00000389048.3:c.1105_1126del	p.Asn369SerfsTer2	p.N369Sfs*2	ENST00000389048	NM_004304.4	369	AACGAGGCTGCAAGAGAGATCCtc/tc	4/29	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	FALSE	1	0.214336395060215	2		441	233	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0039077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	25	622	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.859	0.677	1	0.859	0.677	1	CLONAL	1	TRUE	1	0.16	2		622	364	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs985033810	NA	P-0039077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	33	623	0	ENST00000269305.4:c.731G>T	p.Gly244Val	p.G244V	ENST00000269305	NM_001126112.2	244	gGc/gTc	7/11	1	2	FACETS	0.669	0.543	0.811	0.669	0.543	0.811	SUBCLONAL	1	TRUE	1	0.16	2		623	617	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220706	1220706	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555738475	NA	P-0039077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	55	746	0	ENST00000326873.7:c.727del	p.Val243SerfsTer44	p.V243Sfs*44	ENST00000326873	NM_000455.4	242	Ggg/gg	5/10	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.16	2		746	631	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196270	108196270	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	21	256	0	ENST00000278616.4:c.6806A>T	p.Gln2269Leu	p.Q2269L	ENST00000278616	NM_000051.3	2269	cAg/cTg	46/63	1	2	FACETS	0.67	0.515	0.851	0.67	0.515	0.851	SUBCLONAL	1	TRUE	1	0.16	2		256	392	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145653	11145653	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	60	829	2	ENST00000358026.2:c.4015G>T	p.Glu1339Ter	p.E1339*	ENST00000358026	NM_001128849.1	1339	Gag/Tag	29/36	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.16	2		831	734	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576377	67576377	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs373220196	NA	P-0039077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	15	159	0	ENST00000274335.5:c.656A>G	p.Tyr219Cys	p.Y219C	ENST00000274335		219	tAt/tGt	5/15	1	2	FACETS	0.88	0.645	1	0.88	0.645	1	CLONAL	1	TRUE	1	0.16	2		159	213	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852201	128852201	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	52	869	0	ENST00000249373.3:c.2273G>T	p.Trp758Leu	p.W758L	ENST00000249373	NM_005631.4	758	tGg/tTg	12/12	1	2	FACETS	0.803	0.682	0.937	0.803	0.682	0.937	CLONAL	1	TRUE	1	0.16	2		869	809	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	383	731	2	ENST00000269305.4:c.880del	p.Glu294SerfsTer51	p.E294Sfs*51	ENST00000269305	NM_001126112.2	294	Gag/ag	8/11	0.394740479122297	6	FACETS	1	0.973	1			1	CLONAL	4	FALSE	NA	0.394740479122297	6		733	846	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914790	32914790	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs746661607	NA	P-0039123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	57	497	0	ENST00000380152.3:c.6298C>T	p.Gln2100Ter	p.Q2100*	ENST00000380152		2100	Caa/Taa	11/27	0.382307984732996	2	FACETS	1	0.97	1	0.737	0.642	0.836	CLONAL	1	FALSE	0	0.394740479122297	2		497	196	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17389783	17389783	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	180	763	0	ENST00000359435.4:c.917del	p.Pro306LeufsTer63	p.P306Lfs*63	ENST00000359435	NM_001033549.1	306	Cct/ct	9/9	0.304191037197264	5	FACETS	1	0.956	1	0.697	0.645	0.751	CLONAL	2	FALSE	2	0.394740479122297	5		763	694	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117861252	117861252	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	58	443	0	ENST00000297338.2:c.1637G>C	p.Gly546Ala	p.G546A	ENST00000297338	NM_006265.2	546	gGg/gCg	13/14	0.394740479122297	9	FACETS	0.816	0.703	0.938	0.233	0.2	0.268	CLONAL	2	FALSE	2	0.394740479122297	9		443	429	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123159740	123159740	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	73	382	2	ENST00000218089.9:c.95G>T	p.Gly32Val	p.G32V	ENST00000218089	NM_001042749.1	32	gGa/gTa	4/35	0.394740479122297	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	0	0.394740479122297	1		384	208	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	125	578	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.295512793594442	1	FACETS	0.794	0.723	0.868	0.794	0.723	0.868	INDETERMINATE	1	TRUE	0	0.494748146957642	1		578	479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0039141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	288	803	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.494748146957642	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.494748146957642	1		803	844	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068351	26068360	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TGATTTCTTT	TGATTTCTTT	CTC	novel	NA	P-0039141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	56	429	2	ENST00000435504.4:c.130_139delinsGAG	p.Lys44GlufsTer11	p.K44Efs*11	ENST00000435504		44	AAAGAAATCAga/GAGga	2/13	0.283044762001072	1	FACETS	0.283	0.242	0.328	0.283	0.242	0.328	INDETERMINATE	1	TRUE	0	0.494748146957642	1		431	602	SUCCESS
APC	324	MSKCC	GRCh37	5	112116526	112116527	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATGA	novel	NA	P-0039141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	90	434	0	ENST00000257430.4:c.573_576dup	p.Ala193Ter	p.A193*	ENST00000257430	NM_000038.5	191	tat/tATGAat	6/16	0.494748146957642	1	FACETS	0.719	0.642	0.799	0.719	0.642	0.799	SUBCLONAL	1	TRUE	0	0.494748146957642	1		434	381	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209110083	209110083	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001258-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	53	564	0	ENST00000345146.2:c.480C>G	p.Asp160Glu	p.D160E	ENST00000345146	NM_005896.2	160	gaC/gaG	5/10	0.413388395951674	1	FACETS	0.456	0.395	0.522	0.456	0.395	0.522	INDETERMINATE	1	TRUE	0	0.746508394122808	1		564	195	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415537	152415537	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519714	NA	P-0001258-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	174	406	0	ENST00000206249.3:c.1387T>C	p.Ser463Pro	p.S463P	ENST00000206249	NM_000125.3	463	Tcc/Ccc	7/8	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.746508394122808	2		406	354	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111517	8111518	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0001258-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	301	562	0	ENST00000346208.3:c.1004dup	p.Asp335GlufsTer17	p.D335Efs*17	ENST00000346208		335	gac/gAac	5/6	0.282775551180626	5	FACETS	1	0.985	1	0.736	0.697	0.776	INDETERMINATE	2	TRUE	2	0.746508394122808	5		562	774	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325747	30325749	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0001258-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	54	291	0	ENST00000322652.5:c.1950_1952del	p.Lys650del	p.K650del	ENST00000322652	NM_015355.2	649	AAG/-	16/16	0.280297372971255	1	FACETS	0.55	0.479	0.624	0.55	0.479	0.624	INDETERMINATE	1	TRUE	0	0.746508394122808	1		291	165	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209110083	209110083	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001258-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	273	564	0	ENST00000345146.2:c.480C>G	p.Asp160Glu	p.D160E	ENST00000345146	NM_005896.2	160	gaC/gaG	5/10	0.663012691924828	3	FACETS	1	0.965	1	0.52	0.488	0.552	CLONAL	1	TRUE	1	0.663012691924828	3		564	1055	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415537	152415537	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519714	NA	P-0001258-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	209	406	0	ENST00000206249.3:c.1387T>C	p.Ser463Pro	p.S463P	ENST00000206249	NM_000125.3	463	Tcc/Ccc	7/8	0.648693849257456	3	FACETS	1	0.98	1	0.379	0.353	0.406	CLONAL	1	TRUE	0	0.663012691924828	3		406	738	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111517	8111518	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0001258-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	486	562	0	ENST00000346208.3:c.1004dup	p.Asp335GlufsTer17	p.D335Efs*17	ENST00000346208		335	gac/gAac	5/6	0.362532313587009	6	FACETS	0.897	0.859	0.935	0.897	0.859	0.935	INDETERMINATE	3	TRUE	3	0.663012691924828	6		562	1267	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325747	30325749	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0001258-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	292	291	0	ENST00000322652.5:c.1950_1952del	p.Lys650del	p.K650del	ENST00000322652	NM_015355.2	649	AAG/-	16/16	0.663012691924828	4	FACETS	0.969	0.916	1			1	CLONAL	2	TRUE	NA	0.663012691924828	4		291	756	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619238	37619238	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1461056187	NA	P-0001258-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	58	399	0	ENST00000447079.4:c.914A>G	p.Tyr305Cys	p.Y305C	ENST00000447079	NM_015083.1	305	tAt/tGt	1/14	0.31797220336319	5	FACETS	0.544	0.466	0.628	0.181	0.155	0.21	INDETERMINATE	1	TRUE	2	0.663012691924828	5		399	642	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375001	45375295	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCATAATATGCTATCGAACACCAAAATGCAGGTTCTGAGTAAGTAACTGGCTGTAAATCTGAAAAAGAAAAAAATAAAAAAATAATAAAAGGAAGAAATGCGTGAACAATTCAAGCCAAAAATAGATTTAATATAATCATCTTTACATGCTCTATGCCAGCCTGCACTGGCAAAAGCTCAGGAAGTAGACATAGTATCTGTATCGGTTTCCACAGATGATACCAGATTTTCAGTATTTTTCACACAAAACTCCAGTTTCATAGATCATACCAGATTTTTTCAAATTTCTCCCATG	TCATAATATGCTATCGAACACCAAAATGCAGGTTCTGAGTAAGTAACTGGCTGTAAATCTGAAAAAGAAAAAAATAAAAAAATAATAAAAGGAAGAAATGCGTGAACAATTCAAGCCAAAAATAGATTTAATATAATCATCTTTACATGCTCTATGCCAGCCTGCACTGGCAAAAGCTCAGGAAGTAGACATAGTATCTGTATCGGTTTCCACAGATGATACCAGATTTTCAGTATTTTTCACACAAAACTCCAGTTTCATAGATCATACCAGATTTTTTCAAATTTCTCCCATG	-	novel	NA	P-0001258-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	131	521	0	ENST00000262160.6:c.785-237_842del		p.X262_splice	ENST00000262160	NM_005901.5	262		8/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.663012691924828	2		521	319	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294312	1294312	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs957794083	NA	P-0001258-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	179	495	0	ENST00000310581.5:c.689G>A	p.Arg230Gln	p.R230Q	ENST00000310581	NM_198253.2	230	cGa/cAa	2/16	0.556270380806291	4	FACETS	0.987	0.91	1			1	CLONAL	1	TRUE	NA	0.663012691924828	4		495	910	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0002324-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	278	701	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	FALSE	1	0.879087432334883	2		701	586	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002324-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	251	420	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.482897062033074	5	FACETS	1	0.987	1			1	INDETERMINATE	1	FALSE	NA	0.879087432334883	5		420	1097	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240732	53240732	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002324-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	342	668	0	ENST00000375401.3:c.1348G>C	p.Gly450Arg	p.G450R	ENST00000375401	NM_004187.3	450	Ggc/Cgc	10/26	1	2	FACETS	0.984	0.936	1	0.984	0.936	1	CLONAL	1	FALSE	1	0.879087432334883	2		668	791	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002324-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	303	635	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	1	2	FACETS	0.939	0.89	0.989	0.939	0.89	0.989	CLONAL	1	FALSE	1	0.879087432334883	2		635	734	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94908684	94908684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760970492	NA	P-0002324-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	294	472	0	ENST00000536441.1:c.1370G>A	p.Arg457Gln	p.R457Q	ENST00000536441	NM_144665.3	457	cGg/cAg	9/10	0.879087432334883	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	0	0.879087432334883	1		472	375	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	112	313	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.862787154704113	2		315	250	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0004224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	401	359	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.81179193646615	4	FACETS	0.945	0.924	0.964	0.945	0.924	0.964	CLONAL	4	TRUE	0	0.862787154704113	4		359	458	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123705	11123705	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	579	665	0	ENST00000358026.2:c.2355G>C	p.Lys785Asn	p.K785N	ENST00000358026	NM_001128849.1	785	aaG/aaC	16/36	0.344389230078161	6	FACETS	1	0.99	1	1	0.99	1	INDETERMINATE	3	TRUE	3	0.862787154704113	6		665	1145	SUCCESS
AR	367	MSKCC	GRCh37	X	66766450	66766450	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	235	164	0	ENST00000374690.3:c.1462C>T	p.Gln488Ter	p.Q488*	ENST00000374690	NM_000044.3	488	Cag/Tag	1/8	0.862787154704113	2	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.862787154704113	2		164	258	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0004224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	614	656	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.839141701081915	2	FACETS	0.995	0.977	1	0.995	0.977	1	CLONAL	2	TRUE	0	0.862787154704113	2		656	715	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247367	153247367	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747241612	NA	P-0004224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	280	307	0	ENST00000281708.4:c.1435C>G	p.Arg479Gly	p.R479G	ENST00000281708	NM_033632.3	479	Cga/Gga	10/12	0.826536115470001	4	FACETS	0.951	0.911	0.989	0.951	0.911	0.989	CLONAL	3	TRUE	1	0.862787154704113	4		307	424	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911098	32911098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80358523	NA	P-0004224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	95	420	0	ENST00000380152.3:c.2606C>T	p.Ser869Leu	p.S869L	ENST00000380152		869	tCa/tTa	11/27	0.344389230078161	6	FACETS	0.962	0.876	1	0.962	0.876	1	INDETERMINATE	3	TRUE	3	0.862787154704113	6		420	208	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949038	44949038	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	418	296	0	ENST00000377967.4:c.3599T>G	p.Leu1200Arg	p.L1200R	ENST00000377967	NM_021140.2	1200	cTt/cGt	25/29	0.862787154704113	3	FACETS	1	0.996	1			1	CLONAL	3	TRUE	NA	0.862787154704113	3		296	443	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784035	120784035	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	311	728	0	ENST00000257552.2:c.950C>G	p.Ala317Gly	p.A317G	ENST00000257552	NM_002442.3	317	gCc/gGc	13/15	0.862787154704113	4	FACETS	1	0.964	1	0.515	0.485	0.546	CLONAL	1	TRUE	2	0.862787154704113	4		728	1303	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256685	19256685	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	183	511	0	ENST00000162023.5:c.1028T>G	p.Leu343Arg	p.L343R	ENST00000162023		343	cTc/cGc	13/13	0.344389230078161	6	FACETS	1	0.987	1	0.445	0.41	0.48	INDETERMINATE	1	TRUE	3	0.862787154704113	6		511	867	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034493	47034493	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0004224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	10	314	0	ENST00000377604.3:c.576+2T>A		p.X192_splice	ENST00000377604	NM_001204468.1	192			0.862787154704113	2	FACETS	0.455	0.316	0.619			1	SUBCLONAL	1	TRUE	NA	0.862787154704113	2		314	51	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0004739-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	506	447	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.520815178296154	2	FACETS	0.974	0.937	1	0.974	0.937	1	CLONAL	2	TRUE	0	0.518662342458001	2		447	1002	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0004739-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	693	630	1	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	0.518662342458001	8	FACETS	1	0.994	1	0.897	0.867	0.927	CLONAL	4	TRUE	3	0.518662342458001	8		631	1523	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199431	11199431	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004739-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	175	881	0	ENST00000361445.4:c.5060A>T	p.His1687Leu	p.H1687L	ENST00000361445	NM_004958.3	1687	cAt/cTt	36/58	0.522706179830969	4	FACETS	0.86	0.79	0.933	0.287	0.263	0.311	CLONAL	1	TRUE	1	0.518662342458001	4		881	1192	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263895	133263895	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004739-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	35	452	0	ENST00000320574.5:c.7C>A	p.Leu3Met	p.L3M	ENST00000320574	NM_006231.2	3	Ctg/Atg	1/49	0.522706179830969	3	FACETS	0.274	0.223	0.33	0.091	0.074	0.11	SUBCLONAL	1	TRUE	0	0.518662342458001	3		452	621	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15967433	15967433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004739-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1354	213	755	1	ENST00000268712.3:c.5170C>T	p.Arg1724Trp	p.R1724W	ENST00000268712	NM_006311.3	1724	Cgg/Tgg	35/46	0.518662342458001	6	FACETS	1	0.965	1			1	CLONAL	1	TRUE	NA	0.518662342458001	6		756	1567	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0004742-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	225	636	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.937378644553252	1	FACETS	0.921	0.888	0.951	0.921	0.888	0.951	CLONAL	1	TRUE	0	0.937378644553252	1		637	277	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0004742-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	233	403	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.937378644553252	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.937378644553252	1		403	253	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61712950	61712950	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004742-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	128	410	0	ENST00000401558.2:c.2461C>G	p.Gln821Glu	p.Q821E	ENST00000401558	NM_003400.3	821	Caa/Gaa	20/25	0.60926968973929	3	FACETS	0.518	0.469	0.569	0.173	0.156	0.19	SUBCLONAL	1	TRUE	0	0.937378644553252	3		410	775	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519920	NA	P-0004742-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	207	267	0	ENST00000397062.3:c.85G>C	p.Asp29His	p.D29H	ENST00000397062	NM_006164.4	29	Gat/Cat	2/5	0.481640621111044	3	FACETS	1	0.986	1	0.594	0.556	0.633	INDETERMINATE	1	TRUE	1	0.937378644553252	3		267	546	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750684	128750684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1294281543	NA	P-0004742-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	776	535	0	ENST00000377970.2:c.221C>T	p.Pro74Leu	p.P74L	ENST00000377970	NM_002467.4	74	cCg/cTg	2/3	0.937378644553252	3	FACETS	1	0.976	1			1	CLONAL	2	TRUE	NA	0.937378644553252	3		535	1213	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829423	72829423	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004742-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	540	540	1	ENST00000268489.5:c.7158G>A	p.Met2386Ile	p.M2386I	ENST00000268489	NM_006885.3	2386	atG/atA	9/10	0.922776764373658	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.937378644553252	2		541	574	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925484	114925486	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0004742-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	203	678	0	ENST00000543371.1:c.1562_1564del	p.Leu521_Lys522delinsGln	p.L521_K522delinsQ	ENST00000543371	NM_001198531.1	521	cTGAag/cag	14/14	0.454281864003308	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.937378644553252	0		678	486	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16041505	16041505	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004742-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	60	275	0	ENST00000268712.3:c.1374C>G	p.Asn458Lys	p.N458K	ENST00000268712	NM_006311.3	458	aaC/aaG	13/46	0.937378644553252	1	FACETS	0.349	0.305	0.394	0.349	0.305	0.394	SUBCLONAL	1	TRUE	0	0.937378644553252	1		275	195	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105558	30105558	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004742-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	388	584	0	ENST00000331968.5:c.1128del	p.Asn377ThrfsTer31	p.N377Tfs*31	ENST00000331968	NM_002742.2	376	caG/ca	7/18	0.937378644553252	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.937378644553252	1		584	431	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38137159	38137159	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004742-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1417	225	611	0	ENST00000317025.8:c.3659G>C	p.Arg1220Pro	p.R1220P	ENST00000317025	NM_023034.1	1220	cGc/cCc	21/24	0.937378644553252	4	FACETS	0.566	0.525	0.609			1	SUBCLONAL	1	TRUE	NA	0.937378644553252	4		611	1642	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271165	38271166	+	inframe_insertion	In_Frame_Ins	INS	-	-	CATTGG	novel	NA	P-0004742-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1327	138	507	0	ENST00000425967.3:c.2537_2542dup	p.Ala846_Asn847dup	p.A846_N847dup	ENST00000425967	NM_001174067.1	846	ggc/gCCAATGgc	19/19	0.937378644553252	4	FACETS	0.389	0.353	0.428			1	SUBCLONAL	1	TRUE	NA	0.937378644553252	4		507	1465	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005143-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	29	313	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.623826008847324	2		315	81	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0005143-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	74	359	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.623826008847324	2		359	170	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097631	27097631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005143-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	17	652	1	ENST00000324856.7:c.3220C>T	p.Arg1074Trp	p.R1074W	ENST00000324856	NM_006015.4	1074	Cgg/Tgg	12/20	0.220406019351775	3	FACETS	0.941	0.719	1	0.47	0.359	0.596	INDETERMINATE	1	TRUE	1	0.623826008847324	3		653	76	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361160	70361160	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs79912241	NA	P-0005143-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	17	488	0	ENST00000374080.3:c.6348C>A	p.His2116Gln	p.H2116Q	ENST00000374080		2116	caC/caA	43/45	1	1	FACETS	0.264	0.198	0.341	0.264	0.198	0.341	SUBCLONAL	1	TRUE	0	0.623826008847324	1		488	142	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165020	47165020	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005143-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	12	331	0	ENST00000409792.3:c.1106C>A	p.Ser369Tyr	p.S369Y	ENST00000409792	NM_014159.6	369	tCt/tAt	3/21	1	2	FACETS	0.916	0.669	1	0.916	0.669	1	CLONAL	1	TRUE	1	0.623826008847324	2		331	42	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770626	40770626	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005143-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	19	452	0	ENST00000373198.4:c.2756A>G	p.Gln919Arg	p.Q919R	ENST00000373198	NM_133170.3	919	cAg/cGg	19/32	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.623826008847324	2		452	50	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820754	3820775	+	frameshift_variant	Frame_Shift_Del	DEL	GGGAGTCTGCCCGGAAGACGAC	GGGAGTCTGCCCGGAAGACGAC	-	novel	NA	P-0005143-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	52	1309	1	ENST00000262367.5:c.2676_2697del	p.Ser893ProfsTer27	p.S893Pfs*27	ENST00000262367	NM_004380.2	892	gtGTCGTCTTCCGGGCAGACTCCC/gt	14/31	1	2	FACETS	0.892	0.771	1	0.892	0.771	1	CLONAL	1	TRUE	1	0.623826008847324	2		1310	187	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786956	135786956	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0005143-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	11	375	0	ENST00000298552.3:c.914-1G>A		p.X305_splice	ENST00000298552	NM_001162426.1	305			0.623826008847324	1	FACETS	0.693	0.502	0.906	0.693	0.502	0.906	SUBCLONAL	1	TRUE	0	0.623826008847324	1		375	35	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266102	+	inframe_deletion	In_Frame_Del	DEL	GACTCT	GACTCT	-	novel	NA	P-0006035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	142	432	0	ENST00000349496.5:c.95_100del	p.Asp32_Ser33del	p.D32_S33del	ENST00000349496	NM_001904.3	32	GACTCT/-	3/15	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		432	593	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0006328-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	108	411	0	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	0.34654146989811	2	FACETS	1	0.902	1	0.501	0.451	0.555	CLONAL	1	TRUE	0	0.355524710851021	2		411	606	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434857	99434857	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006328-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	75	397	0	ENST00000268035.6:c.944G>A	p.Gly315Asp	p.G315D	ENST00000268035	NM_000875.3	315	gGc/gAc	3/21	0.300719349734147	3	FACETS	0.817	0.717	0.926	0.409	0.358	0.463	CLONAL	1	TRUE	1	0.355524710851021	3		397	608	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788561	3788561	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006328-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	71	271	0	ENST00000262367.5:c.4393G>A	p.Gly1465Arg	p.G1465R	ENST00000262367	NM_004380.2	1465	Ggg/Agg	26/31	1	2	FACETS	0.979	0.858	1	0.979	0.858	1	CLONAL	1	TRUE	1	0.355524710851021	2		271	408	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89807250	89807252	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs397507553	NA	P-0006328-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	52	362	0	ENST00000389301.3:c.3788_3790del	p.Phe1263del	p.F1263del	ENST00000389301	NM_000135.2	1263	tTCTcc/tcc	38/43	1	2	FACETS	0.549	0.467	0.638	0.549	0.467	0.638	SUBCLONAL	1	TRUE	1	0.355524710851021	2		362	533	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438542	52438542	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006328-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	278	571	0	ENST00000460680.1:c.1177C>T	p.Gln393Ter	p.Q393*	ENST00000460680	NM_004656.3	393	Cag/Tag	12/17	0.340623359189639	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.355524710851021	2		571	734	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150022977	150022977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55945045	NA	P-0006799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	105	610	0	ENST00000253339.5:c.286C>T	p.Arg96Trp	p.R96W	ENST00000253339		96	Cgg/Tgg	1/7	0.237099161783559	3	FACETS	1	0.899	1	0.501	0.449	0.556	CLONAL	1	TRUE	1	0.374196163425503	3		610	665	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606696	29606696	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769910087	NA	P-0006799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	85	537	0	ENST00000389048.3:c.1184G>A	p.Arg395His	p.R395H	ENST00000389048	NM_004304.4	395	cGt/cAt	5/29	1	2	FACETS	0.882	0.782	0.989	0.882	0.782	0.989	CLONAL	1	TRUE	1	0.374196163425503	2		537	515	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021785	71021785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs112795301	NA	P-0006908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	391	400	3	ENST00000318789.4:c.1573C>T	p.Arg525Ter	p.R525*	ENST00000318789	NM_032682.5	525	Cga/Tga	18/21	0.850185926033281	3	FACETS	0.792	0.757	0.826	0.528	0.504	0.551	SUBCLONAL	2	TRUE	0	0.850185926033281	3		403	828	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021785	71021785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs112795301	NA	P-0006908-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	157	400	3	ENST00000318789.4:c.1573C>T	p.Arg525Ter	p.R525*	ENST00000318789	NM_032682.5	525	Cga/Tga	18/21	0.404787994251076	3	FACETS	0.976	0.901	1	0.65	0.601	0.702	CLONAL	2	TRUE	0	0.404787994251076	3		403	478	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944553	71944553	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006908-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	2574	625	0	ENST00000298229.2:c.2109C>G	p.Ile703Met	p.I703M	ENST00000298229	NM_001567.3	703	atC/atG	18/28	0.404787994251076	19	FACETS	0.979	0.967	0.99			1	CLONAL	17	TRUE	NA	0.404787994251076	19		625	3395	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223162	41223162	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006908-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	103	675	0	ENST00000357654.3:c.4769T>G	p.Val1590Gly	p.V1590G	ENST00000357654	NM_007294.3	1590	gTt/gGt	15/23	0.404787994251076	3	FACETS	0.684	0.611	0.761	0.342	0.305	0.381	SUBCLONAL	1	TRUE	1	0.404787994251076	3		675	895	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728742	39728742	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006908-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	114	506	0	ENST00000361337.2:c.1022G>A	p.Cys341Tyr	p.C341Y	ENST00000361337	NM_003286.2	341	tGt/tAt	12/21	0.404787994251076	4	FACETS	0.93	0.837	1	0.465	0.418	0.514	CLONAL	1	TRUE	2	0.404787994251076	4		506	851	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021785	71021785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs112795301	NA	P-0006908-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	169	400	3	ENST00000318789.4:c.1573C>T	p.Arg525Ter	p.R525*	ENST00000318789	NM_032682.5	525	Cga/Tga	18/21	0.457807197502536	3	FACETS	0.98	0.91	1	0.653	0.607	0.701	CLONAL	2	TRUE	0	0.474081209651453	3		403	450	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944553	71944553	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006908-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	1115	625	0	ENST00000298229.2:c.2109C>G	p.Ile703Met	p.I703M	ENST00000298229	NM_001567.3	703	atC/atG	18/28	0.474081209651453	11	FACETS	0.958	0.937	0.978			1	CLONAL	9	TRUE	NA	0.474081209651453	11		625	1710	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407519	407519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006908-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	95	548	0	ENST00000380956.4:c.1277G>A	p.Arg426Lys	p.R426K	ENST00000380956	NM_001195286.1	426	aGg/aAg	9/9	0.186432117189238	5	FACETS	1	0.955	1			1	INDETERMINATE	1	TRUE	NA	0.474081209651453	5		548	603	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560139	29560139	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006908-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	90	353	0	ENST00000356175.3:c.3616G>T	p.Glu1206Ter	p.E1206*	ENST00000356175	NM_000267.3	1206	Gag/Tag	27/57	0.474081209651453	5	FACETS	1	0.904	1	0.34	0.302	0.381	CLONAL	1	TRUE	2	0.474081209651453	5		353	637	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93627350	93627350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756047567	NA	P-0007237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	77	356	0	ENST00000375746.1:c.817C>T	p.Arg273Cys	p.R273C	ENST00000375746	NM_001174167.1	273	Cgt/Tgt	6/14	1	2	FACETS	0.645	0.565	0.731	0.645	0.565	0.731	SUBCLONAL	1	FALSE	1	0.273901707063964	2		356	872	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046743	180046743	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	93	221	1	ENST00000261937.6:c.2569G>T	p.Gly857Trp	p.G857W	ENST00000261937	NM_182925.4	857	Ggg/Tgg	18/30	0.210917578666424	2	FACETS	0.996	0.886	1	0.498	0.443	0.557	CLONAL	1	FALSE	0	0.273901707063964	2		222	682	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281322	15281322	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	96	201	0	ENST00000263388.2:c.4934C>G	p.Pro1645Arg	p.P1645R	ENST00000263388	NM_000435.2	1645	cCa/cGa	27/33	1	2	FACETS	0.943	0.841	1	0.943	0.841	1	CLONAL	1	FALSE	1	0.273901707063964	2		201	743	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0007702-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	302	495	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	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.955861187471297	2		495	629	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594258	55594258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913523	NA	P-0007702-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	182	542	0	ENST00000288135.5:c.1961T>C	p.Val654Ala	p.V654A	ENST00000288135	NM_000222.2	654	gTg/gCg	13/21	1	2	FACETS	0.495	0.457	0.533	0.495	0.457	0.533	SUBCLONAL	1	TRUE	1	0.955861187471297	2		542	770	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913237	NA	P-0007884-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	23	403	0	ENST00000369535.4:c.35G>C	p.Gly12Ala	p.G12A	ENST00000369535	NM_002524.4	12	gGt/gCt	2/7	0.148084179161482	3	FACETS	0.138	0.106	0.174	0.069	0.053	0.087	INDETERMINATE	1	FALSE	1	0.382993443949085	3		403	1039	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599321	55599321	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913507	NA	P-0007884-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	53	507	0	ENST00000288135.5:c.2447A>T	p.Asp816Val	p.D816V	ENST00000288135	NM_000222.2	816	gAc/gTc	17/21	0.382993443949085	1	FACETS	0.565	0.483	0.654	0.565	0.483	0.654	SUBCLONAL	1	FALSE	0	0.382993443949085	1		507	396	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259334	89259334	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007884-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	38	551	1	ENST00000336596.2:c.478C>A	p.Arg160Ser	p.R160S	ENST00000336596	NM_005233.5	160	Cgt/Agt	3/17	1	2	FACETS	0.514	0.425	0.613	0.514	0.425	0.613	SUBCLONAL	1	FALSE	1	0.382993443949085	2		552	386	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340138	116340138	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	108	284	0	ENST00000397752.3:c.1000G>C	p.Gly334Arg	p.G334R	ENST00000397752	NM_000245.2	334	Gga/Cga	2/21	0.158873737261092	3	FACETS	1	0.966	1	0.581	0.523	0.641	INDETERMINATE	1	TRUE	1	0.45799283700115	3		284	499	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931463	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622007	NA	P-0008339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	209	261	1	ENST00000374690.3:c.2105T>A	p.Leu702His	p.L702H	ENST00000374690	NM_000044.3	702	cTc/cAc	4/8	1	1	FACETS	1	0.974	1	1	0.994	1	CLONAL	2	TRUE	0	0.32	1		262	512	SUCCESS
AR	367	MSKCC	GRCh37	X	66943552	66943552	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137852578	NA	P-0008339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	71	163	0	ENST00000374690.3:c.2632A>G	p.Thr878Ala	p.T878A	ENST00000374690	NM_000044.3	878	Act/Gct	8/8	1	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.32	1		163	331	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051246	128051246	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	98	470	0	ENST00000285398.2:c.77A>G	p.Glu26Gly	p.E26G	ENST00000285398	NM_000122.1	26	gAa/gGa	2/15	1	2	FACETS	0.879	0.784	0.979	0.879	0.784	0.979	CLONAL	1	TRUE	1	0.32	2		470	697	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061221	38061232	+	inframe_deletion	In_Frame_Del	DEL	GTTCTCGAACAT	GTTCTCGAACAT	-	novel	NA	P-0008339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	70	351	0	ENST00000250448.2:c.757_768del	p.Met253_Asn256del	p.M253_N256del	ENST00000250448	NM_004496.3	253	ATGTTCGAGAAC/-	2/2	1	2	FACETS	0.819	0.715	0.931	0.819	0.715	0.931	CLONAL	1	TRUE	1	0.32	2		351	534	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917733	29917733	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs772219619	NA	P-0008339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	96	543	0	ENST00000389048.3:c.935C>A	p.Ser312Tyr	p.S312Y	ENST00000389048	NM_004304.4	312	tCt/tAt	3/29	1	2	FACETS	0.754	0.671	0.842	0.754	0.671	0.842	SUBCLONAL	1	TRUE	1	0.32	2		543	796	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0008559-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	54	367	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.492432641894802	3	FACETS	0.887	0.775	1	0.887	0.775	1	CLONAL	2	TRUE	1	0.517970718464746	3		367	148	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008559-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	84	548	1	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	0.478452920465807	1	FACETS	0.932	0.835	1	0.932	0.835	1	CLONAL	1	TRUE	0	0.517970718464746	1		549	258	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027248	49027248	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0008559-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	59	327	0	ENST00000267163.4:c.1814+1G>A		p.X605_splice	ENST00000267163	NM_000321.2	605			0.508996228085322	2	FACETS	0.99	0.884	1	0.99	0.884	1	CLONAL	2	TRUE	0	0.517970718464746	2		327	115	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747889	41747889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772358257	NA	P-0008559-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	59	324	1	ENST00000226382.2:c.880G>A	p.Val294Ile	p.V294I	ENST00000226382	NM_003924.3	294	Gtc/Atc	3/3	1	2	FACETS	0.726	0.628	0.83	0.726	0.628	0.83	SUBCLONAL	1	TRUE	1	0.517970718464746	2		325	314	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600336	10600336	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs751088754	NA	P-0008559-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	81	571	1	ENST00000171111.5:c.1519C>T	p.Arg507Ter	p.R507*	ENST00000171111	NM_203500.1	507	Cga/Tga	4/6	0.517970718464746	1	FACETS	0.81	0.722	0.903	0.81	0.722	0.903	CLONAL	1	TRUE	0	0.517970718464746	1		572	286	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666400	206666400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008559-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	41	531	1	ENST00000367120.3:c.1880C>T	p.Ser627Phe	p.S627F	ENST00000367120	NM_014002.3	627	tCt/tTt	19/22	0.517970718464746		FACETS		0.286	0.41				SUBCLONAL	1	TRUE	1	0.517970718464746	4		532	698	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12043972	12043972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008559-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	11	221	0	ENST00000396373.4:c.1351G>A	p.Glu451Lys	p.E451K	ENST00000396373	NM_001987.4	451	Gaa/Aaa	8/8	0.517970718464746	1	FACETS	0.208	0.144	0.288	0.208	0.144	0.288	SUBCLONAL	1	TRUE	0	0.517970718464746	1		221	151	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861264	57861264	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008559-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	50	423	1	ENST00000228682.2:c.1061G>T	p.Arg354Leu	p.R354L	ENST00000228682	NM_005269.2	354	cGg/cTg	9/12	1	2	FACETS	0.631	0.538	0.731	0.631	0.538	0.731	SUBCLONAL	1	TRUE	1	0.517970718464746	2		424	306	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379685	17379685	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371905545	NA	P-0008559-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	88	510	1	ENST00000359435.4:c.70C>T	p.Arg24Trp	p.R24W	ENST00000359435	NM_001033549.1	24	Cgg/Tgg	2/9	0.337109365939861	5	FACETS	0.86	0.762	0.965			1	CLONAL	1	TRUE	NA	0.517970718464746	5		511	702	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250606	99250849	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGCCAGCTAACTGGTTAGCCACCTAAACTGTCAGTCTGCAACCCACAGCTCTGCAGTGAACAATTGAACCTCATTTCTTTAATAATAATACAGGATTCCTGAAAACCAACTGTATTATTGTTTGGAAAATAGTTTAAAAATTATTTCCTTCTAACTGAGACGTTTACCCTCTTGTCTCCCTTCAGTCTGCGGGCCAGGCATCGACATCCGCAACGACTATCAGCAGCTGAAGCGCCTGGAGAAC	TGCCAGCTAACTGGTTAGCCACCTAAACTGTCAGTCTGCAACCCACAGCTCTGCAGTGAACAATTGAACCTCATTTCTTTAATAATAATACAGGATTCCTGAAAACCAACTGTATTATTGTTTGGAAAATAGTTTAAAAATTATTTCCTTCTAACTGAGACGTTTACCCTCTTGTCTCCCTTCAGTCTGCGGGCCAGGCATCGACATCCGCAACGACTATCAGCAGCTGAAGCGCCTGGAGAAC	-	novel	NA	P-0008569-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	70	12	0	ENST00000268035.6:c.95-182_156del		p.X32_splice	ENST00000268035	NM_000875.3	32		2/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		12	92	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148936	119148936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	91	524	1	ENST00000264033.4:c.1156G>A	p.Glu386Lys	p.E386K	ENST00000264033	NM_005188.3	386	Gaa/Aaa	8/16	0.288261281261154	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.32200306019064	1		525	345	SUCCESS
AR	367	MSKCC	GRCh37	X	66937417	66937417	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	148	365	0	ENST00000374690.3:c.2271T>A	p.Asn757Lys	p.N757K	ENST00000374690	NM_000044.3	757	aaT/aaA	5/8	0.32200306019064	2	FACETS	0.886	0.821	0.951			1	CLONAL	3	TRUE	NA	0.32200306019064	2		365	346	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925435	114925435	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs375657594	NA	P-0008842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	271	750	2	ENST00000543371.1:c.1513C>T	p.Arg505Ter	p.R505*	ENST00000543371	NM_001198531.1	505	Cga/Tga	14/14	0.489903932251263	2	FACETS	0.854	0.8	0.909	0.427	0.4	0.455	CLONAL	1	TRUE	0	0.489903932251263	2		752	1296	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879657	37879657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377979176	NA	P-0008842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	133	283	0	ENST00000269571.5:c.2032C>T	p.Arg678Trp	p.R678W	ENST00000269571		678	Cgg/Tgg	17/27	0.489903932251263	3	FACETS	0.899	0.817	0.985	0.449	0.408	0.493	CLONAL	1	TRUE	1	0.489903932251263	3		283	752	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0008885-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	320	835	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.295969768654691	2	FACETS	0.942	0.89	0.995	0.942	0.89	0.995	CLONAL	2	TRUE	0	0.31	2		835	1096	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775907	9775907	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008885-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	155	356	0	ENST00000377346.4:c.371G>A	p.Gly124Asp	p.G124D	ENST00000377346	NM_005026.3	124	gGc/gAc	5/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.31	2		356	769	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133748326	133748326	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs753103329	NA	P-0008885-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	208	439	0	ENST00000318560.5:c.987G>T	p.Glu329Asp	p.E329D	ENST00000318560	NM_005157.4	329	gaG/gaT	6/11	0.256921900803837	2	FACETS	0.827	0.77	0.887	0.827	0.77	0.887	CLONAL	2	TRUE	0	0.31	2		439	811	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0008978-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	360	952	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.41171582845289	5	FACETS	1	0.98	1			1	CLONAL	3	TRUE	NA	0.41171582845289	5		952	893	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0008978-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	311	447	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.340750075452557	3	FACETS	1	0.989	1	0.774	0.733	0.814	CLONAL	2	TRUE	0	0.41171582845289	3		447	785	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0008978-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	467	846	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.41171582845289	5	FACETS	0.923	0.882	0.964			1	CLONAL	3	TRUE	NA	0.41171582845289	5		846	1325	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976922	18976922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008978-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	77	847	1	ENST00000262803.5:c.3307G>A	p.Gly1103Arg	p.G1103R	ENST00000262803	NM_002911.3	1103	Gga/Aga	23/24	1	2	FACETS	0.521	0.457	0.59	0.521	0.457	0.59	SUBCLONAL	1	TRUE	1	0.41171582845289	2		848	718	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249092	55249092	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008978-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1285	93	878	0	ENST00000275493.2:c.2390G>C	p.Cys797Ser	p.C797S	ENST00000275493	NM_005228.3	797	tGc/tCc	20/28	0.41171582845289	5	FACETS	0.53	0.47	0.596			1	SUBCLONAL	1	TRUE	NA	0.41171582845289	5		878	1378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0008995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	421	316	0	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.308471724602869	4	FACETS	1	0.993	1	0.865	0.83	0.9	CLONAL	3	TRUE	0	0.431097853836669	4		316	808	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599338	55599338	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	54	396	0	ENST00000288135.5:c.2464A>T	p.Asn822Tyr	p.N822Y	ENST00000288135	NM_000222.2	822	Aat/Tat	17/21	0.260999644769057	3	FACETS	1	0.959	1	0.656	0.567	0.752	CLONAL	1	TRUE	1	0.431097853836669	3		396	232	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680683	30680683	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	65	387	0	ENST00000376406.3:c.1036C>G	p.Pro346Ala	p.P346A	ENST00000376406	NM_014641.2	346	Cct/Gct	5/15	1	2	FACETS	0.831	0.719	0.954	0.831	0.719	0.954	CLONAL	1	TRUE	1	0.171258369124679	2		387	913	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55209982	55209982	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	78	283	2	ENST00000275493.2:c.92G>T	p.Cys31Phe	p.C31F	ENST00000275493	NM_005228.3	31	tGc/tTc	2/28	0.103106740057665	4	FACETS	1	0.948	1	0.577	0.506	0.654	CLONAL	1	TRUE	2	0.171258369124679	4		285	924	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843546	3843546	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	48	255	0	ENST00000262367.5:c.1057C>G	p.Leu353Val	p.L353V	ENST00000262367	NM_004380.2	353	Ctg/Gtg	4/31	0.171258369124679	2	FACETS	0.925	0.781	1	0.463	0.39	0.542	CLONAL	1	TRUE	0	0.171258369124679	2		255	606	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003192	42003192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764724458	NA	P-0009797-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	261	825	1	ENST00000219905.7:c.2729G>A	p.Arg910Gln	p.R910Q	ENST00000219905	NM_001164273.1	910	cGa/cAa	8/24	1	2	FACETS	0.766	0.715	0.818	0.766	0.715	0.818	SUBCLONAL	1	TRUE	1	0.456646138219459	2		826	1493	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979532	55979532	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1205	151	580	0	ENST00000263923.4:c.915C>A	p.Tyr305Ter	p.Y305*	ENST00000263923	NM_002253.2	305	taC/taA	7/30	0.285575678040858	1	FACETS	0.274	0.25	0.3	0.274	0.25	0.3	INDETERMINATE	1	TRUE	0	0.577761502268923	1		580	1356	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564631	139564631	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	241	472	0	ENST00000308874.7:c.420A>C	p.Glu140Asp	p.E140D	ENST00000308874		140	gaA/gaC	7/10	0.554346679643215	2	FACETS	0.708	0.66	0.757	0.354	0.33	0.379	SUBCLONAL	1	TRUE	0	0.577761502268923	2		472	1179	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947823	178947823	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010972-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1364	114	568	0	ENST00000263967.3:c.2698T>A	p.Ser900Thr	p.S900T	ENST00000263967	NM_006218.2	900	Tca/Aca	19/21	0.347726229916184	3	FACETS	0.491	0.44	0.545	0.245	0.22	0.273	SUBCLONAL	1	TRUE	1	0.372874627107904	3		568	1478	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0010974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	23	482	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.147207379974012	2		482	256	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	123	313	2				ENST00000310581	NM_198253.2	-/1132			0.147207379974012	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	3	TRUE	0	0.147207379974012	3		315	535	SUCCESS
APC	324	MSKCC	GRCh37	5	112103020	112103020	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	63	399	0	ENST00000257430.4:c.355C>G	p.Pro119Ala	p.P119A	ENST00000257430	NM_000038.5	119	Cca/Gca	4/16	1	2	FACETS	1	0.935	1	1	0.981	1	CLONAL	2	TRUE	1	0.147207379974012	2		399	380	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197187	26197187	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	37	433	0	ENST00000356476.2:c.292G>C	p.Glu98Gln	p.E98Q	ENST00000356476		98	Gag/Cag	1/1	1	2	FACETS	0.848	0.698	1	0.848	0.698	1	CLONAL	1	TRUE	1	0.147207379974012	2		433	593	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680695	30680695	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	49	537	0	ENST00000376406.3:c.1024C>T	p.Pro342Ser	p.P342S	ENST00000376406	NM_014641.2	342	Cca/Tca	5/15	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.147207379974012	2		537	650	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610074	81610074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	36	335	0	ENST00000298171.2:c.1672G>A	p.Val558Met	p.V558M	ENST00000298171	NM_000369.2	558	Gtg/Atg	10/10	1	2	FACETS	0.849	0.697	1	0.849	0.697	1	CLONAL	1	TRUE	1	0.147207379974012	2		335	576	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821416	32821416	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	60	663	0	ENST00000354258.4:c.178C>A	p.Pro60Thr	p.P60T	ENST00000354258	NM_000593.5	60	Cca/Aca	1/11	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.147207379974012	2		663	726	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0011136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	502	918	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.526649991252375	4	FACETS	1	0.995	1	0.871	0.842	0.901	CLONAL	3	TRUE	0	0.526649991252375	4		919	835	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790455	3790455	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783490	NA	P-0011136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	141	500	0	ENST00000262367.5:c.4078C>T	p.Arg1360Ter	p.R1360*	ENST00000262367	NM_004380.2	1360	Cga/Tga	24/31	0.440233449039193	3	FACETS	0.806	0.735	0.881	0.403	0.367	0.441	CLONAL	1	TRUE	1	0.526649991252375	3		500	839	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259192	36259192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	301	504	0	ENST00000300305.3:c.299C>T	p.Ser100Phe	p.S100F	ENST00000300305		100	tCc/tTc	3/8	0.379826678049187	3	FACETS	0.933	0.883	0.983	0.622	0.589	0.656	CLONAL	2	TRUE	0	0.526649991252375	3		504	774	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163522	108163522	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0011136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	103	329	1	ENST00000278616.4:c.4611+2T>C		p.X1537_splice	ENST00000278616	NM_000051.3	1537			0.471444227691505	1	FACETS	0.961	0.871	1	0.961	0.871	1	CLONAL	1	TRUE	0	0.526649991252375	1		330	300	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495355	149495355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600485	NA	P-0011136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	97	509	0	ENST00000261799.4:c.3292C>T	p.Arg1098Trp	p.R1098W	ENST00000261799	NM_002609.3	1098	Cgg/Tgg	23/23	0.35191726856595	1	FACETS	0.537	0.481	0.597	0.537	0.481	0.597	SUBCLONAL	1	TRUE	0	0.526649991252375	1		509	505	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089727	27089727	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	127	423	0	ENST00000324856.7:c.2683C>T	p.Gln895Ter	p.Q895*	ENST00000324856	NM_006015.4	895	Caa/Taa	8/20	1	2	FACETS	0.807	0.733	0.883	0.807	0.733	0.883	CLONAL	1	TRUE	1	0.526649991252375	2		423	598	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799156	42799156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778746549	NA	P-0011421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	34	328	0	ENST00000575354.2:c.4640C>T	p.Pro1547Leu	p.P1547L	ENST00000575354	NM_015125.3	1547	cCt/cTt	20/20	0.1896944129663	2	FACETS	0.602	0.491	0.728	0.301	0.245	0.364	SUBCLONAL	1	TRUE	0	0.1896944129663	2		328	595	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40761115	40761116	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCAGGCAGCGTATGACAAAGGTGTTGGCG	novel	NA	P-0011429-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	259	913	0	ENST00000392038.2:c.236_237insCGCCAACACCTTTGTCATACGCTGCCTGCA	p.Leu78_Gln79insHisAlaAsnThrPheValIleArgCysLeu	p.L78_Q79insHANTFVIRCL	ENST00000392038	NM_001626.4	79	cag/caCGCCAACACCTTTGTCATACGCTGCCTGCAg	4/14	1	2	FACETS	0.599	0.56	0.64	0.599	0.56	0.64	SUBCLONAL	1	TRUE	1	0.617553679237357	2		913	1400	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792784	33792785	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0011429-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	86	132	0	ENST00000498907.2:c.536dup	p.Tyr181LeufsTer140	p.Y181Lfs*140	ENST00000498907	NM_004364.3	179	ttc/ttTc	1/1	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.617553679237357	2		132	244	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0011430-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	961	823	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.690680621312548	3	FACETS	0.983	0.964	1	0.983	0.964	1	CLONAL	3	TRUE	0	0.702662944627884	3		823	1254	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878512	151878512	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011430-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1555	92	532	0	ENST00000262189.6:c.6433T>G	p.Tyr2145Asp	p.Y2145D	ENST00000262189	NM_170606.2	2145	Tat/Gat	36/59	0.624954416308378	4	FACETS	0.271	0.239	0.305	0.135	0.119	0.153	SUBCLONAL	1	TRUE	2	0.702662944627884	4		532	1647	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474419	40474420	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0011466-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	55	807	1	ENST00000264657.5:c.1981_1982delinsTT	p.Asp661Phe	p.D661F	ENST00000264657	NM_139276.2	661	GAt/TTt	21/24	1	2	FACETS	0.737	0.629	0.856	0.737	0.629	0.856	SUBCLONAL	1	TRUE	1	0.17	2		808	878	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922364	178922364	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012601-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	9	483	0	ENST00000263967.3:c.1133G>T	p.Cys378Phe	p.C378F	ENST00000263967	NM_006218.2	378	tGt/tTt	6/21	1	2	FACETS	0.166	0.109	0.24	0.166	0.109	0.24	SUBCLONAL	1	TRUE	1	0.29	2		483	373	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0012601-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	44	794	1	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	0.687	0.576	0.808	0.687	0.576	0.808	SUBCLONAL	1	TRUE	1	0.29	2		795	442	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0012649-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	101	918	1	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	0.363016891671905	2		919	553	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602446	10602446	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012649-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	321	581	0	ENST00000171111.5:c.1132G>T	p.Gly378Cys	p.G378C	ENST00000171111	NM_203500.1	378	Ggc/Tgc	3/6	0.363016891671905	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.363016891671905	2		581	799	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40761161	40761161	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012649-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	134	458	0	ENST00000392038.2:c.191A>T	p.Lys64Met	p.K64M	ENST00000392038	NM_001626.4	64	aAg/aTg	4/14	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.363016891671905	2		458	691	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670816	134670816	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012649-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	98	373	0	ENST00000398015.3:c.727G>T	p.Asp243Tyr	p.D243Y	ENST00000398015	NM_004441.4	243	Gat/Tat	3/16	1	2	FACETS	0.969	0.867	1	0.969	0.867	1	CLONAL	1	TRUE	1	0.363016891671905	2		373	557	SUCCESS
ATR	545	MSKCC	GRCh37	3	142241612	142241612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012649-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	90	440	0	ENST00000350721.4:c.4224del	p.Asp1409IlefsTer46	p.D1409Ifs*46	ENST00000350721	NM_001184.3	1408	gcT/gc	23/47	1	2	FACETS	0.782	0.695	0.875	0.782	0.695	0.875	SUBCLONAL	1	TRUE	1	0.363016891671905	2		440	634	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185186	123185186	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012649-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	120	434	1	ENST00000218089.9:c.1138C>A	p.Leu380Ile	p.L380I	ENST00000218089	NM_001042749.1	380	Ctt/Att	13/35	1	2	FACETS	0.946	0.855	1	0.946	0.855	1	CLONAL	1	TRUE	1	0.363016891671905	2		435	699	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0012983-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	11	587	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.285	0.196	0.397	0.285	0.196	0.397	SUBCLONAL	1	TRUE	1	0.224349762358187	2		587	344	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186804	11186804	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012983-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	49	561	0	ENST00000361445.4:c.6401G>C	p.Arg2134Pro	p.R2134P	ENST00000361445	NM_004958.3	2134	cGg/cCg	46/58	1	2	FACETS	0.462	0.39	0.542	0.462	0.39	0.542	SUBCLONAL	1	TRUE	1	0.224349762358187	2		561	946	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333779	70333779	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012983-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1241	70	792	0	ENST00000373644.4:c.1684G>T	p.Val562Leu	p.V562L	ENST00000373644	NM_030625.2	562	Gtg/Ttg	2/12	1	2	FACETS	0.476	0.413	0.544	0.476	0.413	0.544	SUBCLONAL	1	TRUE	1	0.224349762358187	2		792	1311	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0013217-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	1145	294	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.68641997462209	4	FACETS	0.989	0.967	1	0.989	0.967	1	CLONAL	3	TRUE	1	0.725852052631938	4		294	1836	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106058	8106058	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013217-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	289	542	0	ENST00000346208.3:c.878T>G	p.Met293Arg	p.M293R	ENST00000346208		293	aTg/aGg	4/6	1	2	FACETS	0.963	0.909	1	0.963	0.909	1	CLONAL	1	TRUE	1	0.725852052631938	2		542	827	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061313	38061313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1204900727	NA	P-0013217-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	537	918	0	ENST00000250448.2:c.676G>A	p.Asp226Asn	p.D226N	ENST00000250448	NM_004496.3	226	Gac/Aac	2/2	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.725852052631938	2		918	1451	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0013297-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	312	725	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.251982750279315	3	FACETS	1	0.985	1	0.748	0.705	0.793	CLONAL	2	TRUE	0	0.251982750279315	3		725	1242	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206892	36206892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1229231012	NA	P-0013297-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	45	269	0	ENST00000300305.3:c.620G>A	p.Arg207Gln	p.R207Q	ENST00000300305		207	cGg/cAg	6/8	0.237088777301396	4	FACETS	0.738	0.619	0.869	0.369	0.309	0.435	SUBCLONAL	1	TRUE	2	0.251982750279315	4		269	606	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965736	93965736	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013297-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1312	339	743	1	ENST00000369303.4:c.2192C>T	p.Thr731Ile	p.T731I	ENST00000369303	NM_004440.3	731	aCa/aTa	13/17	0.237088777301396	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.251982750279315	4		744	1651	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063718	67063719	+	splice_donor_variant,intron_variant	Splice_Site	DEL	TA	TA	-	novel	NA	P-0013297-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	74	275	0	ENST00000412916.2:c.165+2_165+3del		p.X55_splice	ENST00000412916		55			0.251982750279315	2	FACETS	0.825	0.727	0.929	0.825	0.727	0.929	CLONAL	2	TRUE	0	0.251982750279315	2		275	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0013775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	324	636	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.746041598501183	1	FACETS	0.888	0.848	0.929	0.888	0.848	0.929	CLONAL	1	TRUE	0	0.746041598501183	1		637	613	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023696	27023696	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	299	763	1	ENST00000324856.7:c.802C>T	p.Gln268Ter	p.Q268*	ENST00000324856	NM_006015.4	268	Cag/Tag	1/20	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.746041598501183	2		764	799	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032069	26032069	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	478	377	0	ENST00000244661.2:c.220G>C	p.Glu74Gln	p.E74Q	ENST00000244661	NM_003537.3	74	Gaa/Caa	1/1	1	2	FACETS	0.912	0.872	0.953	0.912	0.872	0.953	CLONAL	1	TRUE	1	0.746041598501183	2		377	1405	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0013775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	422	970	2	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	1	2	FACETS	0.988	0.943	1	0.988	0.943	1	CLONAL	1	TRUE	1	0.746041598501183	2		972	1145	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720801	89720802	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	50	200	0	ENST00000371953.3:c.954dup	p.Thr319TyrfsTer6	p.T319Yfs*6	ENST00000371953	NM_000314.4	318	ctt/cTtt	8/9	1	2	FACETS	0.59	0.506	0.681	0.59	0.506	0.681	SUBCLONAL	1	TRUE	1	0.746041598501183	2		200	227	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226550857	226550857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	237	854	0	ENST00000366794.5:c.2791G>A	p.Glu931Lys	p.E931K	ENST00000366794	NM_001618.3	931	Gaa/Aaa	21/23	0.738091614269855	3	FACETS	0.702	0.654	0.751	0.351	0.327	0.376	SUBCLONAL	1	TRUE	1	0.746041598501183	3		854	1243	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100403	8100403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	51	1042	1	ENST00000346208.3:c.377C>T	p.Ser126Phe	p.S126F	ENST00000346208		126	tCc/tTc	3/6	1	2	FACETS	0.14	0.118	0.164	0.14	0.118	0.164	SUBCLONAL	1	TRUE	1	0.746041598501183	2		1043	976	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742878	17742878	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	165	530	0	ENST00000250003.3:c.786G>C	p.Glu262Asp	p.E262D	ENST00000250003	NM_002478.4	262	gaG/gaC	3/3	1	2	FACETS	0.933	0.864	1	0.933	0.864	1	CLONAL	1	TRUE	1	0.746041598501183	2		530	474	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557737	21557737	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	339	983	1	ENST00000382592.4:c.2108A>G	p.Asp703Gly	p.D703G	ENST00000382592	NM_014572.2	703	gAt/gGt	5/8	1	2	FACETS	0.912	0.864	0.96	0.912	0.864	0.96	CLONAL	1	TRUE	1	0.746041598501183	2		984	997	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562438	95562438	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs189119295	NA	P-0013775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	256	737	0	ENST00000393063.1:c.4819C>T	p.Arg1607Trp	p.R1607W	ENST00000393063	NM_030621.3	1607	Cgg/Tgg	24/28	1	2	FACETS	0.92	0.865	0.976	0.92	0.865	0.976	CLONAL	1	TRUE	1	0.746041598501183	2		737	746	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434613	99434613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253103806	NA	P-0013775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	270	669	0	ENST00000268035.6:c.700G>A	p.Glu234Lys	p.E234K	ENST00000268035	NM_000875.3	234	Gag/Aag	3/21	0.722294095996751	2	FACETS	1	0.977	1	0.531	0.502	0.562	CLONAL	1	TRUE	0	0.746041598501183	2		669	681	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456292	99456292	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	205	662	0	ENST00000268035.6:c.1609G>C	p.Glu537Gln	p.E537Q	ENST00000268035	NM_000875.3	537	Gag/Cag	8/21	0.722294095996751	2	FACETS	0.758	0.705	0.812	0.379	0.352	0.406	SUBCLONAL	1	TRUE	0	0.746041598501183	2		662	725	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879592	37879592	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	215	607	0	ENST00000269571.5:c.1967C>G	p.Ser656Cys	p.S656C	ENST00000269571		656	tCt/tGt	17/27	1	2	FACETS	0.951	0.89	1	0.951	0.89	1	CLONAL	1	TRUE	1	0.746041598501183	2		607	606	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273528	5273528	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	340	943	1	ENST00000357368.4:c.304G>A	p.Glu102Lys	p.E102K	ENST00000357368	NM_002850.3	102	Gaa/Aaa	4/38	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.746041598501183	2		944	884	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031197	36031197	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs745612156	NA	P-0013775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	322	905	0	ENST00000358208.4:c.1316A>G	p.Tyr439Cys	p.Y439C	ENST00000358208		439	tAt/tGt	11/12	1	2	FACETS	0.972	0.921	1	0.972	0.921	1	CLONAL	1	TRUE	1	0.746041598501183	2		905	888	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188379	142188379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	228	588	0	ENST00000350721.4:c.6352G>A	p.Asp2118Asn	p.D2118N	ENST00000350721	NM_001184.3	2118	Gat/Aat	38/47	1	2	FACETS	0.872	0.816	0.929	0.872	0.816	0.929	CLONAL	1	TRUE	1	0.746041598501183	2		588	701	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637199	176637199	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0013775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	345	731	0	ENST00000439151.2:c.1799C>G	p.Ser600Ter	p.S600*	ENST00000439151	NM_022455.4	600	tCa/tGa	5/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.746041598501183	2		731	895	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665280	176665280	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784107	NA	P-0013775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	353	861	1	ENST00000439151.2:c.3964C>T	p.Arg1322Ter	p.R1322*	ENST00000439151	NM_022455.4	1322	Cga/Tga	7/23	1	2	FACETS	0.959	0.911	1	0.959	0.911	1	CLONAL	1	TRUE	1	0.746041598501183	2		862	987	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126347	5126347	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	233	629	0	ENST00000381652.3:c.3192G>C	p.Met1064Ile	p.M1064I	ENST00000381652	NM_004972.3	1064	atG/atC	24/25	0.547830692598036	3	FACETS	0.917	0.856	0.98			1	CLONAL	1	TRUE	NA	0.746041598501183	3		629	935	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126393	5126393	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	291	646	0	ENST00000381652.3:c.3238G>C	p.Glu1080Gln	p.E1080Q	ENST00000381652	NM_004972.3	1080	Gaa/Caa	24/25	0.547830692598036	3	FACETS	0.991	0.933	1			1	CLONAL	1	TRUE	NA	0.746041598501183	3		646	1081	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250268	110250268	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs756511308	NA	P-0013775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	225	833	0	ENST00000374672.4:c.407C>G	p.Pro136Arg	p.P136R	ENST00000374672	NM_004235.4	136	cCg/cGg	3/5	0.746041598501183	1	FACETS	0.848	0.801	0.895	0.848	0.801	0.895	CLONAL	1	TRUE	0	0.746041598501183	1		833	446	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0013987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	25	497	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	1	2	FACETS	0.094	0.073	0.118	0.094	0.073	0.118	SUBCLONAL	1	TRUE	1	0.79795224945616	2		497	666	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0013987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	238	547	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.896	0.841	0.951	0.896	0.841	0.951	CLONAL	1	TRUE	1	0.79795224945616	2		547	666	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0013987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	353	742	0	ENST00000346208.3:c.1002_1003dup	p.Asp335GlyfsTer21	p.D335Gfs*21	ENST00000346208		333	-/GG	5/6	1	2	FACETS	0.921	0.875	0.967	0.921	0.875	0.967	CLONAL	1	TRUE	1	0.79795224945616	2		742	961	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063636	67063637	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0013987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	300	593	1	ENST00000412916.2:c.88_89dup	p.Gly31ArgfsTer59	p.G31Rfs*59	ENST00000412916		29	tac/tACac	2/6	0.79795224945616	1	FACETS	0.94	0.9	0.979	0.94	0.9	0.979	CLONAL	1	TRUE	0	0.79795224945616	1		594	481	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857490	68857490	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	11	442	0	ENST00000261769.5:c.2125del	p.Ala709ProfsTer13	p.A709Pfs*13	ENST00000261769	NM_004360.3	709	Gcc/cc	13/16	0.79795224945616	1	FACETS	0.113	0.078	0.156	0.113	0.078	0.156	SUBCLONAL	1	TRUE	0	0.79795224945616	1		442	147	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0014035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	286	367	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.666736164681258	2	FACETS	0.946	0.91	0.981	0.946	0.91	0.981	CLONAL	2	TRUE	0	0.755715150243637	2		367	400	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	147	609	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.622998304873758	4	FACETS	1	0.976	1	0.294	0.269	0.32	CLONAL	1	TRUE	0	0.755715150243637	4		609	581	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206647734	206647734	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782440026	NA	P-0014035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	127	501	2	ENST00000367120.3:c.148G>A	p.Glu50Lys	p.E50K	ENST00000367120	NM_014002.3	50	Gag/Aag	4/22	0.646140174555698	4	FACETS	0.794	0.72	0.872	0.397	0.36	0.436	SUBCLONAL	1	TRUE	2	0.755715150243637	4		503	743	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831946	72831946	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0014035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	479	1208	0	ENST00000268489.5:c.4635C>G	p.Tyr1545Ter	p.Y1545*	ENST00000268489	NM_006885.3	1545	taC/taG	9/10	0.413671644061021	1	FACETS	1	0.997	1	1	0.997	1	INDETERMINATE	1	TRUE	0	0.755715150243637	1		1208	636	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663346	227663346	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1024227751	NA	P-0014035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	133	187	0	ENST00000305123.5:c.109G>C	p.Glu37Gln	p.E37Q	ENST00000305123	NM_005544.2	37	Gag/Cag	1/2	0.755715150243637	3	FACETS	0.926	0.859	0.992			1	CLONAL	2	TRUE	NA	0.755715150243637	3		187	262	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280049	18280070	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTGGCGCACCCAGTGCGCGC	CCCTGGCGCACCCAGTGCGCGC	-	novel	NA	P-0014138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	50	151	0	ENST00000222254.8:c.2135_2156del	p.Leu712ArgfsTer155	p.L712Rfs*155	ENST00000222254	NM_005027.3	711	aCCCTGGCGCACCCAGTGCGCGCc/ac	16/16	0.179238896988122	11	FACETS	0.935	0.81	1			1	CLONAL	7	FALSE	NA	0.179238896988122	11		151	154	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794748	42794748	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	141	563	1	ENST00000575354.2:c.1828G>T	p.Glu610Ter	p.E610*	ENST00000575354	NM_015125.3	610	Gag/Tag	10/20	0.179238896988122	7	FACETS	1	0.929	1	0.844	0.775	0.915	CLONAL	5	FALSE	1	0.179238896988122	7		564	450	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880270	155880270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	383	420	3	ENST00000368323.3:c.134G>A	p.Arg45Gln	p.R45Q	ENST00000368323	NM_006912.5	45	cGa/cAa	3/6	0.417587869268587	5	FACETS	0.893	0.855	0.931	0.893	0.855	0.931	CLONAL	4	TRUE	1	0.50736527574942	5		423	744	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574650	64574650	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1060499976	NA	P-0014374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	132	538	0	ENST00000312049.6:c.824+1G>T		p.X275_splice	ENST00000312049	NM_130799.2	275			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.50736527574942	NA		538	382	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061462	38061462	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	65	516	0	ENST00000250448.2:c.527T>C	p.Ile176Thr	p.I176T	ENST00000250448	NM_004496.3	176	aTc/aCc	2/2	1	2	FACETS	0.566	0.492	0.645	0.566	0.492	0.645	SUBCLONAL	1	TRUE	1	0.50736527574942	2		516	453	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013742	12013742	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	86	311	0	ENST00000353533.5:c.684A>T	p.Arg228Ser	p.R228S	ENST00000353533	NM_003010.3	228	agA/agT	6/11	0.50736527574942	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.50736527574942	1		311	177	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0014378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	379	701	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.54298175338092	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.54298175338092	3		701	880	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372117	55372118	+	missense_variant	Missense_Mutation	DNP	CA	CA	AT	rs1563871910	NA	P-0014378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	264	194	147	ENST00000297316.4:c.807_808delinsAT	p.Met270Leu	p.M270L	ENST00000297316	NM_022454.3	269	ccCAtg/ccATtg	2/2	1	2	FACETS	0.833	0.788	0.878	1	0.995	1	CLONAL	2	TRUE	1	0.54298175338092	2		341	584	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022853	31022853	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs751021760	NA	P-0014378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	169	576	1	ENST00000375687.4:c.2338C>T	p.Gln780Ter	p.Q780*	ENST00000375687	NM_015338.5	780	Cag/Tag	13/13	0.54298175338092	3	FACETS	0.948	0.872	1	0.474	0.436	0.514	CLONAL	1	TRUE	1	0.54298175338092	3		577	835	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115711	8115711	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	118	281	0	ENST00000346208.3:c.1060del	p.Leu354Ter	p.L354*	ENST00000346208		353	Ccc/cc	6/6	NA	2	FACETS	0.809	0.733	0.889			1	INDETERMINATE	1	TRUE	NA	0.54298175338092	2		281	537	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063717	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs924551538	NA	P-0014378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	219	265	0	ENST00000412916.2:c.165+1G>A		p.X55_splice	ENST00000412916		55			0.54298175338092	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.54298175338092	2		265	357	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0014378-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	333	701	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.737153068129829	3	FACETS	0.992	0.948	1	0.992	0.948	1	CLONAL	2	TRUE	1	0.737153068129829	3		701	623	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014378-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	396	609	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.737153068129829	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.737153068129829	3		609	711	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022853	31022853	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs751021760	NA	P-0014378-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	187	576	1	ENST00000375687.4:c.2338C>T	p.Gln780Ter	p.Q780*	ENST00000375687	NM_015338.5	780	Cag/Tag	13/13	0.737153068129829	3	FACETS	1	0.959	1	0.524	0.486	0.564	CLONAL	1	TRUE	1	0.737153068129829	3		577	662	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115711	8115711	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014378-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	102	281	0	ENST00000346208.3:c.1060del	p.Leu354Ter	p.L354*	ENST00000346208		353	Ccc/cc	6/6	NA	2	FACETS	0.958	0.869	1			1	INDETERMINATE	1	TRUE	NA	0.737153068129829	2		281	289	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063717	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs924551538	NA	P-0014378-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	159	265	0	ENST00000412916.2:c.165+1G>A		p.X55_splice	ENST00000412916		55			0.737153068129829	2	FACETS	0.863	0.813	0.911	0.863	0.813	0.911	CLONAL	2	TRUE	0	0.737153068129829	2		265	250	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138409957	138409957	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014378-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	119	386	1	ENST00000289153.2:c.1921C>T	p.Gln641Ter	p.Q641*	ENST00000289153	NM_006219.2	641	Caa/Taa	13/22	1	2	FACETS	0.892	0.814	0.972	0.892	0.814	0.972	CLONAL	1	TRUE	1	0.737153068129829	2		387	362	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027245	49027246	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0014378-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	146	464	1	ENST00000267163.4:c.1813dup	p.Met605AsnfsTer48	p.M605Nfs*48	ENST00000267163	NM_000321.2	604	-/A	18/27	1	2	FACETS	0.973	0.898	1	0.973	0.898	1	CLONAL	1	TRUE	1	0.737153068129829	2		465	407	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0014384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	203	701	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.842	0.781	0.905	1	0.992	1	CLONAL	2	TRUE	1	0.26139943692143	2		701	922	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0014384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	183	676	0	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	0.26139943692143	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.26139943692143	1		676	1031	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844247	68844247	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	G	rs1555515469	NA	P-0014384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	83	500	0	ENST00000261769.5:c.832+3A>G		p.X278_splice	ENST00000261769	NM_004360.3	278			0.26139943692143	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.26139943692143	1		500	509	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106162505	106162505	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	48	306	0	ENST00000380013.4:c.3419T>C	p.Ile1140Thr	p.I1140T	ENST00000380013	NM_001127208.2	1140	aTt/aCt	4/11	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.26139943692143	2		306	316	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058476	69058476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267601977	NA	P-0014384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	148	605	1	ENST00000288368.4:c.4120C>T	p.Arg1374Trp	p.R1374W	ENST00000288368	NM_024870.2	1374	Cgg/Tgg	34/40	0.219485969304058	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	1	0.26139943692143	3		606	604	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0014384-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	316	701	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.433505586571362	3	FACETS	0.878	0.837	0.92			1	CLONAL	3	TRUE	NA	0.473136652255384	3		701	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0014384-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	238	676	0	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	0.473136652255384	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.473136652255384	1		676	637	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844247	68844247	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	G	rs1555515469	NA	P-0014384-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	324	500	0	ENST00000261769.5:c.832+3A>G		p.X278_splice	ENST00000261769	NM_004360.3	278			0.473136652255384	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.473136652255384	2		500	646	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106162505	106162505	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014384-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	97	306	0	ENST00000380013.4:c.3419T>C	p.Ile1140Thr	p.I1140T	ENST00000380013	NM_001127208.2	1140	aTt/aCt	4/11	0.473136652255384	1	FACETS	0.991	0.893	1	0.991	0.893	1	CLONAL	1	TRUE	0	0.473136652255384	1		306	316	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058476	69058476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267601977	NA	P-0014384-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	145	605	1	ENST00000288368.4:c.4120C>T	p.Arg1374Trp	p.R1374W	ENST00000288368	NM_024870.2	1374	Cgg/Tgg	34/40	1	2	FACETS	0.946	0.866	1	0.946	0.866	1	CLONAL	1	TRUE	1	0.473136652255384	2		606	648	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730868	40730868	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014384-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	207	725	0	ENST00000373198.4:c.3667G>A	p.Asp1223Asn	p.D1223N	ENST00000373198	NM_133170.3	1223	Gat/Aat	27/32	0.262093442036109	1	FACETS	1	0.962	1	1	0.962	1	INDETERMINATE	1	TRUE	0	0.473136652255384	1		725	639	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246113	41246113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064794100	NA	P-0014384-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	240	716	0	ENST00000357654.3:c.1435G>A	p.Glu479Lys	p.E479K	ENST00000357654	NM_007294.3	479	Gaa/Aaa	10/23	0.473136652255384	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.473136652255384	1		716	723	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	229	503	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	0.708739252990839	2		503	640	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0014543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	167	285	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.869	0.804	0.937	0.869	0.804	0.937	CLONAL	1	TRUE	1	0.708739252990839	2		285	542	SUCCESS
APC	324	MSKCC	GRCh37	5	112175536	112175536	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	203	330	0	ENST00000257430.4:c.4245del	p.Ser1415ArgfsTer4	p.S1415Rfs*4	ENST00000257430	NM_000038.5	1415	agT/ag	16/16	1	2	FACETS	0.961	0.897	1	0.961	0.897	1	CLONAL	1	TRUE	1	0.708739252990839	2		330	596	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983121	201983122	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGACC	novel	NA	P-0014543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	451	643	0	ENST00000359651.3:c.972_976dup	p.Tyr326Ter	p.Y326*	ENST00000359651		324	atg/aTGACCtg	7/8	1	2	FACETS	0.972	0.928	1	0.972	0.928	1	CLONAL	1	TRUE	1	0.708739252990839	2		643	1309	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119816	70119817	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGACATCGGC	novel	NA	P-0014543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	424	732	1	ENST00000245479.2:c.820_829dup	p.Glu277GlyfsTer22	p.E277Gfs*22	ENST00000245479	NM_000346.3	273	gtg/gtGGACATCGGCg	3/3	1	2	FACETS	0.85	0.81	0.892	0.85	0.81	0.892	CLONAL	1	TRUE	1	0.708739252990839	2		733	1407	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0014642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	468	447	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.595951369086523	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.591235163711578	3		447	593	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521544	8521544	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	236	496	1	ENST00000356435.5:c.694C>T	p.Arg232Cys	p.R232C	ENST00000356435		232	Cgc/Tgc	9/35	0.450793044299788	4	FACETS	0.859	0.811	0.907	1	0.991	1	CLONAL	3	TRUE	2	0.591235163711578	4		497	493	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589015	67589016	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0014642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	337	302	0	ENST00000274335.5:c.1108_1109del	p.Leu370TyrfsTer8	p.L370Yfs*8	ENST00000274335		369	aCT/a	8/15	0.595951369086523	4	FACETS	0.989	0.969	1	1	0.997	1	CLONAL	5	TRUE	0	0.591235163711578	4		302	367	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542584	141542584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1238499211	NA	P-0014642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1675	169	663	1	ENST00000220592.5:c.2402C>T	p.Ala801Val	p.A801V	ENST00000220592	NM_012154.3	801	gCg/gTg	18/19	0.591235163711578	16	FACETS	0.797	0.729	0.868			1	SUBCLONAL	2	TRUE	NA	0.591235163711578	16		664	1844	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111509	8111519	+	frameshift_variant	Frame_Shift_Del	DEL	CCAATGGGGAC	CCAATGGGGAC	-	novel	NA	P-0014941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	213	670	0	ENST00000346208.3:c.997_1007del	p.Asn333CysfsTer15	p.N333Cfs*15	ENST00000346208		332	gCCAATGGGGAC/g	5/6	0.442495871928413	3	FACETS	0.973	0.903	1	0.487	0.451	0.523	CLONAL	1	TRUE	1	0.449226629133835	3		670	1193	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0014944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	191	662	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.156103948201362	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	FALSE	0	0.156103948201362	2		662	1098	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936103	178936103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519699	NA	P-0014944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	40	780	0	ENST00000263967.3:c.1645G>A	p.Asp549Asn	p.D549N	ENST00000263967	NM_006218.2	549	Gat/Aat	10/21	1	2	FACETS	0.922	0.765	1	0.922	0.765	1	CLONAL	1	FALSE	1	0.156103948201362	2		780	556	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212252696	212252696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	19	161	1	ENST00000342788.4:c.3157C>T	p.Pro1053Ser	p.P1053S	ENST00000342788	NM_005235.2	1053	Cct/Tct	26/28	1	2	FACETS	0.998	0.759	1	0.998	0.759	1	CLONAL	1	FALSE	1	0.156103948201362	2		162	244	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499579	18499579	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	40	468	0	ENST00000266497.5:c.1434G>C	p.Leu478Phe	p.L478F	ENST00000266497		478	ttG/ttC	10/31	1	2	FACETS	0.993	0.825	1	0.993	0.825	1	CLONAL	1	FALSE	1	0.156103948201362	2		468	516	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998898	11998898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	40	266	1	ENST00000353533.5:c.400C>T	p.Arg134Trp	p.R134W	ENST00000353533	NM_003010.3	134	Cgg/Tgg	4/11	0.156103948201362	2	FACETS	0.867	0.729	1	1	0.943	1	CLONAL	3	FALSE	0	0.156103948201362	2		267	197	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316067	11316067	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	50	517	0	ENST00000361445.4:c.687G>C	p.Gln229His	p.Q229H	ENST00000361445	NM_004958.3	229	caG/caC	5/58	1	2	FACETS	0.817	0.692	0.956	0.817	0.692	0.956	CLONAL	1	FALSE	1	0.156103948201362	2		517	784	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245912910	245912910	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	44	452	0	ENST00000388985.4:c.1242G>C	p.Leu414Phe	p.L414F	ENST00000388985		414	ttG/ttC	12/12	1	2	FACETS	0.806	0.675	0.953	0.806	0.675	0.953	CLONAL	1	FALSE	1	0.156103948201362	2		452	699	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377078	118377078	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	50	343	1	ENST00000534358.1:c.10471G>T	p.Asp3491Tyr	p.D3491Y	ENST00000534358	NM_005933.3	3491	Gac/Tac	27/36	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	FALSE	1	0.156103948201362	2		344	597	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988535	41988535	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	36	510	0	ENST00000219905.7:c.1327T>C	p.Ser443Pro	p.S443P	ENST00000219905	NM_001164273.1	443	Tct/Cct	3/24	1	2	FACETS	0.856	0.702	1	0.856	0.702	1	CLONAL	1	FALSE	1	0.156103948201362	2		510	539	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216406	2216406	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	53	709	0	ENST00000398665.3:c.2050G>T	p.Glu684Ter	p.E684*	ENST00000398665	NM_032482.2	684	Gag/Tag	20/28	0.156103948201362	2	FACETS	0.901	0.766	1	0.45	0.383	0.524	CLONAL	1	FALSE	0	0.156103948201362	2		709	754	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295779	15295779	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	85	809	0	ENST00000263388.2:c.2348G>T	p.Gly783Val	p.G783V	ENST00000263388	NM_000435.2	783	gGg/gTg	15/33	0.156103948201362	2	FACETS	0.931	0.82	1	0.465	0.41	0.525	CLONAL	1	FALSE	0	0.156103948201362	2		809	1170	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96930909	96930909	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142947571	NA	P-0014944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	65	763	1	ENST00000258439.3:c.211G>A	p.Val71Met	p.V71M	ENST00000258439	NM_001193304.2	71	Gtg/Atg	2/4	1	2	FACETS	0.742	0.641	0.853	0.742	0.641	0.853	SUBCLONAL	1	FALSE	1	0.156103948201362	2		764	1122	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466809	57466809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	62	193	0	ENST00000371085.3:c.28G>A	p.Glu10Lys	p.E10K	ENST00000371085	NM_000516.4	10	Gag/Aag	1/13	0.156103948201362	17	FACETS	1	0.966	1			1	CLONAL	1	FALSE	NA	0.156103948201362	17		193	1200	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775559	39775559	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	49	574	0	ENST00000288319.7:c.461A>G	p.Asp154Gly	p.D154G	ENST00000288319	NM_182918.3	154	gAc/gGc	4/10	0.108817659639465	4	FACETS	0.795	0.671	0.932	0.397	0.335	0.466	CLONAL	1	FALSE	2	0.156103948201362	4		574	913	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683765	162683765	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	54	495	0	ENST00000366898.1:c.204C>G	p.His68Gln	p.H68Q	ENST00000366898	NM_004562.2	68	caC/caG	3/12	1	2	FACETS	0.91	0.776	1	0.91	0.776	1	CLONAL	1	FALSE	1	0.156103948201362	2		495	760	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0014944-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	158	662	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.158159063455513	2	FACETS	0.859	0.786	0.936	0.859	0.786	0.936	CLONAL	2	FALSE	0	0.158159063455513	2		662	1163	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936103	178936103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519699	NA	P-0014944-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	86	780	0	ENST00000263967.3:c.1645G>A	p.Asp549Asn	p.D549N	ENST00000263967	NM_006218.2	549	Gat/Aat	10/21	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	FALSE	1	0.158159063455513	2		780	1085	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212252696	212252696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014944-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	20	161	1	ENST00000342788.4:c.3157C>T	p.Pro1053Ser	p.P1053S	ENST00000342788	NM_005235.2	1053	Cct/Tct	26/28	1	2	FACETS	0.9	0.689	1	0.9	0.689	1	CLONAL	1	FALSE	1	0.158159063455513	2		162	281	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499579	18499579	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014944-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	55	468	0	ENST00000266497.5:c.1434G>C	p.Leu478Phe	p.L478F	ENST00000266497		478	ttG/ttC	10/31	1	2	FACETS	0.883	0.753	1	0.883	0.753	1	CLONAL	1	FALSE	1	0.158159063455513	2		468	788	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998898	11998898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014944-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	68	266	1	ENST00000353533.5:c.400C>T	p.Arg134Trp	p.R134W	ENST00000353533	NM_003010.3	134	Cgg/Tgg	4/11	0.158159063455513	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	2	FALSE	0	0.158159063455513	2		267	421	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316067	11316067	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014944-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	70	517	0	ENST00000361445.4:c.687G>C	p.Gln229His	p.Q229H	ENST00000361445	NM_004958.3	229	caG/caC	5/58	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	FALSE	1	0.158159063455513	2		517	802	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377078	118377078	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014944-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	55	343	1	ENST00000534358.1:c.10471G>T	p.Asp3491Tyr	p.D3491Y	ENST00000534358	NM_005933.3	3491	Gac/Tac	27/36	1	2	FACETS	0.959	0.819	1	0.959	0.819	1	CLONAL	1	FALSE	1	0.158159063455513	2		344	725	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988535	41988535	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014944-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	65	510	0	ENST00000219905.7:c.1327T>C	p.Ser443Pro	p.S443P	ENST00000219905	NM_001164273.1	443	Tct/Cct	3/24	1	2	FACETS	0.887	0.767	1	0.887	0.767	1	CLONAL	1	FALSE	1	0.158159063455513	2		510	927	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216406	2216406	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014944-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	104	709	0	ENST00000398665.3:c.2050G>T	p.Glu684Ter	p.E684*	ENST00000398665	NM_032482.2	684	Gag/Tag	20/28	0.156132107488441	2	FACETS	1	0.958	1	0.572	0.511	0.638	CLONAL	1	FALSE	0	0.158159063455513	2		709	1149	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295779	15295779	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014944-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	87	809	0	ENST00000263388.2:c.2348G>T	p.Gly783Val	p.G783V	ENST00000263388	NM_000435.2	783	gGg/gTg	15/33	0.156132107488441	2	FACETS	0.878	0.775	0.989	0.439	0.387	0.495	CLONAL	1	FALSE	0	0.158159063455513	2		809	1253	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466809	57466809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014944-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	63	193	0	ENST00000371085.3:c.28G>A	p.Glu10Lys	p.E10K	ENST00000371085	NM_000516.4	10	Gag/Aag	1/13	0.158159063455513	18	FACETS	0.944	0.814	1			1	CLONAL	2	FALSE	NA	0.158159063455513	18		193	956	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775559	39775559	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014944-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	65	574	0	ENST00000288319.7:c.461A>G	p.Asp154Gly	p.D154G	ENST00000288319	NM_182918.3	154	gAc/gGc	4/10	1	2	FACETS	0.732	0.632	0.841	0.732	0.632	0.841	SUBCLONAL	1	FALSE	1	0.158159063455513	2		574	1123	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683765	162683765	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014944-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	59	495	0	ENST00000366898.1:c.204C>G	p.His68Gln	p.H68Q	ENST00000366898	NM_004562.2	68	caC/caG	3/12	1	2	FACETS	0.861	0.738	0.994	0.861	0.738	0.994	CLONAL	1	FALSE	1	0.158159063455513	2		495	867	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922156	100922156	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1165724245	NA	P-0014944-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	38	378	0	ENST00000325455.5:c.2356G>A	p.Glu786Lys	p.E786K	ENST00000325455	NM_001202474.3	786	Gaa/Aaa	5/8	1	2	FACETS	0.775	0.639	0.927	0.775	0.639	0.927	CLONAL	1	FALSE	1	0.158159063455513	2		378	620	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745966	745966	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014944-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	78	632	0	ENST00000314574.4:c.556G>C	p.Glu186Gln	p.E186Q	ENST00000314574	NM_005433.3	186	Gag/Cag	5/12	0.158159063455513	2	FACETS	0.913	0.8	1	0.457	0.4	0.518	CLONAL	1	FALSE	0	0.158159063455513	2		632	1080	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952348	38952348	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752956118	NA	P-0014944-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	49	356	0	ENST00000357387.3:c.3077C>T	p.Ser1026Leu	p.S1026L	ENST00000357387	NM_152756.3	1026	tCg/tTg	30/38	0.158159063455513	4	FACETS	0.968	0.818	1	0.484	0.409	0.567	CLONAL	1	FALSE	2	0.158159063455513	4		356	741	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115928	8115929	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0014974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	250	403	0	ENST00000346208.3:c.1275dup	p.Ser426IlefsTer81	p.S426Ifs*81	ENST00000346208		425	cca/ccAa	6/6	1	2	FACETS	1	0.957	1	1	0.996	1	CLONAL	4	TRUE	1	0.188594819080385	2		403	650	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974783	21974783	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658556	NA	P-0014974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	120	334	1	ENST00000304494.5:c.44G>A	p.Trp15Ter	p.W15*	ENST00000304494	NM_000077.4	15	tGg/tAg	1/3	1	2	FACETS	1	0.957	1	1	0.993	1	CLONAL	4	TRUE	1	0.188594819080385	2		335	298	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118361956	118361956	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1565293702	NA	P-0014974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	195	374	0	ENST00000534358.1:c.4742A>G	p.Tyr1581Cys	p.Y1581C	ENST00000534358	NM_005933.3	1581	tAt/tGt	14/36	1	2	FACETS	0.903	0.845	0.961	1	0.995	1	CLONAL	5	TRUE	1	0.188594819080385	2		374	458	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974675	21974675	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1060501265	NA	P-0014974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	212	501	0	ENST00000304494.5:c.150+2T>C		p.X50_splice	ENST00000304494	NM_000077.4	50			1	2	FACETS	0.905	0.846	0.966	1	0.995	1	CLONAL	4	TRUE	1	0.188594819080385	2		501	621	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968257	18968257	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	211	747	0	ENST00000262803.5:c.2098del	p.Val700SerfsTer32	p.V700Sfs*32	ENST00000262803	NM_002911.3	699	caG/ca	15/24	1	2	FACETS	0.875	0.813	0.939	0.875	0.813	0.939	CLONAL	1	TRUE	1	0.508841882191804	2		747	948	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579341	7579341	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	531	546	0	ENST00000269305.4:c.346del	p.Ser116LeufsTer7	p.S116Lfs*7	ENST00000269305	NM_001126112.2	116	Tct/ct	4/11	NA	2	FACETS	0.942	0.917	0.967			1	INDETERMINATE	2	TRUE	NA	0.791492957954418	2		546	712	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624290	89624295	+	inframe_deletion	In_Frame_Del	DEL	GACTTA	GACTTA	-	novel	NA	P-0015224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	89	369	0	ENST00000371953.3:c.69_74del	p.Asp24_Leu25del	p.D24_L25del	ENST00000371953	NM_000314.4	22	GACTTA/-	1/9	0.239172734878074	4	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.275455011722619	4		369	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578502	7578503	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGGG	novel	NA	P-0015224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	101	806	1	ENST00000269305.4:c.423_427dup	p.Val143AlafsTer29	p.V143Afs*29	ENST00000269305	NM_001126112.2	143	gtg/gCCCTGtg	5/11	0.26044465994496	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.275455011722619	1		807	608	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578515	7578515	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	111	810	0	ENST00000269305.4:c.415A>C	p.Lys139Gln	p.K139Q	ENST00000269305	NM_001126112.2	139	Aag/Cag	5/11	0.26044465994496	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.275455011722619	1		810	612	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907665	111907666	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGATCGCCCA	novel	NA	P-0015224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	52	266	0	ENST00000393256.3:c.440_449dup	p.Glu151AspfsTer13	p.E151Dfs*13	ENST00000393256	NM_006538.4	147	tgg/tGGATCGCCCAgg	3/4	NA	2	FACETS	0.966	0.825	1			1	INDETERMINATE	1	TRUE	NA	0.275455011722619	2		266	391	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0015299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	114	294	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	0.417309226190898	2		294	538	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495473	56495474	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TATG	novel	NA	P-0015299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	129	752	0	ENST00000267101.3:c.3664_3667dup	p.Glu1223ValfsTer2	p.E1223Vfs*2	ENST00000267101	NM_001982.3	1221	-/TATG	28/28	1	2	FACETS	0.733	0.664	0.805	0.733	0.664	0.805	SUBCLONAL	1	TRUE	1	0.417309226190898	2		752	844	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247454	71247454	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	143	744	0	ENST00000318789.4:c.79C>G	p.Leu27Val	p.L27V	ENST00000318789	NM_032682.5	27	Cta/Gta	6/21	1	2	FACETS	0.831	0.758	0.907	0.831	0.758	0.907	CLONAL	1	TRUE	1	0.417309226190898	2		744	825	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0015354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	52	186	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.327194951577962	1	FACETS	0.715	0.615	0.822	0.715	0.615	0.822	SUBCLONAL	1	TRUE	0	0.477285944263653	1		186	232	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0015354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	263	447	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.477285944263653	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.477285944263653	1		447	651	SUCCESS
APC	324	MSKCC	GRCh37	5	112174502	112174502	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876659539	NA	P-0015354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	50	265	0	ENST00000257430.4:c.3211C>T	p.Gln1071Ter	p.Q1071*	ENST00000257430	NM_000038.5	1071	Caa/Taa	16/16	0.327194951577962	1	FACETS	0.722	0.619	0.832	0.722	0.619	0.832	SUBCLONAL	1	TRUE	0	0.477285944263653	1		265	221	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885531	111885531	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	99	402	0	ENST00000341259.2:c.1308C>A	p.Asp436Glu	p.D436E	ENST00000341259	NM_005475.2	436	gaC/gaA	7/8	0.220571737699662	2	FACETS	0.623	0.556	0.693	0.311	0.278	0.347	INDETERMINATE	1	TRUE	0	0.477285944263653	2		402	666	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609744	81609744	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201889708	NA	P-0015354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	180	330	0	ENST00000298171.2:c.1342G>A	p.Val448Ile	p.V448I	ENST00000298171	NM_000369.2	448	Gtc/Atc	10/10	0.477285944263653	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.477285944263653	1		330	412	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118876	70118876	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	202	353	0	ENST00000245479.2:c.448G>T	p.Glu150Ter	p.E150*	ENST00000245479	NM_000346.3	150	Gag/Tag	2/3	0.209035439850281	3	FACETS	0.84	0.783	0.898	0.84	0.783	0.898	INDETERMINATE	2	TRUE	1	0.477285944263653	3		353	624	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158637064	158637064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	96	500	1	ENST00000263640.3:c.116G>A	p.Gly39Asp	p.G39D	ENST00000263640	NM_001105.4	39	gGt/gAt	4/11	0.252273073142008	2	FACETS	0.589	0.525	0.657	0.294	0.262	0.329	INDETERMINATE	1	TRUE	0	0.477285944263653	2		501	683	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	195	420	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.39312798366121	1	FACETS	0.87	0.807	0.936	0.87	0.807	0.936	CLONAL	1	TRUE	0	0.42515146027953	1		420	830	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927979	178927984	+	inframe_deletion	In_Frame_Del	DEL	CTGTCC	CTGTCC	-	novel	NA	P-0015379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	91	212	0	ENST00000263967.3:c.1257_1262del	p.His419_Pro421delinsGln	p.H419_P421delinsQ	ENST00000263967	NM_006218.2	419	caCTGTCCa/caa	8/21	0.42515146027953	1	FACETS	0.911	0.815	1	0.911	0.815	1	CLONAL	1	TRUE	0	0.42515146027953	1		212	370	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879474	151879474	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0015379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	283	317	0	ENST00000262189.6:c.5471C>G	p.Ser1824Ter	p.S1824*	ENST00000262189	NM_170606.2	1824	tCa/tGa	36/59	0.39312798366121	1	FACETS	0.944	0.898	0.991	1	0.996	1	CLONAL	2	TRUE	0	0.42515146027953	1		317	555	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952077	+	missense_variant	Missense_Mutation	ONP	ATGAAT	ATGAAT	GTGAAG	novel	NA	P-0015379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	330	348	0	ENST00000263967.3:c.3127_3132delinsGTGAAG	p.Met1043_Asn1044delinsValLys	p.M1043_N1044delinsVK	ENST00000263967	NM_006218.2	1043	ATGAAT/GTGAAG	21/21	0.42515146027953	1	FACETS	0.904	0.862	0.947	1	0.996	1	CLONAL	2	TRUE	0	0.42515146027953	1		348	676	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231773	36231773	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	C	C	AGAGGTTA	novel	NA	P-0015379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	669	530	0	ENST00000300305.3:c.611delinsTAACCTCT	p.Arg204LeufsTer11	p.R204Lfs*11	ENST00000300305		204	cGa/cTAACCTCTa	5/8	0.406699006843154	2	FACETS	0.836	0.809	0.862	1	0.997	1	CLONAL	3	TRUE	0	0.42515146027953	2		530	1255	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0015425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	575	294	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.529376297833068	5	FACETS	1	0.994	1	1	0.994	1	CLONAL	5	TRUE	0	0.529376297833068	5		294	736	SUCCESS
ATM	472	MSKCC	GRCh37	11	108100048	108100048	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	58	346	0	ENST00000278616.4:c.329G>C	p.Arg110Thr	p.R110T	ENST00000278616	NM_000051.3	110	aGa/aCa	4/63	0.448965016433092	3	FACETS	0.725	0.626	0.833			1	SUBCLONAL	1	TRUE	NA	0.529376297833068	3		346	382	SUCCESS
ATR	545	MSKCC	GRCh37	3	142259862	142259862	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	92	485	0	ENST00000350721.4:c.3465G>C	p.Leu1155Phe	p.L1155F	ENST00000350721	NM_001184.3	1155	ttG/ttC	18/47	0.448880116152026	4	FACETS	0.87	0.774	0.972			1	CLONAL	1	TRUE	NA	0.529376297833068	4		485	611	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949138	151949138	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	92	530	0	ENST00000262189.6:c.1507G>T	p.Glu503Ter	p.E503*	ENST00000262189	NM_170606.2	503	Gaa/Taa	11/59	0.529376297833068	2	FACETS	0.759	0.677	0.845	0.379	0.338	0.423	SUBCLONAL	1	TRUE	0	0.529376297833068	2		530	458	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045498	47045498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	186	680	0	ENST00000377604.3:c.2465G>A	p.Arg822Lys	p.R822K	ENST00000377604	NM_001204468.1	822	aGa/aAa	22/24	0.294779339528421	5	FACETS	1	0.977	1	0.382	0.352	0.413	INDETERMINATE	1	TRUE	2	0.529376297833068	5		680	1100	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0015435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	364	497	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.580172335119141	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.580172335119141	1		497	819	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217909	2217909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1230117726	NA	P-0015435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	354	521	1	ENST00000398665.3:c.2683G>A	p.Glu895Lys	p.E895K	ENST00000398665	NM_032482.2	895	Gag/Aag	22/28	1	2	FACETS	0.936	0.886	0.987	0.936	0.886	0.987	CLONAL	1	TRUE	1	0.580172335119141	2		522	1304	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99192881	99192881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1013771934	NA	P-0015435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	174	268	0	ENST00000268035.6:c.71C>T	p.Ser24Leu	p.S24L	ENST00000268035	NM_000875.3	24	tCg/tTg	1/21	1	2	FACETS	0.967	0.895	1	0.967	0.895	1	CLONAL	1	TRUE	1	0.580172335119141	2		268	620	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403538	138403538	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	79	458	0	ENST00000289153.2:c.2244G>C	p.Gln748His	p.Q748H	ENST00000289153	NM_006219.2	748	caG/caC	15/22	1	2	FACETS	0.231	0.202	0.262	0.231	0.202	0.262	SUBCLONAL	1	TRUE	1	0.580172335119141	2		458	1178	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420158	420158	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	289	326	0	ENST00000399788.2:c.3109C>G	p.Leu1037Val	p.L1037V	ENST00000399788	NM_001042603.1	1037	Ctt/Gtt	21/28	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.580172335119141	2		326	990	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69230464	69230464	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	190	292	0	ENST00000462284.1:c.853A>C	p.Thr285Pro	p.T285P	ENST00000462284	NM_002392.5	285	Act/Cct	10/11	1	2	FACETS	0.891	0.826	0.958	0.891	0.826	0.958	CLONAL	1	TRUE	1	0.580172335119141	2		292	735	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001425	29001425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	151	215	0	ENST00000282397.4:c.1307C>T	p.Ser436Leu	p.S436L	ENST00000282397	NM_002019.4	436	tCa/tTa	10/30	1	2	FACETS	0.836	0.767	0.907	0.836	0.767	0.907	CLONAL	1	TRUE	1	0.580172335119141	2		215	623	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082546	16082546	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs748818541	NA	P-0015435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	253	372	0	ENST00000281043.3:c.360C>G	p.Phe120Leu	p.F120L	ENST00000281043	NM_005378.4	120	ttC/ttG	2/3	1	2	FACETS	0.919	0.861	0.979	0.919	0.861	0.979	CLONAL	1	TRUE	1	0.580172335119141	2		372	949	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480468	57480468	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	198	280	2	ENST00000371085.3:c.463G>A	p.Glu155Lys	p.E155K	ENST00000371085	NM_000516.4	155	Gag/Aag	6/13	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.580172335119141	2		282	660	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447410	12447410	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766913119	NA	P-0015435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	234	399	0	ENST00000287820.6:c.649G>A	p.Glu217Lys	p.E217K	ENST00000287820	NM_015869.4	217	Gag/Aag	5/7	1	2	FACETS	0.879	0.821	0.938	0.879	0.821	0.938	CLONAL	1	TRUE	1	0.580172335119141	2		399	918	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879643	151879643	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	111	147	0	ENST00000262189.6:c.5302G>T	p.Glu1768Ter	p.E1768*	ENST00000262189	NM_170606.2	1768	Gaa/Taa	36/59	1	2	FACETS	0.999	0.906	1	0.999	0.906	1	CLONAL	1	TRUE	1	0.580172335119141	2		147	383	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	339	440	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.468147001449804	2	FACETS	0.983	0.936	1	0.983	0.936	1	CLONAL	2	TRUE	0	0.468147001449804	2		440	737	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551661	150551661	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	223	275	0	ENST00000369026.2:c.346G>C	p.Ala116Pro	p.A116P	ENST00000369026	NM_021960.4	116	Gct/Cct	1/3	0.468147001449804	6	FACETS	1	0.971	1			1	CLONAL	2	TRUE	NA	0.468147001449804	6		275	859	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137726	64137726	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	405	552	0	ENST00000334205.4:c.1827C>G	p.Phe609Leu	p.F609L	ENST00000334205	NM_003942.2	609	ttC/ttG	15/17	0.297381450587766	5	FACETS	1	0.992	1	0.801	0.763	0.841	CLONAL	2	TRUE	2	0.468147001449804	5		552	1225	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497509	125497511	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0015496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	103	163	0	ENST00000428830.2:c.73_75del	p.Leu25del	p.L25del	ENST00000428830	NM_001114121.2	25	CTT/-	3/14	0.307166178534482	5	FACETS	1	0.924	1			1	CLONAL	2	TRUE	NA	0.468147001449804	5		163	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573958	7574277	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCCAGCCTGGGCATCCTTGAGTTCCAAGGCCTCATTCAGCTCTCGGAACATCTCGAAGCGCTCACGCCCACGGATCTGCAGCAACAGAGGAGGGGGAGAAGTAAGTATATACACAGTACCTGAGTTAAAAGATGGTTCAAGTTACAATTGTTTGACTTTATGACGGTACAAAAGCAACATGCATTTAGTAGAAACTGCACTTCAAGTACCTATACAGCTGACTTTTAAAAATATTTATTTATTTATTTTGAGATGGGGTCTCACTCTGTTGCCCAGGCGGGAGTGCAATGGTGCAATCTTGGCTGATTGCAATCTCCGC	TCCCAGCCTGGGCATCCTTGAGTTCCAAGGCCTCATTCAGCTCTCGGAACATCTCGAAGCGCTCACGCCCACGGATCTGCAGCAACAGAGGAGGGGGAGAAGTAAGTATATACACAGTACCTGAGTTAAAAGATGGTTCAAGTTACAATTGTTTGACTTTATGACGGTACAAAAGCAACATGCATTTAGTAGAAACTGCACTTCAAGTACCTATACAGCTGACTTTTAAAAATATTTATTTATTTATTTTGAGATGGGGTCTCACTCTGTTGCCCAGGCGGGAGTGCAATGGTGCAATCTTGGCTGATTGCAATCTCCGC	-	novel	NA	P-0015496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	84	433	0	ENST00000269305.4:c.994-244_1069del		p.X332_splice	ENST00000269305	NM_001126112.2	332		10/11	0.468147001449804	2	FACETS	0.867	0.77	0.97	0.433	0.385	0.485	CLONAL	1	TRUE	0	0.468147001449804	2		433	414	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164817	36164818	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGGC	novel	NA	P-0015496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	380	567	0	ENST00000300305.3:c.1054_1057dup	p.Phe353CysfsTer248	p.F353Cfs*248	ENST00000300305		353	ttc/tGCCTtc	8/8	0.307166178534482	5	FACETS	1	0.981	1			1	CLONAL	2	TRUE	NA	0.468147001449804	5		567	1296	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206763	36206764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	361	362	1	ENST00000300305.3:c.748_749insT	p.Arg250LeufsTer11	p.R250Lfs*11	ENST00000300305		250	cgt/cTgt	6/8	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.468147001449804	2		363	699	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643829	52643841	+	frameshift_variant	Frame_Shift_Del	DEL	AGAGGGAAGCCTC	AGAGGGAAGCCTC	-	novel	NA	P-0015496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	205	270	0	ENST00000394830.3:c.2055_2067del	p.Arg686AspfsTer9	p.R686Dfs*9	ENST00000394830	NM_018313.4	685	ctGAGGCTTCCCTCT/ct	17/30	0.297381450587766	5	FACETS	1	0.967	1	0.708	0.659	0.758	CLONAL	2	TRUE	2	0.468147001449804	5		270	702	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845545	151845545	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	309	405	0	ENST00000262189.6:c.13467T>G	p.Ile4489Met	p.I4489M	ENST00000262189	NM_170606.2	4489	atT/atG	52/59	0.297381450587766	5	FACETS	1	0.986	1	0.756	0.714	0.799	CLONAL	2	TRUE	2	0.468147001449804	5		405	991	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971167	21971167	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	172	274	0	ENST00000304494.5:c.191T>C	p.Leu64Pro	p.L64P	ENST00000304494	NM_000077.4	64	cTg/cCg	2/3	0.468147001449804	2	FACETS	0.972	0.907	1	0.972	0.907	1	CLONAL	2	TRUE	0	0.468147001449804	2		274	378	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024535	16024555	+	frameshift_variant	Frame_Shift_Del	DEL	AGTTTCTTCTGCTGTACCATC	AGTTTCTTCTGCTGTACCATC	T	novel	NA	P-0015496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	184	354	0	ENST00000268712.3:c.1663_1683delinsA	p.Asp555ArgfsTer21	p.D555Rfs*21	ENST00000268712	NM_006311.3	555	GATGGTACAGCAGAAGAAACT/A	16/46	0.468147001449804	2	FACETS	0.895	0.836	0.955	0.895	0.836	0.955	CLONAL	2	TRUE	0	0.468147001449804	2		354	439	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	138	313	2				ENST00000310581	NM_198253.2	-/1132			0.1324352705714	4	FACETS	0.999	0.92	1	0.999	0.92	1	INDETERMINATE	2	TRUE	2	0.611812808607232	4		315	364	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0015507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	286	294	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.533183126807834	5	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	2	0.611812808607232	5		294	577	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0015507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	111	472	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.611812808607232	3	FACETS	1	0.98	1	0.658	0.598	0.721	CLONAL	1	TRUE	1	0.611812808607232	3		472	360	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430385	47430385	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs947894890	NA	P-0015507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	172	554	0	ENST00000377045.4:c.1660C>T	p.Arg554Trp	p.R554W	ENST00000377045	NM_001654.4	554	Cgg/Tgg	15/16	0.611812808607232	4	FACETS	1	0.956	1			1	CLONAL	1	TRUE	NA	0.611812808607232	4		554	859	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101213	27101213	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	335	609	1	ENST00000324856.7:c.4495C>T	p.Gln1499Ter	p.Q1499*	ENST00000324856	NM_006015.4	1499	Cag/Tag	18/20	0.611812808607232	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.611812808607232	2		610	476	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653799	89653800	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0015507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	146	354	0	ENST00000371953.3:c.98_99dup	p.Ala34LeufsTer21	p.A34Lfs*21	ENST00000371953	NM_000314.4	33	att/aTTtt	2/9	0.611812808607232	3	FACETS	1	0.954	1	0.531	0.486	0.577	CLONAL	1	TRUE	1	0.611812808607232	3		354	587	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36421086	36421192	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTACAGGCAAAGCTGAGCAAAAGTAGATATTACAAGACCAGCATGTACTCACCTCTCATGAAGCACTGTGGGTACGAAGGAAATGACTCAAATATGCTGTCTGAAG	ATTACAGGCAAAGCTGAGCAAAAGTAGATATTACAAGACCAGCATGTACTCACCTCTCATGAAGCACTGTGGGTACGAAGGAAATGACTCAAATATGCTGTCTGAAG	-	novel	NA	P-0015507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	38	136	0	ENST00000300305.3:c.5_58+53del		p.X2_splice	ENST00000300305		2		1/8	0.609595325487916	4	FACETS	1	0.925	1	0.596	0.499	0.7	CLONAL	1	TRUE	2	0.611812808607232	4		136	168	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	144	511	1	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	NA	2	FACETS	1	0.937	1			1	INDETERMINATE	1	FALSE	NA	0.643780576819887	2		512	438	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10264991	10264991	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	97	393	0	ENST00000340748.4:c.1949G>T	p.Arg650Leu	p.R650L	ENST00000340748		650	cGc/cTc	21/40	0.486802561873144	4	FACETS	1	0.964	1			1	CLONAL	1	FALSE	NA	0.643780576819887	4		393	425	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910674	29910674	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	76	899	0	ENST00000376809.5:c.214C>G	p.Arg72Gly	p.R72G	ENST00000376809	NM_002116.7	72	Cgg/Ggg	2/8	0.631855353862946	2	FACETS	0.343	0.3	0.388	0.171	0.15	0.194	SUBCLONAL	1	FALSE	0	0.643780576819887	2		899	689	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752651	128752653	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs761021550	NA	P-0015710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	60	230	0	ENST00000377970.2:c.816_818del	p.Glu272del	p.E272del	ENST00000377970	NM_002467.4	271	cAAGaa/caa	3/3	0.643780576819887	7	FACETS	0.939	0.81	1	0.156	0.135	0.18	CLONAL	1	FALSE	1	0.643780576819887	7		230	518	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261309	115261309	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	69	442	0	ENST00000438362.2:c.2412G>T	p.Lys804Asn	p.K804N	ENST00000438362	NM_001242891.1	804	aaG/aaT	19/20	0.643780576819887	3	FACETS	0.471	0.411	0.537	0.236	0.205	0.269	SUBCLONAL	1	FALSE	1	0.643780576819887	3		442	601	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578369	212578369	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	36	268	1	ENST00000342788.4:c.888C>A	p.Asn296Lys	p.N296K	ENST00000342788	NM_005235.2	296	aaC/aaA	8/28	0.643780576819887	3	FACETS	0.485	0.4	0.579	0.242	0.2	0.29	SUBCLONAL	1	FALSE	1	0.643780576819887	3		269	305	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451439	187451439	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	56	348	0	ENST00000232014.4:c.43G>T	p.Ala15Ser	p.A15S	ENST00000232014	NM_001130845.1	15	Gcc/Tcc	3/10	0.643780576819887	3	FACETS	0.488	0.419	0.564	0.244	0.209	0.282	SUBCLONAL	1	FALSE	1	0.643780576819887	3		348	471	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674246	117674246	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	75	620	0	ENST00000368508.3:c.4228G>C	p.Ala1410Pro	p.A1410P	ENST00000368508	NM_002944.2	1410	Gca/Cca	26/43	0.643780576819887	2	FACETS	0.477	0.419	0.54	0.239	0.209	0.27	SUBCLONAL	1	FALSE	0	0.643780576819887	2		620	488	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913248	39913248	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	111	530	0	ENST00000378444.4:c.4867C>G	p.Pro1623Ala	p.P1623A	ENST00000378444	NM_001123385.1	1623	Cca/Gca	14/15	0.183186804773034	2	FACETS	0.837	0.758	0.919	0.418	0.379	0.46	INDETERMINATE	1	FALSE	0	0.643780576819887	2		530	412	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	271	340	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.362162774164642	5	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	2	0.362162774164642	5		340	660	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs967461896	NA	P-0015760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	261	635	0	ENST00000269305.4:c.526T>C	p.Cys176Arg	p.C176R	ENST00000269305	NM_001126112.2	176	Tgc/Cgc	5/11	0.362162774164642	3	FACETS	0.892	0.848	0.936	1	0.991	1	CLONAL	4	TRUE	0	0.362162774164642	3		635	477	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0015760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	2761	746	2	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.362162774164642	30	FACETS	0.995	0.988	1			1	CLONAL	31	TRUE	NA	0.362162774164642	30		748	3001	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584693	187584693	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	176	756	0	ENST00000441802.2:c.3340C>T	p.Gln1114Ter	p.Q1114*	ENST00000441802	NM_005245.3	1114	Cag/Tag	3/27	0.362162774164642	4	FACETS	0.807	0.745	0.872	0.538	0.496	0.582	CLONAL	2	TRUE	1	0.362162774164642	4		756	820	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830412	72830412	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	56	300	0	ENST00000268489.5:c.6169C>T	p.Gln2057Ter	p.Q2057*	ENST00000268489	NM_006885.3	2057	Cag/Tag	9/10	0.362162774164642	2	FACETS	0.758	0.659	0.863	0.758	0.659	0.863	SUBCLONAL	2	TRUE	0	0.362162774164642	2		300	204	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487561	38487561	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1313589879	NA	P-0015760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	171	680	0	ENST00000254066.5:c.91A>G	p.Met31Val	p.M31V	ENST00000254066	NM_000964.3	31	Atg/Gtg	2/9	0.362162774164642	1	FACETS	0.786	0.729	0.844	1	0.991	1	SUBCLONAL	2	TRUE	0	0.362162774164642	1		680	492	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59934581	59934581	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	532	321	0	ENST00000259008.2:c.217G>A	p.Asp73Asn	p.D73N	ENST00000259008	NM_032043.2	73	Gat/Aat	4/20	0.362162774164642	5	FACETS	1	0.978	1	1	0.997	1	CLONAL	5	TRUE	2	0.362162774164642	5		321	893	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15378237	15378237	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	270	596	0	ENST00000263377.2:c.549G>C	p.Arg183Ser	p.R183S	ENST00000263377	NM_058243.2	183	agG/agC	4/20	0.297723742281835	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	1	0.362162774164642	4		596	636	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004998	150004998	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	84	456	0	ENST00000253339.5:c.1227G>C	p.Met409Ile	p.M409I	ENST00000253339		409	atG/atC	3/7	0.362162774164642	6	FACETS	1	0.956	1	0.39	0.345	0.439	CLONAL	1	TRUE	3	0.362162774164642	6		456	683	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	105	609	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.161212672321958	3	FACETS	1	0.977	1	0.645	0.581	0.711	INDETERMINATE	1	TRUE	1	0.468674095013567	3		609	429	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257071	16257071	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	89	732	0	ENST00000375759.3:c.4336G>A	p.Ala1446Thr	p.A1446T	ENST00000375759	NM_015001.2	1446	Gct/Act	11/15	1	2	FACETS	0.913	0.814	1	0.913	0.814	1	CLONAL	1	TRUE	1	0.468674095013567	2		732	416	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061132	38061183	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCT	CCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCT	GC	novel	NA	P-0015793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	91	410	2	ENST00000250448.2:c.806_857delinsGC	p.Glu269GlyfsTer7	p.E269Gfs*7	ENST00000250448	NM_004496.3	269	gAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGCGGc/gGCc	2/2	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.468674095013567	2		412	286	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831946	72831946	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	71	788	0	ENST00000268489.5:c.4635C>A	p.Tyr1545Ter	p.Y1545*	ENST00000268489	NM_006885.3	1545	taC/taA	9/10	0.468674095013567	1	FACETS	0.776	0.683	0.874	0.776	0.683	0.874	SUBCLONAL	1	TRUE	0	0.468674095013567	1		788	299	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068418	26068418	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	55	481	0	ENST00000435504.4:c.72C>A	p.Tyr24Ter	p.Y24*	ENST00000435504		24	taC/taA	2/13	1	2	FACETS	0.876	0.756	1	0.876	0.756	1	CLONAL	1	TRUE	1	0.468674095013567	2		481	268	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591076	67591076	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	127	410	0	ENST00000274335.5:c.1669C>G	p.Arg557Gly	p.R557G	ENST00000274335		557	Cga/Gga	12/15	0.468674095013567	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.468674095013567	2		410	257	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717710	89717714	+	protein_altering_variant	In_Frame_Ins	INS	GCCGT	GCCGT	AGTACATGAATATC	novel	NA	P-0015793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	63	544	0	ENST00000371953.3:c.735_739delinsAGTACATGAATATC	p.Pro246delinsValHisGluTyr	p.P246delinsVHEY	ENST00000371953	NM_000314.4	245	caGCCGTta/caAGTACATGAATATCta	7/9	0.468674095013567	2	FACETS	1	0.889	1	0.509	0.445	0.577	CLONAL	1	TRUE	0	0.468674095013567	2		544	264	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0015838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	37	701	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.33638437252737	3	FACETS	1	0.948	1	0.685	0.576	0.803	CLONAL	1	TRUE	1	0.490954729267422	3		701	137	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	13	700	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.429477535640289	3	FACETS	0.297	0.212	0.401	0.149	0.106	0.201	SUBCLONAL	1	TRUE	1	0.490954729267422	3		700	222	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044464	5044464	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	12	630	0	ENST00000381652.3:c.412C>T	p.Arg138Ter	p.R138*	ENST00000381652	NM_004972.3	138	Cga/Tga	5/25	1	2	FACETS	0.263	0.185	0.359	0.263	0.185	0.359	SUBCLONAL	1	TRUE	1	0.490954729267422	2		630	186	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0015838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	100	701	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.212252012851236	4	FACETS	0.866	0.786	0.947	1	0.979	1	INDETERMINATE	3	FALSE	2	0.42311175764976	4		701	259	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	27	700	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.21862667280304	3	FACETS	0.515	0.411	0.635	0.258	0.205	0.318	INDETERMINATE	1	FALSE	1	0.42311175764976	3		700	300	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044464	5044464	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	33	630	0	ENST00000381652.3:c.412C>T	p.Arg138Ter	p.R138*	ENST00000381652	NM_004972.3	138	Cga/Tga	5/25	1	2	FACETS	0.503	0.411	0.607	0.503	0.411	0.607	SUBCLONAL	1	FALSE	1	0.42311175764976	2		630	310	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0015868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	55	467	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	0.631	0.54	0.73	0.631	0.54	0.73	SUBCLONAL	1	TRUE	1	0.334122832074142	2		467	522	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0015868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	240	845	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.334122832074142	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.334122832074142	1		845	950	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0015868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	117	493	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.334122832074142	2		493	614	SUCCESS
APC	324	MSKCC	GRCh37	5	112175328	112175328	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	59	228	0	ENST00000257430.4:c.4037C>A	p.Ser1346Ter	p.S1346*	ENST00000257430	NM_000038.5	1346	tCa/tAa	16/16	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.334122832074142	2		228	347	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	307	698	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	0.635828376137616	1	FACETS	0.996	0.947	1	0.996	0.947	1	CLONAL	1	TRUE	0	0.635828376137616	1		699	661	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	167	390	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.629942284625949	1	FACETS	0.746	0.692	0.802	0.746	0.692	0.802	SUBCLONAL	1	TRUE	0	0.635828376137616	1		390	480	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182192	99182192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763716402	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	176	593	0	ENST00000074304.5:c.2257G>A	p.Ala753Thr	p.A753T	ENST00000074304	NM_001134224.1	753	Gcc/Acc	21/26	0.635828376137616	1	FACETS	0.487	0.449	0.526	0.487	0.449	0.526	SUBCLONAL	1	TRUE	0	0.635828376137616	1		593	776	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	260	468	2	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	0.635828376137616	1	FACETS	0.878	0.829	0.929	0.878	0.829	0.929	CLONAL	1	TRUE	0	0.635828376137616	1		470	635	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440912	52440912	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1205668341	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	287	481	1	ENST00000460680.1:c.592del	p.Glu198ArgfsTer33	p.E198Rfs*33	ENST00000460680	NM_004656.3	198	Gag/ag	8/17	0.635828376137616	1	FACETS	0.914	0.865	0.962	0.914	0.865	0.962	CLONAL	1	TRUE	0	0.635828376137616	1		482	674	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29579996	29579996	+	intron_variant	Intron	DEL	A	A	-	rs1567859802	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	130	362	2	ENST00000356175.3:c.4110+3865del		p.*1370*	ENST00000356175	NM_000267.3	1384/2839			0.635828376137616	1	FACETS	0.55	0.502	0.601	0.55	0.502	0.601	SUBCLONAL	1	TRUE	0	0.635828376137616	1		364	507	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241726	55241726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767505234	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	269	449	0	ENST00000275493.2:c.2174C>T	p.Thr725Met	p.T725M	ENST00000275493	NM_005228.3	725	aCg/aTg	18/28	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.635828376137616	2		449	817	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56787259	56787259	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28363311	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	163	558	0	ENST00000337432.4:c.745C>T	p.Arg249Cys	p.R249C	ENST00000337432	NM_058216.2	249	Cgt/Tgt	5/9	0.635828376137616	1	FACETS	0.425	0.39	0.461	0.425	0.39	0.461	SUBCLONAL	1	TRUE	0	0.635828376137616	1		558	823	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370236	40370236	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs761761205	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	201	717	8	ENST00000293328.3:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000293328	NM_012448.3	368	Cag/ag	9/19	0.635828376137616	1	FACETS	0.651	0.606	0.698	0.651	0.606	0.698	SUBCLONAL	1	TRUE	0	0.635828376137616	1		725	662	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023289	27023290	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	133	271	0	ENST00000324856.7:c.400dup	p.Ala134GlyfsTer266	p.A134Gfs*266	ENST00000324856	NM_006015.4	132	gtg/gtGg	1/20	0.635828376137616	1	FACETS	0.802	0.737	0.867	0.802	0.737	0.867	CLONAL	1	TRUE	0	0.635828376137616	1		271	356	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138915	64138915	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	292	675	2	ENST00000334205.4:c.2287del	p.Arg763AlafsTer21	p.R763Afs*21	ENST00000334205	NM_003942.2	761	gCc/gc	17/17	0.635828376137616	1	FACETS	0.956	0.907	1	0.956	0.907	1	CLONAL	1	TRUE	0	0.635828376137616	1		677	655	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219907	133219907	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs973405989	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	101	536	3	ENST00000320574.5:c.4454G>A	p.Arg1485His	p.R1485H	ENST00000320574	NM_006231.2	1485	cGc/cAc	35/49	0.635828376137616	1	FACETS	0.427	0.383	0.474	0.427	0.383	0.474	SUBCLONAL	1	TRUE	0	0.635828376137616	1		539	507	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100999	41100999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1371429276	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	221	498	2	ENST00000373198.4:c.1357C>T	p.Arg453Cys	p.R453C	ENST00000373198	NM_133170.3	453	Cgc/Tgc	8/32	0.635828376137616	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.635828376137616	1		500	448	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562641	29562641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854562	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	226	424	3	ENST00000356175.3:c.3721C>T	p.Arg1241Ter	p.R1241*	ENST00000356175	NM_000267.3	1241	Cga/Tga	28/57	0.635828376137616	1	FACETS	0.895	0.841	0.949	0.895	0.841	0.949	CLONAL	1	TRUE	0	0.635828376137616	1		427	542	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254522	1254522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	188	762	0	ENST00000310581.5:c.3256C>T	p.Arg1086Cys	p.R1086C	ENST00000310581	NM_198253.2	1086	Cgt/Tgt	15/16	0.635828376137616	1	FACETS	0.557	0.516	0.599	0.557	0.516	0.599	SUBCLONAL	1	TRUE	0	0.635828376137616	1		762	724	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5258031	5258031	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	58	318	0	ENST00000357368.4:c.703C>T	p.Arg235Ter	p.R235*	ENST00000357368	NM_002850.3	235	Cga/Tga	8/38	0.635828376137616	1	FACETS	0.399	0.345	0.457	0.399	0.345	0.457	SUBCLONAL	1	TRUE	0	0.635828376137616	1		318	312	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512084	148512084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	321	533	3	ENST00000320356.2:c.1594C>T	p.Arg532Trp	p.R532W	ENST00000320356	NM_004456.4	532	Cgg/Tgg	14/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.635828376137616	2		536	985	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073547	8073547	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	52	343	0	ENST00000377482.5:c.1112G>A	p.Gly371Glu	p.G371E	ENST00000377482	NM_018948.3	371	gGa/gAa	4/4	0.635828376137616	1	FACETS	0.24	0.205	0.28	0.24	0.205	0.28	SUBCLONAL	1	TRUE	0	0.635828376137616	1		343	464	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690829	89690829	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	181	333	0	ENST00000371953.3:c.237del	p.Lys80AsnfsTer19	p.K80Nfs*19	ENST00000371953	NM_000314.4	79	gCc/gc	4/9	0.635828376137616	1	FACETS	0.83	0.773	0.888	0.83	0.773	0.888	CLONAL	1	TRUE	0	0.635828376137616	1		333	468	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944132	71944134	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs746559845	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	267	582	1	ENST00000298229.2:c.1967_1969del	p.Ser656del	p.S656del	ENST00000298229	NM_001567.3	655	atCTCc/atc	17/28	0.635828376137616	1	FACETS	0.998	0.945	1	0.998	0.945	1	CLONAL	1	TRUE	0	0.635828376137616	1		583	574	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230605	46230605	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303729294	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	271	388	0	ENST00000334344.6:c.854G>A	p.Arg285Gln	p.R285Q	ENST00000334344	NM_152641.2	285	cGg/cAg	8/21	0.629942284625949	1	FACETS	0.997	0.945	1	0.997	0.945	1	CLONAL	1	TRUE	0	0.635828376137616	1		388	583	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620101	21620101	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	114	587	0	ENST00000382592.4:c.65T>C	p.Ile22Thr	p.I22T	ENST00000382592	NM_014572.2	22	aTt/aCt	2/8	0.635828376137616	1	FACETS	0.325	0.293	0.36	0.325	0.293	0.36	SUBCLONAL	1	TRUE	0	0.635828376137616	1		587	752	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132982	30132982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750421913	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	391	695	1	ENST00000331968.5:c.619G>A	p.Val207Ile	p.V207I	ENST00000331968	NM_002742.2	207	Gtt/Att	4/18	0.398050604375648	1	FACETS	0.806	0.768	0.844	0.806	0.768	0.844	CLONAL	1	TRUE	0	0.635828376137616	1		696	1041	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239279	105239279	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs549370342	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	327	611	2	ENST00000349310.3:c.1108C>T	p.Arg370Cys	p.R370C	ENST00000349310	NM_001014432.1	370	Cgc/Tgc	12/15	0.398050604375648	1	FACETS	0.832	0.79	0.875	0.832	0.79	0.875	CLONAL	1	TRUE	0	0.635828376137616	1		613	843	SUCCESS
BLM	641	MSKCC	GRCh37	15	91328208	91328208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367953471	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	324	501	1	ENST00000355112.3:c.2720C>T	p.Thr907Met	p.T907M	ENST00000355112	NM_000057.2	907	aCg/aTg	14/22	NA	2	FACETS	0.957	0.905	1			1	INDETERMINATE	1	TRUE	NA	0.635828376137616	2		502	1065	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2221350	2221350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768242605	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	128	631	0	ENST00000326181.6:c.434C>T	p.Thr145Met	p.T145M	ENST00000326181	NM_032271.2	145	aCg/aTg	6/21	0.635828376137616	1	FACETS	0.455	0.414	0.499	0.455	0.414	0.499	SUBCLONAL	1	TRUE	0	0.635828376137616	1		631	603	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944308	81944308	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	286	544	2	ENST00000359376.3:c.1921del	p.His641ThrfsTer11	p.H641Tfs*11	ENST00000359376	NM_002661.3	639	aaC/aa	18/33	0.635828376137616	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.635828376137616	1		546	573	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428051	33428051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	249	486	0	ENST00000345365.6:c.908C>T	p.Thr303Ile	p.T303I	ENST00000345365	NM_002878.3	303	aCa/aTa	10/10	0.635828376137616	1	FACETS	0.952	0.899	1	0.952	0.899	1	CLONAL	1	TRUE	0	0.635828376137616	1		486	561	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40461085	40461085	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	345	698	0	ENST00000345506.4:c.2083G>A	p.Val695Met	p.V695M	ENST00000345506	NM_003152.3	695	Gtg/Atg	18/20	0.635828376137616	1	FACETS	0.954	0.908	1	0.954	0.908	1	CLONAL	1	TRUE	0	0.635828376137616	1		698	776	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47710084	47710084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779969	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	119	182	0	ENST00000233146.2:c.2801C>T	p.Thr934Met	p.T934M	ENST00000233146	NM_000251.2	934	aCg/aTg	16/16	0.629942284625949	1	FACETS	0.953	0.876	1	0.953	0.876	1	CLONAL	1	TRUE	0	0.635828376137616	1		182	268	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659941	227659941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	196	701	2	ENST00000305123.5:c.3514G>A	p.Gly1172Ser	p.G1172S	ENST00000305123	NM_005544.2	1172	Ggt/Agt	1/2	0.635828376137616	1	FACETS	0.542	0.503	0.582	0.542	0.503	0.582	SUBCLONAL	1	TRUE	0	0.635828376137616	1		703	776	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526970	31526970	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	415	703	1	ENST00000344624.3:c.70G>T	p.Gly24Ter	p.G24*	ENST00000344624		24	Gga/Tga	2/33	0.629942284625949	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.635828376137616	1		704	835	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665694	86665694	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	207	359	2	ENST00000274376.6:c.1675G>A	p.Gly559Arg	p.G559R	ENST00000274376	NM_002890.2	559	Gga/Aga	12/25	0.629942284625949	1	FACETS	0.873	0.817	0.928	0.873	0.817	0.928	CLONAL	1	TRUE	0	0.635828376137616	1		361	509	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180040092	180040092	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	275	689	0	ENST00000261937.6:c.3350G>T	p.Gly1117Val	p.G1117V	ENST00000261937	NM_182925.4	1117	gGg/gTg	25/30	0.635828376137616	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.635828376137616	1		689	587	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821418	32821418	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	147	717	0	ENST00000354258.4:c.176T>C	p.Val59Ala	p.V59A	ENST00000354258	NM_000593.5	59	gTg/gCg	1/11	0.635828376137616	1	FACETS	0.429	0.392	0.467	0.429	0.392	0.467	SUBCLONAL	1	TRUE	0	0.635828376137616	1		717	736	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979269	93979269	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs986768697	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	138	442	0	ENST00000369303.4:c.1559C>A	p.Ala520Asp	p.A520D	ENST00000369303	NM_004440.3	520	gCt/gAt	7/17	0.635828376137616	1	FACETS	0.538	0.492	0.586	0.538	0.492	0.586	SUBCLONAL	1	TRUE	0	0.635828376137616	1		442	550	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553233	106553233	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	287	610	1	ENST00000369096.4:c.1198C>A	p.Pro400Thr	p.P400T	ENST00000369096	NM_001198.3	400	Cca/Aca	5/7	0.635828376137616	1	FACETS	0.899	0.851	0.947	0.899	0.851	0.947	CLONAL	1	TRUE	0	0.635828376137616	1		611	685	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527565	157527565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1280712992	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	90	528	3	ENST00000346085.5:c.5290G>A	p.Ala1764Thr	p.A1764T	ENST00000346085	NM_020732.3	1764	Gct/Act	20/20	0.635828376137616	1	FACETS	0.264	0.234	0.296	0.264	0.234	0.296	SUBCLONAL	1	TRUE	0	0.635828376137616	1		531	732	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	154	574	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	0.451	0.412	0.492	0.451	0.412	0.492	SUBCLONAL	1	TRUE	1	0.635828376137616	2		574	1074	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878175	151878175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1456698574	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	251	468	1	ENST00000262189.6:c.6770G>A	p.Arg2257Gln	p.R2257Q	ENST00000262189	NM_170606.2	2257	cGa/cAa	36/59	1	2	FACETS	0.91	0.853	0.968	0.91	0.853	0.968	CLONAL	1	TRUE	1	0.635828376137616	2		469	868	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391656	139391656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768400804	NA	P-0016019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	403	781	4	ENST00000277541.6:c.6535C>T	p.Arg2179Trp	p.R2179W	ENST00000277541	NM_017617.3	2179	Cgg/Tgg	34/34	0.635828376137616	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.635828376137616	1		785	740	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0016024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	225	367	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.4376057912581	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	1	0.516497146912735	4		367	389	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231783	36231783	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057519748	NA	P-0016024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	51	606	0	ENST00000300305.3:c.601C>T	p.Arg201Ter	p.R201*	ENST00000300305		201	Cga/Tga	5/8	0.514243831991132	3	FACETS	0.319	0.27	0.373	0.16	0.135	0.187	SUBCLONAL	1	TRUE	1	0.516497146912735	3		606	778	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324674	31324674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11546719	NA	P-0016024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	10	88	1	ENST00000412585.2:c.134G>A	p.Arg45His	p.R45H	ENST00000412585	NM_005514.6	45	cGc/cAc	2/8	0.516497146912735	5	FACETS	0.687	0.469	0.956	0.229	0.156	0.319	SUBCLONAL	1	TRUE	2	0.516497146912735	5		89	100	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853186	68853204	+	frameshift_variant	Frame_Shift_Del	DEL	TCGGATTTGGAGAGACACT	TCGGATTTGGAGAGACACT	-	novel	NA	P-0016024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	14	394	0	ENST00000261769.5:c.1569_1587del	p.Tyr523Ter	p.Y523*	ENST00000261769	NM_004360.3	523	taTCGGATTTGGAGAGACACT/ta	11/16	0.516497146912735	1	FACETS	0.15	0.108	0.201	0.15	0.108	0.201	SUBCLONAL	1	TRUE	0	0.516497146912735	1		394	268	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252856	36252856	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	116	311	0	ENST00000300305.3:c.506G>C	p.Arg169Thr	p.R169T	ENST00000300305		169	aGa/aCa	4/8	0.514243831991132	3	FACETS	1	0.917	1	0.507	0.459	0.558	CLONAL	1	TRUE	1	0.516497146912735	3		311	557	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160738	56160739	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0016024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	83	327	0	ENST00000399503.3:c.1013dup	p.Tyr338Ter	p.Y338*	ENST00000399503	NM_005921.1	338	tac/tAac	4/20	0.501698035941372	4	FACETS	0.963	0.853	1			1	CLONAL	1	TRUE	NA	0.516497146912735	4		327	506	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183217	56183217	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	179	293	0	ENST00000399503.3:c.4127T>G	p.Leu1376Arg	p.L1376R	ENST00000399503	NM_005921.1	1376	cTa/cGa	18/20	0.501698035941372	4	FACETS	0.896	0.838	0.955			1	CLONAL	3	TRUE	NA	0.516497146912735	4		293	391	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845340	151845340	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs759388071	NA	P-0016024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	172	449	0	ENST00000262189.6:c.13672A>G	p.Ile4558Val	p.I4558V	ENST00000262189	NM_170606.2	4558	Att/Gtt	52/59	0.122236591224281	3	FACETS	1	0.957	1	0.691	0.644	0.739	INDETERMINATE	2	TRUE	0	0.516497146912735	3		449	404	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	577	313	2				ENST00000310581	NM_198253.2	-/1132			0.887845299160568	3	FACETS	0.995	0.964	1	0.995	0.964	1	CLONAL	2	TRUE	1	0.887845299160568	3		315	943	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019428	42019428	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	466	726	0	ENST00000219905.7:c.3481G>T	p.Val1161Leu	p.V1161L	ENST00000219905	NM_001164273.1	1161	Gta/Tta	10/24	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.887845299160568	2		726	980	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858321	27858321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868712730	NA	P-0016113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	387	481	0	ENST00000359303.2:c.250C>T	p.Arg84Cys	p.R84C	ENST00000359303	NM_003535.2	84	Cgt/Tgt	1/1	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.887845299160568	2		481	781	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934576	NA	P-0016140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	311	761	0	ENST00000269305.4:c.818G>C	p.Arg273Pro	p.R273P	ENST00000269305	NM_001126112.2	273	cGt/cCt	8/11	0.192916093321333	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	1	0.193122665535721	4		761	1112	SUCCESS
APC	324	MSKCC	GRCh37	5	112175513	112175513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	45	362	0	ENST00000257430.4:c.4222G>T	p.Glu1408Ter	p.E1408*	ENST00000257430	NM_000038.5	1408	Gaa/Taa	16/16	NA	2	FACETS	1	0.887	1			1	INDETERMINATE	1	TRUE	NA	0.193122665535721	2		362	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0016200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	318	780	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.595387824498697	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.595387824498697	1		780	745	SUCCESS
APC	324	MSKCC	GRCh37	5	112175536	112175536	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	59	330	0	ENST00000257430.4:c.4245del	p.Ser1415ArgfsTer4	p.S1415Rfs*4	ENST00000257430	NM_000038.5	1415	agT/ag	16/16	0.595387824498697	1	FACETS	0.542	0.471	0.617	0.542	0.471	0.617	SUBCLONAL	1	TRUE	0	0.595387824498697	1		330	257	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	180	710	0	ENST00000267101.3:c.310G>C	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ctg	3/28	0.430877846122786	1	FACETS	0.443	0.408	0.479	0.443	0.408	0.479	SUBCLONAL	1	TRUE	0	0.595387824498697	1		710	959	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664915	138664915	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	93	221	0	ENST00000330315.3:c.650C>G	p.Ser217Cys	p.S217C	ENST00000330315	NM_023067.3	217	tCc/tGc	1/1	0.582559288892186	2	FACETS	0.989	0.889	1	0.494	0.444	0.546	CLONAL	1	TRUE	0	0.595387824498697	2		221	316	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912094	114912094	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	161	316	0	ENST00000543371.1:c.1164G>A	p.Trp388Ter	p.W388*	ENST00000543371	NM_001198531.1	388	tgG/tgA	11/14	0.430877846122786	1	FACETS	0.838	0.776	0.902	0.838	0.776	0.902	CLONAL	1	TRUE	0	0.595387824498697	1		316	453	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81534666	81534666	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	98	441	0	ENST00000298171.2:c.311C>G	p.Thr104Ser	p.T104S	ENST00000298171	NM_000369.2	104	aCt/aGt	3/10	0.375052117676303	1	FACETS	0.646	0.581	0.713	0.646	0.581	0.713	SUBCLONAL	1	TRUE	0	0.595387824498697	1		441	358	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940458	31940458	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	78	580	0	ENST00000375333.2:c.491A>G	p.Asp164Gly	p.D164G	ENST00000375333	NM_032454.1	164	gAc/gGc	3/8	1	2	FACETS	0.253	0.221	0.287	0.253	0.221	0.287	SUBCLONAL	1	TRUE	1	0.595387824498697	2		580	1037	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577095	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519984	NA	P-0016279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	542	864	0	ENST00000269305.4:c.843C>A	p.Asp281Glu	p.D281E	ENST00000269305	NM_001126112.2	281	gaC/gaA	8/11	0.597635728311099	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.597635728311099	2		864	822	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984378	201984416	+	inframe_deletion	In_Frame_Del	DEL	GGCGACTCGTCTACAAGTTTGGCAAAAACTCAAGCGGCT	GGCGACTCGTCTACAAGTTTGGCAAAAACTCAAGCGGCT	-	novel	NA	P-0016279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	759	763	2	ENST00000359651.3:c.1045_1083del	p.Arg349_Trp361del	p.R349_W361del	ENST00000359651		348	cGGCGACTCGTCTACAAGTTTGGCAAAAACTCAAGCGGCTgg/cgg	8/8	0.597635728311099	6	FACETS	0.899	0.871	0.927	0.899	0.871	0.927	CLONAL	4	TRUE	2	0.597635728311099	6		765	1550	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457183	25457183	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	170	583	0	ENST00000264709.3:c.2704T>G	p.Phe902Val	p.F902V	ENST00000264709	NM_175629.2	902	Ttc/Gtc	23/23	0.597635728311099	3	FACETS	0.993	0.915	1	0.497	0.457	0.537	CLONAL	1	TRUE	1	0.597635728311099	3		583	744	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242800953	242800953	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777215737	NA	P-0016279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	442	686	4	ENST00000334409.5:c.38C>T	p.Ala13Val	p.A13V	ENST00000334409	NM_005018.2	13	gCg/gTg	1/5	0.410630751786381	3	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.597635728311099	3		690	841	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845367	42845367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757466150	NA	P-0016279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	197	597	0	ENST00000398585.3:c.895G>A	p.Ala299Thr	p.A299T	ENST00000398585	NM_001135099.1	299	Gcg/Acg	9/14	0.597635728311099	7	FACETS	1	0.987	1	0.22	0.203	0.238	CLONAL	1	TRUE	1	0.597635728311099	7		597	1247	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896496	151896496	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	116	410	0	ENST00000262189.6:c.4141A>G	p.Ile1381Val	p.I1381V	ENST00000262189	NM_170606.2	1381	Ata/Gta	27/59	0.597635728311099	3	FACETS	1	0.939	1	0.524	0.475	0.576	CLONAL	1	TRUE	1	0.597635728311099	3		410	481	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	68	313	2				ENST00000310581	NM_198253.2	-/1132			0.2562966154185	2	FACETS	0.924	0.812	1	0.924	0.812	1	CLONAL	2	TRUE	0	0.26570975246466	2		315	277	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228613019	228613019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773567566	NA	P-0016282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	30	169	0	ENST00000366696.1:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000366696	NM_003493.2	3	cGa/cAa	1/1	0.215135587278759	3	FACETS	0.92	0.744	1	0.46	0.372	0.56	CLONAL	1	TRUE	1	0.26570975246466	3		169	278	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561263	9561263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769939031	NA	P-0016282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	90	375	0	ENST00000353224.5:c.519G>A	p.Met173Ile	p.M173I	ENST00000353224	NM_177990.2	173	atG/atA	4/10	0.215135587278759	3	FACETS	1	0.927	1	0.53	0.47	0.594	CLONAL	1	TRUE	1	0.26570975246466	3		375	724	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121913370	NA	P-0016282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	105	286	0	ENST00000288602.6:c.1742A>G	p.Asn581Ser	p.N581S	ENST00000288602	NM_004333.4	581	aAt/aGt	15/18	0.26570975246466	5	FACETS	0.814	0.73	0.903	0.543	0.486	0.602	CLONAL	2	TRUE	2	0.26570975246466	5		286	679	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750440	41750440	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	62	355	0	ENST00000226382.2:c.188G>A	p.Gly63Glu	p.G63E	ENST00000226382	NM_003924.3	63	gGa/gAa	1/3	1	2	FACETS	0.844	0.729	0.968	0.844	0.729	0.968	CLONAL	1	TRUE	1	0.26570975246466	2		355	553	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259262	89259262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770780950	NA	P-0016282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	117	291	0	ENST00000336596.2:c.406C>T	p.Arg136Ter	p.R136*	ENST00000336596	NM_005233.5	136	Cga/Tga	3/17	0.212680057141537	3	FACETS	0.912	0.826	1	0.912	0.826	1	CLONAL	2	TRUE	1	0.26570975246466	3		291	547	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0016282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	92	294	0	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	0.215135587278759	3	FACETS	0.883	0.789	0.983	0.883	0.789	0.983	CLONAL	2	TRUE	1	0.26570975246466	3		294	444	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740665	58740665	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	120	760	0	ENST00000305921.3:c.1570C>T	p.Gln524Ter	p.Q524*	ENST00000305921	NM_003620.3	524	Caa/Taa	6/6	0.215135587278759	3	FACETS	0.787	0.708	0.871	0.394	0.354	0.436	SUBCLONAL	1	TRUE	1	0.26570975246466	3		760	1300	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979257	93979257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	76	437	0	ENST00000369303.4:c.1571G>A	p.Gly524Glu	p.G524E	ENST00000369303	NM_004440.3	524	gGa/gAa	7/17	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.26570975246466	2		437	536	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176461	142176461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	118	353	0	ENST00000350721.4:c.7640G>A	p.Arg2547Gln	p.R2547Q	ENST00000350721	NM_001184.3	2547	cGa/cAa	45/47	0.212680057141537	3	FACETS	0.892	0.808	0.98	0.892	0.808	0.98	CLONAL	2	TRUE	1	0.26570975246466	3		353	564	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560019	29560019	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1555615004	NA	P-0016282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	84	265	0	ENST00000356175.3:c.3497-1G>A		p.X1166_splice	ENST00000356175	NM_000267.3	1166			0.215135587278759	3	FACETS	0.945	0.84	1	0.945	0.84	1	CLONAL	2	TRUE	1	0.26570975246466	3		265	379	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530108	63530108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	256	637	1	ENST00000307078.5:c.2327C>T	p.Pro776Leu	p.P776L	ENST00000307078	NM_004655.3	776	cCa/cTa	10/11	0.215135587278759	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.26570975246466	3		638	1041	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857878	9857878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867464241	NA	P-0016282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	139	413	0	ENST00000330684.3:c.3523G>A	p.Glu1175Lys	p.E1175K	ENST00000330684	NM_001134407.1	1175	Gaa/Aaa	13/13	0.212680057141537	3	FACETS	0.759	0.691	0.83	0.759	0.691	0.83	SUBCLONAL	2	TRUE	1	0.26570975246466	3		413	781	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933735	36933736	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0016282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	95	539	1	ENST00000361632.4:c.1663_1664delinsAA	p.Gly555Lys	p.G555K	ENST00000361632		555	GGg/AAg	12/16	1	2	FACETS	0.943	0.84	1	0.943	0.84	1	CLONAL	1	TRUE	1	0.26570975246466	2		540	758	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165729	108165729	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs762083530	NA	P-0016282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	123	432	1	ENST00000278616.4:c.4852C>T	p.Arg1618Ter	p.R1618*	ENST00000278616	NM_000051.3	1618	Cga/Tga	32/63	0.2562966154185	2	FACETS	0.818	0.742	0.897	0.818	0.742	0.897	CLONAL	2	TRUE	0	0.26570975246466	2		433	566	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149289	119149289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	168	462	0	ENST00000264033.4:c.1297C>T	p.Pro433Ser	p.P433S	ENST00000264033	NM_005188.3	433	Ccg/Tcg	9/16	0.2562966154185	2	FACETS	0.849	0.782	0.918	0.849	0.782	0.918	CLONAL	2	TRUE	0	0.26570975246466	2		462	745	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427504	427504	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	102	513	0	ENST00000399788.2:c.2665C>T	p.Pro889Ser	p.P889S	ENST00000399788	NM_001042603.1	889	Cct/Tct	19/28	0.0832811185740447	4	FACETS	0.983	0.877	1	0.491	0.438	0.548	INDETERMINATE	1	TRUE	2	0.26570975246466	4		513	989	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716366	18716366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs935135637	NA	P-0016282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	113	435	0	ENST00000266497.5:c.3713C>T	p.Ser1238Leu	p.S1238L	ENST00000266497		1238	tCa/tTa	26/31	0.0832811185740447	4	FACETS	1	0.975	1	0.633	0.569	0.7	INDETERMINATE	1	TRUE	2	0.26570975246466	4		435	851	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504584	103504584	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	108	319	0	ENST00000355739.4:c.205C>T	p.Arg69Ter	p.R69*	ENST00000355739	NM_000123.3	69	Cga/Tga	2/15	0.0832811185740447	4	FACETS	0.801	0.72	0.887	0.801	0.72	0.887	INDETERMINATE	2	TRUE	2	0.26570975246466	4		319	642	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2090049	2090049	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0016282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	180	651	0	ENST00000219066.1:c.816-1G>A		p.X272_splice	ENST00000219066	NM_002528.5	272			0.212680057141537	3	FACETS	1	0.988	1	0.705	0.649	0.763	CLONAL	1	TRUE	1	0.26570975246466	3		651	1089	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813768	50813768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	256	672	2	ENST00000398568.2:c.1322C>T	p.Ser441Phe	p.S441F	ENST00000398568	NM_001042412.1	441	tCt/tTt	8/18	0.212680057141537	3	FACETS	0.802	0.749	0.857	0.802	0.749	0.857	CLONAL	2	TRUE	1	0.26570975246466	3		674	1361	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979035	7979035	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0016282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	162	422	0	ENST00000319144.4:c.1533-1G>A		p.X511_splice	ENST00000319144	NM_001139.2	511			0.215135587278759	3	FACETS	0.854	0.784	0.926	0.854	0.784	0.926	CLONAL	2	TRUE	1	0.26570975246466	3		422	809	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210422	2210422	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	184	530	0	ENST00000398665.3:c.1030del	p.Arg344AlafsTer43	p.R344Afs*43	ENST00000398665	NM_032482.2	343	cgC/cg	13/28	0.165205070347176	3	FACETS	1	0.963	1	0.711	0.658	0.765	CLONAL	2	TRUE	0	0.26570975246466	3		530	736	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141112	55141112	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	63	324	0	ENST00000257290.5:c.1758G>A	p.Trp586Ter	p.W586*	ENST00000257290	NM_006206.4	586	tgG/tgA	12/23	1	2	FACETS	0.886	0.767	1	0.886	0.767	1	CLONAL	1	TRUE	1	0.26570975246466	2		324	535	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670909	30670909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	480	588	0	ENST00000376406.3:c.5837C>T	p.Pro1946Leu	p.P1946L	ENST00000376406	NM_014641.2	1946	cCc/cTc	12/15	0.26570975246466	5	FACETS	0.958	0.917	1	0.958	0.917	1	CLONAL	4	TRUE	1	0.26570975246466	5		588	1318	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323111	31323111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151341370	NA	P-0016282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	51	510	1	ENST00000412585.2:c.878C>T	p.Pro293Leu	p.P293L	ENST00000412585	NM_005514.6	293	cCc/cTc	4/8	0.26570975246466	5	FACETS	0.556	0.471	0.651	0.139	0.117	0.163	SUBCLONAL	1	TRUE	1	0.26570975246466	5		511	965	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813435	32813436	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0016282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1341	115	693	3	ENST00000354258.4:c.2347_2348delinsAA	p.Gly783Lys	p.G783K	ENST00000354258	NM_000593.5	783	GGg/AAg	11/11	0.26570975246466	5	FACETS	0.831	0.746	0.922	0.208	0.186	0.231	CLONAL	1	TRUE	1	0.26570975246466	5		696	1456	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117630024	117630024	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746642345	NA	P-0016282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	64	490	0	ENST00000368508.3:c.6502C>T	p.Leu2168Phe	p.L2168F	ENST00000368508	NM_002944.2	2168	Ctt/Ttt	41/43	1	2	FACETS	0.748	0.647	0.857	0.748	0.647	0.857	SUBCLONAL	1	TRUE	1	0.26570975246466	2		490	644	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117746758	117746758	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	87	542	1	ENST00000368508.3:c.62G>A	p.Trp21Ter	p.W21*	ENST00000368508	NM_002944.2	21	tGg/tAg	1/43	1	2	FACETS	0.942	0.834	1	0.942	0.834	1	CLONAL	1	TRUE	1	0.26570975246466	2		543	695	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976676	2976676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	114	348	0	ENST00000396946.4:c.1336G>A	p.Asp446Asn	p.D446N	ENST00000396946	NM_032415.4	446	Gac/Aac	9/25	0.0832811185740447	4	FACETS	1	0.966	1	1	0.966	1	INDETERMINATE	2	TRUE	2	0.26570975246466	4		348	474	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157949	27157949	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	202	548	0	ENST00000380036.4:c.173G>A	p.Gly58Glu	p.G58E	ENST00000380036	NM_000459.3	58	gGa/gAa	2/23	0.2562966154185	2	FACETS	0.822	0.762	0.884	0.822	0.762	0.884	CLONAL	2	TRUE	0	0.26570975246466	2		548	925	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0016387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	416	454	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.832162790117994	1	FACETS	0.957	0.926	0.988	0.957	0.926	0.988	CLONAL	1	TRUE	0	0.843284478849607	1		454	596	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424968	49424978	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGGGGTACC	CTGGGGGTACC	-	novel	NA	P-0016387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	386	449	0	ENST00000301067.7:c.13510_13520del	p.Gly4504GlnfsTer67	p.G4504Qfs*67	ENST00000301067	NM_003482.3	4504	GGTACCCCCAGc/c	39/54	0.843284478849607	1	FACETS	0.964	0.932	0.996	0.964	0.932	0.996	CLONAL	1	TRUE	0	0.843284478849607	1		449	549	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515419	149515420	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0016387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	319	455	0	ENST00000261799.4:c.62_63del	p.Leu21ProfsTer83	p.L21Pfs*83	ENST00000261799	NM_002609.3	21	cTC/c	3/23	0.843284478849607	1	FACETS	0.908	0.872	0.943	0.908	0.872	0.943	CLONAL	1	TRUE	0	0.843284478849607	1		455	482	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785964	135785964	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs118203506	NA	P-0016439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	73	434	2	ENST00000298552.3:c.1257del	p.Arg420GlyfsTer20	p.R420Gfs*20	ENST00000298552	NM_001162426.1	419	ccC/cc	12/23	1	2	FACETS	0.995	0.872	1	0.995	0.872	1	CLONAL	1	TRUE	1	0.271247647117072	2		436	541	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690834	89690834	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	59	394	0	ENST00000371953.3:c.243del	p.Phe81LeufsTer18	p.F81Lfs*18	ENST00000371953	NM_000314.4	81	Ttt/tt	4/9	0.271247647117072	1	FACETS	0.859	0.741	0.986	0.859	0.741	0.986	CLONAL	1	TRUE	0	0.271247647117072	1		394	438	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098398	47098398	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	53	462	0	ENST00000409792.3:c.6876del	p.Ala2293GlnfsTer16	p.A2293Qfs*16	ENST00000409792	NM_014159.6	2292	caA/ca	15/21	0.271247647117072	1	FACETS	0.742	0.634	0.861	0.742	0.634	0.861	SUBCLONAL	1	TRUE	0	0.271247647117072	1		462	455	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623251	52623251	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	50	267	0	ENST00000394830.3:c.2800del	p.Ser934ProfsTer74	p.S934Pfs*74	ENST00000394830	NM_018313.4	934	Tcc/cc	19/30	0.271247647117072	1	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	0	0.271247647117072	1		267	302	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	182	313	2				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		315	429	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225400359	225400359	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0016448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	86	274	0	ENST00000264414.4:c.265-1G>T		p.X89_splice	ENST00000264414	NM_003590.4	89			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		274	434	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836798	151836798	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016498-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	288	609	0	ENST00000262189.6:c.14422G>T	p.Glu4808Ter	p.E4808*	ENST00000262189	NM_170606.2	4808	Gaa/Taa	56/59	0.575424690071114	3	FACETS	0.802	0.759	0.845	0.802	0.759	0.845	CLONAL	2	TRUE	1	0.687878996919089	3		609	702	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151932966	151932966	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016498-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	15	11	0	ENST00000262189.6:c.2705C>A	p.Ser902Ter	p.S902*	ENST00000262189	NM_170606.2	902	tCg/tAg	16/59	0.575424690071114	3	FACETS	0.977	0.769	1	0.977	0.769	1	CLONAL	2	TRUE	1	0.687878996919089	3		11	30	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188219	10188219	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs5030832	NA	P-0016523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	109	485	0	ENST00000256474.2:c.362A>G	p.Asp121Gly	p.D121G	ENST00000256474	NM_000551.3	121	gAt/gGt	2/3	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.247677045063786	2		485	756	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	44	413	0	ENST00000269305.4:c.569del	p.Pro190LeufsTer57	p.P190Lfs*57	ENST00000269305	NM_001126112.2	190	cCt/ct	6/11	1	2	FACETS	0.638	0.534	0.753	0.638	0.534	0.753	SUBCLONAL	1	TRUE	1	0.247677045063786	2		413	557	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158140	47158140	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	70	571	0	ENST00000409792.3:c.4559G>C	p.Cys1520Ser	p.C1520S	ENST00000409792	NM_014159.6	1520	tGt/tCt	4/21	1	2	FACETS	0.906	0.79	1	0.906	0.79	1	CLONAL	1	TRUE	1	0.247677045063786	2		571	624	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610580	52610585	+	inframe_deletion	In_Frame_Del	DEL	GTTTCT	GTTTCT	-	novel	NA	P-0016523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	63	388	0	ENST00000394830.3:c.3588_3593del	p.Glu1196_Thr1198delinsAsp	p.E1196_T1198delinsD	ENST00000394830	NM_018313.4	1196	gaAGAAACc/gac	23/30	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.247677045063786	2		388	491	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638724	176638725	+	missense_variant	Missense_Mutation	DNP	GC	GC	TA	novel	NA	P-0016523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	89	538	1	ENST00000439151.2:c.3324_3325delinsTA	p.His1109Asn	p.H1109N	ENST00000439151	NM_022455.4	1108	gtGCat/gtTAat	5/23	0.247677045063786	3	FACETS	0.919	0.813	1	0.459	0.406	0.516	CLONAL	1	TRUE	1	0.247677045063786	3		539	879	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045006	47045006	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	71	272	0	ENST00000377604.3:c.2332C>G	p.Gln778Glu	p.Q778E	ENST00000377604	NM_001204468.1	778	Cag/Gag	20/24	1	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.247677045063786	1		272	366	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188219	10188219	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs5030832	NA	P-0016523-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	188	485	0	ENST00000256474.2:c.362A>G	p.Asp121Gly	p.D121G	ENST00000256474	NM_000551.3	121	gAt/gGt	2/3	0.250200032981818	2	FACETS	1	0.988	1	0.673	0.622	0.725	CLONAL	1	TRUE	0	0.337120851566707	2		485	829	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016523-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	47	413	0	ENST00000269305.4:c.569del	p.Pro190LeufsTer57	p.P190Lfs*57	ENST00000269305	NM_001126112.2	190	cCt/ct	6/11	0.125716676031124	4	FACETS	0.437	0.367	0.514	0.218	0.183	0.257	INDETERMINATE	1	TRUE	2	0.337120851566707	4		413	854	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158140	47158140	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016523-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	33	571	0	ENST00000409792.3:c.4559G>C	p.Cys1520Ser	p.C1520S	ENST00000409792	NM_014159.6	1520	tGt/tCt	4/21	0.250200032981818	2	FACETS	0.303	0.246	0.368	0.152	0.123	0.184	SUBCLONAL	1	TRUE	0	0.337120851566707	2		571	646	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610580	52610585	+	inframe_deletion	In_Frame_Del	DEL	GTTTCT	GTTTCT	-	novel	NA	P-0016523-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	84	388	0	ENST00000394830.3:c.3588_3593del	p.Glu1196_Thr1198delinsAsp	p.E1196_T1198delinsD	ENST00000394830	NM_018313.4	1196	gaAGAAACc/gac	23/30	0.250200032981818	2	FACETS	0.975	0.864	1	0.488	0.432	0.547	CLONAL	1	TRUE	0	0.337120851566707	2		388	511	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638724	176638725	+	missense_variant	Missense_Mutation	DNP	GC	GC	TA	novel	NA	P-0016523-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	136	538	1	ENST00000439151.2:c.3324_3325delinsTA	p.His1109Asn	p.H1109N	ENST00000439151	NM_022455.4	1108	gtGCat/gtTAat	5/23	0.337120851566707	4	FACETS	1	0.954	1	0.54	0.49	0.592	CLONAL	1	TRUE	2	0.337120851566707	4		539	999	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045006	47045006	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016523-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	55	272	0	ENST00000377604.3:c.2332C>G	p.Gln778Glu	p.Q778E	ENST00000377604	NM_001204468.1	778	Cag/Gag	20/24	0.337120851566707	2	FACETS	0.587	0.502	0.68			1	SUBCLONAL	1	TRUE	NA	0.337120851566707	2		272	556	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972657	25972657	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016523-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	75	254	0	ENST00000435504.4:c.1768A>C	p.Asn590His	p.N590H	ENST00000435504		590	Aat/Cat	12/13	0.13758322633125	5	FACETS	1	0.932	1	0.365	0.32	0.414	INDETERMINATE	1	TRUE	2	0.337120851566707	5		254	612	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628782	187628782	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016523-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	125	476	0	ENST00000441802.2:c.2200T>C	p.Ser734Pro	p.S734P	ENST00000441802	NM_005245.3	734	Tcc/Ccc	2/27	0.16067599832941	3	FACETS	1	0.952	1	0.542	0.49	0.596	INDETERMINATE	1	TRUE	1	0.337120851566707	3		476	800	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0016530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	155	291	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.8	0.736	0.866	0.8	0.736	0.866	SUBCLONAL	1	TRUE	1	0.679033336601779	2		291	571	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727453	66727453	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397516790	NA	P-0016530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	257	345	0	ENST00000307102.5:c.169A>G	p.Lys57Glu	p.K57E	ENST00000307102	NM_002755.3	57	Aag/Gag	2/11	1	2	FACETS	0.909	0.853	0.965	0.909	0.853	0.965	CLONAL	1	TRUE	1	0.679033336601779	2		345	833	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459498	40459499	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0016530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	264	423	1	ENST00000345506.4:c.1759_1760delinsTT	p.Pro587Phe	p.P587F	ENST00000345506	NM_003152.3	587	CCc/TTc	15/20	1	2	FACETS	0.93	0.874	0.987	0.93	0.874	0.987	CLONAL	1	TRUE	1	0.679033336601779	2		424	836	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050307	13050307	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0016530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	301	435	3	ENST00000316448.5:c.259A>T	p.Lys87Ter	p.K87*	ENST00000316448	NM_004343.3	87	Aaa/Taa	3/9	1	2	FACETS	0.86	0.811	0.91	0.86	0.811	0.91	CLONAL	1	TRUE	1	0.679033336601779	2		438	1031	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932644	49932644	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	386	573	1	ENST00000296474.3:c.3227C>T	p.Pro1076Leu	p.P1076L	ENST00000296474	NM_002447.2	1076	cCc/cTc	14/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.679033336601779	2		574	1123	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259646	89259646	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	147	255	0	ENST00000336596.2:c.790G>A	p.Glu264Lys	p.E264K	ENST00000336596	NM_005233.5	264	Gaa/Aaa	3/17	1	2	FACETS	0.921	0.848	0.997	0.921	0.848	0.997	CLONAL	1	TRUE	1	0.679033336601779	2		255	470	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710585	117710585	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	197	257	0	ENST00000368508.3:c.1687G>A	p.Glu563Lys	p.E563K	ENST00000368508	NM_002944.2	563	Gag/Aag	12/43	0.679033336601779	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.679033336601779	1		257	346	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545622	106545622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	309	522	2	ENST00000359195.3:c.3099G>A	p.Met1033Ile	p.M1033I	ENST00000359195	NM_002649.2	1033	atG/atA	11/11	1	2	FACETS	0.854	0.806	0.903	0.854	0.806	0.903	CLONAL	1	TRUE	1	0.679033336601779	2		524	1066	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508284	106508284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	102	213	0	ENST00000359195.3:c.278C>T	p.Pro93Leu	p.P93L	ENST00000359195	NM_002649.2	93	cCg/cTg	2/11	1	2	FACETS	0.944	0.85	1	0.944	0.85	1	CLONAL	1	TRUE	1	0.510736271881284	2		213	423	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174437	11174437	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1553171141	NA	P-0016600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	165	479	0	ENST00000361445.4:c.7238G>T	p.Ser2413Ile	p.S2413I	ENST00000361445	NM_004958.3	2413	aGt/aTt	53/58	0.421772406276325	0	FACETS	0.61	0.564	0.658			1	SUBCLONAL	1	TRUE	0	0.510736271881284	0		479	518	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147196	61147196	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	249	446	0	ENST00000295025.8:c.874A>G	p.Lys292Glu	p.K292E	ENST00000295025	NM_002908.2	292	Aag/Gag	8/11	1	2	FACETS	0.993	0.929	1	0.993	0.929	1	CLONAL	1	TRUE	1	0.510736271881284	2		446	982	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188227	10188227	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	212	454	0	ENST00000256474.2:c.370del	p.Thr124HisfsTer35	p.T124Hfs*35	ENST00000256474	NM_000551.3	124	Aca/ca	2/3	0.510736271881284	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.510736271881284	1		454	594	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241485	105241485	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	226	557	0	ENST00000349310.3:c.495C>G	p.Ile165Met	p.I165M	ENST00000349310	NM_001014432.1	165	atC/atG	7/15	1	2	FACETS	0.885	0.823	0.949	0.885	0.823	0.949	CLONAL	1	TRUE	1	0.436525140971948	2		557	1170	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653829	89653829	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554893808	NA	P-0016658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	237	310	0	ENST00000371953.3:c.127G>T	p.Glu43Ter	p.E43*	ENST00000371953	NM_000314.4	43	Gaa/Taa	2/9	0.917334441486945	1	FACETS	0.995	0.963	1	0.995	0.963	1	CLONAL	1	TRUE	0	0.917334441486945	1		310	281	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578517	7578517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750600586	NA	P-0016688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	634	1296	0	ENST00000269305.4:c.413C>T	p.Ala138Val	p.A138V	ENST00000269305	NM_001126112.2	138	gCc/gTc	5/11	0.757371046467708	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.757371046467708	1		1296	981	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183739	10183739	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs5030802	NA	P-0016688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	335	825	2	ENST00000256474.2:c.208G>T	p.Glu70Ter	p.E70*	ENST00000256474	NM_000551.3	70	Gag/Tag	1/3	0.757371046467708	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.757371046467708	1		827	541	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926254	112926254	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	63	477	0	ENST00000351677.2:c.1387A>G	p.Ile463Val	p.I463V	ENST00000351677	NM_002834.3	463	Att/Gtt	12/16	1	2	FACETS	0.281	0.242	0.322	0.281	0.242	0.322	SUBCLONAL	1	TRUE	1	0.757371046467708	2		477	593	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623174	52623175	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0016688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	276	658	0	ENST00000394830.3:c.2876_2877del	p.His959ArgfsTer22	p.H959Rfs*22	ENST00000394830	NM_018313.4	959	cAT/c	19/30	0.757371046467708	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.757371046467708	1		658	410	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0016695-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	54	595	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.26859607865711	4	FACETS	0.968	0.845	1	1	0.969	1	CLONAL	3	TRUE	2	0.315793542331182	4		595	155	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577505	7577505	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs745425759	NA	P-0016695-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	67	699	0	ENST00000269305.4:c.776A>T	p.Asp259Val	p.D259V	ENST00000269305	NM_001126112.2	259	gAc/gTc	7/11	0.315793542331182	3	FACETS	0.89	0.789	0.994	0.89	0.789	0.994	CLONAL	3	TRUE	0	0.315793542331182	3		699	184	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118911	115118911	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016695-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	12	382	0	ENST00000257566.3:c.430G>T	p.Asp144Tyr	p.D144Y	ENST00000257566	NM_016569.3	144	Gat/Tat	2/8	0.315793542331182	2	FACETS	1	0.792	1	0.567	0.407	0.756	CLONAL	1	TRUE	0	0.315793542331182	2		382	67	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58700884	58700884	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016695-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	17	447	0	ENST00000305921.3:c.475G>A	p.Glu159Lys	p.E159K	ENST00000305921	NM_003620.3	159	Gaa/Aaa	2/6	0.315793542331182	5	FACETS	0.95	0.713	1	0.317	0.237	0.41	CLONAL	1	TRUE	2	0.315793542331182	5		447	167	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985887	60985887	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016695-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	14	425	0	ENST00000333681.4:c.13G>C	p.Gly5Arg	p.G5R	ENST00000333681		5	Ggg/Cgg	2/3	0.315793542331182	3	FACETS	0.703	0.511	0.933	0.352	0.255	0.467	CLONAL	1	TRUE	1	0.315793542331182	3		425	146	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247373	153247373	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016695-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	18	239	0	ENST00000281708.4:c.1429G>T	p.Gly477Cys	p.G477C	ENST00000281708	NM_033632.3	477	Ggt/Tgt	10/12	0.26859607865711	4	FACETS	0.937	0.722	1	0.937	0.722	1	CLONAL	2	TRUE	2	0.315793542331182	4		239	80	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797005	42797005	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148703020	NA	P-0016695-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	23	955	0	ENST00000575354.2:c.3463G>A	p.Ala1155Thr	p.A1155T	ENST00000575354	NM_015125.3	1155	Gcc/Acc	14/20	0.315793542331182	3	FACETS	0.774	0.606	0.966	0.387	0.303	0.483	CLONAL	1	TRUE	1	0.315793542331182	3		955	218	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4123778	4123778	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	G	novel	NA	P-0016728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	49	294	0	ENST00000262948.5:c.92+3G>C		p.X31_splice	ENST00000262948	NM_030662.3	31			1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.226758001441049	2		294	402	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027644	48027644	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	44	257	0	ENST00000234420.5:c.2522G>C	p.Arg841Thr	p.R841T	ENST00000234420	NM_000179.2	841	aGg/aCg	4/10	1	2	FACETS	0.933	0.784	1	0.933	0.784	1	CLONAL	1	TRUE	1	0.226758001441049	2		257	416	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191460	10191470	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TGCCCTTCCAG	TGCCCTTCCAG	-	novel	NA	P-0016728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	52	203	0	ENST00000256474.2:c.464-9_465del		p.X155_splice	ENST00000256474	NM_000551.3	155			0.226758001441049	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.226758001441049	1		203	353	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439780	52439780	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0016728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	74	346	0	ENST00000460680.1:c.931+1G>T		p.X311_splice	ENST00000460680	NM_004656.3	311			0.226758001441049	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.226758001441049	1		346	510	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056313	180056313	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	189	694	0	ENST00000261937.6:c.931A>C	p.Lys311Gln	p.K311Q	ENST00000261937	NM_182925.4	311	Aag/Cag	7/30	0.226758001441049	5	FACETS	0.879	0.81	0.95	0.586	0.54	0.634	CLONAL	2	TRUE	2	0.226758001441049	5		694	1271	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	468	979	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.532238320590128	3	FACETS	0.939	0.909	0.969	0.939	0.909	0.969	CLONAL	3	TRUE	0	0.614023350811359	3		979	707	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814797	139814797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144427288	NA	P-0016787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	141	703	0	ENST00000247668.2:c.790G>A	p.Ala264Thr	p.A264T	ENST00000247668	NM_021138.3	264	Gcg/Acg	8/11	0.614023350811359	3	FACETS	1	0.955	1	0.533	0.488	0.58	CLONAL	1	TRUE	1	0.614023350811359	3		703	563	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992208	72992208	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	288	779	0	ENST00000268489.5:c.1837G>T	p.Asp613Tyr	p.D613Y	ENST00000268489	NM_006885.3	613	Gat/Tat	2/10	0.604309657951699	2	FACETS	0.931	0.888	0.973	0.931	0.888	0.973	CLONAL	2	TRUE	0	0.614023350811359	2		779	504	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992253	72992253	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	377	919	0	ENST00000268489.5:c.1792G>T	p.Asp598Tyr	p.D598Y	ENST00000268489	NM_006885.3	598	Gac/Tac	2/10	0.604309657951699	2	FACETS	0.976	0.938	1	0.976	0.938	1	CLONAL	2	TRUE	0	0.614023350811359	2		919	629	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942181	81942181	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	224	547	0	ENST00000359376.3:c.1718A>T	p.Tyr573Phe	p.Y573F	ENST00000359376	NM_002661.3	573	tAc/tTc	17/33	0.604309657951699	2	FACETS	0.986	0.936	1	0.986	0.936	1	CLONAL	2	TRUE	0	0.614023350811359	2		547	370	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976115	7976115	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	174	658	0	ENST00000319144.4:c.2080C>G	p.Leu694Val	p.L694V	ENST00000319144	NM_001139.2	694	Ctg/Gtg	15/15	0.532238320590128	3	FACETS	1	0.989	1	0.463	0.429	0.498	CLONAL	1	TRUE	0	0.614023350811359	3		658	533	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064418	30064418	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	188	533	0	ENST00000338641.4:c.982G>T	p.Glu328Ter	p.E328*	ENST00000338641	NM_000268.3	328	Gag/Tag	10/16	0.5944109474695	2	FACETS	0.855	0.804	0.906	0.855	0.804	0.906	CLONAL	2	TRUE	0	0.614023350811359	2		533	358	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340398	8340398	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	170	466	0	ENST00000356435.5:c.5198G>A	p.Trp1733Ter	p.W1733*	ENST00000356435		1733	tGg/tAg	31/35	0.614023350811359	3	FACETS	1	0.989	1	0.721	0.668	0.775	CLONAL	1	TRUE	1	0.614023350811359	3		466	502	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174395	11174395	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1085307113	NA	P-0016803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	153	502	0	ENST00000361445.4:c.7280T>A	p.Leu2427Gln	p.L2427Q	ENST00000361445	NM_004958.3	2427	cTg/cAg	53/58	1	2	FACETS	0.959	0.877	1	0.959	0.877	1	CLONAL	1	TRUE	1	0.365678683320887	2		502	873	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183734	10183734	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs869025617	NA	P-0016803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	171	600	0	ENST00000256474.2:c.203C>A	p.Ser68Ter	p.S68*	ENST00000256474	NM_000551.3	68	tCg/tAg	1/3	0.365678683320887	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.365678683320887	1		600	703	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180952	108180952	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	46	311	0	ENST00000278616.4:c.5828A>T	p.Lys1943Met	p.K1943M	ENST00000278616	NM_000051.3	1943	aAg/aTg	39/63	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.365678683320887	2		311	234	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959347	26959347	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0016803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	26	244	0	ENST00000381527.3:c.515-1G>A		p.X172_splice	ENST00000381527	NM_001260.1	172			0.365678683320887	1	FACETS	0.731	0.585	0.894	0.731	0.585	0.894	SUBCLONAL	1	TRUE	0	0.365678683320887	1		244	159	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620696	52620698	+	frameshift_variant	Frame_Shift_Del	DEL	AAA	AAA	TC	novel	NA	P-0016803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	40	252	1	ENST00000394830.3:c.3055_3057delinsGA	p.Phe1019GlufsTer115	p.F1019Efs*115	ENST00000394830	NM_018313.4	1019	TTT/GA	21/30	0.365678683320887	1	FACETS	0.771	0.646	0.907	0.771	0.646	0.907	CLONAL	1	TRUE	0	0.365678683320887	1		253	232	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579321	7579322	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs587780067	NA	P-0016834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	232	418	0	ENST00000269305.4:c.365_366del	p.Val122AspfsTer26	p.V122Dfs*26	ENST00000269305	NM_001126112.2	122	gTG/g	4/11	0.368579146403546	2	FACETS	0.904	0.85	0.959	0.904	0.85	0.959	CLONAL	2	TRUE	0	0.44474984310343	2		418	577	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213640	2213640	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1167722438	NA	P-0016897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	121	584	0	ENST00000398665.3:c.1659+1G>A		p.X553_splice	ENST00000398665	NM_032482.2	553			1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.20018721376455	2		584	1160	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188249	10188250	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0016897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	151	599	0	ENST00000256474.2:c.394dup	p.Gln132ProfsTer3	p.Q132Pfs*3	ENST00000256474	NM_000551.3	131	aac/aaCc	2/3	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.20018721376455	2		599	1383	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441226	52441226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	73	346	0	ENST00000460680.1:c.544G>A	p.Glu182Lys	p.E182K	ENST00000460680	NM_004656.3	182	Gag/Aag	7/17	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.20018721376455	2		346	687	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584550	52584551	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0016897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	97	451	0	ENST00000394830.3:c.4462_4463del	p.Val1488SerfsTer20	p.V1488Sfs*20	ENST00000394830	NM_018313.4	1488	GTa/a	29/30	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.20018721376455	2		451	888	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103828	47103828	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs976581260	NA	P-0016971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	115	302	1	ENST00000409792.3:c.6118C>T	p.Arg2040Ter	p.R2040*	ENST00000409792	NM_014159.6	2040	Cga/Tga	14/21	0.532935120859974	1	FACETS	0.726	0.659	0.796	0.726	0.659	0.796	SUBCLONAL	1	TRUE	0	0.532935120859974	1		303	436	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953945	32953945	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	47	593	0	ENST00000380152.3:c.9012G>T	p.Lys3004Asn	p.K3004N	ENST00000380152		3004	aaG/aaT	23/27	1	2	FACETS	0.226	0.19	0.267	0.226	0.19	0.267	SUBCLONAL	1	TRUE	1	0.532935120859974	2		593	779	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183863	10183881	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTACCGAGGTACGGGCCC	GCTACCGAGGTACGGGCCC	-	novel	NA	P-0016971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	160	544	0	ENST00000256474.2:c.333_340+11del		p.X111_splice	ENST00000256474	NM_000551.3	111		1/3	0.532935120859974	1	FACETS	0.847	0.782	0.914	0.847	0.782	0.914	CLONAL	1	TRUE	0	0.532935120859974	1		544	520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577085	+	missense_variant	Missense_Mutation	ONP	CCTC	CCTC	TCTT	novel	NA	P-0017014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	465	924	1	ENST00000269305.4:c.853_856delinsAAGA	p.Glu285_Glu286delinsLysLys	p.E285_E286delinsKK	ENST00000269305	NM_001126112.2	285	GAGGaa/AAGAaa	8/11	0.535593967600241	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.544805413012952	2		925	811	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675064	40675064	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	184	923	0	ENST00000249776.8:c.28G>A	p.Asp10Asn	p.D10N	ENST00000249776	NM_033286.3	10	Gac/Aac	1/9	0.535593967600241	2	FACETS	0.903	0.836	0.973	0.452	0.418	0.487	CLONAL	1	TRUE	0	0.544805413012952	2		923	748	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793057	42793057	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs746104382	NA	P-0017014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	225	764	0	ENST00000575354.2:c.949T>A	p.Ser317Thr	p.S317T	ENST00000575354	NM_015125.3	317	Tcc/Acc	7/20	0.276166919489841	3	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.544805413012952	3		764	966	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881703	111881703	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0017014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	166	714	0	ENST00000393256.3:c.381T>G	p.Tyr127Ter	p.Y127*	ENST00000393256	NM_006538.4	127	taT/taG	2/4	0.544805413012952	2	FACETS	0.857	0.789	0.927	0.429	0.394	0.464	CLONAL	1	TRUE	0	0.544805413012952	2		714	711	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971140	21971140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	104	492	0	ENST00000304494.5:c.218C>T	p.Ala73Val	p.A73V	ENST00000304494	NM_000077.4	73	gCc/gTc	2/3	0.544805413012952	4	FACETS	0.907	0.814	1	0.302	0.271	0.336	CLONAL	1	TRUE	1	0.544805413012952	4		492	650	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0017054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	10	482	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.417	0.281	0.589	0.417	0.281	0.589	SUBCLONAL	1	TRUE	1	0.12	2		482	400	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508728	148508728	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs267601395	NA	P-0017054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	19	402	0	ENST00000320356.2:c.1936T>C	p.Tyr646His	p.Y646H	ENST00000320356	NM_004456.4	646	Tac/Cac	16/20	1	2	FACETS	1	0.781	1	1	0.781	1	CLONAL	1	TRUE	1	0.12	2		402	307	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0017055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	292	587	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.61338040154493	3	FACETS	0.986	0.936	1	0.986	0.936	1	CLONAL	2	TRUE	1	0.61338040154493	3		587	631	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039133	49039133	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0017055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	103	192	0	ENST00000267163.4:c.2212-1G>C		p.X738_splice	ENST00000267163	NM_000321.2	738			0.61338040154493	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	0	0.61338040154493	2		192	166	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176104169	176104169	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	104	429	0	ENST00000367669.3:c.945T>A	p.Phe315Leu	p.F315L	ENST00000367669	NM_022457.5	315	ttT/ttA	8/20	0.61338040154493	6	FACETS	0.89	0.797	0.99	0.178	0.159	0.198	CLONAL	1	TRUE	1	0.61338040154493	6		429	848	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870862	12870862	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	72	213	0	ENST00000228872.4:c.90del	p.Asn31ThrfsTer11	p.N31Tfs*11	ENST00000228872	NM_004064.3	30	aGg/ag	1/3	0.61001538960999	1	FACETS	0.904	0.808	1	0.904	0.808	1	CLONAL	1	TRUE	0	0.61338040154493	1		213	180	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288412	15288412	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	256	505	1	ENST00000263388.2:c.4327G>A	p.Asp1443Asn	p.D1443N	ENST00000263388	NM_000435.2	1443	Gac/Aac	24/33	0.61338040154493	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.61338040154493	3		506	515	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47643569	47643569	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs267607940	NA	P-0017055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	64	352	2	ENST00000233146.2:c.1076+1G>T		p.X359_splice	ENST00000233146	NM_000251.2	359			1	2	FACETS	0.77	0.674	0.872	0.77	0.674	0.872	SUBCLONAL	1	TRUE	1	0.61338040154493	2		354	271	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997410	149997410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	386	651	0	ENST00000253339.5:c.2869G>A	p.Glu957Lys	p.E957K	ENST00000253339		957	Gaa/Aaa	6/7	0.61338040154493	3	FACETS	0.996	0.952	1	0.996	0.952	1	CLONAL	2	TRUE	1	0.61338040154493	3		651	826	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836846	151836846	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	332	595	0	ENST00000262189.6:c.14374G>T	p.Glu4792Ter	p.E4792*	ENST00000262189	NM_170606.2	4792	Gag/Tag	56/59	0.61338040154493	3	FACETS	0.999	0.952	1	0.999	0.952	1	CLONAL	2	TRUE	1	0.61338040154493	3		595	708	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949218	71949218	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	155	621	2	ENST00000298229.2:c.3685A>G	p.Ser1229Gly	p.S1229G	ENST00000298229	NM_001567.3	1229	Agt/Ggt	27/28	1	2	FACETS	0.921	0.842	1	0.921	0.842	1	CLONAL	1	TRUE	1	0.31	2		623	1086	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188296	10188297	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0017059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	197	573	0	ENST00000256474.2:c.443_444dup	p.Ala149LeufsTer11	p.A149Lfs*11	ENST00000256474	NM_000551.3	147	att/aTTtt	2/3	0.303872458837382	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.31	1		573	959	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651275	52651278	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TACC	TACC	-	novel	NA	P-0017059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	130	371	0	ENST00000394830.3:c.1818_1818+3del		p.X606_splice	ENST00000394830	NM_018313.4	606		15/30	0.303872458837382	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.31	1		371	652	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412449	63412449	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	42	288	0	ENST00000330258.3:c.718T>C	p.Ser240Pro	p.S240P	ENST00000330258	NM_152424.3	240	Tct/Cct	2/2	1	1	FACETS	0.337	0.28	0.4	0.337	0.28	0.4	SUBCLONAL	1	TRUE	0	0.31	1		288	680	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654627	67654627	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	107	370	0	ENST00000264010.4:c.1114T>C	p.Ser372Pro	p.S372P	ENST00000264010	NM_006565.3	372	Tct/Cct	6/12	1	2	FACETS	0.711	0.636	0.79	0.711	0.636	0.79	SUBCLONAL	1	TRUE	1	0.292599432426332	2		370	1029	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162012	47162012	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	90	235	0	ENST00000409792.3:c.4114del	p.Ile1372Ter	p.I1372*	ENST00000409792	NM_014159.6	1372	Ata/ta	3/21	0.292599432426332	1	FACETS	0.941	0.837	1	0.941	0.837	1	CLONAL	1	TRUE	0	0.292599432426332	1		235	558	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620685	52620703	+	stop_gained,protein_altering_variant,splice_region_variant	Nonsense_Mutation	DEL	GGGCATAACTTAAAGTATT	GGGCATAACTTAAAGTATT	TATG	novel	NA	P-0017101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	68	237	2	ENST00000394830.3:c.3050_3068delinsCATA	p.Glu1017_Pro1023delinsAlaTer	p.E1017_P1023delinsA*	ENST00000394830	NM_018313.4	1017	gAATACTTTAAGTTATGCCCa/gCATAa	21/30	0.292599432426332	1	FACETS	0.803	0.7	0.914	0.803	0.7	0.914	CLONAL	1	TRUE	0	0.292599432426332	1		239	494	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157957	106157960	+	frameshift_variant	Frame_Shift_Del	DEL	GGTG	GGTG	AGT	novel	NA	P-0017101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	148	333	2	ENST00000380013.4:c.2858_2861delinsAGT	p.Arg953LysfsTer54	p.R953Kfs*54	ENST00000380013	NM_001127208.2	953	aGGTGg/aAGTg	3/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.292599432426332	2		335	874	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191513	10191513	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1131690962	NA	P-0017115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	68	588	0	ENST00000256474.2:c.506T>C	p.Leu169Pro	p.L169P	ENST00000256474	NM_000551.3	169	cTa/cCa	3/3	0.255950198293383	1	FACETS	0.918	0.8	1	0.918	0.8	1	CLONAL	1	TRUE	0	0.255950198293383	1		588	505	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111959683	111959683	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	38	383	0	ENST00000375549.3:c.262T>A	p.Cys88Ser	p.C88S	ENST00000375549	NM_003002.3	88	Tgc/Agc	3/4	1	2	FACETS	0.881	0.73	1	0.881	0.73	1	CLONAL	1	TRUE	1	0.255950198293383	2		383	337	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245003	46245003	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	172	783	1	ENST00000334344.6:c.3100del	p.Gln1034AsnfsTer26	p.Q1034Nfs*26	ENST00000334344	NM_152641.2	1033	Ccc/cc	15/21	0.239189147627721	3	FACETS	0.793	0.729	0.859	0.793	0.729	0.859	SUBCLONAL	2	TRUE	1	0.255950198293383	3		784	956	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726668	88726668	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	49	599	0	ENST00000360948.2:c.376A>G	p.Asn126Asp	p.N126D	ENST00000360948	NM_001012338.2	126	Aac/Gac	4/19	1	2	FACETS	0.788	0.668	0.92	0.788	0.668	0.92	CLONAL	1	TRUE	1	0.255950198293383	2		599	486	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597477	52597477	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	39	643	0	ENST00000394830.3:c.3833del	p.Pro1278LeufsTer10	p.P1278Lfs*10	ENST00000394830	NM_018313.4	1278	cCt/ct	25/30	0.255950198293383	1	FACETS	0.72	0.598	0.856	0.72	0.598	0.856	SUBCLONAL	1	TRUE	0	0.255950198293383	1		643	369	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524543	176524543	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	218	1109	4	ENST00000292408.4:c.2275C>A	p.Leu759Met	p.L759M	ENST00000292408	NM_213647.1	759	Ctg/Atg	18/18	0.0794901530464325	3	FACETS	0.97	0.903	1	0.97	0.903	1	INDETERMINATE	2	TRUE	1	0.255950198293383	3		1113	990	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289076	33289076	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	79	672	2	ENST00000374542.5:c.476A>G	p.Asn159Ser	p.N159S	ENST00000374542	NM_001141970.1	159	aAc/aGc	3/8	0.0794901530464325	3	FACETS	1	0.889	1	0.506	0.445	0.572	INDETERMINATE	1	TRUE	1	0.255950198293383	3		674	688	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247529	53247529	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	104	466	1	ENST00000375401.3:c.280G>T	p.Glu94Ter	p.E94*	ENST00000375401	NM_004187.3	94	Gaa/Taa	3/26	1	1	FACETS	0.945	0.854	1	1	0.988	1	CLONAL	2	TRUE	0	0.255950198293383	1		467	375	SUCCESS
AR	367	MSKCC	GRCh37	X	66931504	66931504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1340026226	NA	P-0017169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3852	3066	370	1	ENST00000374690.3:c.2146G>A	p.Val716Met	p.V716M	ENST00000374690	NM_000044.3	716	Gtg/Atg	4/8	0.322947536810722	28	FACETS	1	0.994	1			1	CLONAL	14	TRUE	NA	0.322947536810722	28		371	6918	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464410	120464421	+	inframe_deletion	In_Frame_Del	DEL	CTGAGACTTGCA	CTGAGACTTGCA	-	novel	NA	P-0017169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	109	734	0	ENST00000256646.2:c.5225_5236del	p.Val1742_Ser1745del	p.V1742_S1745del	ENST00000256646	NM_024408.3	1742	gTGCAAGTCTCAGaa/gaa	29/34	1	2	FACETS	0.697	0.624	0.773	0.697	0.624	0.773	SUBCLONAL	1	TRUE	1	0.322947536810722	2		734	969	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431254	49431258	+	frameshift_variant	Frame_Shift_Del	DEL	CATGG	CATGG	-	novel	NA	P-0017169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	173	445	0	ENST00000301067.7:c.9881_9885del	p.Ala3294ValfsTer5	p.A3294Vfs*5	ENST00000301067	NM_003482.3	3294	gCCATG/g	34/54	1	2	FACETS	0.857	0.792	0.924	1	0.992	1	CLONAL	2	TRUE	1	0.322947536810722	2		445	625	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274157	10274158	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0017169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	196	566	0	ENST00000330684.3:c.111_112delinsTT	p.Val38Leu	p.V38L	ENST00000330684	NM_001134407.1	37	gcGGtg/gcTTtg	2/13	1	2	FACETS	0.839	0.78	0.901	1	0.992	1	CLONAL	2	TRUE	1	0.322947536810722	2		566	723	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056353	26056353	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	55	391	0	ENST00000343677.2:c.304del	p.Ser102LeufsTer65	p.S102Lfs*65	ENST00000343677	NM_005319.3	102	Tct/ct	1/1	0.291925473937972	1	FACETS	0.571	0.489	0.661	0.571	0.489	0.661	SUBCLONAL	1	TRUE	0	0.322947536810722	1		391	500	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188758	32188758	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	138	613	0	ENST00000375023.3:c.796C>A	p.Pro266Thr	p.P266T	ENST00000375023	NM_004557.3	266	Cca/Aca	4/30	0.291925473937972	1	FACETS	0.884	0.804	0.967	0.884	0.804	0.967	CLONAL	1	TRUE	0	0.322947536810722	1		613	811	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013719	12013719	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017181-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	11	309	0	ENST00000353533.5:c.661G>T	p.Glu221Ter	p.E221*	ENST00000353533	NM_003010.3	221	Gaa/Taa	6/11	0.511293362274	1	FACETS	0.207	0.143	0.285	0.207	0.143	0.285	SUBCLONAL	1	TRUE	0	0.590268740329016	1		309	127	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0017181-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	129	450	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	0.976	0.891	1	0.976	0.891	1	CLONAL	1	TRUE	1	0.590268740329016	2		450	448	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865239	57865239	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	77	926	0	ENST00000228682.2:c.2716C>A	p.Gln906Lys	p.Q906K	ENST00000228682	NM_005269.2	906	Cag/Aag	12/12	1	2	FACETS	0.816	0.715	0.926	0.816	0.715	0.926	CLONAL	1	TRUE	1	0.193095337599666	2		926	977	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183752	10183752	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs5030803	NA	P-0017192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	75	905	1	ENST00000256474.2:c.221T>C	p.Val74Ala	p.V74A	ENST00000256474	NM_000551.3	74	gTc/gCc	1/3	0.17608275572803	2	FACETS	0.813	0.711	0.924	0.407	0.355	0.462	CLONAL	1	TRUE	0	0.193095337599666	2		906	955	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183848	10183849	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCGCCT	novel	NA	P-0017192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	97	832	0	ENST00000256474.2:c.322_323insTCCGCC	p.Arg107_Arg108insLeuArg	p.R107_R108insLR	ENST00000256474	NM_000551.3	106	ggc/ggCCGCCTc	1/3	0.17608275572803	2	FACETS	1	0.963	1	0.596	0.531	0.666	CLONAL	1	TRUE	0	0.193095337599666	2		832	843	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441989	52442010	+	frameshift_variant	Frame_Shift_Del	DEL	CTTGGTGAAGTCCTTCATGCGA	CTTGGTGAAGTCCTTCATGCGA	-	novel	NA	P-0017192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	31	553	0	ENST00000460680.1:c.339_360del	p.Ser113ArgfsTer67	p.S113Rfs*67	ENST00000460680	NM_004656.3	113	agTCGCATGAAGGACTTCACCAAG/ag	5/17	0.193095337599666	1	FACETS	0.536	0.433	0.654	0.536	0.433	0.654	SUBCLONAL	1	TRUE	0	0.193095337599666	1		553	541	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752836	57752868	+	inframe_deletion	In_Frame_Del	DEL	AAAGAAATTCTTAGCTGGGCTTGATAAGTGGAA	AAAGAAATTCTTAGCTGGGCTTGATAAGTGGAA	-	novel	NA	P-0017192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	65	566	0	ENST00000274289.3:c.1060_1092del	p.Phe354_Phe364del	p.F354_F364del	ENST00000274289	NM_006622.3	354	TTCCACTTATCAAGCCCAGCTAAGAATTTCTTT/-	8/14	1	2	FACETS	0.894	0.774	1	0.894	0.774	1	CLONAL	1	TRUE	1	0.193095337599666	2		566	753	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709068	117709068	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1224165751	NA	P-0017192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	67	803	0	ENST00000368508.3:c.1889G>A	p.Ser630Asn	p.S630N	ENST00000368508	NM_002944.2	630	aGt/aAt	13/43	1	2	FACETS	0.676	0.586	0.775	0.676	0.586	0.775	SUBCLONAL	1	TRUE	1	0.193095337599666	2		803	1026	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0017205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	57	499	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.3	1	FACETS	0.83	0.715	0.955	0.83	0.715	0.955	CLONAL	1	TRUE	0	0.3	1		499	389	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	33	313	2				ENST00000310581	NM_198253.2	-/1132			0.160821758260189	0	FACETS	0.562	0.46	0.676			1	INDETERMINATE	1	TRUE	0	0.3	0		315	274	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637653	52637653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	87	802	0	ENST00000394830.3:c.2663C>T	p.Ser888Leu	p.S888L	ENST00000394830	NM_018313.4	888	tCa/tTa	18/30	0.3	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.3	1		802	439	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183770	10183770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs5030805	NA	P-0017205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	145	969	1	ENST00000256474.2:c.239G>A	p.Ser80Asn	p.S80N	ENST00000256474	NM_000551.3	80	aGt/aAt	1/3	0.3	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.3	1		970	610	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273221	115273221	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	116	1035	0	ENST00000438362.2:c.1237G>A	p.Asp413Asn	p.D413N	ENST00000438362	NM_001242891.1	413	Gat/Aat	11/20	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.3	2		1035	735	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690786	89690808	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTAAACTTTTCTTTTAGTTGTGC	TTAAACTTTTCTTTTAGTTGTGC	-	novel	NA	P-0017205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	21	435	0	ENST00000371953.3:c.210-16_216del		p.X70_splice	ENST00000371953	NM_000314.4	70		4/9	1	2	FACETS	0.44	0.339	0.559	0.44	0.339	0.559	SUBCLONAL	1	TRUE	1	0.3	2		435	318	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819648	81819648	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	35	629	0	ENST00000359376.3:c.54C>G	p.Ile18Met	p.I18M	ENST00000359376	NM_002661.3	18	atC/atG	2/33	1	2	FACETS	0.39	0.318	0.47	0.39	0.318	0.47	SUBCLONAL	1	TRUE	1	0.3	2		629	599	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528559	89528559	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	41	417	0	ENST00000336596.2:c.2859G>C	p.Lys953Asn	p.K953N	ENST00000336596	NM_005233.5	953	aaG/aaC	17/17	1	2	FACETS	0.774	0.647	0.915	0.774	0.647	0.915	CLONAL	1	TRUE	1	0.3	2		417	353	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589589	67589594	+	inframe_deletion	In_Frame_Del	DEL	AATATA	AATATA	-	novel	NA	P-0017205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	29	563	0	ENST00000274335.5:c.1353_1358del	p.Glu451_Asn453delinsAsp	p.E451_N453delinsD	ENST00000274335		451	gAATATAac/gac	10/15	0.160821758260189	0	FACETS	0.349	0.28	0.427			1	INDETERMINATE	1	TRUE	0	0.3	0		563	388	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188078	11188078	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	155	316	0	ENST00000361445.4:c.6016G>T	p.Val2006Phe	p.V2006F	ENST00000361445	NM_004958.3	2006	Gtc/Ttc	43/58	0.508157675049809	2	FACETS	0.979	0.913	1	0.979	0.913	1	CLONAL	2	TRUE	0	0.510699227279914	2		316	310	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14031715	14031715	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	88	366	1	ENST00000311895.7:c.1904G>A	p.Arg635Lys	p.R635K	ENST00000311895	NM_005236.2	635	aGg/aAg	9/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.510699227279914	2		367	250	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188287	10188287	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs869025650	NA	P-0017234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	162	750	2	ENST00000256474.2:c.430G>T	p.Gly144Ter	p.G144*	ENST00000256474	NM_000551.3	144	Gga/Tga	2/3	0.5103792351236	1	FACETS	0.982	0.909	1	0.982	0.909	1	CLONAL	1	TRUE	0	0.510699227279914	1		752	481	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52649376	52649377	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	116	607	0	ENST00000394830.3:c.1914dup	p.Leu639ThrfsTer5	p.L639Tfs*5	ENST00000394830	NM_018313.4	638	-/A	16/30	0.5103792351236	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.510699227279914	1		607	306	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057607	180057607	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	352	801	0	ENST00000261937.6:c.348C>G	p.Ile116Met	p.I116M	ENST00000261937	NM_182925.4	116	atC/atG	3/30	0.469269890208728	3	FACETS	0.922	0.877	0.969	0.922	0.877	0.969	CLONAL	2	TRUE	1	0.510699227279914	3		801	938	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	186	503	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.241879015666319	4	FACETS	0.944	0.874	1	0.944	0.874	1	CLONAL	2	TRUE	2	0.373337046610089	4		503	725	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0017351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	344	862	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.36042652126006	3	FACETS	0.93	0.885	0.975	0.93	0.885	0.975	CLONAL	3	TRUE	0	0.373337046610089	3		864	784	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741870	17741870	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	60	291	0	ENST00000250003.3:c.541C>A	p.Pro181Thr	p.P181T	ENST00000250003	NM_002478.4	181	Ccg/Acg	1/3	0.373337046610089	3	FACETS	0.971	0.84	1	0.485	0.42	0.556	CLONAL	1	TRUE	1	0.373337046610089	3		291	393	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724433	724433	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1230365377	NA	P-0017351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	136	620	0	ENST00000314574.4:c.1623A>C	p.Glu541Asp	p.E541D	ENST00000314574	NM_005433.3	541	gaA/gaC	12/12	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.373337046610089	NA		620	1211	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101135	41101135	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	225	435	0	ENST00000373198.4:c.1221G>T	p.Trp407Cys	p.W407C	ENST00000373198	NM_133170.3	407	tgG/tgT	8/32	0.313672604211883	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.373337046610089	4		435	767	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380101	116380101	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	156	555	0	ENST00000397752.3:c.1490A>T	p.Asn497Ile	p.N497I	ENST00000397752	NM_000245.2	497	aAc/aTc	4/21	0.373337046610089	7	FACETS	1	0.98	1	0.25	0.228	0.274	CLONAL	1	TRUE	2	0.373337046610089	7		555	1290	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0017353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	375	482	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.692743964345113	3	FACETS	0.989	0.946	1	0.989	0.946	1	CLONAL	2	TRUE	1	0.707263590774276	3		482	726	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	167	313	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.707263590774276	2		315	427	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394065	31394066	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	199	462	0	ENST00000328111.2:c.2357dup	p.Asn786LysfsTer19	p.N786Kfs*19	ENST00000328111	NM_006892.3	784	-/A	22/23	1	2	FACETS	0.816	0.758	0.874	0.816	0.758	0.874	CLONAL	1	TRUE	1	0.707263590774276	2		462	690	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498403	89498403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	94	184	0	ENST00000336596.2:c.2375C>T	p.Ser792Leu	p.S792L	ENST00000336596	NM_005233.5	792	tCa/tTa	14/17	1	2	FACETS	0.946	0.853	1	0.946	0.853	1	CLONAL	1	TRUE	1	0.707263590774276	2		184	281	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955874	55955874	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	205	578	0	ENST00000263923.4:c.3288G>A	p.Trp1096Ter	p.W1096*	ENST00000263923	NM_002253.2	1096	tgG/tgA	24/30	1	2	FACETS	0.878	0.819	0.94	0.878	0.819	0.94	CLONAL	1	TRUE	1	0.707263590774276	2		578	660	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818768	170818768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	169	332	0	ENST00000296930.5:c.317C>T	p.Ser106Leu	p.S106L	ENST00000296930	NM_002520.6	106	tCa/tTa	4/11	NA	2	FACETS	0.987	0.916	1			1	INDETERMINATE	1	TRUE	NA	0.707263590774276	2		332	484	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920137	76920137	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	207	528	0	ENST00000373344.5:c.3940G>T	p.Glu1314Ter	p.E1314*	ENST00000373344	NM_000489.3	1314	Gag/Tag	11/35	1	2	FACETS	0.848	0.791	0.908	0.848	0.791	0.908	CLONAL	1	TRUE	1	0.707263590774276	2		528	690	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534705	18534705	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	279	297	1	ENST00000266497.5:c.1763C>A	p.Ser588Tyr	p.S588Y	ENST00000266497		588	tCc/tAc	12/31	0.736055917393967	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	1	0.736095781155142	3		298	517	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222330	39222330	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	206	584	0	ENST00000402219.2:c.3280G>C	p.Gly1094Arg	p.G1094R	ENST00000402219	NM_005633.3	1094	Ggt/Cgt	20/23	0.736055917393967	3	FACETS	0.828	0.768	0.889	0.414	0.384	0.445	CLONAL	1	TRUE	1	0.736095781155142	3		584	925	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230820	66230820	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	238	388	1	ENST00000273854.3:c.2151A>T	p.Gln717His	p.Q717H	ENST00000273854	NM_004439.5	717	caA/caT	12/18	0.736095781155142	6	FACETS	0.894	0.836	0.954			1	CLONAL	2	TRUE	NA	0.736095781155142	6		389	894	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554535	29554557	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTAGGCTTGGGAAGATACACA	TTTTAGGCTTGGGAAGATACACA	-	novel	NA	P-0017356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	353	257	0	ENST00000356175.3:c.2326-5_2343del		p.X776_splice	ENST00000356175	NM_000267.3	776		20/57	0.736055917393967	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.736095781155142	2		257	442	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213944	2213944	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368909792	NA	P-0017384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	159	521	0	ENST00000326181.6:c.23G>A	p.Arg8His	p.R8H	ENST00000326181	NM_032271.2	8	cGc/cAc	2/21	1	2	FACETS	0.779	0.718	0.842	0.779	0.718	0.842	SUBCLONAL	1	TRUE	1	0.723503454782992	2		521	564	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0017384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	69	347	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	1	2	FACETS	0.521	0.456	0.59	0.521	0.456	0.59	SUBCLONAL	1	TRUE	1	0.723503454782992	2		347	366	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156631	106156631	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	25	353	0	ENST00000380013.4:c.1532A>G	p.His511Arg	p.H511R	ENST00000380013	NM_001127208.2	511	cAc/cGc	3/11	0.431783029219053	1	FACETS	0.286	0.228	0.352	0.286	0.228	0.352	INDETERMINATE	1	TRUE	0	0.723503454782992	1		353	154	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637443	176637443	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	45	358	0	ENST00000439151.2:c.2043T>G	p.Asn681Lys	p.N681K	ENST00000439151	NM_022455.4	681	aaT/aaG	5/23	0.431783029219053	1	FACETS	0.363	0.308	0.422	0.363	0.308	0.422	INDETERMINATE	1	TRUE	0	0.723503454782992	1		358	219	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0017425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	474	340	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.491490262603713	6	FACETS	0.847	0.81	0.885	0.847	0.81	0.885	CLONAL	3	TRUE	3	0.604158457300413	6		340	1364	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382236	152382236	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	145	521	0	ENST00000206249.3:c.1346A>G	p.Lys449Arg	p.K449R	ENST00000206249	NM_000125.3	449	aAa/aGa	6/8	0.109615996862228	4	FACETS	1	0.987	1	0.713	0.654	0.774	INDETERMINATE	1	TRUE	2	0.604158457300413	4		521	540	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205563	61205563	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	165	616	0	ENST00000301761.2:c.348G>A	p.Trp116Ter	p.W116*	ENST00000301761	NM_017841.2	116	tgG/tgA	3/4	1	2	FACETS	0.94	0.868	1	0.94	0.868	1	CLONAL	1	TRUE	1	0.604158457300413	2		616	581	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988061	85988061	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	120	273	0	ENST00000263360.6:c.1006A>G	p.Met336Val	p.M336V	ENST00000263360	NM_003797.3	336	Atg/Gtg	10/12	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.604158457300413	2		273	357	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188309	10188309	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	90	523	1	ENST00000256474.2:c.452T>A	p.Ile151Asn	p.I151N	ENST00000256474	NM_000551.3	151	aTc/aAc	2/3	0.673084695895597	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.673084695895597	1		524	160	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480557	50480557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	143	547	0	ENST00000394963.4:c.427G>A	p.Glu143Lys	p.E143K	ENST00000394963	NM_003076.4	143	Gaa/Aaa	4/13	0.393490737661689	3	FACETS	1	0.942	1	1	0.942	1	INDETERMINATE	2	TRUE	1	0.673084695895597	3		547	280	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379441	225379441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	100	737	0	ENST00000264414.4:c.427G>A	p.Gly143Arg	p.G143R	ENST00000264414	NM_003590.4	143	Gga/Aga	4/16	0.673084695895597	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.673084695895597	1		737	186	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439162	52439162	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	101	617	0	ENST00000460680.1:c.1080del	p.Leu361Ter	p.L361*	ENST00000460680	NM_004656.3	360	ttT/tt	11/17	0.673084695895597	1	FACETS	0.967	0.885	1	0.967	0.885	1	CLONAL	1	TRUE	0	0.673084695895597	1		617	206	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188309	10188309	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017430-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	65	523	1	ENST00000256474.2:c.452T>A	p.Ile151Asn	p.I151N	ENST00000256474	NM_000551.3	151	aTc/aAc	2/3	1	2	FACETS	0.887	0.767	1	0.887	0.767	1	CLONAL	1	TRUE	1	0.15	2		524	977	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480557	50480557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017430-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	66	547	0	ENST00000394963.4:c.427G>A	p.Glu143Lys	p.E143K	ENST00000394963	NM_003076.4	143	Gaa/Aaa	4/13	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.15	2		547	869	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379441	225379441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017430-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	67	737	0	ENST00000264414.4:c.427G>A	p.Gly143Arg	p.G143R	ENST00000264414	NM_003590.4	143	Gga/Aga	4/16	1	2	FACETS	0.833	0.722	0.955	0.833	0.722	0.955	CLONAL	1	TRUE	1	0.15	2		737	1072	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439162	52439162	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017430-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	56	617	0	ENST00000460680.1:c.1080del	p.Leu361Ter	p.L361*	ENST00000460680	NM_004656.3	360	ttT/tt	11/17	1	2	FACETS	0.833	0.712	0.967	0.833	0.712	0.967	CLONAL	1	TRUE	1	0.15	2		617	896	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884020	37884020	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017430-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	76	724	0	ENST00000269571.5:c.3491G>C	p.Gly1164Ala	p.G1164A	ENST00000269571		1164	gGt/gCt	27/27	1	2	FACETS	0.855	0.747	0.972	0.855	0.747	0.972	CLONAL	1	TRUE	1	0.15	2		724	1185	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607192	189607192	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017430-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1458	113	802	2	ENST00000264731.3:c.1571C>T	p.Ala524Val	p.A524V	ENST00000264731	NM_003722.4	524	gCa/gTa	12/14	1	2	FACETS	0.959	0.86	1	0.959	0.86	1	CLONAL	1	TRUE	1	0.15	2		804	1571	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0017435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	178	294	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.549514041563802	4	FACETS	0.992	0.933	1	0.992	0.933	1	CLONAL	3	FALSE	1	0.599975595937742	4		294	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0017435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	13	831	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.415669745940769	5	FACETS	0.134	0.095	0.183	0.045	0.031	0.061	SUBCLONAL	1	FALSE	2	0.599975595937742	5		832	613	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428511	78428511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408536007	NA	P-0017435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	9	478	1	ENST00000370768.2:c.1288C>T	p.Arg430Cys	p.R430C	ENST00000370768	NM_003902.3	430	Cgt/Tgt	14/20	0.420840426334725	4	FACETS	0.127	0.083	0.183	0.063	0.041	0.092	SUBCLONAL	1	FALSE	2	0.599975595937742	4		479	379	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236086	108236086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782292	NA	P-0017435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	9	475	0	ENST00000278616.4:c.9022C>T	p.Arg3008Cys	p.R3008C	ENST00000278616	NM_000051.3	3008	Cgt/Tgt	63/63	0.599975595937742	3	FACETS	0.131	0.086	0.188	0.065	0.043	0.094	SUBCLONAL	1	FALSE	1	0.599975595937742	3		475	298	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171608	36171618	+	frameshift_variant	Frame_Shift_Del	DEL	ACTGGAAAGTT	ACTGGAAAGTT	-	novel	NA	P-0017435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	106	167	0	ENST00000300305.3:c.947_957del	p.Glu316AlafsTer280	p.E316Afs*280	ENST00000300305		316	gAACTTTCCAGT/g	7/8	0.421540572566805	5	FACETS	1	0.916	1	0.674	0.611	0.739	CLONAL	2	FALSE	2	0.599975595937742	5		167	332	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231810	36231810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	207	652	0	ENST00000300305.3:c.574G>A	p.Ala192Thr	p.A192T	ENST00000300305		192	Gcc/Acc	5/8	0.421540572566805	5	FACETS	0.809	0.753	0.868	0.54	0.502	0.579	CLONAL	2	FALSE	2	0.599975595937742	5		652	810	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0017463-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	88	280	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.945	0.845	1	1	0.985	1	CLONAL	2	TRUE	1	0.281326322980143	2		281	331	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940000	76940000	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1311466929	NA	P-0017463-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	132	529	0	ENST00000373344.5:c.748C>T	p.Arg250Ter	p.R250*	ENST00000373344	NM_000489.3	250	Cga/Tga	9/35	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.281326322980143	2		529	634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577152	7577154	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	ACC	ACC	-	rs1567548347	NA	P-0017463-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	308	501	0	ENST00000269305.4:c.784_786del	p.Gly262del	p.G262del	ENST00000269305	NM_001126112.2	262	GGT/-	8/11	0.281326322980143	2	FACETS	1	0.979	1	1	0.996	1	CLONAL	4	TRUE	0	0.281326322980143	2		501	527	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665641	86665641	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017463-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	18	106	0	ENST00000274376.6:c.1622T>C	p.Phe541Ser	p.F541S	ENST00000274376	NM_002890.2	541	tTt/tCt	12/25	1	2	FACETS	0.384	0.289	0.497	0.384	0.289	0.497	SUBCLONAL	1	TRUE	1	0.281326322980143	2		106	333	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164058	47164058	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0017473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	100	296	0	ENST00000409792.3:c.2068A>T	p.Lys690Ter	p.K690*	ENST00000409792	NM_014159.6	690	Aaa/Taa	3/21	0.27121342338098	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	0	0.27121342338098	2		296	349	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188296	10188297	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs869025653	NA	P-0017473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	206	413	0	ENST00000256474.2:c.444dup	p.Ala149CysfsTer25	p.A149Cfs*25	ENST00000256474	NM_000551.3	147	att/aTtt	2/3	0.27121342338098	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.27121342338098	2		413	669	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52676017	52676018	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	92	444	0	ENST00000394830.3:c.1039dup	p.Met347AsnfsTer10	p.M347Nfs*10	ENST00000394830	NM_018313.4	347	atg/aAtg	11/30	0.27121342338098	2	FACETS	1	0.976	1	0.677	0.604	0.755	CLONAL	1	TRUE	0	0.27121342338098	2		444	501	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720843	89720843	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	44	325	0	ENST00000371953.3:c.996del	p.Ala333ProfsTer11	p.A333Pfs*11	ENST00000371953	NM_000314.4	332	Aaa/aa	8/9	1	2	FACETS	0.818	0.687	0.962	0.818	0.687	0.962	CLONAL	1	TRUE	1	0.267092322913879	2		325	403	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720806	89720807	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0017474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	31	215	0	ENST00000371953.3:c.958_959del	p.Leu320AsnfsTer4	p.L320Nfs*4	ENST00000371953	NM_000314.4	319	acTTta/acta	8/9	1	2	FACETS	0.932	0.758	1	0.932	0.758	1	CLONAL	1	TRUE	1	0.267092322913879	2		215	249	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425091	49425091	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	116	551	0	ENST00000301067.7:c.13397T>C	p.Leu4466Pro	p.L4466P	ENST00000301067	NM_003482.3	4466	cTa/cCa	39/54	0.134636874854746	3	FACETS	1	0.981	1	0.686	0.618	0.757	INDETERMINATE	1	TRUE	1	0.267092322913879	3		551	718	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431978	121431978	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	106	457	0	ENST00000257555.6:c.725T>C	p.Ile242Thr	p.I242T	ENST00000257555		242	aTc/aCc	4/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.267092322913879	2		457	621	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785518	50785518	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	79	385	0	ENST00000398568.2:c.508G>A	p.Glu170Lys	p.E170K	ENST00000398568	NM_001042412.1	170	Gaa/Aaa	4/18	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.267092322913879	2		385	570	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463541	25463541	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	21	460	0	ENST00000264709.3:c.2141C>A	p.Ser714Tyr	p.S714Y	ENST00000264709	NM_175629.2	714	tCc/tAc	18/23	1	2	FACETS	0.274	0.21	0.349	0.274	0.21	0.349	SUBCLONAL	1	TRUE	1	0.267092322913879	2		460	574	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191469	10191469	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs5030816	NA	P-0017474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	68	319	0	ENST00000256474.2:c.464-2A>G		p.X155_splice	ENST00000256474	NM_000551.3	155			0.267092322913879	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.267092322913879	1		319	360	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142991	47142991	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	86	655	0	ENST00000409792.3:c.4972del	p.Ser1658GlnfsTer5	p.S1658Qfs*5	ENST00000409792	NM_014159.6	1658	Tca/ca	8/21	0.267092322913879	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.267092322913879	1		655	516	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	268	313	2				ENST00000310581	NM_198253.2	-/1132			0.311213978772551	3	FACETS	1	0.991	1	0.778	0.743	0.813	INDETERMINATE	2	TRUE	0	0.719246863812358	3		315	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577098	7577098	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	381	536	0	ENST00000269305.4:c.840A>T	p.Arg280Ser	p.R280S	ENST00000269305	NM_001126112.2	280	agA/agT	8/11	0.564330719925536	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.719246863812358	1		536	661	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797221	135797222	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs118203417	NA	P-0017499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	165	235	0	ENST00000298552.3:c.647_648del	p.Phe216Ter	p.F216*	ENST00000298552	NM_001162426.1	216	tTT/t	7/23	0.713957472892363	1	FACETS	0.757	0.704	0.811	0.757	0.704	0.811	SUBCLONAL	1	TRUE	0	0.719246863812358	1		235	388	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057894	27057894	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	351	511	0	ENST00000324856.7:c.1602C>A	p.Tyr534Ter	p.Y534*	ENST00000324856	NM_006015.4	534	taC/taA	3/20	0.693469729270718	1	FACETS	0.925	0.884	0.965	0.925	0.884	0.965	CLONAL	1	TRUE	0	0.719246863812358	1		511	676	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121574	2121574	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	280	503	0	ENST00000219476.3:c.1903G>T	p.Asp635Tyr	p.D635Y	ENST00000219476	NM_000548.3	635	Gat/Tat	18/42	0.364523191929539	1	FACETS	0.798	0.756	0.84	0.798	0.756	0.84	INDETERMINATE	1	TRUE	0	0.719246863812358	1		503	625	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137357	202137373	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTAGAACCTGCTGGATA	TTAGAACCTGCTGGATA	-	novel	NA	P-0017499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	290	260	0	ENST00000358485.4:c.589-2_603del		p.X197_splice	ENST00000358485	NM_001080125.1	197		4/9	0.695484396700037	2	FACETS	0.862	0.824	0.898	0.862	0.824	0.898	CLONAL	2	TRUE	0	0.719246863812358	2		260	468	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069652	69069652	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1520	81	509	0	ENST00000288368.4:c.4327del	p.Gln1443SerfsTer27	p.Q1443Sfs*27	ENST00000288368	NM_024870.2	1443	Cag/ag	35/40	0.113836414249214	5	FACETS	0.292	0.256	0.332			1	INDETERMINATE	1	TRUE	NA	0.719246863812358	5		509	1601	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87338531	87338578	+	inframe_deletion	In_Frame_Del	DEL	GGAAGGAAAGTCTATCACATTATCCTGTAGTGTGGCAGGTGATCCGGT	GGAAGGAAAGTCTATCACATTATCCTGTAGTGTGGCAGGTGATCCGGT	-	novel	NA	P-0017499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	38	375	0	ENST00000277120.3:c.627_674del	p.Glu209_Val225delinsAsp	p.E209_V225delinsD	ENST00000277120		209	gaGGAAGGAAAGTCTATCACATTATCCTGTAGTGTGGCAGGTGATCCGGTt/gat	7/19	0.719246863812358	1	FACETS	0.166	0.137	0.199	0.166	0.137	0.199	SUBCLONAL	1	TRUE	0	0.719246863812358	1		375	407	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0017512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	753	482	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.508701152639234	4	FACETS	0.996	0.968	1	1	0.998	1	CLONAL	3	TRUE	2	0.61822563419846	4		482	1319	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0017512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	38	312	2				ENST00000310581	NM_198253.2	-/1132			0.627155654057436	0	FACETS	0.69	0.602	0.777			1	SUBCLONAL	1	TRUE	0	0.61822563419846	0		314	68	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857500	9857500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	34	312	0	ENST00000330684.3:c.3901G>A	p.Glu1301Lys	p.E1301K	ENST00000330684	NM_001134407.1	1301	Gag/Aag	13/13	0.627155654057436	1	FACETS	0.458	0.379	0.544	0.458	0.379	0.544	SUBCLONAL	1	TRUE	0	0.61822563419846	1		312	166	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456315	32456315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377072761	NA	P-0017512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	66	732	0	ENST00000332351.3:c.577G>A	p.Ala193Thr	p.A193T	ENST00000332351	NM_024426.4	193	Gcc/Acc	1/10	0.225909949045204	0	FACETS	0.26	0.227	0.295			1	INDETERMINATE	1	TRUE	0	0.61822563419846	0		732	313	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729115	66729115	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs727504819	NA	P-0017512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	128	570	2	ENST00000307102.5:c.323G>T	p.Arg108Leu	p.R108L	ENST00000307102	NM_002755.3	108	cGg/cTg	3/11	0.117589648462065	6	FACETS	1	0.961	1	0.371	0.336	0.407	INDETERMINATE	1	TRUE	3	0.61822563419846	6		572	833	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830881	156830881	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	62	499	2	ENST00000524377.1:c.155G>T	p.Arg52Leu	p.R52L	ENST00000524377	NM_002529.3	52	cGg/cTg	1/17	0.48791920490476	3	FACETS	0.51	0.441	0.585	0.255	0.22	0.293	SUBCLONAL	1	TRUE	1	0.61822563419846	3		501	515	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533945	533945	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0017512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	71	292	1	ENST00000451590.1:c.112-1G>T		p.X38_splice	ENST00000451590	NM_001130442.1	38			0.225909949045204	0	FACETS	0.25	0.219	0.282			1	INDETERMINATE	1	TRUE	0	0.61822563419846	0		293	351	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870793	12870793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	129	124	0	ENST00000228872.4:c.20C>T	p.Ser7Phe	p.S7F	ENST00000228872	NM_004064.3	7	tCt/tTt	1/3	0.61822563419846	6	FACETS	1	0.979	1			1	CLONAL	3	TRUE	NA	0.61822563419846	6		124	267	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438035	49438035	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	183	492	0	ENST00000301067.7:c.5136G>T	p.Lys1712Asn	p.K1712N	ENST00000301067	NM_003482.3	1712	aaG/aaT	21/54	0.602722208690774	4	FACETS	1	0.97	1			1	CLONAL	1	TRUE	NA	0.61822563419846	4		492	873	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675109	40675109	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	225	701	0	ENST00000249776.8:c.73C>A	p.His25Asn	p.H25N	ENST00000249776	NM_033286.3	25	Cac/Aac	1/9	0.117589648462065	6	FACETS	0.858	0.799	0.918	0.572	0.533	0.612	INDETERMINATE	2	TRUE	3	0.61822563419846	6		701	949	SUCCESS
BLM	641	MSKCC	GRCh37	15	91295137	91295137	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	512	489	0	ENST00000355112.3:c.920A>C	p.Glu307Ala	p.E307A	ENST00000355112	NM_000057.2	307	gAa/gCa	4/22	0.171054254012306	4	FACETS	1	0.989	1	1	0.989	1	INDETERMINATE	2	TRUE	2	0.61822563419846	4		489	1238	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100636	67100636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	141	452	0	ENST00000412916.2:c.334G>A	p.Gly112Ser	p.G112S	ENST00000412916		112	Ggc/Agc	4/6	0.128643899671572	3	FACETS	0.753	0.686	0.823	0.377	0.343	0.412	INDETERMINATE	1	TRUE	1	0.61822563419846	3		452	793	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428315	33428315	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	74	392	0	ENST00000345365.6:c.808T>A	p.Phe270Ile	p.F270I	ENST00000345365	NM_002878.3	270	Ttt/Att	9/10	1	2	FACETS	0.534	0.469	0.604	0.534	0.469	0.604	SUBCLONAL	1	TRUE	1	0.61822563419846	2		392	448	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752332	55752332	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0017512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	177	559	0	ENST00000284073.2:c.791-1G>T		p.X264_splice	ENST00000284073	NM_138962.2	264			1	2	FACETS	0.772	0.713	0.833	0.772	0.713	0.833	SUBCLONAL	1	TRUE	1	0.61822563419846	2		559	742	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313251	30313251	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1333385090	NA	P-0017512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	114	407	0	ENST00000262643.3:c.945G>T	p.Lys315Asn	p.K315N	ENST00000262643	NM_001238.2	315	aaG/aaT	10/12	1	2	FACETS	0.695	0.628	0.764	0.695	0.628	0.764	SUBCLONAL	1	TRUE	1	0.61822563419846	2		407	531	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469139	25469139	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	180	506	1	ENST00000264709.3:c.1319G>T	p.Trp440Leu	p.W440L	ENST00000264709	NM_175629.2	440	tGg/tTg	11/23	0.28795623712361	4	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.61822563419846	4		507	738	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162048	47162049	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0017512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	83	322	0	ENST00000409792.3:c.4077_4078delinsTT	p.Leu1360Phe	p.L1360F	ENST00000409792	NM_014159.6	1359	tcCCtt/tcTTtt	3/21	0.276541686188448	2	FACETS	0.718	0.638	0.802	0.359	0.319	0.401	INDETERMINATE	1	TRUE	0	0.61822563419846	2		322	374	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948770	55948770	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368229220	NA	P-0017512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	64	560	0	ENST00000263923.4:c.3695G>A	p.Arg1232Gln	p.R1232Q	ENST00000263923	NM_002253.2	1232	cGg/cAg	28/30	0.100781062633065	3	FACETS	0.324	0.28	0.373	0.162	0.14	0.187	INDETERMINATE	1	TRUE	1	0.61822563419846	3		560	836	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637707	176637707	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	237	660	2	ENST00000439151.2:c.2307G>T	p.Lys769Asn	p.K769N	ENST00000439151	NM_022455.4	769	aaG/aaT	5/23	0.276541686188448	2	FACETS	0.89	0.833	0.95	0.445	0.416	0.475	INDETERMINATE	1	TRUE	0	0.61822563419846	2		662	861	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536160	106536160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	87	266	0	ENST00000369096.4:c.127G>A	p.Asp43Asn	p.D43N	ENST00000369096	NM_001198.3	43	Gat/Aat	2/7	0.396820282729746	3	FACETS	1	0.941	1			1	CLONAL	1	TRUE	NA	0.61822563419846	3		266	341	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026416	6026417	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0017512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	216	329	1	ENST00000265849.7:c.1979_1980delinsTT	p.Ala660Val	p.A660V	ENST00000265849	NM_000535.5	660	gCC/gTT	11/15	0.50580319836428	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.61822563419846	3		330	395	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509118	106509119	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0017512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	180	462	3	ENST00000359195.3:c.1112_1113delinsTT	p.Pro371Leu	p.P371L	ENST00000359195	NM_002649.2	371	cCC/cTT	2/11	0.508701152639234	4	FACETS	0.767	0.706	0.831	0.384	0.353	0.416	SUBCLONAL	1	TRUE	2	0.61822563419846	4		465	1228	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617167	100617167	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	130	229	0	ENST00000308731.7:c.582G>T	p.Glu194Asp	p.E194D	ENST00000308731	NM_000061.2	194	gaG/gaT	7/19	1	1	FACETS	0.862	0.793	0.933	0.862	0.793	0.933	CLONAL	1	TRUE	0	0.61822563419846	1		229	337	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774893	73774893	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	105	772	0	ENST00000254810.4:c.280C>G	p.Gln94Glu	p.Q94E	ENST00000254810	NM_005324.3	94	Cag/Gag	3/4	0.241546160587856	1	FACETS	0.69	0.616	0.768	0.69	0.616	0.768	SUBCLONAL	1	FALSE	0	0.241546160587856	1		772	1108	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210734	2210734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	115	530	0	ENST00000398665.3:c.1231C>T	p.Arg411Cys	p.R411C	ENST00000398665	NM_032482.2	411	Cgc/Tgc	14/28	0.241546160587856	0	FACETS	1	0.943	1			1	CLONAL	1	FALSE	0	0.241546160587856	0		530	678	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977997	131977997	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	125	263	0	ENST00000265335.6:c.3880G>T	p.Asp1294Tyr	p.D1294Y	ENST00000265335		1294	Gat/Tat	25/25	0.241546160587856	3	FACETS	1	0.964	1	0.745	0.678	0.815	CLONAL	2	FALSE	0	0.241546160587856	3		263	519	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0017559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	163	340	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.361260495439702	3	FACETS	0.898	0.828	0.97	0.898	0.828	0.97	CLONAL	2	TRUE	1	0.361260495439702	3		340	593	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	422	313	2				ENST00000310581	NM_198253.2	-/1132			0.596039587495868	6	FACETS	0.998	0.965	1	0.998	0.965	1	CLONAL	5	TRUE	1	0.596039587495868	6		315	622	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574000	7574000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	832	747	1	ENST00000269305.4:c.1027G>T	p.Glu343Ter	p.E343*	ENST00000269305	NM_001126112.2	343	Gag/Tag	10/11	0.548530527675639	3	FACETS	0.927	0.904	0.95	0.927	0.904	0.95	CLONAL	3	TRUE	0	0.596039587495868	3		748	1303	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164713	36164713	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	244	622	0	ENST00000300305.3:c.1162T>A	p.Ser388Thr	p.S388T	ENST00000300305		388	Tcg/Acg	8/8	0.568633225697563	3	FACETS	1	0.972	1	0.356	0.333	0.381	CLONAL	1	TRUE	0	0.596039587495868	3		622	994	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808842	1808842	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0017561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	139	958	0	ENST00000260795.2:c.2275-1G>A		p.X759_splice	ENST00000260795		759			1	2	FACETS	0.369	0.335	0.405	0.369	0.335	0.405	SUBCLONAL	1	TRUE	1	0.596039587495868	2		958	1264	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372124	55372124	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	103	126	0	ENST00000297316.4:c.814C>G	p.Pro272Ala	p.P272A	ENST00000297316	NM_022454.3	272	Ccc/Gcc	2/2	0.596039587495868	3	FACETS	0.927	0.846	1	0.927	0.846	1	CLONAL	2	TRUE	1	0.596039587495868	3		126	242	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489863	2489863	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	134	449	1	ENST00000355716.4:c.260T>C	p.Leu87Pro	p.L87P	ENST00000355716	NM_003820.2	87	cTc/cCc	3/8	0.366293874718623	3	FACETS	0.68	0.618	0.746	0.227	0.206	0.249	SUBCLONAL	1	TRUE	0	0.60438330434346	3		450	849	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402219	402242	+	inframe_deletion	In_Frame_Del	DEL	GGACTTCTGTTTTCCTTCTCCAAA	GGACTTCTGTTTTCCTTCTCCAAA	-	novel	NA	P-0017563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1463	514	543	2	ENST00000399788.2:c.4549_4572del	p.Phe1517_Ser1524del	p.F1517_S1524del	ENST00000399788	NM_001042603.1	1517	TTTGGAGAAGGAAAACAGAAGTCC/-	27/28	0.60438330434346	7	FACETS	1	0.987	1	0.36	0.344	0.377	CLONAL	2	TRUE	1	0.60438330434346	7		545	1977	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569828	95569828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	125	379	0	ENST00000393063.1:c.3905C>T	p.Thr1302Ile	p.T1302I	ENST00000393063	NM_030621.3	1302	aCt/aTt	22/28	0.52187268921033	4	FACETS	0.802	0.726	0.883	0.267	0.242	0.295	CLONAL	1	TRUE	1	0.60438330434346	4		379	827	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578232	7578232	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	972	566	0	ENST00000269305.4:c.617del	p.Leu206TrpfsTer41	p.L206Wfs*41	ENST00000269305	NM_001126112.2	206	tTg/tg	6/11	0.375349054521514	4	FACETS	0.997	0.977	1			1	CLONAL	4	TRUE	NA	0.60438330434346	4		566	1294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0017595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	60	813	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.637	0.549	0.733	0.637	0.549	0.733	SUBCLONAL	1	TRUE	1	0.324824683145815	2		813	580	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103396	77103397	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATCGGAAAA	novel	NA	P-0017595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	326	627	0	ENST00000356341.3:c.169_170insTTTTCCGAT	p.Arg56_Ser57insPhePheArg	p.R56_S57insFFR	ENST00000356341	NM_002576.4	57	tcc/tTTTTCCGATcc	2/15	0.302946365104925	2	FACETS	0.777	0.733	0.822	0.777	0.733	0.822	SUBCLONAL	2	TRUE	0	0.324824683145815	2		627	1292	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998625	100998625	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1330	173	766	1	ENST00000325455.5:c.1177G>T	p.Gly393Cys	p.G393C	ENST00000325455	NM_001202474.3	393	Ggc/Tgc	1/8	0.302946365104925	2	FACETS	0.709	0.65	0.77	0.354	0.325	0.385	SUBCLONAL	1	TRUE	0	0.324824683145815	2		767	1503	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042325	42042325	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1411875020	NA	P-0017595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1876	162	1092	0	ENST00000219905.7:c.6520T>C	p.Trp2174Arg	p.W2174R	ENST00000219905	NM_001164273.1	2174	Tgg/Cgg	17/24	1	2	FACETS	0.489	0.447	0.535	0.489	0.447	0.535	SUBCLONAL	1	TRUE	1	0.324824683145815	2		1092	2038	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472532	88472532	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1216	112	627	0	ENST00000360948.2:c.2023T>G	p.Phe675Val	p.F675V	ENST00000360948	NM_001012338.2	675	Ttt/Gtt	16/19	1	2	FACETS	0.519	0.465	0.577	0.519	0.465	0.577	SUBCLONAL	1	TRUE	1	0.324824683145815	2		627	1328	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141548	202141548	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0017595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	160	455	0	ENST00000358485.4:c.838-2A>C		p.X280_splice	ENST00000358485	NM_001080125.1	280			1	2	FACETS	0.925	0.847	1	0.925	0.847	1	CLONAL	1	TRUE	1	0.324824683145815	2		455	1065	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021721	31021721	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1311986203	NA	P-0017595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	48	172	0	ENST00000375687.4:c.1719+1G>T		p.X573_splice	ENST00000375687	NM_015338.5	573			1	2	FACETS	0.78	0.661	0.91	0.78	0.661	0.91	CLONAL	1	TRUE	1	0.324824683145815	2		172	379	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670468	134670468	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	137	443	0	ENST00000398015.3:c.379G>T	p.Ala127Ser	p.A127S	ENST00000398015	NM_004441.4	127	Gcc/Tcc	3/16	0.132352719675736	3	FACETS	0.904	0.821	0.991	0.452	0.41	0.496	INDETERMINATE	1	TRUE	1	0.324824683145815	3		443	1085	SUCCESS
ATR	545	MSKCC	GRCh37	3	142212150	142212150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	36	363	0	ENST00000350721.4:c.5902G>A	p.Asp1968Asn	p.D1968N	ENST00000350721	NM_001184.3	1968	Gat/Aat	35/47	0.132352719675736	3	FACETS	0.381	0.312	0.458	0.19	0.156	0.229	INDETERMINATE	1	TRUE	1	0.324824683145815	3		363	677	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319934	8319934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764537367	NA	P-0017595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	154	525	1	ENST00000356435.5:c.5567C>T	p.Thr1856Met	p.T1856M	ENST00000356435		1856	aCg/aTg	34/35	0.182949998742795	1	FACETS	0.771	0.705	0.841	0.771	0.705	0.841	INDETERMINATE	1	TRUE	0	0.324824683145815	1		526	1030	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0017636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	19	482	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.595	0.452	0.764	0.595	0.452	0.764	SUBCLONAL	1	TRUE	1	0.21	2		482	304	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295138	15295138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	19	683	3	ENST00000263388.2:c.2534C>T	p.Ser845Phe	p.S845F	ENST00000263388	NM_000435.2	845	tCc/tTc	16/33	1	2	FACETS	0.51	0.386	0.655	0.51	0.386	0.655	SUBCLONAL	1	TRUE	1	0.21	2		686	355	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487556	38487556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017693-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	135	433	0	ENST00000254066.5:c.86C>T	p.Pro29Leu	p.P29L	ENST00000254066	NM_000964.3	29	cCc/cTc	2/9	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		433	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	229	447	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.209558035583173	3	FACETS	0.938	0.876	1	1	0.991	1	CLONAL	3	TRUE	1	0.209558035583173	3		447	858	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	65	281	2	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.209558035583173	3	FACETS	0.751	0.653	0.857	0.751	0.653	0.857	SUBCLONAL	2	TRUE	1	0.209558035583173	3		283	456	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720805	89720808	+	frameshift_variant	Frame_Shift_Del	DEL	CTTT	CTTT	-	rs398123330	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	23	215	1	ENST00000371953.3:c.956_959del	p.Thr319LysfsTer24	p.T319Kfs*24	ENST00000371953	NM_000314.4	319	aCTTTa/aa	8/9	0.209558035583173	3	FACETS	1	0.926	1	0.748	0.589	0.93	CLONAL	1	TRUE	1	0.209558035583173	3		216	162	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165213	47165213	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	49	217	1	ENST00000409792.3:c.913del	p.Thr305GlnfsTer35	p.T305Qfs*35	ENST00000409792	NM_014159.6	305	Aca/ca	3/21	0.209558035583173	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	2	TRUE	0	0.209558035583173	2		218	231	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692981	89692982	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	22	328	0	ENST00000371953.3:c.469dup	p.Glu157GlyfsTer23	p.E157Gfs*23	ENST00000371953	NM_000314.4	155	-/G	5/9	0.209558035583173	3	FACETS	0.866	0.672	1	0.433	0.336	0.545	CLONAL	1	TRUE	1	0.209558035583173	3		328	268	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163553	32163554	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs777647776	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	88	329	3	ENST00000375023.3:c.5672dup	p.Gly1892ArgfsTer24	p.G1892Rfs*24	ENST00000375023	NM_004557.3	1891	ggc/ggGc	30/30	0.209558035583173	2	FACETS	1	0.979	1	0.747	0.663	0.836	CLONAL	1	TRUE	0	0.209558035583173	2		332	562	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646866	37646866	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141353560	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	61	506	0	ENST00000447079.4:c.1988G>A	p.Arg663His	p.R663H	ENST00000447079	NM_015083.1	663	cGt/cAt	3/14	0.209558035583173	3	FACETS	0.846	0.729	0.975	0.423	0.364	0.488	CLONAL	1	TRUE	1	0.209558035583173	3		506	760	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379486	225379486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	29	315	2	ENST00000264414.4:c.382C>T	p.Arg128Cys	p.R128C	ENST00000264414	NM_003590.4	128	Cgt/Tgt	4/16	0.203579111134989	3	FACETS	0.977	0.786	1			1	CLONAL	1	TRUE	NA	0.209558035583173	3		317	313	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413710	138413710	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	55	307	0	ENST00000289153.2:c.1810del	p.Arg604GlyfsTer4	p.R604Gfs*4	ENST00000289153	NM_006219.2	604	Cgg/gg	12/22	0.159334919406404	4	FACETS	1	0.926	1	0.567	0.485	0.657	CLONAL	1	TRUE	2	0.209558035583173	4		307	560	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368387	225368388	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	66	282	0	ENST00000264414.4:c.1358dup	p.Asn453LysfsTer5	p.N453Kfs*5	ENST00000264414	NM_003590.4	453	aac/aaAc	9/16	0.203579111134989	3	FACETS	1	0.943	1			1	CLONAL	2	TRUE	NA	0.209558035583173	3		282	305	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818405	43818405	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	79	429	0	ENST00000372470.3:c.1870C>A	p.His624Asn	p.H624N	ENST00000372470	NM_005373.2	624	Cat/Aat	12/12	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.209558035583173	2		429	657	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202744	108202744	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs876659561	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	67	362	0	ENST00000278616.4:c.7768C>G	p.Gln2590Glu	p.Q2590E	ENST00000278616	NM_000051.3	2590	Caa/Gaa	52/63	0.209558035583173	3	FACETS	0.839	0.732	0.954	0.839	0.732	0.954	CLONAL	2	TRUE	1	0.209558035583173	3		362	421	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	73	424	4	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	0.209558035583173	3	FACETS	1	0.917	1	0.532	0.465	0.605	CLONAL	1	TRUE	1	0.209558035583173	3		428	723	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425023	49425023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200574556	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	77	437	0	ENST00000301067.7:c.13465G>A	p.Gly4489Arg	p.G4489R	ENST00000301067	NM_003482.3	4489	Ggg/Agg	39/54	0.209558035583173	3	FACETS	1	0.918	1	0.53	0.465	0.6	CLONAL	1	TRUE	1	0.209558035583173	3		437	766	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488264	56488264	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	57	286	0	ENST00000267101.3:c.1783G>T	p.Gly595Cys	p.G595C	ENST00000267101	NM_001982.3	595	Ggt/Tgt	15/28	0.209558035583173	3	FACETS	0.877	0.752	1	0.439	0.376	0.508	CLONAL	1	TRUE	1	0.209558035583173	3		286	685	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562146	21562147	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	250	679	0	ENST00000382592.4:c.1772_1773del	p.Glu591ValfsTer12	p.E591Vfs*12	ENST00000382592	NM_014572.2	591	gAG/g	4/8	0.209558035583173	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.209558035583173	2		679	1171	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103510684	103510685	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	27	374	0	ENST00000355739.4:c.593dup	p.Glu199Ter	p.E199*	ENST00000355739	NM_000123.3	196	-/C	6/15	0.159334919406404	4	FACETS	0.956	0.762	1	0.478	0.381	0.589	CLONAL	1	TRUE	2	0.209558035583173	4		374	326	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99452047	99452047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1009888118	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	43	319	0	ENST00000268035.6:c.1381C>T	p.Arg461Cys	p.R461C	ENST00000268035	NM_000875.3	461	Cgc/Tgc	6/21	1	2	FACETS	0.839	0.702	0.991	0.839	0.702	0.991	CLONAL	1	TRUE	1	0.209558035583173	2		319	489	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783697	50783697	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs912795080	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	47	439	1	ENST00000398568.2:c.88G>A	p.Val30Ile	p.V30I	ENST00000398568	NM_001042412.1	30	Gtt/Att	3/18	0.209558035583173	5	FACETS	0.904	0.762	1	0.301	0.254	0.354	CLONAL	1	TRUE	2	0.209558035583173	5		440	652	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830386	72830386	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	24	129	0	ENST00000268489.5:c.6195del	p.Ala2066HisfsTer35	p.A2066Hfs*35	ENST00000268489	NM_006885.3	2065	ccC/cc	9/10	0.209558035583173	5	FACETS	1	0.902	1	0.429	0.337	0.534	CLONAL	1	TRUE	2	0.209558035583173	5		129	234	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969797	81969797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759995209	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	164	395	3	ENST00000359376.3:c.2866C>T	p.Arg956Cys	p.R956C	ENST00000359376	NM_002661.3	956	Cgc/Tgc	27/33	0.209558035583173	5	FACETS	0.888	0.817	0.963	0.888	0.817	0.963	CLONAL	3	TRUE	2	0.209558035583173	5		398	772	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347579	89347579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	52	349	0	ENST00000301030.4:c.5371G>A	p.Val1791Ile	p.V1791I	ENST00000301030	NM_001256183.1	1791	Gtc/Atc	9/13	0.209558035583173	5	FACETS	0.936	0.795	1	0.312	0.265	0.364	CLONAL	1	TRUE	2	0.209558035583173	5		349	697	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362446	40362447	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1202978138	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	76	473	2	ENST00000293328.3:c.1749dup	p.His584ThrfsTer8	p.H584Tfs*8	ENST00000293328	NM_012448.3	583	-/A	14/19	0.209558035583173	3	FACETS	1	0.925	1	0.539	0.472	0.611	CLONAL	1	TRUE	1	0.209558035583173	3		475	744	SUCCESS
YES1	7525	MSKCC	GRCh37	18	751705	751705	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs374613149	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	49	366	0	ENST00000314574.4:c.371C>T	p.Thr124Met	p.T124M	ENST00000314574	NM_005433.3	124	aCg/aTg	3/12	0.209558035583173	3	FACETS	0.879	0.744	1	0.439	0.372	0.514	CLONAL	1	TRUE	1	0.209558035583173	3		366	588	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591806	48591806	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	45	269	0	ENST00000342988.3:c.969G>A	p.Trp323Ter	p.W323*	ENST00000342988	NM_005359.5	323	tgG/tgA	9/12	0.209558035583173	3	FACETS	1	0.875	1	1	0.875	1	CLONAL	2	TRUE	1	0.209558035583173	3		269	229	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135016	11135016	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	102	359	3	ENST00000358026.2:c.2983G>A	p.Val995Ile	p.V995I	ENST00000358026	NM_001128849.1	995	Gtc/Atc	21/36	0.155951635543405	5	FACETS	1	0.961	1	0.574	0.515	0.637	CLONAL	2	TRUE	1	0.209558035583173	5		362	557	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741869	40741869	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768703735	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	60	381	2	ENST00000392038.2:c.1103G>A	p.Arg368His	p.R368H	ENST00000392038	NM_001626.4	368	cGc/cAc	11/14	0.209558035583173	3	FACETS	1	0.899	1	0.527	0.454	0.607	CLONAL	1	TRUE	1	0.209558035583173	3		383	600	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868098	45868098	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	70	460	1	ENST00000391945.4:c.592T>C	p.Ser198Pro	p.S198P	ENST00000391945	NM_000400.3	198	Tca/Cca	7/23	0.209558035583173	3	FACETS	0.981	0.855	1	0.491	0.427	0.56	CLONAL	1	TRUE	1	0.209558035583173	3		461	752	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183871	10183871	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs869025636	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	99	280	0	ENST00000256474.2:c.340G>C	p.Gly114Arg	p.G114R	ENST00000256474	NM_000551.3	114	Ggt/Cgt	1/3	0.209558035583173	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.209558035583173	2		280	437	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050304	37050304	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs193922370	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	72	371	0	ENST00000231790.2:c.454-1G>C		p.X152_splice	ENST00000231790	NM_000249.3	152			0.209558035583173	2	FACETS	0.876	0.77	0.99	0.876	0.77	0.99	CLONAL	2	TRUE	0	0.209558035583173	2		371	392	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397689	49397689	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	149	407	1	ENST00000418115.1:c.535C>A	p.Leu179Met	p.L179M	ENST00000418115	NM_001664.2	179	Ctg/Atg	5/5	0.209558035583173	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	TRUE	0	0.209558035583173	2		408	701	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281578	142281578	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	77	515	0	ENST00000350721.4:c.666del	p.Phe222LeufsTer11	p.F222Lfs*11	ENST00000350721	NM_001184.3	222	ttT/tt	4/47	0.159334919406404	4	FACETS	0.956	0.842	1	0.956	0.842	1	CLONAL	2	TRUE	2	0.209558035583173	4		515	465	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79965968	79965968	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	25	473	0	ENST00000265081.6:c.635del	p.Asn212IlefsTer21	p.N212Ifs*21	ENST00000265081	NM_002439.4	211	gAa/ga	4/24	1	2	FACETS	0.561	0.442	0.699	0.561	0.442	0.699	SUBCLONAL	1	TRUE	1	0.209558035583173	2		473	425	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79966072	79966072	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	29	416	1	ENST00000265081.6:c.736G>A	p.Ala246Thr	p.A246T	ENST00000265081	NM_002439.4	246	Gca/Aca	4/24	1	2	FACETS	0.754	0.606	0.923	0.754	0.606	0.923	CLONAL	1	TRUE	1	0.209558035583173	2		417	367	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041197	112041197	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs759104731	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	48	291	0	ENST00000368678.4:c.58G>T	p.Gly20Cys	p.G20C	ENST00000368678		20	Ggc/Tgc	3/13	0.209558035583173	3	FACETS	1	0.851	1	0.503	0.425	0.589	CLONAL	1	TRUE	1	0.209558035583173	3		291	503	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163760	152163760	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	42	306	0	ENST00000206249.3:c.481G>T	p.Gly161Cys	p.G161C	ENST00000206249	NM_000125.3	161	Ggc/Tgc	2/8	0.209558035583173	3	FACETS	0.978	0.817	1	0.489	0.408	0.578	CLONAL	1	TRUE	1	0.209558035583173	3		306	453	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0017894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	93	559	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	0.331116430094964	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.331116430094964	2		559	238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577084	7577084	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121912667	NA	P-0017894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	312	930	2	ENST00000269305.4:c.854A>T	p.Glu285Val	p.E285V	ENST00000269305	NM_001126112.2	285	gAg/gTg	8/11	0.331116430094964	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.331116430094964	2		932	797	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120181	70120182	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CG	novel	NA	P-0017894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	305	660	0	ENST00000245479.2:c.1185_1186dup	p.His396ArgfsTer8	p.H396Rfs*8	ENST00000245479	NM_000346.3	395	acg/aCGcg	3/3	0.331116430094964	4	FACETS	0.904	0.859	0.95	1	0.991	1	CLONAL	4	TRUE	1	0.331116430094964	4		660	678	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393189	393189	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	33	383	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	TRUE	NA	0.331116430094964	NA		383	232	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932068	39932068	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140780988	NA	P-0017894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	111	819	1	ENST00000378444.4:c.2531C>T	p.Pro844Leu	p.P844L	ENST00000378444	NM_001123385.1	844	cCg/cTg	4/15	0.269425910573696	4	FACETS	0.834	0.753	0.92	0.834	0.753	0.92	CLONAL	2	TRUE	2	0.331116430094964	4		820	535	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578177	7578177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	232	967	0	ENST00000269305.4:c.672G>C	p.Glu224Asp	p.E224D	ENST00000269305	NM_001126112.2	224	gaG/gaC	6/11	0.221335907239129	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.221335907239129	2		967	952	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458447	120458496	+	frameshift_variant	Frame_Shift_Del	DEL	GCTCCCGAGGGGTGGTTATGTGCTTCCCTTCAGGTGGCCTGCTCTGGGGA	GCTCCCGAGGGGTGGTTATGTGCTTCCCTTCAGGTGGCCTGCTCTGGGGA	-	novel	NA	P-0017897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	349	578	0	ENST00000256646.2:c.6849_6898del	p.Pro2284LeufsTer12	p.P2284Lfs*12	ENST00000256646	NM_024408.3	2283	gcTCCCCAGAGCAGGCCACCTGAAGGGAAGCACATAACCACCCCTCGGGAGCcc/gccc	34/34	0.221335907239129	6	FACETS	1	0.97	1			1	CLONAL	6	TRUE	NA	0.221335907239129	6		578	742	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346568	89346568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	44	465	0	ENST00000301030.4:c.6382G>A	p.Glu2128Lys	p.E2128K	ENST00000301030	NM_001256183.1	2128	Gag/Aag	9/13	0.0863818476152149	5	FACETS	1	0.917	1			1	INDETERMINATE	1	TRUE	NA	0.221335907239129	5		465	460	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587261	212587261	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0017897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	23	484	0	ENST00000342788.4:c.742-2A>G		p.X248_splice	ENST00000342788	NM_005235.2	248			1	2	FACETS	0.534	0.416	0.672	0.534	0.416	0.672	SUBCLONAL	1	TRUE	1	0.221335907239129	2		484	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578177	7578177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017897-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	790	967	0	ENST00000269305.4:c.672G>C	p.Glu224Asp	p.E224D	ENST00000269305	NM_001126112.2	224	gaG/gaC	6/11	0.655113574549161	2	FACETS	0.984	0.96	1	0.984	0.96	1	CLONAL	2	TRUE	0	0.698251151917353	2		967	1150	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458447	120458496	+	frameshift_variant	Frame_Shift_Del	DEL	GCTCCCGAGGGGTGGTTATGTGCTTCCCTTCAGGTGGCCTGCTCTGGGGA	GCTCCCGAGGGGTGGTTATGTGCTTCCCTTCAGGTGGCCTGCTCTGGGGA	-	novel	NA	P-0017897-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	329	578	0	ENST00000256646.2:c.6849_6898del	p.Pro2284LeufsTer12	p.P2284Lfs*12	ENST00000256646	NM_024408.3	2283	gcTCCCCAGAGCAGGCCACCTGAAGGGAAGCACATAACCACCCCTCGGGAGCcc/gccc	34/34	0.698251151917353	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.698251151917353	3		578	547	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346568	89346568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017897-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	112	465	0	ENST00000301030.4:c.6382G>A	p.Glu2128Lys	p.E2128K	ENST00000301030	NM_001256183.1	2128	Gag/Aag	9/13	0.529544702139178	4	FACETS	0.982	0.886	1			1	CLONAL	1	TRUE	NA	0.698251151917353	4		465	555	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	600	503	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	0.96	0.93	0.989			1	INDETERMINATE	2	TRUE	NA	0.622110880973942	2		503	1005	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0017900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	186	813	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.622110880973942	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.622110880973942	1		813	399	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971021	21971021	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	365	300	0	ENST00000579755.1:c.380C>T	p.Ser127Phe	p.S127F	ENST00000579755		127	tCt/tTt	2/3	0.127140930159621	6	FACETS	1	0.988	1			1	INDETERMINATE	5	TRUE	NA	0.622110880973942	6		300	502	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971100	21971100	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1001405220	NA	P-0017900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	292	234	0	ENST00000579755.1:c.301C>T	p.Pro101Ser	p.P101S	ENST00000579755		101	Ccg/Tcg	2/3	0.127140930159621	6	FACETS	0.944	0.912	0.974			1	INDETERMINATE	6	TRUE	NA	0.622110880973942	6		234	372	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	49	503	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.54	0.457	0.632	0.54	0.457	0.632	SUBCLONAL	1	TRUE	1	0.326261407221753	2		503	556	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579575	7579575	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555526795	NA	P-0017901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	93	483	0	ENST00000269305.4:c.112del	p.Gln38LysfsTer6	p.Q38Kfs*6	ENST00000269305	NM_001126112.2	38	Caa/aa	4/11	0.250009953028366	1	FACETS	0.669	0.595	0.748	0.669	0.595	0.748	SUBCLONAL	1	TRUE	0	0.326261407221753	1		483	713	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15273337	15273337	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	218	731	0	ENST00000263388.2:c.5852A>C	p.Asn1951Thr	p.N1951T	ENST00000263388	NM_000435.2	1951	aAc/aCc	32/33	1	2	FACETS	0.954	0.886	1	0.954	0.886	1	CLONAL	1	TRUE	1	0.425360042297605	2		731	1075	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183784	10183785	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCCT	novel	NA	P-0017931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	259	606	0	ENST00000256474.2:c.258_259insTTGCCC	p.Leu85_Pro86dup	p.L85_P86dup	ENST00000256474	NM_000551.3	85	ctg/cTGCCCTtg	1/3	0.403196578612572	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.425360042297605	1		606	896	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613127	52613138	+	inframe_deletion	In_Frame_Del	DEL	TTCAGCCACATG	TTCAGCCACATG	-	novel	NA	P-0017931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	178	506	0	ENST00000394830.3:c.3390_3401del	p.Asp1130_Lys1134delinsGlu	p.D1130_K1134delinsE	ENST00000394830	NM_018313.4	1130	gaCATGTGGCTGAAg/gag	22/30	0.403196578612572	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.425360042297605	1		506	643	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797690	32797707	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAATTTGTAGAAGATACC	CAATTTGTAGAAGATACC	-	novel	NA	P-0017931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	129	528	0	ENST00000374899.4:c.1795_1795+17del		p.X599_splice	ENST00000374899	NM_018833.2	599		10/12	0.403196578612572	1	FACETS	0.775	0.705	0.849	0.775	0.705	0.849	SUBCLONAL	1	TRUE	0	0.425360042297605	1		528	616	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185169115	185169115	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	166	857	0	ENST00000265026.3:c.1210C>G	p.Leu404Val	p.L404V	ENST00000265026	NM_004721.4	404	Ctc/Gtc	7/14	0.408455661439857	3	FACETS	1	0.953	1	0.527	0.484	0.572	CLONAL	1	TRUE	1	0.408455661439857	3		857	929	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217150	66217150	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771424766	NA	P-0017972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	137	759	0	ENST00000273854.3:c.2465C>T	p.Ser822Phe	p.S822F	ENST00000273854	NM_004439.5	822	tCc/tTc	14/18	1	2	FACETS	0.991	0.903	1	0.991	0.903	1	CLONAL	1	TRUE	1	0.408455661439857	2		759	677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0018199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	389	767	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.615136003486381	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.615136003486381	1		770	778	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851683	134851683	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	132	533	1	ENST00000398015.3:c.1089C>A	p.Cys363Ter	p.C363*	ENST00000398015	NM_004441.4	363	tgC/tgA	5/16	0.552969592061116	1	FACETS	0.563	0.513	0.614	0.563	0.513	0.614	SUBCLONAL	1	TRUE	0	0.615136003486381	1		534	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0018199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	82	862	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.200130309512683	3	FACETS	1	0.973	1	0.687	0.606	0.774	CLONAL	1	TRUE	1	0.200130309512683	3		864	656	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40500441	40500441	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	64	712	1	ENST00000264657.5:c.94C>T	p.Gln32Ter	p.Q32*	ENST00000264657	NM_139276.2	32	Cag/Tag	2/24	0.200130309512683	5	FACETS	1	0.957	1	0.424	0.367	0.486	CLONAL	1	TRUE	2	0.200130309512683	5		713	654	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	62	503	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.23755586291885	3	FACETS	0.451	0.388	0.52	0.226	0.194	0.26	SUBCLONAL	1	FALSE	1	0.307307077937438	3		503	1032	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0018203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	81	745	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.255198115698148	3	FACETS	1	0.919	1	0.526	0.464	0.593	CLONAL	1	FALSE	1	0.307307077937438	3		745	578	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473723	67473723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223740	NA	P-0018203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	52	701	0	ENST00000327367.4:c.803G>A	p.Arg268His	p.R268H	ENST00000327367	NM_005902.3	268	cGc/cAc	6/9	0.23755586291885	3	FACETS	0.757	0.644	0.88	0.378	0.322	0.44	SUBCLONAL	1	FALSE	1	0.307307077937438	3		701	516	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528133	157528133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	38	605	1	ENST00000346085.5:c.5858G>A	p.Arg1953His	p.R1953H	ENST00000346085	NM_020732.3	1953	cGt/cAt	20/20	0.23755586291885	3	FACETS	0.48	0.395	0.574	0.24	0.197	0.287	SUBCLONAL	1	FALSE	1	0.307307077937438	3		606	595	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732688	204732688	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	40	499	0	ENST00000302823.3:c.24del	p.His9ThrfsTer5	p.H9Tfs*5	ENST00000302823	NM_005214.4	8	cGg/cg	1/4	0.207090488807922	4	FACETS	0.53	0.439	0.632	0.265	0.219	0.316	SUBCLONAL	1	FALSE	2	0.307307077937438	4		499	642	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451888	29451888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764014697	NA	P-0018208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	112	870	4	ENST00000389048.3:c.2677G>A	p.Gly893Arg	p.G893R	ENST00000389048	NM_004304.4	893	Gga/Aga	16/29	0.288172477972064	1	FACETS	0.792	0.714	0.874	0.792	0.714	0.874	SUBCLONAL	1	TRUE	0	0.372488996079416	1		874	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0018208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	233	926	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.201037363866208	2	FACETS	1	0.978	1	0.556	0.518	0.595	INDETERMINATE	1	TRUE	0	0.372488996079416	2		926	1125	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224726	36224726	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	266	963	0	ENST00000222270.7:c.7112A>G	p.Asp2371Gly	p.D2371G	ENST00000222270	NM_014727.1	2371	gAt/gGt	30/37	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.372488996079416	2		963	1004	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952064	178952064	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	85	623	1	ENST00000263967.3:c.3119T>A	p.Met1040Lys	p.M1040K	ENST00000263967	NM_006218.2	1040	aTg/aAg	21/21	1	2	FACETS	0.764	0.677	0.858	0.764	0.677	0.858	SUBCLONAL	1	TRUE	1	0.372488996079416	2		624	597	SUCCESS
APC	324	MSKCC	GRCh37	5	112174170	112174170	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0018208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	96	582	0	ENST00000257430.4:c.2879C>G	p.Ser960Ter	p.S960*	ENST00000257430	NM_000038.5	960	tCa/tGa	16/16	0.201037363866208	2	FACETS	1	0.919	1	0.516	0.462	0.574	INDETERMINATE	1	TRUE	0	0.372488996079416	2		582	499	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004222	150004234	+	frameshift_variant	Frame_Shift_Del	DEL	ATTTCATTCTCTA	ATTTCATTCTCTA	-	novel	NA	P-0018208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	44	549	0	ENST00000253339.5:c.1991_2003del	p.Leu664Ter	p.L664*	ENST00000253339		664	tTAGAGAATGAAATg/tg	3/7	1	2	FACETS	0.385	0.322	0.455	0.385	0.322	0.455	SUBCLONAL	1	TRUE	1	0.372488996079416	2		549	614	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106300	27106300	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	208	777	0	ENST00000324856.7:c.5911C>G	p.Leu1971Val	p.L1971V	ENST00000324856	NM_006015.4	1971	Ctg/Gtg	20/20	1	2	FACETS	0.893	0.834	0.954	0.893	0.834	0.954	CLONAL	1	TRUE	1	0.746223050591199	2		777	624	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107195	27107195	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0018211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	186	621	0	ENST00000324856.7:c.6806C>G	p.Ser2269Ter	p.S2269*	ENST00000324856	NM_006015.4	2269	tCa/tGa	20/20	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.746223050591199	2		621	498	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099447	27099447	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	157	595	0	ENST00000324856.7:c.3686del	p.Asn1229IlefsTer8	p.N1229Ifs*8	ENST00000324856	NM_006015.4	1228	ccA/cc	14/20	1	2	FACETS	0.985	0.912	1	0.985	0.912	1	CLONAL	1	TRUE	1	0.746223050591199	2		595	427	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713457	30713457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	197	647	0	ENST00000295754.5:c.782C>T	p.Ala261Val	p.A261V	ENST00000295754	NM_003242.5	261	gCc/gTc	4/7	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.746223050591199	2		647	498	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164697	47164697	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	114	466	0	ENST00000409792.3:c.1429T>C	p.Ser477Pro	p.S477P	ENST00000409792	NM_014159.6	477	Tcc/Ccc	3/21	1	2	FACETS	0.915	0.834	0.998	0.915	0.834	0.998	CLONAL	1	TRUE	1	0.746223050591199	2		466	334	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250829	26250829	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs761937041	NA	P-0018211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	59	239	0	ENST00000446824.2:c.5C>G	p.Ala2Gly	p.A2G	ENST00000446824	NM_021018.2	2	gCa/gGa	1/1	1	2	FACETS	0.93	0.817	1	0.93	0.817	1	CLONAL	1	TRUE	1	0.746223050591199	2		239	170	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469924	157469925	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	156	659	0	ENST00000346085.5:c.2719dup	p.Arg907LysfsTer35	p.R907Kfs*35	ENST00000346085	NM_020732.3	906	-/A	9/20	1	2	FACETS	0.942	0.871	1	0.942	0.871	1	CLONAL	1	TRUE	1	0.746223050591199	2		659	444	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591144	67591154	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ATACTTGATGT	ATACTTGATGT	C	novel	NA	P-0018211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	226	500	0	ENST00000274335.5:c.1737_1745+2delinsC		p.X579_splice	ENST00000274335		579		12/15	0.746223050591199	2	FACETS	0.983	0.942	1	0.983	0.942	1	CLONAL	2	TRUE	0	0.746223050591199	2		500	308	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0018215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	549	701	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.882706855268856	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.882706855268856	2		701	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0018215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	597	975	3	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.882706855268856	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.882706855268856	1		978	721	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954203	48954206	+	frameshift_variant	Frame_Shift_Del	DEL	ATCC	ATCC	-	novel	NA	P-0018215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	140	538	0	ENST00000267163.4:c.1406_1409del	p.Ser469PhefsTer8	p.S469Ffs*8	ENST00000267163	NM_000321.2	468	ttATCC/tt	15/27	0.882706855268856	1	FACETS	0.802	0.752	0.85	0.802	0.752	0.85	CLONAL	1	TRUE	0	0.882706855268856	1		538	221	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840609	36840609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1384582231	NA	P-0018215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	295	678	0	ENST00000358127.4:c.1124C>T	p.Ala375Val	p.A375V	ENST00000358127	NM_001280556.1	375	gCc/gTc	10/10	1	2	FACETS	0.97	0.92	1	0.97	0.92	1	CLONAL	1	TRUE	1	0.882706855268856	2		678	689	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0018249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	346	770	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.185201350116714	5	FACETS	0.901	0.856	0.947	1	0.992	1	INDETERMINATE	4	TRUE	2	0.311962336805434	5		770	903	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0018249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	221	786	1	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	0.311962336805434	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.311962336805434	2		787	684	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102196281	102196281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	25	316	0	ENST00000263464.3:c.938C>T	p.Ala313Val	p.A313V	ENST00000263464	NM_001165.4	313	gCc/gTc	3/9	1	2	FACETS	0.621	0.491	0.77	0.621	0.491	0.77	SUBCLONAL	1	TRUE	1	0.311962336805434	2		316	258	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554003	63554013	+	frameshift_variant	Frame_Shift_Del	DEL	TTGGCGAAAGT	TTGGCGAAAGT	-	novel	NA	P-0018249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	240	567	0	ENST00000307078.5:c.726_736del	p.Lys242AsnfsTer23	p.K242Nfs*23	ENST00000307078	NM_004655.3	242	aaACTTTCGCCAAcc/aacc	2/11	0.311962336805434	3	FACETS	0.998	0.939	1	0.998	0.939	1	CLONAL	3	TRUE	0	0.311962336805434	3		567	594	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919203	178919203	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1482313267	NA	P-0018249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	60	430	0	ENST00000263967.3:c.688C>G	p.Arg230Gly	p.R230G	ENST00000263967	NM_006218.2	230	Cga/Gga	4/21	0.308355345713515	3	FACETS	1	0.887	1	0.515	0.444	0.591	CLONAL	1	TRUE	1	0.311962336805434	3		430	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0018282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	329	780	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.749249943968935	2	FACETS	0.844	0.811	0.876	0.844	0.811	0.876	CLONAL	2	TRUE	0	0.775032660187469	2		780	503	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029333	14029333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766111215	NA	P-0018282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	30	323	0	ENST00000311895.7:c.1544G>A	p.Arg515His	p.R515H	ENST00000311895	NM_005236.2	515	cGt/cAt	8/11	0.739369370698322	2	FACETS	0.26	0.21	0.316	0.13	0.105	0.158	SUBCLONAL	1	TRUE	0	0.775032660187469	2		323	298	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670756	67670756	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0018282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	257	488	0	ENST00000264010.4:c.1999+2T>G		p.X667_splice	ENST00000264010	NM_006565.3	667			0.739369370698322	2	FACETS	0.906	0.869	0.942	0.906	0.869	0.942	CLONAL	2	TRUE	0	0.775032660187469	2		488	366	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056574	26056575	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0018335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	70	255	0	ENST00000343677.2:c.82_83delinsAA	p.Ala28Asn	p.A28N	ENST00000343677	NM_005319.3	28	GCt/AAt	1/1	0.619877477894927	2	FACETS	0.9	0.795	1	0.45	0.397	0.505	CLONAL	1	TRUE	0	0.619877477894927	2		255	251	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181973	32181974	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0018335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	257	726	0	ENST00000375023.3:c.2080_2081del	p.Gly694LeufsTer33	p.G694Lfs*33	ENST00000375023	NM_004557.3	694	GGc/c	13/30	0.619877477894927	2	FACETS	0.944	0.886	1	0.472	0.443	0.502	CLONAL	1	TRUE	0	0.619877477894927	2		726	878	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	42	503	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.211762968902569	4	FACETS	1	0.954	1	0.711	0.598	0.835	CLONAL	1	FALSE	2	0.314114589287694	4		503	247	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641063	117641063	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	18	742	0	ENST00000368508.3:c.5908G>A	p.Val1970Ile	p.V1970I	ENST00000368508	NM_002944.2	1970	Gtt/Att	36/43	0.314114589287694	3	FACETS	0.436	0.328	0.564	0.218	0.164	0.282	SUBCLONAL	1	FALSE	1	0.314114589287694	3		742	304	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956205	55956205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148668147	NA	P-0018390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	31	759	1	ENST00000263923.4:c.3110C>T	p.Ser1037Leu	p.S1037L	ENST00000263923	NM_002253.2	1037	tCg/tTg	23/30	1	2	FACETS	0.484	0.391	0.589	0.484	0.391	0.589	SUBCLONAL	1	FALSE	1	0.314114589287694	2		760	408	SUCCESS
APC	324	MSKCC	GRCh37	5	112175673	112175673	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	133	575	0	ENST00000257430.4:c.4385del	p.Lys1462ArgfsTer11	p.K1462Rfs*11	ENST00000257430	NM_000038.5	1461	gAa/ga	16/16	0.314114589287694	3	FACETS	0.888	0.816	0.961	0.888	0.816	0.961	CLONAL	3	FALSE	0	0.314114589287694	3		575	368	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778168	3778168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763223282	NA	P-0018390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	141	794	2	ENST00000262367.5:c.6880C>T	p.Arg2294Trp	p.R2294W	ENST00000262367	NM_004380.2	2294	Cgg/Tgg	31/31	0.314114589287694	4	FACETS	1	0.985	1	0.712	0.648	0.778	CLONAL	1	FALSE	2	0.314114589287694	4		796	829	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644832	67644832	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	122	642	0	ENST00000264010.4:c.97C>T	p.Gln33Ter	p.Q33*	ENST00000264010	NM_006565.3	33	Cag/Tag	3/12	0.314114589287694	4	FACETS	0.784	0.71	0.862	0.784	0.71	0.862	SUBCLONAL	2	FALSE	2	0.314114589287694	4		642	651	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057520008	NA	P-0018390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	157	962	0	ENST00000269305.4:c.613T>A	p.Tyr205Asn	p.Y205N	ENST00000269305	NM_001126112.2	205	Tat/Aat	6/11	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	FALSE	NA	0.314114589287694	2		962	743	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630549	187630549	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	39	980	0	ENST00000441802.2:c.433T>G	p.Leu145Val	p.L145V	ENST00000441802	NM_005245.3	145	Ttg/Gtg	2/27	1	2	FACETS	0.536	0.444	0.639	0.536	0.444	0.639	SUBCLONAL	1	FALSE	1	0.314114589287694	2		980	463	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0018526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	39	400	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.642	0.533	0.763	0.642	0.533	0.763	SUBCLONAL	1	TRUE	1	0.329166893840903	2		401	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0018526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	194	636	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.324130937888573	2	FACETS	0.786	0.729	0.844	0.786	0.729	0.844	SUBCLONAL	2	TRUE	0	0.329166893840903	2		637	750	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405452	70405452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	52	894	1	ENST00000373644.4:c.2966C>T	p.Ala989Val	p.A989V	ENST00000373644	NM_030625.2	989	gCa/gTa	4/12	0.246795786920418	2	FACETS	0.449	0.382	0.524	0.225	0.191	0.262	SUBCLONAL	1	TRUE	0	0.329166893840903	2		895	703	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376326	118376326	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	44	659	1	ENST00000534358.1:c.9719C>G	p.Ser3240Cys	p.S3240C	ENST00000534358	NM_005933.3	3240	tCt/tGt	27/36	1	2	FACETS	0.413	0.346	0.488	0.413	0.346	0.488	SUBCLONAL	1	TRUE	1	0.329166893840903	2		660	647	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28882996	28882996	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867799392	NA	P-0018526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	129	624	1	ENST00000282397.4:c.3704C>T	p.Ala1235Val	p.A1235V	ENST00000282397	NM_002019.4	1235	gCc/gTc	28/30	0.230881388066371	3	FACETS	1	0.982	1	0.451	0.409	0.494	CLONAL	1	TRUE	0	0.329166893840903	3		625	675	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100398	2100398	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0018526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	97	450	0	ENST00000219476.3:c.139-3C>T		p.X47_splice	ENST00000219476	NM_000548.3	47			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.329166893840903	2		450	492	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016596	12016596	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	19	324	0	ENST00000353533.5:c.732G>C	p.Lys244Asn	p.K244N	ENST00000353533	NM_003010.3	244	aaG/aaC	7/11	0.324130937888573	2	FACETS	0.36	0.273	0.462	0.18	0.136	0.231	SUBCLONAL	1	TRUE	0	0.329166893840903	2		324	321	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752949	42752949	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	35	715	0	ENST00000222329.4:c.1315G>T	p.Glu439Ter	p.E439*	ENST00000222329	NM_006494.2	439	Gag/Tag	4/4	1	2	FACETS	0.316	0.258	0.381	0.316	0.258	0.381	SUBCLONAL	1	TRUE	1	0.329166893840903	2		715	673	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177491	56177491	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	18	352	0	ENST00000399503.3:c.2464A>T	p.Ser822Cys	p.S822C	ENST00000399503	NM_005921.1	822	Agt/Tgt	14/20	1	2	FACETS	0.314	0.236	0.407	0.314	0.236	0.407	SUBCLONAL	1	TRUE	1	0.329166893840903	2		352	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064794618	NA	P-0018570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	38	649	1	ENST00000269305.4:c.159G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgG/tgA	4/11	0.32174456481355	3	FACETS	0.965	0.803	1	0.483	0.401	0.572	CLONAL	1	TRUE	1	0.370369358459505	3		650	252	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0018606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	214	658	1	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.26176473819748	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.26176473819748	2		659	791	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114755	73114755	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	52	217	0	ENST00000356692.5:c.1136A>T	p.Glu379Val	p.E379V	ENST00000356692		379	gAa/gTa	9/9	0.59697276314973	6	FACETS	1	0.953	1			1	CLONAL	2	FALSE	NA	0.753840669937391	6		217	142	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0018615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	293	564	1	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	0.559783726457245	1	FACETS	0.917	0.866	0.968	0.917	0.866	0.968	CLONAL	1	TRUE	0	0.567892271015093	1		565	806	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623853	28623853	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	112	472	0	ENST00000241453.7:c.801del	p.Leu268TyrfsTer3	p.L268Yfs*3	ENST00000241453	NM_004119.2	267	ccC/cc	7/24	1	2	FACETS	0.741	0.669	0.817	0.741	0.669	0.817	SUBCLONAL	1	TRUE	1	0.567892271015093	2		472	532	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134716	2134716	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs137854879	NA	P-0018615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	436	552	0	ENST00000219476.3:c.4493G>A	p.Ser1498Asn	p.S1498N	ENST00000219476	NM_000548.3	1498	aGt/aAt	34/42	0.567892271015093	2	FACETS	0.969	0.932	1	0.969	0.932	1	CLONAL	2	TRUE	0	0.567892271015093	2		552	792	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226490	1226490	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	184	659	0	ENST00000326873.7:c.1146G>C	p.Gln382His	p.Q382H	ENST00000326873	NM_000455.4	382	caG/caC	9/10	1	2	FACETS	0.645	0.595	0.698	0.645	0.595	0.698	SUBCLONAL	1	TRUE	1	0.567892271015093	2		659	1004	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191570	10191570	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1559429824	NA	P-0018615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	226	416	0	ENST00000256474.2:c.563T>C	p.Leu188Pro	p.L188P	ENST00000256474	NM_000551.3	188	cTg/cCg	3/3	0.559783726457245	1	FACETS	0.986	0.926	1	0.986	0.926	1	CLONAL	1	TRUE	0	0.567892271015093	1		416	578	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441416	52441416	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	241	463	0	ENST00000460680.1:c.436A>G	p.Arg146Gly	p.R146G	ENST00000460680	NM_004656.3	146	Agg/Ggg	6/17	0.559783726457245	1	FACETS	0.963	0.906	1	0.963	0.906	1	CLONAL	1	TRUE	0	0.567892271015093	1		463	631	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226214	53226214	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	261	468	0	ENST00000375401.3:c.2635C>A	p.Gln879Lys	p.Q879K	ENST00000375401	NM_004187.3	879	Cag/Aag	19/26	1	2	FACETS	0.994	0.933	1	0.994	0.933	1	CLONAL	1	TRUE	1	0.567892271015093	2		468	925	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047626	180047626	+	protein_altering_variant	In_Frame_Ins	INS	A	A	GGAT	novel	NA	P-0018615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	172	457	0	ENST00000261937.6:c.2389delinsATCC	p.Phe797delinsIleLeu	p.F797delinsIL	ENST00000261937	NM_182925.4	797	Ttc/ATCCtc	16/30	0.436347503484784	3	FACETS	0.834	0.767	0.903	0.417	0.383	0.452	CLONAL	1	TRUE	1	0.567892271015093	3		457	933	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0018615-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	136	564	1	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	0.264537158424241	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.264537158424241	1		565	873	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623853	28623853	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018615-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	97	472	0	ENST00000241453.7:c.801del	p.Leu268TyrfsTer3	p.L268Yfs*3	ENST00000241453	NM_004119.2	267	ccC/cc	7/24	1	2	FACETS	0.952	0.849	1	0.952	0.849	1	CLONAL	1	TRUE	1	0.264537158424241	2		472	770	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134716	2134716	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs137854879	NA	P-0018615-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	222	552	0	ENST00000219476.3:c.4493G>A	p.Ser1498Asn	p.S1498N	ENST00000219476	NM_000548.3	1498	aGt/aAt	34/42	0.150271106513989	1	FACETS	0.836	0.779	0.894	1	0.993	1	INDETERMINATE	2	TRUE	0	0.264537158424241	1		552	871	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191570	10191570	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1559429824	NA	P-0018615-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	102	416	0	ENST00000256474.2:c.563T>C	p.Leu188Pro	p.L188P	ENST00000256474	NM_000551.3	188	cTg/cCg	3/3	0.264537158424241	1	FACETS	0.984	0.881	1	0.984	0.881	1	CLONAL	1	TRUE	0	0.264537158424241	1		416	680	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441416	52441416	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018615-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	103	463	0	ENST00000460680.1:c.436A>G	p.Arg146Gly	p.R146G	ENST00000460680	NM_004656.3	146	Agg/Ggg	6/17	0.264537158424241	1	FACETS	0.875	0.783	0.973	0.875	0.783	0.973	CLONAL	1	TRUE	0	0.264537158424241	1		463	772	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226214	53226214	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018615-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	87	468	0	ENST00000375401.3:c.2635C>A	p.Gln879Lys	p.Q879K	ENST00000375401	NM_004187.3	879	Cag/Aag	19/26	1	2	FACETS	0.852	0.754	0.957	0.852	0.754	0.957	CLONAL	1	TRUE	1	0.264537158424241	2		468	772	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047626	180047626	+	protein_altering_variant	In_Frame_Ins	INS	A	A	GGAT	novel	NA	P-0018615-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	74	457	0	ENST00000261937.6:c.2389delinsATCC	p.Phe797delinsIleLeu	p.F797delinsIL	ENST00000261937	NM_182925.4	797	Ttc/ATCCtc	16/30	0.106456718846164	0	FACETS	0.516	0.451	0.586			1	INDETERMINATE	1	TRUE	0	0.264537158424241	0		457	798	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154324	2154324	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018615-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	77	737	0	ENST00000434045.2:c.604C>G	p.Leu202Val	p.L202V	ENST00000434045	NM_001127598.1	202	Ctc/Gtc	5/5	1	2	FACETS	0.464	0.405	0.527	0.464	0.405	0.527	SUBCLONAL	1	TRUE	1	0.264537158424241	2		737	1255	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459946	99459946	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs200059469	NA	P-0018687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	79	386	0	ENST00000268035.6:c.2042A>G	p.Glu681Gly	p.E681G	ENST00000268035	NM_000875.3	681	gAg/gGg	10/21	1	2	FACETS	0.911	0.801	1	0.911	0.801	1	CLONAL	1	TRUE	1	0.26	2		386	667	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81887548	81888083	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTGCCTTCATTTCCTCTTCCCCCTTTAATTGAGCCACAGAGCATTTGTAGCTTTTGGGACTCAAGGGAAAAGGTCATCAAGGTCAAGGTCAACCGGACAGTTGACCTTTAGGCTGCCTAGAGTGATCTCTAGTGAGCATCAATTTGGTCTCTTGTTTTTTTTTGGTAGAATAGTCTGTGCTTATTTCCTGAAATCTCAGTTGCATTACAAAAATTAATTGTCCTAGTTTAAAATGTGTCTGTCTGAGAAACAGGGTGAGCGGAAACCCCAAACTCTTCAGACTCCAGGGGTTTGTGGGGTGGCAGCAAATGCCCGGGTAGGGTCTTAGCCCTTTGTCCATTTCCAGAAGGAGGGGACACTGAGTCCAGACGCAGAGATAGCTTTGCGGGATCCTGTTGGGGAAGGAAGGAGCCAGGCTGTGCCTGGGCTGCAGTTGTGTGGCTGCATCCTCAGGTGGAGGGAACTCCAGCTTCTAATTGGCTCATGTTAATTTCATTTTAGTGGATATCATGGAAATAAAAGAAATCCGCCCAGGG	GTGCCTTCATTTCCTCTTCCCCCTTTAATTGAGCCACAGAGCATTTGTAGCTTTTGGGACTCAAGGGAAAAGGTCATCAAGGTCAAGGTCAACCGGACAGTTGACCTTTAGGCTGCCTAGAGTGATCTCTAGTGAGCATCAATTTGGTCTCTTGTTTTTTTTTGGTAGAATAGTCTGTGCTTATTTCCTGAAATCTCAGTTGCATTACAAAAATTAATTGTCCTAGTTTAAAATGTGTCTGTCTGAGAAACAGGGTGAGCGGAAACCCCAAACTCTTCAGACTCCAGGGGTTTGTGGGGTGGCAGCAAATGCCCGGGTAGGGTCTTAGCCCTTTGTCCATTTCCAGAAGGAGGGGACACTGAGTCCAGACGCAGAGATAGCTTTGCGGGATCCTGTTGGGGAAGGAAGGAGCCAGGCTGTGCCTGGGCTGCAGTTGTGTGGCTGCATCCTCAGGTGGAGGGAACTCCAGCTTCTAATTGGCTCATGTTAATTTCATTTTAGTGGATATCATGGAAATAAAAGAAATCCGCCCAGGG	-	novel	NA	P-0018687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1	69	0	0	ENST00000359376.3:c.194-501_228del		p.X65_splice	ENST00000359376	NM_002661.3	65		3/33	0.298682022788892	1	FACETS		NA	1	1	0.989	1	NA	7	TRUE	0	0.26	1		0	70	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157851	106157851	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	67	269	0	ENST00000380013.4:c.2752A>G	p.Arg918Gly	p.R918G	ENST00000380013	NM_001127208.2	918	Agg/Ggg	3/11	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.26	2		269	514	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0018758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	240	547	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.294742665732176	4	FACETS	1	0.951	1	0.679	0.635	0.725	CLONAL	2	TRUE	1	0.352277387637479	4		547	904	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0018758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	366	816	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.224193646752269	2	FACETS	0.972	0.923	1	0.972	0.923	1	CLONAL	2	TRUE	0	0.352277387637479	2		816	1069	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0018758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	294	418	1	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	0.352277387637479	3	FACETS	0.977	0.926	1	1	0.994	1	CLONAL	3	TRUE	1	0.352277387637479	3		419	670	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717678	89717678	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554825200	NA	P-0018758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	442	734	2	ENST00000371953.3:c.703G>T	p.Glu235Ter	p.E235*	ENST00000371953	NM_000314.4	235	Gaa/Taa	7/9	0.294742665732176	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	3	TRUE	1	0.352277387637479	4		736	1124	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591133	67591134	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0018758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	191	471	0	ENST00000274335.5:c.1727dup	p.Arg577GlufsTer25	p.R577Efs*25	ENST00000274335		576	acg/aCcg	12/15	1	2	FACETS	0.843	0.783	0.905	1	0.992	1	CLONAL	2	TRUE	1	0.352277387637479	2		471	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0018794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	104	813	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.584950877249141	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.634622493206883	1		813	206	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0018794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	121	796	7	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.17955837562282	0	FACETS	0.321	0.292	0.351			1	INDETERMINATE	1	TRUE	0	0.634622493206883	0		803	434	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0018794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	83	534	2	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.836	0.745	0.931	0.836	0.745	0.931	CLONAL	1	TRUE	1	0.634622493206883	2		536	313	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368202	45368202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	78	353	3	ENST00000262160.6:c.1400C>T	p.Ser467Leu	p.S467L	ENST00000262160	NM_005901.5	467	tCa/tTa	11/11	0.595387104649008	1	FACETS	0.912	0.82	1	0.912	0.82	1	CLONAL	1	TRUE	0	0.634622493206883	1		356	184	SUCCESS
APC	324	MSKCC	GRCh37	5	112175153	112175153	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	42	244	1	ENST00000257430.4:c.3862G>T	p.Gly1288Ter	p.G1288*	ENST00000257430	NM_000038.5	1288	Gga/Tga	16/16	1	2	FACETS	0.838	0.711	0.973	0.838	0.711	0.973	CLONAL	1	TRUE	1	0.634622493206883	2		245	158	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101750	71101751	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	52	270	2	ENST00000318789.4:c.447dup	p.Gln150ThrfsTer20	p.Q150Tfs*20	ENST00000318789	NM_032682.5	149	-/A	9/21	1	2	FACETS	0.926	0.802	1	0.926	0.802	1	CLONAL	1	TRUE	1	0.634622493206883	2		272	177	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245393	153245393	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	143	645	10	ENST00000281708.4:c.1798G>T	p.Asp600Tyr	p.D600Y	ENST00000281708	NM_033632.3	600	Gat/Tat	11/12	0.595387104649008	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.634622493206883	1		655	278	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984408	201984409	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	184	766	9	ENST00000359651.3:c.1075dup	p.Ser359LysfsTer112	p.S359Kfs*112	ENST00000359651		358	tca/tcAa	8/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.634622493206883	2		775	532	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715875	61715875	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	23	560	0	ENST00000401558.2:c.2054T>C	p.Val685Ala	p.V685A	ENST00000401558	NM_003400.3	685	gTc/gCc	18/25	1	2	FACETS	0.187	0.145	0.235	0.187	0.145	0.235	SUBCLONAL	1	TRUE	1	0.634622493206883	2		560	388	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032069	26032069	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	11	377	0	ENST00000244661.2:c.220G>C	p.Glu74Gln	p.E74Q	ENST00000244661	NM_003537.3	74	Gaa/Caa	1/1	0.1650009255732	3	FACETS	0.237	0.163	0.33	0.118	0.081	0.166	SUBCLONAL	1	TRUE	1	0.19	3		377	535	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416189	416189	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	77	587	0	ENST00000399788.2:c.3997C>T	p.Arg1333Ter	p.R1333*	ENST00000399788	NM_001042603.1	1333	Cga/Tga	24/28	0.3	2	FACETS	0.93	0.815	1			1	CLONAL	1	TRUE	NA	0.19	2		587	872	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577549	64577549	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	58	338	0	ENST00000312049.6:c.33C>A	p.Phe11Leu	p.F11L	ENST00000312049	NM_130799.2	11	ttC/ttA	2/10	0.1650009255732	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.19	1		338	427	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94964022	94964022	+	start_lost	Translation_Start_Site	SNP	C	C	A	novel	NA	P-0018796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	23	107	1	ENST00000536441.1:c.3G>T	p.Met1?	p.M1?	ENST00000536441	NM_144665.3	1	atG/atT	1/10	0.121147347582587	3	FACETS	1	0.837	1	0.362	0.283	0.453	CLONAL	1	TRUE	0	0.19	3		108	244	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579579	7579579	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	51	612	0	ENST00000269305.4:c.108del	p.Ser37ProfsTer7	p.S37Pfs*7	ENST00000269305	NM_001126112.2	36	ccG/cc	4/11	0.1650009255732	3	FACETS	0.65	0.551	0.76	0.325	0.275	0.38	SUBCLONAL	1	TRUE	1	0.19	3		612	904	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602724	10602724	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	105	730	0	ENST00000171111.5:c.854T>A	p.Leu285Gln	p.L285Q	ENST00000171111	NM_203500.1	285	cTg/cAg	3/6	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.19	2		730	1041	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40747909	40747909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	55	730	1	ENST00000392038.2:c.509G>T	p.Arg170Leu	p.R170L	ENST00000392038	NM_001626.4	170	cGg/cTg	6/14	1	2	FACETS	0.541	0.461	0.629	0.541	0.461	0.629	SUBCLONAL	1	TRUE	1	0.19	2		731	1071	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639607	47639607	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1212577306	NA	P-0018796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	50	797	1	ENST00000233146.2:c.700A>T	p.Thr234Ser	p.T234S	ENST00000233146	NM_000251.2	234	Aca/Tca	4/16	1	2	FACETS	0.534	0.452	0.626	0.534	0.452	0.626	SUBCLONAL	1	TRUE	1	0.19	2		798	985	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021433	31021433	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	57	472	0	ENST00000375687.4:c.1432G>T	p.Gly478Cys	p.G478C	ENST00000375687	NM_015338.5	478	Ggt/Tgt	12/13	0.3	3	FACETS	0.916	0.785	1			1	CLONAL	1	TRUE	NA	0.19	3		472	717	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252859	36252859	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	57	451	0	ENST00000300305.3:c.503G>A	p.Gly168Glu	p.G168E	ENST00000300305		168	gGa/gAa	4/8	1	2	FACETS	0.804	0.689	0.931	0.804	0.689	0.931	CLONAL	1	TRUE	1	0.19	2		451	746	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252892	36252892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	74	522	1	ENST00000300305.3:c.470G>A	p.Arg157Lys	p.R157K	ENST00000300305		157	aGa/aAa	4/8	1	2	FACETS	0.904	0.79	1	0.904	0.79	1	CLONAL	1	TRUE	1	0.19	2		523	862	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480429	89480429	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	38	411	0	ENST00000336596.2:c.2266A>T	p.Ser756Cys	p.S756C	ENST00000336596	NM_005233.5	756	Agt/Tgt	13/17	1	2	FACETS	0.712	0.587	0.851	0.712	0.587	0.851	SUBCLONAL	1	TRUE	1	0.19	2		411	562	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161234	185161234	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	72	561	1	ENST00000265026.3:c.661G>T	p.Gly221Cys	p.G221C	ENST00000265026	NM_004721.4	221	Ggt/Tgt	4/14	0.1650009255732	3	FACETS	0.979	0.853	1	0.489	0.426	0.557	CLONAL	1	TRUE	1	0.19	3		562	848	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225771	26225771	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	52	457	0	ENST00000360408.1:c.389G>T	p.Arg130Leu	p.R130L	ENST00000360408	NM_003532.2	130	cGc/cTc	1/1	0.1650009255732	3	FACETS	0.86	0.731	1	0.43	0.365	0.501	CLONAL	1	TRUE	1	0.19	3		457	697	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821308	32821308	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1198	66	792	0	ENST00000354258.4:c.286C>T	p.Leu96Phe	p.L96F	ENST00000354258	NM_000593.5	96	Ctc/Ttc	1/11	0.1650009255732	3	FACETS	0.602	0.52	0.691	0.301	0.26	0.346	SUBCLONAL	1	TRUE	1	0.19	3		792	1264	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346557	81346557	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	51	409	0	ENST00000222390.5:c.1396A>G	p.Ile466Val	p.I466V	ENST00000222390	NM_000601.4	466	Att/Gtt	11/18	0.1650009255732	3	FACETS	0.993	0.843	1	0.496	0.421	0.579	CLONAL	1	TRUE	1	0.19	3		409	592	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508283	106508283	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	52	286	0	ENST00000359195.3:c.277C>A	p.Pro93Thr	p.P93T	ENST00000359195	NM_002649.2	93	Ccg/Acg	2/11	0.1650009255732	3	FACETS	1	0.942	1	0.61	0.52	0.709	CLONAL	1	TRUE	1	0.19	3		286	491	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526580	106526580	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	64	403	0	ENST00000359195.3:c.2873G>C	p.Gly958Ala	p.G958A	ENST00000359195	NM_002649.2	958	gGa/gCa	10/11	0.1650009255732	3	FACETS	1	0.963	1	0.668	0.579	0.765	CLONAL	1	TRUE	1	0.19	3		403	552	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412774	116412774	+	intron_variant	Intron	SNP	G	G	C	novel	NA	P-0018796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	112	1052	0	ENST00000397752.3:c.3028+731G>C		p.*1010*	ENST00000397752	NM_000245.2	-/1390			0.1650009255732	3	FACETS	0.997	0.894	1	0.498	0.447	0.554	CLONAL	1	TRUE	1	0.19	3		1052	1295	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864829	117864829	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	63	520	0	ENST00000297338.2:c.1280G>T	p.Arg427Ile	p.R427I	ENST00000297338	NM_006265.2	427	aGa/aTa	10/14	1	2	FACETS	0.895	0.773	1	0.895	0.773	1	CLONAL	1	TRUE	1	0.19	2		520	741	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652338	48652338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	72	448	1	ENST00000376670.3:c.1009G>A	p.Val337Met	p.V337M	ENST00000376670	NM_002049.3	337	Gtg/Atg	6/6	1	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	0	0.19	1		449	655	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023732	27023734	+	frameshift_variant	Frame_Shift_Ins	INS	TCC	TCC	CTTT	novel	NA	P-0018796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	45	445	1	ENST00000324856.7:c.838_840delinsCTTT	p.Ser280LeufsTer120	p.S280Lfs*120	ENST00000324856	NM_006015.4	280	TCC/CTTT	1/20	1	2	FACETS	0.631	0.529	0.744	0.631	0.529	0.744	SUBCLONAL	1	TRUE	1	0.19	2		446	751	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0018832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	26	587	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.907	0.736	1	0.907	0.736	1	CLONAL	1	TRUE	1	0.61	2		587	94	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0018832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	30	874	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	0.13062255926844	3	FACETS	1	0.885	1	0.553	0.455	0.66	INDETERMINATE	1	TRUE	1	0.61	3		874	116	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100661	67100661	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	19	543	0	ENST00000412916.2:c.359del	p.Asp120ValfsTer19	p.D120Vfs*19	ENST00000412916		120	gAt/gt	4/6	0.297780055549888	0	FACETS	0.458	0.362	0.561			1	INDETERMINATE	1	TRUE	0	0.61	0		543	53	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716214	52716214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	19	397	0	ENST00000322088.6:c.658G>A	p.Val220Met	p.V220M	ENST00000322088	NM_014225.5	220	Gtg/Atg	6/15	0.297780055549888	1	FACETS	0.921	0.734	1	0.921	0.734	1	INDETERMINATE	1	TRUE	0	0.61	1		397	47	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873933	151873934	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	T	novel	NA	P-0018832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	40	400	0	ENST00000262189.6:c.8604_8605delinsA	p.Ser2869LeufsTer37	p.S2869Lfs*37	ENST00000262189	NM_170606.2	2868	acTTct/acAct	38/59	0.297780055549888	5	FACETS	1	0.901	1			1	INDETERMINATE	3	TRUE	NA	0.61	5		400	80	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	307	503	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.280688497704926	3	FACETS	0.787	0.74	0.835	0.787	0.74	0.835	SUBCLONAL	2	TRUE	1	0.31	3		503	1453	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0018853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	107	373	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.295545604156362	1	FACETS	0.765	0.686	0.848	0.765	0.686	0.848	SUBCLONAL	1	TRUE	0	0.31	1		373	763	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578177	7578177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs267605076	NA	P-0018853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1416	208	968	0	ENST00000269305.4:c.672G>T	p.Glu224Asp	p.E224D	ENST00000269305	NM_001126112.2	224	gaG/gaT	6/11	0.253514311677669	1	FACETS	0.698	0.646	0.753	0.698	0.646	0.753	SUBCLONAL	1	TRUE	0	0.31	1		968	1624	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625278	69625292	+	protein_altering_variant	In_Frame_Del	DEL	GTGCGGCGGGTCTTG	GTGCGGCGGGTCTTG	TTA	novel	NA	P-0018853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1233	67	750	5	ENST00000334134.2:c.501_515delinsTAA	p.Thr169_Thr172del	p.T169_T172del	ENST00000334134	NM_005247.2	167	ttCAAGACCCGCCGCACa/ttTAAa	3/3	1	2	FACETS	0.333	0.287	0.382	0.333	0.287	0.382	SUBCLONAL	1	TRUE	1	0.31	2		755	1300	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8525009	8525009	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	57	561	0	ENST00000356435.5:c.595G>A	p.Glu199Lys	p.E199K	ENST00000356435		199	Gag/Aag	7/35	0.295545604156362	1	FACETS	0.356	0.305	0.413	0.356	0.305	0.413	SUBCLONAL	1	TRUE	0	0.31	1		561	872	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22161980	22161980	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	61	714	0	ENST00000215832.6:c.275C>T	p.Ala92Val	p.A92V	ENST00000215832	NM_002745.4	92	gCa/gTa	2/9	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.335376397629455	2		714	353	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417861	138417861	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	70	867	0	ENST00000289153.2:c.1658A>G	p.Asn553Ser	p.N553S	ENST00000289153	NM_006219.2	553	aAt/aGt	11/22	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.335376397629455	2		867	381	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522551	176522551	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	624	615	0	ENST00000292408.4:c.1648G>C	p.Val550Leu	p.V550L	ENST00000292408	NM_213647.1	550	Gtg/Ctg	13/18	0.831907159972375	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.831907159972375	3		615	1041	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193110979	193110979	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0018919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	124	251	0	ENST00000367435.3:c.513-1G>C		p.X171_splice	ENST00000367435	NM_024529.4	171			0.831907159972375	5	FACETS	0.978	0.887	1	0.245	0.221	0.269	CLONAL	1	TRUE	1	0.831907159972375	5		251	685	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351814	89351814	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	427	798	1	ENST00000301030.4:c.1136G>T	p.Ser379Ile	p.S379I	ENST00000301030	NM_001256183.1	379	aGt/aTt	9/13	1	2	FACETS	0.983	0.94	1	0.983	0.94	1	CLONAL	1	TRUE	1	0.831907159972375	2		799	1044	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272037	15272063	+	frameshift_variant	Frame_Shift_Del	DEL	TGCAGTGGCAGTGGCAGCTGCATAGGG	TGCAGTGGCAGTGGCAGCTGCATAGGG	AGCTTGAATT	novel	NA	P-0018919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	242	501	2	ENST00000263388.2:c.6376_6402delinsAATTCAAGCT	p.Pro2126AsnfsTer110	p.P2126Nfs*110	ENST00000263388	NM_000435.2	2126	CCCTATGCAGCTGCCACTGCCACTGCA/AATTCAAGCT	33/33	0.831907159972375	3	FACETS	0.86	0.804	0.917	0.43	0.402	0.459	CLONAL	1	TRUE	1	0.831907159972375	3		503	958	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0019092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	560	918	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.276509920661408	6	FACETS	1	0.989	1			1	INDETERMINATE	3	TRUE	NA	0.596486670458555	6		919	1282	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982405	201982405	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	806	1051	3	ENST00000359651.3:c.784G>T	p.Glu262Ter	p.E262*	ENST00000359651		262	Gag/Tag	6/8	0.537037631147346	6	FACETS	0.946	0.922	0.97	0.946	0.922	0.97	CLONAL	5	TRUE	1	0.596486670458555	6		1054	1253	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248569	8248569	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	174	986	1	ENST00000335790.3:c.318C>A	p.Asp106Glu	p.D106E	ENST00000335790	NM_002315.2	106	gaC/gaA	3/4	1	2	FACETS	0.916	0.847	0.987	0.916	0.847	0.987	CLONAL	1	TRUE	1	0.596486670458555	2		987	637	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589843	69589843	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1367222161	NA	P-0019092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	27	58	0	ENST00000168712.1:c.10C>A	p.Pro4Thr	p.P4T	ENST00000168712	NM_002007.2	4	Ccc/Acc	1/3	0.594696034334696	3	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	1	0.596486670458555	3		58	49	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933240	100933240	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	149	750	0	ENST00000325455.5:c.2150G>T	p.Ser717Ile	p.S717I	ENST00000325455	NM_001202474.3	717	aGt/aTt	4/8	0.594696034334696	3	FACETS	0.919	0.841	1	0.459	0.42	0.5	CLONAL	1	TRUE	1	0.596486670458555	3		750	706	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445766	49445768	+	inframe_deletion	In_Frame_Del	DEL	GGT	GGT	-	novel	NA	P-0019092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1788	244	1551	0	ENST00000301067.7:c.1698_1700del	p.Pro567del	p.P567del	ENST00000301067	NM_003482.3	566	ccACCt/cct	10/54	0.596486670458555	5	FACETS	0.763	0.71	0.818	0.254	0.236	0.273	SUBCLONAL	1	TRUE	2	0.596486670458555	5		1551	2032	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32969050	32969050	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	259	607	0	ENST00000380152.3:c.9481A>C	p.Lys3161Gln	p.K3161Q	ENST00000380152		3161	Aaa/Caa	25/27	0.594696034334696	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.596486670458555	3		607	558	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226447	41226447	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs878853294	NA	P-0019092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	486	994	0	ENST00000357654.3:c.4576G>T	p.Glu1526Ter	p.E1526*	ENST00000357654	NM_007294.3	1526	Gag/Tag	14/23	0.584404684486381	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.596486670458555	4		994	1209	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872681	136872681	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	247	647	0	ENST00000241393.3:c.817G>T	p.Gly273Trp	p.G273W	ENST00000241393	NM_003467.2	273	Ggg/Tgg	2/2	0.584404684486381	4	FACETS	0.965	0.907	1	0.965	0.907	1	CLONAL	2	TRUE	2	0.596486670458555	4		647	685	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161862	47161862	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	373	805	0	ENST00000409792.3:c.4264C>T	p.Gln1422Ter	p.Q1422*	ENST00000409792	NM_014159.6	1422	Cag/Tag	3/21	0.596486670458555	3	FACETS	1	0.976	1	0.689	0.658	0.72	CLONAL	2	TRUE	0	0.596486670458555	3		805	786	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440906	52440906	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs867342588	NA	P-0019092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	458	784	3	ENST00000460680.1:c.598G>T	p.Glu200Ter	p.E200*	ENST00000460680	NM_004656.3	200	Gag/Tag	8/17	0.596486670458555	3	FACETS	0.965	0.933	0.995	0.965	0.933	0.995	CLONAL	3	TRUE	0	0.596486670458555	3		787	689	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144602	55144602	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	296	656	1	ENST00000257290.5:c.2076C>A	p.Ser692Arg	p.S692R	ENST00000257290	NM_006206.4	692	agC/agA	15/23	0.536354580830474	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.596486670458555	4		657	772	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31435899	31435899	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	152	783	1	ENST00000344624.3:c.3015G>T	p.Gln1005His	p.Q1005H	ENST00000344624		1005	caG/caT	22/33	0.596486670458555	6	FACETS	0.908	0.828	0.992	0.303	0.276	0.331	CLONAL	1	TRUE	3	0.596486670458555	6		784	1231	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056449	26056449	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs760498539	NA	P-0019092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	73	341	0	ENST00000343677.2:c.208G>C	p.Gly70Arg	p.G70R	ENST00000343677	NM_005319.3	70	Ggc/Cgc	1/1	0.594696034334696	3	FACETS	0.913	0.804	1	0.457	0.402	0.515	CLONAL	1	TRUE	1	0.596486670458555	3		341	348	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800547	32800547	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	522	1207	0	ENST00000374899.4:c.1000G>T	p.Glu334Ter	p.E334*	ENST00000374899	NM_018833.2	334	Gaa/Taa	6/12	0.594696034334696	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.596486670458555	3		1207	1118	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647493	117647493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	341	861	0	ENST00000368508.3:c.5451G>T	p.Trp1817Cys	p.W1817C	ENST00000368508	NM_002944.2	1817	tgG/tgT	33/43	0.596486670458555	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.596486670458555	2		861	548	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855966	76855966	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	315	1004	0	ENST00000373344.5:c.5634G>T	p.Met1878Ile	p.M1878I	ENST00000373344	NM_000489.3	1878	atG/atT	23/35	0.594696034334696	3	FACETS	0.847	0.803	0.892	0.847	0.803	0.892	CLONAL	2	TRUE	1	0.596486670458555	3		1004	809	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0019138-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	44	465	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.969	0.813	1	0.969	0.813	1	CLONAL	1	TRUE	1	0.2	2		465	454	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488657	212488657	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374970657	NA	P-0019138-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	41	311	0	ENST00000342788.4:c.2192C>T	p.Thr731Met	p.T731M	ENST00000342788	NM_005235.2	731	aCg/aTg	18/28	1	2	FACETS	0.872	0.727	1	0.872	0.727	1	CLONAL	1	TRUE	1	0.2	2		311	470	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135409	30135409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780784905	NA	P-0019138-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	32	206	0	ENST00000331968.5:c.409G>A	p.Ala137Thr	p.A137T	ENST00000331968	NM_002742.2	137	Gcc/Acc	3/18	1	2	FACETS	0.858	0.697	1	0.858	0.697	1	CLONAL	1	TRUE	1	0.2	2		206	373	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118862	115118864	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	novel	NA	P-0019223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	175	653	0	ENST00000257566.3:c.477_479del	p.Asp160del	p.D160del	ENST00000257566	NM_016569.3	159	gaTGAc/gac	2/8	1	2	FACETS	0.79	0.73	0.852	1	0.991	1	SUBCLONAL	2	TRUE	1	0.336719572368634	2		653	658	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120776	115120780	+	frameshift_variant	Frame_Shift_Del	DEL	GGGAT	GGGAT	-	novel	NA	P-0019223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	152	596	0	ENST00000257566.3:c.226_230del	p.Ile76ValfsTer33	p.I76Vfs*33	ENST00000257566	NM_016569.3	76	ATCCCg/g	1/8	1	2	FACETS	0.863	0.794	0.934	1	0.991	1	CLONAL	2	TRUE	1	0.336719572368634	2		596	523	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772199	68772199	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0019223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	186	799	0	ENST00000261769.5:c.49-1G>A		p.X17_splice	ENST00000261769	NM_004360.3	17			0.306043420642668	0	FACETS	0.803	0.75	0.858			1	CLONAL	2	TRUE	0	0.336719572368634	0		799	456	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881001	37881002	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGCTCCCC	rs397516981	NA	P-0019223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	174	900	0	ENST00000269571.5:c.2331_2339dup	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	gtg/gtGGGCTCCCCg	20/27	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.336719572368634	2		900	815	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0019223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	29	244	2	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.797	0.654	0.953	1	0.949	1	CLONAL	2	TRUE	1	0.336719572368634	2		246	108	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164863	36164864	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1439534438	NA	P-0019223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	194	734	0	ENST00000300305.3:c.1011dup	p.Ala338ArgfsTer262	p.A338Rfs*262	ENST00000300305		337	-/C	8/8	0.321880773316571	1	FACETS	0.751	0.698	0.805	1	0.991	1	SUBCLONAL	2	TRUE	0	0.336719572368634	1		734	638	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111495	8111496	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGGA	novel	NA	P-0019254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	458	812	0	ENST00000346208.3:c.982_985dup	p.Arg329MetfsTer24	p.R329Mfs*24	ENST00000346208		327	-/TGGA	5/6	0.71488415082065	4	FACETS	0.908	0.87	0.946	0.908	0.87	0.946	CLONAL	2	TRUE	2	0.885604679318136	4		812	1074	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465622	99465622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	193	529	1	ENST00000268035.6:c.2447G>A	p.Ser816Asn	p.S816N	ENST00000268035	NM_000875.3	816	aGc/aAc	11/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.885604679318136	2		530	394	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035097	37035097	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	129	497	0	ENST00000231790.2:c.59C>G	p.Ala20Gly	p.A20G	ENST00000231790	NM_000249.3	20	gCg/gGg	1/19	0.885604679318136	2	FACETS	0.946	0.871	1	0.473	0.435	0.511	CLONAL	1	TRUE	0	0.885604679318136	2		497	308	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469672	NA	P-0019256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	342	901	1	ENST00000374080.3:c.131G>A	p.Gly44Asp	p.G44D	ENST00000374080		44	gGt/gAt	2/45	0.935603665223106	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.935603665223106	1		902	374	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178016	56178016	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1446404328	NA	P-0019256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	52	669	0	ENST00000399503.3:c.2989A>G	p.Thr997Ala	p.T997A	ENST00000399503	NM_005921.1	997	Act/Gct	14/20	1	2	FACETS	0.22	0.187	0.256	0.22	0.187	0.256	SUBCLONAL	1	TRUE	1	0.935603665223106	2		669	506	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15978955	15978955	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779823128	NA	P-0019342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	323	788	1	ENST00000268712.3:c.3563C>T	p.Ser1188Leu	p.S1188L	ENST00000268712	NM_006311.3	1188	tCg/tTg	27/46	0.872147938748888	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.872147938748888	1		789	402	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478100	138478100	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	106	771	0	ENST00000289153.2:c.86C>A	p.Ser29Tyr	p.S29Y	ENST00000289153	NM_006219.2	29	tCc/tAc	1/22	1	2	FACETS	0.315	0.282	0.35	0.315	0.282	0.35	SUBCLONAL	1	TRUE	1	0.872147938748888	2		771	771	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	186	294	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.838	0.78	0.898	1	0.994	1	CLONAL	3	TRUE	1	0.27960642651758	2		294	529	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111554	8111554	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	200	616	2	ENST00000346208.3:c.1040T>G	p.Leu347Arg	p.L347R	ENST00000346208		347	cTt/cGt	5/6	1	2	FACETS	1	0.983	1	1	0.994	1	CLONAL	2	TRUE	1	0.27960642651758	2		618	612	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494187	140494187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1158980679	NA	P-0019343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	274	882	3	ENST00000288602.6:c.1061G>A	p.Arg354Gln	p.R354Q	ENST00000288602	NM_004333.4	354	cGa/cAa	8/18	1	2	FACETS	1	0.98	1	1	0.995	1	CLONAL	2	TRUE	1	0.27960642651758	2		885	899	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100725	8100726	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1564399278	NA	P-0019343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	243	729	1	ENST00000346208.3:c.701dup	p.Ser237GlnfsTer66	p.S237Qfs*66	ENST00000346208		233	-/T	3/6	1	2	FACETS	1	0.968	1	1	0.995	1	CLONAL	2	TRUE	1	0.27960642651758	2		730	827	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579312	7579315	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CGTG	CGTG	-	novel	NA	P-0019366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	69	563	0	ENST00000269305.4:c.372_375del	p.Tyr126ProfsTer43	p.Y126Pfs*43	ENST00000269305	NM_001126112.2	124	tgCACG/tg	4/11	1	2	FACETS	0.725	0.631	0.827	0.725	0.631	0.827	SUBCLONAL	1	TRUE	1	0.26	2		563	732	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246365	41246366	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACCTAAC	novel	NA	P-0019366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	85	695	0	ENST00000357654.3:c.1176_1182dup	p.Ser395ValfsTer4	p.S395Vfs*4	ENST00000357654	NM_007294.3	394	-/GTTAGGT	10/23	1	2	FACETS	0.609	0.537	0.687	0.609	0.537	0.687	SUBCLONAL	1	TRUE	1	0.26	2		695	1073	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	473	635	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	0.755560237354214	3	FACETS	0.754	0.722	0.786	0.754	0.722	0.786	SUBCLONAL	2	TRUE	1	0.755560237354214	3		635	1144	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461166	120461166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200693165	NA	P-0019453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	373	604	1	ENST00000256646.2:c.5792G>A	p.Arg1931His	p.R1931H	ENST00000256646	NM_024408.3	1931	cGc/cAc	32/34	0.755560237354214	3	FACETS	0.957	0.916	0.997	0.957	0.916	0.997	CLONAL	2	TRUE	1	0.755560237354214	3		605	711	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100073	11100073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1246299696	NA	P-0019453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	304	827	0	ENST00000358026.2:c.1199C>T	p.Ala400Val	p.A400V	ENST00000358026	NM_001128849.1	400	gCg/gTg	7/36	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.755560237354214	2		827	704	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426089	138426089	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1152	75	570	0	ENST00000289153.2:c.1442C>G	p.Thr481Arg	p.T481R	ENST00000289153	NM_006219.2	481	aCa/aGa	9/22	0.658964705365433	5	FACETS	0.345	0.301	0.393	0.115	0.1	0.131	SUBCLONAL	1	TRUE	2	0.755560237354214	5		570	1227	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524725	187524725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756919389	NA	P-0019453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	74	812	0	ENST00000441802.2:c.10955C>T	p.Pro3652Leu	p.P3652L	ENST00000441802	NM_005245.3	3652	cCg/cTg	19/27	0.755560237354214	3	FACETS	0.29	0.253	0.33	0.145	0.126	0.165	SUBCLONAL	1	TRUE	1	0.755560237354214	3		812	930	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750772	57750772	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1392	407	577	1	ENST00000274289.3:c.1832C>G	p.Ala611Gly	p.A611G	ENST00000274289	NM_006622.3	611	gCc/gGc	13/14	0.755560237354214	8	FACETS	0.978	0.928	1			1	CLONAL	2	TRUE	NA	0.755560237354214	8		578	1799	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910587	29910587	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	295	336	0	ENST00000376809.5:c.127G>T	p.Glu43Ter	p.E43*	ENST00000376809	NM_002116.7	43	Gag/Tag	2/8	0.675335119490066	2	FACETS	0.979	0.939	1	0.979	0.939	1	CLONAL	2	TRUE	0	0.675335119490066	2		336	446	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204513771	204513771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	192	431	3	ENST00000367182.3:c.781G>A	p.Glu261Lys	p.E261K	ENST00000367182	NM_001278516.1	261	Gaa/Aaa	9/11	0.675335119490066	3	FACETS	1	0.972	1	0.547	0.508	0.588	CLONAL	1	TRUE	1	0.675335119490066	3		434	695	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651144	206651144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs533634715	NA	P-0019645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	366	917	4	ENST00000367120.3:c.754C>T	p.Arg252Trp	p.R252W	ENST00000367120	NM_014002.3	252	Cgg/Tgg	8/22	0.675335119490066	3	FACETS	1	0.965	1	0.512	0.485	0.54	CLONAL	1	TRUE	1	0.675335119490066	3		921	1415	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877365	28877365	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199779462	NA	P-0019645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	219	590	0	ENST00000282397.4:c.3956C>T	p.Ala1319Val	p.A1319V	ENST00000282397	NM_002019.4	1319	gCg/gTg	30/30	0.675335119490066	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.675335119490066	1		590	410	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103767	47103767	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0019645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	86	559	0	ENST00000409792.3:c.6179C>G	p.Ser2060Ter	p.S2060*	ENST00000409792	NM_014159.6	2060	tCa/tGa	14/21	0.675335119490066	3	FACETS	0.365	0.322	0.411	0.182	0.161	0.206	SUBCLONAL	1	TRUE	1	0.675335119490066	3		559	934	SUCCESS
ATR	545	MSKCC	GRCh37	3	142285015	142285016	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0019645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	205	621	1	ENST00000350721.4:c.238_239dup	p.Leu81HisfsTer5	p.L81Hfs*5	ENST00000350721	NM_001184.3	80	cca/ccCCa	3/47	0.675335119490066	3	FACETS	0.814	0.755	0.875	0.407	0.377	0.438	CLONAL	1	TRUE	1	0.675335119490066	3		622	998	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896411	151896411	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	60	584	0	ENST00000262189.6:c.4226A>T	p.Asp1409Val	p.D1409V	ENST00000262189	NM_170606.2	1409	gAt/gTt	27/59	0.376498396132332	4	FACETS	0.4	0.343	0.461			1	INDETERMINATE	1	TRUE	NA	0.675335119490066	4		584	745	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0019652-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	104	739	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.23989008720553	2	FACETS	0.792	0.712	0.875	0.792	0.712	0.875	SUBCLONAL	2	TRUE	0	0.272564033108589	2		739	482	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429319	78429326	+	frameshift_variant	Frame_Shift_Del	DEL	CACCAGGT	CACCAGGT	-	novel	NA	P-0019652-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	40	709	3	ENST00000370768.2:c.1116_1123del	p.Pro373ThrfsTer5	p.P373Tfs*5	ENST00000370768	NM_003902.3	372	ccACCTGGTGga/ccga	13/20	0.282377622986254	3	FACETS	0.592	0.491	0.705	0.296	0.245	0.353	SUBCLONAL	1	TRUE	1	0.272564033108589	3		712	563	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244759	41244759	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019652-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	68	858	0	ENST00000357654.3:c.2789del	p.Pro930LeufsTer70	p.P930Lfs*70	ENST00000357654	NM_007294.3	930	cCt/ct	10/23	0.23989008720553	2	FACETS	1	0.964	1	0.648	0.566	0.735	CLONAL	1	TRUE	0	0.272564033108589	2		858	385	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215381	5215381	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019652-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	36	690	0	ENST00000357368.4:c.4237C>G	p.Leu1413Val	p.L1413V	ENST00000357368	NM_002850.3	1413	Ctg/Gtg	28/38	0.147758787698525	1	FACETS	0.627	0.516	0.75	0.627	0.516	0.75	INDETERMINATE	1	TRUE	0	0.272564033108589	1		690	364	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794491	242794491	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019652-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	36	771	1	ENST00000334409.5:c.451G>T	p.Val151Leu	p.V151L	ENST00000334409	NM_005018.2	151	Gtg/Ttg	3/5	0.251806002992517	3	FACETS	0.701	0.577	0.841	0.351	0.288	0.421	SUBCLONAL	1	TRUE	1	0.272564033108589	3		772	428	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484779	57484779	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019652-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	35	622	1	ENST00000371085.3:c.759C>A	p.Tyr253Ter	p.Y253*	ENST00000371085	NM_000516.4	253	taC/taA	10/13	1	2	FACETS	0.572	0.469	0.688	0.572	0.469	0.688	SUBCLONAL	1	TRUE	1	0.272564033108589	2		623	449	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458554	12458554	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019652-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	29	781	1	ENST00000287820.6:c.1171T>A	p.Phe391Ile	p.F391I	ENST00000287820	NM_015869.4	391	Ttt/Att	6/7	1	2	FACETS	0.423	0.339	0.519	0.423	0.339	0.519	SUBCLONAL	1	TRUE	1	0.272564033108589	2		782	503	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221995	1221995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201090	NA	P-0019655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	145	664	0	ENST00000326873.7:c.910C>T	p.Arg304Trp	p.R304W	ENST00000326873	NM_000455.4	304	Cgg/Tgg	7/10	0.314605050320698	2	FACETS	0.944	0.868	1	0.944	0.868	1	CLONAL	2	TRUE	0	0.314605050320698	2		664	488	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120509023	120509023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782444829	NA	P-0019655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	97	678	1	ENST00000256646.2:c.1543C>T	p.Arg515Cys	p.R515C	ENST00000256646	NM_024408.3	515	Cgt/Tgt	9/34	0.314605050320698	3	FACETS	0.946	0.844	1	0.473	0.422	0.528	CLONAL	1	TRUE	1	0.314605050320698	3		679	754	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243313	123243313	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	135	916	0	ENST00000358487.5:c.2200A>C	p.Met734Leu	p.M734L	ENST00000358487	NM_000141.4	734	Atg/Ctg	17/18	0.314605050320698	2	FACETS	1	0.955	1	0.54	0.491	0.591	CLONAL	1	TRUE	0	0.314605050320698	2		916	795	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435109	110435109	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	105	735	2	ENST00000375856.3:c.3292G>T	p.Val1098Leu	p.V1098L	ENST00000375856	NM_003749.2	1098	Gtg/Ttg	1/2	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.314605050320698	2		737	656	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719312	52719312	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	181	717	0	ENST00000322088.6:c.978C>G	p.Ile326Met	p.I326M	ENST00000322088	NM_014225.5	326	atC/atG	8/15	0.298434348460632	4	FACETS	0.904	0.834	0.975	0.904	0.834	0.975	CLONAL	2	TRUE	2	0.314605050320698	4		717	837	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864725	68864725	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	83	519	0	ENST00000288368.4:c.96G>C	p.Gln32His	p.Q32H	ENST00000288368	NM_024870.2	32	caG/caC	1/40	0.314605050320698	3	FACETS	1	0.962	1	0.603	0.534	0.677	CLONAL	1	TRUE	1	0.314605050320698	3		519	506	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981970	70981970	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1438472553	NA	P-0019655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	75	1030	1	ENST00000276594.2:c.126C>A	p.Ser42Arg	p.S42R	ENST00000276594	NM_024504.3	42	agC/agA	2/8	0.314605050320698	3	FACETS	0.553	0.483	0.629	0.277	0.241	0.315	SUBCLONAL	1	TRUE	1	0.314605050320698	3		1031	997	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587781525	NA	P-0019831-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	269	690	0	ENST00000269305.4:c.842A>G	p.Asp281Gly	p.D281G	ENST00000269305	NM_001126112.2	281	gAc/gGc	8/11	0.295779036084861	2	FACETS	0.791	0.743	0.839	0.791	0.743	0.839	SUBCLONAL	2	FALSE	0	0.384880123614777	2		690	884	SUCCESS
APC	324	MSKCC	GRCh37	5	112174835	112174835	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0019831-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	104	256	0	ENST00000257430.4:c.3544A>T	p.Lys1182Ter	p.K1182*	ENST00000257430	NM_000038.5	1182	Aaa/Taa	16/16	0.25067051476487	4	FACETS	0.945	0.853	1	0.945	0.853	1	CLONAL	2	FALSE	2	0.384880123614777	4		256	396	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122518	17122518	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019831-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	216	650	0	ENST00000285071.4:c.877G>T	p.Glu293Ter	p.E293*	ENST00000285071	NM_144997.5	293	Gaa/Taa	9/14	0.295779036084861	2	FACETS	0.755	0.705	0.807	0.755	0.705	0.807	SUBCLONAL	2	FALSE	0	0.384880123614777	2		650	743	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221909	98221909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019831-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	152	583	0	ENST00000331920.6:c.2860G>T	p.Asp954Tyr	p.D954Y	ENST00000331920	NM_000264.3	954	Gac/Tac	17/24	0.167099875990683	3	FACETS	1	0.98	1	0.612	0.56	0.666	INDETERMINATE	1	FALSE	1	0.384880123614777	3		583	770	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720826	89720826	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	75	388	0	ENST00000371953.3:c.977A>T	p.Asp326Val	p.D326V	ENST00000371953	NM_000314.4	326	gAc/gTc	8/9	0.390240151191843	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.390240151191843	1		388	294	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039504	49039504	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	229	714	0	ENST00000267163.4:c.2489G>C	p.Arg830Thr	p.R830T	ENST00000267163	NM_000321.2	830	aGa/aCa	23/27	0.372236926976222	2	FACETS	0.923	0.865	0.981	0.923	0.865	0.981	CLONAL	2	TRUE	0	0.390240151191843	2		714	636	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913901	32913902	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs80359512	NA	P-0019975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	85	762	0	ENST00000380152.3:c.5410_5411del	p.Val1804LysfsTer2	p.V1804Kfs*2	ENST00000380152		1803	acTGta/acta	11/27	0.583113571925215	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.583113571925215	1		762	200	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226520	1226520	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	193	861	0	ENST00000326873.7:c.1176G>T	p.Met392Ile	p.M392I	ENST00000326873	NM_000455.4	392	atG/atT	9/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.583113571925215	2		861	604	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290069	15290069	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	213	852	0	ENST00000263388.2:c.3485A>G	p.Asp1162Gly	p.D1162G	ENST00000263388	NM_000435.2	1162	gAt/gGt	22/33	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.583113571925215	2		852	635	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973009	25973010	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0019975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	105	563	0	ENST00000435504.4:c.1414_1415dup	p.Glu473MetfsTer50	p.E473Mfs*50	ENST00000435504		472	cat/caCAt	12/13	1	2	FACETS	0.916	0.828	1	0.916	0.828	1	CLONAL	1	TRUE	1	0.583113571925215	2		563	393	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973016	25973016	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	130	597	0	ENST00000435504.4:c.1409A>C	p.Asn470Thr	p.N470T	ENST00000435504		470	aAt/aCt	12/13	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.583113571925215	2		597	408	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240234	5240247	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGAGGAGCTCGT	GAAGAGGAGCTCGT	C	novel	NA	P-0019975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	158	870	0	ENST00000357368.4:c.1667_1680delinsG	p.Tyr556CysfsTer25	p.Y556Cfs*25	ENST00000357368	NM_002850.3	556	tACGAGCTCCTCTTC/tG	12/38	1	2	FACETS	0.894	0.823	0.968	0.894	0.823	0.968	CLONAL	1	TRUE	1	0.583113571925215	2		870	606	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0019983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	279	432	3	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.787949707547966	3	FACETS	0.875	0.822	0.93	0.438	0.411	0.465	CLONAL	1	TRUE	1	0.787949707547966	3		435	1128	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577507	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	436	650	2	ENST00000269305.4:c.774dup	p.Asp259ArgfsTer5	p.D259Rfs*5	ENST00000269305	NM_001126112.2	258	-/A	7/11	0.787949707547966	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.787949707547966	1		652	645	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0019983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	554	536	5	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			0.701248408725694	3	FACETS	0.952	0.919	0.984			1	CLONAL	2	TRUE	NA	0.787949707547966	3		541	1030	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43806105	43806105	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	429	637	0	ENST00000372470.3:c.901T>A	p.Cys301Ser	p.C301S	ENST00000372470	NM_005373.2	301	Tgt/Agt	6/12	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.787949707547966	2		637	1084	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0020021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	921	411	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.794858002389025	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.794858002389025	2		411	1143	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11273604	11273604	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	393	260	0	ENST00000361445.4:c.3137C>G	p.Thr1046Ser	p.T1046S	ENST00000361445	NM_004958.3	1046	aCc/aGc	21/58	0.743663978386887	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.794858002389025	2		260	491	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258338	16258338	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0020021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	814	475	0	ENST00000375759.3:c.5603T>A	p.Leu1868Ter	p.L1868*	ENST00000375759	NM_015001.2	1868	tTg/tAg	11/15	0.743663978386887	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.794858002389025	2		475	1008	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936841	48936948	+	splice_region_variant,intron_variant	Splice_Region	DEL	AGTAGTAGAATGTTACCAAGATTATTTTTGACCTAAGTTATAGTTAGAATACTTCATTATTTTATATGATGGATGTACAATTGTTCTTATCTAATTTACCACTTTTAC	AGTAGTAGAATGTTACCAAGATTATTTTTGACCTAAGTTATAGTTAGAATACTTCATTATTTTATATGATGGATGTACAATTGTTCTTATCTAATTTACCACTTTTAC	-	novel	NA	P-0020021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	151	48	0	ENST00000267163.4:c.719-108_719-1del		p.X240_splice	ENST00000267163	NM_000321.2	240			0.791568283770814	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.794858002389025	1		48	174	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163678	32163678	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs988401099	NA	P-0020021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	263	306	0	ENST00000375023.3:c.5548G>A	p.Val1850Met	p.V1850M	ENST00000375023	NM_004557.3	1850	Gtg/Atg	30/30	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.794858002389025	2		306	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577557	7577557	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519982	NA	P-0020105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	352	797	1	ENST00000269305.4:c.724T>C	p.Cys242Arg	p.C242R	ENST00000269305	NM_001126112.2	242	Tgc/Cgc	7/11	0.422112645655658	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.422112645655658	2		798	825	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259258	16259258	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	117	575	0	ENST00000375759.3:c.6523G>T	p.Val2175Leu	p.V2175L	ENST00000375759	NM_015001.2	2175	Gtg/Ttg	11/15	0.143401060108051	5	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.422112645655658	5		575	657	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261562	16261562	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs893727176	NA	P-0020105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	191	776	0	ENST00000375759.3:c.8827G>C	p.Val2943Leu	p.V2943L	ENST00000375759	NM_015001.2	2943	Gtt/Ctt	11/15	0.143401060108051	5	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.422112645655658	5		776	1049	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831165	72831165	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	126	611	0	ENST00000268489.5:c.5416G>T	p.Glu1806Ter	p.E1806*	ENST00000268489	NM_006885.3	1806	Gag/Tag	9/10	0.143401060108051	5	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.422112645655658	5		611	782	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643869	52643869	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	142	652	0	ENST00000394830.3:c.2027G>C	p.Arg676Thr	p.R676T	ENST00000394830	NM_018313.4	676	aGg/aCg	17/30	0.231837083893111	5	FACETS	1	0.982	1	0.433	0.395	0.474	INDETERMINATE	1	TRUE	2	0.422112645655658	5		652	845	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961420	1961420	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	359	847	0	ENST00000382891.5:c.3208A>G	p.Thr1070Ala	p.T1070A	ENST00000382891	NM_133335.3	1070	Aca/Gca	17/22	0.422112645655658	5	FACETS	0.94	0.89	0.992			1	CLONAL	2	TRUE	NA	0.422112645655658	5		847	1477	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0020137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	289	952	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.345337051613001	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.345337051613001	3		952	947	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974783	21974783	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658556	NA	P-0020137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	42	334	1	ENST00000304494.5:c.44G>A	p.Trp15Ter	p.W15*	ENST00000304494	NM_000077.4	15	tGg/tAg	1/3	0.345337051613001	1	FACETS	0.972	0.821	1	0.972	0.821	1	CLONAL	1	TRUE	0	0.345337051613001	1		335	207	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005625	42005625	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	72	672	0	ENST00000219905.7:c.3361G>T	p.Glu1121Ter	p.E1121*	ENST00000219905	NM_001164273.1	1121	Gag/Tag	9/24	0.345337051613001	1	FACETS	0.887	0.779	1	0.887	0.779	1	CLONAL	1	TRUE	0	0.345337051613001	1		672	389	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739340	46739340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540912131	NA	P-0020159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	144	717	0	ENST00000371975.4:c.1531C>T	p.Arg511Cys	p.R511C	ENST00000371975	NM_003579.3	511	Cgt/Tgt	14/18	1	2	FACETS	0.764	0.698	0.834	0.764	0.698	0.834	SUBCLONAL	1	TRUE	1	0.492104406605625	2		717	766	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743919	41743920	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0020159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	231	997	0	ENST00000301178.4:c.855_856insGG	p.Gln286GlyfsTer12	p.Q286Gfs*12	ENST00000301178	NM_021913.4	285	tcg/tcGGg	7/20	1	2	FACETS	0.689	0.641	0.739	0.689	0.641	0.739	SUBCLONAL	1	TRUE	1	0.492104406605625	2		997	1362	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266509	198266509	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	38	756	0	ENST00000335508.6:c.2327A>C	p.Glu776Ala	p.E776A	ENST00000335508	NM_012433.2	776	gAa/gCa	16/25	1	2	FACETS	0.61	0.508	0.724	0.61	0.508	0.724	SUBCLONAL	1	TRUE	1	0.492104406605625	2		756	253	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436639	8436639	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	39	897	0	ENST00000356435.5:c.4039del	p.Glu1347LysfsTer3	p.E1347Kfs*3	ENST00000356435		1347	Gaa/aa	24/35	1	2	FACETS	0.495	0.412	0.588	0.495	0.412	0.588	SUBCLONAL	1	TRUE	1	0.492104406605625	2		897	320	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245587	41245587	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357522	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	390	789	3	ENST00000357654.3:c.1961del	p.Lys654SerfsTer47	p.K654Sfs*47	ENST00000357654	NM_007294.3	654	aAg/ag	10/23	1	2	FACETS	0.967	0.917	1	0.967	0.917	1	CLONAL	1	TRUE	1	0.570338586915073	2		792	1415	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	234	520	4	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.891	0.832	0.952	0.891	0.832	0.952	CLONAL	1	TRUE	1	0.570338586915073	2		524	921	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927443	245927443	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	64	578	5	ENST00000388985.4:c.1085del	p.Phe362SerfsTer12	p.F362Sfs*12	ENST00000388985		362	tTc/tc	11/12	0.545554205193534	3	FACETS	0.272	0.234	0.313	0.091	0.078	0.105	SUBCLONAL	1	TRUE	0	0.570338586915073	3		583	1062	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	235	504	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.570338586915073	2		504	821	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	394	764	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.570338586915073	2		770	1320	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992721	68992721	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs764112302	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	251	819	4	ENST00000288368.4:c.1693del	p.Ser565ArgfsTer10	p.S565Rfs*10	ENST00000288368	NM_024870.2	562	cgT/cg	16/40	1	2	FACETS	0.852	0.797	0.908	0.852	0.797	0.908	CLONAL	1	TRUE	1	0.570338586915073	2		823	1033	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189883	11189883	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	237	472	0	ENST00000361445.4:c.5626A>C	p.Thr1876Pro	p.T1876P	ENST00000361445	NM_004958.3	1876	Acc/Ccc	40/58	1	2	FACETS	0.994	0.93	1	0.994	0.93	1	CLONAL	1	TRUE	1	0.570338586915073	2		472	836	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088659	27088659	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	418	907	1	ENST00000324856.7:c.2272del	p.Gln758ArgfsTer75	p.Q758Rfs*75	ENST00000324856	NM_006015.4	756	aaC/aa	7/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.570338586915073	2		908	1379	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937848	36937848	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	400	877	0	ENST00000361632.4:c.988A>G	p.Thr330Ala	p.T330A	ENST00000361632		330	Acc/Gcc	7/16	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.570338586915073	2		877	1388	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649922	88649922	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786201038	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	280	659	0	ENST00000372037.3:c.176del	p.Leu59Ter	p.L59*	ENST00000372037	NM_004329.2	57	ccT/cc	4/13	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.570338586915073	2		659	962	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912183	114912183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	331	679	0	ENST00000543371.1:c.1253C>T	p.Ser418Phe	p.S418F	ENST00000543371	NM_001198531.1	418	tCc/tTc	11/14	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.570338586915073	2		679	1139	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944170	71944170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773191339	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	319	769	1	ENST00000298229.2:c.2003G>A	p.Arg668Gln	p.R668Q	ENST00000298229	NM_001567.3	668	cGg/cAg	17/28	1	2	FACETS	0.99	0.935	1	0.99	0.935	1	CLONAL	1	TRUE	1	0.570338586915073	2		770	1130	SUCCESS
CBL	867	MSKCC	GRCh37	11	119077232	119077233	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAC	rs373212940	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	169	653	0	ENST00000264033.4:c.125_127dup	p.His42dup	p.H42dup	ENST00000264033	NM_005188.3	42	-/CAC	1/16	1	2	FACETS	0.608	0.559	0.66	0.608	0.559	0.66	SUBCLONAL	1	TRUE	1	0.570338586915073	2		653	974	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431719	431719	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs768653465	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	292	686	0	ENST00000399788.2:c.2290C>T	p.Arg764Ter	p.R764*	ENST00000399788	NM_001042603.1	764	Cga/Tga	17/28	1	2	FACETS	0.953	0.898	1	0.953	0.898	1	CLONAL	1	TRUE	1	0.570338586915073	2		686	1074	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123837	46123837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	179	370	0	ENST00000334344.6:c.109del	p.Ile37SerfsTer21	p.I37Sfs*21	ENST00000334344	NM_152641.2	35	Aaa/aa	2/21	1	2	FACETS	0.895	0.828	0.965	0.895	0.828	0.965	CLONAL	1	TRUE	1	0.570338586915073	2		370	701	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416546	49416546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	311	610	1	ENST00000301067.7:c.16165C>T	p.Arg5389Trp	p.R5389W	ENST00000301067	NM_003482.3	5389	Cgg/Tgg	51/54	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.570338586915073	2		611	1008	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431746	49431748	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs748239185	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	299	745	1	ENST00000301067.7:c.9391_9393del	p.Pro3131del	p.P3131del	ENST00000301067	NM_003482.3	3131	CCT/-	34/54	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.570338586915073	2		746	1046	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438688	49438688	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749039924	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	404	827	0	ENST00000301067.7:c.4802G>A	p.Arg1601His	p.R1601H	ENST00000301067	NM_003482.3	1601	cGt/cAt	19/54	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.570338586915073	2		827	1358	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885996	111885996	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	312	662	0	ENST00000341259.2:c.1618C>T	p.Gln540Ter	p.Q540*	ENST00000341259	NM_005475.2	540	Cag/Tag	8/8	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.570338586915073	2		662	1067	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	192	451	8	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	1	2	FACETS	0.997	0.926	1	0.997	0.926	1	CLONAL	1	TRUE	1	0.570338586915073	2		459	675	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436635	110436635	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	379	1097	0	ENST00000375856.3:c.1766A>G	p.Gln589Arg	p.Q589R	ENST00000375856	NM_003749.2	589	cAg/cGg	1/2	1	2	FACETS	0.911	0.864	0.959	0.911	0.864	0.959	CLONAL	1	TRUE	1	0.570338586915073	2		1097	1459	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777898	3777898	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	400	982	5	ENST00000262367.5:c.7150del	p.His2384ThrfsTer12	p.H2384Tfs*12	ENST00000262367	NM_004380.2	2384	Cac/ac	31/31	1	2	FACETS	0.901	0.856	0.948	0.901	0.856	0.948	CLONAL	1	TRUE	1	0.570338586915073	2		987	1556	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778302	3778302	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs794727551	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	322	658	1	ENST00000262367.5:c.6746G>A	p.Arg2249His	p.R2249H	ENST00000262367	NM_004380.2	2249	cGc/cAc	31/31	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.570338586915073	2		659	1062	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	212	450	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.934	0.87	1	0.934	0.87	1	CLONAL	1	TRUE	1	0.570338586915073	2		450	796	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830937	72830937	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	247	531	0	ENST00000268489.5:c.5644A>G	p.Ile1882Val	p.I1882V	ENST00000268489	NM_006885.3	1882	Atc/Gtc	9/10	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.570338586915073	2		531	844	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993143	72993143	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375991410	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1368	159	945	0	ENST00000268489.5:c.902C>T	p.Ala301Val	p.A301V	ENST00000268489	NM_006885.3	301	gCg/gTg	2/10	1	2	FACETS	0.365	0.333	0.399	0.365	0.333	0.399	SUBCLONAL	1	TRUE	1	0.570338586915073	2		945	1527	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687471	37687472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	73	350	0	ENST00000447079.4:c.4381_4382dup	p.Pro1462AlafsTer38	p.P1462Afs*38	ENST00000447079	NM_015083.1	1459	tgg/tGGgg	14/14	1	2	FACETS	0.499	0.437	0.565	0.499	0.437	0.565	SUBCLONAL	1	TRUE	1	0.570338586915073	2		350	513	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868201	37868201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776515406	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	322	695	1	ENST00000269571.5:c.922G>A	p.Val308Met	p.V308M	ENST00000269571		308	Gtg/Atg	8/27	1	2	FACETS	0.922	0.87	0.975	0.922	0.87	0.975	CLONAL	1	TRUE	1	0.570338586915073	2		696	1225	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38506084	38506084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs976474384	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	322	711	1	ENST00000254066.5:c.376C>T	p.Arg126Trp	p.R126W	ENST00000254066	NM_000964.3	126	Cgg/Tgg	4/9	1	2	FACETS	0.997	0.941	1	0.997	0.941	1	CLONAL	1	TRUE	1	0.570338586915073	2		712	1133	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56801430	56801430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881932	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	276	648	1	ENST00000337432.4:c.934C>T	p.Arg312Trp	p.R312W	ENST00000337432	NM_058216.2	312	Cgg/Tgg	7/9	1	2	FACETS	0.979	0.92	1	0.979	0.92	1	CLONAL	1	TRUE	1	0.570338586915073	2		649	989	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821817	59821817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780235	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	308	744	4	ENST00000259008.2:c.2233G>A	p.Ala745Thr	p.A745T	ENST00000259008	NM_032043.2	745	Gca/Aca	15/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.570338586915073	2		748	1035	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533027	63533027	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	365	780	0	ENST00000307078.5:c.1867A>G	p.Met623Val	p.M623V	ENST00000307078	NM_004655.3	623	Atg/Gtg	7/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.570338586915073	2		780	1199	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533767	63533767	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	284	659	0	ENST00000307078.5:c.1387C>A	p.Arg463Ser	p.R463S	ENST00000307078	NM_004655.3	463	Cgc/Agc	6/11	1	2	FACETS	0.981	0.923	1	0.981	0.923	1	CLONAL	1	TRUE	1	0.570338586915073	2		659	1015	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78935227	78935227	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	399	852	0	ENST00000306801.3:c.3639G>T	p.Trp1213Cys	p.W1213C	ENST00000306801	NM_020761.2	1213	tgG/tgT	31/34	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.570338586915073	2		852	1305	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207593	2207593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1309017440	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	305	699	0	ENST00000398665.3:c.877G>A	p.Val293Met	p.V293M	ENST00000398665	NM_032482.2	293	Gtg/Atg	11/28	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.570338586915073	2		699	1048	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	60	158	1	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	0.832	0.724	0.946	0.832	0.724	0.946	CLONAL	1	TRUE	1	0.570338586915073	2		159	253	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10259657	10259657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749258509	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	289	587	3	ENST00000340748.4:c.2575G>A	p.Asp859Asn	p.D859N	ENST00000340748		859	Gac/Aac	26/40	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.570338586915073	2		590	932	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054390	13054390	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	331	674	0	ENST00000316448.5:c.1000A>G	p.Asn334Asp	p.N334D	ENST00000316448	NM_004343.3	334	Aac/Gac	8/9	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.570338586915073	2		674	1092	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272336	15272337	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs771517374	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	316	1003	5	ENST00000263388.2:c.6102dup	p.Gly2035ArgfsTer60	p.G2035Rfs*60	ENST00000263388	NM_000435.2	2034	-/C	33/33	1	2	FACETS	0.817	0.769	0.865	0.817	0.769	0.865	CLONAL	1	TRUE	1	0.570338586915073	2		1008	1357	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303262	15303262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1306893382	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1655	174	1211	2	ENST00000263388.2:c.266G>A	p.Gly89Asp	p.G89D	ENST00000263388	NM_000435.2	89	gGc/gAc	3/33	1	2	FACETS	0.334	0.305	0.363	0.334	0.305	0.363	SUBCLONAL	1	TRUE	1	0.570338586915073	2		1213	1829	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214884	36214884	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1403628021	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	367	949	0	ENST00000222270.7:c.3310C>T	p.Arg1104Trp	p.R1104W	ENST00000222270	NM_014727.1	1104	Cgg/Tgg	8/37	1	2	FACETS	0.962	0.912	1	0.962	0.912	1	CLONAL	1	TRUE	1	0.570338586915073	2		949	1338	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227675	36227675	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	342	807	0	ENST00000222270.7:c.7244G>A	p.Arg2415His	p.R2415H	ENST00000222270	NM_014727.1	2415	cGc/cAc	31/37	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.570338586915073	2		807	1158	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609673	46609673	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	370	774	2	ENST00000263734.3:c.2402del	p.Pro801HisfsTer39	p.P801Hfs*39	ENST00000263734	NM_001430.4	799	ttC/tt	15/16	1	2	FACETS	0.963	0.912	1	0.963	0.912	1	CLONAL	1	TRUE	1	0.570338586915073	2		776	1348	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703523	47703524	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	276	715	0	ENST00000233146.2:c.2024_2025del	p.Lys675IlefsTer23	p.K675Ifs*23	ENST00000233146	NM_000251.2	675	AAa/a	13/16	1	2	FACETS	0.943	0.886	1	0.943	0.886	1	CLONAL	1	TRUE	1	0.570338586915073	2		715	1026	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707957	47707957	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	248	570	0	ENST00000233146.2:c.2581C>A	p.Gln861Lys	p.Q861K	ENST00000233146	NM_000251.2	861	Caa/Aaa	15/16	1	2	FACETS	0.982	0.92	1	0.982	0.92	1	CLONAL	1	TRUE	1	0.570338586915073	2		570	886	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	350	953	1	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.919	0.87	0.97	0.919	0.87	0.97	CLONAL	1	TRUE	1	0.570338586915073	2		954	1335	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	242	287	4	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	1	0.965	1	1	0.995	1	CLONAL	2	TRUE	1	0.570338586915073	2		291	416	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735559	40735559	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	234	541	1	ENST00000373198.4:c.3314C>T	p.Ala1105Val	p.A1105V	ENST00000373198	NM_133170.3	1105	gCt/gTt	25/32	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.570338586915073	2		542	811	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764347	39764347	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	275	648	2	ENST00000288319.7:c.765del	p.Arg256GlyfsTer35	p.R256Gfs*35	ENST00000288319	NM_182918.3	255	ccC/cc	7/10	1	2	FACETS	0.96	0.902	1	0.96	0.902	1	CLONAL	1	TRUE	1	0.570338586915073	2		650	1005	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288437	21288437	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1477769854	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	349	791	1	ENST00000354336.3:c.682A>G	p.Thr228Ala	p.T228A	ENST00000354336	NM_005207.3	228	Acc/Gcc	2/3	1	2	FACETS	0.983	0.931	1	0.983	0.931	1	CLONAL	1	TRUE	1	0.570338586915073	2		792	1245	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032747	30032747	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555986860	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	185	354	0	ENST00000338641.4:c.122G>A	p.Trp41Ter	p.W41*	ENST00000338641	NM_000268.3	41	tGg/tAg	2/16	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.570338586915073	2		354	636	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732969	30732969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893810	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	226	468	1	ENST00000295754.5:c.1582C>T	p.Arg528Cys	p.R528C	ENST00000295754	NM_003242.5	528	Cgt/Tgt	7/7	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.570338586915073	2		469	691	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405932	49405932	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	355	774	0	ENST00000418115.1:c.206T>C	p.Leu69Pro	p.L69P	ENST00000418115	NM_001664.2	69	cTg/cCg	3/5	1	2	FACETS	0.964	0.912	1	0.964	0.912	1	CLONAL	1	TRUE	1	0.570338586915073	2		774	1292	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725085	49725085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1189053822	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	328	759	1	ENST00000449682.2:c.259G>A	p.Val87Met	p.V87M	ENST00000449682	NM_020998.3	87	Gtg/Atg	3/18	1	2	FACETS	0.974	0.92	1	0.974	0.92	1	CLONAL	1	TRUE	1	0.570338586915073	2		760	1181	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631596	119631596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	221	536	1	ENST00000316626.5:c.670G>A	p.Ala224Thr	p.A224T	ENST00000316626		224	Gca/Aca	6/12	1	2	FACETS	0.93	0.868	0.995	0.93	0.868	0.995	CLONAL	1	TRUE	1	0.570338586915073	2		537	833	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670333	134670333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	237	472	1	ENST00000398015.3:c.244G>A	p.Ala82Thr	p.A82T	ENST00000398015	NM_004441.4	82	Gcc/Acc	3/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.570338586915073	2		473	769	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274740	142274741	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	176	455	2	ENST00000350721.4:c.2319_2320del	p.Lys773AsnfsTer3	p.K773Nfs*3	ENST00000350721	NM_001184.3	773	aaAAta/aata	10/47	1	2	FACETS	0.808	0.746	0.872	0.808	0.746	0.872	CLONAL	1	TRUE	1	0.570338586915073	2		457	764	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749415085	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	233	460	1	ENST00000263967.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000263967	NM_006218.2	38	Cgt/Tgt	2/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.570338586915073	2		461	745	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165687	185165687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	64	524	1	ENST00000265026.3:c.962C>T	p.Ala321Val	p.A321V	ENST00000265026	NM_004721.4	321	gCg/gTg	5/14	1	2	FACETS	0.245	0.211	0.282	0.245	0.211	0.282	SUBCLONAL	1	TRUE	1	0.570338586915073	2		525	917	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447033	187447033	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	351	825	0	ENST00000232014.4:c.1160A>C	p.Asn387Thr	p.N387T	ENST00000232014	NM_001130845.1	387	aAc/aCc	5/10	1	2	FACETS	0.995	0.942	1	0.995	0.942	1	CLONAL	1	TRUE	1	0.570338586915073	2		825	1237	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806176	1806176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370064407	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1246	82	865	1	ENST00000260795.2:c.1195C>T	p.Arg399Cys	p.R399C	ENST00000260795		399	Cgc/Tgc	8/17	1	2	FACETS	0.217	0.19	0.245	0.217	0.19	0.245	SUBCLONAL	1	TRUE	1	0.570338586915073	2		866	1328	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806234	1806234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781361431	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	357	850	1	ENST00000260795.2:c.1253C>T	p.Pro418Leu	p.P418L	ENST00000260795		418	cCg/cTg	8/17	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.570338586915073	2		851	1185	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158453	106158453	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	172	402	0	ENST00000380013.4:c.3354T>A	p.Asn1118Lys	p.N1118K	ENST00000380013	NM_001127208.2	1118	aaT/aaA	3/11	1	2	FACETS	0.973	0.899	1	0.973	0.899	1	CLONAL	1	TRUE	1	0.570338586915073	2		402	620	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264539	1264539	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	235	533	0	ENST00000310581.5:c.2823G>T	p.Glu941Asp	p.E941D	ENST00000310581	NM_198253.2	941	gaG/gaT	11/16	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.570338586915073	2		533	819	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410918	31410918	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	419	858	0	ENST00000344624.3:c.3602T>C	p.Ile1201Thr	p.I1201T	ENST00000344624		1201	aTa/aCa	28/33	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.570338586915073	2		858	1326	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944382	131944382	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs748536322	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	211	443	5	ENST00000265335.6:c.2801del	p.Asn934IlefsTer6	p.N934Ifs*6	ENST00000265335		932	Aaa/aa	17/25	1	2	FACETS	0.926	0.862	0.992	0.926	0.862	0.992	CLONAL	1	TRUE	1	0.570338586915073	2		448	799	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522599	176522599	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748021462	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	407	890	1	ENST00000292408.4:c.1696C>T	p.Arg566Cys	p.R566C	ENST00000292408	NM_213647.1	566	Cgc/Tgc	13/18	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.570338586915073	2		891	1221	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	311	810	2	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	1	2	FACETS	0.912	0.86	0.965	0.912	0.86	0.965	CLONAL	1	TRUE	1	0.570338586915073	2		812	1196	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032075	26032075	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	228	605	1	ENST00000244661.2:c.214G>T	p.Val72Leu	p.V72L	ENST00000244661	NM_003537.3	72	Gtg/Ttg	1/1	1	2	FACETS	0.966	0.902	1	0.966	0.902	1	CLONAL	1	TRUE	1	0.570338586915073	2		606	828	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225432	26225432	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	159	326	0	ENST00000360408.1:c.50C>T	p.Pro17Leu	p.P17L	ENST00000360408	NM_003532.2	17	cCg/cTg	1/1	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.570338586915073	2		326	537	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324210	31324211	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	126	365	0	ENST00000412585.2:c.352_353del	p.Thr118ProfsTer20	p.T118Pfs*20	ENST00000412585	NM_005514.6	118	ACc/c	3/8	1	2	FACETS	0.812	0.739	0.889	0.812	0.739	0.889	CLONAL	1	TRUE	1	0.570338586915073	2		365	544	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43746203	43746203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs114262569	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	292	764	2	ENST00000523873.1:c.322C>T	p.Arg108Trp	p.R108W	ENST00000523873		108	Cgg/Tgg	4/8	1	2	FACETS	0.952	0.896	1	0.952	0.896	1	CLONAL	1	TRUE	1	0.570338586915073	2		766	1076	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120866	94120866	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	206	670	0	ENST00000369303.4:c.185A>G	p.Asp62Gly	p.D62G	ENST00000369303	NM_004440.3	62	gAt/gGt	3/17	1	2	FACETS	0.895	0.832	0.96	0.895	0.832	0.96	CLONAL	1	TRUE	1	0.570338586915073	2		670	807	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129130	152129130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	343	865	6	ENST00000206249.3:c.83G>A	p.Arg28His	p.R28H	ENST00000206249	NM_000125.3	28	cGt/cAt	1/8	1	2	FACETS	0.995	0.941	1	0.995	0.941	1	CLONAL	1	TRUE	1	0.570338586915073	2		871	1209	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521872	157521872	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	247	536	0	ENST00000346085.5:c.4148del	p.Pro1383GlnfsTer65	p.P1383Qfs*65	ENST00000346085	NM_020732.3	1382	Ccc/cc	18/20	1	2	FACETS	0.97	0.908	1	0.97	0.908	1	CLONAL	1	TRUE	1	0.570338586915073	2		536	893	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434413	140434413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775889922	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	233	575	1	ENST00000288602.6:c.2285C>T	p.Ala762Val	p.A762V	ENST00000288602	NM_004333.4	762	gCg/gTg	18/18	1	2	FACETS	0.924	0.863	0.987	0.924	0.863	0.987	CLONAL	1	TRUE	1	0.570338586915073	2		576	884	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974775	21974775	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs758455611	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	78	291	0	ENST00000304494.5:c.52A>G	p.Thr18Ala	p.T18A	ENST00000304494	NM_000077.4	18	Acg/Gcg	1/3	1	2	FACETS	0.784	0.694	0.879	0.784	0.694	0.879	SUBCLONAL	1	TRUE	1	0.570338586915073	2		291	349	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209424	98209424	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	276	662	1	ENST00000331920.6:c.4114A>G	p.Thr1372Ala	p.T1372A	ENST00000331920	NM_000264.3	1372	Acg/Gcg	23/24	1	2	FACETS	0.972	0.913	1	0.972	0.913	1	CLONAL	1	TRUE	1	0.570338586915073	2		663	996	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209648	98209648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs386833412	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	264	631	0	ENST00000331920.6:c.3890G>A	p.Arg1297Gln	p.R1297Q	ENST00000331920	NM_000264.3	1297	cGg/cAg	23/24	1	2	FACETS	0.992	0.932	1	0.992	0.932	1	CLONAL	1	TRUE	1	0.570338586915073	2		631	933	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412243	139412243	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	430	875	1	ENST00000277541.6:c.1402C>A	p.Leu468Met	p.L468M	ENST00000277541	NM_017617.3	468	Ctg/Atg	8/34	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.570338586915073	2		876	1386	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044904	47044904	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	40	502	2	ENST00000377604.3:c.2230C>A	p.Arg744Ser	p.R744S	ENST00000377604	NM_001204468.1	744	Cgt/Agt	20/24	1	1	FACETS	0.133	0.11	0.159	0.133	0.11	0.159	SUBCLONAL	1	TRUE	0	0.570338586915073	1		504	754	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650362	48650362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	411	365	0	ENST00000376670.3:c.332C>T	p.Pro111Leu	p.P111L	ENST00000376670	NM_002049.3	111	cCc/cTc	3/6	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.570338586915073	1		365	700	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222725	53222725	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1179389525	NA	P-0020221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	433	480	0	ENST00000375401.3:c.4211T>C	p.Met1404Thr	p.M1404T	ENST00000375401	NM_004187.3	1404	aTg/aCg	25/26	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.570338586915073	1		480	749	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0020224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	819	823	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.696623466787804	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.696623466787804	2		823	1117	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163820	72163820	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	127	454	0	ENST00000357731.5:c.538A>C	p.Lys180Gln	p.K180Q	ENST00000357731	NM_173808.2	180	Aaa/Caa	4/7	0.696623466787804	6	FACETS	0.732	0.661	0.807	0.183	0.165	0.202	SUBCLONAL	1	TRUE	2	0.696623466787804	6		454	1192	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342971	118342971	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	137	306	0	ENST00000534358.1:c.1097G>C	p.Arg366Thr	p.R366T	ENST00000534358	NM_005933.3	366	aGg/aCg	3/36	0.696623466787804	3	FACETS	0.885	0.808	0.966	0.443	0.404	0.483	CLONAL	1	TRUE	1	0.696623466787804	3		306	599	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628754	21628754	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	349	596	1	ENST00000421138.2:c.954C>G	p.Ile318Met	p.I318M	ENST00000421138		318	atC/atG	10/16	0.416832139616729	3	FACETS	0.913	0.871	0.955			1	INDETERMINATE	2	TRUE	NA	0.696623466787804	3		597	740	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647140	2647140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	168	582	0	ENST00000342085.4:c.1418G>A	p.Arg473Gln	p.R473Q	ENST00000342085	NM_002613.4	473	cGa/cAa	13/14	0.421300219822794	3	FACETS	0.702	0.645	0.762	0.351	0.322	0.381	SUBCLONAL	1	TRUE	1	0.696623466787804	3		582	926	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857159	9857159	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	152	510	1	ENST00000330684.3:c.4242G>T	p.Arg1414Ser	p.R1414S	ENST00000330684	NM_001134407.1	1414	agG/agT	13/13	0.421300219822794	3	FACETS	0.813	0.745	0.884	0.406	0.372	0.442	CLONAL	1	TRUE	1	0.696623466787804	3		511	724	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217877	2217877	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	337	931	2	ENST00000398665.3:c.2651C>T	p.Pro884Leu	p.P884L	ENST00000398665	NM_032482.2	884	cCc/cTc	22/28	0.696623466787804	3	FACETS	0.963	0.909	1	0.481	0.454	0.509	CLONAL	1	TRUE	1	0.696623466787804	3		933	1355	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141517	11141517	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	327	792	0	ENST00000358026.2:c.3494T>A	p.Leu1165His	p.L1165H	ENST00000358026	NM_001128849.1	1165	cTc/cAc	25/36	0.696623466787804	3	FACETS	1	0.959	1	0.509	0.481	0.538	CLONAL	1	TRUE	1	0.696623466787804	3		792	1243	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170797	11170801	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGA	GCCGA	-	novel	NA	P-0020224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	239	738	0	ENST00000358026.2:c.4947_4951del	p.Ser1649ArgfsTer10	p.S1649Rfs*10	ENST00000358026	NM_001128849.1	1647	cgGCCGAgc/cggc	35/36	0.696623466787804	3	FACETS	0.843	0.786	0.901	0.421	0.393	0.451	CLONAL	1	TRUE	1	0.696623466787804	3		738	1098	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561561	9561561	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	403	550	0	ENST00000353224.5:c.221A>G	p.Asn74Ser	p.N74S	ENST00000353224	NM_177990.2	74	aAc/aGc	4/10	0.422020701384427	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.696623466787804	4		550	962	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944533	40944533	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	305	668	0	ENST00000373198.4:c.1969A>T	p.Ser657Cys	p.S657C	ENST00000373198	NM_133170.3	657	Agc/Tgc	12/32	0.421300219822794	3	FACETS	1	0.986	1	0.57	0.538	0.604	CLONAL	1	TRUE	1	0.696623466787804	3		668	1035	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390917	89390917	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1273217724	NA	P-0020224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	106	581	0	ENST00000336596.2:c.983C>T	p.Ser328Leu	p.S328L	ENST00000336596	NM_005233.5	328	tCa/tTa	5/17	0.388005128406455	2	FACETS	0.494	0.444	0.547	0.247	0.222	0.274	INDETERMINATE	1	TRUE	0	0.696623466787804	2		581	616	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539771	187539771	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs745468634	NA	P-0020224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	232	492	0	ENST00000441802.2:c.7969A>G	p.Thr2657Ala	p.T2657A	ENST00000441802	NM_005245.3	2657	Aca/Gca	10/27	0.696623466787804	3	FACETS	0.975	0.91	1	0.488	0.455	0.521	CLONAL	1	TRUE	1	0.696623466787804	3		492	921	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629919	187629919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	308	665	1	ENST00000441802.2:c.1063G>A	p.Val355Met	p.V355M	ENST00000441802	NM_005245.3	355	Gtg/Atg	2/27	0.696623466787804	3	FACETS	0.892	0.839	0.945	0.446	0.419	0.473	CLONAL	1	TRUE	1	0.696623466787804	3		666	1337	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505014	149505014	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	193	436	0	ENST00000261799.4:c.1801G>T	p.Val601Leu	p.V601L	ENST00000261799	NM_002609.3	601	Gtg/Ttg	12/23	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.696623466787804	2		436	522	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637556	176637557	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	320	700	0	ENST00000439151.2:c.2157dup	p.Glu720ArgfsTer10	p.E720Rfs*10	ENST00000439151	NM_022455.4	719	gca/gcAa	5/23	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.696623466787804	2		700	918	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680441	30680441	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	610	658	2	ENST00000376406.3:c.1278A>G	p.Ile426Met	p.I426M	ENST00000376406	NM_014641.2	426	atA/atG	5/15	0.696623466787804	3	FACETS	0.984	0.95	1	0.984	0.95	1	CLONAL	2	TRUE	1	0.696623466787804	3		660	1200	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800169	32800169	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	222	505	0	ENST00000374899.4:c.1213A>T	p.Thr405Ser	p.T405S	ENST00000374899	NM_018833.2	405	Acc/Tcc	7/12	0.696623466787804	3	FACETS	0.962	0.897	1	0.481	0.448	0.515	CLONAL	1	TRUE	1	0.696623466787804	3		505	893	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271246	38271246	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1154	332	895	1	ENST00000425967.3:c.2462C>A	p.Ser821Ter	p.S821*	ENST00000425967	NM_001174067.1	821	tCa/tAa	19/19	0.696623466787804	3	FACETS	0.865	0.816	0.915			1	CLONAL	1	TRUE	NA	0.696623466787804	3		896	1486	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863308	56863308	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	871	680	0	ENST00000519728.1:c.452G>T	p.Gly151Val	p.G151V	ENST00000519728	NM_002350.3	151	gGa/gTa	6/13	0.677369989212226	5	FACETS	0.924	0.901	0.947	0.924	0.901	0.947	CLONAL	4	TRUE	1	0.696623466787804	5		680	1384	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061223	38061228	+	inframe_deletion	In_Frame_Del	DEL	TCTCGA	TCTCGA	-	novel	NA	P-0020379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	79	1050	3	ENST00000250448.2:c.761_766del	p.Phe254_Asn256delinsTyr	p.F254_N256delinsY	ENST00000250448	NM_004496.3	254	tTCGAGAac/tac	2/2	0.296207833811483	5	FACETS	1	0.944	1	1	0.98	1	CLONAL	4	TRUE	2	0.33	5		1053	168	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871889	12871889	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0020379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	46	251	0	ENST00000228872.4:c.*8+1G>T			ENST00000228872	NM_004064.3	-/198			0.250208836166995	4	FACETS	0.997	0.874	1	1	0.977	1	CLONAL	4	TRUE	2	0.33	4		251	93	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220473	123220473	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	18	435	1	ENST00000218089.9:c.3130T>C	p.Tyr1044His	p.Y1044H	ENST00000218089	NM_001042749.1	1044	Tac/Cac	30/35	0.193471059776264	2	FACETS	0.826	0.641	1			1	INDETERMINATE	2	TRUE	NA	0.33	2		436	66	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578204	7578204	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520001	NA	P-0020405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	297	983	4	ENST00000269305.4:c.645T>G	p.Ser215Arg	p.S215R	ENST00000269305	NM_001126112.2	215	agT/agG	6/11	0.633454325415391	1	FACETS	0.937	0.888	0.986	0.937	0.888	0.986	CLONAL	1	TRUE	0	0.633454325415391	1		987	684	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112029147	112029147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	180	528	0	ENST00000368678.4:c.421G>A	p.Val141Ile	p.V141I	ENST00000368678		141	Gtt/Att	5/13	0.633454325415391	1	FACETS	0.897	0.837	0.958	0.897	0.837	0.958	CLONAL	1	TRUE	0	0.633454325415391	1		528	433	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240039	41240039	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs963605898	NA	P-0020405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	19	13	1	ENST00000379561.5:c.311G>C	p.Gly104Ala	p.G104A	ENST00000379561	NM_002015.3	104	gGg/gCg	1/3	1	2	FACETS	1	0.86	1	1	0.953	1	CLONAL	2	TRUE	1	0.633454325415391	2		14	29	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100133	30100133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370296777	NA	P-0020405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	321	911	1	ENST00000331968.5:c.1487C>T	p.Thr496Met	p.T496M	ENST00000331968	NM_002742.2	496	aCg/aTg	10/18	0.633454325415391	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.633454325415391	1		912	680	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445662	49445777	+	frameshift_variant	Frame_Shift_Del	DEL	GTGGGAACAGACGAGATGCCTCCGGTGGTGGAGACATGGGTGACTCTTCAGGTGGAGGGGACATGGGTGACTCCTCAGGTGGTGGAGACAGGCGAGATGCTTCAGGTGGCGGGGAA	GTGGGAACAGACGAGATGCCTCCGGTGGTGGAGACATGGGTGACTCTTCAGGTGGAGGGGACATGGGTGACTCCTCAGGTGGTGGAGACAGGCGAGATGCTTCAGGTGGCGGGGAA	-	novel	NA	P-0020405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	416	1367	4	ENST00000301067.7:c.1689_1804del	p.Ser564IlefsTer2	p.S564Ifs*2	ENST00000301067	NM_003482.3	563	acTTCCCCGCCACCTGAAGCATCTCGCCTGTCTCCACCACCTGAGGAGTCACCCATGTCCCCTCCACCTGAAGAGTCACCCATGTCTCCACCACCGGAGGCATCTCGTCTGTTCCCACca/acca	10/54	0.633454325415391	1	FACETS	0.932	0.891	0.973	0.932	0.891	0.973	CLONAL	1	TRUE	0	0.633454325415391	1		1371	963	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257911	198257911	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	136	451	1	ENST00000335508.6:c.3541G>C	p.Asp1181His	p.D1181H	ENST00000335508	NM_012433.2	1181	Gac/Cac	24/25	1	2	FACETS	0.906	0.83	0.985	0.906	0.83	0.985	CLONAL	1	TRUE	1	0.633454325415391	2		452	474	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410511	139410511	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs937879671	NA	P-0020405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	352	1109	1	ENST00000277541.6:c.1591G>A	p.Glu531Lys	p.E531K	ENST00000277541	NM_017617.3	531	Gag/Aag	10/34	1	2	FACETS	0.996	0.944	1	0.996	0.944	1	CLONAL	1	TRUE	1	0.633454325415391	2		1110	1116	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0020411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	235	573	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.31199382748366	3	FACETS	1	0.99	1	0.831	0.781	0.88	CLONAL	2	TRUE	0	0.394911265776857	3		573	572	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755666	39755666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	128	876	0	ENST00000288319.7:c.1099C>T	p.Arg367Cys	p.R367C	ENST00000288319	NM_182918.3	367	Cgc/Tgc	10/10	1	2	FACETS	0.852	0.773	0.935	0.852	0.773	0.935	CLONAL	1	TRUE	1	0.394911265776857	2		876	761	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264329	16264354	+	frameshift_variant	Frame_Shift_Del	DEL	GCCTGCTGGCCCTCAAGAATGACACA	GCCTGCTGGCCCTCAAGAATGACACA	-	novel	NA	P-0020411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	36	773	0	ENST00000375759.3:c.10534_10559del	p.Leu3512CysfsTer22	p.L3512Cfs*22	ENST00000375759	NM_015001.2	3511	gGCCTGCTGGCCCTCAAGAATGACACA/g	13/15	0.375756138430427	1	FACETS	0.309	0.253	0.371	0.309	0.253	0.371	SUBCLONAL	1	TRUE	0	0.394911265776857	1		773	474	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845642	68845642	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	156	958	0	ENST00000261769.5:c.888C>A	p.Tyr296Ter	p.Y296*	ENST00000261769	NM_004360.3	296	taC/taA	7/16	0.394911265776857	1	FACETS	0.916	0.841	0.994	0.916	0.841	0.994	CLONAL	1	TRUE	0	0.394911265776857	1		958	692	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793273	242793292	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTGAGCCCCTGCGGGCGG	AGCTGAGCCCCTGCGGGCGG	-	novel	NA	P-0020411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	167	1091	0	ENST00000334409.5:c.785_804del	p.Pro262ArgfsTer12	p.P262Rfs*12	ENST00000334409	NM_005018.2	262	cCCGCCCGCAGGGGCTCAGCT/c	5/5	0.353769472097718	1	FACETS	0.909	0.837	0.983	0.909	0.837	0.983	CLONAL	1	TRUE	0	0.394911265776857	1		1091	747	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630593	187630593	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	111	821	0	ENST00000441802.2:c.389A>G	p.Glu130Gly	p.E130G	ENST00000441802	NM_005245.3	130	gAg/gGg	2/27	1	2	FACETS	0.746	0.67	0.825	0.746	0.67	0.825	SUBCLONAL	1	TRUE	1	0.394911265776857	2		821	754	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925399	131925399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	56	325	0	ENST00000265335.6:c.1322G>A	p.Arg441Lys	p.R441K	ENST00000265335		441	aGa/aAa	9/25	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.394911265776857	2		325	250	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730259	133730259	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	73	716	0	ENST00000318560.5:c.325G>C	p.Gly109Arg	p.G109R	ENST00000318560	NM_005157.4	109	Ggc/Cgc	3/11	0.356061120986168	4	FACETS	0.62	0.541	0.705	0.207	0.18	0.235	SUBCLONAL	1	TRUE	1	0.394911265776857	4		716	832	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922181	39922181	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	163	865	1	ENST00000378444.4:c.3991G>A	p.Asp1331Asn	p.D1331N	ENST00000378444	NM_001123385.1	1331	Gat/Aat	9/15	0.24279058694758	3	FACETS	1	0.922	1			1	CLONAL	1	TRUE	NA	0.394911265776857	3		866	983	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663934	29663934	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0020415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	70	335	0	ENST00000356175.3:c.6364+2T>C		p.X2122_splice	ENST00000356175	NM_000267.3	2122			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		335	109	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663934	29663934	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0020415-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	183	335	0	ENST00000356175.3:c.6364+2T>C		p.X2122_splice	ENST00000356175	NM_000267.3	2122			0.768349302433551	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.768349302433551	1		335	292	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781374	135781374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377279170	NA	P-0020415-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	148	640	1	ENST00000298552.3:c.1591G>A	p.Val531Met	p.V531M	ENST00000298552	NM_001162426.1	531	Gtg/Atg	15/23	1	2	FACETS	0.412	0.376	0.45	0.412	0.376	0.45	SUBCLONAL	1	TRUE	1	0.768349302433551	2		641	935	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0020433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	8	524	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	0.827	0.534	1	0.827	0.534	1	CLONAL	1	TRUE	1	0.15	2		524	129	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0020433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	32	641	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	0.124427176714407	3	FACETS	0.854	0.701	1	1	0.927	1	CLONAL	3	TRUE	1	0.15	3		641	179	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0020453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	217	680	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.302028763202211	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.309465937307119	2		680	609	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862076	68862076	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0020453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	141	440	0	ENST00000261769.5:c.2165-1G>A		p.X722_splice	ENST00000261769	NM_004360.3	722			0.302028763202211	2	FACETS	0.951	0.873	1	0.951	0.873	1	CLONAL	2	TRUE	0	0.309465937307119	2		440	479	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41560079	41560079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373249130	NA	P-0020453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	106	564	0	ENST00000263253.7:c.3751G>A	p.Gly1251Arg	p.G1251R	ENST00000263253	NM_001429.3	1251	Gga/Aga	22/31	0.309465937307119	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.309465937307119	1		564	468	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061007	38061022	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCGGGGGCCGGCGC	GCCCGGGGGCCGGCGC	-	novel	NA	P-0020454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	19	460	0	ENST00000250448.2:c.967_982del	p.Ala323ProfsTer22	p.A323Pfs*22	ENST00000250448	NM_004496.3	323	GCGCCGGCCCCCGGGCcc/cc	2/2	0.349941233998591	5	FACETS	0.459	0.348	0.589	0.153	0.116	0.197	SUBCLONAL	1	FALSE	2	0.476011122716557	5		460	298	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201089	108201089	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	41	595	0	ENST00000278616.4:c.7456C>G	p.Arg2486Gly	p.R2486G	ENST00000278616	NM_000051.3	2486	Cga/Gga	50/63	0.476011122716557	3	FACETS	0.793	0.664	0.934	0.396	0.332	0.467	CLONAL	1	FALSE	1	0.476011122716557	3		595	269	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061121	38061192	+	inframe_deletion	In_Frame_Del	DEL	CGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGA	CGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGA	-	novel	NA	P-0020454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	147	345	0	ENST00000250448.2:c.797_868del	p.Phe266_Gly290delinsCys	p.F266_G290delinsC	ENST00000250448	NM_004496.3	266	tTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGCGGCGCCAAGGGCGgc/tgc	2/2	0.349941233998591	5	FACETS	0.888	0.826	0.95	1	0.983	1	CLONAL	4	FALSE	2	0.476011122716557	5		345	298	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193733	106193733	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	19	281	0	ENST00000380013.4:c.4195A>G	p.Thr1399Ala	p.T1399A	ENST00000380013	NM_001127208.2	1399	Act/Gct	10/11	0.476011122716557	4	FACETS	0.623	0.475	0.796	0.312	0.237	0.398	SUBCLONAL	1	FALSE	2	0.476011122716557	4		281	189	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696169	52696169	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	138	1423	1	ENST00000394830.3:c.508C>T	p.Gln170Ter	p.Q170*	ENST00000394830	NM_018313.4	170	Cag/Tag	5/30	0.539775055492695	1	FACETS	0.889	0.816	0.963	0.889	0.816	0.963	CLONAL	1	TRUE	0	0.539775055492695	1		1424	420	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330531	65330531	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	99	866	1	ENST00000342505.4:c.1115T>A	p.Ile372Asn	p.I372N	ENST00000342505	NM_002227.2	372	aTc/aAc	8/25	0.539775055492695	1	FACETS	0.842	0.761	0.927	0.842	0.761	0.927	CLONAL	1	TRUE	0	0.539775055492695	1		867	318	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106537	108106537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	56	626	0	ENST00000278616.4:c.472G>A	p.Glu158Lys	p.E158K	ENST00000278616	NM_000051.3	158	Gaa/Aaa	5/63	1	2	FACETS	0.665	0.573	0.764	0.665	0.573	0.764	SUBCLONAL	1	TRUE	1	0.539775055492695	2		626	312	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437500	110437500	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	115	1258	1	ENST00000375856.3:c.901del	p.Arg301GlyfsTer90	p.R301Gfs*90	ENST00000375856	NM_003749.2	301	Cgg/gg	1/2	0.248102687974044	3	FACETS	1	0.982	1	0.683	0.621	0.748	INDETERMINATE	1	TRUE	1	0.539775055492695	3		1259	396	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982492	10982773	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CACCATCGGCGACGCGAACGGCGAGATCCAGCGGCACGCGGAGCAGCAGGCGCTGCGCCTCGAGGTGCGCGCCGGCCCGGACTCGGCGGGCATCGCCCTCTACAGCCGTGAGTACGGGGCCCCGGGGCAGGCGCAGGGCCGGGGCTGCTCACGAGGCCGGCCCGGGGCGGGGGCCGGCGGGGAGGGGCCCTGAGCGCGGGGGCCTGGCGTGGGGTCCCCGGGACTGAGCCGGTGGCCTGCAGGGAGCGACCGTGGAGGGCCGGTGCCAGGGGACAGACAGAG	CACCATCGGCGACGCGAACGGCGAGATCCAGCGGCACGCGGAGCAGCAGGCGCTGCGCCTCGAGGTGCGCGCCGGCCCGGACTCGGCGGGCATCGCCCTCTACAGCCGTGAGTACGGGGCCCCGGGGCAGGCGCAGGGCCGGGGCTGCTCACGAGGCCGGCCCGGGGCGGGGGCCGGCGGGGAGGGGCCCTGAGCGCGGGGGCCTGGCGTGGGGTCCCCGGGACTGAGCCGGTGGCCTGCAGGGAGCGACCGTGGAGGGCCGGTGCCAGGGGACAGACAGAG	-	novel	NA	P-0020459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	17	384	0	ENST00000327064.4:c.114_220+175del		p.X38_splice	ENST00000327064	NM_199141.1	38		1/16	0.359867722299845	1	FACETS	0.222	0.166	0.288	0.222	0.166	0.288	SUBCLONAL	1	TRUE	0	0.539775055492695	1		384	207	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169993073	169993073	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	75	857	0	ENST00000295797.4:c.703G>A	p.Glu235Lys	p.E235K	ENST00000295797	NM_002740.5	235	Gag/Aag	8/18	1	2	FACETS	0.803	0.709	0.903	0.803	0.709	0.903	CLONAL	1	TRUE	1	0.539775055492695	2		857	346	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949143	44949143	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	10	423	0	ENST00000377967.4:c.3704A>G	p.Asn1235Ser	p.N1235S	ENST00000377967	NM_021140.2	1235	aAc/aGc	25/29	1	1	FACETS	0.153	0.103	0.215	0.153	0.103	0.215	SUBCLONAL	1	TRUE	0	0.539775055492695	1		423	177	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039310	47039310	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	23	705	0	ENST00000377604.3:c.933C>G	p.Ser311Arg	p.S311R	ENST00000377604	NM_001204468.1	311	agC/agG	10/24	1	1	FACETS	0.254	0.198	0.318	0.254	0.198	0.318	SUBCLONAL	1	TRUE	0	0.539775055492695	1		705	245	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185002	123185002	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	11	288	0	ENST00000218089.9:c.1049C>G	p.Ala350Gly	p.A350G	ENST00000218089	NM_001042749.1	350	gCt/gGt	12/35	1	1	FACETS	0.224	0.155	0.308	0.224	0.155	0.308	SUBCLONAL	1	TRUE	0	0.539775055492695	1		288	133	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215276	123215276	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0020459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	73	486	0	ENST00000218089.9:c.2822C>G	p.Ser941Ter	p.S941*	ENST00000218089	NM_001042749.1	941	tCa/tGa	28/35	1	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.539775055492695	1		486	162	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206665052	206665052	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs12059562	NA	P-0020479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	99	555	0	ENST00000367120.3:c.1805C>T	p.Ala602Val	p.A602V	ENST00000367120	NM_014002.3	602	gCg/gTg	18/22	0.600081893888066	5	FACETS	0.57	0.507	0.637			1	SUBCLONAL	1	TRUE	NA	0.612811959899435	5		555	1088	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89837864	89838100	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCCAAAATTAAATAAATAAATAAAATGTAAAAGGAGCTCTTCATACACAAACAGACTGTGGCAGCTGACCCTGGTACACCGCTGCCTGGCCCTGGAACATCTGATACGACACTAACTGAGCAAGTCAAACAGAAATTGAGAGAAGGCTCCATGCGTCTAATGCCTCTGCCTAATGGAAAATGGTGAAGACCCCCTGCTTTGTTCTGAGCCCCTACACCTACCATGTGTTCCCGTGG	CTCCAAAATTAAATAAATAAATAAAATGTAAAAGGAGCTCTTCATACACAAACAGACTGTGGCAGCTGACCCTGGTACACCGCTGCCTGGCCCTGGAACATCTGATACGACACTAACTGAGCAAGTCAAACAGAAATTGAGAGAAGGCTCCATGCGTCTAATGCCTCTGCCTAATGGAAAATGGTGAAGACCCCCTGCTTTGTTCTGAGCCCCTACACCTACCATGTGTTCCCGTGG	-	novel	NA	P-0020479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	68	16	0	ENST00000389301.3:c.2137_2151+222del		p.X713_splice	ENST00000389301	NM_000135.2	713		23/43	0.466078066765079	2	FACETS	1	0.966	1	1	0.988	1	CLONAL	3	TRUE	0	0.612811959899435	2		16	73	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879881	37879881	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	196	824	0	ENST00000269571.5:c.2176C>G	p.Leu726Val	p.L726V	ENST00000269571		726	Ctt/Gtt	18/27	0.463268676841533	4	FACETS	0.915	0.846	0.987	0.458	0.423	0.494	CLONAL	1	TRUE	2	0.612811959899435	4		824	1127	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510560	38510560	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	144	454	0	ENST00000254066.5:c.814C>G	p.Arg272Gly	p.R272G	ENST00000254066	NM_000964.3	272	Cgg/Ggg	7/9	0.463268676841533	4	FACETS	1	0.954	1	0.533	0.487	0.581	CLONAL	1	TRUE	2	0.612811959899435	4		454	711	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737675	145737685	+	frameshift_variant	Frame_Shift_Del	DEL	ACTCCACAAGC	ACTCCACAAGC	-	novel	NA	P-0020479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1224	129	729	0	ENST00000428558.2:c.3078_3088del	p.Leu1027GlnfsTer2	p.L1027Qfs*2	ENST00000428558	NM_004260.3	1026	gtGCTTGTGGAGTtc/gttc	19/22	0.600081893888066	5	FACETS	0.597	0.54	0.658			1	SUBCLONAL	1	TRUE	NA	0.612811959899435	5		729	1353	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737845	145737845	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1451	203	907	0	ENST00000428558.2:c.2985del	p.Met996TrpfsTer48	p.M996Wfs*48	ENST00000428558	NM_004260.3	995	tcC/tc	18/22	0.600081893888066	5	FACETS	0.769	0.71	0.83			1	SUBCLONAL	1	TRUE	NA	0.612811959899435	5		907	1654	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971101	21971101	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	130	556	2	ENST00000304494.5:c.257C>T	p.Ala86Val	p.A86V	ENST00000304494	NM_000077.4	86	gCc/gTc	2/3	0.477917815028244	2	FACETS	0.905	0.826	0.986	0.452	0.413	0.493	CLONAL	1	TRUE	0	0.612811959899435	2		558	469	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956238	175956255	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCTGAAAACAAATAATA	TCCTGAAAACAAATAATA	-	novel	NA	P-0020479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	35	353	0	ENST00000367669.3:c.1973-16_1974del		p.X658_splice	ENST00000367669	NM_022457.5	658		18/20	0.612811959899435	6	FACETS	0.431	0.352	0.52			1	SUBCLONAL	1	TRUE	NA	0.612811959899435	6		353	590	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	105	503	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.613922423093036	4	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	2	0.61789246067406	4		503	265	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292481	15292481	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	177	1259	0	ENST00000263388.2:c.2698A>G	p.Thr900Ala	p.T900A	ENST00000263388	NM_000435.2	900	Acc/Gcc	17/33	0.191440859615371	1	FACETS	0.797	0.74	0.854	0.797	0.74	0.854	INDETERMINATE	1	TRUE	0	0.61789246067406	1		1259	497	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0020574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	22	315	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.577975908485386	1	FACETS	0.342	0.268	0.427	0.342	0.268	0.427	SUBCLONAL	1	TRUE	0	0.626045457602802	1		315	141	SUCCESS
APC	324	MSKCC	GRCh37	5	112176020	112176020	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	53	404	3	ENST00000257430.4:c.4729G>T	p.Glu1577Ter	p.E1577*	ENST00000257430	NM_000038.5	1577	Gaa/Taa	16/16	0.577975908485386	1	FACETS	0.692	0.602	0.788	0.692	0.602	0.788	SUBCLONAL	1	TRUE	0	0.626045457602802	1		407	168	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030460	49030463	+	frameshift_variant	Frame_Shift_Del	DEL	CTCT	CTCT	-	novel	NA	P-0020574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	131	666	0	ENST00000267163.4:c.1937_1940del	p.Ser646PhefsTer11	p.S646Ffs*11	ENST00000267163	NM_000321.2	645	acCTCT/ac	19/27	0.626045457602802	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.626045457602802	1		666	267	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061243	38061243	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	148	952	0	ENST00000250448.2:c.746A>T	p.Asp249Val	p.D249V	ENST00000250448	NM_004496.3	249	gAc/gTc	2/2	0.626045457602802	3	FACETS	1	0.97	1	0.56	0.514	0.608	CLONAL	1	TRUE	1	0.626045457602802	3		952	554	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627445	14627445	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	104	785	0	ENST00000254322.2:c.625A>G	p.Lys209Glu	p.K209E	ENST00000254322	NM_006145.1	209	Aag/Gag	2/3	0.332201968875141	1	FACETS	0.692	0.626	0.759	0.692	0.626	0.759	INDETERMINATE	1	TRUE	0	0.626045457602802	1		785	330	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	272	450	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	0.89	0.835	0.947	0.89	0.835	0.947	CLONAL	1	TRUE	1	0.523607431412144	2		450	1167	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057600	180057600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1267101992	NA	P-0020637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	220	1129	0	ENST00000261937.6:c.355C>T	p.Arg119Cys	p.R119C	ENST00000261937	NM_182925.4	119	Cgc/Tgc	3/30	NA	2	FACETS	0.632	0.588	0.677			1	INDETERMINATE	1	TRUE	NA	0.734973467980474	2		1129	947	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610705	52610705	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	94	427	0	ENST00000394830.3:c.3468del	p.Val1157TyrfsTer36	p.V1157Yfs*36	ENST00000394830	NM_018313.4	1156	aaA/aa	23/30	0.734973467980474	1	FACETS	0.856	0.782	0.93	0.856	0.782	0.93	CLONAL	1	TRUE	0	0.734973467980474	1		427	189	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252776	10252776	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	207	794	0	ENST00000340748.4:c.3189G>C	p.Glu1063Asp	p.E1063D	ENST00000340748		1063	gaG/gaC	29/40	1	2	FACETS	0.981	0.917	1	0.981	0.917	1	CLONAL	1	TRUE	1	0.734973467980474	2		794	574	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196958	106196958	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1368741274	NA	P-0020637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	87	268	0	ENST00000380013.4:c.5291A>G	p.His1764Arg	p.H1764R	ENST00000380013	NM_001127208.2	1764	cAt/cGt	11/11	0.734973467980474	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.734973467980474	1		268	144	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606314	93606314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs16906862	NA	P-0020637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	156	829	1	ENST00000375746.1:c.134G>A	p.Arg45His	p.R45H	ENST00000375746	NM_001174167.1	45	cGc/cAc	2/14	0.38538498277642	1	FACETS	0.516	0.476	0.558	0.516	0.476	0.558	INDETERMINATE	1	TRUE	0	0.734973467980474	1		830	520	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	48	503	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		503	608	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0020672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	18	564	3	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		567	527	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0020713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	240	834	1	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.499352854483804	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.499352854483804	1		835	664	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185050	123185050	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	146	351	0	ENST00000218089.9:c.1097T>G	p.Leu366Arg	p.L366R	ENST00000218089	NM_001042749.1	366	cTt/cGt	12/35	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.499352854483804	1		351	366	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0020770-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	296	745	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.626558073504612	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.687016520057389	1		745	524	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28897002	28897002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554058758	NA	P-0020770-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	222	469	0	ENST00000282397.4:c.2878G>A	p.Val960Ile	p.V960I	ENST00000282397	NM_002019.4	960	Gtc/Atc	21/30	1	2	FACETS	0.887	0.828	0.946	0.887	0.828	0.946	CLONAL	1	TRUE	1	0.687016520057389	2		469	729	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658535	206658535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1281179215	NA	P-0020770-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	130	324	0	ENST00000367120.3:c.1508C>T	p.Ala503Val	p.A503V	ENST00000367120	NM_014002.3	503	gCg/gTg	15/22	0.339460280894212	4	FACETS	1	0.97	1	0.288	0.262	0.315	INDETERMINATE	1	TRUE	0	0.687016520057389	4		324	555	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060568	38060571	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	AGCT	AGCT	-	novel	NA	P-0020770-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	270	622	0	ENST00000250448.2:c.1418_*2del		p.*473*	ENST00000250448	NM_004496.3	473		2/2	1	2	FACETS	0.872	0.82	0.926	0.872	0.82	0.926	CLONAL	1	TRUE	1	0.687016520057389	2		622	901	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467921	50467921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020770-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	90	374	0	ENST00000331340.3:c.1156C>T	p.Arg386Cys	p.R386C	ENST00000331340	NM_006060.4	386	Cgc/Tgc	8/8	1	2	FACETS	0.611	0.545	0.68	0.611	0.545	0.68	SUBCLONAL	1	TRUE	1	0.687016520057389	2		374	429	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56882298	56882298	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020770-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	240	544	0	ENST00000519728.1:c.996G>T	p.Lys332Asn	p.K332N	ENST00000519728	NM_002350.3	332	aaG/aaT	10/13	0.632533575689403	3	FACETS	0.86	0.802	0.919			1	CLONAL	1	TRUE	NA	0.687016520057389	3		544	1092	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936542	49936563	+	frameshift_variant	Frame_Shift_Del	DEL	GCCACTGTGACGTTGTCAAGGC	GCCACTGTGACGTTGTCAAGGC	-	novel	NA	P-0020770-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	126	663	0	ENST00000296474.3:c.1364_1385del	p.Arg455HisfsTer19	p.R455Hfs*19	ENST00000296474	NM_002447.2	455	cGCCTTGACAACGTCACAGTGGCa/ca	2/20	0.368183926376159	1	FACETS	0.372	0.337	0.408	0.372	0.337	0.408	INDETERMINATE	1	TRUE	0	0.687016520057389	1		663	648	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38954964	38954964	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0020770-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	49	165	0	ENST00000357387.3:c.2610-1G>C		p.X870_splice	ENST00000357387	NM_152756.3	870			0.687016520057389	4	FACETS	0.402	0.34	0.47	0.134	0.113	0.157	SUBCLONAL	1	TRUE	1	0.687016520057389	4		165	599	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0020804-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	333	294	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.892158201302604	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.892158201302604	2		294	358	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225674	26225674	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020804-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	199	687	0	ENST00000360408.1:c.292G>C	p.Glu98Gln	p.E98Q	ENST00000360408	NM_003532.2	98	Gag/Cag	1/1	0.830921751511013	3	FACETS	0.935	0.87	1	0.467	0.435	0.501	CLONAL	1	TRUE	1	0.892158201302604	3		687	690	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250440	26250440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020804-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	182	596	1	ENST00000446824.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000446824	NM_021018.2	132	Cgc/Tgc	1/1	0.830921751511013	3	FACETS	1	0.952	1	0.517	0.479	0.555	CLONAL	1	TRUE	1	0.892158201302604	3		597	571	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885344	111885344	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1474199230	NA	P-0020804-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	87	303	0	ENST00000341259.2:c.1232C>G	p.Ala411Gly	p.A411G	ENST00000341259	NM_005475.2	411	gCc/gGc	6/8	0.892158201302604	5	FACETS	0.825	0.732	0.924			1	CLONAL	1	TRUE	NA	0.892158201302604	5		303	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577157	7577157	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0020804-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	441	541	0	ENST00000269305.4:c.783-2A>C		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.892158201302604	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.892158201302604	2		541	462	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684314	29684314	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020804-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	399	618	3	ENST00000356175.3:c.7834G>T	p.Glu2612Ter	p.E2612*	ENST00000356175	NM_000267.3	2612	Gag/Tag	53/57	0.892158201302604	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.892158201302604	2		621	427	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27220086	27220086	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020804-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	299	830	1	ENST00000380036.4:c.3143A>T	p.Tyr1048Phe	p.Y1048F	ENST00000380036	NM_000459.3	1048	tAc/tTc	21/23	0.892158201302604	3	FACETS	1	0.981	1	0.361	0.34	0.381	CLONAL	1	TRUE	0	0.892158201302604	3		831	896	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	123	813	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.202072387884987	3	FACETS	0.801	0.724	0.882	0.534	0.482	0.588	CLONAL	2	TRUE	0	0.202879073285043	3		813	834	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254165	133254165	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	32	529	0	ENST00000320574.5:c.719T>C	p.Val240Ala	p.V240A	ENST00000320574	NM_006231.2	240	gTg/gCg	7/49	NA	2	FACETS	0.548	0.443	0.666			1	INDETERMINATE	1	TRUE	NA	0.202879073285043	2		529	576	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022914	27022942	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCCGCCGCCAGCAGCCTGGGCAACCCG	CCGCCGCCGCCAGCAGCCTGGGCAACCCG	-	novel	NA	P-0020814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	30	103	0	ENST00000324856.7:c.31_59del	p.Ser11AlafsTer90	p.S11Afs*90	ENST00000324856	NM_006015.4	7	cCCGCCGCCGCCAGCAGCCTGGGCAACCCG/c	1/20	NA	2	FACETS	0.98	0.816	1			1	INDETERMINATE	2	TRUE	NA	0.368660626932239	2		103	83	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578446	7578455	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCCATGGC	TGGCCATGGC	-	novel	NA	P-0020814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	457	1111	0	ENST00000269305.4:c.475_484del	p.Ala159SerfsTer8	p.A159Sfs*8	ENST00000269305	NM_001126112.2	159	GCCATGGCCAtc/tc	5/11	0.361172811729482	2	FACETS	0.979	0.936	1	0.979	0.936	1	CLONAL	2	TRUE	0	0.368660626932239	2		1111	1266	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207059	1207059	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	182	1102	1	ENST00000326873.7:c.147C>A	p.Tyr49Ter	p.Y49*	ENST00000326873	NM_000455.4	49	taC/taA	1/10	0.368660626932239	1	FACETS	0.845	0.78	0.913	0.845	0.78	0.913	CLONAL	1	TRUE	0	0.368660626932239	1		1103	953	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0020844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	238	802	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.438416166444036	1	FACETS	0.899	0.841	0.958	0.899	0.841	0.958	CLONAL	1	TRUE	0	0.482930948617037	1		802	832	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169853	32169853	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs751390609	NA	P-0020844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	219	730	0	ENST00000375023.3:c.3755C>T	p.Thr1252Ile	p.T1252I	ENST00000375023	NM_004557.3	1252	aCt/aTt	21/30	1	2	FACETS	0.985	0.917	1	0.985	0.917	1	CLONAL	1	TRUE	1	0.482930948617037	2		730	921	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258712	16258713	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0020844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	147	589	2	ENST00000375759.3:c.5977_5978delinsTT	p.Gly1993Phe	p.G1993F	ENST00000375759	NM_015001.2	1993	GGt/TTt	11/15	1	2	FACETS	0.811	0.741	0.883	0.811	0.741	0.883	CLONAL	1	TRUE	1	0.482930948617037	2		591	751	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831390	72831390	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	63	402	0	ENST00000268489.5:c.5191C>T	p.Gln1731Ter	p.Q1731*	ENST00000268489	NM_006885.3	1731	Cag/Tag	9/10	0.482930948617037	1	FACETS	0.533	0.463	0.609	0.533	0.463	0.609	SUBCLONAL	1	TRUE	0	0.482930948617037	1		402	371	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0021271-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	54	341	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	1	2	FACETS	0.816	0.699	0.943	0.816	0.699	0.943	CLONAL	1	TRUE	1	0.33350634395919	2		341	397	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249338	133249338	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021271-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	133	669	0	ENST00000320574.5:c.1561G>T	p.Glu521Ter	p.E521*	ENST00000320574	NM_006231.2	521	Gag/Tag	15/49	1	2	FACETS	0.944	0.857	1	0.944	0.857	1	CLONAL	1	TRUE	1	0.33350634395919	2		669	845	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066937	30066937	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771413120	NA	P-0021271-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	84	421	1	ENST00000331968.5:c.2194C>T	p.Arg732Trp	p.R732W	ENST00000331968	NM_002742.2	732	Cgg/Tgg	16/18	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.33350634395919	2		422	501	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133887	41133887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755827604	NA	P-0021271-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	81	349	0	ENST00000379561.5:c.1741G>A	p.Val581Met	p.V581M	ENST00000379561	NM_002015.3	581	Gtg/Atg	2/3	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.33350634395919	2		349	437	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	133	313	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.916	0.842	0.992	0.916	0.842	0.992	CLONAL	1	TRUE	1	0.8	2		315	363	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458196	120458196	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	320	610	1	ENST00000256646.2:c.7149C>A	p.Tyr2383Ter	p.Y2383*	ENST00000256646	NM_024408.3	2383	taC/taA	34/34	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.8	2		611	715	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435228	18435228	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	27	399	0	ENST00000266497.5:c.213G>T	p.Trp71Cys	p.W71C	ENST00000266497		71	tgG/tgT	1/31	1	2	FACETS	0.157	0.125	0.195	0.157	0.125	0.195	SUBCLONAL	1	TRUE	1	0.8	2		399	429	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521172	187521172	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	302	684	0	ENST00000441802.2:c.11983A>G	p.Ser3995Gly	p.S3995G	ENST00000441802	NM_005245.3	3995	Agc/Ggc	22/27	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.8	2		684	729	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591131	67591132	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0021353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	245	424	0	ENST00000274335.5:c.1725_1726del	p.Lys575AsnfsTer26	p.K575Nfs*26	ENST00000274335		575	aAG/a	12/15	1	2	FACETS	0.887	0.836	0.939	0.887	0.836	0.939	CLONAL	1	TRUE	1	0.937827884683342	2		424	589	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909587	76909587	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0021353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	390	818	1	ENST00000373344.5:c.4317+1G>A		p.X1439_splice	ENST00000373344	NM_000489.3	1439			0.227351945390395	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.937827884683342	0		819	690	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0021428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	24	830	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		830	652	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916957	178916957	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	25	508	0	ENST00000263967.3:c.344G>C	p.Arg115Pro	p.R115P	ENST00000263967	NM_006218.2	115	cGa/cCa	2/21	0.152347562231839	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		508	402	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061144	38061165	+	frameshift_variant	Frame_Shift_Del	DEL	CTTCCGCTCCCGCCCCCGCCGC	CTTCCGCTCCCGCCCCCGCCGC	-	novel	NA	P-0021673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	26	361	1	ENST00000250448.2:c.824_845del	p.Gly275AlafsTer39	p.G275Afs*39	ENST00000250448	NM_004496.3	275	gGCGGCGGGGGCGGGAGCGGAAGc/gc	2/2	1	2	FACETS	0.154	0.121	0.191	0.154	0.121	0.191	SUBCLONAL	1	TRUE	1	0.801870502075402	2		362	422	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0021739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	99	352	0	ENST00000374080.3:c.3670C>T	p.Leu1224Phe	p.L1224F	ENST00000374080		1224	Ctc/Ttc	26/45	0.167020449992995	2	FACETS	0.899	0.81	0.992			1	CLONAL	3	TRUE	NA	0.203893587292171	2		352	360	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509382	46509382	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	95	583	0	ENST00000262741.5:c.1349A>G	p.Tyr450Cys	p.Y450C	ENST00000262741	NM_003629.3	450	tAc/tGc	10/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.203893587292171	2		583	625	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231410	98231410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	214	453	0	ENST00000331920.6:c.1873G>A	p.Val625Ile	p.V625I	ENST00000331920	NM_000264.3	625	Gtt/Att	14/24	0.203893587292171	3	FACETS	1	0.947	1	1	0.992	1	CLONAL	3	TRUE	1	0.203893587292171	3		453	757	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0021741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	191	672	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	0.871	0.809	0.934	0.871	0.809	0.934	CLONAL	1	TRUE	1	0.690620129286588	2		672	635	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215201	142215201	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0021741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	50	293	0	ENST00000350721.4:c.5898+2T>C		p.X1966_splice	ENST00000350721	NM_001184.3	1966			0.508397125993716	3	FACETS	0.555	0.473	0.645	0.277	0.236	0.323	SUBCLONAL	1	TRUE	1	0.690620129286588	3		293	351	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874338	151874338	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	136	584	0	ENST00000262189.6:c.8200A>C	p.Thr2734Pro	p.T2734P	ENST00000262189	NM_170606.2	2734	Act/Cct	38/59	0.509490974528358	4	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.690620129286588	4		584	574	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0021821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	339	820	2	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	0.334976720563562	3	FACETS	0.84	0.797	0.883	0.84	0.797	0.883	CLONAL	3	TRUE	0	0.359602325849967	3		822	883	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888199	112888199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918454	NA	P-0021821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	17	721	0	ENST00000351677.2:c.215C>T	p.Ala72Val	p.A72V	ENST00000351677	NM_002834.3	72	gCc/gTc	3/16	0.324373250416205	3	FACETS	0.283	0.21	0.37	0.094	0.07	0.124	SUBCLONAL	1	TRUE	0	0.359602325849967	3		721	394	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597500	28597500	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	18	677	0	ENST00000241453.7:c.2405T>A	p.Leu802Gln	p.L802Q	ENST00000241453	NM_004119.2	802	cTg/cAg	19/24	1	2	FACETS	0.285	0.214	0.369	0.285	0.214	0.369	SUBCLONAL	1	TRUE	1	0.359602325849967	2		677	351	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623628	28623628	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	77	828	0	ENST00000241453.7:c.929T>G	p.Ile310Arg	p.I310R	ENST00000241453	NM_004119.2	310	aTa/aGa	8/24	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.359602325849967	2		828	381	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96930938	96930938	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs886056448	NA	P-0021821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	100	779	0	ENST00000258439.3:c.182G>C	p.Cys61Ser	p.C61S	ENST00000258439	NM_001193304.2	61	tGt/tCt	2/4	0.359602325849967	3	FACETS	0.767	0.685	0.856	0.384	0.342	0.428	SUBCLONAL	1	TRUE	1	0.359602325849967	3		779	855	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27228259	27228259	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	78	814	0	ENST00000380036.4:c.3256G>C	p.Ala1086Pro	p.A1086P	ENST00000380036	NM_000459.3	1086	Gcc/Ccc	22/23	0.359602325849967	2	FACETS	1	0.908	1	0.516	0.456	0.581	CLONAL	1	TRUE	0	0.359602325849967	2		814	420	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412476	63412476	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	191	906	1	ENST00000330258.3:c.691C>T	p.Pro231Ser	p.P231S	ENST00000330258	NM_152424.3	231	Ccc/Tcc	2/2	0.359602325849967	2	FACETS	0.948	0.883	1	0.948	0.883	1	CLONAL	2	TRUE	0	0.359602325849967	2		907	560	SUCCESS
AR	367	MSKCC	GRCh37	X	66942707	66942707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	112	601	0	ENST00000374690.3:c.2488G>A	p.Glu830Lys	p.E830K	ENST00000374690	NM_000044.3	830	Gaa/Aaa	7/8	0.85243121919168	4	FACETS	0.859	0.775	0.947			1	CLONAL	1	FALSE	NA	0.843776452807298	4		601	570	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484206	8484206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768568228	NA	P-0021825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	147	656	1	ENST00000356435.5:c.3326G>A	p.Arg1109His	p.R1109H	ENST00000356435		1109	cGt/cAt	19/35	NA	2	FACETS	0.924	0.854	0.995			1	INDETERMINATE	1	FALSE	NA	0.843776452807298	2		657	377	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174912	56174913	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0021825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	257	492	0	ENST00000399503.3:c.2073_2074del	p.Ala692ArgfsTer4	p.A692Rfs*4	ENST00000399503	NM_005921.1	691	TGt/t	11/20	0.843776452807298	7	FACETS	0.964	0.909	1			1	CLONAL	3	FALSE	NA	0.843776452807298	7		492	655	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189472	56189472	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	336	574	0	ENST00000399503.3:c.4504del	p.Leu1502TyrfsTer2	p.L1502Yfs*2	ENST00000399503	NM_005921.1	1502	Cta/ta	20/20	0.843776452807298	7	FACETS	0.972	0.924	1			1	CLONAL	3	FALSE	NA	0.843776452807298	7		574	849	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934574	NA	P-0021973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	129	690	0	ENST00000269305.4:c.844C>G	p.Arg282Gly	p.R282G	ENST00000269305	NM_001126112.2	282	Cgg/Ggg	8/11	0.206419782965347	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	0	0.206419782965347	1		690	841	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183748	10183748	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs869025619	NA	P-0021973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	51	685	0	ENST00000256474.2:c.217C>T	p.Gln73Ter	p.Q73*	ENST00000256474	NM_000551.3	73	Cag/Tag	1/3	0.206419782965347	1	FACETS	0.576	0.488	0.673	0.576	0.488	0.673	SUBCLONAL	1	FALSE	0	0.206419782965347	1		685	769	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692831	89692839	+	inframe_deletion	In_Frame_Del	DEL	TGAAGATCT	TGAAGATCT	-	novel	NA	P-0021973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	24	177	0	ENST00000371953.3:c.318_326del	p.Glu106_Leu108del	p.E106_L108del	ENST00000371953	NM_000314.4	105	tgTGAAGATCTt/tgt	5/9	0.206419782965347	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	FALSE	0	0.206419782965347	1		177	149	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383852	15383852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1290547844	NA	P-0021973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	255	686	1	ENST00000263377.2:c.59G>A	p.Gly20Glu	p.G20E	ENST00000263377	NM_058243.2	20	gGa/gAa	2/20	0.206419782965347	5	FACETS	0.908	0.849	0.969			1	CLONAL	3	FALSE	NA	0.206419782965347	5		687	1188	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143167	30143167	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	77	520	2	ENST00000389048.3:c.359C>A	p.Ala120Asp	p.A120D	ENST00000389048	NM_004304.4	120	gCc/gAc	1/29	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	FALSE	1	0.206419782965347	2		522	700	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183789	10183793	+	frameshift_variant	Frame_Shift_Del	DEL	CGTAT	CGTAT	-	novel	NA	P-0021973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	52	661	0	ENST00000256474.2:c.258_262del	p.Val87AlafsTer43	p.V87Afs*43	ENST00000256474	NM_000551.3	86	ccCGTATgg/ccgg	1/3	0.206419782965347	1	FACETS	0.593	0.504	0.691	0.593	0.504	0.691	SUBCLONAL	1	FALSE	0	0.206419782965347	1		661	762	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138407721	138407721	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	72	448	0	ENST00000289153.2:c.2132del	p.Lys711SerfsTer9	p.K711Sfs*9	ENST00000289153	NM_006219.2	711	aAg/ag	14/22	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.206419782965347	2		448	578	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0021986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	16	587	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.2	0.146	0.264	0.2	0.146	0.264	SUBCLONAL	1	TRUE	1	0.254009672606401	2		587	631	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023702	31023702	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1311033207	NA	P-0021986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	141	641	1	ENST00000375687.4:c.3187C>T	p.Gln1063Ter	p.Q1063*	ENST00000375687	NM_015338.5	1063	Cag/Tag	13/13	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.254009672606401	2		642	995	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190666	11190666	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762176419	NA	P-0021986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	137	611	0	ENST00000361445.4:c.5533G>A	p.Glu1845Lys	p.E1845K	ENST00000361445	NM_004958.3	1845	Gag/Aag	39/58	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.254009672606401	2		611	899	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670417	246670417	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	97	546	0	ENST00000388985.4:c.103C>T	p.Pro35Ser	p.P35S	ENST00000388985		35	Ccc/Tcc	1/12	0.243067805687601	3	FACETS	0.909	0.809	1	0.454	0.404	0.508	CLONAL	1	TRUE	1	0.254009672606401	3		546	947	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115442	115115444	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0021986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	120	646	0	ENST00000257566.3:c.882_884del	p.Asp295del	p.D295del	ENST00000257566	NM_016569.3	294	atAGAc/atc	5/8	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.254009672606401	2		646	925	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061244	38061244	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	118	576	0	ENST00000250448.2:c.745G>T	p.Asp249Tyr	p.D249Y	ENST00000250448	NM_004496.3	249	Gac/Tac	2/2	1	2	FACETS	0.989	0.892	1	0.989	0.892	1	CLONAL	1	TRUE	1	0.254009672606401	2		576	939	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856032	68856048	+	frameshift_variant	Frame_Shift_Del	DEL	ATCATTGATGCAGACCT	ATCATTGATGCAGACCT	-	novel	NA	P-0021986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	129	681	0	ENST00000261769.5:c.1840_1856del	p.Ile614SerfsTer43	p.I614Sfs*43	ENST00000261769	NM_004360.3	614	ATCATTGATGCAGACCTt/t	12/16	0.254009672606401	1	FACETS	0.98	0.888	1	0.98	0.888	1	CLONAL	1	TRUE	0	0.254009672606401	1		681	905	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822187	72822187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755178587	NA	P-0021986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	109	603	2	ENST00000268489.5:c.9988G>A	p.Gly3330Arg	p.G3330R	ENST00000268489	NM_006885.3	3330	Ggg/Agg	10/10	0.254009672606401	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.254009672606401	1		605	704	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458392	12458392	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	117	662	0	ENST00000287820.6:c.1009C>G	p.Leu337Val	p.L337V	ENST00000287820	NM_015869.4	337	Ctt/Gtt	6/7	1	2	FACETS	0.904	0.814	1	0.904	0.814	1	CLONAL	1	TRUE	1	0.254009672606401	2		662	1019	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056559	26056559	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs147592392	NA	P-0021986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	54	256	0	ENST00000343677.2:c.98G>C	p.Arg33Pro	p.R33P	ENST00000343677	NM_005319.3	33	cGt/cCt	1/1	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.254009672606401	2		256	387	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164124	32164124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773802121	NA	P-0021986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	121	604	0	ENST00000375023.3:c.5275G>A	p.Asp1759Asn	p.D1759N	ENST00000375023	NM_004557.3	1759	Gat/Aat	29/30	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.254009672606401	2		604	881	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506170	148506171	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs797045568	NA	P-0021986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	124	509	0	ENST00000320356.2:c.2187dup	p.Asp730Ter	p.D730*	ENST00000320356	NM_004456.4	729	-/T	19/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.254009672606401	2		509	869	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667423	241667423	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913122	NA	P-0021996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	106	627	0	ENST00000366560.3:c.1027C>T	p.Arg343Ter	p.R343*	ENST00000366560	NM_000143.3	343	Cga/Tga	7/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.646714466154171	2		627	289	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39744051	39744051	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	46	555	0	ENST00000361337.2:c.1679C>G	p.Pro560Arg	p.P560R	ENST00000361337	NM_003286.2	560	cCc/cGc	16/21	0.601079916538262	5	FACETS	0.376	0.316	0.444	0.094	0.079	0.111	SUBCLONAL	1	TRUE	1	0.592769943924175	5		555	779	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092948	29092948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201206424	NA	P-0022026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	191	698	0	ENST00000328354.6:c.1036C>T	p.Arg346Cys	p.R346C	ENST00000328354	NM_007194.3	346	Cgt/Tgt	10/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.605886864215559	2		698	579	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0022079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	11	363	1	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	0.793771391025051	3	FACETS	0.079	0.054	0.11	0.039	0.027	0.055	SUBCLONAL	1	TRUE	1	0.793771391025051	3		364	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0022079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	505	739	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	0.793771391025051	2		739	614	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245759	41245759	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs55650082	NA	P-0022079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	163	675	1	ENST00000357654.3:c.1789G>T	p.Glu597Ter	p.E597*	ENST00000357654	NM_007294.3	597	Gaa/Taa	10/23	0.793771391025051	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.793771391025051	1		676	229	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103520607	103520607	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs763466582	NA	P-0022079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	92	319	0	ENST00000355739.4:c.2678C>T	p.Ser893Leu	p.S893L	ENST00000355739	NM_000123.3	893	tCa/tTa	12/15	0.785827134488924	2	FACETS	0.892	0.83	0.949	0.892	0.83	0.949	CLONAL	2	TRUE	0	0.793771391025051	2		319	130	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	284	503	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.288061563518666	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	1	0.288061563518666	4		503	792	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0022112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	82	403	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.226268666029519	3	FACETS	1	0.97	1	0.651	0.576	0.732	CLONAL	1	TRUE	1	0.288061563518666	3		403	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0022112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	150	802	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.288061563518666	2		802	744	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555929	226555929	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	62	690	0	ENST00000366794.5:c.2248C>T	p.Pro750Ser	p.P750S	ENST00000366794	NM_001618.3	750	Ccg/Tcg	16/23	0.170824569411929	4	FACETS	0.877	0.757	1	0.439	0.378	0.504	INDETERMINATE	1	TRUE	2	0.288061563518666	4		690	632	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346841	89346841	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs891424039	NA	P-0022112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	47	317	0	ENST00000301030.4:c.6109G>A	p.Val2037Ile	p.V2037I	ENST00000301030	NM_001256183.1	2037	Gtc/Atc	9/13	0.260122455860885	3	FACETS	1	0.954	1	0.676	0.574	0.787	CLONAL	1	TRUE	1	0.288061563518666	3		317	276	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	132	503	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.217400400739621	5	FACETS	0.914	0.841	0.988	1	0.98	1	CLONAL	4	TRUE	2	0.31167946733561	5		503	340	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0022112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	79	403	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.194053643020692	3	FACETS	1	0.906	1	1	0.906	1	CLONAL	2	TRUE	1	0.31167946733561	3		403	287	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0022112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	68	802	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.133200620064551	3	FACETS	1	0.971	1	0.472	0.413	0.535	INDETERMINATE	1	TRUE	0	0.31167946733561	3		802	356	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346841	89346841	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs891424039	NA	P-0022112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	17	317	0	ENST00000301030.4:c.6109G>A	p.Val2037Ile	p.V2037I	ENST00000301030	NM_001256183.1	2037	Gtc/Atc	9/13	0.31167946733561	3	FACETS	1	0.824	1	0.558	0.421	0.716	CLONAL	1	TRUE	1	0.31167946733561	3		317	113	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0022112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	8	819	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.133200620064551	3	FACETS	0.179	0.115	0.264	0.06	0.038	0.088	INDETERMINATE	1	TRUE	0	0.31167946733561	3		819	331	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573581	48573585	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTT	TTCTT	-	novel	NA	P-0022112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	22	399	0	ENST00000342988.3:c.166_170del	p.Ser56AsnfsTer12	p.S56Nfs*12	ENST00000342988	NM_005359.5	55	gaTTCTTta/gata	2/12	0.223365476850818	2	FACETS	1	0.882	1	0.598	0.47	0.742	CLONAL	1	TRUE	0	0.31167946733561	2		399	118	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0022135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	36	701	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.303	0.249	0.363	0.303	0.249	0.363	SUBCLONAL	1	TRUE	1	0.532046923849682	2		701	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0022135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	9	831	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.532046923849682	1	FACETS	0.074	0.049	0.107	0.074	0.049	0.107	SUBCLONAL	1	TRUE	0	0.532046923849682	1		832	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577069	7577069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55819519	NA	P-0022135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	14	995	2	ENST00000269305.4:c.869G>A	p.Arg290His	p.R290H	ENST00000269305	NM_001126112.2	290	cGc/cAc	8/11	0.532046923849682	1	FACETS	0.079	0.056	0.106	0.079	0.056	0.106	SUBCLONAL	1	TRUE	0	0.532046923849682	1		997	490	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0022135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	9	932	2	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	0.08	0.052	0.116	0.08	0.052	0.116	SUBCLONAL	1	TRUE	1	0.532046923849682	2		934	423	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715368	61715368	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	13	948	2	ENST00000401558.2:c.2245C>T	p.Arg749Ter	p.R749*	ENST00000401558	NM_003400.3	749	Cga/Tga	19/25	0.163844331476925	0	FACETS	0.039	0.027	0.053			1	INDETERMINATE	1	TRUE	0	0.532046923849682	0		950	589	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967543	26967543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	12	654	0	ENST00000381527.3:c.686C>T	p.Thr229Met	p.T229M	ENST00000381527	NM_001260.1	229	aCg/aTg	7/13	0.532046923849682	1	FACETS	0.151	0.106	0.207	0.151	0.106	0.207	SUBCLONAL	1	TRUE	0	0.532046923849682	1		654	219	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112939969	112939969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs186919241	NA	P-0022135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	12	537	0	ENST00000351677.2:c.1621G>A	p.Glu541Lys	p.E541K	ENST00000351677	NM_002834.3	541	Gaa/Aaa	14/16	1	2	FACETS	0.287	0.202	0.391	0.287	0.202	0.391	SUBCLONAL	1	TRUE	1	0.532046923849682	2		537	157	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088733	27088734	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	179	903	1	ENST00000324856.7:c.2343dup	p.His782ThrfsTer35	p.H782Tfs*35	ENST00000324856	NM_006015.4	781	ata/atAa	7/20	0.241780184456278	3	FACETS	0.773	0.717	0.83	0.773	0.717	0.83	INDETERMINATE	2	TRUE	1	0.532046923849682	3		904	551	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31369198	31369198	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752329190	NA	P-0022135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	50	841	2	ENST00000328111.2:c.182C>T	p.Ser61Phe	p.S61F	ENST00000328111	NM_006892.3	61	tCc/tTc	3/23	0.24690856379469	2	FACETS	0.399	0.339	0.465	0.2	0.169	0.233	INDETERMINATE	1	TRUE	0	0.532046923849682	2		843	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577095	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519984	NA	P-0022139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	175	1306	0	ENST00000269305.4:c.843C>G	p.Asp281Glu	p.D281E	ENST00000269305	NM_001126112.2	281	gaC/gaG	8/11	0.279963693197345	2	FACETS	0.84	0.775	0.907	0.84	0.775	0.907	CLONAL	2	TRUE	0	0.279963693197345	2		1306	744	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63810707	63810707	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	67	709	0	ENST00000279873.7:c.794T>C	p.Phe265Ser	p.F265S	ENST00000279873	NM_032199.2	265	tTc/tCc	5/10	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.279963693197345	2		709	477	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625191	69625191	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	156	1243	1	ENST00000334134.2:c.602C>A	p.Pro201His	p.P201H	ENST00000334134	NM_005247.2	201	cCc/cAc	3/3	0.218166000565286	4	FACETS	1	0.944	1			1	CLONAL	2	TRUE	NA	0.279963693197345	4		1244	689	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406315	406315	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	85	1093	0	ENST00000399788.2:c.4126G>C	p.Asp1376His	p.D1376H	ENST00000399788	NM_001042603.1	1376	Gat/Cat	25/28	0.279963693197345	3	FACETS	0.947	0.837	1	0.473	0.418	0.533	CLONAL	1	TRUE	1	0.279963693197345	3		1093	731	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433565	49433566	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0022139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	109	1743	5	ENST00000301067.7:c.7987_7988delinsTT	p.Gly2663Phe	p.G2663F	ENST00000301067	NM_003482.3	2663	GGt/TTt	31/54	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.279963693197345	2		1748	747	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448335	49448335	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1311872208	NA	P-0022139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	59	1249	0	ENST00000301067.7:c.376C>G	p.Pro126Ala	p.P126A	ENST00000301067	NM_003482.3	126	Cct/Gct	3/54	1	2	FACETS	0.691	0.594	0.796	0.691	0.594	0.796	SUBCLONAL	1	TRUE	1	0.279963693197345	2		1249	610	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271967	15271967	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	164	1334	2	ENST00000263388.2:c.6472C>A	p.Leu2158Ile	p.L2158I	ENST00000263388	NM_000435.2	2158	Ctc/Atc	33/33	0.272534168421217	2	FACETS	0.93	0.857	1	0.93	0.857	1	CLONAL	2	TRUE	0	0.279963693197345	2		1336	630	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211505	36211505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	119	1244	1	ENST00000222270.7:c.1256C>T	p.Pro419Leu	p.P419L	ENST00000222270	NM_014727.1	419	cCc/cTc	3/37	0.141480218055739	5	FACETS	0.773	0.698	0.852	0.515	0.465	0.568	INDETERMINATE	2	TRUE	2	0.279963693197345	5		1245	781	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872936	136872936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	47	641	0	ENST00000241393.3:c.562C>T	p.Arg188Cys	p.R188C	ENST00000241393	NM_003467.2	188	Cgc/Tgc	2/2	0.153134417481114	3	FACETS	0.916	0.774	1			1	INDETERMINATE	1	TRUE	NA	0.279963693197345	3		641	418	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215881	142215882	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0022139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	90	691	2	ENST00000350721.4:c.5711_5712delinsAT	p.Arg1904His	p.R1904H	ENST00000350721	NM_001184.3	1904	cGG/cAT	33/47	0.265407431580696	3	FACETS	0.925	0.827	1	0.925	0.827	1	CLONAL	2	TRUE	1	0.279963693197345	3		693	396	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974708	21974717	+	frameshift_variant	Frame_Shift_Del	DEL	GCGTTGGGCA	GCGTTGGGCA	-	novel	NA	P-0022139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	91	712	0	ENST00000304494.5:c.110_119del	p.Leu37HisfsTer13	p.L37Hfs*13	ENST00000304494	NM_000077.4	37	cTGCCCAACGCa/ca	1/3	0.272534168421217	2	FACETS	0.827	0.739	0.919	0.827	0.739	0.919	CLONAL	2	TRUE	0	0.279963693197345	2		712	393	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211530	98211530	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1259134617	NA	P-0022139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	48	957	0	ENST00000331920.6:c.3625A>G	p.Met1209Val	p.M1209V	ENST00000331920	NM_000264.3	1209	Atg/Gtg	22/24	0.272534168421217	2	FACETS	0.713	0.603	0.834	0.356	0.301	0.417	SUBCLONAL	1	TRUE	0	0.279963693197345	2		957	481	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916480	39916480	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1569142538	NA	P-0022139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	231	1442	0	ENST00000378444.4:c.4523G>C	p.Gly1508Ala	p.G1508A	ENST00000378444	NM_001123385.1	1508	gGc/gCc	11/15	0.265407431580696	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.279963693197345	3		1442	891	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937344	76937344	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	98	931	0	ENST00000373344.5:c.3404G>A	p.Arg1135Lys	p.R1135K	ENST00000373344	NM_000489.3	1135	aGg/aAg	9/35	0.265407431580696	3	FACETS	1	0.979	1	0.71	0.635	0.789	CLONAL	1	TRUE	1	0.279963693197345	3		931	562	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	66	294	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.219641813723816	3	FACETS	1	0.885	1	0.507	0.443	0.576	INDETERMINATE	1	FALSE	1	0.445593526120284	3		294	357	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0022309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	117	737	0	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	NA	2	FACETS	1	0.921	1			1	INDETERMINATE	1	FALSE	NA	0.445593526120284	2		737	516	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209556	98209556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	46	601	0	ENST00000331920.6:c.3982G>A	p.Glu1328Lys	p.E1328K	ENST00000331920	NM_000264.3	1328	Gaa/Aaa	23/24	NA	2	FACETS	0.545	0.46	0.638			1	INDETERMINATE	1	FALSE	NA	0.445593526120284	2		601	379	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298621	11298621	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	54	578	0	ENST00000361445.4:c.1840G>T	p.Glu614Ter	p.E614*	ENST00000361445	NM_004958.3	614	Gag/Tag	12/58	0.214645149540662	2	FACETS	0.522	0.447	0.605	0.261	0.223	0.303	INDETERMINATE	1	FALSE	0	0.445593526120284	2		578	464	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716389	18716389	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	46	492	0	ENST00000266497.5:c.3736C>G	p.His1246Asp	p.H1246D	ENST00000266497		1246	Cac/Gac	26/31	1	2	FACETS	0.465	0.392	0.546	0.465	0.392	0.546	SUBCLONAL	1	FALSE	1	0.445593526120284	2		492	444	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56474145	56474145	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	83	690	0	ENST00000267101.3:c.61G>C	p.Glu21Gln	p.E21Q	ENST00000267101	NM_001982.3	21	Gag/Cag	1/28	0.303108464936504	4	FACETS	0.722	0.637	0.813	0.361	0.318	0.407	SUBCLONAL	1	FALSE	2	0.445593526120284	4		690	746	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941691	48941691	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	45	436	0	ENST00000267163.4:c.1001G>C	p.Arg334Thr	p.R334T	ENST00000267163	NM_000321.2	334	aGa/aCa	10/27	0.167783390908939	3	FACETS	0.648	0.546	0.761	0.216	0.182	0.254	INDETERMINATE	1	FALSE	0	0.445593526120284	3		436	381	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355960	73355960	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	131	973	4	ENST00000377767.4:c.11C>T	p.Ser4Phe	p.S4F	ENST00000377767	NM_014953.3	4	tCc/tTc	1/21	0.167783390908939	3	FACETS	0.745	0.675	0.819	0.248	0.225	0.273	INDETERMINATE	1	FALSE	0	0.445593526120284	3		977	965	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37876079	37876079	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	75	725	0	ENST00000269571.5:c.1938G>C	p.Gln646His	p.Q646H	ENST00000269571		646	caG/caC	16/27	0.445593526120284	7	FACETS	0.63	0.55	0.717			1	SUBCLONAL	1	FALSE	NA	0.445593526120284	7		725	1129	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883158	37883158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	91	826	0	ENST00000269571.5:c.3061G>A	p.Glu1021Lys	p.E1021K	ENST00000269571		1021	Gag/Aag	25/27	0.445593526120284	7	FACETS	0.646	0.572	0.727			1	SUBCLONAL	1	FALSE	NA	0.445593526120284	7		826	1336	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883728	37883728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1332	95	901	0	ENST00000269571.5:c.3340G>A	p.Glu1114Lys	p.E1114K	ENST00000269571		1114	Gag/Aag	26/27	0.445593526120284	7	FACETS	0.632	0.56	0.709			1	SUBCLONAL	1	FALSE	NA	0.445593526120284	7		901	1427	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128018917	128018917	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	42	458	0	ENST00000285398.2:c.1951G>C	p.Val651Leu	p.V651L	ENST00000285398	NM_000122.1	651	Gtt/Ctt	13/15	NA	2	FACETS	0.527	0.441	0.621			1	INDETERMINATE	1	FALSE	NA	0.445593526120284	2		458	358	SUCCESS
APC	324	MSKCC	GRCh37	5	112157678	112157678	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	48	427	0	ENST00000257430.4:c.1398G>C	p.Met466Ile	p.M466I	ENST00000257430	NM_000038.5	466	atG/atC	11/16	0.342998458512071	3	FACETS	0.681	0.577	0.794			1	SUBCLONAL	1	FALSE	NA	0.445593526120284	3		427	387	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508213	106508213	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	16	252	0	ENST00000359195.3:c.207G>C	p.Gln69His	p.Q69H	ENST00000359195	NM_002649.2	69	caG/caC	2/11	1	2	FACETS	0.386	0.286	0.504	0.386	0.286	0.504	SUBCLONAL	1	FALSE	1	0.445593526120284	2		252	186	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39935756	39935756	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0022309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	51	688	0	ENST00000378444.4:c.116C>G	p.Ser39Ter	p.S39*	ENST00000378444	NM_001123385.1	39	tCa/tGa	3/15	0.449034790039662	1	FACETS	0.352	0.299	0.41	0.352	0.299	0.41	SUBCLONAL	1	FALSE	0	0.445593526120284	1		688	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578277	7578307	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGAGGGGCCAGACCTAAGAGCAATCAGTGAG	GGAGGGGCCAGACCTAAGAGCAATCAGTGAG	-	novel	NA	P-0022374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	181	561	1	ENST00000269305.4:c.560-18_572del		p.X187_splice	ENST00000269305	NM_001126112.2	187		6/11	0.468935221083206	2	FACETS	0.974	0.913	1	0.974	0.913	1	CLONAL	2	TRUE	0	0.490072562080079	2		562	379	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145599	24145599	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	226	559	0	ENST00000263121.7:c.618G>T	p.Trp206Cys	p.W206C	ENST00000263121	NM_003073.3	206	tgG/tgT	5/9	0.38729235528826	3	FACETS	0.963	0.904	1	0.963	0.904	1	CLONAL	2	TRUE	1	0.490072562080079	3		559	596	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6048638	6048638	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs372539944	NA	P-0022374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	130	602	0	ENST00000265849.7:c.13G>C	p.Glu5Gln	p.E5Q	ENST00000265849	NM_000535.5	5	Gag/Cag	1/15	0.485538890040975	1	FACETS	0.795	0.725	0.867	0.795	0.725	0.867	SUBCLONAL	1	TRUE	0	0.490072562080079	1		602	504	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508860	106508860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1251220989	NA	P-0022374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	23	380	0	ENST00000359195.3:c.854C>T	p.Thr285Met	p.T285M	ENST00000359195	NM_002649.2	285	aCg/aTg	2/11	1	2	FACETS	0.265	0.206	0.333	0.265	0.206	0.333	SUBCLONAL	1	TRUE	1	0.490072562080079	2		380	354	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	105	313	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.829	0.751	0.909	0.829	0.751	0.909	CLONAL	1	TRUE	1	0.775126856589414	2		315	327	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0022469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11814	1129	514	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.775126856589414	28	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.775126856589414	28		514	12943	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439596	51439597	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAGACTGCTACTTAGAGGTGCTAATCCCGATTTGAA	novel	NA	P-0022469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	87	290	0	ENST00000262662.1:c.162_197dup	p.Arg55_Lys66dup	p.R55_K66dup	ENST00000262662		55	agg/agGAGACTGCTACTTAGAGGTGCTAATCCCGATTTGAAg	4/4	1	2	FACETS	0.445	0.395	0.498	0.445	0.395	0.498	SUBCLONAL	1	TRUE	1	0.775126856589414	2		290	505	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692793	89692793	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786204927	NA	P-0022469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	10	279	0	ENST00000371953.3:c.277C>G	p.His93Asp	p.H93D	ENST00000371953	NM_000314.4	93	Cat/Gat	5/9	0.775126856589414	1	FACETS	0.077	0.052	0.109	0.077	0.052	0.109	SUBCLONAL	1	TRUE	0	0.775126856589414	1		279	204	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201946	102201946	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	59	198	0	ENST00000263464.3:c.1298A>G	p.Glu433Gly	p.E433G	ENST00000263464	NM_001165.4	433	gAa/gGa	6/9	1	2	FACETS	0.87	0.763	0.981	0.87	0.763	0.981	CLONAL	1	TRUE	1	0.775126856589414	2		198	175	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041141	29041141	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	230	584	0	ENST00000282397.4:c.287C>G	p.Thr96Arg	p.T96R	ENST00000282397	NM_002019.4	96	aCa/aGa	3/30	1	2	FACETS	0.989	0.929	1	0.989	0.929	1	CLONAL	1	TRUE	1	0.775126856589414	2		584	600	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015040	27015040	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	185	347	0	ENST00000335756.4:c.142C>G	p.Leu48Val	p.L48V	ENST00000335756	NM_001809.3	48	Cta/Gta	2/5	1	2	FACETS	0.907	0.844	0.972	0.907	0.844	0.972	CLONAL	1	TRUE	1	0.775126856589414	2		347	526	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168516	56168516	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	52	254	0	ENST00000399503.3:c.1472G>T	p.Cys491Phe	p.C491F	ENST00000399503	NM_005921.1	491	tGt/tTt	8/20	1	2	FACETS	0.504	0.433	0.581	0.504	0.433	0.581	SUBCLONAL	1	TRUE	1	0.775126856589414	2		254	266	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	87	294	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	FALSE	1	0.229385649984065	2		294	511	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0022531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	82	450	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	0.736	0.648	0.832	0.736	0.648	0.832	SUBCLONAL	1	FALSE	1	0.229385649984065	2		450	971	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	254	294	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	0.846206729993459	2		294	594	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922364	178922364	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	273	483	0	ENST00000263967.3:c.1133G>T	p.Cys378Phe	p.C378F	ENST00000263967	NM_006218.2	378	tGt/tTt	6/21	1	2	FACETS	0.954	0.902	1	0.954	0.902	1	CLONAL	1	TRUE	1	0.846206729993459	2		483	676	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0022565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	362	936	2	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	1	2	FACETS	0.823	0.782	0.865	0.823	0.782	0.865	CLONAL	1	TRUE	1	0.846206729993459	2		938	1039	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	194	294	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	FALSE	1	0.637390768385246	2		294	579	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217479	142217479	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	69	673	0	ENST00000350721.4:c.5518G>C	p.Glu1840Gln	p.E1840Q	ENST00000350721	NM_001184.3	1840	Gaa/Caa	32/47	1	2	FACETS	0.294	0.256	0.336	0.294	0.256	0.336	SUBCLONAL	1	FALSE	1	0.637390768385246	2		673	736	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29090070	29090070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	37	270	0	ENST00000328354.6:c.1411C>T	p.Pro471Ser	p.P471S	ENST00000328354	NM_007194.3	471	Cca/Tca	13/15	1	2	FACETS	0.474	0.393	0.563	0.474	0.393	0.563	SUBCLONAL	1	FALSE	1	0.637390768385246	2		270	245	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100949	27100949	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	72	780	3	ENST00000324856.7:c.4231C>T	p.Gln1411Ter	p.Q1411*	ENST00000324856	NM_006015.4	1411	Cag/Tag	18/20	0.249507668603695	5	FACETS	0.887	0.783	0.998	0.887	0.783	0.998	CLONAL	3	FALSE	2	0.249507668603695	5		783	298	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111501	8111502	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0022574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	168	883	1	ENST00000346208.3:c.988_989del	p.Arg330GlufsTer21	p.R330Efs*21	ENST00000346208		329	agGAgg/aggg	5/6	0.176809165231458	3	FACETS	0.878	0.811	0.947	1	0.986	1	CLONAL	3	FALSE	1	0.249507668603695	3		884	575	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107095	27107098	+	frameshift_variant	Frame_Shift_Ins	INS	CGCG	CGCG	GCGCC	novel	NA	P-0022574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	84	647	1	ENST00000324856.7:c.6706_6709delinsGCGCC	p.Arg2236AlafsTer42	p.R2236Afs*42	ENST00000324856	NM_006015.4	2236	CGCGcg/GCGCCcg	20/20	0.249507668603695	5	FACETS	1	0.9	1	1	0.9	1	CLONAL	3	FALSE	2	0.249507668603695	5		648	306	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0022575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	67	813	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.12	2		813	997	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916940	178916948	+	inframe_deletion	In_Frame_Del	DEL	AGAAAAGAT	AGAAAAGAT	-	novel	NA	P-0022596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	126	869	0	ENST00000263967.3:c.327_335del	p.Glu109_Ile112delinsAsp	p.E109_I112delinsD	ENST00000263967	NM_006218.2	109	gaAGAAAAGATc/gac	2/21	0.427433087238044	3	FACETS	0.908	0.83	0.988	0.908	0.83	0.988	CLONAL	2	FALSE	1	0.427433087238044	3		869	394	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0022596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	9	932	2	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	0.125	0.082	0.181	0.125	0.082	0.181	SUBCLONAL	1	FALSE	1	0.427433087238044	2		934	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519999	NA	P-0022596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	90	1020	0	ENST00000269305.4:c.716A>C	p.Asn239Thr	p.N239T	ENST00000269305	NM_001126112.2	239	aAc/aCc	7/11	0.258209484133322	2	FACETS	0.977	0.872	1	0.489	0.436	0.544	CLONAL	1	FALSE	0	0.427433087238044	2		1020	431	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231770	36231770	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0022596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	161	1004	1	ENST00000300305.3:c.613+1G>A		p.X205_splice	ENST00000300305		205			0.294067882665981	3	FACETS	0.768	0.708	0.831	0.512	0.472	0.554	SUBCLONAL	2	FALSE	0	0.427433087238044	3		1005	595	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342777	87342777	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	38	775	0	ENST00000277120.3:c.1062G>A	p.Met354Ile	p.M354I	ENST00000277120		354	atG/atA	9/19	0.258209484133322	2	FACETS	0.77	0.641	0.911	0.385	0.32	0.456	CLONAL	1	FALSE	0	0.427433087238044	2		775	231	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032554	47032554	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	37	1000	0	ENST00000377604.3:c.460G>T	p.Val154Leu	p.V154L	ENST00000377604	NM_001204468.1	154	Gtg/Ttg	5/24	0.237086622563319	1	FACETS	0.225	0.185	0.27	0.225	0.185	0.27	INDETERMINATE	1	FALSE	0	0.427433087238044	1		1000	605	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916940	178916948	+	inframe_deletion	In_Frame_Del	DEL	AGAAAAGAT	AGAAAAGAT	-	novel	NA	P-0022596-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	356	869	0	ENST00000263967.3:c.327_335del	p.Glu109_Ile112delinsAsp	p.E109_I112delinsD	ENST00000263967	NM_006218.2	109	gaAGAAAAGATc/gac	2/21	0.644266618698401	6	FACETS	1	0.991	1	0.859	0.82	0.898	CLONAL	3	FALSE	2	0.644266618698401	6		869	736	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519999	NA	P-0022596-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	219	1020	0	ENST00000269305.4:c.716A>C	p.Asn239Thr	p.N239T	ENST00000269305	NM_001126112.2	239	aAc/aCc	7/11	0.373395931512706	3	FACETS	1	0.99	1	0.808	0.766	0.849	INDETERMINATE	2	FALSE	0	0.644266618698401	3		1020	371	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231770	36231770	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0022596-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	392	1004	1	ENST00000300305.3:c.613+1G>A		p.X205_splice	ENST00000300305		205			0.644266618698401	6	FACETS	0.914	0.875	0.952	0.914	0.875	0.952	CLONAL	4	FALSE	2	0.644266618698401	6		1005	762	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342777	87342777	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022596-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	69	775	0	ENST00000277120.3:c.1062G>A	p.Met354Ile	p.M354I	ENST00000277120		354	atG/atA	9/19	0.593327939805259	2	FACETS	0.885	0.781	0.994	0.443	0.39	0.497	CLONAL	1	FALSE	0	0.644266618698401	2		775	242	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032554	47032554	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022596-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	41	1000	0	ENST00000377604.3:c.460G>T	p.Val154Leu	p.V154L	ENST00000377604	NM_001204468.1	154	Gtg/Ttg	5/24	0.473857631799459	3	FACETS	0.448	0.373	0.53	0.149	0.124	0.177	SUBCLONAL	1	FALSE	0	0.644266618698401	3		1000	376	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544748	65544748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022596-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	11	995	1	ENST00000358664.4:c.178C>T	p.Arg60Trp	p.R60W	ENST00000358664	NM_002382.4	60	Cgg/Tgg	4/5	0.644868622811977	4	FACETS	0.108	0.074	0.151	0.054	0.037	0.076	SUBCLONAL	1	FALSE	2	0.644266618698401	4		996	519	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749515	41749515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022596-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	17	784	0	ENST00000226382.2:c.280G>A	p.Glu94Lys	p.E94K	ENST00000226382	NM_003924.3	94	Gag/Aag	2/3	0.24704486001554	3	FACETS	0.247	0.184	0.322	0.082	0.061	0.108	INDETERMINATE	1	FALSE	0	0.644266618698401	3		784	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0022597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	232	1070	2	ENST00000269305.4:c.376-1G>T		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.406767464283225	2	FACETS	0.955	0.898	1	0.955	0.898	1	CLONAL	2	TRUE	0	0.406767464283225	2		1072	597	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165522	118165522	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	42	301	0	ENST00000369448.3:c.32del	p.Cys11SerfsTer36	p.C11Sfs*36	ENST00000369448	NM_017709.3	11	tGc/tc	2/2	0.406767464283225	4	FACETS	0.875	0.733	1	0.438	0.366	0.516	CLONAL	1	TRUE	2	0.406767464283225	4		301	332	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961517	54961517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1315333827	NA	P-0022597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	53	294	0	ENST00000312783.6:c.115G>A	p.Val39Ile	p.V39I	ENST00000312783	NM_198436.1	39	Gta/Ata	4/10	0.388963349260639	5	FACETS	1	0.959	1	0.45	0.386	0.519	CLONAL	1	TRUE	2	0.406767464283225	5		294	311	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857531	68857531	+	splice_donor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0022679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	22	557	0	ENST00000261769.5:c.2164+2del		p.X722_splice	ENST00000261769	NM_004360.3	722			0.192113954458405	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		557	337	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705367	43705368	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	93	959	0	ENST00000382044.4:c.5254dup	p.Ser1752LysfsTer14	p.S1752Kfs*14	ENST00000382044	NM_001141980.1	1752	agc/aAgc	24/28	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		959	937	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372205	55372205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs904970570	NA	P-0022927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	150	437	0	ENST00000297316.4:c.895G>A	p.Ala299Thr	p.A299T	ENST00000297316	NM_022454.3	299	Gcg/Acg	2/2	1	2	FACETS	0.925	0.852	0.999	0.925	0.852	0.999	CLONAL	1	TRUE	1	0.688892971303785	2		437	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578476	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTGCCGGGCGG	GGGTGCCGGGCGG	-	rs876659215	NA	P-0022927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	313	902	1	ENST00000269305.4:c.454_466del	p.Pro152AlafsTer14	p.P152Afs*14	ENST00000269305	NM_001126112.2	152	CCGCCCGGCACCCgc/gc	5/11	0.688892971303785	1	FACETS	0.986	0.94	1	0.986	0.94	1	CLONAL	1	TRUE	0	0.688892971303785	1		903	604	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268895	115268895	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	256	770	0	ENST00000438362.2:c.1715T>A	p.Leu572Gln	p.L572Q	ENST00000438362	NM_001242891.1	572	cTg/cAg	14/20	1	2	FACETS	0.977	0.918	1	0.977	0.918	1	CLONAL	1	TRUE	1	0.688892971303785	2		770	761	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589186	67589274	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTCTGACCCATTAACCTTCAGTTCTGTGGTTGAATTAATAAACCACTACCGGAATGAATCTCTAGCTCAGTATAATCCCAAATTGGA	TTCTCTGACCCATTAACCTTCAGTTCTGTGGTTGAATTAATAAACCACTACCGGAATGAATCTCTAGCTCAGTATAATCCCAAATTGGA	-	novel	NA	P-0022927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	40	465	0	ENST00000274335.5:c.1175_1263del	p.Phe392CysfsTer20	p.F392Cfs*20	ENST00000274335		392	TTCTCTGACCCATTAACCTTCAGTTCTGTGGTTGAATTAATAAACCACTACCGGAATGAATCTCTAGCTCAGTATAATCCCAAATTGGAt/t	9/15	0.688892971303785	1	FACETS	0.44	0.371	0.515	0.44	0.371	0.515	SUBCLONAL	1	TRUE	0	0.688892971303785	1		465	173	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772818	135772823	+	inframe_deletion	In_Frame_Del	DEL	GAGTTT	GAGTTT	-	novel	NA	P-0022927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	77	751	0	ENST00000298552.3:c.2800_2805del	p.Lys934_Leu935del	p.K934_L935del	ENST00000298552	NM_001162426.1	934	AAACTC/-	21/23	0.688892971303785	1	FACETS	0.33	0.291	0.372	0.33	0.291	0.372	SUBCLONAL	1	TRUE	0	0.688892971303785	1		751	444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578525	7578525	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519976	NA	P-0022987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	184	1117	2	ENST00000269305.4:c.405C>G	p.Cys135Trp	p.C135W	ENST00000269305	NM_001126112.2	135	tgC/tgG	5/11	0.406658625303415	0	FACETS	0.699	0.647	0.753			1	SUBCLONAL	1	FALSE	0	0.406658625303415	0		1119	768	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167602	24167602	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	72	610	0	ENST00000263121.7:c.986G>C	p.Ser329Thr	p.S329T	ENST00000263121	NM_003073.3	329	aGc/aCc	7/9	0.406658625303415	0	FACETS	0.585	0.514	0.661			1	SUBCLONAL	1	FALSE	0	0.406658625303415	0		610	359	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	135	313	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.834824880670338	2		315	277	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233037	55233037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1477025000	NA	P-0022991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	26580	629	1	ENST00000275493.2:c.1787C>T	p.Pro596Leu	p.P596L	ENST00000275493	NM_005228.3	596	cCg/cTg	15/28	0.834824880670338	75	FACETS	1	0.999	1			1	CLONAL	74	TRUE	NA	0.834824880670338	75		630	27034	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	269	772	0	ENST00000269305.4:c.517G>C	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ctg	5/11	0.834824880670338	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.834824880670338	1		772	337	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624242	89624243	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs121913290	NA	P-0022991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	91	248	0	ENST00000371953.3:c.17_18del	p.Lys6ArgfsTer4	p.K6Rfs*4	ENST00000371953	NM_000314.4	6	AAa/a	1/9	0.834824880670338	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.834824880670338	1		248	112	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041175	180041175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1400220848	NA	P-0022991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	238	1121	1	ENST00000261937.6:c.3224G>A	p.Arg1075Gln	p.R1075Q	ENST00000261937	NM_182925.4	1075	cGg/cAg	24/30	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.834824880670338	2		1122	549	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383227	31383227	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148132847	NA	P-0022991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	209	520	1	ENST00000328111.2:c.1139G>A	p.Arg380Gln	p.R380Q	ENST00000328111	NM_006892.3	380	cGa/cAa	11/23	0.834824880670338	3	FACETS	1	0.979	1	0.558	0.521	0.596	CLONAL	1	TRUE	1	0.834824880670338	3		521	636	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848043	151848043	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	219	564	0	ENST00000262189.6:c.12716G>A	p.Ser4239Asn	p.S4239N	ENST00000262189	NM_170606.2	4239	aGt/aAt	51/59	0.148666328415087	4	FACETS	1	0.986	1	0.572	0.54	0.604	INDETERMINATE	2	TRUE	0	0.834824880670338	4		564	421	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156040	119156040	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	67	863	0	ENST00000264033.4:c.1705C>T	p.Pro569Ser	p.P569S	ENST00000264033	NM_005188.3	569	Cca/Tca	11/16	0.183705400285826	4	FACETS	0.438	0.38	0.501	0.146	0.126	0.167	INDETERMINATE	1	TRUE	1	0.834824880670338	4		863	672	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434711	49434711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	64	863	2	ENST00000301067.7:c.6842C>T	p.Ser2281Phe	p.S2281F	ENST00000301067	NM_003482.3	2281	tCc/tTc	31/54	0.130857427686539	4	FACETS	0.467	0.404	0.535	0.156	0.134	0.179	INDETERMINATE	1	TRUE	1	0.834824880670338	4		865	602	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250793	10250793	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	34	850	0	ENST00000340748.4:c.3687C>A	p.Phe1229Leu	p.F1229L	ENST00000340748		1229	ttC/ttA	32/40	0.834824880670338	3	FACETS	0.173	0.141	0.21	0.058	0.047	0.07	SUBCLONAL	1	TRUE	0	0.834824880670338	3		850	667	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096096	178096096	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	56	464	0	ENST00000397062.3:c.1235G>A	p.Gly412Glu	p.G412E	ENST00000397062	NM_006164.4	412	gGg/gAg	5/5	0.300017793348842	2	FACETS	0.373	0.32	0.429	0.186	0.16	0.215	INDETERMINATE	1	TRUE	0	0.834824880670338	2		464	360	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801119	1801119	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	64	1050	0	ENST00000260795.2:c.248C>T	p.Pro83Leu	p.P83L	ENST00000260795		83	cCc/cTc	2/17	0.146026657525394	3	FACETS	0.436	0.378	0.499	0.145	0.126	0.167	INDETERMINATE	1	TRUE	0	0.834824880670338	3		1050	498	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874065	151874065	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	149	767	1	ENST00000262189.6:c.8473G>C	p.Glu2825Gln	p.E2825Q	ENST00000262189	NM_170606.2	2825	Gaa/Caa	38/59	0.148666328415087	4	FACETS	1	0.981	1	0.305	0.28	0.331	INDETERMINATE	1	TRUE	0	0.834824880670338	4		768	537	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0022992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	79	680	0	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	0.616216665981535	2		680	196	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457243	25457243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377577594	NA	P-0022992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	9	704	1	ENST00000264709.3:c.2644C>T	p.Arg882Cys	p.R882C	ENST00000264709	NM_175629.2	882	Cgc/Tgc	23/23	1	2	FACETS	0.07	0.045	0.101	0.07	0.045	0.101	SUBCLONAL	1	TRUE	1	0.616216665981535	2		705	420	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115745	8115745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	27	597	1	ENST00000346208.3:c.1091G>A	p.Arg364Lys	p.R364K	ENST00000346208		364	aGa/aAa	6/6	1	2	FACETS	0.333	0.266	0.41	0.333	0.266	0.41	SUBCLONAL	1	TRUE	1	0.616216665981535	2		598	263	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411522	63411522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746279756	NA	P-0022992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	11	980	3	ENST00000330258.3:c.1645C>T	p.Arg549Trp	p.R549W	ENST00000330258	NM_152424.3	549	Cgg/Tgg	2/2	0.378678939338119	1	FACETS	0.125	0.086	0.173	0.125	0.086	0.173	SUBCLONAL	1	TRUE	0	0.616216665981535	1		983	198	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115751	8115751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	69	626	0	ENST00000346208.3:c.1097G>A	p.Arg366Gln	p.R366Q	ENST00000346208		366	cGa/cAa	6/6	1	2	FACETS	0.78	0.686	0.88	0.78	0.686	0.88	SUBCLONAL	1	TRUE	1	0.616216665981535	2		626	287	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429367	78429367	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	11	713	3	ENST00000370768.2:c.1075C>T	p.Arg359Ter	p.R359*	ENST00000370768	NM_003902.3	359	Cga/Tga	13/20	1	2	FACETS	0.173	0.119	0.24	0.173	0.119	0.24	SUBCLONAL	1	TRUE	1	0.616216665981535	2		716	206	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252993	36252994	+	frameshift_variant	Frame_Shift_Ins	INS	AT	AT	GGG	novel	NA	P-0022992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	99	590	0	ENST00000300305.3:c.368_369delinsCCC	p.Asp123AlafsTer15	p.D123Afs*15	ENST00000300305		123	gAT/gCCC	4/8	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.616216665981535	2		590	301	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0022993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	295	482	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.294247081054534	3	FACETS	1	0.994	1	0.742	0.702	0.784	INDETERMINATE	1	TRUE	1	0.655530057038064	3		482	805	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	80	313	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.427	0.376	0.481	0.427	0.376	0.481	SUBCLONAL	1	TRUE	1	0.655530057038064	2		315	572	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924707	94924711	+	frameshift_variant	Frame_Shift_Del	DEL	GTAGA	GTAGA	-	rs1388190639	NA	P-0022993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	172	696	0	ENST00000536441.1:c.199_203del	p.Ser67IlefsTer50	p.S67Ifs*50	ENST00000536441	NM_144665.3	67	TCTACa/a	3/10	0.620074420350029	2	FACETS	0.486	0.447	0.528	0.243	0.223	0.264	SUBCLONAL	1	TRUE	0	0.655530057038064	2		696	1079	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817482	39817482	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1154	81	584	0	ENST00000288319.7:c.81C>A	p.His27Gln	p.H27Q	ENST00000288319	NM_182918.3	27	caC/caA	2/10	0.655530057038064	3	FACETS	0.266	0.233	0.301	0.133	0.116	0.151	SUBCLONAL	1	TRUE	1	0.655530057038064	3		584	1235	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187383	38187383	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	65	653	0	ENST00000317025.8:c.1094G>A	p.Arg365His	p.R365H	ENST00000317025	NM_023034.1	365	cGt/cAt	6/24	0.392848384366255	1	FACETS	0.199	0.172	0.229	0.199	0.172	0.229	INDETERMINATE	1	TRUE	0	0.655530057038064	1		653	669	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229254	123229255	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0022993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	98	203	0	ENST00000218089.9:c.3739_3740dup	p.Lys1248Ter	p.K1248*	ENST00000218089	NM_001042749.1	1246	-/CT	34/35	1	1	FACETS	0.584	0.526	0.645	0.584	0.526	0.645	SUBCLONAL	1	TRUE	0	0.655530057038064	1		203	344	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0022993-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	215	482	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.122826405908568	5	FACETS	1	0.95	1			1	INDETERMINATE	2	TRUE	NA	0.395832765577148	5		482	845	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022993-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	43	313	2				ENST00000310581	NM_198253.2	-/1132			0.251942869648936	4	FACETS	0.678	0.568	0.801	0.339	0.284	0.401	SUBCLONAL	1	TRUE	2	0.395832765577148	4		315	447	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924707	94924711	+	frameshift_variant	Frame_Shift_Del	DEL	GTAGA	GTAGA	-	rs1388190639	NA	P-0022993-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	152	696	0	ENST00000536441.1:c.199_203del	p.Ser67IlefsTer50	p.S67Ifs*50	ENST00000536441	NM_144665.3	67	TCTACa/a	3/10	0.373231304374291	2	FACETS	0.867	0.793	0.944	0.433	0.396	0.472	CLONAL	1	TRUE	0	0.395832765577148	2		696	886	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817482	39817482	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022993-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	83	584	0	ENST00000288319.7:c.81C>A	p.His27Gln	p.H27Q	ENST00000288319	NM_182918.3	27	caC/caA	2/10	0.38968923605037	5	FACETS	0.702	0.618	0.792	0.234	0.206	0.264	SUBCLONAL	1	TRUE	2	0.395832765577148	5		584	952	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229254	123229255	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0022993-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	85	203	0	ENST00000218089.9:c.3739_3740dup	p.Lys1248Ter	p.K1248*	ENST00000218089	NM_001042749.1	1246	-/CT	34/35	1	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.395832765577148	1		203	315	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730916	40730916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765075213	NA	P-0023203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	42	583	2	ENST00000373198.4:c.3619C>T	p.Arg1207Cys	p.R1207C	ENST00000373198	NM_133170.3	1207	Cgt/Tgt	27/32	0.3	3	FACETS	0.877	0.738	1	1	0.946	1	CLONAL	3	TRUE	1	0.14	3		585	244	SUCCESS
APC	324	MSKCC	GRCh37	5	112102927	112102927	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746592911	NA	P-0023203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	16	438	0	ENST00000257430.4:c.262C>T	p.Arg88Trp	p.R88W	ENST00000257430	NM_000038.5	88	Cgg/Tgg	4/16	1	2	FACETS	0.796	0.588	1	0.796	0.588	1	CLONAL	1	TRUE	1	0.14	2		438	287	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271596	26271596	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	11	330	0	ENST00000305910.3:c.17A>T	p.Gln6Leu	p.Q6L	ENST00000305910	NM_003534.2	6	cAg/cTg	1/1	0.3	5	FACETS	1	0.707	1	0.341	0.235	0.471	CLONAL	1	TRUE	2	0.14	5		330	186	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969194	93969194	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	18	400	1	ENST00000369303.4:c.1802A>C	p.Lys601Thr	p.K601T	ENST00000369303	NM_004440.3	601	aAa/aCa	10/17	0.3	3	FACETS	1	0.898	1	0.717	0.542	0.921	CLONAL	1	TRUE	1	0.14	3		401	192	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579379	7579385	+	frameshift_variant	Frame_Shift_Del	DEL	TAGGTTT	TAGGTTT	-	novel	NA	P-0023210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	96	1001	0	ENST00000269305.4:c.302_308del	p.Lys101ThrfsTer20	p.K101Tfs*20	ENST00000269305	NM_001126112.2	101	aAAACCTAc/ac	4/11	0.498238370509667	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.486443937786662	1		1001	231	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441464	40441464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	71	779	0	ENST00000345506.4:c.35G>A	p.Gly12Glu	p.G12E	ENST00000345506	NM_003152.3	12	gGa/gAa	3/20	0.498238370509667	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.486443937786662	1		779	183	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427726	72427737	+	inframe_deletion	In_Frame_Del	DEL	ACGTTGCCCACA	ACGTTGCCCACA	-	novel	NA	P-0023210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	38	450	0	ENST00000477973.2:c.751_762del	p.Val252_Val255del	p.V252_V255del	ENST00000477973	NM_012234.5	251	acTGTGGGCAACGTc/acc	4/4	1	2	FACETS	0.964	0.809	1	0.964	0.809	1	CLONAL	1	TRUE	1	0.486443937786662	2		450	162	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79966110	79966110	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	14	630	0	ENST00000265081.6:c.774C>G	p.Phe258Leu	p.F258L	ENST00000265081	NM_002439.4	258	ttC/ttG	4/24	NA	2	FACETS	0.215	0.155	0.287			1	INDETERMINATE	1	TRUE	NA	0.486443937786662	2		630	268	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27173319	27173319	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	24	931	0	ENST00000380036.4:c.860G>T	p.Cys287Phe	p.C287F	ENST00000380036	NM_000459.3	287	tGt/tTt	6/23	0.498238370509667	1	FACETS	0.526	0.417	0.648	0.526	0.417	0.648	SUBCLONAL	1	TRUE	0	0.486443937786662	1		931	142	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	67	688	6	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	0.166476991409113	3	FACETS	1	0.966	1	0.677	0.59	0.77	CLONAL	1	FALSE	1	0.256717131899498	3		694	435	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	135	472	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.94	0.864	1	1	0.993	1	CLONAL	3	FALSE	1	0.256717131899498	2		472	373	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591144	67591154	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ATACTTGATGT	ATACTTGATGT	C	novel	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	176	500	0	ENST00000274335.5:c.1737_1745+2delinsC		p.X579_splice	ENST00000274335		579		12/15	1	2	FACETS	0.923	0.858	0.99	1	0.994	1	CLONAL	3	FALSE	1	0.256717131899498	2		500	495	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	220	844	6	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.978	0.917	1	1	0.995	1	CLONAL	3	FALSE	1	0.256717131899498	2		850	584	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	228	857	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.256717131899498	1	FACETS	0.906	0.858	0.955	1	0.996	1	CLONAL	4	FALSE	0	0.256717131899498	1		857	427	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720808	89720808	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	88	387	0	ENST00000371953.3:c.959T>C	p.Leu320Ser	p.L320S	ENST00000371953	NM_000314.4	320	tTa/tCa	8/9	1	2	FACETS	0.929	0.829	1	1	0.985	1	CLONAL	2	FALSE	1	0.256717131899498	2		387	369	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717769	89717770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	164	445	0	ENST00000371953.3:c.800dup	p.Asp268GlyfsTer30	p.D268Gfs*30	ENST00000371953	NM_000314.4	265	cta/ctAa	7/9	1	2	FACETS	0.885	0.82	0.953	1	0.994	1	CLONAL	3	FALSE	1	0.256717131899498	2		445	481	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	184	587	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	1	0.958	1	1	0.995	1	CLONAL	3	FALSE	1	0.256717131899498	2		587	461	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849514	68849514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs36087757	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	265	921	0	ENST00000261769.5:c.1417G>A	p.Val473Ile	p.V473I	ENST00000261769	NM_004360.3	473	Gtc/Atc	10/16	1	2	FACETS	0.975	0.919	1	1	0.996	1	CLONAL	3	FALSE	1	0.256717131899498	2		921	706	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155972	119155972	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751274314	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	317	1073	0	ENST00000264033.4:c.1637C>T	p.Pro546Leu	p.P546L	ENST00000264033	NM_005188.3	546	cCg/cTg	11/16	1	2	FACETS	0.955	0.905	1	1	0.997	1	CLONAL	3	FALSE	1	0.256717131899498	2		1073	862	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831357	72831358	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTG	rs34918837	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	51	518	1	ENST00000268489.5:c.5221_5223dup	p.Gln1741dup	p.Q1741dup	ENST00000268489	NM_006885.3	1741	-/CAA	9/10	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.256717131899498	2		519	294	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255142	16255143	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	rs764595221	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	216	573	8	ENST00000375759.3:c.2417_2418del	p.Arg806ThrfsTer14	p.R806Tfs*14	ENST00000375759	NM_015001.2	803	GAg/g	11/15	0.166476991409113	3	FACETS	1	0.964	1	1	0.993	1	CLONAL	3	FALSE	1	0.256717131899498	3		581	607	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482926	140482927	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs777474487	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	252	866	0	ENST00000288602.6:c.1208dup	p.Ala404CysfsTer9	p.A404Cfs*9	ENST00000288602	NM_004333.4	403	cct/ccCt	10/18	1	2	FACETS	0.901	0.847	0.956	1	0.996	1	CLONAL	3	FALSE	1	0.256717131899498	2		866	726	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591154	67591154	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	180	495	0	ENST00000274335.5:c.1745+2T>C		p.X582_splice	ENST00000274335		582			1	2	FACETS	0.978	0.91	1	1	0.994	1	CLONAL	3	FALSE	1	0.256717131899498	2		495	478	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002734	37002734	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	30	746	1	ENST00000358127.4:c.515C>T	p.Thr172Met	p.T172M	ENST00000358127	NM_001280556.1	172	aCg/aTg	5/10	0.256717131899498	1	FACETS	0.423	0.34	0.517	0.423	0.34	0.517	SUBCLONAL	1	FALSE	0	0.256717131899498	1		747	482	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444932	49444933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs767415197	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	183	665	0	ENST00000301067.7:c.2533dup	p.Arg845ProfsTer3	p.R845Pfs*3	ENST00000301067	NM_003482.3	845	cgg/cCgg	10/54	0.179469051801533	4	FACETS	0.971	0.901	1	1	0.99	1	CLONAL	3	FALSE	2	0.256717131899498	4		665	615	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131403	17131403	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs758385503	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	246	964	1	ENST00000285071.4:c.49del	p.Arg17AlafsTer38	p.R17Afs*38	ENST00000285071	NM_144997.5	17	Cgc/gc	4/14	0.166476991409113	3	FACETS	1	0.98	1	1	0.994	1	CLONAL	3	FALSE	1	0.256717131899498	3		965	660	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712000	89712000	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	205	401	0	ENST00000371953.3:c.618del	p.Phe206LeufsTer15	p.F206Lfs*15	ENST00000371953	NM_000314.4	206	ttC/tt	6/9	1	2	FACETS	0.881	0.827	0.936	1	0.995	1	CLONAL	4	FALSE	1	0.256717131899498	2		401	453	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224111	36224111	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	94	975	1	ENST00000222270.7:c.6666del	p.Thr2223ProfsTer38	p.T2223Pfs*38	ENST00000222270	NM_014727.1	2221	Ccc/cc	28/37	0.0991368606988909	3	FACETS	1	0.961	1			1	INDETERMINATE	1	FALSE	NA	0.256717131899498	3		976	701	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736511	85736511	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs387906351	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	194	597	15	ENST00000370580.1:c.136del	p.Ile46TyrfsTer24	p.I46Yfs*24	ENST00000370580	NM_003921.4	46	Ata/ta	2/3	1	2	FACETS	0.971	0.906	1	1	0.995	1	CLONAL	3	FALSE	1	0.256717131899498	2		612	519	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127791	64127791	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	244	868	1	ENST00000334205.4:c.284C>T	p.Ala95Val	p.A95V	ENST00000334205	NM_003942.2	95	gCg/gTg	3/17	1	2	FACETS	0.951	0.894	1	1	0.996	1	CLONAL	3	FALSE	1	0.256717131899498	2		869	666	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39321493	39321493	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	319	924	0	ENST00000373001.3:c.528del	p.Phe176LeufsTer14	p.F176Lfs*14	ENST00000373001	NM_022157.3	176	ttT/tt	3/7	1	2	FACETS	0.998	0.946	1	1	0.997	1	CLONAL	3	FALSE	1	0.256717131899498	2		924	830	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799269	45799269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553130580	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	143	581	0	ENST00000450313.1:c.164C>T	p.Ala55Val	p.A55V	ENST00000450313	NM_012222.2	55	gCa/gTa	3/16	1	2	FACETS	0.977	0.902	1	1	0.993	1	CLONAL	3	FALSE	1	0.256717131899498	2		581	380	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226566960	226566960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371066735	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	173	600	2	ENST00000366794.5:c.1628C>T	p.Ala543Val	p.A543V	ENST00000366794	NM_001618.3	543	gCg/gTg	12/23	0.256717131899498	7	FACETS	1	0.98	1	0.399	0.367	0.432	CLONAL	2	FALSE	1	0.256717131899498	7		602	925	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246093233	246093233	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	220	780	0	ENST00000388985.4:c.538T>C	p.Cys180Arg	p.C180R	ENST00000388985		180	Tgc/Cgc	6/12	0.256717131899498	7	FACETS	0.907	0.844	0.973	0.454	0.422	0.487	CLONAL	3	FALSE	1	0.256717131899498	7		780	1034	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333547	70333548	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	243	759	0	ENST00000373644.4:c.1457dup	p.Asn486LysfsTer15	p.N486Kfs*15	ENST00000373644	NM_030625.2	484	-/A	2/12	1	2	FACETS	1	0.944	1	1	0.996	1	CLONAL	3	FALSE	1	0.256717131899498	2		759	629	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309777	104309777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745958724	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	312	922	0	ENST00000369902.3:c.368G>A	p.Arg123His	p.R123H	ENST00000369902	NM_016169.3	123	cGt/cAt	3/12	1	2	FACETS	0.987	0.935	1	1	0.997	1	CLONAL	3	FALSE	1	0.256717131899498	2		922	821	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924617	94924617	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	284	977	0	ENST00000536441.1:c.293del	p.Arg98ProfsTer16	p.R98Pfs*16	ENST00000536441	NM_144665.3	98	cGc/cc	3/10	1	2	FACETS	0.944	0.892	0.998	1	0.996	1	CLONAL	3	FALSE	1	0.256717131899498	2		977	781	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434005	49434005	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	336	941	1	ENST00000301067.7:c.7548del	p.Asn2517IlefsTer26	p.N2517Ifs*26	ENST00000301067	NM_003482.3	2516	ccC/cc	31/54	0.179469051801533	4	FACETS	0.922	0.875	0.97	1	0.996	1	CLONAL	4	FALSE	2	0.256717131899498	4		942	892	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121888	2121888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779275341	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	329	1020	2	ENST00000219476.3:c.2050G>A	p.Val684Met	p.V684M	ENST00000219476	NM_000548.3	684	Gtg/Atg	19/42	1	2	FACETS	1	0.986	1	1	0.997	1	CLONAL	3	FALSE	1	0.256717131899498	2		1022	777	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72833973	72833973	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	234	832	0	ENST00000268489.5:c.3920del	p.Pro1307GlnfsTer38	p.P1307Qfs*38	ENST00000268489	NM_006885.3	1307	cCa/ca	8/10	1	2	FACETS	1	0.963	1	1	0.996	1	CLONAL	3	FALSE	1	0.256717131899498	2		832	588	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350203	89350203	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	299	1152	0	ENST00000301030.4:c.2747del	p.Asn916ThrfsTer61	p.N916Tfs*61	ENST00000301030	NM_001256183.1	916	aAc/ac	9/13	0.104476662672058	3	FACETS	0.968	0.914	1			1	INDETERMINATE	3	FALSE	NA	0.256717131899498	3		1152	905	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45423025	45423025	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	245	675	0	ENST00000262160.6:c.103G>A	p.Gly35Arg	p.G35R	ENST00000262160	NM_005901.5	35	Ggg/Agg	2/11	1	2	FACETS	1	0.951	1	1	0.996	1	CLONAL	3	FALSE	1	0.256717131899498	2		675	629	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226871	2226871	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	170	380	2	ENST00000398665.3:c.4351G>T	p.Ala1451Ser	p.A1451S	ENST00000398665	NM_032482.2	1451	Gca/Tca	27/28	1	2	FACETS	1	0.981	1	1	0.995	1	CLONAL	3	FALSE	1	0.256717131899498	2		382	385	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354033	15354033	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	151	511	0	ENST00000263377.2:c.2847G>T	p.Lys949Asn	p.K949N	ENST00000263377	NM_058243.2	949	aaG/aaT	14/20	1	2	FACETS	0.954	0.882	1	1	0.993	1	CLONAL	3	FALSE	1	0.256717131899498	2		511	411	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36217149	36217149	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	98	974	0	ENST00000222270.7:c.3898T>C	p.Cys1300Arg	p.C1300R	ENST00000222270	NM_014727.1	1300	Tgt/Cgt	14/37	0.0991368606988909	3	FACETS	1	0.957	1			1	INDETERMINATE	1	FALSE	NA	0.256717131899498	3		974	752	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223020	36223020	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	47	1030	0	ENST00000222270.7:c.5653del	p.Leu1885CysfsTer10	p.L1885Cfs*10	ENST00000222270	NM_014727.1	1883	ggC/gg	27/37	0.0991368606988909	3	FACETS	0.497	0.418	0.585			1	INDETERMINATE	1	FALSE	NA	0.256717131899498	3		1030	831	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45854922	45854922	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	99	980	1	ENST00000391945.4:c.2248C>A	p.Leu750Met	p.L750M	ENST00000391945	NM_000400.3	750	Ctg/Atg	23/23	0.250208575926148	3	FACETS	1	0.945	1			1	CLONAL	1	FALSE	NA	0.256717131899498	3		981	796	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145579	61145579	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	267	760	1	ENST00000295025.8:c.694del	p.Ser232HisfsTer9	p.S232Hfs*9	ENST00000295025	NM_002908.2	231	Ttt/tt	7/11	1	2	FACETS	0.906	0.854	0.96	1	0.996	1	CLONAL	3	FALSE	1	0.256717131899498	2		761	765	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750588	41750588	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	243	835	0	ENST00000226382.2:c.40T>C	p.Tyr14His	p.Y14H	ENST00000226382	NM_003924.3	14	Tac/Cac	1/3	1	2	FACETS	1	0.941	1	1	0.996	1	CLONAL	3	FALSE	1	0.256717131899498	2		835	631	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356254	66356254	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	240	882	0	ENST00000273854.3:c.1243C>A	p.Leu415Ile	p.L415I	ENST00000273854	NM_004439.5	415	Ctt/Att	5/18	1	2	FACETS	0.933	0.876	0.991	1	0.996	1	CLONAL	3	FALSE	1	0.256717131899498	2		882	668	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114316	143114316	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	190	718	2	ENST00000262992.4:c.1105C>T	p.Pro369Ser	p.P369S	ENST00000262992	NM_001101669.1	369	Cca/Tca	13/24	1	2	FACETS	1	0.969	1	1	0.995	1	CLONAL	3	FALSE	1	0.256717131899498	2		720	465	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503836	149503836	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	225	878	0	ENST00000261799.4:c.2000T>C	p.Leu667Pro	p.L667P	ENST00000261799	NM_002609.3	667	cTg/cCg	14/23	0.256717131899498	1	FACETS	0.906	0.851	0.962	1	0.995	1	CLONAL	3	FALSE	0	0.256717131899498	1		878	562	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805361	32805361	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	261	795	0	ENST00000374899.4:c.561T>G	p.His187Gln	p.H187Q	ENST00000374899	NM_018833.2	187	caT/caG	3/12	0.166476991409113	3	FACETS	1	0.951	1	1	0.994	1	CLONAL	3	FALSE	1	0.256717131899498	3		795	756	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836295	151836295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	64	864	0	ENST00000262189.6:c.14510C>T	p.Ala4837Val	p.A4837V	ENST00000262189	NM_170606.2	4837	gCg/gTg	57/59	0.250208575926148	3	FACETS	0.792	0.685	0.909			1	CLONAL	1	FALSE	NA	0.256717131899498	3		864	710	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418406	139418406	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1348892740	NA	P-0023286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	273	1000	2	ENST00000277541.6:c.166C>T	p.Arg56Ter	p.R56*	ENST00000277541	NM_017617.3	56	Cga/Tga	3/34	1	2	FACETS	1	0.953	1	1	0.996	1	CLONAL	3	FALSE	1	0.256717131899498	2		1002	702	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0023294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	55	794	1	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	0.995	0.851	1	0.995	0.851	1	CLONAL	1	TRUE	1	0.20102324544973	2		795	550	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243394	46243394	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	43	620	1	ENST00000334344.6:c.1747G>T	p.Val583Leu	p.V583L	ENST00000334344	NM_152641.2	583	Gtg/Ttg	14/21	0.20102324544973	1	FACETS	0.822	0.688	0.971	0.822	0.688	0.971	CLONAL	1	TRUE	0	0.20102324544973	1		621	468	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117406	115117409	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0023294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	53	799	0	ENST00000257566.3:c.765_768del	p.Arg256ProfsTer5	p.R256Pfs*5	ENST00000257566	NM_016569.3	255	gtAAGA/gt	4/8	1	2	FACETS	0.769	0.654	0.894	0.769	0.654	0.894	SUBCLONAL	1	TRUE	1	0.20102324544973	2		799	686	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867258	68867258	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0023294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	96	1021	0	ENST00000261769.5:c.2505T>A	p.Tyr835Ter	p.Y835*	ENST00000261769	NM_004360.3	835	taT/taA	16/16	0.20102324544973	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.20102324544973	1		1021	822	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270007	198270007	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	55	689	0	ENST00000335508.6:c.1429A>C	p.Lys477Gln	p.K477Q	ENST00000335508	NM_012433.2	477	Aaa/Caa	10/25	1	2	FACETS	0.854	0.73	0.99	0.854	0.73	0.99	CLONAL	1	TRUE	1	0.20102324544973	2		689	641	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202710	128202710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	91	1094	2	ENST00000341105.2:c.1010G>A	p.Arg337Gln	p.R337Q	ENST00000341105	NM_032638.4	337	cGa/cAa	4/6	1	2	FACETS	0.972	0.862	1	0.972	0.862	1	CLONAL	1	TRUE	1	0.20102324544973	2		1096	931	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0023295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	158	612	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.448914277935697	2		612	543	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028657	12028657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	146	780	1	ENST00000353533.5:c.860G>A	p.Arg287His	p.R287H	ENST00000353533	NM_003010.3	287	cGc/cAc	8/11	0.289643601517463	1	FACETS	0.788	0.731	0.846	1	0.99	1	SUBCLONAL	2	TRUE	0	0.448914277935697	1		781	320	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0023295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	371	989	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.406901523260409	3	FACETS	0.913	0.873	0.953			1	CLONAL	3	TRUE	NA	0.448914277935697	3		989	739	SUCCESS
APC	324	MSKCC	GRCh37	5	112174884	112174885	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs864622106	NA	P-0023295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	106	564	2	ENST00000257430.4:c.3596dup	p.Ser1200GlufsTer8	p.S1200Efs*8	ENST00000257430	NM_000038.5	1198	tca/tcAa	16/16	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.448914277935697	2		566	453	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117614	70117614	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	529	972	3	ENST00000245479.2:c.82G>T	p.Glu28Ter	p.E28*	ENST00000245479	NM_000346.3	28	Gag/Tag	1/3	0.452631981023475	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	4	TRUE	0	0.448914277935697	4		975	773	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950709	79950717	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGGCC	GCAGCGGCC	-	rs758960105	NA	P-0023295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	77	365	2	ENST00000265081.6:c.178_186del	p.Ala60_Ala62del	p.A60_A62del	ENST00000265081	NM_002439.4	55	GCAGCGGCC/-	1/24	0.232515182193655	4	FACETS	0.784	0.694	0.878	0.784	0.694	0.878	INDETERMINATE	2	TRUE	2	0.448914277935697	4		367	317	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693002	89693003	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	86	351	0	ENST00000371953.3:c.491dup	p.Val166SerfsTer14	p.V166Sfs*14	ENST00000371953	NM_000314.4	162	-/A	5/9	0.831956622429172	1	FACETS	0.844	0.775	0.911	0.844	0.775	0.911	CLONAL	1	TRUE	0	0.831956622429172	1		351	143	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378292	225378310	+	frameshift_variant	Frame_Shift_Del	DEL	ATAGACTGATCTTCCTTCG	ATAGACTGATCTTCCTTCG	-	novel	NA	P-0023301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	129	520	0	ENST00000264414.4:c.585_603del	p.Glu196LysfsTer24	p.E196Kfs*24	ENST00000264414	NM_003590.4	195	ctCGAAGGAAGATCAGTCTAT/ct	5/16	1	2	FACETS	0.818	0.75	0.889	0.818	0.75	0.889	CLONAL	1	TRUE	1	0.831956622429172	2		520	379	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977928	131977928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	197	565	1	ENST00000265335.6:c.3811G>A	p.Glu1271Lys	p.E1271K	ENST00000265335		1271	Gaa/Aaa	25/25	1	2	FACETS	0.968	0.906	1	0.968	0.906	1	CLONAL	1	TRUE	1	0.831956622429172	2		566	489	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508813	148508813	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0023301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	151	406	2	ENST00000320356.2:c.1852-1G>T		p.X618_splice	ENST00000320356	NM_004456.4	618			0.831956622429172	1	FACETS	0.914	0.861	0.965	0.914	0.861	0.965	CLONAL	1	TRUE	0	0.831956622429172	1		408	232	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0023370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	52	587	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.42193143050068	5	FACETS	0.861	0.734	0.999	0.215	0.183	0.25	CLONAL	1	FALSE	1	0.468657725718529	5		587	439	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031979	10031979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	107	600	2	ENST00000330684.3:c.844G>A	p.Asp282Asn	p.D282N	ENST00000330684	NM_001134407.1	282	Gat/Aat	3/13	0.468657725718529	5	FACETS	1	0.903	1			1	CLONAL	1	FALSE	NA	0.468657725718529	5		602	772	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99451967	99451967	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	26	463	0	ENST00000268035.6:c.1301G>A	p.Trp434Ter	p.W434*	ENST00000268035	NM_000875.3	434	tGg/tAg	6/21	0.468657725718529	3	FACETS	0.277	0.219	0.344	0.139	0.109	0.172	SUBCLONAL	1	FALSE	1	0.468657725718529	3		463	494	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198262832	198262832	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	41	372	0	ENST00000335508.6:c.3143A>G	p.Glu1048Gly	p.E1048G	ENST00000335508	NM_012433.2	1048	gAa/gGa	22/25	0.46244079973027	3	FACETS	0.9	0.756	1	0.45	0.378	0.529	CLONAL	1	FALSE	1	0.468657725718529	3		372	240	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743367	162743367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	65	380	0	ENST00000367921.3:c.1837G>A	p.Asp613Asn	p.D613N	ENST00000367921	NM_006182.2	613	Gat/Aat	14/18	0.468657725718529	6	FACETS	1	0.878	1	0.253	0.219	0.289	CLONAL	1	FALSE	2	0.468657725718529	6		380	531	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99440029	99440029	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	79	488	0	ENST00000268035.6:c.997G>A	p.Glu333Lys	p.E333K	ENST00000268035	NM_000875.3	333	Gag/Aag	4/21	0.468657725718529	3	FACETS	0.683	0.601	0.771	0.342	0.3	0.386	SUBCLONAL	1	FALSE	1	0.468657725718529	3		488	609	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541783	187541783	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs896060735	NA	P-0023370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	27	473	2	ENST00000441802.2:c.5957C>T	p.Ala1986Val	p.A1986V	ENST00000441802	NM_005245.3	1986	gCg/gTg	10/27	0.17312759102147	2	FACETS	0.317	0.252	0.391	0.158	0.126	0.196	INDETERMINATE	1	FALSE	0	0.468657725718529	2		475	364	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184818	32184818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	93	502	0	ENST00000375023.3:c.1765G>A	p.Glu589Lys	p.E589K	ENST00000375023	NM_004557.3	589	Gag/Aag	11/30	0.468657725718529	3	FACETS	1	0.926	1	0.349	0.311	0.389	CLONAL	1	FALSE	0	0.468657725718529	3		502	468	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139440237	139440237	+	start_lost	Translation_Start_Site	SNP	A	A	C	novel	NA	P-0023370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	32	69	0	ENST00000277541.6:c.2T>G	p.Met1?	p.M1?	ENST00000277541	NM_017617.3	1	aTg/aGg	1/34	0.468657725718529	3	FACETS	1	0.916	1	0.759	0.642	0.88	CLONAL	2	FALSE	0	0.468657725718529	3		69	74	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0023390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	13	835	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.590436770288406	4	FACETS	0.143	0.101	0.195	0.072	0.05	0.098	SUBCLONAL	1	TRUE	2	0.48	4		835	559	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0023410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	109	465	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.245816093738557	4	FACETS	0.988	0.89	1	0.988	0.89	1	CLONAL	2	TRUE	2	0.245816093738557	4		465	559	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264398	16264398	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	48	911	0	ENST00000375759.3:c.10601C>T	p.Ala3534Val	p.A3534V	ENST00000375759	NM_015001.2	3534	gCc/gTc	13/15	1	2	FACETS	0.776	0.656	0.908	0.776	0.656	0.908	CLONAL	1	TRUE	1	0.245816093738557	2		911	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577521	7577523	+	inframe_deletion	In_Frame_Del	DEL	TGG	TGG	-	novel	NA	P-0023410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	123	870	1	ENST00000269305.4:c.758_760del	p.Thr253del	p.T253del	ENST00000269305	NM_001126112.2	253	aCCAtc/atc	7/11	0.221200742414686	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.245816093738557	2		871	446	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821446	32821446	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	63	871	0	ENST00000354258.4:c.148C>A	p.Pro50Thr	p.P50T	ENST00000354258	NM_000593.5	50	Ccc/Acc	1/11	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.245816093738557	2		871	511	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0023528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	304	294	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.663799922935771	7	FACETS	0.931	0.896	0.966	1	0.992	1	CLONAL	6	TRUE	2	0.663799922935771	7		294	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579418	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	GAG	GAG	CA	novel	NA	P-0023528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	134	1039	3	ENST00000269305.4:c.267_269delinsTG	p.Ser90AlafsTer33	p.S90Afs*33	ENST00000269305	NM_001126112.2	89	ccCTCc/ccTGc	4/11	0.663799922935771	3	FACETS	0.948	0.895	0.999	0.948	0.895	0.999	CLONAL	3	TRUE	0	0.663799922935771	3		1042	189	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543656	9543656	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	21	678	0	ENST00000353224.5:c.1498del	p.Asp500IlefsTer27	p.D500Ifs*27	ENST00000353224	NM_177990.2	500	Gat/at	6/10	0.328154721561034	5	FACETS	0.896	0.727	1	0.896	0.727	1	INDETERMINATE	3	TRUE	2	0.663799922935771	5		678	47	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180497	56180498	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0023528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	46	428	0	ENST00000399503.3:c.3827_3828del	p.Tyr1276CysfsTer7	p.Y1276Cfs*7	ENST00000399503	NM_005921.1	1276	TAt/t	16/20	0.328154721561034	5	FACETS	1	0.953	1	0.831	0.722	0.943	INDETERMINATE	2	TRUE	2	0.663799922935771	5		428	111	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184095	56184095	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	82	705	0	ENST00000399503.3:c.4300A>C	p.Ser1434Arg	p.S1434R	ENST00000399503	NM_005921.1	1434	Agt/Cgt	19/20	0.328154721561034	5	FACETS	1	0.914	1	0.682	0.611	0.756	INDETERMINATE	2	TRUE	2	0.663799922935771	5		705	241	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884462	151884463	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0023528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	75	684	0	ENST00000262189.6:c.4892_4893del	p.Asn1631SerfsTer7	p.N1631Sfs*7	ENST00000262189	NM_170606.2	1631	aAT/a	33/59	0.269208030861089	3	FACETS	1	0.976	1	1	0.976	1	INDETERMINATE	3	TRUE	0	0.663799922935771	3		684	91	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965670	90965670	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	82	678	1	ENST00000265433.3:c.1647A>T	p.Lys549Asn	p.K549N	ENST00000265433	NM_002485.4	549	aaA/aaT	11/16	0.663799922935771	8	FACETS	0.999	0.887	1	0.333	0.295	0.373	CLONAL	2	TRUE	2	0.663799922935771	8		679	370	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0023748-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	24	294	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.599082572454428	4	FACETS	0.872	0.723	1	0.872	0.723	1	CLONAL	3	TRUE	1	0.599082572454428	4		294	49	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0023748-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	25	587	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.599082572454428	4	FACETS	0.981	0.803	1	0.654	0.535	0.78	CLONAL	2	TRUE	1	0.599082572454428	4		587	68	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832398	72832398	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023748-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	67	393	0	ENST00000268489.5:c.4183G>C	p.Asp1395His	p.D1395H	ENST00000268489	NM_006885.3	1395	Gat/Cat	9/10	0.501324929353572	3	FACETS	0.995	0.873	1	0.332	0.291	0.375	CLONAL	1	TRUE	0	0.599082572454428	3		393	292	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577596	7577597	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0023748-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	101	472	0	ENST00000269305.4:c.683_684dup	p.Cys229ThrfsTer19	p.C229Tfs*19	ENST00000269305	NM_001126112.2	228	-/AC	7/11	0.458089333320922	2	FACETS	1	0.979	1	0.648	0.589	0.709	CLONAL	1	TRUE	0	0.599082572454428	2		472	260	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526700	106526700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023748-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	22	345	2	ENST00000359195.3:c.2993C>T	p.Ser998Phe	p.S998F	ENST00000359195	NM_002649.2	998	tCt/tTt	10/11	1	2	FACETS	0.854	0.678	1	0.854	0.678	1	CLONAL	1	TRUE	1	0.599082572454428	2		347	86	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0023762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	36	450	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	0.906	0.755	1	0.906	0.755	1	CLONAL	1	FALSE	1	0.493872186181213	2		450	161	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977949	134977949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56186270	NA	P-0023762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	19	381	0	ENST00000398015.3:c.2942C>T	p.Thr981Met	p.T981M	ENST00000398015	NM_004441.4	981	aCg/aTg	16/16	1	2	FACETS	0.874	0.7	1	1	0.939	1	CLONAL	2	FALSE	1	0.493872186181213	2		381	44	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043904	180043904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56082504	NA	P-0023762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	11	430	1	ENST00000261937.6:c.3092G>A	p.Arg1031Gln	p.R1031Q	ENST00000261937	NM_182925.4	1031	cGa/cAa	22/30	0.329806108285193	1	FACETS	0.645	0.458	0.863	0.645	0.458	0.863	SUBCLONAL	1	FALSE	0	0.493872186181213	1		431	52	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776660	9776660	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	21	477	0	ENST00000377346.4:c.763C>G	p.Pro255Ala	p.P255A	ENST00000377346	NM_005026.3	255	Ccg/Gcg	6/24	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	FALSE	1	0.493872186181213	2		477	58	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023201	27023201	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	23	119	0	ENST00000324856.7:c.307del	p.Ser103ArgfsTer11	p.S103Rfs*11	ENST00000324856	NM_006015.4	103	Tcg/cg	1/20	1	2	FACETS	0.855	0.678	1	0.855	0.678	1	CLONAL	1	FALSE	1	0.493872186181213	2		119	109	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928080	178928080	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	10	389	0	ENST00000263967.3:c.1358A>T	p.Glu453Val	p.E453V	ENST00000263967	NM_006218.2	453	gAa/gTa	8/21	1	2	FACETS	0.664	0.459	0.91	0.664	0.459	0.91	SUBCLONAL	1	FALSE	1	0.493872186181213	2		389	61	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	117	646	4	ENST00000347630.2:c.397T>C	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	Ttc/Ctc	6/11	1	2	FACETS	0.786	0.713	0.863	0.786	0.713	0.863	SUBCLONAL	1	TRUE	1	0.62	2		650	480	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274121	10274121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	63	612	4	ENST00000330684.3:c.148G>A	p.Glu50Lys	p.E50K	ENST00000330684	NM_001134407.1	50	Gaa/Aaa	2/13	1	2	FACETS	0.987	0.867	1	0.987	0.867	1	CLONAL	1	TRUE	1	0.62	2		616	206	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128676	64128676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	33	614	2	ENST00000334205.4:c.533C>T	p.Thr178Met	p.T178M	ENST00000334205	NM_003942.2	178	aCg/aTg	5/17	1	2	FACETS	0.263	0.214	0.319	0.263	0.214	0.319	SUBCLONAL	1	TRUE	1	0.62	2		616	404	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061004	38061005	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0023864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	61	373	0	ENST00000250448.2:c.984dup	p.Ala329ArgfsTer86	p.A329Rfs*86	ENST00000250448	NM_004496.3	328	-/C	2/2	1	2	FACETS	0.965	0.845	1	0.965	0.845	1	CLONAL	1	TRUE	1	0.62	2		373	204	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0023929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	86	767	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.461568402878462	1	FACETS	0.814	0.726	0.907	0.814	0.726	0.907	CLONAL	1	TRUE	0	0.461568402878462	1		770	352	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293871	1293871	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756954938	NA	P-0023929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	123	770	3	ENST00000310581.5:c.1130G>A	p.Arg377His	p.R377H	ENST00000310581	NM_198253.2	377	cGc/cAc	2/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.461568402878462	2		773	478	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487277	56487277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035001455	NA	P-0023929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	109	653	1	ENST00000267101.3:c.1423C>T	p.Arg475Trp	p.R475W	ENST00000267101	NM_001982.3	475	Cgg/Tgg	12/28	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.461568402878462	2		654	414	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134251	11134251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1218643327	NA	P-0023929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	91	630	6	ENST00000358026.2:c.2917C>T	p.Arg973Trp	p.R973W	ENST00000358026	NM_001128849.1	973	Cgg/Tgg	20/36	1	2	FACETS	0.964	0.861	1	0.964	0.861	1	CLONAL	1	TRUE	1	0.461568402878462	2		636	409	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775601	39775601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146705250	NA	P-0023929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	53	476	1	ENST00000288319.7:c.419G>A	p.Arg140Gln	p.R140Q	ENST00000288319	NM_182918.3	140	cGg/cAg	4/10	1	2	FACETS	0.748	0.642	0.863	0.748	0.642	0.863	SUBCLONAL	1	TRUE	1	0.461568402878462	2		477	307	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63760024	63760024	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	80	412	5	ENST00000279873.7:c.677G>T	p.Arg226Leu	p.R226L	ENST00000279873	NM_032199.2	226	cGg/cTg	4/10	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.461568402878462	2		417	338	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478815	56478815	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	112	773	3	ENST00000267101.3:c.271A>T	p.Met91Leu	p.M91L	ENST00000267101	NM_001982.3	91	Atg/Ttg	3/28	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.461568402878462	2		776	482	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019389	31019389	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	112	537	4	ENST00000375687.4:c.886G>T	p.Gly296Trp	p.G296W	ENST00000375687	NM_015338.5	296	Ggg/Tgg	10/13	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.461568402878462	2		541	424	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713733	30713733	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553630235	NA	P-0023929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	99	506	2	ENST00000295754.5:c.1058C>T	p.Ser353Phe	p.S353F	ENST00000295754	NM_003242.5	353	tCc/tTc	4/7	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.461568402878462	2		508	395	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067431	37067431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	84	547	2	ENST00000231790.2:c.1342G>A	p.Glu448Lys	p.E448K	ENST00000231790	NM_000249.3	448	Gag/Aag	12/19	1	2	FACETS	0.936	0.832	1	0.936	0.832	1	CLONAL	1	TRUE	1	0.461568402878462	2		549	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578400	7578400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751477326	NA	P-0023930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	166	715	1	ENST00000269305.4:c.530C>T	p.Pro177Leu	p.P177L	ENST00000269305	NM_001126112.2	177	cCc/cTc	5/11	0.476815250362543	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.476815250362543	1		716	483	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257227	16257227	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0023930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	390	796	0	ENST00000375759.3:c.4492A>T	p.Lys1498Ter	p.K1498*	ENST00000375759	NM_015001.2	1498	Aag/Tag	11/15	0.386659253946627	3	FACETS	1	0.993	1	0.805	0.769	0.841	CLONAL	2	TRUE	0	0.476815250362543	3		796	839	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562207	21562207	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	29	972	0	ENST00000382592.4:c.1712A>G	p.Lys571Arg	p.K571R	ENST00000382592	NM_014572.2	571	aAg/aGg	4/8	1	2	FACETS	0.219	0.175	0.269	0.219	0.175	0.269	SUBCLONAL	1	TRUE	1	0.476815250362543	2		972	555	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10284550	10284550	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	164	723	1	ENST00000340748.4:c.632A>T	p.Glu211Val	p.E211V	ENST00000340748		211	gAa/gTa	7/40	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.476815250362543	2		724	656	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799131	42799131	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	48	823	0	ENST00000575354.2:c.4620del	p.Thr1541LeufsTer79	p.T1541Lfs*79	ENST00000575354	NM_015125.3	1539	Ccc/cc	20/20	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	FALSE	1	0.330091391698473	2		823	263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	35	447	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.768	0.633	0.919	0.768	0.633	0.919	CLONAL	1	FALSE	1	0.330091391698473	2		447	276	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	13	770	5	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.324	0.231	0.438	0.324	0.231	0.438	SUBCLONAL	1	FALSE	1	0.330091391698473	2		775	243	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657066	47657066	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	17	269	0	ENST00000233146.2:c.1262T>G	p.Leu421Arg	p.L421R	ENST00000233146	NM_000251.2	421	cTg/cGg	7/16	1	2	FACETS	0.512	0.383	0.664	0.512	0.383	0.664	SUBCLONAL	1	FALSE	1	0.330091391698473	2		269	201	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	22	725	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	1	2	FACETS	0.511	0.396	0.643	0.511	0.396	0.643	SUBCLONAL	1	FALSE	1	0.330091391698473	2		725	261	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	15	975	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	NA	2	FACETS	0.371	0.271	0.491			1	INDETERMINATE	1	FALSE	NA	0.330091391698473	2		975	245	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289107	33289107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760147301	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	22	699	2	ENST00000374542.5:c.445G>A	p.Ala149Thr	p.A149T	ENST00000374542	NM_001141970.1	149	Gcc/Acc	3/8	1	2	FACETS	0.444	0.344	0.56	0.444	0.344	0.56	SUBCLONAL	1	FALSE	1	0.330091391698473	2		701	300	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729687	41729687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	12	540	1	ENST00000242208.4:c.842C>T	p.Ala281Val	p.A281V	ENST00000242208	NM_002192.2	281	gCa/gTa	3/3	1	2	FACETS	0.326	0.229	0.446	0.326	0.229	0.446	SUBCLONAL	1	FALSE	1	0.330091391698473	2		541	223	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034435	47034435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	14	344	2	ENST00000377604.3:c.520G>A	p.Ala174Thr	p.A174T	ENST00000377604	NM_001204468.1	174	Gcc/Acc	6/24	1	1	FACETS	0.463	0.336	0.615	0.463	0.336	0.615	SUBCLONAL	1	FALSE	0	0.330091391698473	1		346	153	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372205	55372205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs904970570	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	10	437	0	ENST00000297316.4:c.895G>A	p.Ala299Thr	p.A299T	ENST00000297316	NM_022454.3	299	Gcg/Acg	2/2	1	2	FACETS	0.376	0.255	0.528	0.376	0.255	0.528	SUBCLONAL	1	FALSE	1	0.330091391698473	2		437	161	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138614	11138614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	38	519	0	ENST00000358026.2:c.3370C>T	p.Leu1124Phe	p.L1124F	ENST00000358026	NM_001128849.1	1124	Ctc/Ttc	24/36	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	FALSE	1	0.330091391698473	2		519	223	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	rs267608078	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	16	526	0	ENST00000234420.5:c.3260_3261dup	p.Phe1088ProfsTer3	p.F1088Pfs*3	ENST00000234420	NM_000179.2	1085	acc/aCCcc	5/10	1	2	FACETS	0.383	0.283	0.503	0.383	0.283	0.503	SUBCLONAL	1	FALSE	1	0.330091391698473	2		526	253	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40743886	40743886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434593	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	16	590	1	ENST00000392038.2:c.821G>A	p.Arg274His	p.R274H	ENST00000392038	NM_001626.4	274	cGc/cAc	9/14	1	2	FACETS	0.399	0.295	0.523	0.399	0.295	0.523	SUBCLONAL	1	FALSE	1	0.330091391698473	2		591	243	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189867	11189867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	32	539	1	ENST00000361445.4:c.5642C>T	p.Thr1881Met	p.T1881M	ENST00000361445	NM_004958.3	1881	aCg/aTg	40/58	1	2	FACETS	0.71	0.579	0.857	0.71	0.579	0.857	SUBCLONAL	1	FALSE	1	0.330091391698473	2		540	273	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571907	64571907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	36	1048	0	ENST00000312049.6:c.1732C>T	p.Gln578Ter	p.Q578*	ENST00000312049	NM_130799.2	578	Caa/Taa	10/10	1	2	FACETS	0.73	0.602	0.871	0.73	0.602	0.871	SUBCLONAL	1	FALSE	1	0.330091391698473	2		1048	299	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991059	41991059	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	16	322	0	ENST00000219905.7:c.2014-2A>G		p.X672_splice	ENST00000219905	NM_001164273.1	672			1	2	FACETS	0.455	0.337	0.596	0.455	0.337	0.596	SUBCLONAL	1	FALSE	1	0.330091391698473	2		322	213	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950271	15950271	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	40	691	0	ENST00000268712.3:c.6673G>C	p.Asp2225His	p.D2225H	ENST00000268712	NM_006311.3	2225	Gat/Cat	42/46	1	2	FACETS	0.885	0.739	1	0.885	0.739	1	CLONAL	1	FALSE	1	0.330091391698473	2		691	274	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508827	31508827	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	17	622	0	ENST00000344624.3:c.1488C>G	p.Ser496Arg	p.S496R	ENST00000344624		496	agC/agG	7/33	1	2	FACETS	0.363	0.27	0.472	0.363	0.27	0.472	SUBCLONAL	1	FALSE	1	0.330091391698473	2		622	284	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753013	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	10	384	0	ENST00000274289.3:c.1003_1004del	p.Leu335AlafsTer11	p.L335Afs*11	ENST00000274289	NM_006622.3	335	TTg/g	7/14	0.330091391698473	3	FACETS	0.355	0.24	0.499	0.177	0.12	0.25	SUBCLONAL	1	FALSE	1	0.330091391698473	3		384	199	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593301	67593301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	10	330	0	ENST00000274335.5:c.2047G>A	p.Glu683Lys	p.E683K	ENST00000274335		683	Gag/Aag	15/15	0.330091391698473	3	FACETS	0.37	0.25	0.519	0.185	0.125	0.26	SUBCLONAL	1	FALSE	1	0.330091391698473	3		330	191	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166736	32166736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867581638	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	37	873	1	ENST00000375023.3:c.4502G>A	p.Arg1501Gln	p.R1501Q	ENST00000375023	NM_004557.3	1501	cGg/cAg	24/30	1	2	FACETS	0.833	0.691	0.991	0.833	0.691	0.991	CLONAL	1	FALSE	1	0.330091391698473	2		874	269	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715470	117715470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	25	388	0	ENST00000368508.3:c.1019C>T	p.Ser340Phe	p.S340F	ENST00000368508	NM_002944.2	340	tCt/tTt	10/43	1	2	FACETS	0.682	0.54	0.844	0.682	0.54	0.844	SUBCLONAL	1	FALSE	1	0.330091391698473	2		388	222	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434247	49434247	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	18	1121	1	ENST00000301067.7:c.7306del	p.Cys2436AlafsTer49	p.C2436Afs*49	ENST00000301067	NM_003482.3	2436	Tgc/gc	31/54	1	2	FACETS	0.383	0.288	0.495	0.383	0.288	0.495	SUBCLONAL	1	FALSE	1	0.330091391698473	2		1122	285	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352988	70352988	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	12	309	1	ENST00000374080.3:c.4543C>T	p.Arg1515Ter	p.R1515*	ENST00000374080		1515	Cga/Tga	33/45	1	1	FACETS	0.502	0.355	0.679	0.502	0.355	0.679	SUBCLONAL	1	FALSE	0	0.330091391698473	1		310	121	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800903	120800903	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748469666	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	24	717	2	ENST00000257552.2:c.345del	p.Leu116CysfsTer3	p.L116Cfs*3	ENST00000257552	NM_002442.3	115	ggG/gg	6/15	1	2	FACETS	0.564	0.443	0.702	0.564	0.443	0.702	SUBCLONAL	1	FALSE	1	0.330091391698473	2		719	258	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372513	118372513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782124549	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	12	563	0	ENST00000534358.1:c.6446G>A	p.Arg2149Gln	p.R2149Q	ENST00000534358	NM_005933.3	2149	cGa/cAa	26/36	1	2	FACETS	0.309	0.217	0.423	0.309	0.217	0.423	SUBCLONAL	1	FALSE	1	0.330091391698473	2		563	235	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2093613	2093613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	25	831	8	ENST00000219066.1:c.664G>A	p.Ala222Thr	p.A222T	ENST00000219066	NM_002528.5	222	Gca/Aca	4/6	1	2	FACETS	0.547	0.432	0.678	0.547	0.432	0.678	SUBCLONAL	1	FALSE	1	0.330091391698473	2		839	277	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821944	72821944	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	11	589	0	ENST00000268489.5:c.10231G>T	p.Asp3411Tyr	p.D3411Y	ENST00000268489	NM_006885.3	3411	Gac/Tac	10/10	1	2	FACETS	0.328	0.227	0.455	0.328	0.227	0.455	SUBCLONAL	1	FALSE	1	0.330091391698473	2		589	203	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353767	40353767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760771231	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	15	571	0	ENST00000293328.3:c.2353G>A	p.Ala785Thr	p.A785T	ENST00000293328	NM_012448.3	785	Gca/Aca	19/19	1	2	FACETS	0.382	0.279	0.505	0.382	0.279	0.505	SUBCLONAL	1	FALSE	1	0.330091391698473	2		571	238	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097089	11097089	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	14	851	5	ENST00000358026.2:c.580C>T	p.Gln194Ter	p.Q194*	ENST00000358026	NM_001128849.1	194	Cag/Tag	4/36	1	2	FACETS	0.352	0.254	0.47	0.352	0.254	0.47	SUBCLONAL	1	FALSE	1	0.330091391698473	2		856	241	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123752	11123752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568471266	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	16	600	0	ENST00000358026.2:c.2402G>A	p.Arg801His	p.R801H	ENST00000358026	NM_001128849.1	801	cGc/cAc	16/36	1	2	FACETS	0.48	0.355	0.628	0.48	0.355	0.628	SUBCLONAL	1	FALSE	1	0.330091391698473	2		600	202	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211774	36211774	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	22	869	0	ENST00000222270.7:c.1525G>A	p.Asp509Asn	p.D509N	ENST00000222270	NM_014727.1	509	Gac/Aac	3/37	1	2	FACETS	0.481	0.373	0.606	0.481	0.373	0.606	SUBCLONAL	1	FALSE	1	0.330091391698473	2		869	277	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662038	227662038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775717471	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	29	655	0	ENST00000305123.5:c.1417C>T	p.Pro473Ser	p.P473S	ENST00000305123	NM_005544.2	473	Ccc/Tcc	1/2	1	2	FACETS	0.706	0.569	0.86	0.706	0.569	0.86	SUBCLONAL	1	FALSE	1	0.330091391698473	2		655	249	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022331	31022331	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746515791	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	17	385	2	ENST00000375687.4:c.1816C>T	p.Arg606Trp	p.R606W	ENST00000375687	NM_015338.5	606	Cgg/Tgg	13/13	1	2	FACETS	0.542	0.406	0.702	0.542	0.406	0.702	SUBCLONAL	1	FALSE	1	0.330091391698473	2		387	190	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053520	37053520	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750085	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	14	594	0	ENST00000231790.2:c.607G>A	p.Asp203Asn	p.D203N	ENST00000231790	NM_000249.3	203	Gat/Aat	8/19	1	2	FACETS	0.352	0.254	0.47	0.352	0.254	0.47	SUBCLONAL	1	FALSE	1	0.330091391698473	2		594	241	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588122	67588122	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	12	344	0	ENST00000274335.5:c.952G>A	p.Ala318Thr	p.A318T	ENST00000274335		318	Gcc/Acc	7/15	0.330091391698473	3	FACETS	0.373	0.262	0.51	0.187	0.131	0.255	SUBCLONAL	1	FALSE	1	0.330091391698473	3		344	227	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525584	137525584	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	15	588	0	ENST00000367739.4:c.431A>G	p.Asp144Gly	p.D144G	ENST00000367739	NM_000416.2	144	gAc/gGc	4/7	1	2	FACETS	0.33	0.241	0.438	0.33	0.241	0.438	SUBCLONAL	1	FALSE	1	0.330091391698473	2		588	275	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391869	139391869	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780963597	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	11	861	1	ENST00000277541.6:c.6322G>A	p.Asp2108Asn	p.D2108N	ENST00000277541	NM_017617.3	2108	Gac/Aac	34/34	1	2	FACETS	0.314	0.217	0.435	0.314	0.217	0.435	SUBCLONAL	1	FALSE	1	0.330091391698473	2		862	212	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225148	53225148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	11	380	1	ENST00000375401.3:c.3070G>A	p.Glu1024Lys	p.E1024K	ENST00000375401	NM_004187.3	1024	Gag/Aag	20/26	1	1	FACETS	0.354	0.245	0.489	0.354	0.245	0.489	SUBCLONAL	1	FALSE	0	0.330091391698473	1		381	157	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617586	100617587	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	11	344	0	ENST00000308731.7:c.482dup	p.Asn161LysfsTer33	p.N161Kfs*33	ENST00000308731	NM_000061.2	161	aat/aaAt	6/19	1	1	FACETS	0.384	0.266	0.529	0.384	0.266	0.529	SUBCLONAL	1	FALSE	0	0.330091391698473	1		344	145	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0025859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	123	310	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.581194304243412	4	FACETS	0.95	0.872	1	0.633	0.581	0.686	CLONAL	2	TRUE	1	0.721534104557233	4		310	309	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	446	745	0	ENST00000269305.4:c.383del	p.Pro128LeufsTer42	p.P128Lfs*42	ENST00000269305	NM_001126112.2	128	cCt/ct	5/11	NA	2	FACETS	0.994	0.963	1			1	INDETERMINATE	2	TRUE	NA	0.721534104557233	2		745	622	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149238613	149238613	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1483683545	NA	P-0025859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	344	477	0	ENST00000360632.3:c.1182G>T	p.Glu394Asp	p.E394D	ENST00000360632	NM_015472.4	394	gaG/gaT	7/7	0.581194304243412	4	FACETS	0.958	0.919	0.997	0.958	0.919	0.997	CLONAL	3	TRUE	1	0.721534104557233	4		477	571	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346025	73346025	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025928-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	56	331	0	ENST00000377767.4:c.1513C>T	p.His505Tyr	p.H505Y	ENST00000377767	NM_014953.3	505	Cat/Tat	11/21	0.252058753047069	3	FACETS	0.51	0.436	0.591	0.255	0.218	0.296	INDETERMINATE	1	TRUE	1	0.425313516220127	3		331	626	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248572	10248572	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025928-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	220	629	0	ENST00000340748.4:c.4181C>G	p.Ser1394Cys	p.S1394C	ENST00000340748		1394	tCc/tGc	35/40	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.425313516220127	2		629	1009	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161850	47161850	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0025928-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	222	446	0	ENST00000409792.3:c.4276A>T	p.Lys1426Ter	p.K1426*	ENST00000409792	NM_014159.6	1426	Aaa/Taa	3/21	0.425313516220127	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.425313516220127	1		446	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0026021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	193	767	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.619773844608155	1	FACETS	0.909	0.849	0.969	0.909	0.849	0.969	CLONAL	1	TRUE	0	0.619773844608155	1		770	473	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007870	45007871	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0026021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	89	446	0	ENST00000558401.1:c.320dup	p.Leu107PhefsTer8	p.L107Ffs*8	ENST00000558401	NM_004048.2	106	act/acTt	2/4	0.619773844608155	1	FACETS	0.656	0.588	0.727	0.656	0.588	0.727	SUBCLONAL	1	TRUE	0	0.619773844608155	1		446	302	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37666014	37666014	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	124	346	0	ENST00000447079.4:c.2666+1del		p.S889fs	ENST00000447079	NM_015083.1	889	aGt/at	7/14	0.619773844608155	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.619773844608155	1		346	260	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106543539	106543631	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GACCCCTAATAGGTGAAATCTACACCAATGACACAGTTCCTAAGAACGCCAACAGGAAATATTTTTGGAGGGTAAGTAAGGGAAATTTCTTCA	GACCCCTAATAGGTGAAATCTACACCAATGACACAGTTCCTAAGAACGCCAACAGGAAATATTTTTGGAGGGTAAGTAAGGGAAATTTCTTCA	-	novel	NA	P-0026021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	52	287	0	ENST00000369096.4:c.346_411+27del		p.X116_splice	ENST00000369096	NM_001198.3	116		3/7	0.113931304069555	5	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.619773844608155	5		287	241	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0026526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	15	835	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.211645984044473	3	FACETS	1	0.844	1	1	0.844	1	CLONAL	2	TRUE	1	0.211645984044473	3		835	66	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0026526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	12	735	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.211645984044473	3	FACETS	0.883	0.632	1	0.883	0.632	1	CLONAL	2	TRUE	1	0.211645984044473	3		735	71	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95584011	95584011	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	10	400	0	ENST00000393063.1:c.1457A>G	p.Lys486Arg	p.K486R	ENST00000393063	NM_030621.3	486	aAg/aGg	10/28	0.196241906536729	5	FACETS	1	0.711	1	0.349	0.237	0.487	CLONAL	1	TRUE	2	0.211645984044473	5		400	119	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843501	3843501	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	22	637	1	ENST00000262367.5:c.1102C>T	p.Gln368Ter	p.Q368*	ENST00000262367	NM_004380.2	368	Cag/Tag	4/31	1	2	FACETS	1	0.887	1	1	0.953	1	CLONAL	2	TRUE	1	0.211645984044473	2		638	87	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219748	36219748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	17	1012	0	ENST00000222270.7:c.4645G>A	p.Glu1549Lys	p.E1549K	ENST00000222270	NM_014727.1	1549	Gag/Aag	20/37	0.142118270797791	0	FACETS	0.782	0.596	0.992			1	CLONAL	2	TRUE	0	0.211645984044473	0		1012	81	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155267	185155267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	18	518	0	ENST00000265026.3:c.508G>A	p.Glu170Lys	p.E170K	ENST00000265026	NM_004721.4	170	Gag/Aag	3/14	0.211645984044473	5	FACETS	0.842	0.641	1	0.562	0.427	0.717	CLONAL	2	TRUE	2	0.211645984044473	5		518	133	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0026589-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	49	283	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.873	0.742	1	0.873	0.742	1	CLONAL	1	TRUE	1	0.293855566329152	2		283	382	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917634	94917635	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0026589-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	114	598	0	ENST00000536441.1:c.886_887del	p.Glu296LysfsTer19	p.E296Kfs*19	ENST00000536441	NM_144665.3	296	GAa/a	6/10	0.281575694271382	3	FACETS	1	0.979	1	0.661	0.596	0.73	CLONAL	1	TRUE	1	0.293855566329152	3		598	673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577530	7577530	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026769-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	64	553	0	ENST00000269305.4:c.751A>T	p.Ile251Phe	p.I251F	ENST00000269305	NM_001126112.2	251	Atc/Ttc	7/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.13	2		553	753	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027230-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	640	503	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.629924219291704	2	FACETS	0.908	0.881	0.935	0.908	0.881	0.935	CLONAL	2	FALSE	0	0.678401286477158	2		503	1039	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913343	NA	P-0027230-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	932	709	1	ENST00000269305.4:c.817C>A	p.Arg273Ser	p.R273S	ENST00000269305	NM_001126112.2	273	Cgt/Agt	8/11	NA	2	FACETS		NA	1			1	INDETERMINATE	3	FALSE	NA	0.678401286477158	2		710	1036	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092780	27092780	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027230-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	380	656	0	ENST00000324856.7:c.2802del	p.Asn935IlefsTer6	p.N935Ifs*6	ENST00000324856	NM_006015.4	934	aTt/at	9/20	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	FALSE	1	0.678401286477158	2		656	911	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	12	503	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		503	508	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	22	313	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.81	0.626	1	0.81	0.626	1	CLONAL	1	TRUE	1	0.13	2		315	418	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0028777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	69	359	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.88	0.767	1	1	0.978	1	CLONAL	2	TRUE	1	0.13	2		359	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0028777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	34	477	0	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	1	2	FACETS	0.819	0.667	0.99	0.819	0.667	0.99	CLONAL	1	TRUE	1	0.13	2		477	639	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281802	46281802	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs769002244	NA	P-0028777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	38	454	0	ENST00000371998.3:c.4249A>G	p.Met1417Val	p.M1417V	ENST00000371998		1417	Atg/Gtg	22/23	1	2	FACETS	0.906	0.748	1	0.906	0.748	1	CLONAL	1	TRUE	1	0.13	2		454	645	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573052	41573052	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	45	633	0	ENST00000263253.7:c.5337C>A	p.Cys1779Ter	p.C1779*	ENST00000263253	NM_001429.3	1779	tgC/tgA	31/31	1	2	FACETS	0.851	0.713	1	0.851	0.713	1	CLONAL	1	TRUE	1	0.13	2		633	814	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0029167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	104	739	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.640989363449557	3	FACETS	0.807	0.725	0.893	0.403	0.362	0.447	CLONAL	1	TRUE	1	0.640989363449557	3		739	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs864622237	NA	P-0029167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	221	469	0	ENST00000269305.4:c.700T>C	p.Tyr234His	p.Y234H	ENST00000269305	NM_001126112.2	234	Tac/Cac	7/11	0.640989363449557	3	FACETS	0.973	0.916	1	0.973	0.916	1	CLONAL	2	TRUE	1	0.640989363449557	3		469	468	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149218	119149218	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs727504426	NA	P-0029167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	296	374	0	ENST00000264033.4:c.1228-2A>G		p.X410_splice	ENST00000264033	NM_005188.3	410			0.640989363449557	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	0	0.640989363449557	3		374	402	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913237	NA	P-0029167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	130	337	0	ENST00000369535.4:c.35G>T	p.Gly12Val	p.G12V	ENST00000369535	NM_002524.4	12	gGt/gTt	2/7	0.640989363449557	3	FACETS	1	0.95	1	0.53	0.484	0.579	CLONAL	1	TRUE	1	0.640989363449557	3		337	505	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589651	69589651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	18	83	0	ENST00000168712.1:c.202G>A	p.Ala68Thr	p.A68T	ENST00000168712	NM_002007.2	68	Gcc/Acc	1/3	0.640989363449557	3	FACETS	0.749	0.573	0.949	0.375	0.286	0.475	CLONAL	1	TRUE	1	0.640989363449557	3		83	99	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64126715	64126715	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	27	275	2	ENST00000334205.4:c.8A>T	p.Asp3Val	p.D3V	ENST00000334205	NM_003942.2	3	gAc/gTc	1/17	0.640989363449557	3	FACETS	0.426	0.34	0.524	0.213	0.17	0.262	SUBCLONAL	1	TRUE	1	0.640989363449557	3		277	261	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676323	37676323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	44	470	0	ENST00000447079.4:c.3078C>A	p.Ser1026Arg	p.S1026R	ENST00000447079	NM_015083.1	1026	agC/agA	11/14	0.640989363449557	3	FACETS	0.358	0.3	0.423	0.179	0.15	0.212	SUBCLONAL	1	TRUE	1	0.640989363449557	3		470	506	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029976-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	10	340	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	TRUE	1	0.396442392517065	2		340	36	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602532	10602532	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1237235830	NA	P-0029976-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	52	533	0	ENST00000171111.5:c.1046A>G	p.Asp349Gly	p.D349G	ENST00000171111	NM_203500.1	349	gAc/gGc	3/6	0.396442392517065	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.396442392517065	1		533	154	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578183	7578210	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCTCATAGGGCACCACCACACTATGT	CGGCTCATAGGGCACCACCACACTATGT	-	novel	NA	P-0029976-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	63	526	0	ENST00000269305.4:c.639_666del	p.His214LeufsTer24	p.H214Lfs*24	ENST00000269305	NM_001126112.2	213	cgACATAGTGTGGTGGTGCCCTATGAGCCG/cg	6/11	0.295538256001928	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.396442392517065	2		526	131	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0030094-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	54	595	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.9	0.767	1	0.9	0.767	1	CLONAL	1	TRUE	1	0.17	2		595	706	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577115	7577115	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519983	NA	P-0030094-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	86	826	0	ENST00000269305.4:c.823T>C	p.Cys275Arg	p.C275R	ENST00000269305	NM_001126112.2	275	Tgt/Cgt	8/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.17	2		826	827	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199364	16199364	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030094-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	30	495	0	ENST00000375759.3:c.137G>T	p.Gly46Val	p.G46V	ENST00000375759	NM_015001.2	46	gGa/gTa	2/15	1	2	FACETS	0.594	0.477	0.727	0.594	0.477	0.727	SUBCLONAL	1	TRUE	1	0.17	2		495	594	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176104215	176104215	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030094-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	47	362	0	ENST00000367669.3:c.899G>C	p.Ser300Thr	p.S300T	ENST00000367669	NM_022457.5	300	aGt/aCt	8/20	0.102391131200592	3	FACETS	1	0.95	1	0.664	0.56	0.777	CLONAL	1	TRUE	1	0.17	3		362	452	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865641	57865641	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030094-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	45	940	0	ENST00000228682.2:c.3118C>A	p.Leu1040Ile	p.L1040I	ENST00000228682	NM_005269.2	1040	Ctt/Att	12/12	1	2	FACETS	0.618	0.518	0.73	0.618	0.518	0.73	SUBCLONAL	1	TRUE	1	0.17	2		940	856	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281393	49281393	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030094-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	43	930	1	ENST00000282018.3:c.440T>A	p.Leu147Gln	p.L147Q	ENST00000282018	NM_020377.2	147	cTg/cAg	1/1	1	2	FACETS	0.61	0.509	0.723	0.61	0.509	0.723	SUBCLONAL	1	TRUE	1	0.17	2		931	829	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986589	36986589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030094-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	110	459	0	ENST00000354822.5:c.1100C>T	p.Pro367Leu	p.P367L	ENST00000354822	NM_001079668.2	367	cCc/cTc	3/3	0.141907358776323	6	FACETS	0.905	0.814	1			1	CLONAL	3	TRUE	NA	0.17	6		459	639	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991701	72991701	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030094-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	27	442	0	ENST00000268489.5:c.2344G>C	p.Ala782Pro	p.A782P	ENST00000268489	NM_006885.3	782	Gcg/Ccg	2/10	1	2	FACETS	0.88	0.7	1	0.88	0.7	1	CLONAL	1	TRUE	1	0.17	2		442	361	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40879774	40879774	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030094-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	54	537	2	ENST00000428826.2:c.125A>G	p.Tyr42Cys	p.Y42C	ENST00000428826		42	tAt/tGt	4/21	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.17	2		539	623	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638641	176638641	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030094-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	59	890	0	ENST00000439151.2:c.3244del	p.Ala1082GlnfsTer12	p.A1082Qfs*12	ENST00000439151	NM_022455.4	1081	Ggg/gg	5/23	1	2	FACETS	0.785	0.674	0.907	0.785	0.674	0.907	CLONAL	1	TRUE	1	0.17	2		890	884	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058261	42058261	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	267	450	0	ENST00000219905.7:c.7981G>C	p.Gly2661Arg	p.G2661R	ENST00000219905	NM_001164273.1	2661	Gga/Cga	24/24	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.79	2		450	676	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984070	7984070	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	339	583	0	ENST00000319144.4:c.556A>G	p.Ile186Val	p.I186V	ENST00000319144	NM_001139.2	186	Att/Gtt	5/15	1	2	FACETS	0.959	0.91	1	0.959	0.91	1	CLONAL	1	TRUE	1	0.79	2		583	895	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0031304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	200	435	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.472029743686383	3	FACETS	1	0.988	1	0.666	0.619	0.715	CLONAL	1	TRUE	1	0.472029743686383	3		435	786	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397800	49397800	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	136	556	0	ENST00000418115.1:c.424G>A	p.Glu142Lys	p.E142K	ENST00000418115	NM_001664.2	142	Gaa/Aaa	5/5	0.472029743686383	1	FACETS	0.588	0.535	0.643	0.588	0.535	0.643	SUBCLONAL	1	TRUE	0	0.472029743686383	1		556	749	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0031304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	284	845	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.472029743686383	1	FACETS	0.903	0.85	0.958	0.903	0.85	0.958	CLONAL	1	TRUE	0	0.472029743686383	1		845	1018	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26046026	26046026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	131	396	1	ENST00000540144.1:c.388C>T	p.Arg130Cys	p.R130C	ENST00000540144	NM_003531.2	130	Cgc/Tgc	1/1	1	2	FACETS	0.904	0.823	0.989	0.904	0.823	0.989	CLONAL	1	TRUE	1	0.472029743686383	2		397	614	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939473	71939473	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1169	353	736	0	ENST00000298229.2:c.328G>C	p.Val110Leu	p.V110L	ENST00000298229	NM_001567.3	110	Gtg/Ctg	3/28	1	2	FACETS	0.983	0.929	1	0.983	0.929	1	CLONAL	1	TRUE	1	0.472029743686383	2		736	1522	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800822	18800822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	110	389	0	ENST00000266497.5:c.4198G>A	p.Glu1400Lys	p.E1400K	ENST00000266497		1400	Gaa/Aaa	31/31	0.429439137927808	1	FACETS	0.693	0.625	0.764	0.693	0.625	0.764	SUBCLONAL	1	TRUE	0	0.472029743686383	1		389	514	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223138	1223138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060499967	NA	P-0031304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	263	699	0	ENST00000326873.7:c.1075G>A	p.Asp359Asn	p.D359N	ENST00000326873	NM_000455.4	359	Gac/Aac	8/10	0.472029743686383	1	FACETS	0.923	0.867	0.981	0.923	0.867	0.981	CLONAL	1	TRUE	0	0.472029743686383	1		699	922	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122607	2122852	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTCCCATCTGTGCTTTTCCTAAGTGGGGCTCCCGTGCCGTTCACCTCACATTCCTGGTGTGTTACTTGGCAGGCACTCCCACCACTCCGAAAGGGAGGCCCTTCCTGGGAGGGAGGCAAGAAGGCTCCCCAGCCCCTTTGCCCCCTTTCCTGGGCCTGCGTTCCCAGGGCCTCCCCAGCCCCTCTGGCTACCCCGTGACCTGGCCGCTGGGGAGAGGTTTCATGCCTGGATTTGGTCATCAGCTT	TCTCCCATCTGTGCTTTTCCTAAGTGGGGCTCCCGTGCCGTTCACCTCACATTCCTGGTGTGTTACTTGGCAGGCACTCCCACCACTCCGAAAGGGAGGCCCTTCCTGGGAGGGAGGCAAGAAGGCTCCCCAGCCCCTTTGCCCCCTTTCCTGGGCCTGCGTTCCCAGGGCCTCCCCAGCCCCTCTGGCTACCCCGTGACCTGGCCGCTGGGGAGAGGTTTCATGCCTGGATTTGGTCATCAGCTT	-	novel	NA	P-0031304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	10	134	0	ENST00000219476.3:c.2221-241_2225del		p.X741_splice	ENST00000219476	NM_000548.3	741		21/42	0.411391087688196	0	FACETS	0.35	0.241	0.48			1	SUBCLONAL	1	TRUE	0	0.472029743686383	0		134	64	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578189	7578189	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0031827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	278	562	0	ENST00000269305.4:c.660T>G	p.Tyr220Ter	p.Y220*	ENST00000269305	NM_001126112.2	220	taT/taG	6/11	0.302228432609006	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.302228432609006	2		562	866	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759697	133759697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776289598	NA	P-0031827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	226	521	0	ENST00000318560.5:c.2020C>T	p.Arg674Trp	p.R674W	ENST00000318560	NM_005157.4	674	Cgg/Tgg	11/11	0.302228432609006	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.302228432609006	2		521	725	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098898	47098898	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	139	580	0	ENST00000409792.3:c.6376G>T	p.Glu2126Ter	p.E2126*	ENST00000409792	NM_014159.6	2126	Gag/Tag	15/21	1	2	FACETS	0.951	0.865	1	0.951	0.865	1	CLONAL	1	TRUE	1	0.302228432609006	2		580	967	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163374	47163387	+	frameshift_variant	Frame_Shift_Del	DEL	AACTTTTTTTACTC	AACTTTTTTTACTC	-	novel	NA	P-0031827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	79	325	0	ENST00000409792.3:c.2739_2752del	p.Lys913AsnfsTer17	p.K913Nfs*17	ENST00000409792	NM_014159.6	913	aaGAGTAAAAAAAGTTca/aaca	3/21	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.302228432609006	2		325	485	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620104	21620104	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031932-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	108	369	0	ENST00000382592.4:c.62A>G	p.Glu21Gly	p.E21G	ENST00000382592	NM_014572.2	21	gAg/gGg	2/8	0.252714771148842	1	FACETS	0.518	0.467	0.572	0.518	0.467	0.572	INDETERMINATE	1	TRUE	0	0.579372089313256	1		369	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578217	7578218	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0031932-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	209	495	0	ENST00000269305.4:c.631_632del	p.Thr211PhefsTer4	p.T211Ffs*4	ENST00000269305	NM_001126112.2	211	ACt/t	6/11	0.515618434257481	1	FACETS	0.917	0.858	0.977	0.917	0.858	0.977	CLONAL	1	TRUE	0	0.579372089313256	1		495	559	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753915	133753915	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031932-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	115	378	0	ENST00000318560.5:c.1384G>C	p.Glu462Gln	p.E462Q	ENST00000318560	NM_005157.4	462	Gaa/Caa	8/11	0.430083418566696	3	FACETS	1	0.954	1	0.544	0.492	0.597	CLONAL	1	TRUE	1	0.579372089313256	3		378	471	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949091	71949120	+	inframe_deletion	In_Frame_Del	DEL	GTGCCTGCAGGGCGGGCGGGCCAGCGGGCT	GTGCCTGCAGGGCGGGCGGGCCAGCGGGCT	-	novel	NA	P-0031932-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	73	398	0	ENST00000298229.2:c.3559_3588del	p.Cys1187_Leu1196del	p.C1187_L1196del	ENST00000298229	NM_001567.3	1186	ccGTGCCTGCAGGGCGGGCGGGCCAGCGGGCTg/ccg	27/28	1	2	FACETS	0.432	0.378	0.49	0.432	0.378	0.49	SUBCLONAL	1	TRUE	1	0.579372089313256	2		398	583	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0032827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	108	952	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.666817375636771	2	FACETS	0.996	0.929	1	0.996	0.929	1	CLONAL	2	TRUE	0	0.673645244425912	2		952	161	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0032827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	304	849	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.670076655207346	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.673645244425912	2		849	405	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954327	48954328	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0032827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	116	290	0	ENST00000267163.4:c.1450_1451del	p.Met484ValfsTer8	p.M484Vfs*8	ENST00000267163	NM_000321.2	483	cAT/c	16/27	0.666817375636771	2	FACETS	0.87	0.808	0.931	0.87	0.808	0.931	CLONAL	2	TRUE	0	0.673645244425912	2		290	198	SUCCESS
APC	324	MSKCC	GRCh37	5	112178355	112178355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	72	367	0	ENST00000257430.4:c.7064C>T	p.Ser2355Leu	p.S2355L	ENST00000257430	NM_000038.5	2355	tCa/tTa	16/16	0.615669656895586	2	FACETS	0.763	0.689	0.837	0.763	0.689	0.837	SUBCLONAL	2	TRUE	0	0.673645244425912	2		367	140	SUCCESS
APC	324	MSKCC	GRCh37	5	112173600	112173600	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1060503310	NA	P-0032827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	33	284	0	ENST00000257430.4:c.2309C>G	p.Ser770Ter	p.S770*	ENST00000257430	NM_000038.5	770	tCa/tGa	16/16	0.615669656895586	2	FACETS	0.742	0.615	0.879	0.371	0.307	0.44	SUBCLONAL	1	TRUE	0	0.673645244425912	2		284	132	SUCCESS
APC	324	MSKCC	GRCh37	5	112175842	112175842	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	29	268	0	ENST00000257430.4:c.4551G>C	p.Gln1517His	p.Q1517H	ENST00000257430	NM_000038.5	1517	caG/caC	16/16	0.615669656895586	2	FACETS	0.797	0.654	0.952	0.399	0.327	0.476	CLONAL	1	TRUE	0	0.673645244425912	2		268	108	SUCCESS
APC	324	MSKCC	GRCh37	5	112177323	112177323	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554087155	NA	P-0032827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	46	341	0	ENST00000257430.4:c.6032C>T	p.Ser2011Leu	p.S2011L	ENST00000257430	NM_000038.5	2011	tCa/tTa	16/16	0.615669656895586	2	FACETS	1	0.963	1	0.676	0.59	0.764	CLONAL	1	TRUE	0	0.673645244425912	2		341	101	SUCCESS
APC	324	MSKCC	GRCh37	5	112173275	112173275	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	35	193	0	ENST00000257430.4:c.1984C>G	p.Leu662Val	p.L662V	ENST00000257430	NM_000038.5	662	Cta/Gta	16/16	0.615669656895586	2	FACETS	0.904	0.758	1	0.452	0.379	0.529	CLONAL	1	TRUE	0	0.673645244425912	2		193	115	SUCCESS
APC	324	MSKCC	GRCh37	5	112173642	112173642	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs778287168	NA	P-0032827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	34	324	0	ENST00000257430.4:c.2351C>G	p.Ser784Cys	p.S784C	ENST00000257430	NM_000038.5	784	tCt/tGt	16/16	0.615669656895586	2	FACETS	0.742	0.617	0.877	0.371	0.308	0.439	SUBCLONAL	1	TRUE	0	0.673645244425912	2		324	136	SUCCESS
APC	324	MSKCC	GRCh37	5	112173836	112173836	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	65	338	0	ENST00000257430.4:c.2545G>C	p.Asp849His	p.D849H	ENST00000257430	NM_000038.5	849	Gat/Cat	16/16	0.615669656895586	2	FACETS	1	0.948	1	0.564	0.5	0.63	CLONAL	1	TRUE	0	0.673645244425912	2		338	171	SUCCESS
APC	324	MSKCC	GRCh37	5	112173992	112173992	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	53	345	0	ENST00000257430.4:c.2701C>G	p.Gln901Glu	p.Q901E	ENST00000257430	NM_000038.5	901	Cag/Gag	16/16	0.615669656895586	2	FACETS	0.894	0.776	1	0.447	0.388	0.509	CLONAL	1	TRUE	0	0.673645244425912	2		345	176	SUCCESS
APC	324	MSKCC	GRCh37	5	112174979	112174979	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	29	220	0	ENST00000257430.4:c.3688C>G	p.Gln1230Glu	p.Q1230E	ENST00000257430	NM_000038.5	1230	Cag/Gag	16/16	0.615669656895586	2	FACETS	0.657	0.536	0.79	0.329	0.268	0.395	SUBCLONAL	1	TRUE	0	0.673645244425912	2		220	131	SUCCESS
APC	324	MSKCC	GRCh37	5	112175502	112175502	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	46	324	0	ENST00000257430.4:c.4211C>G	p.Ser1404Cys	p.S1404C	ENST00000257430	NM_000038.5	1404	tCc/tGc	16/16	0.615669656895586	2	FACETS	0.828	0.709	0.954	0.414	0.354	0.477	CLONAL	1	TRUE	0	0.673645244425912	2		324	165	SUCCESS
APC	324	MSKCC	GRCh37	5	112175537	112175537	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	59	318	0	ENST00000257430.4:c.4246G>C	p.Gly1416Arg	p.G1416R	ENST00000257430	NM_000038.5	1416	Ggc/Cgc	16/16	0.615669656895586	2	FACETS	1	0.934	1	0.547	0.481	0.616	CLONAL	1	TRUE	0	0.673645244425912	2		318	160	SUCCESS
APC	324	MSKCC	GRCh37	5	112175878	112175878	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	20	249	0	ENST00000257430.4:c.4587G>C	p.Gln1529His	p.Q1529H	ENST00000257430	NM_000038.5	1529	caG/caC	16/16	0.615669656895586	2	FACETS	0.632	0.492	0.788	0.316	0.246	0.394	SUBCLONAL	1	TRUE	0	0.673645244425912	2		249	94	SUCCESS
APC	324	MSKCC	GRCh37	5	112175885	112175885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881251	NA	P-0032827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	21	243	0	ENST00000257430.4:c.4594G>A	p.Asp1532Asn	p.D1532N	ENST00000257430	NM_000038.5	1532	Gac/Aac	16/16	0.615669656895586	2	FACETS	0.643	0.504	0.797	0.321	0.252	0.399	SUBCLONAL	1	TRUE	0	0.673645244425912	2		243	97	SUCCESS
APC	324	MSKCC	GRCh37	5	112176234	112176234	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	78	435	0	ENST00000257430.4:c.4943C>G	p.Pro1648Arg	p.P1648R	ENST00000257430	NM_000038.5	1648	cCt/cGt	16/16	0.615669656895586	2	FACETS	0.777	0.705	0.849	0.777	0.705	0.849	SUBCLONAL	2	TRUE	0	0.673645244425912	2		435	149	SUCCESS
APC	324	MSKCC	GRCh37	5	112176269	112176269	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs767271480	NA	P-0032827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	57	426	0	ENST00000257430.4:c.4978C>G	p.Leu1660Val	p.L1660V	ENST00000257430	NM_000038.5	1660	Cta/Gta	16/16	0.615669656895586	2	FACETS	1	0.971	1	0.688	0.609	0.767	CLONAL	1	TRUE	0	0.673645244425912	2		426	123	SUCCESS
APC	324	MSKCC	GRCh37	5	112176285	112176287	+	frameshift_variant	Frame_Shift_Del	DEL	CTC	CTC	TT	novel	NA	P-0032827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	41	427	0	ENST00000257430.4:c.4994_4996delinsTT	p.Pro1665LeufsTer5	p.P1665Lfs*5	ENST00000257430	NM_000038.5	1665	cCTCca/cTTca	16/16	0.615669656895586	2	FACETS	1	0.928	1	0.569	0.488	0.653	CLONAL	1	TRUE	0	0.673645244425912	2		427	107	SUCCESS
APC	324	MSKCC	GRCh37	5	112176774	112176774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs971100064	NA	P-0032827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	52	297	0	ENST00000257430.4:c.5483C>T	p.Pro1828Leu	p.P1828L	ENST00000257430	NM_000038.5	1828	cCa/cTa	16/16	0.615669656895586	2	FACETS	1	0.97	1	0.702	0.619	0.786	CLONAL	1	TRUE	0	0.673645244425912	2		297	110	SUCCESS
APC	324	MSKCC	GRCh37	5	112178385	112178385	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0032827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	78	365	0	ENST00000257430.4:c.7094C>G	p.Ser2365Ter	p.S2365*	ENST00000257430	NM_000038.5	2365	tCa/tGa	16/16	0.615669656895586	2	FACETS	0.815	0.742	0.888	0.815	0.742	0.888	CLONAL	2	TRUE	0	0.673645244425912	2		365	142	SUCCESS
APC	324	MSKCC	GRCh37	5	112178562	112178562	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	45	342	0	ENST00000257430.4:c.7271C>T	p.Ser2424Leu	p.S2424L	ENST00000257430	NM_000038.5	2424	tCa/tTa	16/16	0.615669656895586	2	FACETS	1	0.955	1	0.63	0.547	0.715	CLONAL	1	TRUE	0	0.673645244425912	2		342	106	SUCCESS
APC	324	MSKCC	GRCh37	5	112178633	112178633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561614782	NA	P-0032827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	49	317	0	ENST00000257430.4:c.7342C>T	p.Pro2448Ser	p.P2448S	ENST00000257430	NM_000038.5	2448	Cca/Tca	16/16	0.615669656895586	2	FACETS	1	0.971	1	0.735	0.647	0.823	CLONAL	1	TRUE	0	0.673645244425912	2		317	99	SUCCESS
APC	324	MSKCC	GRCh37	5	112178753	112178753	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	60	398	0	ENST00000257430.4:c.7462C>G	p.Leu2488Val	p.L2488V	ENST00000257430	NM_000038.5	2488	Ctt/Gtt	16/16	0.615669656895586	2	FACETS	1	0.97	1	0.66	0.585	0.735	CLONAL	1	TRUE	0	0.673645244425912	2		398	135	SUCCESS
APC	324	MSKCC	GRCh37	5	112179591	112179591	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0032827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	72	353	0	ENST00000257430.4:c.8300C>G	p.Ser2767Ter	p.S2767*	ENST00000257430	NM_000038.5	2767	tCa/tGa	16/16	0.615669656895586	2	FACETS	0.906	0.826	0.983	0.906	0.826	0.983	CLONAL	2	TRUE	0	0.673645244425912	2		353	118	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907702	76907702	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	83	452	0	ENST00000373344.5:c.4459G>A	p.Asp1487Asn	p.D1487N	ENST00000373344	NM_000489.3	1487	Gat/Aat	15/35	1	2	FACETS	0.859	0.767	0.955	0.859	0.767	0.955	CLONAL	1	TRUE	1	0.673645244425912	2		452	287	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033735-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	119	503	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	0.229606013480734	2		503	884	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114773	108114773	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753806542	NA	P-0033735-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	239	581	0	ENST00000278616.4:c.590G>A	p.Gly197Glu	p.G197E	ENST00000278616	NM_000051.3	197	gGa/gAa	6/63	0.185830893601278	3	FACETS	0.958	0.893	1			1	CLONAL	2	TRUE	NA	0.229606013480734	3		581	1211	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26974649	26974649	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033735-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	48	641	0	ENST00000381527.3:c.993G>C	p.Gln331His	p.Q331H	ENST00000381527	NM_001260.1	331	caG/caC	10/13	0.229606013480734	1	FACETS	0.437	0.368	0.514	0.437	0.368	0.514	SUBCLONAL	1	TRUE	0	0.229606013480734	1		641	846	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614539	38614539	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754706111	NA	P-0033735-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	159	671	0	ENST00000299084.4:c.305C>T	p.Thr102Met	p.T102M	ENST00000299084	NM_152594.2	102	aCg/aTg	3/7	0.229606013480734	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.229606013480734	1		671	1069	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180417	38180417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746126009	NA	P-0033735-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	72	873	0	ENST00000396334.3:c.265G>A	p.Asp89Asn	p.D89N	ENST00000396334	NM_002468.4	89	Gac/Aac	1/5	1	2	FACETS	0.57	0.496	0.65	0.57	0.496	0.65	SUBCLONAL	1	TRUE	1	0.229606013480734	2		873	1101	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781232	161781232	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033735-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	48	658	0	ENST00000366898.1:c.1173C>A	p.Tyr391Ter	p.Y391*	ENST00000366898	NM_004562.2	391	taC/taA	11/12	1	2	FACETS	0.544	0.459	0.639	0.544	0.459	0.639	SUBCLONAL	1	TRUE	1	0.229606013480734	2		658	768	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197411	27197411	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033735-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	103	746	0	ENST00000380036.4:c.1723T>C	p.Tyr575His	p.Y575H	ENST00000380036	NM_000459.3	575	Tat/Cat	12/23	0.227172442064556	1	FACETS	0.671	0.599	0.749	0.671	0.599	0.749	SUBCLONAL	1	TRUE	0	0.229606013480734	1		746	1183	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636315	87636315	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033735-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	53	750	1	ENST00000277120.3:c.2480C>T	p.Ala827Val	p.A827V	ENST00000277120		827	gCc/gTc	19/19	0.227172442064556	1	FACETS	0.478	0.406	0.557	0.478	0.406	0.557	SUBCLONAL	1	TRUE	0	0.229606013480734	1		751	855	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851574	134851574	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747682274	NA	P-0034363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	192	383	0	ENST00000398015.3:c.980G>A	p.Arg327His	p.R327H	ENST00000398015	NM_004441.4	327	cGc/cAc	5/16	1	2	FACETS	0.926	0.86	0.994	0.926	0.86	0.994	CLONAL	1	TRUE	1	0.62	2		383	669	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0034363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	182	343	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.936	0.868	1	0.936	0.868	1	CLONAL	1	TRUE	1	0.62	2		343	627	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0034363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	147	267	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.99	0.911	1	0.99	0.911	1	CLONAL	1	TRUE	1	0.62	2		267	479	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0034363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	112	472	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.838	0.759	0.921	0.838	0.759	0.921	CLONAL	1	TRUE	1	0.62	2		472	431	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436297	110436305	+	inframe_deletion	In_Frame_Del	DEL	CGGCGGCGG	CGGCGGCGG	-	rs34412495	NA	P-0034363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	118	129	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	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.62	2		129	323	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617589	158617589	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121912679	NA	P-0034363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	130	282	0	ENST00000263640.3:c.1067G>A	p.Gly356Asp	p.G356D	ENST00000263640	NM_001105.4	356	gGc/gAc	9/11	1	2	FACETS	0.87	0.794	0.949	0.87	0.794	0.949	CLONAL	1	TRUE	1	0.62	2		282	482	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057850	27057850	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	314	585	0	ENST00000324856.7:c.1558C>T	p.Gln520Ter	p.Q520*	ENST00000324856	NM_006015.4	520	Cag/Tag	3/20	1	2	FACETS	0.967	0.914	1	0.967	0.914	1	CLONAL	1	TRUE	1	0.62	2		585	1047	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273869	18273869	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	259	523	0	ENST00000222254.8:c.1202T>G	p.Leu401Arg	p.L401R	ENST00000222254	NM_005027.3	401	cTc/cGc	10/16	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.62	2		523	833	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514650	103514650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	147	293	0	ENST00000355739.4:c.1151C>T	p.Ser384Leu	p.S384L	ENST00000355739	NM_000123.3	384	tCa/tTa	8/15	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.62	2		293	473	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106994	27106998	+	frameshift_variant	Frame_Shift_Del	DEL	GCCTT	GCCTT	-	novel	NA	P-0034363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	180	361	0	ENST00000324856.7:c.6608_6612del	p.Leu2203ArgfsTer20	p.L2203Rfs*20	ENST00000324856	NM_006015.4	2202	aGCCTT/a	20/20	1	2	FACETS	0.926	0.858	0.996	0.926	0.858	0.996	CLONAL	1	TRUE	1	0.62	2		361	627	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654607	67654607	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	214	368	0	ENST00000264010.4:c.1094A>C	p.Lys365Thr	p.K365T	ENST00000264010	NM_006565.3	365	aAa/aCa	6/12	1	2	FACETS	0.989	0.923	1	0.989	0.923	1	CLONAL	1	TRUE	1	0.62	2		368	698	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591039	67591040	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTGGAAGAAGAC	novel	NA	P-0034363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	60	204	0	ENST00000274335.5:c.1636_1647dup	p.Glu546_Leu549dup	p.E546_L549dup	ENST00000274335		546	-/TTGGAAGAAGAC	12/15	1	2	FACETS	0.52	0.45	0.596	0.52	0.45	0.596	SUBCLONAL	1	TRUE	1	0.62	2		204	372	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720798	89720801	+	frameshift_variant	Frame_Shift_Del	DEL	GTAC	GTAC	AG	novel	NA	P-0034363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	51	157	1	ENST00000371953.3:c.949_952delinsAG	p.Val317SerfsTer7	p.V317Sfs*7	ENST00000371953	NM_000314.4	317	GTACtt/AGtt	8/9	1	2	FACETS	0.63	0.54	0.727	0.63	0.54	0.727	SUBCLONAL	1	TRUE	1	0.62	2		158	261	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578485	7578485	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1064793929	NA	P-0034484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	471	768	0	ENST00000269305.4:c.445del	p.Ser149ProfsTer21	p.S149Pfs*21	ENST00000269305	NM_001126112.2	149	Tcc/cc	5/11	0.543265445913818	4	FACETS	1	0.993	1	0.824	0.798	0.85	CLONAL	3	FALSE	0	0.696101368784712	4		768	696	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972621	76972621	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	53	600	0	ENST00000373344.5:c.120G>A	p.Met40Ile	p.M40I	ENST00000373344	NM_000489.3	40	atG/atA	2/35	0.523204435791083	3	FACETS	0.503	0.43	0.583	0.168	0.143	0.195	SUBCLONAL	1	FALSE	0	0.696101368784712	3		600	408	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248636	10248636	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1356963122	NA	P-0034484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	88	510	0	ENST00000340748.4:c.4117G>A	p.Asp1373Asn	p.D1373N	ENST00000340748		1373	Gac/Aac	35/40	0.696101368784712	6	FACETS	1	0.966	1	0.407	0.362	0.456	CLONAL	1	FALSE	3	0.696101368784712	6		510	495	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023559	27023560	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0034705-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	160	318	0	ENST00000324856.7:c.671dup	p.Pro225AlafsTer175	p.P225Afs*175	ENST00000324856	NM_006015.4	222	tac/taCc	1/20	1	2	FACETS	0.68	0.626	0.735	0.68	0.626	0.735	SUBCLONAL	1	TRUE	1	0.784604783248878	2		318	600	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591108	67591128	+	inframe_deletion	In_Frame_Del	DEL	ACCAGACCTTATCCAGCTGAG	ACCAGACCTTATCCAGCTGAG	-	novel	NA	P-0034705-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	148	339	0	ENST00000274335.5:c.1702_1722del	p.Pro568_Arg574del	p.P568_R574del	ENST00000274335		567	aaACCAGACCTTATCCAGCTGAGa/aaa	12/15	0.563223257220097	4	FACETS	0.987	0.915	1	0.658	0.61	0.707	CLONAL	2	TRUE	1	0.784604783248878	4		339	341	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252873	36252889	+	frameshift_variant	Frame_Shift_Del	DEL	AAACCTGAGGTCATTAA	AAACCTGAGGTCATTAA	-	novel	NA	P-0034705-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	142	358	0	ENST00000300305.3:c.473_489del	p.Phe158CysfsTer49	p.F158Cfs*49	ENST00000300305		158	tTTAATGACCTCAGGTTT/t	4/8	0.158092235660015	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.784604783248878	0		358	462	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645996	215645996	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034813-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	359	563	0	ENST00000260947.4:c.602G>T	p.Arg201Ile	p.R201I	ENST00000260947	NM_000465.2	201	aGa/aTa	4/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.782145991350185	2		563	902	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937059	48937059	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034813-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	221	431	0	ENST00000267163.4:c.828del	p.Leu277SerfsTer9	p.L277Sfs*9	ENST00000267163	NM_000321.2	276	gTt/gt	8/27	0.782145991350185	1	FACETS	0.948	0.9	0.995	0.948	0.9	0.995	CLONAL	1	TRUE	0	0.782145991350185	1		431	363	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0035025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	456	780	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.889912991605063	1	FACETS	0.972	0.946	0.997	0.972	0.946	0.997	CLONAL	1	TRUE	0	0.893446392126852	1		780	581	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033844	49033844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853294	NA	P-0035025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	319	295	0	ENST00000267163.4:c.1981C>T	p.Arg661Trp	p.R661W	ENST00000267163	NM_000321.2	661	Cgg/Tgg	20/27	0.893446392126852	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.893446392126852	1		295	391	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201684	67201684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376762664	NA	P-0035025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	456	499	0	ENST00000312629.5:c.985C>T	p.Arg329Trp	p.R329W	ENST00000312629	NM_003952.2	329	Cgg/Tgg	12/15	0.893446392126852	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.893446392126852	1		499	554	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044850	47044850	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	276	664	1	ENST00000377604.3:c.2176C>T	p.Arg726Ter	p.R726*	ENST00000377604	NM_001204468.1	726	Cga/Tga	20/24	0.893446392126852	1	FACETS	0.469	0.442	0.496	0.469	0.442	0.496	SUBCLONAL	1	TRUE	0	0.893446392126852	1		665	729	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942052	71942053	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1326136034	NA	P-0035025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	502	599	1	ENST00000298229.2:c.1322dup	p.Asn441LysfsTer25	p.N441Kfs*25	ENST00000298229	NM_001567.3	439	cca/ccAa	12/28	0.893446392126852	1	FACETS	0.954	0.929	0.978	0.954	0.929	0.978	CLONAL	1	TRUE	0	0.893446392126852	1		600	652	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275311	115275311	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1307490780	NA	P-0035025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	500	507	0	ENST00000438362.2:c.1102A>G	p.Thr368Ala	p.T368A	ENST00000438362	NM_001242891.1	368	Aca/Gca	10/20	0.893446392126852	1	FACETS	0.985	0.96	1	0.985	0.96	1	CLONAL	1	TRUE	0	0.893446392126852	1		507	629	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577567	64577568	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0035025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	293	308	0	ENST00000312049.6:c.14_15del	p.Ala5GlyfsTer111	p.A5Gfs*111	ENST00000312049	NM_130799.2	5	gCC/g	2/10	0.893446392126852	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.893446392126852	1		308	363	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992792	72992792	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	438	509	0	ENST00000268489.5:c.1253del	p.Val418AlafsTer39	p.V418Afs*39	ENST00000268489	NM_006885.3	418	gTc/gc	2/10	0.889912991605063	1	FACETS	0.97	0.944	0.996	0.97	0.944	0.996	CLONAL	1	TRUE	0	0.893446392126852	1		509	559	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912114	76912117	+	frameshift_variant	Frame_Shift_Del	DEL	AATC	AATC	-	novel	NA	P-0035025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	252	365	0	ENST00000373344.5:c.4147_4150del	p.Asp1383PhefsTer106	p.D1383Ffs*106	ENST00000373344	NM_000489.3	1383	GATTtt/tt	13/35	0.893446392126852	1	FACETS	0.991	0.956	1	0.991	0.956	1	CLONAL	1	TRUE	0	0.893446392126852	1		365	315	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272264	15272264	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	369	506	0	ENST00000263388.2:c.6175G>A	p.Gly2059Arg	p.G2059R	ENST00000263388	NM_000435.2	2059	Ggg/Agg	33/33	1	2	FACETS	0.825	0.785	0.866	0.825	0.785	0.866	CLONAL	1	TRUE	1	0.893446392126852	2		506	1001	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673728	30673728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778019975	NA	P-0035025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	77	451	0	ENST00000376406.3:c.3232G>A	p.Val1078Ile	p.V1078I	ENST00000376406	NM_014641.2	1078	Gtt/Att	10/15	0.889912991605063	1	FACETS	0.15	0.131	0.17	0.15	0.131	0.17	SUBCLONAL	1	TRUE	0	0.893446392126852	1		451	635	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161970020	161970020	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	185	507	0	ENST00000366898.1:c.949C>A	p.Gln317Lys	p.Q317K	ENST00000366898	NM_004562.2	317	Cag/Aag	9/12	0.889912991605063	1	FACETS	0.372	0.345	0.4	0.372	0.345	0.4	SUBCLONAL	1	TRUE	0	0.893446392126852	1		507	616	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0035733-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	234	595	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.233250055379355	6	FACETS	0.852	0.794	0.912	0.639	0.595	0.684	CLONAL	3	TRUE	2	0.233250055379355	6		595	1151	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0035733-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	108	709	0	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	1	2	FACETS	0.959	0.859	1	0.959	0.859	1	CLONAL	1	TRUE	1	0.233250055379355	2		709	966	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041657	47041657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035733-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	201	401	2	ENST00000377604.3:c.1882G>T	p.Glu628Ter	p.E628*	ENST00000377604	NM_001204468.1	628	Gag/Tag	17/24	0.215195178019026	2	FACETS	0.94	0.877	1			1	CLONAL	3	TRUE	NA	0.233250055379355	2		403	611	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971090	21971090	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035733-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	32	459	0	ENST00000304494.5:c.268T>A	p.Phe90Ile	p.F90I	ENST00000304494	NM_000077.4	90	Ttc/Atc	2/3	1	2	FACETS	0.502	0.406	0.61	0.502	0.406	0.61	SUBCLONAL	1	TRUE	1	0.233250055379355	2		459	547	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	84	780	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.588	0.518	0.663	0.588	0.518	0.663	SUBCLONAL	1	TRUE	1	0.33	2		780	866	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	161	629	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	0.771	0.71	0.834	1	0.989	1	SUBCLONAL	2	TRUE	1	0.33	2		629	633	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	72	365	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.33	2		365	360	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	130	693	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.33	2		693	764	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	65	366	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.33	2		366	279	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346284	152346284	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs778698188	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	39	733	0	ENST00000359321.1:c.286C>A	p.Leu96Ile	p.L96I	ENST00000359321	NM_005431.1	96	Ctt/Att	3/3	1	2	FACETS	0.35	0.289	0.418	0.35	0.289	0.418	SUBCLONAL	1	TRUE	1	0.33	2		733	676	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122680	108122680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	23	560	0	ENST00000278616.4:c.1724C>T	p.Ser575Leu	p.S575L	ENST00000278616	NM_000051.3	575	tCa/tTa	11/63	1	2	FACETS	0.324	0.252	0.408	0.324	0.252	0.408	SUBCLONAL	1	TRUE	1	0.33	2		560	430	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192435	138192435	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	43	385	1	ENST00000237289.4:c.71G>T	p.Arg24Ile	p.R24I	ENST00000237289	NM_001270507.1	24	aGa/aTa	2/9	1	2	FACETS	0.74	0.621	0.871	0.74	0.621	0.871	SUBCLONAL	1	TRUE	1	0.33	2		386	352	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	167	704	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	0.33	2		704	710	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926518	59926518	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1330277587	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	47	985	2	ENST00000259008.2:c.479G>T	p.Arg160Ile	p.R160I	ENST00000259008	NM_032043.2	160	aGa/aTa	5/20	1	2	FACETS	0.415	0.349	0.488	0.415	0.349	0.488	SUBCLONAL	1	TRUE	1	0.33	2		987	686	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	35	613	1	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	1	2	FACETS	0.388	0.317	0.467	0.388	0.317	0.467	SUBCLONAL	1	TRUE	1	0.33	2		614	547	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811758	102811758	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	118	773	0	ENST00000307046.8:c.426G>T	p.Lys142Asn	p.K142N	ENST00000307046	NM_001111285.1	142	aaG/aaT	4/4	1	2	FACETS	0.951	0.858	1	0.951	0.858	1	CLONAL	1	TRUE	1	0.33	2		773	752	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	36	637	3	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.333	0.272	0.4	0.333	0.272	0.4	SUBCLONAL	1	TRUE	1	0.33	2		640	656	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509637	106509637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766453335	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	171	573	0	ENST00000359195.3:c.1631G>A	p.Arg544Gln	p.R544Q	ENST00000359195	NM_002649.2	544	cGa/cAa	2/11	1	2	FACETS	0.828	0.765	0.893	1	0.991	1	CLONAL	2	TRUE	1	0.33	2		573	626	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	119	631	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.782	0.711	0.857	1	0.986	1	SUBCLONAL	2	TRUE	1	0.33	2		631	461	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333143	70333143	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767493807	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	47	824	0	ENST00000373644.4:c.1048G>A	p.Glu350Lys	p.E350K	ENST00000373644	NM_030625.2	350	Gaa/Aaa	2/12	1	2	FACETS	0.357	0.3	0.421	0.357	0.3	0.421	SUBCLONAL	1	TRUE	1	0.33	2		824	797	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285327	212285327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143134749	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	48	486	1	ENST00000342788.4:c.2974C>T	p.Arg992Cys	p.R992C	ENST00000342788	NM_005235.2	992	Cgt/Tgt	25/28	1	2	FACETS	0.71	0.601	0.829	0.71	0.601	0.829	SUBCLONAL	1	TRUE	1	0.33	2		487	410	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068357	26068357	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	30	626	0	ENST00000435504.4:c.133G>T	p.Glu45Ter	p.E45*	ENST00000435504		45	Gaa/Taa	2/13	1	2	FACETS	0.481	0.388	0.587	0.481	0.388	0.587	SUBCLONAL	1	TRUE	1	0.33	2		626	378	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404538	70404538	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	65	441	0	ENST00000373644.4:c.2052A>C	p.Lys684Asn	p.K684N	ENST00000373644	NM_030625.2	684	aaA/aaC	4/12	1	2	FACETS	0.91	0.791	1	0.91	0.791	1	CLONAL	1	TRUE	1	0.33	2		441	433	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965543	15965543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	39	345	0	ENST00000268712.3:c.5263C>T	p.Arg1755Cys	p.R1755C	ENST00000268712	NM_006311.3	1755	Cgc/Tgc	36/46	1	2	FACETS	0.589	0.489	0.701	0.589	0.489	0.701	SUBCLONAL	1	TRUE	1	0.33	2		345	401	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604736	48604736	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	53	478	0	ENST00000342988.3:c.1558G>T	p.Glu520Ter	p.E520*	ENST00000342988	NM_005359.5	520	Gaa/Taa	12/12	1	2	FACETS	0.57	0.485	0.662	0.57	0.485	0.662	SUBCLONAL	1	TRUE	1	0.33	2		478	564	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440346	187440346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	41	710	0	ENST00000232014.4:c.2021G>A	p.Arg674Gln	p.R674Q	ENST00000232014	NM_001130845.1	674	cGa/cAa	10/10	1	2	FACETS	0.359	0.298	0.427	0.359	0.298	0.427	SUBCLONAL	1	TRUE	1	0.33	2		710	693	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471047	8471047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201751722	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	86	564	1	ENST00000356435.5:c.3452G>A	p.Arg1151His	p.R1151H	ENST00000356435		1151	cGc/cAc	20/35	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.33	2		565	506	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164703	36164703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	79	897	0	ENST00000300305.3:c.1172C>T	p.Ala391Val	p.A391V	ENST00000300305		391	gCg/gTg	8/8	1	2	FACETS	0.518	0.454	0.586	0.518	0.454	0.586	SUBCLONAL	1	TRUE	1	0.33	2		897	925	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032822	30032822	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	25	400	0	ENST00000338641.4:c.197A>G	p.Tyr66Cys	p.Y66C	ENST00000338641	NM_000268.3	66	tAc/tGc	2/16	1	2	FACETS	0.322	0.253	0.401	0.322	0.253	0.401	SUBCLONAL	1	TRUE	1	0.33	2		400	471	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089730	27089730	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	43	642	0	ENST00000324856.7:c.2686G>T	p.Glu896Ter	p.E896*	ENST00000324856	NM_006015.4	896	Gaa/Taa	8/20	1	2	FACETS	0.356	0.297	0.422	0.356	0.297	0.422	SUBCLONAL	1	TRUE	1	0.33	2		642	732	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117629975	117629975	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	66	454	0	ENST00000368508.3:c.6551G>T	p.Arg2184Ile	p.R2184I	ENST00000368508	NM_002944.2	2184	aGa/aTa	41/43	0.3	1	FACETS	0.825	0.719	0.938	0.825	0.719	0.938	CLONAL	1	TRUE	0	0.33	1		454	405	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337650	73337650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	61	356	0	ENST00000377767.4:c.2066G>A	p.Arg689Gln	p.R689Q	ENST00000377767	NM_014953.3	689	cGa/cAa	16/21	1	2	FACETS	0.999	0.866	1	0.999	0.866	1	CLONAL	1	TRUE	1	0.33	2		356	370	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332565	70332565	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs185830524	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	40	677	0	ENST00000373644.4:c.470C>T	p.Ser157Leu	p.S157L	ENST00000373644	NM_030625.2	157	tCg/tTg	2/12	1	2	FACETS	0.389	0.322	0.464	0.389	0.322	0.464	SUBCLONAL	1	TRUE	1	0.33	2		677	623	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168741	56168741	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775802110	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	90	496	0	ENST00000399503.3:c.1595G>A	p.Arg532Gln	p.R532Q	ENST00000399503	NM_005921.1	532	cGa/cAa	9/20	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.33	2		496	533	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	95	457	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.33	2		457	438	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954587	17954587	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs761583890	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	54	821	0	ENST00000458235.1:c.307C>T	p.Arg103Cys	p.R103C	ENST00000458235	NM_000215.3	103	Cgc/Tgc	3/24	1	2	FACETS	0.394	0.336	0.459	0.394	0.336	0.459	SUBCLONAL	1	TRUE	1	0.33	2		821	830	SUCCESS
ALK	238	MSKCC	GRCh37	2	29450509	29450509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774004991	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	65	1010	0	ENST00000389048.3:c.2845G>A	p.Glu949Lys	p.E949K	ENST00000389048	NM_004304.4	949	Gaa/Aaa	17/29	1	2	FACETS	0.398	0.343	0.457	0.398	0.343	0.457	SUBCLONAL	1	TRUE	1	0.33	2		1010	991	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922301	178922301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	56	421	0	ENST00000263967.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000263967	NM_006218.2	357	cGa/cAa	6/21	1	2	FACETS	0.992	0.855	1	0.992	0.855	1	CLONAL	1	TRUE	1	0.33	2		421	342	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953748	48953748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759079385	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	21	314	0	ENST00000267163.4:c.1351C>T	p.Arg451Cys	p.R451C	ENST00000267163	NM_000321.2	451	Cgc/Tgc	14/27	1	2	FACETS	0.323	0.248	0.411	0.323	0.248	0.411	SUBCLONAL	1	TRUE	1	0.33	2		314	394	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649442	23649442	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	59	415	0	ENST00000261584.4:c.57G>T	p.Glu19Asp	p.E19D	ENST00000261584	NM_024675.3	19	gaG/gaT	2/13	1	2	FACETS	0.954	0.824	1	0.954	0.824	1	CLONAL	1	TRUE	1	0.33	2		415	375	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832557	72832557	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141100730	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	58	563	0	ENST00000268489.5:c.4024G>A	p.Gly1342Arg	p.G1342R	ENST00000268489	NM_006885.3	1342	Gga/Aga	9/10	1	2	FACETS	0.599	0.514	0.691	0.599	0.514	0.691	SUBCLONAL	1	TRUE	1	0.33	2		563	587	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394849	394849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1377317453	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	69	429	0	ENST00000380956.4:c.245G>A	p.Arg82Gln	p.R82Q	ENST00000380956	NM_001195286.1	82	cGa/cAa	3/9	1	2	FACETS	0.877	0.765	0.996	0.877	0.765	0.996	CLONAL	1	TRUE	1	0.33	2		429	477	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729613	41729613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs564878978	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	130	591	0	ENST00000242208.4:c.916C>T	p.Arg306Cys	p.R306C	ENST00000242208	NM_002192.2	306	Cgc/Tgc	3/3	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.33	2		591	694	SUCCESS
APC	324	MSKCC	GRCh37	5	112177901	112177901	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs752654519	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	57	369	0	ENST00000257430.4:c.6610C>T	p.Arg2204Ter	p.R2204*	ENST00000257430	NM_000038.5	2204	Cga/Tga	16/16	1	2	FACETS	0.881	0.759	1	0.881	0.759	1	CLONAL	1	TRUE	1	0.33	2		369	392	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115600	108115600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772821016	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	122	641	1	ENST00000278616.4:c.748C>T	p.Arg250Ter	p.R250*	ENST00000278616	NM_000051.3	250	Cga/Tga	7/63	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.33	2		642	500	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604790	48604790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	26	389	1	ENST00000342988.3:c.1612G>A	p.Glu538Lys	p.E538K	ENST00000342988	NM_005359.5	538	Gaa/Aaa	12/12	1	2	FACETS	0.338	0.267	0.42	0.338	0.267	0.42	SUBCLONAL	1	TRUE	1	0.33	2		390	466	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29090089	29090089	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764396738	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	16	210	0	ENST00000328354.6:c.1392G>T	p.Lys464Asn	p.K464N	ENST00000328354	NM_007194.3	464	aaG/aaT	13/15	1	2	FACETS	0.495	0.367	0.647	0.495	0.367	0.647	SUBCLONAL	1	TRUE	1	0.33	2		210	196	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94170371	94170371	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745614941	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	28	523	1	ENST00000323929.3:c.1898G>A	p.Arg633Gln	p.R633Q	ENST00000323929	NM_005591.3	633	cGa/cAa	17/20	1	2	FACETS	0.4	0.319	0.493	0.4	0.319	0.493	SUBCLONAL	1	TRUE	1	0.33	2		524	424	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915952	127915952	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs865855853	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	33	731	1	ENST00000373547.4:c.529C>T	p.Arg177Ter	p.R177*	ENST00000373547	NM_002721.4	177	Cga/Tga	6/7	1	2	FACETS	0.332	0.27	0.403	0.332	0.27	0.403	SUBCLONAL	1	TRUE	1	0.33	2		732	602	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131412	202131412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339962485	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	36	540	1	ENST00000358485.4:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000358485	NM_001080125.1	127	cGa/cAa	2/9	1	2	FACETS	0.419	0.344	0.503	0.419	0.344	0.503	SUBCLONAL	1	TRUE	1	0.33	2		541	521	SUCCESS
APC	324	MSKCC	GRCh37	5	112178211	112178211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs901983934	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	105	448	0	ENST00000257430.4:c.6920C>T	p.Ser2307Leu	p.S2307L	ENST00000257430	NM_000038.5	2307	tCg/tTg	16/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.33	2		448	425	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120360	94120360	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs749418654	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	24	371	1	ENST00000369303.4:c.691C>T	p.Arg231Ter	p.R231*	ENST00000369303	NM_004440.3	231	Cga/Tga	3/17	1	2	FACETS	0.358	0.28	0.448	0.358	0.28	0.448	SUBCLONAL	1	TRUE	1	0.33	2		372	406	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287387	33287387	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	123	684	0	ENST00000374542.5:c.1710G>T	p.Glu570Asp	p.E570D	ENST00000374542	NM_001141970.1	570	gaG/gaT	6/8	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.33	2		684	644	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662433	227662433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751685762	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	139	671	0	ENST00000305123.5:c.1022C>T	p.Ser341Leu	p.S341L	ENST00000305123	NM_005544.2	341	tCg/tTg	1/2	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.33	2		671	714	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711911	89711911	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	98	761	0	ENST00000371953.3:c.529T>G	p.Tyr177Asp	p.Y177D	ENST00000371953	NM_000314.4	177	Tat/Gat	6/9	1	2	FACETS	0.922	0.824	1	0.922	0.824	1	CLONAL	1	TRUE	1	0.33	2		761	644	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228613019	228613019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773567566	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	29	169	0	ENST00000366696.1:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000366696	NM_003493.2	3	cGa/cAa	1/1	1	2	FACETS	0.357	0.285	0.438	0.357	0.285	0.438	SUBCLONAL	1	TRUE	1	0.33	2		169	493	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687329	117687329	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	26	506	0	ENST00000368508.3:c.2722G>T	p.Glu908Ter	p.E908*	ENST00000368508	NM_002944.2	908	Gaa/Taa	18/43	1	2	FACETS	0.336	0.265	0.417	0.336	0.265	0.417	SUBCLONAL	1	TRUE	1	0.33	2		506	469	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153445	108153445	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	78	575	0	ENST00000278616.4:c.3585G>T	p.Glu1195Asp	p.E1195D	ENST00000278616	NM_000051.3	1195	gaG/gaT	25/63	1	2	FACETS	0.963	0.849	1	0.963	0.849	1	CLONAL	1	TRUE	1	0.33	2		575	491	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266679	142266679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146504354	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	33	593	3	ENST00000350721.4:c.3245G>A	p.Arg1082His	p.R1082H	ENST00000350721	NM_001184.3	1082	cGt/cAt	16/47	1	2	FACETS	0.443	0.361	0.537	0.443	0.361	0.537	SUBCLONAL	1	TRUE	1	0.33	2		596	451	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201816	66201816	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556854839	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	83	555	1	ENST00000273854.3:c.2686C>T	p.Arg896Cys	p.R896C	ENST00000273854	NM_004439.5	896	Cgt/Tgt	16/18	1	2	FACETS	0.942	0.833	1	0.942	0.833	1	CLONAL	1	TRUE	1	0.33	2		556	534	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161405	185161405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	105	591	0	ENST00000265026.3:c.832C>T	p.Arg278Cys	p.R278C	ENST00000265026	NM_004721.4	278	Cgt/Tgt	4/14	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.33	2		591	591	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9787030	9787030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397518423	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	40	562	2	ENST00000377346.4:c.3061G>A	p.Glu1021Lys	p.E1021K	ENST00000377346	NM_005026.3	1021	Gaa/Aaa	24/24	1	2	FACETS	0.363	0.301	0.433	0.363	0.301	0.433	SUBCLONAL	1	TRUE	1	0.33	2		564	668	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352373	70352373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	38	530	0	ENST00000374080.3:c.4400G>A	p.Arg1467Gln	p.R1467Q	ENST00000374080		1467	cGa/cAa	31/45	1	2	FACETS	0.445	0.368	0.532	0.445	0.368	0.532	SUBCLONAL	1	TRUE	1	0.33	2		530	517	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8733794	8733794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs949202374	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	82	571	0	ENST00000356435.5:c.50G>A	p.Arg17His	p.R17H	ENST00000356435		17	cGc/cAc	1/35	1	2	FACETS	0.842	0.744	0.948	0.842	0.744	0.948	CLONAL	1	TRUE	1	0.33	2		571	590	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190748	108190748	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1339238483	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	57	488	0	ENST00000278616.4:c.6415G>T	p.Glu2139Ter	p.E2139*	ENST00000278616	NM_000051.3	2139	Gaa/Taa	44/63	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.33	2		488	324	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742515	17742515	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768652299	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	130	634	1	ENST00000250003.3:c.697G>A	p.Glu233Lys	p.E233K	ENST00000250003	NM_002478.4	233	Gag/Aag	2/3	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.33	2		635	742	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844172	68844172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	48	758	1	ENST00000261769.5:c.760G>A	p.Asp254Asn	p.D254N	ENST00000261769	NM_004360.3	254	Gat/Aat	6/16	1	2	FACETS	0.361	0.304	0.425	0.361	0.304	0.425	SUBCLONAL	1	TRUE	1	0.33	2		759	805	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15967454	15967454	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1204491653	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	73	589	0	ENST00000268712.3:c.5149G>A	p.Glu1717Lys	p.E1717K	ENST00000268712	NM_006311.3	1717	Gaa/Aaa	35/46	1	2	FACETS	0.604	0.528	0.687	0.604	0.528	0.687	SUBCLONAL	1	TRUE	1	0.33	2		589	732	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908873	101908873	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200595614	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	234	810	0	ENST00000374994.4:c.1237C>T	p.Arg413Ter	p.R413*	ENST00000374994	NM_004612.2	413	Cga/Tga	7/9	1	2	FACETS	0.973	0.911	1	1	0.994	1	CLONAL	2	TRUE	1	0.33	2		810	729	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101082	4101082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778895928	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	30	442	1	ENST00000262948.5:c.640G>A	p.Gly214Arg	p.G214R	ENST00000262948	NM_030662.3	214	Ggg/Agg	6/11	1	2	FACETS	0.385	0.31	0.471	0.385	0.31	0.471	SUBCLONAL	1	TRUE	1	0.33	2		443	472	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164913	106164913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs898441677	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	21	386	0	ENST00000380013.4:c.3781C>T	p.Arg1261Cys	p.R1261C	ENST00000380013	NM_001127208.2	1261	Cgc/Tgc	6/11	1	2	FACETS	0.281	0.216	0.358	0.281	0.216	0.358	SUBCLONAL	1	TRUE	1	0.33	2		386	453	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349918	15349918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293348757	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	45	792	0	ENST00000263377.2:c.3734C>T	p.Ala1245Val	p.A1245V	ENST00000263377	NM_058243.2	1245	gCc/gTc	18/20	1	2	FACETS	0.318	0.266	0.376	0.318	0.266	0.376	SUBCLONAL	1	TRUE	1	0.33	2		792	857	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319348	11319348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	52	793	3	ENST00000361445.4:c.119C>T	p.Ala40Val	p.A40V	ENST00000361445	NM_004958.3	40	gCc/gTc	2/58	1	2	FACETS	0.366	0.311	0.428	0.366	0.311	0.428	SUBCLONAL	1	TRUE	1	0.33	2		796	860	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542357	187542357	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs769432838	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	54	487	0	ENST00000441802.2:c.5383C>T	p.Arg1795Ter	p.R1795*	ENST00000441802	NM_005245.3	1795	Cga/Tga	10/27	1	2	FACETS	0.671	0.573	0.777	0.671	0.573	0.777	SUBCLONAL	1	TRUE	1	0.33	2		487	488	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812205	43812205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866559375	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	118	694	1	ENST00000372470.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000372470	NM_005373.2	357	cGa/cAa	7/12	1	2	FACETS	0.997	0.901	1	0.997	0.901	1	CLONAL	1	TRUE	1	0.33	2		695	717	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624245	89624245	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554890335	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	34	283	1	ENST00000371953.3:c.19G>T	p.Glu7Ter	p.E7*	ENST00000371953	NM_000314.4	7	Gag/Tag	1/9	1	2	FACETS	0.896	0.737	1	0.896	0.737	1	CLONAL	1	TRUE	1	0.33	2		284	230	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073928	8073928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746056102	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	181	578	0	ENST00000377482.5:c.731G>A	p.Arg244Gln	p.R244Q	ENST00000377482	NM_018948.3	244	cGa/cAa	4/4	1	2	FACETS	0.868	0.804	0.933	1	0.992	1	CLONAL	2	TRUE	1	0.33	2		578	632	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630638	158630638	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs387906591	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	54	277	0	ENST00000263640.3:c.605G>T	p.Arg202Ile	p.R202I	ENST00000263640	NM_001105.4	202	aGa/aTa	6/11	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.33	2		277	290	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291528	10291528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755995375	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	37	706	1	ENST00000340748.4:c.151G>A	p.Glu51Lys	p.E51K	ENST00000340748		51	Gaa/Aaa	3/40	1	2	FACETS	0.335	0.275	0.402	0.335	0.275	0.402	SUBCLONAL	1	TRUE	1	0.33	2		707	670	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793432	18793432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs187869576	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	87	604	1	ENST00000266497.5:c.4129C>T	p.Arg1377Cys	p.R1377C	ENST00000266497		1377	Cgt/Tgt	30/31	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.33	2		605	512	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398896	398896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	43	635	0	ENST00000380956.4:c.706G>A	p.Glu236Lys	p.E236K	ENST00000380956	NM_001195286.1	236	Gag/Aag	6/9	1	2	FACETS	0.405	0.338	0.479	0.405	0.338	0.479	SUBCLONAL	1	TRUE	1	0.33	2		635	644	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281219	46281219	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	44	621	1	ENST00000371998.3:c.4016G>T	p.Arg1339Ile	p.R1339I	ENST00000371998		1339	aGa/aTa	21/23	1	2	FACETS	0.407	0.341	0.481	0.407	0.341	0.481	SUBCLONAL	1	TRUE	1	0.33	2		622	655	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633825	86633825	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	40	401	0	ENST00000274376.6:c.934G>T	p.Glu312Ter	p.E312*	ENST00000274376	NM_002890.2	312	Gaa/Taa	5/25	1	2	FACETS	0.94	0.786	1	0.94	0.786	1	CLONAL	1	TRUE	1	0.33	2		401	258	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937950	76937950	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	41	796	2	ENST00000373344.5:c.2798C>A	p.Ser933Tyr	p.S933Y	ENST00000373344	NM_000489.3	933	tCt/tAt	9/35	1	2	FACETS	0.329	0.273	0.391	0.329	0.273	0.391	SUBCLONAL	1	TRUE	1	0.33	2		798	756	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143035	30143035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	54	942	0	ENST00000389048.3:c.491G>A	p.Gly164Glu	p.G164E	ENST00000389048	NM_004304.4	164	gGg/gAg	1/29	1	2	FACETS	0.33	0.281	0.385	0.33	0.281	0.385	SUBCLONAL	1	TRUE	1	0.33	2		942	991	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976703	2976703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	58	609	0	ENST00000396946.4:c.1309C>T	p.Arg437Cys	p.R437C	ENST00000396946	NM_032415.4	437	Cgc/Tgc	9/25	1	2	FACETS	0.476	0.408	0.551	0.476	0.408	0.551	SUBCLONAL	1	TRUE	1	0.33	2		609	738	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584489	39584489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1403147154	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	81	409	0	ENST00000262039.4:c.1154G>A	p.Arg385Gln	p.R385Q	ENST00000262039	NM_002647.2	385	cGa/cAa	10/25	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.33	2		409	487	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5065040	5065040	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs267602253	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	17	372	0	ENST00000381652.3:c.1214C>T	p.Ser405Leu	p.S405L	ENST00000381652	NM_004972.3	405	tCg/tTg	9/25	1	2	FACETS	0.311	0.232	0.406	0.311	0.232	0.406	SUBCLONAL	1	TRUE	1	0.33	2		372	331	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170815004	170815004	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	28	425	0	ENST00000296930.5:c.52C>A	p.Leu18Ile	p.L18I	ENST00000296930	NM_002520.6	18	Ctt/Att	1/11	1	2	FACETS	0.341	0.272	0.42	0.341	0.272	0.42	SUBCLONAL	1	TRUE	1	0.33	2		425	498	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5077508	5077508	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	42	460	0	ENST00000381652.3:c.1920G>T	p.Lys640Asn	p.K640N	ENST00000381652	NM_004972.3	640	aaG/aaT	15/25	1	2	FACETS	0.811	0.68	0.955	0.811	0.68	0.955	CLONAL	1	TRUE	1	0.33	2		460	314	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740436	58740436	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs769061997	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	137	742	0	ENST00000305921.3:c.1341G>T	p.Glu447Asp	p.E447D	ENST00000305921	NM_003620.3	447	gaG/gaT	6/6	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.33	2		742	662	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100016	11100016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749059769	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	162	742	2	ENST00000358026.2:c.1142G>A	p.Arg381Gln	p.R381Q	ENST00000358026	NM_001128849.1	381	cGa/cAa	7/36	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.33	2		744	801	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121756	108121756	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	104	695	0	ENST00000278616.4:c.1564G>T	p.Glu522Ter	p.E522*	ENST00000278616	NM_000051.3	522	Gaa/Taa	10/63	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.33	2		695	612	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136182	11136182	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs267605281	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	123	642	1	ENST00000358026.2:c.3166G>A	p.Glu1056Lys	p.E1056K	ENST00000358026	NM_001128849.1	1056	Gag/Aag	22/36	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.33	2		643	693	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854897	76854897	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	95	781	0	ENST00000373344.5:c.5939C>T	p.Ser1980Phe	p.S1980F	ENST00000373344	NM_000489.3	1980	tCt/tTt	25/35	1	2	FACETS	0.986	0.88	1	0.986	0.88	1	CLONAL	1	TRUE	1	0.33	2		781	584	SUCCESS
APC	324	MSKCC	GRCh37	5	112178781	112178781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141010008	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	38	581	0	ENST00000257430.4:c.7490C>T	p.Ser2497Leu	p.S2497L	ENST00000257430	NM_000038.5	2497	tCg/tTg	16/16	1	2	FACETS	0.413	0.34	0.494	0.413	0.34	0.494	SUBCLONAL	1	TRUE	1	0.33	2		581	558	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6029587	6029587	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	109	605	0	ENST00000265849.7:c.989-1G>A		p.X330_splice	ENST00000265849	NM_000535.5	330			1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.33	2		605	612	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934284	68934284	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146218789	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	26	517	0	ENST00000288368.4:c.350G>A	p.Arg117His	p.R117H	ENST00000288368	NM_024870.2	117	cGt/cAt	4/40	1	2	FACETS	0.329	0.26	0.409	0.329	0.26	0.409	SUBCLONAL	1	TRUE	1	0.33	2		517	479	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004277	29004277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370686484	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	28	441	2	ENST00000282397.4:c.1016G>A	p.Arg339Gln	p.R339Q	ENST00000282397	NM_002019.4	339	cGa/cAa	8/30	1	2	FACETS	0.372	0.297	0.458	0.372	0.297	0.458	SUBCLONAL	1	TRUE	1	0.33	2		443	456	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953887	17953887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750606059	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	57	960	1	ENST00000458235.1:c.515G>A	p.Arg172Gln	p.R172Q	ENST00000458235	NM_000215.3	172	cGg/cAg	5/24	1	2	FACETS	0.337	0.288	0.391	0.337	0.288	0.391	SUBCLONAL	1	TRUE	1	0.33	2		961	1024	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826539	50826539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1315227790	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	21	468	0	ENST00000398568.2:c.2264G>A	p.Arg755Gln	p.R755Q	ENST00000398568	NM_001042412.1	755	cGa/cAa	15/18	1	2	FACETS	0.335	0.257	0.426	0.335	0.257	0.426	SUBCLONAL	1	TRUE	1	0.33	2		468	380	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804348	46804348	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	39	622	1	ENST00000290295.7:c.659G>A	p.Arg220His	p.R220H	ENST00000290295	NM_006361.5	220	cGc/cAc	2/2	1	2	FACETS	0.305	0.251	0.364	0.305	0.251	0.364	SUBCLONAL	1	TRUE	1	0.33	2		623	776	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342507	118342507	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	12	223	0	ENST00000534358.1:c.633G>T	p.Lys211Asn	p.K211N	ENST00000534358	NM_005933.3	211	aaG/aaT	3/36	1	2	FACETS	0.355	0.249	0.484	0.355	0.249	0.484	SUBCLONAL	1	TRUE	1	0.33	2		223	205	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679798	88679798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774739739	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	37	650	0	ENST00000360948.2:c.665G>A	p.Arg222Gln	p.R222Q	ENST00000360948	NM_001012338.2	222	cGa/cAa	7/19	1	2	FACETS	0.314	0.257	0.377	0.314	0.257	0.377	SUBCLONAL	1	TRUE	1	0.33	2		650	715	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955524	90955524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753270166	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	135	659	1	ENST00000265433.3:c.2141G>A	p.Arg714Gln	p.R714Q	ENST00000265433	NM_002485.4	714	cGa/cAa	14/16	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.33	2		660	581	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031979	10031979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	130	600	2	ENST00000330684.3:c.844G>A	p.Asp282Asn	p.D282N	ENST00000330684	NM_001134407.1	282	Gat/Aat	3/13	1	2	FACETS	0.934	0.847	1	0.934	0.847	1	CLONAL	1	TRUE	1	0.33	2		602	844	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873661	35873661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs193922644	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	30	376	0	ENST00000303115.3:c.617G>A	p.Arg206Gln	p.R206Q	ENST00000303115	NM_002185.3	206	cGa/cAa	5/8	1	2	FACETS	0.457	0.368	0.558	0.457	0.368	0.558	SUBCLONAL	1	TRUE	1	0.33	2		376	398	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125533	7125533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867354196	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	34	542	1	ENST00000302850.5:c.3019C>T	p.Pro1007Ser	p.P1007S	ENST00000302850	NM_000208.2	1007	Cca/Tca	17/22	1	2	FACETS	0.341	0.277	0.412	0.341	0.277	0.412	SUBCLONAL	1	TRUE	1	0.33	2		543	605	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610715	52610715	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	26	441	0	ENST00000394830.3:c.3459-1G>T		p.X1153_splice	ENST00000394830	NM_018313.4	1153			1	2	FACETS	0.39	0.308	0.484	0.39	0.308	0.484	SUBCLONAL	1	TRUE	1	0.33	2		441	404	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650720	67650720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	164	780	0	ENST00000264010.4:c.1025G>A	p.Arg342His	p.R342H	ENST00000264010	NM_006565.3	342	cGt/cAt	5/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.33	2		780	809	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76919048	76919048	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	45	365	0	ENST00000373344.5:c.3944-1G>T		p.X1315_splice	ENST00000373344	NM_000489.3	1315			1	2	FACETS	0.733	0.618	0.86	0.733	0.618	0.86	SUBCLONAL	1	TRUE	1	0.33	2		365	372	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43769902	43769902	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	149	718	1	ENST00000382044.4:c.844G>T	p.Glu282Ter	p.E282*	ENST00000382044	NM_001141980.1	282	Gaa/Taa	8/28	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.33	2		719	651	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073692	8073692	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	120	442	1	ENST00000377482.5:c.967G>T	p.Glu323Ter	p.E323*	ENST00000377482	NM_018948.3	323	Gaa/Taa	4/4	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.33	2		443	557	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434118	12434118	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	31	401	0	ENST00000287820.6:c.486C>A	p.Phe162Leu	p.F162L	ENST00000287820	NM_015869.4	162	ttC/ttA	4/7	1	2	FACETS	0.471	0.381	0.573	0.471	0.381	0.573	SUBCLONAL	1	TRUE	1	0.33	2		401	399	SUCCESS
APC	324	MSKCC	GRCh37	5	112177368	112177368	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	60	395	0	ENST00000257430.4:c.6077C>T	p.Ser2026Phe	p.S2026F	ENST00000257430	NM_000038.5	2026	tCt/tTt	16/16	1	2	FACETS	0.921	0.796	1	0.921	0.796	1	CLONAL	1	TRUE	1	0.33	2		395	395	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724138	112724138	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	19	320	0	ENST00000369452.4:c.22G>T	p.Glu8Ter	p.E8*	ENST00000369452	NM_007373.3	8	Gaa/Taa	2/9	1	2	FACETS	0.379	0.287	0.486	0.379	0.287	0.486	SUBCLONAL	1	TRUE	1	0.33	2		320	304	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796753	135796753	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755859330	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	26	390	0	ENST00000298552.3:c.734G>A	p.Arg245Gln	p.R245Q	ENST00000298552	NM_001162426.1	245	cGa/cAa	8/23	1	2	FACETS	0.44	0.348	0.545	0.44	0.348	0.545	SUBCLONAL	1	TRUE	1	0.33	2		390	358	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884466	151884466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1435892915	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	30	498	1	ENST00000262189.6:c.4889C>T	p.Ser1630Leu	p.S1630L	ENST00000262189	NM_170606.2	1630	tCg/tTg	33/59	1	2	FACETS	0.311	0.249	0.381	0.311	0.249	0.381	SUBCLONAL	1	TRUE	1	0.33	2		499	585	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714237	43714237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1171556914	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	183	1061	1	ENST00000382044.4:c.3916G>A	p.Asp1306Asn	p.D1306N	ENST00000382044	NM_001141980.1	1306	Gat/Aat	19/28	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.33	2		1062	994	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259681	11259681	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs939676380	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	46	651	1	ENST00000361445.4:c.4024G>A	p.Glu1342Lys	p.E1342K	ENST00000361445	NM_004958.3	1342	Gag/Aag	27/58	1	2	FACETS	0.389	0.326	0.458	0.389	0.326	0.458	SUBCLONAL	1	TRUE	1	0.33	2		652	717	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776309	76776309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	86	988	1	ENST00000373344.5:c.7157G>A	p.Arg2386Gln	p.R2386Q	ENST00000373344	NM_000489.3	2386	cGa/cAa	34/35	1	2	FACETS	0.69	0.61	0.776	0.69	0.61	0.776	SUBCLONAL	1	TRUE	1	0.33	2		989	755	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435188	56435188	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1348340748	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	142	829	0	ENST00000407977.2:c.1949G>A	p.Arg650Gln	p.R650Q	ENST00000407977		650	cGa/cAa	9/10	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.33	2		829	843	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16056687	16056687	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs767188997	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	23	446	0	ENST00000268712.3:c.755A>C	p.Lys252Thr	p.K252T	ENST00000268712	NM_006311.3	252	aAa/aCa	7/46	1	2	FACETS	0.37	0.288	0.465	0.37	0.288	0.465	SUBCLONAL	1	TRUE	1	0.33	2		446	377	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803500	32803500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550712305	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	59	907	0	ENST00000374899.4:c.659G>A	p.Arg220Gln	p.R220Q	ENST00000374899	NM_018833.2	220	cGa/cAa	4/12	1	2	FACETS	0.363	0.311	0.42	0.363	0.311	0.42	SUBCLONAL	1	TRUE	1	0.33	2		907	986	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202926	27202926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772637203	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	91	644	0	ENST00000380036.4:c.2018G>A	p.Arg673His	p.R673H	ENST00000380036	NM_000459.3	673	cGt/cAt	13/23	1	2	FACETS	0.921	0.819	1	0.921	0.819	1	CLONAL	1	TRUE	1	0.33	2		644	599	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984079	2984079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	37	643	0	ENST00000396946.4:c.451G>A	p.Glu151Lys	p.E151K	ENST00000396946	NM_032415.4	151	Gag/Aag	5/25	1	2	FACETS	0.321	0.263	0.385	0.321	0.263	0.385	SUBCLONAL	1	TRUE	1	0.33	2		643	699	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805352	89805352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745882980	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	39	706	0	ENST00000389301.3:c.4198C>T	p.Arg1400Cys	p.R1400C	ENST00000389301	NM_000135.2	1400	Cgt/Tgt	42/43	1	2	FACETS	0.313	0.258	0.374	0.313	0.258	0.374	SUBCLONAL	1	TRUE	1	0.33	2		706	755	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162750028	162750028	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771898787	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	83	425	1	ENST00000367921.3:c.2560G>A	p.Asp854Asn	p.D854N	ENST00000367921	NM_006182.2	854	Gac/Aac	18/18	0.139888192623542	1	FACETS	0.89	0.788	0.998	0.89	0.788	0.998	INDETERMINATE	1	TRUE	0	0.33	1		426	472	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069620	69069620	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	76	613	0	ENST00000288368.4:c.4295A>G	p.Gln1432Arg	p.Q1432R	ENST00000288368	NM_024870.2	1432	cAg/cGg	35/40	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.33	2		613	453	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665109	182665109	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	90	535	0	ENST00000292782.4:c.617G>A	p.Arg206Gln	p.R206Q	ENST00000292782	NM_020640.2	206	cGa/cAa	6/7	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.33	2		535	438	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851828	63851828	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs201944744	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	75	677	0	ENST00000279873.7:c.2606C>A	p.Ser869Tyr	p.S869Y	ENST00000279873	NM_032199.2	869	tCt/tAt	10/10	1	2	FACETS	0.653	0.572	0.741	0.653	0.572	0.741	SUBCLONAL	1	TRUE	1	0.33	2		677	696	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060728	38060728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	212	1126	2	ENST00000250448.2:c.1261G>A	p.Glu421Lys	p.E421K	ENST00000250448	NM_004496.3	421	Gaa/Aaa	2/2	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.33	2		1128	1180	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141012	55141012	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501502	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	69	428	0	ENST00000257290.5:c.1658C>T	p.Pro553Leu	p.P553L	ENST00000257290	NM_006206.4	553	cCg/cTg	12/23	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.33	2		428	375	SUCCESS
APC	324	MSKCC	GRCh37	5	112177377	112177377	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	22	371	0	ENST00000257430.4:c.6086C>A	p.Ser2029Tyr	p.S2029Y	ENST00000257430	NM_000038.5	2029	tCt/tAt	16/16	1	2	FACETS	0.337	0.26	0.426	0.337	0.26	0.426	SUBCLONAL	1	TRUE	1	0.33	2		371	396	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173730	108173730	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	19	418	0	ENST00000278616.4:c.5470C>A	p.Leu1824Ile	p.L1824I	ENST00000278616	NM_000051.3	1824	Ctt/Att	36/63	1	2	FACETS	0.366	0.277	0.47	0.366	0.277	0.47	SUBCLONAL	1	TRUE	1	0.33	2		418	315	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729635	162729635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	39	656	0	ENST00000367921.3:c.721G>A	p.Asp241Asn	p.D241N	ENST00000367921	NM_006182.2	241	Gat/Aat	8/18	1	2	FACETS	0.341	0.281	0.407	0.341	0.281	0.407	SUBCLONAL	1	TRUE	1	0.33	2		656	694	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143494	108143494	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs766342338	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	60	719	0	ENST00000278616.4:c.3199G>T	p.Asp1067Tyr	p.D1067Y	ENST00000278616	NM_000051.3	1067	Gac/Tac	22/63	1	2	FACETS	0.766	0.661	0.879	0.766	0.661	0.879	SUBCLONAL	1	TRUE	1	0.33	2		719	475	SUCCESS
APC	324	MSKCC	GRCh37	5	112177354	112177354	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	27	423	0	ENST00000257430.4:c.6063C>A	p.Phe2021Leu	p.F2021L	ENST00000257430	NM_000038.5	2021	ttC/ttA	16/16	1	2	FACETS	0.413	0.328	0.51	0.413	0.328	0.51	SUBCLONAL	1	TRUE	1	0.33	2		423	396	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103322	119103322	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	96	576	0	ENST00000264033.4:c.360G>T	p.Glu120Asp	p.E120D	ENST00000264033	NM_005188.3	120	gaG/gaT	2/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.33	2		576	456	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646149	215646149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881412	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	32	703	0	ENST00000260947.4:c.449G>A	p.Arg150Gln	p.R150Q	ENST00000260947	NM_000465.2	150	cGa/cAa	4/11	1	2	FACETS	0.321	0.26	0.391	0.321	0.26	0.391	SUBCLONAL	1	TRUE	1	0.33	2		703	604	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509660	106509660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757849968	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	98	602	4	ENST00000359195.3:c.1654C>T	p.Arg552Cys	p.R552C	ENST00000359195	NM_002649.2	552	Cgc/Tgc	2/11	1	2	FACETS	0.935	0.836	1	0.935	0.836	1	CLONAL	1	TRUE	1	0.33	2		606	635	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467884	66467884	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	57	487	0	ENST00000273854.3:c.385G>T	p.Glu129Ter	p.E129*	ENST00000273854	NM_004439.5	129	Gaa/Taa	3/18	1	2	FACETS	0.753	0.647	0.868	0.753	0.647	0.868	SUBCLONAL	1	TRUE	1	0.33	2		487	459	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710875	117710875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140178288	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	100	608	1	ENST00000368508.3:c.1397G>A	p.Arg466Gln	p.R466Q	ENST00000368508	NM_002944.2	466	cGa/cAa	12/43	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.33	2		609	577	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001373	150001373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200119992	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	38	895	2	ENST00000253339.5:c.2231G>A	p.Arg744Gln	p.R744Q	ENST00000253339		744	cGa/cAa	4/7	1	2	FACETS	0.349	0.288	0.419	0.349	0.288	0.419	SUBCLONAL	1	TRUE	1	0.33	2		897	659	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590927	95590927	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	23	448	1	ENST00000393063.1:c.982G>T	p.Glu328Ter	p.E328*	ENST00000393063	NM_030621.3	328	Gaa/Taa	9/28	1	2	FACETS	0.33	0.256	0.415	0.33	0.256	0.415	SUBCLONAL	1	TRUE	1	0.33	2		449	423	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710987	117710987	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	19	305	0	ENST00000368508.3:c.1285G>T	p.Asp429Tyr	p.D429Y	ENST00000368508	NM_002944.2	429	Gat/Tat	12/43	1	2	FACETS	0.397	0.301	0.51	0.397	0.301	0.51	SUBCLONAL	1	TRUE	1	0.33	2		305	290	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243030	105243030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1566818890	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	66	880	2	ENST00000349310.3:c.253G>A	p.Glu85Lys	p.E85K	ENST00000349310	NM_001014432.1	85	Gaa/Aaa	5/15	1	2	FACETS	0.384	0.332	0.441	0.384	0.332	0.441	SUBCLONAL	1	TRUE	1	0.33	2		882	1041	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170832364	170832364	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	18	311	1	ENST00000296930.5:c.728C>A	p.Ser243Tyr	p.S243Y	ENST00000296930	NM_002520.6	243	tCt/tAt	9/11	1	2	FACETS	0.41	0.309	0.53	0.41	0.309	0.53	SUBCLONAL	1	TRUE	1	0.33	2		312	266	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972866	25972866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	105	703	1	ENST00000435504.4:c.1559C>T	p.Ser520Phe	p.S520F	ENST00000435504		520	tCt/tTt	12/13	1	2	FACETS	0.899	0.806	0.997	0.899	0.806	0.997	CLONAL	1	TRUE	1	0.33	2		704	708	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939483	68939483	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs772266269	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	70	492	0	ENST00000288368.4:c.468G>T	p.Lys156Asn	p.K156N	ENST00000288368	NM_024870.2	156	aaG/aaT	5/40	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.33	2		492	409	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158129	106158129	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs770136804	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	22	372	0	ENST00000380013.4:c.3030G>T	p.Glu1010Asp	p.E1010D	ENST00000380013	NM_001127208.2	1010	gaG/gaT	3/11	1	2	FACETS	0.32	0.247	0.404	0.32	0.247	0.404	SUBCLONAL	1	TRUE	1	0.33	2		372	417	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752361	57752361	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	27	546	0	ENST00000274289.3:c.1212G>T	p.Lys404Asn	p.K404N	ENST00000274289	NM_006622.3	404	aaG/aaT	9/14	1	2	FACETS	0.323	0.256	0.4	0.323	0.256	0.4	SUBCLONAL	1	TRUE	1	0.33	2		546	506	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131315	202131315	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	33	571	0	ENST00000358485.4:c.283G>T	p.Glu95Ter	p.E95*	ENST00000358485	NM_001080125.1	95	Gaa/Taa	2/9	1	2	FACETS	0.377	0.307	0.457	0.377	0.307	0.457	SUBCLONAL	1	TRUE	1	0.33	2		571	530	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690570	88690570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	35	483	1	ENST00000360948.2:c.460G>A	p.Glu154Lys	p.E154K	ENST00000360948	NM_001012338.2	154	Gaa/Aaa	5/19	1	2	FACETS	0.419	0.343	0.505	0.419	0.343	0.505	SUBCLONAL	1	TRUE	1	0.33	2		484	506	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537246	80537246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	38	742	0	ENST00000286548.4:c.152G>A	p.Gly51Asp	p.G51D	ENST00000286548	NM_002072.3	51	gGc/gAc	2/7	1	2	FACETS	0.31	0.255	0.372	0.31	0.255	0.372	SUBCLONAL	1	TRUE	1	0.33	2		742	742	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939158	76939158	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	42	777	0	ENST00000373344.5:c.1590G>T	p.Glu530Asp	p.E530D	ENST00000373344	NM_000489.3	530	gaG/gaT	9/35	1	2	FACETS	0.33	0.274	0.392	0.33	0.274	0.392	SUBCLONAL	1	TRUE	1	0.33	2		777	772	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073350	8073350	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	100	738	0	ENST00000377482.5:c.1309G>T	p.Glu437Ter	p.E437*	ENST00000377482	NM_018948.3	437	Gaa/Taa	4/4	1	2	FACETS	0.837	0.748	0.932	0.837	0.748	0.932	CLONAL	1	TRUE	1	0.33	2		738	724	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073509	8073509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	147	541	0	ENST00000377482.5:c.1150G>T	p.Glu384Ter	p.E384*	ENST00000377482	NM_018948.3	384	Gaa/Taa	4/4	1	2	FACETS	0.755	0.692	0.82	1	0.988	1	SUBCLONAL	2	TRUE	1	0.33	2		541	590	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11193205	11193205	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	58	841	0	ENST00000361445.4:c.5296G>T	p.Glu1766Ter	p.E1766*	ENST00000361445	NM_004958.3	1766	Gag/Tag	38/58	1	2	FACETS	0.406	0.348	0.47	0.406	0.348	0.47	SUBCLONAL	1	TRUE	1	0.33	2		841	866	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257985	16257985	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	40	535	0	ENST00000375759.3:c.5250T>G	p.Asp1750Glu	p.D1750E	ENST00000375759	NM_015001.2	1750	gaT/gaG	11/15	1	2	FACETS	0.419	0.347	0.499	0.419	0.347	0.499	SUBCLONAL	1	TRUE	1	0.33	2		535	579	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22413036	22413036	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	64	310	0	ENST00000344548.3:c.283G>T	p.Glu95Ter	p.E95*	ENST00000344548	NM_001039802.1	95	Gaa/Taa	5/7	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.33	2		310	318	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023682	27023682	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	102	647	0	ENST00000324856.7:c.788C>A	p.Ser263Tyr	p.S263Y	ENST00000324856	NM_006015.4	263	tCt/tAt	1/20	1	2	FACETS	0.953	0.853	1	0.953	0.853	1	CLONAL	1	TRUE	1	0.33	2		647	649	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36931961	36931961	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	132	549	1	ENST00000361632.4:c.2508C>A	p.Phe836Leu	p.F836L	ENST00000361632		836	ttC/ttA	16/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.33	2		550	588	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937934	36937934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	174	1015	0	ENST00000361632.4:c.902C>T	p.Thr301Met	p.T301M	ENST00000361632		301	aCg/aTg	7/16	1	2	FACETS	0.996	0.916	1	0.996	0.916	1	CLONAL	1	TRUE	1	0.33	2		1015	1059	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436146	51436146	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	53	368	0	ENST00000262662.1:c.106G>T	p.Gly36Ter	p.G36*	ENST00000262662		36	Gga/Tga	3/4	1	2	FACETS	0.822	0.703	0.951	0.822	0.703	0.951	CLONAL	1	TRUE	1	0.33	2		368	391	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313289	65313289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	35	736	0	ENST00000342505.4:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000342505	NM_002227.2	609	Gaa/Aaa	13/25	1	2	FACETS	0.307	0.251	0.371	0.307	0.251	0.371	SUBCLONAL	1	TRUE	1	0.33	2		736	690	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330476	65330476	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	73	561	0	ENST00000342505.4:c.1170G>T	p.Lys390Asn	p.K390N	ENST00000342505	NM_002227.2	390	aaG/aaT	8/25	1	2	FACETS	0.822	0.72	0.932	0.822	0.72	0.932	CLONAL	1	TRUE	1	0.33	2		561	538	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78426167	78426167	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	57	305	0	ENST00000370768.2:c.1358C>A	p.Pro453His	p.P453H	ENST00000370768	NM_003902.3	453	cCt/cAt	15/20	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.33	2		305	320	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115272882	115272882	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	91	760	0	ENST00000438362.2:c.1491G>T	p.Glu497Asp	p.E497D	ENST00000438362	NM_001242891.1	497	gaG/gaT	12/20	1	2	FACETS	0.89	0.791	0.995	0.89	0.791	0.995	CLONAL	1	TRUE	1	0.33	2		760	620	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115284149	115284149	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	88	563	0	ENST00000438362.2:c.137C>A	p.Ser46Tyr	p.S46Y	ENST00000438362	NM_001242891.1	46	tCt/tAt	2/20	1	2	FACETS	0.942	0.837	1	0.942	0.837	1	CLONAL	1	TRUE	1	0.33	2		563	566	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729663	162729663	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	41	672	0	ENST00000367921.3:c.749T>C	p.Val250Ala	p.V250A	ENST00000367921	NM_006182.2	250	gTg/gCg	8/18	1	2	FACETS	0.343	0.284	0.408	0.343	0.284	0.408	SUBCLONAL	1	TRUE	1	0.33	2		672	725	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737039	162737039	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1403575672	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	37	672	0	ENST00000367921.3:c.1183G>T	p.Asp395Tyr	p.D395Y	ENST00000367921	NM_006182.2	395	Gac/Tac	11/18	1	2	FACETS	0.318	0.261	0.382	0.318	0.261	0.382	SUBCLONAL	1	TRUE	1	0.33	2		672	705	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984340	201984340	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	40	578	0	ENST00000359651.3:c.1005C>A	p.Tyr335Ter	p.Y335*	ENST00000359651		335	taC/taA	8/8	1	2	FACETS	0.371	0.307	0.442	0.371	0.307	0.442	SUBCLONAL	1	TRUE	1	0.33	2		578	654	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63661997	63661997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	106	572	0	ENST00000279873.7:c.101G>A	p.Arg34Lys	p.R34K	ENST00000279873	NM_032199.2	34	aGa/aAa	2/10	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.33	2		572	618	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332679	70332679	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	102	706	0	ENST00000373644.4:c.584G>T	p.Arg195Ile	p.R195I	ENST00000373644	NM_030625.2	195	aGa/aTa	2/12	1	2	FACETS	0.873	0.781	0.971	0.873	0.781	0.971	CLONAL	1	TRUE	1	0.33	2		706	708	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333925	70333925	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	77	346	1	ENST00000373644.4:c.1830G>T	p.Lys610Asn	p.K610N	ENST00000373644	NM_030625.2	610	aaG/aaT	2/12	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.33	2		347	441	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685303	89685303	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	33	422	0	ENST00000371953.3:c.198G>T	p.Lys66Asn	p.K66N	ENST00000371953	NM_000314.4	66	aaG/aaT	3/9	1	2	FACETS	0.901	0.739	1	0.901	0.739	1	CLONAL	1	TRUE	1	0.33	2		422	222	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94908801	94908801	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	32	599	0	ENST00000536441.1:c.1253A>G	p.Asp418Gly	p.D418G	ENST00000536441	NM_144665.3	418	gAt/gGt	9/10	1	2	FACETS	0.389	0.315	0.473	0.389	0.315	0.473	SUBCLONAL	1	TRUE	1	0.33	2		599	498	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999575	100999575	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	65	1226	0	ENST00000325455.5:c.227A>G	p.Asp76Gly	p.D76G	ENST00000325455	NM_001202474.3	76	gAc/gGc	1/8	1	2	FACETS	0.315	0.271	0.362	0.315	0.271	0.362	SUBCLONAL	1	TRUE	1	0.33	2		1226	1252	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142118	108142118	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	66	622	0	ENST00000278616.4:c.3062T>C	p.Val1021Ala	p.V1021A	ENST00000278616	NM_000051.3	1021	gTa/gCa	20/63	1	2	FACETS	0.82	0.713	0.935	0.82	0.713	0.935	CLONAL	1	TRUE	1	0.33	2		622	488	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235887	108235887	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	32	616	0	ENST00000278616.4:c.8929G>T	p.Glu2977Ter	p.E2977*	ENST00000278616	NM_000051.3	2977	Gaa/Taa	62/63	1	2	FACETS	0.354	0.286	0.43	0.354	0.286	0.43	SUBCLONAL	1	TRUE	1	0.33	2		616	548	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375326	118375326	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	120	491	0	ENST00000534358.1:c.8719A>G	p.Thr2907Ala	p.T2907A	ENST00000534358	NM_005933.3	2907	Aca/Gca	27/36	1	2	FACETS	0.766	0.695	0.839	1	0.986	1	SUBCLONAL	2	TRUE	1	0.33	2		491	475	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380671	118380671	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	47	365	0	ENST00000534358.1:c.10909A>G	p.Thr3637Ala	p.T3637A	ENST00000534358	NM_005933.3	3637	Aca/Gca	30/36	1	2	FACETS	0.861	0.729	1	0.861	0.729	1	CLONAL	1	TRUE	1	0.33	2		365	331	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385325	4385325	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867376054	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	83	430	2	ENST00000261254.3:c.350C>T	p.Pro117Leu	p.P117L	ENST00000261254	NM_001759.3	117	cCg/cTg	2/5	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.33	2		432	470	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544146	18544146	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	19	454	0	ENST00000266497.5:c.1963A>C	p.Lys655Gln	p.K655Q	ENST00000266497		655	Aaa/Caa	13/31	1	2	FACETS	0.322	0.244	0.414	0.322	0.244	0.414	SUBCLONAL	1	TRUE	1	0.33	2		454	358	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719938	18719938	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	48	648	0	ENST00000266497.5:c.3835G>T	p.Asp1279Tyr	p.D1279Y	ENST00000266497		1279	Gat/Tat	27/31	1	2	FACETS	0.63	0.533	0.736	0.63	0.533	0.736	SUBCLONAL	1	TRUE	1	0.33	2		648	462	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944931	31944931	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	30	383	0	ENST00000340398.3:c.170C>A	p.Ser57Ter	p.S57*	ENST00000340398	NM_001013699.2	57	tCg/tAg	1/1	1	2	FACETS	0.378	0.304	0.462	0.378	0.304	0.462	SUBCLONAL	1	TRUE	1	0.33	2		383	481	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123662	46123662	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs774482788	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	45	323	0	ENST00000334344.6:c.43A>C	p.Lys15Gln	p.K15Q	ENST00000334344	NM_152641.2	15	Aag/Cag	1/21	1	2	FACETS	0.696	0.586	0.817	0.696	0.586	0.817	SUBCLONAL	1	TRUE	1	0.33	2		323	392	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231350	46231350	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	31	643	0	ENST00000334344.6:c.1190A>C	p.Gln397Pro	p.Q397P	ENST00000334344	NM_152641.2	397	cAg/cCg	10/21	1	2	FACETS	0.364	0.294	0.444	0.364	0.294	0.444	SUBCLONAL	1	TRUE	1	0.33	2		643	516	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479996	50479996	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	57	784	0	ENST00000394963.4:c.230G>T	p.Gly77Val	p.G77V	ENST00000394963	NM_003076.4	77	gGa/gTa	2/13	1	2	FACETS	0.437	0.374	0.506	0.437	0.374	0.506	SUBCLONAL	1	TRUE	1	0.33	2		784	791	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144740	58144740	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	101	615	0	ENST00000257904.6:c.488G>T	p.Arg163Ile	p.R163I	ENST00000257904	NM_000075.3	163	aGa/aTa	4/8	1	2	FACETS	0.965	0.864	1	0.965	0.864	1	CLONAL	1	TRUE	1	0.33	2		615	634	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145001	58145001	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772938517	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	125	623	0	ENST00000257904.6:c.343G>A	p.Glu115Lys	p.E115K	ENST00000257904	NM_000075.3	115	Gaa/Aaa	3/8	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.33	2		623	707	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975698	26975698	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	34	518	0	ENST00000381527.3:c.1206G>T	p.Lys402Asn	p.K402N	ENST00000381527	NM_001260.1	402	aaG/aaT	12/13	1	2	FACETS	0.362	0.295	0.437	0.362	0.295	0.437	SUBCLONAL	1	TRUE	1	0.33	2		518	570	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041067	29041067	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	37	583	0	ENST00000282397.4:c.361G>T	p.Glu121Ter	p.E121*	ENST00000282397	NM_002019.4	121	Gaa/Taa	3/30	1	2	FACETS	0.342	0.281	0.411	0.342	0.281	0.411	SUBCLONAL	1	TRUE	1	0.33	2		583	655	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912291	32912291	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	30	596	0	ENST00000380152.3:c.3799G>T	p.Asp1267Tyr	p.D1267Y	ENST00000380152		1267	Gat/Tat	11/27	1	2	FACETS	0.321	0.258	0.393	0.321	0.258	0.393	SUBCLONAL	1	TRUE	1	0.33	2		596	566	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915273	32915273	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs876660812	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	41	786	1	ENST00000380152.3:c.6781G>T	p.Glu2261Ter	p.E2261*	ENST00000380152		2261	Gaa/Taa	11/27	1	2	FACETS	0.433	0.36	0.514	0.433	0.36	0.514	SUBCLONAL	1	TRUE	1	0.33	2		787	574	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878068	48878068	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	41	301	0	ENST00000267163.4:c.20del	p.Arg7GlnfsTer58	p.R7Qfs*58	ENST00000267163	NM_000321.2	7	cGa/ca	1/27	1	2	FACETS	0.804	0.673	0.949	0.804	0.673	0.949	CLONAL	1	TRUE	1	0.33	2		301	309	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941739	48941739	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1368390928	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	16	420	0	ENST00000267163.4:c.1049G>T	p.Ser350Ile	p.S350I	ENST00000267163	NM_000321.2	350	aGt/aTt	10/27	1	2	FACETS	0.334	0.247	0.439	0.334	0.247	0.439	SUBCLONAL	1	TRUE	1	0.33	2		420	290	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955517	48955517	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	28	526	0	ENST00000267163.4:c.1633G>T	p.Glu545Ter	p.E545*	ENST00000267163	NM_000321.2	545	Gaa/Taa	17/27	1	2	FACETS	0.438	0.35	0.539	0.438	0.35	0.539	SUBCLONAL	1	TRUE	1	0.33	2		526	387	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281864	49281864	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	43	832	0	ENST00000282018.3:c.911T>C	p.Leu304Pro	p.L304P	ENST00000282018	NM_020377.2	304	cTc/cCc	1/1	1	2	FACETS	0.318	0.265	0.377	0.318	0.265	0.377	SUBCLONAL	1	TRUE	1	0.33	2		832	819	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73333958	73333958	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	80	741	0	ENST00000377767.4:c.2852A>C	p.Lys951Thr	p.K951T	ENST00000377767	NM_014953.3	951	aAa/aCa	21/21	1	2	FACETS	0.867	0.765	0.977	0.867	0.765	0.977	CLONAL	1	TRUE	1	0.33	2		741	559	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506717	103506717	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	31	184	0	ENST00000355739.4:c.460A>C	p.Lys154Gln	p.K154Q	ENST00000355739	NM_000123.3	154	Aaa/Caa	4/15	1	2	FACETS	0.912	0.743	1	0.912	0.743	1	CLONAL	1	TRUE	1	0.33	2		184	206	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103510633	103510633	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	38	448	0	ENST00000355739.4:c.537C>A	p.Phe179Leu	p.F179L	ENST00000355739	NM_000123.3	179	ttC/ttA	6/15	1	2	FACETS	0.647	0.536	0.77	0.647	0.536	0.77	SUBCLONAL	1	TRUE	1	0.33	2		448	356	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527822	103527822	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs768440346	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	68	402	0	ENST00000355739.4:c.3130G>T	p.Glu1044Ter	p.E1044*	ENST00000355739	NM_000123.3	1044	Gaa/Taa	15/15	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.33	2		402	392	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438161	110438161	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	28	389	0	ENST00000375856.3:c.240A>C	p.Lys80Asn	p.K80N	ENST00000375856	NM_003749.2	80	aaA/aaC	1/2	1	2	FACETS	0.366	0.292	0.45	0.366	0.292	0.45	SUBCLONAL	1	TRUE	1	0.33	2		389	464	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68934929	68934929	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	90	561	0	ENST00000487270.1:c.998T>G	p.Phe333Cys	p.F333C	ENST00000487270	NM_133509.3	333	tTt/tGt	10/11	1	2	FACETS	0.926	0.823	1	0.926	0.823	1	CLONAL	1	TRUE	1	0.33	2		561	589	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609650	81609650	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	76	783	1	ENST00000298171.2:c.1248C>A	p.Phe416Leu	p.F416L	ENST00000298171	NM_000369.2	416	ttC/ttA	10/10	1	2	FACETS	0.606	0.531	0.687	0.606	0.531	0.687	SUBCLONAL	1	TRUE	1	0.33	2		784	760	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614570	38614570	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	29	791	0	ENST00000299084.4:c.336T>G	p.Phe112Leu	p.F112L	ENST00000299084	NM_152594.2	112	ttT/ttG	3/7	1	2	FACETS	0.328	0.262	0.403	0.328	0.262	0.403	SUBCLONAL	1	TRUE	1	0.33	2		791	536	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988360	41988360	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	119	687	0	ENST00000219905.7:c.1152A>T	p.Glu384Asp	p.E384D	ENST00000219905	NM_001164273.1	384	gaA/gaT	3/24	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.33	2		687	716	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41999967	41999967	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	110	846	0	ENST00000219905.7:c.2230G>T	p.Asp744Tyr	p.D744Y	ENST00000219905	NM_001164273.1	744	Gat/Tat	6/24	1	2	FACETS	0.95	0.854	1	0.95	0.854	1	CLONAL	1	TRUE	1	0.33	2		846	702	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701145	43701145	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	33	602	0	ENST00000382044.4:c.5550T>G	p.Asn1850Lys	p.N1850K	ENST00000382044	NM_001141980.1	1850	aaT/aaG	26/28	1	2	FACETS	0.325	0.264	0.395	0.325	0.264	0.395	SUBCLONAL	1	TRUE	1	0.33	2		602	615	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748591	43748591	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	69	1161	0	ENST00000382044.4:c.2215C>A	p.Leu739Ile	p.L739I	ENST00000382044	NM_001141980.1	739	Ctt/Att	12/28	1	2	FACETS	0.388	0.336	0.443	0.388	0.336	0.443	SUBCLONAL	1	TRUE	1	0.33	2		1161	1079	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292688	91292688	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	28	476	0	ENST00000355112.3:c.190G>T	p.Asp64Tyr	p.D64Y	ENST00000355112	NM_000057.2	64	Gat/Tat	3/22	1	2	FACETS	0.374	0.298	0.46	0.374	0.298	0.46	SUBCLONAL	1	TRUE	1	0.33	2		476	454	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104300	2104300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397515021	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	99	577	0	ENST00000219476.3:c.340G>A	p.Glu114Lys	p.E114K	ENST00000219476	NM_000548.3	114	Gag/Aag	5/42	1	2	FACETS	0.86	0.768	0.957	0.86	0.768	0.957	CLONAL	1	TRUE	1	0.33	2		577	698	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652187	3652187	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	55	1002	1	ENST00000294008.3:c.882C>A	p.Phe294Leu	p.F294L	ENST00000294008	NM_032444.2	294	ttC/ttA	4/15	1	2	FACETS	0.319	0.272	0.372	0.319	0.272	0.372	SUBCLONAL	1	TRUE	1	0.33	2		1003	1044	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658656	3658656	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	66	1244	1	ENST00000294008.3:c.310C>A	p.Gln104Lys	p.Q104K	ENST00000294008	NM_032444.2	104	Caa/Aaa	2/15	1	2	FACETS	0.322	0.278	0.369	0.322	0.278	0.369	SUBCLONAL	1	TRUE	1	0.33	2		1245	1244	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857199	9857199	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	91	542	0	ENST00000330684.3:c.4202T>G	p.Leu1401Arg	p.L1401R	ENST00000330684	NM_001134407.1	1401	cTt/cGt	13/13	1	2	FACETS	0.951	0.846	1	0.951	0.846	1	CLONAL	1	TRUE	1	0.33	2		542	580	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641346	23641346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759024828	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	142	921	3	ENST00000261584.4:c.2129C>T	p.Thr710Met	p.T710M	ENST00000261584	NM_024675.3	710	aCg/aTg	5/13	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.33	2		924	847	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783853	50783853	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	71	811	2	ENST00000398568.2:c.244C>A	p.Leu82Ile	p.L82I	ENST00000398568	NM_001042412.1	82	Ctc/Atc	3/18	1	2	FACETS	0.638	0.557	0.727	0.638	0.557	0.727	SUBCLONAL	1	TRUE	1	0.33	2		813	674	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829522	72829522	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	47	855	0	ENST00000268489.5:c.7059G>T	p.Lys2353Asn	p.K2353N	ENST00000268489	NM_006885.3	2353	aaG/aaT	9/10	1	2	FACETS	0.308	0.259	0.363	0.308	0.259	0.363	SUBCLONAL	1	TRUE	1	0.33	2		855	925	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830406	72830406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	63	404	0	ENST00000268489.5:c.6175G>A	p.Ala2059Thr	p.A2059T	ENST00000268489	NM_006885.3	2059	Gcg/Acg	9/10	1	2	FACETS	0.868	0.753	0.992	0.868	0.753	0.992	CLONAL	1	TRUE	1	0.33	2		404	440	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991576	72991576	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	64	1018	0	ENST00000268489.5:c.2469G>T	p.Met823Ile	p.M823I	ENST00000268489	NM_006885.3	823	atG/atT	2/10	1	2	FACETS	0.342	0.295	0.394	0.342	0.295	0.394	SUBCLONAL	1	TRUE	1	0.33	2		1018	1134	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992568	72992568	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	100	818	0	ENST00000268489.5:c.1477G>T	p.Gly493Ter	p.G493*	ENST00000268489	NM_006885.3	493	Gga/Tga	2/10	1	2	FACETS	0.662	0.59	0.738	0.662	0.59	0.738	SUBCLONAL	1	TRUE	1	0.33	2		818	916	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509673	29509673	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs778606171	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	23	546	0	ENST00000356175.3:c.878A>C	p.Asn293Thr	p.N293T	ENST00000356175	NM_000267.3	293	aAc/aCc	8/57	1	2	FACETS	0.365	0.284	0.459	0.365	0.284	0.459	SUBCLONAL	1	TRUE	1	0.33	2		546	382	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553692	29553692	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	35	785	0	ENST00000356175.3:c.2241G>T	p.Met747Ile	p.M747I	ENST00000356175	NM_000267.3	747	atG/atT	18/57	1	2	FACETS	0.319	0.261	0.386	0.319	0.261	0.386	SUBCLONAL	1	TRUE	1	0.33	2		785	664	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556440	29556440	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	38	709	0	ENST00000356175.3:c.2807A>C	p.Lys936Thr	p.K936T	ENST00000356175	NM_000267.3	936	aAa/aCa	21/57	1	2	FACETS	0.353	0.291	0.422	0.353	0.291	0.422	SUBCLONAL	1	TRUE	1	0.33	2		709	653	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37672011	37672011	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	103	730	1	ENST00000447079.4:c.2796G>T	p.Lys932Asn	p.K932N	ENST00000447079	NM_015083.1	932	aaG/aaT	9/14	1	2	FACETS	0.983	0.881	1	0.983	0.881	1	CLONAL	1	TRUE	1	0.33	2		731	635	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244543	41244543	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	120	957	1	ENST00000357654.3:c.3005A>G	p.Asn1002Ser	p.N1002S	ENST00000357654	NM_007294.3	1002	aAc/aGc	10/23	1	2	FACETS	0.97	0.876	1	0.97	0.876	1	CLONAL	1	TRUE	1	0.33	2		958	750	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245047	41245047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757383244	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	59	1163	0	ENST00000357654.3:c.2501G>A	p.Gly834Glu	p.G834E	ENST00000357654	NM_007294.3	834	gGa/gAa	10/23	1	2	FACETS	0.394	0.338	0.455	0.394	0.338	0.455	SUBCLONAL	1	TRUE	1	0.33	2		1163	908	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245278	41245278	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	51	1022	0	ENST00000357654.3:c.2270T>C	p.Val757Ala	p.V757A	ENST00000357654	NM_007294.3	757	gTt/gCt	10/23	1	2	FACETS	0.32	0.27	0.374	0.32	0.27	0.374	SUBCLONAL	1	TRUE	1	0.33	2		1022	967	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246166	41246166	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	44	815	0	ENST00000357654.3:c.1382T>G	p.Phe461Cys	p.F461C	ENST00000357654	NM_007294.3	461	tTt/tGt	10/23	1	2	FACETS	0.349	0.292	0.413	0.349	0.292	0.413	SUBCLONAL	1	TRUE	1	0.33	2		815	764	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41247926	41247926	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	33	587	1	ENST00000357654.3:c.607G>T	p.Glu203Ter	p.E203*	ENST00000357654	NM_007294.3	203	Gaa/Taa	9/23	1	2	FACETS	0.351	0.285	0.426	0.351	0.285	0.426	SUBCLONAL	1	TRUE	1	0.33	2		588	569	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804291	46804291	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	46	787	0	ENST00000290295.7:c.716A>C	p.Lys239Thr	p.K239T	ENST00000290295	NM_006361.5	239	aAg/aCg	2/2	1	2	FACETS	0.304	0.255	0.359	0.304	0.255	0.359	SUBCLONAL	1	TRUE	1	0.33	2		787	916	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55334859	55334859	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	139	584	0	ENST00000284073.2:c.136G>A	p.Glu46Lys	p.E46K	ENST00000284073	NM_138962.2	46	Gaa/Aaa	3/14	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.33	2		584	575	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59861674	59861674	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	100	616	0	ENST00000259008.2:c.1585G>T	p.Gly529Ter	p.G529*	ENST00000259008	NM_032043.2	529	Gga/Tga	11/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.33	2		616	498	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117780	70117780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	46	780	0	ENST00000245479.2:c.248G>A	p.Gly83Asp	p.G83D	ENST00000245479	NM_000346.3	83	gGc/gAc	1/3	1	2	FACETS	0.317	0.266	0.374	0.317	0.266	0.374	SUBCLONAL	1	TRUE	1	0.33	2		780	880	SUCCESS
YES1	7525	MSKCC	GRCh37	18	739800	739800	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1432620928	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	73	509	0	ENST00000314574.4:c.1072G>T	p.Asp358Tyr	p.D358Y	ENST00000314574	NM_005433.3	358	Gat/Tat	9/12	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.33	2		509	440	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39593530	39593530	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	35	355	0	ENST00000262039.4:c.1295A>C	p.Asn432Thr	p.N432T	ENST00000262039	NM_002647.2	432	aAt/aCt	11/25	1	2	FACETS	0.884	0.729	1	0.884	0.729	1	CLONAL	1	TRUE	1	0.33	2		355	240	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395710	45395710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	81	495	0	ENST00000262160.6:c.424G>A	p.Glu142Lys	p.E142K	ENST00000262160	NM_005901.5	142	Gaa/Aaa	4/11	1	2	FACETS	0.907	0.801	1	0.907	0.801	1	CLONAL	1	TRUE	1	0.33	2		495	541	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172323	7172323	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs778989302	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	39	513	0	ENST00000302850.5:c.1246C>T	p.Arg416Ter	p.R416*	ENST00000302850	NM_000208.2	416	Cga/Tga	5/22	1	2	FACETS	0.435	0.36	0.519	0.435	0.36	0.519	SUBCLONAL	1	TRUE	1	0.33	2		513	543	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051462	13051462	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	86	447	0	ENST00000316448.5:c.810G>T	p.Glu270Asp	p.E270D	ENST00000316448	NM_004343.3	270	gaG/gaT	6/9	1	2	FACETS	0.978	0.867	1	0.978	0.867	1	CLONAL	1	TRUE	1	0.33	2		447	533	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278158	15278158	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	53	946	0	ENST00000263388.2:c.5264T>C	p.Leu1755Pro	p.L1755P	ENST00000263388	NM_000435.2	1755	cTg/cCg	29/33	1	2	FACETS	0.304	0.258	0.354	0.304	0.258	0.354	SUBCLONAL	1	TRUE	1	0.33	2		946	1058	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300127	15300127	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	58	924	0	ENST00000263388.2:c.1149C>A	p.Phe383Leu	p.F383L	ENST00000263388	NM_000435.2	383	ttC/ttA	7/33	1	2	FACETS	0.374	0.32	0.433	0.374	0.32	0.433	SUBCLONAL	1	TRUE	1	0.33	2		924	940	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355299	15355299	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1465213842	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	93	478	0	ENST00000263377.2:c.2324A>C	p.Gln775Pro	p.Q775P	ENST00000263377	NM_058243.2	775	cAg/cCg	13/20	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.33	2		478	502	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942524	17942524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763951351	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	135	813	0	ENST00000458235.1:c.2764G>A	p.Asp922Asn	p.D922N	ENST00000458235	NM_000215.3	922	Gat/Aat	20/24	1	2	FACETS	0.981	0.892	1	0.981	0.892	1	CLONAL	1	TRUE	1	0.33	2		813	834	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951074	17951074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	41	706	1	ENST00000458235.1:c.1219G>A	p.Asp407Asn	p.D407N	ENST00000458235	NM_000215.3	407	Gac/Aac	9/24	1	2	FACETS	0.319	0.264	0.379	0.319	0.264	0.379	SUBCLONAL	1	TRUE	1	0.33	2		707	780	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303897	30303897	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	39	657	0	ENST00000262643.3:c.133G>T	p.Glu45Ter	p.E45*	ENST00000262643	NM_001238.2	45	Gaa/Taa	4/12	1	2	FACETS	0.306	0.253	0.366	0.306	0.253	0.366	SUBCLONAL	1	TRUE	1	0.33	2		657	772	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744410	41744410	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148886744	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	123	860	0	ENST00000301178.4:c.1030C>T	p.Arg344Trp	p.R344W	ENST00000301178	NM_021913.4	344	Cgg/Tgg	8/20	1	2	FACETS	0.857	0.774	0.944	0.857	0.774	0.944	CLONAL	1	TRUE	1	0.33	2		860	870	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446389	29446389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774836034	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	57	1019	0	ENST00000389048.3:c.3178C>T	p.Arg1060Cys	p.R1060C	ENST00000389048	NM_004304.4	1060	Cgc/Tgc	20/29	1	2	FACETS	0.322	0.275	0.374	0.322	0.275	0.374	SUBCLONAL	1	TRUE	1	0.33	2		1019	1073	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018209	48018209	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	118	723	0	ENST00000234420.5:c.404A>G	p.Asp135Gly	p.D135G	ENST00000234420	NM_000179.2	135	gAt/gGt	2/10	1	2	FACETS	0.881	0.794	0.972	0.881	0.794	0.972	CLONAL	1	TRUE	1	0.33	2		723	812	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026567	48026567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773226008	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	100	516	0	ENST00000234420.5:c.1445G>A	p.Arg482Gln	p.R482Q	ENST00000234420	NM_000179.2	482	cGa/cAa	4/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.33	2		516	535	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027593	48027593	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	89	405	0	ENST00000234420.5:c.2471A>C	p.Lys824Thr	p.K824T	ENST00000234420	NM_000179.2	824	aAa/aCa	4/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.33	2		405	393	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028004	48028004	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	24	370	0	ENST00000234420.5:c.2882G>A	p.Arg961Lys	p.R961K	ENST00000234420	NM_000179.2	961	aGa/aAa	4/10	1	2	FACETS	0.376	0.294	0.47	0.376	0.294	0.47	SUBCLONAL	1	TRUE	1	0.33	2		370	387	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147190	61147190	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	64	411	0	ENST00000295025.8:c.868A>G	p.Lys290Glu	p.K290E	ENST00000295025	NM_002908.2	290	Aaa/Gaa	8/11	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.33	2		411	361	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096082	178096082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746016111	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	71	632	0	ENST00000397062.3:c.1249G>A	p.Val417Met	p.V417M	ENST00000397062	NM_006164.4	417	Gtg/Atg	5/5	1	2	FACETS	0.668	0.583	0.76	0.668	0.583	0.76	SUBCLONAL	1	TRUE	1	0.33	2		632	644	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131183	202131183	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	48	399	0	ENST00000358485.4:c.152-1G>T		p.X51_splice	ENST00000358485	NM_001080125.1	51			1	2	FACETS	0.788	0.669	0.919	0.788	0.669	0.919	CLONAL	1	TRUE	1	0.33	2		399	369	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131364	202131364	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	93	526	0	ENST00000358485.4:c.332G>T	p.Arg111Ile	p.R111I	ENST00000358485	NM_001080125.1	111	aGa/aTa	2/9	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.33	2		526	526	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131375	202131375	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	116	538	0	ENST00000358485.4:c.343G>A	p.Glu115Lys	p.E115K	ENST00000358485	NM_001080125.1	115	Gaa/Aaa	2/9	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.33	2		538	529	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209101875	209101875	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	68	570	1	ENST00000345146.2:c.1173C>A	p.Tyr391Ter	p.Y391*	ENST00000345146	NM_005896.2	391	taC/taA	10/10	1	2	FACETS	0.954	0.833	1	0.954	0.833	1	CLONAL	1	TRUE	1	0.33	2		571	432	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209108298	209108298	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	32	575	0	ENST00000345146.2:c.551A>C	p.Asn184Thr	p.N184T	ENST00000345146	NM_005896.2	184	aAt/aCt	6/10	1	2	FACETS	0.357	0.289	0.434	0.357	0.289	0.434	SUBCLONAL	1	TRUE	1	0.33	2		575	544	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645784	215645784	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	104	719	0	ENST00000260947.4:c.814T>G	p.Phe272Val	p.F272V	ENST00000260947	NM_000465.2	272	Ttt/Gtt	4/11	1	2	FACETS	0.954	0.855	1	0.954	0.855	1	CLONAL	1	TRUE	1	0.33	2		719	661	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662805	227662805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	59	802	1	ENST00000305123.5:c.650C>T	p.Ser217Leu	p.S217L	ENST00000305123	NM_005544.2	217	tCg/tTg	1/2	1	2	FACETS	0.37	0.317	0.428	0.37	0.317	0.428	SUBCLONAL	1	TRUE	1	0.33	2		803	966	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385260	41385260	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	36	670	0	ENST00000373198.4:c.701A>G	p.Asp234Gly	p.D234G	ENST00000373198	NM_133170.3	234	gAc/gGc	6/32	1	2	FACETS	0.358	0.294	0.431	0.358	0.294	0.431	SUBCLONAL	1	TRUE	1	0.33	2		670	609	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958042	54958042	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs779964295	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	36	300	0	ENST00000312783.6:c.565C>T	p.Arg189Trp	p.R189W	ENST00000312783	NM_198436.1	189	Cgg/Tgg	6/10	1	2	FACETS	0.699	0.577	0.836	0.699	0.577	0.836	SUBCLONAL	1	TRUE	1	0.33	2		300	312	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145583	24145583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555877287	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	45	801	0	ENST00000263121.7:c.602G>A	p.Arg201Gln	p.R201Q	ENST00000263121	NM_003073.3	201	cGa/cAa	5/9	1	2	FACETS	0.318	0.266	0.376	0.318	0.266	0.376	SUBCLONAL	1	TRUE	1	0.33	2		801	858	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519889	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	23	599	1	ENST00000263253.7:c.4195G>T	p.Asp1399Tyr	p.D1399Y	ENST00000263253	NM_001429.3	1399	Gat/Tat	26/31	1	2	FACETS	0.262	0.203	0.33	0.262	0.203	0.33	SUBCLONAL	1	TRUE	1	0.33	2		600	532	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37092144	37092144	+	stop_lost	Nonstop_Mutation	SNP	A	A	C	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	27	483	0	ENST00000231790.2:c.2271A>C	p.Ter757TyrextTer36	p.*757Yext*36	ENST00000231790	NM_000249.3	757	taA/taC	19/19	1	2	FACETS	0.35	0.278	0.433	0.35	0.278	0.433	SUBCLONAL	1	TRUE	1	0.33	2		483	467	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267225	41267225	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	37	507	0	ENST00000349496.5:c.809A>C	p.Lys270Thr	p.K270T	ENST00000349496	NM_001904.3	270	aAa/aCa	6/15	1	2	FACETS	0.369	0.304	0.443	0.369	0.304	0.443	SUBCLONAL	1	TRUE	1	0.33	2		507	607	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47061326	47061326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775780402	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	25	489	0	ENST00000409792.3:c.7355C>T	p.Ser2452Leu	p.S2452L	ENST00000409792	NM_014159.6	2452	tCg/tTg	19/21	1	2	FACETS	0.321	0.252	0.4	0.321	0.252	0.4	SUBCLONAL	1	TRUE	1	0.33	2		489	472	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443599	52443599	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	83	557	0	ENST00000460680.1:c.93G>T	p.Glu31Asp	p.E31D	ENST00000460680	NM_004656.3	31	gaG/gaT	3/17	1	2	FACETS	0.833	0.736	0.937	0.833	0.736	0.937	CLONAL	1	TRUE	1	0.33	2		557	604	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72897372	72897372	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	60	388	1	ENST00000325599.8:c.120C>A	p.Phe40Leu	p.F40L	ENST00000325599	NM_018130.2	40	ttC/ttA	1/11	1	2	FACETS	0.767	0.662	0.881	0.767	0.662	0.881	SUBCLONAL	1	TRUE	1	0.33	2		389	474	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390088	89390088	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	62	424	0	ENST00000336596.2:c.837G>T	p.Lys279Asn	p.K279N	ENST00000336596	NM_005233.5	279	aaG/aaT	4/17	1	2	FACETS	0.848	0.735	0.971	0.848	0.735	0.971	CLONAL	1	TRUE	1	0.33	2		424	443	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119624700	119624700	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	20	431	0	ENST00000316626.5:c.716-1G>T		p.X239_splice	ENST00000316626		239			1	2	FACETS	0.306	0.233	0.392	0.306	0.233	0.392	SUBCLONAL	1	TRUE	1	0.33	2		431	396	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453575	138453575	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	82	592	0	ENST00000289153.2:c.873A>C	p.Lys291Asn	p.K291N	ENST00000289153	NM_006219.2	291	aaA/aaC	5/22	1	2	FACETS	0.986	0.872	1	0.986	0.872	1	CLONAL	1	TRUE	1	0.33	2		592	504	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474805	138474805	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	68	473	0	ENST00000289153.2:c.188T>C	p.Val63Ala	p.V63A	ENST00000289153	NM_006219.2	63	gTt/gCt	2/22	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.33	2		473	403	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226779	142226779	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	74	437	0	ENST00000350721.4:c.5025T>G	p.Phe1675Leu	p.F1675L	ENST00000350721	NM_001184.3	1675	ttT/ttG	28/47	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.33	2		437	440	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272100	142272100	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	36	650	0	ENST00000350721.4:c.2774T>G	p.Phe925Cys	p.F925C	ENST00000350721	NM_001184.3	925	tTt/tGt	13/47	1	2	FACETS	0.376	0.308	0.452	0.376	0.308	0.452	SUBCLONAL	1	TRUE	1	0.33	2		650	580	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281515	142281515	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	45	754	0	ENST00000350721.4:c.729A>C	p.Lys243Asn	p.K243N	ENST00000350721	NM_001184.3	243	aaA/aaC	4/47	1	2	FACETS	0.39	0.327	0.46	0.39	0.327	0.46	SUBCLONAL	1	TRUE	1	0.33	2		754	699	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170020884	170020884	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	35	270	1	ENST00000295797.4:c.1760C>A	p.Pro587His	p.P587H	ENST00000295797	NM_002740.5	587	cCt/cAt	18/18	1	2	FACETS	0.996	0.823	1	0.996	0.823	1	CLONAL	1	TRUE	1	0.33	2		271	213	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182662938	182662938	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	89	552	0	ENST00000292782.4:c.724G>T	p.Asp242Tyr	p.D242Y	ENST00000292782	NM_020640.2	242	Gac/Tac	7/7	1	2	FACETS	0.916	0.813	1	0.916	0.813	1	CLONAL	1	TRUE	1	0.33	2		552	589	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665375	182665375	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	16	328	0	ENST00000292782.4:c.566G>T	p.Arg189Ile	p.R189I	ENST00000292782	NM_020640.2	189	aGa/aTa	5/7	1	2	FACETS	0.325	0.24	0.428	0.325	0.24	0.428	SUBCLONAL	1	TRUE	1	0.33	2		328	298	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1795732	1795732	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	84	357	0	ENST00000260795.2:c.71C>A	p.Ser24Tyr	p.S24Y	ENST00000260795		24	tCc/tAc	1/17	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.33	2		357	435	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141007	55141007	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	54	411	0	ENST00000257290.5:c.1654-1G>T		p.X552_splice	ENST00000257290	NM_006206.4	552			1	2	FACETS	0.88	0.754	1	0.88	0.754	1	CLONAL	1	TRUE	1	0.33	2		411	372	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970882	55970882	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	40	684	1	ENST00000263923.4:c.1915G>T	p.Asp639Tyr	p.D639Y	ENST00000263923	NM_002253.2	639	Gac/Tac	13/30	1	2	FACETS	0.349	0.289	0.416	0.349	0.289	0.416	SUBCLONAL	1	TRUE	1	0.33	2		685	695	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218777	66218777	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	68	374	0	ENST00000273854.3:c.2281T>G	p.Leu761Val	p.L761V	ENST00000273854	NM_004439.5	761	Tta/Gta	13/18	1	2	FACETS	0.818	0.72	0.92	1	0.978	1	CLONAL	2	TRUE	1	0.33	2		374	252	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356339	66356339	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	107	587	0	ENST00000273854.3:c.1158G>T	p.Arg386Ser	p.R386S	ENST00000273854	NM_004439.5	386	agG/agT	5/18	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.33	2		587	618	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467988	66467988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	54	473	1	ENST00000273854.3:c.281C>T	p.Ala94Val	p.A94V	ENST00000273854	NM_004439.5	94	gCc/gTc	3/18	1	2	FACETS	0.892	0.765	1	0.892	0.765	1	CLONAL	1	TRUE	1	0.33	2		474	367	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197568	106197568	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	31	473	0	ENST00000380013.4:c.5901C>A	p.Phe1967Leu	p.F1967L	ENST00000380013	NM_001127208.2	1967	ttC/ttA	11/11	1	2	FACETS	0.445	0.36	0.542	0.445	0.36	0.542	SUBCLONAL	1	TRUE	1	0.33	2		473	422	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130067	143130067	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	23	695	0	ENST00000262992.4:c.949G>T	p.Glu317Ter	p.E317*	ENST00000262992	NM_001101669.1	317	Gaa/Taa	11/24	1	2	FACETS	0.318	0.247	0.4	0.318	0.247	0.4	SUBCLONAL	1	TRUE	1	0.33	2		695	439	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245420	153245420	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	97	783	0	ENST00000281708.4:c.1771G>T	p.Asp591Tyr	p.D591Y	ENST00000281708	NM_033632.3	591	Gac/Tac	11/12	1	2	FACETS	0.87	0.776	0.969	0.87	0.776	0.969	CLONAL	1	TRUE	1	0.33	2		783	676	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245518	153245518	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	89	512	0	ENST00000281708.4:c.1673C>A	p.Ser558Tyr	p.S558Y	ENST00000281708	NM_033632.3	558	tCt/tAt	11/12	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.33	2		512	492	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268093	153268093	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	56	340	0	ENST00000281708.4:c.715A>C	p.Lys239Gln	p.K239Q	ENST00000281708	NM_033632.3	239	Aaa/Caa	4/12	1	2	FACETS	0.8	0.688	0.923	0.8	0.688	0.923	CLONAL	1	TRUE	1	0.33	2		340	424	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527366	187527366	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	86	462	0	ENST00000441802.2:c.10208T>G	p.Ile3403Ser	p.I3403S	ENST00000441802	NM_005245.3	3403	aTt/aGt	17/27	1	2	FACETS	0.991	0.879	1	0.991	0.879	1	CLONAL	1	TRUE	1	0.33	2		462	526	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532659	187532659	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs758260235	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	91	591	0	ENST00000441802.2:c.9734T>C	p.Val3245Ala	p.V3245A	ENST00000441802	NM_005245.3	3245	gTt/gCt	14/27	1	2	FACETS	0.904	0.804	1	0.904	0.804	1	CLONAL	1	TRUE	1	0.33	2		591	610	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542914	187542914	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	50	332	0	ENST00000441802.2:c.4826C>A	p.Ser1609Tyr	p.S1609Y	ENST00000441802	NM_005245.3	1609	tCt/tAt	10/27	1	2	FACETS	0.902	0.769	1	0.902	0.769	1	CLONAL	1	TRUE	1	0.33	2		332	336	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293671	1293671	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	185	958	1	ENST00000310581.5:c.1330G>T	p.Asp444Tyr	p.D444Y	ENST00000310581	NM_198253.2	444	Gac/Tac	2/16	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.33	2		959	1086	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31401601	31401601	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	143	787	0	ENST00000344624.3:c.4063A>C	p.Met1355Leu	p.M1355L	ENST00000344624		1355	Atg/Ctg	33/33	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.33	2		787	818	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867477	35867477	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	49	341	0	ENST00000303115.3:c.291G>T	p.Lys97Asn	p.K97N	ENST00000303115	NM_002185.3	97	aaG/aaT	3/8	1	2	FACETS	0.9	0.766	1	0.9	0.766	1	CLONAL	1	TRUE	1	0.33	2		341	330	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876302	35876302	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	38	647	1	ENST00000303115.3:c.1094C>A	p.Ser365Ter	p.S365*	ENST00000303115	NM_002185.3	365	tCa/tAa	8/8	1	2	FACETS	0.34	0.28	0.407	0.34	0.28	0.407	SUBCLONAL	1	TRUE	1	0.33	2		648	677	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953100	38953100	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	33	323	0	ENST00000357387.3:c.2884C>A	p.Leu962Ile	p.L962I	ENST00000357387	NM_152756.3	962	Ctt/Att	29/38	1	2	FACETS	0.877	0.719	1	0.877	0.719	1	CLONAL	1	TRUE	1	0.33	2		323	228	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38955713	38955713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	44	468	0	ENST00000357387.3:c.2593C>T	p.Arg865Cys	p.R865C	ENST00000357387	NM_152756.3	865	Cgt/Tgt	26/38	1	2	FACETS	0.725	0.609	0.852	0.725	0.609	0.852	SUBCLONAL	1	TRUE	1	0.33	2		468	368	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181803	56181803	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	63	457	0	ENST00000399503.3:c.4027G>T	p.Glu1343Ter	p.E1343*	ENST00000399503	NM_005921.1	1343	Gaa/Taa	17/20	1	2	FACETS	0.945	0.821	1	0.945	0.821	1	CLONAL	1	TRUE	1	0.33	2		457	404	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80057444	80057444	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	20	487	0	ENST00000265081.6:c.1843C>G	p.Leu615Val	p.L615V	ENST00000265081	NM_002439.4	615	Cta/Gta	13/24	1	2	FACETS	0.312	0.238	0.4	0.312	0.238	0.4	SUBCLONAL	1	TRUE	1	0.33	2		487	388	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80071522	80071522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	54	447	0	ENST00000265081.6:c.2263G>A	p.Glu755Lys	p.E755K	ENST00000265081	NM_002439.4	755	Gaa/Aaa	16/24	1	2	FACETS	0.885	0.758	1	0.885	0.758	1	CLONAL	1	TRUE	1	0.33	2		447	370	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627247	86627247	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	51	519	0	ENST00000274376.6:c.622G>T	p.Glu208Ter	p.E208*	ENST00000274376	NM_002890.2	208	Gag/Tag	2/25	1	2	FACETS	0.707	0.602	0.822	0.707	0.602	0.822	SUBCLONAL	1	TRUE	1	0.33	2		519	437	SUCCESS
APC	324	MSKCC	GRCh37	5	112174376	112174376	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	14	331	0	ENST00000257430.4:c.3085C>A	p.Leu1029Ile	p.L1029I	ENST00000257430	NM_000038.5	1029	Ctt/Att	16/16	1	2	FACETS	0.337	0.243	0.45	0.337	0.243	0.45	SUBCLONAL	1	TRUE	1	0.33	2		331	252	SUCCESS
APC	324	MSKCC	GRCh37	5	112179452	112179452	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782312	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	37	554	0	ENST00000257430.4:c.8161C>T	p.Arg2721Cys	p.R2721C	ENST00000257430	NM_000038.5	2721	Cgc/Tgc	16/16	1	2	FACETS	0.414	0.341	0.497	0.414	0.341	0.497	SUBCLONAL	1	TRUE	1	0.33	2		554	541	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923308	131923308	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	10	230	0	ENST00000265335.6:c.811G>T	p.Glu271Ter	p.E271*	ENST00000265335		271	Gaa/Taa	6/25	1	2	FACETS	0.322	0.218	0.453	0.322	0.218	0.453	SUBCLONAL	1	TRUE	1	0.33	2		230	188	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149434859	149434859	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	51	824	0	ENST00000286301.3:c.2595C>A	p.Phe865Leu	p.F865L	ENST00000286301	NM_005211.3	865	ttC/ttA	20/22	1	2	FACETS	0.394	0.334	0.46	0.394	0.334	0.46	SUBCLONAL	1	TRUE	1	0.33	2		824	785	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562927	176562927	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs754265807	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	33	589	0	ENST00000439151.2:c.823A>C	p.Asn275His	p.N275H	ENST00000439151	NM_022455.4	275	Aat/Cat	2/23	1	2	FACETS	0.351	0.285	0.426	0.351	0.285	0.426	SUBCLONAL	1	TRUE	1	0.33	2		589	569	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637673	176637673	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	39	725	0	ENST00000439151.2:c.2273C>A	p.Ser758Ter	p.S758*	ENST00000439151	NM_022455.4	758	tCa/tAa	5/23	1	2	FACETS	0.304	0.251	0.364	0.304	0.251	0.364	SUBCLONAL	1	TRUE	1	0.33	2		725	777	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694671	176694671	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs754939355	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	83	585	0	ENST00000439151.2:c.5255A>G	p.Lys1752Arg	p.K1752R	ENST00000439151	NM_022455.4	1752	aAa/aGa	15/23	1	2	FACETS	0.944	0.835	1	0.944	0.835	1	CLONAL	1	TRUE	1	0.33	2		585	533	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709561	176709561	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	32	458	0	ENST00000439151.2:c.5988C>A	p.Phe1996Leu	p.F1996L	ENST00000439151	NM_022455.4	1996	ttC/ttA	19/23	1	2	FACETS	0.42	0.34	0.51	0.42	0.34	0.51	SUBCLONAL	1	TRUE	1	0.33	2		458	462	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20486969	20486969	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	24	425	1	ENST00000346618.3:c.934G>T	p.Asp312Tyr	p.D312Y	ENST00000346618	NM_001949.4	312	Gac/Tac	5/7	1	2	FACETS	0.33	0.258	0.413	0.33	0.258	0.413	SUBCLONAL	1	TRUE	1	0.33	2		426	441	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056484	26056484	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs550065694	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	61	322	0	ENST00000343677.2:c.173C>A	p.Ser58Tyr	p.S58Y	ENST00000343677	NM_005319.3	58	tCt/tAt	1/1	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.33	2		322	342	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911143	29911143	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	125	382	0	ENST00000376809.5:c.442A>C	p.Ile148Leu	p.I148L	ENST00000376809	NM_002116.7	148	Atc/Ctc	3/8	1	2	FACETS	0.924	0.844	1	1	0.99	1	CLONAL	2	TRUE	1	0.33	2		382	410	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324054	31324054	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	102	587	0	ENST00000412585.2:c.509A>C	p.Lys170Thr	p.K170T	ENST00000412585	NM_005514.6	170	aAg/aCg	3/8	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.33	2		587	558	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908170	41908170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1278695873	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	62	869	0	ENST00000372991.4:c.352C>T	p.Pro118Ser	p.P118S	ENST00000372991	NM_001760.3	118	Ccc/Tcc	2/5	1	2	FACETS	0.361	0.31	0.416	0.361	0.31	0.416	SUBCLONAL	1	TRUE	1	0.33	2		869	1042	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120683	94120683	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	103	626	0	ENST00000369303.4:c.368T>G	p.Phe123Cys	p.F123C	ENST00000369303	NM_004440.3	123	tTt/tGt	3/17	1	2	FACETS	0.988	0.885	1	0.988	0.885	1	CLONAL	1	TRUE	1	0.33	2		626	632	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674241	117674241	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	48	770	0	ENST00000368508.3:c.4233G>T	p.Lys1411Asn	p.K1411N	ENST00000368508	NM_002944.2	1411	aaG/aaT	26/43	1	2	FACETS	0.383	0.323	0.45	0.383	0.323	0.45	SUBCLONAL	1	TRUE	1	0.33	2		770	759	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686368	117686368	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	34	219	0	ENST00000368508.3:c.2974-1G>A		p.X992_splice	ENST00000368508	NM_002944.2	992			1	2	FACETS	1	0.84	1	1	0.84	1	CLONAL	1	TRUE	1	0.33	2		219	202	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708061	117708061	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	21	523	0	ENST00000368508.3:c.2116A>C	p.Asn706His	p.N706H	ENST00000368508	NM_002944.2	706	Aat/Cat	14/43	1	2	FACETS	0.311	0.239	0.396	0.311	0.239	0.396	SUBCLONAL	1	TRUE	1	0.33	2		523	409	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997696	149997696	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749907686	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	27	452	0	ENST00000253339.5:c.2771G>A	p.Arg924Gln	p.R924Q	ENST00000253339		924	cGa/cAa	5/7	1	2	FACETS	0.345	0.274	0.427	0.345	0.274	0.427	SUBCLONAL	1	TRUE	1	0.33	2		452	474	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157488266	157488266	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	94	545	0	ENST00000346085.5:c.2972A>G	p.Asn991Ser	p.N991S	ENST00000346085	NM_020732.3	991	aAc/aGc	10/20	1	2	FACETS	0.953	0.849	1	0.953	0.849	1	CLONAL	1	TRUE	1	0.33	2		545	598	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55225369	55225369	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	42	625	0	ENST00000275493.2:c.1221T>G	p.Ile407Met	p.I407M	ENST00000275493	NM_005228.3	407	atT/atG	11/28	1	2	FACETS	0.386	0.322	0.458	0.386	0.322	0.458	SUBCLONAL	1	TRUE	1	0.33	2		625	659	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340068	116340068	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	56	307	0	ENST00000397752.3:c.930G>T	p.Lys310Asn	p.K310N	ENST00000397752	NM_000245.2	310	aaG/aaT	2/21	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.33	2		307	333	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845577	128845577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	125	704	0	ENST00000249373.3:c.874G>A	p.Glu292Lys	p.E292K	ENST00000249373	NM_005631.4	292	Gag/Aag	4/12	1	2	FACETS	0.925	0.837	1	0.925	0.837	1	CLONAL	1	TRUE	1	0.33	2		704	819	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846014	128846014	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	138	846	1	ENST00000249373.3:c.944T>C	p.Val315Ala	p.V315A	ENST00000249373	NM_005631.4	315	gTc/gCc	5/12	1	2	FACETS	0.936	0.851	1	0.936	0.851	1	CLONAL	1	TRUE	1	0.33	2		847	894	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481471	140481471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	82	760	0	ENST00000288602.6:c.1337C>T	p.Ser446Leu	p.S446L	ENST00000288602	NM_004333.4	446	tCg/tTg	11/18	1	2	FACETS	0.744	0.656	0.838	0.744	0.656	0.838	SUBCLONAL	1	TRUE	1	0.33	2		760	668	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864405	151864405	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	105	650	0	ENST00000262189.6:c.9576A>C	p.Gln3192His	p.Q3192H	ENST00000262189	NM_170606.2	3192	caA/caC	42/59	1	2	FACETS	0.953	0.855	1	0.953	0.855	1	CLONAL	1	TRUE	1	0.33	2		650	668	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205681	38205681	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	46	833	0	ENST00000317025.8:c.9C>A	p.Phe3Leu	p.F3L	ENST00000317025	NM_023034.1	3	ttC/ttA	2/24	1	2	FACETS	0.341	0.286	0.402	0.341	0.286	0.402	SUBCLONAL	1	TRUE	1	0.33	2		833	818	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56854504	56854504	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1285322860	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	49	550	1	ENST00000519728.1:c.86G>T	p.Arg29Ile	p.R29I	ENST00000519728	NM_002350.3	29	aGa/aTa	2/13	1	2	FACETS	0.583	0.494	0.682	0.583	0.494	0.682	SUBCLONAL	1	TRUE	1	0.33	2		551	509	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866415	56866415	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	42	650	0	ENST00000519728.1:c.662G>T	p.Arg221Ile	p.R221I	ENST00000519728	NM_002350.3	221	aGa/aTa	8/13	1	2	FACETS	0.354	0.295	0.42	0.354	0.295	0.42	SUBCLONAL	1	TRUE	1	0.33	2		650	719	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942858	68942858	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	165	734	0	ENST00000288368.4:c.670T>G	p.Leu224Val	p.L224V	ENST00000288368	NM_024870.2	224	Tta/Gta	6/40	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.33	2		734	730	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68993020	68993020	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	53	491	0	ENST00000288368.4:c.1825G>T	p.Asp609Tyr	p.D609Y	ENST00000288368	NM_024870.2	609	Gac/Tac	17/40	1	2	FACETS	0.803	0.687	0.93	0.803	0.687	0.93	CLONAL	1	TRUE	1	0.33	2		491	400	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981645	70981645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	211	1157	1	ENST00000276594.2:c.451C>A	p.Pro151Thr	p.P151T	ENST00000276594	NM_024504.3	151	Cca/Aca	2/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.33	2		1158	1216	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753155	128753155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148863193	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	67	331	0	ENST00000377970.2:c.1316G>A	p.Arg439Gln	p.R439Q	ENST00000377970	NM_002467.4	439	cGa/cAa	3/3	1	2	FACETS	0.995	0.869	1	0.995	0.869	1	CLONAL	1	TRUE	1	0.33	2		331	408	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072601	5072601	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	22	394	0	ENST00000381652.3:c.1751A>G	p.Asp584Gly	p.D584G	ENST00000381652	NM_004972.3	584	gAt/gGt	13/25	1	2	FACETS	0.403	0.312	0.508	0.403	0.312	0.508	SUBCLONAL	1	TRUE	1	0.33	2		394	331	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341925	8341925	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	28	593	0	ENST00000356435.5:c.4715G>T	p.Arg1572Ile	p.R1572I	ENST00000356435		1572	aGa/aTa	29/35	1	2	FACETS	0.322	0.256	0.397	0.322	0.256	0.397	SUBCLONAL	1	TRUE	1	0.33	2		593	527	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485310	8485310	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	24	485	0	ENST00000356435.5:c.3070T>G	p.Phe1024Val	p.F1024V	ENST00000356435		1024	Ttt/Gtt	18/35	1	2	FACETS	0.341	0.267	0.428	0.341	0.267	0.428	SUBCLONAL	1	TRUE	1	0.33	2		485	426	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528777	8528777	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs763617561	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	54	339	0	ENST00000356435.5:c.355G>A	p.Asp119Asn	p.D119N	ENST00000356435		119	Gat/Aat	4/35	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.33	2		339	326	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158005	27158005	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	130	734	1	ENST00000380036.4:c.229G>T	p.Asp77Tyr	p.D77Y	ENST00000380036	NM_000459.3	77	Gat/Tat	2/23	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.33	2		735	772	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212761	27212761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	160	904	1	ENST00000380036.4:c.2743C>T	p.Arg915Cys	p.R915C	ENST00000380036	NM_000459.3	915	Cgc/Tgc	17/23	1	2	FACETS	0.97	0.888	1	0.97	0.888	1	CLONAL	1	TRUE	1	0.33	2		905	1000	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27229182	27229182	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	39	710	0	ENST00000380036.4:c.3327G>T	p.Glu1109Asp	p.E1109D	ENST00000380036	NM_000459.3	1109	gaG/gaT	23/23	1	2	FACETS	0.352	0.291	0.421	0.352	0.291	0.421	SUBCLONAL	1	TRUE	1	0.33	2		710	671	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336400	80336400	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	75	473	0	ENST00000286548.4:c.919G>T	p.Glu307Ter	p.E307*	ENST00000286548	NM_002072.3	307	Gaa/Taa	7/7	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.33	2		473	445	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537181	80537181	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	60	517	1	ENST00000286548.4:c.217A>G	p.Arg73Gly	p.R73G	ENST00000286548	NM_002072.3	73	Agg/Ggg	2/7	1	2	FACETS	0.686	0.592	0.789	0.686	0.592	0.789	SUBCLONAL	1	TRUE	1	0.33	2		518	530	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908801	101908801	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	92	620	0	ENST00000374994.4:c.1165A>C	p.Asn389His	p.N389H	ENST00000374994	NM_004612.2	389	Aat/Cat	7/9	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.33	2		620	484	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772658	135772658	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	46	783	0	ENST00000298552.3:c.2888T>C	p.Leu963Ser	p.L963S	ENST00000298552	NM_001162426.1	963	tTa/tCa	22/23	1	2	FACETS	0.366	0.307	0.431	0.366	0.307	0.431	SUBCLONAL	1	TRUE	1	0.33	2		783	762	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321286	1321286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780766655	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	42	494	1	ENST00000400841.2:c.469G>A	p.Asp157Asn	p.D157N	ENST00000400841		157	Gac/Aac	4/6	1	2	FACETS	0.415	0.345	0.492	0.415	0.345	0.492	SUBCLONAL	1	TRUE	1	0.33	2		495	614	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321386	1321386	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	37	520	1	ENST00000400841.2:c.369G>T	p.Lys123Asn	p.K123N	ENST00000400841		123	aaG/aaT	4/6	1	2	FACETS	0.374	0.307	0.448	0.374	0.307	0.448	SUBCLONAL	1	TRUE	1	0.33	2		521	600	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930944	39930944	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	48	462	0	ENST00000378444.4:c.2998-1G>T		p.X1000_splice	ENST00000378444	NM_001123385.1	1000			1	2	FACETS	0.724	0.613	0.845	0.724	0.613	0.845	SUBCLONAL	1	TRUE	1	0.33	2		462	402	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933787	39933787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748212546	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	147	735	1	ENST00000378444.4:c.812C>T	p.Ser271Leu	p.S271L	ENST00000378444	NM_001123385.1	271	tCg/tTg	4/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.33	2		736	827	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966665	44966665	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	56	471	0	ENST00000377967.4:c.3889C>A	p.Leu1297Ile	p.L1297I	ENST00000377967	NM_021140.2	1297	Cta/Ata	27/29	1	2	FACETS	0.822	0.706	0.947	0.822	0.706	0.947	CLONAL	1	TRUE	1	0.33	2		471	413	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430770	47430770	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	153	936	1	ENST00000377045.4:c.1735C>T	p.Arg579Trp	p.R579W	ENST00000377045	NM_001654.4	579	Cgg/Tgg	16/16	1	2	FACETS	0.86	0.786	0.938	0.86	0.786	0.938	CLONAL	1	TRUE	1	0.33	2		937	1078	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650816	48650816	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	55	876	0	ENST00000376670.3:c.685G>T	p.Gly229Cys	p.G229C	ENST00000376670	NM_002049.3	229	Ggc/Tgc	4/6	1	2	FACETS	0.347	0.295	0.403	0.347	0.295	0.403	SUBCLONAL	1	TRUE	1	0.33	2		876	961	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342687	70342687	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	135	801	0	ENST00000374080.3:c.1448G>T	p.Arg483Leu	p.R483L	ENST00000374080		483	cGa/cTa	10/45	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.33	2		801	818	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829731	76829731	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	94	728	0	ENST00000373344.5:c.6310G>T	p.Asp2104Tyr	p.D2104Y	ENST00000373344	NM_000489.3	2104	Gat/Tat	28/35	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.33	2		728	554	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938244	76938244	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	47	838	0	ENST00000373344.5:c.2504G>T	p.Arg835Ile	p.R835I	ENST00000373344	NM_000489.3	835	aGa/aTa	9/35	1	2	FACETS	0.401	0.337	0.471	0.401	0.337	0.471	SUBCLONAL	1	TRUE	1	0.33	2		838	711	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939468	76939468	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	143	963	1	ENST00000373344.5:c.1280A>T	p.Lys427Ile	p.K427I	ENST00000373344	NM_000489.3	427	aAa/aTa	9/35	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.33	2		964	804	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76949345	76949345	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	64	726	0	ENST00000373344.5:c.452A>C	p.Lys151Thr	p.K151T	ENST00000373344	NM_000489.3	151	aAa/aCa	6/35	1	2	FACETS	0.752	0.652	0.86	0.752	0.652	0.86	SUBCLONAL	1	TRUE	1	0.33	2		726	516	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176443	123176443	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	23	446	0	ENST00000218089.9:c.410G>A	p.Arg137Lys	p.R137K	ENST00000218089	NM_001042749.1	137	aGa/aAa	7/35	1	2	FACETS	0.337	0.262	0.424	0.337	0.262	0.424	SUBCLONAL	1	TRUE	1	0.33	2		446	414	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227989	123227989	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	45	486	0	ENST00000218089.9:c.3700G>T	p.Asp1234Tyr	p.D1234Y	ENST00000218089	NM_001042749.1	1234	Gat/Tat	33/35	1	2	FACETS	0.819	0.691	0.959	0.819	0.691	0.959	CLONAL	1	TRUE	1	0.33	2		486	333	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139572	47139572	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0035770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	18	312	0	ENST00000409792.3:c.5016-1G>T		p.X1672_splice	ENST00000409792	NM_014159.6	1672			1	2	FACETS	0.303	0.227	0.393	0.303	0.227	0.393	SUBCLONAL	1	TRUE	1	0.33	2		312	360	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945331	71945331	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0036014-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	236	817	0	ENST00000298229.2:c.2219C>G	p.Ser740Ter	p.S740*	ENST00000298229	NM_001567.3	740	tCa/tGa	20/28	0.718382896587523	1	FACETS	0.959	0.908	1	0.959	0.908	1	CLONAL	1	TRUE	0	0.718382896587523	1		817	439	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832744	3832744	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036014-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	58	612	0	ENST00000262367.5:c.1514del	p.Pro505LeufsTer14	p.P505Lfs*14	ENST00000262367	NM_004380.2	505	cCt/ct	6/31	1	2	FACETS	0.212	0.182	0.246	0.212	0.182	0.246	SUBCLONAL	1	TRUE	1	0.718382896587523	2		612	761	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10267110	10267114	+	frameshift_variant	Frame_Shift_Del	DEL	AGAAA	AGAAA	-	novel	NA	P-0036014-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	226	584	0	ENST00000340748.4:c.1304_1308del	p.Phe435TrpfsTer8	p.F435Wfs*8	ENST00000340748		435	tTTTCT/t	17/40	1	2	FACETS	0.977	0.915	1	0.977	0.915	1	CLONAL	1	TRUE	1	0.718382896587523	2		584	644	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32802929	32802929	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0036014-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	22	382	0	ENST00000374899.4:c.945+2T>C		p.X315_splice	ENST00000374899	NM_018833.2	315			0.718382896587523	1	FACETS	0.15	0.116	0.19	0.15	0.116	0.19	SUBCLONAL	1	TRUE	0	0.718382896587523	1		382	261	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137524800	137524801	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0036014-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	143	502	0	ENST00000367739.4:c.568dup	p.Gln190ProfsTer5	p.Q190Pfs*5	ENST00000367739	NM_000416.2	190	cag/cCag	5/7	0.718382896587523	1	FACETS	0.993	0.927	1	0.993	0.927	1	CLONAL	1	TRUE	0	0.718382896587523	1		502	257	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981455	70981455	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1397743336	NA	P-0036014-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	341	944	0	ENST00000276594.2:c.641A>G	p.Glu214Gly	p.E214G	ENST00000276594	NM_024504.3	214	gAg/gGg	2/8	0.718382896587523	3	FACETS	1	0.95	1	0.502	0.475	0.531	CLONAL	1	TRUE	1	0.718382896587523	3		944	1284	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434754	128434754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036014-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	224	724	0	ENST00000265960.3:c.100C>T	p.His34Tyr	p.H34Y	ENST00000265960	NM_001006617.1	34	Cat/Tat	2/12	1	2	FACETS	0.982	0.92	1	0.982	0.92	1	CLONAL	1	TRUE	1	0.718382896587523	2		724	635	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	80	313	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.863	0.771	0.958	0.863	0.771	0.958	CLONAL	1	TRUE	1	0.753993461042097	2		315	246	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233037	55233037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1477025000	NA	P-0036016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9662	697	629	1	ENST00000275493.2:c.1787C>T	p.Pro596Leu	p.P596L	ENST00000275493	NM_005228.3	596	cCg/cTg	15/28	0.753993461042097	39	FACETS	0.889	0.851	0.929			1	CLONAL	3	TRUE	NA	0.753993461042097	39		630	10359	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898755	134898755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs546798910	NA	P-0036016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	132	474	0	ENST00000398015.3:c.1813G>A	p.Glu605Lys	p.E605K	ENST00000398015	NM_004441.4	605	Gaa/Aaa	10/16	1	2	FACETS	0.878	0.805	0.953	0.878	0.805	0.953	CLONAL	1	TRUE	1	0.753993461042097	2		474	399	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220290	55220290	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1046438724	NA	P-0036016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3659	11591	893	0	ENST00000275493.2:c.680C>T	p.Ser227Phe	p.S227F	ENST00000275493	NM_005228.3	227	tCc/tTc	6/28	0.753993461042097	39	FACETS	1	0.997	1			1	CLONAL	30	TRUE	NA	0.753993461042097	39		893	15250	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166292	118166292	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761103312	NA	P-0036016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	112	344	0	ENST00000369448.3:c.802C>T	p.Arg268Cys	p.R268C	ENST00000369448	NM_017709.3	268	Cgc/Tgc	2/2	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.753993461042097	2		344	270	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428417	72428417	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	323	830	1	ENST00000477973.2:c.587C>A	p.Thr196Asn	p.T196N	ENST00000477973	NM_012234.5	196	aCc/aAc	2/4	1	2	FACETS	0.968	0.917	1	0.968	0.917	1	CLONAL	1	TRUE	1	0.753993461042097	2		831	885	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0036440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	135	294	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.591620373607078	5	FACETS	0.912	0.851	0.973	1	0.985	1	CLONAL	4	TRUE	2	0.591620373607078	5		294	236	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0036440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	77	502	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.354471216841168	3	FACETS	1	0.978	1	0.73	0.651	0.812	INDETERMINATE	1	TRUE	1	0.591620373607078	3		502	231	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519938	NA	P-0036440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	92	348	0	ENST00000263967.3:c.1034A>T	p.Asn345Ile	p.N345I	ENST00000263967	NM_006218.2	345	aAt/aTt	5/21	0.591620373607078	5	FACETS	1	0.951	1	1	0.951	1	CLONAL	3	TRUE	2	0.591620373607078	5		348	184	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610077	43610077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1432069386	NA	P-0036440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	11	718	0	ENST00000355710.3:c.2029C>T	p.Arg677Trp	p.R677W	ENST00000355710	NM_020975.4	677	Cgg/Tgg	11/20	0.219245648798774	4	FACETS	0.312	0.215	0.431	0.156	0.107	0.216	INDETERMINATE	1	TRUE	2	0.591620373607078	4		718	190	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271471	26271471	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	59	446	1	ENST00000305910.3:c.142G>A	p.Ala48Thr	p.A48T	ENST00000305910	NM_003534.2	48	Gct/Act	1/1	0.591620373607078	9	FACETS	1	0.922	1	0.436	0.378	0.498	CLONAL	2	TRUE	4	0.591620373607078	9		447	281	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760592	133760607	+	protein_altering_variant	In_Frame_Del	DEL	CGGGGACCCCCATCAG	CGGGGACCCCCATCAG	GGTC	novel	NA	P-0036440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	58	817	3	ENST00000318560.5:c.2915_2930delinsGGTC	p.Ser972_Ile976delinsTrp	p.S972_I976delinsW	ENST00000318560	NM_005157.4	972	tCGGGGACCCCCATCAGc/tGGTCc	11/11	0.290520450795436	1	FACETS	0.78	0.683	0.881	0.78	0.683	0.881	INDETERMINATE	1	TRUE	0	0.591620373607078	1		820	177	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0036525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	86	455	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.551550309598157	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.551550309598157	1		455	206	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0036525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	88	340	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.313236946951183	1	FACETS	0.943	0.85	1	0.943	0.85	1	INDETERMINATE	1	TRUE	0	0.551550309598157	1		340	245	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175951	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1392778905	NA	P-0036525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	57	212	0	ENST00000257430.4:c.4660G>T	p.Glu1554Ter	p.E1554*	ENST00000257430	NM_000038.5	1554	Gaa/Taa	16/16	0.18625553401057	4	FACETS	0.966	0.846	1	0.966	0.846	1	INDETERMINATE	2	TRUE	2	0.551550309598157	4		212	166	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076862	41076862	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs750249800	NA	P-0036525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	151	389	0	ENST00000373198.4:c.1558G>A	p.Glu520Lys	p.E520K	ENST00000373198	NM_133170.3	520	Gag/Aag	9/32	0.257214481070934	3	FACETS	1	0.989	1	0.75	0.691	0.81	INDETERMINATE	1	TRUE	1	0.551550309598157	3		389	466	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411678	63411678	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	258	365	0	ENST00000330258.3:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000330258	NM_152424.3	497	Cga/Tga	2/2	0.424787606145228	2	FACETS	0.843	0.808	0.877			1	CLONAL	3	TRUE	NA	0.551550309598157	2		365	370	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184592	11184592	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs774204282	NA	P-0036525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	112	542	0	ENST00000361445.4:c.6625C>G	p.Leu2209Val	p.L2209V	ENST00000361445	NM_004958.3	2209	Ctg/Gtg	47/58	0.508340827280449	1	FACETS	0.562	0.508	0.62	0.562	0.508	0.62	SUBCLONAL	1	TRUE	0	0.551550309598157	1		542	523	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274610	198274610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139577219	NA	P-0036525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	236	551	0	ENST00000335508.6:c.788C>T	p.Ala263Val	p.A263V	ENST00000335508	NM_012433.2	263	gCg/gTg	7/25	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.551550309598157	2		551	722	SUCCESS
APC	324	MSKCC	GRCh37	5	112173531	112173531	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs773020689	NA	P-0036525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	57	314	0	ENST00000257430.4:c.2240C>G	p.Ser747Ter	p.S747*	ENST00000257430	NM_000038.5	747	tCa/tGa	16/16	0.18625553401057	4	FACETS	0.798	0.695	0.906	0.798	0.695	0.906	INDETERMINATE	2	TRUE	2	0.551550309598157	4		314	201	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59886111	59886111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	83	342	0	ENST00000259008.2:c.635G>A	p.Gly212Asp	p.G212D	ENST00000259008	NM_032043.2	212	gGc/gAc	7/20	0.302277646540606	1	FACETS	1	0.928	1	1	0.928	1	INDETERMINATE	1	TRUE	0	0.551550309598157	1		342	210	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918753	50918753	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751565067	NA	P-0036525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	102	670	0	ENST00000440232.2:c.2623C>T	p.Arg875Cys	p.R875C	ENST00000440232	NM_002691.3	875	Cgc/Tgc	21/27	1	2	FACETS	0.438	0.391	0.488	0.438	0.391	0.488	SUBCLONAL	1	TRUE	1	0.551550309598157	2		670	845	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938501	44938501	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	182	565	0	ENST00000377967.4:c.3049A>G	p.Thr1017Ala	p.T1017A	ENST00000377967	NM_021140.2	1017	Aca/Gca	20/29	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		565	752	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0036703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	201	612	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.734580480715438	2	FACETS	0.883	0.838	0.926	0.883	0.838	0.926	CLONAL	2	TRUE	0	0.734580480715438	2		612	310	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056104	26056104	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375520468	NA	P-0036703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	225	474	0	ENST00000343677.2:c.553G>A	p.Ala185Thr	p.A185T	ENST00000343677	NM_005319.3	185	Gct/Act	1/1	1	2	FACETS	0.969	0.908	1	0.969	0.908	1	CLONAL	1	TRUE	1	0.734580480715438	2		474	632	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0036728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	160	502	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.679852125391631	4	FACETS	1	0.983	1	0.414	0.381	0.448	CLONAL	1	TRUE	1	0.723123909207706	4		502	614	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112322	115112323	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0036728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	157	290	0	ENST00000257566.3:c.1416_1417dup	p.Leu473ArgfsTer160	p.L473Rfs*160	ENST00000257566	NM_016569.3	473	ctc/cGCtc	7/8	0.723123909207706	4	FACETS	0.938	0.88	0.994	0.938	0.88	0.994	CLONAL	3	TRUE	1	0.723123909207706	4		290	266	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006836	47006836	+	5_prime_UTR_variant	5'UTR	SNP	C	C	T	rs781915889	NA	P-0036870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	76	330	1	ENST00000377604.3:c.-45C>T		p.*15*	ENST00000377604	NM_001204468.1	-/852		2/24	0.37811051441586	2	FACETS	1	0.973	1			1	CLONAL	1	FALSE	NA	0.37811051441586	2		331	296	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022903	31022903	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	31	622	0	ENST00000375687.4:c.2388G>A	p.Trp796Ter	p.W796*	ENST00000375687	NM_015338.5	796	tgG/tgA	13/13	1	2	FACETS	0.531	0.43	0.644	0.531	0.43	0.644	SUBCLONAL	1	FALSE	1	0.37811051441586	2		622	309	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027051	71027051	+	frameshift_variant	Frame_Shift_Ins	INS	T	T	CTG	novel	NA	P-0036870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	109	587	0	ENST00000318789.4:c.1276delinsCAG	p.Thr426GlnfsTer49	p.T426Qfs*49	ENST00000318789	NM_032682.5	426	Acc/CAGcc	15/21	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.37811051441586	2		587	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0036881-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	253	780	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.215216299127643	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.280832166758768	2		780	875	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0036881-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	123	796	7	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.215216299127643	2	FACETS	0.828	0.752	0.907	0.828	0.752	0.907	CLONAL	2	TRUE	0	0.280832166758768	2		803	529	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0036881-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	132	365	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.220419565821102	3	FACETS	1	0.961	1	0.728	0.665	0.793	CLONAL	2	TRUE	0	0.280832166758768	3		365	491	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990481	69990481	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs201247895	NA	P-0036881-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	46	361	0	ENST00000394351.3:c.440C>T	p.Thr147Met	p.T147M	ENST00000394351	NM_000248.3	147	aCg/aTg	4/9	0.211069224195179	3	FACETS	1	0.924	1	0.578	0.489	0.676	CLONAL	1	TRUE	1	0.280832166758768	3		361	323	SUCCESS
APC	324	MSKCC	GRCh37	5	112090657	112090657	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs145945630	NA	P-0036881-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	104	390	0	ENST00000257430.4:c.70C>T	p.Arg24Ter	p.R24*	ENST00000257430	NM_000038.5	24	Cga/Tga	2/16	0.220419565821102	3	FACETS	1	0.966	1	0.769	0.695	0.846	CLONAL	2	TRUE	0	0.280832166758768	3		390	366	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224532	36224532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759167832	NA	P-0036881-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	248	916	0	ENST00000222270.7:c.6994C>T	p.Arg2332Cys	p.R2332C	ENST00000222270	NM_014727.1	2332	Cgt/Tgt	29/37	0.211069224195179	3	FACETS	0.934	0.873	0.997	0.934	0.873	0.997	CLONAL	2	TRUE	1	0.280832166758768	3		916	1078	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851561	63851561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567464868	NA	P-0036881-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	150	630	0	ENST00000279873.7:c.2339G>A	p.Arg780Gln	p.R780Q	ENST00000279873	NM_032199.2	780	cGa/cAa	10/10	0.276803124228211	3	FACETS	1	0.985	1	0.681	0.622	0.742	CLONAL	1	TRUE	1	0.280832166758768	3		630	895	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43745205	43745205	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0036881-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	143	537	0	ENST00000523873.1:c.119-1G>A		p.X40_splice	ENST00000523873		40			0.186153728334973	4	FACETS	0.961	0.878	1	0.961	0.878	1	CLONAL	2	TRUE	2	0.280832166758768	4		537	679	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0036883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	129	465	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.216475220883649	4	FACETS	0.928	0.842	1	0.928	0.842	1	CLONAL	2	TRUE	2	0.227160299380127	4		465	751	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249348	110249348	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	231	775	0	ENST00000374672.4:c.1225A>C	p.Lys409Gln	p.K409Q	ENST00000374672	NM_004235.4	409	Aag/Cag	4/5	0.227160299380127	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.227160299380127	2		775	992	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578415	7578415	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	175	624	0	ENST00000269305.4:c.515T>A	p.Val172Asp	p.V172D	ENST00000269305	NM_001126112.2	172	gTt/gAt	5/11	0.227160299380127	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.227160299380127	2		624	721	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878749	151878749	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1211949081	NA	P-0036883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	139	484	1	ENST00000262189.6:c.6196C>T	p.Arg2066Ter	p.R2066*	ENST00000262189	NM_170606.2	2066	Cga/Tga	36/59	0.227160299380127	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	2	TRUE	0	0.227160299380127	2		485	607	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974676	21974676	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0036883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	172	386	0	ENST00000304494.5:c.150+1G>T		p.X50_splice	ENST00000304494	NM_000077.4	50			0.227160299380127	3	FACETS	0.993	0.919	1	0.993	0.919	1	CLONAL	3	TRUE	0	0.227160299380127	3		386	566	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0036885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	256	918	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.32513765528971	5	FACETS	0.947	0.898	0.995	0.947	0.898	0.995	CLONAL	5	TRUE	0	0.32513765528971	5		919	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs985033810	NA	P-0036885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	73	632	0	ENST00000269305.4:c.731G>T	p.Gly244Val	p.G244V	ENST00000269305	NM_001126112.2	244	gGc/gTc	7/11	0.298862027162542	2	FACETS	1	0.959	1	0.607	0.534	0.685	CLONAL	1	TRUE	0	0.32513765528971	2		632	370	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163297333	163297333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767890204	NA	P-0036885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	30	577	1	ENST00000271452.3:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000271452	NM_145697.2	60	cGa/cAa	3/14	1	2	FACETS	0.586	0.473	0.713	0.586	0.473	0.713	SUBCLONAL	1	TRUE	1	0.32513765528971	2		578	315	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256158	123256158	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	26	598	0	ENST00000358487.5:c.1751T>A	p.Met584Lys	p.M584K	ENST00000358487	NM_000141.4	584	aTg/aAg	13/18	0.234955948078853	1	FACETS	0.433	0.344	0.536	0.433	0.344	0.536	SUBCLONAL	1	TRUE	0	0.32513765528971	1		598	309	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103203	119103203	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	41	563	0	ENST00000264033.4:c.241C>T	p.Pro81Ser	p.P81S	ENST00000264033	NM_005188.3	81	Cca/Tca	2/16	0.158171506099754	3	FACETS	0.819	0.684	0.968			1	INDETERMINATE	1	TRUE	NA	0.32513765528971	3		563	358	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060939	38060939	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs999746832	NA	P-0036885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	46	394	0	ENST00000250448.2:c.1050G>C	p.Lys350Asn	p.K350N	ENST00000250448	NM_004496.3	350	aaG/aaC	2/2	0.0984780616478305	4	FACETS	1	0.949	1	0.653	0.553	0.762	INDETERMINATE	1	TRUE	2	0.32513765528971	4		394	287	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677800	58677800	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	79	604	3	ENST00000305921.3:c.25G>T	p.Val9Leu	p.V9L	ENST00000305921	NM_003620.3	9	Gtg/Ttg	1/6	0.201104754812293	4	FACETS	1	0.964	1	0.624	0.55	0.703	CLONAL	1	TRUE	2	0.32513765528971	4		607	516	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610526	10610526	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	87	785	0	ENST00000171111.5:c.184C>T	p.Gln62Ter	p.Q62*	ENST00000171111	NM_203500.1	62	Cag/Tag	2/6	0.189341577938742	2	FACETS	1	0.966	1	0.614	0.546	0.685	INDETERMINATE	1	TRUE	0	0.32513765528971	2		785	436	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274088	18274088	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	45	537	1	ENST00000222254.8:c.1306G>A	p.Glu436Lys	p.E436K	ENST00000222254	NM_005027.3	436	Gag/Aag	11/16	0.189341577938742	2	FACETS	0.854	0.721	1	0.427	0.36	0.5	INDETERMINATE	1	TRUE	0	0.32513765528971	2		538	324	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661749	227661749	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	44	638	1	ENST00000305123.5:c.1706C>A	p.Pro569Gln	p.P569Q	ENST00000305123	NM_005544.2	569	cCg/cAg	1/2	0.156161582169402	3	FACETS	0.725	0.609	0.854	0.242	0.203	0.285	INDETERMINATE	1	TRUE	0	0.32513765528971	3		639	434	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662158	227662158	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	45	628	0	ENST00000305123.5:c.1297T>C	p.Ser433Pro	p.S433P	ENST00000305123	NM_005544.2	433	Tcc/Ccc	1/2	0.156161582169402	3	FACETS	0.697	0.586	0.819	0.232	0.195	0.273	INDETERMINATE	1	TRUE	0	0.32513765528971	3		628	462	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799468	72799468	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	61	756	0	ENST00000325599.8:c.1701G>T	p.Gln567His	p.Q567H	ENST00000325599	NM_018130.2	567	caG/caT	11/11	0.286099244713363	3	FACETS	1	0.897	1	0.522	0.451	0.598	CLONAL	1	TRUE	1	0.32513765528971	3		756	418	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156709	55156709	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	27	369	1	ENST00000257290.5:c.3110G>C	p.Arg1037Thr	p.R1037T	ENST00000257290	NM_006206.4	1037	aGg/aCg	22/23	0.32513765528971	1	FACETS	0.589	0.471	0.723	0.589	0.471	0.723	SUBCLONAL	1	TRUE	0	0.32513765528971	1		370	236	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280128	66280128	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	40	420	0	ENST00000273854.3:c.1561A>C	p.Lys521Gln	p.K521Q	ENST00000273854	NM_004439.5	521	Aaa/Caa	7/18	0.189341577938742	2	FACETS	1	0.884	1	0.535	0.448	0.63	INDETERMINATE	1	TRUE	0	0.32513765528971	2		420	230	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007296	143007296	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0036885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	54	524	0	ENST00000262992.4:c.2487+1G>T		p.X829_splice	ENST00000262992	NM_001101669.1	829			0.189341577938742	2	FACETS	1	0.922	1	0.555	0.477	0.639	INDETERMINATE	1	TRUE	0	0.32513765528971	2		524	299	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509966	187509966	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	62	545	0	ENST00000441802.2:c.13547A>G	p.His4516Arg	p.H4516R	ENST00000441802	NM_005245.3	4516	cAt/cGt	27/27	0.189341577938742	2	FACETS	1	0.965	1	0.674	0.587	0.766	INDETERMINATE	1	TRUE	0	0.32513765528971	2		545	283	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79966110	79966110	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	82	545	0	ENST00000265081.6:c.774C>A	p.Phe258Leu	p.F258L	ENST00000265081	NM_002439.4	258	ttC/ttA	4/24	1	2	FACETS	0.764	0.68	0.853	1	0.98	1	SUBCLONAL	2	TRUE	1	0.32513765528971	2		545	330	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933121	39933121	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	60	847	0	ENST00000378444.4:c.1478G>T	p.Gly493Val	p.G493V	ENST00000378444	NM_001123385.1	493	gGt/gTt	4/15	0.32513765528971	1	FACETS	0.901	0.781	1	0.901	0.781	1	CLONAL	1	TRUE	0	0.32513765528971	1		847	343	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165349	32165399	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGACATCAGGGGTGTCACCCCATCTGTTGGTAAGACAGAGTAATGGGTCAA	TGACATCAGGGGTGTCACCCCATCTGTTGGTAAGACAGAGTAATGGGTCAA	CACGCCTGGCTAATTTTGTAGAGAGGGGGTTTTGCCATG	novel	NA	P-0036885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	98	709	0	ENST00000375023.3:c.4757-28_4779delinsCATGGCAAAACCCCCTCTCTACAAAATTAGCCAGGCGTG		p.X1586_splice	ENST00000375023	NM_004557.3	1586		27/30	0.278467337247255	3	FACETS	1	0.951	1	0.37	0.33	0.412	CLONAL	1	TRUE	0	0.32513765528971	3		709	631	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577595	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0036886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	320	726	0	ENST00000269305.4:c.686_687del	p.Cys229TyrfsTer10	p.C229Yfs*10	ENST00000269305	NM_001126112.2	229	tGT/t	7/11	0.329337769289087	3	FACETS	1	0.988	1	0.758	0.719	0.798	CLONAL	2	TRUE	0	0.411055110500916	3		726	825	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396600	30396600	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1264254616	NA	P-0036886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	45	207	0	ENST00000331968.5:c.119C>G	p.Ala40Gly	p.A40G	ENST00000331968	NM_002742.2	40	gCt/gGt	1/18	0.379519536521287	2	FACETS	0.862	0.73	1	0.431	0.365	0.503	CLONAL	1	TRUE	0	0.411055110500916	2		207	254	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49724991	49724991	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	118	498	0	ENST00000449682.2:c.353A>T	p.Lys118Ile	p.K118I	ENST00000449682	NM_020998.3	118	aAa/aTa	3/18	0.411055110500916	2	FACETS	1	0.905	1	0.5	0.452	0.55	CLONAL	1	TRUE	0	0.411055110500916	2		498	574	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031900	26031900	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	78	412	0	ENST00000244661.2:c.389G>A	p.Arg130His	p.R130H	ENST00000244661	NM_003537.3	130	cGc/cAc	1/1	0.41155614014673	3	FACETS	0.857	0.754	0.966	0.428	0.377	0.483	CLONAL	1	TRUE	1	0.411055110500916	3		412	534	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31468154	31468154	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1226092566	NA	P-0036960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	176	443	2	ENST00000344624.3:c.2258G>A	p.Arg753His	p.R753H	ENST00000344624		753	cGt/cAt	15/33	0.365893002954807	5	FACETS	0.868	0.8	0.939	0.579	0.533	0.626	CLONAL	2	TRUE	2	0.365893002954807	5		445	858	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750323	133750323	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	64	469	0	ENST00000318560.5:c.1154G>A	p.Ser385Asn	p.S385N	ENST00000318560	NM_005157.4	385	aGc/aAc	7/11	0.256868492929916	1	FACETS	0.472	0.409	0.541	0.472	0.409	0.541	SUBCLONAL	1	TRUE	0	0.365893002954807	1		469	605	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0037003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	1062	294	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.882477524855257	5	FACETS	0.991	0.972	1	0.991	0.972	1	CLONAL	4	TRUE	1	0.882477524855257	5		294	1411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0037003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	656	739	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.859317002306597	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.882477524855257	1		739	789	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027244	49027244	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	226	312	0	ENST00000267163.4:c.1811A>G	p.Asp604Gly	p.D604G	ENST00000267163	NM_000321.2	604	gAt/gGt	18/27	0.859317002306597	1	FACETS	0.923	0.884	0.96	0.923	0.884	0.96	CLONAL	1	TRUE	0	0.882477524855257	1		312	310	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291915	15291915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775964142	NA	P-0037003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	701	962	3	ENST00000263388.2:c.2851C>T	p.Arg951Cys	p.R951C	ENST00000263388	NM_000435.2	951	Cgt/Tgt	18/33	0.418117135174867	3	FACETS	1	0.996	1	0.61	0.588	0.632	INDETERMINATE	1	TRUE	1	0.882477524855257	3		965	1878	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588174	67588174	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	109	329	0	ENST00000274335.5:c.1004G>A	p.Trp335Ter	p.W335*	ENST00000274335		335	tGg/tAg	7/15	0.489052823989514	1	FACETS	0.268	0.241	0.295	0.268	0.241	0.295	INDETERMINATE	1	TRUE	0	0.882477524855257	1		329	516	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0037101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	1024	595	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.850698194681638	5	FACETS	1	0.991	1			1	CLONAL	4	TRUE	NA	0.930814299698334	5		595	1301	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0037101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	251	587	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.54481430641979	4	FACETS	1	0.986	1	0.391	0.367	0.417	INDETERMINATE	1	TRUE	1	0.930814299698334	4		587	887	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117707	70117707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367592961	NA	P-0037101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	376	702	0	ENST00000245479.2:c.175G>A	p.Asp59Asn	p.D59N	ENST00000245479	NM_000346.3	59	Gat/Aat	1/3	0.850276180984755	3	FACETS	1	0.955	1	0.503	0.477	0.529	CLONAL	1	TRUE	1	0.930814299698334	3		702	1177	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160489	108160489	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	94	597	0	ENST00000278616.4:c.4397G>C	p.Arg1466Pro	p.R1466P	ENST00000278616	NM_000051.3	1466	cGa/cCa	29/63	0.923121021653819	2	FACETS	0.304	0.27	0.339	0.152	0.135	0.17	SUBCLONAL	1	TRUE	0	0.930814299698334	2		597	665	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577088	7577088	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1204379654	NA	P-0037101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	353	780	0	ENST00000269305.4:c.850A>C	p.Thr284Pro	p.T284P	ENST00000269305	NM_001126112.2	284	Aca/Cca	8/11	0.408969331382454	4	FACETS	0.976	0.923	1			1	INDETERMINATE	1	TRUE	NA	0.930814299698334	4		780	1500	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437384	110437384	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	651	283	0	ENST00000375856.3:c.1017del	p.Arg340AlafsTer51	p.R340Afs*51	ENST00000375856	NM_003749.2	339	gtG/gt	1/2	0.913521361852503	5	FACETS	1	0.982	1	0.804	0.786	0.821	CLONAL	4	TRUE	0	0.930814299698334	5		283	834	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292803	91292803	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	262	487	2	ENST00000355112.3:c.305G>T	p.Gly102Val	p.G102V	ENST00000355112	NM_000057.2	102	gGt/gTt	3/22	NA	2	FACETS	0.949	0.897	1			1	INDETERMINATE	1	TRUE	NA	0.930814299698334	2		489	593	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786144	3786144	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1266	402	778	0	ENST00000262367.5:c.4621G>C	p.Glu1541Gln	p.E1541Q	ENST00000262367	NM_004380.2	1541	Gaa/Caa	28/31	0.735345623369149	4	FACETS	1	0.949	1			1	CLONAL	1	TRUE	NA	0.930814299698334	4		778	1668	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577606	7577615	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AACCTAGGAG	AACCTAGGAG	-	novel	NA	P-0037101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	575	565	0	ENST00000269305.4:c.673-7_675del		p.X225_splice	ENST00000269305	NM_001126112.2	225		7/11	0.408969331382454	4	FACETS	0.875	0.848	0.901			1	INDETERMINATE	3	TRUE	NA	0.930814299698334	4		565	909	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220138	36220138	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1574	391	817	0	ENST00000222270.7:c.4858G>C	p.Glu1620Gln	p.E1620Q	ENST00000222270	NM_014727.1	1620	Gag/Cag	22/37	0.92382208590566	5	FACETS	1	0.965	1	0.341	0.323	0.36	CLONAL	1	TRUE	2	0.930814299698334	5		817	1965	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919929	50919929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376197467	NA	P-0037101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1530	382	778	1	ENST00000440232.2:c.3016G>A	p.Ala1006Thr	p.A1006T	ENST00000440232	NM_002691.3	1006	Gcc/Acc	24/27	0.92382208590566	5	FACETS	1	0.967	1	0.343	0.324	0.362	CLONAL	1	TRUE	2	0.930814299698334	5		779	1912	SUCCESS
ATR	545	MSKCC	GRCh37	3	142185372	142185372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	147	294	0	ENST00000350721.4:c.6691G>A	p.Asp2231Asn	p.D2231N	ENST00000350721	NM_001184.3	2231	Gat/Aat	40/47	0.54481430641979	4	FACETS	1	0.98	1	0.402	0.369	0.436	INDETERMINATE	1	TRUE	1	0.930814299698334	4		294	506	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157168	106157168	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	117	395	0	ENST00000380013.4:c.2069A>T	p.Gln690Leu	p.Q690L	ENST00000380013	NM_001127208.2	690	cAa/cTa	3/11	0.512951384481069	3	FACETS	0.666	0.603	0.733	0.222	0.201	0.245	INDETERMINATE	1	TRUE	0	0.930814299698334	3		395	553	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	63	313	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.979	0.851	1	0.979	0.851	1	CLONAL	1	TRUE	1	0.349699088404459	2		315	368	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779191	3779191	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	83	613	2	ENST00000262367.5:c.5857C>T	p.Pro1953Ser	p.P1953S	ENST00000262367	NM_004380.2	1953	Cct/Tct	31/31	1	2	FACETS	0.918	0.812	1	0.918	0.812	1	CLONAL	1	TRUE	1	0.349699088404459	2		615	517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs878854073	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	94	549	0	ENST00000269305.4:c.673-1G>A		p.X225_splice	ENST00000269305	NM_001126112.2	225			1	2	FACETS	0.914	0.815	1	0.914	0.815	1	CLONAL	1	TRUE	1	0.349699088404459	2		549	588	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395074	139395074	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	278	913	2	ENST00000277541.6:c.5864A>G	p.Asn1955Ser	p.N1955S	ENST00000277541	NM_017617.3	1955	aAc/aGc	31/34	0.347916120185866	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.349699088404459	2		915	740	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790776	89790776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757768258	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	303	1086	2	ENST00000336032.3:c.163C>T	p.Leu55Phe	p.L55F	ENST00000336032	NM_006813.2	55	Ctc/Ttc	1/2	0.349699088404459	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.349699088404459	3		1088	994	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675112	40675112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	143	989	0	ENST00000249776.8:c.76C>T	p.Pro26Ser	p.P26S	ENST00000249776	NM_033286.3	26	Cca/Tca	1/9	1	2	FACETS	0.968	0.883	1	0.968	0.883	1	CLONAL	1	TRUE	1	0.349699088404459	2		989	845	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713205	30713205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	80	411	0	ENST00000295754.5:c.530G>A	p.Gly177Glu	p.G177E	ENST00000295754	NM_003242.5	177	gGa/gAa	4/7	0.349699088404459	1	FACETS	0.973	0.862	1	0.973	0.862	1	CLONAL	1	TRUE	0	0.349699088404459	1		411	388	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120496297	120496297	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	60	443	0	ENST00000256646.2:c.2234G>T	p.Cys745Phe	p.C745F	ENST00000256646	NM_024408.3	745	tGt/tTt	14/34	1	2	FACETS	0.732	0.632	0.84	0.732	0.632	0.84	SUBCLONAL	1	TRUE	1	0.349699088404459	2		443	469	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204855	94204855	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	102	516	0	ENST00000323929.3:c.730G>A	p.Gly244Ser	p.G244S	ENST00000323929	NM_005591.3	244	Ggc/Agc	8/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.349699088404459	2		516	476	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374285	118374285	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	89	445	0	ENST00000534358.1:c.7678G>A	p.Glu2560Lys	p.E2560K	ENST00000534358	NM_005933.3	2560	Gaa/Aaa	27/36	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.349699088404459	2		445	486	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245376	46245376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	78	508	0	ENST00000334344.6:c.3470C>T	p.Ser1157Leu	p.S1157L	ENST00000334344	NM_152641.2	1157	tCa/tTa	15/21	1	2	FACETS	0.865	0.761	0.975	0.865	0.761	0.975	CLONAL	1	TRUE	1	0.349699088404459	2		508	516	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298782	46298783	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	71	356	0	ENST00000334344.6:c.5429_5430delinsTT	p.Thr1810Ile	p.T1810I	ENST00000334344	NM_152641.2	1810	aCC/aTT	21/21	1	2	FACETS	0.976	0.856	1	0.976	0.856	1	CLONAL	1	TRUE	1	0.349699088404459	2		356	416	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610588	81610588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs903686564	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	73	300	0	ENST00000298171.2:c.2186G>A	p.Arg729Lys	p.R729K	ENST00000298171	NM_000369.2	729	aGg/aAg	10/10	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.349699088404459	2		300	377	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610660	81610660	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	63	310	0	ENST00000298171.2:c.2258G>A	p.Gly753Asp	p.G753D	ENST00000298171	NM_000369.2	753	gGc/gAc	10/10	1	2	FACETS	0.892	0.774	1	0.892	0.774	1	CLONAL	1	TRUE	1	0.349699088404459	2		310	404	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50827460	50827460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	91	368	0	ENST00000398568.2:c.2345C>T	p.Pro782Leu	p.P782L	ENST00000398568	NM_001042412.1	782	cCc/cTc	16/18	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.349699088404459	2		368	519	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33430500	33430501	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	115	698	2	ENST00000345365.6:c.639_640delinsTT	p.Pro214Ser	p.P214S	ENST00000345365	NM_002878.3	213	tcCCca/tcTTca	7/10	1	2	FACETS	0.933	0.841	1	0.933	0.841	1	CLONAL	1	TRUE	1	0.349699088404459	2		700	705	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246903	10246903	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	143	966	2	ENST00000340748.4:c.4502C>T	p.Pro1501Leu	p.P1501L	ENST00000340748		1501	cCc/cTc	37/40	1	2	FACETS	0.985	0.899	1	0.985	0.899	1	CLONAL	1	TRUE	1	0.349699088404459	2		968	830	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296080	15296080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772155427	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	152	951	0	ENST00000263388.2:c.2284C>T	p.Pro762Ser	p.P762S	ENST00000263388	NM_000435.2	762	Cct/Tct	14/33	1	2	FACETS	0.863	0.789	0.942	0.863	0.789	0.942	CLONAL	1	TRUE	1	0.349699088404459	2		951	1007	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355099	15355099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	189	1155	3	ENST00000263377.2:c.2524C>T	p.Pro842Ser	p.P842S	ENST00000263377	NM_058243.2	842	Ccg/Tcg	13/20	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.349699088404459	2		1158	1053	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50138855	50138855	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	211	1157	0	ENST00000246792.3:c.635G>A	p.Gly212Asp	p.G212D	ENST00000246792	NM_006270.3	212	gGc/gAc	6/6	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.349699088404459	2		1157	1062	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474088	29474088	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	152	780	0	ENST00000389048.3:c.2087C>T	p.Pro696Leu	p.P696L	ENST00000389048	NM_004304.4	696	cCc/cTc	12/29	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.349699088404459	2		780	751	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944543	40944544	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	75	532	0	ENST00000373198.4:c.1958_1959delinsAA	p.Arg653Gln	p.R653Q	ENST00000373198	NM_133170.3	653	cGG/cAA	12/32	1	2	FACETS	0.841	0.739	0.951	0.841	0.739	0.951	CLONAL	1	TRUE	1	0.349699088404459	2		532	510	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268835	41268835	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	116	454	0	ENST00000349496.5:c.1073del	p.Val358GlufsTer9	p.V358Efs*9	ENST00000349496	NM_001904.3	358	gTa/ga	7/15	0.349699088404459	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.349699088404459	1		454	495	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890215	72890215	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs755200026	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	87	496	0	ENST00000325599.8:c.467G>T	p.Gly156Val	p.G156V	ENST00000325599	NM_018130.2	156	gGa/gTa	4/11	NA	2	FACETS	0.885	0.785	0.992			1	INDETERMINATE	1	TRUE	NA	0.349699088404459	2		496	562	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582058	189582058	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	97	446	0	ENST00000264731.3:c.617C>A	p.Ala206Glu	p.A206E	ENST00000264731	NM_003722.4	206	gCa/gAa	5/14	0.349699088404459	3	FACETS	1	0.944	1	0.544	0.486	0.606	CLONAL	1	TRUE	1	0.349699088404459	3		446	599	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1795726	1795726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	42	418	0	ENST00000260795.2:c.65C>T	p.Ser22Leu	p.S22L	ENST00000260795		22	tCg/tTg	1/17	1	2	FACETS	0.748	0.627	0.882	0.748	0.627	0.882	SUBCLONAL	1	TRUE	1	0.349699088404459	2		418	321	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807114	1807114	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	147	964	2	ENST00000260795.2:c.1445G>T	p.Cys482Phe	p.C482F	ENST00000260795		482	tGc/tTc	10/17	1	2	FACETS	0.987	0.901	1	0.987	0.901	1	CLONAL	1	TRUE	1	0.349699088404459	2		966	852	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55597524	55597524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	92	420	1	ENST00000288135.5:c.2172G>A	p.Met724Ile	p.M724I	ENST00000288135	NM_000222.2	724	atG/atA	15/21	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.349699088404459	2		421	519	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007329	143007329	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	195	535	0	ENST00000262992.4:c.2455A>C	p.Lys819Gln	p.K819Q	ENST00000262992	NM_001101669.1	819	Aag/Cag	22/24	0.349699088404459	3	FACETS	0.869	0.806	0.933	0.869	0.806	0.933	CLONAL	2	TRUE	1	0.349699088404459	3		535	754	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541795	187541808	+	frameshift_variant	Frame_Shift_Del	DEL	TCCTGGGTAAACTT	TCCTGGGTAAACTT	-	novel	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	168	511	0	ENST00000441802.2:c.5932_5945del	p.Lys1978CysfsTer28	p.K1978Cfs*28	ENST00000441802	NM_005245.3	1978	AAGTTTACCCAGGAt/t	10/27	0.349699088404459	3	FACETS	0.863	0.796	0.932	0.863	0.796	0.932	CLONAL	2	TRUE	1	0.349699088404459	3		511	654	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490506	20490506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	100	599	0	ENST00000346618.3:c.1243C>T	p.Pro415Ser	p.P415S	ENST00000346618	NM_001949.4	415	Cct/Tct	7/7	1	2	FACETS	0.905	0.81	1	0.905	0.81	1	CLONAL	1	TRUE	1	0.349699088404459	2		599	632	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14017076	14017076	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1403337828	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	57	360	1	ENST00000405192.2:c.211G>T	p.Val71Leu	p.V71L	ENST00000405192	NM_001163147.1	71	Gta/Tta	5/12	0.349699088404459	3	FACETS	0.717	0.616	0.828	0.359	0.308	0.414	SUBCLONAL	1	TRUE	1	0.349699088404459	3		361	534	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340071	116340072	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	43	250	0	ENST00000397752.3:c.933_934delinsAA	p.Glu312Lys	p.E312K	ENST00000397752	NM_000245.2	311	aaGGaa/aaAAaa	2/21	1	2	FACETS	0.869	0.731	1	0.869	0.731	1	CLONAL	1	TRUE	1	0.349699088404459	2		250	283	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239064	98239064	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	180	461	0	ENST00000331920.6:c.1579C>A	p.Gln527Lys	p.Q527K	ENST00000331920	NM_000264.3	527	Cag/Aag	11/24	0.347916120185866	2	FACETS	0.921	0.855	0.989	0.921	0.855	0.989	CLONAL	2	TRUE	0	0.349699088404459	2		461	559	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399537	139399537	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	243	914	0	ENST00000277541.6:c.4606T>G	p.Cys1536Gly	p.C1536G	ENST00000277541	NM_017617.3	1536	Tgc/Ggc	26/34	0.347916120185866	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.349699088404459	2		914	686	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55693432	55693472	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CATGGGGATGCTGGGTGAGTCTGGACAGGACCGCAGGTCAC	CATGGGGATGCTGGGTGAGTCTGGACAGGACCGCAGGTCAC	-	novel	NA	P-0037117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	75	696	0	ENST00000284073.2:c.644_652+32del		p.X215_splice	ENST00000284073	NM_138962.2	215		9/14	1	2	FACETS	0.599	0.524	0.68	0.599	0.524	0.68	SUBCLONAL	1	TRUE	1	0.349699088404459	2		696	716	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207021	1207021	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913324	NA	P-0037149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	124	464	0	ENST00000326873.7:c.109C>T	p.Gln37Ter	p.Q37*	ENST00000326873	NM_000455.4	37	Cag/Tag	1/10	0.28571701401176	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.28571701401176	1		464	670	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24133958	24133958	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	17	218	0	ENST00000263121.7:c.109C>T	p.Arg37Cys	p.R37C	ENST00000263121	NM_003073.3	37	Cgt/Tgt	2/9	0.28571701401176	1	FACETS	0.395	0.295	0.514	0.395	0.295	0.514	SUBCLONAL	1	TRUE	0	0.28571701401176	1		218	258	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547198	106547198	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	54	233	0	ENST00000369096.4:c.435C>A	p.His145Gln	p.H145Q	ENST00000369096	NM_001198.3	145	caC/caA	4/7	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.28571701401176	2		233	354	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017597	112017597	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	45	459	0	ENST00000368678.4:c.916del	p.Glu306AsnfsTer10	p.E306Nfs*10	ENST00000368678		306	Gaa/aa	9/13	1	2	FACETS	0.452	0.379	0.533	0.452	0.379	0.533	SUBCLONAL	1	TRUE	1	0.28571701401176	2		459	697	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97934393	97934393	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	20	270	0	ENST00000289081.3:c.382G>C	p.Asp128His	p.D128H	ENST00000289081	NM_000136.2	128	Gat/Cat	5/15	1	2	FACETS	0.543	0.415	0.691	0.543	0.415	0.691	SUBCLONAL	1	TRUE	1	0.28571701401176	2		270	258	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0037161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	260	550	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.364525056376201	3	FACETS	0.909	0.859	0.961	1	0.993	1	CLONAL	3	TRUE	1	0.362569108208943	3		550	621	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243675668	243675668	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	46	445	0	ENST00000263826.5:c.1312G>T	p.Glu438Ter	p.E438*	ENST00000263826	NM_005465.4	438	Gaa/Taa	12/13	NA	2	FACETS	0.86	0.728	1			1	INDETERMINATE	1	TRUE	NA	0.362569108208943	2		445	295	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726671	88726671	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	39	417	0	ENST00000360948.2:c.373A>G	p.Lys125Glu	p.K125E	ENST00000360948	NM_001012338.2	125	Aag/Gag	4/19	0.364525056376201	0	FACETS	0.635	0.531	0.748			1	SUBCLONAL	1	TRUE	0	0.362569108208943	0		417	216	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044985	47044985	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	73	364	0	ENST00000377604.3:c.2313del	p.Glu772ArgfsTer30	p.E772Rfs*30	ENST00000377604	NM_001204468.1	771	Aaa/aa	20/24	0.195281622284683	2	FACETS	1	0.929	1			1	INDETERMINATE	2	TRUE	NA	0.362569108208943	2		364	191	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0037179-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	179	686	1	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.477282150741818	2	FACETS	0.905	0.848	0.961	0.905	0.848	0.961	CLONAL	2	TRUE	0	0.555707346117832	2		687	356	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0037179-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	51	365	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.16991996109705	1	FACETS	0.828	0.718	0.944	0.828	0.718	0.944	INDETERMINATE	1	TRUE	0	0.555707346117832	1		365	160	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0037221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	937	964	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.937452313006916	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.943879491379787	2		964	989	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801012	135801013	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	rs397514795	NA	P-0037221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	617	459	0	ENST00000298552.3:c.324_325del	p.Gln109SerfsTer16	p.Q109Sfs*16	ENST00000298552	NM_001162426.1	108	tcTCaa/tcaa	5/23	0.919149634520485	3	FACETS	0.972	0.959	0.984			1	CLONAL	3	TRUE	NA	0.943879491379787	3		459	660	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532664	46532664	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	27	487	1	ENST00000262741.5:c.414C>A	p.Asn138Lys	p.N138K	ENST00000262741	NM_003629.3	138	aaC/aaA	4/10	1	2	FACETS	0.128	0.101	0.158	0.128	0.101	0.158	SUBCLONAL	1	TRUE	1	0.943879491379787	2		488	448	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65300339	65301076	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACCTGTAAAAAGAAAGAAGTAACAACAGTAAAAATGTTAGATCTGGGAACTTTAAAAAATAACAGAAATATCAAGAGTAAGAAAATAATTTTGGAAATGCAATGACTTTTCCTTAAAGACTAGAAAAACAAGAGTATTTGAATAGTTTAAAACACAGAAAATGGGATACAACTCTAGTTCATAAATAATATTTTAACATTTGAGAAGCTCAAGGGTTGACTGGCTGCAATAAAATCCAGGTCATTCCTGTAAACCAGTTAGAGGGTGAAGCAGAATCTCAGTTCAGACTTGAACTTTCCAGACTGGCTGCCTCACTCTCTGACTCATACTGTTCAGTGTGTCTTACACAGTCTCAAGAGTTTAGTATTAAAGGCTCAATTCACTTAGAAAACTGAATTATAAATGCTAATAAGTGGGATAAACTTACACACAAAAAATGCAATTATATGTATTTGTCACACTAAGGCTACACCAAAACCTGTCCCTCTGGGGCAAGCAAGTGGATAAAGAGGGGCTGGCTTTTGGAGGGAATCCTTGCTCTGAACCTAACTGGTGGCTATCATCTAGCCCCAAAGGCGATTTCTCAGTTATCTTATGTGAAATTCAGCTTCAGAAAACTATTTTACAAGGACTTCACTGCATCATTTCCTCGCTCTCCCCTCTACCCATTGCTGGACAACTCAAGCTGCGAAAACATAATAGAAATGGAGTGTTATTACTGTGACGTGGCCCATAGAT	ACCTGTAAAAAGAAAGAAGTAACAACAGTAAAAATGTTAGATCTGGGAACTTTAAAAAATAACAGAAATATCAAGAGTAAGAAAATAATTTTGGAAATGCAATGACTTTTCCTTAAAGACTAGAAAAACAAGAGTATTTGAATAGTTTAAAACACAGAAAATGGGATACAACTCTAGTTCATAAATAATATTTTAACATTTGAGAAGCTCAAGGGTTGACTGGCTGCAATAAAATCCAGGTCATTCCTGTAAACCAGTTAGAGGGTGAAGCAGAATCTCAGTTCAGACTTGAACTTTCCAGACTGGCTGCCTCACTCTCTGACTCATACTGTTCAGTGTGTCTTACACAGTCTCAAGAGTTTAGTATTAAAGGCTCAATTCACTTAGAAAACTGAATTATAAATGCTAATAAGTGGGATAAACTTACACACAAAAAATGCAATTATATGTATTTGTCACACTAAGGCTACACCAAAACCTGTCCCTCTGGGGCAAGCAAGTGGATAAAGAGGGGCTGGCTTTTGGAGGGAATCCTTGCTCTGAACCTAACTGGTGGCTATCATCTAGCCCCAAAGGCGATTTCTCAGTTATCTTATGTGAAATTCAGCTTCAGAAAACTATTTTACAAGGACTTCACTGCATCATTTCCTCGCTCTCCCCTCTACCCATTGCTGGACAACTCAAGCTGCGAAAACATAATAGAAATGGAGTGTTATTACTGTGACGTGGCCCATAGAT	-	novel	NA	P-0037221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	235	331	0	ENST00000342505.4:c.3369+3_3371del		p.X1123_splice	ENST00000342505	NM_002227.2	1123		25/25	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.943879491379787	2		331	491	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301190	65301780	+	splice_donor_variant,splice_acceptor_variant,intron_variant	Splice_Site	DEL	CTATATAAAATAAAATCAAACAAAACGTTTAACTTTGCAAGTATTTACATAAATGCCAAACAGATTAAGGTGAAATTTCTACAATCAACTGGAAATTTAAGTAGCAATAAAAAGGCTTTTCTCCTTAGTAACTTTAAATAAAAATCCAAAATCCTTATTAGCTTTCAATGATCTGTCTCTAACCAGTGTCTTAGACTCTACCAACCACTCCTTGTGCTTGTGCTGGTCAAGGAGTCTGTTCCCAAGAAAATGATCTGATTTAGGAATGAAGGAGGCACAGACAAGGCTGGTCCCTACCCAGTGCTACCCCACTTAACTTGCTCATTTTCCCATAAAACTGCCCTTCATCTCTACACAGATAAGATCCTTGAGAGTCAAGGTCATCCTATAGAACTCCGGGCTCGTTGTGAAAGCAAGACTTTAGAGATTCACAAATAACTGTCAAGTAGCAAACCAAGTTAATGGGAAAGTGACATTTTCCATTATAATACATTCATTGGATTCCATTTAAAAACAAAAGTTAACCAAGCAGAGGGATGGACACATTTTAAATGGGTACTGGATTCAAATGAAGAGAAAAGTAGGACTTAC	CTATATAAAATAAAATCAAACAAAACGTTTAACTTTGCAAGTATTTACATAAATGCCAAACAGATTAAGGTGAAATTTCTACAATCAACTGGAAATTTAAGTAGCAATAAAAAGGCTTTTCTCCTTAGTAACTTTAAATAAAAATCCAAAATCCTTATTAGCTTTCAATGATCTGTCTCTAACCAGTGTCTTAGACTCTACCAACCACTCCTTGTGCTTGTGCTGGTCAAGGAGTCTGTTCCCAAGAAAATGATCTGATTTAGGAATGAAGGAGGCACAGACAAGGCTGGTCCCTACCCAGTGCTACCCCACTTAACTTGCTCATTTTCCCATAAAACTGCCCTTCATCTCTACACAGATAAGATCCTTGAGAGTCAAGGTCATCCTATAGAACTCCGGGCTCGTTGTGAAAGCAAGACTTTAGAGATTCACAAATAACTGTCAAGTAGCAAACCAAGTTAATGGGAAAGTGACATTTTCCATTATAATACATTCATTGGATTCCATTTAAAAACAAAAGTTAACCAAGCAGAGGGATGGACACATTTTAAATGGGTACTGGATTCAAATGAAGAGAAAAGTAGGACTTAC	-	novel	NA	P-0037221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	198	245	0	ENST00000342505.4:c.3258+1_3259-1del		p.X1086_splice	ENST00000342505	NM_002227.2	1086			1	2	FACETS	0.947	0.888	1	0.947	0.888	1	CLONAL	1	TRUE	1	0.943879491379787	2		245	443	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303787	65304146	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTGAGAGAGAGAAGTAAAAGTCAAGCACATTGCTAAAGTCACTTTAGATTGTATTATCTATCACTTCATCAGAAAAAATAGAAATGTCATTTCATTCACATATCACTGACAATTTTTTTGGTTCTGACTTTTATGCAAGAATATTAAGAACAAACTGATTCAAATAAATACACATTAAAATAACCATATTTAAATCCGTTTACTTTCTTAGTAGAAGCTAACTTTTCATCTAAATAATGCAGAGAAAAACAAACAGTATAATTATCATAAACTTACCCACTTAGAGTCAAATTACAAACCAATTACCCAGGACAGAGTGCCTGATGTCTTAATCTGTAACATGATGTCTTTATTTTTTA	CCTGAGAGAGAGAAGTAAAAGTCAAGCACATTGCTAAAGTCACTTTAGATTGTATTATCTATCACTTCATCAGAAAAAATAGAAATGTCATTTCATTCACATATCACTGACAATTTTTTTGGTTCTGACTTTTATGCAAGAATATTAAGAACAAACTGATTCAAATAAATACACATTAAAATAACCATATTTAAATCCGTTTACTTTCTTAGTAGAAGCTAACTTTTCATCTAAATAATGCAGAGAAAAACAAACAGTATAATTATCATAAACTTACCCACTTAGAGTCAAATTACAAACCAATTACCCAGGACAGAGTGCCTGATGTCTTAATCTGTAACATGATGTCTTTATTTTTTA	-	novel	NA	P-0037221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	297	452	0	ENST00000342505.4:c.2967+2_2968del		p.X989_splice	ENST00000342505	NM_002227.2	989		22/25	1	2	FACETS	0.838	0.793	0.883	0.838	0.793	0.883	CLONAL	1	TRUE	1	0.943879491379787	2		452	751	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65304272	65305284	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTGTTTAGAAAAAACATCCATCAGTCTGAGGCTGCCAAATGAGGGAACCATGGGAGAGGCAAGGGCACAGGATATGAGACAGAGGCCCTGAGGTGACGCCAGCTTCGCCCCTTCATTACAGGCATGTTACTTGACCTCTTATGCCTCAAGATCCTCAGCAGTGAATGGAGATGGTAACAATGGTGTACCTACCTCACAGGCATAAGCACTCACTGAGATAACAGTCAGAGTGCTCTGTAAACCACAGGCAAATGACTGTTTTCAAAAATTATCGGGCTGGGCGCGGTGGCTCACGCTTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAAATTAGCCGGGCGTGATGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCAGTCCAGCCTGGGCCACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAATTATCATCAGCTGTCAATTTCACTACCATGAGTAGATGCTGGCTTGCAAATAAGATACAATTATTAGTAAATATTACTTGCCACTTTGATTTAGACAACTAGAAAATGAAATACCCTGGCTAGTATTGGATCAGAACAGGAAGTGGGTGGAGGTAGAGTAGGAATCAGTTTCATAAGGCATAAGTGCAAGTGACGTGGAGAGACAGTGCTGGAACCAGCCCCTGGATGGAGGGGCCTGGGTGGCCTCCTCAGGAGCCCTGCAGCTGCTGAGGGATTTGACATATGACTTGGAAGCCTTGAGAGTGTGTGGGAACCACCAGCTAGCATGTCAGACGCCCAGGTAAGGCCACGGAGTGCCTGTTTTGCACTGGCCTTTATGACCCTAGACAGTCACCAAATCTTTAAACCGGACCCCAGCCTTGCATAACATA	CCTGTTTAGAAAAAACATCCATCAGTCTGAGGCTGCCAAATGAGGGAACCATGGGAGAGGCAAGGGCACAGGATATGAGACAGAGGCCCTGAGGTGACGCCAGCTTCGCCCCTTCATTACAGGCATGTTACTTGACCTCTTATGCCTCAAGATCCTCAGCAGTGAATGGAGATGGTAACAATGGTGTACCTACCTCACAGGCATAAGCACTCACTGAGATAACAGTCAGAGTGCTCTGTAAACCACAGGCAAATGACTGTTTTCAAAAATTATCGGGCTGGGCGCGGTGGCTCACGCTTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAAATTAGCCGGGCGTGATGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCAGTCCAGCCTGGGCCACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAATTATCATCAGCTGTCAATTTCACTACCATGAGTAGATGCTGGCTTGCAAATAAGATACAATTATTAGTAAATATTACTTGCCACTTTGATTTAGACAACTAGAAAATGAAATACCCTGGCTAGTATTGGATCAGAACAGGAAGTGGGTGGAGGTAGAGTAGGAATCAGTTTCATAAGGCATAAGTGCAAGTGACGTGGAGAGACAGTGCTGGAACCAGCCCCTGGATGGAGGGGCCTGGGTGGCCTCCTCAGGAGCCCTGCAGCTGCTGAGGGATTTGACATATGACTTGGAAGCCTTGAGAGTGTGTGGGAACCACCAGCTAGCATGTCAGACGCCCAGGTAAGGCCACGGAGTGCCTGTTTTGCACTGGCCTTTATGACCCTAGACAGTCACCAAATCTTTAAACCGGACCCCAGCCTTGCATAACATA	-	novel	NA	P-0037221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	257	373	0	ENST00000342505.4:c.2842+2_2843del		p.X948_splice	ENST00000342505	NM_002227.2	948		21/25	1	2	FACETS	0.84	0.792	0.889	0.84	0.792	0.889	CLONAL	1	TRUE	1	0.943879491379787	2		373	648	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562393	95562393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1007550524	NA	P-0037221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	544	561	1	ENST00000393063.1:c.4864G>A	p.Ala1622Thr	p.A1622T	ENST00000393063	NM_030621.3	1622	Gct/Act	24/28	0.910785876130386	3	FACETS	0.967	0.937	0.998	0.967	0.937	0.998	CLONAL	2	TRUE	1	0.943879491379787	3		562	877	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315366	30315366	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	545	514	0	ENST00000322652.5:c.1051C>T	p.Gln351Ter	p.Q351*	ENST00000322652	NM_015355.2	351	Cag/Tag	10/16	0.937452313006916	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.943879491379787	2		514	572	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967076	25967162	+	inframe_deletion	In_Frame_Del	DEL	AGCAGTCTGCCCTTCACCACCCTCTCCTGGACCTTGTCCACCCCCTGGGCCAGGTCCTGGAATGGTCCCTCCAACTGAGGCGGCTGC	AGCAGTCTGCCCTTCACCACCCTCTCCTGGACCTTGTCCACCCCCTGGGCCAGGTCCTGGAATGGTCCCTCCAACTGAGGCGGCTGC	-	novel	NA	P-0037221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	95	646	0	ENST00000435504.4:c.2044_2130del	p.Ala682_Ala710del	p.A682_A710del	ENST00000435504		682	GCAGCCGCCTCAGTTGGAGGGACCATTCCAGGACCTGGCCCAGGGGGTGGACAAGGTCCAGGAGAGGGTGGTGAAGGGCAGACTGCT/-	13/13	0.80958190672392	3	FACETS	0.297	0.263	0.333			1	SUBCLONAL	1	TRUE	NA	0.943879491379787	3		646	998	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250193	39250193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1320	777	954	0	ENST00000402219.2:c.1376G>A	p.Arg459Lys	p.R459K	ENST00000402219	NM_005633.3	459	aGa/aAa	10/23	0.68458960834331	6	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.943879491379787	6		954	2097	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155426	99155426	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	750	463	0	ENST00000074304.5:c.652G>C	p.Asp218His	p.D218H	ENST00000074304	NM_001134224.1	218	Gac/Cac	9/26	0.68458960834331	6	FACETS	0.91	0.884	0.935			1	CLONAL	4	TRUE	NA	0.943879491379787	6		463	1261	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096522	178096522	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	396	480	0	ENST00000397062.3:c.809C>A	p.Ser270Ter	p.S270*	ENST00000397062	NM_006164.4	270	tCa/tAa	5/5	0.943880985675483	3	FACETS	0.915	0.879	0.95	0.915	0.879	0.95	CLONAL	2	TRUE	1	0.943879491379787	3		480	675	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514465	41514465	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	284	591	0	ENST00000373198.4:c.196G>T	p.Asp66Tyr	p.D66Y	ENST00000373198	NM_133170.3	66	Gac/Tac	2/32	0.501644133883719	3	FACETS	0.981	0.924	1			1	INDETERMINATE	1	TRUE	NA	0.943879491379787	3		591	903	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486167	8486167	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	254	592	1	ENST00000356435.5:c.2650G>C	p.Asp884His	p.D884H	ENST00000356435		884	Gac/Cac	17/35	0.943880985675483	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.943879491379787	1		593	274	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911401	39911401	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	291	640	0	ENST00000378444.4:c.5229G>T	p.Trp1743Cys	p.W1743C	ENST00000378444	NM_001123385.1	1743	tgG/tgT	15/15	NA	2	FACETS	0.952	0.902	1			1	INDETERMINATE	1	TRUE	NA	0.943879491379787	2		640	648	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428159	47428159	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	454	983	0	ENST00000377045.4:c.1119G>C	p.Met373Ile	p.M373I	ENST00000377045	NM_001654.4	373	atG/atC	11/16	NA	2	FACETS	0.934	0.895	0.973			1	INDETERMINATE	1	TRUE	NA	0.943879491379787	2		983	1030	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602872	10602872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	298	967	1	ENST00000171111.5:c.706G>A	p.Asp236Asn	p.D236N	ENST00000171111	NM_203500.1	236	Gac/Aac	3/6	0.282527367471332	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.306628339150611	2		968	959	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480306	89480306	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	42	314	0	ENST00000336596.2:c.2143G>T	p.Asp715Tyr	p.D715Y	ENST00000336596	NM_005233.5	715	Gat/Tat	13/17	0.306628339150611	1	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	TRUE	0	0.306628339150611	1		314	228	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0037222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	189	475	1	ENST00000269305.4:c.96+1G>A		p.X32_splice	ENST00000269305	NM_001126112.2	32			0.284485527085835	3	FACETS	0.86	0.801	0.921	0.86	0.801	0.921	CLONAL	3	TRUE	0	0.306628339150611	3		476	551	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438225	49438225	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	203	767	0	ENST00000301067.7:c.5044G>T	p.Glu1682Ter	p.E1682*	ENST00000301067	NM_003482.3	1682	Gag/Tag	20/54	0.266635282420681	5	FACETS	0.979	0.908	1	0.653	0.605	0.702	CLONAL	2	TRUE	2	0.306628339150611	5		767	987	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438364	110438364	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	29	144	0	ENST00000375856.3:c.37G>T	p.Ala13Ser	p.A13S	ENST00000375856	NM_003749.2	13	Gcg/Tcg	1/2	0.306628339150611	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.306628339150611	1		144	116	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566487	41566487	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	65	450	0	ENST00000263253.7:c.4364A>G	p.Gln1455Arg	p.Q1455R	ENST00000263253	NM_001429.3	1455	cAg/cGg	27/31	1	2	FACETS	0.85	0.738	0.97	0.85	0.738	0.97	CLONAL	1	TRUE	1	0.306628339150611	2		450	499	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86667969	86667969	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0037222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	101	340	0	ENST00000274376.6:c.1733T>G	p.Leu578Ter	p.L578*	ENST00000274376	NM_002890.2	578	tTa/tGa	13/25	0.302373804787679	2	FACETS	0.832	0.749	0.918	0.832	0.749	0.918	CLONAL	2	TRUE	0	0.306628339150611	2		340	396	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012425	152012425	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0037222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	76	306	0	ENST00000262189.6:c.390-2A>G		p.X130_splice	ENST00000262189	NM_170606.2	130			0.286039299336402	3	FACETS	0.831	0.734	0.933	0.831	0.734	0.933	CLONAL	2	TRUE	1	0.306628339150611	3		306	344	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396891	139396892	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0037222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	160	534	0	ENST00000277541.6:c.5216dup	p.Ala1740GlyfsTer32	p.A1740Gfs*32	ENST00000277541	NM_017617.3	1739	gtg/gtTg	28/34	0.275217939362294	2	FACETS	0.985	0.909	1	0.985	0.909	1	CLONAL	2	TRUE	0	0.306628339150611	2		534	530	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354951	70354951	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	94	293	0	ENST00000374080.3:c.4873G>T	p.Gly1625Trp	p.G1625W	ENST00000374080		1625	Ggg/Tgg	36/45	1	1	FACETS	0.75	0.674	0.83	1	0.982	1	SUBCLONAL	2	TRUE	0	0.306628339150611	1		293	346	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0037272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	190	587	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.537842144213096	2		587	629	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111877	56111878	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0037272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	11	13	0	ENST00000399503.3:c.478dup	p.Ala160GlyfsTer4	p.A160Gfs*4	ENST00000399503	NM_005921.1	159	-/G	1/20	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.537842144213096	2		13	28	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445068	49445068	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	196	645	0	ENST00000301067.7:c.2398C>T	p.Gln800Ter	p.Q800*	ENST00000301067	NM_003482.3	800	Cag/Tag	10/54	1	2	FACETS	0.983	0.91	1	0.983	0.91	1	CLONAL	1	TRUE	1	0.401454873717418	2		645	993	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0037296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	244	587	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.338543528776798	5	FACETS	1	0.981	1	0.558	0.522	0.594	CLONAL	2	TRUE	1	0.401454873717418	5		587	873	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0037296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	215	735	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.961	0.893	1	0.961	0.893	1	CLONAL	1	TRUE	1	0.401454873717418	2		735	1114	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457242	25457242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147001633	NA	P-0037296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	202	675	3	ENST00000264709.3:c.2645G>A	p.Arg882His	p.R882H	ENST00000264709	NM_175629.2	882	cGc/cAc	23/23	1	2	FACETS	0.909	0.842	0.979	0.909	0.842	0.979	CLONAL	1	TRUE	1	0.401454873717418	2		678	1107	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519896	NA	P-0037296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	339	448	0	ENST00000281708.4:c.1514G>T	p.Arg505Leu	p.R505L	ENST00000281708	NM_033632.3	505	cGc/cTc	10/12	0.401454873717418	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.401454873717418	3		448	951	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851900	128851900	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	231	823	0	ENST00000249373.3:c.1972G>A	p.Glu658Lys	p.E658K	ENST00000249373	NM_005631.4	658	Gag/Aag	12/12	0.401454873717418	1	FACETS	0.989	0.923	1	0.989	0.923	1	CLONAL	1	TRUE	0	0.401454873717418	1		823	930	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939843	76939843	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	147	386	0	ENST00000373344.5:c.905G>T	p.Ser302Ile	p.S302I	ENST00000373344	NM_000489.3	302	aGt/aTt	9/35	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.401454873717418	1		386	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	346	979	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.724895004841112	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.724895004841112	1		979	600	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672758	86672758	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1204340475	NA	P-0037306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	118	353	0	ENST00000274376.6:c.2245C>T	p.Arg749Ter	p.R749*	ENST00000274376	NM_002890.2	749	Cga/Tga	17/25	0.724895004841112	1	FACETS	0.91	0.841	0.979	0.91	0.841	0.979	CLONAL	1	TRUE	0	0.724895004841112	1		353	228	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932274	36932274	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	381	689	1	ENST00000361632.4:c.2195A>T	p.Asp732Val	p.D732V	ENST00000361632		732	gAc/gTc	16/16	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.724895004841112	2		690	1047	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332741	70332741	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	283	466	0	ENST00000373644.4:c.646G>T	p.Gly216Trp	p.G216W	ENST00000373644	NM_030625.2	216	Ggg/Tgg	2/12	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.724895004841112	2		466	681	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77064582	77064582	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	272	467	0	ENST00000356341.3:c.835G>T	p.Gly279Cys	p.G279C	ENST00000356341	NM_002576.4	279	Ggt/Tgt	8/15	1	2	FACETS	0.967	0.911	1	0.967	0.911	1	CLONAL	1	TRUE	1	0.724895004841112	2		467	776	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239420	105239420	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	496	533	0	ENST00000349310.3:c.967G>T	p.Asp323Tyr	p.D323Y	ENST00000349310	NM_001014432.1	323	Gac/Tac	12/15	0.273885728743908	5	FACETS	0.854	0.82	0.888	0.854	0.82	0.888	INDETERMINATE	3	TRUE	2	0.724895004841112	5		533	1115	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819735	81819735	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	294	464	0	ENST00000359376.3:c.141G>C	p.Met47Ile	p.M47I	ENST00000359376	NM_002661.3	47	atG/atC	2/33	1	2	FACETS	0.98	0.926	1	0.98	0.926	1	CLONAL	1	TRUE	1	0.724895004841112	2		464	828	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670120	29670120	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	232	454	0	ENST00000356175.3:c.7093T>A	p.Phe2365Ile	p.F2365I	ENST00000356175	NM_000267.3	2365	Ttt/Att	47/57	0.496456473981943	1	FACETS	0.993	0.942	1	0.993	0.942	1	CLONAL	1	TRUE	0	0.724895004841112	1		454	411	SUCCESS
APC	324	MSKCC	GRCh37	5	112176194	112176194	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	226	379	0	ENST00000257430.4:c.4903G>T	p.Gly1635Trp	p.G1635W	ENST00000257430	NM_000038.5	1635	Ggg/Tgg	16/16	0.724895004841112	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.724895004841112	1		379	365	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752965	128752965	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1276187525	NA	P-0037306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	104	377	0	ENST00000377970.2:c.1126G>A	p.Val376Ile	p.V376I	ENST00000377970	NM_002467.4	376	Gtc/Atc	3/3	1	2	FACETS	0.459	0.412	0.509	0.459	0.412	0.509	SUBCLONAL	1	TRUE	1	0.724895004841112	2		377	625	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934574	NA	P-0037314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	14	690	0	ENST00000269305.4:c.844C>G	p.Arg282Gly	p.R282G	ENST00000269305	NM_001126112.2	282	Cgg/Ggg	8/11	0.120128473667291	3	FACETS	0.492	0.354	0.66	0.246	0.177	0.33	SUBCLONAL	1	TRUE	1	0.15	3		690	408	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577138	7577138	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587780075	NA	P-0037314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	22	517	0	ENST00000269305.4:c.800G>C	p.Arg267Pro	p.R267P	ENST00000269305	NM_001126112.2	267	cGg/cCg	8/11	0.120128473667291	3	FACETS	0.925	0.717	1	0.462	0.358	0.584	CLONAL	1	TRUE	1	0.15	3		517	341	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624918	9624918	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	15	425	0	ENST00000353224.5:c.59G>A	p.Arg20Lys	p.R20K	ENST00000353224	NM_177990.2	20	aGg/aAg	3/10	1	2	FACETS	0.709	0.518	0.939	0.709	0.518	0.939	CLONAL	1	TRUE	1	0.15	2		425	282	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471599	120471599	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	13	276	0	ENST00000256646.2:c.3892G>A	p.Gly1298Ser	p.G1298S	ENST00000256646	NM_024408.3	1298	Ggc/Agc	23/34	0.207702240353742	3	FACETS	1	0.773	1	0.548	0.392	0.737	CLONAL	1	TRUE	1	0.15	3		276	170	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865242	57865242	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	21	648	1	ENST00000228682.2:c.2719G>A	p.Glu907Lys	p.E907K	ENST00000228682	NM_005269.2	907	Gag/Aag	12/12	0.403640937750067	4	FACETS	0.877	0.675	1	0.439	0.337	0.557	CLONAL	1	TRUE	2	0.15	4		649	367	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829887	72829887	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	21	666	0	ENST00000268489.5:c.6694G>A	p.Glu2232Lys	p.E2232K	ENST00000268489	NM_006885.3	2232	Gaa/Aaa	9/10	1	2	FACETS	0.969	0.747	1	0.969	0.747	1	CLONAL	1	TRUE	1	0.15	2		666	289	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075269	16075269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	19	395	2	ENST00000268712.3:c.283G>A	p.Gly95Ser	p.G95S	ENST00000268712	NM_006311.3	95	Ggc/Agc	4/46	0.120128473667291	3	FACETS	0.785	0.595	1	0.392	0.297	0.505	CLONAL	1	TRUE	1	0.15	3		397	347	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086121	16086121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	24	446	0	ENST00000281043.3:c.1297C>T	p.Leu433Phe	p.L433F	ENST00000281043	NM_005378.4	433	Ctc/Ttc	3/3	0.120128473667291	3	FACETS	1	0.885	1	0.606	0.476	0.755	CLONAL	1	TRUE	1	0.15	3		446	284	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182135	99182135	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766270566	NA	P-0037314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	12	415	0	ENST00000074304.5:c.2200C>T	p.Leu734Phe	p.L734F	ENST00000074304	NM_001134224.1	734	Ctt/Ttt	21/26	0.207702240353742	4	FACETS	0.8	0.562	1	0.4	0.281	0.547	CLONAL	1	TRUE	2	0.15	4		415	230	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572913	41572913	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	22	634	0	ENST00000263253.7:c.5198T>C	p.Leu1733Pro	p.L1733P	ENST00000263253	NM_001429.3	1733	cTg/cCg	31/31	1	2	FACETS	0.892	0.691	1	0.892	0.691	1	CLONAL	1	TRUE	1	0.15	2		634	329	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729896	30729897	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0037314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	15	280	0	ENST00000295754.5:c.1417_1418delinsTT	p.Pro473Leu	p.P473L	ENST00000295754	NM_003242.5	473	CCa/TTa	6/7	0.207702240353742	3	FACETS	0.76	0.555	1	0.38	0.277	0.503	CLONAL	1	TRUE	1	0.15	3		280	283	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430489	181430489	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	12	435	0	ENST00000325404.1:c.341G>A	p.Arg114Gln	p.R114Q	ENST00000325404	NM_003106.3	114	cGg/cAg	1/1	0.207702240353742	3	FACETS	0.726	0.51	0.992	0.363	0.255	0.496	CLONAL	1	TRUE	1	0.15	3		435	237	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450371	50450372	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0037314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	18	407	2	ENST00000331340.3:c.555_556delinsAA	p.Asp186Asn	p.D186N	ENST00000331340	NM_006060.4	185	agGGac/agAAac	5/8	0.120128473667291	3	FACETS	0.966	0.728	1	0.483	0.364	0.624	CLONAL	1	TRUE	1	0.15	3		409	267	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206730	27206730	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	22	484	0	ENST00000380036.4:c.2515C>T	p.Leu839Phe	p.L839F	ENST00000380036	NM_000459.3	839	Ctt/Ttt	15/23	1	2	FACETS	0.886	0.687	1	0.886	0.687	1	CLONAL	1	TRUE	1	0.15	2		484	331	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404328	139404328	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	25	746	1	ENST00000277541.6:c.2826T>G	p.Cys942Trp	p.C942W	ENST00000277541	NM_017617.3	942	tgT/tgG	18/34	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.15	2		747	235	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418387	139418387	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749947050	NA	P-0037314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	25	837	1	ENST00000277541.6:c.185C>T	p.Pro62Leu	p.P62L	ENST00000277541	NM_017617.3	62	cCg/cTg	3/34	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.15	2		838	274	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426675	47426675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	27	306	0	ENST00000377045.4:c.920C>T	p.Pro307Leu	p.P307L	ENST00000377045	NM_001654.4	307	cCc/cTc	10/16	0.3	2	FACETS	0.887	0.71	1	0.887	0.71	1	CLONAL	2	TRUE	0	0.15	2		306	203	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0037319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	314	780	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.745294275718918	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.745294275718918	1		780	485	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267836	7267836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs52836744	NA	P-0037319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	129	432	0	ENST00000302850.5:c.172G>A	p.Gly58Arg	p.G58R	ENST00000302850	NM_000208.2	58	Gga/Aga	2/22	0.158891401149651	4	FACETS	0.899	0.817	0.985	0.45	0.408	0.493	INDETERMINATE	1	TRUE	2	0.745294275718918	4		432	672	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927989	49927989	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374259168	NA	P-0037319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	161	472	1	ENST00000296474.3:c.3739G>A	p.Ala1247Thr	p.A1247T	ENST00000296474	NM_002447.2	1247	Gct/Act	18/20	0.198491244331639	3	FACETS	0.819	0.753	0.888	0.273	0.251	0.296	INDETERMINATE	1	TRUE	0	0.745294275718918	3		473	724	SUCCESS
APC	324	MSKCC	GRCh37	5	112128142	112128144	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GCG	GCG	-	novel	NA	P-0037319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	146	187	0	ENST00000257430.4:c.646-1_647del		p.X216_splice	ENST00000257430	NM_000038.5	216		7/16	0.745294275718918	2	FACETS	0.92	0.868	0.969	0.92	0.868	0.969	CLONAL	2	TRUE	0	0.745294275718918	2		187	213	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057573	180057573	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs866678855	NA	P-0037319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	178	573	0	ENST00000261937.6:c.382T>C	p.Ser128Pro	p.S128P	ENST00000261937	NM_182925.4	128	Tcc/Ccc	3/30	0.745294275718918	2	FACETS	0.68	0.629	0.734	0.34	0.314	0.367	SUBCLONAL	1	TRUE	0	0.745294275718918	2		573	702	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922762	44922762	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	80	318	0	ENST00000377967.4:c.1623G>T	p.Gln541His	p.Q541H	ENST00000377967	NM_021140.2	541	caG/caT	16/29	0.37347252927613	2	FACETS	0.538	0.476	0.604	0.269	0.238	0.302	INDETERMINATE	1	TRUE	0	0.745294275718918	2		318	399	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0037332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	238	499	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.882611880325477	1	FACETS	0.943	0.906	0.979	0.943	0.906	0.979	CLONAL	1	TRUE	0	0.884722001975001	1		499	318	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0037332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	470	662	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	NA	2	FACETS	0.98	0.96	0.999			1	INDETERMINATE	2	TRUE	NA	0.884722001975001	2		662	542	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940000	76940000	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1311466929	NA	P-0037332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	123	529	0	ENST00000373344.5:c.748C>T	p.Arg250Ter	p.R250*	ENST00000373344	NM_000489.3	250	Cga/Tga	9/35	0.486746796895155	2	FACETS	0.764	0.716	0.809			1	INDETERMINATE	2	TRUE	NA	0.884722001975001	2		529	182	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740098	162740098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781104392	NA	P-0037332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	100	305	0	ENST00000367921.3:c.1300C>T	p.Arg434Trp	p.R434W	ENST00000367921	NM_006182.2	434	Cgg/Tgg	12/18	0.884722001975001	4	FACETS	0.886	0.795	0.981	0.443	0.397	0.491	CLONAL	1	TRUE	2	0.884722001975001	4		305	481	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753752	42753757	+	inframe_deletion	In_Frame_Del	DEL	GAAGAT	GAAGAT	-	rs749503353	NA	P-0037332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	60	723	0	ENST00000222329.4:c.507_512del	p.Ser170_Ser171del	p.S170_S171del	ENST00000222329	NM_006494.2	169	tcATCTTCc/tcc	4/4	0.879742733789695	2	FACETS	0.23	0.197	0.264	0.115	0.098	0.132	SUBCLONAL	1	TRUE	0	0.884722001975001	2		723	591	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271209	26271209	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1318299590	NA	P-0037332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	135	332	0	ENST00000305910.3:c.404G>A	p.Arg135Lys	p.R135K	ENST00000305910	NM_003534.2	135	aGa/aAa	1/1	0.863565507368377	5	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.884722001975001	5		332	559	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276633	115276633	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	126	541	0	ENST00000438362.2:c.826G>C	p.Glu276Gln	p.E276Q	ENST00000438362	NM_001242891.1	276	Gaa/Caa	8/20	0.884722001975001	4	FACETS	1	0.941	1	0.522	0.475	0.571	CLONAL	1	TRUE	2	0.884722001975001	4		541	514	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983065	201983065	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	303	652	0	ENST00000359651.3:c.914T>C	p.Phe305Ser	p.F305S	ENST00000359651		305	tTc/tCc	7/8	0.884722001975001	3	FACETS	1	0.979	1	0.535	0.505	0.566	CLONAL	1	TRUE	1	0.884722001975001	3		652	923	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649115	37649115	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	73	342	0	ENST00000447079.4:c.2220A>T	p.Gln740His	p.Q740H	ENST00000447079	NM_015083.1	740	caA/caT	4/14	0.349842315354937	5	FACETS	1	0.936	1	0.274	0.241	0.309	INDETERMINATE	1	TRUE	1	0.884722001975001	5		342	350	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72873575	72873575	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	23	380	0	ENST00000325599.8:c.727G>C	p.Val243Leu	p.V243L	ENST00000325599	NM_018130.2	243	Gtg/Ctg	6/11	0.884722001975001	3	FACETS	0.258	0.201	0.323			1	SUBCLONAL	1	TRUE	NA	0.884722001975001	3		380	291	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231668	66231668	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	62	428	0	ENST00000273854.3:c.2032G>C	p.Glu678Gln	p.E678Q	ENST00000273854	NM_004439.5	678	Gag/Cag	11/18	0.862969291294967	2	FACETS	0.806	0.71	0.904	0.403	0.355	0.452	CLONAL	1	TRUE	0	0.884722001975001	2		428	174	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39021200	39021200	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1246966013	NA	P-0037332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	97	405	2	ENST00000357387.3:c.136G>T	p.Ala46Ser	p.A46S	ENST00000357387	NM_152756.3	46	Gcc/Tcc	3/38	0.877485761775837	5	FACETS	1	0.977	1	0.33	0.296	0.365	CLONAL	1	TRUE	1	0.884722001975001	5		407	387	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411182	63411182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	231	328	0	ENST00000330258.3:c.1985C>T	p.Ser662Leu	p.S662L	ENST00000330258	NM_152424.3	662	tCa/tTa	2/2	0.486746796895155	2	FACETS	1	0.982	1			1	INDETERMINATE	2	TRUE	NA	0.884722001975001	2		328	258	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0037370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	76	493	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	NA	4	FACETS	1	0.933	1	1	0.933	1	INDETERMINATE	2	FALSE	2	0.177318429940348	4		493	463	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576870	7576870	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs876659384	NA	P-0037370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	98	548	0	ENST00000269305.4:c.976G>T	p.Glu326Ter	p.E326*	ENST00000269305	NM_001126112.2	326	Gaa/Taa	9/11	0.177318429940348	2	FACETS	0.9	0.804	1	0.9	0.804	1	CLONAL	2	FALSE	0	0.177318429940348	2		548	614	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0037370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	36	268	2	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.169872632215109	3	FACETS	1	0.852	1	0.52	0.427	0.624	CLONAL	1	FALSE	1	0.177318429940348	3		270	425	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111012	193111012	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	30	164	0	ENST00000367435.3:c.545T>A	p.Ile182Asn	p.I182N	ENST00000367435	NM_024529.4	182	aTt/aAt	7/17	0.169872632215109	3	FACETS	1	0.868	1	1	0.868	1	CLONAL	2	FALSE	1	0.177318429940348	3		164	170	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3795351	3795351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201874248	NA	P-0037370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	34	241	1	ENST00000262367.5:c.3841G>A	p.Val1281Ile	p.V1281I	ENST00000262367	NM_004380.2	1281	Gtt/Att	22/31	0.169872632215109	3	FACETS	1	0.933	1	0.665	0.545	0.799	CLONAL	1	FALSE	1	0.177318429940348	3		242	314	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808911	3808911	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	107	491	0	ENST00000262367.5:c.3313G>T	p.Asp1105Tyr	p.D1105Y	ENST00000262367	NM_004380.2	1105	Gac/Tac	17/31	0.169872632215109	3	FACETS	0.985	0.885	1	0.985	0.885	1	CLONAL	2	FALSE	1	0.177318429940348	3		491	667	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205019	128205019	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	53	548	0	ENST00000341105.2:c.422A>G	p.Tyr141Cys	p.Y141C	ENST00000341105	NM_032638.4	141	tAc/tGc	3/6	0.0386428041274536	4	FACETS	0.85	0.727	0.984	0.85	0.727	0.984	INDETERMINATE	2	FALSE	2	0.177318429940348	4		548	414	SUCCESS
ATR	545	MSKCC	GRCh37	3	142204115	142204115	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201091477	NA	P-0037370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	56	363	0	ENST00000350721.4:c.6088G>A	p.Ala2030Thr	p.A2030T	ENST00000350721	NM_001184.3	2030	Gcg/Acg	36/47	0.0386428041274536	4	FACETS	0.871	0.748	1	0.871	0.748	1	INDETERMINATE	2	FALSE	2	0.177318429940348	4		363	427	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557967	187557967	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	24	380	0	ENST00000441802.2:c.3744del	p.Lys1248AsnfsTer28	p.K1248Nfs*28	ENST00000441802	NM_005245.3	1248	aaG/aa	5/27	1	2	FACETS	0.645	0.505	0.806	0.645	0.505	0.806	SUBCLONAL	1	FALSE	1	0.177318429940348	2		380	420	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0037406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	173	294	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.412434616638669	5	FACETS	0.963	0.897	1	0.963	0.897	1	CLONAL	3	TRUE	2	0.50063276038485	5		294	419	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs80338963	NA	P-0037406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	200	383	0	ENST00000342988.3:c.1081C>G	p.Arg361Gly	p.R361G	ENST00000342988	NM_005359.5	361	Cgc/Ggc	9/12	0.50063276038485	3	FACETS	0.874	0.823	0.925	0.874	0.823	0.925	CLONAL	3	TRUE	0	0.50063276038485	3		383	381	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196258	108196267	+	frameshift_variant	Frame_Shift_Del	DEL	TCAAGAACAC	TCAAGAACAC	-	novel	NA	P-0037406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	121	298	0	ENST00000278616.4:c.6797_6806del	p.Lys2266SerfsTer41	p.K2266Sfs*41	ENST00000278616	NM_000051.3	2265	tTCAAGAACACt/tt	46/63	0.50063276038485	2	FACETS	0.909	0.837	0.981	0.909	0.837	0.981	CLONAL	2	TRUE	0	0.50063276038485	2		298	266	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661942	29661942	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	204	441	0	ENST00000356175.3:c.5838del	p.Lys1946AsnfsTer12	p.K1946Nfs*12	ENST00000356175	NM_000267.3	1946	Aaa/aa	39/57	0.50063276038485	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.50063276038485	2		441	378	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853838	59853838	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	161	314	0	ENST00000259008.2:c.2021A>T	p.Asp674Val	p.D674V	ENST00000259008	NM_032043.2	674	gAt/gTt	14/20	0.160925416978897	6	FACETS	0.901	0.834	0.971	0.901	0.834	0.971	INDETERMINATE	3	TRUE	3	0.50063276038485	6		314	476	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138447	2138447	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	287	649	0	ENST00000219476.3:c.5260A>T	p.Ile1754Phe	p.I1754F	ENST00000219476	NM_000548.3	1754	Atc/Ttc	42/42	0.275035290586522	1	FACETS	0.764	0.723	0.804	0.764	0.723	0.804	INDETERMINATE	1	TRUE	0	0.719434652465928	1		649	669	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890106	76890106	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	192	490	1	ENST00000373344.5:c.4788G>A	p.Met1596Ile	p.M1596I	ENST00000373344	NM_000489.3	1596	atG/atA	17/35	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.585927532299342	2		491	553	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057302	30057302	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315496	NA	P-0037525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	251	434	0	ENST00000338641.4:c.784C>T	p.Arg262Ter	p.R262*	ENST00000338641	NM_000268.3	262	Cga/Tga	8/16	0.590165700873682	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.590165700873682	2		434	411	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39251221	39251221	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	141	633	0	ENST00000402219.2:c.1132A>T	p.Thr378Ser	p.T378S	ENST00000402219	NM_005633.3	378	Aca/Tca	9/23	0.588834171267644	3	FACETS	0.676	0.615	0.739	0.338	0.307	0.37	SUBCLONAL	1	TRUE	1	0.590165700873682	3		633	916	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591145	67591154	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TACTTGATGT	TACTTGATGT	-	novel	NA	P-0037530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	97	252	0	ENST00000274335.5:c.1738_1745+2del		p.X580_splice	ENST00000274335		580		12/15	0.60896471795475	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.638705219421555	1		252	203	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36024647	36024668	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCGGCTTCTACATCACCTCC	CGGCGGCTTCTACATCACCTCC	-	novel	NA	P-0037530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	195	584	0	ENST00000358208.4:c.638_659del	p.Gly213AlafsTer81	p.G213Afs*81	ENST00000358208		212	agCGGCGGCTTCTACATCACCTCC/ag	6/12	1	2	FACETS	0.888	0.825	0.952	0.888	0.825	0.952	CLONAL	1	TRUE	1	0.638705219421555	2		584	688	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940445	49940445	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	243	562	1	ENST00000296474.3:c.598G>A	p.Ala200Thr	p.A200T	ENST00000296474	NM_002447.2	200	Gca/Aca	1/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.638705219421555	2		563	718	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001395	150001395	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	211	666	2	ENST00000253339.5:c.2209C>T	p.Arg737Ter	p.R737*	ENST00000253339		737	Cga/Tga	4/7	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.520311303387739	2		668	730	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131421	202131421	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	141	507	2	ENST00000358485.4:c.389G>T	p.Arg130Ile	p.R130I	ENST00000358485	NM_001080125.1	130	aGa/aTa	2/9	1	2	FACETS	0.97	0.888	1	0.97	0.888	1	CLONAL	1	TRUE	1	0.520311303387739	2		509	559	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374881	45374881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	243	591	0	ENST00000262160.6:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000262160	NM_005901.5	321	cGa/cAa	8/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.520311303387739	2		591	775	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	174	583	2	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.520311303387739	2		585	577	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	131	396	0	ENST00000263967.3:c.333G>T	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaT	2/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.520311303387739	2		396	476	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479811	67479811	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500766	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	158	557	0	ENST00000327367.4:c.1118G>A	p.Arg373His	p.R373H	ENST00000327367	NM_005902.3	373	cGc/cAc	8/9	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.520311303387739	2		557	607	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	126	285	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.520311303387739	2		285	484	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273297	55273297	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1301373415	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	141	416	0	ENST00000275493.2:c.3620T>G	p.Phe1207Cys	p.F1207C	ENST00000275493	NM_005228.3	1207	tTt/tGt	28/28	0.520311303387739	3	FACETS	1	0.972	1	0.572	0.523	0.623	CLONAL	1	TRUE	1	0.520311303387739	3		416	597	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	186	704	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	0.520311303387739	2		704	602	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457303	67457303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768713596	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	169	617	2	ENST00000327367.4:c.277C>T	p.Arg93Ter	p.R93*	ENST00000327367	NM_005902.3	93	Cga/Tga	2/9	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.520311303387739	2		619	544	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440943	56440943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786205215	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	168	568	2	ENST00000407977.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000407977		132	Cga/Tga	4/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.520311303387739	2		570	604	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007681	45007681	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	35	467	0	ENST00000558401.1:c.128T>G	p.Leu43Arg	p.L43R	ENST00000558401	NM_004048.2	43	cTg/cGg	2/4	1	2	FACETS	0.23	0.188	0.278	0.23	0.188	0.278	SUBCLONAL	1	TRUE	1	0.520311303387739	2		467	585	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663722	29663722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1026776734	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	224	581	1	ENST00000356175.3:c.6154C>T	p.Leu2052Phe	p.L2052F	ENST00000356175	NM_000267.3	2052	Ctt/Ttt	41/57	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.520311303387739	2		582	685	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374245	138374245	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	170	578	0	ENST00000289153.2:c.3199G>T	p.Asp1067Tyr	p.D1067Y	ENST00000289153	NM_006219.2	1067	Gac/Tac	22/22	1	2	FACETS	0.942	0.869	1	0.942	0.869	1	CLONAL	1	TRUE	1	0.520311303387739	2		578	694	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857127	9857127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs976259560	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	116	384	1	ENST00000330684.3:c.4274C>T	p.Ser1425Leu	p.S1425L	ENST00000330684	NM_001134407.1	1425	tCg/tTg	13/13	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.520311303387739	2		385	434	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	172	468	0	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.520311303387739	2		468	517	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495372	149495372	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146614144	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	123	567	1	ENST00000261799.4:c.3275C>T	p.Ser1092Leu	p.S1092L	ENST00000261799	NM_002609.3	1092	tCg/tTg	23/23	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.520311303387739	2		568	467	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101170	41101170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41279256	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	32	650	0	ENST00000373198.4:c.1186G>A	p.Val396Ile	p.V396I	ENST00000373198	NM_133170.3	396	Gta/Ata	8/32	1	2	FACETS	0.222	0.179	0.27	0.222	0.179	0.27	SUBCLONAL	1	TRUE	1	0.520311303387739	2		650	554	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011200	12011200	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	142	434	0	ENST00000353533.5:c.607G>T	p.Glu203Ter	p.E203*	ENST00000353533	NM_003010.3	203	Gaa/Taa	5/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.520311303387739	2		434	514	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591076	67591076	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	108	293	0	ENST00000274335.5:c.1669C>T	p.Arg557Ter	p.R557*	ENST00000274335		557	Cga/Tga	12/15	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.520311303387739	2		293	395	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525883	148525883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778968366	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	306	541	2	ENST00000320356.2:c.574G>A	p.Asp192Asn	p.D192N	ENST00000320356	NM_004456.4	192	Gat/Aat	6/20	0.520311303387739	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.520311303387739	3		543	735	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832265	72832265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267604632	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	154	534	1	ENST00000268489.5:c.4316G>A	p.Arg1439Gln	p.R1439Q	ENST00000268489	NM_006885.3	1439	cGa/cAa	9/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.520311303387739	2		535	508	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007752	45007753	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	165	483	0	ENST00000558401.1:c.204dup	p.Val69SerfsTer21	p.V69Sfs*21	ENST00000558401	NM_004048.2	67	gaa/gAaa	2/4	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.520311303387739	2		483	614	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003779	45003779	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	32	528	0	ENST00000558401.1:c.35T>G	p.Leu12Arg	p.L12R	ENST00000558401	NM_004048.2	12	cTa/cGa	1/4	1	2	FACETS	0.197	0.159	0.24	0.197	0.159	0.24	SUBCLONAL	1	TRUE	1	0.520311303387739	2		528	625	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251901	153251901	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	43	561	0	ENST00000281708.4:c.1105G>T	p.Glu369Ter	p.E369*	ENST00000281708	NM_033632.3	369	Gaa/Taa	7/12	1	2	FACETS	0.235	0.196	0.279	0.235	0.196	0.279	SUBCLONAL	1	TRUE	1	0.520311303387739	2		561	702	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007672	45007672	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	161	463	0	ENST00000558401.1:c.119C>A	p.Ser40Ter	p.S40*	ENST00000558401	NM_004048.2	40	tCa/tAa	2/4	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.520311303387739	2		463	576	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911435	134911435	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	151	531	1	ENST00000398015.3:c.1900T>C	p.Tyr634His	p.Y634H	ENST00000398015	NM_004441.4	634	Tac/Cac	11/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.520311303387739	2		532	500	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433373	49433373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771966959	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	190	654	0	ENST00000301067.7:c.8074C>T	p.Arg2692Trp	p.R2692W	ENST00000301067	NM_003482.3	2692	Cgg/Tgg	32/54	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.520311303387739	2		654	610	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027887	48027887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752839086	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	30	350	0	ENST00000234420.5:c.2765G>A	p.Arg922Gln	p.R922Q	ENST00000234420	NM_000179.2	922	cGa/cAa	4/10	1	2	FACETS	0.242	0.195	0.296	0.242	0.195	0.296	SUBCLONAL	1	TRUE	1	0.520311303387739	2		350	476	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808966	1808966	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	96	492	0	ENST00000260795.2:c.2398A>G	p.Ser800Gly	p.S800G	ENST00000260795		800	Agc/Ggc	17/17	NA	2	FACETS	0.904	0.811	1			1	INDETERMINATE	1	TRUE	NA	0.520311303387739	2		492	408	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419841	41419841	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	87	399	3	ENST00000373198.4:c.480C>A	p.Phe160Leu	p.F160L	ENST00000373198	NM_133170.3	160	ttC/ttA	3/32	1	2	FACETS	0.878	0.783	0.978	0.878	0.783	0.978	CLONAL	1	TRUE	1	0.520311303387739	2		402	381	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395710	45395710	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	186	478	1	ENST00000262160.6:c.424G>T	p.Glu142Ter	p.E142*	ENST00000262160	NM_005901.5	142	Gaa/Taa	4/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.520311303387739	2		479	624	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412196	63412196	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	228	424	0	ENST00000330258.3:c.971C>A	p.Ser324Ter	p.S324*	ENST00000330258	NM_152424.3	324	tCa/tAa	2/2	1	1	FACETS	0.883	0.84	0.926	1	0.995	1	CLONAL	2	TRUE	0	0.520311303387739	1		424	367	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926518	59926518	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1330277587	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	273	985	2	ENST00000259008.2:c.479G>T	p.Arg160Ile	p.R160I	ENST00000259008	NM_032043.2	160	aGa/aTa	5/20	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.520311303387739	2		987	796	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998919	11998919	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	112	346	1	ENST00000353533.5:c.421G>T	p.Glu141Ter	p.E141*	ENST00000353533	NM_003010.3	141	Gaa/Taa	4/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.520311303387739	2		347	392	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073637	8073637	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	205	510	0	ENST00000377482.5:c.1022A>G	p.Tyr341Cys	p.Y341C	ENST00000377482	NM_018948.3	341	tAc/tGc	4/4	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.520311303387739	2		510	585	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11210264	11210264	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	34	556	0	ENST00000361445.4:c.4489T>C	p.Cys1497Arg	p.C1497R	ENST00000361445	NM_004958.3	1497	Tgc/Cgc	31/58	1	2	FACETS	0.211	0.172	0.256	0.211	0.172	0.256	SUBCLONAL	1	TRUE	1	0.520311303387739	2		556	618	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46527623	46527623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	231	539	0	ENST00000262741.5:c.742G>A	p.Gly248Arg	p.G248R	ENST00000262741	NM_003629.3	248	Ggg/Agg	6/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.520311303387739	2		539	772	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248740	59248740	+	start_lost	Translation_Start_Site	SNP	C	C	A	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	39	703	0	ENST00000371222.2:c.3G>T	p.Met1?	p.M1?	ENST00000371222	NM_002228.3	1	atG/atT	1/1	1	2	FACETS	0.204	0.168	0.244	0.204	0.168	0.244	SUBCLONAL	1	TRUE	1	0.520311303387739	2		703	734	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054937	176054937	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	136	497	0	ENST00000367669.3:c.1116T>G	p.Phe372Leu	p.F372L	ENST00000367669	NM_022457.5	372	ttT/ttG	10/20	1	2	FACETS	0.871	0.795	0.951	0.871	0.795	0.951	CLONAL	1	TRUE	1	0.520311303387739	2		497	600	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692997	89692997	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	109	374	0	ENST00000371953.3:c.481A>G	p.Arg161Gly	p.R161G	ENST00000371953	NM_000314.4	161	Aga/Gga	5/9	1	2	FACETS	0.993	0.898	1	0.993	0.898	1	CLONAL	1	TRUE	1	0.520311303387739	2		374	422	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711999	89711999	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	137	288	0	ENST00000371953.3:c.617T>C	p.Phe206Ser	p.F206S	ENST00000371953	NM_000314.4	206	tTc/tCc	6/9	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.520311303387739	2		288	400	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104356918	104356918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775245784	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	193	572	0	ENST00000369902.3:c.778G>A	p.Glu260Lys	p.E260K	ENST00000369902	NM_016169.3	260	Gag/Aag	7/12	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.520311303387739	2		572	617	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8246247	8246247	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	123	425	0	ENST00000335790.3:c.387C>A	p.Phe129Leu	p.F129L	ENST00000335790	NM_002315.2	129	ttC/ttA	4/4	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.520311303387739	2		425	456	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32439136	32439136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	153	678	0	ENST00000332351.3:c.937G>A	p.Ala313Thr	p.A313T	ENST00000332351	NM_024426.4	313	Gcc/Acc	4/10	1	2	FACETS	0.977	0.898	1	0.977	0.898	1	CLONAL	1	TRUE	1	0.520311303387739	2		678	602	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944790	71944790	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	37	618	1	ENST00000298229.2:c.2212+2T>C		p.X738_splice	ENST00000298229	NM_001567.3	738			1	2	FACETS	0.208	0.171	0.25	0.208	0.171	0.25	SUBCLONAL	1	TRUE	1	0.520311303387739	2		619	683	SUCCESS
EED	8726	MSKCC	GRCh37	11	85977174	85977174	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	126	466	2	ENST00000263360.6:c.776C>A	p.Ser259Tyr	p.S259Y	ENST00000263360	NM_003797.3	259	tCt/tAt	8/12	1	2	FACETS	0.866	0.788	0.949	0.866	0.788	0.949	CLONAL	1	TRUE	1	0.520311303387739	2		468	559	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918552	94918552	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	38	590	0	ENST00000536441.1:c.630T>G	p.Ser210Arg	p.S210R	ENST00000536441	NM_144665.3	210	agT/agG	5/10	1	2	FACETS	0.213	0.175	0.255	0.213	0.175	0.255	SUBCLONAL	1	TRUE	1	0.520311303387739	2		590	686	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933474	100933474	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	88	316	1	ENST00000325455.5:c.1916T>G	p.Phe639Cys	p.F639C	ENST00000325455	NM_001202474.3	639	tTt/tGt	4/8	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.520311303387739	2		317	321	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118850	115118850	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	184	486	0	ENST00000257566.3:c.491A>C	p.Lys164Thr	p.K164T	ENST00000257566	NM_016569.3	164	aAa/aCa	2/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.520311303387739	2		486	596	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588621	28588621	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	173	478	2	ENST00000241453.7:c.2827T>G	p.Leu943Val	p.L943V	ENST00000241453	NM_004119.2	943	Tta/Gta	23/24	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.520311303387739	2		480	631	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28644627	28644627	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	206	568	0	ENST00000241453.7:c.165+1G>A		p.X55_splice	ENST00000241453	NM_004119.2	55			1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.520311303387739	2		568	646	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041120	29041120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	282	761	1	ENST00000282397.4:c.308G>A	p.Gly103Asp	p.G103D	ENST00000282397	NM_002019.4	103	gGc/gAc	3/30	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.520311303387739	2		762	998	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910767	32910767	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	143	403	0	ENST00000380152.3:c.2275C>A	p.Leu759Ile	p.L759I	ENST00000380152		759	Ctt/Att	11/27	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.520311303387739	2		403	487	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919228	48919228	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	72	201	1	ENST00000267163.4:c.393C>A	p.Phe131Leu	p.F131L	ENST00000267163	NM_000321.2	131	ttC/ttA	4/27	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.520311303387739	2		202	241	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039490	49039490	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	186	541	0	ENST00000267163.4:c.2475G>T	p.Met825Ile	p.M825I	ENST00000267163	NM_000321.2	825	atG/atT	23/27	1	2	FACETS	0.977	0.905	1	0.977	0.905	1	CLONAL	1	TRUE	1	0.520311303387739	2		541	732	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281262	49281262	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	53	864	0	ENST00000282018.3:c.309T>G	p.Asn103Lys	p.N103K	ENST00000282018	NM_020377.2	103	aaT/aaG	1/1	1	2	FACETS	0.253	0.215	0.295	0.253	0.215	0.295	SUBCLONAL	1	TRUE	1	0.520311303387739	2		864	806	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346835	73346835	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	22	241	0	ENST00000377767.4:c.1382A>C	p.Glu461Ala	p.E461A	ENST00000377767	NM_014953.3	461	gAa/gCa	9/21	1	2	FACETS	0.268	0.207	0.338	0.268	0.207	0.338	SUBCLONAL	1	TRUE	1	0.520311303387739	2		241	316	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093363	30093363	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	201	584	0	ENST00000331968.5:c.1900C>A	p.Leu634Ile	p.L634I	ENST00000331968	NM_002742.2	634	Cta/Ata	13/18	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.520311303387739	2		584	633	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003288	42003288	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	219	701	0	ENST00000219905.7:c.2825C>A	p.Ser942Tyr	p.S942Y	ENST00000219905	NM_001164273.1	942	tCt/tAt	8/24	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.520311303387739	2		701	786	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707910	43707910	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	226	743	0	ENST00000382044.4:c.4971G>T	p.Lys1657Asn	p.K1657N	ENST00000382044	NM_001141980.1	1657	aaG/aaT	23/28	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.520311303387739	2		743	829	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43738647	43738647	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	241	604	0	ENST00000382044.4:c.2978G>T	p.Arg993Ile	p.R993I	ENST00000382044	NM_001141980.1	993	aGa/aTa	14/28	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.520311303387739	2		604	762	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482863	67482863	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	156	458	0	ENST00000327367.4:c.1267A>C	p.Ser423Arg	p.S423R	ENST00000327367	NM_005902.3	423	Agt/Cgt	9/9	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.520311303387739	2		458	505	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3841993	3841993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1208256956	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	180	444	1	ENST00000262367.5:c.1319G>A	p.Arg440Gln	p.R440Q	ENST00000262367	NM_004380.2	440	cGa/cAa	5/31	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.520311303387739	2		445	617	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81904512	81904512	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	103	390	0	ENST00000359376.3:c.620A>C	p.Lys207Thr	p.K207T	ENST00000359376	NM_002661.3	207	aAa/aCa	7/33	0.198791785039625	0	FACETS	0.386	0.347	0.427			1	INDETERMINATE	1	TRUE	0	0.520311303387739	0		390	492	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350695	89350695	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	69	943	1	ENST00000301030.4:c.2255C>T	p.Ser752Phe	p.S752F	ENST00000301030	NM_001256183.1	752	tCt/tTt	9/13	1	2	FACETS	0.217	0.188	0.249	0.217	0.188	0.249	SUBCLONAL	1	TRUE	1	0.520311303387739	2		944	1222	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813065	89813065	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	143	541	0	ENST00000389301.3:c.3440A>C	p.Asp1147Ala	p.D1147A	ENST00000389301	NM_000135.2	1147	gAc/gCc	35/43	1	2	FACETS	0.954	0.874	1	0.954	0.874	1	CLONAL	1	TRUE	1	0.520311303387739	2		541	576	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89818606	89818606	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	174	463	0	ENST00000389301.3:c.3006A>C	p.Glu1002Asp	p.E1002D	ENST00000389301	NM_000135.2	1002	gaA/gaC	31/43	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.520311303387739	2		463	647	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971372	15971372	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	194	643	0	ENST00000268712.3:c.4577G>T	p.Arg1526Met	p.R1526M	ENST00000268712	NM_006311.3	1526	aGg/aTg	32/46	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.520311303387739	2		643	710	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322615	30322615	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	38	542	0	ENST00000322652.5:c.1628T>G	p.Phe543Cys	p.F543C	ENST00000322652	NM_015355.2	543	tTt/tGt	14/16	1	2	FACETS	0.257	0.212	0.307	0.257	0.212	0.307	SUBCLONAL	1	TRUE	1	0.520311303387739	2		542	569	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618830	37618830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	182	453	1	ENST00000447079.4:c.506G>A	p.Ser169Asn	p.S169N	ENST00000447079	NM_015083.1	169	aGc/aAc	1/14	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.520311303387739	2		454	527	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243902	41243902	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	203	641	0	ENST00000357654.3:c.3646T>G	p.Leu1216Val	p.L1216V	ENST00000357654	NM_007294.3	1216	Tta/Gta	10/23	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.520311303387739	2		641	731	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256254	41256254	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs750275408	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	170	435	0	ENST00000357654.3:c.326A>G	p.Lys109Arg	p.K109R	ENST00000357654	NM_007294.3	109	aAa/aGa	6/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.520311303387739	2		435	556	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858223	59858223	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	205	495	0	ENST00000259008.2:c.1772T>C	p.Phe591Ser	p.F591S	ENST00000259008	NM_032043.2	591	tTt/tCt	12/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.520311303387739	2		495	656	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626891	14626891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778737677	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	46	630	0	ENST00000254322.2:c.884G>A	p.Arg295Gln	p.R295Q	ENST00000254322	NM_006145.1	295	cGa/cAa	3/3	1	2	FACETS	0.233	0.195	0.275	0.233	0.195	0.275	SUBCLONAL	1	TRUE	1	0.520311303387739	2		630	759	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754974	29754974	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	31	463	0	ENST00000389048.3:c.961C>A	p.Leu321Ile	p.L321I	ENST00000389048	NM_004304.4	321	Ctc/Atc	4/29	1	2	FACETS	0.244	0.196	0.297	0.244	0.196	0.297	SUBCLONAL	1	TRUE	1	0.520311303387739	2		463	489	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250088	39250088	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	260	712	0	ENST00000402219.2:c.1481T>G	p.Phe494Cys	p.F494C	ENST00000402219	NM_005633.3	494	tTt/tGt	10/23	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.520311303387739	2		712	838	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728733	190728733	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	105	326	1	ENST00000441310.2:c.2121A>C	p.Lys707Asn	p.K707N	ENST00000441310	NM_000534.4	707	aaA/aaC	10/13	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.520311303387739	2		327	392	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149929	202149929	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	41	636	0	ENST00000358485.4:c.1370A>C	p.Asp457Ala	p.D457A	ENST00000358485	NM_001080125.1	457	gAc/gCc	8/9	1	2	FACETS	0.235	0.195	0.279	0.235	0.195	0.279	SUBCLONAL	1	TRUE	1	0.520311303387739	2		636	672	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422537	225422537	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	126	411	0	ENST00000264414.4:c.103G>A	p.Asp35Asn	p.D35N	ENST00000264414	NM_003590.4	35	Gac/Aac	2/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.520311303387739	2		411	458	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538308	9538308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	237	619	1	ENST00000353224.5:c.1690G>A	p.Val564Met	p.V564M	ENST00000353224	NM_177990.2	564	Gtg/Atg	7/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.520311303387739	2		620	738	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538359	9538359	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	166	540	0	ENST00000353224.5:c.1639A>G	p.Thr547Ala	p.T547A	ENST00000353224	NM_177990.2	547	Act/Gct	7/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.520311303387739	2		540	548	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385039	31385039	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	41	598	1	ENST00000328111.2:c.1424A>C	p.Gln475Pro	p.Q475P	ENST00000328111	NM_006892.3	475	cAg/cCg	14/23	1	2	FACETS	0.218	0.181	0.26	0.218	0.181	0.26	SUBCLONAL	1	TRUE	1	0.520311303387739	2		599	722	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980849	40980849	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	161	552	0	ENST00000373198.4:c.1637G>T	p.Arg546Leu	p.R546L	ENST00000373198	NM_133170.3	546	cGg/cTg	10/32	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.520311303387739	2		552	517	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101174	41101174	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	124	637	0	ENST00000373198.4:c.1182A>C	p.Glu394Asp	p.E394D	ENST00000373198	NM_133170.3	394	gaA/gaC	8/32	1	2	FACETS	0.883	0.802	0.967	0.883	0.802	0.967	CLONAL	1	TRUE	1	0.520311303387739	2		637	540	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574576	41574576	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	221	739	2	ENST00000263253.7:c.6861T>G	p.Asn2287Lys	p.N2287K	ENST00000263253	NM_001429.3	2287	aaT/aaG	31/31	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.520311303387739	2		741	652	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164310	47164310	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	161	424	0	ENST00000409792.3:c.1816A>C	p.Asn606His	p.N606H	ENST00000409792	NM_014159.6	606	Aat/Cat	3/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.520311303387739	2		424	551	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610660	52610660	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	35	545	1	ENST00000394830.3:c.3513C>A	p.Phe1171Leu	p.F1171L	ENST00000394830	NM_018313.4	1171	ttC/ttA	23/30	1	2	FACETS	0.218	0.178	0.263	0.218	0.178	0.263	SUBCLONAL	1	TRUE	1	0.520311303387739	2		546	618	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89176383	89176383	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	110	379	0	ENST00000336596.2:c.113T>C	p.Ile38Thr	p.I38T	ENST00000336596	NM_005233.5	38	aTt/aCt	2/17	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.520311303387739	2		379	397	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541967	187541967	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	226	582	0	ENST00000441802.2:c.5773G>C	p.Glu1925Gln	p.E1925Q	ENST00000441802	NM_005245.3	1925	Gag/Cag	10/27	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.520311303387739	2		582	729	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630731	187630731	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs774253076	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	50	692	0	ENST00000441802.2:c.251A>G	p.Lys84Arg	p.K84R	ENST00000441802	NM_005245.3	84	aAa/aGa	2/27	1	2	FACETS	0.221	0.187	0.259	0.221	0.187	0.259	SUBCLONAL	1	TRUE	1	0.520311303387739	2		692	869	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526439	31526439	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	54	860	0	ENST00000344624.3:c.601A>C	p.Ser201Arg	p.S201R	ENST00000344624		201	Agt/Cgt	2/33	1	2	FACETS	0.223	0.19	0.26	0.223	0.19	0.26	SUBCLONAL	1	TRUE	1	0.520311303387739	2		860	929	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959416	38959416	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	20	365	0	ENST00000357387.3:c.2059A>C	p.Asn687His	p.N687H	ENST00000357387	NM_152756.3	687	Aat/Cat	22/38	1	2	FACETS	0.216	0.165	0.276	0.216	0.165	0.276	SUBCLONAL	1	TRUE	1	0.520311303387739	2		365	356	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178044	56178044	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	32	403	0	ENST00000399503.3:c.3017T>G	p.Leu1006Arg	p.L1006R	ENST00000399503	NM_005921.1	1006	cTt/cGt	14/20	1	2	FACETS	0.251	0.203	0.305	0.251	0.203	0.305	SUBCLONAL	1	TRUE	1	0.520311303387739	2		403	490	SUCCESS
APC	324	MSKCC	GRCh37	5	112154938	112154938	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	209	609	0	ENST00000257430.4:c.1209A>C	p.Glu403Asp	p.E403D	ENST00000257430	NM_000038.5	403	gaA/gaC	10/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.520311303387739	2		609	738	SUCCESS
APC	324	MSKCC	GRCh37	5	112176017	112176017	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554086134	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	115	340	1	ENST00000257430.4:c.4726G>T	p.Glu1576Ter	p.E1576*	ENST00000257430	NM_000038.5	1576	Gaa/Taa	16/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.520311303387739	2		341	389	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120633	94120633	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	124	524	0	ENST00000369303.4:c.418G>T	p.Glu140Ter	p.E140*	ENST00000369303	NM_004440.3	140	Gaa/Taa	3/17	1	2	FACETS	0.8	0.726	0.877	0.8	0.726	0.877	SUBCLONAL	1	TRUE	1	0.520311303387739	2		524	596	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109319879	109319879	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	178	642	0	ENST00000436639.2:c.809C>A	p.Ser270Tyr	p.S270Y	ENST00000436639	NM_014454.2	270	tCt/tAt	5/10	1	2	FACETS	0.964	0.891	1	0.964	0.891	1	CLONAL	1	TRUE	1	0.520311303387739	2		642	710	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609778	117609778	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	190	613	0	ENST00000368508.3:c.6921G>T	p.Lys2307Asn	p.K2307N	ENST00000368508	NM_002944.2	2307	aaG/aaT	43/43	1	2	FACETS	0.951	0.881	1	0.951	0.881	1	CLONAL	1	TRUE	1	0.520311303387739	2		613	768	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642492	117642492	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	187	695	0	ENST00000368508.3:c.5707G>T	p.Asp1903Tyr	p.D1903Y	ENST00000368508	NM_002944.2	1903	Gac/Tac	35/43	1	2	FACETS	0.926	0.858	0.997	0.926	0.858	0.997	CLONAL	1	TRUE	1	0.520311303387739	2		695	776	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663633	117663633	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	225	579	1	ENST00000368508.3:c.4599A>C	p.Lys1533Asn	p.K1533N	ENST00000368508	NM_002944.2	1533	aaA/aaC	28/43	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.520311303387739	2		580	659	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508373	106508373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	17	352	0	ENST00000359195.3:c.367C>T	p.Arg123Cys	p.R123C	ENST00000359195	NM_002649.2	123	Cgc/Tgc	2/11	0.520311303387739	3	FACETS	0.278	0.207	0.363	0.139	0.103	0.182	SUBCLONAL	1	TRUE	1	0.520311303387739	3		352	296	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515072	148515072	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	368	569	0	ENST00000320356.2:c.1137A>C	p.Glu379Asp	p.E379D	ENST00000320356	NM_004456.4	379	gaA/gaC	10/20	0.520311303387739	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.520311303387739	3		569	842	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860075	151860075	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	228	447	0	ENST00000262189.6:c.10587T>G	p.Phe3529Leu	p.F3529L	ENST00000262189	NM_170606.2	3529	ttT/ttG	43/59	0.520311303387739	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.520311303387739	3		447	528	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020361	69020361	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	30	495	2	ENST00000288368.4:c.2733G>T	p.Lys911Asn	p.K911N	ENST00000288368	NM_024870.2	911	aaG/aaT	24/40	1	2	FACETS	0.195	0.157	0.24	0.195	0.157	0.24	SUBCLONAL	1	TRUE	1	0.520311303387739	2		497	590	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028080	69028080	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	167	604	0	ENST00000288368.4:c.3239G>T	p.Arg1080Ile	p.R1080I	ENST00000288368	NM_024870.2	1080	aGa/aTa	26/40	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.520311303387739	2		604	571	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970968	70970968	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	103	723	0	ENST00000276594.2:c.1293A>C	p.Lys431Asn	p.K431N	ENST00000276594	NM_024504.3	431	aaA/aaC	6/8	1	2	FACETS	0.496	0.444	0.552	0.496	0.444	0.552	SUBCLONAL	1	TRUE	1	0.520311303387739	2		723	798	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70971015	70971015	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	271	720	0	ENST00000276594.2:c.1246G>T	p.Asp416Tyr	p.D416Y	ENST00000276594	NM_024504.3	416	Gat/Tat	6/8	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.520311303387739	2		720	810	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559216	141559216	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	26	544	0	ENST00000220592.5:c.1585T>C	p.Tyr529His	p.Y529H	ENST00000220592	NM_012154.3	529	Tac/Cac	12/19	1	2	FACETS	0.194	0.153	0.242	0.194	0.153	0.242	SUBCLONAL	1	TRUE	1	0.520311303387739	2		544	514	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249847	110249847	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	35	652	0	ENST00000374672.4:c.828G>T	p.Lys276Asn	p.K276N	ENST00000374672	NM_004235.4	276	aaG/aaT	3/5	1	2	FACETS	0.256	0.209	0.309	0.256	0.209	0.309	SUBCLONAL	1	TRUE	1	0.520311303387739	2		652	525	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912136	127912136	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	81	412	0	ENST00000373547.4:c.734A>C	p.Lys245Thr	p.K245T	ENST00000373547	NM_002721.4	245	aAa/aCa	7/7	1	2	FACETS	0.646	0.571	0.726	0.646	0.571	0.726	SUBCLONAL	1	TRUE	1	0.520311303387739	2		412	482	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0037606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	120	482	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.856	0.774	0.944	0.856	0.774	0.944	CLONAL	1	TRUE	1	0.364951937809485	2		482	768	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043479	180043479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	128	609	0	ENST00000261937.6:c.3107G>A	p.Arg1036Lys	p.R1036K	ENST00000261937	NM_182925.4	1036	aGa/aAa	23/30	1	2	FACETS	0.991	0.899	1	0.991	0.899	1	CLONAL	1	TRUE	1	0.364951937809485	2		609	708	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442008	52442008	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	45	520	0	ENST00000460680.1:c.341del	p.Arg114ProfsTer2	p.R114Pfs*2	ENST00000460680	NM_004656.3	114	cGc/cc	5/17	0.364951937809485	1	FACETS	0.333	0.279	0.393	0.333	0.279	0.393	SUBCLONAL	1	TRUE	0	0.364951937809485	1		520	605	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442009	52442009	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	72	528	0	ENST00000460680.1:c.340del	p.Arg114AlafsTer2	p.R114Afs*2	ENST00000460680	NM_004656.3	114	Cgc/gc	5/17	0.364951937809485	1	FACETS	0.529	0.462	0.601	0.529	0.462	0.601	SUBCLONAL	1	TRUE	0	0.364951937809485	1		528	610	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142132	108142132	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	40	318	0	ENST00000278616.4:c.3076T>C	p.Trp1026Arg	p.W1026R	ENST00000278616	NM_000051.3	1026	Tgg/Cgg	20/63	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.18	2		318	361	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023190	150023204	+	inframe_deletion	In_Frame_Del	DEL	CAGTATAGTTACTGG	CAGTATAGTTACTGG	-	novel	NA	P-0037619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	119	604	0	ENST00000253339.5:c.59_73del	p.Ala20_Thr24del	p.A20_T24del	ENST00000253339		20	gCCAGTAACTATACTGtc/gtc	1/7	0.157878467630368	5	FACETS	1	0.968	1	0.776	0.701	0.855	CLONAL	2	TRUE	2	0.18	5		604	721	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0037622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	100	482	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.489481397219108	2		482	371	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	53	313	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.489481397219108	2		315	170	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933755	36933756	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0037622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	36	557	0	ENST00000361632.4:c.1643_1644del	p.Val548AlafsTer2	p.V548Afs*2	ENST00000361632		548	gTG/g	12/16	1	2	FACETS	0.226	0.185	0.272	0.226	0.185	0.272	SUBCLONAL	1	TRUE	1	0.489481397219108	2		557	652	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0037636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	474	918	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.511448573691705	3	FACETS	0.999	0.966	1	0.999	0.966	1	CLONAL	3	TRUE	0	0.531652092257453	3		919	753	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670486	134670486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	222	840	1	ENST00000398015.3:c.397C>T	p.Pro133Ser	p.P133S	ENST00000398015	NM_004441.4	133	Ccc/Tcc	3/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.531652092257453	2		841	790	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971194	21971194	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs561034503	NA	P-0037636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	193	593	0	ENST00000304494.5:c.164G>T	p.Gly55Val	p.G55V	ENST00000304494	NM_000077.4	55	gGc/gTc	2/3	0.531652092257453	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.531652092257453	1		593	423	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748739	43748739	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	331	1297	0	ENST00000382044.4:c.2067G>A	p.Met689Ile	p.M689I	ENST00000382044	NM_001141980.1	689	atG/atA	12/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.531652092257453	2		1297	1193	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180333	32180333	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	117	848	0	ENST00000375023.3:c.2598C>A	p.Phe866Leu	p.F866L	ENST00000375023	NM_004557.3	866	ttC/ttA	17/30	0.366343632883994	1	FACETS	0.401	0.362	0.443	0.401	0.362	0.443	SUBCLONAL	1	TRUE	0	0.531652092257453	1		848	805	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344849	118344849	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	209	403	0	ENST00000534358.1:c.2975C>T	p.Ser992Phe	p.S992F	ENST00000534358	NM_005933.3	992	tCc/tTc	3/36	0.491132998188839	2	FACETS	0.975	0.92	1	0.975	0.92	1	CLONAL	2	TRUE	0	0.531652092257453	2		403	403	SUCCESS
CBL	867	MSKCC	GRCh37	11	119158601	119158601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	298	754	0	ENST00000264033.4:c.1981C>T	p.His661Tyr	p.H661Y	ENST00000264033	NM_005188.3	661	Cac/Tac	12/16	0.491132998188839	2	FACETS	0.827	0.784	0.87	0.827	0.784	0.87	CLONAL	2	TRUE	0	0.531652092257453	2		754	678	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218479	1218479	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	328	659	0	ENST00000326873.7:c.354C>A	p.Tyr118Ter	p.Y118*	ENST00000326873	NM_000455.4	118	taC/taA	2/10	0.531652092257453	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.531652092257453	2		659	613	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218580	1219602	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCTTCCCGTCTCCTTGAAGGAGACTGGCACACGAGGGCCGTGGCCTTCCCTGGTTCCCCGGAAGTCAGCCATTGTGGCAATGGCTGCGCAGCTTGCTGAAAGGGGCCCTGAGCCCTGGCCCCTGTGTCTTGGGCCCGTGGGGTGTCAAGTCCCTTTTTTCTCAGAGTCTCCTCCCAGGCTAACCAGGGGTGTAGCCACGGTCTGCCTGAGACAGGCCACGCGGGCTGACCGTTGTGGGCCATTTTGGTCGTGGCTGGGCGTGTCCTCGTGTCATCTGTGGACACCCCCATGGGTCTTACGGGCACAGCCTCCCTACGGGGACTTTGCTTCCTAAGGCCCTGTGCCCAGAGCAAGAGCCAGAAGTGGTCCTGAGGCTGGGGCTGTGTTCCCTGAGCCACGCGGTCAGGGGCCCTGGGACCGTCCTGCATGGGCCCGAGCCTGCTTGGGGGGGCGTCCAGGAGGCACCATCCCCCGCCCATGGGCAGGGTGGGGGACGTGAGCCCCGCAGGAACGCTGCCCCAAGAGTCAGCCCTGTCCTCCCCTTCCCCGTAGGCTCCTTCCTCCTGGGACGCTGGGGCCCCTGGGCCTTTTCAGAGGGGTGGCTGAGGGCAGGGTGGGCCCTGGTCCCGAGGAGGGGCAAGGTGGGTGCAGAGGGTCCCTCCAGAGCCCCTTTTCTGGCCCCCGTGCTCCCTGGGCCTGTGAGTGGGGCCGCCCCCTGAGCTGTGTGTCCTTAGCGCCCCACGTATATGGTGATGGAGTACTGCGTGTGTGGCATGCAGGAAATGCTGGACAGCGTGCCGGAGAAGCGTTTCCCAGTGTGCCAGGCCCACGGGTGCGTGCGCGGGGCAGGGGCCAGGGTGGGGCGGGGGCCGGGGGCCAGGCAGGGCAGGCTCCTTTCCGTGAGGCCACACTGCTTGTCCTGATATTCATTGACATGAAGGCCCAAGTTTTTTTGTTTTTTTGTTTTTTTGTGTTTTTTTTCGAGATGGAGTCTCACTCTGTCGCCCAGGCTGGAGTGCAAT	CTCTTCCCGTCTCCTTGAAGGAGACTGGCACACGAGGGCCGTGGCCTTCCCTGGTTCCCCGGAAGTCAGCCATTGTGGCAATGGCTGCGCAGCTTGCTGAAAGGGGCCCTGAGCCCTGGCCCCTGTGTCTTGGGCCCGTGGGGTGTCAAGTCCCTTTTTTCTCAGAGTCTCCTCCCAGGCTAACCAGGGGTGTAGCCACGGTCTGCCTGAGACAGGCCACGCGGGCTGACCGTTGTGGGCCATTTTGGTCGTGGCTGGGCGTGTCCTCGTGTCATCTGTGGACACCCCCATGGGTCTTACGGGCACAGCCTCCCTACGGGGACTTTGCTTCCTAAGGCCCTGTGCCCAGAGCAAGAGCCAGAAGTGGTCCTGAGGCTGGGGCTGTGTTCCCTGAGCCACGCGGTCAGGGGCCCTGGGACCGTCCTGCATGGGCCCGAGCCTGCTTGGGGGGGCGTCCAGGAGGCACCATCCCCCGCCCATGGGCAGGGTGGGGGACGTGAGCCCCGCAGGAACGCTGCCCCAAGAGTCAGCCCTGTCCTCCCCTTCCCCGTAGGCTCCTTCCTCCTGGGACGCTGGGGCCCCTGGGCCTTTTCAGAGGGGTGGCTGAGGGCAGGGTGGGCCCTGGTCCCGAGGAGGGGCAAGGTGGGTGCAGAGGGTCCCTCCAGAGCCCCTTTTCTGGCCCCCGTGCTCCCTGGGCCTGTGAGTGGGGCCGCCCCCTGAGCTGTGTGTCCTTAGCGCCCCACGTATATGGTGATGGAGTACTGCGTGTGTGGCATGCAGGAAATGCTGGACAGCGTGCCGGAGAAGCGTTTCCCAGTGTGCCAGGCCCACGGGTGCGTGCGCGGGGCAGGGGCCAGGGTGGGGCGGGGGCCGGGGGCCAGGCAGGGCAGGCTCCTTTCCGTGAGGCCACACTGCTTGTCCTGATATTCATTGACATGAAGGCCCAAGTTTTTTTGTTTTTTTGTTTTTTTGTGTTTTTTTTCGAGATGGAGTCTCACTCTGTCGCCCAGGCTGGAGTGCAAT	-	novel	NA	P-0037636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	90	196	0	ENST00000326873.7:c.374+81_464+190del		p.X125_splice	ENST00000326873	NM_000455.4	125		3/10	0.531652092257453	2	FACETS	0.967	0.883	1	0.967	0.883	1	CLONAL	2	TRUE	0	0.531652092257453	2		196	175	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602650	10602650	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	485	1104	0	ENST00000171111.5:c.928del	p.Leu310CysfsTer7	p.L310Cfs*7	ENST00000171111	NM_203500.1	310	Ctg/tg	3/6	0.531652092257453	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.531652092257453	2		1104	910	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144030	11144030	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	452	851	0	ENST00000358026.2:c.3611T>A	p.Leu1204His	p.L1204H	ENST00000358026	NM_001128849.1	1204	cTc/cAc	26/36	0.531652092257453	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.531652092257453	2		851	785	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905744	50905744	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	610	1207	0	ENST00000440232.2:c.792C>G	p.Asn264Lys	p.N264K	ENST00000440232	NM_002691.3	264	aaC/aaG	7/27	0.497695751268391	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.531652092257453	3		1207	1349	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713332	40713332	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	115	719	0	ENST00000373198.4:c.4183G>T	p.Val1395Phe	p.V1395F	ENST00000373198	NM_133170.3	1395	Gtc/Ttc	30/32	0.283344263554036	1	FACETS	0.451	0.406	0.497	0.451	0.406	0.497	INDETERMINATE	1	TRUE	0	0.531652092257453	1		719	705	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448582	89448582	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	237	687	1	ENST00000336596.2:c.1546G>T	p.Gly516Ter	p.G516*	ENST00000336596	NM_005233.5	516	Gga/Tga	7/17	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.531652092257453	2		688	840	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361218	70361218	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	281	817	0	ENST00000374080.3:c.6406C>T	p.Gln2136Ter	p.Q2136*	ENST00000374080		2136	Cag/Tag	43/45	0.278857130243773	3	FACETS	1	0.991	1	0.655	0.616	0.695	INDETERMINATE	1	TRUE	1	0.531652092257453	3		817	1021	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517201	NA	P-0037667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	168	424	0	ENST00000263967.3:c.1637A>C	p.Gln546Pro	p.Q546P	ENST00000263967	NM_006218.2	546	cAg/cCg	10/21	0.812494084447271	3	FACETS	0.944	0.872	1	0.472	0.436	0.51	CLONAL	1	TRUE	1	0.812494084447271	3		424	616	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916766	48916766	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	96	223	0	ENST00000267163.4:c.299del	p.Gly100GlufsTer11	p.G100Efs*11	ENST00000267163	NM_000321.2	99	tGg/tg	3/27	0.812494084447271	1	FACETS	0.84	0.773	0.906	0.84	0.773	0.906	CLONAL	1	TRUE	0	0.812494084447271	1		223	167	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578539	7578539	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782160	NA	P-0037667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	1212	482	1	ENST00000269305.4:c.391A>T	p.Asn131Tyr	p.N131Y	ENST00000269305	NM_001126112.2	131	Aac/Tac	5/11	0.812494084447271	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.812494084447271	2		483	1427	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021741	69021741	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	242	297	0	ENST00000288368.4:c.3029G>T	p.Gly1010Val	p.G1010V	ENST00000288368	NM_024870.2	1010	gGt/gTt	25/40	0.812494084447271	3	FACETS	0.973	0.911	1	0.486	0.455	0.519	CLONAL	1	TRUE	1	0.812494084447271	3		297	861	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781470	3781475	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AAGACC	AAGACC	-	novel	NA	P-0037667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	185	178	0	ENST00000262367.5:c.4891-1_4895del		p.X1631_splice	ENST00000262367	NM_004380.2	1631		30/31	1	2	FACETS	0.918	0.855	0.982	0.918	0.855	0.982	CLONAL	1	TRUE	1	0.812494084447271	2		178	496	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348782	89348782	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	664	621	0	ENST00000301030.4:c.4168G>C	p.Gly1390Arg	p.G1390R	ENST00000301030	NM_001256183.1	1390	Ggc/Cgc	9/13	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.812494084447271	2		621	1561	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498285	29498285	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	269	306	0	ENST00000389048.3:c.1895T>C	p.Leu632Pro	p.L632P	ENST00000389048	NM_004304.4	632	cTg/cCg	10/29	1	2	FACETS	0.917	0.865	0.97	0.917	0.865	0.97	CLONAL	1	TRUE	1	0.812494084447271	2		306	722	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573689	41573689	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1332146367	NA	P-0037667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	427	367	0	ENST00000263253.7:c.5974C>A	p.Gln1992Lys	p.Q1992K	ENST00000263253	NM_001429.3	1992	Cag/Aag	31/31	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.812494084447271	2		367	1029	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73108249	73108249	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	55	107	0	ENST00000356692.5:c.350del	p.Gly117GlufsTer9	p.G117Efs*9	ENST00000356692		117	Gga/ga	4/9	0.798236869230444	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.812494084447271	1		107	77	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55963933	55963933	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	157	202	0	ENST00000263923.4:c.2510del	p.Gly837ValfsTer12	p.G837Vfs*12	ENST00000263923	NM_002253.2	837	gGt/gt	18/30	1	2	FACETS	0.824	0.761	0.888	0.824	0.761	0.888	CLONAL	1	TRUE	1	0.812494084447271	2		202	469	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094859	143094859	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	235	347	0	ENST00000262992.4:c.1285G>A	p.Asp429Asn	p.D429N	ENST00000262992	NM_001101669.1	429	Gac/Aac	14/24	1	2	FACETS	0.908	0.853	0.964	0.908	0.853	0.964	CLONAL	1	TRUE	1	0.812494084447271	2		347	637	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395864	395864	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	317	304	0	ENST00000380956.4:c.421C>A	p.Leu141Met	p.L141M	ENST00000380956	NM_001195286.1	141	Ctg/Atg	4/9	0.812494084447271	3	FACETS	0.959	0.905	1	0.48	0.452	0.507	CLONAL	1	TRUE	1	0.812494084447271	3		304	1144	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739869	41739869	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	213	237	0	ENST00000242208.4:c.104G>T	p.Cys35Phe	p.C35F	ENST00000242208	NM_002192.2	35	tGt/tTt	2/3	1	2	FACETS	0.858	0.802	0.915	0.858	0.802	0.915	CLONAL	1	TRUE	1	0.812494084447271	2		237	611	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459532	50459532	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	109	141	0	ENST00000331340.3:c.821G>T	p.Arg274Leu	p.R274L	ENST00000331340	NM_006060.4	274	cGt/cTt	7/8	1	2	FACETS	0.676	0.612	0.743	0.676	0.612	0.743	SUBCLONAL	1	TRUE	1	0.812494084447271	2		141	397	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046350	69046350	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	272	334	0	ENST00000288368.4:c.3823G>C	p.Val1275Leu	p.V1275L	ENST00000288368	NM_024870.2	1275	Gtc/Ctc	32/40	0.812494084447271	3	FACETS	0.911	0.856	0.969	0.456	0.428	0.485	CLONAL	1	TRUE	1	0.812494084447271	3		334	1033	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410338	63410338	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	314	509	0	ENST00000330258.3:c.2829C>A	p.Asp943Glu	p.D943E	ENST00000330258	NM_152424.3	943	gaC/gaA	2/2	0.364804469607871	1	FACETS	0.493	0.467	0.521	0.493	0.467	0.521	INDETERMINATE	1	TRUE	0	0.812494084447271	1		509	930	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411529	63411529	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	351	503	0	ENST00000330258.3:c.1638G>C	p.Leu546Phe	p.L546F	ENST00000330258	NM_152424.3	546	ttG/ttC	2/2	0.364804469607871	1	FACETS	0.573	0.545	0.602	0.573	0.545	0.602	INDETERMINATE	1	TRUE	0	0.812494084447271	1		503	895	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829817	76829817	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	75	273	0	ENST00000373344.5:c.6224G>T	p.Gly2075Val	p.G2075V	ENST00000373344	NM_000489.3	2075	gGg/gTg	28/35	0.364804469607871	1	FACETS	0.386	0.342	0.433	0.386	0.342	0.433	INDETERMINATE	1	TRUE	0	0.812494084447271	1		273	284	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626659	100626659	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	266	266	0	ENST00000308731.7:c.271C>A	p.Gln91Lys	p.Q91K	ENST00000308731	NM_000061.2	91	Caa/Aaa	4/19	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.812494084447271	2		266	622	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484596	57484596	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913494	NA	P-0037688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	130	712	0	ENST00000371085.3:c.680A>T	p.Gln227Leu	p.Q227L	ENST00000371085	NM_000516.4	227	cAg/cTg	9/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		712	697	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56871638	56871638	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs199837299	NA	P-0037688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	36	437	1	ENST00000308159.5:c.2018G>A	p.Arg673Gln	p.R673Q	ENST00000308159	NM_014669.4	673	cGg/cAg	18/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		438	488	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56867237	56867237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138281575	NA	P-0037688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	185	625	1	ENST00000308159.5:c.1456C>T	p.Arg486Cys	p.R486C	ENST00000308159	NM_014669.4	486	Cgc/Tgc	13/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		626	789	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867320	68867321	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0037688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	125	666	0	ENST00000261769.5:c.2569dup	p.Gln857ProfsTer4	p.Q857Pfs*4	ENST00000261769	NM_004360.3	856	gac/gaCc	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		666	551	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290067	15290067	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	71	913	1	ENST00000263388.2:c.3487G>T	p.Asp1163Tyr	p.D1163Y	ENST00000263388	NM_000435.2	1163	Gac/Tac	22/33	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		914	796	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	85	313	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.718903083098628	2		315	203	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0037725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	224	495	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	0.718903083098628	2		495	532	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531904	41531904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	151	404	0	ENST00000263253.7:c.1616C>T	p.Ser539Phe	p.S539F	ENST00000263253	NM_001429.3	539	tCt/tTt	7/31	1	2	FACETS	0.911	0.839	0.986	0.911	0.839	0.986	CLONAL	1	TRUE	1	0.661530493874074	2		404	501	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0037737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	374	728	1	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.644856955469503	2	FACETS	0.883	0.848	0.918	0.883	0.848	0.918	CLONAL	2	TRUE	0	0.661530493874074	2		729	640	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720808	89720808	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs1114167667	NA	P-0037738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	75	313	0	ENST00000371953.3:c.959T>G	p.Leu320Ter	p.L320*	ENST00000371953	NM_000314.4	320	tTa/tGa	8/9	0.395811998132732	2	FACETS	0.713	0.633	0.798	0.357	0.316	0.399	INDETERMINATE	1	TRUE	0	0.778675173546184	2		313	270	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543324	65543324	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0037738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	94	619	0	ENST00000358664.4:c.353C>G	p.Ser118Ter	p.S118*	ENST00000358664	NM_002382.4	118	tCa/tGa	5/5	0.778675173546184	3	FACETS	0.5	0.445	0.558	0.25	0.222	0.279	SUBCLONAL	1	TRUE	1	0.778675173546184	3		619	671	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100944	41100944	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	118	643	0	ENST00000373198.4:c.1412T>A	p.Met471Lys	p.M471K	ENST00000373198	NM_133170.3	471	aTg/aAg	8/32	0.778675173546184	1	FACETS	0.603	0.552	0.655	0.603	0.552	0.655	SUBCLONAL	1	TRUE	0	0.778675173546184	1		643	307	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868962	117868962	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415135262	NA	P-0037738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	151	381	0	ENST00000297338.2:c.737C>T	p.Pro246Leu	p.P246L	ENST00000297338	NM_006265.2	246	cCt/cTt	7/14	0.665200572063441	4	FACETS	1	0.988	1	0.488	0.45	0.528	CLONAL	1	TRUE	1	0.778675173546184	4		381	471	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196261	106196261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	20	292	0	ENST00000380013.4:c.4594C>T	p.Gln1532Ter	p.Q1532*	ENST00000380013	NM_001127208.2	1532	Cag/Tag	11/11	1	2	FACETS	0.716	0.547	0.915	0.716	0.547	0.915	CLONAL	1	TRUE	1	0.16	2		292	349	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023696	27023696	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	53	763	1	ENST00000324856.7:c.802C>T	p.Gln268Ter	p.Q268*	ENST00000324856	NM_006015.4	268	Cag/Tag	1/20	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.16	2		764	651	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591888	48591888	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519739	NA	P-0037739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	29	534	0	ENST00000342988.3:c.1051G>C	p.Asp351His	p.D351H	ENST00000342988	NM_005359.5	351	Gat/Cat	9/12	1	2	FACETS	0.851	0.682	1	0.851	0.682	1	CLONAL	1	TRUE	1	0.16	2		534	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0037741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	32	686	1	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	0.356	0.287	0.434	0.356	0.287	0.434	SUBCLONAL	1	TRUE	1	0.2	2		687	900	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546085	29546086	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0037741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	76	529	1	ENST00000356175.3:c.1590_1591delinsTT	p.Gln531Ter	p.Q531*	ENST00000356175	NM_000267.3	530	gtCCaa/gtTTaa	14/57	1	2	FACETS	0.984	0.863	1	0.984	0.863	1	CLONAL	1	TRUE	1	0.2	2		530	772	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871940	45871940	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142462393	NA	P-0037742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	157	626	0	ENST00000391945.4:c.308C>T	p.Pro103Leu	p.P103L	ENST00000391945	NM_000400.3	103	cCg/cTg	5/23	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.415384727458652	2		626	642	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916205	9916205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555491654	NA	P-0037742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	125	481	1	ENST00000330684.3:c.2084G>A	p.Arg695Gln	p.R695Q	ENST00000330684	NM_001134407.1	695	cGg/cAg	10/13	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.415384727458652	2		482	419	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528215	103528215	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	84	335	0	ENST00000355739.4:c.3523A>C	p.Lys1175Gln	p.K1175Q	ENST00000355739	NM_000123.3	1175	Aaa/Caa	15/15	1	2	FACETS	0.825	0.731	0.925	0.825	0.731	0.925	CLONAL	1	FALSE	1	0.415384727458652	2		335	490	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443861	52443861	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	161	610	0	ENST00000460680.1:c.34C>T	p.Pro12Ser	p.P12S	ENST00000460680	NM_004656.3	12	Cca/Tca	1/17	0.415384727458652	1	FACETS	0.812	0.755	0.87	1	0.991	1	CLONAL	2	FALSE	0	0.415384727458652	1		610	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579494	7579494	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1555526721	NA	P-0037743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	77	815	0	ENST00000269305.4:c.193A>T	p.Arg65Ter	p.R65*	ENST00000269305	NM_001126112.2	65	Aga/Tga	4/11	0.242598607539805	1	FACETS	0.74	0.65	0.836	0.74	0.65	0.836	SUBCLONAL	1	TRUE	0	0.282469379947717	1		815	633	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303964	91303964	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	57	613	0	ENST00000355112.3:c.1361A>T	p.Asn454Ile	p.N454I	ENST00000355112	NM_000057.2	454	aAt/aTt	7/22	0.282469379947717	1	FACETS	0.522	0.447	0.604	0.522	0.447	0.604	SUBCLONAL	1	TRUE	0	0.282469379947717	1		613	664	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40740974	40740974	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	58	801	0	ENST00000392038.2:c.1344C>G	p.Ile448Met	p.I448M	ENST00000392038	NM_001626.4	448	atC/atG	13/14	1	2	FACETS	0.6	0.514	0.693	0.6	0.514	0.693	SUBCLONAL	1	TRUE	1	0.282469379947717	2		801	685	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0037746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	63	813	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.885	0.765	1	0.885	0.765	1	CLONAL	1	TRUE	1	0.23	2		813	619	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028657	12028657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	59	780	1	ENST00000353533.5:c.860G>A	p.Arg287His	p.R287H	ENST00000353533	NM_003010.3	287	cGc/cAc	8/11	1	2	FACETS	0.975	0.84	1	0.975	0.84	1	CLONAL	1	TRUE	1	0.23	2		781	526	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023447	27023447	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	79	528	0	ENST00000324856.7:c.553C>T	p.Gln185Ter	p.Q185*	ENST00000324856	NM_006015.4	185	Cag/Tag	1/20	0.173058771313341	3	FACETS	1	0.963	1	0.621	0.546	0.701	CLONAL	1	TRUE	1	0.23	3		528	617	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983094	201983094	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	117	693	0	ENST00000359651.3:c.943T>C	p.Trp315Arg	p.W315R	ENST00000359651		315	Tgg/Cgg	7/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.23	2		693	721	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984428	201984429	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0037746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	104	657	0	ENST00000359651.3:c.1094dup	p.Val366GlyfsTer105	p.V366Gfs*105	ENST00000359651		365	gag/gAag	8/8	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.23	2		657	798	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424541	49425125	+	splice_donor_variant,splice_acceptor_variant,frameshift_variant,stop_lost,intron_variant	Splice_Site	DEL	AGGGACAGCTCCTACAAGGGGCAAGATGACAAAGTTCAAAACCTGCAGCGTTTGCATCGCTGTCTTGCACAGCTGGGGGACAGGGTGCCCCCTATCCTGGGATGGGACCAGGGGGACTGTCTCCTGGGGGGTCACCTGTTTCAGCTGTTTCAGCAAGGCCTCGCTGGCCCTGACCCCGTCCTCCTTCCGCAGCTTCTTTCGGGAGCTCACCAACCTGTCGCTTGCCTTCTGTACCCGCTTGGGCTTCGGTGTCAAAGGCTTCCTTGCTGCTGCATCCTAAGCCAAATAAGCCCATTGAAGGCTGCTACCCTCCTCCTCAGAGCCCTCATCTCTTCTGTCTGACCCAGGCTCACTCATTCTGCCCCCCGCTGGCTCTAGGACCCACTCTACCTGCTCCACTCTACTCAGAGTACTCACCTCCTTGTTGCTGGGGGTACCCTGTAGTTTCTGCTCCAGCCCAGCCAGCTTGCTGTCAATGTGCCCGTTGATCTCAGCTCGCAGCCCCTCGGACCCCCGCCCAGTGCTGAGTTGCACATTCTTTGCCCGGAGTAGCTTCTGCAAGAGCAGATGCCCAGCTTCTGAGCG	AGGGACAGCTCCTACAAGGGGCAAGATGACAAAGTTCAAAACCTGCAGCGTTTGCATCGCTGTCTTGCACAGCTGGGGGACAGGGTGCCCCCTATCCTGGGATGGGACCAGGGGGACTGTCTCCTGGGGGGTCACCTGTTTCAGCTGTTTCAGCAAGGCCTCGCTGGCCCTGACCCCGTCCTCCTTCCGCAGCTTCTTTCGGGAGCTCACCAACCTGTCGCTTGCCTTCTGTACCCGCTTGGGCTTCGGTGTCAAAGGCTTCCTTGCTGCTGCATCCTAAGCCAAATAAGCCCATTGAAGGCTGCTACCCTCCTCCTCAGAGCCCTCATCTCTTCTGTCTGACCCAGGCTCACTCATTCTGCCCCCCGCTGGCTCTAGGACCCACTCTACCTGCTCCACTCTACTCAGAGTACTCACCTCCTTGTTGCTGGGGGTACCCTGTAGTTTCTGCTCCAGCCCAGCCAGCTTGCTGTCAATGTGCCCGTTGATCTCAGCTCGCAGCCCCTCGGACCCCCGCCCAGTGCTGAGTTGCACATTCTTTGCCCGGAGTAGCTTCTGCAAGAGCAGATGCCCAGCTTCTGAGCG	-	novel	NA	P-0037746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	63	631	0	ENST00000301067.7:c.13363_13682del		p.X4455_splice	ENST00000301067	NM_003482.3	4455	CGCTCAGAAGCTGGGCATCTGCTCTTGCAGAAGCTACTCCGGGCAAAGAATGTGCAACTCAGCACTGGGCGGGGGTCCGAGGGGCTGCGAGCTGAGATCAACGGGCACATTGACAGCAAGCTGGCTGGGCTGGAGCAGAAACTACAGGGTACCCCCAGCAACAAGGAGGTGAGTACTCTGAGTAGAGTGGAGCAGGTAGAGTGGGTCCTAGAGCCAGCGGGGGGCAGAATGAGTGAGCCTGGGTCAGACAGAAGAGATGAGGGCTCTGAGGAGGAGGGTAGCAGCCTTCAATGGGCTTATTTGGCTTAGGATGCAGCAGCAAGGAAGCCTTTGACACCGAAGCCCAAGCGGGTACAGAAGGCAAGCGACAGGTTGGTGAGCTCCCGAAAGAAGCTGCGGAAGGAGGACGGGGTCAGGGCCAGCGAGGCCTTGCTGAAACAGCTGAAACAGGTGACCCCCCAGGAGACAGTCCCCCTGGTCCCATCCCAGGATAGGGGGCACCCTGTCCCCCAGCTGTGCAAGACAGCGATGCAAACGCTGCAGGTTTTGAACTTTGTCATCTTGCCCCTTGTAGGAGCTGTCCCTg/g	39-41/54	0.191891190457606	3	FACETS	0.9	0.777	1	0.45	0.388	0.517	CLONAL	1	TRUE	1	0.23	3		631	679	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	88	557	1	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	0.191891190457606	3	FACETS	1	0.964	1	0.611	0.541	0.686	CLONAL	1	TRUE	1	0.23	3		558	698	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052633	42052633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	75	474	0	ENST00000219905.7:c.7304G>A	p.Arg2435Gln	p.R2435Q	ENST00000219905	NM_001164273.1	2435	cGg/cAg	20/24	1	2	FACETS	0.917	0.803	1	0.917	0.803	1	CLONAL	1	TRUE	1	0.23	2		474	711	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085659	16085659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs794727503	NA	P-0037746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	75	641	0	ENST00000281043.3:c.835G>A	p.Val279Met	p.V279M	ENST00000281043	NM_005378.4	279	Gtg/Atg	3/3	NA	2	FACETS	1	0.904	1			1	INDETERMINATE	1	TRUE	NA	0.23	2		641	629	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728486	190728486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	52	366	0	ENST00000441310.2:c.1874C>T	p.Thr625Ile	p.T625I	ENST00000441310	NM_000534.4	625	aCt/aTt	10/13	0.101601738286946	3	FACETS	1	0.948	1	0.63	0.538	0.731	INDETERMINATE	1	TRUE	1	0.23	3		366	400	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150003	202150003	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	78	623	0	ENST00000358485.4:c.1444C>T	p.Gln482Ter	p.Q482*	ENST00000358485	NM_001080125.1	482	Cag/Tag	8/9	0.101601738286946	3	FACETS	1	0.91	1	0.522	0.458	0.59	INDETERMINATE	1	TRUE	1	0.23	3		623	725	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696169	52696169	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	78	1423	1	ENST00000394830.3:c.508C>T	p.Gln170Ter	p.Q170*	ENST00000394830	NM_018313.4	170	Cag/Tag	5/30	0.101601738286946	3	FACETS	0.96	0.842	1	0.48	0.421	0.543	INDETERMINATE	1	TRUE	1	0.23	3		1424	788	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356269	66356269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200754741	NA	P-0037746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	50	560	0	ENST00000273854.3:c.1228G>A	p.Gly410Ser	p.G410S	ENST00000273854	NM_004439.5	410	Ggt/Agt	5/18	1	2	FACETS	0.792	0.672	0.924	0.792	0.672	0.924	CLONAL	1	TRUE	1	0.23	2		560	549	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508580	106508580	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs796052174	NA	P-0037746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	47	449	0	ENST00000359195.3:c.574G>A	p.Asp192Asn	p.D192N	ENST00000359195	NM_002649.2	192	Gac/Aac	2/11	0.173058771313341	3	FACETS	0.881	0.744	1	0.441	0.372	0.517	CLONAL	1	TRUE	1	0.23	3		449	517	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151844647	151845669	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCGGGCATGGTAGCGCAAGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCACTTGAACCCAGGAGGCGGAGGTTGCAGGGAACTGAGATCGCGCCATTGCAGTCCAGCCTGTGCAACAAAAGAGAAACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAGAAAAAGAAAAAGAAAAAGGAGGTCCCCAATGCAAATGACAGGCAACCTTTATCTACAAATCATTCTCGGATTTACCTCACCAACTCGTATGTTCAAAGATATATTGATTATGAAAGTGTTTAGACAACTGTATAGCAAAGAGAGCAAGGTGTGAGAACACAAACATTGGCATTTGTAAATGAAAAATACACATTATAAAATATAAAACTAACATGAGACAAACATGGAAAATTGACAAAATACATTCATTAGCCTGACATCAGAGTAAGTAGCACTGCACAGCATGTGAACGGCAGACGTTACCTTTAGGTGAGATGTCACTTAGAACCAGGTCTTCATGGCCTTGTTCCACAATCCTGATGACAAACACTGGGCGCCCATCCTTCTCCTCAATGGAGCACAGGTAGCGGCAGCGCCTATTGGCATAGCGAGTGCTCCAGTACAGCCGGCTGGCTTCATAGCCCACAGGGAAGAGTGCTTTAGGAGAATGGAATGCTTGCATCTGCTGTGGAAGCAGCTGACCAATTGTGTGGAAGATGAGGCTACCCACGCGAAAGGTATGGTCCCGTTCTCCTCGTTGCACGATGCTAGCAATCTGTCGCACCTCATCACGCTGAACATAGACCCTCCTGAAGACTGCAAAGTAACTTAATTCTTGCTCATGAATTCCCTTTGGTTTGTGCATGGGGCAAAGCATAGTTTTGTCCTTAAAAAACATGCATTGTGCTTTAATGGCGCAAGTGAAGTGATAAATGTTGGTGCATCGAAATCTGTGGCATCCACTAGTGGCACCCGTCTTGTGACAGAAGACACATTTCATTTGTAGGCCTCTCCTCAGAGCTAGCTCCACATTTA	CCGGGCATGGTAGCGCAAGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCACTTGAACCCAGGAGGCGGAGGTTGCAGGGAACTGAGATCGCGCCATTGCAGTCCAGCCTGTGCAACAAAAGAGAAACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAGAAAAAGAAAAAGAAAAAGGAGGTCCCCAATGCAAATGACAGGCAACCTTTATCTACAAATCATTCTCGGATTTACCTCACCAACTCGTATGTTCAAAGATATATTGATTATGAAAGTGTTTAGACAACTGTATAGCAAAGAGAGCAAGGTGTGAGAACACAAACATTGGCATTTGTAAATGAAAAATACACATTATAAAATATAAAACTAACATGAGACAAACATGGAAAATTGACAAAATACATTCATTAGCCTGACATCAGAGTAAGTAGCACTGCACAGCATGTGAACGGCAGACGTTACCTTTAGGTGAGATGTCACTTAGAACCAGGTCTTCATGGCCTTGTTCCACAATCCTGATGACAAACACTGGGCGCCCATCCTTCTCCTCAATGGAGCACAGGTAGCGGCAGCGCCTATTGGCATAGCGAGTGCTCCAGTACAGCCGGCTGGCTTCATAGCCCACAGGGAAGAGTGCTTTAGGAGAATGGAATGCTTGCATCTGCTGTGGAAGCAGCTGACCAATTGTGTGGAAGATGAGGCTACCCACGCGAAAGGTATGGTCCCGTTCTCCTCGTTGCACGATGCTAGCAATCTGTCGCACCTCATCACGCTGAACATAGACCCTCCTGAAGACTGCAAAGTAACTTAATTCTTGCTCATGAATTCCCTTTGGTTTGTGCATGGGGCAAAGCATAGTTTTGTCCTTAAAAAACATGCATTGTGCTTTAATGGCGCAAGTGAAGTGATAAATGTTGGTGCATCGAAATCTGTGGCATCCACTAGTGGCACCCGTCTTGTGACAGAAGACACATTTCATTTGTAGGCCTCTCCTCAGAGCTAGCTCCACATTTA	-	novel	NA	P-0037746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	0	31	1	0	ENST00000262189.6:c.13343_13894+471del		p.X4448_splice	ENST00000262189	NM_170606.2	4448		52/59	0.173058771313341	3	FACETS		NA	1	1	0.977	1	NA	10	TRUE	1	0.23	3		1	31	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0037747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	36	701	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.206	0.169	0.248	0.206	0.169	0.248	SUBCLONAL	1	TRUE	1	0.504965107257856	2		701	692	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115708	8115708	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	26	429	0	ENST00000346208.3:c.1054A>G	p.Arg352Gly	p.R352G	ENST00000346208		352	Aga/Gga	6/6	1	2	FACETS	0.218	0.172	0.271	0.218	0.172	0.271	SUBCLONAL	1	TRUE	1	0.504965107257856	2		429	472	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857466	68857466	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	244	647	1	ENST00000261769.5:c.2101del	p.Val701SerfsTer21	p.V701Sfs*21	ENST00000261769	NM_004360.3	701	Gtc/tc	13/16	0.504965107257856	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.504965107257856	1		648	701	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0037762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	56	659	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	1	2	FACETS	0.671	0.575	0.776	0.671	0.575	0.776	SUBCLONAL	1	FALSE	1	0.291701884065637	2		659	572	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061334	38061334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	209	626	0	ENST00000250448.2:c.655C>A	p.Arg219Ser	p.R219S	ENST00000250448	NM_004496.3	219	Cgc/Agc	2/2	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.423993307135933	2		626	966	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199908	108199908	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	76	313	0	ENST00000278616.4:c.7250T>C	p.Leu2417Pro	p.L2417P	ENST00000278616	NM_000051.3	2417	cTg/cCg	49/63	0.423993307135933	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.423993307135933	1		313	233	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895599	28895599	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0037765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	104	425	0	ENST00000282397.4:c.3174+1G>A		p.X1058_splice	ENST00000282397	NM_002019.4	1058			1	2	FACETS	0.898	0.807	0.995	0.898	0.807	0.995	CLONAL	1	TRUE	1	0.423993307135933	2		425	546	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732283	74732283	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	35	342	0	ENST00000359995.5:c.626C>A	p.Pro209His	p.P209H	ENST00000359995	NM_001195427.1	209	cCc/cAc	2/3	1	2	FACETS	0.365	0.299	0.44	0.365	0.299	0.44	SUBCLONAL	1	TRUE	1	0.423993307135933	2		342	452	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729162	66729162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519732	NA	P-0037766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	45	632	0	ENST00000307102.5:c.370C>T	p.Pro124Ser	p.P124S	ENST00000307102	NM_002755.3	124	Ccg/Tcg	3/11	1	2	FACETS	0.806	0.675	0.952	0.806	0.675	0.952	CLONAL	1	TRUE	1	0.13	2		632	859	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315468	30315468	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	54	568	0	ENST00000322652.5:c.1153C>T	p.Leu385Phe	p.L385F	ENST00000322652	NM_015355.2	385	Ctc/Ttc	10/16	1	2	FACETS	0.996	0.849	1	0.996	0.849	1	CLONAL	1	TRUE	1	0.13	2		568	834	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0037767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	39	595	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.208256714250906	5	FACETS	1	0.951	1	0.485	0.403	0.575	CLONAL	1	TRUE	2	0.247560822034956	5		595	297	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396746	396746	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	26	579	0	ENST00000262320.3:c.280G>T	p.Asp94Tyr	p.D94Y	ENST00000262320	NM_003502.3	94	Gat/Tat	2/11	0.208256714250906	5	FACETS	0.967	0.767	1	0.322	0.255	0.398	CLONAL	1	TRUE	2	0.247560822034956	5		579	298	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0037777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	71	735	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.365	0.317	0.417	0.365	0.317	0.417	SUBCLONAL	1	TRUE	1	0.368900474026936	2		735	1055	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94209538	94209538	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	46	362	0	ENST00000323929.3:c.576G>A	p.Met192Ile	p.M192I	ENST00000323929	NM_005591.3	192	atG/atA	7/20	1	2	FACETS	0.509	0.429	0.598	0.509	0.429	0.598	SUBCLONAL	1	TRUE	1	0.368900474026936	2		362	490	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434736	99434736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374358935	NA	P-0037777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	379	686	0	ENST00000268035.6:c.823C>T	p.Arg275Cys	p.R275C	ENST00000268035	NM_000875.3	275	Cgc/Tgc	3/21	0.325034693060035	3	FACETS	0.991	0.941	1	0.991	0.941	1	CLONAL	2	TRUE	1	0.368900474026936	3		686	1228	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2107113	2107113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45502703	NA	P-0037777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	121	752	1	ENST00000219476.3:c.782G>A	p.Arg261Gln	p.R261Q	ENST00000219476	NM_000548.3	261	cGg/cAg	9/42	0.290796398006839	1	FACETS	0.488	0.439	0.539	0.488	0.439	0.539	SUBCLONAL	1	TRUE	0	0.368900474026936	1		753	1097	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0037777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	201	622	1	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	0.262351830499375	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.368900474026936	1		623	821	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8111076	8111076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201438176	NA	P-0037777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	232	743	3	ENST00000585124.1:c.131G>A	p.Arg44His	p.R44H	ENST00000585124	NM_004217.3	44	cGc/cAc	3/9	0.262351830499375	1	FACETS	0.973	0.907	1	0.973	0.907	1	CLONAL	1	TRUE	0	0.368900474026936	1		746	1054	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119719	17119719	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	92	568	0	ENST00000285071.4:c.1275G>T	p.Gln425His	p.Q425H	ENST00000285071	NM_144997.5	425	caG/caT	11/14	1	2	FACETS	0.547	0.485	0.613	0.547	0.485	0.613	SUBCLONAL	1	TRUE	1	0.368900474026936	2		568	912	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149542	202149542	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	61	483	0	ENST00000358485.4:c.983C>G	p.Ala328Gly	p.A328G	ENST00000358485	NM_001080125.1	328	gCt/gGt	8/9	1	2	FACETS	0.465	0.401	0.536	0.465	0.401	0.536	SUBCLONAL	1	TRUE	1	0.368900474026936	2		483	711	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221725	55221725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138847501	NA	P-0037777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	56	451	0	ENST00000275493.2:c.769G>A	p.Glu257Lys	p.E257K	ENST00000275493	NM_005228.3	257	Gaa/Aaa	7/28	1	2	FACETS	0.382	0.327	0.444	0.382	0.327	0.444	SUBCLONAL	1	TRUE	1	0.368900474026936	2		451	794	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0037786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	129	400	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	0.858	0.781	0.939	0.858	0.781	0.939	CLONAL	1	TRUE	1	0.514707494195827	2		400	584	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096580	178096580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	71	320	0	ENST00000397062.3:c.751G>A	p.Glu251Lys	p.E251K	ENST00000397062	NM_006164.4	251	Gag/Aag	5/5	1	2	FACETS	0.851	0.749	0.96	0.851	0.749	0.96	CLONAL	1	TRUE	1	0.514707494195827	2		320	324	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948083	178948083	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	40	284	0	ENST00000263967.3:c.2855T>C	p.Val952Ala	p.V952A	ENST00000263967	NM_006218.2	952	gTg/gCg	20/21	0.514707494195827	3	FACETS	0.537	0.447	0.636	0.268	0.223	0.318	SUBCLONAL	1	TRUE	1	0.514707494195827	3		284	364	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0037793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	372	980	5	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	0.551407585030047	4	FACETS	0.912	0.866	0.958	0.912	0.866	0.958	CLONAL	2	TRUE	2	0.551407585030047	4		985	1148	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691025	NA	P-0037793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	329	724	0	ENST00000269305.4:c.785G>T	p.Gly262Val	p.G262V	ENST00000269305	NM_001126112.2	262	gGt/gTt	8/11	0.529279698015177	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.551407585030047	2		724	566	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245779	41245779	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	137	717	0	ENST00000357654.3:c.1769G>C	p.Ser590Thr	p.S590T	ENST00000357654	NM_007294.3	590	aGt/aCt	10/23	0.551407585030047	3	FACETS	0.974	0.888	1	0.487	0.444	0.532	CLONAL	1	TRUE	1	0.551407585030047	3		717	651	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467502	25467502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	78	833	1	ENST00000264709.3:c.1574C>T	p.Ala525Val	p.A525V	ENST00000264709	NM_175629.2	525	gCg/gTg	14/23	0.549271534020497	3	FACETS	0.442	0.387	0.5	0.221	0.193	0.25	SUBCLONAL	1	TRUE	1	0.551407585030047	3		834	817	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683358	88683358	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	446	977	0	ENST00000372037.3:c.1481G>T	p.Arg494Leu	p.R494L	ENST00000372037	NM_004329.2	494	cGa/cTa	13/13	0.551407585030047	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.551407585030047	3		977	888	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246226	41246226	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1163497041	NA	P-0037793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	114	615	0	ENST00000357654.3:c.1322T>C	p.Ile441Thr	p.I441T	ENST00000357654	NM_007294.3	441	aTa/aCa	10/23	0.551407585030047	3	FACETS	0.939	0.848	1	0.469	0.424	0.517	CLONAL	1	TRUE	1	0.551407585030047	3		615	562	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39567809	39567809	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	90	315	0	ENST00000262039.4:c.567del	p.Val190Ter	p.V190*	ENST00000262039	NM_002647.2	189	Aaa/aa	5/25	0.232462302905817	3	FACETS	0.921	0.833	1			1	INDETERMINATE	2	TRUE	NA	0.551407585030047	3		315	226	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121160	11121160	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	683	1002	1	ENST00000358026.2:c.2227G>T	p.Asp743Tyr	p.D743Y	ENST00000358026	NM_001128849.1	743	Gac/Tac	15/36	0.551407585030047	3	FACETS	0.997	0.969	1	0.997	0.969	1	CLONAL	3	TRUE	0	0.551407585030047	3		1003	1057	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121163	11121163	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0037793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	672	995	1	ENST00000358026.2:c.2230A>T	p.Lys744Ter	p.K744*	ENST00000358026	NM_001128849.1	744	Aag/Tag	15/36	0.551407585030047	3	FACETS	0.994	0.966	1	0.994	0.966	1	CLONAL	3	TRUE	0	0.551407585030047	3		996	1043	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295777	15295777	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	731	1209	1	ENST00000263388.2:c.2350G>T	p.Gly784Cys	p.G784C	ENST00000263388	NM_000435.2	784	Ggc/Tgc	15/33	0.551407585030047	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.551407585030047	3		1210	1094	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077432	30077432	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	146	290	0	ENST00000338641.4:c.1579G>A	p.Glu527Lys	p.E527K	ENST00000338641	NM_000268.3	527	Gaa/Aaa	15/16	0.529279698015177	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	0	0.551407585030047	2		290	262	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119634996	119634996	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	53	300	0	ENST00000316626.5:c.503G>T	p.Ser168Ile	p.S168I	ENST00000316626		168	aGt/aTt	5/12	1	2	FACETS	0.947	0.819	1	0.947	0.819	1	CLONAL	1	TRUE	1	0.551407585030047	2		300	203	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911427	134911427	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	107	611	2	ENST00000398015.3:c.1892G>T	p.Gly631Val	p.G631V	ENST00000398015	NM_004441.4	631	gGa/gTa	11/16	1	2	FACETS	0.874	0.789	0.963	0.874	0.789	0.963	CLONAL	1	TRUE	1	0.551407585030047	2		613	444	SUCCESS
APC	324	MSKCC	GRCh37	5	112175957	112175958	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0037793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	124	335	0	ENST00000257430.4:c.4666_4667insG	p.Thr1556SerfsTer3	p.T1556Sfs*3	ENST00000257430	NM_000038.5	1556	act/aGct	16/16	0.551407585030047	2	FACETS	0.969	0.899	1	0.969	0.899	1	CLONAL	2	TRUE	0	0.551407585030047	2		335	232	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046063	180046063	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	137	222	0	ENST00000261937.6:c.2808del	p.Asn937ThrfsTer70	p.N937Tfs*70	ENST00000261937	NM_182925.4	936	tcC/tc	20/30	0.164948337983285	3	FACETS	1	0.952	1	0.693	0.641	0.745	INDETERMINATE	2	TRUE	0	0.551407585030047	3		222	305	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975472	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	190	406	0	ENST00000405192.2:c.415A>G	p.Thr139Ala	p.T139A	ENST00000405192	NM_001163147.1	139	Aca/Gca	7/12	0.551407585030047	4	FACETS	0.951	0.885	1			1	CLONAL	2	TRUE	NA	0.551407585030047	4		406	562	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0037795-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	451	630	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.683656310744221	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.683656310744221	2		630	620	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0037795-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	60	186	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	1	2	FACETS	0.848	0.742	0.96	0.848	0.742	0.96	CLONAL	1	TRUE	1	0.683656310744221	2		186	207	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0037795-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	102	612	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.862	0.779	0.949	0.862	0.779	0.949	CLONAL	1	TRUE	1	0.683656310744221	2		612	346	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471048	8471048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037795-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	78	354	0	ENST00000356435.5:c.3451C>T	p.Arg1151Cys	p.R1151C	ENST00000356435		1151	Cgc/Tgc	20/35	0.291172195288505	3	FACETS	0.709	0.625	0.797	0.236	0.208	0.266	INDETERMINATE	1	TRUE	0	0.683656310744221	3		354	432	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856554	111856554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs953545115	NA	P-0037795-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	79	211	0	ENST00000341259.2:c.605G>A	p.Arg202His	p.R202H	ENST00000341259	NM_005475.2	202	cGc/cAc	2/8	0.683656310744221	3	FACETS	1	0.905	1	0.51	0.453	0.57	CLONAL	1	TRUE	1	0.683656310744221	3		211	304	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0037798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	46	707	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	1	2	FACETS	0.481	0.404	0.566	0.481	0.404	0.566	SUBCLONAL	1	FALSE	1	0.3	2		707	638	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28929495	NA	P-0037798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	52	670	0	ENST00000275493.2:c.2155G>A	p.Gly719Ser	p.G719S	ENST00000275493	NM_005228.3	719	Ggc/Agc	18/28	1	2	FACETS	0.556	0.473	0.648	0.556	0.473	0.648	SUBCLONAL	1	FALSE	1	0.3	2		670	623	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	62	635	0	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS	0.625	0.539	0.718	0.625	0.539	0.718	SUBCLONAL	1	TRUE	1	0.28	2		635	709	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604790	48604790	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1568211615	NA	P-0037799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	58	345	0	ENST00000342988.3:c.1612G>T	p.Glu538Ter	p.E538*	ENST00000342988	NM_005359.5	538	Gaa/Taa	12/12	1	2	FACETS	0.895	0.77	1	0.895	0.77	1	CLONAL	1	TRUE	1	0.28	2		345	463	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0037799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	46	277	1	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	0.3	1	FACETS	0.81	0.684	0.947	0.81	0.684	0.947	CLONAL	1	TRUE	0	0.28	1		278	349	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49413009	49413009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519953	NA	P-0037799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	96	596	3	ENST00000418115.1:c.14G>A	p.Arg5Gln	p.R5Q	ENST00000418115	NM_001664.2	5	cGg/cAg	2/5	1	2	FACETS	0.912	0.812	1	0.912	0.812	1	CLONAL	1	TRUE	1	0.28	2		599	752	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858783	9858783	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	28	222	0	ENST00000330684.3:c.2618G>C	p.Gly873Ala	p.G873A	ENST00000330684	NM_001134407.1	873	gGa/gCa	13/13	1	2	FACETS	0.794	0.637	0.971	0.794	0.637	0.971	CLONAL	1	TRUE	1	0.28	2		222	252	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0037799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	61	534	0	ENST00000269305.4:c.97-1G>C		p.X33_splice	ENST00000269305	NM_001126112.2	33			1	2	FACETS	0.882	0.762	1	0.882	0.762	1	CLONAL	1	TRUE	1	0.28	2		534	494	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606368	93606368	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1388733927	NA	P-0037799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	70	693	1	ENST00000375746.1:c.188A>G	p.His63Arg	p.H63R	ENST00000375746	NM_001174167.1	63	cAc/cGc	2/14	1	2	FACETS	0.717	0.625	0.817	0.717	0.625	0.817	SUBCLONAL	1	TRUE	1	0.28	2		694	697	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930087	68930087	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	74	362	0	ENST00000288368.4:c.148T>G	p.Leu50Val	p.L50V	ENST00000288368	NM_024870.2	50	Tta/Gta	2/40	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.28	2		362	525	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780812	9780812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765797019	NA	P-0037799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	77	665	1	ENST00000377346.4:c.1534C>T	p.Arg512Trp	p.R512W	ENST00000377346	NM_005026.3	512	Cgg/Tgg	13/24	1	2	FACETS	0.724	0.635	0.82	0.724	0.635	0.82	SUBCLONAL	1	TRUE	1	0.28	2		666	760	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089510	27089514	+	frameshift_variant	Frame_Shift_Del	DEL	CTACC	CTACC	-	novel	NA	P-0037799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	92	627	0	ENST00000324856.7:c.2467_2471del	p.Tyr823GlnfsTer47	p.Y823Qfs*47	ENST00000324856	NM_006015.4	822	aaCTACCcc/aacc	8/20	1	2	FACETS	0.797	0.707	0.892	0.797	0.707	0.892	SUBCLONAL	1	TRUE	1	0.28	2		627	825	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424741	49424741	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783692	NA	P-0037799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	93	681	0	ENST00000301067.7:c.13606C>T	p.Arg4536Ter	p.R4536*	ENST00000301067	NM_003482.3	4536	Cga/Tga	40/54	1	2	FACETS	0.79	0.701	0.884	0.79	0.701	0.884	SUBCLONAL	1	TRUE	1	0.28	2		681	841	SUCCESS
BLM	641	MSKCC	GRCh37	15	91352417	91352417	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	54	375	1	ENST00000355112.3:c.3802G>A	p.Glu1268Lys	p.E1268K	ENST00000355112	NM_000057.2	1268	Gaa/Aaa	20/22	1	2	FACETS	0.724	0.618	0.839	0.724	0.618	0.839	SUBCLONAL	1	TRUE	1	0.28	2		376	533	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197085	26197085	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	61	443	0	ENST00000356476.2:c.394C>A	p.Arg132Ser	p.R132S	ENST00000356476		132	Cgt/Agt	1/1	1	2	FACETS	0.756	0.653	0.869	0.756	0.653	0.869	SUBCLONAL	1	TRUE	1	0.28	2		443	576	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859687	151859687	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	82	338	0	ENST00000262189.6:c.10975G>T	p.Glu3659Ter	p.E3659*	ENST00000262189	NM_170606.2	3659	Gag/Tag	43/59	0.195414165389188	2	FACETS	1	0.972	1	0.667	0.591	0.748	CLONAL	1	TRUE	0	0.28	2		338	439	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519886	NA	P-0037800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	68	512	0	ENST00000349496.5:c.97T>C	p.Ser33Pro	p.S33P	ENST00000349496	NM_001904.3	33	Tct/Cct	3/15	1	2	FACETS	0.651	0.566	0.743	0.651	0.566	0.743	SUBCLONAL	1	TRUE	1	0.324044189980161	2		512	645	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441884	40441884	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	241	967	0	ENST00000345506.4:c.129G>A	p.Trp43Ter	p.W43*	ENST00000345506	NM_003152.3	43	tgG/tgA	4/20	0.29981718688238	3	FACETS	1	0.988	1	0.635	0.591	0.679	CLONAL	1	TRUE	1	0.324044189980161	3		967	1362	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143181719	143181719	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0037800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	81	359	0	ENST00000262992.4:c.616-2A>T		p.X206_splice	ENST00000262992	NM_001101669.1	206			1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.324044189980161	2		359	451	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176683976	176683976	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	194	670	0	ENST00000439151.2:c.4790A>T	p.Lys1597Met	p.K1597M	ENST00000439151	NM_022455.4	1597	aAg/aTg	13/23	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.324044189980161	2		670	980	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	36	503	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		503	404	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034471	47034471	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	63	405	0	ENST00000377604.3:c.556C>T	p.Arg186Ter	p.R186*	ENST00000377604	NM_001204468.1	186	Cga/Tga	6/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		405	364	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492813	56492813	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	98	574	1	ENST00000407977.2:c.126del	p.Glu43AsnfsTer8	p.E43Nfs*8	ENST00000407977		42	gcA/gc	2/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		575	595	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219361	1219361	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	122	650	0	ENST00000326873.7:c.415del	p.Met139CysfsTer22	p.M139Cfs*22	ENST00000326873	NM_000455.4	138	gAa/ga	3/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		650	716	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691779	30691792	+	frameshift_variant	Frame_Shift_Del	DEL	ACATAACACTAGAG	ACATAACACTAGAG	-	novel	NA	P-0037802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	30	503	0	ENST00000295754.5:c.284_297del	p.Ile95SerfsTer4	p.I95Sfs*4	ENST00000295754	NM_003242.5	94	aACATAACACTAGAG/a	3/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		503	460	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971105	21971107	+	inframe_deletion	In_Frame_Del	DEL	CGT	CGT	-	novel	NA	P-0037802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	25	287	0	ENST00000304494.5:c.251_253del	p.Asp84del	p.D84del	ENST00000304494	NM_000077.4	84	gACGct/gct	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		287	348	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0037803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	83	493	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.43110523846269	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	0	0.43110523846269	2		493	187	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0037803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	48	283	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.43110523846269	2		283	196	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285816	46285816	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	53	474	0	ENST00000334344.6:c.5086del	p.Leu1696TyrfsTer5	p.L1696Yfs*5	ENST00000334344	NM_152641.2	1695	gCc/gc	18/21	0.41137919932416	1	FACETS	0.901	0.779	1	0.901	0.779	1	CLONAL	1	TRUE	0	0.43110523846269	1		474	214	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831203	3831225	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ACTTTGTGGCCCCCAGGGAAGTC	ACTTTGTGGCCCCCAGGGAAGTC	-	novel	NA	P-0037803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	46	301	0	ENST00000262367.5:c.1656_1676+2del		p.X552_splice	ENST00000262367	NM_004380.2	552		7/31	1	2	FACETS	0.912	0.775	1	0.912	0.775	1	CLONAL	1	TRUE	1	0.43110523846269	2		301	234	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579335	7579336	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0037803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	54	681	0	ENST00000269305.4:c.351_352insC	p.Thr118HisfsTer31	p.T118Hfs*31	ENST00000269305	NM_001126112.2	117	-/C	4/11	0.399095989053377	1	FACETS	0.968	0.839	1	0.968	0.839	1	CLONAL	1	TRUE	0	0.43110523846269	1		681	203	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62325749	62325749	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	55	723	0	ENST00000360203.5:c.3017T>C	p.Leu1006Pro	p.L1006P	ENST00000360203	NM_001283009.1	1006	cTg/cCg	31/35	1	2	FACETS	0.845	0.728	0.971	0.845	0.728	0.971	CLONAL	1	TRUE	1	0.43110523846269	2		723	302	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536164	41536178	+	inframe_deletion	In_Frame_Del	DEL	CGCCGGATCCTGCTG	CGCCGGATCCTGCTG	-	novel	NA	P-0037814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	86	644	0	ENST00000263253.7:c.1782_1796del	p.Pro595_Ala599del	p.P595_A599del	ENST00000263253	NM_001429.3	594	aCGCCGGATCCTGCTGct/act	9/31	1	2	FACETS	0.881	0.793	0.972	1	0.985	1	CLONAL	2	FALSE	1	0.420615669510222	2		644	232	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0037817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	133	450	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	0.35403015426472	5	FACETS	1	0.929	1	0.677	0.62	0.735	CLONAL	2	TRUE	2	0.578636189321696	5		450	423	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857336	9857336	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	41	555	0	ENST00000330684.3:c.4065G>T	p.Lys1355Asn	p.K1355N	ENST00000330684	NM_001134407.1	1355	aaG/aaT	13/13	0.336020089833013	3	FACETS	1	0.927	1	0.586	0.496	0.682	INDETERMINATE	1	TRUE	1	0.578636189321696	3		555	156	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776195	135776195	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	68	478	0	ENST00000298552.3:c.2532G>C	p.Gln844His	p.Q844H	ENST00000298552	NM_001162426.1	844	caG/caC	20/23	0.578636189321696	1	FACETS	0.949	0.844	1	0.949	0.844	1	CLONAL	1	TRUE	0	0.578636189321696	1		478	176	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776201	135776201	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	65	463	0	ENST00000298552.3:c.2526G>C	p.Gln842His	p.Q842H	ENST00000298552	NM_001162426.1	842	caG/caC	20/23	0.578636189321696	1	FACETS	0.95	0.843	1	0.95	0.843	1	CLONAL	1	TRUE	0	0.578636189321696	1		463	168	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0037818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	47	386	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.418993891325269	2		386	178	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934576	NA	P-0037818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	212	761	0	ENST00000269305.4:c.818G>C	p.Arg273Pro	p.R273P	ENST00000269305	NM_001126112.2	273	cGt/cCt	8/11	0.418993891325269	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.418993891325269	1		761	765	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070631	67070631	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs760230354	NA	P-0037818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	139	235	0	ENST00000412916.2:c.255T>A	p.Tyr85Ter	p.Y85*	ENST00000412916		85	taT/taA	3/6	0.364559618291228	2	FACETS	0.987	0.912	1	0.987	0.912	1	CLONAL	2	TRUE	0	0.418993891325269	2		235	336	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734016	58734016	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	140	554	0	ENST00000305921.3:c.1074G>C	p.Trp358Cys	p.W358C	ENST00000305921	NM_003620.3	358	tgG/tgC	5/6	0.358230049989664	3	FACETS	0.955	0.87	1			1	CLONAL	1	TRUE	NA	0.418993891325269	3		554	846	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734074	58734074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	127	718	0	ENST00000305921.3:c.1132G>A	p.Glu378Lys	p.E378K	ENST00000305921	NM_003620.3	378	Gaa/Aaa	5/6	0.358230049989664	3	FACETS	0.897	0.813	0.986			1	CLONAL	1	TRUE	NA	0.418993891325269	3		718	817	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734107	58734107	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	115	758	0	ENST00000305921.3:c.1165G>A	p.Asp389Asn	p.D389N	ENST00000305921	NM_003620.3	389	Gat/Aat	5/6	0.358230049989664	3	FACETS	0.856	0.771	0.945			1	CLONAL	1	TRUE	NA	0.418993891325269	3		758	776	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577537	7577538	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0037819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	196	639	0	ENST00000269305.4:c.743_744delinsTT	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGG/cTT	7/11	0.513731914725333	2	FACETS	0.855	0.801	0.91	0.855	0.801	0.91	CLONAL	2	TRUE	0	0.513826468383957	2		639	446	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0037831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	238	340	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.231601868925375	6	FACETS	0.97	0.909	1			1	CLONAL	4	FALSE	NA	0.231601868925375	6		340	775	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044853	47044853	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	110	795	0	ENST00000377604.3:c.2179G>T	p.Gly727Ter	p.G727*	ENST00000377604	NM_001204468.1	727	Gga/Tga	20/24	0.197015872100672	1	FACETS	0.712	0.638	0.791	0.712	0.638	0.791	SUBCLONAL	1	FALSE	0	0.231601868925375	1		795	1179	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203511	108203511	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	39	211	0	ENST00000278616.4:c.7811G>C	p.Arg2604Thr	p.R2604T	ENST00000278616	NM_000051.3	2604	aGa/aCa	53/63	0.149812529215294	4	FACETS	1	0.902	1	0.564	0.468	0.67	CLONAL	1	FALSE	2	0.231601868925375	4		211	368	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263856	133263856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241114520	NA	P-0037831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	34	172	0	ENST00000320574.5:c.46G>A	p.Asp16Asn	p.D16N	ENST00000320574	NM_006231.2	16	Gat/Aat	1/49	0.149812529215294	4	FACETS	1	0.887	1	0.558	0.457	0.671	CLONAL	1	FALSE	2	0.231601868925375	4		172	324	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599926	28599926	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	113	647	1	ENST00000253063.3:c.808G>T	p.Glu270Ter	p.E270*	ENST00000253063	NM_031459.4	270	Gag/Tag	6/10	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	FALSE	1	0.231601868925375	2		648	971	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263359	123263359	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	91	446	0	ENST00000358487.5:c.1384G>T	p.Gly462Trp	p.G462W	ENST00000358487	NM_000141.4	462	Ggg/Tgg	10/18	0.175713773020981	3	FACETS	1	0.963	1	0.601	0.533	0.673	CLONAL	1	FALSE	1	0.231601868925375	3		446	730	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066848	77066848	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs776284597	NA	P-0037831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	33	336	0	ENST00000356341.3:c.637C>G	p.Pro213Ala	p.P213A	ENST00000356341	NM_002576.4	213	Cca/Gca	7/15	0.149812529215294	4	FACETS	0.591	0.48	0.716	0.295	0.24	0.358	SUBCLONAL	1	FALSE	2	0.231601868925375	4		336	594	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203561	108203561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	59	273	0	ENST00000278616.4:c.7861G>A	p.Glu2621Lys	p.E2621K	ENST00000278616	NM_000051.3	2621	Gag/Aag	53/63	0.149812529215294	4	FACETS	1	0.959	1	0.661	0.569	0.76	CLONAL	1	FALSE	2	0.231601868925375	4		273	475	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218013	108218013	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	52	207	0	ENST00000278616.4:c.8592C>A	p.Tyr2864Ter	p.Y2864*	ENST00000278616	NM_000051.3	2864	taC/taA	59/63	0.149812529215294	4	FACETS	1	0.946	1	0.623	0.531	0.723	CLONAL	1	FALSE	2	0.231601868925375	4		207	444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577055	7577067	+	frameshift_variant	Frame_Shift_Del	DEL	GCTCCCCTTTCTT	GCTCCCCTTTCTT	-	novel	NA	P-0037831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	188	766	0	ENST00000269305.4:c.871_883del	p.Lys291LeufsTer50	p.K291Lfs*50	ENST00000269305	NM_001126112.2	291	AAGAAAGGGGAGCct/ct	8/11	0.156384362228528	2	FACETS	1	0.988	1	0.684	0.631	0.739	CLONAL	1	FALSE	0	0.231601868925375	2		766	1187	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22161984	22161984	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	49	431	0	ENST00000215832.6:c.271C>G	p.Arg91Gly	p.R91G	ENST00000215832	NM_002745.4	91	Cga/Gga	2/9	0.175713773020981	3	FACETS	0.688	0.582	0.806	0.344	0.291	0.403	SUBCLONAL	1	FALSE	1	0.231601868925375	3		431	686	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467686	66467686	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	46	300	0	ENST00000273854.3:c.583C>A	p.Leu195Met	p.L195M	ENST00000273854	NM_004439.5	195	Ctg/Atg	3/18	0.231601868925375	3	FACETS	0.786	0.661	0.924	0.262	0.22	0.308	CLONAL	1	FALSE	0	0.231601868925375	3		300	564	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178313	56178313	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	58	258	0	ENST00000399503.3:c.3286G>A	p.Gly1096Ser	p.G1096S	ENST00000399503	NM_005921.1	1096	Ggc/Agc	14/20	0.231803048818537	3	FACETS	1	0.906	1	0.535	0.46	0.617	CLONAL	1	FALSE	1	0.231601868925375	3		258	522	SUCCESS
APC	324	MSKCC	GRCh37	5	112177253	112177253	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	97	293	0	ENST00000257430.4:c.5962A>G	p.Lys1988Glu	p.K1988E	ENST00000257430	NM_000038.5	1988	Aaa/Gaa	16/16	0.231803048818537	3	FACETS	0.97	0.868	1	0.97	0.868	1	CLONAL	2	FALSE	1	0.231601868925375	3		293	482	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020847	26020847	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138723860	NA	P-0037831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	32	387	0	ENST00000357647.3:c.130C>T	p.Pro44Ser	p.P44S	ENST00000357647	NM_003529.2	44	Ccg/Tcg	1/1	1	2	FACETS	0.529	0.429	0.643	0.529	0.429	0.643	SUBCLONAL	1	FALSE	1	0.231601868925375	2		387	522	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165272	32165272	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1272865229	NA	P-0037831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	205	769	0	ENST00000375023.3:c.4856T>G	p.Leu1619Arg	p.L1619R	ENST00000375023	NM_004557.3	1619	cTg/cGg	27/30	0.231803048818537	3	FACETS	1	0.99	1	0.721	0.667	0.778	CLONAL	1	FALSE	1	0.231601868925375	3		769	1369	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339523	81339523	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	78	368	0	ENST00000222390.5:c.1481G>T	p.Arg494Leu	p.R494L	ENST00000222390	NM_000601.4	494	cGa/cTa	13/18	0.175713773020981	3	FACETS	1	0.957	1	0.598	0.526	0.676	CLONAL	1	FALSE	1	0.231601868925375	3		368	628	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87475993	87475993	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	87	801	0	ENST00000277120.3:c.1435C>T	p.Gln479Ter	p.Q479*	ENST00000277120		479	Caa/Taa	13/19	1	2	FACETS	0.608	0.537	0.686	0.608	0.537	0.686	SUBCLONAL	1	FALSE	1	0.231601868925375	2		801	1235	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0037832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	286	587	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.18445092380693	2	FACETS	1	0.993	1	0.688	0.652	0.725	INDETERMINATE	1	TRUE	0	0.620213539255657	2		587	670	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944257	206944257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	111	421	0	ENST00000423557.1:c.373C>T	p.Arg125Cys	p.R125C	ENST00000423557	NM_000572.2	125	Cgc/Tgc	3/5	0.620213539255657	4	FACETS	0.647	0.58	0.717	0.216	0.193	0.239	SUBCLONAL	1	TRUE	1	0.620213539255657	4		421	897	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663825	29663825	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	236	584	0	ENST00000356175.3:c.6257T>C	p.Val2086Ala	p.V2086A	ENST00000356175	NM_000267.3	2086	gTt/gCt	41/57	1	2	FACETS	0.995	0.932	1	0.995	0.932	1	CLONAL	1	TRUE	1	0.620213539255657	2		584	765	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441283	52441283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1385279115	NA	P-0037832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	160	630	2	ENST00000460680.1:c.487C>T	p.Arg163Trp	p.R163W	ENST00000460680	NM_004656.3	163	Cgg/Tgg	7/17	0.18445092380693	2	FACETS	0.694	0.638	0.753	0.347	0.319	0.377	INDETERMINATE	1	TRUE	0	0.620213539255657	2		632	743	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0037833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	124	918	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.893	0.81	0.98	1	0.988	1	CLONAL	2	TRUE	1	0.22	2		919	631	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156609	2156609	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs868067982	NA	P-0037833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	55	736	0	ENST00000434045.2:c.313G>T	p.Gly105Cys	p.G105C	ENST00000434045	NM_001127598.1	105	Ggc/Tgc	3/5	1	2	FACETS	0.745	0.637	0.864	0.745	0.637	0.864	SUBCLONAL	1	TRUE	1	0.22	2		736	671	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626628	100626628	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	55	379	0	ENST00000308731.7:c.302C>A	p.Pro101His	p.P101H	ENST00000308731	NM_000061.2	101	cCc/cAc	4/19	1	2	FACETS	0.967	0.828	1	0.967	0.828	1	CLONAL	1	TRUE	1	0.22	2		379	517	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098795	47098795	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	64	834	0	ENST00000409792.3:c.6479del	p.Pro2160ArgfsTer88	p.P2160Rfs*88	ENST00000409792	NM_014159.6	2160	cCg/cg	15/21	1	2	FACETS	0.782	0.676	0.897	0.782	0.676	0.897	SUBCLONAL	1	TRUE	1	0.22	2		834	744	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47087982	47087982	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	40	418	0	ENST00000409792.3:c.7093C>T	p.Gln2365Ter	p.Q2365*	ENST00000409792	NM_014159.6	2365	Cag/Tag	16/21	1	2	FACETS	0.645	0.535	0.767	0.645	0.535	0.767	SUBCLONAL	1	TRUE	1	0.22	2		418	564	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29195912	29195912	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	77	859	0	ENST00000240100.2:c.686C>G	p.Ser229Cys	p.S229C	ENST00000240100	NM_001394.6	229	tCc/tGc	3/4	1	2	FACETS	0.958	0.84	1	0.958	0.84	1	CLONAL	1	TRUE	1	0.22	2		859	731	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045547	47045547	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	56	678	0	ENST00000377604.3:c.2514C>A	p.Tyr838Ter	p.Y838*	ENST00000377604	NM_001204468.1	838	taC/taA	22/24	1	2	FACETS	0.863	0.739	0.998	0.863	0.739	0.998	CLONAL	1	TRUE	1	0.22	2		678	590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0037858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	135	636	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.151784548045526	3	FACETS	0.974	0.918	1			1	INDETERMINATE	3	TRUE	NA	0.629585317782236	3		637	193	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776783	NA	P-0037858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	47	224	1	ENST00000267163.4:c.1215+1G>A		p.X405_splice	ENST00000267163	NM_000321.2	405			0.629585317782236	2	FACETS	0.868	0.767	0.968	0.868	0.767	0.968	CLONAL	2	TRUE	0	0.629585317782236	2		225	86	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099124	27099124	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0037858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	76	354	1	ENST00000324856.7:c.3539+1G>T		p.X1180_splice	ENST00000324856	NM_006015.4	1180			0.629585317782236	4	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	2	0.629585317782236	4		355	189	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778812	76778818	+	frameshift_variant	Frame_Shift_Del	DEL	GAATCAT	GAATCAT	-	novel	NA	P-0037858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	65	414	0	ENST00000373344.5:c.6761_6767del	p.His2254LeufsTer11	p.H2254Lfs*11	ENST00000373344	NM_000489.3	2254	cATGATTCt/ct	31/35	0.629585317782236	5	FACETS	0.797	0.699	0.9	0.531	0.466	0.6	SUBCLONAL	2	TRUE	2	0.629585317782236	5		414	252	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185195	123185195	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	20	443	0	ENST00000218089.9:c.1147G>T	p.Glu383Ter	p.E383*	ENST00000218089	NM_001042749.1	383	Gaa/Taa	13/35	0.629585317782236	3	FACETS	0.4	0.307	0.508			1	SUBCLONAL	1	TRUE	NA	0.629585317782236	3		443	209	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0037859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	33	291	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.905	0.739	1	0.905	0.739	1	CLONAL	1	TRUE	1	0.24	2		291	304	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578502	7578502	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555526241	NA	P-0037859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	174	755	0	ENST00000269305.4:c.428T>G	p.Val143Gly	p.V143G	ENST00000269305	NM_001126112.2	143	gTg/gGg	5/11	0.286259382862912	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.24	1		755	906	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	43	313	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.24935246289181	2		315	278	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803721	1803721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780313125	NA	P-0037861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	83	801	0	ENST00000260795.2:c.899C>T	p.Pro300Leu	p.P300L	ENST00000260795		300	cCg/cTg	6/17	0.24935246289181	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.24935246289181	1		801	522	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243424	46243424	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	40	351	0	ENST00000334344.6:c.1777del	p.His593IlefsTer5	p.H593Ifs*5	ENST00000334344	NM_152641.2	593	Cat/at	14/21	0.24935246289181	1	FACETS	0.962	0.803	1	0.962	0.803	1	CLONAL	1	TRUE	0	0.24935246289181	1		351	292	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101977	11101977	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	75	710	0	ENST00000358026.2:c.1397G>T	p.Arg466Leu	p.R466L	ENST00000358026	NM_001128849.1	466	cGc/cTc	8/36	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.24935246289181	2		710	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0037870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	56	813	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.19	2		813	581	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0037870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	99	595	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.798	0.713	0.888	1	0.983	1	SUBCLONAL	2	TRUE	1	0.19	2		595	653	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78831603	78831603	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	67	451	1	ENST00000306801.3:c.1412G>T	p.Gly471Val	p.G471V	ENST00000306801	NM_020761.2	471	gGc/gTc	13/34	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.19	2		452	536	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37876033	37876048	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTGCAGCTGTGTGGA	CCTGCAGCTGTGTGGA	-	novel	NA	P-0037872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	426	434	0	ENST00000269571.5:c.1899-3_1911del		p.X633_splice	ENST00000269571		633		16/27	0.204548117577805	6	FACETS	0.932	0.898	0.966			1	INDETERMINATE	5	TRUE	NA	0.535658571700959	6		434	707	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177699	56177699	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs768354073	NA	P-0037872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	141	218	0	ENST00000399503.3:c.2672A>G	p.Asn891Ser	p.N891S	ENST00000399503	NM_005921.1	891	aAc/aGc	14/20	0.452330524791519	4	FACETS	0.881	0.809	0.955	0.881	0.809	0.955	CLONAL	2	TRUE	2	0.535658571700959	4		218	459	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	79	688	6	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.858	0.759	0.964	0.858	0.759	0.964	CLONAL	1	TRUE	1	0.469501661430774	2		694	392	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	191	506	9	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	0.412088160087611	3	FACETS	0.814	0.757	0.873	0.814	0.757	0.873	CLONAL	2	TRUE	1	0.469501661430774	3		515	617	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	100	504	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.469501661430774	2		504	413	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	59	246	0	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	1	2	FACETS	0.982	0.854	1	0.982	0.854	1	CLONAL	1	TRUE	1	0.469501661430774	2		246	256	SUCCESS
BTK	695	MSKCC	GRCh37	X	100624988	100624988	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs864321664	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	63	152	2	ENST00000308731.7:c.389del	p.Asn130ThrfsTer2	p.N130Tfs*2	ENST00000308731	NM_000061.2	130	aAc/ac	5/19	1	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.469501661430774	1		154	196	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088788	27088788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	85	434	1	ENST00000324856.7:c.2402del	p.Gly801ValfsTer32	p.G801Vfs*32	ENST00000324856	NM_006015.4	799	caG/ca	7/20	1	2	FACETS	0.806	0.716	0.902	0.806	0.716	0.902	CLONAL	1	TRUE	1	0.469501661430774	2		435	449	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	51	202	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	1	2	FACETS	0.811	0.695	0.936	0.811	0.695	0.936	CLONAL	1	TRUE	1	0.469501661430774	2		202	268	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821594	72821596	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	rs374416547	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	13	92	1	ENST00000268489.5:c.10579_10581del	p.Gly3527del	p.G3527del	ENST00000268489	NM_006885.3	3527	GGC/-	10/10	1	2	FACETS	0.583	0.421	0.775	0.583	0.421	0.775	SUBCLONAL	1	TRUE	1	0.469501661430774	2		93	95	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	83	300	2	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	0.469501661430774	3	FACETS	0.979	0.868	1	0.489	0.434	0.549	CLONAL	1	TRUE	1	0.469501661430774	3		302	446	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	37	354	0	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	0.364	0.3	0.436	0.364	0.3	0.436	SUBCLONAL	1	TRUE	1	0.469501661430774	2		354	433	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921737	111921737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1170116948	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	77	221	0	ENST00000393256.3:c.526G>A	p.Glu176Lys	p.E176K	ENST00000393256	NM_006538.4	176	Gaa/Aaa	4/4	1	2	FACETS	0.877	0.775	0.985	0.877	0.775	0.985	CLONAL	1	TRUE	1	0.469501661430774	2		221	374	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461543	138461543	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	100	332	1	ENST00000289153.2:c.478del	p.Ile160SerfsTer13	p.I160Sfs*13	ENST00000289153	NM_006219.2	160	Atc/tc	3/22	1	2	FACETS	0.908	0.815	1	0.908	0.815	1	CLONAL	1	TRUE	1	0.469501661430774	2		333	469	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	47	294	0	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	1	2	FACETS	0.52	0.44	0.608	0.52	0.44	0.608	SUBCLONAL	1	TRUE	1	0.469501661430774	2		294	385	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	93	323	2	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.923	0.826	1	0.923	0.826	1	CLONAL	1	TRUE	1	0.469501661430774	2		325	429	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934243	49934243	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1407832113	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	61	505	5	ENST00000296474.3:c.2264del	p.Gly755ValfsTer19	p.G755Vfs*19	ENST00000296474	NM_002447.2	755	gGt/gt	8/20	0.431839709947084	2	FACETS	0.534	0.461	0.612	0.267	0.23	0.306	SUBCLONAL	1	TRUE	0	0.469501661430774	2		510	487	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	33	305	0	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	0.465	0.38	0.561	0.465	0.38	0.561	SUBCLONAL	1	TRUE	1	0.469501661430774	2		305	302	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120031	70120031	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	13	58	0	ENST00000245479.2:c.1037del	p.Pro346ArgfsTer37	p.P346Rfs*37	ENST00000245479	NM_000346.3	345	Ccc/cc	3/3	1	2	FACETS	0.814	0.593	1	0.814	0.593	1	CLONAL	1	TRUE	1	0.469501661430774	2		58	68	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14026116	14026116	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	21	178	0	ENST00000311895.7:c.1081del	p.Met361TrpfsTer15	p.M361Wfs*15	ENST00000311895	NM_005236.2	359	gAa/ga	6/11	1	2	FACETS	0.333	0.256	0.421	0.333	0.256	0.421	SUBCLONAL	1	TRUE	1	0.469501661430774	2		178	269	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140870	37140870	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	44	391	0	ENST00000373509.5:c.706G>A	p.Val236Met	p.V236M	ENST00000373509	NM_002648.3	236	Gtg/Atg	5/6	1	2	FACETS	0.442	0.371	0.521	0.442	0.371	0.521	SUBCLONAL	1	TRUE	1	0.469501661430774	2		391	424	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910684	29910684	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs41542016	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	130	835	0	ENST00000376809.5:c.224G>A	p.Trp75Ter	p.W75*	ENST00000376809	NM_002116.7	75	tGg/tAg	2/8	1	2	FACETS	0.69	0.626	0.758	0.69	0.626	0.758	SUBCLONAL	1	TRUE	1	0.469501661430774	2		835	802	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	82	698	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.75	0.663	0.841	0.75	0.663	0.841	SUBCLONAL	1	TRUE	1	0.469501661430774	2		699	466	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	216	764	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.759	0.71	0.809	1	0.992	1	SUBCLONAL	2	TRUE	1	0.469501661430774	2		770	606	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539104	23539104	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	72	367	0	ENST00000380871.4:c.335C>T	p.Ala112Val	p.A112V	ENST00000380871	NM_006167.3	112	gCc/gTc	2/2	1	2	FACETS	0.786	0.691	0.889	0.786	0.691	0.889	SUBCLONAL	1	TRUE	1	0.469501661430774	2		367	390	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56811497	56811497	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1567818564	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	80	258	0	ENST00000337432.4:c.1045A>G	p.Thr349Ala	p.T349A	ENST00000337432	NM_058216.2	349	Act/Gct	9/9	1	2	FACETS	0.881	0.78	0.987	0.881	0.78	0.987	CLONAL	1	TRUE	1	0.469501661430774	2		258	387	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352784	70352784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1369442321	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	124	253	0	ENST00000374080.3:c.4505C>T	p.Ser1502Phe	p.S1502F	ENST00000374080		1502	tCc/tTc	32/45	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.469501661430774	1		253	280	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	213	578	1	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	0.412088160087611	3	FACETS	0.906	0.847	0.967	0.906	0.847	0.967	CLONAL	2	TRUE	1	0.469501661430774	3		579	618	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412647	63412648	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	84	221	0	ENST00000330258.3:c.519dup	p.Ser174Ter	p.S174*	ENST00000330258	NM_152424.3	173	-/T	2/2	1	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.469501661430774	1		221	248	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883774	37883774	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	132	627	2	ENST00000269571.5:c.3391del	p.Leu1131Ter	p.L1131*	ENST00000269571		1129	gCc/gc	26/27	1	2	FACETS	0.891	0.811	0.975	0.891	0.811	0.975	CLONAL	1	TRUE	1	0.469501661430774	2		629	631	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324596	31324596	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs778050851	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	69	401	1	ENST00000412585.2:c.212C>A	p.Pro71Gln	p.P71Q	ENST00000412585	NM_005514.6	71	cCg/cAg	2/8	1	2	FACETS	0.728	0.636	0.825	0.728	0.636	0.825	SUBCLONAL	1	TRUE	1	0.469501661430774	2		402	404	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1620979	1620979	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1329397192	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	83	697	1	ENST00000344749.5:c.1081del	p.Gln361ArgfsTer33	p.Q361Rfs*33	ENST00000344749	NM_001136139.2	361	Cag/ag	13/19	1	2	FACETS	0.507	0.447	0.571	0.507	0.447	0.571	SUBCLONAL	1	TRUE	1	0.469501661430774	2		698	698	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322882	31322882	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1476457470	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	51	419	0	ENST00000412585.2:c.1012+2T>C		p.X338_splice	ENST00000412585	NM_005514.6	338			1	2	FACETS	0.499	0.425	0.581	0.499	0.425	0.581	SUBCLONAL	1	TRUE	1	0.469501661430774	2		419	435	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654615	67654615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	81	281	0	ENST00000264010.4:c.1102C>T	p.Arg368Cys	p.R368C	ENST00000264010	NM_006565.3	368	Cgt/Tgt	6/12	1	2	FACETS	0.808	0.715	0.907	0.808	0.715	0.907	CLONAL	1	TRUE	1	0.469501661430774	2		281	427	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526271	189526271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	86	329	3	ENST00000264731.3:c.535G>A	p.Val179Met	p.V179M	ENST00000264731	NM_003722.4	179	Gtg/Atg	4/14	1	2	FACETS	0.905	0.805	1	0.905	0.805	1	CLONAL	1	TRUE	1	0.469501661430774	2		332	405	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347111	347111	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	148	604	0	ENST00000262320.3:c.1900C>T	p.Gln634Ter	p.Q634*	ENST00000262320	NM_003502.3	634	Cag/Tag	7/11	1	2	FACETS	0.924	0.846	1	0.924	0.846	1	CLONAL	1	TRUE	1	0.469501661430774	2		604	682	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594228	55594228	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	55	259	0	ENST00000288135.5:c.1931T>C	p.Leu644Pro	p.L644P	ENST00000288135	NM_000222.2	644	cTg/cCg	13/21	1	2	FACETS	0.861	0.743	0.988	0.861	0.743	0.988	CLONAL	1	TRUE	1	0.469501661430774	2		259	272	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118901	70118901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	139	550	0	ENST00000245479.2:c.473C>T	p.Ala158Val	p.A158V	ENST00000245479	NM_000346.3	158	gCg/gTg	2/3	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.469501661430774	2		550	554	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784041	9784041	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752328071	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	106	486	0	ENST00000377346.4:c.2609G>A	p.Arg870Gln	p.R870Q	ENST00000377346	NM_005026.3	870	cGa/cAa	21/24	1	2	FACETS	0.905	0.815	0.999	0.905	0.815	0.999	CLONAL	1	TRUE	1	0.469501661430774	2		486	499	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46736401	46736401	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	84	356	0	ENST00000371975.4:c.1113G>T	p.Glu371Asp	p.E371D	ENST00000371975	NM_003579.3	371	gaG/gaT	10/18	1	2	FACETS	0.842	0.747	0.942	0.842	0.747	0.942	CLONAL	1	TRUE	1	0.469501661430774	2		356	425	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980427	201980427	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	96	462	0	ENST00000359651.3:c.163G>T	p.Glu55Ter	p.E55*	ENST00000359651		55	Gag/Tag	1/8	1	2	FACETS	0.868	0.777	0.964	0.868	0.777	0.964	CLONAL	1	TRUE	1	0.469501661430774	2		462	471	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567709	226567709	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	21	415	0	ENST00000366794.5:c.1457A>C	p.Lys486Thr	p.K486T	ENST00000366794	NM_001618.3	486	aAg/aCg	10/23	1	2	FACETS	0.216	0.166	0.275	0.216	0.166	0.275	SUBCLONAL	1	TRUE	1	0.469501661430774	2		415	414	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659802	88659802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	77	296	0	ENST00000372037.3:c.449G>A	p.Ser150Asn	p.S150N	ENST00000372037	NM_004329.2	150	aGc/aAc	7/13	1	2	FACETS	0.71	0.625	0.8	0.71	0.625	0.8	SUBCLONAL	1	TRUE	1	0.469501661430774	2		296	462	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14317322	14317322	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782597266	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	74	257	2	ENST00000256196.4:c.188G>A	p.Arg63Gln	p.R63Q	ENST00000256196		63	cGg/cAg	2/6	1	2	FACETS	0.778	0.685	0.878	0.778	0.685	0.878	SUBCLONAL	1	TRUE	1	0.469501661430774	2		259	405	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741603	17741603	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749172312	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	25	338	0	ENST00000250003.3:c.274C>T	p.Arg92Cys	p.R92C	ENST00000250003	NM_002478.4	92	Cgc/Tgc	1/3	1	2	FACETS	0.336	0.265	0.418	0.336	0.265	0.418	SUBCLONAL	1	TRUE	1	0.469501661430774	2		338	317	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200258	67200258	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767094407	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	48	497	0	ENST00000312629.5:c.566G>A	p.Gly189Asp	p.G189D	ENST00000312629	NM_003952.2	189	gGc/gAc	7/15	1	2	FACETS	0.358	0.302	0.42	0.358	0.302	0.42	SUBCLONAL	1	TRUE	1	0.469501661430774	2		497	571	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433980	49433980	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	131	596	0	ENST00000301067.7:c.7573G>T	p.Gly2525Cys	p.G2525C	ENST00000301067	NM_003482.3	2525	Ggt/Tgt	31/54	0.412088160087611	3	FACETS	1	0.918	1	0.505	0.459	0.553	CLONAL	1	TRUE	1	0.469501661430774	3		596	682	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779515	3779515	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	155	721	0	ENST00000262367.5:c.5533A>G	p.Asn1845Asp	p.N1845D	ENST00000262367	NM_004380.2	1845	Aac/Gac	31/31	1	2	FACETS	0.841	0.771	0.914	0.841	0.771	0.914	CLONAL	1	TRUE	1	0.469501661430774	2		721	785	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56852610	56852610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764790250	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	89	343	0	ENST00000308159.5:c.524G>A	p.Arg175Gln	p.R175Q	ENST00000308159	NM_014669.4	175	cGa/cAa	6/22	1	2	FACETS	0.788	0.702	0.88	0.788	0.702	0.88	SUBCLONAL	1	TRUE	1	0.469501661430774	2		343	481	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829269	72829269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200921039	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	55	527	0	ENST00000268489.5:c.7312G>A	p.Ala2438Thr	p.A2438T	ENST00000268489	NM_006885.3	2438	Gca/Aca	9/10	1	2	FACETS	0.444	0.38	0.514	0.444	0.38	0.514	SUBCLONAL	1	TRUE	1	0.469501661430774	2		527	528	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217646	7217647	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	67	310	0	ENST00000380728.2:c.280_281del	p.Leu94ThrfsTer2	p.L94Tfs*2	ENST00000380728		94	TTa/a	4/11	1	2	FACETS	0.739	0.646	0.84	0.739	0.646	0.84	SUBCLONAL	1	TRUE	1	0.469501661430774	2		310	386	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676297	37676297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752787823	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	119	400	0	ENST00000447079.4:c.3052G>A	p.Asp1018Asn	p.D1018N	ENST00000447079	NM_015083.1	1018	Gac/Aac	11/14	1	2	FACETS	0.883	0.8	0.97	0.883	0.8	0.97	CLONAL	1	TRUE	1	0.469501661430774	2		400	574	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40477012	40477012	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	75	414	0	ENST00000264657.5:c.1433T>G	p.Leu478Arg	p.L478R	ENST00000264657	NM_139276.2	478	cTg/cGg	16/24	1	2	FACETS	0.718	0.631	0.81	0.718	0.631	0.81	SUBCLONAL	1	TRUE	1	0.469501661430774	2		414	445	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41228547	41228547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	110	413	0	ENST00000357654.3:c.4442C>T	p.Ala1481Val	p.A1481V	ENST00000357654	NM_007294.3	1481	gCa/gTa	13/23	1	2	FACETS	0.828	0.746	0.914	0.828	0.746	0.914	CLONAL	1	TRUE	1	0.469501661430774	2		413	566	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246874	41246874	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567802483	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	45	197	0	ENST00000357654.3:c.674C>T	p.Ala225Val	p.A225V	ENST00000357654	NM_007294.3	225	gCt/gTt	10/23	1	2	FACETS	0.826	0.701	0.962	0.826	0.701	0.962	CLONAL	1	TRUE	1	0.469501661430774	2		197	232	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211194	2211194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769199900	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	114	584	0	ENST00000398665.3:c.1448C>T	p.Ala483Val	p.A483V	ENST00000398665	NM_032482.2	483	gCg/gTg	15/28	1	2	FACETS	0.824	0.744	0.909	0.824	0.744	0.909	CLONAL	1	TRUE	1	0.469501661430774	2		584	589	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291625	15291625	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	113	624	0	ENST00000263388.2:c.3009G>A	p.Trp1003Ter	p.W1003*	ENST00000263388	NM_000435.2	1003	tgG/tgA	19/33	1	2	FACETS	0.747	0.674	0.825	0.747	0.674	0.825	SUBCLONAL	1	TRUE	1	0.469501661430774	2		624	644	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943697	17943697	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1463023314	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	118	535	0	ENST00000458235.1:c.2392C>G	p.Pro798Ala	p.P798A	ENST00000458235	NM_000215.3	798	Cct/Gct	18/24	1	2	FACETS	0.934	0.846	1	0.934	0.846	1	CLONAL	1	TRUE	1	0.469501661430774	2		535	538	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279544	18279544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	87	442	2	ENST00000222254.8:c.1817C>T	p.Ala606Val	p.A606V	ENST00000222254	NM_005027.3	606	gCa/gTa	15/16	1	2	FACETS	0.862	0.767	0.962	0.862	0.767	0.962	CLONAL	1	TRUE	1	0.469501661430774	2		444	430	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905567	50905567	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	125	639	0	ENST00000440232.2:c.695G>T	p.Arg232Leu	p.R232L	ENST00000440232	NM_002691.3	232	cGt/cTt	6/27	1	2	FACETS	0.859	0.779	0.942	0.859	0.779	0.942	CLONAL	1	TRUE	1	0.469501661430774	2		639	620	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026161	48026161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	49	251	0	ENST00000234420.5:c.1039G>A	p.Glu347Lys	p.E347K	ENST00000234420	NM_000179.2	347	Gaa/Aaa	4/10	1	2	FACETS	0.73	0.622	0.847	0.73	0.622	0.847	SUBCLONAL	1	TRUE	1	0.469501661430774	2		251	286	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99180068	99180068	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	93	445	0	ENST00000074304.5:c.2011C>T	p.Gln671Ter	p.Q671*	ENST00000074304	NM_001134224.1	671	Cag/Tag	19/26	1	2	FACETS	0.928	0.83	1	0.928	0.83	1	CLONAL	1	TRUE	1	0.469501661430774	2		445	427	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182583	99182583	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	45	375	0	ENST00000074304.5:c.2386C>T	p.Pro796Ser	p.P796S	ENST00000074304	NM_001134224.1	796	Ccc/Tcc	22/26	1	2	FACETS	0.517	0.435	0.606	0.517	0.435	0.606	SUBCLONAL	1	TRUE	1	0.469501661430774	2		375	371	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790170	40790170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373191879	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	73	289	0	ENST00000373198.4:c.2561G>A	p.Arg854His	p.R854H	ENST00000373198	NM_133170.3	854	cGc/cAc	18/32	1	2	FACETS	0.945	0.833	1	0.945	0.833	1	CLONAL	1	TRUE	1	0.469501661430774	2		289	329	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713309	30713309	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	63	279	0	ENST00000295754.5:c.634T>C	p.Phe212Leu	p.F212L	ENST00000295754	NM_003242.5	212	Ttc/Ctc	4/7	0.431839709947084	2	FACETS	0.792	0.689	0.902	0.396	0.344	0.451	CLONAL	1	TRUE	0	0.469501661430774	2		279	339	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196325	106196325	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	20	163	0	ENST00000380013.4:c.4658A>G	p.Gln1553Arg	p.Q1553R	ENST00000380013	NM_001127208.2	1553	cAg/cGg	11/11	1	2	FACETS	0.43	0.33	0.546	0.43	0.33	0.546	SUBCLONAL	1	TRUE	1	0.469501661430774	2		163	198	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627885	187627885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752785176	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	130	489	1	ENST00000441802.2:c.3097G>A	p.Val1033Met	p.V1033M	ENST00000441802	NM_005245.3	1033	Gtg/Atg	2/27	1	2	FACETS	0.952	0.866	1	0.952	0.866	1	CLONAL	1	TRUE	1	0.469501661430774	2		490	582	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202370	138202370	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867951430	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	55	477	0	ENST00000237289.4:c.2287C>T	p.Arg763Trp	p.R763W	ENST00000237289	NM_001270507.1	763	Cgg/Tgg	9/9	1	2	FACETS	0.503	0.431	0.581	0.503	0.431	0.581	SUBCLONAL	1	TRUE	1	0.469501661430774	2		477	466	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205354	38205356	+	inframe_deletion	In_Frame_Del	DEL	ATA	ATA	-	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	123	559	0	ENST00000317025.8:c.334_336del	p.Tyr112del	p.Y112del	ENST00000317025	NM_023034.1	112	TAT/-	2/24	1	2	FACETS	0.825	0.748	0.906	0.825	0.748	0.906	CLONAL	1	TRUE	1	0.469501661430774	2		559	635	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551418	141551418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	86	491	1	ENST00000220592.5:c.1879G>A	p.Ala627Thr	p.A627T	ENST00000220592	NM_012154.3	627	Gcc/Acc	15/19	1	2	FACETS	0.796	0.707	0.891	0.796	0.707	0.891	SUBCLONAL	1	TRUE	1	0.469501661430774	2		492	460	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741463	145741463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757988816	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	159	636	1	ENST00000428558.2:c.1040G>A	p.Arg347His	p.R347H	ENST00000428558	NM_004260.3	347	cGc/cAc	5/22	1	2	FACETS	0.982	0.902	1	0.982	0.902	1	CLONAL	1	TRUE	1	0.469501661430774	2		637	690	SUCCESS
AR	367	MSKCC	GRCh37	X	66765110	66765111	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0037875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	79	252	0	ENST00000374690.3:c.125dup	p.Glu43ArgfsTer41	p.E43Rfs*41	ENST00000374690	NM_000044.3	41	cac/caCc	1/8	1	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.469501661430774	1		252	211	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	117	503	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.384575544314141	3	FACETS	0.887	0.807	0.97	0.887	0.807	0.97	CLONAL	2	TRUE	1	0.385630803373961	3		503	408	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0037877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	193	473	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	0.371709358696698	4	FACETS	0.836	0.774	0.899	0.836	0.774	0.899	CLONAL	2	TRUE	2	0.385630803373961	4		473	830	SUCCESS
APC	324	MSKCC	GRCh37	5	112175651	112175651	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	167	246	0	ENST00000257430.4:c.4364del	p.Asn1455IlefsTer18	p.N1455Ifs*18	ENST00000257430	NM_000038.5	1454	Aaa/aa	16/16	0.385630803373961	3	FACETS	0.883	0.822	0.945	0.883	0.822	0.945	CLONAL	3	TRUE	0	0.385630803373961	3		246	390	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646335	3646335	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	289	721	0	ENST00000294008.3:c.1743G>T	p.Glu581Asp	p.E581D	ENST00000294008	NM_032444.2	581	gaG/gaT	8/15	0.384575544314141	3	FACETS	0.961	0.906	1	0.961	0.906	1	CLONAL	2	TRUE	1	0.385630803373961	3		721	930	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116189	209116189	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	57	288	0	ENST00000345146.2:c.87A>T	p.Lys29Asn	p.K29N	ENST00000345146	NM_005896.2	29	aaA/aaT	3/10	0.371709358696698	4	FACETS	0.877	0.754	1	0.439	0.377	0.506	CLONAL	1	TRUE	2	0.385630803373961	4		288	467	SUCCESS
APC	324	MSKCC	GRCh37	5	112154842	112154842	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	101	357	0	ENST00000257430.4:c.1115del	p.Asn372IlefsTer82	p.N372Ifs*82	ENST00000257430	NM_000038.5	371	ggA/gg	10/16	0.385630803373961	3	FACETS	1	0.897	1	0.334	0.299	0.371	CLONAL	1	TRUE	0	0.385630803373961	3		357	624	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0037885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	293	767	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.926987793776471	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.926987793776471	1		770	306	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148513811	148513812	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0037885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	298	278	0	ENST00000320356.2:c.1469_1470del	p.Val490GlyfsTer30	p.V490Gfs*30	ENST00000320356	NM_004456.4	490	gTG/g	12/20	0.926987793776471	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.926987793776471	1		278	317	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	40	503	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	0.156984586077223	2		503	367	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0037886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	38	388	2	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.156984586077223	2		390	371	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711883	89711884	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0037886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	15	342	0	ENST00000371953.3:c.502_503del	p.Ile168SerfsTer11	p.I168Sfs*11	ENST00000371953	NM_000314.4	167	acTAtt/actt	6/9	0.156984586077223	2	FACETS	0.671	0.49	0.888	0.335	0.245	0.444	SUBCLONAL	1	TRUE	0	0.156984586077223	2		342	285	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274911	41274911	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs868651538	NA	P-0037886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	35	331	0	ENST00000349496.5:c.1161T>A	p.Asn387Lys	p.N387K	ENST00000349496	NM_001904.3	387	aaT/aaA	8/15	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.156984586077223	2		331	398	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692886	89692886	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121909223	NA	P-0037886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	75	273	0	ENST00000371953.3:c.370T>G	p.Cys124Gly	p.C124G	ENST00000371953	NM_000314.4	124	Tgt/Ggt	5/9	0.156984586077223	2	FACETS	0.888	0.788	0.993	1	0.982	1	CLONAL	4	TRUE	0	0.156984586077223	2		273	269	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262102	10262102	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	57	471	0	ENST00000340748.4:c.2189G>T	p.Arg730Leu	p.R730L	ENST00000340748		730	cGc/cTc	23/40	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.156984586077223	2		471	654	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	115	482	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.826	0.75	0.905	1	0.987	1	CLONAL	2	TRUE	1	0.345472113564869	2		482	403	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	118	520	4	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.8	0.727	0.876	1	0.987	1	SUBCLONAL	2	TRUE	1	0.345472113564869	2		524	427	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	134	698	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.825	0.755	0.898	1	0.989	1	CLONAL	2	TRUE	1	0.345472113564869	2		699	470	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	189	764	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.857	0.796	0.92	1	0.992	1	CLONAL	2	TRUE	1	0.345472113564869	2		770	638	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	288	578	1	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	0.248049891071653	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	1	0.345472113564869	4		579	672	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	68	355	2	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.854	0.745	0.971	0.854	0.745	0.971	CLONAL	1	TRUE	1	0.345472113564869	2		357	461	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097751	27097751	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	144	424	0	ENST00000324856.7:c.3344del	p.Pro1115GlnfsTer46	p.P1115Qfs*46	ENST00000324856	NM_006015.4	1114	Ccc/cc	12/20	1	2	FACETS	0.847	0.778	0.919	1	0.99	1	CLONAL	2	TRUE	1	0.345472113564869	2		424	492	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231357	5231357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	143	553	0	ENST00000357368.4:c.2119G>A	p.Glu707Lys	p.E707K	ENST00000357368	NM_002850.3	707	Gag/Aag	14/38	1	2	FACETS	0.796	0.73	0.864	1	0.989	1	SUBCLONAL	2	TRUE	1	0.345472113564869	2		553	520	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332273	70332273	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	128	357	0	ENST00000373644.4:c.184del	p.Thr62GlnfsTer13	p.T62Qfs*13	ENST00000373644	NM_030625.2	60	Aaa/aa	2/12	1	2	FACETS	0.827	0.755	0.901	1	0.988	1	CLONAL	2	TRUE	1	0.345472113564869	2		357	448	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744385	41744385	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	31	512	0	ENST00000301178.4:c.1010del	p.Pro337LeufsTer29	p.P337Lfs*29	ENST00000301178	NM_021913.4	335	ggC/gg	8/20	1	2	FACETS	0.411	0.332	0.5	0.411	0.332	0.5	SUBCLONAL	1	TRUE	1	0.345472113564869	2		512	437	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	155	327	6	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	0.848	0.781	0.917	1	0.991	1	CLONAL	2	TRUE	1	0.345472113564869	2		333	529	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	121	564	0	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	0.345472113564869	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.345472113564869	1		564	413	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533939	63533940	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs771001164	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	75	393	0	ENST00000307078.5:c.1214_1215del	p.Glu405GlyfsTer56	p.E405Gfs*56	ENST00000307078	NM_004655.3	405	gAG/g	6/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.345472113564869	2		393	347	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568865	212568866	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	42	394	0	ENST00000342788.4:c.1252dup	p.Ser418PhefsTer2	p.S418Ffs*2	ENST00000342788	NM_005235.2	418	tct/tTct	11/28	1	2	FACETS	0.668	0.559	0.788	0.668	0.559	0.788	SUBCLONAL	1	TRUE	1	0.345472113564869	2		394	364	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390736	139390736	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	161	665	0	ENST00000277541.6:c.7455del	p.Ser2486ArgfsTer103	p.S2486Rfs*103	ENST00000277541	NM_017617.3	2485	ccC/cc	34/34	0.345472113564869	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.345472113564869	1		665	674	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909851	100909851	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	33	172	0	ENST00000325455.5:c.2798del	p.Lys933SerfsTer11	p.K933Sfs*11	ENST00000325455	NM_001202474.3	933	aAg/ag	8/8	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.345472113564869	2		172	169	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384650	31384651	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs756395138	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	256	538	0	ENST00000328111.2:c.1359dup	p.Leu454AlafsTer11	p.L454Afs*11	ENST00000328111	NM_006892.3	451	gag/gaGg	13/23	0.345472113564869	3	FACETS	0.858	0.808	0.909	1	0.991	1	CLONAL	3	TRUE	1	0.345472113564869	3		538	675	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29083899	29083900	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	31	141	0	ENST00000328354.6:c.1617_1618del	p.Ala540CysfsTer9	p.A540Cfs*9	ENST00000328354	NM_007194.3	539	tgTGct/tgct	15/15	1	2	FACETS	0.945	0.771	1	0.945	0.771	1	CLONAL	1	TRUE	1	0.345472113564869	2		141	190	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538941	187538941	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs113224498	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	120	343	1	ENST00000441802.2:c.8799del	p.Gly2934ValfsTer3	p.G2934Vfs*3	ENST00000441802	NM_005245.3	2933	caA/ca	10/27	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.345472113564869	2		344	481	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	84	249	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	0.871	0.779	0.967	1	0.984	1	CLONAL	2	TRUE	1	0.345472113564869	2		249	279	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212450	5212450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196839847	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	156	566	0	ENST00000357368.4:c.4667C>T	p.Pro1556Leu	p.P1556L	ENST00000357368	NM_002850.3	1556	cCg/cTg	31/38	1	2	FACETS	0.846	0.779	0.914	1	0.991	1	CLONAL	2	TRUE	1	0.345472113564869	2		566	534	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8525030	8525030	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	79	237	0	ENST00000356435.5:c.574C>A	p.Leu192Ile	p.L192I	ENST00000356435		192	Ctt/Att	7/35	0.345472113564869	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.345472113564869	1		237	285	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492812	56492812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	130	424	1	ENST00000407977.2:c.127G>A	p.Glu43Lys	p.E43K	ENST00000407977		43	Gaa/Aaa	2/10	1	2	FACETS	0.791	0.722	0.862	1	0.988	1	SUBCLONAL	2	TRUE	1	0.345472113564869	2		425	476	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349688	70349688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	102	432	0	ENST00000374080.3:c.3850C>T	p.Arg1284Cys	p.R1284C	ENST00000374080		1284	Cgc/Tgc	27/45	0.345472113564869	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.345472113564869	1		432	425	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435162	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	137	612	0	ENST00000407977.2:c.1975_1976del	p.Gly659SerfsTer87	p.G659Sfs*87	ENST00000407977		659	GGt/t	9/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.345472113564869	2		612	566	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295278	1295278	+	upstream_gene_variant	5'Flank	SNP	C	C	T	rs914835735	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	99	186	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.974	1	1	0.99	1	CLONAL	2	TRUE	1	0.345472113564869	2		186	239	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497542	125497542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753180922	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	94	227	0	ENST00000428830.2:c.106G>A	p.Ala36Thr	p.A36T	ENST00000428830	NM_001114121.2	36	Gca/Aca	3/14	1	2	FACETS	0.972	0.877	1	1	0.987	1	CLONAL	2	TRUE	1	0.345472113564869	2		227	280	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939453	36939453	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	179	572	0	ENST00000361632.4:c.397A>G	p.Met133Val	p.M133V	ENST00000361632		133	Atg/Gtg	4/16	1	2	FACETS	0.816	0.756	0.878	1	0.991	1	CLONAL	2	TRUE	1	0.345472113564869	2		572	635	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695886	117695886	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	195	525	0	ENST00000369458.3:c.551A>G	p.Gln184Arg	p.Q184R	ENST00000369458	NM_024626.3	184	cAa/cGa	4/6	1	2	FACETS	0.833	0.774	0.893	1	0.992	1	CLONAL	2	TRUE	1	0.345472113564869	2		525	678	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406388	70406388	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs766616425	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	218	546	0	ENST00000373644.4:c.3902A>G	p.Gln1301Arg	p.Q1301R	ENST00000373644	NM_030625.2	1301	cAg/cGg	4/12	1	2	FACETS	0.92	0.86	0.982	1	0.994	1	CLONAL	2	TRUE	1	0.345472113564869	2		546	686	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456675	32456675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	105	216	0	ENST00000332351.3:c.217G>A	p.Val73Met	p.V73M	ENST00000332351	NM_024426.4	73	Gtg/Atg	1/10	1	2	FACETS	0.91	0.824	0.998	1	0.988	1	CLONAL	2	TRUE	1	0.345472113564869	2		216	334	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203653	94203653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	70	264	0	ENST00000323929.3:c.1001G>A	p.Ser334Asn	p.S334N	ENST00000323929	NM_005591.3	334	aGc/aAc	9/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.345472113564869	2		264	275	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390432	118390432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781945281	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	170	401	0	ENST00000534358.1:c.11246G>A	p.Arg3749His	p.R3749H	ENST00000534358	NM_005933.3	3749	cGt/cAt	32/36	1	2	FACETS	0.905	0.837	0.974	1	0.992	1	CLONAL	2	TRUE	1	0.345472113564869	2		401	544	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022738	12022738	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772622167	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	45	473	0	ENST00000396373.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000396373	NM_001987.4	282	Cgg/Tgg	5/8	0.345472113564869	5	FACETS	0.879	0.739	1	0.293	0.246	0.345	CLONAL	1	TRUE	2	0.345472113564869	5		473	450	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426021	49426022	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	311	616	0	ENST00000301067.7:c.12466dup	p.Gln4156ProfsTer12	p.Q4156Pfs*12	ENST00000301067	NM_003482.3	4156	caa/cCaa	39/54	0.248049891071653	4	FACETS	0.979	0.927	1	0.979	0.927	1	CLONAL	3	TRUE	1	0.345472113564869	4		616	825	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30069016	30069016	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	107	356	0	ENST00000331968.5:c.1913A>T	p.His638Leu	p.H638L	ENST00000331968	NM_002742.2	638	cAt/cTt	14/18	1	2	FACETS	0.844	0.764	0.927	1	0.987	1	CLONAL	2	TRUE	1	0.345472113564869	2		356	367	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041485	42041485	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	169	455	0	ENST00000219905.7:c.5680del	p.Val1894CysfsTer7	p.V1894Cfs*7	ENST00000219905	NM_001164273.1	1894	Gtg/tg	17/24	1	2	FACETS	0.855	0.791	0.922	1	0.991	1	CLONAL	2	TRUE	1	0.345472113564869	2		455	572	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500539	99500539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	138	543	0	ENST00000268035.6:c.3972G>T	p.Lys1324Asn	p.K1324N	ENST00000268035	NM_000875.3	1324	aaG/aaT	21/21	1	2	FACETS	0.876	0.803	0.951	1	0.99	1	CLONAL	2	TRUE	1	0.345472113564869	2		543	456	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50821755	50821755	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	65	268	0	ENST00000398568.2:c.2095del	p.Ile699Ter	p.I699*	ENST00000398568	NM_001042412.1	697	ctA/ct	13/18	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.345472113564869	2		268	338	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827267	72827267	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	115	505	0	ENST00000268489.5:c.9314C>A	p.Pro3105His	p.P3105H	ENST00000268489	NM_006885.3	3105	cCt/cAt	9/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.345472113564869	2		505	539	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376191	15376191	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	160	515	0	ENST00000263377.2:c.823A>G	p.Ile275Val	p.I275V	ENST00000263377	NM_058243.2	275	Atc/Gtc	5/20	1	2	FACETS	0.896	0.827	0.967	1	0.991	1	CLONAL	2	TRUE	1	0.345472113564869	2		515	517	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906768	50906768	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373046355	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	166	554	0	ENST00000440232.2:c.1156C>T	p.Arg386Cys	p.R386C	ENST00000440232	NM_002691.3	386	Cgt/Tgt	10/27	1	2	FACETS	0.819	0.756	0.883	1	0.991	1	CLONAL	2	TRUE	1	0.345472113564869	2		554	587	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978937	25978939	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	novel	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	111	346	0	ENST00000435504.4:c.984_986del	p.Asn329del	p.N329del	ENST00000435504		328	aaCAAt/aat	10/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.345472113564869	2		346	439	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62298880	62298880	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1309066366	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	83	550	0	ENST00000360203.5:c.673C>T	p.Pro225Ser	p.P225S	ENST00000360203	NM_001283009.1	225	Ccg/Tcg	8/35	0.345472113564869	3	FACETS	0.829	0.731	0.933	0.414	0.365	0.467	CLONAL	1	TRUE	1	0.345472113564869	3		550	680	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205208	128205208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867138640	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	121	470	0	ENST00000341105.2:c.233G>A	p.Arg78His	p.R78H	ENST00000341105	NM_032638.4	78	cGc/cAc	3/6	1	2	FACETS	0.785	0.714	0.859	1	0.987	1	SUBCLONAL	2	TRUE	1	0.345472113564869	2		470	446	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443296	187443296	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	70	215	0	ENST00000232014.4:c.1830A>T	p.Arg610Ser	p.R610S	ENST00000232014	NM_001130845.1	610	agA/agT	8/10	1	2	FACETS	0.82	0.725	0.921	1	0.979	1	CLONAL	2	TRUE	1	0.345472113564869	2		215	247	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526256	189526256	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	124	448	0	ENST00000264731.3:c.520C>T	p.Pro174Ser	p.P174S	ENST00000264731	NM_003722.4	174	Ccg/Tcg	4/14	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.345472113564869	2		448	515	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324680	31324681	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	43	112	0	ENST00000412585.2:c.127dup	p.Glu43GlyfsTer56	p.E43Gfs*56	ENST00000412585	NM_005514.6	43	gag/gGag	2/8	1	2	FACETS	1	0.926	1	1	0.98	1	CLONAL	3	TRUE	1	0.345472113564869	2		112	77	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547362	106547362	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	157	362	0	ENST00000369096.4:c.599A>G	p.Tyr200Cys	p.Y200C	ENST00000369096	NM_001198.3	200	tAt/tGt	4/7	1	2	FACETS	0.864	0.797	0.933	1	0.991	1	CLONAL	2	TRUE	1	0.345472113564869	2		362	526	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394364	162394364	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	104	304	0	ENST00000366898.1:c.704A>C	p.Asn235Thr	p.N235T	ENST00000366898	NM_004562.2	235	aAc/aCc	6/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.345472113564869	2		304	423	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509583	106509583	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749714535	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	123	520	0	ENST00000359195.3:c.1577C>T	p.Pro526Leu	p.P526L	ENST00000359195	NM_002649.2	526	cCg/cTg	2/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.345472113564869	2		520	491	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15826355	15826355	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	86	320	0	ENST00000307771.7:c.400-1G>T		p.X134_splice	ENST00000307771	NM_005089.3	134			0.345472113564869	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.345472113564869	1		320	390	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229291	123229291	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	52	213	0	ENST00000218089.9:c.3775G>T	p.Asp1259Tyr	p.D1259Y	ENST00000218089	NM_001042749.1	1259	Gat/Tat	34/35	0.345472113564869	1	FACETS	0.847	0.726	0.978	0.847	0.726	0.978	CLONAL	1	TRUE	0	0.345472113564869	1		213	294	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831385	72831386	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGC	rs759114423	NA	P-0037887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	16	316	0	ENST00000268489.5:c.5193_5195dup	p.Gln1741dup	p.Q1741dup	ENST00000268489	NM_006885.3	1741	caa/caGCAa	9/10	1	2	FACETS	0.377	0.278	0.494	0.377	0.278	0.494	SUBCLONAL	1	TRUE	1	0.345472113564869	2		316	246	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579393	7579394	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGGACAGAAGATGACAG	novel	NA	P-0037894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	139	690	0	ENST00000269305.4:c.277_293dup	p.Ser99CysfsTer30	p.S99Cfs*30	ENST00000269305	NM_001126112.2	98	cct/ccCTGTCATCTTCTGTCCCt	4/11	NA	2	FACETS	0.795	0.723	0.871			1	INDETERMINATE	1	TRUE	NA	0.359278067531203	2		690	973	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858201	9858201	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	61	277	0	ENST00000330684.3:c.3200G>C	p.Arg1067Pro	p.R1067P	ENST00000330684	NM_001134407.1	1067	cGg/cCg	13/13	1	2	FACETS	0.831	0.716	0.956	0.831	0.716	0.956	CLONAL	1	FALSE	1	0.211809628097465	2		277	693	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	43	262	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.959	0.814	1	0.959	0.814	1	CLONAL	1	TRUE	1	0.49	2		262	183	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667784	37667784	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	35	273	0	ENST00000447079.4:c.2669G>A	p.Arg890His	p.R890H	ENST00000447079	NM_015083.1	890	cGc/cAc	8/14	1	2	FACETS	0.916	0.762	1	0.916	0.762	1	CLONAL	1	TRUE	1	0.49	2		273	156	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	84	422	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.49	2		422	317	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	21	197	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.772	0.604	0.961	0.772	0.604	0.961	CLONAL	1	TRUE	1	0.49	2		197	111	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028657	12028657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	48	780	1	ENST00000353533.5:c.860G>A	p.Arg287His	p.R287H	ENST00000353533	NM_003010.3	287	cGc/cAc	8/11	1	2	FACETS	0.96	0.822	1	0.96	0.822	1	CLONAL	1	TRUE	1	0.49	2		781	204	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	28	559	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.922	0.749	1	0.922	0.749	1	CLONAL	1	TRUE	1	0.49	2		559	124	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979448	2979448	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	61	445	0	ENST00000396946.4:c.799C>A	p.Leu267Met	p.L267M	ENST00000396946	NM_032415.4	267	Ctg/Atg	6/25	1	2	FACETS	0.859	0.747	0.978	0.859	0.747	0.978	CLONAL	1	TRUE	1	0.49	2		445	290	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845433	156845433	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	60	605	0	ENST00000524377.1:c.1476G>T	p.Glu492Asp	p.E492D	ENST00000524377	NM_002529.3	492	gaG/gaT	12/17	1	2	FACETS	0.547	0.472	0.628	0.547	0.472	0.628	SUBCLONAL	1	TRUE	1	0.49	2		605	448	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606679	29606679	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs865931787	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	88	396	0	ENST00000389048.3:c.1201C>T	p.Arg401Ter	p.R401*	ENST00000389048	NM_004304.4	401	Cga/Tga	5/29	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.49	2		396	353	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86686647	86686647	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	11	169	0	ENST00000274376.6:c.3091G>T	p.Glu1031Ter	p.E1031*	ENST00000274376	NM_002890.2	1031	Gaa/Taa	25/25	1	2	FACETS	0.277	0.192	0.383	0.277	0.192	0.383	SUBCLONAL	1	TRUE	1	0.49	2		169	162	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224793	123224793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	13	162	0	ENST00000218089.9:c.3557G>A	p.Arg1186Gln	p.R1186Q	ENST00000218089	NM_001042749.1	1186	cGa/cAa	32/35	0.3	2	FACETS	0.411	0.295	0.551	0.206	0.147	0.276	SUBCLONAL	1	TRUE	0	0.49	2		162	129	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	112	693	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.49	2		693	377	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919203	178919203	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	10	166	0	ENST00000263967.3:c.688C>T	p.Arg230Ter	p.R230*	ENST00000263967	NM_006218.2	230	Cga/Tga	4/21	1	2	FACETS	0.408	0.279	0.568	0.408	0.279	0.568	SUBCLONAL	1	TRUE	1	0.49	2		166	100	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013719	12013719	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	40	309	0	ENST00000353533.5:c.661G>T	p.Glu221Ter	p.E221*	ENST00000353533	NM_003010.3	221	Gaa/Taa	6/11	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.49	2		309	162	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240785	55240785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1417155613	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	136	626	1	ENST00000275493.2:c.2029C>T	p.Arg677Cys	p.R677C	ENST00000275493	NM_005228.3	677	Cgc/Tgc	17/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.49	2		627	468	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141989	108141989	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	20	232	0	ENST00000278616.4:c.2933C>A	p.Ser978Tyr	p.S978Y	ENST00000278616	NM_000051.3	978	tCt/tAt	20/63	1	2	FACETS	0.492	0.379	0.622	0.492	0.379	0.622	SUBCLONAL	1	TRUE	1	0.49	2		232	166	SUCCESS
APC	324	MSKCC	GRCh37	5	112178000	112178000	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768922431	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	39	266	0	ENST00000257430.4:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000257430	NM_000038.5	2237	Cga/Tga	16/16	1	2	FACETS	0.92	0.773	1	0.92	0.773	1	CLONAL	1	TRUE	1	0.49	2		266	173	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525044	157525044	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	26	195	0	ENST00000346085.5:c.4939C>A	p.Leu1647Ile	p.L1647I	ENST00000346085	NM_020732.3	1647	Ctt/Att	19/20	0.163447526461599	3	FACETS	0.551	0.438	0.679	0.275	0.219	0.34	INDETERMINATE	1	TRUE	1	0.49	3		195	240	SUCCESS
APC	324	MSKCC	GRCh37	5	112175457	112175457	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	34	243	0	ENST00000257430.4:c.4166C>A	p.Ser1389Tyr	p.S1389Y	ENST00000257430	NM_000038.5	1389	tCt/tAt	16/16	1	2	FACETS	0.998	0.83	1	0.998	0.83	1	CLONAL	1	TRUE	1	0.49	2		243	139	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216568	108216568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs767845728	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	39	193	0	ENST00000278616.4:c.8517C>A	p.Phe2839Leu	p.F2839L	ENST00000278616	NM_000051.3	2839	ttC/ttA	58/63	1	2	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	TRUE	1	0.49	2		193	157	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209264	98209264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778630	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	107	500	1	ENST00000331920.6:c.4274C>T	p.Ser1425Leu	p.S1425L	ENST00000331920	NM_000264.3	1425	tCg/tTg	23/24	1	2	FACETS	0.973	0.878	1	0.973	0.878	1	CLONAL	1	TRUE	1	0.49	2		501	449	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622457	28622457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751562024	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	37	333	0	ENST00000241453.7:c.1160G>A	p.Arg387Gln	p.R387Q	ENST00000241453	NM_004119.2	387	cGa/cAa	9/24	1	2	FACETS	0.699	0.581	0.828	0.699	0.581	0.828	SUBCLONAL	1	TRUE	1	0.49	2		333	216	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	41	366	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.49	2		366	157	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693887	47693887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778523	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	23	207	0	ENST00000233146.2:c.1601G>A	p.Arg534His	p.R534H	ENST00000233146	NM_000251.2	534	cGt/cAt	10/16	1	2	FACETS	0.846	0.671	1	0.846	0.671	1	CLONAL	1	TRUE	1	0.49	2		207	111	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584684	187584684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149295542	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	36	341	1	ENST00000441802.2:c.3349G>A	p.Val1117Met	p.V1117M	ENST00000441802	NM_005245.3	1117	Gtg/Atg	3/27	1	2	FACETS	0.422	0.348	0.505	0.422	0.348	0.505	SUBCLONAL	1	TRUE	1	0.49	2		342	348	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	11	384	0	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	1	2	FACETS	0.159	0.109	0.221	0.159	0.109	0.221	SUBCLONAL	1	TRUE	1	0.49	2		384	283	SUCCESS
APC	324	MSKCC	GRCh37	5	112174119	112174119	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1554084512	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	31	240	0	ENST00000257430.4:c.2828C>A	p.Ser943Ter	p.S943*	ENST00000257430	NM_000038.5	943	tCa/tAa	16/16	1	2	FACETS	0.966	0.795	1	0.966	0.795	1	CLONAL	1	TRUE	1	0.49	2		240	131	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765576	41765576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763066660	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	29	516	1	ENST00000301178.4:c.2452G>A	p.Glu818Lys	p.E818K	ENST00000301178	NM_021913.4	818	Gaa/Aaa	20/20	1	2	FACETS	0.289	0.232	0.355	0.289	0.232	0.355	SUBCLONAL	1	TRUE	1	0.49	2		517	409	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482242	87482242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	57	434	0	ENST00000277120.3:c.1529C>T	p.Ser510Leu	p.S510L	ENST00000277120		510	tCg/tTg	14/19	1	2	FACETS	0.931	0.807	1	0.931	0.807	1	CLONAL	1	TRUE	1	0.49	2		434	250	SUCCESS
ATR	545	MSKCC	GRCh37	3	142168429	142168429	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	47	230	0	ENST00000350721.4:c.7777C>A	p.Leu2593Ile	p.L2593I	ENST00000350721	NM_001184.3	2593	Ctt/Att	47/47	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.49	2		230	178	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148513849	148513849	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	18	290	0	ENST00000320356.2:c.1432G>T	p.Glu478Ter	p.E478*	ENST00000320356	NM_004456.4	478	Gaa/Taa	12/20	1	2	FACETS	0.367	0.277	0.473	0.367	0.277	0.473	SUBCLONAL	1	TRUE	1	0.49	2		290	200	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232137	98232137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1382474804	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	14	301	0	ENST00000331920.6:c.1805G>A	p.Arg602Gln	p.R602Q	ENST00000331920	NM_000264.3	602	cGa/cAa	13/24	1	2	FACETS	0.316	0.229	0.42	0.316	0.229	0.42	SUBCLONAL	1	TRUE	1	0.49	2		301	181	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856181	111856181	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754838420	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	47	214	2	ENST00000341259.2:c.232G>A	p.Glu78Lys	p.E78K	ENST00000341259	NM_005475.2	78	Gag/Aag	2/8	0.163447526461599	3	FACETS	0.627	0.53	0.733	0.313	0.265	0.367	INDETERMINATE	1	TRUE	1	0.49	3		216	381	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542861	187542861	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1340793072	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	22	217	0	ENST00000441802.2:c.4879C>T	p.Arg1627Ter	p.R1627*	ENST00000441802	NM_005245.3	1627	Cga/Tga	10/27	1	2	FACETS	0.538	0.42	0.672	0.538	0.42	0.672	SUBCLONAL	1	TRUE	1	0.49	2		217	167	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604707	48604707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	15	301	0	ENST00000342988.3:c.1529G>A	p.Gly510Glu	p.G510E	ENST00000342988	NM_005359.5	510	gGa/gAa	12/12	1	2	FACETS	0.24	0.175	0.318	0.24	0.175	0.318	SUBCLONAL	1	TRUE	1	0.49	2		301	255	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649005	86649005	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	14	205	0	ENST00000274376.6:c.1285G>T	p.Glu429Ter	p.E429*	ENST00000274376	NM_002890.2	429	Gaa/Taa	9/25	1	2	FACETS	0.325	0.235	0.432	0.325	0.235	0.432	SUBCLONAL	1	TRUE	1	0.49	2		205	176	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160663	56160663	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558965285	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	52	288	0	ENST00000399503.3:c.937C>T	p.Arg313Trp	p.R313W	ENST00000399503	NM_005921.1	313	Cgg/Tgg	4/20	1	2	FACETS	0.789	0.677	0.909	0.789	0.677	0.909	CLONAL	1	TRUE	1	0.49	2		288	269	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346284	152346284	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs778698188	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	36	733	0	ENST00000359321.1:c.286C>A	p.Leu96Ile	p.L96I	ENST00000359321	NM_005431.1	96	Ctt/Att	3/3	1	2	FACETS	0.794	0.66	0.941	0.794	0.66	0.941	CLONAL	1	TRUE	1	0.49	2		733	185	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030396	49030396	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	26	276	0	ENST00000267163.4:c.1871C>A	p.Ser624Tyr	p.S624Y	ENST00000267163	NM_000321.2	624	tCt/tAt	19/27	1	2	FACETS	0.694	0.556	0.848	0.694	0.556	0.848	SUBCLONAL	1	TRUE	1	0.49	2		276	153	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42050032	42050032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	47	232	0	ENST00000219905.7:c.7186C>T	p.Arg2396Ter	p.R2396*	ENST00000219905	NM_001164273.1	2396	Cga/Tga	19/24	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.49	2		232	169	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99203950	99203950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755469992	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	20	203	0	ENST00000074304.5:c.2813G>A	p.Arg938Gln	p.R938Q	ENST00000074304	NM_001134224.1	938	cGa/cAa	26/26	1	2	FACETS	0.664	0.514	0.834	0.664	0.514	0.834	SUBCLONAL	1	TRUE	1	0.49	2		203	123	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918695	44918695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746746824	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	13	142	0	ENST00000377967.4:c.1178G>A	p.Arg393Gln	p.R393Q	ENST00000377967	NM_021140.2	393	cGa/cAa	12/29	0.3	2	FACETS	0.424	0.305	0.568	0.212	0.152	0.284	SUBCLONAL	1	TRUE	0	0.49	2		142	125	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709529	176709529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777258117	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	10	204	0	ENST00000439151.2:c.5956C>T	p.Arg1986Cys	p.R1986C	ENST00000439151	NM_022455.4	1986	Cgc/Tgc	19/23	1	2	FACETS	0.211	0.143	0.298	0.211	0.143	0.298	SUBCLONAL	1	TRUE	1	0.49	2		204	193	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796804	135796804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223799508	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	70	185	0	ENST00000298552.3:c.683G>A	p.Arg228Gln	p.R228Q	ENST00000298552	NM_001162426.1	228	cGa/cAa	8/23	1	2	FACETS	1	0.917	1	1	0.985	1	CLONAL	2	TRUE	1	0.49	2		185	140	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94201000	94201000	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	20	257	0	ENST00000323929.3:c.1077G>T	p.Glu359Asp	p.E359D	ENST00000323929	NM_005591.3	359	gaG/gaT	10/20	1	2	FACETS	0.332	0.254	0.422	0.332	0.254	0.422	SUBCLONAL	1	TRUE	1	0.49	2		257	246	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830958	72830958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393698686	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	58	324	0	ENST00000268489.5:c.5623G>A	p.Glu1875Lys	p.E1875K	ENST00000268489	NM_006885.3	1875	Gaa/Aaa	9/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.49	2		324	179	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827900	40827900	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	84	358	1	ENST00000373198.4:c.2528C>A	p.Ser843Tyr	p.S843Y	ENST00000373198	NM_133170.3	843	tCt/tAt	17/32	0.163447526461599	0	FACETS	0.575	0.513	0.64			1	INDETERMINATE	1	TRUE	0	0.49	0		359	304	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027511	48027511	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	40	242	0	ENST00000234420.5:c.2389G>T	p.Asp797Tyr	p.D797Y	ENST00000234420	NM_000179.2	797	Gac/Tac	4/10	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.49	2		242	144	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164855	47164855	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424607930	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	29	207	0	ENST00000409792.3:c.1271G>A	p.Arg424Gln	p.R424Q	ENST00000409792	NM_014159.6	424	cGa/cAa	3/21	1	2	FACETS	0.705	0.571	0.852	0.705	0.571	0.852	SUBCLONAL	1	TRUE	1	0.49	2		207	168	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026290	48026290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147737737	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	15	253	0	ENST00000234420.5:c.1168G>A	p.Asp390Asn	p.D390N	ENST00000234420	NM_000179.2	390	Gat/Aat	4/10	1	2	FACETS	0.486	0.358	0.636	0.486	0.358	0.636	SUBCLONAL	1	TRUE	1	0.49	2		253	126	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030293	180030293	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	65	552	0	ENST00000261937.6:c.3991G>T	p.Val1331Leu	p.V1331L	ENST00000261937	NM_182925.4	1331	Gtg/Ttg	30/30	1	2	FACETS	0.663	0.577	0.756	0.663	0.577	0.756	SUBCLONAL	1	TRUE	1	0.49	2		552	400	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710593	117710593	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145765584	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	70	209	0	ENST00000368508.3:c.1679G>A	p.Arg560His	p.R560H	ENST00000368508	NM_002944.2	560	cGc/cAc	12/43	0.163447526461599	3	FACETS	0.763	0.675	0.856	0.763	0.675	0.856	INDETERMINATE	2	TRUE	1	0.49	3		209	233	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645910	67645910	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	49	355	0	ENST00000264010.4:c.838A>C	p.Asn280His	p.N280H	ENST00000264010	NM_006565.3	280	Aat/Cat	4/12	1	2	FACETS	0.484	0.411	0.565	0.484	0.411	0.565	SUBCLONAL	1	TRUE	1	0.49	2		355	413	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394902	394902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767879003	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	86	363	0	ENST00000380956.4:c.298G>A	p.Ala100Thr	p.A100T	ENST00000380956	NM_001195286.1	100	Gct/Act	3/9	0.3	2	FACETS	0.902	0.804	1			1	CLONAL	1	TRUE	NA	0.49	2		363	389	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728847	39728847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	61	237	0	ENST00000361337.2:c.1127G>A	p.Arg376Gln	p.R376Q	ENST00000361337	NM_003286.2	376	cGa/cAa	12/21	0.163447526461599	0	FACETS	0.525	0.458	0.596			1	INDETERMINATE	1	TRUE	0	0.49	0		237	242	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319887	62319887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371161995	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	112	500	0	ENST00000360203.5:c.1729G>A	p.Asp577Asn	p.D577N	ENST00000360203	NM_001283009.1	577	Gac/Aac	21/35	0.163447526461599	0	FACETS	0.506	0.457	0.556			1	INDETERMINATE	1	TRUE	0	0.49	0		500	461	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794394	42794394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373584239	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	45	595	0	ENST00000575354.2:c.1474C>T	p.Arg492Trp	p.R492W	ENST00000575354	NM_015125.3	492	Cgg/Tgg	10/20	1	2	FACETS	0.364	0.305	0.428	0.364	0.305	0.428	SUBCLONAL	1	TRUE	1	0.49	2		595	505	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001395	150001395	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	18	666	2	ENST00000253339.5:c.2209C>T	p.Arg737Ter	p.R737*	ENST00000253339		737	Cga/Tga	4/7	0.163447526461599	3	FACETS	0.471	0.356	0.606	0.236	0.178	0.303	INDETERMINATE	1	TRUE	1	0.49	3		668	194	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56787287	56787287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267606997	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	54	371	0	ENST00000337432.4:c.773G>A	p.Arg258His	p.R258H	ENST00000337432	NM_058216.2	258	cGt/cAt	5/9	1	2	FACETS	0.9	0.776	1	0.9	0.776	1	CLONAL	1	TRUE	1	0.49	2		371	245	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58711261	58711261	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571290585	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	19	413	0	ENST00000305921.3:c.749G>A	p.Arg250Gln	p.R250Q	ENST00000305921	NM_003620.3	250	cGa/cAa	3/6	1	2	FACETS	0.259	0.197	0.333	0.259	0.197	0.333	SUBCLONAL	1	TRUE	1	0.49	2		413	299	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729889	41729889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs923669088	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	76	385	0	ENST00000242208.4:c.640C>T	p.Arg214Trp	p.R214W	ENST00000242208	NM_002192.2	214	Cgg/Tgg	3/3	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.49	2		385	279	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131421	202131421	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	50	507	2	ENST00000358485.4:c.389G>T	p.Arg130Ile	p.R130I	ENST00000358485	NM_001080125.1	130	aGa/aTa	2/9	1	2	FACETS	0.773	0.661	0.894	0.773	0.661	0.894	SUBCLONAL	1	TRUE	1	0.49	2		509	264	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673482	30673482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775535131	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	70	377	1	ENST00000376406.3:c.3478C>T	p.Pro1160Ser	p.P1160S	ENST00000376406	NM_014641.2	1160	Cca/Tca	10/15	0.163447526461599	3	FACETS	1	0.921	1	0.533	0.467	0.602	INDETERMINATE	1	TRUE	1	0.49	3		378	334	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983784	15983784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150513105	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	65	354	0	ENST00000268712.3:c.3338G>A	p.Arg1113Gln	p.R1113Q	ENST00000268712	NM_006311.3	1113	cGa/cAa	25/46	1	2	FACETS	0.824	0.72	0.935	0.824	0.72	0.935	CLONAL	1	TRUE	1	0.49	2		354	322	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231239	98231239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs570441437	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	127	489	0	ENST00000331920.6:c.2044C>T	p.Arg682Cys	p.R682C	ENST00000331920	NM_000264.3	682	Cgc/Tgc	14/24	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.49	2		489	472	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807914	3807914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	72	352	0	ENST00000262367.5:c.3505C>T	p.Arg1169Cys	p.R1169C	ENST00000262367	NM_004380.2	1169	Cgc/Tgc	18/31	1	2	FACETS	0.993	0.876	1	0.993	0.876	1	CLONAL	1	TRUE	1	0.49	2		352	296	SUCCESS
APC	324	MSKCC	GRCh37	5	112173365	112173365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561574669	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	26	223	0	ENST00000257430.4:c.2074C>T	p.Pro692Ser	p.P692S	ENST00000257430	NM_000038.5	692	Cct/Tct	16/16	1	2	FACETS	0.849	0.683	1	0.849	0.683	1	CLONAL	1	TRUE	1	0.49	2		223	125	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383654	84383654	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	21	327	0	ENST00000321945.7:c.1198T>G	p.Phe400Val	p.F400V	ENST00000321945	NM_139076.2	400	Ttt/Gtt	9/9	1	2	FACETS	0.307	0.237	0.389	0.307	0.237	0.389	SUBCLONAL	1	TRUE	1	0.49	2		327	279	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276798	15276798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763602970	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	116	553	0	ENST00000263388.2:c.5467G>A	p.Asp1823Asn	p.D1823N	ENST00000263388	NM_000435.2	1823	Gac/Aac	30/33	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.49	2		553	379	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27172623	27172623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	18	340	0	ENST00000380036.4:c.638C>T	p.Ala213Val	p.A213V	ENST00000380036	NM_000459.3	213	gCc/gTc	5/23	1	2	FACETS	0.393	0.297	0.505	0.393	0.297	0.505	SUBCLONAL	1	TRUE	1	0.49	2		340	187	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286215	66286215	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	14	244	0	ENST00000273854.3:c.1471G>T	p.Glu491Ter	p.E491*	ENST00000273854	NM_004439.5	491	Gaa/Taa	6/18	1	2	FACETS	0.384	0.278	0.509	0.384	0.278	0.509	SUBCLONAL	1	TRUE	1	0.49	2		244	149	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199878	108199878	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1555122149	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	14	128	0	ENST00000278616.4:c.7220C>A	p.Ser2407Ter	p.S2407*	ENST00000278616	NM_000051.3	2407	tCa/tAa	49/63	1	2	FACETS	0.515	0.376	0.679	0.515	0.376	0.679	SUBCLONAL	1	TRUE	1	0.49	2		128	111	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233141	66233141	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs146757388	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	43	230	1	ENST00000273854.3:c.1858C>T	p.Arg620Trp	p.R620W	ENST00000273854	NM_004439.5	620	Cgg/Tgg	10/18	1	2	FACETS	0.939	0.796	1	0.939	0.796	1	CLONAL	1	TRUE	1	0.49	2		231	187	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614469	38614469	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	35	293	0	ENST00000299084.4:c.235G>T	p.Asp79Tyr	p.D79Y	ENST00000299084	NM_152594.2	79	Gac/Tac	3/7	1	2	FACETS	0.776	0.643	0.922	0.776	0.643	0.922	CLONAL	1	TRUE	1	0.49	2		293	184	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818213	32818213	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs143800384	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	135	473	0	ENST00000354258.4:c.1312C>T	p.Arg438Ter	p.R438*	ENST00000354258	NM_000593.5	438	Cga/Tga	5/11	0.163447526461599	3	FACETS	1	0.971	1	0.575	0.524	0.627	INDETERMINATE	1	TRUE	1	0.49	3		473	597	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546618	9546618	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	66	369	0	ENST00000353224.5:c.1404G>T	p.Glu468Asp	p.E468D	ENST00000353224	NM_177990.2	468	gaG/gaT	5/10	0.163447526461599	0	FACETS	0.509	0.446	0.575			1	INDETERMINATE	1	TRUE	0	0.49	0		369	270	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70411605	70411605	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs868611128	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	33	217	0	ENST00000373644.4:c.4279C>T	p.Arg1427Ter	p.R1427*	ENST00000373644	NM_030625.2	1427	Cga/Tga	5/12	1	2	FACETS	0.962	0.797	1	0.962	0.797	1	CLONAL	1	TRUE	1	0.49	2		217	140	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447841	49447841	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748834953	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	72	487	1	ENST00000301067.7:c.593C>T	p.Ala198Val	p.A198V	ENST00000301067	NM_003482.3	198	gCg/gTg	5/54	0.163447526461599	3	FACETS	0.709	0.621	0.804	0.355	0.31	0.402	INDETERMINATE	1	TRUE	1	0.49	3		488	516	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28631537	28631537	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	37	217	0	ENST00000241453.7:c.431T>G	p.Phe144Cys	p.F144C	ENST00000241453	NM_004119.2	144	tTt/tGt	4/24	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.49	2		217	138	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31472277	31472277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	64	359	0	ENST00000344624.3:c.2134G>A	p.Ala712Thr	p.A712T	ENST00000344624		712	Gcc/Acc	14/33	1	2	FACETS	0.827	0.721	0.939	0.827	0.721	0.939	CLONAL	1	TRUE	1	0.49	2		359	316	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644715	134644715	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs556035012	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	66	345	0	ENST00000398015.3:c.116C>T	p.Ala39Val	p.A39V	ENST00000398015	NM_004441.4	39	gCg/gTg	2/16	1	2	FACETS	0.91	0.797	1	0.91	0.797	1	CLONAL	1	TRUE	1	0.49	2		345	296	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814756	139814756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376884527	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	99	558	0	ENST00000247668.2:c.749C>T	p.Ser250Leu	p.S250L	ENST00000247668	NM_021138.3	250	tCg/tTg	8/11	1	2	FACETS	0.967	0.869	1	0.967	0.869	1	CLONAL	1	TRUE	1	0.49	2		558	418	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526195	63526195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	105	420	0	ENST00000307078.5:c.2431G>A	p.Glu811Lys	p.E811K	ENST00000307078	NM_004655.3	811	Gag/Aag	11/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.49	2		420	380	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688800	47688800	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	20	230	0	ENST00000347630.2:c.500C>A	p.Ser167Tyr	p.S167Y	ENST00000347630	NM_001007230.1	167	tCt/tAt	7/11	1	2	FACETS	0.352	0.27	0.448	0.352	0.27	0.448	SUBCLONAL	1	TRUE	1	0.49	2		230	232	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243927	41243927	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	17	392	0	ENST00000357654.3:c.3621G>T	p.Lys1207Asn	p.K1207N	ENST00000357654	NM_007294.3	1207	aaG/aaT	10/23	1	2	FACETS	0.235	0.175	0.307	0.235	0.175	0.307	SUBCLONAL	1	TRUE	1	0.49	2		392	295	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444026	49444026	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	40	472	0	ENST00000301067.7:c.3345C>A	p.Phe1115Leu	p.F1115L	ENST00000301067	NM_003482.3	1115	ttC/ttA	11/54	0.163447526461599	3	FACETS	0.594	0.495	0.704	0.297	0.247	0.352	INDETERMINATE	1	TRUE	1	0.49	3		472	342	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026853	71026853	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	34	189	0	ENST00000318789.4:c.1369G>T	p.Glu457Ter	p.E457*	ENST00000318789	NM_032682.5	457	Gaa/Taa	16/21	1	2	FACETS	0.957	0.795	1	0.957	0.795	1	CLONAL	1	TRUE	1	0.49	2		189	145	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122680	108122680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	30	560	0	ENST00000278616.4:c.1724C>T	p.Ser575Leu	p.S575L	ENST00000278616	NM_000051.3	575	tCa/tTa	11/63	1	2	FACETS	0.765	0.624	0.921	0.765	0.624	0.921	CLONAL	1	TRUE	1	0.49	2		560	160	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192435	138192435	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	39	385	1	ENST00000237289.4:c.71G>T	p.Arg24Ile	p.R24I	ENST00000237289	NM_001270507.1	24	aGa/aTa	2/9	0.163447526461599	3	FACETS	0.833	0.695	0.983	0.416	0.347	0.492	INDETERMINATE	1	TRUE	1	0.49	3		386	238	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435382	18435382	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	25	232	0	ENST00000266497.5:c.367G>T	p.Glu123Ter	p.E123*	ENST00000266497		123	Gaa/Taa	1/31	0.163447526461599	3	FACETS	1	0.865	1	0.552	0.443	0.673	INDETERMINATE	1	TRUE	1	0.49	3		232	115	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76953080	76953080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	45	190	0	ENST00000373344.5:c.233G>A	p.Arg78Gln	p.R78Q	ENST00000373344	NM_000489.3	78	cGa/cAa	4/35	0.3	2	FACETS	0.778	0.673	0.888	0.778	0.673	0.888	SUBCLONAL	2	TRUE	0	0.49	2		190	118	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17354361	17354361	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	21	172	0	ENST00000375499.3:c.424-1G>T		p.X142_splice	ENST00000375499	NM_003000.2	142			1	2	FACETS	0.733	0.572	0.914	0.733	0.572	0.914	CLONAL	1	TRUE	1	0.49	2		172	117	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739368	46739368	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759993383	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	79	376	0	ENST00000371975.4:c.1559C>T	p.Ser520Leu	p.S520L	ENST00000371975	NM_003579.3	520	tCg/tTg	14/18	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.49	2		376	320	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166274	118166274	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	51	270	0	ENST00000369448.3:c.784G>T	p.Glu262Ter	p.E262*	ENST00000369448	NM_017709.3	262	Gaa/Taa	2/2	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.49	2		270	179	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120496301	120496301	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	20	204	0	ENST00000256646.2:c.2230C>A	p.Leu744Ile	p.L744I	ENST00000256646	NM_024408.3	744	Ctc/Atc	14/34	1	2	FACETS	0.68	0.527	0.854	0.68	0.527	0.854	SUBCLONAL	1	TRUE	1	0.49	2		204	120	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870306	155870306	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	77	372	0	ENST00000368323.3:c.533T>G	p.Leu178Arg	p.L178R	ENST00000368323	NM_006912.5	178	cTt/cGt	6/6	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.49	2		372	289	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667455	241667455	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	44	236	0	ENST00000366560.3:c.995C>T	p.Ala332Val	p.A332V	ENST00000366560	NM_000143.3	332	gCc/gTc	7/10	1	2	FACETS	0.971	0.825	1	0.971	0.825	1	CLONAL	1	TRUE	1	0.49	2		236	185	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596047	43596047	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	93	514	0	ENST00000355710.3:c.214C>A	p.Leu72Ile	p.L72I	ENST00000355710	NM_020975.4	72	Ctc/Atc	2/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.49	2		514	355	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850697	63850697	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	27	240	0	ENST00000279873.7:c.1475A>C	p.Asp492Ala	p.D492A	ENST00000279873	NM_032199.2	492	gAc/gCc	10/10	1	2	FACETS	0.568	0.455	0.695	0.568	0.455	0.695	SUBCLONAL	1	TRUE	1	0.49	2		240	194	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88635831	88635831	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	13	299	0	ENST00000372037.3:c.56C>A	p.Ser19Tyr	p.S19Y	ENST00000372037	NM_004329.2	19	tCt/tAt	3/13	1	2	FACETS	0.256	0.183	0.346	0.256	0.183	0.346	SUBCLONAL	1	TRUE	1	0.49	2		299	207	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32449530	32449530	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	58	531	0	ENST00000332351.3:c.844G>A	p.Ala282Thr	p.A282T	ENST00000332351	NM_024426.4	282	Gct/Act	3/10	1	2	FACETS	0.596	0.514	0.685	0.596	0.514	0.685	SUBCLONAL	1	TRUE	1	0.49	2		531	397	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988112	85988112	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	35	240	0	ENST00000263360.6:c.1057C>A	p.Leu353Ile	p.L353I	ENST00000263360	NM_003797.3	353	Ctt/Att	10/12	1	2	FACETS	0.972	0.81	1	0.972	0.81	1	CLONAL	1	TRUE	1	0.49	2		240	147	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194195	94194195	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	35	212	0	ENST00000323929.3:c.1233G>T	p.Glu411Asp	p.E411D	ENST00000323929	NM_005591.3	411	gaG/gaT	12/20	1	2	FACETS	0.992	0.827	1	0.992	0.827	1	CLONAL	1	TRUE	1	0.49	2		212	144	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098563	108098563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3218684	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	18	181	0	ENST00000278616.4:c.133C>T	p.Arg45Trp	p.R45W	ENST00000278616	NM_000051.3	45	Cgg/Tgg	3/63	1	2	FACETS	0.364	0.275	0.468	0.364	0.275	0.468	SUBCLONAL	1	TRUE	1	0.49	2		181	202	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163347	108163347	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	22	258	0	ENST00000278616.4:c.4438C>T	p.Pro1480Ser	p.P1480S	ENST00000278616	NM_000051.3	1480	Cct/Tct	30/63	1	2	FACETS	0.781	0.615	0.967	0.781	0.615	0.967	CLONAL	1	TRUE	1	0.49	2		258	115	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188130	108188130	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	27	187	0	ENST00000278616.4:c.6229C>A	p.Leu2077Ile	p.L2077I	ENST00000278616	NM_000051.3	2077	Ctt/Att	43/63	1	2	FACETS	0.689	0.554	0.839	0.689	0.554	0.839	SUBCLONAL	1	TRUE	1	0.49	2		187	160	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343697	118343697	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	42	300	0	ENST00000534358.1:c.1823G>A	p.Arg608Gln	p.R608Q	ENST00000534358	NM_005933.3	608	cGa/cAa	3/36	1	2	FACETS	0.947	0.802	1	0.947	0.802	1	CLONAL	1	TRUE	1	0.49	2		300	181	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380757	118380757	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	42	287	0	ENST00000534358.1:c.10995G>T	p.Glu3665Asp	p.E3665D	ENST00000534358	NM_005933.3	3665	gaG/gaT	30/36	1	2	FACETS	0.917	0.775	1	0.917	0.775	1	CLONAL	1	TRUE	1	0.49	2		287	187	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103249	119103249	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781738309	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	45	289	0	ENST00000264033.4:c.287G>A	p.Arg96His	p.R96H	ENST00000264033	NM_005188.3	96	cGt/cAt	2/16	1	2	FACETS	0.854	0.726	0.993	0.854	0.726	0.993	CLONAL	1	TRUE	1	0.49	2		289	215	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417093	417093	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	16	217	0	ENST00000399788.2:c.3457A>C	p.Thr1153Pro	p.T1153P	ENST00000399788	NM_001042603.1	1153	Aca/Cca	23/28	0.3	2	FACETS	0.357	0.265	0.466			1	SUBCLONAL	1	TRUE	NA	0.49	2		217	183	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475224	475224	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	37	382	0	ENST00000399788.2:c.413A>C	p.Lys138Thr	p.K138T	ENST00000399788	NM_001042603.1	138	aAa/aCa	4/28	0.3	2	FACETS	0.528	0.437	0.629			1	SUBCLONAL	1	TRUE	NA	0.49	2		382	286	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435250	18435250	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	20	253	0	ENST00000266497.5:c.235A>C	p.Asn79His	p.N79H	ENST00000266497		79	Aat/Cat	1/31	0.163447526461599	3	FACETS	0.916	0.711	1	0.458	0.355	0.574	INDETERMINATE	1	TRUE	1	0.49	3		253	111	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378706	25378706	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	19	171	0	ENST00000311936.3:c.292G>T	p.Glu98Ter	p.E98*	ENST00000311936	NM_004985.3	98	Gaa/Taa	4/5	0.163447526461599	3	FACETS	1	0.915	1	0.721	0.564	0.893	INDETERMINATE	1	TRUE	1	0.49	3		171	67	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246617	46246617	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	15	139	1	ENST00000334344.6:c.4711G>T	p.Glu1571Ter	p.E1571*	ENST00000334344	NM_152641.2	1571	Gaa/Taa	15/21	0.163447526461599	3	FACETS	0.615	0.453	0.805	0.307	0.226	0.403	INDETERMINATE	1	TRUE	1	0.49	3		140	124	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425221	49425221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	53	663	0	ENST00000301067.7:c.13267C>T	p.Pro4423Ser	p.P4423S	ENST00000301067	NM_003482.3	4423	Cca/Tca	39/54	0.163447526461599	3	FACETS	0.542	0.462	0.629	0.271	0.231	0.315	INDETERMINATE	1	TRUE	1	0.49	3		663	497	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443712	49443712	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	66	546	0	ENST00000301067.7:c.3659T>G	p.Phe1220Cys	p.F1220C	ENST00000301067	NM_003482.3	1220	tTt/tGt	11/54	0.163447526461599	3	FACETS	0.828	0.722	0.942	0.414	0.361	0.471	INDETERMINATE	1	TRUE	1	0.49	3		546	405	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120806669	120806669	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	31	186	0	ENST00000257552.2:c.67T>G	p.Phe23Val	p.F23V	ENST00000257552	NM_002442.3	23	Ttc/Gtc	2/15	0.163447526461599	3	FACETS	0.538	0.436	0.652	0.269	0.218	0.326	INDETERMINATE	1	TRUE	1	0.49	3		186	293	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250189	133250189	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	95	410	0	ENST00000320574.5:c.1331T>A	p.Met444Lys	p.M444K	ENST00000320574	NM_006231.2	444	aTg/aAg	13/49	0.163447526461599	3	FACETS	1	0.979	1	0.686	0.616	0.758	INDETERMINATE	1	TRUE	1	0.49	3		410	352	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28886195	28886195	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	45	338	0	ENST00000282397.4:c.3427G>T	p.Glu1143Ter	p.E1143*	ENST00000282397	NM_002019.4	1143	Gaa/Taa	26/30	1	2	FACETS	0.765	0.649	0.892	0.765	0.649	0.892	SUBCLONAL	1	TRUE	1	0.49	2		338	240	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955551	48955551	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773116120	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	12	246	0	ENST00000267163.4:c.1667G>A	p.Arg556Gln	p.R556Q	ENST00000267163	NM_000321.2	556	cGa/cAa	17/27	1	2	FACETS	0.35	0.247	0.475	0.35	0.247	0.475	SUBCLONAL	1	TRUE	1	0.49	2		246	140	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003117	42003117	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	15	440	1	ENST00000219905.7:c.2654C>A	p.Ser885Tyr	p.S885Y	ENST00000219905	NM_001164273.1	885	tCt/tAt	8/24	1	2	FACETS	0.263	0.192	0.348	0.263	0.192	0.348	SUBCLONAL	1	TRUE	1	0.49	2		441	233	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749187	43749187	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	55	492	0	ENST00000382044.4:c.1619G>T	p.Arg540Ile	p.R540I	ENST00000382044	NM_001141980.1	540	aGa/aTa	12/28	1	2	FACETS	0.867	0.748	0.993	0.867	0.748	0.993	CLONAL	1	TRUE	1	0.49	2		492	259	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420199	88420199	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	77	339	0	ENST00000360948.2:c.2487G>T	p.Lys829Asn	p.K829N	ENST00000360948	NM_001012338.2	829	aaG/aaT	19/19	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.49	2		339	253	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636680	2636680	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	61	317	1	ENST00000342085.4:c.1129G>T	p.Asp377Tyr	p.D377Y	ENST00000342085	NM_002613.4	377	Gac/Tac	11/14	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.49	2		318	198	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645270	67645270	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	74	428	0	ENST00000264010.4:c.535G>T	p.Glu179Ter	p.E179*	ENST00000264010	NM_006565.3	179	Gaa/Taa	3/12	1	2	FACETS	0.95	0.839	1	0.95	0.839	1	CLONAL	1	TRUE	1	0.49	2		428	318	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992719	72992719	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	66	514	0	ENST00000268489.5:c.1326G>T	p.Glu442Asp	p.E442D	ENST00000268489	NM_006885.3	442	gaG/gaT	2/10	1	2	FACETS	0.673	0.587	0.766	0.673	0.587	0.766	SUBCLONAL	1	TRUE	1	0.49	2		514	400	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337244	89337244	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	129	443	0	ENST00000301030.4:c.7787A>G	p.Asp2596Gly	p.D2596G	ENST00000301030	NM_001256183.1	2596	gAc/gGc	12/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.49	2		443	389	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7218340	7218340	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	123	407	1	ENST00000380728.2:c.32C>T	p.Ser11Phe	p.S11F	ENST00000380728		11	tCc/tTc	2/11	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.49	2		408	474	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16001809	16001809	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	25	272	0	ENST00000268712.3:c.2692A>C	p.Met898Leu	p.M898L	ENST00000268712	NM_006311.3	898	Atg/Ctg	21/46	1	2	FACETS	0.5	0.396	0.618	0.5	0.396	0.618	SUBCLONAL	1	TRUE	1	0.49	2		272	204	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684049	29684049	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	35	365	0	ENST00000356175.3:c.7747C>A	p.Leu2583Ile	p.L2583I	ENST00000356175	NM_000267.3	2583	Ctc/Atc	52/57	1	2	FACETS	0.479	0.394	0.574	0.479	0.394	0.574	SUBCLONAL	1	TRUE	1	0.49	2		365	298	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685996	29685996	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	25	187	0	ENST00000356175.3:c.8060T>G	p.Phe2687Cys	p.F2687C	ENST00000356175	NM_000267.3	2687	tTt/tGt	55/57	1	2	FACETS	0.593	0.472	0.731	0.593	0.472	0.731	SUBCLONAL	1	TRUE	1	0.49	2		187	172	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489867	40489867	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	39	334	0	ENST00000264657.5:c.559G>T	p.Asp187Tyr	p.D187Y	ENST00000264657	NM_139276.2	187	Gat/Tat	7/24	1	2	FACETS	0.451	0.374	0.536	0.451	0.374	0.536	SUBCLONAL	1	TRUE	1	0.49	2		334	353	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234450	41234450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs4986849	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	28	338	0	ENST00000357654.3:c.4328G>A	p.Arg1443Gln	p.R1443Q	ENST00000357654	NM_007294.3	1443	cGa/cAa	12/23	1	2	FACETS	0.455	0.365	0.557	0.455	0.365	0.557	SUBCLONAL	1	TRUE	1	0.49	2		338	251	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47684678	47684678	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	69	339	0	ENST00000347630.2:c.771C>A	p.Phe257Leu	p.F257L	ENST00000347630	NM_001007230.1	257	ttC/ttA	9/11	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.49	2		339	265	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734177	58734177	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	39	316	0	ENST00000305921.3:c.1235C>T	p.Ser412Phe	p.S412F	ENST00000305921	NM_003620.3	412	tCc/tTc	5/6	1	2	FACETS	0.707	0.591	0.835	0.707	0.591	0.835	SUBCLONAL	1	TRUE	1	0.49	2		316	225	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117851	70117851	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	43	379	0	ENST00000245479.2:c.319C>T	p.Arg107Trp	p.R107W	ENST00000245479	NM_000346.3	107	Cgg/Tgg	1/3	1	2	FACETS	0.524	0.44	0.616	0.524	0.44	0.616	SUBCLONAL	1	TRUE	1	0.49	2		379	335	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374867	45374867	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	33	338	0	ENST00000262160.6:c.976G>T	p.Glu326Ter	p.E326*	ENST00000262160	NM_005901.5	326	Gaa/Taa	8/11	1	2	FACETS	0.783	0.645	0.934	0.783	0.645	0.934	CLONAL	1	TRUE	1	0.49	2		338	172	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394784	45394784	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	34	197	0	ENST00000262160.6:c.565G>T	p.Glu189Ter	p.E189*	ENST00000262160	NM_005901.5	189	Gaa/Taa	5/11	1	2	FACETS	0.684	0.563	0.816	0.684	0.563	0.816	SUBCLONAL	1	TRUE	1	0.49	2		197	203	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573637	48573637	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	17	254	0	ENST00000342988.3:c.221T>C	p.Ile74Thr	p.I74T	ENST00000342988	NM_005359.5	74	aTa/aCa	2/12	1	2	FACETS	0.448	0.336	0.578	0.448	0.336	0.578	SUBCLONAL	1	TRUE	1	0.49	2		254	155	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291617	15291617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150941674	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	28	560	0	ENST00000263388.2:c.3017G>A	p.Arg1006His	p.R1006H	ENST00000263388	NM_000435.2	1006	cGc/cAc	19/33	1	2	FACETS	0.224	0.178	0.276	0.224	0.178	0.276	SUBCLONAL	1	TRUE	1	0.49	2		560	511	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976479	18976479	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	132	647	0	ENST00000262803.5:c.3129T>G	p.Asp1043Glu	p.D1043E	ENST00000262803	NM_002911.3	1043	gaT/gaG	22/24	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.49	2		647	454	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258614	19258614	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138148108	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	94	543	0	ENST00000162023.5:c.286G>A	p.Asp96Asn	p.D96N	ENST00000162023		96	Gat/Aat	8/13	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.49	2		543	377	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798413	42798413	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	114	538	2	ENST00000575354.2:c.4284G>T	p.Lys1428Asn	p.K1428N	ENST00000575354	NM_015125.3	1428	aaG/aaT	18/20	1	2	FACETS	0.865	0.782	0.952	0.865	0.782	0.952	CLONAL	1	TRUE	1	0.49	2		540	538	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872210	45872210	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	82	515	0	ENST00000391945.4:c.224G>T	p.Arg75Ile	p.R75I	ENST00000391945	NM_000400.3	75	aGa/aTa	4/23	1	2	FACETS	0.841	0.746	0.942	0.841	0.746	0.942	CLONAL	1	TRUE	1	0.49	2		515	398	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52705261	52705261	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770424653	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	31	317	0	ENST00000322088.6:c.143G>A	p.Arg48Gln	p.R48Q	ENST00000322088	NM_014225.5	48	cGa/cAa	2/15	1	2	FACETS	0.416	0.337	0.505	0.416	0.337	0.505	SUBCLONAL	1	TRUE	1	0.49	2		317	304	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068390	26068390	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	18	229	0	ENST00000435504.4:c.100A>C	p.Ile34Leu	p.I34L	ENST00000435504		34	Att/Ctt	2/13	1	2	FACETS	0.281	0.212	0.364	0.281	0.212	0.364	SUBCLONAL	1	TRUE	1	0.49	2		229	261	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46588129	46588129	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	28	492	0	ENST00000263734.3:c.679G>T	p.Glu227Ter	p.E227*	ENST00000263734	NM_001430.4	227	Gaa/Taa	6/16	1	2	FACETS	0.282	0.225	0.347	0.282	0.225	0.347	SUBCLONAL	1	TRUE	1	0.49	2		492	405	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46611713	46611713	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	106	551	0	ENST00000263734.3:c.2527G>T	p.Asp843Tyr	p.D843Y	ENST00000263734	NM_001430.4	843	Gac/Tac	16/16	1	2	FACETS	0.824	0.742	0.911	0.824	0.742	0.911	CLONAL	1	TRUE	1	0.49	2		551	525	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637284	47637284	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779803074	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	77	402	0	ENST00000233146.2:c.418G>T	p.Asp140Tyr	p.D140Y	ENST00000233146	NM_000251.2	140	Gat/Tat	3/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.49	2		402	269	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47643558	47643558	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	36	312	0	ENST00000233146.2:c.1066A>C	p.Ile356Leu	p.I356L	ENST00000233146	NM_000251.2	356	Ata/Cta	6/16	1	2	FACETS	0.79	0.657	0.936	0.79	0.657	0.936	CLONAL	1	TRUE	1	0.49	2		312	186	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693878	47693878	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	22	213	0	ENST00000233146.2:c.1592A>C	p.Lys531Thr	p.K531T	ENST00000233146	NM_000251.2	531	aAa/aCa	10/16	1	2	FACETS	0.755	0.593	0.936	0.755	0.593	0.936	CLONAL	1	TRUE	1	0.49	2		213	119	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147198	61147198	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	45	228	0	ENST00000295025.8:c.876G>T	p.Lys292Asn	p.K292N	ENST00000295025	NM_002908.2	292	aaG/aaT	8/11	1	2	FACETS	0.952	0.81	1	0.952	0.81	1	CLONAL	1	TRUE	1	0.49	2		228	193	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726852	61726852	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	23	208	0	ENST00000401558.2:c.586G>T	p.Asp196Tyr	p.D196Y	ENST00000401558	NM_003400.3	196	Gac/Tac	7/25	1	2	FACETS	0.706	0.557	0.873	0.706	0.557	0.873	SUBCLONAL	1	TRUE	1	0.49	2		208	133	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158637027	158637027	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1320913728	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	71	358	1	ENST00000263640.3:c.153G>T	p.Gln51His	p.Q51H	ENST00000263640	NM_001105.4	51	caG/caT	4/11	1	2	FACETS	0.821	0.721	0.927	0.821	0.721	0.927	CLONAL	1	TRUE	1	0.49	2		359	353	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270150	198270150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1421809024	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	72	288	0	ENST00000335508.6:c.1286G>A	p.Arg429Gln	p.R429Q	ENST00000335508	NM_012433.2	429	cGa/cAa	10/25	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.49	2		288	260	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495224	212495224	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	10	278	0	ENST00000342788.4:c.2042A>C	p.Lys681Thr	p.K681T	ENST00000342788	NM_005235.2	681	aAa/aCa	17/28	1	2	FACETS	0.214	0.144	0.301	0.214	0.144	0.301	SUBCLONAL	1	TRUE	1	0.49	2		278	191	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730788	40730788	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	75	427	0	ENST00000373198.4:c.3747T>G	p.Asn1249Lys	p.N1249K	ENST00000373198	NM_133170.3	1249	aaT/aaG	27/32	0.163447526461599	0	FACETS	0.535	0.473	0.599			1	INDETERMINATE	1	TRUE	0	0.49	0		427	292	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980728	40980728	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	45	316	0	ENST00000373198.4:c.1758T>G	p.Ile586Met	p.I586M	ENST00000373198	NM_133170.3	586	atT/atG	10/32	0.163447526461599	0	FACETS	0.466	0.396	0.541			1	INDETERMINATE	1	TRUE	0	0.49	0		316	201	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206833	36206833	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1555889984	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	88	335	0	ENST00000300305.3:c.679G>T	p.Glu227Ter	p.E227*	ENST00000300305		227	Gaa/Taa	6/8	0.163447526461599	4	FACETS	0.904	0.81	1	0.904	0.81	1	INDETERMINATE	2	TRUE	2	0.49	4		335	296	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032808	30032808	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	96	303	0	ENST00000338641.4:c.183C>A	p.Phe61Leu	p.F61L	ENST00000338641	NM_000268.3	61	ttC/ttA	2/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.49	2		303	299	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513615	41513615	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	32	480	0	ENST00000263253.7:c.519G>T	p.Met173Ile	p.M173I	ENST00000263253	NM_001429.3	173	atG/atT	2/31	1	2	FACETS	0.428	0.348	0.518	0.428	0.348	0.518	SUBCLONAL	1	TRUE	1	0.49	2		480	305	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574278	41574278	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	77	506	0	ENST00000263253.7:c.6563T>C	p.Met2188Thr	p.M2188T	ENST00000263253	NM_001429.3	2188	aTg/aCg	31/31	1	2	FACETS	0.964	0.854	1	0.964	0.854	1	CLONAL	1	TRUE	1	0.49	2		506	326	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627220	12627220	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	59	319	0	ENST00000251849.4:c.1496C>A	p.Ser499Tyr	p.S499Y	ENST00000251849	NM_002880.3	499	tCt/tAt	14/17	1	2	FACETS	0.866	0.752	0.988	0.866	0.752	0.988	CLONAL	1	TRUE	1	0.49	2		319	278	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090071	37090071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1559591314	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	24	346	0	ENST00000231790.2:c.1960C>T	p.Pro654Ser	p.P654S	ENST00000231790	NM_000249.3	654	Cct/Tct	17/19	1	2	FACETS	0.38	0.298	0.473	0.38	0.298	0.473	SUBCLONAL	1	TRUE	1	0.49	2		346	258	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47108598	47108598	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	22	208	0	ENST00000409792.3:c.6071G>T	p.Arg2024Leu	p.R2024L	ENST00000409792	NM_014159.6	2024	cGa/cTa	13/21	1	2	FACETS	0.655	0.514	0.816	0.655	0.514	0.816	SUBCLONAL	1	TRUE	1	0.49	2		208	137	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161991	47161991	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	29	261	0	ENST00000409792.3:c.4135G>T	p.Asp1379Tyr	p.D1379Y	ENST00000409792	NM_014159.6	1379	Gac/Tac	3/21	1	2	FACETS	0.947	0.773	1	0.947	0.773	1	CLONAL	1	TRUE	1	0.49	2		261	125	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162333	47162333	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	12	263	0	ENST00000409792.3:c.3793G>T	p.Glu1265Ter	p.E1265*	ENST00000409792	NM_014159.6	1265	Gaa/Taa	3/21	1	2	FACETS	0.302	0.213	0.412	0.302	0.213	0.412	SUBCLONAL	1	TRUE	1	0.49	2		263	162	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72873590	72873590	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	23	259	0	ENST00000325599.8:c.712A>C	p.Asn238His	p.N238H	ENST00000325599	NM_018130.2	238	Aat/Cat	6/11	1	2	FACETS	0.546	0.429	0.679	0.546	0.429	0.679	SUBCLONAL	1	TRUE	1	0.49	2		259	172	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156963	89156963	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	95	381	0	ENST00000336596.2:c.65T>G	p.Leu22Arg	p.L22R	ENST00000336596	NM_005233.5	22	cTg/cGg	1/17	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.49	2		381	363	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274944	142274944	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	35	272	0	ENST00000350721.4:c.2116G>T	p.Glu706Ter	p.E706*	ENST00000350721	NM_001184.3	706	Gaa/Taa	10/47	1	2	FACETS	0.803	0.666	0.952	0.803	0.666	0.952	CLONAL	1	TRUE	1	0.49	2		272	178	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281302	142281302	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	62	342	0	ENST00000350721.4:c.942A>C	p.Glu314Asp	p.E314D	ENST00000350721	NM_001184.3	314	gaA/gaC	4/47	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.49	2		342	211	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952012	178952012	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	33	254	0	ENST00000263967.3:c.3067C>T	p.Arg1023Ter	p.R1023*	ENST00000263967	NM_006218.2	1023	Cga/Tga	21/21	1	2	FACETS	0.886	0.732	1	0.886	0.732	1	CLONAL	1	TRUE	1	0.49	2		254	152	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665348	182665348	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1553838648	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	22	151	0	ENST00000292782.4:c.593A>C	p.Lys198Thr	p.K198T	ENST00000292782	NM_020640.2	198	aAa/aCa	5/7	1	2	FACETS	0.691	0.542	0.859	0.691	0.542	0.859	SUBCLONAL	1	TRUE	1	0.49	2		151	130	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182681676	182681676	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	36	246	0	ENST00000292782.4:c.382G>T	p.Glu128Ter	p.E128*	ENST00000292782	NM_020640.2	128	Gaa/Taa	3/7	1	2	FACETS	0.769	0.639	0.912	0.769	0.639	0.912	CLONAL	1	TRUE	1	0.49	2		246	191	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155354	185155354	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	53	340	0	ENST00000265026.3:c.595G>T	p.Glu199Ter	p.E199*	ENST00000265026	NM_004721.4	199	Gaa/Taa	3/14	1	2	FACETS	0.603	0.516	0.697	0.603	0.516	0.697	SUBCLONAL	1	TRUE	1	0.49	2		340	359	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442741	187442741	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	38	252	0	ENST00000232014.4:c.1965G>T	p.Glu655Asp	p.E655D	ENST00000232014	NM_001130845.1	655	gaG/gaT	9/10	1	2	FACETS	0.535	0.444	0.635	0.535	0.444	0.635	SUBCLONAL	1	TRUE	1	0.49	2		252	290	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607164	189607164	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	28	498	0	ENST00000264731.3:c.1543G>T	p.Asp515Tyr	p.D515Y	ENST00000264731	NM_003722.4	515	Gac/Tac	12/14	1	2	FACETS	0.297	0.237	0.365	0.297	0.237	0.365	SUBCLONAL	1	TRUE	1	0.49	2		498	385	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1978263	1978263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	93	567	0	ENST00000382891.5:c.3683G>A	p.Arg1228His	p.R1228H	ENST00000382891	NM_133335.3	1228	cGc/cAc	21/22	1	2	FACETS	0.831	0.742	0.924	0.831	0.742	0.924	CLONAL	1	TRUE	1	0.49	2		567	457	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133455	55133455	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	39	291	0	ENST00000257290.5:c.760-1G>A		p.X254_splice	ENST00000257290	NM_006206.4	254			1	2	FACETS	0.899	0.755	1	0.899	0.755	1	CLONAL	1	TRUE	1	0.49	2		291	177	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156540	55156540	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775205485	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	55	383	0	ENST00000257290.5:c.2941C>T	p.Arg981Cys	p.R981C	ENST00000257290	NM_006206.4	981	Cgt/Tgt	22/23	1	2	FACETS	0.968	0.837	1	0.968	0.837	1	CLONAL	1	TRUE	1	0.49	2		383	232	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565835	55565835	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	44	388	0	ENST00000288135.5:c.659G>T	p.Ser220Ile	p.S220I	ENST00000288135	NM_000222.2	220	aGc/aTc	4/21	1	2	FACETS	0.805	0.682	0.939	0.805	0.682	0.939	CLONAL	1	TRUE	1	0.49	2		388	223	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972933	55972933	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	10	286	0	ENST00000263923.4:c.1457G>T	p.Arg486Ile	p.R486I	ENST00000263923	NM_002253.2	486	aGa/aTa	11/30	1	2	FACETS	0.267	0.181	0.374	0.267	0.181	0.374	SUBCLONAL	1	TRUE	1	0.49	2		286	153	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467748	66467748	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	21	224	0	ENST00000273854.3:c.521T>G	p.Ile174Ser	p.I174S	ENST00000273854	NM_004439.5	174	aTt/aGt	3/18	1	2	FACETS	0.703	0.548	0.877	0.703	0.548	0.877	SUBCLONAL	1	TRUE	1	0.49	2		224	122	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156426	106156426	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	19	270	0	ENST00000380013.4:c.1327A>G	p.Thr443Ala	p.T443A	ENST00000380013	NM_001127208.2	443	Aca/Gca	3/11	1	2	FACETS	0.454	0.346	0.578	0.454	0.346	0.578	SUBCLONAL	1	TRUE	1	0.49	2		270	171	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106183003	106183003	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	10	147	0	ENST00000380013.4:c.4042C>A	p.Gln1348Lys	p.Q1348K	ENST00000380013	NM_001127208.2	1348	Cag/Aag	8/11	1	2	FACETS	0.412	0.281	0.573	0.412	0.281	0.573	SUBCLONAL	1	TRUE	1	0.49	2		147	99	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250828	153250828	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	30	262	0	ENST00000281708.4:c.1232G>A	p.Gly411Asp	p.G411D	ENST00000281708	NM_033632.3	411	gGc/gAc	8/12	1	2	FACETS	0.641	0.521	0.775	0.641	0.521	0.775	SUBCLONAL	1	TRUE	1	0.49	2		262	191	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517885	187517885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1222913841	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	34	299	0	ENST00000441802.2:c.12809G>A	p.Arg4270Gln	p.R4270Q	ENST00000441802	NM_005245.3	4270	cGa/cAa	25/27	1	2	FACETS	0.557	0.458	0.668	0.557	0.458	0.668	SUBCLONAL	1	TRUE	1	0.49	2		299	249	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525683	187525683	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	17	292	0	ENST00000441802.2:c.10396G>T	p.Asp3466Tyr	p.D3466Y	ENST00000441802	NM_005245.3	3466	Gat/Tat	18/27	1	2	FACETS	0.397	0.297	0.513	0.397	0.297	0.513	SUBCLONAL	1	TRUE	1	0.49	2		292	175	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534451	187534451	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	40	270	0	ENST00000441802.2:c.9275T>C	p.Val3092Ala	p.V3092A	ENST00000441802	NM_005245.3	3092	gTt/gCt	13/27	1	2	FACETS	0.553	0.462	0.654	0.553	0.462	0.654	SUBCLONAL	1	TRUE	1	0.49	2		270	295	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542918	187542918	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1408700232	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	22	137	0	ENST00000441802.2:c.4822A>C	p.Asn1608His	p.N1608H	ENST00000441802	NM_005245.3	1608	Aat/Cat	10/27	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.49	2		137	79	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628899	187628899	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	83	403	0	ENST00000441802.2:c.2083A>T	p.Asn695Tyr	p.N695Y	ENST00000441802	NM_005245.3	695	Aac/Tac	2/27	1	2	FACETS	0.946	0.842	1	0.946	0.842	1	CLONAL	1	TRUE	1	0.49	2		403	358	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629270	187629270	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	80	417	0	ENST00000441802.2:c.1712A>C	p.Lys571Thr	p.K571T	ENST00000441802	NM_005245.3	571	aAa/aCa	2/27	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.49	2		417	305	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633900	86633900	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	13	207	0	ENST00000274376.6:c.1009G>T	p.Glu337Ter	p.E337*	ENST00000274376	NM_002890.2	337	Gaa/Taa	5/25	1	2	FACETS	0.359	0.257	0.481	0.359	0.257	0.481	SUBCLONAL	1	TRUE	1	0.49	2		207	148	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645079	86645079	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	48	212	1	ENST00000274376.6:c.1151G>A	p.Gly384Asp	p.G384D	ENST00000274376	NM_002890.2	384	gGc/gAc	8/25	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.49	2		213	179	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672056	30672056	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	39	497	0	ENST00000376406.3:c.4904C>A	p.Ser1635Tyr	p.S1635Y	ENST00000376406	NM_014641.2	1635	tCt/tAt	10/15	0.163447526461599	3	FACETS	0.478	0.396	0.568	0.239	0.198	0.284	INDETERMINATE	1	TRUE	1	0.49	3		497	415	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190436	32190436	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs758283279	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	74	622	2	ENST00000375023.3:c.303C>A	p.Phe101Leu	p.F101L	ENST00000375023	NM_004557.3	101	ttC/ttA	3/30	0.163447526461599	3	FACETS	0.845	0.742	0.955	0.423	0.371	0.478	INDETERMINATE	1	TRUE	1	0.49	3		624	445	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820952	32820952	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1160841627	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	137	652	0	ENST00000354258.4:c.642G>A	p.Trp214Ter	p.W214*	ENST00000354258	NM_000593.5	214	tgG/tgA	1/11	0.163447526461599	3	FACETS	1	0.967	1	0.561	0.512	0.613	INDETERMINATE	1	TRUE	1	0.49	3		652	620	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967945	93967945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745827385	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	20	302	1	ENST00000369303.4:c.1982C>T	p.Ala661Val	p.A661V	ENST00000369303	NM_004440.3	661	gCa/gTa	11/17	0.163447526461599	3	FACETS	0.538	0.413	0.682	0.269	0.206	0.341	INDETERMINATE	1	TRUE	1	0.49	3		303	189	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982028	93982028	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	42	229	0	ENST00000369303.4:c.1437G>T	p.Lys479Asn	p.K479N	ENST00000369303	NM_004440.3	479	aaG/aaT	6/17	0.163447526461599	3	FACETS	1	0.958	1	0.716	0.609	0.83	INDETERMINATE	1	TRUE	1	0.49	3		229	149	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120442	94120442	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	26	240	0	ENST00000369303.4:c.609G>T	p.Lys203Asn	p.K203N	ENST00000369303	NM_004440.3	203	aaG/aaT	3/17	0.163447526461599	3	FACETS	1	0.879	1	0.565	0.455	0.685	INDETERMINATE	1	TRUE	1	0.49	3		240	117	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663635	117663635	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs755903627	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	45	281	0	ENST00000368508.3:c.4597A>C	p.Lys1533Gln	p.K1533Q	ENST00000368508	NM_002944.2	1533	Aaa/Caa	28/43	0.163447526461599	3	FACETS	1	0.96	1	0.706	0.603	0.815	INDETERMINATE	1	TRUE	1	0.49	3		281	162	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725561	117725561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	46	287	0	ENST00000368508.3:c.320C>T	p.Ala107Val	p.A107V	ENST00000368508	NM_002944.2	107	gCt/gTt	5/43	0.163447526461599	3	FACETS	1	0.896	1	0.534	0.454	0.62	INDETERMINATE	1	TRUE	1	0.49	3		287	219	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419939	152419939	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	100	403	0	ENST00000206249.3:c.1626G>T	p.Glu542Asp	p.E542D	ENST00000206249	NM_000125.3	542	gaG/gaT	8/8	0.163447526461599	3	FACETS	1	0.976	1	0.648	0.583	0.716	INDETERMINATE	1	TRUE	1	0.49	3		403	392	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978836	13978836	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	57	296	0	ENST00000405192.2:c.271G>T	p.Glu91Ter	p.E91*	ENST00000405192	NM_001163147.1	91	Gaa/Taa	6/12	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.49	2		296	223	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335663	81335663	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	24	341	0	ENST00000222390.5:c.1697A>G	p.Asn566Ser	p.N566S	ENST00000222390	NM_000601.4	566	aAt/aGt	15/18	1	2	FACETS	0.406	0.32	0.506	0.406	0.32	0.506	SUBCLONAL	1	TRUE	1	0.49	2		341	241	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508803	106508803	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	41	434	0	ENST00000359195.3:c.797G>T	p.Ser266Ile	p.S266I	ENST00000359195	NM_002649.2	266	aGc/aTc	2/11	1	2	FACETS	0.414	0.345	0.491	0.414	0.345	0.491	SUBCLONAL	1	TRUE	1	0.49	2		434	404	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512039	148512039	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	28	253	0	ENST00000320356.2:c.1639T>G	p.Phe547Val	p.F547V	ENST00000320356	NM_004456.4	547	Ttt/Gtt	14/20	1	2	FACETS	0.574	0.462	0.7	0.574	0.462	0.7	SUBCLONAL	1	TRUE	1	0.49	2		253	199	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873742	151873742	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	54	365	0	ENST00000262189.6:c.8796T>G	p.Ile2932Met	p.I2932M	ENST00000262189	NM_170606.2	2932	atT/atG	38/59	1	2	FACETS	0.745	0.64	0.857	0.745	0.64	0.857	SUBCLONAL	1	TRUE	1	0.49	2		365	296	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272107	38272107	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	101	417	0	ENST00000425967.3:c.2111T>G	p.Phe704Cys	p.F704C	ENST00000425967	NM_001174067.1	704	tTt/tGt	16/19	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.49	2		417	333	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864548	56864548	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	55	356	0	ENST00000519728.1:c.511G>T	p.Asp171Tyr	p.D171Y	ENST00000519728	NM_002350.3	171	Gac/Tac	7/13	1	2	FACETS	0.968	0.837	1	0.968	0.837	1	CLONAL	1	TRUE	1	0.49	2		356	232	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74858960	74858960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1297079854	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	40	291	1	ENST00000284811.8:c.244C>T	p.Arg82Cys	p.R82C	ENST00000284811		82	Cgc/Tgc	4/4	1	2	FACETS	0.746	0.625	0.877	0.746	0.625	0.877	SUBCLONAL	1	TRUE	1	0.49	2		292	219	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158053	27158053	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1364627600	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	72	465	1	ENST00000380036.4:c.277G>T	p.Ala93Ser	p.A93S	ENST00000380036	NM_000459.3	93	Gct/Tct	2/23	1	2	FACETS	0.986	0.87	1	0.986	0.87	1	CLONAL	1	TRUE	1	0.49	2		466	298	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202881	27202881	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs886063822	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	44	331	0	ENST00000380036.4:c.1973C>A	p.Ser658Tyr	p.S658Y	ENST00000380036	NM_000459.3	658	tCt/tAt	13/23	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.49	2		331	170	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1331500	1331500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	100	383	0	ENST00000400841.2:c.28G>A	p.Ala10Thr	p.A10T	ENST00000400841		10	Gct/Act	1/6	0.3	2	FACETS	0.945	0.849	1	0.472	0.424	0.523	CLONAL	1	TRUE	0	0.49	2		383	432	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933989	39933989	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	53	266	0	ENST00000378444.4:c.610T>G	p.Tyr204Asp	p.Y204D	ENST00000378444	NM_001123385.1	204	Tac/Gac	4/15	0.3	2	FACETS	0.983	0.849	1	0.492	0.424	0.564	CLONAL	1	TRUE	0	0.49	2		266	220	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945125	44945125	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	35	138	0	ENST00000377967.4:c.3449A>G	p.Asn1150Ser	p.N1150S	ENST00000377967	NM_021140.2	1150	aAc/aGc	24/29	0.3	2	FACETS	0.85	0.723	0.981	0.85	0.723	0.981	CLONAL	2	TRUE	0	0.49	2		138	84	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989087	41989087	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	120	360	0	ENST00000219905.7:c.1879C>T	p.Arg627Ter	p.R627*	ENST00000219905	NM_001164273.1	627	Cga/Tga	3/24	0.211601194931805	2	FACETS	0.952	0.863	1	0.952	0.863	1	CLONAL	2	TRUE	0	0.22	2		360	573	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686961	37686961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367703051	NA	P-0037900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	118	314	0	ENST00000447079.4:c.3865G>A	p.Ala1289Thr	p.A1289T	ENST00000447079	NM_015083.1	1289	Gcc/Acc	14/14	0.211601194931805	2	FACETS	0.93	0.841	1	0.93	0.841	1	CLONAL	2	TRUE	0	0.22	2		314	577	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374882	45374882	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs776149698	NA	P-0037900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	86	335	0	ENST00000262160.6:c.961C>T	p.Arg321Ter	p.R321*	ENST00000262160	NM_005901.5	321	Cga/Tga	8/11	0.211601194931805	2	FACETS	0.842	0.748	0.942	0.842	0.748	0.942	CLONAL	2	TRUE	0	0.22	2		335	464	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584526	52584526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs563717316	NA	P-0037900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	135	380	0	ENST00000394830.3:c.4487G>A	p.Arg1496Gln	p.R1496Q	ENST00000394830	NM_018313.4	1496	cGg/cAg	29/30	0.211601194931805	2	FACETS	0.904	0.823	0.988	0.904	0.823	0.988	CLONAL	2	TRUE	0	0.22	2		380	679	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724421	112724421	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0037900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	99	395	0	ENST00000369452.4:c.305C>G	p.Ser102Ter	p.S102*	ENST00000369452	NM_007373.3	102	tCa/tGa	2/9	0.26325615527373	4	FACETS	0.759	0.678	0.846	0.759	0.678	0.846	SUBCLONAL	2	TRUE	2	0.22	4		395	723	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572604	64572604	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894264	NA	P-0037900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	160	489	1	ENST00000312049.6:c.1252G>A	p.Asp418Asn	p.D418N	ENST00000312049	NM_130799.2	418	Gac/Aac	9/10	0.210555749946966	2	FACETS	0.89	0.817	0.967	0.89	0.817	0.967	CLONAL	2	TRUE	0	0.22	2		490	817	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36989289	36989289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	49	379	0	ENST00000354822.5:c.46G>A	p.Ala16Thr	p.A16T	ENST00000354822	NM_001079668.2	16	Gcg/Acg	1/3	0.194796615353515	4	FACETS	0.898	0.76	1	0.449	0.38	0.526	CLONAL	1	TRUE	2	0.22	4		379	605	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238990	5238990	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778054699	NA	P-0037900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	141	351	0	ENST00000357368.4:c.1789C>T	p.Arg597Cys	p.R597C	ENST00000357368	NM_002850.3	597	Cgc/Tgc	13/38	0.166915790372782	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.22	3		351	652	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528079	157528079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1282942992	NA	P-0037902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	83	410	0	ENST00000346085.5:c.5804C>T	p.Ala1935Val	p.A1935V	ENST00000346085	NM_020732.3	1935	gCg/gTg	20/20	1	2	FACETS	0.493	0.437	0.553	0.493	0.437	0.553	SUBCLONAL	1	TRUE	1	0.749571620222608	2		410	449	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871873	12871873	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	128	161	0	ENST00000228872.4:c.592del	p.Thr198ArgfsTer27	p.T198Rfs*27	ENST00000228872	NM_004064.3	197	cAa/ca	2/3	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.749571620222608	2		161	292	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0037914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	582	600	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.697436975958056	3	FACETS	0.92	0.896	0.943	0.92	0.896	0.943	CLONAL	3	TRUE	0	0.722007227787723	3		600	795	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319369	62319369	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774688252	NA	P-0037914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1154	276	937	1	ENST00000360203.5:c.1561G>A	p.Asp521Asn	p.D521N	ENST00000360203	NM_001283009.1	521	Gat/Aat	18/35	0.202117314740371	6	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.722007227787723	6		938	1430	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344973	70344973	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756039521	NA	P-0037914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	77	623	1	ENST00000374080.3:c.2203G>A	p.Ala735Thr	p.A735T	ENST00000374080		735	Gcc/Acc	15/45	0.509048183114318	1	FACETS	0.313	0.275	0.352	0.313	0.275	0.352	SUBCLONAL	1	TRUE	0	0.722007227787723	1		624	436	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332884	65332884	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	84	191	0	ENST00000342505.4:c.655C>T	p.Arg219Ter	p.R219*	ENST00000342505	NM_002227.2	219	Cga/Tga	7/25	0.722007227787723	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.722007227787723	1		191	122	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980726	70980726	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	141	596	0	ENST00000276594.2:c.742C>T	p.Gln248Ter	p.Q248*	ENST00000276594	NM_024504.3	248	Caa/Taa	3/8	0.558544020874973	3	FACETS	0.795	0.726	0.867	0.397	0.363	0.434	SUBCLONAL	1	TRUE	1	0.722007227787723	3		596	669	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110704	2110704	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	269	821	0	ENST00000219476.3:c.1009G>C	p.Glu337Gln	p.E337Q	ENST00000219476	NM_000548.3	337	Gag/Cag	11/42	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.722007227787723	2		821	741	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861085	35861085	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	71	283	0	ENST00000303115.3:c.214G>A	p.Glu72Lys	p.E72K	ENST00000303115	NM_002185.3	72	Gaa/Aaa	2/8	1	2	FACETS	0.806	0.713	0.903	0.806	0.713	0.903	CLONAL	1	TRUE	1	0.722007227787723	2		283	244	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622086	43622086	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	103	412	0	ENST00000355710.3:c.3103G>A	p.Glu1035Lys	p.E1035K	ENST00000355710	NM_020975.4	1035	Gag/Aag	19/20	0.28468490193396	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.722007227787723	0		412	345	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248117	59248117	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	65	201	0	ENST00000371222.2:c.626A>C	p.His209Pro	p.H209P	ENST00000371222	NM_002228.3	209	cAc/cCc	1/1	0.217500395114276	3	FACETS	0.984	0.864	1	0.492	0.432	0.556	INDETERMINATE	1	TRUE	1	0.722007227787723	3		201	249	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145018	58145018	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	395	564	0	ENST00000257904.6:c.326del	p.Pro109HisfsTer12	p.P109Hfs*12	ENST00000257904	NM_000075.3	109	cCa/ca	3/8	0.481249530038096	5	FACETS	1	0.987	1	0.728	0.693	0.762	CLONAL	2	TRUE	2	0.722007227787723	5		564	1044	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132919	30132919	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	282	513	0	ENST00000331968.5:c.682G>T	p.Asp228Tyr	p.D228Y	ENST00000331968	NM_002742.2	228	Gat/Tat	4/18	0.256578016358825	3	FACETS	0.97	0.922	1	0.647	0.615	0.679	INDETERMINATE	2	TRUE	0	0.722007227787723	3		513	548	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858291	9858291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	113	432	0	ENST00000330684.3:c.3110C>T	p.Ala1037Val	p.A1037V	ENST00000330684	NM_001134407.1	1037	gCa/gTa	13/13	1	2	FACETS	0.865	0.786	0.946	0.865	0.786	0.946	CLONAL	1	TRUE	1	0.722007227787723	2		432	362	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600446	10600446	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	652	829	1	ENST00000171111.5:c.1409G>T	p.Arg470Leu	p.R470L	ENST00000171111	NM_203500.1	470	cGt/cTt	4/6	0.0723441138545623	5	FACETS	1	0.996	1			1	INDETERMINATE	4	TRUE	NA	0.722007227787723	5		830	854	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461527	138461528	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0037914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	129	455	0	ENST00000289153.2:c.493_494delinsTT	p.Gly165Leu	p.G165L	ENST00000289153	NM_006219.2	165	GGa/TTa	3/22	0.722007227787723	3	FACETS	0.932	0.849	1	0.466	0.424	0.509	CLONAL	1	TRUE	1	0.722007227787723	3		455	522	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467410	66467410	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	61	237	0	ENST00000273854.3:c.859G>T	p.Gly287Trp	p.G287W	ENST00000273854	NM_004439.5	287	Ggg/Tgg	3/18	NA	2	FACETS	0.63	0.549	0.717			1	INDETERMINATE	1	TRUE	NA	0.722007227787723	2		237	268	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86681162	86681162	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0037914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	79	255	0	ENST00000274376.6:c.2803A>T	p.Lys935Ter	p.K935*	ENST00000274376	NM_002890.2	935	Aaa/Taa	22/25	0.722007227787723	1	FACETS	0.964	0.877	1	0.964	0.877	1	CLONAL	1	TRUE	0	0.722007227787723	1		255	145	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521544	8521544	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	115	450	1	ENST00000356435.5:c.694C>A	p.Arg232Ser	p.R232S	ENST00000356435		232	Cgc/Agc	9/35	0.722007227787723	1	FACETS	0.817	0.751	0.884	0.817	0.751	0.884	CLONAL	1	TRUE	0	0.722007227787723	1		451	249	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0037917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	143	422	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.875	0.802	0.952	1	0.99	1	CLONAL	2	TRUE	1	0.281167044157761	2		422	581	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0037917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	126	784	8	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.96	0.875	1	1	0.99	1	CLONAL	2	TRUE	1	0.281167044157761	2		792	467	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0037917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	24	770	5	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.363	0.284	0.455	0.363	0.284	0.455	SUBCLONAL	1	TRUE	1	0.281167044157761	2		775	470	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988309	36988309	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776709	NA	P-0037917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	72	522	1	ENST00000354822.5:c.344del	p.Gly115AlafsTer10	p.G115Afs*10	ENST00000354822	NM_001079668.2	115	gGc/gc	2/3	1	2	FACETS	0.842	0.743	0.948	1	0.98	1	CLONAL	2	TRUE	1	0.281167044157761	2		523	304	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339328	70339328	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0037917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	118	469	0	ENST00000374080.3:c.204+1G>T		p.X68_splice	ENST00000374080		68			0.281167044157761	1	FACETS	1	0.974	1	1	0.991	1	CLONAL	2	TRUE	0	0.281167044157761	1		469	309	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354375	354375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910854855	NA	P-0037917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	223	851	0	ENST00000262320.3:c.1183C>T	p.Arg395Cys	p.R395C	ENST00000262320	NM_003502.3	395	Cgc/Tgc	5/11	0.146475220184636	0	FACETS	0.902	0.845	0.96			1	INDETERMINATE	2	TRUE	0	0.281167044157761	0		851	632	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624296	89624296	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786201995	NA	P-0037917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	148	540	0	ENST00000371953.3:c.70G>T	p.Asp24Tyr	p.D24Y	ENST00000371953	NM_000314.4	24	Gac/Tac	1/9	1	2	FACETS	1	0.947	1	1	0.992	1	CLONAL	2	TRUE	1	0.281167044157761	2		540	507	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692818	89692818	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	69	257	0	ENST00000371953.3:c.302del	p.Ile101ThrfsTer12	p.I101Tfs*12	ENST00000371953	NM_000314.4	101	aTc/ac	5/9	1	2	FACETS	0.866	0.769	0.965	1	0.986	1	CLONAL	3	TRUE	1	0.281167044157761	2		257	189	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927443	245927443	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	88	578	5	ENST00000388985.4:c.1085del	p.Phe362SerfsTer12	p.F362Sfs*12	ENST00000388985		362	tTc/tc	11/12	0.281167044157761	4	FACETS	1	0.979	1	0.493	0.438	0.552	CLONAL	1	TRUE	1	0.281167044157761	4		583	542	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210725	36210725	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	151	919	0	ENST00000222270.7:c.481del	p.Leu161PhefsTer6	p.L161Ffs*6	ENST00000222270	NM_014727.1	159	aCc/ac	3/37	0.123425703319859	0	FACETS	0.775	0.714	0.839			1	INDETERMINATE	2	TRUE	0	0.281167044157761	0		919	498	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648218	206648218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782466362	NA	P-0037917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	68	451	0	ENST00000367120.3:c.239G>A	p.Arg80Gln	p.R80Q	ENST00000367120	NM_014002.3	80	cGg/cAg	5/22	0.281167044157761	4	FACETS	0.759	0.663	0.862	0.506	0.442	0.575	SUBCLONAL	2	TRUE	1	0.281167044157761	4		451	408	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646190	3646190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376620029	NA	P-0037917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	40	928	0	ENST00000294008.3:c.1888G>A	p.Gly630Ser	p.G630S	ENST00000294008	NM_032444.2	630	Ggc/Agc	8/15	0.146475220184636	0	FACETS	0.449	0.373	0.533			1	INDETERMINATE	1	TRUE	0	0.281167044157761	0		928	456	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492704	56492706	+	inframe_deletion	In_Frame_Del	DEL	CTG	CTG	-	novel	NA	P-0037917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	107	503	0	ENST00000407977.2:c.233_235del	p.Ala78del	p.A78del	ENST00000407977		78	gCAGaa/gaa	2/10	1	2	FACETS	0.968	0.876	1	1	0.988	1	CLONAL	2	TRUE	1	0.281167044157761	2		503	393	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350605	15350605	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	197	965	0	ENST00000263377.2:c.3310C>G	p.Pro1104Ala	p.P1104A	ENST00000263377	NM_058243.2	1104	Ccc/Gcc	16/20	0.123425703319859	0	FACETS	0.895	0.834	0.956			1	INDETERMINATE	2	TRUE	0	0.281167044157761	0		965	563	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046915	128046915	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	29	505	0	ENST00000285398.2:c.820C>T	p.Gln274Ter	p.Q274*	ENST00000285398	NM_000122.1	274	Cag/Tag	6/15	1	2	FACETS	0.501	0.401	0.614	0.501	0.401	0.614	SUBCLONAL	1	TRUE	1	0.281167044157761	2		505	412	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829195	128829195	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	13	347	0	ENST00000249373.3:c.207del	p.Cys70AlafsTer52	p.C70Afs*52	ENST00000249373	NM_005631.4	68	gCc/gc	1/12	1	2	FACETS	0.399	0.284	0.538	0.399	0.284	0.538	SUBCLONAL	1	TRUE	1	0.281167044157761	2		347	232	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0037938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	23	294	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.301617498861238	5	FACETS	1	0.801	1	1	0.801	1	CLONAL	2	TRUE	3	0.42	5		294	89	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855935	68855936	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0037938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	22	435	0	ENST00000261769.5:c.1744_1745del	p.Leu582AlafsTer5	p.L582Afs*5	ENST00000261769	NM_004360.3	581	ctTCtg/cttg	12/16	0.234282746254576	3	FACETS	1	0.922	1	0.475	0.376	0.583	INDETERMINATE	1	TRUE	0	0.42	3		435	89	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96931038	96931038	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	27	180	0	ENST00000258439.3:c.82G>A	p.Glu28Lys	p.E28K	ENST00000258439	NM_001193304.2	28	Gag/Aag	2/4	0.121373748935634	0	FACETS	0.544	0.439	0.661			1	INDETERMINATE	1	TRUE	0	0.42	0		180	137	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55269017	55269017	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	37	530	0	ENST00000275493.2:c.3083C>G	p.Ser1028Cys	p.S1028C	ENST00000275493	NM_005228.3	1028	tCc/tGc	25/28	0.214568803005089	5	FACETS	0.92	0.771	1	0.614	0.514	0.722	INDETERMINATE	2	TRUE	2	0.42	5		530	156	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0037939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	141	816	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.288310331105576	5	FACETS	0.94	0.862	1			1	CLONAL	3	FALSE	NA	0.288310331105576	5		816	497	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913355	NA	P-0037946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	46	314	0	ENST00000288602.6:c.1406G>T	p.Gly469Val	p.G469V	ENST00000288602	NM_004333.4	469	gGa/gTa	11/18	1	2	FACETS	0.622	0.524	0.731	0.622	0.524	0.731	SUBCLONAL	1	TRUE	1	0.279026607430095	2		314	530	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610265	10610265	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	170	629	0	ENST00000171111.5:c.445G>T	p.Glu149Ter	p.E149*	ENST00000171111	NM_203500.1	149	Gag/Tag	2/6	0.170621915182853	2	FACETS	1	0.983	1	0.629	0.578	0.683	CLONAL	1	TRUE	0	0.279026607430095	2		629	968	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793427	242793427	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	52	495	0	ENST00000334409.5:c.650C>A	p.Pro217His	p.P217H	ENST00000334409	NM_005018.2	217	cCt/cAt	5/5	0.183694187494944	3	FACETS	0.495	0.42	0.578	0.248	0.21	0.289	SUBCLONAL	1	TRUE	1	0.279026607430095	3		495	858	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598839	28598839	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	156	568	0	ENST00000253063.3:c.399G>T	p.Met133Ile	p.M133I	ENST00000253063	NM_031459.4	133	atG/atT	4/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.279026607430095	2		568	908	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78426138	78426138	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	42	306	0	ENST00000370768.2:c.1387del	p.His463MetfsTer202	p.H463Mfs*202	ENST00000370768	NM_003902.3	463	Cat/at	15/20	1	2	FACETS	0.599	0.499	0.709	0.599	0.499	0.709	SUBCLONAL	1	TRUE	1	0.279026607430095	2		306	503	SUCCESS
EED	8726	MSKCC	GRCh37	11	85956278	85956278	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	66	213	0	ENST00000263360.6:c.7G>T	p.Glu3Ter	p.E3*	ENST00000263360	NM_003797.3	3	Gag/Tag	1/12	0.183694187494944	3	FACETS	1	0.962	1	0.645	0.562	0.734	CLONAL	1	TRUE	1	0.279026607430095	3		213	418	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909882	100909882	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	31	292	0	ENST00000325455.5:c.2767G>T	p.Gly923Trp	p.G923W	ENST00000325455	NM_001202474.3	923	Ggg/Tgg	8/8	0.183694187494944	3	FACETS	0.622	0.503	0.757	0.311	0.251	0.379	SUBCLONAL	1	TRUE	1	0.279026607430095	3		292	407	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962607	100962607	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	78	297	0	ENST00000325455.5:c.1790G>T	p.Gly597Val	p.G597V	ENST00000325455	NM_001202474.3	597	gGg/gTg	3/8	0.183694187494944	3	FACETS	1	0.969	1	0.662	0.584	0.746	CLONAL	1	TRUE	1	0.279026607430095	3		297	481	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112532	115112532	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	128	511	0	ENST00000257566.3:c.1208C>A	p.Pro403His	p.P403H	ENST00000257566	NM_016569.3	403	cCc/cAc	7/8	0.170621915182853	2	FACETS	1	0.98	1	0.652	0.591	0.715	CLONAL	1	TRUE	0	0.279026607430095	2		511	704	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434730	99434730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269644208	NA	P-0037946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	76	509	0	ENST00000268035.6:c.817G>A	p.Gly273Ser	p.G273S	ENST00000268035	NM_000875.3	273	Ggc/Agc	3/21	0.170621915182853	2	FACETS	0.693	0.607	0.786	0.347	0.303	0.393	SUBCLONAL	1	TRUE	0	0.279026607430095	2		509	786	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684018	29684018	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	134	492	0	ENST00000356175.3:c.7716A>C	p.Leu2572Phe	p.L2572F	ENST00000356175	NM_000267.3	2572	ttA/ttC	52/57	0.170621915182853	2	FACETS	1	0.985	1	0.711	0.648	0.778	CLONAL	1	TRUE	0	0.279026607430095	2		492	675	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117733	70117733	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	70	498	0	ENST00000245479.2:c.201C>G	p.Asp67Glu	p.D67E	ENST00000245479	NM_000346.3	67	gaC/gaG	1/3	0.183694187494944	3	FACETS	0.653	0.568	0.746	0.327	0.284	0.373	SUBCLONAL	1	TRUE	1	0.279026607430095	3		498	875	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219328	5219328	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	163	549	0	ENST00000357368.4:c.3916T>C	p.Tyr1306His	p.Y1306H	ENST00000357368	NM_002850.3	1306	Tac/Cac	23/38	0.170621915182853	2	FACETS	0.766	0.704	0.83	0.766	0.704	0.83	SUBCLONAL	2	TRUE	0	0.279026607430095	2		549	763	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437170	220437170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	79	585	0	ENST00000243786.2:c.74C>T	p.Ala25Val	p.A25V	ENST00000243786	NM_002191.3	25	gCc/gTc	1/2	0.183694187494944	3	FACETS	0.686	0.602	0.777	0.343	0.301	0.389	SUBCLONAL	1	TRUE	1	0.279026607430095	3		585	940	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439821	220439821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	79	570	0	ENST00000243786.2:c.674G>A	p.Ser225Asn	p.S225N	ENST00000243786	NM_002191.3	225	aGt/aAt	2/2	0.183694187494944	3	FACETS	0.804	0.706	0.909	0.402	0.353	0.455	CLONAL	1	TRUE	1	0.279026607430095	3		570	803	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670789	134670789	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	110	408	0	ENST00000398015.3:c.700G>T	p.Val234Leu	p.V234L	ENST00000398015	NM_004441.4	234	Gtg/Ttg	3/16	0.246284532600528	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.279026607430095	1		408	647	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196724	106196724	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	47	395	0	ENST00000380013.4:c.5057G>T	p.Ser1686Ile	p.S1686I	ENST00000380013	NM_001127208.2	1686	aGc/aTc	11/11	0.183694187494944	3	FACETS	0.676	0.57	0.793	0.338	0.285	0.397	SUBCLONAL	1	TRUE	1	0.279026607430095	3		395	568	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500522	149500522	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	69	463	0	ENST00000261799.4:c.2515C>A	p.Leu839Met	p.L839M	ENST00000261799	NM_002609.3	839	Ctg/Atg	18/23	0.246284532600528	1	FACETS	0.649	0.565	0.74	0.649	0.565	0.74	SUBCLONAL	1	TRUE	0	0.279026607430095	1		463	656	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168624	32168624	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	147	499	0	ENST00000375023.3:c.4299C>A	p.His1433Gln	p.H1433Q	ENST00000375023	NM_004557.3	1433	caC/caA	23/30	0.271578605556144	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.279026607430095	1		499	786	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346428	152346428	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	42	350	1	ENST00000359321.1:c.142G>T	p.Gly48Cys	p.G48C	ENST00000359321	NM_005431.1	48	Ggc/Tgc	3/3	1	2	FACETS	0.614	0.513	0.727	0.614	0.513	0.727	SUBCLONAL	1	TRUE	1	0.279026607430095	2		351	490	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518114	8518114	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	207	400	1	ENST00000356435.5:c.1277C>A	p.Ala426Glu	p.A426E	ENST00000356435		426	gCa/gAa	10/35	0.279026607430095	3	FACETS	0.912	0.851	0.974	0.912	0.851	0.974	CLONAL	3	TRUE	0	0.279026607430095	3		401	618	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874314	76874314	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	115	466	0	ENST00000373344.5:c.5408G>T	p.Arg1803Leu	p.R1803L	ENST00000373344	NM_000489.3	1803	cGt/cTt	21/35	0.183694187494944	3	FACETS	1	0.977	1	0.642	0.578	0.709	CLONAL	1	TRUE	1	0.279026607430095	3		466	732	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909691	76909691	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0037946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	22	266	0	ENST00000373344.5:c.4215-1G>T		p.X1405_splice	ENST00000373344	NM_000489.3	1405			0.183694187494944	3	FACETS	0.461	0.356	0.582	0.23	0.178	0.291	SUBCLONAL	1	TRUE	1	0.279026607430095	3		266	390	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0037955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	305	482	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.261483929513659	3	FACETS	0.802	0.761	0.843	0.802	0.761	0.843	INDETERMINATE	2	TRUE	1	0.748821599449953	3		482	698	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0037955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	313	643	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.748821599449953	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.748821599449953	1		643	474	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971116	21971116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552823	NA	P-0037955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	187	324	0	ENST00000304494.5:c.242C>T	p.Pro81Leu	p.P81L	ENST00000304494	NM_000077.4	81	cCc/cTc	2/3	0.748821599449953	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.748821599449953	1		324	286	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344985	70344985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1365839691	NA	P-0037955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	284	568	0	ENST00000374080.3:c.2215C>T	p.Pro739Ser	p.P739S	ENST00000374080		739	Ccc/Tcc	15/45	0.748821599449953	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.748821599449953	1		568	434	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630303	187630303	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774143174	NA	P-0037955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	291	605	0	ENST00000441802.2:c.679C>T	p.Arg227Cys	p.R227C	ENST00000441802	NM_005245.3	227	Cgt/Tgt	2/27	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.748821599449953	2		605	763	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0037955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	117	200	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.748821599449953	2		201	269	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445847	49445847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	302	950	0	ENST00000301067.7:c.1619C>T	p.Pro540Leu	p.P540L	ENST00000301067	NM_003482.3	540	cCt/cTt	10/54	1	2	FACETS	0.881	0.832	0.93	0.881	0.832	0.93	CLONAL	1	TRUE	1	0.748821599449953	2		950	916	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223063	5223078	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGGCCGCCGCGGCT	CCAGGCCGCCGCGGCT	-	rs1174523743	NA	P-0037955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	181	404	0	ENST00000357368.4:c.2725_2740del	p.Ser909AlafsTer8	p.S909Afs*8	ENST00000357368	NM_002850.3	909	AGCCGCGGCGGCCTGGgc/gc	18/38	1	2	FACETS	0.885	0.822	0.95	0.885	0.822	0.95	CLONAL	1	TRUE	1	0.748821599449953	2		404	546	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272825	18272825	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	338	644	0	ENST00000222254.8:c.865C>T	p.Gln289Ter	p.Q289*	ENST00000222254	NM_005027.3	289	Cag/Tag	7/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.748821599449953	2		644	855	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961752	55961752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	98	379	0	ENST00000263923.4:c.2809C>T	p.Pro937Ser	p.P937S	ENST00000263923	NM_002253.2	937	Ccc/Tcc	20/30	1	2	FACETS	0.411	0.367	0.458	0.411	0.367	0.458	SUBCLONAL	1	TRUE	1	0.748821599449953	2		379	637	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523607	176523607	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	403	721	0	ENST00000292408.4:c.2018G>A	p.Trp673Ter	p.W673*	ENST00000292408	NM_213647.1	673	tGg/tAg	16/18	0.748821599449953	3	FACETS	0.91	0.871	0.948	0.91	0.871	0.948	CLONAL	2	TRUE	1	0.748821599449953	3		721	813	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673324	30673325	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0037955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	352	812	2	ENST00000376406.3:c.3635_3636delinsTT	p.Ser1212Phe	p.S1212F	ENST00000376406	NM_014641.2	1212	tCC/tTT	10/15	1	2	FACETS	0.956	0.908	1	0.956	0.908	1	CLONAL	1	TRUE	1	0.748821599449953	2		814	983	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120509	94120509	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	205	332	0	ENST00000369303.4:c.542G>A	p.Gly181Glu	p.G181E	ENST00000369303	NM_004440.3	181	gGa/gAa	3/17	0.748821599449953	1	FACETS	0.641	0.6	0.684	0.641	0.6	0.684	SUBCLONAL	1	TRUE	0	0.748821599449953	1		332	534	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372349	55372349	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	242	561	0	ENST00000297316.4:c.1039G>A	p.Asp347Asn	p.D347N	ENST00000297316	NM_022454.3	347	Gac/Aac	2/2	0.748821599449953	3	FACETS	0.975	0.912	1	0.488	0.456	0.52	CLONAL	1	TRUE	1	0.748821599449953	3		561	911	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396919	139396919	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	15	348	0	ENST00000277541.6:c.5189del	p.Pro1730ArgfsTer68	p.P1730Rfs*68	ENST00000277541	NM_017617.3	1730	cCg/cg	28/34	0.748821599449953	1	FACETS	0.089	0.065	0.119	0.089	0.065	0.119	SUBCLONAL	1	TRUE	0	0.748821599449953	1		348	281	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399887	139399887	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	35	762	0	ENST00000277541.6:c.4461G>A	p.Trp1487Ter	p.W1487*	ENST00000277541	NM_017617.3	1487	tgG/tgA	25/34	0.748821599449953	1	FACETS	0.106	0.086	0.128	0.106	0.086	0.128	SUBCLONAL	1	TRUE	0	0.748821599449953	1		762	551	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	146	503	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.0957277534345624	3	FACETS	1	0.987	1	0.72	0.658	0.783	INDETERMINATE	1	TRUE	1	0.362604747850781	3		503	661	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591892	48591892	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	122	481	0	ENST00000342988.3:c.1055G>C	p.Gly352Ala	p.G352A	ENST00000342988	NM_005359.5	352	gGa/gCa	9/12	0.34678754327365	0	FACETS	1	0.939	1			1	CLONAL	1	TRUE	0	0.362604747850781	0		481	413	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374881	45374881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	72	591	0	ENST00000262160.6:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000262160	NM_005901.5	321	cGa/cAa	8/11	0.34678754327365	0	FACETS	0.483	0.423	0.548			1	SUBCLONAL	1	TRUE	0	0.362604747850781	0		591	524	SUCCESS
APC	324	MSKCC	GRCh37	5	112178268	112178268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs531178000	NA	P-0037957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	31	421	1	ENST00000257430.4:c.6977G>A	p.Arg2326Gln	p.R2326Q	ENST00000257430	NM_000038.5	2326	cGa/cAa	16/16	0.362604747850781	1	FACETS	0.357	0.289	0.435	0.357	0.289	0.435	SUBCLONAL	1	TRUE	0	0.362604747850781	1		422	392	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118881	70118882	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0037957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	185	593	1	ENST00000245479.2:c.454dup	p.Arg152ProfsTer100	p.R152Pfs*100	ENST00000245479	NM_000346.3	151	-/C	2/3	1	2	FACETS	0.933	0.867	1	1	0.993	1	CLONAL	2	TRUE	1	0.362604747850781	2		594	547	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857885	9857885	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs746944419	NA	P-0037957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	107	603	1	ENST00000330684.3:c.3516G>T	p.Leu1172Phe	p.L1172F	ENST00000330684	NM_001134407.1	1172	ttG/ttT	13/13	0.362604747850781	1	FACETS	0.942	0.848	1	0.942	0.848	1	CLONAL	1	TRUE	0	0.362604747850781	1		604	513	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56870564	56870564	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	115	428	0	ENST00000308159.5:c.1834G>A	p.Val612Ile	p.V612I	ENST00000308159	NM_014669.4	612	Gtt/Att	17/22	0.362604747850781	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.362604747850781	1		428	487	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374762	149374762	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	39	281	1	ENST00000360632.3:c.332C>T	p.Ala111Val	p.A111V	ENST00000360632	NM_015472.4	111	gCg/gTg	2/7	1	2	FACETS	0.64	0.532	0.76	0.64	0.532	0.76	SUBCLONAL	1	TRUE	1	0.362604747850781	2		282	336	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0037964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	338	493	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.629939598590261	3	FACETS	0.933	0.889	0.977	0.933	0.889	0.977	CLONAL	2	TRUE	1	0.661324454019989	3		493	729	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0037964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	141	365	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.661324454019989	3	FACETS	0.874	0.799	0.953	0.437	0.399	0.477	CLONAL	1	TRUE	1	0.661324454019989	3		365	649	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120787	115120787	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	184	631	0	ENST00000257566.3:c.219G>T	p.Glu73Asp	p.E73D	ENST00000257566	NM_016569.3	73	gaG/gaT	1/8	0.661324454019989	3	FACETS	1	0.95	1	0.516	0.478	0.556	CLONAL	1	TRUE	1	0.661324454019989	3		631	717	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262126	10262126	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	213	786	0	ENST00000340748.4:c.2165A>G	p.Lys722Arg	p.K722R	ENST00000340748		722	aAg/aGg	23/40	1	2	FACETS	0.719	0.669	0.771	0.719	0.669	0.771	SUBCLONAL	1	TRUE	1	0.661324454019989	2		786	896	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623236	52623236	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1232278552	NA	P-0037964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	152	416	0	ENST00000394830.3:c.2815G>A	p.Gly939Ser	p.G939S	ENST00000394830	NM_018313.4	939	Ggc/Agc	19/30	1	2	FACETS	0.962	0.886	1	0.962	0.886	1	CLONAL	1	TRUE	1	0.661324454019989	2		416	478	SUCCESS
APC	324	MSKCC	GRCh37	5	112174031	112174032	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0037964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	326	480	0	ENST00000257430.4:c.2744_2745del	p.Val915AspfsTer3	p.V915Dfs*3	ENST00000257430	NM_000038.5	914	TGt/t	16/16	0.661324454019989	3	FACETS	0.942	0.897	0.988	0.942	0.897	0.988	CLONAL	2	TRUE	1	0.661324454019989	3		480	696	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0037965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	31	680	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		680	468	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	108	503	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		503	693	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879885	37879885	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	85	792	0	ENST00000269571.5:c.2180G>C	p.Gly727Ala	p.G727A	ENST00000269571		727	gGa/gCa	18/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		792	1136	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	73	469	0	ENST00000304494.5:c.262G>A	p.Glu88Lys	p.E88K	ENST00000304494	NM_000077.4	88	Gag/Aag	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		469	716	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352697	NA	P-0037965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	82	679	1	ENST00000269305.4:c.587G>A	p.Arg196Gln	p.R196Q	ENST00000269305	NM_001126112.2	196	cGa/cAa	6/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		680	1022	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244706	46244706	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	60	642	0	ENST00000334344.6:c.2800C>T	p.Gln934Ter	p.Q934*	ENST00000334344	NM_152641.2	934	Caa/Taa	15/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		642	928	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202753	108202753	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs781215442	NA	P-0037965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	102	418	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		418	702	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970945	21970945	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	102	636	0	ENST00000304494.5:c.413G>C	p.Arg138Thr	p.R138T	ENST00000304494	NM_000077.4	138	aGa/aCa	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		636	980	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224531	108224531	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	79	390	0	ENST00000278616.4:c.8710G>C	p.Glu2904Gln	p.E2904Q	ENST00000278616	NM_000051.3	2904	Gag/Cag	60/63	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		390	758	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90976662	90976662	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	44	492	0	ENST00000265433.3:c.970G>A	p.Asp324Asn	p.D324N	ENST00000265433	NM_002485.4	324	Gat/Aat	8/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		492	708	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110031	115110031	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	89	711	0	ENST00000257566.3:c.1847C>T	p.Ser616Phe	p.S616F	ENST00000257566	NM_016569.3	616	tCt/tTt	8/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		711	1048	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400810	72400810	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	42	402	0	ENST00000357731.5:c.361C>T	p.Gln121Ter	p.Q121*	ENST00000357731	NM_173808.2	121	Cag/Tag	2/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		402	549	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164054	108164054	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	54	222	0	ENST00000278616.4:c.4626G>C	p.Leu1542Phe	p.L1542F	ENST00000278616	NM_000051.3	1542	ttG/ttC	31/63	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		222	338	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377033	118377033	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	98	511	0	ENST00000534358.1:c.10426G>C	p.Asp3476His	p.D3476H	ENST00000534358	NM_005933.3	3476	Gat/Cat	27/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		511	871	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164457	36164457	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	36	256	0	ENST00000300305.3:c.1418A>T	p.Glu473Val	p.E473V	ENST00000300305		473	gAg/gTg	8/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		256	491	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155416	185155416	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	46	376	0	ENST00000265026.3:c.657C>G	p.Phe219Leu	p.F219L	ENST00000265026	NM_004721.4	219	ttC/ttG	3/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		376	641	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401687	401687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	75	638	1	ENST00000380956.4:c.1009G>A	p.Asp337Asn	p.D337N	ENST00000380956	NM_001195286.1	337	Gac/Aac	7/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		639	918	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0037966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	152	813	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.791	0.724	0.861	1	0.989	1	SUBCLONAL	2	TRUE	1	0.229567965634662	2		813	837	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	117	375	0	ENST00000257430.4:c.4199C>A	p.Ser1400Ter	p.S1400*	ENST00000257430	NM_000038.5	1400	tCg/tAg	16/16	0.216837712970078	2	FACETS	0.988	0.895	1	0.988	0.895	1	CLONAL	2	TRUE	0	0.229567965634662	2		375	516	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591114	67591124	+	protein_altering_variant	In_Frame_Del	DEL	CCTTATCCAGC	CCTTATCCAGC	TA	novel	NA	P-0037966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	45	437	1	ENST00000274335.5:c.1707_1717delinsTA	p.Leu570_Leu573delinsMet	p.L570_L573delinsM	ENST00000274335		569	gaCCTTATCCAGCtg/gaTAtg	12/15	0.216837712970078	2	FACETS	0.674	0.565	0.794	0.337	0.282	0.397	SUBCLONAL	1	TRUE	0	0.229567965634662	2		438	582	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683812	117683812	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	104	578	2	ENST00000368508.3:c.3335C>A	p.Ser1112Tyr	p.S1112Y	ENST00000368508	NM_002944.2	1112	tCt/tAt	21/43	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.229567965634662	2		580	687	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	151	503	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.111287630234248	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.829684342635303	0		503	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0037967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	178	813	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.829684342635303	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.829684342635303	1		813	245	SUCCESS
APC	324	MSKCC	GRCh37	5	112175235	112175235	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0037967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	103	223	0	ENST00000257430.4:c.3944C>G	p.Ser1315Ter	p.S1315*	ENST00000257430	NM_000038.5	1315	tCa/tGa	16/16	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.829684342635303	2		223	234	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38178604	38178606	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0037967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	161	270	0	ENST00000317025.8:c.1793_1795del	p.Lys598del	p.K598del	ENST00000317025	NM_023034.1	598	aAGAtc/atc	8/24	NA	2	FACETS	0.828	0.766	0.891			1	INDETERMINATE	1	TRUE	NA	0.829684342635303	2		270	469	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581086	48581160	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAAGATTTTTTTTTCTGGGAATAGAAGCTTATAAAAATTTAAAATATGTTTAATTTTCTATATAGCTCCATCAAG	TAAGATTTTTTTTTCTGGGAATAGAAGCTTATAAAAATTTAAAATATGTTTAATTTTCTATATAGCTCCATCAAG	-	novel	NA	P-0037967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	83	89	0	ENST00000342988.3:c.455-63_466del		p.X152_splice	ENST00000342988	NM_005359.5	152		5/12	0.829684342635303	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.829684342635303	1		89	97	SUCCESS
APC	324	MSKCC	GRCh37	5	112175015	112175015	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1460397656	NA	P-0037967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	95	178	0	ENST00000257430.4:c.3724C>T	p.Gln1242Ter	p.Q1242*	ENST00000257430	NM_000038.5	1242	Cag/Tag	16/16	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.829684342635303	2		178	224	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0037970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	27	587	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.270540716506622	3	FACETS	1	0.831	1	1	0.831	1	CLONAL	2	TRUE	1	0.15	3		587	186	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578507	7578507	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519977	NA	P-0037970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	48	807	0	ENST00000269305.4:c.423C>G	p.Cys141Trp	p.C141W	ENST00000269305	NM_001126112.2	141	tgC/tgG	5/11	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.15	2		807	583	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287398	38287398	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778531708	NA	P-0037970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	41	580	0	ENST00000425967.3:c.259C>T	p.Arg87Cys	p.R87C	ENST00000425967	NM_001174067.1	87	Cgc/Tgc	4/19	0.298387283473635	4	FACETS	0.969	0.805	1			1	CLONAL	1	TRUE	NA	0.15	4		580	649	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879322	151879322	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	26	539	0	ENST00000262189.6:c.5623C>T	p.Gln1875Ter	p.Q1875*	ENST00000262189	NM_170606.2	1875	Cag/Tag	36/59	0.100093864771957	5	FACETS	0.854	0.675	1	0.214	0.168	0.266	CLONAL	1	TRUE	1	0.15	5		539	497	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339856	116339856	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	27	517	0	ENST00000397752.3:c.718G>C	p.Glu240Gln	p.E240Q	ENST00000397752	NM_000245.2	240	Gag/Cag	2/21	0.184788566082078	3	FACETS	0.951	0.756	1	0.475	0.378	0.587	CLONAL	1	TRUE	1	0.15	3		517	407	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255445	16255445	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	32	561	0	ENST00000375759.3:c.2710G>C	p.Asp904His	p.D904H	ENST00000375759	NM_015001.2	904	Gat/Cat	11/15	1	2	FACETS	0.981	0.796	1	0.981	0.796	1	CLONAL	1	TRUE	1	0.15	2		561	435	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333593	70333593	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	26	497	0	ENST00000373644.4:c.1498G>C	p.Glu500Gln	p.E500Q	ENST00000373644	NM_030625.2	500	Gag/Cag	2/12	1	2	FACETS	0.757	0.598	0.939	0.757	0.598	0.939	CLONAL	1	TRUE	1	0.15	2		497	458	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135688	64135688	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	30	705	0	ENST00000334205.4:c.1156G>C	p.Asp386His	p.D386H	ENST00000334205	NM_003942.2	386	Gac/Cac	10/17	0.157547732075042	1	FACETS	0.799	0.643	0.977	0.799	0.643	0.977	CLONAL	1	TRUE	0	0.15	1		705	463	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025650	1025650	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0037970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	29	464	0	ENST00000358495.3:c.726-1G>C		p.X242_splice	ENST00000358495	NM_134424.2	242			0.184788566082078	3	FACETS	1	0.807	1	0.503	0.403	0.617	CLONAL	1	TRUE	1	0.15	3		464	413	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428425	49428425	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	31	656	0	ENST00000301067.7:c.10380G>C	p.Gln3460His	p.Q3460H	ENST00000301067	NM_003482.3	3460	caG/caC	36/54	1	2	FACETS	0.844	0.681	1	0.844	0.681	1	CLONAL	1	TRUE	1	0.15	2		656	490	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490340	29490340	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0037970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	28	551	0	ENST00000356175.3:c.425T>G	p.Leu142Ter	p.L142*	ENST00000356175	NM_000267.3	142	tTa/tGa	4/57	1	2	FACETS	1	0.807	1	1	0.807	1	CLONAL	1	TRUE	1	0.15	2		551	370	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359627	40359627	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	32	631	0	ENST00000293328.3:c.2026G>C	p.Asp676His	p.D676H	ENST00000293328	NM_012448.3	676	Gat/Cat	16/19	1	2	FACETS	0.845	0.685	1	0.845	0.685	1	CLONAL	1	TRUE	1	0.15	2		631	505	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362282	40362282	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	38	636	0	ENST00000293328.3:c.1813G>C	p.Asp605His	p.D605H	ENST00000293328	NM_012448.3	605	Gac/Cac	15/19	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.15	2		636	484	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7119488	7119488	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	31	710	0	ENST00000302850.5:c.3766G>T	p.Asp1256Tyr	p.D1256Y	ENST00000302850	NM_000208.2	1256	Gat/Tat	21/22	0.157547732075042	1	FACETS	0.668	0.539	0.815	0.668	0.539	0.815	SUBCLONAL	1	TRUE	0	0.15	1		710	572	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17941003	17941003	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	29	705	0	ENST00000458235.1:c.3121G>C	p.Glu1041Gln	p.E1041Q	ENST00000458235	NM_000215.3	1041	Gag/Cag	23/24	1	2	FACETS	0.716	0.573	0.879	0.716	0.573	0.879	SUBCLONAL	1	TRUE	1	0.15	2		705	540	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655200	45655200	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1199628286	NA	P-0037970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	27	535	0	ENST00000407780.3:c.652G>T	p.Glu218Ter	p.E218*	ENST00000407780	NM_001283052.1	218	Gag/Tag	4/7	1	2	FACETS	0.778	0.618	0.961	0.778	0.618	0.961	CLONAL	1	TRUE	1	0.15	2		535	463	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835900	151835900	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	20	452	0	ENST00000262189.6:c.14624G>C	p.Arg4875Thr	p.R4875T	ENST00000262189	NM_170606.2	4875	aGa/aCa	58/59	0.100093864771957	5	FACETS	0.918	0.701	1	0.229	0.175	0.293	CLONAL	1	TRUE	1	0.15	5		452	356	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349586	70349586	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1164353230	NA	P-0037970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	38	696	0	ENST00000374080.3:c.3748C>A	p.Pro1250Thr	p.P1250T	ENST00000374080		1250	Cca/Aca	27/45	1	2	FACETS	0.931	0.769	1	0.931	0.769	1	CLONAL	1	TRUE	1	0.15	2		696	544	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	18	503	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.117	0.087	0.153	0.117	0.087	0.153	SUBCLONAL	1	TRUE	1	0.404526062795543	2		503	760	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0037971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	28	343	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.404526062795543	1	FACETS	0.169	0.134	0.209	0.169	0.134	0.209	SUBCLONAL	1	TRUE	0	0.404526062795543	1		343	654	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0037971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	173	559	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	0.404526062795543	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.404526062795543	1		559	559	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0037971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	200	434	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.404526062795543	2		434	812	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302801	15302801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756520455	NA	P-0037971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	263	759	0	ENST00000263388.2:c.649G>A	p.Asp217Asn	p.D217N	ENST00000263388	NM_000435.2	217	Gac/Aac	4/33	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.404526062795543	2		759	1060	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514277	69514277	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	243	731	0	ENST00000294312.3:c.404G>T	p.Arg135Leu	p.R135L	ENST00000294312	NM_005117.2	135	cGa/cTa	3/3	0.404526062795543	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.404526062795543	1		731	780	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579318	7579325	+	frameshift_variant	Frame_Shift_Del	DEL	AGTCACAG	AGTCACAG	-	novel	NA	P-0037971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	268	596	0	ENST00000269305.4:c.362_369del	p.Ser121LeufsTer25	p.S121Lfs*25	ENST00000269305	NM_001126112.2	121	tCTGTGACT/t	4/11	NA	2	FACETS	0.845	0.796	0.895			1	INDETERMINATE	2	TRUE	NA	0.404526062795543	2		596	784	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534428	63534429	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0037971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	204	634	0	ENST00000307078.5:c.1092dup	p.Val365ArgfsTer9	p.V365Rfs*9	ENST00000307078	NM_004655.3	364	-/C	5/11	1	2	FACETS	0.964	0.894	1	0.964	0.894	1	CLONAL	1	TRUE	1	0.404526062795543	2		634	1046	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577074	7577075	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0037972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	627	730	0	ENST00000269305.4:c.863dup	p.Asn288LysfsTer18	p.N288Kfs*18	ENST00000269305	NM_001126112.2	288	aat/aaAt	8/11	0.80501898590618	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.80501898590618	1		730	868	SUCCESS
APC	324	MSKCC	GRCh37	5	112175447	112175447	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0037972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	208	376	0	ENST00000257430.4:c.4156A>T	p.Arg1386Ter	p.R1386*	ENST00000257430	NM_000038.5	1386	Aga/Tga	16/16	0.79223215946423	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.80501898590618	1		376	290	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968196	55968196	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0037972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	228	452	0	ENST00000263923.4:c.2135-1G>T		p.X712_splice	ENST00000263923	NM_002253.2	712			0.263933033144607	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.80501898590618	0		452	602	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011106	12011106	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0037972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	237	299	0	ENST00000353533.5:c.514-1G>T		p.X172_splice	ENST00000353533	NM_003010.3	172			0.80501898590618	1	FACETS	0.969	0.924	1	0.969	0.924	1	CLONAL	1	TRUE	0	0.80501898590618	1		299	363	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470014	25470014	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	36	465	0	ENST00000264709.3:c.1028A>C	p.Lys343Thr	p.K343T	ENST00000264709	NM_175629.2	343	aAg/aCg	9/23	0.170475955646803	3	FACETS	0.19	0.155	0.229	0.095	0.077	0.115	INDETERMINATE	1	TRUE	1	0.80501898590618	3		465	661	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349029	70349029	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	216	683	1	ENST00000374080.3:c.3541A>G	p.Lys1181Glu	p.K1181E	ENST00000374080		1181	Aag/Gag	25/45	0.57981258939468	1	FACETS	0.4	0.372	0.428	0.4	0.372	0.428	SUBCLONAL	1	TRUE	0	0.80501898590618	1		684	802	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0037975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	354	725	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.301250128763735	4	FACETS	0.836	0.792	0.881	0.836	0.792	0.881	CLONAL	3	TRUE	1	0.31	4		725	1193	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982416	201982417	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0037975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	129	739	0	ENST00000359651.3:c.796dup	p.Ser266LysfsTer35	p.S266Kfs*35	ENST00000359651		265	-/A	6/8	0.225967457565987	2	FACETS	0.782	0.708	0.861	0.391	0.354	0.431	SUBCLONAL	1	TRUE	0	0.31	2		739	1064	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560248	95560248	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	95	444	1	ENST00000393063.1:c.5341G>T	p.Glu1781Ter	p.E1781*	ENST00000393063	NM_030621.3	1781	Gaa/Taa	25/28	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.31	2		445	613	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324684	31324684	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	121	549	0	ENST00000412585.2:c.124G>A	p.Gly42Arg	p.G42R	ENST00000412585	NM_005514.6	42	Ggg/Agg	2/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.31	2		549	592	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197803	123197803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	67	281	1	ENST00000218089.9:c.1927G>A	p.Glu643Lys	p.E643K	ENST00000218089	NM_001042749.1	643	Gag/Aag	20/35	0.215543907585043	2	FACETS	1	0.963	1			1	CLONAL	1	TRUE	NA	0.31	2		282	337	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	104	313	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.341835381920741	2		315	574	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221954	1221954	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057524439	NA	P-0037976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	185	752	0	ENST00000326873.7:c.869T>C	p.Leu290Pro	p.L290P	ENST00000326873	NM_000455.4	290	cTt/cCt	7/10	0.341835381920741	1	FACETS	0.993	0.917	1	0.993	0.917	1	CLONAL	1	TRUE	0	0.341835381920741	1		752	904	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271301	1271301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	150	611	0	ENST00000310581.5:c.2401G>A	p.Ala801Thr	p.A801T	ENST00000310581	NM_198253.2	801	Gcc/Acc	8/16	1	2	FACETS	0.875	0.799	0.955	0.875	0.799	0.955	CLONAL	1	TRUE	1	0.341835381920741	2		611	1003	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983059	201983060	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0037976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	363	835	0	ENST00000359651.3:c.909dup	p.Lys304GlnfsTer167	p.K304Qfs*167	ENST00000359651		303	ttc/ttCc	7/8	0.306245003853295	3	FACETS	0.879	0.832	0.927	0.879	0.832	0.927	CLONAL	2	TRUE	1	0.341835381920741	3		835	1415	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40998451	40998451	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	150	703	0	ENST00000267868.3:c.302A>G	p.Gln101Arg	p.Q101R	ENST00000267868	NM_002875.4	101	cAg/cGg	4/10	1	2	FACETS	0.856	0.782	0.935	0.856	0.782	0.935	CLONAL	1	TRUE	1	0.341835381920741	2		703	1025	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161783	47161783	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1192116385	NA	P-0037976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	115	412	0	ENST00000409792.3:c.4343C>T	p.Ser1448Phe	p.S1448F	ENST00000409792	NM_014159.6	1448	tCc/tTc	3/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.341835381920741	2		412	590	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439227	52439227	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	81	791	0	ENST00000460680.1:c.1015C>G	p.Pro339Ala	p.P339A	ENST00000460680	NM_004656.3	339	Cca/Gca	11/17	1	2	FACETS	0.443	0.389	0.502	0.443	0.389	0.502	SUBCLONAL	1	TRUE	1	0.341835381920741	2		791	1069	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944566	38944566	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	72	444	0	ENST00000357387.3:c.4895A>G	p.His1632Arg	p.H1632R	ENST00000357387	NM_152756.3	1632	cAt/cGt	36/38	1	2	FACETS	0.829	0.726	0.94	0.829	0.726	0.94	CLONAL	1	TRUE	1	0.341835381920741	2		444	508	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467751	50467751	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	62	655	0	ENST00000331340.3:c.986C>T	p.Pro329Leu	p.P329L	ENST00000331340	NM_006060.4	329	cCg/cTg	8/8	1	2	FACETS	0.353	0.304	0.407	0.353	0.304	0.407	SUBCLONAL	1	TRUE	1	0.341835381920741	2		655	1028	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249124	55249124	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	179	801	0	ENST00000275493.2:c.2422A>G	p.Asn808Asp	p.N808D	ENST00000275493	NM_005228.3	808	Aat/Gat	20/28	1	2	FACETS	0.904	0.832	0.98	0.904	0.832	0.98	CLONAL	1	TRUE	1	0.341835381920741	2		801	1158	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842703	68842703	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	201	282	1	ENST00000261769.5:c.639G>A	p.Trp213Ter	p.W213*	ENST00000261769	NM_004360.3	213	tgG/tgA	5/16	0.681482101503374	1	FACETS	0.88	0.826	0.934	0.88	0.826	0.934	CLONAL	1	TRUE	0	0.681482101503374	1		283	442	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256313	16256314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGT	novel	NA	P-0037981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	192	337	0	ENST00000375759.3:c.3580_3583dup	p.Pro1195GlnfsTer3	p.P1195Qfs*3	ENST00000375759	NM_015001.2	1193	ggc/ggCAGTc	11/15	0.681482101503374	1	FACETS	0.82	0.767	0.874	0.82	0.767	0.874	CLONAL	1	TRUE	0	0.681482101503374	1		337	453	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575361	64575361	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0037981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	242	519	0	ENST00000312049.6:c.654+2T>C		p.X218_splice	ENST00000312049	NM_130799.2	218			0.681482101503374	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.681482101503374	1		519	466	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860532	45860532	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	368	767	0	ENST00000391945.4:c.1475C>G	p.Pro492Arg	p.P492R	ENST00000391945	NM_000400.3	492	cCt/cGt	15/23	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.649796273599852	2		767	1121	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11292504	11292504	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	63	466	0	ENST00000361445.4:c.2503G>T	p.Ala835Ser	p.A835S	ENST00000361445	NM_004958.3	835	Gcc/Tcc	16/58	0.329802674854812	3	FACETS	0.857	0.742	0.981	0.429	0.371	0.491	CLONAL	1	TRUE	1	0.336038956351269	3		466	511	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246498766	246498766	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	82	523	1	ENST00000388985.4:c.239G>A	p.Trp80Ter	p.W80*	ENST00000388985		80	tGg/tAg	3/12	0.336038956351269	7	FACETS	1	0.892	1	0.203	0.178	0.229	CLONAL	1	TRUE	2	0.336038956351269	7		524	886	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114197	115114198	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0037983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	228	738	1	ENST00000257566.3:c.1019_1020delinsAA	p.Ser340Ter	p.S340*	ENST00000257566	NM_016569.3	340	tCC/tAA	6/8	0.329802674854812	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.336038956351269	3		739	772	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256598	133256598	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	185	577	1	ENST00000320574.5:c.365A>T	p.Lys122Met	p.K122M	ENST00000320574	NM_006231.2	122	aAg/aTg	5/49	0.329802674854812	3	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	1	0.336038956351269	3		578	640	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937579	32937579	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	185	619	0	ENST00000380152.3:c.8240T>A	p.Val2747Asp	p.V2747D	ENST00000380152		2747	gTt/gAt	18/27	0.336038956351269	2	FACETS	0.98	0.911	1	0.98	0.911	1	CLONAL	2	TRUE	0	0.336038956351269	2		619	562	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781368	3781368	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	146	957	0	ENST00000262367.5:c.4997C>G	p.Ala1666Gly	p.A1666G	ENST00000262367	NM_004380.2	1666	gCc/gGc	30/31	0.336038956351269	3	FACETS	0.929	0.847	1	0.465	0.423	0.508	CLONAL	1	TRUE	1	0.336038956351269	3		957	1092	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578404	+	missense_variant	Missense_Mutation	DNP	CA	CA	AC	novel	NA	P-0037983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	219	813	0	ENST00000269305.4:c.526_527delinsGT	p.Cys176Val	p.C176V	ENST00000269305	NM_001126112.2	176	TGc/GTc	5/11	0.336038956351269	2	FACETS	0.919	0.859	0.981	0.919	0.859	0.981	CLONAL	2	TRUE	0	0.336038956351269	2		813	709	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557319	29557320	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0037983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	54	331	0	ENST00000356175.3:c.3037dup	p.Thr1013AsnfsTer8	p.T1013Nfs*8	ENST00000356175	NM_000267.3	1011	ata/atAa	23/57	1	2	FACETS	0.929	0.797	1	0.929	0.797	1	CLONAL	1	TRUE	1	0.336038956351269	2		331	346	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683525	29683525	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0037983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	57	369	0	ENST00000356175.3:c.7600A>T	p.Lys2534Ter	p.K2534*	ENST00000356175	NM_000267.3	2534	Aaa/Taa	51/57	1	2	FACETS	0.919	0.792	1	0.919	0.792	1	CLONAL	1	TRUE	1	0.336038956351269	2		369	369	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735634	204735634	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	139	464	0	ENST00000302823.3:c.435C>G	p.Asn145Lys	p.N145K	ENST00000302823	NM_005214.4	145	aaC/aaG	2/4	0.336038956351269	3	FACETS	0.896	0.82	0.975	0.896	0.82	0.975	CLONAL	2	TRUE	1	0.336038956351269	3		464	539	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483916	212483916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375308478	NA	P-0037983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	60	528	0	ENST00000342788.4:c.2287G>A	p.Val763Met	p.V763M	ENST00000342788	NM_005235.2	763	Gtg/Atg	19/28	0.329802674854812	3	FACETS	0.871	0.752	1	0.435	0.376	0.5	CLONAL	1	TRUE	1	0.336038956351269	3		528	479	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39721121	39721121	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	85	482	0	ENST00000361337.2:c.624A>T	p.Glu208Asp	p.E208D	ENST00000361337	NM_003286.2	208	gaA/gaT	9/21	0.336038956351269	7	FACETS	1	0.948	1	0.189	0.166	0.213	CLONAL	1	TRUE	1	0.336038956351269	7		482	822	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143033764	143033764	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	204	441	0	ENST00000262992.4:c.2207G>T	p.Gly736Val	p.G736V	ENST00000262992	NM_001101669.1	736	gGa/gTa	20/24	0.336038956351269	4	FACETS	0.971	0.907	1	0.971	0.907	1	CLONAL	3	TRUE	1	0.336038956351269	4		441	557	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540425	187540425	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	157	478	0	ENST00000441802.2:c.7315G>T	p.Val2439Phe	p.V2439F	ENST00000441802	NM_005245.3	2439	Gtc/Ttc	10/27	NA	2	FACETS	0.905	0.835	0.978			1	INDETERMINATE	2	TRUE	NA	0.336038956351269	2		478	516	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542306	187542307	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0037983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	146	403	0	ENST00000441802.2:c.5433dup	p.Val1812CysfsTer2	p.V1812Cfs*2	ENST00000441802	NM_005245.3	1811	-/T	10/27	NA	2	FACETS	0.942	0.867	1			1	INDETERMINATE	2	TRUE	NA	0.336038956351269	2		403	461	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120648	94120648	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	89	447	0	ENST00000369303.4:c.403G>C	p.Gly135Arg	p.G135R	ENST00000369303	NM_004440.3	135	Ggc/Cgc	3/17	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.336038956351269	2		447	442	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332890	152332890	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	63	454	0	ENST00000206249.3:c.1196C>A	p.Pro399Gln	p.P399Q	ENST00000206249	NM_000125.3	399	cCa/cAa	5/8	1	2	FACETS	0.874	0.758	0.999	0.874	0.758	0.999	CLONAL	1	TRUE	1	0.336038956351269	2		454	429	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50358686	50358686	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	97	261	0	ENST00000331340.3:c.31del	p.Gln11LysfsTer10	p.Q11Kfs*10	ENST00000331340	NM_006060.4	10	tCc/tc	2/8	0.336038956351269	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.336038956351269	4		261	343	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350081	81350081	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	130	406	0	ENST00000222390.5:c.1251G>T	p.Lys417Asn	p.K417N	ENST00000222390	NM_000601.4	417	aaG/aaT	10/18	0.336038956351269	4	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	2	0.336038956351269	4		406	503	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913355	NA	P-0037983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	153	314	0	ENST00000288602.6:c.1406G>T	p.Gly469Val	p.G469V	ENST00000288602	NM_004333.4	469	gGa/gTa	11/18	0.336038956351269	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.336038956351269	4		314	509	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945134	151945134	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	18	422	0	ENST00000262189.6:c.2385C>A	p.Asp795Glu	p.D795E	ENST00000262189	NM_170606.2	795	gaC/gaA	14/59	0.336038956351269	4	FACETS	0.407	0.305	0.526	0.203	0.152	0.263	SUBCLONAL	1	TRUE	2	0.336038956351269	4		422	352	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507429	8507429	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	176	290	0	ENST00000356435.5:c.1549G>T	p.Gly517Trp	p.G517W	ENST00000356435		517	Ggg/Tgg	11/35	0.336038956351269	6	FACETS	0.954	0.888	1	0.954	0.888	1	CLONAL	4	TRUE	2	0.336038956351269	6		290	459	SUCCESS
AR	367	MSKCC	GRCh37	X	66765413	66765413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1260562254	NA	P-0037983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	120	901	0	ENST00000374690.3:c.425G>A	p.Ser142Asn	p.S142N	ENST00000374690	NM_000044.3	142	aGc/aAc	1/8	0.100591373830299	5	FACETS	1	0.979	1	0.329	0.297	0.363	INDETERMINATE	1	TRUE	1	0.336038956351269	5		901	816	SUCCESS
AR	367	MSKCC	GRCh37	X	66765802	66765802	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	298	1138	0	ENST00000374690.3:c.814C>A	p.Leu272Ile	p.L272I	ENST00000374690	NM_000044.3	272	Ctt/Att	1/8	0.100591373830299	5	FACETS	1	0.99	1	0.619	0.583	0.655	INDETERMINATE	2	TRUE	1	0.336038956351269	5		1138	1078	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154432	2154432	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	115	903	1	ENST00000434045.2:c.496del	p.Val166TrpfsTer49	p.V166Wfs*49	ENST00000434045	NM_001127598.1	166	Gtg/tg	5/5	0.177988213987324	2	FACETS	0.979	0.883	1	0.49	0.441	0.541	INDETERMINATE	1	TRUE	0	0.336038956351269	2		904	699	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0038013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	1956	918	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.379170234865048	25	FACETS	0.979	0.968	0.99			1	CLONAL	24	TRUE	NA	0.379170234865048	25		919	2353	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988352	41988353	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0038013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	126	385	0	ENST00000219905.7:c.1145_1146del	p.Lys382ArgfsTer6	p.K382Rfs*6	ENST00000219905	NM_001164273.1	382	AAa/a	3/24	1	2	FACETS	0.996	0.904	1	0.996	0.904	1	CLONAL	1	TRUE	1	0.379170234865048	2		385	667	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671216	30671216	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	118	573	0	ENST00000376406.3:c.5661C>G	p.Asn1887Lys	p.N1887K	ENST00000376406	NM_014641.2	1887	aaC/aaG	11/15	1	2	FACETS	0.905	0.817	0.997	0.905	0.817	0.997	CLONAL	1	TRUE	1	0.379170234865048	2		573	688	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552921	106552921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	172	618	0	ENST00000369096.4:c.886C>T	p.Arg296Trp	p.R296W	ENST00000369096	NM_001198.3	296	Cgg/Tgg	5/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.379170234865048	2		618	787	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169513	27169513	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs891063377	NA	P-0038013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	196	417	0	ENST00000380036.4:c.514G>C	p.Asp172His	p.D172H	ENST00000380036	NM_000459.3	172	Gat/Cat	4/23	0.379170234865048	3	FACETS	0.791	0.734	0.85	0.528	0.489	0.567	SUBCLONAL	2	TRUE	0	0.379170234865048	3		417	777	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0038036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	75	186	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.325712750077925	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	0	0.338382355574874	2		186	208	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578441	7578441	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	215	916	0	ENST00000269305.4:c.489C>A	p.Tyr163Ter	p.Y163*	ENST00000269305	NM_001126112.2	163	taC/taA	5/11	0.325712750077925	2	FACETS	0.961	0.898	1	0.961	0.898	1	CLONAL	2	TRUE	0	0.338382355574874	2		916	661	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992721	68992721	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs764112302	NA	P-0038036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	72	819	4	ENST00000288368.4:c.1693del	p.Ser565ArgfsTer10	p.S565Rfs*10	ENST00000288368	NM_024870.2	562	cgT/cg	16/40	0.325712750077925	2	FACETS	0.839	0.735	0.952	0.42	0.367	0.476	CLONAL	1	TRUE	0	0.338382355574874	2		823	507	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277482	142277482	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	17	291	0	ENST00000350721.4:c.1869G>C	p.Arg623Ser	p.R623S	ENST00000350721	NM_001184.3	623	agG/agC	8/47	0.235522312446014	2	FACETS	0.328	0.245	0.428	0.164	0.122	0.214	SUBCLONAL	1	TRUE	0	0.338382355574874	2		291	306	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467845	66467845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	15	324	0	ENST00000273854.3:c.424G>A	p.Gly142Arg	p.G142R	ENST00000273854	NM_004439.5	142	Gga/Aga	3/18	1	2	FACETS	0.324	0.236	0.429	0.324	0.236	0.429	SUBCLONAL	1	TRUE	1	0.338382355574874	2		324	274	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0038038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	59	796	7	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.277814376760704	2		803	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0038038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	161	802	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.824	0.758	0.893	1	0.99	1	CLONAL	2	TRUE	1	0.277814376760704	2		802	703	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0038038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	33	315	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	0.919	1	CLONAL	1	TRUE	1	0.277814376760704	2		315	194	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0038038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	69	294	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	1	2	FACETS	0.833	0.732	0.94	1	0.978	1	CLONAL	2	TRUE	1	0.277814376760704	2		294	298	SUCCESS
APC	324	MSKCC	GRCh37	5	112173995	112173995	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	59	329	0	ENST00000257430.4:c.2704G>T	p.Glu902Ter	p.E902*	ENST00000257430	NM_000038.5	902	Gaa/Taa	16/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.277814376760704	2		329	311	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374935	45374935	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	167	467	0	ENST00000262160.6:c.908C>G	p.Thr303Arg	p.T303R	ENST00000262160	NM_005901.5	303	aCa/aGa	8/11	0.253832056422764	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.277814376760704	2		467	486	SUCCESS
APC	324	MSKCC	GRCh37	5	112102044	112102044	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	28	279	0	ENST00000257430.4:c.158del	p.Gly53GlufsTer17	p.G53Efs*17	ENST00000257430	NM_000038.5	53	Gga/ga	3/16	1	2	FACETS	0.816	0.655	0.998	0.816	0.655	0.998	CLONAL	1	TRUE	1	0.277814376760704	2		279	247	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482804	67482804	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	82	654	0	ENST00000327367.4:c.1208C>T	p.Pro403Leu	p.P403L	ENST00000327367	NM_005902.3	403	cCt/cTt	9/9	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.277814376760704	2		654	430	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0038041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	151	340	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	0.993	1	CLONAL	2	TRUE	1	0.38	2		340	341	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0038041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	170	406	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.978	1	1	0.994	1	CLONAL	2	TRUE	1	0.38	2		406	398	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699372	47699372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	201	292	0	ENST00000347630.2:c.136G>A	p.Glu46Lys	p.E46K	ENST00000347630	NM_001007230.1	46	Gag/Aag	4/11	0.3	1	FACETS	1	0.991	1	1	0.996	1	CLONAL	3	TRUE	0	0.38	1		292	251	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs199469669	NA	P-0038041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	185	489	0	ENST00000374080.3:c.130G>C	p.Gly44Arg	p.G44R	ENST00000374080		44	Ggt/Cgt	2/45	0.3	0	FACETS	0.946	0.892	0.999			1	CLONAL	2	TRUE	0	0.38	0		489	319	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056207	27056207	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0038041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	226	507	0	ENST00000324856.7:c.1203C>G	p.Tyr401Ter	p.Y401*	ENST00000324856	NM_006015.4	401	taC/taG	2/20	1	2	FACETS	1	0.981	1	1	0.995	1	CLONAL	2	TRUE	1	0.38	2		507	540	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466026	69466031	+	inframe_deletion	In_Frame_Del	DEL	CGACGT	CGACGT	-	novel	NA	P-0038041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	274	523	0	ENST00000227507.2:c.864_869del	p.Asp289_Val290del	p.D289_V290del	ENST00000227507	NM_053056.2	288	acCGACGTg/acg	5/5	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.38	2		523	613	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	18	313	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.814	0.615	1	0.814	0.615	1	CLONAL	1	TRUE	1	0.219054014847976	2		315	202	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0038042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	42	321	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	1	2	FACETS	0.888	0.742	1	0.888	0.742	1	CLONAL	1	TRUE	1	0.219054014847976	2		321	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0038042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	76	786	1	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	1	2	FACETS	0.953	0.835	1	0.953	0.835	1	CLONAL	1	TRUE	1	0.219054014847976	2		787	728	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660070	12660070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	37	377	0	ENST00000251849.4:c.151C>T	p.Pro51Ser	p.P51S	ENST00000251849	NM_002880.3	51	Cct/Tct	2/17	1	2	FACETS	0.742	0.612	0.888	0.742	0.612	0.888	SUBCLONAL	1	TRUE	1	0.219054014847976	2		377	455	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166811	32166811	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142608082	NA	P-0038042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	67	667	1	ENST00000375023.3:c.4427G>A	p.Arg1476Gln	p.R1476Q	ENST00000375023	NM_004557.3	1476	cGa/cAa	24/30	1	2	FACETS	0.977	0.849	1	0.977	0.849	1	CLONAL	1	TRUE	1	0.219054014847976	2		668	626	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781060	135781061	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs118203597	NA	P-0038042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	45	566	0	ENST00000298552.3:c.1904_1905del	p.Thr635ArgfsTer52	p.T635Rfs*52	ENST00000298552	NM_001162426.1	635	aCA/a	15/23	0.219054014847976	1	FACETS	0.605	0.507	0.713	0.605	0.507	0.713	SUBCLONAL	1	TRUE	0	0.219054014847976	1		566	605	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753170	42753170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753965187	NA	P-0038042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	70	597	0	ENST00000222329.4:c.1094C>T	p.Ser365Leu	p.S365L	ENST00000222329	NM_006494.2	365	tCg/tTg	4/4	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.219054014847976	2		597	606	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675049	40675049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764271025	NA	P-0038042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	38	611	0	ENST00000249776.8:c.13G>A	p.Glu5Lys	p.E5K	ENST00000249776	NM_033286.3	5	Gaa/Aaa	1/9	1	2	FACETS	0.513	0.423	0.615	0.513	0.423	0.615	SUBCLONAL	1	TRUE	1	0.219054014847976	2		611	676	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927368	245927368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	38	396	0	ENST00000388985.4:c.1160C>T	p.Pro387Leu	p.P387L	ENST00000388985		387	cCc/cTc	11/12	1	2	FACETS	0.756	0.625	0.902	0.756	0.625	0.902	CLONAL	1	TRUE	1	0.219054014847976	2		396	459	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874034	151874034	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	46	417	0	ENST00000262189.6:c.8504C>T	p.Ser2835Phe	p.S2835F	ENST00000262189	NM_170606.2	2835	tCc/tTc	38/59	1	2	FACETS	0.862	0.726	1	0.862	0.726	1	CLONAL	1	TRUE	1	0.219054014847976	2		417	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577115	7577116	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0038042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	51	678	0	ENST00000269305.4:c.822_823del	p.Ala276LeufsTer29	p.A276Lfs*29	ENST00000269305	NM_001126112.2	274	gtTTgt/gtgt	8/11	1	2	FACETS	0.662	0.562	0.773	0.662	0.562	0.773	SUBCLONAL	1	TRUE	1	0.219054014847976	2		678	703	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727836	41727836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765828639	NA	P-0038042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	65	717	0	ENST00000301178.4:c.461C>T	p.Thr154Ile	p.T154I	ENST00000301178	NM_021913.4	154	aCc/aTc	4/20	1	2	FACETS	0.847	0.733	0.97	0.847	0.733	0.97	CLONAL	1	TRUE	1	0.219054014847976	2		717	701	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262523	16262523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	21	300	1	ENST00000375759.3:c.9788C>T	p.Pro3263Leu	p.P3263L	ENST00000375759	NM_015001.2	3263	cCt/cTt	11/15	1	2	FACETS	0.71	0.548	0.899	0.71	0.548	0.899	SUBCLONAL	1	TRUE	1	0.219054014847976	2		301	270	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325280	39325281	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0038042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	31	314	1	ENST00000373001.3:c.38_39delinsTT	p.Ala13Val	p.A13V	ENST00000373001	NM_022157.3	13	gCC/gTT	1/7	1	2	FACETS	0.676	0.546	0.822	0.676	0.546	0.822	SUBCLONAL	1	TRUE	1	0.219054014847976	2		315	419	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166388	118166388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	29	351	0	ENST00000369448.3:c.898G>A	p.Glu300Lys	p.E300K	ENST00000369448	NM_017709.3	300	Gag/Aag	2/2	1	2	FACETS	0.714	0.573	0.874	0.714	0.573	0.874	SUBCLONAL	1	TRUE	1	0.219054014847976	2		351	371	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156836751	156836751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	55	673	0	ENST00000524377.1:c.409G>A	p.Gly137Ser	p.G137S	ENST00000524377	NM_002529.3	137	Ggc/Agc	4/17	1	2	FACETS	0.817	0.698	0.946	0.817	0.698	0.946	CLONAL	1	TRUE	1	0.219054014847976	2		673	615	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999727	100999728	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0038042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	47	794	1	ENST00000325455.5:c.74_75delinsTT	p.Ser25Phe	p.S25F	ENST00000325455	NM_001202474.3	25	tCC/tTT	1/8	1	2	FACETS	0.721	0.608	0.847	0.721	0.608	0.847	SUBCLONAL	1	TRUE	1	0.219054014847976	2		795	595	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644452	21644452	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0038042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	24	242	0	ENST00000421138.2:c.214+1G>A		p.X72_splice	ENST00000421138		72			1	2	FACETS	0.905	0.712	1	0.905	0.712	1	CLONAL	1	TRUE	1	0.219054014847976	2		242	242	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354437	91354437	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	25	272	0	ENST00000355112.3:c.3877G>A	p.Glu1293Lys	p.E1293K	ENST00000355112	NM_000057.2	1293	Gaa/Aaa	21/22	1	2	FACETS	0.756	0.596	0.938	0.756	0.596	0.938	CLONAL	1	TRUE	1	0.219054014847976	2		272	302	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639398	3639399	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0038042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	42	695	0	ENST00000294008.3:c.4240_4241delinsTT	p.Pro1414Leu	p.P1414L	ENST00000294008	NM_032444.2	1414	CCa/TTa	12/15	1	2	FACETS	0.635	0.529	0.753	0.635	0.529	0.753	SUBCLONAL	1	TRUE	1	0.219054014847976	2		695	604	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971159	18971159	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	72	668	0	ENST00000262803.5:c.2212C>T	p.Gln738Ter	p.Q738*	ENST00000262803	NM_002911.3	738	Cag/Tag	16/24	1	2	FACETS	0.815	0.711	0.927	0.815	0.711	0.927	CLONAL	1	TRUE	1	0.219054014847976	2		668	807	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606688	29606688	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	30	468	0	ENST00000389048.3:c.1192A>C	p.Asn398His	p.N398H	ENST00000389048	NM_004304.4	398	Aac/Cac	5/29	1	2	FACETS	0.522	0.419	0.638	0.522	0.419	0.638	SUBCLONAL	1	TRUE	1	0.219054014847976	2		468	525	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010406	48010406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782084	NA	P-0038042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	40	396	0	ENST00000234420.5:c.34C>T	p.Pro12Ser	p.P12S	ENST00000234420	NM_000179.2	12	Ccc/Tcc	1/10	1	2	FACETS	0.64	0.531	0.761	0.64	0.531	0.761	SUBCLONAL	1	TRUE	1	0.219054014847976	2		396	571	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270048	198270048	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	30	347	0	ENST00000335508.6:c.1388A>G	p.Asn463Ser	p.N463S	ENST00000335508	NM_012433.2	463	aAt/aGt	10/25	1	2	FACETS	0.617	0.497	0.754	0.617	0.497	0.754	SUBCLONAL	1	TRUE	1	0.219054014847976	2		347	444	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067198	37067198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	21	293	0	ENST00000231790.2:c.1109C>T	p.Ser370Phe	p.S370F	ENST00000231790	NM_000249.3	370	tCt/tTt	12/19	1	2	FACETS	0.49	0.377	0.623	0.49	0.377	0.623	SUBCLONAL	1	TRUE	1	0.219054014847976	2		293	391	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398882	398882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	42	457	0	ENST00000380956.4:c.692C>T	p.Pro231Leu	p.P231L	ENST00000380956	NM_001195286.1	231	cCc/cTc	6/9	1	2	FACETS	0.858	0.717	1	0.858	0.717	1	CLONAL	1	TRUE	1	0.219054014847976	2		457	447	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405056	405057	+	stop_gained	Nonsense_Mutation	DNP	AG	AG	TA	novel	NA	P-0038042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	44	406	0	ENST00000380956.4:c.1138_1139delinsTA	p.Arg380Ter	p.R380*	ENST00000380956	NM_001195286.1	380	AGa/TAa	8/9	1	2	FACETS	0.887	0.744	1	0.887	0.744	1	CLONAL	1	TRUE	1	0.219054014847976	2		406	453	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020752	26020752	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144334321	NA	P-0038042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	12	186	0	ENST00000357647.3:c.35C>T	p.Thr12Ile	p.T12I	ENST00000357647	NM_003529.2	12	aCt/aTt	1/1	1	2	FACETS	0.512	0.36	0.699	0.512	0.36	0.699	SUBCLONAL	1	TRUE	1	0.219054014847976	2		186	214	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032282	26032282	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	19	191	0	ENST00000244661.2:c.7C>G	p.Arg3Gly	p.R3G	ENST00000244661	NM_003537.3	3	Cgt/Ggt	1/1	1	2	FACETS	0.785	0.598	1	0.785	0.598	1	CLONAL	1	TRUE	1	0.219054014847976	2		191	221	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738745	145738746	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0038042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	73	649	2	ENST00000428558.2:c.2318_2319delinsTT	p.Ala773Val	p.A773V	ENST00000428558	NM_004260.3	773	gCC/gTT	15/22	1	2	FACETS	0.972	0.849	1	0.972	0.849	1	CLONAL	1	TRUE	1	0.219054014847976	2		651	686	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974679	21974680	+	stop_gained,splice_region_variant	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0038042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	21	353	0	ENST00000304494.5:c.147_148delinsTT	p.Gln50Ter	p.Q50*	ENST00000304494	NM_000077.4	49	atCCag/atTTag	1/3	0.219054014847976	1	FACETS	0.472	0.363	0.599	0.472	0.363	0.599	SUBCLONAL	1	TRUE	0	0.219054014847976	1		353	362	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759413	133759413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778013	NA	P-0038042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	63	661	0	ENST00000318560.5:c.1736C>T	p.Pro579Leu	p.P579L	ENST00000318560	NM_005157.4	579	cCc/cTc	11/11	0.219054014847976	1	FACETS	0.82	0.709	0.94	0.82	0.709	0.94	CLONAL	1	TRUE	0	0.219054014847976	1		661	625	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227768	53227768	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	53	319	0	ENST00000375401.3:c.2420C>T	p.Pro807Leu	p.P807L	ENST00000375401	NM_004187.3	807	cCt/cTt	17/26	1	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.219054014847976	1		319	333	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0038043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	20	701	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.796	1	1	0.796	1	CLONAL	1	TRUE	1	0.12	2		701	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0038043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	22	447	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.863	0.667	1	0.863	0.667	1	CLONAL	1	TRUE	1	0.12	2		447	425	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274171	10274171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs960622904	NA	P-0038044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	99	562	0	ENST00000330684.3:c.98C>T	p.Ala33Val	p.A33V	ENST00000330684	NM_001134407.1	33	gCg/gTg	2/13	0.31415622957506	1	FACETS	0.781	0.707	0.857	0.781	0.707	0.857	INDETERMINATE	1	TRUE	0	0.618957448822236	1		562	283	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11177076	11177076	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0038044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	51	430	0	ENST00000361445.4:c.7001del	p.Leu2334Ter	p.L2334*	ENST00000361445	NM_004958.3	2334	tTa/ta	50/58	0.393026428189513	0	FACETS	0.237	0.203	0.274			1	SUBCLONAL	1	TRUE	0	0.618957448822236	0		430	265	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935714	13935716	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TGA	TGA	-	novel	NA	P-0038044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	116	393	0	ENST00000405192.2:c.1144-4_1144-2del		p.X382_splice	ENST00000405192	NM_001163147.1	382			1	2	FACETS	0.901	0.819	0.987	0.901	0.819	0.987	CLONAL	1	TRUE	1	0.618957448822236	2		393	416	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0038045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	19	796	7	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.485	0.367	0.625	0.485	0.367	0.625	SUBCLONAL	1	TRUE	1	0.17	2		803	461	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0038045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	29	547	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.714	0.572	0.876	0.714	0.572	0.876	SUBCLONAL	1	TRUE	1	0.17	2		547	478	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0038045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	24	341	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	1	2	FACETS	0.902	0.708	1	0.902	0.708	1	CLONAL	1	TRUE	1	0.17	2		341	313	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370985	55370985	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	61	646	0	ENST00000297316.4:c.287C>G	p.Ala96Gly	p.A96G	ENST00000297316	NM_022454.3	96	gCc/gGc	1/2	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.17	2		646	605	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106766	27106766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	95	730	0	ENST00000324856.7:c.6377G>A	p.Ser2126Asn	p.S2126N	ENST00000324856	NM_006015.4	2126	aGc/aAc	20/20	1	2	FACETS	0.936	0.835	1	1	0.985	1	CLONAL	2	TRUE	1	0.17	2		730	597	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380348	14380349	+	missense_variant	Missense_Mutation	DNP	GC	GC	TA	novel	NA	P-0038045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	21	239	1	ENST00000256196.4:c.68_69delinsTA	p.Gly23Val	p.G23V	ENST00000256196		23	gGC/gTA	1/6	1	2	FACETS	0.824	0.634	1	0.824	0.634	1	CLONAL	1	TRUE	1	0.17	2		240	300	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820749	3820749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1485287458	NA	P-0038045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	73	1071	0	ENST00000262367.5:c.2702C>T	p.Pro901Leu	p.P901L	ENST00000262367	NM_004380.2	901	cCg/cTg	14/31	1	2	FACETS	0.854	0.745	0.972	0.854	0.745	0.972	CLONAL	1	TRUE	1	0.17	2		1071	1006	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0038046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	40	406	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.291465418439141	3	FACETS	1	0.95	1			1	CLONAL	1	FALSE	NA	0.291465418439141	3		406	226	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0038046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	15	633	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	1	2	FACETS	0.464	0.339	0.613	0.464	0.339	0.613	SUBCLONAL	1	FALSE	1	0.291465418439141	2		633	222	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197273	106197273	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	56	248	0	ENST00000380013.4:c.5606G>T	p.Gly1869Val	p.G1869V	ENST00000380013	NM_001127208.2	1869	gGg/gTg	11/11	0.291465418439141	3	FACETS	1	0.916	1	1	0.916	1	CLONAL	2	FALSE	1	0.291465418439141	3		248	205	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245229	133245229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	19	686	2	ENST00000320574.5:c.2018G>A	p.Gly673Asp	p.G673D	ENST00000320574	NM_006231.2	673	gGc/gAc	18/49	0.291465418439141	1	FACETS	0.533	0.406	0.681	0.533	0.406	0.681	SUBCLONAL	1	FALSE	0	0.291465418439141	1		688	209	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047247	180047247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765671332	NA	P-0038046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	34	749	0	ENST00000261937.6:c.2468C>T	p.Pro823Leu	p.P823L	ENST00000261937	NM_182925.4	823	cCt/cTt	17/30	0.117389149673764	1	FACETS	0.898	0.739	1	0.898	0.739	1	INDETERMINATE	1	FALSE	0	0.291465418439141	1		749	222	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940109	31940109	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1348516957	NA	P-0038046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	52	618	0	ENST00000375333.2:c.251G>T	p.Cys84Phe	p.C84F	ENST00000375333	NM_032454.1	84	tGc/tTc	2/8	0.291465418439141	4	FACETS	0.797	0.684	0.92	0.532	0.456	0.614	CLONAL	2	FALSE	1	0.291465418439141	4		618	289	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55225418	55225418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	32	373	0	ENST00000275493.2:c.1270G>A	p.Glu424Lys	p.E424K	ENST00000275493	NM_005228.3	424	Gaa/Aaa	11/28	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	FALSE	1	0.291465418439141	2		373	207	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420219	88420219	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	269	495	0	ENST00000360948.2:c.2467A>G	p.Ile823Val	p.I823V	ENST00000360948	NM_001012338.2	823	Atc/Gtc	19/19	0.560514234706374	3	FACETS	1	0.982	1			1	CLONAL	2	TRUE	NA	0.643648894949973	3		495	515	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578192	7578192	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	548	753	1	ENST00000269305.4:c.657del	p.Tyr220MetfsTer27	p.Y220Mfs*27	ENST00000269305	NM_001126112.2	219	ccC/cc	6/11	0.643648894949973	3	FACETS	0.996	0.969	1	0.996	0.969	1	CLONAL	3	TRUE	0	0.643648894949973	3		754	753	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155262	55155262	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	124	519	0	ENST00000257290.5:c.2861T>G	p.Leu954Arg	p.L954R	ENST00000257290	NM_006206.4	954	cTg/cGg	21/23	0.321900298178436	5	FACETS	1	0.96	1	0.37	0.335	0.406	INDETERMINATE	1	TRUE	2	0.643648894949973	5		519	683	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637338	176637361	+	inframe_deletion	In_Frame_Del	DEL	CAGTGACCTGGATCCCATAGAACA	CAGTGACCTGGATCCCATAGAACA	-	novel	NA	P-0038047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	31	666	0	ENST00000439151.2:c.1941_1964del	p.Asp648_Ser655del	p.D648_S655del	ENST00000439151	NM_022455.4	646	agCAGTGACCTGGATCCCATAGAACAc/agc	5/23	1	2	FACETS	0.197	0.159	0.241	0.197	0.159	0.241	SUBCLONAL	1	TRUE	1	0.643648894949973	2		666	488	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840557	36840557	+	stop_lost	Nonstop_Mutation	SNP	T	T	A	novel	NA	P-0038047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	186	912	0	ENST00000358127.4:c.1176A>T	p.Ter392CysextTer111	p.*392Cext*111	ENST00000358127	NM_001280556.1	392	tgA/tgT	10/10	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.643648894949973	NA		912	1088	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0038052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	71	465	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.886	0.774	1	0.886	0.774	1	CLONAL	1	TRUE	1	0.272459310007821	2		465	588	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0038052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	86	570	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.986	0.873	1	0.986	0.873	1	CLONAL	1	TRUE	1	0.272459310007821	2		570	640	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593417	48593417	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	80	458	0	ENST00000342988.3:c.1168G>T	p.Glu390Ter	p.E390*	ENST00000342988	NM_005359.5	390	Gaa/Taa	10/12	0.272459310007821	1	FACETS	0.979	0.864	1	0.979	0.864	1	CLONAL	1	TRUE	0	0.272459310007821	1		458	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577508	7577508	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060501201	NA	P-0038052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	129	752	0	ENST00000269305.4:c.773A>G	p.Glu258Gly	p.E258G	ENST00000269305	NM_001126112.2	258	gAa/gGa	7/11	0.272459310007821	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.272459310007821	1		752	737	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971053	21971053	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137854598	NA	P-0038052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	93	614	0	ENST00000304494.5:c.305C>T	p.Ala102Val	p.A102V	ENST00000304494	NM_000077.4	102	gCg/gTg	2/3	0.272459310007821	1	FACETS	0.965	0.859	1	0.965	0.859	1	CLONAL	1	TRUE	0	0.272459310007821	1		614	611	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691809	30691809	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	42	592	0	ENST00000295754.5:c.311C>T	p.Pro104Leu	p.P104L	ENST00000295754	NM_003242.5	104	cCc/cTc	3/7	1	2	FACETS	0.384	0.32	0.457	0.384	0.32	0.457	SUBCLONAL	1	TRUE	1	0.272459310007821	2		592	802	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0038067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	182	547	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	0.604298590332185	2		547	543	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624275	89624275	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204910	NA	P-0038067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	142	320	1	ENST00000371953.3:c.49C>T	p.Gln17Ter	p.Q17*	ENST00000371953	NM_000314.4	17	Caa/Taa	1/9	1	2	FACETS	0.878	0.805	0.955	0.878	0.805	0.955	CLONAL	1	TRUE	1	0.604298590332185	2		321	535	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574024	7574025	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0038067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	214	483	0	ENST00000269305.4:c.1002dup	p.Arg335AlafsTer2	p.R335Afs*2	ENST00000269305	NM_001126112.2	334	-/G	10/11	0.599626356759368	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.604298590332185	1		483	466	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952075	178952075	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	92	256	0	ENST00000263967.3:c.3130A>C	p.Asn1044His	p.N1044H	ENST00000263967	NM_006218.2	1044	Aat/Cat	21/21	1	2	FACETS	0.917	0.823	1	0.917	0.823	1	CLONAL	1	TRUE	1	0.604298590332185	2		256	332	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919836	96919836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772153618	NA	P-0038067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	224	337	0	ENST00000258439.3:c.427G>A	p.Val143Ile	p.V143I	ENST00000258439	NM_001193304.2	143	Gtc/Atc	4/4	NA	2	FACETS	0.842	0.796	0.889			1	INDETERMINATE	2	TRUE	NA	0.604298590332185	2		337	440	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952065	178952065	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	93	264	0	ENST00000263967.3:c.3120G>A	p.Met1040Ile	p.M1040I	ENST00000263967	NM_006218.2	1040	atG/atA	21/21	1	2	FACETS	0.924	0.83	1	0.924	0.83	1	CLONAL	1	TRUE	1	0.604298590332185	2		264	333	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0038069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	76	294	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.54159125182098	6	FACETS	0.857	0.752	0.971			1	CLONAL	1	TRUE	NA	0.54159125182098	6		294	682	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0038069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	146	281	2	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.532793662986919	2	FACETS	0.926	0.849	1	0.463	0.424	0.503	CLONAL	1	TRUE	0	0.54159125182098	2		283	582	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456599	32456599	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	337	136	0	ENST00000332351.3:c.293G>T	p.Gly98Val	p.G98V	ENST00000332351	NM_024426.4	98	gGc/gTc	1/10	0.526527317390641	5	FACETS	1	0.971	1			1	CLONAL	5	TRUE	NA	0.54159125182098	5		136	449	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244567	46244567	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	36	424	0	ENST00000334344.6:c.2661A>C	p.Gln887His	p.Q887H	ENST00000334344	NM_152641.2	887	caA/caC	15/21	0.54159125182098	3	FACETS	0.238	0.195	0.287	0.119	0.097	0.144	SUBCLONAL	1	TRUE	1	0.54159125182098	3		424	709	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420661	49420661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555185875	NA	P-0038069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	231	477	0	ENST00000301067.7:c.15088C>T	p.Arg5030Cys	p.R5030C	ENST00000301067	NM_003482.3	5030	Cgt/Tgt	48/54	0.54159125182098	3	FACETS	1	0.988	1	0.62	0.579	0.662	CLONAL	1	TRUE	1	0.54159125182098	3		477	874	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863391	57863391	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139792497	NA	P-0038069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	223	543	0	ENST00000228682.2:c.1486C>T	p.Arg496Cys	p.R496C	ENST00000228682	NM_005269.2	496	Cgc/Tgc	11/12	0.54159125182098	3	FACETS	1	0.963	1	0.525	0.489	0.563	CLONAL	1	TRUE	1	0.54159125182098	3		543	996	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514944	103514944	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	66	259	0	ENST00000355739.4:c.1445G>T	p.Gly482Val	p.G482V	ENST00000355739	NM_000123.3	482	gGg/gTg	8/15	0.483313925265231	3	FACETS	0.626	0.544	0.714			1	SUBCLONAL	1	TRUE	NA	0.54159125182098	3		259	495	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028715	42028715	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	193	440	0	ENST00000219905.7:c.4253A>G	p.Asp1418Gly	p.D1418G	ENST00000219905	NM_001164273.1	1418	gAt/gGt	13/24	0.54159125182098	3	FACETS	1	0.98	1	0.578	0.536	0.622	CLONAL	1	TRUE	1	0.54159125182098	3		440	783	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830754	3830754	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	137	292	0	ENST00000262367.5:c.1802G>T	p.Arg601Leu	p.R601L	ENST00000262367	NM_004380.2	601	cGg/cTg	8/31	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.54159125182098	2		292	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0038069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	391	470	0	ENST00000269305.4:c.560-1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.54159125182098	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.54159125182098	2		470	676	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676284	37676284	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	227	473	0	ENST00000447079.4:c.3039G>C	p.Gln1013His	p.Q1013H	ENST00000447079	NM_015083.1	1013	caG/caC	11/14	0.532793662986919	2	FACETS	1	0.981	1	0.561	0.524	0.599	CLONAL	1	TRUE	0	0.54159125182098	2		473	747	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215336	5215336	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	204	496	0	ENST00000357368.4:c.4282T>C	p.Tyr1428His	p.Y1428H	ENST00000357368	NM_002850.3	1428	Tat/Cat	28/38	0.54159125182098	3	FACETS	1	0.979	1	0.57	0.529	0.612	CLONAL	1	TRUE	1	0.54159125182098	3		496	840	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627293	14627293	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs779148550	NA	P-0038069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2209	237	666	0	ENST00000254322.2:c.777G>C	p.Arg259Ser	p.R259S	ENST00000254322	NM_006145.1	259	agG/agC	2/3	0.54159125182098	5	FACETS	0.648	0.602	0.697	0.216	0.2	0.233	SUBCLONAL	1	TRUE	2	0.54159125182098	5		666	2446	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143051	30143052	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1244823020	NA	P-0038069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	185	712	4	ENST00000389048.3:c.474dup	p.Gly159ArgfsTer67	p.G159Rfs*67	ENST00000389048	NM_004304.4	158	-/C	1/29	0.340369047795665	1	FACETS	0.619	0.572	0.667	0.619	0.572	0.667	SUBCLONAL	1	TRUE	0	0.54159125182098	1		716	805	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607416	46607416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	260	719	1	ENST00000263734.3:c.1605G>A	p.Met535Ile	p.M535I	ENST00000263734	NM_001430.4	535	atG/atA	12/16	1	2	FACETS	0.868	0.813	0.925	0.868	0.813	0.925	CLONAL	1	TRUE	1	0.54159125182098	2		720	1106	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713346	40713346	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	204	542	0	ENST00000373198.4:c.4169A>T	p.Glu1390Val	p.E1390V	ENST00000373198	NM_133170.3	1390	gAg/gTg	30/32	0.54159125182098	3	FACETS	1	0.952	1	0.516	0.479	0.555	CLONAL	1	TRUE	1	0.54159125182098	3		542	927	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755426	39755427	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	157	422	1	ENST00000288319.7:c.1338dup	p.Ala447CysfsTer19	p.A447Cfs*19	ENST00000288319	NM_182918.3	446	-/T	10/10	0.54159125182098	3	FACETS	0.992	0.91	1	0.496	0.455	0.539	CLONAL	1	TRUE	1	0.54159125182098	3		423	743	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541087	187541087	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	94	286	0	ENST00000441802.2:c.6653T>C	p.Ile2218Thr	p.I2218T	ENST00000441802	NM_005245.3	2218	aTc/aCc	10/27	1	2	FACETS	0.962	0.863	1	0.962	0.863	1	CLONAL	1	TRUE	1	0.54159125182098	2		286	361	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052920	180052920	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	300	673	0	ENST00000261937.6:c.1370A>G	p.Gln457Arg	p.Q457R	ENST00000261937	NM_182925.4	457	cAg/cGg	10/30	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.54159125182098	2		673	937	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120287	94120287	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	83	225	0	ENST00000369303.4:c.764A>T	p.Glu255Val	p.E255V	ENST00000369303	NM_004440.3	255	gAa/gTa	3/17	0.54159125182098	3	FACETS	1	0.961	1	0.588	0.524	0.656	CLONAL	1	TRUE	1	0.54159125182098	3		225	331	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439721	140439721	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	134	363	0	ENST00000288602.6:c.2018A>G	p.Tyr673Cys	p.Y673C	ENST00000288602	NM_004333.4	673	tAc/tGc	17/18	0.518320865640661	4	FACETS	1	0.96	1	0.365	0.332	0.4	CLONAL	1	TRUE	1	0.54159125182098	4		363	696	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494139	140494139	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	224	580	0	ENST00000288602.6:c.1109A>T	p.His370Leu	p.H370L	ENST00000288602	NM_004333.4	370	cAt/cTt	8/18	0.518320865640661	4	FACETS	0.947	0.88	1	0.316	0.293	0.339	CLONAL	1	TRUE	1	0.54159125182098	4		580	1347	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151168675	151168675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	73	350	0	ENST00000262187.5:c.292G>A	p.Val98Ile	p.V98I	ENST00000262187	NM_005614.3	98	Gtt/Att	5/8	0.494477685968118	1	FACETS	0.69	0.609	0.774	0.69	0.609	0.774	SUBCLONAL	1	TRUE	0	0.54159125182098	1		350	285	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981791	70981791	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	650	661	0	ENST00000276594.2:c.305A>G	p.Tyr102Cys	p.Y102C	ENST00000276594	NM_024504.3	102	tAc/tGc	2/8	0.54159125182098	4	FACETS	0.912	0.881	0.943			1	CLONAL	3	TRUE	NA	0.54159125182098	4		661	1352	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430637	80430637	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	60	252	0	ENST00000286548.4:c.371T>A	p.Phe124Tyr	p.F124Y	ENST00000286548	NM_002072.3	124	tTt/tAt	3/7	0.518320865640661	4	FACETS	0.921	0.797	1	0.307	0.265	0.352	CLONAL	1	TRUE	1	0.54159125182098	4		252	371	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238393	98238393	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs774082990	NA	P-0038069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	130	386	0	ENST00000331920.6:c.1651A>G	p.Thr551Ala	p.T551A	ENST00000331920	NM_000264.3	551	Acg/Gcg	12/24	NA	2	FACETS	0.887	0.809	0.969			1	INDETERMINATE	1	TRUE	NA	0.54159125182098	2		386	541	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913137	44913137	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1740	121	388	0	ENST00000377967.4:c.812A>G	p.Gln271Arg	p.Q271R	ENST00000377967	NM_021140.2	271	cAg/cGg	10/29	0.54159125182098	13	FACETS	0.955	0.859	1			1	CLONAL	1	TRUE	NA	0.54159125182098	13		388	1861	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045893	47045894	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCCGGCCTGGGTGCACCGGCCTG	novel	NA	P-0038069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1230	125	454	0	ENST00000377604.3:c.2704_2705insCGGCCTGTCCGGCCTGGGTGCAC	p.Arg902ProfsTer30	p.R902Pfs*30	ENST00000377604	NM_001204468.1	896	-/TCCGGCCTGGGTGCACCGGCCTG	24/24	0.54159125182098	5	FACETS	0.617	0.557	0.682			1	SUBCLONAL	1	TRUE	NA	0.54159125182098	5		454	1355	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649532	48649532	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	1014	573	0	ENST00000376670.3:c.16C>G	p.Leu6Val	p.L6V	ENST00000376670	NM_002049.3	6	Ctg/Gtg	2/6	0.54159125182098	5	FACETS	1	0.997	1			1	CLONAL	4	TRUE	NA	0.54159125182098	5		573	1533	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608307	100608308	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0038069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	108	524	0	ENST00000308731.7:c.1782dup	p.Lys595GlufsTer5	p.K595Efs*5	ENST00000308731	NM_000061.2	594	-/G	18/19	0.325105081559173	4	FACETS	0.704	0.631	0.782			1	SUBCLONAL	1	TRUE	NA	0.54159125182098	4		524	873	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453397	40453398	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0038069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	28	370	0	ENST00000345506.4:c.1094_1095insC	p.Pro366SerfsTer11	p.P366Sfs*11	ENST00000345506	NM_003152.3	365	aat/aaCt	10/20	0.54159125182098	2	FACETS	0.364	0.291	0.446	0.182	0.145	0.223	SUBCLONAL	1	TRUE	0	0.54159125182098	2		370	284	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	136	277	0	ENST00000397062.3:c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	NM_006164.4	34	Cga/Gga	2/5	0.292953424063527	1	FACETS	0.835	0.766	0.906	0.835	0.766	0.906	INDETERMINATE	1	TRUE	0	0.550227521413218	1		277	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578441	7578441	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	443	916	0	ENST00000269305.4:c.489C>A	p.Tyr163Ter	p.Y163*	ENST00000269305	NM_001126112.2	163	taC/taA	5/11	0.503285129175427	2	FACETS	0.904	0.867	0.94	0.904	0.867	0.94	CLONAL	2	TRUE	0	0.550227521413218	2		916	891	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724530	162724530	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	250	551	0	ENST00000367921.3:c.302G>T	p.Gly101Val	p.G101V	ENST00000367921	NM_006182.2	101	gGg/gTg	5/18	0.278873055570611	3	FACETS	1	0.993	1	0.732	0.686	0.778	INDETERMINATE	1	TRUE	1	0.550227521413218	3		551	792	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28605715	28605715	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	279	715	0	ENST00000253063.3:c.1319A>G	p.Tyr440Cys	p.Y440C	ENST00000253063	NM_031459.4	440	tAc/tGc	9/10	0.332465064205763	1	FACETS	0.913	0.861	0.966	0.913	0.861	0.966	CLONAL	1	TRUE	0	0.550227521413218	1		715	805	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166098	118166098	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	71	402	0	ENST00000369448.3:c.608C>T	p.Ser203Phe	p.S203F	ENST00000369448	NM_017709.3	203	tCt/tTt	2/2	0.550227521413218	1	FACETS	0.549	0.482	0.619	0.549	0.482	0.619	SUBCLONAL	1	TRUE	0	0.550227521413218	1		402	341	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671197	30671197	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0038080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	243	754	0	ENST00000376406.3:c.5680A>T	p.Lys1894Ter	p.K1894*	ENST00000376406	NM_014641.2	1894	Aaa/Taa	11/15	0.276929825827857	1	FACETS	0.772	0.723	0.822	0.772	0.723	0.822	INDETERMINATE	1	TRUE	0	0.550227521413218	1		754	829	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127920606	127920606	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	134	538	0	ENST00000373547.4:c.293C>A	p.Ala98Glu	p.A98E	ENST00000373547	NM_002721.4	98	gCa/gAa	4/7	0.511607596451252	2	FACETS	0.813	0.741	0.888	0.407	0.37	0.444	CLONAL	1	TRUE	0	0.550227521413218	2		538	599	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0038081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	157	403	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.252148898218184	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	0	0.281141449015179	2		403	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0038081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	230	987	1	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.240360696496626	2	FACETS	0.9	0.84	0.962	0.9	0.84	0.962	CLONAL	2	TRUE	0	0.281141449015179	2		988	909	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64288917	64288917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755475012	NA	P-0038081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	147	535	1	ENST00000370651.3:c.313G>A	p.Val105Ile	p.V105I	ENST00000370651	NM_003463.4	105	Gtt/Att	4/6	0.281392974801665	3	FACETS	0.807	0.738	0.879	0.807	0.738	0.879	CLONAL	2	TRUE	1	0.281141449015179	3		536	739	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0038082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	111	382	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.95	0.861	1	0.95	0.861	1	CLONAL	1	TRUE	1	0.59160785052622	2		382	395	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717730	89717730	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121909239	NA	P-0038082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	149	444	0	ENST00000371953.3:c.755A>T	p.Asp252Val	p.D252V	ENST00000371953	NM_000314.4	252	gAt/gTt	7/9	0.59160785052622	3	FACETS	0.871	0.797	0.949	0.436	0.398	0.475	CLONAL	1	TRUE	1	0.59160785052622	3		444	749	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936083	178936083	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519927	NA	P-0038082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	168	573	0	ENST00000263967.3:c.1625A>C	p.Glu542Ala	p.E542A	ENST00000263967	NM_006218.2	542	gAa/gCa	10/21	1	2	FACETS	0.973	0.899	1	0.973	0.899	1	CLONAL	1	TRUE	1	0.59160785052622	2		573	584	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711875	89711875	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	rs587782603	NA	P-0038082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	260	405	0	ENST00000371953.3:c.493G>T	p.Gly165Ter	p.G165*	ENST00000371953	NM_000314.4	165	Gga/Tga	6/9	0.59160785052622	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.59160785052622	3		405	546	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650654	67650654	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	128	428	0	ENST00000264010.4:c.959G>A	p.Arg320His	p.R320H	ENST00000264010	NM_006565.3	320	cGt/cAt	5/12	1	2	FACETS	0.874	0.797	0.954	0.874	0.797	0.954	CLONAL	1	TRUE	1	0.59160785052622	2		428	495	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644528	3644528	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	230	949	0	ENST00000294008.3:c.2086C>G	p.Gln696Glu	p.Q696E	ENST00000294008	NM_032444.2	696	Cag/Gag	10/15	1	2	FACETS	0.895	0.836	0.956	0.895	0.836	0.956	CLONAL	1	TRUE	1	0.59160785052622	2		949	869	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967464	38967464	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs376772272	NA	P-0038082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	131	369	0	ENST00000357387.3:c.1126A>G	p.Ile376Val	p.I376V	ENST00000357387	NM_152756.3	376	Att/Gtt	13/38	1	2	FACETS	0.946	0.865	1	0.946	0.865	1	CLONAL	1	TRUE	1	0.59160785052622	2		369	468	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591077	67591079	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0038082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	72	335	0	ENST00000274335.5:c.1670_1672del	p.Arg557_Glu558delinsGln	p.R557_E558delinsQ	ENST00000274335		557	cGAGaa/caa	12/15	1	2	FACETS	0.691	0.608	0.78	0.691	0.608	0.78	SUBCLONAL	1	TRUE	1	0.59160785052622	2		335	352	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0038085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	82	482	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		482	421	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913499	NA	P-0038088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	98	230	0	ENST00000345146.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000345146	NM_005896.2	132	Cgt/Ggt	4/10	1	2	FACETS	0.974	0.877	1	0.974	0.877	1	CLONAL	1	TRUE	1	0.576558981441214	2		230	349	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938089	76938092	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	novel	NA	P-0038088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	218	254	0	ENST00000373344.5:c.2656_2659del	p.Glu886LeufsTer18	p.E886Lfs*18	ENST00000373344	NM_000489.3	886	GAGAct/ct	9/35	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.576558981441214	1		254	443	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965248	81965248	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	157	410	0	ENST00000359376.3:c.2728A>T	p.Ile910Phe	p.I910F	ENST00000359376	NM_002661.3	910	Att/Ttt	25/33	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.576558981441214	2		410	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579480	7579487	+	frameshift_variant	Frame_Shift_Del	DEL	AGCCTCTG	AGCCTCTG	-	novel	NA	P-0038088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	478	707	0	ENST00000269305.4:c.200_207del	p.Pro67ArgfsTer79	p.P67Rfs*79	ENST00000269305	NM_001126112.2	67	cCAGAGGCT/c	4/11	1	2	FACETS	1	0.991	1	1	0.998	1	CLONAL	2	TRUE	1	0.576558981441214	2		707	775	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588175	67588175	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	112	258	0	ENST00000274335.5:c.1005G>A	p.Trp335Ter	p.W335*	ENST00000274335		335	tgG/tgA	7/15	0.539699343172874	1	FACETS	0.743	0.675	0.814	0.743	0.675	0.814	SUBCLONAL	1	TRUE	0	0.576558981441214	1		258	372	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0038089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	176	294	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.381986005450492	2	FACETS	1	0.99	1	0.698	0.651	0.746	CLONAL	1	TRUE	0	0.601401891675722	2		294	419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0038089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	23	831	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.425340120302427	1	FACETS	0.064	0.049	0.081	0.064	0.049	0.081	SUBCLONAL	1	TRUE	0	0.601401891675722	1		832	839	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0038089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	10	493	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.282858939385601	1	FACETS	0.05	0.033	0.071	0.05	0.033	0.071	INDETERMINATE	1	TRUE	0	0.601401891675722	1		493	467	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0038089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	41	770	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.282858939385601	1	FACETS	0.205	0.17	0.243	0.205	0.17	0.243	INDETERMINATE	1	TRUE	0	0.601401891675722	1		770	465	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0038089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	126	283	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.88	0.802	0.961	0.88	0.802	0.961	CLONAL	1	TRUE	1	0.601401891675722	2		283	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0038089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	279	802	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.425340120302427	1	FACETS	0.578	0.542	0.614	0.578	0.542	0.614	SUBCLONAL	1	TRUE	0	0.601401891675722	1		802	1123	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0038089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	302	365	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.601401891675722	2	FACETS	0.94	0.898	0.983	0.94	0.898	0.983	CLONAL	2	TRUE	0	0.601401891675722	2		365	534	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200118	128200118	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553770434	NA	P-0038089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	486	737	0	ENST00000341105.2:c.1187G>A	p.Arg396Gln	p.R396Q	ENST00000341105	NM_032638.4	396	cGg/cAg	6/6	0.381986005450492	2	FACETS	1	0.995	1	0.646	0.619	0.674	CLONAL	1	TRUE	0	0.601401891675722	2		737	1250	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135385	30135385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	124	378	0	ENST00000331968.5:c.433C>T	p.Arg145Cys	p.R145C	ENST00000331968	NM_002742.2	145	Cgt/Tgt	3/18	1	2	FACETS	0.687	0.624	0.754	0.687	0.624	0.754	SUBCLONAL	1	TRUE	1	0.601401891675722	2		378	600	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490599	20490599	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749949370	NA	P-0038089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	173	563	0	ENST00000346618.3:c.1336G>A	p.Asp446Asn	p.D446N	ENST00000346618	NM_001949.4	446	Gat/Aat	7/7	1	2	FACETS	0.653	0.601	0.707	0.653	0.601	0.707	SUBCLONAL	1	TRUE	1	0.601401891675722	2		563	881	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94923095	94923095	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	27	431	1	ENST00000536441.1:c.373del	p.Ile125Ter	p.I125*	ENST00000536441	NM_144665.3	125	Ata/ta	4/10	1	2	FACETS	0.242	0.192	0.299	0.242	0.192	0.299	SUBCLONAL	1	TRUE	1	0.601401891675722	2		432	371	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120258	70120259	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0038089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1421	83	865	0	ENST00000245479.2:c.1261_1262dup	p.Ser421ArgfsTer50	p.S421Rfs*50	ENST00000245479	NM_000346.3	420	-/AG	3/3	1	2	FACETS	0.184	0.161	0.208	0.184	0.161	0.208	SUBCLONAL	1	TRUE	1	0.601401891675722	2		865	1504	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224198	36224198	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1351767688	NA	P-0038089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	295	718	0	ENST00000222270.7:c.6748C>T	p.Arg2250Cys	p.R2250C	ENST00000222270	NM_014727.1	2250	Cgc/Tgc	28/37	1	2	FACETS	0.761	0.715	0.808	0.761	0.715	0.808	SUBCLONAL	1	TRUE	1	0.601401891675722	2		718	1289	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0038091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	107	403	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.209483397014294	4	FACETS	0.91	0.818	1	0.91	0.818	1	CLONAL	2	TRUE	2	0.23	4		403	629	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578463	7578463	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371524413	NA	P-0038091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	57	953	0	ENST00000269305.4:c.467G>C	p.Arg156Pro	p.R156P	ENST00000269305	NM_001126112.2	156	cGc/cCc	5/11	1	2	FACETS	0.513	0.439	0.595	0.513	0.439	0.595	SUBCLONAL	1	TRUE	1	0.23	2		953	966	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617419	158617419	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	33	471	0	ENST00000263640.3:c.1237del	p.Glu413LysfsTer7	p.E413Kfs*7	ENST00000263640	NM_001105.4	413	Gaa/aa	9/11	1	2	FACETS	0.451	0.366	0.547	0.451	0.366	0.547	SUBCLONAL	1	TRUE	1	0.23	2		471	636	SUCCESS
APC	324	MSKCC	GRCh37	5	112154719	112154719	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	89	495	0	ENST00000257430.4:c.990G>A	p.Met330Ile	p.M330I	ENST00000257430	NM_000038.5	330	atG/atA	10/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.23	2		495	598	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486221	8486221	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1392599086	NA	P-0038091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	30	428	0	ENST00000356435.5:c.2596G>C	p.Glu866Gln	p.E866Q	ENST00000356435		866	Gag/Cag	17/35	1	2	FACETS	0.488	0.392	0.597	0.488	0.392	0.597	SUBCLONAL	1	TRUE	1	0.23	2		428	535	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0038095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	115	567	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.148841109895534	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	FALSE	2	0.192205397894586	4		567	588	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0038095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	90	514	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.148841109895534	4	FACETS	0.979	0.871	1	0.979	0.871	1	CLONAL	2	FALSE	2	0.192205397894586	4		514	570	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038613	14038613	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	31	334	0	ENST00000311895.7:c.1938A>T	p.Arg646Ser	p.R646S	ENST00000311895	NM_005236.2	646	agA/agT	10/11	0.192205397894586	9	FACETS	0.902	0.728	1			1	CLONAL	1	FALSE	NA	0.192205397894586	9		334	598	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993216	72993216	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	138	717	1	ENST00000268489.5:c.829A>G	p.Lys277Glu	p.K277E	ENST00000268489	NM_006885.3	277	Aag/Gag	2/10	0.192205397894586	5	FACETS	0.955	0.868	1	0.636	0.578	0.697	CLONAL	2	FALSE	2	0.192205397894586	5		718	969	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933468	49933468	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	47	708	0	ENST00000296474.3:c.2722G>T	p.Glu908Ter	p.E908*	ENST00000296474	NM_002447.2	908	Gag/Tag	11/20	0.192205397894586	3	FACETS	0.942	0.794	1	0.471	0.397	0.553	CLONAL	1	FALSE	1	0.192205397894586	3		708	569	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658464	117658464	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	40	519	1	ENST00000368508.3:c.5119A>G	p.Ser1707Gly	p.S1707G	ENST00000368508	NM_002944.2	1707	Agc/Ggc	31/43	0.192205397894586	3	FACETS	0.834	0.692	0.992	0.417	0.346	0.496	CLONAL	1	FALSE	1	0.192205397894586	3		520	547	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521531	8521531	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	40	408	0	ENST00000356435.5:c.707C>G	p.Pro236Arg	p.P236R	ENST00000356435		236	cCa/cGa	9/35	1	2	FACETS	0.921	0.765	1	0.921	0.765	1	CLONAL	1	FALSE	1	0.192205397894586	2		408	452	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120612003	120612004	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	rs372504208	NA	P-0038096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	10	24	0	ENST00000256646.2:c.17_18del	p.Pro6ArgfsTer27	p.P6Rfs*27	ENST00000256646	NM_024408.3	6	cCC/c	1/34	0.237264527629959	3	FACETS	0.827	0.573	1	0.827	0.573	1	CLONAL	2	TRUE	1	0.237264527629959	3		24	57	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577102	7577102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793881	NA	P-0038096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	219	710	0	ENST00000269305.4:c.836G>A	p.Gly279Glu	p.G279E	ENST00000269305	NM_001126112.2	279	gGg/gAg	8/11	0.163002005921678	3	FACETS	1	0.982	1	0.767	0.715	0.822	CLONAL	2	TRUE	0	0.237264527629959	3		710	897	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733461	85733461	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	60	382	0	ENST00000370580.1:c.551A>C	p.Asn184Thr	p.N184T	ENST00000370580	NM_003921.4	184	aAt/aCt	3/3	0.237264527629959	3	FACETS	0.884	0.761	1	0.442	0.38	0.509	CLONAL	1	TRUE	1	0.237264527629959	3		382	640	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844791	156844798	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GGGATCAA	GGGATCAA	CTC	novel	NA	P-0038096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	267	655	1	ENST00000524377.1:c.1345_1352delinsCTC	p.Gly449LeufsTer49	p.G449Lfs*49	ENST00000524377	NM_002529.3	449	GGGATCAAc/CTCc	11/17	0.237264527629959	4	FACETS	0.936	0.878	0.995	0.936	0.878	0.995	CLONAL	3	TRUE	1	0.237264527629959	4		656	992	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609991	43609991	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs864622505	NA	P-0038096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	99	814	1	ENST00000355710.3:c.1943T>C	p.Val648Ala	p.V648A	ENST00000355710	NM_020975.4	648	gTc/gCc	11/20	0.237264527629959	3	FACETS	0.926	0.825	1	0.463	0.412	0.517	CLONAL	1	TRUE	1	0.237264527629959	3		815	1008	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919634	28919634	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	48	499	0	ENST00000282397.4:c.2303C>A	p.Ala768Asp	p.A768D	ENST00000282397	NM_002019.4	768	gCt/gAt	16/30	0.163002005921678	3	FACETS	0.617	0.521	0.725	0.206	0.173	0.242	SUBCLONAL	1	TRUE	0	0.237264527629959	3		499	733	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105236683	105236683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	259	677	0	ENST00000349310.3:c.1438G>A	p.Ala480Thr	p.A480T	ENST00000349310	NM_001014432.1	480	Gcc/Acc	15/15	0.237264527629959	6	FACETS	0.959	0.898	1			1	CLONAL	3	TRUE	NA	0.237264527629959	6		677	1119	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16021267	16021267	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	42	243	0	ENST00000268712.3:c.1990A>G	p.Asn664Asp	p.N664D	ENST00000268712	NM_006311.3	664	Aac/Gac	18/46	0.237264527629959	3	FACETS	1	0.898	1	0.55	0.46	0.649	CLONAL	1	TRUE	1	0.237264527629959	3		243	360	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234518	41234518	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	66	462	0	ENST00000357654.3:c.4260G>C	p.Gln1420His	p.Q1420H	ENST00000357654	NM_007294.3	1420	caG/caC	12/23	0.223554201130603	4	FACETS	1	0.872	1	0.251	0.218	0.288	CLONAL	1	TRUE	0	0.237264527629959	4		462	685	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234520	41234520	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs80357305	NA	P-0038096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	198	473	0	ENST00000357654.3:c.4258C>T	p.Gln1420Ter	p.Q1420*	ENST00000357654	NM_007294.3	1420	Cag/Tag	12/23	0.223554201130603	4	FACETS	1	0.945	1	0.764	0.71	0.819	CLONAL	3	TRUE	0	0.237264527629959	4		473	676	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533095	63533095	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	78	537	0	ENST00000307078.5:c.1799C>G	p.Pro600Arg	p.P600R	ENST00000307078	NM_004655.3	600	cCc/cGc	7/11	0.237264527629959	5	FACETS	1	0.911	1	0.209	0.183	0.237	CLONAL	1	TRUE	0	0.237264527629959	5		537	852	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680238	30680238	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	103	658	0	ENST00000376406.3:c.1481A>T	p.Asp494Val	p.D494V	ENST00000376406	NM_014641.2	494	gAc/gTc	5/15	0.237264527629959	6	FACETS	1	0.912	1	0.256	0.228	0.286	CLONAL	1	TRUE	2	0.237264527629959	6		658	1248	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30682881	30682881	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	73	512	0	ENST00000376406.3:c.72G>C	p.Leu24Phe	p.L24F	ENST00000376406	NM_014641.2	24	ttG/ttC	2/15	0.237264527629959	6	FACETS	0.945	0.825	1	0.236	0.206	0.269	CLONAL	1	TRUE	2	0.237264527629959	6		512	960	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527479	157527479	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	119	428	0	ENST00000346085.5:c.5204C>G	p.Ala1735Gly	p.A1735G	ENST00000346085	NM_020732.3	1735	gCt/gGt	20/20	0.237264527629959	3	FACETS	0.901	0.815	0.991	0.6	0.543	0.661	CLONAL	2	TRUE	0	0.237264527629959	3		428	623	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355277	81355277	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	90	290	0	ENST00000222390.5:c.1097T>C	p.Phe366Ser	p.F366S	ENST00000222390	NM_000601.4	366	tTt/tCt	9/18	0.237264527629959	3	FACETS	0.935	0.833	1			1	CLONAL	2	TRUE	NA	0.237264527629959	3		290	454	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869712	117869712	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	38	249	0	ENST00000297338.2:c.482G>T	p.Gly161Val	p.G161V	ENST00000297338	NM_006265.2	161	gGt/gTt	6/14	0.237264527629959	6	FACETS	1	0.879	1	0.216	0.178	0.258	CLONAL	1	TRUE	1	0.237264527629959	6		249	437	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131780	2131839	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTGCCTCGCTCCAACACAGGTGAGTGGCATGGCGGGCCTTGGCACGGGCTCTGCTCCCA	TCTGCCTCGCTCCAACACAGGTGAGTGGCATGGCGGGCCTTGGCACGGGCTCTGCTCCCA	GCTGCTCCTCCTC	novel	NA	P-0038096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	198	653	0	ENST00000219476.3:c.3795_3814+40delinsGCTGCTCCTCCTC		p.X1265_splice	ENST00000219476	NM_000548.3	1265		31/42	0.230811682339764	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.237264527629959	2		653	739	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0038099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	29	770	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	1	0.206942415073092	2		770	266	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207021	1207021	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913324	NA	P-0038099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	120	464	0	ENST00000326873.7:c.109C>T	p.Gln37Ter	p.Q37*	ENST00000326873	NM_000455.4	37	Cag/Tag	1/10	0.206942415073092	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.206942415073092	1		464	993	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095002	11095002	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1315494799	NA	P-0038099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	107	878	0	ENST00000358026.2:c.175C>T	p.Gln59Ter	p.Q59*	ENST00000358026	NM_001128849.1	59	Cag/Tag	2/36	0.206942415073092	1	FACETS	0.929	0.832	1	0.929	0.832	1	CLONAL	1	TRUE	0	0.206942415073092	1		878	998	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713522	30713522	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	44	530	0	ENST00000295754.5:c.847G>T	p.Glu283Ter	p.E283*	ENST00000295754	NM_003242.5	283	Gag/Tag	4/7	0.206942415073092	1	FACETS	0.752	0.63	0.887	0.752	0.63	0.887	SUBCLONAL	1	TRUE	0	0.206942415073092	1		530	507	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743580	46743580	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs888235109	NA	P-0038099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	71	685	0	ENST00000371975.4:c.1961G>A	p.Arg654His	p.R654H	ENST00000371975	NM_003579.3	654	cGc/cAc	17/18	1	2	FACETS	0.811	0.707	0.924	0.811	0.707	0.924	CLONAL	1	TRUE	1	0.206942415073092	2		685	846	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602413	10602413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	76	789	2	ENST00000171111.5:c.1165G>A	p.Asp389Asn	p.D389N	ENST00000171111	NM_203500.1	389	Gac/Aac	3/6	0.206942415073092	1	FACETS	0.8	0.701	0.908	0.8	0.701	0.908	CLONAL	1	TRUE	0	0.206942415073092	1		791	823	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29197685	29197685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371579846	NA	P-0038099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	85	706	0	ENST00000240100.2:c.509C>T	p.Pro170Leu	p.P170L	ENST00000240100	NM_001394.6	170	cCg/cTg	2/4	1	2	FACETS	0.865	0.763	0.974	0.865	0.763	0.974	CLONAL	1	TRUE	1	0.206942415073092	2		706	950	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0038100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	29	331	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	1	2	FACETS	0.908	0.737	1	0.908	0.737	1	CLONAL	1	TRUE	1	0.39178048661274	2		331	163	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984680	11984681	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGAGAACACACAGCAT	novel	NA	P-0038100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	14	279	1	ENST00000353533.5:c.231_246dup	p.Ser83AsnfsTer5	p.S83Nfs*5	ENST00000353533	NM_003010.3	76	ctg/cTGAGAACACACAGCATtg	3/11	0.349785247946129	1	FACETS	0.58	0.425	0.764	0.58	0.425	0.764	SUBCLONAL	1	TRUE	0	0.39178048661274	1		280	99	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696452	47696452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	54	476	0	ENST00000347630.2:c.371G>A	p.Arg124Lys	p.R124K	ENST00000347630	NM_001007230.1	124	aGg/aAg	6/11	1	2	FACETS	0.872	0.75	1	0.872	0.75	1	CLONAL	1	TRUE	1	0.39178048661274	2		476	316	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0038101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	198	488	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	1	2	FACETS	0.868	0.811	0.927	0.868	0.811	0.927	CLONAL	1	TRUE	1	0.836661808384371	2		488	545	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202743	16202743	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	59	406	0	ENST00000375759.3:c.451C>A	p.His151Asn	p.H151N	ENST00000375759	NM_015001.2	151	Cac/Aac	3/15	1	2	FACETS	0.934	0.805	1	0.934	0.805	1	CLONAL	1	FALSE	1	0.287206447964844	2		406	440	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	55	437	1	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	0.876	0.751	1	0.876	0.751	1	CLONAL	1	FALSE	1	0.287206447964844	2		438	437	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102157	27102158	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	49	395	0	ENST00000324856.7:c.5084dup	p.Tyr1696ValfsTer2	p.Y1696Vfs*2	ENST00000324856	NM_006015.4	1695	ctg/cTtg	19/20	1	2	FACETS	0.742	0.629	0.866	0.742	0.629	0.866	SUBCLONAL	1	FALSE	1	0.287206447964844	2		395	460	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430879	78430879	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	47	385	1	ENST00000370768.2:c.510del	p.Gly171GlufsTer21	p.G171Efs*21	ENST00000370768	NM_003902.3	170	aaA/aa	8/20	1	2	FACETS	0.648	0.547	0.76	0.648	0.547	0.76	SUBCLONAL	1	FALSE	1	0.287206447964844	2		386	505	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717728	89717728	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	99	364	0	ENST00000371953.3:c.753del	p.Asp252IlefsTer4	p.D252Ifs*4	ENST00000371953	NM_000314.4	251	ggT/gg	7/9	0.228411950954342	2	FACETS	0.905	0.814	0.999	0.905	0.814	0.999	CLONAL	2	FALSE	0	0.287206447964844	2		364	381	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533881	533881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs727503093	NA	P-0038102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	83	637	1	ENST00000451590.1:c.175G>A	p.Ala59Thr	p.A59T	ENST00000451590	NM_001130442.1	59	Gcc/Acc	3/5	1	2	FACETS	0.973	0.86	1	0.973	0.86	1	CLONAL	1	FALSE	1	0.287206447964844	2		638	594	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137357	64137357	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	73	539	0	ENST00000334205.4:c.1789G>A	p.Val597Ile	p.V597I	ENST00000334205	NM_003942.2	597	Gtc/Atc	14/17	1	2	FACETS	0.777	0.68	0.883	0.777	0.68	0.883	SUBCLONAL	1	FALSE	1	0.287206447964844	2		539	654	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466019	69466019	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	86	615	0	ENST00000227507.2:c.857C>A	p.Thr286Lys	p.T286K	ENST00000227507	NM_053056.2	286	aCa/aAa	5/5	1	2	FACETS	0.926	0.819	1	0.926	0.819	1	CLONAL	1	FALSE	1	0.287206447964844	2		615	647	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374507	118374507	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	34	323	0	ENST00000534358.1:c.7900C>T	p.Leu2634Phe	p.L2634F	ENST00000534358	NM_005933.3	2634	Ctt/Ttt	27/36	1	2	FACETS	0.64	0.523	0.771	0.64	0.523	0.771	SUBCLONAL	1	FALSE	1	0.287206447964844	2		323	370	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434270	49434270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776887182	NA	P-0038102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	108	819	0	ENST00000301067.7:c.7283G>A	p.Arg2428Gln	p.R2428Q	ENST00000301067	NM_003482.3	2428	cGg/cAg	31/54	1	2	FACETS	0.813	0.729	0.903	0.813	0.729	0.903	CLONAL	1	FALSE	1	0.287206447964844	2		819	925	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915180	32915180	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	46	478	0	ENST00000380152.3:c.6688A>T	p.Ile2230Phe	p.I2230F	ENST00000380152		2230	Att/Ttt	11/27	1	2	FACETS	0.836	0.706	0.979	0.836	0.706	0.979	CLONAL	1	FALSE	1	0.287206447964844	2		478	383	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346220	89346220	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	15	257	0	ENST00000301030.4:c.6730del	p.Val2244PhefsTer93	p.V2244Ffs*93	ENST00000301030	NM_001256183.1	2244	Gtt/tt	9/13	NA	2	FACETS	0.452	0.331	0.598			1	INDETERMINATE	1	FALSE	NA	0.287206447964844	2		257	231	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752444	55752444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1422545682	NA	P-0038102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	103	702	0	ENST00000284073.2:c.902C>T	p.Ala301Val	p.A301V	ENST00000284073	NM_138962.2	301	gCg/gTg	12/14	1	2	FACETS	0.939	0.84	1	0.939	0.84	1	CLONAL	1	FALSE	1	0.287206447964844	2		702	764	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27016012	27016012	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0038102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	49	398	0	ENST00000335756.4:c.289-1G>C		p.X97_splice	ENST00000335756	NM_001809.3	97			1	2	FACETS	0.857	0.728	0.999	0.857	0.728	0.999	CLONAL	1	FALSE	1	0.287206447964844	2		398	398	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712520	52712520	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	55	393	0	ENST00000394830.3:c.232C>T	p.Arg78Ter	p.R78*	ENST00000394830	NM_018313.4	78	Cga/Tga	3/30	1	2	FACETS	0.735	0.629	0.851	0.735	0.629	0.851	SUBCLONAL	1	FALSE	1	0.287206447964844	2		393	521	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119635014	119635034	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATATACAACTGGAATAGATAG	ATATACAACTGGAATAGATAG	-	novel	NA	P-0038102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	27	156	0	ENST00000316626.5:c.478-13_485del		p.X160_splice	ENST00000316626		160		5/12	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	FALSE	1	0.287206447964844	2		156	151	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916726	178916726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772110575	NA	P-0038102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	35	301	2	ENST00000263967.3:c.113G>A	p.Arg38His	p.R38H	ENST00000263967	NM_006218.2	38	cGt/cAt	2/21	1	2	FACETS	0.81	0.666	0.97	0.81	0.666	0.97	CLONAL	1	FALSE	1	0.287206447964844	2		303	301	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	25	222	0	ENST00000263967.3:c.1034A>G	p.Asn345Ser	p.N345S	ENST00000263967	NM_006218.2	345	aAt/aGt	5/21	1	2	FACETS	0.767	0.607	0.949	0.767	0.607	0.949	CLONAL	1	FALSE	1	0.287206447964844	2		222	227	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637210	176637210	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	73	546	0	ENST00000439151.2:c.1810C>G	p.Arg604Gly	p.R604G	ENST00000439151	NM_022455.4	604	Cga/Gga	5/23	1	2	FACETS	0.794	0.695	0.902	0.794	0.695	0.902	CLONAL	1	FALSE	1	0.287206447964844	2		546	640	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268090	55268090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745490627	NA	P-0038102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	103	698	1	ENST00000275493.2:c.2930G>A	p.Arg977His	p.R977H	ENST00000275493	NM_005228.3	977	cGc/cAc	24/28	1	2	FACETS	0.87	0.778	0.968	0.87	0.778	0.968	CLONAL	1	FALSE	1	0.287206447964844	2		699	824	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508253	106508253	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	42	297	0	ENST00000359195.3:c.247G>A	p.Val83Met	p.V83M	ENST00000359195	NM_002649.2	83	Gtg/Atg	2/11	1	2	FACETS	0.863	0.723	1	0.863	0.723	1	CLONAL	1	FALSE	1	0.287206447964844	2		297	339	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0038102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	37	250	3	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	1	2	FACETS	0.976	0.809	1	0.976	0.809	1	CLONAL	1	FALSE	1	0.287206447964844	2		253	264	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993640	90993640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	32	264	0	ENST00000265433.3:c.283del	p.Asp95MetfsTer14	p.D95Mfs*14	ENST00000265433	NM_002485.4	95	Gat/at	3/16	1	2	FACETS	0.609	0.495	0.738	0.609	0.495	0.738	SUBCLONAL	1	FALSE	1	0.287206447964844	2		264	366	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041666	47041666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	100	579	1	ENST00000377604.3:c.1891G>A	p.Ala631Thr	p.A631T	ENST00000377604	NM_001204468.1	631	Gca/Aca	17/24	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.287206447964844	2		580	627	SUCCESS
BTK	695	MSKCC	GRCh37	X	100629549	100629549	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	74	452	1	ENST00000308731.7:c.215del	p.Asn72IlefsTer49	p.N72Ifs*49	ENST00000308731	NM_000061.2	72	aAt/at	3/19	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	FALSE	1	0.287206447964844	2		453	507	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0038120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	296	680	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.539813099652671	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	1	0.539813099652671	3		680	693	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	122	313	2				ENST00000310581	NM_198253.2	-/1132			0.165055969856231	3	FACETS	1	0.945	1			1	INDETERMINATE	1	TRUE	NA	0.539813099652671	3		315	543	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0038120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	373	359	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.539813099652671	3	FACETS	0.942	0.897	0.987	0.942	0.897	0.987	CLONAL	2	TRUE	1	0.539813099652671	3		359	932	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653808	89653808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	36	508	0	ENST00000371953.3:c.106G>A	p.Gly36Arg	p.G36R	ENST00000371953	NM_000314.4	36	Gga/Aga	2/9	0.534670964069416	2	FACETS	0.246	0.201	0.295	0.123	0.1	0.148	SUBCLONAL	1	TRUE	0	0.539813099652671	2		508	543	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981167	201981168	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	292	1002	0	ENST00000359651.3:c.248dup	p.Asn83LysfsTer9	p.N83Kfs*9	ENST00000359651		82	-/A	2/8	0.539813099652671	3	FACETS	1	0.961	1	0.515	0.484	0.547	CLONAL	1	TRUE	1	0.539813099652671	3		1002	1334	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092737	27092738	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	54	566	0	ENST00000324856.7:c.2760dup	p.Gly921ArgfsTer15	p.G921Rfs*15	ENST00000324856	NM_006015.4	920	caa/cAaa	9/20	0.539813099652671	3	FACETS	0.311	0.265	0.362	0.156	0.132	0.181	SUBCLONAL	1	TRUE	1	0.539813099652671	3		566	816	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998727	100998727	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751642083	NA	P-0038120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	50	881	0	ENST00000325455.5:c.1075C>T	p.Pro359Ser	p.P359S	ENST00000325455	NM_001202474.3	359	Ccc/Tcc	1/8	0.539813099652671	2	FACETS	0.208	0.176	0.244	0.104	0.088	0.122	SUBCLONAL	1	TRUE	0	0.539813099652671	2		881	890	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427251	49427271	+	inframe_deletion	In_Frame_Del	DEL	TGCTGCTGCTGCTGTTGCTGC	TGCTGCTGCTGCTGTTGCTGC	-	rs1565778850	NA	P-0038120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	189	759	0	ENST00000301067.7:c.11217_11237del	p.Gln3739_Gln3745del	p.Q3739_Q3745del	ENST00000301067	NM_003482.3	3739	caGCAGCAACAGCAGCAGCAGCAc/cac	39/54	0.539813099652671	3	FACETS	0.784	0.724	0.847	0.392	0.362	0.424	SUBCLONAL	1	TRUE	1	0.539813099652671	3		759	1134	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149452969	149452969	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	53	665	0	ENST00000286301.3:c.977A>G	p.Glu326Gly	p.E326G	ENST00000286301	NM_005211.3	326	gAg/gGg	7/22	0.285145639104442	3	FACETS	0.268	0.228	0.313	0.134	0.114	0.157	INDETERMINATE	1	TRUE	1	0.539813099652671	3		665	930	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941833	44941837	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	novel	NA	P-0038120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	231	222	0	ENST00000377967.4:c.3159_3163del	p.Arg1054SerfsTer3	p.R1054Sfs*3	ENST00000377967	NM_021140.2	1053	AAAAGa/a	21/29	0.523136076270114	2	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.539813099652671	2		222	360	SUCCESS
AR	367	MSKCC	GRCh37	X	66943634	66943634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	101	395	0	ENST00000374690.3:c.2714C>T	p.Pro905Leu	p.P905L	ENST00000374690	NM_000044.3	905	cCc/cTc	8/8	0.523136076270114	2	FACETS	0.592	0.53	0.658			1	SUBCLONAL	1	TRUE	NA	0.539813099652671	2		395	632	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0038121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	125	363	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	0.557426237925072	2	FACETS	0.813	0.752	0.874	0.813	0.752	0.874	CLONAL	2	TRUE	0	0.615086494748115	2		363	250	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141586	202141586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760898260	NA	P-0038121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	53	422	0	ENST00000358485.4:c.874C>T	p.Arg292Trp	p.R292W	ENST00000358485	NM_001080125.1	292	Cgg/Tgg	7/9	1	2	FACETS	0.56	0.48	0.645	0.56	0.48	0.645	SUBCLONAL	1	TRUE	1	0.615086494748115	2		422	308	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826538	50826538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121908388	NA	P-0038121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	57	304	0	ENST00000398568.2:c.2263C>T	p.Arg755Ter	p.R755*	ENST00000398568	NM_001042412.1	755	Cga/Tga	15/18	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.615086494748115	2		304	148	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46270974	46270974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	125	534	0	ENST00000371998.3:c.3098C>T	p.Ser1033Phe	p.S1033F	ENST00000371998		1033	tCc/tTc	17/23	1	2	FACETS	0.932	0.85	1	0.932	0.85	1	CLONAL	1	TRUE	1	0.615086494748115	2		534	436	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483904	88483904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371770675	NA	P-0038121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	124	703	0	ENST00000360948.2:c.1666G>A	p.Glu556Lys	p.E556K	ENST00000360948	NM_001012338.2	556	Gag/Aag	14/19	0.229730944400183	1	FACETS	0.468	0.424	0.513	0.468	0.424	0.513	INDETERMINATE	1	TRUE	0	0.615086494748115	1		703	597	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312779	91312779	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1238410843	NA	P-0038121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	132	516	0	ENST00000355112.3:c.2518G>A	p.Asp840Asn	p.D840N	ENST00000355112	NM_000057.2	840	Gac/Aac	12/22	0.229730944400183	1	FACETS	0.526	0.479	0.575	0.526	0.479	0.575	INDETERMINATE	1	TRUE	0	0.615086494748115	1		516	565	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790845	89790845	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1316435868	NA	P-0038121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	220	609	0	ENST00000336032.3:c.232C>G	p.Leu78Val	p.L78V	ENST00000336032	NM_006813.2	78	Ctg/Gtg	1/2	0.176700944650585	4	FACETS	1	0.991	1	0.707	0.659	0.756	INDETERMINATE	1	TRUE	2	0.615086494748115	4		609	817	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0038122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	298	422	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.837	0.789	0.887	0.837	0.789	0.887	CLONAL	1	TRUE	1	0.665287150595057	2		422	1070	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0038122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	395	759	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.665287150595057	1	FACETS	0.972	0.931	1	0.972	0.931	1	CLONAL	1	TRUE	0	0.665287150595057	1		759	815	SUCCESS
APC	324	MSKCC	GRCh37	5	112170652	112170652	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0038122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	381	337	0	ENST00000257430.4:c.1748C>G	p.Ser583Ter	p.S583*	ENST00000257430	NM_000038.5	583	tCa/tGa	15/16	0.62408918220964	2	FACETS	0.925	0.89	0.96	0.925	0.89	0.96	CLONAL	2	TRUE	0	0.665287150595057	2		337	619	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624294	89624294	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0038122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	277	521	0	ENST00000371953.3:c.68T>G	p.Leu23Ter	p.L23*	ENST00000371953	NM_000314.4	23	tTa/tGa	1/9	0.665287150595057	1	FACETS	0.936	0.887	0.984	0.936	0.887	0.984	CLONAL	1	TRUE	0	0.665287150595057	1		521	594	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937166	39937166	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	382	842	1	ENST00000378444.4:c.17C>T	p.Pro6Leu	p.P6L	ENST00000378444	NM_001123385.1	6	cCc/cTc	2/15	1	2	FACETS	0.937	0.891	0.985	0.937	0.891	0.985	CLONAL	1	TRUE	1	0.665287150595057	2		843	1225	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0038123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	152	340	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.275089094150083	3	FACETS	0.894	0.82	0.972	0.894	0.82	0.972	CLONAL	2	TRUE	1	0.275089094150083	3		340	703	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578419	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587781845	NA	P-0038123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	127	731	3	ENST00000269305.4:c.511G>T	p.Glu171Ter	p.E171*	ENST00000269305	NM_001126112.2	171	Gag/Tag	5/11	0.275089094150083	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.275089094150083	1		734	790	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612878	228612878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	54	633	1	ENST00000366696.1:c.149G>A	p.Arg50His	p.R50H	ENST00000366696	NM_003493.2	50	cGc/cAc	1/1	1	2	FACETS	0.501	0.427	0.582	0.501	0.427	0.582	SUBCLONAL	1	TRUE	1	0.275089094150083	2		634	784	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129246	152129246	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	67	678	1	ENST00000206249.3:c.199G>A	p.Ala67Thr	p.A67T	ENST00000206249	NM_000125.3	67	Gcc/Acc	1/8	1	2	FACETS	0.539	0.467	0.618	0.539	0.467	0.618	SUBCLONAL	1	TRUE	1	0.275089094150083	2		679	903	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8252034	8252034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536636517	NA	P-0038124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	81	701	1	ENST00000335790.3:c.43G>A	p.Val15Ile	p.V15I	ENST00000335790	NM_002315.2	15	Gtc/Atc	2/4	0.329001455180994	1	FACETS	0.824	0.728	0.927	0.824	0.728	0.927	CLONAL	1	TRUE	0	0.329001455180994	1		702	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520008	NA	P-0038124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	270	789	0	ENST00000269305.4:c.613T>C	p.Tyr205His	p.Y205H	ENST00000269305	NM_001126112.2	205	Tat/Cat	6/11	0.0824028804709869	3	FACETS	0.861	0.812	0.911			1	INDETERMINATE	3	TRUE	NA	0.329001455180994	3		789	740	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960042	134960042	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	138	699	0	ENST00000398015.3:c.2399A>C	p.Lys800Thr	p.K800T	ENST00000398015	NM_004441.4	800	aAg/aCg	13/16	1	2	FACETS	0.811	0.742	0.883	1	0.989	1	CLONAL	2	TRUE	1	0.329001455180994	2		699	517	SUCCESS
APC	324	MSKCC	GRCh37	5	112174670	112174670	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	107	419	0	ENST00000257430.4:c.3379C>T	p.Gln1127Ter	p.Q1127*	ENST00000257430	NM_000038.5	1127	Cag/Tag	16/16	0.323798041813868	2	FACETS	0.906	0.821	0.994	0.906	0.821	0.994	CLONAL	2	TRUE	0	0.329001455180994	2		419	359	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134482	41134483	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0038125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	90	630	0	ENST00000379561.5:c.1144_1145dup	p.Ser383HisfsTer6	p.S383Hfs*6	ENST00000379561	NM_002015.3	382	tca/tcTCa	2/3	1	2	FACETS	0.369	0.328	0.413	0.369	0.328	0.413	SUBCLONAL	1	FALSE	1	0.831584828202921	2		630	586	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0038128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	283	767	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.47420523573828	1	FACETS	0.973	0.916	1	0.973	0.916	1	CLONAL	1	TRUE	0	0.47420523573828	1		770	936	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121852	2121870	+	frameshift_variant	Frame_Shift_Del	DEL	CCGGCGCCTGCAGGCCCCG	CCGGCGCCTGCAGGCCCCG	-	novel	NA	P-0038128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	138	644	0	ENST00000219476.3:c.2017_2035del	p.Ala673CysfsTer19	p.A673Cfs*19	ENST00000219476	NM_000548.3	672	CCGGCGCCTGCAGGCCCCGcc/cc	19/42	0.47420523573828	1	FACETS	0.717	0.655	0.783	0.717	0.655	0.783	SUBCLONAL	1	TRUE	0	0.47420523573828	1		644	619	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654857	29654857	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	94	352	0	ENST00000356175.3:c.5546G>T	p.Arg1849Leu	p.R1849L	ENST00000356175	NM_000267.3	1849	cGg/cTg	37/57	0.47420523573828	1	FACETS	0.963	0.867	1	0.963	0.867	1	CLONAL	1	TRUE	0	0.47420523573828	1		352	314	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829066	128829066	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs41304185	NA	P-0038129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	18	13	1	ENST00000249373.3:c.74A>G	p.Asp25Gly	p.D25G	ENST00000249373	NM_005631.4	25	gAc/gGc	1/12	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.738105415415908	2		14	42	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916940	178916948	+	inframe_deletion	In_Frame_Del	DEL	AGAAAAGAT	AGAAAAGAT	-	novel	NA	P-0038129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	1616	869	0	ENST00000263967.3:c.327_335del	p.Glu109_Ile112delinsAsp	p.E109_I112delinsD	ENST00000263967	NM_006218.2	109	gaAGAAAAGATc/gac	2/21	0.738105415415908	8	FACETS	0.942	0.928	0.956			1	CLONAL	7	TRUE	NA	0.738105415415908	8		869	2134	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579702	7579703	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	242	631	0	ENST00000269305.4:c.93_94insA	p.Leu32ThrfsTer11	p.L32Tfs*11	ENST00000269305	NM_001126112.2	31	-/A	3/11	0.738105415415908	1	FACETS	0.829	0.784	0.875	0.829	0.784	0.875	CLONAL	1	TRUE	0	0.738105415415908	1		631	499	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924315	11924315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1355620714	NA	P-0038129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	90	150	0	ENST00000353533.5:c.112C>T	p.Gln38Ter	p.Q38*	ENST00000353533	NM_003010.3	38	Cag/Tag	1/11	0.738105415415908	1	FACETS	0.884	0.808	0.961	0.884	0.808	0.961	CLONAL	1	TRUE	0	0.738105415415908	1		150	174	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021631	31021631	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	364	588	0	ENST00000375687.4:c.1630G>T	p.Asp544Tyr	p.D544Y	ENST00000375687	NM_015338.5	544	Gat/Tat	12/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.738105415415908	2		588	924	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126345	5126345	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	205	286	0	ENST00000381652.3:c.3190A>G	p.Met1064Val	p.M1064V	ENST00000381652	NM_004972.3	1064	Atg/Gtg	24/25	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.824696000241512	2		286	489	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295170	1295170	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0038131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	48	184	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		184	292	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061185	38061185	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1449268552	NA	P-0038132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	33	429	0	ENST00000250448.2:c.804C>A	p.Cys268Ter	p.C268*	ENST00000250448	NM_004496.3	268	tgC/tgA	2/2	1	2	FACETS	0.687	0.558	0.832	0.687	0.558	0.832	SUBCLONAL	1	FALSE	1	0.160766666438938	2		429	598	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	118	313	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.821	0.75	0.893	0.821	0.75	0.893	CLONAL	1	TRUE	1	0.871575865863399	2		315	330	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322591	30322591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	211	428	0	ENST00000322652.5:c.1604G>A	p.Arg535Gln	p.R535Q	ENST00000322652	NM_015355.2	535	cGa/cAa	14/16	1	2	FACETS	0.976	0.916	1	0.976	0.916	1	CLONAL	1	TRUE	1	0.871575865863399	2		428	496	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581268	48581268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752575871	NA	P-0038138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	329	623	0	ENST00000342988.3:c.572C>T	p.Ser191Leu	p.S191L	ENST00000342988	NM_005359.5	191	tCg/tTg	5/12	1	2	FACETS	0.958	0.91	1	0.958	0.91	1	CLONAL	1	TRUE	1	0.871575865863399	2		623	788	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636133	28636133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	326	728	1	ENST00000241453.7:c.239C>T	p.Ala80Val	p.A80V	ENST00000241453	NM_004119.2	80	gCt/gTt	3/24	1	2	FACETS	0.927	0.88	0.974	0.927	0.88	0.974	CLONAL	1	TRUE	1	0.871575865863399	2		729	807	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971128	55971128	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	291	645	0	ENST00000263923.4:c.1669C>A	p.Pro557Thr	p.P557T	ENST00000263923	NM_002253.2	557	Cct/Act	13/30	1	2	FACETS	0.888	0.84	0.937	0.888	0.84	0.937	CLONAL	1	TRUE	1	0.871575865863399	2		645	752	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0038139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	56	369	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.22105806683911	3	FACETS	1	0.961	1	0.654	0.569	0.744	INDETERMINATE	1	TRUE	1	0.558982082527491	3		369	196	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0038139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	122	343	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.22105806683911	3	FACETS	0.751	0.686	0.818	0.751	0.686	0.818	INDETERMINATE	2	TRUE	1	0.558982082527491	3		343	372	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0038139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	127	267	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.20453773647335	4	FACETS	1	0.943	1	1	0.943	1	INDETERMINATE	2	TRUE	2	0.558982082527491	4		267	342	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916957	178916957	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200018596	NA	P-0038139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	57	458	0	ENST00000263967.3:c.344G>T	p.Arg115Leu	p.R115L	ENST00000263967	NM_006218.2	115	cGa/cTa	2/21	0.22105806683911	3	FACETS	1	0.952	1	0.607	0.528	0.691	INDETERMINATE	1	TRUE	1	0.558982082527491	3		458	215	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591126	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAGAAAGAC	GAGAAAGAC	-	novel	NA	P-0038139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	215	394	0	ENST00000274335.5:c.1723_1731del	p.Lys575_Arg577del	p.K575_R577del	ENST00000274335		573	ctGAGAAAGACg/ctg	12/15	0.558982082527491	8	FACETS	0.877	0.821	0.934			1	CLONAL	4	TRUE	NA	0.558982082527491	8		394	587	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386512	81386512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	30	444	0	ENST00000222390.5:c.475G>A	p.Glu159Lys	p.E159K	ENST00000222390	NM_000601.4	159	Gaa/Aaa	4/18	1	2	FACETS	0.725	0.592	0.871	0.725	0.592	0.871	SUBCLONAL	1	TRUE	1	0.558982082527491	2		444	148	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510570	38510570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757750800	NA	P-0038139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	122	628	0	ENST00000254066.5:c.824C>T	p.Thr275Met	p.T275M	ENST00000254066	NM_000964.3	275	aCg/aTg	7/9	0.20453773647335	4	FACETS	0.967	0.884	1	0.967	0.884	1	INDETERMINATE	2	TRUE	2	0.558982082527491	4		628	352	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437603	56437603	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770023953	NA	P-0038139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	145	532	0	ENST00000407977.2:c.859G>A	p.Val287Ile	p.V287I	ENST00000407977		287	Gtc/Atc	8/10	0.20453773647335	4	FACETS	1	0.972	1	1	0.972	1	INDETERMINATE	2	TRUE	2	0.558982082527491	4		532	364	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187315	38187315	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	135	651	0	ENST00000317025.8:c.1162G>C	p.Glu388Gln	p.E388Q	ENST00000317025	NM_023034.1	388	Gaa/Caa	6/24	0.485627584310633	3	FACETS	0.756	0.693	0.82	0.756	0.693	0.82	SUBCLONAL	2	TRUE	1	0.558982082527491	3		651	409	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344104	70344116	+	frameshift_variant	Frame_Shift_Del	DEL	TATACTTGCACTC	TATACTTGCACTC	-	novel	NA	P-0038139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	16	829	0	ENST00000374080.3:c.1841_1853del	p.Tyr614SerfsTer93	p.Y614Sfs*93	ENST00000374080		614	TATACTTGCACTCtc/tc	13/45	0.46071406099608	1	FACETS	0.168	0.124	0.22	0.168	0.124	0.22	SUBCLONAL	1	TRUE	0	0.558982082527491	1		829	246	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344185	70344185	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	16	515	0	ENST00000374080.3:c.1921del	p.Ala641ProfsTer70	p.A641Pfs*70	ENST00000374080		641	Gcc/cc	13/45	0.46071406099608	1	FACETS	0.268	0.199	0.349	0.268	0.199	0.349	SUBCLONAL	1	TRUE	0	0.558982082527491	1		515	154	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981153	201981154	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACCA	novel	NA	P-0038140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	435	778	1	ENST00000359651.3:c.234_237dup	p.Val80ProfsTer13	p.V80Pfs*13	ENST00000359651		78	tac/tACCAac	2/8	0.82037199608376	3	FACETS	0.918	0.874	0.963	0.459	0.437	0.482	CLONAL	1	TRUE	1	0.842806638019248	3		779	1598	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111958634	111958634	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs104894303	NA	P-0038140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	248	402	0	ENST00000375549.3:c.106C>T	p.Gln36Ter	p.Q36*	ENST00000375549	NM_003002.3	36	Cag/Tag	2/4	1	2	FACETS	0.999	0.942	1	0.999	0.942	1	CLONAL	1	TRUE	1	0.842806638019248	2		402	589	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774064	56774064	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	210	513	2	ENST00000337432.4:c.415G>A	p.Ala139Thr	p.A139T	ENST00000337432	NM_058216.2	139	Gca/Aca	3/9	0.82037199608376	3	FACETS	0.926	0.862	0.991	0.463	0.431	0.496	CLONAL	1	TRUE	1	0.842806638019248	3		515	765	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597496	10597497	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TG	TG	-	novel	NA	P-0038140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	344	557	0	ENST00000171111.5:c.1709-3_1709-2del		p.X570_splice	ENST00000171111	NM_203500.1	570			0.842806638019248	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.842806638019248	1		557	457	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069472	30069472	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	416	593	0	ENST00000338641.4:c.1338del	p.Arg447GlyfsTer8	p.R447Gfs*8	ENST00000338641	NM_000268.3	446	aGg/ag	12/16	0.842806638019248	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.842806638019248	1		593	544	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131893037	131893037	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	243	418	0	ENST00000265335.6:c.21G>T	p.Met7Ile	p.M7I	ENST00000265335		7	atG/atT	1/25	1	2	FACETS	0.987	0.93	1	0.987	0.93	1	CLONAL	1	TRUE	1	0.842806638019248	2		418	584	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	312	918	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.427124451876402	5	FACETS	1	0.954	1	1	0.954	1	CLONAL	3	TRUE	2	0.515798704238274	5		919	712	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	585	762	0	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	0.456323503990641	5	FACETS	1	0.993	1	0.865	0.839	0.891	CLONAL	4	TRUE	0	0.515798704238274	5		762	930	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951053	48951053	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	57	276	0	ENST00000267163.4:c.1216-1G>T		p.X406_splice	ENST00000267163	NM_000321.2	406			0.486741359731022	3	FACETS	0.885	0.777	0.998	0.59	0.518	0.665	CLONAL	2	TRUE	0	0.515798704238274	3		276	157	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480538	120480538	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	153	600	0	ENST00000256646.2:c.3279G>T	p.Trp1093Cys	p.W1093C	ENST00000256646	NM_024408.3	1093	tgG/tgT	20/34	0.515798704238274	3	FACETS	1	0.967	1	0.551	0.505	0.599	CLONAL	1	TRUE	1	0.515798704238274	3		600	677	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245873	41245873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	138	644	0	ENST00000357654.3:c.1675G>T	p.Gly559Cys	p.G559C	ENST00000357654	NM_007294.3	559	Ggt/Tgt	10/23	0.427124451876402	5	FACETS	0.861	0.787	0.938	0.574	0.525	0.625	CLONAL	2	TRUE	2	0.515798704238274	5		644	551	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888171	81888171	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	213	628	0	ENST00000359376.3:c.316C>T	p.Leu106Phe	p.L106F	ENST00000359376	NM_002661.3	106	Ctc/Ttc	3/33	0.321521649844161	5	FACETS	0.898	0.836	0.961	0.598	0.557	0.641	CLONAL	2	TRUE	2	0.515798704238274	5		628	816	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324917	31324917	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs776780353	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	82	639	0	ENST00000412585.2:c.19C>T	p.Arg7Ter	p.R7*	ENST00000412585	NM_005514.6	7	Cga/Tga	1/8	0.515798704238274	3	FACETS	0.516	0.454	0.582	0.258	0.227	0.291	SUBCLONAL	1	TRUE	1	0.515798704238274	3		639	775	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226549779	226549779	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	105	508	0	ENST00000366794.5:c.2854G>T	p.Gly952Cys	p.G952C	ENST00000366794	NM_001618.3	952	Ggc/Tgc	22/23	0.492795045580688	5	FACETS	0.885	0.792	0.983	0.221	0.198	0.246	CLONAL	1	TRUE	1	0.515798704238274	5		508	816	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21639413	21639413	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	110	342	0	ENST00000421138.2:c.501G>T	p.Lys167Asn	p.K167N	ENST00000421138		167	aaG/aaT	6/16	0.427124451876402	5	FACETS	1	0.965	1	0.753	0.684	0.824	CLONAL	2	TRUE	2	0.515798704238274	5		342	335	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245527	46245527	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	190	485	0	ENST00000334344.6:c.3621G>C	p.Gln1207His	p.Q1207H	ENST00000334344	NM_152641.2	1207	caG/caC	15/21	0.515798704238274	4	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	2	0.515798704238274	4		485	550	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959024	28959024	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	138	401	2	ENST00000282397.4:c.2114C>T	p.Pro705Leu	p.P705L	ENST00000282397	NM_002019.4	705	cCt/cTt	14/30	0.493353835116924	2	FACETS	0.836	0.773	0.9	0.836	0.773	0.9	CLONAL	2	TRUE	0	0.515798704238274	2		403	320	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423568	88423568	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	251	721	0	ENST00000360948.2:c.2267T>A	p.Phe756Tyr	p.F756Y	ENST00000360948	NM_001012338.2	756	tTc/tAc	18/19	0.514770368928764	2	FACETS	0.913	0.863	0.963	0.913	0.863	0.963	CLONAL	2	TRUE	0	0.515798704238274	2		721	533	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78923341	78923341	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	212	519	0	ENST00000306801.3:c.3364A>T	p.Thr1122Ser	p.T1122S	ENST00000306801	NM_020761.2	1122	Acg/Tcg	28/34	0.427124451876402	5	FACETS	1	0.984	1	0.779	0.728	0.831	CLONAL	2	TRUE	2	0.515798704238274	5		519	624	SUCCESS
YES1	7525	MSKCC	GRCh37	18	739760	739760	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	210	634	0	ENST00000314574.4:c.1112C>A	p.Pro371Gln	p.P371Q	ENST00000314574	NM_005433.3	371	cCa/cAa	9/12	0.103529218371514	1	FACETS	1	0.985	1	1	0.985	1	INDETERMINATE	1	TRUE	0	0.515798704238274	1		634	516	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101142	4101142	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	68	727	0	ENST00000262948.5:c.581-1G>C		p.X194_splice	ENST00000262948	NM_030662.3	194			0.514770368928764	2	FACETS	0.426	0.37	0.486	0.213	0.185	0.243	SUBCLONAL	1	TRUE	0	0.515798704238274	2		727	619	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798089	42798089	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	249	741	0	ENST00000575354.2:c.4043G>C	p.Arg1348Thr	p.R1348T	ENST00000575354	NM_015125.3	1348	aGg/aCg	17/20	0.515798704238274	3	FACETS	0.921	0.867	0.977	0.921	0.867	0.977	CLONAL	2	TRUE	1	0.515798704238274	3		741	659	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860551	45860551	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	199	725	0	ENST00000391945.4:c.1456G>T	p.Ala486Ser	p.A486S	ENST00000391945	NM_000400.3	486	Gca/Tca	15/23	0.515798704238274	3	FACETS	1	0.945	1	0.511	0.474	0.551	CLONAL	1	TRUE	1	0.515798704238274	3		725	949	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659953	227659953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	359	785	0	ENST00000305123.5:c.3502G>A	p.Gly1168Arg	p.G1168R	ENST00000305123	NM_005544.2	1168	Ggg/Agg	1/2	0.413017260068634	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.515798704238274	4		785	989	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663018	227663018	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	314	708	2	ENST00000305123.5:c.437G>T	p.Gly146Val	p.G146V	ENST00000305123	NM_005544.2	146	gGg/gTg	1/2	0.413017260068634	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.515798704238274	4		710	830	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561004	9561004	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	243	511	0	ENST00000353224.5:c.778A>T	p.Ser260Cys	p.S260C	ENST00000353224	NM_177990.2	260	Agc/Tgc	4/10	0.321521649844161	5	FACETS	0.845	0.795	0.897	0.845	0.795	0.897	CLONAL	3	TRUE	2	0.515798704238274	5		511	659	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130427	29130427	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587781269	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	160	649	0	ENST00000328354.6:c.283C>G	p.Arg95Gly	p.R95G	ENST00000328354	NM_007194.3	95	Cga/Gga	2/15	0.515798704238274	3	FACETS	0.977	0.897	1	0.488	0.448	0.53	CLONAL	1	TRUE	1	0.515798704238274	3		649	799	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390992	89390992	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	198	627	0	ENST00000336596.2:c.1058G>T	p.Gly353Val	p.G353V	ENST00000336596	NM_005233.5	353	gGc/gTc	5/17	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.515798704238274	2		627	562	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119585459	119585459	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	169	440	0	ENST00000316626.5:c.926G>A	p.Gly309Glu	p.G309E	ENST00000316626		309	gGa/gAa	9/12	0.266910548954006	4	FACETS	0.905	0.844	0.965	0.678	0.633	0.724	INDETERMINATE	3	TRUE	0	0.515798704238274	4		440	366	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1941462	1941462	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	65	619	0	ENST00000382891.5:c.1838T>C	p.Phe613Ser	p.F613S	ENST00000382891	NM_133335.3	613	tTt/tCt	9/22	0.321521649844161	5	FACETS	0.461	0.398	0.529	0.154	0.132	0.177	SUBCLONAL	1	TRUE	2	0.515798704238274	5		619	970	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356349	66356349	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	188	576	0	ENST00000273854.3:c.1148C>G	p.Thr383Ser	p.T383S	ENST00000273854	NM_004439.5	383	aCt/aGt	5/18	0.321521649844161	5	FACETS	1	0.932	1	0.669	0.621	0.719	CLONAL	2	TRUE	2	0.515798704238274	5		576	644	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84406222	84406222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	88	314	0	ENST00000321945.7:c.4G>A	p.Glu2Lys	p.E2K	ENST00000321945	NM_139076.2	2	Gag/Aag	1/9	0.321521649844161	5	FACETS	1	0.905	1	0.341	0.302	0.382	CLONAL	1	TRUE	2	0.515798704238274	5		314	592	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159146	143159146	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	55	371	0	ENST00000262992.4:c.707G>C	p.Cys236Ser	p.C236S	ENST00000262992	NM_001101669.1	236	tGt/tCt	10/24	0.515798704238274	3	FACETS	1	0.945	1	0.593	0.514	0.678	CLONAL	1	TRUE	1	0.515798704238274	3		371	226	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170827906	170827907	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAT	novel	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	121	587	0	ENST00000296930.5:c.652_654dup	p.Ser218dup	p.S218dup	ENST00000296930	NM_002520.6	218	cca/cCATca	8/11	0.515798704238274	6	FACETS	0.976	0.88	1	0.244	0.22	0.27	CLONAL	1	TRUE	2	0.515798704238274	6		587	977	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30668411	30668411	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	141	555	0	ENST00000376406.3:c.6103-2A>T		p.X2035_splice	ENST00000376406	NM_014641.2	2035			0.515798704238274	3	FACETS	1	0.917	1	0.502	0.458	0.548	CLONAL	1	TRUE	1	0.515798704238274	3		555	685	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206824	162206824	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	205	582	0	ENST00000366898.1:c.851G>T	p.Gly284Val	p.G284V	ENST00000366898	NM_004562.2	284	gGc/gTc	7/12	0.506309626262525	3	FACETS	0.886	0.828	0.946	0.886	0.828	0.946	CLONAL	2	TRUE	1	0.515798704238274	3		582	564	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358929	81358929	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	278	552	0	ENST00000222390.5:c.1032C>A	p.Phe344Leu	p.F344L	ENST00000222390	NM_000601.4	344	ttC/ttA	8/18	0.515798704238274	5	FACETS	0.993	0.94	1	0.993	0.94	1	CLONAL	3	TRUE	2	0.515798704238274	5		552	642	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374356	81374356	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	160	465	2	ENST00000222390.5:c.706G>T	p.Asp236Tyr	p.D236Y	ENST00000222390	NM_000601.4	236	Gat/Tat	6/18	0.515798704238274	5	FACETS	0.85	0.782	0.921	0.567	0.521	0.614	CLONAL	2	TRUE	2	0.515798704238274	5		467	647	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521421	8521421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769639520	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	57	772	0	ENST00000356435.5:c.817G>A	p.Ala273Thr	p.A273T	ENST00000356435		273	Gca/Aca	9/35	0.497542081395061	2	FACETS	0.36	0.308	0.416	0.18	0.154	0.208	SUBCLONAL	1	TRUE	0	0.515798704238274	2		772	614	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342670	87342670	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	253	711	2	ENST00000277120.3:c.955T>C	p.Tyr319His	p.Y319H	ENST00000277120		319	Tat/Cat	9/19	0.506309626262525	3	FACETS	0.925	0.871	0.98	0.925	0.871	0.98	CLONAL	2	TRUE	1	0.515798704238274	3		713	667	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239956	98239956	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	248	573	0	ENST00000331920.6:c.1376G>T	p.Arg459Leu	p.R459L	ENST00000331920	NM_000264.3	459	cGc/cTc	10/24	0.506309626262525	3	FACETS	0.971	0.914	1	0.971	0.914	1	CLONAL	2	TRUE	1	0.515798704238274	3		573	623	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918903	76918903	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	177	701	0	ENST00000373344.5:c.4088A>T	p.His1363Leu	p.H1363L	ENST00000373344	NM_000489.3	1363	cAt/cTt	12/35	0.515798704238274	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.515798704238274	1		701	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0038145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	74	722	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	1	2	FACETS	0.532	0.464	0.605	0.532	0.464	0.605	SUBCLONAL	1	TRUE	1	0.263843582590787	2		722	1055	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445068	49445068	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	54	645	0	ENST00000301067.7:c.2398C>T	p.Gln800Ter	p.Q800*	ENST00000301067	NM_003482.3	800	Cag/Tag	10/54	1	2	FACETS	0.562	0.479	0.654	0.562	0.479	0.654	SUBCLONAL	1	TRUE	1	0.263843582590787	2		645	728	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115960	8115960	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	49	389	0	ENST00000346208.3:c.1306del	p.Ser436ProfsTer39	p.S436Pfs*39	ENST00000346208		436	Tcc/cc	6/6	1	2	FACETS	0.705	0.597	0.824	0.705	0.597	0.824	SUBCLONAL	1	TRUE	1	0.263843582590787	2		389	527	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770029	56770029	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	58	598	2	ENST00000337432.4:c.25G>T	p.Glu9Ter	p.E9*	ENST00000337432	NM_058216.2	9	Gaa/Taa	1/9	1	2	FACETS	0.635	0.545	0.734	0.635	0.545	0.734	SUBCLONAL	1	TRUE	1	0.263843582590787	2		600	692	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912194	127912194	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	45	310	0	ENST00000373547.4:c.676C>G	p.His226Asp	p.H226D	ENST00000373547	NM_002721.4	226	Cat/Gat	7/7	1	2	FACETS	0.872	0.735	1	0.872	0.735	1	CLONAL	1	TRUE	1	0.263843582590787	2		310	391	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801050	135801050	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	94	627	0	ENST00000298552.3:c.287T>A	p.Val96Asp	p.V96D	ENST00000298552	NM_001162426.1	96	gTc/gAc	5/23	1	2	FACETS	0.84	0.747	0.94	0.84	0.747	0.94	CLONAL	1	TRUE	1	0.263843582590787	2		627	848	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341249	70341249	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	62	589	1	ENST00000374080.3:c.808G>A	p.Asp270Asn	p.D270N	ENST00000374080		270	Gat/Aat	6/45	1	2	FACETS	0.602	0.519	0.692	0.602	0.519	0.692	SUBCLONAL	1	TRUE	1	0.263843582590787	2		590	781	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576858	7576858	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	404	664	0	ENST00000269305.4:c.988del	p.Leu330PhefsTer15	p.L330Ffs*15	ENST00000269305	NM_001126112.2	330	Ctt/tt	9/11	0.117106637839429	6	FACETS	1	0.982	1			1	INDETERMINATE	3	TRUE	NA	0.43741251976505	6		664	1089	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405218	70405218	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0038147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	60	604	0	ENST00000373644.4:c.2732C>G	p.Ser911Ter	p.S911*	ENST00000373644	NM_030625.2	911	tCa/tGa	4/12	0.175212519889527	3	FACETS	0.355	0.305	0.41	0.177	0.152	0.205	INDETERMINATE	1	TRUE	1	0.43741251976505	3		604	942	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636509	21636509	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs773801667	NA	P-0038147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	69	367	1	ENST00000421138.2:c.502-1G>C		p.X168_splice	ENST00000421138		168			1	2	FACETS	0.509	0.443	0.58	0.509	0.443	0.58	SUBCLONAL	1	TRUE	1	0.43741251976505	2		368	620	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074251	30074254	+	frameshift_variant	Frame_Shift_Del	DEL	CTGT	CTGT	-	novel	NA	P-0038147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	208	589	0	ENST00000338641.4:c.1515_1518del	p.Phe507ThrfsTer7	p.F507Tfs*7	ENST00000338641	NM_000268.3	505	CTGTct/ct	14/16	0.414930839401846	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.43741251976505	1		589	685	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888189	112888189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507511	NA	P-0121568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	241	740	0	ENST00000351677.2:c.205G>A	p.Glu69Lys	p.E69K	ENST00000351677	NM_002834.3	69	Gag/Aag	3/16	1	2	FACETS	0.498	0.464	0.532	0.498	0.464	0.532	SUBCLONAL	1	NA	1	0.879557952083302	2		740	1101	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884191	37884191	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs568793816	NA	P-0121568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	274	792	0	ENST00000269571.5:c.3662A>G	p.Tyr1221Cys	p.Y1221C	ENST00000269571		1221	tAt/tGt	27/27	1	2	FACETS	0.545	0.511	0.579	0.545	0.511	0.579	SUBCLONAL	1	NA	1	0.879557952083302	2		792	1144	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196750	106196751	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTTATGGAAACCAAAATATGCAGGGAGATGGTTTCAGCA	novel	NA	P-0121568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	58	627	0	ENST00000380013.4:c.5087_5125dup	p.Tyr1696_Ser1708dup	p.Y1696_S1708dup	ENST00000380013	NM_001127208.2	1696	ggt/gGTTATGGAAACCAAAATATGCAGGGAGATGGTTTCAGCAgt	11/11	0.466654244817887	1	FACETS	0.103	0.088	0.12	0.103	0.088	0.12	INDETERMINATE	1	NA	0	0.879557952083302	1		627	717	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048553	180048553	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0121568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	230	767	1	ENST00000261937.6:c.2009T>A	p.Leu670Gln	p.L670Q	ENST00000261937	NM_182925.4	670	cTg/cAg	13/30	NA	2	FACETS	0.538	0.502	0.576			1	INDETERMINATE	1	NA	NA	0.879557952083302	2		768	972	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0038149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	135	482	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		482	563	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560937	9560937	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs372728080	NA	P-0038149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	147	541	0	ENST00000353224.5:c.845T>C	p.Met282Thr	p.M282T	ENST00000353224	NM_177990.2	282	aTg/aCg	4/10	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		541	661	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396359	139396359	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	94	793	1	ENST00000277541.6:c.5479G>T	p.Glu1827Ter	p.E1827*	ENST00000277541	NM_017617.3	1827	Gag/Tag	30/34	1	2	FACETS	0.886	0.786	0.993	0.886	0.786	0.993	CLONAL	1	TRUE	1	0.2	2		794	1061	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0038151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	174	918	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.363461198657731	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.363461198657731	1		919	705	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0038151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	79	314	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	1	2	FACETS	0.866	0.764	0.975	0.866	0.764	0.975	CLONAL	1	TRUE	1	0.363461198657731	2		314	502	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161949	47161949	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1469670151	NA	P-0038151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	161	456	0	ENST00000409792.3:c.4177T>G	p.Leu1393Val	p.L1393V	ENST00000409792	NM_014159.6	1393	Tta/Gta	3/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.363461198657731	2		456	732	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747945	41747945	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	99	196	0	ENST00000226382.2:c.824C>A	p.Pro275His	p.P275H	ENST00000226382	NM_003924.3	275	cCc/cAc	3/3	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.363461198657731	2		196	467	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345907	70345907	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762905361	NA	P-0038151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	150	476	0	ENST00000374080.3:c.2444G>A	p.Arg815Gln	p.R815Q	ENST00000374080		815	cGg/cAg	18/45	0.363461198657731	3	FACETS	1	0.927	1	0.509	0.464	0.555	CLONAL	1	TRUE	1	0.363461198657731	3		476	959	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281768	49281768	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	103	921	0	ENST00000282018.3:c.815C>A	p.Thr272Lys	p.T272K	ENST00000282018	NM_020377.2	272	aCg/aAg	1/1	0.190201345218402	0	FACETS	0.348	0.31	0.388			1	INDETERMINATE	1	TRUE	0	0.363461198657731	0		921	1038	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578195	7578199	+	frameshift_variant	Frame_Shift_Del	DEL	CACCA	CACCA	-	novel	NA	P-0038151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	175	777	0	ENST00000269305.4:c.650_654del	p.Val217AlafsTer3	p.V217Afs*3	ENST00000269305	NM_001126112.2	217	gTGGTG/g	6/11	0.363461198657731	1	FACETS	0.811	0.747	0.879	0.811	0.747	0.879	CLONAL	1	TRUE	0	0.363461198657731	1		777	971	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16005051	16005051	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752014552	NA	P-0038151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	165	705	0	ENST00000268712.3:c.2203G>A	p.Glu735Lys	p.E735K	ENST00000268712	NM_006311.3	735	Gag/Aag	20/46	1	2	FACETS	0.871	0.798	0.946	0.871	0.798	0.946	CLONAL	1	TRUE	1	0.363461198657731	2		705	1043	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190742126	190742126	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	103	454	0	ENST00000441310.2:c.2763T>G	p.Phe921Leu	p.F921L	ENST00000441310	NM_000534.4	921	ttT/ttG	13/13	1	2	FACETS	0.803	0.719	0.892	0.803	0.719	0.892	CLONAL	1	TRUE	1	0.363461198657731	2		454	706	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965644	93965644	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	137	578	0	ENST00000369303.4:c.2284C>G	p.Arg762Gly	p.R762G	ENST00000369303	NM_004440.3	762	Cgc/Ggc	13/17	0.363461198657731	1	FACETS	0.932	0.85	1	0.932	0.85	1	CLONAL	1	TRUE	0	0.363461198657731	1		578	662	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69011960	69011960	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1242	108	735	0	ENST00000288368.4:c.2597A>G	p.Asn866Ser	p.N866S	ENST00000288368	NM_024870.2	866	aAc/aGc	23/40	0.332690357561549	3	FACETS	0.52	0.465	0.579	0.26	0.232	0.29	SUBCLONAL	1	TRUE	1	0.363461198657731	3		735	1350	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197014	123197014	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	98	454	0	ENST00000218089.9:c.1780T>A	p.Tyr594Asn	p.Y594N	ENST00000218089	NM_001042749.1	594	Tac/Aac	19/35	0.363461198657731	3	FACETS	0.785	0.7	0.876	0.392	0.35	0.438	SUBCLONAL	1	TRUE	1	0.363461198657731	3		454	812	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	153	313	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.928	0.852	1	0.928	0.852	1	CLONAL	1	TRUE	1	0.532841168942517	2		315	619	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720857	89720857	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	184	408	0	ENST00000371953.3:c.1008C>A	p.Tyr336Ter	p.Y336*	ENST00000371953	NM_000314.4	336	taC/taA	8/9	0.532841168942517	1	FACETS	0.988	0.919	1	0.988	0.919	1	CLONAL	1	TRUE	0	0.532841168942517	1		408	513	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936064	178936064	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	122	405	0	ENST00000263967.3:c.1606A>G	p.Thr536Ala	p.T536A	ENST00000263967	NM_006218.2	536	Aca/Gca	10/21	1	2	FACETS	0.91	0.827	0.997	0.91	0.827	0.997	CLONAL	1	TRUE	1	0.532841168942517	2		405	503	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0038153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	216	744	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	0.39879083310919	4	FACETS	0.885	0.828	0.941	0.885	0.828	0.941	INDETERMINATE	2	TRUE	2	0.733797436431735	4		744	577	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056053	26056067	+	inframe_deletion	In_Frame_Del	DEL	CCTTGGGCTTAGCGG	CCTTGGGCTTAGCGG	-	rs756916945	NA	P-0038153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	67	486	0	ENST00000343677.2:c.590_604del	p.Ala197_Lys201del	p.A197_K201del	ENST00000343677	NM_005319.3	197	gCCGCTAAGCCCAAGGtt/gtt	1/1	0.444838808037893	3	FACETS	0.626	0.546	0.711	0.313	0.273	0.356	SUBCLONAL	1	TRUE	1	0.733797436431735	3		486	399	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770139	56770139	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs371608994	NA	P-0038153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	214	640	0	ENST00000337432.4:c.135G>C	p.Glu45Asp	p.E45D	ENST00000337432	NM_058216.2	45	gaG/gaC	1/9	1	2	FACETS	0.932	0.871	0.994	0.932	0.871	0.994	CLONAL	1	TRUE	1	0.733797436431735	2		640	626	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285779	198285779	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	29	532	0	ENST00000335508.6:c.274A>C	p.Asn92His	p.N92H	ENST00000335508	NM_012433.2	92	Aat/Cat	3/25	0.212698517000913	4	FACETS	0.523	0.421	0.638	0.262	0.21	0.319	INDETERMINATE	1	TRUE	2	0.733797436431735	4		532	262	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437846	52437846	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1559587112	NA	P-0038153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	294	945	0	ENST00000460680.1:c.1315G>T	p.Val439Leu	p.V439L	ENST00000460680	NM_004656.3	439	Gtg/Ttg	13/17	0.722253040682407	1	FACETS	0.981	0.936	1	0.981	0.936	1	CLONAL	1	TRUE	0	0.733797436431735	1		945	517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574030	7574030	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	337	634	0	ENST00000269305.4:c.997del	p.Arg333ValfsTer12	p.R333Vfs*12	ENST00000269305	NM_001126112.2	333	Cgt/gt	10/11	0.684109388064889	2	FACETS	0.949	0.912	0.984	0.949	0.912	0.984	CLONAL	2	TRUE	0	0.699289310533674	2		634	508	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839802	27839802	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	39	627	0	ENST00000328488.2:c.292G>C	p.Glu98Gln	p.E98Q	ENST00000328488	NM_003533.2	98	Gag/Cag	1/1	0.699289310533674	5	FACETS	0.295	0.243	0.353	0.074	0.06	0.089	SUBCLONAL	1	TRUE	1	0.699289310533674	5		627	775	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684380	29684415	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTGTTGTGTAAGTATCTCCTTTTGATTTTAATTCA	CCTGTTGTGTAAGTATCTCCTTTTGATTTTAATTCA	-	novel	NA	P-0038154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	159	470	0	ENST00000356175.3:c.7903_7907+31del		p.X2635_splice	ENST00000356175	NM_000267.3	2635		53/57	0.684109388064889	2	FACETS	0.815	0.764	0.865	0.815	0.764	0.865	CLONAL	2	TRUE	0	0.699289310533674	2		470	279	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202785	128202785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866549293	NA	P-0038154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	398	748	0	ENST00000341105.2:c.935G>A	p.Gly312Asp	p.G312D	ENST00000341105	NM_032638.4	312	gGc/gAc	4/6	0.643870740518849	6	FACETS	1	0.986	1	0.545	0.518	0.572	CLONAL	2	TRUE	2	0.699289310533674	6		748	1252	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984821	55984821	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	299	647	0	ENST00000263923.4:c.308G>T	p.Cys103Phe	p.C103F	ENST00000263923	NM_002253.2	103	tGc/tTc	3/30	0.305762957157421	5	FACETS	1	0.979	1	0.712	0.673	0.752	INDETERMINATE	2	TRUE	2	0.699289310533674	5		647	820	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163739	32163739	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs768765460	NA	P-0038154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	243	693	0	ENST00000375023.3:c.5487C>A	p.His1829Gln	p.H1829Q	ENST00000375023	NM_004557.3	1829	caC/caA	30/30	0.699289310533674	6	FACETS	1	0.986	1	0.468	0.439	0.497	CLONAL	2	TRUE	1	0.699289310533674	6		693	713	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0038156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	721	701	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.549174167026214	4	FACETS	0.941	0.912	0.969			1	CLONAL	3	TRUE	NA	0.616897177290213	4		701	1339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	377	944	0	ENST00000269305.4:c.853G>T	p.Glu285Ter	p.E285*	ENST00000269305	NM_001126112.2	285	Gag/Tag	8/11	0.609380269539769	1	FACETS	0.991	0.946	1	0.991	0.946	1	CLONAL	1	TRUE	0	0.616897177290213	1		944	853	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551898	150551898	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	183	551	0	ENST00000369026.2:c.109G>C	p.Ala37Pro	p.A37P	ENST00000369026	NM_021960.4	37	Gct/Cct	1/3	0.578221286404792	4	FACETS	0.865	0.797	0.936	0.288	0.265	0.312	CLONAL	1	TRUE	1	0.616897177290213	4		551	1109	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512090	148512090	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	236	621	0	ENST00000320356.2:c.1588C>T	p.His530Tyr	p.H530Y	ENST00000320356	NM_004456.4	530	Cat/Tat	14/20	0.616897177290213	3	FACETS	0.965	0.901	1	0.483	0.45	0.516	CLONAL	1	TRUE	1	0.616897177290213	3		621	1037	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538766	23538766	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	214	506	0	ENST00000380871.4:c.673T>C	p.Cys225Arg	p.C225R	ENST00000380871	NM_006167.3	225	Tgc/Cgc	2/2	0.616897177290213	1	FACETS	0.981	0.922	1	0.981	0.922	1	CLONAL	1	TRUE	0	0.616897177290213	1		506	489	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845580	151845580	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1287135873	NA	P-0038157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	82	834	1	ENST00000262189.6:c.13432C>T	p.Arg4478Ter	p.R4478*	ENST00000262189	NM_170606.2	4478	Cga/Tga	52/59	0.286176312811053	4	FACETS	1	0.976	1	0.706	0.628	0.788	INDETERMINATE	1	FALSE	2	0.526231606371324	4		835	337	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844215	68844216	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0038157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	133	815	0	ENST00000261769.5:c.807dup	p.Ser270ValfsTer23	p.S270Vfs*23	ENST00000261769	NM_004360.3	268	aag/aaGg	6/16	0.311266407269265	1	FACETS	1	0.987	1	1	0.987	1	INDETERMINATE	1	FALSE	0	0.526231606371324	1		815	275	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028689	12028689	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0038157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	45	492	0	ENST00000353533.5:c.891+1G>C		p.X297_splice	ENST00000353533	NM_003010.3	297			0.52961021490614	1	FACETS	0.768	0.657	0.887	0.768	0.657	0.887	SUBCLONAL	1	FALSE	0	0.526231606371324	1		492	164	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	186	313	2				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		315	1224	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	123	482	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.981	0.891	1	0.981	0.891	1	CLONAL	1	TRUE	1	0.47320191049849	2		482	530	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	147	701	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.47320191049849	2		701	592	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	96	612	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.782	0.699	0.869	0.782	0.699	0.869	SUBCLONAL	1	TRUE	1	0.47320191049849	2		612	519	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	94	300	1	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	1	2	FACETS	0.854	0.764	0.95	0.854	0.764	0.95	CLONAL	1	TRUE	1	0.47320191049849	2		301	465	SUCCESS
APC	324	MSKCC	GRCh37	5	112175970	112175970	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1114167552	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	58	230	0	ENST00000257430.4:c.4682del	p.Lys1561ArgfsTer4	p.K1561Rfs*4	ENST00000257430	NM_000038.5	1560	gAa/ga	16/16	1	2	FACETS	0.704	0.608	0.808	0.704	0.608	0.808	SUBCLONAL	1	TRUE	1	0.47320191049849	2		230	348	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	128	499	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.951	0.865	1	0.951	0.865	1	CLONAL	1	TRUE	1	0.47320191049849	2		499	569	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438316	110438317	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	rs532810290	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	36	110	0	ENST00000375856.3:c.82_84dup	p.Asn28dup	p.N28dup	ENST00000375856	NM_003749.2	28	-/AAC	1/2	1	2	FACETS	0.566	0.467	0.675	0.566	0.467	0.675	SUBCLONAL	1	TRUE	1	0.47320191049849	2		110	269	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238958	5238958	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	99	396	0	ENST00000357368.4:c.1821del	p.Val608TrpfsTer30	p.V608Wfs*30	ENST00000357368	NM_002850.3	607	ccC/cc	13/38	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.47320191049849	2		396	417	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	205	611	2	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.47320191049849	2		613	814	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885956	59885956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28997569	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	160	401	0	ENST00000259008.2:c.790C>T	p.Arg264Trp	p.R264W	ENST00000259008	NM_032043.2	264	Cgg/Tgg	7/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.47320191049849	2		401	663	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	83	980	5	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	0.504	0.445	0.568	0.504	0.445	0.568	SUBCLONAL	1	TRUE	1	0.47320191049849	2		985	696	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245587	41245587	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357522	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	178	789	3	ENST00000357654.3:c.1961del	p.Lys654SerfsTer47	p.K654Sfs*47	ENST00000357654	NM_007294.3	654	aAg/ag	10/23	1	2	FACETS	0.931	0.859	1	0.931	0.859	1	CLONAL	1	TRUE	1	0.47320191049849	2		792	808	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	80	520	4	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.713	0.63	0.802	0.713	0.63	0.802	SUBCLONAL	1	TRUE	1	0.47320191049849	2		524	474	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	138	688	6	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	0.47320191049849	2		694	553	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149917	202149917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	145	522	1	ENST00000358485.4:c.1358C>T	p.Pro453Leu	p.P453L	ENST00000358485	NM_001080125.1	453	cCg/cTg	8/9	1	2	FACETS	0.868	0.794	0.946	0.868	0.794	0.946	CLONAL	1	TRUE	1	0.47320191049849	2		523	706	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375459	40375459	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	52	482	0	ENST00000293328.3:c.491del	p.Lys164SerfsTer17	p.K164Sfs*17	ENST00000293328	NM_012448.3	164	aAg/ag	5/19	1	2	FACETS	0.29	0.246	0.338	0.29	0.246	0.338	SUBCLONAL	1	TRUE	1	0.47320191049849	2		482	759	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905055	50905055	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	111	412	0	ENST00000440232.2:c.342del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	113	Ggg/gg	4/27	1	2	FACETS	0.961	0.869	1	0.961	0.869	1	CLONAL	1	TRUE	1	0.47320191049849	2		412	488	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117854	70117854	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	53	424	0	ENST00000245479.2:c.322C>T	p.Pro108Ser	p.P108S	ENST00000245479	NM_000346.3	108	Ccc/Tcc	1/3	1	2	FACETS	0.446	0.381	0.518	0.446	0.381	0.518	SUBCLONAL	1	TRUE	1	0.47320191049849	2		424	502	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220098	133220099	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	rs758487568	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	155	548	2	ENST00000320574.5:c.4337_4338dup	p.Val1447TrpfsTer7	p.V1447Wfs*7	ENST00000320574	NM_006231.2	1446	-/TG	34/49	1	2	FACETS	0.836	0.766	0.908	0.836	0.766	0.908	CLONAL	1	TRUE	1	0.47320191049849	2		550	784	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799131	42799131	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	157	823	0	ENST00000575354.2:c.4620del	p.Thr1541LeufsTer79	p.T1541Lfs*79	ENST00000575354	NM_015125.3	1539	Ccc/cc	20/20	1	2	FACETS	0.943	0.866	1	0.943	0.866	1	CLONAL	1	TRUE	1	0.47320191049849	2		823	704	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821620	72821620	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751386892	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	20	50	0	ENST00000268489.5:c.10555G>A	p.Gly3519Ser	p.G3519S	ENST00000268489	NM_006885.3	3519	Ggt/Agt	10/10	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.47320191049849	2		50	58	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269072	142269072	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	148	305	0	ENST00000350721.4:c.2878C>T	p.Arg960Ter	p.R960*	ENST00000350721	NM_001184.3	960	Cga/Tga	14/47	1	2	FACETS	0.959	0.879	1	0.959	0.879	1	CLONAL	1	TRUE	1	0.47320191049849	2		305	652	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324892	31324892	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs765875917	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	82	160	0	ENST00000412585.2:c.44del	p.Ala15GlyfsTer5	p.A15Gfs*5	ENST00000412585	NM_005514.6	15	gCg/gg	1/8	1	2	FACETS	0.784	0.704	0.866	1	0.982	1	SUBCLONAL	2	TRUE	1	0.47320191049849	2		160	221	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	187	655	5	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	1	2	FACETS	0.862	0.796	0.93	0.862	0.796	0.93	CLONAL	1	TRUE	1	0.47320191049849	2		660	917	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	152	400	10	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.846	0.775	0.921	0.846	0.775	0.921	CLONAL	1	TRUE	1	0.47320191049849	2		410	759	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	171	616	0	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.95	0.875	1	0.95	0.875	1	CLONAL	1	TRUE	1	0.47320191049849	2		616	761	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120148	70120148	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	61	221	0	ENST00000245479.2:c.1150A>G	p.Thr384Ala	p.T384A	ENST00000245479	NM_000346.3	384	Acg/Gcg	3/3	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.47320191049849	2		221	241	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733223	74733223	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	127	439	0	ENST00000359995.5:c.20del	p.Pro7LeufsTer7	p.P7Lfs*7	ENST00000359995	NM_001195427.1	7	cCt/ct	1/3	1	2	FACETS	0.981	0.893	1	0.981	0.893	1	CLONAL	1	TRUE	1	0.47320191049849	2		439	547	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998128	169998128	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs753143066	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	174	574	4	ENST00000295797.4:c.826del	p.Thr276GlnfsTer7	p.T276Qfs*7	ENST00000295797	NM_002740.5	273	ttA/tt	9/18	1	2	FACETS	0.792	0.729	0.857	0.792	0.729	0.857	SUBCLONAL	1	TRUE	1	0.47320191049849	2		578	929	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569955	95569955	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763425076	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	91	329	0	ENST00000393063.1:c.3778G>A	p.Val1260Ile	p.V1260I	ENST00000393063	NM_030621.3	1260	Gta/Ata	22/28	1	2	FACETS	0.811	0.723	0.904	0.811	0.723	0.904	CLONAL	1	TRUE	1	0.47320191049849	2		329	474	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425124	49425124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372839823	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	221	602	0	ENST00000301067.7:c.13364G>A	p.Arg4455His	p.R4455H	ENST00000301067	NM_003482.3	4455	cGc/cAc	39/54	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.47320191049849	2		602	842	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39726940	39726940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757344214	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	83	202	0	ENST00000361337.2:c.938C>T	p.Thr313Met	p.T313M	ENST00000361337	NM_003286.2	313	aCg/aTg	11/21	1	2	FACETS	0.953	0.847	1	0.953	0.847	1	CLONAL	1	TRUE	1	0.47320191049849	2		202	368	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133756012	133756012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs574660646	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	144	409	1	ENST00000318560.5:c.1639G>A	p.Val547Met	p.V547M	ENST00000318560	NM_005157.4	547	Gtg/Atg	10/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.47320191049849	2		410	576	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84393376	84393376	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	91	242	0	ENST00000321945.7:c.281del	p.Lys94ArgfsTer4	p.K94Rfs*4	ENST00000321945	NM_139076.2	94	aAg/ag	4/9	1	2	FACETS	0.81	0.722	0.903	0.81	0.722	0.903	CLONAL	1	TRUE	1	0.47320191049849	2		242	475	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863053	56863054	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	88	421	0	ENST00000519728.1:c.327dup	p.Glu110ArgfsTer40	p.E110Rfs*40	ENST00000519728	NM_002350.3	107	aca/acAa	5/13	1	2	FACETS	0.518	0.459	0.581	0.518	0.459	0.581	SUBCLONAL	1	TRUE	1	0.47320191049849	2		421	718	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953633	32953633	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359732	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	99	337	0	ENST00000380152.3:c.8940del	p.Glu2981LysfsTer7	p.E2981Kfs*7	ENST00000380152		2978	tcA/tc	22/27	1	2	FACETS	0.829	0.743	0.919	0.829	0.743	0.919	CLONAL	1	TRUE	1	0.47320191049849	2		337	505	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148507423	148507423	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	85	238	0	ENST00000320356.2:c.2029+2T>C		p.X677_splice	ENST00000320356	NM_004456.4	677			1	2	FACETS	0.771	0.684	0.863	0.771	0.684	0.863	SUBCLONAL	1	TRUE	1	0.47320191049849	2		238	466	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62325754	62325754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145335410	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	145	470	0	ENST00000360203.5:c.3022G>A	p.Val1008Met	p.V1008M	ENST00000360203	NM_001283009.1	1008	Gtg/Atg	31/35	1	2	FACETS	0.889	0.813	0.969	0.889	0.813	0.969	CLONAL	1	TRUE	1	0.47320191049849	2		470	689	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117191	7117191	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	151	532	0	ENST00000302850.5:c.4025del	p.Gly1342AlafsTer23	p.G1342Afs*23	ENST00000302850	NM_000208.2	1342	gGc/gc	22/22	1	2	FACETS	0.937	0.859	1	0.937	0.859	1	CLONAL	1	TRUE	1	0.47320191049849	2		532	681	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41249283	41249283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80357090	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	189	299	0	ENST00000357654.3:c.571G>A	p.Val191Ile	p.V191I	ENST00000357654	NM_007294.3	191	Gtt/Att	8/23	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.47320191049849	2		299	785	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778894	9778894	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	168	479	0	ENST00000377346.4:c.1165del	p.Arg389ValfsTer9	p.R389Vfs*9	ENST00000377346	NM_005026.3	388	gCc/gc	9/24	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.47320191049849	2		479	705	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812238	43812238	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	109	426	0	ENST00000372470.3:c.1103T>C	p.Val368Ala	p.V368A	ENST00000372470	NM_005373.2	368	gTg/gCg	7/12	1	2	FACETS	0.644	0.579	0.714	0.644	0.579	0.714	SUBCLONAL	1	TRUE	1	0.47320191049849	2		426	715	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226590047	226590047	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	138	487	0	ENST00000366794.5:c.154T>C	p.Tyr52His	p.Y52H	ENST00000366794	NM_001618.3	52	Tac/Cac	2/23	1	2	FACETS	0.86	0.785	0.939	0.86	0.785	0.939	CLONAL	1	TRUE	1	0.47320191049849	2		487	678	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104353782	104353782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1403040084	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	138	424	0	ENST00000369902.3:c.716G>A	p.Arg239Gln	p.R239Q	ENST00000369902	NM_016169.3	239	cGg/cAg	6/12	1	2	FACETS	0.874	0.798	0.955	0.874	0.798	0.955	CLONAL	1	TRUE	1	0.47320191049849	2		424	667	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999149	100999149	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	127	598	1	ENST00000325455.5:c.653C>T	p.Ala218Val	p.A218V	ENST00000325455	NM_001202474.3	218	gCg/gTg	1/8	1	2	FACETS	0.898	0.816	0.983	0.898	0.816	0.983	CLONAL	1	TRUE	1	0.47320191049849	2		599	598	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139213	108139213	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	171	471	1	ENST00000278616.4:c.2717del	p.Leu906CysfsTer3	p.L906Cfs*3	ENST00000278616	NM_000051.3	905	tgT/tg	18/63	1	2	FACETS	0.982	0.905	1	0.982	0.905	1	CLONAL	1	TRUE	1	0.47320191049849	2		472	736	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498103	498103	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	125	327	0	ENST00000399788.2:c.155G>A	p.Arg52Gln	p.R52Q	ENST00000399788	NM_001042603.1	52	cGg/cAg	1/28	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.47320191049849	2		327	528	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641409	18641409	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	29	182	0	ENST00000266497.5:c.2408C>T	p.Ala803Val	p.A803V	ENST00000266497		803	gCt/gTt	17/31	1	2	FACETS	0.382	0.307	0.467	0.382	0.307	0.467	SUBCLONAL	1	TRUE	1	0.47320191049849	2		182	321	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249393	133249393	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	151	396	0	ENST00000320574.5:c.1506G>T	p.Glu502Asp	p.E502D	ENST00000320574	NM_006231.2	502	gaG/gaT	15/49	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.47320191049849	2		396	580	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052627	42052627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	175	341	0	ENST00000219905.7:c.7298G>A	p.Arg2433Gln	p.R2433Q	ENST00000219905	NM_001164273.1	2433	cGg/cAg	20/24	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.47320191049849	2		341	675	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481600	40481600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	44	451	0	ENST00000264657.5:c.1205G>A	p.Gly402Asp	p.G402D	ENST00000264657	NM_139276.2	402	gGc/gAc	13/24	1	2	FACETS	0.282	0.236	0.334	0.282	0.236	0.334	SUBCLONAL	1	TRUE	1	0.47320191049849	2		451	659	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435761	56435761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	114	371	0	ENST00000407977.2:c.1376C>T	p.Ala459Val	p.A459V	ENST00000407977		459	gCa/gTa	9/10	1	2	FACETS	0.987	0.894	1	0.987	0.894	1	CLONAL	1	TRUE	1	0.47320191049849	2		371	488	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119815	70119816	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	165	497	0	ENST00000245479.2:c.818dup	p.Asp274GlyfsTer22	p.D274Gfs*22	ENST00000245479	NM_000346.3	273	gtg/gTtg	3/3	1	2	FACETS	0.981	0.903	1	0.981	0.903	1	CLONAL	1	TRUE	1	0.47320191049849	2		497	711	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229609	5229609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1399739848	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	22	46	0	ENST00000357368.4:c.2242C>T	p.Arg748Trp	p.R748W	ENST00000357368	NM_002850.3	748	Cgg/Tgg	15/38	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.47320191049849	2		46	83	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556645	41556645	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	116	293	0	ENST00000263253.7:c.3591-1G>A		p.X1197_splice	ENST00000263253	NM_001429.3	1197			1	2	FACETS	0.92	0.833	1	0.92	0.833	1	CLONAL	1	TRUE	1	0.47320191049849	2		293	533	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266877	41266877	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	29	292	0	ENST00000349496.5:c.548C>T	p.Ala183Val	p.A183V	ENST00000349496	NM_001904.3	183	gCt/gTt	5/15	1	2	FACETS	0.259	0.207	0.317	0.259	0.207	0.317	SUBCLONAL	1	TRUE	1	0.47320191049849	2		292	474	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969147	93969147	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	86	286	0	ENST00000369303.4:c.1849C>T	p.Pro617Ser	p.P617S	ENST00000369303	NM_004440.3	617	Cca/Tca	10/17	1	2	FACETS	0.799	0.71	0.893	0.799	0.71	0.893	SUBCLONAL	1	TRUE	1	0.47320191049849	2		286	455	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015614	112015614	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1223286930	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	136	326	0	ENST00000368678.4:c.1228C>T	p.Arg410Ter	p.R410*	ENST00000368678		410	Cga/Tga	11/13	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.47320191049849	2		326	545	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271764	38271764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	153	624	0	ENST00000425967.3:c.2185G>A	p.Gly729Ser	p.G729S	ENST00000425967	NM_001174067.1	729	Ggc/Agc	17/19	1	2	FACETS	0.91	0.834	0.988	0.91	0.834	0.988	CLONAL	1	TRUE	1	0.47320191049849	2		624	711	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923410	36923410	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	188	575	0	ENST00000358127.4:c.852del	p.Thr285ProfsTer18	p.T285Pfs*18	ENST00000358127	NM_001280556.1	284	ccC/cc	7/10	1	2	FACETS	0.969	0.897	1	0.969	0.897	1	CLONAL	1	TRUE	1	0.47320191049849	2		575	820	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393629	139393629	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	195	622	1	ENST00000277541.6:c.6017C>T	p.Ala2006Val	p.A2006V	ENST00000277541	NM_017617.3	2006	gCc/gTc	32/34	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.47320191049849	2		623	789	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0038165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	224	393	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.893	0.843	0.942	1	0.994	1	CLONAL	2	TRUE	1	0.569068334816205	2		393	441	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346365	73346365	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	58	304	0	ENST00000377767.4:c.1435G>T	p.Asp479Tyr	p.D479Y	ENST00000377767	NM_014953.3	479	Gac/Tac	10/21	0.529061461814348	1	FACETS	0.61	0.53	0.695	0.61	0.53	0.695	SUBCLONAL	1	TRUE	0	0.569068334816205	1		304	239	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378306	225378306	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	74	310	0	ENST00000264414.4:c.589G>T	p.Gly197Ter	p.G197*	ENST00000264414	NM_003590.4	197	Gga/Tga	5/16	0.334051996118942	1	FACETS	0.608	0.537	0.683	0.608	0.537	0.683	INDETERMINATE	1	TRUE	0	0.569068334816205	1		310	306	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324509	31324509	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs41553715	NA	P-0038165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	12	50	0	ENST00000412585.2:c.299A>T	p.Glu100Val	p.E100V	ENST00000412585	NM_005514.6	100	gAg/gTg	2/8	0.492149068812642	1	FACETS	0.464	0.333	0.618	0.464	0.333	0.618	SUBCLONAL	1	TRUE	0	0.569068334816205	1		50	65	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295755	212295755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	52	463	0	ENST00000342788.4:c.2558C>T	p.Ser853Phe	p.S853F	ENST00000342788	NM_005235.2	853	tCt/tTt	21/28	0.334051996118942	1	FACETS	0.265	0.226	0.309	0.265	0.226	0.309	INDETERMINATE	1	TRUE	0	0.569068334816205	1		463	493	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006897	47006897	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	186	705	0	ENST00000377604.3:c.17G>T	p.Arg6Leu	p.R6L	ENST00000377604	NM_001204468.1	6	cGt/cTt	2/24	0.446274711822609	0	FACETS	0.408	0.378	0.439			1	SUBCLONAL	1	TRUE	0	0.569068334816205	0		705	691	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266549	115266549	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	184	528	0	ENST00000438362.2:c.1966C>T	p.Pro656Ser	p.P656S	ENST00000438362	NM_001242891.1	656	Cca/Tca	16/20	1	2	FACETS	0.906	0.839	0.975	0.906	0.839	0.975	CLONAL	1	TRUE	1	0.569068334816205	2		528	714	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46240663	46240663	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	46	302	0	ENST00000334344.6:c.1523A>C	p.His508Pro	p.H508P	ENST00000334344	NM_152641.2	508	cAt/cCt	12/21	1	2	FACETS	0.7	0.595	0.813	0.7	0.595	0.813	SUBCLONAL	1	TRUE	1	0.569068334816205	2		302	231	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437508	49437508	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	247	631	0	ENST00000301067.7:c.5377G>T	p.Gly1793Trp	p.G1793W	ENST00000301067	NM_003482.3	1793	Ggg/Tgg	23/54	1	2	FACETS	0.892	0.835	0.951	0.892	0.835	0.951	CLONAL	1	TRUE	1	0.569068334816205	2		631	973	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061009	38061009	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs568751362	NA	P-0038165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	226	351	0	ENST00000250448.2:c.980G>T	p.Gly327Val	p.G327V	ENST00000250448	NM_004496.3	327	gGg/gTg	2/2	0.0926187020136111	4	FACETS	1	0.985	1			1	INDETERMINATE	2	TRUE	NA	0.569068334816205	4		351	541	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609565	81609565	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	72	529	0	ENST00000298171.2:c.1163C>G	p.Thr388Ser	p.T388S	ENST00000298171	NM_000369.2	388	aCc/aGc	10/10	0.248950700896235	0	FACETS	0.229	0.2	0.259			1	INDETERMINATE	1	TRUE	0	0.569068334816205	0		529	477	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609626	81609626	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0038165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	89	576	0	ENST00000298171.2:c.1224T>A	p.Cys408Ter	p.C408*	ENST00000298171	NM_000369.2	408	tgT/tgA	10/10	0.248950700896235	0	FACETS	0.225	0.199	0.252			1	INDETERMINATE	1	TRUE	0	0.569068334816205	0		576	599	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669536	88669536	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	57	490	0	ENST00000360948.2:c.1362C>A	p.Asn454Lys	p.N454K	ENST00000360948	NM_001012338.2	454	aaC/aaA	12/19	0.431956562537059	1	FACETS	0.255	0.219	0.295	0.255	0.219	0.295	SUBCLONAL	1	TRUE	0	0.569068334816205	1		490	561	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923449	9923449	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	170	575	0	ENST00000330684.3:c.1838T>A	p.Phe613Tyr	p.F613Y	ENST00000330684	NM_001134407.1	613	tTc/tAc	9/13	0.434088531269212	1	FACETS	0.682	0.63	0.736	0.682	0.63	0.736	SUBCLONAL	1	TRUE	0	0.569068334816205	1		575	627	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923773	72923773	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	111	620	0	ENST00000268489.5:c.3305A>T	p.Asn1102Ile	p.N1102I	ENST00000268489	NM_006885.3	1102	aAc/aTc	4/10	0.434088531269212	1	FACETS	0.413	0.371	0.457	0.413	0.371	0.457	SUBCLONAL	1	TRUE	0	0.569068334816205	1		620	676	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528428	29528428	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs876660782	NA	P-0038165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	118	327	0	ENST00000356175.3:c.1186-1G>C		p.X396_splice	ENST00000356175	NM_000267.3	396			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.569068334816205	2		327	342	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684345	29684345	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0038165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	84	464	0	ENST00000356175.3:c.7865T>A	p.Leu2622Ter	p.L2622*	ENST00000356175	NM_000267.3	2622	tTa/tAa	53/57	1	2	FACETS	0.717	0.636	0.801	0.717	0.636	0.801	SUBCLONAL	1	TRUE	1	0.569068334816205	2		464	412	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965713	25965713	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	197	664	0	ENST00000435504.4:c.3493G>T	p.Asp1165Tyr	p.D1165Y	ENST00000435504		1165	Gac/Tac	13/13	1	2	FACETS	0.771	0.714	0.83	0.771	0.714	0.83	SUBCLONAL	1	TRUE	1	0.569068334816205	2		664	898	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521664	89521664	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs17801309	NA	P-0038165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	151	493	0	ENST00000336596.2:c.2741G>T	p.Arg914Leu	p.R914L	ENST00000336596	NM_005233.5	914	cGc/cTc	16/17	0.521273516685297	1	FACETS	0.764	0.703	0.826	0.764	0.703	0.826	SUBCLONAL	1	TRUE	0	0.569068334816205	1		493	497	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898726	134898726	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs750940800	NA	P-0038165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	105	318	0	ENST00000398015.3:c.1784T>C	p.Ile595Thr	p.I595T	ENST00000398015	NM_004441.4	595	aTt/aCt	10/16	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.569068334816205	2		318	353	SUCCESS
ATR	545	MSKCC	GRCh37	3	142185376	142185376	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0038165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	57	264	0	ENST00000350721.4:c.6688-1G>T		p.X2230_splice	ENST00000350721	NM_001184.3	2230			1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.569068334816205	2		264	174	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467487	66467487	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	143	339	0	ENST00000273854.3:c.782C>A	p.Ser261Tyr	p.S261Y	ENST00000273854	NM_004439.5	261	tCc/tAc	3/18	1	2	FACETS	0.978	0.897	1	0.978	0.897	1	CLONAL	1	TRUE	1	0.569068334816205	2		339	514	SUCCESS
APC	324	MSKCC	GRCh37	5	112173667	112173667	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	93	355	0	ENST00000257430.4:c.2376del	p.Lys792AsnfsTer28	p.K792Nfs*28	ENST00000257430	NM_000038.5	792	aaG/aa	16/16	1	2	FACETS	0.851	0.762	0.944	0.851	0.762	0.944	CLONAL	1	TRUE	1	0.569068334816205	2		355	384	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486227	8486227	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	132	399	0	ENST00000356435.5:c.2590G>C	p.Asp864His	p.D864H	ENST00000356435		864	Gat/Cat	17/35	0.569068334816205	1	FACETS	0.842	0.773	0.914	0.842	0.773	0.914	CLONAL	1	TRUE	0	0.569068334816205	1		399	394	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032557	47032557	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	146	658	1	ENST00000377604.3:c.463C>T	p.Gln155Ter	p.Q155*	ENST00000377604	NM_001204468.1	155	Caa/Taa	5/24	0.446274711822609	0	FACETS	0.39	0.357	0.424			1	SUBCLONAL	1	TRUE	0	0.569068334816205	0		659	567	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123026618	123026618	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	143	486	0	ENST00000355640.3:c.1094G>T	p.Arg365Ile	p.R365I	ENST00000355640		365	aGa/aTa	5/7	0.569068334816205	1	FACETS	0.892	0.822	0.964	0.892	0.822	0.964	CLONAL	1	TRUE	0	0.569068334816205	1		486	403	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	125	503	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.459124712759808	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.459124712759808	1		503	389	SUCCESS
APC	324	MSKCC	GRCh37	5	112163677	112163677	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0038168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	107	229	0	ENST00000257430.4:c.1600A>T	p.Lys534Ter	p.K534*	ENST00000257430	NM_000038.5	534	Aaa/Taa	13/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.459124712759808	2		229	385	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555687605	NA	P-0038168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	28	390	0	ENST00000342988.3:c.1610A>G	p.Asp537Gly	p.D537G	ENST00000342988	NM_005359.5	537	gAc/gGc	12/12	0.459124712759808	1	FACETS	0.348	0.279	0.426	0.348	0.279	0.426	SUBCLONAL	1	TRUE	0	0.459124712759808	1		390	270	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250883	153250883	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	117	331	2	ENST00000281708.4:c.1177C>T	p.Arg393Ter	p.R393*	ENST00000281708	NM_033632.3	393	Cga/Tga	8/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.459124712759808	2		333	424	SUCCESS
APC	324	MSKCC	GRCh37	5	112175198	112175198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	88	211	0	ENST00000257430.4:c.3907C>T	p.Gln1303Ter	p.Q1303*	ENST00000257430	NM_000038.5	1303	Caa/Taa	16/16	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.459124712759808	2		211	372	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912188	114912188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	216	412	4	ENST00000543371.1:c.1258C>T	p.Arg420Trp	p.R420W	ENST00000543371	NM_001198531.1	420	Cgg/Tgg	11/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.459124712759808	2		416	830	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	267	700	1	ENST00000269305.4:c.388del	p.Leu130SerfsTer40	p.L130Sfs*40	ENST00000269305	NM_001126112.2	130	Ctc/tc	5/11	0.459124712759808	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.459124712759808	1		701	861	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127460	55127460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779332376	NA	P-0038168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	252	446	7	ENST00000257290.5:c.248C>T	p.Thr83Met	p.T83M	ENST00000257290	NM_006206.4	83	aCg/aTg	3/23	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.459124712759808	2		453	855	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245462	153245462	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	199	425	1	ENST00000281708.4:c.1729T>G	p.Leu577Val	p.L577V	ENST00000281708	NM_033632.3	577	Tta/Gta	11/12	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.459124712759808	2		426	765	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478927	56478927	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	360	539	1	ENST00000267101.3:c.383G>T	p.Ser128Ile	p.S128I	ENST00000267101	NM_001982.3	128	aGc/aTc	3/28	0.271824349540198	2	FACETS	0.759	0.721	0.798	0.759	0.721	0.798	INDETERMINATE	2	TRUE	0	0.459124712759808	2		540	1033	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	125	313	2				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.824	0.754	0.896			1	INDETERMINATE	1	TRUE	NA	0.833290420614029	2		315	364	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586502	189586502	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757536818	NA	P-0038169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	180	333	0	ENST00000264731.3:c.1126C>T	p.Arg376Cys	p.R376C	ENST00000264731	NM_003722.4	376	Cgc/Tgc	8/14	1	2	FACETS	0.911	0.849	0.975	0.911	0.849	0.975	CLONAL	1	TRUE	1	0.833290420614029	2		333	474	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519923	66519923	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	197	475	0	ENST00000358598.2:c.406G>A	p.Val136Met	p.V136M	ENST00000358598	NM_212471.2	136	Gtg/Atg	4/11	1	2	FACETS	0.869	0.811	0.928	0.869	0.811	0.928	CLONAL	1	TRUE	1	0.833290420614029	2		475	544	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797898	42797898	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0038169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	356	780	0	ENST00000575354.2:c.3950del	p.Asp1317AlafsTer15	p.D1317Afs*15	ENST00000575354	NM_015125.3	1317	gAc/gc	16/20	0.833290420614029	3	FACETS	1	0.955	1	0.504	0.477	0.531	CLONAL	1	TRUE	1	0.833290420614029	3		780	1201	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0038186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	75	482	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		482	513	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	198	882	1	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.50656876240707	1	FACETS	0.524	0.486	0.562	0.524	0.486	0.562	SUBCLONAL	1	TRUE	0	0.693769289496612	1		883	712	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0038189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	144	467	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.693769289496612	1	FACETS	0.863	0.801	0.926	0.863	0.801	0.926	CLONAL	1	TRUE	0	0.693769289496612	1		467	314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579419	7579420	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs587783062	NA	P-0038189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	568	970	0	ENST00000269305.4:c.267dup	p.Ser90LeufsTer59	p.S90Lfs*59	ENST00000269305	NM_001126112.2	89	-/C	4/11	0.693769289496612	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.693769289496612	1		970	941	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672219	86672219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194205020	NA	P-0038189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	188	445	0	ENST00000274376.6:c.2021G>A	p.Arg674His	p.R674H	ENST00000274376	NM_002890.2	674	cGc/cAc	16/25	0.693769289496612	1	FACETS	0.989	0.93	1	0.989	0.93	1	CLONAL	1	TRUE	0	0.693769289496612	1		445	358	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27213564	27213564	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	121	761	0	ENST00000380036.4:c.2960G>A	p.Arg987Gln	p.R987Q	ENST00000380036	NM_000459.3	987	cGa/cAa	18/23	1	2	FACETS	0.473	0.428	0.521	0.473	0.428	0.521	SUBCLONAL	1	TRUE	1	0.693769289496612	2		761	737	SUCCESS
RET	5979	MSKCC	GRCh37	10	43613921	43613921	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	47	741	0	ENST00000355710.3:c.2385C>A	p.Ser795Arg	p.S795R	ENST00000355710	NM_020975.4	795	agC/agA	13/20	1	2	FACETS	0.185	0.155	0.217	0.185	0.155	0.217	SUBCLONAL	1	TRUE	1	0.693769289496612	2		741	734	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447846	49447846	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	340	828	2	ENST00000301067.7:c.588del	p.Cys197AlafsTer11	p.C197Afs*11	ENST00000301067	NM_003482.3	196	ccC/cc	5/54	0.495743996864764	1	FACETS	0.756	0.718	0.794	0.756	0.718	0.794	SUBCLONAL	1	TRUE	0	0.693769289496612	1		830	847	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0038192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	27	151	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	0.666	0.531	0.821	0.666	0.531	0.821	SUBCLONAL	1	TRUE	1	0.246286149121527	2		151	329	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443880	52443880	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs916069743	NA	P-0038192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	24	146	0	ENST00000460680.1:c.15G>A	p.Trp5Ter	p.W5*	ENST00000460680	NM_004656.3	5	tgG/tgA	1/17	0.243945359788171	1	FACETS	0.712	0.56	0.886	0.712	0.56	0.886	SUBCLONAL	1	TRUE	0	0.246286149121527	1		146	240	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412483	63412483	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	24	139	0	ENST00000330258.3:c.684T>A	p.Asn228Lys	p.N228K	ENST00000330258	NM_152424.3	228	aaT/aaA	2/2	1	2	FACETS	0.776	0.611	0.966	0.776	0.611	0.966	CLONAL	1	TRUE	1	0.246286149121527	2		139	251	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306599	41306599	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778985729	NA	P-0038192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	29	161	0	ENST00000373198.4:c.1060G>A	p.Val354Ile	p.V354I	ENST00000373198	NM_133170.3	354	Gtt/Att	7/32	1	2	FACETS	0.815	0.656	0.995	0.815	0.656	0.995	CLONAL	1	TRUE	1	0.246286149121527	2		161	289	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	107	503	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		503	966	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591719	38591736	+	inframe_deletion	In_Frame_Del	DEL	ATCCGTGGAGAGCGACTC	ATCCGTGGAGAGCGACTC	-	novel	NA	P-0038193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	47	582	0	ENST00000299084.4:c.179_196del	p.Ile60_Leu65del	p.I60_L65del	ENST00000299084	NM_152594.2	60	ATCCGTGGAGAGCGACTC/-	2/7	0.0771154644230078	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		582	878	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161222	56161222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	357	516	0	ENST00000399503.3:c.1091G>A	p.Arg364Gln	p.R364Q	ENST00000399503	NM_005921.1	364	cGg/cAg	5/20	1	2	FACETS	0.991	0.943	1	0.991	0.943	1	CLONAL	1	TRUE	1	0.81041017295273	2		516	889	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571966	64571966	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	513	881	0	ENST00000312049.6:c.1673T>A	p.Met558Lys	p.M558K	ENST00000312049	NM_130799.2	558	aTg/aAg	10/10	0.81041017295273	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.81041017295273	1		881	747	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426767	121426767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	70	673	0	ENST00000257555.6:c.458C>T	p.Pro153Leu	p.P153L	ENST00000257555		153	cCc/cTc	2/10	1	2	FACETS	0.162	0.141	0.186	0.162	0.141	0.186	SUBCLONAL	1	TRUE	1	0.81041017295273	2		673	1064	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913237	NA	P-0038195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	536	403	0	ENST00000369535.4:c.35G>C	p.Gly12Ala	p.G12A	ENST00000369535	NM_002524.4	12	gGt/gCt	2/7	0.762457451925613	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.762457451925613	3		403	933	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285694	87285694	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs78936193	NA	P-0038195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	771	824	0	ENST00000277120.3:c.31G>A	p.Ala11Thr	p.A11T	ENST00000277120		11	Gcc/Acc	2/19	0.584270913937924	4	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	2	0.762457451925613	4		824	1591	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845590	128845590	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772693769	NA	P-0038195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	734	766	5	ENST00000249373.3:c.887G>A	p.Arg296His	p.R296H	ENST00000249373	NM_005631.4	296	cGt/cAt	4/12	0.715286990884966	4	FACETS	1	0.987	1	0.691	0.668	0.714	CLONAL	2	TRUE	1	0.762457451925613	4		771	1637	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577477	7577502	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGGTGGCAAGTGGCTCCTGACCTGG	AGGGTGGCAAGTGGCTCCTGACCTGG	-	novel	NA	P-0038195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	334	703	0	ENST00000269305.4:c.779_782+22del		p.X260_splice	ENST00000269305	NM_001126112.2	260		7/11	0.762457451925613	2	FACETS	0.775	0.743	0.808	0.775	0.743	0.808	SUBCLONAL	2	TRUE	0	0.762457451925613	2		703	565	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400691	56400691	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	168	509	4	ENST00000348428.3:c.1285G>T	p.Asp429Tyr	p.D429Y	ENST00000348428	NM_006785.3	429	Gat/Tat	11/17	0.762457451925613	2	FACETS	0.888	0.841	0.934	0.888	0.841	0.934	CLONAL	2	TRUE	0	0.762457451925613	2		513	248	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574814	41574814	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	511	916	2	ENST00000263253.7:c.7099C>A	p.Pro2367Thr	p.P2367T	ENST00000263253	NM_001429.3	2367	Ccg/Acg	31/31	0.762457451925613	2	FACETS	1	0.993	1	0.567	0.545	0.59	CLONAL	1	TRUE	0	0.762457451925613	2		918	1181	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937133	39937133	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1195	123	540	0	ENST00000378444.4:c.50G>T	p.Ser17Ile	p.S17I	ENST00000378444	NM_001123385.1	17	aGc/aTc	2/15	0.729454921084737	2	FACETS	0.245	0.22	0.271			1	SUBCLONAL	1	TRUE	NA	0.762457451925613	2		540	1318	SUCCESS
APC	324	MSKCC	GRCh37	5	112175477	112175479	+	frameshift_variant	Frame_Shift_Del	DEL	TTT	TTT	A	novel	NA	P-0038195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	349	480	0	ENST00000257430.4:c.4186_4188delinsA	p.Phe1396ArgfsTer12	p.F1396Rfs*12	ENST00000257430	NM_000038.5	1396	TTT/A	16/16	0.762457451925613	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.762457451925613	2		480	440	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464952	120464952	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	48	602	0	ENST00000256646.2:c.5120G>C	p.Gly1707Ala	p.G1707A	ENST00000256646	NM_024408.3	1707	gGc/gCc	28/34	1	2	FACETS	0.281	0.237	0.331	0.281	0.237	0.331	SUBCLONAL	1	TRUE	1	0.410563080329745	2		602	831	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385195	4385196	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	296	546	0	ENST00000261254.3:c.222dup	p.Glu75ArgfsTer84	p.E75Rfs*84	ENST00000261254	NM_001759.3	74	gaa/gAaa	2/5	1	2	FACETS	1	0.963	1	1	0.996	1	CLONAL	2	TRUE	1	0.410563080329745	2		546	707	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851574	134851574	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747682274	NA	P-0038198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	206	383	0	ENST00000398015.3:c.980G>A	p.Arg327His	p.R327H	ENST00000398015	NM_004441.4	327	cGc/cAc	5/16	1	2	FACETS	0.464	0.43	0.5	0.464	0.43	0.5	SUBCLONAL	1	TRUE	1	0.71519033810192	2		383	1241	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921167	50921167	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1322	301	944	2	ENST00000440232.2:c.3287T>A	p.Leu1096Gln	p.L1096Q	ENST00000440232	NM_002691.3	1096	cTg/cAg	27/27	1	2	FACETS	0.519	0.487	0.551	0.519	0.487	0.551	SUBCLONAL	1	TRUE	1	0.71519033810192	2		946	1623	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395598	31395598	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	264	895	0	ENST00000328111.2:c.2451C>G	p.Asp817Glu	p.D817E	ENST00000328111	NM_006892.3	817	gaC/gaG	23/23	0.358321292971955	1	FACETS	0.395	0.37	0.421	0.395	0.37	0.421	INDETERMINATE	1	TRUE	0	0.71519033810192	1		895	1201	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593331	67593331	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	166	514	0	ENST00000274335.5:c.2077G>T	p.Glu693Ter	p.E693*	ENST00000274335		693	Gaa/Taa	15/15	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.71519033810192	NA		514	735	SUCCESS
APC	324	MSKCC	GRCh37	5	112175940	112175940	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0038198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	240	394	0	ENST00000257430.4:c.4649del	p.Glu1550GlyfsTer15	p.E1550Gfs*15	ENST00000257430	NM_000038.5	1550	gAg/gg	16/16	0.292728847800141	1	FACETS	0.704	0.663	0.747	0.704	0.663	0.747	INDETERMINATE	1	TRUE	0	0.71519033810192	1		394	612	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555687605	NA	P-0038199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	112	390	0	ENST00000342988.3:c.1610A>G	p.Asp537Gly	p.D537G	ENST00000342988	NM_005359.5	537	gAc/gGc	12/12	0.421872640681342	1	FACETS	0.853	0.771	0.939	0.853	0.771	0.939	CLONAL	1	FALSE	0	0.421872640681342	1		390	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0038199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	272	707	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.341557116659925	2	FACETS	0.862	0.813	0.912	0.862	0.813	0.912	CLONAL	2	FALSE	0	0.421872640681342	2		707	748	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336625	81336625	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs527951814	NA	P-0038199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	118	440	0	ENST00000222390.5:c.1597C>T	p.Arg533Ter	p.R533*	ENST00000222390	NM_000601.4	533	Cga/Tga	14/18	0.368875314451715	3	FACETS	1	0.981	1	0.665	0.603	0.731	CLONAL	1	FALSE	1	0.421872640681342	3		440	509	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40860032	40860032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	140	749	0	ENST00000428826.2:c.1604G>A	p.Cys535Tyr	p.C535Y	ENST00000428826		535	tGc/tAc	15/21	0.113587180373051	3	FACETS	0.85	0.774	0.931	0.283	0.258	0.311	INDETERMINATE	1	FALSE	0	0.421872640681342	3		749	945	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0038202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	143	367	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.862	0.79	0.936	0.862	0.79	0.936	CLONAL	1	TRUE	1	0.620426570948017	2		367	535	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0038202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	185	262	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	0.620426570948017	2		262	590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0038202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	511	447	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	2	TRUE	NA	0.620426570948017	2		447	809	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0038202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	107	390	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	0.107444164550484	3	FACETS	1	0.969	1	0.585	0.529	0.644	INDETERMINATE	1	TRUE	1	0.620426570948017	3		390	386	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467748	50467748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	144	679	0	ENST00000331340.3:c.983G>A	p.Arg328His	p.R328H	ENST00000331340	NM_006060.4	328	cGc/cAc	8/8	1	2	FACETS	0.765	0.7	0.832	0.765	0.7	0.832	SUBCLONAL	1	TRUE	1	0.620426570948017	2		679	607	SUCCESS
APC	324	MSKCC	GRCh37	5	112175681	112175682	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	137	479	0	ENST00000257430.4:c.4391dup	p.Ser1465GlufsTer4	p.S1465Efs*4	ENST00000257430	NM_000038.5	1464	gag/gAag	16/16	0.107444164550484	3	FACETS	1	0.974	1	0.58	0.531	0.631	INDETERMINATE	1	TRUE	1	0.620426570948017	3		479	499	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411786	63411786	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	476	936	1	ENST00000330258.3:c.1381C>T	p.Gln461Ter	p.Q461*	ENST00000330258	NM_152424.3	461	Caa/Taa	2/2	0.620426570948017	2	FACETS	0.998	0.964	1	0.998	0.964	1	CLONAL	2	TRUE	0	0.620426570948017	2		937	769	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	306	503	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.239878776066246	4	FACETS	0.917	0.871	0.964	1	0.992	1	CLONAL	4	TRUE	1	0.315807813414453	4		503	695	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	89	313	2				ENST00000310581	NM_198253.2	-/1132			0.063338638385763	4	FACETS	1	0.964	1	1	0.964	1	INDETERMINATE	2	TRUE	2	0.315807813414453	4		315	315	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858709	9858709	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	27	566	0	ENST00000330684.3:c.2692C>T	p.Leu898Phe	p.L898F	ENST00000330684	NM_001134407.1	898	Ctc/Ttc	13/13	0.251209114329917	3	FACETS	0.386	0.306	0.478	0.193	0.153	0.239	SUBCLONAL	1	TRUE	1	0.315807813414453	3		566	513	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258079	16258079	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	49	634	1	ENST00000375759.3:c.5344G>A	p.Asp1782Asn	p.D1782N	ENST00000375759	NM_015001.2	1782	Gat/Aat	11/15	0.063338638385763	4	FACETS	0.865	0.733	1	0.433	0.366	0.505	INDETERMINATE	1	TRUE	2	0.315807813414453	4		635	472	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258085	16258085	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	50	644	0	ENST00000375759.3:c.5350G>A	p.Glu1784Lys	p.E1784K	ENST00000375759	NM_015001.2	1784	Gag/Aag	11/15	0.063338638385763	4	FACETS	0.886	0.753	1	0.443	0.376	0.517	INDETERMINATE	1	TRUE	2	0.315807813414453	4		644	470	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258858	16258858	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	83	799	1	ENST00000375759.3:c.6123G>C	p.Gln2041His	p.Q2041H	ENST00000375759	NM_015001.2	2041	caG/caC	11/15	0.063338638385763	4	FACETS	1	0.933	1	0.541	0.478	0.609	INDETERMINATE	1	TRUE	2	0.315807813414453	4		800	639	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352591	118352591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370374383	NA	P-0038203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	63	636	0	ENST00000534358.1:c.3796C>T	p.Pro1266Ser	p.P1266S	ENST00000534358	NM_005933.3	1266	Ccc/Tcc	7/36	1	2	FACETS	0.773	0.67	0.885	0.773	0.67	0.885	SUBCLONAL	1	TRUE	1	0.315807813414453	2		636	516	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372403	118372418	+	frameshift_variant	Frame_Shift_Del	DEL	GAGTCAAAACACAGCT	GAGTCAAAACACAGCT	-	novel	NA	P-0038203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	76	624	0	ENST00000534358.1:c.6338_6353del	p.Ser2113LysfsTer3	p.S2113Kfs*3	ENST00000534358	NM_005933.3	2112	gaGAGTCAAAACACAGCT/ga	26/36	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.315807813414453	2		624	403	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438297	49438297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	101	584	0	ENST00000301067.7:c.4972G>A	p.Glu1658Lys	p.E1658K	ENST00000301067	NM_003482.3	1658	Gag/Aag	20/54	0.239878776066246	4	FACETS	1	0.908	1	0.673	0.605	0.743	CLONAL	2	TRUE	1	0.315807813414453	4		584	417	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68878227	68878227	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769705231	NA	P-0038203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	53	461	0	ENST00000487270.1:c.940G>A	p.Asp314Asn	p.D314N	ENST00000487270	NM_133509.3	314	Gat/Aat	9/11	0.00558590429306349	4	FACETS	0.887	0.757	1	0.443	0.378	0.515	INDETERMINATE	1	TRUE	2	0.315807813414453	4		461	498	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075245	16075245	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	100	625	0	ENST00000268712.3:c.307T>G	p.Ser103Ala	p.S103A	ENST00000268712	NM_006311.3	103	Tca/Gca	4/46	0.00558590429306349	4	FACETS	1	0.98	1	0.721	0.645	0.801	INDETERMINATE	1	TRUE	2	0.315807813414453	4		625	578	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953269	17953269	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	56	825	0	ENST00000458235.1:c.717C>G	p.Ile239Met	p.I239M	ENST00000458235	NM_000215.3	239	atC/atG	6/24	0.251209114329917	3	FACETS	0.799	0.685	0.923	0.399	0.342	0.462	CLONAL	1	TRUE	1	0.315807813414453	3		825	514	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867774	45867774	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	190	908	1	ENST00000391945.4:c.626A>G	p.Tyr209Cys	p.Y209C	ENST00000391945	NM_000400.3	209	tAc/tGc	8/23	0.0694801728608744	6	FACETS	1	0.942	1	1	0.942	1	INDETERMINATE	3	TRUE	3	0.315807813414453	6		909	644	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022371	26022371	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	69	624	0	ENST00000435504.4:c.286G>A	p.Glu96Lys	p.E96K	ENST00000435504		96	Gaa/Aaa	5/13	0.063338638385763	4	FACETS	0.871	0.758	0.993	0.436	0.379	0.497	INDETERMINATE	1	TRUE	2	0.315807813414453	4		624	660	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795376	39795376	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	38	770	0	ENST00000288319.7:c.344C>G	p.Pro115Arg	p.P115R	ENST00000288319	NM_182918.3	115	cCc/cGc	3/10	NA	3	FACETS	0.441	0.363	0.528	0.22	0.181	0.264	INDETERMINATE	1	TRUE	1	0.315807813414453	3		770	632	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12393114	12393114	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	56	716	0	ENST00000287820.6:c.23C>G	p.Ser8Cys	p.S8C	ENST00000287820	NM_015869.4	8	tCt/tGt	1/7	0.251209114329917	3	FACETS	0.83	0.711	0.958	0.415	0.355	0.479	CLONAL	1	TRUE	1	0.315807813414453	3		716	495	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808907	1808907	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs140616343	NA	P-0038203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	59	908	0	ENST00000260795.2:c.2339C>G	p.Ser780Cys	p.S780C	ENST00000260795		780	tCc/tGc	17/17	1	2	FACETS	0.77	0.664	0.886	0.77	0.664	0.886	SUBCLONAL	1	TRUE	1	0.315807813414453	2		908	485	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776217	135776217	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	43	536	0	ENST00000298552.3:c.2510del	p.Asn837ThrfsTer12	p.N837Tfs*12	ENST00000298552	NM_001162426.1	837	aAc/ac	20/23	0.315807813414453	2	FACETS	0.615	0.515	0.725	0.307	0.257	0.363	SUBCLONAL	1	TRUE	0	0.315807813414453	2		536	443	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950056	44950056	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	57	360	0	ENST00000377967.4:c.3825G>A	p.Trp1275Ter	p.W1275*	ENST00000377967	NM_021140.2	1275	tgG/tgA	26/29	0.0907986111837613	2	FACETS	1	0.953	1			1	INDETERMINATE	1	TRUE	NA	0.315807813414453	2		360	290	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533904	63533904	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201460658	NA	P-0038204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	218	398	0	ENST00000307078.5:c.1250C>T	p.Ala417Val	p.A417V	ENST00000307078	NM_004655.3	417	gCg/gTg	6/11	0.578441929345895	5	FACETS	1	0.962	1	0.694	0.649	0.739	CLONAL	2	TRUE	2	0.65524569156002	5		398	634	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0038204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	214	455	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.65524569156002	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.65524569156002	2		455	316	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578214	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs864309495	NA	P-0038204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	455	604	0	ENST00000269305.4:c.635_636del	p.Phe212SerfsTer3	p.F212Sfs*3	ENST00000269305	NM_001126112.2	212	tTT/t	6/11	0.641659651974208	3	FACETS	0.99	0.96	1	0.99	0.96	1	CLONAL	3	TRUE	0	0.65524569156002	3		604	621	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667784	37667784	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	250	273	0	ENST00000447079.4:c.2669G>A	p.Arg890His	p.R890H	ENST00000447079	NM_015083.1	890	cGc/cAc	8/14	0.578441929345895	5	FACETS	0.952	0.9	1	0.952	0.9	1	CLONAL	3	TRUE	2	0.65524569156002	5		273	530	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246448	46246449	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0038204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	185	223	0	ENST00000334344.6:c.4543_4544del	p.Val1515LysfsTer8	p.V1515Kfs*8	ENST00000334344	NM_152641.2	1514	acTGta/acta	15/21	0.538000584167159	5	FACETS	1	0.946	1	1	0.946	1	CLONAL	3	TRUE	2	0.65524569156002	5		223	370	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522123	157522123	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554235726	NA	P-0038204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	159	502	0	ENST00000346085.5:c.4395G>A	p.Trp1465Ter	p.W1465*	ENST00000346085	NM_020732.3	1465	tgG/tgA	18/20	0.651834543696062	3	FACETS	1	0.973	1	0.561	0.517	0.607	CLONAL	1	TRUE	1	0.65524569156002	3		502	574	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054998	176054998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757438162	NA	P-0038204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	30	408	0	ENST00000367669.3:c.1055C>T	p.Thr352Met	p.T352M	ENST00000367669	NM_022457.5	352	aCg/aTg	10/20	0.340054044825878	4	FACETS	0.317	0.255	0.388	0.159	0.127	0.194	INDETERMINATE	1	TRUE	2	0.65524569156002	4		408	478	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201955	67202051	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTGAGTGCGGGGGCCTGAGGCCTGTGGGACCAGGGCACGGATCGTGACTAAGGATGGCAGGCACTGAGTGTCGCATGGCCCTGCCTCCGCCCCCCA	GGTGAGTGCGGGGGCCTGAGGCCTGTGGGACCAGGGCACGGATCGTGACTAAGGATGGCAGGCACTGAGTGTCGCATGGCCCTGCCTCCGCCCCCCA	-	novel	NA	P-0038204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	52	538	0	ENST00000312629.5:c.1155+2_1156del		p.X385_splice	ENST00000312629	NM_003952.2	385		13/15	0.407127519234778	5	FACETS	0.378	0.321	0.441	0.126	0.107	0.147	SUBCLONAL	1	TRUE	2	0.65524569156002	5		538	833	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202163	67202456	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGGTACTGAGGGACGTGGGGGTGTGTGGCTGGGTTAGGGACGCTGGCAGGCAGGATGCCAGCTCCAGCCTTGGGTGCCTTGGCCACGTCTGTCGGCCAGTGTTGGCTTCGGTTGCTGTGTCTATCATGGGGACCTCAGTTCCTACACCCCTTGTGGCCAGGCTGCCTGGATGGGAGTTTGTGGAGCCCGCGGCCTGTGTGCCTGGGCAGGTGGGAAAGGCTGCCTTCCCTGACTGAGTGCTGGGAGCCTCTGGCAGGGCCTAGGAGGCTCTTATTCTGCCTTGGTTTCCCCTG	CAGGTACTGAGGGACGTGGGGGTGTGTGGCTGGGTTAGGGACGCTGGCAGGCAGGATGCCAGCTCCAGCCTTGGGTGCCTTGGCCACGTCTGTCGGCCAGTGTTGGCTTCGGTTGCTGTGTCTATCATGGGGACCTCAGTTCCTACACCCCTTGTGGCCAGGCTGCCTGGATGGGAGTTTGTGGAGCCCGCGGCCTGTGTGCCTGGGCAGGTGGGAAAGGCTGCCTTCCCTGACTGAGTGCTGGGAGCCTCTGGCAGGGCCTAGGAGGCTCTTATTCTGCCTTGGTTTCCCCTG	-	novel	NA	P-0038204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	51	592	0	ENST00000312629.5:c.1268+1_1269-1del		p.X423_splice	ENST00000312629	NM_003952.2	423		14/15	0.407127519234778	5	FACETS	0.352	0.298	0.412	0.117	0.099	0.138	SUBCLONAL	1	TRUE	2	0.65524569156002	5		592	876	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046477	69046477	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	34	495	0	ENST00000288368.4:c.3950T>A	p.Leu1317His	p.L1317H	ENST00000288368	NM_024870.2	1317	cTt/cAt	32/40	0.65524569156002	3	FACETS	0.303	0.248	0.366	0.152	0.124	0.183	SUBCLONAL	1	TRUE	1	0.65524569156002	3		495	454	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0038205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	317	367	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.300662461174081	6	FACETS	1	0.989	1	0.74	0.706	0.773	CLONAL	4	TRUE	0	0.463477293129099	6		367	594	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0038205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	260	620	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.352135526292078	2	FACETS	0.804	0.757	0.851	0.804	0.757	0.851	CLONAL	2	TRUE	0	0.463477293129099	2		620	698	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561767	55561767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780349712	NA	P-0038205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	59	289	0	ENST00000288135.5:c.157G>A	p.Glu53Lys	p.E53K	ENST00000288135	NM_000222.2	53	Gag/Aag	2/21	0.323154879517595	3	FACETS	0.774	0.668	0.889	0.387	0.334	0.445	SUBCLONAL	1	TRUE	1	0.463477293129099	3		289	405	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637115	176637115	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	134	562	0	ENST00000439151.2:c.1715C>G	p.Ser572Cys	p.S572C	ENST00000439151	NM_022455.4	572	tCc/tGc	5/23	1	2	FACETS	0.873	0.795	0.955	0.873	0.795	0.955	CLONAL	1	TRUE	1	0.463477293129099	2		562	662	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0038207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	207	813	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.501071452434243	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.501071452434243	1		813	536	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0038207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	260	406	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.501071452434243	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.501071452434243	3		406	629	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867632	78867632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196323454	NA	P-0038207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	218	733	1	ENST00000306801.3:c.2368G>A	p.Ala790Thr	p.A790T	ENST00000306801	NM_020761.2	790	Gcc/Acc	20/34	0.501071452434243	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.501071452434243	1		734	568	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	493220	493220	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	106	368	0	ENST00000399788.2:c.343C>G	p.Leu115Val	p.L115V	ENST00000399788	NM_001042603.1	115	Ctg/Gtg	3/28	0.501071452434243	3	FACETS	0.996	0.897	1	0.498	0.448	0.551	CLONAL	1	TRUE	1	0.501071452434243	3		368	531	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435889	56435889	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	156	514	1	ENST00000407977.2:c.1248G>A	p.Trp416Ter	p.W416*	ENST00000407977		416	tgG/tgA	9/10	0.501071452434243	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.501071452434243	1		515	390	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272335	15272335	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1361834674	NA	P-0038207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	189	844	0	ENST00000263388.2:c.6104del	p.Gly2035ValfsTer50	p.G2035Vfs*50	ENST00000263388	NM_000435.2	2035	gGt/gt	33/33	1	2	FACETS	0.909	0.841	0.979	0.909	0.841	0.979	CLONAL	1	TRUE	1	0.501071452434243	2		844	830	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0038208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	202	918	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.282585802952931	5	FACETS	0.99	0.926	1			1	CLONAL	4	TRUE	NA	0.282585802952931	5		919	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519989	NA	P-0038208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	198	485	0	ENST00000269305.4:c.730G>C	p.Gly244Arg	p.G244R	ENST00000269305	NM_001126112.2	244	Ggc/Cgc	7/11	0.237618519352058	2	FACETS	0.868	0.806	0.933	0.868	0.806	0.933	CLONAL	2	TRUE	0	0.282585802952931	2		485	807	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948654	71948655	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0038208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	121	695	1	ENST00000298229.2:c.3366_3367delinsTT	p.Val1123Leu	p.V1123L	ENST00000298229	NM_001567.3	1122	tcGGtg/tcTTtg	26/28	1	2	FACETS	0.864	0.779	0.954	0.864	0.779	0.954	CLONAL	1	TRUE	1	0.282585802952931	2		696	991	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118345013	118345013	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	21	218	0	ENST00000534358.1:c.3139G>T	p.Asp1047Tyr	p.D1047Y	ENST00000534358	NM_005933.3	1047	Gac/Tac	3/36	1	2	FACETS	0.533	0.411	0.675	0.533	0.411	0.675	SUBCLONAL	1	TRUE	1	0.282585802952931	2		218	279	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040835	42040835	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	62	304	0	ENST00000219905.7:c.5213A>C	p.Glu1738Ala	p.E1738A	ENST00000219905	NM_001164273.1	1738	gAa/gCa	16/24	0.270247309281379	3	FACETS	0.948	0.82	1	0.474	0.41	0.544	CLONAL	1	TRUE	1	0.282585802952931	3		304	528	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467927	50467927	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	78	471	0	ENST00000331340.3:c.1162G>A	p.Ala388Thr	p.A388T	ENST00000331340	NM_006060.4	388	Gcg/Acg	8/8	0.270247309281379	3	FACETS	0.935	0.821	1	0.467	0.41	0.529	CLONAL	1	TRUE	1	0.282585802952931	3		471	674	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206751	102206753	+	missense_variant	Missense_Mutation	TNP	GTG	GTG	TTT	novel	NA	P-0038208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	50	338	0	ENST00000263464.3:c.1379_1381delinsTTT	p.Cys460_Val461delinsPheLeu	p.C460_V461delinsFL	ENST00000263464	NM_001165.4	460	tGTGta/tTTTta	7/9	1	2	FACETS	0.815	0.693	0.949	0.815	0.693	0.949	CLONAL	1	TRUE	1	0.282585802952931	2		338	434	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0038210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	65	340	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.323076241538942	2		340	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	100	700	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.323076241538942	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.323076241538942	1		700	470	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332010	81332010	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	47	289	0	ENST00000222390.5:c.2074G>T	p.Val692Phe	p.V692F	ENST00000222390	NM_000601.4	692	Gtt/Ttt	18/18	1	2	FACETS	0.909	0.771	1	0.909	0.771	1	CLONAL	1	TRUE	1	0.323076241538942	2		289	320	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593357	48593397	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGATAAAATGTAATTTCTTTTTTCTTCCTAAGGTTGCACAT	AGATAAAATGTAATTTCTTTTTTCTTCCTAAGGTTGCACAT	-	novel	NA	P-0038210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	43	165	0	ENST00000342988.3:c.1140-30_1150del		p.X380_splice	ENST00000342988	NM_005359.5	380		10/12	0.323076241538942	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.323076241538942	1		165	170	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593405	48593406	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0038210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	16	275	0	ENST00000342988.3:c.1160_1161dup	p.Gln388CysfsTer28	p.Q388Cfs*28	ENST00000342988	NM_005359.5	386	ggt/gGTgt	10/12	0.323076241538942	1	FACETS	0.262	0.193	0.344	0.262	0.193	0.344	SUBCLONAL	1	TRUE	0	0.323076241538942	1		275	317	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0038213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	21	780	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.3	1	FACETS	0.172	0.131	0.22	0.172	0.131	0.22	SUBCLONAL	1	TRUE	0	0.26	1		780	817	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0038213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	54	294	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.26	2		294	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0038213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	34	652	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.3	1	FACETS	0.31	0.252	0.375	0.31	0.252	0.375	SUBCLONAL	1	TRUE	0	0.26	1		652	734	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844246	68844246	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0038213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	66	455	0	ENST00000261769.5:c.832+2T>C		p.X278_splice	ENST00000261769	NM_004360.3	278			0.3	1	FACETS	0.882	0.767	1	0.882	0.767	1	CLONAL	1	TRUE	0	0.26	1		455	501	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934208	48934208	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0038213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	38	322	1	ENST00000267163.4:c.663T>A	p.Cys221Ter	p.C221*	ENST00000267163	NM_000321.2	221	tgT/tgA	7/27	1	2	FACETS	0.661	0.547	0.789	0.661	0.547	0.789	SUBCLONAL	1	TRUE	1	0.26	2		323	442	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0038216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	36	400	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.898	0.74	1	0.898	0.74	1	CLONAL	1	TRUE	1	0.234467760323704	2		401	342	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	69	291	0	ENST00000262160.6:c.1391C>A	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tAa	11/11	0.199901144470701	2	FACETS	0.943	0.828	1	0.943	0.828	1	CLONAL	2	TRUE	0	0.234467760323704	2		291	312	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175481	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0038216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	34	300	0	ENST00000257430.4:c.4192_4193del	p.Arg1399PhefsTer9	p.R1399Ffs*9	ENST00000257430	NM_000038.5	1397	GAg/g	16/16	1	2	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	1	0.234467760323704	2		300	279	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs770248150	NA	P-0038216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	88	329	0	ENST00000311936.3:c.351A>T	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaT	4/5	0.184686749353663	3	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	1	0.234467760323704	3		329	390	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	61	481	0	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	1	2	FACETS	0.95	0.82	1	0.95	0.82	1	CLONAL	1	TRUE	1	0.234467760323704	2		481	548	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249501	153249501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1316840275	NA	P-0038216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	46	486	1	ENST00000281708.4:c.1277C>T	p.Ser426Leu	p.S426L	ENST00000281708	NM_033632.3	426	tCa/tTa	9/12	1	2	FACETS	0.847	0.714	0.994	0.847	0.714	0.994	CLONAL	1	TRUE	1	0.234467760323704	2		487	463	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67462938	67462939	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	98	459	0	ENST00000327367.4:c.656dup	p.Leu219PhefsTer92	p.L219Ffs*92	ENST00000327367	NM_005902.3	218	-/T	5/9	0.199901144470701	2	FACETS	0.846	0.758	0.939	0.846	0.758	0.939	CLONAL	2	TRUE	0	0.234467760323704	2		459	494	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218520	5218520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs936142250	NA	P-0038216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	53	797	0	ENST00000357368.4:c.3959G>A	p.Arg1320His	p.R1320H	ENST00000357368	NM_002850.3	1320	cGc/cAc	25/38	1	2	FACETS	0.653	0.556	0.76	0.653	0.556	0.76	SUBCLONAL	1	TRUE	1	0.234467760323704	2		797	692	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0038217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	104	447	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.905	0.817	0.996	1	0.99	1	CLONAL	3	FALSE	1	0.19953540607885	2		447	384	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0038217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	31	280	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.19953540607885	3	FACETS	0.87	0.716	1	1	0.931	1	CLONAL	3	FALSE	1	0.19953540607885	3		281	131	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519998	NA	P-0038217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	68	583	0	ENST00000269305.4:c.581T>C	p.Leu194Pro	p.L194P	ENST00000269305	NM_001126112.2	194	cTt/cCt	6/11	1	2	FACETS	0.947	0.835	1	1	0.985	1	CLONAL	3	FALSE	1	0.19953540607885	2		583	240	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451561	70451561	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	16	429	0	ENST00000373644.4:c.6401A>G	p.His2134Arg	p.H2134R	ENST00000373644	NM_030625.2	2134	cAt/cGt	12/12	0.19953540607885	1	FACETS	0.476	0.352	0.626	0.476	0.352	0.626	SUBCLONAL	1	FALSE	0	0.19953540607885	1		429	303	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0038221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	202	587	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.92	0.862	0.978	0.92	0.862	0.978	CLONAL	1	TRUE	1	0.934576744684871	2		587	470	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039424	49039425	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	210	388	0	ENST00000267163.4:c.2410dup	p.Ile804AsnfsTer11	p.I804Nfs*11	ENST00000267163	NM_000321.2	803	-/A	23/27	0.934576744684871	1	FACETS	0.852	0.816	0.886	0.852	0.816	0.886	CLONAL	1	TRUE	0	0.934576744684871	1		388	281	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259067	153259068	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	57	161	0	ENST00000281708.4:c.747dup	p.Leu250IlefsTer6	p.L250Ifs*6	ENST00000281708	NM_033632.3	249	-/A	5/12	1	2	FACETS	0.853	0.751	0.958	0.853	0.751	0.958	CLONAL	1	TRUE	1	0.934576744684871	2		161	143	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0038227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	15	367	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.717	0.523	0.95	0.717	0.523	0.95	CLONAL	1	TRUE	1	0.13	2		367	322	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0038227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	8	363	1	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS	0.438	0.281	0.643	0.438	0.281	0.643	SUBCLONAL	1	TRUE	1	0.13	2		364	281	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0038227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	32	392	1	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	0.825	0.668	1	0.825	0.668	1	CLONAL	1	TRUE	1	0.13	2		393	597	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	29	301	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.84	0.673	1	0.84	0.673	1	CLONAL	1	TRUE	1	0.13	2		301	531	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772950	135772951	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs118203724	NA	P-0038227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	24	307	0	ENST00000298552.3:c.2672dup	p.Asn891LysfsTer13	p.N891Kfs*13	ENST00000298552	NM_001162426.1	891	aac/aaAc	21/23	1	2	FACETS	0.847	0.663	1	0.847	0.663	1	CLONAL	1	TRUE	1	0.13	2		307	436	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282115	38282115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554562012	NA	P-0038227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	51	598	0	ENST00000425967.3:c.941C>T	p.Pro314Leu	p.P314L	ENST00000425967	NM_001174067.1	314	cCg/cTg	8/19	1	2	FACETS	0.836	0.708	0.977	0.836	0.708	0.977	CLONAL	1	TRUE	1	0.13	2		598	939	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512402	38512402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	51	595	3	ENST00000254066.5:c.1319del	p.Pro440ArgfsTer203	p.P440Rfs*203	ENST00000254066	NM_000964.3	438	gCc/gc	9/9	1	2	FACETS	0.894	0.757	1	0.894	0.757	1	CLONAL	1	TRUE	1	0.13	2		598	878	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436044	51436044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	21	257	0	ENST00000262662.1:c.4G>A	p.Ala2Thr	p.A2T	ENST00000262662		2	Gcc/Acc	3/4	1	2	FACETS	0.862	0.663	1	0.862	0.663	1	CLONAL	1	TRUE	1	0.13	2		257	375	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437382	110437382	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1473105634	NA	P-0038227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	24	219	1	ENST00000375856.3:c.1019G>A	p.Arg340His	p.R340H	ENST00000375856	NM_003749.2	340	cGc/cAc	1/2	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.13	2		220	301	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647857	3647857	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773539191	NA	P-0038227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	57	587	1	ENST00000294008.3:c.1307C>T	p.Ala436Val	p.A436V	ENST00000294008	NM_032444.2	436	gCg/gTg	6/15	1	2	FACETS	0.925	0.791	1	0.925	0.791	1	CLONAL	1	TRUE	1	0.13	2		588	948	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39347514	39347514	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	59	441	0	ENST00000402219.2:c.50C>A	p.Pro17His	p.P17H	ENST00000402219	NM_005633.3	17	cCc/cAc	1/23	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.13	2		441	794	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902538	1902538	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	45	527	0	ENST00000382891.5:c.157C>A	p.Leu53Ile	p.L53I	ENST00000382891	NM_133335.3	53	Ctc/Atc	2/22	1	2	FACETS	0.792	0.663	0.935	0.792	0.663	0.935	CLONAL	1	TRUE	1	0.13	2		527	874	SUCCESS
APC	324	MSKCC	GRCh37	5	112103057	112103057	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	22	229	0	ENST00000257430.4:c.392C>A	p.Thr131Asn	p.T131N	ENST00000257430	NM_000038.5	131	aCt/aAt	4/16	1	2	FACETS	0.85	0.658	1	0.85	0.658	1	CLONAL	1	TRUE	1	0.13	2		229	398	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652077	36652077	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	68	594	0	ENST00000244741.5:c.199C>A	p.Arg67Ser	p.R67S	ENST00000244741	NM_000389.4	67	Cgt/Agt	2/3	1	2	FACETS	0.956	0.829	1	0.956	0.829	1	CLONAL	1	TRUE	1	0.13	2		594	1094	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555164	106555164	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	46	421	0	ENST00000369096.4:c.2281G>A	p.Ala761Thr	p.A761T	ENST00000369096	NM_001198.3	761	Gcc/Acc	7/7	1	2	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	TRUE	1	0.13	2		421	702	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372219	55372234	+	frameshift_variant	Frame_Shift_Del	DEL	CGGGGCGGGCGGCGGG	CGGGGCGGGCGGCGGG	-	novel	NA	P-0038227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	65	380	0	ENST00000297316.4:c.911_926del	p.Gly304AlafsTer78	p.G304Afs*78	ENST00000297316	NM_022454.3	303	ccCGGGGCGGGCGGCGGG/cc	2/2	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.13	2		380	753	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0038229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	41	482	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.783	0.658	0.919	0.783	0.658	0.919	CLONAL	1	TRUE	1	0.459295023434953	2		482	228	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0038236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	75	612	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.286318910559941	3	FACETS	1	0.968	1	0.659	0.578	0.744	CLONAL	1	TRUE	1	0.26	3		612	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0038236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	239	769	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.217042212665081	2	FACETS	0.94	0.878	1	0.94	0.878	1	CLONAL	2	TRUE	0	0.26	2		770	978	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0038236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	80	304	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	0.286318910559941	3	FACETS	1	0.977	1	0.749	0.662	0.842	CLONAL	1	TRUE	1	0.26	3		304	464	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911548	114911548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	73	533	0	ENST00000543371.1:c.1066G>A	p.Ala356Thr	p.A356T	ENST00000543371	NM_001198531.1	356	Gca/Aca	10/14	0.26974394264551	3	FACETS	0.95	0.831	1	0.475	0.415	0.54	CLONAL	1	TRUE	1	0.26	3		533	668	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031954	10031954	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199528312	NA	P-0038236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	119	752	1	ENST00000330684.3:c.869C>T	p.Ala290Val	p.A290V	ENST00000330684	NM_001134407.1	290	gCg/gTg	3/13	0.3	3	FACETS	1	0.924	1	0.515	0.464	0.569	CLONAL	1	TRUE	1	0.26	3		753	1004	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161846	47161846	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	87	402	0	ENST00000409792.3:c.4280T>G	p.Val1427Gly	p.V1427G	ENST00000409792	NM_014159.6	1427	gTt/gGt	3/21	0.26974394264551	3	FACETS	1	0.963	1	0.608	0.539	0.682	CLONAL	1	TRUE	1	0.26	3		402	622	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112276	115112292	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGTCCGTCTGCACCG	CGCGTCCGTCTGCACCG	-	novel	NA	P-0038237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	73	182	0	ENST00000257566.3:c.1448_1464del	p.Thr483SerfsTer203	p.T483Sfs*203	ENST00000257566	NM_016569.3	483	aCGGTGCAGACGGACGCG/a	7/8	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.744075202640885	2		182	183	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15978934	15978935	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0038237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	229	546	0	ENST00000268712.3:c.3583_3584del	p.Ser1195GlnfsTer3	p.S1195Qfs*3	ENST00000268712	NM_006311.3	1195	AGc/c	27/46	0.728001626804521	1	FACETS	0.871	0.823	0.918	0.871	0.823	0.918	CLONAL	1	TRUE	0	0.744075202640885	1		546	444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0038238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	939	447	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.795893519118611	3	FACETS	1	0.998	1	1	0.998	1	CLONAL	3	TRUE	0	0.795893519118611	3		447	1038	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564327	86564327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	36	569	0	ENST00000274376.6:c.59G>A	p.Gly20Glu	p.G20E	ENST00000274376	NM_002890.2	20	gGa/gAa	1/25	0.795893519118611	3	FACETS	0.183	0.15	0.221	0.092	0.075	0.111	SUBCLONAL	1	TRUE	1	0.795893519118611	3		569	691	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137696	64137696	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0038238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	289	748	0	ENST00000334205.4:c.1798-1G>A		p.X600_splice	ENST00000334205	NM_003942.2	600			0.795893519118611	3	FACETS	0.97	0.913	1	0.485	0.456	0.514	CLONAL	1	TRUE	1	0.795893519118611	3		748	1047	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369209	118369209	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	173	426	0	ENST00000534358.1:c.5927A>G	p.Tyr1976Cys	p.Y1976C	ENST00000534358	NM_005933.3	1976	tAt/tGt	22/36	0.795893519118611	3	FACETS	0.945	0.874	1	0.473	0.437	0.51	CLONAL	1	TRUE	1	0.795893519118611	3		426	643	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346373	89346373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	170	697	0	ENST00000301030.4:c.6577G>A	p.Asp2193Asn	p.D2193N	ENST00000301030	NM_001256183.1	2193	Gac/Aac	9/13	0.486081583580373	3	FACETS	0.788	0.726	0.852	0.394	0.363	0.426	SUBCLONAL	1	TRUE	1	0.795893519118611	3		697	758	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748003	41748003	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	31	51	0	ENST00000226382.2:c.766G>T	p.Ala256Ser	p.A256S	ENST00000226382	NM_003924.3	256	Gca/Tca	3/3	0.795893519118611	3	FACETS	1	0.947	1	0.698	0.586	0.815	CLONAL	1	TRUE	1	0.795893519118611	3		51	78	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286160	66286160	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	95	287	0	ENST00000273854.3:c.1526del	p.Lys509ArgfsTer22	p.K509Rfs*22	ENST00000273854	NM_004439.5	509	aAg/ag	6/18	0.795893519118611	3	FACETS	0.824	0.739	0.914	0.412	0.369	0.457	CLONAL	1	TRUE	1	0.795893519118611	3		287	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0038239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	222	447	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.518983204456238	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.518983204456238	1		447	619	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604789	48604789	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	137	479	0	ENST00000342988.3:c.1611C>G	p.Asp537Glu	p.D537E	ENST00000342988	NM_005359.5	537	gaC/gaG	12/12	0.518983204456238	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.518983204456238	1		479	368	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118885	70118885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	211	623	2	ENST00000245479.2:c.457C>T	p.Pro153Ser	p.P153S	ENST00000245479	NM_000346.3	153	Ccc/Tcc	2/3	0.518983204456238	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.518983204456238	1		625	508	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857476	9857476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145602289	NA	P-0038239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	141	547	1	ENST00000330684.3:c.3925C>T	p.Arg1309Trp	p.R1309W	ENST00000330684	NM_001134407.1	1309	Cgg/Tgg	13/13	1	2	FACETS	0.937	0.857	1	0.937	0.857	1	CLONAL	1	TRUE	1	0.518983204456238	2		548	580	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4387952	4387952	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	814	584	0	ENST00000261254.3:c.438G>C	p.Lys146Asn	p.K146N	ENST00000261254	NM_001759.3	146	aaG/aaC	3/5	0.518983204456238	5	FACETS	1	0.993	1	1	0.993	1	CLONAL	4	TRUE	1	0.518983204456238	5		584	1318	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392119	81392119	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	100	323	0	ENST00000222390.5:c.158T>G	p.Ile53Arg	p.I53R	ENST00000222390	NM_000601.4	53	aTa/aGa	2/18	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.518983204456238	2		323	383	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517201	NA	P-0038240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	135	424	0	ENST00000263967.3:c.1637A>C	p.Gln546Pro	p.Q546P	ENST00000263967	NM_006218.2	546	cAg/cCg	10/21	0.485341040013279	2	FACETS	1	0.959	1	0.541	0.495	0.589	CLONAL	1	TRUE	0	0.495962770410287	2		424	503	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259397	11259397	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	419	680	0	ENST00000361445.4:c.4171C>G	p.Arg1391Gly	p.R1391G	ENST00000361445	NM_004958.3	1391	Cga/Gga	28/58	0.439961926688528	3	FACETS	0.853	0.813	0.894	0.853	0.813	0.894	CLONAL	2	TRUE	1	0.495962770410287	3		680	1236	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577515	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	560	727	0	ENST00000269305.4:c.766del	p.Thr256HisfsTer89	p.T256Hfs*89	ENST00000269305	NM_001126112.2	256	Aca/ca	7/11	0.369965385768241	3	FACETS	1	0.994	1	0.77	0.741	0.799	CLONAL	2	TRUE	0	0.495962770410287	3		727	1220	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211660	36211660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	584	678	0	ENST00000222270.7:c.1411C>T	p.Arg471Trp	p.R471W	ENST00000222270	NM_014727.1	471	Cgg/Tgg	3/37	0.495962770410287	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.495962770410287	3		678	1409	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433333	78433333	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	48	534	0	ENST00000370768.2:c.268C>G	p.Pro90Ala	p.P90A	ENST00000370768	NM_003902.3	90	Cca/Gca	4/20	1	2	FACETS	0.429	0.363	0.502	0.429	0.363	0.502	SUBCLONAL	1	TRUE	1	0.495962770410287	2		534	451	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857364	68857369	+	inframe_deletion	In_Frame_Del	DEL	CTCAAG	CTCAAG	-	novel	NA	P-0038240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	74	606	0	ENST00000261769.5:c.2003_2008del	p.Lys668_Leu669del	p.K668_L669del	ENST00000261769	NM_004360.3	667	CTCAAG/-	13/16	NA	2	FACETS	0.319	0.279	0.364			1	INDETERMINATE	1	TRUE	NA	0.495962770410287	2		606	934	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0038241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	29	465	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.85	0.681	1	0.85	0.681	1	CLONAL	1	TRUE	1	0.11	2		465	620	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397740	49397740	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	49	657	0	ENST00000418115.1:c.484A>G	p.Lys162Glu	p.K162E	ENST00000418115	NM_001664.2	162	Aag/Gag	5/5	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.11	2		657	883	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732930	30732931	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0038241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	23	412	0	ENST00000295754.5:c.1545_1546del	p.Glu515AspfsTer4	p.E515Dfs*4	ENST00000295754	NM_003242.5	515	GAg/g	7/7	1	2	FACETS	0.961	0.748	1	0.961	0.748	1	CLONAL	1	TRUE	1	0.11	2		412	435	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0038243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	201	363	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	1	2	FACETS	0.861	0.806	0.918	0.861	0.806	0.918	CLONAL	1	TRUE	1	0.918826177970405	2		363	508	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562746	29562746	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs199474742	NA	P-0038243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	325	492	0	ENST00000356175.3:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000356175	NM_000267.3	1276	Cga/Tga	28/57	0.918826177970405	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.918826177970405	1		492	352	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375975	118375975	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	330	673	0	ENST00000534358.1:c.9368C>T	p.Ser3123Leu	p.S3123L	ENST00000534358	NM_005933.3	3123	tCa/tTa	27/36	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.918826177970405	2		673	705	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503838	149503838	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs864309711	NA	P-0038244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	778	701	0	ENST00000261799.4:c.1998C>A	p.Asn666Lys	p.N666K	ENST00000261799	NM_002609.3	666	aaC/aaA	14/23	0.719290972757329	3	FACETS	0.998	0.968	1	0.998	0.968	1	CLONAL	2	TRUE	1	0.719290972757329	3		701	1474	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891466	76891466	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	399	336	1	ENST00000373344.5:c.4639G>T	p.Glu1547Ter	p.E1547*	ENST00000373344	NM_000489.3	1547	Gaa/Taa	16/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.719290972757329	1		337	547	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0038245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	117	862	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.507	0.456	0.56	0.507	0.456	0.56	SUBCLONAL	1	FALSE	1	0.490426045823821	2		864	942	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023897	27023897	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	38	105	0	ENST00000324856.7:c.1003C>A	p.Gln335Lys	p.Q335K	ENST00000324856	NM_006015.4	335	Cag/Aag	1/20	1	2	FACETS	0.752	0.628	0.888	0.752	0.628	0.888	SUBCLONAL	1	FALSE	1	0.490426045823821	2		105	206	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195413	102195413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	38	360	0	ENST00000263464.3:c.173C>T	p.Thr58Ile	p.T58I	ENST00000263464	NM_001165.4	58	aCt/aTt	2/9	1	2	FACETS	0.236	0.194	0.282	0.236	0.194	0.282	SUBCLONAL	1	FALSE	1	0.490426045823821	2		360	658	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929182	32929182	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	120	487	0	ENST00000380152.3:c.7192A>C	p.Thr2398Pro	p.T2398P	ENST00000380152		2398	Act/Cct	14/27	1	2	FACETS	0.517	0.466	0.571	0.517	0.466	0.571	SUBCLONAL	1	FALSE	1	0.490426045823821	2		487	947	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210444	36210444	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0038245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	117	544	0	ENST00000222270.7:c.436+1G>A		p.X146_splice	ENST00000222270	NM_014727.1	146			1	2	FACETS	0.504	0.454	0.558	0.504	0.454	0.558	SUBCLONAL	1	FALSE	1	0.490426045823821	2		544	946	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051174	128051174	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759337466	NA	P-0038245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	62	654	0	ENST00000285398.2:c.149G>A	p.Gly50Asp	p.G50D	ENST00000285398	NM_000122.1	50	gGc/gAc	2/15	1	2	FACETS	0.237	0.204	0.274	0.237	0.204	0.274	SUBCLONAL	1	FALSE	1	0.490426045823821	2		654	1065	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818198	32818198	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746163946	NA	P-0038245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	66	615	1	ENST00000354258.4:c.1327G>A	p.Glu443Lys	p.E443K	ENST00000354258	NM_000593.5	443	Gag/Aag	5/11	1	2	FACETS	0.234	0.202	0.269	0.234	0.202	0.269	SUBCLONAL	1	FALSE	1	0.490426045823821	2		616	1150	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0038246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	151	564	3	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.894	0.817	0.974	0.894	0.817	0.974	CLONAL	1	TRUE	1	0.38	2		567	889	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0038246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	63	780	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	1	2	FACETS	0.285	0.245	0.328	0.285	0.245	0.328	SUBCLONAL	1	TRUE	1	0.38	2		780	1164	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0038246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	109	426	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	1	2	FACETS	0.905	0.814	1	0.905	0.814	1	CLONAL	1	TRUE	1	0.38	2		426	634	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0038246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	106	796	7	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.784	0.703	0.869	0.784	0.703	0.869	SUBCLONAL	1	TRUE	1	0.38	2		803	712	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332739	153332739	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	157	524	0	ENST00000281708.4:c.217C>T	p.Gln73Ter	p.Q73*	ENST00000281708	NM_033632.3	73	Cag/Tag	2/12	1	2	FACETS	0.991	0.908	1	0.991	0.908	1	CLONAL	1	TRUE	1	0.38	2		524	834	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785525	50785525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219465670	NA	P-0038246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	151	579	0	ENST00000398568.2:c.515G>A	p.Arg172His	p.R172H	ENST00000398568	NM_001042412.1	172	cGt/cAt	4/18	1	2	FACETS	0.912	0.834	0.994	0.912	0.834	0.994	CLONAL	1	TRUE	1	0.38	2		579	871	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120279	70120280	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0038246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	214	749	0	ENST00000245479.2:c.1282_1283dup	p.Ser429ThrfsTer42	p.S429Tfs*42	ENST00000245479	NM_000346.3	427	-/TA	3/3	1	2	FACETS	0.877	0.814	0.943	0.877	0.814	0.943	CLONAL	1	TRUE	1	0.38	2		749	1284	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371723	45371723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	117	421	0	ENST00000262160.6:c.1268G>A	p.Gly423Glu	p.G423E	ENST00000262160	NM_005901.5	423	gGa/gAa	10/11	1	2	FACETS	0.881	0.795	0.971	0.881	0.795	0.971	CLONAL	1	TRUE	1	0.38	2		421	699	SUCCESS
APC	324	MSKCC	GRCh37	5	112174685	112174685	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	100	382	0	ENST00000257430.4:c.3394G>T	p.Glu1132Ter	p.E1132*	ENST00000257430	NM_000038.5	1132	Gaa/Taa	16/16	1	2	FACETS	0.904	0.81	1	0.904	0.81	1	CLONAL	1	TRUE	1	0.38	2		382	582	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056032	26056032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754560095	NA	P-0038246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	98	388	0	ENST00000343677.2:c.625G>A	p.Ala209Thr	p.A209T	ENST00000343677	NM_005319.3	209	Gcg/Acg	1/1	1	2	FACETS	0.85	0.759	0.945	0.85	0.759	0.945	CLONAL	1	TRUE	1	0.38	2		388	607	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954187	48954187	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	rs1555286568	NA	P-0038247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	117	208	0	ENST00000267163.4:c.1390-2A>C		p.X464_splice	ENST00000267163	NM_000321.2	464			0.742468076020273	2	FACETS	0.825	0.768	0.881	0.825	0.768	0.881	CLONAL	2	TRUE	0	0.742468076020273	2		208	191	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579461	7579467	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGGGC	CAGGGGC	-	novel	NA	P-0038247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	801	758	3	ENST00000269305.4:c.220_226del	p.Ala74HisfsTer47	p.A74Hfs*47	ENST00000269305	NM_001126112.2	74	GCCCCTGca/ca	4/11	0.742468076020273	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.742468076020273	2		761	1048	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394091	31394091	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	283	460	0	ENST00000328111.2:c.2378T>C	p.Met793Thr	p.M793T	ENST00000328111	NM_006892.3	793	aTg/aCg	22/23	1	2	FACETS	0.972	0.918	1	0.972	0.918	1	CLONAL	1	TRUE	1	0.742468076020273	2		460	784	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861051	35861051	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	502	322	0	ENST00000303115.3:c.180G>T	p.Glu60Asp	p.E60D	ENST00000303115	NM_002185.3	60	gaG/gaT	2/8	0.558370160752853	4	FACETS	0.934	0.902	0.965	0.934	0.902	0.965	CLONAL	3	TRUE	1	0.742468076020273	4		322	841	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878849	117878849	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	134	399	0	ENST00000297338.2:c.120C>G	p.Ser40Arg	p.S40R	ENST00000297338	NM_006265.2	40	agC/agG	2/14	1	2	FACETS	0.628	0.573	0.685	0.628	0.573	0.685	SUBCLONAL	1	TRUE	1	0.742468076020273	2		399	575	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76777866	76777866	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	215	236	0	ENST00000373344.5:c.6850G>T	p.Gly2284Ter	p.G2284*	ENST00000373344	NM_000489.3	2284	Gga/Tga	32/35	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.742468076020273	1		236	333	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867041	45867041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	243	571	0	ENST00000391945.4:c.1078G>A	p.Gly360Ser	p.G360S	ENST00000391945	NM_000400.3	360	Ggc/Agc	11/23	0.551769776133695	1	FACETS	0.982	0.927	1	0.982	0.927	1	CLONAL	1	TRUE	0	0.641525662395633	1		571	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578525	7578525	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519976	NA	P-0038252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	302	1117	2	ENST00000269305.4:c.405C>G	p.Cys135Trp	p.C135W	ENST00000269305	NM_001126112.2	135	tgC/tgG	5/11	0.641525662395633	1	FACETS	0.996	0.947	1	0.996	0.947	1	CLONAL	1	TRUE	0	0.641525662395633	1		1119	642	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441436	52441436	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	55	492	0	ENST00000460680.1:c.416del	p.Lys139ArgfsTer48	p.K139Rfs*48	ENST00000460680	NM_004656.3	139	aAg/ag	6/17	0.641525662395633	1	FACETS	0.308	0.264	0.356	0.308	0.264	0.356	SUBCLONAL	1	TRUE	0	0.641525662395633	1		492	378	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0038254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	74	701	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.813	0.718	0.913	0.813	0.718	0.913	CLONAL	1	TRUE	1	0.591205946282721	2		701	308	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0038254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	118	340	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.591205946282721	3	FACETS	0.816	0.746	0.887	0.816	0.746	0.887	CLONAL	2	TRUE	1	0.591205946282721	3		340	317	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615045	43615045	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	244	712	1	ENST00000355710.3:c.2459G>A	p.Arg820His	p.R820H	ENST00000355710	NM_020975.4	820	cGc/cAc	14/20	0.591205946282721	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.591205946282721	3		713	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0038255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	82	637	1	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	1	2	FACETS	0.817	0.72	0.922	0.817	0.72	0.922	CLONAL	1	TRUE	1	0.261696000420457	2		638	767	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847198	68847218	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CATCTCTTTGCTCTGCAGTAC	CATCTCTTTGCTCTGCAGTAC	-	novel	NA	P-0038255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	71	376	0	ENST00000261769.5:c.1138-18_1140del		p.X380_splice	ENST00000261769	NM_004360.3	380		9/16	NA	2	FACETS	1	0.937	1			1	INDETERMINATE	1	TRUE	NA	0.261696000420457	2		376	487	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0038258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	91	482	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		482	462	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0038258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	106	701	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		701	469	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602493	10602493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	389	566	0	ENST00000171111.5:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000171111	NM_203500.1	362	cGg/cAg	3/6	0.645054938814904	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.645054938814904	1		566	717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0038259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	326	551	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	0.645054938814904	1	FACETS	0.975	0.929	1	0.975	0.929	1	CLONAL	1	TRUE	0	0.645054938814904	1		551	702	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170761	11170761	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1948	395	623	0	ENST00000358026.2:c.4905del	p.Lys1636ArgfsTer6	p.K1636Rfs*6	ENST00000358026	NM_001128849.1	1635	gaG/ga	35/36	0.645054938814904	5	FACETS	1	0.966	1	0.257	0.243	0.272	CLONAL	1	TRUE	1	0.645054938814904	5		623	2343	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0038260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	197	918	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.327617270056437	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.327617270056437	2		919	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0038260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	230	705	1	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.280203270288049	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.327617270056437	1		706	980	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044967	47044967	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	227	708	0	ENST00000377604.3:c.2293C>T	p.Arg765Ter	p.R765*	ENST00000377604	NM_001204468.1	765	Cga/Tga	20/24	0.327617270056437	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.327617270056437	1		708	1006	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223057	1223063	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCGCA	TGGCGCA	GGGCG	novel	NA	P-0038260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	310	700	2	ENST00000326873.7:c.994_1000delinsGGGCG	p.Trp332GlyfsTer27	p.W332Gfs*27	ENST00000326873	NM_000455.4	332	TGGCGCAgc/GGGCGgc	8/10	0.276695411437073	2	FACETS	0.914	0.863	0.966	0.914	0.863	0.966	CLONAL	2	TRUE	0	0.327617270056437	2		702	1035	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602417	10602418	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	308	762	0	ENST00000171111.5:c.1160dup	p.Asn387LysfsTer28	p.N387Kfs*28	ENST00000171111	NM_203500.1	387	aac/aaAc	3/6	0.273637560646429	2	FACETS	0.921	0.869	0.973	0.921	0.869	0.973	CLONAL	2	TRUE	0	0.327617270056437	2		762	1021	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0038261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	66	387	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	1	2	FACETS	0.415	0.36	0.475	0.415	0.36	0.475	SUBCLONAL	1	TRUE	1	0.524457421399972	2		387	606	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241042	133241042	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	41	437	0	ENST00000320574.5:c.2475del	p.Trp826GlyfsTer24	p.W826Gfs*24	ENST00000320574	NM_006231.2	825	cgC/cg	22/49	1	2	FACETS	0.292	0.242	0.347	0.292	0.242	0.347	SUBCLONAL	1	TRUE	1	0.524457421399972	2		437	536	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185870	32185870	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs765298875	NA	P-0038261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	34	552	0	ENST00000375023.3:c.1526T>C	p.Leu509Pro	p.L509P	ENST00000375023	NM_004557.3	509	cTc/cCc	9/30	1	2	FACETS	0.21	0.171	0.255	0.21	0.171	0.255	SUBCLONAL	1	TRUE	1	0.524457421399972	2		552	616	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006099	22006099	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	69	413	0	ENST00000276925.6:c.304del	p.Ala102ProfsTer63	p.A102Pfs*63	ENST00000276925	NM_004936.3	102	Gcc/cc	2/2	1	2	FACETS	0.447	0.39	0.51	0.447	0.39	0.51	SUBCLONAL	1	TRUE	1	0.524457421399972	2		413	588	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	232	882	1	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.711013202090953	3	FACETS	0.882	0.823	0.943	0.441	0.411	0.472	CLONAL	1	TRUE	1	0.711013202090953	3		883	1003	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579381	7579381	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	909	683	0	ENST00000269305.4:c.306del	p.Tyr103ThrfsTer20	p.Y103Tfs*20	ENST00000269305	NM_001126112.2	102	acC/ac	4/11	0.711013202090953	3	FACETS	0.958	0.939	0.977			1	CLONAL	3	TRUE	NA	0.711013202090953	3		683	1206	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362015	118362015	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	190	322	0	ENST00000534358.1:c.4801A>G	p.Asn1601Asp	p.N1601D	ENST00000534358	NM_005933.3	1601	Aat/Gat	14/36	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.711013202090953	2		322	517	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68878212	68878212	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	128	342	0	ENST00000487270.1:c.925A>T	p.Ile309Phe	p.I309F	ENST00000487270	NM_133509.3	309	Atc/Ttc	9/11	1	2	FACETS	0.657	0.598	0.719	0.657	0.598	0.719	SUBCLONAL	1	TRUE	1	0.711013202090953	2		342	548	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369283	40369283	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	279	442	0	ENST00000293328.3:c.1275G>C	p.Lys425Asn	p.K425N	ENST00000293328	NM_012448.3	425	aaG/aaC	11/19	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.711013202090953	2		442	765	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008964	152008964	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	206	453	0	ENST00000262189.6:c.658C>T	p.Gln220Ter	p.Q220*	ENST00000262189	NM_170606.2	220	Caa/Taa	5/59	NA	2	FACETS	0.857	0.799	0.917			1	INDETERMINATE	1	TRUE	NA	0.711013202090953	2		453	676	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0038264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	306	842	0	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	0.268442039382159	3	FACETS	1	0.984	1	0.729	0.691	0.768	CLONAL	2	TRUE	0	0.436858445167143	3		842	780	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402690	139402690	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs41309764	NA	P-0038264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	277	794	0	ENST00000277541.6:c.3319C>T	p.Arg1107Ter	p.R1107*	ENST00000277541	NM_017617.3	1107	Cga/Tga	20/34	0.436858445167143	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.436858445167143	2		794	633	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910617	29910617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199474377	NA	P-0038264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	140	820	0	ENST00000376809.5:c.157G>A	p.Asp53Asn	p.D53N	ENST00000376809	NM_002116.7	53	Gac/Aac	2/8	0.296390777783098	3	FACETS	1	0.964	1	0.369	0.337	0.403	CLONAL	1	TRUE	0	0.436858445167143	3		820	705	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549788	187549788	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	72	455	0	ENST00000441802.2:c.4453G>A	p.Glu1485Lys	p.E1485K	ENST00000441802	NM_005245.3	1485	Gag/Aag	8/27	0.437279019868829	3	FACETS	1	0.92	1	0.354	0.311	0.4	CLONAL	1	TRUE	0	0.436858445167143	3		455	378	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400794	72400794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	61	375	0	ENST00000357731.5:c.377C>T	p.Pro126Leu	p.P126L	ENST00000357731	NM_173808.2	126	cCc/cTc	2/7	0.396911858564291	3	FACETS	0.972	0.843	1	0.486	0.421	0.556	CLONAL	1	TRUE	1	0.436858445167143	3		375	350	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253843	30253843	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568844220	NA	P-0038264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	201	673	0	ENST00000307677.4:c.611G>A	p.Arg204Gln	p.R204Q	ENST00000307677	NM_138578.1	204	cGa/cAa	3/3	0.437279019868829	5	FACETS	0.957	0.889	1	0.638	0.592	0.685	CLONAL	2	TRUE	2	0.436858445167143	5		673	796	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518865	187518865	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	287	571	0	ENST00000441802.2:c.12339T>G	p.Cys4113Trp	p.C4113W	ENST00000441802	NM_005245.3	4113	tgT/tgG	24/27	0.437279019868829	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.436858445167143	3		571	494	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205641	38205641	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2607	145	736	1	ENST00000317025.8:c.49C>T	p.Gln17Ter	p.Q17*	ENST00000317025	NM_023034.1	17	Cag/Tag	2/24	0.436858445167143	16	FACETS	0.979	0.888	1			1	CLONAL	1	TRUE	NA	0.436858445167143	16		737	2752	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0038266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	445	952	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.760261670074566	5	FACETS	0.835	0.8	0.871	0.835	0.8	0.871	CLONAL	3	TRUE	2	0.760261670074566	5		952	1000	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579494	7579494	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1555526721	NA	P-0038266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	666	815	0	ENST00000269305.4:c.193A>T	p.Arg65Ter	p.R65*	ENST00000269305	NM_001126112.2	65	Aga/Tga	4/11	0.760261670074566	2	FACETS	0.984	0.961	1	0.984	0.961	1	CLONAL	2	TRUE	0	0.760261670074566	2		815	890	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878151	48878151	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778869	NA	P-0038266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	59	118	1	ENST00000267163.4:c.103C>T	p.Gln35Ter	p.Q35*	ENST00000267163	NM_000321.2	35	Cag/Tag	1/27	0.75984965684031	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.760261670074566	1		119	94	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777925	27777925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1269049636	NA	P-0038266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	154	372	0	ENST00000369163.2:c.74C>T	p.Ala25Val	p.A25V	ENST00000369163	NM_003536.2	25	gCg/gTg	1/1	0.760261670074566	3	FACETS	0.822	0.755	0.893	0.411	0.377	0.447	CLONAL	1	TRUE	1	0.760261670074566	3		372	680	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0038267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	216	680	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.469545034825404	3	FACETS	1	0.984	1			1	CLONAL	2	TRUE	NA	0.547246291575125	3		680	445	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763912	76763912	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs782540364	NA	P-0038267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	194	1079	1	ENST00000373344.5:c.7396G>T	p.Gly2466Cys	p.G2466C	ENST00000373344	NM_000489.3	2466	Ggt/Tgt	35/35	0.234054376889733	1	FACETS	0.684	0.634	0.735	0.684	0.634	0.735	INDETERMINATE	1	TRUE	0	0.547246291575125	1		1080	753	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540652	NA	P-0038268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	130	532	2	ENST00000269305.4:c.743G>C	p.Arg248Pro	p.R248P	ENST00000269305	NM_001126112.2	248	cGg/cCg	7/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.239420404293002	2		534	806	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0038268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	30	427	0	ENST00000311936.3:c.34_35delinsTT	p.Gly12Phe	p.G12F	ENST00000311936	NM_004985.3	12	GGt/TTt	2/5	1	2	FACETS	0.539	0.434	0.659	0.539	0.434	0.659	SUBCLONAL	1	TRUE	1	0.239420404293002	2		427	465	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539513	187539513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	29	379	0	ENST00000441802.2:c.8227C>T	p.Pro2743Ser	p.P2743S	ENST00000441802	NM_005245.3	2743	Cca/Tca	10/27	1	2	FACETS	0.489	0.392	0.601	0.489	0.392	0.601	SUBCLONAL	1	TRUE	1	0.239420404293002	2		379	495	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220506	1220506	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0038268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	75	635	0	ENST00000326873.7:c.597+2T>A		p.X199_splice	ENST00000326873	NM_000455.4	199			0.239420404293002	1	FACETS	0.922	0.809	1	0.922	0.809	1	CLONAL	1	TRUE	0	0.239420404293002	1		635	598	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249229	10249229	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766051225	NA	P-0038268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	80	593	0	ENST00000340748.4:c.3953C>T	p.Ala1318Val	p.A1318V	ENST00000340748		1318	gCg/gTg	34/40	0.239420404293002	1	FACETS	0.994	0.876	1	0.994	0.876	1	CLONAL	1	TRUE	0	0.239420404293002	1		593	592	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739391	46739391	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	60	445	0	ENST00000371975.4:c.1582C>G	p.Leu528Val	p.L528V	ENST00000371975	NM_003579.3	528	Ctc/Gtc	14/18	1	2	FACETS	0.751	0.647	0.866	0.751	0.647	0.866	SUBCLONAL	1	TRUE	1	0.239420404293002	2		445	667	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610369	10610369	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	118	689	1	ENST00000171111.5:c.341G>T	p.Gly114Val	p.G114V	ENST00000171111	NM_203500.1	114	gGg/gTg	2/6	0.239420404293002	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.239420404293002	1		690	787	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871956	45871956	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	60	620	0	ENST00000391945.4:c.292G>T	p.Glu98Ter	p.E98*	ENST00000391945	NM_000400.3	98	Gag/Tag	5/23	1	2	FACETS	0.683	0.587	0.787	0.683	0.587	0.787	SUBCLONAL	1	TRUE	1	0.239420404293002	2		620	734	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142950	30142950	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	90	695	0	ENST00000389048.3:c.576G>T	p.Glu192Asp	p.E192D	ENST00000389048	NM_004304.4	192	gaG/gaT	1/29	1	2	FACETS	0.946	0.838	1	0.946	0.838	1	CLONAL	1	TRUE	1	0.239420404293002	2		695	795	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561250	9561250	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	70	471	0	ENST00000353224.5:c.532G>T	p.Gly178Trp	p.G178W	ENST00000353224	NM_177990.2	178	Ggg/Tgg	4/10	0.155546778518052	3	FACETS	1	0.931	1	0.552	0.481	0.628	CLONAL	1	TRUE	1	0.239420404293002	3		471	593	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533686	41533686	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	65	522	0	ENST00000263253.7:c.1652C>G	p.Pro551Arg	p.P551R	ENST00000263253	NM_001429.3	551	cCc/cGc	8/31	1	2	FACETS	0.772	0.669	0.885	0.772	0.669	0.885	SUBCLONAL	1	TRUE	1	0.239420404293002	2		522	703	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272756	142272756	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs768453013	NA	P-0038268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	56	513	0	ENST00000350721.4:c.2443G>T	p.Asp815Tyr	p.D815Y	ENST00000350721	NM_001184.3	815	Gat/Tat	11/47	1	2	FACETS	0.818	0.701	0.946	0.818	0.701	0.946	CLONAL	1	TRUE	1	0.239420404293002	2		513	572	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939030	76939030	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	53	550	0	ENST00000373344.5:c.1718G>T	p.Gly573Val	p.G573V	ENST00000373344	NM_000489.3	573	gGt/gTt	9/35	1	2	FACETS	0.668	0.569	0.777	0.668	0.569	0.777	SUBCLONAL	1	TRUE	1	0.239420404293002	2		550	663	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0038269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	84	403	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.176408583198967	1	FACETS	0.572	0.507	0.641	0.572	0.507	0.641	INDETERMINATE	1	TRUE	0	0.462787915797907	1		403	488	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193172931	193172931	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	48	338	0	ENST00000367435.3:c.979G>T	p.Ala327Ser	p.A327S	ENST00000367435	NM_024529.4	327	Gca/Tca	11/17	0.462787915797907	3	FACETS	0.464	0.392	0.544	0.232	0.196	0.272	SUBCLONAL	1	TRUE	1	0.462787915797907	3		338	550	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852089	63852089	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	81	563	0	ENST00000279873.7:c.2867G>T	p.Arg956Leu	p.R956L	ENST00000279873	NM_032199.2	956	cGg/cTg	10/10	1	2	FACETS	0.459	0.404	0.518	0.459	0.404	0.518	SUBCLONAL	1	TRUE	1	0.462787915797907	2		563	763	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186748	108186748	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	133	417	0	ENST00000278616.4:c.6106T>C	p.Tyr2036His	p.Y2036H	ENST00000278616	NM_000051.3	2036	Tat/Cat	42/63	0.462787915797907	1	FACETS	0.977	0.895	1	0.977	0.895	1	CLONAL	1	TRUE	0	0.462787915797907	1		417	452	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112472	115112472	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	124	535	0	ENST00000257566.3:c.1268G>T	p.Arg423Leu	p.R423L	ENST00000257566	NM_016569.3	423	cGg/cTg	7/8	1	2	FACETS	0.814	0.738	0.894	0.814	0.738	0.894	CLONAL	1	TRUE	1	0.462787915797907	2		535	658	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462547	29462547	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1441640593	NA	P-0038269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	164	451	1	ENST00000389048.3:c.2354G>A	p.Ser785Asn	p.S785N	ENST00000389048	NM_004304.4	785	aGt/aAt	13/29	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.462787915797907	2		452	669	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1331447	1331447	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0038269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	83	454	0	ENST00000400841.2:c.79+2T>C		p.X27_splice	ENST00000400841		27			1	2	FACETS	0.677	0.599	0.76	0.677	0.599	0.76	SUBCLONAL	1	TRUE	1	0.462787915797907	2		454	530	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954198	48954198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123331	NA	P-0038270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	357	217	0	ENST00000267163.4:c.1399C>T	p.Arg467Ter	p.R467*	ENST00000267163	NM_000321.2	467	Cga/Tga	15/27	0.792896585962677	5	FACETS	0.981	0.959	1	0.981	0.959	1	CLONAL	5	TRUE	0	0.792896585962677	5		217	402	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517201	NA	P-0038270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	684	424	0	ENST00000263967.3:c.1637A>C	p.Gln546Pro	p.Q546P	ENST00000263967	NM_006218.2	546	cAg/cCg	10/21	0.792896585962677	8	FACETS	0.979	0.946	1	0.652	0.63	0.675	CLONAL	4	TRUE	2	0.792896585962677	8		424	1489	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354330	354330	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	389	672	0	ENST00000262320.3:c.1228G>T	p.Glu410Ter	p.E410*	ENST00000262320	NM_003502.3	410	Gag/Tag	5/11	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	2	TRUE	NA	0.792896585962677	2		672	481	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659851	227659851	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	152	489	0	ENST00000305123.5:c.3604C>T	p.Pro1202Ser	p.P1202S	ENST00000305123	NM_005544.2	1202	Ccc/Tcc	1/2	0.792896585962677	3	FACETS	0.991	0.912	1	0.496	0.456	0.537	CLONAL	1	TRUE	1	0.792896585962677	3		489	540	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843495	3843495	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1384496494	NA	P-0038270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	227	546	0	ENST00000262367.5:c.1108C>G	p.Arg370Gly	p.R370G	ENST00000262367	NM_004380.2	370	Cga/Gga	4/31	0.792896585962677	3	FACETS	1	0.985	1	0.584	0.546	0.622	CLONAL	1	TRUE	1	0.792896585962677	3		546	685	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462884	120462884	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	197	357	0	ENST00000256646.2:c.5447T>C	p.Val1816Ala	p.V1816A	ENST00000256646	NM_024408.3	1816	gTg/gCg	30/34	0.792896585962677	3	FACETS	0.956	0.901	1	0.956	0.901	1	CLONAL	2	TRUE	1	0.792896585962677	3		357	363	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253191	133253191	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	191	554	0	ENST00000320574.5:c.850A>C	p.Lys284Gln	p.K284Q	ENST00000320574	NM_006231.2	284	Aag/Cag	9/49	0.792896585962677	3	FACETS	1	0.946	1	0.511	0.475	0.549	CLONAL	1	TRUE	1	0.792896585962677	3		554	658	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577137	7577152	+	frameshift_variant	Frame_Shift_Del	DEL	CCGTCCCAGTAGATTA	CCGTCCCAGTAGATTA	-	novel	NA	P-0038270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	352	561	0	ENST00000269305.4:c.786_801del	p.Asn263ThrfsTer77	p.N263Tfs*77	ENST00000269305	NM_001126112.2	262	ggTAATCTACTGGGACGG/gg	8/11	0.792896585962677	2	FACETS	0.955	0.924	0.984	0.955	0.924	0.984	CLONAL	2	TRUE	0	0.792896585962677	2		561	465	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474104	29474104	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	361	542	1	ENST00000389048.3:c.2071A>T	p.Ser691Cys	p.S691C	ENST00000389048	NM_004304.4	691	Agc/Tgc	12/29	0.792896585962677	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.792896585962677	3		543	598	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225343015	225343015	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	334	482	0	ENST00000264414.4:c.2077C>T	p.Gln693Ter	p.Q693*	ENST00000264414	NM_003590.4	693	Cag/Tag	15/16	0.792896585962677	3	FACETS	0.969	0.927	1	0.969	0.927	1	CLONAL	2	TRUE	1	0.792896585962677	3		482	607	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391088	89391088	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	417	601	0	ENST00000336596.2:c.1154G>T	p.Arg385Leu	p.R385L	ENST00000336596	NM_005233.5	385	cGa/cTa	5/17	0.792896585962677	2	FACETS	0.989	0.961	1	0.989	0.961	1	CLONAL	2	TRUE	0	0.792896585962677	2		601	532	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176684102	176684103	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTGTATAACCTGTCATG	novel	NA	P-0038270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	144	462	0	ENST00000439151.2:c.4920_4936dup	p.Ala1646ValfsTer2	p.A1646Vfs*2	ENST00000439151	NM_022455.4	1639	atc/atCTGTATAACCTGTCATGc	13/23	0.792896585962677	4	FACETS	0.863	0.788	0.941			1	CLONAL	1	TRUE	NA	0.792896585962677	4		462	755	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176684128	176684129	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGCCAATGTTATCCAGCTGAGG	novel	NA	P-0038270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	91	418	0	ENST00000439151.2:c.4953_4954insATCCAGCTGAGGCAGCCAATGTT	p.Ser1652IlefsTer15	p.S1652Ifs*15	ENST00000439151	NM_022455.4	1648	cca/cCAGCCAATGTTATCCAGCTGAGGca	13/23	0.792896585962677	4	FACETS	0.71	0.631	0.793			1	SUBCLONAL	1	TRUE	NA	0.792896585962677	4		418	580	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	219	821	0	ENST00000269305.4:c.880del	p.Glu294SerfsTer51	p.E294Sfs*51	ENST00000269305	NM_001126112.2	294	Gag/ag	8/11	0.193415903487871	3	FACETS	1	0.986	1	0.812	0.758	0.868	CLONAL	2	FALSE	0	0.266594499329437	3		821	764	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31015952	31015952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781684559	NA	P-0023985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	154	479	0	ENST00000375687.4:c.274C>T	p.Arg92Cys	p.R92C	ENST00000375687	NM_015338.5	92	Cgc/Tgc	5/13	0.257350567993019	3	FACETS	0.889	0.82	0.96	1	0.986	1	CLONAL	3	FALSE	1	0.266594499329437	3		479	491	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809507	36809507	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	46	798	0	ENST00000373129.3:c.958G>C	p.Ala320Pro	p.A320P	ENST00000373129	NM_032017.1	320	Gcc/Ccc	10/12	0.266594499329437	4	FACETS	0.624	0.524	0.734	0.208	0.174	0.245	SUBCLONAL	1	FALSE	1	0.266594499329437	4		798	701	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330514	65330514	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1340	78	697	0	ENST00000342505.4:c.1132A>C	p.Lys378Gln	p.K378Q	ENST00000342505	NM_002227.2	378	Aag/Cag	8/25	0.266594499329437	7	FACETS	0.688	0.602	0.781			1	SUBCLONAL	1	FALSE	NA	0.266594499329437	7		697	1418	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551937	150551937	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	132	638	0	ENST00000369026.2:c.70G>T	p.Gly24Cys	p.G24C	ENST00000369026	NM_021960.4	24	Ggc/Tgc	1/3	0.266594499329437	5	FACETS	1	0.932	1	0.686	0.624	0.751	CLONAL	2	FALSE	2	0.266594499329437	5		638	674	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740219	162740219	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs958394700	NA	P-0023985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	69	662	0	ENST00000367921.3:c.1421T>A	p.Ile474Asn	p.I474N	ENST00000367921	NM_006182.2	474	aTc/aAc	12/18	0.266594499329437	5	FACETS	0.899	0.782	1	0.3	0.26	0.342	CLONAL	1	FALSE	2	0.266594499329437	5		662	806	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243708849	243708849	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	76	718	0	ENST00000263826.5:c.1214T>C	p.Phe405Ser	p.F405S	ENST00000263826	NM_005465.4	405	tTc/tCc	11/13	0.266594499329437	5	FACETS	0.684	0.598	0.777	0.228	0.199	0.259	SUBCLONAL	1	FALSE	2	0.266594499329437	5		718	1167	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864846	57864846	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs200374961	NA	P-0023985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	59	791	0	ENST00000228682.2:c.2323C>G	p.Pro775Ala	p.P775A	ENST00000228682	NM_005269.2	775	Ccc/Gcc	12/12	0.266594499329437	4	FACETS	0.773	0.664	0.892	0.258	0.221	0.298	SUBCLONAL	1	FALSE	1	0.266594499329437	4		791	725	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626812	28626812	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0023985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	48	496	0	ENST00000241453.7:c.485-1G>T		p.X162_splice	ENST00000241453	NM_004119.2	162			0.266594499329437	5	FACETS	0.744	0.627	0.872	0.186	0.156	0.218	SUBCLONAL	1	FALSE	1	0.266594499329437	5		496	678	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2093643	2093643	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	107	886	0	ENST00000219066.1:c.634G>C	p.Val212Leu	p.V212L	ENST00000219066	NM_002528.5	212	Gtg/Ctg	4/6	0.266594499329437	5	FACETS	1	0.945	1	0.362	0.324	0.403	CLONAL	1	FALSE	2	0.266594499329437	5		886	1034	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719002	190719002	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	78	448	0	ENST00000441310.2:c.1004C>G	p.Thr335Ser	p.T335S	ENST00000441310	NM_000534.4	335	aCt/aGt	9/13	0.230448852228374	5	FACETS	1	0.975	1	0.487	0.428	0.549	CLONAL	1	FALSE	2	0.266594499329437	5		448	561	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267222	41267222	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1392093769	NA	P-0023985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	52	693	0	ENST00000349496.5:c.806C>G	p.Ala269Gly	p.A269G	ENST00000349496	NM_001904.3	269	gCt/gGt	6/15	0.180923066661096	4	FACETS	0.659	0.56	0.768	0.22	0.186	0.256	SUBCLONAL	1	FALSE	1	0.266594499329437	4		693	750	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031713	69031713	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	156	826	0	ENST00000288368.4:c.3468C>G	p.Asp1156Glu	p.D1156E	ENST00000288368	NM_024870.2	1156	gaC/gaG	28/40	0.266594499329437	7	FACETS	1	0.987	1	0.294	0.268	0.321	CLONAL	1	FALSE	2	0.266594499329437	7		826	1328	SUCCESS
BTK	695	MSKCC	GRCh37	X	100604908	100604908	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	53	695	0	ENST00000308731.7:c.1945A>T	p.Ser649Cys	p.S649C	ENST00000308731	NM_000061.2	649	Agc/Tgc	19/19	0.123696525555747	5	FACETS	0.647	0.55	0.754	0.216	0.183	0.252	INDETERMINATE	1	FALSE	2	0.266594499329437	5		695	860	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0024047-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3254	175	427	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.421719625887034	31	FACETS	0.861	0.788	0.938			1	CLONAL	2	TRUE	NA	0.421719625887034	31		427	3429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0024047-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	160	577	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.28826619227622	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.421719625887034	1		577	524	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023280	27023284	+	frameshift_variant	Frame_Shift_Del	DEL	GCGAT	GCGAT	-	novel	NA	P-0024047-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	15	102	0	ENST00000324856.7:c.387_391del	p.Ser129ArgfsTer269	p.S129Rfs*269	ENST00000324856	NM_006015.4	129	aGCGAT/a	1/20	1	2	FACETS	0.9	0.671	1	0.9	0.671	1	CLONAL	1	TRUE	1	0.421719625887034	2		102	79	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383231	4383231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024047-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	106	342	0	ENST00000261254.3:c.25G>A	p.Asp9Asn	p.D9N	ENST00000261254	NM_001759.3	9	Gac/Aac	1/5	0.421719625887034	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.421719625887034	1		342	298	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517753	187517753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024047-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	52	245	0	ENST00000441802.2:c.12941C>T	p.Ser4314Leu	p.S4314L	ENST00000441802	NM_005245.3	4314	tCa/tTa	25/27	1	2	FACETS	0.975	0.838	1	0.975	0.838	1	CLONAL	1	TRUE	1	0.421719625887034	2		245	253	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2966396	2966396	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024047-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	41	511	0	ENST00000396946.4:c.1784G>T	p.Gly595Val	p.G595V	ENST00000396946	NM_032415.4	595	gGg/gTg	14/25	0.421719625887034	4	FACETS	0.396	0.329	0.471	0.198	0.164	0.236	SUBCLONAL	1	TRUE	2	0.421719625887034	4		511	698	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0024142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	54	290	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.332164522408849	4	FACETS	0.859	0.743	0.982	0.859	0.743	0.982	CLONAL	2	FALSE	2	0.405435852349014	4		290	218	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112547	2112547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs796053485	NA	P-0024142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	141	765	0	ENST00000219476.3:c.1307C>T	p.Pro436Leu	p.P436L	ENST00000219476	NM_000548.3	436	cCg/cTg	13/42	0.259537586624415	5	FACETS	0.892	0.82	0.965			1	CLONAL	3	FALSE	NA	0.405435852349014	5		765	418	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105623	27105623	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	78	723	0	ENST00000324856.7:c.5234del	p.Leu1745ArgfsTer25	p.L1745Rfs*25	ENST00000324856	NM_006015.4	1745	cTg/cg	20/20	0.405435852349014	3	FACETS	1	0.972	1	0.669	0.592	0.75	CLONAL	1	FALSE	1	0.405435852349014	3		723	346	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133185	30133185	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	19	584	0	ENST00000263025.4:c.313G>C	p.Asp105His	p.D105H	ENST00000263025	NM_002746.2	105	Gac/Cac	2/9	0.332164522408849	4	FACETS	0.379	0.287	0.487	0.189	0.143	0.244	SUBCLONAL	1	FALSE	2	0.405435852349014	4		584	348	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277037	18277037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	141	670	0	ENST00000222254.8:c.1484G>A	p.Gly495Asp	p.G495D	ENST00000222254	NM_005027.3	495	gGc/gAc	12/16	0.124849838153457	3	FACETS	0.905	0.839	0.972	0.905	0.839	0.972	INDETERMINATE	3	FALSE	0	0.405435852349014	3		670	308	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922553	56922555	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	novel	NA	P-0024142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	52	678	0	ENST00000519728.1:c.1425_1427del	p.Ile475del	p.I475del	ENST00000519728	NM_002350.3	475	ATT/-	13/13	0.405435852349014	4	FACETS	0.939	0.802	1	0.469	0.401	0.544	CLONAL	1	FALSE	2	0.405435852349014	4		678	384	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504330	8504330	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	33	684	0	ENST00000356435.5:c.1753C>G	p.Leu585Val	p.L585V	ENST00000356435		585	Ctg/Gtg	12/35	0.405435852349014	6	FACETS	0.491	0.399	0.596	0.164	0.133	0.199	SUBCLONAL	1	FALSE	3	0.405435852349014	6		684	600	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0024231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	537	809	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.773714419192454	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.773714419192454	1		809	845	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0024231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	3122	866	9	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	0.773714419192454	8	FACETS	0.983	0.973	0.993			1	CLONAL	7	TRUE	NA	0.773714419192454	8		875	3894	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057642	27057655	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GATTCCTCCTTATG	GATTCCTCCTTATG	-	novel	NA	P-0024231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	385	619	3	ENST00000324856.7:c.1352_1365del		p.X451_splice	ENST00000324856	NM_006015.4	451		3/20	0.368345142255648	1	FACETS	0.748	0.715	0.781	0.748	0.715	0.781	INDETERMINATE	1	TRUE	0	0.773714419192454	1		622	816	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928076	178928084	+	inframe_deletion	In_Frame_Del	DEL	TTAGAAGAT	TTAGAAGAT	-	novel	NA	P-0024231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3567	556	807	0	ENST00000263967.3:c.1356_1364del	p.Glu453_Leu455del	p.E453_L455del	ENST00000263967	NM_006218.2	452	TTAGAAGAT/-	8/21	0.773714419192454	8	FACETS	1	0.992	1			1	CLONAL	1	TRUE	NA	0.773714419192454	8		807	4123	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508825	31508825	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0024231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	53	851	0	ENST00000344624.3:c.1490C>G	p.Ser497Ter	p.S497*	ENST00000344624		497	tCa/tGa	7/33	0.773714419192454	1	FACETS	0.105	0.089	0.123	0.105	0.089	0.123	SUBCLONAL	1	TRUE	0	0.773714419192454	1		851	801	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133710868	133710870	+	inframe_deletion	In_Frame_Del	DEL	AAT	AAT	-	novel	NA	P-0024231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	167	631	0	ENST00000318560.5:c.35_37del	p.Lys12_Ser13delinsThr	p.K12_S13delinsT	ENST00000318560	NM_005157.4	12	aAATcc/acc	1/11	NA	2	FACETS	0.453	0.416	0.492			1	INDETERMINATE	1	TRUE	NA	0.773714419192454	2		631	952	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	832	503	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.761281777877099	37	FACETS	1	0.992	1			1	CLONAL	33	TRUE	NA	0.761281777877099	37		503	939	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057520006	NA	P-0024326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	334	924	2	ENST00000269305.4:c.821T>A	p.Val274Asp	p.V274D	ENST00000269305	NM_001126112.2	274	gTt/gAt	8/11	0.757638622744302	4	FACETS	0.986	0.96	1	0.986	0.96	1	CLONAL	4	TRUE	0	0.761281777877099	4		926	392	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878887	151878887	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	67	922	0	ENST00000262189.6:c.6058C>T	p.Gln2020Ter	p.Q2020*	ENST00000262189	NM_170606.2	2020	Caa/Taa	36/59	0.761281777877099	2	FACETS	0.978	0.903	1	0.978	0.903	1	CLONAL	2	TRUE	0	0.761281777877099	2		922	90	SUCCESS
AR	367	MSKCC	GRCh37	X	66937439	66937439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	149	955	0	ENST00000374690.3:c.2294del	p.Phe765SerfsTer24	p.F765Sfs*24	ENST00000374690	NM_000044.3	765	Ttc/tc	5/8	0.205878924118607	5	FACETS	1	0.984	1	0.815	0.756	0.875	INDETERMINATE	2	TRUE	2	0.761281777877099	5		955	343	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	99	503	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.306310800802531	6	FACETS	1	0.939	1	0.778	0.709	0.848	INDETERMINATE	3	FALSE	2	0.650831046536871	6		503	225	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155725	56155726	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0024332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	188	496	0	ENST00000399503.3:c.819_820del	p.Arg273SerfsTer27	p.R273Sfs*27	ENST00000399503	NM_005921.1	273	AGa/a	3/20	0.660730506700388	5	FACETS	0.91	0.869	0.948	0.91	0.869	0.948	CLONAL	5	FALSE	0	0.650831046536871	5		496	251	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180845	106180845	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	22	544	0	ENST00000380013.4:c.3873G>C	p.Trp1291Cys	p.W1291C	ENST00000380013	NM_001127208.2	1291	tgG/tgC	7/11	0.291953953482569	4	FACETS	0.729	0.571	0.91	0.365	0.285	0.455	INDETERMINATE	1	FALSE	2	0.650831046536871	4		544	153	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794132	242794132	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	10	883	0	ENST00000334409.5:c.596C>A	p.Thr199Lys	p.T199K	ENST00000334409	NM_005018.2	199	aCa/aAa	4/5	0.183052499716629	3	FACETS	0.224	0.151	0.315			1	INDETERMINATE	1	FALSE	NA	0.650831046536871	3		883	182	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643726	52643726	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	113	885	0	ENST00000394830.3:c.2170A>G	p.Met724Val	p.M724V	ENST00000394830	NM_018313.4	724	Atg/Gtg	17/30	0.623339192894095	5	FACETS	1	0.981	1	0.457	0.413	0.504	CLONAL	1	FALSE	2	0.650831046536871	5		885	500	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	127	503	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.974	0.893	1	0.974	0.893	1	CLONAL	1	TRUE	1	0.749411475261162	2		503	348	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258581	16258582	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0024361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	161	416	1	ENST00000375759.3:c.5846_5847del	p.Arg1949GlnfsTer13	p.R1949Qfs*13	ENST00000375759	NM_015001.2	1949	cGG/c	11/15	1	2	FACETS	0.92	0.851	0.99	0.92	0.851	0.99	CLONAL	1	TRUE	1	0.749411475261162	2		417	467	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56171042	56171042	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	79	257	1	ENST00000399503.3:c.1870C>T	p.Gln624Ter	p.Q624*	ENST00000399503	NM_005921.1	624	Cag/Tag	10/20	1	2	FACETS	0.837	0.746	0.931	0.837	0.746	0.931	CLONAL	1	TRUE	1	0.749411475261162	2		258	252	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087944	27087944	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0024463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	167	790	0	ENST00000324856.7:c.2231C>G	p.Ser744Ter	p.S744*	ENST00000324856	NM_006015.4	744	tCa/tGa	6/20	0.56631762561486	6	FACETS	0.774	0.712	0.839			1	SUBCLONAL	2	TRUE	NA	0.56631762561486	6		790	812	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518692	204518692	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	175	483	3	ENST00000367182.3:c.1355G>T	p.Gly452Val	p.G452V	ENST00000367182	NM_001278516.1	452	gGa/gTa	11/11	0.534689043748355	5	FACETS	1	0.968	1	0.718	0.665	0.771	CLONAL	2	TRUE	2	0.56631762561486	5		486	531	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998186	100998186	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745472229	NA	P-0024463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	30	476	0	ENST00000325455.5:c.1616C>T	p.Pro539Leu	p.P539L	ENST00000325455	NM_001202474.3	539	cCg/cTg	1/8	0.573706839471841	1	FACETS	0.298	0.241	0.362	0.298	0.241	0.362	SUBCLONAL	1	TRUE	0	0.56631762561486	1		476	255	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240978	133240978	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	150	711	2	ENST00000320574.5:c.2539C>G	p.Arg847Gly	p.R847G	ENST00000320574	NM_006231.2	847	Cgg/Ggg	22/49	0.573706839471841	4	FACETS	0.978	0.895	1	0.326	0.298	0.356	CLONAL	1	TRUE	1	0.56631762561486	4		713	848	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3824656	3824656	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	423	568	0	ENST00000262367.5:c.2197C>T	p.Gln733Ter	p.Q733*	ENST00000262367	NM_004380.2	733	Cag/Tag	12/31	0.56631762561486	5	FACETS	1	0.991	1	0.829	0.795	0.863	CLONAL	3	TRUE	1	0.56631762561486	5		568	833	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0024463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	392	468	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.534992303696445	4	FACETS	1	0.983	1			1	CLONAL	3	TRUE	NA	0.56631762561486	4		468	693	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186507029	186507040	+	inframe_deletion	In_Frame_Del	DEL	ATGCCCATGAAT	ATGCCCATGAAT	-	novel	NA	P-0024463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	67	331	0	ENST00000323963.5:c.1195_1206del	p.Met399_Asn402del	p.M399_N402del	ENST00000323963		399	ATGCCCATGAAT/-	11/11	0.56631762561486	6	FACETS	0.805	0.699	0.919	0.201	0.174	0.23	CLONAL	1	TRUE	2	0.56631762561486	6		331	627	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670564	30670564	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764807291	NA	P-0024463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	351	646	0	ENST00000376406.3:c.5956G>A	p.Ala1986Thr	p.A1986T	ENST00000376406	NM_014641.2	1986	Gca/Aca	13/15	0.56631762561486	9	FACETS	1	0.982	1			1	CLONAL	3	TRUE	NA	0.56631762561486	9		646	1142	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199702	138199702	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	105	588	0	ENST00000237289.4:c.1120G>T	p.Glu374Ter	p.E374*	ENST00000237289	NM_001270507.1	374	Gaa/Taa	7/9	0.56631762561486	8	FACETS	1	0.963	1			1	CLONAL	1	TRUE	NA	0.56631762561486	8		588	859	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021838	69021838	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1244359757	NA	P-0024463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	52	639	0	ENST00000288368.4:c.3126G>A	p.Met1042Ile	p.M1042I	ENST00000288368	NM_024870.2	1042	atG/atA	25/40	0.366877615562823	1	FACETS	0.495	0.425	0.57	0.495	0.425	0.57	SUBCLONAL	1	TRUE	0	0.56631762561486	1		639	266	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0024468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	82	359	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.344607431663242	5	FACETS	1	0.941	1	0.721	0.644	0.802	CLONAL	2	TRUE	2	0.481810967986366	5		359	271	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670597	134670597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1330628001	NA	P-0024468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	14	992	1	ENST00000398015.3:c.508C>T	p.Arg170Trp	p.R170W	ENST00000398015	NM_004441.4	170	Cgg/Tgg	3/16	0.481810967986366	1	FACETS	0.075	0.054	0.102	0.075	0.054	0.102	SUBCLONAL	1	TRUE	0	0.481810967986366	1		993	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574002	7574002	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	378	970	0	ENST00000269305.4:c.1025del	p.Arg342GlnfsTer3	p.R342Qfs*3	ENST00000269305	NM_001126112.2	342	cGa/ca	10/11	0.392812371068332	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.481810967986366	2		970	779	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376425	118376425	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	29	663	0	ENST00000534358.1:c.9818A>G	p.Asp3273Gly	p.D3273G	ENST00000534358	NM_005933.3	3273	gAt/gGt	27/36	0.481810967986366	1	FACETS	0.249	0.2	0.305	0.249	0.2	0.305	SUBCLONAL	1	TRUE	0	0.481810967986366	1		663	367	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28903743	28903769	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCCATTACCTCCTTGCTTGGTGCAGG	CTCCATTACCTCCTTGCTTGGTGCAGG	-	novel	NA	P-0024468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	42	587	1	ENST00000282397.4:c.2690_2707+9del		p.X897_splice	ENST00000282397	NM_002019.4	897		19/30	1	2	FACETS	0.479	0.401	0.565	0.479	0.401	0.565	SUBCLONAL	1	TRUE	1	0.481810967986366	2		588	364	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477082	67477083	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACTACATC	novel	NA	P-0024468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	119	664	0	ENST00000327367.4:c.890_897dup	p.Gly300ThrfsTer44	p.G300Tfs*44	ENST00000327367	NM_005902.3	297	tac/tACTACATCac	7/9	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.481810967986366	2		664	494	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401777	401777	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	270	684	0	ENST00000380956.4:c.1099G>T	p.Glu367Ter	p.E367*	ENST00000380956	NM_001195286.1	367	Gag/Tag	7/9	0.481810967986366	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.481810967986366	3		684	684	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672243	30672243	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	53	926	0	ENST00000376406.3:c.4717C>G	p.Pro1573Ala	p.P1573A	ENST00000376406	NM_014641.2	1573	Cct/Gct	10/15	0.481810967986366	3	FACETS	0.325	0.276	0.378	0.162	0.138	0.189	SUBCLONAL	1	TRUE	1	0.481810967986366	3		926	841	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956724	68956724	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs372931548	NA	P-0024468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	121	752	1	ENST00000288368.4:c.842G>A	p.Arg281Gln	p.R281Q	ENST00000288368	NM_024870.2	281	cGg/cAg	8/40	0.344206764363683	3	FACETS	1	0.954	1	0.543	0.492	0.596	CLONAL	1	TRUE	1	0.481810967986366	3		753	574	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0024471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	95	290	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.887	0.802	0.975	0.887	0.802	0.975	CLONAL	1	TRUE	1	0.808131932939664	2		290	265	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862100	68862100	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	241	724	0	ENST00000261769.5:c.2190del	p.Leu731PhefsTer39	p.L731Ffs*39	ENST00000261769	NM_004360.3	730	Ttt/tt	14/16	0.808131932939664	1	FACETS	0.974	0.93	1	0.974	0.93	1	CLONAL	1	TRUE	0	0.808131932939664	1		724	365	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	34	408	1	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.201506524047585	1	FACETS	0.503	0.41	0.608	0.503	0.41	0.608	SUBCLONAL	1	TRUE	0	0.21	1		409	576	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177920	56177920	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	66	658	0	ENST00000399503.3:c.2893C>T	p.Gln965Ter	p.Q965*	ENST00000399503	NM_005921.1	965	Cag/Tag	14/20	0.0928106277854649	3	FACETS	1	0.912	1	0.533	0.463	0.61	INDETERMINATE	1	TRUE	1	0.21	3		658	651	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118355686	118355687	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	rs1555040480	NA	P-0024496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	79	705	1	ENST00000534358.1:c.4331_4332dup	p.Phe1445SerfsTer17	p.F1445Sfs*17	ENST00000534358	NM_005933.3	1443	gta/gtAGa	10/36	0.201506524047585	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.21	1		706	518	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879885	37879885	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1949	551	846	0	ENST00000269571.5:c.2180G>C	p.Gly727Ala	p.G727A	ENST00000269571		727	gGa/gCa	18/27	0.450996893028049	13	FACETS	1	0.991	1			1	CLONAL	3	TRUE	NA	0.450996893028049	13		846	2500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578191	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs530941076	NA	P-0024504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	413	740	0	ENST00000269305.4:c.658T>C	p.Tyr220His	p.Y220H	ENST00000269305	NM_001126112.2	220	Tat/Cat	6/11	0.372568294295089	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.450996893028049	2		740	853	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359594	40359594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758951069	NA	P-0024504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	110	610	0	ENST00000293328.3:c.2059C>T	p.Pro687Ser	p.P687S	ENST00000293328	NM_012448.3	687	Ccc/Tcc	16/19	0.450996893028049	2	FACETS	0.863	0.778	0.953	0.432	0.389	0.477	CLONAL	1	TRUE	0	0.450996893028049	2		610	565	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567311	226567311	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	89	608	0	ENST00000366794.5:c.1575A>C	p.Leu525Phe	p.L525F	ENST00000366794	NM_001618.3	525	ttA/ttC	11/23	0.450996893028049	5	FACETS	0.761	0.673	0.854	0.254	0.224	0.285	SUBCLONAL	1	TRUE	2	0.450996893028049	5		608	870	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567323	226567323	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	92	449	0	ENST00000366794.5:c.1563G>C	p.Lys521Asn	p.K521N	ENST00000366794	NM_001618.3	521	aaG/aaC	11/23	0.450996893028049	5	FACETS	0.797	0.707	0.893	0.266	0.235	0.298	SUBCLONAL	1	TRUE	2	0.450996893028049	5		449	858	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375770	118375770	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	115	614	0	ENST00000534358.1:c.9163G>C	p.Asp3055His	p.D3055H	ENST00000534358	NM_005933.3	3055	Gat/Cat	27/36	0.450996893028049	2	FACETS	1	0.95	1	0.538	0.487	0.591	CLONAL	1	TRUE	0	0.450996893028049	2		614	474	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448103	49448103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	85	547	2	ENST00000301067.7:c.497C>T	p.Ser166Leu	p.S166L	ENST00000301067	NM_003482.3	166	tCa/tTa	4/54	0.450996893028049	3	FACETS	0.857	0.759	0.961	0.429	0.379	0.481	CLONAL	1	TRUE	1	0.450996893028049	3		549	539	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489566	56489566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	97	485	0	ENST00000267101.3:c.2031G>A	p.Met677Ile	p.M677I	ENST00000267101	NM_001982.3	677	atG/atA	17/28	0.450996893028049	3	FACETS	0.864	0.772	0.962	0.432	0.386	0.481	CLONAL	1	TRUE	1	0.450996893028049	3		485	610	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842400	68842400	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	135	721	0	ENST00000261769.5:c.461G>C	p.Arg154Thr	p.R154T	ENST00000261769	NM_004360.3	154	aGa/aCa	4/16	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.450996893028049	2		721	571	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676228	37676228	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2072	110	610	0	ENST00000447079.4:c.2983G>C	p.Asp995His	p.D995H	ENST00000447079	NM_015083.1	995	Gat/Cat	11/14	0.450996893028049	13	FACETS	0.778	0.695	0.867			1	SUBCLONAL	1	TRUE	NA	0.450996893028049	13		610	2182	SUCCESS
YES1	7525	MSKCC	GRCh37	18	751748	751748	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747726944	NA	P-0024504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	144	577	0	ENST00000314574.4:c.328C>T	p.Leu110Phe	p.L110F	ENST00000314574	NM_005433.3	110	Ctt/Ttt	3/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.450996893028049	2		577	559	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353725	15353725	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	156	935	0	ENST00000263377.2:c.3155A>C	p.Asp1052Ala	p.D1052A	ENST00000263377	NM_058243.2	1052	gAc/gCc	14/20	1	2	FACETS	0.839	0.768	0.912	0.839	0.768	0.912	CLONAL	1	TRUE	1	0.450996893028049	2		935	825	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719851	61719851	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	128	587	0	ENST00000401558.2:c.1417G>C	p.Glu473Gln	p.E473Q	ENST00000401558	NM_003400.3	473	Gaa/Caa	14/25	0.450996893028049	3	FACETS	1	0.959	1	0.549	0.499	0.602	CLONAL	1	TRUE	1	0.450996893028049	3		587	633	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171584	32171584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	120	769	0	ENST00000375023.3:c.3194C>T	p.Ala1065Val	p.A1065V	ENST00000375023	NM_004557.3	1065	gCa/gTa	20/30	0.450996893028049	3	FACETS	0.897	0.811	0.988	0.449	0.405	0.494	CLONAL	1	TRUE	1	0.450996893028049	3		769	727	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946412	2946412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1362125570	NA	P-0024504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	157	890	0	ENST00000396946.4:c.3325G>A	p.Glu1109Lys	p.E1109K	ENST00000396946	NM_032415.4	1109	Gag/Aag	25/25	0.121187024188711	4	FACETS	0.982	0.898	1	0.491	0.449	0.535	INDETERMINATE	1	TRUE	2	0.450996893028049	4		890	1029	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205323	38205323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	174	1004	0	ENST00000317025.8:c.367G>A	p.Glu123Lys	p.E123K	ENST00000317025	NM_023034.1	123	Gaa/Aaa	2/24	0.450996893028049	3	FACETS	0.81	0.744	0.878	0.405	0.372	0.439	CLONAL	1	TRUE	1	0.450996893028049	3		1004	1168	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222677	53222677	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	130	885	0	ENST00000375401.3:c.4259G>T	p.Trp1420Leu	p.W1420L	ENST00000375401	NM_004187.3	1420	tGg/tTg	25/26	0.450996893028049	1	FACETS	0.881	0.803	0.961	0.881	0.803	0.961	CLONAL	1	TRUE	0	0.450996893028049	1		885	507	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222686	53222686	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	129	877	0	ENST00000375401.3:c.4250A>G	p.His1417Arg	p.H1417R	ENST00000375401	NM_004187.3	1417	cAc/cGc	25/26	0.450996893028049	1	FACETS	0.877	0.8	0.958	0.877	0.8	0.958	CLONAL	1	TRUE	0	0.450996893028049	1		877	505	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641503	23641503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555460542	NA	P-0024506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	76	818	0	ENST00000261584.4:c.1972G>A	p.Glu658Lys	p.E658K	ENST00000261584	NM_024675.3	658	Gaa/Aaa	5/13	1	2	FACETS	0.676	0.591	0.768	0.676	0.591	0.768	SUBCLONAL	1	TRUE	1	0.219861893473295	2		818	1023	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0024506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	163	715	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.219861893473295	3	FACETS	1	0.935	1	0.68	0.624	0.737	CLONAL	2	TRUE	0	0.219861893473295	3		715	807	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117535	70117535	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0024506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	94	505	1	ENST00000245479.2:c.3G>A	p.Met1?	p.M1?	ENST00000245479	NM_000346.3	1	atG/atA	1/3	0.219861893473295	2	FACETS	0.814	0.727	0.907	0.814	0.727	0.907	CLONAL	2	TRUE	0	0.219861893473295	2		506	525	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0024506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	146	483	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.219861893473295	3	FACETS	0.837	0.767	0.91	0.837	0.767	0.91	CLONAL	3	TRUE	0	0.219861893473295	3		483	587	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395937	395937	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0024506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	40	381	0	ENST00000380956.4:c.492+2T>C		p.X164_splice	ENST00000380956	NM_001195286.1	164			0.219861893473295	4	FACETS	0.875	0.727	1	0.438	0.363	0.521	CLONAL	1	TRUE	2	0.219861893473295	4		381	507	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933956	39933956	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	156	777	0	ENST00000378444.4:c.643C>G	p.Leu215Val	p.L215V	ENST00000378444	NM_001123385.1	215	Ctg/Gtg	4/15	0.211106821153518	2	FACETS	0.863	0.791	0.938	0.863	0.791	0.938	CLONAL	2	TRUE	0	0.219861893473295	2		777	822	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725042	89725042	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0024509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	117	291	0	ENST00000371953.3:c.1027-2A>T		p.X343_splice	ENST00000371953	NM_000314.4	343			1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.685608443738801	2		291	323	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653860	89653860	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786203375	NA	P-0024509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	175	505	0	ENST00000371953.3:c.158T>A	p.Val53Glu	p.V53E	ENST00000371953	NM_000314.4	53	gTa/gAa	2/9	1	2	FACETS	0.972	0.902	1	0.972	0.902	1	CLONAL	1	TRUE	1	0.685608443738801	2		505	525	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624976	9624976	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0024509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	78	276	0	ENST00000353224.5:c.1A>G	p.Met1?	p.M1?	ENST00000353224	NM_177990.2	1	Atg/Gtg	3/10	0.685608443738801	3	FACETS	0.995	0.883	1	0.498	0.441	0.557	CLONAL	1	TRUE	1	0.685608443738801	3		276	307	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	185	674	0	ENST00000206249.3:c.1607T>A	p.Leu536His	p.L536H	ENST00000206249	NM_000125.3	536	cTc/cAc	8/8	0.546943111019037	2	FACETS	1	0.959	1	0.524	0.486	0.564	CLONAL	1	TRUE	0	0.546943111019037	2		674	645	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934190	39934190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146403660	NA	P-0024512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	204	676	4	ENST00000378444.4:c.409G>A	p.Val137Ile	p.V137I	ENST00000378444	NM_001123385.1	137	Gtc/Atc	4/15	0.546943111019037	3	FACETS	1	0.948	1	0.513	0.476	0.551	CLONAL	1	TRUE	1	0.546943111019037	3		680	926	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217312	11217312	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	281	804	1	ENST00000361445.4:c.4366T>A	p.Trp1456Arg	p.W1456R	ENST00000361445	NM_004958.3	1456	Tgg/Agg	30/58	0.480984390890319	3	FACETS	1	0.992	1	0.672	0.632	0.712	CLONAL	1	TRUE	1	0.546943111019037	3		805	974	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163715	47163728	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGAAGGGTTGCT	AAAGAAGGGTTGCT	-	novel	NA	P-0024512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	196	536	0	ENST00000409792.3:c.2398_2411del	p.Ser800ValfsTer2	p.S800Vfs*2	ENST00000409792	NM_014159.6	800	AGCAACCCTTCTTTg/g	3/21	0.546943111019037	4	FACETS	0.824	0.766	0.883	0.824	0.766	0.883	CLONAL	2	TRUE	2	0.546943111019037	4		536	673	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927959	49927959	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	342	691	1	ENST00000296474.3:c.3769G>A	p.Glu1257Lys	p.E1257K	ENST00000296474	NM_002447.2	1257	Gag/Aag	18/20	0.368251635457677	4	FACETS	0.955	0.905	1			1	CLONAL	2	TRUE	NA	0.546943111019037	4		692	1013	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180542	56180543	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	206	421	0	ENST00000399503.3:c.3872dup	p.Arg1292LysfsTer17	p.R1292Kfs*17	ENST00000399503	NM_005921.1	1291	cta/cTta	16/20	0.546943111019037	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	2	0.546943111019037	4		421	562	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491645	56491645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	175	623	0	ENST00000267101.3:c.2537G>T	p.Ser846Ile	p.S846I	ENST00000267101	NM_001982.3	846	aGt/aTt	21/28	1	2	FACETS	0.904	0.836	0.974	0.904	0.836	0.974	CLONAL	1	TRUE	1	0.613444635496356	2		623	631	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164860	36164872	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCGGGGAACTG	GCGCGGGGAACTG	-	novel	NA	P-0024517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	227	752	0	ENST00000300305.3:c.1003_1015del	p.Gln335CysfsTer255	p.Q335Cfs*255	ENST00000300305		335	CAGTTCCCCGCGCtg/tg	8/8	0.15590764718036	4	FACETS	1	0.989	1	0.656	0.612	0.702	INDETERMINATE	1	TRUE	2	0.613444635496356	4		752	910	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867264	68867264	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	205	555	0	ENST00000261769.5:c.2512del	p.Ser838AlafsTer8	p.S838Afs*8	ENST00000261769	NM_004360.3	837	ggA/gg	16/16	0.613444635496356	1	FACETS	0.951	0.892	1	0.951	0.892	1	CLONAL	1	TRUE	0	0.613444635496356	1		555	487	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349694	89349695	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0024519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	82	764	2	ENST00000301030.4:c.3255_3256del	p.Lys1086GlufsTer15	p.K1086Efs*15	ENST00000301030	NM_001256183.1	1085	gaGAag/gaag	9/13	0.354188579736847	5	FACETS	0.938	0.826	1			1	CLONAL	1	FALSE	NA	0.354188579736847	5		766	756	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591888	48591888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519739	NA	P-0024519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	8	537	0	ENST00000342988.3:c.1051G>A	p.Asp351Asn	p.D351N	ENST00000342988	NM_005359.5	351	Gat/Aat	9/12	0.334009808851291	3	FACETS	0.148	0.094	0.217	0.049	0.031	0.073	SUBCLONAL	1	FALSE	0	0.354188579736847	3		537	360	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	31	408	1	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.257167517756491	3	FACETS	0.587	0.475	0.714	0.196	0.158	0.238	SUBCLONAL	1	FALSE	0	0.305040409126938	3		409	399	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39647472	39647472	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	21	695	1	ENST00000262039.4:c.2644G>T	p.Ala882Ser	p.A882S	ENST00000262039	NM_002647.2	882	Gcc/Tcc	24/25	0.305040409126938	4	FACETS	0.488	0.375	0.62	0.244	0.187	0.31	SUBCLONAL	1	FALSE	2	0.305040409126938	4		696	368	SUCCESS
AR	367	MSKCC	GRCh37	X	66942818	66942818	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs137852564	NA	P-0024565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	68	843	1	ENST00000374690.3:c.2599G>T	p.Val867Leu	p.V867L	ENST00000374690	NM_000044.3	867	Gtg/Ttg	7/8	0.302420031222159	1	FACETS	0.7	0.609	0.798	0.7	0.609	0.798	SUBCLONAL	1	TRUE	0	0.28	1		844	597	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309749	65309749	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	53	638	1	ENST00000342505.4:c.2401G>A	p.Glu801Lys	p.E801K	ENST00000342505	NM_002227.2	801	Gag/Aag	17/25	0.196384748881951	3	FACETS	0.658	0.56	0.765	0.329	0.28	0.383	SUBCLONAL	1	TRUE	1	0.28	3		639	656	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0024902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	135	314	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.242343517886899	0	FACETS	0.785	0.735	0.834			1	SUBCLONAL	5	FALSE	0	0.239847333807809	0		314	218	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980892	40980892	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	50	538	0	ENST00000373198.4:c.1594A>C	p.Ser532Arg	p.S532R	ENST00000373198	NM_133170.3	532	Agt/Cgt	10/32	0.216366390176706	6	FACETS	0.842	0.713	0.986	0.211	0.178	0.247	CLONAL	1	TRUE	2	0.216366390176706	6		538	786	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876659802	NA	P-0024944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	253	814	4	ENST00000269305.4:c.833C>A	p.Pro278His	p.P278H	ENST00000269305	NM_001126112.2	278	cCt/cAt	8/11	0.216366390176706	3	FACETS	0.842	0.788	0.897	0.842	0.788	0.897	CLONAL	3	TRUE	0	0.216366390176706	3		818	1026	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022344	26022344	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	219	799	3	ENST00000435504.4:c.313C>T	p.Gln105Ter	p.Q105*	ENST00000435504		105	Cag/Tag	5/13	0.216366390176706	4	FACETS	1	0.982	1	0.778	0.723	0.835	CLONAL	2	TRUE	1	0.216366390176706	4		802	1055	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656585	3656585	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1247	91	959	0	ENST00000294008.3:c.650A>C	p.Lys217Thr	p.K217T	ENST00000294008	NM_032444.2	217	aAg/aCg	3/15	0.216366390176706	5	FACETS	0.833	0.737	0.936	0.278	0.245	0.312	CLONAL	1	TRUE	2	0.216366390176706	5		959	1338	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942124	81942124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781434235	NA	P-0024944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	205	756	2	ENST00000359376.3:c.1661C>T	p.Thr554Met	p.T554M	ENST00000359376	NM_002661.3	554	aCg/aTg	17/33	0.216366390176706	5	FACETS	0.864	0.802	0.929	0.864	0.802	0.929	CLONAL	3	TRUE	2	0.216366390176706	5		758	968	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164964	47164964	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779126757	NA	P-0024944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	103	423	1	ENST00000409792.3:c.1162C>T	p.Arg388Trp	p.R388W	ENST00000409792	NM_014159.6	388	Cgg/Tgg	3/21	0.216366390176706	4	FACETS	1	0.906	1	0.674	0.604	0.747	CLONAL	2	TRUE	1	0.216366390176706	4		424	573	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269021	142269021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	67	564	1	ENST00000350721.4:c.2929G>A	p.Glu977Lys	p.E977K	ENST00000350721	NM_001184.3	977	Gaa/Aaa	14/47	0.216366390176706	5	FACETS	0.935	0.811	1	0.312	0.27	0.357	CLONAL	1	TRUE	2	0.216366390176706	5		565	877	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220483	98220483	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	90	800	0	ENST00000331920.6:c.2980G>C	p.Val994Leu	p.V994L	ENST00000331920	NM_000264.3	994	Gta/Cta	18/24	0.197785945684246	5	FACETS	1	0.887	1	0.334	0.295	0.376	CLONAL	1	TRUE	2	0.216366390176706	5		800	1099	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772976	135772976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs118203721	NA	P-0024944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	54	311	0	ENST00000298552.3:c.2647G>A	p.Ala883Thr	p.A883T	ENST00000298552	NM_001162426.1	883	Gcc/Acc	21/23	0.197785945684246	5	FACETS	1	0.965	1	0.494	0.423	0.572	CLONAL	1	TRUE	2	0.216366390176706	5		311	446	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004247	150004247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	318	452	0	ENST00000253339.5:c.1978C>T	p.Arg660Cys	p.R660C	ENST00000253339		660	Cgt/Tgt	3/7	0.466159394975877	3	FACETS	0.935	0.885	0.985	0.935	0.885	0.985	CLONAL	2	TRUE	1	0.466159394975877	3		452	900	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907651	76907651	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	216	848	4	ENST00000373344.5:c.4510C>T	p.Arg1504Ter	p.R1504*	ENST00000373344	NM_000489.3	1504	Cga/Tga	15/35	0.126608144201429	4	FACETS	0.987	0.916	1			1	INDETERMINATE	1	TRUE	NA	0.466159394975877	4		852	1376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs878854073	NA	P-0024946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	1063	656	1	ENST00000269305.4:c.673-1G>A		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.466159394975877	6	FACETS	0.988	0.968	1			1	CLONAL	6	TRUE	NA	0.466159394975877	6		657	1487	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314876	1314876	+	downstream_gene_variant	3'Flank	SNP	G	G	A	rs757104826	NA	P-0024946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	105	354	0				ENST00000400841		-/233			0.466159394975877	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.466159394975877	1		354	320	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166387	118166388	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0024946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1256	95	410	0	ENST00000369448.3:c.902_903del	p.Arg301LysfsTer24	p.R301Kfs*24	ENST00000369448	NM_017709.3	299	gaAGag/gaag	2/2	0.466159394975877	9	FACETS	0.794	0.704	0.89			1	SUBCLONAL	1	TRUE	NA	0.466159394975877	9		410	1351	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145038	58145039	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	GTCCTTAG	novel	NA	P-0024946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1205	164	738	0	ENST00000257904.6:c.298_305dup	p.Tyr103Ter	p.Y103*	ENST00000257904	NM_000075.3	102	aca/acCTAAGGACa	3/8	0.466159394975877	3	FACETS	0.634	0.58	0.69	0.317	0.29	0.345	SUBCLONAL	1	TRUE	1	0.466159394975877	3		738	1369	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435771	110435771	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775002025	NA	P-0024946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	332	379	0	ENST00000375856.3:c.2630C>T	p.Pro877Leu	p.P877L	ENST00000375856	NM_003749.2	877	cCg/cTg	1/2	0.466159394975877	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.466159394975877	3		379	551	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707971	47707971	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	157	555	0	ENST00000233146.2:c.2595C>G	p.Ile865Met	p.I865M	ENST00000233146	NM_000251.2	865	atC/atG	15/16	0.425986568148257	5	FACETS	0.916	0.837	0.999	0.305	0.279	0.333	CLONAL	1	TRUE	2	0.466159394975877	5		555	1250	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575481	67575481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	172	521	0	ENST00000274335.5:c.554C>T	p.Ala185Val	p.A185V	ENST00000274335		185	gCt/gTt	4/15	0.466159394975877	2	FACETS	1	0.967	1	0.543	0.501	0.586	CLONAL	1	TRUE	0	0.466159394975877	2		521	680	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115971	8115972	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0024982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	59	220	0	ENST00000346208.3:c.1318dup	p.Thr440AsnfsTer67	p.T440Nfs*67	ENST00000346208		439	-/A	6/6	0.304449951068411	7	FACETS	1	0.967	1			1	CLONAL	1	TRUE	NA	0.29	7		220	484	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114799801	114799801	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	58	346	1	ENST00000543371.1:c.468G>T	p.Trp156Cys	p.W156C	ENST00000543371	NM_001198531.1	156	tgG/tgT	5/14	1	2	FACETS	0.608	0.522	0.702	0.608	0.522	0.702	SUBCLONAL	1	TRUE	1	0.29	2		347	658	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0024989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	291	720	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	NA	2	FACETS	0.888	0.842	0.935			1	INDETERMINATE	2	TRUE	NA	0.489602621105421	2		720	669	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	113	544	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.383493577543062	5	FACETS	1	0.97	1	0.4	0.36	0.441	CLONAL	1	TRUE	2	0.489602621105421	5		544	668	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878151	48878151	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	AG	novel	NA	P-0024989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	58	91	0	ENST00000267163.4:c.103delinsAG	p.Gln35ArgfsTer14	p.Q35Rfs*14	ENST00000267163	NM_000321.2	35	Cag/AGag	1/27	0.489602621105421	3	FACETS	0.91	0.799	1	0.91	0.799	1	CLONAL	2	TRUE	1	0.489602621105421	3		91	162	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0025021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	244	403	2	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.667104823983805	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.667104823983805	2		405	359	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579366	7579366	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs770776262	NA	P-0025021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	642	526	0	ENST00000269305.4:c.321C>A	p.Tyr107Ter	p.Y107*	ENST00000269305	NM_001126112.2	107	taC/taA	4/11	0.640406484944866	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	4	TRUE	0	0.667104823983805	4		526	781	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807635	1807635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	286	556	1	ENST00000260795.2:c.1804G>A	p.Ala602Thr	p.A602T	ENST00000260795		602	Gcc/Acc	12/17	0.667104823983805	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.667104823983805	2		557	398	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0025039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	61	359	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.898	0.782	1	0.898	0.782	1	CLONAL	1	TRUE	1	0.499387054050027	2		359	272	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938462	76938462	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1490691498	NA	P-0025039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	28	619	0	ENST00000373344.5:c.2286G>C	p.Lys762Asn	p.K762N	ENST00000373344	NM_000489.3	762	aaG/aaC	9/35	0.499387054050027	1	FACETS	0.223	0.178	0.275	0.223	0.178	0.275	SUBCLONAL	1	TRUE	0	0.499387054050027	1		619	377	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905073	50905073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747614571	NA	P-0025039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	51	683	3	ENST00000440232.2:c.355C>T	p.Arg119Cys	p.R119C	ENST00000440232	NM_002691.3	119	Cgc/Tgc	4/27	1	2	FACETS	0.49	0.417	0.569	0.49	0.417	0.569	SUBCLONAL	1	TRUE	1	0.499387054050027	2		686	417	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027245	49027246	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0025039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	29	582	0	ENST00000267163.4:c.1813dup	p.Met605AsnfsTer48	p.M605Nfs*48	ENST00000267163	NM_000321.2	604	-/A	18/27	0.499387054050027	1	FACETS	0.308	0.248	0.376	0.308	0.248	0.376	SUBCLONAL	1	TRUE	0	0.499387054050027	1		582	283	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0025039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	118	359	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.697531013526986	2		359	331	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905073	50905073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747614571	NA	P-0025039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	271	683	3	ENST00000440232.2:c.355C>T	p.Arg119Cys	p.R119C	ENST00000440232	NM_002691.3	119	Cgc/Tgc	4/27	1	2	FACETS	0.963	0.907	1	0.963	0.907	1	CLONAL	1	TRUE	1	0.697531013526986	2		686	807	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	207	408	1	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.510876393056576	1	FACETS	0.88	0.821	0.941	0.88	0.821	0.941	CLONAL	1	FALSE	0	0.537451917035324	1		409	640	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166354	7166354	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	236	573	0	ENST00000302850.5:c.1672G>T	p.Val558Leu	p.V558L	ENST00000302850	NM_000208.2	558	Gtg/Ttg	8/22	1	2	FACETS	0.918	0.857	0.98	0.918	0.857	0.98	CLONAL	1	FALSE	1	0.537451917035324	2		573	957	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932585	39932585	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	127	625	0	ENST00000378444.4:c.2014T>C	p.Ser672Pro	p.S672P	ENST00000378444	NM_001123385.1	672	Tcc/Ccc	4/15	0.489886400041506	1	FACETS	0.461	0.418	0.506	0.461	0.418	0.506	SUBCLONAL	1	FALSE	0	0.537451917035324	1		625	750	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070577	67070578	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	44	196	0	ENST00000412916.2:c.207dup	p.Pro70SerfsTer13	p.P70Sfs*13	ENST00000412916		67	-/T	3/6	0.386133247793791	1	FACETS	0.505	0.425	0.594	0.505	0.425	0.594	SUBCLONAL	1	TRUE	0	0.386133247793791	1		196	364	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	92	698	0	ENST00000267101.3:c.850G>C	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Cga	7/28	1	2	FACETS	0.79	0.703	0.883	0.79	0.703	0.883	SUBCLONAL	1	TRUE	1	0.386133247793791	2		698	603	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910399	29910399	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	47	530	0	ENST00000376809.5:c.69G>A	p.Trp23Ter	p.W23*	ENST00000376809	NM_002116.7	23	tgG/tgA	1/8	0.138688161698817	4	FACETS	0.839	0.71	0.982	0.42	0.355	0.491	INDETERMINATE	1	TRUE	2	0.386133247793791	4		530	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0025052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	220	585	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.522762118716809	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.533950847124281	2		585	403	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440303	187440303	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	29	417	0	ENST00000232014.4:c.2064G>C	p.Lys688Asn	p.K688N	ENST00000232014	NM_001130845.1	688	aaG/aaC	10/10	0.420086165026522	3	FACETS	0.277	0.222	0.341	0.139	0.111	0.171	SUBCLONAL	1	TRUE	1	0.533950847124281	3		417	496	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517405	176517405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	57	331	0	ENST00000292408.4:c.106C>T	p.Pro36Ser	p.P36S	ENST00000292408	NM_213647.1	36	Ccc/Tcc	3/18	0.185799915556463	3	FACETS	1	0.888	1	0.343	0.297	0.392	INDETERMINATE	1	TRUE	0	0.533950847124281	3		331	263	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202835	27202835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	192	513	0	ENST00000380036.4:c.1927G>A	p.Glu643Lys	p.E643K	ENST00000380036	NM_000459.3	643	Gaa/Aaa	13/23	0.533950847124281	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.533950847124281	1		513	493	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202895	27202895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751169842	NA	P-0025052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	357	588	0	ENST00000380036.4:c.1987G>A	p.Asp663Asn	p.D663N	ENST00000380036	NM_000459.3	663	Gat/Aat	13/23	0.533950847124281	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.533950847124281	1		588	692	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202952	27202952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	301	509	0	ENST00000380036.4:c.2044G>A	p.Asp682Asn	p.D682N	ENST00000380036	NM_000459.3	682	Gac/Aac	13/23	0.533950847124281	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.533950847124281	1		509	571	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202964	27202964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	298	513	1	ENST00000380036.4:c.2056G>A	p.Asp686Asn	p.D686N	ENST00000380036	NM_000459.3	686	Gat/Aat	13/23	0.533950847124281	1	FACETS	0.76	0.725	0.795	1	0.995	1	SUBCLONAL	2	TRUE	0	0.533950847124281	1		514	538	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27203039	27203039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	355	546	1	ENST00000380036.4:c.2131G>A	p.Asp711Asn	p.D711N	ENST00000380036	NM_000459.3	711	Gac/Aac	13/23	0.533950847124281	1	FACETS	0.752	0.72	0.784	1	0.996	1	SUBCLONAL	2	TRUE	0	0.533950847124281	1		547	648	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555787	21555787	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	215	581	0	ENST00000382592.4:c.2483G>A	p.Gly828Glu	p.G828E	ENST00000382592	NM_014572.2	828	gGg/gAg	6/8	0.78532188638981	2	FACETS	1	0.948	1	0.506	0.474	0.538	CLONAL	1	TRUE	0	0.78532188638981	2		581	541	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868662	56868662	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1377003104	NA	P-0025101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	88	418	0	ENST00000308159.5:c.1754G>A	p.Gly585Glu	p.G585E	ENST00000308159	NM_014669.4	585	gGg/gAg	16/22	1	2	FACETS	0.789	0.708	0.873	0.789	0.708	0.873	SUBCLONAL	1	TRUE	1	0.78532188638981	2		418	284	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579338	7579339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGAATGCAAGAAGCCCAGACGG	novel	NA	P-0025101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	317	683	0	ENST00000269305.4:c.327_348dup	p.Gly117ProfsTer39	p.G117Pfs*39	ENST00000269305	NM_001126112.2	116	-/CCGTCTGGGCTTCTTGCATTCT	4/11	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.78532188638981	2		683	634	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726645	41726645	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	206	676	1	ENST00000301178.4:c.190C>A	p.Pro64Thr	p.P64T	ENST00000301178	NM_021913.4	64	Ccc/Acc	2/20	0.782535788875702	2	FACETS	0.933	0.873	0.995	0.467	0.436	0.498	CLONAL	1	TRUE	0	0.78532188638981	2		677	562	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064681	80064681	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	90	525	0	ENST00000265081.6:c.2112A>T	p.Lys704Asn	p.K704N	ENST00000265081	NM_002439.4	704	aaA/aaT	15/24	0.782535788875702	2	FACETS	0.84	0.755	0.927	0.42	0.377	0.464	CLONAL	1	TRUE	0	0.78532188638981	2		525	273	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942710	44942743	+	frameshift_variant	Frame_Shift_Del	DEL	AGTTGCAGCTACATGAGCTGACTAAACTTCCTGC	AGTTGCAGCTACATGAGCTGACTAAACTTCCTGC	-	novel	NA	P-0025101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	142	452	0	ENST00000377967.4:c.3290_3323del	p.Lys1097IlefsTer12	p.K1097Ifs*12	ENST00000377967	NM_021140.2	1097	aAGTTGCAGCTACATGAGCTGACTAAACTTCCTGCt/at	23/29	0.772284471205846	1	FACETS	0.886	0.828	0.943	0.886	0.828	0.943	CLONAL	1	TRUE	0	0.78532188638981	1		452	248	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0025141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	243	400	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.264450746998169	6	FACETS	1	0.976	1			1	CLONAL	4	TRUE	NA	0.264450746998169	6		400	655	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868516	117868516	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	56	391	0	ENST00000297338.2:c.826G>C	p.Asp276His	p.D276H	ENST00000297338	NM_006265.2	276	Gat/Cat	8/14	0.264450746998169	7	FACETS	1	0.88	1	0.172	0.147	0.2	CLONAL	1	TRUE	1	0.264450746998169	7		391	682	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226579937	226579937	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1481258529	NA	P-0025141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	85	756	0	ENST00000366794.5:c.365G>A	p.Arg122Lys	p.R122K	ENST00000366794	NM_001618.3	122	aGa/aAa	3/23	0.264450746998169	4	FACETS	0.913	0.806	1	0.304	0.268	0.343	CLONAL	1	TRUE	1	0.264450746998169	4		756	890	SUCCESS
ATM	472	MSKCC	GRCh37	11	108168043	108168046	+	frameshift_variant	Frame_Shift_Del	DEL	CTAG	CTAG	-	novel	NA	P-0025141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	40	433	0	ENST00000278616.4:c.4939_4942del	p.Val1648SerfsTer11	p.V1648Sfs*11	ENST00000278616	NM_000051.3	1647	CTAGtt/tt	33/63	0.234328886318071	1	FACETS	0.647	0.538	0.767	0.647	0.538	0.767	SUBCLONAL	1	TRUE	0	0.264450746998169	1		433	406	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0025191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	150	398	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.988	0.913	1	0.988	0.913	1	CLONAL	1	TRUE	1	0.755032744925663	2		398	402	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0025191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	288	471	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.755032744925663	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.755032744925663	1		471	446	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981047	55981047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145458680	NA	P-0025191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	308	433	0	ENST00000263923.4:c.652G>A	p.Val218Ile	p.V218I	ENST00000263923	NM_002253.2	218	Gtt/Att	5/30	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.755032744925663	2		433	785	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039349	49039350	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0025191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	382	657	1	ENST00000267163.4:c.2334_2335del	p.Leu779ValfsTer15	p.L779Vfs*15	ENST00000267163	NM_000321.2	778	acCTtg/actg	23/27	0.755032744925663	1	FACETS	0.977	0.938	1	0.977	0.938	1	CLONAL	1	TRUE	0	0.755032744925663	1		658	645	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028893	47028893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556771063	NA	P-0025191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	223	512	2	ENST00000377604.3:c.197C>T	p.Ala66Val	p.A66V	ENST00000377604	NM_001204468.1	66	gCg/gTg	3/24	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.755032744925663	2		514	589	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860120	152860120	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	261	606	0	ENST00000406277.2:c.308del	p.Gly103ValfsTer25	p.G103Vfs*25	ENST00000406277	NM_152274.4	103	gGt/gt	5/7	1		FACETS		0.864	0.973				CLONAL	1	TRUE	1	0.755032744925663	2		606	753	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0025191-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	217	471	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.839860183468252	1	FACETS	0.934	0.89	0.976	0.934	0.89	0.976	CLONAL	1	TRUE	0	0.839860183468252	1		471	321	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860120	152860120	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025191-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	208	606	0	ENST00000406277.2:c.308del	p.Gly103ValfsTer25	p.G103Vfs*25	ENST00000406277	NM_152274.4	103	gGt/gt	5/7	1		FACETS		0.821	0.936				CLONAL	1	TRUE	1	0.839860183468252	2		606	564	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0025191-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	145	340	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.839860183468252	2		340	315	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748282	41748282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767837376	NA	P-0025191-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	333	632	1	ENST00000226382.2:c.487G>A	p.Ala163Thr	p.A163T	ENST00000226382	NM_003924.3	163	Gca/Aca	3/3	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.839860183468252	2		633	733	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0025196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	103	503	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.631447083413866	4	FACETS	0.856	0.775	0.939	0.856	0.775	0.939	CLONAL	2	FALSE	2	0.631447083413866	4		503	311	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578266	7578266	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs942158624	NA	P-0025196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	187	471	0	ENST00000269305.4:c.583A>T	p.Ile195Phe	p.I195F	ENST00000269305	NM_001126112.2	195	Atc/Ttc	6/11	0.526493561549067	3	FACETS	1	0.979	1	0.73	0.686	0.773	CLONAL	2	FALSE	0	0.631447083413866	3		471	356	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264338	46264338	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	84	409	0	ENST00000371998.3:c.1385A>G	p.Asn462Ser	p.N462S	ENST00000371998		462	aAc/aGc	11/23	0.553242551216888	4	FACETS	1	0.963	1	0.6	0.533	0.669	CLONAL	1	FALSE	2	0.631447083413866	4		409	362	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164563	36164602	+	frameshift_variant	Frame_Shift_Del	DEL	CGGTGGAGGCGTTGGTGCAGGGCGGCAGGATGCGCGGCGG	CGGTGGAGGCGTTGGTGCAGGGCGGCAGGATGCGCGGCGG	-	novel	NA	P-0025196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	78	356	0	ENST00000300305.3:c.1273_1312del	p.Pro425AlafsTer156	p.P425Afs*156	ENST00000300305		425	CCGCCGCGCATCCTGCCGCCCTGCACCAACGCCTCCACCGgc/gc	8/8	0.366456056561825	4	FACETS	0.797	0.71	0.887	0.797	0.71	0.887	INDETERMINATE	2	FALSE	2	0.631447083413866	4		356	253	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818810	32818810	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	135	532	0	ENST00000354258.4:c.1141C>G	p.Leu381Val	p.L381V	ENST00000354258	NM_000593.5	381	Ctc/Gtc	4/11	0.366456056561825	4	FACETS	0.813	0.745	0.883	0.813	0.745	0.883	INDETERMINATE	2	FALSE	2	0.631447083413866	4		532	429	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829040	128829042	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	rs570242755	NA	P-0025249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	11	39	0	ENST00000249373.3:c.67_69del	p.Leu23del	p.L23del	ENST00000249373	NM_005631.4	16	ggGCTg/ggg	1/12	1	2	FACETS	0.281	0.195	0.386	0.281	0.195	0.386	SUBCLONAL	1	TRUE	1	0.657702351618576	2		39	119	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0025265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	193	585	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.351116241215175	2	FACETS	0.837	0.782	0.893	0.837	0.782	0.893	CLONAL	2	TRUE	0	0.480212213311467	2		585	480	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347617	89347617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1319171561	NA	P-0025265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	30	559	0	ENST00000301030.4:c.5333C>T	p.Ala1778Val	p.A1778V	ENST00000301030	NM_001256183.1	1778	gCt/gTt	9/13	1	2	FACETS	0.345	0.278	0.421	0.345	0.278	0.421	SUBCLONAL	1	TRUE	1	0.480212213311467	2		559	362	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351745	89351745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201526691	NA	P-0025265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	45	862	0	ENST00000301030.4:c.1205C>T	p.Ala402Val	p.A402V	ENST00000301030	NM_001256183.1	402	gCg/gTg	9/13	1	2	FACETS	0.285	0.239	0.337	0.285	0.239	0.337	SUBCLONAL	1	TRUE	1	0.480212213311467	2		862	657	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028657	12028657	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	25	516	0	ENST00000353533.5:c.860G>T	p.Arg287Leu	p.R287L	ENST00000353533	NM_003010.3	287	cGc/cTc	8/11	0.351116241215175	2	FACETS	0.283	0.223	0.352	0.141	0.111	0.176	SUBCLONAL	1	TRUE	0	0.480212213311467	2		516	368	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591108	67591119	+	inframe_deletion	In_Frame_Del	DEL	ACCAGACCTTAT	ACCAGACCTTAT	-	novel	NA	P-0025265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	85	323	0	ENST00000274335.5:c.1701_1712del	p.Lys567_Ile571delinsAsn	p.K567_I571delinsN	ENST00000274335		567	aaACCAGACCTTATc/aac	12/15	0.335058116317022	2	FACETS	1	0.979	1	0.711	0.638	0.786	CLONAL	1	TRUE	0	0.480212213311467	2		323	249	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0025268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	22	434	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	1	2	FACETS	0.547	0.427	0.686	0.547	0.427	0.686	SUBCLONAL	1	TRUE	1	0.425271467122226	2		434	189	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654622	29654622	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	36	365	0	ENST00000356175.3:c.5311T>G	p.Cys1771Gly	p.C1771G	ENST00000356175	NM_000267.3	1771	Tgc/Ggc	37/57	1	2	FACETS	0.685	0.567	0.816	0.685	0.567	0.816	SUBCLONAL	1	TRUE	1	0.425271467122226	2		365	247	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058446	69058446	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	57	439	0	ENST00000288368.4:c.4090G>A	p.Val1364Ile	p.V1364I	ENST00000288368	NM_024870.2	1364	Gtt/Att	34/40	0.425271467122226	3	FACETS	0.801	0.697	0.91	0.801	0.697	0.91	CLONAL	2	TRUE	1	0.425271467122226	3		439	203	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252994	36252995	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0025270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	161	507	2	ENST00000300305.3:c.367dup	p.Asp123GlyfsTer15	p.D123Gfs*15	ENST00000300305		123	gat/gGat	4/8	1	2	FACETS	0.692	0.636	0.751	0.692	0.636	0.751	SUBCLONAL	1	TRUE	1	0.631196918018588	2		509	737	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853195	68853195	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886039590	NA	P-0025270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	262	528	11	ENST00000261769.5:c.1578G>A	p.Trp526Ter	p.W526*	ENST00000261769	NM_004360.3	526	tgG/tgA	11/16	0.631196918018588	1	FACETS	0.997	0.943	1	0.997	0.943	1	CLONAL	1	TRUE	0	0.631196918018588	1		539	570	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101434	27101434	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	59	565	0	ENST00000324856.7:c.4716C>A	p.Tyr1572Ter	p.Y1572*	ENST00000324856	NM_006015.4	1572	taC/taA	18/20	0.631196918018588	1	FACETS	0.161	0.138	0.186	0.161	0.138	0.186	SUBCLONAL	1	TRUE	0	0.631196918018588	1		565	796	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061190	38061192	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	TGA	TGA	CT	novel	NA	P-0025270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	199	407	7	ENST00000250448.2:c.797_799delinsAG	p.Phe266Ter	p.F266*	ENST00000250448	NM_004496.3	266	tTCAag/tAGag	2/2	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.631196918018588	2		414	580	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0025277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	123	280	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.609453819419334	2		280	401	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063353	67063353	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1334157952	NA	P-0025277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	160	332	1	ENST00000412916.2:c.43G>T	p.Glu15Ter	p.E15*	ENST00000412916		15	Gag/Tag	1/6	0.609453819419334	1	FACETS	0.913	0.847	0.979	0.913	0.847	0.979	CLONAL	1	TRUE	0	0.609453819419334	1		333	400	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119754	70119755	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0025277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	79	547	0	ENST00000245479.2:c.758dup	p.Arg254AlafsTer42	p.R254Afs*42	ENST00000245479	NM_000346.3	252	-/A	3/3	1	2	FACETS	0.402	0.353	0.454	0.402	0.353	0.454	SUBCLONAL	1	TRUE	1	0.609453819419334	2		547	645	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945521	151945525	+	frameshift_variant	Frame_Shift_Del	DEL	TTGTT	TTGTT	-	novel	NA	P-0025277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	81	540	0	ENST00000262189.6:c.1994_1998del	p.Glu665AlafsTer8	p.E665Afs*8	ENST00000262189	NM_170606.2	665	gAACAA/g	14/59	1	2	FACETS	0.637	0.564	0.715	0.637	0.564	0.715	SUBCLONAL	1	TRUE	1	0.609453819419334	2		540	417	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	308	768	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.662512879162698	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.662512879162698	1		768	561	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349058	89349058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555528234	NA	P-0025282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	148	794	1	ENST00000301030.4:c.3892G>A	p.Asp1298Asn	p.D1298N	ENST00000301030	NM_001256183.1	1298	Gat/Aat	9/13	0.662512879162698	1	FACETS	0.394	0.36	0.429	0.394	0.36	0.429	SUBCLONAL	1	TRUE	0	0.662512879162698	1		795	759	SUCCESS
APC	324	MSKCC	GRCh37	5	112178969	112178969	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	171	311	0	ENST00000257430.4:c.7678C>T	p.Arg2560Ter	p.R2560*	ENST00000257430	NM_000038.5	2560	Cga/Tga	16/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.662512879162698	2		311	476	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343021	70343021	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs875989806	NA	P-0025282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	228	589	1	ENST00000374080.3:c.1562G>A	p.Arg521His	p.R521H	ENST00000374080		521	cGt/cAt	11/45	1	2	FACETS	0.766	0.714	0.818	0.766	0.714	0.818	SUBCLONAL	1	TRUE	1	0.662512879162698	2		590	899	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0025291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	668	503	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.820705132505729	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	1	0.820705132505729	3		503	1064	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361160	70361160	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs79912241	NA	P-0025291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	36	704	0	ENST00000374080.3:c.6348C>A	p.His2116Gln	p.H2116Q	ENST00000374080		2116	caC/caA	43/45	0.334721248742575	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.820705132505729	0		704	613	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005296	150005296	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	243	476	0	ENST00000253339.5:c.929T>C	p.Met310Thr	p.M310T	ENST00000253339		310	aTg/aCg	3/7	1	2	FACETS	0.999	0.941	1	0.999	0.941	1	CLONAL	1	TRUE	1	0.820705132505729	2		476	593	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0025310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	996	407	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.425845730639292	5	FACETS	0.959	0.945	0.972			1	INDETERMINATE	5	TRUE	NA	0.779742564423333	5		407	1156	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167801	56167802	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	218	504	0	ENST00000399503.3:c.1368dup	p.Thr457TyrfsTer4	p.T457Yfs*4	ENST00000399503	NM_005921.1	456	ctt/cTtt	7/20	0.779742564423333	1	FACETS	0.95	0.902	0.998	0.95	0.902	0.998	CLONAL	1	TRUE	0	0.779742564423333	1		504	359	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878863	151878863	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1563288201	NA	P-0025310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	234	569	0	ENST00000262189.6:c.6082C>T	p.Arg2028Ter	p.R2028*	ENST00000262189	NM_170606.2	2028	Cga/Tga	36/59	0.382459514207683	1	FACETS	0.667	0.628	0.707	0.667	0.628	0.707	INDETERMINATE	1	TRUE	0	0.779742564423333	1		569	549	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061232	38061232	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1486264414	NA	P-0025310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	314	692	2	ENST00000250448.2:c.757A>G	p.Met253Val	p.M253V	ENST00000250448	NM_004496.3	253	Atg/Gtg	2/2	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.779742564423333	2		694	757	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943936	71943936	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	304	804	0	ENST00000298229.2:c.1869C>G	p.Ile623Met	p.I623M	ENST00000298229	NM_001567.3	623	atC/atG	16/28	NA	2	FACETS	0.801	0.756	0.846			1	INDETERMINATE	1	TRUE	NA	0.779742564423333	2		804	974	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948231	71948231	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	350	1020	0	ENST00000298229.2:c.2943C>G	p.Phe981Leu	p.F981L	ENST00000298229	NM_001567.3	981	ttC/ttG	26/28	NA	2	FACETS	0.818	0.775	0.861			1	INDETERMINATE	1	TRUE	NA	0.779742564423333	2		1020	1098	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913422	32913422	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	100	578	0	ENST00000380152.3:c.4930G>T	p.Glu1644Ter	p.E1644*	ENST00000380152		1644	Gaa/Taa	11/27	0.162895188548448	2	FACETS	1	0.972	1	0.632	0.565	0.703	CLONAL	1	TRUE	0	0.237249285104096	2		578	667	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0025446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	197	558	0	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.355668050592888	1	FACETS	0.949	0.879	1	0.949	0.879	1	CLONAL	1	TRUE	0	0.364688111132944	1		558	931	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415856	49415858	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	rs587783704	NA	P-0025446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	38	404	2	ENST00000301067.7:c.16489_16491del	p.Ile5497del	p.I5497del	ENST00000301067	NM_003482.3	5497	ATC/-	53/54	0.355668050592888	1	FACETS	0.254	0.209	0.305	0.254	0.209	0.305	SUBCLONAL	1	TRUE	0	0.364688111132944	1		406	670	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11204784	11204784	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	139	444	0	ENST00000361445.4:c.4793A>G	p.Glu1598Gly	p.E1598G	ENST00000361445	NM_004958.3	1598	gAg/gGg	34/58	0.355668050592888	1	FACETS	0.816	0.743	0.892	0.816	0.743	0.892	CLONAL	1	TRUE	0	0.364688111132944	1		444	764	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725042	89725042	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1085308041	NA	P-0025456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	23	219	0	ENST00000371953.3:c.1027-2A>G		p.X343_splice	ENST00000371953	NM_000314.4	343			0.275665925001103	3	FACETS	1	0.926	1	0.483	0.384	0.592	CLONAL	1	TRUE	0	0.381810103969744	3		219	99	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211940	36211940	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374728315	NA	P-0025456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	91	831	2	ENST00000222270.7:c.1691G>A	p.Arg564Gln	p.R564Q	ENST00000222270	NM_014727.1	564	cGa/cAa	3/37	0.168850155798629	4	FACETS	0.864	0.767	0.968	0.288	0.255	0.323	INDETERMINATE	1	TRUE	1	0.381810103969744	4		833	762	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974801	21974801	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs145445140	NA	P-0025456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	21	131	0	ENST00000304494.5:c.26T>A	p.Met9Lys	p.M9K	ENST00000304494	NM_000077.4	9	aTg/aAg	1/3	0.363862708172284	0	FACETS	0.708	0.556	0.878			1	SUBCLONAL	1	TRUE	0	0.381810103969744	0		131	96	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0025464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	160	280	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.453542060225408	3	FACETS	0.984	0.911	1	0.984	0.911	1	CLONAL	2	TRUE	1	0.453542060225408	3		280	440	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999518	100999518	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	195	856	0	ENST00000325455.5:c.284G>T	p.Gly95Val	p.G95V	ENST00000325455	NM_001202474.3	95	gGt/gTt	1/8	0.453542060225408	3	FACETS	1	0.963	1	0.533	0.493	0.574	CLONAL	1	TRUE	1	0.453542060225408	3		856	990	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719877	61719877	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	86	407	0	ENST00000401558.2:c.1391T>G	p.Leu464Arg	p.L464R	ENST00000401558	NM_003400.3	464	cTt/cGt	14/25	0.453542060225408	3	FACETS	0.969	0.861	1	0.485	0.43	0.543	CLONAL	1	TRUE	1	0.453542060225408	3		407	480	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171683	36171684	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0025464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	210	425	0	ENST00000300305.3:c.881dup	p.Ser295PhefsTer305	p.S295Ffs*305	ENST00000300305		294	cct/ccCt	7/8	0.453542060225408	3	FACETS	0.976	0.913	1	0.976	0.913	1	CLONAL	2	TRUE	1	0.453542060225408	3		425	582	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206710	36206710	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	187	673	0	ENST00000300305.3:c.802C>T	p.Gln268Ter	p.Q268*	ENST00000300305		268	Cag/Tag	6/8	0.453542060225408	3	FACETS	1	0.981	1	0.591	0.546	0.637	CLONAL	1	TRUE	1	0.453542060225408	3		673	856	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836340	151836340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1260358874	NA	P-0025464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	217	473	0	ENST00000262189.6:c.14465G>A	p.Arg4822His	p.R4822H	ENST00000262189	NM_170606.2	4822	cGt/cAt	57/59	0.453542060225408	3	FACETS	0.863	0.806	0.921	0.863	0.806	0.921	CLONAL	2	TRUE	1	0.453542060225408	3		473	680	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	63	483	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.938	0.812	1	0.938	0.812	1	CLONAL	1	TRUE	1	0.253061570279297	2		483	531	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202801	16202801	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	93	432	0	ENST00000375759.3:c.509del	p.Tyr170LeufsTer196	p.Y170Lfs*196	ENST00000375759	NM_015001.2	170	tAt/tt	3/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.253061570279297	2		432	592	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450080	32450080	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1060501259	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	103	522	0	ENST00000332351.3:c.732C>G	p.Phe244Leu	p.F244L	ENST00000332351	NM_024426.4	244	ttC/ttG	2/10	0.212945027247758	1	FACETS	0.986	0.883	1	0.986	0.883	1	CLONAL	1	TRUE	0	0.253061570279297	1		522	721	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103416	77103416	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	70	422	0	ENST00000356341.3:c.150G>C	p.Lys50Asn	p.K50N	ENST00000356341	NM_002576.4	50	aaG/aaC	2/15	1	2	FACETS	0.895	0.781	1	0.895	0.781	1	CLONAL	1	TRUE	1	0.253061570279297	2		422	618	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383225	4383225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	41	323	0	ENST00000261254.3:c.19G>A	p.Glu7Lys	p.E7K	ENST00000261254	NM_001759.3	7	Gag/Aag	1/5	1	2	FACETS	0.959	0.801	1	0.959	0.801	1	CLONAL	1	TRUE	1	0.253061570279297	2		323	338	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443518	49443518	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	33	507	0	ENST00000301067.7:c.3853G>C	p.Glu1285Gln	p.E1285Q	ENST00000301067	NM_003482.3	1285	Gag/Cag	11/54	1	2	FACETS	0.421	0.342	0.511	0.421	0.342	0.511	SUBCLONAL	1	TRUE	1	0.253061570279297	2		507	619	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005643	42005643	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	40	325	0	ENST00000219905.7:c.3379G>C	p.Glu1127Gln	p.E1127Q	ENST00000219905	NM_001164273.1	1127	Gag/Cag	9/24	1	2	FACETS	0.751	0.624	0.891	0.751	0.624	0.891	SUBCLONAL	1	TRUE	1	0.253061570279297	2		325	421	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867215	68867216	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	90	543	0	ENST00000261769.5:c.2466dup	p.Thr823HisfsTer6	p.T823Hfs*6	ENST00000261769	NM_004360.3	821	gac/gaCc	16/16	0.253061570279297	1	FACETS	0.977	0.868	1	0.977	0.868	1	CLONAL	1	TRUE	0	0.253061570279297	1		543	636	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832413	72832413	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	71	333	1	ENST00000268489.5:c.4168C>T	p.Gln1390Ter	p.Q1390*	ENST00000268489	NM_006885.3	1390	Cag/Tag	9/10	0.253061570279297	1	FACETS	0.914	0.799	1	0.914	0.799	1	CLONAL	1	TRUE	0	0.253061570279297	1		334	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	76	526	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.253061570279297	1	FACETS	0.897	0.787	1	0.897	0.787	1	CLONAL	1	TRUE	0	0.253061570279297	1		526	585	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004630	16004630	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	61	608	0	ENST00000268712.3:c.2624C>G	p.Ser875Ter	p.S875*	ENST00000268712	NM_006311.3	875	tCa/tGa	20/46	0.253061570279297	1	FACETS	0.639	0.551	0.735	0.639	0.551	0.735	SUBCLONAL	1	TRUE	0	0.253061570279297	1		608	659	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576091	29576091	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1131691087	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	82	520	0	ENST00000356175.3:c.4064C>G	p.Ser1355Ter	p.S1355*	ENST00000356175	NM_000267.3	1355	tCa/tGa	30/57	0.253061570279297	1	FACETS	0.723	0.637	0.816	0.723	0.637	0.816	SUBCLONAL	1	TRUE	0	0.253061570279297	1		520	783	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244499	41244499	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	85	638	0	ENST00000357654.3:c.3049G>C	p.Glu1017Gln	p.E1017Q	ENST00000357654	NM_007294.3	1017	Gag/Cag	10/23	0.253061570279297	1	FACETS	0.928	0.821	1	0.928	0.821	1	CLONAL	1	TRUE	0	0.253061570279297	1		638	632	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761121	59761121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	95	624	0	ENST00000259008.2:c.3286G>A	p.Glu1096Lys	p.E1096K	ENST00000259008	NM_032043.2	1096	Gaa/Aaa	20/20	0.253061570279297	1	FACETS	0.934	0.832	1	0.934	0.832	1	CLONAL	1	TRUE	0	0.253061570279297	1		624	702	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604655	48604655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	54	288	0	ENST00000342988.3:c.1477G>A	p.Asp493Asn	p.D493N	ENST00000342988	NM_005359.5	493	Gat/Aat	12/12	0.212945027247758	1	FACETS	0.786	0.673	0.911	0.786	0.673	0.911	CLONAL	1	TRUE	0	0.253061570279297	1		288	474	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621184	1621184	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	73	564	2	ENST00000344749.5:c.962G>T	p.Arg321Leu	p.R321L	ENST00000344749	NM_001136139.2	321	cGa/cTa	12/19	1	2	FACETS	0.791	0.691	0.899	0.791	0.691	0.899	SUBCLONAL	1	TRUE	1	0.253061570279297	2		566	729	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281228	15281228	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	93	667	0	ENST00000263388.2:c.5028C>A	p.Phe1676Leu	p.F1676L	ENST00000263388	NM_000435.2	1676	ttC/ttA	27/33	1	2	FACETS	0.86	0.763	0.963	0.86	0.763	0.963	CLONAL	1	TRUE	1	0.253061570279297	2		667	855	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366234	15366234	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	75	597	0	ENST00000263377.2:c.1921G>A	p.Glu641Lys	p.E641K	ENST00000263377	NM_058243.2	641	Gag/Aag	10/20	1	2	FACETS	0.785	0.687	0.891	0.785	0.687	0.891	SUBCLONAL	1	TRUE	1	0.253061570279297	2		597	755	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279355	18279355	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	66	473	1	ENST00000222254.8:c.1807G>A	p.Asp603Asn	p.D603N	ENST00000222254	NM_005027.3	603	Gac/Aac	14/16	1	2	FACETS	0.835	0.724	0.954	0.835	0.724	0.954	CLONAL	1	TRUE	1	0.253061570279297	2		474	625	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416740	29416740	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	55	408	0	ENST00000389048.3:c.4213G>C	p.Val1405Leu	p.V1405L	ENST00000389048	NM_004304.4	1405	Gtg/Ctg	29/29	1	2	FACETS	0.768	0.657	0.89	0.768	0.657	0.89	SUBCLONAL	1	TRUE	1	0.253061570279297	2		408	566	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212615408	212615408	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	105	541	0	ENST00000342788.4:c.578G>A	p.Cys193Tyr	p.C193Y	ENST00000342788	NM_005235.2	193	tGt/tAt	5/28	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.253061570279297	2		541	736	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652755	212652755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760630823	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	43	384	3	ENST00000342788.4:c.551C>T	p.Ser184Leu	p.S184L	ENST00000342788	NM_005235.2	184	tCa/tTa	4/28	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.253061570279297	2		387	318	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370699	225370699	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	83	489	0	ENST00000264414.4:c.1180G>C	p.Asp394His	p.D394H	ENST00000264414	NM_003590.4	394	Gat/Cat	8/16	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.253061570279297	2		489	624	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637539	52637539	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	72	565	0	ENST00000394830.3:c.2777G>C	p.Arg926Thr	p.R926T	ENST00000394830	NM_018313.4	926	aGa/aCa	18/30	1	2	FACETS	0.79	0.69	0.899	0.79	0.69	0.899	SUBCLONAL	1	TRUE	1	0.253061570279297	2		565	720	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	62	316	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.817	0.705	0.938	0.817	0.705	0.938	CLONAL	1	TRUE	1	0.253061570279297	2		316	600	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157673	106157673	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	48	346	0	ENST00000380013.4:c.2574G>C	p.Lys858Asn	p.K858N	ENST00000380013	NM_001127208.2	858	aaG/aaC	3/11	1	2	FACETS	0.941	0.798	1	0.941	0.798	1	CLONAL	1	TRUE	1	0.253061570279297	2		346	403	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196705	106196705	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs997900764	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	79	487	0	ENST00000380013.4:c.5038C>T	p.Gln1680Ter	p.Q1680*	ENST00000380013	NM_001127208.2	1680	Cag/Tag	11/11	1	2	FACETS	0.855	0.752	0.967	0.855	0.752	0.967	CLONAL	1	TRUE	1	0.253061570279297	2		487	730	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509446	149509446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41287110	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	110	692	0	ENST00000261799.4:c.1453G>A	p.Glu485Lys	p.E485K	ENST00000261799	NM_002609.3	485	Gag/Aag	10/23	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.253061570279297	2		692	864	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672139	30672139	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	43	594	0	ENST00000376406.3:c.4821G>C	p.Lys1607Asn	p.K1607N	ENST00000376406	NM_014641.2	1607	aaG/aaC	10/15	1	2	FACETS	0.439	0.366	0.52	0.439	0.366	0.52	SUBCLONAL	1	TRUE	1	0.253061570279297	2		594	775	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673215	30673215	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	35	469	0	ENST00000376406.3:c.3745G>C	p.Glu1249Gln	p.E1249Q	ENST00000376406	NM_014641.2	1249	Gag/Cag	10/15	1	2	FACETS	0.441	0.36	0.532	0.441	0.36	0.532	SUBCLONAL	1	TRUE	1	0.253061570279297	2		469	627	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673391	30673391	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	53	647	0	ENST00000376406.3:c.3569G>C	p.Arg1190Thr	p.R1190T	ENST00000376406	NM_014641.2	1190	aGa/aCa	10/15	1	2	FACETS	0.485	0.413	0.566	0.485	0.413	0.566	SUBCLONAL	1	TRUE	1	0.253061570279297	2		647	863	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675523	30675523	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1260988837	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	55	716	0	ENST00000376406.3:c.2833G>C	p.Asp945His	p.D945H	ENST00000376406	NM_014641.2	945	Gat/Cat	8/15	1	2	FACETS	0.413	0.352	0.481	0.413	0.352	0.481	SUBCLONAL	1	TRUE	1	0.253061570279297	2		716	1052	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798524	32798524	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	91	618	0	ENST00000374899.4:c.1332C>G	p.Phe444Leu	p.F444L	ENST00000374899	NM_018833.2	444	ttC/ttG	8/12	1	2	FACETS	0.806	0.715	0.904	0.806	0.715	0.904	CLONAL	1	TRUE	1	0.253061570279297	2		618	892	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97897771	97897771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	56	388	0	ENST00000289081.3:c.700C>T	p.Leu234Phe	p.L234F	ENST00000289081	NM_000136.2	234	Ctc/Ttc	8/15	1	2	FACETS	0.75	0.642	0.868	0.75	0.642	0.868	SUBCLONAL	1	TRUE	1	0.253061570279297	2		388	590	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209357	98209357	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748812637	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	30	505	2	ENST00000331920.6:c.4181G>A	p.Arg1394Gln	p.R1394Q	ENST00000331920	NM_000264.3	1394	cGa/cAa	23/24	1	2	FACETS	0.431	0.346	0.528	0.431	0.346	0.528	SUBCLONAL	1	TRUE	1	0.253061570279297	2		507	550	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787747	135787747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1467020958	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	100	508	0	ENST00000298552.3:c.835C>T	p.His279Tyr	p.H279Y	ENST00000298552	NM_001162426.1	279	Cac/Tac	9/23	1	2	FACETS	0.979	0.874	1	0.979	0.874	1	CLONAL	1	TRUE	1	0.253061570279297	2		508	807	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413088	139413088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	82	585	0	ENST00000277541.6:c.1054G>A	p.Asp352Asn	p.D352N	ENST00000277541	NM_017617.3	352	Gac/Aac	6/34	1	2	FACETS	0.927	0.817	1	0.927	0.817	1	CLONAL	1	TRUE	1	0.253061570279297	2		585	699	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577129	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519986	NA	P-0025690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	196	742	0	ENST00000269305.4:c.809T>G	p.Phe270Cys	p.F270C	ENST00000269305	NM_001126112.2	270	tTt/tGt	8/11	0.233770693068613	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.235325789729545	2		742	738	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609754	117609754	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1281	118	569	0	ENST00000368508.3:c.6945C>A	p.Phe2315Leu	p.F2315L	ENST00000368508	NM_002944.2	2315	ttC/ttA	43/43	0.235325789729545	10	FACETS	1	0.981	1	0.155	0.139	0.172	CLONAL	1	TRUE	1	0.235325789729545	10		569	1399	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001184	150001184	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	103	684	0	ENST00000253339.5:c.2420T>C	p.Phe807Ser	p.F807S	ENST00000253339		807	tTc/tCc	4/7	0.235325789729545	1	FACETS	0.975	0.872	1	0.975	0.872	1	CLONAL	1	TRUE	0	0.235325789729545	1		684	792	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543653	148543653	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752284693	NA	P-0025690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	62	489	0	ENST00000320356.2:c.155G>A	p.Arg52Lys	p.R52K	ENST00000320356	NM_004456.4	52	aGa/aAa	3/20	0.233770693068613	2	FACETS	0.769	0.664	0.884	0.385	0.332	0.442	SUBCLONAL	1	TRUE	0	0.235325789729545	2		489	685	SUCCESS
BTK	695	MSKCC	GRCh37	X	100612532	100612532	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	53	561	0	ENST00000308731.7:c.1142A>G	p.Asn381Ser	p.N381S	ENST00000308731	NM_000061.2	381	aAc/aGc	13/19	0.235325789729545	3	FACETS	0.65	0.553	0.757	0.325	0.276	0.379	SUBCLONAL	1	TRUE	1	0.235325789729545	3		561	774	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0025697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	171	483	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.548293560608895	2		483	613	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716095	243716095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	260	552	0	ENST00000263826.5:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000263826	NM_005465.4	367	Cga/Tga	10/13	0.478541398340981	4	FACETS	1	0.991	1	0.447	0.418	0.476	CLONAL	1	TRUE	1	0.548293560608895	4		552	1095	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862084	68862085	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0025697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	211	391	0	ENST00000261769.5:c.2173_2174del	p.Leu725AlafsTer22	p.L725Afs*22	ENST00000261769	NM_004360.3	724	atTCtg/attg	14/16	0.548293560608895	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.548293560608895	1		391	467	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174806	56174807	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0025697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	75	269	0	ENST00000399503.3:c.1968_1969dup	p.Thr657LysfsTer3	p.T657Kfs*3	ENST00000399503	NM_005921.1	655	-/AA		1	2	FACETS	0.724	0.638	0.815	0.724	0.638	0.815	SUBCLONAL	1	TRUE	1	0.548293560608895	2		269	378	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177456	56177456	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0025697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	41	337	0	ENST00000399503.3:c.2429C>G	p.Ser810Ter	p.S810*	ENST00000399503	NM_005921.1	810	tCa/tGa	14/20	NA	2	FACETS	0.369	0.308	0.437			1	INDETERMINATE	1	TRUE	NA	0.548293560608895	2		337	405	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187954	32187954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1366333651	NA	P-0025697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	106	584	1	ENST00000375023.3:c.1267G>A	p.Gly423Ser	p.G423S	ENST00000375023	NM_004557.3	423	Ggc/Agc	7/30	1	2	FACETS	0.525	0.47	0.582	0.525	0.47	0.582	SUBCLONAL	1	TRUE	1	0.548293560608895	2		585	737	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0025728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	236	290	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.343865994289964	4	FACETS	0.839	0.786	0.893	0.839	0.786	0.893	CLONAL	3	TRUE	1	0.343865994289964	4		290	733	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs17849781	NA	P-0025728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	122	583	0	ENST00000269305.4:c.832C>G	p.Pro278Ala	p.P278A	ENST00000269305	NM_001126112.2	278	Cct/Gct	8/11	0.304263935865477	1	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	0	0.343865994289964	1		583	585	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415858	49415859	+	inframe_insertion	In_Frame_Ins	INS	-	-	GATGATGATTTTGTCCTC	novel	NA	P-0025728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	53	344	0	ENST00000301067.7:c.16471_16488dup	p.Glu5491_Ile5496dup	p.E5491_I5496dup	ENST00000301067	NM_003482.3	5491	-/GAGGACAAAATCATCATC	53/54	0.343865994289964	2	FACETS	0.641	0.547	0.743	0.32	0.273	0.372	SUBCLONAL	1	TRUE	0	0.343865994289964	2		344	481	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504413	186504417	+	frameshift_variant	Frame_Shift_Del	DEL	TTATA	TTATA	-	novel	NA	P-0025728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	95	533	0	ENST00000323963.5:c.753_757del	p.Tyr251Ter	p.Y251*	ENST00000323963		250	ttTTATAtt/tttt	7/11	0.343865994289964	3	FACETS	0.845	0.752	0.945	0.282	0.25	0.315	CLONAL	1	TRUE	0	0.343865994289964	3		533	766	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs121913468	NA	P-0025732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	27	675	0	ENST00000269571.5:c.2305G>C	p.Asp769His	p.D769H	ENST00000269571		769	Gac/Cac	19/27	1	2	FACETS	0.784	0.622	0.97	0.784	0.622	0.97	CLONAL	1	TRUE	1	0.12	2		675	574	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0025732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	41	767	2	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	1	2	FACETS	0.99	0.823	1	0.99	0.823	1	CLONAL	1	TRUE	1	0.12	2		769	690	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844180	68844180	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	35	845	0	ENST00000261769.5:c.768T>A	p.Asn256Lys	p.N256K	ENST00000261769	NM_004360.3	256	aaT/aaA	6/16	1	2	FACETS	0.868	0.71	1	0.868	0.71	1	CLONAL	1	TRUE	1	0.12	2		845	672	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0025740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	221	336	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.345143905597419	4	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	2	0.542891011803574	4		336	628	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0026150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	120	403	2	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.631143924465603	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.631143924465603	1		405	224	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0026232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	397	615	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.527347593457802	2	FACETS	0.923	0.885	0.96	0.923	0.885	0.96	CLONAL	2	TRUE	0	0.57905918759838	2		615	743	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298516	11298516	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	86	568	0	ENST00000361445.4:c.1945G>C	p.Val649Leu	p.V649L	ENST00000361445	NM_004958.3	649	Gtg/Ctg	12/58	0.162960972651217	5	FACETS	0.57	0.503	0.642	0.19	0.167	0.214	INDETERMINATE	1	TRUE	2	0.57905918759838	5		568	974	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648245	206648245	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	124	540	0	ENST00000367120.3:c.266G>C	p.Cys89Ser	p.C89S	ENST00000367120	NM_014002.3	89	tGc/tCc	5/22	1	2	FACETS	0.584	0.529	0.643	0.584	0.529	0.643	SUBCLONAL	1	TRUE	1	0.57905918759838	2		540	733	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13949280	13949280	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	44	215	0	ENST00000405192.2:c.848G>C	p.Cys283Ser	p.C283S	ENST00000405192	NM_001163147.1	283	tGt/tCt	9/12	0.396845951837727	0	FACETS	0.299	0.253	0.349			1	SUBCLONAL	1	TRUE	0	0.57905918759838	0		215	214	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271298	38271298	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	61	730	0	ENST00000425967.3:c.2410C>G	p.Leu804Val	p.L804V	ENST00000425967	NM_001174067.1	804	Ctg/Gtg	19/19	0.57905918759838	1	FACETS	0.186	0.159	0.214	0.186	0.159	0.214	SUBCLONAL	1	TRUE	0	0.57905918759838	1		730	806	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0026238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	44	185	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.719	0.607	0.84	0.719	0.607	0.84	SUBCLONAL	1	TRUE	1	0.480301484881685	2		185	255	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0026238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	12	270	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	0.22	0.154	0.301	0.22	0.154	0.301	SUBCLONAL	1	TRUE	1	0.480301484881685	2		270	227	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449806	29449806	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	120	488	2	ENST00000389048.3:c.3049G>A	p.Asp1017Asn	p.D1017N	ENST00000389048	NM_004304.4	1017	Gat/Aat	18/29	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.480301484881685	2		490	479	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380907	116380907	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	52	211	0	ENST00000397752.3:c.1529T>A	p.Ile510Asn	p.I510N	ENST00000397752	NM_000245.2	510	aTc/aAc	5/21	1	2	FACETS	0.898	0.773	1	0.898	0.773	1	CLONAL	1	TRUE	1	0.480301484881685	2		211	241	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0026240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	47	400	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.817	0.694	0.95	1	0.967	1	CLONAL	2	TRUE	1	0.21	2		400	274	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs17849781	NA	P-0026240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	72	935	0	ENST00000269305.4:c.832C>A	p.Pro278Thr	p.P278T	ENST00000269305	NM_001126112.2	278	Cct/Act	8/11	0.302461732803703	1	FACETS	1	0.929	1	1	0.984	1	CLONAL	2	TRUE	0	0.21	1		935	286	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	9	425	0	ENST00000263121.7:c.1130G>T	p.Arg377Leu	p.R377L	ENST00000263121	NM_003073.3	377	cGt/cTt	9/9	1	2	FACETS	0.291	0.191	0.418	0.291	0.191	0.418	SUBCLONAL	1	TRUE	1	0.21	2		425	295	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2214485	2214485	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	78	352	0	ENST00000398665.3:c.1813G>T	p.Glu605Ter	p.E605*	ENST00000398665	NM_032482.2	605	Gag/Tag	19/28	1	2	FACETS	0.919	0.812	1	1	0.982	1	CLONAL	2	TRUE	1	0.21	2		352	404	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754088	42754088	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0026240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	40	294	0	ENST00000222329.4:c.264C>G	p.Tyr88Ter	p.Y88*	ENST00000222329	NM_006494.2	88	taC/taG	3/4	1	2	FACETS	0.876	0.741	1	1	0.975	1	CLONAL	3	TRUE	1	0.21	2		294	145	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857867	89857867	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148473140	NA	P-0026244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	92	378	0	ENST00000389301.3:c.1303C>T	p.Arg435Cys	p.R435C	ENST00000389301	NM_000135.2	435	Cgc/Tgc	14/43	1	2	FACETS	0.851	0.762	0.943	0.851	0.762	0.943	CLONAL	1	TRUE	1	0.594313531955883	2		378	364	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251184	99251184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182472366	NA	P-0026244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	115	395	0	ENST00000268035.6:c.488C>T	p.Ala163Val	p.A163V	ENST00000268035	NM_000875.3	163	gCg/gTg	2/21	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.594313531955883	2		395	378	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	91	441	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.73217111777592	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.73217111777592	3		441	160	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95595814	95595814	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	36	249	0	ENST00000393063.1:c.729A>T	p.Leu243Phe	p.L243F	ENST00000393063	NM_030621.3	243	ttA/ttT	7/28	0.73217111777592	3	FACETS	0.988	0.827	1	0.494	0.413	0.58	CLONAL	1	TRUE	1	0.73217111777592	3		249	136	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660534	227660534	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	106	235	0	ENST00000305123.5:c.2921G>C	p.Ser974Thr	p.S974T	ENST00000305123	NM_005544.2	974	aGc/aCc	1/2	0.73217111777592	3	FACETS	1	0.962	1	0.562	0.509	0.617	CLONAL	1	TRUE	1	0.73217111777592	3		235	352	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721789	176721789	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	82	246	0	ENST00000439151.2:c.7420C>T	p.Gln2474Ter	p.Q2474*	ENST00000439151	NM_022455.4	2474	Cag/Tag	23/23	0.73217111777592	3	FACETS	1	0.921	1	0.52	0.464	0.58	CLONAL	1	TRUE	1	0.73217111777592	3		246	294	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412721	63412721	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	97	244	0	ENST00000330258.3:c.446G>C	p.Gly149Ala	p.G149A	ENST00000330258	NM_152424.3	149	gGa/gCa	2/2	0.73217111777592	3	FACETS	1	0.907	1	0.504	0.453	0.557	CLONAL	1	TRUE	1	0.73217111777592	3		244	359	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0026288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	281	654	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.537896709856469	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	3	TRUE	0	0.538760432739173	3		654	439	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820570	3820570	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0026288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	374	537	0	ENST00000262367.5:c.2880+1G>T		p.X960_splice	ENST00000262367	NM_004380.2	960			0.497904125100898	4	FACETS	0.886	0.852	0.919	0.886	0.852	0.919	CLONAL	4	TRUE	0	0.538760432739173	4		537	603	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120798	94120798	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	79	291	1	ENST00000369303.4:c.253C>A	p.Leu85Met	p.L85M	ENST00000369303	NM_004440.3	85	Ctg/Atg	3/17	0.537896709856469	4	FACETS	1	0.914	1	0.347	0.307	0.391	CLONAL	1	TRUE	1	0.538760432739173	4		292	433	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099359	157099359	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1188660877	NA	P-0026288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	59	150	0	ENST00000346085.5:c.296A>T	p.His99Leu	p.H99L	ENST00000346085	NM_020732.3	99	cAc/cTc	1/20	0.537896709856469	4	FACETS	1	0.965	1	0.453	0.394	0.516	CLONAL	1	TRUE	1	0.538760432739173	4		150	248	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928070	178928085	+	protein_altering_variant	In_Frame_Del	DEL	CATGGATTAGAAGATT	CATGGATTAGAAGATT	G	novel	NA	P-0026288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	105	466	0	ENST00000263967.3:c.1348_1363delinsG	p.His450_Leu455delinsVal	p.H450_L455delinsV	ENST00000263967	NM_006218.2	450	CATGGATTAGAAGATTtg/Gtg	8/21	0.537896709856469	5	FACETS	1	0.977	1	0.435	0.391	0.482	CLONAL	1	TRUE	2	0.538760432739173	5		466	540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0026288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	61	654	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.328498831432849	1	FACETS	0.657	0.568	0.752	0.657	0.568	0.752	SUBCLONAL	1	FALSE	0	0.360081681583348	1		654	423	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820570	3820570	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0026288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	85	537	0	ENST00000262367.5:c.2880+1G>T		p.X960_splice	ENST00000262367	NM_004380.2	960			1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	FALSE	1	0.360081681583348	2		537	438	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928070	178928085	+	protein_altering_variant	In_Frame_Del	DEL	CATGGATTAGAAGATT	CATGGATTAGAAGATT	G	novel	NA	P-0026288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	51	466	0	ENST00000263967.3:c.1348_1363delinsG	p.His450_Leu455delinsVal	p.H450_L455delinsV	ENST00000263967	NM_006218.2	450	CATGGATTAGAAGATTtg/Gtg	8/21	1	2	FACETS	0.493	0.418	0.574	0.493	0.418	0.574	SUBCLONAL	1	FALSE	1	0.360081681583348	2		466	575	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0026330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	107	400	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.667097387913192	3	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	1	0.692219831773859	3		400	204	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0026330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	63	594	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.667097387913192	3	FACETS	1	0.896	1	0.513	0.449	0.58	CLONAL	1	TRUE	1	0.692219831773859	3		594	239	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	93	556	0	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	0.667097387913192	3	FACETS	0.869	0.791	0.949	0.869	0.791	0.949	CLONAL	2	TRUE	1	0.692219831773859	3		556	208	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272447	15272447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201105335	NA	P-0026330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	112	586	2	ENST00000263388.2:c.5992C>T	p.Arg1998Cys	p.R1998C	ENST00000263388	NM_000435.2	1998	Cgt/Tgt	33/33	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.692219831773859	2		588	286	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851456	63851456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201542647	NA	P-0026330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	61	326	1	ENST00000279873.7:c.2234C>T	p.Ala745Val	p.A745V	ENST00000279873	NM_032199.2	745	gCg/gTg	10/10	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.692219831773859	2		327	160	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045967	26045968	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs761955716	NA	P-0026330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	47	290	0	ENST00000540144.1:c.331_332del	p.Cys111ArgfsTer5	p.C111Rfs*5	ENST00000540144	NM_003531.2	110	cTG/c	1/1	0.667097387913192	3	FACETS	1	0.915	1	0.547	0.47	0.63	CLONAL	1	TRUE	1	0.692219831773859	3		290	167	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0026332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	51	444	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.982	0.853	1	0.982	0.853	1	CLONAL	1	TRUE	1	0.702084348962456	2		444	148	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs730881677	NA	P-0026332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	41	240	0	ENST00000304494.5:c.151-1G>C		p.X51_splice	ENST00000304494	NM_000077.4	51			0.702084348962456	1	FACETS	0.947	0.826	1	0.947	0.826	1	CLONAL	1	TRUE	0	0.702084348962456	1		240	80	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610478	10610478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	55	378	0	ENST00000171111.5:c.232G>A	p.Asp78Asn	p.D78N	ENST00000171111	NM_203500.1	78	Gac/Aac	2/6	0.702084348962456	1	FACETS	0.764	0.672	0.859	0.764	0.672	0.859	SUBCLONAL	1	TRUE	0	0.702084348962456	1		378	133	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097143	11097143	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886937766	NA	P-0026332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	57	346	0	ENST00000358026.2:c.634G>A	p.Gly212Arg	p.G212R	ENST00000358026	NM_001128849.1	212	Ggg/Agg	4/36	0.702084348962456	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.702084348962456	1		346	103	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118641	11118641	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0026332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	59	481	0	ENST00000358026.2:c.2065A>T	p.Lys689Ter	p.K689*	ENST00000358026	NM_001128849.1	689	Aag/Tag	14/36	0.702084348962456	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.702084348962456	1		481	93	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636770	8636771	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0026332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	29	342	0	ENST00000356435.5:c.138dup	p.Ala47SerfsTer8	p.A47Sfs*8	ENST00000356435		46	-/A	2/35	0.702084348962456	1	FACETS	0.654	0.542	0.772	0.654	0.542	0.772	SUBCLONAL	1	TRUE	0	0.702084348962456	1		342	82	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023720	27023721	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0026384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	37	495	0	ENST00000324856.7:c.828_829dup	p.Gly277GlufsTer87	p.G277Efs*87	ENST00000324856	NM_006015.4	276	gga/gGAga	1/20	1	2	FACETS	0.188	0.154	0.226	0.188	0.154	0.226	SUBCLONAL	1	TRUE	1	0.53632932210174	2		495	734	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118890	70118890	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	89	667	0	ENST00000245479.2:c.462C>A	p.Phe154Leu	p.F154L	ENST00000245479	NM_000346.3	154	ttC/ttA	2/3	1	2	FACETS	0.432	0.383	0.485	0.432	0.383	0.485	SUBCLONAL	1	TRUE	1	0.53632932210174	2		667	768	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349948	70349948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	59	834	0	ENST00000374080.3:c.3931G>A	p.Val1311Met	p.V1311M	ENST00000374080		1311	Gtg/Atg	28/45	1	2	FACETS	0.192	0.164	0.223	0.192	0.164	0.223	SUBCLONAL	1	TRUE	1	0.53632932210174	2		834	1144	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519893	NA	P-0026403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	201	805	0	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	0.306586803472273	2		805	1151	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913471	NA	P-0026403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	37	727	1	ENST00000269571.5:c.2329G>A	p.Val777Met	p.V777M	ENST00000269571		777	Gtg/Atg	20/27	1	2	FACETS	0.255	0.209	0.307	0.255	0.209	0.307	SUBCLONAL	1	TRUE	1	0.306586803472273	2		728	946	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604764	48604765	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs377767376	NA	P-0026403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	95	608	0	ENST00000342988.3:c.1587dup	p.His530ThrfsTer47	p.H530Tfs*47	ENST00000342988	NM_005359.5	529	tta/ttAa	12/12	0.306586803472273	1	FACETS	0.682	0.607	0.763	0.682	0.607	0.763	SUBCLONAL	1	TRUE	0	0.306586803472273	1		608	769	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089513	27089513	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	130	791	1	ENST00000324856.7:c.2472del	p.Ser825ValfsTer8	p.S825Vfs*8	ENST00000324856	NM_006015.4	823	taC/ta	8/20	0.299712056969058	2	FACETS	0.804	0.728	0.884	0.402	0.364	0.442	CLONAL	1	TRUE	0	0.306586803472273	2		792	1055	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983120	201983121	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	66	747	0	ENST00000359651.3:c.970dup	p.Met324AsnfsTer147	p.M324Nfs*147	ENST00000359651		323	-/A	7/8	1	2	FACETS	0.425	0.368	0.488	0.425	0.368	0.488	SUBCLONAL	1	TRUE	1	0.306586803472273	2		747	1013	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052635	42052635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	161	614	2	ENST00000219905.7:c.7306C>T	p.Arg2436Cys	p.R2436C	ENST00000219905	NM_001164273.1	2436	Cgt/Tgt	20/24	1	2	FACETS	0.991	0.908	1	0.991	0.908	1	CLONAL	1	TRUE	1	0.306586803472273	2		616	1060	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441542	40441542	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	98	804	0	ENST00000345506.4:c.113T>A	p.Ile38Asn	p.I38N	ENST00000345506	NM_003152.3	38	aTt/aAt	3/20	1	2	FACETS	0.654	0.582	0.731	0.654	0.582	0.731	SUBCLONAL	1	TRUE	1	0.306586803472273	2		804	977	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440662	56440662	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	136	692	0	ENST00000407977.2:c.556A>T	p.Ile186Phe	p.I186F	ENST00000407977		186	Att/Ttt	5/10	1	2	FACETS	0.906	0.823	0.994	0.906	0.823	0.994	CLONAL	1	TRUE	1	0.306586803472273	2		692	979	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111780	56111780	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	24	33	1	ENST00000399503.3:c.380C>A	p.Ser127Ter	p.S127*	ENST00000399503	NM_005921.1	127	tCg/tAg	1/20	1	2	FACETS	0.824	0.661	1	1	0.941	1	CLONAL	2	TRUE	1	0.306586803472273	2		34	95	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873587	151873588	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	110	645	0	ENST00000262189.6:c.8950dup	p.Ser2984PhefsTer18	p.S2984Ffs*18	ENST00000262189	NM_170606.2	2984	tct/tTct	38/59	1	2	FACETS	0.867	0.778	0.96	0.867	0.778	0.96	CLONAL	1	TRUE	1	0.306586803472273	2		645	828	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040963	47040964	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0026403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	168	736	0	ENST00000377604.3:c.1494dup	p.Ala499ArgfsTer19	p.A499Rfs*19	ENST00000377604	NM_001204468.1	498	cgc/cgCc	14/24	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.306586803472273	2		736	985	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429809	78429809	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	218	474	10	ENST00000370768.2:c.979G>A	p.Gly327Arg	p.G327R	ENST00000370768	NM_003902.3	327	Gga/Aga	12/20	0.673199889205483	3	FACETS	0.996	0.928	1	0.498	0.464	0.533	CLONAL	1	TRUE	1	0.673199889205483	3		484	869	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151688	108151738	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTACATTACATTTTTTTTTTAATTTCTTTTTAAGTCCCATAGTGCTGAGAA	TTACATTACATTTTTTTTTTAATTTCTTTTTAAGTCCCATAGTGCTGAGAA	-	novel	NA	P-0026439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	87	120	4	ENST00000278616.4:c.3403-34_3419del		p.X1135_splice	ENST00000278616	NM_000051.3	1135		24/63	1	2	FACETS	0.788	0.719	0.856	1	0.985	1	SUBCLONAL	2	TRUE	1	0.673199889205483	2		124	164	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579532	7579533	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	786	757	16	ENST00000269305.4:c.154dup	p.Gln52ProfsTer5	p.Q52Pfs*5	ENST00000269305	NM_001126112.2	52	caa/cCaa	4/11	0.66358727370508	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.673199889205483	2		773	1137	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495376	149495376	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	670	646	33	ENST00000261799.4:c.3271G>C	p.Asp1091His	p.D1091H	ENST00000261799	NM_002609.3	1091	Gat/Cat	23/23	0.673199889205483	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.673199889205483	2		679	940	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	310	441	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.451435207775531	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.452497007737267	2		441	653	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0026465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	199	688	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.452497007737267	1	FACETS	0.943	0.876	1	0.943	0.876	1	CLONAL	1	TRUE	0	0.452497007737267	1		688	722	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0026465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	140	337	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.452497007737267	1	FACETS	0.954	0.874	1	0.954	0.874	1	CLONAL	1	TRUE	0	0.452497007737267	1		337	502	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440904	56440904	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1458799446	NA	P-0026465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	217	719	0	ENST00000407977.2:c.433C>T	p.Arg145Ter	p.R145*	ENST00000407977		145	Cga/Tga	4/10	0.452959211346966	3	FACETS	1	0.945	1	0.51	0.474	0.548	CLONAL	1	TRUE	1	0.452497007737267	3		719	1152	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593405	48593405	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519962	NA	P-0026465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	129	425	0	ENST00000342988.3:c.1156G>A	p.Gly386Ser	p.G386S	ENST00000342988	NM_005359.5	386	Ggt/Agt	10/12	0.452497007737267	1	FACETS	0.895	0.816	0.977	0.895	0.816	0.977	CLONAL	1	TRUE	0	0.452497007737267	1		425	493	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119906	70119907	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0026465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	168	529	0	ENST00000245479.2:c.911dup	p.Val306GlyfsTer272	p.V306Gfs*272	ENST00000245479	NM_000346.3	303	cac/caCc	3/3	0.452959211346966	3	FACETS	1	0.972	1	0.561	0.516	0.608	CLONAL	1	TRUE	1	0.452497007737267	3		529	811	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200991	108200991	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587781361	NA	P-0026465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	156	548	0	ENST00000278616.4:c.7358G>C	p.Arg2453Pro	p.R2453P	ENST00000278616	NM_000051.3	2453	cGt/cCt	50/63	1	2	FACETS	0.977	0.897	1	0.977	0.897	1	CLONAL	1	TRUE	1	0.452497007737267	2		548	706	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423596	88423596	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	153	624	0	ENST00000360948.2:c.2239T>G	p.Phe747Val	p.F747V	ENST00000360948	NM_001012338.2	747	Ttc/Gtc	18/19	1	2	FACETS	0.897	0.822	0.975	0.897	0.822	0.975	CLONAL	1	TRUE	1	0.452497007737267	2		624	754	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435160	56435160	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	350	614	0	ENST00000407977.2:c.1977del	p.Ser661ProfsTer39	p.S661Pfs*39	ENST00000407977		659	ggT/gg	9/10	0.452959211346966	3	FACETS	0.907	0.86	0.954	0.907	0.86	0.954	CLONAL	2	TRUE	1	0.452497007737267	3		614	1046	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526205	189526205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	240	700	1	ENST00000264731.3:c.469G>A	p.Asp157Asn	p.D157N	ENST00000264731	NM_003722.4	157	Gat/Aat	4/14	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.452497007737267	2		701	923	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217150	66217150	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	185	588	0	ENST00000273854.3:c.2465C>G	p.Ser822Cys	p.S822C	ENST00000273854	NM_004439.5	822	tCc/tGc	14/18	0.452497007737267	1	FACETS	0.972	0.901	1	0.972	0.901	1	CLONAL	1	TRUE	0	0.452497007737267	1		588	651	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672278	86672278	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	181	589	0	ENST00000274376.6:c.2080T>C	p.Ser694Pro	p.S694P	ENST00000274376	NM_002890.2	694	Tcc/Ccc	16/25	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.452497007737267	2		589	758	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129946	69129946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759522634	NA	P-0026465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	89	384	0	ENST00000288368.4:c.4700G>A	p.Arg1567Gln	p.R1567Q	ENST00000288368	NM_024870.2	1567	cGg/cAg	38/40	0.452959211346966	3	FACETS	0.791	0.702	0.885	0.395	0.351	0.443	SUBCLONAL	1	TRUE	1	0.452497007737267	3		384	610	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127794	47127794	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0026481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	91	429	0	ENST00000409792.3:c.5288C>G	p.Ser1763Ter	p.S1763*	ENST00000409792	NM_014159.6	1763	tCa/tGa	11/21	1	2	FACETS	0.748	0.664	0.836	0.748	0.664	0.836	SUBCLONAL	1	TRUE	1	0.380932651942402	2		429	639	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591894	48591906	+	protein_altering_variant	In_Frame_Del	DEL	TACGTGGACCCTT	TACGTGGACCCTT	GGAGTAA	novel	NA	P-0026481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	56	438	2	ENST00000342988.3:c.1057_1069delinsGGAGTAA	p.Tyr353_Ser357delinsGlyValThr	p.Y353_S357delinsGVT	ENST00000342988	NM_005359.5	353	TACGTGGACCCTTct/GGAGTAAct	9/12	0.32327069347577	1	FACETS	0.481	0.412	0.556	0.481	0.412	0.556	SUBCLONAL	1	TRUE	0	0.380932651942402	1		440	495	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249278	10249278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	88	395	0	ENST00000340748.4:c.3904G>A	p.Gly1302Ser	p.G1302S	ENST00000340748		1302	Ggt/Agt	34/40	1	2	FACETS	0.894	0.794	0.999	0.894	0.794	0.999	CLONAL	1	TRUE	1	0.380932651942402	2		395	517	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582093	189582093	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	129	540	0	ENST00000264731.3:c.652C>A	p.Pro218Thr	p.P218T	ENST00000264731	NM_003722.4	218	Cca/Aca	5/14	0.29102342463955	4	FACETS	0.866	0.784	0.953	0.433	0.392	0.477	CLONAL	1	TRUE	2	0.380932651942402	4		540	1080	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295365	1295365	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0026481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	37	296	0				ENST00000310581	NM_198253.2	-/1132			0.380932651942402	3	FACETS	0.459	0.378	0.55	0.229	0.189	0.275	SUBCLONAL	1	TRUE	1	0.380932651942402	3		296	504	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186757	108186757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs864622251	NA	P-0026615-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	232	497	1	ENST00000278616.4:c.6115G>A	p.Glu2039Lys	p.E2039K	ENST00000278616	NM_000051.3	2039	Gaa/Aaa	42/63	NA	2	FACETS	0.837	0.803	0.868			1	INDETERMINATE	2	TRUE	NA	0.900372556815293	2		498	308	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844202	68844202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026615-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	341	713	0	ENST00000261769.5:c.790C>T	p.Gln264Ter	p.Q264*	ENST00000261769	NM_004360.3	264	Cag/Tag	6/16	NA	2	FACETS	0.871	0.844	0.896			1	INDETERMINATE	2	TRUE	NA	0.900372556815293	2		713	435	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184561	11184561	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	102	575	0	ENST00000361445.4:c.6656del	p.Asn2219ThrfsTer60	p.N2219Tfs*60	ENST00000361445	NM_004958.3	2219	aAc/ac	47/58	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.489843599072747	2		575	365	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061248	38061248	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	330	852	0	ENST00000250448.2:c.741C>A	p.His247Gln	p.H247Q	ENST00000250448	NM_004496.3	247	caC/caA	2/2	0.275475679985944	3	FACETS	1	0.993	1	1	0.993	1	INDETERMINATE	2	TRUE	1	0.489843599072747	3		852	685	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197498	106197498	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	49	349	0	ENST00000380013.4:c.5831C>T	p.Ser1944Phe	p.S1944F	ENST00000380013	NM_001127208.2	1944	tCc/tTc	11/11	1	2	FACETS	0.747	0.637	0.865	0.747	0.637	0.865	SUBCLONAL	1	TRUE	1	0.489843599072747	2		349	268	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	106	441	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.12857982240631	3	FACETS	1	0.98	1	0.664	0.603	0.728	INDETERMINATE	1	TRUE	1	0.658961965717677	3		441	322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0026681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	175	688	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.658961965717677	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.658961965717677	1		688	314	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591916	48591916	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	87	290	1	ENST00000342988.3:c.1079A>T	p.Asp360Val	p.D360V	ENST00000342988	NM_005359.5	360	gAt/gTt	9/12	0.658961965717677	1	FACETS	0.927	0.841	1	0.927	0.841	1	CLONAL	1	TRUE	0	0.658961965717677	1		291	191	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397540	116397540	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1060503536	NA	P-0026681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	59	325	0	ENST00000397752.3:c.1912A>G	p.Ile638Val	p.I638V	ENST00000397752	NM_000245.2	638	Ata/Gta	7/21	0.658961965717677	5	FACETS	0.674	0.581	0.776	0.225	0.193	0.259	SUBCLONAL	1	TRUE	2	0.658961965717677	5		325	528	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427883	49427905	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTGTAACCAGCTTGAGCTTCT	CTCTGTAACCAGCTTGAGCTTCT	-	novel	NA	P-0026852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	22	563	0	ENST00000301067.7:c.10685_10707del	p.Glu3562AlafsTer21	p.E3562Afs*21	ENST00000301067	NM_003482.3	3562	gAGAAGCTCAAGCTGGTTACAGAG/g	38/54	NA	2	FACETS	0.358	0.278	0.449			1	INDETERMINATE	1	TRUE	NA	0.566634491628245	2		563	217	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916776	48916776	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	28	393	0	ENST00000267163.4:c.306T>G	p.Cys102Trp	p.C102W	ENST00000267163	NM_000321.2	102	tgT/tgG	3/27	0.353820585518611	5	FACETS	0.781	0.628	0.955	0.26	0.209	0.319	CLONAL	1	TRUE	2	0.566634491628245	5		393	234	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95597932	95597932	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	10	400	1	ENST00000393063.1:c.352G>T	p.Asp118Tyr	p.D118Y	ENST00000393063	NM_030621.3	118	Gat/Tat	5/28	0.46264572311151	5	FACETS	0.349	0.236	0.491	0.116	0.078	0.164	SUBCLONAL	1	TRUE	2	0.566634491628245	5		401	187	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813274	89813274	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	15	590	0	ENST00000389301.3:c.3373G>C	p.Ala1125Pro	p.A1125P	ENST00000389301	NM_000135.2	1125	Gcc/Ccc	34/43	0.327936685578573	3	FACETS	0.384	0.282	0.506	0.192	0.141	0.253	INDETERMINATE	1	TRUE	1	0.566634491628245	3		590	177	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281365	15281365	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0026852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	32	548	1	ENST00000263388.2:c.4892-1G>A		p.X1631_splice	ENST00000263388	NM_000435.2	1631			0.266740542797069	1	FACETS	0.373	0.305	0.449	0.373	0.305	0.449	INDETERMINATE	1	TRUE	0	0.566634491628245	1		549	217	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157814	106157844	+	frameshift_variant	Frame_Shift_Del	DEL	TATGTCTGGTCAACAAGCTGCGCAACTTGCT	TATGTCTGGTCAACAAGCTGCGCAACTTGCT	GCG	novel	NA	P-0026852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	12	319	2	ENST00000380013.4:c.2715_2745delinsGCG	p.Asp905GlufsTer7	p.D905Efs*7	ENST00000380013	NM_001127208.2	905	gaTATGTCTGGTCAACAAGCTGCGCAACTTGCT/gaGCG	3/11	0.46264572311151	5	FACETS	0.38	0.267	0.519	0.127	0.089	0.173	SUBCLONAL	1	TRUE	2	0.566634491628245	5		321	206	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293686	1293686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	117	656	0	ENST00000310581.5:c.1315G>A	p.Glu439Lys	p.E439K	ENST00000310581	NM_198253.2	439	Gag/Aag	2/16	0.192352352736193	4	FACETS	0.989	0.904	1	0.989	0.904	1	INDETERMINATE	2	TRUE	2	0.566634491628245	4		656	327	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449762	8449762	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	30	436	3	ENST00000356435.5:c.3951C>A	p.Asp1317Glu	p.D1317E	ENST00000356435		1317	gaC/gaA	23/35	0.57096462358798	3	FACETS	0.785	0.64	0.947	0.393	0.32	0.474	CLONAL	1	TRUE	1	0.566634491628245	3		439	173	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685315	89685315	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1554897280	NA	P-0027255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	146	276	0	ENST00000371953.3:c.209+1G>A		p.X70_splice	ENST00000371953	NM_000314.4	70			0.566785381576152	2	FACETS	1	0.989	1	0.735	0.681	0.789	CLONAL	1	TRUE	0	0.605740969259514	2		276	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576901	7576901	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	253	526	0	ENST00000269305.4:c.945del	p.Gln317SerfsTer28	p.Q317Sfs*28	ENST00000269305	NM_001126112.2	315	tcT/tc	9/11	NA	2	FACETS	0.825	0.782	0.869			1	INDETERMINATE	2	TRUE	NA	0.605740969259514	2		526	506	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446422	49446422	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	223	522	0	ENST00000301067.7:c.1183C>T	p.Gln395Ter	p.Q395*	ENST00000301067	NM_003482.3	395	Cag/Tag	9/54	0.605740969259514	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.605740969259514	1		522	458	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15960883	15960883	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	179	294	1	ENST00000268712.3:c.6337C>G	p.Gln2113Glu	p.Q2113E	ENST00000268712	NM_006311.3	2113	Caa/Gaa	40/46	0.363385441995433	4	FACETS	0.882	0.819	0.947	0.588	0.546	0.631	INDETERMINATE	2	TRUE	1	0.605740969259514	4		295	538	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721909	176721909	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	92	477	0	ENST00000439151.2:c.7540C>G	p.Gln2514Glu	p.Q2514E	ENST00000439151	NM_022455.4	2514	Cag/Gag	23/23	0.191421734413836	2	FACETS	0.514	0.457	0.574	0.257	0.228	0.287	INDETERMINATE	1	TRUE	0	0.605740969259514	2		477	591	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0027296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	229	398	0				ENST00000310581	NM_198253.2	-/1132			0.322868788528756	7	FACETS	0.966	0.909	1	0.966	0.909	1	CLONAL	5	TRUE	2	0.322868788528756	7		398	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0027296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	218	582	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.322868788528756	4	FACETS	0.936	0.881	0.992	1	0.99	1	CLONAL	4	TRUE	1	0.322868788528756	4		582	477	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0027296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	56	160	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	0.26064112742096	3	FACETS	0.895	0.785	1			1	CLONAL	3	TRUE	NA	0.322868788528756	3		160	150	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37622766	37622766	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773894520	NA	P-0027296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	84	553	0	ENST00000249071.6:c.526G>A	p.Val176Met	p.V176M	ENST00000249071	NM_002872.4	176	Gtg/Atg	6/7	0.322868788528756	3	FACETS	0.92	0.813	1	0.46	0.406	0.517	CLONAL	1	TRUE	1	0.322868788528756	3		553	657	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772584	135772584	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	32	276	0	ENST00000298552.3:c.2962G>A	p.Ala988Thr	p.A988T	ENST00000298552	NM_001162426.1	988	Gca/Aca	22/23	0.322868788528756	5	FACETS	0.718	0.582	0.87	0.239	0.194	0.29	SUBCLONAL	1	TRUE	2	0.322868788528756	5		276	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0027303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	146	688	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.252035982298937	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.252035982298937	1		688	949	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0027303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	48	474	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.252035982298937	1	FACETS	0.946	0.803	1	0.946	0.803	1	CLONAL	1	TRUE	0	0.252035982298937	1		474	352	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435234	110435234	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769819684	NA	P-0027409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	53	397	1	ENST00000375856.3:c.3167C>T	p.Pro1056Leu	p.P1056L	ENST00000375856	NM_003749.2	1056	cCg/cTg	1/2	0.660410992880551	1	FACETS	0.546	0.472	0.624	0.546	0.472	0.624	SUBCLONAL	1	TRUE	0	0.660410992880551	1		398	197	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579545	7579546	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0027409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	210	739	0	ENST00000269305.4:c.141_142del	p.Asp48ArgfsTer3	p.D48Rfs*3	ENST00000269305	NM_001126112.2	47	ccGGac/ccac	4/11	0.660410992880551	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.660410992880551	1		739	394	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46254130	46254130	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	104	517	0	ENST00000371998.3:c.262A>C	p.Thr88Pro	p.T88P	ENST00000371998		88	Act/Cct	5/23	0.54900340534489	1	FACETS	0.314	0.281	0.349	0.314	0.281	0.349	SUBCLONAL	1	TRUE	0	0.660410992880551	1		517	671	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484267	8484267	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	160	613	0	ENST00000356435.5:c.3265G>A	p.Gly1089Arg	p.G1089R	ENST00000356435		1089	Gga/Aga	19/35	0.33563910251473	1	FACETS	0.648	0.598	0.699	0.648	0.598	0.699	INDETERMINATE	1	TRUE	0	0.660410992880551	1		613	501	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0027476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	78	280	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	0.278720583335274	2		280	436	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0027476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	133	560	2	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.27862147289059	3	FACETS	0.961	0.876	1	0.961	0.876	1	CLONAL	2	TRUE	1	0.278720583335274	3		562	566	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0027476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	58	593	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.278720583335274	2		593	414	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0027476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	90	320	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	0.278720583335274	2		320	597	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0027476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	18	645	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.172	0.128	0.224	0.172	0.128	0.224	SUBCLONAL	1	TRUE	1	0.278720583335274	2		645	751	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425086	49425086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761717148	NA	P-0027476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	152	908	3	ENST00000301067.7:c.13402C>T	p.Arg4468Trp	p.R4468W	ENST00000301067	NM_003482.3	4468	Cgg/Tgg	39/54	0.27862147289059	3	FACETS	0.992	0.905	1	0.496	0.452	0.542	CLONAL	1	TRUE	1	0.278720583335274	3		911	1253	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618570	37618572	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0027476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	139	680	0	ENST00000447079.4:c.248_250del	p.Phe83del	p.F83del	ENST00000447079	NM_015083.1	82	acCTTc/acc	1/14	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.278720583335274	2		680	803	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448508	89448508	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773835698	NA	P-0027476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	56	586	0	ENST00000336596.2:c.1472G>A	p.Gly491Asp	p.G491D	ENST00000336596	NM_005233.5	491	gGc/gAc	7/17	1	2	FACETS	0.747	0.64	0.863	0.747	0.64	0.863	SUBCLONAL	1	TRUE	1	0.278720583335274	2		586	538	SUCCESS
APC	324	MSKCC	GRCh37	5	112173602	112173602	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	67	459	0	ENST00000257430.4:c.2311G>T	p.Glu771Ter	p.E771*	ENST00000257430	NM_000038.5	771	Gaa/Taa	16/16	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.278720583335274	2		459	457	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289317	33289317	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	90	436	1	ENST00000374542.5:c.235G>A	p.Ala79Thr	p.A79T	ENST00000374542	NM_001141970.1	79	Gca/Aca	3/8	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.278720583335274	2		437	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0027478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	64	513	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.179818932278511	3	FACETS	0.389	0.335	0.447			1	INDETERMINATE	1	TRUE	NA	0.349060464362174	3		513	1108	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259249	36259250	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0027478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	131	479	0	ENST00000300305.3:c.241dup	p.Val81GlyfsTer57	p.V81Gfs*57	ENST00000300305		81	gtg/gGtg	3/8	1	2	FACETS	0.745	0.675	0.819	0.745	0.675	0.819	SUBCLONAL	1	TRUE	1	0.349060464362174	2		479	1008	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106662	27106662	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	143	413	0	ENST00000324856.7:c.6273G>A	p.Trp2091Ter	p.W2091*	ENST00000324856	NM_006015.4	2091	tgG/tgA	20/20	0.145298070927875	4	FACETS	1	0.969	1	0.569	0.518	0.623	INDETERMINATE	1	TRUE	2	0.349060464362174	4		413	971	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939464	71939464	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	270	658	0	ENST00000298229.2:c.319C>T	p.Gln107Ter	p.Q107*	ENST00000298229	NM_001567.3	107	Cag/Tag	3/28	0.156554026802332	3	FACETS	0.824	0.773	0.877	0.55	0.515	0.585	INDETERMINATE	2	TRUE	0	0.349060464362174	3		658	1102	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849577	68849577	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs778871891	NA	P-0027478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	150	535	0	ENST00000261769.5:c.1480G>T	p.Glu494Ter	p.E494*	ENST00000261769	NM_004360.3	494	Gaa/Taa	10/16	0.349060464362174	1	FACETS	0.774	0.707	0.844	0.774	0.707	0.844	SUBCLONAL	1	TRUE	0	0.349060464362174	1		535	917	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206732	36206736	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	GTTAA	GTTAA	TTT	novel	NA	P-0027478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	146	536	2	ENST00000300305.3:c.776_780delinsAAA	p.Phe259Ter	p.F259*	ENST00000300305		259	tTTAAC/tAAA	6/8	1	2	FACETS	0.777	0.708	0.849	0.777	0.708	0.849	SUBCLONAL	1	TRUE	1	0.349060464362174	2		538	1077	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959323	38959323	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	121	408	0	ENST00000357387.3:c.2152T>C	p.Ser718Pro	p.S718P	ENST00000357387	NM_152756.3	718	Tcc/Ccc	22/38	0.2095478658078	4	FACETS	0.983	0.887	1	0.492	0.443	0.543	CLONAL	1	TRUE	2	0.349060464362174	4		408	951	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0027507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	55	263	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	0.20906805126493	2		263	447	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0027507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	77	505	2	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	1	2	FACETS	0.952	0.835	1	0.952	0.835	1	CLONAL	1	TRUE	1	0.20906805126493	2		507	774	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242511	55242511	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913418	NA	P-0027507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	69	319	0	ENST00000275493.2:c.2281G>T	p.Asp761Tyr	p.D761Y	ENST00000275493	NM_005228.3	761	Gat/Tat	19/28	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.20906805126493	2		319	560	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710610	114710610	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	54	364	0	ENST00000543371.1:c.95C>T	p.Ser32Phe	p.S32F	ENST00000543371	NM_001198531.1	32	tCc/tTc	1/14	1	2	FACETS	0.9	0.768	1	0.9	0.768	1	CLONAL	1	TRUE	1	0.20906805126493	2		364	574	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633594	69633594	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	23	128	0	ENST00000334134.2:c.108C>A	p.Tyr36Ter	p.Y36*	ENST00000334134	NM_005247.2	36	taC/taA	1/3	1	2	FACETS	0.902	0.705	1	0.902	0.705	1	CLONAL	1	TRUE	1	0.20906805126493	2		128	244	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366483	118366483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782730461	NA	P-0027507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	56	331	0	ENST00000534358.1:c.5432G>A	p.Arg1811Gln	p.R1811Q	ENST00000534358	NM_005933.3	1811	cGa/cAa	19/36	0.204830977827496	1	FACETS	0.915	0.785	1	0.915	0.785	1	CLONAL	1	TRUE	0	0.20906805126493	1		331	524	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684286	29684286	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0027507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	37	250	1	ENST00000356175.3:c.7807-1G>T		p.X2603_splice	ENST00000356175	NM_000267.3	2603			1	2	FACETS	0.773	0.637	0.925	0.773	0.637	0.925	CLONAL	1	TRUE	1	0.20906805126493	2		251	458	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184992	32184992	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	80	559	0	ENST00000375023.3:c.1676C>G	p.Pro559Arg	p.P559R	ENST00000375023	NM_004557.3	559	cCc/cGc	10/30	1	2	FACETS	0.938	0.824	1	0.938	0.824	1	CLONAL	1	TRUE	1	0.20906805126493	2		559	816	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061465	38061465	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	82	443	0	ENST00000250448.2:c.524A>G	p.Tyr175Cys	p.Y175C	ENST00000250448	NM_004496.3	175	tAc/tGc	2/2	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.19	2		443	798	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863683	68863683	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	31	322	0	ENST00000261769.5:c.2422G>T	p.Gly808Ter	p.G808*	ENST00000261769	NM_004360.3	808	Gga/Tga	15/16	1	2	FACETS	0.588	0.474	0.717	0.588	0.474	0.717	SUBCLONAL	1	TRUE	1	0.19	2		322	555	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654642	67654642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027725-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	68	577	1	ENST00000264010.4:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000264010	NM_006565.3	377	Cgt/Tgt	6/12	0.660545195804369	1	FACETS	0.46	0.403	0.519	0.46	0.403	0.519	SUBCLONAL	1	TRUE	0	0.660545195804369	1		578	300	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168830	56168830	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027725-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	151	473	0	ENST00000399503.3:c.1684C>T	p.Gln562Ter	p.Q562*	ENST00000399503	NM_005921.1	562	Cag/Tag	9/20	0.20926157205368	5	FACETS	0.985	0.908	1	0.657	0.605	0.709	INDETERMINATE	2	TRUE	2	0.660545195804369	5		473	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0027738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	152	721	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.276607536635572	2		721	1053	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101154	41101154	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200302453	NA	P-0027738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	69	587	5	ENST00000373198.4:c.1202G>A	p.Arg401Gln	p.R401Q	ENST00000373198	NM_133170.3	401	cGg/cAg	8/32	1	2	FACETS	0.806	0.702	0.918	0.806	0.702	0.918	CLONAL	1	TRUE	1	0.276607536635572	2		592	619	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210743	5210743	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	59	663	0	ENST00000357368.4:c.5308G>T	p.Glu1770Ter	p.E1770*	ENST00000357368	NM_002850.3	1770	Gag/Tag	34/38	0.276607536635572	1	FACETS	0.546	0.469	0.63	0.546	0.469	0.63	SUBCLONAL	1	TRUE	0	0.276607536635572	1		663	673	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0028008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	53	336	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.37370313635733	2		336	228	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0028008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	20	582	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.261	0.199	0.334	0.261	0.199	0.334	SUBCLONAL	1	TRUE	1	0.37370313635733	2		582	410	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	39	264	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.822	0.686	0.971	0.822	0.686	0.971	CLONAL	1	TRUE	1	0.37370313635733	2		264	254	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830590	72830593	+	frameshift_variant	Frame_Shift_Del	DEL	AATC	AATC	-	novel	NA	P-0028010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	56	539	0	ENST00000268489.5:c.5988_5991del	p.Leu1996PhefsTer2	p.L1996Ffs*2	ENST00000268489	NM_006885.3	1996	ttGATT/tt	9/10	1	2	FACETS	0.997	0.868	1	0.997	0.868	1	CLONAL	1	TRUE	1	0.585006669658681	2		539	192	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0028016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	41	424	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	0.26	0.216	0.31	0.26	0.216	0.31	SUBCLONAL	1	TRUE	1	0.517242420024872	2		424	609	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs985033810	NA	P-0028016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	48	522	0	ENST00000269305.4:c.731G>T	p.Gly244Val	p.G244V	ENST00000269305	NM_001126112.2	244	gGc/gTc	7/11	1	2	FACETS	0.263	0.221	0.309	0.263	0.221	0.309	SUBCLONAL	1	TRUE	1	0.517242420024872	2		522	706	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0028169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	709	720	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.723544685929509	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.723544685929509	2		720	939	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0028169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	148	586	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.686001204207932	3	FACETS	0.8	0.733	0.871	0.4	0.366	0.436	SUBCLONAL	1	TRUE	1	0.723544685929509	3		586	696	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0028169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	630	291	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	0.723544685929509	5	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	2	0.723544685929509	5		291	1132	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411868	63411868	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1500	81	714	1	ENST00000330258.3:c.1299C>A	p.His433Gln	p.H433Q	ENST00000330258	NM_152424.3	433	caC/caA	2/2	0.458478124772247	4	FACETS	0.244	0.214	0.277	0.122	0.107	0.139	SUBCLONAL	1	TRUE	2	0.723544685929509	4		715	1581	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120971	115120971	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	35	440	0	ENST00000257566.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000257566	NM_016569.3	12	gGg/gTg	1/8	1	2	FACETS	0.16	0.13	0.193	0.16	0.13	0.193	SUBCLONAL	1	TRUE	1	0.723544685929509	2		440	606	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412657	139412691	+	frameshift_variant	Frame_Shift_Del	DEL	GCCTTGCCATTGACAGGGTTGGTGTCGCAGTTGGA	GCCTTGCCATTGACAGGGTTGGTGTCGCAGTTGGA	-	novel	NA	P-0028169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	134	545	0	ENST00000277541.6:c.1153_1187del	p.Ser385HisfsTer19	p.S385Hfs*19	ENST00000277541	NM_017617.3	385	TCCAACTGCGACACCAACCCTGTCAATGGCAAGGCc/c	7/34	0.686001204207932	3	FACETS	0.573	0.52	0.629	0.287	0.26	0.315	SUBCLONAL	1	TRUE	1	0.723544685929509	3		545	880	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0028258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	30	703	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.083	0.066	0.102	0.083	0.066	0.102	SUBCLONAL	1	TRUE	1	0.71908379236688	2		703	1007	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162336	47162336	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	186	299	0	ENST00000409792.3:c.3790C>T	p.Gln1264Ter	p.Q1264*	ENST00000409792	NM_014159.6	1264	Caa/Taa	3/21	1	2	FACETS	0.976	0.908	1	0.976	0.908	1	CLONAL	1	TRUE	1	0.71908379236688	2		299	530	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557385	187557385	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	31	357	0	ENST00000441802.2:c.3977del	p.Lys1326ArgfsTer42	p.K1326Rfs*42	ENST00000441802	NM_005245.3	1326	aAg/ag	6/27	1	2	FACETS	0.17	0.137	0.208	0.17	0.137	0.208	SUBCLONAL	1	TRUE	1	0.71908379236688	2		357	506	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0028292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	99	400	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.841	0.756	0.931	1	0.985	1	CLONAL	2	TRUE	1	0.278913233504809	2		400	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579538	7579538	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs370502517	NA	P-0028292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	113	438	0	ENST00000269305.4:c.149T>C	p.Ile50Thr	p.I50T	ENST00000269305	NM_001126112.2	50	aTt/aCt	4/11	0.278913233504809	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.278913233504809	1		438	493	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0028298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	329	703	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.625346358642312	5	FACETS	1	0.981	1	0.711	0.674	0.748	CLONAL	2	TRUE	2	0.780626722900955	5		703	858	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614537	38614538	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1555391053	NA	P-0028298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	281	443	0	ENST00000299084.4:c.304dup	p.Thr102AsnfsTer7	p.T102Nfs*7	ENST00000299084	NM_152594.2	101	-/A	3/7	0.780626722900955	2	FACETS	0.918	0.883	0.952	0.918	0.883	0.952	CLONAL	2	TRUE	0	0.780626722900955	2		443	392	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482606	56482606	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	108	426	0	ENST00000267101.3:c.1063A>G	p.Thr355Ala	p.T355A	ENST00000267101	NM_001982.3	355	Acc/Gcc	9/28	0.747596682734794	4	FACETS	0.651	0.584	0.722	0.325	0.292	0.361	SUBCLONAL	1	TRUE	2	0.780626722900955	4		426	757	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479255	50479255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	75	109	0	ENST00000394963.4:c.103G>A	p.Gly35Arg	p.G35R	ENST00000394963	NM_003076.4	35	Ggg/Agg	1/13	0.747596682734794	4	FACETS	1	0.964	1	0.615	0.545	0.689	CLONAL	1	TRUE	2	0.780626722900955	4		109	278	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436728	110436728	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs569788055	NA	P-0028298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	51	334	0	ENST00000375856.3:c.1673G>C	p.Arg558Pro	p.R558P	ENST00000375856	NM_003749.2	558	cGg/cCg	1/2	0.538433904659881	4	FACETS	0.44	0.374	0.512	0.22	0.187	0.256	SUBCLONAL	1	TRUE	2	0.780626722900955	4		334	529	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026652	6026653	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	61	837	1	ENST00000265849.7:c.1743dup	p.Glu582ArgfsTer8	p.E582Rfs*8	ENST00000265849	NM_000535.5	581	-/A	11/15	0.217036913294231	3	FACETS	0.549	0.472	0.634	0.275	0.236	0.317	SUBCLONAL	1	TRUE	1	0.217036913294231	3		838	1135	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841443	156841443	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	63	542	0	ENST00000524377.1:c.746T>A	p.Leu249Gln	p.L249Q	ENST00000524377	NM_002529.3	249	cTg/cAg	7/17	0.217036913294231	3	FACETS	0.878	0.758	1	0.439	0.379	0.504	CLONAL	1	TRUE	1	0.217036913294231	3		542	733	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154831	2154831	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	93	746	1	ENST00000434045.2:c.390C>A	p.Ser130Arg	p.S130R	ENST00000434045	NM_001127598.1	130	agC/agA	4/5	0.200757840294698	3	FACETS	1	0.919	1	0.348	0.308	0.39	CLONAL	1	TRUE	0	0.217036913294231	3		747	911	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625434	69625434	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs571671602	NA	P-0028304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	89	716	1	ENST00000334134.2:c.359G>A	p.Arg120Gln	p.R120Q	ENST00000334134	NM_005247.2	120	cGg/cAg	3/3	0.200757840294698	3	FACETS	1	0.952	1	0.38	0.337	0.427	CLONAL	1	TRUE	0	0.217036913294231	3		717	797	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125507408	125507408	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1275492676	NA	P-0028304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	53	544	0	ENST00000428830.2:c.783A>C	p.Lys261Asn	p.K261N	ENST00000428830	NM_001114121.2	261	aaA/aaC	8/14	NA	2	FACETS	0.874	0.745	1			1	INDETERMINATE	1	TRUE	NA	0.217036913294231	2		544	559	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235954	133235954	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	75	563	0	ENST00000320574.5:c.3202A>T	p.Met1068Leu	p.M1068L	ENST00000320574	NM_006231.2	1068	Atg/Ttg	26/49	0.214595572974993	2	FACETS	1	0.939	1	0.558	0.489	0.633	CLONAL	1	TRUE	0	0.217036913294231	2		563	619	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281900	49281900	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	55	538	0	ENST00000282018.3:c.947T>C	p.Leu316Pro	p.L316P	ENST00000282018	NM_020377.2	316	cTa/cCa	1/1	0.217036913294231	5	FACETS	0.722	0.615	0.839	0.241	0.205	0.28	SUBCLONAL	1	TRUE	2	0.217036913294231	5		538	931	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524586	103524587	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0028304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	27	322	0	ENST00000355739.4:c.2717_2718delinsTT	p.Arg906Ile	p.R906I	ENST00000355739	NM_000123.3	906	aGA/aTT	13/15	0.192795496022267	3	FACETS	0.597	0.474	0.738	0.298	0.237	0.369	SUBCLONAL	1	TRUE	1	0.217036913294231	3		322	462	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221212	5221212	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	68	679	0	ENST00000357368.4:c.3254T>A	p.Leu1085His	p.L1085H	ENST00000357368	NM_002850.3	1085	cTc/cAc	20/38	0.214595572974993	2	FACETS	0.759	0.659	0.867	0.379	0.329	0.434	SUBCLONAL	1	TRUE	0	0.217036913294231	2		679	826	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109312026	109312026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1391783010	NA	P-0028304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	113	625	0	ENST00000436639.2:c.1246G>A	p.Glu416Lys	p.E416K	ENST00000436639	NM_014454.2	416	Gaa/Aaa	8/10	0.170011914408073	4	FACETS	0.883	0.795	0.975			1	CLONAL	2	TRUE	NA	0.217036913294231	4		625	718	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725470	117725470	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	29	515	0	ENST00000368508.3:c.411A>C	p.Gln137His	p.Q137H	ENST00000368508	NM_002944.2	137	caA/caC	5/43	0.217036913294231	1	FACETS	0.432	0.345	0.53	0.432	0.345	0.53	SUBCLONAL	1	TRUE	0	0.217036913294231	1		515	552	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194626	29194626	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	89	706	0	ENST00000240100.2:c.1102T>G	p.Phe368Val	p.F368V	ENST00000240100	NM_001394.6	368	Ttt/Gtt	4/4	0.150703705006858	4	FACETS	0.939	0.83	1	0.469	0.415	0.528	CLONAL	1	TRUE	2	0.217036913294231	4		706	1063	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370937	55370937	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	54	684	2	ENST00000297316.4:c.239A>C	p.Lys80Thr	p.K80T	ENST00000297316	NM_022454.3	80	aAg/aCg	1/2	0.150703705006858	4	FACETS	0.803	0.685	0.934	0.402	0.342	0.467	CLONAL	1	TRUE	2	0.217036913294231	4		686	754	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981555	70981555	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	77	861	1	ENST00000276594.2:c.541G>T	p.Gly181Cys	p.G181C	ENST00000276594	NM_024504.3	181	Ggt/Tgt	2/8	0.217036913294231	5	FACETS	0.84	0.735	0.953	0.28	0.245	0.318	CLONAL	1	TRUE	2	0.217036913294231	5		862	1120	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730271	133730271	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	73	569	0	ENST00000318560.5:c.337A>C	p.Ser113Arg	p.S113R	ENST00000318560	NM_005157.4	113	Agc/Cgc	3/11	0.217036913294231	3	FACETS	0.875	0.764	0.996	0.292	0.254	0.332	CLONAL	1	TRUE	0	0.217036913294231	3		569	852	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139411756	139411756	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	61	718	1	ENST00000277541.6:c.1523A>T	p.Lys508Met	p.K508M	ENST00000277541	NM_017617.3	508	aAg/aTg	9/34	0.217036913294231	3	FACETS	0.697	0.6	0.803	0.232	0.2	0.268	SUBCLONAL	1	TRUE	0	0.217036913294231	3		719	894	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944312	76944312	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1180790039	NA	P-0028304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	40	481	0	ENST00000373344.5:c.593A>G	p.Lys198Arg	p.K198R	ENST00000373344	NM_000489.3	198	aAg/aGg	7/35	0.217036913294231	1	FACETS	0.77	0.64	0.914	0.77	0.64	0.914	CLONAL	1	TRUE	0	0.217036913294231	1		481	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578177	7578177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	141	535	0	ENST00000269305.4:c.672G>C	p.Glu224Asp	p.E224D	ENST00000269305	NM_001126112.2	224	gaG/gaC	6/11	0.658587231831896	4	FACETS	0.91	0.83	0.995	0.303	0.276	0.332	CLONAL	1	TRUE	1	0.658587231831896	4		535	780	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778389	3778389	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	71	459	0	ENST00000262367.5:c.6659del	p.Gly2220AlafsTer82	p.G2220Afs*82	ENST00000262367	NM_004380.2	2220	gGc/gc	31/31	0.658587231831896	4	FACETS	0.543	0.473	0.618	0.271	0.236	0.309	SUBCLONAL	1	TRUE	2	0.658587231831896	4		459	659	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487604	38487604	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	67	465	0	ENST00000254066.5:c.134A>G	p.Gln45Arg	p.Q45R	ENST00000254066	NM_000964.3	45	cAg/cGg	2/9	0.658587231831896	3	FACETS	0.503	0.437	0.573	0.251	0.218	0.287	SUBCLONAL	1	TRUE	1	0.658587231831896	3		465	538	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182049	38182049	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	180	346	0	ENST00000396334.3:c.673A>T	p.Ile225Phe	p.I225F	ENST00000396334	NM_002468.4	225	Atc/Ttc	3/5	0.658587231831896	3	FACETS	0.92	0.86	0.98	0.92	0.86	0.98	CLONAL	2	TRUE	1	0.658587231831896	3		346	395	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0028383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	302	596	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	1	2	FACETS	0.924	0.873	0.976	0.924	0.873	0.976	CLONAL	1	TRUE	1	0.724871773695652	2		596	902	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520006	NA	P-0028383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	388	776	1	ENST00000269305.4:c.821T>C	p.Val274Ala	p.V274A	ENST00000269305	NM_001126112.2	274	gTt/gCt	8/11	0.441231632355196	1	FACETS	0.785	0.749	0.82	0.785	0.749	0.82	SUBCLONAL	1	TRUE	0	0.724871773695652	1		777	870	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653780	89653781	+	splice_acceptor_variant	Splice_Site	DEL	AG	AG	-	rs1554893747	NA	P-0028383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	58	333	0	ENST00000371953.3:c.80-1_80del		p.X27_splice	ENST00000371953	NM_000314.4	27			0.719437033582577	1	FACETS	0.508	0.443	0.576	0.508	0.443	0.576	SUBCLONAL	1	TRUE	0	0.724871773695652	1		333	201	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0028463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	93	503	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.31	2		503	588	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171593	36171596	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CTTA	CTTA	-	novel	NA	P-0028463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	31	188	0	ENST00000300305.3:c.967+2_967+5del		p.X323_splice	ENST00000300305		323			1	2	FACETS	0.866	0.704	1	0.866	0.704	1	CLONAL	1	TRUE	1	0.31	2		188	231	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936104	178936104	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	108	481	0	ENST00000263967.3:c.1646A>T	p.Asp549Val	p.D549V	ENST00000263967	NM_006218.2	549	gAt/gTt	10/21	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.31	2		481	680	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38966790	38966790	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145165444	NA	P-0028463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	48	213	0	ENST00000357387.3:c.1252C>T	p.His418Tyr	p.H418Y	ENST00000357387	NM_152756.3	418	Cat/Tat	15/38	1	2	FACETS	0.837	0.71	0.976	0.837	0.71	0.976	CLONAL	1	TRUE	1	0.31	2		213	370	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058446	69058446	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	90	295	0	ENST00000288368.4:c.4090G>T	p.Val1364Phe	p.V1364F	ENST00000288368	NM_024870.2	1364	Gtt/Ttt	34/40	NA	2	FACETS	0.917	0.829	1			1	INDETERMINATE	1	TRUE	NA	0.83505265426184	2		295	235	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274636	123274636	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	18	276	0	ENST00000358487.5:c.1282del	p.Val428Ter	p.V428*	ENST00000358487	NM_000141.4	428	Gta/ta	9/18	0.3	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		276	87	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589546	69589546	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1401762674	NA	P-0028471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	144	173	0	ENST00000168712.1:c.307C>A	p.Arg103Ser	p.R103S	ENST00000168712	NM_002007.2	103	Cgc/Agc	1/3	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.754384344723329	2		173	312	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138294	2138294	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45517412	NA	P-0028471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	318	638	0	ENST00000219476.3:c.5227C>T	p.Arg1743Trp	p.R1743W	ENST00000219476	NM_000548.3	1743	Cgg/Tgg	41/42	0.754384344723329	1	FACETS	0.994	0.952	1	0.994	0.952	1	CLONAL	1	TRUE	0	0.754384344723329	1		638	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0028481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	375	443	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.786454336310181	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.786454336310181	1		444	543	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0028481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	140	254	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.786454336310181	1	FACETS	0.854	0.796	0.911	0.854	0.796	0.911	CLONAL	1	TRUE	0	0.786454336310181	1		254	253	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481403	140481403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913357	NA	P-0028481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	114	311	0	ENST00000288602.6:c.1405G>A	p.Gly469Arg	p.G469R	ENST00000288602	NM_004333.4	469	Gga/Aga	11/18	1	2	FACETS	0.863	0.786	0.942	0.863	0.786	0.942	CLONAL	1	TRUE	1	0.786454336310181	2		311	336	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238951	5238951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237159914	NA	P-0028481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	305	381	0	ENST00000357368.4:c.1828C>T	p.Arg610Trp	p.R610W	ENST00000357368	NM_002850.3	610	Cgg/Tgg	13/38	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.786454336310181	2		381	740	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235920	108235920	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	161	403	0	ENST00000278616.4:c.8962G>T	p.Asp2988Tyr	p.D2988Y	ENST00000278616	NM_000051.3	2988	Gac/Tac	62/63	1	2	FACETS	0.884	0.818	0.952	0.884	0.818	0.952	CLONAL	1	TRUE	1	0.786454336310181	2		403	463	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3795351	3795351	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	299	356	0	ENST00000262367.5:c.3841G>T	p.Val1281Phe	p.V1281F	ENST00000262367	NM_004380.2	1281	Gtt/Ttt	22/31	1	2	FACETS	0.991	0.938	1	0.991	0.938	1	CLONAL	1	TRUE	1	0.786454336310181	2		356	767	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120114	70120115	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGTGC	novel	NA	P-0028481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	81	120	0	ENST00000245479.2:c.1117_1118insGTGCC	p.Pro373ArgfsTer12	p.P373Rfs*12	ENST00000245479	NM_000346.3	372	-/CGTGC	3/3	0.786454336310181	1	FACETS	0.933	0.855	1	0.933	0.855	1	CLONAL	1	TRUE	0	0.786454336310181	1		120	134	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575077	48575077	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	117	317	0	ENST00000342988.3:c.271C>A	p.Pro91Thr	p.P91T	ENST00000342988	NM_005359.5	91	Cct/Act	3/12	0.786454336310181	1	FACETS	0.872	0.809	0.935	0.872	0.809	0.935	CLONAL	1	TRUE	0	0.786454336310181	1		317	207	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210419	36210419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs567944243	NA	P-0028481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	434	464	0	ENST00000222270.7:c.412C>T	p.Arg138Cys	p.R138C	ENST00000222270	NM_014727.1	138	Cgc/Tgc	2/37	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.786454336310181	2		464	963	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719655	190719655	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	44	235	0	ENST00000441310.2:c.1657A>C	p.Ile553Leu	p.I553L	ENST00000441310	NM_000534.4	553	Ata/Cta	9/13	1	2	FACETS	0.956	0.825	1	0.956	0.825	1	CLONAL	1	TRUE	1	0.786454336310181	2		235	117	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0028493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	73	586	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.16104962298757	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.16104962298757	1		586	663	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109924	115109924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754142951	NA	P-0028493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	45	574	2	ENST00000257566.3:c.1954G>A	p.Gly652Ser	p.G652S	ENST00000257566	NM_016569.3	652	Ggc/Agc	8/8	1	2	FACETS	0.946	0.794	1	0.946	0.794	1	CLONAL	1	TRUE	1	0.16104962298757	2		576	591	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168978	11168978	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1388483526	NA	P-0028493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	46	707	0	ENST00000358026.2:c.4568G>A	p.Arg1523Gln	p.R1523Q	ENST00000358026	NM_001128849.1	1523	cGa/cAa	32/36	0.16104962298757	1	FACETS	0.698	0.587	0.823	0.698	0.587	0.823	SUBCLONAL	1	TRUE	0	0.16104962298757	1		707	752	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764146326	NA	P-0028493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	193	746	0	ENST00000269305.4:c.841G>T	p.Asp281Tyr	p.D281Y	ENST00000269305	NM_001126112.2	281	Gac/Tac	8/11	1	2	FACETS	0.851	0.787	0.917	1	0.994	1	CLONAL	3	TRUE	1	0.16104962298757	2		746	939	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933305	39933305	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774884449	NA	P-0028493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	46	715	0	ENST00000378444.4:c.1294G>A	p.Val432Ile	p.V432I	ENST00000378444	NM_001123385.1	432	Gtt/Att	4/15	0.16104962298757	1	FACETS	0.611	0.513	0.721	0.611	0.513	0.721	SUBCLONAL	1	TRUE	0	0.16104962298757	1		715	859	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812567	43812567	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028509-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	325	461	0	ENST00000372470.3:c.1270C>T	p.Gln424Ter	p.Q424*	ENST00000372470	NM_005373.2	424	Caa/Taa	8/12	0.700298284904542	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.700298284904542	2		461	463	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134267	2134268	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0028509-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	422	702	0	ENST00000219476.3:c.4046_4047del	p.Ala1349GlyfsTer64	p.A1349Gfs*64	ENST00000219476	NM_000548.3	1348	caCGcg/cacg	34/42	0.700298284904542	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.700298284904542	2		702	583	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266736	18266736	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1215895377	NA	P-0028509-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	390	577	0	ENST00000222254.8:c.47G>A	p.Arg16His	p.R16H	ENST00000222254	NM_005027.3	16	cGc/cAc	2/16	0.700298284904542	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.700298284904542	3		577	740	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183763	10183763	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs869025621	NA	P-0028521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	68	650	1	ENST00000256474.2:c.232A>T	p.Asn78Tyr	p.N78Y	ENST00000256474	NM_000551.3	78	Aat/Tat	1/3	0.135832663929297	5	FACETS	1	0.92	1	1	0.966	1	CLONAL	6	TRUE	0	0.135832663929297	5		651	192	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651382	52651382	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	43	587	0	ENST00000394830.3:c.1714G>T	p.Glu572Ter	p.E572*	ENST00000394830	NM_018313.4	572	Gag/Tag	15/30	0.135832663929297	5	FACETS	1	0.867	1	0.819	0.695	0.954	CLONAL	4	TRUE	0	0.135832663929297	5		587	186	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239740	53239740	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	40	321	0	ENST00000375401.3:c.1602G>C	p.Trp534Cys	p.W534C	ENST00000375401	NM_004187.3	534	tgG/tgC	12/26	1	1	FACETS	0.945	0.819	1	1	0.981	1	CLONAL	7	TRUE	0	0.135832663929297	1		321	83	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120795695	120795695	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	14	444	0	ENST00000257552.2:c.458G>C	p.Gly153Ala	p.G153A	ENST00000257552	NM_002442.3	153	gGg/gCg	8/15	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		444	246	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0028586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	59	425	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.769	0.663	0.884	0.769	0.663	0.884	SUBCLONAL	1	TRUE	1	0.317030114995678	2		425	484	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249002	55249003	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCGTGGA	rs397517109	NA	P-0028586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	699	526	0	ENST00000275493.2:c.2303_2311dup	p.Ser768_Asp770dup	p.S768_D770dup	ENST00000275493	NM_005228.3	768	gcc/gcCAGCGTGGAc	20/28	0.317030114995678	11	FACETS	0.943	0.913	0.974			1	CLONAL	8	TRUE	NA	0.317030114995678	11		526	1418	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528707	8528707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs545049137	NA	P-0028586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	83	434	0	ENST00000356435.5:c.425C>T	p.Thr142Met	p.T142M	ENST00000356435		142	aCg/aTg	4/35	1	2	FACETS	0.79	0.697	0.889	0.79	0.697	0.889	SUBCLONAL	1	TRUE	1	0.317030114995678	2		434	663	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873661	35873661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs193922644	NA	P-0028586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	41	430	0	ENST00000303115.3:c.617G>A	p.Arg206Gln	p.R206Q	ENST00000303115	NM_002185.3	206	cGa/cAa	5/8	0.286735102837642	4	FACETS	0.668	0.556	0.793	0.223	0.185	0.265	SUBCLONAL	1	TRUE	1	0.317030114995678	4		430	510	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038684	14038684	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56129764	NA	P-0028586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	61	377	0	ENST00000311895.7:c.2009G>A	p.Arg670Gln	p.R670Q	ENST00000311895	NM_005236.2	670	cGg/cAg	10/11	0.309543154782457	3	FACETS	0.721	0.622	0.83	0.361	0.311	0.415	SUBCLONAL	1	TRUE	1	0.317030114995678	3		377	618	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0028604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	76	560	2	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.0604221336679869	3	FACETS	0.906	0.793	1	0.453	0.396	0.514	INDETERMINATE	1	TRUE	1	0.227611006963218	3		562	821	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482864	67482864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555414503	NA	P-0028604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	136	473	1	ENST00000327367.4:c.1268G>A	p.Ser423Asn	p.S423N	ENST00000327367	NM_005902.3	423	aGt/aAt	9/9	0.18514862496069	2	FACETS	0.852	0.776	0.932	0.852	0.776	0.932	CLONAL	2	TRUE	0	0.227611006963218	2		474	701	SUCCESS
APC	324	MSKCC	GRCh37	5	112175488	112175488	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	121	415	0	ENST00000257430.4:c.4198del	p.Ser1400ArgfsTer15	p.S1400Rfs*15	ENST00000257430	NM_000038.5	1399	cgT/cg	16/16	0.224702505131605	2	FACETS	0.931	0.844	1	0.931	0.844	1	CLONAL	2	TRUE	0	0.227611006963218	2		415	571	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395739	45395739	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	54	448	0	ENST00000262160.6:c.395G>A	p.Trp132Ter	p.W132*	ENST00000262160	NM_005901.5	132	tGg/tAg	4/11	0.227611006963218	1	FACETS	0.666	0.569	0.774	0.666	0.569	0.774	SUBCLONAL	1	TRUE	0	0.227611006963218	1		448	631	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939908	76939910	+	missense_variant	Missense_Mutation	TNP	ACA	ACA	CAT	novel	NA	P-0028604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	73	279	0	ENST00000373344.5:c.838_840delinsATG	p.Cys280Met	p.C280M	ENST00000373344	NM_000489.3	280	TGT/ATG	9/35	1	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.227611006963218	1		279	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0028872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	79	552	1	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.143495049160515	3	FACETS	0.768	0.675	0.868	0.256	0.225	0.29	INDETERMINATE	1	TRUE	0	0.333715740234797	3		553	719	SUCCESS
APC	324	MSKCC	GRCh37	5	112175246	112175246	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1057517558	NA	P-0028872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	90	227	0	ENST00000257430.4:c.3956del	p.Pro1319LeufsTer2	p.P1319Lfs*2	ENST00000257430	NM_000038.5	1319	Cct/ct	16/16	0.333715740234797	2	FACETS	0.893	0.802	0.988	0.893	0.802	0.988	CLONAL	2	TRUE	0	0.333715740234797	2		227	302	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398220	25398220	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	230	396	0	ENST00000311936.3:c.99T>G	p.Asp33Glu	p.D33E	ENST00000311936	NM_004985.3	33	gaT/gaG	2/5	0.316757638603272	4	FACETS	0.875	0.82	0.932	1	0.99	1	CLONAL	3	TRUE	2	0.333715740234797	4		396	700	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971053	21971053	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137854598	NA	P-0028872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	52	186	0	ENST00000304494.5:c.305C>T	p.Ala102Val	p.A102V	ENST00000304494	NM_000077.4	102	gCg/gTg	2/3	0.306296055466793	3	FACETS	1	0.941	1	0.598	0.512	0.691	CLONAL	1	TRUE	1	0.333715740234797	3		186	304	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577589	7577590	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	149	510	0	ENST00000269305.4:c.691dup	p.Thr231AsnfsTer9	p.T231Nfs*9	ENST00000269305	NM_001126112.2	231	acc/aAcc	7/11	0.143495049160515	3	FACETS	0.994	0.914	1	0.663	0.609	0.718	INDETERMINATE	2	TRUE	0	0.333715740234797	3		510	524	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900995	114900995	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	93	518	0	ENST00000543371.1:c.605C>T	p.Pro202Leu	p.P202L	ENST00000543371	NM_001198531.1	202	cCt/cTt	6/14	1	2	FACETS	0.926	0.825	1	0.926	0.825	1	CLONAL	1	TRUE	1	0.333715740234797	2		518	602	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916954	178916956	+	inframe_deletion	In_Frame_Del	DEL	ATC	ATC	-	novel	NA	P-0028872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	188	331	0	ENST00000263967.3:c.341_343del	p.Asn114del	p.N114del	ENST00000263967	NM_006218.2	114	aATCga/aga	2/21	0.333715740234797	3	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	1	0.333715740234797	3		331	650	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155389	47155389	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	127	468	0	ENST00000409792.3:c.4692G>C	p.Leu1564Phe	p.L1564F	ENST00000409792	NM_014159.6	1564	ttG/ttC	5/21	0.289711035040826	2	FACETS	0.808	0.736	0.884	0.808	0.736	0.884	CLONAL	2	TRUE	0	0.301046244805749	2		468	522	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964865	55964865	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs758102038	NA	P-0028968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	19	351	2	ENST00000263923.4:c.2372G>A	p.Arg791Gln	p.R791Q	ENST00000263923	NM_002253.2	791	cGg/cAg	16/30	0.17727258146753	3	FACETS	0.75	0.569	0.962	0.375	0.284	0.481	CLONAL	1	TRUE	1	0.18	3		353	307	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610450	81610450	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	28	463	0	ENST00000298171.2:c.2048A>G	p.Lys683Arg	p.K683R	ENST00000298171	NM_000369.2	683	aAg/aGg	10/10	1	2	FACETS	1	0.806	1	1	0.806	1	CLONAL	1	TRUE	1	0.18	2		463	309	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166333	7166333	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	32	745	0	ENST00000302850.5:c.1693del	p.Leu565Ter	p.L565*	ENST00000302850	NM_000208.2	565	Ctg/tg	8/22	0.3	1	FACETS	0.819	0.665	0.993	0.819	0.665	0.993	CLONAL	1	TRUE	0	0.18	1		745	395	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0028973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	137	483	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.958	0.877	1	0.958	0.877	1	CLONAL	1	TRUE	1	0.560623392428587	2		483	510	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0028973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	143	474	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.936	0.858	1	0.936	0.858	1	CLONAL	1	TRUE	1	0.560623392428587	2		474	545	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534788	18534788	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1436795840	NA	P-0028973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	197	554	0	ENST00000266497.5:c.1846A>C	p.Ser616Arg	p.S616R	ENST00000266497		616	Agt/Cgt	12/31	1	2	FACETS	0.887	0.823	0.953	0.887	0.823	0.953	CLONAL	1	TRUE	1	0.560623392428587	2		554	792	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	158	424	0	ENST00000342988.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000342988	NM_005359.5	356	cCt/cTt	9/12	0.560623392428587	1	FACETS	0.823	0.76	0.888	0.823	0.76	0.888	CLONAL	1	TRUE	0	0.560623392428587	1		424	493	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445005	89445005	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112239794	NA	P-0028973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	157	526	0	ENST00000336596.2:c.1325C>T	p.Thr442Met	p.T442M	ENST00000336596	NM_005233.5	442	aCg/aTg	6/17	1	2	FACETS	0.818	0.751	0.887	0.818	0.751	0.887	CLONAL	1	TRUE	1	0.560623392428587	2		526	685	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874011	123874013	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs780061449	NA	P-0028973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	11	33	0	ENST00000330479.4:c.62_64del	p.Ala21del	p.A21del	ENST00000330479	NM_020382.3	14	gaGGCg/gag	2/9	1	2	FACETS	0.392	0.273	0.537	0.392	0.273	0.537	SUBCLONAL	1	TRUE	1	0.560623392428587	2		33	100	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575122	64575122	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754378887	NA	P-0028973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	244	630	0	ENST00000312049.6:c.685C>T	p.Arg229Cys	p.R229C	ENST00000312049	NM_130799.2	229	Cgc/Tgc	4/10	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.560623392428587	2		630	867	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003780	45003781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0028973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	153	392	0	ENST00000558401.1:c.37_38insCC	p.Leu13ProfsTer32	p.L13Pfs*32	ENST00000558401	NM_004048.2	12	-/CC	1/4	1	2	FACETS	0.968	0.89	1	0.968	0.89	1	CLONAL	1	TRUE	1	0.560623392428587	2		392	564	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62008694	62008694	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0028973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	207	620	1	ENST00000392795.3:c.121+1G>A		p.X41_splice	ENST00000392795	NM_001039933.1	41			1	2	FACETS	0.921	0.856	0.987	0.921	0.856	0.987	CLONAL	1	TRUE	1	0.560623392428587	2		621	802	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374849	45374850	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0028973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	171	558	0	ENST00000262160.6:c.993_994insTA	p.Ile332Ter	p.I332*	ENST00000262160	NM_005901.5	331	-/TA	8/11	1	2	FACETS	0.851	0.785	0.919	0.851	0.785	0.919	CLONAL	1	TRUE	1	0.560623392428587	2		558	717	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626969	14626969	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	267	811	0	ENST00000254322.2:c.806G>T	p.Cys269Phe	p.C269F	ENST00000254322	NM_006145.1	269	tGc/tTc	3/3	1	2	FACETS	0.942	0.884	1	0.942	0.884	1	CLONAL	1	TRUE	1	0.560623392428587	2		811	1011	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397664	49397664	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	188	497	0	ENST00000418115.1:c.560A>T	p.Lys187Ile	p.K187I	ENST00000418115	NM_001664.2	187	aAa/aTa	5/5	1	2	FACETS	0.849	0.786	0.914	0.849	0.786	0.914	CLONAL	1	TRUE	1	0.560623392428587	2		497	790	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0028990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	63	546	0	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	1	2	FACETS	0.814	0.702	0.935	0.814	0.702	0.935	CLONAL	1	TRUE	1	0.19	2		546	815	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967350	134967350	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs61736108	NA	P-0028990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	61	438	1	ENST00000398015.3:c.2689G>A	p.Val897Met	p.V897M	ENST00000398015	NM_004441.4	897	Gtg/Atg	14/16	1	2	FACETS	0.977	0.843	1	0.977	0.843	1	CLONAL	1	TRUE	1	0.19	2		439	657	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247168	153247168	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1560758208	NA	P-0028990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	25	331	0	ENST00000281708.4:c.1634A>G	p.Tyr545Cys	p.Y545C	ENST00000281708	NM_033632.3	545	tAt/tGt	10/12	1	2	FACETS	0.911	0.719	1	0.911	0.719	1	CLONAL	1	TRUE	1	0.19	2		331	289	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0028990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	42	551	0	ENST00000311936.3:c.180_181delinsAA	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggAAaa	3/5	1	2	FACETS	0.795	0.663	0.942	0.795	0.663	0.942	CLONAL	1	TRUE	1	0.19	2		551	556	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844179	156844181	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs891423027	NA	P-0028990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	48	701	0	ENST00000524377.1:c.1184_1186del	p.Phe395del	p.F395del	ENST00000524377	NM_002529.3	394	tcCTTc/tcc	9/17	1	2	FACETS	0.634	0.534	0.744	0.634	0.534	0.744	SUBCLONAL	1	TRUE	1	0.19	2		701	797	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428026	49428026	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	71	535	0	ENST00000301067.7:c.10564C>T	p.Gln3522Ter	p.Q3522*	ENST00000301067	NM_003482.3	3522	Cag/Tag	38/54	1	2	FACETS	0.983	0.857	1	0.983	0.857	1	CLONAL	1	TRUE	1	0.19	2		535	760	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473696	67473696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	64	541	1	ENST00000327367.4:c.776G>A	p.Gly259Asp	p.G259D	ENST00000327367	NM_005902.3	259	gGc/gAc	6/9	1	2	FACETS	0.914	0.79	1	0.914	0.79	1	CLONAL	1	TRUE	1	0.19	2		542	737	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63545729	63545732	+	frameshift_variant	Frame_Shift_Del	DEL	AGCC	AGCC	-	novel	NA	P-0028990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	136	514	1	ENST00000307078.5:c.862_865del	p.Gly288MetfsTer19	p.G288Mfs*19	ENST00000307078	NM_004655.3	288	GGCTat/at	3/11	1	2	FACETS	0.841	0.765	0.921	1	0.988	1	CLONAL	2	TRUE	1	0.19	2		515	851	SUCCESS
APC	324	MSKCC	GRCh37	5	112174101	112174268	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	TCACTAAGTCGGAAAATTCAAATAGGACATGTTCTATGCCTTATGCCAAATTAGAATACAAGAGATCTTCAAATGATAGTTTAAATAGTGTCAGTAGTAGTGATGGTTATGGTAAAAGAGGTCAAATGAAACCCTCGATTGAATCCTATTCTGAAGATGATGAAAGTA	TCACTAAGTCGGAAAATTCAAATAGGACATGTTCTATGCCTTATGCCAAATTAGAATACAAGAGATCTTCAAATGATAGTTTAAATAGTGTCAGTAGTAGTGATGGTTATGGTAAAAGAGGTCAAATGAAACCCTCGATTGAATCCTATTCTGAAGATGATGAAAGTA	-	novel	NA	P-0028990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	25	333	0	ENST00000257430.4:c.2810_2977del	p.Phe937_Lys993delinsTer	p.F937_K993delins*	ENST00000257430	NM_000038.5	937	tTCACTAAGTCGGAAAATTCAAATAGGACATGTTCTATGCCTTATGCCAAATTAGAATACAAGAGATCTTCAAATGATAGTTTAAATAGTGTCAGTAGTAGTGATGGTTATGGTAAAAGAGGTCAAATGAAACCCTCGATTGAATCCTATTCTGAAGATGATGAAAGTAag/tag	16/16	1	2	FACETS	0.781	0.616	0.971	0.781	0.616	0.971	CLONAL	1	TRUE	1	0.19	2		333	337	SUCCESS
APC	324	MSKCC	GRCh37	5	112175621	112175622	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0028990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	39	398	0	ENST00000257430.4:c.4333dup	p.Thr1445AsnfsTer10	p.T1445Nfs*10	ENST00000257430	NM_000038.5	1444	caa/cAaa	16/16	1	2	FACETS	0.685	0.567	0.818	0.685	0.567	0.818	SUBCLONAL	1	TRUE	1	0.19	2		398	599	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522188	157522188	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370838091	NA	P-0028990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	53	525	1	ENST00000346085.5:c.4460C>T	p.Ala1487Val	p.A1487V	ENST00000346085	NM_020732.3	1487	gCg/gTg	18/20	1	2	FACETS	0.868	0.739	1	0.868	0.739	1	CLONAL	1	TRUE	1	0.19	2		526	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577095	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519984	NA	P-0029163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	291	688	0	ENST00000269305.4:c.843C>G	p.Asp281Glu	p.D281E	ENST00000269305	NM_001126112.2	281	gaC/gaG	8/11	0.3	0	FACETS	0.752	0.71	0.794			1	SUBCLONAL	3	TRUE	0	0.24	0		688	817	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061093	38061102	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGAGGGGT	CCAGAGGGGT	-	novel	NA	P-0029163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	18	123	0	ENST00000250448.2:c.887_896del	p.Asp296AlafsTer22	p.D296Afs*22	ENST00000250448	NM_004496.3	296	gACCCCTCTGGc/gc	2/2	1	2	FACETS	0.732	0.553	0.942	0.732	0.553	0.942	CLONAL	1	TRUE	1	0.24	2		123	205	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	248	474	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.228762704158898	2	FACETS	1	0.993	1	0.744	0.697	0.793	CLONAL	1	TRUE	0	0.364185615116334	2		474	915	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371409680	NA	P-0029377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	193	774	0	ENST00000269305.4:c.848G>C	p.Arg283Pro	p.R283P	ENST00000269305	NM_001126112.2	283	cGc/cCc	8/11	0.364185615116334	1	FACETS	0.95	0.879	1	0.95	0.879	1	CLONAL	1	TRUE	0	0.364185615116334	1		774	913	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540790	187540793	+	missense_variant	Missense_Mutation	ONP	CCTC	CCTC	TCTT	novel	NA	P-0029377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	56	329	0	ENST00000441802.2:c.6947_6950delinsAAGA	p.Arg2316_Gly2317delinsLysGlu	p.R2316_G2317delinsKE	ENST00000441802	NM_005245.3	2316	aGAGGa/aAAGAa	10/27	1	2	FACETS	0.611	0.524	0.706	0.611	0.524	0.706	SUBCLONAL	1	TRUE	1	0.364185615116334	2		329	503	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0029383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	230	483	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.853	0.803	0.903	1	0.994	1	CLONAL	2	TRUE	1	0.524762538698878	2		483	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0029383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	329	699	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.324981074675977	3	FACETS	0.931	0.884	0.979	0.621	0.589	0.653	CLONAL	2	TRUE	0	0.524762538698878	3		699	850	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032033	10032033	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	65	588	0	ENST00000330684.3:c.790A>G	p.Asn264Asp	p.N264D	ENST00000330684	NM_001134407.1	264	Aac/Gac	3/13	0.116777136040057	3	FACETS	0.67	0.582	0.764	0.223	0.194	0.255	INDETERMINATE	1	TRUE	0	0.524762538698878	3		588	467	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708132	117708132	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	160	552	0	ENST00000368508.3:c.2045A>G	p.Lys682Arg	p.K682R	ENST00000368508	NM_002944.2	682	aAa/aGa	14/43	0.331737111324398	1	FACETS	0.974	0.901	1	0.974	0.901	1	CLONAL	1	TRUE	0	0.524762538698878	1		552	462	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489566	56489566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	182	485	0	ENST00000267101.3:c.2031G>A	p.Met677Ile	p.M677I	ENST00000267101	NM_001982.3	677	atG/atA	17/28	0.419145140525114	1	FACETS	0.816	0.754	0.881	0.816	0.754	0.881	CLONAL	1	TRUE	0	0.419145140525114	1		485	841	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0029385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	239	681	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.419145140525114	1	FACETS	0.832	0.777	0.89	0.832	0.777	0.89	CLONAL	1	TRUE	0	0.419145140525114	1		681	1083	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0029385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	146	540	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.904	0.826	0.985	0.904	0.826	0.985	CLONAL	1	TRUE	1	0.419145140525114	2		541	771	SUCCESS
APC	324	MSKCC	GRCh37	5	112175786	112175786	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs756912930	NA	P-0029385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	46	275	1	ENST00000257430.4:c.4495G>T	p.Gly1499Ter	p.G1499*	ENST00000257430	NM_000038.5	1499	Gga/Tga	16/16	0.419145140525114	1	FACETS	0.414	0.349	0.486	0.414	0.349	0.486	SUBCLONAL	1	TRUE	0	0.419145140525114	1		276	419	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246051	46246051	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	170	392	0	ENST00000334344.6:c.4146del	p.Asn1383IlefsTer3	p.N1383Ifs*3	ENST00000334344	NM_152641.2	1382	tCc/tc	15/21	0.419145140525114	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.419145140525114	1		392	566	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037972	49037972	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0029385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	335	448	0	ENST00000267163.4:c.2211+1G>C		p.X737_splice	ENST00000267163	NM_000321.2	737			0.419145140525114	2	FACETS	0.928	0.881	0.976	0.928	0.881	0.976	CLONAL	2	TRUE	0	0.419145140525114	2		448	861	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934035	49934035	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs756528902	NA	P-0029385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	191	711	0	ENST00000296474.3:c.2377C>G	p.Leu793Val	p.L793V	ENST00000296474	NM_002447.2	793	Cta/Gta	9/20	0.419145140525114	1	FACETS	0.815	0.754	0.878	0.815	0.754	0.878	CLONAL	1	TRUE	0	0.419145140525114	1		711	884	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467856	50467856	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	137	402	0	ENST00000331340.3:c.1091C>G	p.Ser364Trp	p.S364W	ENST00000331340	NM_006060.4	364	tCg/tGg	8/8	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.419145140525114	2		402	621	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0029388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	421	503	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.817891189627526	1	FACETS	0.95	0.92	0.98	0.95	0.92	0.98	CLONAL	1	FALSE	0	0.852676027530552	1		503	596	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	660	768	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.852676027530552	2		768	1521	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	321	474	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.121517042013365	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.852676027530552	0		474	884	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087503	27087503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	583	702	2	ENST00000324856.7:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000324856	NM_006015.4	693	Cga/Tga	5/20	0.682311543112157	1	FACETS	0.914	0.888	0.94	0.914	0.888	0.94	CLONAL	1	FALSE	0	0.852676027530552	1		704	858	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174458	11174458	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	417	617	0	ENST00000361445.4:c.7217T>C	p.Val2406Ala	p.V2406A	ENST00000361445	NM_004958.3	2406	gTg/gCg	53/58	0.852676027530552	1	FACETS	0.983	0.952	1	0.983	0.952	1	CLONAL	1	FALSE	0	0.852676027530552	1		617	571	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326285	62326285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746445840	NA	P-0029388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	550	769	2	ENST00000360203.5:c.3301G>A	p.Ala1101Thr	p.A1101T	ENST00000360203	NM_001283009.1	1101	Gcc/Acc	32/35	1	2	FACETS	0.985	0.947	1	0.985	0.947	1	CLONAL	1	FALSE	1	0.852676027530552	2		771	1310	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265746	41266234	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAA	CAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAA	-	novel	NA	P-0029388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	32	44	0	ENST00000349496.5:c.13+176_233del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.817891189627526	1	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	FALSE	0	0.852676027530552	1		44	43	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99451990	99451990	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	144	505	0	ENST00000268035.6:c.1326del	p.Ala443GlnfsTer23	p.A443Qfs*23	ENST00000268035	NM_000875.3	442	Aaa/aa	6/21	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.539916780671471	2		505	528	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354661	70354661	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	402	773	0	ENST00000374080.3:c.4826A>G	p.Asn1609Ser	p.N1609S	ENST00000374080		1609	aAc/aGc	35/45	1	2	FACETS	0.956	0.911	1	0.956	0.911	1	CLONAL	1	TRUE	1	0.740461030662016	2		773	1136	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246153	46246153	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	28	314	0	ENST00000334344.6:c.4247C>G	p.Ser1416Cys	p.S1416C	ENST00000334344	NM_152641.2	1416	tCt/tGt	15/21	0.192098443649185	4	FACETS	0.456	0.363	0.561	0.228	0.181	0.281	INDETERMINATE	1	TRUE	2	0.352155369323603	4		314	472	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610546	81610546	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	33	298	0	ENST00000298171.2:c.2144A>G	p.Asn715Ser	p.N715S	ENST00000298171	NM_000369.2	715	aAc/aGc	10/10	0.281557106843417	2	FACETS	0.464	0.378	0.561	0.232	0.189	0.281	SUBCLONAL	1	TRUE	0	0.352155369323603	2		298	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577563	+	frameshift_variant	Frame_Shift_Del	DEL	GAACT	GAACT	-	novel	NA	P-0029753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	309	429	0	ENST00000269305.4:c.718_722del	p.Ser240LeufsTer22	p.S240Lfs*22	ENST00000269305	NM_001126112.2	240	AGTTCc/c	7/11	0.300611155286914	4	FACETS	1	0.977	1	0.79	0.749	0.831	CLONAL	3	TRUE	0	0.352155369323603	4		429	751	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217597	142217597	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	213	391	0	ENST00000350721.4:c.5400G>C	p.Trp1800Cys	p.W1800C	ENST00000350721	NM_001184.3	1800	tgG/tgC	32/47	0.352155369323603	5	FACETS	0.939	0.877	1			1	CLONAL	3	TRUE	NA	0.352155369323603	5		391	656	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157971	106157971	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs749121114	NA	P-0029753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	108	258	0	ENST00000380013.4:c.2872C>T	p.Gln958Ter	p.Q958*	ENST00000380013	NM_001127208.2	958	Cag/Tag	3/11	0.281557106843417	2	FACETS	0.797	0.721	0.875	0.797	0.721	0.875	SUBCLONAL	2	TRUE	0	0.352155369323603	2		258	385	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242796	98242796	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	38	407	0	ENST00000331920.6:c.821A>C	p.Gln274Pro	p.Q274P	ENST00000331920	NM_000264.3	274	cAa/cCa	6/24	0.352155369323603	3	FACETS	0.354	0.291	0.424	0.118	0.097	0.142	SUBCLONAL	1	TRUE	0	0.352155369323603	3		407	718	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0029755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	563	732	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.592227953752773	4	FACETS	0.956	0.929	0.981	1	0.998	1	CLONAL	4	TRUE	2	0.592227953752773	4		732	792	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0029755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	110	326	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.592227953752773	3	FACETS	0.882	0.818	0.944	0.882	0.818	0.944	CLONAL	3	TRUE	0	0.592227953752773	3		326	182	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0029755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	39	527	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	0.592227953752773	4	FACETS	0.21	0.173	0.252	0.105	0.086	0.126	SUBCLONAL	1	TRUE	2	0.592227953752773	4		527	999	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821572	72821572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457944892	NA	P-0029755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	114	161	0	ENST00000268489.5:c.10603G>A	p.Glu3535Lys	p.E3535K	ENST00000268489	NM_006885.3	3535	Gag/Aag	10/10	0.588602796204326	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.592227953752773	2		161	166	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944504	71944504	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0029755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	145	492	0	ENST00000298229.2:c.2060C>G	p.Ser687Ter	p.S687*	ENST00000298229	NM_001567.3	687	tCa/tGa	18/28	0.414683107183989	3	FACETS	1	0.965	1	0.55	0.504	0.598	CLONAL	1	TRUE	1	0.592227953752773	3		492	577	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515418	149515418	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	110	368	0	ENST00000261799.4:c.64C>G	p.Leu22Val	p.L22V	ENST00000261799	NM_002609.3	22	Ctg/Gtg	3/23	0.588602796204326	2	FACETS	0.659	0.594	0.727	0.329	0.297	0.364	SUBCLONAL	1	TRUE	0	0.592227953752773	2		368	564	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128347922	128347922	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369629455	NA	P-0029755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	156	491	1	ENST00000265960.3:c.583G>A	p.Val195Met	p.V195M	ENST00000265960	NM_001006617.1	195	Gtg/Atg	5/12	0.414683107183989	3	FACETS	0.561	0.512	0.612	0.28	0.256	0.306	SUBCLONAL	1	TRUE	1	0.592227953752773	3		492	1218	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	219	474	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.679237340443466	3	FACETS	0.934	0.881	0.988	0.934	0.881	0.988	CLONAL	2	TRUE	1	0.706407766458435	3		474	449	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0029807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	71	254	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.874	0.774	0.978	0.874	0.774	0.978	CLONAL	1	TRUE	1	0.706407766458435	2		254	230	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	125	424	0	ENST00000342988.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000342988	NM_005359.5	356	cCt/cTt	9/12	0.706407766458435	1	FACETS	0.958	0.888	1	0.958	0.888	1	CLONAL	1	TRUE	0	0.706407766458435	1		424	239	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0029807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	138	338	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.965	0.887	1	0.965	0.887	1	CLONAL	1	TRUE	1	0.706407766458435	2		338	405	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430936	181430936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	314	672	0	ENST00000325404.1:c.788C>T	p.Ala263Val	p.A263V	ENST00000325404	NM_003106.3	263	gCg/gTg	1/1	1	2	FACETS	0.989	0.936	1	0.989	0.936	1	CLONAL	1	TRUE	1	0.706407766458435	2		672	899	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779102	135779102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs986350787	NA	P-0029807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	206	400	0	ENST00000298552.3:c.2144G>A	p.Arg715Gln	p.R715Q	ENST00000298552	NM_001162426.1	715	cGg/cAg	17/23	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.706407766458435	2		400	555	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936191	71936191	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	93	466	0	ENST00000298229.2:c.163G>C	p.Ala55Pro	p.A55P	ENST00000298229	NM_001567.3	55	Gcc/Ccc	1/28	1	2	FACETS	0.422	0.375	0.471	0.422	0.375	0.471	SUBCLONAL	1	TRUE	1	0.706407766458435	2		466	624	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514496	149514496	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs199522807	NA	P-0029811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	131	485	0	ENST00000261799.4:c.448C>T	p.Arg150Ter	p.R150*	ENST00000261799	NM_002609.3	150	Cga/Tga	4/23	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.260752561892988	2		485	700	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027168	49027168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913305	NA	P-0029815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	95	404	0	ENST00000267163.4:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	579	Cga/Tga	18/27	1	2	FACETS	0.909	0.811	1	0.909	0.811	1	CLONAL	1	TRUE	1	0.351977100778625	2		404	594	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536713	120536713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748118400	NA	P-0029815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	112	578	1	ENST00000229340.5:c.379C>T	p.Arg127Trp	p.R127W	ENST00000229340	NM_006861.6	127	Cgg/Tgg	5/6	0.291003065993445	2	FACETS	0.769	0.691	0.851	0.384	0.345	0.426	SUBCLONAL	1	TRUE	0	0.351977100778625	2		579	828	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303266	15303266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	158	791	0	ENST00000263388.2:c.262G>A	p.Ala88Thr	p.A88T	ENST00000263388	NM_000435.2	88	Gct/Act	3/33	0.310106360510424	3	FACETS	0.905	0.827	0.986	0.452	0.413	0.493	CLONAL	1	TRUE	1	0.351977100778625	3		791	1167	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553159	41553180	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTTGTCTTTCTAGGATTACTT	ACTTGTCTTTCTAGGATTACTT	-	novel	NA	P-0029815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	130	261	0	ENST00000263253.7:c.3262-14_3269del		p.X1088_splice	ENST00000263253	NM_001429.3	1088		18/31	0.217507035780627	3	FACETS	1	0.923	1	0.673	0.616	0.733	CLONAL	2	TRUE	0	0.351977100778625	3		261	430	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0029825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	325	461	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.332654960333625	2	FACETS	0.836	0.791	0.881	0.836	0.791	0.881	CLONAL	2	TRUE	0	0.415529126610818	2		461	936	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141507	11141507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	149	630	0	ENST00000358026.2:c.3484G>A	p.Gly1162Ser	p.G1162S	ENST00000358026	NM_001128849.1	1162	Ggc/Agc	25/36	0.336090113699158	3	FACETS	0.847	0.773	0.925	0.423	0.386	0.463	CLONAL	1	TRUE	1	0.415529126610818	3		630	1023	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060992	38061010	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGGCTGGCGGCGGGCCC	GGGGGCTGGCGGCGGGCCC	-	novel	NA	P-0029875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	45	271	0	ENST00000250448.2:c.979_997del	p.Gly327ArgfsTer17	p.G327Rfs*17	ENST00000250448	NM_004496.3	327	GGGCCCGCCGCCAGCCCCCag/ag	2/2	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	FALSE	1	0.517007461800654	2		271	168	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0030003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	204	525	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.216763774835534	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	0	0.223771981740596	2		525	902	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247168	153247168	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	77	292	0	ENST00000281708.4:c.1634A>T	p.Tyr545Phe	p.Y545F	ENST00000281708	NM_033632.3	545	tAt/tTt	10/12	0.223771981740596	3	FACETS	0.784	0.69	0.884	0.523	0.46	0.59	SUBCLONAL	2	TRUE	0	0.223771981740596	3		292	488	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478544	99478544	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0030003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	23	268	0	ENST00000268035.6:c.3187-1G>A		p.X1063_splice	ENST00000268035	NM_000875.3	1063			0.223771981740596	1	FACETS	0.458	0.356	0.575	0.458	0.356	0.575	SUBCLONAL	1	TRUE	0	0.223771981740596	1		268	399	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967881	93967881	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	75	563	0	ENST00000369303.4:c.2046A>C	p.Glu682Asp	p.E682D	ENST00000369303	NM_004440.3	682	gaA/gaC	11/17	1	2	FACETS	0.742	0.649	0.843	0.742	0.649	0.843	SUBCLONAL	1	TRUE	1	0.223771981740596	2		563	903	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0030006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	24	483	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.539	0.422	0.674	0.539	0.422	0.674	SUBCLONAL	1	TRUE	1	0.240666130590631	2		483	370	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0030006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	53	441	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.805	0.687	0.935	0.805	0.687	0.935	CLONAL	1	TRUE	1	0.240666130590631	2		441	547	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920447	114920447	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	34	413	0	ENST00000543371.1:c.1388G>T	p.Cys463Phe	p.C463F	ENST00000543371	NM_001198531.1	463	tGc/tTc	13/14	1	2	FACETS	0.481	0.392	0.582	0.481	0.392	0.582	SUBCLONAL	1	TRUE	1	0.240666130590631	2		413	587	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252991	36252992	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CATCC	novel	NA	P-0030006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	37	363	0	ENST00000300305.3:c.366_370dup	p.Val124GlyfsTer11	p.V124Gfs*11	ENST00000300305		124	gtt/gGGATGtt	4/8	1	2	FACETS	0.566	0.466	0.679	0.566	0.466	0.679	SUBCLONAL	1	TRUE	1	0.240666130590631	2		363	543	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183254	56183254	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	28	473	0	ENST00000399503.3:c.4164T>A	p.Asp1388Glu	p.D1388E	ENST00000399503	NM_005921.1	1388	gaT/gaA	18/20	1	2	FACETS	0.419	0.334	0.517	0.419	0.334	0.517	SUBCLONAL	1	TRUE	1	0.240666130590631	2		473	555	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0030030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	26	400	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.295	0.233	0.365	0.295	0.233	0.365	SUBCLONAL	1	FALSE	1	0.442491036358492	2		400	399	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84384746	84384747	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	11	252	1	ENST00000321945.7:c.696dup	p.Val233SerfsTer5	p.V233Sfs*5	ENST00000321945	NM_139076.2	232	-/A	8/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.442491036358492	NA		253	157	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209062	133209062	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	73	404	0	ENST00000320574.5:c.6169A>C	p.Asn2057His	p.N2057H	ENST00000320574	NM_006231.2	2057	Aat/Cat	45/49	1	2	FACETS	0.954	0.84	1	0.954	0.84	1	CLONAL	1	FALSE	1	0.442491036358492	2		404	346	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165290	47165290	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	34	350	1	ENST00000409792.3:c.836C>A	p.Ser279Ter	p.S279*	ENST00000409792	NM_014159.6	279	tCa/tAa	3/21	0.442491036358492	1	FACETS	0.928	0.773	1	0.928	0.773	1	CLONAL	1	FALSE	0	0.442491036358492	1		351	129	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53254020	53254020	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	17	243	1	ENST00000375401.3:c.52G>T	p.Glu18Ter	p.E18*	ENST00000375401	NM_004187.3	18	Gag/Tag	1/26	1	1	FACETS	0.299	0.224	0.388	0.299	0.224	0.388	SUBCLONAL	1	FALSE	0	0.442491036358492	1		244	200	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228274	53228282	+	inframe_deletion	In_Frame_Del	DEL	ACTTGATAC	ACTTGATAC	-	novel	NA	P-0030030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	26	313	0	ENST00000375401.3:c.2121_2129del	p.Ile708_Cys710del	p.I708_C710del	ENST00000375401	NM_004187.3	707	tGTATCAAGTgc/tgc	15/26	1	1	FACETS	0.276	0.219	0.342	0.276	0.219	0.342	SUBCLONAL	1	FALSE	0	0.442491036358492	1		313	331	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503838	149503838	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs864309711	NA	P-0030045-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	329	465	0	ENST00000261799.4:c.1998C>A	p.Asn666Lys	p.N666K	ENST00000261799	NM_002609.3	666	aaC/aaA	14/23	0.672763595137774	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.672763595137774	2		465	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579329	7579329	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912658	NA	P-0030045-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	319	459	0	ENST00000269305.4:c.358A>G	p.Lys120Glu	p.K120E	ENST00000269305	NM_001126112.2	120	Aag/Gag	4/11	0.672763595137774	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.672763595137774	3		459	616	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953785	48953785	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0030045-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	130	216	0	ENST00000267163.4:c.1388C>G	p.Ser463Ter	p.S463*	ENST00000267163	NM_000321.2	463	tCa/tGa	14/27	NA	2	FACETS	0.87	0.812	0.928			1	INDETERMINATE	2	TRUE	NA	0.672763595137774	2		216	222	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577590	7577590	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030045-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	159	512	0	ENST00000269305.4:c.691A>G	p.Thr231Ala	p.T231A	ENST00000269305	NM_001126112.2	231	Acc/Gcc	7/11	0.672763595137774	3	FACETS	0.909	0.835	0.985	0.454	0.417	0.493	CLONAL	1	TRUE	1	0.672763595137774	3		512	695	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872626	136872626	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030045-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	26	379	0	ENST00000241393.3:c.872C>A	p.Ala291Asp	p.A291D	ENST00000241393	NM_003467.2	291	gCt/gAt	2/2	0.565263252453446	2	FACETS	0.194	0.153	0.24	0.097	0.076	0.12	SUBCLONAL	1	TRUE	0	0.672763595137774	2		379	399	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56854492	56854492	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030045-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	225	386	0	ENST00000519728.1:c.74G>C	p.Arg25Pro	p.R25P	ENST00000519728	NM_002350.3	25	cGt/cCt	2/13	0.501050940439376	4	FACETS	0.866	0.811	0.922	0.866	0.811	0.922	CLONAL	2	TRUE	2	0.672763595137774	4		386	646	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0030053-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	306	427	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.584408193410276	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	2	0.877710865670792	4		427	636	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998756	100998756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749674024	NA	P-0030053-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	96	459	1	ENST00000325455.5:c.1046C>T	p.Ser349Leu	p.S349L	ENST00000325455	NM_001202474.3	349	tCg/tTg	1/8	0.873787485496449	4	FACETS	0.761	0.68	0.846	0.38	0.34	0.423	SUBCLONAL	1	TRUE	2	0.877710865670792	4		460	540	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259442	55259442	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397517127	NA	P-0030053-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	218	344	0	ENST00000275493.2:c.2500G>T	p.Val834Leu	p.V834L	ENST00000275493	NM_005228.3	834	Gtg/Ttg	21/28	0.584408193410276	4	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	2	0.877710865670792	4		344	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0030053-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	269	503	1	ENST00000269305.4:c.559+1G>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.336403261041466	3	FACETS	0.93	0.903	0.955	0.93	0.903	0.955	INDETERMINATE	3	TRUE	0	0.877710865670792	3		504	316	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550938	150550938	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030053-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	124	354	0	ENST00000369026.2:c.718G>A	p.Glu240Lys	p.E240K	ENST00000369026	NM_021960.4	240	Gaa/Aaa	2/3	0.877710865670792	7	FACETS	1	0.938	1			1	CLONAL	1	TRUE	NA	0.877710865670792	7		354	860	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942698	48942701	+	frameshift_variant	Frame_Shift_Del	DEL	TTGA	TTGA	-	novel	NA	P-0030053-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	177	293	0	ENST00000267163.4:c.1086_1089del	p.Asp363LysfsTer3	p.D363Kfs*3	ENST00000267163	NM_000321.2	362	cTTGAt/ct	11/27	0.850163105689678	2	FACETS	0.942	0.906	0.976	0.942	0.906	0.976	CLONAL	2	TRUE	0	0.877710865670792	2		293	214	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500777	149500777	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030053-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	240	414	0	ENST00000261799.4:c.2453C>A	p.Ala818Asp	p.A818D	ENST00000261799	NM_002609.3	818	gCc/gAc	17/23	0.868751416737325	5	FACETS	0.835	0.782	0.888	0.334	0.313	0.356	CLONAL	2	TRUE	0	0.877710865670792	5		414	759	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520432	176520432	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030053-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	343	643	0	ENST00000292408.4:c.1277G>T	p.Gly426Val	p.G426V	ENST00000292408	NM_213647.1	426	gGc/gTc	10/18	0.868751416737325	5	FACETS	1	0.991	1	0.463	0.441	0.486	CLONAL	2	TRUE	0	0.877710865670792	5		643	782	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6442022	6442022	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030053-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	197	185	0	ENST00000356142.4:c.581C>G	p.Ala194Gly	p.A194G	ENST00000356142	NM_018890.3	194	gCa/gGa	7/7	0.584408193410276	4	FACETS	0.865	0.818	0.91	1	0.991	1	CLONAL	3	TRUE	2	0.877710865670792	4		185	325	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668811	52668811	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030053-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	27	331	0	ENST00000394830.3:c.1108G>C	p.Glu370Gln	p.E370Q	ENST00000394830	NM_018313.4	370	Gag/Cag	12/30	0.840792941236602	2	FACETS	0.289	0.231	0.354	0.144	0.115	0.177	SUBCLONAL	1	TRUE	0	0.877710865670792	2		331	213	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	218	264	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.867612565633475	2		264	488	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117632202	117632202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139881304	NA	P-0030101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	333	397	0	ENST00000368508.3:c.6214C>T	p.Arg2072Trp	p.R2072W	ENST00000368508	NM_002944.2	2072	Cgg/Tgg	39/43	1	2	FACETS	0.997	0.948	1	0.997	0.948	1	CLONAL	1	TRUE	1	0.867612565633475	2		397	770	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003149	42003149	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1225212904	NA	P-0030101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	381	670	1	ENST00000219905.7:c.2686C>T	p.Arg896Ter	p.R896*	ENST00000219905	NM_001164273.1	896	Cga/Tga	8/24	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.867612565633475	2		671	833	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534744	18534744	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	231	479	0	ENST00000266497.5:c.1802G>T	p.Ser601Ile	p.S601I	ENST00000266497		601	aGt/aTt	12/31	1	2	FACETS	0.928	0.872	0.984	0.928	0.872	0.984	CLONAL	1	TRUE	1	0.867612565633475	2		479	574	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0030102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	48	280	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	0.177333930721336	2		280	382	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971156	21971156	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	28	297	1	ENST00000304494.5:c.202G>A	p.Ala68Thr	p.A68T	ENST00000304494	NM_000077.4	68	Gcg/Acg	2/3	1	2	FACETS	0.648	0.517	0.799	0.648	0.517	0.799	SUBCLONAL	1	TRUE	1	0.177333930721336	2		298	487	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572254	41572254	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	34	375	0	ENST00000263253.7:c.4784del	p.Phe1595SerfsTer3	p.F1595Sfs*3	ENST00000263253	NM_001429.3	1595	Ttc/tc	30/31	1	2	FACETS	0.736	0.6	0.889	0.736	0.6	0.889	SUBCLONAL	1	TRUE	1	0.177333930721336	2		375	521	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955550	48955550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913304	NA	P-0030124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	67	402	0	ENST00000267163.4:c.1666C>T	p.Arg556Ter	p.R556*	ENST00000267163	NM_000321.2	556	Cga/Tga	17/27	0.270515251242369	2	FACETS	1	0.959	1	0.622	0.544	0.704	CLONAL	1	TRUE	0	0.330630652577894	2		402	326	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148991	119148991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs192712314	NA	P-0030124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	17	537	3	ENST00000264033.4:c.1211G>A	p.Cys404Tyr	p.C404Y	ENST00000264033	NM_005188.3	404	tGt/tAt	8/16	0.224850758107139	3	FACETS	0.259	0.192	0.338	0.086	0.064	0.113	SUBCLONAL	1	TRUE	0	0.330630652577894	3		540	463	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519991	NA	P-0030124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	258	640	0	ENST00000269305.4:c.536A>C	p.His179Pro	p.H179P	ENST00000269305	NM_001126112.2	179	cAt/cCt	5/11	0.286936147430896	4	FACETS	1	0.981	1	0.815	0.769	0.862	CLONAL	3	TRUE	0	0.330630652577894	4		640	637	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781636	9781636	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	136	630	0	ENST00000377346.4:c.1946G>T	p.Trp649Leu	p.W649L	ENST00000377346	NM_005026.3	649	tGg/tTg	15/24	0.307863512359051	4	FACETS	0.798	0.727	0.872	0.798	0.727	0.872	SUBCLONAL	2	TRUE	2	0.330630652577894	4		630	686	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989507	7989507	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1314147344	NA	P-0030124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	240	612	0	ENST00000319144.4:c.179A>T	p.Asp60Val	p.D60V	ENST00000319144	NM_001139.2	60	gAc/gTc	2/15	0.286936147430896	4	FACETS	1	0.955	1	0.764	0.718	0.811	CLONAL	3	TRUE	0	0.330630652577894	4		612	632	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934578	NA	P-0030182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	734	521	0	ENST00000269305.4:c.524G>T	p.Arg175Leu	p.R175L	ENST00000269305	NM_001126112.2	175	cGc/cTc	5/11	0.782228453295142	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.782228453295142	2		521	897	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164887	36164887	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	131	575	0	ENST00000300305.3:c.988T>C	p.Phe330Leu	p.F330L	ENST00000300305		330	Ttc/Ctc	8/8	0.521271709478651	3	FACETS	0.425	0.384	0.467	0.212	0.192	0.234	SUBCLONAL	1	TRUE	1	0.782228453295142	3		575	1097	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661395	227661396	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGC	rs138975702	NA	P-0030182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	187	445	1	ENST00000305123.5:c.2057_2059dup	p.Ser686dup	p.S686dup	ENST00000305123	NM_005544.2	686	aac/aGCAac	1/2	0.269435869761534	3	FACETS	0.947	0.878	1	0.474	0.439	0.51	INDETERMINATE	1	TRUE	1	0.782228453295142	3		446	702	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692877	89692877	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	208	250	0	ENST00000371953.3:c.361G>A	p.Ala121Thr	p.A121T	ENST00000371953	NM_000314.4	121	Gca/Aca	5/9	NA	2	FACETS	0.911	0.869	0.95			1	INDETERMINATE	2	TRUE	NA	0.782228453295142	2		250	292	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189846	11189846	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	536	412	0	ENST00000361445.4:c.5663T>C	p.Phe1888Ser	p.F1888S	ENST00000361445	NM_004958.3	1888	tTc/tCc	40/58	0.762473782921458	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.782228453295142	2		412	662	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556395	29556396	+	missense_variant	Missense_Mutation	DNP	TG	TG	GT	novel	NA	P-0030182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	40	481	0	ENST00000356175.3:c.2762_2763delinsGT	p.Val921Gly	p.V921G	ENST00000356175	NM_000267.3	921	gTG/gGT	21/57	0.779391521508834	3	FACETS	0.185	0.153	0.221	0.062	0.051	0.074	SUBCLONAL	1	TRUE	0	0.782228453295142	3		481	770	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556891	29556893	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	novel	NA	P-0030182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	286	263	1	ENST00000356175.3:c.2889_2891del	p.Gln963_Thr964delinsHis	p.Q963_T964delinsH	ENST00000356175	NM_000267.3	963	caAACc/cac	22/57	0.779391521508834	3	FACETS	0.939	0.908	0.969	0.939	0.908	0.969	CLONAL	3	TRUE	0	0.782228453295142	3		264	361	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224566	36224566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	321	793	2	ENST00000222270.7:c.7028C>T	p.Pro2343Leu	p.P2343L	ENST00000222270	NM_014727.1	2343	cCc/cTc	29/37	0.782228453295142	3	FACETS	0.792	0.746	0.839	0.396	0.373	0.42	SUBCLONAL	1	TRUE	1	0.782228453295142	3		795	1442	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943796	71943797	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	196	505	1	ENST00000298229.2:c.1840dup	p.Met614AsnfsTer16	p.M614Nfs*16	ENST00000298229	NM_001567.3	613	-/A	15/28	0.343196712661899	3	FACETS	0.938	0.872	1	0.938	0.872	1	CLONAL	2	TRUE	1	0.343196712661899	3		506	713	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0030214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	72	703	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	FALSE	1	0.250324811893272	2		703	540	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0030214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	58	297	0	ENST00000262160.6:c.1391C>G	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tGa	11/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.250324811893272	2		297	358	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249022	55249022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567477136	NA	P-0030214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	63	431	0	ENST00000275493.2:c.2320G>A	p.Val774Met	p.V774M	ENST00000275493	NM_005228.3	774	Gtg/Atg	20/28	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.250324811893272	2		431	383	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482861	67482861	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	32	286	1	ENST00000327367.4:c.1265C>T	p.Ser422Phe	p.S422F	ENST00000327367	NM_005902.3	422	tCc/tTc	9/9	1	2	FACETS	0.695	0.564	0.842	0.695	0.564	0.842	SUBCLONAL	1	FALSE	1	0.250324811893272	2		287	368	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804345	43804345	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	70	445	0	ENST00000372470.3:c.345C>G	p.Phe115Leu	p.F115L	ENST00000372470	NM_005373.2	115	ttC/ttG	3/12	0.170187604828323	2	FACETS	1	0.95	1	0.589	0.514	0.668	CLONAL	1	FALSE	0	0.250324811893272	2		445	475	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645228	67645228	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	89	538	0	ENST00000264010.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000264010	NM_006565.3	165	Cag/Tag	3/12	0.247643203716253	2	FACETS	1	0.971	1	0.644	0.572	0.72	CLONAL	1	FALSE	0	0.250324811893272	2		538	552	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842456	68842488	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAAAACCTGGTTCAGGTAGAGAAAGAAGTTCTC	AAAAACCTGGTTCAGGTAGAGAAAGAAGTTCTC	CTG	novel	NA	P-0030214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	74	544	2	ENST00000261769.5:c.517_531+18delinsCTG		p.X173_splice	ENST00000261769	NM_004360.3	173		4/16	0.247643203716253	2	FACETS	1	0.965	1	0.641	0.563	0.725	CLONAL	1	FALSE	0	0.250324811893272	2		546	461	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346750	225346750	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	75	425	0	ENST00000264414.4:c.1888G>A	p.Ala630Thr	p.A630T	ENST00000264414	NM_003590.4	630	Gcc/Acc	14/16	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	1	0.250324811893272	2		425	525	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151833982	151833982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	39	467	0	ENST00000262189.6:c.14671G>A	p.Glu4891Lys	p.E4891K	ENST00000262189	NM_170606.2	4891	Gaa/Aaa	59/59	1	2	FACETS	0.558	0.462	0.666	0.558	0.462	0.666	SUBCLONAL	1	FALSE	1	0.250324811893272	2		467	558	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151932982	151932982	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	12	50	0	ENST00000262189.6:c.2689C>G	p.Arg897Gly	p.R897G	ENST00000262189	NM_170606.2	897	Cga/Gga	16/59	1	2	FACETS	1	0.746	1	1	0.746	1	CLONAL	1	FALSE	1	0.250324811893272	2		50	91	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0030216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	42	258	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.267994947922445	3	FACETS	0.912	0.763	1	0.456	0.381	0.538	CLONAL	1	TRUE	1	0.28264248449036	3		258	372	SUCCESS
APC	324	MSKCC	GRCh37	5	112175225	112175225	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	67	259	0	ENST00000257430.4:c.3934G>T	p.Gly1312Ter	p.G1312*	ENST00000257430	NM_000038.5	1312	Gga/Tga	16/16	0.267994947922445	3	FACETS	1	0.911	1	1	0.911	1	CLONAL	2	TRUE	1	0.28264248449036	3		259	259	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578262	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs483352697	NA	P-0030216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	141	631	0	ENST00000269305.4:c.587G>C	p.Arg196Pro	p.R196P	ENST00000269305	NM_001126112.2	196	cGa/cCa	6/11	0.23544489971602	2	FACETS	0.889	0.814	0.967	0.889	0.814	0.967	CLONAL	2	TRUE	0	0.28264248449036	2		631	561	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128047	64128047	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	145	633	0	ENST00000334205.4:c.445C>G	p.Leu149Val	p.L149V	ENST00000334205	NM_003942.2	149	Ctg/Gtg	4/17	0.238711909209459	3	FACETS	0.782	0.714	0.852	0.782	0.714	0.852	SUBCLONAL	2	TRUE	1	0.28264248449036	3		633	749	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420841	49420841	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	44	563	0	ENST00000301067.7:c.14908G>A	p.Glu4970Lys	p.E4970K	ENST00000301067	NM_003482.3	4970	Gaa/Aaa	48/54	1	2	FACETS	0.545	0.457	0.644	0.545	0.457	0.644	SUBCLONAL	1	TRUE	1	0.28264248449036	2		563	571	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139818399	139818399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	83	606	0	ENST00000247668.2:c.1234G>A	p.Val412Met	p.V412M	ENST00000247668	NM_021138.3	412	Gtg/Atg	10/11	1	2	FACETS	0.856	0.756	0.964	0.856	0.756	0.964	CLONAL	1	TRUE	1	0.28264248449036	2		606	686	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357138	70357138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762659794	NA	P-0030241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	134	641	0	ENST00000374080.3:c.5653G>A	p.Val1885Ile	p.V1885I	ENST00000374080		1885	Gtc/Atc	39/45	0.230783970884267	1	FACETS	1	0.979	1	1	0.992	1	CLONAL	2	TRUE	0	0.230783970884267	1		641	422	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100613	67100613	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	140	509	0	ENST00000412916.2:c.311A>G	p.Asn104Ser	p.N104S	ENST00000412916		104	aAt/aGt	4/6	0.230783970884267	0	FACETS	0.827	0.784	0.868			1	CLONAL	6	TRUE	0	0.230783970884267	0		509	188	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111434	8111434	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs111853237	NA	P-0030241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	140	387	0	ENST00000346208.3:c.922-2A>T		p.X308_splice	ENST00000346208		308			0.17720933132981	3	FACETS	1	0.95	1	1	0.992	1	CLONAL	4	TRUE	1	0.230783970884267	3		387	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0030250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	78	585	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	1	2	FACETS	0.643	0.563	0.728	0.643	0.563	0.728	SUBCLONAL	1	TRUE	1	0.262699085112128	2		585	924	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351980	89351980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	106	813	0	ENST00000301030.4:c.970G>A	p.Glu324Lys	p.E324K	ENST00000301030	NM_001256183.1	324	Gaa/Aaa	9/13	1	2	FACETS	0.675	0.603	0.751	0.675	0.603	0.751	SUBCLONAL	1	TRUE	1	0.262699085112128	2		813	1196	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489538	40489538	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	67	519	0	ENST00000264657.5:c.712G>T	p.Glu238Ter	p.E238*	ENST00000264657	NM_139276.2	238	Gag/Tag	8/24	1	2	FACETS	0.708	0.615	0.81	0.708	0.615	0.81	SUBCLONAL	1	TRUE	1	0.262699085112128	2		519	720	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242672	46242673	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0030250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	29	344	0	ENST00000334344.6:c.1635_1636del	p.Met545IlefsTer3	p.M545Ifs*3	ENST00000334344	NM_152641.2	545	aTG/a	13/21	1	2	FACETS	0.655	0.526	0.801	0.655	0.526	0.801	SUBCLONAL	1	TRUE	1	0.262699085112128	2		344	337	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0030254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	881	483	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.581778526765664	5	FACETS	1	0.978	1	1	0.978	1	CLONAL	4	TRUE	1	0.581778526765664	5		483	1413	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145657	61145657	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748863675	NA	P-0030254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	271	518	0	ENST00000295025.8:c.769G>A	p.Val257Ile	p.V257I	ENST00000295025	NM_002908.2	257	Gta/Ata	7/11	1	2	FACETS	0.945	0.888	1	0.945	0.888	1	CLONAL	1	TRUE	1	0.581778526765664	2		518	986	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944243	81944243	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759496244	NA	P-0030254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1449	175	532	1	ENST00000359376.3:c.1852C>T	p.Arg618Cys	p.R618C	ENST00000359376	NM_002661.3	618	Cgc/Tgc	18/33	0.270354036639579	5	FACETS	0.694	0.636	0.754	0.139	0.127	0.151	INDETERMINATE	1	TRUE	0	0.581778526765664	5		533	1624	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143033725	143033725	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	198	412	0	ENST00000262992.4:c.2246G>C	p.Gly749Ala	p.G749A	ENST00000262992	NM_001101669.1	749	gGa/gCa	20/24	1	2	FACETS	0.934	0.868	1	0.934	0.868	1	CLONAL	1	TRUE	1	0.581778526765664	2		412	729	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525080	9525080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	51	462	1	ENST00000353224.5:c.1805C>T	p.Ser602Leu	p.S602L	ENST00000353224	NM_177990.2	602	tCa/tTa	8/10	0.278389719573174	1	FACETS	0.147	0.124	0.172	0.147	0.124	0.172	INDETERMINATE	1	TRUE	0	0.581778526765664	1		463	845	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30323835	30323835	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	132	277	0	ENST00000322652.5:c.1813G>C	p.Asp605His	p.D605H	ENST00000322652	NM_015355.2	605	Gat/Cat	15/16	1	2	FACETS	0.749	0.682	0.819	0.749	0.682	0.819	SUBCLONAL	1	TRUE	1	0.581778526765664	2		277	606	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883101	37883101	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	147	584	0	ENST00000269571.5:c.3004A>T	p.Ser1002Cys	p.S1002C	ENST00000269571		1002	Agc/Tgc	25/27	1	2	FACETS	0.446	0.407	0.488	0.446	0.407	0.488	SUBCLONAL	1	TRUE	1	0.581778526765664	2		584	1132	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744465	41744465	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	169	509	1	ENST00000301178.4:c.1085G>T	p.Gly362Val	p.G362V	ENST00000301178	NM_021913.4	362	gGt/gTt	8/20	1	2	FACETS	0.474	0.434	0.515	0.474	0.434	0.515	SUBCLONAL	1	TRUE	1	0.581778526765664	2		510	1226	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319400	62319401	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GA	GA	CT	novel	NA	P-0030254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1480	119	548	2	ENST00000360203.5:c.1592_1593delinsCT	p.Arg531Thr	p.R531T	ENST00000360203	NM_001283009.1	531	aGA/aCT	18/35	0.582062813946086	3	FACETS	0.33	0.297	0.366	0.165	0.148	0.183	SUBCLONAL	1	TRUE	1	0.581778526765664	3		550	1599	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121248	29121248	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	309	628	0	ENST00000328354.6:c.427C>G	p.His143Asp	p.H143D	ENST00000328354	NM_007194.3	143	Cac/Gac	3/15	1	2	FACETS	0.931	0.878	0.985	0.931	0.878	0.985	CLONAL	1	TRUE	1	0.581778526765664	2		628	1141	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295310	1295310	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0030254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	152	371	2				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.493	0.45	0.539			1	INDETERMINATE	1	TRUE	NA	0.581778526765664	2		373	1059	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679912	30679912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	166	260	0	ENST00000376406.3:c.1807G>A	p.Glu603Lys	p.E603K	ENST00000376406	NM_014641.2	603	Gaa/Aaa	5/15	0.565728912642471	2	FACETS	1	0.963	1	0.533	0.493	0.575	CLONAL	1	TRUE	0	0.581778526765664	2		260	535	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	193	264	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.77430595029237	2		264	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0030263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	283	410	1	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.756782748828513	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.77430595029237	1		411	428	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061333	38061333	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	300	494	0	ENST00000250448.2:c.656G>A	p.Arg219His	p.R219H	ENST00000250448	NM_004496.3	219	cGc/cAc	2/2	1	2	FACETS	0.997	0.944	1	0.997	0.944	1	CLONAL	1	TRUE	1	0.77430595029237	2		494	777	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628403	187628403	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0030263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	310	539	0	ENST00000441802.2:c.2579C>G	p.Ser860Ter	p.S860*	ENST00000441802	NM_005245.3	860	tCa/tGa	2/27	1	2	FACETS	0.982	0.931	1	0.982	0.931	1	CLONAL	1	TRUE	1	0.77430595029237	2		539	815	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902229	151902229	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0030263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	160	431	0	ENST00000262189.6:c.3923C>G	p.Ser1308Ter	p.S1308*	ENST00000262189	NM_170606.2	1308	tCa/tGa	25/59	1	2	FACETS	0.979	0.908	1	0.979	0.908	1	CLONAL	1	TRUE	1	0.77430595029237	2		431	422	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236097	108236097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565608982	NA	P-0030263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	213	497	1	ENST00000278616.4:c.9033G>A	p.Met3011Ile	p.M3011I	ENST00000278616	NM_000051.3	3011	atG/atA	63/63	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.77430595029237	2		498	530	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445302	49445302	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	411	684	1	ENST00000301067.7:c.2164G>T	p.Glu722Ter	p.E722*	ENST00000301067	NM_003482.3	722	Gag/Tag	10/54	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.77430595029237	2		685	1053	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257206	133257206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376348304	NA	P-0030263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	210	398	0	ENST00000320574.5:c.272G>A	p.Gly91Glu	p.G91E	ENST00000320574	NM_006231.2	91	gGa/gAa	3/49	1	2	FACETS	0.913	0.854	0.974	0.913	0.854	0.974	CLONAL	1	TRUE	1	0.77430595029237	2		398	594	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28979985	28979985	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	173	534	0	ENST00000282397.4:c.1483G>A	p.Asp495Asn	p.D495N	ENST00000282397	NM_002019.4	495	Gac/Aac	11/30	1	2	FACETS	0.978	0.909	1	0.978	0.909	1	CLONAL	1	TRUE	1	0.77430595029237	2		534	457	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035073	42035073	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	300	556	0	ENST00000219905.7:c.4915G>C	p.Glu1639Gln	p.E1639Q	ENST00000219905	NM_001164273.1	1639	Gag/Cag	15/24	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.77430595029237	2		556	768	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90645531	90645531	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	53	46	0	ENST00000330062.3:c.92C>A	p.Ser31Ter	p.S31*	ENST00000330062	NM_002168.2	31	tCg/tAg	1/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.77430595029237	2		46	105	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778807	3778807	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886041518	NA	P-0030263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	363	573	0	ENST00000262367.5:c.6241C>T	p.Gln2081Ter	p.Q2081*	ENST00000262367	NM_004380.2	2081	Cag/Tag	31/31	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.77430595029237	2		573	854	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857494	9857494	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	156	336	0	ENST00000330684.3:c.3907G>C	p.Asp1303His	p.D1303H	ENST00000330684	NM_001134407.1	1303	Gac/Cac	13/13	1	2	FACETS	0.971	0.899	1	0.971	0.899	1	CLONAL	1	TRUE	1	0.77430595029237	2		336	415	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169506	11169512	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	GAGAAGG	GAGAAGG	TAAAGA	novel	NA	P-0030263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	347	533	2	ENST00000358026.2:c.4672_4678delinsTAAAGA	p.Glu1558Ter	p.E1558*	ENST00000358026	NM_001128849.1	1558	GAGAAGGac/TAAAGAac	33/36	0.77430595029237	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.77430595029237	1		535	501	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795787	42795787	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	308	513	0	ENST00000575354.2:c.2776C>G	p.Leu926Val	p.L926V	ENST00000575354	NM_015125.3	926	Ctg/Gtg	11/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.77430595029237	2		513	772	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244080	153244080	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	254	387	0	ENST00000281708.4:c.2077G>T	p.Glu693Ter	p.E693*	ENST00000281708	NM_033632.3	693	Gaa/Taa	12/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.77430595029237	2		387	602	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592047	67592047	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	117	247	0	ENST00000274335.5:c.1863G>C	p.Glu621Asp	p.E621D	ENST00000274335		621	gaG/gaC	14/15	1	2	FACETS	0.93	0.85	1	0.93	0.85	1	CLONAL	1	TRUE	1	0.77430595029237	2		247	325	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592111	67592111	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	129	263	0	ENST00000274335.5:c.1927G>C	p.Asp643His	p.D643H	ENST00000274335		643	Gat/Cat	14/15	1	2	FACETS	0.931	0.854	1	0.931	0.854	1	CLONAL	1	TRUE	1	0.77430595029237	2		263	358	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674318	86674318	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1236053304	NA	P-0030263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	109	354	0	ENST00000274376.6:c.2450C>G	p.Ser817Cys	p.S817C	ENST00000274376	NM_002890.2	817	tCt/tGt	18/25	1	2	FACETS	0.92	0.838	1	0.92	0.838	1	CLONAL	1	TRUE	1	0.77430595029237	2		354	306	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652178	36652196	+	frameshift_variant	Frame_Shift_Del	DEL	TCTGCTGCAGGGGACAGCA	TCTGCTGCAGGGGACAGCA	AG	novel	NA	P-0030263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	273	382	2	ENST00000244741.5:c.300_318delinsAG	p.Leu101GlyfsTer22	p.L101Gfs*22	ENST00000244741	NM_000389.4	100	gcTCTGCTGCAGGGGACAGCA/gcAG	2/3	1	2	FACETS	0.948	0.894	1	0.948	0.894	1	CLONAL	1	TRUE	1	0.77430595029237	2		384	744	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039829	47039829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	373	292	0	ENST00000377604.3:c.1172C>T	p.Ser391Phe	p.S391F	ENST00000377604	NM_001204468.1	391	tCc/tTc	12/24	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.77430595029237	1		292	458	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045656	47045656	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0030263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	301	211	0	ENST00000377604.3:c.2538-1G>A		p.X846_splice	ENST00000377604	NM_001204468.1	846			1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.77430595029237	1		211	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0030305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	238	693	0	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.491372827306132	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.491372827306132	1		693	679	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111494	8111495	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTGGAGG	novel	NA	P-0030305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	414	615	0	ENST00000346208.3:c.981_987dup	p.Arg330LeufsTer24	p.R330Lfs*24	ENST00000346208		327	ctc/ctCTGGAGGc	5/6	0.491372827306132	3	FACETS	0.876	0.835	0.918	0.876	0.835	0.918	CLONAL	2	TRUE	1	0.491372827306132	3		615	1198	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251601	212251601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs905120734	NA	P-0030305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	148	437	0	ENST00000342788.4:c.3458C>T	p.Pro1153Leu	p.P1153L	ENST00000342788	NM_005235.2	1153	cCt/cTt	27/28	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.491372827306132	2		437	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0030334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	306	468	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.618981707840044	2	FACETS	0.895	0.855	0.936	0.895	0.855	0.936	CLONAL	2	TRUE	0	0.619119005793285	2		468	552	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627928	37627929	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	545	641	0	ENST00000447079.4:c.1844dup	p.Thr616AsnfsTer25	p.T616Nfs*25	ENST00000447079	NM_015083.1	615	gta/gTta	2/14	0.618981707840044	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.619119005793285	2		641	774	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921540	178921540	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	67	432	0	ENST00000263967.3:c.1022C>G	p.Ala341Gly	p.A341G	ENST00000263967	NM_006218.2	341	gCa/gGa	5/21	0.618981707840044	3	FACETS	0.718	0.626	0.815	0.359	0.313	0.408	SUBCLONAL	1	TRUE	1	0.619119005793285	3		432	395	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31493382	31493382	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	92	386	0	ENST00000344624.3:c.1774del	p.Ile592Ter	p.I592*	ENST00000344624		592	Ata/ta	10/33	0.537214174419268	4	FACETS	1	0.908	1	0.51	0.455	0.568	CLONAL	1	TRUE	2	0.619119005793285	4		386	472	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595255	141595255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1234	154	678	0	ENST00000220592.5:c.178G>T	p.Asp60Tyr	p.D60Y	ENST00000220592	NM_012154.3	60	Gat/Tat	2/19	0.619119005793285	7	FACETS	0.913	0.833	0.997	0.183	0.166	0.2	CLONAL	1	TRUE	2	0.619119005793285	7		678	1388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782144	NA	P-0030335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	122	608	0	ENST00000269305.4:c.473G>C	p.Arg158Pro	p.R158P	ENST00000269305	NM_001126112.2	158	cGc/cCc	5/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.346521990942121	2		608	523	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41022087	41022087	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	61	537	0	ENST00000267868.3:c.811G>A	p.Ala271Thr	p.A271T	ENST00000267868	NM_002875.4	271	Gct/Act	9/10	1	2	FACETS	0.744	0.643	0.854	0.744	0.643	0.854	SUBCLONAL	1	TRUE	1	0.346521990942121	2		537	473	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098790	178098806	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGAGAAATTCACCTG	TGGGAGAAATTCACCTG	-	novel	NA	P-0030335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	90	531	0	ENST00000397062.3:c.239_255del	p.Thr80AsnfsTer32	p.T80Nfs*32	ENST00000397062	NM_006164.4	80	aCAGGTGAATTTCTCCCA/a	2/5	1	2	FACETS	0.821	0.729	0.918	0.821	0.729	0.918	CLONAL	1	TRUE	1	0.346521990942121	2		531	633	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945418	71945422	+	frameshift_variant	Frame_Shift_Del	DEL	TCTAC	TCTAC	-	novel	NA	P-0030370-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	101	709	0	ENST00000298229.2:c.2311_2315del	p.Ser771LeufsTer10	p.S771Lfs*10	ENST00000298229	NM_001567.3	769	tTCTAC/t	20/28	0.31865419784278	1	FACETS	0.821	0.735	0.913	0.821	0.735	0.913	CLONAL	1	TRUE	0	0.31865419784278	1		709	649	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867255	68867256	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030370-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	121	562	0	ENST00000261769.5:c.2503dup	p.Tyr835LeufsTer2	p.Y835Lfs*2	ENST00000261769	NM_004360.3	834	-/T	16/16	0.31865419784278	1	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	0	0.31865419784278	1		562	634	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0030392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	105	503	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.461011437921518	1	FACETS	0.93	0.84	1	0.93	0.84	1	CLONAL	1	TRUE	0	0.461011437921518	1		503	377	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0030392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	51	475	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.461011437921518	1	FACETS	0.402	0.342	0.467	0.402	0.342	0.467	SUBCLONAL	1	TRUE	0	0.461011437921518	1		475	424	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863699	68863702	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	AAGT	AAGT	-	rs587782810	NA	P-0030392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	78	289	0	ENST00000261769.5:c.2439+5_2439+8del		p.X813_splice	ENST00000261769	NM_004360.3	813		15/16	0.461011437921518	1	FACETS	0.799	0.708	0.894	0.799	0.708	0.894	SUBCLONAL	1	TRUE	0	0.461011437921518	1		289	326	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229441	36229441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	76	339	0	ENST00000222270.7:c.8131C>T	p.Arg2711Cys	p.R2711C	ENST00000222270	NM_014727.1	2711	Cgt/Tgt	37/37	1	2	FACETS	0.533	0.467	0.603	0.533	0.467	0.603	SUBCLONAL	1	TRUE	1	0.461011437921518	2		339	619	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220139	36220139	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	68	543	0	ENST00000222270.7:c.4859A>T	p.Glu1620Val	p.E1620V	ENST00000222270	NM_014727.1	1620	gAg/gTg	22/37	1	2	FACETS	0.321	0.278	0.367	0.321	0.278	0.367	SUBCLONAL	1	TRUE	1	0.461011437921518	2		543	920	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	353	451	1	ENST00000269305.4:c.528C>A	p.Cys176Ter	p.C176*	ENST00000269305	NM_001126112.2	176	tgC/tgA	5/11	0.453870488026728	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.453870488026728	1		452	926	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280636	41280636	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768012106	NA	P-0030393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	48	449	2	ENST00000349496.5:c.2149C>T	p.Arg717Cys	p.R717C	ENST00000349496	NM_001904.3	717	Cgt/Tgt	15/15	0.453870488026728	1	FACETS	0.332	0.281	0.389	0.332	0.281	0.389	SUBCLONAL	1	TRUE	0	0.453870488026728	1		451	492	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462132	120462132	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	88	467	0	ENST00000256646.2:c.5584T>A	p.Leu1862Met	p.L1862M	ENST00000256646	NM_024408.3	1862	Ttg/Atg	31/34	0.226706813834785	3	FACETS	0.503	0.445	0.566	0.252	0.222	0.283	INDETERMINATE	1	TRUE	1	0.453870488026728	3		467	945	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434791	110434791	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1273138872	NA	P-0030393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	95	659	1	ENST00000375856.3:c.3610C>A	p.Pro1204Thr	p.P1204T	ENST00000375856	NM_003749.2	1204	Cca/Aca	1/2	0.453870488026728	1	FACETS	0.319	0.283	0.358	0.319	0.283	0.358	SUBCLONAL	1	TRUE	0	0.453870488026728	1		660	1014	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47643498	47643498	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs63751062	NA	P-0030393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	33	494	1	ENST00000233146.2:c.1006C>A	p.Pro336Thr	p.P336T	ENST00000233146	NM_000251.2	336	Cct/Act	6/16	0.439681721892648	1	FACETS	0.245	0.199	0.297	0.245	0.199	0.297	SUBCLONAL	1	TRUE	0	0.453870488026728	1		495	458	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564468	55564468	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	49	326	0	ENST00000288135.5:c.356T>G	p.Leu119Arg	p.L119R	ENST00000288135	NM_000222.2	119	cTt/cGt	3/21	0.453870488026728	1	FACETS	0.477	0.405	0.555	0.477	0.405	0.555	SUBCLONAL	1	TRUE	0	0.453870488026728	1		326	350	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288636	33288636	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	47	291	0	ENST00000374542.5:c.916C>G	p.Arg306Gly	p.R306G	ENST00000374542	NM_001141970.1	306	Cga/Gga	3/8	0.362396561060625	2	FACETS	0.433	0.366	0.508	0.217	0.183	0.254	SUBCLONAL	1	TRUE	0	0.453870488026728	2		291	478	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49430952	49430952	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	138	409	0	ENST00000301067.7:c.10187del	p.Leu3396TrpfsTer37	p.L3396Wfs*37	ENST00000301067	NM_003482.3	3396	tTg/tg	34/54	0.110593255689307	4	FACETS	0.868	0.797	0.941	0.868	0.797	0.941	INDETERMINATE	2	TRUE	2	0.613920563374372	4		409	418	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827929	72827930	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0030474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	204	666	0	ENST00000268489.5:c.8651_8652insGT	p.Glu2885LeufsTer70	p.E2885Lfs*70	ENST00000268489	NM_006885.3	2884	tct/tcGTt	9/10	0.613920563374372	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.613920563374372	1		666	448	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976373	18976373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746427790	NA	P-0030474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	65	764	0	ENST00000262803.5:c.3023G>A	p.Arg1008Gln	p.R1008Q	ENST00000262803	NM_002911.3	1008	cGa/cAa	22/24	1	2	FACETS	0.359	0.311	0.411	0.359	0.311	0.411	SUBCLONAL	1	TRUE	1	0.613920563374372	2		764	590	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670727	134670727	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	63	461	0	ENST00000398015.3:c.638C>T	p.Ala213Val	p.A213V	ENST00000398015	NM_004441.4	213	gCa/gTa	3/16	1	2	FACETS	0.497	0.431	0.568	0.497	0.431	0.568	SUBCLONAL	1	TRUE	1	0.613920563374372	2		461	413	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0030561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	150	461	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.438626034004181	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.438626034004181	1		461	497	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098391	108098391	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	117	270	0	ENST00000278616.4:c.40C>T	p.Gln14Ter	p.Q14*	ENST00000278616	NM_000051.3	14	Caa/Taa	2/63	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.438626034004181	2		270	519	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99452006	99452006	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	127	370	0	ENST00000268035.6:c.1340A>T	p.Tyr447Phe	p.Y447F	ENST00000268035	NM_000875.3	447	tAc/tTc	6/21	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.438626034004181	2		370	554	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183857	10183857	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	130	366	0	ENST00000256474.2:c.326del	p.Ile109ThrfsTer50	p.I109Tfs*50	ENST00000256474	NM_000551.3	109	aTc/ac	1/3	0.438626034004181	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.438626034004181	1		366	426	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143038	47143038	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	151	334	0	ENST00000409792.3:c.4925T>A	p.Val1642Glu	p.V1642E	ENST00000409792	NM_014159.6	1642	gTg/gAg	8/21	0.438626034004181	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.438626034004181	1		334	499	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623115	52623115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	127	355	0	ENST00000394830.3:c.2936G>A	p.Cys979Tyr	p.C979Y	ENST00000394830	NM_018313.4	979	tGt/tAt	19/30	0.438626034004181	1	FACETS	0.926	0.844	1	0.926	0.844	1	CLONAL	1	TRUE	0	0.438626034004181	1		355	488	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0030588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	38	280	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.978	0.81	1	0.978	0.81	1	CLONAL	1	TRUE	1	0.21	2		280	370	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184574	11184574	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519917	NA	P-0030588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	57	478	0	ENST00000361445.4:c.6643T>A	p.Ser2215Thr	p.S2215T	ENST00000361445	NM_004958.3	2215	Tct/Act	47/58	1	2	FACETS	0.721	0.617	0.834	0.721	0.617	0.834	SUBCLONAL	1	TRUE	1	0.21	2		478	753	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211840	2211840	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	57	471	0	ENST00000398665.3:c.1556A>C	p.Lys519Thr	p.K519T	ENST00000398665	NM_032482.2	519	aAg/aCg	16/28	1	2	FACETS	0.591	0.505	0.685	0.591	0.505	0.685	SUBCLONAL	1	TRUE	1	0.21	2		471	919	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191532	10191549	+	inframe_deletion	In_Frame_Del	DEL	CAGGAGACTGGACATCGT	CAGGAGACTGGACATCGT	-	novel	NA	P-0030588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	40	393	0	ENST00000256474.2:c.529_546del	p.Arg177_Arg182del	p.R177_R182del	ENST00000256474	NM_000551.3	175	taCAGGAGACTGGACATCGTc/tac	3/3	1	2	FACETS	0.547	0.453	0.651	0.547	0.453	0.651	SUBCLONAL	1	TRUE	1	0.21	2		393	697	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643375	52643375	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	33	395	0	ENST00000394830.3:c.2521C>T	p.Gln841Ter	p.Q841*	ENST00000394830	NM_018313.4	841	Caa/Taa	17/30	1	2	FACETS	0.733	0.596	0.886	0.733	0.596	0.886	SUBCLONAL	1	TRUE	1	0.21	2		395	429	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155526	106155526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749618735	NA	P-0030590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	145	308	0	ENST00000380013.4:c.427G>A	p.Asp143Asn	p.D143N	ENST00000380013	NM_001127208.2	143	Gat/Aat	3/11	0.689776992583093	4	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.689776992583093	4		308	548	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876659675	NA	P-0030590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	309	378	0	ENST00000269305.4:c.764T>G	p.Ile255Ser	p.I255S	ENST00000269305	NM_001126112.2	255	aTc/aGc	7/11	0.55121078142945	3	FACETS	1	0.992	1	0.771	0.737	0.804	CLONAL	2	TRUE	0	0.689776992583093	3		378	521	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020769	37020769	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	78	327	0	ENST00000358127.4:c.76G>T	p.Val26Phe	p.V26F	ENST00000358127	NM_001280556.1	26	Gtt/Ttt	2/10	0.533056736039898	6	FACETS	0.65	0.57	0.736	0.217	0.19	0.246	SUBCLONAL	1	TRUE	3	0.689776992583093	6		327	828	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422196	81422208	+	splice_donor_variant,intron_variant	Splice_Site	DEL	TGAGTACCCGGGA	TGAGTACCCGGGA	-	novel	NA	P-0030590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	62	313	0	ENST00000298171.2:c.170+2_170+14del		p.X57_splice	ENST00000298171	NM_000369.2	57			0.55121078142945	3	FACETS	0.693	0.602	0.79	0.231	0.2	0.264	SUBCLONAL	1	TRUE	0	0.689776992583093	3		313	349	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721198	61721198	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	409	327	0	ENST00000401558.2:c.1076A>C	p.Glu359Ala	p.E359A	ENST00000401558	NM_003400.3	359	gAa/gCa	12/25	0.684417542283791	5	FACETS	0.938	0.904	0.971			1	CLONAL	4	TRUE	NA	0.689776992583093	5		327	643	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1956895	1956895	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	255	385	1	ENST00000382891.5:c.2346G>T	p.Met782Ile	p.M782I	ENST00000382891	NM_133335.3	782	atG/atT	13/22	0.545655076927616	3	FACETS	0.783	0.738	0.828	0.522	0.492	0.552	SUBCLONAL	2	TRUE	0	0.689776992583093	3		386	635	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969138	93969139	+	missense_variant	Missense_Mutation	DNP	CT	CT	GC	novel	NA	P-0030590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	45	259	0	ENST00000369303.4:c.1857_1858delinsGC	p.Ala620Pro	p.A620P	ENST00000369303	NM_004440.3	619	agAGct/agGCct	10/17	0.533056736039898	6	FACETS	0.604	0.507	0.711	0.201	0.169	0.237	SUBCLONAL	1	TRUE	3	0.689776992583093	6		259	514	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923137	39923138	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0030590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	248	361	1	ENST00000378444.4:c.3570_3571delinsTT	p.Glu1190Asp	p.E1190D	ENST00000378444	NM_001123385.1	1190	gaGCtg/gaTTtg	8/15	0.689776992583093	8	FACETS	1	0.967	1			1	CLONAL	2	TRUE	NA	0.689776992583093	8		362	1047	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0030692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	588	773	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.404181135483583	2	FACETS		NA	1	1	0.998	1	NA	5	FALSE	0	0.404181135483583	2		773	639	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0030692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	110	264	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.404181135483583	1	FACETS	0.932	0.856	1	1	0.989	1	CLONAL	2	FALSE	0	0.404181135483583	1		264	233	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141492	11141492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	192	417	0	ENST00000358026.2:c.3469C>T	p.Arg1157Trp	p.R1157W	ENST00000358026	NM_001128849.1	1157	Cgg/Tgg	25/36	0.146225504507135	3	FACETS	0.959	0.9	1	1	0.992	1	INDETERMINATE	3	FALSE	1	0.404181135483583	3		417	397	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253781	153253781	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	72	288	0	ENST00000281708.4:c.952A>G	p.Asn318Asp	p.N318D	ENST00000281708	NM_033632.3	318	Aac/Gac	6/12	0.336796219263041	0	FACETS	1	0.94	1			1	CLONAL	1	FALSE	0	0.404181135483583	0		288	196	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271525	26271525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	58	243	0	ENST00000305910.3:c.88G>A	p.Ala30Thr	p.A30T	ENST00000305910	NM_003534.2	30	Gcg/Acg	1/1	0.404181135483583	4	FACETS	0.752	0.652	0.859			1	SUBCLONAL	2	FALSE	NA	0.404181135483583	4		243	268	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849164	76849164	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0030692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	44	264	0	ENST00000373344.5:c.6110+2T>G		p.X2037_splice	ENST00000373344	NM_000489.3	2037			0.404181135483583	0	FACETS	0.612	0.53	0.696			1	SUBCLONAL	2	FALSE	0	0.404181135483583	0		264	106	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0030697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	102	714	0	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	0.677587120037993	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.717171265123785	2		714	136	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506972	186506972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	91	335	0	ENST00000323963.5:c.1138G>A	p.Glu380Lys	p.E380K	ENST00000323963		380	Gaa/Aaa	11/11	0.717171265123785	5	FACETS	1	0.977	1	0.343	0.306	0.381	CLONAL	1	TRUE	1	0.717171265123785	5		335	384	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736492	85736492	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	66	406	0	ENST00000370580.1:c.155C>A	p.Thr52Asn	p.T52N	ENST00000370580	NM_003921.4	52	aCt/aAt	2/3	0.458756272800779	4	FACETS	1	0.953	1	0.592	0.519	0.669	CLONAL	1	TRUE	2	0.717171265123785	4		406	267	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617708	39617708	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	42	497	0	ENST00000262039.4:c.1892A>G	p.Tyr631Cys	p.Y631C	ENST00000262039	NM_002647.2	631	tAt/tGt	17/25	0.399971517422298	3	FACETS	1	0.884	1	0.349	0.296	0.405	INDETERMINATE	1	TRUE	0	0.717171265123785	3		497	152	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0030754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	165	582	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.174978496235737	4	FACETS	0.973	0.904	1			1	INDETERMINATE	3	TRUE	NA	0.37923682356131	4		582	411	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723047	52723047	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	116	383	0	ENST00000322088.6:c.1232T>G	p.Leu411Arg	p.L411R	ENST00000322088	NM_014225.5	411	cTg/cGg	10/15	0.37923682356131	3	FACETS	1	0.974	1	0.78	0.713	0.849	CLONAL	2	TRUE	0	0.37923682356131	3		383	311	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38957782	38957782	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	33	273	0	ENST00000357387.3:c.2471T>C	p.Val824Ala	p.V824A	ENST00000357387	NM_152756.3	824	gTa/gCa	25/38	0.209337711291751	2	FACETS	0.719	0.589	0.864	0.36	0.294	0.432	INDETERMINATE	1	TRUE	0	0.37923682356131	2		273	242	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138729528	NA	P-0030777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	365	474	0	ENST00000269305.4:c.523C>G	p.Arg175Gly	p.R175G	ENST00000269305	NM_001126112.2	175	Cgc/Ggc	5/11	0.808177670873996	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.808177670873996	2		474	449	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038811	47038811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	180	606	0	ENST00000377604.3:c.818C>T	p.Pro273Leu	p.P273L	ENST00000377604	NM_001204468.1	273	cCg/cTg	9/24	0.808177670873996	1	FACETS	0.667	0.623	0.711	0.667	0.623	0.711	SUBCLONAL	1	TRUE	0	0.808177670873996	1		606	398	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805538	46805538	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	589	618	2	ENST00000290295.7:c.418A>G	p.Met140Val	p.M140V	ENST00000290295	NM_006361.5	140	Atg/Gtg	1/2	0.396986552546775	4	FACETS	0.913	0.885	0.941	0.913	0.885	0.941	INDETERMINATE	3	TRUE	1	0.808177670873996	4		620	962	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971030	55971030	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	118	420	0	ENST00000263923.4:c.1767G>T	p.Gln589His	p.Q589H	ENST00000263923	NM_002253.2	589	caG/caT	13/30	0.778296065209196	3	FACETS	0.863	0.783	0.946	0.432	0.391	0.473	CLONAL	1	TRUE	1	0.808177670873996	3		420	475	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0030825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	153	398	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.982	0.907	1	0.982	0.907	1	CLONAL	1	TRUE	1	0.71624558334942	2		398	435	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0030825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	131	335	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.912	0.836	0.991	0.912	0.836	0.991	CLONAL	1	TRUE	1	0.71624558334942	2		335	401	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295774	15295774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1289281166	NA	P-0030825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	316	965	1	ENST00000263388.2:c.2353C>T	p.Arg785Cys	p.R785C	ENST00000263388	NM_000435.2	785	Cgc/Tgc	15/33	1	2	FACETS	0.897	0.848	0.947	0.897	0.848	0.947	CLONAL	1	TRUE	1	0.71624558334942	2		966	984	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870236	155870237	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	213	644	0	ENST00000368323.3:c.602dup	p.Asn201LysfsTer40	p.N201Kfs*40	ENST00000368323	NM_006912.5	201	aac/aaAc	6/6	1	2	FACETS	0.924	0.863	0.986	0.924	0.863	0.986	CLONAL	1	TRUE	1	0.71624558334942	2		644	644	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624270	89624270	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs398123324	NA	P-0030825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	153	356	0	ENST00000371953.3:c.44G>C	p.Arg15Thr	p.R15T	ENST00000371953	NM_000314.4	15	aGa/aCa	1/9	0.71624558334942	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.71624558334942	1		356	269	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs17849781	NA	P-0030827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	304	583	0	ENST00000269305.4:c.832C>G	p.Pro278Ala	p.P278A	ENST00000269305	NM_001126112.2	278	Cct/Gct	8/11	0.390678421187495	2	FACETS	0.959	0.908	1	0.959	0.908	1	CLONAL	2	TRUE	0	0.390678421187495	2		583	811	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3634842	3634842	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	112	553	0	ENST00000294008.3:c.4667C>A	p.Pro1556His	p.P1556H	ENST00000294008	NM_032444.2	1556	cCc/cAc	13/15	0.389370795961439	3	FACETS	0.825	0.741	0.913	0.412	0.37	0.457	CLONAL	1	TRUE	1	0.390678421187495	3		553	831	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692795	89692796	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	64	291	0	ENST00000371953.3:c.281dup	p.Asn94LysfsTer13	p.N94Kfs*13	ENST00000371953	NM_000314.4	93	-/A	5/9	0.390678421187495	2	FACETS	0.996	0.868	1	0.498	0.434	0.566	CLONAL	1	TRUE	0	0.390678421187495	2		291	329	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001933	29001933	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	90	420	0	ENST00000282397.4:c.1232A>T	p.Gln411Leu	p.Q411L	ENST00000282397	NM_002019.4	411	cAg/cTg	9/30	0.390678421187495	3	FACETS	0.923	0.82	1	0.461	0.41	0.516	CLONAL	1	TRUE	1	0.390678421187495	3		420	597	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89809312	89809312	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	88	412	0	ENST00000389301.3:c.3661A>G	p.Asn1221Asp	p.N1221D	ENST00000389301	NM_000135.2	1221	Aac/Gac	37/43	0.389370795961439	3	FACETS	0.884	0.784	0.991	0.442	0.392	0.496	CLONAL	1	TRUE	1	0.390678421187495	3		412	609	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663365	227663367	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0030827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	82	392	0	ENST00000305123.5:c.88_90del	p.Phe30del	p.F30del	ENST00000305123	NM_005544.2	30	TTC/-	1/2	0.390678421187495	2	FACETS	0.923	0.817	1	0.461	0.408	0.518	CLONAL	1	TRUE	0	0.390678421187495	2		392	455	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274859	41274859	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	103	329	0	ENST00000349496.5:c.1109T>A	p.Leu370Gln	p.L370Q	ENST00000349496	NM_001904.3	370	cTg/cAg	8/15	0.389370795961439	3	FACETS	1	0.965	1	0.585	0.525	0.648	CLONAL	1	TRUE	1	0.390678421187495	3		329	539	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233729	233729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760598746	NA	P-0030827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	117	428	0	ENST00000264932.6:c.1033C>T	p.Arg345Trp	p.R345W	ENST00000264932	NM_004168.2	345	Cgg/Tgg	8/15	0.204639266405404	4	FACETS	1	0.963	1	0.57	0.514	0.629	INDETERMINATE	1	TRUE	2	0.390678421187495	4		428	731	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061240	38061240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	328	686	0	ENST00000250448.2:c.749C>T	p.Ser250Phe	p.S250F	ENST00000250448	NM_004496.3	250	tCc/tTc	2/2	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.849740377199299	2		686	767	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0030831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	107	561	0	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	1	2	FACETS	0.884	0.805	0.965	0.884	0.805	0.965	CLONAL	1	TRUE	1	0.849740377199299	2		561	285	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0030831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	163	506	0	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	0.849740377199299	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.849740377199299	1		506	214	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980344	201980350	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCTGT	CCTCTGT	-	novel	NA	P-0030831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	818	830	0	ENST00000359651.3:c.80_86del	p.Ala27ValfsTer14	p.A27Vfs*14	ENST00000359651		27	gCCTCTGTt/gt	1/8	0.84278915620981	3	FACETS	0.957	0.931	0.983	0.957	0.931	0.983	CLONAL	2	TRUE	1	0.849740377199299	3		830	1433	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874021	123874021	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6	72	31	0	ENST00000330479.4:c.52G>A	p.Ala18Thr	p.A18T	ENST00000330479	NM_020382.3	18	Gcg/Acg	2/9	0.849740377199299	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.849740377199299	2		31	78	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914923	32914923	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359587	NA	P-0030831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	86	486	0	ENST00000380152.3:c.6434del	p.Asn2145IlefsTer23	p.N2145Ifs*23	ENST00000380152		2144	gAa/ga	11/27	0.849740377199299	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.849740377199299	1		486	114	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061280	38061281	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTCCGGGGAGCGTGCCACCTTGACGAAGCA	novel	NA	P-0030831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	266	705	0	ENST00000250448.2:c.679_708dup	p.Cys227_Asp236dup	p.C227_D236dup	ENST00000250448	NM_004496.3	227	-/TGCTTCGTCAAGGTGGCACGCTCCCCGGAC	2/2	1	2	FACETS	0.584	0.547	0.622	0.584	0.547	0.622	SUBCLONAL	1	TRUE	1	0.849740377199299	2		705	1072	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763475	59763478	+	frameshift_variant	Frame_Shift_Del	DEL	CTTT	CTTT	-	novel	NA	P-0030831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	116	541	0	ENST00000259008.2:c.2624_2627del	p.Glu875ValfsTer21	p.E875Vfs*21	ENST00000259008	NM_032043.2	875	gAAAGt/gt	19/20	0.849740377199299	3	FACETS	1	0.925	1	0.509	0.463	0.557	CLONAL	1	TRUE	1	0.849740377199299	3		541	382	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033653	48033653	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	138	516	0	ENST00000234420.5:c.3864A>C	p.Lys1288Asn	p.K1288N	ENST00000234420	NM_000179.2	1288	aaA/aaC	9/10	1	2	FACETS	0.955	0.882	1	0.955	0.882	1	CLONAL	1	TRUE	1	0.849740377199299	2		516	340	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125644	47125644	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	139	419	0	ENST00000409792.3:c.5626C>A	p.Leu1876Ile	p.L1876I	ENST00000409792	NM_014159.6	1876	Cta/Ata	12/21	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.849740377199299	2		419	315	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674163	117674163	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	168	546	0	ENST00000368508.3:c.4311G>T	p.Gln1437His	p.Q1437H	ENST00000368508	NM_002944.2	1437	caG/caT	26/43	1	2	FACETS	0.903	0.839	0.968	0.903	0.839	0.968	CLONAL	1	TRUE	1	0.849740377199299	2		546	438	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709571	176709571	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	168	425	2	ENST00000439151.2:c.5998A>G	p.Thr2000Ala	p.T2000A	ENST00000439151	NM_022455.4	2000	Acc/Gcc	19/23	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.512396361196433	2		427	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578491	7578491	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1567553924	NA	P-0030881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	289	712	1	ENST00000269305.4:c.439del	p.Val147LeufsTer23	p.V147Lfs*23	ENST00000269305	NM_001126112.2	147	Gtt/tt	5/11	0.671112654212961	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.671112654212961	1		713	513	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	65	356	0	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	0.671112654212961	1	FACETS	0.562	0.494	0.634	0.562	0.494	0.634	SUBCLONAL	1	TRUE	0	0.671112654212961	1		356	229	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342651	70342651	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1373901177	NA	P-0030881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	27	586	0	ENST00000374080.3:c.1412C>G	p.Ser471Cys	p.S471C	ENST00000374080		471	tCt/tGt	10/45	0.671112654212961	1	FACETS	0.379	0.306	0.461	0.379	0.306	0.461	SUBCLONAL	1	TRUE	0	0.671112654212961	1		586	141	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	40	264	0				ENST00000310581	NM_198253.2	-/1132			0.284091471065745	1	FACETS	0.542	0.45	0.644	0.542	0.45	0.644	SUBCLONAL	1	FALSE	0	0.284091471065745	1		264	446	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118870	70118870	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs886041242	NA	P-0030887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	91	426	0	ENST00000245479.2:c.442G>T	p.Glu148Ter	p.E148*	ENST00000245479	NM_000346.3	148	Gag/Tag	2/3	0.284091471065745	1	FACETS	0.615	0.545	0.69	0.615	0.545	0.69	SUBCLONAL	1	FALSE	0	0.284091471065745	1		426	894	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692790	89692790	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	28	301	0	ENST00000371953.3:c.274G>C	p.Asp92His	p.D92H	ENST00000371953	NM_000314.4	92	Gac/Cac	5/9	0.279618154791995	3	FACETS	0.996	0.801	1	0.498	0.4	0.608	CLONAL	1	FALSE	1	0.284091471065745	3		301	226	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311619	15311621	+	inframe_deletion	In_Frame_Del	DEL	AGC	AGC	-	rs746497955	NA	P-0030887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	11	54	0	ENST00000263388.2:c.96_98del	p.Leu33del	p.L33del	ENST00000263388	NM_000435.2	32	ctGCTa/cta	1/33	0.224666049874671	3	FACETS	0.502	0.348	0.694	0.251	0.174	0.347	SUBCLONAL	1	FALSE	1	0.284091471065745	3		54	176	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577569	7577569	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519981	NA	P-0030887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	75	547	0	ENST00000269305.4:c.712T>C	p.Cys238Arg	p.C238R	ENST00000269305	NM_001126112.2	238	Tgt/Cgt	7/11	0.284091471065745	1	FACETS	0.582	0.509	0.661	0.582	0.509	0.661	SUBCLONAL	1	FALSE	0	0.284091471065745	1		547	778	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112884189	112884189	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397507501	NA	P-0030887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	33	516	0	ENST00000351677.2:c.124A>G	p.Thr42Ala	p.T42A	ENST00000351677	NM_002834.3	42	Aca/Gca	2/16	0.224666049874671	3	FACETS	0.416	0.338	0.505	0.208	0.169	0.253	SUBCLONAL	1	FALSE	1	0.284091471065745	3		516	638	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606840	43606840	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0030887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	169	667	0	ENST00000355710.3:c.1449C>G	p.Tyr483Ter	p.Y483*	ENST00000355710	NM_020975.4	483	taC/taG	7/20	0.279618154791995	3	FACETS	1	0.982	1	0.625	0.574	0.679	CLONAL	1	FALSE	1	0.284091471065745	3		667	1087	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223159	5223159	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1568407818	NA	P-0030887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	97	465	0	ENST00000357368.4:c.2644G>T	p.Glu882Ter	p.E882*	ENST00000357368	NM_002850.3	882	Gag/Tag	18/38	0.224666049874671	3	FACETS	0.808	0.719	0.903	0.404	0.359	0.452	CLONAL	1	FALSE	1	0.284091471065745	3		465	965	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082752	16082752	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	26	63	0	ENST00000281043.3:c.566C>T	p.Pro189Leu	p.P189L	ENST00000281043	NM_005378.4	189	cCc/cTc	2/3	1	2	FACETS	0.606	0.481	0.749	0.606	0.481	0.749	SUBCLONAL	1	FALSE	1	0.284091471065745	2		63	302	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62293870	62293870	+	intron_variant	Intron	SNP	C	C	A	novel	NA	P-0030887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	56	586	0	ENST00000360203.5:c.396-29C>A		p.*132*	ENST00000360203	NM_001283009.1	147/1243			1	2	FACETS	0.406	0.347	0.472	0.406	0.347	0.472	SUBCLONAL	1	FALSE	1	0.284091471065745	2		586	970	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143129657	143129657	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	27	514	2	ENST00000262992.4:c.993C>A	p.Ser331Arg	p.S331R	ENST00000262992	NM_001101669.1	331	agC/agA	12/24	1	2	FACETS	0.598	0.476	0.736	0.598	0.476	0.736	SUBCLONAL	1	FALSE	1	0.284091471065745	2		516	318	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871287	35871287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149161098	NA	P-0030887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	29	388	1	ENST00000303115.3:c.509G>A	p.Arg170His	p.R170H	ENST00000303115	NM_002185.3	170	cGc/cAc	4/8	0.284091471065745	1	FACETS	0.553	0.444	0.675	0.553	0.444	0.675	SUBCLONAL	1	FALSE	0	0.284091471065745	1		389	317	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271770	38271770	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	57	597	1	ENST00000425967.3:c.2179C>A	p.Leu727Met	p.L727M	ENST00000425967	NM_001174067.1	727	Ctg/Atg	17/19	1	2	FACETS	0.412	0.352	0.477	0.412	0.352	0.477	SUBCLONAL	1	FALSE	1	0.284091471065745	2		598	975	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939072	76939072	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060499760	NA	P-0030887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	16	287	0	ENST00000373344.5:c.1676C>T	p.Ser559Leu	p.S559L	ENST00000373344	NM_000489.3	559	tCa/tTa	9/35	0.253468067965135	2	FACETS	0.647	0.481	0.845			1	SUBCLONAL	1	FALSE	NA	0.284091471065745	2		287	174	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111499	8111500	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0030918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	293	555	0	ENST00000346208.3:c.987dup	p.Arg330GlufsTer22	p.R330Efs*22	ENST00000346208		329	agg/aGgg	5/6	0.251827407574496	3	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	1	0.292924688694096	3		555	1133	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0030970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	480	732	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	NA	2	FACETS	0.968	0.94	0.996			1	INDETERMINATE	3	TRUE	NA	0.497826086207696	2		732	664	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20153856	20153857	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	196	371	0	ENST00000379607.5:c.203dup	p.Val69GlyfsTer19	p.V69Gfs*19	ENST00000379607	NM_001412.3	68	aag/aaAg	3/7	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.497826086207696	2		371	563	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972362	32972362	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0030970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	374	460	0	ENST00000380152.3:c.9712A>T	p.Lys3238Ter	p.K3238*	ENST00000380152		3238	Aag/Tag	27/27	0.462168694518607	5	FACETS	0.891	0.848	0.934			1	CLONAL	3	TRUE	NA	0.497826086207696	5		460	982	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888051	81888051	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	101	296	0	ENST00000359376.3:c.196G>C	p.Asp66His	p.D66H	ENST00000359376	NM_002661.3	66	Gat/Cat	3/33	0.497826086207696	2	FACETS	1	0.97	1	0.597	0.539	0.657	CLONAL	1	TRUE	0	0.497826086207696	2		296	340	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370213	40370213	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	150	599	0	ENST00000293328.3:c.1125T>A	p.Ser375Arg	p.S375R	ENST00000293328	NM_012448.3	375	agT/agA	9/19	0.383480796541434	1	FACETS	0.731	0.671	0.794	0.731	0.671	0.794	SUBCLONAL	1	TRUE	0	0.497826086207696	1		599	619	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748576	40748576	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	146	293	0	ENST00000373198.4:c.2940A>C	p.Gln980His	p.Q980H	ENST00000373198	NM_133170.3	980	caA/caC	21/32	0.36409003568242	0	FACETS	0.834	0.772	0.898			1	CLONAL	1	TRUE	0	0.497826086207696	0		293	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0030979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	476	782	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.538956932423304	4	FACETS	0.937	0.906	0.966			1	CLONAL	4	TRUE	NA	0.539584802348843	4		784	725	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279674	123279674	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs77543610	NA	P-0030979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	110	215	0	ENST00000358487.5:c.758C>G	p.Pro253Arg	p.P253R	ENST00000358487	NM_000141.4	253	cCt/cGt	7/18	0.443405581043826	2	FACETS	0.906	0.833	0.979	0.906	0.833	0.979	CLONAL	2	TRUE	0	0.539584802348843	2		215	225	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030426	49030433	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCCTTC	CAGCCTTC	-	novel	NA	P-0030979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	41	272	0	ENST00000267163.4:c.1904_1911del	p.Ala635AspfsTer15	p.A635Dfs*15	ENST00000267163	NM_000321.2	634	tCAGCCTTC/t	19/27	0.443405581043826	2	FACETS	0.434	0.362	0.513	0.217	0.181	0.257	SUBCLONAL	1	TRUE	0	0.539584802348843	2		272	350	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5073748	5073748	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	82	253	0	ENST00000381652.3:c.1827G>C	p.Leu609Phe	p.L609F	ENST00000381652	NM_004972.3	609	ttG/ttC	14/25	0.539584802348843	5	FACETS	1	0.961	1	0.24	0.212	0.27	CLONAL	1	TRUE	0	0.539584802348843	5		253	458	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786876	135786885	+	frameshift_variant	Frame_Shift_Del	DEL	ACTCAGAGTC	ACTCAGAGTC	-	novel	NA	P-0030979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	93	287	0	ENST00000298552.3:c.984_993del	p.Gln328HisfsTer7	p.Q328Hfs*7	ENST00000298552	NM_001162426.1	328	caGACTCTGAGT/ca	10/23	0.365035430531423	3	FACETS	1	0.942	1	0.359	0.321	0.399	CLONAL	1	TRUE	0	0.539584802348843	3		287	406	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0031002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	15	335	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.897	0.657	1	0.897	0.657	1	CLONAL	1	TRUE	1	0.15	2		335	223	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448518	49448518	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1189364625	NA	P-0031002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	19	583	1	ENST00000301067.7:c.193C>T	p.Arg65Cys	p.R65C	ENST00000301067	NM_003482.3	65	Cgt/Tgt	3/54	1	2	FACETS	0.67	0.508	0.862	0.67	0.508	0.862	SUBCLONAL	1	TRUE	1	0.15	2		584	378	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891268	101891268	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs753933625	NA	P-0031002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	20	621	0	ENST00000374994.4:c.229T>G	p.Leu77Val	p.L77V	ENST00000374994	NM_004612.2	77	Tta/Gta	2/9	1	2	FACETS	1	0.822	1	1	0.822	1	CLONAL	1	TRUE	1	0.15	2		621	245	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937139	39937139	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	25	741	0	ENST00000378444.4:c.44T>A	p.Met15Lys	p.M15K	ENST00000378444	NM_001123385.1	15	aTg/aAg	2/15	0.117498796140308	0	FACETS	0.721	0.568	0.897			1	SUBCLONAL	1	TRUE	0	0.15	0		741	393	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410346	63410346	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	22	785	0	ENST00000330258.3:c.2821A>T	p.Ser941Cys	p.S941C	ENST00000330258	NM_152424.3	941	Agc/Tgc	2/2	0.117498796140308	0	FACETS	0.782	0.606	0.986			1	CLONAL	1	TRUE	0	0.15	0		785	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0031045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	90	513	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.537414541631942	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.537414541631942	1		513	192	SUCCESS
APC	324	MSKCC	GRCh37	5	112175358	112175358	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1554085480	NA	P-0031045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	38	150	0	ENST00000257430.4:c.4067C>G	p.Ser1356Ter	p.S1356*	ENST00000257430	NM_000038.5	1356	tCa/tGa	16/16	0.537414541631942	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	0	0.537414541631942	2		150	65	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913237	NA	P-0031045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	105	335	0	ENST00000369535.4:c.35G>T	p.Gly12Val	p.G12V	ENST00000369535	NM_002524.4	12	gGt/gTt	2/7	0.529266530535743	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.537414541631942	2		335	175	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965472	68965472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200682883	NA	P-0031045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	24	641	1	ENST00000288368.4:c.1084C>T	p.Arg362Trp	p.R362W	ENST00000288368	NM_024870.2	362	Cgg/Tgg	9/40	1	2	FACETS	0.558	0.442	0.69	0.558	0.442	0.69	SUBCLONAL	1	TRUE	1	0.537414541631942	2		642	160	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982105	201982106	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0031045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	112	594	0	ENST00000359651.3:c.630dup	p.Asp211ArgfsTer6	p.D211Rfs*6	ENST00000359651		210	tca/tcAa	5/8	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.537414541631942	2		594	297	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217304	66217304	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs549914252	NA	P-0031045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	17	186	0	ENST00000273854.3:c.2311C>A	p.Gln771Lys	p.Q771K	ENST00000273854	NM_004439.5	771	Cag/Aag	14/18	0.224693205316224	0	FACETS	0.552	0.428	0.687			1	INDETERMINATE	1	TRUE	0	0.537414541631942	0		186	53	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433696	149433696	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs557980960	NA	P-0031045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	10	533	0	ENST00000286301.3:c.2855C>A	p.Thr952Asn	p.T952N	ENST00000286301	NM_005211.3	952	aCc/aAc	22/22	0.537414541631942	2	FACETS	0.195	0.132	0.274	0.097	0.066	0.137	SUBCLONAL	1	TRUE	0	0.537414541631942	2		533	191	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028854	42028855	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TATA	novel	NA	P-0031048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	34	582	0	ENST00000219905.7:c.4393_4396dup	p.Lys1466IlefsTer2	p.K1466Ifs*2	ENST00000219905	NM_001164273.1	1464	-/TATA	13/24	1	2	FACETS	0.694	0.566	0.838	0.694	0.566	0.838	SUBCLONAL	1	TRUE	1	0.2	2		582	490	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207176	1207176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	210	811	0	ENST00000326873.7:c.267del	p.Asn90ThrfsTer6	p.N90Tfs*6	ENST00000326873	NM_000455.4	88	atC/at	1/10	0.554859357763852	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.554859357763852	1		811	506	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056059	26056059	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	105	375	0	ENST00000343677.2:c.598C>A	p.Pro200Thr	p.P200T	ENST00000343677	NM_005319.3	200	Ccc/Acc	1/1	1	2	FACETS	0.953	0.861	1	0.953	0.861	1	CLONAL	1	TRUE	1	0.554859357763852	2		375	397	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864697	57864697	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	192	730	0	ENST00000228682.2:c.2174C>T	p.Pro725Leu	p.P725L	ENST00000228682	NM_005269.2	725	cCa/cTa	12/12	1	2	FACETS	0.948	0.879	1	0.948	0.879	1	CLONAL	1	TRUE	1	0.554859357763852	2		730	730	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865711	57865711	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	42	748	2	ENST00000228682.2:c.3188C>A	p.Pro1063His	p.P1063H	ENST00000228682	NM_005269.2	1063	cCt/cAt	12/12	1	2	FACETS	0.235	0.196	0.279	0.235	0.196	0.279	SUBCLONAL	1	TRUE	1	0.554859357763852	2		750	644	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910564	32910565	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0031048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	31	566	0	ENST00000380152.3:c.2076dup	p.Cys693MetfsTer2	p.C693Mfs*2	ENST00000380152		691	gca/gcAa	11/27	0.554859357763852	1	FACETS	0.211	0.17	0.257	0.211	0.17	0.257	SUBCLONAL	1	TRUE	0	0.554859357763852	1		566	383	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032125	10032125	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	38	730	0	ENST00000330684.3:c.698A>C	p.Lys233Thr	p.K233T	ENST00000330684	NM_001134407.1	233	aAa/aCa	3/13	1	2	FACETS	0.195	0.16	0.234	0.195	0.16	0.234	SUBCLONAL	1	TRUE	1	0.554859357763852	2		730	703	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222107	2222107	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	80	698	0	ENST00000398665.3:c.2941del	p.Arg981AlafsTer87	p.R981Afs*87	ENST00000398665	NM_032482.2	980	tCc/tc	24/28	0.554859357763852	1	FACETS	0.429	0.378	0.482	0.429	0.378	0.482	SUBCLONAL	1	TRUE	0	0.554859357763852	1		698	486	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602836	10602836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	199	844	3	ENST00000171111.5:c.742G>A	p.Ala248Thr	p.A248T	ENST00000171111	NM_203500.1	248	Gcc/Acc	3/6	0.554859357763852	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.554859357763852	1		847	516	SUCCESS
APC	324	MSKCC	GRCh37	5	112178031	112178031	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	82	553	0	ENST00000257430.4:c.6740C>G	p.Ser2247Cys	p.S2247C	ENST00000257430	NM_000038.5	2247	tCt/tGt	16/16	1	2	FACETS	0.523	0.462	0.589	0.523	0.462	0.589	SUBCLONAL	1	TRUE	1	0.554859357763852	2		553	565	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884484	151884484	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	37	470	0	ENST00000262189.6:c.4871G>A	p.Gly1624Glu	p.G1624E	ENST00000262189	NM_170606.2	1624	gGa/gAa	33/59	1	2	FACETS	0.259	0.213	0.311	0.259	0.213	0.311	SUBCLONAL	1	TRUE	1	0.554859357763852	2		470	515	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486196	8486196	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	33	457	0	ENST00000356435.5:c.2621C>G	p.Ser874Cys	p.S874C	ENST00000356435		874	tCt/tGt	17/35	0.554859357763852	1	FACETS	0.246	0.2	0.297	0.246	0.2	0.297	SUBCLONAL	1	TRUE	0	0.554859357763852	1		457	350	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200067	123200067	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0031048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	117	251	0	ENST00000218089.9:c.2139C>G	p.Tyr713Ter	p.Y713*	ENST00000218089	NM_001042749.1	713	taC/taG	22/35	1	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.554859357763852	1		251	244	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0031063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	219	582	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.3430592153751	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	0	0.3430592153751	1		582	856	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827567	72827567	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	67	410	0	ENST00000268489.5:c.9014A>T	p.Lys3005Met	p.K3005M	ENST00000268489	NM_006885.3	3005	aAg/aTg	9/10	1	2	FACETS	0.412	0.357	0.472	0.412	0.357	0.472	SUBCLONAL	1	FALSE	1	0.3430592153751	2		410	948	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52722992	52722992	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1362406458	NA	P-0031063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	69	450	0	ENST00000322088.6:c.1177G>A	p.Glu393Lys	p.E393K	ENST00000322088	NM_014225.5	393	Gag/Aag	10/15	NA	2	FACETS	0.396	0.343	0.452			1	INDETERMINATE	1	FALSE	NA	0.3430592153751	2		450	1017	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266001	41266212	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATT	TGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATT	-	novel	NA	P-0031063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	43	69	0	ENST00000349496.5:c.14-15_210del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.281859450449734	2	FACETS	1	0.939	1	0.617	0.522	0.72	CLONAL	1	FALSE	0	0.3430592153751	2		69	203	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169869	32169869	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	206	649	0	ENST00000375023.3:c.3739A>G	p.Thr1247Ala	p.T1247A	ENST00000375023	NM_004557.3	1247	Acc/Gcc	21/30	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.3430592153751	2		649	1155	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0031183-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	262	280	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.794190810896785	3	FACETS	0.993	0.945	1	0.993	0.945	1	CLONAL	2	TRUE	1	0.794190810896785	3		280	464	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937044	178937044	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031183-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	167	350	0	ENST00000263967.3:c.1725T>A	p.Asn575Lys	p.N575K	ENST00000263967	NM_006218.2	575	aaT/aaA	11/21	0.794190810896785	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.794190810896785	3		350	268	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160555	56160639	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTGAAGTTTCAGAGTGGCAGAATCACACCACCCCGAAGAGCCCCTTCACCAGATGGCTTCTCACCATATAGCCCTGAGGAAACAA	GTGAAGTTTCAGAGTGGCAGAATCACACCACCCCGAAGAGCCCCTTCACCAGATGGCTTCTCACCATATAGCCCTGAGGAAACAA	-	novel	NA	P-0031183-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	218	162	0	ENST00000399503.3:c.835-6_913del		p.X279_splice	ENST00000399503	NM_005921.1	279		4/20	0.794190810896785	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.794190810896785	3		162	362	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161768	56161768	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031183-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	162	450	0	ENST00000399503.3:c.1265C>A	p.Ser422Ter	p.S422*	ENST00000399503	NM_005921.1	422	tCa/tAa	6/20	0.794190810896785	3	FACETS	0.936	0.863	1	0.468	0.431	0.506	CLONAL	1	TRUE	1	0.794190810896785	3		450	609	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836258	151836273	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCGCTGTCTCACCTT	CTCGCTGTCTCACCTT	G	novel	NA	P-0031183-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	369	326	0	ENST00000262189.6:c.14532_14534+13delinsC		p.X4844_splice	ENST00000262189	NM_170606.2	4844		57/59	0.794190810896785	3	FACETS	0.942	0.902	0.982	0.942	0.902	0.982	CLONAL	2	TRUE	1	0.794190810896785	3		326	689	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0031280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	361	503	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.529656421275213	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	1	0.529656421275213	3		503	861	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604655	48604655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	222	288	0	ENST00000342988.3:c.1477G>A	p.Asp493Asn	p.D493N	ENST00000342988	NM_005359.5	493	Gat/Aat	12/12	0.529656421275213	2	FACETS	0.964	0.91	1	0.964	0.91	1	CLONAL	2	TRUE	0	0.529656421275213	2		288	435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0031280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	515	732	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.529656421275213	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.529656421275213	2		732	879	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777894	NA	P-0031280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	221	523	0	ENST00000361445.4:c.6644C>T	p.Ser2215Phe	p.S2215F	ENST00000361445	NM_004958.3	2215	tCt/tTt	47/58	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.529656421275213	2		523	793	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0031280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	138	431	1	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	0.529656421275213	3	FACETS	1	0.951	1	0.531	0.484	0.579	CLONAL	1	TRUE	1	0.529656421275213	3		432	621	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41242963	41242963	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	206	344	0	ENST00000357654.3:c.4183C>G	p.Gln1395Glu	p.Q1395E	ENST00000357654	NM_007294.3	1395	Cag/Gag	11/23	0.469161463735355	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.529656421275213	1		344	444	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149440518	149440518	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1228572300	NA	P-0031280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	218	588	0	ENST00000286301.3:c.1876G>A	p.Glu626Lys	p.E626K	ENST00000286301	NM_005211.3	626	Gag/Aag	14/22	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.529656421275213	2		588	784	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937067	36937067	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767670169	NA	P-0031280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	184	495	0	ENST00000361632.4:c.1252C>T	p.Arg418Cys	p.R418C	ENST00000361632		418	Cgt/Tgt	9/16	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.529656421275213	2		495	671	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528428	29528428	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0031280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	146	352	0	ENST00000356175.3:c.1186-1G>A		p.X396_splice	ENST00000356175	NM_000267.3	396			0.36628676860624	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.529656421275213	1		352	359	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956084	175956084	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	154	387	1	ENST00000367669.3:c.2128G>A	p.Asp710Asn	p.D710N	ENST00000367669	NM_022457.5	710	Gat/Aat	18/20	NA	2	FACETS	0.96	0.882	1			1	INDETERMINATE	1	TRUE	NA	0.529656421275213	2		388	606	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170336	119170336	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	118	323	1	ENST00000264033.4:c.2566C>T	p.Gln856Ter	p.Q856*	ENST00000264033	NM_005188.3	856	Cag/Tag	16/16	1	2	FACETS	0.995	0.903	1	0.995	0.903	1	CLONAL	1	TRUE	1	0.529656421275213	2		324	448	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942674	48942675	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1131690861	NA	P-0031280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	108	330	0	ENST00000267163.4:c.1064_1065del	p.Arg355AsnfsTer6	p.R355Nfs*6	ENST00000267163	NM_000321.2	354	cAG/c	11/27	0.529656421275213	1	FACETS	0.884	0.803	0.969	0.884	0.803	0.969	CLONAL	1	TRUE	0	0.529656421275213	1		330	339	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66777430	66777430	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	204	613	1	ENST00000307102.5:c.796C>T	p.Pro266Ser	p.P266S	ENST00000307102	NM_002755.3	266	Cca/Tca	7/11	0.529656421275213	1	FACETS	0.938	0.875	1	0.938	0.875	1	CLONAL	1	TRUE	0	0.529656421275213	1		614	604	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221697	22221697	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	32	64	0	ENST00000215832.6:c.34G>C	p.Glu12Gln	p.E12Q	ENST00000215832	NM_002745.4	12	Gag/Cag	1/9	1	2	FACETS	0.746	0.613	0.892	0.746	0.613	0.892	SUBCLONAL	1	TRUE	1	0.529656421275213	2		64	162	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673637	30673637	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	187	610	0	ENST00000376406.3:c.3323G>C	p.Arg1108Thr	p.R1108T	ENST00000376406	NM_014641.2	1108	aGa/aCa	10/15	1	2	FACETS	0.939	0.87	1	0.939	0.87	1	CLONAL	1	TRUE	1	0.529656421275213	2		610	752	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981736	70981736	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	304	783	0	ENST00000276594.2:c.360G>T	p.Glu120Asp	p.E120D	ENST00000276594	NM_024504.3	120	gaG/gaT	2/8	0.529656421275213	3	FACETS	1	0.978	1	0.541	0.508	0.574	CLONAL	1	TRUE	1	0.529656421275213	3		783	1343	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	210	264	0				ENST00000310581	NM_198253.2	-/1132			0.313646387746311	3	FACETS	0.864	0.811	0.917	0.864	0.811	0.917	INDETERMINATE	2	TRUE	1	0.689648394870781	3		264	474	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169869	32169869	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	224	649	0	ENST00000375023.3:c.3739A>G	p.Thr1247Ala	p.T1247A	ENST00000375023	NM_004557.3	1247	Acc/Gcc	21/30	0.689648394870781	3	FACETS	0.951	0.886	1	0.317	0.295	0.339	CLONAL	1	TRUE	0	0.689648394870781	3		649	919	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057857	27057857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	301	774	0	ENST00000324856.7:c.1565C>T	p.Pro522Leu	p.P522L	ENST00000324856	NM_006015.4	522	cCa/cTa	3/20	1	2	FACETS	0.911	0.86	0.963	0.911	0.86	0.963	CLONAL	1	TRUE	1	0.689648394870781	2		774	958	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166091	118166091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	109	395	0	ENST00000369448.3:c.601C>T	p.Pro201Ser	p.P201S	ENST00000369448	NM_017709.3	201	Ccc/Tcc	2/2	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.689648394870781	2		395	310	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458221	120458221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	191	576	0	ENST00000256646.2:c.7124C>T	p.Pro2375Leu	p.P2375L	ENST00000256646	NM_024408.3	2375	cCt/cTt	34/34	1	2	FACETS	0.898	0.835	0.963	0.898	0.835	0.963	CLONAL	1	TRUE	1	0.689648394870781	2		576	617	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458845	120458845	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746028501	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	178	712	1	ENST00000256646.2:c.6500C>T	p.Ser2167Phe	p.S2167F	ENST00000256646	NM_024408.3	2167	tCt/tTt	34/34	1	2	FACETS	0.841	0.779	0.905	0.841	0.779	0.905	CLONAL	1	TRUE	1	0.689648394870781	2		713	614	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451005	70451005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	289	585	0	ENST00000373644.4:c.5845C>T	p.Pro1949Ser	p.P1949S	ENST00000373644	NM_030625.2	1949	Cct/Tct	12/12	0.561278301392563	3	FACETS	0.906	0.86	0.953	0.906	0.86	0.953	CLONAL	2	TRUE	1	0.689648394870781	3		585	622	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123245022	123245022	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	114	395	2	ENST00000358487.5:c.2082G>A	p.Trp694Ter	p.W694*	ENST00000358487	NM_000141.4	694	tgG/tgA	16/18	0.561278301392563	3	FACETS	1	0.91	1	0.502	0.455	0.551	CLONAL	1	TRUE	1	0.689648394870781	3		397	443	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200942	108200942	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	50	391	0	ENST00000278616.4:c.7309T>G	p.Tyr2437Asp	p.Y2437D	ENST00000278616	NM_000051.3	2437	Tac/Gac	50/63	0.669401469881058	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.689648394870781	1		391	89	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409088	4409089	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	109	332	0	ENST00000261254.3:c.783_784delinsTT	p.Arg262Cys	p.R262C	ENST00000261254	NM_001759.3	261	taCCgt/taTTgt	5/5	1	2	FACETS	0.961	0.873	1	0.961	0.873	1	CLONAL	1	TRUE	1	0.689648394870781	2		332	329	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494872	56494872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112651994	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	212	462	0	ENST00000267101.3:c.3229C>T	p.Arg1077Trp	p.R1077W	ENST00000267101	NM_001982.3	1077	Cgg/Tgg	27/28	1	2	FACETS	0.974	0.91	1	0.974	0.91	1	CLONAL	1	TRUE	1	0.689648394870781	2		462	631	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32899288	32899288	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	42	328	0	ENST00000380152.3:c.392C>T	p.Ser131Phe	p.S131F	ENST00000380152		131	tCc/tTc	4/27	0.689648394870781	1	FACETS	0.782	0.675	0.893	0.782	0.675	0.893	SUBCLONAL	1	TRUE	0	0.689648394870781	1		328	102	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134480	41134480	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	194	581	0	ENST00000379561.5:c.1148C>T	p.Ser383Leu	p.S383L	ENST00000379561	NM_002015.3	383	tCa/tTa	2/3	0.689648394870781	1	FACETS	0.996	0.938	1	0.996	0.938	1	CLONAL	1	TRUE	0	0.689648394870781	1		581	370	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955535	48955550	+	frameshift_variant	Frame_Shift_Del	DEL	GAACGATGTGAACATC	GAACGATGTGAACATC	-	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	32	383	0	ENST00000267163.4:c.1654_1669del	p.Arg552SerfsTer54	p.R552Sfs*54	ENST00000267163	NM_000321.2	551	GAACGATGTGAACATCga/ga	17/27	0.689648394870781	1	FACETS	0.647	0.54	0.759	0.647	0.54	0.759	SUBCLONAL	1	TRUE	0	0.689648394870781	1		383	94	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643248	38643248	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	68	407	0	ENST00000299084.4:c.718C>T	p.Gln240Ter	p.Q240*	ENST00000299084	NM_152594.2	240	Caa/Taa	7/7	0.689648394870781	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.689648394870781	1		407	114	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858201	9858201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	121	570	1	ENST00000330684.3:c.3200G>A	p.Arg1067Gln	p.R1067Q	ENST00000330684	NM_001134407.1	1067	cGg/cAg	13/13	1	2	FACETS	0.771	0.701	0.844	0.771	0.701	0.844	SUBCLONAL	1	TRUE	1	0.689648394870781	2		571	455	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849631	68849631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659244	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	139	546	0	ENST00000261769.5:c.1534G>A	p.Glu512Lys	p.E512K	ENST00000261769	NM_004360.3	512	Gag/Aag	10/16	1	2	FACETS	0.876	0.804	0.951	0.876	0.804	0.951	CLONAL	1	TRUE	1	0.689648394870781	2		546	460	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828150	72828150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377589097	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	174	682	0	ENST00000268489.5:c.8431G>A	p.Glu2811Lys	p.E2811K	ENST00000268489	NM_006885.3	2811	Gaa/Aaa	9/10	1	2	FACETS	0.945	0.876	1	0.945	0.876	1	CLONAL	1	TRUE	1	0.689648394870781	2		682	534	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347110	89347110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	142	472	0	ENST00000301030.4:c.5840C>T	p.Pro1947Leu	p.P1947L	ENST00000301030	NM_001256183.1	1947	cCc/cTc	9/13	1	2	FACETS	0.955	0.879	1	0.955	0.879	1	CLONAL	1	TRUE	1	0.689648394870781	2		472	431	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29422344	29422344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs864622210	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	212	423	0	ENST00000356175.3:c.17C>T	p.Pro6Leu	p.P6L	ENST00000356175	NM_000267.3	6	cCg/cTg	1/57	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.689648394870781	2		423	555	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41251898	41251898	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	80	390	0	ENST00000357654.3:c.442-1G>A		p.X148_splice	ENST00000357654	NM_007294.3	148			1	2	FACETS	0.826	0.735	0.92	0.826	0.735	0.92	CLONAL	1	TRUE	1	0.689648394870781	2		390	281	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435533	56435533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369428576	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	216	602	1	ENST00000407977.2:c.1604C>T	p.Ser535Leu	p.S535L	ENST00000407977		535	tCg/tTg	9/10	1	2	FACETS	0.904	0.844	0.965	0.904	0.844	0.965	CLONAL	1	TRUE	1	0.689648394870781	2		603	693	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761264	59761264	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	72	772	0	ENST00000259008.2:c.3143C>T	p.Pro1048Leu	p.P1048L	ENST00000259008	NM_032043.2	1048	cCc/cTc	20/20	1	2	FACETS	0.806	0.713	0.904	0.806	0.713	0.904	CLONAL	1	TRUE	1	0.689648394870781	2		772	259	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821921	59821921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768393936	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	61	416	1	ENST00000259008.2:c.2129C>T	p.Ser710Phe	p.S710F	ENST00000259008	NM_032043.2	710	tCt/tTt	15/20	1	2	FACETS	0.941	0.827	1	0.941	0.827	1	CLONAL	1	TRUE	1	0.689648394870781	2		417	188	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220920	36220920	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	120	351	0	ENST00000222270.7:c.4970C>T	p.Ser1657Phe	p.S1657F	ENST00000222270	NM_014727.1	1657	tCc/tTc	23/37	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.689648394870781	2		351	311	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383075	42383076	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	98	418	0	ENST00000221972.3:c.95_96delinsTT	p.Ala32Val	p.A32V	ENST00000221972	NM_021601.3	32	gCC/gTT	2/5	1	2	FACETS	0.866	0.781	0.955	0.866	0.781	0.955	CLONAL	1	TRUE	1	0.689648394870781	2		418	328	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449836	29449836	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	348	976	0	ENST00000389048.3:c.3019T>A	p.Phe1007Ile	p.F1007I	ENST00000389048	NM_004304.4	1007	Ttc/Atc	18/29	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.689648394870781	2		976	1000	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736159	204736160	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	107	474	1	ENST00000302823.3:c.516_517delinsAA	p.Gly173Arg	p.G173R	ENST00000302823	NM_005214.4	172	tcGGgg/tcAAgg	3/4	1	2	FACETS	0.766	0.692	0.843	0.766	0.692	0.843	SUBCLONAL	1	TRUE	1	0.689648394870781	2		475	405	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212252681	212252681	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	34	171	0	ENST00000342788.4:c.3172C>T	p.Pro1058Ser	p.P1058S	ENST00000342788	NM_005235.2	1058	Ccc/Tcc	26/28	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.689648394870781	2		171	83	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546683	9546683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	125	379	0	ENST00000353224.5:c.1339G>A	p.Glu447Lys	p.E447K	ENST00000353224	NM_177990.2	447	Gaa/Aaa	5/10	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.689648394870781	2		379	346	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40709548	40709548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754318111	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	131	523	0	ENST00000373198.4:c.4354G>A	p.Val1452Met	p.V1452M	ENST00000373198	NM_133170.3	1452	Gtg/Atg	32/32	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.689648394870781	2		523	377	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40709549	40709549	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	131	525	0	ENST00000373198.4:c.4353G>T	p.Glu1451Asp	p.E1451D	ENST00000373198	NM_133170.3	1451	gaG/gaT	32/32	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.689648394870781	2		525	378	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633229	12633229	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs368807126	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	374	560	0	ENST00000251849.4:c.1171A>T	p.Arg391Trp	p.R391W	ENST00000251849	NM_002880.3	391	Agg/Tgg	11/17	0.676259823032356	2	FACETS	0.986	0.951	1	0.986	0.951	1	CLONAL	2	TRUE	0	0.689648394870781	2		560	550	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902755	1902755	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	134	586	0	ENST00000382891.5:c.374A>G	p.Lys125Arg	p.K125R	ENST00000382891	NM_133335.3	125	aAg/aGg	2/22	1	2	FACETS	0.881	0.807	0.958	0.881	0.807	0.958	CLONAL	1	TRUE	1	0.689648394870781	2		586	441	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604638	55604638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	179	548	0	ENST00000288135.5:c.2846C>T	p.Pro949Leu	p.P949L	ENST00000288135	NM_000222.2	949	cCc/cTc	21/21	1	2	FACETS	0.877	0.813	0.943	0.877	0.813	0.943	CLONAL	1	TRUE	1	0.689648394870781	2		548	592	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156493	106156493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	69	312	0	ENST00000380013.4:c.1394C>T	p.Pro465Leu	p.P465L	ENST00000380013	NM_001127208.2	465	cCa/cTa	3/11	1	2	FACETS	0.957	0.848	1	0.957	0.848	1	CLONAL	1	TRUE	1	0.689648394870781	2		312	209	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1268645	1268645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1322978833	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	208	599	0	ENST00000310581.5:c.2572C>T	p.Arg858Trp	p.R858W	ENST00000310581	NM_198253.2	858	Cgg/Tgg	9/16	0.313646387746311	3	FACETS	1	0.947	1	0.51	0.474	0.547	INDETERMINATE	1	TRUE	1	0.689648394870781	3		599	795	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873657	35873657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	45	305	0	ENST00000303115.3:c.613G>A	p.Val205Ile	p.V205I	ENST00000303115	NM_002185.3	205	Gtt/Att	5/8	0.313646387746311	3	FACETS	0.886	0.754	1	0.443	0.377	0.514	INDETERMINATE	1	TRUE	1	0.689648394870781	3		305	198	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875648	35875648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	143	380	0	ENST00000303115.3:c.835C>T	p.His279Tyr	p.H279Y	ENST00000303115	NM_002185.3	279	Cat/Tat	7/8	0.313646387746311	3	FACETS	0.871	0.807	0.936	0.871	0.807	0.936	INDETERMINATE	2	TRUE	1	0.689648394870781	3		380	320	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924381	131924381	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1341798216	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	32	233	0	ENST00000265335.6:c.1054C>T	p.Arg352Cys	p.R352C	ENST00000265335		352	Cgt/Tgt	8/25	0.686672657445484	3	FACETS	0.891	0.735	1	0.446	0.367	0.531	CLONAL	1	TRUE	1	0.689648394870781	3		233	140	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522582	176522582	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	219	681	0	ENST00000292408.4:c.1679A>T	p.Glu560Val	p.E560V	ENST00000292408	NM_213647.1	560	gAg/gTg	13/18	0.686672657445484	3	FACETS	0.961	0.895	1	0.48	0.447	0.515	CLONAL	1	TRUE	1	0.689648394870781	3		681	889	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547241	106547241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	98	332	0	ENST00000369096.4:c.478C>T	p.Arg160Cys	p.R160C	ENST00000369096	NM_001198.3	160	Cgc/Tgc	4/7	0.689648394870781	1	FACETS	0.95	0.87	1	0.95	0.87	1	CLONAL	1	TRUE	0	0.689648394870781	1		332	196	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641180	117641180	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	125	779	0	ENST00000368508.3:c.5791C>T	p.Gln1931Ter	p.Q1931*	ENST00000368508	NM_002944.2	1931	Caa/Taa	36/43	0.689648394870781	1	FACETS	0.973	0.901	1	0.973	0.901	1	CLONAL	1	TRUE	0	0.689648394870781	1		779	244	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979457	2979457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769402864	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	620	678	0	ENST00000396946.4:c.790G>A	p.Glu264Lys	p.E264K	ENST00000396946	NM_032415.4	264	Gag/Aag	6/25	0.65377408764409	4	FACETS	0.976	0.946	1	0.976	0.946	1	CLONAL	3	TRUE	1	0.689648394870781	4		678	1038	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987422	2987422	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	369	463	0	ENST00000396946.4:c.8-1G>A		p.X3_splice	ENST00000396946	NM_032415.4	3			0.65377408764409	4	FACETS	0.893	0.855	0.93	0.893	0.855	0.93	CLONAL	3	TRUE	1	0.689648394870781	4		463	675	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514433	148514433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	196	508	1	ENST00000320356.2:c.1291C>T	p.Pro431Ser	p.P431S	ENST00000320356	NM_004456.4	431	Cct/Tct	11/20	0.689648394870781	3	FACETS	0.999	0.957	1	0.999	0.957	1	CLONAL	3	TRUE	0	0.689648394870781	3		509	255	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992794	68992794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	64	584	0	ENST00000288368.4:c.1759G>A	p.Glu587Lys	p.E587K	ENST00000288368	NM_024870.2	587	Gaa/Aaa	16/40	0.689648394870781	3	FACETS	0.942	0.824	1	0.471	0.412	0.534	CLONAL	1	TRUE	1	0.689648394870781	3		584	265	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995553	68995553	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771763123	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	73	702	0	ENST00000288368.4:c.1957G>A	p.Asp653Asn	p.D653N	ENST00000288368	NM_024870.2	653	Gat/Aat	18/40	0.689648394870781	3	FACETS	0.845	0.744	0.951	0.422	0.372	0.476	CLONAL	1	TRUE	1	0.689648394870781	3		702	337	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069640	69069640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	57	454	0	ENST00000288368.4:c.4315G>A	p.Glu1439Lys	p.E1439K	ENST00000288368	NM_024870.2	1439	Gaa/Aaa	35/40	0.689648394870781	3	FACETS	1	0.902	1	0.522	0.454	0.594	CLONAL	1	TRUE	1	0.689648394870781	3		454	213	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136794	69136794	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs372981486	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	130	373	0	ENST00000288368.4:c.4708G>A	p.Gly1570Arg	p.G1570R	ENST00000288368	NM_024870.2	1570	Gga/Aga	39/40	0.689648394870781	3	FACETS	0.854	0.787	0.92	0.854	0.787	0.92	CLONAL	2	TRUE	1	0.689648394870781	3		373	297	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964333	70964333	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	113	326	0	ENST00000276594.2:c.1695G>A	p.Met565Ile	p.M565I	ENST00000276594	NM_024504.3	565	atG/atA	8/8	0.689648394870781	3	FACETS	1	0.929	1	0.515	0.466	0.565	CLONAL	1	TRUE	1	0.689648394870781	3		326	428	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8497247	8497247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	22	246	0	ENST00000356435.5:c.2344G>A	p.Glu782Lys	p.E782K	ENST00000356435		782	Gaa/Aaa	15/35	0.689648394870781	1	FACETS	0.746	0.604	0.895	0.746	0.604	0.895	SUBCLONAL	1	TRUE	0	0.689648394870781	1		246	56	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27183567	27183567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1296261695	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	101	400	0	ENST00000380036.4:c.1141G>A	p.Glu381Lys	p.E381K	ENST00000380036	NM_000459.3	381	Gaa/Aaa	8/23	0.689648394870781	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.689648394870781	1		400	184	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778168	135778168	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554815054	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	176	585	1	ENST00000298552.3:c.2215C>T	p.Gln739Ter	p.Q739*	ENST00000298552	NM_001162426.1	739	Cag/Tag	18/23	0.669401469881058	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.689648394870781	1		586	326	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860118	152860118	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	235	309	0	ENST00000406277.2:c.310G>T	p.Glu104Ter	p.E104*	ENST00000406277	NM_152274.4	104	Gag/Tag	5/7	1		FACETS		0.995	1				CLONAL	1	TRUE	0	0.689648394870781	1		309	311	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383075	42383075	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	98	408	0	ENST00000221972.3:c.95C>T	p.Ala32Val	p.A32V	ENST00000221972	NM_021601.3	32	gCc/gTc	2/5	1	2	FACETS	0.866	0.781	0.955	0.866	0.781	0.955	CLONAL	1	TRUE	1	0.689648394870781	2		408	328	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031309-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	71	441	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.357349187353465	2	FACETS	0.948	0.843	1	0.948	0.843	1	CLONAL	2	TRUE	0	0.370755301132162	2		441	202	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031349-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	142	683	1	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	0.490800016204764	3	FACETS	0.916	0.836	1	0.458	0.418	0.501	CLONAL	1	TRUE	1	0.490311187747892	3		684	787	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099423	27099424	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0031349-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	324	527	2	ENST00000324856.7:c.3661_3662dup	p.Met1221IlefsTer17	p.M1221Ifs*17	ENST00000324856	NM_006015.4	1220	-/AT	14/20	0.422622067485628	4	FACETS	1	0.987	1	0.819	0.782	0.856	CLONAL	3	TRUE	0	0.490311187747892	4		529	601	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30102089	30102089	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031349-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	49	573	0	ENST00000331968.5:c.1378A>C	p.Ser460Arg	p.S460R	ENST00000331968	NM_002742.2	460	Agc/Cgc	9/18	0.46541449387305	3	FACETS	0.756	0.644	0.879	0.378	0.322	0.44	SUBCLONAL	1	TRUE	1	0.490311187747892	3		573	329	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579563	7579566	+	frameshift_variant	Frame_Shift_Del	DEL	CATC	CATC	-	novel	NA	P-0031349-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	228	658	0	ENST00000269305.4:c.121_124del	p.Asp41IlefsTer2	p.D41Ifs*2	ENST00000269305	NM_001126112.2	41	GATGat/at	4/11	NA	2	FACETS	0.989	0.934	1			1	INDETERMINATE	2	TRUE	NA	0.490311187747892	2		658	470	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158731	26158731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031349-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	84	436	0	ENST00000289316.2:c.334G>A	p.Val112Met	p.V112M	ENST00000289316	NM_138720.2	112	Gtg/Atg	1/2	0.490800016204764	3	FACETS	0.893	0.791	1	0.446	0.395	0.5	CLONAL	1	TRUE	1	0.490311187747892	3		436	478	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205250	61205250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565128535	NA	P-0031365-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	298	590	0	ENST00000301761.2:c.190G>A	p.Glu64Lys	p.E64K	ENST00000301761	NM_017841.2	64	Gaa/Aaa	2/4	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.932498556380683	2		590	582	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031388-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	137	264	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.991	0.917	1	1	0.994	1	CLONAL	4	FALSE	1	0.225861882283051	2		264	306	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0031388-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	108	335	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.188073596167551	3	FACETS	1	0.917	1	1	0.989	1	CLONAL	4	FALSE	1	0.225861882283051	3		335	265	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944134	71944134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1208152317	NA	P-0031388-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	224	454	0	ENST00000298229.2:c.1967C>T	p.Ser656Phe	p.S656F	ENST00000298229	NM_001567.3	656	tCc/tTc	17/28	1	2	FACETS	0.91	0.855	0.966	1	0.996	1	CLONAL	4	FALSE	1	0.225861882283051	2		454	545	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992152	11992152	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031388-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	227	368	0	ENST00000396373.4:c.242C>T	p.Pro81Leu	p.P81L	ENST00000396373	NM_001987.4	81	cCa/cTa	3/8	0.225861882283051	7	FACETS	0.946	0.889	1			1	CLONAL	6	FALSE	NA	0.225861882283051	7		368	554	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0031400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	59	336	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.580447385362581	2		336	202	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178643	56178643	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	46	237	0	ENST00000399503.3:c.3617del	p.Pro1206LeufsTer39	p.P1206Lfs*39	ENST00000399503	NM_005921.1	1206	Cct/ct	14/20	1	2	FACETS	0.895	0.766	1	0.895	0.766	1	CLONAL	1	TRUE	1	0.580447385362581	2		237	177	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427948	49427948	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	198	575	0	ENST00000301067.7:c.10642A>C	p.Thr3548Pro	p.T3548P	ENST00000301067	NM_003482.3	3548	Act/Cct	38/54	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.580447385362581	2		575	554	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179416	56179416	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	44	277	0	ENST00000399503.3:c.3729G>T	p.Trp1243Cys	p.W1243C	ENST00000399503	NM_005921.1	1243	tgG/tgT	15/20	1	2	FACETS	0.966	0.824	1	0.966	0.824	1	CLONAL	1	TRUE	1	0.580447385362581	2		277	157	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271228	26271228	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	119	437	0	ENST00000305910.3:c.385C>T	p.Arg129Cys	p.R129C	ENST00000305910	NM_003534.2	129	Cgc/Tgc	1/1	0.123503200567561	4	FACETS	1	0.982	1	0.685	0.622	0.751	INDETERMINATE	1	TRUE	2	0.580447385362581	4		437	473	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183776	10183776	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs794726890	NA	P-0031408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	140	556	0	ENST00000256474.2:c.245G>C	p.Arg82Pro	p.R82P	ENST00000256474	NM_000551.3	82	cGc/cCc	1/3	0.215717247412438	2	FACETS	1	0.968	1	0.566	0.516	0.619	CLONAL	1	TRUE	0	0.33	2		556	749	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262642	16262643	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0031408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	61	360	0	ENST00000375759.3:c.9908_9909del	p.Phe3303SerfsTer44	p.F3303Sfs*44	ENST00000375759	NM_015001.2	3303	TTt/t	11/15	1	2	FACETS	0.973	0.843	1	0.973	0.843	1	CLONAL	1	TRUE	1	0.33	2		360	380	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729625	162729625	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	78	456	0	ENST00000367921.3:c.711del	p.Gly238AlafsTer47	p.G238Afs*47	ENST00000367921	NM_006182.2	237	tcT/tc	8/18	1	2	FACETS	0.826	0.727	0.933	0.826	0.727	0.933	CLONAL	1	TRUE	1	0.33	2		456	572	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183776	10183777	+	missense_variant	Missense_Mutation	DNP	GC	GC	CG	novel	NA	P-0031408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	144	558	1	ENST00000256474.2:c.245_246delinsCG	p.Arg82Pro	p.R82P	ENST00000256474	NM_000551.3	82	cGC/cCG	1/3	0.215717247412438	2	FACETS	1	0.973	1	0.58	0.529	0.632	CLONAL	1	TRUE	0	0.33	2		559	753	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163106	47163139	+	frameshift_variant	Frame_Shift_Del	DEL	AAATTCAAATCACAAGAAGAAAATACAACTTCTG	AAATTCAAATCACAAGAAGAAAATACAACTTCTG	-	novel	NA	P-0031408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	84	360	0	ENST00000409792.3:c.2987_3020del	p.Ser996Ter	p.S996*	ENST00000409792	NM_014159.6	996	tCAGAAGTTGTATTTTCTTCTTGTGATTTGAATTTa/ta	3/21	0.215717247412438	2	FACETS	1	0.958	1	0.587	0.52	0.657	CLONAL	1	TRUE	0	0.33	2		360	434	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643843	52643847	+	frameshift_variant	Frame_Shift_Del	DEL	GAAAT	GAAAT	-	novel	NA	P-0031408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	122	433	0	ENST00000394830.3:c.2049_2053del	p.Phe684GlufsTer5	p.F684Efs*5	ENST00000394830	NM_018313.4	683	atATTTCtg/attg	17/30	0.215717247412438	2	FACETS	1	0.984	1	0.706	0.641	0.773	CLONAL	1	TRUE	0	0.33	2		433	524	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545641	106545641	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	125	494	1	ENST00000359195.3:c.3118C>A	p.Pro1040Thr	p.P1040T	ENST00000359195	NM_002649.2	1040	Ccc/Acc	11/11	0.298526843881376	4	FACETS	1	0.976	1	0.414	0.374	0.455	CLONAL	1	TRUE	1	0.33	4		495	812	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950724	79950725	+	missense_variant	Missense_Mutation	DNP	GC	GC	AT	novel	NA	P-0031434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	152	208	1	ENST00000265081.6:c.178_179delinsAT	p.Ala60Ile	p.A60I	ENST00000265081	NM_002439.4	60	GCc/ATc	1/24	0.472913964854207	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.483730585044717	4		209	378	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	101	264	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.519235430268809	2		264	360	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0031504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	110	335	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.868	0.784	0.956	0.868	0.784	0.956	CLONAL	1	TRUE	1	0.519235430268809	2		335	488	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28601450	28601450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	204	628	0	ENST00000253063.3:c.1135G>A	p.Ala379Thr	p.A379T	ENST00000253063	NM_031459.4	379	Gcc/Acc	8/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.519235430268809	2		628	747	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316331	14316331	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782166268	NA	P-0031504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	125	680	1	ENST00000256196.4:c.274G>A	p.Val92Ile	p.V92I	ENST00000256196		92	Gtc/Atc	3/6	1	2	FACETS	0.833	0.757	0.913	0.833	0.757	0.913	CLONAL	1	TRUE	1	0.519235430268809	2		681	578	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755626	57755626	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	177	594	2	ENST00000274289.3:c.161C>T	p.Ala54Val	p.A54V	ENST00000274289	NM_006622.3	54	gCg/gTg	1/14	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.519235430268809	2		596	599	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681650	30681650	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	152	544	0	ENST00000376406.3:c.447G>C	p.Glu149Asp	p.E149D	ENST00000376406	NM_014641.2	149	gaG/gaC	3/15	1	2	FACETS	0.974	0.895	1	0.974	0.895	1	CLONAL	1	TRUE	1	0.519235430268809	2		544	601	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0031505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	94	444	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.10254400787382	3	FACETS	0.84	0.751	0.934	0.84	0.751	0.934	INDETERMINATE	2	TRUE	1	0.268245208844171	3		444	473	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006898	47006898	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1556762493	NA	P-0031505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	56	624	0	ENST00000377604.3:c.17+1G>T		p.X6_splice	ENST00000377604	NM_001204468.1	6			0.268245208844171	1	FACETS	0.561	0.48	0.649	0.561	0.48	0.649	SUBCLONAL	1	TRUE	0	0.268245208844171	1		624	645	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199939	128199939	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	32	463	0	ENST00000341105.2:c.1366C>A	p.Pro456Thr	p.P456T	ENST00000341105	NM_032638.4	456	Ccg/Acg	6/6	1	2	FACETS	0.574	0.465	0.696	0.574	0.465	0.696	SUBCLONAL	1	TRUE	1	0.268245208844171	2		463	416	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458330	120458330	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	41	499	0	ENST00000256646.2:c.7015A>G	p.Met2339Val	p.M2339V	ENST00000256646	NM_024408.3	2339	Atg/Gtg	34/34	1	2	FACETS	0.559	0.465	0.664	0.559	0.465	0.664	SUBCLONAL	1	TRUE	1	0.268245208844171	2		499	547	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551703	150551703	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	41	227	1	ENST00000369026.2:c.304A>T	p.Thr102Ser	p.T102S	ENST00000369026	NM_021960.4	102	Acc/Tcc	1/3	1	2	FACETS	0.672	0.56	0.796	0.672	0.56	0.796	SUBCLONAL	1	TRUE	1	0.268245208844171	2		228	455	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343359	118343359	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	38	347	0	ENST00000534358.1:c.1485G>T	p.Glu495Asp	p.E495D	ENST00000534358	NM_005933.3	495	gaG/gaT	3/36	1	2	FACETS	0.725	0.6	0.864	0.725	0.6	0.864	SUBCLONAL	1	TRUE	1	0.268245208844171	2		347	391	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422032	81422032	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1263008401	NA	P-0031505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	27	333	0	ENST00000298171.2:c.8C>A	p.Pro3Gln	p.P3Q	ENST00000298171	NM_000369.2	3	cCg/cAg	1/10	1	2	FACETS	0.458	0.363	0.565	0.458	0.363	0.565	SUBCLONAL	1	TRUE	1	0.268245208844171	2		333	440	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354621	91354621	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	38	482	0	ENST00000355112.3:c.4061G>T	p.Gly1354Val	p.G1354V	ENST00000355112	NM_000057.2	1354	gGt/gTt	21/22	0.268245208844171	1	FACETS	0.513	0.424	0.613	0.513	0.424	0.613	SUBCLONAL	1	TRUE	0	0.268245208844171	1		482	478	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578175	7578175	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0031505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	40	580	0	ENST00000269305.4:c.672+2T>C		p.X224_splice	ENST00000269305	NM_001126112.2	224			1	2	FACETS	0.534	0.443	0.635	0.534	0.443	0.635	SUBCLONAL	1	TRUE	1	0.268245208844171	2		580	559	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508727	29508727	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0031505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	32	458	1	ENST00000356175.3:c.655-1G>T		p.X219_splice	ENST00000356175	NM_000267.3	219			1	2	FACETS	0.628	0.51	0.761	0.628	0.51	0.761	SUBCLONAL	1	TRUE	1	0.268245208844171	2		459	380	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022248	31022248	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	15	269	0	ENST00000375687.4:c.1733G>C	p.Arg578Pro	p.R578P	ENST00000375687	NM_015338.5	578	cGt/cCt	13/13	0.268245208844171	1	FACETS	0.353	0.258	0.468	0.353	0.258	0.468	SUBCLONAL	1	TRUE	0	0.268245208844171	1		269	274	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0031505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	82	444	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.998	0.884	1	1	0.984	1	CLONAL	2	TRUE	1	0.19377959603299	2		444	424	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006898	47006898	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1556762493	NA	P-0031505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	62	624	0	ENST00000377604.3:c.17+1G>T		p.X6_splice	ENST00000377604	NM_001204468.1	6			0.19377959603299	0	FACETS	0.784	0.677	0.901			1	CLONAL	1	TRUE	0	0.19377959603299	0		624	658	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199939	128199939	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	38	463	0	ENST00000341105.2:c.1366C>A	p.Pro456Thr	p.P456T	ENST00000341105	NM_032638.4	456	Ccg/Acg	6/6	1	2	FACETS	0.747	0.617	0.893	0.747	0.617	0.893	SUBCLONAL	1	TRUE	1	0.19377959603299	2		463	525	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458330	120458330	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	48	499	0	ENST00000256646.2:c.7015A>G	p.Met2339Val	p.M2339V	ENST00000256646	NM_024408.3	2339	Atg/Gtg	34/34	1	2	FACETS	0.85	0.718	0.995	0.85	0.718	0.995	CLONAL	1	TRUE	1	0.19377959603299	2		499	583	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551703	150551703	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	12	227	1	ENST00000369026.2:c.304A>T	p.Thr102Ser	p.T102S	ENST00000369026	NM_021960.4	102	Acc/Tcc	1/3	1	2	FACETS	0.391	0.274	0.536	0.391	0.274	0.536	SUBCLONAL	1	TRUE	1	0.19377959603299	2		228	317	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343359	118343359	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	40	347	0	ENST00000534358.1:c.1485G>T	p.Glu495Asp	p.E495D	ENST00000534358	NM_005933.3	495	gaG/gaT	3/36	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.19377959603299	2		347	368	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422032	81422032	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1263008401	NA	P-0031505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	21	333	0	ENST00000298171.2:c.8C>A	p.Pro3Gln	p.P3Q	ENST00000298171	NM_000369.2	3	cCg/cAg	1/10	1	2	FACETS	0.53	0.407	0.674	0.53	0.407	0.674	SUBCLONAL	1	TRUE	1	0.19377959603299	2		333	409	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354621	91354621	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	33	482	0	ENST00000355112.3:c.4061G>T	p.Gly1354Val	p.G1354V	ENST00000355112	NM_000057.2	1354	gGt/gTt	21/22	0.19377959603299	1	FACETS	0.673	0.548	0.815	0.673	0.548	0.815	SUBCLONAL	1	TRUE	0	0.19377959603299	1		482	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578175	7578175	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0031505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	66	580	0	ENST00000269305.4:c.672+2T>C		p.X224_splice	ENST00000269305	NM_001126112.2	224			1	2	FACETS	0.931	0.807	1	0.931	0.807	1	CLONAL	1	TRUE	1	0.19377959603299	2		580	732	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508727	29508727	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0031505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	18	458	1	ENST00000356175.3:c.655-1G>T		p.X219_splice	ENST00000356175	NM_000267.3	219			1	2	FACETS	0.491	0.369	0.637	0.491	0.369	0.637	SUBCLONAL	1	TRUE	1	0.19377959603299	2		459	378	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022248	31022248	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	17	269	0	ENST00000375687.4:c.1733G>C	p.Arg578Pro	p.R578P	ENST00000375687	NM_015338.5	578	cGt/cCt	13/13	1	2	FACETS	0.575	0.429	0.749	0.575	0.429	0.749	SUBCLONAL	1	TRUE	1	0.19377959603299	2		269	305	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225399	2225399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	46	558	1	ENST00000326181.6:c.1484G>A	p.Gly495Asp	p.G495D	ENST00000326181	NM_032271.2	495	gGc/gAc	16/21	1	2	FACETS	0.642	0.539	0.756	0.642	0.539	0.756	SUBCLONAL	1	TRUE	1	0.19377959603299	2		559	740	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0031511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	215	589	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.522879855116188	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.522879855116188	1		589	553	SUCCESS
APC	324	MSKCC	GRCh37	5	112174835	112174835	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0031511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	109	283	0	ENST00000257430.4:c.3544A>T	p.Lys1182Ter	p.K1182*	ENST00000257430	NM_000038.5	1182	Aaa/Taa	16/16	1	2	FACETS	0.988	0.894	1	0.988	0.894	1	CLONAL	1	TRUE	1	0.522879855116188	2		283	422	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920401	114920401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1422891742	NA	P-0031511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	170	400	0	ENST00000543371.1:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000543371	NM_001198531.1	448	Cgg/Tgg	13/14	1	2	FACETS	0.963	0.889	1	0.963	0.889	1	CLONAL	1	TRUE	1	0.522879855116188	2		400	675	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916931	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0031511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	69	467	1	ENST00000263967.3:c.317_318delinsTT	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGC/gTT	2/21	1	2	FACETS	0.509	0.443	0.579	0.509	0.443	0.579	SUBCLONAL	1	TRUE	1	0.522879855116188	2		468	519	SUCCESS
APC	324	MSKCC	GRCh37	5	112175136	112175136	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	96	263	0	ENST00000257430.4:c.3845del	p.Ser1282Ter	p.S1282*	ENST00000257430	NM_000038.5	1282	tCa/ta	16/16	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.522879855116188	2		263	337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0031596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	68	589	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.216410601423489	2		589	425	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0031596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	78	389	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.175476154865529	1	FACETS	0.908	0.804	1	1	0.982	1	CLONAL	2	TRUE	0	0.216410601423489	1		389	354	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108010	30108010	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	31	615	1	ENST00000331968.5:c.797A>T	p.Lys266Ile	p.K266I	ENST00000331968	NM_002742.2	266	aAa/aTa	5/18	1	2	FACETS	0.549	0.443	0.669	0.549	0.443	0.669	SUBCLONAL	1	TRUE	1	0.216410601423489	2		616	522	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483953	212483953	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	69	423	0	ENST00000342788.4:c.2250del	p.Lys751ArgfsTer20	p.K751Rfs*20	ENST00000342788	NM_005235.2	750	atT/at	19/28	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.367806725535988	2		423	351	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668751	52668751	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	81	456	0	ENST00000394830.3:c.1168T>A	p.Tyr390Asn	p.Y390N	ENST00000394830	NM_018313.4	390	Tat/Aat	12/30	0.367806725535988	1	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	0	0.367806725535988	1		456	352	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243870	53243870	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0031597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	138	293	0	ENST00000375401.3:c.1122+1G>T		p.X374_splice	ENST00000375401	NM_004187.3	374			1	1	FACETS	0.804	0.74	0.869	1	0.989	1	CLONAL	2	TRUE	0	0.367806725535988	1		293	381	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518262	8518262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	64	216	1	ENST00000356435.5:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000356435		377	Cgc/Tgc	10/35	0.517191541446824	3	FACETS	1	0.952	1	0.592	0.518	0.671	CLONAL	1	TRUE	1	0.517191541446824	3		217	263	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502662	149502662	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759436020	NA	P-0031599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	48	344	0	ENST00000261799.4:c.2126G>A	p.Arg709His	p.R709H	ENST00000261799	NM_002609.3	709	cGc/cAc	15/23	0.191724217117715	4	FACETS	0.545	0.46	0.638	0.182	0.153	0.213	INDETERMINATE	1	TRUE	1	0.517191541446824	4		344	517	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0031666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	135	337	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.79939539208572	1	FACETS	0.757	0.702	0.811	0.757	0.702	0.811	SUBCLONAL	1	TRUE	0	0.79939539208572	1		337	268	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504584	103504584	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	184	464	0	ENST00000355739.4:c.205C>T	p.Arg69Ter	p.R69*	ENST00000355739	NM_000123.3	69	Cga/Tga	2/15	0.382353938477393	3	FACETS	1	0.96	1	0.526	0.487	0.565	INDETERMINATE	1	TRUE	1	0.79939539208572	3		464	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579556	7579594	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATCAAATCATCCATTGCTTGGGACGGCAAGGGGGACTGT	ATCAAATCATCCATTGCTTGGGACGGCAAGGGGGACTGT	-	novel	NA	P-0031666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	267	747	1	ENST00000269305.4:c.97-4_131del		p.X33_splice	ENST00000269305	NM_001126112.2	33		4/11	0.79939539208572	1	FACETS	0.859	0.818	0.899	0.859	0.818	0.899	CLONAL	1	TRUE	0	0.79939539208572	1		748	467	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444356	50444356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	153	497	1	ENST00000331340.3:c.286C>T	p.His96Tyr	p.H96Y	ENST00000331340	NM_006060.4	96	Cac/Tac	4/8	0.418388230578753	1	FACETS	0.395	0.363	0.428	0.395	0.363	0.428	INDETERMINATE	1	TRUE	0	0.79939539208572	1		498	582	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801023	135801023	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs758924121	NA	P-0031666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	411	598	1	ENST00000298552.3:c.314A>G	p.His105Arg	p.H105R	ENST00000298552	NM_001162426.1	105	cAt/cGt	5/23	0.264625034983789	2	FACETS	1	0.995	1	0.664	0.637	0.691	INDETERMINATE	1	TRUE	0	0.79939539208572	2		599	774	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937372	76937372	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	46	630	0	ENST00000373344.5:c.3376G>T	p.Asp1126Tyr	p.D1126Y	ENST00000373344	NM_000489.3	1126	Gat/Tat	9/35	0.435280415125741	2	FACETS	0.404	0.342	0.471	0.202	0.171	0.236	INDETERMINATE	1	TRUE	0	0.79939539208572	2		630	285	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871037	12871037	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	93	535	0	ENST00000228872.4:c.264del	p.Tyr89ThrfsTer30	p.Y89Tfs*30	ENST00000228872	NM_004064.3	88	taC/ta	1/3	1	2	FACETS	0.546	0.487	0.608	0.546	0.487	0.608	SUBCLONAL	1	TRUE	1	0.664235571568657	2		535	513	SUCCESS
APC	324	MSKCC	GRCh37	5	112164575	112164575	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	70	370	0	ENST00000257430.4:c.1649A>G	p.Asn550Ser	p.N550S	ENST00000257430	NM_000038.5	550	aAt/aGt	14/16	0.60010363414905	3	FACETS	0.939	0.826	1	0.47	0.413	0.529	CLONAL	1	TRUE	1	0.664235571568657	3		370	299	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0031823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	242	400	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	0.988	1	CLONAL	1	TRUE	1	0.620267386999844	2		400	648	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871249	12871249	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0031823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	15	132	1	ENST00000228872.4:c.475+1G>A		p.X159_splice	ENST00000228872	NM_004064.3	159			0.405572517999614	3	FACETS	0.32	0.234	0.422	0.16	0.117	0.211	SUBCLONAL	1	TRUE	1	0.620267386999844	3		133	198	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061463	38061463	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	225	579	0	ENST00000250448.2:c.526A>G	p.Ile176Val	p.I176V	ENST00000250448	NM_004496.3	176	Atc/Gtc	2/2	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.620267386999844	2		579	659	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944257	206944257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	68	423	0	ENST00000423557.1:c.373C>T	p.Arg125Cys	p.R125C	ENST00000423557	NM_000572.2	125	Cgc/Tgc	3/5	0.583332118116097	4	FACETS	0.391	0.339	0.448	0.13	0.113	0.15	SUBCLONAL	1	TRUE	1	0.620267386999844	4		423	908	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178151	56178152	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0031823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	12	378	0	ENST00000399503.3:c.3127dup	p.Ser1043PhefsTer14	p.S1043Ffs*14	ENST00000399503	NM_005921.1	1042	ctt/cTtt	14/20	0.620267386999844	1	FACETS	0.112	0.078	0.154	0.112	0.078	0.154	SUBCLONAL	1	TRUE	0	0.620267386999844	1		378	238	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44733235	44733235	+	splice_donor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0031823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	51	416	0	ENST00000377967.4:c.225+2del		p.X75_splice	ENST00000377967	NM_021140.2	75			1	2	FACETS	0.363	0.309	0.422	0.363	0.309	0.422	SUBCLONAL	1	TRUE	1	0.620267386999844	2		416	453	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0031833-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	106	474	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.402665231319739	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.767566747319639	0		474	361	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0031833-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	64	389	0	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	0.174189507064519	4	FACETS	0.833	0.736	0.933	0.833	0.736	0.933	INDETERMINATE	2	FALSE	2	0.767566747319639	4		389	177	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519980	NA	P-0031833-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	182	641	0	ENST00000269305.4:c.528C>G	p.Cys176Trp	p.C176W	ENST00000269305	NM_001126112.2	176	tgC/tgG	5/11	0.689667976173893	1	FACETS	0.994	0.939	1	0.994	0.939	1	CLONAL	1	FALSE	0	0.767566747319639	1		641	294	SUCCESS
APC	324	MSKCC	GRCh37	5	112175213	112175213	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0031833-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	29	314	0	ENST00000257430.4:c.3922A>T	p.Lys1308Ter	p.K1308*	ENST00000257430	NM_000038.5	1308	Aaa/Taa	16/16	0.174189507064519	4	FACETS	1	0.88	1	0.552	0.451	0.662	INDETERMINATE	1	FALSE	2	0.767566747319639	4		314	121	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237659	133237659	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031833-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	113	635	4	ENST00000320574.5:c.2956C>T	p.Gln986Ter	p.Q986*	ENST00000320574	NM_006231.2	986	Caa/Taa	25/49	1	2	FACETS	0.813	0.739	0.89	0.813	0.739	0.89	CLONAL	1	FALSE	1	0.767566747319639	2		639	362	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468368	89468368	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031833-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	30	257	0	ENST00000336596.2:c.1902G>T	p.Glu634Asp	p.E634D	ENST00000336596	NM_005233.5	634	gaG/gaT	11/17	0.153243009456885	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.767566747319639	0		257	99	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0031848-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	170	439	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.715464039581535	6	FACETS	0.907	0.837	0.978			1	CLONAL	2	TRUE	NA	0.715464039581535	6		439	637	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031848-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	213	783	0	ENST00000256196.4:c.68G>A	p.Gly23Asp	p.G23D	ENST00000256196		23	gGc/gAc	1/6	0.442785406693304	1	FACETS	0.993	0.939	1	0.993	0.939	1	CLONAL	1	TRUE	0	0.715464039581535	1		783	385	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0032006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	42	223	3	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.797	0.679	0.923	0.797	0.679	0.923	CLONAL	1	TRUE	1	0.747088982073099	2		226	141	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061202	+	inframe_deletion	In_Frame_Del	DEL	GAAGCGCTTCTG	GAAGCGCTTCTG	-	novel	NA	P-0032006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	156	336	1	ENST00000250448.2:c.787_798del	p.Gln263_Phe266del	p.Q263_F266del	ENST00000250448	NM_004496.3	263	CAGAAGCGCTTC/-	2/2	1	2	FACETS	0.994	0.92	1	0.994	0.92	1	CLONAL	1	TRUE	1	0.747088982073099	2		337	420	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538865	23538865	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	71	430	0	ENST00000380871.4:c.574G>C	p.Glu192Gln	p.E192Q	ENST00000380871	NM_006167.3	192	Gag/Cag	2/2	0.747088982073099	1	FACETS	0.342	0.3	0.387	0.342	0.3	0.387	SUBCLONAL	1	TRUE	0	0.747088982073099	1		430	348	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742507	145742507	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	291	627	5	ENST00000428558.2:c.281C>A	p.Pro94Gln	p.P94Q	ENST00000428558	NM_004260.3	94	cCa/cAa	4/22	0.639109751649476	4	FACETS	1	0.98	1	0.364	0.342	0.387	CLONAL	1	TRUE	1	0.747088982073099	4		632	1247	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0032108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	61	503	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.178479858428672	2		503	552	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	116	474	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.0537793814062082	4	FACETS	1	0.935	1	1	0.935	1	INDETERMINATE	2	TRUE	2	0.178479858428672	4		474	731	SUCCESS
APC	324	MSKCC	GRCh37	5	112173668	112173668	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	34	459	1	ENST00000257430.4:c.2377C>T	p.Gln793Ter	p.Q793*	ENST00000257430	NM_000038.5	793	Caa/Taa	16/16	0.161841131540642	3	FACETS	0.838	0.684	1	0.419	0.342	0.506	CLONAL	1	TRUE	1	0.178479858428672	3		460	495	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445697	49445697	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	139	982	0	ENST00000301067.7:c.1769T>G	p.Met590Arg	p.M590R	ENST00000301067	NM_003482.3	590	aTg/aGg	10/54	0.0537793814062082	4	FACETS	1	0.979	1	1	0.979	1	INDETERMINATE	2	TRUE	2	0.178479858428672	4		982	742	SUCCESS
APC	324	MSKCC	GRCh37	5	112175723	112175724	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0032108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	37	391	0	ENST00000257430.4:c.4435dup	p.Val1479GlyfsTer8	p.V1479Gfs*8	ENST00000257430	NM_000038.5	1478	agg/aGgg	16/16	0.161841131540642	3	FACETS	0.997	0.822	1	0.498	0.411	0.597	CLONAL	1	TRUE	1	0.178479858428672	3		391	453	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120152	70120165	+	frameshift_variant	Frame_Shift_Del	DEL	TGAGCAGCGAGCCG	TGAGCAGCGAGCCG	-	novel	NA	P-0032108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	28	298	0	ENST00000245479.2:c.1154_1167del	p.Leu385ArgfsTer188	p.L385Rfs*188	ENST00000245479	NM_000346.3	385	cTGAGCAGCGAGCCG/c	3/3	0.178479858428672	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.178479858428672	1		298	209	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0032110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	28	503	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.988	0.789	1	0.988	0.789	1	CLONAL	1	TRUE	1	0.14	2		503	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0032110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	43	513	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.906	0.757	1	0.906	0.757	1	CLONAL	1	TRUE	1	0.14	2		513	678	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853281	68853281	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	43	563	0	ENST00000261769.5:c.1664del	p.His555ProfsTer2	p.H555Pfs*2	ENST00000261769	NM_004360.3	555	cAc/cc	11/16	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.14	2		563	598	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939126	76939126	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	39	622	0	ENST00000373344.5:c.1622C>T	p.Ser541Leu	p.S541L	ENST00000373344	NM_000489.3	541	tCa/tTa	9/35	1	2	FACETS	0.862	0.713	1	0.862	0.713	1	CLONAL	1	TRUE	1	0.14	2		622	646	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0032114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	27	407	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.325627031571196	6	FACETS	0.227	0.179	0.282			1	SUBCLONAL	1	TRUE	NA	0.325627031571196	6		407	1207	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	64	264	0				ENST00000310581	NM_198253.2	-/1132			0.148042500480489	2	FACETS	0.835	0.724	0.954	0.417	0.362	0.477	INDETERMINATE	1	TRUE	0	0.325627031571196	2		264	471	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0032114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1521	57	703	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.325627031571196	6	FACETS	0.366	0.312	0.426			1	SUBCLONAL	1	TRUE	NA	0.325627031571196	6		703	1578	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0032114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	205	437	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	0.325627031571196	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.325627031571196	2		437	522	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	13	438	0	ENST00000397062.3:c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	NM_006164.4	34	Cga/Gga	2/5	1	2	FACETS	0.149	0.106	0.203	0.149	0.106	0.203	SUBCLONAL	1	TRUE	1	0.325627031571196	2		438	535	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469672	NA	P-0032114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	166	331	0	ENST00000374080.3:c.131G>A	p.Gly44Asp	p.G44D	ENST00000374080		44	gGt/gAt	2/45	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	2	TRUE	NA	0.325627031571196	2		331	433	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482607	56482607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs993665271	NA	P-0032114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	301	767	0	ENST00000267101.3:c.1064C>T	p.Thr355Ile	p.T355I	ENST00000267101	NM_001982.3	355	aCc/aTc	9/28	0.206994875244632	4	FACETS	1	0.988	1	0.783	0.738	0.829	CLONAL	2	TRUE	1	0.325627031571196	4		767	1043	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317010	11317010	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	82	483	0	ENST00000361445.4:c.484G>A	p.Glu162Lys	p.E162K	ENST00000361445	NM_004958.3	162	Gag/Aag	4/58	1	2	FACETS	0.899	0.794	1	0.899	0.794	1	CLONAL	1	TRUE	1	0.325627031571196	2		483	560	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984329	201984340	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCACCCAGGTAC	TCACCCAGGTAC	-	novel	NA	P-0032114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	104	568	0	ENST00000359651.3:c.1002-7_1006del		p.X334_splice	ENST00000359651		334		8/8	0.325627031571196	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.325627031571196	1		568	517	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374204	118374204	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	121	430	0	ENST00000534358.1:c.7597G>T	p.Glu2533Ter	p.E2533*	ENST00000534358	NM_005933.3	2533	Gaa/Taa	27/36	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.325627031571196	2		430	520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	172	843	0	ENST00000269305.4:c.856del	p.Glu286LysfsTer59	p.E286Kfs*59	ENST00000269305	NM_001126112.2	286	Gaa/aa	8/11	0.325627031571196	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.325627031571196	1		843	792	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47643463	47643463	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	118	629	0	ENST00000233146.2:c.971A>G	p.Gln324Arg	p.Q324R	ENST00000233146	NM_000251.2	324	cAg/cGg	6/16	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.325627031571196	2		629	708	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526384	31526384	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1306	207	1043	1	ENST00000344624.3:c.656G>A	p.Arg219Lys	p.R219K	ENST00000344624		219	aGa/aAa	2/33	0.148042500480489	2	FACETS	0.84	0.777	0.906	0.42	0.388	0.453	INDETERMINATE	1	TRUE	0	0.325627031571196	2		1044	1513	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878025	151878025	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	91	480	0	ENST00000262189.6:c.6920G>A	p.Arg2307Lys	p.R2307K	ENST00000262189	NM_170606.2	2307	aGa/aAa	36/59	0.111102949738892	3	FACETS	1	0.964	1	0.602	0.536	0.672	INDETERMINATE	1	TRUE	1	0.325627031571196	3		480	540	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040746	47040746	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	140	433	0	ENST00000377604.3:c.1382del	p.Lys461ArgfsTer24	p.K461Rfs*24	ENST00000377604	NM_001204468.1	461	Aag/ag	13/24	NA	2	FACETS	0.975	0.896	1			1	INDETERMINATE	2	TRUE	NA	0.325627031571196	2		433	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519988	NA	P-0032114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	258	589	0	ENST00000269305.4:c.808T>C	p.Phe270Leu	p.F270L	ENST00000269305	NM_001126112.2	270	Ttt/Ctt	8/11	0.564136549059368	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.564136549059368	2		589	451	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0032114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	235	448	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.564136549059368	4	FACETS	0.874	0.825	0.923	0.874	0.825	0.923	CLONAL	3	TRUE	1	0.564136549059368	4		449	497	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302604	15302604	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115836330	NA	P-0032114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	133	803	1	ENST00000263388.2:c.754G>A	p.Val252Met	p.V252M	ENST00000263388	NM_000435.2	252	Gtg/Atg	5/33	0.564136549059368	3	FACETS	0.983	0.896	1	0.491	0.448	0.537	CLONAL	1	TRUE	1	0.564136549059368	3		804	615	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165698	118165698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1432369724	NA	P-0032114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	36	344	0	ENST00000369448.3:c.208C>T	p.Arg70Trp	p.R70W	ENST00000369448	NM_017709.3	70	Cgg/Tgg	2/2	0.483885170320869	4	FACETS	0.555	0.456	0.664	0.277	0.228	0.332	SUBCLONAL	1	TRUE	2	0.564136549059368	4		344	360	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29002002	29002002	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1437659960	NA	P-0032114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	227	459	0	ENST00000282397.4:c.1163A>G	p.Tyr388Cys	p.Y388C	ENST00000282397	NM_002019.4	388	tAc/tGc	9/30	0.545386476003678	3	FACETS	0.925	0.879	0.97	0.925	0.879	0.97	CLONAL	3	TRUE	0	0.564136549059368	3		459	372	SUCCESS
APC	324	MSKCC	GRCh37	5	112170685	112170686	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	127	411	0	ENST00000257430.4:c.1784dup	p.Leu595PhefsTer7	p.L595Ffs*7	ENST00000257430	NM_000038.5	594	aat/aaTt	15/16	0.564136549059368	2	FACETS	0.84	0.776	0.904	0.84	0.776	0.904	CLONAL	2	TRUE	0	0.564136549059368	2		411	268	SUCCESS
APC	324	MSKCC	GRCh37	5	112178663	112178663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	122	362	0	ENST00000257430.4:c.7372G>A	p.Glu2458Lys	p.E2458K	ENST00000257430	NM_000038.5	2458	Gaa/Aaa	16/16	0.564136549059368	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	0	0.564136549059368	2		362	215	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100403	8100403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	215	757	0	ENST00000346208.3:c.377C>T	p.Ser126Phe	p.S126F	ENST00000346208		126	tCc/tTc	3/6	1	2	FACETS	0.987	0.924	1	0.987	0.924	1	CLONAL	1	TRUE	1	0.72096337404564	2		757	604	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263973	104263974	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776579	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	56	170	0	ENST00000369902.3:c.71dup	p.Ala25GlyfsTer23	p.A25Gfs*23	ENST00000369902	NM_016169.3	22	gcc/gCcc	1/12	1	2	FACETS	0.894	0.777	1	0.894	0.777	1	CLONAL	1	TRUE	1	0.60804130006725	2		170	206	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913400	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	119	384	0	ENST00000349496.5:c.98C>A	p.Ser33Tyr	p.S33Y	ENST00000349496	NM_001904.3	33	tCt/tAt	3/15	0.599784773334719	2	FACETS	1	0.944	1	0.523	0.477	0.571	CLONAL	1	TRUE	0	0.60804130006725	2		384	374	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	165	715	0	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.60804130006725	2		715	539	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	83	374	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.965	0.862	1	0.965	0.862	1	CLONAL	1	TRUE	1	0.60804130006725	2		374	283	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	159	636	5	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.936	0.862	1	0.936	0.862	1	CLONAL	1	TRUE	1	0.60804130006725	2		641	559	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170088	32170088	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775047010	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	234	825	0	ENST00000375023.3:c.3520G>A	p.Gly1174Arg	p.G1174R	ENST00000375023	NM_004557.3	1174	Gga/Aga	21/30	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.60804130006725	2		825	723	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	99	474	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.831	0.747	0.918	0.831	0.747	0.918	CLONAL	1	TRUE	1	0.60804130006725	2		474	392	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	139	658	1	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.776	0.709	0.846	0.776	0.709	0.846	SUBCLONAL	1	TRUE	1	0.60804130006725	2		659	589	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625080	69625080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782166974	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	35	538	1	ENST00000334134.2:c.713C>T	p.Ala238Val	p.A238V	ENST00000334134	NM_005247.2	238	gCg/gTg	3/3	1	2	FACETS	0.329	0.27	0.395	0.329	0.27	0.395	SUBCLONAL	1	TRUE	1	0.60804130006725	2		539	350	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154242	2154242	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755455183	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	36	741	5	ENST00000434045.2:c.686del	p.Pro229GlnfsTer27	p.P229Qfs*27	ENST00000434045	NM_001127598.1	229	cCa/ca	5/5	1	2	FACETS	0.22	0.18	0.264	0.22	0.18	0.264	SUBCLONAL	1	TRUE	1	0.60804130006725	2		746	539	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	194	653	13	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.60804130006725	2		666	620	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	121	776	0	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.547	0.495	0.603	0.547	0.495	0.603	SUBCLONAL	1	TRUE	1	0.60804130006725	2		776	727	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	115	422	1	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.60804130006725	2		423	367	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306996	65306997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	132	519	9	ENST00000342505.4:c.2580dup	p.Pro861ThrfsTer4	p.P861Tfs*4	ENST00000342505	NM_002227.2	860	-/A	19/25	1	2	FACETS	0.912	0.834	0.993	0.912	0.834	0.993	CLONAL	1	TRUE	1	0.60804130006725	2		528	476	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647028	23647028	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1555461597	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	173	811	2	ENST00000261584.4:c.839del	p.Asn280ThrfsTer8	p.N280Tfs*8	ENST00000261584	NM_024675.3	280	aAc/ac	4/13	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.60804130006725	2		813	564	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	146	604	1	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	0.998	0.918	1	0.998	0.918	1	CLONAL	1	TRUE	1	0.60804130006725	2		605	481	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760024	133760024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	210	647	1	ENST00000318560.5:c.2352del	p.Arg785GlyfsTer3	p.R785Gfs*3	ENST00000318560	NM_005157.4	783	Ccc/cc	11/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.60804130006725	2		648	637	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696757	176696757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752685166	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	132	461	0	ENST00000439151.2:c.5458G>A	p.Val1820Met	p.V1820M	ENST00000439151	NM_022455.4	1820	Gtg/Atg	16/23	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.60804130006725	2		461	424	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096048	11096048	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	61	799	0	ENST00000358026.2:c.326del	p.Pro109ArgfsTer194	p.P109Rfs*194	ENST00000358026	NM_001128849.1	108	Ccc/cc	3/36	1	2	FACETS	0.324	0.279	0.372	0.324	0.279	0.372	SUBCLONAL	1	TRUE	1	0.60804130006725	2		799	620	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303224	15303224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753596637	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	104	940	1	ENST00000263388.2:c.304G>A	p.Ala102Thr	p.A102T	ENST00000263388	NM_000435.2	102	Gcc/Acc	3/33	1	2	FACETS	0.514	0.46	0.57	0.514	0.46	0.57	SUBCLONAL	1	TRUE	1	0.60804130006725	2		941	666	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023954	27023954	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	30	55	0	ENST00000324856.7:c.1060C>T	p.Gln354Ter	p.Q354*	ENST00000324856	NM_006015.4	354	Caa/Taa	1/20	1	2	FACETS	0.759	0.64	0.88	1	0.955	1	SUBCLONAL	2	TRUE	1	0.60804130006725	2		55	65	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347875	73347875	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs917054849	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	76	442	0	ENST00000377767.4:c.1186C>T	p.Arg396Trp	p.R396W	ENST00000377767	NM_014953.3	396	Cgg/Tgg	8/21	1	2	FACETS	0.916	0.813	1	0.916	0.813	1	CLONAL	1	TRUE	1	0.60804130006725	2		442	273	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	208	653	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.60804130006725	2		658	611	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480010	50480010	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	195	695	5	ENST00000394963.4:c.249del	p.Asn84ThrfsTer79	p.N84Tfs*79	ENST00000394963	NM_003076.4	82	Ggg/gg	2/13	1	2	FACETS	0.993	0.923	1	0.993	0.923	1	CLONAL	1	TRUE	1	0.60804130006725	2		700	646	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99181137	99181137	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	204	675	0	ENST00000074304.5:c.2078T>C	p.Leu693Pro	p.L693P	ENST00000074304	NM_001134224.1	693	cTg/cCg	20/26	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.60804130006725	2		675	653	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	176	819	4	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.946	0.876	1	0.946	0.876	1	CLONAL	1	TRUE	1	0.60804130006725	2		823	612	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542455	187542455	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376944386	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	69	607	2	ENST00000441802.2:c.5285C>T	p.Ala1762Val	p.A1762V	ENST00000441802	NM_005245.3	1762	gCg/gTg	10/27	1	2	FACETS	0.457	0.398	0.519	0.457	0.398	0.519	SUBCLONAL	1	TRUE	1	0.60804130006725	2		609	497	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793208	139793208	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561210418	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	192	662	0	ENST00000247668.2:c.16G>A	p.Val6Met	p.V6M	ENST00000247668	NM_021138.3	6	Gtg/Atg	2/11	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.60804130006725	2		662	615	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118633	11118635	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs765524239	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	185	651	3	ENST00000358026.2:c.2066_2068del	p.Lys689del	p.K689del	ENST00000358026	NM_001128849.1	686	gAGAag/gag	14/36	1	2	FACETS	0.981	0.911	1	0.981	0.911	1	CLONAL	1	TRUE	1	0.60804130006725	2		654	620	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925402	114925402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748822481	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	196	739	1	ENST00000543371.1:c.1485del	p.Ser496ProfsTer5	p.S496Pfs*5	ENST00000543371	NM_001198531.1	494	Ccc/cc	14/14	1	2	FACETS	0.998	0.928	1	0.998	0.928	1	CLONAL	1	TRUE	1	0.60804130006725	2		740	646	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948755	71948755	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1565399032	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	195	791	4	ENST00000298229.2:c.3470del	p.Gly1157AspfsTer45	p.G1157Dfs*45	ENST00000298229	NM_001567.3	1156	cGg/cg	26/28	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.60804130006725	2		795	599	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605204	46605204	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1459319402	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	77	389	2	ENST00000263734.3:c.1421G>C	p.Ser474Thr	p.S474T	ENST00000263734	NM_001430.4	474	aGc/aCc	10/16	1	2	FACETS	0.993	0.884	1	0.993	0.884	1	CLONAL	1	TRUE	1	0.60804130006725	2		391	255	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172509	108172510	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	43	345	1	ENST00000278616.4:c.5318dup	p.Phe1774ValfsTer8	p.F1774Vfs*8	ENST00000278616	NM_000051.3	1771	aga/agAa	35/63	1	2	FACETS	0.733	0.621	0.854	0.733	0.621	0.854	SUBCLONAL	1	TRUE	1	0.60804130006725	2		346	193	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515145	31515145	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1202201920	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	206	874	0	ENST00000344624.3:c.1240C>T	p.Arg414Ter	p.R414*	ENST00000344624		414	Cga/Tga	5/33	1	2	FACETS	0.899	0.836	0.963	0.899	0.836	0.963	CLONAL	1	TRUE	1	0.60804130006725	2		874	754	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27098990	27098990	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1191305197	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	28	535	0	ENST00000324856.7:c.3407-1G>A		p.X1136_splice	ENST00000324856	NM_006015.4	1136			1	2	FACETS	0.202	0.161	0.249	0.202	0.161	0.249	SUBCLONAL	1	TRUE	1	0.60804130006725	2		535	456	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309821	65309821	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	226	690	0	ENST00000342505.4:c.2329T>A	p.Trp777Arg	p.W777R	ENST00000342505	NM_002227.2	777	Tgg/Agg	17/25	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.60804130006725	2		690	707	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193205403	193205403	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	216	606	0	ENST00000367435.3:c.1338del	p.Phe446LeufsTer33	p.F446Lfs*33	ENST00000367435	NM_024529.4	445	gTt/gt	15/17	1	2	FACETS	0.998	0.932	1	0.998	0.932	1	CLONAL	1	TRUE	1	0.60804130006725	2		606	712	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943783	71943783	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	224	815	0	ENST00000298229.2:c.1826A>G	p.Asn609Ser	p.N609S	ENST00000298229	NM_001567.3	609	aAc/aGc	15/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.60804130006725	2		815	670	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911021	94911021	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	76	783	0	ENST00000536441.1:c.1109A>G	p.Asp370Gly	p.D370G	ENST00000536441	NM_144665.3	370	gAc/gGc	8/10	1	2	FACETS	0.495	0.435	0.559	0.495	0.435	0.559	SUBCLONAL	1	TRUE	1	0.60804130006725	2		783	505	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444210	49444210	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	114	814	0	ENST00000301067.7:c.3161C>A	p.Pro1054Gln	p.P1054Q	ENST00000301067	NM_003482.3	1054	cCg/cAg	11/54	1	2	FACETS	0.49	0.441	0.541	0.49	0.441	0.541	SUBCLONAL	1	TRUE	1	0.60804130006725	2		814	766	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448524	49448524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767327365	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	167	571	2	ENST00000301067.7:c.187G>A	p.Val63Met	p.V63M	ENST00000301067	NM_003482.3	63	Gtg/Atg	3/54	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.60804130006725	2		573	509	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69207391	69207391	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1487823798	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	79	506	0	ENST00000462284.1:c.157A>T	p.Thr53Ser	p.T53S	ENST00000462284	NM_002392.5	53	Act/Tct	3/11	1	2	FACETS	0.78	0.692	0.873	0.78	0.692	0.873	SUBCLONAL	1	TRUE	1	0.60804130006725	2		506	333	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878097	48878097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1566174092	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	49	57	0	ENST00000267163.4:c.49G>A	p.Ala17Thr	p.A17T	ENST00000267163	NM_000321.2	17	Gcc/Acc	1/27	1	2	FACETS	0.767	0.674	0.862	1	0.972	1	SUBCLONAL	2	TRUE	1	0.60804130006725	2		57	105	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068234	30068234	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	37	572	0	ENST00000331968.5:c.2165A>G	p.Gln722Arg	p.Q722R	ENST00000331968	NM_002742.2	722	cAg/cGg	15/18	1	2	FACETS	0.284	0.234	0.34	0.284	0.234	0.34	SUBCLONAL	1	TRUE	1	0.60804130006725	2		572	428	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934831	9934831	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	164	695	1	ENST00000330684.3:c.1459A>G	p.Lys487Glu	p.K487E	ENST00000330684	NM_001134407.1	487	Aag/Gag	6/13	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.60804130006725	2		696	514	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032092	10032092	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201674066	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	184	724	1	ENST00000330684.3:c.731G>A	p.Arg244His	p.R244H	ENST00000330684	NM_001134407.1	244	cGc/cAc	3/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.60804130006725	2		725	550	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830959	72830959	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	190	595	0	ENST00000268489.5:c.5622del	p.Glu1875LysfsTer39	p.E1875Kfs*39	ENST00000268489	NM_006885.3	1874	ccC/cc	9/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.60804130006725	2		595	556	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89806443	89806447	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTT	CTCTT	-	novel	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	185	703	0	ENST00000389301.3:c.3889_3893del	p.Lys1297GlufsTer14	p.K1297Efs*14	ENST00000389301	NM_000135.2	1297	AAGAGg/g	39/43	1	2	FACETS	0.903	0.837	0.971	0.903	0.837	0.971	CLONAL	1	TRUE	1	0.60804130006725	2		703	674	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30302676	30302676	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	67	509	0	ENST00000322652.5:c.767G>A	p.Arg256His	p.R256H	ENST00000322652	NM_015355.2	256	cGt/cAt	7/16	1	2	FACETS	0.687	0.601	0.778	0.687	0.601	0.778	SUBCLONAL	1	TRUE	1	0.60804130006725	2		509	321	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265416	10265416	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375474222	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	194	780	1	ENST00000340748.4:c.1630C>T	p.Arg544Cys	p.R544C	ENST00000340748		544	Cgc/Tgc	20/40	1	2	FACETS	0.88	0.817	0.945	0.88	0.817	0.945	CLONAL	1	TRUE	1	0.60804130006725	2		781	725	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135101	11135101	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	181	854	0	ENST00000358026.2:c.3068A>G	p.Glu1023Gly	p.E1023G	ENST00000358026	NM_001128849.1	1023	gAg/gGg	21/36	1	2	FACETS	0.932	0.863	1	0.932	0.863	1	CLONAL	1	TRUE	1	0.60804130006725	2		854	639	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955219	17955219	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	193	807	1	ENST00000458235.1:c.8C>A	p.Pro3His	p.P3H	ENST00000458235	NM_000215.3	3	cCt/cAt	2/24	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.60804130006725	2		808	611	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266831	18266831	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1011337615	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	112	373	0	ENST00000222254.8:c.142G>C	p.Glu48Gln	p.E48Q	ENST00000222254	NM_005027.3	48	Gag/Cag	2/16	1	2	FACETS	0.93	0.844	1	0.93	0.844	1	CLONAL	1	TRUE	1	0.60804130006725	2		373	396	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724300	52724300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	46	594	0	ENST00000322088.6:c.1432G>A	p.Ala478Thr	p.A478T	ENST00000322088	NM_014225.5	478	Gcc/Acc	12/15	1	2	FACETS	0.261	0.219	0.308	0.261	0.219	0.308	SUBCLONAL	1	TRUE	1	0.60804130006725	2		594	579	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607667	46607667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769628339	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	240	811	0	ENST00000263734.3:c.1856C>T	p.Pro619Leu	p.P619L	ENST00000263734	NM_001430.4	619	cCg/cTg	12/16	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.60804130006725	2		811	629	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37083823	37083823	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs267607853	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	275	576	0	ENST00000231790.2:c.1731+1G>A		p.X577_splice	ENST00000231790	NM_000249.3	577			0.599784773334719	2	FACETS	0.956	0.912	1	0.956	0.912	1	CLONAL	2	TRUE	0	0.60804130006725	2		576	473	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405961	49405961	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	182	583	0	ENST00000418115.1:c.177C>A	p.Asp59Glu	p.D59E	ENST00000418115	NM_001664.2	59	gaC/gaA	3/5	0.599784773334719	2	FACETS	1	0.954	1	0.519	0.481	0.557	CLONAL	1	TRUE	0	0.60804130006725	2		583	577	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428523	72428523	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	41	593	0	ENST00000477973.2:c.481A>G	p.Thr161Ala	p.T161A	ENST00000477973	NM_012234.5	161	Acc/Gcc	2/4	1	2	FACETS	0.318	0.265	0.377	0.318	0.265	0.377	SUBCLONAL	1	TRUE	1	0.60804130006725	2		593	424	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259220	89259220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	114	524	2	ENST00000336596.2:c.364C>A	p.Leu122Met	p.L122M	ENST00000336596	NM_005233.5	122	Ctg/Atg	3/17	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.60804130006725	2		526	374	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608629	189608629	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	202	684	0	ENST00000264731.3:c.1707del	p.Leu570Ter	p.L570*	ENST00000264731	NM_003722.4	568	caG/ca	13/14	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.60804130006725	2		684	622	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521932	157521932	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554235555	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	129	521	0	ENST00000346085.5:c.4204G>T	p.Glu1402Ter	p.E1402*	ENST00000346085	NM_020732.3	1402	Gag/Tag	18/20	1	2	FACETS	0.905	0.826	0.986	0.905	0.826	0.986	CLONAL	1	TRUE	1	0.60804130006725	2		521	469	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879570	151879570	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs755216963	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	147	479	0	ENST00000262189.6:c.5375A>G	p.His1792Arg	p.H1792R	ENST00000262189	NM_170606.2	1792	cAt/cGt	36/59	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.60804130006725	2		479	397	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207530	29207530	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	34	508	1	ENST00000240100.2:c.266C>T	p.Ala89Val	p.A89V	ENST00000240100	NM_001394.6	89	gCc/gTc	1/4	1	2	FACETS	0.268	0.218	0.323	0.268	0.218	0.323	SUBCLONAL	1	TRUE	1	0.60804130006725	2		509	418	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046324	69046324	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	53	596	0	ENST00000288368.4:c.3800del	p.Phe1267SerfsTer20	p.F1267Sfs*20	ENST00000288368	NM_024870.2	1266	gTt/gt	32/40	1	2	FACETS	0.339	0.289	0.393	0.339	0.289	0.393	SUBCLONAL	1	TRUE	1	0.60804130006725	2		596	515	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028731	47028731	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	183	706	1	ENST00000377604.3:c.35G>T	p.Arg12Met	p.R12M	ENST00000377604	NM_001204468.1	12	aGg/aTg	3/24	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.60804130006725	2		707	591	SUCCESS
AR	367	MSKCC	GRCh37	X	66766381	66766381	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	18	43	0	ENST00000374690.3:c.1393G>A	p.Gly465Ser	p.G465S	ENST00000374690	NM_000044.3	465	Ggc/Agc	1/8	1	2	FACETS	1	0.808	1	1	0.808	1	CLONAL	1	TRUE	1	0.60804130006725	2		43	57	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0032228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	49	525	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	1	2	FACETS	0.803	0.681	0.936	0.803	0.681	0.936	CLONAL	1	TRUE	1	0.292115171697409	2		525	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0032228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	18	714	0	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	1	2	FACETS	0.24	0.18	0.311	0.24	0.18	0.311	SUBCLONAL	1	TRUE	1	0.292115171697409	2		714	514	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511750	46511750	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	54	526	2	ENST00000262741.5:c.1027A>T	p.Ile343Phe	p.I343F	ENST00000262741	NM_003629.3	343	Atc/Ttc	9/10	0.292115171697409	1	FACETS	0.695	0.595	0.805	0.695	0.595	0.805	SUBCLONAL	1	TRUE	0	0.292115171697409	1		528	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578501	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	AA	novel	NA	P-0032228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	79	804	0	ENST00000269305.4:c.429_430delinsTT	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	143	gtGCag/gtTTag	5/11	1	2	FACETS	0.904	0.796	1	0.904	0.796	1	CLONAL	1	TRUE	1	0.292115171697409	2		804	598	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0032318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	150	400	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.48675453291052	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	FALSE	1	0.486444263314512	3		400	362	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727483	66727483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504317	NA	P-0032318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	12	511	1	ENST00000307102.5:c.199G>A	p.Asp67Asn	p.D67N	ENST00000307102	NM_002755.3	67	Gac/Aac	2/11	0.167961710829462	3	FACETS	0.149	0.104	0.204	0.05	0.034	0.068	INDETERMINATE	1	FALSE	0	0.486444263314512	3		512	413	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162860	47162860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536163785	NA	P-0032318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	10	440	0	ENST00000409792.3:c.3266G>A	p.Arg1089Gln	p.R1089Q	ENST00000409792	NM_014159.6	1089	cGg/cAg	3/21	0.149404933328131	2	FACETS	0.206	0.139	0.289	0.103	0.069	0.145	INDETERMINATE	1	FALSE	0	0.486444263314512	2		440	200	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593606	55593650	+	inframe_deletion	In_Frame_Del	DEL	AAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGAC	AAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGAC	-	novel	NA	P-0032319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	233	512	0	ENST00000288135.5:c.1672_1716del	p.Lys558_Asp572del	p.K558_D572del	ENST00000288135	NM_000222.2	558	AAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGAC/-	11/21	1	2	FACETS	0.934	0.879	0.99	0.934	0.879	0.99	CLONAL	1	TRUE	1	0.908665752662651	2		512	549	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352258	70352258	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	114	731	0	ENST00000374080.3:c.4285G>C	p.Ala1429Pro	p.A1429P	ENST00000374080		1429	Gcc/Ccc	31/45	1	2	FACETS	0.293	0.263	0.324	0.293	0.263	0.324	SUBCLONAL	1	TRUE	1	0.908665752662651	2		731	857	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578260	7578260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204041	NA	P-0032379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	180	630	0	ENST00000269305.4:c.589G>A	p.Val197Met	p.V197M	ENST00000269305	NM_001126112.2	197	Gtg/Atg	6/11	0.455291326763387	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.513271334913786	1		630	505	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412581	63412581	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs751224138	NA	P-0032379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	190	274	0	ENST00000330258.3:c.586G>T	p.Gly196Trp	p.G196W	ENST00000330258	NM_152424.3	196	Ggg/Tgg	2/2	1	1	FACETS	0.805	0.758	0.851	1	0.993	1	CLONAL	2	TRUE	0	0.513271334913786	1		274	342	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589666	69589666	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	23	87	0	ENST00000168712.1:c.187C>T	p.Gln63Ter	p.Q63*	ENST00000168712	NM_002007.2	63	Cag/Tag	1/3	1	2	FACETS	0.546	0.43	0.679	0.546	0.43	0.679	SUBCLONAL	1	TRUE	1	0.513271334913786	2		87	164	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15365069	15365069	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	40	447	0	ENST00000263377.2:c.2052G>C	p.Glu684Asp	p.E684D	ENST00000263377	NM_058243.2	684	gaG/gaC	11/20	1	2	FACETS	0.25	0.207	0.298	0.25	0.207	0.298	SUBCLONAL	1	TRUE	1	0.513271334913786	2		447	624	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390812	139390814	+	missense_variant	Missense_Mutation	TNP	TCC	TCC	AAT	novel	NA	P-0032379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	56	772	1	ENST00000277541.6:c.7377_7379delinsATT	p.Glu2460Leu	p.E2460L	ENST00000277541	NM_017617.3	2459	caGGAg/caATTg	34/34	1	2	FACETS	0.256	0.218	0.297	0.256	0.218	0.297	SUBCLONAL	1	TRUE	1	0.513271334913786	2		773	853	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391424	139391424	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759225800	NA	P-0032379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	86	664	2	ENST00000277541.6:c.6767C>T	p.Ala2256Val	p.A2256V	ENST00000277541	NM_017617.3	2256	gCg/gTg	34/34	1	2	FACETS	0.455	0.402	0.511	0.455	0.402	0.511	SUBCLONAL	1	TRUE	1	0.513271334913786	2		666	737	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	234	408	1	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.988	0.929	1	0.988	0.929	1	CLONAL	1	TRUE	1	0.825612476033781	2		409	574	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0032381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	214	462	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	1	2	FACETS	0.943	0.883	1	0.943	0.883	1	CLONAL	1	TRUE	1	0.825612476033781	2		462	550	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821594	72821602	+	inframe_deletion	In_Frame_Del	DEL	GCCGCCGCC	GCCGCCGCC	-	rs374416547	NA	P-0032381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	14	88	0	ENST00000268489.5:c.10573_10581del	p.Gly3525_Gly3527del	p.G3525_G3527del	ENST00000268489	NM_006885.3	3525	GGCGGCGGC/-	10/10	1	2	FACETS	0.239	0.173	0.317	0.239	0.173	0.317	SUBCLONAL	1	TRUE	1	0.825612476033781	2		88	142	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163774	72163774	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	245	474	0	ENST00000357731.5:c.584G>A	p.Arg195Lys	p.R195K	ENST00000357731	NM_173808.2	195	aGg/aAg	4/7	1	2	FACETS	0.962	0.906	1	0.962	0.906	1	CLONAL	1	TRUE	1	0.825612476033781	2		474	617	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	115	768	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.33615191079831	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.33615191079831	1		768	561	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045522	47045522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	109	597	0	ENST00000377604.3:c.2489C>T	p.Pro830Leu	p.P830L	ENST00000377604	NM_001204468.1	830	cCg/cTg	22/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.33615191079831	2		597	548	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120019	70120020	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGC	rs776337541	NA	P-0032409-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	31	82	5	ENST00000245479.2:c.1029_1031dup	p.Pro346dup	p.P346dup	ENST00000245479	NM_000346.3	346	gcg/gCGCcg	3/3	NA	2	FACETS	1	0.863	1			1	INDETERMINATE	2	TRUE	NA	0.330933365711444	2		87	90	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432610	78432610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1397698903	NA	P-0032409-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	86	606	1	ENST00000370768.2:c.373C>T	p.Arg125Cys	p.R125C	ENST00000370768	NM_003902.3	125	Cgc/Tgc	6/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.330933365711444	2		607	394	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966768	44966768	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032409-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	66	316	0	ENST00000377967.4:c.3992G>A	p.Cys1331Tyr	p.C1331Y	ENST00000377967	NM_021140.2	1331	tGt/tAt	27/29	1	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.330933365711444	1		316	240	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0032489-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	71	195	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.455028710828356	2	FACETS	0.906	0.811	1	0.906	0.811	1	CLONAL	2	TRUE	0	0.480818074780241	2		195	163	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40828000	40828000	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032489-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	66	447	0	ENST00000373198.4:c.2428C>A	p.Gln810Lys	p.Q810K	ENST00000373198	NM_133170.3	810	Cag/Aag	17/32	1	2	FACETS	0.503	0.437	0.574	0.503	0.437	0.574	SUBCLONAL	1	TRUE	1	0.480818074780241	2		447	546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0032489-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	249	674	0	ENST00000269305.4:c.672+1G>C		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.447460850770494	2	FACETS	0.898	0.847	0.949	0.898	0.847	0.949	CLONAL	2	TRUE	0	0.480818074780241	2		674	577	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0032490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	78	258	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.405157608749287	3	FACETS	1	0.931	1	0.687	0.624	0.749	INDETERMINATE	2	TRUE	0	0.70687399961431	3		258	145	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850991	63850991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	41	518	0	ENST00000279873.7:c.1769C>T	p.Pro590Leu	p.P590L	ENST00000279873	NM_032199.2	590	cCc/cTc	10/10	0.633357401164892	4	FACETS	0.407	0.339	0.483	0.102	0.084	0.121	SUBCLONAL	1	TRUE	0	0.70687399961431	4		518	486	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692949	89692949	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	246	560	0	ENST00000371953.3:c.433T>G	p.Phe145Val	p.F145V	ENST00000371953	NM_000314.4	145	Ttt/Gtt	5/9	0.633357401164892	4	FACETS	1	0.99	1	0.839	0.803	0.874	CLONAL	3	TRUE	0	0.70687399961431	4		560	354	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779623	3779623	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	219	749	0	ENST00000262367.5:c.5425A>C	p.Lys1809Gln	p.K1809Q	ENST00000262367	NM_004380.2	1809	Aaa/Caa	31/31	0.70687399961431	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.70687399961431	3		749	374	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027198	48027198	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	130	603	0	ENST00000234420.5:c.2076A>T	p.Lys692Asn	p.K692N	ENST00000234420	NM_000179.2	692	aaA/aaT	4/10	0.305824150357995	6	FACETS	0.902	0.83	0.976	0.902	0.83	0.976	INDETERMINATE	3	TRUE	3	0.70687399961431	6		603	328	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573282	41573282	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	44	743	0	ENST00000263253.7:c.5567C>G	p.Thr1856Arg	p.T1856R	ENST00000263253	NM_001429.3	1856	aCg/aGg	31/31	0.661257656458232	2	FACETS	0.336	0.283	0.396	0.168	0.141	0.198	SUBCLONAL	1	TRUE	0	0.70687399961431	2		743	370	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916860	178916863	+	missense_variant	Missense_Mutation	ONP	TTTG	TTTG	AAGA	novel	NA	P-0032490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	186	672	2	ENST00000263967.3:c.247_250delinsAAGA	p.Phe83_Asp84delinsLysAsn	p.F83_D84delinsKN	ENST00000263967	NM_006218.2	83	TTTGat/AAGAat	2/21	0.70687399961431	5	FACETS	1	0.985	1	0.796	0.743	0.85	CLONAL	2	TRUE	2	0.70687399961431	5		674	454	SUCCESS
APC	324	MSKCC	GRCh37	5	112174840	112174840	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs1561585641	NA	P-0032490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	10	334	0	ENST00000257430.4:c.3549T>G	p.Tyr1183Ter	p.Y1183*	ENST00000257430	NM_000038.5	1183	taT/taG	16/16	0.405157608749287	3	FACETS	0.282	0.191	0.394	0.094	0.063	0.132	INDETERMINATE	1	TRUE	0	0.70687399961431	3		334	136	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577523	7577524	+	protein_altering_variant	In_Frame_Ins	INS	-	-	CAT	novel	NA	P-0032490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	212	637	0	ENST00000269305.4:c.757_758insATG	p.Thr253delinsAsnAla	p.T253delinsNA	ENST00000269305	NM_001126112.2	253	acc/aATGcc	7/11	0.661257656458232	2	FACETS	0.926	0.881	0.969	0.926	0.881	0.969	CLONAL	2	TRUE	0	0.70687399961431	2		637	324	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0032491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	65	531	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.16	2		531	702	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0032491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	22	336	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	0.137148239100903	0	FACETS	0.831	0.645	1			1	CLONAL	1	TRUE	0	0.16	0		336	278	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624301	89624301	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	38	536	0	ENST00000371953.3:c.75del	p.Thr26ProfsTer28	p.T26Pfs*28	ENST00000371953	NM_000314.4	25	ttG/tt	1/9	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.16	2		536	358	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0032492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	272	732	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.382050722735159	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.388749191204065	2		732	678	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0032492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	88	258	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.386815857710701	3	FACETS	0.832	0.744	0.923	0.832	0.744	0.923	CLONAL	2	TRUE	1	0.388749191204065	3		258	325	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634449	23634449	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	63	424	0	ENST00000261584.4:c.2837C>T	p.Ala946Val	p.A946V	ENST00000261584	NM_024675.3	946	gCa/gTa	9/13	0.386815857710701	3	FACETS	1	0.897	1	0.519	0.451	0.592	CLONAL	1	TRUE	1	0.388749191204065	3		424	373	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016126	31016126	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs780099677	NA	P-0032492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	119	635	1	ENST00000375687.4:c.374-2A>G		p.X125_splice	ENST00000375687	NM_015338.5	125			0.388749191204065	6	FACETS	0.985	0.887	1	0.197	0.177	0.218	CLONAL	1	TRUE	1	0.388749191204065	6		636	1105	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0032492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	111	423	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	0.388749191204065	3	FACETS	1	0.983	1	0.729	0.659	0.802	CLONAL	1	TRUE	1	0.388749191204065	3		423	468	SUCCESS
APC	324	MSKCC	GRCh37	5	112175388	112175389	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	54	350	0	ENST00000257430.4:c.4098dup	p.Gln1367SerfsTer8	p.Q1367Sfs*8	ENST00000257430	NM_000038.5	1366	gct/gcTt	16/16	0.386815857710701	3	FACETS	0.885	0.759	1	0.442	0.379	0.511	CLONAL	1	TRUE	1	0.388749191204065	3		350	375	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864361	151864361	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	85	609	0	ENST00000262189.6:c.9620A>C	p.Lys3207Thr	p.K3207T	ENST00000262189	NM_170606.2	3207	aAa/aCa	42/59	0.388749191204065	3	FACETS	0.76	0.672	0.855	0.38	0.336	0.428	SUBCLONAL	1	TRUE	1	0.388749191204065	3		609	687	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0032494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	327	468	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA	2	FACETS	0.97	0.923	1			1	INDETERMINATE	2	TRUE	NA	0.480274413389429	2		468	702	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813333	102813333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs539899150	NA	P-0032494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	205	518	2	ENST00000307046.8:c.356G>A	p.Arg119His	p.R119H	ENST00000307046	NM_001111285.1	119	cGc/cAc	3/4	0.476847779852687	3	FACETS	0.839	0.782	0.897	0.839	0.782	0.897	CLONAL	2	TRUE	1	0.480274413389429	3		520	631	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775601	39775601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146705250	NA	P-0032494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	148	442	0	ENST00000288319.7:c.419G>A	p.Arg140Gln	p.R140Q	ENST00000288319	NM_182918.3	140	cGg/cAg	4/10	0.443697065726608	3	FACETS	0.758	0.697	0.821	0.505	0.465	0.548	SUBCLONAL	2	TRUE	0	0.480274413389429	3		442	504	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433995	49433995	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759516070	NA	P-0032494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	130	638	0	ENST00000301067.7:c.7558C>T	p.Arg2520Trp	p.R2520W	ENST00000301067	NM_003482.3	2520	Cgg/Tgg	31/54	0.480274413389429	4	FACETS	1	0.921	1	0.339	0.307	0.372	CLONAL	1	TRUE	1	0.480274413389429	4		638	789	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737400	145737400	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765087683	NA	P-0032494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	212	674	1	ENST00000428558.2:c.3287G>A	p.Arg1096His	p.R1096H	ENST00000428558	NM_004260.3	1096	cGc/cAc	20/22	0.480274413389429	3	FACETS	1	0.979	1	0.567	0.526	0.608	CLONAL	1	TRUE	1	0.480274413389429	3		675	966	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36989268	36989268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773410433	NA	P-0032494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	81	442	0	ENST00000354822.5:c.67G>A	p.Gly23Ser	p.G23S	ENST00000354822	NM_001079668.2	23	Ggc/Agc	1/3	0.467732795746535	3	FACETS	0.78	0.689	0.878	0.39	0.344	0.439	SUBCLONAL	1	TRUE	1	0.480274413389429	3		442	536	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50810095	50810095	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	75	498	0	ENST00000398568.2:c.919G>T	p.Val307Leu	p.V307L	ENST00000398568	NM_001042412.1	307	Gtg/Ttg	6/18	0.438416834994888	3	FACETS	0.772	0.678	0.872	0.257	0.226	0.291	SUBCLONAL	1	TRUE	0	0.480274413389429	3		498	502	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677779	58677779	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	99	424	0	ENST00000305921.3:c.4G>T	p.Ala2Ser	p.A2S	ENST00000305921	NM_003620.3	2	Gcg/Tcg	1/6	0.429948094723876	4	FACETS	1	0.959	1	0.57	0.511	0.633	CLONAL	1	TRUE	2	0.480274413389429	4		424	535	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467605	66467605	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	146	438	0	ENST00000273854.3:c.664G>T	p.Ala222Ser	p.A222S	ENST00000273854	NM_004439.5	222	Gct/Tct	3/18	0.447827586327834	2	FACETS	0.783	0.723	0.845	0.783	0.723	0.845	SUBCLONAL	2	TRUE	0	0.480274413389429	2		438	388	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389240	8389240	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0032494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	97	549	0	ENST00000356435.5:c.4378A>T	p.Arg1460Ter	p.R1460*	ENST00000356435		1460	Aga/Tga	26/35	0.447827586327834	2	FACETS	0.784	0.702	0.872	0.392	0.351	0.436	SUBCLONAL	1	TRUE	0	0.480274413389429	2		549	515	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265814	16265814	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032499-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	201	615	0	ENST00000375759.3:c.10889del	p.Pro3630ArgfsTer29	p.P3630Rfs*29	ENST00000375759	NM_015001.2	3629	ttC/tt	15/15	0.489811260469791	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.48	1		615	586	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859467	151859488	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTGGCCTGGGCAGGACTCTG	TCTTGGCCTGGGCAGGACTCTG	-	novel	NA	P-0032499-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	160	607	0	ENST00000262189.6:c.11174_11195del	p.Thr3725ArgfsTer13	p.T3725Rfs*13	ENST00000262189	NM_170606.2	3725	aCAGAGTCCTGCCCAGGCCAAGAg/ag	43/59	1	2	FACETS	0.931	0.856	1	0.931	0.856	1	CLONAL	1	TRUE	1	0.48	2		607	716	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	169	264	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.991	0.925	1	1	0.994	1	CLONAL	3	TRUE	1	0.308100650196841	2		264	369	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106562	27106562	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	245	557	0	ENST00000324856.7:c.6176del	p.Asn2059ThrfsTer76	p.N2059Tfs*76	ENST00000324856	NM_006015.4	2058	gAa/ga	20/20	1	2	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	1	0.308100650196841	2		557	677	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0032509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	214	340	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.906751326443313	2		340	471	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913444	NA	P-0032509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10622	949	430	0	ENST00000275493.2:c.2582T>G	p.Leu861Arg	p.L861R	ENST00000275493	NM_005228.3	861	cTg/cGg	21/28	0.906751326443313	29	FACETS	1	0.995	1	0.083	0.079	0.086	CLONAL	2	TRUE	0	0.906751326443313	29		430	11571	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641492	18641492	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	141	316	0	ENST00000266497.5:c.2491G>C	p.Glu831Gln	p.E831Q	ENST00000266497		831	Gag/Cag	17/31	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.906751326443313	2		316	304	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166824	32166824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs544666247	NA	P-0032509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	330	610	0	ENST00000375023.3:c.4414C>T	p.Arg1472Trp	p.R1472W	ENST00000375023	NM_004557.3	1472	Cgg/Tgg	24/30	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.906751326443313	2		610	701	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604697	48604697	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	35	327	0	ENST00000342988.3:c.1519A>G	p.Lys507Glu	p.K507E	ENST00000342988	NM_005359.5	507	Aaa/Gaa	12/12	0.3	1	FACETS	0.805	0.66	0.968	0.805	0.66	0.968	CLONAL	1	TRUE	0	0.19	1		327	414	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970979	21970979	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	95	611	0	ENST00000304494.5:c.379del	p.Ala127HisfsTer19	p.A127Hfs*19	ENST00000304494	NM_000077.4	127	Gca/ca	2/3	0.3	1	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	0	0.19	1		611	901	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0032511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	104	732	0	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.19	2		732	997	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242495	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAGCAACATCTCCGAAAGCC	TTAAGAGAAGCAACATCTCCGAAAGCC	GCAACA	novel	NA	P-0032511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	30	338	1	ENST00000275493.2:c.2239_2265delinsGCAACA	p.Leu747_Ala755delinsAlaThr	p.L747_A755delinsAT	ENST00000275493	NM_005228.3	747	TTAAGAGAAGCAACATCTCCGAAAGCC/GCAACA	19/28	1	2	FACETS	0.651	0.524	0.796	0.651	0.524	0.796	SUBCLONAL	1	TRUE	1	0.19	2		339	485	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509734	106509734	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	85	439	2	ENST00000359195.3:c.1728G>T	p.Trp576Cys	p.W576C	ENST00000359195	NM_002649.2	576	tgG/tgT	2/11	1	2	FACETS	0.751	0.664	0.843	1	0.978	1	SUBCLONAL	2	TRUE	1	0.19	2		441	596	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0032512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	251	607	2	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.293321814900248	2	FACETS	0.964	0.905	1	0.964	0.905	1	CLONAL	2	TRUE	0	0.313215269795856	2		609	831	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284907	15284907	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs551991530	NA	P-0032512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	64	832	0	ENST00000263388.2:c.4708C>T	p.Arg1570Cys	p.R1570C	ENST00000263388	NM_000435.2	1570	Cgt/Tgt	25/33	0.22074422457009	2	FACETS	0.439	0.379	0.505	0.22	0.189	0.253	SUBCLONAL	1	TRUE	0	0.313215269795856	2		832	930	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984897	55984897	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	58	410	0	ENST00000263923.4:c.232G>A	p.Glu78Lys	p.E78K	ENST00000263923	NM_002253.2	78	Gag/Aag	3/30	0.22074422457009	2	FACETS	0.615	0.528	0.71	0.308	0.264	0.355	SUBCLONAL	1	TRUE	0	0.313215269795856	2		410	602	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435493	110435493	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	65	559	1	ENST00000375856.3:c.2908C>T	p.Arg970Trp	p.R970W	ENST00000375856	NM_003749.2	970	Cgg/Tgg	1/2	1	2	FACETS	0.565	0.489	0.647	0.565	0.489	0.647	SUBCLONAL	1	TRUE	1	0.313215269795856	2		560	735	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282681	1282681	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	162	505	0	ENST00000310581.5:c.1632C>G	p.Phe544Leu	p.F544L	ENST00000310581	NM_198253.2	544	ttC/ttG	3/16	0.205718381138029	4	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.313215269795856	4		505	947	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547263	106547263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1317403077	NA	P-0032512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	43	288	0	ENST00000369096.4:c.500C>T	p.Ser167Phe	p.S167F	ENST00000369096	NM_001198.3	167	tCt/tTt	4/7	0.22074422457009	2	FACETS	0.69	0.578	0.813	0.345	0.289	0.407	SUBCLONAL	1	TRUE	0	0.313215269795856	2		288	398	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410005	139410005	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1458	92	903	0	ENST00000277541.6:c.1833del	p.Cys612AlafsTer19	p.C612Afs*19	ENST00000277541	NM_017617.3	611	ccC/cc	11/34	0.308383957257347	4	FACETS	0.498	0.44	0.56	0.124	0.11	0.14	SUBCLONAL	1	TRUE	0	0.313215269795856	4		903	1550	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0032529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	73	251	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.899070557925458	2	FACETS	1	0.976	1	0.634	0.576	0.691	CLONAL	1	TRUE	0	0.899070557925458	2		251	128	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579364	7579376	+	frameshift_variant	Frame_Shift_Del	DEL	CCGTAGCTGCCCT	CCGTAGCTGCCCT	-	novel	NA	P-0032529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	726	689	0	ENST00000269305.4:c.311_323del	p.Gln104LeufsTer15	p.Q104Lfs*15	ENST00000269305	NM_001126112.2	104	cAGGGCAGCTACGGt/ct	4/11	NA	2	FACETS	0.976	0.961	0.991			1	INDETERMINATE	2	TRUE	NA	0.899070557925458	2		689	827	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29422364	29422366	+	inframe_deletion	In_Frame_Del	DEL	GTG	GTG	-	novel	NA	P-0032529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	479	409	0	ENST00000356175.3:c.39_41del	p.Val14del	p.V14del	ENST00000356175	NM_000267.3	13	GTG/-	1/57	0.530162323737602	1	FACETS	1	0.997	1	1	0.997	1	INDETERMINATE	1	TRUE	0	0.899070557925458	1		409	535	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0032531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	428	448	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.785920745675622	5	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	TRUE	2	0.785920745675622	5		449	782	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0032531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	293	369	3	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	0.785920745675622	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.785920745675622	2		372	366	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577575	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587782289	NA	P-0032531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	439	627	10	ENST00000269305.4:c.706T>A	p.Tyr236Asn	p.Y236N	ENST00000269305	NM_001126112.2	236	Tac/Aac	7/11	0.781057384703686	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.785920745675622	2		637	550	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484075	50484076	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0032531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	424	674	5	ENST00000394963.4:c.928dup	p.Gln310ProfsTer15	p.Q310Pfs*15	ENST00000394963	NM_003076.4	309	acc/aCcc	8/13	0.769382489658639	3	FACETS	0.905	0.869	0.942	0.905	0.869	0.942	CLONAL	2	TRUE	1	0.785920745675622	3		679	830	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644524	3644524	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs554989399	NA	P-0032531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	326	752	7	ENST00000294008.3:c.2090C>T	p.Thr697Met	p.T697M	ENST00000294008	NM_032444.2	697	aCg/aTg	10/15	0.78144445001295	4	FACETS	1	0.992	1	0.642	0.607	0.679	CLONAL	1	TRUE	2	0.785920745675622	4		759	1153	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349548	70349548	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	164	550	0	ENST00000374080.3:c.3710G>T	p.Gly1237Val	p.G1237V	ENST00000374080		1237	gGt/gTt	27/45	0.647451227299146	4	FACETS	1	0.942	1			1	CLONAL	1	TRUE	NA	0.785920745675622	4		550	724	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0032535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	68	582	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	0.937	1	CLONAL	1	TRUE	1	0.17	2		582	706	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	42	474	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.809	0.674	0.959	0.809	0.674	0.959	CLONAL	1	TRUE	1	0.17	2		474	611	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0032535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	19	428	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	0.616	0.467	0.792	0.616	0.467	0.792	SUBCLONAL	1	TRUE	1	0.17	2		428	363	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0032543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	650	586	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.706302271419749	11	FACETS	0.918	0.884	0.952			1	CLONAL	5	TRUE	NA	0.706302271419749	11		586	1676	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0032543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	1440	589	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.706302271419749	7	FACETS	0.991	0.98	1			1	CLONAL	7	TRUE	NA	0.706302271419749	7		589	1626	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847399	68847399	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0032544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	180	522	0	ENST00000261769.5:c.1320+1G>T		p.X440_splice	ENST00000261769	NM_004360.3	440			0.551358288575629	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.551358288575629	1		522	456	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0032544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	125	285	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.945	0.86	1	0.945	0.86	1	CLONAL	1	TRUE	1	0.551358288575629	2		285	480	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043464	180043464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	107	694	1	ENST00000261937.6:c.3122G>A	p.Arg1041Gln	p.R1041Q	ENST00000261937	NM_182925.4	1041	cGg/cAg	23/30	1	2	FACETS	0.472	0.423	0.524	0.472	0.423	0.524	SUBCLONAL	1	TRUE	1	0.551358288575629	2		695	823	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778597	3778597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1361732490	NA	P-0032544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	187	693	1	ENST00000262367.5:c.6451C>T	p.Arg2151Trp	p.R2151W	ENST00000262367	NM_004380.2	2151	Cgg/Tgg	31/31	0.50867769765652	3	FACETS	0.967	0.894	1	0.483	0.447	0.522	CLONAL	1	TRUE	1	0.551358288575629	3		694	895	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100690	67100690	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	247	655	0	ENST00000412916.2:c.388G>T	p.Glu130Ter	p.E130*	ENST00000412916		130	Gag/Tag	4/6	0.551358288575629	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.551358288575629	1		655	635	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284972	15284972	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	229	688	0	ENST00000263388.2:c.4643A>T	p.Asp1548Val	p.D1548V	ENST00000263388	NM_000435.2	1548	gAc/gTc	25/33	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.551358288575629	2		688	735	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397811	49397811	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	165	407	1	ENST00000418115.1:c.413C>T	p.Pro138Leu	p.P138L	ENST00000418115	NM_001664.2	138	cCg/cTg	5/5	1	2	FACETS	0.968	0.893	1	0.968	0.893	1	CLONAL	1	TRUE	1	0.551358288575629	2		408	618	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157431696	157431696	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0032544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	45	533	0	ENST00000346085.5:c.2371+1G>T		p.X791_splice	ENST00000346085	NM_020732.3	791			1	2	FACETS	0.264	0.221	0.312	0.264	0.221	0.312	SUBCLONAL	1	TRUE	1	0.551358288575629	2		533	618	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938996	76938997	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0032544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	74	758	0	ENST00000373344.5:c.1751_1752del	p.Lys584ArgfsTer5	p.K584Rfs*5	ENST00000373344	NM_000489.3	584	aAA/a	9/35	1	2	FACETS	0.444	0.388	0.503	0.444	0.388	0.503	SUBCLONAL	1	TRUE	1	0.551358288575629	2		758	605	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0032545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	104	602	0	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	0.287351501535569	1	FACETS	0.795	0.717	0.875	1	0.985	1	SUBCLONAL	2	TRUE	0	0.287351501535569	1		602	390	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671650	67671650	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	48	468	1	ENST00000264010.4:c.2059G>A	p.Glu687Lys	p.E687K	ENST00000264010	NM_006565.3	687	Gaa/Aaa	12/12	0.286080585094039	2	FACETS	1	0.889	1	0.529	0.449	0.615	CLONAL	1	TRUE	0	0.287351501535569	2		469	316	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197399	26197399	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	20	368	1	ENST00000356476.2:c.80G>T	p.Arg27Leu	p.R27L	ENST00000356476		27	cGa/cTa	1/1	0.287351501535569	4	FACETS	0.61	0.466	0.777	0.305	0.233	0.389	SUBCLONAL	1	TRUE	2	0.287351501535569	4		369	294	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680662	88680662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	34	595	1	ENST00000360948.2:c.595C>T	p.Leu199Phe	p.L199F	ENST00000360948	NM_001012338.2	199	Ctc/Ttc	6/19	0.25493096541488	4	FACETS	0.696	0.568	0.839	0.232	0.189	0.28	SUBCLONAL	1	TRUE	1	0.287351501535569	4		596	438	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373751	118373751	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	23	421	0	ENST00000534358.1:c.7144C>G	p.Arg2382Gly	p.R2382G	ENST00000534358	NM_005933.3	2382	Cga/Gga	27/36	0.287351501535569	3	FACETS	0.509	0.396	0.639	0.254	0.198	0.32	SUBCLONAL	1	TRUE	1	0.287351501535569	3		421	360	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373911	118373911	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs76721917	NA	P-0032545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	17	338	0	ENST00000534358.1:c.7304C>G	p.Ser2435Cys	p.S2435C	ENST00000534358	NM_005933.3	2435	tCc/tGc	27/36	0.287351501535569	3	FACETS	0.562	0.419	0.73	0.281	0.209	0.365	SUBCLONAL	1	TRUE	1	0.287351501535569	3		338	241	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066841	30066841	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	42	622	1	ENST00000331968.5:c.2290C>G	p.Leu764Val	p.L764V	ENST00000331968	NM_002742.2	764	Cta/Gta	16/18	0.287351501535569	3	FACETS	0.732	0.611	0.865	0.244	0.203	0.289	SUBCLONAL	1	TRUE	0	0.287351501535569	3		623	457	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72866434	72866434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	28	454	1	ENST00000325599.8:c.829G>A	p.Asp277Asn	p.D277N	ENST00000325599	NM_018130.2	277	Gat/Aat	7/11	0.287351501535569	3	FACETS	0.612	0.489	0.752	0.306	0.244	0.376	SUBCLONAL	1	TRUE	1	0.287351501535569	3		455	364	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374892	149374892	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	28	368	0	ENST00000360632.3:c.202G>T	p.Asp68Tyr	p.D68Y	ENST00000360632	NM_015472.4	68	Gac/Tac	2/7	0.287351501535569	3	FACETS	0.771	0.618	0.945	0.386	0.309	0.473	CLONAL	1	TRUE	1	0.287351501535569	3		368	289	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957529	1957529	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	79	759	0	ENST00000382891.5:c.2628G>C	p.Lys876Asn	p.K876N	ENST00000382891	NM_133335.3	876	aaG/aaC	14/22	0.287351501535569	3	FACETS	1	0.959	1	0.602	0.531	0.679	CLONAL	1	TRUE	1	0.287351501535569	3		759	522	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637697	176637697	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	26	613	0	ENST00000439151.2:c.2297C>G	p.Ser766Trp	p.S766W	ENST00000439151	NM_022455.4	766	tCg/tGg	5/23	1	2	FACETS	0.433	0.342	0.537	0.433	0.342	0.537	SUBCLONAL	1	TRUE	1	0.287351501535569	2		613	418	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37141799	37141799	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	36	524	0	ENST00000373509.5:c.874G>C	p.Asp292His	p.D292H	ENST00000373509	NM_002648.3	292	Gat/Cat	6/6	0.287351501535569	5	FACETS	0.554	0.454	0.667	0.185	0.151	0.223	SUBCLONAL	1	TRUE	2	0.287351501535569	5		524	647	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975372	13975372	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761565850	NA	P-0032545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	24	476	0	ENST00000405192.2:c.515C>T	p.Ser172Leu	p.S172L	ENST00000405192	NM_001163147.1	172	tCg/tTg	7/12	0.201488276035574	4	FACETS	0.539	0.422	0.674	0.269	0.211	0.337	SUBCLONAL	1	TRUE	2	0.287351501535569	4		476	399	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240810	55240810	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	88	797	1	ENST00000275493.2:c.2054A>G	p.Glu685Gly	p.E685G	ENST00000275493	NM_005228.3	685	gAg/gGg	17/28	0.201488276035574	4	FACETS	0.764	0.679	0.854	0.764	0.679	0.854	SUBCLONAL	2	TRUE	2	0.287351501535569	4		798	516	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509089	106509089	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs746626966	NA	P-0032545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	26	529	0	ENST00000359195.3:c.1083C>A	p.Phe361Leu	p.F361L	ENST00000359195	NM_002649.2	361	ttC/ttA	2/11	0.287351501535569	3	FACETS	0.521	0.412	0.646	0.261	0.206	0.323	SUBCLONAL	1	TRUE	1	0.287351501535569	3		529	397	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157960	27157960	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	21	574	0	ENST00000380036.4:c.184G>C	p.Glu62Gln	p.E62Q	ENST00000380036	NM_000459.3	62	Gaa/Caa	2/23	0.286080585094039	2	FACETS	0.426	0.328	0.541	0.213	0.164	0.271	SUBCLONAL	1	TRUE	0	0.287351501535569	2		574	343	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030547	47030547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1489483300	NA	P-0032545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	31	659	0	ENST00000377604.3:c.322C>T	p.Arg108Trp	p.R108W	ENST00000377604	NM_001204468.1	108	Cgg/Tgg	4/24	0.286080585094039	2	FACETS	0.574	0.464	0.698	0.287	0.232	0.349	SUBCLONAL	1	TRUE	0	0.287351501535569	2		659	376	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0032569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	50	400	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.44713754081153	3	FACETS	0.393	0.332	0.459	0.196	0.166	0.23	SUBCLONAL	1	TRUE	1	0.44713754081153	3		400	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0032569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	276	782	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.445658650179047	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.44713754081153	2		784	583	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555216	226555216	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374662166	NA	P-0032569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	45	508	1	ENST00000366794.5:c.2371G>A	p.Asp791Asn	p.D791N	ENST00000366794	NM_001618.3	791	Gat/Aat	17/23	0.105156013865773	6	FACETS	0.488	0.409	0.576	0.163	0.136	0.192	INDETERMINATE	1	TRUE	3	0.44713754081153	6		509	781	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436026	56436026	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771831816	NA	P-0032569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	135	431	0	ENST00000407977.2:c.1111C>T	p.Arg371Ter	p.R371*	ENST00000407977		371	Cga/Tga	9/10	0.44713754081153	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	0	0.44713754081153	2		431	302	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161398	55161398	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752633017	NA	P-0032569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	245	443	0	ENST00000257290.5:c.3229G>A	p.Gly1077Ser	p.G1077S	ENST00000257290	NM_006206.4	1077	Ggc/Agc	23/23	0.44713754081153	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.44713754081153	2		443	486	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012660	36012660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	70	149	0	ENST00000358208.4:c.104C>T	p.Ser35Leu	p.S35L	ENST00000358208		35	tCg/tTg	2/12	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.701434709162504	2		149	185	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36823931	36823931	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747619342	NA	P-0032573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	304	749	0	ENST00000373129.3:c.251G>A	p.Arg84Gln	p.R84Q	ENST00000373129	NM_032017.1	84	cGg/cAg	5/12	1	2	FACETS	0.992	0.938	1	0.992	0.938	1	CLONAL	1	TRUE	1	0.701434709162504	2		749	874	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427962	49427962	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763174410	NA	P-0032573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	282	791	0	ENST00000301067.7:c.10628G>T	p.Cys3543Phe	p.C3543F	ENST00000301067	NM_003482.3	3543	tGt/tTt	38/54	1	2	FACETS	0.926	0.873	0.981	0.926	0.873	0.981	CLONAL	1	TRUE	1	0.701434709162504	2		791	868	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929322	44929325	+	frameshift_variant	Frame_Shift_Del	DEL	CATA	CATA	-	novel	NA	P-0032588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	907	382	0	ENST00000377967.4:c.2424_2427del	p.His808GlnfsTer58	p.H808Qfs*58	ENST00000377967	NM_021140.2	808	CATAca/ca	17/29	0.762520533510423	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.794039678653078	2		382	1073	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43783895	43783895	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	404	700	1	ENST00000382044.4:c.343C>T	p.Gln115Ter	p.Q115*	ENST00000382044	NM_001141980.1	115	Cag/Tag	4/28	0.794039678653078	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.794039678653078	1		701	611	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588949	67588949	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	157	326	0	ENST00000274335.5:c.1040T>C	p.Leu347Pro	p.L347P	ENST00000274335		347	cTt/cCt	8/15	0.794039678653078	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.794039678653078	1		326	221	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578250	7578274	+	protein_altering_variant	In_Frame_Del	DEL	TTTCCTTCCACTCGGATAAGATGCT	TTTCCTTCCACTCGGATAAGATGCT	G	novel	NA	P-0032588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	478	792	0	ENST00000269305.4:c.575_599delinsC	p.Gln192_Asn200delinsPro	p.Q192_N200delinsP	ENST00000269305	NM_001126112.2	192	cAGCATCTTATCCGAGTGGAAGGAAAt/cCt	6/11	0.794039678653078	1	FACETS	0.985	0.953	1	0.985	0.953	1	CLONAL	1	TRUE	0	0.794039678653078	1		792	737	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	117	264	0				ENST00000310581	NM_198253.2	-/1132			0.348153319932279	6	FACETS	1	0.977	1	0.622	0.565	0.682	CLONAL	2	TRUE	2	0.348153319932279	6		264	458	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658294	18658294	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	48	588	0	ENST00000266497.5:c.3100del	p.Arg1034ValfsTer8	p.R1034Vfs*8	ENST00000266497		1033	gaC/ga	22/31	0.348153319932279	3	FACETS	0.843	0.715	0.984	0.422	0.357	0.492	CLONAL	1	TRUE	1	0.348153319932279	3		588	384	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039457	49039457	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1566237790	NA	P-0032595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	200	547	0	ENST00000267163.4:c.2442A>C	p.Lys814Asn	p.K814N	ENST00000267163	NM_000321.2	814	aaA/aaC	23/27	1	2	FACETS	0.868	0.815	0.923	1	0.995	1	CLONAL	3	TRUE	1	0.348153319932279	2		547	441	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183871	10183871	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	13	526	0	ENST00000256474.2:c.340G>T	p.Gly114Cys	p.G114C	ENST00000256474	NM_000551.3	114	Ggt/Tgt	1/3	0.135132723772869	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		526	214	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873789	151873789	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs752041568	NA	P-0032596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	28	581	0	ENST00000262189.6:c.8749G>C	p.Val2917Leu	p.V2917L	ENST00000262189	NM_170606.2	2917	Gtt/Ctt	38/59	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		581	312	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183769	10183769	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs786202787	NA	P-0032596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	54	722	0	ENST00000256474.2:c.238A>C	p.Ser80Arg	p.S80R	ENST00000256474	NM_000551.3	80	Agt/Cgt	1/3	0.252403134778878	2	FACETS	1	0.939	1	0.585	0.504	0.673	CLONAL	1	TRUE	0	0.32719535550036	2		722	282	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562190	176562190	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	74	785	0	ENST00000439151.2:c.86del	p.Asp29AlafsTer53	p.D29Afs*53	ENST00000439151	NM_022455.4	29	gAc/gc	2/23	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.32719535550036	2		785	394	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624275	89624275	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204910	NA	P-0032601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	37	390	1	ENST00000371953.3:c.49C>T	p.Gln17Ter	p.Q17*	ENST00000371953	NM_000314.4	17	Caa/Taa	1/9	1	2	FACETS	0.673	0.556	0.802	0.673	0.556	0.802	SUBCLONAL	1	TRUE	1	0.338447367474758	2		391	325	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78435689	78435690	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	C	novel	NA	P-0032601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	16	390	0	ENST00000370768.2:c.130_131delinsG	p.Lys44GlufsTer10	p.K44Efs*10	ENST00000370768	NM_003902.3	44	AAa/Ga	2/20	1	2	FACETS	0.936	0.702	1	0.936	0.702	1	CLONAL	1	TRUE	1	0.338447367474758	2		390	101	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577500	7577503	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	TGGA	TGGA	ACACAC	novel	NA	P-0032603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	177	678	6	ENST00000269305.4:c.778_781delinsGTGTGT	p.Ser260ValfsTer86	p.S260Vfs*86	ENST00000269305	NM_001126112.2	260	TCCAgt/GTGTGTgt	7/11	0.332558292127032	1	FACETS	0.915	0.843	0.99	0.915	0.843	0.99	CLONAL	1	TRUE	0	0.332558292127032	1		684	970	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427664	49427665	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCTGC	novel	NA	P-0032604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	138	709	0	ENST00000301067.7:c.10818_10823dup	p.Gln3611_Gln3612dup	p.Q3611_Q3612dup	ENST00000301067	NM_003482.3	3611	caa/caGCAGCAa	39/54	0.407430284452869	2	FACETS	1	0.985	1	0.68	0.623	0.739	CLONAL	1	TRUE	0	0.419316391006046	2		709	484	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221448	36221448	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	60	923	0	ENST00000222270.7:c.5207G>T	p.Arg1736Leu	p.R1736L	ENST00000222270	NM_014727.1	1736	cGc/cTc	25/37	0.134519878621205	3	FACETS	0.549	0.472	0.632	0.183	0.157	0.211	INDETERMINATE	1	TRUE	0	0.419316391006046	3		923	631	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137528131	137528131	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	33	333	0	ENST00000367739.4:c.169C>A	p.Pro57Thr	p.P57T	ENST00000367739	NM_000416.2	57	Cct/Act	2/7	0.0708322329808593	3	FACETS	0.835	0.685	1			1	INDETERMINATE	1	TRUE	NA	0.419316391006046	3		333	228	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517910	8517910	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	52	435	0	ENST00000356435.5:c.1481C>A	p.Ala494Asp	p.A494D	ENST00000356435		494	gCt/gAt	10/35	0.419316391006046	1	FACETS	0.674	0.577	0.778	0.674	0.577	0.778	SUBCLONAL	1	TRUE	0	0.419316391006046	1		435	291	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27217757	27217757	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0032604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	59	697	1	ENST00000380036.4:c.3062+1G>A		p.X1021_splice	ENST00000380036	NM_000459.3	1021			0.419316391006046	1	FACETS	0.65	0.563	0.745	0.65	0.563	0.745	SUBCLONAL	1	TRUE	0	0.419316391006046	1		698	342	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0032605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	206	157	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.853	0.803	0.902	1	0.994	1	CLONAL	2	TRUE	1	0.594999868217919	2		157	406	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591132	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	rs1057519842	NA	P-0032605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	111	92	0	ENST00000274335.5:c.1727_1729del	p.Thr576del	p.T576del	ENST00000274335		575	aaGACg/aag	12/15	0.594999868217919	4	FACETS	1	0.982	1	0.461	0.417	0.507	CLONAL	1	TRUE	1	0.594999868217919	4		92	430	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105892	27105892	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	363	508	0	ENST00000324856.7:c.5503C>T	p.Gln1835Ter	p.Q1835*	ENST00000324856	NM_006015.4	1835	Cag/Tag	20/20	1	2	FACETS	0.828	0.791	0.865	1	0.996	1	CLONAL	2	TRUE	1	0.594999868217919	2		508	737	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023968	27024010	+	frameshift_variant	Frame_Shift_Del	DEL	CCACGCGCCCATGAGCCCCGGGAGCAGCGGCGGCGGGGGGCAG	CCACGCGCCCATGAGCCCCGGGAGCAGCGGCGGCGGGGGGCAG	-	novel	NA	P-0032605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	30	68	0	ENST00000324856.7:c.1076_1118del	p.His359ArgfsTer18	p.H359Rfs*18	ENST00000324856	NM_006015.4	358	caCCACGCGCCCATGAGCCCCGGGAGCAGCGGCGGCGGGGGGCAG/ca	1/20	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.594999868217919	2		68	95	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692922	89692922	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	495	174	0	ENST00000371953.3:c.406del	p.Cys136ValfsTer11	p.C136Vfs*11	ENST00000371953	NM_000314.4	136	Tgt/gt	5/9	0.594999868217919	2	FACETS	1	0.997	1	1	0.998	1	CLONAL	3	TRUE	0	0.594999868217919	2		174	516	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410678	32410678	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	310	389	0	ENST00000332351.3:c.1480G>T	p.Ala494Ser	p.A494S	ENST00000332351	NM_024426.4	494	Gcc/Tcc	10/10	1	2	FACETS	0.797	0.758	0.836	1	0.995	1	SUBCLONAL	2	TRUE	1	0.594999868217919	2		389	654	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593368	67593368	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	341	159	0	ENST00000274335.5:c.2114A>C	p.Gln705Pro	p.Q705P	ENST00000274335		705	cAg/cCg	15/15	0.594999868217919	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	1	0.594999868217919	4		159	523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0032607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	350	623	0	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	0.678758110406852	3	FACETS	0.928	0.898	0.956	0.928	0.898	0.956	CLONAL	3	TRUE	0	0.743720318748201	3		623	464	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522274	157522274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567836947	NA	P-0032607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	224	652	0	ENST00000346085.5:c.4546G>A	p.Val1516Ile	p.V1516I	ENST00000346085	NM_020732.3	1516	Gtc/Atc	18/20	0.71322718309106	2	FACETS	0.801	0.76	0.841	0.801	0.76	0.841	CLONAL	2	TRUE	0	0.743720318748201	2		652	376	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582030	189582030	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	99	353	0	ENST00000264731.3:c.589G>A	p.Glu197Lys	p.E197K	ENST00000264731	NM_003722.4	197	Gaa/Aaa	5/14	0.372897207607428	5	FACETS	1	0.982	1	0.491	0.442	0.543	INDETERMINATE	1	TRUE	2	0.743720318748201	5		353	382	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038881	12038881	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	35	283	0	ENST00000396373.4:c.1174G>C	p.Glu392Gln	p.E392Q	ENST00000396373	NM_001987.4	392	Gag/Cag	7/8	0.743720318748201	4	FACETS	0.38	0.311	0.457	0.127	0.103	0.153	SUBCLONAL	1	TRUE	1	0.743720318748201	4		283	432	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416417	49416417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565753611	NA	P-0032607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	151	615	1	ENST00000301067.7:c.16294C>T	p.Arg5432Trp	p.R5432W	ENST00000301067	NM_003482.3	5432	Cgg/Tgg	51/54	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.743720318748201	2		616	355	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443761	52443761	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0032607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	294	548	1	ENST00000460680.1:c.38-2A>G		p.X13_splice	ENST00000460680	NM_004656.3	13			0.71322718309106	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.743720318748201	2		549	392	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286516	33286536	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	GCAGCTAATCAGAGTCTGAGA	GCAGCTAATCAGAGTCTGAGA	-	novel	NA	P-0032607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	166	333	0	ENST00000374542.5:c.2207_*4del		p.*736*	ENST00000374542	NM_001141970.1	736		8/8	0.743720318748201	4	FACETS	1	0.931	1	0.667	0.621	0.714	CLONAL	2	TRUE	1	0.743720318748201	4		333	389	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389335	8389335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	161	725	0	ENST00000356435.5:c.4283C>T	p.Thr1428Ile	p.T1428I	ENST00000356435		1428	aCa/aTa	26/35	0.442984690119721	3	FACETS	1	0.987	1	0.443	0.41	0.477	INDETERMINATE	1	TRUE	0	0.743720318748201	3		725	447	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436624	8436624	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	130	601	0	ENST00000356435.5:c.4054A>C	p.Asn1352His	p.N1352H	ENST00000356435		1352	Aat/Cat	24/35	0.442984690119721	3	FACETS	1	0.979	1	0.408	0.373	0.443	INDETERMINATE	1	TRUE	0	0.743720318748201	3		601	392	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44894177	44894201	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	ATTTTCAGTTAGCTTTGGTTGACTG	ATTTTCAGTTAGCTTTGGTTGACTG	-	novel	NA	P-0032607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	77	642	0	ENST00000377967.4:c.566_590del	p.His189LeufsTer45	p.H189Lfs*45	ENST00000377967	NM_021140.2	189	cATTTTCAGTTAGCTTTGGTTGACTGt/ct	7/29	0.743720318748201	1	FACETS	0.891	0.808	0.973	0.891	0.808	0.973	CLONAL	1	TRUE	0	0.743720318748201	1		642	146	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	391	441	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.616845583632387	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	FALSE	1	0.616845583632387	3		441	676	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860619	45860619	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	28	826	0	ENST00000391945.4:c.1388C>T	p.Pro463Leu	p.P463L	ENST00000391945	NM_000400.3	463	cCg/cTg	15/23	0.37853057471566	4	FACETS	0.56	0.449	0.686			1	SUBCLONAL	1	FALSE	NA	0.616845583632387	4		826	262	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231383	98231383	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764218645	NA	P-0032608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	60	702	0	ENST00000331920.6:c.1900C>T	p.His634Tyr	p.H634Y	ENST00000331920	NM_000264.3	634	Cac/Tac	14/24	0.270002790981745	1	FACETS	0.549	0.478	0.624	0.549	0.478	0.624	INDETERMINATE	1	FALSE	0	0.616845583632387	1		702	245	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692792	89692792	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	115	435	0	ENST00000371953.3:c.277del	p.His93IlefsTer6	p.H93Ifs*6	ENST00000371953	NM_000314.4	92	gaC/ga	5/9	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.616845583632387	2		435	308	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922072	39922075	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	novel	NA	P-0032608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	61	792	0	ENST00000378444.4:c.4097_4100del	p.Lys1366ThrfsTer2	p.K1366Tfs*2	ENST00000378444	NM_001123385.1	1366	aAACAc/ac	9/15	0.593165997074697	1	FACETS	0.795	0.7	0.894	0.795	0.7	0.894	SUBCLONAL	1	FALSE	0	0.616845583632387	1		792	172	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922115	39922119	+	frameshift_variant	Frame_Shift_Del	DEL	TGTCG	TGTCG	-	novel	NA	P-0032608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	22	835	0	ENST00000378444.4:c.4053_4057del	p.Asp1352GlnfsTer55	p.D1352Qfs*55	ENST00000378444	NM_001123385.1	1351	acCGACAac/acac	9/15	0.593165997074697	1	FACETS	0.314	0.245	0.392	0.314	0.245	0.392	SUBCLONAL	1	FALSE	0	0.616845583632387	1		835	157	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412200	63412200	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	48	969	0	ENST00000330258.3:c.967G>C	p.Asp323His	p.D323H	ENST00000330258	NM_152424.3	323	Gat/Cat	2/2	0.593165997074697	1	FACETS	0.797	0.69	0.908	0.797	0.69	0.908	CLONAL	1	FALSE	0	0.616845583632387	1		969	135	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0032609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	160	280	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.370532397536624	1	FACETS	0.629	0.587	0.671	0.629	0.587	0.671	INDETERMINATE	1	TRUE	0	0.875053855614167	1		280	327	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794800	120794800	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	588	859	1	ENST00000257552.2:c.557C>T	p.Pro186Leu	p.P186L	ENST00000257552	NM_002442.3	186	cCa/cTa	9/15	1	2	FACETS	0.955	0.919	0.991	0.955	0.919	0.991	CLONAL	1	TRUE	1	0.875053855614167	2		860	1407	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449790	149449790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	412	592	1	ENST00000286301.3:c.1274C>T	p.Pro425Leu	p.P425L	ENST00000286301	NM_005211.3	425	cCc/cTc	9/22	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.875053855614167	2		593	934	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549481	187549481	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	17	479	0	ENST00000441802.2:c.4637C>A	p.Ala1546Glu	p.A1546E	ENST00000441802	NM_005245.3	1546	gCa/gAa	9/27	1	2	FACETS	0.166	0.123	0.216	0.166	0.123	0.216	SUBCLONAL	1	TRUE	1	0.65607926662697	2		479	313	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015676	112015676	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	51	470	0	ENST00000368678.4:c.1166G>T	p.Arg389Leu	p.R389L	ENST00000368678		389	cGa/cTa	11/13	0.65607926662697	3	FACETS	0.765	0.655	0.883	0.382	0.327	0.442	SUBCLONAL	1	TRUE	1	0.65607926662697	3		470	270	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0032612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	223	688	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.26542618023934	2	FACETS	0.817	0.762	0.873	0.817	0.762	0.873	CLONAL	2	TRUE	0	0.335506398616816	2		688	814	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0032612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	39	258	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.605	0.502	0.72	0.605	0.502	0.72	SUBCLONAL	1	TRUE	1	0.335506398616816	2		258	384	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0032612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	75	196	2	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.676	0.593	0.767	0.676	0.593	0.767	SUBCLONAL	1	TRUE	1	0.335506398616816	2		198	661	SUCCESS
APC	324	MSKCC	GRCh37	5	112175198	112175198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	26	216	0	ENST00000257430.4:c.3907C>T	p.Gln1303Ter	p.Q1303*	ENST00000257430	NM_000038.5	1303	Caa/Taa	16/16	1	2	FACETS	0.654	0.52	0.806	0.654	0.52	0.806	SUBCLONAL	1	TRUE	1	0.335506398616816	2		216	237	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31025008	31025008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150119795	NA	P-0032612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	341	567	0	ENST00000375687.4:c.4493C>T	p.Thr1498Met	p.T1498M	ENST00000375687	NM_015338.5	1498	aCg/aTg	13/13	0.335506398616816	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	1	0.335506398616816	4		567	838	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829895	72829895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	111	737	0	ENST00000268489.5:c.6686C>T	p.Pro2229Leu	p.P2229L	ENST00000268489	NM_006885.3	2229	cCt/cTt	9/10	1	2	FACETS	0.891	0.801	0.985	0.891	0.801	0.985	CLONAL	1	TRUE	1	0.335506398616816	2		737	743	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682173	37682173	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	181	597	0	ENST00000447079.4:c.3364C>A	p.Leu1122Met	p.L1122M	ENST00000447079	NM_015083.1	1122	Ctg/Atg	13/14	0.107758821727178	4	FACETS	0.84	0.775	0.907			1	INDETERMINATE	2	TRUE	NA	0.335506398616816	4		597	858	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910785	29910785	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs45572937	NA	P-0032612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	80	738	0	ENST00000376809.5:c.325T>A	p.Tyr109Asn	p.Y109N	ENST00000376809	NM_002116.7	109	Tac/Aac	2/8	0.282240903869039	3	FACETS	0.697	0.613	0.788	0.348	0.306	0.394	SUBCLONAL	1	TRUE	1	0.335506398616816	3		738	799	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852272	128852272	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	142	736	0	ENST00000249373.3:c.2344G>T	p.Asp782Tyr	p.D782Y	ENST00000249373	NM_005631.4	782	Gat/Tat	12/12	0.105473475121012	4	FACETS	0.793	0.724	0.865	0.793	0.724	0.865	INDETERMINATE	2	TRUE	2	0.335506398616816	4		736	713	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044952	47044952	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	167	477	1	ENST00000377604.3:c.2278G>T	p.Ala760Ser	p.A760S	ENST00000377604	NM_001204468.1	760	Gcc/Tcc	20/24	0.0975861907103068	2	FACETS	1	0.97	1			1	INDETERMINATE	2	TRUE	NA	0.335506398616816	2		478	458	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0032614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	18	503	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.787	1	1	0.787	1	CLONAL	1	TRUE	1	0.172072707391687	2		503	200	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0032614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	10	483	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.646	0.438	0.907	0.646	0.438	0.907	SUBCLONAL	1	TRUE	1	0.172072707391687	2		483	180	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337314	89337314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	24	393	0	ENST00000301030.4:c.7717G>A	p.Asp2573Asn	p.D2573N	ENST00000301030	NM_001256183.1	2573	Gac/Aac	12/13	1	2	FACETS	0.633	0.495	0.792	0.633	0.495	0.792	SUBCLONAL	1	TRUE	1	0.172072707391687	2		393	441	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564633	86564633	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	36	609	0	ENST00000274376.6:c.365C>A	p.Ser122Ter	p.S122*	ENST00000274376	NM_002890.2	122	tCg/tAg	1/25	1	2	FACETS	0.61	0.5	0.734	0.61	0.5	0.734	SUBCLONAL	1	TRUE	1	0.172072707391687	2		609	686	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533772	41533772	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853038	NA	P-0032614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	20	420	0	ENST00000263253.7:c.1738C>T	p.Arg580Ter	p.R580*	ENST00000263253	NM_001429.3	580	Cga/Tga	8/31	1	2	FACETS	0.609	0.465	0.778	0.609	0.465	0.778	SUBCLONAL	1	TRUE	1	0.172072707391687	2		420	382	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41011095	41011095	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	34	458	0	ENST00000267868.3:c.528G>C	p.Glu176Asp	p.E176D	ENST00000267868	NM_002875.4	176	gaG/gaC	6/10	1	2	FACETS	0.776	0.634	0.938	0.776	0.634	0.938	CLONAL	1	TRUE	1	0.172072707391687	2		458	509	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611758	1611758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	48	649	0	ENST00000344749.5:c.1904C>T	p.Ser635Leu	p.S635L	ENST00000344749	NM_001136139.2	635	tCa/tTa	19/19	1	2	FACETS	0.798	0.673	0.936	0.798	0.673	0.936	CLONAL	1	TRUE	1	0.172072707391687	2		649	699	SUCCESS
ATM	472	MSKCC	GRCh37	11	108168092	108168092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	26	294	0	ENST00000278616.4:c.4988G>A	p.Gly1663Asp	p.G1663D	ENST00000278616	NM_000051.3	1663	gGt/gAt	33/63	0.172072707391687	2	FACETS	0.783	0.625	0.962	0.783	0.625	0.962	CLONAL	2	TRUE	0	0.172072707391687	2		294	193	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666374	206666374	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	40	535	1	ENST00000367120.3:c.1854G>T	p.Arg618Ser	p.R618S	ENST00000367120	NM_014002.3	618	agG/agT	19/22	1		FACETS		0.564	0.811				SUBCLONAL	1	TRUE	1	0.172072707391687	2		536	683	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066809	77066809	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	52	388	0	ENST00000356341.3:c.676G>A	p.Glu226Lys	p.E226K	ENST00000356341	NM_002576.4	226	Gaa/Aaa	7/15	0.172072707391687	2	FACETS	1	0.963	1	0.73	0.623	0.847	CLONAL	1	TRUE	0	0.172072707391687	2		388	414	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	464338	464338	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	40	598	0	ENST00000399788.2:c.856C>G	p.Leu286Val	p.L286V	ENST00000399788	NM_001042603.1	286	Ctc/Gtc	7/28	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.172072707391687	2		598	389	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916825	48916825	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	25	349	0	ENST00000267163.4:c.355G>T	p.Glu119Ter	p.E119*	ENST00000267163	NM_000321.2	119	Gag/Tag	3/27	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.172072707391687	2		349	208	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068864	30068864	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	11	489	0	ENST00000331968.5:c.2065C>T	p.Gln689Ter	p.Q689*	ENST00000331968	NM_002742.2	689	Cag/Tag	14/18	1	2	FACETS	0.618	0.427	0.855	0.618	0.427	0.855	SUBCLONAL	1	TRUE	1	0.172072707391687	2		489	207	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133764	2133764	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1064793797	NA	P-0032614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	37	681	0	ENST00000219476.3:c.3952G>T	p.Glu1318Ter	p.E1318*	ENST00000219476	NM_000548.3	1318	Gag/Tag	33/42	1	2	FACETS	0.673	0.553	0.807	0.673	0.553	0.807	SUBCLONAL	1	TRUE	1	0.172072707391687	2		681	639	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647331	23647331	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	33	582	0	ENST00000261584.4:c.536A>G	p.Gln179Arg	p.Q179R	ENST00000261584	NM_024675.3	179	cAg/cGg	4/13	1	2	FACETS	1	0.831	1	1	0.831	1	CLONAL	1	TRUE	1	0.172072707391687	2		582	376	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483022	29483022	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs771764281	NA	P-0032614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	14	314	1	ENST00000356175.3:c.82C>T	p.Gln28Ter	p.Q28*	ENST00000356175	NM_000267.3	28	Cag/Tag	2/57	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.172072707391687	2		315	116	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37865624	37865624	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	66	619	0	ENST00000269571.5:c.493G>T	p.Asp165Tyr	p.D165Y	ENST00000269571		165	Gac/Tac	4/27	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.172072707391687	2		619	689	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095749	178095749	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	19	381	0	ENST00000397062.3:c.1582G>C	p.Asp528His	p.D528H	ENST00000397062	NM_006164.4	528	Gat/Cat	5/5	1	2	FACETS	1	0.803	1	1	0.803	1	CLONAL	1	TRUE	1	0.172072707391687	2		381	208	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252903	36252904	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	33	380	0	ENST00000300305.3:c.458dup	p.Asn153LysfsTer7	p.N153Kfs*7	ENST00000300305		153	aac/aaAc	4/8	1	2	FACETS	0.878	0.715	1	0.878	0.715	1	CLONAL	1	TRUE	1	0.172072707391687	2		380	437	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523735	41523735	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0032614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	28	577	0	ENST00000263253.7:c.1151C>G	p.Ser384Ter	p.S384*	ENST00000263253	NM_001429.3	384	tCa/tGa	4/31	1	2	FACETS	0.621	0.495	0.765	0.621	0.495	0.765	SUBCLONAL	1	TRUE	1	0.172072707391687	2		577	524	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165347	47165347	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	19	399	0	ENST00000409792.3:c.779C>G	p.Ser260Cys	p.S260C	ENST00000409792	NM_014159.6	260	tCt/tGt	3/21	1	2	FACETS	1	0.806	1	1	0.806	1	CLONAL	1	TRUE	1	0.172072707391687	2		399	207	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808320	1808320	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760292339	NA	P-0032614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	47	845	0	ENST00000260795.2:c.2078C>T	p.Ser693Phe	p.S693F	ENST00000260795		693	tCc/tTc	15/17	1	2	FACETS	0.856	0.721	1	0.856	0.721	1	CLONAL	1	TRUE	1	0.172072707391687	2		845	638	SUCCESS
APC	324	MSKCC	GRCh37	5	112176210	112176210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529480958	NA	P-0032614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	45	351	1	ENST00000257430.4:c.4919G>A	p.Arg1640Gln	p.R1640Q	ENST00000257430	NM_000038.5	1640	cGg/cAg	16/16	1	2	FACETS	0.767	0.647	0.899	1	0.961	1	SUBCLONAL	2	TRUE	1	0.172072707391687	2		352	341	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439357	149439357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	52	578	0	ENST00000286301.3:c.2038G>A	p.Glu680Lys	p.E680K	ENST00000286301	NM_005211.3	680	Gag/Aag	15/22	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.172072707391687	2		578	539	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056403	180056403	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	30	488	0	ENST00000261937.6:c.841G>C	p.Glu281Gln	p.E281Q	ENST00000261937	NM_182925.4	281	Gag/Cag	7/30	1	2	FACETS	0.72	0.58	0.881	0.72	0.58	0.881	SUBCLONAL	1	TRUE	1	0.172072707391687	2		488	484	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0032617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	34	340	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.959	0.784	1	0.959	0.784	1	CLONAL	1	TRUE	1	0.17	2		340	417	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0032617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	38	335	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.17	2		335	322	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40467773	40467773	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1191676333	NA	P-0032617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	51	477	0	ENST00000264657.5:c.2303C>T	p.Ser768Phe	p.S768F	ENST00000264657	NM_139276.2	768	tCc/tTc	24/24	1	2	FACETS	0.92	0.781	1	0.92	0.781	1	CLONAL	1	TRUE	1	0.17	2		477	652	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112035584	112035584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	38	451	0	ENST00000368678.4:c.310C>T	p.His104Tyr	p.H104Y	ENST00000368678		104	Cac/Tac	4/13	0.140323634640961	0	FACETS	0.718	0.593	0.858			1	SUBCLONAL	1	TRUE	0	0.17	0		451	517	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845847	151845847	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	92	728	0	ENST00000262189.6:c.13165T>A	p.Ser4389Thr	p.S4389T	ENST00000262189	NM_170606.2	4389	Tcc/Acc	52/59	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.17	2		728	752	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0032628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	742	745	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.743632462879295	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.743632462879295	2		745	971	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201874	152201874	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753014570	NA	P-0032628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	135	343	3	ENST00000206249.3:c.728G>A	p.Arg243His	p.R243H	ENST00000206249	NM_000125.3	243	cGt/cAt	3/8	0.743632462879295	3	FACETS	0.956	0.874	1	0.478	0.437	0.521	CLONAL	1	TRUE	1	0.743632462879295	3		346	521	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933510	36933510	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	328	810	0	ENST00000361632.4:c.1777G>T	p.Ala593Ser	p.A593S	ENST00000361632		593	Gcc/Tcc	13/16	1	2	FACETS	0.962	0.912	1	0.962	0.912	1	CLONAL	1	TRUE	1	0.743632462879295	2		810	917	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342376	118342376	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0032628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	47	165	0	ENST00000534358.1:c.503-1G>C		p.X168_splice	ENST00000534358	NM_005933.3	168			0.733938977569472	3	FACETS	0.876	0.767	0.985	0.876	0.767	0.985	CLONAL	2	TRUE	1	0.743632462879295	3		165	99	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669604	88669604	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs771227484	NA	P-0032628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	90	270	0	ENST00000360948.2:c.1294G>A	p.Val432Ile	p.V432I	ENST00000360948	NM_001012338.2	432	Gta/Ata	12/19	0.743632462879295	3	FACETS	0.639	0.568	0.713	0.319	0.284	0.357	SUBCLONAL	1	TRUE	1	0.743632462879295	3		270	520	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119892	70119988	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGCCCAACGGCCACCCGGGGGTGCCGGCCACGCACGGCCAGGTCACCTACACGGGCAGCTACGGCATCAGCAGCACCGCGGCCACCCCGGCGAGC	GCCGCCCAACGGCCACCCGGGGGTGCCGGCCACGCACGGCCAGGTCACCTACACGGGCAGCTACGGCATCAGCAGCACCGCGGCCACCCCGGCGAGC	-	novel	NA	P-0032628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	175	620	0	ENST00000245479.2:c.896_992del	p.Pro299ArgfsTer52	p.P299Rfs*52	ENST00000245479	NM_000346.3	298	ctGCCGCCCAACGGCCACCCGGGGGTGCCGGCCACGCACGGCCAGGTCACCTACACGGGCAGCTACGGCATCAGCAGCACCGCGGCCACCCCGGCGAGC/ct	3/3	0.743632462879295	2	FACETS	0.698	0.645	0.753	0.349	0.322	0.377	SUBCLONAL	1	TRUE	0	0.743632462879295	2		620	674	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90971055	90971055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	272	349	0	ENST00000265433.3:c.1022G>A	p.Ser341Asn	p.S341N	ENST00000265433	NM_002485.4	341	aGc/aAc	9/16	0.472140127075911	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.743632462879295	4		349	609	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577494	64577495	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCGGCCCAGCTCGGCAGCAAACAGGCGCACCACGTCGTCGATGGAGCGCAGCGG	novel	NA	P-0032629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	27	512	0	ENST00000312049.6:c.34_87dup	p.Pro12_Arg29dup	p.P12_R29dup	ENST00000312049	NM_130799.2	12	-/CCGCTGCGCTCCATCGACGACGTGGTGCGCCTGTTTGCTGCCGAGCTGGGCCGA	2/10	0.286610325579843	1	FACETS	0.367	0.291	0.453	0.367	0.291	0.453	SUBCLONAL	1	TRUE	0	0.286610325579843	1		512	440	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937813	76937815	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	CAG	CAG	-	novel	NA	P-0032629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	57	349	0	ENST00000373344.5:c.2933_2935del	p.Ser978_Glu979delinsTer	p.S978_E979delins*	ENST00000373344	NM_000489.3	978	tCTGaa/taa	9/35	1	1	FACETS	0.767	0.667	0.874	1	0.972	1	SUBCLONAL	2	TRUE	0	0.286610325579843	1		349	222	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0032631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	122	656	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	0.189612941778388	5	FACETS	0.86	0.779	0.944	0.645	0.584	0.708	CLONAL	3	TRUE	1	0.189612941778388	5		656	641	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524486	44524486	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	22	300	0	ENST00000291552.4:c.71T>C	p.Ile24Thr	p.I24T	ENST00000291552	NM_006758.2	24	aTt/aCt	2/8	1	2	FACETS	0.756	0.586	0.953	0.756	0.586	0.953	CLONAL	1	TRUE	1	0.189612941778388	2		300	307	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	111	861	0	ENST00000269305.4:c.772del	p.Glu258LysfsTer87	p.E258Kfs*87	ENST00000269305	NM_001126112.2	258	Gaa/aa	7/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.189612941778388	2		861	965	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465886	69465886	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1772	117	745	0	ENST00000227507.2:c.724G>T	p.Asp242Tyr	p.D242Y	ENST00000227507	NM_053056.2	242	Gac/Tac	5/5	0.189612941778388	9	FACETS	1	0.947	1			1	CLONAL	1	TRUE	NA	0.189612941778388	9		745	1889	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380328	25380328	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	87	512	0	ENST00000311936.3:c.130G>C	p.Val44Leu	p.V44L	ENST00000311936	NM_004985.3	44	Gta/Cta	3/5	0.189612941778388	5	FACETS	0.879	0.782	0.982	0.659	0.586	0.736	CLONAL	3	TRUE	1	0.189612941778388	5		512	447	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715828	61715828	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	28	567	0	ENST00000401558.2:c.2101G>C	p.Ala701Pro	p.A701P	ENST00000401558	NM_003400.3	701	Gct/Cct	18/25	1	2	FACETS	0.55	0.438	0.678	0.55	0.438	0.678	SUBCLONAL	1	TRUE	1	0.189612941778388	2		567	537	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	149	441	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.190143962567109	0	FACETS	0.434	0.401	0.468			1	INDETERMINATE	1	TRUE	0	0.637257395870445	0		441	391	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0032633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	142	337	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.637257395870445	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.637257395870445	1		337	282	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0032633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	96	335	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	1	2	FACETS	0.913	0.822	1	0.913	0.822	1	CLONAL	1	TRUE	1	0.637257395870445	2		335	330	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411276	63411276	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	481	886	1	ENST00000330258.3:c.1891C>T	p.Arg631Ter	p.R631*	ENST00000330258	NM_152424.3	631	Cga/Tga	2/2	0.637257395870445	2	FACETS	0.964	0.931	0.996	0.964	0.931	0.996	CLONAL	2	TRUE	0	0.637257395870445	2		887	783	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119974	70120026	+	frameshift_variant	Frame_Shift_Del	DEL	GCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAGGCGCCGCC	GCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAGGCGCCGCC	-	novel	NA	P-0032633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	44	288	0	ENST00000245479.2:c.984_1036del	p.Ser330AlafsTer230	p.S330Afs*230	ENST00000245479	NM_000346.3	326	GCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAGGCGCCGCCg/g	3/3	1	2	FACETS	0.457	0.385	0.536	0.457	0.385	0.536	SUBCLONAL	1	TRUE	1	0.637257395870445	2		288	302	SUCCESS
APC	324	MSKCC	GRCh37	5	112162813	112162813	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658868	NA	P-0032633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	97	405	0	ENST00000257430.4:c.1417C>T	p.Gln473Ter	p.Q473*	ENST00000257430	NM_000038.5	473	Cag/Tag	12/16	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.637257395870445	2		405	301	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0032637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	172	539	0	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	0.219505497062666	0	FACETS	0.991	0.916	1			1	CLONAL	2	TRUE	0	0.219505497062666	0		539	617	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40367096	40367097	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGTA	novel	NA	P-0032637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	219	613	0	ENST00000397332.2:c.97_100dup	p.Asp34ValfsTer12	p.D34Vfs*12	ENST00000397332	NM_001033082.2	34	gac/gTACGac	2/3	1	2	FACETS	0.861	0.8	0.924	1	0.993	1	CLONAL	2	TRUE	1	0.219505497062666	2		613	1159	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711879	89711880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0032637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	68	497	0	ENST00000371953.3:c.498_499dup	p.Thr167LysfsTer17	p.T167Kfs*17	ENST00000371953	NM_000314.4	166	gta/gtAAa	6/9	0.219505497062666	0	FACETS	0.959	0.836	1			1	CLONAL	1	TRUE	0	0.219505497062666	0		497	504	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588756	29588756	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	88	293	0	ENST00000356175.3:c.4545del	p.Phe1515LeufsTer38	p.F1515Lfs*38	ENST00000356175	NM_000267.3	1514	ccT/cc	34/57	0.219505497062666	1	FACETS	0.883	0.788	0.985	1	0.984	1	CLONAL	2	TRUE	0	0.219505497062666	1		293	404	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575690	48575691	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AATG	novel	NA	P-0032637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	122	520	0	ENST00000342988.3:c.451_454dup	p.Ala152GlufsTer11	p.A152Efs*11	ENST00000342988	NM_005359.5	150	-/AATG	4/12	0.219505497062666	0	FACETS	0.834	0.758	0.914			1	CLONAL	2	TRUE	0	0.219505497062666	0		520	520	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259663	89259674	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTGCCAAGGTAA	GTGCCAAGGTAA	-	novel	NA	P-0032637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	49	314	0	ENST00000336596.2:c.808_814+5del		p.X270_splice	ENST00000336596	NM_005233.5	270		3/17	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.219505497062666	2		314	349	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181827	56181830	+	frameshift_variant	Frame_Shift_Del	DEL	GAAC	GAAC	-	novel	NA	P-0032637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	103	405	0	ENST00000399503.3:c.4051_4054del	p.Glu1351SerfsTer25	p.E1351Sfs*25	ENST00000399503	NM_005921.1	1351	GAACag/ag	17/20	0.219505497062666	1	FACETS	0.912	0.821	1	1	0.987	1	CLONAL	2	TRUE	0	0.219505497062666	1		405	458	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845741	151845755	+	inframe_deletion	In_Frame_Del	DEL	AAGTCAAGGTTGAGT	AAGTCAAGGTTGAGT	-	novel	NA	P-0032637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	179	691	0	ENST00000262189.6:c.13257_13271del	p.Leu4420_Leu4424del	p.L4420_L4424del	ENST00000262189	NM_170606.2	4419	ctACTCAACCTTGACTTg/ctg	52/59	0.219505497062666	3	FACETS	0.824	0.759	0.892	0.824	0.759	0.892	CLONAL	2	TRUE	1	0.219505497062666	3		691	1098	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625218	69625218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1168737490	NA	P-0032640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1666	106	634	0	ENST00000334134.2:c.575G>A	p.Arg192Gln	p.R192Q	ENST00000334134	NM_005247.2	192	cGg/cAg	3/3	0.397989377034045	4	FACETS	0.36	0.321	0.401			1	SUBCLONAL	1	TRUE	NA	0.498570283429963	4		634	1772	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953214	81953214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369516453	NA	P-0032640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	211	385	1	ENST00000359376.3:c.2180G>A	p.Arg727Gln	p.R727Q	ENST00000359376	NM_002661.3	727	cGa/cAa	20/33	0.326236540178808	2	FACETS	0.828	0.777	0.88	0.828	0.777	0.88	CLONAL	2	TRUE	0	0.498570283429963	2		386	511	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346897	89346897	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1175676213	NA	P-0032640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	30	277	0	ENST00000301030.4:c.6053C>T	p.Pro2018Leu	p.P2018L	ENST00000301030	NM_001256183.1	2018	cCt/cTt	9/13	0.326236540178808	2	FACETS	0.377	0.304	0.46	0.189	0.152	0.23	SUBCLONAL	1	TRUE	0	0.498570283429963	2		277	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0032640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	517	693	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.470721098694646	3	FACETS	0.925	0.892	0.957	0.925	0.892	0.957	CLONAL	3	TRUE	0	0.498570283429963	3		693	934	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374930	45374930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	199	508	0	ENST00000262160.6:c.913C>T	p.Pro305Ser	p.P305S	ENST00000262160	NM_005901.5	305	Cca/Tca	8/11	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.498570283429963	2		508	794	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855469	45855469	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	372	680	0	ENST00000391945.4:c.2188C>G	p.Arg730Gly	p.R730G	ENST00000391945	NM_000400.3	730	Cgg/Ggg	22/23	0.498570283429963	2	FACETS	0.979	0.936	1	0.979	0.936	1	CLONAL	2	TRUE	0	0.498570283429963	2		680	762	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285815	39285815	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	54	483	0	ENST00000402219.2:c.344A>C	p.Lys115Thr	p.K115T	ENST00000402219	NM_005633.3	115	aAg/aCg	3/23	1	2	FACETS	0.264	0.224	0.307	0.264	0.224	0.307	SUBCLONAL	1	TRUE	1	0.498570283429963	2		483	822	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141609	202141612	+	frameshift_variant	Frame_Shift_Del	DEL	CAAT	CAAT	-	novel	NA	P-0032640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	63	381	0	ENST00000358485.4:c.899_902del	p.Asn300ThrfsTer29	p.N300Tfs*29	ENST00000358485	NM_001080125.1	299	aaCAAT/aa	7/9	0.498570283429963	3	FACETS	0.481	0.416	0.553	0.241	0.208	0.277	SUBCLONAL	1	TRUE	1	0.498570283429963	3		381	656	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380450	31380450	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	84	508	1	ENST00000328111.2:c.940G>T	p.Gly314Cys	p.G314C	ENST00000328111	NM_006892.3	314	Ggc/Tgc	9/23	0.301042437946323	3	FACETS	0.539	0.475	0.607	0.27	0.237	0.304	SUBCLONAL	1	TRUE	1	0.498570283429963	3		509	781	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275191	41275191	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770598744	NA	P-0032640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	62	434	0	ENST00000349496.5:c.1357C>T	p.Arg453Trp	p.R453W	ENST00000349496	NM_001904.3	453	Cgg/Tgg	9/15	0.279857671427595	1	FACETS	0.338	0.292	0.388	0.338	0.292	0.388	INDETERMINATE	1	TRUE	0	0.498570283429963	1		434	553	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161264	185161264	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	285	650	0	ENST00000265026.3:c.691A>G	p.Ile231Val	p.I231V	ENST00000265026	NM_004721.4	231	Att/Gtt	4/14	0.267941559981192	3	FACETS	1	0.991	1	0.434	0.408	0.461	INDETERMINATE	1	TRUE	0	0.498570283429963	3		650	1096	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374432	81374432	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	88	416	0	ENST00000222390.5:c.630A>T	p.Glu210Asp	p.E210D	ENST00000222390	NM_000601.4	210	gaA/gaT	6/18	0.257791951453244	3	FACETS	0.625	0.553	0.701	0.312	0.276	0.351	INDETERMINATE	1	TRUE	1	0.498570283429963	3		416	706	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407967	139407967	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	149	831	1	ENST00000277541.6:c.2230G>T	p.Gly744Trp	p.G744W	ENST00000277541	NM_017617.3	744	Ggg/Tgg	14/34	1	2	FACETS	0.547	0.499	0.598	0.547	0.499	0.598	SUBCLONAL	1	TRUE	1	0.498570283429963	2		832	1093	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097240	11097240	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778683	NA	P-0032643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	117	794	0	ENST00000358026.2:c.731C>T	p.Pro244Leu	p.P244L	ENST00000358026	NM_001128849.1	244	cCg/cTg	4/36	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.34016242530168	2		794	626	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050657	30050658	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GACCCCAGTGTTCACAA	novel	NA	P-0032643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	40	373	0	ENST00000338641.4:c.461_477dup	p.Arg160ThrfsTer20	p.R160Tfs*20	ENST00000338641	NM_000268.3	153	-/GACCCCAGTGTTCACAA	5/16	0.34016242530168	1	FACETS	0.422	0.351	0.502	0.422	0.351	0.502	SUBCLONAL	1	TRUE	0	0.34016242530168	1		373	462	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050659	30050660	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCCAGT	novel	NA	P-0032643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	28	378	0	ENST00000338641.4:c.462_468dup	p.Val157ProfsTer48	p.V157Pfs*48	ENST00000338641	NM_000268.3	154	gac/gaCCCCAGTc	5/16	0.34016242530168	1	FACETS	0.291	0.232	0.358	0.291	0.232	0.358	SUBCLONAL	1	TRUE	0	0.34016242530168	1		378	470	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436304	52436304	+	stop_lost	Nonstop_Mutation	SNP	T	T	G	novel	NA	P-0032643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	101	634	0	ENST00000460680.1:c.2190A>C	p.Ter730CysextTer205	p.*730Cext*205	ENST00000460680	NM_004656.3	730	tgA/tgC	17/17	0.321728782361914	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.34016242530168	1		634	456	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	158	264	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.555034158356905	2		264	465	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0032662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	75	264	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.986	0.874	1	0.986	0.874	1	CLONAL	1	TRUE	1	0.555034158356905	2		264	274	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791772	42791772	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	42	795	0	ENST00000575354.2:c.658C>T	p.Gln220Ter	p.Q220*	ENST00000575354	NM_015125.3	220	Cag/Tag	5/20	0.555034158356905	1	FACETS	0.152	0.126	0.181	0.152	0.126	0.181	SUBCLONAL	1	TRUE	0	0.555034158356905	1		795	720	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591145	67591146	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0032662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	64	407	0	ENST00000274335.5:c.1738_1739insTG	p.Tyr580LeufsTer3	p.Y580Lfs*3	ENST00000274335		580	tac/tTGac	12/15	1	2	FACETS	0.842	0.736	0.954	0.842	0.736	0.954	CLONAL	1	TRUE	1	0.555034158356905	2		407	274	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0032667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	73	338	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.271088190424485	4	FACETS	0.848	0.754	0.946	0.848	0.754	0.946	INDETERMINATE	2	TRUE	2	0.642376092823097	4		338	220	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0032667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	194	448	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.176537222577051	3	FACETS	0.803	0.75	0.857	0.535	0.5	0.571	INDETERMINATE	2	TRUE	0	0.642376092823097	3		449	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0032667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	285	916	3	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.370175340686328	2	FACETS	0.78	0.741	0.819	0.78	0.741	0.819	INDETERMINATE	2	TRUE	0	0.642376092823097	2		919	569	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715847	117715847	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	59	440	0	ENST00000368508.3:c.911G>T	p.Arg304Ile	p.R304I	ENST00000368508	NM_002944.2	304	aGa/aTa	9/43	0.162038828335707	0	FACETS	0.268	0.233	0.305			1	INDETERMINATE	1	TRUE	0	0.642376092823097	0		440	245	SUCCESS
APC	324	MSKCC	GRCh37	5	112175547	112175548	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1554085679	NA	P-0032667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	67	378	1	ENST00000257430.4:c.4260dup	p.Ser1421GlnfsTer2	p.S1421Qfs*2	ENST00000257430	NM_000038.5	1419	agc/agCc	16/16	0.271088190424485	4	FACETS	1	0.974	1	0.735	0.648	0.827	INDETERMINATE	1	TRUE	2	0.642376092823097	4		379	233	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	97	441	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.922	0.83	1	0.922	0.83	1	CLONAL	1	TRUE	1	0.602709983496393	2		441	349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577567	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1567549651	NA	P-0032668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	167	654	0	ENST00000269305.4:c.714dup	p.Asn239Ter	p.N239*	ENST00000269305	NM_001126112.2	238	-/T	7/11	0.602709983496393	1	FACETS	0.762	0.706	0.82	0.762	0.706	0.82	SUBCLONAL	1	TRUE	0	0.602709983496393	1		654	508	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0032668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	53	149	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.602709983496393	2		149	152	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996797	100996797	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs757498161	NA	P-0032668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	113	367	0	ENST00000325455.5:c.1730G>C	p.Cys577Ser	p.C577S	ENST00000325455	NM_001202474.3	577	tGt/tCt	2/8	1	2	FACETS	0.8	0.724	0.879	0.8	0.724	0.879	SUBCLONAL	1	TRUE	1	0.602709983496393	2		367	469	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527892	103527892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1256557967	NA	P-0032668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	35	196	0	ENST00000355739.4:c.3200C>T	p.Ser1067Leu	p.S1067L	ENST00000355739	NM_000123.3	1067	tCa/tTa	15/15	0.602709983496393	6	FACETS	0.477	0.39	0.575	0.095	0.078	0.115	SUBCLONAL	1	TRUE	1	0.602709983496393	6		196	537	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480107	20480107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1221089278	NA	P-0032668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	103	304	0	ENST00000346618.3:c.424G>A	p.Gly142Ser	p.G142S	ENST00000346618	NM_001949.4	142	Ggt/Agt	2/7	1	2	FACETS	0.872	0.786	0.961	0.872	0.786	0.961	CLONAL	1	TRUE	1	0.602709983496393	2		304	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0032669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	43	809	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.695	0.582	0.82	0.695	0.582	0.82	SUBCLONAL	1	TRUE	1	0.26	2		809	476	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0032669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	28	503	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.3	1	FACETS	0.872	0.701	1	0.872	0.701	1	CLONAL	1	TRUE	0	0.26	1		503	215	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	41	441	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.254065671210304	0	FACETS	0.871	0.73	1			1	CLONAL	1	TRUE	0	0.26	0		441	268	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0032669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	18	338	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.607	0.458	0.783	0.607	0.458	0.783	SUBCLONAL	1	TRUE	1	0.26	2		338	228	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167577	NA	P-0032669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	16	352	0	ENST00000257430.4:c.4463del	p.Leu1488TyrfsTer19	p.L1488Yfs*19	ENST00000257430	NM_000038.5	1487	acT/ac	16/16	1	2	FACETS	0.628	0.465	0.821	0.628	0.465	0.821	SUBCLONAL	1	TRUE	1	0.26	2		352	196	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32455870	32456600	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTGGCGTTTCCTTAATTAACAAAACTCTCCCCAAGGCAGAGCCAGACACTGCGCCGGTCTCCTGGTTCCACTCCCGTGGGGACTAGCAGTCCCGGAATCTCTCGGACTCTAAGGGGCCCCAGACGCCCTCCCGGCTCTTGCGAACAGTCAGGCTCCTAGCTCTGCCTGGCTTTGGAGGATGTCGGGGGCCAGTGCCTGCGTGCACTCCCACTCTCCGGCCTCCTCCCCAGCCGCCGCTTCCGCTATCCTCACGGCCCTTGGGAAGCAGCTGGGTAAGAGCTGCGGTCAAAAGGGGTAGGAGAGGGGGGTGTCCTAGAGCGGAGAGTCCCTGGCGCCACTGCCCCGCGCGTAGGGGGCGCTCCCCGGCCTACTTACCCTGATTGCGAATAGCGGGCTGGCTCTCGAGGCAGCTGGGCAGGTAGGGCGCGTTAGGAAACATCCTGGCCTGGCCGGATGACGCCTGGCTGGGCGGAGGAGGACCGAAGGGCCCGTAGCGACAGGCTCCGGCTGTGCCAGTGAACTGGCCGGAAAAGTGGACAGTGAAGGCGCTCAGGCACTGCTCCTCGTGCGGCTCCGCGCCGCCCCAGCTCGGCTCCTGTTTGATGAAGGAGTGAGGCGGCGGCGGCGGGGGTGGCGGCGGAGCCGGTGGCGGCGCGGGGCCGCCCAACGACCCGTAAGCCGAAGCGCCCGGGGGCGCAAAGTCCAGCACCGGCGCCCACTGCGCCGCGCC	TTTGGCGTTTCCTTAATTAACAAAACTCTCCCCAAGGCAGAGCCAGACACTGCGCCGGTCTCCTGGTTCCACTCCCGTGGGGACTAGCAGTCCCGGAATCTCTCGGACTCTAAGGGGCCCCAGACGCCCTCCCGGCTCTTGCGAACAGTCAGGCTCCTAGCTCTGCCTGGCTTTGGAGGATGTCGGGGGCCAGTGCCTGCGTGCACTCCCACTCTCCGGCCTCCTCCCCAGCCGCCGCTTCCGCTATCCTCACGGCCCTTGGGAAGCAGCTGGGTAAGAGCTGCGGTCAAAAGGGGTAGGAGAGGGGGGTGTCCTAGAGCGGAGAGTCCCTGGCGCCACTGCCCCGCGCGTAGGGGGCGCTCCCCGGCCTACTTACCCTGATTGCGAATAGCGGGCTGGCTCTCGAGGCAGCTGGGCAGGTAGGGCGCGTTAGGAAACATCCTGGCCTGGCCGGATGACGCCTGGCTGGGCGGAGGAGGACCGAAGGGCCCGTAGCGACAGGCTCCGGCTGTGCCAGTGAACTGGCCGGAAAAGTGGACAGTGAAGGCGCTCAGGCACTGCTCCTCGTGCGGCTCCGCGCCGCCCCAGCTCGGCTCCTGTTTGATGAAGGAGTGAGGCGGCGGCGGCGGGGGTGGCGGCGGAGCCGGTGGCGGCGCGGGGCCGCCCAACGACCCGTAAGCCGAAGCGCCCGGGGGCGCAAAGTCCAGCACCGGCGCCCACTGCGCCGCGCC	-	novel	NA	P-0032669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	0	22	11	0	ENST00000332351.3:c.292_646+376del		p.X98_splice	ENST00000332351	NM_024426.4	98		1/10	1	2	FACETS		NA	1	1	0.968	1	NA	8	TRUE	1	0.26	2		11	22	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244227	153244227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	41	455	0	ENST00000281708.4:c.1930G>A	p.Gly644Arg	p.G644R	ENST00000281708	NM_033632.3	644	Gga/Aga	12/12	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.26	2		455	281	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730008	41730008	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs537531066	NA	P-0032669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	84	680	1	ENST00000242208.4:c.521G>T	p.Arg174Leu	p.R174L	ENST00000242208	NM_002192.2	174	cGc/cTc	3/3	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.26	2		681	522	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	78	264	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.473809594730794	2		264	290	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0032672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	80	335	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.868	0.769	0.973	0.868	0.769	0.973	CLONAL	1	TRUE	1	0.473809594730794	2		335	389	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0032673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	149	400	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.159670773581208	3	FACETS	0.84	0.772	0.91	0.84	0.772	0.91	INDETERMINATE	2	TRUE	1	0.405640216242743	3		400	526	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196830	123196830	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	16	393	0	ENST00000218089.9:c.1717C>T	p.Gln573Ter	p.Q573*	ENST00000218089	NM_001042749.1	573	Cag/Tag	18/35	0.216869347659957	0	FACETS	0.251	0.186	0.328			1	INDETERMINATE	1	TRUE	0	0.405640216242743	0		393	187	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856020	68856020	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	72	413	0	ENST00000261769.5:c.1828C>T	p.Gln610Ter	p.Q610*	ENST00000261769	NM_004360.3	610	Cag/Tag	12/16	0.405640216242743	1	FACETS	0.718	0.631	0.812	0.718	0.631	0.812	SUBCLONAL	1	TRUE	0	0.405640216242743	1		413	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578371	7578371	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs776167460	NA	P-0032673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	79	420	0	ENST00000269305.4:c.559G>A	p.Gly187Ser	p.G187S	ENST00000269305	NM_001126112.2	187	Ggt/Agt	5/11	0.405640216242743	1	FACETS	0.935	0.83	1	0.935	0.83	1	CLONAL	1	TRUE	0	0.405640216242743	1		420	332	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100219	157100219	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	15	7	0	ENST00000346085.5:c.1156G>A	p.Gly386Arg	p.G386R	ENST00000346085	NM_020732.3	386	Ggg/Agg	1/20	0.159670773581208	3	FACETS	0.767	0.578	0.978	0.767	0.578	0.978	INDETERMINATE	2	TRUE	1	0.405640216242743	3		7	58	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998913	11998913	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	22	211	0	ENST00000353533.5:c.415del	p.Glu139LysfsTer13	p.E139Kfs*13	ENST00000353533	NM_003010.3	139	Gaa/aa	4/11	0.405640216242743	1	FACETS	0.67	0.526	0.833	0.67	0.526	0.833	SUBCLONAL	1	TRUE	0	0.405640216242743	1		211	129	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218849	36218849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753899619	NA	P-0032673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	113	548	0	ENST00000222270.7:c.4460G>A	p.Arg1487His	p.R1487H	ENST00000222270	NM_014727.1	1487	cGc/cAc	18/37	0.405640216242743	1	FACETS	0.873	0.789	0.96	0.873	0.789	0.96	CLONAL	1	TRUE	0	0.405640216242743	1		548	509	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426637	212426637	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	44	406	0	ENST00000342788.4:c.2478G>C	p.Gln826His	p.Q826H	ENST00000342788	NM_005235.2	826	caG/caC	20/28	1	2	FACETS	0.518	0.435	0.609	0.518	0.435	0.609	SUBCLONAL	1	TRUE	1	0.405640216242743	2		406	419	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165165	32165165	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	69	511	0	ENST00000375023.3:c.4963G>C	p.Glu1655Gln	p.E1655Q	ENST00000375023	NM_004557.3	1655	Gag/Cag	27/30	0.159670773581208	3	FACETS	0.663	0.578	0.756	0.332	0.289	0.378	INDETERMINATE	1	TRUE	1	0.405640216242743	3		511	617	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129132	152129132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	81	565	0	ENST00000206249.3:c.85C>T	p.Pro29Ser	p.P29S	ENST00000206249	NM_000125.3	29	Ccg/Tcg	1/8	0.159670773581208	3	FACETS	0.938	0.829	1	0.469	0.414	0.528	INDETERMINATE	1	TRUE	1	0.405640216242743	3		565	512	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247813	59247814	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTTTAAGCTG	novel	NA	P-0032674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1264	72	968	0	ENST00000371222.2:c.919_929dup	p.Gln310HisfsTer8	p.Q310Hfs*8	ENST00000371222	NM_002228.3	310	cag/caCAGCTTAAACAg	1/1	1	2	FACETS	0.493	0.428	0.562	0.493	0.428	0.562	SUBCLONAL	1	TRUE	1	0.21881163127479	2		968	1336	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180949	108180949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881394	NA	P-0032674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	35	347	1	ENST00000278616.4:c.5825C>T	p.Ala1942Val	p.A1942V	ENST00000278616	NM_000051.3	1942	gCc/gTc	39/63	1	2	FACETS	0.773	0.634	0.929	0.773	0.634	0.929	CLONAL	1	TRUE	1	0.21881163127479	2		348	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0032688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	149	468	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.426481772613	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.426481772613	1		468	511	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0032688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	78	444	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.792	0.698	0.892	0.792	0.698	0.892	SUBCLONAL	1	TRUE	1	0.426481772613	2		444	462	SUCCESS
APC	324	MSKCC	GRCh37	5	112175246	112175246	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1057517558	NA	P-0032688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	54	227	0	ENST00000257430.4:c.3956del	p.Pro1319LeufsTer2	p.P1319Lfs*2	ENST00000257430	NM_000038.5	1319	Cct/ct	16/16	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.426481772613	2		227	241	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0032688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	100	474	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.864	0.774	0.958	0.864	0.774	0.958	CLONAL	1	TRUE	1	0.426481772613	2		474	543	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0032688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	72	335	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	1	2	FACETS	0.896	0.787	1	0.896	0.787	1	CLONAL	1	TRUE	1	0.426481772613	2		335	377	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720699	89720699	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs786202840	NA	P-0032688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	21	114	0	ENST00000371953.3:c.850G>T	p.Glu284Ter	p.E284*	ENST00000371953	NM_000314.4	284	Gag/Tag	8/9	1	2	FACETS	0.794	0.62	0.992	0.794	0.62	0.992	CLONAL	1	TRUE	1	0.426481772613	2		114	124	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63531763	63531763	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370503213	NA	P-0032688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	123	582	0	ENST00000307078.5:c.2218C>T	p.Pro740Ser	p.P740S	ENST00000307078	NM_004655.3	740	Cca/Tca	9/11	1	2	FACETS	0.991	0.899	1	0.991	0.899	1	CLONAL	1	TRUE	1	0.426481772613	2		582	582	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268138	153268138	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1406877044	NA	P-0032688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	211	337	0	ENST00000281708.4:c.670C>T	p.Arg224Ter	p.R224*	ENST00000281708	NM_033632.3	224	Cga/Tga	4/12	1	2	FACETS	1	0.975	1	1	0.995	1	CLONAL	2	TRUE	1	0.426481772613	2		337	463	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911625	114911625	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	96	378	0	ENST00000543371.1:c.1143C>G	p.Asn381Lys	p.N381K	ENST00000543371	NM_001198531.1	381	aaC/aaG	10/14	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.426481772613	2		378	446	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104636	69104636	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757884988	NA	P-0032688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	157	600	0	ENST00000288368.4:c.4480C>T	p.Arg1494Cys	p.R1494C	ENST00000288368	NM_024870.2	1494	Cgc/Tgc	37/40	0.426481772613	4	FACETS	0.929	0.849	1	0.31	0.283	0.338	CLONAL	1	TRUE	1	0.426481772613	4		600	1131	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435744	56435744	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	620	585	0	ENST00000407977.2:c.1393G>A	p.Asp465Asn	p.D465N	ENST00000407977		465	Gac/Aac	9/10	0.834597631309808	7	FACETS	0.91	0.883	0.937	0.758	0.735	0.781	CLONAL	5	TRUE	1	0.834597631309808	7		585	1008	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911757	32911757	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs80358573	NA	P-0032697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	275	500	0	ENST00000380152.3:c.3265C>T	p.Gln1089Ter	p.Q1089*	ENST00000380152		1089	Cag/Tag	11/27	0.356982549890178	4	FACETS	0.929	0.878	0.979			1	INDETERMINATE	2	TRUE	NA	0.834597631309808	4		500	651	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579371	7579371	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	255	616	0	ENST00000269305.4:c.316del	p.Ser106AlafsTer17	p.S106Afs*17	ENST00000269305	NM_001126112.2	106	Agc/gc	4/11	0.834597631309808	1	FACETS	0.981	0.94	1	0.981	0.94	1	CLONAL	1	TRUE	0	0.834597631309808	1		616	363	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523630	41523630	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	268	701	1	ENST00000263253.7:c.1046A>G	p.His349Arg	p.H349R	ENST00000263253	NM_001429.3	349	cAc/cGc	4/31	1	2	FACETS	0.923	0.871	0.976	0.923	0.871	0.976	CLONAL	1	TRUE	1	0.834597631309808	2		702	696	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79952295	79952298	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	rs1259647122	NA	P-0032697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	144	366	0	ENST00000265081.6:c.307_310del	p.Lys103SerfsTer22	p.K103Sfs*22	ENST00000265081	NM_002439.4	101	gtAAAG/gt	2/24	1	2	FACETS	0.91	0.84	0.982	0.91	0.84	0.982	CLONAL	1	TRUE	1	0.834597631309808	2		366	379	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435744	56435744	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032697-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	658	585	0	ENST00000407977.2:c.1393G>A	p.Asp465Asn	p.D465N	ENST00000407977		465	Gac/Aac	9/10	0.795481932523031	12	FACETS	0.979	0.951	1	0.783	0.761	0.806	CLONAL	8	TRUE	2	0.795481932523031	12		585	1051	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911757	32911757	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs80358573	NA	P-0032697-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	251	500	0	ENST00000380152.3:c.3265C>T	p.Gln1089Ter	p.Q1089*	ENST00000380152		1089	Cag/Tag	11/27	0.795481932523031	6	FACETS	0.951	0.898	1			1	CLONAL	3	TRUE	NA	0.795481932523031	6		500	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579371	7579371	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032697-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	245	616	0	ENST00000269305.4:c.316del	p.Ser106AlafsTer17	p.S106Afs*17	ENST00000269305	NM_001126112.2	106	Agc/gc	4/11	0.770472854853145	2	FACETS	0.981	0.945	1	0.981	0.945	1	CLONAL	2	TRUE	0	0.795481932523031	2		616	314	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523630	41523630	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032697-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	294	701	1	ENST00000263253.7:c.1046A>G	p.His349Arg	p.H349R	ENST00000263253	NM_001429.3	349	cAc/cGc	4/31	0.795481932523031	4	FACETS	0.936	0.887	0.986	0.936	0.887	0.986	CLONAL	2	TRUE	2	0.795481932523031	4		702	709	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79952295	79952298	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	rs1259647122	NA	P-0032697-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	168	366	0	ENST00000265081.6:c.307_310del	p.Lys103SerfsTer22	p.K103Sfs*22	ENST00000265081	NM_002439.4	101	gtAAAG/gt	2/24	0.513616238395402	4	FACETS	0.962	0.896	1	0.962	0.896	1	CLONAL	2	TRUE	2	0.795481932523031	4		366	394	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	69	280	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.964	0.844	1	0.964	0.844	1	CLONAL	1	TRUE	1	0.374745465169081	2		280	382	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	59	441	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.641	0.552	0.738	0.641	0.552	0.738	SUBCLONAL	1	TRUE	1	0.374745465169081	2		441	491	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760024	133760024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	118	647	1	ENST00000318560.5:c.2352del	p.Arg785GlyfsTer3	p.R785Gfs*3	ENST00000318560	NM_005157.4	783	Ccc/cc	11/11	1	2	FACETS	0.834	0.753	0.92	0.834	0.753	0.92	CLONAL	1	TRUE	1	0.374745465169081	2		648	755	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	135	653	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.885	0.805	0.97	0.885	0.805	0.97	CLONAL	1	TRUE	1	0.374745465169081	2		658	814	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609894	117609894	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs202153378	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	129	637	2	ENST00000368508.3:c.6805C>T	p.Arg2269Ter	p.R2269*	ENST00000368508	NM_002944.2	2269	Cga/Tga	43/43	1	2	FACETS	0.982	0.892	1	0.982	0.892	1	CLONAL	1	TRUE	1	0.374745465169081	2		639	701	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	146	576	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.985	0.9	1	0.985	0.9	1	CLONAL	1	TRUE	1	0.374745465169081	2		576	791	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	85	275	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.374745465169081	2		275	401	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	117	660	7	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.955	0.863	1	0.955	0.863	1	CLONAL	1	TRUE	1	0.374745465169081	2		667	654	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	187	590	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.374745465169081	2	FACETS	0.795	0.738	0.853	0.795	0.738	0.853	SUBCLONAL	2	TRUE	0	0.374745465169081	2		590	628	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735470	40735470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761910971	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	128	575	0	ENST00000373198.4:c.3403G>A	p.Val1135Met	p.V1135M	ENST00000373198	NM_133170.3	1135	Gtg/Atg	25/32	1	2	FACETS	0.999	0.907	1	0.999	0.907	1	CLONAL	1	TRUE	1	0.374745465169081	2		575	684	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277275	41277275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	118	361	2	ENST00000349496.5:c.1744C>T	p.Arg582Trp	p.R582W	ENST00000349496	NM_001904.3	582	Cgg/Tgg	11/15	0.374745465169081	2	FACETS	1	0.97	1	0.585	0.53	0.643	CLONAL	1	TRUE	0	0.374745465169081	2		363	538	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521299	187521299	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1166479124	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	129	586	3	ENST00000441802.2:c.11856del	p.Phe3952LeufsTer31	p.F3952Lfs*31	ENST00000441802	NM_005245.3	3952	ttT/tt	22/27	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.374745465169081	2		589	685	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953730	48953730	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs3092891	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	73	219	0	ENST00000267163.4:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000267163	NM_000321.2	445	Cga/Tga	14/27	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.374745465169081	2		219	350	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	140	612	3	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.374745465169081	2		615	643	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219579	133219579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542430685	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	87	527	2	ENST00000320574.5:c.4555C>T	p.Arg1519Cys	p.R1519C	ENST00000320574	NM_006231.2	1519	Cgc/Tgc	36/49	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.374745465169081	2		529	432	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	153	381	1	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.878	0.81	0.948	1	0.991	1	CLONAL	2	TRUE	1	0.374745465169081	2		382	465	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222708	5222708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370399999	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	100	403	0	ENST00000357368.4:c.3095G>A	p.Arg1032Gln	p.R1032Q	ENST00000357368	NM_002850.3	1032	cGg/cAg	18/38	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.374745465169081	2		403	456	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120115	70120115	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	20	106	0	ENST00000245479.2:c.1121del	p.Pro374ArgfsTer9	p.P374Rfs*9	ENST00000245479	NM_000346.3	373	Ccc/cc	3/3	1	2	FACETS	0.905	0.701	1	0.905	0.701	1	CLONAL	1	TRUE	1	0.374745465169081	2		106	118	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412058	63412059	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	169	899	0	ENST00000330258.3:c.1108dup	p.Glu370GlyfsTer8	p.E370Gfs*8	ENST00000330258	NM_152424.3	370	gag/gGag	2/2	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.374745465169081	2		899	739	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836985	89836985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs539161141	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	115	547	2	ENST00000389301.3:c.2209G>A	p.Ala737Thr	p.A737T	ENST00000389301	NM_000135.2	737	Gct/Act	24/43	1	2	FACETS	0.968	0.874	1	0.968	0.874	1	CLONAL	1	TRUE	1	0.374745465169081	2		549	634	SUCCESS
APC	324	MSKCC	GRCh37	5	112175952	112175952	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587783031	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	60	240	0	ENST00000257430.4:c.4666del	p.Thr1556LeufsTer9	p.T1556Lfs*9	ENST00000257430	NM_000038.5	1554	gAa/ga	16/16	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.374745465169081	2		240	263	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958190	2958190	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753952757	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	123	625	1	ENST00000396946.4:c.2542C>T	p.Arg848Cys	p.R848C	ENST00000396946	NM_032415.4	848	Cgc/Tgc	19/25	1	2	FACETS	0.993	0.9	1	0.993	0.9	1	CLONAL	1	TRUE	1	0.374745465169081	2		626	661	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11032084	11032084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	106	651	0	ENST00000327064.4:c.1649G>A	p.Arg550Gln	p.R550Q	ENST00000327064	NM_199141.1	550	cGg/cAg	15/16	1	2	FACETS	0.892	0.801	0.988	0.892	0.801	0.988	CLONAL	1	TRUE	1	0.374745465169081	2		651	634	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022990	33022990	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	77	403	0	ENST00000300177.4:c.104del	p.Pro35ArgfsTer49	p.P35Rfs*49	ENST00000300177	NM_001191322.1	33	atC/at	2/2	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.374745465169081	2		403	396	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041262	29041262	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	87	460	1	ENST00000282397.4:c.166del	p.Glu56LysfsTer12	p.E56Kfs*12	ENST00000282397	NM_002019.4	56	Gaa/aa	3/30	1	2	FACETS	0.934	0.83	1	0.934	0.83	1	CLONAL	1	TRUE	1	0.374745465169081	2		461	497	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204992	128204992	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	90	651	1	ENST00000341105.2:c.449del	p.Gly150GlufsTer68	p.G150Efs*68	ENST00000341105	NM_032638.4	150	gGa/ga	3/6	1	2	FACETS	0.778	0.692	0.871	0.778	0.692	0.871	SUBCLONAL	1	TRUE	1	0.374745465169081	2		652	617	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	106	631	1	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.946	0.85	1	0.946	0.85	1	CLONAL	1	TRUE	1	0.374745465169081	2		632	598	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952013	178952013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	95	429	1	ENST00000263967.3:c.3068G>A	p.Arg1023Gln	p.R1023Q	ENST00000263967	NM_006218.2	1023	cGa/cAa	21/21	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.374745465169081	2		430	500	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349594	70349594	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	131	604	0	ENST00000374080.3:c.3756G>T	p.Glu1252Asp	p.E1252D	ENST00000374080		1252	gaG/gaT	27/45	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.374745465169081	2		604	604	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281255	46281255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781251226	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	66	390	0	ENST00000371998.3:c.4052C>T	p.Pro1351Leu	p.P1351L	ENST00000371998		1351	cCg/cTg	21/23	1	2	FACETS	0.823	0.717	0.937	0.823	0.717	0.937	CLONAL	1	TRUE	1	0.374745465169081	2		390	428	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281305	15281305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	115	549	0	ENST00000263388.2:c.4951G>A	p.Ala1651Thr	p.A1651T	ENST00000263388	NM_000435.2	1651	Gct/Act	27/33	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.374745465169081	2		549	602	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095665	178095666	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	123	560	0	ENST00000397062.3:c.1665dup	p.Gln556ThrfsTer15	p.Q556Tfs*15	ENST00000397062	NM_006164.4	555	-/A	5/5	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.374745465169081	2		560	618	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477073	67477073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223744	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	188	424	0	ENST00000327367.4:c.880G>A	p.Val294Met	p.V294M	ENST00000327367	NM_005902.3	294	Gtg/Atg	7/9	0.374745465169081	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	0	0.374745465169081	2		424	501	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446229	29446229	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199987354	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	95	509	1	ENST00000389048.3:c.3338G>A	p.Arg1113Gln	p.R1113Q	ENST00000389048	NM_004304.4	1113	cGg/cAg	20/29	1	2	FACETS	0.927	0.828	1	0.927	0.828	1	CLONAL	1	TRUE	1	0.374745465169081	2		510	547	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874749	151874749	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	86	413	0	ENST00000262189.6:c.7789C>G	p.Pro2597Ala	p.P2597A	ENST00000262189	NM_170606.2	2597	Cca/Gca	38/59	1	2	FACETS	0.937	0.832	1	0.937	0.832	1	CLONAL	1	TRUE	1	0.374745465169081	2		413	490	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259567	16259567	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	111	441	0	ENST00000375759.3:c.6832G>A	p.Ala2278Thr	p.A2278T	ENST00000375759	NM_015001.2	2278	Gct/Act	11/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.374745465169081	2		441	489	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46512252	46512252	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	94	482	1	ENST00000262741.5:c.987G>A	p.Trp329Ter	p.W329*	ENST00000262741	NM_003629.3	329	tgG/tgA	8/10	1	2	FACETS	0.852	0.759	0.95	0.852	0.759	0.95	CLONAL	1	TRUE	1	0.374745465169081	2		483	589	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648237	206648237	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	98	543	0	ENST00000367120.3:c.258G>T	p.Met86Ile	p.M86I	ENST00000367120	NM_014002.3	86	atG/atT	5/22	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.374745465169081	2		543	491	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139302	108139302	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3218708	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	124	600	2	ENST00000278616.4:c.2804C>T	p.Thr935Met	p.T935M	ENST00000278616	NM_000051.3	935	aCg/aTg	18/63	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.374745465169081	2		602	635	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118354958	118354958	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	105	407	0	ENST00000534358.1:c.4147C>A	p.Leu1383Ile	p.L1383I	ENST00000534358	NM_005933.3	1383	Ctc/Atc	9/36	1	2	FACETS	0.913	0.819	1	0.913	0.819	1	CLONAL	1	TRUE	1	0.374745465169081	2		407	614	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503064	125503064	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	66	351	0	ENST00000428830.2:c.431T>A	p.Leu144His	p.L144H	ENST00000428830	NM_001114121.2	144	cTc/cAc	6/14	1	2	FACETS	0.841	0.732	0.957	0.841	0.732	0.957	CLONAL	1	TRUE	1	0.374745465169081	2		351	419	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574716	95574716	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	95	404	2	ENST00000393063.1:c.2381C>A	p.Pro794His	p.P794H	ENST00000393063	NM_030621.3	794	cCt/cAt	16/28	1	2	FACETS	0.951	0.85	1	0.951	0.85	1	CLONAL	1	TRUE	1	0.374745465169081	2		406	533	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646298	3646298	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	54	885	0	ENST00000294008.3:c.1780G>T	p.Gly594Cys	p.G594C	ENST00000294008	NM_032444.2	594	Ggc/Tgc	8/15	1	2	FACETS	0.349	0.297	0.407	0.349	0.297	0.407	SUBCLONAL	1	TRUE	1	0.374745465169081	2		885	825	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89862403	89862403	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370852532	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	115	551	1	ENST00000389301.3:c.917C>T	p.Thr306Met	p.T306M	ENST00000389301	NM_000135.2	306	aCg/aTg	11/43	1	2	FACETS	0.967	0.873	1	0.967	0.873	1	CLONAL	1	TRUE	1	0.374745465169081	2		552	635	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573010	7573010	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	36	439	0	ENST00000269305.4:c.1101-2A>C		p.X367_splice	ENST00000269305	NM_001126112.2	367			1	2	FACETS	0.363	0.298	0.437	0.363	0.298	0.437	SUBCLONAL	1	TRUE	1	0.374745465169081	2		439	529	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40444065	40444065	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	93	547	0	ENST00000345506.4:c.361C>T	p.Arg121Ter	p.R121*	ENST00000345506	NM_003152.3	121	Cga/Tga	5/20	1	2	FACETS	0.771	0.686	0.861	0.771	0.686	0.861	SUBCLONAL	1	TRUE	1	0.374745465169081	2		547	644	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7152805	7152805	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	157	644	0	ENST00000302850.5:c.2163G>T	p.Lys721Asn	p.K721N	ENST00000302850	NM_000208.2	721	aaG/aaT	10/22	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.374745465169081	2		644	802	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303080	15303080	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	44	834	0	ENST00000263388.2:c.370C>A	p.Leu124Ile	p.L124I	ENST00000263388	NM_000435.2	124	Ctc/Atc	4/33	1	2	FACETS	0.28	0.234	0.331	0.28	0.234	0.331	SUBCLONAL	1	TRUE	1	0.374745465169081	2		834	839	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349722	15349722	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1369312862	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	158	724	0	ENST00000263377.2:c.3852G>T	p.Glu1284Asp	p.E1284D	ENST00000263377	NM_058243.2	1284	gaG/gaT	19/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.374745465169081	2		724	667	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383353	42383353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs548487112	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	96	441	2	ENST00000221972.3:c.373G>A	p.Val125Met	p.V125M	ENST00000221972	NM_021601.3	125	Gtg/Atg	2/5	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.374745465169081	2		443	478	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467164	25467164	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	65	518	2	ENST00000264709.3:c.1711del	p.Ala571LeufsTer80	p.A571Lfs*80	ENST00000264709	NM_175629.2	571	Gct/ct	15/23	1	2	FACETS	0.754	0.655	0.86	0.754	0.655	0.86	SUBCLONAL	1	TRUE	1	0.374745465169081	2		520	460	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137460	202137460	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	91	377	0	ENST00000358485.4:c.688C>A	p.Leu230Met	p.L230M	ENST00000358485	NM_001080125.1	230	Ctg/Atg	4/9	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.374745465169081	2		377	478	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380472	31380472	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	108	516	1	ENST00000328111.2:c.962C>A	p.Pro321His	p.P321H	ENST00000328111	NM_006892.3	321	cCt/cAt	9/23	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.374745465169081	2		517	531	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62317157	62317157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	167	682	1	ENST00000360203.5:c.1280C>T	p.Pro427Leu	p.P427L	ENST00000360203	NM_001283009.1	427	cCt/cTt	16/35	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.374745465169081	2		683	717	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319059	62319059	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1409999749	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	164	806	0	ENST00000360203.5:c.1417C>T	p.Arg473Cys	p.R473C	ENST00000360203	NM_001283009.1	473	Cgc/Tgc	17/35	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.374745465169081	2		806	850	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574371	41574371	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	120	640	0	ENST00000263253.7:c.6656A>G	p.Tyr2219Cys	p.Y2219C	ENST00000263253	NM_001429.3	2219	tAc/tGc	31/31	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.374745465169081	2		640	603	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37092009	37092009	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs63750499	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	244	508	1	ENST00000231790.2:c.2136G>A	p.Trp712Ter	p.W712*	ENST00000231790	NM_000249.3	712	tgG/tgA	19/19	0.374745465169081	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.374745465169081	2		509	600	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933628	49933628	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	157	867	1	ENST00000296474.3:c.2649G>T	p.Glu883Asp	p.E883D	ENST00000296474	NM_002447.2	883	gaG/gaT	10/20	0.374745465169081	2	FACETS	0.968	0.887	1	0.484	0.443	0.526	CLONAL	1	TRUE	0	0.374745465169081	2		868	866	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612282	189612282	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	70	338	0	ENST00000264731.3:c.2038del	p.Glu680SerfsTer24	p.E680Sfs*24	ENST00000264731	NM_003722.4	678	gaG/ga	14/14	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.374745465169081	2		338	350	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1941440	1941440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1299648042	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	50	564	0	ENST00000382891.5:c.1816G>A	p.Ala606Thr	p.A606T	ENST00000382891	NM_133335.3	606	Gca/Aca	9/22	1	2	FACETS	0.337	0.285	0.395	0.337	0.285	0.395	SUBCLONAL	1	TRUE	1	0.374745465169081	2		564	791	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968667	55968667	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	107	444	0	ENST00000263923.4:c.1996G>A	p.Ala666Thr	p.A666T	ENST00000263923	NM_002253.2	666	Gca/Aca	14/30	1	2	FACETS	0.988	0.889	1	0.988	0.889	1	CLONAL	1	TRUE	1	0.374745465169081	2		444	578	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84384747	84384747	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1390153317	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	71	351	0	ENST00000321945.7:c.696del	p.Val233TrpfsTer8	p.V233Wfs*8	ENST00000321945	NM_139076.2	232	aaA/aa	8/9	1	2	FACETS	0.783	0.685	0.888	0.783	0.685	0.888	SUBCLONAL	1	TRUE	1	0.374745465169081	2		351	484	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526204	31526204	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377246504	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	179	834	0	ENST00000344624.3:c.836G>A	p.Arg279His	p.R279H	ENST00000344624		279	cGc/cAc	2/33	1	2	FACETS	0.978	0.901	1	0.978	0.901	1	CLONAL	1	TRUE	1	0.374745465169081	2		834	977	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161222	56161222	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	125	526	0	ENST00000399503.3:c.1093del	p.Val365CysfsTer4	p.V365Cfs*4	ENST00000399503	NM_005921.1	364	cGg/cg	5/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.374745465169081	2		526	594	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829017	128829017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	18	29	0	ENST00000249373.3:c.25G>A	p.Gly9Arg	p.G9R	ENST00000249373	NM_005631.4	9	Ggg/Agg	1/12	1	2	FACETS	0.961	0.755	1	1	0.938	1	CLONAL	2	TRUE	1	0.374745465169081	2		29	50	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485992	8485992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	106	524	0	ENST00000356435.5:c.2825C>T	p.Pro942Leu	p.P942L	ENST00000356435		942	cCt/cTt	17/35	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.374745465169081	2		524	550	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196796	123196796	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	24	440	0	ENST00000218089.9:c.1687del	p.Ile563SerfsTer13	p.I563Sfs*13	ENST00000218089	NM_001042749.1	561	acA/ac	18/35	1	2	FACETS	0.368	0.288	0.46	0.368	0.288	0.46	SUBCLONAL	1	TRUE	1	0.374745465169081	2		440	348	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224493	108224493	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs748192003	NA	P-0032710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	116	224	0	ENST00000278616.4:c.8672G>A	p.Gly2891Asp	p.G2891D	ENST00000278616	NM_000051.3	2891	gGt/gAt	60/63	0.590395860539429	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.590395860539429	2		224	179	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602719	55602719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752695117	NA	P-0032710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	176	424	1	ENST00000288135.5:c.2540C>T	p.Thr847Met	p.T847M	ENST00000288135	NM_000222.2	847	aCg/aTg	18/21	0.590395860539429	3	FACETS	0.963	0.899	1	0.963	0.899	1	CLONAL	2	TRUE	1	0.590395860539429	3		425	401	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585431	29585431	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	243	514	0	ENST00000356175.3:c.4180A>T	p.Asn1394Tyr	p.N1394Y	ENST00000356175	NM_000267.3	1394	Aat/Tat	31/57	0.590395860539429	3	FACETS	0.93	0.887	0.973	1	0.994	1	CLONAL	3	TRUE	1	0.590395860539429	3		514	382	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748455	40748455	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	80	490	0	ENST00000392038.2:c.427G>C	p.Ala143Pro	p.A143P	ENST00000392038	NM_001626.4	143	Gca/Cca	5/14	0.577471477762339	3	FACETS	0.737	0.651	0.829	0.369	0.325	0.415	SUBCLONAL	1	TRUE	1	0.590395860539429	3		490	476	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267337	198267338	+	inframe_insertion	In_Frame_Ins	INS	-	-	AATAGCTATCTGTTGTACAATCTTAATACC	novel	NA	P-0032710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	57	440	0	ENST00000335508.6:c.1990_2019dup	p.Gly664_Ile673dup	p.G664_I673dup	ENST00000335508	NM_012433.2	664	-/GGTATTAAGATTGTACAACAGATAGCTATT	14/25	0.577471477762339	3	FACETS	0.531	0.456	0.612	0.265	0.228	0.306	SUBCLONAL	1	TRUE	1	0.590395860539429	3		440	471	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	132	407	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.353623340650644	2		407	685	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	139	441	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.246120927696646	3	FACETS	1	0.985	1	0.703	0.642	0.767	CLONAL	1	TRUE	1	0.353623340650644	3		441	658	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	186	653	5	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	0.353623340650644	2		658	784	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	159	381	1	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.809	0.745	0.874	1	0.99	1	CLONAL	2	TRUE	1	0.353623340650644	2		382	556	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257842	16257842	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	68	438	0	ENST00000375759.3:c.5111del	p.Pro1704GlnfsTer11	p.P1704Qfs*11	ENST00000375759	NM_015001.2	1703	Ccc/cc	11/15	1	2	FACETS	0.592	0.514	0.675	0.592	0.514	0.675	SUBCLONAL	1	TRUE	1	0.353623340650644	2		438	650	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106330	27106330	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	122	503	0	ENST00000324856.7:c.5941T>C	p.Cys1981Arg	p.C1981R	ENST00000324856	NM_006015.4	1981	Tgc/Cgc	20/20	1	2	FACETS	0.801	0.724	0.883	0.801	0.724	0.883	CLONAL	1	TRUE	1	0.353623340650644	2		503	861	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803901	43803901	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs780738649	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	154	408	0	ENST00000372470.3:c.211C>T	p.Arg71Trp	p.R71W	ENST00000372470	NM_005373.2	71	Cgg/Tgg	2/12	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.353623340650644	2		408	609	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46715742	46715742	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	95	472	0	ENST00000371975.4:c.161C>A	p.Pro54His	p.P54H	ENST00000371975	NM_003579.3	54	cCt/cAt	3/18	1	2	FACETS	0.695	0.619	0.777	0.695	0.619	0.777	SUBCLONAL	1	TRUE	1	0.353623340650644	2		472	773	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115252188	115252188	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	75	334	0	ENST00000369535.4:c.450+2T>C		p.X150_splice	ENST00000369535	NM_002524.4	150			1	2	FACETS	0.73	0.64	0.827	0.73	0.64	0.827	SUBCLONAL	1	TRUE	1	0.353623340650644	2		334	581	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849855	156849855	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	106	549	0	ENST00000524377.1:c.2111T>C	p.Phe704Ser	p.F704S	ENST00000524377	NM_002529.3	704	tTc/tCc	16/17	1	2	FACETS	0.74	0.663	0.822	0.74	0.663	0.822	SUBCLONAL	1	TRUE	1	0.353623340650644	2		549	810	SUCCESS
RET	5979	MSKCC	GRCh37	10	43572711	43572711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	57	123	0	ENST00000355710.3:c.5C>T	p.Ala2Val	p.A2V	ENST00000355710	NM_020975.4	2	gCg/gTg	1/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.353623340650644	2		123	245	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136040	64136040	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	99	595	0	ENST00000334205.4:c.1301G>A	p.Gly434Asp	p.G434D	ENST00000334205	NM_003942.2	434	gGc/gAc	11/17	1	2	FACETS	0.654	0.583	0.73	0.654	0.583	0.73	SUBCLONAL	1	TRUE	1	0.353623340650644	2		595	856	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137791	64137791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	126	706	2	ENST00000334205.4:c.1892G>A	p.Gly631Glu	p.G631E	ENST00000334205	NM_003942.2	631	gGg/gAg	15/17	1	2	FACETS	0.685	0.619	0.755	0.685	0.619	0.755	SUBCLONAL	1	TRUE	1	0.353623340650644	2		708	1040	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111965527	111965527	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	109	303	0	ENST00000375549.3:c.315-2A>G		p.X105_splice	ENST00000375549	NM_003002.3	105			1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.353623340650644	2		303	431	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307348	118307348	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	10	10	0	ENST00000534358.1:c.126del	p.Pro45ArgfsTer105	p.P45Rfs*105	ENST00000534358	NM_005933.3	41	Ccc/cc	1/36	1	2	FACETS	1	0.774	1	1	0.902	1	CLONAL	2	TRUE	1	0.353623340650644	2		10	26	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	104	635	2	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.63	0.563	0.701	0.63	0.563	0.701	SUBCLONAL	1	TRUE	1	0.353623340650644	2		637	934	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505404	125505404	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	132	319	0	ENST00000428830.2:c.694A>G	p.Lys232Glu	p.K232E	ENST00000428830	NM_001114121.2	232	Aaa/Gaa	7/14	1	2	FACETS	0.757	0.692	0.825	1	0.987	1	SUBCLONAL	2	TRUE	1	0.353623340650644	2		319	493	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498235	498235	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	35	189	2	ENST00000399788.2:c.23del	p.Gly8AlafsTer58	p.G8Afs*58	ENST00000399788	NM_001042603.1	8	gGc/gc	1/28	0.246120927696646	3	FACETS	0.693	0.569	0.832	0.347	0.284	0.416	SUBCLONAL	1	TRUE	1	0.353623340650644	3		191	336	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644434	18644434	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	70	400	0	ENST00000266497.5:c.2612T>C	p.Val871Ala	p.V871A	ENST00000266497		871	gTa/gCa	18/31	0.246120927696646	3	FACETS	0.744	0.649	0.847	0.372	0.324	0.424	SUBCLONAL	1	TRUE	1	0.353623340650644	3		400	626	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	113	557	4	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	0.246120927696646	3	FACETS	0.786	0.706	0.871	0.393	0.353	0.436	SUBCLONAL	1	TRUE	1	0.353623340650644	3		561	957	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246076	46246076	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	110	336	0	ENST00000334344.6:c.4170A>G	p.Ile1390Met	p.I1390M	ENST00000334344	NM_152641.2	1390	atA/atG	15/21	0.246120927696646	3	FACETS	0.756	0.683	0.833	0.756	0.683	0.833	SUBCLONAL	2	TRUE	1	0.353623340650644	3		336	484	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427129	49427129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	310	583	0	ENST00000301067.7:c.11359G>A	p.Val3787Ile	p.V3787I	ENST00000301067	NM_003482.3	3787	Gtc/Atc	39/54	0.246120927696646	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.353623340650644	3		583	878	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427708	49427708	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	332	613	0	ENST00000301067.7:c.10780G>T	p.Glu3594Ter	p.E3594*	ENST00000301067	NM_003482.3	3594	Gaa/Taa	39/54	0.246120927696646	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.353623340650644	3		613	999	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	197	651	1	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.246120927696646	3	FACETS	1	0.99	1	0.737	0.683	0.793	CLONAL	1	TRUE	1	0.353623340650644	3		652	889	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	283	454	0	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	0.246120927696646	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.353623340650644	3		454	862	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112218	115112218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs994091095	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	155	334	0	ENST00000257566.3:c.1522G>A	p.Ala508Thr	p.A508T	ENST00000257566	NM_016569.3	508	Gcg/Acg	7/8	0.246120927696646	3	FACETS	0.961	0.885	1	0.961	0.885	1	CLONAL	2	TRUE	1	0.353623340650644	3		334	537	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112283	115112283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1018135320	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	119	94	0	ENST00000257566.3:c.1457C>T	p.Thr486Met	p.T486M	ENST00000257566	NM_016569.3	486	aCg/aTg	7/8	0.246120927696646	3	FACETS	1	0.968	1	1	0.989	1	CLONAL	3	TRUE	1	0.353623340650644	3		94	241	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118854	115118854	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	83	435	0	ENST00000257566.3:c.487T>C	p.Tyr163His	p.Y163H	ENST00000257566	NM_016569.3	163	Tat/Cat	2/8	0.246120927696646	3	FACETS	0.69	0.608	0.778	0.345	0.304	0.389	SUBCLONAL	1	TRUE	1	0.353623340650644	3		435	801	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800916	120800916	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	86	540	0	ENST00000257552.2:c.332T>C	p.Ile111Thr	p.I111T	ENST00000257552	NM_002442.3	111	aTc/aCc	6/15	0.246120927696646	3	FACETS	0.591	0.522	0.666	0.296	0.261	0.333	SUBCLONAL	1	TRUE	1	0.353623340650644	3		540	968	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562618	21562618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	48	201	0	ENST00000382592.4:c.1301C>T	p.Ala434Val	p.A434V	ENST00000382592	NM_014572.2	434	gCt/gTt	4/8	1	2	FACETS	0.689	0.584	0.804	0.689	0.584	0.804	SUBCLONAL	1	TRUE	1	0.353623340650644	2		201	394	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26927982	26927982	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1339818101	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	73	478	0	ENST00000381527.3:c.421T>C	p.Tyr141His	p.Y141H	ENST00000381527	NM_001260.1	141	Tac/Cac	4/13	1	2	FACETS	0.651	0.569	0.739	0.651	0.569	0.739	SUBCLONAL	1	TRUE	1	0.353623340650644	2		478	634	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896469	28896470	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	124	332	0	ENST00000282397.4:c.2980dup	p.Ile994AsnfsTer39	p.I994Nfs*39	ENST00000282397	NM_002019.4	994	atc/aAtc	22/30	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.353623340650644	2		332	495	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916852	48916852	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	41	298	0	ENST00000267163.4:c.380+2T>C		p.X127_splice	ENST00000267163	NM_000321.2	127			1	2	FACETS	0.622	0.519	0.735	0.622	0.519	0.735	SUBCLONAL	1	TRUE	1	0.353623340650644	2		298	373	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030368	49030368	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	59	279	0	ENST00000267163.4:c.1848del	p.Gly617ValfsTer6	p.G617Vfs*6	ENST00000267163	NM_000321.2	615	Aaa/aa	19/27	1	2	FACETS	0.802	0.692	0.921	0.802	0.692	0.921	CLONAL	1	TRUE	1	0.353623340650644	2		279	416	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518670	103518670	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	36	297	0	ENST00000355739.4:c.2262del	p.Lys754AsnfsTer46	p.K754Nfs*46	ENST00000355739	NM_000123.3	753	cAa/ca	10/15	1	2	FACETS	0.448	0.368	0.538	0.448	0.368	0.538	SUBCLONAL	1	TRUE	1	0.353623340650644	2		297	454	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482771	67482771	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	193	415	0	ENST00000327367.4:c.1179del	p.Cys394AlafsTer7	p.C394Afs*7	ENST00000327367	NM_005902.3	392	aCc/ac	9/9	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.353623340650644	2		415	735	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640518	3640518	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	110	695	1	ENST00000294008.3:c.3121del	p.Gln1041ArgfsTer75	p.Q1041Rfs*75	ENST00000294008	NM_032444.2	1041	Cag/ag	12/15	1	2	FACETS	0.688	0.617	0.763	0.688	0.617	0.763	SUBCLONAL	1	TRUE	1	0.353623340650644	2		696	904	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777952	3777952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	165	771	0	ENST00000262367.5:c.7096C>T	p.Arg2366Trp	p.R2366W	ENST00000262367	NM_004380.2	2366	Cgg/Tgg	31/31	1	2	FACETS	0.845	0.774	0.918	0.845	0.774	0.918	CLONAL	1	TRUE	1	0.353623340650644	2		771	1105	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786703	3786703	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587783497	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	98	601	0	ENST00000262367.5:c.4508A>G	p.Tyr1503Cys	p.Y1503C	ENST00000262367	NM_004380.2	1503	tAc/tGc	27/31	1	2	FACETS	0.536	0.476	0.599	0.536	0.476	0.599	SUBCLONAL	1	TRUE	1	0.353623340650644	2		601	1035	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	99	348	4	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.788	0.703	0.877	0.788	0.703	0.877	SUBCLONAL	1	TRUE	1	0.353623340650644	2		352	711	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56857698	56857698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	174	393	0	ENST00000308159.5:c.734G>A	p.Arg245His	p.R245H	ENST00000308159	NM_014669.4	245	cGc/cAc	8/22	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.353623340650644	2		393	673	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	102	423	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.353623340650644	2		423	492	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827589	72827589	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343025200	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	226	643	0	ENST00000268489.5:c.8992C>T	p.Arg2998Trp	p.R2998W	ENST00000268489	NM_006885.3	2998	Cgg/Tgg	9/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.353623340650644	2		643	923	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831764	72831764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	109	627	0	ENST00000268489.5:c.4817G>A	p.Ser1606Asn	p.S1606N	ENST00000268489	NM_006885.3	1606	aGc/aAc	9/10	1	2	FACETS	0.703	0.631	0.78	0.703	0.631	0.78	SUBCLONAL	1	TRUE	1	0.353623340650644	2		627	877	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127270	17127270	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs878855217	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	204	543	1	ENST00000285071.4:c.584del	p.Gly195GlufsTer28	p.G195Efs*28	ENST00000285071	NM_144997.5	195	gGa/ga	6/14	1	2	FACETS	0.794	0.738	0.85	1	0.992	1	SUBCLONAL	2	TRUE	1	0.353623340650644	2		544	727	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120043	70120043	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	14	19	0	ENST00000245479.2:c.1049del	p.Pro350HisfsTer33	p.P350Hfs*33	ENST00000245479	NM_000346.3	349	Ccc/cc	3/3	1	2	FACETS	0.966	0.731	1	1	0.921	1	CLONAL	2	TRUE	1	0.353623340650644	2		19	41	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78599498	78599498	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	169	403	0	ENST00000306801.3:c.170del	p.Thr57LysfsTer6	p.T57Kfs*6	ENST00000306801	NM_020761.2	57	aCa/aa	2/34	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.353623340650644	2		403	657	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612377	1612377	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753978381	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	251	604	0	ENST00000344749.5:c.1642C>T	p.Arg548Cys	p.R548C	ENST00000344749	NM_001136139.2	548	Cgc/Tgc	18/19	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.353623340650644	2		604	960	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208031	5208031	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	76	499	0	ENST00000357368.4:c.5680A>G	p.Ser1894Gly	p.S1894G	ENST00000357368	NM_002850.3	1894	Agc/Ggc	37/38	1	2	FACETS	0.602	0.528	0.682	0.602	0.528	0.682	SUBCLONAL	1	TRUE	1	0.353623340650644	2		499	714	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210704	5210704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766174955	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	95	586	0	ENST00000357368.4:c.5347C>T	p.Arg1783Trp	p.R1783W	ENST00000357368	NM_002850.3	1783	Cgg/Tgg	34/38	1	2	FACETS	0.59	0.525	0.661	0.59	0.525	0.661	SUBCLONAL	1	TRUE	1	0.353623340650644	2		586	910	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5216772	5216772	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1403235094	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	91	233	0	ENST00000357368.4:c.4055G>A	p.Gly1352Asp	p.G1352D	ENST00000357368	NM_002850.3	1352	gGc/gAc	26/38	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.353623340650644	2		233	375	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288447	15288447	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	53	373	0	ENST00000263388.2:c.4292T>C	p.Leu1431Pro	p.L1431P	ENST00000263388	NM_000435.2	1431	cTg/cCg	24/33	1	2	FACETS	0.628	0.536	0.729	0.628	0.536	0.729	SUBCLONAL	1	TRUE	1	0.353623340650644	2		373	477	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288456	15288456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	60	338	0	ENST00000263388.2:c.4283G>A	p.Cys1428Tyr	p.C1428Y	ENST00000263388	NM_000435.2	1428	tGc/tAc	24/33	1	2	FACETS	0.733	0.633	0.842	0.733	0.633	0.842	SUBCLONAL	1	TRUE	1	0.353623340650644	2		338	463	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353819	15353819	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	116	470	3	ENST00000263377.2:c.3061del	p.His1021IlefsTer47	p.H1021Ifs*47	ENST00000263377	NM_058243.2	1021	Cat/at	14/20	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.353623340650644	2		473	655	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214398	36214398	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs868041281	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	175	485	2	ENST00000222270.7:c.3057del	p.Gly1020AlafsTer4	p.G1020Afs*4	ENST00000222270	NM_014727.1	1018	Aaa/aa	7/37	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.353623340650644	2		487	704	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223328	36223328	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	298	723	0	ENST00000222270.7:c.5882del	p.Pro1961LeufsTer26	p.P1961Lfs*26	ENST00000222270	NM_014727.1	1960	Ccc/cc	28/37	1	2	FACETS	0.775	0.73	0.821	1	0.994	1	SUBCLONAL	2	TRUE	1	0.353623340650644	2		723	1088	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966873	25966873	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1271466699	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	97	553	3	ENST00000435504.4:c.2333del	p.Pro778GlnfsTer21	p.P778Qfs*21	ENST00000435504		778	cCa/ca	13/13	0.246120927696646	3	FACETS	0.739	0.658	0.825	0.369	0.329	0.413	SUBCLONAL	1	TRUE	1	0.353623340650644	3		556	874	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39239433	39239433	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	186	573	0	ENST00000402219.2:c.2224del	p.Ile742LeufsTer24	p.I742Lfs*24	ENST00000402219	NM_005633.3	742	Att/tt	14/23	0.246120927696646	3	FACETS	1	0.987	1	0.667	0.616	0.72	CLONAL	1	TRUE	1	0.353623340650644	3		573	928	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170890	99170890	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	224	536	0	ENST00000074304.5:c.1519G>A	p.Ala507Thr	p.A507T	ENST00000074304	NM_001134224.1	507	Gcc/Acc	16/26	0.246120927696646	3	FACETS	0.831	0.775	0.889	0.831	0.775	0.889	CLONAL	2	TRUE	1	0.353623340650644	3		536	897	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	157	473	2	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	0.246120927696646	3	FACETS	1	0.986	1	0.696	0.638	0.756	CLONAL	1	TRUE	1	0.353623340650644	3		475	751	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662980	227662980	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1215890148	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	119	551	0	ENST00000305123.5:c.475G>A	p.Ala159Thr	p.A159T	ENST00000305123	NM_005544.2	159	Gca/Aca	1/2	0.246120927696646	3	FACETS	0.856	0.772	0.945	0.428	0.386	0.473	CLONAL	1	TRUE	1	0.353623340650644	3		551	925	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817415	39817415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148089492	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	84	441	0	ENST00000288319.7:c.148C>T	p.Arg50Cys	p.R50C	ENST00000288319	NM_182918.3	50	Cgc/Tgc	2/10	1	2	FACETS	0.696	0.614	0.783	0.696	0.614	0.783	SUBCLONAL	1	TRUE	1	0.353623340650644	2		441	683	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37637690	37637690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	95	511	0	ENST00000249071.6:c.44G>A	p.Gly15Asp	p.G15D	ENST00000249071	NM_002872.4	15	gGc/gAc	2/7	1	2	FACETS	0.729	0.649	0.814	0.729	0.649	0.814	SUBCLONAL	1	TRUE	1	0.353623340650644	2		511	737	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566570	41566570	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	56	282	0	ENST00000263253.7:c.4447T>C	p.Tyr1483His	p.Y1483H	ENST00000263253	NM_001429.3	1483	Tac/Cac	27/31	1	2	FACETS	0.74	0.636	0.854	0.74	0.636	0.854	SUBCLONAL	1	TRUE	1	0.353623340650644	2		282	428	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089123	37089125	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs63751247	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	176	412	0	ENST00000231790.2:c.1852_1854del	p.Lys618del	p.K618del	ENST00000231790	NM_000249.3	615	ctGAAg/ctg	16/19	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.353623340650644	2		412	717	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722213	49722213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	161	392	0	ENST00000449682.2:c.1727G>A	p.Cys576Tyr	p.C576Y	ENST00000449682	NM_020998.3	576	tGt/tAt	15/18	1	2	FACETS	0.785	0.724	0.848	1	0.99	1	SUBCLONAL	2	TRUE	1	0.353623340650644	2		392	580	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722791	49722791	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316094064	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	10	52	0	ENST00000449682.2:c.1448G>A	p.Gly483Asp	p.G483D	ENST00000449682	NM_020998.3	483	gGc/gAc	13/18	1	2	FACETS	0.832	0.573	1	0.832	0.573	1	CLONAL	1	TRUE	1	0.353623340650644	2		52	68	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	123	302	0	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.353623340650644	2		302	576	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119642242	119642242	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs72546695	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	97	467	0	ENST00000316626.5:c.455C>T	p.Thr152Met	p.T152M	ENST00000316626		152	aCg/aTg	4/12	1	2	FACETS	0.767	0.684	0.856	0.767	0.684	0.856	SUBCLONAL	1	TRUE	1	0.353623340650644	2		467	715	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851558	134851558	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs770155473	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	146	392	0	ENST00000398015.3:c.964G>A	p.Val322Ile	p.V322I	ENST00000398015	NM_004441.4	322	Gtc/Atc	5/16	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.353623340650644	2		392	578	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374697	149374697	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	88	503	0	ENST00000360632.3:c.397A>G	p.Thr133Ala	p.T133A	ENST00000360632	NM_015472.4	133	Acc/Gcc	2/7	1	2	FACETS	0.654	0.579	0.734	0.654	0.579	0.734	SUBCLONAL	1	TRUE	1	0.353623340650644	2		503	761	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55130038	55130038	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	112	480	0	ENST00000257290.5:c.572C>T	p.Ala191Val	p.A191V	ENST00000257290	NM_006206.4	191	gCc/gTc	4/23	0.328217058530803	1	FACETS	0.795	0.716	0.878	0.795	0.716	0.878	SUBCLONAL	1	TRUE	0	0.353623340650644	1		480	656	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155778	106155779	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs759055581	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	73	416	0	ENST00000380013.4:c.685dup	p.Thr229AsnfsTer25	p.T229Nfs*25	ENST00000380013	NM_001127208.2	227	gaa/gAaa	3/11	0.328217058530803	1	FACETS	0.603	0.527	0.683	0.603	0.527	0.683	SUBCLONAL	1	TRUE	0	0.353623340650644	1		416	564	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251907	153251907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	155	520	0	ENST00000281708.4:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000281708	NM_033632.3	367	Cga/Tga	7/12	0.328217058530803	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.353623340650644	1		520	599	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293896	1293896	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1561213793	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	144	712	0	ENST00000310581.5:c.1105A>G	p.Arg369Gly	p.R369G	ENST00000310581	NM_198253.2	369	Agg/Ggg	2/16	1	2	FACETS	0.765	0.696	0.837	0.765	0.696	0.837	SUBCLONAL	1	TRUE	1	0.353623340650644	2		712	1065	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876532	35876532	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	67	450	0	ENST00000303115.3:c.1324G>T	p.Gly442Ter	p.G442*	ENST00000303115	NM_002185.3	442	Gga/Tga	8/8	1	2	FACETS	0.571	0.495	0.652	0.571	0.495	0.652	SUBCLONAL	1	TRUE	1	0.353623340650644	2		450	664	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	116	404	1	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.353623340650644	2		405	529	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	100	260	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.353623340650644	2		260	429	SUCCESS
APC	324	MSKCC	GRCh37	5	112155032	112155032	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554080162	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	124	421	0	ENST00000257430.4:c.1307del	p.Asn436IlefsTer18	p.N436Ifs*18	ENST00000257430	NM_000038.5	435	Aaa/aa	10/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.353623340650644	2		421	617	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638363	176638363	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	135	638	0	ENST00000439151.2:c.2963C>A	p.Ser988Tyr	p.S988Y	ENST00000439151	NM_022455.4	988	tCt/tAt	5/23	1	2	FACETS	0.817	0.742	0.897	0.817	0.742	0.897	CLONAL	1	TRUE	1	0.353623340650644	2		638	934	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20488470	20488470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147333935	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	49	299	0	ENST00000346618.3:c.1126G>A	p.Ala376Thr	p.A376T	ENST00000346618	NM_001949.4	376	Gct/Act	6/7	0.353623340650644	2	FACETS	0.679	0.576	0.792	0.34	0.288	0.396	SUBCLONAL	1	TRUE	0	0.353623340650644	2		299	408	SUCCESS
MET	4233	MSKCC	GRCh37	7	116417506	116417506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	47	346	0	ENST00000397752.3:c.3323C>T	p.Ala1108Val	p.A1108V	ENST00000397752	NM_000245.2	1108	gCt/gTt	16/21	1	2	FACETS	0.562	0.474	0.658	0.562	0.474	0.658	SUBCLONAL	1	TRUE	1	0.353623340650644	2		346	473	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739732	145739732	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	110	578	0	ENST00000428558.2:c.1719G>T	p.Gln573His	p.Q573H	ENST00000428558	NM_004260.3	573	caG/caT	11/22	1	2	FACETS	0.86	0.774	0.952	0.86	0.774	0.952	CLONAL	1	TRUE	1	0.353623340650644	2		578	723	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	189	485	0	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.353623340650644	2		485	724	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412249	139412249	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	104	645	0	ENST00000277541.6:c.1396A>G	p.Thr466Ala	p.T466A	ENST00000277541	NM_017617.3	466	Acc/Gcc	8/34	1	2	FACETS	0.576	0.514	0.641	0.576	0.514	0.641	SUBCLONAL	1	TRUE	1	0.353623340650644	2		645	1022	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223533	53223533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	144	481	0	ENST00000375401.3:c.3826G>A	p.Glu1276Lys	p.E1276K	ENST00000375401	NM_004187.3	1276	Gag/Aag	23/26	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.353623340650644	2		481	563	SUCCESS
AR	367	MSKCC	GRCh37	X	66765088	66765088	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	86	512	0	ENST00000374690.3:c.100A>G	p.Ile34Val	p.I34V	ENST00000374690	NM_000044.3	34	Atc/Gtc	1/8	1	2	FACETS	0.673	0.595	0.756	0.673	0.595	0.756	SUBCLONAL	1	TRUE	1	0.353623340650644	2		512	723	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858098	152858098	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782309279	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	97	564	0	ENST00000406277.2:c.517C>T	p.Arg173Trp	p.R173W	ENST00000406277	NM_152274.4	173	Cgg/Tgg	6/7	1	2	FACETS	0.726	0.647	0.81	0.726	0.647	0.81	SUBCLONAL	1	TRUE	1	0.353623340650644	2		564	756	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37056038	37056038	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	C	novel	NA	P-0032718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	89	249	0	ENST00000231790.2:c.790+3A>C		p.X264_splice	ENST00000231790	NM_000249.3	264			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.353623340650644	2		249	399	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0032719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	306	809	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.505928424066312	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.505928424066312	1		809	689	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0032719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	76	280	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.180267595249411	3	FACETS	1	0.973	1	0.682	0.605	0.763	INDETERMINATE	1	TRUE	1	0.505928424066312	3		280	276	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576091	29576091	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1131691087	NA	P-0032719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	134	520	0	ENST00000356175.3:c.4064C>G	p.Ser1355Ter	p.S1355*	ENST00000356175	NM_000267.3	1355	tCa/tGa	30/57	0.49330776729482	1	FACETS	0.972	0.892	1	0.972	0.892	1	CLONAL	1	TRUE	0	0.505928424066312	1		520	407	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713171	30713171	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	167	401	0	ENST00000295754.5:c.496C>T	p.Gln166Ter	p.Q166*	ENST00000295754	NM_003242.5	166	Caa/Taa	4/7	0.505928424066312	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.505928424066312	1		401	388	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446249	187446249	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	293	571	0	ENST00000232014.4:c.1439C>G	p.Ser480Cys	p.S480C	ENST00000232014	NM_001130845.1	480	tCt/tGt	6/10	0.180267595249411	3	FACETS	0.754	0.711	0.799	0.754	0.711	0.799	INDETERMINATE	2	TRUE	1	0.505928424066312	3		571	962	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458050	120458050	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	233	515	0	ENST00000256646.2:c.7295C>G	p.Ser2432Cys	p.S2432C	ENST00000256646	NM_024408.3	2432	tCt/tGt	34/34	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.505928424066312	2		515	773	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576105	29576105	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	125	511	0	ENST00000356175.3:c.4078C>A	p.Gln1360Lys	p.Q1360K	ENST00000356175	NM_000267.3	1360	Caa/Aaa	30/57	0.49330776729482	1	FACETS	0.942	0.861	1	0.942	0.861	1	CLONAL	1	TRUE	0	0.505928424066312	1		511	392	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58701007	58701007	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	65	541	0	ENST00000305921.3:c.598C>G	p.Gln200Glu	p.Q200E	ENST00000305921	NM_003620.3	200	Cag/Gag	2/6	NA	2	FACETS	0.324	0.28	0.371			1	INDETERMINATE	1	TRUE	NA	0.505928424066312	2		541	794	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754509	41754509	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	240	525	0	ENST00000301178.4:c.1628G>T	p.Gly543Val	p.G543V	ENST00000301178	NM_021913.4	543	gGa/gTa	13/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.505928424066312	2		525	808	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713217	30713217	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	198	381	0	ENST00000295754.5:c.542C>G	p.Ser181Cys	p.S181C	ENST00000295754	NM_003242.5	181	tCt/tGt	4/7	0.505928424066312	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.505928424066312	1		381	423	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178547	56178550	+	frameshift_variant	Frame_Shift_Del	DEL	AATC	AATC	-	novel	NA	P-0032719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	63	232	0	ENST00000399503.3:c.3522_3525del	p.Asn1174LysfsTer15	p.N1174Kfs*15	ENST00000399503	NM_005921.1	1174	AATCaa/aa	14/20	0.505928424066312	1	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	0	0.505928424066312	1		232	179	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90995048	90995048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781748	NA	P-0032719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	74	458	0	ENST00000265433.3:c.73G>A	p.Val25Ile	p.V25I	ENST00000265433	NM_002485.4	25	Gtt/Att	2/16	0.505928424066312	3	FACETS	0.972	0.856	1	0.324	0.285	0.366	CLONAL	1	TRUE	0	0.505928424066312	3		458	377	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5066725	5066725	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	63	397	0	ENST00000381652.3:c.1262G>C	p.Gly421Ala	p.G421A	ENST00000381652	NM_004972.3	421	gGa/gCa	10/25	1	2	FACETS	0.996	0.872	1	0.996	0.872	1	CLONAL	1	TRUE	1	0.505928424066312	2		397	250	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	120	441	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.405210202773697	3	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	1	0.405210202773697	3		441	345	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176338	24176338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	10	503	0	ENST00000263121.7:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000263121	NM_003073.3	377	Cgt/Tgt	9/9	0.405210202773697	3	FACETS	0.195	0.131	0.276	0.098	0.065	0.138	SUBCLONAL	1	TRUE	1	0.405210202773697	3		503	304	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346338	73346338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	9	391	0	ENST00000377767.4:c.1462G>A	p.Asp488Asn	p.D488N	ENST00000377767	NM_014953.3	488	Gat/Aat	10/21	0.405210202773697	6	FACETS	0.266	0.175	0.383	0.067	0.043	0.096	SUBCLONAL	1	TRUE	2	0.405210202773697	6		391	302	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561352	9561352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773981325	NA	P-0032720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	8	453	1	ENST00000353224.5:c.430G>A	p.Glu144Lys	p.E144K	ENST00000353224	NM_177990.2	144	Gaa/Aaa	4/10	0.405210202773697	4	FACETS	0.189	0.121	0.278	0.095	0.06	0.139	SUBCLONAL	1	TRUE	2	0.405210202773697	4		454	293	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74858884	74858884	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	14	490	0	ENST00000284811.8:c.320C>T	p.Ala107Val	p.A107V	ENST00000284811		107	gCg/gTg	4/4	1	2	FACETS	0.286	0.206	0.382	0.286	0.206	0.382	SUBCLONAL	1	TRUE	1	0.405210202773697	2		490	242	SUCCESS
APC	324	MSKCC	GRCh37	5	112175351	112175351	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	55	251	0	ENST00000257430.4:c.4063del	p.Ser1355LeufsTer60	p.S1355Lfs*60	ENST00000257430	NM_000038.5	1354	Ttt/tt	16/16	0.405210202773697	3	FACETS	1	0.895	1	1	0.976	1	CLONAL	3	TRUE	1	0.405210202773697	3		251	108	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106169	27106170	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	65	383	0	ENST00000324856.7:c.5781dup	p.Lys1928Ter	p.K1928*	ENST00000324856	NM_006015.4	1927	gct/gcTt	20/20	0.227621548432125	3	FACETS	1	0.892	1	0.673	0.595	0.755	INDETERMINATE	2	TRUE	0	0.405210202773697	3		383	191	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81927333	81927333	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	85	462	0	ENST00000359376.3:c.1006C>G	p.Leu336Val	p.L336V	ENST00000359376	NM_002661.3	336	Ctg/Gtg	12/33	1	2	FACETS	1	0.906	1	1	0.987	1	CLONAL	2	TRUE	1	0.405210202773697	2		462	209	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119714	70119714	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	310	453	0	ENST00000245479.2:c.717del	p.Thr240ProfsTer13	p.T240Pfs*13	ENST00000245479	NM_000346.3	239	aCc/ac	3/3	0.405210202773697	4	FACETS	1	0.99	1	1	0.996	1	CLONAL	4	TRUE	1	0.405210202773697	4		453	484	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243983	5243983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762898326	NA	P-0032720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	51	530	0	ENST00000357368.4:c.1499G>A	p.Arg500Gln	p.R500Q	ENST00000357368	NM_002850.3	500	cGg/cAg	11/38	0.369815842805898	4	FACETS	1	0.964	1	0.485	0.416	0.559	CLONAL	1	TRUE	1	0.405210202773697	4		530	243	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092929	29092929	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs764181318	NA	P-0032720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	80	460	0	ENST00000328354.6:c.1055A>G	p.Asn352Ser	p.N352S	ENST00000328354	NM_007194.3	352	aAt/aGt	10/15	0.405210202773697	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.405210202773697	3		460	190	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0032721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	125	503	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.324699159254177	4	FACETS	0.773	0.702	0.847	0.773	0.702	0.847	SUBCLONAL	2	TRUE	2	0.384991781639389	4		503	582	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578509	7578509	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519978	NA	P-0032721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	250	849	0	ENST00000269305.4:c.421T>C	p.Cys141Arg	p.C141R	ENST00000269305	NM_001126112.2	141	Tgc/Cgc	5/11	0.310931004685899	2	FACETS	0.78	0.732	0.83	0.78	0.732	0.83	SUBCLONAL	2	TRUE	0	0.384991781639389	2		849	832	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318754	163318755	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	100	329	0	ENST00000271452.3:c.1150dup	p.Arg384LysfsTer6	p.R384Kfs*6	ENST00000271452	NM_145697.2	382	gaa/gAaa	13/14	0.384991781639389	4	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.384991781639389	4		329	536	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213345	36213345	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	121	619	0	ENST00000222270.7:c.2542T>C	p.Ser848Pro	p.S848P	ENST00000222270	NM_014727.1	848	Tcg/Ccg	4/37	0.310673341349703	5	FACETS	0.869	0.783	0.96	0.29	0.261	0.32	CLONAL	1	TRUE	2	0.384991781639389	5		619	1141	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228801	36228801	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	111	709	0	ENST00000222270.7:c.7700G>A	p.Arg2567His	p.R2567H	ENST00000222270	NM_014727.1	2567	cGt/cAt	35/37	0.310673341349703	5	FACETS	0.814	0.73	0.903	0.271	0.243	0.301	CLONAL	1	TRUE	2	0.384991781639389	5		709	1118	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342860	87342860	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	71	436	0	ENST00000277120.3:c.1145C>T	p.Pro382Leu	p.P382L	ENST00000277120		382	cCt/cTt	9/19	1	2	FACETS	0.711	0.621	0.807	0.711	0.621	0.807	SUBCLONAL	1	TRUE	1	0.384991781639389	2		436	519	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0032722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	259	428	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.785421176932442	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.785421176932442	1		428	381	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348930	11348930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	254	379	0	ENST00000332029.2:c.406C>T	p.His136Tyr	p.H136Y	ENST00000332029	NM_003745.1	136	Cac/Tac	2/2	0.756287301018309	3	FACETS	1	0.972	1	0.53	0.498	0.564	CLONAL	1	TRUE	1	0.785421176932442	3		379	849	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555525857	NA	P-0032724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	116	608	1	ENST00000269305.4:c.596G>A	p.Gly199Glu	p.G199E	ENST00000269305	NM_001126112.2	199	gGa/gAa	6/11	0.346693291187033	1	FACETS	0.863	0.782	0.948	0.863	0.782	0.948	CLONAL	1	FALSE	0	0.426310689826334	1		609	496	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	206	474	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.303573575596502	2	FACETS	1	0.936	1	0.503	0.468	0.539	INDETERMINATE	1	TRUE	0	0.525062199666461	2		474	780	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578262	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs483352697	NA	P-0032725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	122	631	0	ENST00000269305.4:c.587G>C	p.Arg196Pro	p.R196P	ENST00000269305	NM_001126112.2	196	cGa/cCa	6/11	0.525062199666461	1	FACETS	0.844	0.77	0.921	0.844	0.77	0.921	CLONAL	1	TRUE	0	0.525062199666461	1		631	406	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030645	48030645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750998	NA	P-0032725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	160	531	0	ENST00000234420.5:c.3259C>T	p.Pro1087Ser	p.P1087S	ENST00000234420	NM_000179.2	1087	Ccc/Tcc	5/10	1	2	FACETS	0.925	0.851	1	0.925	0.851	1	CLONAL	1	TRUE	1	0.525062199666461	2		531	659	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729958	30729973	+	frameshift_variant	Frame_Shift_Del	DEL	AGATCGAGGGCGACCA	AGATCGAGGGCGACCA	-	novel	NA	P-0032725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	114	367	0	ENST00000295754.5:c.1479_1494del	p.Asp494LysfsTer19	p.D494Kfs*19	ENST00000295754	NM_003242.5	493	agAGATCGAGGGCGACCA/ag	6/7	0.525062199666461	1	FACETS	0.787	0.714	0.862	0.787	0.714	0.862	SUBCLONAL	1	TRUE	0	0.525062199666461	1		367	407	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971205	21971206	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0032725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	122	360	0	ENST00000304494.5:c.152_153delinsAT	p.Val51Asp	p.V51D	ENST00000304494	NM_000077.4	51	gTC/gAT	2/3	0.200714193969198	1	FACETS	1	0.961	1	1	0.961	1	INDETERMINATE	1	TRUE	0	0.525062199666461	1		360	317	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	213	474	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.562697554563535	2		474	537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0032726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	326	732	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.562697554563535	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.562697554563535	1		732	784	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0032726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	62	258	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.938	0.82	1	0.938	0.82	1	CLONAL	1	TRUE	1	0.562697554563535	2		258	235	SUCCESS
APC	324	MSKCC	GRCh37	5	112175225	112175225	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	83	259	0	ENST00000257430.4:c.3934G>T	p.Gly1312Ter	p.G1312*	ENST00000257430	NM_000038.5	1312	Gga/Tga	16/16	1	2	FACETS	0.911	0.811	1	0.911	0.811	1	CLONAL	1	TRUE	1	0.562697554563535	2		259	324	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157924	27157924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775700953	NA	P-0032726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	509	474	2	ENST00000380036.4:c.148C>T	p.Arg50Cys	p.R50C	ENST00000380036	NM_000459.3	50	Cgc/Tgc	2/23	0.562697554563535	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.562697554563535	2		476	894	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0032728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	164	579	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.398325016321542	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.39858589428942	1		579	641	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543637	29543637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	77	468	0	ENST00000389048.3:c.1526C>T	p.Ala509Val	p.A509V	ENST00000389048	NM_004304.4	509	gCc/gTc	7/29	0.275957964074505	1	FACETS	0.535	0.47	0.605	0.535	0.47	0.605	SUBCLONAL	1	TRUE	0	0.39858589428942	1		468	578	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572556	64572556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767854775	NA	P-0032738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	81	468	1	ENST00000312049.6:c.1300G>A	p.Val434Met	p.V434M	ENST00000312049	NM_130799.2	434	Gtg/Atg	9/10	1	2	FACETS	0.822	0.726	0.925	0.822	0.726	0.925	CLONAL	1	TRUE	1	0.374687504141766	2		469	526	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436390	49436390	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs372271746	NA	P-0032738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	81	423	0	ENST00000301067.7:c.5821A>G	p.Met1941Val	p.M1941V	ENST00000301067	NM_003482.3	1941	Atg/Gtg	27/54	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.374687504141766	2		423	398	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846150	68846171	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTTCAATCCCACCACGGTAAT	TCTTCAATCCCACCACGGTAAT	-	novel	NA	P-0032738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	42	485	0	ENST00000261769.5:c.1124_1137+8del		p.X375_splice	ENST00000261769	NM_004360.3	375		8/16	0.374687504141766	1	FACETS	0.698	0.587	0.82	0.698	0.587	0.82	SUBCLONAL	1	TRUE	0	0.374687504141766	1		485	261	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0032742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	58	340	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.22	2		340	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0032742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	93	709	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	1	2	FACETS	0.873	0.775	0.979	0.873	0.775	0.979	CLONAL	1	TRUE	1	0.22	2		709	968	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0032742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	91	671	0	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	1	2	FACETS	0.832	0.737	0.934	0.832	0.737	0.934	CLONAL	1	TRUE	1	0.22	2		671	994	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214019	36214019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	85	772	0	ENST00000222270.7:c.2845C>T	p.Pro949Ser	p.P949S	ENST00000222270	NM_014727.1	949	Ccc/Tcc	6/37	1	2	FACETS	0.797	0.703	0.899	0.797	0.703	0.899	SUBCLONAL	1	TRUE	1	0.22	2		772	969	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403352	139403352	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	165	571	0	ENST00000277541.6:c.3141C>G	p.Cys1047Trp	p.C1047W	ENST00000277541	NM_017617.3	1047	tgC/tgG	19/34	0.3	3	FACETS	0.999	0.919	1	0.999	0.919	1	CLONAL	2	TRUE	1	0.22	3		571	833	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057302	30057302	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315496	NA	P-0032745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	27	397	0	ENST00000338641.4:c.784C>T	p.Arg262Ter	p.R262*	ENST00000338641	NM_000268.3	262	Cga/Tga	8/16	1	2	FACETS	0.121	0.096	0.151	0.121	0.096	0.151	SUBCLONAL	1	TRUE	1	0.905398655538234	2		397	491	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155365	47155365	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0032745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	39	350	0	ENST00000409792.3:c.4715+1G>T		p.X1572_splice	ENST00000409792	NM_014159.6	1572			1	2	FACETS	0.179	0.148	0.214	0.179	0.148	0.214	SUBCLONAL	1	TRUE	1	0.905398655538234	2		350	481	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0032748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	79	444	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.283070615030797	1	FACETS	0.751	0.667	0.84	1	0.978	1	SUBCLONAL	2	TRUE	0	0.283070615030797	1		444	319	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068922	30068922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	69	486	2	ENST00000331968.5:c.2007G>A	p.Met669Ile	p.M669I	ENST00000331968	NM_002742.2	669	atG/atA	14/18	NA	2	FACETS	1	0.93	1			1	INDETERMINATE	1	TRUE	NA	0.283070615030797	2		488	444	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068938	30068938	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	65	481	0	ENST00000331968.5:c.1991G>A	p.Gly664Glu	p.G664E	ENST00000331968	NM_002742.2	664	gGa/gAa	14/18	NA	2	FACETS	1	0.886	1			1	INDETERMINATE	1	TRUE	NA	0.283070615030797	2		481	450	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068981	30068981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	52	450	0	ENST00000331968.5:c.1948G>A	p.Glu650Lys	p.E650K	ENST00000331968	NM_002742.2	650	Gag/Aag	14/18	NA	2	FACETS	0.975	0.833	1			1	INDETERMINATE	1	TRUE	NA	0.283070615030797	2		450	377	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560535	65560535	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0032748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	71	307	0	ENST00000358664.4:c.64-2A>T		p.X22_splice	ENST00000358664	NM_002382.4	22			0.220787011817014	2	FACETS	0.845	0.744	0.951	0.845	0.744	0.951	CLONAL	2	TRUE	0	0.283070615030797	2		307	297	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713871	30713871	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	43	443	0	ENST00000295754.5:c.1196G>T	p.Gly399Val	p.G399V	ENST00000295754	NM_003242.5	399	gGg/gTg	4/7	1	2	FACETS	0.876	0.735	1	0.876	0.735	1	CLONAL	1	TRUE	1	0.283070615030797	2		443	347	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	37	441	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.26653837905423	1	FACETS	0.735	0.608	0.876	0.735	0.608	0.876	SUBCLONAL	1	TRUE	0	0.268260673375188	1		441	325	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0032749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	90	576	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.26653837905423	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.268260673375188	1		576	544	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267383	198267383	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	57	495	0	ENST00000335508.6:c.1974G>C	p.Trp658Cys	p.W658C	ENST00000335508	NM_012433.2	658	tgG/tgC	14/25	1	2	FACETS	0.902	0.775	1	0.902	0.775	1	CLONAL	1	TRUE	1	0.268260673375188	2		495	471	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874092	151874093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	69	484	0	ENST00000262189.6:c.8445dup	p.Ser2816IlefsTer6	p.S2816Ifs*6	ENST00000262189	NM_170606.2	2815	-/A	38/59	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.268260673375188	2		484	433	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416774	416774	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	57	272	0	ENST00000399788.2:c.3776G>C	p.Arg1259Thr	p.R1259T	ENST00000399788	NM_001042603.1	1259	aGa/aCa	23/28	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.268260673375188	2		272	337	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	129	441	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.66736122032021	1	FACETS	0.924	0.855	0.993	0.924	0.855	0.993	CLONAL	1	TRUE	0	0.690096787220802	1		441	265	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0032750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	130	335	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	1	2	FACETS	0.891	0.815	0.969	0.891	0.815	0.969	CLONAL	1	TRUE	1	0.690096787220802	2		335	423	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0032750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	100	284	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.690096787220802	2		284	277	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0032750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	112	223	1	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	0.690096787220802	2		224	305	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114917797	114917798	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0032750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	76	272	0	ENST00000543371.1:c.1290_1291dup	p.Arg431LysfsTer61	p.R431Kfs*61	ENST00000543371	NM_001198531.1	429	-/AA	12/14	0.397842140376889	1	FACETS	0.416	0.367	0.467	0.416	0.367	0.467	INDETERMINATE	1	TRUE	0	0.690096787220802	1		272	347	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125323	47125323	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	194	442	0	ENST00000409792.3:c.5947G>T	p.Glu1983Ter	p.E1983*	ENST00000409792	NM_014159.6	1983	Gaa/Taa	12/21	0.424239664539906	1	FACETS	0.789	0.737	0.84	0.789	0.737	0.84	SUBCLONAL	1	TRUE	0	0.690096787220802	1		442	467	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437273	52437273	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	250	528	0	ENST00000460680.1:c.1771G>A	p.Gly591Ser	p.G591S	ENST00000460680	NM_004656.3	591	Ggc/Agc	14/17	0.424239664539906	1	FACETS	0.834	0.787	0.881	0.834	0.787	0.881	CLONAL	1	TRUE	0	0.690096787220802	1		528	569	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101612	27101612	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	211	563	0	ENST00000324856.7:c.4899del	p.Met1634Ter	p.M1634*	ENST00000324856	NM_006015.4	1632	Ccc/cc	18/20	0.273412647638448	2	FACETS	0.972	0.905	1	0.972	0.905	1	CLONAL	2	FALSE	0	0.273412647638448	2		563	794	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0032752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	58	301	0	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	0.273412647638448	2	FACETS	0.754	0.648	0.869	0.377	0.324	0.435	SUBCLONAL	1	FALSE	0	0.273412647638448	2		301	563	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444659	78444659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs908264837	NA	P-0032752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	137	308	1	ENST00000370768.2:c.30del	p.Ser11LeufsTer43	p.S11Lfs*43	ENST00000370768	NM_003902.3	10	ccC/cc	1/20	0.273412647638448	2	FACETS	0.919	0.84	1	0.919	0.84	1	CLONAL	2	FALSE	0	0.273412647638448	2		309	545	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720709	89720709	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs863224909	NA	P-0032752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	33	83	0	ENST00000371953.3:c.860C>A	p.Ser287Ter	p.S287*	ENST00000371953	NM_000314.4	287	tCa/tAa	8/9	0.273412647638448	2	FACETS	0.925	0.779	1	1	0.949	1	CLONAL	3	FALSE	0	0.273412647638448	2		83	87	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900958	114900958	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	180	394	0	ENST00000543371.1:c.568G>A	p.Val190Met	p.V190M	ENST00000543371	NM_001198531.1	190	Gtg/Atg	6/14	0.273412647638448	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	FALSE	0	0.273412647638448	2		394	636	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942123	71942123	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	202	534	0	ENST00000298229.2:c.1390del	p.His464MetfsTer67	p.H464Mfs*67	ENST00000298229	NM_001567.3	463	Ccc/cc	12/28	0.273412647638448	2	FACETS	0.979	0.91	1	0.979	0.91	1	CLONAL	2	FALSE	0	0.273412647638448	2		534	755	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236207	108236207	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1555152058	NA	P-0032752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	165	441	1	ENST00000278616.4:c.9146del	p.Phe3049SerfsTer26	p.F3049Sfs*26	ENST00000278616	NM_000051.3	3048	cTt/ct	63/63	0.273412647638448	2	FACETS	0.943	0.869	1	0.943	0.869	1	CLONAL	2	FALSE	0	0.273412647638448	2		442	640	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143020	58143020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144657355	NA	P-0032752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	227	458	1	ENST00000257904.6:c.764G>A	p.Arg255His	p.R255H	ENST00000257904	NM_000075.3	255	cGc/cAc	7/8	0.273412647638448	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	FALSE	0	0.273412647638448	2		459	763	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820602	3820602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749011678	NA	P-0032752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	193	491	0	ENST00000262367.5:c.2849C>T	p.Thr950Met	p.T950M	ENST00000262367	NM_004380.2	950	aCg/aTg	14/31	0.2642287335043	2	FACETS	0.917	0.85	0.986	0.917	0.85	0.986	CLONAL	2	FALSE	0	0.273412647638448	2		491	770	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677249	29677250	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0032752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	88	370	0	ENST00000356175.3:c.7308_7309del	p.His2436GlnfsTer8	p.H2436Qfs*8	ENST00000356175	NM_000267.3	2436	cAT/c	49/57	0.273412647638448	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	FALSE	0	0.273412647638448	2		370	286	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210725	36210725	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	196	496	0	ENST00000222270.7:c.481del	p.Leu161PhefsTer6	p.L161Ffs*6	ENST00000222270	NM_014727.1	159	aCc/ac	3/37	0.273412647638448	2	FACETS	0.929	0.862	0.998	0.929	0.862	0.998	CLONAL	2	FALSE	0	0.273412647638448	2		496	772	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86648999	86648999	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs975191415	NA	P-0032752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	57	270	0	ENST00000274376.6:c.1279C>T	p.Arg427Ter	p.R427*	ENST00000274376	NM_002890.2	427	Cga/Tga	9/25	0.273412647638448	2	FACETS	0.983	0.856	1	0.983	0.856	1	CLONAL	2	FALSE	0	0.273412647638448	2		270	212	SUCCESS
APC	324	MSKCC	GRCh37	5	112170822	112170822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1114167575	NA	P-0032752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	146	461	0	ENST00000257430.4:c.1918C>T	p.Arg640Trp	p.R640W	ENST00000257430	NM_000038.5	640	Cgg/Tgg	15/16	0.273412647638448	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	FALSE	0	0.273412647638448	2		461	471	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391728	139391728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035043614	NA	P-0032752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	39	503	0	ENST00000277541.6:c.6463G>A	p.Gly2155Ser	p.G2155S	ENST00000277541	NM_017617.3	2155	Ggc/Agc	34/34	0.273412647638448	2	FACETS	0.389	0.321	0.465	0.195	0.16	0.233	SUBCLONAL	1	FALSE	0	0.273412647638448	2		503	733	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578509	7578509	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519978	NA	P-0032753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	182	603	0	ENST00000269305.4:c.421T>G	p.Cys141Gly	p.C141G	ENST00000269305	NM_001126112.2	141	Tgc/Ggc	5/11	0.52762688183318	1	FACETS	0.996	0.926	1	0.996	0.926	1	CLONAL	1	TRUE	0	0.52762688183318	1		603	510	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023249	27023249	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	44	113	0	ENST00000324856.7:c.355G>T	p.Glu119Ter	p.E119*	ENST00000324856	NM_006015.4	119	Gag/Tag	1/20	1	2	FACETS	0.864	0.734	1	0.864	0.734	1	CLONAL	1	TRUE	1	0.52762688183318	2		113	193	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610093	10610093	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	143	499	1	ENST00000171111.5:c.617A>G	p.Tyr206Cys	p.Y206C	ENST00000171111	NM_203500.1	206	tAc/tGc	2/6	0.52762688183318	1	FACETS	0.976	0.899	1	0.976	0.899	1	CLONAL	1	TRUE	0	0.52762688183318	1		500	409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0032754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	121	720	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.327946346584295	4	FACETS	0.939	0.873	1	0.939	0.873	1	CLONAL	4	FALSE	0	0.445817058060662	4		720	209	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0032754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	79	296	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.327946346584295	4	FACETS	1	0.969	1	0.871	0.792	0.95	CLONAL	3	FALSE	0	0.445817058060662	4		296	147	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913351	NA	P-0032754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	14	392	1	ENST00000288602.6:c.1397G>A	p.Gly466Glu	p.G466E	ENST00000288602	NM_004333.4	466	gGa/gAa	11/18	0.378153070944972	4	FACETS	0.811	0.592	1	0.405	0.296	0.535	CLONAL	1	FALSE	2	0.445817058060662	4		393	112	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046356	128046356	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	34	394	0	ENST00000285398.2:c.907A>C	p.Asn303His	p.N303H	ENST00000285398	NM_000122.1	303	Aac/Cac	7/15	0.418994632622464	4	FACETS	1	0.917	1	0.4	0.33	0.476	CLONAL	1	FALSE	1	0.445817058060662	4		394	184	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660087	227660087	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1274307554	NA	P-0032754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	66	430	0	ENST00000305123.5:c.3368C>A	p.Ala1123Glu	p.A1123E	ENST00000305123	NM_005544.2	1123	gCa/gAa	1/2	0.337125564402323	4	FACETS	0.945	0.843	1	0.945	0.843	1	CLONAL	3	FALSE	1	0.445817058060662	4		430	151	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081573	143081573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	16	455	0	ENST00000262992.4:c.1501C>T	p.Pro501Ser	p.P501S	ENST00000262992	NM_001101669.1	501	Ccc/Tcc	15/24	1	2	FACETS	0.552	0.412	0.717	0.552	0.412	0.717	SUBCLONAL	1	FALSE	1	0.445817058060662	2		455	130	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	46	264	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.728	0.618	0.848	0.728	0.618	0.848	SUBCLONAL	1	TRUE	1	0.497456596138811	2		264	254	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717679	89717696	+	inframe_deletion	In_Frame_Del	DEL	AAGACAAGTTCATGTACT	AAGACAAGTTCATGTACT	-	novel	NA	P-0032759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	43	398	0	ENST00000371953.3:c.704_721del	p.Glu235_Phe241delinsVal	p.E235_F241delinsV	ENST00000371953	NM_000314.4	235	gAAGACAAGTTCATGTACTtt/gtt	7/9	0.497456596138811	1	FACETS	0.496	0.417	0.581	0.496	0.417	0.581	SUBCLONAL	1	TRUE	0	0.497456596138811	1		398	262	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953844	17953844	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	113	469	1	ENST00000458235.1:c.558G>T	p.Lys186Asn	p.K186N	ENST00000458235	NM_000215.3	186	aaG/aaT	5/24	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.497456596138811	2		470	424	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	155	653	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.757	0.697	0.819	1	0.989	1	SUBCLONAL	2	FALSE	1	0.373708474338663	2		658	548	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	154	460	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	0.311230114005267	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	FALSE	0	0.373708474338663	2		460	332	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023699	27023699	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	35	290	0	ENST00000324856.7:c.805C>T	p.Gln269Ter	p.Q269*	ENST00000324856	NM_006015.4	269	Cag/Tag	1/20	0.311230114005267	2	FACETS	0.746	0.615	0.892	0.373	0.307	0.446	SUBCLONAL	1	FALSE	0	0.373708474338663	2		290	251	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690819	89690820	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	202	350	0	ENST00000371953.3:c.227_228del	p.Tyr76Ter	p.Y76*	ENST00000371953	NM_000314.4	76	TAt/t	4/9	0.373708474338663	2	FACETS	0.91	0.857	0.963	1	0.992	1	CLONAL	3	FALSE	0	0.373708474338663	2		350	396	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948136	178948136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	61	213	0	ENST00000263967.3:c.2908G>A	p.Glu970Lys	p.E970K	ENST00000263967	NM_006218.2	970	Gaa/Aaa	20/21	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.373708474338663	2		213	221	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275399	142275399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202162034	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	66	310	0	ENST00000350721.4:c.1904G>A	p.Arg635Gln	p.R635Q	ENST00000350721	NM_001184.3	635	cGa/cAa	9/47	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	1	0.373708474338663	2		310	308	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	56	335	1	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.373708474338663	2		336	233	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517445	157517445	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs773740590	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	79	355	0	ENST00000346085.5:c.4009C>T	p.Arg1337Ter	p.R1337*	ENST00000346085	NM_020732.3	1337	Cga/Tga	16/20	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	FALSE	1	0.373708474338663	2		355	412	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063359	67063359	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	55	205	0	ENST00000412916.2:c.54del	p.Phe18LeufsTer4	p.F18Lfs*4	ENST00000412916		17	Ttt/tt	1/6	0.373708474338663	1	FACETS	0.855	0.75	0.962	1	0.977	1	CLONAL	2	FALSE	0	0.373708474338663	1		205	140	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771903	135771903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	100	525	0	ENST00000298552.3:c.3214G>A	p.Ala1072Thr	p.A1072T	ENST00000298552	NM_001162426.1	1072	Gcc/Acc	23/23	1	2	FACETS	0.773	0.698	0.852	1	0.984	1	SUBCLONAL	2	FALSE	1	0.373708474338663	2		525	346	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2125894	2125894	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs45517252	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	33	528	0	ENST00000219476.3:c.2639+1G>A		p.X880_splice	ENST00000219476	NM_000548.3	880			1	2	FACETS	0.54	0.441	0.652	0.54	0.441	0.652	SUBCLONAL	1	FALSE	1	0.373708474338663	2		528	327	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042077	42042077	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	94	442	0	ENST00000219905.7:c.6276del	p.Ala2093ProfsTer9	p.A2093Pfs*9	ENST00000219905	NM_001164273.1	2091	gAa/ga	17/24	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.373708474338663	2		442	365	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682810	190682810	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	83	475	2	ENST00000441310.2:c.492del	p.Lys164AsnfsTer6	p.K164Nfs*6	ENST00000441310	NM_000534.4	162	gcA/gc	5/13	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.373708474338663	2		477	370	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119780	70119781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	123	485	0	ENST00000245479.2:c.788dup	p.Arg264GlnfsTer32	p.R264Qfs*32	ENST00000245479	NM_000346.3	261	gag/gaGg	3/3	1	2	FACETS	0.899	0.822	0.979	1	0.989	1	CLONAL	2	FALSE	1	0.373708474338663	2		485	366	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660999	227660999	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	67	440	0	ENST00000305123.5:c.2456del	p.Gly819AspfsTer124	p.G819Dfs*124	ENST00000305123	NM_005544.2	819	gGa/ga	1/2	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.373708474338663	2		440	249	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11270924	11270924	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	41	392	0	ENST00000361445.4:c.3601C>T	p.Arg1201Ter	p.R1201*	ENST00000361445	NM_004958.3	1201	Cga/Tga	24/58	1	2	FACETS	0.657	0.549	0.776	0.657	0.549	0.776	SUBCLONAL	1	FALSE	1	0.373708474338663	2		392	334	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	128	657	1	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	FALSE	1	0.373708474338663	2		658	503	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	97	993	5	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.88	0.795	0.968	1	0.986	1	CLONAL	2	FALSE	1	0.373708474338663	2		998	295	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402714	139402714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	127	551	0	ENST00000277541.6:c.3295G>A	p.Val1099Met	p.V1099M	ENST00000277541	NM_017617.3	1099	Gtg/Atg	20/34	1	2	FACETS	0.794	0.725	0.865	1	0.988	1	SUBCLONAL	2	FALSE	1	0.373708474338663	2		551	428	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214871	36214871	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	84	527	2	ENST00000222270.7:c.3302del	p.Pro1101LeufsTer81	p.P1101Lfs*81	ENST00000222270	NM_014727.1	1099	ggC/gg	8/37	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	FALSE	1	0.373708474338663	2		529	430	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821381	72821382	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	53	378	0	ENST00000268489.5:c.10793dup	p.Pro3599SerfsTer67	p.P3599Sfs*67	ENST00000268489	NM_006885.3	3598	cct/ccCt	10/10	0.373708474338663	1	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	FALSE	0	0.373708474338663	1		378	223	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099941	27099941	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	168	447	1	ENST00000324856.7:c.3820G>T	p.Gly1274Ter	p.G1274*	ENST00000324856	NM_006015.4	1274	Gga/Tga	15/20	0.311230114005267	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	FALSE	0	0.373708474338663	2		448	414	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796213	45796213	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780085	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	15	346	0	ENST00000450313.1:c.1493A>G	p.Gln498Arg	p.Q498R	ENST00000450313	NM_012222.2	498	cAg/cGg	15/16	0.311230114005267	2	FACETS	0.287	0.209	0.38	0.143	0.104	0.19	SUBCLONAL	1	FALSE	0	0.373708474338663	2		346	280	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163297290	163297290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	108	446	0	ENST00000271452.3:c.136C>T	p.His46Tyr	p.H46Y	ENST00000271452	NM_145697.2	46	Cac/Tac	3/14	0.373708474338663	3	FACETS	1	0.95	1	0.545	0.49	0.604	CLONAL	1	FALSE	1	0.373708474338663	3		446	629	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77051783	77051783	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	114	420	0	ENST00000356341.3:c.1024G>T	p.Val342Phe	p.V342F	ENST00000356341	NM_002576.4	342	Gtt/Ttt	11/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.373708474338663	2		420	409	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557816	21557816	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1458859481	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	145	577	0	ENST00000382592.4:c.2029G>A	p.Gly677Ser	p.G677S	ENST00000382592	NM_014572.2	677	Ggt/Agt	5/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.373708474338663	2		577	560	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877434	28877434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	23	400	0	ENST00000282397.4:c.3887G>A	p.Ser1296Asn	p.S1296N	ENST00000282397	NM_002019.4	1296	aGc/aAc	30/30	1	2	FACETS	0.303	0.236	0.381	0.303	0.236	0.381	SUBCLONAL	1	FALSE	1	0.373708474338663	2		400	406	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134497	2134497	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	80	575	0	ENST00000219476.3:c.4274G>T	p.Gly1425Val	p.G1425V	ENST00000219476	NM_000548.3	1425	gGg/gTg	34/42	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	FALSE	1	0.373708474338663	2		575	392	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136314	2136315	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGGCCTGGACGTGTGTGGTGAGGAAGGCCAGTTCACCTACTGCTGGCACGAT	novel	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	61	578	0	ENST00000219476.3:c.4808_4809insAGGCCAGTTCACCTACTGCTGGCACGATGAGGCCTGGACGTGTGTGGTGAGGA	p.Asp1603GlufsTer40	p.D1603Efs*40	ENST00000219476	NM_000548.3	1595	gga/gGAGGCCTGGACGTGTGTGGTGAGGAAGGCCAGTTCACCTACTGCTGGCACGATga	37/42	1	2	FACETS	0.652	0.563	0.748	0.652	0.563	0.748	SUBCLONAL	1	FALSE	1	0.373708474338663	2		578	501	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55693436	55693436	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	42	441	0	ENST00000284073.2:c.643G>T	p.Gly215Trp	p.G215W	ENST00000284073	NM_138962.2	215	Ggg/Tgg	9/14	1	2	FACETS	0.501	0.418	0.592	0.501	0.418	0.592	SUBCLONAL	1	FALSE	1	0.373708474338663	2		441	449	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218430	1218430	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555737397	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	63	471	0	ENST00000326873.7:c.305T>C	p.Leu102Pro	p.L102P	ENST00000326873	NM_000455.4	102	cTg/cCg	2/10	1	2	FACETS	0.909	0.79	1	0.909	0.79	1	CLONAL	1	FALSE	1	0.373708474338663	2		471	371	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11015633	11015634	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	104	396	0	ENST00000327064.4:c.235_236dup	p.Phe80SerfsTer46	p.F80Sfs*46	ENST00000327064	NM_199141.1	76	gat/gaTGt	2/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.373708474338663	2		396	374	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79968139	79968142	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs763478027	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	146	590	0	ENST00000265081.6:c.873_876del	p.Val292MetfsTer15	p.V292Mfs*15	ENST00000265081	NM_002439.4	290	cTGTTt/ct	5/24	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.373708474338663	2		590	553	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405795	157405795	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	14	263	0	ENST00000346085.5:c.2038-1G>T		p.X680_splice	ENST00000346085	NM_020732.3	680			1	2	FACETS	0.288	0.208	0.385	0.288	0.208	0.385	SUBCLONAL	1	FALSE	1	0.373708474338663	2		263	260	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287268	38287268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	92	555	0	ENST00000425967.3:c.389G>A	p.Gly130Asp	p.G130D	ENST00000425967	NM_001174067.1	130	gGc/gAc	4/19	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	FALSE	1	0.373708474338663	2		555	483	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402824	139402824	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	114	488	0	ENST00000277541.6:c.3185G>A	p.Trp1062Ter	p.W1062*	ENST00000277541	NM_017617.3	1062	tGg/tAg	20/34	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.373708474338663	2		488	423	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418378	139418378	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	131	544	0	ENST00000277541.6:c.194G>A	p.Ser65Asn	p.S65N	ENST00000277541	NM_017617.3	65	aGc/aAc	3/34	1	2	FACETS	0.855	0.783	0.929	1	0.989	1	CLONAL	2	FALSE	1	0.373708474338663	2		544	410	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222499	53222499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556832647	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	106	563	0	ENST00000375401.3:c.4333C>T	p.Arg1445Cys	p.R1445C	ENST00000375401	NM_004187.3	1445	Cgt/Tgt	26/26	1	2	FACETS	0.849	0.77	0.931	1	0.987	1	CLONAL	2	FALSE	1	0.373708474338663	2		563	334	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136340	2136340	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	42	550	0	ENST00000219476.3:c.4809C>A	p.Asp1603Glu	p.D1603E	ENST00000219476	NM_000548.3	1603	gaC/gaA	37/42	1	2	FACETS	0.533	0.445	0.63	0.533	0.445	0.63	SUBCLONAL	1	FALSE	1	0.373708474338663	2		550	422	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0032776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	81	284	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.953	1	1	0.986	1	CLONAL	2	TRUE	1	0.257756512471728	2		284	279	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0032776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	391	528	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.257756512471728	4	FACETS	0.945	0.917	0.971	1	0.997	1	CLONAL	8	TRUE	0	0.257756512471728	4		528	505	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937121	39937121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778129253	NA	P-0032776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	18	611	0	ENST00000378444.4:c.62G>A	p.Arg21His	p.R21H	ENST00000378444	NM_001123385.1	21	cGc/cAc	2/15	0.257756512471728	0	FACETS	0.294	0.22	0.38			1	SUBCLONAL	1	TRUE	0	0.257756512471728	0		611	353	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918608	44918608	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778404068	NA	P-0032776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	111	515	0	ENST00000377967.4:c.1091C>T	p.Ser364Phe	p.S364F	ENST00000377967	NM_021140.2	364	tCc/tTc	12/29	0.257756512471728	0	FACETS	0.793	0.719	0.871			1	SUBCLONAL	2	TRUE	0	0.257756512471728	0		515	403	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872200	76872200	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0032776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	78	374	0	ENST00000373344.5:c.5449-2A>G		p.X1817_splice	ENST00000373344	NM_000489.3	1817			0.257756512471728	0	FACETS	0.888	0.791	0.989			1	CLONAL	2	TRUE	0	0.257756512471728	0		374	253	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562746	29562746	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs199474742	NA	P-0032785-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	203	454	0	ENST00000356175.3:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000356175	NM_000267.3	1276	Cga/Tga	28/57	1	2	FACETS	0.915	0.852	0.981	0.915	0.852	0.981	CLONAL	1	TRUE	1	0.615964775193507	2		454	720	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199469672	NA	P-0032785-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	254	466	0	ENST00000374080.3:c.131G>T	p.Gly44Val	p.G44V	ENST00000374080		44	gGt/gTt	2/45	0.403018564801871	1	FACETS	0.951	0.898	1	0.951	0.898	1	CLONAL	1	TRUE	0	0.615964775193507	1		466	600	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0032796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	735	587	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.631119943505517	10	FACETS	1	0.99	1	0.802	0.781	0.823	CLONAL	7	TRUE	1	0.631119943505517	10		587	1137	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664534	29664535	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0032796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	110	537	0	ENST00000356175.3:c.6522_6523dup	p.Thr2175ArgfsTer5	p.T2175Rfs*5	ENST00000356175	NM_000267.3	2171	-/GA	42/57	0.526676724793661	3	FACETS	0.656	0.59	0.726	0.328	0.295	0.363	SUBCLONAL	1	TRUE	1	0.631119943505517	3		537	699	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280099	18280099	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	15	32	0	ENST00000222254.8:c.2182C>T	p.Arg728Cys	p.R728C	ENST00000222254	NM_005027.3	728	Cgc/Tgc	16/16	0.477263806030265	4	FACETS	0.775	0.588	0.981	0.517	0.392	0.654	CLONAL	2	TRUE	1	0.631119943505517	4		32	50	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31486629	31486629	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756470214	NA	P-0032796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	58	373	1	ENST00000344624.3:c.1883C>T	p.Thr628Met	p.T628M	ENST00000344624		628	aCg/aTg	11/33	0.160877976888319	6	FACETS	0.859	0.739	0.989	0.286	0.246	0.33	INDETERMINATE	1	TRUE	3	0.631119943505517	6		374	484	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533536	533536	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369106578	NA	P-0032796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	164	755	0	ENST00000451590.1:c.367C>T	p.Arg123Cys	p.R123C	ENST00000451590	NM_001130442.1	123	Cgc/Tgc	4/5	0.526676724793661	3	FACETS	0.883	0.812	0.957	0.442	0.406	0.479	CLONAL	1	TRUE	1	0.631119943505517	3		755	774	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274163	18274163	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	101	491	0	ENST00000222254.8:c.1381G>T	p.Asp461Tyr	p.D461Y	ENST00000222254	NM_005027.3	461	Gac/Tac	11/16	0.477263806030265	4	FACETS	0.735	0.657	0.818	0.245	0.219	0.273	SUBCLONAL	1	TRUE	1	0.631119943505517	4		491	710	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278071	18278071	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	124	619	0	ENST00000222254.8:c.1691A>T	p.Lys564Met	p.K564M	ENST00000222254	NM_005027.3	564	aAg/aTg	13/16	0.477263806030265	4	FACETS	0.72	0.651	0.793	0.24	0.217	0.265	SUBCLONAL	1	TRUE	1	0.631119943505517	4		619	890	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336612	81336612	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	22	232	1	ENST00000222390.5:c.1610C>A	p.Pro537His	p.P537H	ENST00000222390	NM_000601.4	537	cCt/cAt	14/18	0.281504062148889	3	FACETS	0.409	0.318	0.514	0.205	0.159	0.257	INDETERMINATE	1	TRUE	1	0.631119943505517	3		233	224	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874556	151874556	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	46	415	0	ENST00000262189.6:c.7982C>G	p.Pro2661Arg	p.P2661R	ENST00000262189	NM_170606.2	2661	cCt/cGt	38/59	0.281504062148889	3	FACETS	0.554	0.468	0.648	0.277	0.234	0.324	INDETERMINATE	1	TRUE	1	0.631119943505517	3		415	346	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659912	227659912	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	66	560	0	ENST00000305123.5:c.3543C>A	p.Asp1181Glu	p.D1181E	ENST00000305123	NM_005544.2	1181	gaC/gaA	1/2	0.113401050088287	5	FACETS	0.907	0.788	1	0.227	0.197	0.259	INDETERMINATE	1	FALSE	1	0.476024427813807	5		560	524	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265049	46265049	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs778829476	NA	P-0032798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	15	480	0	ENST00000371998.3:c.1919C>G	p.Ser640Cys	p.S640C	ENST00000371998		640	tCc/tGc	12/23	0.17721016191663	5	FACETS	0.794	0.585	1	0.265	0.195	0.347	INDETERMINATE	1	FALSE	2	0.476024427813807	5		480	136	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169953136	169953136	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	68	372	0	ENST00000295797.4:c.220G>T	p.Glu74Ter	p.E74*	ENST00000295797	NM_002740.5	74	Gaa/Taa	2/18	0.146838693605412	3	FACETS	0.953	0.836	1	1	0.972	1	CLONAL	3	TRUE	1	0.164435398537285	3		372	313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0032804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	316	693	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.272945413465339	5	FACETS	0.909	0.866	0.952	0.909	0.866	0.952	CLONAL	5	FALSE	0	0.334845058002387	5		693	624	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145582	24145582	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555877286	NA	P-0032804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	154	594	1	ENST00000263121.7:c.601C>T	p.Arg201Ter	p.R201*	ENST00000263121	NM_003073.3	201	Cga/Tga	5/9	0.304048497691838	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	FALSE	0	0.334845058002387	2		595	446	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492769	56492769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	150	658	0	ENST00000407977.2:c.170C>T	p.Pro57Leu	p.P57L	ENST00000407977		57	cCc/cTc	2/10	0.0946025329079454	4	FACETS	1	0.949	1	1	0.949	1	INDETERMINATE	2	FALSE	2	0.334845058002387	4		658	572	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135804152	135804185	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ACCAGAATTGAGGTTCTCTTTAAAGACAGCTGTC	ACCAGAATTGAGGTTCTCTTTAAAGACAGCTGTC	-	novel	NA	P-0032804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	41	333	0	ENST00000298552.3:c.75_106+2del		p.X25_splice	ENST00000298552	NM_001162426.1	25		3/23	0.174826041747877	3	FACETS	1	0.902	1	0.554	0.464	0.652	INDETERMINATE	1	FALSE	1	0.334845058002387	3		333	258	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567323	226567323	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	132	449	0	ENST00000366794.5:c.1563G>C	p.Lys521Asn	p.K521N	ENST00000366794	NM_001618.3	521	aaG/aaC	11/23	1	2	FACETS	0.73	0.665	0.798	0.73	0.665	0.798	SUBCLONAL	1	TRUE	1	0.595867941139046	2		449	607	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0032808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	102	280	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	0.595867941139046	2		280	287	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577102	7577102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793881	NA	P-0032808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	230	587	0	ENST00000269305.4:c.836G>A	p.Gly279Glu	p.G279E	ENST00000269305	NM_001126112.2	279	gGg/gAg	8/11	0.548169969032445	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.595867941139046	1		587	505	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105547	27105553	+	frameshift_variant	Frame_Shift_Del	DEL	TTCCGAC	TTCCGAC	-	novel	NA	P-0032808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	116	428	0	ENST00000324856.7:c.5158_5164del	p.Phe1720AspfsTer3	p.F1720Dfs*3	ENST00000324856	NM_006015.4	1720	TTCCGACga/ga	20/20	1	2	FACETS	0.929	0.844	1	0.929	0.844	1	CLONAL	1	TRUE	1	0.595867941139046	2		428	419	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860622	151860622	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs536894778	NA	P-0032814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	48	499	0	ENST00000262189.6:c.10040A>G	p.Asn3347Ser	p.N3347S	ENST00000262189	NM_170606.2	3347	aAt/aGt	43/59	1	2	FACETS	0.815	0.688	0.955	0.815	0.688	0.955	CLONAL	1	TRUE	1	0.19	2		499	620	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746032	162746032	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	81	328	0	ENST00000367921.3:c.2155G>A	p.Gly719Ser	p.G719S	ENST00000367921	NM_006182.2	719	Ggt/Agt	16/18	0.257872948056126	3	FACETS	0.934	0.825	1	0.934	0.825	1	CLONAL	2	TRUE	1	0.19	3		328	500	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915753	112915753	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	38	318	0	ENST00000351677.2:c.1026G>A	p.Trp342Ter	p.W342*	ENST00000351677	NM_002834.3	342	tgG/tgA	9/16	1	2	FACETS	1	0.844	1	1	0.844	1	CLONAL	1	TRUE	1	0.19	2		318	392	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66735644	66735644	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	110	377	1	ENST00000307102.5:c.465del	p.Lys156ArgfsTer11	p.K156Rfs*11	ENST00000307102	NM_002755.3	155	ctG/ct	4/11	0.193047633191961	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.19	2		378	506	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900720	3900720	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	33	488	0	ENST00000262367.5:c.376G>T	p.Gly126Ter	p.G126*	ENST00000262367	NM_004380.2	126	Gga/Tga	2/31	1	2	FACETS	0.741	0.603	0.896	0.741	0.603	0.896	SUBCLONAL	1	TRUE	1	0.19	2		488	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577585	7577600	+	frameshift_variant	Frame_Shift_Del	DEL	GATGGTGGTACAGTCA	GATGGTGGTACAGTCA	-	novel	NA	P-0032814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	32	419	0	ENST00000269305.4:c.681_696del	p.Asp228ThrfsTer14	p.D228Tfs*14	ENST00000269305	NM_001126112.2	227	tcTGACTGTACCACCATC/tc	7/11	1	2	FACETS	0.634	0.514	0.771	0.634	0.514	0.771	SUBCLONAL	1	TRUE	1	0.19	2		419	531	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	82	645	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.538	0.474	0.606	0.538	0.474	0.606	SUBCLONAL	1	TRUE	1	0.44	2		645	693	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	189	693	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.781	0.727	0.836	1	0.992	1	SUBCLONAL	2	TRUE	1	0.44	2		693	550	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715847	117715847	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	47	440	0	ENST00000368508.3:c.911G>T	p.Arg304Ile	p.R304I	ENST00000368508	NM_002944.2	304	aGa/aTa	9/43	1	2	FACETS	0.521	0.44	0.61	0.521	0.44	0.61	SUBCLONAL	1	TRUE	1	0.44	2		440	410	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219579	133219579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542430685	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	13	527	2	ENST00000320574.5:c.4555C>T	p.Arg1519Cys	p.R1519C	ENST00000320574	NM_006231.2	1519	Cgc/Tgc	36/49	1	2	FACETS	0.3	0.214	0.404	0.3	0.214	0.404	SUBCLONAL	1	TRUE	1	0.44	2		529	197	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188823	32188823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs8192585	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	21	739	1	ENST00000375023.3:c.731C>T	p.Ser244Leu	p.S244L	ENST00000375023	NM_004557.3	244	tCg/tTg	4/30	1	2	FACETS	0.3	0.231	0.381	0.3	0.231	0.381	SUBCLONAL	1	TRUE	1	0.44	2		740	318	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241895	133241895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1483635586	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	21	560	1	ENST00000320574.5:c.2461C>T	p.Arg821Cys	p.R821C	ENST00000320574	NM_006231.2	821	Cgc/Tgc	21/49	1	2	FACETS	0.275	0.211	0.349	0.275	0.211	0.349	SUBCLONAL	1	TRUE	1	0.44	2		561	347	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276316	15276316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372834264	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	33	731	0	ENST00000263388.2:c.5678G>A	p.Arg1893Gln	p.R1893Q	ENST00000263388	NM_000435.2	1893	cGa/cAa	31/33	1	2	FACETS	0.343	0.279	0.415	0.343	0.279	0.415	SUBCLONAL	1	TRUE	1	0.44	2		731	437	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	127	597	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.44	2		597	440	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	171	596	1	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.44	2		597	576	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518099	8518099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764400127	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	69	499	0	ENST00000356435.5:c.1292C>T	p.Ser431Leu	p.S431L	ENST00000356435		431	tCg/tTg	10/35	1	2	FACETS	0.852	0.747	0.965	0.852	0.747	0.965	CLONAL	1	TRUE	1	0.44	2		499	368	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244872	46244872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766470086	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	37	631	1	ENST00000334344.6:c.2966C>T	p.Ser989Leu	p.S989L	ENST00000334344	NM_152641.2	989	tCg/tTg	15/21	0.210001659018759	4	FACETS	0.49	0.404	0.587	0.245	0.202	0.294	INDETERMINATE	1	TRUE	2	0.44	4		632	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	19	785	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	1	2	FACETS	0.199	0.151	0.257	0.199	0.151	0.257	SUBCLONAL	1	TRUE	1	0.44	2		785	433	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916248	9916248	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397518472	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	19	470	0	ENST00000330684.3:c.2041C>T	p.Arg681Ter	p.R681*	ENST00000330684	NM_001134407.1	681	Cga/Tga	10/13	1	2	FACETS	0.393	0.299	0.502	0.393	0.299	0.502	SUBCLONAL	1	TRUE	1	0.44	2		470	220	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247028	53247028	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	22	742	0	ENST00000375401.3:c.472G>A	p.Glu158Lys	p.E158K	ENST00000375401	NM_004187.3	158	Gaa/Aaa	4/26	0.294472231170961	0	FACETS	0.136	0.104	0.172			1	SUBCLONAL	1	TRUE	0	0.44	0		742	413	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134252	11134252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	37	624	0	ENST00000358026.2:c.2918G>A	p.Arg973Gln	p.R973Q	ENST00000358026	NM_001128849.1	973	cGg/cAg	20/36	1	2	FACETS	0.316	0.26	0.379	0.316	0.26	0.379	SUBCLONAL	1	TRUE	1	0.44	2		624	532	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335121	65335121	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	43	495	0	ENST00000342505.4:c.520C>T	p.Arg174Ter	p.R174*	ENST00000342505	NM_002227.2	174	Cga/Tga	6/25	1	2	FACETS	0.495	0.415	0.583	0.495	0.415	0.583	SUBCLONAL	1	TRUE	1	0.44	2		495	395	SUCCESS
APC	324	MSKCC	GRCh37	5	112179011	112179011	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876659753	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	17	297	0	ENST00000257430.4:c.7720C>A	p.Leu2574Ile	p.L2574I	ENST00000257430	NM_000038.5	2574	Ctt/Att	16/16	0.130861378403997	3	FACETS	0.374	0.279	0.487	0.187	0.139	0.244	INDETERMINATE	1	TRUE	1	0.44	3		297	252	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	88	615	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.873	0.777	0.975	0.873	0.777	0.975	CLONAL	1	TRUE	1	0.44	2		615	458	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539951	187539951	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs777631605	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	36	446	0	ENST00000441802.2:c.7789C>T	p.Arg2597Ter	p.R2597*	ENST00000441802	NM_005245.3	2597	Cga/Tga	10/27	1	2	FACETS	0.473	0.389	0.566	0.473	0.389	0.566	SUBCLONAL	1	TRUE	1	0.44	2		446	346	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143216	30143216	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs576431612	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	11	525	0	ENST00000389048.3:c.310C>T	p.Pro104Ser	p.P104S	ENST00000389048	NM_004304.4	104	Ccg/Tcg	1/29	1	2	FACETS	0.245	0.169	0.339	0.245	0.169	0.339	SUBCLONAL	1	TRUE	1	0.44	2		525	204	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129655	11129655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	41	728	0	ENST00000358026.2:c.2461G>A	p.Glu821Lys	p.E821K	ENST00000358026	NM_001128849.1	821	Gag/Aag	17/36	1	2	FACETS	0.3	0.249	0.357	0.3	0.249	0.357	SUBCLONAL	1	TRUE	1	0.44	2		728	621	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	18	327	0	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	1	2	FACETS	0.23	0.172	0.298	0.23	0.172	0.298	SUBCLONAL	1	TRUE	1	0.44	2		327	356	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001374	150001374	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	70	738	1	ENST00000253339.5:c.2230C>T	p.Arg744Ter	p.R744*	ENST00000253339		744	Cga/Tga	4/7	1	2	FACETS	0.576	0.503	0.656	0.576	0.503	0.656	SUBCLONAL	1	TRUE	1	0.44	2		739	552	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923805	39923805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	31	794	0	ENST00000378444.4:c.3286G>A	p.Glu1096Lys	p.E1096K	ENST00000378444	NM_001123385.1	1096	Gag/Aag	7/15	0.294472231170961	0	FACETS	0.183	0.147	0.223			1	SUBCLONAL	1	TRUE	0	0.44	0		794	432	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201702	67201702	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373702089	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	30	654	0	ENST00000312629.5:c.1003G>A	p.Asp335Asn	p.D335N	ENST00000312629	NM_003952.2	335	Gac/Aac	12/15	1	2	FACETS	0.257	0.206	0.314	0.257	0.206	0.314	SUBCLONAL	1	TRUE	1	0.44	2		654	531	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	45	577	0	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	1	2	FACETS	0.419	0.352	0.493	0.419	0.352	0.493	SUBCLONAL	1	TRUE	1	0.44	2		577	488	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931589	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	24	326	0	ENST00000349496.5:c.101G>A	p.Gly34Glu	p.G34E	ENST00000349496	NM_001904.3	34	gGa/gAa	3/15	1	2	FACETS	0.354	0.278	0.442	0.354	0.278	0.442	SUBCLONAL	1	TRUE	1	0.44	2		326	308	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374317	31374317	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	13	423	0	ENST00000328111.2:c.316C>T	p.Arg106Ter	p.R106*	ENST00000328111	NM_006892.3	106	Cga/Tga	5/23	1	2	FACETS	0.227	0.162	0.307	0.227	0.162	0.307	SUBCLONAL	1	TRUE	1	0.44	2		423	260	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188288	142188288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1470834016	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	67	458	0	ENST00000350721.4:c.6443G>A	p.Arg2148Gln	p.R2148Q	ENST00000350721	NM_001184.3	2148	cGa/cAa	38/47	1	2	FACETS	0.689	0.601	0.784	0.689	0.601	0.784	SUBCLONAL	1	TRUE	1	0.44	2		458	442	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944865	131944865	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	10	252	0	ENST00000265335.6:c.2886G>T	p.Glu962Asp	p.E962D	ENST00000265335		962	gaG/gaT	18/25	0.130861378403997	3	FACETS	0.283	0.191	0.398	0.141	0.095	0.199	INDETERMINATE	1	TRUE	1	0.44	3		252	196	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515141	103515141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770246574	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	16	358	0	ENST00000355739.4:c.1642G>A	p.Glu548Lys	p.E548K	ENST00000355739	NM_000123.3	548	Gaa/Aaa	8/15	1	2	FACETS	0.364	0.269	0.476	0.364	0.269	0.476	SUBCLONAL	1	TRUE	1	0.44	2		358	200	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650710	67650710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243010179	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	58	606	0	ENST00000264010.4:c.1015C>T	p.Arg339Trp	p.R339W	ENST00000264010	NM_006565.3	339	Cgg/Tgg	5/12	1	2	FACETS	0.368	0.316	0.426	0.368	0.316	0.426	SUBCLONAL	1	TRUE	1	0.44	2		606	716	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939417	76939417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781932965	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	44	935	1	ENST00000373344.5:c.1331G>A	p.Arg444Gln	p.R444Q	ENST00000373344	NM_000489.3	444	cGa/cAa	9/35	0.294472231170961	0	FACETS	0.201	0.168	0.237			1	SUBCLONAL	1	TRUE	0	0.44	0		936	558	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693002	89693003	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	33	425	0	ENST00000371953.3:c.491dup	p.Val166SerfsTer14	p.V166Sfs*14	ENST00000371953	NM_000314.4	162	-/A	5/9	1	2	FACETS	0.524	0.429	0.632	0.524	0.429	0.632	SUBCLONAL	1	TRUE	1	0.44	2		425	286	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023019	150023019	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	168	754	0	ENST00000253339.5:c.244C>T	p.Arg82Ter	p.R82*	ENST00000253339		82	Cga/Tga	1/7	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.44	2		754	640	SUCCESS
AR	367	MSKCC	GRCh37	X	66943532	66943532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143040492	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	43	434	0	ENST00000374690.3:c.2612C>T	p.Ala871Val	p.A871V	ENST00000374690	NM_000044.3	871	gCg/gTg	8/8	0.294472231170961	0	FACETS	0.507	0.428	0.592			1	SUBCLONAL	1	TRUE	0	0.44	0		434	216	SUCCESS
ALK	238	MSKCC	GRCh37	2	29430047	29430047	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1553390742	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	20	696	0	ENST00000389048.3:c.3928A>G	p.Thr1310Ala	p.T1310A	ENST00000389048	NM_004304.4	1310	Aca/Gca	26/29	1	2	FACETS	0.229	0.174	0.293	0.229	0.174	0.293	SUBCLONAL	1	TRUE	1	0.44	2		696	397	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	133	406	1	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.777	0.713	0.843	1	0.988	1	SUBCLONAL	2	TRUE	1	0.44	2		407	389	SUCCESS
APC	324	MSKCC	GRCh37	5	112176873	112176873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	27	466	1	ENST00000257430.4:c.5582C>A	p.Ser1861Tyr	p.S1861Y	ENST00000257430	NM_000038.5	1861	tCt/tAt	16/16	0.130861378403997	3	FACETS	0.431	0.343	0.532	0.216	0.171	0.266	INDETERMINATE	1	TRUE	1	0.44	3		467	347	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115600	108115600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772821016	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	168	578	1	ENST00000278616.4:c.748C>T	p.Arg250Ter	p.R250*	ENST00000278616	NM_000051.3	250	Cga/Tga	7/63	1	2	FACETS	0.804	0.745	0.864	1	0.991	1	CLONAL	2	TRUE	1	0.44	2		579	475	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10267124	10267124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751093624	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	26	595	0	ENST00000340748.4:c.1294G>A	p.Glu432Lys	p.E432K	ENST00000340748		432	Gaa/Aaa	17/40	1	2	FACETS	0.215	0.17	0.268	0.215	0.17	0.268	SUBCLONAL	1	TRUE	1	0.44	2		595	549	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980297	55980297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs539911006	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	54	540	0	ENST00000263923.4:c.794C>T	p.Ser265Leu	p.S265L	ENST00000263923	NM_002253.2	265	tCg/tTg	6/30	1	2	FACETS	0.609	0.522	0.704	0.609	0.522	0.704	SUBCLONAL	1	TRUE	1	0.44	2		540	403	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627773	187627773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200050180	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	61	577	1	ENST00000441802.2:c.3209G>A	p.Arg1070Gln	p.R1070Q	ENST00000441802	NM_005245.3	1070	cGa/cAa	2/27	1	2	FACETS	0.686	0.594	0.786	0.686	0.594	0.786	SUBCLONAL	1	TRUE	1	0.44	2		578	404	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	53	276	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	0.130861378403997	3	FACETS	0.842	0.721	0.973	0.421	0.36	0.487	INDETERMINATE	1	TRUE	1	0.44	3		276	349	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37865572	37865572	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	31	639	0	ENST00000269571.5:c.441G>T	p.Glu147Asp	p.E147D	ENST00000269571		147	gaG/gaT	4/27	1	2	FACETS	0.3	0.242	0.365	0.3	0.242	0.365	SUBCLONAL	1	TRUE	1	0.44	2		639	470	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780684	9780684	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	29	773	0	ENST00000377346.4:c.1486C>T	p.Arg496Ter	p.R496*	ENST00000377346	NM_005026.3	496	Cga/Tga	12/24	0.3	2	FACETS	0.309	0.248	0.38			1	SUBCLONAL	1	TRUE	NA	0.44	2		773	426	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467865	66467865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs939351025	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	61	446	0	ENST00000273854.3:c.404G>A	p.Arg135Gln	p.R135Q	ENST00000273854	NM_004439.5	135	cGg/cAg	3/18	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.44	2		446	254	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6031648	6031648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs116314131	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	25	499	0	ENST00000265849.7:c.944G>A	p.Arg315Gln	p.R315Q	ENST00000265849	NM_000535.5	315	cGa/cAa	9/15	1	2	FACETS	0.247	0.194	0.308	0.247	0.194	0.308	SUBCLONAL	1	TRUE	1	0.44	2		499	460	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347916	73347916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139907646	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	12	392	0	ENST00000377767.4:c.1145G>A	p.Arg382Gln	p.R382Q	ENST00000377767	NM_014953.3	382	cGa/cAa	8/21	1	2	FACETS	0.188	0.132	0.258	0.188	0.132	0.258	SUBCLONAL	1	TRUE	1	0.44	2		392	290	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775985	9775985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201492009	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	30	677	0	ENST00000377346.4:c.449C>T	p.Ala150Val	p.A150V	ENST00000377346	NM_005026.3	150	gCg/gTg	5/24	0.3	2	FACETS	0.377	0.303	0.46			1	SUBCLONAL	1	TRUE	NA	0.44	2		677	362	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582439	119582439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775606264	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	14	241	0	ENST00000316626.5:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000316626		321	cGa/cAa	10/12	1	2	FACETS	0.284	0.205	0.379	0.284	0.205	0.379	SUBCLONAL	1	TRUE	1	0.44	2		241	224	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751902	57751902	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	41	557	0	ENST00000274289.3:c.1335T>G	p.Ile445Met	p.I445M	ENST00000274289	NM_006622.3	445	atT/atG	10/14	0.130861378403997	3	FACETS	0.427	0.355	0.507	0.214	0.177	0.254	INDETERMINATE	1	TRUE	1	0.44	3		557	532	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858253	59858253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778133	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	38	691	0	ENST00000259008.2:c.1742G>A	p.Arg581Gln	p.R581Q	ENST00000259008	NM_032043.2	581	cGa/cAa	12/20	1	2	FACETS	0.292	0.24	0.349	0.292	0.24	0.349	SUBCLONAL	1	TRUE	1	0.44	2		691	592	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972440	81972440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs891516801	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	30	503	0	ENST00000359376.3:c.3233G>A	p.Arg1078Gln	p.R1078Q	ENST00000359376	NM_002661.3	1078	cGa/cAa	29/33	1	2	FACETS	0.345	0.278	0.422	0.345	0.278	0.422	SUBCLONAL	1	TRUE	1	0.44	2		503	395	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741493	17741493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	33	593	0	ENST00000250003.3:c.164C>T	p.Ala55Val	p.A55V	ENST00000250003	NM_002478.4	55	gCg/gTg	1/3	1	2	FACETS	0.449	0.366	0.542	0.449	0.366	0.542	SUBCLONAL	1	TRUE	1	0.44	2		593	334	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685281	89685281	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	63	273	0	ENST00000371953.3:c.176C>A	p.Ser59Ter	p.S59*	ENST00000371953	NM_000314.4	59	tCa/tAa	3/9	1	2	FACETS	0.734	0.638	0.838	0.734	0.638	0.838	SUBCLONAL	1	TRUE	1	0.44	2		273	390	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845507	128845507	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	36	823	0	ENST00000249373.3:c.804C>A	p.Phe268Leu	p.F268L	ENST00000249373	NM_005631.4	268	ttC/ttA	4/12	1	2	FACETS	0.287	0.235	0.345	0.287	0.235	0.345	SUBCLONAL	1	TRUE	1	0.44	2		823	570	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220476	133220476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372901803	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	26	697	0	ENST00000320574.5:c.4237G>A	p.Glu1413Lys	p.E1413K	ENST00000320574	NM_006231.2	1413	Gag/Aag	33/49	1	2	FACETS	0.257	0.203	0.32	0.257	0.203	0.32	SUBCLONAL	1	TRUE	1	0.44	2		697	459	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032002	10032002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs539907710	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	16	695	0	ENST00000330684.3:c.821C>T	p.Ser274Leu	p.S274L	ENST00000330684	NM_001134407.1	274	tCg/tTg	3/13	1	2	FACETS	0.239	0.176	0.315	0.239	0.176	0.315	SUBCLONAL	1	TRUE	1	0.44	2		695	304	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120496243	120496243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782306821	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	98	585	0	ENST00000256646.2:c.2288C>T	p.Ser763Leu	p.S763L	ENST00000256646	NM_024408.3	763	tCg/tTg	14/34	1	2	FACETS	0.94	0.842	1	0.94	0.842	1	CLONAL	1	TRUE	1	0.44	2		585	474	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562641	29562641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854562	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	33	569	1	ENST00000356175.3:c.3721C>T	p.Arg1241Ter	p.R1241*	ENST00000356175	NM_000267.3	1241	Cga/Tga	28/57	1	2	FACETS	0.308	0.25	0.373	0.308	0.25	0.373	SUBCLONAL	1	TRUE	1	0.44	2		570	487	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542861	187542861	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1340793072	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	34	457	1	ENST00000441802.2:c.4879C>T	p.Arg1627Ter	p.R1627*	ENST00000441802	NM_005245.3	1627	Cga/Tga	10/27	1	2	FACETS	0.527	0.432	0.634	0.527	0.432	0.634	SUBCLONAL	1	TRUE	1	0.44	2		458	293	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461167	120461167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs983208690	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	16	400	0	ENST00000256646.2:c.5791C>T	p.Arg1931Cys	p.R1931C	ENST00000256646	NM_024408.3	1931	Cgc/Tgc	32/34	1	2	FACETS	0.232	0.171	0.306	0.232	0.171	0.306	SUBCLONAL	1	TRUE	1	0.44	2		400	313	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158212	47158212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553699111	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	48	516	0	ENST00000409792.3:c.4487G>A	p.Arg1496Gln	p.R1496Q	ENST00000409792	NM_014159.6	1496	cGa/cAa	4/21	1	2	FACETS	0.406	0.342	0.475	0.406	0.342	0.475	SUBCLONAL	1	TRUE	1	0.44	2		516	538	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961109	55961109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374755237	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	40	663	0	ENST00000263923.4:c.2831G>A	p.Arg944Gln	p.R944Q	ENST00000263923	NM_002253.2	944	cGa/cAa	21/30	1	2	FACETS	0.425	0.353	0.505	0.425	0.353	0.505	SUBCLONAL	1	TRUE	1	0.44	2		663	428	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	45	604	0	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	1	2	FACETS	0.409	0.344	0.482	0.409	0.344	0.482	SUBCLONAL	1	TRUE	1	0.44	2		604	500	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685312	86685312	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	16	186	0	ENST00000274376.6:c.3028C>T	p.Arg1010Ter	p.R1010*	ENST00000274376	NM_002890.2	1010	Cga/Tga	24/25	0.130861378403997	3	FACETS	0.415	0.307	0.543	0.207	0.153	0.272	INDETERMINATE	1	TRUE	1	0.44	3		186	214	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	86	455	0	ENST00000320574.5:c.1231G>C	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ctg	13/49	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.44	2		455	265	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565543	41565543	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	23	525	0	ENST00000263253.7:c.4209C>A	p.Phe1403Leu	p.F1403L	ENST00000263253	NM_001429.3	1403	ttC/ttA	26/31	1	2	FACETS	0.229	0.178	0.288	0.229	0.178	0.288	SUBCLONAL	1	TRUE	1	0.44	2		525	457	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946809	17946809	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257320432	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	133	799	1	ENST00000458235.1:c.1838G>A	p.Arg613Gln	p.R613Q	ENST00000458235	NM_000215.3	613	cGa/cAa	14/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.44	2		800	436	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521544	8521544	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	21	483	0	ENST00000356435.5:c.694C>T	p.Arg232Cys	p.R232C	ENST00000356435		232	Cgc/Tgc	9/35	1	2	FACETS	0.299	0.23	0.38	0.299	0.23	0.38	SUBCLONAL	1	TRUE	1	0.44	2		483	319	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539690	187539690	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs748166431	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	49	404	1	ENST00000441802.2:c.8050G>T	p.Glu2684Ter	p.E2684*	ENST00000441802	NM_005245.3	2684	Gaa/Taa	10/27	1	2	FACETS	0.853	0.729	0.988	0.853	0.729	0.988	CLONAL	1	TRUE	1	0.44	2		405	261	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763428	59763428	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	28	778	1	ENST00000259008.2:c.2674C>A	p.Leu892Ile	p.L892I	ENST00000259008	NM_032043.2	892	Ctt/Att	19/20	1	2	FACETS	0.234	0.187	0.289	0.234	0.187	0.289	SUBCLONAL	1	TRUE	1	0.44	2		779	543	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888102	81888102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	36	491	0	ENST00000359376.3:c.247G>A	p.Glu83Lys	p.E83K	ENST00000359376	NM_002661.3	83	Gag/Aag	3/33	1	2	FACETS	0.474	0.391	0.568	0.474	0.391	0.568	SUBCLONAL	1	TRUE	1	0.44	2		491	345	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950099	38950099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757900166	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	20	569	0	ENST00000357387.3:c.3851C>T	p.Ser1284Leu	p.S1284L	ENST00000357387	NM_152756.3	1284	tCg/tTg	31/38	0.130861378403997	3	FACETS	0.282	0.215	0.361	0.141	0.107	0.181	INDETERMINATE	1	TRUE	1	0.44	3		569	393	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670234	134670234	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764139128	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	13	427	0	ENST00000398015.3:c.145G>A	p.Asp49Asn	p.D49N	ENST00000398015	NM_004441.4	49	Gat/Aat	3/16	1	2	FACETS	0.266	0.19	0.359	0.266	0.19	0.359	SUBCLONAL	1	TRUE	1	0.44	2		427	222	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105736	27105736	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	23	404	1	ENST00000324856.7:c.5347G>T	p.Glu1783Ter	p.E1783*	ENST00000324856	NM_006015.4	1783	Gaa/Taa	20/20	1	2	FACETS	0.43	0.336	0.538	0.43	0.336	0.538	SUBCLONAL	1	TRUE	1	0.44	2		405	243	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916957	178916957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	26	368	1	ENST00000263967.3:c.344G>A	p.Arg115Gln	p.R115Q	ENST00000263967	NM_006218.2	115	cGa/cAa	2/21	1	2	FACETS	0.368	0.292	0.456	0.368	0.292	0.456	SUBCLONAL	1	TRUE	1	0.44	2		369	321	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830535	72830535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776901666	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	39	750	0	ENST00000268489.5:c.6046G>A	p.Glu2016Lys	p.E2016K	ENST00000268489	NM_006885.3	2016	Gag/Aag	9/10	1	2	FACETS	0.362	0.299	0.431	0.362	0.299	0.431	SUBCLONAL	1	TRUE	1	0.44	2		750	490	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609786	117609786	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs141670885	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	26	690	1	ENST00000368508.3:c.6913G>T	p.Glu2305Ter	p.E2305*	ENST00000368508	NM_002944.2	2305	Gaa/Taa	43/43	1	2	FACETS	0.279	0.221	0.347	0.279	0.221	0.347	SUBCLONAL	1	TRUE	1	0.44	2		691	423	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343020	70343020	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	81	687	0	ENST00000374080.3:c.1561C>T	p.Arg521Cys	p.R521C	ENST00000374080		521	Cgt/Tgt	11/45	0.294472231170961	0	FACETS	0.505	0.447	0.567			1	SUBCLONAL	1	TRUE	0	0.44	0		687	408	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212572	133212572	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	68	557	0	ENST00000320574.5:c.5717C>A	p.Ser1906Tyr	p.S1906Y	ENST00000320574	NM_006231.2	1906	tCt/tAt	42/49	1	2	FACETS	0.981	0.861	1	0.981	0.861	1	CLONAL	1	TRUE	1	0.44	2		557	315	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930610	32930610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358973	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	21	423	0	ENST00000380152.3:c.7481G>A	p.Arg2494Gln	p.R2494Q	ENST00000380152		2494	cGa/cAa	15/27	0.294472231170961	4	FACETS	0.383	0.294	0.486	0.191	0.147	0.243	SUBCLONAL	1	TRUE	2	0.44	4		423	359	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740436	58740436	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs769061997	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	56	591	1	ENST00000305921.3:c.1341G>T	p.Glu447Asp	p.E447D	ENST00000305921	NM_003620.3	447	gaG/gaT	6/6	1	2	FACETS	0.582	0.5	0.672	0.582	0.5	0.672	SUBCLONAL	1	TRUE	1	0.44	2		592	437	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765472	41765472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775504685	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	25	608	1	ENST00000301178.4:c.2348C>T	p.Ser783Leu	p.S783L	ENST00000301178	NM_021913.4	783	tCg/tTg	20/20	1	2	FACETS	0.247	0.194	0.308	0.247	0.194	0.308	SUBCLONAL	1	TRUE	1	0.44	2		609	460	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176504	142176504	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1196005889	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	21	477	2	ENST00000350721.4:c.7597C>T	p.Arg2533Ter	p.R2533*	ENST00000350721	NM_001184.3	2533	Cga/Tga	45/47	1	2	FACETS	0.253	0.194	0.322	0.253	0.194	0.322	SUBCLONAL	1	TRUE	1	0.44	2		479	377	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421355	12421355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777334819	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	79	790	0	ENST00000287820.6:c.235G>A	p.Glu79Lys	p.E79K	ENST00000287820	NM_015869.4	79	Gaa/Aaa	2/7	1	2	FACETS	0.559	0.492	0.632	0.559	0.492	0.632	SUBCLONAL	1	TRUE	1	0.44	2		790	642	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528078	103528078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368829739	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	13	317	0	ENST00000355739.4:c.3386C>T	p.Ser1129Leu	p.S1129L	ENST00000355739	NM_000123.3	1129	tCg/tTg	15/15	1	2	FACETS	0.264	0.188	0.356	0.264	0.188	0.356	SUBCLONAL	1	TRUE	1	0.44	2		317	224	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306558	163306558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	29	507	0	ENST00000271452.3:c.355C>T	p.Arg119Trp	p.R119W	ENST00000271452	NM_145697.2	119	Cgg/Tgg	6/14	1	2	FACETS	0.257	0.206	0.316	0.257	0.206	0.316	SUBCLONAL	1	TRUE	1	0.44	2		507	512	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828503	72828503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	55	712	0	ENST00000268489.5:c.8078G>A	p.Arg2693Gln	p.R2693Q	ENST00000268489	NM_006885.3	2693	cGa/cAa	9/10	1	2	FACETS	0.556	0.476	0.642	0.556	0.476	0.642	SUBCLONAL	1	TRUE	1	0.44	2		712	450	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672800	86672800	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764802465	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	116	373	0	ENST00000274376.6:c.2287G>A	p.Glu763Lys	p.E763K	ENST00000274376	NM_002890.2	763	Gaa/Aaa	17/25	0.130861378403997	3	FACETS	0.827	0.752	0.904	0.827	0.752	0.904	INDETERMINATE	2	TRUE	1	0.44	3		373	389	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538990	23538990	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775943527	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	23	697	0	ENST00000380871.4:c.449C>T	p.Ser150Leu	p.S150L	ENST00000380871	NM_006167.3	150	tCg/tTg	2/2	1	2	FACETS	0.265	0.206	0.333	0.265	0.206	0.333	SUBCLONAL	1	TRUE	1	0.44	2		697	395	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165729	108165729	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs762083530	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	34	408	1	ENST00000278616.4:c.4852C>T	p.Arg1618Ter	p.R1618*	ENST00000278616	NM_000051.3	1618	Cga/Tga	32/63	1	2	FACETS	0.437	0.357	0.526	0.437	0.357	0.526	SUBCLONAL	1	TRUE	1	0.44	2		409	354	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180441	94180441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139461096	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	29	629	0	ENST00000323929.3:c.1727G>A	p.Arg576Gln	p.R576Q	ENST00000323929	NM_005591.3	576	cGa/cAa	15/20	1	2	FACETS	0.263	0.21	0.323	0.263	0.21	0.323	SUBCLONAL	1	TRUE	1	0.44	2		629	502	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944983	31944983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1175067252	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	57	760	0	ENST00000340398.3:c.118C>T	p.Arg40Cys	p.R40C	ENST00000340398	NM_001013699.2	40	Cgc/Tgc	1/1	0.210001659018759	4	FACETS	0.584	0.5	0.675	0.292	0.25	0.338	INDETERMINATE	1	TRUE	2	0.44	4		760	639	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928067	178928067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	150	672	0	ENST00000263967.3:c.1345C>T	p.Pro449Ser	p.P449S	ENST00000263967	NM_006218.2	449	Cct/Tct	8/21	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.44	2		672	544	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197721	66197721	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	26	526	0	ENST00000273854.3:c.2978C>A	p.Ser993Ter	p.S993*	ENST00000273854	NM_004439.5	993	tCa/tAa	17/18	1	2	FACETS	0.33	0.261	0.409	0.33	0.261	0.409	SUBCLONAL	1	TRUE	1	0.44	2		526	358	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965644	93965644	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	22	484	0	ENST00000369303.4:c.2284C>T	p.Arg762Cys	p.R762C	ENST00000369303	NM_004440.3	762	Cgc/Tgc	13/17	1	2	FACETS	0.25	0.193	0.316	0.25	0.193	0.316	SUBCLONAL	1	TRUE	1	0.44	2		484	400	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535426	187535426	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370628880	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	26	526	0	ENST00000441802.2:c.9148G>A	p.Ala3050Thr	p.A3050T	ENST00000441802	NM_005245.3	3050	Gca/Aca	12/27	1	2	FACETS	0.341	0.27	0.422	0.341	0.27	0.422	SUBCLONAL	1	TRUE	1	0.44	2		526	347	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725528	117725528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867759865	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	105	602	1	ENST00000368508.3:c.353G>A	p.Arg118Gln	p.R118Q	ENST00000368508	NM_002944.2	118	cGa/cAa	5/43	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.44	2		603	362	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741688	17741688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	108	430	0	ENST00000250003.3:c.359G>A	p.Arg120His	p.R120H	ENST00000250003	NM_002478.4	120	cGc/cAc	1/3	1	2	FACETS	0.963	0.88	1	1	0.989	1	CLONAL	2	TRUE	1	0.44	2		430	255	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246091297	246091297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758081490	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	20	420	0	ENST00000388985.4:c.638C>T	p.Ser213Leu	p.S213L	ENST00000388985		213	tCg/tTg	7/12	1	2	FACETS	0.253	0.193	0.324	0.253	0.193	0.324	SUBCLONAL	1	TRUE	1	0.44	2		420	359	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054649	5054649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373174105	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	46	343	0	ENST00000381652.3:c.701G>A	p.Arg234His	p.R234H	ENST00000381652	NM_004972.3	234	cGc/cAc	7/25	1	2	FACETS	0.672	0.569	0.785	0.672	0.569	0.785	SUBCLONAL	1	TRUE	1	0.44	2		343	311	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476364	88476364	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780933441	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	54	677	2	ENST00000360948.2:c.1768G>A	p.Glu590Lys	p.E590K	ENST00000360948	NM_001012338.2	590	Gag/Aag	15/19	1	2	FACETS	0.688	0.59	0.794	0.688	0.59	0.794	SUBCLONAL	1	TRUE	1	0.44	2		679	357	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47700132	47700132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1412582124	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	106	450	0	ENST00000347630.2:c.41C>T	p.Ser14Leu	p.S14L	ENST00000347630	NM_001007230.1	14	tCg/tTg	3/11	1	2	FACETS	0.975	0.878	1	0.975	0.878	1	CLONAL	1	TRUE	1	0.44	2		450	494	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740204	162740204	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749040833	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	29	569	0	ENST00000367921.3:c.1406C>T	p.Ser469Leu	p.S469L	ENST00000367921	NM_006182.2	469	tCg/tTg	12/18	1	2	FACETS	0.313	0.251	0.384	0.313	0.251	0.384	SUBCLONAL	1	TRUE	1	0.44	2		569	421	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446447	70446447	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	107	474	0	ENST00000373644.4:c.5387C>T	p.Ser1796Leu	p.S1796L	ENST00000373644	NM_030625.2	1796	tCg/tTg	11/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.44	2		474	402	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803500	32803500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550712305	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	36	812	0	ENST00000374899.4:c.659G>A	p.Arg220Gln	p.R220Q	ENST00000374899	NM_018833.2	220	cGa/cAa	4/12	1	2	FACETS	0.269	0.22	0.324	0.269	0.22	0.324	SUBCLONAL	1	TRUE	1	0.44	2		812	608	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594061	55594061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs891140054	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	51	531	0	ENST00000288135.5:c.1847C>T	p.Ala616Val	p.A616V	ENST00000288135	NM_000222.2	616	gCg/gTg	12/21	1	2	FACETS	0.642	0.548	0.745	0.642	0.548	0.745	SUBCLONAL	1	TRUE	1	0.44	2		531	361	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857686	59857686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781321	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	33	447	0	ENST00000259008.2:c.1871C>T	p.Ser624Leu	p.S624L	ENST00000259008	NM_032043.2	624	tCg/tTg	13/20	1	2	FACETS	0.41	0.334	0.495	0.41	0.334	0.495	SUBCLONAL	1	TRUE	1	0.44	2		447	366	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754974	29754974	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	44	532	0	ENST00000389048.3:c.961C>T	p.Leu321Phe	p.L321F	ENST00000389048	NM_004304.4	321	Ctc/Ttc	4/29	1	2	FACETS	0.637	0.536	0.747	0.637	0.536	0.747	SUBCLONAL	1	TRUE	1	0.44	2		532	314	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443676	29443676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56315533	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	25	678	1	ENST00000389048.3:c.3541C>T	p.Arg1181Cys	p.R1181C	ENST00000389048	NM_004304.4	1181	Cgc/Tgc	23/29	1	2	FACETS	0.288	0.226	0.358	0.288	0.226	0.358	SUBCLONAL	1	TRUE	1	0.44	2		679	395	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532474	63532474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757100957	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	32	761	1	ENST00000307078.5:c.2105G>A	p.Arg702His	p.R702H	ENST00000307078	NM_004655.3	702	cGc/cAc	8/11	1	2	FACETS	0.358	0.291	0.435	0.358	0.291	0.435	SUBCLONAL	1	TRUE	1	0.44	2		762	406	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6442009	6442009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	27	346	0	ENST00000356142.4:c.568G>A	p.Glu190Lys	p.E190K	ENST00000356142	NM_018890.3	190	Gaa/Aaa	7/7	1	2	FACETS	0.425	0.338	0.523	0.425	0.338	0.523	SUBCLONAL	1	TRUE	1	0.44	2		346	289	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741894	40741894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs930976777	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	68	811	1	ENST00000392038.2:c.1078G>A	p.Glu360Lys	p.E360K	ENST00000392038	NM_001626.4	360	Gag/Aag	11/14	1	2	FACETS	0.688	0.601	0.783	0.688	0.601	0.783	SUBCLONAL	1	TRUE	1	0.44	2		812	449	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751487	57751487	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	25	404	0	ENST00000274289.3:c.1504C>T	p.Gln502Ter	p.Q502*	ENST00000274289	NM_006622.3	502	Cag/Tag	11/14	0.130861378403997	3	FACETS	0.414	0.326	0.515	0.207	0.163	0.258	INDETERMINATE	1	TRUE	1	0.44	3		404	335	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42050033	42050033	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs548371365	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	25	391	1	ENST00000219905.7:c.7187G>A	p.Arg2396Gln	p.R2396Q	ENST00000219905	NM_001164273.1	2396	cGa/cAa	19/24	1	2	FACETS	0.276	0.217	0.344	0.276	0.217	0.344	SUBCLONAL	1	TRUE	1	0.44	2		392	412	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929510	81929510	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	25	557	0	ENST00000359376.3:c.1171G>T	p.Asp391Tyr	p.D391Y	ENST00000359376	NM_002661.3	391	Gac/Tac	13/33	1	2	FACETS	0.259	0.203	0.323	0.259	0.203	0.323	SUBCLONAL	1	TRUE	1	0.44	2		557	439	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426543	49426543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760983900	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	51	998	1	ENST00000301067.7:c.11945G>A	p.Arg3982Gln	p.R3982Q	ENST00000301067	NM_003482.3	3982	cGa/cAa	39/54	0.210001659018759	4	FACETS	0.411	0.348	0.48	0.206	0.174	0.24	INDETERMINATE	1	TRUE	2	0.44	4		999	812	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222953	36222953	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753685124	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	33	1005	0	ENST00000222270.7:c.5582C>T	p.Ser1861Leu	p.S1861L	ENST00000222270	NM_014727.1	1861	tCg/tTg	27/37	1	2	FACETS	0.268	0.217	0.325	0.268	0.217	0.325	SUBCLONAL	1	TRUE	1	0.44	2		1005	560	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349471	73349471	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777245855	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	25	572	0	ENST00000377767.4:c.865G>A	p.Glu289Lys	p.E289K	ENST00000377767	NM_014953.3	289	Gaa/Aaa	6/21	1	2	FACETS	0.231	0.181	0.288	0.231	0.181	0.288	SUBCLONAL	1	TRUE	1	0.44	2		572	492	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873932	151873932	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	155	573	0	ENST00000262189.6:c.8606C>A	p.Ser2869Tyr	p.S2869Y	ENST00000262189	NM_170606.2	2869	tCt/tAt	38/59	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.44	2		573	529	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41279559	41279559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200308943	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	36	480	1	ENST00000349496.5:c.2129G>A	p.Arg710His	p.R710H	ENST00000349496	NM_001904.3	710	cGc/cAc	14/15	1	2	FACETS	0.398	0.327	0.477	0.398	0.327	0.477	SUBCLONAL	1	TRUE	1	0.44	2		481	411	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257957	16257957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762412019	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	28	556	0	ENST00000375759.3:c.5222C>T	p.Ser1741Leu	p.S1741L	ENST00000375759	NM_015001.2	1741	tCg/tTg	11/15	0.3	5	FACETS	0.566	0.453	0.696			1	SUBCLONAL	1	TRUE	NA	0.44	5		556	373	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346631	81346631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	16	358	0	ENST00000222390.5:c.1322G>A	p.Arg441Gln	p.R441Q	ENST00000222390	NM_000601.4	441	cGa/cAa	11/18	1	2	FACETS	0.263	0.194	0.345	0.263	0.194	0.345	SUBCLONAL	1	TRUE	1	0.44	2		358	277	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710875	117710875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140178288	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	22	523	2	ENST00000368508.3:c.1397G>A	p.Arg466Gln	p.R466Q	ENST00000368508	NM_002944.2	466	cGa/cAa	12/43	1	2	FACETS	0.282	0.218	0.356	0.282	0.218	0.356	SUBCLONAL	1	TRUE	1	0.44	2		525	355	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438282	49438282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs192216625	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	49	665	0	ENST00000301067.7:c.4987G>A	p.Glu1663Lys	p.E1663K	ENST00000301067	NM_003482.3	1663	Gaa/Aaa	20/54	0.210001659018759	4	FACETS	0.685	0.581	0.8	0.343	0.29	0.4	INDETERMINATE	1	TRUE	2	0.44	4		665	468	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938325	76938325	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782181535	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	110	771	0	ENST00000373344.5:c.2423G>A	p.Arg808Gln	p.R808Q	ENST00000373344	NM_000489.3	808	cGa/cAa	9/35	0.294472231170961	0	FACETS	0.585	0.528	0.644			1	SUBCLONAL	1	TRUE	0	0.44	0		771	479	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599908	28599908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756414646	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	32	669	0	ENST00000253063.3:c.790C>T	p.Arg264Cys	p.R264C	ENST00000253063	NM_031459.4	264	Cgc/Tgc	6/10	1	2	FACETS	0.422	0.342	0.511	0.422	0.342	0.511	SUBCLONAL	1	TRUE	1	0.44	2		669	345	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307169	65307169	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	24	518	0	ENST00000342505.4:c.2519C>T	p.Ala840Val	p.A840V	ENST00000342505	NM_002227.2	840	gCc/gTc	18/25	1	2	FACETS	0.325	0.254	0.406	0.325	0.254	0.406	SUBCLONAL	1	TRUE	1	0.44	2		518	336	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400879	72400879	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs372543475	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	28	392	0	ENST00000357731.5:c.292A>G	p.Lys98Glu	p.K98E	ENST00000357731	NM_173808.2	98	Aaa/Gaa	2/7	1	2	FACETS	0.36	0.287	0.442	0.36	0.287	0.442	SUBCLONAL	1	TRUE	1	0.44	2		392	354	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115251226	115251226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	32	690	0	ENST00000369535.4:c.500G>A	p.Arg167Gln	p.R167Q	ENST00000369535	NM_002524.4	167	cGa/cAa	5/7	1	2	FACETS	0.263	0.212	0.319	0.263	0.212	0.319	SUBCLONAL	1	TRUE	1	0.44	2		690	554	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261329	115261329	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	41	421	0	ENST00000438362.2:c.2392C>T	p.Arg798Trp	p.R798W	ENST00000438362	NM_001242891.1	798	Cgg/Tgg	19/20	1	2	FACETS	0.525	0.438	0.621	0.525	0.438	0.621	SUBCLONAL	1	TRUE	1	0.44	2		421	355	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849833	156849833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758876909	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	28	618	0	ENST00000524377.1:c.2089G>A	p.Glu697Lys	p.E697K	ENST00000524377	NM_002529.3	697	Gag/Aag	16/17	1	2	FACETS	0.349	0.278	0.429	0.349	0.278	0.429	SUBCLONAL	1	TRUE	1	0.44	2		618	365	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731019	162731019	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	17	383	0	ENST00000367921.3:c.874T>C	p.Phe292Leu	p.F292L	ENST00000367921	NM_006182.2	292	Ttt/Ctt	9/18	1	2	FACETS	0.285	0.213	0.371	0.285	0.213	0.371	SUBCLONAL	1	TRUE	1	0.44	2		383	271	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743338	162743338	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1221368862	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	25	424	0	ENST00000367921.3:c.1808T>C	p.Val603Ala	p.V603A	ENST00000367921	NM_006182.2	603	gTc/gCc	14/18	1	2	FACETS	0.335	0.264	0.417	0.335	0.264	0.417	SUBCLONAL	1	TRUE	1	0.44	2		424	339	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246091247	246091247	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147009044	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	19	400	0	ENST00000388985.4:c.688G>A	p.Glu230Lys	p.E230K	ENST00000388985		230	Gag/Aag	7/12	1	2	FACETS	0.23	0.174	0.296	0.23	0.174	0.296	SUBCLONAL	1	TRUE	1	0.44	2		400	376	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724411	112724411	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	25	554	0	ENST00000369452.4:c.295G>A	p.Glu99Lys	p.E99K	ENST00000369452	NM_007373.3	99	Gaa/Aaa	2/9	1	2	FACETS	0.266	0.209	0.331	0.266	0.209	0.331	SUBCLONAL	1	TRUE	1	0.44	2		554	428	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573758	64573758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	41	708	0	ENST00000312049.6:c.995G>A	p.Arg332His	p.R332H	ENST00000312049	NM_130799.2	332	cGc/cAc	7/10	1	2	FACETS	0.327	0.272	0.389	0.327	0.272	0.389	SUBCLONAL	1	TRUE	1	0.44	2		708	570	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94153298	94153298	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1403179982	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	24	624	0	ENST00000323929.3:c.2120G>A	p.Arg707Lys	p.R707K	ENST00000323929	NM_005591.3	707	aGa/aAa	20/20	1	2	FACETS	0.228	0.178	0.286	0.228	0.178	0.286	SUBCLONAL	1	TRUE	1	0.44	2		624	478	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918657	94918657	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	14	350	0	ENST00000536441.1:c.526-1G>A		p.X176_splice	ENST00000536441	NM_144665.3	176			1	2	FACETS	0.229	0.165	0.306	0.229	0.165	0.306	SUBCLONAL	1	TRUE	1	0.44	2		350	278	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342647	118342647	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	12	227	0	ENST00000534358.1:c.773G>T	p.Arg258Met	p.R258M	ENST00000534358	NM_005933.3	258	aGg/aTg	3/36	1	2	FACETS	0.345	0.243	0.47	0.345	0.243	0.47	SUBCLONAL	1	TRUE	1	0.44	2		227	158	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344036	118344036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	17	458	0	ENST00000534358.1:c.2162G>A	p.Arg721Gln	p.R721Q	ENST00000534358	NM_005933.3	721	cGa/cAa	3/36	1	2	FACETS	0.241	0.179	0.314	0.241	0.179	0.314	SUBCLONAL	1	TRUE	1	0.44	2		458	321	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348826	118348826	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	39	334	1	ENST00000534358.1:c.3479G>A	p.Gly1160Asp	p.G1160D	ENST00000534358	NM_005933.3	1160	gGc/gAc	5/36	1	2	FACETS	0.539	0.448	0.64	0.539	0.448	0.64	SUBCLONAL	1	TRUE	1	0.44	2		335	329	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375267	118375267	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	25	433	0	ENST00000534358.1:c.8660A>G	p.Asp2887Gly	p.D2887G	ENST00000534358	NM_005933.3	2887	gAc/gGc	27/36	1	2	FACETS	0.373	0.294	0.463	0.373	0.294	0.463	SUBCLONAL	1	TRUE	1	0.44	2		433	305	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	464344	464344	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	49	712	0	ENST00000399788.2:c.850G>A	p.Gly284Ser	p.G284S	ENST00000399788	NM_001042603.1	284	Ggc/Agc	7/28	0.3	2	FACETS	0.301	0.254	0.353			1	SUBCLONAL	1	TRUE	NA	0.44	2		712	739	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435508	18435508	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	36	270	0	ENST00000266497.5:c.493C>A	p.His165Asn	p.H165N	ENST00000266497		165	Cat/Aat	1/31	0.210001659018759	4	FACETS	1	0.925	1	0.61	0.507	0.724	INDETERMINATE	1	TRUE	2	0.44	4		270	193	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544169	18544169	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	21	427	0	ENST00000266497.5:c.1986G>T	p.Gln662His	p.Q662H	ENST00000266497		662	caG/caT	13/31	0.210001659018759	4	FACETS	0.382	0.293	0.485	0.191	0.146	0.243	INDETERMINATE	1	TRUE	2	0.44	4		427	360	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245985	46245985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	14	341	0	ENST00000334344.6:c.4079G>A	p.Gly1360Glu	p.G1360E	ENST00000334344	NM_152641.2	1360	gGa/gAa	15/21	0.210001659018759	4	FACETS	0.359	0.259	0.48	0.18	0.129	0.24	INDETERMINATE	1	TRUE	2	0.44	4		341	255	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428642	49428642	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	31	875	0	ENST00000301067.7:c.10308G>T	p.Lys3436Asn	p.K3436N	ENST00000301067	NM_003482.3	3436	aaG/aaT	35/54	0.210001659018759	4	FACETS	0.351	0.283	0.428	0.176	0.141	0.214	INDETERMINATE	1	TRUE	2	0.44	4		875	578	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441791	49441791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1389196402	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	27	528	1	ENST00000301067.7:c.4193C>T	p.Ser1398Leu	p.S1398L	ENST00000301067	NM_003482.3	1398	tCg/tTg	14/54	0.210001659018759	4	FACETS	0.359	0.285	0.444	0.18	0.142	0.222	INDETERMINATE	1	TRUE	2	0.44	4		529	492	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488219	56488219	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs371577741	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	41	635	0	ENST00000267101.3:c.1738C>T	p.Arg580Ter	p.R580*	ENST00000267101	NM_001982.3	580	Cga/Tga	15/28	0.210001659018759	4	FACETS	0.525	0.437	0.623	0.263	0.218	0.312	INDETERMINATE	1	TRUE	2	0.44	4		635	511	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541733	120541733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	67	646	0	ENST00000229340.5:c.124G>A	p.Gly42Arg	p.G42R	ENST00000229340	NM_006861.6	42	Gga/Aga	3/6	1	2	FACETS	0.624	0.543	0.711	0.624	0.543	0.711	SUBCLONAL	1	TRUE	1	0.44	2		646	488	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431969	121431969	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs587778397	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	18	490	0	ENST00000257555.6:c.716C>T	p.Ala239Val	p.A239V	ENST00000257555		239	gCg/gTg	4/10	1	2	FACETS	0.233	0.175	0.302	0.233	0.175	0.302	SUBCLONAL	1	TRUE	1	0.44	2		490	351	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29068923	29068923	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1304722504	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	10	221	0	ENST00000282397.4:c.58C>T	p.Leu20Phe	p.L20F	ENST00000282397	NM_002019.4	20	Ctc/Ttc	1/30	0.210001659018759	0	FACETS	0.166	0.113	0.233			1	INDETERMINATE	1	TRUE	0	0.44	0		221	153	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900279	32900279	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs68071147	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	27	417	0	ENST00000380152.3:c.467A>C	p.Asp156Ala	p.D156A	ENST00000380152		156	gAt/gCt	5/27	0.294472231170961	4	FACETS	0.426	0.338	0.526	0.213	0.169	0.263	SUBCLONAL	1	TRUE	2	0.44	4		417	415	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912069	32912069	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	31	714	0	ENST00000380152.3:c.3577G>T	p.Ala1193Ser	p.A1193S	ENST00000380152		1193	Gct/Tct	11/27	0.294472231170961	4	FACETS	0.433	0.349	0.527	0.216	0.174	0.264	SUBCLONAL	1	TRUE	2	0.44	4		714	469	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504600	103504600	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	26	402	0	ENST00000355739.4:c.221T>G	p.Phe74Cys	p.F74C	ENST00000355739	NM_000123.3	74	tTt/tGt	2/15	1	2	FACETS	0.297	0.235	0.368	0.297	0.235	0.368	SUBCLONAL	1	TRUE	1	0.44	2		402	398	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435568	110435568	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	13	327	0	ENST00000375856.3:c.2833T>C	p.Ser945Pro	p.S945P	ENST00000375856	NM_003749.2	945	Tcc/Ccc	1/2	1	2	FACETS	0.229	0.163	0.31	0.229	0.163	0.31	SUBCLONAL	1	TRUE	1	0.44	2		327	258	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060892	38060892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	14	564	0	ENST00000250448.2:c.1097C>T	p.Ala366Val	p.A366V	ENST00000250448	NM_004496.3	366	gCg/gTg	2/2	1	2	FACETS	0.235	0.169	0.314	0.235	0.169	0.314	SUBCLONAL	1	TRUE	1	0.44	2		564	271	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061760	38061760	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	39	516	0	ENST00000250448.2:c.229C>A	p.Leu77Met	p.L77M	ENST00000250448	NM_004496.3	77	Ctg/Atg	2/2	1	2	FACETS	0.504	0.418	0.598	0.504	0.418	0.598	SUBCLONAL	1	TRUE	1	0.44	2		516	352	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566271	95566271	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	18	442	0	ENST00000393063.1:c.4052T>C	p.Val1351Ala	p.V1351A	ENST00000393063	NM_030621.3	1351	gTc/gCc	23/28	1	2	FACETS	0.272	0.204	0.352	0.272	0.204	0.352	SUBCLONAL	1	TRUE	1	0.44	2		442	301	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961511	41961511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528733174	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	29	722	0	ENST00000219905.7:c.419G>A	p.Arg140His	p.R140H	ENST00000219905	NM_001164273.1	140	cGt/cAt	2/24	1	2	FACETS	0.243	0.194	0.299	0.243	0.194	0.299	SUBCLONAL	1	TRUE	1	0.44	2		722	542	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705429	43705429	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs752678808	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	31	810	0	ENST00000382044.4:c.5193G>T	p.Lys1731Asn	p.K1731N	ENST00000382044	NM_001141980.1	1731	aaG/aaT	24/28	1	2	FACETS	0.254	0.205	0.31	0.254	0.205	0.31	SUBCLONAL	1	TRUE	1	0.44	2		810	554	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853227	68853227	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881667	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	42	570	0	ENST00000261769.5:c.1610C>T	p.Pro537Leu	p.P537L	ENST00000261769	NM_004360.3	537	cCg/cTg	11/16	1	2	FACETS	0.416	0.347	0.492	0.416	0.347	0.492	SUBCLONAL	1	TRUE	1	0.44	2		570	459	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992970	72992970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	83	1022	0	ENST00000268489.5:c.1075G>A	p.Gly359Ser	p.G359S	ENST00000268489	NM_006885.3	359	Ggc/Agc	2/10	1	2	FACETS	0.487	0.429	0.549	0.487	0.429	0.549	SUBCLONAL	1	TRUE	1	0.44	2		1022	775	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350752	89350752	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373946350	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	69	1015	0	ENST00000301030.4:c.2198G>A	p.Arg733Gln	p.R733Q	ENST00000301030	NM_001256183.1	733	cGa/cAa	9/13	1	2	FACETS	0.383	0.333	0.438	0.383	0.333	0.438	SUBCLONAL	1	TRUE	1	0.44	2		1015	819	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541484	29541484	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	14	189	0	ENST00000356175.3:c.1408G>T	p.Glu470Ter	p.E470*	ENST00000356175	NM_000267.3	470	Gaa/Taa	13/57	1	2	FACETS	0.333	0.241	0.444	0.333	0.241	0.444	SUBCLONAL	1	TRUE	1	0.44	2		189	191	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40855800	40855800	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1458266017	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	50	668	0	ENST00000428826.2:c.2056C>T	p.Arg686Ter	p.R686*	ENST00000428826		686	Cga/Tga	19/21	1	2	FACETS	0.346	0.293	0.405	0.346	0.293	0.405	SUBCLONAL	1	TRUE	1	0.44	2		668	656	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41276073	41276073	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	40	652	0	ENST00000357654.3:c.41T>C	p.Val14Ala	p.V14A	ENST00000357654	NM_007294.3	14	gTc/gCc	2/23	1	2	FACETS	0.251	0.207	0.299	0.251	0.207	0.299	SUBCLONAL	1	TRUE	1	0.44	2		652	725	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55478759	55478759	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	42	511	0	ENST00000284073.2:c.332A>G	p.Lys111Arg	p.K111R	ENST00000284073	NM_138962.2	111	aAa/aGa	6/14	1	2	FACETS	0.42	0.35	0.496	0.42	0.35	0.496	SUBCLONAL	1	TRUE	1	0.44	2		511	455	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858328	59858328	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	30	574	0	ENST00000259008.2:c.1667A>G	p.Tyr556Cys	p.Y556C	ENST00000259008	NM_032043.2	556	tAc/tGc	12/20	1	2	FACETS	0.265	0.213	0.324	0.265	0.213	0.324	SUBCLONAL	1	TRUE	1	0.44	2		574	515	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926518	59926518	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	50	822	0	ENST00000259008.2:c.479G>A	p.Arg160Lys	p.R160K	ENST00000259008	NM_032043.2	160	aGa/aAa	5/20	1	2	FACETS	0.321	0.272	0.376	0.321	0.272	0.376	SUBCLONAL	1	TRUE	1	0.44	2		822	708	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226388	2226388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs112052747	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	47	873	2	ENST00000398665.3:c.3868G>A	p.Ala1290Thr	p.A1290T	ENST00000398665	NM_032482.2	1290	Gct/Act	27/28	1	2	FACETS	0.457	0.386	0.536	0.457	0.386	0.536	SUBCLONAL	1	TRUE	1	0.44	2		875	467	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117578	4117578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1295043645	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	37	649	0	ENST00000262948.5:c.142G>A	p.Glu48Lys	p.E48K	ENST00000262948	NM_030662.3	48	Gag/Aag	2/11	1	2	FACETS	0.406	0.335	0.486	0.406	0.335	0.486	SUBCLONAL	1	TRUE	1	0.44	2		649	414	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247856	10247856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	52	818	0	ENST00000340748.4:c.4346G>A	p.Gly1449Asp	p.G1449D	ENST00000340748		1449	gGc/gAc	36/40	1	2	FACETS	0.456	0.388	0.531	0.456	0.388	0.531	SUBCLONAL	1	TRUE	1	0.44	2		818	518	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258567	19258567	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	55	874	1	ENST00000162023.5:c.333G>T	p.Glu111Asp	p.E111D	ENST00000162023		111	gaG/gaT	8/13	1	2	FACETS	0.446	0.381	0.516	0.446	0.381	0.516	SUBCLONAL	1	TRUE	1	0.44	2		875	561	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469074	25469074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	35	867	0	ENST00000264709.3:c.1384G>A	p.Ala462Thr	p.A462T	ENST00000264709	NM_175629.2	462	Gcg/Acg	11/23	1	2	FACETS	0.231	0.189	0.279	0.231	0.189	0.279	SUBCLONAL	1	TRUE	1	0.44	2		867	688	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46597034	46597034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767899036	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	26	565	0	ENST00000263734.3:c.848C>T	p.Ala283Val	p.A283V	ENST00000263734	NM_001430.4	283	gCg/gTg	7/16	1	2	FACETS	0.261	0.206	0.324	0.261	0.206	0.324	SUBCLONAL	1	TRUE	1	0.44	2		565	453	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46608793	46608793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	19	777	1	ENST00000263734.3:c.2104C>T	p.Leu702Phe	p.L702F	ENST00000263734	NM_001430.4	702	Ctc/Ttc	13/16	1	2	FACETS	0.241	0.182	0.31	0.241	0.182	0.31	SUBCLONAL	1	TRUE	1	0.44	2		778	359	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657054	47657054	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	22	283	0	ENST00000233146.2:c.1250T>C	p.Val417Ala	p.V417A	ENST00000233146	NM_000251.2	417	gTt/gCt	7/16	1	2	FACETS	0.352	0.273	0.444	0.352	0.273	0.444	SUBCLONAL	1	TRUE	1	0.44	2		283	284	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707989	47707989	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1156823520	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	24	456	0	ENST00000233146.2:c.2613G>T	p.Lys871Asn	p.K871N	ENST00000233146	NM_000251.2	871	aaG/aaT	15/16	1	2	FACETS	0.37	0.29	0.461	0.37	0.29	0.461	SUBCLONAL	1	TRUE	1	0.44	2		456	295	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026549	48026549	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	34	524	0	ENST00000234420.5:c.1427A>C	p.Lys476Thr	p.K476T	ENST00000234420	NM_000179.2	476	aAg/aCg	4/10	1	2	FACETS	0.465	0.381	0.56	0.465	0.381	0.56	SUBCLONAL	1	TRUE	1	0.44	2		524	332	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033609	48033609	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs587779294	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	27	485	0	ENST00000234420.5:c.3820G>T	p.Glu1274Ter	p.E1274*	ENST00000234420	NM_000179.2	1274	Gaa/Taa	9/10	1	2	FACETS	0.412	0.328	0.507	0.412	0.328	0.507	SUBCLONAL	1	TRUE	1	0.44	2		485	298	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726900	61726900	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	38	573	0	ENST00000401558.2:c.538G>A	p.Asp180Asn	p.D180N	ENST00000401558	NM_003400.3	180	Gat/Aat	7/25	1	2	FACETS	0.31	0.256	0.371	0.31	0.256	0.371	SUBCLONAL	1	TRUE	1	0.44	2		573	557	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155400	99155400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs965243879	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	21	442	1	ENST00000074304.5:c.626G>A	p.Arg209Gln	p.R209Q	ENST00000074304	NM_001134224.1	209	cGa/cAa	9/26	1	2	FACETS	0.236	0.181	0.3	0.236	0.181	0.3	SUBCLONAL	1	TRUE	1	0.44	2		443	405	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204737491	204737491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	19	372	0	ENST00000302823.3:c.628G>A	p.Glu210Lys	p.E210K	ENST00000302823	NM_005214.4	210	Gaa/Aaa	4/4	1	2	FACETS	0.263	0.199	0.339	0.263	0.199	0.339	SUBCLONAL	1	TRUE	1	0.44	2		372	328	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646225	215646225	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1553622720	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	25	385	1	ENST00000260947.4:c.373G>T	p.Glu125Ter	p.E125*	ENST00000260947	NM_000465.2	125	Gaa/Taa	4/11	1	2	FACETS	0.367	0.289	0.456	0.367	0.289	0.456	SUBCLONAL	1	TRUE	1	0.44	2		386	310	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017155	31017155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	15	258	0	ENST00000375687.4:c.486G>T	p.Lys162Asn	p.K162N	ENST00000375687	NM_015338.5	162	aaG/aaT	7/13	1	2	FACETS	0.253	0.185	0.336	0.253	0.185	0.336	SUBCLONAL	1	TRUE	1	0.44	2		258	269	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024945	31024945	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	24	601	0	ENST00000375687.4:c.4430A>C	p.Lys1477Thr	p.K1477T	ENST00000375687	NM_015338.5	1477	aAa/aCa	13/13	1	2	FACETS	0.261	0.204	0.327	0.261	0.204	0.327	SUBCLONAL	1	TRUE	1	0.44	2		601	418	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980829	40980829	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	16	510	0	ENST00000373198.4:c.1657T>G	p.Phe553Val	p.F553V	ENST00000373198	NM_133170.3	553	Ttt/Gtt	10/32	0.3	0	FACETS	0.135	0.099	0.177			1	SUBCLONAL	1	TRUE	0	0.44	0		510	302	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46271024	46271024	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772403773	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	50	620	0	ENST00000371998.3:c.3148G>A	p.Glu1050Lys	p.E1050K	ENST00000371998		1050	Gaa/Aaa	17/23	1	2	FACETS	0.47	0.398	0.548	0.47	0.398	0.548	SUBCLONAL	1	TRUE	1	0.44	2		620	484	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62322268	62322268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465400494	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	26	917	0	ENST00000360203.5:c.2524G>A	p.Glu842Lys	p.E842K	ENST00000360203	NM_001283009.1	842	Gaa/Aaa	27/35	1	2	FACETS	0.273	0.216	0.339	0.273	0.216	0.339	SUBCLONAL	1	TRUE	1	0.44	2		917	433	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121316	29121316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202246	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	101	852	1	ENST00000328354.6:c.359G>A	p.Ser120Asn	p.S120N	ENST00000328354	NM_007194.3	120	aGc/aAc	3/15	1	2	FACETS	0.685	0.613	0.762	0.685	0.613	0.762	SUBCLONAL	1	TRUE	1	0.44	2		853	670	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042455	37042455	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs766608278	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	24	439	0	ENST00000231790.2:c.217C>A	p.Leu73Met	p.L73M	ENST00000231790	NM_000249.3	73	Ctg/Atg	3/19	1	2	FACETS	0.241	0.188	0.302	0.241	0.188	0.302	SUBCLONAL	1	TRUE	1	0.44	2		439	453	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125834	47125834	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	26	343	0	ENST00000409792.3:c.5436A>C	p.Lys1812Asn	p.K1812N	ENST00000409792	NM_014159.6	1812	aaA/aaC	12/21	1	2	FACETS	0.408	0.323	0.504	0.408	0.323	0.504	SUBCLONAL	1	TRUE	1	0.44	2		343	290	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162432	47162432	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	82	510	0	ENST00000409792.3:c.3694A>C	p.Lys1232Gln	p.K1232Q	ENST00000409792	NM_014159.6	1232	Aaa/Caa	3/21	1	2	FACETS	0.869	0.77	0.974	0.869	0.77	0.974	CLONAL	1	TRUE	1	0.44	2		510	429	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162522	47162522	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	28	457	0	ENST00000409792.3:c.3604C>A	p.Leu1202Met	p.L1202M	ENST00000409792	NM_014159.6	1202	Ctg/Atg	3/21	1	2	FACETS	0.366	0.292	0.449	0.366	0.292	0.449	SUBCLONAL	1	TRUE	1	0.44	2		457	348	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163610	47163610	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	19	444	0	ENST00000409792.3:c.2516G>T	p.Arg839Ile	p.R839I	ENST00000409792	NM_014159.6	839	aGa/aTa	3/21	1	2	FACETS	0.259	0.196	0.333	0.259	0.196	0.333	SUBCLONAL	1	TRUE	1	0.44	2		444	334	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165049	47165049	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	85	418	0	ENST00000409792.3:c.1077A>C	p.Lys359Asn	p.K359N	ENST00000409792	NM_014159.6	359	aaA/aaC	3/21	1	2	FACETS	0.781	0.692	0.874	0.781	0.692	0.874	SUBCLONAL	1	TRUE	1	0.44	2		418	495	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165255	47165255	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	139	480	0	ENST00000409792.3:c.871G>T	p.Glu291Ter	p.E291*	ENST00000409792	NM_014159.6	291	Gaa/Taa	3/21	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.44	2		480	448	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165906	47165906	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	30	584	0	ENST00000409792.3:c.220T>C	p.Ser74Pro	p.S74P	ENST00000409792	NM_014159.6	74	Tca/Cca	3/21	1	2	FACETS	0.245	0.196	0.3	0.245	0.196	0.3	SUBCLONAL	1	TRUE	1	0.44	2		584	557	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49929220	49929220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147999292	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	38	880	0	ENST00000296474.3:c.3323G>A	p.Arg1108Gln	p.R1108Q	ENST00000296474	NM_002447.2	1108	cGa/cAa	15/20	1	2	FACETS	0.283	0.233	0.339	0.283	0.233	0.339	SUBCLONAL	1	TRUE	1	0.44	2		880	610	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662933	52662933	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	33	520	1	ENST00000394830.3:c.1420C>A	p.Leu474Ile	p.L474I	ENST00000394830	NM_018313.4	474	Cta/Ata	13/30	1	2	FACETS	0.278	0.226	0.337	0.278	0.226	0.337	SUBCLONAL	1	TRUE	1	0.44	2		521	540	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69788814	69788814	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	27	266	0	ENST00000352241.4:c.66A>C	p.Lys22Asn	p.K22N	ENST00000352241	NM_198159.2	22	aaA/aaC	1/10	1	2	FACETS	0.451	0.36	0.555	0.451	0.36	0.555	SUBCLONAL	1	TRUE	1	0.44	2		266	272	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495737	72495737	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	32	576	0	ENST00000477973.2:c.335G>A	p.Gly112Glu	p.G112E	ENST00000477973	NM_012234.5	112	gGg/gAg	1/4	1	2	FACETS	0.249	0.201	0.303	0.249	0.201	0.303	SUBCLONAL	1	TRUE	1	0.44	2		576	585	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670468	134670468	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1404562506	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	22	585	2	ENST00000398015.3:c.379G>A	p.Ala127Thr	p.A127T	ENST00000398015	NM_004441.4	127	Gcc/Acc	3/16	1	2	FACETS	0.336	0.26	0.423	0.336	0.26	0.423	SUBCLONAL	1	TRUE	1	0.44	2		587	298	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138382759	138382759	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	27	524	0	ENST00000289153.2:c.2785A>C	p.Lys929Gln	p.K929Q	ENST00000289153	NM_006219.2	929	Aaa/Caa	19/22	1	2	FACETS	0.294	0.233	0.363	0.294	0.233	0.363	SUBCLONAL	1	TRUE	1	0.44	2		524	418	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242885	142242885	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1194388677	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	45	619	0	ENST00000350721.4:c.4102C>T	p.Arg1368Ter	p.R1368*	ENST00000350721	NM_001184.3	1368	Cga/Tga	22/47	1	2	FACETS	0.384	0.322	0.452	0.384	0.322	0.452	SUBCLONAL	1	TRUE	1	0.44	2		619	533	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169953092	169953092	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	29	577	0	ENST00000295797.4:c.176C>A	p.Ser59Tyr	p.S59Y	ENST00000295797	NM_002740.5	59	tCt/tAt	2/18	1	2	FACETS	0.242	0.194	0.298	0.242	0.194	0.298	SUBCLONAL	1	TRUE	1	0.44	2		577	544	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430807	181430807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	30	785	0	ENST00000325404.1:c.659C>T	p.Ser220Leu	p.S220L	ENST00000325404	NM_003106.3	220	tCg/tTg	1/1	1	2	FACETS	0.313	0.252	0.382	0.313	0.252	0.382	SUBCLONAL	1	TRUE	1	0.44	2		785	436	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198077	185198077	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	75	464	0	ENST00000265026.3:c.2559C>A	p.Phe853Leu	p.F853L	ENST00000265026	NM_004721.4	853	ttC/ttA	13/14	1	2	FACETS	0.997	0.88	1	0.997	0.88	1	CLONAL	1	TRUE	1	0.44	2		464	342	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129932	55129932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760631068	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	37	655	0	ENST00000257290.5:c.466G>A	p.Glu156Lys	p.E156K	ENST00000257290	NM_006206.4	156	Gag/Aag	4/23	1	2	FACETS	0.36	0.297	0.431	0.36	0.297	0.431	SUBCLONAL	1	TRUE	1	0.44	2		655	467	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151564	55151564	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	45	545	0	ENST00000257290.5:c.2350G>A	p.Asp784Asn	p.D784N	ENST00000257290	NM_006206.4	784	Gat/Aat	17/23	1	2	FACETS	0.522	0.439	0.613	0.522	0.439	0.613	SUBCLONAL	1	TRUE	1	0.44	2		545	392	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956151	55956151	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	102	590	2	ENST00000263923.4:c.3164A>C	p.Lys1055Thr	p.K1055T	ENST00000263923	NM_002253.2	1055	aAa/aCa	23/30	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.44	2		592	435	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189871	66189871	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	23	533	0	ENST00000273854.3:c.3075A>C	p.Glu1025Asp	p.E1025D	ENST00000273854	NM_004439.5	1025	gaA/gaC	18/18	1	2	FACETS	0.24	0.187	0.303	0.24	0.187	0.303	SUBCLONAL	1	TRUE	1	0.44	2		533	435	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217217	66217217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	19	447	0	ENST00000273854.3:c.2398G>A	p.Asp800Asn	p.D800N	ENST00000273854	NM_004439.5	800	Gat/Aat	14/18	1	2	FACETS	0.286	0.217	0.367	0.286	0.217	0.367	SUBCLONAL	1	TRUE	1	0.44	2		447	302	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251906	153251906	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745418631	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	60	603	0	ENST00000281708.4:c.1100G>A	p.Arg367Gln	p.R367Q	ENST00000281708	NM_033632.3	367	cGa/cAa	7/12	1	2	FACETS	0.552	0.476	0.634	0.552	0.476	0.634	SUBCLONAL	1	TRUE	1	0.44	2		603	494	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521515	187521515	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	13	397	0	ENST00000441802.2:c.11641-1G>T		p.X3881_splice	ENST00000441802	NM_005245.3	3881			1	2	FACETS	0.284	0.203	0.383	0.284	0.203	0.383	SUBCLONAL	1	TRUE	1	0.44	2		397	208	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630452	187630452	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	28	888	0	ENST00000441802.2:c.530A>C	p.Asp177Ala	p.D177A	ENST00000441802	NM_005245.3	177	gAc/gCc	2/27	1	2	FACETS	0.249	0.198	0.307	0.249	0.198	0.307	SUBCLONAL	1	TRUE	1	0.44	2		888	511	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410988	31410988	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1295265844	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	51	621	0	ENST00000344624.3:c.3532C>T	p.Arg1178Ter	p.R1178*	ENST00000344624		1178	Cga/Tga	28/33	0.210001659018759	0	FACETS	0.284	0.241	0.331			1	INDETERMINATE	1	TRUE	0	0.44	0		621	457	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31421411	31421411	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	54	571	0	ENST00000344624.3:c.3493C>A	p.His1165Asn	p.H1165N	ENST00000344624		1165	Cat/Aat	27/33	0.210001659018759	0	FACETS	0.32	0.274	0.371			1	INDETERMINATE	1	TRUE	0	0.44	0		571	429	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31431764	31431764	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	29	403	0	ENST00000344624.3:c.3064A>T	p.Met1022Leu	p.M1022L	ENST00000344624		1022	Atg/Ttg	23/33	0.210001659018759	0	FACETS	0.177	0.142	0.218			1	INDETERMINATE	1	TRUE	0	0.44	0		403	416	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161263	56161263	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	29	466	0	ENST00000399503.3:c.1132A>C	p.Lys378Gln	p.K378Q	ENST00000399503	NM_005921.1	378	Aaa/Caa	5/20	0.130861378403997	3	FACETS	0.336	0.269	0.412	0.168	0.134	0.206	INDETERMINATE	1	TRUE	1	0.44	3		466	479	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590496	67590496	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	67	233	0	ENST00000274335.5:c.1558G>T	p.Glu520Ter	p.E520*	ENST00000274335		520	Gaa/Taa	11/15	0.130861378403997	3	FACETS	0.764	0.673	0.861	0.764	0.673	0.861	INDETERMINATE	2	TRUE	1	0.44	3		233	243	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064769	80064769	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770330684	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	24	429	0	ENST00000265081.6:c.2200C>T	p.Arg734Ter	p.R734*	ENST00000265081	NM_002439.4	734	Cga/Tga	15/24	0.130861378403997	3	FACETS	0.348	0.273	0.436	0.174	0.136	0.218	INDETERMINATE	1	TRUE	1	0.44	3		429	382	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940093	31940093	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	49	780	0	ENST00000375333.2:c.235G>A	p.Glu79Lys	p.E79K	ENST00000375333	NM_032454.1	79	Gag/Aag	2/8	1	2	FACETS	0.332	0.28	0.389	0.332	0.28	0.389	SUBCLONAL	1	TRUE	1	0.44	2		780	671	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805781	32805781	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	99	792	0	ENST00000374899.4:c.230T>C	p.Val77Ala	p.V77A	ENST00000374899	NM_018833.2	77	gTc/gCc	2/12	1	2	FACETS	0.904	0.81	1	0.904	0.81	1	CLONAL	1	TRUE	1	0.44	2		792	498	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748591	43748591	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	rs1205123562	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	16	356	0	ENST00000523873.1:c.545A>C	p.His182Pro	p.H182P	ENST00000523873		182	cAt/cCt	6/8	1	2	FACETS	0.253	0.187	0.333	0.253	0.187	0.333	SUBCLONAL	1	TRUE	1	0.44	2		356	287	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004348	150004348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766836005	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	73	643	0	ENST00000253339.5:c.1877G>A	p.Arg626Gln	p.R626Q	ENST00000253339		626	cGa/cAa	3/7	1	2	FACETS	0.583	0.51	0.661	0.583	0.51	0.661	SUBCLONAL	1	TRUE	1	0.44	2		643	569	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201850	152201850	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	30	422	0	ENST00000206249.3:c.704A>C	p.Lys235Thr	p.K235T	ENST00000206249	NM_000125.3	235	aAg/aCg	3/8	1	2	FACETS	0.351	0.283	0.429	0.351	0.283	0.429	SUBCLONAL	1	TRUE	1	0.44	2		422	388	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6031615	6031615	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	14	299	0	ENST00000265849.7:c.977C>A	p.Ser326Tyr	p.S326Y	ENST00000265849	NM_000535.5	326	tCt/tAt	9/15	1	2	FACETS	0.269	0.194	0.359	0.269	0.194	0.359	SUBCLONAL	1	TRUE	1	0.44	2		299	237	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386574	81386574	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs894908363	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	44	665	1	ENST00000222390.5:c.413G>A	p.Gly138Glu	p.G138E	ENST00000222390	NM_000601.4	138	gGa/gAa	4/18	1	2	FACETS	0.404	0.339	0.476	0.404	0.339	0.476	SUBCLONAL	1	TRUE	1	0.44	2		666	495	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534476	140534476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs557241012	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	27	447	0	ENST00000288602.6:c.437G>A	p.Arg146Gln	p.R146Q	ENST00000288602	NM_004333.4	146	cGg/cAg	3/18	1	2	FACETS	0.276	0.219	0.342	0.276	0.219	0.342	SUBCLONAL	1	TRUE	1	0.44	2		447	444	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508748	148508748	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	72	615	0	ENST00000320356.2:c.1916A>C	p.Lys639Thr	p.K639T	ENST00000320356	NM_004456.4	639	aAa/aCa	16/20	1	2	FACETS	0.808	0.709	0.914	0.808	0.709	0.914	CLONAL	1	TRUE	1	0.44	2		615	405	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523717	148523717	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	13	271	0	ENST00000320356.2:c.736G>T	p.Glu246Ter	p.E246*	ENST00000320356	NM_004456.4	246	Gaa/Taa	8/20	1	2	FACETS	0.319	0.228	0.43	0.319	0.228	0.43	SUBCLONAL	1	TRUE	1	0.44	2		271	185	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939483	68939483	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs772266269	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	18	423	1	ENST00000288368.4:c.468G>T	p.Lys156Asn	p.K156N	ENST00000288368	NM_024870.2	156	aaG/aaT	5/40	1	2	FACETS	0.244	0.183	0.316	0.244	0.183	0.316	SUBCLONAL	1	TRUE	1	0.44	2		424	335	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970919	70970919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1563439440	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	37	733	4	ENST00000276594.2:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000276594	NM_024504.3	448	Cgg/Tgg	6/8	1	2	FACETS	0.408	0.337	0.488	0.408	0.337	0.488	SUBCLONAL	1	TRUE	1	0.44	2		737	412	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465627	8465627	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	29	605	0	ENST00000356435.5:c.3553G>T	p.Glu1185Ter	p.E1185*	ENST00000356435		1185	Gaa/Taa	21/35	1	2	FACETS	0.341	0.274	0.418	0.341	0.274	0.418	SUBCLONAL	1	TRUE	1	0.44	2		605	386	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002719	37002719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757277825	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	15	568	0	ENST00000358127.4:c.530C>T	p.Ser177Leu	p.S177L	ENST00000358127	NM_001280556.1	177	tCg/tTg	5/10	1	2	FACETS	0.237	0.173	0.314	0.237	0.173	0.314	SUBCLONAL	1	TRUE	1	0.44	2		568	288	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339142	87339142	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	22	365	1	ENST00000277120.3:c.724G>T	p.Glu242Ter	p.E242*	ENST00000277120		242	Gaa/Taa	8/19	1	2	FACETS	0.444	0.345	0.558	0.444	0.345	0.558	SUBCLONAL	1	TRUE	1	0.44	2		366	225	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549140	87549140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	68	569	0	ENST00000277120.3:c.1697G>A	p.Gly566Glu	p.G566E	ENST00000277120		566	gGa/gAa	15/19	1	2	FACETS	0.912	0.799	1	0.912	0.799	1	CLONAL	1	TRUE	1	0.44	2		569	339	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98011502	98011502	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	28	589	0	ENST00000289081.3:c.72G>T	p.Gln24His	p.Q24H	ENST00000289081	NM_000136.2	24	caG/caT	2/15	1	2	FACETS	0.244	0.194	0.301	0.244	0.194	0.301	SUBCLONAL	1	TRUE	1	0.44	2		589	521	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128322038	128322038	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	27	554	0	ENST00000265960.3:c.722T>C	p.Val241Ala	p.V241A	ENST00000265960	NM_001006617.1	241	gTg/gCg	6/12	1	2	FACETS	0.282	0.224	0.349	0.282	0.224	0.349	SUBCLONAL	1	TRUE	1	0.44	2		554	435	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139794123	139794123	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs200834553	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	79	557	0	ENST00000247668.2:c.266C>T	p.Ser89Leu	p.S89L	ENST00000247668	NM_021138.3	89	tCg/tTg	3/11	1	2	FACETS	0.759	0.67	0.854	0.759	0.67	0.854	SUBCLONAL	1	TRUE	1	0.44	2		557	473	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841131	15841131	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	22	471	0	ENST00000307771.7:c.1215G>T	p.Lys405Asn	p.K405N	ENST00000307771	NM_005089.3	405	aaG/aaT	11/11	0.294472231170961	0	FACETS	0.177	0.137	0.224			1	SUBCLONAL	1	TRUE	0	0.44	0		471	316	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222782	53222782	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	32	968	3	ENST00000375401.3:c.4154C>T	p.Thr1385Ile	p.T1385I	ENST00000375401	NM_004187.3	1385	aCt/aTt	25/26	0.294472231170961	0	FACETS	0.213	0.172	0.258			1	SUBCLONAL	1	TRUE	0	0.44	0		971	383	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410985	63410985	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	19	811	0	ENST00000330258.3:c.2182T>C	p.Phe728Leu	p.F728L	ENST00000330258	NM_152424.3	728	Ttt/Ctt	2/2	0.294472231170961	0	FACETS	0.179	0.136	0.23			1	SUBCLONAL	1	TRUE	0	0.44	0		811	270	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907615	76907615	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	61	611	0	ENST00000373344.5:c.4546A>C	p.Lys1516Gln	p.K1516Q	ENST00000373344	NM_000489.3	1516	Aaa/Caa	15/35	0.294472231170961	0	FACETS	0.374	0.324	0.429			1	SUBCLONAL	1	TRUE	0	0.44	0		611	415	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938444	76938444	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	32	795	0	ENST00000373344.5:c.2304G>T	p.Lys768Asn	p.K768N	ENST00000373344	NM_000489.3	768	aaG/aaT	9/35	0.294472231170961	0	FACETS	0.183	0.148	0.223			1	SUBCLONAL	1	TRUE	0	0.44	0		795	445	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617194	100617194	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	59	705	0	ENST00000308731.7:c.555A>C	p.Lys185Asn	p.K185N	ENST00000308731	NM_000061.2	185	aaA/aaC	7/19	0.294472231170961	0	FACETS	0.378	0.326	0.434			1	SUBCLONAL	1	TRUE	0	0.44	0		705	397	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210280	123210280	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	126	562	1	ENST00000218089.9:c.2632G>A	p.Glu878Lys	p.E878K	ENST00000218089	NM_001042749.1	878	Gag/Aag	26/35	0.294472231170961	0	FACETS	0.993	0.912	1			1	CLONAL	1	TRUE	0	0.44	0		563	323	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438333	110438333	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	12	175	0	ENST00000375856.3:c.68A>G	p.Asn23Ser	p.N23S	ENST00000375856	NM_003749.2	23	aAc/aGc	1/2	1	2	FACETS	0.331	0.233	0.45	0.331	0.233	0.45	SUBCLONAL	1	TRUE	1	0.44	2		175	165	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0032821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	197	439	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.361965924044308	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.361965924044308	3		439	549	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0032821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	247	732	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.361965924044308	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.361965924044308	1		732	933	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0032821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	142	504	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.182846195566176	2	FACETS	1	0.988	1	0.746	0.684	0.81	INDETERMINATE	1	TRUE	0	0.361965924044308	2		504	526	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0032821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	107	298	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.361965924044308	3	FACETS	0.816	0.737	0.898	0.816	0.737	0.898	CLONAL	2	TRUE	1	0.361965924044308	3		298	428	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0032821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	81	286	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.361965924044308	3	FACETS	0.99	0.874	1	0.495	0.437	0.557	CLONAL	1	TRUE	1	0.361965924044308	3		286	534	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615812	1615812	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771807324	NA	P-0032821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	109	501	1	ENST00000344749.5:c.1459C>T	p.Arg487Ter	p.R487*	ENST00000344749	NM_001136139.2	487	Cga/Tga	17/19	1	2	FACETS	0.938	0.844	1	0.938	0.844	1	CLONAL	1	TRUE	1	0.361965924044308	2		502	642	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912185	114912185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs976821949	NA	P-0032821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	300	530	1	ENST00000543371.1:c.1255G>A	p.Ala419Thr	p.A419T	ENST00000543371	NM_001198531.1	419	Gcg/Acg	11/14	0.361965924044308	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.361965924044308	2		531	792	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741519	17741519	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	233	519	0	ENST00000250003.3:c.190C>G	p.His64Asp	p.H64D	ENST00000250003	NM_002478.4	64	Cac/Gac	1/3	0.361965924044308	3	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	1	0.361965924044308	3		519	758	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163345	108163345	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs759520465	NA	P-0032821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	137	397	0	ENST00000278616.4:c.4437-1G>C		p.X1479_splice	ENST00000278616	NM_000051.3	1479			0.361965924044308	3	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	1	0.361965924044308	3		397	435	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358516	67358517	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0032821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	77	272	0	ENST00000327367.4:c.29dup	p.Ile11AspfsTer100	p.I11Dfs*100	ENST00000327367	NM_005902.3	8	-/C	1/9	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.361965924044308	2		272	401	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983945	15983945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759870954	NA	P-0032821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	129	432	0	ENST00000268712.3:c.3274C>T	p.Arg1092Trp	p.R1092W	ENST00000268712	NM_006311.3	1092	Cgg/Tgg	24/46	0.361965924044308	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.361965924044308	1		432	581	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119066	70119066	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	220	371	0	ENST00000245479.2:c.638A>T	p.His213Leu	p.H213L	ENST00000245479	NM_000346.3	213	cAc/cTc	2/3	0.361965924044308	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.361965924044308	3		371	596	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40747909	40747909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	203	686	0	ENST00000392038.2:c.509G>A	p.Arg170Gln	p.R170Q	ENST00000392038	NM_001626.4	170	cGg/cAg	6/14	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.361965924044308	2		686	901	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0032827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	257	290	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.837627288200222	5	FACETS	0.881	0.842	0.919	0.881	0.842	0.919	CLONAL	4	TRUE	1	0.837627288200222	5		290	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0032827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	346	791	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.837627288200222	2	FACETS	0.986	0.958	1	0.986	0.958	1	CLONAL	2	TRUE	0	0.837627288200222	2		791	419	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954327	48954328	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0032827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	153	333	0	ENST00000267163.4:c.1450_1451del	p.Met484ValfsTer8	p.M484Vfs*8	ENST00000267163	NM_000321.2	483	cAT/c	16/27	0.837627288200222	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.837627288200222	2		333	177	SUCCESS
APC	324	MSKCC	GRCh37	5	112178355	112178355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	80	386	0	ENST00000257430.4:c.7064C>T	p.Ser2355Leu	p.S2355L	ENST00000257430	NM_000038.5	2355	tCa/tTa	16/16	0.837627288200222	2	FACETS	0.901	0.839	0.957	0.901	0.839	0.957	CLONAL	2	TRUE	0	0.837627288200222	2		386	106	SUCCESS
APC	324	MSKCC	GRCh37	5	112173600	112173600	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1060503310	NA	P-0032827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	61	300	0	ENST00000257430.4:c.2309C>G	p.Ser770Ter	p.S770*	ENST00000257430	NM_000038.5	770	tCa/tGa	16/16	0.837627288200222	2	FACETS	0.828	0.728	0.931	0.414	0.364	0.466	CLONAL	1	TRUE	0	0.837627288200222	2		300	176	SUCCESS
APC	324	MSKCC	GRCh37	5	112175842	112175842	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	41	236	0	ENST00000257430.4:c.4551G>C	p.Gln1517His	p.Q1517H	ENST00000257430	NM_000038.5	1517	caG/caC	16/16	0.837627288200222	2	FACETS	0.866	0.742	0.996	0.433	0.371	0.498	CLONAL	1	TRUE	0	0.837627288200222	2		236	113	SUCCESS
APC	324	MSKCC	GRCh37	5	112177323	112177323	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554087155	NA	P-0032827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	60	309	0	ENST00000257430.4:c.6032C>T	p.Ser2011Leu	p.S2011L	ENST00000257430	NM_000038.5	2011	tCa/tTa	16/16	0.837627288200222	2	FACETS	0.823	0.751	0.891	0.823	0.751	0.891	CLONAL	2	TRUE	0	0.837627288200222	2		309	87	SUCCESS
APC	324	MSKCC	GRCh37	5	112173275	112173275	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	45	158	0	ENST00000257430.4:c.1984C>G	p.Leu662Val	p.L662V	ENST00000257430	NM_000038.5	662	Cta/Gta	16/16	0.837627288200222	2	FACETS	1	0.931	1	0.554	0.483	0.626	CLONAL	1	TRUE	0	0.837627288200222	2		158	97	SUCCESS
APC	324	MSKCC	GRCh37	5	112173642	112173642	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs778287168	NA	P-0032827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	53	316	0	ENST00000257430.4:c.2351C>G	p.Ser784Cys	p.S784C	ENST00000257430	NM_000038.5	784	tCt/tGt	16/16	0.837627288200222	2	FACETS	0.74	0.643	0.842	0.37	0.321	0.421	SUBCLONAL	1	TRUE	0	0.837627288200222	2		316	171	SUCCESS
APC	324	MSKCC	GRCh37	5	112173836	112173836	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	59	312	0	ENST00000257430.4:c.2545G>C	p.Asp849His	p.D849H	ENST00000257430	NM_000038.5	849	Gat/Cat	16/16	0.837627288200222	2	FACETS	0.886	0.78	0.996	0.443	0.39	0.498	CLONAL	1	TRUE	0	0.837627288200222	2		312	159	SUCCESS
APC	324	MSKCC	GRCh37	5	112173992	112173992	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	66	291	0	ENST00000257430.4:c.2701C>G	p.Gln901Glu	p.Q901E	ENST00000257430	NM_000038.5	901	Cag/Gag	16/16	0.837627288200222	2	FACETS	0.944	0.838	1	0.472	0.419	0.526	CLONAL	1	TRUE	0	0.837627288200222	2		291	167	SUCCESS
APC	324	MSKCC	GRCh37	5	112174979	112174979	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	59	236	0	ENST00000257430.4:c.3688C>G	p.Gln1230Glu	p.Q1230E	ENST00000257430	NM_000038.5	1230	Cag/Gag	16/16	0.837627288200222	2	FACETS	1	0.89	1	0.503	0.445	0.563	CLONAL	1	TRUE	0	0.837627288200222	2		236	140	SUCCESS
APC	324	MSKCC	GRCh37	5	112175502	112175502	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	113	332	0	ENST00000257430.4:c.4211C>G	p.Ser1404Cys	p.S1404C	ENST00000257430	NM_000038.5	1404	tCc/tGc	16/16	0.837627288200222	2	FACETS	1	0.965	1	0.548	0.503	0.594	CLONAL	1	TRUE	0	0.837627288200222	2		332	246	SUCCESS
APC	324	MSKCC	GRCh37	5	112175537	112175537	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	96	299	0	ENST00000257430.4:c.4246G>C	p.Gly1416Arg	p.G1416R	ENST00000257430	NM_000038.5	1416	Ggc/Cgc	16/16	0.837627288200222	2	FACETS	1	0.91	1	0.5	0.455	0.547	CLONAL	1	TRUE	0	0.837627288200222	2		299	229	SUCCESS
APC	324	MSKCC	GRCh37	5	112175878	112175878	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	36	207	0	ENST00000257430.4:c.4587G>C	p.Gln1529His	p.Q1529H	ENST00000257430	NM_000038.5	1529	caG/caC	16/16	0.837627288200222	2	FACETS	0.827	0.699	0.961	0.413	0.349	0.481	CLONAL	1	TRUE	0	0.837627288200222	2		207	104	SUCCESS
APC	324	MSKCC	GRCh37	5	112175885	112175885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881251	NA	P-0032827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	41	203	0	ENST00000257430.4:c.4594G>A	p.Asp1532Asn	p.D1532N	ENST00000257430	NM_000038.5	1532	Gac/Aac	16/16	0.837627288200222	2	FACETS	0.924	0.793	1	0.462	0.396	0.53	CLONAL	1	TRUE	0	0.837627288200222	2		203	106	SUCCESS
APC	324	MSKCC	GRCh37	5	112176234	112176234	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	107	346	0	ENST00000257430.4:c.4943C>G	p.Pro1648Arg	p.P1648R	ENST00000257430	NM_000038.5	1648	cCt/cGt	16/16	0.837627288200222	2	FACETS	0.912	0.86	0.961	0.912	0.86	0.961	CLONAL	2	TRUE	0	0.837627288200222	2		346	140	SUCCESS
APC	324	MSKCC	GRCh37	5	112176269	112176269	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs767271480	NA	P-0032827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	67	320	0	ENST00000257430.4:c.4978C>G	p.Leu1660Val	p.L1660V	ENST00000257430	NM_000038.5	1660	Cta/Gta	16/16	0.837627288200222	2	FACETS	0.86	0.792	0.923	0.86	0.792	0.923	CLONAL	2	TRUE	0	0.837627288200222	2		320	93	SUCCESS
APC	324	MSKCC	GRCh37	5	112176285	112176287	+	frameshift_variant	Frame_Shift_Del	DEL	CTC	CTC	TT	novel	NA	P-0032827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	56	295	0	ENST00000257430.4:c.4994_4996delinsTT	p.Pro1665LeufsTer5	p.P1665Lfs*5	ENST00000257430	NM_000038.5	1665	cCTCca/cTTca	16/16	0.837627288200222	2	FACETS	0.796	0.721	0.866	0.796	0.721	0.866	SUBCLONAL	2	TRUE	0	0.837627288200222	2		295	84	SUCCESS
APC	324	MSKCC	GRCh37	5	112176774	112176774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs971100064	NA	P-0032827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	49	272	1	ENST00000257430.4:c.5483C>T	p.Pro1828Leu	p.P1828L	ENST00000257430	NM_000038.5	1828	cCa/cTa	16/16	0.837627288200222	2	FACETS	0.848	0.768	0.921	0.848	0.768	0.921	CLONAL	2	TRUE	0	0.837627288200222	2		273	69	SUCCESS
APC	324	MSKCC	GRCh37	5	112178385	112178385	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0032827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	71	363	0	ENST00000257430.4:c.7094C>G	p.Ser2365Ter	p.S2365*	ENST00000257430	NM_000038.5	2365	tCa/tGa	16/16	0.837627288200222	2	FACETS	0.931	0.867	0.989	0.931	0.867	0.989	CLONAL	2	TRUE	0	0.837627288200222	2		363	91	SUCCESS
APC	324	MSKCC	GRCh37	5	112178562	112178562	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	55	264	0	ENST00000257430.4:c.7271C>T	p.Ser2424Leu	p.S2424L	ENST00000257430	NM_000038.5	2424	tCa/tTa	16/16	0.837627288200222	2	FACETS	0.875	0.8	0.944	0.875	0.8	0.944	CLONAL	2	TRUE	0	0.837627288200222	2		264	75	SUCCESS
APC	324	MSKCC	GRCh37	5	112178633	112178633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561614782	NA	P-0032827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	57	332	0	ENST00000257430.4:c.7342C>T	p.Pro2448Ser	p.P2448S	ENST00000257430	NM_000038.5	2448	Cca/Tca	16/16	0.837627288200222	2	FACETS	0.895	0.822	0.962	0.895	0.822	0.962	CLONAL	2	TRUE	0	0.837627288200222	2		332	76	SUCCESS
APC	324	MSKCC	GRCh37	5	112178753	112178753	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	120	436	0	ENST00000257430.4:c.7462C>G	p.Leu2488Val	p.L2488V	ENST00000257430	NM_000038.5	2488	Ctt/Gtt	16/16	0.837627288200222	2	FACETS	0.901	0.851	0.948	0.901	0.851	0.948	CLONAL	2	TRUE	0	0.837627288200222	2		436	159	SUCCESS
APC	324	MSKCC	GRCh37	5	112179591	112179591	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0032827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	102	333	0	ENST00000257430.4:c.8300C>G	p.Ser2767Ter	p.S2767*	ENST00000257430	NM_000038.5	2767	tCa/tGa	16/16	0.837627288200222	2	FACETS	0.902	0.848	0.952	0.902	0.848	0.952	CLONAL	2	TRUE	0	0.837627288200222	2		333	135	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907702	76907702	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	83	569	0	ENST00000373344.5:c.4459G>A	p.Asp1487Asn	p.D1487N	ENST00000373344	NM_000489.3	1487	Gat/Aat	15/35	0.280817927368413	1	FACETS	0.452	0.404	0.501	0.452	0.404	0.501	INDETERMINATE	1	TRUE	0	0.837627288200222	1		569	255	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0032828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	408	400	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.333412407227731	3	FACETS	1	0.992	1	0.755	0.726	0.785	INDETERMINATE	2	TRUE	0	0.665828363443198	3		400	721	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0032828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	282	582	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.665828363443198	1	FACETS	0.956	0.907	1	0.956	0.907	1	CLONAL	1	TRUE	0	0.665828363443198	1		582	591	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0032828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	134	335	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.316932131975133	3	FACETS	1	0.939	1	0.517	0.472	0.563	INDETERMINATE	1	TRUE	1	0.665828363443198	3		335	519	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16235922	16235922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	100	502	0	ENST00000375759.3:c.988G>A	p.Glu330Lys	p.E330K	ENST00000375759	NM_015001.2	330	Gag/Aag	4/15	1	2	FACETS	0.386	0.344	0.43	0.386	0.344	0.43	SUBCLONAL	1	TRUE	1	0.665828363443198	2		502	778	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643371	38643371	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	83	508	0	ENST00000299084.4:c.841C>G	p.Gln281Glu	p.Q281E	ENST00000299084	NM_152594.2	281	Cag/Gag	7/7	0.426479867545924	1	FACETS	0.335	0.297	0.377	0.335	0.297	0.377	SUBCLONAL	1	TRUE	0	0.665828363443198	1		508	496	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041686	42041686	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	163	455	2	ENST00000219905.7:c.5881C>T	p.Gln1961Ter	p.Q1961*	ENST00000219905	NM_001164273.1	1961	Cag/Tag	17/24	0.426479867545924	1	FACETS	0.736	0.682	0.791	0.736	0.682	0.791	SUBCLONAL	1	TRUE	0	0.665828363443198	1		457	444	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584560	48584560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	219	474	0	ENST00000342988.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000342988	NM_005359.5	245	Cag/Tag	6/12	0.665828363443198	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.665828363443198	1		474	428	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057292	30057292	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	145	397	0	ENST00000338641.4:c.774G>C	p.Trp258Cys	p.W258C	ENST00000338641	NM_000268.3	258	tgG/tgC	8/16	1	2	FACETS	0.844	0.775	0.916	0.844	0.775	0.916	CLONAL	1	TRUE	1	0.665828363443198	2		397	516	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564849	41564849	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	221	634	0	ENST00000263253.7:c.4150G>C	p.Asp1384His	p.D1384H	ENST00000263253	NM_001429.3	1384	Gac/Cac	25/31	1	2	FACETS	0.921	0.86	0.983	0.921	0.86	0.983	CLONAL	1	TRUE	1	0.665828363443198	2		634	721	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035095	37035095	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	188	414	0	ENST00000231790.2:c.57C>G	p.Ile19Met	p.I19M	ENST00000231790	NM_000249.3	19	atC/atG	1/19	1	2	FACETS	0.891	0.827	0.956	0.891	0.827	0.956	CLONAL	1	TRUE	1	0.665828363443198	2		414	634	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098382	47098382	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	234	634	0	ENST00000409792.3:c.6892C>T	p.Gln2298Ter	p.Q2298*	ENST00000409792	NM_014159.6	2298	Caa/Taa	15/21	1	2	FACETS	0.907	0.849	0.966	0.907	0.849	0.966	CLONAL	1	TRUE	1	0.665828363443198	2		634	775	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164118	47164118	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	116	362	0	ENST00000409792.3:c.2008G>T	p.Glu670Ter	p.E670*	ENST00000409792	NM_014159.6	670	Gaa/Taa	3/21	1	2	FACETS	0.929	0.846	1	0.929	0.846	1	CLONAL	1	TRUE	1	0.665828363443198	2		362	375	SUCCESS
APC	324	MSKCC	GRCh37	5	112178410	112178410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	111	311	1	ENST00000257430.4:c.7119G>A	p.Met2373Ile	p.M2373I	ENST00000257430	NM_000038.5	2373	atG/atA	16/16	1	2	FACETS	0.807	0.731	0.886	0.807	0.731	0.886	CLONAL	1	TRUE	1	0.665828363443198	2		312	413	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911487	131911487	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	146	382	0	ENST00000265335.6:c.232G>T	p.Val78Leu	p.V78L	ENST00000265335		78	Gtg/Ttg	3/25	1	2	FACETS	0.877	0.806	0.951	0.877	0.806	0.951	CLONAL	1	TRUE	1	0.665828363443198	2		382	500	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859845	151859845	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1421487755	NA	P-0032828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	143	395	0	ENST00000262189.6:c.10817G>C	p.Arg3606Thr	p.R3606T	ENST00000262189	NM_170606.2	3606	aGa/aCa	43/59	0.316932131975133	3	FACETS	1	0.965	1	0.548	0.503	0.596	INDETERMINATE	1	TRUE	1	0.665828363443198	3		395	522	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76812923	76812964	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TTTGGCAGCATGGGAGTATCCCTCTTCTTCTTCTTTTCTGAA	TTTGGCAGCATGGGAGTATCCCTCTTCTTCTTCTTTTCTGAA	-	novel	NA	P-0032828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	58	611	0	ENST00000373344.5:c.6657_6698del	p.Asn2219_Pro2232del	p.N2219_P2232del	ENST00000373344	NM_000489.3	2219	aaTTCAGAAAAGAAGAAGAAGAGGGATACTCCCATGCTGCCAAAg/aag	30/35	0.469335244897732	1	FACETS	0.223	0.192	0.258	0.223	0.192	0.258	SUBCLONAL	1	TRUE	0	0.665828363443198	1		611	520	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198455	108198455	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	19	409	0	ENST00000278616.4:c.7059del	p.Ala2354ArgfsTer8	p.A2354Rfs*8	ENST00000278616	NM_000051.3	2353	ccT/cc	48/63	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	FALSE	1	0.255302854177005	2		409	125	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923438	9923438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	35	619	0	ENST00000330684.3:c.1849G>A	p.Val617Met	p.V617M	ENST00000330684	NM_001134407.1	617	Gtg/Atg	9/13	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	1	0.255302854177005	2		619	195	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578401	7578402	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCA	novel	NA	P-0032841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	62	601	0	ENST00000269305.4:c.526_528dup	p.Cys176dup	p.C176dup	ENST00000269305	NM_001126112.2	176	-/TGC	5/11	1	2	FACETS	0.505	0.436	0.581	0.505	0.436	0.581	SUBCLONAL	1	TRUE	1	0.35	2		601	701	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0032843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	167	439	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.715645018849672	7	FACETS	1	0.981	1	0.743	0.698	0.787	CLONAL	4	TRUE	1	0.715645018849672	7		439	292	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	128	264	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	FALSE	1	0.725257760590585	2		264	345	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692920	89692921	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs398123323	NA	P-0032844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	222	492	0	ENST00000371953.3:c.405dup	p.Cys136MetfsTer44	p.C136Mfs*44	ENST00000371953	NM_000314.4	135	ata/atAa	5/9	0.725257760590585	1	FACETS	0.854	0.805	0.903	0.854	0.805	0.903	CLONAL	1	FALSE	0	0.725257760590585	1		492	457	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610695	52610695	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	242	416	0	ENST00000394830.3:c.3478C>T	p.Arg1160Ter	p.R1160*	ENST00000394830	NM_018313.4	1160	Cga/Tga	23/30	0.376286931820192	1	FACETS	0.776	0.732	0.821	0.776	0.732	0.821	INDETERMINATE	1	FALSE	0	0.725257760590585	1		416	548	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561861	55561861	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201872586	NA	P-0032844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	156	263	1	ENST00000288135.5:c.251C>T	p.Thr84Met	p.T84M	ENST00000288135	NM_000222.2	84	aCg/aTg	2/21	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	1	0.725257760590585	2		264	422	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483113	29483113	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	301	504	0	ENST00000356175.3:c.173T>A	p.Leu58His	p.L58H	ENST00000356175	NM_000267.3	58	cTc/cAc	2/57	0.725257760590585	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	0	0.725257760590585	1		504	518	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141036	55141036	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121908586	NA	P-0032848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	177	353	0	ENST00000257290.5:c.1682T>A	p.Val561Asp	p.V561D	ENST00000257290	NM_006206.4	561	gTc/gAc	12/23	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.701681122077984	2		353	488	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352540	118352540	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	159	428	0	ENST00000534358.1:c.3745A>G	p.Arg1249Gly	p.R1249G	ENST00000534358	NM_005933.3	1249	Aga/Gga	7/36	1	2	FACETS	0.78	0.719	0.844	0.78	0.719	0.844	SUBCLONAL	1	TRUE	1	0.701681122077984	2		428	581	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578260	7578260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204041	NA	P-0032854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	176	630	0	ENST00000269305.4:c.589G>A	p.Val197Met	p.V197M	ENST00000269305	NM_001126112.2	197	Gtg/Atg	6/11	0.409248119510295	0	FACETS	0.746	0.69	0.805			1	SUBCLONAL	1	FALSE	0	0.409248119510295	0		630	681	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662481	227662481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	62	484	0	ENST00000305123.5:c.974G>A	p.Arg325His	p.R325H	ENST00000305123	NM_005544.2	325	cGt/cAt	1/2	0.409248119510295	0	FACETS	0.357	0.309	0.41			1	SUBCLONAL	1	FALSE	0	0.409248119510295	0		484	501	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	67	382	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	0.739	0.644	0.841	0.739	0.644	0.841	SUBCLONAL	1	FALSE	1	0.409248119510295	2		382	443	SUCCESS
APC	324	MSKCC	GRCh37	5	112175419	112175420	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0032854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	44	345	0	ENST00000257430.4:c.4129_4130del	p.Val1377SerfsTer8	p.V1377Sfs*8	ENST00000257430	NM_000038.5	1376	taTGtt/tatt	16/16	0.409248119510295	1	FACETS	0.576	0.485	0.675	0.576	0.485	0.675	SUBCLONAL	1	FALSE	0	0.409248119510295	1		345	297	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609957	81609957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756016910	NA	P-0032854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	27	379	0	ENST00000298171.2:c.1555C>T	p.Arg519Cys	p.R519C	ENST00000298171	NM_000369.2	519	Cgc/Tgc	10/10	1	2	FACETS	0.405	0.322	0.499	0.405	0.322	0.499	SUBCLONAL	1	FALSE	1	0.409248119510295	2		379	326	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945777	206945777	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	38	553	0	ENST00000423557.1:c.4C>G	p.His2Asp	p.H2D	ENST00000423557	NM_000572.2	2	Cac/Gac	1/5	1	2	FACETS	0.253	0.208	0.304	0.253	0.208	0.304	SUBCLONAL	1	FALSE	1	0.409248119510295	2		553	733	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615533	43615533	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	57	512	0	ENST00000355710.3:c.2612T>C	p.Val871Ala	p.V871A	ENST00000355710	NM_020975.4	871	gTt/gCt	15/20	1	2	FACETS	0.487	0.418	0.563	0.487	0.418	0.563	SUBCLONAL	1	FALSE	1	0.409248119510295	2		512	572	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440097	49440097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	54	691	1	ENST00000301067.7:c.4529G>A	p.Cys1510Tyr	p.C1510Y	ENST00000301067	NM_003482.3	1510	tGt/tAt	16/54	1	2	FACETS	0.34	0.289	0.395	0.34	0.289	0.395	SUBCLONAL	1	FALSE	1	0.409248119510295	2		692	777	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911298	32911301	+	frameshift_variant	Frame_Shift_Del	DEL	AAAC	AAAC	-	rs80359351	NA	P-0032854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	90	528	0	ENST00000380152.3:c.2808_2811del	p.Ala938ProfsTer21	p.A938Pfs*21	ENST00000380152		936	AAACaa/aa	11/27	0.287048827128933	2	FACETS	0.938	0.836	1	0.469	0.418	0.523	CLONAL	1	FALSE	0	0.409248119510295	2		528	469	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251886	153251891	+	stop_gained,inframe_deletion,splice_region_variant	Nonsense_Mutation	DEL	TAGGAG	TAGGAG	-	novel	NA	P-0032854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	122	518	0	ENST00000281708.4:c.1115_1120del	p.Ser372_Lys374delinsTer	p.S372_K374delins*	ENST00000281708	NM_033632.3	372	tCTCCTAag/tag	7/12	1	2	FACETS	0.994	0.901	1	0.994	0.901	1	CLONAL	1	FALSE	1	0.409248119510295	2		518	600	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562922	176562922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	83	504	0	ENST00000439151.2:c.818C>T	p.Ser273Leu	p.S273L	ENST00000439151	NM_022455.4	273	tCa/tTa	2/23	0.409248119510295	1	FACETS	0.54	0.476	0.607	0.54	0.476	0.607	SUBCLONAL	1	FALSE	0	0.409248119510295	1		504	598	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372544	55372544	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs773818791	NA	P-0032854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	209	780	0	ENST00000297316.4:c.1234C>G	p.Pro412Ala	p.P412A	ENST00000297316	NM_022454.3	412	Cct/Gct	2/2	0.228780686936923	3	FACETS	0.9	0.833	0.969	0.3	0.277	0.323	INDETERMINATE	1	FALSE	0	0.409248119510295	3		780	1367	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517908	8517918	+	frameshift_variant	Frame_Shift_Del	DEL	AAGCCAGGACT	AAGCCAGGACT	-	novel	NA	P-0032854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	76	396	0	ENST00000356435.5:c.1473_1483del	p.Lys491AsnfsTer12	p.K491Nfs*12	ENST00000356435		491	aaAGTCCTGGCTTtt/aatt	10/35	1	2	FACETS	0.868	0.764	0.978	0.868	0.764	0.978	CLONAL	1	FALSE	1	0.409248119510295	2		396	428	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889133	76889133	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	43	436	1	ENST00000373344.5:c.4877G>A	p.Cys1626Tyr	p.C1626Y	ENST00000373344	NM_000489.3	1626	tGt/tAt	18/35	0.409248119510295	1	FACETS	0.369	0.309	0.436	0.369	0.309	0.436	SUBCLONAL	1	FALSE	0	0.409248119510295	1		437	453	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486575	56486575	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs12320176	NA	P-0032856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1319	243	651	0	ENST00000267101.3:c.1154A>G	p.Asn385Ser	p.N385S	ENST00000267101	NM_001982.3	385	aAt/aGt	10/28	0.853167901629784	4	FACETS	0.676	0.629	0.724	0.225	0.209	0.242	SUBCLONAL	1	TRUE	1	0.853167901629784	4		651	1562	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560464	95560464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	747	505	0	ENST00000393063.1:c.5125G>A	p.Asp1709Asn	p.D1709N	ENST00000393063	NM_030621.3	1709	Gat/Aat	25/28	0.853167901629784	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.853167901629784	3		505	829	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946008	17946008	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	306	664	0	ENST00000458235.1:c.1931C>G	p.Pro644Arg	p.P644R	ENST00000458235	NM_000215.3	644	cCc/cGc	15/24	0.853167901629784	3	FACETS	1	0.962	1	0.512	0.483	0.542	CLONAL	1	TRUE	1	0.853167901629784	3		664	999	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0032860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	175	483	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.362943004365616	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.362943004365616	1		483	615	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	249	441	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.362943004365616	1	FACETS	0.788	0.74	0.836	1	0.994	1	SUBCLONAL	2	TRUE	0	0.362943004365616	1		441	713	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0032860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	102	320	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.362943004365616	2		320	414	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0032860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	111	438	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.362943004365616	2		438	488	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604773	48604773	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	56	327	0	ENST00000342988.3:c.1595C>A	p.Ala532Asp	p.A532D	ENST00000342988	NM_005359.5	532	gCc/gAc	12/12	0.362943004365616	1	FACETS	0.784	0.676	0.901	0.784	0.676	0.901	CLONAL	1	TRUE	0	0.362943004365616	1		327	322	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243975	5243975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1488811231	NA	P-0032860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	234	639	0	ENST00000357368.4:c.1507G>A	p.Ala503Thr	p.A503T	ENST00000357368	NM_002850.3	503	Gcc/Acc	11/38	1	2	FACETS	0.777	0.726	0.829	1	0.993	1	SUBCLONAL	2	TRUE	1	0.362943004365616	2		639	830	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839930	27839930	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	85	638	0	ENST00000328488.2:c.164A>G	p.Tyr55Cys	p.Y55C	ENST00000328488	NM_003533.2	55	tAc/tGc	1/1	1	2	FACETS	0.579	0.511	0.652	0.579	0.511	0.652	SUBCLONAL	1	TRUE	1	0.362943004365616	2		638	809	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188866	32188866	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767567419	NA	P-0032860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	88	713	1	ENST00000375023.3:c.688C>T	p.Arg230Cys	p.R230C	ENST00000375023	NM_004557.3	230	Cgt/Tgt	4/30	1	2	FACETS	0.822	0.729	0.921	0.822	0.729	0.921	CLONAL	1	TRUE	1	0.362943004365616	2		714	590	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0032860-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	21	483	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.25	2		483	130	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032860-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	17	441	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.938	0.705	1	0.938	0.705	1	CLONAL	1	TRUE	1	0.25	2		441	145	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0032860-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	19	320	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.741	0.565	0.947	0.741	0.565	0.947	CLONAL	1	TRUE	1	0.25	2		320	205	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727483	66727483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504317	NA	P-0032860-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	8	511	1	ENST00000307102.5:c.199G>A	p.Asp67Asn	p.D67N	ENST00000307102	NM_002755.3	67	Gac/Aac	2/11	0.165379581927003	1	FACETS	0.145	0.093	0.214	0.145	0.093	0.214	SUBCLONAL	1	TRUE	0	0.25	1		512	386	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0032860-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	10	438	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.516	0.35	0.723	0.516	0.35	0.723	SUBCLONAL	1	TRUE	1	0.25	2		438	155	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243975	5243975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1488811231	NA	P-0032860-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	51	639	0	ENST00000357368.4:c.1507G>A	p.Ala503Thr	p.A503T	ENST00000357368	NM_002850.3	503	Gcc/Acc	11/38	1	2	FACETS	0.802	0.682	0.933	0.802	0.682	0.933	CLONAL	1	TRUE	1	0.25	2		639	509	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188866	32188866	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767567419	NA	P-0032860-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	28	713	1	ENST00000375023.3:c.688C>T	p.Arg230Cys	p.R230C	ENST00000375023	NM_004557.3	230	Cgt/Tgt	4/30	1	2	FACETS	0.519	0.414	0.638	0.519	0.414	0.638	SUBCLONAL	1	TRUE	1	0.25	2		714	432	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682399	52682400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	62	371	2	ENST00000394830.3:c.773dup	p.Asn258LysfsTer6	p.N258Kfs*6	ENST00000394830	NM_018313.4	258	aat/aaAt	8/30	0.343414639322085	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.343414639322085	1		373	202	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0032872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	119	716	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	0.343414639322085	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.343414639322085	1		716	480	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337698	73337702	+	frameshift_variant	Frame_Shift_Del	DEL	GAAAT	GAAAT	-	novel	NA	P-0032872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	21	225	0	ENST00000377767.4:c.2014_2018del	p.Ile672CysfsTer7	p.I672Cfs*7	ENST00000377767	NM_014953.3	672	ATTTCt/t	16/21	1	2	FACETS	1	0.807	1	1	0.807	1	CLONAL	1	TRUE	1	0.343414639322085	2		225	118	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22142560	22142560	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	47	442	0	ENST00000215832.6:c.842A>G	p.Asn281Ser	p.N281S	ENST00000215832	NM_002745.4	281	aAt/aGt	6/9	0.343414639322085	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.343414639322085	1		442	175	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106058	8106058	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	219	331	0	ENST00000346208.3:c.878T>G	p.Met293Arg	p.M293R	ENST00000346208		293	aTg/aGg	4/6	0.230269439607857	5	FACETS	0.887	0.832	0.943	0.887	0.832	0.943	INDETERMINATE	3	FALSE	2	0.525414614880597	5		331	560	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518634	204518634	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	52	224	0	ENST00000367182.3:c.1297C>A	p.Leu433Ile	p.L433I	ENST00000367182	NM_001278516.1	433	Ctc/Atc	11/11	0.303043394450085	4	FACETS	0.987	0.845	1	0.493	0.422	0.57	INDETERMINATE	1	FALSE	2	0.525414614880597	4		224	306	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060817	38060818	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0032889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	290	479	0	ENST00000250448.2:c.1171dup	p.Asp391GlyfsTer24	p.D391Gfs*24	ENST00000250448	NM_004496.3	391	gac/gGac	2/2	0.485808779755351	3	FACETS	0.928	0.878	0.979	0.928	0.878	0.979	CLONAL	2	FALSE	1	0.525414614880597	3		479	751	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214573	5214573	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs748467965	NA	P-0032889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	230	385	0	ENST00000357368.4:c.4493G>A	p.Arg1498Gln	p.R1498Q	ENST00000357368	NM_002850.3	1498	cGg/cAg	29/38	0.482578240698157	4	FACETS	0.966	0.905	1	0.966	0.905	1	CLONAL	2	FALSE	2	0.525414614880597	4		385	691	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0032890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	191	440	2	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.327852096182599	2	FACETS	0.941	0.876	1	0.941	0.876	1	CLONAL	2	TRUE	0	0.366548329245281	2		442	554	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0032890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	44	228	1	ENST00000267163.4:c.1215+1G>T		p.X405_splice	ENST00000267163	NM_000321.2	405			0.327852096182599	2	FACETS	1	0.939	1	0.612	0.52	0.712	CLONAL	1	TRUE	0	0.366548329245281	2		229	196	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226539	41226539	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs80358189	NA	P-0032890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	83	262	2	ENST00000357654.3:c.4485-1G>T		p.X1495_splice	ENST00000357654	NM_007294.3	1495			0.152428871946316	4	FACETS	0.862	0.766	0.963	0.862	0.766	0.963	INDETERMINATE	2	TRUE	2	0.366548329245281	4		264	359	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207658	102207658	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	53	287	2	ENST00000263464.3:c.1640A>G	p.Gln547Arg	p.Q547R	ENST00000263464	NM_001165.4	547	cAa/cGa	9/9	0.327852096182599	2	FACETS	0.822	0.713	0.936	0.822	0.713	0.936	CLONAL	2	TRUE	0	0.366548329245281	2		289	176	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287250	46287250	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	58	350	1	ENST00000334344.6:c.5195C>G	p.Ala1732Gly	p.A1732G	ENST00000334344	NM_152641.2	1732	gCc/gGc	19/21	0.292740090060891	3	FACETS	0.752	0.647	0.866	0.376	0.323	0.433	SUBCLONAL	1	TRUE	1	0.366548329245281	3		351	498	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396504	30396504	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	276	255	4	ENST00000331968.5:c.215A>G	p.Tyr72Cys	p.Y72C	ENST00000331968	NM_002742.2	72	tAc/tGc	1/18	0.335349769746545	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	4	TRUE	0	0.366548329245281	4		259	490	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680676	88680676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	165	417	2	ENST00000360948.2:c.581G>A	p.Gly194Asp	p.G194D	ENST00000360948	NM_001012338.2	194	gGc/gAc	6/19	0.314146367134338	2	FACETS	0.917	0.849	0.987	0.917	0.849	0.987	CLONAL	2	TRUE	0	0.366548329245281	2		419	491	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350276	89350276	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	135	603	0	ENST00000301030.4:c.2674A>T	p.Ser892Cys	p.S892C	ENST00000301030	NM_001256183.1	892	Agc/Tgc	9/13	0.292740090060891	3	FACETS	0.994	0.903	1	0.497	0.451	0.545	CLONAL	1	TRUE	1	0.366548329245281	3		603	877	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295690	212295690	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	125	361	3	ENST00000342788.4:c.2623T>A	p.Tyr875Asn	p.Y875N	ENST00000342788	NM_005235.2	875	Tac/Aac	21/28	0.284403893628049	3	FACETS	1	0.917	1	1	0.917	1	CLONAL	2	TRUE	1	0.366548329245281	3		364	402	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426718	212426718	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	127	387	3	ENST00000342788.4:c.2397G>T	p.Met799Ile	p.M799I	ENST00000342788	NM_005235.2	799	atG/atT	20/28	0.284403893628049	3	FACETS	0.872	0.795	0.952	0.872	0.795	0.952	CLONAL	2	TRUE	1	0.366548329245281	3		390	470	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659783	227659783	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	120	341	2	ENST00000305123.5:c.3672G>T	p.Glu1224Asp	p.E1224D	ENST00000305123	NM_005544.2	1224	gaG/gaT	1/2	0.284403893628049	3	FACETS	0.911	0.83	0.996	0.911	0.83	0.996	CLONAL	2	TRUE	1	0.366548329245281	3		343	425	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747048	40747048	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	143	404	0	ENST00000373198.4:c.3034G>A	p.Gly1012Ser	p.G1012S	ENST00000373198	NM_133170.3	1012	Ggc/Agc	22/32	0.292740090060891	3	FACETS	0.92	0.844	0.998	0.92	0.844	0.998	CLONAL	2	TRUE	1	0.366548329245281	3		404	502	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641241	12641241	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs946464136	NA	P-0032890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	78	337	0	ENST00000251849.4:c.1057A>G	p.Thr353Ala	p.T353A	ENST00000251849	NM_002880.3	353	Act/Gct	10/17	0.366548329245281	1	FACETS	0.937	0.829	1	0.937	0.829	1	CLONAL	1	TRUE	0	0.366548329245281	1		337	371	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670372	134670372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	169	314	3	ENST00000398015.3:c.283G>A	p.Asp95Asn	p.D95N	ENST00000398015	NM_004441.4	95	Gac/Aac	3/16	0.366548329245281	5	FACETS	0.854	0.79	0.92	0.854	0.79	0.92	CLONAL	3	TRUE	2	0.366548329245281	5		317	558	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969968	161969968	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	136	331	1	ENST00000366898.1:c.1001del	p.Arg334ProfsTer101	p.R334Pfs*101	ENST00000366898	NM_004562.2	334	cGc/cc	9/12	0.152428871946316	4	FACETS	0.833	0.76	0.909	0.833	0.76	0.909	INDETERMINATE	2	TRUE	2	0.366548329245281	4		332	609	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55229216	55229216	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	92	263	6	ENST00000275493.2:c.1523C>T	p.Ala508Val	p.A508V	ENST00000275493	NM_005228.3	508	gCc/gTc	13/28	0.152428871946316	4	FACETS	0.811	0.725	0.902	0.811	0.725	0.902	INDETERMINATE	2	TRUE	2	0.366548329245281	4		269	423	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938408	44938408	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	72	172	0	ENST00000377967.4:c.2956A>G	p.Thr986Ala	p.T986A	ENST00000377967	NM_021140.2	986	Act/Gct	20/29	0.223191555109332	2	FACETS	1	0.933	1			1	CLONAL	2	TRUE	NA	0.366548329245281	2		172	185	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0032891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	373	607	2	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.832457544811926	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.832457544811926	1		609	478	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247280	153247280	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	190	262	0	ENST00000281708.4:c.1522C>T	p.Gln508Ter	p.Q508*	ENST00000281708	NM_033632.3	508	Caa/Taa	10/12	0.832457544811926	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.832457544811926	2		262	227	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257459	16257459	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	106	342	0	ENST00000375759.3:c.4724C>A	p.Ser1575Tyr	p.S1575Y	ENST00000375759	NM_015001.2	1575	tCc/tAc	11/15	0.832457544811926	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.832457544811926	1		342	148	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111490	8111490	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs964378376	NA	P-0032891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	298	383	0	ENST00000346208.3:c.976A>G	p.Thr326Ala	p.T326A	ENST00000346208		326	Aca/Gca	5/6	0.573275877481946	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.832457544811926	1		383	392	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679838	88679838	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs542205293	NA	P-0032891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	162	275	0	ENST00000360948.2:c.625C>A	p.Leu209Ile	p.L209I	ENST00000360948	NM_001012338.2	209	Ctt/Att	7/19	0.328881115306712	1	FACETS	0.664	0.619	0.709	0.664	0.619	0.709	INDETERMINATE	1	TRUE	0	0.832457544811926	1		275	342	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857044	9857044	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs201707833	NA	P-0032891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	65	239	0	ENST00000330684.3:c.4357G>T	p.Val1453Leu	p.V1453L	ENST00000330684	NM_001134407.1	1453	Gtg/Ttg	13/13	0.832457544811926	1	FACETS	0.98	0.899	1	0.98	0.899	1	CLONAL	1	TRUE	0	0.832457544811926	1		239	93	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760778	59760778	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs112214651	NA	P-0032891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	111	505	0	ENST00000259008.2:c.3629A>G	p.Asp1210Gly	p.D1210G	ENST00000259008	NM_032043.2	1210	gAt/gGt	20/20	0.423057407673738	1	FACETS	0.782	0.723	0.84	0.782	0.723	0.84	INDETERMINATE	1	TRUE	0	0.832457544811926	1		505	199	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211188	2211188	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	402	490	0	ENST00000398665.3:c.1442C>A	p.Pro481Gln	p.P481Q	ENST00000398665	NM_032482.2	481	cCg/cAg	15/28	0.184573613995937	2	FACETS	1	0.994	1	0.624	0.598	0.65	INDETERMINATE	1	TRUE	0	0.832457544811926	2		490	774	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948775	17948775	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	458	552	0	ENST00000458235.1:c.1667A>G	p.Lys556Arg	p.K556R	ENST00000458235	NM_000215.3	556	aAg/aGg	12/24	0.310068850927532	4	FACETS	0.969	0.929	1	0.969	0.929	1	INDETERMINATE	2	TRUE	2	0.832457544811926	4		552	1040	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860357	42860357	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	359	394	0	ENST00000398585.3:c.520T>A	p.Ser174Thr	p.S174T	ENST00000398585	NM_001135099.1	174	Tca/Aca	5/14	0.832457544811926	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.832457544811926	1		394	452	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462353	89462353	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	66	402	0	ENST00000336596.2:c.1825G>C	p.Val609Leu	p.V609L	ENST00000336596	NM_005233.5	609	Gtt/Ctt	10/17	0.832457544811926	1	FACETS	0.917	0.836	0.993	0.917	0.836	0.993	CLONAL	1	TRUE	0	0.832457544811926	1		402	101	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100000	157100008	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGA	GGCGGCGGA	-	rs1200163659	NA	P-0032891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	39	49	1	ENST00000346085.5:c.939_947del	p.Gly317_Gly319del	p.G317_G319del	ENST00000346085	NM_020732.3	313	GGCGGCGGA/-	1/20	0.300809611607717	2	FACETS	0.726	0.615	0.844	0.363	0.307	0.422	INDETERMINATE	1	TRUE	0	0.832457544811926	2		50	129	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431629	6431631	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0032891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	48	243	0	ENST00000356142.4:c.186_188del	p.Glu62del	p.E62del	ENST00000356142	NM_018890.3	61	cAAGaa/caa	3/7	0.198045361013311	3	FACETS	0.785	0.672	0.907	0.393	0.336	0.454	INDETERMINATE	1	TRUE	1	0.832457544811926	3		243	208	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376087	8376087	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	153	207	0	ENST00000356435.5:c.4510G>C	p.Gly1504Arg	p.G1504R	ENST00000356435		1504	Ggt/Cgt	28/35	0.832457544811926	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	0	0.832457544811926	3		207	170	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346338	73346338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	93	391	0	ENST00000377767.4:c.1462G>A	p.Asp488Asn	p.D488N	ENST00000377767	NM_014953.3	488	Gat/Aat	10/21	1	2	FACETS	0.71	0.639	0.785	0.71	0.639	0.785	SUBCLONAL	1	TRUE	1	0.852911942968468	2		391	307	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575462	67575462	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	190	335	0	ENST00000274335.5:c.535del	p.Val179CysfsTer28	p.V179Cfs*28	ENST00000274335		179	Gtg/tg	4/15	1	2	FACETS	0.909	0.849	0.971	0.909	0.849	0.971	CLONAL	1	TRUE	1	0.852911942968468	2		335	490	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061249	38061249	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	299	402	0	ENST00000250448.2:c.740A>T	p.His247Leu	p.H247L	ENST00000250448	NM_004496.3	247	cAc/cTc	2/2	1	2	FACETS	0.959	0.91	1	1	0.997	1	CLONAL	3	FALSE	1	0.308269402857727	2		402	674	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344348	118344348	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	189	288	0	ENST00000534358.1:c.2474A>T	p.Glu825Val	p.E825V	ENST00000534358	NM_005933.3	825	gAg/gTg	3/36	NA	2	FACETS	0.978	0.916	1			1	INDETERMINATE	3	FALSE	NA	0.308269402857727	2		288	418	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643348	52643348	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	66	347	0	ENST00000394830.3:c.2548C>T	p.Arg850Ter	p.R850*	ENST00000394830	NM_018313.4	850	Cga/Tga	17/30	0.291804149894186	1	FACETS	0.899	0.783	1	0.899	0.783	1	CLONAL	1	TRUE	0	0.291804149894186	1		347	430	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784077	120784077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1210006090	NA	P-0032897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	235	547	3	ENST00000257552.2:c.908G>A	p.Arg303His	p.R303H	ENST00000257552	NM_002442.3	303	cGc/cAc	13/15	0.274964851239023	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.291804149894186	3		550	887	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105659	30105659	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	76	488	0	ENST00000331968.5:c.1027G>C	p.Glu343Gln	p.E343Q	ENST00000331968	NM_002742.2	343	Gaa/Caa	7/18	1	2	FACETS	0.68	0.596	0.771	0.68	0.596	0.771	SUBCLONAL	1	TRUE	1	0.291804149894186	2		488	766	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183848	10183850	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	novel	NA	P-0032897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	74	407	0	ENST00000256474.2:c.322_324del	p.Arg108del	p.R108del	ENST00000256474	NM_000551.3	106	gGCCgc/ggc	1/3	0.291804149894186	1	FACETS	0.958	0.842	1	0.958	0.842	1	CLONAL	1	TRUE	0	0.291804149894186	1		407	452	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155483	47155483	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	46	269	0	ENST00000409792.3:c.4598G>T	p.Cys1533Phe	p.C1533F	ENST00000409792	NM_014159.6	1533	tGt/tTt	5/21	0.291804149894186	1	FACETS	0.806	0.682	0.942	0.806	0.682	0.942	CLONAL	1	TRUE	0	0.291804149894186	1		269	334	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589581	67589585	+	protein_altering_variant	In_Frame_Del	DEL	ATTAC	ATTAC	TT	novel	NA	P-0032897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	21	209	1	ENST00000274335.5:c.1344_1348delinsTT	p.Lys448_His450delinsAsnTyr	p.K448_H450delinsNY	ENST00000274335		448	aaATTACat/aaTTat	10/15	1	2	FACETS	0.72	0.557	0.907	0.72	0.557	0.907	CLONAL	1	TRUE	1	0.291804149894186	2		210	200	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287235	33287235	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	72	442	0	ENST00000374542.5:c.1862A>C	p.Asn621Thr	p.N621T	ENST00000374542	NM_001141970.1	621	aAc/aCc	6/8	1	2	FACETS	0.814	0.712	0.925	0.814	0.712	0.925	CLONAL	1	TRUE	1	0.291804149894186	2		442	606	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223423	53223424	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGGAGCTCAGCCAGCCGTCC	novel	NA	P-0032897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	74	260	0	ENST00000375401.3:c.3916_3935dup	p.Gln1313AspfsTer52	p.Q1313Dfs*52	ENST00000375401	NM_004187.3	1312	cgc/cgGGACGGCTGGCTGAGCTCCGc	23/26	1	1	FACETS	0.982	0.863	1	0.982	0.863	1	CLONAL	1	TRUE	0	0.291804149894186	1		260	441	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0032899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	89	280	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.270087363494052	3	FACETS	0.868	0.774	0.967	0.868	0.774	0.967	CLONAL	2	TRUE	1	0.270087363494052	3		280	431	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351379	89351379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1040338311	NA	P-0032899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	85	566	1	ENST00000301030.4:c.1571C>T	p.Ser524Leu	p.S524L	ENST00000301030	NM_001256183.1	524	tCg/tTg	9/13	0.270087363494052	2	FACETS	0.939	0.831	1	0.47	0.415	0.528	CLONAL	1	TRUE	0	0.270087363494052	2		567	670	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160677	56160678	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	99	259	0	ENST00000399503.3:c.953dup	p.Leu318PhefsTer8	p.L318Ffs*8	ENST00000399503	NM_005921.1	317	-/T	4/20	0.270087363494052	4	FACETS	0.851	0.762	0.945	0.851	0.762	0.945	CLONAL	2	TRUE	2	0.270087363494052	4		259	547	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164182	108164182	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	45	224	0	ENST00000278616.4:c.4754G>C	p.Arg1585Thr	p.R1585T	ENST00000278616	NM_000051.3	1585	aGa/aCa	31/63	0.270087363494052	3	FACETS	0.988	0.832	1	0.494	0.416	0.58	CLONAL	1	TRUE	1	0.270087363494052	3		224	383	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942670	48942671	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs587778829	NA	P-0032899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	51	204	0	ENST00000267163.4:c.1060_1061del	p.Gln354GlufsTer7	p.Q354Efs*7	ENST00000267163	NM_000321.2	353	ACa/a	11/27	0.270087363494052	1	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	0	0.270087363494052	1		204	318	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138569	37138569	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	65	269	0	ENST00000373509.5:c.103G>C	p.Glu35Gln	p.E35Q	ENST00000373509	NM_002648.3	35	Gag/Cag	2/6	0.270087363494052	3	FACETS	1	0.946	1	0.587	0.51	0.67	CLONAL	1	TRUE	1	0.270087363494052	3		269	465	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258036	123258036	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	74	477	0	ENST00000358487.5:c.1645A>G	p.Asn549Asp	p.N549D	ENST00000358487	NM_000141.4	549	Aat/Gat	12/18	0.270087363494052	2	FACETS	0.946	0.829	1	0.473	0.414	0.536	CLONAL	1	TRUE	0	0.270087363494052	2		477	579	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258061	123258061	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	71	517	0	ENST00000358487.5:c.1620G>T	p.Met540Ile	p.M540I	ENST00000358487	NM_000141.4	540	atG/atT	12/18	0.270087363494052	2	FACETS	0.851	0.743	0.967	0.425	0.371	0.484	CLONAL	1	TRUE	0	0.270087363494052	2		517	618	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267518	198267518	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	46	310	0	ENST00000335508.6:c.1839G>C	p.Met613Ile	p.M613I	ENST00000335508	NM_012433.2	613	atG/atC	14/25	0.270087363494052	3	FACETS	0.796	0.67	0.934	0.398	0.335	0.467	CLONAL	1	TRUE	1	0.270087363494052	3		310	486	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177845	56177851	+	frameshift_variant	Frame_Shift_Del	DEL	AGTTCAA	AGTTCAA	-	novel	NA	P-0032899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	115	262	0	ENST00000399503.3:c.2818_2824del	p.Ser940GlnfsTer26	p.S940Qfs*26	ENST00000399503	NM_005921.1	940	AGTTCAAca/ca	14/20	0.270087363494052	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	2	0.270087363494052	4		262	497	SUCCESS
APC	324	MSKCC	GRCh37	5	112175232	112175232	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	88	199	0	ENST00000257430.4:c.3941G>C	p.Arg1314Thr	p.R1314T	ENST00000257430	NM_000038.5	1314	aGg/aCg	16/16	0.270087363494052	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.270087363494052	4		199	346	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197326	26197326	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	33	254	0	ENST00000356476.2:c.153G>T	p.Glu51Asp	p.E51D	ENST00000356476		51	gaG/gaT	1/1	0.270087363494052	3	FACETS	0.675	0.55	0.816	0.337	0.275	0.408	SUBCLONAL	1	TRUE	1	0.270087363494052	3		254	411	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878332	151878332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	85	443	0	ENST00000262189.6:c.6613C>T	p.His2205Tyr	p.H2205Y	ENST00000262189	NM_170606.2	2205	Cat/Tat	36/59	0.270087363494052	3	FACETS	1	0.922	1	0.528	0.466	0.593	CLONAL	1	TRUE	1	0.270087363494052	3		443	677	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0032911-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	84	270	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	0.287574160908217	3	FACETS	1	0.975	1	0.65	0.584	0.718	INDETERMINATE	1	TRUE	1	0.771790895773704	3		270	232	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488657	212488657	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374970657	NA	P-0032911-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	145	426	0	ENST00000342788.4:c.2192C>T	p.Thr731Met	p.T731M	ENST00000342788	NM_005235.2	731	aCg/aTg	18/28	1	2	FACETS	0.963	0.889	1	0.963	0.889	1	CLONAL	1	TRUE	1	0.771790895773704	2		426	390	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0032911-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	136	260	0	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.771790895773704	2		260	316	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624274	89624274	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs587782187	NA	P-0032911-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	231	358	0	ENST00000371953.3:c.48T>A	p.Tyr16Ter	p.Y16*	ENST00000371953	NM_000314.4	16	taT/taA	1/9	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.771790895773704	2		358	429	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947540	48947540	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0032911-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	145	424	0	ENST00000267163.4:c.1128-1G>A		p.X376_splice	ENST00000267163	NM_000321.2	376			0.771790895773704	1	FACETS	0.99	0.93	1	0.99	0.93	1	CLONAL	1	TRUE	0	0.771790895773704	1		424	233	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692823	89692823	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1554898088	NA	P-0032911-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	60	207	0	ENST00000371953.3:c.309del	p.Cys105ValfsTer8	p.C105Vfs*8	ENST00000371953	NM_000314.4	103	Ccc/cc	5/9	1	2	FACETS	0.888	0.781	1	0.888	0.781	1	CLONAL	1	TRUE	1	0.771790895773704	2		207	175	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131776	2131777	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0032911-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	230	544	0	ENST00000219476.3:c.3791_3792insGG	p.Pro1265ValfsTer61	p.P1265Vfs*61	ENST00000219476	NM_000548.3	1264	cct/ccGGt	31/42	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.771790895773704	2		544	582	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577075	7577076	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	rs1555525158	NA	P-0032911-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	624	711	0	ENST00000269305.4:c.861_862dup	p.Asn288ArgfsTer58	p.N288Rfs*58	ENST00000269305	NM_001126112.2	288	aat/aGAat	8/11	0.770384268626989	2	FACETS	0.899	0.875	0.923	0.899	0.875	0.923	CLONAL	2	TRUE	0	0.771790895773704	2		711	899	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839860	27839860	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032911-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	114	504	0	ENST00000328488.2:c.234C>A	p.Asp78Glu	p.D78E	ENST00000328488	NM_003533.2	78	gaC/gaA	1/1	0.771790895773704	4	FACETS	0.575	0.517	0.637	0.288	0.258	0.319	SUBCLONAL	1	TRUE	2	0.771790895773704	4		504	910	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851095	151851095	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032911-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	60	159	0	ENST00000262189.6:c.12276G>C	p.Glu4092Asp	p.E4092D	ENST00000262189	NM_170606.2	4092	gaG/gaC	48/59	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.771790895773704	2		159	153	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	80	264	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.35	2		264	332	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0032933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	285	588	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	NA	2	FACETS	0.837	0.788	0.887			1	INDETERMINATE	2	TRUE	NA	0.35	2		588	973	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037966	49037966	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	72	428	0	ENST00000267163.4:c.2206C>T	p.Gln736Ter	p.Q736*	ENST00000267163	NM_000321.2	736	Cag/Tag	21/27	0.301838475789746	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.35	1		428	320	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045016	47045016	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0032933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	161	335	0	ENST00000377604.3:c.2342C>G	p.Ser781Ter	p.S781*	ENST00000377604	NM_001204468.1	781	tCa/tGa	20/24	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.35	1		335	516	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481811	56481811	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767905298	NA	P-0032933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	110	613	0	ENST00000267101.3:c.739C>T	p.Arg247Trp	p.R247W	ENST00000267101	NM_001982.3	247	Cgg/Tgg	7/28	1	2	FACETS	0.761	0.683	0.843	0.761	0.683	0.843	SUBCLONAL	1	TRUE	1	0.35	2		613	826	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432535	49432554	+	frameshift_variant	Frame_Shift_Del	DEL	CACTGGCTCACCAGGGCCTG	CACTGGCTCACCAGGGCCTG	T	novel	NA	P-0032933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	147	582	0	ENST00000301067.7:c.8585_8604delinsA	p.Pro2862HisfsTer42	p.P2862Hfs*42	ENST00000301067	NM_003482.3	2862	cCAGGCCCTGGTGAGCCAGTG/cA	34/54	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.35	2		582	788	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0032934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	205	448	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.547600431017909	3	FACETS	0.799	0.747	0.852	0.799	0.747	0.852	SUBCLONAL	2	TRUE	1	0.626051743162497	3		449	538	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562850	21562850	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1418882962	NA	P-0032934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	471	405	0	ENST00000382592.4:c.1069G>A	p.Val357Met	p.V357M	ENST00000382592	NM_014572.2	357	Gtg/Atg	4/8	0.569078016748209	5	FACETS	0.943	0.905	0.982	0.943	0.905	0.982	CLONAL	3	TRUE	2	0.626051743162497	5		405	1031	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121561	108121561	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs749036865	NA	P-0032934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	96	515	0	ENST00000278616.4:c.1369C>T	p.Arg457Ter	p.R457*	ENST00000278616	NM_000051.3	457	Cga/Tga	10/63	0.150663388305252	3	FACETS	0.64	0.571	0.714	0.213	0.19	0.238	INDETERMINATE	1	TRUE	0	0.626051743162497	3		515	629	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121466	108121467	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	128	392	0	ENST00000278616.4:c.1276dup	p.Ser426LysfsTer4	p.S426Kfs*4	ENST00000278616	NM_000051.3	425	gca/gcAa	10/63	0.150663388305252	3	FACETS	1	0.981	1	0.426	0.389	0.464	INDETERMINATE	1	TRUE	0	0.626051743162497	3		392	420	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447099	49447099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	127	470	0	ENST00000301067.7:c.845C>T	p.Pro282Leu	p.P282L	ENST00000301067	NM_003482.3	282	cCt/cTt	7/54	0.547600431017909	3	FACETS	0.9	0.818	0.986	0.45	0.409	0.493	CLONAL	1	TRUE	1	0.626051743162497	3		470	592	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098369	47098369	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	124	563	0	ENST00000409792.3:c.6905G>T	p.Cys2302Phe	p.C2302F	ENST00000409792	NM_014159.6	2302	tGt/tTt	15/21	0.150663388305252	3	FACETS	0.734	0.664	0.806	0.245	0.221	0.269	INDETERMINATE	1	TRUE	0	0.626051743162497	3		563	709	SUCCESS
APC	324	MSKCC	GRCh37	5	112175319	112175320	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	157	268	0	ENST00000257430.4:c.4030dup	p.Ser1344PhefsTer10	p.S1344Ffs*10	ENST00000257430	NM_000038.5	1343	tct/tcTt	16/16	0.52874180430585	2	FACETS	0.883	0.827	0.939	0.883	0.827	0.939	CLONAL	2	TRUE	0	0.626051743162497	2		268	284	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27205020	27205020	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	46	559	0	ENST00000380036.4:c.2321G>A	p.Arg774Lys	p.R774K	ENST00000380036	NM_000459.3	774	aGg/aAg	14/23	0.267770030941533	3	FACETS	0.232	0.195	0.274	0.116	0.097	0.137	INDETERMINATE	1	TRUE	1	0.626051743162497	3		559	830	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105635	11105636	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0032935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	64	579	0	ENST00000358026.2:c.1554_1555del	p.Asn519ArgfsTer14	p.N519Rfs*14	ENST00000358026	NM_001128849.1	517	aaAGag/aaag	9/36	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.28	2		579	406	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618950	37618950	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	62	547	0	ENST00000447079.4:c.626G>C	p.Ser209Thr	p.S209T	ENST00000447079	NM_015083.1	209	aGt/aCt	1/14	0.301361051170192	3	FACETS	0.867	0.749	0.996	0.434	0.374	0.498	CLONAL	1	TRUE	1	0.28	3		547	582	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268438	46268438	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	47	386	1	ENST00000371998.3:c.2825G>T	p.Gly942Val	p.G942V	ENST00000371998		942	gGa/gTa	15/23	0.301361051170192	3	FACETS	0.828	0.7	0.97	0.414	0.35	0.485	CLONAL	1	TRUE	1	0.28	3		387	462	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257104	198257104	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs759773104	NA	P-0032939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	327	450	0	ENST00000335508.6:c.3838C>G	p.Leu1280Val	p.L1280V	ENST00000335508	NM_012433.2	1280	Ctc/Gtc	25/25	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.864774337565246	2		450	741	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0032949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	122	280	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.776	0.704	0.851	1	0.986	1	SUBCLONAL	2	TRUE	1	0.29	2		280	542	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0032949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	188	800	0	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.29	2		800	910	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115964	8115964	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	27	347	0	ENST00000346208.3:c.1310G>C	p.Ser437Thr	p.S437T	ENST00000346208		437	aGc/aCc	6/6	1	2	FACETS	0.424	0.337	0.524	0.424	0.337	0.524	SUBCLONAL	1	TRUE	1	0.29	2		347	439	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95584081	95584081	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	37	473	0	ENST00000393063.1:c.1387G>T	p.Glu463Ter	p.E463*	ENST00000393063	NM_030621.3	463	Gaa/Taa	10/28	1	2	FACETS	0.363	0.299	0.437	0.363	0.299	0.437	SUBCLONAL	1	TRUE	1	0.29	2		473	702	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830115	72830115	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	51	656	0	ENST00000268489.5:c.6466C>T	p.Gln2156Ter	p.Q2156*	ENST00000268489	NM_006885.3	2156	Cag/Tag	9/10	1	2	FACETS	0.465	0.394	0.543	0.465	0.394	0.543	SUBCLONAL	1	TRUE	1	0.29	2		656	757	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0032959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	123	264	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.867	0.796	0.94	1	0.992	1	CLONAL	3	TRUE	1	0.308940106807387	2		264	306	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56852643	56852643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs966758586	NA	P-0032959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	168	404	3	ENST00000308159.5:c.557C>T	p.Ala186Val	p.A186V	ENST00000308159	NM_014669.4	186	gCg/gTg	6/22	1	2	FACETS	0.865	0.804	0.927	1	0.994	1	CLONAL	3	TRUE	1	0.308940106807387	2		407	419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576900	7576901	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	217	657	0	ENST00000269305.4:c.945dup	p.Pro316SerfsTer21	p.P316Sfs*21	ENST00000269305	NM_001126112.2	315	-/T	9/11	1	2	FACETS	0.864	0.81	0.918	1	0.995	1	CLONAL	3	TRUE	1	0.308940106807387	2		657	542	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430639	181430639	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	154	431	0	ENST00000325404.1:c.491A>G	p.Asn164Ser	p.N164S	ENST00000325404	NM_003106.3	164	aAc/aGc	1/1	1	2	FACETS	0.97	0.894	1	1	0.992	1	CLONAL	2	TRUE	1	0.308940106807387	2		431	514	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106872	27106872	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	31	546	0	ENST00000324856.7:c.6484del	p.Val2162CysfsTer38	p.V2162Cfs*38	ENST00000324856	NM_006015.4	2161	ccG/cc	20/20	1	2	FACETS	0.585	0.474	0.711	0.585	0.474	0.711	SUBCLONAL	1	TRUE	1	0.308940106807387	2		546	343	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576885	7576886	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0032959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	243	686	0	ENST00000269305.4:c.960dup	p.Lys321GlufsTer16	p.K321Efs*16	ENST00000269305	NM_001126112.2	320	-/G	9/11	1	2	FACETS	0.915	0.862	0.968	1	0.996	1	CLONAL	3	TRUE	1	0.308940106807387	2		686	573	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939756	76939757	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	206	561	0	ENST00000373344.5:c.991_992insA	p.Leu331TyrfsTer3	p.L331Yfs*3	ENST00000373344	NM_000489.3	331	tta/tAta	9/35	0.308940106807387	1	FACETS	1	0.968	1	1	0.994	1	CLONAL	2	TRUE	0	0.308940106807387	1		561	534	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120789192	120789192	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	55	295	0	ENST00000257552.2:c.745G>C	p.Glu249Gln	p.E249Q	ENST00000257552	NM_002442.3	249	Gag/Cag	11/15	0.340220243273807	5	FACETS	0.955	0.819	1	0.239	0.204	0.276	CLONAL	1	TRUE	1	0.416761499831402	5		295	449	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984782	11984788	+	frameshift_variant	Frame_Shift_Del	DEL	CGAGGAG	CGAGGAG	-	novel	NA	P-0032960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	26	280	0	ENST00000353533.5:c.329_335del	p.Arg110LeufsTer16	p.R110Lfs*16	ENST00000353533	NM_003010.3	110	CGAGGAGct/ct	3/11	0.416761499831402	1	FACETS	0.558	0.446	0.684	0.558	0.446	0.684	SUBCLONAL	1	TRUE	0	0.416761499831402	1		280	177	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15943760	15943760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571174228	NA	P-0032960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	85	352	1	ENST00000268712.3:c.6728C>T	p.Thr2243Met	p.T2243M	ENST00000268712	NM_006311.3	2243	aCg/aTg	43/46	0.416761499831402	1	FACETS	0.92	0.82	1	0.92	0.82	1	CLONAL	1	TRUE	0	0.416761499831402	1		353	351	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872218	45872223	+	inframe_deletion	In_Frame_Del	DEL	GTAGAT	GTAGAT	-	novel	NA	P-0032960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	62	580	0	ENST00000391945.4:c.211_216del	p.Ile71_Tyr72del	p.I71_Y72del	ENST00000391945	NM_000400.3	71	ATCTAC/-	4/23	0.407989387725351	1	FACETS	0.471	0.407	0.54	0.471	0.407	0.54	SUBCLONAL	1	TRUE	0	0.416761499831402	1		580	500	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430992	181430992	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	71	513	0	ENST00000325404.1:c.844G>C	p.Glu282Gln	p.E282Q	ENST00000325404	NM_003106.3	282	Gag/Cag	1/1	1	2	FACETS	0.783	0.686	0.887	0.783	0.686	0.887	SUBCLONAL	1	TRUE	1	0.416761499831402	2		513	435	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345803	152345803	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	99	413	0	ENST00000359321.1:c.767T>C	p.Val256Ala	p.V256A	ENST00000359321	NM_005431.1	256	gTt/gCt	3/3	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.416761499831402	2		413	410	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431969	121431969	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs587778397	NA	P-0032961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	177	490	0	ENST00000257555.6:c.716C>T	p.Ala239Val	p.A239V	ENST00000257555		239	gCg/gTg	4/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.868566161786244	2		490	371	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520027	106520027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370034420	NA	P-0032961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	95	252	1	ENST00000359195.3:c.2455G>A	p.Asp819Asn	p.D819N	ENST00000359195	NM_002649.2	819	Gat/Aat	6/11	0.868566161786244	2	FACETS	0.911	0.826	0.998	0.456	0.413	0.499	CLONAL	1	TRUE	0	0.868566161786244	2		253	240	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120247	70120247	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886043831	NA	P-0032961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	614	611	0	ENST00000245479.2:c.1249C>T	p.Gln417Ter	p.Q417*	ENST00000245479	NM_000346.3	417	Cag/Tag	3/3	0.869366727750519	3	FACETS	0.984	0.954	1	0.984	0.954	1	CLONAL	2	TRUE	1	0.868566161786244	3		611	1030	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932705	49932705	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	262	607	0	ENST00000296474.3:c.3166T>G	p.Ser1056Ala	p.S1056A	ENST00000296474	NM_002447.2	1056	Tcc/Gcc	14/20	0.842966191761053	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.868566161786244	1		607	323	SUCCESS
APC	324	MSKCC	GRCh37	5	112174183	112174183	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554084575	NA	P-0032961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	95	313	0	ENST00000257430.4:c.2894del	p.Asn965IlefsTer15	p.N965Ifs*15	ENST00000257430	NM_000038.5	964	ttA/tt	16/16	0.836410100290837	1	FACETS	0.938	0.875	0.996	0.938	0.875	0.996	CLONAL	1	TRUE	0	0.868566161786244	1		313	132	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0032962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	388	468	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.924895535433242	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.924895535433242	1		468	436	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872497	136872497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748189454	NA	P-0032962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	193	170	1	ENST00000241393.3:c.1001G>A	p.Arg334Gln	p.R334Q	ENST00000241393	NM_003467.2	334	cGa/cAa	2/2	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.924895535433242	2		171	395	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643614	52643614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	410	257	0	ENST00000394830.3:c.2282G>A	p.Arg761Lys	p.R761K	ENST00000394830	NM_018313.4	761	aGa/aAa	17/30	0.924895535433242	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.924895535433242	1		257	449	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955875	55955875	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	216	155	0	ENST00000263923.4:c.3287G>A	p.Trp1096Ter	p.W1096*	ENST00000263923	NM_002253.2	1096	tGg/tAg	24/30	0.34555701273791	1	FACETS	0.568	0.535	0.601	0.568	0.535	0.601	INDETERMINATE	1	TRUE	0	0.924895535433242	1		155	442	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202443	123202443	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	159	178	0	ENST00000218089.9:c.2295G>C	p.Met765Ile	p.M765I	ENST00000218089	NM_001042749.1	765	atG/atC	24/35	1	2	FACETS	0.914	0.85	0.98	0.914	0.85	0.98	CLONAL	1	TRUE	1	0.924895535433242	2		178	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0032980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	80	505	1	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	0.255954783725713	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.406564487248888	2		506	167	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673694	37673694	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	54	488	2	ENST00000447079.4:c.2848C>T	p.Arg950Ter	p.R950*	ENST00000447079	NM_015083.1	950	Cga/Tga	10/14	0.255954783725713	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	0	0.406564487248888	2		490	121	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188098	11188098	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	32	438	0	ENST00000361445.4:c.5996G>A	p.Cys1999Tyr	p.C1999Y	ENST00000361445	NM_004958.3	1999	tGt/tAt	43/58	1	2	FACETS	0.816	0.668	0.979	0.816	0.668	0.979	CLONAL	1	TRUE	1	0.406564487248888	2		438	193	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560068	29560068	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	36	250	0	ENST00000356175.3:c.3545T>A	p.Val1182Asp	p.V1182D	ENST00000356175	NM_000267.3	1182	gTt/gAt	27/57	0.255954783725713	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	2	TRUE	0	0.406564487248888	2		250	80	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15273364	15273364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	91	346	2	ENST00000263388.2:c.5825C>T	p.Ala1942Val	p.A1942V	ENST00000263388	NM_000435.2	1942	gCc/gTc	32/33	1	2	FACETS	0.974	0.871	1	0.974	0.871	1	CLONAL	1	TRUE	1	0.476457857281718	2		348	392	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0032985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	42	424	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	0.35988658102536	3	FACETS	1	0.903	1	0.548	0.463	0.64	CLONAL	1	TRUE	1	0.498904066921144	3		424	192	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579315	7579316	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1267047192	NA	P-0032985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	329	559	0	ENST00000269305.4:c.371dup	p.Cys124TrpfsTer25	p.C124Wfs*25	ENST00000269305	NM_001126112.2	124	tgc/tgGc	4/11	0.498904066921144	3	FACETS	0.947	0.906	0.988	0.947	0.906	0.988	CLONAL	3	TRUE	0	0.498904066921144	3		559	580	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404720	70404720	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369109149	NA	P-0032985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	49	476	0	ENST00000373644.4:c.2234G>A	p.Arg745Gln	p.R745Q	ENST00000373644	NM_030625.2	745	cGa/cAa	4/12	0.47042225719529	5	FACETS	0.962	0.818	1			1	CLONAL	1	TRUE	NA	0.498904066921144	5		476	357	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041110	180041110	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781402372	NA	P-0032985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	155	806	1	ENST00000261937.6:c.3289G>A	p.Val1097Met	p.V1097M	ENST00000261937	NM_182925.4	1097	Gtg/Atg	24/30	0.269215098161427	4	FACETS	0.937	0.857	1	0.468	0.428	0.511	INDETERMINATE	1	TRUE	2	0.498904066921144	4		807	994	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410987	31410987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1236254462	NA	P-0032985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	122	577	0	ENST00000344624.3:c.3533G>A	p.Arg1178Gln	p.R1178Q	ENST00000344624		1178	cGa/cAa	28/33	0.498904066921144	6	FACETS	0.903	0.815	0.997	0.301	0.271	0.333	CLONAL	1	TRUE	3	0.498904066921144	6		577	1082	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916932	178916932	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	45	470	0	ENST00000263967.3:c.319A>C	p.Asn107His	p.N107H	ENST00000263967	NM_006218.2	107	Aac/Cac	2/21	0.35988658102536	3	FACETS	1	0.878	1	0.519	0.441	0.604	CLONAL	1	TRUE	1	0.498904066921144	3		470	217	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598128	55598128	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	407	545	0	ENST00000288135.5:c.2325G>C	p.Gln775His	p.Q775H	ENST00000288135	NM_000222.2	775	caG/caC	16/21	0.47042225719529	5	FACETS	0.889	0.852	0.926			1	CLONAL	4	TRUE	NA	0.498904066921144	5		545	802	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738211	133738211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370646520	NA	P-0032989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	46	470	0	ENST00000318560.5:c.611C>T	p.Thr204Met	p.T204M	ENST00000318560	NM_005157.4	204	aCg/aTg	4/11	1	2	FACETS	0.518	0.436	0.61	0.518	0.436	0.61	SUBCLONAL	1	TRUE	1	0.29	2		470	612	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894230	NA	P-0032989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	187	508	0	ENST00000451590.1:c.35G>A	p.Gly12Asp	p.G12D	ENST00000451590	NM_001130442.1	12	gGc/gAc	2/5	1	2	FACETS	1	0.979	1	1	0.994	1	CLONAL	2	TRUE	1	0.29	2		508	570	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860619	45860619	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	319	731	0	ENST00000391945.4:c.1388C>A	p.Pro463Gln	p.P463Q	ENST00000391945	NM_000400.3	463	cCg/cAg	15/23	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.29	2		731	962	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526071	189526071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	66	388	1	ENST00000264731.3:c.335C>T	p.Thr112Met	p.T112M	ENST00000264731	NM_003722.4	112	aCg/aTg	4/14	1	2	FACETS	0.803	0.697	0.917	0.803	0.697	0.917	CLONAL	1	TRUE	1	0.29	2		389	567	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696642	47696642	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	14	500	0	ENST00000347630.2:c.306C>A	p.Phe102Leu	p.F102L	ENST00000347630	NM_001007230.1	102	ttC/ttA	5/11	1	2	FACETS	0.249	0.179	0.334	0.249	0.179	0.334	SUBCLONAL	1	TRUE	1	0.29	2		500	388	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023246	33023247	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0032989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	68	652	0	ENST00000300177.4:c.356dup	p.Tyr119Ter	p.Y119*	ENST00000300177	NM_001191322.1	119	tac/tAac	2/2	1	2	FACETS	0.714	0.621	0.815	0.714	0.621	0.815	SUBCLONAL	1	TRUE	1	0.29	2		652	657	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955626	55955626	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	11	427	0	ENST00000263923.4:c.3319C>T	p.Pro1107Ser	p.P1107S	ENST00000263923	NM_002253.2	1107	Cct/Tct	25/30	1	2	FACETS	0.37	0.255	0.512	0.37	0.255	0.512	SUBCLONAL	1	TRUE	1	0.29	2		427	205	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251195	251195	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	32	314	0	ENST00000264932.6:c.1640A>T	p.Lys547Met	p.K547M	ENST00000264932	NM_004168.2	547	aAg/aTg	12/15	1	2	FACETS	0.437	0.354	0.531	0.437	0.354	0.531	SUBCLONAL	1	TRUE	1	0.29	2		314	505	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878900	117878900	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	18	405	0	ENST00000297338.2:c.69G>T	p.Trp23Cys	p.W23C	ENST00000297338	NM_006265.2	23	tgG/tgT	2/14	1	2	FACETS	0.404	0.304	0.523	0.404	0.304	0.523	SUBCLONAL	1	TRUE	1	0.29	2		405	307	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15826392	15826392	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	48	230	0	ENST00000307771.7:c.436G>A	p.Glu146Lys	p.E146K	ENST00000307771	NM_005089.3	146	Gag/Aag	6/11	1	1	FACETS	0.813	0.699	0.935	1	0.969	1	CLONAL	2	TRUE	0	0.29	1		230	174	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	22	441	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.143425567132697	4	FACETS	1	0.829	1	0.538	0.419	0.674	INDETERMINATE	1	FALSE	2	0.276296599312411	4		441	189	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	62	683	1	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	0.143425567132697	4	FACETS	0.899	0.776	1	0.45	0.388	0.517	INDETERMINATE	1	FALSE	2	0.276296599312411	4		684	637	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0032990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	15	423	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	0.106161142137397	4	FACETS	1	0.771	1	0.525	0.387	0.688	INDETERMINATE	1	FALSE	2	0.276296599312411	4		423	132	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0032990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	29	993	5	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.595	0.478	0.728	0.595	0.478	0.728	SUBCLONAL	1	FALSE	1	0.276296599312411	2		998	353	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692920	89692921	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs398123323	NA	P-0032990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	48	492	0	ENST00000371953.3:c.405dup	p.Cys136MetfsTer44	p.C136Mfs*44	ENST00000371953	NM_000314.4	135	ata/atAa	5/9	0.276296599312411	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	2	FALSE	0	0.276296599312411	2		492	170	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0032990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	23	570	2	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.339	0.263	0.427	0.339	0.263	0.427	SUBCLONAL	1	FALSE	1	0.276296599312411	2		572	491	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158153	47158153	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	12	528	0	ENST00000409792.3:c.4546T>C	p.Cys1516Arg	p.C1516R	ENST00000409792	NM_014159.6	1516	Tgt/Cgt	4/21	1	2	FACETS	0.408	0.286	0.557	0.408	0.286	0.557	SUBCLONAL	1	FALSE	1	0.276296599312411	2		528	213	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845621	63845621	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	11	194	0	ENST00000279873.7:c.1360G>T	p.Glu454Ter	p.E454*	ENST00000279873	NM_032199.2	454	Gaa/Taa	9/10	0.202873425983743	4	FACETS	0.758	0.526	1	0.379	0.263	0.522	CLONAL	1	FALSE	2	0.276296599312411	4		194	134	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885578	111885578	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs751470371	NA	P-0032990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	39	673	0	ENST00000341259.2:c.1355C>G	p.Ala452Gly	p.A452G	ENST00000341259	NM_005475.2	452	gCc/gGc	7/8	0.143425567132697	4	FACETS	0.567	0.469	0.677	0.284	0.234	0.339	INDETERMINATE	1	FALSE	2	0.276296599312411	4		673	635	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466022	69466022	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	67	620	0	ENST00000227507.2:c.860C>A	p.Pro287His	p.P287H	ENST00000227507	NM_053056.2	287	cCc/cAc	5/5	1	2	FACETS	0.951	0.828	1	0.951	0.828	1	CLONAL	1	FALSE	1	0.276296599312411	2		620	510	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180586	56180588	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	rs1357146419	NA	P-0032990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	10	383	0	ENST00000399503.3:c.3918_3920del	p.Ile1307del	p.I1307del	ENST00000399503	NM_005921.1	1305	aaCATc/aac	16/20	1	2	FACETS	0.566	0.385	0.79	0.566	0.385	0.79	SUBCLONAL	1	FALSE	1	0.276296599312411	2		383	128	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864291	57864291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758959112	NA	P-0032990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	34	556	1	ENST00000228682.2:c.1768C>T	p.Arg590Trp	p.R590W	ENST00000228682	NM_005269.2	590	Cgg/Tgg	12/12	0.143425567132697	4	FACETS	0.964	0.789	1	0.482	0.394	0.579	INDETERMINATE	1	FALSE	2	0.276296599312411	4		557	326	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107014	27107014	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	43	432	0	ENST00000324856.7:c.6625C>T	p.Gln2209Ter	p.Q2209*	ENST00000324856	NM_006015.4	2209	Cag/Tag	20/20	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	FALSE	1	0.276296599312411	2		432	304	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229229	36229229	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	66	699	0	ENST00000222270.7:c.7919A>G	p.Asp2640Gly	p.D2640G	ENST00000222270	NM_014727.1	2640	gAc/gGc	37/37	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	FALSE	1	0.276296599312411	2		699	417	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46603752	46603752	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs770217055	NA	P-0032990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	23	598	0	ENST00000263734.3:c.1109T>C	p.Met370Thr	p.M370T	ENST00000263734	NM_001430.4	370	aTg/aCg	9/16	1	2	FACETS	0.474	0.369	0.596	0.474	0.369	0.596	SUBCLONAL	1	FALSE	1	0.276296599312411	2		598	351	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158636870	158636870	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	33	514	0	ENST00000263640.3:c.310A>G	p.Thr104Ala	p.T104A	ENST00000263640	NM_001105.4	104	Acg/Gcg	4/11	1	2	FACETS	0.756	0.617	0.911	0.756	0.617	0.911	CLONAL	1	FALSE	1	0.276296599312411	2		514	316	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422522	225422522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	11	492	0	ENST00000264414.4:c.118G>A	p.Ala40Thr	p.A40T	ENST00000264414	NM_003590.4	40	Gca/Aca	2/16	1	2	FACETS	0.577	0.4	0.794	0.577	0.4	0.794	SUBCLONAL	1	FALSE	1	0.276296599312411	2		492	138	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160701	56160702	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0032990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	40	399	0	ENST00000399503.3:c.977_978del	p.Ser326PhefsTer11	p.S326Ffs*11	ENST00000399503	NM_005921.1	325	aaCTct/aact	4/20	1	2	FACETS	0.852	0.718	0.996	1	0.965	1	CLONAL	2	FALSE	1	0.276296599312411	2		399	170	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449848	149449848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377213618	NA	P-0032990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	46	636	1	ENST00000286301.3:c.1216G>A	p.Val406Ile	p.V406I	ENST00000286301	NM_005211.3	406	Gtc/Atc	9/22	1	2	FACETS	0.845	0.713	0.99	0.845	0.713	0.99	CLONAL	1	FALSE	1	0.276296599312411	2		637	394	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117861195	117861195	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1299225160	NA	P-0032990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	14	435	0	ENST00000297338.2:c.1694A>G	p.His565Arg	p.H565R	ENST00000297338	NM_006265.2	565	cAt/cGt	13/14	1	2	FACETS	0.426	0.308	0.569	0.426	0.308	0.569	SUBCLONAL	1	FALSE	1	0.276296599312411	2		435	238	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402519	139402519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	31	676	1	ENST00000277541.6:c.3398G>A	p.Cys1133Tyr	p.C1133Y	ENST00000277541	NM_017617.3	1133	tGc/tAc	21/34	1	2	FACETS	0.435	0.351	0.53	0.435	0.351	0.53	SUBCLONAL	1	FALSE	1	0.276296599312411	2		677	516	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357049	70357049	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	25	698	0	ENST00000374080.3:c.5564T>C	p.Val1855Ala	p.V1855A	ENST00000374080		1855	gTg/gCg	39/45	1	2	FACETS	0.46	0.362	0.573	0.46	0.362	0.573	SUBCLONAL	1	FALSE	1	0.276296599312411	2		698	393	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193121546	193121546	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	38	262	0	ENST00000367435.3:c.944A>G	p.Tyr315Cys	p.Y315C	ENST00000367435	NM_024529.4	315	tAc/tGc	10/17	0.534338134433185	3	FACETS	1	0.867	1	0.517	0.435	0.606	CLONAL	1	TRUE	1	0.666236552616408	3		262	147	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0032998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	394	582	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.677661045032979	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.677661045032979	2		582	571	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11308151	11308151	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1451713797	NA	P-0032998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	234	359	0	ENST00000361445.4:c.841C>T	p.Arg281Cys	p.R281C	ENST00000361445	NM_004958.3	281	Cgt/Tgt	7/58	0.504269768125669	4	FACETS	0.997	0.938	1	0.997	0.938	1	CLONAL	2	TRUE	2	0.677661045032979	4		359	581	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390713	118390713	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	233	412	0	ENST00000534358.1:c.11363A>T	p.His3788Leu	p.H3788L	ENST00000534358	NM_005933.3	3788	cAt/cTt	33/36	0.677661045032979	2	FACETS	0.971	0.926	1	0.971	0.926	1	CLONAL	2	TRUE	0	0.677661045032979	2		412	354	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631265	117631265	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	140	410	0	ENST00000368508.3:c.6413T>C	p.Phe2138Ser	p.F2138S	ENST00000368508	NM_002944.2	2138	tTc/tCc	40/43	0.677661045032979	2	FACETS	1	0.963	1	0.538	0.495	0.582	CLONAL	1	TRUE	0	0.677661045032979	2		410	384	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029527	14029527	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	29	330	0	ENST00000311895.7:c.1738C>G	p.Leu580Val	p.L580V	ENST00000311895	NM_005236.2	580	Ctt/Gtt	8/11	1	2	FACETS	0.996	0.814	1	0.996	0.814	1	CLONAL	1	TRUE	1	0.481467076526541	2		330	121	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220488	1220488	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	117	506	0	ENST00000326873.7:c.581A>C	p.Asp194Ala	p.D194A	ENST00000326873	NM_000455.4	194	gAc/gCc	4/10	0.481467076526541	2	FACETS	1	0.988	1	1	0.992	1	CLONAL	3	TRUE	0	0.481467076526541	2		506	139	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	26	441	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.767	0.611	0.943	1	0.935	1	CLONAL	2	TRUE	1	0.16	2		441	212	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0033011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	52	491	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.16	2		491	519	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271447	38271447	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	55	586	0	ENST00000425967.3:c.2374A>G	p.Thr792Ala	p.T792A	ENST00000425967	NM_001174067.1	792	Acc/Gcc	18/19	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.16	2		586	635	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041423	47041423	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	68	307	1	ENST00000377604.3:c.1767C>A	p.Tyr589Ter	p.Y589*	ENST00000377604	NM_001204468.1	589	taC/taA	16/24	0.142711641952306	2	FACETS	1	0.916	1			1	CLONAL	3	TRUE	NA	0.16	2		308	269	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0033012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	301	543	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.559530115933582	2	FACETS	0.996	0.951	1	0.996	0.951	1	CLONAL	2	TRUE	0	0.559530115933582	2		543	540	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223193	36223193	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471456268	NA	P-0033012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	775	736	0	ENST00000222270.7:c.5743C>T	p.Arg1915Cys	p.R1915C	ENST00000222270	NM_014727.1	1915	Cgt/Tgt	28/37	0.559530115933582	7	FACETS	0.956	0.926	0.987			1	CLONAL	4	TRUE	NA	0.559530115933582	7		736	1737	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0033012-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	317	543	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.500564142808515	2	FACETS	0.944	0.898	0.99	0.944	0.898	0.99	CLONAL	2	TRUE	0	0.500564142808515	2		543	671	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223193	36223193	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471456268	NA	P-0033012-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	530	736	0	ENST00000222270.7:c.5743C>T	p.Arg1915Cys	p.R1915C	ENST00000222270	NM_014727.1	1915	Cgt/Tgt	28/37	0.500564142808515	5	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.500564142808515	5		736	1601	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0033012-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	29	714	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.164	0.131	0.202	0.164	0.131	0.202	SUBCLONAL	1	TRUE	1	0.500564142808515	2		714	707	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0033012-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	70	533	1	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	0.393	0.342	0.448	0.393	0.342	0.448	SUBCLONAL	1	TRUE	1	0.500564142808515	2		534	712	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183787	10183787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123481	NA	P-0033013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	222	550	2	ENST00000256474.2:c.256C>T	p.Pro86Ser	p.P86S	ENST00000256474	NM_000551.3	86	Ccc/Tcc	1/3	0.783459376781632	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.783459376781632	1		552	343	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508614	106508614	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377001952	NA	P-0033013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	147	398	0	ENST00000359195.3:c.608C>T	p.Thr203Met	p.T203M	ENST00000359195	NM_002649.2	203	aCg/aTg	2/11	1	2	FACETS	0.977	0.903	1	0.977	0.903	1	CLONAL	1	TRUE	1	0.783459376781632	2		398	384	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405201	139405201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767886377	NA	P-0033013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	268	669	1	ENST00000277541.6:c.2644G>A	p.Ala882Thr	p.A882T	ENST00000277541	NM_017617.3	882	Gca/Aca	17/34	0.783459376781632	1	FACETS	0.959	0.915	1	0.959	0.915	1	CLONAL	1	TRUE	0	0.783459376781632	1		670	434	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443870	52443870	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	208	645	0	ENST00000460680.1:c.25G>T	p.Glu9Ter	p.E9*	ENST00000460680	NM_004656.3	9	Gag/Tag	1/17	0.783459376781632	1	FACETS	0.982	0.932	1	0.982	0.932	1	CLONAL	1	TRUE	0	0.783459376781632	1		645	329	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442863	187442863	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	109	273	0	ENST00000232014.4:c.1843G>T	p.Ala615Ser	p.A615S	ENST00000232014	NM_001130845.1	615	Gcc/Tcc	9/10	0.738386190784376	3	FACETS	1	0.949	1	0.535	0.485	0.587	CLONAL	1	TRUE	1	0.783459376781632	3		273	362	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631253	117631253	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	115	464	0	ENST00000368508.3:c.6425C>A	p.Ser2142Tyr	p.S2142Y	ENST00000368508	NM_002944.2	2142	tCt/tAt	40/43	1	2	FACETS	0.903	0.824	0.984	0.903	0.824	0.984	CLONAL	1	TRUE	1	0.783459376781632	2		464	325	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194620	29194620	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	272	734	0	ENST00000240100.2:c.1108G>C	p.Val370Leu	p.V370L	ENST00000240100	NM_001394.6	370	Gtc/Ctc	4/4	0.783459376781632	1	FACETS	0.953	0.91	0.996	0.953	0.91	0.996	CLONAL	1	TRUE	0	0.783459376781632	1		734	443	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738964	145738964	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	566	564	1	ENST00000428558.2:c.2191G>T	p.Gly731Trp	p.G731W	ENST00000428558	NM_004260.3	731	Ggg/Tgg	13/22	0.646786328822863	4	FACETS	1	0.987	1			1	CLONAL	3	TRUE	NA	0.783459376781632	4		565	836	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183787	10183787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123481	NA	P-0033013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	79	550	2	ENST00000256474.2:c.256C>T	p.Pro86Ser	p.P86S	ENST00000256474	NM_000551.3	86	Ccc/Tcc	1/3	0.582141731996453	1	FACETS	0.91	0.82	1	0.91	0.82	1	CLONAL	1	TRUE	0	0.638539302102539	1		552	185	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443870	52443870	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	84	645	0	ENST00000460680.1:c.25G>T	p.Glu9Ter	p.E9*	ENST00000460680	NM_004656.3	9	Gag/Tag	1/17	0.582141731996453	1	FACETS	0.782	0.703	0.864	0.782	0.703	0.864	SUBCLONAL	1	TRUE	0	0.638539302102539	1		645	229	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631253	117631253	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	37	464	0	ENST00000368508.3:c.6425C>A	p.Ser2142Tyr	p.S2142Y	ENST00000368508	NM_002944.2	2142	tCt/tAt	40/43	0.235753219180357	3	FACETS	0.974	0.815	1	0.487	0.407	0.573	INDETERMINATE	1	TRUE	1	0.638539302102539	3		464	157	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194620	29194620	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	68	734	0	ENST00000240100.2:c.1108G>C	p.Val370Leu	p.V370L	ENST00000240100	NM_001394.6	370	Gtc/Ctc	4/4	0.638539302102539	1	FACETS	0.853	0.759	0.949	0.853	0.759	0.949	CLONAL	1	TRUE	0	0.638539302102539	1		734	170	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738964	145738964	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	117	564	1	ENST00000428558.2:c.2191G>T	p.Gly731Trp	p.G731W	ENST00000428558	NM_004260.3	731	Ggg/Tgg	13/22	0.638539302102539	3	FACETS	0.876	0.804	0.949	0.876	0.804	0.949	CLONAL	2	TRUE	1	0.638539302102539	3		565	276	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265353	152265353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188957694	NA	P-0033013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	69	455	0	ENST00000206249.3:c.806G>A	p.Arg269His	p.R269H	ENST00000206249	NM_000125.3	269	cGc/cAc	4/8	0.235753219180357	3	FACETS	1	0.97	1	0.663	0.587	0.742	INDETERMINATE	1	TRUE	1	0.638539302102539	3		455	215	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0033014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16123	5606	715	1	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.921379310489203	26	FACETS	0.965	0.951	0.978			1	CLONAL	7	TRUE	NA	0.921379310489203	26		716	21729	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456310	32456310	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	190	628	0	ENST00000332351.3:c.582G>C	p.Arg194Ser	p.R194S	ENST00000332351	NM_024426.4	194	agG/agC	1/10	1	2	FACETS	0.596	0.551	0.642	0.596	0.551	0.642	SUBCLONAL	1	TRUE	1	0.753358477954428	2		628	847	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656255	18656255	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	150	433	0	ENST00000266497.5:c.2934G>T	p.Lys978Asn	p.K978N	ENST00000266497		978	aaG/aaT	21/31	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.753358477954428	2		433	371	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448574	89448574	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	35	498	0	ENST00000336596.2:c.1538C>G	p.Thr513Arg	p.T513R	ENST00000336596	NM_005233.5	513	aCa/aGa	7/17	1	2	FACETS	0.145	0.118	0.175	0.145	0.118	0.175	SUBCLONAL	1	TRUE	1	0.753358477954428	2		498	642	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178199	142178199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746049210	NA	P-0033018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	74	270	0	ENST00000350721.4:c.7219C>T	p.Arg2407Cys	p.R2407C	ENST00000350721	NM_001184.3	2407	Cgc/Tgc	43/47	1	2	FACETS	0.854	0.754	0.959	0.854	0.754	0.959	CLONAL	1	TRUE	1	0.545063735642143	2		270	318	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748093	43748093	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	143	408	0	ENST00000382044.4:c.2713A>G	p.Ser905Gly	p.S905G	ENST00000382044	NM_001141980.1	905	Agt/Ggt	12/28	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.545063735642143	2		408	517	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644474	3644474	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	158	623	0	ENST00000294008.3:c.2140T>G	p.Cys714Gly	p.C714G	ENST00000294008	NM_032444.2	714	Tgc/Ggc	10/15	1	2	FACETS	0.877	0.806	0.951	0.877	0.806	0.951	CLONAL	1	TRUE	1	0.545063735642143	2		623	661	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178199	142178199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746049210	NA	P-0033018-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	79	270	0	ENST00000350721.4:c.7219C>T	p.Arg2407Cys	p.R2407C	ENST00000350721	NM_001184.3	2407	Cgc/Tgc	43/47	0.130914273339489	0	FACETS	0.827	0.737	0.921			1	INDETERMINATE	1	TRUE	0	0.420734109740869	0		270	263	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748093	43748093	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033018-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	73	408	0	ENST00000382044.4:c.2713A>G	p.Ser905Gly	p.S905G	ENST00000382044	NM_001141980.1	905	Agt/Ggt	12/28	0.372551030455759	3	FACETS	0.811	0.718	0.908	0.811	0.718	0.908	CLONAL	2	TRUE	1	0.420734109740869	3		408	259	SUCCESS
YES1	7525	MSKCC	GRCh37	18	732848	732848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755971181	NA	P-0033018-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	39	572	1	ENST00000314574.4:c.1409G>A	p.Arg470Gln	p.R470Q	ENST00000314574	NM_005433.3	470	cGa/cAa	11/12	0.420734109740869	2	FACETS	0.719	0.599	0.85	0.359	0.299	0.425	SUBCLONAL	1	TRUE	0	0.420734109740869	2		573	258	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993094	90993094	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033018-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	32	317	0	ENST00000265433.3:c.348C>G	p.Cys116Trp	p.C116W	ENST00000265433	NM_002485.4	116	tgC/tgG	4/16	0.420734109740869	7	FACETS	0.604	0.489	0.734	0.151	0.122	0.184	SUBCLONAL	1	TRUE	3	0.420734109740869	7		317	517	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115871	8115872	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0033019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	163	535	0	ENST00000346208.3:c.1219_1220del	p.Ser407AlafsTer99	p.S407Afs*99	ENST00000346208		406	aTC/a	6/6	1	2	FACETS	0.999	0.923	1	0.999	0.923	1	CLONAL	1	TRUE	1	0.613602855223874	2		535	532	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968235	2968235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1188731718	NA	P-0033019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	357	586	2	ENST00000396946.4:c.1751G>A	p.Arg584His	p.R584H	ENST00000396946	NM_032415.4	584	cGc/cAc	13/25	0.613602855223874	3	FACETS	0.989	0.943	1	0.989	0.943	1	CLONAL	2	TRUE	1	0.613602855223874	3		588	769	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026811	71026812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0033019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	113	309	0	ENST00000318789.4:c.1409_1410dup	p.Ala471MetfsTer4	p.A471Mfs*4	ENST00000318789	NM_032682.5	470	-/AT	16/21	0.613602855223874	1	FACETS	0.967	0.886	1	0.967	0.886	1	CLONAL	1	TRUE	0	0.613602855223874	1		309	264	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0033022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	47	419	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.745	0.63	0.87	0.745	0.63	0.87	SUBCLONAL	1	TRUE	1	0.343862081971646	2		419	367	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961999	41961999	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	56	534	0	ENST00000219905.7:c.907C>T	p.Gln303Ter	p.Q303*	ENST00000219905	NM_001164273.1	303	Caa/Taa	2/24	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.343862081971646	2		534	310	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593397	48593397	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs377767355	NA	P-0033022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	50	377	0	ENST00000342988.3:c.1148T>C	p.Ile383Thr	p.I383T	ENST00000342988	NM_005359.5	383	aTa/aCa	10/12	0.343862081971646	1	FACETS	0.895	0.766	1	0.895	0.766	1	CLONAL	1	TRUE	0	0.343862081971646	1		377	269	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799159	42799159	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1482360658	NA	P-0033022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	102	496	0	ENST00000575354.2:c.4643C>T	p.Ala1548Val	p.A1548V	ENST00000575354	NM_015125.3	1548	gCc/gTc	20/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.343862081971646	2		496	480	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440897	52440897	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	80	516	0	ENST00000460680.1:c.607A>G	p.Thr203Ala	p.T203A	ENST00000460680	NM_004656.3	203	Aca/Gca	8/17	0.343862081971646	1	FACETS	0.937	0.83	1	0.937	0.83	1	CLONAL	1	TRUE	0	0.343862081971646	1		516	411	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0033023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	75	483	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.374554992989977	7	FACETS	0.727	0.635	0.827	0.182	0.158	0.207	SUBCLONAL	1	FALSE	3	0.374554992989977	7		483	1066	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098953	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	190	311	0	ENST00000397062.3:c.92G>C	p.Gly31Ala	p.G31A	ENST00000397062	NM_006164.4	31	gGa/gCa	2/5	0.299865119062903	4	FACETS	0.874	0.814	0.935			1	CLONAL	3	FALSE	NA	0.374554992989977	4		311	532	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164916	106164916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1361899165	NA	P-0033023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	44	343	0	ENST00000380013.4:c.3784C>T	p.Arg1262Trp	p.R1262W	ENST00000380013	NM_001127208.2	1262	Cgg/Tgg	6/11	0.126803916961086	4	FACETS	0.942	0.792	1	0.471	0.396	0.553	INDETERMINATE	1	FALSE	2	0.374554992989977	4		343	343	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010455	48010455	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	55	315	0	ENST00000234420.5:c.83C>A	p.Ser28Ter	p.S28*	ENST00000234420	NM_000179.2	28	tCa/tAa	1/10	0.35871557095045	4	FACETS	0.762	0.652	0.882	0.381	0.326	0.441	SUBCLONAL	1	FALSE	2	0.374554992989977	4		315	530	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004574	16004574	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	47	394	1	ENST00000268712.3:c.2680G>A	p.Glu894Lys	p.E894K	ENST00000268712	NM_006311.3	894	Gag/Aag	20/46	0.374554992989977	1	FACETS	0.526	0.444	0.615	0.526	0.444	0.615	SUBCLONAL	1	FALSE	0	0.374554992989977	1		395	388	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877084	151877084	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	45	467	0	ENST00000262189.6:c.7277A>G	p.Glu2426Gly	p.E2426G	ENST00000262189	NM_170606.2	2426	gAg/gGg	37/59	0.374554992989977	3	FACETS	0.482	0.404	0.568	0.241	0.202	0.284	SUBCLONAL	1	FALSE	1	0.374554992989977	3		467	592	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257690	16257690	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0033023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	105	433	0	ENST00000375759.3:c.4955C>G	p.Ser1652Ter	p.S1652*	ENST00000375759	NM_015001.2	1652	tCa/tGa	11/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.374554992989977	2		433	459	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941233	36941233	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	133	596	0	ENST00000361632.4:c.106G>T	p.Val36Phe	p.V36F	ENST00000361632		36	Gtc/Ttc	3/16	0.374554992989977	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	0	0.374554992989977	1		596	497	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246498772	246498772	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	64	463	0	ENST00000388985.4:c.233A>T	p.Lys78Ile	p.K78I	ENST00000388985		78	aAa/aTa	3/12	0.35871557095045	4	FACETS	0.566	0.489	0.65	0.283	0.244	0.325	SUBCLONAL	1	FALSE	2	0.374554992989977	4		463	830	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200084	67200084	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	61	497	0	ENST00000312629.5:c.471C>A	p.Phe157Leu	p.F157L	ENST00000312629	NM_003952.2	157	ttC/ttA	6/15	0.113535733398867	3	FACETS	0.571	0.492	0.657	0.286	0.246	0.329	INDETERMINATE	1	FALSE	1	0.374554992989977	3		497	677	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631131	69631131	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	113	602	0	ENST00000334134.2:c.281G>T	p.Gly94Val	p.G94V	ENST00000334134	NM_005247.2	94	gGg/gTg	2/3	0.113535733398867	3	FACETS	1	0.965	1	0.577	0.52	0.637	INDETERMINATE	1	FALSE	1	0.374554992989977	3		602	621	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579461	7579462	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	112	621	1	ENST00000269305.4:c.225dup	p.Ala76CysfsTer73	p.A76Cfs*73	ENST00000269305	NM_001126112.2	75	-/T	4/11	0.374554992989977	1	FACETS	0.921	0.831	1	0.921	0.831	1	CLONAL	1	FALSE	0	0.374554992989977	1		622	528	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626850	14626850	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs749934387	NA	P-0033023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	85	691	0	ENST00000254322.2:c.925G>C	p.Glu309Gln	p.E309Q	ENST00000254322	NM_006145.1	309	Gag/Cag	3/3	0.374554992989977	5	FACETS	0.723	0.638	0.815	0.241	0.212	0.272	SUBCLONAL	1	FALSE	2	0.374554992989977	5		691	980	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297919	15297919	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	444	606	1	ENST00000263388.2:c.1837A>T	p.Thr613Ser	p.T613S	ENST00000263388	NM_000435.2	613	Aca/Tca	11/33	0.374554992989977	5	FACETS	0.911	0.873	0.95	1	0.994	1	CLONAL	4	FALSE	2	0.374554992989977	5		607	1016	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299079	15299079	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	76	545	0	ENST00000263388.2:c.1459C>G	p.Arg487Gly	p.R487G	ENST00000263388	NM_000435.2	487	Cga/Gga	9/33	0.374554992989977	5	FACETS	0.654	0.572	0.743	0.218	0.19	0.248	SUBCLONAL	1	FALSE	2	0.374554992989977	5		545	969	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952229	17952229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	62	623	0	ENST00000458235.1:c.1111G>A	p.Glu371Lys	p.E371K	ENST00000458235	NM_000215.3	371	Gaa/Aaa	8/24	0.345324640321897	1	FACETS	0.47	0.406	0.54	0.47	0.406	0.54	SUBCLONAL	1	FALSE	0	0.374554992989977	1		623	572	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466819	25466819	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	61	536	0	ENST00000264709.3:c.1884del	p.Glu629ArgfsTer22	p.E629Rfs*22	ENST00000264709	NM_175629.2	628	gcT/gc	16/23	NA	2	FACETS	0.524	0.451	0.602			1	INDETERMINATE	1	FALSE	NA	0.374554992989977	2		536	622	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056417	180056417	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1164739687	NA	P-0033023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	41	437	0	ENST00000261937.6:c.827G>T	p.Gly276Val	p.G276V	ENST00000261937	NM_182925.4	276	gGt/gTt	7/30	NA	2	FACETS	0.501	0.417	0.594			1	INDETERMINATE	1	FALSE	NA	0.374554992989977	2		437	437	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045874	26045874	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	120	425	0	ENST00000540144.1:c.236T>A	p.Phe79Tyr	p.F79Y	ENST00000540144	NM_003531.2	79	tTc/tAc	1/1	0.113535733398867	3	FACETS	1	0.98	1	0.657	0.595	0.722	INDETERMINATE	1	FALSE	1	0.374554992989977	3		425	579	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271255	26271255	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs756096962	NA	P-0033023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	112	478	0	ENST00000305910.3:c.358A>G	p.Ile120Val	p.I120V	ENST00000305910	NM_003534.2	120	Atc/Gtc	1/1	0.113535733398867	3	FACETS	1	0.977	1	0.637	0.575	0.703	INDETERMINATE	1	FALSE	1	0.374554992989977	3		478	557	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188304	32188304	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1260037526	NA	P-0033023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	132	688	1	ENST00000375023.3:c.1037G>T	p.Gly346Val	p.G346V	ENST00000375023	NM_004557.3	346	gGc/gTc	6/30	1	2	FACETS	0.944	0.857	1	0.944	0.857	1	CLONAL	1	FALSE	1	0.374554992989977	2		689	747	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555194	106555194	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	48	449	0	ENST00000369096.4:c.2311G>T	p.Gly771Cys	p.G771C	ENST00000369096	NM_001198.3	771	Ggc/Tgc	7/7	0.139547802195339	0	FACETS	0.345	0.291	0.403			1	INDETERMINATE	1	FALSE	0	0.374554992989977	0		449	465	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962373	2962373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560138497	NA	P-0033023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	155	648	0	ENST00000396946.4:c.2164G>A	p.Glu722Lys	p.E722K	ENST00000396946	NM_032415.4	722	Gag/Aag	17/25	0.126803916961086	4	FACETS	0.82	0.752	0.89	0.82	0.752	0.89	INDETERMINATE	2	FALSE	2	0.374554992989977	4		648	694	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455101	50455101	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	117	282	0	ENST00000331340.3:c.648A>T	p.Leu216Phe	p.L216F	ENST00000331340	NM_006060.4	216	ttA/ttT	6/8	0.126803916961086	4	FACETS	1	0.916	1	1	0.916	1	INDETERMINATE	2	FALSE	2	0.374554992989977	4		282	426	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332052	81332052	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	35	260	1	ENST00000222390.5:c.2032G>T	p.Val678Phe	p.V678F	ENST00000222390	NM_000601.4	678	Gtt/Ttt	18/18	0.374554992989977	3	FACETS	0.57	0.468	0.685	0.285	0.234	0.343	SUBCLONAL	1	FALSE	1	0.374554992989977	3		261	389	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859492	151859492	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	64	501	0	ENST00000262189.6:c.11170G>C	p.Glu3724Gln	p.E3724Q	ENST00000262189	NM_170606.2	3724	Gag/Cag	43/59	0.374554992989977	3	FACETS	0.65	0.563	0.745	0.325	0.281	0.373	SUBCLONAL	1	FALSE	1	0.374554992989977	3		501	624	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945357	151945357	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	42	217	0	ENST00000262189.6:c.2162A>T	p.Gln721Leu	p.Q721L	ENST00000262189	NM_170606.2	721	cAa/cTa	14/59	0.374554992989977	3	FACETS	1	0.887	1	0.535	0.45	0.628	CLONAL	1	FALSE	1	0.374554992989977	3		217	249	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117870603	117870603	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	118	314	0	ENST00000297338.2:c.469G>C	p.Glu157Gln	p.E157Q	ENST00000297338	NM_006265.2	157	Gaa/Caa	5/14	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.374554992989977	2		314	445	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285787	87285787	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	135	588	0	ENST00000277120.3:c.124C>G	p.Arg42Gly	p.R42G	ENST00000277120		42	Cgg/Ggg	2/19	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.374554992989977	2		588	585	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931926	39931926	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	148	675	0	ENST00000378444.4:c.2673C>A	p.Asn891Lys	p.N891K	ENST00000378444	NM_001123385.1	891	aaC/aaA	4/15	0.113535733398867	3	FACETS	1	0.977	1	0.599	0.548	0.653	INDETERMINATE	1	FALSE	1	0.374554992989977	3		675	783	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224583	123224583	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	111	486	1	ENST00000218089.9:c.3436A>T	p.Thr1146Ser	p.T1146S	ENST00000218089	NM_001042749.1	1146	Act/Tct	31/35	0.126803916961086	4	FACETS	1	0.964	1	0.578	0.52	0.639	INDETERMINATE	1	FALSE	2	0.374554992989977	4		487	705	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224762	123224762	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	114	556	0	ENST00000218089.9:c.3526G>A	p.Glu1176Lys	p.E1176K	ENST00000218089	NM_001042749.1	1176	Gag/Aag	32/35	0.126803916961086	4	FACETS	1	0.973	1	0.614	0.554	0.678	INDETERMINATE	1	FALSE	2	0.374554992989977	4		556	681	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498428	89498428	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	102	400	0	ENST00000336596.2:c.2400G>T	p.Lys800Asn	p.K800N	ENST00000336596	NM_005233.5	800	aaG/aaT	14/17	0.180801648436645	4	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	2	0.21	4		400	561	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101353	27101353	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	133	554	0	ENST00000324856.7:c.4635G>T	p.Trp1545Cys	p.W1545C	ENST00000324856	NM_006015.4	1545	tgG/tgT	18/20	0.212690104684374	3	FACETS	0.838	0.761	0.919	0.838	0.761	0.919	CLONAL	2	TRUE	1	0.21	3		554	835	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5225780	5225780	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	237	636	0	ENST00000357368.4:c.2452G>C	p.Gly818Arg	p.G818R	ENST00000357368	NM_002850.3	818	Ggc/Cgc	17/38	0.180801648436645	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.21	4		636	1119	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262542	39262542	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	64	420	0	ENST00000402219.2:c.964C>A	p.Leu322Ile	p.L322I	ENST00000402219	NM_005633.3	322	Ctt/Att	7/23	0.150590966947243	4	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	2	0.21	4		420	313	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812302	212812302	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	95	310	0	ENST00000342788.4:c.274A>G	p.Asn92Asp	p.N92D	ENST00000342788	NM_005235.2	92	Aat/Gat	3/28	0.150590966947243	4	FACETS	0.835	0.748	0.927	1	0.971	1	CLONAL	3	TRUE	2	0.21	4		310	437	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183817	10183826	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCCCTACC	CAGCCCTACC	-	novel	NA	P-0033032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	140	599	0	ENST00000256474.2:c.288_297del	p.Pro97ArgfsTer59	p.P97Rfs*59	ENST00000256474	NM_000551.3	96	CAGCCCTACCca/ca	1/3	0.291243276174156	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.21	2		599	601	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162045	47162045	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	154	452	1	ENST00000409792.3:c.4081C>T	p.Gln1361Ter	p.Q1361*	ENST00000409792	NM_014159.6	1361	Cag/Tag	3/21	0.291243276174156	2	FACETS	0.986	0.909	1	1	0.989	1	CLONAL	3	TRUE	0	0.21	2		453	496	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931382	131931382	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	161	462	0	ENST00000265335.6:c.2087A>T	p.Glu696Val	p.E696V	ENST00000265335		696	gAa/gTa	13/25	0.3	5	FACETS	1	0.973	1	0.759	0.696	0.824	CLONAL	2	TRUE	2	0.21	5		462	886	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391944	139391944	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	159	846	0	ENST00000277541.6:c.6247C>G	p.His2083Asp	p.H2083D	ENST00000277541	NM_017617.3	2083	Cac/Gac	34/34	1	2	FACETS	0.815	0.747	0.886	1	0.99	1	CLONAL	2	TRUE	1	0.21	2		846	929	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53253947	53253947	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	138	210	0	ENST00000375401.3:c.125G>T	p.Gly42Val	p.G42V	ENST00000375401	NM_004187.3	42	gGc/gTc	1/26	0.3	2	FACETS	1	0.971	1			1	CLONAL	3	TRUE	NA	0.21	2		210	391	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0033033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	137	594	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.951	0.871	1	0.951	0.871	1	CLONAL	1	TRUE	1	0.606705522817241	2		594	475	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958228	11958228	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	188	331	0	ENST00000353533.5:c.138del	p.Asn47IlefsTer15	p.N47Ifs*15	ENST00000353533	NM_003010.3	46	ttG/tt	2/11	0.597139340935644	2	FACETS	0.956	0.902	1	0.956	0.902	1	CLONAL	2	TRUE	0	0.606705522817241	2		331	324	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411522	63411522	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	222	724	0	ENST00000330258.3:c.1645del	p.Arg549GlyfsTer13	p.R549Gfs*13	ENST00000330258	NM_152424.3	549	Cgg/gg	2/2	0.66932661038607	1	FACETS	0.83	0.779	0.88	0.83	0.779	0.88	CLONAL	1	TRUE	0	0.669320576015948	1		724	532	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115751	8115751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	76	376	0	ENST00000346208.3:c.1097G>A	p.Arg366Gln	p.R366Q	ENST00000346208		366	cGa/cAa	6/6	0.263822170920686	1	FACETS	0.643	0.565	0.725	0.643	0.565	0.725	SUBCLONAL	1	TRUE	0	0.391493613688856	1		376	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0033038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	360	663	0	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	0.328926671066528	3	FACETS	0.881	0.84	0.922	0.881	0.84	0.922	CLONAL	3	TRUE	0	0.423175078473543	3		663	780	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907047	101907047	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0033038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	80	382	0	ENST00000374994.4:c.1007C>G	p.Ser336Ter	p.S336*	ENST00000374994	NM_004612.2	336	tCa/tGa	6/9	0.39162676919016	2	FACETS	1	0.979	1	0.733	0.654	0.815	CLONAL	1	TRUE	0	0.423175078473543	2		382	258	SUCCESS
RET	5979	MSKCC	GRCh37	10	43614987	43614987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1364361946	NA	P-0033038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	76	582	0	ENST00000355710.3:c.2401C>T	p.Leu801Phe	p.L801F	ENST00000355710	NM_020975.4	801	Ctc/Ttc	14/20	1	2	FACETS	0.883	0.778	0.994	0.883	0.778	0.994	CLONAL	1	TRUE	1	0.423175078473543	2		582	407	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695760	117695760	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	122	488	0	ENST00000369458.3:c.677T>C	p.Met226Thr	p.M226T	ENST00000369458	NM_024626.3	226	aTg/aCg	4/6	0.345194569848698	2	FACETS	0.853	0.781	0.927	0.853	0.781	0.927	CLONAL	2	TRUE	0	0.423175078473543	2		488	338	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166100	118166100	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	26	407	0	ENST00000369448.3:c.610G>C	p.Glu204Gln	p.E204Q	ENST00000369448	NM_017709.3	204	Gag/Cag	2/2	0.345194569848698	2	FACETS	0.339	0.268	0.419	0.169	0.134	0.21	SUBCLONAL	1	TRUE	0	0.423175078473543	2		407	363	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658640	206658640	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	36	464	0	ENST00000367120.3:c.1613G>C	p.Arg538Thr	p.R538T	ENST00000367120	NM_014002.3	538	aGa/aCa	15/22	0.310019454992102	3	FACETS	0.454	0.373	0.545	0.151	0.124	0.182	SUBCLONAL	1	TRUE	0	0.423175078473543	3		464	454	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426790	121426790	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	123	524	1	ENST00000257555.6:c.481G>T	p.Ala161Ser	p.A161S	ENST00000257555		161	Gcc/Tcc	2/10	0.1387395387672	4	FACETS	0.752	0.683	0.824	0.752	0.683	0.824	INDETERMINATE	2	TRUE	2	0.423175078473543	4		525	550	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781797	3781797	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	129	528	0	ENST00000262367.5:c.4870A>G	p.Thr1624Ala	p.T1624A	ENST00000262367	NM_004380.2	1624	Acc/Gcc	29/31	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.423175078473543	2		528	573	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81892744	81892744	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	116	456	1	ENST00000359376.3:c.455C>T	p.Ser152Phe	p.S152F	ENST00000359376	NM_002661.3	152	tCt/tTt	5/33	0.212746961848667	5	FACETS	1	0.915	1	0.673	0.61	0.738	INDETERMINATE	2	TRUE	2	0.423175078473543	5		457	444	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56912085	56912085	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	102	662	0	ENST00000519728.1:c.1313C>A	p.Thr438Asn	p.T438N	ENST00000519728	NM_002350.3	438	aCc/aAc	12/13	0.423175078473543	4	FACETS	0.718	0.641	0.801			1	SUBCLONAL	1	TRUE	NA	0.423175078473543	4		662	955	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0033041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	77	474	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.788	0.694	0.888	1	0.978	1	SUBCLONAL	2	TRUE	1	0.206697818811768	2		474	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0033041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	73	513	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.965	0.843	1	0.965	0.843	1	CLONAL	1	TRUE	1	0.206697818811768	2		513	732	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501279	140501279	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs397516905	NA	P-0033041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	19	393	0	ENST00000288602.6:c.793G>C	p.Gly265Arg	p.G265R	ENST00000288602	NM_004333.4	265	Ggt/Cgt	6/18	1	2	FACETS	0.521	0.395	0.67	0.521	0.395	0.67	SUBCLONAL	1	TRUE	1	0.206697818811768	2		393	353	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343512	343512	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	46	786	0	ENST00000262320.3:c.2162C>G	p.Ala721Gly	p.A721G	ENST00000262320	NM_003502.3	721	gCc/gGc	8/11	1	2	FACETS	0.597	0.502	0.704	0.597	0.502	0.704	SUBCLONAL	1	TRUE	1	0.206697818811768	2		786	745	SUCCESS
APC	324	MSKCC	GRCh37	5	112174337	112174337	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	17	284	0	ENST00000257430.4:c.3046G>C	p.Asp1016His	p.D1016H	ENST00000257430	NM_000038.5	1016	Gat/Cat	16/16	1	2	FACETS	0.594	0.443	0.773	0.594	0.443	0.773	SUBCLONAL	1	TRUE	1	0.206697818811768	2		284	277	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036949	180036949	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	140	522	0	ENST00000261937.6:c.3763T>G	p.Phe1255Val	p.F1255V	ENST00000261937	NM_182925.4	1255	Ttt/Gtt	28/30	0.460285824498115	1	FACETS	0.922	0.845	1	0.922	0.845	1	CLONAL	1	TRUE	0	0.460285824498115	1		522	508	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206661310	206661310	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	113	418	0	ENST00000367120.3:c.1676A>T	p.Lys559Met	p.K559M	ENST00000367120	NM_014002.3	559	aAg/aTg	16/22	NA	2	FACETS	0.919	0.831	1			1	INDETERMINATE	1	TRUE	NA	0.460285824498115	2		418	534	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217003	7217003	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	95	420	0	ENST00000380728.2:c.518G>C	p.Gly173Ala	p.G173A	ENST00000380728		173	gGg/gCg	7/11	0.460285824498115	2	FACETS	0.803	0.717	0.894	0.402	0.358	0.447	CLONAL	1	TRUE	0	0.460285824498115	2		420	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578261	7578262	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGGA	novel	NA	P-0033055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	271	507	0	ENST00000269305.4:c.584_587dup	p.Val197ProfsTer13	p.V197Pfs*13	ENST00000269305	NM_001126112.2	196	cga/cgTCCGa	6/11	0.460285824498115	2	FACETS	0.884	0.835	0.933	0.884	0.835	0.933	CLONAL	2	TRUE	0	0.460285824498115	2		507	666	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538298	9538298	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	143	465	0	ENST00000353224.5:c.1700G>C	p.Arg567Thr	p.R567T	ENST00000353224	NM_177990.2	567	aGg/aCg	7/10	1	2	FACETS	0.988	0.904	1	0.988	0.904	1	CLONAL	1	TRUE	1	0.460285824498115	2		465	629	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0033060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	117	280	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	0.439152766615404	2		280	483	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0033060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	121	444	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.13264431501674	0	FACETS	0.541	0.491	0.594			1	INDETERMINATE	1	TRUE	0	0.439152766615404	0		444	571	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0033060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	19	474	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.13264431501674	0	FACETS	0.086	0.064	0.111			1	INDETERMINATE	1	TRUE	0	0.439152766615404	0		474	567	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0033060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	95	320	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.981	0.878	1	0.981	0.878	1	CLONAL	1	TRUE	1	0.439152766615404	2		320	441	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625218	69625218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1168737490	NA	P-0033060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	162	634	0	ENST00000334134.2:c.575G>A	p.Arg192Gln	p.R192Q	ENST00000334134	NM_005247.2	192	cGg/cAg	3/3	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.439152766615404	2		634	670	SUCCESS
APC	324	MSKCC	GRCh37	5	112174094	112174095	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs863225332	NA	P-0033060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	113	333	0	ENST00000257430.4:c.2804dup	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	tac/tAac	16/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.439152766615404	2		333	468	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805351	89805351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149851163	NA	P-0033060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	174	492	0	ENST00000389301.3:c.4199G>A	p.Arg1400His	p.R1400H	ENST00000389301	NM_000135.2	1400	cGt/cAt	42/43	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.439152766615404	2		492	792	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95596505	95596505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745802492	NA	P-0033060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	62	289	0	ENST00000393063.1:c.463G>A	p.Ala155Thr	p.A155T	ENST00000393063	NM_030621.3	155	Gcc/Acc	6/28	1	2	FACETS	0.807	0.701	0.92	0.807	0.701	0.92	CLONAL	1	TRUE	1	0.439152766615404	2		289	350	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57567412	57567412	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0033064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	239	338	0	ENST00000316660.6:c.3G>A	p.Met1?	p.M1?	ENST00000316660	NM_021127.2	1	atG/atA	1/2	0.704891947922725	2	FACETS	0.901	0.859	0.943	0.901	0.859	0.943	CLONAL	2	TRUE	0	0.707215222825007	2		338	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	59	468	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.226027385585492	2	FACETS	1	0.944	1	0.594	0.512	0.682	CLONAL	1	TRUE	0	0.23	2		468	432	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030613	48030613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779617676	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	75	534	0	ENST00000234420.5:c.3227G>A	p.Arg1076His	p.R1076H	ENST00000234420	NM_000179.2	1076	cGc/cAc	5/10	0.3	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.23	1		534	482	SUCCESS
BTK	695	MSKCC	GRCh37	X	100625055	100625055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	28	262	0	ENST00000308731.7:c.322G>A	p.Glu108Lys	p.E108K	ENST00000308731	NM_000061.2	108	Gaa/Aaa	5/19	1	1	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	0	0.23	1		262	173	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058569	69058569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	21	717	0	ENST00000288368.4:c.4213C>T	p.Pro1405Ser	p.P1405S	ENST00000288368	NM_024870.2	1405	Cct/Tct	34/40	1	2	FACETS	0.992	0.769	1	0.992	0.769	1	CLONAL	1	TRUE	1	0.23	2		717	184	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802635	135802635	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203343	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	59	493	1	ENST00000298552.3:c.163C>T	p.Gln55Ter	p.Q55*	ENST00000298552	NM_001162426.1	55	Cag/Tag	4/23	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.23	2		494	434	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406306	70406306	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752696543	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	50	607	0	ENST00000373644.4:c.3820G>A	p.Gly1274Arg	p.G1274R	ENST00000373644	NM_030625.2	1274	Ggg/Agg	4/12	0.177873963156565	3	FACETS	1	0.952	1	0.655	0.558	0.761	CLONAL	1	TRUE	1	0.23	3		607	370	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809766	36809766	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	75	552	0	ENST00000373129.3:c.839A>T	p.Gln280Leu	p.Q280L	ENST00000373129	NM_032017.1	280	cAg/cTg	9/12	1	2	FACETS	0.908	0.801	1	1	0.982	1	CLONAL	2	TRUE	1	0.23	2		552	359	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226589943	226589943	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	64	506	0	ENST00000366794.5:c.258G>C	p.Lys86Asn	p.K86N	ENST00000366794	NM_001618.3	86	aaG/aaC	2/23	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.23	2		506	444	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333970	70333971	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	22	346	0	ENST00000373644.4:c.1875_1876delinsTT	p.Glu625_Glu626delinsAspTer	p.E625_E626delinsD*	ENST00000373644	NM_030625.2	625	gaGGag/gaTTag	2/12	0.177873963156565	3	FACETS	0.931	0.724	1	0.466	0.362	0.585	CLONAL	1	TRUE	1	0.23	3		346	229	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	35	551	0	ENST00000371953.3:c.511C>G	p.Gln171Glu	p.Q171E	ENST00000371953	NM_000314.4	171	Cag/Gag	6/9	0.3	1	FACETS	0.88	0.732	1	1	0.961	1	CLONAL	2	TRUE	0	0.23	1		551	153	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446701	49446701	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	51	499	0	ENST00000301067.7:c.1109G>T	p.Ser370Ile	p.S370I	ENST00000301067	NM_003482.3	370	aGc/aTc	8/54	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.23	2		499	394	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888153	112888153	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	35	666	0	ENST00000351677.2:c.169C>G	p.Gln57Glu	p.Q57E	ENST00000351677	NM_002834.3	57	Cag/Gag	3/16	1	2	FACETS	0.845	0.694	1	0.845	0.694	1	CLONAL	1	TRUE	1	0.23	2		666	360	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233778	133233778	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	48	680	0	ENST00000320574.5:c.3526G>A	p.Asp1176Asn	p.D1176N	ENST00000320574	NM_006231.2	1176	Gat/Aat	29/49	1	2	FACETS	0.82	0.693	0.96	0.82	0.693	0.96	CLONAL	1	TRUE	1	0.23	2		680	509	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911961	32911961	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	36	588	0	ENST00000380152.3:c.3469G>C	p.Glu1157Gln	p.E1157Q	ENST00000380152		1157	Gag/Cag	11/27	0.3	1	FACETS	0.894	0.737	1	0.894	0.737	1	CLONAL	1	TRUE	0	0.23	1		588	310	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951087	48951087	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	23	348	0	ENST00000267163.4:c.1252del	p.Arg418GlufsTer2	p.R418Efs*2	ENST00000267163	NM_000321.2	417	Aaa/aa	13/27	0.3	1	FACETS	0.885	0.704	1	1	0.943	1	CLONAL	2	TRUE	0	0.23	1		348	100	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639152	3639152	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	70	634	0	ENST00000294008.3:c.4487G>C	p.Gly1496Ala	p.G1496A	ENST00000294008	NM_032444.2	1496	gGc/gCc	12/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.23	2		634	439	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857650	9857650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	50	484	0	ENST00000330684.3:c.3751G>A	p.Asp1251Asn	p.D1251N	ENST00000330684	NM_001134407.1	1251	Gac/Aac	13/13	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.23	2		484	368	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632742	23632742	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs183489969	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	34	628	0	ENST00000261584.4:c.3054G>T	p.Glu1018Asp	p.E1018D	ENST00000261584	NM_024675.3	1018	gaG/gaT	10/13	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.23	2		628	274	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032469	12032469	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	34	432	0	ENST00000353533.5:c.905C>T	p.Thr302Ile	p.T302I	ENST00000353533	NM_003010.3	302	aCa/aTa	9/11	0.226027385585492	2	FACETS	1	0.94	1	0.688	0.566	0.822	CLONAL	1	TRUE	0	0.23	2		432	215	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29422349	29422349	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	65	485	0	ENST00000356175.3:c.22G>T	p.Glu8Ter	p.E8*	ENST00000356175	NM_000267.3	8	Gaa/Taa	1/57	0.226027385585492	2	FACETS	0.805	0.702	0.915	0.805	0.702	0.915	CLONAL	2	TRUE	0	0.23	2		485	351	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30314520	30315411	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTGTCAGTGAAACTGAGAGAAGTCAAAGAAAATTACTAATTGAAAAGCTGTTCAATTTACAAAAAAAAAAGTAATTGGTCACCTAAGAGCAAAGGTTGCATGCTGGTGGGCTTTGGGTACCACAATTTTATTTTTAAGACATTTCAAGGCCAGGCGTGGTGGCTCATGCCTGTAACCCCAGCACTTTGGGAGGCCGAGGCAGGCAAATCACCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAAGATGATGAAACCCCGTCTCTACTAAAAACACACACACAAAAAATTAGCTGGGCGTGACGGCAGGTGCCTGTAATCCCAGCTACTTGGGAGGCTGAGACAGGAGAATTGCTTGAACCTGGGAGGGGGAGGTTGCAGTGAGCTGAGACCATGCCAGTTGCACACTAGCCTGGGCGACAAGAGTGAAACTCCATCTCAAAAAAAAAAAAAGACATTTGAACTGGTTAGCAACAACCTAAATGGGAAATTTTCCCATGATAACTTTGATTTCTGACCTATTTGGAAAAATCTGAAAATCTGTCTGTGTTGGACGAGTGTTTTCACATGGCAACAATTCACCTGTTGCTGATCAGTGGTCGCCTCTTTTAGACAGCCTGTGCTCTCCAGTTCAAGTTCTACAGTGTCTGGTCCATACTTTTACTTTGTTTGCCTAGCCGTCTCAGTCAGCATTTGGATTTTCAAGACAAATCTATTAAGGCAAATCCACATTGACTTATAATGAATTTTTTTTAATTTCTACAATTTATTTGAATTCATTATCTGAGTCTCCAGTCTTTGCATGTTTTTTATTTTTTAGAGGCTGCCTCCATTCGAAACATTTTCTCAGGGACCTACGTTGCAGTTCACTCTTCGTTGGACAGGAGAGACCA	ATTGTCAGTGAAACTGAGAGAAGTCAAAGAAAATTACTAATTGAAAAGCTGTTCAATTTACAAAAAAAAAAGTAATTGGTCACCTAAGAGCAAAGGTTGCATGCTGGTGGGCTTTGGGTACCACAATTTTATTTTTAAGACATTTCAAGGCCAGGCGTGGTGGCTCATGCCTGTAACCCCAGCACTTTGGGAGGCCGAGGCAGGCAAATCACCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAAGATGATGAAACCCCGTCTCTACTAAAAACACACACACAAAAAATTAGCTGGGCGTGACGGCAGGTGCCTGTAATCCCAGCTACTTGGGAGGCTGAGACAGGAGAATTGCTTGAACCTGGGAGGGGGAGGTTGCAGTGAGCTGAGACCATGCCAGTTGCACACTAGCCTGGGCGACAAGAGTGAAACTCCATCTCAAAAAAAAAAAAAGACATTTGAACTGGTTAGCAACAACCTAAATGGGAAATTTTCCCATGATAACTTTGATTTCTGACCTATTTGGAAAAATCTGAAAATCTGTCTGTGTTGGACGAGTGTTTTCACATGGCAACAATTCACCTGTTGCTGATCAGTGGTCGCCTCTTTTAGACAGCCTGTGCTCTCCAGTTCAAGTTCTACAGTGTCTGGTCCATACTTTTACTTTGTTTGCCTAGCCGTCTCAGTCAGCATTTGGATTTTCAAGACAAATCTATTAAGGCAAATCCACATTGACTTATAATGAATTTTTTTTAATTTCTACAATTTATTTGAATTCATTATCTGAGTCTCCAGTCTTTGCATGTTTTTTATTTTTTAGAGGCTGCCTCCATTCGAAACATTTTCTCAGGGACCTACGTTGCAGTTCACTCTTCGTTGGACAGGAGAGACCA	-	novel	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1	34	1	0	ENST00000322652.5:c.1024-817_1098del		p.X342_splice	ENST00000322652	NM_015355.2	342		10/16	0.226027385585492	2	FACETS	1	0.971	1	1	0.979	1	CLONAL	8	TRUE	0	0.23	2		1	35	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353782	40353782	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	62	622	0	ENST00000293328.3:c.2338C>T	p.Gln780Ter	p.Q780*	ENST00000293328	NM_012448.3	780	Cag/Tag	19/19	0.226027385585492	2	FACETS	0.943	0.814	1	0.471	0.407	0.541	CLONAL	1	TRUE	0	0.23	2		622	572	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117445	4117445	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	33	551	0	ENST00000262948.5:c.275G>A	p.Arg92Lys	p.R92K	ENST00000262948	NM_030662.3	92	aGa/aAa	2/11	0.3	1	FACETS	0.765	0.624	0.923	0.765	0.624	0.923	CLONAL	1	TRUE	0	0.23	1		551	332	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295205	15295205	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	38	706	0	ENST00000263388.2:c.2467C>G	p.His823Asp	p.H823D	ENST00000263388	NM_000435.2	823	Cat/Gat	16/33	0.3	1	FACETS	0.64	0.529	0.764	0.64	0.529	0.764	SUBCLONAL	1	TRUE	0	0.23	1		706	457	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312707	30312707	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	19	610	0	ENST00000262643.3:c.688G>C	p.Glu230Gln	p.E230Q	ENST00000262643	NM_001238.2	230	Gaa/Caa	8/12	0.0892141831437887	3	FACETS	0.543	0.412	0.698	0.272	0.206	0.349	INDETERMINATE	1	TRUE	1	0.23	3		610	339	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211135	36211135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201417711	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	98	805	0	ENST00000222270.7:c.886G>A	p.Gly296Ser	p.G296S	ENST00000222270	NM_014727.1	296	Ggc/Agc	3/37	0.0892141831437887	3	FACETS	0.774	0.691	0.861	0.774	0.691	0.861	INDETERMINATE	2	TRUE	1	0.23	3		805	614	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067878	30067878	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	56	511	0	ENST00000338641.4:c.1063G>C	p.Glu355Gln	p.E355Q	ENST00000338641	NM_000268.3	355	Gag/Cag	11/16	0.3	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.23	1		511	373	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723615	49723615	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	19	110	0	ENST00000449682.2:c.1027G>C	p.Glu343Gln	p.E343Q	ENST00000449682	NM_020998.3	343	Gag/Cag	9/18	1	2	FACETS	1	0.818	1	1	0.941	1	CLONAL	2	TRUE	1	0.23	2		110	78	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874618	35874618	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	18	532	0	ENST00000303115.3:c.774C>G	p.Ile258Met	p.I258M	ENST00000303115	NM_002185.3	258	atC/atG	6/8	1	2	FACETS	0.435	0.327	0.563	0.435	0.327	0.563	SUBCLONAL	1	TRUE	1	0.23	2		532	360	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449519	149449519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	74	629	1	ENST00000286301.3:c.1427C>T	p.Thr476Ile	p.T476I	ENST00000286301	NM_005211.3	476	aCc/aTc	10/22	0.3	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.23	1		630	407	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032128	26032128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	55	438	0	ENST00000244661.2:c.161G>A	p.Arg54His	p.R54H	ENST00000244661	NM_003537.3	54	cGc/cAc	1/1	0.164710536394049	5	FACETS	0.858	0.737	0.989	0.572	0.491	0.659	CLONAL	2	TRUE	2	0.23	5		438	375	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271355	26271355	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	27	447	0	ENST00000305910.3:c.258G>C	p.Gln86His	p.Q86H	ENST00000305910	NM_003534.2	86	caG/caC	1/1	0.164710536394049	5	FACETS	0.763	0.606	0.942	0.254	0.202	0.314	CLONAL	1	TRUE	2	0.23	5		447	414	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190381	32190381	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748704745	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	27	721	1	ENST00000375023.3:c.358G>A	p.Asp120Asn	p.D120N	ENST00000375023	NM_004557.3	120	Gac/Aac	3/30	0.164710536394049	5	FACETS	0.65	0.516	0.803	0.217	0.172	0.268	SUBCLONAL	1	TRUE	2	0.23	5		722	486	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878674	151878674	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	22	539	0	ENST00000262189.6:c.6271A>T	p.Asn2091Tyr	p.N2091Y	ENST00000262189	NM_170606.2	2091	Aat/Tat	36/59	1	2	FACETS	0.669	0.519	0.843	0.669	0.519	0.843	SUBCLONAL	1	TRUE	1	0.23	2		539	286	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005915	69005915	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	46	578	1	ENST00000288368.4:c.2326C>T	p.Pro776Ser	p.P776S	ENST00000288368	NM_024870.2	776	Cct/Tct	21/40	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.23	2		579	268	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139438540	139438540	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1217905346	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	64	608	0	ENST00000277541.6:c.76C>T	p.Gln26Ter	p.Q26*	ENST00000277541	NM_017617.3	26	Cag/Tag	2/34	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.23	2		608	524	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197808	123197808	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	20	307	0	ENST00000218089.9:c.1932C>G	p.Phe644Leu	p.F644L	ENST00000218089	NM_001042749.1	644	ttC/ttG	20/35	1	1	FACETS	0.999	0.784	1	1	0.942	1	CLONAL	2	TRUE	0	0.23	1		307	77	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39746835	39746839	+	missense_variant	Missense_Mutation	ONP	CTTTC	CTTTC	TTTTG	novel	NA	P-0033067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	33	384	0	ENST00000361337.2:c.1849_1853delinsTTTTG	p.Leu617_Ser618delinsPheCys	p.L617_S618delinsFC	ENST00000361337	NM_003286.2	617	CTTTCt/TTTTGt	18/21	0.0892141831437887	3	FACETS	1	0.923	1	0.63	0.516	0.757	INDETERMINATE	1	TRUE	1	0.23	3		384	254	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210075	55210075	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	18513	500	0	ENST00000275493.2:c.185T>G	p.Leu62Arg	p.L62R	ENST00000275493	NM_005228.3	62	cTt/cGt	2/28	0.536421063507225	67	FACETS	0.995	0.993	0.997	0.995	0.993	0.997	CLONAL	67	TRUE	0	0.536421063507225	67		500	19087	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720680	89720681	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	59	191	0	ENST00000371953.3:c.833dup	p.Phe279LeufsTer19	p.F279Lfs*19	ENST00000371953	NM_000314.4	277	-/T	8/9	0.536421063507225	1	FACETS	0.654	0.569	0.745	0.654	0.569	0.745	SUBCLONAL	1	TRUE	0	0.536421063507225	1		191	246	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943950	71943950	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	158	560	0	ENST00000298229.2:c.1883T>C	p.Phe628Ser	p.F628S	ENST00000298229	NM_001567.3	628	tTt/tCt	16/28	1	2	FACETS	0.919	0.845	0.996	0.919	0.845	0.996	CLONAL	1	TRUE	1	0.536421063507225	2		560	641	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801737	3801737	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	111	443	1	ENST00000262367.5:c.3769C>T	p.Gln1257Ter	p.Q1257*	ENST00000262367	NM_004380.2	1257	Cag/Tag	20/31	1	2	FACETS	0.8	0.723	0.882	0.8	0.723	0.882	SUBCLONAL	1	TRUE	1	0.536421063507225	2		444	517	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753279	42753279	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1307797425	NA	P-0033073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	171	609	0	ENST00000222329.4:c.985C>T	p.Arg329Cys	p.R329C	ENST00000222329	NM_006494.2	329	Cgc/Tgc	4/4	1	2	FACETS	0.836	0.77	0.904	0.836	0.77	0.904	CLONAL	1	TRUE	1	0.536421063507225	2		609	763	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535358	66535358	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	121	378	0	ENST00000273854.3:c.103C>A	p.Pro35Thr	p.P35T	ENST00000273854	NM_004439.5	35	Cct/Act	1/18	1	2	FACETS	0.921	0.836	1	0.921	0.836	1	CLONAL	1	TRUE	1	0.536421063507225	2		378	490	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0033076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	16	439	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	0.076	0.056	0.101	0.076	0.056	0.101	SUBCLONAL	1	TRUE	1	0.613034763569404	2		439	686	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426733	121426736	+	protein_altering_variant	In_Frame_Del	DEL	TCCC	TCCC	G	novel	NA	P-0033076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	176	504	0	ENST00000257555.6:c.424_427delinsG	p.Ser142_His143delinsAsp	p.S142_H143delinsD	ENST00000257555		142	TCCCac/Gac	2/10	0.21414140951252	3	FACETS	1	0.973	1	0.555	0.513	0.598	INDETERMINATE	1	TRUE	1	0.613034763569404	3		504	676	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578509	7578509	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519978	NA	P-0033080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	76	849	0	ENST00000269305.4:c.421T>C	p.Cys141Arg	p.C141R	ENST00000269305	NM_001126112.2	141	Tgc/Cgc	5/11	0.362417177868157	2	FACETS	1	0.97	1	0.643	0.572	0.717	CLONAL	1	TRUE	0	0.474815620904658	2		849	249	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0033080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	27	419	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.377868148837139	3	FACETS	1	0.893	1	0.582	0.471	0.703	CLONAL	1	TRUE	1	0.474815620904658	3		419	121	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0033080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	43	468	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	0.377156223740083	1	FACETS	0.794	0.674	0.922	0.794	0.674	0.922	CLONAL	1	TRUE	0	0.474815620904658	1		468	174	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0033081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	293	280	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.382223727349607	2	FACETS	0.965	0.918	1	0.965	0.918	1	CLONAL	2	TRUE	0	0.533817395219563	2		280	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0033081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	505	607	2	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	2	TRUE	NA	0.533817395219563	2		609	922	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228801	36228801	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	193	709	0	ENST00000222270.7:c.7700G>A	p.Arg2567His	p.R2567H	ENST00000222270	NM_014727.1	2567	cGt/cAt	35/37	1	2	FACETS	0.721	0.667	0.777	0.721	0.667	0.777	SUBCLONAL	1	TRUE	1	0.533817395219563	2		709	1003	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89335072	89335074	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CTG	CTG	-	novel	NA	P-0033081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	115	385	0	ENST00000301030.4:c.7807-3_7807-1del		p.X2603_splice	ENST00000301030	NM_001256183.1	2603			0.533817395219563	1	FACETS	0.833	0.758	0.912	0.833	0.758	0.912	CLONAL	1	TRUE	0	0.533817395219563	1		385	379	SUCCESS
YES1	7525	MSKCC	GRCh37	18	732846	732846	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	239	705	0	ENST00000314574.4:c.1411G>C	p.Val471Leu	p.V471L	ENST00000314574	NM_005433.3	471	Gtg/Ctg	11/12	0.533817395219563	1	FACETS	0.972	0.913	1	0.972	0.913	1	CLONAL	1	TRUE	0	0.533817395219563	1		705	675	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189416	56189416	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	251	652	0	ENST00000399503.3:c.4448A>G	p.Asp1483Gly	p.D1483G	ENST00000399503	NM_005921.1	1483	gAt/gGt	20/20	1	2	FACETS	0.936	0.876	0.997	0.936	0.876	0.997	CLONAL	1	TRUE	1	0.533817395219563	2		652	1005	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528945	157528945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	42	562	1	ENST00000346085.5:c.6670G>A	p.Asp2224Asn	p.D2224N	ENST00000346085	NM_020732.3	2224	Gat/Aat	20/20	0.533817395219563	1	FACETS	0.184	0.153	0.218	0.184	0.153	0.218	SUBCLONAL	1	TRUE	0	0.533817395219563	1		563	628	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0033083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	220	693	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.226090559347866	2	FACETS	0.791	0.736	0.848	0.791	0.736	0.848	SUBCLONAL	2	TRUE	0	0.279066652292768	2		693	997	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750945	128750945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	151	489	1	ENST00000377970.2:c.482C>T	p.Ser161Leu	p.S161L	ENST00000377970	NM_002467.4	161	tCa/tTa	2/3	0.279087056273971	3	FACETS	0.965	0.885	1	0.965	0.885	1	CLONAL	2	TRUE	1	0.279066652292768	3		490	639	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879156	151879156	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0033083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	161	714	1	ENST00000262189.6:c.5789C>G	p.Ser1930Ter	p.S1930*	ENST00000262189	NM_170606.2	1930	tCa/tGa	36/59	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.279066652292768	2		715	953	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0033085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	162	290	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.346192057891091	4	FACETS	0.773	0.71	0.839	0.773	0.71	0.839	SUBCLONAL	2	TRUE	2	0.346192057891091	4		290	815	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0033085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	264	709	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.340765500277721	3	FACETS	0.855	0.802	0.91	0.855	0.802	0.91	CLONAL	2	TRUE	1	0.346192057891091	3		709	1046	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574026	+	inframe_deletion	In_Frame_Del	DEL	CACGCC	CACGCC	-	novel	NA	P-0033085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	139	655	0	ENST00000269305.4:c.1001_1006del	p.Gly334_Arg335del	p.G334_R335del	ENST00000269305	NM_001126112.2	334	gGGCGTGag/gag	10/11	0.340765500277721	3	FACETS	0.864	0.785	0.947	0.432	0.392	0.474	CLONAL	1	TRUE	1	0.346192057891091	3		655	1090	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0033087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	120	340	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.706738994669317	2		340	301	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0033087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	106	335	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.984	0.894	1	0.984	0.894	1	CLONAL	1	TRUE	1	0.706738994669317	2		335	305	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968265	15968265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	176	404	0	ENST00000268712.3:c.5020C>T	p.Pro1674Ser	p.P1674S	ENST00000268712	NM_006311.3	1674	Ccc/Tcc	34/46	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.706738994669317	2		404	476	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	76	264	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.927	1			1	INDETERMINATE	1	TRUE	NA	0.590453423218322	2		264	244	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0033092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	268	732	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.590964971078249	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.590453423218322	1		732	584	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061646	38061646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	97	125	0	ENST00000250448.2:c.343G>A	p.Ala115Thr	p.A115T	ENST00000250448	NM_004496.3	115	Gcc/Acc	2/2	0.364213223489977	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.590453423218322	1		125	166	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953760	48953760	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913302	NA	P-0033092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	115	344	0	ENST00000267163.4:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000267163	NM_000321.2	455	Cga/Tga	14/27	0.447529077557385	1	FACETS	0.906	0.828	0.986	0.906	0.828	0.986	CLONAL	1	TRUE	0	0.590453423218322	1		344	303	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711873	89711873	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs587781784	NA	P-0033092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	153	409	0	ENST00000371953.3:c.493-2A>G		p.X165_splice	ENST00000371953	NM_000314.4	165			0.590453423218322	1	FACETS	0.946	0.876	1	0.946	0.876	1	CLONAL	1	TRUE	0	0.590453423218322	1		409	386	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0033094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	163	424	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	0.267689219080143	5	FACETS	0.979	0.905	1	0.652	0.603	0.703	INDETERMINATE	2	TRUE	2	0.660603794589126	5		424	502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	799	636	0	ENST00000269305.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	336	Gag/Tag	10/11	0.656973381198586	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.660603794589126	3		636	1016	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	763	481	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.660603794589126	4	FACETS	0.923	0.896	0.95	0.923	0.896	0.95	CLONAL	3	TRUE	1	0.660603794589126	4		481	1385	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0033094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	212	440	0	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	0.267689219080143	5	FACETS	0.806	0.75	0.863	0.537	0.5	0.575	INDETERMINATE	2	TRUE	2	0.660603794589126	5		440	793	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996868	100996869	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	271	641	0	ENST00000325455.5:c.1658dup	p.Ser554GlufsTer20	p.S554Efs*20	ENST00000325455	NM_001202474.3	553	cag/caAg	2/8	0.660603794589126	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.660603794589126	1		641	508	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379644	17379644	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	354	352	0	ENST00000359435.4:c.29C>A	p.Thr10Asn	p.T10N	ENST00000359435	NM_001033549.1	10	aCt/aAt	2/9	0.372925275033026	4	FACETS	0.969	0.929	1	0.969	0.929	1	INDETERMINATE	3	TRUE	1	0.660603794589126	4		352	612	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176666804	176666804	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	48	408	0	ENST00000439151.2:c.4240G>A	p.Glu1414Lys	p.E1414K	ENST00000439151	NM_022455.4	1414	Gaa/Aaa	8/23	1	2	FACETS	0.488	0.414	0.567	0.488	0.414	0.567	SUBCLONAL	1	TRUE	1	0.660603794589126	2		408	298	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200324	138200324	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	171	440	1	ENST00000237289.4:c.1742G>A	p.Arg581Lys	p.R581K	ENST00000237289	NM_001270507.1	581	aGa/aAa	7/9	0.146263802277849	3	FACETS	1	0.985	1	0.633	0.586	0.681	INDETERMINATE	1	TRUE	1	0.660603794589126	3		441	544	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878827	117878827	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	69	380	0	ENST00000297338.2:c.142A>C	p.Lys48Gln	p.K48Q	ENST00000297338	NM_006265.2	48	Aag/Cag	2/14	0.660603794589126	5	FACETS	0.528	0.459	0.603	0.176	0.153	0.201	SUBCLONAL	1	TRUE	2	0.660603794589126	5		380	788	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0033096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	169	525	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.485532322172693	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.49120679061345	1		525	510	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985510	2985510	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	172	452	0	ENST00000396946.4:c.301G>C	p.Glu101Gln	p.E101Q	ENST00000396946	NM_032415.4	101	Gaa/Caa	4/25	0.132376092696439	4	FACETS	1	0.987	1	0.451	0.415	0.488	INDETERMINATE	1	TRUE	1	0.49120679061345	4		452	772	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343334	118343334	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	70	346	0	ENST00000534358.1:c.1460C>G	p.Ser487Cys	p.S487C	ENST00000534358	NM_005933.3	487	tCc/tGc	3/36	0.227493412791283	2	FACETS	0.774	0.679	0.876	0.387	0.339	0.438	INDETERMINATE	1	TRUE	0	0.49120679061345	2		346	368	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786110	3786110	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	133	672	1	ENST00000262367.5:c.4655G>T	p.Ser1552Ile	p.S1552I	ENST00000262367	NM_004380.2	1552	aGc/aTc	28/31	0.485532322172693	1	FACETS	0.588	0.535	0.644	0.588	0.535	0.644	SUBCLONAL	1	TRUE	0	0.49120679061345	1		673	695	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685315	89685315	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0033099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	79	336	0	ENST00000371953.3:c.209+1G>C		p.X70_splice	ENST00000371953	NM_000314.4	70			NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.52842180735161	2		336	219	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865476	57865481	+	inframe_deletion	In_Frame_Del	DEL	GCAGCA	GCAGCA	-	novel	NA	P-0033099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	41	564	0	ENST00000228682.2:c.2956_2961del	p.Ala986_Ala987del	p.A986_A987del	ENST00000228682	NM_005269.2	985	GCAGCA/-	12/12	0.379157876338232	4	FACETS	0.608	0.507	0.72	0.304	0.253	0.36	SUBCLONAL	1	TRUE	2	0.52842180735161	4		564	390	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907210	32907210	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359292	NA	P-0033099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	96	435	0	ENST00000380152.3:c.1597del	p.Thr533LeufsTer25	p.T533Lfs*25	ENST00000380152		532	gAa/ga	10/27	0.512253352717405	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	2	TRUE	0	0.52842180735161	2		435	181	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554306	81554306	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908865	NA	P-0033099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	57	398	0	ENST00000298171.2:c.326G>A	p.Arg109Gln	p.R109Q	ENST00000298171	NM_000369.2	109	cGg/cAg	4/10	0.18905356785446	4	FACETS	1	0.966	1	0.699	0.606	0.797	INDETERMINATE	1	TRUE	2	0.52842180735161	4		398	236	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089923	16089923	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	167	365	0	ENST00000268712.3:c.187C>T	p.Gln63Ter	p.Q63*	ENST00000268712	NM_006311.3	63	Caa/Taa	3/46	0.52842180735161	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.52842180735161	1		365	340	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504259	8504259	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0033099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	12	365	0	ENST00000356435.5:c.1822+2T>A		p.X608_splice	ENST00000356435		608			0.306955607162598	1	FACETS	0.169	0.118	0.231	0.169	0.118	0.231	INDETERMINATE	1	TRUE	0	0.52842180735161	1		365	198	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	20	280	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.275	0.21	0.352	0.275	0.21	0.352	SUBCLONAL	1	TRUE	1	0.355585862015741	2		280	409	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	26	444	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.244	0.192	0.303	0.244	0.192	0.303	SUBCLONAL	1	TRUE	1	0.355585862015741	2		444	600	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	13	645	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.112	0.079	0.153	0.112	0.079	0.153	SUBCLONAL	1	TRUE	1	0.355585862015741	2		645	650	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	72	448	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.667	0.583	0.758	0.667	0.583	0.758	SUBCLONAL	1	TRUE	1	0.355585862015741	2		449	607	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	130	776	0	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.355585862015741	2		776	724	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	139	653	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.355585862015741	2		658	712	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	126	335	1	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.83	0.758	0.905	1	0.988	1	CLONAL	2	TRUE	1	0.355585862015741	2		336	427	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073804	8073804	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1557463619	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	67	423	2	ENST00000377482.5:c.855del	p.Arg286GlufsTer9	p.R286Efs*9	ENST00000377482	NM_018948.3	285	ccC/cc	4/4	1	2	FACETS	0.883	0.77	1	0.883	0.77	1	CLONAL	1	TRUE	1	0.355585862015741	2		425	427	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256640	16256640	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	85	560	0	ENST00000375759.3:c.3905T>C	p.Val1302Ala	p.V1302A	ENST00000375759	NM_015001.2	1302	gTc/gCc	11/15	1	2	FACETS	0.968	0.858	1	0.968	0.858	1	CLONAL	1	TRUE	1	0.355585862015741	2		560	494	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258454	16258454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752378818	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	98	630	0	ENST00000375759.3:c.5719G>A	p.Val1907Ile	p.V1907I	ENST00000375759	NM_015001.2	1907	Gtc/Atc	11/15	1	2	FACETS	0.947	0.847	1	0.947	0.847	1	CLONAL	1	TRUE	1	0.355585862015741	2		630	582	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	47	284	0	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	0.806	0.683	0.94	0.806	0.683	0.94	CLONAL	1	TRUE	1	0.355585862015741	2		284	328	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305247	39305247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	117	659	1	ENST00000373001.3:c.1178G>A	p.Gly393Asp	p.G393D	ENST00000373001	NM_022157.3	393	gGc/gAc	7/7	1	2	FACETS	0.994	0.898	1	0.994	0.898	1	CLONAL	1	TRUE	1	0.355585862015741	2		660	662	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429978	78429978	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	56	562	0	ENST00000370768.2:c.901del	p.Ile301TyrfsTer22	p.I301Yfs*22	ENST00000370768	NM_003902.3	301	Ata/ta	11/20	1	2	FACETS	0.636	0.546	0.735	0.636	0.546	0.735	SUBCLONAL	1	TRUE	1	0.355585862015741	2		562	495	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851429	156851429	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	88	768	0	ENST00000524377.1:c.2386G>A	p.Gly796Ser	p.G796S	ENST00000524377	NM_002529.3	796	Ggc/Agc	17/17	1	2	FACETS	0.719	0.637	0.807	0.719	0.637	0.807	SUBCLONAL	1	TRUE	1	0.355585862015741	2		768	688	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	61	305	4	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.355585862015741	2		309	310	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683247	88683247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752802257	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	119	685	0	ENST00000372037.3:c.1457G>A	p.Arg486Gln	p.R486Q	ENST00000372037	NM_004329.2	486	cGg/cAg	12/13	1	2	FACETS	0.959	0.867	1	0.959	0.867	1	CLONAL	1	TRUE	1	0.355585862015741	2		685	698	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104359271	104359271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141359583	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	64	444	2	ENST00000369902.3:c.992G>A	p.Arg331Gln	p.R331Q	ENST00000369902	NM_016169.3	331	cGg/cAg	8/12	1	2	FACETS	0.758	0.658	0.866	0.758	0.658	0.866	SUBCLONAL	1	TRUE	1	0.355585862015741	2		446	475	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900984	114900984	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778855667	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	117	629	0	ENST00000543371.1:c.598del	p.Leu200SerfsTer25	p.L200Sfs*25	ENST00000543371	NM_001198531.1	198	caC/ca	6/14	1	2	FACETS	0.978	0.883	1	0.978	0.883	1	CLONAL	1	TRUE	1	0.355585862015741	2		629	673	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942053	71942053	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	105	636	1	ENST00000298229.2:c.1322del	p.Asn441ThrfsTer2	p.N441Tfs*2	ENST00000298229	NM_001567.3	439	ccA/cc	12/28	1	2	FACETS	0.96	0.862	1	0.96	0.862	1	CLONAL	1	TRUE	1	0.355585862015741	2		637	615	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344599	118344599	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	93	592	1	ENST00000534358.1:c.2725G>T	p.Gly909Cys	p.G909C	ENST00000534358	NM_005933.3	909	Ggt/Tgt	3/36	1	2	FACETS	0.896	0.798	0.999	0.896	0.798	0.999	CLONAL	1	TRUE	1	0.355585862015741	2		593	584	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118368739	118368739	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	113	648	0	ENST00000534358.1:c.5753A>G	p.Asp1918Gly	p.D1918G	ENST00000534358	NM_005933.3	1918	gAc/gGc	21/36	1	2	FACETS	0.947	0.854	1	0.947	0.854	1	CLONAL	1	TRUE	1	0.355585862015741	2		648	671	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	63	476	0	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.864	0.75	0.987	0.864	0.75	0.987	CLONAL	1	TRUE	1	0.355585862015741	2		476	410	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244077	46244077	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	102	626	0	ENST00000334344.6:c.2171C>T	p.Pro724Leu	p.P724L	ENST00000334344	NM_152641.2	724	cCc/cTc	15/21	1	2	FACETS	0.94	0.843	1	0.94	0.843	1	CLONAL	1	TRUE	1	0.355585862015741	2		626	610	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245712	46245712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752984515	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	79	462	0	ENST00000334344.6:c.3806C>T	p.Pro1269Leu	p.P1269L	ENST00000334344	NM_152641.2	1269	cCg/cTg	15/21	1	2	FACETS	0.983	0.868	1	0.983	0.868	1	CLONAL	1	TRUE	1	0.355585862015741	2		462	452	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865044	57865044	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	118	803	1	ENST00000228682.2:c.2525del	p.Pro842HisfsTer104	p.P842Hfs*104	ENST00000228682	NM_005269.2	841	Ccc/cc	12/12	1	2	FACETS	0.876	0.79	0.966	0.876	0.79	0.966	CLONAL	1	TRUE	1	0.355585862015741	2		804	758	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233090	69233090	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746910913	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	41	246	1	ENST00000462284.1:c.961del	p.Leu321PhefsTer52	p.L321Ffs*52	ENST00000462284	NM_002392.5	319	Ccc/cc	11/11	1	2	FACETS	0.524	0.437	0.621	0.524	0.437	0.621	SUBCLONAL	1	TRUE	1	0.355585862015741	2		247	440	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434356	121434356	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	110	654	1	ENST00000257555.6:c.1124del	p.Gly375AlafsTer9	p.G375Afs*9	ENST00000257555		374	Ggg/gg	6/10	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.355585862015741	2		655	601	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245435	133245435	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs754925525	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	56	649	2	ENST00000320574.5:c.1885del	p.Ala629ProfsTer8	p.A629Pfs*8	ENST00000320574	NM_006231.2	629	Gcc/cc	17/49	1	2	FACETS	0.491	0.42	0.569	0.491	0.42	0.569	SUBCLONAL	1	TRUE	1	0.355585862015741	2		651	641	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477077	67477077	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	69	505	1	ENST00000327367.4:c.884G>T	p.Arg295Leu	p.R295L	ENST00000327367	NM_005902.3	295	cGg/cTg	7/9	1	2	FACETS	0.913	0.798	1	0.913	0.798	1	CLONAL	1	TRUE	1	0.355585862015741	2		506	425	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99482514	99482514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777966016	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	109	642	2	ENST00000268035.6:c.3382G>A	p.Ala1128Thr	p.A1128T	ENST00000268035	NM_000875.3	1128	Gcc/Acc	18/21	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.355585862015741	2		644	595	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2224005	2224005	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	110	858	0	ENST00000326181.6:c.1219A>G	p.Met407Val	p.M407V	ENST00000326181	NM_032271.2	407	Atg/Gtg	13/21	1	2	FACETS	0.857	0.77	0.948	0.857	0.77	0.948	CLONAL	1	TRUE	1	0.355585862015741	2		858	722	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129042	30129042	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745793573	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	120	671	0	ENST00000263025.4:c.724C>T	p.Arg242Trp	p.R242W	ENST00000263025	NM_002746.2	242	Cgg/Tgg	5/9	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.355585862015741	2		671	661	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	76	444	1	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.95	0.836	1	0.95	0.836	1	CLONAL	1	TRUE	1	0.355585862015741	2		445	450	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827511	72827511	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	94	808	0	ENST00000268489.5:c.9070del	p.Thr3024GlnfsTer52	p.T3024Qfs*52	ENST00000268489	NM_006885.3	3024	Aca/ca	9/10	1	2	FACETS	0.663	0.589	0.741	0.663	0.589	0.741	SUBCLONAL	1	TRUE	1	0.355585862015741	2		808	798	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508736	29508736	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	78	619	1	ENST00000356175.3:c.663G>T	p.Trp221Cys	p.W221C	ENST00000356175	NM_000267.3	221	tgG/tgT	7/57	1	2	FACETS	0.854	0.752	0.962	0.854	0.752	0.962	CLONAL	1	TRUE	1	0.355585862015741	2		620	514	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243835	41243835	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	129	757	1	ENST00000357654.3:c.3713C>A	p.Pro1238His	p.P1238H	ENST00000357654	NM_007294.3	1238	cCt/cAt	10/23	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.355585862015741	2		758	666	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	206	679	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.355585862015741	2	FACETS	0.87	0.811	0.93	0.87	0.811	0.93	CLONAL	2	TRUE	0	0.355585862015741	2		686	666	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448297	56448298	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1567880599	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	221	720	0	ENST00000407977.2:c.349dup	p.Arg117ProfsTer8	p.R117Pfs*8	ENST00000407977		117	cgc/cCgc	3/10	0.355585862015741	2	FACETS	0.915	0.856	0.976	0.915	0.856	0.976	CLONAL	2	TRUE	0	0.355585862015741	2		720	679	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	102	730	6	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	0.355585862015741	2	FACETS	0.889	0.797	0.988	0.445	0.398	0.494	CLONAL	1	TRUE	0	0.355585862015741	2		736	645	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575123	48575123	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	91	492	1	ENST00000342988.3:c.317A>G	p.Lys106Arg	p.K106R	ENST00000342988	NM_005359.5	106	aAa/aGa	3/12	1	2	FACETS	0.984	0.877	1	0.984	0.877	1	CLONAL	1	TRUE	1	0.355585862015741	2		493	520	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	71	449	3	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.355585862015741	2		452	392	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231610	5231611	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	13	160	0	ENST00000357368.4:c.1865dup	p.Gln623SerfsTer4	p.Q623Sfs*4	ENST00000357368	NM_002850.3	622	cct/ccCt	14/38	1	2	FACETS	0.451	0.323	0.607	0.451	0.323	0.607	SUBCLONAL	1	TRUE	1	0.355585862015741	2		160	162	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7174729	7174729	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	84	467	0	ENST00000302850.5:c.988C>A	p.Pro330Thr	p.P330T	ENST00000302850	NM_000208.2	330	Cca/Aca	4/22	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.355585862015741	2		467	462	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299864	15299864	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	116	797	0	ENST00000263388.2:c.1314del	p.Cys440AlafsTer11	p.C440Afs*11	ENST00000263388	NM_000435.2	438	ggG/gg	8/33	1	2	FACETS	0.905	0.816	0.998	0.905	0.816	0.998	CLONAL	1	TRUE	1	0.355585862015741	2		797	721	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387698	17387698	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199960321	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	83	605	1	ENST00000359435.4:c.766G>A	p.Glu256Lys	p.E256K	ENST00000359435	NM_001033549.1	256	Gag/Aag	8/9	1	2	FACETS	0.753	0.665	0.847	0.753	0.665	0.847	SUBCLONAL	1	TRUE	1	0.355585862015741	2		606	620	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214025	36214025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766488321	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	127	794	0	ENST00000222270.7:c.2851C>T	p.Arg951Cys	p.R951C	ENST00000222270	NM_014727.1	951	Cgc/Tgc	6/37	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.355585862015741	2		794	679	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224124	36224124	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	59	691	0	ENST00000222270.7:c.6678del	p.Thr2227ArgfsTer34	p.T2227Rfs*34	ENST00000222270	NM_014727.1	2225	tCc/tc	28/37	1	2	FACETS	0.567	0.488	0.654	0.567	0.488	0.654	SUBCLONAL	1	TRUE	1	0.355585862015741	2		691	585	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799050	42799050	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	146	884	1	ENST00000575354.2:c.4534C>T	p.Arg1512Cys	p.R1512C	ENST00000575354	NM_015125.3	1512	Cgt/Tgt	20/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.355585862015741	2		885	742	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902265	50902265	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	136	852	0	ENST00000440232.2:c.157C>G	p.Gln53Glu	p.Q53E	ENST00000440232	NM_002691.3	53	Cag/Gag	2/27	1	2	FACETS	0.996	0.906	1	0.996	0.906	1	CLONAL	1	TRUE	1	0.355585862015741	2		852	768	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467065	25467065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1368287759	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	110	646	0	ENST00000264709.3:c.1810C>T	p.Arg604Trp	p.R604W	ENST00000264709	NM_175629.2	604	Cgg/Tgg	15/23	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.355585862015741	2		646	562	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982440	25982440	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	96	534	0	ENST00000435504.4:c.850C>T	p.Arg284Ter	p.R284*	ENST00000435504		284	Cga/Tga	9/13	1	2	FACETS	0.926	0.827	1	0.926	0.827	1	CLONAL	1	TRUE	1	0.355585862015741	2		534	583	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732730	204732730	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	83	596	3	ENST00000302823.3:c.65G>A	p.Cys22Tyr	p.C22Y	ENST00000302823	NM_005214.4	22	tGc/tAc	1/4	1	2	FACETS	0.785	0.693	0.882	0.785	0.693	0.882	SUBCLONAL	1	TRUE	1	0.355585862015741	2		599	595	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793290	242793291	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	78	787	0	ENST00000334409.5:c.786dup	p.Ala263ArgfsTer7	p.A263Rfs*7	ENST00000334409	NM_005018.2	262	-/C	5/5	1	2	FACETS	0.676	0.594	0.764	0.676	0.594	0.764	SUBCLONAL	1	TRUE	1	0.355585862015741	2		787	649	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	103	472	0	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.858	0.769	0.953	0.858	0.769	0.953	CLONAL	1	TRUE	1	0.355585862015741	2		472	675	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560913	9560913	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559720359	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	85	620	2	ENST00000353224.5:c.869C>T	p.Ser290Leu	p.S290L	ENST00000353224	NM_177990.2	290	tCg/tTg	4/10	1	2	FACETS	0.814	0.721	0.914	0.814	0.721	0.914	CLONAL	1	TRUE	1	0.355585862015741	2		622	587	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	93	468	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.878	0.782	0.98	0.878	0.782	0.98	CLONAL	1	TRUE	1	0.355585862015741	2		468	596	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266927	41266927	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139085081	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	107	569	0	ENST00000349496.5:c.598C>T	p.Arg200Cys	p.R200C	ENST00000349496	NM_001904.3	200	Cgt/Tgt	5/15	0.355585862015741	2	FACETS	1	0.92	1	0.514	0.462	0.568	CLONAL	1	TRUE	0	0.355585862015741	2		569	586	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161907	47161907	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	107	572	9	ENST00000409792.3:c.4219del	p.Arg1407GlyfsTer5	p.R1407Gfs*5	ENST00000409792	NM_014159.6	1407	Agg/gg	3/21	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.355585862015741	2		581	572	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405962	49405962	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	122	598	0	ENST00000418115.1:c.176A>G	p.Asp59Gly	p.D59G	ENST00000418115	NM_001664.2	59	gAc/gGc	3/5	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.355585862015741	2		598	639	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70001016	70001016	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	81	502	1	ENST00000394351.3:c.617del	p.Lys206ArgfsTer6	p.K206Rfs*6	ENST00000394351	NM_000248.3	205	Aaa/aa	6/9	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.355585862015741	2		503	455	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413710	138413710	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	65	460	3	ENST00000289153.2:c.1810del	p.Arg604GlyfsTer4	p.R604Gfs*4	ENST00000289153	NM_006219.2	604	Cgg/gg	12/22	1	2	FACETS	0.79	0.686	0.901	0.79	0.686	0.901	CLONAL	1	TRUE	1	0.355585862015741	2		463	463	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919312	178919312	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	40	303	0	ENST00000263967.3:c.797C>A	p.Pro266His	p.P266H	ENST00000263967	NM_006218.2	266	cCt/cAt	4/21	1	2	FACETS	0.784	0.655	0.926	0.784	0.655	0.926	CLONAL	1	TRUE	1	0.355585862015741	2		303	287	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950763	38950763	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	43	360	0	ENST00000357387.3:c.3187G>A	p.Asp1063Asn	p.D1063N	ENST00000357387	NM_152756.3	1063	Gat/Aat	31/38	1	2	FACETS	0.756	0.635	0.888	0.756	0.635	0.888	SUBCLONAL	1	TRUE	1	0.355585862015741	2		360	320	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177608	56177608	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	101	469	0	ENST00000399503.3:c.2581G>T	p.Asp861Tyr	p.D861Y	ENST00000399503	NM_005921.1	861	Gat/Tat	14/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.355585862015741	2		469	506	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645099	86645099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1305400293	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	63	464	0	ENST00000274376.6:c.1171C>T	p.Arg391Trp	p.R391W	ENST00000274376	NM_002890.2	391	Cgg/Tgg	8/25	1	2	FACETS	0.854	0.741	0.975	0.854	0.741	0.975	CLONAL	1	TRUE	1	0.355585862015741	2		464	415	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131930612	131930612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	51	469	0	ENST00000265335.6:c.1849del	p.Arg617GlufsTer26	p.R617Efs*26	ENST00000265335		615	ctA/ct	12/25	1	2	FACETS	0.7	0.596	0.813	0.7	0.596	0.813	SUBCLONAL	1	TRUE	1	0.355585862015741	2		469	410	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694718	176694718	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	64	448	0	ENST00000439151.2:c.5302A>G	p.Arg1768Gly	p.R1768G	ENST00000439151	NM_022455.4	1768	Agg/Ggg	15/23	1	2	FACETS	0.793	0.688	0.906	0.793	0.688	0.906	CLONAL	1	TRUE	1	0.355585862015741	2		448	454	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176700778	176700779	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs587784152	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	65	359	0	ENST00000439151.2:c.5618_5619del	p.Ile1873LysfsTer18	p.I1873Kfs*18	ENST00000439151	NM_022455.4	1872	cAT/c	17/23	1	2	FACETS	0.926	0.806	1	0.926	0.806	1	CLONAL	1	TRUE	1	0.355585862015741	2		359	395	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225789	26225789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	64	381	1	ENST00000360408.1:c.407C>T	p.Ala136Val	p.A136V	ENST00000360408	NM_003532.2	136	gCg/gTg	1/1	1	2	FACETS	0.978	0.852	1	0.978	0.852	1	CLONAL	1	TRUE	1	0.355585862015741	2		382	368	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673037	30673037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201814179	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	117	774	1	ENST00000376406.3:c.3923G>A	p.Arg1308Gln	p.R1308Q	ENST00000376406	NM_014641.2	1308	cGg/cAg	10/15	1	2	FACETS	0.855	0.771	0.943	0.855	0.771	0.943	CLONAL	1	TRUE	1	0.355585862015741	2		775	770	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821533	32821533	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	74	701	0	ENST00000354258.4:c.61C>T	p.Pro21Ser	p.P21S	ENST00000354258	NM_000593.5	21	Ccc/Tcc	1/11	1	2	FACETS	0.768	0.673	0.87	0.768	0.673	0.87	SUBCLONAL	1	TRUE	1	0.355585862015741	2		701	542	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43745376	43745376	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1187507161	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	121	685	0	ENST00000523873.1:c.289A>G	p.Thr97Ala	p.T97A	ENST00000523873		97	Act/Gct	3/8	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.355585862015741	2		685	651	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946173	13946173	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1419836219	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	120	662	0	ENST00000405192.2:c.923G>A	p.Arg308Gln	p.R308Q	ENST00000405192	NM_001163147.1	308	cGg/cAg	10/12	1	2	FACETS	0.993	0.898	1	0.993	0.898	1	CLONAL	1	TRUE	1	0.355585862015741	2		662	680	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340178	116340178	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	96	356	0	ENST00000397752.3:c.1040C>T	p.Ala347Val	p.A347V	ENST00000397752	NM_000245.2	347	gCa/gTa	2/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.355585862015741	2		356	402	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273432	38273432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1412996644	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	83	888	0	ENST00000425967.3:c.1903G>A	p.Ala635Thr	p.A635T	ENST00000425967	NM_001174067.1	635	Gcc/Acc	14/19	1	2	FACETS	0.566	0.499	0.638	0.566	0.499	0.638	SUBCLONAL	1	TRUE	1	0.355585862015741	2		888	825	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054648	5054648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765286468	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	64	447	0	ENST00000381652.3:c.700C>T	p.Arg234Cys	p.R234C	ENST00000381652	NM_004972.3	234	Cgc/Tgc	7/25	1	2	FACETS	0.865	0.752	0.987	0.865	0.752	0.987	CLONAL	1	TRUE	1	0.355585862015741	2		447	416	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933594	39933594	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	84	288	0	ENST00000378444.4:c.1005del	p.Ser336ArgfsTer42	p.S336Rfs*42	ENST00000378444	NM_001123385.1	335	ccC/cc	4/15	1	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.355585862015741	1		288	285	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181284	123181284	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	61	206	0	ENST00000218089.9:c.748G>A	p.Ala250Thr	p.A250T	ENST00000218089	NM_001042749.1	250	Gca/Aca	9/35	1	1	FACETS	0.845	0.745	0.948	1	0.978	1	CLONAL	2	TRUE	0	0.355585862015741	1		206	167	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0033101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	169	582	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.465514330886689	1	FACETS	0.95	0.878	1	0.95	0.878	1	CLONAL	1	TRUE	0	0.473244518772924	1		582	574	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0033101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	177	448	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.897	0.827	0.969	0.897	0.827	0.969	CLONAL	1	TRUE	1	0.473244518772924	2		449	834	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581229	48581229	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs377767331	NA	P-0033101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	156	431	0	ENST00000342988.3:c.533C>G	p.Ser178Ter	p.S178*	ENST00000342988	NM_005359.5	178	tCa/tGa	5/12	0.465514330886689	1	FACETS	0.868	0.799	0.939	0.868	0.799	0.939	CLONAL	1	TRUE	0	0.473244518772924	1		431	580	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0033101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	143	423	1	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.867	0.792	0.945	0.867	0.792	0.945	CLONAL	1	TRUE	1	0.473244518772924	2		424	697	SUCCESS
APC	324	MSKCC	GRCh37	5	112175419	112175419	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0033101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	203	304	0	ENST00000257430.4:c.4128T>A	p.Tyr1376Ter	p.Y1376*	ENST00000257430	NM_000038.5	1376	taT/taA	16/16	0.459184072326031	2	FACETS	0.883	0.827	0.939	0.883	0.827	0.939	CLONAL	2	TRUE	0	0.473244518772924	2		304	486	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057955	27057955	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	117	517	1	ENST00000324856.7:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000324856	NM_006015.4	555	Cag/Tag	3/20	0.25100401325096	1	FACETS	0.506	0.456	0.558	0.506	0.456	0.558	INDETERMINATE	1	TRUE	0	0.473244518772924	1		518	746	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480430	50480430	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1446694595	NA	P-0033101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	149	405	0	ENST00000394963.4:c.392A>G	p.Lys131Arg	p.K131R	ENST00000394963	NM_003076.4	131	aAa/aGa	3/13	1	2	FACETS	0.826	0.756	0.9	0.826	0.756	0.9	CLONAL	1	TRUE	1	0.473244518772924	2		405	762	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119775	70119776	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0033101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	159	459	0	ENST00000245479.2:c.779dup	p.Glu261ArgfsTer35	p.E261Rfs*35	ENST00000245479	NM_000346.3	259	-/C	3/3	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.473244518772924	2		459	671	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221944	98221944	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767225445	NA	P-0033101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	43	494	0	ENST00000331920.6:c.2825G>A	p.Arg942Gln	p.R942Q	ENST00000331920	NM_000264.3	942	cGg/cAg	17/24	1	2	FACETS	0.234	0.195	0.277	0.234	0.195	0.277	SUBCLONAL	1	TRUE	1	0.473244518772924	2		494	778	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039708	47039708	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	375	603	1	ENST00000377604.3:c.1160G>A	p.Arg387Lys	p.R387K	ENST00000377604	NM_001204468.1	387	aGg/aAg	11/24	0.41446542551921	3	FACETS	0.974	0.927	1	0.974	0.927	1	CLONAL	2	TRUE	1	0.473244518772924	3		604	1006	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114901018	114901020	+	frameshift_variant	Frame_Shift_Del	DEL	CAC	CAC	A	novel	NA	P-0033101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	168	446	1	ENST00000543371.1:c.628_630delinsA	p.His210IlefsTer117	p.H210Ifs*117	ENST00000543371	NM_001198531.1	210	CAC/A	6/14	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.473244518772924	2		447	696	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	75	264	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.54	2		264	276	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453136	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	rs397516897	NA	P-0033106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	87	497	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	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.54	2		497	291	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784869	9784869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	91	557	0	ENST00000377346.4:c.2872G>A	p.Gly958Ser	p.G958S	ENST00000377346	NM_005026.3	958	Ggc/Agc	23/24	1	2	FACETS	0.648	0.577	0.723	0.648	0.577	0.723	SUBCLONAL	1	TRUE	1	0.54	2		557	520	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0033111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	129	280	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	0.485265133650389	2		280	501	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0033111-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	275	280	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.958	0.908	1	0.958	0.908	1	CLONAL	1	TRUE	1	0.937696354344653	2		280	612	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0033112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	166	474	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.169112358938031	3	FACETS	0.878	0.813	0.945	0.878	0.813	0.945	INDETERMINATE	3	TRUE	0	0.285714523105809	3		474	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0033112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	91	576	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.158914573719232	1	FACETS	1	0.965	1	1	0.965	1	INDETERMINATE	1	TRUE	0	0.285714523105809	1		576	455	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0033112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	28	590	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.391	0.312	0.482	0.391	0.312	0.482	SUBCLONAL	1	TRUE	1	0.285714523105809	2		590	501	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956221	55956221	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs767542615	NA	P-0033112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	84	559	0	ENST00000263923.4:c.3094C>T	p.Arg1032Ter	p.R1032*	ENST00000263923	NM_002253.2	1032	Cga/Tga	23/30	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.285714523105809	2		559	504	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597813	43597813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770548816	NA	P-0033112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	92	761	0	ENST00000355710.3:c.361G>A	p.Val121Ile	p.V121I	ENST00000355710	NM_020975.4	121	Gtc/Atc	3/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.285714523105809	2		761	535	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910587	29910587	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	104	728	0	ENST00000376809.5:c.127G>T	p.Glu43Ter	p.E43*	ENST00000376809	NM_002116.7	43	Gag/Tag	2/8	0.169112358938031	3	FACETS	0.86	0.773	0.95	0.573	0.515	0.634	INDETERMINATE	2	TRUE	0	0.285714523105809	3		728	484	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175217	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	64	307	0	ENST00000257430.4:c.3929dup	p.Ile1311AspfsTer4	p.I1311Dfs*4	ENST00000257430	NM_000038.5	1309	gaa/gAaa	16/16	0.285714523105809	3	FACETS	0.918	0.81	1	0.918	0.81	1	CLONAL	3	TRUE	0	0.285714523105809	3		307	186	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864003	97864003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs370974124	NA	P-0033112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	28	571	0	ENST00000289081.3:c.1663C>T	p.Arg555Ter	p.R555*	ENST00000289081	NM_000136.2	555	Cga/Tga	15/15	1	2	FACETS	0.394	0.314	0.485	0.394	0.314	0.485	SUBCLONAL	1	TRUE	1	0.285714523105809	2		571	498	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551940	150551941	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0033112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	73	421	0	ENST00000369026.2:c.66_67del	p.Ala23ArgfsTer86	p.A23Rfs*86	ENST00000369026	NM_021960.4	22	ggGGcc/ggcc	1/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.285714523105809	2		421	364	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735470	40735470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761910971	NA	P-0033119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	174	575	0	ENST00000373198.4:c.3403G>A	p.Val1135Met	p.V1135M	ENST00000373198	NM_133170.3	1135	Gtg/Atg	25/32	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.285988497474755	2		575	865	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141426	11141426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	55	501	0	ENST00000358026.2:c.3403C>T	p.Arg1135Trp	p.R1135W	ENST00000358026	NM_001128849.1	1135	Cgg/Tgg	25/36	1	2	FACETS	0.542	0.463	0.63	0.542	0.463	0.63	SUBCLONAL	1	FALSE	1	0.285988497474755	2		501	709	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618395	37618395	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0033119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	50	338	0	ENST00000447079.4:c.71C>G	p.Ser24Ter	p.S24*	ENST00000447079	NM_015083.1	24	tCa/tGa	1/14	1	2	FACETS	0.705	0.598	0.822	0.705	0.598	0.822	SUBCLONAL	1	FALSE	1	0.285988497474755	2		338	496	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486145	8486145	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	68	468	0	ENST00000356435.5:c.2672A>G	p.Tyr891Cys	p.Y891C	ENST00000356435		891	tAc/tGc	17/35	0.222893736407155	1	FACETS	0.776	0.676	0.884	0.776	0.676	0.884	SUBCLONAL	1	FALSE	0	0.285988497474755	1		468	525	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	177	264	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.978	1	1	0.995	1	CLONAL	3	FALSE	1	0.267416773758572	2		264	398	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453136	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	rs397516897	NA	P-0033121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	264	497	0	ENST00000288602.6:c.1799_1801del	p.Val600_Lys601delinsGlu	p.V600_K601delinsE	ENST00000288602	NM_004333.4	600	gTGAaa/gaa	15/18	0.267416773758572	2	FACETS	0.968	0.933	1	1	0.997	1	CLONAL	6	FALSE	0	0.267416773758572	2		497	340	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217296	123217296	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	179	307	0	ENST00000218089.9:c.2950G>T	p.Glu984Ter	p.E984*	ENST00000218089	NM_001042749.1	984	Gag/Tag	29/35	0.267416773758572	2	FACETS	0.934	0.891	0.974			1	CLONAL	6	FALSE	NA	0.267416773758572	2		307	239	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	128	441	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.843	0.766	0.923	0.843	0.766	0.923	CLONAL	1	TRUE	1	0.48	2		441	633	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	63	431	1	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS	0.805	0.701	0.917	0.805	0.701	0.917	CLONAL	1	TRUE	1	0.48	2		432	326	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	172	374	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.953	0.89	1	1	0.993	1	CLONAL	2	TRUE	1	0.48	2		374	376	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	127	423	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.796	0.722	0.873	0.796	0.722	0.873	SUBCLONAL	1	TRUE	1	0.48	2		423	665	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	195	460	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.48	2		460	725	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	135	335	1	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.792	0.721	0.867	0.792	0.721	0.867	SUBCLONAL	1	TRUE	1	0.48	2		336	710	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682810	190682810	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	84	475	2	ENST00000441310.2:c.492del	p.Lys164AsnfsTer6	p.K164Nfs*6	ENST00000441310	NM_000534.4	162	gcA/gc	5/13	1	2	FACETS	0.956	0.851	1	0.956	0.851	1	CLONAL	1	TRUE	1	0.48	2		477	366	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	426	993	5	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.879	0.84	0.917	1	0.997	1	CLONAL	2	TRUE	1	0.48	2		998	1010	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101402	27101402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	147	403	0	ENST00000324856.7:c.4689del	p.Met1564Ter	p.M1564*	ENST00000324856	NM_006015.4	1562	Ccc/cc	18/20	1	2	FACETS	0.848	0.776	0.924	0.848	0.776	0.924	CLONAL	1	TRUE	1	0.48	2		403	722	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	166	262	1	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	1	2	FACETS	0.83	0.763	0.9	0.83	0.763	0.9	CLONAL	1	TRUE	1	0.48	2		263	833	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	185	591	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.775	0.716	0.838	0.775	0.716	0.838	SUBCLONAL	1	TRUE	1	0.48	2		592	994	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656951	47656951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63749849	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	104	467	0	ENST00000233146.2:c.1147C>T	p.Arg383Ter	p.R383*	ENST00000233146	NM_000251.2	383	Cga/Tga	7/16	1	2	FACETS	0.825	0.742	0.913	0.825	0.742	0.913	CLONAL	1	TRUE	1	0.48	2		467	525	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129428	64129428	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61736650	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	209	625	0	ENST00000334205.4:c.860C>T	p.Ala287Val	p.A287V	ENST00000334205	NM_003942.2	287	gCg/gTg	8/17	1	2	FACETS	0.872	0.809	0.936	0.872	0.809	0.936	CLONAL	1	TRUE	1	0.48	2		625	999	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636729	8636729	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	135	388	0	ENST00000356435.5:c.180del	p.Gly61GlufsTer11	p.G61Efs*11	ENST00000356435		60	aaA/aa	2/35	1	2	FACETS	0.942	0.86	1	0.942	0.86	1	CLONAL	1	TRUE	1	0.48	2		388	597	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	255	500	3	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.48	2		503	944	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422384	47422384	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	134	478	0	ENST00000377045.4:c.23del	p.Pro8LeufsTer26	p.P8Lfs*26	ENST00000377045	NM_001654.4	6	ggC/gg	2/16	1	2	FACETS	0.784	0.714	0.858	0.784	0.714	0.858	SUBCLONAL	1	TRUE	1	0.48	2		478	712	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	377	578	9	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	0.91	0.868	0.952	1	0.996	1	CLONAL	2	TRUE	1	0.48	2		587	863	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944382	131944382	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs748536322	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	53	230	4	ENST00000265335.6:c.2801del	p.Asn934IlefsTer6	p.N934Ifs*6	ENST00000265335		932	Aaa/aa	17/25	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.48	2		234	217	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347983	347983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760961378	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	234	778	2	ENST00000262320.3:c.1523del	p.Gly508ValfsTer197	p.G508Vfs*197	ENST00000262320	NM_003502.3	508	gGt/gt	6/11	1	2	FACETS	0.878	0.819	0.94	0.878	0.819	0.94	CLONAL	1	TRUE	1	0.48	2		780	1110	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029576	14029576	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751782722	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	153	355	0	ENST00000311895.7:c.1787C>T	p.Ala596Val	p.A596V	ENST00000311895	NM_005236.2	596	gCg/gTg	8/11	1	2	FACETS	0.99	0.909	1	0.99	0.909	1	CLONAL	1	TRUE	1	0.48	2		355	644	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905055	50905055	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	181	539	3	ENST00000440232.2:c.342del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	113	Ggg/gg	4/27	1	2	FACETS	0.888	0.82	0.959	0.888	0.82	0.959	CLONAL	1	TRUE	1	0.48	2		542	849	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649051	37649051	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	157	485	1	ENST00000447079.4:c.2160del	p.Lys721AsnfsTer32	p.K721Nfs*32	ENST00000447079	NM_015083.1	719	tGg/tg	4/14	1	2	FACETS	0.894	0.82	0.97	0.894	0.82	0.97	CLONAL	1	TRUE	1	0.48	2		486	732	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120031	70120031	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	11	25	0	ENST00000245479.2:c.1037del	p.Pro346ArgfsTer37	p.P346Rfs*37	ENST00000245479	NM_000346.3	345	Ccc/cc	3/3	1	2	FACETS	0.588	0.412	0.799	0.588	0.412	0.799	SUBCLONAL	1	TRUE	1	0.48	2		25	78	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519505	137519506	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs780346130	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	174	489	8	ENST00000367739.4:c.1132_1133del	p.Ser378PhefsTer6	p.S378Ffs*6	ENST00000367739	NM_000416.2	378	AGt/t	7/7	0.0984246449379452	3	FACETS	1	0.978	1	0.579	0.534	0.626	INDETERMINATE	1	TRUE	1	0.48	3		497	776	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510806	157510806	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	236	616	3	ENST00000346085.5:c.3586del	p.Gln1196SerfsTer15	p.Q1196Sfs*15	ENST00000346085	NM_020732.3	1194	aCc/ac	14/20	0.0984246449379452	3	FACETS	1	0.987	1	0.613	0.572	0.656	INDETERMINATE	1	TRUE	1	0.48	3		619	994	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696461	47696461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	164	559	1	ENST00000347630.2:c.362G>A	p.Arg121Gln	p.R121Q	ENST00000347630	NM_001007230.1	121	cGg/cAg	6/11	1	2	FACETS	0.943	0.867	1	0.943	0.867	1	CLONAL	1	TRUE	1	0.48	2		560	725	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455576	189455576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754361670	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	186	598	0	ENST00000264731.3:c.110G>A	p.Arg37Gln	p.R37Q	ENST00000264731	NM_003722.4	37	cGa/cAa	2/14	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.48	2		598	646	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912716	100912716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1450222910	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	130	543	0	ENST00000325455.5:c.2606G>A	p.Arg869His	p.R869H	ENST00000325455	NM_001202474.3	869	cGt/cAt	7/8	1	2	FACETS	0.897	0.816	0.981	0.897	0.816	0.981	CLONAL	1	TRUE	1	0.48	2		543	604	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050708	30050708	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	151	382	0	ENST00000338641.4:c.514del	p.Arg172GlyfsTer2	p.R172Gfs*2	ENST00000338641	NM_000268.3	170	ccA/cc	5/16	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.48	2		382	623	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834548	156834548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763164402	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	250	852	0	ENST00000524377.1:c.316G>A	p.Val106Met	p.V106M	ENST00000524377	NM_002529.3	106	Gtg/Atg	3/17	1	2	FACETS	0.884	0.826	0.943	0.884	0.826	0.943	CLONAL	1	TRUE	1	0.48	2		852	1179	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264348	46264348	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	48	437	0	ENST00000371998.3:c.1400del	p.Pro467HisfsTer15	p.P467Hfs*15	ENST00000371998		465	agC/ag	11/23	1	2	FACETS	0.258	0.218	0.304	0.258	0.218	0.304	SUBCLONAL	1	TRUE	1	0.48	2		437	774	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864757	57864757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138157845	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	275	703	1	ENST00000228682.2:c.2234C>T	p.Ala745Val	p.A745V	ENST00000228682	NM_005269.2	745	gCg/gTg	12/12	0.200709584188044	4	FACETS	0.777	0.73	0.826	0.777	0.73	0.826	INDETERMINATE	2	TRUE	2	0.48	4		704	1091	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714679	52714679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	227	658	0	ENST00000322088.6:c.437C>T	p.Ser146Leu	p.S146L	ENST00000322088	NM_014225.5	146	tCg/tTg	4/15	1	2	FACETS	0.872	0.812	0.934	0.872	0.812	0.934	CLONAL	1	TRUE	1	0.48	2		658	1085	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499362	89499363	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	191	444	2	ENST00000336596.2:c.2538dup	p.Met847HisfsTer26	p.M847Hfs*26	ENST00000336596	NM_005233.5	844	-/C	15/17	1	2	FACETS	0.944	0.874	1	0.944	0.874	1	CLONAL	1	TRUE	1	0.48	2		446	843	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511116	148511116	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139878257	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	212	590	2	ENST00000320356.2:c.1786G>A	p.Ala596Thr	p.A596T	ENST00000320356	NM_004456.4	596	Gct/Act	15/20	1	2	FACETS	0.923	0.858	0.99	0.923	0.858	0.99	CLONAL	1	TRUE	1	0.48	2		592	957	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619821	1619821	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	215	655	0	ENST00000344749.5:c.1125del	p.Gly376ValfsTer18	p.G376Vfs*18	ENST00000344749	NM_001136139.2	375	ccC/cc	14/19	1	2	FACETS	0.783	0.727	0.841	0.783	0.727	0.841	SUBCLONAL	1	TRUE	1	0.48	2		655	1144	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129397	30129397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764219989	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	216	681	3	ENST00000263025.4:c.631C>T	p.Arg211Trp	p.R211W	ENST00000263025	NM_002746.2	211	Cgg/Tgg	4/9	1	2	FACETS	0.87	0.809	0.934	0.87	0.809	0.934	CLONAL	1	TRUE	1	0.48	2		684	1034	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710566	40710566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760820896	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	248	694	0	ENST00000373198.4:c.4285G>A	p.Val1429Met	p.V1429M	ENST00000373198	NM_133170.3	1429	Gtg/Atg	31/32	1	2	FACETS	0.865	0.808	0.924	0.865	0.808	0.924	CLONAL	1	TRUE	1	0.48	2		694	1194	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600424	10600425	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	245	679	0	ENST00000171111.5:c.1430dup	p.Phe478LeufsTer2	p.F478Lfs*2	ENST00000171111	NM_203500.1	477	ggc/ggGc	4/6	1	2	FACETS	0.824	0.769	0.881	0.824	0.769	0.881	CLONAL	1	TRUE	1	0.48	2		679	1239	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401008	139401008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763098618	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	228	700	0	ENST00000277541.6:c.3985G>A	p.Ala1329Thr	p.A1329T	ENST00000277541	NM_017617.3	1329	Gcc/Acc	24/34	1	2	FACETS	0.918	0.855	0.983	0.918	0.855	0.983	CLONAL	1	TRUE	1	0.48	2		700	1035	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775756	9775756	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	216	701	0	ENST00000377346.4:c.299G>A	p.Arg100His	p.R100H	ENST00000377346	NM_005026.3	100	cGc/cAc	4/24	1	2	FACETS	0.864	0.803	0.927	0.864	0.803	0.927	CLONAL	1	TRUE	1	0.48	2		701	1042	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784974	9784974	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	200	529	1	ENST00000377346.4:c.2977A>G	p.Lys993Glu	p.K993E	ENST00000377346	NM_005026.3	993	Aaa/Gaa	23/24	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.48	2		530	828	SUCCESS
H3C13	653604	MSKCC	GRCh37	1	149784868	149784868	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	88	230	0	ENST00000331491.1:c.369G>T	p.Lys123Asn	p.K123N	ENST00000331491	NM_001123375.2	123	aaG/aaT	1/1	1	2	FACETS	0.943	0.841	1	0.943	0.841	1	CLONAL	1	TRUE	1	0.48	2		230	389	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193202218	193202218	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	158	458	0	ENST00000367435.3:c.1250C>T	p.Thr417Ile	p.T417I	ENST00000367435	NM_024529.4	417	aCt/aTt	14/17	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.48	2		458	568	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942124	71942124	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	221	732	0	ENST00000298229.2:c.1388C>A	p.Pro463His	p.P463H	ENST00000298229	NM_001567.3	463	cCc/cAc	12/28	1	2	FACETS	0.848	0.789	0.909	0.848	0.789	0.909	CLONAL	1	TRUE	1	0.48	2		732	1086	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245688	46245688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1199501070	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	160	406	0	ENST00000334344.6:c.3782G>A	p.Arg1261His	p.R1261H	ENST00000334344	NM_152641.2	1261	cGt/cAt	15/21	0.200709584188044	4	FACETS	1	0.985	1	0.668	0.613	0.724	INDETERMINATE	1	TRUE	2	0.48	4		406	739	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424177	49424178	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	89	415	1	ENST00000301067.7:c.13884dup	p.Thr4629HisfsTer18	p.T4629Hfs*18	ENST00000301067	NM_003482.3	4628	-/C	42/54	0.200709584188044	4	FACETS	0.938	0.833	1	0.469	0.416	0.525	INDETERMINATE	1	TRUE	2	0.48	4		416	585	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331817	68331817	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	227	565	0	ENST00000487270.1:c.413T>C	p.Val138Ala	p.V138A	ENST00000487270	NM_133509.3	138	gTg/gCg	5/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.48	2		565	786	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058576	42058577	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	113	407	0	ENST00000219905.7:c.8301_8302del	p.Arg2767SerfsTer10	p.R2767Sfs*10	ENST00000219905	NM_001164273.1	2766	GAg/g	24/24	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.48	2		407	388	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701293	43701293	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	190	403	0	ENST00000382044.4:c.5402G>A	p.Cys1801Tyr	p.C1801Y	ENST00000382044	NM_001141980.1	1801	tGt/tAt	26/28	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.48	2		403	789	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992861	72992862	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	206	550	0	ENST00000268489.5:c.1183_1184del	p.Leu395AspfsTer59	p.L395Dfs*59	ENST00000268489	NM_006885.3	395	TTg/g	2/10	1	2	FACETS	0.933	0.866	1	0.933	0.866	1	CLONAL	1	TRUE	1	0.48	2		550	920	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896593	78896593	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	166	607	0	ENST00000306801.3:c.2590C>T	p.Pro864Ser	p.P864S	ENST00000306801	NM_020761.2	864	Ccc/Tcc	22/34	1	2	FACETS	0.771	0.708	0.837	0.771	0.708	0.837	SUBCLONAL	1	TRUE	1	0.48	2		607	897	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267523	7267523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	148	700	2	ENST00000302850.5:c.485G>A	p.Arg162His	p.R162H	ENST00000302850	NM_000208.2	162	cGt/cAt	2/22	1	2	FACETS	0.575	0.524	0.628	0.575	0.524	0.628	SUBCLONAL	1	TRUE	1	0.48	2		702	1073	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610292	10610292	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201447398	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	272	800	1	ENST00000171111.5:c.418G>A	p.Ala140Thr	p.A140T	ENST00000171111	NM_203500.1	140	Gcc/Acc	2/6	1	2	FACETS	0.864	0.809	0.92	0.864	0.809	0.92	CLONAL	1	TRUE	1	0.48	2		801	1312	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976896	18976896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1333445130	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	241	596	0	ENST00000262803.5:c.3281C>T	p.Ala1094Val	p.A1094V	ENST00000262803	NM_002911.3	1094	gCg/gTg	23/24	1	2	FACETS	0.95	0.887	1	0.95	0.887	1	CLONAL	1	TRUE	1	0.48	2		596	1057	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228051	36228051	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	233	742	0	ENST00000222270.7:c.7440del	p.Gly2481GlufsTer24	p.G2481Efs*24	ENST00000222270	NM_014727.1	2479	ctC/ct	33/37	1	2	FACETS	0.833	0.776	0.892	0.833	0.776	0.892	CLONAL	1	TRUE	1	0.48	2		742	1166	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724280	52724280	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	238	555	0	ENST00000322088.6:c.1415del	p.Lys472SerfsTer28	p.K472Sfs*28	ENST00000322088	NM_014225.5	471	gAa/ga	12/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.48	2		555	934	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249950	39249950	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	177	743	0	ENST00000402219.2:c.1619C>T	p.Ala540Val	p.A540V	ENST00000402219	NM_005633.3	540	gCa/gTa	10/23	1	2	FACETS	0.869	0.801	0.939	0.869	0.801	0.939	CLONAL	1	TRUE	1	0.48	2		743	849	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46602864	46602864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1245767976	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	248	614	0	ENST00000263734.3:c.922C>T	p.Arg308Trp	p.R308W	ENST00000263734	NM_001430.4	308	Cgg/Tgg	8/16	1	2	FACETS	0.906	0.846	0.967	0.906	0.846	0.967	CLONAL	1	TRUE	1	0.48	2		614	1141	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607400	46607400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	257	752	0	ENST00000263734.3:c.1589C>T	p.Ala530Val	p.A530V	ENST00000263734	NM_001430.4	530	gCa/gTa	12/16	1	2	FACETS	0.943	0.882	1	0.943	0.882	1	CLONAL	1	TRUE	1	0.48	2		752	1136	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702411	47702411	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	49	221	0	ENST00000233146.2:c.2005+2T>G		p.X669_splice	ENST00000233146	NM_000251.2	669			1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.48	2		221	186	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209110041	209110041	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	139	508	0	ENST00000345146.2:c.520+2T>C		p.X174_splice	ENST00000345146	NM_005896.2	174			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.48	2		508	499	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225367767	225367767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753045999	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	119	509	0	ENST00000264414.4:c.1400C>T	p.Thr467Met	p.T467M	ENST00000264414	NM_003590.4	467	aCg/aTg	10/16	1	2	FACETS	0.952	0.863	1	0.952	0.863	1	CLONAL	1	TRUE	1	0.48	2		509	521	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661675	227661675	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753804742	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	185	539	2	ENST00000305123.5:c.1780C>T	p.Arg594Cys	p.R594C	ENST00000305123	NM_005544.2	594	Cgt/Tgt	1/2	1	2	FACETS	0.924	0.854	0.997	0.924	0.854	0.997	CLONAL	1	TRUE	1	0.48	2		541	834	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561033	9561033	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	198	495	0	ENST00000353224.5:c.749T>C	p.Leu250Pro	p.L250P	ENST00000353224	NM_177990.2	250	cTg/cCg	4/10	1	2	FACETS	0.984	0.913	1	0.984	0.913	1	CLONAL	1	TRUE	1	0.48	2		495	838	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509756	187509756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376922855	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	105	297	1	ENST00000441802.2:c.13757C>T	p.Thr4586Met	p.T4586M	ENST00000441802	NM_005245.3	4586	aCg/aTg	27/27	1	2	FACETS	0.943	0.849	1	0.943	0.849	1	CLONAL	1	TRUE	1	0.48	2		298	464	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522579	176522579	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	200	655	1	ENST00000292408.4:c.1676G>T	p.Arg559Leu	p.R559L	ENST00000292408	NM_213647.1	559	cGg/cTg	13/18	1	2	FACETS	0.856	0.793	0.921	0.856	0.793	0.921	CLONAL	1	TRUE	1	0.48	2		656	974	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638879	176638879	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	231	663	0	ENST00000439151.2:c.3479G>A	p.Trp1160Ter	p.W1160*	ENST00000439151	NM_022455.4	1160	tGg/tAg	5/23	1	2	FACETS	0.989	0.923	1	0.989	0.923	1	CLONAL	1	TRUE	1	0.48	2		663	973	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820017	32820017	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	238	676	1	ENST00000354258.4:c.894-1G>A		p.X298_splice	ENST00000354258	NM_000593.5	298			0.0984246449379452	3	FACETS	1	0.982	1	0.571	0.533	0.61	INDETERMINATE	1	TRUE	1	0.48	3		677	1077	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066671	94066671	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	255	588	0	ENST00000369303.4:c.1088T>C	p.Val363Ala	p.V363A	ENST00000369303	NM_004440.3	363	gTg/gCg	5/17	0.0984246449379452	3	FACETS	1	0.991	1	0.663	0.621	0.706	INDETERMINATE	1	TRUE	1	0.48	3		588	994	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266457	55266457	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775695605	NA	P-0033122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	274	596	0	ENST00000275493.2:c.2749G>A	p.Gly917Arg	p.G917R	ENST00000275493	NM_005228.3	917	Gga/Aga	23/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.48	2		596	1053	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0033123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	152	645	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.170415178227765	0	FACETS	0.741	0.687	0.795			1	INDETERMINATE	2	FALSE	0	0.361786811958394	0		645	362	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0033123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	112	531	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.361786811958394	1	FACETS	1	0.982	1	1	0.991	1	CLONAL	2	FALSE	0	0.361786811958394	1		531	204	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0033123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	147	236	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	0.937	0.873	1	1	0.994	1	CLONAL	3	FALSE	1	0.361786811958394	2		236	289	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087452	27087452	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	354	676	0	ENST00000324856.7:c.2027del	p.Pro676GlnfsTer66	p.P676Qfs*66	ENST00000324856	NM_006015.4	676	Cca/ca	5/20	0.361786811958394	2	FACETS	0.991	0.969	1	1	0.997	1	CLONAL	5	FALSE	0	0.361786811958394	2		676	395	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95577653	95577653	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691231	NA	P-0033123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	53	478	2	ENST00000393063.1:c.2256+1G>A		p.X752_splice	ENST00000393063	NM_030621.3	752			1	2	FACETS	0.993	0.853	1	0.993	0.853	1	CLONAL	1	FALSE	1	0.361786811958394	2		480	295	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860517	151860517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772864510	NA	P-0033123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	72	677	0	ENST00000262189.6:c.10145G>A	p.Arg3382Gln	p.R3382Q	ENST00000262189	NM_170606.2	3382	cGg/cAg	43/59	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	FALSE	1	0.361786811958394	2		677	385	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497808	25497808	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0033128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	49	542	0	ENST00000264709.3:c.639+2T>C		p.X213_splice	ENST00000264709	NM_175629.2	213			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		542	156	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0033131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	187	483	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.288755981087863	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.288755981087863	2		483	588	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	170	441	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.288755981087863	3	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	TRUE	1	0.288755981087863	3		441	670	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0033131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	76	196	2	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.756	0.663	0.857	0.756	0.663	0.857	SUBCLONAL	1	TRUE	1	0.288755981087863	2		198	696	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136799	2136799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137854153	NA	P-0033131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	141	758	1	ENST00000219476.3:c.4916G>A	p.Arg1639His	p.R1639H	ENST00000219476	NM_000548.3	1639	cGc/cAc	38/42	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.288755981087863	2		759	829	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830754	3830754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	82	445	0	ENST00000262367.5:c.1802G>A	p.Arg601Gln	p.R601Q	ENST00000262367	NM_004380.2	601	cGg/cAg	8/31	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.288755981087863	2		445	527	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409146	4409146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587777621	NA	P-0033131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	140	366	0	ENST00000261254.3:c.841C>T	p.Pro281Ser	p.P281S	ENST00000261254	NM_001759.3	281	Cct/Tct	5/5	0.288755981087863	3	FACETS	0.984	0.9	1	0.984	0.9	1	CLONAL	2	TRUE	1	0.288755981087863	3		366	564	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903736	114903736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	71	502	0	ENST00000543371.1:c.740C>T	p.Pro247Leu	p.P247L	ENST00000543371	NM_001198531.1	247	cCt/cTt	7/14	1	2	FACETS	0.762	0.665	0.867	0.762	0.665	0.867	SUBCLONAL	1	TRUE	1	0.288755981087863	2		502	645	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117861	70117861	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	125	446	1	ENST00000245479.2:c.329A>G	p.Asn110Ser	p.N110S	ENST00000245479	NM_000346.3	110	aAc/aGc	1/3	0.288755981087863	3	FACETS	0.968	0.88	1	0.968	0.88	1	CLONAL	2	TRUE	1	0.288755981087863	3		447	512	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374931	45374931	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	69	525	0	ENST00000262160.6:c.912C>G	p.Asp304Glu	p.D304E	ENST00000262160	NM_005901.5	304	gaC/gaG	8/11	1	2	FACETS	0.708	0.616	0.807	0.708	0.616	0.807	SUBCLONAL	1	TRUE	1	0.288755981087863	2		525	675	SUCCESS
ALK	238	MSKCC	GRCh37	2	29448363	29448363	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	97	921	0	ENST00000389048.3:c.3136G>A	p.Ala1046Thr	p.A1046T	ENST00000389048	NM_004304.4	1046	Gcc/Acc	19/29	1	2	FACETS	0.715	0.636	0.799	0.715	0.636	0.799	SUBCLONAL	1	TRUE	1	0.288755981087863	2		921	940	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568576	41568576	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	88	664	0	ENST00000263253.7:c.4526G>C	p.Trp1509Ser	p.W1509S	ENST00000263253	NM_001429.3	1509	tGg/tCg	28/31	1	2	FACETS	0.908	0.805	1	0.908	0.805	1	CLONAL	1	TRUE	1	0.288755981087863	2		664	671	SUCCESS
APC	324	MSKCC	GRCh37	5	112175199	112175199	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	84	243	0	ENST00000257430.4:c.3910del	p.Ile1304Ter	p.I1304*	ENST00000257430	NM_000038.5	1303	cAa/ca	16/16	0.288755981087863	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.288755981087863	2		243	268	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467831	50467831	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	53	390	0	ENST00000331340.3:c.1066G>A	p.Glu356Lys	p.E356K	ENST00000331340	NM_006060.4	356	Gag/Aag	8/8	0.288755981087863	3	FACETS	0.979	0.837	1	0.49	0.418	0.567	CLONAL	1	TRUE	1	0.288755981087863	3		390	429	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877870	151877870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	90	438	0	ENST00000262189.6:c.7075G>A	p.Val2359Met	p.V2359M	ENST00000262189	NM_170606.2	2359	Gtg/Atg	36/59	0.288755981087863	3	FACETS	1	0.957	1	0.58	0.515	0.649	CLONAL	1	TRUE	1	0.288755981087863	3		438	615	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864280	117864283	+	frameshift_variant	Frame_Shift_Del	DEL	GCTG	GCTG	-	novel	NA	P-0033131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	67	522	0	ENST00000297338.2:c.1374_1377del	p.Ser459GlufsTer4	p.S459Efs*4	ENST00000297338	NM_006265.2	458	gcCAGC/gc	11/14	1	2	FACETS	0.768	0.668	0.877	0.768	0.668	0.877	SUBCLONAL	1	TRUE	1	0.288755981087863	2		522	604	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211545	98211545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370675945	NA	P-0033131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	74	507	1	ENST00000331920.6:c.3610G>A	p.Val1204Met	p.V1204M	ENST00000331920	NM_000264.3	1204	Gtg/Atg	22/24	1	2	FACETS	0.915	0.802	1	0.915	0.802	1	CLONAL	1	TRUE	1	0.288755981087863	2		508	560	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	100	264	0				ENST00000310581	NM_198253.2	-/1132			0.376306040729145	1	FACETS	0.793	0.724	0.862	0.793	0.724	0.862	INDETERMINATE	1	TRUE	0	0.732939694137278	1		264	218	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0033132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	287	743	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.732939694137278	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.732939694137278	1		743	436	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434498	121434498	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	332	770	0	ENST00000257555.6:c.1262C>T	p.Ser421Phe	p.S421F	ENST00000257555		421	tCc/tTc	6/10	0.410178483504378	3	FACETS	0.882	0.84	0.924	0.882	0.84	0.924	INDETERMINATE	2	TRUE	1	0.732939694137278	3		770	702	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929432	81929432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775728338	NA	P-0033132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	204	503	0	ENST00000359376.3:c.1093G>A	p.Asp365Asn	p.D365N	ENST00000359376	NM_002661.3	365	Gat/Aat	13/33	0.309325787171752	3	FACETS	0.801	0.751	0.851	0.801	0.751	0.851	INDETERMINATE	2	TRUE	1	0.732939694137278	3		503	475	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422845	12422845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	335	483	2	ENST00000287820.6:c.335C>T	p.Ser112Phe	p.S112F	ENST00000287820	NM_015869.4	112	tCt/tTt	3/7	0.533783746250652	3	FACETS	0.886	0.844	0.928			1	CLONAL	2	TRUE	NA	0.732939694137278	3		485	705	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252162	226252162	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	86	116	0	ENST00000366813.1:c.110A>G	p.Lys37Arg	p.K37R	ENST00000366813		37	aAg/aGg	1/3	0.312896537363894	2	FACETS	0.782	0.716	0.847	0.782	0.716	0.847	INDETERMINATE	2	TRUE	0	0.732939694137278	2		116	150	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983016	149983016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326200282	NA	P-0033132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	186	657	1	ENST00000253339.5:c.3242G>A	p.Arg1081Gln	p.R1081Q	ENST00000253339		1081	cGa/cAa	7/7	1	2	FACETS	0.999	0.931	1	0.999	0.931	1	CLONAL	1	TRUE	1	0.732939694137278	2		658	508	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164142	47164142	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	106	406	0	ENST00000409792.3:c.1984C>T	p.Gln662Ter	p.Q662*	ENST00000409792	NM_014159.6	662	Caa/Taa	3/21	0.268669834077434	3	FACETS	0.859	0.775	0.948	0.286	0.258	0.316	INDETERMINATE	1	TRUE	0	0.732939694137278	3		406	460	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004664	16004664	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	303	673	0	ENST00000268712.3:c.2590C>T	p.Gln864Ter	p.Q864*	ENST00000268712	NM_006311.3	864	Cag/Tag	20/46	0.732939694137278	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.732939694137278	1		673	454	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983019	201983019	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	14	753	0	ENST00000359651.3:c.868G>T	p.Glu290Ter	p.E290*	ENST00000359651		290	Gag/Tag	7/8	0.732939694137278	1	FACETS	0.091	0.065	0.122	0.091	0.065	0.122	SUBCLONAL	1	TRUE	0	0.732939694137278	1		753	267	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999656	100999656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1349242903	NA	P-0033132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	284	873	0	ENST00000325455.5:c.146C>T	p.Ser49Leu	p.S49L	ENST00000325455	NM_001202474.3	49	tCg/tTg	1/8	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.732939694137278	2		873	623	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938517	44938517	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs865968726	NA	P-0033132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	157	260	0	ENST00000377967.4:c.3065A>G	p.His1022Arg	p.H1022R	ENST00000377967	NM_021140.2	1022	cAt/cGt	20/29	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.732939694137278	1		260	229	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	126	290	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.966	0.882	1	1	0.992	1	CLONAL	3	TRUE	1	0.208053383764427	2		290	418	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	190	471	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.897	0.832	0.963	1	0.994	1	CLONAL	3	TRUE	1	0.208053383764427	2		471	679	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547241	106547241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	26	332	0	ENST00000369096.4:c.478C>T	p.Arg160Cys	p.R160C	ENST00000369096	NM_001198.3	160	Cgc/Tgc	4/7	0.152716978965641	3	FACETS	0.532	0.42	0.66	0.266	0.21	0.33	SUBCLONAL	1	TRUE	1	0.208053383764427	3		332	519	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201874	152201874	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753014570	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	34	343	3	ENST00000206249.3:c.728G>A	p.Arg243His	p.R243H	ENST00000206249	NM_000125.3	243	cGt/cAt	3/8	0.152716978965641	3	FACETS	0.629	0.513	0.76	0.314	0.256	0.38	SUBCLONAL	1	TRUE	1	0.208053383764427	3		346	574	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	52	651	1	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.152716978965641	3	FACETS	0.794	0.675	0.925	0.397	0.337	0.463	CLONAL	1	TRUE	1	0.208053383764427	3		652	695	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	119	348	4	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	0.208053383764427	1	FACETS	0.864	0.782	0.95	1	0.987	1	CLONAL	2	TRUE	0	0.208053383764427	1		352	593	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942053	71942053	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	70	636	1	ENST00000298229.2:c.1322del	p.Asn441ThrfsTer2	p.N441Tfs*2	ENST00000298229	NM_001567.3	439	ccA/cc	12/28	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.208053383764427	2		637	615	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11193150	11193150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764395301	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	66	496	1	ENST00000361445.4:c.5351G>A	p.Arg1784His	p.R1784H	ENST00000361445	NM_004958.3	1784	cGc/cAc	38/58	0.208053383764427	1	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	0	0.208053383764427	1		497	564	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317108	11317108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	104	520	0	ENST00000361445.4:c.386C>T	p.Ala129Val	p.A129V	ENST00000361445	NM_004958.3	129	gCc/gTc	4/58	0.208053383764427	1	FACETS	0.813	0.73	0.9	1	0.984	1	CLONAL	2	TRUE	0	0.208053383764427	1		520	551	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101004	27101004	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	56	551	0	ENST00000324856.7:c.4286A>C	p.Asn1429Thr	p.N1429T	ENST00000324856	NM_006015.4	1429	aAc/aCc	18/20	0.109200409370778	3	FACETS	0.957	0.819	1			1	INDETERMINATE	1	TRUE	NA	0.208053383764427	3		551	621	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101138	27101138	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1476360310	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	147	660	1	ENST00000324856.7:c.4420C>T	p.Gln1474Ter	p.Q1474*	ENST00000324856	NM_006015.4	1474	Caa/Taa	18/20	0.109200409370778	3	FACETS	1	0.972	1			1	INDETERMINATE	2	TRUE	NA	0.208053383764427	3		661	682	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101375	27101375	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	191	363	0	ENST00000324856.7:c.4661del	p.Pro1554HisfsTer11	p.P1554Hfs*11	ENST00000324856	NM_006015.4	1553	Ccc/cc	18/20	0.109200409370778	3	FACETS	0.891	0.829	0.954			1	INDETERMINATE	4	TRUE	NA	0.208053383764427	3		363	569	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058517	72058517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372023233	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	115	520	0	ENST00000357731.5:c.923C>T	p.Ala308Val	p.A308V	ENST00000357731	NM_173808.2	308	gCg/gTg	6/7	1	2	FACETS	0.79	0.712	0.871	1	0.985	1	SUBCLONAL	2	TRUE	1	0.208053383764427	2		520	700	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262207	115262207	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	102	313	1	ENST00000438362.2:c.2347C>T	p.Arg783Ter	p.R783*	ENST00000438362	NM_001242891.1	783	Cga/Tga	18/20	1	2	FACETS	0.911	0.818	1	1	0.986	1	CLONAL	2	TRUE	1	0.208053383764427	2		314	538	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690377	117690377	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs940554533	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	41	544	1	ENST00000369458.3:c.752T>C	p.Leu251Pro	p.L251P	ENST00000369458	NM_024626.3	251	cTa/cCa	5/6	1	2	FACETS	0.547	0.455	0.651	0.547	0.455	0.651	SUBCLONAL	1	TRUE	1	0.208053383764427	2		545	720	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870336	155870336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs938749530	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	129	545	0	ENST00000368323.3:c.503G>A	p.Arg168His	p.R168H	ENST00000368323	NM_006912.5	168	cGc/cAc	6/6	0.208053383764427	5	FACETS	0.843	0.763	0.927	0.562	0.509	0.618	CLONAL	2	TRUE	2	0.208053383764427	5		545	965	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843626	156843626	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	181	739	0	ENST00000524377.1:c.1052C>A	p.Pro351His	p.P351H	ENST00000524377	NM_002529.3	351	cCc/cAc	8/17	0.208053383764427	4	FACETS	1	0.982	1	0.81	0.748	0.875	CLONAL	2	TRUE	1	0.208053383764427	4		739	865	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724571	162724571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	57	518	1	ENST00000367921.3:c.343G>A	p.Ala115Thr	p.A115T	ENST00000367921	NM_006182.2	115	Gcc/Acc	5/18	0.208053383764427	4	FACETS	0.966	0.828	1	0.322	0.276	0.373	CLONAL	1	TRUE	1	0.208053383764427	4		519	685	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226573273	226573273	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	191	576	0	ENST00000366794.5:c.943G>A	p.Val315Ile	p.V315I	ENST00000366794	NM_001618.3	315	Gtc/Atc	7/23	0.208053383764427	4	FACETS	0.911	0.843	0.98	0.911	0.843	0.98	CLONAL	3	TRUE	1	0.208053383764427	4		576	812	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332286	70332286	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	25	321	0	ENST00000373644.4:c.191C>A	p.Pro64His	p.P64H	ENST00000373644	NM_030625.2	64	cCt/cAt	2/12	1	2	FACETS	0.562	0.442	0.7	0.562	0.442	0.7	SUBCLONAL	1	TRUE	1	0.208053383764427	2		321	428	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720805	89720805	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	85	248	0	ENST00000371953.3:c.956del	p.Thr319IlefsTer2	p.T319Ifs*2	ENST00000371953	NM_000314.4	319	aCt/at	8/9	1	2	FACETS	1	0.965	1	1	0.987	1	CLONAL	2	TRUE	1	0.208053383764427	2		248	340	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	131	304	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.999	0.915	1	1	0.992	1	CLONAL	3	TRUE	1	0.208053383764427	2		304	420	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741954	17741954	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	76	217	1	ENST00000250003.3:c.625G>T	p.Gly209Cys	p.G209C	ENST00000250003	NM_002478.4	209	Ggc/Tgc	1/3	1	2	FACETS	1	0.958	1	1	0.988	1	CLONAL	3	TRUE	1	0.208053383764427	2		218	212	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943290	71943290	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	110	573	0	ENST00000298229.2:c.1622A>C	p.Lys541Thr	p.K541T	ENST00000298229	NM_001567.3	541	aAg/aCg	14/28	1	2	FACETS	0.843	0.759	0.932	1	0.986	1	CLONAL	2	TRUE	1	0.208053383764427	2		573	627	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090968	77090968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	110	491	0	ENST00000356341.3:c.262G>A	p.Gly88Ser	p.G88S	ENST00000356341	NM_002576.4	88	Ggt/Agt	3/15	1	2	FACETS	0.867	0.781	0.958	1	0.986	1	CLONAL	2	TRUE	1	0.208053383764427	2		491	610	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212851	94212851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368403414	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	58	363	0	ENST00000323929.3:c.391G>A	p.Asp131Asn	p.D131N	ENST00000323929	NM_005591.3	131	Gat/Aat	5/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.208053383764427	2		363	436	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196880	108196880	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	48	387	1	ENST00000278616.4:c.6908del	p.Lys2303ArgfsTer7	p.K2303Rfs*7	ENST00000278616	NM_000051.3	2301	gcA/gc	47/63	1	2	FACETS	0.821	0.694	0.962	0.821	0.694	0.962	CLONAL	1	TRUE	1	0.208053383764427	2		388	562	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343381	118343381	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	70	355	0	ENST00000534358.1:c.1507C>T	p.Arg503Trp	p.R503W	ENST00000534358	NM_005933.3	503	Cgg/Tgg	3/36	1	2	FACETS	0.823	0.72	0.932	1	0.977	1	CLONAL	2	TRUE	1	0.208053383764427	2		355	409	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376554	118376554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201447376	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	23	402	1	ENST00000534358.1:c.9947C>T	p.Ala3316Val	p.A3316V	ENST00000534358	NM_005933.3	3316	gCg/gTg	27/36	1	2	FACETS	0.509	0.396	0.641	0.509	0.396	0.641	SUBCLONAL	1	TRUE	1	0.208053383764427	2		403	434	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534734	18534734	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	55	429	0	ENST00000266497.5:c.1792A>C	p.Thr598Pro	p.T598P	ENST00000266497		598	Aca/Cca	12/31	NA	2	FACETS	0.754	0.644	0.875			1	INDETERMINATE	1	TRUE	NA	0.208053383764427	2		429	701	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656251	18656251	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	178	441	0	ENST00000266497.5:c.2930C>T	p.Ala977Val	p.A977V	ENST00000266497		977	gCa/gTa	21/31	NA	2	FACETS	0.987	0.915	1			1	INDETERMINATE	3	TRUE	NA	0.208053383764427	2		441	578	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433525	49433526	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555191665	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	61	822	0	ENST00000301067.7:c.8027_8028del	p.Glu2676AlafsTer47	p.E2676Afs*47	ENST00000301067	NM_003482.3	2676	gAG/g	31/54	0.152716978965641	3	FACETS	0.725	0.624	0.836	0.362	0.312	0.418	SUBCLONAL	1	TRUE	1	0.208053383764427	3		822	893	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439884	49439884	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	115	572	1	ENST00000301067.7:c.4657T>C	p.Cys1553Arg	p.C1553R	ENST00000301067	NM_003482.3	1553	Tgt/Cgt	17/54	0.152716978965641	3	FACETS	0.884	0.798	0.976	0.884	0.798	0.976	CLONAL	2	TRUE	1	0.208053383764427	3		573	690	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488312	56488312	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373609369	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	187	461	0	ENST00000267101.3:c.1831C>T	p.Arg611Trp	p.R611W	ENST00000267101	NM_001982.3	611	Cgg/Tgg	15/28	0.152716978965641	3	FACETS	1	0.954	1	1	0.991	1	CLONAL	3	TRUE	1	0.208053383764427	3		461	638	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117762	115117762	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1400959825	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	68	310	0	ENST00000257566.3:c.673A>C	p.Ser225Arg	p.S225R	ENST00000257566	NM_016569.3	225	Agt/Cgt	3/8	0.208053383764427	1	FACETS	0.765	0.668	0.867	1	0.974	1	SUBCLONAL	2	TRUE	0	0.208053383764427	1		310	383	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220142	133220142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371712284	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	77	485	0	ENST00000320574.5:c.4295C>T	p.Pro1432Leu	p.P1432L	ENST00000320574	NM_006231.2	1432	cCg/cTg	34/49	0.208053383764427	1	FACETS	0.786	0.693	0.885	1	0.978	1	SUBCLONAL	2	TRUE	0	0.208053383764427	1		485	422	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249308	133249308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748489355	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	38	721	0	ENST00000320574.5:c.1591G>A	p.Gly531Arg	p.G531R	ENST00000320574	NM_006231.2	531	Gga/Aga	15/49	0.208053383764427	1	FACETS	0.469	0.386	0.562	0.469	0.386	0.562	SUBCLONAL	1	TRUE	0	0.208053383764427	1		721	698	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249850	133249850	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	70	347	0	ENST00000320574.5:c.1373A>G	p.Tyr458Cys	p.Y458C	ENST00000320574	NM_006231.2	458	tAt/tGt	14/49	0.208053383764427	1	FACETS	0.922	0.81	1	1	0.981	1	CLONAL	2	TRUE	0	0.208053383764427	1		347	327	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562756	21562756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs12867400	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	119	480	0	ENST00000382592.4:c.1163C>T	p.Ala388Val	p.A388V	ENST00000382592	NM_014572.2	388	gCg/gTg	4/8	0.208053383764427	1	FACETS	0.991	0.899	1	1	0.989	1	CLONAL	2	TRUE	0	0.208053383764427	1		480	517	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008057	29008057	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139202898	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	81	395	0	ENST00000282397.4:c.712C>T	p.Arg238Cys	p.R238C	ENST00000282397	NM_002019.4	238	Cgc/Tgc	6/30	0.208053383764427	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.208053383764427	1		395	478	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907347	32907347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	89	399	0	ENST00000380152.3:c.1732G>A	p.Gly578Ser	p.G578S	ENST00000380152		578	Ggt/Agt	10/27	0.208053383764427	1	FACETS	0.768	0.683	0.858	1	0.98	1	SUBCLONAL	2	TRUE	0	0.208053383764427	1		399	499	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913837	32913837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359507	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	164	423	4	ENST00000380152.3:c.5351del	p.Asn1784ThrfsTer7	p.N1784Tfs*7	ENST00000380152		1782	cAa/ca	11/27	0.208053383764427	1	FACETS	1	0.983	1	1	0.993	1	CLONAL	2	TRUE	0	0.208053383764427	1		427	571	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355090	73355090	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	155	484	0	ENST00000377767.4:c.280G>A	p.Val94Ile	p.V94I	ENST00000377767	NM_014953.3	94	Gtt/Att	2/21	1	2	FACETS	0.89	0.815	0.968	1	0.99	1	CLONAL	2	TRUE	1	0.208053383764427	2		484	837	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524567	103524568	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs759551120	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	40	181	0	ENST00000355739.4:c.2705dup	p.Asn902LysfsTer7	p.N902Kfs*7	ENST00000355739	NM_000123.3	900	caa/cAaa	13/15	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.208053383764427	2		181	287	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435263	110435263	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	15	208	0	ENST00000375856.3:c.3138del	p.Ala1047ProfsTer59	p.A1047Pfs*59	ENST00000375856	NM_003749.2	1046	ccC/cc	1/2	0.207751498600347	1	FACETS	0.55	0.402	0.727	0.55	0.402	0.727	SUBCLONAL	1	TRUE	0	0.208053383764427	1		208	235	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435613	110435613	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	75	372	0	ENST00000375856.3:c.2788C>T	p.Arg930Cys	p.R930C	ENST00000375856	NM_003749.2	930	Cgc/Tgc	1/2	0.207751498600347	1	FACETS	0.839	0.739	0.945	1	0.98	1	CLONAL	2	TRUE	0	0.208053383764427	1		372	385	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068872	30068872	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	68	619	1	ENST00000331968.5:c.2057del	p.Leu686Ter	p.L686*	ENST00000331968	NM_002742.2	686	tTa/ta	14/18	1	2	FACETS	0.87	0.756	0.994	0.87	0.756	0.994	CLONAL	1	TRUE	1	0.208053383764427	2		620	751	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194853	30194853	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs778489882	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	110	491	0	ENST00000331968.5:c.292T>C	p.Tyr98His	p.Y98H	ENST00000331968	NM_002742.2	98	Tat/Cat	2/18	1	2	FACETS	0.794	0.714	0.878	1	0.985	1	SUBCLONAL	2	TRUE	1	0.208053383764427	2		491	666	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988217	36988217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	53	373	0	ENST00000354822.5:c.436G>A	p.Ala146Thr	p.A146T	ENST00000354822	NM_001079668.2	146	Gcc/Acc	2/3	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.208053383764427	2		373	410	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590730	95590730	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	111	427	2	ENST00000393063.1:c.1179G>T	p.Gln393His	p.Q393H	ENST00000393063	NM_030621.3	393	caG/caT	9/28	1	2	FACETS	0.876	0.789	0.967	1	0.987	1	CLONAL	2	TRUE	1	0.208053383764427	2		429	609	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708519	43708519	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	162	755	1	ENST00000382044.4:c.4777C>A	p.Leu1593Met	p.L1593M	ENST00000382044	NM_001141980.1	1593	Ctg/Atg	22/28	1	2	FACETS	0.882	0.809	0.958	1	0.991	1	CLONAL	2	TRUE	1	0.208053383764427	2		756	883	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473717	67473717	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753486471	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	99	539	0	ENST00000327367.4:c.797C>T	p.Ser266Leu	p.S266L	ENST00000327367	NM_005902.3	266	tCg/tTg	6/9	1	2	FACETS	0.884	0.792	0.982	1	0.985	1	CLONAL	2	TRUE	1	0.208053383764427	2		539	538	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476259	88476259	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	75	507	0	ENST00000360948.2:c.1873C>A	p.Leu625Met	p.L625M	ENST00000360948	NM_001012338.2	625	Ctg/Atg	15/19	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.208053383764427	2		507	553	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354308	354308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757610038	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	114	498	0	ENST00000262320.3:c.1250G>A	p.Arg417His	p.R417H	ENST00000262320	NM_003502.3	417	cGc/cAc	5/11	0.208053383764427	1	FACETS	0.984	0.89	1	1	0.989	1	CLONAL	2	TRUE	0	0.208053383764427	1		498	499	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130243	2130243	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45517295	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	88	610	0	ENST00000219476.3:c.3475C>T	p.Arg1159Trp	p.R1159W	ENST00000219476	NM_000548.3	1159	Cgg/Tgg	30/42	0.208053383764427	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.208053383764427	1		610	597	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222242	2222242	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs892092927	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	115	536	0	ENST00000326181.6:c.526G>A	p.Ala176Thr	p.A176T	ENST00000326181	NM_032271.2	176	Gcg/Acg	8/21	0.208053383764427	1	FACETS	0.837	0.756	0.922	1	0.986	1	CLONAL	2	TRUE	0	0.208053383764427	1		536	592	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223535	2223535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	125	554	1	ENST00000326181.6:c.1066C>T	p.Arg356Trp	p.R356W	ENST00000326181	NM_032271.2	356	Cgg/Tgg	11/21	0.208053383764427	1	FACETS	0.943	0.857	1	1	0.989	1	CLONAL	2	TRUE	0	0.208053383764427	1		555	571	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632671	3632671	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752633436	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	167	696	1	ENST00000294008.3:c.5177C>T	p.Ala1726Val	p.A1726V	ENST00000294008	NM_032444.2	1726	gCg/gTg	15/15	0.208053383764427	1	FACETS	1	0.979	1	1	0.993	1	CLONAL	2	TRUE	0	0.208053383764427	1		697	615	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640698	3640698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs546628836	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	126	683	1	ENST00000294008.3:c.2941G>A	p.Gly981Arg	p.G981R	ENST00000294008	NM_032444.2	981	Ggg/Agg	12/15	0.208053383764427	1	FACETS	0.789	0.715	0.866	1	0.986	1	SUBCLONAL	2	TRUE	0	0.208053383764427	1		684	688	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900611	3900611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757321118	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	120	578	2	ENST00000262367.5:c.485C>T	p.Ala162Val	p.A162V	ENST00000262367	NM_004380.2	162	gCg/gTg	2/31	0.208053383764427	1	FACETS	0.894	0.81	0.982	1	0.988	1	CLONAL	2	TRUE	0	0.208053383764427	1		580	578	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862833	9862833	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	84	540	1	ENST00000330684.3:c.2470C>A	p.Leu824Met	p.L824M	ENST00000330684	NM_001134407.1	824	Ctg/Atg	12/13	0.208053383764427	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.208053383764427	1		541	578	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892274	9892274	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	80	412	1	ENST00000330684.3:c.2216C>T	p.Ala739Val	p.A739V	ENST00000330684	NM_001134407.1	739	gCt/gTt	11/13	0.208053383764427	1	FACETS	0.788	0.697	0.886	1	0.979	1	SUBCLONAL	2	TRUE	0	0.208053383764427	1		413	437	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50820786	50820786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	65	399	1	ENST00000398568.2:c.1961C>T	p.Thr654Ile	p.T654I	ENST00000398568	NM_001042412.1	654	aCa/aTa	12/18	0.208053383764427	0	FACETS	0.79	0.691	0.897			1	SUBCLONAL	2	TRUE	0	0.208053383764427	0		400	313	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348283	89348283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781186923	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	149	938	0	ENST00000301030.4:c.4667C>T	p.Ala1556Val	p.A1556V	ENST00000301030	NM_001256183.1	1556	gCg/gTg	9/13	0.208053383764427	0	FACETS	0.936	0.859	1			1	CLONAL	2	TRUE	0	0.208053383764427	0		938	606	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89851341	89851341	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1226302370	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	20	428	0	ENST00000389301.3:c.1391G>A	p.Gly464Asp	p.G464D	ENST00000389301	NM_000135.2	464	gGc/gAc	15/43	0.208053383764427	0	FACETS	0.436	0.333	0.557			1	SUBCLONAL	1	TRUE	0	0.208053383764427	0		428	349	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89880998	89880998	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	24	484	0	ENST00000389301.3:c.213del	p.Lys71AsnfsTer7	p.K71Nfs*7	ENST00000389301	NM_000135.2	71	aaA/aa	3/43	0.208053383764427	0	FACETS	0.407	0.318	0.51			1	SUBCLONAL	1	TRUE	0	0.208053383764427	0		484	449	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108301	8108301	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	123	578	0	ENST00000585124.1:c.923T>G	p.Leu308Arg	p.L308R	ENST00000585124	NM_004217.3	308	cTc/cGc	9/9	1	2	FACETS	0.778	0.704	0.856	1	0.986	1	SUBCLONAL	2	TRUE	1	0.208053383764427	2		578	760	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984785	11984785	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	67	383	0	ENST00000353533.5:c.331G>A	p.Gly111Arg	p.G111R	ENST00000353533	NM_003010.3	111	Gga/Aga	3/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.208053383764427	2		383	441	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044570	12044570	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	59	510	0	ENST00000353533.5:c.1193T>C	p.Val398Ala	p.V398A	ENST00000353533	NM_003010.3	398	gTc/gCc	11/11	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.208053383764427	2		510	558	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559807	29559807	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	73	315	1	ENST00000356175.3:c.3404C>A	p.Ser1135Tyr	p.S1135Y	ENST00000356175	NM_000267.3	1135	tCt/tAt	26/57	1	2	FACETS	0.822	0.722	0.929	1	0.978	1	CLONAL	2	TRUE	1	0.208053383764427	2		316	427	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322675	30322675	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	115	578	1	ENST00000322652.5:c.1688G>A	p.Arg563His	p.R563H	ENST00000322652	NM_015355.2	563	cGt/cAt	14/16	1	2	FACETS	0.798	0.719	0.88	1	0.985	1	SUBCLONAL	2	TRUE	1	0.208053383764427	2		579	693	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243953	41243953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	122	639	0	ENST00000357654.3:c.3595G>A	p.Ala1199Thr	p.A1199T	ENST00000357654	NM_007294.3	1199	Gct/Act	10/23	1	2	FACETS	0.769	0.695	0.846	1	0.985	1	SUBCLONAL	2	TRUE	1	0.208053383764427	2		639	763	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47685275	47685275	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	89	415	0	ENST00000347630.2:c.675del	p.Phe225LeufsTer30	p.F225Lfs*30	ENST00000347630	NM_001007230.1	225	ttT/tt	8/11	1	2	FACETS	0.864	0.769	0.965	1	0.983	1	CLONAL	2	TRUE	1	0.208053383764427	2		415	495	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532456	63532456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780123	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	129	580	1	ENST00000307078.5:c.2123C>T	p.Ser708Leu	p.S708L	ENST00000307078	NM_004655.3	708	tCg/tTg	8/11	1	2	FACETS	0.963	0.875	1	1	0.99	1	CLONAL	2	TRUE	1	0.208053383764427	2		581	644	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612376	1612376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763884772	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	39	665	0	ENST00000344749.5:c.1643G>A	p.Arg548His	p.R548H	ENST00000344749	NM_001136139.2	548	cGc/cAc	18/19	0.208053383764427	1	FACETS	0.443	0.365	0.529	0.443	0.365	0.529	SUBCLONAL	1	TRUE	0	0.208053383764427	1		665	759	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632402	1632402	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	45	564	0	ENST00000344749.5:c.148C>A	p.Leu50Ile	p.L50I	ENST00000344749	NM_001136139.2	50	Ctt/Att	4/19	0.208053383764427	1	FACETS	0.649	0.545	0.765	0.649	0.545	0.765	SUBCLONAL	1	TRUE	0	0.208053383764427	1		564	597	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226943	2226943	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150855728	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	91	444	1	ENST00000398665.3:c.4423G>A	p.Ala1475Thr	p.A1475T	ENST00000398665	NM_032482.2	1475	Gcg/Acg	27/28	0.208053383764427	1	FACETS	0.885	0.789	0.985	1	0.984	1	CLONAL	2	TRUE	0	0.208053383764427	1		445	443	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3120995	3120995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1461947710	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	76	383	2	ENST00000078429.4:c.898C>T	p.Arg300Trp	p.R300W	ENST00000078429	NM_002067.2	300	Cgg/Tgg	7/7	0.208053383764427	1	FACETS	0.841	0.742	0.947	1	0.98	1	CLONAL	2	TRUE	0	0.208053383764427	1		385	389	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220303	5220303	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	77	633	0	ENST00000357368.4:c.3517C>A	p.Leu1173Met	p.L1173M	ENST00000357368	NM_002850.3	1173	Ctg/Atg	21/38	0.208053383764427	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.208053383764427	1		633	477	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244100	5244100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1174113999	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	36	735	0	ENST00000357368.4:c.1382G>A	p.Arg461His	p.R461H	ENST00000357368	NM_002850.3	461	cGc/cAc	11/38	0.208053383764427	1	FACETS	0.528	0.433	0.635	0.528	0.433	0.635	SUBCLONAL	1	TRUE	0	0.208053383764427	1		735	587	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7168029	7168029	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	32	523	0	ENST00000302850.5:c.1560G>C	p.Trp520Cys	p.W520C	ENST00000302850	NM_000208.2	520	tgG/tgC	7/22	0.208053383764427	1	FACETS	0.456	0.369	0.555	0.456	0.369	0.555	SUBCLONAL	1	TRUE	0	0.208053383764427	1		523	604	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247892	10247892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	149	607	0	ENST00000340748.4:c.4310G>A	p.Arg1437His	p.R1437H	ENST00000340748		1437	cGc/cAc	36/40	0.208053383764427	1	FACETS	1	0.924	1	1	0.991	1	CLONAL	2	TRUE	0	0.208053383764427	1		607	636	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123688	11123688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	163	509	0	ENST00000358026.2:c.2338G>A	p.Glu780Lys	p.E780K	ENST00000358026	NM_001128849.1	780	Gag/Aag	16/36	1	2	FACETS	1	0.966	1	1	0.993	1	CLONAL	2	TRUE	1	0.208053383764427	2		509	717	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132498	11132498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	131	641	0	ENST00000358026.2:c.2714G>A	p.Arg905His	p.R905H	ENST00000358026	NM_001128849.1	905	cGc/cAc	19/36	1	2	FACETS	0.891	0.809	0.976	1	0.989	1	CLONAL	2	TRUE	1	0.208053383764427	2		641	707	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627456	14627456	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	106	630	0	ENST00000254322.2:c.614C>T	p.Thr205Ile	p.T205I	ENST00000254322	NM_006145.1	205	aCc/aTc	2/3	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.208053383764427	2		630	783	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271531	15271531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	130	813	0	ENST00000263388.2:c.6908C>T	p.Ala2303Val	p.A2303V	ENST00000263388	NM_000435.2	2303	gCc/gTc	33/33	0.146173484516265	0	FACETS	0.735	0.668	0.806			1	SUBCLONAL	2	TRUE	0	0.208053383764427	0		813	673	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349892	15349892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1427595023	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	106	524	1	ENST00000263377.2:c.3760C>T	p.Arg1254Trp	p.R1254W	ENST00000263377	NM_058243.2	1254	Cgg/Tgg	18/20	0.146173484516265	0	FACETS	0.802	0.722	0.886			1	CLONAL	2	TRUE	0	0.208053383764427	0		525	503	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19261510	19261510	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	201	651	1	ENST00000162023.5:c.35T>G	p.Leu12Arg	p.L12R	ENST00000162023		12	cTg/cGg	6/13	0.146173484516265	0	FACETS	0.762	0.71	0.817			1	SUBCLONAL	3	TRUE	0	0.208053383764427	0		652	669	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221756	36221756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377420237	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	89	666	0	ENST00000222270.7:c.5425G>A	p.Ala1809Thr	p.A1809T	ENST00000222270	NM_014727.1	1809	Gcc/Acc	26/37	0.146173484516265	0	FACETS	0.932	0.826	1			1	CLONAL	1	TRUE	0	0.208053383764427	0		666	727	SUCCESS
AXL	558	MSKCC	GRCh37	19	41759547	41759547	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	31	650	0	ENST00000301178.4:c.1970C>T	p.Ala657Val	p.A657V	ENST00000301178	NM_021913.4	657	gCc/gTc	17/20	0.146173484516265	0	FACETS	0.402	0.324	0.491			1	SUBCLONAL	1	TRUE	0	0.208053383764427	0		650	587	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467204	25467204	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	69	397	0	ENST00000264709.3:c.1671C>A	p.Cys557Ter	p.C557*	ENST00000264709	NM_175629.2	557	tgC/tgA	15/23	1	2	FACETS	0.831	0.727	0.942	1	0.977	1	CLONAL	2	TRUE	1	0.208053383764427	2		397	399	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505508	25505508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753287419	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	109	660	0	ENST00000264709.3:c.250G>A	p.Ala84Thr	p.A84T	ENST00000264709	NM_175629.2	84	Gcc/Acc	4/23	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.208053383764427	2		660	724	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213372	39213372	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	50	790	0	ENST00000402219.2:c.3595T>G	p.Ser1199Ala	p.S1199A	ENST00000402219	NM_005633.3	1199	Tca/Gca	23/23	1	2	FACETS	0.499	0.422	0.585	0.499	0.422	0.585	SUBCLONAL	1	TRUE	1	0.208053383764427	2		790	963	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224164	39224164	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	32	464	0	ENST00000402219.2:c.2980T>G	p.Leu994Val	p.L994V	ENST00000402219	NM_005633.3	994	Ttg/Gtg	19/23	1	2	FACETS	0.547	0.443	0.666	0.547	0.443	0.666	SUBCLONAL	1	TRUE	1	0.208053383764427	2		464	562	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637326	47637326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759712763	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	153	737	3	ENST00000233146.2:c.460G>A	p.Ala154Thr	p.A154T	ENST00000233146	NM_000251.2	154	Gca/Aca	3/16	1	2	FACETS	0.85	0.778	0.926	1	0.99	1	CLONAL	2	TRUE	1	0.208053383764427	2		740	865	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025857	48025857	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs267608041	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	83	300	2	ENST00000234420.5:c.741del	p.Lys247AsnfsTer32	p.K247Nfs*32	ENST00000234420	NM_000179.2	245	atA/at	4/10	1	2	FACETS	0.934	0.829	1	1	0.984	1	CLONAL	2	TRUE	1	0.208053383764427	2		302	427	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027196	48027196	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs267608083	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	84	487	1	ENST00000234420.5:c.2079del	p.Lys693AsnfsTer43	p.K693Nfs*43	ENST00000234420	NM_000179.2	692	Aaa/aa	4/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.208053383764427	2		488	609	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	108	476	2	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	0.208053383764427	2		478	735	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617517	158617517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	113	461	0	ENST00000263640.3:c.1139G>A	p.Arg380His	p.R380H	ENST00000263640	NM_001105.4	380	cGc/cAc	9/11	1	2	FACETS	0.875	0.789	0.965	1	0.987	1	CLONAL	2	TRUE	1	0.208053383764427	2		461	621	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593542	215593542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782248	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	86	361	0	ENST00000260947.4:c.2192G>A	p.Arg731His	p.R731H	ENST00000260947	NM_000465.2	731	cGc/cAc	11/11	1	2	FACETS	0.827	0.734	0.926	1	0.982	1	CLONAL	2	TRUE	1	0.208053383764427	2		361	500	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439887	220439887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751673614	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	119	708	1	ENST00000243786.2:c.740G>A	p.Arg247His	p.R247H	ENST00000243786	NM_002191.3	247	cGc/cAc	2/2	1	2	FACETS	0.945	0.856	1	1	0.989	1	CLONAL	2	TRUE	1	0.208053383764427	2		709	605	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342941	225342941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	125	536	0	ENST00000264414.4:c.2151G>A	p.Met717Ile	p.M717I	ENST00000264414	NM_003590.4	717	atG/atA	15/16	1	2	FACETS	0.777	0.704	0.855	1	0.986	1	SUBCLONAL	2	TRUE	1	0.208053383764427	2		536	773	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624802	9624802	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	87	388	0	ENST00000353224.5:c.175A>G	p.Ile59Val	p.I59V	ENST00000353224	NM_177990.2	59	Atc/Gtc	3/10	0.208053383764427	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.208053383764427	1		388	582	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714455	40714455	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	25	469	0	ENST00000373198.4:c.3942C>A	p.Cys1314Ter	p.C1314*	ENST00000373198	NM_133170.3	1314	tgC/tgA	29/32	0.208053383764427	0	FACETS	0.402	0.316	0.502			1	SUBCLONAL	1	TRUE	0	0.208053383764427	0		469	473	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385195	41385195	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	99	564	0	ENST00000373198.4:c.766G>T	p.Asp256Tyr	p.D256Y	ENST00000373198	NM_133170.3	256	Gac/Tac	6/32	0.208053383764427	0	FACETS	1	0.975	1			1	CLONAL	1	TRUE	0	0.208053383764427	0		564	572	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321444	62321444	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200003693	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	29	547	1	ENST00000360203.5:c.2146G>A	p.Ala716Thr	p.A716T	ENST00000360203	NM_001283009.1	716	Gcc/Acc	25/35	0.208053383764427	1	FACETS	0.467	0.374	0.573	0.467	0.374	0.573	SUBCLONAL	1	TRUE	0	0.208053383764427	1		548	535	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326522	62326522	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	102	716	0	ENST00000360203.5:c.3447G>T	p.Gln1149His	p.Q1149H	ENST00000360203	NM_001283009.1	1149	caG/caT	33/35	0.208053383764427	1	FACETS	0.767	0.687	0.85	1	0.983	1	SUBCLONAL	2	TRUE	0	0.208053383764427	1		716	573	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171607	36171607	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1569008655	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	101	305	0	ENST00000300305.3:c.958C>T	p.Arg320Ter	p.R320*	ENST00000300305		320	Cga/Tga	7/8	1	2	FACETS	1	0.956	1	1	0.988	1	CLONAL	2	TRUE	1	0.208053383764427	2		305	436	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817460	39817460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774083516	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	53	455	0	ENST00000288319.7:c.103G>A	p.Ala35Thr	p.A35T	ENST00000288319	NM_182918.3	35	Gcg/Acg	2/10	1	2	FACETS	0.839	0.715	0.976	0.839	0.715	0.976	CLONAL	1	TRUE	1	0.208053383764427	2		455	607	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513259	44513259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	124	495	0	ENST00000291552.4:c.676C>T	p.Arg226Cys	p.R226C	ENST00000291552	NM_006758.2	226	Cgt/Tgt	8/8	1	2	FACETS	1	0.938	1	1	0.99	1	CLONAL	2	TRUE	1	0.208053383764427	2		495	572	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095874	29095874	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	128	644	0	ENST00000328354.6:c.960A>C	p.Lys320Asn	p.K320N	ENST00000328354	NM_007194.3	320	aaA/aaC	9/15	1	2	FACETS	0.853	0.774	0.936	1	0.988	1	CLONAL	2	TRUE	1	0.208053383764427	2		644	721	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121015	29121015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121908701	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	156	650	1	ENST00000328354.6:c.542G>A	p.Arg181His	p.R181H	ENST00000328354	NM_007194.3	181	cGt/cAt	4/15	1	2	FACETS	0.883	0.809	0.961	1	0.99	1	CLONAL	2	TRUE	1	0.208053383764427	2		651	849	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447543	12447543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	99	519	0	ENST00000287820.6:c.782C>T	p.Ala261Val	p.A261V	ENST00000287820	NM_015869.4	261	gCg/gTg	5/7	1	2	FACETS	0.801	0.717	0.891	1	0.983	1	CLONAL	2	TRUE	1	0.208053383764427	2		519	594	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053542	37053542	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	87	630	0	ENST00000231790.2:c.629C>A	p.Ala210Asp	p.A210D	ENST00000231790	NM_000249.3	210	gCc/gAc	8/19	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.208053383764427	2		630	727	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412959	49412959	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	135	646	0	ENST00000418115.1:c.64C>A	p.Leu22Ile	p.L22I	ENST00000418115	NM_001664.2	22	Ctc/Atc	2/5	1	2	FACETS	0.761	0.691	0.834	1	0.986	1	SUBCLONAL	2	TRUE	1	0.208053383764427	2		646	853	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932636	49932636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780949671	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	123	590	1	ENST00000296474.3:c.3235C>T	p.Arg1079Trp	p.R1079W	ENST00000296474	NM_002447.2	1079	Cgg/Tgg	14/20	1	2	FACETS	0.914	0.828	1	1	0.988	1	CLONAL	2	TRUE	1	0.208053383764427	2		591	647	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932677	49932677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754028685	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	156	679	0	ENST00000296474.3:c.3194C>T	p.Ala1065Val	p.A1065V	ENST00000296474	NM_002447.2	1065	gCg/gTg	14/20	1	2	FACETS	1	0.932	1	1	0.992	1	CLONAL	2	TRUE	1	0.208053383764427	2		679	737	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439262	52439262	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	103	610	0	ENST00000460680.1:c.980G>T	p.Ser327Ile	p.S327I	ENST00000460680	NM_004656.3	327	aGc/aTc	11/17	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.208053383764427	2		610	735	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582302	119582302	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	131	440	1	ENST00000316626.5:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000316626		367	Cga/Tga	10/12	1	2	FACETS	0.919	0.836	1	1	0.989	1	CLONAL	2	TRUE	1	0.208053383764427	2		441	685	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138402527	138402528	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	46	355	0	ENST00000289153.2:c.2417dup	p.Asn806LysfsTer3	p.N806Kfs*3	ENST00000289153	NM_006219.2	806	aat/aaAt	16/22	1	2	FACETS	0.927	0.781	1	0.927	0.781	1	CLONAL	1	TRUE	1	0.208053383764427	2		355	477	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242963	142242963	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	55	516	0	ENST00000350721.4:c.4024G>T	p.Gly1342Cys	p.G1342C	ENST00000350721	NM_001184.3	1342	Ggt/Tgt	22/47	1	2	FACETS	0.689	0.588	0.8	0.689	0.588	0.8	SUBCLONAL	1	TRUE	1	0.208053383764427	2		516	767	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374675	149374675	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	40	521	0	ENST00000360632.3:c.419G>T	p.Arg140Met	p.R140M	ENST00000360632	NM_015472.4	140	aGg/aTg	2/7	1	2	FACETS	0.496	0.41	0.591	0.496	0.41	0.591	SUBCLONAL	1	TRUE	1	0.208053383764427	2		521	776	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504039	186504040	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	38	281	0	ENST00000323963.5:c.609dup	p.Leu204ThrfsTer17	p.L204Tfs*17	ENST00000323963		202	caa/cAaa	6/11	1	2	FACETS	0.742	0.613	0.887	0.742	0.613	0.887	SUBCLONAL	1	TRUE	1	0.208053383764427	2		281	492	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806180	1806181	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760502257	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	139	615	2	ENST00000260795.2:c.1206dup	p.Lys403GlnfsTer93	p.K403Qfs*93	ENST00000260795		400	agc/agCc	8/17	1	2	FACETS	0.99	0.903	1	1	0.991	1	CLONAL	2	TRUE	1	0.208053383764427	2		617	675	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747837	41747837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762234006	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	64	323	1	ENST00000226382.2:c.932G>A	p.Ser311Asn	p.S311N	ENST00000226382	NM_003924.3	311	aGc/aAc	3/3	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.208053383764427	2		324	460	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286238	66286238	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	96	489	0	ENST00000273854.3:c.1448del	p.Asn483ThrfsTer18	p.N483Tfs*18	ENST00000273854	NM_004439.5	483	aAc/ac	6/18	0.152716978965641	3	FACETS	0.828	0.739	0.923	0.828	0.739	0.923	CLONAL	2	TRUE	1	0.208053383764427	3		489	615	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356200	66356200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770587480	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	96	541	1	ENST00000273854.3:c.1297G>A	p.Ala433Thr	p.A433T	ENST00000273854	NM_004439.5	433	Gct/Act	5/18	0.152716978965641	3	FACETS	1	0.945	1	0.551	0.49	0.617	CLONAL	1	TRUE	1	0.208053383764427	3		542	924	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045827	143045827	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	44	488	0	ENST00000262992.4:c.1807A>G	p.Thr603Ala	p.T603A	ENST00000262992	NM_001101669.1	603	Aca/Gca	17/24	0.152716978965641	3	FACETS	0.653	0.546	0.772	0.327	0.273	0.386	SUBCLONAL	1	TRUE	1	0.208053383764427	3		488	715	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530425	187530425	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199995119	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	84	378	0	ENST00000441802.2:c.10118C>T	p.Ser3373Leu	p.S3373L	ENST00000441802	NM_005245.3	3373	tCa/tTa	16/27	1	2	FACETS	0.812	0.72	0.911	1	0.981	1	CLONAL	2	TRUE	1	0.208053383764427	2		378	497	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630890	187630890	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	137	501	0	ENST00000441802.2:c.92C>T	p.Pro31Leu	p.P31L	ENST00000441802	NM_005245.3	31	cCt/cTt	2/27	1	2	FACETS	1	0.921	1	1	0.991	1	CLONAL	2	TRUE	1	0.208053383764427	2		501	652	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874637	35874637	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	69	395	4	ENST00000303115.3:c.799del	p.Arg267GlyfsTer28	p.R267Gfs*28	ENST00000303115	NM_002185.3	265	Aaa/aa	6/8	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.208053383764427	2		399	539	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456910	149456910	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	124	688	0	ENST00000286301.3:c.818C>A	p.Ala273Asp	p.A273D	ENST00000286301	NM_005211.3	273	gCc/gAc	6/22	1	2	FACETS	0.795	0.719	0.874	1	0.986	1	SUBCLONAL	2	TRUE	1	0.208053383764427	2		688	750	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519352	176519352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	135	456	0	ENST00000292408.4:c.758C>T	p.Ala253Val	p.A253V	ENST00000292408	NM_213647.1	253	gCc/gTc	7/18	1	2	FACETS	1	0.92	1	1	0.993	1	CLONAL	3	TRUE	1	0.208053383764427	2		456	431	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522668	176522668	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	99	632	0	ENST00000292408.4:c.1765C>A	p.Leu589Met	p.L589M	ENST00000292408	NM_213647.1	589	Ctg/Atg	13/18	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.208053383764427	2		632	699	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523709	176523709	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761135791	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	34	619	1	ENST00000292408.4:c.2120G>A	p.Arg707Gln	p.R707Q	ENST00000292408	NM_213647.1	707	cGg/cAg	16/18	1	2	FACETS	0.52	0.424	0.629	0.52	0.424	0.629	SUBCLONAL	1	TRUE	1	0.208053383764427	2		620	628	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	31	275	0	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.671	0.542	0.817	0.671	0.542	0.817	SUBCLONAL	1	TRUE	1	0.208053383764427	2		275	444	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675592	30675592	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	57	913	1	ENST00000376406.3:c.2764C>T	p.Pro922Ser	p.P922S	ENST00000376406	NM_014641.2	922	Cca/Tca	8/15	0.152716978965641	3	FACETS	0.539	0.461	0.626	0.27	0.23	0.313	SUBCLONAL	1	TRUE	1	0.208053383764427	3		914	1122	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680481	30680481	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764808773	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	131	618	0	ENST00000376406.3:c.1238C>T	p.Ala413Val	p.A413V	ENST00000376406	NM_014641.2	413	gCg/gTg	5/15	0.152716978965641	3	FACETS	0.921	0.836	1	0.921	0.836	1	CLONAL	2	TRUE	1	0.208053383764427	3		618	755	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323230	31323230	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	31	524	0	ENST00000412585.2:c.759G>T	p.Glu253Asp	p.E253D	ENST00000412585	NM_005514.6	253	gaG/gaT	4/8	0.152716978965641	3	FACETS	0.56	0.451	0.683	0.28	0.225	0.342	SUBCLONAL	1	TRUE	1	0.208053383764427	3		524	588	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185886	32185886	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	102	524	2	ENST00000375023.3:c.1511-1G>T		p.X504_splice	ENST00000375023	NM_004557.3	504			0.152716978965641	3	FACETS	1	0.92	1	1	0.92	1	CLONAL	2	TRUE	1	0.208053383764427	3		526	526	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903822	41903822	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	91	513	1	ENST00000372991.4:c.735G>T	p.Glu245Asp	p.E245D	ENST00000372991	NM_001760.3	245	gaG/gaT	5/5	0.152716978965641	3	FACETS	0.976	0.869	1	0.976	0.869	1	CLONAL	2	TRUE	1	0.208053383764427	3		514	495	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553111	106553111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	92	459	0	ENST00000369096.4:c.1076C>T	p.Thr359Met	p.T359M	ENST00000369096	NM_001198.3	359	aCg/aTg	5/7	0.152716978965641	3	FACETS	0.776	0.69	0.867	0.776	0.69	0.867	SUBCLONAL	2	TRUE	1	0.208053383764427	3		459	629	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117645566	117645566	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	82	483	0	ENST00000368508.3:c.5570T>C	p.Ile1857Thr	p.I1857T	ENST00000368508	NM_002944.2	1857	aTa/aCa	34/43	0.152716978965641	3	FACETS	1	0.955	1	0.587	0.517	0.662	CLONAL	1	TRUE	1	0.208053383764427	3		483	741	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196093	138196093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1405321250	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	69	271	0	ENST00000237289.4:c.407G>A	p.Arg136His	p.R136H	ENST00000237289	NM_001270507.1	136	cGc/cAc	3/9	0.152716978965641	3	FACETS	1	0.971	1	0.721	0.629	0.82	CLONAL	1	TRUE	1	0.208053383764427	3		271	508	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200459	138200459	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	98	436	0	ENST00000237289.4:c.1877T>C	p.Leu626Pro	p.L626P	ENST00000237289	NM_001270507.1	626	cTg/cCg	7/9	0.152716978965641	3	FACETS	0.886	0.792	0.985	0.886	0.792	0.985	CLONAL	2	TRUE	1	0.208053383764427	3		436	587	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161807881	161807881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375036403	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	28	464	1	ENST00000366898.1:c.1112C>T	p.Ala371Val	p.A371V	ENST00000366898	NM_004562.2	371	gCg/gTg	10/12	NA	2	FACETS	0.502	0.4	0.619			1	INDETERMINATE	1	TRUE	NA	0.208053383764427	2		465	536	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508567	106508567	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	57	292	0	ENST00000359195.3:c.561G>T	p.Glu187Asp	p.E187D	ENST00000359195	NM_002649.2	187	gaG/gaT	2/11	1	2	FACETS	0.856	0.739	0.982	1	0.974	1	CLONAL	2	TRUE	1	0.208053383764427	2		292	320	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509748	106509748	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	103	489	2	ENST00000359195.3:c.1742A>T	p.Glu581Val	p.E581V	ENST00000359195	NM_002649.2	581	gAa/gTa	2/11	1	2	FACETS	0.831	0.745	0.921	1	0.985	1	CLONAL	2	TRUE	1	0.208053383764427	2		491	596	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412677	116412677	+	intron_variant	Intron	SNP	C	C	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	221	949	0	ENST00000397752.3:c.3028+634C>T		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.874	0.812	0.939	1	0.993	1	CLONAL	2	TRUE	1	0.208053383764427	2		949	1215	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860073	151860074	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	98	405	0	ENST00000262189.6:c.10588dup	p.Ser3530PhefsTer36	p.S3530Ffs*36	ENST00000262189	NM_170606.2	3530	tct/tTct	43/59	1	2	FACETS	0.92	0.824	1	1	0.986	1	CLONAL	2	TRUE	1	0.208053383764427	2		405	512	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860481	151860481	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	104	580	0	ENST00000262189.6:c.10181G>T	p.Ser3394Ile	p.S3394I	ENST00000262189	NM_170606.2	3394	aGt/aTt	43/59	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.208053383764427	2		580	803	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29197723	29197723	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs774219516	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	133	652	1	ENST00000240100.2:c.471C>A	p.Phe157Leu	p.F157L	ENST00000240100	NM_001394.6	157	ttC/ttA	2/4	1	2	FACETS	0.841	0.765	0.922	1	0.988	1	CLONAL	2	TRUE	1	0.208053383764427	2		653	760	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133958	38133958	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	307	791	1	ENST00000317025.8:c.3928C>T	p.Arg1310Ter	p.R1310*	ENST00000317025	NM_023034.1	1310	Cga/Tga	23/24	1	2	FACETS	0.915	0.863	0.968	1	0.996	1	CLONAL	3	TRUE	1	0.208053383764427	2		792	1075	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38184347	38184347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	95	483	0	ENST00000317025.8:c.1609G>A	p.Val537Ile	p.V537I	ENST00000317025	NM_023034.1	537	Gtc/Atc	7/24	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.208053383764427	2		483	705	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372454	55372454	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	137	814	0	ENST00000297316.4:c.1144C>T	p.His382Tyr	p.H382Y	ENST00000297316	NM_022454.3	382	Cat/Tat	2/2	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.208053383764427	2		814	1049	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002849	69002849	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	42	318	0	ENST00000288368.4:c.2149C>T	p.Gln717Ter	p.Q717*	ENST00000288368	NM_024870.2	717	Cag/Tag	20/40	1	2	FACETS	0.913	0.763	1	0.913	0.763	1	CLONAL	1	TRUE	1	0.208053383764427	2		318	442	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864944	117864944	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	78	333	0	ENST00000297338.2:c.1165T>G	p.Phe389Val	p.F389V	ENST00000297338	NM_006265.2	389	Ttt/Gtt	10/14	1	2	FACETS	0.91	0.804	1	1	0.982	1	CLONAL	2	TRUE	1	0.208053383764427	2		333	412	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974742	21974742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554656382	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	14	253	0	ENST00000304494.5:c.85C>T	p.Arg29Trp	p.R29W	ENST00000304494	NM_000077.4	29	Cgg/Tgg	1/3	1	2	FACETS	0.482	0.348	0.645	0.482	0.348	0.645	SUBCLONAL	1	TRUE	1	0.208053383764427	2		253	279	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285800	87285800	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1171041569	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	41	540	0	ENST00000277120.3:c.137G>A	p.Ser46Asn	p.S46N	ENST00000277120		46	aGc/aAc	2/19	1	2	FACETS	0.681	0.566	0.808	0.681	0.566	0.808	SUBCLONAL	1	TRUE	1	0.208053383764427	2		540	579	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128246746	128246746	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	36	597	1	ENST00000265960.3:c.1183C>T	p.Arg395Ter	p.R395*	ENST00000265960	NM_001006617.1	395	Cga/Tga	9/12	1	2	FACETS	0.481	0.394	0.579	0.481	0.394	0.579	SUBCLONAL	1	TRUE	1	0.208053383764427	2		598	719	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759406	133759406	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1371645607	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	99	587	2	ENST00000318560.5:c.1729C>T	p.Arg577Ter	p.R577*	ENST00000318560	NM_005157.4	577	Cga/Tga	11/11	0.208053383764427	1	FACETS	0.838	0.751	0.929	1	0.984	1	CLONAL	2	TRUE	0	0.208053383764427	1		589	509	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401088	139401088	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762091081	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	33	615	0	ENST00000277541.6:c.3905G>A	p.Arg1302His	p.R1302H	ENST00000277541	NM_017617.3	1302	cGc/cAc	24/34	1	2	FACETS	0.522	0.424	0.633	0.522	0.424	0.633	SUBCLONAL	1	TRUE	1	0.208053383764427	2		615	608	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417466	139417466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774966208	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	131	737	1	ENST00000277541.6:c.578G>A	p.Gly193Asp	p.G193D	ENST00000277541	NM_017617.3	193	gGc/gAc	4/34	1	2	FACETS	0.97	0.883	1	1	0.99	1	CLONAL	2	TRUE	1	0.208053383764427	2		738	649	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20153857	20153857	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	32	483	0	ENST00000379607.5:c.203del	p.Lys68ArgfsTer4	p.K68Rfs*4	ENST00000379607	NM_001412.3	68	aAg/ag	3/7	0.208053383764427	1	FACETS	0.48	0.389	0.584	0.48	0.389	0.584	SUBCLONAL	1	TRUE	0	0.208053383764427	1		483	574	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916463	39916463	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	54	685	1	ENST00000378444.4:c.4540C>T	p.Arg1514Ter	p.R1514*	ENST00000378444	NM_001123385.1	1514	Cga/Tga	11/15	0.208053383764427	1	FACETS	0.698	0.596	0.811	0.698	0.596	0.811	SUBCLONAL	1	TRUE	0	0.208053383764427	1		686	666	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937657	44937657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	102	447	0	ENST00000377967.4:c.2845C>T	p.Arg949Cys	p.R949C	ENST00000377967	NM_021140.2	949	Cgt/Tgt	19/29	0.208053383764427	1	FACETS	0.759	0.68	0.842	1	0.982	1	SUBCLONAL	2	TRUE	0	0.208053383764427	1		447	579	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346303	70346303	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	52	784	0	ENST00000374080.3:c.2654G>T	p.Ser885Ile	p.S885I	ENST00000374080		885	aGc/aTc	19/45	0.199942720992942	0	FACETS	0.545	0.463	0.636			1	SUBCLONAL	1	TRUE	0	0.208053383764427	0		784	726	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70353023	70353023	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	76	600	0	ENST00000374080.3:c.4578G>T	p.Lys1526Asn	p.K1526N	ENST00000374080		1526	aaG/aaT	33/45	0.199942720992942	0	FACETS	1	0.952	1			1	CLONAL	1	TRUE	0	0.208053383764427	0		600	497	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855019	76855019	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	86	455	4	ENST00000373344.5:c.5817del	p.Asp1940IlefsTer15	p.D1940Ifs*15	ENST00000373344	NM_000489.3	1939	aaA/aa	25/35	0.199942720992942	0	FACETS	1	0.943	1			1	CLONAL	1	TRUE	0	0.208053383764427	0		459	593	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891548	76891548	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0033133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	65	486	0	ENST00000373344.5:c.4558-1G>T		p.X1520_splice	ENST00000373344	NM_000489.3	1520			0.199942720992942	0	FACETS	1	0.901	1			1	CLONAL	1	TRUE	0	0.208053383764427	0		486	474	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023094	27023095	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0033134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	12	49	0	ENST00000324856.7:c.200_201del	p.Gln67ProfsTer43	p.Q67Pfs*43	ENST00000324856	NM_006015.4	67	cAG/c	1/20	0.524687545736855	1	FACETS	0.964	0.712	1	0.964	0.712	1	CLONAL	1	TRUE	0	0.524687545736855	1		49	35	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183692	10183693	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs869025615	NA	P-0033134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	72	590	0	ENST00000256474.2:c.163dup	p.Glu55GlyfsTer77	p.E55Gfs*77	ENST00000256474	NM_000551.3	54	atg/atGg	1/3	0.508647305351891	1	FACETS	0.837	0.741	0.936	0.837	0.741	0.936	CLONAL	1	TRUE	0	0.524687545736855	1		590	242	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584457	52584457	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	67	473	0	ENST00000394830.3:c.4556del	p.Lys1519SerfsTer28	p.K1519Sfs*28	ENST00000394830	NM_018313.4	1519	aAg/ag	29/30	0.508647305351891	1	FACETS	0.571	0.499	0.647	0.571	0.499	0.647	SUBCLONAL	1	TRUE	0	0.524687545736855	1		473	330	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668643	52668643	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	23	458	0	ENST00000394830.3:c.1276del	p.Met426CysfsTer12	p.M426Cfs*12	ENST00000394830	NM_018313.4	426	Atg/tg	12/30	0.508647305351891	1	FACETS	0.16	0.125	0.202	0.16	0.125	0.202	SUBCLONAL	1	TRUE	0	0.524687545736855	1		458	403	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41904365	41904365	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	103	538	1	ENST00000372991.4:c.643C>A	p.Leu215Met	p.L215M	ENST00000372991	NM_001760.3	215	Ctg/Atg	4/5	1	2	FACETS	0.852	0.766	0.941	0.852	0.766	0.941	CLONAL	1	TRUE	1	0.524687545736855	2		539	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578220	7578220	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	340	566	0	ENST00000269305.4:c.629del	p.Asn210ThrfsTer37	p.N210Tfs*37	ENST00000269305	NM_001126112.2	210	aAc/ac	6/11	0.597566830799322	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.597566830799322	1		566	701	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266546	198266546	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	163	377	0	ENST00000335508.6:c.2290T>G	p.Tyr764Asp	p.Y764D	ENST00000335508	NM_012433.2	764	Tac/Gac	16/25	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.597566830799322	2		377	519	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518257	8518261	+	frameshift_variant	Frame_Shift_Del	DEL	GTAGC	GTAGC	T	novel	NA	P-0033137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	157	348	0	ENST00000356435.5:c.1130_1134delinsA	p.Arg377GlnfsTer6	p.R377Qfs*6	ENST00000356435		377	cGCTAC/cA	10/35	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.597566830799322	2		348	476	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793219	42793219	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	94	664	0	ENST00000575354.2:c.1111C>A	p.Gln371Lys	p.Q371K	ENST00000575354	NM_015125.3	371	Cag/Aag	7/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.37	2		664	408	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0033149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	258	280	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.986	0.931	1	0.986	0.931	1	CLONAL	1	TRUE	1	0.894955689538432	2		280	585	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	171	264	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.894955689538432	2		264	378	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0033149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	320	456	0	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.849857572751526	5	FACETS	1	0.979	1	0.36	0.338	0.382	CLONAL	1	TRUE	2	0.894955689538432	5		456	1552	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913428	NA	P-0033149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1385	364	600	1	ENST00000275493.2:c.2156G>A	p.Gly719Asp	p.G719D	ENST00000275493	NM_005228.3	719	gGc/gAc	18/28	0.849857572751526	5	FACETS	1	0.982	1	0.363	0.343	0.384	CLONAL	1	TRUE	2	0.894955689538432	5		601	1749	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223604	55223604	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	319	530	1	ENST00000275493.2:c.971G>T	p.Arg324Leu	p.R324L	ENST00000275493	NM_005228.3	324	cGc/cTc	8/28	0.849857572751526	5	FACETS	1	0.983	1	0.37	0.348	0.392	CLONAL	1	TRUE	2	0.894955689538432	5		531	1506	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104356996	104356996	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	288	500	0	ENST00000369902.3:c.856del	p.Glu286ArgfsTer27	p.E286Rfs*27	ENST00000369902	NM_016169.3	286	Gag/ag	7/12	0.894955689538432	1	FACETS	0.938	0.905	0.97	0.938	0.905	0.97	CLONAL	1	TRUE	0	0.894955689538432	1		500	379	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820638	44820638	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0033149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	192	428	0	ENST00000377967.4:c.334+1G>C		p.X112_splice	ENST00000377967	NM_021140.2	112			0.894955689538432	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.894955689538432	1		428	237	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0033152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	15	471	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		471	582	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0033152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	52	576	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		576	949	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0033153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	145	503	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.702337616184172	3	FACETS	1	0.922	1	0.503	0.461	0.546	CLONAL	1	TRUE	1	0.702337616184172	3		503	555	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798761	42798761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	120	577	1	ENST00000575354.2:c.4333G>A	p.Glu1445Lys	p.E1445K	ENST00000575354	NM_015125.3	1445	Gaa/Aaa	19/20	1	2	FACETS	0.926	0.845	1	0.926	0.845	1	CLONAL	1	TRUE	1	0.702337616184172	2		578	369	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411640	116411640	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	265	745	1	ENST00000397752.3:c.2819C>T	p.Ser940Leu	p.S940L	ENST00000397752	NM_000245.2	940	tCa/tTa	13/21	0.0816966329338882	4	FACETS	0.956	0.902	1	0.956	0.902	1	INDETERMINATE	2	TRUE	2	0.702337616184172	4		746	672	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907692	111907692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775080943	NA	P-0033154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	305	585	0	ENST00000393256.3:c.466G>A	p.Gly156Arg	p.G156R	ENST00000393256	NM_006538.4	156	Gga/Aga	3/4	0.32709832660379	5	FACETS	0.844	0.8	0.889	0.844	0.8	0.889	INDETERMINATE	3	TRUE	2	0.605342999000649	5		585	759	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578507	7578507	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519977	NA	P-0033154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	409	798	0	ENST00000269305.4:c.423C>G	p.Cys141Trp	p.C141W	ENST00000269305	NM_001126112.2	141	tgC/tgG	5/11	0.586238882328699	2	FACETS	0.988	0.951	1	0.988	0.951	1	CLONAL	2	TRUE	0	0.605342999000649	2		798	684	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830603	72830603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	286	774	0	ENST00000268489.5:c.5978C>T	p.Ser1993Phe	p.S1993F	ENST00000268489	NM_006885.3	1993	tCc/tTc	9/10	0.605342999000649	2	FACETS	0.958	0.914	1	0.958	0.914	1	CLONAL	2	TRUE	0	0.605342999000649	2		774	493	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0033155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	277	400	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.430223391059385	4	FACETS	1	0.963	1	1	0.963	1	CLONAL	4	TRUE	0	0.430223391059385	4		400	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0033155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	251	732	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.42920314867703	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.430223391059385	2		732	529	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	187	264	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.96353066314976	2		264	337	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0033158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	280	264	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	0.96353066314976	2		264	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0033158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	969	623	0	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	2	TRUE	NA	0.96353066314976	2		623	1002	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169168	32169168	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	347	639	1	ENST00000375023.3:c.3865G>A	p.Gly1289Arg	p.G1289R	ENST00000375023	NM_004557.3	1289	Ggg/Agg	22/30	0.170546143097193	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.96353066314976	0		640	732	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0033175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	229	789	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.175408196821748	2		789	1108	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627647	37627647	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	226	624	1	ENST00000447079.4:c.1562del	p.Ser521Ter	p.S521*	ENST00000447079	NM_015083.1	521	tCa/ta	2/14	0.175408196821748	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	TRUE	0	0.175408196821748	3		625	852	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250471	26250471	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	116	504	1	ENST00000446824.2:c.363G>T	p.Met121Ile	p.M121I	ENST00000446824	NM_021018.2	121	atG/atT	1/1	0.175408196821748	3	FACETS	0.788	0.709	0.871	0.788	0.709	0.871	SUBCLONAL	2	TRUE	1	0.175408196821748	3		505	913	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615644	100615644	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	137	358	0	ENST00000308731.7:c.688G>T	p.Ala230Ser	p.A230S	ENST00000308731	NM_000061.2	230	Gca/Tca	8/19	0.175408196821748	2	FACETS	0.877	0.8	0.956			1	CLONAL	3	TRUE	NA	0.175408196821748	2		358	594	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0033176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	398	514	0	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	0.904593026102453	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.904593026102453	1		514	462	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508514	106508514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1406220505	NA	P-0033176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	106	197	2	ENST00000359195.3:c.508G>A	p.Asp170Asn	p.D170N	ENST00000359195	NM_002649.2	170	Gac/Aac	2/11	0.389972928178321	1	FACETS	0.709	0.656	0.761	0.709	0.656	0.761	INDETERMINATE	1	TRUE	0	0.904593026102453	1		199	181	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206862	102206862	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs373311655	NA	P-0033176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	254	315	0	ENST00000263464.3:c.1490A>G	p.Asp497Gly	p.D497G	ENST00000263464	NM_001165.4	497	gAt/gGt	7/9	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.904593026102453	2		315	528	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29120987	29120987	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	349	509	0	ENST00000328354.6:c.570del	p.Leu191CysfsTer3	p.L191Cfs*3	ENST00000328354	NM_007194.3	190	gcA/gc	4/15	0.158168307007215	3	FACETS	1	0.995	1	0.705	0.671	0.739	INDETERMINATE	1	TRUE	1	0.904593026102453	3		509	795	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629223	187629223	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	324	516	1	ENST00000441802.2:c.1759C>T	p.Gln587Ter	p.Q587*	ENST00000441802	NM_005245.3	587	Caa/Taa	2/27	0.904593026102453	1	FACETS	0.978	0.949	1	0.978	0.949	1	CLONAL	1	TRUE	0	0.904593026102453	1		517	401	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913514	NA	P-0033188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	153	363	0	ENST00000288135.5:c.2466T>A	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaA	17/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.87624708386027	2		363	313	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544735	65544735	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	278	437	1	ENST00000358664.4:c.191T>C	p.Leu64Pro	p.L64P	ENST00000358664	NM_002382.4	64	cTa/cCa	4/5	0.87624708386027	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.87624708386027	1		438	342	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0033192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	70	340	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.326027508636558	2		340	352	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032794	30032794	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121434259	NA	P-0033192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	50	290	0	ENST00000338641.4:c.169C>T	p.Arg57Ter	p.R57*	ENST00000338641	NM_000268.3	57	Cga/Tga	2/16	0.326027508636558	1	FACETS	0.574	0.488	0.669	0.574	0.488	0.669	SUBCLONAL	1	TRUE	0	0.326027508636558	1		290	447	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657517	29657517	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs876658854	NA	P-0033192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	77	237	0	ENST00000356175.3:c.5749+1G>A		p.X1917_splice	ENST00000356175	NM_000267.3	1917			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.326027508636558	2		237	357	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478756	57478757	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0033192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	67	307	0	ENST00000371085.3:c.348dup	p.Val117ArgfsTer23	p.V117Rfs*23	ENST00000371085	NM_000516.4	114	-/C	5/13	0.302087526035858	3	FACETS	0.84	0.731	0.958	0.42	0.365	0.479	CLONAL	1	TRUE	1	0.326027508636558	3		307	569	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527477	29527478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0033192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	116	383	0	ENST00000356175.3:c.928dup	p.His310ProfsTer5	p.H310Pfs*5	ENST00000356175	NM_000267.3	309	ggc/ggCc	9/57	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.326027508636558	2		383	672	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36265222	36265222	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs781761402	NA	P-0033192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	33	243	0	ENST00000300305.3:c.97G>A	p.Asp33Asn	p.D33N	ENST00000300305		33	Gat/Aat	2/8	1	2	FACETS	0.723	0.591	0.87	0.723	0.591	0.87	SUBCLONAL	1	TRUE	1	0.326027508636558	2		243	280	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0033197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	36	335	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		335	237	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0033200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	109	483	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.578082884331956	2	FACETS	0.982	0.89	1	0.491	0.445	0.539	CLONAL	1	TRUE	0	0.578082884331956	2		483	384	SUCCESS
APC	324	MSKCC	GRCh37	5	112174956	112174956	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1114167614	NA	P-0033200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	191	202	0	ENST00000257430.4:c.3665C>A	p.Ser1222Ter	p.S1222*	ENST00000257430	NM_000038.5	1222	tCa/tAa	16/16	0.573551736989988	2	FACETS	0.972	0.916	1	0.972	0.916	1	CLONAL	2	TRUE	0	0.578082884331956	2		202	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579528	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CAGTGAAC	CAGTGAAC	-	novel	NA	P-0033200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	765	634	0	ENST00000269305.4:c.159_166del	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgGTTCACTGaa/tgaa	4/11	0.578082884331956	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.578082884331956	2		634	1298	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437669	52437669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	364	534	1	ENST00000460680.1:c.1492G>A	p.Glu498Lys	p.E498K	ENST00000460680	NM_004656.3	498	Gag/Aag	13/17	0.578082884331956	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.578082884331956	1		535	843	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941858	44941858	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0033200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	124	176	0	ENST00000377967.4:c.3182C>G	p.Ser1061Ter	p.S1061*	ENST00000377967	NM_021140.2	1061	tCa/tGa	21/29	1	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.578082884331956	1		176	259	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562918	95562918	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	179	340	0	ENST00000393063.1:c.4339C>G	p.Gln1447Glu	p.Q1447E	ENST00000393063	NM_030621.3	1447	Cag/Gag	24/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.578082884331956	2		340	571	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483325	120483325	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	183	317	0	ENST00000256646.2:c.3036G>T	p.Leu1012Phe	p.L1012F	ENST00000256646	NM_024408.3	1012	ttG/ttT	19/34	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.578082884331956	2		317	616	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745597	162745630	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCTAATTCTTCCTCCAGCGATGTACGCACTGT	CCCCTAATTCTTCCTCCAGCGATGTACGCACTGT	-	novel	NA	P-0033200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	125	389	0	ENST00000367921.3:c.2013_2046del	p.Pro672ValfsTer5	p.P672Vfs*5	ENST00000367921	NM_006182.2	671	cCCCCTAATTCTTCCTCCAGCGATGTACGCACTGTc/cc	15/18	1	2	FACETS	0.565	0.511	0.621	0.565	0.511	0.621	SUBCLONAL	1	TRUE	1	0.578082884331956	2		389	766	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437424	121437424	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	235	465	0	ENST00000257555.6:c.1762C>A	p.Pro588Thr	p.P588T	ENST00000257555		588	Ccc/Acc	9/10	1	2	FACETS	0.923	0.863	0.985	0.923	0.863	0.985	CLONAL	1	TRUE	1	0.578082884331956	2		465	881	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964094	28964094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	211	507	0	ENST00000282397.4:c.1808G>A	p.Ser603Asn	p.S603N	ENST00000282397	NM_002019.4	603	aGt/aAt	13/30	0.578082884331956	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.578082884331956	1		507	511	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554272	29554272	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199474762	NA	P-0033200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	702	468	0	ENST00000356175.3:c.2288T>C	p.Leu763Pro	p.L763P	ENST00000356175	NM_000267.3	763	cTg/cCg	19/57	0.578082884331956	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.578082884331956	2		468	1116	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46583399	46583399	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	251	394	0	ENST00000263734.3:c.327C>G	p.Ile109Met	p.I109M	ENST00000263734	NM_001430.4	109	atC/atG	3/16	1	2	FACETS	0.914	0.856	0.974	0.914	0.856	0.974	CLONAL	1	TRUE	1	0.578082884331956	2		394	950	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182192	99182192	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	207	456	0	ENST00000074304.5:c.2257G>T	p.Ala753Ser	p.A753S	ENST00000074304	NM_001134224.1	753	Gcc/Tcc	21/26	1	2	FACETS	0.876	0.814	0.939	0.876	0.814	0.939	CLONAL	1	TRUE	1	0.578082884331956	2		456	818	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008471	70008471	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	172	231	0	ENST00000394351.3:c.758A>C	p.Tyr253Ser	p.Y253S	ENST00000394351	NM_000248.3	253	tAt/tCt	8/9	0.578082884331956	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.578082884331956	1		231	390	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919155	178919155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	91	238	0	ENST00000263967.3:c.640G>T	p.Asp214Tyr	p.D214Y	ENST00000263967	NM_006218.2	214	Gac/Tac	4/21	0.578082884331956	2	FACETS	0.875	0.783	0.97	0.437	0.391	0.485	CLONAL	1	TRUE	0	0.578082884331956	2		238	360	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674350	86674351	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0033200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	99	312	1	ENST00000274376.6:c.2484_2485del	p.Cys828Ter	p.C828*	ENST00000274376	NM_002890.2	828	TGt/t	18/25	0.578082884331956	1	FACETS	0.848	0.768	0.931	0.848	0.768	0.931	CLONAL	1	TRUE	0	0.578082884331956	1		313	287	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056745	180056745	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	693	634	1	ENST00000261937.6:c.767C>A	p.Ala256Asp	p.A256D	ENST00000261937	NM_182925.4	256	gCt/gAt	6/30	0.573551736989988	2	FACETS	0.959	0.93	0.988	0.959	0.93	0.988	CLONAL	2	TRUE	0	0.578082884331956	2		635	1250	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001033	150001033	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	107	362	0	ENST00000253339.5:c.2571C>G	p.His857Gln	p.H857Q	ENST00000253339		857	caC/caG	4/7	0.578082884331956	2	FACETS	0.824	0.744	0.909	0.412	0.372	0.455	CLONAL	1	TRUE	0	0.578082884331956	2		362	449	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	147	441	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.885	0.814	0.959	0.885	0.814	0.959	CLONAL	1	TRUE	1	0.669737352123064	2		441	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578207	7578215	+	inframe_deletion	In_Frame_Del	DEL	ATGTCGAAA	ATGTCGAAA	-	novel	NA	P-0033201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	210	620	0	ENST00000269305.4:c.634_642del	p.Phe212_His214del	p.F212_H214del	ENST00000269305	NM_001126112.2	212	TTTCGACAT/-	6/11	0.669737352123064	1	FACETS	0.946	0.89	1	0.946	0.89	1	CLONAL	1	TRUE	0	0.669737352123064	1		620	441	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16097858	16097858	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	142	320	0	ENST00000268712.3:c.26A>G	p.Asn9Ser	p.N9S	ENST00000268712	NM_006311.3	9	aAc/aGc	2/46	0.669737352123064	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.669737352123064	1		320	273	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971175	21971207	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CTCCGCCACTCGGGCGCTGCCCATCATCATGAC	CTCCGCCACTCGGGCGCTGCCCATCATCATGAC	-	novel	NA	P-0033201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	91	295	0	ENST00000304494.5:c.151_183del	p.Val51_Glu61del	p.V51_E61del	ENST00000304494	NM_000077.4	51	GTCATGATGATGGGCAGCGCCCGAGTGGCGGAG/-	2/3	0.669737352123064	1	FACETS	0.845	0.766	0.925	0.845	0.766	0.925	CLONAL	1	TRUE	0	0.669737352123064	1		295	214	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759366	133759376	+	frameshift_variant	Frame_Shift_Del	DEL	CCATGAGCCTG	CCATGAGCCTG	-	novel	NA	P-0033201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	128	553	0	ENST00000318560.5:c.1691_1701del	p.His564ArgfsTer19	p.H564Rfs*19	ENST00000318560	NM_005157.4	563	gaCCATGAGCCTGcc/gacc	11/11	1	2	FACETS	0.774	0.705	0.845	0.774	0.705	0.845	SUBCLONAL	1	TRUE	1	0.669737352123064	2		553	494	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242716	46242716	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	96	293	0	ENST00000334344.6:c.1678G>T	p.Gly560Ter	p.G560*	ENST00000334344	NM_152641.2	560	Gga/Tga	13/21	0.140487555510729	3	FACETS	1	0.924	1	0.69	0.619	0.763	INDETERMINATE	2	TRUE	0	0.279053668117692	3		293	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579362	7579363	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	T	novel	NA	P-0033207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	229	460	0	ENST00000269305.4:c.324_325delinsA	p.Phe109SerfsTer14	p.F109Sfs*14	ENST00000269305	NM_001126112.2	108	ggTTtc/ggAtc	4/11	0.184055936597659	3	FACETS	0.978	0.912	1	0.652	0.608	0.698	CLONAL	2	TRUE	0	0.279053668117692	3		460	956	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0033209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	26	423	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	0.902	0.713	1	0.902	0.713	1	CLONAL	1	TRUE	1	0.14	2		423	412	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023559	27023560	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0033209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	17	313	2	ENST00000324856.7:c.671dup	p.Pro225AlafsTer175	p.P225Afs*175	ENST00000324856	NM_006015.4	222	tac/taCc	1/20	1	2	FACETS	0.949	0.709	1	0.949	0.709	1	CLONAL	1	TRUE	1	0.14	2		315	256	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400179	41400179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	25	391	1	ENST00000373198.4:c.580C>T	p.His194Tyr	p.H194Y	ENST00000373198	NM_133170.3	194	Cat/Tat	5/32	1	2	FACETS	0.747	0.588	0.931	0.747	0.588	0.931	CLONAL	1	TRUE	1	0.14	2		392	478	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457265	67457265	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758823376	NA	P-0033209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	26	591	0	ENST00000327367.4:c.239G>A	p.Arg80Gln	p.R80Q	ENST00000327367	NM_005902.3	80	cGg/cAg	2/9	1	2	FACETS	0.769	0.608	0.954	0.769	0.608	0.954	CLONAL	1	TRUE	1	0.14	2		591	483	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842471	68842471	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0033209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	72	472	0	ENST00000261769.5:c.531+1G>C		p.X177_splice	ENST00000261769	NM_004360.3	177			1	2	FACETS	1	0.907	1	1	0.983	1	CLONAL	2	TRUE	1	0.14	2		472	493	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	40	556	0	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	0.3	2	FACETS	0.609	0.505	0.725			1	SUBCLONAL	1	TRUE	NA	0.22	2		556	597	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835633	68835643	+	frameshift_variant	Frame_Shift_Del	DEL	TCAAAGTGGGC	TCAAAGTGGGC	-	novel	NA	P-0033220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	45	622	1	ENST00000261769.5:c.224_234del	p.Phe75TyrfsTer15	p.F75Yfs*15	ENST00000261769	NM_004360.3	75	tTCAAAGTGGGC/t	3/16	1	2	FACETS	0.715	0.6	0.842	0.715	0.6	0.842	SUBCLONAL	1	TRUE	1	0.22	2		623	572	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376708	31376708	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	35	470	0	ENST00000328111.2:c.703G>C	p.Gly235Arg	p.G235R	ENST00000328111	NM_006892.3	235	Ggc/Cgc	7/23	1	2	FACETS	0.57	0.466	0.687	0.57	0.466	0.687	SUBCLONAL	1	TRUE	1	0.22	2		470	558	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938535	44938535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	35	492	0	ENST00000377967.4:c.3083C>T	p.Ser1028Phe	p.S1028F	ENST00000377967	NM_021140.2	1028	tCt/tTt	20/29	1	2	FACETS	0.606	0.496	0.73	0.606	0.496	0.73	SUBCLONAL	1	TRUE	1	0.22	2		492	525	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	105	264	0				ENST00000310581	NM_198253.2	-/1132			0.313952378762163	1	FACETS	0.614	0.556	0.674	0.614	0.556	0.674	INDETERMINATE	1	TRUE	0	0.669155955319765	1		264	340	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105761	27105761	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	351	373	0	ENST00000324856.7:c.5372C>A	p.Ser1791Ter	p.S1791*	ENST00000324856	NM_006015.4	1791	tCa/tAa	20/20	0.669155955319765	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.669155955319765	2		373	475	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744494	41744494	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	251	540	0	ENST00000301178.4:c.1114C>G	p.Gln372Glu	p.Q372E	ENST00000301178	NM_021913.4	372	Caa/Gaa	8/20	0.161207811037422	3	FACETS	1	0.976	1	0.362	0.338	0.385	INDETERMINATE	1	TRUE	0	0.669155955319765	3		540	923	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879256	151879256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761429170	NA	P-0033221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	48	400	0	ENST00000262189.6:c.5689C>T	p.Pro1897Ser	p.P1897S	ENST00000262189	NM_170606.2	1897	Cca/Tca	36/59	1	2	FACETS	0.258	0.218	0.303	0.258	0.218	0.303	SUBCLONAL	1	TRUE	1	0.669155955319765	2		400	555	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794756	120794756	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	204	658	0	ENST00000257552.2:c.601C>T	p.Arg201Ter	p.R201*	ENST00000257552	NM_002442.3	201	Cga/Tga	9/15	0.161207811037422	3	FACETS	0.801	0.742	0.862	0.267	0.247	0.288	INDETERMINATE	1	TRUE	0	0.669155955319765	3		658	1016	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81971431	81971431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	193	346	0	ENST00000359376.3:c.3121G>A	p.Glu1041Lys	p.E1041K	ENST00000359376	NM_002661.3	1041	Gag/Aag	28/33	0.12715195089945	4	FACETS	0.752	0.699	0.807	0.752	0.699	0.807	INDETERMINATE	2	TRUE	2	0.669155955319765	4		346	640	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138497	11138497	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	220	387	1	ENST00000358026.2:c.3253C>T	p.Leu1085Phe	p.L1085F	ENST00000358026	NM_001128849.1	1085	Ctt/Ttt	24/36	0.319021033631449	1	FACETS	0.796	0.746	0.845	0.796	0.746	0.845	INDETERMINATE	1	TRUE	0	0.669155955319765	1		388	550	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564865	41564865	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	259	453	1	ENST00000263253.7:c.4166A>T	p.Asn1389Ile	p.N1389I	ENST00000263253	NM_001429.3	1389	aAc/aTc	25/31	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.669155955319765	2		454	694	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084182	47084182	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1213736696	NA	P-0033221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	88	348	0	ENST00000409792.3:c.7107G>T	p.Met2369Ile	p.M2369I	ENST00000409792	NM_014159.6	2369	atG/atT	17/21	0.609099767354881	1	FACETS	0.507	0.453	0.564	0.507	0.453	0.564	SUBCLONAL	1	TRUE	0	0.669155955319765	1		348	345	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436815	52436815	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	191	529	0	ENST00000460680.1:c.1963G>T	p.Glu655Ter	p.E655*	ENST00000460680	NM_004656.3	655	Gag/Tag	15/17	0.158701363317108	2	FACETS	0.762	0.707	0.82	0.381	0.353	0.41	INDETERMINATE	1	TRUE	0	0.669155955319765	2		529	749	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440374	52440374	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	232	429	0	ENST00000460680.1:c.678C>G	p.Ile226Met	p.I226M	ENST00000460680	NM_004656.3	226	atC/atG	9/17	0.158701363317108	2	FACETS	1	0.989	1	0.615	0.578	0.652	INDETERMINATE	1	TRUE	0	0.669155955319765	2		429	564	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670591	134670591	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	153	641	0	ENST00000398015.3:c.502C>G	p.Leu168Val	p.L168V	ENST00000398015	NM_004441.4	168	Ctt/Gtt	3/16	0.158701363317108	2	FACETS	0.438	0.4	0.478	0.219	0.2	0.239	INDETERMINATE	1	TRUE	0	0.669155955319765	2		641	1045	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808870	1808870	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs560280646	NA	P-0033221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	734	603	0	ENST00000260795.2:c.2302G>T	p.Glu768Ter	p.E768*	ENST00000260795		768	Gag/Tag	17/17	0.161207811037422	3	FACETS	0.989	0.966	1	0.989	0.966	1	INDETERMINATE	3	TRUE	0	0.669155955319765	3		603	987	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522771	67522771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141974044	NA	P-0033221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	75	217	0	ENST00000274335.5:c.268C>T	p.Arg90Trp	p.R90W	ENST00000274335		90	Cgg/Tgg	1/15	0.158701363317108	2	FACETS	0.671	0.593	0.754	0.336	0.296	0.377	INDETERMINATE	1	TRUE	0	0.669155955319765	2		217	334	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910601	29910601	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs199474370	NA	P-0033221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	76	361	0	ENST00000376809.5:c.141C>G	p.Ile47Met	p.I47M	ENST00000376809	NM_002116.7	47	atC/atG	2/8	0.319021033631449	1	FACETS	0.339	0.298	0.382	0.339	0.298	0.382	INDETERMINATE	1	TRUE	0	0.669155955319765	1		361	446	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099409	157099409	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	56	162	0	ENST00000346085.5:c.346C>T	p.Gln116Ter	p.Q116*	ENST00000346085	NM_020732.3	116	Cag/Tag	1/20	0.319021033631449	1	FACETS	0.466	0.403	0.533	0.466	0.403	0.533	INDETERMINATE	1	TRUE	0	0.669155955319765	1		162	239	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878533	151878533	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	67	569	0	ENST00000262189.6:c.6412C>G	p.Pro2138Ala	p.P2138A	ENST00000262189	NM_170606.2	2138	Cca/Gca	36/59	1	2	FACETS	0.245	0.212	0.28	0.245	0.212	0.28	SUBCLONAL	1	TRUE	1	0.669155955319765	2		569	818	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878769	151878769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	59	395	0	ENST00000262189.6:c.6176C>T	p.Ser2059Leu	p.S2059L	ENST00000262189	NM_170606.2	2059	tCa/tTa	36/59	1	2	FACETS	0.333	0.287	0.384	0.333	0.287	0.384	SUBCLONAL	1	TRUE	1	0.669155955319765	2		395	529	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879084	151879084	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	81	604	0	ENST00000262189.6:c.5861C>A	p.Ser1954Tyr	p.S1954Y	ENST00000262189	NM_170606.2	1954	tCt/tAt	36/59	1	2	FACETS	0.29	0.255	0.328	0.29	0.255	0.328	SUBCLONAL	1	TRUE	1	0.669155955319765	2		604	835	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879343	151879343	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	58	385	0	ENST00000262189.6:c.5602C>T	p.Leu1868Phe	p.L1868F	ENST00000262189	NM_170606.2	1868	Ctt/Ttt	36/59	1	2	FACETS	0.304	0.261	0.351	0.304	0.261	0.351	SUBCLONAL	1	TRUE	1	0.669155955319765	2		385	570	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884505	151884505	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0033221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	63	373	0	ENST00000262189.6:c.4850C>G	p.Ser1617Ter	p.S1617*	ENST00000262189	NM_170606.2	1617	tCa/tGa	33/59	1	2	FACETS	0.329	0.284	0.377	0.329	0.284	0.377	SUBCLONAL	1	TRUE	1	0.669155955319765	2		373	573	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540222	23540222	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	54	262	0	ENST00000380871.4:c.181G>C	p.Glu61Gln	p.E61Q	ENST00000380871	NM_006167.3	61	Gag/Cag	1/2	0.375213546688896	3	FACETS	0.444	0.38	0.515	0.148	0.126	0.172	INDETERMINATE	1	TRUE	0	0.669155955319765	3		262	485	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0033237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	39	236	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.308196664626766	2		236	244	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0033237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	77	574	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.1928124991868	3	FACETS	0.887	0.786	0.994	0.887	0.786	0.994	CLONAL	2	TRUE	1	0.308196664626766	3		574	325	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589581	67589583	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	novel	NA	P-0033237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	30	164	0	ENST00000274335.5:c.1345_1347del	p.Leu449del	p.L449del	ENST00000274335		448	aaATTa/aaa	10/15	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.308196664626766	2		164	173	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0033237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	106	354	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.308196664626766	2		354	464	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057811	27057811	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	179	631	0	ENST00000324856.7:c.1519C>T	p.Gln507Ter	p.Q507*	ENST00000324856	NM_006015.4	507	Caa/Taa	3/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.308196664626766	2		631	807	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653794	89653794	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	59	295	0	ENST00000371953.3:c.92A>G	p.Asn31Ser	p.N31S	ENST00000371953	NM_000314.4	31	aAc/aGc	2/9	0.1928124991868	3	FACETS	1	0.968	1	0.727	0.63	0.831	CLONAL	1	TRUE	1	0.308196664626766	3		295	304	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009344	69009344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	31	357	0	ENST00000288368.4:c.2461G>A	p.Val821Ile	p.V821I	ENST00000288368	NM_024870.2	821	Gtc/Atc	22/40	1	2	FACETS	0.507	0.41	0.616	0.507	0.41	0.616	SUBCLONAL	1	TRUE	1	0.308196664626766	2		357	397	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	119	264	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.681359611214782	2		264	305	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720649	89720649	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs587782455	NA	P-0033248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	18	154	0	ENST00000371953.3:c.802-2A>T		p.X268_splice	ENST00000371953	NM_000314.4	268			0.681359611214782	1	FACETS	0.645	0.505	0.796	0.645	0.505	0.796	SUBCLONAL	1	FALSE	0	0.681359611214782	1		154	54	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654616	67654616	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1259610303	NA	P-0033248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	84	318	0	ENST00000264010.4:c.1103G>A	p.Arg368His	p.R368H	ENST00000264010	NM_006565.3	368	cGt/cAt	6/12	1	2	FACETS	0.842	0.752	0.935	0.842	0.752	0.935	CLONAL	1	FALSE	1	0.681359611214782	2		318	293	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120529666	120529666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	100	334	0	ENST00000256646.2:c.791G>A	p.Cys264Tyr	p.C264Y	ENST00000256646	NM_024408.3	264	tGc/tAc	5/34	1	2	FACETS	0.929	0.84	1	0.929	0.84	1	CLONAL	1	FALSE	1	0.681359611214782	2		334	316	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0033250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	78	732	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.324476763349425	1	FACETS	0.778	0.692	0.866	1	0.98	1	SUBCLONAL	2	TRUE	0	0.324476763349425	1		732	259	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412252	139412252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057523819	NA	P-0033250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	17	523	0	ENST00000277541.6:c.1393G>A	p.Ala465Thr	p.A465T	ENST00000277541	NM_017617.3	465	Gcc/Acc	8/34	0.204290192125185	1	FACETS	0.354	0.264	0.46	0.354	0.264	0.46	SUBCLONAL	1	TRUE	0	0.324476763349425	1		523	248	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78935253	78935253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143802144	NA	P-0033250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	11	427	0	ENST00000306801.3:c.3665G>A	p.Arg1222His	p.R1222H	ENST00000306801	NM_020761.2	1222	cGt/cAt	31/34	0.324476763349425	1	FACETS	0.262	0.18	0.363	0.262	0.18	0.363	SUBCLONAL	1	TRUE	0	0.324476763349425	1		427	217	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411267	63411267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866313799	NA	P-0033250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	43	267	1	ENST00000330258.3:c.1900C>T	p.Arg634Cys	p.R634C	ENST00000330258	NM_152424.3	634	Cgt/Tgt	2/2	0.187912930267763	0	FACETS	0.772	0.664	0.884			1	INDETERMINATE	2	TRUE	NA	0.324476763349425	0		268	116	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612095	43612095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	34	389	0	ENST00000355710.3:c.2200G>A	p.Glu734Lys	p.E734K	ENST00000355710	NM_020975.4	734	Gaa/Aaa	12/20	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.324476763349425	2		389	178	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435689	56435689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779655071	NA	P-0033250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	96	401	0	ENST00000407977.2:c.1448C>T	p.Thr483Met	p.T483M	ENST00000407977		483	aCg/aTg	9/10	0.27107924665372	3	FACETS	1	0.963	1	0.762	0.687	0.839	CLONAL	2	TRUE	0	0.324476763349425	3		401	301	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843706	156843706	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	68	604	0	ENST00000524377.1:c.1132T>G	p.Phe378Val	p.F378V	ENST00000524377	NM_002529.3	378	Ttc/Gtc	8/17	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.324476763349425	2		604	344	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609689	46609689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147672406	NA	P-0033250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	53	481	0	ENST00000263734.3:c.2413G>A	p.Ala805Thr	p.A805T	ENST00000263734	NM_001430.4	805	Gcc/Acc	15/16	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.324476763349425	2		481	297	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578370	212578370	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	14	221	0	ENST00000342788.4:c.887A>C	p.Asn296Thr	p.N296T	ENST00000342788	NM_005235.2	296	aAc/aCc	8/28	1	2	FACETS	0.872	0.638	1	0.872	0.638	1	CLONAL	1	TRUE	1	0.324476763349425	2		221	99	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	48	264	0				ENST00000310581	NM_198253.2	-/1132			0.366452994066258	3	FACETS	1	0.949	1	0.638	0.544	0.739	CLONAL	1	TRUE	1	0.366452994066258	3		264	243	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	308	773	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.335107851346915	3	FACETS	1	0.984	1			1	CLONAL	3	TRUE	NA	0.366452994066258	3		773	615	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325846	65325846	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747767226	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	75	315	1	ENST00000342505.4:c.1276G>A	p.Asp426Asn	p.D426N	ENST00000342505	NM_002227.2	426	Gac/Aac	9/25	0.366452994066258	3	FACETS	1	0.929	1	0.541	0.475	0.61	CLONAL	1	TRUE	1	0.366452994066258	3		316	448	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	67	489	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	0.366452994066258	4	FACETS	0.908	0.79	1	0.454	0.395	0.518	CLONAL	1	TRUE	2	0.366452994066258	4		489	550	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459215	120459215	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1221302379	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	177	381	1	ENST00000256646.2:c.6130C>T	p.Arg2044Cys	p.R2044C	ENST00000256646	NM_024408.3	2044	Cgt/Tgt	34/34	0.366452994066258	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.366452994066258	4		382	579	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497699	120497699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	149	303	0	ENST00000256646.2:c.2183C>T	p.Pro728Leu	p.P728L	ENST00000256646	NM_024408.3	728	cCc/cTc	13/34	0.366452994066258	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.366452994066258	4		303	453	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849128	156849128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	225	661	0	ENST00000524377.1:c.2020G>A	p.Asp674Asn	p.D674N	ENST00000524377	NM_002529.3	674	Gat/Aat	15/17	0.366452994066258	4	FACETS	0.974	0.909	1	0.974	0.909	1	CLONAL	2	TRUE	2	0.366452994066258	4		661	861	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597801	43597801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868523779	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	108	501	0	ENST00000355710.3:c.349C>T	p.Pro117Ser	p.P117S	ENST00000355710	NM_020975.4	117	Ccc/Tcc	3/20	0.363182928421357	3	FACETS	1	0.97	1	0.601	0.541	0.665	CLONAL	1	TRUE	1	0.366452994066258	3		501	580	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572587	64572587	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1114167533	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	273	432	0	ENST00000312049.6:c.1269G>A	p.Trp423Ter	p.W423*	ENST00000312049	NM_130799.2	423	tgG/tgA	9/10	0.366452994066258	3	FACETS	1	0.985	1			1	CLONAL	3	TRUE	NA	0.366452994066258	3		432	535	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77043873	77043873	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	224	546	0	ENST00000356341.3:c.1453C>T	p.Gln485Ter	p.Q485*	ENST00000356341	NM_002576.4	485	Cag/Tag	14/15	0.366452994066258	3	FACETS	1	0.967	1			1	CLONAL	2	TRUE	NA	0.366452994066258	3		546	688	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374666	118374666	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs782087392	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	162	288	0	ENST00000534358.1:c.8059T>C	p.Phe2687Leu	p.F2687L	ENST00000534358	NM_005933.3	2687	Ttc/Ctc	27/36	0.366452994066258	3	FACETS	1	0.968	1			1	CLONAL	3	TRUE	NA	0.366452994066258	3		288	329	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149247	119149247	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	219	419	0	ENST00000264033.4:c.1255T>A	p.Cys419Ser	p.C419S	ENST00000264033	NM_005188.3	419	Tgc/Agc	9/16	0.366452994066258	3	FACETS	0.962	0.905	1			1	CLONAL	3	TRUE	NA	0.366452994066258	3		419	490	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641487	18641487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	37	318	0	ENST00000266497.5:c.2486C>T	p.Ser829Phe	p.S829F	ENST00000266497		829	tCc/tTc	17/31	0.324710503008618	4	FACETS	0.809	0.669	0.965	0.27	0.223	0.322	CLONAL	1	TRUE	1	0.366452994066258	4		318	341	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18747427	18747427	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	78	250	0	ENST00000266497.5:c.3889-1G>A		p.X1297_splice	ENST00000266497		1297			0.324710503008618	4	FACETS	1	0.958	1	0.773	0.688	0.86	CLONAL	2	TRUE	1	0.366452994066258	4		250	251	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230405	46230405	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1391481708	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	48	323	0	ENST00000334344.6:c.739C>T	p.Arg247Cys	p.R247C	ENST00000334344	NM_152641.2	247	Cgt/Tgt	7/21	0.324710503008618	4	FACETS	1	0.879	1	0.347	0.294	0.404	CLONAL	1	TRUE	1	0.366452994066258	4		323	344	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491600	56491600	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	201	341	0	ENST00000267101.3:c.2492T>G	p.Val831Gly	p.V831G	ENST00000267101	NM_001982.3	831	gTg/gGg	21/28	0.324710503008618	4	FACETS	1	0.939	1	1	0.939	1	CLONAL	3	TRUE	1	0.366452994066258	4		341	498	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120621	115120621	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	321	524	0	ENST00000257566.3:c.385G>A	p.Gly129Arg	p.G129R	ENST00000257566	NM_016569.3	129	Gga/Aga	1/8	0.324710503008618	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	1	0.366452994066258	4		524	738	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608060	28608060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	164	470	0	ENST00000241453.7:c.1906G>A	p.Gly636Arg	p.G636R	ENST00000241453	NM_004119.2	636	Gga/Aga	15/24	0.35082098088518	4	FACETS	0.988	0.911	1	0.988	0.911	1	CLONAL	2	TRUE	2	0.366452994066258	4		470	619	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622440	28622440	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	122	418	0	ENST00000241453.7:c.1177G>A	p.Glu393Lys	p.E393K	ENST00000241453	NM_004119.2	393	Gag/Aag	9/24	0.35082098088518	4	FACETS	0.903	0.82	0.989	0.903	0.82	0.989	CLONAL	2	TRUE	2	0.366452994066258	4		418	504	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893589	28893589	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	120	295	1	ENST00000282397.4:c.3257G>A	p.Gly1086Glu	p.G1086E	ENST00000282397	NM_002019.4	1086	gGa/gAa	24/30	0.35082098088518	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	2	0.366452994066258	4		296	414	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32918761	32918761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1239798218	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	49	193	0	ENST00000380152.3:c.6908C>T	p.Ser2303Phe	p.S2303F	ENST00000380152		2303	tCc/tTc	12/27	0.35082098088518	4	FACETS	0.909	0.78	1	0.909	0.78	1	CLONAL	2	TRUE	2	0.366452994066258	4		193	201	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951120	48951120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	77	264	0	ENST00000267163.4:c.1282G>A	p.Glu428Lys	p.E428K	ENST00000267163	NM_000321.2	428	Gag/Aag	13/27	0.35082098088518	4	FACETS	0.837	0.741	0.939	0.837	0.741	0.939	CLONAL	2	TRUE	2	0.366452994066258	4		264	343	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955563	48955563	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	71	234	0	ENST00000267163.4:c.1679C>T	p.Ser560Phe	p.S560F	ENST00000267163	NM_000321.2	560	tCc/tTc	17/27	0.35082098088518	4	FACETS	0.846	0.745	0.953	0.846	0.745	0.953	CLONAL	2	TRUE	2	0.366452994066258	4		234	313	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437754	110437755	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	190	468	1	ENST00000375856.3:c.646dup	p.Val216GlyfsTer90	p.V216Gfs*90	ENST00000375856	NM_003749.2	216	gtg/gGtg	1/2	0.35082098088518	4	FACETS	0.985	0.914	1	0.985	0.914	1	CLONAL	2	TRUE	2	0.366452994066258	4		469	719	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007681	45007681	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	118	309	1	ENST00000558401.1:c.128T>C	p.Leu43Pro	p.L43P	ENST00000558401	NM_004048.2	43	cTg/cCg	2/4	0.331508899831486	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.366452994066258	2		310	298	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	263	706	0	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	0.29895953111526	5	FACETS	1	0.989	1	0.817	0.768	0.869	CLONAL	2	TRUE	2	0.366452994066258	5		706	907	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396349	396349	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	113	616	1	ENST00000262320.3:c.677C>T	p.Ser226Phe	p.S226F	ENST00000262320	NM_003502.3	226	tCt/tTt	2/11	0.363182928421357	3	FACETS	1	0.962	1	0.568	0.512	0.627	CLONAL	1	TRUE	1	0.366452994066258	3		617	642	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828063	3828063	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369233303	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	177	432	0	ENST00000262367.5:c.2062C>T	p.Pro688Ser	p.P688S	ENST00000262367	NM_004380.2	688	Ccg/Tcg	10/31	0.363182928421357	3	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	1	0.366452994066258	3		432	563	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900518	3900518	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	244	597	2	ENST00000262367.5:c.578C>T	p.Ser193Phe	p.S193F	ENST00000262367	NM_004380.2	193	tCt/tTt	2/31	0.363182928421357	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.366452994066258	3		599	762	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858784	9858784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	31	198	0	ENST00000330684.3:c.2617G>A	p.Gly873Arg	p.G873R	ENST00000330684	NM_001134407.1	873	Gga/Aga	13/13	0.363182928421357	3	FACETS	0.804	0.653	0.972	0.402	0.326	0.486	CLONAL	1	TRUE	1	0.366452994066258	3		198	249	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81941310	81941310	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	136	465	0	ENST00000359376.3:c.1488C>G	p.Cys496Trp	p.C496W	ENST00000359376	NM_002661.3	496	tgC/tgG	16/33	0.366452994066258	4	FACETS	0.929	0.849	1	0.464	0.424	0.506	CLONAL	2	TRUE	0	0.366452994066258	4		465	546	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831297	89831297	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs140180549	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	77	380	0	ENST00000389301.3:c.2778+1G>A		p.X926_splice	ENST00000389301	NM_000135.2	926			0.366452994066258	2	FACETS	1	0.898	1	0.51	0.45	0.574	CLONAL	1	TRUE	0	0.366452994066258	2		380	412	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586051	29586051	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	22	291	0	ENST00000356175.3:c.4271T>G	p.Ile1424Arg	p.I1424R	ENST00000356175	NM_000267.3	1424	aTa/aGa	32/57	0.366452994066258	3	FACETS	0.549	0.426	0.69	0.274	0.213	0.345	SUBCLONAL	1	TRUE	1	0.366452994066258	3		291	259	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804277	46804277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372121677	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	106	478	0	ENST00000290295.7:c.730G>A	p.Asp244Asn	p.D244N	ENST00000290295	NM_006361.5	244	Gac/Aac	2/2	0.366452994066258	3	FACETS	1	0.96	1	0.568	0.51	0.629	CLONAL	1	TRUE	1	0.366452994066258	3		478	603	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532460	63532460	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	81	470	0	ENST00000307078.5:c.2119G>T	p.Val707Leu	p.V707L	ENST00000307078	NM_004655.3	707	Gtg/Ttg	8/11	0.366452994066258	4	FACETS	0.942	0.831	1	0.471	0.415	0.531	CLONAL	1	TRUE	2	0.366452994066258	4		470	641	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573505	48573505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	33	211	0	ENST00000342988.3:c.89G>A	p.Gly30Glu	p.G30E	ENST00000342988	NM_005359.5	30	gGa/gAa	2/12	0.363182928421357	3	FACETS	1	0.922	1	0.616	0.507	0.735	CLONAL	1	TRUE	1	0.366452994066258	3		211	173	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226931	2226931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1287116735	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	114	356	0	ENST00000398665.3:c.4411G>A	p.Gly1471Arg	p.G1471R	ENST00000398665	NM_032482.2	1471	Gga/Aga	27/28	0.363182928421357	3	FACETS	0.92	0.836	1	0.92	0.836	1	CLONAL	2	TRUE	1	0.366452994066258	3		356	400	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15273319	15273319	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	239	544	0	ENST00000263388.2:c.5870C>T	p.Ala1957Val	p.A1957V	ENST00000263388	NM_000435.2	1957	gCc/gTc	32/33	0.366452994066258	5	FACETS	1	0.979	1	0.738	0.69	0.787	CLONAL	2	TRUE	2	0.366452994066258	5		544	913	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353986	15353986	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	93	138	0	ENST00000263377.2:c.2894C>T	p.Ser965Phe	p.S965F	ENST00000263377	NM_058243.2	965	tCt/tTt	14/20	0.366452994066258	5	FACETS	0.894	0.811	0.978	1	0.972	1	CLONAL	4	TRUE	2	0.366452994066258	5		138	220	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17941028	17941028	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	287	462	0	ENST00000458235.1:c.3097-1G>A		p.X1033_splice	ENST00000458235	NM_000215.3	1033			0.366452994066258	5	FACETS	1	0.959	1	1	0.959	1	CLONAL	3	TRUE	2	0.366452994066258	5		462	794	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220154	36220154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	193	524	0	ENST00000222270.7:c.4874C>T	p.Ser1625Phe	p.S1625F	ENST00000222270	NM_014727.1	1625	tCc/tTc	22/37	0.35082098088518	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.366452994066258	4		524	683	SUCCESS
AXL	558	MSKCC	GRCh37	19	41759589	41759589	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	195	416	0	ENST00000301178.4:c.2012G>C	p.Arg671Pro	p.R671P	ENST00000301178	NM_021913.4	671	cGg/cCg	17/20	0.35082098088518	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.366452994066258	4		416	643	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295786	212295786	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751446160	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	132	407	0	ENST00000342788.4:c.2527G>A	p.Asp843Asn	p.D843N	ENST00000342788	NM_005235.2	843	Gat/Aat	21/28	0.366452994066258	3	FACETS	0.975	0.893	1	0.975	0.893	1	CLONAL	2	TRUE	1	0.366452994066258	3		407	437	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440206	220440206	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	368	584	0	ENST00000243786.2:c.1059G>C	p.Glu353Asp	p.E353D	ENST00000243786	NM_002191.3	353	gaG/gaC	2/2	0.366452994066258	5	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	2	0.366452994066258	5		584	939	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659979	227659979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1310675277	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	173	402	0	ENST00000305123.5:c.3476C>T	p.Ala1159Val	p.A1159V	ENST00000305123	NM_005544.2	1159	gCc/gTc	1/2	0.366452994066258	5	FACETS	1	0.962	1	0.711	0.656	0.767	CLONAL	2	TRUE	2	0.366452994066258	5		402	686	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561450	9561450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	170	398	0	ENST00000353224.5:c.332G>A	p.Gly111Glu	p.G111E	ENST00000353224	NM_177990.2	111	gGa/gAa	4/10	0.366452994066258	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.366452994066258	3		398	481	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730799	40730799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	203	446	0	ENST00000373198.4:c.3736G>A	p.Glu1246Lys	p.E1246K	ENST00000373198	NM_133170.3	1246	Gaa/Aaa	27/32	0.366452994066258	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.366452994066258	3		446	535	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743942	40743942	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868489194	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	51	422	0	ENST00000373198.4:c.3053G>A	p.Arg1018Gln	p.R1018Q	ENST00000373198	NM_133170.3	1018	cGa/cAa	23/32	0.366452994066258	3	FACETS	0.738	0.629	0.859	0.369	0.314	0.43	SUBCLONAL	1	TRUE	1	0.366452994066258	3		422	446	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256317	46256317	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	34	216	0	ENST00000371998.3:c.545C>T	p.Ser182Phe	p.S182F	ENST00000371998		182	tCc/tTc	7/23	0.366452994066258	3	FACETS	0.861	0.707	1	0.431	0.353	0.516	CLONAL	1	TRUE	1	0.366452994066258	3		216	255	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264737	46264737	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	78	257	0	ENST00000371998.3:c.1607C>T	p.Ser536Phe	p.S536F	ENST00000371998		536	tCc/tTc	12/23	0.366452994066258	3	FACETS	1	0.953	1	0.579	0.511	0.652	CLONAL	1	TRUE	1	0.366452994066258	3		257	435	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436635	52436635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1482394743	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	91	463	0	ENST00000460680.1:c.2039C>T	p.Ser680Phe	p.S680F	ENST00000460680	NM_004656.3	680	tCc/tTc	16/17	0.366452994066258	4	FACETS	1	0.92	1	0.348	0.309	0.39	CLONAL	1	TRUE	1	0.366452994066258	4		463	650	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149238714	149238714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	267	625	0	ENST00000360632.3:c.1081C>T	p.Leu361Phe	p.L361F	ENST00000360632	NM_015472.4	361	Ctt/Ttt	7/7	0.366452994066258	4	FACETS	0.948	0.894	1	0.948	0.894	1	CLONAL	3	TRUE	1	0.366452994066258	4		625	700	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916863	178916863	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	78	481	1	ENST00000263967.3:c.250G>A	p.Asp84Asn	p.D84N	ENST00000263967	NM_006218.2	84	Gat/Aat	2/21	0.366452994066258	3	FACETS	1	0.9	1	0.512	0.451	0.577	CLONAL	1	TRUE	1	0.366452994066258	3		482	492	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612140	189612140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	142	436	0	ENST00000264731.3:c.1892G>A	p.Ser631Asn	p.S631N	ENST00000264731	NM_003722.4	631	aGt/aAt	14/14	0.366452994066258	4	FACETS	0.966	0.885	1	0.966	0.885	1	CLONAL	2	TRUE	2	0.366452994066258	4		436	548	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127289	55127289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	73	412	1	ENST00000257290.5:c.77C>T	p.Ser26Leu	p.S26L	ENST00000257290	NM_006206.4	26	tCa/tTa	3/23	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.366452994066258	2		413	382	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193721	106193721	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	25	138	0	ENST00000380013.4:c.4183G>A	p.Val1395Ile	p.V1395I	ENST00000380013	NM_001127208.2	1395	Gta/Ata	10/11	1	2	FACETS	0.864	0.688	1	0.864	0.688	1	CLONAL	1	TRUE	1	0.366452994066258	2		138	158	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539277	187539277	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	54	307	0	ENST00000441802.2:c.8463C>G	p.Asn2821Lys	p.N2821K	ENST00000441802	NM_005245.3	2821	aaC/aaG	10/27	0.366452994066258	1	FACETS	0.863	0.743	0.992	0.863	0.743	0.992	CLONAL	1	TRUE	0	0.366452994066258	1		307	279	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871312	35871312	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs754827305	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	62	211	0	ENST00000303115.3:c.534G>A	p.Trp178Ter	p.W178*	ENST00000303115	NM_002185.3	178	tgG/tgA	4/8	0.366452994066258	3	FACETS	0.845	0.739	0.957	0.845	0.739	0.957	CLONAL	2	TRUE	1	0.366452994066258	3		211	237	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873675	35873675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	98	249	0	ENST00000303115.3:c.631C>T	p.His211Tyr	p.H211Y	ENST00000303115	NM_002185.3	211	Cac/Tac	5/8	0.366452994066258	3	FACETS	1	0.917	1	1	0.917	1	CLONAL	2	TRUE	1	0.366452994066258	3		249	311	SUCCESS
APC	324	MSKCC	GRCh37	5	112116563	112116563	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	64	242	0	ENST00000257430.4:c.609del	p.Gln203HisfsTer2	p.Q203Hfs*2	ENST00000257430	NM_000038.5	203	cAa/ca	6/16	0.366452994066258	3	FACETS	0.879	0.771	0.993	0.879	0.771	0.993	CLONAL	2	TRUE	1	0.366452994066258	3		242	235	SUCCESS
APC	324	MSKCC	GRCh37	5	112128185	112128185	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779805	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	81	264	0	ENST00000257430.4:c.688C>T	p.Arg230Cys	p.R230C	ENST00000257430	NM_000038.5	230	Cgt/Tgt	7/16	0.366452994066258	3	FACETS	0.931	0.83	1	0.931	0.83	1	CLONAL	2	TRUE	1	0.366452994066258	3		264	281	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514520	149514520	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	170	403	0	ENST00000261799.4:c.424A>T	p.Ile142Leu	p.I142L	ENST00000261799	NM_002609.3	142	Ata/Tta	4/23	0.363182928421357	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	1	0.366452994066258	3		403	533	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514556	149514556	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	136	329	0	ENST00000261799.4:c.388A>G	p.Asn130Asp	p.N130D	ENST00000261799	NM_002609.3	130	Aat/Gat	4/23	0.363182928421357	3	FACETS	0.991	0.909	1	0.991	0.909	1	CLONAL	2	TRUE	1	0.366452994066258	3		329	443	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520211	176520211	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	144	588	0	ENST00000292408.4:c.1130C>T	p.Ser377Phe	p.S377F	ENST00000292408	NM_213647.1	377	tCc/tTc	9/18	0.363182928421357	3	FACETS	1	0.977	1	0.601	0.549	0.656	CLONAL	1	TRUE	1	0.366452994066258	3		588	773	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520497	176520498	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	224	583	1	ENST00000292408.4:c.1342_1343delinsAA	p.Gly448Asn	p.G448N	ENST00000292408	NM_213647.1	448	GGc/AAc	10/18	0.363182928421357	3	FACETS	0.992	0.927	1	0.992	0.927	1	CLONAL	2	TRUE	1	0.366452994066258	3		584	729	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056611	26056611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746599723	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	76	122	0	ENST00000343677.2:c.46G>A	p.Glu16Lys	p.E16K	ENST00000343677	NM_005319.3	16	Gag/Aag	1/1	0.29895953111526	5	FACETS	0.864	0.768	0.964	0.864	0.768	0.964	CLONAL	3	TRUE	2	0.366452994066258	5		122	248	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168678	32168678	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775488332	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	110	483	0	ENST00000375023.3:c.4245G>A	p.Met1415Ile	p.M1415I	ENST00000375023	NM_004557.3	1415	atG/atA	23/30	0.333299364913664	4	FACETS	1	0.964	1	0.578	0.519	0.639	CLONAL	1	TRUE	2	0.366452994066258	4		483	710	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187552	32187552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	180	418	0	ENST00000375023.3:c.1327C>T	p.Pro443Ser	p.P443S	ENST00000375023	NM_004557.3	443	Cca/Tca	8/30	0.333299364913664	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.366452994066258	4		418	604	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287233	33287233	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	187	438	0	ENST00000374542.5:c.1864T>C	p.Trp622Arg	p.W622R	ENST00000374542	NM_001141970.1	622	Tgg/Cgg	6/8	0.366452994066258	4	FACETS	0.989	0.917	1			1	CLONAL	2	TRUE	NA	0.366452994066258	4		438	705	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956682	93956682	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	42	281	0	ENST00000369303.4:c.2554G>T	p.Gly852Cys	p.G852C	ENST00000369303	NM_004440.3	852	Ggt/Tgt	15/17	0.366452994066258	2	FACETS	0.782	0.656	0.92	0.391	0.328	0.46	CLONAL	1	TRUE	0	0.366452994066258	2		281	293	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553594	106553594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs960785645	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	72	232	0	ENST00000369096.4:c.1559G>A	p.Gly520Glu	p.G520E	ENST00000369096	NM_001198.3	520	gGa/gAa	5/7	0.366452994066258	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	2	TRUE	0	0.366452994066258	2		232	195	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864464	162864464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	102	311	0	ENST00000366898.1:c.49G>A	p.Val17Ile	p.V17I	ENST00000366898	NM_004562.2	17	Gtc/Atc	2/12	0.366452994066258	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	0	0.366452994066258	2		311	269	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	123	466	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.366452994066258	5	FACETS	0.763	0.691	0.838	0.508	0.46	0.559	SUBCLONAL	2	TRUE	2	0.366452994066258	5		466	682	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444362	50444362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	80	286	0	ENST00000331340.3:c.292G>A	p.Asp98Asn	p.D98N	ENST00000331340	NM_006060.4	98	Gac/Aac	4/8	0.366452994066258	5	FACETS	0.785	0.694	0.881	0.523	0.463	0.588	SUBCLONAL	2	TRUE	2	0.366452994066258	5		286	431	SUCCESS
MET	4233	MSKCC	GRCh37	7	116409831	116409831	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778115147	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	98	252	0	ENST00000397752.3:c.2716G>A	p.Glu906Lys	p.E906K	ENST00000397752	NM_000245.2	906	Gag/Aag	12/21	0.29895953111526	5	FACETS	0.835	0.753	0.92	0.835	0.753	0.92	CLONAL	3	TRUE	2	0.366452994066258	5		252	331	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172261	38172261	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	54	264	1	ENST00000317025.8:c.2146C>T	p.Pro716Ser	p.P716S	ENST00000317025	NM_023034.1	716	Cct/Tct	12/24	1	2	FACETS	0.933	0.801	1	0.933	0.801	1	CLONAL	1	TRUE	1	0.366452994066258	2		265	316	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992692	68992692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529924687	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	39	470	0	ENST00000288368.4:c.1657G>A	p.Glu553Lys	p.E553K	ENST00000288368	NM_024870.2	553	Gaa/Aaa	16/40	1	2	FACETS	0.737	0.613	0.872	0.737	0.613	0.872	SUBCLONAL	1	TRUE	1	0.366452994066258	2		470	289	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090902	5090902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	29	95	0	ENST00000381652.3:c.3050C>T	p.Pro1017Leu	p.P1017L	ENST00000381652	NM_004972.3	1017	cCc/cTc	22/25	0.366452994066258	5	FACETS	1	0.841	1	0.687	0.562	0.823	CLONAL	2	TRUE	2	0.366452994066258	5		95	119	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549574	5549574	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528056151	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	179	471	0	ENST00000397747.3:c.601G>A	p.Glu201Lys	p.E201K	ENST00000397747	NM_025239.3	201	Gaa/Aaa	4/7	0.366452994066258	5	FACETS	0.982	0.907	1	0.655	0.604	0.706	CLONAL	2	TRUE	2	0.366452994066258	5		471	771	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484293	8484293	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	134	432	0	ENST00000356435.5:c.3239C>T	p.Ser1080Leu	p.S1080L	ENST00000356435		1080	tCa/tTa	19/35	0.366452994066258	5	FACETS	0.898	0.818	0.981	0.599	0.545	0.654	CLONAL	2	TRUE	2	0.366452994066258	5		432	631	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500886	8500886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	183	426	0	ENST00000356435.5:c.1996C>T	p.Pro666Ser	p.P666S	ENST00000356435		666	Cct/Tct	13/35	0.366452994066258	5	FACETS	1	0.981	1	0.783	0.725	0.842	CLONAL	2	TRUE	2	0.366452994066258	5		426	659	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521528	8521528	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	165	373	0	ENST00000356435.5:c.710G>A	p.Arg237Lys	p.R237K	ENST00000356435		237	aGa/aAa	9/35	0.366452994066258	5	FACETS	1	0.98	1	0.791	0.73	0.854	CLONAL	2	TRUE	2	0.366452994066258	5		373	588	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27168576	27168576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753021890	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	82	443	0	ENST00000380036.4:c.448G>A	p.Glu150Lys	p.E150K	ENST00000380036	NM_000459.3	150	Gaa/Aaa	3/23	0.366452994066258	4	FACETS	1	0.968	1			1	CLONAL	1	TRUE	NA	0.366452994066258	4		443	479	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27213548	27213548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	187	408	0	ENST00000380036.4:c.2944G>A	p.Asp982Asn	p.D982N	ENST00000380036	NM_000459.3	982	Gat/Aat	18/23	0.366452994066258	4	FACETS	0.932	0.868	0.996			1	CLONAL	3	TRUE	NA	0.366452994066258	4		408	499	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482167	87482167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	94	490	1	ENST00000277120.3:c.1454C>T	p.Ser485Phe	p.S485F	ENST00000277120		485	tCc/tTc	14/19	0.366452994066258	3	FACETS	1	0.94	1	0.54	0.481	0.602	CLONAL	1	TRUE	1	0.366452994066258	3		491	562	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915924	127915924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	156	424	0	ENST00000373547.4:c.557C>T	p.Pro186Leu	p.P186L	ENST00000373547	NM_002721.4	186	cCt/cTt	6/7	0.366452994066258	3	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	1	0.366452994066258	3		424	491	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293556	137293556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766062086	NA	P-0033251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	242	696	0	ENST00000481739.1:c.107C>T	p.Ser36Phe	p.S36F	ENST00000481739	NM_002957.4	36	tCc/tTc	2/10	0.366452994066258	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.366452994066258	3		696	757	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0033252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	124	594	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.621124160203385	3	FACETS	0.925	0.851	0.999	0.925	0.851	0.999	CLONAL	2	TRUE	1	0.621124160203385	3		594	283	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063717	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0033252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	49	141	0	ENST00000412916.2:c.165+1G>T		p.X55_splice	ENST00000412916		55			0.603222083738251	2	FACETS	0.822	0.725	0.918	0.822	0.725	0.918	CLONAL	2	TRUE	0	0.621124160203385	2		141	96	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772227	68772228	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	142	583	0	ENST00000261769.5:c.77dup	p.Pro27AlafsTer7	p.P27Afs*7	ENST00000261769	NM_004360.3	26	gag/gAag	2/16	0.603222083738251	2	FACETS	0.994	0.932	1	0.994	0.932	1	CLONAL	2	TRUE	0	0.621124160203385	2		583	230	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591850	48591850	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	25	433	0	ENST00000342988.3:c.1013C>A	p.Thr338Lys	p.T338K	ENST00000342988	NM_005359.5	338	aCa/aAa	9/12	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.309116536050217	2		433	145	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007742	45007795	+	frameshift_variant	Frame_Shift_Del	DEL	AGAGAGAATTGAAAAAGTGGAGCATTCAGACTTGTCTTTCAGCAAGGACTGGTC	AGAGAGAATTGAAAAAGTGGAGCATTCAGACTTGTCTTTCAGCAAGGACTGGTC	T	novel	NA	P-0033256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	19	362	0	ENST00000558401.1:c.189_242delinsT	p.Glu64PhefsTer8	p.E64Ffs*8	ENST00000558401	NM_004048.2	63	ggAGAGAGAATTGAAAAAGTGGAGCATTCAGACTTGTCTTTCAGCAAGGACTGGTCt/ggTt	2/4	0.309116536050217	0	FACETS	0.965	0.748	1			1	CLONAL	1	TRUE	0	0.309116536050217	0		362	88	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0033259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	232	468	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.459390006588968	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.459390006588968	2		468	485	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711879	89711880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	88	344	0	ENST00000371953.3:c.499dup	p.Thr167AsnfsTer13	p.T167Nfs*13	ENST00000371953	NM_000314.4	166	gta/gtAa	6/9	0.421033338509945	3	FACETS	0.899	0.808	0.993	0.899	0.808	0.993	CLONAL	2	TRUE	1	0.459390006588968	3		344	262	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795223	42795223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774119037	NA	P-0033259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	114	489	2	ENST00000575354.2:c.2303C>T	p.Pro768Leu	p.P768L	ENST00000575354	NM_015125.3	768	cCg/cTg	10/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.459390006588968	2		491	386	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782694	135782695	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1064795285	NA	P-0033259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	62	362	0	ENST00000298552.3:c.1326_1327del	p.Gly443IlefsTer15	p.G443Ifs*15	ENST00000298552	NM_001162426.1	442	agAGga/agga	13/23	0.406774651877815	4	FACETS	0.872	0.755	0.998	0.436	0.377	0.499	CLONAL	1	TRUE	2	0.459390006588968	4		362	452	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	85	264	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.673267920573451	2		264	225	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0033279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	199	335	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.673267920573451	2		335	581	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0033291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	64	785	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	1	2	FACETS	0.429	0.371	0.493	0.429	0.371	0.493	SUBCLONAL	1	TRUE	1	0.353658463298604	2		785	843	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843622	156843622	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1214	105	1171	0	ENST00000524377.1:c.1048C>A	p.Gln350Lys	p.Q350K	ENST00000524377	NM_002529.3	350	Cag/Aag	8/17	1	2	FACETS	0.45	0.402	0.502	0.45	0.402	0.502	SUBCLONAL	1	TRUE	1	0.353658463298604	2		1171	1319	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0033299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	13	474	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.756	1	1	0.756	1	CLONAL	1	TRUE	1	0.15	2		474	163	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0033299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	26	732	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.703	0.556	0.873	0.703	0.556	0.873	SUBCLONAL	1	TRUE	1	0.15	2		732	493	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923737	131923737	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs771068208	NA	P-0033301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	68	246	0	ENST00000265335.6:c.1007C>G	p.Ser336Cys	p.S336C	ENST00000265335		336	tCt/tGt	7/25	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		246	279	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0033302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	469	732	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.558564420494407	2	FACETS	0.821	0.791	0.851	0.821	0.791	0.851	CLONAL	2	TRUE	0	0.682539349765543	2		732	837	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	468	481	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.682539349765543	3	FACETS	0.915	0.878	0.952	0.915	0.878	0.952	CLONAL	2	TRUE	1	0.682539349765543	3		481	1005	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489543	40489543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	146	776	0	ENST00000264657.5:c.707C>T	p.Thr236Met	p.T236M	ENST00000264657	NM_139276.2	236	aCg/aTg	8/24	0.585146019367336	3	FACETS	0.593	0.541	0.648	0.297	0.27	0.324	SUBCLONAL	1	TRUE	1	0.682539349765543	3		776	967	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95583999	95583999	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1006363970	NA	P-0033302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	306	561	0	ENST00000393063.1:c.1469G>T	p.Arg490Leu	p.R490L	ENST00000393063	NM_030621.3	490	cGc/cTc	10/28	0.682539349765543	4	FACETS	0.941	0.891	0.991	0.941	0.891	0.991	CLONAL	2	TRUE	2	0.682539349765543	4		561	802	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030326	180030326	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs150279372	NA	P-0033302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	221	1056	0	ENST00000261937.6:c.3958C>G	p.Arg1320Gly	p.R1320G	ENST00000261937	NM_182925.4	1320	Cgg/Ggg	30/30	0.502721314151964	4	FACETS	0.809	0.751	0.869	0.404	0.375	0.435	CLONAL	1	TRUE	2	0.682539349765543	4		1056	1347	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897399	78897399	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144539543	NA	P-0033303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	339	964	1	ENST00000306801.3:c.2734G>A	p.Ala912Thr	p.A912T	ENST00000306801	NM_020761.2	912	Gct/Act	23/34	0.266614722721017	3	FACETS	0.815	0.771	0.86	0.815	0.771	0.86	CLONAL	2	TRUE	1	0.432050649163844	3		965	1171	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374828	149374828	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	482	556	0	ENST00000360632.3:c.266C>G	p.Ser89Trp	p.S89W	ENST00000360632	NM_015472.4	89	tCg/tGg	2/7	1	2	FACETS	0.885	0.854	0.917	1	0.998	1	CLONAL	3	TRUE	1	0.432050649163844	2		556	840	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762863	40762863	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	252	614	0	ENST00000392038.2:c.145C>A	p.Leu49Ile	p.L49I	ENST00000392038	NM_001626.4	49	Cta/Ata	3/14	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.432050649163844	2		614	790	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116149	67116149	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	153	444	0	ENST00000412916.2:c.433G>C	p.Glu145Gln	p.E145Q	ENST00000412916		145	Gag/Cag	5/6	0.432050649163844	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.432050649163844	1		444	513	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29083926	29083926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781710	NA	P-0033303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	84	363	0	ENST00000328354.6:c.1591G>A	p.Glu531Lys	p.E531K	ENST00000328354	NM_007194.3	531	Gag/Aag	15/15	0.266614722721017	3	FACETS	0.961	0.852	1	0.481	0.426	0.539	CLONAL	1	TRUE	1	0.432050649163844	3		363	492	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805914	32805914	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	412	1209	2	ENST00000374899.4:c.97C>T	p.Gln33Ter	p.Q33*	ENST00000374899	NM_018833.2	33	Caa/Taa	2/12	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.432050649163844	2		1211	1322	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852183	128852183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	434	1453	1	ENST00000249373.3:c.2255C>T	p.Ala752Val	p.A752V	ENST00000249373	NM_005631.4	752	gCa/gTa	12/12	1	2	FACETS	0.832	0.794	0.871	1	0.996	1	CLONAL	2	TRUE	1	0.432050649163844	2		1454	1207	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875031	151875031	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	66	271	0	ENST00000262189.6:c.7507C>T	p.Gln2503Ter	p.Q2503*	ENST00000262189	NM_170606.2	2503	Cag/Tag	38/59	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.432050649163844	2		271	227	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012228	152012228	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	188	547	0	ENST00000262189.6:c.585G>C	p.Gln195His	p.Q195H	ENST00000262189	NM_170606.2	195	caG/caC	4/59	1	2	FACETS	0.794	0.739	0.85	1	0.992	1	SUBCLONAL	2	TRUE	1	0.432050649163844	2		547	548	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs17849781	NA	P-0033304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	191	935	0	ENST00000269305.4:c.832C>A	p.Pro278Thr	p.P278T	ENST00000269305	NM_001126112.2	278	Cct/Act	8/11	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.285598216955527	2		935	1291	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	81	264	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.285598216955527	2		264	533	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692844	89692844	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1114167629	NA	P-0033304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	42	267	0	ENST00000371953.3:c.328C>T	p.Gln110Ter	p.Q110*	ENST00000371953	NM_000314.4	110	Caa/Taa	5/9	0.285598216955527	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.285598216955527	1		267	201	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463182	25463182	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs779626155	NA	P-0033304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	72	584	0	ENST00000264709.3:c.2311C>T	p.Arg771Ter	p.R771*	ENST00000264709	NM_175629.2	771	Cga/Tga	19/23	1	2	FACETS	0.739	0.646	0.841	0.739	0.646	0.841	SUBCLONAL	1	TRUE	1	0.285598216955527	2		584	682	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041121	180041121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770869636	NA	P-0033304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1309	203	1240	0	ENST00000261937.6:c.3278C>T	p.Thr1093Met	p.T1093M	ENST00000261937	NM_182925.4	1093	aCg/aTg	24/30	1	2	FACETS	0.94	0.869	1	0.94	0.869	1	CLONAL	1	TRUE	1	0.285598216955527	2		1240	1512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576912	7576912	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	157	884	0	ENST00000269305.4:c.934del	p.Thr312ProfsTer33	p.T312Pfs*33	ENST00000269305	NM_001126112.2	312	Acc/cc	9/11	1	2	FACETS	0.976	0.893	1	0.976	0.893	1	CLONAL	1	TRUE	1	0.285598216955527	2		884	1126	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0033305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	262	340	0				ENST00000310581	NM_198253.2	-/1132			0.638980980601548	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.638980980601548	1		340	525	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0033305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	344	693	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.638980980601548	1	FACETS	0.974	0.928	1	0.974	0.928	1	CLONAL	1	TRUE	0	0.638980980601548	1		693	752	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431400	49431400	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	341	1010	1	ENST00000301067.7:c.9739del	p.Leu3247CysfsTer83	p.L3247Cfs*83	ENST00000301067	NM_003482.3	3247	Ctg/tg	34/54	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.638980980601548	2		1011	1053	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431404	49431404	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	364	1007	1	ENST00000301067.7:c.9735A>T	p.Leu3245Phe	p.L3245F	ENST00000301067	NM_003482.3	3245	ttA/ttT	34/54	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.638980980601548	2		1008	1077	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290199	15290199	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	495	1156	0	ENST00000263388.2:c.3436T>G	p.Cys1146Gly	p.C1146G	ENST00000263388	NM_000435.2	1146	Tgc/Ggc	21/33	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.638980980601548	2		1156	1432	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632207	215632207	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	141	383	0	ENST00000260947.4:c.1567G>T	p.Val523Phe	p.V523F	ENST00000260947	NM_000465.2	523	Gtt/Ttt	6/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.638980980601548	2		383	407	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	66	264	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.575198979954648	2		264	215	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0033308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	39	581	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.997	0.843	1	0.997	0.843	1	CLONAL	1	TRUE	1	0.575198979954648	2		581	136	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263910	16263910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	139	905	0	ENST00000375759.3:c.10279G>A	p.Gly3427Ser	p.G3427S	ENST00000375759	NM_015001.2	3427	Ggc/Agc	12/15	1	2	FACETS	0.803	0.744	0.862	1	0.99	1	CLONAL	2	TRUE	1	0.575198979954648	2		905	301	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170436	119170436	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1369884955	NA	P-0033308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	81	332	0	ENST00000264033.4:c.2666A>G	p.Lys889Arg	p.K889R	ENST00000264033	NM_005188.3	889	aAa/aGa	16/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.575198979954648	2		332	243	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123875297	123875297	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	61	297	0	ENST00000330479.4:c.253G>A	p.Gly85Arg	p.G85R	ENST00000330479	NM_020382.3	85	Ggg/Agg	3/9	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.575198979954648	2		297	189	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133238270	133238270	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	67	345	0	ENST00000320574.5:c.2707G>A	p.Glu903Lys	p.E903K	ENST00000320574	NM_006231.2	903	Gaa/Aaa	24/49	1	2	FACETS	0.983	0.866	1	0.983	0.866	1	CLONAL	1	TRUE	1	0.575198979954648	2		345	237	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515004	103515004	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1430769122	NA	P-0033308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	44	266	0	ENST00000355739.4:c.1505C>T	p.Pro502Leu	p.P502L	ENST00000355739	NM_000123.3	502	cCt/cTt	8/15	0.575198979954648	1	FACETS	0.965	0.833	1	0.965	0.833	1	CLONAL	1	TRUE	0	0.575198979954648	1		266	113	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402491	20402491	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1304084051	NA	P-0033308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	146	556	0	ENST00000346618.3:c.28G>A	p.Glu10Lys	p.E10K	ENST00000346618	NM_001949.4	10	Gag/Aag	1/7	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.575198979954648	2		556	445	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852168	128852168	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	164	1062	0	ENST00000249373.3:c.2240C>T	p.Pro747Leu	p.P747L	ENST00000249373	NM_005631.4	747	cCa/cTa	12/12	1	2	FACETS	0.932	0.859	1	0.932	0.859	1	CLONAL	1	TRUE	1	0.575198979954648	2		1062	612	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021725	69021725	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	82	398	0	ENST00000288368.4:c.3013C>T	p.Gln1005Ter	p.Q1005*	ENST00000288368	NM_024870.2	1005	Cag/Tag	25/40	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.575198979954648	2		398	276	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738359	133738359	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	8	391	0	ENST00000318560.5:c.759C>A	p.Tyr253Ter	p.Y253*	ENST00000318560	NM_005157.4	253	taC/taA	4/11	0.188501323463709	1	FACETS	0.051	0.032	0.075	0.051	0.032	0.075	INDETERMINATE	1	TRUE	0	0.575198979954648	1		391	392	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115983	8116011	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	TTAGAGCCCTGCTCGATGCTCACAGGGCC	TTAGAGCCCTGCTCGATGCTCACAGGGCC	-	novel	NA	P-0033310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	84	264	0	ENST00000346208.3:c.1329_*25del		p.*443*	ENST00000346208		443		6/6	1	2	FACETS	0.694	0.618	0.773	0.694	0.618	0.773	SUBCLONAL	1	TRUE	1	0.740617245644779	2		264	327	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945512	151945513	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	390	709	0	ENST00000262189.6:c.2006dup	p.Leu669PhefsTer6	p.L669Ffs*6	ENST00000262189	NM_170606.2	669	ttg/ttTg	14/59	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.740617245644779	2		709	1017	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	183	264	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.875308024765727	2		264	387	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0033311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	318	716	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	1	2	FACETS	0.929	0.882	0.977	0.929	0.882	0.977	CLONAL	1	TRUE	1	0.875308024765727	2		716	782	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413070	139413072	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0033311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	57	682	0	ENST00000277541.6:c.1070_1072del	p.Phe357del	p.F357del	ENST00000277541	NM_017617.3	357	tTCTac/tac	6/34	1	2	FACETS	0.17	0.145	0.197	0.17	0.145	0.197	SUBCLONAL	1	TRUE	1	0.875308024765727	2		682	767	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463298	25463300	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs761103716	NA	P-0033311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	27	394	0	ENST00000264709.3:c.2193_2195del	p.Phe732del	p.F732del	ENST00000264709	NM_175629.2	731	ttCTTt/ttt	19/23	1	2	FACETS	0.126	0.1	0.156	0.126	0.1	0.156	SUBCLONAL	1	TRUE	1	0.875308024765727	2		394	489	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562708	29562710	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0033311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	56	521	0	ENST00000356175.3:c.3791_3793del	p.Glu1264del	p.E1264del	ENST00000356175	NM_000267.3	1263	aAAGaa/aaa	28/57	1	2	FACETS	0.175	0.149	0.203	0.175	0.149	0.203	SUBCLONAL	1	TRUE	1	0.875308024765727	2		521	732	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754617	42754619	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0033311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	62	910	0	ENST00000222329.4:c.121_123del	p.Glu41del	p.E41del	ENST00000222329	NM_006494.2	41	GAG/-	2/4	0.875308024765727	1	FACETS	0.123	0.105	0.141	0.123	0.105	0.141	SUBCLONAL	1	TRUE	0	0.875308024765727	1		910	650	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793528	42793529	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0033311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	94	1069	0	ENST00000575354.2:c.1332_1333del	p.Cys444Ter	p.C444*	ENST00000575354	NM_015125.3	444	TGt/t	8/20	0.875308024765727	1	FACETS	0.184	0.164	0.206	0.184	0.164	0.206	SUBCLONAL	1	TRUE	0	0.875308024765727	1		1069	655	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796793	42796794	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCA	novel	NA	P-0033311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	386	1214	0	ENST00000575354.2:c.3252_3255dup	p.Ala1086CysfsTer66	p.A1086Cfs*66	ENST00000575354	NM_015125.3	1084	tgt/tgTGCAt	14/20	0.875308024765727	1	FACETS	0.713	0.684	0.742	0.713	0.684	0.742	SUBCLONAL	1	TRUE	0	0.875308024765727	1		1214	696	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0033313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	513	290	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.636544777686559	11	FACETS	1	0.974	1	0.869	0.837	0.901	CLONAL	6	TRUE	4	0.636544777686559	11		290	1024	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0033313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	764	698	1	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.621401153363594	4	FACETS	0.969	0.947	0.989	0.969	0.947	0.989	CLONAL	4	TRUE	0	0.636544777686559	4		699	1014	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214612	5214612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139132124	NA	P-0033313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	132	734	1	ENST00000357368.4:c.4454C>T	p.Ala1485Val	p.A1485V	ENST00000357368	NM_002850.3	1485	gCg/gTg	29/38	0.53089582112379	4	FACETS	0.621	0.562	0.683	0.31	0.281	0.342	SUBCLONAL	1	TRUE	2	0.636544777686559	4		735	1093	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578532	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	178	993	0	ENST00000269305.4:c.398T>G	p.Met133Arg	p.M133R	ENST00000269305	NM_001126112.2	133	aTg/aGg	5/11	0.178847613398173	3	FACETS	0.98	0.902	1	0.98	0.902	1	CLONAL	2	TRUE	1	0.178847613398173	3		993	1106	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242486	+	inframe_deletion	In_Frame_Del	DEL	TTAAGAGAAGCAACATCT	TTAAGAGAAGCAACATCT	-	rs121913440	NA	P-0033314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	398	382	0	ENST00000275493.2:c.2239_2256del	p.Leu747_Ser752del	p.L747_S752del	ENST00000275493	NM_005228.3	747	TTAAGAGAAGCAACATCT/-	19/28	0.178847613398173	19	FACETS	1	0.976	1	0.845	0.809	0.88	CLONAL	14	TRUE	2	0.178847613398173	19		382	781	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562708	29562710	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0033324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	88	521	0	ENST00000356175.3:c.3791_3793del	p.Glu1264del	p.E1264del	ENST00000356175	NM_000267.3	1263	aAAGaa/aaa	28/57	0.451310597330076	4	FACETS	0.955	0.847	1	0.477	0.423	0.535	CLONAL	1	TRUE	2	0.463489747755178	4		521	582	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850272	128850272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777204354	NA	P-0033324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	147	617	0	ENST00000249373.3:c.1535G>A	p.Arg512His	p.R512H	ENST00000249373	NM_005631.4	512	cGc/cAc	9/12	1	2	FACETS	0.914	0.836	0.995	0.914	0.836	0.995	CLONAL	1	TRUE	1	0.463489747755178	2		617	694	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057848	27057848	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	216	862	0	ENST00000324856.7:c.1558del	p.Gln520SerfsTer99	p.Q520Sfs*99	ENST00000324856	NM_006015.4	519	tCc/tc	3/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.463489747755178	2		862	885	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101135	27101135	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	171	610	0	ENST00000324856.7:c.4417C>T	p.Gln1473Ter	p.Q1473*	ENST00000324856	NM_006015.4	1473	Cag/Tag	18/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.463489747755178	2		610	639	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	56	441	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	0.31	2		441	350	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181757	56181757	+	splice_acceptor_variant	Splice_Site	DEL	A	A	-	novel	NA	P-0033330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	24	265	0	ENST00000399503.3:c.3983-2del		p.X1328_splice	ENST00000399503	NM_005921.1	1328			1	2	FACETS	0.846	0.668	1	0.846	0.668	1	CLONAL	1	TRUE	1	0.31	2		265	183	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578201	7578202	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACA	novel	NA	P-0033330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	55	641	0	ENST00000269305.4:c.645_647dup	p.Val218dup	p.V218dup	ENST00000269305	NM_001126112.2	218	gtg/gtTGTg	6/11	0.3	1	FACETS	0.813	0.698	0.937	0.813	0.698	0.937	CLONAL	1	TRUE	0	0.31	1		641	369	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	45	264	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.873	0.754	0.997	0.873	0.754	0.997	CLONAL	1	TRUE	1	0.844871843761343	2		264	122	SUCCESS
AR	367	MSKCC	GRCh37	X	66765142	66765142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747293337	NA	P-0033342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	99	225	0	ENST00000374690.3:c.154G>A	p.Ala52Thr	p.A52T	ENST00000374690	NM_000044.3	52	Gcc/Acc	1/8	0.844871843761343	3	FACETS	1	0.933	1	0.521	0.47	0.573	CLONAL	1	TRUE	1	0.844871843761343	3		225	320	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430342	181430342	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	211	240	0	ENST00000325404.1:c.194A>G	p.Lys65Arg	p.K65R	ENST00000325404	NM_003106.3	65	aAg/aGg	1/1	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.844871843761343	2		240	352	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0033344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	18	337	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.147066632392434	3	FACETS	0.473	0.36	0.602	0.236	0.18	0.301	INDETERMINATE	1	FALSE	1	0.964551894422979	3		337	117	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117958	70117959	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	34	214	0	ENST00000245479.2:c.427dup	p.Trp143LeufsTer109	p.W143Lfs*109	ENST00000245479	NM_000346.3	142	-/T	1/3	0.213845326274742	3	FACETS	0.843	0.727	0.956	0.562	0.485	0.637	INDETERMINATE	2	FALSE	0	0.964551894422979	3		214	62	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211899	36211899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	25	772	1	ENST00000222270.7:c.1656del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	550	gaC/ga	3/37	0.147066632392434	3	FACETS	0.276	0.218	0.343	0.138	0.109	0.172	INDETERMINATE	1	FALSE	1	0.964551894422979	3		773	278	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114218	115114218	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	58	872	0	ENST00000257566.3:c.999del	p.Asn333LysfsTer28	p.N333Kfs*28	ENST00000257566	NM_016569.3	333	aaT/aa	6/8	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		872	1080	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0033349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	69	531	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.996	0.865	1	0.996	0.865	1	CLONAL	1	TRUE	1	0.15	2		531	924	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0033349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	188	993	5	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.941	1	1	0.993	1	CLONAL	2	TRUE	1	0.15	2		998	1224	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0033349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	40	574	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.788	0.653	0.939	0.788	0.653	0.939	CLONAL	1	TRUE	1	0.15	2		574	677	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374293	138374293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	82	672	1	ENST00000289153.2:c.3151G>A	p.Glu1051Lys	p.E1051K	ENST00000289153	NM_006219.2	1051	Gaa/Aaa	22/22	1	2	FACETS	0.961	0.845	1	0.961	0.845	1	CLONAL	1	TRUE	1	0.15	2		673	1138	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	57	639	1	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.784	0.67	0.908	0.784	0.67	0.908	CLONAL	1	TRUE	1	0.15	2		640	970	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582117	189582117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	49	430	0	ENST00000264731.3:c.676C>T	p.Arg226Cys	p.R226C	ENST00000264731	NM_003722.4	226	Cgc/Tgc	5/14	1	2	FACETS	0.85	0.718	0.995	0.85	0.718	0.995	CLONAL	1	TRUE	1	0.15	2		430	769	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0033349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	79	638	0	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	1	2	FACETS	0.998	0.876	1	0.998	0.876	1	CLONAL	1	TRUE	1	0.15	2		638	1055	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426973	49426973	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1565778024	NA	P-0033349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	87	616	1	ENST00000301067.7:c.11515del	p.Gln3839SerfsTer42	p.Q3839Sfs*42	ENST00000301067	NM_003482.3	3839	Cag/ag	39/54	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.15	2		617	930	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1620979	1620979	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1329397192	NA	P-0033349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1482	104	1079	2	ENST00000344749.5:c.1081del	p.Gln361ArgfsTer33	p.Q361Rfs*33	ENST00000344749	NM_001136139.2	361	Cag/ag	13/19	1	2	FACETS	0.874	0.78	0.976	0.874	0.78	0.976	CLONAL	1	TRUE	1	0.15	2		1081	1586	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057840	27057840	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1488	110	941	0	ENST00000324856.7:c.1548del	p.Pro517HisfsTer102	p.P517Hfs*102	ENST00000324856	NM_006015.4	516	ccT/cc	3/20	1	2	FACETS	0.918	0.821	1	0.918	0.821	1	CLONAL	1	TRUE	1	0.15	2		941	1598	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544167	18544167	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	19	358	0	ENST00000266497.5:c.1984C>T	p.Gln662Ter	p.Q662*	ENST00000266497		662	Cag/Tag	13/31	1	2	FACETS	0.679	0.515	0.873	0.679	0.515	0.873	SUBCLONAL	1	TRUE	1	0.15	2		358	373	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475163	40475164	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TG	TG	-	novel	NA	P-0033349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	50	525	0	ENST00000264657.5:c.1749-3_1749-2del		p.X583_splice	ENST00000264657	NM_139276.2	583			1	2	FACETS	0.88	0.744	1	0.88	0.744	1	CLONAL	1	TRUE	1	0.15	2		525	758	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619452	1619452	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1530	107	1015	0	ENST00000344749.5:c.1189C>A	p.Leu397Met	p.L397M	ENST00000344749	NM_001136139.2	397	Ctg/Atg	15/19	1	2	FACETS	0.872	0.778	0.971	0.872	0.778	0.971	CLONAL	1	TRUE	1	0.15	2		1015	1637	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627294	37627294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1676	146	1211	1	ENST00000249071.6:c.425G>A	p.Gly142Asp	p.G142D	ENST00000249071	NM_002872.4	142	gGc/gAc	5/7	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.15	2		1212	1822	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568503	41568503	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	31	398	1	ENST00000263253.7:c.4453G>T	p.Asp1485Tyr	p.D1485Y	ENST00000263253	NM_001429.3	1485	Gat/Tat	28/31	1	2	FACETS	0.832	0.672	1	0.832	0.672	1	CLONAL	1	TRUE	1	0.15	2		399	497	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777854	27777854	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs752719435	NA	P-0033349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	24	307	0	ENST00000369163.2:c.3G>A	p.Met1?	p.M1?	ENST00000369163	NM_003536.2	1	atG/atA	1/1	1	2	FACETS	0.802	0.628	1	0.802	0.628	1	CLONAL	1	TRUE	1	0.15	2		307	399	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323968	31323968	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs151341328	NA	P-0033349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	44	491	0	ENST00000412585.2:c.595G>C	p.Gly199Arg	p.G199R	ENST00000412585	NM_005514.6	199	Ggg/Cgg	3/8	1	2	FACETS	0.797	0.667	0.942	0.797	0.667	0.942	CLONAL	1	TRUE	1	0.15	2		491	736	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900206	101900206	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs727503470	NA	P-0033349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	29	410	0	ENST00000374994.4:c.640G>T	p.Gly214Cys	p.G214C	ENST00000374994	NM_004612.2	214	Ggt/Tgt	4/9	1	2	FACETS	0.692	0.554	0.849	0.692	0.554	0.849	SUBCLONAL	1	TRUE	1	0.15	2		410	559	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407522	139407522	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0033349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1400	90	960	0	ENST00000277541.6:c.2418T>A	p.Cys806Ter	p.C806*	ENST00000277541	NM_017617.3	806	tgT/tgA	15/34	1	2	FACETS	0.805	0.712	0.906	0.805	0.712	0.906	CLONAL	1	TRUE	1	0.15	2		960	1490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0033350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	116	809	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.282	0.253	0.313	0.282	0.253	0.313	SUBCLONAL	1	TRUE	1	0.66047537582998	2		809	1244	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0033350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	238	474	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.998	0.936	1	0.998	0.936	1	CLONAL	1	TRUE	1	0.66047537582998	2		474	722	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0033350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	300	286	1	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.66047537582998	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.66047537582998	2		287	434	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444566	78444567	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	A	novel	NA	P-0033350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	172	376	0	ENST00000370768.2:c.120+2dup		p.X40_splice	ENST00000370768	NM_003902.3	40			1	2	FACETS	0.872	0.807	0.94	0.872	0.807	0.94	CLONAL	1	TRUE	1	0.66047537582998	2		376	597	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923160	48923161	+	splice_donor_variant	Splice_Site	INS	-	-	T	rs1131690895	NA	P-0033350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	121	326	0	ENST00000267163.4:c.607+2dup		p.X203_splice	ENST00000267163	NM_000321.2	203			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.66047537582998	2		326	344	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944447	40944447	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	447	716	0	ENST00000373198.4:c.2055G>T	p.Lys685Asn	p.K685N	ENST00000373198	NM_133170.3	685	aaG/aaT	12/32	0.281355266444619	3	FACETS	0.781	0.747	0.816	0.781	0.747	0.816	INDETERMINATE	2	TRUE	1	0.66047537582998	3		716	1152	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265289	46265289	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1349873682	NA	P-0033350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	184	353	0	ENST00000371998.3:c.2159A>G	p.Asn720Ser	p.N720S	ENST00000371998		720	aAt/aGt	12/23	0.281355266444619	3	FACETS	1	0.978	1	0.568	0.527	0.611	INDETERMINATE	1	TRUE	1	0.66047537582998	3		353	652	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582154	189582154	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377757904	NA	P-0033350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	258	492	0	ENST00000264731.3:c.713C>T	p.Thr238Met	p.T238M	ENST00000264731	NM_003722.4	238	aCg/aTg	5/14	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.66047537582998	2		492	727	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0033352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	246	596	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	1	2	FACETS	0.866	0.812	0.922	0.866	0.812	0.922	CLONAL	1	TRUE	1	0.665790517404413	2		596	853	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0033355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	515	720	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.631189240677671	2	FACETS	0.943	0.913	0.973	0.943	0.913	0.973	CLONAL	2	TRUE	0	0.678140453053398	2		720	805	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307414	118307416	+	inframe_deletion	In_Frame_Del	DEL	GCG	GCG	-	rs781936420	NA	P-0033355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	10	40	0	ENST00000534358.1:c.200_202del	p.Ala67del	p.A67del	ENST00000534358	NM_005933.3	63	GCG/-	1/36	0.678140453053398	4	FACETS	0.384	0.261	0.536			1	SUBCLONAL	1	TRUE	NA	0.678140453053398	4		40	129	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345208	70345208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	345	340	0	ENST00000374080.3:c.2234C>T	p.Ser745Leu	p.S745L	ENST00000374080		745	tCa/tTa	16/45	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.678140453053398	1		340	464	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562482	95562482	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	71	457	0	ENST00000393063.1:c.4775C>G	p.Pro1592Arg	p.P1592R	ENST00000393063	NM_030621.3	1592	cCg/cGg	24/28	NA	2	FACETS	0.3	0.262	0.342			1	INDETERMINATE	1	TRUE	NA	0.678140453053398	2		457	697	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498289	29498289	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	47	605	0	ENST00000389048.3:c.1891A>T	p.Ser631Cys	p.S631C	ENST00000389048	NM_004304.4	631	Agc/Tgc	10/29	1	2	FACETS	0.171	0.144	0.202	0.171	0.144	0.202	SUBCLONAL	1	TRUE	1	0.678140453053398	2		605	810	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141549	202141549	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0033355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	121	348	0	ENST00000358485.4:c.838-1G>T		p.X280_splice	ENST00000358485	NM_001080125.1	280			0.479780817922049	4	FACETS	0.792	0.716	0.872			1	SUBCLONAL	1	TRUE	NA	0.678140453053398	4		348	756	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165510	47165510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	124	594	1	ENST00000409792.3:c.616G>A	p.Ala206Thr	p.A206T	ENST00000409792	NM_014159.6	206	Gca/Aca	3/21	0.652246004135441	2	FACETS	0.547	0.496	0.601	0.274	0.248	0.301	SUBCLONAL	1	TRUE	0	0.678140453053398	2		595	668	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168767	32168767	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	297	761	2	ENST00000375023.3:c.4156G>T	p.Gly1386Cys	p.G1386C	ENST00000375023	NM_004557.3	1386	Ggt/Tgt	23/30	0.678140453053398	3	FACETS	0.878	0.825	0.932	0.439	0.412	0.466	CLONAL	1	TRUE	1	0.678140453053398	3		763	1336	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169209	32169209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1390	383	969	0	ENST00000375023.3:c.3824C>T	p.Ala1275Val	p.A1275V	ENST00000375023	NM_004557.3	1275	gCa/gTa	22/30	0.678140453053398	3	FACETS	0.853	0.808	0.9	0.427	0.404	0.45	CLONAL	1	TRUE	1	0.678140453053398	3		969	1773	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964420	93964420	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	214	630	0	ENST00000369303.4:c.2477T>A	p.Met826Lys	p.M826K	ENST00000369303	NM_004440.3	826	aTg/aAg	14/17	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.678140453053398	2		630	587	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778056	135778056	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	512	750	0	ENST00000298552.3:c.2327A>T	p.His776Leu	p.H776L	ENST00000298552	NM_001162426.1	776	cAc/cTc	18/23	0.423091156277738	4	FACETS	0.873	0.836	0.91			1	CLONAL	2	TRUE	NA	0.678140453053398	4		750	1452	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778083	135778083	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	499	744	0	ENST00000298552.3:c.2300A>C	p.Gln767Pro	p.Q767P	ENST00000298552	NM_001162426.1	767	cAg/cCg	18/23	0.423091156277738	4	FACETS	0.871	0.834	0.909			1	CLONAL	2	TRUE	NA	0.678140453053398	4		744	1417	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70350054	70350073	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCATTCTCCAGGTAGGCCAA	GCATTCTCCAGGTAGGCCAA	T	novel	NA	P-0033355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	222	261	0	ENST00000374080.3:c.4037_4047+9delinsT		p.X1346_splice	ENST00000374080		1346		28/45	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.678140453053398	1		261	332	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587780070	NA	P-0033384-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	351	666	0	ENST00000269305.4:c.535C>G	p.His179Asp	p.H179D	ENST00000269305	NM_001126112.2	179	Cat/Gat	5/11	0.604019062022377	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	FALSE	0	0.6288038086608	2		666	542	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110073	115110073	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033384-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	206	783	0	ENST00000257566.3:c.1805del	p.Pro602LeufsTer30	p.P602Lfs*30	ENST00000257566	NM_016569.3	602	cCt/ct	8/8	0.531070394380893	4	FACETS	1	0.977	1	0.374	0.347	0.402	CLONAL	1	FALSE	1	0.6288038086608	4		783	951	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806242	1806242	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033384-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	163	636	0	ENST00000260795.2:c.1261C>T	p.Arg421Ter	p.R421*	ENST00000260795		421	Cga/Tga	8/17	0.221353223598968	4	FACETS	1	0.982	1	0.615	0.566	0.666	INDETERMINATE	1	FALSE	2	0.6288038086608	4		636	686	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73047240	73047246	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGGAA	GGGGGAA	AG	novel	NA	P-0033384-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	77	451	1	ENST00000356692.5:c.47_53delinsAG	p.Arg16LysfsTer29	p.R16Kfs*29	ENST00000356692		16	aGGGGGAAa/aAGa	2/9	0.6288038086608	3	FACETS	0.863	0.762	0.97	0.432	0.381	0.485	CLONAL	1	FALSE	1	0.6288038086608	3		452	373	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199313	16199313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033384-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	30	326	0	ENST00000375759.3:c.86A>G	p.Tyr29Cys	p.Y29C	ENST00000375759	NM_015001.2	29	tAt/tGt	2/15	0.360329941209619	4	FACETS	0.474	0.382	0.577			1	INDETERMINATE	1	FALSE	NA	0.6288038086608	4		326	328	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267490	7267490	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033384-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	105	614	0	ENST00000302850.5:c.518T>C	p.Val173Ala	p.V173A	ENST00000302850	NM_000208.2	173	gTg/gCg	2/22	0.319205959249372	2	FACETS	0.392	0.351	0.436	0.196	0.175	0.218	INDETERMINATE	1	FALSE	0	0.6288038086608	2		614	851	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399539	139399539	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033384-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	110	607	0	ENST00000277541.6:c.4604A>T	p.Tyr1535Phe	p.Y1535F	ENST00000277541	NM_017617.3	1535	tAc/tTc	26/34	0.280710806571062	5	FACETS	0.851	0.764	0.943	0.284	0.254	0.315	INDETERMINATE	1	FALSE	2	0.6288038086608	5		607	799	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0033394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	37	419	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.19619076483038	4	FACETS	0.896	0.753	1	0.896	0.753	1	INDETERMINATE	2	FALSE	2	0.418174177595271	4		419	140	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	101	592	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.372402416091961	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	0	0.418174177595271	1		592	293	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0033394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	59	342	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.418174177595271	2	FACETS	0.847	0.758	0.936	1	0.969	1	CLONAL	3	FALSE	0	0.418174177595271	2		342	111	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs371769427	NA	P-0033394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	24	242	0	ENST00000291552.4:c.101C>A	p.Ser34Tyr	p.S34Y	ENST00000291552	NM_006758.2	34	tCt/tAt	2/8	1	2	FACETS	1	0.835	1	1	0.835	1	CLONAL	1	FALSE	1	0.418174177595271	2		242	109	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940262	71940262	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777010283	NA	P-0033394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	64	534	2	ENST00000298229.2:c.647G>A	p.Arg216Gln	p.R216Q	ENST00000298229	NM_001567.3	216	cGg/cAg	5/28	1	2	FACETS	0.93	0.811	1	0.93	0.811	1	CLONAL	1	FALSE	1	0.418174177595271	2		536	329	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832423	72832423	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	45	443	0	ENST00000268489.5:c.4158del	p.Lys1387ArgfsTer38	p.K1387Rfs*38	ENST00000268489	NM_006885.3	1386	gcC/gc	9/10	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	FALSE	1	0.418174177595271	2		443	178	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794868	42794869	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0033394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	79	550	0	ENST00000575354.2:c.1953dup	p.Ala652ArgfsTer38	p.A652Rfs*38	ENST00000575354	NM_015125.3	650	gcc/gCcc	10/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.418174177595271	2		550	306	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257052	198257052	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1352116876	NA	P-0033394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	16	383	0	ENST00000335508.6:c.3890G>A	p.Arg1297His	p.R1297H	ENST00000335508	NM_012433.2	1297	cGt/cAt	25/25	1	2	FACETS	0.994	0.751	1	0.994	0.751	1	CLONAL	1	FALSE	1	0.418174177595271	2		383	77	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0033403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	199	531	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	0.742167996358044	2		531	516	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335121	65335121	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	145	495	0	ENST00000342505.4:c.520C>T	p.Arg174Ter	p.R174*	ENST00000342505	NM_002227.2	174	Cga/Tga	6/25	1	2	FACETS	0.771	0.708	0.836	0.771	0.708	0.836	SUBCLONAL	1	TRUE	1	0.742167996358044	2		495	507	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0033403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	208	714	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.961	0.899	1	0.961	0.899	1	CLONAL	1	TRUE	1	0.742167996358044	2		714	583	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0033403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	225	581	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.742167996358044	2		581	556	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117958	70117959	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	73	214	0	ENST00000245479.2:c.427dup	p.Trp143LeufsTer109	p.W143Lfs*109	ENST00000245479	NM_000346.3	142	-/T	1/3	1	2	FACETS	0.994	0.886	1	0.994	0.886	1	CLONAL	1	TRUE	1	0.742167996358044	2		214	198	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446313	187446313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137878288	NA	P-0033403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	143	498	0	ENST00000232014.4:c.1375C>T	p.Arg459Cys	p.R459C	ENST00000232014	NM_001130845.1	459	Cgc/Tgc	6/10	1	2	FACETS	0.892	0.821	0.965	0.892	0.821	0.965	CLONAL	1	TRUE	1	0.742167996358044	2		498	432	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306959	65306959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1358494508	NA	P-0033403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	151	436	0	ENST00000342505.4:c.2618G>A	p.Arg873His	p.R873H	ENST00000342505	NM_002227.2	873	cGc/cAc	19/25	1	2	FACETS	0.938	0.865	1	0.938	0.865	1	CLONAL	1	TRUE	1	0.742167996358044	2		436	434	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241679	55241681	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	rs397517086	NA	P-0033403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	380	602	0	ENST00000275493.2:c.2127_2129del	p.Glu709_Thr710delinsAsp	p.E709_T710delinsD	ENST00000275493	NM_005228.3	709	gaAACt/gat	18/28	0.729074484391635	3	FACETS	0.922	0.883	0.962	0.922	0.883	0.962	CLONAL	2	TRUE	1	0.742167996358044	3		602	761	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720671	89720671	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587782607	NA	P-0033403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	111	211	0	ENST00000371953.3:c.822G>A	p.Trp274Ter	p.W274*	ENST00000371953	NM_000314.4	274	tgG/tgA	8/9	0.742167996358044	3	FACETS	0.765	0.7	0.832	0.765	0.7	0.832	SUBCLONAL	2	TRUE	1	0.742167996358044	3		211	268	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720711	89720712	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	44	126	0	ENST00000371953.3:c.867dup	p.Val290SerfsTer8	p.V290Sfs*8	ENST00000371953	NM_000314.4	288	gaa/gAaa	8/9	0.742167996358044	3	FACETS	0.763	0.647	0.889	0.382	0.323	0.445	SUBCLONAL	1	TRUE	1	0.742167996358044	3		126	213	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625252	69625252	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782761826	NA	P-0033403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	193	751	1	ENST00000334134.2:c.541C>T	p.Arg181Cys	p.R181C	ENST00000334134	NM_005247.2	181	Cgc/Tgc	3/3	1	2	FACETS	0.983	0.917	1	0.983	0.917	1	CLONAL	1	TRUE	1	0.742167996358044	2		752	529	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088734	27088735	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0033403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	202	584	1	ENST00000324856.7:c.2348_2349del	p.Thr783ArgfsTer33	p.T783Rfs*33	ENST00000324856	NM_006015.4	781	atACac/atac	7/20	1	2	FACETS	0.923	0.861	0.986	0.923	0.861	0.986	CLONAL	1	TRUE	1	0.742167996358044	2		585	590	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052630	42052630	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	182	502	0	ENST00000219905.7:c.7301G>C	p.Arg2434Pro	p.R2434P	ENST00000219905	NM_001164273.1	2434	cGg/cCg	20/24	1	2	FACETS	0.995	0.926	1	0.995	0.926	1	CLONAL	1	TRUE	1	0.742167996358044	2		502	493	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500388	99500388	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	192	657	0	ENST00000268035.6:c.3821T>C	p.Phe1274Ser	p.F1274S	ENST00000268035	NM_000875.3	1274	tTc/tCc	21/21	1	2	FACETS	0.914	0.851	0.978	0.914	0.851	0.978	CLONAL	1	TRUE	1	0.742167996358044	2		657	566	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120253	70120254	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0033403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	288	736	0	ENST00000245479.2:c.1257dup	p.Tyr420LeufsTer158	p.Y420Lfs*158	ENST00000245479	NM_000346.3	419	gcc/gCcc	3/3	1	2	FACETS	0.956	0.902	1	0.956	0.902	1	CLONAL	1	TRUE	1	0.742167996358044	2		736	812	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591139	67591140	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACC	novel	NA	P-0033403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	84	279	0	ENST00000274335.5:c.1734_1736dup	p.Asp578_Gln579insHis	p.D578_Q579insH	ENST00000274335		578	gac/gACCac	12/15	1	2	FACETS	0.881	0.789	0.976	0.881	0.789	0.976	CLONAL	1	TRUE	1	0.742167996358044	2		279	257	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449438	149449438	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	111	440	0	ENST00000286301.3:c.1508C>A	p.Ala503Glu	p.A503E	ENST00000286301	NM_005211.3	503	gCa/gAa	10/22	1	2	FACETS	0.86	0.781	0.941	0.86	0.781	0.941	CLONAL	1	TRUE	1	0.742167996358044	2		440	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578259	7578259	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1567551903	NA	P-0033404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	288	671	0	ENST00000269305.4:c.590T>A	p.Val197Glu	p.V197E	ENST00000269305	NM_001126112.2	197	gTg/gAg	6/11	0.685703044093066	4	FACETS	0.999	0.945	1	0.999	0.945	1	CLONAL	2	TRUE	2	0.685703044093066	4		671	709	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258406	16258406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766484681	NA	P-0033404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	228	578	0	ENST00000375759.3:c.5671G>A	p.Glu1891Lys	p.E1891K	ENST00000375759	NM_015001.2	1891	Gaa/Aaa	11/15	0.685703044093066	4	FACETS	0.845	0.792	0.9	0.845	0.792	0.9	CLONAL	2	TRUE	2	0.685703044093066	4		578	663	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186751	108186751	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1448711296	NA	P-0033404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	49	397	0	ENST00000278616.4:c.6109G>A	p.Glu2037Lys	p.E2037K	ENST00000278616	NM_000051.3	2037	Gaa/Aaa	42/63	0.685703044093066	3	FACETS	0.52	0.442	0.606	0.26	0.221	0.303	SUBCLONAL	1	TRUE	1	0.685703044093066	3		397	369	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439299	52439299	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	311	587	1	ENST00000460680.1:c.943G>T	p.Glu315Ter	p.E315*	ENST00000460680	NM_004656.3	315	Gag/Tag	11/17	NA	2	FACETS	0.98	0.941	1			1	INDETERMINATE	2	TRUE	NA	0.685703044093066	2		588	463	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501563	149501563	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	242	671	0	ENST00000261799.4:c.2224G>A	p.Asp742Asn	p.D742N	ENST00000261799	NM_002609.3	742	Gac/Aac	16/23	0.685703044093066	4	FACETS	0.952	0.895	1	0.952	0.895	1	CLONAL	2	TRUE	2	0.685703044093066	4		671	625	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513186	106513186	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1428197771	NA	P-0033404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	119	348	0	ENST00000359195.3:c.2090G>T	p.Trp697Leu	p.W697L	ENST00000359195	NM_002649.2	697	tGg/tTg	4/11	0.685703044093066	4	FACETS	1	0.986	1	0.744	0.678	0.813	CLONAL	1	TRUE	2	0.685703044093066	4		348	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0033411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	343	720	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.339925902486849	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.365187170407874	3		720	647	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs770248150	NA	P-0033411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	186	503	0	ENST00000311936.3:c.351A>C	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaC	4/5	0.343726529570866	4	FACETS	0.986	0.92	1	0.986	0.92	1	CLONAL	3	TRUE	1	0.365187170407874	4		503	470	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523271	9523271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775109543	NA	P-0033411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	71	615	0	ENST00000353224.5:c.1966C>T	p.Arg656Trp	p.R656W	ENST00000353224	NM_177990.2	656	Cgg/Tgg	9/10	0.306519371724793	4	FACETS	0.812	0.708	0.923	0.406	0.354	0.462	CLONAL	1	TRUE	2	0.365187170407874	4		615	654	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217301	11217303	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	novel	NA	P-0033411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	95	786	0	ENST00000361445.4:c.4375_4377del	p.Ala1459del	p.A1459del	ENST00000361445	NM_004958.3	1459	GCC/-	30/58	0.342036636245263	3	FACETS	0.974	0.868	1	0.487	0.434	0.543	CLONAL	1	TRUE	1	0.365187170407874	3		786	632	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843574	156843575	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0033411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	60	874	1	ENST00000524377.1:c.1000_1001delinsAT	p.Glu334Met	p.E334M	ENST00000524377	NM_002529.3	334	GAg/ATg	8/17	0.181605788238121	5	FACETS	0.665	0.572	0.767	0.222	0.19	0.256	INDETERMINATE	1	TRUE	2	0.365187170407874	5		875	765	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646476	23646476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	56	753	0	ENST00000261584.4:c.1391G>A	p.Arg464Lys	p.R464K	ENST00000261584	NM_024675.3	464	aGg/aAg	4/13	0.342036636245263	3	FACETS	0.58	0.497	0.672	0.29	0.248	0.336	SUBCLONAL	1	TRUE	1	0.365187170407874	3		753	625	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273265	18273265	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	79	407	0	ENST00000222254.8:c.1058T>C	p.Leu353Pro	p.L353P	ENST00000222254	NM_005027.3	353	cTa/cCa	9/16	0.100875831337766	5	FACETS	0.854	0.756	0.959	0.569	0.504	0.639	INDETERMINATE	2	TRUE	2	0.365187170407874	5		407	392	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169979	32169979	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	48	770	0	ENST00000375023.3:c.3629C>T	p.Pro1210Leu	p.P1210L	ENST00000375023	NM_004557.3	1210	cCc/cTc	21/30	0.228451951925196	4	FACETS	0.532	0.448	0.624	0.266	0.224	0.312	SUBCLONAL	1	TRUE	2	0.365187170407874	4		770	675	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932188	39932188	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	80	497	0	ENST00000378444.4:c.2411del	p.Val804AlafsTer3	p.V804Afs*3	ENST00000378444	NM_001123385.1	804	gTc/gc	4/15	0.231640538552186	2	FACETS	0.978	0.864	1			1	CLONAL	1	TRUE	NA	0.365187170407874	2		497	448	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0033414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	101	444	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.275469574146273	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.275469574146273	1		444	528	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456555	32456555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253163678	NA	P-0033414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	16	24	0	ENST00000332351.3:c.337G>A	p.Ala113Thr	p.A113T	ENST00000332351	NM_024426.4	113	Gct/Act	1/10	1	2	FACETS	1	0.764	1	1	0.93	1	CLONAL	2	TRUE	1	0.275469574146273	2		24	58	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247865	59247865	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	146	883	0	ENST00000371222.2:c.878A>G	p.Glu293Gly	p.E293G	ENST00000371222	NM_002228.3	293	gAg/gGg	1/1	0.275469574146273	1	FACETS	0.972	0.887	1	0.972	0.887	1	CLONAL	1	TRUE	0	0.275469574146273	1		883	940	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982401	201982402	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0033414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	195	635	0	ENST00000359651.3:c.782_783del	p.Leu261ArgfsTer39	p.L261Rfs*39	ENST00000359651		260	tgTCtc/tgtc	6/8	0.275469574146273	3	FACETS	0.96	0.89	1	0.96	0.89	1	CLONAL	2	TRUE	1	0.275469574146273	3		635	839	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851764	63851764	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	42	519	0	ENST00000279873.7:c.2542C>G	p.Leu848Val	p.L848V	ENST00000279873	NM_032199.2	848	Ctt/Gtt	10/10	1	2	FACETS	0.468	0.389	0.555	0.468	0.389	0.555	SUBCLONAL	1	TRUE	1	0.275469574146273	2		519	652	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28903831	28903831	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	135	556	0	ENST00000282397.4:c.2628G>T	p.Met876Ile	p.M876I	ENST00000282397	NM_002019.4	876	atG/atT	19/30	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.275469574146273	2		556	721	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675061	40675061	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	115	639	0	ENST00000249776.8:c.25C>A	p.Leu9Met	p.L9M	ENST00000249776	NM_033286.3	9	Ctg/Atg	1/9	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.275469574146273	2		639	759	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566819	212566819	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	53	318	1	ENST00000342788.4:c.1362C>A	p.Ser454Arg	p.S454R	ENST00000342788	NM_005235.2	454	agC/agA	12/28	1	2	FACETS	0.846	0.722	0.98	0.846	0.722	0.98	CLONAL	1	TRUE	1	0.275469574146273	2		319	455	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657156	215657156	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	55	275	0	ENST00000260947.4:c.229G>T	p.Asp77Tyr	p.D77Y	ENST00000260947	NM_000465.2	77	Gac/Tac	3/11	1	2	FACETS	0.96	0.823	1	0.96	0.823	1	CLONAL	1	TRUE	1	0.275469574146273	2		275	416	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437594	52437600	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGGCT	CAGGGCT	-	novel	NA	P-0033414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	109	633	0	ENST00000460680.1:c.1561_1567del	p.Val523ProfsTer46	p.V523Pfs*46	ENST00000460680	NM_004656.3	521	AGCCCTGtc/tc	13/17	0.275469574146273	1	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	0	0.275469574146273	1		633	669	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741925	17741925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765066996	NA	P-0033416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	24	156	0	ENST00000250003.3:c.596C>T	p.Ala199Val	p.A199V	ENST00000250003	NM_002478.4	199	gCg/gTg	1/3	0.245937837349574	2	FACETS	1	0.907	1	0.642	0.51	0.79	CLONAL	1	FALSE	0	0.283153490959348	2		156	132	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218656	98218656	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	30	339	0	ENST00000331920.6:c.3208A>C	p.Met1070Leu	p.M1070L	ENST00000331920	NM_000264.3	1070	Atg/Ctg	19/24	0.226310963633228	2	FACETS	0.771	0.623	0.937	0.385	0.311	0.469	CLONAL	1	FALSE	0	0.283153490959348	2		339	275	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0033417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	245	654	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.504500275710251	2	FACETS	0.878	0.831	0.925	0.878	0.831	0.925	CLONAL	2	TRUE	0	0.571637495523416	2		654	488	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022747	12022747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376242225	NA	P-0033417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	54	386	0	ENST00000396373.4:c.853G>A	p.Val285Met	p.V285M	ENST00000396373	NM_001987.4	285	Gtg/Atg	5/8	0.571637495523416	3	FACETS	0.802	0.689	0.923	0.401	0.344	0.462	CLONAL	1	TRUE	1	0.571637495523416	3		386	303	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604789	48604789	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	25	320	0	ENST00000342988.3:c.1611C>A	p.Asp537Glu	p.D537E	ENST00000342988	NM_005359.5	537	gaC/gaA	12/12	0.279191088538231	0	FACETS	0.196	0.155	0.242			1	INDETERMINATE	1	TRUE	0	0.571637495523416	0		320	191	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156848995	156849007	+	frameshift_variant	Frame_Shift_Del	DEL	CGTGGCTAGCCAG	CGTGGCTAGCCAG	-	novel	NA	P-0033417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	126	679	0	ENST00000524377.1:c.1887_1899del	p.Val630SerfsTer24	p.V630Sfs*24	ENST00000524377	NM_002529.3	629	gcCGTGGCTAGCCAG/gc	15/17	NA	2	FACETS	0.938	0.855	1			1	INDETERMINATE	1	TRUE	NA	0.571637495523416	2		679	470	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133169	30133169	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	65	355	0	ENST00000263025.4:c.329C>T	p.Ser110Phe	p.S110F	ENST00000263025	NM_002746.2	110	tCc/tTc	2/9	0.551754906105386	3	FACETS	0.581	0.505	0.664	0.194	0.168	0.222	SUBCLONAL	1	TRUE	0	0.571637495523416	3		355	503	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589782	55589782	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	62	388	0	ENST00000288135.5:c.1264G>C	p.Val422Leu	p.V422L	ENST00000288135	NM_000222.2	422	Gtg/Ctg	8/21	0.571637495523416	1	FACETS	0.885	0.781	0.994	0.885	0.781	0.994	CLONAL	1	TRUE	0	0.571637495523416	1		388	175	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0033420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	177	689	1	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.575470829803102	1	FACETS	0.843	0.782	0.904	0.843	0.782	0.904	CLONAL	1	TRUE	0	0.575470829803102	1		690	520	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016603	12016603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	151	440	0	ENST00000353533.5:c.739G>A	p.Asp247Asn	p.D247N	ENST00000353533	NM_003010.3	247	Gac/Aac	7/11	0.575470829803102	1	FACETS	0.984	0.911	1	0.984	0.911	1	CLONAL	1	TRUE	0	0.575470829803102	1		440	380	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591118	67591150	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	ATCCAGCTGAGAAAGACGAGAGACCAATACTTG	ATCCAGCTGAGAAAGACGAGAGACCAATACTTG	-	novel	NA	P-0033420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	57	284	0	ENST00000274335.5:c.1713_1745del	p.Ile571_Leu581del	p.I571_L581del	ENST00000274335		571	ATCCAGCTGAGAAAGACGAGAGACCAATACTTG/-	12/15	1	2	FACETS	0.569	0.491	0.654	0.569	0.491	0.654	SUBCLONAL	1	TRUE	1	0.575470829803102	2		284	348	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592170	67592170	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0033420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	65	200	1	ENST00000274335.5:c.1985+1G>A		p.X662_splice	ENST00000274335		662			1	2	FACETS	0.949	0.834	1	0.949	0.834	1	CLONAL	1	TRUE	1	0.575470829803102	2		201	238	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0033421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	45	280	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.952	0.818	1	0.952	0.818	1	CLONAL	1	FALSE	1	0.684738136578764	2		280	138	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	154	768	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.684738136578764	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	0	0.684738136578764	1		768	244	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245343	46245343	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	10	465	0	ENST00000334344.6:c.3437C>T	p.Ser1146Leu	p.S1146L	ENST00000334344	NM_152641.2	1146	tCg/tTg	15/21	0.345017014119474	4	FACETS	0.313	0.212	0.44	0.157	0.106	0.22	INDETERMINATE	1	FALSE	2	0.684738136578764	4		465	157	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579542	7579542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780728	NA	P-0033421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	9	775	0	ENST00000269305.4:c.145G>A	p.Asp49Asn	p.D49N	ENST00000269305	NM_001126112.2	49	Gat/Aat	4/11	0.16868659176572	1	FACETS	0.062	0.041	0.09	0.062	0.041	0.09	INDETERMINATE	1	FALSE	0	0.684738136578764	1		775	277	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112473	115112473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	171	700	2	ENST00000257566.3:c.1267del	p.Arg423GlyfsTer209	p.R423Gfs*209	ENST00000257566	NM_016569.3	423	Cgg/gg	7/8	0.182821497849279	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.684738136578764	0		702	447	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562961	95562966	+	inframe_deletion	In_Frame_Del	DEL	CGGAGC	CGGAGC	-	novel	NA	P-0033421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	30	419	0	ENST00000393063.1:c.4291_4296del	p.Ala1431_Pro1432del	p.A1431_P1432del	ENST00000393063	NM_030621.3	1431	GCTCCG/-	24/28	1	2	FACETS	0.362	0.293	0.44	0.362	0.293	0.44	SUBCLONAL	1	FALSE	1	0.684738136578764	2		419	242	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004862	150004862	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	41	514	0	ENST00000253339.5:c.1363C>T	p.Gln455Ter	p.Q455*	ENST00000253339		455	Caa/Taa	3/7	1	2	FACETS	0.677	0.571	0.79	0.677	0.571	0.79	SUBCLONAL	1	FALSE	1	0.684738136578764	2		514	177	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0033422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	334	732	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.500499472059622	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.500182258376172	2		732	597	SUCCESS
AR	367	MSKCC	GRCh37	X	66766357	66766395	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	-	rs746853821	NA	P-0033422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	61	138	0	ENST00000374690.3:c.1382_1420del	p.Gly461_Gly473del	p.G461_G473del	ENST00000374690	NM_000044.3	457	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC/-	1/8	0.500499472059622	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.500182258376172	2		138	101	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968120	55968120	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1516	807	541	0	ENST00000263923.4:c.2210G>T	p.Cys737Phe	p.C737F	ENST00000263923	NM_002253.2	737	tGc/tTc	15/30	0.500182258376172	16	FACETS	1	0.987	1			1	CLONAL	6	TRUE	NA	0.500182258376172	16		541	2323	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163466	108163467	+	missense_variant	Missense_Mutation	DNP	TA	TA	CT	novel	NA	P-0033422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	285	700	0	ENST00000278616.4:c.4557_4558delinsCT	p.Ile1520Phe	p.I1520F	ENST00000278616	NM_000051.3	1519	gtTAtt/gtCTtt	30/63	0.500499472059622	3	FACETS	0.94	0.888	0.992	0.94	0.888	0.992	CLONAL	2	TRUE	1	0.500182258376172	3		700	758	SUCCESS
ALK	238	MSKCC	GRCh37	2	29450475	29450475	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs986532632	NA	P-0033422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	131	1011	2	ENST00000389048.3:c.2879G>T	p.Ser960Ile	p.S960I	ENST00000389048	NM_004304.4	960	aGt/aTt	17/29	NA	2	FACETS	0.677	0.614	0.742			1	INDETERMINATE	1	TRUE	NA	0.500182258376172	2		1013	774	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542471	187542471	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369520905	NA	P-0033422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	106	524	0	ENST00000441802.2:c.5269G>A	p.Asp1757Asn	p.D1757N	ENST00000441802	NM_005245.3	1757	Gat/Aat	10/27	0.14839422006023	0	FACETS	0.468	0.421	0.516			1	INDETERMINATE	1	TRUE	0	0.500182258376172	0		524	453	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671603	30671603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	158	769	1	ENST00000376406.3:c.5357C>T	p.Ser1786Phe	p.S1786F	ENST00000376406	NM_014641.2	1786	tCc/tTc	10/15	0.500499472059622	3	FACETS	1	0.923	1	0.503	0.461	0.547	CLONAL	1	TRUE	1	0.500182258376172	3		770	785	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878779	151878779	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	195	449	0	ENST00000262189.6:c.6166C>T	p.Pro2056Ser	p.P2056S	ENST00000262189	NM_170606.2	2056	Cct/Tct	36/59	0.500182258376172	6	FACETS	0.943	0.874	1	0.471	0.437	0.507	CLONAL	2	TRUE	2	0.500182258376172	6		449	827	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0033424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	167	428	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.176927797847944	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.205915492487676	2		428	696	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0033424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	31	196	2	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.513	0.414	0.626	0.513	0.414	0.626	SUBCLONAL	1	TRUE	1	0.205915492487676	2		198	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0033424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	133	758	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.156889706683701	0	FACETS	0.938	0.85	1			1	CLONAL	1	TRUE	0	0.205915492487676	0		758	1094	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121909229	NA	P-0033424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	44	166	0	ENST00000371953.3:c.389G>C	p.Arg130Pro	p.R130P	ENST00000371953	NM_000314.4	130	cGa/cCa	5/9	1	2	FACETS	0.833	0.698	0.982	0.833	0.698	0.982	CLONAL	1	TRUE	1	0.205915492487676	2		166	513	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979261	93979261	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs954614070	NA	P-0033424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	21	106	0	ENST00000369303.4:c.1567T>C	p.Tyr523His	p.Y523H	ENST00000369303	NM_004440.3	523	Tat/Cat	7/17	1	2	FACETS	0.559	0.43	0.71	0.559	0.43	0.71	SUBCLONAL	1	TRUE	1	0.205915492487676	2		106	365	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711880	89711880	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	29	192	0	ENST00000371953.3:c.499del	p.Thr167LeufsTer16	p.T167Lfs*16	ENST00000371953	NM_000314.4	166	gtA/gt	6/9	1	2	FACETS	0.592	0.474	0.726	0.592	0.474	0.726	SUBCLONAL	1	TRUE	1	0.205915492487676	2		192	476	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0033434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	206	503	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	TRUE	1	0.717817321429917	2		503	553	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	239	544	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.717817321429917	2		544	655	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0033434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	251	477	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.717817321429917	1	FACETS	0.988	0.938	1	0.988	0.938	1	CLONAL	1	TRUE	0	0.717817321429917	1		477	454	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221800	55221800	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199796955	NA	P-0033434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	272	547	0	ENST00000275493.2:c.844G>A	p.Glu282Lys	p.E282K	ENST00000275493	NM_005228.3	282	Gag/Aag	7/28	1	2	FACETS	0.912	0.859	0.966	0.912	0.859	0.966	CLONAL	1	TRUE	1	0.717817321429917	2		547	831	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193530	99193530	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	222	423	0	ENST00000074304.5:c.2725G>A	p.Glu909Lys	p.E909K	ENST00000074304	NM_001134224.1	909	Gag/Aag	25/26	1	2	FACETS	0.874	0.817	0.932	0.874	0.817	0.932	CLONAL	1	TRUE	1	0.717817321429917	2		423	708	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021779	71021805	+	inframe_deletion	In_Frame_Del	DEL	CTACTCGCACAAAACACTTGTGAAGAC	CTACTCGCACAAAACACTTGTGAAGAC	-	novel	NA	P-0033434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	28	270	0	ENST00000318789.4:c.1553_1579del	p.Ser518_Glu527delinsLys	p.S518_E527delinsK	ENST00000318789	NM_032682.5	518	aGTCTTCACAAGTGTTTTGTGCGAGTAGaa/aaa	18/21	1	2	FACETS	0.174	0.138	0.214	0.174	0.138	0.214	SUBCLONAL	1	TRUE	1	0.717817321429917	2		270	449	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322932	31322932	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	338	565	0	ENST00000412585.2:c.964G>C	p.Val322Leu	p.V322L	ENST00000412585	NM_005514.6	322	Gtc/Ctc	5/8	1	2	FACETS	0.972	0.922	1	0.972	0.922	1	CLONAL	1	TRUE	1	0.717817321429917	2		565	969	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109322547	109322547	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	288	535	0	ENST00000436639.2:c.490C>G	p.Leu164Val	p.L164V	ENST00000436639	NM_014454.2	164	Cta/Gta	3/10	1	2	FACETS	0.946	0.893	1	0.946	0.893	1	CLONAL	1	TRUE	1	0.717817321429917	2		535	848	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	32	513	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.93	0.766	1	1	0.969	1	CLONAL	3	FALSE	1	0.155996658542814	2		513	147	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	33	348	4	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	0.155996658542814	0	FACETS	1	0.865	1			1	CLONAL	3	FALSE	0	0.155996658542814	0		352	114	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	13	335	1	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.829	1	1	0.921	1	CLONAL	2	FALSE	1	0.155996658542814	2		336	69	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233090	69233090	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746910913	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	13	246	1	ENST00000462284.1:c.961del	p.Leu321PhefsTer52	p.L321Ffs*52	ENST00000462284	NM_002392.5	319	Ccc/cc	11/11	0.155996658542814	12	FACETS	1	0.867	1	0.162	0.115	0.218	CLONAL	1	FALSE	3	0.155996658542814	12		247	204	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	19	472	0	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	1	0.814	1	1	0.94	1	CLONAL	2	FALSE	1	0.155996658542814	2		472	114	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	27	262	1	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	1	2	FACETS	0.986	0.799	1	1	0.965	1	CLONAL	3	FALSE	1	0.155996658542814	2		263	117	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882019	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	32	600	4	ENST00000269305.4:c.455del	p.Pro152ArgfsTer18	p.P152Rfs*18	ENST00000269305	NM_001126112.2	152	cCg/cg	5/11	1	2	FACETS	1	0.887	1	1	0.964	1	CLONAL	2	FALSE	1	0.155996658542814	2		604	184	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760967	59760967	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	27	512	0	ENST00000259008.2:c.3440del	p.Asn1147MetfsTer3	p.N1147Mfs*3	ENST00000259008	NM_032043.2	1147	aAt/at	20/20	0.155996658542814	2	FACETS	1	0.817	1	1	0.817	1	CLONAL	2	FALSE	0	0.155996658542814	2		512	170	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339111	65339111	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	23	455	3	ENST00000342505.4:c.425del	p.Lys142ArgfsTer26	p.K142Rfs*26	ENST00000342505	NM_002227.2	142	aAg/ag	5/25	1	2	FACETS	0.87	0.69	1	1	0.956	1	CLONAL	3	FALSE	1	0.155996658542814	2		458	113	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574678	41574679	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs754418509	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	16	501	0	ENST00000263253.7:c.6970dup	p.His2324ProfsTer55	p.H2324Pfs*55	ENST00000263253	NM_001429.3	2321	-/C	31/31	1	2	FACETS	0.789	0.588	1	1	0.903	1	CLONAL	2	FALSE	1	0.155996658542814	2		501	130	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088788	27088788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	11	319	1	ENST00000324856.7:c.2402del	p.Gly801ValfsTer32	p.G801Vfs*32	ENST00000324856	NM_006015.4	799	caG/ca	7/20	0.155996658542814	3	FACETS	1	0.786	1	0.589	0.409	0.81	CLONAL	1	FALSE	1	0.155996658542814	3		320	129	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007332	143007332	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	34	324	0	ENST00000262992.4:c.2452del	p.Arg818GlufsTer4	p.R818Efs*4	ENST00000262992	NM_001101669.1	818	Aga/ga	22/24	0.155996658542814	1	FACETS	1	0.916	1	1	0.968	1	CLONAL	2	FALSE	0	0.155996658542814	1		324	169	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	24	550	7	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	1	0.877	1	1	0.954	1	CLONAL	2	FALSE	1	0.155996658542814	2		557	133	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910372	29910372	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs41548119	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	22	483	0	ENST00000376809.5:c.46del	p.Ala16ProfsTer4	p.A16Pfs*4	ENST00000376809	NM_002116.7	14	tcG/tc	1/8	0.155996658542814	7	FACETS	1	0.89	1	0.624	0.488	0.779	CLONAL	2	FALSE	3	0.155996658542814	7		483	157	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276618	15276618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	49	439	1	ENST00000263388.2:c.5647G>A	p.Asp1883Asn	p.D1883N	ENST00000263388	NM_000435.2	1883	Gat/Aat	30/33	1	2	FACETS	0.952	0.827	1	1	0.983	1	CLONAL	5	FALSE	1	0.155996658542814	2		440	132	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262326	46262326	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	23	382	1	ENST00000371998.3:c.915del	p.Phe305LeufsTer3	p.F305Lfs*3	ENST00000371998		304	Ttt/tt	9/23	1	2	FACETS	1	0.858	1	1	0.951	1	CLONAL	2	FALSE	1	0.155996658542814	2		383	132	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073668	8073668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768497001	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	21	276	1	ENST00000377482.5:c.991C>T	p.Arg331Cys	p.R331C	ENST00000377482	NM_018948.3	331	Cgc/Tgc	4/4	0.155996658542814	1	FACETS	0.962	0.75	1	1	0.94	1	CLONAL	2	FALSE	0	0.155996658542814	1		277	129	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912218	97912218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374176091	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	32	301	0	ENST00000289081.3:c.673G>A	p.Glu225Lys	p.E225K	ENST00000289081	NM_000136.2	225	Gag/Aag	7/15	0.155996658542814	2	FACETS	0.998	0.824	1	1	0.948	1	CLONAL	3	FALSE	0	0.155996658542814	2		301	137	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524834	187524834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771664786	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	16	450	0	ENST00000441802.2:c.10846G>A	p.Val3616Ile	p.V3616I	ENST00000441802	NM_005245.3	3616	Gta/Ata	19/27	0.155996658542814	1	FACETS	0.775	0.579	1	1	0.902	1	CLONAL	2	FALSE	0	0.155996658542814	1		450	122	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057937	27057937	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	21	491	0	ENST00000324856.7:c.1650del	p.Tyr551ThrfsTer68	p.Y551Tfs*68	ENST00000324856	NM_006015.4	549	Ccc/cc	3/20	0.155996658542814	3	FACETS	0.885	0.687	1	0.885	0.687	1	CLONAL	2	FALSE	1	0.155996658542814	3		491	164	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346158	89346158	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs878855327	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	11	83	0	ENST00000301030.4:c.6792del	p.Ala2265ProfsTer72	p.A2265Pfs*72	ENST00000301030	NM_001256183.1	2264	ccC/cc	9/13	0.155996658542814	1	FACETS	0.879	0.634	1	1	0.923	1	CLONAL	4	FALSE	0	0.155996658542814	1		83	37	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808898	1808898	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1416045205	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	10	440	0	ENST00000260795.2:c.2334del	p.Ser779AlafsTer41	p.S779Afs*41	ENST00000260795		777	aCc/ac	17/17	1	2	FACETS	1	0.682	1	1	0.682	1	CLONAL	1	FALSE	1	0.155996658542814	2		440	128	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926270	112926270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918457	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	54	424	0	ENST00000351677.2:c.1403C>T	p.Thr468Met	p.T468M	ENST00000351677	NM_002834.3	468	aCg/aTg	12/16	0.152682069237085	3	FACETS	1	0.919	1	1	0.968	1	CLONAL	4	FALSE	0	0.155996658542814	3		424	173	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287213	33287213	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	33	377	2	ENST00000374542.5:c.1884del	p.Cys629AlafsTer16	p.C629Afs*16	ENST00000374542	NM_001141970.1	628	ccC/cc	6/8	0.155996658542814	3	FACETS	1	0.896	1	1	0.896	1	CLONAL	2	FALSE	1	0.155996658542814	3		379	201	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953114	81953114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764736362	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	14	182	0	ENST00000359376.3:c.2080C>T	p.Arg694Cys	p.R694C	ENST00000359376	NM_002661.3	694	Cgc/Tgc	20/33	0.155996658542814	1	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	FALSE	0	0.155996658542814	1		182	130	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032104	48032104	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	21	287	0	ENST00000234420.5:c.3494G>A	p.Cys1165Tyr	p.C1165Y	ENST00000234420	NM_000179.2	1165	tGc/tAc	6/10	0.0825750781059644	4	FACETS	0.961	0.746	1	0.961	0.746	1	INDETERMINATE	2	FALSE	2	0.155996658542814	4		287	162	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755426	39755427	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	11	321	0	ENST00000288319.7:c.1338dup	p.Ala447CysfsTer19	p.A447Cfs*19	ENST00000288319	NM_182918.3	446	-/T	10/10	1	2	FACETS	1	0.845	1	1	0.845	1	CLONAL	1	FALSE	1	0.155996658542814	2		321	100	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671654	67671655	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	18	300	0	ENST00000264010.4:c.2070dup	p.Glu691ArgfsTer5	p.E691Rfs*5	ENST00000264010	NM_006565.3	688	gta/gtAa	12/12	0.155996658542814	1	FACETS	0.858	0.653	1	1	0.922	1	CLONAL	2	FALSE	0	0.155996658542814	1		300	124	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165282	47165283	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	40	327	0	ENST00000409792.3:c.843dup	p.Glu282ArgfsTer9	p.E282Rfs*9	ENST00000409792	NM_014159.6	281	-/A	3/21	1	2	FACETS	0.89	0.749	1	1	0.974	1	CLONAL	3	FALSE	1	0.155996658542814	2		327	192	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405954	157405954	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	36	330	0	ENST00000346085.5:c.2201del	p.Gly734AlafsTer11	p.G734Afs*11	ENST00000346085	NM_020732.3	732	ccG/cc	6/20	0.155996658542814	1	FACETS	0.849	0.708	1	1	0.971	1	CLONAL	3	FALSE	0	0.155996658542814	1		330	167	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579547	7579547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567557016	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	22	523	0	ENST00000269305.4:c.140del	p.Pro47ArgfsTer76	p.P47Rfs*76	ENST00000269305	NM_001126112.2	47	cCg/cg	4/11	1	2	FACETS	1	0.839	1	1	0.948	1	CLONAL	2	FALSE	1	0.155996658542814	2		523	130	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442024	52442024	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	30	297	0	ENST00000460680.1:c.325G>T	p.Gly109Ter	p.G109*	ENST00000460680	NM_004656.3	109	Gga/Tga	5/17	1	2	FACETS	0.866	0.708	1	1	0.966	1	CLONAL	3	FALSE	1	0.155996658542814	2		297	148	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431395	121431395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs893256143	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	24	366	0	ENST00000257555.6:c.599G>A	p.Arg200Gln	p.R200Q	ENST00000257555		200	cGg/cAg	3/10	0.152682069237085	3	FACETS	1	0.846	1	0.723	0.572	0.892	CLONAL	2	FALSE	0	0.155996658542814	3		366	153	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726651	46726651	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237327590	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	22	263	0	ENST00000371975.4:c.730G>A	p.Asp244Asn	p.D244N	ENST00000371975	NM_003579.3	244	Gat/Aat	7/18	1	2	FACETS	1	0.817	1	1	0.958	1	CLONAL	3	FALSE	1	0.155996658542814	2		263	91	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97873912	97873912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371897078	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	34	369	1	ENST00000289081.3:c.1162G>A	p.Gly388Arg	p.G388R	ENST00000289081	NM_000136.2	388	Gga/Aga	13/15	0.155996658542814	2	FACETS	1	0.89	1	1	0.968	1	CLONAL	4	FALSE	0	0.155996658542814	2		370	101	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900661	3900661	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	16	415	1	ENST00000262367.5:c.435del	p.Ala146LeufsTer6	p.A146Lfs*6	ENST00000262367	NM_004380.2	145	ccC/cc	2/31	0.155996658542814	0	FACETS	0.849	0.636	1			1	CLONAL	2	FALSE	0	0.155996658542814	0		416	102	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998127	169998128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs753143066	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	28	476	1	ENST00000295797.4:c.826dup	p.Thr276AsnfsTer16	p.T276Nfs*16	ENST00000295797	NM_002740.5	273	tta/ttAa	9/18	1	2	FACETS	0.93	0.749	1	1	0.953	1	CLONAL	2	FALSE	1	0.155996658542814	2		477	193	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	50	510	3	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	1	2	FACETS	1	0.927	1	1	0.983	1	CLONAL	4	FALSE	1	0.155996658542814	2		513	145	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65311270	65311270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	27	292	1	ENST00000342505.4:c.2041C>T	p.Arg681Trp	p.R681W	ENST00000342505	NM_002227.2	681	Cgg/Tgg	15/25	1	2	FACETS	1	0.89	1	1	0.967	1	CLONAL	3	FALSE	1	0.155996658542814	2		293	101	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141027	55141027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761924292	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	16	273	0	ENST00000257290.5:c.1673G>A	p.Arg558His	p.R558H	ENST00000257290	NM_006206.4	558	cGc/cAc	12/23	0.155996658542814	0	FACETS	0.951	0.715	1			1	CLONAL	2	FALSE	0	0.155996658542814	0		273	91	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948747	71948748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760925109	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	17	505	12	ENST00000298229.2:c.3466dup	p.Arg1156ProfsTer59	p.R1156Pfs*59	ENST00000298229	NM_001567.3	1153	-/C	26/28	0.155996658542814	5	FACETS	1	0.803	1	0.538	0.405	0.692	CLONAL	2	FALSE	1	0.155996658542814	5		517	125	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445203	49445203	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	38	475	1	ENST00000301067.7:c.2263del	p.Arg755GlyfsTer175	p.R755Gfs*175	ENST00000301067	NM_003482.3	755	Cgg/gg	10/54	0.155996658542814	6	FACETS	1	0.885	1			1	CLONAL	4	FALSE	NA	0.155996658542814	6		476	150	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112323	115112324	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	rs1381943852	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	14	26	0	ENST00000257566.3:c.1416_1417del	p.Leu473ProfsTer218	p.L473Pfs*218	ENST00000257566	NM_016569.3	472	gcGCtc/gctc	7/8	0.152682069237085	3	FACETS	1	0.811	1	1	0.919	1	CLONAL	5	FALSE	0	0.155996658542814	3		26	36	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478947	56478947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760053751	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	37	456	1	ENST00000267101.3:c.403C>T	p.Arg135Cys	p.R135C	ENST00000267101	NM_001982.3	135	Cgc/Tgc	3/28	0.155996658542814	12	FACETS	0.891	0.74	1	0.396	0.328	0.47	CLONAL	4	FALSE	3	0.155996658542814	12		457	237	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400299	139400299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150343794	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	21	375	1	ENST00000277541.6:c.4049G>A	p.Arg1350His	p.R1350H	ENST00000277541	NM_017617.3	1350	cGt/cAt	25/34	0.155996658542814	0	FACETS	0.842	0.662	1			1	CLONAL	3	FALSE	0	0.155996658542814	0		376	90	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797830	32797830	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759127287	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	21	322	0	ENST00000374899.4:c.1672G>A	p.Gly558Ser	p.G558S	ENST00000374899	NM_018833.2	558	Ggt/Agt	10/12	0.155996658542814	3	FACETS	1	0.794	1	1	0.794	1	CLONAL	2	FALSE	1	0.155996658542814	3		322	142	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910632	50910632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1354117345	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	15	457	0	ENST00000440232.2:c.1735G>A	p.Glu579Lys	p.E579K	ENST00000440232	NM_002691.3	579	Gag/Aag	14/27	1	2	FACETS	0.808	0.597	1	1	0.901	1	CLONAL	2	FALSE	1	0.155996658542814	2		457	119	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516867	187516867	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	23	311	0	ENST00000441802.2:c.13114C>T	p.Gln4372Ter	p.Q4372*	ENST00000441802	NM_005245.3	4372	Cag/Tag	26/27	0.155996658542814	1	FACETS	0.855	0.679	1	1	0.956	1	CLONAL	3	FALSE	0	0.155996658542814	1		311	106	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073712	8073712	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs374638182	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	20	228	0	ENST00000377482.5:c.947C>A	p.Pro316His	p.P316H	ENST00000377482	NM_018948.3	316	cCt/cAt	4/4	0.155996658542814	1	FACETS	1	0.825	1	1	0.943	1	CLONAL	2	FALSE	0	0.155996658542814	1		228	110	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598311	28598311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1480732926	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	21	531	0	ENST00000253063.3:c.283C>T	p.Arg95Cys	p.R95C	ENST00000253063	NM_031459.4	95	Cgc/Tgc	3/10	0.155996658542814	1	FACETS	0.856	0.666	1	1	0.932	1	CLONAL	2	FALSE	0	0.155996658542814	1		531	145	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193205402	193205403	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	43	314	0	ENST00000367435.3:c.1338dup	p.Val447CysfsTer17	p.V447Cfs*17	ENST00000367435	NM_024529.4	445	gtt/gTtt	15/17	1	2	FACETS	0.947	0.803	1	1	0.977	1	CLONAL	3	FALSE	1	0.155996658542814	2		314	194	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852590	63852590	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	29	351	0	ENST00000279873.7:c.3368C>T	p.Ser1123Leu	p.S1123L	ENST00000279873	NM_032199.2	1123	tCg/tTg	10/10	0.155996658542814	10	FACETS	1	0.834	1			1	CLONAL	4	FALSE	NA	0.155996658542814	10		351	147	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999078	100999078	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200987911	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	10	301	0	ENST00000325455.5:c.724C>T	p.Arg242Trp	p.R242W	ENST00000325455	NM_001202474.3	242	Cgg/Tgg	1/8	0.155996658542814	5	FACETS	1	0.767	1	0.573	0.395	0.789	CLONAL	2	FALSE	1	0.155996658542814	5		301	69	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437749	49437749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1355098421	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	26	387	0	ENST00000301067.7:c.5221G>A	p.Val1741Met	p.V1741M	ENST00000301067	NM_003482.3	1741	Gtg/Atg	22/54	0.155996658542814	6	FACETS	1	0.877	1			1	CLONAL	3	FALSE	NA	0.155996658542814	6		387	129	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50490676	50490676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777367839	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	16	299	1	ENST00000394963.4:c.1313G>A	p.Arg438Gln	p.R438Q	ENST00000394963	NM_003076.4	438	cGg/cAg	11/13	0.155996658542814	6	FACETS	0.88	0.654	1			1	CLONAL	2	FALSE	NA	0.155996658542814	6		300	153	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422182	81422182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	14	261	0	ENST00000298171.2:c.158G>A	p.Ser53Asn	p.S53N	ENST00000298171	NM_000369.2	53	aGt/aAt	1/10	1	2	FACETS	0.925	0.678	1	1	0.909	1	CLONAL	2	FALSE	1	0.155996658542814	2		261	97	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81927375	81927375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1272100050	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	18	432	0	ENST00000359376.3:c.1048C>T	p.Arg350Cys	p.R350C	ENST00000359376	NM_002661.3	350	Cgc/Tgc	12/33	0.155996658542814	1	FACETS	0.771	0.586	0.985	1	0.911	1	CLONAL	2	FALSE	0	0.155996658542814	1		432	138	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15975498	15975498	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	30	335	0	ENST00000268712.3:c.3856C>A	p.Leu1286Ile	p.L1286I	ENST00000268712	NM_006311.3	1286	Ctc/Atc	29/46	1	2	FACETS	1	0.895	1	1	0.963	1	CLONAL	2	FALSE	1	0.155996658542814	2		335	167	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244398	41244398	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	36	589	0	ENST00000357654.3:c.3150T>A	p.Ser1050Arg	p.S1050R	ENST00000357654	NM_007294.3	1050	agT/agA	10/23	0.155996658542814	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	2	FALSE	0	0.155996658542814	2		589	209	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47679356	47679356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	13	263	0	ENST00000347630.2:c.851G>A	p.Arg284His	p.R284H	ENST00000347630	NM_001007230.1	284	cGc/cAc	10/11	0.155996658542814	2	FACETS	1	0.844	1	0.651	0.468	0.871	CLONAL	1	FALSE	0	0.155996658542814	2		263	128	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172413	7172413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764221583	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	19	329	1	ENST00000302850.5:c.1156G>A	p.Gly386Ser	p.G386S	ENST00000302850	NM_000208.2	386	Ggc/Agc	5/22	1	2	FACETS	0.902	0.692	1	1	0.93	1	CLONAL	2	FALSE	1	0.155996658542814	2		330	135	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968216	18968216	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	31	457	0	ENST00000262803.5:c.2056G>A	p.Glu686Lys	p.E686K	ENST00000262803	NM_002911.3	686	Gag/Aag	15/24	1	2	FACETS	0.903	0.747	1	1	0.972	1	CLONAL	4	FALSE	1	0.155996658542814	2		457	110	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228086	36228086	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	53	446	1	ENST00000222270.7:c.7472G>A	p.Arg2491His	p.R2491H	ENST00000222270	NM_014727.1	2491	cGt/cAt	33/37	1	2	FACETS	0.95	0.83	1	1	0.984	1	CLONAL	5	FALSE	1	0.155996658542814	2		447	143	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229369	36229369	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	16	367	0	ENST00000222270.7:c.8059A>G	p.Thr2687Ala	p.T2687A	ENST00000222270	NM_014727.1	2687	Acc/Gcc	37/37	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	FALSE	1	0.155996658542814	2		367	167	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765606	41765606	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	32	448	1	ENST00000301178.4:c.2482G>A	p.Gly828Arg	p.G828R	ENST00000301178	NM_021913.4	828	Gga/Aga	20/20	1	2	FACETS	0.882	0.726	1	1	0.968	1	CLONAL	3	FALSE	1	0.155996658542814	2		449	155	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383281	42383281	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	34	376	1	ENST00000221972.3:c.305del	p.Gly102AlafsTer90	p.G102Afs*90	ENST00000221972	NM_021601.3	101	Ggg/gg	2/5	1	2	FACETS	1	0.903	1	1	0.973	1	CLONAL	3	FALSE	1	0.155996658542814	2		377	129	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641550	47641550	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs796532309	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	19	186	1	ENST00000233146.2:c.939del	p.Gln314ArgfsTer17	p.Q314Rfs*17	ENST00000233146	NM_000251.2	312	cTt/ct	5/16	0.0825750781059644	4	FACETS	1	0.819	1	1	0.923	1	INDETERMINATE	3	FALSE	2	0.155996658542814	4		187	88	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47672790	47672790	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	38	351	0	ENST00000233146.2:c.1381del	p.Asp461IlefsTer10	p.D461Ifs*10	ENST00000233146	NM_000251.2	460	atG/at	8/16	0.0825750781059644	4	FACETS	1	0.912	1	1	0.963	1	INDETERMINATE	3	FALSE	2	0.155996658542814	4		351	165	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051629	128051629	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs113310650	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	17	254	0	ENST00000285398.2:c.28+1G>A		p.X10_splice	ENST00000285398	NM_000122.1	10			0.155996658542814	1	FACETS	1	0.783	1	1	0.932	1	CLONAL	2	FALSE	0	0.155996658542814	1		254	97	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998041	169998041	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	10	468	0	ENST00000295797.4:c.732A>C	p.Lys244Asn	p.K244N	ENST00000295797	NM_002740.5	244	aaA/aaC	9/18	1	2	FACETS	0.754	0.512	1	0.754	0.512	1	CLONAL	1	FALSE	1	0.155996658542814	2		468	170	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55124939	55124939	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	39	472	0	ENST00000257290.5:c.4G>A	p.Gly2Arg	p.G2R	ENST00000257290	NM_006206.4	2	Ggg/Agg	2/23	0.155996658542814	0	FACETS	0.938	0.791	1			1	CLONAL	3	FALSE	0	0.155996658542814	0		472	150	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293920	1293920	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	15	592	0	ENST00000310581.5:c.1081G>A	p.Val361Met	p.V361M	ENST00000310581	NM_198253.2	361	Gtg/Atg	2/16	0.155996658542814	0	FACETS	1	0.782	1			1	CLONAL	2	FALSE	0	0.155996658542814	0		592	77	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294126	1294126	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	12	535	3	ENST00000310581.5:c.875C>T	p.Thr292Met	p.T292M	ENST00000310581	NM_198253.2	292	aCg/aTg	2/16	0.155996658542814	0	FACETS	1	0.844	1			1	CLONAL	1	FALSE	0	0.155996658542814	0		538	97	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636933	176636934	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	26	335	0	ENST00000439151.2:c.1538dup	p.His515ProfsTer5	p.H515Pfs*5	ENST00000439151	NM_022455.4	511	-/A	5/23	1	2	FACETS	1	0.887	1	1	0.958	1	CLONAL	2	FALSE	1	0.155996658542814	2		335	143	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401454	401454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781276700	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	10	159	0	ENST00000380956.4:c.776G>A	p.Arg259Gln	p.R259Q	ENST00000380956	NM_001195286.1	259	cGg/cAg	7/9	NA	2	FACETS	1	0.762	1			1	INDETERMINATE	2	FALSE	NA	0.155996658542814	2		159	57	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323262	31323262	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs77665001	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	37	299	1	ENST00000412585.2:c.727C>T	p.Arg243Trp	p.R243W	ENST00000412585	NM_005514.6	243	Cgg/Tgg	4/8	0.155996658542814	7	FACETS	0.929	0.779	1	1	0.918	1	CLONAL	5	FALSE	3	0.155996658542814	7		300	142	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066682	94066683	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	29	404	0	ENST00000369303.4:c.1076dup	p.Arg360LysfsTer11	p.R360Kfs*11	ENST00000369303	NM_004440.3	359	gga/ggGa	5/17	0.155996658542814	3	FACETS	1	0.876	1	1	0.95	1	CLONAL	3	FALSE	1	0.155996658542814	3		404	122	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026780	6026780	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138222146	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	15	373	1	ENST00000265849.7:c.1616C>T	p.Ala539Val	p.A539V	ENST00000265849	NM_000535.5	539	gCg/gTg	11/15	0.152682069237085	3	FACETS	1	0.809	1	0.743	0.552	0.965	CLONAL	2	FALSE	0	0.155996658542814	3		374	93	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272116	38272116	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	54	382	0	ENST00000425967.3:c.2102A>C	p.Glu701Ala	p.E701A	ENST00000425967	NM_001174067.1	701	gAg/gCg	16/19	0.152682069237085	3	FACETS	1	0.929	1	1	0.978	1	CLONAL	5	FALSE	0	0.155996658542814	3		382	137	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551406	141551406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035096734	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	11	456	1	ENST00000220592.5:c.1891G>A	p.Val631Met	p.V631M	ENST00000220592	NM_012154.3	631	Gtg/Atg	15/19	0.155996658542814	5	FACETS	0.763	0.531	1	0.382	0.265	0.524	CLONAL	2	FALSE	1	0.155996658542814	5		457	114	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742531	145742531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	20	351	0	ENST00000428558.2:c.257C>T	p.Ala86Val	p.A86V	ENST00000428558	NM_004260.3	86	gCg/gTg	4/22	0.155996658542814	5	FACETS	1	0.822	1	0.799	0.622	0.998	CLONAL	3	FALSE	1	0.155996658542814	5		351	99	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250298	110250298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763201664	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	18	390	0	ENST00000374672.4:c.377C>T	p.Ser126Leu	p.S126L	ENST00000374672	NM_004235.4	126	tCg/tTg	3/5	0.155996658542814	0	FACETS	0.877	0.677	1			1	CLONAL	3	FALSE	0	0.155996658542814	0		390	74	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650478	48650478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	21	627	0	ENST00000376670.3:c.448C>T	p.Pro150Ser	p.P150S	ENST00000376670	NM_002049.3	150	Cct/Tct	3/6	0.155996658542814	0	FACETS	0.861	0.678	1			1	CLONAL	3	FALSE	0	0.155996658542814	0		627	88	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939558	76939558	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	33	486	0	ENST00000373344.5:c.1190C>A	p.Ser397Tyr	p.S397Y	ENST00000373344	NM_000489.3	397	tCt/tAt	9/35	0.155996658542814	0	FACETS	0.832	0.689	0.988			1	CLONAL	3	FALSE	0	0.155996658542814	0		486	143	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0033436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	340	528	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.623178253929961	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	FALSE	0	0.623178253929961	3		528	460	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435317	56435317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200066146	NA	P-0033436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	324	496	0	ENST00000407977.2:c.1820C>T	p.Ser607Leu	p.S607L	ENST00000407977		607	tCg/tTg	9/10	0.541397371295159	5	FACETS	0.976	0.929	1	0.976	0.929	1	CLONAL	3	FALSE	2	0.623178253929961	5		496	687	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444987	49444987	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	193	428	1	ENST00000301067.7:c.2479del	p.Gln827AsnfsTer103	p.Q827Nfs*103	ENST00000301067	NM_003482.3	827	Caa/aa	10/54	0.623178253929961	2	FACETS	0.974	0.921	1	0.974	0.921	1	CLONAL	2	FALSE	0	0.623178253929961	2		429	318	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982529	10982529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1163340108	NA	P-0033436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	47	29	1	ENST00000327064.4:c.151G>A	p.Ala51Thr	p.A51T	ENST00000327064	NM_199141.1	51	Gcg/Acg	1/16	0.547409117831365	4	FACETS	0.85	0.746	0.955	1	0.96	1	CLONAL	3	FALSE	2	0.623178253929961	4		30	96	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638273	176638273	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0033436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	294	662	0	ENST00000439151.2:c.2873C>G	p.Ser958Ter	p.S958*	ENST00000439151	NM_022455.4	958	tCa/tGa	5/23	0.192965258250513	3	FACETS	0.993	0.943	1	0.662	0.629	0.696	INDETERMINATE	2	FALSE	0	0.623178253929961	3		662	623	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880071	151880071	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	261	384	0	ENST00000262189.6:c.5253G>A	p.Trp1751Ter	p.W1751*	ENST00000262189	NM_170606.2	1751	tgG/tgA	35/59	0.541397371295159	5	FACETS	0.986	0.927	1	0.657	0.618	0.698	CLONAL	2	FALSE	2	0.623178253929961	5		384	822	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087426	27087426	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	53	676	0	ENST00000324856.7:c.2001del	p.Ser668AlafsTer74	p.S668Afs*74	ENST00000324856	NM_006015.4	667	tCc/tc	5/20	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	FALSE	1	0.260931760114633	2		676	359	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006247	22006247	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0033438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	45	271	1	ENST00000276925.6:c.157-1G>A		p.X53_splice	ENST00000276925	NM_004936.3	53			1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	FALSE	1	0.260931760114633	2		272	307	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	102	441	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	0.410531009323752	2		441	419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576904	7576904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	470	590	1	ENST00000269305.4:c.942del	p.Ser315LeufsTer30	p.S315Lfs*30	ENST00000269305	NM_001126112.2	314	tcC/tc	9/11	0.410531009323752	5	FACETS	0.955	0.922	0.988			1	CLONAL	5	TRUE	NA	0.410531009323752	5		591	775	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546721	9546721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	66	262	0	ENST00000353224.5:c.1301C>T	p.Ala434Val	p.A434V	ENST00000353224	NM_177990.2	434	gCg/gTg	5/10	0.410531009323752	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.410531009323752	1		262	232	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974780	21974780	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs864622263	NA	P-0033439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	31	91	0	ENST00000304494.5:c.47T>A	p.Leu16Gln	p.L16Q	ENST00000304494	NM_000077.4	16	cTg/cAg	1/3	0.410531009323752	1	FACETS	0.75	0.629	0.877	1	0.953	1	SUBCLONAL	2	TRUE	0	0.410531009323752	1		91	80	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220290	55220290	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1046438724	NA	P-0033439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	138	660	1	ENST00000275493.2:c.680C>T	p.Ser227Phe	p.S227F	ENST00000275493	NM_005228.3	227	tCc/tTc	6/28	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.410531009323752	2		661	605	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164802	106164802	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	119	429	0	ENST00000380013.4:c.3670G>T	p.Ala1224Ser	p.A1224S	ENST00000380013	NM_001127208.2	1224	Gca/Tca	6/11	0.410531009323752	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.410531009323752	1		429	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0033440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	275	589	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.537496707049966	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.537496707049966	1		589	641	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0033440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	130	286	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.411534463690441	1	FACETS	0.821	0.751	0.893	0.821	0.751	0.893	CLONAL	1	TRUE	0	0.537496707049966	1		286	431	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867540	35867541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs869312857	NA	P-0033440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	79	168	0	ENST00000303115.3:c.361dup	p.Ile121AsnfsTer8	p.I121Nfs*8	ENST00000303115	NM_002185.3	118	-/A	3/8	0.537496707049966	1	FACETS	0.726	0.645	0.811	0.726	0.645	0.811	SUBCLONAL	1	TRUE	0	0.537496707049966	1		168	296	SUCCESS
APC	324	MSKCC	GRCh37	5	112175174	112175174	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	24	153	0	ENST00000257430.4:c.3883G>T	p.Glu1295Ter	p.E1295*	ENST00000257430	NM_000038.5	1295	Gaa/Taa	16/16	0.411534463690441	1	FACETS	0.268	0.21	0.333	0.268	0.21	0.333	SUBCLONAL	1	TRUE	0	0.537496707049966	1		153	244	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727077	40727077	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	132	363	0	ENST00000373198.4:c.3887A>C	p.Glu1296Ala	p.E1296A	ENST00000373198	NM_133170.3	1296	gAg/gCg	28/32	NA	2	FACETS	0.652	0.593	0.715			1	INDETERMINATE	1	TRUE	NA	0.537496707049966	2		363	753	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961519	41961519	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	245	450	0	ENST00000219905.7:c.427G>T	p.Glu143Ter	p.E143*	ENST00000219905	NM_001164273.1	143	Gaa/Taa	2/24	0.537496707049966	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.537496707049966	1		450	599	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0033441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	36	444	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.2168855007274	1	FACETS	0.615	0.505	0.739	0.615	0.505	0.739	SUBCLONAL	1	TRUE	0	0.2168855007274	1		444	481	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220717	1220717	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587782018	NA	P-0033441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	50	407	0	ENST00000326873.7:c.734+1G>T		p.X245_splice	ENST00000326873	NM_000455.4	245			0.2168855007274	1	FACETS	0.75	0.636	0.875	0.75	0.636	0.875	SUBCLONAL	1	TRUE	0	0.2168855007274	1		407	548	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602581	10602581	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	66	447	0	ENST00000171111.5:c.997G>A	p.Gly333Ser	p.G333S	ENST00000171111	NM_203500.1	333	Ggc/Agc	3/6	0.2168855007274	1	FACETS	0.849	0.737	0.971	0.849	0.737	0.971	CLONAL	1	TRUE	0	0.2168855007274	1		447	639	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739114	40739115	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0033441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	37	400	1	ENST00000373198.4:c.3169_3170delinsTT	p.Glu1057Leu	p.E1057L	ENST00000373198	NM_133170.3	1057	GAg/TTg	24/32	1	2	FACETS	0.532	0.438	0.639	0.532	0.438	0.639	SUBCLONAL	1	TRUE	1	0.2168855007274	2		401	641	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170011171	170011171	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs773224124	NA	P-0033441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	47	446	0	ENST00000295797.4:c.1292G>T	p.Gly431Val	p.G431V	ENST00000295797	NM_002740.5	431	gGt/gTt	14/18	1	2	FACETS	0.75	0.632	0.88	0.75	0.632	0.88	SUBCLONAL	1	TRUE	1	0.2168855007274	2		446	578	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	79	264	0				ENST00000310581	NM_198253.2	-/1132			0.594665376804673	3	FACETS	0.916	0.825	1	0.916	0.825	1	CLONAL	2	TRUE	1	0.625669207547263	3		264	181	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs967461896	NA	P-0033443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	168	653	0	ENST00000269305.4:c.526T>C	p.Cys176Arg	p.C176R	ENST00000269305	NM_001126112.2	176	Tgc/Cgc	5/11	0.625669207547263	1	FACETS	0.85	0.79	0.912	0.85	0.79	0.912	CLONAL	1	TRUE	0	0.625669207547263	1		653	434	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099102	27099103	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0033443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	114	393	0	ENST00000324856.7:c.3524dup	p.Leu1176IlefsTer17	p.L1176Ifs*17	ENST00000324856	NM_006015.4	1173	atc/atCc	13/20	1	2	FACETS	0.821	0.744	0.901	0.821	0.744	0.901	CLONAL	1	TRUE	1	0.625669207547263	2		393	444	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526176	189526176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747354750	NA	P-0033443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	187	559	0	ENST00000264731.3:c.440C>T	p.Ser147Leu	p.S147L	ENST00000264731	NM_003722.4	147	tCg/tTg	4/14	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.625669207547263	2		559	591	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106457	27106457	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	173	517	0	ENST00000324856.7:c.6069del	p.Glu2023AspfsTer7	p.E2023Dfs*7	ENST00000324856	NM_006015.4	2023	gAa/ga	20/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.625669207547263	2		517	536	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553177	41553177	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	134	452	0	ENST00000263253.7:c.3266A>T	p.Tyr1089Phe	p.Y1089F	ENST00000263253	NM_001429.3	1089	tAc/tTc	18/31	1	2	FACETS	0.96	0.88	1	0.96	0.88	1	CLONAL	1	TRUE	1	0.625669207547263	2		452	446	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553232	41553232	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	195	658	1	ENST00000263253.7:c.3321C>A	p.Asp1107Glu	p.D1107E	ENST00000263253	NM_001429.3	1107	gaC/gaA	18/31	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.625669207547263	2		659	623	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	21	264	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.664	0.517	0.832	0.664	0.517	0.832	SUBCLONAL	1	TRUE	1	0.448478618239246	2		264	141	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0033445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	58	337	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.731	0.631	0.838	0.731	0.631	0.838	SUBCLONAL	1	TRUE	1	0.448478618239246	2		337	354	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645294	67645294	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	105	414	0	ENST00000264010.4:c.559G>T	p.Glu187Ter	p.E187*	ENST00000264010	NM_006565.3	187	Gaa/Taa	3/12	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.448478618239246	2		414	440	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266018	41266622	+	splice_donor_variant,splice_acceptor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	TGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGAT	TGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGAT	-	novel	NA	P-0033445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	55	188	0	ENST00000349496.5:c.16_420del		p.X6_splice	ENST00000349496	NM_001904.3	6	gcTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATt/gct	3-4/15	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.448478618239246	2		188	212	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186501400	186501400	+	start_lost	Translation_Start_Site	SNP	A	A	C	novel	NA	P-0033445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	62	234	0	ENST00000323963.5:c.1A>C	p.Met1?	p.M1?	ENST00000323963		1	Atg/Ctg	1/11	1	2	FACETS	0.867	0.754	0.987	0.867	0.754	0.987	CLONAL	1	TRUE	1	0.448478618239246	2		234	319	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056493	26056493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	31	167	0	ENST00000343677.2:c.164G>T	p.Ser55Ile	p.S55I	ENST00000343677	NM_005319.3	55	aGc/aTc	1/1	0.409772154328855	3	FACETS	0.62	0.503	0.751	0.31	0.251	0.376	SUBCLONAL	1	TRUE	1	0.448478618239246	3		167	273	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983284	149983285	+	missense_variant	Missense_Mutation	DNP	GT	GT	TC	novel	NA	P-0033445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	50	541	1	ENST00000253339.5:c.2973_2974delinsGA	p.Pro992Thr	p.P992T	ENST00000253339		991	ggACcc/ggGAcc	7/7	1	2	FACETS	0.436	0.37	0.509	0.436	0.37	0.509	SUBCLONAL	1	TRUE	1	0.448478618239246	2		542	511	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851515	63851515	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033453-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	152	470	0	ENST00000279873.7:c.2293G>A	p.Glu765Lys	p.E765K	ENST00000279873	NM_032199.2	765	Gag/Aag	10/10	0.115878988667424	5	FACETS	0.936	0.863	1	1	0.985	1	CLONAL	7	FALSE	0	0.115878988667424	5		470	470	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943664	9943664	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033453-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	113	591	0	ENST00000330684.3:c.1277C>A	p.Thr426Asn	p.T426N	ENST00000330684	NM_001134407.1	426	aCc/aAc	5/13	0.115878988667424	11	FACETS	1	0.911	1	0.675	0.607	0.746	CLONAL	4	FALSE	5	0.115878988667424	11		591	733	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418370	139418371	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0033453-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	448	830	2	ENST00000277541.6:c.201dup	p.Cys68LeufsTer75	p.C68Lfs*75	ENST00000277541	NM_017617.3	67	-/C	3/34	0.115878988667424	12	FACETS	1	0.955	1	0.802	0.764	0.84	CLONAL	8	FALSE	2	0.115878988667424	12		832	1523	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	162	400	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.984	0.908	1	0.984	0.908	1	CLONAL	1	TRUE	1	0.609962631537162	2		400	540	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	24	587	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.126	0.098	0.159	0.126	0.098	0.159	SUBCLONAL	1	TRUE	1	0.609962631537162	2		587	623	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	21	480	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.5034862809904	4	FACETS	0.141	0.108	0.18	0.07	0.054	0.09	SUBCLONAL	1	TRUE	2	0.609962631537162	4		480	787	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	15	407	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	0.5034862809904	4	FACETS	0.107	0.077	0.142	0.053	0.038	0.071	SUBCLONAL	1	TRUE	2	0.609962631537162	4		407	743	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	313	858	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.609962631537162	2		858	1017	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132428	11132428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	246	913	0	ENST00000358026.2:c.2644G>A	p.Glu882Lys	p.E882K	ENST00000358026	NM_001128849.1	882	Gaa/Aaa	19/36	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.609962631537162	2		913	772	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629902	187629902	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	260	802	0	ENST00000441802.2:c.1080C>G	p.Phe360Leu	p.F360L	ENST00000441802	NM_005245.3	360	ttC/ttG	2/27	1	2	FACETS	0.957	0.898	1	0.957	0.898	1	CLONAL	1	TRUE	1	0.609962631537162	2		802	891	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267680	7267680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	45	680	0	ENST00000302850.5:c.328C>T	p.Arg110Trp	p.R110W	ENST00000302850	NM_000208.2	110	Cgg/Tgg	2/22	0.488197672536671	1	FACETS	0.166	0.139	0.197	0.166	0.139	0.197	SUBCLONAL	1	TRUE	0	0.609962631537162	1		680	616	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33446593	33446593	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	39	778	0	ENST00000345365.6:c.40G>C	p.Glu14Gln	p.E14Q	ENST00000345365	NM_002878.3	14	Gag/Cag	1/10	1	2	FACETS	0.183	0.151	0.22	0.183	0.151	0.22	SUBCLONAL	1	TRUE	1	0.609962631537162	2		778	697	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475599	12475599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	41	557	0	ENST00000287820.6:c.1473G>A	p.Met491Ile	p.M491I	ENST00000287820	NM_015869.4	491	atG/atA	7/7	0.609962631537162	1	FACETS	0.243	0.203	0.288	0.243	0.203	0.288	SUBCLONAL	1	TRUE	0	0.609962631537162	1		557	384	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223466	53223466	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	39	783	0	ENST00000375401.3:c.3893C>G	p.Ser1298Cys	p.S1298C	ENST00000375401	NM_004187.3	1298	tCt/tGt	23/26	1	2	FACETS	0.193	0.159	0.231	0.193	0.159	0.231	SUBCLONAL	1	TRUE	1	0.609962631537162	2		783	663	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261194	16261194	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	27	631	1	ENST00000375759.3:c.8459C>T	p.Ser2820Leu	p.S2820L	ENST00000375759	NM_015001.2	2820	tCa/tTa	11/15	1	2	FACETS	0.164	0.13	0.203	0.164	0.13	0.203	SUBCLONAL	1	TRUE	1	0.609962631537162	2		632	540	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106255	27106255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1483998772	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	188	761	0	ENST00000324856.7:c.5866G>A	p.Glu1956Lys	p.E1956K	ENST00000324856	NM_006015.4	1956	Gag/Aag	20/20	1	2	FACETS	0.895	0.83	0.962	0.895	0.83	0.962	CLONAL	1	TRUE	1	0.609962631537162	2		761	689	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176176050	176176050	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	229	614	1	ENST00000367669.3:c.65C>G	p.Ser22Cys	p.S22C	ENST00000367669	NM_022457.5	22	tCc/tGc	1/20	0.562248241348036	4	FACETS	1	0.984	1	0.393	0.366	0.421	CLONAL	1	TRUE	1	0.609962631537162	4		615	1026	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983150	201983150	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	54	609	1	ENST00000359651.3:c.999G>A	p.Met333Ile	p.M333I	ENST00000359651		333	atG/atA	7/8	0.562248241348036	4	FACETS	0.29	0.246	0.338	0.097	0.082	0.113	SUBCLONAL	1	TRUE	1	0.609962631537162	4		610	984	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197299	94197299	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs778211645	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	140	512	0	ENST00000323929.3:c.1205G>C	p.Arg402Thr	p.R402T	ENST00000323929	NM_005591.3	402	aGa/aCa	11/20	1	2	FACETS	0.904	0.828	0.982	0.904	0.828	0.982	CLONAL	1	TRUE	1	0.609962631537162	2		512	508	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376338	118376338	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	41	672	0	ENST00000534358.1:c.9731C>G	p.Ser3244Ter	p.S3244*	ENST00000534358	NM_005933.3	3244	tCa/tGa	27/36	1	2	FACETS	0.207	0.172	0.247	0.207	0.172	0.247	SUBCLONAL	1	TRUE	1	0.609962631537162	2		672	648	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647596	23647596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	34	626	0	ENST00000261584.4:c.271G>A	p.Glu91Lys	p.E91K	ENST00000261584	NM_024675.3	91	Gaa/Aaa	4/13	1	2	FACETS	0.167	0.136	0.202	0.167	0.136	0.202	SUBCLONAL	1	TRUE	1	0.609962631537162	2		626	668	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618559	37618559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	45	652	0	ENST00000447079.4:c.235G>A	p.Asp79Asn	p.D79N	ENST00000447079	NM_015083.1	79	Gat/Aat	1/14	1	2	FACETS	0.218	0.182	0.257	0.218	0.182	0.257	SUBCLONAL	1	TRUE	1	0.609962631537162	2		652	677	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883987	37883987	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758365405	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	63	859	1	ENST00000269571.5:c.3458G>A	p.Arg1153Gln	p.R1153Q	ENST00000269571		1153	cGa/cAa	27/27	1	2	FACETS	0.272	0.235	0.313	0.272	0.235	0.313	SUBCLONAL	1	TRUE	1	0.609962631537162	2		860	759	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375505	40375505	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	202	831	0	ENST00000293328.3:c.445G>C	p.Glu149Gln	p.E149Q	ENST00000293328	NM_012448.3	149	Gag/Cag	5/19	1	2	FACETS	0.786	0.729	0.844	0.786	0.729	0.844	SUBCLONAL	1	TRUE	1	0.609962631537162	2		831	843	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40462628	40462628	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	174	690	0	ENST00000345506.4:c.2326G>C	p.Asp776His	p.D776H	ENST00000345506	NM_003152.3	776	Gac/Cac	20/20	1	2	FACETS	0.813	0.75	0.877	0.813	0.75	0.877	CLONAL	1	TRUE	1	0.609962631537162	2		690	702	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724522	724522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	25	270	0	ENST00000314574.4:c.1534G>A	p.Asp512Asn	p.D512N	ENST00000314574	NM_005433.3	512	Gac/Aac	12/12	1	2	FACETS	0.277	0.218	0.344	0.277	0.218	0.344	SUBCLONAL	1	TRUE	1	0.609962631537162	2		270	296	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910239	50910239	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	38	654	0	ENST00000440232.2:c.1495-1G>A		p.X499_splice	ENST00000440232	NM_002691.3	499			1	2	FACETS	0.211	0.174	0.253	0.211	0.174	0.253	SUBCLONAL	1	TRUE	1	0.609962631537162	2		654	590	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919751	50919751	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	63	854	0	ENST00000440232.2:c.2919C>G	p.Ile973Met	p.I973M	ENST00000440232	NM_002691.3	973	atC/atG	23/27	0.464189400772106	1	FACETS	0.208	0.179	0.239	0.208	0.179	0.239	SUBCLONAL	1	TRUE	0	0.609962631537162	1		854	691	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098867	178098867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	302	787	0	ENST00000397062.3:c.178G>A	p.Glu60Lys	p.E60K	ENST00000397062	NM_006164.4	60	Gaa/Aaa	2/5	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.609962631537162	2		787	963	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209108162	209108162	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	30	411	0	ENST00000345146.2:c.687G>C	p.Glu229Asp	p.E229D	ENST00000345146	NM_005896.2	229	gaG/gaC	6/10	1	2	FACETS	0.219	0.176	0.267	0.219	0.176	0.267	SUBCLONAL	1	TRUE	1	0.609962631537162	2		411	450	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663008	227663008	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	146	783	0	ENST00000305123.5:c.447G>T	p.Leu149Phe	p.L149F	ENST00000305123	NM_005544.2	149	ttG/ttT	1/2	1	2	FACETS	0.736	0.674	0.801	0.736	0.674	0.801	SUBCLONAL	1	TRUE	1	0.609962631537162	2		783	650	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119562156	119562156	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	113	507	0	ENST00000316626.5:c.1180C>G	p.His394Asp	p.H394D	ENST00000316626		394	Cat/Gat	11/12	1	2	FACETS	0.624	0.563	0.688	0.624	0.563	0.688	SUBCLONAL	1	TRUE	1	0.609962631537162	2		507	594	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915124	131915124	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	44	660	0	ENST00000265335.6:c.481G>C	p.Asp161His	p.D161H	ENST00000265335		161	Gat/Cat	4/25	1	2	FACETS	0.203	0.169	0.24	0.203	0.169	0.24	SUBCLONAL	1	TRUE	1	0.609962631537162	2		660	712	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562452	176562452	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	70	879	0	ENST00000439151.2:c.348G>C	p.Leu116Phe	p.L116F	ENST00000439151	NM_022455.4	116	ttG/ttC	2/23	1	2	FACETS	0.249	0.216	0.284	0.249	0.216	0.284	SUBCLONAL	1	TRUE	1	0.609962631537162	2		879	923	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180049758	180049758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	49	846	0	ENST00000261937.6:c.1630G>A	p.Glu544Lys	p.E544K	ENST00000261937	NM_182925.4	544	Gag/Aag	12/30	1	2	FACETS	0.222	0.187	0.26	0.222	0.187	0.26	SUBCLONAL	1	TRUE	1	0.609962631537162	2		846	724	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187551	32187551	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	43	738	0	ENST00000375023.3:c.1328C>G	p.Pro443Arg	p.P443R	ENST00000375023	NM_004557.3	443	cCa/cGa	8/30	0.609962631537162	1	FACETS	0.209	0.175	0.248	0.209	0.175	0.248	SUBCLONAL	1	TRUE	0	0.609962631537162	1		738	468	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725558	117725558	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	64	659	0	ENST00000368508.3:c.323C>A	p.Ser108Tyr	p.S108Y	ENST00000368508	NM_002944.2	108	tCt/tAt	5/43	0.609962631537162	1	FACETS	0.301	0.261	0.345	0.301	0.261	0.345	SUBCLONAL	1	TRUE	0	0.609962631537162	1		659	484	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525053	157525053	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554236623	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	60	500	0	ENST00000346085.5:c.4948G>T	p.Glu1650Ter	p.E1650*	ENST00000346085	NM_020732.3	1650	Gag/Tag	19/20	0.609962631537162	1	FACETS	0.28	0.241	0.322	0.28	0.241	0.322	SUBCLONAL	1	TRUE	0	0.609962631537162	1		500	489	SUCCESS
MET	4233	MSKCC	GRCh37	7	116399528	116399528	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	186	521	0	ENST00000397752.3:c.2348G>A	p.Gly783Glu	p.G783E	ENST00000397752	NM_000245.2	783	gGa/gAa	10/21	0.5034862809904	4	FACETS	0.967	0.893	1	0.484	0.446	0.523	CLONAL	1	TRUE	2	0.609962631537162	4		521	1015	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624401	140624401	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	86	184	0	ENST00000288602.6:c.103G>A	p.Ala35Thr	p.A35T	ENST00000288602	NM_004333.4	35	Gcc/Acc	1/18	0.5034862809904	4	FACETS	1	0.965	1	0.604	0.538	0.673	CLONAL	1	TRUE	2	0.609962631537162	4		184	376	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859839	151859839	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	138	513	0	ENST00000262189.6:c.10823G>A	p.Arg3608Lys	p.R3608K	ENST00000262189	NM_170606.2	3608	aGa/aAa	43/59	0.5034862809904	4	FACETS	1	0.918	1	0.504	0.459	0.551	CLONAL	1	TRUE	2	0.609962631537162	4		513	723	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132717	152132717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	39	253	1	ENST00000262189.6:c.155G>A	p.Arg52Lys	p.R52K	ENST00000262189	NM_170606.2	52	aGa/aAa	1/59	0.5034862809904	4	FACETS	0.446	0.369	0.531	0.223	0.184	0.266	SUBCLONAL	1	TRUE	2	0.609962631537162	4		254	462	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912141	29912141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs281864770	NA	P-0033463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	11	50	0	ENST00000376809.5:c.862G>A	p.Glu288Lys	p.E288K	ENST00000376809	NM_002116.7	288	Gag/Aag	4/8	0.609962631537162	1	FACETS	0.864	0.634	1	0.864	0.634	1	CLONAL	1	TRUE	0	0.609962631537162	1		50	29	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0033466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	304	582	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.723056996510755	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.723931484332159	1		582	481	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189455	94189455	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	55	551	0	ENST00000323929.3:c.1550A>C	p.Asp517Ala	p.D517A	ENST00000323929	NM_005591.3	517	gAt/gCt	14/20	0.184881698549042	4	FACETS	0.577	0.494	0.667	0.288	0.247	0.334	INDETERMINATE	1	TRUE	2	0.723931484332159	4		551	454	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-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	106	560	0	ENST00000264033.4:c.1214_1431+593del		p.X405_splice	ENST00000264033	NM_005188.3	405		8-9/16	0.184881698549042	4	FACETS	1	0.904	1	0.502	0.452	0.555	INDETERMINATE	1	TRUE	2	0.723931484332159	4		560	503	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89881018	89881018	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	151	470	0	ENST00000389301.3:c.193G>C	p.Glu65Gln	p.E65Q	ENST00000389301	NM_000135.2	65	Gaa/Caa	3/43	1	2	FACETS	0.925	0.853	0.999	0.925	0.853	0.999	CLONAL	1	TRUE	1	0.723931484332159	2		470	451	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222777	5222777	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	188	655	0	ENST00000357368.4:c.3026A>C	p.Gln1009Pro	p.Q1009P	ENST00000357368	NM_002850.3	1009	cAa/cCa	18/38	0.217171239719743	1	FACETS	0.736	0.688	0.785	0.736	0.688	0.785	INDETERMINATE	1	TRUE	0	0.723931484332159	1		655	450	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379803	17379804	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0033466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	367	917	0	ENST00000359435.4:c.189dup	p.Asn64GlnfsTer8	p.N64Qfs*8	ENST00000359435	NM_001033549.1	63	ctc/ctCc	2/9	0.122317433030472	5	FACETS	1	0.982	1	0.712	0.677	0.748	INDETERMINATE	2	TRUE	2	0.723931484332159	5		917	990	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976392	18976392	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	197	872	0	ENST00000262803.5:c.3042G>C	p.Lys1014Asn	p.K1014N	ENST00000262803	NM_002911.3	1014	aaG/aaC	22/24	0.122317433030472	5	FACETS	0.918	0.855	0.983	0.612	0.57	0.656	INDETERMINATE	2	TRUE	2	0.723931484332159	5		872	618	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31015950	31015950	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	181	409	0	ENST00000375687.4:c.272C>A	p.Ser91Tyr	p.S91Y	ENST00000375687	NM_015338.5	91	tCt/tAt	5/13	1	2	FACETS	0.956	0.889	1	0.956	0.889	1	CLONAL	1	TRUE	1	0.723931484332159	2		409	523	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720924	119720924	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	123	612	0	ENST00000316626.5:c.251T>A	p.Ile84Asn	p.I84N	ENST00000316626		84	aTc/aAc	2/12	0.185276928073516	2	FACETS	0.725	0.659	0.792	0.362	0.329	0.396	INDETERMINATE	1	TRUE	0	0.723931484332159	2		612	469	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459223	99459257	+	frameshift_variant	Frame_Shift_Del	DEL	CATCGAACTCCTCTTCTCAGTTAATCGTGAAGTGG	CATCGAACTCCTCTTCTCAGTTAATCGTGAAGTGG	T	novel	NA	P-0033466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	253	789	0	ENST00000268035.6:c.1859_1893delinsT	p.Ala620ValfsTer11	p.A620Vfs*11	ENST00000268035	NM_000875.3	620	gCATCGAACTCCTCTTCTCAGTTAATCGTGAAGTGG/gT	9/21	1	2	FACETS	0.963	0.905	1	0.963	0.905	1	CLONAL	1	TRUE	1	0.723931484332159	2		789	726	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954198	48954198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123331	NA	P-0033472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	160	260	0	ENST00000267163.4:c.1399C>T	p.Arg467Ter	p.R467*	ENST00000267163	NM_000321.2	467	Cga/Tga	15/27	0.92965558403132	1	FACETS	0.959	0.921	0.995	0.959	0.921	0.995	CLONAL	1	TRUE	0	0.92965558403132	1		260	192	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577069	7577069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55819519	NA	P-0033472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	26	889	1	ENST00000269305.4:c.869G>A	p.Arg290His	p.R290H	ENST00000269305	NM_001126112.2	290	cGc/cAc	8/11	1	2	FACETS	0.051	0.04	0.064	0.051	0.04	0.064	SUBCLONAL	1	TRUE	1	0.92965558403132	2		890	1099	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199469669	NA	P-0033472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	415	681	2	ENST00000374080.3:c.130G>T	p.Gly44Cys	p.G44C	ENST00000374080		44	Ggt/Tgt	2/45	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.92965558403132	2		683	785	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579470	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	409	787	0	ENST00000269305.4:c.217del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	73	Gtg/tg	4/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.92965558403132	2		787	870	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176349	24176350	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	344	729	0	ENST00000263121.7:c.1141dup	p.Thr381AsnfsTer64	p.T381Nfs*64	ENST00000263121	NM_003073.3	380	-/A	9/9	0.92965558403132	1	FACETS	0.985	0.96	1	0.985	0.96	1	CLONAL	1	TRUE	0	0.92965558403132	1		729	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0033474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	155	715	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.314967033707981	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.314967033707981	1		715	778	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0033474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	99	406	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	0.314967033707981	2		406	567	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508499	106508499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752602335	NA	P-0033474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	25	324	0	ENST00000359195.3:c.493G>A	p.Val165Ile	p.V165I	ENST00000359195	NM_002649.2	165	Gtc/Atc	2/11	0.314967033707981	1	FACETS	0.497	0.393	0.617	0.497	0.393	0.617	SUBCLONAL	1	TRUE	0	0.314967033707981	1		324	269	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983911	2983911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237589286	NA	P-0033474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	65	1008	1	ENST00000396946.4:c.619C>T	p.Arg207Cys	p.R207C	ENST00000396946	NM_032415.4	207	Cgc/Tgc	5/25	0.294229099671224	2	FACETS	0.349	0.301	0.401	0.174	0.15	0.201	SUBCLONAL	1	TRUE	0	0.314967033707981	2		1009	1183	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937309	76937309	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	20	651	0	ENST00000373344.5:c.3439A>C	p.Lys1147Gln	p.K1147Q	ENST00000373344	NM_000489.3	1147	Aag/Cag	9/35	0.314967033707981	1	FACETS	0.272	0.208	0.348	0.272	0.208	0.348	SUBCLONAL	1	TRUE	0	0.314967033707981	1		651	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0033481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	623	732	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.935674160362369	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.935674160362369	1		732	692	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276974	123276974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918504	NA	P-0033481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	232	340	0	ENST00000358487.5:c.943G>A	p.Ala315Thr	p.A315T	ENST00000358487	NM_000141.4	315	Gcc/Acc	8/18	0.935674160362369	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.935674160362369	1		340	246	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246021859	246021859	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	576	958	0	ENST00000388985.4:c.1015A>T	p.Ile339Phe	p.I339F	ENST00000388985		339	Atc/Ttc	10/12	1	2	FACETS	0.943	0.908	0.978	0.943	0.908	0.978	CLONAL	1	TRUE	1	0.935674160362369	2		958	1306	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585494	29585494	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs876660428	NA	P-0033481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	204	358	0	ENST00000356175.3:c.4243G>T	p.Glu1415Ter	p.E1415*	ENST00000356175	NM_000267.3	1415	Gaa/Taa	31/57	1	2	FACETS	0.967	0.908	1	0.967	0.908	1	CLONAL	1	TRUE	1	0.935674160362369	2		358	451	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288839	33288839	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	366	602	1	ENST00000374542.5:c.713G>T	p.Arg238Leu	p.R238L	ENST00000374542	NM_001141970.1	238	cGa/cTa	3/8	1	2	FACETS	0.971	0.926	1	0.971	0.926	1	CLONAL	1	TRUE	1	0.935674160362369	2		603	806	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099997	157099997	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	168	283	0	ENST00000346085.5:c.934G>C	p.Gly312Arg	p.G312R	ENST00000346085	NM_020732.3	312	Ggc/Cgc	1/20	0.935674160362369	3	FACETS	1	0.988	1	0.652	0.607	0.698	CLONAL	1	TRUE	1	0.935674160362369	3		283	404	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978521	70978521	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	458	700	0	ENST00000276594.2:c.1132G>T	p.Val378Leu	p.V378L	ENST00000276594	NM_024504.3	378	Gtg/Ttg	5/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.935674160362369	2		700	949	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412746	139412746	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0033481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	499	718	0	ENST00000277541.6:c.1100-2A>T		p.X367_splice	ENST00000277541	NM_017617.3	367			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.935674160362369	2		718	1025	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	216	503	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.425303267650275	5	FACETS	1	0.987	1	0.818	0.764	0.873	CLONAL	2	TRUE	2	0.425303267650275	5		503	678	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	75	264	0				ENST00000310581	NM_198253.2	-/1132			0.212346390636129	3	FACETS	0.81	0.719	0.906	0.81	0.719	0.906	INDETERMINATE	2	TRUE	1	0.425303267650275	3		264	264	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882019	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	108	600	4	ENST00000269305.4:c.455del	p.Pro152ArgfsTer18	p.P152Rfs*18	ENST00000269305	NM_001126112.2	152	cCg/cg	5/11	0.366766454785146	3	FACETS	0.769	0.69	0.853	0.384	0.345	0.427	SUBCLONAL	1	TRUE	1	0.425303267650275	3		604	801	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	112	336	0	ENST00000397062.3:c.92G>A	p.Gly31Glu	p.G31E	ENST00000397062	NM_006164.4	31	gGa/gAa	2/5	0.366766454785146	3	FACETS	0.762	0.691	0.837	0.762	0.691	0.837	SUBCLONAL	2	TRUE	1	0.425303267650275	3		336	419	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292409	15292409	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	186	542	0	ENST00000263388.2:c.2770G>A	p.Asp924Asn	p.D924N	ENST00000263388	NM_000435.2	924	Gac/Aac	17/33	0.333954993749643	2	FACETS	0.905	0.844	0.968	0.905	0.844	0.968	CLONAL	2	TRUE	0	0.425303267650275	2		542	483	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302560	15302560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	187	607	0	ENST00000263388.2:c.798G>A	p.Trp266Ter	p.W266*	ENST00000263388	NM_000435.2	266	tgG/tgA	5/33	0.333954993749643	2	FACETS	0.866	0.806	0.926	0.866	0.806	0.926	CLONAL	2	TRUE	0	0.425303267650275	2		607	508	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137800	64137801	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	100	655	2	ENST00000334205.4:c.1901_1902delinsTT	p.Ser634Phe	p.S634F	ENST00000334205	NM_003942.2	634	tCC/tTT	15/17	0.4255641797867	3	FACETS	0.658	0.587	0.733	0.329	0.293	0.367	SUBCLONAL	1	TRUE	1	0.425303267650275	3		657	867	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158431	106158431	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs767477894	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	36	279	0	ENST00000380013.4:c.3332T>A	p.Leu1111Ter	p.L1111*	ENST00000380013	NM_001127208.2	1111	tTa/tAa	3/11	1	2	FACETS	0.616	0.508	0.734	0.616	0.508	0.734	SUBCLONAL	1	TRUE	1	0.425303267650275	2		279	275	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520008	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	212	560	0	ENST00000269305.4:c.613T>G	p.Tyr205Asp	p.Y205D	ENST00000269305	NM_001126112.2	205	Tat/Gat	6/11	0.366766454785146	3	FACETS	0.876	0.817	0.936	0.876	0.817	0.936	CLONAL	2	TRUE	1	0.425303267650275	3		560	690	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120469223	120469223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	140	371	0	ENST00000256646.2:c.3904G>A	p.Glu1302Lys	p.E1302K	ENST00000256646	NM_024408.3	1302	Gaa/Aaa	24/34	0.366766454785146	3	FACETS	0.899	0.826	0.975	0.899	0.826	0.975	CLONAL	2	TRUE	1	0.425303267650275	3		371	444	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242646	16242646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	145	448	0	ENST00000375759.3:c.1267C>T	p.Arg423Cys	p.R423C	ENST00000375759	NM_015001.2	423	Cgc/Tgc	6/15	0.366766454785146	3	FACETS	0.807	0.741	0.876	0.807	0.741	0.876	CLONAL	2	TRUE	1	0.425303267650275	3		448	512	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715741	18715741	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	101	326	0	ENST00000266497.5:c.3572C>T	p.Thr1191Ile	p.T1191I	ENST00000266497		1191	aCt/aTt	25/31	0.201159339334717	4	FACETS	0.771	0.693	0.853	0.771	0.693	0.853	INDETERMINATE	2	TRUE	2	0.425303267650275	4		326	439	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40447646	40447646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	89	517	1	ENST00000345506.4:c.385C>T	p.Pro129Ser	p.P129S	ENST00000345506	NM_003152.3	129	Ccg/Tcg	6/20	0.366766454785146	3	FACETS	0.765	0.679	0.858	0.383	0.339	0.429	SUBCLONAL	1	TRUE	1	0.425303267650275	3		518	663	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900639	32900639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41293469	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	120	458	1	ENST00000380152.3:c.520C>T	p.Arg174Cys	p.R174C	ENST00000380152		174	Cgt/Tgt	7/27	0.108250162194734	3	FACETS	0.76	0.691	0.832	0.507	0.461	0.555	INDETERMINATE	2	TRUE	0	0.425303267650275	3		459	450	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030005	36030005	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	172	510	0	ENST00000358208.4:c.1040G>A	p.Gly347Glu	p.G347E	ENST00000358208		347	gGg/gAg	9/12	0.201159339334717	4	FACETS	0.867	0.8	0.935	0.867	0.8	0.935	INDETERMINATE	2	TRUE	2	0.425303267650275	4		510	665	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16248778	16248778	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	144	450	0	ENST00000375759.3:c.1784T>A	p.Phe595Tyr	p.F595Y	ENST00000375759	NM_015001.2	595	tTt/tAt	10/15	0.366766454785146	3	FACETS	0.758	0.695	0.823	0.758	0.695	0.823	SUBCLONAL	2	TRUE	1	0.425303267650275	3		450	542	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46543246	46543247	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	91	493	1	ENST00000262741.5:c.254_255delinsAA	p.Gly85Glu	p.G85E	ENST00000262741	NM_003629.3	85	gGG/gAA	3/10	0.366766454785146	3	FACETS	0.848	0.754	0.948	0.424	0.377	0.474	CLONAL	1	TRUE	1	0.425303267650275	3		494	612	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280590	115280590	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	180	491	1	ENST00000438362.2:c.441T>A	p.Asn147Lys	p.N147K	ENST00000438362	NM_001242891.1	147	aaT/aaA	4/20	0.366766454785146	3	FACETS	0.864	0.801	0.929	0.864	0.801	0.929	CLONAL	2	TRUE	1	0.425303267650275	3		492	594	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200466	67200467	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	229	620	1	ENST00000312629.5:c.660_661delinsTT	p.His221Tyr	p.H221Y	ENST00000312629	NM_003952.2	220	atCCat/atTTat	8/15	0.4255641797867	3	FACETS	0.906	0.848	0.965	0.906	0.848	0.965	CLONAL	2	TRUE	1	0.425303267650275	3		621	721	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342713	118342713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	42	200	0	ENST00000534358.1:c.839C>T	p.Pro280Leu	p.P280L	ENST00000534358	NM_005933.3	280	cCt/cTt	3/36	0.4255641797867	3	FACETS	0.82	0.688	0.965	0.41	0.344	0.483	CLONAL	1	TRUE	1	0.425303267650275	3		200	292	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373988	118373989	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	199	379	0	ENST00000534358.1:c.7381_7382delinsAA	p.Gly2461Lys	p.G2461K	ENST00000534358	NM_005933.3	2461	GGa/AAa	27/36	0.4255641797867	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.425303267650275	3		379	530	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445896	49445896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	273	758	0	ENST00000301067.7:c.1570G>A	p.Glu524Lys	p.E524K	ENST00000301067	NM_003482.3	524	Gaa/Aaa	10/54	0.201159339334717	4	FACETS	0.823	0.773	0.876	0.823	0.773	0.876	INDETERMINATE	2	TRUE	2	0.425303267650275	4		758	1111	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865180	57865181	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	187	723	1	ENST00000228682.2:c.2657_2658delinsTT	p.Pro886Leu	p.P886L	ENST00000228682	NM_005269.2	886	cCC/cTT	12/12	0.201159339334717	4	FACETS	1	0.99	1	0.738	0.683	0.796	INDETERMINATE	1	TRUE	2	0.425303267650275	4		724	849	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120796832	120796832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	184	529	0	ENST00000257552.2:c.427G>A	p.Asp143Asn	p.D143N	ENST00000257552	NM_002442.3	143	Gac/Aac	7/15	0.201159339334717	4	FACETS	0.862	0.798	0.928	0.862	0.798	0.928	INDETERMINATE	2	TRUE	2	0.425303267650275	4		529	715	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622445	28622445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	78	527	0	ENST00000241453.7:c.1172C>T	p.Pro391Leu	p.P391L	ENST00000241453	NM_004119.2	391	cCt/cTt	9/24	0.108250162194734	3	FACETS	0.813	0.716	0.917	0.271	0.238	0.306	INDETERMINATE	1	TRUE	0	0.425303267650275	3		527	547	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913752	32913752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771571938	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	47	421	0	ENST00000380152.3:c.5260G>A	p.Asp1754Asn	p.D1754N	ENST00000380152		1754	Gat/Aat	11/27	0.108250162194734	3	FACETS	0.698	0.59	0.816	0.233	0.196	0.272	INDETERMINATE	1	TRUE	0	0.425303267650275	3		421	384	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239592	105239592	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	188	452	0	ENST00000349310.3:c.953C>T	p.Pro318Leu	p.P318L	ENST00000349310	NM_001014432.1	318	cCc/cTc	11/15	0.258892008846778	4	FACETS	0.935	0.867	1	0.935	0.867	1	CLONAL	2	TRUE	2	0.425303267650275	4		452	674	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988918	41988918	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	158	463	1	ENST00000219905.7:c.1710G>T	p.Lys570Asn	p.K570N	ENST00000219905	NM_001164273.1	570	aaG/aaT	3/24	0.108250162194734	3	FACETS	0.839	0.773	0.906	0.559	0.515	0.604	INDETERMINATE	2	TRUE	0	0.425303267650275	3		464	537	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714110	43714110	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	247	671	0	ENST00000382044.4:c.4043G>A	p.Gly1348Glu	p.G1348E	ENST00000382044	NM_001141980.1	1348	gGg/gAg	19/28	0.108250162194734	3	FACETS	0.884	0.829	0.94	0.589	0.552	0.627	INDETERMINATE	2	TRUE	0	0.425303267650275	3		671	797	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585489	29585489	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	45	311	0	ENST00000356175.3:c.4238G>A	p.Arg1413Lys	p.R1413K	ENST00000356175	NM_000267.3	1413	aGa/aAa	31/57	0.366766454785146	3	FACETS	0.759	0.64	0.889	0.38	0.32	0.445	SUBCLONAL	1	TRUE	1	0.425303267650275	3		311	338	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244816	41244816	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs431825392	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	99	695	0	ENST00000357654.3:c.2732G>A	p.Gly911Glu	p.G911E	ENST00000357654	NM_007294.3	911	gGa/gAa	10/23	0.366766454785146	3	FACETS	0.791	0.706	0.881	0.395	0.353	0.441	SUBCLONAL	1	TRUE	1	0.425303267650275	3		695	714	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740664	58740665	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	141	500	0	ENST00000305921.3:c.1569_1570delinsTT	p.Gln524Ter	p.Q524*	ENST00000305921	NM_003620.3	523	gcCCaa/gcTTaa	6/6	0.116893038303074	5	FACETS	0.895	0.818	0.974	0.596	0.545	0.65	INDETERMINATE	2	TRUE	2	0.425303267650275	5		500	607	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117321	7117321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	175	620	0	ENST00000302850.5:c.3895C>T	p.Pro1299Ser	p.P1299S	ENST00000302850	NM_000208.2	1299	Cca/Tca	22/22	0.116893038303074	5	FACETS	0.881	0.813	0.952	0.587	0.542	0.635	INDETERMINATE	2	TRUE	2	0.425303267650275	5		620	765	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271769	15271770	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	194	664	0	ENST00000263388.2:c.6669_6670delinsAA	p.Ala2224Thr	p.A2224T	ENST00000263388	NM_000435.2	2223	gcGGct/gcAAct	33/33	0.333954993749643	2	FACETS	0.756	0.704	0.81	0.756	0.704	0.81	SUBCLONAL	2	TRUE	0	0.425303267650275	2		664	603	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211342	36211342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	205	594	0	ENST00000222270.7:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000222270	NM_014727.1	365	Gaa/Aaa	3/37	0.201159339334717	4	FACETS	0.848	0.788	0.91	0.848	0.788	0.91	INDETERMINATE	2	TRUE	2	0.425303267650275	4		594	810	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022469	31022470	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	70	250	0	ENST00000375687.4:c.1954_1955delinsAA	p.Gly652Asn	p.G652N	ENST00000375687	NM_015338.5	652	GGc/AAc	13/13	0.201159339334717	4	FACETS	0.859	0.757	0.967	0.859	0.757	0.967	INDETERMINATE	2	TRUE	2	0.425303267650275	4		250	273	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022832	31022832	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	145	494	0	ENST00000375687.4:c.2317G>A	p.Glu773Lys	p.E773K	ENST00000375687	NM_015338.5	773	Gag/Aag	13/13	0.201159339334717	4	FACETS	0.78	0.714	0.849	0.78	0.714	0.849	INDETERMINATE	2	TRUE	2	0.425303267650275	4		494	623	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030027	36030028	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	166	528	0	ENST00000358208.4:c.1062_1063delinsAA	p.Gly355Arg	p.G355R	ENST00000358208		354	aaGGgg/aaAAgg	9/12	0.201159339334717	4	FACETS	0.78	0.718	0.844	0.78	0.718	0.844	INDETERMINATE	2	TRUE	2	0.425303267650275	4		528	713	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980848	40980849	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	131	462	0	ENST00000373198.4:c.1637_1638delinsAA	p.Arg546Gln	p.R546Q	ENST00000373198	NM_133170.3	546	cGG/cAA	10/32	0.201159339334717	4	FACETS	1	0.986	1	0.73	0.665	0.799	INDETERMINATE	1	TRUE	2	0.425303267650275	4		462	601	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484813	57484813	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	169	525	0	ENST00000371085.3:c.793C>G	p.Arg265Gly	p.R265G	ENST00000371085	NM_000516.4	265	Cgc/Ggc	10/13	0.201159339334717	4	FACETS	0.821	0.757	0.887	0.821	0.757	0.887	INDETERMINATE	2	TRUE	2	0.425303267650275	4		525	690	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119595342	119595342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	106	306	1	ENST00000316626.5:c.827C>T	p.Pro276Leu	p.P276L	ENST00000316626		276	cCa/cTa	8/12	0.425303267650275	5	FACETS	0.81	0.729	0.895	0.54	0.486	0.597	CLONAL	2	TRUE	2	0.425303267650275	5		307	504	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138400876	138400876	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	160	449	0	ENST00000289153.2:c.2437G>T	p.Asp813Tyr	p.D813Y	ENST00000289153	NM_006219.2	813	Gat/Tat	17/22	0.425303267650275	5	FACETS	0.8	0.735	0.868	0.534	0.49	0.579	SUBCLONAL	2	TRUE	2	0.425303267650275	5		449	770	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141045	55141045	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	75	411	0	ENST00000257290.5:c.1691C>A	p.Ser564Ter	p.S564*	ENST00000257290	NM_006206.4	564	tCa/tAa	12/23	1	2	FACETS	0.911	0.803	1	0.911	0.803	1	CLONAL	1	TRUE	1	0.425303267650275	2		411	387	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535282	66535282	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	97	383	0	ENST00000273854.3:c.179A>C	p.Glu60Ala	p.E60A	ENST00000273854	NM_004439.5	60	gAa/gCa	1/18	1	2	FACETS	0.973	0.871	1	0.973	0.871	1	CLONAL	1	TRUE	1	0.425303267650275	2		383	469	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542404	187542404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	95	418	0	ENST00000441802.2:c.5336C>T	p.Ser1779Leu	p.S1779L	ENST00000441802	NM_005245.3	1779	tCa/tTa	10/27	1	2	FACETS	0.973	0.871	1	0.973	0.871	1	CLONAL	1	TRUE	1	0.425303267650275	2		418	459	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564306	86564306	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs761910879	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	72	264	0	ENST00000274376.6:c.38C>G	p.Pro13Arg	p.P13R	ENST00000274376	NM_002890.2	13	cCg/cGg	1/25	0.212346390636129	3	FACETS	1	0.946	1	0.569	0.5	0.642	INDETERMINATE	1	TRUE	1	0.425303267650275	3		264	361	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441307	149441307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	189	607	0	ENST00000286301.3:c.1732C>T	p.Pro578Ser	p.P578S	ENST00000286301	NM_005211.3	578	Ccc/Tcc	12/22	0.212346390636129	3	FACETS	0.754	0.699	0.81	0.754	0.699	0.81	INDETERMINATE	2	TRUE	1	0.425303267650275	3		607	715	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495483	149495483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	190	710	1	ENST00000261799.4:c.3164C>T	p.Ser1055Phe	p.S1055F	ENST00000261799	NM_002609.3	1055	tCc/tTc	23/23	0.212346390636129	3	FACETS	1	0.984	1	0.612	0.566	0.66	INDETERMINATE	1	TRUE	1	0.425303267650275	3		711	885	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514562	149514562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	122	349	0	ENST00000261799.4:c.382C>T	p.Leu128Phe	p.L128F	ENST00000261799	NM_002609.3	128	Ctc/Ttc	4/23	0.212346390636129	3	FACETS	1	0.985	1	0.735	0.669	0.805	INDETERMINATE	1	TRUE	1	0.425303267650275	3		349	473	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520291	176520291	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	128	574	0	ENST00000292408.4:c.1210G>C	p.Ala404Pro	p.A404P	ENST00000292408	NM_213647.1	404	Gcc/Ccc	9/18	0.212346390636129	3	FACETS	1	0.977	1	0.619	0.562	0.677	INDETERMINATE	1	TRUE	1	0.425303267650275	3		574	590	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176684093	176684094	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	189	508	1	ENST00000439151.2:c.4907_4908delinsTT	p.Ser1636Phe	p.S1636F	ENST00000439151	NM_022455.4	1636	tCC/tTT	13/23	0.212346390636129	3	FACETS	1	0.99	1	0.726	0.673	0.781	INDETERMINATE	1	TRUE	1	0.425303267650275	3		509	742	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324596	31324597	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	240	384	1	ENST00000412585.2:c.211_212delinsTT	p.Pro71Leu	p.P71L	ENST00000412585	NM_005514.6	71	CCg/TTg	2/8	0.212346390636129	3	FACETS	1	0.972	1	1	0.994	1	INDETERMINATE	3	TRUE	1	0.425303267650275	3		385	440	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192467	138192467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	74	335	0	ENST00000237289.4:c.103G>A	p.Gly35Arg	p.G35R	ENST00000237289	NM_001270507.1	35	Ggg/Agg	2/9	0.212346390636129	3	FACETS	0.923	0.811	1	0.462	0.405	0.522	INDETERMINATE	1	TRUE	1	0.425303267650275	3		335	457	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468132	50468133	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	100	394	1	ENST00000331340.3:c.1367_1368delinsAA	p.Gly456Glu	p.G456E	ENST00000331340	NM_006060.4	456	gGG/gAA	8/8	0.294303349633831	5	FACETS	1	0.974	1	0.429	0.384	0.477	CLONAL	1	TRUE	2	0.425303267650275	5		395	598	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268035	55268036	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	229	503	2	ENST00000275493.2:c.2875_2876delinsTT	p.Pro959Leu	p.P959L	ENST00000275493	NM_005228.3	959	CCa/TTa	24/28	0.294303349633831	5	FACETS	1	0.969	1	0.708	0.661	0.756	CLONAL	2	TRUE	2	0.425303267650275	5		505	831	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845697	151845697	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	191	521	0	ENST00000262189.6:c.13315G>T	p.Val4439Phe	p.V4439F	ENST00000262189	NM_170606.2	4439	Gtc/Ttc	52/59	0.294303349633831	5	FACETS	0.938	0.869	1	0.626	0.579	0.673	CLONAL	2	TRUE	2	0.425303267650275	5		521	784	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878325	151878325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	234	556	0	ENST00000262189.6:c.6620C>T	p.Pro2207Leu	p.P2207L	ENST00000262189	NM_170606.2	2207	cCt/cTt	36/59	0.294303349633831	5	FACETS	1	0.963	1	0.696	0.651	0.743	CLONAL	2	TRUE	2	0.425303267650275	5		556	863	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539126	23539127	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	195	461	0	ENST00000380871.4:c.312_313delinsAA	p.Asp105Asn	p.D105N	ENST00000380871	NM_006167.3	104	ttGGac/ttAAac	2/2	0.34496178432646	3	FACETS	1	0.982	1	0.763	0.713	0.813	CLONAL	2	TRUE	0	0.425303267650275	3		461	486	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5081811	5081811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	236	334	0	ENST00000381652.3:c.2521C>T	p.Pro841Ser	p.P841S	ENST00000381652	NM_004972.3	841	Cct/Tct	19/25	0.42146401347045	4	FACETS	1	0.989	1	0.875	0.828	0.922	CLONAL	3	TRUE	0	0.425303267650275	4		334	452	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393712	139393712	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	365	515	0	ENST00000277541.6:c.5935-1G>A		p.X1979_splice	ENST00000277541	NM_017617.3	1979			0.425303267650275	3	FACETS	0.974	0.932	1	0.974	0.932	1	CLONAL	3	TRUE	0	0.425303267650275	3		515	712	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228248	53228249	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	209	309	0	ENST00000375401.3:c.2153_2154delinsTT	p.Ala718Val	p.A718V	ENST00000375401	NM_004187.3	718	gCC/gTT	15/26	0.254444159595735	2	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.425303267650275	2		309	401	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421839	49421840	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	A	novel	NA	P-0033494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	219	641	0	ENST00000301067.7:c.14467_14468delinsT	p.Pro4823SerfsTer35	p.P4823Sfs*35	ENST00000301067	NM_003482.3	4823	CCc/Tc	46/54	0.201159339334717	4	FACETS	0.861	0.803	0.922	0.861	0.803	0.922	INDETERMINATE	2	TRUE	2	0.425303267650275	4		641	852	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0033495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	179	773	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.37540668574678	1	FACETS	0.972	0.898	1	0.972	0.898	1	CLONAL	1	TRUE	0	0.37540668574678	1		773	797	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0033495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	27	448	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.163342105417824	0	FACETS	0.139	0.11	0.173			1	INDETERMINATE	1	TRUE	0	0.37540668574678	0		449	646	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	28	460	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.267	0.212	0.329	0.267	0.212	0.329	SUBCLONAL	1	TRUE	1	0.37540668574678	2		460	559	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0033495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	93	679	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.37540668574678	1	FACETS	0.588	0.523	0.658	0.588	0.523	0.658	SUBCLONAL	1	TRUE	0	0.37540668574678	1		686	684	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653796	89653798	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs1554893765	NA	P-0033495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	39	459	0	ENST00000371953.3:c.97_99del	p.Ile33del	p.I33del	ENST00000371953	NM_000314.4	32	ATT/-	2/9	1	2	FACETS	0.49	0.406	0.583	0.49	0.406	0.583	SUBCLONAL	1	TRUE	1	0.37540668574678	2		459	424	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556463	29556463	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1567849208	NA	P-0033495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	36	427	0	ENST00000356175.3:c.2835del	p.Phe945LeufsTer9	p.F945Lfs*9	ENST00000356175	NM_000267.3	944	Ttt/tt	21/57	0.37540668574678	1	FACETS	0.376	0.309	0.451	0.376	0.309	0.451	SUBCLONAL	1	TRUE	0	0.37540668574678	1		427	414	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	228	558	1	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.37540668574678	2		559	873	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435128	110435129	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs772322568	NA	P-0033495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	38	481	3	ENST00000375856.3:c.3272dup	p.Lys1092GlufsTer233	p.K1092Efs*233	ENST00000375856	NM_003749.2	1091	ccg/ccCg	1/2	0.37540668574678	1	FACETS	0.28	0.23	0.335	0.28	0.23	0.335	SUBCLONAL	1	TRUE	0	0.37540668574678	1		484	588	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508473	106508473	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370328855	NA	P-0033495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	13	227	0	ENST00000359195.3:c.467C>T	p.Ala156Val	p.A156V	ENST00000359195	NM_002649.2	156	gCg/gTg	2/11	1	2	FACETS	0.296	0.211	0.4	0.296	0.211	0.4	SUBCLONAL	1	TRUE	1	0.37540668574678	2		227	234	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518279	187518279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779582047	NA	P-0033495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	30	345	2	ENST00000441802.2:c.12415G>A	p.Gly4139Arg	p.G4139R	ENST00000441802	NM_005245.3	4139	Ggg/Agg	25/27	1	2	FACETS	0.401	0.322	0.489	0.401	0.322	0.489	SUBCLONAL	1	TRUE	1	0.37540668574678	2		347	399	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041089	180041089	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	60	773	0	ENST00000261937.6:c.3310C>G	p.Leu1104Val	p.L1104V	ENST00000261937	NM_182925.4	1104	Ctc/Gtc	24/30	0.180370626651748	3	FACETS	0.321	0.275	0.371	0.16	0.137	0.186	INDETERMINATE	1	TRUE	1	0.37540668574678	3		773	1184	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075425	8075425	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	29	411	0	ENST00000377482.5:c.145C>A	p.Pro49Thr	p.P49T	ENST00000377482	NM_018948.3	49	Ccg/Acg	3/4	1	2	FACETS	0.369	0.295	0.452	0.369	0.295	0.452	SUBCLONAL	1	TRUE	1	0.37540668574678	2		411	419	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023178	27023196	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCGGAGCCGGACCTGAA	GCGCGGAGCCGGACCTGAA	-	novel	NA	P-0033495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	10	66	0	ENST00000324856.7:c.285_303del	p.Ala96ThrfsTer12	p.A96Tfs*12	ENST00000324856	NM_006015.4	95	gGCGCGGAGCCGGACCTGAAg/gg	1/20	1	2	FACETS	0.65	0.445	0.899	0.65	0.445	0.899	SUBCLONAL	1	TRUE	1	0.37540668574678	2		66	82	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948280	71948280	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	59	869	0	ENST00000298229.2:c.2996del	p.Pro999ArgfsTer132	p.P999Rfs*132	ENST00000298229	NM_001567.3	998	Ccc/cc	26/28	0.180370626651748	3	FACETS	0.317	0.272	0.368	0.159	0.136	0.184	INDETERMINATE	1	TRUE	1	0.37540668574678	3		869	1176	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591713	38591713	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	45	510	0	ENST00000299084.4:c.177del	p.Phe59LeufsTer62	p.F59Lfs*62	ENST00000299084	NM_152594.2	58	Ttt/tt	2/7	0.37540668574678	1	FACETS	0.297	0.249	0.35	0.297	0.249	0.35	SUBCLONAL	1	TRUE	0	0.37540668574678	1		510	656	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641143	23641143	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1567217583	NA	P-0033495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	65	801	0	ENST00000261584.4:c.2332A>G	p.Ser778Gly	p.S778G	ENST00000261584	NM_024675.3	778	Agt/Ggt	5/13	1	2	FACETS	0.314	0.271	0.361	0.314	0.271	0.361	SUBCLONAL	1	TRUE	1	0.37540668574678	2		801	1104	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645045	67645045	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	41	673	0	ENST00000264010.4:c.310G>T	p.Glu104Ter	p.E104*	ENST00000264010	NM_006565.3	104	Gag/Tag	3/12	0.37540668574678	1	FACETS	0.224	0.185	0.267	0.224	0.185	0.267	SUBCLONAL	1	TRUE	0	0.37540668574678	1		673	793	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991765	72991765	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	21	368	0	ENST00000268489.5:c.2280del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	760	ggA/gg	2/10	0.37540668574678	1	FACETS	0.226	0.173	0.288	0.226	0.173	0.288	SUBCLONAL	1	TRUE	0	0.37540668574678	1		368	402	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226965	2226965	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	31	401	0	ENST00000398665.3:c.4445A>T	p.Gln1482Leu	p.Q1482L	ENST00000398665	NM_032482.2	1482	cAg/cTg	27/28	0.37540668574678	1	FACETS	0.24	0.194	0.294	0.24	0.194	0.294	SUBCLONAL	1	TRUE	0	0.37540668574678	1		401	558	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40740952	40740952	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	57	694	0	ENST00000392038.2:c.1366T>C	p.Tyr456His	p.Y456H	ENST00000392038	NM_001626.4	456	Tat/Cat	13/14	0.37540668574678	1	FACETS	0.345	0.295	0.399	0.345	0.295	0.399	SUBCLONAL	1	TRUE	0	0.37540668574678	1		694	715	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321115	62321115	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	116	684	0	ENST00000360203.5:c.2038C>A	p.Gln680Lys	p.Q680K	ENST00000360203	NM_001283009.1	680	Cag/Aag	24/35	1	2	FACETS	0.67	0.603	0.741	0.67	0.603	0.741	SUBCLONAL	1	TRUE	1	0.37540668574678	2		684	922	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436428	52436428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	41	586	0	ENST00000460680.1:c.2066C>T	p.Ala689Val	p.A689V	ENST00000460680	NM_004656.3	689	gCc/gTc	17/17	0.37540668574678	1	FACETS	0.283	0.235	0.336	0.283	0.235	0.336	SUBCLONAL	1	TRUE	0	0.37540668574678	1		586	628	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356403	66356403	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	53	444	0	ENST00000273854.3:c.1094T>A	p.Ile365Asn	p.I365N	ENST00000273854	NM_004439.5	365	aTc/aAc	5/18	1	2	FACETS	0.542	0.462	0.629	0.542	0.462	0.629	SUBCLONAL	1	TRUE	1	0.37540668574678	2		444	521	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293785	1293785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866101734	NA	P-0033495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	42	775	2	ENST00000310581.5:c.1216G>A	p.Gly406Arg	p.G406R	ENST00000310581	NM_198253.2	406	Ggg/Agg	2/16	1	2	FACETS	0.271	0.225	0.322	0.271	0.225	0.322	SUBCLONAL	1	TRUE	1	0.37540668574678	2		777	827	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790614	89790614	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0033495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	56	679	0	ENST00000336032.3:c.1A>G	p.Met1?	p.M1?	ENST00000336032	NM_006813.2	1	Atg/Gtg	1/2	1	2	FACETS	0.323	0.275	0.375	0.323	0.275	0.375	SUBCLONAL	1	TRUE	1	0.37540668574678	2		679	925	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933427	39933427	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1480861473	NA	P-0033495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	44	672	0	ENST00000378444.4:c.1172G>A	p.Gly391Asp	p.G391D	ENST00000378444	NM_001123385.1	391	gGc/gAc	4/15	1	2	FACETS	0.283	0.237	0.336	0.283	0.237	0.336	SUBCLONAL	1	TRUE	1	0.37540668574678	2		672	827	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0033509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	132	474	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.36254749340051	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.36254749340051	1		474	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0033509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	199	693	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.36254749340051	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.36254749340051	1		693	855	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102140	27102140	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	53	645	0	ENST00000324856.7:c.5066A>T	p.Asp1689Val	p.D1689V	ENST00000324856	NM_006015.4	1689	gAt/gTt	19/20	0.36254749340051	1	FACETS	0.332	0.282	0.386	0.332	0.282	0.386	SUBCLONAL	1	TRUE	0	0.36254749340051	1		645	722	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942939	71943961	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCATTGTGCCCAGGTCTCCTGATTTTCGGTCTGGTGCTCTCCCAGGTAGATTCTGCGCAGAATCTGCAGGGCCTTTCAGCTTCACCCTTGGGGTCCCCTGTGATCTCCAGGGGCTCTGCTCACACATACAGACAGACTCAGGCCATCCACACAGACCATGTGTGCCCAATGAGGACCCCCCCCTCCCCCAGGGAAGGTGTGGGTGTGTGCAGGGGCCTGCCCATGTCACAGCGTCTGGTGGGCTCAGCGGGAGGATCCTCTCACTGCAGCTTTGAGAGGCAGAAGGGAGAGTTGGGAGCCCTCTGAGGATGACCCAGGCCTTCCTCTCTTGCTTGCCTTAACAGGGAACAAGGGGGCTGTGGGCGTCTCCTTCATGTTTAATGGCACCTCATTTGGCTTTGTGAATTGTCACCTCACCTCGGGAAATGAGAAGACGGCTCGGTGAGGGGGCGCCTTTCCCATGGTCTCTTTACACCCATCCCATTCACCTGAGGCCTGTTCCCGCTCCCATACCCTAGCCCATGACCCTCCCGCAGGCCTGTCTCCAGAGACCCCCTGCTCTCTTATCCCAATTCAAGACCCTTCTGTTCCTGACCCTAACCTTGTCCCCAGGGGCCCGGATCTTTACCCCATCCCTGACTCCTGAGACTTCTTCCCTTTATGCCTATCCCTGACTTCTGGCCCTGACCCTGGGGATCTACCCCTCCCCACCACGCACCCCTCACCCTAGGAGGAACCAAAACTACTTGGACATCCTGCGGCTGCTCTCGCTGGGCGACCGGCAGCTCAATGCCTTTGACATCTCTCTGCGTTTCACACACCTCTTCTGGTTTGGGGACCTCAACTACCGCCTGGACATGGATATCCAGGTGCGAGCAGGGCCCTGCCATGGCTGTAGGGAGGCTAAGGGCCACATGGGCTATCACCCCTGGCTCTGGCTCCGGAGGAATGTTTCTAGCCTTTGTGTCCTCCACCCCAGGAGATCCTGAACTACATCAGCAGGAAAGAGTTTGAGCCCCTCC	GGCATTGTGCCCAGGTCTCCTGATTTTCGGTCTGGTGCTCTCCCAGGTAGATTCTGCGCAGAATCTGCAGGGCCTTTCAGCTTCACCCTTGGGGTCCCCTGTGATCTCCAGGGGCTCTGCTCACACATACAGACAGACTCAGGCCATCCACACAGACCATGTGTGCCCAATGAGGACCCCCCCCTCCCCCAGGGAAGGTGTGGGTGTGTGCAGGGGCCTGCCCATGTCACAGCGTCTGGTGGGCTCAGCGGGAGGATCCTCTCACTGCAGCTTTGAGAGGCAGAAGGGAGAGTTGGGAGCCCTCTGAGGATGACCCAGGCCTTCCTCTCTTGCTTGCCTTAACAGGGAACAAGGGGGCTGTGGGCGTCTCCTTCATGTTTAATGGCACCTCATTTGGCTTTGTGAATTGTCACCTCACCTCGGGAAATGAGAAGACGGCTCGGTGAGGGGGCGCCTTTCCCATGGTCTCTTTACACCCATCCCATTCACCTGAGGCCTGTTCCCGCTCCCATACCCTAGCCCATGACCCTCCCGCAGGCCTGTCTCCAGAGACCCCCTGCTCTCTTATCCCAATTCAAGACCCTTCTGTTCCTGACCCTAACCTTGTCCCCAGGGGCCCGGATCTTTACCCCATCCCTGACTCCTGAGACTTCTTCCCTTTATGCCTATCCCTGACTTCTGGCCCTGACCCTGGGGATCTACCCCTCCCCACCACGCACCCCTCACCCTAGGAGGAACCAAAACTACTTGGACATCCTGCGGCTGCTCTCGCTGGGCGACCGGCAGCTCAATGCCTTTGACATCTCTCTGCGTTTCACACACCTCTTCTGGTTTGGGGACCTCAACTACCGCCTGGACATGGATATCCAGGTGCGAGCAGGGCCCTGCCATGGCTGTAGGGAGGCTAAGGGCCACATGGGCTATCACCCCTGGCTCTGGCTCCGGAGGAATGTTTCTAGCCTTTGTGTCCTCCACCCCAGGAGATCCTGAACTACATCAGCAGGAAAGAGTTTGAGCCCCTCC	-	novel	NA	P-0033509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	28	23	0	ENST00000298229.2:c.1615+280_1894del		p.X539_splice	ENST00000298229	NM_001567.3	539		14-16/28	0.182298349763563	1	FACETS	0.832	0.689	0.983	1	0.954	1	INDETERMINATE	2	TRUE	0	0.36254749340051	1		23	76	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0033511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	29	474	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.372960456789388	6	FACETS	0.353	0.282	0.434			1	SUBCLONAL	1	TRUE	NA	0.372960456789388	6		474	770	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319853	8319853	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	129	568	0	ENST00000356435.5:c.5648G>A	p.Arg1883Gln	p.R1883Q	ENST00000356435		1883	cGa/cAa	34/35	0.290497936455918	1	FACETS	0.867	0.797	0.938	0.867	0.797	0.938	INDETERMINATE	1	TRUE	0	0.628208212637729	1		568	325	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156734	20156734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	152	550	0	ENST00000379607.5:c.23G>A	p.Gly8Glu	p.G8E	ENST00000379607	NM_001412.3	8	gGa/gAa	2/7	0.288840154394084	4	FACETS	0.987	0.913	1	0.987	0.913	1	INDETERMINATE	2	TRUE	2	0.628208212637729	4		550	399	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924708	94924708	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	258	828	1	ENST00000536441.1:c.202A>T	p.Thr68Ser	p.T68S	ENST00000536441	NM_144665.3	68	Aca/Tca	3/10	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.628208212637729	2		829	579	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543685	29543693	+	inframe_deletion	In_Frame_Del	DEL	GTGCCTTGG	GTGCCTTGG	-	novel	NA	P-0033513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	204	658	0	ENST00000389048.3:c.1470_1478del	p.Gln491_Thr493del	p.Q491_T493del	ENST00000389048	NM_004304.4	490	acCCAAGGCACa/aca	7/29	1	2	FACETS	0.981	0.914	1	0.981	0.914	1	CLONAL	1	TRUE	1	0.628208212637729	2		658	662	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31472316	31472316	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	256	682	0	ENST00000344624.3:c.2095A>G	p.Met699Val	p.M699V	ENST00000344624		699	Atg/Gtg	14/33	0.288840154394084	4	FACETS	1	0.973	1	1	0.973	1	INDETERMINATE	2	TRUE	2	0.628208212637729	4		682	630	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509533	149509533	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0033513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	142	487	0	ENST00000261799.4:c.1368-2A>G		p.X456_splice	ENST00000261799	NM_002609.3	456			0.288840154394084	4	FACETS	0.754	0.692	0.818	0.754	0.692	0.818	INDETERMINATE	2	TRUE	2	0.628208212637729	4		487	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0033526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	8	782	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.255687586636232	3	FACETS	0.132	0.084	0.194	0.066	0.042	0.097	SUBCLONAL	1	FALSE	1	0.381878213756432	3		784	378	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186562	108186562	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	36	365	0	ENST00000278616.4:c.6019del	p.Glu2007LysfsTer6	p.E2007Kfs*6	ENST00000278616	NM_000051.3	2007	Gaa/aa	41/63	0.378817467779377	3	FACETS	1	0.941	1	0.832	0.707	0.96	CLONAL	2	FALSE	0	0.381878213756432	3		365	90	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750351	39750351	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	12	318	0	ENST00000361337.2:c.1966G>T	p.Glu656Ter	p.E656*	ENST00000361337	NM_003286.2	656	Gaa/Taa	19/21	1	2	FACETS	0.321	0.225	0.438	0.321	0.225	0.438	SUBCLONAL	1	FALSE	1	0.381878213756432	2		318	196	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0033528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	536	400	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.478961804705034	3	FACETS	1	0.974	1			1	INDETERMINATE	2	TRUE	NA	0.83570404186894	3		400	902	SUCCESS
APC	324	MSKCC	GRCh37	5	112176020	112176020	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	154	312	0	ENST00000257430.4:c.4729G>T	p.Glu1577Ter	p.E1577*	ENST00000257430	NM_000038.5	1577	Gaa/Taa	16/16	1	2	FACETS	0.993	0.921	1	0.993	0.921	1	CLONAL	1	TRUE	1	0.83570404186894	2		312	371	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188078	11188078	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	252	557	0	ENST00000361445.4:c.6016G>C	p.Val2006Leu	p.V2006L	ENST00000361445	NM_004958.3	2006	Gtc/Ctc	43/58	1	2	FACETS	0.917	0.863	0.971	0.917	0.863	0.971	CLONAL	1	TRUE	1	0.83570404186894	2		557	658	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830866	72830870	+	frameshift_variant	Frame_Shift_Del	DEL	CGGAC	CGGAC	-	novel	NA	P-0033528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	388	656	0	ENST00000268489.5:c.5711_5715del	p.Gly1904GlufsTer23	p.G1904Efs*23	ENST00000268489	NM_006885.3	1904	gGTCCG/g	9/10	0.83570404186894	1	FACETS	0.934	0.901	0.966	0.934	0.901	0.966	CLONAL	1	TRUE	0	0.83570404186894	1		656	579	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40761173	40761173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	273	572	0	ENST00000392038.2:c.179G>A	p.Cys60Tyr	p.C60Y	ENST00000392038	NM_001626.4	60	tGc/tAc	4/14	1	2	FACETS	0.943	0.89	0.996	0.943	0.89	0.996	CLONAL	1	TRUE	1	0.83570404186894	2		572	693	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275057	41275057	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	210	494	0	ENST00000349496.5:c.1223T>C	p.Leu408Pro	p.L408P	ENST00000349496	NM_001904.3	408	cTt/cCt	9/15	1	2	FACETS	0.816	0.762	0.871	0.816	0.762	0.871	CLONAL	1	TRUE	1	0.83570404186894	2		494	616	SUCCESS
APC	324	MSKCC	GRCh37	5	112174424	112174424	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	155	298	0	ENST00000257430.4:c.3133C>T	p.Gln1045Ter	p.Q1045*	ENST00000257430	NM_000038.5	1045	Cag/Tag	16/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.83570404186894	2		298	340	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0033530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	127	594	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.845	0.766	0.928	0.845	0.766	0.928	CLONAL	1	TRUE	1	0.405698856920015	2		594	741	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711281	114711281	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	105	438	0	ENST00000543371.1:c.296C>G	p.Pro99Arg	p.P99R	ENST00000543371	NM_001198531.1	99	cCg/cGg	3/14	1	2	FACETS	0.9	0.809	0.997	0.9	0.809	0.997	CLONAL	1	TRUE	1	0.405698856920015	2		438	575	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144880	47144880	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	129	640	2	ENST00000409792.3:c.4873C>T	p.Arg1625Cys	p.R1625C	ENST00000409792	NM_014159.6	1625	Cgt/Tgt	7/21	1	2	FACETS	0.877	0.796	0.962	0.877	0.796	0.962	CLONAL	1	TRUE	1	0.405698856920015	2		642	725	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523516	41523516	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	114	495	0	ENST00000263253.7:c.932A>C	p.Gln311Pro	p.Q311P	ENST00000263253	NM_001429.3	311	cAg/cCg	4/31	1	2	FACETS	0.834	0.752	0.92	0.834	0.752	0.92	CLONAL	1	TRUE	1	0.405698856920015	2		495	674	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125235	47125235	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	126	578	0	ENST00000409792.3:c.6035T>G	p.Leu2012Arg	p.L2012R	ENST00000409792	NM_014159.6	2012	cTc/cGc	12/21	1	2	FACETS	0.962	0.873	1	0.962	0.873	1	CLONAL	1	TRUE	1	0.405698856920015	2		578	646	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-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1375	430	894	0	ENST00000397752.3:c.2888-11_2953del		p.X963_splice	ENST00000397752	NM_000245.2	963		14/21	0.405698856920015	3	FACETS	1	0.995	1	0.706	0.671	0.742	CLONAL	1	TRUE	1	0.405698856920015	3		894	1805	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0033531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	386	720	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.199045184849287	15	FACETS	1	0.987	1			1	CLONAL	19	FALSE	NA	0.199045184849287	15		720	459	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0033531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	108	264	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.199045184849287	5	FACETS	0.943	0.863	1	1	0.989	1	CLONAL	6	FALSE	2	0.199045184849287	5		264	249	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577530	7577530	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	23	780	0	ENST00000269305.4:c.751A>T	p.Ile251Phe	p.I251F	ENST00000269305	NM_001126112.2	251	Atc/Ttc	7/11	0.199045184849287	15	FACETS	1	0.886	1			1	CLONAL	1	FALSE	NA	0.199045184849287	15		780	428	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991805	72991805	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	44	777	0	ENST00000268489.5:c.2240C>G	p.Ser747Cys	p.S747C	ENST00000268489	NM_006885.3	747	tCt/tGt	2/10	0.153797061984309	4	FACETS	1	0.905	1			1	CLONAL	3	FALSE	NA	0.199045184849287	4		777	163	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413087	139413087	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	22	755	0	ENST00000277541.6:c.1055A>G	p.Asp352Gly	p.D352G	ENST00000277541	NM_017617.3	352	gAc/gGc	6/34	0.199045184849287	5	FACETS	0.97	0.752	1	0.323	0.25	0.408	CLONAL	1	FALSE	2	0.199045184849287	5		755	296	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939496	76939496	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057523785	NA	P-0033531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	105	380	0	ENST00000373344.5:c.1252C>T	p.Arg418Ter	p.R418*	ENST00000373344	NM_000489.3	418	Cga/Tga	9/35	0.199045184849287	2	FACETS	0.992	0.936	1			1	CLONAL	8	FALSE	NA	0.199045184849287	2		380	133	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274123	10274123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774442834	NA	P-0033551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	142	650	0	ENST00000330684.3:c.146G>A	p.Arg49His	p.R49H	ENST00000330684	NM_001134407.1	49	cGc/cAc	2/13	0.629025167817985	3	FACETS	0.644	0.586	0.704	0.322	0.293	0.352	SUBCLONAL	1	TRUE	1	0.682564019365243	3		650	867	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255371	16255371	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	34	422	0	ENST00000375759.3:c.2636T>G	p.Val879Gly	p.V879G	ENST00000375759	NM_015001.2	879	gTt/gGt	11/15	1	2	FACETS	0.209	0.17	0.252	0.209	0.17	0.252	SUBCLONAL	1	TRUE	1	0.682564019365243	2		422	477	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304261	91304261	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	74	392	0	ENST00000355112.3:c.1658T>C	p.Ile553Thr	p.I553T	ENST00000355112	NM_000057.2	553	aTt/aCt	7/22	1	2	FACETS	0.616	0.543	0.694	0.616	0.543	0.694	SUBCLONAL	1	TRUE	1	0.682564019365243	2		392	352	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50827478	50827478	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	36	444	0	ENST00000398568.2:c.2363G>A	p.Cys788Tyr	p.C788Y	ENST00000398568	NM_001042412.1	788	tGt/tAt	16/18	0.682564019365243	1	FACETS	0.234	0.193	0.28	0.234	0.193	0.28	SUBCLONAL	1	TRUE	0	0.682564019365243	1		444	297	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753627	42753627	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	70	782	1	ENST00000222329.4:c.637G>T	p.Asp213Tyr	p.D213Y	ENST00000222329	NM_006494.2	213	Gat/Tat	4/4	1	2	FACETS	0.256	0.223	0.293	0.256	0.223	0.293	SUBCLONAL	1	TRUE	1	0.682564019365243	2		783	800	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0033555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	429	589	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.927892241145922	1	FACETS	0.985	0.963	1	0.985	0.963	1	CLONAL	1	TRUE	0	0.927892241145922	1		589	503	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494902	56494902	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs749837397	NA	P-0033555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	389	517	0	ENST00000267101.3:c.3259A>G	p.Met1087Val	p.M1087V	ENST00000267101	NM_001982.3	1087	Atg/Gtg	27/28	0.911279450130859	3	FACETS	0.988	0.939	1	0.494	0.469	0.519	CLONAL	1	TRUE	1	0.927892241145922	3		517	1242	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	56	441	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	0.16	2		441	529	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346890	89346898	+	inframe_deletion	In_Frame_Del	DEL	GGCGGGAGG	GGCGGGAGG	-	rs775221712	NA	P-0033561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	26	263	0	ENST00000301030.4:c.6052_6060del	p.Pro2018_Ala2020del	p.P2018_A2020del	ENST00000301030	NM_001256183.1	2018	CCTCCCGCC/-	9/13	1	2	FACETS	1	0.81	1	1	0.81	1	CLONAL	1	TRUE	1	0.16	2		263	318	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691938	30691938	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	42	342	2	ENST00000295754.5:c.440T>A	p.Ile147Asn	p.I147N	ENST00000295754	NM_003242.5	147	aTc/aAc	3/7	1	2	FACETS	0.894	0.746	1	0.894	0.746	1	CLONAL	1	TRUE	1	0.16	2		344	587	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044496	47044496	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	66	572	0	ENST00000377604.3:c.1993C>T	p.Gln665Ter	p.Q665*	ENST00000377604	NM_001204468.1	665	Caa/Taa	18/24	1	2	FACETS	0.901	0.78	1	0.901	0.78	1	CLONAL	1	TRUE	1	0.16	2		572	916	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667368	241667368	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	251	501	0	ENST00000366560.3:c.1082A>G	p.Asn361Ser	p.N361S	ENST00000366560	NM_000143.3	361	aAt/aGt	7/10	0.556623024565489	2	FACETS	0.876	0.829	0.923	0.876	0.829	0.923	CLONAL	2	TRUE	0	0.556623024565489	2		501	515	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678001	117678001	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	265	587	0	ENST00000368508.3:c.3932G>C	p.Arg1311Pro	p.R1311P	ENST00000368508	NM_002944.2	1311	cGa/cCa	25/43	0.497518363246418	3	FACETS	0.922	0.87	0.974	0.922	0.87	0.974	CLONAL	2	TRUE	1	0.556623024565489	3		587	660	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875906	76875906	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	259	337	0	ENST00000373344.5:c.5229G>T	p.Arg1743Ser	p.R1743S	ENST00000373344	NM_000489.3	1743	agG/agT	20/35	0.237112746623855	3	FACETS	1	0.988	1			1	INDETERMINATE	3	TRUE	NA	0.556623024565489	3		337	367	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	34	356	0	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	0.755	0.616	0.914	0.755	0.616	0.914	CLONAL	1	TRUE	1	0.14	2		356	643	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117799	108117799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202160435	NA	P-0033565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	17	352	0	ENST00000278616.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000278616	NM_000051.3	337	cGt/cAt	8/63	1	2	FACETS	0.369	0.273	0.483	0.369	0.273	0.483	SUBCLONAL	1	TRUE	1	0.14	2		352	659	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453132	140453132	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913365	NA	P-0033565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	32	247	0	ENST00000288602.6:c.1803A>T	p.Lys601Asn	p.K601N	ENST00000288602	NM_004333.4	601	aaA/aaT	15/18	0.128912322994337	3	FACETS	0.863	0.699	1	0.431	0.349	0.525	CLONAL	1	TRUE	1	0.14	3		247	567	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646981	23646981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	60	691	3	ENST00000261584.4:c.886del	p.Met296Ter	p.M296*	ENST00000261584	NM_024675.3	296	Atg/tg	4/13	1	2	FACETS	0.823	0.707	0.951	0.823	0.707	0.951	CLONAL	1	TRUE	1	0.14	2		694	1041	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561465	9561465	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1407217736	NA	P-0033565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	37	440	0	ENST00000353224.5:c.317C>A	p.Pro106His	p.P106H	ENST00000353224	NM_177990.2	106	cCc/cAc	4/10	1	2	FACETS	0.727	0.598	0.873	0.727	0.598	0.873	SUBCLONAL	1	TRUE	1	0.14	2		440	727	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932289	36932289	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	50	631	0	ENST00000361632.4:c.2180A>G	p.Tyr727Cys	p.Y727C	ENST00000361632		727	tAt/tGt	16/16	1	2	FACETS	0.806	0.682	0.944	0.806	0.682	0.944	CLONAL	1	TRUE	1	0.14	2		631	886	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117921	70117922	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0033565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	29	317	0	ENST00000245479.2:c.390dup	p.His131AlafsTer121	p.H131Afs*121	ENST00000245479	NM_000346.3	130	ttg/ttGg	1/3	1	2	FACETS	0.88	0.705	1	0.88	0.705	1	CLONAL	1	TRUE	1	0.14	2		317	471	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090446	37090446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750217	NA	P-0033565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	52	338	0	ENST00000231790.2:c.2041G>A	p.Ala681Thr	p.A681T	ENST00000231790	NM_000249.3	681	Gct/Act	18/19	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.14	2		338	707	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004882	150004882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	41	459	0	ENST00000253339.5:c.1343G>A	p.Gly448Glu	p.G448E	ENST00000253339		448	gGg/gAg	3/7	1	2	FACETS	0.76	0.631	0.904	0.76	0.631	0.904	CLONAL	1	TRUE	1	0.14	2		459	771	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0033596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	36	419	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.26	2		419	257	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578231	7578232	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	87	593	0	ENST00000269305.4:c.617dup	p.Leu206PhefsTer3	p.L206Ffs*3	ENST00000269305	NM_001126112.2	206	ttg/ttTg	6/11	1	2	FACETS	0.889	0.786	0.998	0.889	0.786	0.998	CLONAL	1	TRUE	1	0.26	2		593	753	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5078351	5078353	+	inframe_deletion	In_Frame_Del	DEL	CTG	CTG	-	novel	NA	P-0033596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	11	367	0	ENST00000381652.3:c.2040_2042del	p.Leu681del	p.L681del	ENST00000381652	NM_004972.3	680	CTG/-	16/25	1	2	FACETS	0.432	0.298	0.597	0.432	0.298	0.597	SUBCLONAL	1	TRUE	1	0.26	2		367	196	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555526097	NA	P-0033597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	180	736	1	ENST00000269305.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000269305	NM_001126112.2	167	Cag/Tag	5/11	0.329985815668769	1	FACETS	0.983	0.906	1	0.983	0.906	1	CLONAL	1	TRUE	0	0.329985815668769	1		737	927	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562347	95562347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140875148	NA	P-0033597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	88	364	0	ENST00000393063.1:c.4910C>T	p.Ser1637Leu	p.S1637L	ENST00000393063	NM_030621.3	1637	tCg/tTg	24/28	1	2	FACETS	0.993	0.882	1	0.993	0.882	1	CLONAL	1	TRUE	1	0.329985815668769	2		364	537	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163246	32163246	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1259	193	891	1	ENST00000375023.3:c.5980C>T	p.Pro1994Ser	p.P1994S	ENST00000375023	NM_004557.3	1994	Ccc/Tcc	30/30	1	2	FACETS	0.806	0.743	0.871	0.806	0.743	0.871	CLONAL	1	TRUE	1	0.329985815668769	2		892	1452	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662427	67662427	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	142	681	0	ENST00000264010.4:c.1673C>G	p.Ser558Cys	p.S558C	ENST00000264010	NM_006565.3	558	tCt/tGt	9/12	1	2	FACETS	0.839	0.763	0.918	0.839	0.763	0.918	CLONAL	1	TRUE	1	0.329985815668769	2		681	1026	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532639	46532639	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1280941990	NA	P-0033597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	79	385	2	ENST00000262741.5:c.439C>T	p.Gln147Ter	p.Q147*	ENST00000262741	NM_003629.3	147	Cag/Tag	4/10	0.302433907765029	2	FACETS	0.973	0.858	1	0.487	0.429	0.548	CLONAL	1	TRUE	0	0.329985815668769	2		387	492	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148638	119149422	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CATTGGAACCCATTGACTAGATTAGTGAATTTGTGTGTATGTGGTTTCACTTTAAACCCTGGAGCTTAAAATAGGACCCAGACTAGATGCTTTCTGGTTTAATAAAAAATAAACCACTGTTGTGACATTTTTATATAAGCAAAATTTGTATAGGAAACAAGTCTTCACTTTTTCTGTTAACATTTATAATTGCAGTTATTTATTCAACTAATAGTCTTTTAATTTTTTTTAATCAAAGGAACAATATGAATTATACTGTGAGATGGGCTCCACATTCCAACTATGTAAAATATGTGCTGAAAATGATAAGGATGTAAAGATTGAGCCCTGTGGACACCTCATGTGCACATCCTGTCTTACATCCTGGCAGGTACGGATCTAAACAGCGACTTTTTTCAGCTATGTAATAACCTTGGAAAATTCGGTATTATATAGCCTTTACTGATACAAGGGGTGGCCTGGCTTTTGGGGTTAGGTTTAAACTTTTACTTTTTTTTGATCTCTAGGAAATGTATTTTCTAGTAGATTAATATTTTAAGTATTTTCAGATGCATCTGTTACTATCTTTTGCTTCTTCTGCAGGAATCAGAAGGTCAGGGCTGTCCTTTCTGCCGATGTGAAATTAAAGGTACTGAACCCATCGTGGTAGATCCGTTTGATCCTAGAGGGAGTGGCAGCCTGTTGAGGCAAGGAGCAGAGGGAGCTCCCTCCCCAAATTATGATGATGATGATGATGAACGAGCTGATGATACTCTCTTCATGATGAAGGAATTGGCTGGTGCCAA	CATTGGAACCCATTGACTAGATTAGTGAATTTGTGTGTATGTGGTTTCACTTTAAACCCTGGAGCTTAAAATAGGACCCAGACTAGATGCTTTCTGGTTTAATAAAAAATAAACCACTGTTGTGACATTTTTATATAAGCAAAATTTGTATAGGAAACAAGTCTTCACTTTTTCTGTTAACATTTATAATTGCAGTTATTTATTCAACTAATAGTCTTTTAATTTTTTTTAATCAAAGGAACAATATGAATTATACTGTGAGATGGGCTCCACATTCCAACTATGTAAAATATGTGCTGAAAATGATAAGGATGTAAAGATTGAGCCCTGTGGACACCTCATGTGCACATCCTGTCTTACATCCTGGCAGGTACGGATCTAAACAGCGACTTTTTTCAGCTATGTAATAACCTTGGAAAATTCGGTATTATATAGCCTTTACTGATACAAGGGGTGGCCTGGCTTTTGGGGTTAGGTTTAAACTTTTACTTTTTTTTGATCTCTAGGAAATGTATTTTCTAGTAGATTAATATTTTAAGTATTTTCAGATGCATCTGTTACTATCTTTTGCTTCTTCTGCAGGAATCAGAAGGTCAGGGCTGTCCTTTCTGCCGATGTGAAATTAAAGGTACTGAACCCATCGTGGTAGATCCGTTTGATCCTAGAGGGAGTGGCAGCCTGTTGAGGCAAGGAGCAGAGGGAGCTCCCTCCCCAAATTATGATGATGATGATGATGAACGAGCTGATGATACTCTCTTCATGATGAAGGAATTGGCTGGTGCCAA	-	novel	NA	P-0033597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	36	109	0	ENST00000264033.4:c.1095+84_1430del		p.X365_splice	ENST00000264033	NM_005188.3	365		8-9/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.329985815668769	2		109	156	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871181	12871184	+	frameshift_variant	Frame_Shift_Del	DEL	TCCG	TCCG	-	novel	NA	P-0033597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	46	190	0	ENST00000228872.4:c.410_413del	p.Pro137ArgfsTer7	p.P137Rfs*7	ENST00000228872	NM_004064.3	136	gaTCCG/ga	1/3	0.231177266528881	3	FACETS	1	0.925	1	0.578	0.49	0.674	CLONAL	1	TRUE	1	0.329985815668769	3		190	281	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745090	41745090	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	123	583	0	ENST00000301178.4:c.1156A>T	p.Arg386Trp	p.R386W	ENST00000301178	NM_021913.4	386	Agg/Tgg	9/20	1	2	FACETS	0.893	0.807	0.983	0.893	0.807	0.983	CLONAL	1	TRUE	1	0.329985815668769	2		583	835	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6038854	6038854	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	137	608	0	ENST00000265849.7:c.590G>T	p.Gly197Val	p.G197V	ENST00000265849	NM_000535.5	197	gGc/gTc	6/15	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.329985815668769	2		608	825	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245374	53245374	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	109	283	0	ENST00000375401.3:c.663A>T	p.Glu221Asp	p.E221D	ENST00000375401	NM_004187.3	221	gaA/gaT	6/26	1	1	FACETS	0.766	0.695	0.84	1	0.985	1	SUBCLONAL	2	TRUE	0	0.329985815668769	1		283	360	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	62	441	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.0778382273613611	0	FACETS	0.806	0.697	0.924			1	INDETERMINATE	1	TRUE	0	0.23	0		441	515	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068375	26068375	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	65	464	0	ENST00000435504.4:c.115C>T	p.Gln39Ter	p.Q39*	ENST00000435504		39	Cag/Tag	2/13	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.23	2		464	473	SUCCESS
AR	367	MSKCC	GRCh37	X	66765121	66765121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	58	500	1	ENST00000374690.3:c.133G>A	p.Ala45Thr	p.A45T	ENST00000374690	NM_000044.3	45	Gcg/Acg	1/8	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.23	2		501	441	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610135	43610135	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564496520	NA	P-0033599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	71	785	0	ENST00000355710.3:c.2087C>T	p.Ser696Leu	p.S696L	ENST00000355710	NM_020975.4	696	tCg/tTg	11/20	1	2	FACETS	0.926	0.808	1	0.926	0.808	1	CLONAL	1	TRUE	1	0.23	2		785	667	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26927926	26927926	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	38	356	0	ENST00000381527.3:c.365A>T	p.Gln122Leu	p.Q122L	ENST00000381527	NM_001260.1	122	cAg/cTg	4/13	1	2	FACETS	0.888	0.736	1	0.888	0.736	1	CLONAL	1	TRUE	1	0.23	2		356	372	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226385	2226385	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	82	794	0	ENST00000326181.6:c.1998G>T	p.Lys666Asn	p.K666N	ENST00000326181	NM_032271.2	666	aaG/aaT	20/21	0.0778382273613611	0	FACETS	0.88	0.776	0.991			1	INDETERMINATE	1	TRUE	0	0.23	0		794	624	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266713	198266713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776846119	NA	P-0033602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	72	430	1	ENST00000335508.6:c.2219G>A	p.Gly740Glu	p.G740E	ENST00000335508	NM_012433.2	740	gGa/gAa	15/25	1	2	FACETS	0.947	0.828	1	0.947	0.828	1	CLONAL	1	TRUE	1	0.230975002995373	2		431	658	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107136	27107137	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0033602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	108	527	0	ENST00000324856.7:c.6749_6750del	p.Glu2250ValfsTer27	p.E2250Vfs*27	ENST00000324856	NM_006015.4	2249	tcAGag/tcag	20/20	0.230975002995373	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.230975002995373	1		527	758	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279672	123279672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	68	314	0	ENST00000358487.5:c.760C>T	p.His254Tyr	p.H254Y	ENST00000358487	NM_000141.4	254	Cac/Tac	7/18	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.230975002995373	2		314	533	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099564	157099582	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCGGCCAGGCCGACCCC	GGGCGGCCAGGCCGACCCC	TGG	novel	NA	P-0033602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	30	106	2	ENST00000346085.5:c.501_519delinsTGG	p.Gly169ArgfsTer6	p.G169Rfs*6	ENST00000346085	NM_020732.3	167	gcGGGCGGCCAGGCCGACCCC/gcTGG	1/20	0.230975002995373	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.230975002995373	1		108	160	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0033604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	167	503	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	0.445482427990664	2		503	745	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0033604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	201	540	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.445482427990664	2		540	872	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81960742	81960742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768839912	NA	P-0033604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	167	428	0	ENST00000359376.3:c.2473G>A	p.Glu825Lys	p.E825K	ENST00000359376	NM_002661.3	825	Gag/Aag	23/33	0.445482427990664	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.445482427990664	1		428	524	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250643	26250643	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	144	581	1	ENST00000446824.2:c.191G>A	p.Arg64His	p.R64H	ENST00000446824	NM_021018.2	64	cGc/cAc	1/1	1	2	FACETS	0.89	0.814	0.971	0.89	0.814	0.971	CLONAL	1	TRUE	1	0.445482427990664	2		582	726	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061208	38061208	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	170	509	0	ENST00000250448.2:c.781C>A	p.Arg261Ser	p.R261S	ENST00000250448	NM_004496.3	261	Cgc/Agc	2/2	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.445482427990664	2		509	700	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105586	27105586	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	179	518	1	ENST00000324856.7:c.5197G>T	p.Glu1733Ter	p.E1733*	ENST00000324856	NM_006015.4	1733	Gag/Tag	20/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.445482427990664	2		519	732	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54959353	54959353	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0033604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	117	422	0	ENST00000312783.6:c.347C>G	p.Ser116Ter	p.S116*	ENST00000312783	NM_198436.1	116	tCa/tGa	5/10	1	2	FACETS	0.941	0.852	1	0.941	0.852	1	CLONAL	1	TRUE	1	0.445482427990664	2		422	558	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332804	152332804	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	184	552	0	ENST00000206249.3:c.1110G>C	p.Leu370Phe	p.L370F	ENST00000206249	NM_000125.3	370	ttG/ttC	5/8	1	2	FACETS	0.999	0.923	1	0.999	0.923	1	CLONAL	1	TRUE	1	0.445482427990664	2		552	827	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562190	21562190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	354	1045	1	ENST00000382592.4:c.1729C>T	p.Pro577Ser	p.P577S	ENST00000382592	NM_014572.2	577	Ccc/Tcc	4/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.445482427990664	2		1046	1505	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863698	68863698	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	112	296	0	ENST00000261769.5:c.2437del	p.Glu813LysfsTer3	p.E813Kfs*3	ENST00000261769	NM_004360.3	813	Gaa/aa	15/16	0.445482427990664	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.445482427990664	1		296	377	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288937	212288937	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	122	443	0	ENST00000342788.4:c.2809G>C	p.Glu937Gln	p.E937Q	ENST00000342788	NM_005235.2	937	Gaa/Caa	23/28	1	2	FACETS	0.944	0.857	1	0.944	0.857	1	CLONAL	1	TRUE	1	0.445482427990664	2		443	580	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805984	32805984	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	202	712	0	ENST00000374899.4:c.27G>C	p.Trp9Cys	p.W9C	ENST00000374899	NM_018833.2	9	tgG/tgC	2/12	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.445482427990664	2		712	857	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087503	27087503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	71	702	2	ENST00000324856.7:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000324856	NM_006015.4	693	Cga/Tga	5/20	1	2	FACETS	0.544	0.473	0.621	0.544	0.473	0.621	SUBCLONAL	1	TRUE	1	0.233427142513196	2		704	1118	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397811	49397811	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	114	407	1	ENST00000418115.1:c.413C>T	p.Pro138Leu	p.P138L	ENST00000418115	NM_001664.2	138	cCg/cTg	5/5	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.233427142513196	2		408	818	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0033605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	44	419	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.554	0.463	0.654	0.554	0.463	0.654	SUBCLONAL	1	TRUE	1	0.233427142513196	2		419	681	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0033605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	99	476	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.922	0.822	1	0.922	0.822	1	CLONAL	1	TRUE	1	0.233427142513196	2		478	920	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022747	12022747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376242225	NA	P-0033605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	49	386	0	ENST00000396373.4:c.853G>A	p.Val285Met	p.V285M	ENST00000396373	NM_001987.4	285	Gtg/Atg	5/8	NA	2	FACETS	0.601	0.508	0.703			1	INDETERMINATE	1	TRUE	NA	0.233427142513196	2		386	699	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339111	65339111	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	103	455	3	ENST00000342505.4:c.425del	p.Lys142ArgfsTer26	p.K142Rfs*26	ENST00000342505	NM_002227.2	142	aAg/ag	5/25	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.233427142513196	2		458	837	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807505	36807505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200986219	NA	P-0033605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	132	691	0	ENST00000373129.3:c.1159G>A	p.Glu387Lys	p.E387K	ENST00000373129	NM_032017.1	387	Gag/Aag	12/12	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.233427142513196	2		691	1023	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335079	65335079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	98	526	0	ENST00000342505.4:c.562G>A	p.Glu188Lys	p.E188K	ENST00000342505	NM_002227.2	188	Gag/Aag	6/25	1	2	FACETS	0.971	0.865	1	0.971	0.865	1	CLONAL	1	TRUE	1	0.233427142513196	2		526	865	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163307847	163307847	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	34	274	0	ENST00000271452.3:c.473C>A	p.Ala158Glu	p.A158E	ENST00000271452	NM_145697.2	158	gCa/gAa	7/14	0.175322710669383	2	FACETS	0.674	0.551	0.813	0.337	0.275	0.407	SUBCLONAL	1	TRUE	0	0.233427142513196	2		274	432	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235879	108235879	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139379666	NA	P-0033605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	40	420	0	ENST00000278616.4:c.8921C>T	p.Pro2974Leu	p.P2974L	ENST00000278616	NM_000051.3	2974	cCg/cTg	62/63	1	2	FACETS	0.457	0.378	0.545	0.457	0.378	0.545	SUBCLONAL	1	TRUE	1	0.233427142513196	2		420	750	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636438	21636438	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	53	629	0	ENST00000421138.2:c.572C>A	p.Pro191Gln	p.P191Q	ENST00000421138		191	cCa/cAa	7/16	1	2	FACETS	0.499	0.424	0.582	0.499	0.424	0.582	SUBCLONAL	1	TRUE	1	0.233427142513196	2		629	910	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434477	110434477	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747968639	NA	P-0033605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	124	498	0	ENST00000375856.3:c.3924del	p.Pro1309ArgfsTer22	p.P1309Rfs*22	ENST00000375856	NM_003749.2	1308	ggG/gg	1/2	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.233427142513196	2		498	949	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019471	42019471	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	75	574	0	ENST00000219905.7:c.3524C>A	p.Pro1175His	p.P1175H	ENST00000219905	NM_001164273.1	1175	cCc/cAc	10/24	1	2	FACETS	0.647	0.565	0.736	0.647	0.565	0.736	SUBCLONAL	1	TRUE	1	0.233427142513196	2		574	993	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28934577	NA	P-0033605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	142	617	0	ENST00000269305.4:c.770T>C	p.Leu257Pro	p.L257P	ENST00000269305	NM_001126112.2	257	cTg/cCg	7/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.233427142513196	2		617	1098	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40371848	40371848	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143092033	NA	P-0033605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1370	84	885	0	ENST00000293328.3:c.563C>T	p.Pro188Leu	p.P188L	ENST00000293328	NM_012448.3	188	cCg/cTg	6/19	1	2	FACETS	0.495	0.435	0.56	0.495	0.435	0.56	SUBCLONAL	1	TRUE	1	0.233427142513196	2		885	1454	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821924	59821924	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1567781600	NA	P-0033605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	65	433	0	ENST00000259008.2:c.2126T>C	p.Leu709Pro	p.L709P	ENST00000259008	NM_032043.2	709	cTc/cCc	15/20	1	2	FACETS	0.884	0.766	1	0.884	0.766	1	CLONAL	1	TRUE	1	0.233427142513196	2		433	630	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615748	1615748	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139492270	NA	P-0033605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	128	737	1	ENST00000344749.5:c.1523C>T	p.Thr508Met	p.T508M	ENST00000344749	NM_001136139.2	508	aCg/aTg	17/19	1	2	FACETS	0.814	0.735	0.897	0.814	0.735	0.897	CLONAL	1	TRUE	1	0.233427142513196	2		738	1348	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222853	5222853	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	86	457	0	ENST00000357368.4:c.2950C>T	p.Pro984Ser	p.P984S	ENST00000357368	NM_002850.3	984	Ccg/Tcg	18/38	1	2	FACETS	0.847	0.748	0.953	0.847	0.748	0.953	CLONAL	1	TRUE	1	0.233427142513196	2		457	870	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794950	42794950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141594034	NA	P-0033605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	145	693	1	ENST00000575354.2:c.2030G>A	p.Arg677Gln	p.R677Q	ENST00000575354	NM_015125.3	677	cGg/cAg	10/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.233427142513196	2		694	1191	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648410	30648410	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	81	434	0	ENST00000295754.5:c.35T>A	p.Leu12Gln	p.L12Q	ENST00000295754	NM_003242.5	12	cTg/cAg	1/7	1	2	FACETS	0.859	0.756	0.97	0.859	0.756	0.97	CLONAL	1	TRUE	1	0.233427142513196	2		434	808	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588757	52588757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269557269	NA	P-0033605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	102	371	0	ENST00000394830.3:c.4271C>T	p.Pro1424Leu	p.P1424L	ENST00000394830	NM_018313.4	1424	cCg/cTg	27/30	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.233427142513196	2		371	710	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189860	66189860	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs144528528	NA	P-0033605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	58	490	0	ENST00000273854.3:c.3086A>G	p.Gln1029Arg	p.Q1029R	ENST00000273854	NM_004439.5	1029	cAg/cGg	18/18	1	2	FACETS	0.699	0.6	0.808	0.699	0.6	0.808	SUBCLONAL	1	TRUE	1	0.233427142513196	2		490	711	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057042	180057042	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	94	682	1	ENST00000261937.6:c.577G>A	p.Val193Met	p.V193M	ENST00000261937	NM_182925.4	193	Gtg/Atg	5/30	1	2	FACETS	0.738	0.655	0.827	0.738	0.655	0.827	SUBCLONAL	1	TRUE	1	0.233427142513196	2		683	1091	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398830	398830	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	82	411	0	ENST00000380956.4:c.640T>C	p.Cys214Arg	p.C214R	ENST00000380956	NM_001195286.1	214	Tgc/Cgc	6/9	NA	2	FACETS	0.947	0.834	1			1	INDETERMINATE	1	TRUE	NA	0.233427142513196	2		411	742	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140508764	140508764	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	95	436	0	ENST00000288602.6:c.536A>G	p.Asp179Gly	p.D179G	ENST00000288602	NM_004333.4	179	gAc/gGc	4/18	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.233427142513196	2		436	769	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874196	151874196	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	63	480	0	ENST00000262189.6:c.8342T>C	p.Ile2781Thr	p.I2781T	ENST00000262189	NM_170606.2	2781	aTt/aCt	38/59	1	2	FACETS	0.72	0.621	0.827	0.72	0.621	0.827	SUBCLONAL	1	TRUE	1	0.233427142513196	2		480	750	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484207	8484207	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773612496	NA	P-0033605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	106	494	1	ENST00000356435.5:c.3325C>T	p.Arg1109Cys	p.R1109C	ENST00000356435		1109	Cgt/Tgt	19/35	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.233427142513196	2		495	881	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753937	133753937	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	86	455	0	ENST00000318560.5:c.1406A>G	p.Tyr469Cys	p.Y469C	ENST00000318560	NM_005157.4	469	tAt/tGt	8/11	1	2	FACETS	0.912	0.806	1	0.912	0.806	1	CLONAL	1	TRUE	1	0.233427142513196	2		455	808	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933209	39933209	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	161	399	0	ENST00000378444.4:c.1390A>G	p.Thr464Ala	p.T464A	ENST00000378444	NM_001123385.1	464	Acg/Gcg	4/15	1	1	FACETS	0.814	0.748	0.883	1	0.99	1	CLONAL	2	TRUE	0	0.233427142513196	1		399	748	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426111	47426111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	66	377	4	ENST00000377045.4:c.631C>T	p.Arg211Cys	p.R211C	ENST00000377045	NM_001654.4	211	Cgc/Tgc	7/16	1	1	FACETS	0.681	0.59	0.779	0.681	0.59	0.779	SUBCLONAL	1	TRUE	0	0.233427142513196	1		381	734	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0033609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	379	444	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.376477309047395	5	FACETS	0.975	0.935	1	0.78	0.748	0.811	CLONAL	4	TRUE	0	0.520809073957385	5		444	665	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257104	198257104	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs759773104	NA	P-0033609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	106	450	0	ENST00000335508.6:c.3838C>G	p.Leu1280Val	p.L1280V	ENST00000335508	NM_012433.2	1280	Ctc/Gtc	25/25	1	2	FACETS	0.915	0.825	1	0.915	0.825	1	CLONAL	1	TRUE	1	0.520809073957385	2		450	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0033609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	344	506	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.435698230085372	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.520809073957385	1		506	962	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226573362	226573362	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	188	367	0	ENST00000366794.5:c.854A>T	p.Asp285Val	p.D285V	ENST00000366794	NM_001618.3	285	gAt/gTt	7/23	0.520809073957385	3	FACETS	0.869	0.802	0.939	0.435	0.401	0.47	CLONAL	1	TRUE	1	0.520809073957385	3		367	1047	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744035	41744035	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1302	283	514	0	ENST00000301178.4:c.970C>A	p.Leu324Ile	p.L324I	ENST00000301178	NM_021913.4	324	Ctt/Att	7/20	0.520809073957385	3	FACETS	0.864	0.81	0.92	0.432	0.405	0.46	CLONAL	1	TRUE	1	0.520809073957385	3		514	1585	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155257	185155257	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	79	306	0	ENST00000265026.3:c.498G>T	p.Glu166Asp	p.E166D	ENST00000265026	NM_004721.4	166	gaG/gaT	3/14	1	2	FACETS	0.396	0.348	0.448	0.396	0.348	0.448	SUBCLONAL	1	TRUE	1	0.520809073957385	2		306	766	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638006	176638006	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs756688297	NA	P-0033609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	195	513	0	ENST00000439151.2:c.2606A>T	p.Tyr869Phe	p.Y869F	ENST00000439151	NM_022455.4	869	tAc/tTc	5/23	0.486630238619482	1	FACETS	0.851	0.791	0.912	0.851	0.791	0.912	CLONAL	1	TRUE	0	0.520809073957385	1		513	651	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412743	63412743	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0033609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	223	475	0	ENST00000330258.3:c.424A>T	p.Arg142Ter	p.R142*	ENST00000330258	NM_152424.3	142	Aga/Tga	2/2	0.326810160689236	1	FACETS	0.695	0.648	0.744	0.695	0.648	0.744	SUBCLONAL	1	TRUE	0	0.520809073957385	1		475	911	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0033610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	114	340	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.811785684770639	2		340	262	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0033610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	277	335	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.811785684770639	3	FACETS	0.993	0.947	1	0.993	0.947	1	CLONAL	2	TRUE	1	0.811785684770639	3		335	483	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648248	206648248	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	159	576	0	ENST00000367120.3:c.269C>T	p.Ser90Phe	p.S90F	ENST00000367120	NM_014002.3	90	tCc/tTc	5/22	0.811785684770639	3	FACETS	0.951	0.876	1	0.476	0.438	0.515	CLONAL	1	TRUE	1	0.811785684770639	3		576	579	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543829	212543829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771154734	NA	P-0033610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	139	325	0	ENST00000342788.4:c.1570C>T	p.Arg524Cys	p.R524C	ENST00000342788	NM_005235.2	524	Cgc/Tgc	13/28	0.8035505005753	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.811785684770639	1		325	203	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953840	131953840	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0033610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	137	329	0	ENST00000265335.6:c.3243T>G	p.Tyr1081Ter	p.Y1081*	ENST00000265335		1081	taT/taG	21/25	0.118272473278371	4	FACETS	0.813	0.748	0.88	0.813	0.748	0.88	INDETERMINATE	2	TRUE	2	0.811785684770639	4		329	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0033617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	441	688	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	NA	2	FACETS	0.922	0.888	0.956			1	INDETERMINATE	2	TRUE	NA	0.621779969452712	2		688	769	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0033617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	285	474	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.501530786171642	3	FACETS	0.779	0.736	0.823	0.779	0.736	0.823	SUBCLONAL	2	TRUE	1	0.621779969452712	3		474	771	SUCCESS
APC	324	MSKCC	GRCh37	5	112175324	112175324	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1211642532	NA	P-0033617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	171	254	0	ENST00000257430.4:c.4033G>T	p.Glu1345Ter	p.E1345*	ENST00000257430	NM_000038.5	1345	Gaa/Taa	16/16	0.475117519684411	3	FACETS	1	0.987	1	0.801	0.753	0.849	CLONAL	2	TRUE	0	0.621779969452712	3		254	300	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295801	212295801	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1423325504	NA	P-0033617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	121	492	0	ENST00000342788.4:c.2512C>T	p.Arg838Ter	p.R838*	ENST00000342788	NM_005235.2	838	Cga/Tga	21/28	0.341389153970974	1	FACETS	0.514	0.466	0.564	0.514	0.466	0.564	INDETERMINATE	1	TRUE	0	0.621779969452712	1		492	522	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346157	89346158	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs878855327	NA	P-0033617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	41	290	0	ENST00000301030.4:c.6792dup	p.Ala2265ArgfsTer8	p.A2265Rfs*8	ENST00000301030	NM_001256183.1	2264	-/C	9/13	1	2	FACETS	0.673	0.567	0.788	0.673	0.567	0.788	SUBCLONAL	1	TRUE	1	0.621779969452712	2		290	196	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845063	128845063	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	175	655	0	ENST00000249373.3:c.557A>T	p.Lys186Met	p.K186M	ENST00000249373	NM_005631.4	186	aAg/aTg	3/12	NA	2	FACETS	0.84	0.776	0.906			1	INDETERMINATE	1	TRUE	NA	0.621779969452712	2		655	670	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247364	153247366	+	missense_variant	Missense_Mutation	TNP	CTC	CTC	TTT	novel	NA	P-0033617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	78	255	0	ENST00000281708.4:c.1436_1438delinsAAA	p.Arg479_Asp480delinsGlnAsn	p.R479_D480delinsQN	ENST00000281708	NM_033632.3	479	cGAGat/cAAAat	10/12	1	2	FACETS	0.85	0.755	0.951	0.85	0.755	0.951	CLONAL	1	TRUE	1	0.621779969452712	2		255	295	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0033618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	680	582	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.730500277698694	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.730500277698694	2		582	833	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867546	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGC	GGCGGCGGC	-	rs11466445	NA	P-0033618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	14	14	0	ENST00000374994.4:c.70_78del	p.Ala24_Ala26del	p.A24_A26del	ENST00000374994	NM_004612.2	17	ctGGCGGCGGCg/ctg	1/9	0.730500277698694	3	FACETS	1	0.889	1	0.459	0.349	0.577	CLONAL	1	TRUE	0	0.730500277698694	3		14	38	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121265	29121265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368570187	NA	P-0033618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	436	862	1	ENST00000328354.6:c.410G>A	p.Arg137Gln	p.R137Q	ENST00000328354	NM_007194.3	137	cGa/cAa	3/15	0.730500277698694	2	FACETS	0.987	0.956	1	0.987	0.956	1	CLONAL	2	TRUE	0	0.730500277698694	2		863	605	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856439	111856439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	335	183	0	ENST00000341259.2:c.490G>A	p.Gly164Arg	p.G164R	ENST00000341259	NM_005475.2	164	Ggg/Agg	2/8	0.727544246642277	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.730500277698694	2		183	415	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763498	41763498	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	236	506	0	ENST00000301178.4:c.2297A>T	p.Asn766Ile	p.N766I	ENST00000301178	NM_021913.4	766	aAt/aTt	19/20	0.730500277698694	3	FACETS	1	0.977	1	0.365	0.341	0.389	CLONAL	1	TRUE	0	0.730500277698694	3		506	806	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139006	37139006	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs778700298	NA	P-0033618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	162	658	0	ENST00000373509.5:c.346T>G	p.Phe116Val	p.F116V	ENST00000373509	NM_002648.3	116	Ttc/Gtc	4/6	0.730500277698694	2	FACETS	0.524	0.481	0.569	0.262	0.24	0.285	SUBCLONAL	1	TRUE	0	0.730500277698694	2		658	846	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111499	8111500	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0033619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	177	555	0	ENST00000346208.3:c.987dup	p.Arg330GlufsTer22	p.R330Efs*22	ENST00000346208		329	agg/aGgg	5/6	0.662928719322662	3	FACETS	0.664	0.611	0.719	0.332	0.305	0.36	SUBCLONAL	1	TRUE	1	0.662928719322662	3		555	1071	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417947	32417947	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1423753702	NA	P-0033619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	100	427	0	ENST00000332351.3:c.1105C>T	p.Arg369Ter	p.R369*	ENST00000332351	NM_024426.4	369	Cga/Tga	7/10	0.468480190043295	3	FACETS	0.93	0.836	1	0.465	0.418	0.515	CLONAL	1	TRUE	1	0.662928719322662	3		427	432	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924997	49924997	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0033619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	88	520	0	ENST00000296474.3:c.3948-2A>G		p.X1316_splice	ENST00000296474	NM_002447.2	1316			0.601570356678867	3	FACETS	0.616	0.546	0.69	0.308	0.273	0.345	SUBCLONAL	1	TRUE	1	0.662928719322662	3		520	574	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867546	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGC	GGCGGCGGC	-	rs11466445	NA	P-0033621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	11	14	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	0.847	1	1	0.847	1	CLONAL	1	TRUE	1	0.48	2		14	35	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099931	27099931	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	77	513	0	ENST00000324856.7:c.3810del	p.Asn1270LysfsTer19	p.N1270Kfs*19	ENST00000324856	NM_006015.4	1270	aaT/aa	15/20	1	2	FACETS	0.671	0.591	0.757	0.671	0.591	0.757	SUBCLONAL	1	TRUE	1	0.48	2		513	478	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183844	10183844	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1553619461	NA	P-0033621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	75	523	0	ENST00000256474.2:c.313A>C	p.Thr105Pro	p.T105P	ENST00000256474	NM_000551.3	105	Acg/Ccg	1/3	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.48	NA		523	452	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158239	47158242	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TTCT	TTCT	-	rs1553699115	NA	P-0033621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	50	341	0	ENST00000409792.3:c.4457_4460del	p.Lys1486ArgfsTer28	p.K1486Rfs*28	ENST00000409792	NM_014159.6	1486	aAGAAg/ag	4/21	0.3	1	FACETS	0.492	0.419	0.571	0.492	0.419	0.571	SUBCLONAL	1	TRUE	0	0.48	1		341	322	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794062	42794062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	59	486	0	ENST00000575354.2:c.1423G>A	p.Glu475Lys	p.E475K	ENST00000575354	NM_015125.3	475	Gag/Aag	9/20	0.388240381108558	3	FACETS	0.556	0.478	0.64	0.278	0.239	0.32	SUBCLONAL	1	TRUE	1	0.443568781466176	3		486	585	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	93	481	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	1	2	FACETS	0.899	0.799	1	0.899	0.799	1	CLONAL	1	TRUE	1	0.284179630533327	2		481	728	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0033630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	150	563	1	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.284179630533327	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.284179630533327	1		564	852	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967635	26967635	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	32	394	0	ENST00000381527.3:c.778G>T	p.Gly260Ter	p.G260*	ENST00000381527	NM_001260.1	260	Gga/Tga	7/13	1	2	FACETS	0.405	0.328	0.493	0.405	0.328	0.493	SUBCLONAL	1	TRUE	1	0.284179630533327	2		394	556	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247105	53247105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	76	443	0	ENST00000375401.3:c.395G>A	p.Arg132His	p.R132H	ENST00000375401	NM_004187.3	132	cGt/cAt	4/26	0.284179630533327	1	FACETS	0.682	0.598	0.772	0.682	0.598	0.772	SUBCLONAL	1	TRUE	0	0.284179630533327	1		443	673	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696450	47696450	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	23	501	0	ENST00000347630.2:c.373T>G	p.Phe125Val	p.F125V	ENST00000347630	NM_001007230.1	125	Ttt/Gtt	6/11	0.124451463665094	1	FACETS	0.412	0.32	0.518	0.412	0.32	0.518	INDETERMINATE	1	TRUE	0	0.23	1		501	430	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164811	47164811	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	68	419	0	ENST00000409792.3:c.1315C>G	p.Pro439Ala	p.P439A	ENST00000409792	NM_014159.6	439	Cct/Gct	3/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.23	2		419	424	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0033644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	155	503	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	0.637091785778855	2		503	471	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070577	67070578	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	104	196	0	ENST00000412916.2:c.207dup	p.Pro70SerfsTer13	p.P70Sfs*13	ENST00000412916		67	-/T	3/6	0.563825669632384	1	FACETS	0.984	0.901	1	0.984	0.901	1	CLONAL	1	TRUE	0	0.637091785778855	1		196	226	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0033644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	346	400	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.637091785778855	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.637091785778855	2		400	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0033644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	213	594	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.637091785778855	1	FACETS	0.887	0.832	0.942	0.887	0.832	0.942	CLONAL	1	TRUE	0	0.637091785778855	1		594	514	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947596	48947596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1566196458	NA	P-0033644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	125	313	0	ENST00000267163.4:c.1183C>T	p.Gln395Ter	p.Q395*	ENST00000267163	NM_000321.2	395	Caa/Taa	12/27	0.637091785778855	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.637091785778855	1		313	247	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0033644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	248	535	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	1	2	FACETS	0.958	0.898	1	0.958	0.898	1	CLONAL	1	TRUE	1	0.637091785778855	2		535	813	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111433	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0033644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	113	298	0	ENST00000346208.3:c.922-3C>T		p.X308_splice	ENST00000346208		308			0.617381659184707	5	FACETS	0.923	0.83	1			1	CLONAL	1	TRUE	NA	0.637091785778855	5		298	752	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210837	133210837	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	203	560	0	ENST00000320574.5:c.5939G>A	p.Trp1980Ter	p.W1980*	ENST00000320574	NM_006231.2	1980	tGg/tAg	43/49	1	2	FACETS	0.9	0.838	0.964	0.9	0.838	0.964	CLONAL	1	TRUE	1	0.637091785778855	2		560	708	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842378	68842378	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	196	434	1	ENST00000261769.5:c.440del	p.Pro147LeufsTer68	p.P147Lfs*68	ENST00000261769	NM_004360.3	147	Cct/ct	4/16	0.637091785778855	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.637091785778855	1		435	413	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0033645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	42	359	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.399	0.334	0.472	0.399	0.334	0.472	SUBCLONAL	1	TRUE	1	0.549051826640509	2		359	383	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	172	544	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.510433980228022	2	FACETS	1	0.985	1	0.622	0.576	0.668	CLONAL	1	TRUE	0	0.549051826640509	2		544	504	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184160	56184163	+	frameshift_variant	Frame_Shift_Del	DEL	CAAT	CAAT	-	rs745497809	NA	P-0033645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	201	333	0	ENST00000399503.3:c.4367_4370del	p.Asn1456IlefsTer4	p.N1456Ifs*4	ENST00000399503	NM_005921.1	1455	tcCAAT/tc	19/20	0.490593282637098	2	FACETS	0.857	0.805	0.91	0.857	0.805	0.91	CLONAL	2	TRUE	0	0.549051826640509	2		333	427	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871792	12871792	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	36	187	0	ENST00000228872.4:c.509del	p.Thr170LysfsTer55	p.T170Kfs*55	ENST00000228872	NM_004064.3	170	aCa/aa	2/3	0.283530735442693	1	FACETS	0.529	0.439	0.626	0.529	0.439	0.626	INDETERMINATE	1	TRUE	0	0.549051826640509	1		187	180	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117945	70117945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	15	250	0	ENST00000245479.2:c.413C>T	p.Thr138Met	p.T138M	ENST00000245479	NM_000346.3	138	aCg/aTg	1/3	0.16387210369657	1	FACETS	0.141	0.103	0.187	0.141	0.103	0.187	INDETERMINATE	1	TRUE	0	0.549051826640509	1		250	281	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0033646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	92	280	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.3	3	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	1	0.2	3		280	463	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0033646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	92	316	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.3	3	FACETS	0.996	0.888	1	0.996	0.888	1	CLONAL	2	TRUE	1	0.2	3		316	508	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540968	187540968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	35	260	0	ENST00000441802.2:c.6772G>A	p.Asp2258Asn	p.D2258N	ENST00000441802	NM_005245.3	2258	Gac/Aac	10/27	NA	2	FACETS	0.916	0.752	1			1	INDETERMINATE	1	TRUE	NA	0.2	2		260	382	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343635	343635	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375187798	NA	P-0033646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	93	598	11	ENST00000262320.3:c.2039G>A	p.Arg680Gln	p.R680Q	ENST00000262320	NM_003502.3	680	cGg/cAg	8/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.2	2		609	800	SUCCESS
RET	5979	MSKCC	GRCh37	10	43613864	43613864	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	65	586	0	ENST00000355710.3:c.2328C>A	p.Phe776Leu	p.F776L	ENST00000355710	NM_020975.4	776	ttC/ttA	13/20	1	2	FACETS	0.842	0.729	0.965	0.842	0.729	0.965	CLONAL	1	TRUE	1	0.2	2		586	772	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446435	49446436	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACGTAC	novel	NA	P-0033646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	50	424	0	ENST00000301067.7:c.1164_1169dup	p.Tyr389_Val390dup	p.Y389_V390dup	ENST00000301067	NM_003482.3	389	gtt/gtGTACGTt	9/54	0.244593734809724	3	FACETS	0.811	0.687	0.948	0.406	0.343	0.474	CLONAL	1	TRUE	1	0.2	3		424	678	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463296	25463296	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	31	302	0	ENST00000264709.3:c.2197G>C	p.Glu733Gln	p.E733Q	ENST00000264709	NM_175629.2	733	Gag/Cag	19/23	1	2	FACETS	0.695	0.562	0.846	0.695	0.562	0.846	SUBCLONAL	1	TRUE	1	0.2	2		302	446	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0033649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	100	773	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.778403909963024	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.800844551947256	1		773	143	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0033649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	91	489	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.800844551947256	2		489	188	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46215212	46215212	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	35	293	2	ENST00000334344.6:c.647C>T	p.Ser216Phe	p.S216F	ENST00000334344	NM_152641.2	216	tCc/tTc	6/21	NA	2	FACETS	1	0.913	1			1	INDETERMINATE	1	TRUE	NA	0.800844551947256	2		295	79	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467933	50467933	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	45	436	0	ENST00000331340.3:c.1168C>T	p.Pro390Ser	p.P390S	ENST00000331340	NM_006060.4	390	Ccg/Tcg	8/8	0.312788057568951	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.800844551947256	0		436	83	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476406	88476406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1395756451	NA	P-0033649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	48	526	0	ENST00000360948.2:c.1726G>A	p.Asp576Asn	p.D576N	ENST00000360948	NM_001012338.2	576	Gat/Aat	15/19	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.800844551947256	2		526	87	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411576	63411576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	27	472	0	ENST00000330258.3:c.1591C>T	p.Arg531Ter	p.R531*	ENST00000330258	NM_152424.3	531	Cga/Tga	2/2	1	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.800844551947256	1		472	35	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390071	89390071	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760135022	NA	P-0033649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	37	338	1	ENST00000336596.2:c.820C>T	p.Arg274Ter	p.R274*	ENST00000336596	NM_005233.5	274	Cga/Tga	4/17	0.256996252276604	1	FACETS	0.71	0.611	0.81	0.71	0.611	0.81	INDETERMINATE	1	TRUE	0	0.800844551947256	1		339	78	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367239	50367239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1045233686	NA	P-0033649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	10	301	0	ENST00000331340.3:c.46G>A	p.Glu16Lys	p.E16K	ENST00000331340	NM_006060.4	16	Gaa/Aaa	3/8	0.312788057568951	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.800844551947256	0		301	54	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909601	76909601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	59	414	2	ENST00000373344.5:c.4304C>T	p.Ser1435Phe	p.S1435F	ENST00000373344	NM_000489.3	1435	tCc/tTc	14/35	1	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.800844551947256	1		416	66	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041220	29041220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1351200892	NA	P-0033649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	38	841	1	ENST00000282397.4:c.208G>A	p.Glu70Lys	p.E70K	ENST00000282397	NM_002019.4	70	Gaa/Aaa	3/30	0.387847613980135	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.800844551947256	0		842	128	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483916	88483916	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	48	830	1	ENST00000360948.2:c.1654G>A	p.Val552Ile	p.V552I	ENST00000360948	NM_001012338.2	552	Gtc/Atc	14/19	1	2	FACETS	0.714	0.614	0.819	0.714	0.614	0.819	SUBCLONAL	1	TRUE	1	0.800844551947256	2		831	168	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220690	2220690	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	15	664	0	ENST00000326181.6:c.307C>G	p.Leu103Val	p.L103V	ENST00000326181	NM_032271.2	103	Ctg/Gtg	5/21	0.800844551947256	1	FACETS	0.162	0.119	0.212	0.162	0.119	0.212	SUBCLONAL	1	TRUE	0	0.800844551947256	1		664	139	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639093	3639093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775915651	NA	P-0033649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	92	791	1	ENST00000294008.3:c.4546G>A	p.Gly1516Arg	p.G1516R	ENST00000294008	NM_032444.2	1516	Ggg/Agg	12/15	0.800844551947256	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.800844551947256	1		792	124	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469955	25469955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	171	838	1	ENST00000264709.3:c.1087C>T	p.Pro363Ser	p.P363S	ENST00000264709	NM_175629.2	363	Ccc/Tcc	9/23	0.554352748167271	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.800844551947256	1		839	220	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566769	212566769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	26	522	0	ENST00000342788.4:c.1412C>T	p.Thr471Ile	p.T471I	ENST00000342788	NM_005235.2	471	aCc/aTc	12/28	0.256996252276604	1	FACETS	0.573	0.471	0.679	0.573	0.471	0.679	INDETERMINATE	1	TRUE	0	0.800844551947256	1		522	68	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247417	71247418	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	114	582	1	ENST00000318789.4:c.115_116delinsAA	p.Gly39Lys	p.G39K	ENST00000318789	NM_032682.5	39	GGa/AAa	6/21	0.256996252276604	1	FACETS	0.745	0.687	0.804	0.745	0.687	0.804	INDETERMINATE	1	TRUE	0	0.800844551947256	1		583	229	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729963	41729963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	60	840	0	ENST00000242208.4:c.566G>A	p.Gly189Glu	p.G189E	ENST00000242208	NM_002192.2	189	gGg/gAg	3/3	0.312788057568951	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.800844551947256	0		840	165	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76876001	76876001	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0033649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3	26	223	0	ENST00000373344.5:c.5135-1G>A		p.X1712_splice	ENST00000373344	NM_000489.3	1712			1	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.800844551947256	1		223	29	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0033650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	371	468	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.618770869931445	3	FACETS	0.931	0.888	0.974	0.931	0.888	0.974	CLONAL	2	TRUE	1	0.623848830471674	3		468	838	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16021266	16021267	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	TTTTACA	novel	NA	P-0033650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	131	374	0	ENST00000268712.3:c.1984_1990dup	p.Asn664MetfsTer2	p.N664Mfs*2	ENST00000268712	NM_006311.3	664	aac/aTGTAAAAac	18/46	1	2	FACETS	0.743	0.677	0.812	0.743	0.677	0.812	SUBCLONAL	1	TRUE	1	0.623848830471674	2		374	565	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144108	11144108	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	240	631	0	ENST00000358026.2:c.3689A>T	p.Gln1230Leu	p.Q1230L	ENST00000358026	NM_001128849.1	1230	cAg/cTg	26/36	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.623848830471674	2		631	615	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0033651-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	227	721	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.492947740028496	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.492947740028496	1		721	679	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654770	29654772	+	frameshift_variant	Frame_Shift_Del	DEL	AAC	AAC	T	novel	NA	P-0033651-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	102	375	0	ENST00000356175.3:c.5459_5461delinsT	p.Gln1820LeufsTer20	p.Q1820Lfs*20	ENST00000356175	NM_000267.3	1820	cAACac/cTac	37/57	0.492947740028496	1	FACETS	0.962	0.871	1	0.962	0.871	1	CLONAL	1	TRUE	0	0.492947740028496	1		375	324	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369169	118369169	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	270	434	0	ENST00000534358.1:c.5887C>T	p.Arg1963Ter	p.R1963*	ENST00000534358	NM_005933.3	1963	Cga/Tga	22/36	0.84505183451535	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.84505183451535	1		434	353	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188200	10188200	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs5030811	NA	P-0033656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	269	523	0	ENST00000256474.2:c.343C>T	p.His115Tyr	p.H115Y	ENST00000256474	NM_000551.3	115	Cac/Tac	2/3	0.292834089309549	3	FACETS	0.948	0.893	1	0.632	0.595	0.67	CLONAL	2	TRUE	0	0.440364939166527	3		523	786	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717695	89717696	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1060500115	NA	P-0033656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	225	431	0	ENST00000371953.3:c.723dup	p.Glu242Ter	p.E242*	ENST00000371953	NM_000314.4	240	-/T	7/9	0.33710534612921	4	FACETS	1	0.983	1	0.57	0.533	0.607	CLONAL	2	TRUE	0	0.440364939166527	4		431	646	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294451	1294451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773758089	NA	P-0033656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	94	483	0	ENST00000310581.5:c.550G>A	p.Ala184Thr	p.A184T	ENST00000310581	NM_198253.2	184	Gcc/Acc	2/16	0.440364939166527	5	FACETS	0.642	0.569	0.719			1	SUBCLONAL	1	TRUE	NA	0.440364939166527	5		483	1105	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798139	32798139	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	143	672	0	ENST00000374899.4:c.1540G>T	p.Ala514Ser	p.A514S	ENST00000374899	NM_018833.2	514	Gcc/Tcc	9/12	0.440364939166527	5	FACETS	1	0.946	1	0.351	0.32	0.385	CLONAL	1	TRUE	2	0.440364939166527	5		672	1023	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992750	68992750	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0033656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1235	202	648	0	ENST00000288368.4:c.1715C>G	p.Ser572Ter	p.S572*	ENST00000288368	NM_024870.2	572	tCa/tGa	16/40	0.440364939166527	6	FACETS	1	0.982	1	0.24	0.222	0.259	CLONAL	1	TRUE	1	0.440364939166527	6		648	1437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0033657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	35	576	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		576	502	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	46	264	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		264	135	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0033665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	364	607	2	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.805195707133944	2	FACETS	0.996	0.967	1	0.996	0.967	1	CLONAL	2	TRUE	0	0.805195707133944	2		609	454	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324690	31324690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1399078190	NA	P-0033665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	12	112	1	ENST00000412585.2:c.118G>A	p.Gly40Ser	p.G40S	ENST00000412585	NM_005514.6	40	Ggc/Agc	2/8	1	2	FACETS	0.42	0.3	0.561	0.42	0.3	0.561	SUBCLONAL	1	TRUE	1	0.805195707133944	2		113	71	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324201	31324201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1071652	NA	P-0033665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	11	151	0	ENST00000412585.2:c.362G>A	p.Ser121Asn	p.S121N	ENST00000412585	NM_005514.6	121	aGc/aAc	3/8	1	2	FACETS	0.183	0.127	0.253	0.183	0.127	0.253	SUBCLONAL	1	TRUE	1	0.805195707133944	2		151	149	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100371	8100372	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0033665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	209	741	2	ENST00000346208.3:c.345_346delinsAA	p.Ser115_Pro116delinsArgThr	p.S115_P116delinsRT	ENST00000346208		115	agCCcc/agAAcc	3/6	1	2	FACETS	0.929	0.869	0.99	0.929	0.869	0.99	CLONAL	1	TRUE	1	0.805195707133944	2		743	559	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115822	8115822	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	171	542	2	ENST00000346208.3:c.1168T>A	p.Ser390Thr	p.S390T	ENST00000346208		390	Tcg/Acg	6/6	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.805195707133944	2		544	419	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869490	102869490	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	134	380	1	ENST00000307046.8:c.151G>T	p.Glu51Ter	p.E51*	ENST00000307046	NM_001111285.1	51	Gag/Tag	2/4	1	2	FACETS	0.973	0.896	1	0.973	0.896	1	CLONAL	1	TRUE	1	0.805195707133944	2		381	342	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120805836	120805836	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	269	642	1	ENST00000257552.2:c.242C>A	p.Ser81Ter	p.S81*	ENST00000257552	NM_002442.3	81	tCg/tAg	4/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.805195707133944	2		643	623	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209004	133209005	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0033665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	127	687	1	ENST00000320574.5:c.6226_6227delinsCT	p.Gly2076Leu	p.G2076L	ENST00000320574	NM_006231.2	2076	GGc/CTc	45/49	1	2	FACETS	0.909	0.834	0.986	0.909	0.834	0.986	CLONAL	1	TRUE	1	0.805195707133944	2		688	347	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033949	49033949	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0033665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	98	392	0	ENST00000267163.4:c.2086A>T	p.Arg696Ter	p.R696*	ENST00000267163	NM_000321.2	696	Aga/Tga	20/27	0.79369077582235	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.805195707133944	1		392	135	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633326	3633326	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	181	819	0	ENST00000294008.3:c.4925A>C	p.His1642Pro	p.H1642P	ENST00000294008	NM_032444.2	1642	cAt/cCt	14/15	1	2	FACETS	0.925	0.861	0.99	0.925	0.861	0.99	CLONAL	1	TRUE	1	0.805195707133944	2		819	486	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217063	2217063	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	157	607	1	ENST00000398665.3:c.2518C>T	p.Leu840Phe	p.L840F	ENST00000398665	NM_032482.2	840	Ctt/Ttt	21/28	1	2	FACETS	0.926	0.858	0.996	0.926	0.858	0.996	CLONAL	1	TRUE	1	0.805195707133944	2		608	421	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298032	15298033	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	237	788	1	ENST00000263388.2:c.1723dup	p.Thr575AsnfsTer48	p.T575Nfs*48	ENST00000263388	NM_000435.2	575	acg/aAcg	11/33	1	2	FACETS	0.975	0.916	1	0.975	0.916	1	CLONAL	1	TRUE	1	0.805195707133944	2		789	604	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300092	15300092	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	163	658	0	ENST00000263388.2:c.1184G>T	p.Cys395Phe	p.C395F	ENST00000263388	NM_000435.2	395	tGc/tTc	7/33	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.805195707133944	2		658	398	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138431130	138431130	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	67	367	1	ENST00000289153.2:c.1319G>T	p.Trp440Leu	p.W440L	ENST00000289153	NM_006219.2	440	tGg/tTg	8/22	0.735422610620226	3	FACETS	1	0.913	1	0.521	0.459	0.586	CLONAL	1	TRUE	1	0.805195707133944	3		368	224	SUCCESS
ATR	545	MSKCC	GRCh37	3	142286985	142286985	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	75	442	1	ENST00000350721.4:c.71A>G	p.Glu24Gly	p.E24G	ENST00000350721	NM_001184.3	24	gAg/gGg	2/47	0.735422610620226	3	FACETS	0.975	0.865	1	0.487	0.432	0.545	CLONAL	1	TRUE	1	0.805195707133944	3		443	268	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253810	153253810	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	64	416	0	ENST00000281708.4:c.923G>T	p.Cys308Phe	p.C308F	ENST00000281708	NM_033632.3	308	tGt/tTt	6/12	0.79369077582235	1	FACETS	0.931	0.845	1	0.931	0.845	1	CLONAL	1	TRUE	0	0.805195707133944	1		416	102	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518242	187518242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	105	303	2	ENST00000441802.2:c.12452G>A	p.Cys4151Tyr	p.C4151Y	ENST00000441802	NM_005245.3	4151	tGc/tAc	25/27	0.79369077582235	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.805195707133944	1		305	150	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449862	149449862	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	148	622	0	ENST00000286301.3:c.1202C>A	p.Pro401His	p.P401H	ENST00000286301	NM_005211.3	401	cCc/cAc	9/22	1	2	FACETS	0.901	0.832	0.972	0.901	0.832	0.972	CLONAL	1	TRUE	1	0.805195707133944	2		622	408	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681084	117681084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	89	466	0	ENST00000368508.3:c.3536C>T	p.Ser1179Leu	p.S1179L	ENST00000368508	NM_002944.2	1179	tCa/tTa	23/43	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.805195707133944	2		466	216	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412179	116412179	+	intron_variant	Intron	SNP	A	A	G	novel	NA	P-0033665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	79	653	0	ENST00000397752.3:c.3028+136A>G		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.805195707133944	2		653	195	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74858903	74858903	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	248	786	2	ENST00000284811.8:c.301C>G	p.Leu101Val	p.L101V	ENST00000284811		101	Ctg/Gtg	4/4	0.805195707133944	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.805195707133944	2		788	291	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941988	44941988	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	30	206	0	ENST00000377967.4:c.3241del	p.Thr1081ProfsTer2	p.T1081Pfs*2	ENST00000377967	NM_021140.2	1080	Aaa/aa	22/29	1	1	FACETS	0.394	0.324	0.47	0.394	0.324	0.47	SUBCLONAL	1	TRUE	0	0.805195707133944	1		206	113	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0033672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	102	280	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	0.840677965354078	2		280	216	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0033672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	167	285	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.840677965354078	2		285	384	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246445	105246445	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	256	476	0	ENST00000349310.3:c.155T>A	p.Leu52His	p.L52H	ENST00000349310	NM_001014432.1	52	cTc/cAc	4/15	1	2	FACETS	0.967	0.912	1	0.967	0.912	1	CLONAL	1	TRUE	1	0.840677965354078	2		476	630	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644826	67644826	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	161	305	0	ENST00000264010.4:c.95del	p.Gly32AlafsTer30	p.G32Afs*30	ENST00000264010	NM_006565.3	31	Ggg/gg	3/12	0.840677965354078	1	FACETS	0.965	0.915	1	0.965	0.915	1	CLONAL	1	TRUE	0	0.840677965354078	1		305	230	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31451746	31451746	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	71	186	0	ENST00000344624.3:c.2576A>G	p.His859Arg	p.H859R	ENST00000344624		859	cAt/cGt	18/33	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.840677965354078	2		186	164	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738311	133738311	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	24	372	0	ENST00000318560.5:c.711G>A	p.Met237Ile	p.M237I	ENST00000318560	NM_005157.4	237	atG/atA	4/11	0.174480587794939	1	FACETS	0.083	0.064	0.104	0.083	0.064	0.104	INDETERMINATE	1	TRUE	0	0.840677965354078	1		372	400	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0033675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	275	589	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.774869231391529	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.774869231391529	1		589	414	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099406	157099426	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAGCAA	CAGCAGCAGCAGCAGCAGCAA	-	rs762617219	NA	P-0033675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	60	202	0	ENST00000346085.5:c.363_383del	p.Gln125_Gln131del	p.Q125_Q131del	ENST00000346085	NM_020732.3	115	CAGCAGCAGCAGCAGCAGCAA/-	1/20	1	2	FACETS	0.571	0.497	0.651	0.571	0.497	0.651	SUBCLONAL	1	TRUE	1	0.774869231391529	2		202	271	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913250	NA	P-0033675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	155	335	0	ENST00000369535.4:c.34G>A	p.Gly12Ser	p.G12S	ENST00000369535	NM_002524.4	12	Ggt/Agt	2/7	1	2	FACETS	0.964	0.892	1	0.964	0.892	1	CLONAL	1	TRUE	1	0.774869231391529	2		335	415	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604656	48604656	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	137	269	0	ENST00000342988.3:c.1478A>G	p.Asp493Gly	p.D493G	ENST00000342988	NM_005359.5	493	gAt/gGt	12/12	0.774869231391529	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.774869231391529	1		269	188	SUCCESS
APC	324	MSKCC	GRCh37	5	112173912	112173913	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs863225330	NA	P-0033675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	96	261	0	ENST00000257430.4:c.2624dup	p.Arg876AlafsTer36	p.R876Afs*36	ENST00000257430	NM_000038.5	874	tca/tcAa	16/16	1	2	FACETS	0.891	0.806	0.98	0.891	0.806	0.98	CLONAL	1	TRUE	1	0.774869231391529	2		261	278	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117600	70117601	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0033675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	176	400	1	ENST00000245479.2:c.72dup	p.Thr25HisfsTer227	p.T25Hfs*227	ENST00000245479	NM_000346.3	23	agc/agCc	1/3	0.774869231391529	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.774869231391529	1		401	266	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911624	114911624	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	263	306	0	ENST00000543371.1:c.1142A>T	p.Asn381Ile	p.N381I	ENST00000543371	NM_001198531.1	381	aAc/aTc	10/14	0.463797689288318	2	FACETS	0.771	0.735	0.807	0.771	0.735	0.807	INDETERMINATE	2	TRUE	0	0.774869231391529	2		306	440	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661996	227661996	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1218652396	NA	P-0033675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	82	426	0	ENST00000305123.5:c.1459C>T	p.Arg487Trp	p.R487W	ENST00000305123	NM_005544.2	487	Cgg/Tgg	1/2	1	2	FACETS	0.466	0.413	0.523	0.466	0.413	0.523	SUBCLONAL	1	TRUE	1	0.774869231391529	2		426	454	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	120	368	0	ENST00000263967.3:c.3062A>T	p.Tyr1021Phe	p.Y1021F	ENST00000263967	NM_006218.2	1021	tAc/tTc	21/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.774869231391529	2		368	276	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0033677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	87	336	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.312498484961372	6	FACETS	1	0.952	1	0.552	0.495	0.61	INDETERMINATE	2	TRUE	2	0.748716029401335	6		336	263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0033677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	303	582	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.694600065392066	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.748716029401335	2		582	375	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0033677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	68	264	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.748716029401335	2		264	156	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180991	108180991	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs876658989	NA	P-0033677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	105	343	0	ENST00000278616.4:c.5867T>A	p.Leu1956His	p.L1956H	ENST00000278616	NM_000051.3	1956	cTc/cAc	39/63	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.748716029401335	2		343	266	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948774	17948774	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	142	673	0	ENST00000458235.1:c.1668G>C	p.Lys556Asn	p.K556N	ENST00000458235	NM_000215.3	556	aaG/aaC	12/24	0.37787534156862	4	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.748716029401335	4		673	553	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938056	76938056	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	156	649	0	ENST00000373344.5:c.2692del	p.Asp898ThrfsTer7	p.D898Tfs*7	ENST00000373344	NM_000489.3	898	Gac/ac	9/35	0.748716029401335	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.748716029401335	1		649	226	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	17	381	1	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.63	0.481	0.797	0.63	0.481	0.797	SUBCLONAL	1	TRUE	1	0.719983226321928	2		382	75	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	19	500	3	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.55	0.425	0.691	0.55	0.425	0.691	SUBCLONAL	1	TRUE	1	0.719983226321928	2		503	96	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782136	9782136	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs964373496	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	44	562	0	ENST00000377346.4:c.2159G>A	p.Arg720Gln	p.R720Q	ENST00000377346	NM_005026.3	720	cGg/cAg	17/24	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.719983226321928	2		562	98	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261140	16261140	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1275384688	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	44	359	0	ENST00000375759.3:c.8405C>T	p.Ser2802Leu	p.S2802L	ENST00000375759	NM_015001.2	2802	tCa/tTa	11/15	0.719983226321928	3	FACETS	1	0.948	1	0.625	0.536	0.718	CLONAL	1	TRUE	1	0.719983226321928	3		359	133	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262695	16262696	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	18	297	0	ENST00000375759.3:c.9967_9968del	p.Thr3323SerfsTer24	p.T3323Sfs*24	ENST00000375759	NM_015001.2	3320	ctCAca/ctca	11/15	0.719983226321928	3	FACETS	0.439	0.332	0.562	0.219	0.166	0.281	SUBCLONAL	1	TRUE	1	0.719983226321928	3		297	155	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22412955	22412955	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	28	134	1	ENST00000344548.3:c.202C>T	p.Arg68Ter	p.R68*	ENST00000344548	NM_001039802.1	68	Cga/Tga	5/7	1	2	FACETS	0.894	0.736	1	0.894	0.736	1	CLONAL	1	TRUE	1	0.719983226321928	2		135	87	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057936	27057937	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1415146710	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	51	525	0	ENST00000324856.7:c.1650dup	p.Tyr551LeufsTer72	p.Y551Lfs*72	ENST00000324856	NM_006015.4	548	-/C	3/20	1	2	FACETS	0.838	0.726	0.957	0.838	0.726	0.957	CLONAL	1	TRUE	1	0.719983226321928	2		525	169	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518437	204518437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201947927	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	32	377	0	ENST00000367182.3:c.1100C>T	p.Ser367Leu	p.S367L	ENST00000367182	NM_001278516.1	367	tCg/tTg	11/11	1	2	FACETS	0.839	0.697	0.989	0.839	0.697	0.989	CLONAL	1	TRUE	1	0.719983226321928	2		377	106	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392700	118392700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	58	495	0	ENST00000534358.1:c.11732C>T	p.Ser3911Leu	p.S3911L	ENST00000534358	NM_005933.3	3911	tCg/tTg	36/36	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.719983226321928	2		495	146	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	87	472	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	0.719983226321928	2		472	188	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398279	25398279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894365	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	54	420	1	ENST00000311936.3:c.40G>A	p.Val14Ile	p.V14I	ENST00000311936	NM_004985.3	14	Gta/Ata	2/5	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.719983226321928	2		421	149	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487277	56487277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035001455	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	59	371	0	ENST00000267101.3:c.1423C>T	p.Arg475Trp	p.R475W	ENST00000267101	NM_001982.3	475	Cgg/Tgg	12/28	1	2	FACETS	0.867	0.759	0.98	0.867	0.759	0.98	CLONAL	1	TRUE	1	0.719983226321928	2		371	189	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109720	115109720	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	54	606	0	ENST00000257566.3:c.2158G>A	p.Glu720Lys	p.E720K	ENST00000257566	NM_016569.3	720	Gaa/Aaa	8/8	1	2	FACETS	0.867	0.754	0.985	0.867	0.754	0.985	CLONAL	1	TRUE	1	0.719983226321928	2		606	173	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240697	133240697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374200895	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	38	608	0	ENST00000320574.5:c.2599G>A	p.Val867Ile	p.V867I	ENST00000320574	NM_006231.2	867	Gtc/Atc	23/49	1	2	FACETS	0.895	0.758	1	0.895	0.758	1	CLONAL	1	TRUE	1	0.719983226321928	2		608	118	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620098	21620098	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	15	529	0	ENST00000382592.4:c.68G>A	p.Arg23His	p.R23H	ENST00000382592	NM_014572.2	23	cGt/cAt	2/8	0.43277535143242	1	FACETS	0.137	0.1	0.181	0.137	0.1	0.181	SUBCLONAL	1	TRUE	0	0.719983226321928	1		529	195	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438316	110438317	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	rs532810290	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	23	128	0	ENST00000375856.3:c.82_84dup	p.Asn28dup	p.N28dup	ENST00000375856	NM_003749.2	28	-/AAC	1/2	1	2	FACETS	0.761	0.608	0.927	0.761	0.608	0.927	CLONAL	1	TRUE	1	0.719983226321928	2		128	84	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396908	396908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753659585	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	63	532	2	ENST00000262320.3:c.118G>A	p.Ala40Thr	p.A40T	ENST00000262320	NM_003502.3	40	Gcc/Acc	2/11	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.719983226321928	2		534	174	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226294	2226294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	50	649	1	ENST00000326181.6:c.1907C>T	p.Thr636Met	p.T636M	ENST00000326181	NM_032271.2	636	aCg/aTg	20/21	1	2	FACETS	0.926	0.803	1	0.926	0.803	1	CLONAL	1	TRUE	1	0.719983226321928	2		650	150	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944250	81944250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147396004	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	33	511	0	ENST00000359376.3:c.1859C>T	p.Thr620Met	p.T620M	ENST00000359376	NM_002661.3	620	aCg/aTg	18/33	1	2	FACETS	0.619	0.512	0.736	0.619	0.512	0.736	SUBCLONAL	1	TRUE	1	0.719983226321928	2		511	148	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980435	7980435	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760428119	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	28	451	0	ENST00000319144.4:c.1148C>T	p.Thr383Met	p.T383M	ENST00000319144	NM_001139.2	383	aCg/aTg	9/15	1	2	FACETS	0.665	0.541	0.8	0.665	0.541	0.8	SUBCLONAL	1	TRUE	1	0.719983226321928	2		451	117	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240271	5240271	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	10	676	0	ENST00000357368.4:c.1643del	p.Pro548ArgfsTer37	p.P548Rfs*37	ENST00000357368	NM_002850.3	548	cCg/cg	12/38	1	2	FACETS	0.176	0.119	0.247	0.176	0.119	0.247	SUBCLONAL	1	TRUE	1	0.719983226321928	2		676	158	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244328	5244328	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs115982731	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	10	622	1	ENST00000357368.4:c.1154C>T	p.Thr385Ile	p.T385I	ENST00000357368	NM_002850.3	385	aCa/aTa	11/38	1	2	FACETS	0.157	0.106	0.221	0.157	0.106	0.221	SUBCLONAL	1	TRUE	1	0.719983226321928	2		623	177	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100015	11100015	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs972341316	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	34	480	0	ENST00000358026.2:c.1141C>T	p.Arg381Ter	p.R381*	ENST00000358026	NM_001128849.1	381	Cga/Tga	7/36	1	2	FACETS	0.572	0.474	0.68	0.572	0.474	0.68	SUBCLONAL	1	TRUE	1	0.719983226321928	2		480	165	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214389	36214389	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	47	466	1	ENST00000222270.7:c.3043C>T	p.Arg1015Ter	p.R1015*	ENST00000222270	NM_014727.1	1015	Cga/Tga	7/37	1	2	FACETS	0.859	0.739	0.985	0.859	0.739	0.985	CLONAL	1	TRUE	1	0.719983226321928	2		467	152	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221481	36221481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	57	659	2	ENST00000222270.7:c.5240C>T	p.Ser1747Leu	p.S1747L	ENST00000222270	NM_014727.1	1747	tCg/tTg	25/37	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.719983226321928	2		661	154	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383185	42383185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782563209	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	17	492	0	ENST00000221972.3:c.205G>A	p.Val69Ile	p.V69I	ENST00000221972	NM_021601.3	69	Gtc/Atc	2/5	1	2	FACETS	0.245	0.183	0.317	0.245	0.183	0.317	SUBCLONAL	1	TRUE	1	0.719983226321928	2		492	193	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912134	50912134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781327088	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	35	683	0	ENST00000440232.2:c.1868G>A	p.Arg623Gln	p.R623Q	ENST00000440232	NM_002691.3	623	cGg/cAg	15/27	1	2	FACETS	0.868	0.729	1	0.868	0.729	1	CLONAL	1	TRUE	1	0.719983226321928	2		683	112	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965839	25965839	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	16	531	0	ENST00000435504.4:c.3367C>T	p.His1123Tyr	p.H1123Y	ENST00000435504		1123	Cac/Tac	13/13	0.719983226321928	2	FACETS	0.339	0.253	0.441	0.17	0.126	0.221	SUBCLONAL	1	TRUE	0	0.719983226321928	2		531	131	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657046	47657050	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTA	ACCTA	-	novel	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	57	276	0	ENST00000233146.2:c.1243_1247del	p.Pro415CysfsTer9	p.P415Cfs*9	ENST00000233146	NM_000251.2	414	ctACCTAat/ctat	7/16	0.719983226321928	2	FACETS	0.954	0.868	1	0.954	0.868	1	CLONAL	2	TRUE	0	0.719983226321928	2		276	83	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794474	242794474	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	48	616	1	ENST00000334409.5:c.468del	p.Ser157AlafsTer28	p.S157Afs*28	ENST00000334409	NM_005018.2	156	ccC/cc	3/5	0.591991194777183	1	FACETS	0.597	0.516	0.682	0.597	0.516	0.682	SUBCLONAL	1	TRUE	0	0.719983226321928	1		617	143	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386387	31386387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs987153673	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	60	449	1	ENST00000328111.2:c.1612C>T	p.Arg538Cys	p.R538C	ENST00000328111	NM_006892.3	538	Cgc/Tgc	15/23	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.719983226321928	2		450	153	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231773	36231773	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1569061762	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	12	466	0	ENST00000300305.3:c.611G>A	p.Arg204Gln	p.R204Q	ENST00000300305		204	cGa/cAa	5/8	1	2	FACETS	0.142	0.099	0.194	0.142	0.099	0.194	SUBCLONAL	1	TRUE	1	0.719983226321928	2		466	235	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	8	378	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	1	2	FACETS	0.16	0.103	0.233	0.16	0.103	0.233	SUBCLONAL	1	TRUE	1	0.719983226321928	2		378	139	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598137	55598137	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	21	376	0	ENST00000288135.5:c.2334G>T	p.Lys778Asn	p.K778N	ENST00000288135	NM_000222.2	778	aaG/aaT	16/21	0.166241672279122	1	FACETS	0.309	0.241	0.385	0.309	0.241	0.385	INDETERMINATE	1	TRUE	0	0.719983226321928	1		376	121	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521120	187521120	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752997628	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	46	413	1	ENST00000441802.2:c.12035C>T	p.Thr4012Met	p.T4012M	ENST00000441802	NM_005245.3	4012	aCg/aTg	22/27	0.166241672279122	1	FACETS	0.644	0.556	0.735	0.644	0.556	0.735	INDETERMINATE	1	TRUE	0	0.719983226321928	1		414	127	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961007	79961007	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	26	433	0	ENST00000265081.6:c.408del	p.Lys136AsnfsTer2	p.K136Nfs*2	ENST00000265081	NM_002439.4	135	gAa/ga	3/24	1	2	FACETS	0.623	0.502	0.756	0.623	0.502	0.756	SUBCLONAL	1	TRUE	1	0.719983226321928	2		433	116	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672747	86672747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	20	312	0	ENST00000274376.6:c.2234G>A	p.Cys745Tyr	p.C745Y	ENST00000274376	NM_002890.2	745	tGt/tAt	17/25	1	2	FACETS	0.539	0.419	0.675	0.539	0.419	0.675	SUBCLONAL	1	TRUE	1	0.719983226321928	2		312	103	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052980	180052980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	60	703	1	ENST00000261937.6:c.1310G>A	p.Arg437His	p.R437H	ENST00000261937	NM_182925.4	437	cGt/cAt	10/30	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.719983226321928	2		704	122	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	32	589	1	ENST00000261937.6:c.89C>T	p.Pro30Leu	p.P30L	ENST00000261937	NM_182925.4	30	cCg/cTg	2/30	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.719983226321928	2		590	86	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372287	55372288	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1170462661	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	18	230	0	ENST00000297316.4:c.983dup	p.Gly331ArgfsTer34	p.G331Rfs*34	ENST00000297316	NM_022454.3	326	cac/caCc	2/2	1	2	FACETS	0.376	0.286	0.48	0.376	0.286	0.48	SUBCLONAL	1	TRUE	1	0.719983226321928	2		230	133	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222978	53222978	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	33	536	0	ENST00000375401.3:c.4094C>A	p.Pro1365Gln	p.P1365Q	ENST00000375401	NM_004187.3	1365	cCg/cAg	24/26	0.176083415110665	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.719983226321928	0		536	114	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577061	7577074	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTCTTGCGGAGA	CTTTCTTGCGGAGA	-	novel	NA	P-0033690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	113	706	0	ENST00000269305.4:c.864_877del	p.Asn288LysfsTer13	p.N288Kfs*13	ENST00000269305	NM_001126112.2	288	aaTCTCCGCAAGAAAGgg/aagg	8/11	0.45675712610406	1	FACETS	0.723	0.654	0.796	0.723	0.654	0.796	SUBCLONAL	1	TRUE	0	0.470394000576262	1		706	508	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246370	41246370	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0033690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	182	614	0	ENST00000357654.3:c.1178T>G	p.Leu393Ter	p.L393*	ENST00000357654	NM_007294.3	393	tTa/tGa	10/23	0.45675712610406	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.470394000576262	1		614	491	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30733037	30733038	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGCTGCTC	novel	NA	P-0033690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	58	303	0	ENST00000295754.5:c.1651_1658dup	p.Glu554AlafsTer13	p.E554Afs*13	ENST00000295754	NM_003242.5	550	-/AGCTGCTC	7/7	1	2	FACETS	0.91	0.789	1	0.91	0.789	1	CLONAL	1	TRUE	1	0.470394000576262	2		303	271	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39074225	39074225	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	34	175	0	ENST00000357387.3:c.85G>C	p.Asp29His	p.D29H	ENST00000357387	NM_152756.3	29	Gat/Cat	2/38	0.250812868871182	2	FACETS	0.86	0.712	1	0.43	0.356	0.512	INDETERMINATE	1	TRUE	0	0.470394000576262	2		175	168	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576900	7576901	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0033720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	93	703	0	ENST00000269305.4:c.945_946del	p.Gln317AlafsTer19	p.Q317Afs*19	ENST00000269305	NM_001126112.2	315	tcTCcc/tccc	9/11	0.218738626145748	1	FACETS	0.872	0.777	0.972	0.872	0.777	0.972	CLONAL	1	TRUE	0	0.33	1		703	540	SUCCESS
APC	324	MSKCC	GRCh37	5	112173837	112173838	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0033720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	33	429	0	ENST00000257430.4:c.2547_2548del	p.Asp849GlufsTer62	p.D849Efs*62	ENST00000257430	NM_000038.5	849	gAT/g	16/16	1	2	FACETS	0.926	0.76	1	0.926	0.76	1	CLONAL	1	TRUE	1	0.33	2		429	216	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293134	91293135	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0033720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	28	511	0	ENST00000355112.3:c.638_639del	p.Ser213Ter	p.S213*	ENST00000355112	NM_000057.2	212	tcCTct/tcct	3/22	1	2	FACETS	0.423	0.338	0.521	0.423	0.338	0.521	SUBCLONAL	1	TRUE	1	0.33	2		511	401	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	85	264	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.946	1			1	INDETERMINATE	1	FALSE	NA	0.633943800632025	2		264	247	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970971	21970971	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	194	575	0	ENST00000304494.5:c.387C>A	p.Tyr129Ter	p.Y129*	ENST00000304494	NM_000077.4	129	taC/taA	2/3	0.518816638132004	1	FACETS	0.937	0.878	0.998	0.937	0.878	0.998	CLONAL	1	FALSE	0	0.633943800632025	1		575	446	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888165	112888165	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397507510	NA	P-0033722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	178	701	0	ENST00000351677.2:c.181G>T	p.Asp61Tyr	p.D61Y	ENST00000351677	NM_002834.3	61	Gat/Tat	3/16	0.158460247785235	0	FACETS	0.325	0.301	0.35			1	INDETERMINATE	1	FALSE	0	0.633943800632025	0		701	632	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692805	89692805	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204928	NA	P-0033722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	142	371	0	ENST00000371953.3:c.289C>T	p.Gln97Ter	p.Q97*	ENST00000371953	NM_000314.4	97	Cag/Tag	5/9	0.633943800632025	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	0	0.633943800632025	1		371	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0033723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	37	732	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.229382907492897	5	FACETS	0.896	0.752	1	0.597	0.501	0.7	INDETERMINATE	2	TRUE	2	0.535956736887503	5		732	139	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098816	178098816	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	10	768	0	ENST00000397062.3:c.229G>C	p.Asp77His	p.D77H	ENST00000397062	NM_006164.4	77	Gat/Cat	2/5	0.229382907492897	5	FACETS	0.647	0.442	0.901	0.216	0.147	0.301	INDETERMINATE	1	TRUE	2	0.535956736887503	5		768	104	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0033723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	23	511	1	ENST00000269305.4:c.673-2A>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.229382907492897	5	FACETS	1	0.807	1	0.67	0.538	0.813	INDETERMINATE	2	TRUE	2	0.535956736887503	5		512	77	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714075	43714075	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs773155828	NA	P-0033723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	17	682	0	ENST00000382044.4:c.4078C>T	p.Arg1360Ter	p.R1360*	ENST00000382044	NM_001141980.1	1360	Cga/Tga	19/28	1	2	FACETS	0.661	0.501	0.844	0.661	0.501	0.844	SUBCLONAL	1	TRUE	1	0.535956736887503	2		682	96	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484228	120484228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1456398532	NA	P-0033723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	10	672	3	ENST00000256646.2:c.2902G>A	p.Val968Ile	p.V968I	ENST00000256646	NM_024408.3	968	Gtc/Atc	18/34	0.535956736887503	1	FACETS	0.402	0.276	0.553	0.402	0.276	0.553	SUBCLONAL	1	TRUE	0	0.535956736887503	1		675	68	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134055	41134055	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1566060553	NA	P-0033723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	19	575	0	ENST00000379561.5:c.1573C>T	p.Pro525Ser	p.P525S	ENST00000379561	NM_002015.3	525	Cct/Tct	2/3	0.289594877551714	5	FACETS	1	0.905	1	0.463	0.358	0.582	INDETERMINATE	1	TRUE	2	0.535956736887503	5		575	92	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098961	+	inframe_insertion	In_Frame_Ins	INS	-	-	TAT	novel	NA	P-0033723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	10	384	0	ENST00000397062.3:c.82_84dup	p.Ile28dup	p.I28dup	ENST00000397062	NM_006164.4	28	-/ATA	2/5	0.229382907492897	5	FACETS	0.68	0.465	0.945	0.227	0.155	0.315	INDETERMINATE	1	TRUE	2	0.535956736887503	5		384	99	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233134	66233134	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	35	568	1	ENST00000273854.3:c.1865G>T	p.Gly622Val	p.G622V	ENST00000273854	NM_004439.5	622	gGc/gTc	10/18	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.535956736887503	2		569	107	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484254	8484254	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	22	591	0	ENST00000356435.5:c.3278G>T	p.Gly1093Val	p.G1093V	ENST00000356435		1093	gGt/gTt	19/35	0.535956736887503	1	FACETS	0.835	0.667	1	0.835	0.667	1	CLONAL	1	TRUE	0	0.535956736887503	1		591	72	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395119	139395119	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	53	659	0	ENST00000277541.6:c.5819G>T	p.Arg1940Leu	p.R1940L	ENST00000277541	NM_017617.3	1940	cGc/cTc	31/34	0.2055451762878	4	FACETS	1	0.95	1	0.785	0.688	0.884	INDETERMINATE	2	TRUE	1	0.535956736887503	4		659	129	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809263	243809263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	34	534	0	ENST00000263826.5:c.361C>T	p.Pro121Ser	p.P121S	ENST00000263826	NM_005465.4	121	Cca/Tca	4/13	1	2	FACETS	0.189	0.154	0.23	0.189	0.154	0.23	SUBCLONAL	1	TRUE	1	0.565171570404269	2		534	635	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624291	89624291	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1554890398	NA	P-0033724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	165	460	0	ENST00000371953.3:c.65A>G	p.Asp22Gly	p.D22G	ENST00000371953	NM_000314.4	22	gAc/gGc	1/9	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.565171570404269	2		460	514	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506687	103506687	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	90	251	2	ENST00000355739.4:c.430T>A	p.Tyr144Asn	p.Y144N	ENST00000355739	NM_000123.3	144	Tat/Aat	4/15	1	2	FACETS	0.998	0.895	1	0.998	0.895	1	CLONAL	1	TRUE	1	0.565171570404269	2		253	319	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241700	55241700	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	232	584	0	ENST00000275493.2:c.2148A>C	p.Lys716Asn	p.K716N	ENST00000275493	NM_005228.3	716	aaA/aaC	18/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.565171570404269	2		584	747	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780071	NA	P-0033726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	289	490	0	ENST00000269305.4:c.580C>T	p.Leu194Phe	p.L194F	ENST00000269305	NM_001126112.2	194	Ctt/Ttt	6/11	0.764913379980619	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.764913379980619	1		490	408	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631937	90631937	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	317	742	0	ENST00000330062.3:c.416T>C	p.Ile139Thr	p.I139T	ENST00000330062	NM_002168.2	139	aTc/aCc	4/11	1	2	FACETS	0.91	0.861	0.959	0.91	0.861	0.959	CLONAL	1	TRUE	1	0.764913379980619	2		742	911	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11803087	11803249	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCATTAAGGTAAAAATCTTCTCCCCTCCTTCTACGTGGTGGAAACCCTGAGCTGCACCGGCCAGGGCAGTCGTGCTGGGCTCCTCAGAGCAGGCTGTTGCAGTTGCTCTGTTCGCAGGAAATTATTTGGGGCGAGAGGGAAAGAGATGCAGCTCGCGGTGGCT	GCATTAAGGTAAAAATCTTCTCCCCTCCTTCTACGTGGTGGAAACCCTGAGCTGCACCGGCCAGGGCAGTCGTGCTGGGCTCCTCAGAGCAGGCTGTTGCAGTTGCTCTGTTCGCAGGAAATTATTTGGGGCGAGAGGGAAAGAGATGCAGCTCGCGGTGGCT	-	novel	NA	P-0033726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	135	358	0	ENST00000396373.4:c.28_33+157del		p.X10_splice	ENST00000396373	NM_001987.4	10		1/8	0.352828925068753	4	FACETS	1	0.985	1	0.677	0.62	0.736	INDETERMINATE	1	TRUE	2	0.764913379980619	4		358	460	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354389	354389	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	339	747	0	ENST00000262320.3:c.1169A>T	p.Glu390Val	p.E390V	ENST00000262320	NM_003502.3	390	gAg/gTg	5/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.764913379980619	2		747	863	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961117	55961117	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	225	593	0	ENST00000263923.4:c.2823A>T	p.Lys941Asn	p.K941N	ENST00000263923	NM_002253.2	941	aaA/aaT	21/30	1	2	FACETS	0.879	0.823	0.937	0.879	0.823	0.937	CLONAL	1	TRUE	1	0.764913379980619	2		593	669	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0033728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	315	880	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.841	0.797	0.886	1	0.995	1	CLONAL	2	TRUE	1	0.444351678027601	2		882	843	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0033728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	186	236	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.887	0.827	0.947	1	0.993	1	CLONAL	2	TRUE	1	0.444351678027601	2		236	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0033728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	181	599	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.444351678027601	2		599	592	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147534	47147534	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	29	525	0	ENST00000409792.3:c.4792C>T	p.Arg1598Ter	p.R1598*	ENST00000409792	NM_014159.6	1598	Cga/Tga	6/21	0.444351678027601	1	FACETS	0.184	0.147	0.226	0.184	0.147	0.226	SUBCLONAL	1	TRUE	0	0.444351678027601	1		525	552	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938003	76938006	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	novel	NA	P-0033728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	321	774	0	ENST00000373344.5:c.2742_2745del	p.Ser915LeufsTer54	p.S915Lfs*54	ENST00000373344	NM_000489.3	914	gcAAGT/gc	9/35	0.350989626279605	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.444351678027601	1		774	806	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	16	460	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.781	1	1	0.781	1	CLONAL	1	TRUE	1	0.262655833612118	2		460	116	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	34	740	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.1606539467716	2	FACETS	0.908	0.765	1	1	0.948	1	CLONAL	3	TRUE	0	0.262655833612118	2		740	95	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0033737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	369	744	1	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.373214371255548	3	FACETS	1	0.992	1	0.787	0.751	0.824	CLONAL	2	TRUE	0	0.466023605338456	3		745	827	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259166	89259166	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	95	321	0	ENST00000336596.2:c.310C>T	p.Arg104Ter	p.R104*	ENST00000336596	NM_005233.5	104	Cga/Tga	3/17	0.355486760151497	2	FACETS	1	0.971	1	0.612	0.55	0.676	CLONAL	1	TRUE	0	0.466023605338456	2		321	333	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414907	78414930	+	inframe_deletion	In_Frame_Del	DEL	CTATAATACTCAGCCCAGGCTGCA	CTATAATACTCAGCCCAGGCTGCA	-	novel	NA	P-0033737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	86	333	0	ENST00000370768.2:c.1836_1859del	p.Ser612_Tyr619del	p.S612_Y619del	ENST00000370768	NM_003902.3	612	agTGCAGCCTGGGCTGAGTATTATAGa/aga	19/20	0.257604087702068	3	FACETS	0.658	0.582	0.739	0.329	0.291	0.37	INDETERMINATE	1	TRUE	1	0.466023605338456	3		333	692	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246726	41246726	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs80357331	NA	P-0033737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	250	486	0	ENST00000357654.3:c.822T>A	p.Cys274Ter	p.C274*	ENST00000357654	NM_007294.3	274	tgT/tgA	10/23	0.355675292547225	2	FACETS	0.896	0.844	0.947	0.896	0.844	0.947	CLONAL	2	TRUE	0	0.466023605338456	2		486	599	SUCCESS
AR	367	MSKCC	GRCh37	X	66863106	66863106	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471576123	NA	P-0033737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	37	519	0	ENST00000374690.3:c.1625C>T	p.Thr542Ile	p.T542I	ENST00000374690	NM_000044.3	542	aCt/aTt	2/8	0.355486760151497	2	FACETS	0.235	0.193	0.283	0.118	0.096	0.142	SUBCLONAL	1	TRUE	0	0.466023605338456	2		519	675	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	218	485	3	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	NA	2	FACETS	1	0.961	1			1	INDETERMINATE	1	TRUE	NA	0.516821109674483	2		488	809	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0033738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	261	501	2	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.501717627123816	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.516821109674483	1		503	711	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716334	18716334	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	100	262	0	ENST00000266497.5:c.3681C>A	p.His1227Gln	p.H1227Q	ENST00000266497		1227	caC/caA	26/31	1	2	FACETS	0.956	0.86	1	0.956	0.86	1	CLONAL	1	TRUE	1	0.516821109674483	2		262	405	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105793	27105793	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	14	384	0	ENST00000324856.7:c.5404G>T	p.Glu1802Ter	p.E1802*	ENST00000324856	NM_006015.4	1802	Gag/Tag	20/20	1	2	FACETS	0.446	0.322	0.596	0.446	0.322	0.596	SUBCLONAL	1	TRUE	1	0.23	2		384	273	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437616	110437616	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	44	529	0	ENST00000375856.3:c.785C>G	p.Ser262Trp	p.S262W	ENST00000375856	NM_003749.2	262	tCg/tGg	1/2	0.194572388924292	3	FACETS	1	0.949	1	0.673	0.567	0.789	CLONAL	1	TRUE	1	0.23	3		529	317	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292679	62292679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1044603913	NA	P-0033739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	25	424	1	ENST00000360203.5:c.131C>T	p.Thr44Met	p.T44M	ENST00000360203	NM_001283009.1	44	aCg/aTg	3/35	1	2	FACETS	0.788	0.622	0.977	0.788	0.622	0.977	CLONAL	1	TRUE	1	0.23	2		425	276	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912793	100912793	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	28	396	0	ENST00000325455.5:c.2529G>C	p.Glu843Asp	p.E843D	ENST00000325455	NM_001202474.3	843	gaG/gaC	7/8	1	2	FACETS	0.775	0.621	0.951	0.775	0.621	0.951	CLONAL	1	TRUE	1	0.23	2		396	314	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	464403	464403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	36	438	0	ENST00000399788.2:c.791G>A	p.Arg264Gln	p.R264Q	ENST00000399788	NM_001042603.1	264	cGa/cAa	7/28	0.202566139885367	4	FACETS	0.995	0.819	1	0.497	0.409	0.596	CLONAL	1	TRUE	2	0.23	4		438	387	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444243	49444243	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	55	657	0	ENST00000301067.7:c.3128C>G	p.Ser1043Cys	p.S1043C	ENST00000301067	NM_003482.3	1043	tCt/tGt	11/54	0.202566139885367	4	FACETS	1	0.948	1	0.621	0.531	0.718	CLONAL	1	TRUE	2	0.23	4		657	474	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437316	121437316	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	51	633	0	ENST00000257555.6:c.1654G>C	p.Glu552Gln	p.E552Q	ENST00000257555		552	Gag/Cag	9/10	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.23	2		633	381	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842631	68842631	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	28	497	0	ENST00000261769.5:c.567C>G	p.Phe189Leu	p.F189L	ENST00000261769	NM_004360.3	189	ttC/ttG	5/16	1	2	FACETS	0.72	0.576	0.884	0.72	0.576	0.884	SUBCLONAL	1	TRUE	1	0.23	2		497	338	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369246	40369246	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	37	430	0	ENST00000293328.3:c.1312G>C	p.Glu438Gln	p.E438Q	ENST00000293328	NM_012448.3	438	Gaa/Caa	11/19	1	2	FACETS	0.787	0.649	0.94	0.787	0.649	0.94	CLONAL	1	TRUE	1	0.23	2		430	409	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370335	40370335	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	19	618	0	ENST00000293328.3:c.1003G>C	p.Glu335Gln	p.E335Q	ENST00000293328	NM_012448.3	335	Gag/Cag	9/19	1	2	FACETS	0.495	0.375	0.636	0.495	0.375	0.636	SUBCLONAL	1	TRUE	1	0.23	2		618	334	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11022869	11022869	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	42	716	0	ENST00000327064.4:c.568G>C	p.Asp190His	p.D190H	ENST00000327064	NM_199141.1	190	Gat/Cat	5/16	0.149797981652318	0	FACETS	0.781	0.654	0.922			1	CLONAL	1	TRUE	0	0.23	0		716	360	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228990	36228990	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	56	597	0	ENST00000222270.7:c.7770C>G	p.Phe2590Leu	p.F2590L	ENST00000222270	NM_014727.1	2590	ttC/ttG	36/37	0.145981090687306	3	FACETS	1	0.942	1	0.398	0.341	0.459	CLONAL	1	TRUE	0	0.23	3		597	455	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146169	38146169	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	43	617	0	ENST00000317025.8:c.3337G>C	p.Glu1113Gln	p.E1113Q	ENST00000317025	NM_023034.1	1113	Gag/Cag	19/24	0.203942534733454	5	FACETS	0.965	0.807	1	0.322	0.269	0.38	CLONAL	1	TRUE	2	0.23	5		617	521	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413021	63413021	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	40	704	0	ENST00000330258.3:c.146C>T	p.Pro49Leu	p.P49L	ENST00000330258	NM_152424.3	49	cCa/cTa	2/2	1	2	FACETS	0.933	0.776	1	0.933	0.776	1	CLONAL	1	TRUE	1	0.23	2		704	373	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918999	76918999	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	23	412	0	ENST00000373344.5:c.3992C>T	p.Ser1331Phe	p.S1331F	ENST00000373344	NM_000489.3	1331	tCt/tTt	12/35	1	2	FACETS	0.633	0.494	0.794	0.633	0.494	0.794	SUBCLONAL	1	TRUE	1	0.23	2		412	316	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0033741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	71	694	3	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	0.254776949504793	2	FACETS	0.657	0.573	0.746	0.328	0.286	0.373	SUBCLONAL	1	TRUE	0	0.373462504726458	2		697	579	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0033741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	21	751	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	0.254776949504793	2	FACETS	0.175	0.134	0.223	0.087	0.067	0.112	SUBCLONAL	1	TRUE	0	0.373462504726458	2		751	644	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	719	657	0	ENST00000397752.3:c.3028G>C	p.Asp1010His	p.D1010H	ENST00000397752	NM_000245.2	1010	Gat/Cat	14/21	0.373462504726458	5	FACETS	1	0.986	1	1	0.986	1	CLONAL	5	TRUE	0	0.373462504726458	5		657	1175	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652872	29652873	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	91	281	0	ENST00000356175.3:c.4808dup	p.Tyr1604IlefsTer16	p.Y1604Ifs*16	ENST00000356175	NM_000267.3	1603	ata/aTta	36/57	0.254776949504793	2	FACETS	1	0.976	1	0.666	0.596	0.739	CLONAL	1	TRUE	0	0.373462504726458	2		281	366	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0033745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	8	339	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.936	0.618	1	0.936	0.618	1	CLONAL	1	TRUE	1	0.38	2		339	45	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426121	47426121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519786	NA	P-0033745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	47	327	0	ENST00000377045.4:c.641C>T	p.Ser214Phe	p.S214F	ENST00000377045	NM_001654.4	214	tCc/tTc	7/16	0.166579560239554	2	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.38	2		327	166	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443881	52443881	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	22	545	0	ENST00000460680.1:c.14G>A	p.Trp5Ter	p.W5*	ENST00000460680	NM_004656.3	5	tGg/tAg	1/17	1	2	FACETS	0.306	0.236	0.386	0.306	0.236	0.386	SUBCLONAL	1	TRUE	1	0.38	2		545	379	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620601	52620601	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	23	491	0	ENST00000394830.3:c.3152G>A	p.Trp1051Ter	p.W1051*	ENST00000394830	NM_018313.4	1051	tGg/tAg	21/30	1	2	FACETS	1	0.823	1	1	0.823	1	CLONAL	1	TRUE	1	0.38	2		491	116	SUCCESS
AR	367	MSKCC	GRCh37	X	66937454	66937454	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	16	250	0	ENST00000374690.3:c.2308G>T	p.Val770Phe	p.V770F	ENST00000374690	NM_000044.3	770	Gtt/Ttt	5/8	0.166579560239554	2	FACETS	1	0.856	1			1	INDETERMINATE	1	TRUE	NA	0.38	2		250	70	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0033750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	78	581	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.721	0.631	0.818	0.721	0.631	0.818	SUBCLONAL	1	FALSE	1	0.188996566695592	2		582	1145	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478888	56478888	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1355	94	648	0	ENST00000267101.3:c.344T>C	p.Phe115Ser	p.F115S	ENST00000267101	NM_001982.3	115	tTt/tCt	3/28	1	2	FACETS	0.686	0.608	0.771	0.686	0.608	0.771	SUBCLONAL	1	FALSE	1	0.188996566695592	2		648	1449	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112445	115112445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	65	677	1	ENST00000257566.3:c.1295C>T	p.Ser432Leu	p.S432L	ENST00000257566	NM_016569.3	432	tCg/tTg	7/8	1	2	FACETS	0.689	0.595	0.791	0.689	0.595	0.791	SUBCLONAL	1	FALSE	1	0.188996566695592	2		678	999	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714543	52714543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	67	450	0	ENST00000322088.6:c.301G>A	p.Glu101Lys	p.E101K	ENST00000322088	NM_014225.5	101	Gag/Aag	4/15	1	2	FACETS	0.67	0.58	0.768	0.67	0.58	0.768	SUBCLONAL	1	FALSE	1	0.188996566695592	2		450	1058	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0033750-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	30	272	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.735	0.595	0.892	0.735	0.595	0.892	SUBCLONAL	1	TRUE	1	0.340194125338749	2		272	240	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121909229	NA	P-0033750-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	18	508	0	ENST00000371953.3:c.389G>T	p.Arg130Leu	p.R130L	ENST00000371953	NM_000314.4	130	cGa/cTa	5/9	1	2	FACETS	0.23	0.172	0.299	0.23	0.172	0.299	SUBCLONAL	1	TRUE	1	0.340194125338749	2		508	460	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952076	178952076	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1064793838	NA	P-0033750-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	52	334	0	ENST00000263967.3:c.3131A>G	p.Asn1044Ser	p.N1044S	ENST00000263967	NM_006218.2	1044	aAt/aGt	21/21	1	2	FACETS	0.993	0.85	1	0.993	0.85	1	CLONAL	1	TRUE	1	0.340194125338749	2		334	308	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106319	27106346	+	frameshift_variant	Frame_Shift_Del	DEL	TTGCCAAGCGCTGCGTCTGTGTGTCCAA	TTGCCAAGCGCTGCGTCTGTGTGTCCAA	-	novel	NA	P-0033750-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	107	596	0	ENST00000324856.7:c.5931_5958del	p.Ala1978ProfsTer28	p.A1978Pfs*28	ENST00000324856	NM_006015.4	1977	cTTGCCAAGCGCTGCGTCTGTGTGTCCAAt/ct	20/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.340194125338749	2		596	596	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488720	212488720	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033750-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	119	513	0	ENST00000342788.4:c.2129T>A	p.Leu710His	p.L710H	ENST00000342788	NM_005235.2	710	cTt/cAt	18/28	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.340194125338749	2		513	627	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0033760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	188	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.485735489527334	3	FACETS	1	0.989	1	0.823	0.773	0.872	CLONAL	2	TRUE	0	0.538606545225349	3		502	359	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0033760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	150	615	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.500723085275862	2	FACETS	0.87	0.809	0.932	0.87	0.809	0.932	CLONAL	2	TRUE	0	0.538606545225349	2		617	320	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604790	48604790	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1568211615	NA	P-0033760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	43	294	0	ENST00000342988.3:c.1612G>T	p.Glu538Ter	p.E538*	ENST00000342988	NM_005359.5	538	Gaa/Taa	12/12	0.538606545225349	1	FACETS	0.743	0.633	0.861	0.743	0.633	0.861	SUBCLONAL	1	TRUE	0	0.538606545225349	1		294	157	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs878854073	NA	P-0033760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	139	410	1	ENST00000269305.4:c.673-1G>A		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.500723085275862	2	FACETS	0.952	0.885	1	0.952	0.885	1	CLONAL	2	TRUE	0	0.538606545225349	2		411	271	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451749	29451749	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0033760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	53	462	0	ENST00000389048.3:c.2815+1G>T		p.X939_splice	ENST00000389048	NM_004304.4	939			0.136854045669515	3	FACETS	0.788	0.676	0.909	0.263	0.225	0.303	INDETERMINATE	1	TRUE	0	0.538606545225349	3		462	317	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662615	117662615	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	48	430	1	ENST00000368508.3:c.4850G>T	p.Arg1617Met	p.R1617M	ENST00000368508	NM_002944.2	1617	aGg/aTg	29/43	1	2	FACETS	0.675	0.575	0.783	0.675	0.575	0.783	SUBCLONAL	1	TRUE	1	0.538606545225349	2		431	264	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0033764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	569	514	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.402693900938937	6	FACETS	1	0.99	1	1	0.99	1	CLONAL	5	TRUE	1	0.402693900938937	6		514	969	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0033764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	439	751	1	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.402693900938937	3	FACETS	0.963	0.923	1	0.963	0.923	1	CLONAL	3	TRUE	0	0.402693900938937	3		752	907	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396464	396464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	150	795	0	ENST00000262320.3:c.562G>A	p.Glu188Lys	p.E188K	ENST00000262320	NM_003502.3	188	Gaa/Aaa	2/11	0.33802288228048	3	FACETS	0.85	0.776	0.928	0.425	0.388	0.464	CLONAL	1	TRUE	1	0.402693900938937	3		795	1053	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056244	26056244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781319824	NA	P-0033764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	93	515	0	ENST00000343677.2:c.413C>T	p.Pro138Leu	p.P138L	ENST00000343677	NM_005319.3	138	cCc/cTc	1/1	0.402693900938937	7	FACETS	0.8	0.709	0.897	0.16	0.141	0.18	SUBCLONAL	1	TRUE	2	0.402693900938937	7		515	1159	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0033768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	202	573	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.252673060543333	3	FACETS	0.914	0.851	0.978	0.914	0.851	0.978	CLONAL	3	TRUE	0	0.252673060543333	3		574	657	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	72	311	2	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	0.252673060543333	3	FACETS	0.779	0.684	0.881	0.779	0.684	0.881	SUBCLONAL	2	TRUE	1	0.252673060543333	3		313	412	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0033768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	44	530	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.252673060543333	3	FACETS	0.866	0.727	1	0.433	0.363	0.51	CLONAL	1	TRUE	1	0.252673060543333	3		530	453	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819651	81819651	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	76	491	0	ENST00000359376.3:c.57G>T	p.Lys19Asn	p.K19N	ENST00000359376	NM_002661.3	19	aaG/aaT	2/33	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.252673060543333	2		491	571	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781440	135781440	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203542	NA	P-0033769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	73	406	0	ENST00000298552.3:c.1525C>T	p.Arg509Ter	p.R509*	ENST00000298552	NM_001162426.1	509	Cga/Tga	15/23	0.308891418839837	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.308891418839837	1		406	329	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411880	116411883	+	intron_variant	Intron	DEL	TCTT	TCTT	-	rs747887276	NA	P-0033769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	133	858	0	ENST00000397752.3:c.2888-16_2888-13del		p.*963*	ENST00000397752	NM_000245.2	-/1390			0.308891418839837	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.308891418839837	1		858	715	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636193	28636193	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	55	368	0	ENST00000241453.7:c.179del	p.Pro60ArgfsTer8	p.P60Rfs*8	ENST00000241453	NM_004119.2	60	cCg/cg	3/24	1	2	FACETS	0.802	0.687	0.927	0.802	0.687	0.927	CLONAL	1	TRUE	1	0.308891418839837	2		368	444	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885972	59885972	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1198536492	NA	P-0033769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	107	585	0	ENST00000259008.2:c.774G>C	p.Gln258His	p.Q258H	ENST00000259008	NM_032043.2	258	caG/caC	7/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.308891418839837	2		585	620	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267500	198267500	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	72	378	4	ENST00000335508.6:c.1857C>G	p.Asn619Lys	p.N619K	ENST00000335508	NM_012433.2	619	aaC/aaG	14/25	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.308891418839837	2		382	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0033770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	73	714	0	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	0.31879713738773	1	FACETS	0.689	0.603	0.781	0.689	0.603	0.781	SUBCLONAL	1	TRUE	0	0.31879713738773	1		714	559	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246048	46246048	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	34	315	0	ENST00000334344.6:c.4142C>G	p.Thr1381Ser	p.T1381S	ENST00000334344	NM_152641.2	1381	aCt/aGt	15/21	1	2	FACETS	0.97	0.798	1	0.97	0.798	1	CLONAL	1	TRUE	1	0.31879713738773	2		315	220	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158715	26158715	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	32	237	0	ENST00000289316.2:c.318G>T	p.Glu106Asp	p.E106D	ENST00000289316	NM_138720.2	106	gaG/gaT	1/2	0.159026402309172	3	FACETS	1	0.86	1	0.531	0.434	0.639	INDETERMINATE	1	TRUE	1	0.31879713738773	3		237	219	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0033771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	106	236	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.758603950244483	2		236	270	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064794618	NA	P-0033771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	409	630	0	ENST00000269305.4:c.159G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgG/tgA	4/11	0.11476026616189	3	FACETS	0.751	0.717	0.785	0.751	0.717	0.785	INDETERMINATE	2	TRUE	1	0.758603950244483	3		630	990	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0033771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	292	421	0	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.11476026616189	3	FACETS	1	0.994	1	0.729	0.69	0.769	INDETERMINATE	1	TRUE	1	0.758603950244483	3		421	728	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139563028	139563028	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758520402	NA	P-0033771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	65	503	1	ENST00000308874.7:c.100C>T	p.Arg34Trp	p.R34W	ENST00000308874		34	Cgg/Tgg	4/10	1	2	FACETS	0.203	0.175	0.234	0.203	0.175	0.234	SUBCLONAL	1	TRUE	1	0.758603950244483	2		504	843	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0033796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	321	458	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.506022485654449	7	FACETS	1	0.982	1	1	0.982	1	CLONAL	4	TRUE	3	0.506022485654449	7		458	676	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983970	2983970	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776851359	NA	P-0033796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	119	826	0	ENST00000396946.4:c.560G>A	p.Arg187Gln	p.R187Q	ENST00000396946	NM_032415.4	187	cGg/cAg	5/25	0.376595519237907	3	FACETS	0.94	0.85	1	0.47	0.425	0.517	CLONAL	1	TRUE	1	0.506022485654449	3		826	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578488	7578494	+	frameshift_variant	Frame_Shift_Del	DEL	CAACCCA	CAACCCA	-	novel	NA	P-0033798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	484	829	0	ENST00000269305.4:c.436_442del	p.Trp146IlefsTer22	p.W146Ifs*22	ENST00000269305	NM_001126112.2	146	TGGGTTGat/at	5/11	0.766925509314333	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.766925509314333	2		829	604	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15952157	15952157	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0033798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	21	530	0	ENST00000268712.3:c.6536+2T>G		p.X2179_splice	ENST00000268712	NM_006311.3	2179			0.766925509314333	2	FACETS	0.136	0.104	0.173	0.068	0.052	0.087	SUBCLONAL	1	TRUE	0	0.766925509314333	2		530	404	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0033803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	42	463	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.5	0.419	0.59	0.5	0.419	0.59	SUBCLONAL	1	TRUE	1	0.514974352302713	2		463	326	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796756	42796756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781265178	NA	P-0033803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	91	680	0	ENST00000575354.2:c.3214G>A	p.Val1072Met	p.V1072M	ENST00000575354	NM_015125.3	1072	Gtg/Atg	14/20	0.419453999801439	3	FACETS	0.439	0.389	0.493	0.22	0.194	0.247	SUBCLONAL	1	TRUE	1	0.514974352302713	3		680	1012	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0033803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	53	338	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	1	2	FACETS	0.891	0.768	1	0.891	0.768	1	CLONAL	1	TRUE	1	0.514974352302713	2		338	231	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs770248150	NA	P-0033803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	107	490	1	ENST00000311936.3:c.351A>T	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaT	4/5	0.419453999801439	3	FACETS	0.904	0.823	0.987	0.904	0.823	0.987	CLONAL	2	TRUE	1	0.514974352302713	3		491	289	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115594	108115594	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730881336	NA	P-0033803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	63	437	1	ENST00000278616.4:c.742C>T	p.Arg248Ter	p.R248*	ENST00000278616	NM_000051.3	248	Cga/Tga	7/63	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.514974352302713	2		438	241	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411678	63411678	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	233	666	1	ENST00000330258.3:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000330258	NM_152424.3	497	Cga/Tga	2/2	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.514974352302713	2		667	743	SUCCESS
APC	324	MSKCC	GRCh37	5	112175952	112175952	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587783031	NA	P-0033803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	24	186	0	ENST00000257430.4:c.4666del	p.Thr1556LeufsTer9	p.T1556Lfs*9	ENST00000257430	NM_000038.5	1554	gAa/ga	16/16	1	2	FACETS	0.533	0.421	0.659	0.533	0.421	0.659	SUBCLONAL	1	TRUE	1	0.514974352302713	2		186	175	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693009	89693010	+	splice_donor_variant	Splice_Site	INS	-	-	TTGT	novel	NA	P-0033803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	10	229	0	ENST00000371953.3:c.492+2_492+3insTGTT		p.X164_splice	ENST00000371953	NM_000314.4	164			1	2	FACETS	0.262	0.178	0.368	0.262	0.178	0.368	SUBCLONAL	1	TRUE	1	0.514974352302713	2		229	148	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588749	29588749	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1060500292	NA	P-0033804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	28	268	0	ENST00000356175.3:c.4535del	p.Arg1512AsnfsTer41	p.R1512Nfs*41	ENST00000356175	NM_000267.3	1512	aGa/aa	34/57	1	2	FACETS	1	0.938	1	1	0.968	1	CLONAL	2	TRUE	1	0.463378586088276	2		268	49	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97869385	97869385	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	23	537	0	ENST00000289081.3:c.1496C>G	p.Pro499Arg	p.P499R	ENST00000289081	NM_000136.2	499	cCt/cGt	14/15	0.325636291306638	1	FACETS	0.625	0.494	0.771	0.625	0.494	0.771	SUBCLONAL	1	TRUE	0	0.463378586088276	1		537	122	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0033809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	65	514	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.791	0.685	0.907	0.791	0.685	0.907	CLONAL	1	TRUE	1	0.234676336658725	2		514	700	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0033809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	69	917	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.234676336658725	1	FACETS	0.532	0.462	0.608	0.532	0.462	0.608	SUBCLONAL	1	TRUE	0	0.234676336658725	1		917	976	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034422	47034438	+	frameshift_variant	Frame_Shift_Del	DEL	GAGCCGGGGCTTCGCCT	GAGCCGGGGCTTCGCCT	-	novel	NA	P-0033809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	108	360	0	ENST00000377604.3:c.507_523del	p.Gln169HisfsTer5	p.Q169Hfs*5	ENST00000377604	NM_001204468.1	169	caGAGCCGGGGCTTCGCCTtc/catc	6/24	1	1	FACETS	0.793	0.715	0.876	1	0.985	1	SUBCLONAL	2	TRUE	0	0.234676336658725	1		360	512	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0033812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	178	663	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.74	0.684	0.798	0.74	0.684	0.798	SUBCLONAL	1	TRUE	1	0.687310647688269	2		663	700	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0033812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	89	438	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.687310647688269	1	FACETS	0.939	0.855	1	0.939	0.855	1	CLONAL	1	TRUE	0	0.687310647688269	1		438	181	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578412	7578412	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519747	NA	P-0033812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	221	576	0	ENST00000269305.4:c.518T>C	p.Val173Ala	p.V173A	ENST00000269305	NM_001126112.2	173	gTg/gCg	5/11	0.629007078846052	1	FACETS	0.867	0.816	0.918	0.867	0.816	0.918	CLONAL	1	TRUE	0	0.687310647688269	1		576	487	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120181	70120182	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CG	novel	NA	P-0033812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	181	378	0	ENST00000245479.2:c.1185_1186dup	p.His396ArgfsTer8	p.H396Rfs*8	ENST00000245479	NM_000346.3	395	acg/aCGcg	3/3	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.687310647688269	2		378	526	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735458	40735458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1243407933	NA	P-0033812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	397	581	0	ENST00000373198.4:c.3415C>T	p.Arg1139Trp	p.R1139W	ENST00000373198	NM_133170.3	1139	Cgg/Tgg	25/32	0.235899085163036	3	FACETS	1	0.986	1	0.706	0.677	0.735	INDETERMINATE	2	TRUE	0	0.687310647688269	3		581	733	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411576	63411576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	212	611	0	ENST00000330258.3:c.1591C>T	p.Arg531Ter	p.R531*	ENST00000330258	NM_152424.3	531	Cga/Tga	2/2	0.306482547240975	1	FACETS	0.599	0.559	0.64	0.599	0.559	0.64	INDETERMINATE	1	TRUE	0	0.687310647688269	1		611	676	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914723	39914723	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	162	413	1	ENST00000378444.4:c.4639C>T	p.Arg1547Ter	p.R1547*	ENST00000378444	NM_001123385.1	1547	Cga/Tga	12/15	0.306482547240975	1	FACETS	0.567	0.523	0.612	0.567	0.523	0.612	INDETERMINATE	1	TRUE	0	0.687310647688269	1		414	546	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197353	26197353	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0033812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	52	318	0	ENST00000356476.2:c.126C>G	p.Tyr42Ter	p.Y42*	ENST00000356476		42	taC/taG	1/1	1	2	FACETS	0.287	0.244	0.334	0.287	0.244	0.334	SUBCLONAL	1	TRUE	1	0.687310647688269	2		318	528	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118377	17118380	+	frameshift_variant	Frame_Shift_Del	DEL	TCAA	TCAA	-	novel	NA	P-0033812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	185	625	0	ENST00000285071.4:c.1457_1460del	p.Ile486LysfsTer4	p.I486Kfs*4	ENST00000285071	NM_144997.5	486	aTTGAa/aa	13/14	0.629007078846052	1	FACETS	0.616	0.572	0.66	0.616	0.572	0.66	SUBCLONAL	1	TRUE	0	0.687310647688269	1		625	574	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420107	41420107	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0033812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	140	221	1	ENST00000373198.4:c.215-1G>A		p.X72_splice	ENST00000373198	NM_133170.3	72			0.235899085163036	3	FACETS	1	0.958	1	0.694	0.646	0.741	INDETERMINATE	2	TRUE	0	0.687310647688269	3		222	263	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045766	143045766	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	45	349	0	ENST00000262992.4:c.1868G>C	p.Arg623Thr	p.R623T	ENST00000262992	NM_001101669.1	623	aGa/aCa	17/24	0.687310647688269	1	FACETS	0.246	0.207	0.288	0.246	0.207	0.288	SUBCLONAL	1	TRUE	0	0.687310647688269	1		349	350	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509870	106509870	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	181	502	0	ENST00000359195.3:c.1864T>G	p.Leu622Val	p.L622V	ENST00000359195	NM_002649.2	622	Ttg/Gtg	2/11	1	2	FACETS	0.788	0.73	0.849	0.788	0.73	0.849	SUBCLONAL	1	TRUE	1	0.687310647688269	2		502	668	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0033813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	244	554	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.51283244851877	3	FACETS	0.916	0.871	0.96	0.916	0.871	0.96	CLONAL	3	FALSE	0	0.546262113796307	3		554	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0033813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	244	540	2	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.546262113796307	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	FALSE	0	0.546262113796307	2		542	446	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101336	27101336	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	199	607	0	ENST00000324856.7:c.4618A>G	p.Asn1540Asp	p.N1540D	ENST00000324856	NM_006015.4	1540	Aac/Gac	18/20	0.301922148570325	4	FACETS	1	0.977	1	1	0.977	1	INDETERMINATE	2	FALSE	2	0.546262113796307	4		607	514	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111437	8111437	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	36	358	0	ENST00000346208.3:c.923C>T	p.Ser308Phe	p.S308F	ENST00000346208		308	tCt/tTt	5/6	0.470809365578485	3	FACETS	0.461	0.379	0.552	0.231	0.189	0.276	SUBCLONAL	1	FALSE	1	0.546262113796307	3		358	364	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219413	1219413	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0033813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	220	509	0	ENST00000326873.7:c.464+1G>A		p.X155_splice	ENST00000326873	NM_000455.4	155			0.546262113796307	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	FALSE	0	0.546262113796307	2		509	395	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198263249	198263249	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	148	527	0	ENST00000335508.6:c.3070T>G	p.Leu1024Val	p.L1024V	ENST00000335508	NM_012433.2	1024	Tta/Gta	21/25	0.41509398275109	5	FACETS	0.774	0.709	0.841			1	SUBCLONAL	2	FALSE	NA	0.546262113796307	5		527	637	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519988	NA	P-0033814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	246	518	0	ENST00000269305.4:c.808T>C	p.Phe270Leu	p.F270L	ENST00000269305	NM_001126112.2	270	Ttt/Ctt	8/11	0.526410174110179	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.543554878143871	1		518	613	SUCCESS
APC	324	MSKCC	GRCh37	5	112175530	112175530	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	89	278	0	ENST00000257430.4:c.4240del	p.Val1414Ter	p.V1414*	ENST00000257430	NM_000038.5	1413	atG/at	16/16	1	2	FACETS	0.84	0.75	0.935	0.84	0.75	0.935	CLONAL	1	TRUE	1	0.543554878143871	2		278	390	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73342975	73342975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757306363	NA	P-0033814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	248	431	1	ENST00000377767.4:c.1831C>T	p.Arg611Cys	p.R611C	ENST00000377767	NM_014953.3	611	Cgt/Tgt	14/21	0.543554878143871	4	FACETS	1	0.968	1	0.696	0.654	0.738	CLONAL	2	TRUE	1	0.543554878143871	4		432	675	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104353811	104353812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0033814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	183	411	0	ENST00000369902.3:c.749_750dup	p.Leu251ThrfsTer17	p.L251Tfs*17	ENST00000369902	NM_016169.3	249	cca/cCAca	6/12	1	2	FACETS	0.938	0.868	1	0.938	0.868	1	CLONAL	1	TRUE	1	0.543554878143871	2		411	718	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120165	70120165	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	179	266	0	ENST00000245479.2:c.1169del	p.Gly390AlafsTer13	p.G390Afs*13	ENST00000245479	NM_000346.3	389	ccG/cc	3/3	0.34785925770496	3	FACETS	0.824	0.766	0.884	0.824	0.766	0.884	CLONAL	2	TRUE	1	0.543554878143871	3		266	508	SUCCESS
APC	324	MSKCC	GRCh37	5	112173728	112173743	+	frameshift_variant	Frame_Shift_Del	DEL	AATTTTAATACTGGCA	AATTTTAATACTGGCA	-	novel	NA	P-0033814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	55	317	0	ENST00000257430.4:c.2438_2453del	p.Asn813ThrfsTer2	p.N813Tfs*2	ENST00000257430	NM_000038.5	813	AATTTTAATACTGGCAac/ac	16/16	1	2	FACETS	0.679	0.585	0.78	0.679	0.585	0.78	SUBCLONAL	1	TRUE	1	0.543554878143871	2		317	298	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5064922	5064922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375678155	NA	P-0033814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	54	370	0	ENST00000381652.3:c.1096G>A	p.Val366Met	p.V366M	ENST00000381652	NM_004972.3	366	Gtg/Atg	9/25	1	2	FACETS	0.656	0.564	0.755	0.656	0.564	0.755	SUBCLONAL	1	TRUE	1	0.543554878143871	2		370	303	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0033816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	79	502	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	0.363104188850235	2		502	384	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0033816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	65	451	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	0.363104188850235	2		451	310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs967461896	NA	P-0033816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	144	670	0	ENST00000269305.4:c.526T>A	p.Cys176Ser	p.C176S	ENST00000269305	NM_001126112.2	176	Tgc/Agc	5/11	0.363104188850235	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.363104188850235	1		670	546	SUCCESS
ATR	545	MSKCC	GRCh37	3	142243013	142243013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	85	441	0	ENST00000350721.4:c.3974G>A	p.Ser1325Asn	p.S1325N	ENST00000350721	NM_001184.3	1325	aGt/aAt	22/47	1	2	FACETS	0.952	0.844	1	0.952	0.844	1	CLONAL	1	TRUE	1	0.363104188850235	2		441	492	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970962	55970962	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	103	572	0	ENST00000263923.4:c.1835T>G	p.Leu612Trp	p.L612W	ENST00000263923	NM_002253.2	612	tTg/tGg	13/30	1	2	FACETS	0.917	0.822	1	0.917	0.822	1	CLONAL	1	TRUE	1	0.363104188850235	2		572	619	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169929	32169929	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	156	735	0	ENST00000375023.3:c.3679G>T	p.Gly1227Trp	p.G1227W	ENST00000375023	NM_004557.3	1227	Ggg/Tgg	21/30	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.363104188850235	2		735	802	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952063	76952063	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0033816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	46	440	0	ENST00000373344.5:c.370+2T>A		p.X124_splice	ENST00000373344	NM_000489.3	124			1	2	FACETS	0.724	0.612	0.847	0.724	0.612	0.847	SUBCLONAL	1	TRUE	1	0.363104188850235	2		440	350	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0033820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	48	451	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.489548126702598	3	FACETS	1	0.961	1	0.697	0.599	0.802	CLONAL	1	TRUE	1	0.489548126702598	3		451	175	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266835	+	missense_variant	Missense_Mutation	DNP	TC	TC	CA	novel	NA	P-0033820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	128	427	0	ENST00000335508.6:c.2097_2098delinsTG	p.Gln699_Lys700delinsHisGlu	p.Q699_K700delinsHE	ENST00000335508	NM_012433.2	699	caGAaa/caTGaa	15/25	0.489548126702598	3	FACETS	0.826	0.756	0.898	0.826	0.756	0.898	CLONAL	2	TRUE	1	0.489548126702598	3		427	394	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31423030	31423030	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	51	404	0	ENST00000344624.3:c.3283C>T	p.Arg1095Ter	p.R1095*	ENST00000344624		1095	Cga/Tga	26/33	0.489548126702598	4	FACETS	0.9	0.768	1	0.45	0.384	0.522	CLONAL	1	TRUE	2	0.489548126702598	4		404	345	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937261	76937261	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	117	488	0	ENST00000373344.5:c.3487G>C	p.Glu1163Gln	p.E1163Q	ENST00000373344	NM_000489.3	1163	Gaa/Caa	9/35	0.318252650928699	5	FACETS	1	0.969	1	0.763	0.696	0.833	CLONAL	2	TRUE	2	0.489548126702598	5		488	362	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261314	16261314	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	GT	novel	NA	P-0033820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	66	518	0	ENST00000375759.3:c.8579delinsGT	p.Ser2860CysfsTer35	p.S2860Cfs*35	ENST00000375759	NM_015001.2	2860	tCt/tGTt	11/15	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.489548126702598	2		518	237	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041788	42041788	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	148	325	0	ENST00000219905.7:c.5983C>T	p.Gln1995Ter	p.Q1995*	ENST00000219905	NM_001164273.1	1995	Cag/Tag	17/24	0.673961894177196	1	FACETS	0.952	0.885	1	0.952	0.885	1	CLONAL	1	TRUE	0	0.673961894177196	1		325	306	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923411	9923411	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	212	554	0	ENST00000330684.3:c.1876A>G	p.Thr626Ala	p.T626A	ENST00000330684	NM_001134407.1	626	Acc/Gcc	9/13	1	2	FACETS	0.983	0.918	1	0.983	0.918	1	CLONAL	1	TRUE	1	0.673961894177196	2		554	640	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132430	11132430	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	237	661	0	ENST00000358026.2:c.2646A>C	p.Glu882Asp	p.E882D	ENST00000358026	NM_001128849.1	882	gaA/gaC	19/36	1	2	FACETS	0.85	0.796	0.907	0.85	0.796	0.907	CLONAL	1	TRUE	1	0.673961894177196	2		661	827	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021446	31021446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	190	358	1	ENST00000375687.4:c.1445C>T	p.Pro482Leu	p.P482L	ENST00000375687	NM_015338.5	482	cCa/cTa	12/13	1	2	FACETS	0.987	0.919	1	0.987	0.919	1	CLONAL	1	TRUE	1	0.673961894177196	2		359	571	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386604	81386604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	128	466	0	ENST00000222390.5:c.383G>A	p.Cys128Tyr	p.C128Y	ENST00000222390	NM_000601.4	128	tGc/tAc	4/18	1	2	FACETS	0.856	0.781	0.932	0.856	0.781	0.932	CLONAL	1	TRUE	1	0.673961894177196	2		466	444	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0033835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	354	463	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.547559911140613	7	FACETS	1	0.992	1	0.414	0.392	0.437	CLONAL	2	TRUE	1	0.547559911140613	7		463	1233	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0033835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	283	440	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	0.547559911140613	3	FACETS	0.893	0.844	0.943	0.893	0.844	0.943	CLONAL	2	TRUE	1	0.547559911140613	3		440	737	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0033835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	176	604	1	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	0.547559911140613	2		605	582	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401074	139401074	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746910989	NA	P-0033835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	222	789	1	ENST00000277541.6:c.3919G>A	p.Val1307Ile	p.V1307I	ENST00000277541	NM_017617.3	1307	Gtc/Atc	24/34	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.547559911140613	2		790	798	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298797	15298797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1208817958	NA	P-0033835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	200	739	0	ENST00000263388.2:c.1501G>A	p.Gly501Ser	p.G501S	ENST00000263388	NM_000435.2	501	Ggc/Agc	10/33	1	2	FACETS	0.946	0.879	1	0.946	0.879	1	CLONAL	1	TRUE	1	0.547559911140613	2		739	772	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517532	176517532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200146267	NA	P-0033835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	258	818	2	ENST00000292408.4:c.233G>A	p.Arg78His	p.R78H	ENST00000292408	NM_213647.1	78	cGt/cAt	3/18	0.547559911140613	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.547559911140613	1		820	608	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210645	2210645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369996787	NA	P-0033835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	143	664	2	ENST00000398665.3:c.1142C>T	p.Ala381Val	p.A381V	ENST00000398665	NM_032482.2	381	gCg/gTg	14/28	1	2	FACETS	0.976	0.895	1	0.976	0.895	1	CLONAL	1	TRUE	1	0.547559911140613	2		666	535	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699324	18699324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369934938	NA	P-0033835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	117	424	0	ENST00000266497.5:c.3425G>A	p.Arg1142His	p.R1142H	ENST00000266497		1142	cGt/cAt	24/31	1	2	FACETS	0.945	0.858	1	0.945	0.858	1	CLONAL	1	TRUE	1	0.547559911140613	2		424	452	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	41	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.744	0.625	0.874	0.744	0.625	0.874	SUBCLONAL	1	TRUE	1	0.474864295009205	2		148	232	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685300	89685300	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs878853936	NA	P-0033883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	61	278	0	ENST00000371953.3:c.195C>A	p.Tyr65Ter	p.Y65*	ENST00000371953	NM_000314.4	65	taC/taA	3/9	0.474864295009205	1	FACETS	0.806	0.704	0.915	0.806	0.704	0.915	CLONAL	1	TRUE	0	0.474864295009205	1		278	243	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684061	29684061	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	101	492	0	ENST00000356175.3:c.7759G>T	p.Glu2587Ter	p.E2587*	ENST00000356175	NM_000267.3	2587	Gaa/Taa	52/57	0.474864295009205	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.474864295009205	1		492	314	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761014	59761017	+	frameshift_variant	Frame_Shift_Del	DEL	ATAG	ATAG	-	rs778664039	NA	P-0033885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	65	267	0	ENST00000259008.2:c.3390_3393del	p.Tyr1131LeufsTer18	p.Y1131Lfs*18	ENST00000259008	NM_032043.2	1130	atCTAT/at	20/20	0.222045975146887	0	FACETS	0.547	0.483	0.613			1	INDETERMINATE	1	FALSE	0	0.551950714383335	0		267	193	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252994	36252995	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0033885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	187	363	0	ENST00000300305.3:c.367dup	p.Asp123GlyfsTer15	p.D123Gfs*15	ENST00000300305		123	gat/gGat	4/8	1	2	FACETS	0.782	0.731	0.834	1	0.992	1	SUBCLONAL	2	FALSE	1	0.551950714383335	2		363	433	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720857	89720857	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs786201816	NA	P-0033885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	152	165	0	ENST00000371953.3:c.1008C>G	p.Tyr336Ter	p.Y336*	ENST00000371953	NM_000314.4	336	taC/taG	8/9	0.28693176300882	1	FACETS	1	0.988	1	1	0.994	1	INDETERMINATE	2	FALSE	0	0.551950714383335	1		165	181	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279674	123279674	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs77543610	NA	P-0033885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	21	348	0	ENST00000358487.5:c.758C>G	p.Pro253Arg	p.P253R	ENST00000358487	NM_000141.4	253	cCt/cGt	7/18	1	2	FACETS	0.277	0.213	0.351	0.277	0.213	0.351	SUBCLONAL	1	FALSE	1	0.551950714383335	2		348	275	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404534	70404534	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	149	350	0	ENST00000373644.4:c.2048A>G	p.Gln683Arg	p.Q683R	ENST00000373644	NM_030625.2	683	cAa/cGa	4/12	0.483019888517795	4	FACETS	1	0.981	1			1	CLONAL	2	FALSE	NA	0.551950714383335	4		350	356	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857388	68857388	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0033885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	176	465	0	ENST00000261769.5:c.2023A>T	p.Lys675Ter	p.K675*	ENST00000261769	NM_004360.3	675	Aaa/Taa	13/16	0.566316034030894	1	FACETS	0.966	0.92	1	1	0.994	1	CLONAL	2	FALSE	0	0.551950714383335	1		465	239	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155236	55155236	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	12	482	0	ENST00000257290.5:c.2835C>A	p.His945Gln	p.H945Q	ENST00000257290	NM_006206.4	945	caC/caA	21/23	0.468958271652794	0	FACETS	0.106	0.075	0.146			1	SUBCLONAL	1	FALSE	0	0.551950714383335	0		482	183	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004907	16004907	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	11	649	1	ENST00000268712.3:c.2347del	p.Gln783ArgfsTer2	p.Q783Rfs*2	ENST00000268712	NM_006311.3	783	Cag/ag	20/46	0.566316034030894	0	FACETS	0.248	0.174	0.337			1	SUBCLONAL	1	FALSE	0	0.551950714383335	0		650	72	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639760	3639760	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	100	759	1	ENST00000294008.3:c.3879G>T	p.Arg1293Ser	p.R1293S	ENST00000294008	NM_032444.2	1293	agG/agT	12/15	0.247192055672929	4	FACETS	0.602	0.536	0.673	0.301	0.268	0.337	SUBCLONAL	1	TRUE	2	0.340963228878146	4		760	1307	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	220	632	0	ENST00000269305.4:c.548C>A	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tAa	5/11	0.313637142337669	2	FACETS	0.95	0.888	1	0.95	0.888	1	CLONAL	2	TRUE	0	0.340963228878146	2		632	679	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715672	30715672	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	124	333	0	ENST00000295754.5:c.1330C>A	p.Gln444Lys	p.Q444K	ENST00000295754	NM_003242.5	444	Cag/Aag	5/7	0.313637142337669	2	FACETS	0.806	0.735	0.881	0.806	0.735	0.881	CLONAL	2	TRUE	0	0.340963228878146	2		333	451	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84384038	84384038	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	198	560	0	ENST00000321945.7:c.814A>G	p.Lys272Glu	p.K272E	ENST00000321945	NM_139076.2	272	Aaa/Gaa	9/9	0.202541309191764	4	FACETS	0.802	0.743	0.863	0.802	0.743	0.863	INDETERMINATE	2	TRUE	2	0.340963228878146	4		560	971	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0033891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	711	896	2	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.804603615908972	2	FACETS	0.984	0.964	1	0.984	0.964	1	CLONAL	2	TRUE	0	0.816624062012397	2		898	885	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572033	64572033	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	529	807	4	ENST00000312049.6:c.1606C>T	p.Gln536Ter	p.Q536*	ENST00000312049	NM_130799.2	536	Cag/Tag	10/10	0.799045982121781	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.816624062012397	2		811	637	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984884	101984884	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	372	566	0	ENST00000282441.5:c.331G>C	p.Asp111His	p.D111H	ENST00000282441	NM_001130145.2	111	Gat/Cat	2/9	0.799045982121781	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.816624062012397	2		566	454	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783667	50783668	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	59	608	0	ENST00000398568.2:c.64dup	p.Tyr22LeufsTer19	p.Y22Lfs*19	ENST00000398568	NM_001042412.1	20	att/aTtt	3/18	0.804603615908972	2	FACETS	0.323	0.278	0.372	0.162	0.139	0.186	SUBCLONAL	1	TRUE	0	0.816624062012397	2		608	447	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744424	41744424	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	233	815	0	ENST00000301178.4:c.1045del	p.Ala349ProfsTer17	p.A349Pfs*17	ENST00000301178	NM_021913.4	348	caG/ca	8/20	0.81381432963139	2	FACETS	0.929	0.873	0.987	0.465	0.436	0.494	CLONAL	1	TRUE	0	0.816624062012397	2		815	614	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55991458	55991458	+	start_lost	Translation_Start_Site	SNP	C	C	A	novel	NA	P-0033891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	349	607	1	ENST00000263923.4:c.3G>T	p.Met1?	p.M1?	ENST00000263923	NM_002253.2	1	atG/atT	1/30	0.804603615908972	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.816624062012397	2		608	417	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884392	151884392	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	43	391	0	ENST00000262189.6:c.4963C>A	p.Leu1655Ile	p.L1655I	ENST00000262189	NM_170606.2	1655	Ctc/Atc	33/59	0.816871491689824	3	FACETS	0.336	0.281	0.396	0.168	0.14	0.198	SUBCLONAL	1	TRUE	1	0.816624062012397	3		391	442	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40742002	40742005	+	missense_variant	Missense_Mutation	ONP	CCTC	CCTC	TCTT	novel	NA	P-0033895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	80	670	0	ENST00000392038.2:c.967_970delinsAAGA	p.Glu323_Asp324delinsLysAsn	p.E323_D324delinsKN	ENST00000392038	NM_001626.4	323	GAGGac/AAGAac	11/14	1	2	FACETS	0.988	0.877	1	0.988	0.877	1	CLONAL	1	TRUE	1	0.492467425983042	2		670	329	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	395	148	0				ENST00000310581	NM_198253.2	-/1132			0.108560327948727	10	FACETS	0.992	0.959	1	1	0.997	1	CLONAL	19	TRUE	1	0.108560327948727	10		148	554	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0033897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	74	451	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.981	0.888	1	1	0.99	1	CLONAL	10	TRUE	1	0.108560327948727	2		451	139	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831326	89831326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747220449	NA	P-0033897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	232	466	0	ENST00000389301.3:c.2750G>A	p.Arg917Gln	p.R917Q	ENST00000389301	NM_000135.2	917	cGa/cAa	28/43	1	2	FACETS	1	0.949	1	1	0.996	1	CLONAL	8	TRUE	1	0.108560327948727	2		466	530	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0033901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	78	236	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.887	0.788	0.992	0.887	0.788	0.992	CLONAL	1	TRUE	1	0.6	2		236	293	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0033901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	73	675	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.373	0.326	0.424	0.373	0.326	0.424	SUBCLONAL	1	TRUE	1	0.6	2		675	652	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0033901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	311	767	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.805	0.766	0.844	1	0.995	1	CLONAL	2	TRUE	1	0.6	2		767	644	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845526	72845526	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	185	616	0	ENST00000268489.5:c.3814A>G	p.Thr1272Ala	p.T1272A	ENST00000268489	NM_006885.3	1272	Acc/Gcc	7/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.6	2		616	591	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224474	224474	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0033901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	10	69	0	ENST00000264932.6:c.151-1G>A		p.X51_splice	ENST00000264932	NM_004168.2	51			0.172757435702807	0	FACETS	0.185	0.127	0.256			1	INDETERMINATE	1	TRUE	0	0.6	0		69	72	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224511	224511	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	43	226	0	ENST00000264932.6:c.187G>A	p.Asp63Asn	p.D63N	ENST00000264932	NM_004168.2	63	Gat/Aat	3/15	0.172757435702807	0	FACETS	0.209	0.176	0.246			1	INDETERMINATE	1	TRUE	0	0.6	0		226	274	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918931	76918934	+	frameshift_variant	Frame_Shift_Del	DEL	CTCC	CTCC	-	novel	NA	P-0033901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	244	346	0	ENST00000373344.5:c.4057_4060del	p.Gly1353LysfsTer21	p.G1353Kfs*21	ENST00000373344	NM_000489.3	1353	GGAGaa/aa	12/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.6	1		346	407	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225549	225549	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	13	111	0	ENST00000264932.6:c.328G>A	p.Ala110Thr	p.A110T	ENST00000264932	NM_004168.2	110	Gct/Act	4/15	0.172757435702807	0	FACETS	0.143	0.103	0.192			1	INDETERMINATE	1	TRUE	0	0.6	0		111	121	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247516	123247516	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519795	NA	P-0033927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	385	680	0	ENST00000358487.5:c.1975A>G	p.Lys659Glu	p.K659E	ENST00000358487	NM_000141.4	659	Aag/Gag	14/18	0.918737899154986	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.918737899154986	1		680	430	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0033929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	35	425	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.613	0.501	0.74	0.613	0.501	0.74	SUBCLONAL	1	TRUE	1	0.15	2		425	761	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922593	56922593	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	50	609	0	ENST00000519728.1:c.1463C>T	p.Pro488Leu	p.P488L	ENST00000519728	NM_002350.3	488	cCa/cTa	13/13	1	2	FACETS	0.848	0.718	0.992	0.848	0.718	0.992	CLONAL	1	TRUE	1	0.15	2		609	786	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933061	39933062	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0033929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	50	920	1	ENST00000378444.4:c.1537_1538delinsCT	p.Gly513Leu	p.G513L	ENST00000378444	NM_001123385.1	513	GGg/CTg	4/15	1	2	FACETS	0.676	0.572	0.792	0.676	0.572	0.792	SUBCLONAL	1	TRUE	1	0.15	2		921	986	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040620	47040620	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033929-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	57	488	5	ENST00000377604.3:c.1255C>T	p.Gln419Ter	p.Q419*	ENST00000377604	NM_001204468.1	419	Caa/Taa	13/24	1	2	FACETS	0.909	0.783	1	0.909	0.783	1	CLONAL	1	FALSE	1	0.325043412115258	2		493	386	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0033929-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	23	666	0	ENST00000311936.3:c.34_35delinsTT	p.Gly12Phe	p.G12F	ENST00000311936	NM_004985.3	12	GGt/TTt	2/5	0.105347292471907	3	FACETS	0.43	0.334	0.54	0.215	0.167	0.27	INDETERMINATE	1	FALSE	1	0.325043412115258	3		666	383	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390649	139390650	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs763016003	NA	P-0033929-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	61	825	9	ENST00000277541.6:c.7541_7542del	p.Pro2514ArgfsTer4	p.P2514Rfs*4	ENST00000277541	NM_017617.3	2514	cCT/c	34/34	0.184895212282338	3	FACETS	0.556	0.478	0.64	0.278	0.239	0.32	INDETERMINATE	1	FALSE	1	0.325043412115258	3		834	785	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829066	128829066	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs41304185	NA	P-0033929-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	17	17	1	ENST00000249373.3:c.74A>G	p.Asp25Gly	p.D25G	ENST00000249373	NM_005631.4	25	gAc/gGc	1/12	1	2	FACETS	1	0.882	1	1	0.944	1	CLONAL	2	FALSE	1	0.325043412115258	2		18	43	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944872	31944872	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033929-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	54	546	2	ENST00000340398.3:c.229G>T	p.Asp77Tyr	p.D77Y	ENST00000340398	NM_001013699.2	77	Gat/Tat	1/1	0.105347292471907	3	FACETS	0.7	0.598	0.812	0.35	0.299	0.406	INDETERMINATE	1	FALSE	1	0.325043412115258	3		548	552	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967836	93967836	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033929-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	34	611	0	ENST00000369303.4:c.2091G>T	p.Leu697Phe	p.L697F	ENST00000369303	NM_004440.3	697	ttG/ttT	11/17	0.325043412115258	0	FACETS	0.948	0.786	1			1	CLONAL	1	FALSE	0	0.325043412115258	0		611	149	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399171	139399187	+	frameshift_variant	Frame_Shift_Del	DEL	CGCTGCCACCAGGGAGC	CGCTGCCACCAGGGAGC	-	novel	NA	P-0033929-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	58	659	0	ENST00000277541.6:c.4956_4972del	p.Leu1653GlyfsTer23	p.L1653Gfs*23	ENST00000277541	NM_017617.3	1652	ctGCTCCCTGGTGGCAGCGag/ctag	26/34	0.184895212282338	3	FACETS	0.685	0.588	0.79	0.342	0.294	0.395	INDETERMINATE	1	FALSE	1	0.325043412115258	3		659	606	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	136	460	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.22431339831634	3	FACETS	0.924	0.844	1	0.924	0.844	1	CLONAL	2	FALSE	1	0.3	3		460	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0033937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	140	694	1	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.214348298028242	2	FACETS	0.755	0.69	0.823	0.755	0.69	0.823	SUBCLONAL	2	FALSE	0	0.3	2		695	618	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573586	48573586	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	20	369	0	ENST00000342988.3:c.170T>C	p.Leu57Ser	p.L57S	ENST00000342988	NM_005359.5	57	tTa/tCa	2/12	0.3	1	FACETS	0.495	0.379	0.629	0.495	0.379	0.629	SUBCLONAL	1	FALSE	0	0.3	1		369	229	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999062	100999062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	22	631	0	ENST00000325455.5:c.740C>T	p.Ala247Val	p.A247V	ENST00000325455	NM_001202474.3	247	gCg/gTg	1/8	0.22431339831634	3	FACETS	0.402	0.31	0.508	0.201	0.155	0.254	SUBCLONAL	1	FALSE	1	0.3	3		631	420	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21565492	21565492	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	58	799	1	ENST00000382592.4:c.394G>T	p.Ala132Ser	p.A132S	ENST00000382592	NM_014572.2	132	Gcc/Tcc	3/8	0.243870363989463	4	FACETS	0.622	0.533	0.72	0.207	0.177	0.24	SUBCLONAL	1	FALSE	1	0.3	4		800	808	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89851354	89851354	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1438828232	NA	P-0033937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	95	579	2	ENST00000389301.3:c.1378C>T	p.Arg460Ter	p.R460*	ENST00000389301	NM_000135.2	460	Cga/Tga	15/43	0.0899755809707381	3	FACETS	1	0.98	1	0.734	0.656	0.817	INDETERMINATE	1	FALSE	1	0.3	3		581	496	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626792	14626793	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0033937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	55	664	0	ENST00000254322.2:c.981_982dup	p.Gln328ProfsTer79	p.Q328Pfs*79	ENST00000254322	NM_006145.1	328	cag/cCCag	3/3	1	2	FACETS	0.523	0.447	0.607	0.523	0.447	0.607	SUBCLONAL	1	FALSE	1	0.3	2		664	701	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039413	47039413	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	53	348	0	ENST00000377604.3:c.1036G>C	p.Ala346Pro	p.A346P	ENST00000377604	NM_001204468.1	346	Gcc/Ccc	10/24	1	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	0	0.3	1		348	237	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0033941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	123	573	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.362358262783	1	FACETS	0.766	0.693	0.842	0.766	0.693	0.842	SUBCLONAL	1	TRUE	0	0.362358262783	1		574	726	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0033941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	152	528	2	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.336074521957957	3	FACETS	0.874	0.809	0.939	1	0.986	1	CLONAL	3	TRUE	1	0.362358262783	3		530	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577578	7577578	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	323	613	0	ENST00000269305.4:c.703A>G	p.Asn235Asp	p.N235D	ENST00000269305	NM_001126112.2	235	Aac/Gac	7/11	0.362358262783	1	FACETS	1	0.971	1	1	0.996	1	CLONAL	2	TRUE	0	0.362358262783	1		613	709	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922097	39922097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1249334408	NA	P-0033941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	170	409	1	ENST00000378444.4:c.4075G>A	p.Gly1359Arg	p.G1359R	ENST00000378444	NM_001123385.1	1359	Ggg/Agg	9/15	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.362358262783	1		410	625	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884908	134884908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202034365	NA	P-0033941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	120	572	2	ENST00000398015.3:c.1684G>A	p.Val562Ile	p.V562I	ENST00000398015	NM_004441.4	562	Gtc/Atc	8/16	0.341534961309627	3	FACETS	0.805	0.726	0.889	0.402	0.363	0.445	CLONAL	1	TRUE	1	0.362358262783	3		574	972	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795037	45795037	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	107	553	0	ENST00000450313.1:c.1591A>G	p.Asn531Asp	p.N531D	ENST00000450313	NM_012222.2	531	Aat/Gat	16/16	0.107822022142387	5	FACETS	0.974	0.872	1	0.243	0.218	0.271	INDETERMINATE	1	TRUE	1	0.362358262783	5		553	936	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710658	114710659	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0033941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	233	385	0	ENST00000543371.1:c.143_144del	p.Leu48ArgfsTer3	p.L48Rfs*3	ENST00000543371	NM_001198531.1	48	cTA/c	1/14	0.186348731542525	3	FACETS	0.934	0.88	0.989			1	INDETERMINATE	3	TRUE	NA	0.362358262783	3		385	542	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375407	40375407	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	267	528	0	ENST00000293328.3:c.543G>T	p.Arg181Ser	p.R181S	ENST00000293328	NM_012448.3	181	agG/agT	5/19	1	2	FACETS	0.957	0.901	1	1	0.995	1	CLONAL	2	TRUE	1	0.362358262783	2		528	770	SUCCESS
APC	324	MSKCC	GRCh37	5	112174132	112174132	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0033941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	93	427	0	ENST00000257430.4:c.2841T>A	p.Cys947Ter	p.C947*	ENST00000257430	NM_000038.5	947	tgT/tgA	16/16	1	2	FACETS	0.844	0.76	0.932	1	0.985	1	CLONAL	2	TRUE	1	0.362358262783	2		427	304	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	21	148	0				ENST00000310581	NM_198253.2	-/1132			0.563852621426363	2	FACETS	0.203	0.156	0.258	0.102	0.078	0.129	SUBCLONAL	1	TRUE	0	0.691741864318532	2		148	299	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0033947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	348	632	0	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	1	2	FACETS	0.76	0.726	0.793	1	0.996	1	SUBCLONAL	2	TRUE	1	0.691741864318532	2		632	662	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857203	9857203	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	111	478	0	ENST00000330684.3:c.4198T>C	p.Tyr1400His	p.Y1400H	ENST00000330684	NM_001134407.1	1400	Tat/Cat	13/13	0.192043851522422	2	FACETS	0.655	0.592	0.721	0.327	0.296	0.361	INDETERMINATE	1	TRUE	0	0.691741864318532	2		478	490	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589630	67589632	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0033947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	78	253	0	ENST00000274335.5:c.1393_1395del	p.Arg465del	p.R465del	ENST00000274335		465	AGA/-	10/15	0.563852621426363	2	FACETS	0.789	0.717	0.859	0.789	0.717	0.859	SUBCLONAL	2	TRUE	0	0.691741864318532	2		253	143	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819326	3819326	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	420	577	0	ENST00000262367.5:c.2909A>C	p.Asn970Thr	p.N970T	ENST00000262367	NM_004380.2	970	aAc/aCc	15/31	0.761278951280202	4	FACETS	0.902	0.863	0.942	0.902	0.863	0.942	CLONAL	2	TRUE	2	0.883962668610238	4		577	992	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602619	10602619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	483	603	0	ENST00000171111.5:c.959G>A	p.Arg320Gln	p.R320Q	ENST00000171111	NM_203500.1	320	cGg/cAg	3/6	0.829151656377594	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	2	0.883962668610238	4		603	1029	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371634	225371634	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	232	563	0	ENST00000264414.4:c.970C>T	p.Gln324Ter	p.Q324*	ENST00000264414	NM_003590.4	324	Caa/Taa	7/16	0.436044210377925	5	FACETS	0.851	0.804	0.899			1	INDETERMINATE	3	TRUE	NA	0.883962668610238	5		563	478	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507374	8507374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	268	368	1	ENST00000356435.5:c.1604C>T	p.Ser535Phe	p.S535F	ENST00000356435		535	tCt/tTt	11/35	0.249832241524837	6	FACETS	0.971	0.92	1	0.971	0.92	1	INDETERMINATE	3	TRUE	3	0.883962668610238	6		369	576	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0033952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	348	317	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	0.249832241524837	6	FACETS	1	0.969	1	1	0.969	1	INDETERMINATE	3	TRUE	3	0.883962668610238	6		317	713	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889150	76889152	+	frameshift_variant	Frame_Shift_Del	DEL	GCT	GCT	CA	novel	NA	P-0033953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	158	149	1	ENST00000373344.5:c.4858_4860delinsTG	p.Ser1620Ter	p.S1620*	ENST00000373344	NM_000489.3	1620	AGC/TG	18/35	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.691288020221118	1		150	237	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0033954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	235	880	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.479367956679491	1	FACETS	0.963	0.902	1	0.963	0.902	1	CLONAL	1	TRUE	0	0.479367956679491	1		882	774	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0033954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	211	608	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	0.479367956679491	2		608	762	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0033954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	73	196	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.479367956679491	2	FACETS	0.828	0.74	0.918	0.828	0.74	0.918	CLONAL	2	TRUE	0	0.479367956679491	2		196	184	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533939	63533940	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs771001164	NA	P-0033954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	116	427	0	ENST00000307078.5:c.1214_1215del	p.Glu405GlyfsTer56	p.E405Gfs*56	ENST00000307078	NM_004655.3	405	gAG/g	6/11	0.281965777516865	3	FACETS	0.924	0.835	1	0.462	0.417	0.51	INDETERMINATE	1	TRUE	1	0.479367956679491	3		427	649	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431018	181431018	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	168	619	0	ENST00000325404.1:c.870C>A	p.Ser290Arg	p.S290R	ENST00000325404	NM_003106.3	290	agC/agA	1/1	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.479367956679491	2		619	585	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922974	44922974	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	85	258	0	ENST00000377967.4:c.1835G>T	p.Arg612Leu	p.R612L	ENST00000377967	NM_021140.2	612	cGa/cTa	16/29	0.276271731571286	3	FACETS	0.814	0.721	0.913			1	INDETERMINATE	1	TRUE	NA	0.479367956679491	3		258	540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0033959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	741	494	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.682993893612414	6	FACETS	1	0.995	1	1	0.995	1	CLONAL	5	FALSE	1	0.682993893612414	6		495	969	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0033959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	57	103	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	0.682993893612414	6	FACETS	0.914	0.816	1	0.914	0.816	1	CLONAL	4	FALSE	2	0.682993893612414	6		103	108	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578441	7578441	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	183	750	1	ENST00000269305.4:c.489C>A	p.Tyr163Ter	p.Y163*	ENST00000269305	NM_001126112.2	163	taC/taA	5/11	0.682993893612414	6	FACETS	1	0.986	1	0.26	0.24	0.281	CLONAL	1	FALSE	1	0.682993893612414	6		751	975	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140726	55140727	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCAGTCCTGGTGCTGTTGGTGATTGTGATCATCTCACTTATG	novel	NA	P-0033959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	334	764	0	ENST00000257290.5:c.1628_1629insGGCAGTCCTGGTGCTGTTGGTGATTGTGATCATCTCACTTAT	p.Leu542_Ile543insMetAlaValLeuValLeuLeuValIleValIleIleSerLeu	p.L542_I543insMAVLVLLVIVIISL	ENST00000257290	NM_006206.4	529	-/GCAGTCCTGGTGCTGTTGGTGATTGTGATCATCTCACTTATG	11/23	0.463485665384492	6	FACETS	0.898	0.848	0.948	0.598	0.565	0.632	CLONAL	2	FALSE	3	0.682993893612414	6		764	1289	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469669	NA	P-0033962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	27	465	0	ENST00000374080.3:c.130G>A	p.Gly44Ser	p.G44S	ENST00000374080		44	Ggt/Agt	2/45	1	2	FACETS	0.115	0.091	0.143	0.115	0.091	0.143	SUBCLONAL	1	TRUE	1	0.69075045609203	2		465	681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577098	7577098	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	336	704	1	ENST00000269305.4:c.840A>T	p.Arg280Ser	p.R280S	ENST00000269305	NM_001126112.2	280	agA/agT	8/11	0.69075045609203	1	FACETS	0.994	0.949	1	0.994	0.949	1	CLONAL	1	TRUE	0	0.69075045609203	1		705	641	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032006	26032006	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	71	388	0	ENST00000244661.2:c.283G>C	p.Glu95Gln	p.E95Q	ENST00000244661	NM_003537.3	95	Gag/Cag	1/1	0.69075045609203	3	FACETS	0.539	0.471	0.612	0.27	0.235	0.306	SUBCLONAL	1	TRUE	1	0.69075045609203	3		388	513	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266862	18266865	+	frameshift_variant	Frame_Shift_Del	DEL	CCGG	CCGG	-	novel	NA	P-0033962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	23	221	0	ENST00000222254.8:c.175_178del	p.Gly59SerfsTer70	p.G59Sfs*70	ENST00000222254	NM_005027.3	58	cCCGGc/cc	2/16	0.20191763020909	1	FACETS	0.128	0.1	0.161	0.128	0.1	0.161	INDETERMINATE	1	TRUE	0	0.69075045609203	1		221	340	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573577	41573578	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	38	687	0	ENST00000263253.7:c.5862_5863delinsTT	p.Gln1955Ter	p.Q1955*	ENST00000263253	NM_001429.3	1954	caCCag/caTTag	31/31	0.443376075209123	1	FACETS	0.12	0.099	0.144	0.12	0.099	0.144	SUBCLONAL	1	TRUE	0	0.69075045609203	1		687	600	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589556	67589558	+	inframe_deletion	In_Frame_Del	DEL	ATA	ATA	-	novel	NA	P-0033962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	44	251	0	ENST00000274335.5:c.1322_1324del	p.Asn441del	p.N441del	ENST00000274335		440	gATAat/gat	10/15	1	2	FACETS	0.801	0.684	0.926	0.801	0.684	0.926	CLONAL	1	TRUE	1	0.69075045609203	2		251	159	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555021	106555021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	155	455	1	ENST00000369096.4:c.2138C>T	p.Ala713Val	p.A713V	ENST00000369096	NM_001198.3	713	gCc/gTc	7/7	0.69075045609203	3	FACETS	0.903	0.829	0.979	0.451	0.414	0.49	CLONAL	1	TRUE	1	0.69075045609203	3		456	669	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845210	128845210	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	29	559	1	ENST00000249373.3:c.704C>A	p.Ala235Glu	p.A235E	ENST00000249373	NM_005631.4	235	gCg/gAg	3/12	1	2	FACETS	0.145	0.116	0.179	0.145	0.116	0.179	SUBCLONAL	1	TRUE	1	0.69075045609203	2		560	579	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498004	29498004	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1208550472	NA	P-0033965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	132	566	0	ENST00000389048.3:c.2002G>A	p.Glu668Lys	p.E668K	ENST00000389048	NM_004304.4	668	Gaa/Aaa	11/29	1	2	FACETS	0.951	0.876	1	0.951	0.876	1	CLONAL	1	TRUE	1	0.849188686539751	2		566	327	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453136	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	rs397516897	NA	P-0033965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	130	296	0	ENST00000288602.6:c.1799_1801del	p.Val600_Lys601delinsGlu	p.V600_K601delinsE	ENST00000288602	NM_004333.4	600	gTGAaa/gaa	15/18	0.46471583018706	4	FACETS	0.886	0.828	0.943	0.886	0.828	0.943	INDETERMINATE	3	TRUE	1	0.849188686539751	4		296	213	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692910	89692910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	77	623	0	ENST00000371953.3:c.394G>A	p.Gly132Ser	p.G132S	ENST00000371953	NM_000314.4	132	Ggt/Agt	5/9	0.849188686539751	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.849188686539751	1		623	99	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048602	180048602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778453271	NA	P-0033965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	210	692	0	ENST00000261937.6:c.1960G>A	p.Glu654Lys	p.E654K	ENST00000261937	NM_182925.4	654	Gaa/Aaa	13/30	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.849188686539751	2		692	471	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450712	70450712	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	116	476	0	ENST00000373644.4:c.5552C>T	p.Ser1851Phe	p.S1851F	ENST00000373644	NM_030625.2	1851	tCc/tTc	12/12	0.849188686539751	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.849188686539751	1		476	155	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78866571	78866571	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	214	633	0	ENST00000306801.3:c.2144C>T	p.Pro715Leu	p.P715L	ENST00000306801	NM_020761.2	715	cCc/cTc	19/34	1	2	FACETS	0.955	0.895	1	0.955	0.895	1	CLONAL	1	TRUE	1	0.849188686539751	2		633	528	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0033965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	98	274	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.849188686539751	2		274	215	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001309	29001309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	57	246	0	ENST00000282397.4:c.1423C>T	p.His475Tyr	p.H475Y	ENST00000282397	NM_002019.4	475	Cat/Tat	10/30	0.651675137834737	1	FACETS	0.56	0.493	0.628	0.56	0.493	0.628	SUBCLONAL	1	TRUE	0	0.849188686539751	1		246	138	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17743029	17743029	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	160	447	0	ENST00000250003.3:c.937C>T	p.Pro313Ser	p.P313S	ENST00000250003	NM_002478.4	313	Ccc/Tcc	3/3	0.365933376336059	1	FACETS	0.706	0.66	0.752	0.706	0.66	0.752	INDETERMINATE	1	TRUE	0	0.849188686539751	1		447	307	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127695	64127696	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	228	617	0	ENST00000334205.4:c.188_189delinsTT	p.Ala63Val	p.A63V	ENST00000334205	NM_003942.2	63	gCC/gTT	3/17	0.365933376336059	1	FACETS	0.687	0.649	0.725	0.687	0.649	0.725	INDETERMINATE	1	TRUE	0	0.849188686539751	1		617	450	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719947	18719947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437834329	NA	P-0033965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	44	394	0	ENST00000266497.5:c.3844C>T	p.His1282Tyr	p.H1282Y	ENST00000266497		1282	Cat/Tat	27/31	NA	2	FACETS	0.934	0.807	1			1	INDETERMINATE	1	TRUE	NA	0.849188686539751	2		394	111	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445662	49445662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	305	976	0	ENST00000301067.7:c.1804C>T	p.Pro602Ser	p.P602S	ENST00000301067	NM_003482.3	602	Cca/Tca	10/54	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.849188686539751	2		976	680	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209001	133209001	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	162	557	0	ENST00000320574.5:c.6230C>T	p.Ser2077Phe	p.S2077F	ENST00000320574	NM_006231.2	2077	tCt/tTt	45/49	1	2	FACETS	0.942	0.875	1	0.942	0.875	1	CLONAL	1	TRUE	1	0.849188686539751	2		557	405	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249337	133249338	+	missense_variant	Missense_Mutation	DNP	TC	TC	CT	novel	NA	P-0033965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	215	793	1	ENST00000320574.5:c.1561_1562delinsAG	p.Glu521Arg	p.E521R	ENST00000320574	NM_006231.2	521	GAg/AGg	15/49	1	2	FACETS	0.985	0.925	1	0.985	0.925	1	CLONAL	1	TRUE	1	0.849188686539751	2		794	514	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434769	110434769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	190	353	0	ENST00000375856.3:c.3632C>T	p.Pro1211Leu	p.P1211L	ENST00000375856	NM_003749.2	1211	cCc/cTc	1/2	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.849188686539751	2		353	388	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453418	40453419	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0033965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	226	742	1	ENST00000345506.4:c.1115_1116delinsAT	p.Thr372Asn	p.T372N	ENST00000345506	NM_003152.3	372	aCC/aAT	10/20	1	2	FACETS	0.975	0.916	1	0.975	0.916	1	CLONAL	1	TRUE	1	0.849188686539751	2		743	546	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221242	36221243	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0033965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	122	686	0	ENST00000222270.7:c.5077-1_5077delinsAA		p.X1693_splice	ENST00000222270	NM_014727.1	1693		24/37	1	2	FACETS	0.653	0.594	0.714	0.653	0.594	0.714	SUBCLONAL	1	TRUE	1	0.849188686539751	2		686	440	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561103	9561104	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	68	384	0	ENST00000353224.5:c.678_679delinsTT	p.Pro227Ser	p.P227S	ENST00000353224	NM_177990.2	226	tcCCct/tcTTct	4/10	1	2	FACETS	0.942	0.839	1	0.942	0.839	1	CLONAL	1	TRUE	1	0.849188686539751	2		384	170	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931860	68931860	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	98	575	1	ENST00000288368.4:c.290C>T	p.Pro97Leu	p.P97L	ENST00000288368	NM_024870.2	97	cCc/cTc	3/40	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.849188686539751	2		576	212	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0033966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	34	240	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.835	0.691	0.992	0.835	0.691	0.992	CLONAL	1	TRUE	1	0.482084759855145	2		240	169	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061249	38061249	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	124	521	0	ENST00000250448.2:c.740A>G	p.His247Arg	p.H247R	ENST00000250448	NM_004496.3	247	cAc/cGc	2/2	1	2	FACETS	0.974	0.886	1	0.974	0.886	1	CLONAL	1	TRUE	1	0.482084759855145	2		521	528	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864193	57864193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746398371	NA	P-0033966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	69	558	1	ENST00000228682.2:c.1670G>A	p.Arg557His	p.R557H	ENST00000228682	NM_005269.2	557	cGc/cAc	12/12	0.170704495784965	3	FACETS	0.866	0.758	0.983	0.433	0.379	0.492	INDETERMINATE	1	TRUE	1	0.482084759855145	3		559	410	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0033971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	16	298	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.222905792526866	1	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	0	0.35	1		298	64	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968237	18968237	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	43	405	0	ENST00000262803.5:c.2077A>G	p.Ile693Val	p.I693V	ENST00000262803	NM_002911.3	693	Atc/Gtc	15/24	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.35	2		405	237	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0033973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	615	609	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.830138753672018	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.830138753672018	2		609	717	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245087	133245087	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	725	498	1	ENST00000320574.5:c.2028G>A	p.Met676Ile	p.M676I	ENST00000320574	NM_006231.2	676	atG/atA	19/49	0.830138753672018	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.830138753672018	2		499	834	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354402	354402	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	785	524	0	ENST00000262320.3:c.1156C>T	p.Gln386Ter	p.Q386*	ENST00000262320	NM_003502.3	386	Cag/Tag	5/11	0.830138753672018	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.830138753672018	2		524	893	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39002737	39002737	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	203	345	0	ENST00000357387.3:c.292G>C	p.Glu98Gln	p.E98Q	ENST00000357387	NM_152756.3	98	Gaa/Caa	5/38	0.830138753672018	2	FACETS	1	0.99	1	0.637	0.6	0.673	CLONAL	1	TRUE	0	0.830138753672018	2		345	384	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859519	151859519	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	461	506	0	ENST00000262189.6:c.11143del	p.Thr3715GlnfsTer4	p.T3715Qfs*4	ENST00000262189	NM_170606.2	3715	Aca/ca	43/59	0.830138753672018	3	FACETS	0.986	0.95	1	0.986	0.95	1	CLONAL	2	TRUE	1	0.830138753672018	3		506	797	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860582	151860587	+	inframe_deletion	In_Frame_Del	DEL	TATTGG	TATTGG	-	novel	NA	P-0033973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	549	507	1	ENST00000262189.6:c.10075_10080del	p.Pro3359_Ile3360del	p.P3359_I3360del	ENST00000262189	NM_170606.2	3359	CCAATA/-	43/59	0.830138753672018	3	FACETS	0.962	0.929	0.994	0.962	0.929	0.994	CLONAL	2	TRUE	1	0.830138753672018	3		508	973	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	41	460	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	0.26	2		460	254	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882019	NA	P-0033982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	50	760	0	ENST00000269305.4:c.455dup	p.Pro153AlafsTer28	p.P153Afs*28	ENST00000269305	NM_001126112.2	152	ccg/ccCg	5/11	0.271133014728443	1	FACETS	0.964	0.822	1	0.964	0.822	1	CLONAL	1	TRUE	0	0.26	1		760	347	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949096	44949096	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	25	447	0	ENST00000377967.4:c.3657G>A	p.Trp1219Ter	p.W1219*	ENST00000377967	NM_021140.2	1219	tgG/tgA	25/29	0.226882802784515	0	FACETS	0.525	0.415	0.651			1	SUBCLONAL	1	TRUE	0	0.26	0		447	271	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987221	2987221	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	429	573	0	ENST00000396946.4:c.208A>G	p.Ile70Val	p.I70V	ENST00000396946	NM_032415.4	70	Atc/Gtc	3/25	0.422597638290815	5	FACETS	0.856	0.818	0.895	0.856	0.818	0.895	CLONAL	3	TRUE	2	0.562988782015757	5		573	1094	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035185	6035185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs182246929	NA	P-0033983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	368	473	0	ENST00000265849.7:c.883C>T	p.Arg295Trp	p.R295W	ENST00000265849	NM_000535.5	295	Cgg/Tgg	8/15	0.422597638290815	5	FACETS	1	0.992	1	0.816	0.776	0.856	CLONAL	2	TRUE	2	0.562988782015757	5		473	985	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805391	32805395	+	missense_variant	Missense_Mutation	ONP	AATCA	AATCA	CATCG	novel	NA	P-0033983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	150	767	0	ENST00000374899.4:c.527_531delinsCGATG	p.Val176_Ile177delinsAlaMet	p.V176_I177delinsAM	ENST00000374899	NM_018833.2	176	gTGATT/gCGATG	3/12	0.463932703260073	3	FACETS	0.796	0.727	0.867	0.398	0.363	0.434	SUBCLONAL	1	TRUE	1	0.562988782015757	3		767	858	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0033986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	115	425	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.407536297997271	2		425	398	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612933	228612933	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	79	481	0	ENST00000366696.1:c.94G>A	p.Ala32Thr	p.A32T	ENST00000366696	NM_003493.2	32	Gcc/Acc	1/1	0.399283532018268	3	FACETS	0.968	0.854	1	0.484	0.427	0.545	CLONAL	1	FALSE	1	0.407536297997271	3		481	482	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115752	8115752	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	135	485	0	ENST00000346208.3:c.1102del	p.Met368CysfsTer36	p.M368Cfs*36	ENST00000346208		366	cgA/cg	6/6	0.401315529561368	2	FACETS	0.839	0.77	0.909	0.839	0.77	0.909	CLONAL	2	FALSE	0	0.407536297997271	2		485	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0033986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	161	461	0	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.379301064208285	2	FACETS	0.983	0.912	1	0.983	0.912	1	CLONAL	2	FALSE	0	0.407536297997271	2		461	402	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56787260	56787260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881925	NA	P-0033986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	113	758	0	ENST00000337432.4:c.746G>A	p.Arg249His	p.R249H	ENST00000337432	NM_058216.2	249	cGt/cAt	5/9	0.379301064208285	2	FACETS	1	0.939	1	0.526	0.475	0.579	CLONAL	1	FALSE	0	0.407536297997271	2		758	527	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763317	59763317	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	87	864	0	ENST00000259008.2:c.2785C>G	p.Leu929Val	p.L929V	ENST00000259008	NM_032043.2	929	Cta/Gta	19/20	0.379301064208285	2	FACETS	0.912	0.811	1	0.456	0.405	0.51	CLONAL	1	FALSE	0	0.407536297997271	2		864	468	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326114	62326114	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	92	593	0	ENST00000360203.5:c.3130C>A	p.Gln1044Lys	p.Q1044K	ENST00000360203	NM_001283009.1	1044	Cag/Aag	32/35	0.407536297997271	5	FACETS	0.999	0.888	1	0.333	0.296	0.373	CLONAL	1	FALSE	2	0.407536297997271	5		593	728	SUCCESS
APC	324	MSKCC	GRCh37	5	112175191	112175192	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554085382	NA	P-0033986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	58	274	0	ENST00000257430.4:c.3901dup	p.Thr1301AsnfsTer14	p.T1301Nfs*14	ENST00000257430	NM_000038.5	1300	-/A	16/16	0.3925924944388	3	FACETS	0.797	0.694	0.905	0.797	0.694	0.905	CLONAL	2	FALSE	1	0.407536297997271	3		274	215	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112025282	112025282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370545141	NA	P-0033986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	91	621	0	ENST00000368678.4:c.467G>A	p.Arg156Gln	p.R156Q	ENST00000368678		156	cGa/cAa	6/13	1	2	FACETS	0.899	0.801	1	0.899	0.801	1	CLONAL	1	FALSE	1	0.407536297997271	2		621	497	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151868387	151868387	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	88	576	0	ENST00000262189.6:c.9415A>T	p.Ser3139Cys	p.S3139C	ENST00000262189	NM_170606.2	3139	Agt/Tgt	40/59	0.104369904475921	6	FACETS	1	0.962	1	0.401	0.356	0.45	INDETERMINATE	1	FALSE	3	0.407536297997271	6		576	651	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0033990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	179	312	1	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.651287011545502	2		313	539	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692790	89692790	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	185	307	0	ENST00000371953.3:c.274G>C	p.Asp92His	p.D92H	ENST00000371953	NM_000314.4	92	Gac/Cac	5/9	0.651287011545502	3	FACETS	0.995	0.921	1	0.497	0.46	0.536	CLONAL	1	TRUE	1	0.651287011545502	3		307	757	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716212	52716212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555791268	NA	P-0033990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	183	568	0	ENST00000322088.6:c.656C>T	p.Ser219Leu	p.S219L	ENST00000322088	NM_014225.5	219	tCg/tTg	6/15	1	2	FACETS	0.83	0.769	0.893	0.83	0.769	0.893	CLONAL	1	TRUE	1	0.651287011545502	2		568	677	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057874	27057874	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	259	663	0	ENST00000324856.7:c.1582C>T	p.Gln528Ter	p.Q528*	ENST00000324856	NM_006015.4	528	Cag/Tag	3/20	1	2	FACETS	0.963	0.905	1	0.963	0.905	1	CLONAL	1	TRUE	1	0.651287011545502	2		663	826	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145689	11145689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318154109	NA	P-0033990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	234	477	0	ENST00000358026.2:c.4051G>A	p.Asp1351Asn	p.D1351N	ENST00000358026	NM_001128849.1	1351	Gac/Aac	29/36	1	2	FACETS	0.967	0.906	1	0.967	0.906	1	CLONAL	1	TRUE	1	0.651287011545502	2		477	743	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023156	27023172	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGGCAGCGGCGGCGG	GCCGGCAGCGGCGGCGG	-	novel	NA	P-0033990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	115	74	0	ENST00000324856.7:c.265_281del	p.Gly89ArgfsTer16	p.G89Rfs*16	ENST00000324856	NM_006015.4	88	GCCGGCAGCGGCGGCGGg/g	1/20	1	2	FACETS	1	0.978	1	1	0.992	1	CLONAL	2	TRUE	1	0.651287011545502	2		74	161	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720677	89720677	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	198	157	0	ENST00000371953.3:c.828T>A	p.Asn276Lys	p.N276K	ENST00000371953	NM_000314.4	276	aaT/aaA	8/9	0.651287011545502	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.651287011545502	3		157	395	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828769	72828771	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs1383573529	NA	P-0033990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	226	494	0	ENST00000268489.5:c.7810_7812del	p.Pro2604del	p.P2604del	ENST00000268489	NM_006885.3	2604	CCT/-	9/10	1	2	FACETS	0.939	0.878	1	0.939	0.878	1	CLONAL	1	TRUE	1	0.651287011545502	2		494	739	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085626	16085637	+	inframe_deletion	In_Frame_Del	DEL	GATGAAGAGGAA	GATGAAGAGGAA	-	rs745328158	NA	P-0033990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	124	356	0	ENST00000281043.3:c.816_827del	p.Asp272_Glu275del	p.D272_E275del	ENST00000281043	NM_005378.4	268	GATGAAGAGGAA/-	3/3	0.651287011545502	3	FACETS	0.66	0.597	0.726	0.33	0.298	0.363	SUBCLONAL	1	TRUE	1	0.651287011545502	3		356	765	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591114	67591115	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTT	novel	NA	P-0033990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	136	242	0	ENST00000274335.5:c.1708_1710dup	p.Leu570dup	p.L570dup	ENST00000274335		570	-/CTT	12/15	1	2	FACETS	0.892	0.817	0.97	0.892	0.817	0.97	CLONAL	1	TRUE	1	0.651287011545502	2		242	468	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0033990-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	100	312	1	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.480892389755547	2		313	410	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692790	89692790	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033990-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	76	307	0	ENST00000371953.3:c.274G>C	p.Asp92His	p.D92H	ENST00000371953	NM_000314.4	92	Gac/Cac	5/9	0.480892389755547	3	FACETS	1	0.935	1	0.545	0.481	0.612	CLONAL	1	TRUE	1	0.480892389755547	3		307	360	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716212	52716212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555791268	NA	P-0033990-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	165	568	0	ENST00000322088.6:c.656C>T	p.Ser219Leu	p.S219L	ENST00000322088	NM_014225.5	219	tCg/tTg	6/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.480892389755547	2		568	632	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057874	27057874	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033990-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	195	663	0	ENST00000324856.7:c.1582C>T	p.Gln528Ter	p.Q528*	ENST00000324856	NM_006015.4	528	Cag/Tag	3/20	1	2	FACETS	0.882	0.817	0.95	0.882	0.817	0.95	CLONAL	1	TRUE	1	0.480892389755547	2		663	919	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145689	11145689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318154109	NA	P-0033990-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	149	477	0	ENST00000358026.2:c.4051G>A	p.Asp1351Asn	p.D1351N	ENST00000358026	NM_001128849.1	1351	Gac/Aac	29/36	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.480892389755547	2		477	609	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023156	27023172	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGGCAGCGGCGGCGG	GCCGGCAGCGGCGGCGG	-	novel	NA	P-0033990-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	93	74	0	ENST00000324856.7:c.265_281del	p.Gly89ArgfsTer16	p.G89Rfs*16	ENST00000324856	NM_006015.4	88	GCCGGCAGCGGCGGCGGg/g	1/20	1	2	FACETS	0.982	0.895	1	1	0.988	1	CLONAL	2	TRUE	1	0.480892389755547	2		74	197	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720677	89720677	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033990-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	78	157	0	ENST00000371953.3:c.828T>A	p.Asn276Lys	p.N276K	ENST00000371953	NM_000314.4	276	aaT/aaA	8/9	0.480892389755547	3	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	1	0.480892389755547	3		157	188	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828769	72828771	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs1383573529	NA	P-0033990-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	149	494	0	ENST00000268489.5:c.7810_7812del	p.Pro2604del	p.P2604del	ENST00000268489	NM_006885.3	2604	CCT/-	9/10	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.480892389755547	2		494	597	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085626	16085637	+	inframe_deletion	In_Frame_Del	DEL	GATGAAGAGGAA	GATGAAGAGGAA	-	rs745328158	NA	P-0033990-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	78	356	0	ENST00000281043.3:c.816_827del	p.Asp272_Glu275del	p.D272_E275del	ENST00000281043	NM_005378.4	268	GATGAAGAGGAA/-	3/3	0.480892389755547	3	FACETS	0.74	0.651	0.835	0.37	0.325	0.418	SUBCLONAL	1	TRUE	1	0.480892389755547	3		356	544	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591114	67591115	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTT	novel	NA	P-0033990-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	35	242	0	ENST00000274335.5:c.1708_1710dup	p.Leu570dup	p.L570dup	ENST00000274335		570	-/CTT	12/15	1	2	FACETS	0.677	0.559	0.807	0.677	0.559	0.807	SUBCLONAL	1	TRUE	1	0.480892389755547	2		242	215	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0034022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	505	472	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.691425098542664	2	FACETS	0.986	0.956	1	0.986	0.956	1	CLONAL	2	TRUE	0	0.691425098542664	2		472	741	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936855	78936855	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	29	312	0	ENST00000306801.3:c.3937T>C	p.Trp1313Arg	p.W1313R	ENST00000306801	NM_020761.2	1313	Tgg/Cgg	33/34	1	2	FACETS	0.22	0.176	0.27	0.22	0.176	0.27	SUBCLONAL	1	TRUE	1	0.691425098542664	2		312	381	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627613	14627613	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	247	460	0	ENST00000254322.2:c.457C>T	p.Gln153Ter	p.Q153*	ENST00000254322	NM_006145.1	153	Caa/Taa	2/3	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.691425098542664	2		460	649	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	94	460	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.200140543371351	3	FACETS	1	0.91	1	1	0.91	1	CLONAL	2	TRUE	1	0.200140543371351	3		460	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0034025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	96	523	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.200140543371351	2	FACETS	0.852	0.761	0.948	0.852	0.761	0.948	CLONAL	2	TRUE	0	0.200140543371351	2		523	563	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964872	55964872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374386254	NA	P-0034025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	38	244	1	ENST00000263923.4:c.2365G>A	p.Val789Ile	p.V789I	ENST00000263923	NM_002253.2	789	Gtt/Att	16/30	1	2	FACETS	0.994	0.823	1	0.994	0.823	1	CLONAL	1	TRUE	1	0.200140543371351	2		245	382	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0034030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	18	690	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.208	0.156	0.271	0.208	0.156	0.271	SUBCLONAL	1	FALSE	1	0.213994627230604	2		690	807	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391168	89391168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772463834	NA	P-0034030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	70	339	0	ENST00000336596.2:c.1234G>A	p.Val412Ile	p.V412I	ENST00000336596	NM_005233.5	412	Gtt/Att	5/17	0.213994627230604	0	FACETS	0.878	0.772	0.989			1	CLONAL	2	FALSE	0	0.213994627230604	0		339	293	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060789	38060792	+	frameshift_variant	Frame_Shift_Del	DEL	GAAC	GAAC	-	novel	NA	P-0034030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	61	642	0	ENST00000250448.2:c.1197_1200del	p.Phe400ProfsTer39	p.F400Pfs*39	ENST00000250448	NM_004496.3	399	ccGTTC/cc	2/2	1	2	FACETS	0.549	0.472	0.634	0.549	0.472	0.634	SUBCLONAL	1	FALSE	1	0.213994627230604	2		642	1038	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061009	38061015	+	frameshift_variant	Frame_Shift_Del	DEL	CCGGGGG	CCGGGGG	-	novel	NA	P-0034030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	17	110	0	ENST00000250448.2:c.974_980del	p.Ala325GlyfsTer23	p.A325Gfs*23	ENST00000250448	NM_004496.3	325	gCCCCCGGg/gg	2/2	1	2	FACETS	1	0.799	1	1	0.799	1	CLONAL	1	FALSE	1	0.213994627230604	2		110	148	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696450	47696450	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	143	365	0	ENST00000347630.2:c.373T>A	p.Phe125Ile	p.F125I	ENST00000347630	NM_001007230.1	125	Ttt/Att	6/11	1	2	FACETS	0.88	0.808	0.956	1	0.993	1	CLONAL	3	FALSE	1	0.213994627230604	2		365	506	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559387	141559387	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	165	456	0	ENST00000220592.5:c.1414G>A	p.Glu472Lys	p.E472K	ENST00000220592	NM_012154.3	472	Gag/Aag	12/19	0.213994627230604	1	FACETS	1	0.935	1	1	0.992	1	CLONAL	2	FALSE	0	0.213994627230604	1		456	677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0034031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	412	675	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.17063023576546	5	FACETS	1	0.99	1			1	INDETERMINATE	4	TRUE	NA	0.450478206702533	5		675	707	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46277807	46277807	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	66	328	0	ENST00000371998.3:c.3605G>A	p.Gly1202Asp	p.G1202D	ENST00000371998		1202	gGt/gAt	19/23	0.294808790914818	4	FACETS	0.893	0.777	1			1	CLONAL	1	TRUE	NA	0.450478206702533	4		328	476	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541045	187541045	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	118	298	0	ENST00000441802.2:c.6695del	p.Asn2232IlefsTer8	p.N2232Ifs*8	ENST00000441802	NM_005245.3	2232	aAt/at	10/27	0.450478206702533	2	FACETS	0.922	0.846	1	0.922	0.846	1	CLONAL	2	TRUE	0	0.450478206702533	2		298	284	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857692	9857692	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1389208302	NA	P-0034034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	38	325	0	ENST00000330684.3:c.3709G>A	p.Asp1237Asn	p.D1237N	ENST00000330684	NM_001134407.1	1237	Gat/Aat	13/13	0.335371057217534	5	FACETS	0.792	0.666	0.929	0.528	0.444	0.619	INDETERMINATE	2	FALSE	2	0.591771248264621	5		325	153	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140786	55140786	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs747156883	NA	P-0034034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	94	408	0	ENST00000257290.5:c.1647G>A	p.Trp549Ter	p.W549*	ENST00000257290	NM_006206.4	549	tgG/tgA	11/23	0.372107551012218	4	FACETS	0.943	0.852	1	0.943	0.852	1	CLONAL	2	FALSE	2	0.591771248264621	4		408	268	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133208969	133208969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749342382	NA	P-0034034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	140	471	0	ENST00000320574.5:c.6262C>T	p.Pro2088Ser	p.P2088S	ENST00000320574	NM_006231.2	2088	Cct/Tct	45/49	0.333403286882724	4	FACETS	1	0.947	1	1	0.947	1	INDETERMINATE	2	FALSE	2	0.591771248264621	4		471	364	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757438	40757438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	67	463	0	ENST00000373198.4:c.2860G>A	p.Asp954Asn	p.D954N	ENST00000373198	NM_133170.3	954	Gat/Aat	20/32	NA	2	FACETS	0.797	0.7	0.901			1	INDETERMINATE	1	FALSE	NA	0.591771248264621	2		463	284	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256531	+	missense_variant	Missense_Mutation	DNP	GT	GT	TC	novel	NA	P-0034034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	349	533	0	ENST00000369535.4:c.180_181delinsGA	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	60	ggACaa/ggGAaa	3/7	0.591771248264621	5	FACETS	1	0.992	1	0.874	0.836	0.911	CLONAL	3	FALSE	1	0.591771248264621	5		533	637	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675631	30675631	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	74	689	0	ENST00000376406.3:c.2725A>G	p.Thr909Ala	p.T909A	ENST00000376406	NM_014641.2	909	Acc/Gcc	8/15	0.591771248264621	5	FACETS	0.559	0.489	0.636	0.186	0.163	0.212	SUBCLONAL	1	FALSE	2	0.591771248264621	5		689	844	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859527	151859528	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0034034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	120	426	1	ENST00000262189.6:c.11134_11135delinsTT	p.Pro3712Phe	p.P3712F	ENST00000262189	NM_170606.2	3712	CCt/TTt	43/59	0.591771248264621	4	FACETS	0.907	0.828	0.988	0.907	0.828	0.988	CLONAL	2	FALSE	2	0.591771248264621	4		427	356	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822678	72822678	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	46	511	0	ENST00000268489.5:c.9497C>A	p.Thr3166Asn	p.T3166N	ENST00000268489	NM_006885.3	3166	aCt/aAt	10/10	1	2	FACETS	0.571	0.482	0.667	0.571	0.482	0.667	SUBCLONAL	1	FALSE	1	0.475518730235988	2		511	339	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386522	81386522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	24	514	0	ENST00000222390.5:c.465G>A	p.Met155Ile	p.M155I	ENST00000222390	NM_000601.4	155	atG/atA	4/18	1	2	FACETS	0.834	0.664	1	0.834	0.664	1	CLONAL	1	FALSE	1	0.475518730235988	2		514	121	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200104	67200104	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	151	477	0	ENST00000312629.5:c.491G>T	p.Gly164Val	p.G164V	ENST00000312629	NM_003952.2	164	gGc/gTc	6/15	0.210888029914699	7	FACETS	1	0.976	1			1	CLONAL	2	FALSE	NA	0.210888029914699	7		477	924	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061132	38061197	+	protein_altering_variant	In_Frame_Del	DEL	CCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGC	CCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGC	GTT	novel	NA	P-0034039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	133	253	2	ENST00000250448.2:c.792_857delinsAAC	p.Arg265_Gly286delinsThr	p.R265_G286delinsT	ENST00000250448	NM_004496.3	264	aaGCGCTTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGCGGc/aaAACc	2/2	0.210888029914699	3	FACETS	0.92	0.845	0.997	1	0.99	1	CLONAL	4	FALSE	1	0.210888029914699	3		255	379	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790454	3790454	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	228	388	0	ENST00000262367.5:c.4079G>C	p.Arg1360Pro	p.R1360P	ENST00000262367	NM_004380.2	1360	cGa/cCa	24/31	0.210888029914699	3	FACETS	0.993	0.932	1	1	0.995	1	CLONAL	4	FALSE	1	0.210888029914699	3		388	602	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618800	37618801	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0034039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	80	297	0	ENST00000447079.4:c.477dup	p.Asp160Ter	p.D160*	ENST00000447079	NM_015083.1	159	gat/gaTt	1/14	1	2	FACETS	0.872	0.771	0.979	1	0.982	1	CLONAL	2	FALSE	1	0.210888029914699	2		297	435	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673746	37673746	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	77	481	0	ENST00000447079.4:c.2900C>T	p.Pro967Leu	p.P967L	ENST00000447079	NM_015083.1	967	cCc/cTc	10/14	1	2	FACETS	0.808	0.712	0.91	1	0.979	1	CLONAL	2	FALSE	1	0.210888029914699	2		481	452	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720981	176720981	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	82	347	0	ENST00000439151.2:c.6612G>C	p.Glu2204Asp	p.E2204D	ENST00000439151	NM_022455.4	2204	gaG/gaC	23/23	1	2	FACETS	0.884	0.783	0.991	1	0.982	1	CLONAL	2	FALSE	1	0.210888029914699	2		347	440	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0034040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	56	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.25857929960318	0	FACETS	0.722	0.622	0.83			1	SUBCLONAL	1	FALSE	0	0.319013570871623	0		502	331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0034040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	63	573	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	FALSE	1	0.319013570871623	2		574	392	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584513	48584514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs377767334	NA	P-0034040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	15	342	0	ENST00000342988.3:c.692dup	p.Ser232GlnfsTer3	p.S232Qfs*3	ENST00000342988	NM_005359.5	229	ctg/ctGg	6/12	0.319013570871623	1	FACETS	0.338	0.247	0.447	0.338	0.247	0.447	SUBCLONAL	1	FALSE	0	0.319013570871623	1		342	234	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867502	45867502	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161399233	NA	P-0034040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	29	742	0	ENST00000391945.4:c.806C>T	p.Thr269Met	p.T269M	ENST00000391945	NM_000400.3	269	aCg/aTg	9/23	0.319013570871623	3	FACETS	0.466	0.374	0.572	0.233	0.187	0.286	SUBCLONAL	1	FALSE	1	0.319013570871623	3		742	452	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434685	99434685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs543792941	NA	P-0034040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	40	636	1	ENST00000268035.6:c.772G>A	p.Gly258Ser	p.G258S	ENST00000268035	NM_000875.3	258	Ggt/Agt	3/21	0.319013570871623	1	FACETS	0.288	0.239	0.344	0.288	0.239	0.344	SUBCLONAL	1	FALSE	0	0.319013570871623	1		637	731	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503977	186503977	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	21	388	0	ENST00000323963.5:c.542T>C	p.Val181Ala	p.V181A	ENST00000323963		181	gTt/gCt	6/11	1	2	FACETS	0.551	0.425	0.696	0.551	0.425	0.696	SUBCLONAL	1	FALSE	1	0.319013570871623	2		388	239	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145689	11145689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318154109	NA	P-0034060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	74	477	0	ENST00000358026.2:c.4051G>A	p.Asp1351Asn	p.D1351N	ENST00000358026	NM_001128849.1	1351	Gac/Aac	29/36	0.167373646206888	3	FACETS	1	0.885	1	1	0.885	1	CLONAL	2	FALSE	1	0.20306939644156	3		477	399	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0034060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	207	504	2	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.20306939644156	6	FACETS	1	0.944	1	1	0.944	1	CLONAL	6	FALSE	0	0.20306939644156	6		506	475	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066627	94066627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	22	412	0	ENST00000369303.4:c.1132G>A	p.Glu378Lys	p.E378K	ENST00000369303	NM_004440.3	378	Gaa/Aaa	5/17	0.20306939644156	0	FACETS	0.664	0.516	0.836			1	SUBCLONAL	1	FALSE	0	0.20306939644156	0		412	260	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578255	7578255	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	14	511	1	ENST00000269305.4:c.594A>T	p.Glu198Asp	p.E198D	ENST00000269305	NM_001126112.2	198	gaA/gaT	6/11	0.20306939644156	6	FACETS	0.414	0.298	0.556	0.069	0.049	0.093	SUBCLONAL	1	FALSE	0	0.20306939644156	6		512	468	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783218	9783218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573872848	NA	P-0034060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	23	416	0	ENST00000377346.4:c.2462G>A	p.Arg821His	p.R821H	ENST00000377346	NM_005026.3	821	cGc/cAc	20/24	1	2	FACETS	0.606	0.472	0.761	0.606	0.472	0.761	SUBCLONAL	1	FALSE	1	0.20306939644156	2		416	374	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054996	176054996	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	19	448	0	ENST00000367669.3:c.1057T>A	p.Leu353Ile	p.L353I	ENST00000367669	NM_022457.5	353	Tta/Ata	10/20	0.10413174555773	5	FACETS	0.733	0.556	0.942	0.244	0.185	0.314	INDETERMINATE	1	FALSE	2	0.20306939644156	5		448	333	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111547	8111547	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	59	401	0	ENST00000346208.3:c.1033T>C	p.Tyr345His	p.Y345H	ENST00000346208		345	Tac/Cac	5/6	0.17938262049295	0	FACETS	0.858	0.745	0.978			1	CLONAL	2	FALSE	0	0.20306939644156	0		401	270	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244097	5244097	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	20	615	0	ENST00000357368.4:c.1385T>G	p.Val462Gly	p.V462G	ENST00000357368	NM_002850.3	462	gTc/gGc	11/38	0.20306939644156	0	FACETS	0.449	0.342	0.573			1	SUBCLONAL	1	FALSE	0	0.20306939644156	0		615	350	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149245621	149245621	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0034060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	61	483	0	ENST00000360632.3:c.905+2T>C		p.X302_splice	ENST00000360632	NM_015472.4	302			0.20306939644156	3	FACETS	0.838	0.726	0.959	0.838	0.726	0.959	CLONAL	2	FALSE	1	0.20306939644156	3		483	395	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412332	139412332	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	26	533	0	ENST00000277541.6:c.1313G>T	p.Cys438Phe	p.C438F	ENST00000277541	NM_017617.3	438	tGc/tTc	8/34	0.20306939644156	3	FACETS	0.668	0.529	0.829	0.334	0.264	0.415	SUBCLONAL	1	FALSE	1	0.20306939644156	3		533	422	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143191881	143191881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs184155869	NA	P-0034064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	205	388	0	ENST00000262992.4:c.550G>A	p.Val184Met	p.V184M	ENST00000262992	NM_001101669.1	184	Gtg/Atg	8/24	1	2	FACETS	0.765	0.715	0.815	1	0.992	1	SUBCLONAL	2	TRUE	1	0.5	2		388	536	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0034069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	139	313	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.949	0.878	1	0.949	0.878	1	CLONAL	1	TRUE	1	0.932948388593012	2		313	314	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399422	139399422	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	894	614	2	ENST00000277541.6:c.4721T>C	p.Leu1574Pro	p.L1574P	ENST00000277541	NM_017617.3	1574	cTg/cCg	26/34	0.932948388593012	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.932948388593012	3		616	1357	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44935947	44935948	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0034069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	114	236	0	ENST00000377967.4:c.2709dup	p.Gly904ArgfsTer2	p.G904Rfs*2	ENST00000377967	NM_021140.2	903	cta/ctAa	18/29	0.932948388593012	1	FACETS	0.938	0.891	0.98	0.938	0.891	0.98	CLONAL	1	TRUE	0	0.932948388593012	1		236	139	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	43	460	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.158804108495281	3	FACETS	1	0.868	1	0.515	0.435	0.601	INDETERMINATE	1	TRUE	1	0.471322426109735	3		460	219	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0034082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	44	757	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	0.109742614285797	0	FACETS	0.574	0.489	0.665			1	INDETERMINATE	1	TRUE	0	0.471322426109735	0		757	172	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143549	108143549	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1284116426	NA	P-0034082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	37	650	0	ENST00000278616.4:c.3254T>A	p.Val1085Asp	p.V1085D	ENST00000278616	NM_000051.3	1085	gTt/gAt	22/63	1	2	FACETS	0.789	0.657	0.933	0.789	0.657	0.933	CLONAL	1	TRUE	1	0.471322426109735	2		650	199	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150300	108150300	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	44	564	0	ENST00000278616.4:c.3367del	p.Ala1123HisfsTer3	p.A1123Hfs*3	ENST00000278616	NM_000051.3	1123	Gca/ca	23/63	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.471322426109735	2		564	184	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604753	48604762	+	frameshift_variant	Frame_Shift_Del	DEL	TGAAATTCAC	TGAAATTCAC	-	novel	NA	P-0034082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	49	546	0	ENST00000342988.3:c.1576_1585del	p.Glu526TyrfsTer8	p.E526Yfs*8	ENST00000342988	NM_005359.5	525	atTGAAATTCAC/at	12/12	0.471322426109735	1	FACETS	0.987	0.852	1	0.987	0.852	1	CLONAL	1	TRUE	0	0.471322426109735	1		546	161	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0034084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	37	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	FALSE	1	0.14870592059818	2		502	469	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440904	56440904	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1458799446	NA	P-0034084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	62	1014	1	ENST00000407977.2:c.433C>T	p.Arg145Ter	p.R145*	ENST00000407977		145	Cga/Tga	4/10	0.14870592059818	0	FACETS	1	0.952	1			1	CLONAL	1	FALSE	0	0.14870592059818	0		1015	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs864622237	NA	P-0034084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	46	937	0	ENST00000269305.4:c.700T>G	p.Tyr234Asp	p.Y234D	ENST00000269305	NM_001126112.2	234	Tac/Gac	7/11	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	FALSE	1	0.14870592059818	2		937	568	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190345	32190345	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1304701623	NA	P-0034084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	30	1006	0	ENST00000375023.3:c.394C>T	p.Arg132Cys	p.R132C	ENST00000375023	NM_004557.3	132	Cgc/Tgc	3/30	1	2	FACETS	0.801	0.644	0.979	0.801	0.644	0.979	CLONAL	1	FALSE	1	0.14870592059818	2		1006	504	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95573982	95573982	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	30	488	0	ENST00000393063.1:c.2767A>G	p.Lys923Glu	p.K923E	ENST00000393063	NM_030621.3	923	Aaa/Gaa	18/28	1	2	FACETS	0.991	0.799	1	0.991	0.799	1	CLONAL	1	FALSE	1	0.14870592059818	2		488	407	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971078	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGCACGTCCAGCCGCGCCCCGGCCCGGTGCAGCACCACCAG	CGCGCACGTCCAGCCGCGCCCCGGCCCGGTGCAGCACCACCAG	-	novel	NA	P-0034084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	44	891	0	ENST00000304494.5:c.280_322del	p.Leu94MetfsTer38	p.L94Mfs*38	ENST00000304494	NM_000077.4	94	CTGGTGGTGCTGCACCGGGCCGGGGCGCGGCTGGACGTGCGCGat/at	2/3	0.14870592059818	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	FALSE	0	0.14870592059818	1		891	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0034088-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	241	880	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.554423864943152	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.554423864943152	1		882	441	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0034088-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	46	196	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.11339036452482	5	FACETS	0.796	0.679	0.92	0.53	0.453	0.614	INDETERMINATE	2	TRUE	2	0.554423864943152	5		196	191	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0034088-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	145	446	0	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	0.207354043234826	2	FACETS	1	0.987	1	0.692	0.639	0.746	INDETERMINATE	1	TRUE	0	0.554423864943152	2		446	378	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46587863	46587863	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747275399	NA	P-0034088-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	62	360	2	ENST00000263734.3:c.541C>T	p.Arg181Cys	p.R181C	ENST00000263734	NM_001430.4	181	Cgt/Tgt	5/16	0.207354043234826	2	FACETS	0.672	0.584	0.766	0.336	0.292	0.383	INDETERMINATE	1	TRUE	0	0.554423864943152	2		362	333	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942874	15942875	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0034088-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	182	408	0	ENST00000268712.3:c.6827_6828del	p.Asp2276GlyfsTer4	p.D2276Gfs*4	ENST00000268712	NM_006311.3	2276	gAT/g	44/46	0.554423864943152	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.554423864943152	1		408	349	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587142	212587142	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034088-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	57	419	0	ENST00000342788.4:c.859G>A	p.Ala287Thr	p.A287T	ENST00000342788	NM_005235.2	287	Gca/Aca	7/28	0.207354043234826	2	FACETS	0.502	0.431	0.577	0.251	0.215	0.289	INDETERMINATE	1	TRUE	0	0.554423864943152	2		419	410	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAAT	novel	NA	P-0034088-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	61	193	0	ENST00000257430.4:c.3920_3923dup	p.Lys1308AsnfsTer8	p.K1308Nfs*8	ENST00000257430	NM_000038.5	1306	gaa/gAAATaa	16/16	0.11339036452482	5	FACETS	1	0.899	1	0.685	0.601	0.774	INDETERMINATE	2	TRUE	2	0.554423864943152	5		193	196	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982010	70982011	+	missense_variant	Missense_Mutation	DNP	TA	TA	GT	novel	NA	P-0034088-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	102	628	0	ENST00000276594.2:c.85_86delinsAC	p.Tyr29Thr	p.Y29T	ENST00000276594	NM_024504.3	29	TAc/ACc	2/8	0.499570865001629	4	FACETS	0.529	0.471	0.59	0.176	0.157	0.197	SUBCLONAL	1	TRUE	1	0.554423864943152	4		628	1082	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942687	48942687	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	62	308	1	ENST00000267163.4:c.1078del	p.Ser360ValfsTer7	p.S360Vfs*7	ENST00000267163	NM_000321.2	358	cgA/cg	11/27	0.382247017815237	1	FACETS	0.902	0.786	1	0.902	0.786	1	CLONAL	1	TRUE	0	0.382247017815237	1		309	291	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0034090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	79	767	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.247414478278685	2	FACETS	0.886	0.791	0.984	0.886	0.791	0.984	CLONAL	2	TRUE	0	0.367103827924759	2		767	243	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117888	70117888	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs886043537	NA	P-0034090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	71	586	0	ENST00000245479.2:c.356C>A	p.Ala119Glu	p.A119E	ENST00000245479	NM_000346.3	119	gCg/gAg	1/3	0.247414478278685	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.367103827924759	2		586	161	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588988	67588988	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	11	344	1	ENST00000274335.5:c.1079C>T	p.Ala360Val	p.A360V	ENST00000274335		360	gCg/gTg	8/15	0.367103827924759	2	FACETS	0.461	0.32	0.634	0.23	0.16	0.317	SUBCLONAL	1	TRUE	0	0.367103827924759	2		345	130	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796883	42796883	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	50	1168	1	ENST00000575354.2:c.3347del	p.Pro1116GlnfsTer45	p.P1116Qfs*45	ENST00000575354	NM_015125.3	1114	gCc/gc	14/20	0.367103827924759	3	FACETS	0.974	0.83	1			1	CLONAL	1	TRUE	NA	0.367103827924759	3		1169	331	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023327	27023327	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	23	304	0	ENST00000324856.7:c.437del	p.Pro146GlnfsTer86	p.P146Qfs*86	ENST00000324856	NM_006015.4	145	Ccc/cc	1/20	1	2	FACETS	0.921	0.727	1	0.921	0.727	1	CLONAL	1	TRUE	1	0.367103827924759	2		304	136	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273105	18273105	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	11	771	3	ENST00000222254.8:c.1000del	p.Asp334ThrfsTer7	p.D334Tfs*7	ENST00000222254	NM_005027.3	332	tGg/tg	8/16	1	2	FACETS	0.276	0.19	0.383	0.276	0.19	0.383	SUBCLONAL	1	TRUE	1	0.367103827924759	2		774	217	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0034090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	15	1072	2	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	1	2	FACETS	0.289	0.211	0.383	0.289	0.211	0.383	SUBCLONAL	1	TRUE	1	0.367103827924759	2		1074	283	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794422	242794422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758959367	NA	P-0034090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	39	964	0	ENST00000334409.5:c.520G>A	p.Val174Met	p.V174M	ENST00000334409	NM_005018.2	174	Gtg/Atg	3/5	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.367103827924759	2		964	196	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278854	1278854	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761116773	NA	P-0034090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	26	906	5	ENST00000310581.5:c.2188G>A	p.Ala730Thr	p.A730T	ENST00000310581	NM_198253.2	730	Gcc/Acc	6/16	1	2	FACETS	0.567	0.45	0.699	0.567	0.45	0.699	SUBCLONAL	1	TRUE	1	0.367103827924759	2		911	250	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881363	111881363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	27	501	1	ENST00000393256.3:c.41G>A	p.Arg14Gln	p.R14Q	ENST00000393256	NM_006538.4	14	cGa/cAa	2/4	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.367103827924759	2		502	123	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922363	178922363	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	24	445	0	ENST00000263967.3:c.1132T>C	p.Cys378Arg	p.C378R	ENST00000263967	NM_006218.2	378	Tgt/Cgt	6/21	1	2	FACETS	0.778	0.615	0.962	0.778	0.615	0.962	CLONAL	1	TRUE	1	0.367103827924759	2		445	168	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231783	36231783	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	32	840	0	ENST00000300305.3:c.601del	p.Arg201GlufsTer10	p.R201Efs*10	ENST00000300305		201	Cga/ga	5/8	1	2	FACETS	0.846	0.692	1	0.846	0.692	1	CLONAL	1	TRUE	1	0.367103827924759	2		840	206	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266175	198266175	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	17	643	2	ENST00000335508.6:c.2445del	p.Phe815LeufsTer19	p.F815Lfs*19	ENST00000335508	NM_012433.2	815	ttT/tt	17/25	1	2	FACETS	0.334	0.249	0.435	0.334	0.249	0.435	SUBCLONAL	1	TRUE	1	0.367103827924759	2		645	277	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210893	36210893	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	43	1003	4	ENST00000222270.7:c.649del	p.Arg217GlyfsTer22	p.R217Gfs*22	ENST00000222270	NM_014727.1	215	aCc/ac	3/37	1	2	FACETS	0.828	0.697	0.971	0.828	0.697	0.971	CLONAL	1	TRUE	1	0.367103827924759	2		1007	283	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981546	201981547	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0034090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	66	1071	0	ENST00000359651.3:c.461dup	p.Asp155ArgfsTer6	p.D155Rfs*6	ENST00000359651		154	cta/cTta	3/8	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.367103827924759	2		1071	321	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109962	115109962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	133	1129	0	ENST00000257566.3:c.1916G>A	p.Arg639His	p.R639H	ENST00000257566	NM_016569.3	639	cGc/cAc	8/8	0.233227339998944	3	FACETS	0.919	0.848	0.991	0.919	0.848	0.991	CLONAL	3	TRUE	0	0.367103827924759	3		1129	311	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610239	81610239	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	10	570	0	ENST00000298171.2:c.1837T>C	p.Tyr613His	p.Y613H	ENST00000298171	NM_000369.2	613	Tac/Cac	10/10	1	2	FACETS	0.29	0.196	0.407	0.29	0.196	0.407	SUBCLONAL	1	TRUE	1	0.367103827924759	2		570	188	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225323	2225323	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	34	868	0	ENST00000326181.6:c.1408C>T	p.Gln470Ter	p.Q470*	ENST00000326181	NM_032271.2	470	Cag/Tag	16/21	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.367103827924759	2		868	166	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633402	3633402	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs768401328	NA	P-0034090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	52	1199	0	ENST00000294008.3:c.4849T>C	p.Ser1617Pro	p.S1617P	ENST00000294008	NM_032444.2	1617	Tca/Cca	14/15	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.367103827924759	2		1199	253	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650698	67650698	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	22	704	1	ENST00000264010.4:c.1003G>T	p.Gly335Ter	p.G335*	ENST00000264010	NM_006565.3	335	Gga/Tga	5/12	1	2	FACETS	0.599	0.467	0.751	0.599	0.467	0.751	SUBCLONAL	1	TRUE	1	0.367103827924759	2		705	200	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216588	2216588	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	31	1125	0	ENST00000398665.3:c.2232C>G	p.Asp744Glu	p.D744E	ENST00000398665	NM_032482.2	744	gaC/gaG	20/28	1	2	FACETS	0.662	0.538	0.801	0.662	0.538	0.801	SUBCLONAL	1	TRUE	1	0.367103827924759	2		1125	255	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101034	4101034	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	19	609	0	ENST00000262948.5:c.688A>G	p.Thr230Ala	p.T230A	ENST00000262948	NM_030662.3	230	Acg/Gcg	6/11	1	2	FACETS	0.592	0.451	0.754	0.592	0.451	0.754	SUBCLONAL	1	TRUE	1	0.367103827924759	2		609	175	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183349	56183349	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0034090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	18	421	0	ENST00000399503.3:c.4257+2T>C		p.X1419_splice	ENST00000399503	NM_005921.1	1419			1	2	FACETS	0.791	0.602	1	0.791	0.602	1	CLONAL	1	TRUE	1	0.367103827924759	2		421	124	SUCCESS
APC	324	MSKCC	GRCh37	5	112175710	112175711	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCTGCAGTTCAGAG	novel	NA	P-0034090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	34	416	0	ENST00000257430.4:c.4421_4434dup	p.Val1479LeufsTer33	p.V1479Lfs*33	ENST00000257430	NM_000038.5	1473	-/GCTGCAGTTCAGAG	16/16	0.367103827924759	2	FACETS	1	0.93	1	0.63	0.523	0.746	CLONAL	1	TRUE	0	0.367103827924759	2		416	147	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020851	26020851	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	43	479	0	ENST00000357647.3:c.134G>A	p.Gly45Asp	p.G45D	ENST00000357647	NM_003529.2	45	gGc/gAc	1/1	1	2	FACETS	0.808	0.689	0.933	1	0.966	1	CLONAL	2	TRUE	1	0.367103827924759	2		479	145	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042269	6042270	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TG	TG	-	novel	NA	P-0034090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	21	453	0	ENST00000265849.7:c.354-3_354-2del		p.X118_splice	ENST00000265849	NM_000535.5	118			0.292746611131161	3	FACETS	0.988	0.77	1	0.494	0.385	0.619	CLONAL	1	TRUE	1	0.367103827924759	3		453	137	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371909	55371909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1200403075	NA	P-0034090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	20	454	0	ENST00000297316.4:c.599G>A	p.Gly200Asp	p.G200D	ENST00000297316	NM_022454.3	200	gGc/gAc	2/2	1	2	FACETS	0.939	0.728	1	0.939	0.728	1	CLONAL	1	TRUE	1	0.367103827924759	2		454	116	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776356	76776356	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	29	421	0	ENST00000373344.5:c.7110G>T	p.Gln2370His	p.Q2370H	ENST00000373344	NM_000489.3	2370	caG/caT	34/35	1	1	FACETS	0.97	0.791	1	0.97	0.791	1	CLONAL	1	TRUE	0	0.367103827924759	1		421	133	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306599	41306599	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778985729	NA	P-0034090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	64	753	0	ENST00000373198.4:c.1060G>A	p.Val354Ile	p.V354I	ENST00000373198	NM_133170.3	354	Gtt/Att	7/32	0.367103827924759	3	FACETS	0.997	0.877	1	0.997	0.877	1	CLONAL	2	TRUE	1	0.367103827924759	3		753	207	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0034096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	75	339	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.46583321149676	3	FACETS	0.904	0.796	1	0.452	0.398	0.51	CLONAL	1	TRUE	1	0.46583321149676	3		339	439	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0034096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	416	482	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	0.46583321149676	3	FACETS	0.965	0.926	1	0.965	0.926	1	CLONAL	3	TRUE	0	0.46583321149676	3		482	761	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0034096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	240	576	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			0.46583321149676	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.46583321149676	3		576	600	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189585638	189585638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886058222	NA	P-0034096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	150	608	1	ENST00000264731.3:c.899C>T	p.Thr300Met	p.T300M	ENST00000264731	NM_003722.4	300	aCg/aTg	7/14	0.46583321149676	4	FACETS	0.98	0.895	1	0.327	0.298	0.357	CLONAL	1	TRUE	1	0.46583321149676	4		609	963	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600016	10600019	+	frameshift_variant	Frame_Shift_Del	DEL	ATAG	ATAG	-	novel	NA	P-0034096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	210	832	0	ENST00000171111.5:c.1557_1560del	p.Ile519MetfsTer12	p.I519Mfs*12	ENST00000171111	NM_203500.1	519	atCTAT/at	5/6	0.46583321149676	3	FACETS	1	0.964	1	0.53	0.492	0.57	CLONAL	1	TRUE	1	0.46583321149676	3		832	1048	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260485	16260485	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	270	571	0	ENST00000375759.3:c.7750G>T	p.Glu2584Ter	p.E2584*	ENST00000375759	NM_015001.2	2584	Gaa/Taa	11/15	0.46583321149676	3	FACETS	0.993	0.945	1	1	0.995	1	CLONAL	3	TRUE	1	0.46583321149676	3		571	480	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871002	12871039	+	frameshift_variant	Frame_Shift_Del	DEL	CAAGAGGTGGAGAAGGGCAGCTTGCCCGAGTTCTACTA	CAAGAGGTGGAGAAGGGCAGCTTGCCCGAGTTCTACTA	-	novel	NA	P-0034096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	116	355	0	ENST00000228872.4:c.231_268del	p.Glu78ThrfsTer34	p.E78Tfs*34	ENST00000228872	NM_004064.3	77	CAAGAGGTGGAGAAGGGCAGCTTGCCCGAGTTCTACTAc/c	1/3	0.46583321149676	3	FACETS	0.823	0.749	0.899	0.823	0.749	0.899	CLONAL	2	TRUE	1	0.46583321149676	3		355	373	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912200	32912200	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	180	739	0	ENST00000380152.3:c.3708A>C	p.Lys1236Asn	p.K1236N	ENST00000380152		1236	aaA/aaC	11/27	0.144590026966118	4	FACETS	1	0.977	1	0.576	0.531	0.623	INDETERMINATE	1	TRUE	2	0.46583321149676	4		739	983	SUCCESS
AR	367	MSKCC	GRCh37	X	66764922	66765210	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	CTCTTCTGAGCAAGAGAAGGGGAGGCGGGGTAAGGGAAGTAGGTGGAAGATTCAGCCAAGCTCAAGGATGGAAGTGCAGTTAGGGCTGGGAAGGGTCTACCCTCGGCCGCCGTCCAAGACCTACCGAGGAGCTTTCCAGAATCTGTTCCAGAGCGTGCGCGAAGTGATCCAGAACCCGGGCCCCAGGCACCCAGAGGCCGCGAGCGCAGCACCTCCCGGCGCCAGTTTGCTGCTGCTGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG	CTCTTCTGAGCAAGAGAAGGGGAGGCGGGGTAAGGGAAGTAGGTGGAAGATTCAGCCAAGCTCAAGGATGGAAGTGCAGTTAGGGCTGGGAAGGGTCTACCCTCGGCCGCCGTCCAAGACCTACCGAGGAGCTTTCCAGAATCTGTTCCAGAGCGTGCGCGAAGTGATCCAGAACCCGGGCCCCAGGCACCCAGAGGCCGCGAGCGCAGCACCTCCCGGCGCCAGTTTGCTGCTGCTGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG	-	novel	NA	P-0034096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	44	286	0	ENST00000374690.3:c.-66_223del		p.*22*	ENST00000374690	NM_000044.3	?-74/920		1/8	0.191208470127435	3	FACETS	0.779	0.657	0.913	0.26	0.219	0.305	INDETERMINATE	1	TRUE	0	0.46583321149676	3		286	299	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181810	56181814	+	frameshift_variant	Frame_Shift_Del	DEL	TAGTT	TAGTT	A	novel	NA	P-0034096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	270	415	0	ENST00000399503.3:c.4034_4038delinsA	p.Val1345GlufsTer31	p.V1345Efs*31	ENST00000399503	NM_005921.1	1345	gTAGTT/gA	17/20	0.323229980688252	3	FACETS	0.873	0.828	0.917	0.873	0.828	0.917	CLONAL	3	TRUE	0	0.46583321149676	3		415	546	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78858829	78858829	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034107-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	46	480	0	ENST00000306801.3:c.1864G>T	p.Ala622Ser	p.A622S	ENST00000306801	NM_020761.2	622	Gcc/Tcc	17/34	0.156187886705361	2	FACETS	0.839	0.719	0.965	1	0.949	1	CLONAL	3	TRUE	0	0.23	2		480	159	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091855	29091855	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034107-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	20	118	0	ENST00000328354.6:c.1102G>T	p.Asp368Tyr	p.D368Y	ENST00000328354	NM_007194.3	368	Gat/Tat	11/15	1	2	FACETS	0.892	0.705	1	1	0.952	1	CLONAL	3	TRUE	1	0.23	2		118	65	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331646	8331646	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1177261686	NA	P-0034107-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	62	440	0	ENST00000356435.5:c.5470A>G	p.Ile1824Val	p.I1824V	ENST00000356435		1824	Atc/Gtc	33/35	0.3	1	FACETS	1	0.959	1	1	0.983	1	CLONAL	2	TRUE	0	0.23	1		440	195	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900314	101900314	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	17	480	0	ENST00000374994.4:c.748C>T	p.Gln250Ter	p.Q250*	ENST00000374994	NM_004612.2	250	Caa/Taa	4/9	1	2	FACETS	1	0.769	1	1	0.769	1	CLONAL	1	TRUE	1	0.280301084146038	2		480	119	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249505	153249505	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	30	716	0	ENST00000281708.4:c.1273T>C	p.Trp425Arg	p.W425R	ENST00000281708	NM_033632.3	425	Tgg/Cgg	9/12	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.280301084146038	2		716	155	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561571	9561571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758518559	NA	P-0034108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	19	559	0	ENST00000353224.5:c.211G>A	p.Val71Ile	p.V71I	ENST00000353224	NM_177990.2	71	Gtt/Att	4/10	0.124867432527442	3	FACETS	0.931	0.712	1	0.466	0.356	0.593	INDETERMINATE	1	TRUE	1	0.280301084146038	3		559	166	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921463	+	frameshift_variant	Frame_Shift_Del	DEL	TTGACAATAAGTCTCCGTGC	TTGACAATAAGTCTCCGTGC	-	novel	NA	P-0034108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	28	376	0	ENST00000378444.4:c.4357_4376del	p.Ala1453Ter	p.A1453*	ENST00000378444	NM_001123385.1	1453	GCACGGAGACTTATTGTCAAt/t	10/15	NA	2	FACETS	1	0.937	1			1	INDETERMINATE	1	TRUE	NA	0.280301084146038	2		376	138	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134305	2134305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762798984	NA	P-0034109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	150	678	0	ENST00000219476.3:c.4082G>A	p.Arg1361Gln	p.R1361Q	ENST00000219476	NM_000548.3	1361	cGa/cAa	34/42	0.321063478784903	15	FACETS	1	0.974	1			1	CLONAL	3	FALSE	NA	0.321063478784903	15		678	825	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115888	8115889	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0034110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	104	587	0	ENST00000346208.3:c.1236dup	p.Ser413GlnfsTer94	p.S413Qfs*94	ENST00000346208		412	tcc/tCcc	6/6	0.306761561496712	1	FACETS	0.353	0.316	0.392	0.353	0.316	0.392	INDETERMINATE	1	TRUE	0	0.580495178521234	1		587	721	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627773	187627773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200050180	NA	P-0034110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	136	548	0	ENST00000441802.2:c.3209G>A	p.Arg1070Gln	p.R1070Q	ENST00000441802	NM_005245.3	1070	cGa/cAa	2/27	1	2	FACETS	0.887	0.811	0.967	0.887	0.811	0.967	CLONAL	1	TRUE	1	0.580495178521234	2		548	528	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572092	64572093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs767319284	NA	P-0034110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	264	646	3	ENST00000312049.6:c.1546dup	p.Arg516ProfsTer15	p.R516Pfs*15	ENST00000312049	NM_130799.2	516	cgg/cCgg	10/10	0.580495178521234	1	FACETS	0.936	0.882	0.99	0.936	0.882	0.99	CLONAL	1	TRUE	0	0.580495178521234	1		649	690	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971137	21971137	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	153	312	0	ENST00000304494.5:c.221A>G	p.Asp74Gly	p.D74G	ENST00000304494	NM_000077.4	74	gAc/gGc	2/3	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.580495178521234	2		312	498	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026675	48026675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	85	480	1	ENST00000234420.5:c.1553C>T	p.Thr518Ile	p.T518I	ENST00000234420	NM_000179.2	518	aCc/aTc	4/10	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.580495178521234	2		481	285	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115727	8115727	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	57	375	0	ENST00000346208.3:c.1073A>C	p.Lys358Thr	p.K358T	ENST00000346208		358	aAg/aCg	6/6	0.306761561496712	1	FACETS	0.469	0.405	0.538	0.469	0.405	0.538	INDETERMINATE	1	TRUE	0	0.580495178521234	1		375	297	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873404	136873404	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	86	469	1	ENST00000241393.3:c.94G>A	p.Glu32Lys	p.E32K	ENST00000241393	NM_003467.2	32	Gaa/Aaa	2/2	1	2	FACETS	0.892	0.797	0.993	0.892	0.797	0.993	CLONAL	1	TRUE	1	0.580495178521234	2		470	332	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458381	12458381	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	180	796	0	ENST00000287820.6:c.998G>C	p.Gly333Ala	p.G333A	ENST00000287820	NM_015869.4	333	gGt/gCt	6/7	0.24587749631039	3	FACETS	0.984	0.909	1	0.492	0.454	0.531	INDETERMINATE	1	TRUE	1	0.580495178521234	3		796	813	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0034114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	222	846	1	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.443250139456736	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.443250139456736	1		847	562	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197149	106197149	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1176763299	NA	P-0034114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	32	370	0	ENST00000380013.4:c.5482C>T	p.Gln1828Ter	p.Q1828*	ENST00000380013	NM_001127208.2	1828	Cag/Tag	11/11	1	2	FACETS	0.525	0.428	0.634	0.525	0.428	0.634	SUBCLONAL	1	TRUE	1	0.443250139456736	2		370	275	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076726	72076726	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	106	555	0	ENST00000357731.5:c.771G>A	p.Trp257Ter	p.W257*	ENST00000357731	NM_173808.2	257	tgG/tgA	5/7	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.443250139456736	2		555	465	SUCCESS
APC	324	MSKCC	GRCh37	5	112128142	112128142	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs78847145	NA	P-0034114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	53	279	0	ENST00000257430.4:c.646-1G>T		p.X216_splice	ENST00000257430	NM_000038.5	216			1	2	FACETS	0.996	0.859	1	0.996	0.859	1	CLONAL	1	TRUE	1	0.443250139456736	2		279	240	SUCCESS
APC	324	MSKCC	GRCh37	5	112162946	112162946	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1057517561	NA	P-0034114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	49	368	0	ENST00000257430.4:c.1548+2T>C		p.X516_splice	ENST00000257430	NM_000038.5	516			1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.443250139456736	2		368	193	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939577	76939577	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0121536-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	273	341	0	ENST00000373344.5:c.1171C>T	p.Gln391Ter	p.Q391*	ENST00000373344	NM_000489.3	391	Cag/Tag	9/35	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	NA	0	0.831033880938498	1		341	323	SUCCESS
AXL	558	MSKCC	GRCh37	19	41749547	41749547	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121536-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	243	533	0	ENST00000301178.4:c.1472G>T	p.Arg491Ile	p.R491I	ENST00000301178	NM_021913.4	491	aGa/aTa	12/20	1	2	FACETS	0.928	0.873	0.984	0.928	0.873	0.984	CLONAL	1	NA	1	0.831033880938498	2		533	630	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660832	227660832	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0121536-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	188	602	0	ENST00000305123.5:c.2623del	p.Arg875GlufsTer68	p.R875Efs*68	ENST00000305123	NM_005544.2	875	Cga/ga	1/2	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	NA	1	0.831033880938498	2		602	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0034116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	213	671	1	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	1	2	FACETS	1	0.977	1	1	0.994	1	CLONAL	2	TRUE	1	0.215054334989089	2		672	890	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0034117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	53	576	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			0.836961559871181	3	FACETS	0.889	0.769	1	0.445	0.384	0.509	CLONAL	1	TRUE	1	0.836961559871181	3		576	202	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0034117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	353	418	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.836961559871181	6	FACETS	0.997	0.98	1			1	CLONAL	6	TRUE	NA	0.836961559871181	6		418	377	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0034117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	112	663	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.749215575311551	5	FACETS	0.934	0.851	1			1	CLONAL	2	TRUE	NA	0.836961559871181	5		663	323	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916744	48916760	+	frameshift_variant	Frame_Shift_Del	DEL	ATTCAAAAGAAAAAGGA	ATTCAAAAGAAAAAGGA	-	novel	NA	P-0034117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	72	502	0	ENST00000267163.4:c.275_291del	p.Ile92ThrfsTer12	p.I92Tfs*12	ENST00000267163	NM_000321.2	92	ATTCAAAAGAAAAAGGAa/a	3/27	0.82103115189696	2	FACETS	0.906	0.84	0.965	0.906	0.84	0.965	CLONAL	2	TRUE	0	0.836961559871181	2		502	95	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578221	7578222	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0034117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	90	884	0	ENST00000269305.4:c.627_628insG	p.Asn210GlufsTer6	p.N210Efs*6	ENST00000269305	NM_001126112.2	209	-/G	6/11	0.836961559871181	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.836961559871181	1		884	104	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350750	15350750	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	87	1110	0	ENST00000263377.2:c.3253C>G	p.Pro1085Ala	p.P1085A	ENST00000263377	NM_058243.2	1085	Ccc/Gcc	15/20	0.240997564814176	3	FACETS	0.81	0.736	0.885	0.81	0.736	0.885	INDETERMINATE	2	TRUE	1	0.836961559871181	3		1110	182	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163570	32163571	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0034117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	133	760	0	ENST00000375023.3:c.5655_5656insA	p.Leu1886IlefsTer30	p.L1886Ifs*30	ENST00000375023	NM_004557.3	1885	-/A	30/30	0.836961559871181	3	FACETS	0.835	0.774	0.896	0.557	0.516	0.598	CLONAL	2	TRUE	0	0.836961559871181	3		760	270	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0034126-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	263	751	1	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.410011961240558	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.410011961240558	1		752	916	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32790091	32790091	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034126-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	61	143	0	ENST00000374899.4:c.1937C>A	p.Thr646Asn	p.T646N	ENST00000374899	NM_018833.2	646	aCc/aAc	12/12	0.410011961240558	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.410011961240558	1		143	200	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31435929	31435931	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0034126-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	60	245	0	ENST00000344624.3:c.2983_2985del	p.Gly995del	p.G995del	ENST00000344624		995	GGA/-	22/33	0.305614777652159	4	FACETS	0.69	0.594	0.794	0.23	0.198	0.265	SUBCLONAL	1	TRUE	1	0.410011961240558	4		245	598	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574030	7574030	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	234	461	0	ENST00000269305.4:c.997del	p.Arg333ValfsTer12	p.R333Vfs*12	ENST00000269305	NM_001126112.2	333	Cgt/gt	10/11	0.120151451919179	5	FACETS	1	0.972	1	0.794	0.746	0.844	INDETERMINATE	3	TRUE	1	0.349782393362009	5		461	642	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0034136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	73	199	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	0.349782393362009	2	FACETS	0.936	0.832	1	0.936	0.832	1	CLONAL	2	TRUE	0	0.349782393362009	2		199	223	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163325216	163325216	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	24	302	0	ENST00000271452.3:c.1352A>G	p.Lys451Arg	p.K451R	ENST00000271452	NM_145697.2	451	aAg/aGg	14/14	0.124499185343205	4	FACETS	0.659	0.518	0.822	0.33	0.259	0.411	INDETERMINATE	1	TRUE	2	0.349782393362009	4		302	281	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105554	30105554	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	100	671	0	ENST00000331968.5:c.1132G>C	p.Asp378His	p.D378H	ENST00000331968	NM_002742.2	378	Gac/Cac	7/18	0.278380943252915	4	FACETS	0.834	0.744	0.931	0.417	0.372	0.466	CLONAL	1	TRUE	2	0.349782393362009	4		671	925	SUCCESS
ATR	545	MSKCC	GRCh37	3	142259848	142259848	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1231282916	NA	P-0034136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	72	470	0	ENST00000350721.4:c.3479A>G	p.Lys1160Arg	p.K1160R	ENST00000350721	NM_001184.3	1160	aAg/aGg	18/47	0.349652805229997	4	FACETS	0.85	0.742	0.966	0.283	0.247	0.322	CLONAL	1	TRUE	1	0.349782393362009	4		470	654	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965406	68965406	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	33	584	0	ENST00000288368.4:c.1018G>T	p.Val340Phe	p.V340F	ENST00000288368	NM_024870.2	340	Gtt/Ttt	9/40	0.278380943252915	4	FACETS	0.396	0.321	0.481	0.198	0.16	0.241	SUBCLONAL	1	TRUE	2	0.349782393362009	4		584	643	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401275	139401276	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0034136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	240	644	0	ENST00000277541.6:c.3793dup	p.Glu1265GlyfsTer26	p.E1265Gfs*26	ENST00000277541	NM_017617.3	1265	gag/gGag	23/34	0.349782393362009	2	FACETS	0.965	0.905	1	0.965	0.905	1	CLONAL	2	TRUE	0	0.349782393362009	2		644	711	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0034137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	288	528	2	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.582448316140215	3	FACETS	0.986	0.936	1	0.986	0.936	1	CLONAL	2	TRUE	1	0.636072528135465	3		530	605	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	199	217	0	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	0.618342279947063	3	FACETS	0.913	0.868	0.957	0.913	0.868	0.957	CLONAL	3	TRUE	0	0.636072528135465	3		217	301	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0034137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	330	569	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.629520255741524	2	FACETS	0.984	0.945	1	0.984	0.945	1	CLONAL	2	TRUE	0	0.636072528135465	2		569	527	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653789	89653789	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0034137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	255	306	0	ENST00000371953.3:c.87T>G	p.Tyr29Ter	p.Y29*	ENST00000371953	NM_000314.4	29	taT/taG	2/9	0.629520255741524	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.636072528135465	2		306	384	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809504	36809504	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1412240338	NA	P-0034137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	172	563	4	ENST00000373129.3:c.961G>A	p.Ala321Thr	p.A321T	ENST00000373129	NM_032017.1	321	Gcc/Acc	10/12	1	2	FACETS	0.941	0.87	1	0.941	0.87	1	CLONAL	1	TRUE	1	0.636072528135465	2		567	575	SUCCESS
FH	2271	MSKCC	GRCh37	1	241665799	241665799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	143	429	0	ENST00000366560.3:c.1180G>T	p.Val394Phe	p.V394F	ENST00000366560	NM_000143.3	394	Gtc/Ttc	8/10	0.289519253420865	1	FACETS	0.7	0.644	0.758	0.7	0.644	0.758	INDETERMINATE	1	TRUE	0	0.636072528135465	1		429	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0034156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	27	744	1	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.300754618021176	3	FACETS	0.368	0.292	0.455	0.184	0.146	0.228	SUBCLONAL	1	TRUE	1	0.356185303710821	3		745	485	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112445	115112445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	127	677	1	ENST00000257566.3:c.1295C>T	p.Ser432Leu	p.S432L	ENST00000257566	NM_016569.3	432	tCg/tTg	7/8	1	2	FACETS	0.786	0.712	0.865	0.786	0.712	0.865	SUBCLONAL	1	TRUE	1	0.356185303710821	2		678	907	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	223	148	0				ENST00000310581	NM_198253.2	-/1132			0.263805620523953	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.356185303710821	3		148	680	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0034156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	33	458	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.263805620523953	3	FACETS	0.866	0.719	1	0.866	0.719	1	CLONAL	2	TRUE	1	0.356185303710821	3		458	126	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0034156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	158	735	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.300754618021176	3	FACETS	1	0.971	1	0.567	0.519	0.617	CLONAL	1	TRUE	1	0.356185303710821	3		735	922	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	171	693	0	ENST00000269571.5:c.829G>C	p.Asp277His	p.D277H	ENST00000269571		277	Gac/Cac	7/27	0.300754618021176	3	FACETS	1	0.969	1	0.554	0.509	0.602	CLONAL	1	TRUE	1	0.356185303710821	3		693	1020	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032069	26032069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	78	355	0	ENST00000244661.2:c.220G>A	p.Glu74Lys	p.E74K	ENST00000244661	NM_003537.3	74	Gaa/Aaa	1/1	0.300149242025772	5	FACETS	1	0.881	1	0.334	0.293	0.378	CLONAL	1	TRUE	2	0.356185303710821	5		355	670	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56477621	56477621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	64	645	1	ENST00000267101.3:c.169G>A	p.Glu57Lys	p.E57K	ENST00000267101	NM_001982.3	57	Gag/Aag	2/28	0.300149242025772	5	FACETS	0.655	0.566	0.752	0.218	0.188	0.251	SUBCLONAL	1	TRUE	2	0.356185303710821	5		646	842	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584674	187584674	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	29	538	0	ENST00000441802.2:c.3359C>T	p.Ser1120Leu	p.S1120L	ENST00000441802	NM_005245.3	1120	tCa/tTa	3/27	0.192560704875125	1	FACETS	0.683	0.552	0.829	0.683	0.552	0.829	INDETERMINATE	1	TRUE	0	0.356185303710821	1		538	196	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874166	155874166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777520196	NA	P-0034156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	57	638	0	ENST00000368323.3:c.365G>A	p.Arg122Gln	p.R122Q	ENST00000368323	NM_006912.5	122	cGa/cAa	5/6	0.300754618021176	3	FACETS	0.952	0.82	1	0.476	0.41	0.548	CLONAL	1	TRUE	1	0.356185303710821	3		638	396	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259830	16259830	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	74	457	0	ENST00000375759.3:c.7095G>C	p.Glu2365Asp	p.E2365D	ENST00000375759	NM_015001.2	2365	gaG/gaC	11/15	0.300754618021176	3	FACETS	0.9	0.789	1	0.45	0.394	0.51	CLONAL	1	TRUE	1	0.356185303710821	3		457	544	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877972	151877972	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	29	386	0	ENST00000262189.6:c.6973C>T	p.Gln2325Ter	p.Q2325*	ENST00000262189	NM_170606.2	2325	Cag/Tag	36/59	0.263805620523953	3	FACETS	0.803	0.647	0.977	0.401	0.323	0.489	CLONAL	1	TRUE	1	0.356185303710821	3		386	239	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599209	28599209	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	146	721	0	ENST00000253063.3:c.655G>C	p.Glu219Gln	p.E219Q	ENST00000253063	NM_031459.4	219	Gag/Cag	5/10	0.300754618021176	3	FACETS	1	0.927	1	0.509	0.464	0.557	CLONAL	1	TRUE	1	0.356185303710821	3		721	948	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598902	28598902	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	169	759	0	ENST00000253063.3:c.462G>C	p.Glu154Asp	p.E154D	ENST00000253063	NM_031459.4	154	gaG/gaC	4/10	0.300754618021176	3	FACETS	1	0.95	1	0.523	0.48	0.568	CLONAL	1	TRUE	1	0.356185303710821	3		759	1068	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471809	120471809	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	34	380	0	ENST00000256646.2:c.3682G>A	p.Asp1228Asn	p.D1228N	ENST00000256646	NM_024408.3	1228	Gac/Aac	23/34	0.300754618021176	3	FACETS	1	0.947	1	0.716	0.593	0.85	CLONAL	1	TRUE	1	0.356185303710821	3		380	157	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939533	71939533	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1223	248	769	0	ENST00000298229.2:c.388G>A	p.Asp130Asn	p.D130N	ENST00000298229	NM_001567.3	130	Gat/Aat	3/28	0.300149242025772	5	FACETS	1	0.992	1	0.484	0.451	0.518	CLONAL	1	TRUE	2	0.356185303710821	5		769	1471	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998871	100998871	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs373360839	NA	P-0034156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	104	765	0	ENST00000325455.5:c.931C>G	p.Leu311Val	p.L311V	ENST00000325455	NM_001202474.3	311	Ctc/Gtc	1/8	0.263805620523953	3	FACETS	0.976	0.874	1	0.488	0.437	0.542	CLONAL	1	TRUE	1	0.356185303710821	3		765	705	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100642	102100642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	26	406	0	ENST00000282441.5:c.1486G>A	p.Asp496Asn	p.D496N	ENST00000282441	NM_001130145.2	496	Gat/Aat	9/9	0.263805620523953	3	FACETS	1	0.923	1	0.672	0.54	0.818	CLONAL	1	TRUE	1	0.356185303710821	3		406	128	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129772	108129772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658688	NA	P-0034156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	18	558	0	ENST00000278616.4:c.2436G>A	p.Met812Ile	p.M812I	ENST00000278616	NM_000051.3	812	atG/atA	16/63	0.263805620523953	3	FACETS	0.758	0.575	0.972	0.379	0.287	0.486	CLONAL	1	TRUE	1	0.356185303710821	3		558	157	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372386	118372386	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0034156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	19	392	0	ENST00000534358.1:c.6320-1G>C		p.X2107_splice	ENST00000534358	NM_005933.3	2107			0.263805620523953	3	FACETS	0.731	0.558	0.931	0.365	0.279	0.466	CLONAL	1	TRUE	1	0.356185303710821	3		392	172	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245258	46245258	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs757890582	NA	P-0034156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	30	475	0	ENST00000334344.6:c.3352C>T	p.Gln1118Ter	p.Q1118*	ENST00000334344	NM_152641.2	1118	Cag/Tag	15/21	0.356185303710821	1	FACETS	0.442	0.357	0.539	0.442	0.357	0.539	SUBCLONAL	1	TRUE	0	0.356185303710821	1		475	313	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780586	56780586	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs531838785	NA	P-0034156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	49	728	0	ENST00000337432.4:c.601C>G	p.Leu201Val	p.L201V	ENST00000337432	NM_058216.2	201	Ctt/Gtt	4/9	0.300754618021176	3	FACETS	1	0.93	1	0.579	0.494	0.671	CLONAL	1	TRUE	1	0.356185303710821	3		728	280	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41521980	41521980	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0034156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	37	538	0	ENST00000263253.7:c.842C>G	p.Ser281Ter	p.S281*	ENST00000263253	NM_001429.3	281	tCa/tGa	3/31	1	2	FACETS	0.824	0.694	0.963	1	0.962	1	CLONAL	2	TRUE	1	0.356185303710821	2		538	126	SUCCESS
ATR	545	MSKCC	GRCh37	3	142224090	142224090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1027616979	NA	P-0034156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	42	605	0	ENST00000350721.4:c.5087G>A	p.Arg1696Lys	p.R1696K	ENST00000350721	NM_001184.3	1696	aGa/aAa	29/47	0.263805620523953	3	FACETS	1	0.955	1	0.709	0.599	0.828	CLONAL	1	TRUE	1	0.356185303710821	3		605	196	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955040	55955040	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	29	451	0	ENST00000263923.4:c.3505C>G	p.Gln1169Glu	p.Q1169E	ENST00000263923	NM_002253.2	1169	Cag/Gag	26/30	0.192560704875125	1	FACETS	0.64	0.517	0.778	0.64	0.517	0.778	INDETERMINATE	1	TRUE	0	0.356185303710821	1		451	209	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509799	106509799	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	21	617	1	ENST00000359195.3:c.1793G>T	p.Trp598Leu	p.W598L	ENST00000359195	NM_002649.2	598	tGg/tTg	2/11	0.263805620523953	3	FACETS	0.62	0.479	0.783	0.31	0.239	0.392	SUBCLONAL	1	TRUE	1	0.356185303710821	3		618	224	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879486	151879486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	22	473	0	ENST00000262189.6:c.5459C>T	p.Ser1820Phe	p.S1820F	ENST00000262189	NM_170606.2	1820	tCt/tTt	36/59	0.263805620523953	3	FACETS	0.856	0.669	1	0.428	0.334	0.535	CLONAL	1	TRUE	1	0.356185303710821	3		473	170	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904851	101904851	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	15	452	0	ENST00000374994.4:c.839C>T	p.Ser280Leu	p.S280L	ENST00000374994	NM_004612.2	280	tCa/tTa	5/9	1	2	FACETS	0.565	0.416	0.743	0.565	0.416	0.743	SUBCLONAL	1	TRUE	1	0.356185303710821	2		452	149	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133756018	133756018	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	81	461	0	ENST00000318560.5:c.1645G>C	p.Glu549Gln	p.E549Q	ENST00000318560	NM_005157.4	549	Gag/Cag	10/11	0.278410198123706	3	FACETS	0.948	0.837	1	0.316	0.279	0.356	CLONAL	1	TRUE	0	0.356185303710821	3		461	565	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889158	76889158	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	11	213	0	ENST00000373344.5:c.4852G>T	p.Asp1618Tyr	p.D1618Y	ENST00000373344	NM_000489.3	1618	Gat/Tat	18/35	0.356185303710821	2	FACETS	1	0.839	1			1	CLONAL	1	TRUE	NA	0.356185303710821	2		213	47	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0034157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	101	369	2	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	0.550629222467884	2		371	366	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692911	89692911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909241	NA	P-0034157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	76	286	0	ENST00000371953.3:c.395G>A	p.Gly132Asp	p.G132D	ENST00000371953	NM_000314.4	132	gGt/gAt	5/9	1	2	FACETS	0.765	0.675	0.86	0.765	0.675	0.86	SUBCLONAL	1	TRUE	1	0.550629222467884	2		286	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0034157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	218	711	0	ENST00000269305.4:c.376-1G>C		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.550629222467884	1	FACETS	0.984	0.922	1	0.984	0.922	1	CLONAL	1	TRUE	0	0.550629222467884	1		711	583	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653043	29653043	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	159	260	0	ENST00000356175.3:c.4979del	p.Asn1660ThrfsTer17	p.N1660Tfs*17	ENST00000356175	NM_000267.3	1660	Aac/ac	36/57	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.550629222467884	2		260	513	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395750	45395750	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0034157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	130	249	0	ENST00000262160.6:c.384T>A	p.Tyr128Ter	p.Y128*	ENST00000262160	NM_005901.5	128	taT/taA	4/11	0.550629222467884	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.550629222467884	1		249	308	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0034157-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	176	369	2	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.936	0.872	1	0.936	0.872	1	CLONAL	1	TRUE	1	0.895831913728652	2		371	420	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692911	89692911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909241	NA	P-0034157-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	211	286	0	ENST00000371953.3:c.395G>A	p.Gly132Asp	p.G132D	ENST00000371953	NM_000314.4	132	gGt/gAt	5/9	1	2	FACETS	0.948	0.889	1	0.948	0.889	1	CLONAL	1	TRUE	1	0.895831913728652	2		286	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0034157-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	398	711	0	ENST00000269305.4:c.376-1G>C		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.895831913728652	1	FACETS	0.983	0.956	1	0.983	0.956	1	CLONAL	1	TRUE	0	0.895831913728652	1		711	499	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653043	29653043	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034157-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	202	260	0	ENST00000356175.3:c.4979del	p.Asn1660ThrfsTer17	p.N1660Tfs*17	ENST00000356175	NM_000267.3	1660	Aac/ac	36/57	1	2	FACETS	0.957	0.897	1	0.957	0.897	1	CLONAL	1	TRUE	1	0.895831913728652	2		260	471	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395750	45395750	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0034157-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	198	249	0	ENST00000262160.6:c.384T>A	p.Tyr128Ter	p.Y128*	ENST00000262160	NM_005901.5	128	taT/taA	4/11	0.895831913728652	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.895831913728652	1		249	234	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266041	41266373	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTA	CCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTA	-	novel	NA	P-0034157-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	151	121	0	ENST00000349496.5:c.42_242-68del		p.X14_splice	ENST00000349496	NM_001904.3	14		3/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.895831913728652	2		121	308	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277882	41277882	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034157-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	195	226	0	ENST00000349496.5:c.1846G>T	p.Gly616Trp	p.G616W	ENST00000349496	NM_001904.3	616	Ggg/Tgg	12/15	1	2	FACETS	0.994	0.931	1	0.994	0.931	1	CLONAL	1	TRUE	1	0.895831913728652	2		226	438	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0034159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	38	451	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	0.19678989551074	2		451	281	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120642	115120642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	110	684	0	ENST00000257566.3:c.364G>A	p.Glu122Lys	p.E122K	ENST00000257566	NM_016569.3	122	Gag/Aag	1/8	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.19678989551074	2		684	1009	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855944	68855944	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	58	473	0	ENST00000261769.5:c.1753del	p.Leu585CysfsTer4	p.L585Cfs*4	ENST00000261769	NM_004360.3	584	atC/at	12/16	0.19678989551074	1	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	0	0.19678989551074	1		473	521	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0034160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	316	425	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	FALSE	1	0.621342008556884	2		425	732	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100292	27100292	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0034160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	367	741	0	ENST00000324856.7:c.4005-1G>A		p.X1335_splice	ENST00000324856	NM_006015.4	1335			0.621342008556884	1	FACETS	0.876	0.85	0.9	1	0.997	1	CLONAL	2	FALSE	0	0.621342008556884	1		741	465	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876392	35876392	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	259	700	0	ENST00000303115.3:c.1184A>C	p.Lys395Thr	p.K395T	ENST00000303115	NM_002185.3	395	aAg/aCg	8/8	0.294210626856498	1	FACETS	0.974	0.92	1	0.974	0.92	1	INDETERMINATE	1	FALSE	0	0.621342008556884	1		700	590	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441763	49441763	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0034160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	249	605	0	ENST00000301067.7:c.4221C>G	p.Tyr1407Ter	p.Y1407*	ENST00000301067	NM_003482.3	1407	taC/taG	14/54	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	FALSE	1	0.621342008556884	2		605	568	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288471	15288471	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	153	430	0	ENST00000263388.2:c.4268A>G	p.Asp1423Gly	p.D1423G	ENST00000263388	NM_000435.2	1423	gAc/gGc	24/33	1	2	FACETS	0.784	0.73	0.838	1	0.991	1	SUBCLONAL	2	FALSE	1	0.621342008556884	2		430	314	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157520043	157520043	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0034160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	186	415	0	ENST00000346085.5:c.4110+2T>G		p.X1370_splice	ENST00000346085	NM_020732.3	1370			1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.621342008556884	2		415	443	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499812	8499812	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	472	567	0	ENST00000356435.5:c.2157G>C	p.Glu719Asp	p.E719D	ENST00000356435		719	gaG/gaC	14/35	0.621342008556884	3	FACETS	0.838	0.809	0.867	1	0.996	1	CLONAL	3	FALSE	1	0.621342008556884	3		567	792	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923073	39923073	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	313	836	1	ENST00000378444.4:c.3635T>C	p.Leu1212Pro	p.L1212P	ENST00000378444	NM_001123385.1	1212	cTg/cCg	8/15	0.294210626856498	1	FACETS	0.936	0.888	0.984	0.936	0.888	0.984	INDETERMINATE	1	FALSE	0	0.621342008556884	1		837	742	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352301	70352301	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	221	744	0	ENST00000374080.3:c.4328T>C	p.Val1443Ala	p.V1443A	ENST00000374080		1443	gTg/gCg	31/45	0.294210626856498	1	FACETS	0.835	0.783	0.889	0.835	0.783	0.889	INDETERMINATE	1	FALSE	0	0.621342008556884	1		744	587	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0034161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	327	463	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.961	0.913	1	0.961	0.913	1	CLONAL	1	TRUE	1	0.869472790501078	2		463	783	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061463	38061463	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	373	671	0	ENST00000250448.2:c.526A>G	p.Ile176Val	p.I176V	ENST00000250448	NM_004496.3	176	Atc/Gtc	2/2	1	2	FACETS	0.911	0.867	0.955	0.911	0.867	0.955	CLONAL	1	TRUE	1	0.869472790501078	2		671	942	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855998	68855998	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	400	627	0	ENST00000261769.5:c.1806del	p.Cys603ValfsTer10	p.C603Vfs*10	ENST00000261769	NM_004360.3	602	ttC/tt	12/16	0.869472790501078	1	FACETS	0.996	0.967	1	0.996	0.967	1	CLONAL	1	TRUE	0	0.869472790501078	1		627	522	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0034162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	165	502	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	0.436123085610857	2		502	710	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0034162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	108	464	1	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.305534205906086	0	FACETS	0.527	0.475	0.582			1	SUBCLONAL	1	TRUE	0	0.436123085610857	0		465	530	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0034162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	133	465	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.436123085610857	2		465	415	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0034162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	39	356	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	1	2	FACETS	0.568	0.472	0.673	0.568	0.472	0.673	SUBCLONAL	1	TRUE	1	0.436123085610857	2		356	315	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604673	48604673	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060500738	NA	P-0034162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	29	512	0	ENST00000342988.3:c.1495T>C	p.Cys499Arg	p.C499R	ENST00000342988	NM_005359.5	499	Tgc/Cgc	12/12	0.305534205906086	0	FACETS	0.16	0.128	0.196			1	SUBCLONAL	1	TRUE	0	0.436123085610857	0		512	469	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119808	70119808	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	112	705	0	ENST00000245479.2:c.811del	p.Arg271AlafsTer8	p.R271Afs*8	ENST00000245479	NM_000346.3	270	ttC/tt	3/3	1	2	FACETS	0.798	0.719	0.881	0.798	0.719	0.881	SUBCLONAL	1	TRUE	1	0.436123085610857	2		705	644	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476811	140476811	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507479	NA	P-0034162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	123	601	0	ENST00000288602.6:c.1595G>A	p.Cys532Tyr	p.C532Y	ENST00000288602	NM_004333.4	532	tGt/tAt	13/18	0.377503064632583	3	FACETS	0.663	0.598	0.731	0.331	0.299	0.366	SUBCLONAL	1	TRUE	1	0.436123085610857	3		601	1037	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982404	201982407	+	frameshift_variant	Frame_Shift_Ins	INS	CGAG	CGAG	TCGAA	novel	NA	P-0034162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	118	786	3	ENST00000359651.3:c.783_786delinsTCGAA	p.Glu262ArgfsTer39	p.E262Rfs*39	ENST00000359651		261	ctCGAG/ctTCGAA	6/8	1	2	FACETS	0.637	0.574	0.703	0.637	0.574	0.703	SUBCLONAL	1	TRUE	1	0.436123085610857	2		789	850	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205824	108205825	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAG	novel	NA	P-0034162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	62	477	0	ENST00000278616.4:c.8141_8143dup	p.Gln2714dup	p.Q2714dup	ENST00000278616	NM_000051.3	2714	-/CAG	55/63	1	2	FACETS	0.702	0.609	0.803	0.702	0.609	0.803	SUBCLONAL	1	TRUE	1	0.436123085610857	2		477	405	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506646	103506650	+	frameshift_variant	Frame_Shift_Del	DEL	CACTA	CACTA	-	novel	NA	P-0034162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	24	252	0	ENST00000355739.4:c.390_394del	p.Leu131GlnfsTer30	p.L131Qfs*30	ENST00000355739	NM_000123.3	130	gCACTA/g	4/15	0.136967258038352	3	FACETS	0.486	0.381	0.605	0.243	0.19	0.303	INDETERMINATE	1	TRUE	1	0.436123085610857	3		252	276	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119830	70119863	+	frameshift_variant	Frame_Shift_Del	DEL	CTGAGCAGCGACGTCATCTCCAACATCGAGACCT	CTGAGCAGCGACGTCATCTCCAACATCGAGACCT	AG	novel	NA	P-0034162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	42	794	2	ENST00000245479.2:c.832_865delinsAG	p.Leu278SerfsTer7	p.L278Sfs*7	ENST00000245479	NM_000346.3	278	CTGAGCAGCGACGTCATCTCCAACATCGAGACCTtc/AGtc	3/3	1	2	FACETS	0.27	0.225	0.321	0.27	0.225	0.321	SUBCLONAL	1	TRUE	1	0.436123085610857	2		796	713	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27016121	27016121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs905314868	NA	P-0034162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	100	634	0	ENST00000335756.4:c.397C>T	p.Arg133Trp	p.R133W	ENST00000335756	NM_001809.3	133	Cgg/Tgg	4/5	1	2	FACETS	0.701	0.627	0.78	0.701	0.627	0.78	SUBCLONAL	1	TRUE	1	0.436123085610857	2		634	654	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097176	178097176	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	104	511	0	ENST00000397062.3:c.538A>G	p.Met180Val	p.M180V	ENST00000397062	NM_006164.4	180	Atg/Gtg	4/5	1	2	FACETS	0.786	0.705	0.871	0.786	0.705	0.871	SUBCLONAL	1	TRUE	1	0.436123085610857	2		511	607	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130105	143130105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	42	803	0	ENST00000262992.4:c.911G>A	p.Cys304Tyr	p.C304Y	ENST00000262992	NM_001101669.1	304	tGt/tAt	11/24	1	2	FACETS	0.286	0.238	0.34	0.286	0.238	0.34	SUBCLONAL	1	TRUE	1	0.436123085610857	2		803	673	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793566	89793566	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	18	399	0	ENST00000336032.3:c.635A>T	p.Asn212Ile	p.N212I	ENST00000336032	NM_006813.2	212	aAc/aTc	2/2	0.43195709563338	1	FACETS	0.2	0.15	0.259	0.2	0.15	0.259	SUBCLONAL	1	TRUE	0	0.436123085610857	1		399	323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0034164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	815	751	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	2	TRUE	NA	0.890685390803925	2		751	894	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	161	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.92	0.854	0.986	0.92	0.854	0.986	CLONAL	1	TRUE	1	0.890685390803925	2		148	393	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720826	89720826	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	229	353	0	ENST00000371953.3:c.977A>G	p.Asp326Gly	p.D326G	ENST00000371953	NM_000314.4	326	gAc/gGc	8/9	0.890685390803925	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.890685390803925	1		353	275	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165930	118165930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781549053	NA	P-0034164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	288	464	0	ENST00000369448.3:c.440C>T	p.Thr147Met	p.T147M	ENST00000369448	NM_017709.3	147	aCg/aTg	2/2	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.890685390803925	2		464	621	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141030	55141035	+	inframe_deletion	In_Frame_Del	DEL	GGAGGG	GGAGGG	-	novel	NA	P-0034164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	2618	431	0	ENST00000257290.5:c.1676_1681del	p.Trp559_Val561delinsPhe	p.W559_V561delinsF	ENST00000257290	NM_006206.4	559	tGGAGGGtc/ttc	12/23	0.890685390803925	14	FACETS	0.965	0.955	0.975	0.891	0.881	0.9	CLONAL	12	TRUE	1	0.890685390803925	14		431	3221	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050714	5050714	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	272	499	0	ENST00000381652.3:c.497T>C	p.Ile166Thr	p.I166T	ENST00000381652	NM_004972.3	166	aTa/aCa	6/25	1	2	FACETS	0.86	0.812	0.909	0.86	0.812	0.909	CLONAL	1	TRUE	1	0.890685390803925	2		499	710	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0034165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	437	738	2	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	0.318402815784299	3	FACETS	0.901	0.861	0.94	0.901	0.861	0.94	CLONAL	3	FALSE	0	0.356961432537366	3		740	1068	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0034165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	96	502	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.279351129987902	4	FACETS	1	0.977	1	0.682	0.61	0.759	CLONAL	1	FALSE	2	0.356961432537366	4		502	535	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951170	48951170	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	38	428	0	ENST00000267163.4:c.1332G>T	p.Gln444His	p.Q444H	ENST00000267163	NM_000321.2	444	caG/caT	13/27	0.32747181821785	2	FACETS	1	0.949	1	0.687	0.577	0.805	CLONAL	1	FALSE	0	0.356961432537366	2		428	155	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122908	2122909	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGACT	novel	NA	P-0034165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	248	809	0	ENST00000219476.3:c.2282_2286dup	p.His763ThrfsTer10	p.H763Tfs*10	ENST00000219476	NM_000548.3	760	act/acTGACTt	21/42	0.253252199305488	3	FACETS	0.945	0.886	1	0.63	0.591	0.671	CLONAL	2	FALSE	0	0.356961432537366	3		809	866	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094979	11094979	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	277	870	0	ENST00000358026.2:c.152C>A	p.Ser51Ter	p.S51*	ENST00000358026	NM_001128849.1	51	tCa/tAa	2/36	0.254318091001934	3	FACETS	1	0.989	1	0.789	0.744	0.834	CLONAL	2	FALSE	0	0.356961432537366	3		870	773	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111422	56111422	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	184	398	0	ENST00000399503.3:c.22C>G	p.Arg8Gly	p.R8G	ENST00000399503	NM_005921.1	8	Cgc/Ggc	1/20	0.316889408368945	3	FACETS	0.835	0.778	0.893	0.835	0.778	0.893	CLONAL	3	FALSE	0	0.356961432537366	3		398	485	SUCCESS
APC	324	MSKCC	GRCh37	5	112176986	112176986	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs878853457	NA	P-0034165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	162	498	0	ENST00000257430.4:c.5695G>C	p.Glu1899Gln	p.E1899Q	ENST00000257430	NM_000038.5	1899	Gaa/Caa	16/16	0.316889408368945	3	FACETS	0.951	0.884	1	0.951	0.884	1	CLONAL	3	FALSE	0	0.356961432537366	3		498	375	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	222	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.973	0.912	1	0.973	0.912	1	CLONAL	1	TRUE	1	0.784414160168908	2		148	582	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0034166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	200	451	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.861	0.803	0.921	0.861	0.803	0.921	CLONAL	1	TRUE	1	0.784414160168908	2		451	592	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181843	56181843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	237	450	0	ENST00000399503.3:c.4067G>A	p.Gly1356Asp	p.G1356D	ENST00000399503	NM_005921.1	1356	gGc/gAc	17/20	0.685273483741083	1	FACETS	0.927	0.882	0.973	0.927	0.882	0.973	CLONAL	1	TRUE	0	0.784414160168908	1		450	396	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs121913292	NA	P-0034166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	318	519	0	ENST00000371953.3:c.389del	p.Arg130GlnfsTer4	p.R130Qfs*4	ENST00000371953	NM_000314.4	130	cGa/ca	5/9	0.784414160168908	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.784414160168908	1		519	437	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512315	38512317	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	novel	NA	P-0034166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	339	656	0	ENST00000254066.5:c.1228_1230del	p.Ile410del	p.I410del	ENST00000254066	NM_000964.3	409	cTCAtc/ctc	9/9	1	2	FACETS	0.788	0.746	0.831	0.788	0.746	0.831	SUBCLONAL	1	TRUE	1	0.784414160168908	2		656	1097	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061261	38061265	+	missense_variant	Missense_Mutation	ONP	TAGGA	TAGGA	CAGGC	novel	NA	P-0034166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	491	701	0	ENST00000250448.2:c.724_728delinsGCCTG	p.Ser242_Tyr243delinsAlaCys	p.S242_Y243delinsAC	ENST00000250448	NM_004496.3	242	TCCTAc/GCCTGc	2/2	0.399770859187904	1	FACETS	0.791	0.761	0.821	0.791	0.761	0.821	INDETERMINATE	1	TRUE	0	0.784414160168908	1		701	962	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	172	460	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.228123726558995	2	FACETS	0.933	0.864	1	1	0.989	1	CLONAL	3	FALSE	0	0.228123726558995	2		460	539	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0034167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	67	356	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	0.218394677141089	3	FACETS	0.804	0.702	0.914	0.804	0.702	0.914	CLONAL	2	FALSE	1	0.228123726558995	3		356	407	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	28	479	0	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	0.220490035346394	0	FACETS	0.495	0.395	0.608			1	SUBCLONAL	1	FALSE	0	0.228123726558995	0		479	383	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577518	7577519	+	inframe_insertion	In_Frame_Ins	INS	-	-	GATGGTGAG	novel	NA	P-0034167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	95	854	1	ENST00000269305.4:c.754_762dup	p.Leu252_Ile254dup	p.L252_I254dup	ENST00000269305	NM_001126112.2	252	-/CTCACCATC	7/11	0.220490035346394	0	FACETS	0.866	0.771	0.968			1	CLONAL	1	FALSE	0	0.228123726558995	0		855	742	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208381	5208381	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161731225	NA	P-0034167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	97	725	1	ENST00000357368.4:c.5509C>T	p.Arg1837Trp	p.R1837W	ENST00000357368	NM_002850.3	1837	Cgg/Tgg	36/38	0.228123726558995	2	FACETS	0.927	0.826	1	0.464	0.413	0.518	CLONAL	1	FALSE	0	0.228123726558995	2		726	917	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155211	55155211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267600188	NA	P-0034167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	84	663	1	ENST00000257290.5:c.2810C>T	p.Pro937Leu	p.P937L	ENST00000257290	NM_006206.4	937	cCg/cTg	21/23	0.228123726558995	1	FACETS	0.764	0.674	0.861	0.764	0.674	0.861	SUBCLONAL	1	FALSE	0	0.228123726558995	1		664	854	SUCCESS
APC	324	MSKCC	GRCh37	5	112175513	112175514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0034167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	169	445	0	ENST00000257430.4:c.4222_4223insTT	p.Glu1408ValfsTer8	p.E1408Vfs*8	ENST00000257430	NM_000038.5	1408	gaa/gTTaa	16/16	0.218394677141089	3	FACETS	0.919	0.849	0.991	1	0.988	1	CLONAL	3	FALSE	1	0.228123726558995	3		445	599	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0034174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	14	463	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		463	338	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0034175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	46	465	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	1	2	FACETS	0.986	0.832	1	0.986	0.832	1	CLONAL	1	TRUE	1	0.216414682642979	2		465	431	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0034175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	51	470	2	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.216414682642979	2		472	449	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032288	26032288	+	start_lost	Translation_Start_Site	SNP	T	T	C	rs748540323	NA	P-0034175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	30	326	0	ENST00000244661.2:c.1A>G	p.Met1?	p.M1?	ENST00000244661	NM_003537.3	1	Atg/Gtg	1/1	0.0611815393245629	3	FACETS	1	0.84	1	0.523	0.422	0.636	INDETERMINATE	1	TRUE	1	0.216414682642979	3		326	294	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056222	27056223	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0034176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	211	561	0	ENST00000324856.7:c.1220dup	p.Pro408SerfsTer215	p.P408Sfs*215	ENST00000324856	NM_006015.4	406	-/C	2/20	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.451324829053802	2		561	932	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0034182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	92	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.265550205836788	3	FACETS	0.784	0.699	0.873	0.784	0.699	0.873	SUBCLONAL	2	TRUE	1	0.285420764756893	3		502	470	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0034182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	96	438	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.27476212432036	3	FACETS	1	0.96	1	0.756	0.68	0.835	CLONAL	2	TRUE	0	0.285420764756893	3		438	339	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0034182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	88	451	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.265550205836788	3	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	1	0.285420764756893	3		451	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0034182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	160	675	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.285420764756893	2	FACETS	0.847	0.779	0.917	0.847	0.779	0.917	CLONAL	2	TRUE	0	0.285420764756893	2		675	662	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858337	9858337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs560057284	NA	P-0034182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	30	513	0	ENST00000330684.3:c.3064C>T	p.Arg1022Cys	p.R1022C	ENST00000330684	NM_001134407.1	1022	Cgc/Tgc	13/13	0.187487176171678	4	FACETS	0.503	0.404	0.616	0.252	0.202	0.308	SUBCLONAL	1	TRUE	2	0.285420764756893	4		513	537	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032481	12032481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	74	343	0	ENST00000353533.5:c.917C>T	p.Pro306Leu	p.P306L	ENST00000353533	NM_003010.3	306	cCt/cTt	9/11	0.285420764756893	2	FACETS	0.919	0.814	1	0.919	0.814	1	CLONAL	2	TRUE	0	0.285420764756893	2		343	282	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678783	52678784	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0034182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	97	407	0	ENST00000394830.3:c.835dup	p.Ile279AsnfsTer8	p.I279Nfs*8	ENST00000394830	NM_018313.4	279	ata/aAta	9/30	0.265550205836788	3	FACETS	0.841	0.753	0.933	0.841	0.753	0.933	CLONAL	2	TRUE	1	0.285420764756893	3		407	462	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933586	39933586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1397661727	NA	P-0034182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	134	605	0	ENST00000378444.4:c.1013G>A	p.Arg338Gln	p.R338Q	ENST00000378444	NM_001123385.1	338	cGg/cAg	4/15	0.285420764756893	5	FACETS	1	0.936	1	0.689	0.627	0.753	CLONAL	2	TRUE	2	0.285420764756893	5		605	649	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411915	63411931	+	frameshift_variant	Frame_Shift_Del	DEL	GTGGATACATTTGGGCA	GTGGATACATTTGGGCA	-	novel	NA	P-0034182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	220	941	0	ENST00000330258.3:c.1236_1252del	p.Met415TyrfsTer20	p.M415Yfs*20	ENST00000330258	NM_152424.3	412	acTGCCCAAATGTATCCACgg/acgg	2/2	0.285420764756893	5	FACETS	1	0.958	1	0.694	0.645	0.744	CLONAL	2	TRUE	2	0.285420764756893	5		941	1058	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0034183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	176	274	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.82	2		274	412	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097674	27097675	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0034183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	115	648	0	ENST00000324856.7:c.3264dup	p.Ala1089CysfsTer16	p.A1089Cfs*16	ENST00000324856	NM_006015.4	1088	gct/gcTt	12/20	1	2	FACETS	0.496	0.448	0.547	0.496	0.448	0.547	SUBCLONAL	1	TRUE	1	0.82	2		648	565	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101225	27101225	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	31	623	0	ENST00000324856.7:c.4507G>C	p.Asp1503His	p.D1503H	ENST00000324856	NM_006015.4	1503	Gac/Cac	18/20	1	2	FACETS	0.138	0.111	0.169	0.138	0.111	0.169	SUBCLONAL	1	TRUE	1	0.82	2		623	546	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444157	49444157	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	300	764	0	ENST00000301067.7:c.3214G>T	p.Glu1072Ter	p.E1072*	ENST00000301067	NM_003482.3	1072	Gag/Tag	11/54	1	2	FACETS	0.991	0.939	1	0.991	0.939	1	CLONAL	1	TRUE	1	0.82	2		764	738	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444206	49444206	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	324	834	0	ENST00000301067.7:c.3165G>C	p.Leu1055Phe	p.L1055F	ENST00000301067	NM_003482.3	1055	ttG/ttC	11/54	1	2	FACETS	0.993	0.943	1	0.993	0.943	1	CLONAL	1	TRUE	1	0.82	2		834	796	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764303	39764303	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1414795545	NA	P-0034186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	182	756	0	ENST00000288319.7:c.809C>T	p.Ser270Leu	p.S270L	ENST00000288319	NM_182918.3	270	tCg/tTg	7/10	1	2	FACETS	0.927	0.856	1	0.927	0.856	1	CLONAL	1	TRUE	1	0.425391157210998	2		756	923	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843622	3843623	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0034186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	144	592	0	ENST00000262367.5:c.980_981insT	p.Gln327HisfsTer23	p.Q327Hfs*23	ENST00000262367	NM_004380.2	327	cag/caTg	4/31	0.425391157210998	3	FACETS	0.938	0.856	1	0.469	0.428	0.513	CLONAL	1	TRUE	1	0.425391157210998	3		592	875	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38173543	38173543	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1953	127	564	1	ENST00000317025.8:c.1873G>T	p.Asp625Tyr	p.D625Y	ENST00000317025	NM_023034.1	625	Gat/Tat	10/24	0.425391157210998	11	FACETS	0.837	0.754	0.924	0.084	0.075	0.093	CLONAL	1	TRUE	1	0.425391157210998	11		565	2080	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0034188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	16	339	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.777	0.572	1	0.777	0.572	1	CLONAL	1	TRUE	1	0.1	2		339	412	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0034188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	23	463	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.813	0.632	1	0.813	0.632	1	CLONAL	1	TRUE	1	0.1	2		463	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0034189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	40	609	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.843	0.699	1	0.843	0.699	1	CLONAL	1	TRUE	1	0.15	2		609	633	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0034189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	59	435	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.165223081244276	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	1	0.15	3		435	355	SUCCESS
APC	324	MSKCC	GRCh37	5	112175751	112175752	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTTAT	novel	NA	P-0034189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	24	406	0	ENST00000257430.4:c.4462_4466dup	p.Leu1489PhefsTer20	p.L1489Ffs*20	ENST00000257430	NM_000038.5	1487	act/acTTTATt	16/16	1	2	FACETS	1	0.826	1	1	0.826	1	CLONAL	1	TRUE	1	0.15	2		406	302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0034193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	218	712	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.854456018800212	1	FACETS	0.879	0.837	0.92	0.879	0.837	0.92	CLONAL	1	TRUE	0	0.856448227874729	1		712	331	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926872	112926872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507541	NA	P-0034193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	213	785	4	ENST00000351677.2:c.1492C>T	p.Arg498Trp	p.R498W	ENST00000351677	NM_002834.3	498	Cgg/Tgg	13/16	1	2	FACETS	0.895	0.838	0.952	0.895	0.838	0.952	CLONAL	1	TRUE	1	0.856448227874729	2		789	556	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295208	15295208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	305	928	2	ENST00000263388.2:c.2464C>T	p.Pro822Ser	p.P822S	ENST00000263388	NM_000435.2	822	Cct/Tct	16/33	0.841701908406297	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.856448227874729	1		930	407	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118368688	118368688	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	217	601	1	ENST00000534358.1:c.5702G>T	p.Trp1901Leu	p.W1901L	ENST00000534358	NM_005933.3	1901	tGg/tTg	21/36	1	2	FACETS	0.999	0.939	1	0.999	0.939	1	CLONAL	1	TRUE	1	0.856448227874729	2		602	507	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478262	99478262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	133	324	0	ENST00000268035.6:c.3166G>A	p.Glu1056Lys	p.E1056K	ENST00000268035	NM_000875.3	1056	Gag/Aag	16/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.856448227874729	2		324	298	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346594	89346594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	205	559	0	ENST00000301030.4:c.6356C>T	p.Pro2119Leu	p.P2119L	ENST00000301030	NM_001256183.1	2119	cCc/cTc	9/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.856448227874729	2		559	447	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273862	18273862	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	255	799	0	ENST00000222254.8:c.1195G>A	p.Val399Met	p.V399M	ENST00000222254	NM_005027.3	399	Gtg/Atg	10/16	0.776627986991994	3	FACETS	0.92	0.863	0.979			1	CLONAL	1	TRUE	NA	0.856448227874729	3		799	924	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794836	42794836	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	199	661	0	ENST00000575354.2:c.1916A>G	p.Glu639Gly	p.E639G	ENST00000575354	NM_015125.3	639	gAg/gGg	10/20	1	2	FACETS	0.92	0.86	0.981	0.92	0.86	0.981	CLONAL	1	TRUE	1	0.856448227874729	2		661	505	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0034213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	167	387	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.430300933396767	6	FACETS	1	0.94	1	1	0.94	1	CLONAL	3	TRUE	3	0.430300933396767	6		387	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577569	7577569	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519981	NA	P-0034213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	226	716	0	ENST00000269305.4:c.712T>G	p.Cys238Gly	p.C238G	ENST00000269305	NM_001126112.2	238	Tgt/Ggt	7/11	0.430300933396767	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.430300933396767	2		716	454	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408878	41408878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768757373	NA	P-0034213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	37	419	0	ENST00000373198.4:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000373198	NM_133170.3	183	cGg/cAg	4/32	NA	2	FACETS	0.531	0.439	0.633			1	INDETERMINATE	1	TRUE	NA	0.430300933396767	2		419	324	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391389	84391389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760079258	NA	P-0034213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	195	858	0	ENST00000321945.7:c.443G>A	p.Arg148Gln	p.R148Q	ENST00000321945	NM_139076.2	148	cGa/cAa	5/9	0.361190377023493	2	FACETS	0.966	0.904	1	0.966	0.904	1	CLONAL	2	TRUE	0	0.430300933396767	2		858	469	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9928076	9928076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	35	300	0	ENST00000330684.3:c.1663G>A	p.Ala555Thr	p.A555T	ENST00000330684	NM_001134407.1	555	Gcc/Acc	8/13	0.363796499951251	3	FACETS	1	0.868	1	0.529	0.438	0.628	CLONAL	1	TRUE	1	0.430300933396767	3		300	187	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987076	36987076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	163	756	0	ENST00000354822.5:c.613G>A	p.Glu205Lys	p.E205K	ENST00000354822	NM_001079668.2	205	Gag/Aag	3/3	0.422545484358598	4	FACETS	0.979	0.911	1	0.979	0.911	1	CLONAL	3	TRUE	1	0.430300933396767	4		756	369	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670360	246670360	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	59	348	0	ENST00000388985.4:c.160C>G	p.Leu54Val	p.L54V	ENST00000388985		54	Ctc/Gtc	1/12	0.295512945602172	4	FACETS	1	0.944	1	0.591	0.511	0.676	CLONAL	1	TRUE	2	0.430300933396767	4		348	332	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650683	18650683	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0034213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	43	466	0	ENST00000266497.5:c.2893+1G>A		p.X965_splice	ENST00000266497		965			1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.430300933396767	2		466	199	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661015	227661015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201133410	NA	P-0034213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	132	608	0	ENST00000305123.5:c.2440G>A	p.Asp814Asn	p.D814N	ENST00000305123	NM_005544.2	814	Gac/Aac	1/2	0.430300933396767	7	FACETS	1	0.974	1			1	CLONAL	2	TRUE	NA	0.430300933396767	7		608	541	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120610	94120610	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	50	526	0	ENST00000369303.4:c.441C>G	p.Asp147Glu	p.D147E	ENST00000369303	NM_004440.3	147	gaC/gaG	3/17	0.430300933396767	3	FACETS	0.747	0.636	0.868	0.374	0.318	0.434	SUBCLONAL	1	TRUE	1	0.430300933396767	3		526	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572932	7572933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0034214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	377	662	0	ENST00000269305.4:c.1176dup	p.Asp393ArgfsTer78	p.D393Rfs*78	ENST00000269305	NM_001126112.2	392	-/A	11/11	0.506981306022759	3	FACETS	0.897	0.861	0.933	0.897	0.861	0.933	CLONAL	3	TRUE	0	0.540914224079862	3		662	658	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520017	NA	P-0034214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	628	939	1	ENST00000326873.7:c.647C>T	p.Ser216Phe	p.S216F	ENST00000326873	NM_000455.4	216	tCc/tTc	5/10	0.52277195197576	4	FACETS	0.89	0.864	0.916	0.89	0.864	0.916	CLONAL	4	TRUE	0	0.540914224079862	4		940	1005	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220640	1220640	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690940	NA	P-0034214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	656	971	2	ENST00000326873.7:c.658C>T	p.Gln220Ter	p.Q220*	ENST00000326873	NM_000455.4	220	Cag/Tag	5/10	0.52277195197576	4	FACETS	0.898	0.873	0.924	0.898	0.873	0.924	CLONAL	4	TRUE	0	0.540914224079862	4		973	1040	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044850	47044850	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	178	965	0	ENST00000377604.3:c.2176C>T	p.Arg726Ter	p.R726*	ENST00000377604	NM_001204468.1	726	Cga/Tga	20/24	0.463696237619096	3	FACETS	0.924	0.852	0.999	0.462	0.426	0.5	CLONAL	1	TRUE	1	0.540914224079862	3		965	905	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256784	19256784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1297266623	NA	P-0034214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	482	424	0	ENST00000162023.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000162023		310	tCc/tTc	13/13	0.540914224079862	6	FACETS	0.95	0.923	0.976	0.95	0.923	0.976	CLONAL	6	TRUE	0	0.540914224079862	6		424	651	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849883	156849883	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	287	876	0	ENST00000524377.1:c.2139C>A	p.Phe713Leu	p.F713L	ENST00000524377	NM_002529.3	713	ttC/ttA	16/17	0.368123710382842	6	FACETS	0.949	0.892	1	0.474	0.446	0.504	CLONAL	2	TRUE	2	0.540914224079862	6		876	1164	SUCCESS
FH	2271	MSKCC	GRCh37	1	241669430	241669430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1044975651	NA	P-0034214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	53	491	0	ENST00000366560.3:c.777G>A	p.Met259Ile	p.M259I	ENST00000366560	NM_000143.3	259	atG/atA	6/10	0.368123710382842	6	FACETS	0.708	0.604	0.823	0.177	0.151	0.206	SUBCLONAL	1	TRUE	2	0.540914224079862	6		491	576	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609656	28609656	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	186	658	0	ENST00000241453.7:c.1573G>C	p.Glu525Gln	p.E525Q	ENST00000241453	NM_004119.2	525	Gag/Cag	12/24	0.515459354930059	2	FACETS	0.966	0.908	1	0.966	0.908	1	CLONAL	2	TRUE	0	0.540914224079862	2		658	356	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39234206	39234206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	235	700	0	ENST00000402219.2:c.2639C>T	p.Ser880Leu	p.S880L	ENST00000402219	NM_005633.3	880	tCa/tTa	16/23	0.422031901980153	4	FACETS	0.998	0.936	1	0.998	0.936	1	CLONAL	2	TRUE	2	0.540914224079862	4		700	671	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948302	31948302	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1009407914	NA	P-0034214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	406	960	2	ENST00000375333.2:c.890G>C	p.Arg297Thr	p.R297T	ENST00000375333	NM_032454.1	297	aGa/aCa	6/8	0.540914224079862	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.540914224079862	3		962	914	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001068	150001068	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	151	550	0	ENST00000253339.5:c.2536G>A	p.Asp846Asn	p.D846N	ENST00000253339		846	Gac/Aac	4/7	0.333144184108218	4	FACETS	0.947	0.874	1	0.474	0.437	0.512	CLONAL	2	TRUE	0	0.540914224079862	4		550	454	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133748316	133748316	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	128	671	0	ENST00000318560.5:c.977A>G	p.Tyr326Cys	p.Y326C	ENST00000318560	NM_005157.4	326	tAc/tGc	6/11	0.501071624010229	3	FACETS	0.937	0.851	1	0.468	0.425	0.513	CLONAL	1	TRUE	1	0.540914224079862	3		671	642	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947827	178947827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	108	400	0	ENST00000263967.3:c.2702G>T	p.Cys901Phe	p.C901F	ENST00000263967	NM_006218.2	901	tGt/tTt	19/21	0.505667896202497	1	FACETS	0.844	0.767	0.924	0.844	0.767	0.924	CLONAL	1	TRUE	0	0.569956019672343	1		400	321	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752656	128752656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	57	285	0	ENST00000377970.2:c.817G>A	p.Asp273Asn	p.D273N	ENST00000377970	NM_002467.4	273	Gat/Aat	3/3	0.133522707418372	4	FACETS	1	0.939	1	0.577	0.499	0.66	INDETERMINATE	1	TRUE	2	0.569956019672343	4		285	272	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0034219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	9	463	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.079	0.051	0.114	0.079	0.051	0.114	SUBCLONAL	1	FALSE	1	0.513402702753614	2		463	445	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0034219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	41	451	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.841	0.709	0.983	0.841	0.709	0.983	CLONAL	1	FALSE	1	0.513402702753614	2		451	190	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109737	115109750	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTCCGCGCAGAG	TTCTCCGCGCAGAG	-	novel	NA	P-0034219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	135	921	0	ENST00000257566.3:c.2128_2141del	p.Leu710ArgfsTer15	p.L710Rfs*15	ENST00000257566	NM_016569.3	710	CTCTGCGCGGAGAAa/a	8/8	0.513402702753614	1	FACETS	0.471	0.428	0.516	0.471	0.428	0.516	SUBCLONAL	1	FALSE	0	0.513402702753614	1		921	830	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117439	115117439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	47	400	0	ENST00000257566.3:c.735G>A	p.Met245Ile	p.M245I	ENST00000257566	NM_016569.3	245	atG/atA	4/8	0.513402702753614	1	FACETS	0.493	0.419	0.574	0.493	0.419	0.574	SUBCLONAL	1	FALSE	0	0.513402702753614	1		400	276	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842388	68842389	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0034219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	65	648	0	ENST00000261769.5:c.451dup	p.Arg151LysfsTer17	p.R151Kfs*17	ENST00000261769	NM_004360.3	150	aga/agAa	4/16	0.513402702753614	1	FACETS	0.596	0.52	0.676	0.596	0.52	0.676	SUBCLONAL	1	FALSE	0	0.513402702753614	1		648	316	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748874	41748874	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	112	738	0	ENST00000301178.4:c.1400del	p.Leu467TrpfsTer29	p.L467Wfs*29	ENST00000301178	NM_021913.4	467	Ttg/tg	11/20	1	2	FACETS	0.736	0.663	0.812	0.736	0.663	0.812	SUBCLONAL	1	FALSE	1	0.513402702753614	2		738	593	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0034223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	284	463	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.971	0.921	1	0.971	0.921	1	CLONAL	1	TRUE	1	0.946448145405638	2		463	618	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206646650	206646650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553384304	NA	P-0034223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	252	809	0	ENST00000367120.3:c.80G>A	p.Arg27His	p.R27H	ENST00000367120	NM_014002.3	27	cGc/cAc	3/22	0.946448145405638	4	FACETS	0.81	0.757	0.866	0.27	0.252	0.289	CLONAL	1	TRUE	1	0.946448145405638	4		809	1279	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114257	115114258	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0034223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	358	695	0	ENST00000257566.3:c.959dup	p.Ser321ValfsTer6	p.S321Vfs*6	ENST00000257566	NM_016569.3	320	cag/caAg	6/8	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.946448145405638	2		695	742	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061309	38061309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	410	733	0	ENST00000250448.2:c.680G>A	p.Cys227Tyr	p.C227Y	ENST00000250448	NM_004496.3	227	tGc/tAc	2/2	1	2	FACETS	0.994	0.951	1	0.994	0.951	1	CLONAL	1	TRUE	1	0.946448145405638	2		733	872	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835773	68835774	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0034223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	285	600	0	ENST00000261769.5:c.364_365insTG	p.His122LeufsTer94	p.H122Lfs*94	ENST00000261769	NM_004360.3	122	cac/cTGac	3/16	0.946448145405638	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.946448145405638	1		600	316	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0034223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	224	428	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	0.974	0.917	1	0.974	0.917	1	CLONAL	1	TRUE	1	0.946448145405638	2		428	486	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0034224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	83	451	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.25297633446606	5	FACETS	0.943	0.835	1	0.629	0.557	0.705	CLONAL	2	TRUE	2	0.25297633446606	5		451	480	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs104886003	NA	P-0034224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	116	707	0	ENST00000263967.3:c.1633G>C	p.Glu545Gln	p.E545Q	ENST00000263967	NM_006218.2	545	Gag/Cag	10/21	0.25297633446606	5	FACETS	0.863	0.778	0.952	0.575	0.519	0.635	CLONAL	2	TRUE	2	0.25297633446606	5		707	733	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	65	826	0	ENST00000269305.4:c.380C>A	p.Ser127Tyr	p.S127Y	ENST00000269305	NM_001126112.2	127	tCc/tAc	5/11	1	2	FACETS	0.768	0.665	0.88	0.768	0.665	0.88	SUBCLONAL	1	TRUE	1	0.25297633446606	2		826	669	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186689	11186689	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	44	451	0	ENST00000361445.4:c.6516G>C	p.Leu2172Phe	p.L2172F	ENST00000361445	NM_004958.3	2172	ttG/ttC	46/58	0.193624593808999	4	FACETS	0.914	0.767	1			1	CLONAL	1	TRUE	NA	0.25297633446606	4		451	477	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478852	56478853	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGTGGTGCGAGGGA	novel	NA	P-0034224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	61	812	0	ENST00000267101.3:c.310_323dup	p.Gln109TrpfsTer18	p.Q109Wfs*18	ENST00000267101	NM_001982.3	103	cgc/cgCGTGGTGCGAGGGAc	3/28	0.230845836812952	4	FACETS	0.831	0.716	0.957	0.416	0.358	0.479	CLONAL	1	TRUE	2	0.25297633446606	4		812	727	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844099	68844099	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0034224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	40	461	0	ENST00000261769.5:c.688-1G>T		p.X230_splice	ENST00000261769	NM_004360.3	230			0.11039772748355	0	FACETS	0.66	0.55	0.782			1	INDETERMINATE	1	TRUE	0	0.25297633446606	0		461	358	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111675	56111675	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	21	166	1	ENST00000399503.3:c.275C>A	p.Ser92Ter	p.S92*	ENST00000399503	NM_005921.1	92	tCg/tAg	1/20	0.230845836812952	4	FACETS	0.819	0.632	1	0.409	0.316	0.518	CLONAL	1	TRUE	2	0.25297633446606	4		167	254	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322273	31322273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	26	308	0	ENST00000412585.2:c.1076C>T	p.Ser359Phe	p.S359F	ENST00000412585	NM_005514.6	359	tCt/tTt	7/8	0.25297633446606	5	FACETS	0.712	0.564	0.883	0.356	0.282	0.442	SUBCLONAL	1	TRUE	3	0.25297633446606	5		308	398	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917637	151917637	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0034224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	99	676	0	ENST00000262189.6:c.3683C>G	p.Ser1228Ter	p.S1228*	ENST00000262189	NM_170606.2	1228	tCa/tGa	23/59	0.25297633446606	4	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.25297633446606	4		676	711	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980620	70980620	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	29	479	0	ENST00000276594.2:c.757C>G	p.Leu253Val	p.L253V	ENST00000276594	NM_024504.3	253	Cta/Gta	4/8	NA	2	FACETS	0.513	0.411	0.629			1	INDETERMINATE	1	TRUE	NA	0.25297633446606	2		479	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0034225-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	206	709	3	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.491902616777487	2	FACETS	0.872	0.819	0.925	0.872	0.819	0.925	CLONAL	2	TRUE	0	0.531998354466316	2		712	444	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	449	148	0				ENST00000310581	NM_198253.2	-/1132			0.517333424128718	5	FACETS	0.987	0.95	1	0.987	0.95	1	CLONAL	4	TRUE	1	0.517333424128718	5		148	781	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0034226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	388	811	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.504006166797806	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.517333424128718	2		811	702	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245378	53245378	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	236	351	1	ENST00000375401.3:c.659C>T	p.Pro220Leu	p.P220L	ENST00000375401	NM_004187.3	220	cCg/cTg	6/26	0.232078756377639	2	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.517333424128718	2		352	365	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199873	128199873	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780263343	NA	P-0034226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	139	491	0	ENST00000341105.2:c.1432G>A	p.Ala478Thr	p.A478T	ENST00000341105	NM_032638.4	478	Gcc/Acc	6/6	0.517333424128718	3	FACETS	1	0.988	1	0.742	0.68	0.805	CLONAL	1	TRUE	1	0.517333424128718	3		491	456	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270419	10270419	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs142673915	NA	P-0034226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	387	892	0	ENST00000340748.4:c.1147A>G	p.Asn383Asp	p.N383D	ENST00000340748		383	Aat/Gat	16/40	0.387840314906624	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	1	0.517333424128718	3		892	941	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860214	151860214	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	100	748	0	ENST00000262189.6:c.10448del	p.Leu3483TyrfsTer28	p.L3483Yfs*28	ENST00000262189	NM_170606.2	3483	tTa/ta	43/59	0.517333424128718	3	FACETS	0.945	0.847	1	0.472	0.423	0.524	CLONAL	1	TRUE	1	0.517333424128718	3		748	515	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0034228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	105	463	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.786961587066924	1	FACETS	0.936	0.867	1	0.936	0.867	1	CLONAL	1	TRUE	0	0.786961587066924	1		463	173	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0034228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	185	557	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.781712408226871	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.786961587066924	1		557	260	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099397	27099397	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	180	505	0	ENST00000324856.7:c.3634C>T	p.Gln1212Ter	p.Q1212*	ENST00000324856	NM_006015.4	1212	Cag/Tag	14/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.786961587066924	2		505	429	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032459	12032459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	124	316	1	ENST00000353533.5:c.895G>A	p.Glu299Lys	p.E299K	ENST00000353533	NM_003010.3	299	Gag/Aag	9/11	0.781712408226871	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.786961587066924	1		317	180	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242761	98242761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	190	562	0	ENST00000331920.6:c.856G>A	p.Glu286Lys	p.E286K	ENST00000331920	NM_000264.3	286	Gag/Aag	6/24	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.786961587066924	2		562	438	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0034228-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	156	463	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.728220269390851	1	FACETS	0.91	0.851	0.968	0.91	0.851	0.968	CLONAL	1	TRUE	0	0.749746943978737	1		463	286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0034228-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	135	557	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.749746943978737	1	FACETS	0.893	0.831	0.955	0.893	0.831	0.955	CLONAL	1	TRUE	0	0.749746943978737	1		557	252	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099397	27099397	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034228-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	149	505	0	ENST00000324856.7:c.3634C>T	p.Gln1212Ter	p.Q1212*	ENST00000324856	NM_006015.4	1212	Cag/Tag	14/20	1	2	FACETS	0.951	0.878	1	0.951	0.878	1	CLONAL	1	TRUE	1	0.749746943978737	2		505	418	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032459	12032459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034228-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	91	316	1	ENST00000353533.5:c.895G>A	p.Glu299Lys	p.E299K	ENST00000353533	NM_003010.3	299	Gag/Aag	9/11	0.749746943978737	1	FACETS	0.914	0.838	0.99	0.914	0.838	0.99	CLONAL	1	TRUE	0	0.749746943978737	1		317	166	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242761	98242761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034228-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	190	562	0	ENST00000331920.6:c.856G>A	p.Glu286Lys	p.E286K	ENST00000331920	NM_000264.3	286	Gag/Aag	6/24	0.319010694479387	1	FACETS	0.671	0.627	0.716	0.671	0.627	0.716	INDETERMINATE	1	TRUE	0	0.749746943978737	1		562	472	SUCCESS
AR	367	MSKCC	GRCh37	X	66765159	66765203	+	inframe_deletion	In_Frame_Del	DEL	GCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA	GCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA	-	rs3032358	NA	P-0034229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	74	277	0	ENST00000374690.3:c.195_239del	p.Gln66_Gln80del	p.Q66_Q80del	ENST00000374690	NM_000044.3	57	ctGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAg/ctg	1/8	0.617336407362055	3	FACETS	0.965	0.852	1	0.483	0.426	0.543	CLONAL	1	TRUE	1	0.617336407362055	3		277	325	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	426	788	0	ENST00000397062.3:c.246A>C	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaC	2/5	0.617336407362055	3	FACETS	0.981	0.939	1	0.981	0.939	1	CLONAL	2	TRUE	1	0.617336407362055	3		788	921	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160679	56160681	+	inframe_deletion	In_Frame_Del	DEL	TAC	TAC	-	novel	NA	P-0034229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	228	429	0	ENST00000399503.3:c.954_956del	p.Leu319del	p.L319del	ENST00000399503	NM_005921.1	318	tTACtg/ttg	4/20	0.617336407362055	4	FACETS	0.971	0.911	1	0.971	0.911	1	CLONAL	2	TRUE	2	0.617336407362055	4		429	615	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178108	56178109	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0034229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	151	320	0	ENST00000399503.3:c.3082_3083del	p.Gln1028IlefsTer7	p.Q1028Ifs*7	ENST00000399503	NM_005921.1	1027	ctACaa/ctaa	14/20	0.617336407362055	4	FACETS	0.967	0.894	1	0.967	0.894	1	CLONAL	2	TRUE	2	0.617336407362055	4		320	409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	552	880	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.924633515498065	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.924633515498065	1		882	620	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775674	9775674	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs745980735	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	28	784	0	ENST00000377346.4:c.217A>G	p.Ile73Val	p.I73V	ENST00000377346	NM_005026.3	73	Atc/Gtc	4/24	0.924633515498065	1	FACETS	0.061	0.048	0.076	0.061	0.048	0.076	SUBCLONAL	1	TRUE	0	0.924633515498065	1		784	533	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780045	9780045	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28730673	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	27	774	1	ENST00000377346.4:c.1309C>T	p.Arg437Cys	p.R437C	ENST00000377346	NM_005026.3	437	Cgc/Tgc	10/24	0.924633515498065	1	FACETS	0.059	0.046	0.073	0.059	0.046	0.073	SUBCLONAL	1	TRUE	0	0.924633515498065	1		775	536	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780878	9780878	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	42	924	1	ENST00000377346.4:c.1600C>A	p.Leu534Met	p.L534M	ENST00000377346	NM_005026.3	534	Ctg/Atg	13/24	0.924633515498065	1	FACETS	0.079	0.066	0.094	0.079	0.066	0.094	SUBCLONAL	1	TRUE	0	0.924633515498065	1		925	616	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780900	9780900	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	38	877	0	ENST00000377346.4:c.1622A>G	p.His541Arg	p.H541R	ENST00000377346	NM_005026.3	541	cAc/cGc	13/24	0.924633515498065	1	FACETS	0.076	0.062	0.091	0.076	0.062	0.091	SUBCLONAL	1	TRUE	0	0.924633515498065	1		877	585	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782096	9782096	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs745781507	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	26	871	0	ENST00000377346.4:c.2119C>A	p.Pro707Thr	p.P707T	ENST00000377346	NM_005026.3	707	Ccc/Acc	17/24	0.924633515498065	1	FACETS	0.06	0.047	0.075	0.06	0.047	0.075	SUBCLONAL	1	TRUE	0	0.924633515498065	1		871	502	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782165	9782165	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	25	726	0	ENST00000377346.4:c.2188C>A	p.His730Asn	p.H730N	ENST00000377346	NM_005026.3	730	Cac/Aac	17/24	0.924633515498065	1	FACETS	0.061	0.047	0.076	0.061	0.047	0.076	SUBCLONAL	1	TRUE	0	0.924633515498065	1		726	479	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202844	16202845	+	missense_variant	Missense_Mutation	DNP	CG	CG	TA	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	35	672	1	ENST00000375759.3:c.552_553delinsTA	p.Ala185Thr	p.A185T	ENST00000375759	NM_015001.2	184	taCGct/taTAct	3/15	0.924633515498065	1	FACETS	0.088	0.072	0.107	0.088	0.072	0.107	SUBCLONAL	1	TRUE	0	0.924633515498065	1		673	460	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023570	27023570	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs746698854	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	30	459	0	ENST00000324856.7:c.676G>C	p.Ala226Pro	p.A226P	ENST00000324856	NM_006015.4	226	Gcc/Ccc	1/20	0.924633515498065	1	FACETS	0.062	0.05	0.077	0.062	0.05	0.077	SUBCLONAL	1	TRUE	0	0.924633515498065	1		459	559	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023574	27023574	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1334915537	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	32	457	0	ENST00000324856.7:c.680C>A	p.Pro227Gln	p.P227Q	ENST00000324856	NM_006015.4	227	cCg/cAg	1/20	0.924633515498065	1	FACETS	0.066	0.053	0.081	0.066	0.053	0.081	SUBCLONAL	1	TRUE	0	0.924633515498065	1		457	565	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057829	27057829	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	44	1037	0	ENST00000324856.7:c.1537T>G	p.Ser513Ala	p.S513A	ENST00000324856	NM_006015.4	513	Tcc/Gcc	3/20	0.924633515498065	1	FACETS	0.064	0.053	0.076	0.064	0.053	0.076	SUBCLONAL	1	TRUE	0	0.924633515498065	1		1037	803	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057885	27057886	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	43	883	1	ENST00000324856.7:c.1593_1594delinsAA	p.Ala532Thr	p.A532T	ENST00000324856	NM_006015.4	531	ccGGct/ccAAct	3/20	0.924633515498065	1	FACETS	0.072	0.059	0.085	0.072	0.059	0.085	SUBCLONAL	1	TRUE	0	0.924633515498065	1		884	697	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057999	27058000	+	missense_variant	Missense_Mutation	DNP	AC	AC	CT	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	31	744	1	ENST00000324856.7:c.1707_1708delinsCT	p.Pro570Ser	p.P570S	ENST00000324856	NM_006015.4	569	gcACcc/gcCTcc	3/20	0.924633515498065	1	FACETS	0.058	0.047	0.072	0.058	0.047	0.072	SUBCLONAL	1	TRUE	0	0.924633515498065	1		745	618	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088734	27088734	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	33	703	0	ENST00000324856.7:c.2343A>G	p.Ile781Met	p.I781M	ENST00000324856	NM_006015.4	781	atA/atG	7/20	0.924633515498065	1	FACETS	0.065	0.053	0.08	0.065	0.053	0.08	SUBCLONAL	1	TRUE	0	0.924633515498065	1		703	586	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097772	27097772	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	28	586	1	ENST00000324856.7:c.3361G>T	p.Ala1121Ser	p.A1121S	ENST00000324856	NM_006015.4	1121	Gct/Tct	12/20	0.924633515498065	1	FACETS	0.095	0.076	0.118	0.095	0.076	0.118	SUBCLONAL	1	TRUE	0	0.924633515498065	1		587	341	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101036	27101036	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	37	738	0	ENST00000324856.7:c.4318A>G	p.Thr1440Ala	p.T1440A	ENST00000324856	NM_006015.4	1440	Aca/Gca	18/20	0.924633515498065	1	FACETS	0.066	0.054	0.079	0.066	0.054	0.079	SUBCLONAL	1	TRUE	0	0.924633515498065	1		738	654	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101126	27101126	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	45	828	0	ENST00000324856.7:c.4408A>T	p.Thr1470Ser	p.T1470S	ENST00000324856	NM_006015.4	1470	Acc/Tcc	18/20	0.924633515498065	1	FACETS	0.087	0.073	0.103	0.087	0.073	0.103	SUBCLONAL	1	TRUE	0	0.924633515498065	1		828	601	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40367099	40367099	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	26	663	3	ENST00000397332.2:c.98A>T	p.Tyr33Phe	p.Y33F	ENST00000397332	NM_001033082.2	33	tAc/tTc	2/3	0.924633515498065	1	FACETS	0.068	0.053	0.084	0.068	0.053	0.084	SUBCLONAL	1	TRUE	0	0.924633515498065	1		666	447	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509420	46509420	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	26	670	0	ENST00000262741.5:c.1311G>C	p.Leu437Phe	p.L437F	ENST00000262741	NM_003629.3	437	ttG/ttC	10/10	0.924633515498065	1	FACETS	0.061	0.048	0.077	0.061	0.048	0.077	SUBCLONAL	1	TRUE	0	0.924633515498065	1		670	493	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726512	46726512	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	23	513	0	ENST00000371975.4:c.591G>A	p.Met197Ile	p.M197I	ENST00000371975	NM_003579.3	197	atG/atA	7/18	0.924633515498065	1	FACETS	0.069	0.053	0.087	0.069	0.053	0.087	SUBCLONAL	1	TRUE	0	0.924633515498065	1		513	389	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743949	46743949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149441991	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	29	478	0	ENST00000371975.4:c.2239C>T	p.Arg747Cys	p.R747C	ENST00000371975	NM_003579.3	747	Cgc/Tgc	18/18	0.924633515498065	1	FACETS	0.075	0.06	0.092	0.075	0.06	0.092	SUBCLONAL	1	TRUE	0	0.924633515498065	1		478	450	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248684	59248684	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	43	964	0	ENST00000371222.2:c.59C>A	p.Pro20Gln	p.P20Q	ENST00000371222	NM_002228.3	20	cCg/cAg	1/1	0.924633515498065	1	FACETS	0.068	0.056	0.081	0.068	0.056	0.081	SUBCLONAL	1	TRUE	0	0.924633515498065	1		964	738	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344734	65344735	+	missense_variant	Missense_Mutation	DNP	CA	CA	TG	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	15	386	0	ENST00000342505.4:c.302_303inv	p.Met101Thr	p.M101T	ENST00000342505	NM_002227.2	101	aTG/aCA	4/25	0.924633515498065	1	FACETS	0.061	0.044	0.081	0.061	0.044	0.081	SUBCLONAL	1	TRUE	0	0.924633515498065	1		386	288	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873157	71873157	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	10	457	0	ENST00000357731.5:c.1037T>G	p.Phe346Cys	p.F346C	ENST00000357731	NM_173808.2	346	tTc/tGc	7/7	0.924633515498065	1	FACETS	0.061	0.041	0.086	0.061	0.041	0.086	SUBCLONAL	1	TRUE	0	0.924633515498065	1		457	191	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273211	115273211	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	17	571	0	ENST00000438362.2:c.1247T>C	p.Val416Ala	p.V416A	ENST00000438362	NM_001242891.1	416	gTt/gCt	11/20	0.924633515498065	1	FACETS	0.075	0.056	0.098	0.075	0.056	0.098	SUBCLONAL	1	TRUE	0	0.924633515498065	1		571	263	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166596	118166596	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1400295239	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	20	356	0	ENST00000369448.3:c.1106G>A	p.Ser369Asn	p.S369N	ENST00000369448	NM_017709.3	369	aGc/aAc	2/2	0.924633515498065	1	FACETS	0.08	0.061	0.103	0.08	0.061	0.103	SUBCLONAL	1	TRUE	0	0.924633515498065	1		356	290	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458273	120458273	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs763117840	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	27	689	0	ENST00000256646.2:c.7072A>G	p.Met2358Val	p.M2358V	ENST00000256646	NM_024408.3	2358	Atg/Gtg	34/34	0.924633515498065	1	FACETS	0.062	0.049	0.077	0.062	0.049	0.077	SUBCLONAL	1	TRUE	0	0.924633515498065	1		689	505	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458384	120458384	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	21	548	1	ENST00000256646.2:c.6961G>A	p.Ala2321Thr	p.A2321T	ENST00000256646	NM_024408.3	2321	Gct/Act	34/34	0.924633515498065	1	FACETS	0.063	0.048	0.081	0.063	0.048	0.081	SUBCLONAL	1	TRUE	0	0.924633515498065	1		549	386	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458570	120458570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1054703109	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	24	765	0	ENST00000256646.2:c.6775G>A	p.Val2259Met	p.V2259M	ENST00000256646	NM_024408.3	2259	Gtg/Atg	34/34	0.924633515498065	1	FACETS	0.062	0.048	0.078	0.062	0.048	0.078	SUBCLONAL	1	TRUE	0	0.924633515498065	1		765	451	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459025	120459025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1031665170	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	30	799	0	ENST00000256646.2:c.6320G>A	p.Ser2107Asn	p.S2107N	ENST00000256646	NM_024408.3	2107	aGt/aAt	34/34	0.924633515498065	1	FACETS	0.065	0.052	0.08	0.065	0.052	0.08	SUBCLONAL	1	TRUE	0	0.924633515498065	1		799	539	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459038	120459038	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	30	792	0	ENST00000256646.2:c.6307T>C	p.Ser2103Pro	p.S2103P	ENST00000256646	NM_024408.3	2103	Tct/Cct	34/34	0.924633515498065	1	FACETS	0.066	0.053	0.081	0.066	0.053	0.081	SUBCLONAL	1	TRUE	0	0.924633515498065	1		792	528	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462164	120462164	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	22	620	0	ENST00000256646.2:c.5552C>G	p.Ala1851Gly	p.A1851G	ENST00000256646	NM_024408.3	1851	gCa/gGa	31/34	1	2	FACETS	0.109	0.084	0.138	0.109	0.084	0.138	SUBCLONAL	1	TRUE	1	0.924633515498065	2		620	438	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120478143	120478143	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1553195628	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	23	557	0	ENST00000256646.2:c.3607A>G	p.Ile1203Val	p.I1203V	ENST00000256646	NM_024408.3	1203	Att/Gtt	22/34	1	2	FACETS	0.122	0.095	0.154	0.122	0.095	0.154	SUBCLONAL	1	TRUE	1	0.924633515498065	2		557	408	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841415	156841415	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	15	455	0	ENST00000524377.1:c.718A>C	p.Lys240Gln	p.K240Q	ENST00000524377	NM_002529.3	240	Aaa/Caa	7/17	0.922759156402067	1	FACETS	0.067	0.048	0.089	0.067	0.048	0.089	SUBCLONAL	1	TRUE	0	0.924633515498065	1		455	262	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841425	156841426	+	missense_variant	Missense_Mutation	DNP	GT	GT	AC	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	17	506	0	ENST00000524377.1:c.728_729inv	p.Gly243Asp	p.G243D	ENST00000524377	NM_002529.3	243	gGT/gAC	7/17	0.922759156402067	1	FACETS	0.064	0.047	0.084	0.064	0.047	0.084	SUBCLONAL	1	TRUE	0	0.924633515498065	1		506	308	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161326520	161326520	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs760678574	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	11	345	0	ENST00000367975.2:c.295T>C	p.Tyr99His	p.Y99H	ENST00000367975	NM_003001.3	99	Tat/Cat	5/6	0.922759156402067	1	FACETS	0.068	0.047	0.095	0.068	0.047	0.095	SUBCLONAL	1	TRUE	0	0.924633515498065	1		345	188	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226562023	226562023	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	18	656	0	ENST00000366794.5:c.1974T>G	p.Asn658Lys	p.N658K	ENST00000366794	NM_001618.3	658	aaT/aaG	14/23	0.922759156402067	1	FACETS	0.062	0.046	0.081	0.062	0.046	0.081	SUBCLONAL	1	TRUE	0	0.924633515498065	1		656	337	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097712	8097712	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	26	495	0	ENST00000346208.3:c.94A>G	p.Ser32Gly	p.S32G	ENST00000346208		32	Agc/Ggc	2/6	0.922759156402067	1	FACETS	0.06	0.047	0.075	0.06	0.047	0.075	SUBCLONAL	1	TRUE	0	0.924633515498065	1		495	503	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097730	8097730	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747477962	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	30	549	0	ENST00000346208.3:c.112G>C	p.Ala38Pro	p.A38P	ENST00000346208		38	Gcg/Ccg	2/6	0.922759156402067	1	FACETS	0.059	0.047	0.073	0.059	0.047	0.073	SUBCLONAL	1	TRUE	0	0.924633515498065	1		549	590	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100462	8100462	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	30	846	0	ENST00000346208.3:c.436G>T	p.Ala146Ser	p.A146S	ENST00000346208		146	Gcc/Tcc	3/6	0.922759156402067	1	FACETS	0.06	0.048	0.074	0.06	0.048	0.074	SUBCLONAL	1	TRUE	0	0.924633515498065	1		846	577	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239394	123239395	+	missense_variant	Missense_Mutation	DNP	TG	TG	CA	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	15	492	0	ENST00000358487.5:c.2442_2443inv	p.Ile815Val	p.I815V	ENST00000358487	NM_000141.4	814	caCAta/caTGta	18/18	0.922759156402067	1	FACETS	0.082	0.059	0.108	0.082	0.059	0.108	SUBCLONAL	1	TRUE	0	0.924633515498065	1		492	214	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274713	123274713	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	31	687	0	ENST00000358487.5:c.1205A>C	p.Asn402Thr	p.N402T	ENST00000358487	NM_000141.4	402	aAc/aCc	9/18	0.922759156402067	1	FACETS	0.074	0.059	0.091	0.074	0.059	0.091	SUBCLONAL	1	TRUE	0	0.924633515498065	1		687	487	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325122	123325123	+	missense_variant	Missense_Mutation	DNP	AC	AC	GT	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	24	727	1	ENST00000358487.5:c.205_206inv	p.Val69Thr	p.V69T	ENST00000358487	NM_000141.4	69	GTg/ACg	3/18	0.922759156402067	1	FACETS	0.06	0.047	0.076	0.06	0.047	0.076	SUBCLONAL	1	TRUE	0	0.924633515498065	1		728	464	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154393	2154393	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	40	909	0	ENST00000434045.2:c.535A>G	p.Thr179Ala	p.T179A	ENST00000434045	NM_001127598.1	179	Acc/Gcc	5/5	0.924633515498065	1	FACETS	0.076	0.063	0.091	0.076	0.063	0.091	SUBCLONAL	1	TRUE	0	0.924633515498065	1		909	611	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137256	64137256	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	37	829	0	ENST00000334205.4:c.1688G>C	p.Gly563Ala	p.G563A	ENST00000334205	NM_003942.2	563	gGg/gCg	14/17	0.924633515498065	1	FACETS	0.069	0.056	0.083	0.069	0.056	0.083	SUBCLONAL	1	TRUE	0	0.924633515498065	1		829	625	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137259	64137259	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	33	828	0	ENST00000334205.4:c.1691T>G	p.Val564Gly	p.V564G	ENST00000334205	NM_003942.2	564	gTg/gGg	14/17	0.924633515498065	1	FACETS	0.062	0.05	0.075	0.062	0.05	0.075	SUBCLONAL	1	TRUE	0	0.924633515498065	1		828	621	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69458005	69458005	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	22	383	0	ENST00000227507.2:c.405G>C	p.Glu135Asp	p.E135D	ENST00000227507	NM_053056.2	135	gaG/gaC	2/5	0.924633515498065	1	FACETS	0.068	0.052	0.086	0.068	0.052	0.086	SUBCLONAL	1	TRUE	0	0.924633515498065	1		383	377	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518444	69518445	+	missense_variant	Missense_Mutation	DNP	GA	GA	CC	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	20	199	1	ENST00000294312.3:c.200_201delinsGG	p.Val67Gly	p.V67G	ENST00000294312	NM_005117.2	67	gTC/gGG	1/3	0.924633515498065	1	FACETS	0.096	0.073	0.123	0.096	0.073	0.123	SUBCLONAL	1	TRUE	0	0.924633515498065	1		200	242	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518497	69518497	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1168889092	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	31	441	0	ENST00000294312.3:c.148T>G	p.Ser50Ala	p.S50A	ENST00000294312	NM_005117.2	50	Tcc/Gcc	1/3	0.924633515498065	1	FACETS	0.076	0.061	0.093	0.076	0.061	0.093	SUBCLONAL	1	TRUE	0	0.924633515498065	1		441	475	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518525	69518525	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	28	509	0	ENST00000294312.3:c.120C>G	p.Asp40Glu	p.D40E	ENST00000294312	NM_005117.2	40	gaC/gaG	1/3	0.924633515498065	1	FACETS	0.063	0.05	0.078	0.063	0.05	0.078	SUBCLONAL	1	TRUE	0	0.924633515498065	1		509	516	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589533	69589533	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	12	151	0	ENST00000168712.1:c.320C>T	p.Ala107Val	p.A107V	ENST00000168712	NM_002007.2	107	gCg/gTg	1/3	0.924633515498065	1	FACETS	0.08	0.056	0.11	0.08	0.056	0.11	SUBCLONAL	1	TRUE	0	0.924633515498065	1		151	174	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589560	69589560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745670123	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	13	227	0	ENST00000168712.1:c.293C>T	p.Ala98Val	p.A98V	ENST00000168712	NM_002007.2	98	gCg/gTg	1/3	0.924633515498065	1	FACETS	0.062	0.044	0.084	0.062	0.044	0.084	SUBCLONAL	1	TRUE	0	0.924633515498065	1		227	245	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948319	71948319	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	41	1072	0	ENST00000298229.2:c.3031T>C	p.Ser1011Pro	p.S1011P	ENST00000298229	NM_001567.3	1011	Tct/Cct	26/28	0.924633515498065	1	FACETS	0.065	0.054	0.078	0.065	0.054	0.078	SUBCLONAL	1	TRUE	0	0.924633515498065	1		1072	730	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948371	71948371	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	53	1125	0	ENST00000298229.2:c.3083A>G	p.His1028Arg	p.H1028R	ENST00000298229	NM_001567.3	1028	cAc/cGc	26/28	0.924633515498065	1	FACETS	0.087	0.074	0.102	0.087	0.074	0.102	SUBCLONAL	1	TRUE	0	0.924633515498065	1		1125	706	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948380	71948380	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	57	1133	0	ENST00000298229.2:c.3092A>C	p.His1031Pro	p.H1031P	ENST00000298229	NM_001567.3	1031	cAc/cCc	26/28	0.924633515498065	1	FACETS	0.094	0.08	0.109	0.094	0.08	0.109	SUBCLONAL	1	TRUE	0	0.924633515498065	1		1133	706	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948528	71948529	+	missense_variant	Missense_Mutation	DNP	TG	TG	CA	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	41	899	1	ENST00000298229.2:c.3240_3241inv	p.Gly1081Ser	p.G1081S	ENST00000298229	NM_001567.3	1080	cgTGgt/cgCAgt	26/28	0.924633515498065	1	FACETS	0.079	0.065	0.094	0.079	0.065	0.094	SUBCLONAL	1	TRUE	0	0.924633515498065	1		900	604	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948603	71948604	+	missense_variant	Missense_Mutation	DNP	AG	AG	TA	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	38	896	1	ENST00000298229.2:c.3315_3316delinsTA	p.Ala1106Thr	p.A1106T	ENST00000298229	NM_001567.3	1105	ccAGcc/ccTAcc	26/28	0.924633515498065	1	FACETS	0.078	0.064	0.094	0.078	0.064	0.094	SUBCLONAL	1	TRUE	0	0.924633515498065	1		897	563	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948710	71948711	+	missense_variant	Missense_Mutation	DNP	CA	CA	GC	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	26	856	1	ENST00000298229.2:c.3422_3423delinsGC	p.Ala1141Gly	p.A1141G	ENST00000298229	NM_001567.3	1141	gCA/gGC	26/28	0.924633515498065	1	FACETS	0.062	0.049	0.078	0.062	0.049	0.078	SUBCLONAL	1	TRUE	0	0.924633515498065	1		857	487	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948719	71948719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778488376	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	34	862	0	ENST00000298229.2:c.3431C>T	p.Ala1144Val	p.A1144V	ENST00000298229	NM_001567.3	1144	gCg/gTg	26/28	0.924633515498065	1	FACETS	0.081	0.066	0.098	0.081	0.066	0.098	SUBCLONAL	1	TRUE	0	0.924633515498065	1		862	487	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924591	94924591	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	18	629	0	ENST00000536441.1:c.319T>C	p.Tyr107His	p.Y107H	ENST00000536441	NM_144665.3	107	Tac/Cac	3/10	0.924633515498065	1	FACETS	0.064	0.048	0.084	0.064	0.048	0.084	SUBCLONAL	1	TRUE	0	0.924633515498065	1		629	326	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924667	94924667	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	23	824	0	ENST00000536441.1:c.243A>C	p.Leu81Phe	p.L81F	ENST00000536441	NM_144665.3	81	ttA/ttC	3/10	0.924633515498065	1	FACETS	0.058	0.045	0.074	0.058	0.045	0.074	SUBCLONAL	1	TRUE	0	0.924633515498065	1		824	459	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344616	118344616	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	14	619	0	ENST00000534358.1:c.2742G>C	p.Glu914Asp	p.E914D	ENST00000534358	NM_005933.3	914	gaG/gaC	3/36	0.781819877310088	1	FACETS	0.059	0.042	0.079	0.059	0.042	0.079	SUBCLONAL	1	TRUE	0	0.924633515498065	1		619	278	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344665	118344665	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555036737	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	12	514	0	ENST00000534358.1:c.2791A>G	p.Thr931Ala	p.T931A	ENST00000534358	NM_005933.3	931	Aca/Gca	3/36	0.781819877310088	1	FACETS	0.061	0.043	0.084	0.061	0.043	0.084	SUBCLONAL	1	TRUE	0	0.924633515498065	1		514	228	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344710	118344710	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	12	433	0	ENST00000534358.1:c.2836A>G	p.Thr946Ala	p.T946A	ENST00000534358	NM_005933.3	946	Act/Gct	3/36	0.781819877310088	1	FACETS	0.067	0.047	0.092	0.067	0.047	0.092	SUBCLONAL	1	TRUE	0	0.924633515498065	1		433	208	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344789	118344789	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs782663858	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	12	384	0	ENST00000534358.1:c.2915C>A	p.Thr972Asn	p.T972N	ENST00000534358	NM_005933.3	972	aCc/aAc	3/36	0.781819877310088	1	FACETS	0.072	0.05	0.099	0.072	0.05	0.099	SUBCLONAL	1	TRUE	0	0.924633515498065	1		384	194	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375672	118375672	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	19	541	0	ENST00000534358.1:c.9065A>G	p.Asn3022Ser	p.N3022S	ENST00000534358	NM_005933.3	3022	aAt/aGt	27/36	0.781819877310088	1	FACETS	0.066	0.05	0.086	0.066	0.05	0.086	SUBCLONAL	1	TRUE	0	0.924633515498065	1		541	333	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375772	118375772	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	32	584	0	ENST00000534358.1:c.9165T>G	p.Asp3055Glu	p.D3055E	ENST00000534358	NM_005933.3	3055	gaT/gaG	27/36	0.781819877310088	1	FACETS	0.097	0.079	0.119	0.097	0.079	0.119	SUBCLONAL	1	TRUE	0	0.924633515498065	1		584	382	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375995	118375995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	15	616	0	ENST00000534358.1:c.9388G>A	p.Gly3130Ser	p.G3130S	ENST00000534358	NM_005933.3	3130	Ggt/Agt	27/36	0.781819877310088	1	FACETS	0.062	0.045	0.082	0.062	0.045	0.082	SUBCLONAL	1	TRUE	0	0.924633515498065	1		616	283	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376044	118376044	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	18	642	0	ENST00000534358.1:c.9437A>C	p.Gln3146Pro	p.Q3146P	ENST00000534358	NM_005933.3	3146	cAa/cCa	27/36	0.781819877310088	1	FACETS	0.066	0.049	0.086	0.066	0.049	0.086	SUBCLONAL	1	TRUE	0	0.924633515498065	1		642	318	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376058	118376058	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555047693	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	16	643	0	ENST00000534358.1:c.9451T>C	p.Ser3151Pro	p.S3151P	ENST00000534358	NM_005933.3	3151	Tct/Cct	27/36	0.781819877310088	1	FACETS	0.059	0.043	0.078	0.059	0.043	0.078	SUBCLONAL	1	TRUE	0	0.924633515498065	1		643	315	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376085	118376085	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555047715	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	20	653	0	ENST00000534358.1:c.9478T>C	p.Ser3160Pro	p.S3160P	ENST00000534358	NM_005933.3	3160	Tct/Cct	27/36	0.781819877310088	1	FACETS	0.067	0.051	0.086	0.067	0.051	0.086	SUBCLONAL	1	TRUE	0	0.924633515498065	1		653	348	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376120	118376121	+	missense_variant	Missense_Mutation	DNP	TA	TA	CG	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	19	623	1	ENST00000534358.1:c.9513_9514delinsCG	p.Thr3172Ala	p.T3172A	ENST00000534358	NM_005933.3	3171	gcTAct/gcCGct	27/36	0.781819877310088	1	FACETS	0.063	0.048	0.082	0.063	0.048	0.082	SUBCLONAL	1	TRUE	0	0.924633515498065	1		624	349	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376217	118376217	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	14	487	0	ENST00000534358.1:c.9610T>G	p.Ser3204Ala	p.S3204A	ENST00000534358	NM_005933.3	3204	Tcc/Gcc	27/36	0.781819877310088	1	FACETS	0.064	0.046	0.086	0.064	0.046	0.086	SUBCLONAL	1	TRUE	0	0.924633515498065	1		487	255	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109744	115109744	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	32	852	0	ENST00000257566.3:c.2134G>C	p.Ala712Pro	p.A712P	ENST00000257566	NM_016569.3	712	Gcg/Ccg	8/8	0.924633515498065	1	FACETS	0.059	0.047	0.072	0.059	0.047	0.072	SUBCLONAL	1	TRUE	0	0.924633515498065	1		852	630	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416694	121416694	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	36	864	0	ENST00000257555.6:c.123A>T	p.Glu41Asp	p.E41D	ENST00000257555		41	gaA/gaT	1/10	0.924633515498065	1	FACETS	0.077	0.063	0.093	0.077	0.063	0.093	SUBCLONAL	1	TRUE	0	0.924633515498065	1		864	542	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434365	121434365	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	25	753	0	ENST00000257555.6:c.1129C>T	p.Leu377Phe	p.L377F	ENST00000257555		377	Ctc/Ttc	6/10	0.924633515498065	1	FACETS	0.06	0.046	0.075	0.06	0.046	0.075	SUBCLONAL	1	TRUE	0	0.924633515498065	1		753	487	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215834	133215834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs777390504	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	21	682	0	ENST00000320574.5:c.5429A>G	p.His1810Arg	p.H1810R	ENST00000320574	NM_006231.2	1810	cAc/cGc	40/49	0.924633515498065	1	FACETS	0.059	0.045	0.075	0.059	0.045	0.075	SUBCLONAL	1	TRUE	0	0.924633515498065	1		682	414	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643444	38643444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	14	695	0	ENST00000299084.4:c.914C>T	p.Pro305Leu	p.P305L	ENST00000299084	NM_152594.2	305	cCc/cTc	7/7	0.924633515498065	1	FACETS	0.068	0.049	0.091	0.068	0.049	0.091	SUBCLONAL	1	TRUE	0	0.924633515498065	1		695	240	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643488	38643488	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	10	617	0	ENST00000299084.4:c.958A>T	p.Ile320Phe	p.I320F	ENST00000299084	NM_152594.2	320	Att/Ttt	7/7	0.924633515498065	1	FACETS	0.06	0.04	0.085	0.06	0.04	0.085	SUBCLONAL	1	TRUE	0	0.924633515498065	1		617	194	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41020959	41020959	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	23	822	0	ENST00000267868.3:c.581C>G	p.Ala194Gly	p.A194G	ENST00000267868	NM_002875.4	194	gCg/gGg	7/10	0.924633515498065	1	FACETS	0.064	0.049	0.081	0.064	0.049	0.081	SUBCLONAL	1	TRUE	0	0.924633515498065	1		822	419	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961226	41961226	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	16	565	0	ENST00000219905.7:c.134A>G	p.Gln45Arg	p.Q45R	ENST00000219905	NM_001164273.1	45	cAg/cGg	2/24	0.924633515498065	1	FACETS	0.073	0.054	0.096	0.073	0.054	0.096	SUBCLONAL	1	TRUE	0	0.924633515498065	1		565	255	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988571	41988571	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	14	544	0	ENST00000219905.7:c.1363A>C	p.Lys455Gln	p.K455Q	ENST00000219905	NM_001164273.1	455	Aaa/Caa	3/24	0.924633515498065	1	FACETS	0.072	0.052	0.097	0.072	0.052	0.097	SUBCLONAL	1	TRUE	0	0.924633515498065	1		544	225	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988595	41988595	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	13	563	0	ENST00000219905.7:c.1387A>G	p.Thr463Ala	p.T463A	ENST00000219905	NM_001164273.1	463	Act/Gct	3/24	0.924633515498065	1	FACETS	0.069	0.049	0.094	0.069	0.049	0.094	SUBCLONAL	1	TRUE	0	0.924633515498065	1		563	218	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988641	41988641	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	13	572	0	ENST00000219905.7:c.1433G>A	p.Arg478Lys	p.R478K	ENST00000219905	NM_001164273.1	478	aGa/aAa	3/24	0.924633515498065	1	FACETS	0.076	0.054	0.102	0.076	0.054	0.102	SUBCLONAL	1	TRUE	0	0.924633515498065	1		572	200	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028743	42028743	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	20	723	0	ENST00000219905.7:c.4281G>T	p.Glu1427Asp	p.E1427D	ENST00000219905	NM_001164273.1	1427	gaG/gaT	13/24	0.924633515498065	1	FACETS	0.07	0.053	0.09	0.07	0.053	0.09	SUBCLONAL	1	TRUE	0	0.924633515498065	1		723	332	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032318	42032318	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	28	638	0	ENST00000219905.7:c.4502C>G	p.Ser1501Cys	p.S1501C	ENST00000219905	NM_001164273.1	1501	tCc/tGc	14/24	0.924633515498065	1	FACETS	0.067	0.053	0.083	0.067	0.053	0.083	SUBCLONAL	1	TRUE	0	0.924633515498065	1		638	485	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034851	42034851	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	21	603	0	ENST00000219905.7:c.4693A>C	p.Thr1565Pro	p.T1565P	ENST00000219905	NM_001164273.1	1565	Aca/Cca	15/24	0.924633515498065	1	FACETS	0.062	0.047	0.079	0.062	0.047	0.079	SUBCLONAL	1	TRUE	0	0.924633515498065	1		603	395	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035007	42035007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	25	726	1	ENST00000219905.7:c.4849G>A	p.Ala1617Thr	p.A1617T	ENST00000219905	NM_001164273.1	1617	Gct/Act	15/24	0.924633515498065	1	FACETS	0.073	0.057	0.091	0.073	0.057	0.091	SUBCLONAL	1	TRUE	0	0.924633515498065	1		727	400	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035023	42035023	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	25	718	0	ENST00000219905.7:c.4865A>G	p.Glu1622Gly	p.E1622G	ENST00000219905	NM_001164273.1	1622	gAa/gGa	15/24	0.924633515498065	1	FACETS	0.082	0.064	0.103	0.082	0.064	0.103	SUBCLONAL	1	TRUE	0	0.924633515498065	1		718	353	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035061	42035061	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1245262572	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	25	724	0	ENST00000219905.7:c.4903A>G	p.Thr1635Ala	p.T1635A	ENST00000219905	NM_001164273.1	1635	Aca/Gca	15/24	0.924633515498065	1	FACETS	0.082	0.064	0.102	0.082	0.064	0.102	SUBCLONAL	1	TRUE	0	0.924633515498065	1		724	355	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035100	42035100	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	23	751	0	ENST00000219905.7:c.4942T>C	p.Ser1648Pro	p.S1648P	ENST00000219905	NM_001164273.1	1648	Tct/Cct	15/24	0.924633515498065	1	FACETS	0.07	0.054	0.089	0.07	0.054	0.089	SUBCLONAL	1	TRUE	0	0.924633515498065	1		751	380	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035103	42035103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	23	752	0	ENST00000219905.7:c.4945G>A	p.Val1649Ile	p.V1649I	ENST00000219905	NM_001164273.1	1649	Gta/Ata	15/24	0.924633515498065	1	FACETS	0.071	0.055	0.089	0.071	0.055	0.089	SUBCLONAL	1	TRUE	0	0.924633515498065	1		752	378	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035109	42035109	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	22	752	0	ENST00000219905.7:c.4951T>C	p.Ser1651Pro	p.S1651P	ENST00000219905	NM_001164273.1	1651	Tct/Cct	15/24	0.924633515498065	1	FACETS	0.066	0.05	0.083	0.066	0.05	0.083	SUBCLONAL	1	TRUE	0	0.924633515498065	1		752	390	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035140	42035140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	28	808	0	ENST00000219905.7:c.4982C>T	p.Thr1661Ile	p.T1661I	ENST00000219905	NM_001164273.1	1661	aCc/aTc	15/24	0.924633515498065	1	FACETS	0.072	0.057	0.09	0.072	0.057	0.09	SUBCLONAL	1	TRUE	0	0.924633515498065	1		808	450	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035208	42035208	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	33	848	0	ENST00000219905.7:c.5050T>C	p.Ser1684Pro	p.S1684P	ENST00000219905	NM_001164273.1	1684	Tca/Cca	15/24	0.924633515498065	1	FACETS	0.073	0.059	0.089	0.073	0.059	0.089	SUBCLONAL	1	TRUE	0	0.924633515498065	1		848	526	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035250	42035250	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	29	774	0	ENST00000219905.7:c.5092T>A	p.Leu1698Ile	p.L1698I	ENST00000219905	NM_001164273.1	1698	Tta/Ata	15/24	0.924633515498065	1	FACETS	0.063	0.05	0.078	0.063	0.05	0.078	SUBCLONAL	1	TRUE	0	0.924633515498065	1		774	532	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035340	42035340	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	17	560	0	ENST00000219905.7:c.5182A>G	p.Asn1728Asp	p.N1728D	ENST00000219905	NM_001164273.1	1728	Aat/Gat	15/24	0.924633515498065	1	FACETS	0.067	0.049	0.087	0.067	0.049	0.087	SUBCLONAL	1	TRUE	0	0.924633515498065	1		560	297	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040894	42040894	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	26	720	1	ENST00000219905.7:c.5272G>A	p.Ala1758Thr	p.A1758T	ENST00000219905	NM_001164273.1	1758	Gct/Act	16/24	0.924633515498065	1	FACETS	0.071	0.056	0.089	0.071	0.056	0.089	SUBCLONAL	1	TRUE	0	0.924633515498065	1		721	425	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040954	42040954	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	28	794	0	ENST00000219905.7:c.5332T>C	p.Ser1778Pro	p.S1778P	ENST00000219905	NM_001164273.1	1778	Tca/Cca	16/24	0.924633515498065	1	FACETS	0.07	0.055	0.087	0.07	0.055	0.087	SUBCLONAL	1	TRUE	0	0.924633515498065	1		794	465	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041494	42041494	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	19	724	0	ENST00000219905.7:c.5689G>T	p.Ala1897Ser	p.A1897S	ENST00000219905	NM_001164273.1	1897	Gct/Tct	17/24	0.924633515498065	1	FACETS	0.062	0.047	0.08	0.062	0.047	0.08	SUBCLONAL	1	TRUE	0	0.924633515498065	1		724	355	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041551	42041551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	25	682	1	ENST00000219905.7:c.5746A>G	p.Thr1916Ala	p.T1916A	ENST00000219905	NM_001164273.1	1916	Aca/Gca	17/24	0.924633515498065	1	FACETS	0.083	0.065	0.104	0.083	0.065	0.104	SUBCLONAL	1	TRUE	0	0.924633515498065	1		683	349	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059015	42059015	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	13	505	0	ENST00000219905.7:c.8735A>C	p.Asn2912Thr	p.N2912T	ENST00000219905	NM_001164273.1	2912	aAt/aCt	24/24	0.924633515498065	1	FACETS	0.066	0.047	0.09	0.066	0.047	0.09	SUBCLONAL	1	TRUE	0	0.924633515498065	1		505	229	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059101	42059101	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	14	431	0	ENST00000219905.7:c.8821A>C	p.Asn2941His	p.N2941H	ENST00000219905	NM_001164273.1	2941	Aac/Cac	24/24	0.924633515498065	1	FACETS	0.072	0.051	0.096	0.072	0.051	0.096	SUBCLONAL	1	TRUE	0	0.924633515498065	1		431	227	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059105	42059105	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	15	420	0	ENST00000219905.7:c.8825A>G	p.Lys2942Arg	p.K2942R	ENST00000219905	NM_001164273.1	2942	aAg/aGg	24/24	0.924633515498065	1	FACETS	0.077	0.056	0.102	0.077	0.056	0.102	SUBCLONAL	1	TRUE	0	0.924633515498065	1		420	228	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059114	42059114	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	13	420	0	ENST00000219905.7:c.8834T>G	p.Ile2945Ser	p.I2945S	ENST00000219905	NM_001164273.1	2945	aTt/aGt	24/24	0.924633515498065	1	FACETS	0.067	0.047	0.09	0.067	0.047	0.09	SUBCLONAL	1	TRUE	0	0.924633515498065	1		420	227	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059129	42059129	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	13	428	0	ENST00000219905.7:c.8849A>G	p.Asn2950Ser	p.N2950S	ENST00000219905	NM_001164273.1	2950	aAt/aGt	24/24	0.924633515498065	1	FACETS	0.065	0.046	0.088	0.065	0.046	0.088	SUBCLONAL	1	TRUE	0	0.924633515498065	1		428	234	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059140	42059140	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs747826631	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	15	421	0	ENST00000219905.7:c.8860C>A	p.Leu2954Ile	p.L2954I	ENST00000219905	NM_001164273.1	2954	Ctc/Atc	24/24	0.924633515498065	1	FACETS	0.075	0.054	0.099	0.075	0.054	0.099	SUBCLONAL	1	TRUE	0	0.924633515498065	1		421	233	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059329	42059329	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1023027876	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	19	454	0	ENST00000219905.7:c.9049A>G	p.Ile3017Val	p.I3017V	ENST00000219905	NM_001164273.1	3017	Ata/Gta	24/24	0.924633515498065	1	FACETS	0.077	0.058	0.1	0.077	0.058	0.1	SUBCLONAL	1	TRUE	0	0.924633515498065	1		454	286	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059372	42059372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	17	431	0	ENST00000219905.7:c.9092C>T	p.Thr3031Ile	p.T3031I	ENST00000219905	NM_001164273.1	3031	aCa/aTa	24/24	0.924633515498065	1	FACETS	0.062	0.046	0.081	0.062	0.046	0.081	SUBCLONAL	1	TRUE	0	0.924633515498065	1		431	320	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059389	42059389	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	18	428	0	ENST00000219905.7:c.9109G>T	p.Gly3037Cys	p.G3037C	ENST00000219905	NM_001164273.1	3037	Ggc/Tgc	24/24	0.924633515498065	1	FACETS	0.062	0.046	0.081	0.062	0.046	0.081	SUBCLONAL	1	TRUE	0	0.924633515498065	1		428	337	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705480	43705481	+	missense_variant	Missense_Mutation	DNP	GG	GG	CA	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	31	815	1	ENST00000382044.4:c.5141_5142delinsTG	p.Thr1714Met	p.T1714M	ENST00000382044	NM_001141980.1	1714	aCC/aTG	24/28	0.924633515498065	1	FACETS	0.06	0.048	0.074	0.06	0.048	0.074	SUBCLONAL	1	TRUE	0	0.924633515498065	1		816	601	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707884	43707885	+	missense_variant	Missense_Mutation	DNP	AT	AT	GA	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	35	1044	2	ENST00000382044.4:c.4996_4997delinsTC	p.Met1666Ser	p.M1666S	ENST00000382044	NM_001141980.1	1666	ATg/TCg	23/28	0.924633515498065	1	FACETS	0.058	0.047	0.071	0.058	0.047	0.071	SUBCLONAL	1	TRUE	0	0.924633515498065	1		1046	696	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714090	43714090	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	39	895	0	ENST00000382044.4:c.4063G>A	p.Ala1355Thr	p.A1355T	ENST00000382044	NM_001141980.1	1355	Gcc/Acc	19/28	0.924633515498065	1	FACETS	0.062	0.05	0.074	0.062	0.05	0.074	SUBCLONAL	1	TRUE	0	0.924633515498065	1		895	737	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714125	43714125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	46	970	0	ENST00000382044.4:c.4028G>A	p.Arg1343Lys	p.R1343K	ENST00000382044	NM_001141980.1	1343	aGa/aAa	19/28	0.924633515498065	1	FACETS	0.072	0.06	0.085	0.072	0.06	0.085	SUBCLONAL	1	TRUE	0	0.924633515498065	1		970	746	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714143	43714143	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	43	964	1	ENST00000382044.4:c.4010A>G	p.Lys1337Arg	p.K1337R	ENST00000382044	NM_001141980.1	1337	aAa/aGa	19/28	0.924633515498065	1	FACETS	0.066	0.055	0.079	0.066	0.055	0.079	SUBCLONAL	1	TRUE	0	0.924633515498065	1		965	759	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500427	99500427	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	26	739	0	ENST00000268035.6:c.3860T>C	p.Leu1287Pro	p.L1287P	ENST00000268035	NM_000875.3	1287	cTg/cCg	21/21	0.924633515498065	1	FACETS	0.059	0.046	0.074	0.059	0.046	0.074	SUBCLONAL	1	TRUE	0	0.924633515498065	1		739	513	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500526	99500526	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	23	633	0	ENST00000268035.6:c.3959A>T	p.His1320Leu	p.H1320L	ENST00000268035	NM_000875.3	1320	cAc/cTc	21/21	0.924633515498065	1	FACETS	0.067	0.051	0.084	0.067	0.051	0.084	SUBCLONAL	1	TRUE	0	0.924633515498065	1		633	401	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396660	396661	+	missense_variant	Missense_Mutation	DNP	AG	AG	GC	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	25	766	0	ENST00000262320.3:c.365_366delinsGC	p.Thr122Ser	p.T122S	ENST00000262320	NM_003502.3	122	aCT/aGC	2/11	0.924633515498065	1	FACETS	0.06	0.047	0.075	0.06	0.047	0.075	SUBCLONAL	1	TRUE	0	0.924633515498065	1		766	484	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2093681	2093681	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1226532313	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	41	1087	2	ENST00000219066.1:c.596A>G	p.His199Arg	p.H199R	ENST00000219066	NM_002528.5	199	cAc/cGc	4/6	0.924633515498065	1	FACETS	0.066	0.054	0.079	0.066	0.054	0.079	SUBCLONAL	1	TRUE	0	0.924633515498065	1		1089	725	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2137891	2137891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45490993	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	36	945	0	ENST00000219476.3:c.5017G>A	p.Val1673Ile	p.V1673I	ENST00000219476	NM_000548.3	1673	Gtc/Atc	39/42	0.924633515498065	1	FACETS	0.061	0.05	0.074	0.061	0.05	0.074	SUBCLONAL	1	TRUE	0	0.924633515498065	1		945	684	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222297	2222297	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	30	761	0	ENST00000326181.6:c.581T>C	p.Val194Ala	p.V194A	ENST00000326181	NM_032271.2	194	gTa/gCa	8/21	0.924633515498065	1	FACETS	0.062	0.05	0.077	0.062	0.05	0.077	SUBCLONAL	1	TRUE	0	0.924633515498065	1		761	559	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222304	2222305	+	missense_variant	Missense_Mutation	DNP	CA	CA	GG	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	32	772	1	ENST00000326181.6:c.588_589delinsGG	p.Ser197Gly	p.S197G	ENST00000326181	NM_032271.2	196	ggCAgc/ggGGgc	8/21	0.924633515498065	1	FACETS	0.068	0.055	0.083	0.068	0.055	0.083	SUBCLONAL	1	TRUE	0	0.924633515498065	1		773	548	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222319	2222320	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	39	802	1	ENST00000326181.6:c.603_604delinsAG	p.Ile202Val	p.I202V	ENST00000326181	NM_032271.2	201	ccCAtc/ccAGtc	8/21	0.924633515498065	1	FACETS	0.085	0.07	0.102	0.085	0.07	0.102	SUBCLONAL	1	TRUE	0	0.924633515498065	1		803	531	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225386	2225386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139483392	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	36	824	1	ENST00000326181.6:c.1471G>A	p.Val491Met	p.V491M	ENST00000326181	NM_032271.2	491	Gtg/Atg	16/21	0.924633515498065	1	FACETS	0.073	0.059	0.088	0.073	0.059	0.088	SUBCLONAL	1	TRUE	0	0.924633515498065	1		825	575	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777801	3777801	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	45	1141	0	ENST00000262367.5:c.7247G>A	p.Ser2416Asn	p.S2416N	ENST00000262367	NM_004380.2	2416	aGc/aAc	31/31	0.924633515498065	1	FACETS	0.063	0.053	0.075	0.063	0.053	0.075	SUBCLONAL	1	TRUE	0	0.924633515498065	1		1141	826	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778234	3778235	+	missense_variant	Missense_Mutation	DNP	CA	CA	TG	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	40	868	3	ENST00000262367.5:c.6813_6814inv	p.Gly2272Ser	p.G2272S	ENST00000262367	NM_004380.2	2271	ctTGgc/ctCAgc	31/31	0.924633515498065	1	FACETS	0.087	0.071	0.104	0.087	0.071	0.104	SUBCLONAL	1	TRUE	0	0.924633515498065	1		871	537	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778282	3778282	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs752887380	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	41	837	0	ENST00000262367.5:c.6766C>A	p.Leu2256Ile	p.L2256I	ENST00000262367	NM_004380.2	2256	Ctc/Atc	31/31	0.924633515498065	1	FACETS	0.086	0.071	0.103	0.086	0.071	0.103	SUBCLONAL	1	TRUE	0	0.924633515498065	1		837	553	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779053	3779053	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	25	664	0	ENST00000262367.5:c.5995A>G	p.Ser1999Gly	p.S1999G	ENST00000262367	NM_004380.2	1999	Agc/Ggc	31/31	0.924633515498065	1	FACETS	0.061	0.048	0.077	0.061	0.048	0.077	SUBCLONAL	1	TRUE	0	0.924633515498065	1		664	474	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779073	3779073	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	27	752	1	ENST00000262367.5:c.5975G>T	p.Gly1992Val	p.G1992V	ENST00000262367	NM_004380.2	1992	gGg/gTg	31/31	0.924633515498065	1	FACETS	0.06	0.047	0.074	0.06	0.047	0.074	SUBCLONAL	1	TRUE	0	0.924633515498065	1		753	527	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779082	3779082	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	28	773	0	ENST00000262367.5:c.5966G>T	p.Gly1989Val	p.G1989V	ENST00000262367	NM_004380.2	1989	gGg/gTg	31/31	0.924633515498065	1	FACETS	0.059	0.047	0.073	0.059	0.047	0.073	SUBCLONAL	1	TRUE	0	0.924633515498065	1		773	552	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779229	3779229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	22	509	1	ENST00000262367.5:c.5819G>A	p.Ser1940Asn	p.S1940N	ENST00000262367	NM_004380.2	1940	aGc/aAc	31/31	0.924633515498065	1	FACETS	0.074	0.057	0.094	0.074	0.057	0.094	SUBCLONAL	1	TRUE	0	0.924633515498065	1		510	346	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820722	3820722	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	54	1065	0	ENST00000262367.5:c.2729C>G	p.Thr910Ser	p.T910S	ENST00000262367	NM_004380.2	910	aCc/aGc	14/31	0.924633515498065	1	FACETS	0.07	0.059	0.081	0.07	0.059	0.081	SUBCLONAL	1	TRUE	0	0.924633515498065	1		1065	903	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832781	3832781	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	36	723	0	ENST00000262367.5:c.1477A>C	p.Met493Leu	p.M493L	ENST00000262367	NM_004380.2	493	Atg/Ctg	6/31	0.924633515498065	1	FACETS	0.064	0.052	0.077	0.064	0.052	0.077	SUBCLONAL	1	TRUE	0	0.924633515498065	1		723	655	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832856	3832856	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	30	649	0	ENST00000262367.5:c.1402A>G	p.Thr468Ala	p.T468A	ENST00000262367	NM_004380.2	468	Act/Gct	6/31	0.924633515498065	1	FACETS	0.069	0.055	0.084	0.069	0.055	0.084	SUBCLONAL	1	TRUE	0	0.924633515498065	1		649	509	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900424	3900424	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	35	880	0	ENST00000262367.5:c.672G>A	p.Met224Ile	p.M224I	ENST00000262367	NM_004380.2	224	atG/atA	2/31	0.924633515498065	1	FACETS	0.06	0.049	0.073	0.06	0.049	0.073	SUBCLONAL	1	TRUE	0	0.924633515498065	1		880	673	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900611	3900611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757321118	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	46	799	3	ENST00000262367.5:c.485C>T	p.Ala162Val	p.A162V	ENST00000262367	NM_004380.2	162	gCg/gTg	2/31	0.924633515498065	1	FACETS	0.09	0.076	0.107	0.09	0.076	0.107	SUBCLONAL	1	TRUE	0	0.924633515498065	1		802	592	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900660	3900660	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	45	690	0	ENST00000262367.5:c.436G>C	p.Ala146Pro	p.A146P	ENST00000262367	NM_004380.2	146	Gct/Cct	2/31	0.924633515498065	1	FACETS	0.099	0.083	0.118	0.099	0.083	0.118	SUBCLONAL	1	TRUE	0	0.924633515498065	1		690	526	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900725	3900725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756967439	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	34	661	0	ENST00000262367.5:c.371G>A	p.Ser124Asn	p.S124N	ENST00000262367	NM_004380.2	124	aGc/aAc	2/31	0.924633515498065	1	FACETS	0.082	0.066	0.099	0.082	0.066	0.099	SUBCLONAL	1	TRUE	0	0.924633515498065	1		661	484	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900750	3900751	+	missense_variant	Missense_Mutation	DNP	TG	TG	CC	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	25	655	1	ENST00000262367.5:c.345_346delinsGG	p.Ser116Gly	p.S116G	ENST00000262367	NM_004380.2	115	ctCAgt/ctGGgt	2/31	0.924633515498065	1	FACETS	0.059	0.046	0.074	0.059	0.046	0.074	SUBCLONAL	1	TRUE	0	0.924633515498065	1		656	493	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900753	3900753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	25	653	0	ENST00000262367.5:c.343C>T	p.Leu115Phe	p.L115F	ENST00000262367	NM_004380.2	115	Ctc/Ttc	2/31	0.924633515498065	1	FACETS	0.059	0.046	0.074	0.059	0.046	0.074	SUBCLONAL	1	TRUE	0	0.924633515498065	1		653	493	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900789	3900789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	33	650	2	ENST00000262367.5:c.307G>A	p.Ala103Thr	p.A103T	ENST00000262367	NM_004380.2	103	Gct/Act	2/31	0.924633515498065	1	FACETS	0.078	0.063	0.094	0.078	0.063	0.094	SUBCLONAL	1	TRUE	0	0.924633515498065	1		652	495	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900798	3900799	+	missense_variant	Missense_Mutation	DNP	CC	CC	TG	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	32	657	0	ENST00000262367.5:c.297_298delinsCA	p.Gly100Ser	p.G100S	ENST00000262367	NM_004380.2	99	ctGGgt/ctCAgt	2/31	0.924633515498065	1	FACETS	0.072	0.058	0.087	0.072	0.058	0.087	SUBCLONAL	1	TRUE	0	0.924633515498065	1		657	520	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032264	10032264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751692867	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	20	751	0	ENST00000330684.3:c.559G>A	p.Val187Ile	p.V187I	ENST00000330684	NM_001134407.1	187	Gtc/Atc	3/13	0.924633515498065	1	FACETS	0.065	0.049	0.084	0.065	0.049	0.084	SUBCLONAL	1	TRUE	0	0.924633515498065	1		751	357	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032277	10032277	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	19	682	0	ENST00000330684.3:c.546A>C	p.Glu182Asp	p.E182D	ENST00000330684	NM_001134407.1	182	gaA/gaC	3/13	0.924633515498065	1	FACETS	0.063	0.047	0.081	0.063	0.047	0.081	SUBCLONAL	1	TRUE	0	0.924633515498065	1		682	353	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274088	10274089	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	33	771	0	ENST00000330684.3:c.180_181delinsAA	p.Ala61Thr	p.A61T	ENST00000330684	NM_001134407.1	60	gcGGcg/gcAAcg	2/13	0.924633515498065	1	FACETS	0.078	0.063	0.095	0.078	0.063	0.095	SUBCLONAL	1	TRUE	0	0.924633515498065	1		771	492	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274196	10274196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	17	422	0	ENST00000330684.3:c.73G>A	p.Ala25Thr	p.A25T	ENST00000330684	NM_001134407.1	25	Gcg/Acg	2/13	0.924633515498065	1	FACETS	0.062	0.046	0.081	0.062	0.046	0.081	SUBCLONAL	1	TRUE	0	0.924633515498065	1		422	318	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274199	10274199	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	16	404	0	ENST00000330684.3:c.70A>G	p.Ser24Gly	p.S24G	ENST00000330684	NM_001134407.1	24	Agc/Ggc	2/13	0.924633515498065	1	FACETS	0.061	0.045	0.081	0.061	0.045	0.081	SUBCLONAL	1	TRUE	0	0.924633515498065	1		404	305	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274201	10274201	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs969233060	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	16	410	0	ENST00000330684.3:c.68C>A	p.Pro23Gln	p.P23Q	ENST00000330684	NM_001134407.1	23	cCg/cAg	2/13	0.924633515498065	1	FACETS	0.061	0.045	0.081	0.061	0.045	0.081	SUBCLONAL	1	TRUE	0	0.924633515498065	1		410	303	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274259	10274259	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	10	345	0	ENST00000330684.3:c.10G>C	p.Val4Leu	p.V4L	ENST00000330684	NM_001134407.1	4	Gtg/Ctg	2/13	0.924633515498065	1	FACETS	0.059	0.039	0.083	0.059	0.039	0.083	SUBCLONAL	1	TRUE	0	0.924633515498065	1		345	198	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129041	30129041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1287735708	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	39	786	1	ENST00000263025.4:c.725G>A	p.Arg242Gln	p.R242Q	ENST00000263025	NM_002746.2	242	cGg/cAg	5/9	0.924633515498065	1	FACETS	0.075	0.061	0.09	0.075	0.061	0.09	SUBCLONAL	1	TRUE	0	0.924633515498065	1		787	607	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129786	30129786	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	58	666	0	ENST00000263025.4:c.427A>G	p.Ile143Val	p.I143V	ENST00000263025	NM_002746.2	143	Atc/Gtc	3/9	0.924633515498065	1	FACETS	0.131	0.112	0.151	0.131	0.112	0.151	SUBCLONAL	1	TRUE	0	0.924633515498065	1		666	515	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134393	30134393	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	69	759	0	ENST00000263025.4:c.138G>C	p.Gln46His	p.Q46H	ENST00000263025	NM_002746.2	46	caG/caC	1/9	0.924633515498065	1	FACETS	0.108	0.093	0.124	0.108	0.093	0.124	SUBCLONAL	1	TRUE	0	0.924633515498065	1		759	744	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134401	30134401	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	67	730	0	ENST00000263025.4:c.130C>G	p.Gln44Glu	p.Q44E	ENST00000263025	NM_002746.2	44	Cag/Gag	1/9	0.924633515498065	1	FACETS	0.103	0.089	0.118	0.103	0.089	0.118	SUBCLONAL	1	TRUE	0	0.924633515498065	1		730	756	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134443	30134443	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	62	656	0	ENST00000263025.4:c.88A>G	p.Met30Val	p.M30V	ENST00000263025	NM_002746.2	30	Atg/Gtg	1/9	0.924633515498065	1	FACETS	0.104	0.089	0.12	0.104	0.089	0.12	SUBCLONAL	1	TRUE	0	0.924633515498065	1		656	694	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134458	30134458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1044163469	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	55	571	0	ENST00000263025.4:c.73C>T	p.Pro25Ser	p.P25S	ENST00000263025	NM_002746.2	25	Ccg/Tcg	1/9	0.924633515498065	1	FACETS	0.109	0.093	0.126	0.109	0.093	0.126	SUBCLONAL	1	TRUE	0	0.924633515498065	1		571	588	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134477	30134477	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	39	484	0	ENST00000263025.4:c.54G>T	p.Glu18Asp	p.E18D	ENST00000263025	NM_002746.2	18	gaG/gaT	1/9	0.924633515498065	1	FACETS	0.098	0.081	0.117	0.098	0.081	0.117	SUBCLONAL	1	TRUE	0	0.924633515498065	1		484	464	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134482	30134482	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	36	452	0	ENST00000263025.4:c.49A>G	p.Thr17Ala	p.T17A	ENST00000263025	NM_002746.2	17	Acc/Gcc	1/9	0.924633515498065	1	FACETS	0.1	0.082	0.12	0.1	0.082	0.12	SUBCLONAL	1	TRUE	0	0.924633515498065	1		452	420	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134485	30134486	+	missense_variant	Missense_Mutation	DNP	TA	TA	CC	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	34	440	1	ENST00000263025.4:c.45_46delinsGG	p.Arg16Gly	p.R16G	ENST00000263025	NM_002746.2	15	cgTAga/cgGGga	1/9	0.924633515498065	1	FACETS	0.1	0.081	0.121	0.1	0.081	0.121	SUBCLONAL	1	TRUE	0	0.924633515498065	1		441	395	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134514	30134516	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	rs572866415	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	20	254	3	ENST00000263025.4:c.15_17del	p.Ala6del	p.A6del	ENST00000263025	NM_002746.2	5	gcGGCt/gct	1/9	0.924633515498065	1	FACETS	0.119	0.091	0.152	0.119	0.091	0.152	SUBCLONAL	1	TRUE	0	0.924633515498065	1		257	195	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56875707	56875707	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	27	563	0	ENST00000308159.5:c.2311T>G	p.Ser771Ala	p.S771A	ENST00000308159	NM_014669.4	771	Tca/Gca	21/22	0.924633515498065	1	FACETS	0.061	0.048	0.076	0.061	0.048	0.076	SUBCLONAL	1	TRUE	0	0.924633515498065	1		563	514	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821896	72821896	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	28	468	1	ENST00000268489.5:c.10279A>G	p.Thr3427Ala	p.T3427A	ENST00000268489	NM_006885.3	3427	Acc/Gcc	10/10	0.924633515498065	1	FACETS	0.098	0.078	0.121	0.098	0.078	0.121	SUBCLONAL	1	TRUE	0	0.924633515498065	1		469	331	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821953	72821953	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	30	437	0	ENST00000268489.5:c.10222C>G	p.Pro3408Ala	p.P3408A	ENST00000268489	NM_006885.3	3408	Cct/Gct	10/10	0.924633515498065	1	FACETS	0.117	0.094	0.143	0.117	0.094	0.143	SUBCLONAL	1	TRUE	0	0.924633515498065	1		437	298	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821989	72821991	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	rs752028320	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	20	443	3	ENST00000268489.5:c.10184_10186del	p.Gln3395del	p.Q3395del	ENST00000268489	NM_006885.3	3395	cAGCcc/ccc	10/10	0.924633515498065	1	FACETS	0.072	0.055	0.093	0.072	0.055	0.093	SUBCLONAL	1	TRUE	0	0.924633515498065	1		446	321	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822603	72822603	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	25	688	0	ENST00000268489.5:c.9572G>C	p.Gly3191Ala	p.G3191A	ENST00000268489	NM_006885.3	3191	gGc/gCc	10/10	0.924633515498065	1	FACETS	0.062	0.048	0.077	0.062	0.048	0.077	SUBCLONAL	1	TRUE	0	0.924633515498065	1		688	472	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827271	72827272	+	missense_variant	Missense_Mutation	DNP	TG	TG	CA	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	30	751	2	ENST00000268489.5:c.9309_9310inv	p.Thr3104Ala	p.T3104A	ENST00000268489	NM_006885.3	3103	aaCAcc/aaTGcc	9/10	0.924633515498065	1	FACETS	0.069	0.055	0.084	0.069	0.055	0.084	SUBCLONAL	1	TRUE	0	0.924633515498065	1		753	508	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829227	72829227	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	40	957	0	ENST00000268489.5:c.7354C>G	p.Pro2452Ala	p.P2452A	ENST00000268489	NM_006885.3	2452	Cca/Gca	9/10	0.924633515498065	1	FACETS	0.062	0.051	0.074	0.062	0.051	0.074	SUBCLONAL	1	TRUE	0	0.924633515498065	1		957	750	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829879	72829880	+	missense_variant	Missense_Mutation	DNP	TG	TG	CT	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	46	926	1	ENST00000268489.5:c.6701_6702delinsAG	p.Pro2234Gln	p.P2234Q	ENST00000268489	NM_006885.3	2234	cCA/cAG	9/10	0.924633515498065	1	FACETS	0.087	0.073	0.103	0.087	0.073	0.103	SUBCLONAL	1	TRUE	0	0.924633515498065	1		927	613	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831477	72831478	+	missense_variant	Missense_Mutation	DNP	CA	CA	TG	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	24	719	0	ENST00000268489.5:c.5103_5104inv	p.Ala1702Thr	p.A1702T	ENST00000268489	NM_006885.3	1701	atTGct/atCAct	9/10	0.924633515498065	1	FACETS	0.061	0.047	0.077	0.061	0.047	0.077	SUBCLONAL	1	TRUE	0	0.924633515498065	1		719	456	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992514	72992514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	42	940	0	ENST00000268489.5:c.1531C>T	p.Pro511Ser	p.P511S	ENST00000268489	NM_006885.3	511	Cct/Tct	2/10	0.924633515498065	1	FACETS	0.065	0.054	0.078	0.065	0.054	0.078	SUBCLONAL	1	TRUE	0	0.924633515498065	1		940	750	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992542	72992542	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	35	878	0	ENST00000268489.5:c.1503G>C	p.Glu501Asp	p.E501D	ENST00000268489	NM_006885.3	501	gaG/gaC	2/10	0.924633515498065	1	FACETS	0.059	0.048	0.072	0.059	0.048	0.072	SUBCLONAL	1	TRUE	0	0.924633515498065	1		878	690	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992865	72992866	+	missense_variant	Missense_Mutation	DNP	GA	GA	TG	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	32	681	1	ENST00000268489.5:c.1179_1180delinsCA	p.Leu394Ile	p.L394I	ENST00000268489	NM_006885.3	393	ggTCtc/ggCAtc	2/10	0.924633515498065	1	FACETS	0.072	0.058	0.088	0.072	0.058	0.088	SUBCLONAL	1	TRUE	0	0.924633515498065	1		682	517	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993381	72993381	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	39	900	0	ENST00000268489.5:c.664G>A	p.Ala222Thr	p.A222T	ENST00000268489	NM_006885.3	222	Gcg/Acg	2/10	0.924633515498065	1	FACETS	0.067	0.055	0.081	0.067	0.055	0.081	SUBCLONAL	1	TRUE	0	0.924633515498065	1		900	673	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993908	72993908	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	41	741	0	ENST00000268489.5:c.137G>C	p.Ser46Thr	p.S46T	ENST00000268489	NM_006885.3	46	aGc/aCc	2/10	0.924633515498065	1	FACETS	0.089	0.074	0.106	0.089	0.074	0.106	SUBCLONAL	1	TRUE	0	0.924633515498065	1		741	534	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993915	72993915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1170016765	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	40	786	0	ENST00000268489.5:c.130G>A	p.Gly44Ser	p.G44S	ENST00000268489	NM_006885.3	44	Ggc/Agc	2/10	0.924633515498065	1	FACETS	0.084	0.069	0.1	0.084	0.069	0.1	SUBCLONAL	1	TRUE	0	0.924633515498065	1		786	555	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993966	72993966	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	46	828	0	ENST00000268489.5:c.79C>G	p.Leu27Val	p.L27V	ENST00000268489	NM_006885.3	27	Ctc/Gtc	2/10	0.924633515498065	1	FACETS	0.078	0.065	0.093	0.078	0.065	0.093	SUBCLONAL	1	TRUE	0	0.924633515498065	1		828	682	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925132	81925132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199636472	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	23	605	2	ENST00000359376.3:c.923C>T	p.Ala308Val	p.A308V	ENST00000359376	NM_002661.3	308	gCg/gTg	11/33	0.924633515498065	1	FACETS	0.069	0.053	0.087	0.069	0.053	0.087	SUBCLONAL	1	TRUE	0	0.924633515498065	1		607	390	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351439	89351439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	29	752	0	ENST00000301030.4:c.1511G>A	p.Gly504Glu	p.G504E	ENST00000301030	NM_001256183.1	504	gGg/gAg	9/13	0.924633515498065	1	FACETS	0.072	0.057	0.088	0.072	0.057	0.088	SUBCLONAL	1	TRUE	0	0.924633515498065	1		752	471	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857901	89857901	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs762502095	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	11	630	0	ENST00000389301.3:c.1269G>C	p.Gln423His	p.Q423H	ENST00000389301	NM_000135.2	423	caG/caC	14/43	0.924633515498065	0	FACETS		NA	1			1	NA	1	TRUE	0	0.924633515498065	0		630	64	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857903	89857903	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	11	638	0	ENST00000389301.3:c.1267C>G	p.Gln423Glu	p.Q423E	ENST00000389301	NM_000135.2	423	Cag/Gag	14/43	0.924633515498065	0	FACETS		NA	1			1	NA	1	TRUE	0	0.924633515498065	0		638	64	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935714	15935714	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	38	533	0	ENST00000268712.3:c.7219G>T	p.Ala2407Ser	p.A2407S	ENST00000268712	NM_006311.3	2407	Gcg/Tcg	46/46	0.924633515498065	1	FACETS	0.085	0.07	0.102	0.085	0.07	0.102	SUBCLONAL	1	TRUE	0	0.924633515498065	1		533	518	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15960901	15960901	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1343654466	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	16	433	0	ENST00000268712.3:c.6319G>T	p.Ala2107Ser	p.A2107S	ENST00000268712	NM_006311.3	2107	Gct/Tct	40/46	0.924633515498065	1	FACETS	0.064	0.047	0.085	0.064	0.047	0.085	SUBCLONAL	1	TRUE	0	0.924633515498065	1		433	290	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964943	15964943	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	31	719	0	ENST00000268712.3:c.5653T>G	p.Ser1885Ala	p.S1885A	ENST00000268712	NM_006311.3	1885	Tca/Gca	37/46	0.924633515498065	1	FACETS	0.103	0.083	0.125	0.103	0.083	0.125	SUBCLONAL	1	TRUE	0	0.924633515498065	1		719	351	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965437	15965437	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	14	470	0	ENST00000268712.3:c.5369C>G	p.Thr1790Ser	p.T1790S	ENST00000268712	NM_006311.3	1790	aCt/aGt	36/46	0.924633515498065	1	FACETS	0.064	0.046	0.086	0.064	0.046	0.086	SUBCLONAL	1	TRUE	0	0.924633515498065	1		470	255	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965519	15965519	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	14	394	0	ENST00000268712.3:c.5287A>G	p.Thr1763Ala	p.T1763A	ENST00000268712	NM_006311.3	1763	Act/Gct	36/46	0.924633515498065	1	FACETS	0.061	0.043	0.082	0.061	0.043	0.082	SUBCLONAL	1	TRUE	0	0.924633515498065	1		394	268	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973706	15973706	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	30	619	0	ENST00000268712.3:c.4286T>C	p.Val1429Ala	p.V1429A	ENST00000268712	NM_006311.3	1429	gTg/gCg	31/46	0.924633515498065	1	FACETS	0.07	0.056	0.087	0.07	0.056	0.087	SUBCLONAL	1	TRUE	0	0.924633515498065	1		619	495	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653120	29653121	+	missense_variant	Missense_Mutation	DNP	TG	TG	CA	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	17	431	1	ENST00000356175.3:c.5055_5056inv	p.Val1686Ile	p.V1686I	ENST00000356175	NM_000267.3	1685	ctTGtt/ctCAtt	36/57	0.924633515498065	1	FACETS	0.072	0.053	0.094	0.072	0.053	0.094	SUBCLONAL	1	TRUE	0	0.924633515498065	1		432	275	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687094	37687094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567586451	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	20	534	2	ENST00000447079.4:c.3998G>A	p.Arg1333His	p.R1333H	ENST00000447079	NM_015083.1	1333	cGt/cAt	14/14	0.924633515498065	1	FACETS	0.067	0.051	0.086	0.067	0.051	0.086	SUBCLONAL	1	TRUE	0	0.924633515498065	1		536	348	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687148	37687148	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1226061741	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	22	584	0	ENST00000447079.4:c.4052T>C	p.Ile1351Thr	p.I1351T	ENST00000447079	NM_015083.1	1351	aTt/aCt	14/14	0.924633515498065	1	FACETS	0.072	0.055	0.091	0.072	0.055	0.091	SUBCLONAL	1	TRUE	0	0.924633515498065	1		584	355	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687195	37687196	+	missense_variant	Missense_Mutation	DNP	GT	GT	AC	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	24	565	2	ENST00000447079.4:c.4099_4100inv	p.Val1367Thr	p.V1367T	ENST00000447079	NM_015083.1	1367	GTc/ACc	14/14	0.924633515498065	1	FACETS	0.077	0.06	0.096	0.077	0.06	0.096	SUBCLONAL	1	TRUE	0	0.924633515498065	1		567	364	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687234	37687234	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	28	614	0	ENST00000447079.4:c.4138C>G	p.Leu1380Val	p.L1380V	ENST00000447079	NM_015083.1	1380	Ctg/Gtg	14/14	0.924633515498065	1	FACETS	0.08	0.063	0.098	0.08	0.063	0.098	SUBCLONAL	1	TRUE	0	0.924633515498065	1		614	409	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687468	37687468	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	18	305	0	ENST00000447079.4:c.4372C>A	p.His1458Asn	p.H1458N	ENST00000447079	NM_015083.1	1458	Cac/Aac	14/14	0.924633515498065	1	FACETS	0.085	0.063	0.11	0.085	0.063	0.11	SUBCLONAL	1	TRUE	0	0.924633515498065	1		305	247	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687483	37687483	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs552842054	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	16	299	0	ENST00000447079.4:c.4387A>G	p.Thr1463Ala	p.T1463A	ENST00000447079	NM_015083.1	1463	Act/Gct	14/14	0.924633515498065	1	FACETS	0.085	0.063	0.112	0.085	0.063	0.112	SUBCLONAL	1	TRUE	0	0.924633515498065	1		299	218	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37865618	37865618	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	30	832	0	ENST00000269571.5:c.487T>C	p.Tyr163His	p.Y163H	ENST00000269571		163	Tac/Cac	4/27	0.924633515498065	1	FACETS	0.067	0.054	0.083	0.067	0.054	0.083	SUBCLONAL	1	TRUE	0	0.924633515498065	1		832	518	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37865645	37865645	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	32	769	0	ENST00000269571.5:c.514A>G	p.Ile172Val	p.I172V	ENST00000269571		172	Atc/Gtc	4/27	0.924633515498065	1	FACETS	0.078	0.063	0.095	0.078	0.063	0.095	SUBCLONAL	1	TRUE	0	0.924633515498065	1		769	476	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872088	37872089	+	missense_variant	Missense_Mutation	DNP	AT	AT	GC	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	38	939	2	ENST00000269571.5:c.1409_1410delinsGC	p.His470Arg	p.H470R	ENST00000269571		470	cAT/cGC	12/27	0.924633515498065	1	FACETS	0.066	0.054	0.08	0.066	0.054	0.08	SUBCLONAL	1	TRUE	0	0.924633515498065	1		941	668	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872093	37872093	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	38	921	0	ENST00000269571.5:c.1414A>G	p.Thr472Ala	p.T472A	ENST00000269571		472	Acc/Gcc	12/27	0.924633515498065	1	FACETS	0.066	0.054	0.079	0.066	0.054	0.079	SUBCLONAL	1	TRUE	0	0.924633515498065	1		921	673	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872097	37872097	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	40	927	0	ENST00000269571.5:c.1418A>G	p.His473Arg	p.H473R	ENST00000269571		473	cAc/cGc	12/27	0.924633515498065	1	FACETS	0.069	0.057	0.082	0.069	0.057	0.082	SUBCLONAL	1	TRUE	0	0.924633515498065	1		927	676	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872574	37872574	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377085949	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	28	628	0	ENST00000269571.5:c.1534C>T	p.His512Tyr	p.H512Y	ENST00000269571		512	Cac/Tac	13/27	0.924633515498065	1	FACETS	0.079	0.063	0.098	0.079	0.063	0.098	SUBCLONAL	1	TRUE	0	0.924633515498065	1		628	412	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872578	37872578	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	30	670	0	ENST00000269571.5:c.1538A>C	p.Gln513Pro	p.Q513P	ENST00000269571		513	cAg/cCg	13/27	0.924633515498065	1	FACETS	0.081	0.065	0.1	0.081	0.065	0.1	SUBCLONAL	1	TRUE	0	0.924633515498065	1		670	429	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872590	37872591	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	31	783	1	ENST00000269571.5:c.1550_1551delinsAT	p.Arg517His	p.R517H	ENST00000269571		517	cGA/cAT	13/27	0.924633515498065	1	FACETS	0.074	0.059	0.091	0.074	0.059	0.091	SUBCLONAL	1	TRUE	0	0.924633515498065	1		784	486	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873664	37873664	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	55	780	0	ENST00000269571.5:c.1829A>T	p.Tyr610Phe	p.Y610F	ENST00000269571		610	tAc/tTc	15/27	0.924633515498065	1	FACETS	0.105	0.089	0.122	0.105	0.089	0.122	SUBCLONAL	1	TRUE	0	0.924633515498065	1		780	611	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873683	37873684	+	missense_variant	Missense_Mutation	DNP	TC	TC	CG	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	44	785	1	ENST00000269571.5:c.1848_1849delinsCG	p.Pro617Ala	p.P617A	ENST00000269571		616	ttTCca/ttCGca	15/27	0.924633515498065	1	FACETS	0.089	0.074	0.106	0.089	0.074	0.106	SUBCLONAL	1	TRUE	0	0.924633515498065	1		786	572	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873699	37873699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766029214	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	28	775	1	ENST00000269571.5:c.1864G>A	p.Ala622Thr	p.A622T	ENST00000269571		622	Gca/Aca	15/27	0.924633515498065	1	FACETS	0.061	0.048	0.075	0.061	0.048	0.075	SUBCLONAL	1	TRUE	0	0.924633515498065	1		776	537	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246665	41246665	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	23	739	0	ENST00000357654.3:c.883G>C	p.Asp295His	p.D295H	ENST00000357654	NM_007294.3	295	Gac/Cac	10/23	0.924633515498065	1	FACETS	0.078	0.061	0.099	0.078	0.061	0.099	SUBCLONAL	1	TRUE	0	0.924633515498065	1		739	342	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55334146	55334146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	43	362	1	ENST00000284073.2:c.43G>A	p.Asp15Asn	p.D15N	ENST00000284073	NM_138962.2	15	Gac/Aac	1/14	0.924633515498065	1	FACETS	0.097	0.08	0.115	0.097	0.08	0.115	SUBCLONAL	1	TRUE	0	0.924633515498065	1		363	518	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436044	56436044	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs79309393	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	18	510	0	ENST00000407977.2:c.1093G>A	p.Ala365Thr	p.A365T	ENST00000407977		365	Gca/Aca	9/10	0.924633515498065	1	FACETS	0.064	0.048	0.083	0.064	0.048	0.083	SUBCLONAL	1	TRUE	0	0.924633515498065	1		510	328	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58711266	58711266	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	18	725	1	ENST00000305921.3:c.754A>T	p.Thr252Ser	p.T252S	ENST00000305921	NM_003620.3	252	Act/Tct	3/6	0.924633515498065	1	FACETS	0.066	0.05	0.086	0.066	0.05	0.086	SUBCLONAL	1	TRUE	0	0.924633515498065	1		726	315	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532990	63532990	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	28	677	0	ENST00000307078.5:c.1904A>C	p.His635Pro	p.H635P	ENST00000307078	NM_004655.3	635	cAt/cCt	7/11	0.924633515498065	1	FACETS	0.064	0.051	0.08	0.064	0.051	0.08	SUBCLONAL	1	TRUE	0	0.924633515498065	1		677	505	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533066	63533066	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	23	712	0	ENST00000307078.5:c.1828C>G	p.Arg610Gly	p.R610G	ENST00000307078	NM_004655.3	610	Cgg/Ggg	7/11	0.924633515498065	1	FACETS	0.059	0.045	0.075	0.059	0.045	0.075	SUBCLONAL	1	TRUE	0	0.924633515498065	1		712	454	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554036	63554036	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	22	646	0	ENST00000307078.5:c.703A>G	p.Thr235Ala	p.T235A	ENST00000307078	NM_004655.3	235	Act/Gct	2/11	0.924633515498065	1	FACETS	0.063	0.048	0.08	0.063	0.048	0.08	SUBCLONAL	1	TRUE	0	0.924633515498065	1		646	409	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120269	70120269	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	54	1045	0	ENST00000245479.2:c.1271A>G	p.Asn424Ser	p.N424S	ENST00000245479	NM_000346.3	424	aAc/aGc	3/3	0.924633515498065	1	FACETS	0.081	0.069	0.095	0.081	0.069	0.095	SUBCLONAL	1	TRUE	0	0.924633515498065	1		1045	775	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120343	70120343	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	44	1178	0	ENST00000245479.2:c.1345A>G	p.Ser449Gly	p.S449G	ENST00000245479	NM_000346.3	449	Agc/Ggc	3/3	0.924633515498065	1	FACETS	0.062	0.052	0.074	0.062	0.052	0.074	SUBCLONAL	1	TRUE	0	0.924633515498065	1		1178	823	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982572	10982572	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	17	79	0	ENST00000327064.4:c.194A>C	p.Asp65Ala	p.D65A	ENST00000327064	NM_199141.1	65	gAc/gCc	1/16	1	2	FACETS	0.108	0.08	0.142	0.108	0.08	0.142	SUBCLONAL	1	TRUE	1	0.924633515498065	2		79	339	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982574	10982574	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	22	79	0	ENST00000327064.4:c.196T>G	p.Ser66Ala	p.S66A	ENST00000327064	NM_199141.1	66	Tcg/Gcg	1/16	1	2	FACETS	0.145	0.112	0.183	0.145	0.112	0.183	SUBCLONAL	1	TRUE	1	0.924633515498065	2		79	329	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741856	40741857	+	missense_variant	Missense_Mutation	DNP	CG	CG	TT	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	68	696	2	ENST00000392038.2:c.1115_1116delinsAA	p.Thr372Lys	p.T372K	ENST00000392038	NM_001626.4	372	aCG/aAA	11/14	1	2	FACETS	0.142	0.123	0.163	0.142	0.123	0.163	SUBCLONAL	1	TRUE	1	0.924633515498065	2		698	1034	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082199	16082199	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs868623724	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	31	937	1	ENST00000281043.3:c.13T>A	p.Ser5Thr	p.S5T	ENST00000281043	NM_005378.4	5	Tcc/Acc	2/3	0.924633515498065	1	FACETS	0.058	0.047	0.072	0.058	0.047	0.072	SUBCLONAL	1	TRUE	0	0.924633515498065	1		938	619	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082383	16082383	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	49	882	0	ENST00000281043.3:c.197G>C	p.Gly66Ala	p.G66A	ENST00000281043	NM_005378.4	66	gGc/gCc	2/3	0.924633515498065	1	FACETS	0.088	0.074	0.104	0.088	0.074	0.104	SUBCLONAL	1	TRUE	0	0.924633515498065	1		882	646	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082388	16082388	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs767463815	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	44	865	0	ENST00000281043.3:c.202G>C	p.Ala68Pro	p.A68P	ENST00000281043	NM_005378.4	68	Gcg/Ccg	2/3	0.924633515498065	1	FACETS	0.083	0.069	0.099	0.083	0.069	0.099	SUBCLONAL	1	TRUE	0	0.924633515498065	1		865	614	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082400	16082400	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	34	856	0	ENST00000281043.3:c.214T>C	p.Ser72Pro	p.S72P	ENST00000281043	NM_005378.4	72	Tcc/Ccc	2/3	0.924633515498065	1	FACETS	0.063	0.051	0.077	0.063	0.051	0.077	SUBCLONAL	1	TRUE	0	0.924633515498065	1		856	627	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082413	16082413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750717149	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	39	855	0	ENST00000281043.3:c.227G>A	p.Ser76Asn	p.S76N	ENST00000281043	NM_005378.4	76	aGc/aAc	2/3	0.924633515498065	1	FACETS	0.07	0.057	0.084	0.07	0.057	0.084	SUBCLONAL	1	TRUE	0	0.924633515498065	1		855	648	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082419	16082419	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	35	867	0	ENST00000281043.3:c.233T>C	p.Val78Ala	p.V78A	ENST00000281043	NM_005378.4	78	gTc/gCc	2/3	0.924633515498065	1	FACETS	0.064	0.052	0.077	0.064	0.052	0.077	SUBCLONAL	1	TRUE	0	0.924633515498065	1		867	638	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082455	16082455	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	34	873	2	ENST00000281043.3:c.269G>A	p.Ser90Asn	p.S90N	ENST00000281043	NM_005378.4	90	aGc/aAc	2/3	0.924633515498065	1	FACETS	0.061	0.049	0.074	0.061	0.049	0.074	SUBCLONAL	1	TRUE	0	0.924633515498065	1		875	651	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457164	25457164	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs780666472	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	55	644	0	ENST00000264709.3:c.2723A>G	p.Tyr908Cys	p.Y908C	ENST00000264709	NM_175629.2	908	tAt/tGt	23/23	0.924633515498065	1	FACETS	0.1	0.085	0.116	0.1	0.085	0.116	SUBCLONAL	1	TRUE	0	0.924633515498065	1		644	641	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457176	25457176	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149095705	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	108	680	0	ENST00000264709.3:c.2711C>T	p.Pro904Leu	p.P904L	ENST00000264709	NM_175629.2	904	cCg/cTg	23/23	0.924633515498065	1	FACETS	0.18	0.161	0.2	0.18	0.161	0.2	SUBCLONAL	1	TRUE	0	0.924633515498065	1		680	697	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457233	25457233	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	92	643	0	ENST00000264709.3:c.2654G>C	p.Arg885Thr	p.R885T	ENST00000264709	NM_175629.2	885	aGg/aCg	23/23	0.924633515498065	1	FACETS	0.144	0.128	0.162	0.144	0.128	0.162	SUBCLONAL	1	TRUE	0	0.924633515498065	1		643	741	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457242	25457242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147001633	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	102	616	0	ENST00000264709.3:c.2645G>A	p.Arg882His	p.R882H	ENST00000264709	NM_175629.2	882	cGc/cAc	23/23	0.924633515498065	1	FACETS	0.164	0.146	0.182	0.164	0.146	0.182	SUBCLONAL	1	TRUE	0	0.924633515498065	1		616	725	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25458586	25458586	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	106	476	0	ENST00000264709.3:c.2587G>A	p.Glu863Lys	p.E863K	ENST00000264709	NM_175629.2	863	Gaa/Aaa	22/23	0.924633515498065	1	FACETS	0.296	0.267	0.327	0.296	0.267	0.327	SUBCLONAL	1	TRUE	0	0.924633515498065	1		476	416	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25458595	25458595	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs373014701	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	103	511	0	ENST00000264709.3:c.2578T>C	p.Trp860Arg	p.W860R	ENST00000264709	NM_175629.2	860	Tgg/Cgg	22/23	0.924633515498065	1	FACETS	0.269	0.241	0.297	0.269	0.241	0.297	SUBCLONAL	1	TRUE	0	0.924633515498065	1		511	446	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25458631	25458631	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	153	658	0	ENST00000264709.3:c.2542T>G	p.Phe848Val	p.F848V	ENST00000264709	NM_175629.2	848	Ttt/Gtt	22/23	0.924633515498065	1	FACETS	0.324	0.297	0.351	0.324	0.297	0.351	SUBCLONAL	1	TRUE	0	0.924633515498065	1		658	550	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25458689	25459711	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTGAACTAGATGAAGAGGAGAAAAGAGGAATAAGCACGAATTCATTCACCAGCCAACACTGGTCATGCGTCTACCAAATATGCCAGGTACTCGCCAAACCCTGACAGGGCCTGGTCCACCCAGGGGGCTGGGTATGGCTCTGAGTGAGCAGAGTTCGCAGGGCAGGAGCCTCCACAGACCCCACAGCCTCACTTTTCTTCCTACTTGGAGGTCACCTGGCCAATCTTAGATCCATCTAGCCACAGACTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCACCCAGGCTGGACTGCAGTGGTGCGATCTCAGCTCACTGTAACCTCCACCTCCCGGGTTCAAGCGATTCTAATGCCTCAGACTCCTGAGTAGCTGGGACTACAGGCGCCCGCCACCATGCCTGGCTAATTTTTATATTTTTAGTCAGACAGGGTTTCACCGTGTCGGCCAGGCTGGTCTCAAACTCCTGACCTCAGGTGATCCGCCTGCCTCGGCCTCCCAAAGTATTGGGATTATAGGCGTGAGCCACCGCACCCGGCCTAGCCACAGACTTTAGAAGTAGAAGCTGTAGCCACTGTACTTTCCAAGTCTTCCAAAGAATTAGTTCTTTCAGAGATGGAGTAACTTGTAGGCTAAAGGATGCCAAGTTACTGAGGGGCTCAAAGATGCCCTCGGAGCTGCCAGTGGTTCTGAATGCTGGAACCTGCTGACACAGAACCCAGTGCCCCAGGTAGTCACTCCGGGAGATTCCAGCTCCAGAGAGAAATGGAGCTTCCACATCACAGGAGGCTGCTTTGAGGGCTTTTGTAATAGGTTTTGGCCAAAAAATTTAAAAATGAAAAAAAAGCCACAGCACAACCAGGTCTTGGTAAAGACTCCTCAGTGTCTACCGGGGGTGATGGGCGACACTCACCAGGGAGGAAGGGCTGAAGGCCAGCAGCCCTGGGCCCTCCTCTGGCTGCCCTGCTGCATGACCCTGCACCGTCTCCTAAATTGCATTCTCCACACTAGCTGGAGA	GCTGAACTAGATGAAGAGGAGAAAAGAGGAATAAGCACGAATTCATTCACCAGCCAACACTGGTCATGCGTCTACCAAATATGCCAGGTACTCGCCAAACCCTGACAGGGCCTGGTCCACCCAGGGGGCTGGGTATGGCTCTGAGTGAGCAGAGTTCGCAGGGCAGGAGCCTCCACAGACCCCACAGCCTCACTTTTCTTCCTACTTGGAGGTCACCTGGCCAATCTTAGATCCATCTAGCCACAGACTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCACCCAGGCTGGACTGCAGTGGTGCGATCTCAGCTCACTGTAACCTCCACCTCCCGGGTTCAAGCGATTCTAATGCCTCAGACTCCTGAGTAGCTGGGACTACAGGCGCCCGCCACCATGCCTGGCTAATTTTTATATTTTTAGTCAGACAGGGTTTCACCGTGTCGGCCAGGCTGGTCTCAAACTCCTGACCTCAGGTGATCCGCCTGCCTCGGCCTCCCAAAGTATTGGGATTATAGGCGTGAGCCACCGCACCCGGCCTAGCCACAGACTTTAGAAGTAGAAGCTGTAGCCACTGTACTTTCCAAGTCTTCCAAAGAATTAGTTCTTTCAGAGATGGAGTAACTTGTAGGCTAAAGGATGCCAAGTTACTGAGGGGCTCAAAGATGCCCTCGGAGCTGCCAGTGGTTCTGAATGCTGGAACCTGCTGACACAGAACCCAGTGCCCCAGGTAGTCACTCCGGGAGATTCCAGCTCCAGAGAGAAATGGAGCTTCCACATCACAGGAGGCTGCTTTGAGGGCTTTTGTAATAGGTTTTGGCCAAAAAATTTAAAAATGAAAAAAAAGCCACAGCACAACCAGGTCTTGGTAAAGACTCCTCAGTGTCTACCGGGGGTGATGGGCGACACTCACCAGGGAGGAAGGGCTGAAGGCCAGCAGCCCTGGGCCCTCCTCTGGCTGCCCTGCTGCATGACCCTGCACCGTCTCCTAAATTGCATTCTCCACACTAGCTGGAGA	-	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	112	594	0	ENST00000264709.3:c.2478+94_2484del		p.X826_splice	ENST00000264709	NM_175629.2	826		22/23	0.924633515498065	1	FACETS	0.281	0.254	0.31	0.281	0.254	0.31	SUBCLONAL	1	TRUE	0	0.924633515498065	1		594	463	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25459816	25459816	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	160	597	0	ENST00000264709.3:c.2467A>T	p.Arg823Trp	p.R823W	ENST00000264709	NM_175629.2	823	Agg/Tgg	21/23	0.924633515498065	1	FACETS	0.266	0.244	0.288	0.266	0.244	0.288	SUBCLONAL	1	TRUE	0	0.924633515498065	1		597	700	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25462032	25462032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774100557	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	216	589	0	ENST00000264709.3:c.2375G>A	p.Arg792His	p.R792H	ENST00000264709	NM_175629.2	792	cGc/cAc	20/23	0.924633515498065	1	FACETS	0.354	0.33	0.379	0.354	0.33	0.379	SUBCLONAL	1	TRUE	0	0.924633515498065	1		589	709	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25462066	25462066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1305828292	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	250	577	0	ENST00000264709.3:c.2341G>A	p.Asp781Asn	p.D781N	ENST00000264709	NM_175629.2	781	Gat/Aat	20/23	0.924633515498065	1	FACETS	0.415	0.39	0.441	0.415	0.39	0.441	SUBCLONAL	1	TRUE	0	0.924633515498065	1		577	700	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25462075	25462075	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	202	573	0	ENST00000264709.3:c.2332G>A	p.Val778Met	p.V778M	ENST00000264709	NM_175629.2	778	Gtg/Atg	20/23	0.924633515498065	1	FACETS	0.359	0.334	0.384	0.359	0.334	0.384	SUBCLONAL	1	TRUE	0	0.924633515498065	1		573	655	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25462085	25463107	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CTACAAAACAGGAGACGGTTTGAAGATGAGCCAAGGAGGAGCATGAAACAGCGCCGGCATGCTGCTGGGGTCGAGCCTTAAAGCCTCAAAGCCTCTTACTTCTCTCTCAGGAGCCACACACTGGGCTAGCCTGCAGCCTCCAGGAGAAGCTGGAATTACACCTAGCCACATTCCACAAGCTGTCACTGGAACGTTCTAGATCAGCATTGTCCAAATGAACTTCTGCGATGGTGGGTTGTCCTCTACACTGTTCAATTCAGTGGCCACTAGCCCACTAGTACAGGTGGCTATTTTGTACCTAAAATGAGGCCAATGTGATTGAGGAGCTGAATGGTTAATGTTAATGTAAACAGCCGCATGTGGCTGGTGGCTACCATATTGCACAGTGCTGCTCTAGACTACCCAGAGGCTGGGAGAGCCCAGGCTCCAGCGAGTATGGGTGTGTTTACCATGAGCCCTGATTAGAACTCAAACAGACGCCTGCTCACACTTACAGTCAGAACACCAGCTCACAGTGTGACCCACCCCAAGACTCAGGAGCACAGGTGGGCTCAAGCTCCCAGAAGGGCCACTCCAAGCACGCCTCTGGCAGCAGAAGCCCTCTGCACGCGGCTCAGACTTGGCTCAGGGTTAAACGGGGACTCACATGATAAGGAATGAAAACTGAGCTAAGTCTTGTTTTCTTCTCAGGTGCCTGTCATGGTACCAGGGAGTGAGGATAGGCCCTTCTTGCTCAGGGAAAACTGATTTTGTCCTCTCAAAGATCCTGGTGTGTAACAAACACCATACAGAATACCCAACCCCAGGAGTCTGGCACCCCACCTGATTGAGTGACAGGTCCTTCAACCCCGGAGGTCCACACCCACAATGCCACCTCTTAGAGTGAGACCACTGGTTCTTTCCGAGGTAGGCCTCTAACCCTGCTTCCTCCCTTTCTATCCAGGAAGCCTGGGGCTTCCCAAACAGGCCCCTTGCAAAGCAGAAGTCACCAGTCCCCAGCTCCACAATGCAGATGAGACAGGA	CTACAAAACAGGAGACGGTTTGAAGATGAGCCAAGGAGGAGCATGAAACAGCGCCGGCATGCTGCTGGGGTCGAGCCTTAAAGCCTCAAAGCCTCTTACTTCTCTCTCAGGAGCCACACACTGGGCTAGCCTGCAGCCTCCAGGAGAAGCTGGAATTACACCTAGCCACATTCCACAAGCTGTCACTGGAACGTTCTAGATCAGCATTGTCCAAATGAACTTCTGCGATGGTGGGTTGTCCTCTACACTGTTCAATTCAGTGGCCACTAGCCCACTAGTACAGGTGGCTATTTTGTACCTAAAATGAGGCCAATGTGATTGAGGAGCTGAATGGTTAATGTTAATGTAAACAGCCGCATGTGGCTGGTGGCTACCATATTGCACAGTGCTGCTCTAGACTACCCAGAGGCTGGGAGAGCCCAGGCTCCAGCGAGTATGGGTGTGTTTACCATGAGCCCTGATTAGAACTCAAACAGACGCCTGCTCACACTTACAGTCAGAACACCAGCTCACAGTGTGACCCACCCCAAGACTCAGGAGCACAGGTGGGCTCAAGCTCCCAGAAGGGCCACTCCAAGCACGCCTCTGGCAGCAGAAGCCCTCTGCACGCGGCTCAGACTTGGCTCAGGGTTAAACGGGGACTCACATGATAAGGAATGAAAACTGAGCTAAGTCTTGTTTTCTTCTCAGGTGCCTGTCATGGTACCAGGGAGTGAGGATAGGCCCTTCTTGCTCAGGGAAAACTGATTTTGTCCTCTCAAAGATCCTGGTGTGTAACAAACACCATACAGAATACCCAACCCCAGGAGTCTGGCACCCCACCTGATTGAGTGACAGGTCCTTCAACCCCGGAGGTCCACACCCACAATGCCACCTCTTAGAGTGAGACCACTGGTTCTTTCCGAGGTAGGCCTCTAACCCTGCTTCCTCCCTTTCTATCCAGGAAGCCTGGGGCTTCCCAAACAGGCCCCTTGCAAAGCAGAAGTCACCAGTCCCCAGCTCCACAATGCAGATGAGACAGGA	-	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	214	546	0	ENST00000264709.3:c.2322+67_2325del		p.X774_splice	ENST00000264709	NM_175629.2	774			0.924633515498065	1	FACETS	0.392	0.366	0.418	0.392	0.366	0.418	SUBCLONAL	1	TRUE	0	0.924633515498065	1		546	635	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463179	25463179	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	213	531	0	ENST00000264709.3:c.2314T>A	p.Phe772Ile	p.F772I	ENST00000264709	NM_175629.2	772	Ttt/Att	19/23	0.924633515498065	1	FACETS	0.374	0.349	0.4	0.374	0.349	0.4	SUBCLONAL	1	TRUE	0	0.924633515498065	1		531	662	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463206	25463206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1369746569	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	220	595	0	ENST00000264709.3:c.2287G>A	p.Val763Ile	p.V763I	ENST00000264709	NM_175629.2	763	Gtt/Att	19/23	0.924633515498065	1	FACETS	0.366	0.342	0.391	0.366	0.342	0.391	SUBCLONAL	1	TRUE	0	0.924633515498065	1		595	699	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463236	25463236	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	157	564	0	ENST00000264709.3:c.2257T>C	p.Trp753Arg	p.W753R	ENST00000264709	NM_175629.2	753	Tgg/Cgg	19/23	0.924633515498065	1	FACETS	0.277	0.254	0.301	0.277	0.254	0.301	SUBCLONAL	1	TRUE	0	0.924633515498065	1		564	659	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463286	25463286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139293773	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	140	507	2	ENST00000264709.3:c.2207G>A	p.Arg736His	p.R736H	ENST00000264709	NM_175629.2	736	cGc/cAc	19/23	0.924633515498065	1	FACETS	0.276	0.252	0.301	0.276	0.252	0.301	SUBCLONAL	1	TRUE	0	0.924633515498065	1		509	590	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463536	25463536	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1418039680	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	54	620	0	ENST00000264709.3:c.2146G>A	p.Val716Ile	p.V716I	ENST00000264709	NM_175629.2	716	Gtc/Atc	18/23	0.924633515498065	1	FACETS	0.116	0.099	0.135	0.116	0.099	0.135	SUBCLONAL	1	TRUE	0	0.924633515498065	1		620	540	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463546	25463547	+	missense_variant	Missense_Mutation	DNP	GT	GT	AC	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	78	632	0	ENST00000264709.3:c.2135_2136inv	p.Asp712Gly	p.D712G	ENST00000264709	NM_175629.2	712	gAC/gGT	18/23	0.924633515498065	1	FACETS	0.159	0.14	0.18	0.159	0.14	0.18	SUBCLONAL	1	TRUE	0	0.924633515498065	1		632	569	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463579	25463579	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	78	549	0	ENST00000264709.3:c.2103C>G	p.Phe701Leu	p.F701L	ENST00000264709	NM_175629.2	701	ttC/ttG	18/23	0.924633515498065	1	FACETS	0.173	0.152	0.196	0.173	0.152	0.196	SUBCLONAL	1	TRUE	0	0.924633515498065	1		549	523	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464514	25464515	+	missense_variant	Missense_Mutation	DNP	CA	CA	TG	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	88	786	3	ENST00000264709.3:c.1998_1999inv	p.Glu667Lys	p.E667K	ENST00000264709	NM_175629.2	666	tgTGag/tgCAag	17/23	0.924633515498065	1	FACETS	0.15	0.133	0.169	0.15	0.133	0.169	SUBCLONAL	1	TRUE	0	0.924633515498065	1		789	682	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464523	25464524	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AG	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	86	795	4	ENST00000264709.3:c.1989_1990delinsCT	p.Glu664Ter	p.E664*	ENST00000264709	NM_175629.2	663	tcGGag/tcCTag	17/23	0.924633515498065	1	FACETS	0.145	0.128	0.163	0.145	0.128	0.163	SUBCLONAL	1	TRUE	0	0.924633515498065	1		799	690	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464538	25464538	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755982635	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	67	826	1	ENST00000264709.3:c.1975C>T	p.Arg659Cys	p.R659C	ENST00000264709	NM_175629.2	659	Cgc/Tgc	17/23	0.924633515498065	1	FACETS	0.112	0.096	0.128	0.112	0.096	0.128	SUBCLONAL	1	TRUE	0	0.924633515498065	1		827	698	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466831	25466832	+	missense_variant	Missense_Mutation	DNP	TG	TG	CA	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	94	632	1	ENST00000264709.3:c.1871_1872inv	p.Pro624Leu	p.P624L	ENST00000264709	NM_175629.2	624	cCA/cTG	16/23	0.924633515498065	1	FACETS	0.209	0.186	0.233	0.209	0.186	0.233	SUBCLONAL	1	TRUE	0	0.924633515498065	1		633	523	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466832	25466832	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	94	618	0	ENST00000264709.3:c.1871C>T	p.Pro624Leu	p.P624L	ENST00000264709	NM_175629.2	624	cCa/cTa	16/23	0.924633515498065	1	FACETS	0.211	0.188	0.235	0.211	0.188	0.235	SUBCLONAL	1	TRUE	0	0.924633515498065	1		618	518	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466851	25467022	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTAAGCAGTGAGCACAACAGGTCAGATGCAGGCCCAGCGGTGTCCCAAGCTCCCACCCAGCGCTGGCCCTCCAGCCAGGCTCCTAGACCCACACACCCTGCGCACAGCTCAGGCCCCACAACCAAGGCTCAGCCAAGGGAGCTCGAGACCGCGCCCCAGGCCCAGCACTCA	CCTAAGCAGTGAGCACAACAGGTCAGATGCAGGCCCAGCGGTGTCCCAAGCTCCCACCCAGCGCTGGCCCTCCAGCCAGGCTCCTAGACCCACACACCCTGCGCACAGCTCAGGCCCCACAACCAAGGCTCAGCCAAGGGAGCTCGAGACCGCGCCCCAGGCCCAGCACTCA	-	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	20	567	0	ENST00000264709.3:c.1851+2_1852del		p.X617_splice	ENST00000264709	NM_175629.2	617		16/23	0.924633515498065	1	FACETS	0.06	0.045	0.077	0.06	0.045	0.077	SUBCLONAL	1	TRUE	0	0.924633515498065	1		567	390	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467078	25467078	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	78	773	0	ENST00000264709.3:c.1797G>C	p.Glu599Asp	p.E599D	ENST00000264709	NM_175629.2	599	gaG/gaC	15/23	0.924633515498065	1	FACETS	0.123	0.107	0.139	0.123	0.107	0.139	SUBCLONAL	1	TRUE	0	0.924633515498065	1		773	739	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467171	25467183	+	frameshift_variant	Frame_Shift_Ins	INS	CCCCACCAAGAGG	CCCCACCAAGAGG	GGCCCACTAAGAGA	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	26	638	2	ENST00000264709.3:c.1692_1704delinsTCTCTTAGTGGGCC	p.Ala571GlyfsTer7	p.A571Gfs*7	ENST00000264709	NM_175629.2	564	gaCCTCTTGGTGGGG/gaTCTCTTAGTGGGCC	15/23	0.924633515498065	1	FACETS	0.068	0.053	0.084	0.068	0.053	0.084	SUBCLONAL	1	TRUE	0	0.924633515498065	1		640	447	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469576	25469576	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	189	841	0	ENST00000264709.3:c.1192G>T	p.Ala398Ser	p.A398S	ENST00000264709	NM_175629.2	398	Gcc/Tcc	10/23	0.924633515498065	1	FACETS	0.258	0.239	0.279	0.258	0.239	0.279	SUBCLONAL	1	TRUE	0	0.924633515498065	1		841	851	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469611	25469611	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	192	750	0	ENST00000264709.3:c.1157T>C	p.Val386Ala	p.V386A	ENST00000264709	NM_175629.2	386	gTg/gCg	10/23	0.924633515498065	1	FACETS	0.271	0.251	0.292	0.271	0.251	0.292	SUBCLONAL	1	TRUE	0	0.924633515498065	1		750	823	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470512	25470512	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	195	802	0	ENST00000264709.3:c.962C>G	p.Ala321Gly	p.A321G	ENST00000264709	NM_175629.2	321	gCa/gGa	8/23	0.924633515498065	1	FACETS	0.235	0.217	0.254	0.235	0.217	0.254	SUBCLONAL	1	TRUE	0	0.924633515498065	1		802	965	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470516	25470516	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs778270132	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	204	831	2	ENST00000264709.3:c.958C>T	p.Arg320Ter	p.R320*	ENST00000264709	NM_175629.2	320	Cga/Tga	8/23	0.924633515498065	1	FACETS	0.246	0.228	0.265	0.246	0.228	0.265	SUBCLONAL	1	TRUE	0	0.924633515498065	1		833	965	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470572	25470572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	69	874	3	ENST00000264709.3:c.902G>A	p.Arg301Gln	p.R301Q	ENST00000264709	NM_175629.2	301	cGg/cAg	8/23	0.924633515498065	1	FACETS	0.082	0.071	0.094	0.082	0.071	0.094	SUBCLONAL	1	TRUE	0	0.924633515498065	1		877	977	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470574	25470575	+	missense_variant	Missense_Mutation	DNP	CA	CA	AC	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	299	874	1	ENST00000264709.3:c.899_900delinsGT	p.Leu300Arg	p.L300R	ENST00000264709	NM_175629.2	300	cTG/cGT	8/23	0.924633515498065	1	FACETS	0.364	0.343	0.385	0.364	0.343	0.385	SUBCLONAL	1	TRUE	0	0.924633515498065	1		875	956	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470599	25470599	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs777306476	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	186	780	0	ENST00000264709.3:c.875T>C	p.Ile292Thr	p.I292T	ENST00000264709	NM_175629.2	292	aTt/aCt	8/23	0.924633515498065	1	FACETS	0.271	0.25	0.292	0.271	0.25	0.292	SUBCLONAL	1	TRUE	0	0.924633515498065	1		780	798	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470941	25470942	+	missense_variant	Missense_Mutation	DNP	CA	CA	TG	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	103	810	1	ENST00000264709.3:c.819_820inv	p.Ala274Thr	p.A274T	ENST00000264709	NM_175629.2	273	aaTGcc/aaCAcc	7/23	0.924633515498065	1	FACETS	0.15	0.134	0.167	0.15	0.134	0.167	SUBCLONAL	1	TRUE	0	0.924633515498065	1		811	800	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470962	25470962	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	148	795	0	ENST00000264709.3:c.799T>G	p.Ser267Ala	p.S267A	ENST00000264709	NM_175629.2	267	Tcc/Gcc	7/23	0.924633515498065	1	FACETS	0.211	0.193	0.231	0.211	0.193	0.231	SUBCLONAL	1	TRUE	0	0.924633515498065	1		795	815	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471007	25471008	+	missense_variant	Missense_Mutation	DNP	CA	CA	TG	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	224	814	1	ENST00000264709.3:c.753_754inv	p.Asp252Asn	p.D252N	ENST00000264709	NM_175629.2	251	acTGac/acCAac	7/23	0.924633515498065	1	FACETS	0.295	0.275	0.316	0.295	0.275	0.316	SUBCLONAL	1	TRUE	0	0.924633515498065	1		815	883	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471022	25471023	+	missense_variant	Missense_Mutation	DNP	CA	CA	TT	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	231	822	1	ENST00000264709.3:c.738_739delinsAA	p.Val247Met	p.V247M	ENST00000264709	NM_175629.2	246	gcTGtg/gcAAtg	7/23	0.924633515498065	1	FACETS	0.304	0.284	0.325	0.304	0.284	0.325	SUBCLONAL	1	TRUE	0	0.924633515498065	1		823	883	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471058	25471059	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AG	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	172	957	3	ENST00000264709.3:c.702_703delinsCT	p.Glu235Ter	p.E235*	ENST00000264709	NM_175629.2	234	ggGGag/ggCTag	7/23	0.924633515498065	1	FACETS	0.245	0.226	0.266	0.245	0.226	0.266	SUBCLONAL	1	TRUE	0	0.924633515498065	1		960	815	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471064	25471064	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	174	962	0	ENST00000264709.3:c.697C>T	p.Pro233Ser	p.P233S	ENST00000264709	NM_175629.2	233	Ccc/Tcc	7/23	0.924633515498065	1	FACETS	0.25	0.23	0.27	0.25	0.23	0.27	SUBCLONAL	1	TRUE	0	0.924633515498065	1		962	811	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471093	25471093	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	167	886	0	ENST00000264709.3:c.668G>T	p.Gly223Val	p.G223V	ENST00000264709	NM_175629.2	223	gGa/gTa	7/23	0.924633515498065	1	FACETS	0.277	0.255	0.3	0.277	0.255	0.3	SUBCLONAL	1	TRUE	0	0.924633515498065	1		886	701	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471097	25471098	+	missense_variant	Missense_Mutation	DNP	CA	CA	TG	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	138	859	3	ENST00000264709.3:c.663_664inv	p.Ala222Thr	p.A222T	ENST00000264709	NM_175629.2	221	atTGca/atCAca	7/23	0.924633515498065	1	FACETS	0.24	0.218	0.262	0.24	0.218	0.262	SUBCLONAL	1	TRUE	0	0.924633515498065	1		862	669	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471109	25471110	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	113	768	0	ENST00000264709.3:c.651dup	p.Ala218SerfsTer35	p.A218Sfs*35	ENST00000264709	NM_175629.2	217	-/A	7/23	0.924633515498065	1	FACETS	0.227	0.204	0.25	0.227	0.204	0.25	SUBCLONAL	1	TRUE	0	0.924633515498065	1		768	580	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523091	25523091	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	34	662	0	ENST00000264709.3:c.94C>G	p.Pro32Ala	p.P32A	ENST00000264709	NM_175629.2	32	Ccg/Gcg	3/23	0.924633515498065	1	FACETS	0.062	0.05	0.076	0.062	0.05	0.076	SUBCLONAL	1	TRUE	0	0.924633515498065	1		662	637	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523110	25523110	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	27	559	0	ENST00000264709.3:c.75C>G	p.Asp25Glu	p.D25E	ENST00000264709	NM_175629.2	25	gaC/gaG	3/23	0.924633515498065	1	FACETS	0.064	0.05	0.08	0.064	0.05	0.08	SUBCLONAL	1	TRUE	0	0.924633515498065	1		559	491	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25536853	25536853	+	start_lost	Translation_Start_Site	SNP	T	T	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	37	733	0	ENST00000264709.3:c.1A>C	p.Met1?	p.M1?	ENST00000264709	NM_175629.2	1	Atg/Ctg	2/23	0.924633515498065	1	FACETS	0.074	0.06	0.089	0.074	0.06	0.089	SUBCLONAL	1	TRUE	0	0.924633515498065	1		733	581	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965935	25965935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749408482	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	28	828	1	ENST00000435504.4:c.3271G>A	p.Ala1091Thr	p.A1091T	ENST00000435504		1091	Gct/Act	13/13	0.924633515498065	1	FACETS	0.064	0.051	0.08	0.064	0.051	0.08	SUBCLONAL	1	TRUE	0	0.924633515498065	1		829	507	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966924	25966931	+	protein_altering_variant	In_Frame_Del	DEL	CTTGGGGT	CTTGGGGT	TCTGG	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	32	759	2	ENST00000435504.4:c.2275_2282delinsCCAGA	p.Thr759_Ser761delinsProAsp	p.T759_S761delinsPD	ENST00000435504		759	ACCCCAAGc/CCAGAc	13/13	0.924633515498065	1	FACETS	0.065	0.052	0.079	0.065	0.052	0.079	SUBCLONAL	1	TRUE	0	0.924633515498065	1		761	573	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967039	25967047	+	missense_variant	Missense_Mutation	ONP	TTTCACTGA	TTTCACTGA	GTGCGTCAC	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	27	762	2	ENST00000435504.4:c.2159_2167delinsGTGACGCAC	p.Val720_Thr723delinsGlyAspAlaPro	p.V720_T723delinsGDAP	ENST00000435504		720	gTCAGTGAAAct/gGTGACGCACct	13/13	0.924633515498065	1	FACETS	0.059	0.046	0.073	0.059	0.046	0.073	SUBCLONAL	1	TRUE	0	0.924633515498065	1		764	533	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967059	25967059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	25	697	1	ENST00000435504.4:c.2147G>A	p.Gly716Asp	p.G716D	ENST00000435504		716	gGc/gAc	13/13	0.924633515498065	1	FACETS	0.059	0.046	0.074	0.059	0.046	0.074	SUBCLONAL	1	TRUE	0	0.924633515498065	1		698	490	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967084	25967084	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	22	641	1	ENST00000435504.4:c.2122C>A	p.Gln708Lys	p.Q708K	ENST00000435504		708	Cag/Aag	13/13	0.924633515498065	1	FACETS	0.06	0.046	0.076	0.06	0.046	0.076	SUBCLONAL	1	TRUE	0	0.924633515498065	1		642	430	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967156	25967156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201808592	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	31	513	1	ENST00000435504.4:c.2050G>A	p.Ala684Thr	p.A684T	ENST00000435504		684	Gcc/Acc	13/13	0.924633515498065	1	FACETS	0.107	0.086	0.13	0.107	0.086	0.13	SUBCLONAL	1	TRUE	0	0.924633515498065	1		514	338	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967160	25967161	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCG	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	24	505	0	ENST00000435504.4:c.2045_2046insCGC	p.Ala684dup	p.A684dup	ENST00000435504		684	gca/gcCGCa	13/13	0.924633515498065	1	FACETS	0.086	0.067	0.108	0.086	0.067	0.108	SUBCLONAL	1	TRUE	0	0.924633515498065	1		505	325	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451875	29451875	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	32	798	0	ENST00000389048.3:c.2690A>T	p.Gln897Leu	p.Q897L	ENST00000389048	NM_004304.4	897	cAg/cTg	16/29	0.924633515498065	1	FACETS	0.076	0.061	0.093	0.076	0.061	0.093	SUBCLONAL	1	TRUE	0	0.924633515498065	1		798	489	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451891	29451891	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	33	817	0	ENST00000389048.3:c.2674G>T	p.Ala892Ser	p.A892S	ENST00000389048	NM_004304.4	892	Gcc/Tcc	16/29	0.924633515498065	1	FACETS	0.077	0.062	0.094	0.077	0.062	0.094	SUBCLONAL	1	TRUE	0	0.924633515498065	1		817	496	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474001	29474001	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	31	858	0	ENST00000389048.3:c.2174T>C	p.Ile725Thr	p.I725T	ENST00000389048	NM_004304.4	725	aTc/aCc	12/29	0.924633515498065	1	FACETS	0.064	0.051	0.078	0.064	0.051	0.078	SUBCLONAL	1	TRUE	0	0.924633515498065	1		858	566	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474037	29474037	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	31	940	0	ENST00000389048.3:c.2138A>T	p.Glu713Val	p.E713V	ENST00000389048	NM_004304.4	713	gAg/gTg	12/29	0.924633515498065	1	FACETS	0.064	0.051	0.079	0.064	0.051	0.079	SUBCLONAL	1	TRUE	0	0.924633515498065	1		940	561	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213012	39213013	+	missense_variant	Missense_Mutation	DNP	TG	TG	CA	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	30	1095	0	ENST00000402219.2:c.3954_3955inv	p.Met1319Val	p.M1319V	ENST00000402219	NM_005633.3	1318	tcCAtg/tcTGtg	23/23	0.924633515498065	1	FACETS	0.059	0.047	0.073	0.059	0.047	0.073	SUBCLONAL	1	TRUE	0	0.924633515498065	1		1095	587	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018065	48018066	+	inframe_insertion,splice_region_variant	In_Frame_Ins	INS	-	-	TTC	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	20	667	0	ENST00000234420.5:c.262_263insCTT	p.Ser87dup	p.S87dup	ENST00000234420	NM_000179.2	87	agt/agTTCt		0.924633515498065	1	FACETS	0.064	0.048	0.082	0.064	0.048	0.082	SUBCLONAL	1	TRUE	0	0.924633515498065	1		667	366	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033968	48033968	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	20	533	0	ENST00000234420.5:c.4052A>C	p.His1351Pro	p.H1351P	ENST00000234420	NM_000179.2	1351	cAt/cCt	10/10	0.924633515498065	1	FACETS	0.114	0.087	0.145	0.114	0.087	0.145	SUBCLONAL	1	TRUE	0	0.924633515498065	1		533	204	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033999	48034002	+	stop_retained_variant,3_prime_UTR_variant	Silent	DEL	GACT	GACT	-	rs765313977	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	15	519	0	ENST00000234420.5:c.*4_*7del			ENST00000234420	NM_000179.2	1361		10/10	0.924633515498065	1	FACETS	0.089	0.065	0.118	0.089	0.065	0.118	SUBCLONAL	1	TRUE	0	0.924633515498065	1		519	195	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881569	111881569	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	30	748	0	ENST00000393256.3:c.247A>G	p.Met83Val	p.M83V	ENST00000393256	NM_006538.4	83	Atg/Gtg	2/4	0.924633515498065	1	FACETS	0.07	0.056	0.086	0.07	0.056	0.086	SUBCLONAL	1	TRUE	0	0.924633515498065	1		748	498	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096502	178096502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	11	462	2	ENST00000397062.3:c.829G>A	p.Val277Ile	p.V277I	ENST00000397062	NM_006164.4	277	Gtc/Atc	5/5	0.924633515498065	1	FACETS	0.058	0.04	0.081	0.058	0.04	0.081	SUBCLONAL	1	TRUE	0	0.924633515498065	1		464	219	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593492	215593492	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253880	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	18	359	0	ENST00000260947.4:c.2242G>A	p.Glu748Lys	p.E748K	ENST00000260947	NM_000465.2	748	Gag/Aag	11/11	0.924633515498065	1	FACETS	0.082	0.061	0.106	0.082	0.061	0.106	SUBCLONAL	1	TRUE	0	0.924633515498065	1		359	255	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593501	215593501	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs771109295	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	16	398	0	ENST00000260947.4:c.2233T>C	p.Tyr745His	p.Y745H	ENST00000260947	NM_000465.2	745	Tat/Cat	11/11	0.924633515498065	1	FACETS	0.071	0.052	0.094	0.071	0.052	0.094	SUBCLONAL	1	TRUE	0	0.924633515498065	1		398	262	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593506	215593506	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1395245809	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	18	390	0	ENST00000260947.4:c.2228G>C	p.Cys743Ser	p.C743S	ENST00000260947	NM_000465.2	743	tGt/tCt	11/11	0.924633515498065	1	FACETS	0.079	0.059	0.102	0.079	0.059	0.102	SUBCLONAL	1	TRUE	0	0.924633515498065	1		390	266	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593630	215593630	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782415	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	28	434	0	ENST00000260947.4:c.2104A>G	p.Ile702Val	p.I702V	ENST00000260947	NM_000465.2	702	Atc/Gtc	11/11	0.924633515498065	1	FACETS	0.084	0.066	0.103	0.084	0.066	0.103	SUBCLONAL	1	TRUE	0	0.924633515498065	1		434	389	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593641	215593641	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	29	468	0	ENST00000260947.4:c.2093G>C	p.Gly698Ala	p.G698A	ENST00000260947	NM_000465.2	698	gGt/gCt	11/11	0.924633515498065	1	FACETS	0.089	0.071	0.109	0.089	0.071	0.109	SUBCLONAL	1	TRUE	0	0.924633515498065	1		468	379	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593696	215593697	+	missense_variant	Missense_Mutation	DNP	AC	AC	CA	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	15	429	2	ENST00000260947.4:c.2037_2038delinsTG	p.Leu679_Trp680delinsPheGly	p.L679_W680delinsFG	ENST00000260947	NM_000465.2	679	ttGTgg/ttTGgg	11/11	0.924633515498065	1	FACETS	0.066	0.048	0.088	0.066	0.048	0.088	SUBCLONAL	1	TRUE	0	0.924633515498065	1		431	264	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225338988	225338988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759758641	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	46	644	0	ENST00000264414.4:c.2281C>T	p.Arg761Cys	p.R761C	ENST00000264414	NM_003590.4	761	Cgc/Tgc	16/16	0.924633515498065	1	FACETS	0.195	0.165	0.228	0.195	0.165	0.228	SUBCLONAL	1	TRUE	0	0.924633515498065	1		644	274	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339038	225339038	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	30	665	0	ENST00000264414.4:c.2231G>A	p.Arg744His	p.R744H	ENST00000264414	NM_003590.4	744	cGt/cAt	16/16	0.924633515498065	1	FACETS	0.134	0.108	0.163	0.134	0.108	0.163	SUBCLONAL	1	TRUE	0	0.924633515498065	1		665	260	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339057	225339057	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	24	580	0	ENST00000264414.4:c.2212C>A	p.Pro738Thr	p.P738T	ENST00000264414	NM_003590.4	738	Cca/Aca	16/16	0.924633515498065	1	FACETS	0.121	0.095	0.151	0.121	0.095	0.151	SUBCLONAL	1	TRUE	0	0.924633515498065	1		580	231	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339064	225339064	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	20	544	0	ENST00000264414.4:c.2205A>C	p.Leu735Phe	p.L735F	ENST00000264414	NM_003590.4	735	ttA/ttC	16/16	0.924633515498065	1	FACETS	0.106	0.081	0.135	0.106	0.081	0.135	SUBCLONAL	1	TRUE	0	0.924633515498065	1		544	219	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339081	225339081	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	13	464	0	ENST00000264414.4:c.2188T>G	p.Leu730Val	p.L730V	ENST00000264414	NM_003590.4	730	Ttg/Gtg	16/16	0.924633515498065	1	FACETS	0.087	0.062	0.117	0.087	0.062	0.117	SUBCLONAL	1	TRUE	0	0.924633515498065	1		464	174	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342960	225342960	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	43	751	0	ENST00000264414.4:c.2132T>C	p.Met711Thr	p.M711T	ENST00000264414	NM_003590.4	711	aTg/aCg	15/16	0.924633515498065	1	FACETS	0.126	0.105	0.149	0.126	0.105	0.149	SUBCLONAL	1	TRUE	0	0.924633515498065	1		751	396	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342970	225342971	+	missense_variant	Missense_Mutation	DNP	CT	CT	GG	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	62	793	0	ENST00000264414.4:c.2121_2122delinsCC	p.Val708Leu	p.V708L	ENST00000264414	NM_003590.4	707	atAGtg/atCCtg	15/16	0.924633515498065	1	FACETS	0.175	0.151	0.201	0.175	0.151	0.201	SUBCLONAL	1	TRUE	0	0.924633515498065	1		793	412	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346617	225346617	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	16	523	0	ENST00000264414.4:c.2021T>C	p.Ile674Thr	p.I674T	ENST00000264414	NM_003590.4	674	aTt/aCt	14/16	0.924633515498065	1	FACETS	0.08	0.058	0.105	0.08	0.058	0.105	SUBCLONAL	1	TRUE	0	0.924633515498065	1		523	234	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346633	225346633	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	30	575	0	ENST00000264414.4:c.2005C>G	p.Leu669Val	p.L669V	ENST00000264414	NM_003590.4	669	Cta/Gta	14/16	0.924633515498065	1	FACETS	0.131	0.105	0.159	0.131	0.105	0.159	SUBCLONAL	1	TRUE	0	0.924633515498065	1		575	267	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346661	225346691	+	missense_variant	Missense_Mutation	ONP	AAATATATGACCATTTTCTATTTCCTTTGAT	AAATATATGACCATTTTCTATTTCCTTTGAT	GAATCTGTGGCCATTTTCTGTTCCCTTGGAC	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	64	637	2	ENST00000264414.4:c.1947_1977delinsGTCCAAGGGAACAGAAAATGGCCACAGATTC	p.Glu652_Ile658delinsGlyThrGluAsnGlyHisArg	p.E652_I658delinsGTENGHR	ENST00000264414	NM_003590.4	649	aaATCAAAGGAAATAGAAAATGGTCATATATTT/aaGTCCAAGGGAACAGAAAATGGCCACAGATTC	14/16	0.924633515498065	1	FACETS	0.246	0.214	0.279	0.246	0.214	0.279	SUBCLONAL	1	TRUE	0	0.924633515498065	1		639	303	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346755	225346755	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	56	657	0	ENST00000264414.4:c.1883T>G	p.Val628Gly	p.V628G	ENST00000264414	NM_003590.4	628	gTt/gGt	14/16	0.924633515498065	1	FACETS	0.223	0.192	0.256	0.223	0.192	0.256	SUBCLONAL	1	TRUE	0	0.924633515498065	1		657	292	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661377	227661377	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	26	687	0	ENST00000305123.5:c.2078C>G	p.Thr693Ser	p.T693S	ENST00000305123	NM_005544.2	693	aCc/aGc	1/2	0.924633515498065	1	FACETS	0.071	0.056	0.088	0.071	0.056	0.088	SUBCLONAL	1	TRUE	0	0.924633515498065	1		687	427	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661417	227661417	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	26	628	0	ENST00000305123.5:c.2038A>G	p.Ser680Gly	p.S680G	ENST00000305123	NM_005544.2	680	Agc/Ggc	1/2	0.924633515498065	1	FACETS	0.074	0.058	0.093	0.074	0.058	0.093	SUBCLONAL	1	TRUE	0	0.924633515498065	1		628	406	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661447	227661448	+	missense_variant	Missense_Mutation	DNP	CA	CA	TG	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	22	714	0	ENST00000305123.5:c.2007_2008inv	p.Gly670Ser	p.G670S	ENST00000305123	NM_005544.2	669	ggTGgc/ggCAgc	1/2	0.924633515498065	1	FACETS	0.06	0.046	0.076	0.06	0.046	0.076	SUBCLONAL	1	TRUE	0	0.924633515498065	1		714	428	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663435	227663435	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	17	422	0	ENST00000305123.5:c.20G>C	p.Ser7Thr	p.S7T	ENST00000305123	NM_005544.2	7	aGc/aCc	1/2	0.924633515498065	1	FACETS	0.064	0.048	0.084	0.064	0.048	0.084	SUBCLONAL	1	TRUE	0	0.924633515498065	1		422	307	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164761	36164761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	52	867	0	ENST00000300305.3:c.1114G>A	p.Gly372Ser	p.G372S	ENST00000300305		372	Ggc/Agc	8/8	0.924633515498065	1	FACETS	0.077	0.065	0.091	0.077	0.065	0.091	SUBCLONAL	1	TRUE	0	0.924633515498065	1		867	782	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817448	39817449	+	missense_variant	Missense_Mutation	DNP	TG	TG	CA	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	30	608	0	ENST00000288319.7:c.114_115inv	p.Ser39Gly	p.S39G	ENST00000288319	NM_182918.3	38	tcCAgc/tcTGgc	2/10	0.924633515498065	1	FACETS	0.073	0.058	0.089	0.073	0.058	0.089	SUBCLONAL	1	TRUE	0	0.924633515498065	1		608	481	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817467	39817467	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	25	644	0	ENST00000288319.7:c.96G>C	p.Glu32Asp	p.E32D	ENST00000288319	NM_182918.3	32	gaG/gaC	2/10	0.924633515498065	1	FACETS	0.061	0.047	0.076	0.061	0.047	0.076	SUBCLONAL	1	TRUE	0	0.924633515498065	1		644	477	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288438	21288438	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	34	747	0	ENST00000354336.3:c.683C>A	p.Thr228Asn	p.T228N	ENST00000354336	NM_005207.3	228	aCc/aAc	2/3	0.924633515498065	1	FACETS	0.067	0.054	0.082	0.067	0.054	0.082	SUBCLONAL	1	TRUE	0	0.924633515498065	1		747	587	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29090062	29090063	+	missense_variant	Missense_Mutation	DNP	TG	TG	CA	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	30	259	1	ENST00000328354.6:c.1418_1419inv	p.Ala473Val	p.A473V	ENST00000328354	NM_007194.3	473	gCA/gTG	13/15	0.924633515498065	1	FACETS	0.159	0.128	0.193	0.159	0.128	0.193	SUBCLONAL	1	TRUE	0	0.924633515498065	1		260	220	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29090079	29090079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660084	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	27	239	0	ENST00000328354.6:c.1402G>A	p.Val468Ile	p.V468I	ENST00000328354	NM_007194.3	468	Gta/Ata	13/15	0.924633515498065	1	FACETS	0.173	0.139	0.212	0.173	0.139	0.212	SUBCLONAL	1	TRUE	0	0.924633515498065	1		239	181	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513542	41513543	+	missense_variant	Missense_Mutation	DNP	AG	AG	CA	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	23	598	0	ENST00000263253.7:c.446_447delinsCA	p.Gln149Pro	p.Q149P	ENST00000263253	NM_001429.3	149	cAG/cCA	2/31	0.924633515498065	1	FACETS	0.07	0.054	0.088	0.07	0.054	0.088	SUBCLONAL	1	TRUE	0	0.924633515498065	1		598	383	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513704	41513705	+	missense_variant	Missense_Mutation	DNP	AG	AG	CT	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	22	668	0	ENST00000263253.7:c.608_609inv	p.Gln203Pro	p.Q203P	ENST00000263253	NM_001429.3	203	cAG/cCT	2/31	0.924633515498065	1	FACETS	0.06	0.046	0.077	0.06	0.046	0.077	SUBCLONAL	1	TRUE	0	0.924633515498065	1		668	425	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523546	41523546	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	28	635	0	ENST00000263253.7:c.962A>C	p.Gln321Pro	p.Q321P	ENST00000263253	NM_001429.3	321	cAa/cCa	4/31	0.924633515498065	1	FACETS	0.062	0.049	0.077	0.062	0.049	0.077	SUBCLONAL	1	TRUE	0	0.924633515498065	1		635	524	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527595	41527595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	21	502	0	ENST00000263253.7:c.1486C>T	p.Pro496Ser	p.P496S	ENST00000263253	NM_001429.3	496	Cct/Tct	6/31	0.924633515498065	1	FACETS	0.059	0.045	0.075	0.059	0.045	0.075	SUBCLONAL	1	TRUE	0	0.924633515498065	1		502	416	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533685	41533685	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1481865764	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	24	585	0	ENST00000263253.7:c.1651C>G	p.Pro551Ala	p.P551A	ENST00000263253	NM_001429.3	551	Ccc/Gcc	8/31	0.924633515498065	1	FACETS	0.07	0.054	0.088	0.07	0.054	0.088	SUBCLONAL	1	TRUE	0	0.924633515498065	1		585	401	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545957	41545957	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs201030855	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	36	858	0	ENST00000263253.7:c.2572A>G	p.Thr858Ala	p.T858A	ENST00000263253	NM_001429.3	858	Aca/Gca	14/31	0.924633515498065	1	FACETS	0.063	0.052	0.077	0.063	0.052	0.077	SUBCLONAL	1	TRUE	0	0.924633515498065	1		858	660	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573588	41573588	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	38	763	0	ENST00000263253.7:c.5873C>A	p.Pro1958Gln	p.P1958Q	ENST00000263253	NM_001429.3	1958	cCg/cAg	31/31	0.924633515498065	1	FACETS	0.09	0.074	0.108	0.09	0.074	0.108	SUBCLONAL	1	TRUE	0	0.924633515498065	1		763	490	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573737	41573737	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	31	775	0	ENST00000263253.7:c.6022T>C	p.Ser2008Pro	p.S2008P	ENST00000263253	NM_001429.3	2008	Tct/Cct	31/31	0.924633515498065	1	FACETS	0.067	0.054	0.082	0.067	0.054	0.082	SUBCLONAL	1	TRUE	0	0.924633515498065	1		775	536	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573784	41573805	+	missense_variant	Missense_Mutation	ONP	ACCTTTGAACATGGCTCCACAA	ACCTTTGAACATGGCTCCACAA	GCCCTTGAATATAGCTCCCCAG	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	33	911	2	ENST00000263253.7:c.6069_6090delinsGCCCTTGAATATAGCTCCCCAG	p.Met2027Ile	p.M2027I	ENST00000263253	NM_001429.3	2023	caACCTTTGAACATGGCTCCACAA/caGCCCTTGAATATAGCTCCCCAG	31/31	0.924633515498065	1	FACETS	0.07	0.056	0.085	0.07	0.056	0.085	SUBCLONAL	1	TRUE	0	0.924633515498065	1		913	549	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573827	41573827	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs761386616	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	39	929	0	ENST00000263253.7:c.6112A>G	p.Ile2038Val	p.I2038V	ENST00000263253	NM_001429.3	2038	Atc/Gtc	31/31	0.924633515498065	1	FACETS	0.08	0.066	0.096	0.08	0.066	0.096	SUBCLONAL	1	TRUE	0	0.924633515498065	1		929	568	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573829	41573829	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	38	931	0	ENST00000263253.7:c.6114C>G	p.Ile2038Met	p.I2038M	ENST00000263253	NM_001429.3	2038	atC/atG	31/31	0.924633515498065	1	FACETS	0.079	0.064	0.094	0.079	0.064	0.094	SUBCLONAL	1	TRUE	0	0.924633515498065	1		931	562	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574013	41574013	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	47	589	0	ENST00000263253.7:c.6298A>C	p.Ile2100Leu	p.I2100L	ENST00000263253	NM_001429.3	2100	Atc/Ctc	31/31	0.924633515498065	1	FACETS	0.154	0.13	0.181	0.154	0.13	0.181	SUBCLONAL	1	TRUE	0	0.924633515498065	1		589	354	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574107	41574107	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	20	540	0	ENST00000263253.7:c.6392A>C	p.Gln2131Pro	p.Q2131P	ENST00000263253	NM_001429.3	2131	cAg/cCg	31/31	0.924633515498065	1	FACETS	0.076	0.058	0.097	0.076	0.058	0.097	SUBCLONAL	1	TRUE	0	0.924633515498065	1		540	306	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574205	41574207	+	frameshift_variant	Frame_Shift_Del	DEL	CAG	CAG	AA	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	20	682	1	ENST00000263253.7:c.6490_6492delinsAA	p.Gln2164LysfsTer5	p.Q2164Kfs*5	ENST00000263253	NM_001429.3	2164	CAG/AA	31/31	0.924633515498065	1	FACETS	0.06	0.045	0.077	0.06	0.045	0.077	SUBCLONAL	1	TRUE	0	0.924633515498065	1		683	390	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574533	41574533	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	50	816	0	ENST00000263253.7:c.6818T>C	p.Val2273Ala	p.V2273A	ENST00000263253	NM_001429.3	2273	gTt/gCt	31/31	0.924633515498065	1	FACETS	0.095	0.08	0.111	0.095	0.08	0.111	SUBCLONAL	1	TRUE	0	0.924633515498065	1		816	614	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574575	41574576	+	missense_variant	Missense_Mutation	DNP	AT	AT	GC	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	68	1012	1	ENST00000263253.7:c.6860_6861delinsGC	p.Asn2287Ser	p.N2287S	ENST00000263253	NM_001429.3	2287	aAT/aGC	31/31	0.924633515498065	1	FACETS	0.109	0.095	0.125	0.109	0.095	0.125	SUBCLONAL	1	TRUE	0	0.924633515498065	1		1013	723	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574616	41574617	+	missense_variant	Missense_Mutation	DNP	AA	AA	TC	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	51	1044	1	ENST00000263253.7:c.6901_6902delinsTC	p.Asn2301Ser	p.N2301S	ENST00000263253	NM_001429.3	2301	AAt/TCt	31/31	0.924633515498065	1	FACETS	0.078	0.066	0.091	0.078	0.066	0.091	SUBCLONAL	1	TRUE	0	0.924633515498065	1		1045	762	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574762	41574763	+	missense_variant	Missense_Mutation	DNP	TG	TG	CA	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	64	881	0	ENST00000263253.7:c.7047_7048inv	p.Gly2350Arg	p.G2350R	ENST00000263253	NM_001429.3	2349	ccTGga/ccCAga	31/31	0.924633515498065	1	FACETS	0.104	0.09	0.12	0.104	0.09	0.12	SUBCLONAL	1	TRUE	0	0.924633515498065	1		881	713	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574807	41574807	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	33	727	0	ENST00000263253.7:c.7092T>G	p.Phe2364Leu	p.F2364L	ENST00000263253	NM_001429.3	2364	ttT/ttG	31/31	0.924633515498065	1	FACETS	0.061	0.049	0.074	0.061	0.049	0.074	SUBCLONAL	1	TRUE	0	0.924633515498065	1		727	629	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574812	41574812	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	35	718	0	ENST00000263253.7:c.7097G>A	p.Ser2366Asn	p.S2366N	ENST00000263253	NM_001429.3	2366	aGc/aAc	31/31	0.924633515498065	1	FACETS	0.065	0.053	0.079	0.065	0.053	0.079	SUBCLONAL	1	TRUE	0	0.924633515498065	1		718	623	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574824	41574824	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs745616467	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	67	709	0	ENST00000263253.7:c.7109A>G	p.Asn2370Ser	p.N2370S	ENST00000263253	NM_001429.3	2370	aAt/aGt	31/31	0.924633515498065	1	FACETS	0.122	0.106	0.14	0.122	0.106	0.14	SUBCLONAL	1	TRUE	0	0.924633515498065	1		709	638	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713775	30713776	+	missense_variant	Missense_Mutation	DNP	CA	CA	TG	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	21	573	2	ENST00000295754.5:c.1100_1101inv	p.Pro367Leu	p.P367L	ENST00000295754	NM_003242.5	367	cCA/cTG	4/7	0.924633515498065	1	FACETS	0.059	0.045	0.076	0.059	0.045	0.076	SUBCLONAL	1	TRUE	0	0.924633515498065	1		575	413	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37092045	37092045	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	19	633	0	ENST00000231790.2:c.2172G>C	p.Leu724Phe	p.L724F	ENST00000231790	NM_000249.3	724	ttG/ttC	19/19	0.924633515498065	1	FACETS	0.069	0.052	0.089	0.069	0.052	0.089	SUBCLONAL	1	TRUE	0	0.924633515498065	1		633	321	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37092055	37092055	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	20	648	0	ENST00000231790.2:c.2182A>C	p.Ile728Leu	p.I728L	ENST00000231790	NM_000249.3	728	Att/Ctt	19/19	0.924633515498065	1	FACETS	0.075	0.057	0.096	0.075	0.057	0.096	SUBCLONAL	1	TRUE	0	0.924633515498065	1		648	311	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098463	47098463	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	22	625	0	ENST00000409792.3:c.6811A>G	p.Ser2271Gly	p.S2271G	ENST00000409792	NM_014159.6	2271	Agt/Ggt	15/21	0.924633515498065	1	FACETS	0.06	0.046	0.077	0.06	0.046	0.077	SUBCLONAL	1	TRUE	0	0.924633515498065	1		625	423	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098511	47098512	+	missense_variant	Missense_Mutation	DNP	CA	CA	TG	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	19	518	2	ENST00000409792.3:c.6762_6763inv	p.Ala2255Thr	p.A2255T	ENST00000409792	NM_014159.6	2254	gtTGct/gtCAct	15/21	0.924633515498065	1	FACETS	0.063	0.048	0.082	0.063	0.048	0.082	SUBCLONAL	1	TRUE	0	0.924633515498065	1		520	349	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098543	47098543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	18	567	0	ENST00000409792.3:c.6731G>A	p.Ser2244Asn	p.S2244N	ENST00000409792	NM_014159.6	2244	aGt/aAt	15/21	0.924633515498065	1	FACETS	0.068	0.051	0.088	0.068	0.051	0.088	SUBCLONAL	1	TRUE	0	0.924633515498065	1		567	308	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098622	47098622	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	28	702	0	ENST00000409792.3:c.6652T>G	p.Ser2218Ala	p.S2218A	ENST00000409792	NM_014159.6	2218	Tct/Gct	15/21	0.924633515498065	1	FACETS	0.081	0.064	0.1	0.081	0.064	0.1	SUBCLONAL	1	TRUE	0	0.924633515498065	1		702	404	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098658	47098658	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	30	752	1	ENST00000409792.3:c.6616G>T	p.Ala2206Ser	p.A2206S	ENST00000409792	NM_014159.6	2206	Gct/Tct	15/21	0.924633515498065	1	FACETS	0.079	0.064	0.098	0.079	0.064	0.098	SUBCLONAL	1	TRUE	0	0.924633515498065	1		753	439	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161932	47161932	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	11	507	0	ENST00000409792.3:c.4194C>G	p.Ile1398Met	p.I1398M	ENST00000409792	NM_014159.6	1398	atC/atG	3/21	0.924633515498065	1	FACETS	0.064	0.044	0.089	0.064	0.044	0.089	SUBCLONAL	1	TRUE	0	0.924633515498065	1		507	201	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162194	47162195	+	protein_altering_variant	In_Frame_Ins	INS	-	-	TTG	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	16	608	0	ENST00000409792.3:c.3931_3932insCAA	p.Gly1311delinsAlaSer	p.G1311delinsAS	ENST00000409792	NM_014159.6	1311	ggt/gCAAgt	3/21	0.924633515498065	1	FACETS	0.06	0.044	0.08	0.06	0.044	0.08	SUBCLONAL	1	TRUE	0	0.924633515498065	1		608	309	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162234	47162235	+	missense_variant	Missense_Mutation	DNP	CA	CA	TC	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	19	573	0	ENST00000409792.3:c.3891_3892delinsGA	p.Asp1298Asn	p.D1298N	ENST00000409792	NM_014159.6	1297	cgTGat/cgGAat	3/21	0.924633515498065	1	FACETS	0.065	0.049	0.083	0.065	0.049	0.083	SUBCLONAL	1	TRUE	0	0.924633515498065	1		573	342	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162260	47162260	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	16	569	0	ENST00000409792.3:c.3866A>G	p.Asn1289Ser	p.N1289S	ENST00000409792	NM_014159.6	1289	aAt/aGt	3/21	0.924633515498065	1	FACETS	0.059	0.043	0.079	0.059	0.043	0.079	SUBCLONAL	1	TRUE	0	0.924633515498065	1		569	313	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405910	49405911	+	missense_variant	Missense_Mutation	DNP	AT	AT	GC	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	25	690	0	ENST00000418115.1:c.227_228delinsGC	p.Asp76Gly	p.D76G	ENST00000418115	NM_001664.2	76	gAT/gGC	3/5	0.924633515498065	1	FACETS	0.059	0.046	0.074	0.059	0.046	0.074	SUBCLONAL	1	TRUE	0	0.924633515498065	1		690	494	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405960	49405961	+	missense_variant	Missense_Mutation	DNP	TG	TG	CA	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	30	623	0	ENST00000418115.1:c.177_178inv	p.Thr60Ala	p.T60A	ENST00000418115	NM_001664.2	59	gaCAca/gaTGca	3/5	0.924633515498065	1	FACETS	0.081	0.065	0.1	0.081	0.065	0.1	SUBCLONAL	1	TRUE	0	0.924633515498065	1		623	430	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412918	49412919	+	missense_variant	Missense_Mutation	DNP	CA	CA	TT	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	33	833	1	ENST00000418115.1:c.104_105delinsAA	p.Val35Glu	p.V35E	ENST00000418115	NM_001664.2	35	gTG/gAA	2/5	0.924633515498065	1	FACETS	0.076	0.062	0.093	0.076	0.062	0.093	SUBCLONAL	1	TRUE	0	0.924633515498065	1		834	502	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721586	49721587	+	missense_variant	Missense_Mutation	DNP	TG	TG	CA	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	16	447	2	ENST00000449682.2:c.2052_2053inv	p.Asn685Asp	p.N685D	ENST00000449682	NM_020998.3	684	caCAac/caTGac	18/18	0.924633515498065	1	FACETS	0.063	0.046	0.083	0.063	0.046	0.083	SUBCLONAL	1	TRUE	0	0.924633515498065	1		449	295	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723323	49723323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	21	141	0	ENST00000449682.2:c.1220G>A	p.Arg407His	p.R407H	ENST00000449682	NM_020998.3	407	cGc/cAc	10/18	0.924633515498065	1	FACETS	0.212	0.166	0.265	0.212	0.166	0.265	SUBCLONAL	1	TRUE	0	0.924633515498065	1		141	115	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723332	49723332	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	21	227	0	ENST00000449682.2:c.1211A>C	p.Gln404Pro	p.Q404P	ENST00000449682	NM_020998.3	404	cAg/cCg	10/18	0.924633515498065	1	FACETS	0.144	0.111	0.181	0.144	0.111	0.181	SUBCLONAL	1	TRUE	0	0.924633515498065	1		227	170	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723350	49723350	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs201339455	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	22	375	0	ENST00000449682.2:c.1193A>G	p.Lys398Arg	p.K398R	ENST00000449682	NM_020998.3	398	aAg/aGg	10/18	0.924633515498065	1	FACETS	0.08	0.061	0.101	0.08	0.061	0.101	SUBCLONAL	1	TRUE	0	0.924633515498065	1		375	321	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49724663	49724664	+	missense_variant	Missense_Mutation	DNP	CA	CA	GG	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	20	467	0	ENST00000449682.2:c.525_526delinsCC	p.Gly176Arg	p.G176R	ENST00000449682	NM_020998.3	175	gaTGgc/gaCCgc	5/18	0.924633515498065	1	FACETS	0.066	0.05	0.085	0.066	0.05	0.085	SUBCLONAL	1	TRUE	0	0.924633515498065	1		467	350	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987175	69987176	+	missense_variant	Missense_Mutation	DNP	CG	CG	AA	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	23	531	0	ENST00000394351.3:c.236_237delinsAA	p.Thr79Lys	p.T79K	ENST00000394351	NM_000248.3	79	aCG/aAA	2/9	0.924633515498065	1	FACETS	0.059	0.046	0.075	0.059	0.046	0.075	SUBCLONAL	1	TRUE	0	0.924633515498065	1		531	452	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014097	70014098	+	missense_variant	Missense_Mutation	DNP	GT	GT	AC	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	26	601	2	ENST00000394351.3:c.958_959inv	p.Val320Thr	p.V320T	ENST00000394351	NM_000248.3	320	GTt/ACt	9/9	0.924633515498065	1	FACETS	0.079	0.062	0.098	0.079	0.062	0.098	SUBCLONAL	1	TRUE	0	0.924633515498065	1		603	384	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014113	70014113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	23	595	1	ENST00000394351.3:c.974G>A	p.Ser325Asn	p.S325N	ENST00000394351	NM_000248.3	325	aGc/aAc	9/9	0.924633515498065	1	FACETS	0.068	0.053	0.086	0.068	0.053	0.086	SUBCLONAL	1	TRUE	0	0.924633515498065	1		596	391	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027087	71027087	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	29	594	0	ENST00000318789.4:c.1240C>A	p.Leu414Met	p.L414M	ENST00000318789	NM_032682.5	414	Ctg/Atg	15/21	0.924633515498065	1	FACETS	0.061	0.048	0.075	0.061	0.048	0.075	SUBCLONAL	1	TRUE	0	0.924633515498065	1		594	553	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259660	89259661	+	missense_variant	Missense_Mutation	DNP	TA	TA	CG	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	11	334	0	ENST00000336596.2:c.804_805delinsCG	p.Met269Val	p.M269V	ENST00000336596	NM_005233.5	268	ttTAtg/ttCGtg	3/17	0.924633515498065	1	FACETS	0.083	0.057	0.114	0.083	0.057	0.114	SUBCLONAL	1	TRUE	0	0.924633515498065	1		334	155	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521704	89521704	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	18	606	0	ENST00000336596.2:c.2781C>G	p.His927Gln	p.H927Q	ENST00000336596	NM_005233.5	927	caC/caG	16/17	0.924633515498065	1	FACETS	0.059	0.044	0.077	0.059	0.044	0.077	SUBCLONAL	1	TRUE	0	0.924633515498065	1		606	355	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204738	128204738	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs988409355	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	39	957	0	ENST00000341105.2:c.703A>G	p.Thr235Ala	p.T235A	ENST00000341105	NM_032638.4	235	Act/Gct	3/6	0.924633515498065	1	FACETS	0.068	0.056	0.081	0.068	0.056	0.081	SUBCLONAL	1	TRUE	0	0.924633515498065	1		957	670	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204784	128204784	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	40	1005	0	ENST00000341105.2:c.657G>T	p.Glu219Asp	p.E219D	ENST00000341105	NM_032638.4	219	gaG/gaT	3/6	0.924633515498065	1	FACETS	0.068	0.056	0.081	0.068	0.056	0.081	SUBCLONAL	1	TRUE	0	0.924633515498065	1		1005	685	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478175	138478175	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	12	468	1	ENST00000289153.2:c.11G>A	p.Ser4Asn	p.S4N	ENST00000289153	NM_006219.2	4	aGt/aAt	1/22	0.924633515498065	1	FACETS	0.059	0.041	0.081	0.059	0.041	0.081	SUBCLONAL	1	TRUE	0	0.924633515498065	1		469	238	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146639	185146639	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	27	544	0	ENST00000265026.3:c.270C>A	p.His90Gln	p.H90Q	ENST00000265026	NM_004721.4	90	caC/caA	2/14	0.924633515498065	1	FACETS	0.071	0.056	0.088	0.071	0.056	0.088	SUBCLONAL	1	TRUE	0	0.924633515498065	1		544	442	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146653	185146653	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs547600832	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	24	525	0	ENST00000265026.3:c.284C>T	p.Thr95Met	p.T95M	ENST00000265026	NM_004721.4	95	aCg/aTg	2/14	0.924633515498065	1	FACETS	0.064	0.05	0.081	0.064	0.05	0.081	SUBCLONAL	1	TRUE	0	0.924633515498065	1		525	433	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146657	185146658	+	missense_variant	Missense_Mutation	DNP	GG	GG	CA	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	27	517	1	ENST00000265026.3:c.288_289delinsCA	p.Val97Met	p.V97M	ENST00000265026	NM_004721.4	96	gcGGtg/gcCAtg	2/14	0.924633515498065	1	FACETS	0.072	0.057	0.09	0.072	0.057	0.09	SUBCLONAL	1	TRUE	0	0.924633515498065	1		518	434	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612075	189612075	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	31	621	0	ENST00000264731.3:c.1827A>C	p.Glu609Asp	p.E609D	ENST00000264731	NM_003722.4	609	gaA/gaC	14/14	0.924633515498065	1	FACETS	0.072	0.058	0.088	0.072	0.058	0.088	SUBCLONAL	1	TRUE	0	0.924633515498065	1		621	500	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361214	66361214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375878596	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	24	381	0	ENST00000273854.3:c.958G>A	p.Gly320Ser	p.G320S	ENST00000273854	NM_004439.5	320	Ggc/Agc	4/18	1	2	FACETS	0.11	0.085	0.138	0.11	0.085	0.138	SUBCLONAL	1	TRUE	1	0.924633515498065	2		381	474	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398887	398887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776593233	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	24	589	3	ENST00000380956.4:c.697G>A	p.Val233Ile	p.V233I	ENST00000380956	NM_001195286.1	233	Gtc/Atc	6/9	0.922390636615551	1	FACETS	0.06	0.047	0.076	0.06	0.047	0.076	SUBCLONAL	1	TRUE	0	0.924633515498065	1		592	462	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398894	398894	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	25	587	0	ENST00000380956.4:c.704C>T	p.Thr235Ile	p.T235I	ENST00000380956	NM_001195286.1	235	aCa/aTa	6/9	0.922390636615551	1	FACETS	0.063	0.049	0.079	0.063	0.049	0.079	SUBCLONAL	1	TRUE	0	0.924633515498065	1		587	460	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31946776	31947190	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTATGTGACTGTGTGCGTCAGGGGTGCTGGGGGGAGGGCACAGGTTGGGGGAGACAGGGAACTTGGGAAACAGAAATAAAAACAAAAGAAAGAATTTCCCTGCCCCCACATCCCATGGAGAGGGCACAGGGCCCTGGTAAATAGTAATATGAGGGAGAGAGACAGGAGGGAAAGAGGGAGGAGTGAGAGGGTAAAGAGGGGGGGAGAGGAGGGGGAGGAGGAGGAAGGAAGGAGGGGGAGGAGGAGGGGGGGAGGAAGAGGGGGAGGAGGATGAAGAGGAGGAGGAAGAAGAAGGGTATGAGAGGTGGAAGGATCTGAGCAAGAGGTAAGACAGGAAGAGAAATGCTGTCCTGGGGGTGGAGGTTGGTAGAGAGTGAGGGTGGGGATGGACCATGTCTCTCATCTCTGCTTGTAG	GTATGTGACTGTGTGCGTCAGGGGTGCTGGGGGGAGGGCACAGGTTGGGGGAGACAGGGAACTTGGGAAACAGAAATAAAAACAAAAGAAAGAATTTCCCTGCCCCCACATCCCATGGAGAGGGCACAGGGCCCTGGTAAATAGTAATATGAGGGAGAGAGACAGGAGGGAAAGAGGGAGGAGTGAGAGGGTAAAGAGGGGGGGAGAGGAGGGGGAGGAGGAGGAAGGAAGGAGGGGGAGGAGGAGGGGGGGAGGAAGAGGGGGAGGAGGATGAAGAGGAGGAGGAAGAAGAAGGGTATGAGAGGTGGAAGGATCTGAGCAAGAGGTAAGACAGGAAGAGAAATGCTGTCCTGGGGGTGGAGGTTGGTAGAGAGTGAGGGTGGGGATGGACCATGTCTCTCATCTCTGCTTGTAG	-	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	28	631	0	ENST00000375333.2:c.666_677del		p.X222_splice	ENST00000375333	NM_032454.1	222		4/8	0.922390636615551	1	FACETS	0.064	0.05	0.079	0.064	0.05	0.079	SUBCLONAL	1	TRUE	0	0.924633515498065	1		631	511	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31947198	31947198	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	41	612	0	ENST00000375333.2:c.683A>G	p.Lys228Arg	p.K228R	ENST00000375333	NM_032454.1	228	aAg/aGg	5/8	0.922390636615551	1	FACETS	0.087	0.072	0.104	0.087	0.072	0.104	SUBCLONAL	1	TRUE	0	0.924633515498065	1		612	545	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31947249	31947250	+	missense_variant	Missense_Mutation	DNP	CA	CA	TG	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	59	819	1	ENST00000375333.2:c.734_735inv	p.Ser245Leu	p.S245L	ENST00000375333	NM_032454.1	245	tCA/tTG	5/8	0.922390636615551	1	FACETS	0.11	0.095	0.128	0.11	0.095	0.128	SUBCLONAL	1	TRUE	0	0.924633515498065	1		820	621	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31947299	31947299	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	51	664	0	ENST00000375333.2:c.784C>G	p.Gln262Glu	p.Q262E	ENST00000375333	NM_032454.1	262	Cag/Gag	5/8	0.922390636615551	1	FACETS	0.117	0.099	0.136	0.117	0.099	0.136	SUBCLONAL	1	TRUE	0	0.924633515498065	1		664	508	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31947320	31947320	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	42	513	2	ENST00000375333.2:c.805T>C	p.Ser269Pro	p.S269P	ENST00000375333	NM_032454.1	269	Tca/Cca	5/8	0.922390636615551	1	FACETS	0.119	0.099	0.141	0.119	0.099	0.141	SUBCLONAL	1	TRUE	0	0.924633515498065	1		515	411	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31947331	31948227	+	splice_acceptor_variant,splice_donor_variant,intron_variant	Splice_Site	DEL	GTGAGACTTGTGGAACCAACCAAAGTCAGGCATCTGGTGCTTCCCTGCCTCCCTCCAGTTCCATCCAGCCTGTCCTCCTGTTTTTTTGGTGAACCTGCCAGAAAAGCTGCCAAAAAGCTGACTCTTCTTGTTAATAAAATGACCCAAGTTTGTATTCCTCCCCACAAGAGAGGAGGCCTATCTTACCTGGGCCTTAGAAAGAGCCCTGAAATAGAATTCAGTTCTTGGTGGCTTATCAAAAGCACACAGGGGCCTGGCAGGAAGTGTAAAAGCTTGATGTTAATCATACTGGGACTAAGAGGATAGAGAATGGTAGGAGCTGGGATACCCCTAAACATTCACATTAAAACAAAAAAAACCCAAAGCTAAAAAACAACTGGGCAGGAGCTAAATAAAAATCTAATTTTGAGAGGCTGTATCTGGCTCAGGCCTCCTACTTTGTAACCCATGGAATATGTGAAAGCATTTGAAAAACTATAGCACTGATCTCACATGGGCAGACACACTCTCAGAGAGATGTGGTGGGAGCCATGGCGCAGTCTGCCTAGGCAGTGGCAGGAGCGCAGAAGACTCTGATTCCTCTCCTCGGTCCTAAGACCGAATGTGTGTCAGGACATGTGGTCAGGGAAGAGAAGCTATTTAACTGAACCAGTAATAGTAGCAGGAAAAGAAAAAGTGGAGGGAGGGCAGTCCAGGTAGGGGGCCTGGAACAAGCAACTGCACCAACAGAGGCAGTTGGTGCGAGCACAGAACCACCCCAGGCTGGGATTTTGTTATCCAGTCTCTCTTGCATGGTTGCCCGTGTTTCTGGAGACTTGTGTAAACATTAATGGATGAGGAGGAGAGATGGTTCTCAGAGCCCAGCCCTCATCTCTGCTGGCTTCCCACTGCCCTCAG	GTGAGACTTGTGGAACCAACCAAAGTCAGGCATCTGGTGCTTCCCTGCCTCCCTCCAGTTCCATCCAGCCTGTCCTCCTGTTTTTTTGGTGAACCTGCCAGAAAAGCTGCCAAAAAGCTGACTCTTCTTGTTAATAAAATGACCCAAGTTTGTATTCCTCCCCACAAGAGAGGAGGCCTATCTTACCTGGGCCTTAGAAAGAGCCCTGAAATAGAATTCAGTTCTTGGTGGCTTATCAAAAGCACACAGGGGCCTGGCAGGAAGTGTAAAAGCTTGATGTTAATCATACTGGGACTAAGAGGATAGAGAATGGTAGGAGCTGGGATACCCCTAAACATTCACATTAAAACAAAAAAAACCCAAAGCTAAAAAACAACTGGGCAGGAGCTAAATAAAAATCTAATTTTGAGAGGCTGTATCTGGCTCAGGCCTCCTACTTTGTAACCCATGGAATATGTGAAAGCATTTGAAAAACTATAGCACTGATCTCACATGGGCAGACACACTCTCAGAGAGATGTGGTGGGAGCCATGGCGCAGTCTGCCTAGGCAGTGGCAGGAGCGCAGAAGACTCTGATTCCTCTCCTCGGTCCTAAGACCGAATGTGTGTCAGGACATGTGGTCAGGGAAGAGAAGCTATTTAACTGAACCAGTAATAGTAGCAGGAAAAGAAAAAGTGGAGGGAGGGCAGTCCAGGTAGGGGGCCTGGAACAAGCAACTGCACCAACAGAGGCAGTTGGTGCGAGCACAGAACCACCCCAGGCTGGGATTTTGTTATCCAGTCTCTCTTGCATGGTTGCCCGTGTTTCTGGAGACTTGTGTAAACATTAATGGATGAGGAGGAGAGATGGTTCTCAGAGCCCAGCCCTCATCTCTGCTGGCTTCCCACTGCCCTCAG	-	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	27	450	0	ENST00000375333.2:c.815+2_816del		p.X272_splice	ENST00000375333	NM_032454.1	272			0.922390636615551	1	FACETS	0.086	0.068	0.107	0.086	0.068	0.107	SUBCLONAL	1	TRUE	0	0.924633515498065	1		450	365	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169901	32169901	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs550006982	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	29	757	0	ENST00000375023.3:c.3707A>C	p.Glu1236Ala	p.E1236A	ENST00000375023	NM_004557.3	1236	gAa/gCa	21/30	0.922390636615551	1	FACETS	0.064	0.05	0.078	0.064	0.05	0.078	SUBCLONAL	1	TRUE	0	0.924633515498065	1		757	531	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815760	32815762	+	missense_variant	Missense_Mutation	TNP	CCG	CCG	TTA	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	35	855	2	ENST00000354258.4:c.1854_1856delinsTAA	p.Gly619Lys	p.G619K	ENST00000354258	NM_000593.5	618	acCGGg/acTAAg	8/11	0.922390636615551	1	FACETS	0.063	0.051	0.076	0.063	0.051	0.076	SUBCLONAL	1	TRUE	0	0.924633515498065	1		857	647	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289202	33289202	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146117896	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	24	574	0	ENST00000374542.5:c.350G>A	p.Arg117Gln	p.R117Q	ENST00000374542	NM_001141970.1	117	cGg/cAg	3/8	0.922390636615551	1	FACETS	0.06	0.047	0.076	0.06	0.047	0.076	SUBCLONAL	1	TRUE	0	0.924633515498065	1		574	465	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64288857	64288857	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	19	841	0	ENST00000370651.3:c.253T>G	p.Leu85Val	p.L85V	ENST00000370651	NM_003463.4	85	Tta/Gta	4/6	0.922390636615551	1	FACETS	0.062	0.046	0.08	0.062	0.046	0.08	SUBCLONAL	1	TRUE	0	0.924633515498065	1		841	359	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64288909	64288910	+	missense_variant	Missense_Mutation	DNP	TT	TT	CC	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	20	817	0	ENST00000370651.3:c.305_306delinsCC	p.Val102Ala	p.V102A	ENST00000370651	NM_003463.4	102	gTT/gCC	4/6	0.922390636615551	1	FACETS	0.066	0.05	0.085	0.066	0.05	0.085	SUBCLONAL	1	TRUE	0	0.924633515498065	1		817	350	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790998	89790998	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	17	168	0	ENST00000336032.3:c.385A>G	p.Ser129Gly	p.S129G	ENST00000336032	NM_006813.2	129	Agc/Ggc	1/2	0.922390636615551	1	FACETS	0.109	0.081	0.141	0.109	0.081	0.141	SUBCLONAL	1	TRUE	0	0.924633515498065	1		168	182	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793511	89793511	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	16	378	0	ENST00000336032.3:c.580C>A	p.Leu194Ile	p.L194I	ENST00000336032	NM_006813.2	194	Ctt/Att	2/2	0.922390636615551	1	FACETS	0.109	0.08	0.142	0.109	0.08	0.142	SUBCLONAL	1	TRUE	0	0.924633515498065	1		378	171	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793515	89793515	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	10	380	0	ENST00000336032.3:c.584C>G	p.Pro195Arg	p.P195R	ENST00000336032	NM_006813.2	195	cCc/cGc	2/2	0.922390636615551	1	FACETS	0.067	0.045	0.095	0.067	0.045	0.095	SUBCLONAL	1	TRUE	0	0.924633515498065	1		380	173	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793548	89793548	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs753147224	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	13	368	0	ENST00000336032.3:c.617A>G	p.Tyr206Cys	p.Y206C	ENST00000336032	NM_006813.2	206	tAt/tGt	2/2	0.922390636615551	1	FACETS	0.094	0.067	0.127	0.094	0.067	0.127	SUBCLONAL	1	TRUE	0	0.924633515498065	1		368	160	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793715	89793716	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	17	410	0	ENST00000336032.3:c.784_785delinsAT	p.Ser262Met	p.S262M	ENST00000336032	NM_006813.2	262	TCg/ATg	2/2	0.922390636615551	1	FACETS	0.1	0.075	0.131	0.1	0.075	0.131	SUBCLONAL	1	TRUE	0	0.924633515498065	1		410	197	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793765	89793765	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	16	523	0	ENST00000336032.3:c.834T>G	p.Asn278Lys	p.N278K	ENST00000336032	NM_006813.2	278	aaT/aaG	2/2	0.922390636615551	1	FACETS	0.07	0.051	0.093	0.07	0.051	0.093	SUBCLONAL	1	TRUE	0	0.924633515498065	1		523	265	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793767	89793767	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	17	522	0	ENST00000336032.3:c.836A>G	p.Tyr279Cys	p.Y279C	ENST00000336032	NM_006813.2	279	tAt/tGt	2/2	0.922390636615551	1	FACETS	0.072	0.054	0.095	0.072	0.054	0.095	SUBCLONAL	1	TRUE	0	0.924633515498065	1		522	273	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793844	89793844	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760936320	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	31	475	1	ENST00000336032.3:c.913G>A	p.Val305Ile	p.V305I	ENST00000336032	NM_006813.2	305	Gtt/Att	2/2	0.922390636615551	1	FACETS	0.155	0.126	0.188	0.155	0.126	0.188	SUBCLONAL	1	TRUE	0	0.924633515498065	1		476	232	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068082	94068082	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	12	343	0	ENST00000369303.4:c.880T>G	p.Ser294Ala	p.S294A	ENST00000369303	NM_004440.3	294	Tct/Gct	4/17	0.922390636615551	1	FACETS	0.067	0.047	0.092	0.067	0.047	0.092	SUBCLONAL	1	TRUE	0	0.924633515498065	1		343	208	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547422	106547422	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	11	401	0	ENST00000369096.4:c.659A>G	p.Asn220Ser	p.N220S	ENST00000369096	NM_001198.3	220	aAt/aGt	4/7	0.922390636615551	1	FACETS	0.095	0.066	0.132	0.095	0.066	0.132	SUBCLONAL	1	TRUE	0	0.924633515498065	1		401	134	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555238	106555240	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	15	538	0	ENST00000369096.4:c.2358_2360del	p.Ser787del	p.S787del	ENST00000369096	NM_001198.3	785	ctCTCc/ctc	7/7	0.922390636615551	1	FACETS	0.059	0.042	0.078	0.059	0.042	0.078	SUBCLONAL	1	TRUE	0	0.924633515498065	1		538	298	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555273	106555273	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	14	517	0	ENST00000369096.4:c.2390T>C	p.Leu797Pro	p.L797P	ENST00000369096	NM_001198.3	797	cTa/cCa	7/7	0.922390636615551	1	FACETS	0.059	0.042	0.079	0.059	0.042	0.079	SUBCLONAL	1	TRUE	0	0.924633515498065	1		517	276	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555290	106555290	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	17	498	0	ENST00000369096.4:c.2407C>G	p.Pro803Ala	p.P803A	ENST00000369096	NM_001198.3	803	Cct/Gct	7/7	0.922390636615551	1	FACETS	0.075	0.055	0.098	0.075	0.055	0.098	SUBCLONAL	1	TRUE	0	0.924633515498065	1		498	264	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555294	106555294	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	18	497	0	ENST00000369096.4:c.2411C>A	p.Pro804His	p.P804H	ENST00000369096	NM_001198.3	804	cCc/cAc	7/7	0.922390636615551	1	FACETS	0.081	0.06	0.105	0.081	0.06	0.105	SUBCLONAL	1	TRUE	0	0.924633515498065	1		497	259	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555315	106555316	+	missense_variant	Missense_Mutation	DNP	TA	TA	GG	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	14	469	1	ENST00000369096.4:c.2432_2433delinsGG	p.Val811Gly	p.V811G	ENST00000369096	NM_001198.3	811	gTA/gGG	7/7	0.922390636615551	1	FACETS	0.066	0.048	0.089	0.066	0.048	0.089	SUBCLONAL	1	TRUE	0	0.924633515498065	1		470	245	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020765	112020765	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	21	367	0	ENST00000368678.4:c.806G>T	p.Cys269Phe	p.C269F	ENST00000368678		269	tGt/tTt	8/13	0.922390636615551	1	FACETS	0.075	0.057	0.095	0.075	0.057	0.095	SUBCLONAL	1	TRUE	0	0.924633515498065	1		367	327	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020774	112020775	+	missense_variant	Missense_Mutation	DNP	CG	CG	TC	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	20	387	1	ENST00000368678.4:c.796_797delinsGA	p.Arg266Asp	p.R266D	ENST00000368678		266	CGt/GAt	8/13	0.922390636615551	1	FACETS	0.073	0.056	0.094	0.073	0.056	0.094	SUBCLONAL	1	TRUE	0	0.924633515498065	1		388	317	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609672	117609672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	18	473	0	ENST00000368508.3:c.7027G>A	p.Gly2343Arg	p.G2343R	ENST00000368508	NM_002944.2	2343	Gga/Aga	43/43	0.922390636615551	1	FACETS	0.107	0.081	0.138	0.107	0.081	0.138	SUBCLONAL	1	TRUE	0	0.924633515498065	1		473	195	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609715	117609715	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	28	664	0	ENST00000368508.3:c.6984G>C	p.Lys2328Asn	p.K2328N	ENST00000368508	NM_002944.2	2328	aaG/aaC	43/43	0.922390636615551	1	FACETS	0.106	0.085	0.131	0.106	0.085	0.131	SUBCLONAL	1	TRUE	0	0.924633515498065	1		664	306	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609723	117609723	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	31	681	0	ENST00000368508.3:c.6976T>C	p.Ser2326Pro	p.S2326P	ENST00000368508	NM_002944.2	2326	Tct/Cct	43/43	0.922390636615551	1	FACETS	0.113	0.091	0.137	0.113	0.091	0.137	SUBCLONAL	1	TRUE	0	0.924633515498065	1		681	320	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609755	117609756	+	missense_variant	Missense_Mutation	DNP	AA	AA	GG	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	23	760	0	ENST00000368508.3:c.6943_6944delinsCC	p.Phe2315Pro	p.F2315P	ENST00000368508	NM_002944.2	2315	TTc/CCc	43/43	0.922390636615551	1	FACETS	0.081	0.062	0.102	0.081	0.062	0.102	SUBCLONAL	1	TRUE	0	0.924633515498065	1		760	332	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004889	150004890	+	missense_variant	Missense_Mutation	DNP	TC	TC	CT	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	31	635	3	ENST00000253339.5:c.1335_1336delinsAG	p.Ser446Gly	p.S446G	ENST00000253339		445	ccGAgc/ccAGgc	3/7	0.922390636615551	1	FACETS	0.083	0.067	0.102	0.083	0.067	0.102	SUBCLONAL	1	TRUE	0	0.924633515498065	1		638	434	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004930	150004930	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	27	563	0	ENST00000253339.5:c.1295A>C	p.Asn432Thr	p.N432T	ENST00000253339		432	aAt/aCt	3/7	0.922390636615551	1	FACETS	0.075	0.059	0.093	0.075	0.059	0.093	SUBCLONAL	1	TRUE	0	0.924633515498065	1		563	419	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004948	150004948	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	25	542	0	ENST00000253339.5:c.1277T>C	p.Val426Ala	p.V426A	ENST00000253339		426	gTa/gCa	3/7	0.922390636615551	1	FACETS	0.084	0.066	0.105	0.084	0.066	0.105	SUBCLONAL	1	TRUE	0	0.924633515498065	1		542	346	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004951	150004951	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	23	543	0	ENST00000253339.5:c.1274G>A	p.Ser425Asn	p.S425N	ENST00000253339		425	aGt/aAt	3/7	0.922390636615551	1	FACETS	0.078	0.06	0.098	0.078	0.06	0.098	SUBCLONAL	1	TRUE	0	0.924633515498065	1		543	344	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005554	150005554	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	14	455	0	ENST00000253339.5:c.671T>C	p.Val224Ala	p.V224A	ENST00000253339		224	gTt/gCt	3/7	0.922390636615551	1	FACETS	0.061	0.044	0.082	0.061	0.044	0.082	SUBCLONAL	1	TRUE	0	0.924633515498065	1		455	267	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005564	150005564	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	14	443	1	ENST00000253339.5:c.661T>A	p.Ser221Thr	p.S221T	ENST00000253339		221	Tca/Aca	3/7	0.922390636615551	1	FACETS	0.062	0.044	0.083	0.062	0.044	0.083	SUBCLONAL	1	TRUE	0	0.924633515498065	1		444	263	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023103	150023103	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs759856872	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	27	853	0	ENST00000253339.5:c.160A>G	p.Met54Val	p.M54V	ENST00000253339		54	Atg/Gtg	1/7	0.922390636615551	1	FACETS	0.082	0.065	0.102	0.082	0.065	0.102	SUBCLONAL	1	TRUE	0	0.924633515498065	1		853	383	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023107	150023107	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	28	855	0	ENST00000253339.5:c.156T>G	p.His52Gln	p.H52Q	ENST00000253339		52	caT/caG	1/7	0.922390636615551	1	FACETS	0.085	0.068	0.105	0.085	0.068	0.105	SUBCLONAL	1	TRUE	0	0.924633515498065	1		855	381	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023115	150023115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	29	837	0	ENST00000253339.5:c.148G>A	p.Ala50Thr	p.A50T	ENST00000253339		50	Gct/Act	1/7	0.922390636615551	1	FACETS	0.093	0.075	0.115	0.093	0.075	0.115	SUBCLONAL	1	TRUE	0	0.924633515498065	1		837	361	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023189	150023189	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	28	719	0	ENST00000253339.5:c.74T>G	p.Val25Gly	p.V25G	ENST00000253339		25	gTc/gGc	1/7	0.922390636615551	1	FACETS	0.106	0.084	0.13	0.106	0.084	0.13	SUBCLONAL	1	TRUE	0	0.924633515498065	1		719	308	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099505	157099505	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	19	263	0	ENST00000346085.5:c.442C>G	p.Pro148Ala	p.P148A	ENST00000346085	NM_020732.3	148	Cct/Gct	1/20	0.922390636615551	1	FACETS	0.07	0.053	0.09	0.07	0.053	0.09	SUBCLONAL	1	TRUE	0	0.924633515498065	1		263	316	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099805	157099805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	28	505	1	ENST00000346085.5:c.742G>A	p.Ala248Thr	p.A248T	ENST00000346085	NM_020732.3	248	Gct/Act	1/20	0.922390636615551	1	FACETS	0.067	0.053	0.083	0.067	0.053	0.083	SUBCLONAL	1	TRUE	0	0.924633515498065	1		506	488	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157454197	157454197	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	20	569	0	ENST00000346085.5:c.2407G>T	p.Ala803Ser	p.A803S	ENST00000346085	NM_020732.3	803	Gct/Tct	8/20	0.922390636615551	1	FACETS	0.063	0.048	0.081	0.063	0.048	0.081	SUBCLONAL	1	TRUE	0	0.924633515498065	1		569	370	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157454266	157454266	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	22	525	0	ENST00000346085.5:c.2476G>C	p.Ala826Pro	p.A826P	ENST00000346085	NM_020732.3	826	Gct/Cct	8/20	0.922390636615551	1	FACETS	0.063	0.048	0.08	0.063	0.048	0.08	SUBCLONAL	1	TRUE	0	0.924633515498065	1		525	407	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469885	157469886	+	missense_variant	Missense_Mutation	DNP	TG	TG	GA	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	30	691	0	ENST00000346085.5:c.2679_2680delinsGA	p.Val894Met	p.V894M	ENST00000346085	NM_020732.3	893	gcTGtg/gcGAtg	9/20	0.922390636615551	1	FACETS	0.061	0.049	0.076	0.061	0.049	0.076	SUBCLONAL	1	TRUE	0	0.924633515498065	1		691	568	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528813	157528813	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	30	568	0	ENST00000346085.5:c.6538A>C	p.Met2180Leu	p.M2180L	ENST00000346085	NM_020732.3	2180	Atg/Ctg	20/20	0.922390636615551	1	FACETS	0.073	0.058	0.089	0.073	0.058	0.089	SUBCLONAL	1	TRUE	0	0.924633515498065	1		568	481	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864400	162864400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1433385523	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	28	507	0	ENST00000366898.1:c.113C>T	p.Ala38Val	p.A38V	ENST00000366898	NM_004562.2	38	gCt/gTt	2/12	0.922390636615551	1	FACETS	0.059	0.046	0.073	0.059	0.046	0.073	SUBCLONAL	1	TRUE	0	0.924633515498065	1		507	554	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864453	162864453	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	31	526	0	ENST00000366898.1:c.60C>A	p.Asp20Glu	p.D20E	ENST00000366898	NM_004562.2	20	gaC/gaA	2/12	0.922390636615551	1	FACETS	0.082	0.066	0.1	0.082	0.066	0.1	SUBCLONAL	1	TRUE	0	0.924633515498065	1		526	441	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207611	29207611	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	38	825	0	ENST00000240100.2:c.185T>G	p.Leu62Arg	p.L62R	ENST00000240100	NM_001394.6	62	cTa/cGa	1/4	0.924633515498065	1	FACETS	0.075	0.061	0.09	0.075	0.061	0.09	SUBCLONAL	1	TRUE	0	0.924633515498065	1		825	591	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287337	38287337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143241978	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	35	790	2	ENST00000425967.3:c.320C>T	p.Ala107Val	p.A107V	ENST00000425967	NM_001174067.1	107	gCg/gTg	4/19	0.924633515498065	1	FACETS	0.073	0.059	0.088	0.073	0.059	0.088	SUBCLONAL	1	TRUE	0	0.924633515498065	1		792	561	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287461	38287461	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1371683958	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	22	491	0	ENST00000425967.3:c.196C>T	p.Pro66Ser	p.P66S	ENST00000425967	NM_001174067.1	66	Ccc/Tcc	4/19	0.924633515498065	1	FACETS	0.082	0.063	0.104	0.082	0.063	0.104	SUBCLONAL	1	TRUE	0	0.924633515498065	1		491	313	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750996	128750996	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	17	490	0	ENST00000377970.2:c.533A>G	p.Asn178Ser	p.N178S	ENST00000377970	NM_002467.4	178	aAc/aGc	2/3	0.924633515498065	1	FACETS	0.058	0.043	0.076	0.058	0.043	0.076	SUBCLONAL	1	TRUE	0	0.924633515498065	1		490	340	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949999	44949999	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	107	586	0	ENST00000377967.4:c.3768C>G	p.Tyr1256Ter	p.Y1256*	ENST00000377967	NM_021140.2	1256	taC/taG	26/29	1	2	FACETS	0.723	0.657	0.792	0.723	0.657	0.792	SUBCLONAL	1	TRUE	1	0.924633515498065	2		586	320	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469886	157469886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	30	691	0	ENST00000346085.5:c.2680G>A	p.Val894Met	p.V894M	ENST00000346085	NM_020732.3	894	Gtg/Atg	9/20	0.922390636615551	1	FACETS	0.061	0.049	0.076	0.061	0.049	0.076	SUBCLONAL	1	TRUE	0	0.924633515498065	1		691	568	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705481	43705481	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1447223433	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	31	806	0	ENST00000382044.4:c.5141C>T	p.Thr1714Ile	p.T1714I	ENST00000382044	NM_001141980.1	1714	aCc/aTc	24/28	0.924633515498065	1	FACETS	0.06	0.048	0.074	0.06	0.048	0.074	SUBCLONAL	1	TRUE	0	0.924633515498065	1		806	601	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470575	25470575	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1180980391	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	206	875	0	ENST00000264709.3:c.899T>G	p.Leu300Arg	p.L300R	ENST00000264709	NM_175629.2	300	cTg/cGg	8/23	0.924633515498065	1	FACETS	0.252	0.233	0.271	0.252	0.233	0.271	SUBCLONAL	1	TRUE	0	0.924633515498065	1		875	951	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967039	25967039	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	27	761	1	ENST00000435504.4:c.2167A>C	p.Thr723Pro	p.T723P	ENST00000435504		723	Act/Cct	13/13	0.924633515498065	1	FACETS	0.059	0.046	0.073	0.059	0.046	0.073	SUBCLONAL	1	TRUE	0	0.924633515498065	1		762	533	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492929	56492929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	13	266	0	ENST00000407977.2:c.10G>A	p.Gly4Ser	p.G4S	ENST00000407977		4	Ggc/Agc	2/10	0.924633515498065	1	FACETS	0.065	0.046	0.088	0.065	0.046	0.088	SUBCLONAL	1	TRUE	0	0.924633515498065	1		266	232	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020774	112020774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777800541	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	20	388	0	ENST00000368678.4:c.797G>A	p.Arg266His	p.R266H	ENST00000368678		266	cGt/cAt	8/13	0.922390636615551	1	FACETS	0.073	0.056	0.094	0.073	0.056	0.094	SUBCLONAL	1	TRUE	0	0.924633515498065	1		388	317	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020775	112020775	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	20	381	0	ENST00000368678.4:c.796C>G	p.Arg266Gly	p.R266G	ENST00000368678		266	Cgt/Ggt	8/13	0.922390636615551	1	FACETS	0.075	0.057	0.096	0.075	0.057	0.096	SUBCLONAL	1	TRUE	0	0.924633515498065	1		381	312	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513542	41513542	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	23	596	0	ENST00000263253.7:c.446A>C	p.Gln149Pro	p.Q149P	ENST00000263253	NM_001429.3	149	cAg/cCg	2/31	0.924633515498065	1	FACETS	0.071	0.055	0.089	0.071	0.055	0.089	SUBCLONAL	1	TRUE	0	0.924633515498065	1		596	378	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25459804	25459804	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs762213449	NA	P-0034230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	164	562	0	ENST00000264709.3:c.2478+1G>T		p.X826_splice	ENST00000264709	NM_175629.2	826			0.924633515498065	1	FACETS	0.295	0.271	0.319	0.295	0.271	0.319	SUBCLONAL	1	TRUE	0	0.924633515498065	1		562	647	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0034231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	883	421	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.312276444592529	26	FACETS	0.992	0.969	1	0.906	0.885	0.926	CLONAL	21	TRUE	3	0.312276444592529	26		421	1289	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0034231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	130	703	0	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	0.309309884935996	2	FACETS	0.913	0.834	0.994	0.913	0.834	0.994	CLONAL	2	TRUE	0	0.312276444592529	2		703	456	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433754	49433754	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs374291343	NA	P-0034231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	62	965	0	ENST00000301067.7:c.7799C>A	p.Ser2600Tyr	p.S2600Y	ENST00000301067	NM_003482.3	2600	tCc/tAc	31/54	0.312276444592529	9	FACETS	0.689	0.592	0.794			1	SUBCLONAL	1	TRUE	NA	0.312276444592529	9		965	1207	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637781	176637781	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	172	675	0	ENST00000439151.2:c.2381A>T	p.His794Leu	p.H794L	ENST00000439151	NM_022455.4	794	cAc/cTc	5/23	0.271641659941166	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.312276444592529	3		675	581	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117874101	117874101	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	85	425	0	ENST00000297338.2:c.353A>G	p.Asp118Gly	p.D118G	ENST00000297338	NM_006265.2	118	gAt/gGt	4/14	0.271641659941166	3	FACETS	0.971	0.867	1	0.971	0.867	1	CLONAL	2	TRUE	1	0.312276444592529	3		425	324	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0034232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	72	528	2	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.859	0.754	0.972	0.859	0.754	0.972	CLONAL	1	TRUE	1	0.401838339988654	2		530	417	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793663	NA	P-0034232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	115	555	0	ENST00000263967.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000263967	NM_006218.2	93	cGg/cAg	2/21	1	2	FACETS	0.992	0.896	1	0.992	0.896	1	CLONAL	1	TRUE	1	0.401838339988654	2		555	577	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0034232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	56	392	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.945	0.815	1	0.945	0.815	1	CLONAL	1	TRUE	1	0.401838339988654	2		392	295	SUCCESS
APC	324	MSKCC	GRCh37	5	112175761	112175761	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	51	390	0	ENST00000257430.4:c.4473del	p.Phe1491LeufsTer16	p.F1491Lfs*16	ENST00000257430	NM_000038.5	1490	caT/ca	16/16	1	2	FACETS	0.694	0.592	0.805	0.694	0.592	0.805	SUBCLONAL	1	TRUE	1	0.401838339988654	2		390	366	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956221	55956221	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs767542615	NA	P-0034232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	128	626	0	ENST00000263923.4:c.3094C>T	p.Arg1032Ter	p.R1032*	ENST00000263923	NM_002253.2	1032	Cga/Tga	23/30	1	2	FACETS	0.997	0.906	1	0.997	0.906	1	CLONAL	1	TRUE	1	0.401838339988654	2		626	639	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922328	178922328	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	71	469	0	ENST00000263967.3:c.1097C>G	p.Pro366Arg	p.P366R	ENST00000263967	NM_006218.2	366	cCc/cGc	6/21	1	2	FACETS	0.856	0.75	0.969	0.856	0.75	0.969	CLONAL	1	TRUE	1	0.401838339988654	2		469	413	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573428	48573428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	26	213	0	ENST00000342988.3:c.12G>A	p.Met4Ile	p.M4I	ENST00000342988	NM_005359.5	4	atG/atA	2/12	0.401838339988654	1	FACETS	0.932	0.752	1	0.932	0.752	1	CLONAL	1	TRUE	0	0.401838339988654	1		213	111	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	342	740	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.660413458839066	4	FACETS	0.889	0.845	0.934			1	CLONAL	2	TRUE	NA	0.821143392451223	4		740	853	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0034249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	415	695	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.660413458839066	4	FACETS	0.975	0.932	1			1	CLONAL	2	TRUE	NA	0.821143392451223	4		695	944	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439847	49439847	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs886041406	NA	P-0034249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	146	664	0	ENST00000301067.7:c.4693+1G>T		p.X1565_splice	ENST00000301067	NM_003482.3	1565			0.784992999254182	4	FACETS	0.999	0.915	1	0.333	0.305	0.363	CLONAL	1	TRUE	1	0.821143392451223	4		664	648	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428417	49428418	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0034249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	514	793	0	ENST00000301067.7:c.10387dup	p.Ser3463PhefsTer5	p.S3463Ffs*5	ENST00000301067	NM_003482.3	3463	tcg/tTcg	36/54	0.784992999254182	4	FACETS	0.972	0.942	1	0.972	0.942	1	CLONAL	3	TRUE	1	0.821143392451223	4		793	782	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437531	49437531	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	445	676	0	ENST00000301067.7:c.5354G>C	p.Ser1785Thr	p.S1785T	ENST00000301067	NM_003482.3	1785	aGc/aCc	23/54	0.784992999254182	4	FACETS	0.948	0.916	0.98	0.948	0.916	0.98	CLONAL	3	TRUE	1	0.821143392451223	4		676	694	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119759	70119759	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	168	654	1	ENST00000245479.2:c.761G>A	p.Arg254Gln	p.R254Q	ENST00000245479	NM_000346.3	254	cGa/cAa	3/3	0.821143392451223	3	FACETS	0.993	0.918	1	0.497	0.459	0.536	CLONAL	1	TRUE	1	0.821143392451223	3		655	581	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244145	153244152	+	frameshift_variant	Frame_Shift_Del	DEL	ACTCCCCC	ACTCCCCC	-	novel	NA	P-0034249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	460	660	0	ENST00000281708.4:c.2005_2012del	p.Gly669CysfsTer22	p.G669Cfs*22	ENST00000281708	NM_033632.3	669	GGGGGAGTt/t	12/12	0.821143392451223	3	FACETS	0.942	0.92	0.964	0.942	0.92	0.964	CLONAL	3	TRUE	0	0.821143392451223	3		660	559	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931621	39931621	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs756356120	NA	P-0034249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	77	537	0	ENST00000378444.4:c.2978G>T	p.Arg993Leu	p.R993L	ENST00000378444	NM_001123385.1	993	cGg/cTg	4/15	0.821143392451223	4	FACETS	0.508	0.446	0.575			1	SUBCLONAL	1	TRUE	NA	0.821143392451223	4		537	672	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937356	76937356	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	141	260	0	ENST00000373344.5:c.3392G>C	p.Arg1131Thr	p.R1131T	ENST00000373344	NM_000489.3	1131	aGa/aCa	9/35	0.821143392451223	4	FACETS	1	0.983	1	0.643	0.59	0.699	CLONAL	1	TRUE	2	0.821143392451223	4		260	486	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	36	563	0	ENST00000347630.2:c.305T>C	p.Phe102Ser	p.F102S	ENST00000347630	NM_001007230.1	102	tTc/tCc	5/11	1	2	FACETS	0.802	0.666	0.952	0.802	0.666	0.952	CLONAL	1	FALSE	1	0.43350964316454	2		563	207	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	193	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.954	1	1	0.994	1	CLONAL	2	FALSE	1	0.492162339563941	2		148	385	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0034252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	300	418	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.492162339563941	1	FACETS	0.986	0.945	1	1	0.996	1	CLONAL	2	FALSE	0	0.492162339563941	1		418	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	407	768	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.448018180309535	0	FACETS		NA	1			1	NA	3	FALSE	0	0.492162339563941	0		768	441	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817754	3817754	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	432	672	3	ENST00000262367.5:c.3217C>T	p.Gln1073Ter	p.Q1073*	ENST00000262367	NM_004380.2	1073	Cag/Tag	16/31	1	2	FACETS	0.874	0.837	0.912	1	0.997	1	CLONAL	2	FALSE	1	0.492162339563941	2		675	1004	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	421	795	3	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	1	2	FACETS	1	0.985	1	1	0.997	1	CLONAL	2	FALSE	1	0.492162339563941	2		798	811	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0034252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	286	364	1	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	0.988	0.939	1	1	0.996	1	CLONAL	2	FALSE	1	0.492162339563941	2		365	588	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363243	40363243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	531	653	1	ENST00000397332.2:c.986C>T	p.Ser329Leu	p.S329L	ENST00000397332	NM_001033082.2	329	tCg/tTg	3/3	0.492162339563941	3	FACETS	0.995	0.962	1	1	0.997	1	CLONAL	3	FALSE	1	0.492162339563941	3		654	901	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147574	61147574	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1476158837	NA	P-0034252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	13	54	0	ENST00000295025.8:c.979G>A	p.Asp327Asn	p.D327N	ENST00000295025	NM_002908.2	327	Gat/Aat	9/11	0.492162339563941	1	FACETS	0.781	0.575	1	0.781	0.575	1	CLONAL	1	FALSE	0	0.492162339563941	1		54	51	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0034252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	54	224	0	ENST00000267163.4:c.1215+1G>C		p.X405_splice	ENST00000267163	NM_000321.2	405			0.492162339563941	0	FACETS		NA	1			1	NA	3	FALSE	0	0.492162339563941	0		224	63	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710984	117710984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	146	262	0	ENST00000368508.3:c.1288G>A	p.Gly430Ser	p.G430S	ENST00000368508	NM_002944.2	430	Ggc/Agc	12/43	1	2	FACETS	0.891	0.826	0.957	1	0.991	1	CLONAL	2	FALSE	1	0.492162339563941	2		262	333	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786117	3786117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	550	946	1	ENST00000262367.5:c.4648G>A	p.Glu1550Lys	p.E1550K	ENST00000262367	NM_004380.2	1550	Gaa/Aaa	28/31	1	2	FACETS	0.974	0.939	1	1	0.998	1	CLONAL	2	FALSE	1	0.492162339563941	2		947	1147	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866626	37866626	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	392	626	2	ENST00000269571.5:c.793G>A	p.Glu265Lys	p.E265K	ENST00000269571		265	Gag/Aag	7/27	1	2	FACETS	0.969	0.927	1	1	0.997	1	CLONAL	2	FALSE	1	0.492162339563941	2		628	822	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798969	45798969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782041	NA	P-0034252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	573	790	2	ENST00000450313.1:c.376C>T	p.Arg126Trp	p.R126W	ENST00000450313	NM_012222.2	126	Cgg/Tgg	4/16	0.492162339563941	3	FACETS	0.881	0.85	0.911	1	0.997	1	CLONAL	3	FALSE	1	0.492162339563941	3		792	1098	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984438	201984450	+	frameshift_variant,stop_lost	Frame_Shift_Del	DEL	AGAGTCGGAACTG	AGAGTCGGAACTG	-	novel	NA	P-0034252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	212	521	1	ENST00000359651.3:c.1105_*1del		p.QSRN*368fs	ENST00000359651		368	cAGAGTCGGAACTGa/ca	8/8	1	2	FACETS	0.766	0.717	0.816	1	0.992	1	SUBCLONAL	2	FALSE	1	0.492162339563941	2		522	562	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435312	49435312	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	365	768	1	ENST00000301067.7:c.6241G>C	p.Glu2081Gln	p.E2081Q	ENST00000301067	NM_003482.3	2081	Gag/Cag	31/54	0.0644941775744472	4	FACETS	0.915	0.873	0.958	1	0.995	1	INDETERMINATE	3	FALSE	2	0.492162339563941	4		769	806	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436013	49436013	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	346	639	1	ENST00000301067.7:c.5968G>T	p.Glu1990Ter	p.E1990*	ENST00000301067	NM_003482.3	1990	Gag/Tag	28/54	0.0644941775744472	4	FACETS	0.955	0.911	1	1	0.995	1	INDETERMINATE	3	FALSE	2	0.492162339563941	4		640	732	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879710	123879710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	16	92	0	ENST00000330479.4:c.406G>A	p.Glu136Lys	p.E136K	ENST00000330479	NM_020382.3	136	Gaa/Aaa	4/9	1	2	FACETS	0.823	0.621	1	0.823	0.621	1	CLONAL	1	FALSE	1	0.492162339563941	2		92	79	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321730	30321730	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	249	497	1	ENST00000322652.5:c.1585C>T	p.Leu529Phe	p.L529F	ENST00000322652	NM_015355.2	529	Ctt/Ttt	13/16	1	2	FACETS	0.889	0.839	0.94	1	0.995	1	CLONAL	2	FALSE	1	0.492162339563941	2		498	569	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7163171	7163171	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	199	710	0	ENST00000302850.5:c.1901C>A	p.Ser634Ter	p.S634*	ENST00000302850	NM_000208.2	634	tCa/tAa	9/22	1	2	FACETS	0.886	0.821	0.953	0.886	0.821	0.953	CLONAL	1	FALSE	1	0.492162339563941	2		710	913	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354168	15354168	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	323	689	3	ENST00000263377.2:c.2712del	p.Met905TrpfsTer44	p.M905Wfs*44	ENST00000263377	NM_058243.2	904	ccC/cc	14/20	1	2	FACETS	0.882	0.838	0.926	1	0.996	1	CLONAL	2	FALSE	1	0.492162339563941	2		692	744	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967007	18967018	+	inframe_deletion	In_Frame_Del	DEL	GCAGAAGCTGCA	GCAGAAGCTGCA	-	novel	NA	P-0034252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	251	586	2	ENST00000262803.5:c.1726_1737del	p.Lys576_Gln579del	p.K576_Q579del	ENST00000262803	NM_002911.3	574	ctGCAGAAGCTGCAg/ctg	13/24	1	2	FACETS	0.964	0.912	1	1	0.995	1	CLONAL	2	FALSE	1	0.492162339563941	2		588	529	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463173	25463173	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs760624806	NA	P-0034252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	265	447	2	ENST00000264709.3:c.2320G>A	p.Glu774Lys	p.E774K	ENST00000264709	NM_175629.2	774	Gag/Aag	19/23	0.492162339563941	1	FACETS	0.929	0.886	0.971	1	0.996	1	CLONAL	2	FALSE	0	0.492162339563941	1		449	437	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721473	49721473	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	157	491	0	ENST00000449682.2:c.2166G>C	p.Met722Ile	p.M722I	ENST00000449682	NM_020998.3	722	atG/atC	18/18	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	FALSE	1	0.492162339563941	2		491	631	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247253	153247253	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	298	409	0	ENST00000281708.4:c.1549G>T	p.Gly517Ter	p.G517*	ENST00000281708	NM_033632.3	517	Gga/Tga	10/12	1	2	FACETS	0.955	0.907	1	1	0.996	1	CLONAL	2	FALSE	1	0.492162339563941	2		409	634	SUCCESS
MET	4233	MSKCC	GRCh37	7	116381050	116381050	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	442	778	2	ENST00000397752.3:c.1672C>T	p.Gln558Ter	p.Q558*	ENST00000397752	NM_000245.2	558	Caa/Taa	5/21	1	2	FACETS	0.922	0.883	0.961	1	0.997	1	CLONAL	2	FALSE	1	0.492162339563941	2		780	974	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172936	38172936	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	210	646	0	ENST00000317025.8:c.2113C>G	p.Gln705Glu	p.Q705E	ENST00000317025	NM_023034.1	705	Cag/Gag	11/24	1	2	FACETS	0.985	0.916	1	0.985	0.916	1	CLONAL	1	FALSE	1	0.492162339563941	2		646	866	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169601	27169601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540914328	NA	P-0034252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	225	752	2	ENST00000380036.4:c.602C>T	p.Ser201Leu	p.S201L	ENST00000380036	NM_000459.3	201	tCg/tTg	4/23	0.492162339563941	1	FACETS	0.92	0.86	0.982	0.92	0.86	0.982	CLONAL	1	FALSE	0	0.492162339563941	1		754	749	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932222	39932222	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	684	529	1	ENST00000378444.4:c.2377C>G	p.Gln793Glu	p.Q793E	ENST00000378444	NM_001123385.1	793	Caa/Gaa	4/15	1	1	FACETS	0.969	0.958	0.979	1	0.998	1	CLONAL	3	FALSE	0	0.492162339563941	1		530	721	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691025	NA	P-0034254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	531	572	0	ENST00000269305.4:c.785G>T	p.Gly262Val	p.G262V	ENST00000269305	NM_001126112.2	262	gGt/gTt	8/11	0.859206425829504	3	FACETS	0.988	0.97	1	0.988	0.97	1	CLONAL	3	FALSE	0	0.859322744142202	3		572	596	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027244	49027244	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	191	409	0	ENST00000267163.4:c.1811A>G	p.Asp604Gly	p.D604G	ENST00000267163	NM_000321.2	604	gAt/gGt	18/27	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	2	FALSE	NA	0.859322744142202	2		409	214	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	459942	459942	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	268	549	0	ENST00000399788.2:c.1153G>A	p.Val385Ile	p.V385I	ENST00000399788	NM_001042603.1	385	Gtt/Att	10/28	0.859322744142202	4	FACETS	0.91	0.86	0.961	0.91	0.86	0.961	CLONAL	2	FALSE	2	0.859322744142202	4		549	637	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857349	9857349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	280	481	0	ENST00000330684.3:c.4052G>A	p.Ser1351Asn	p.S1351N	ENST00000330684	NM_001134407.1	1351	aGc/aAc	13/13	0.759533354826261	4	FACETS	0.969	0.918	1	0.969	0.918	1	CLONAL	2	FALSE	2	0.859322744142202	4		481	625	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553474	29553474	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	226	647	0	ENST00000356175.3:c.2024del	p.Gly675GlufsTer13	p.G675Efs*13	ENST00000356175	NM_000267.3	675	Gga/ga	18/57	0.829569525491853	4	FACETS	1	0.979	1	0.373	0.347	0.399	CLONAL	1	FALSE	1	0.859322744142202	4		647	875	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220874	36220874	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	100	203	0	ENST00000222270.7:c.4924G>C	p.Glu1642Gln	p.E1642Q	ENST00000222270	NM_014727.1	1642	Gag/Cag	23/37	0.693366476924797	4	FACETS	0.933	0.85	1	0.933	0.85	1	CLONAL	2	FALSE	2	0.859322744142202	4		203	232	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726649	41726649	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	400	718	0	ENST00000301178.4:c.194C>A	p.Pro65His	p.P65H	ENST00000301178	NM_021913.4	65	cCc/cAc	2/20	0.693366476924797	4	FACETS	0.939	0.897	0.981	0.939	0.897	0.981	CLONAL	2	FALSE	2	0.859322744142202	4		718	922	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503732	186503732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	286	548	0	ENST00000323963.5:c.409G>A	p.Gly137Ser	p.G137S	ENST00000323963		137	Ggt/Agt	5/11	0.859322744142202	6	FACETS	0.907	0.853	0.961	0.453	0.426	0.481	CLONAL	2	FALSE	2	0.859322744142202	6		548	998	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532749	187532749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756315351	NA	P-0034254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	392	599	1	ENST00000441802.2:c.9644C>T	p.Thr3215Ile	p.T3215I	ENST00000441802	NM_005245.3	3215	aCt/aTt	14/27	0.859171858747175	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	FALSE	1	0.859322744142202	3		600	626	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288801	33288801	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1477247712	NA	P-0034254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	294	454	0	ENST00000374542.5:c.751C>T	p.Arg251Cys	p.R251C	ENST00000374542	NM_001141970.1	251	Cgt/Tgt	3/8	0.859322744142202	3	FACETS	0.976	0.932	1	0.976	0.932	1	CLONAL	2	FALSE	1	0.859322744142202	3		454	501	SUCCESS
AR	367	MSKCC	GRCh37	X	66931501	66931501	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	335	601	0	ENST00000374690.3:c.2143C>A	p.His715Asn	p.H715N	ENST00000374690	NM_000044.3	715	Cac/Aac	4/8	0.655049652994455	4	FACETS	0.965	0.919	1	0.965	0.919	1	CLONAL	2	FALSE	2	0.859322744142202	4		601	751	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940080	76940080	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	205	467	0	ENST00000373344.5:c.668G>T	p.Cys223Phe	p.C223F	ENST00000373344	NM_000489.3	223	tGt/tTt	9/35	0.655049652994455	4	FACETS	0.846	0.792	0.902	0.846	0.792	0.902	CLONAL	2	FALSE	2	0.859322744142202	4		467	524	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0034266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	251	626	1	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.734481669659904	2		627	682	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156713	20156713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	165	299	0	ENST00000379607.5:c.44G>A	p.Gly15Asp	p.G15D	ENST00000379607	NM_001412.3	15	gGt/gAt	2/7	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.734481669659904	1		299	210	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431954	49431954	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	287	742	0	ENST00000301067.7:c.9185A>G	p.Lys3062Arg	p.K3062R	ENST00000301067	NM_003482.3	3062	aAg/aGg	34/54	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.734481669659904	2		742	764	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0034275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	86	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.987	0.882	1	0.987	0.882	1	CLONAL	1	TRUE	1	0.565839155967208	2		502	308	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523142	176523142	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1281	138	676	0	ENST00000292408.4:c.1906G>C	p.Gly636Arg	p.G636R	ENST00000292408	NM_213647.1	636	Ggc/Cgc	14/18	0.565839155967208	9	FACETS	1	0.926	1			1	CLONAL	1	TRUE	NA	0.565839155967208	9		676	1419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577600	7577601	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0034275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	99	502	0	ENST00000269305.4:c.680_681del	p.Ser227Ter	p.S227*	ENST00000269305	NM_001126112.2	227	tCT/t	7/11	0.565839155967208	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.565839155967208	1		502	247	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202170	108202170	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0034275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	52	289	0	ENST00000278616.4:c.7516-1G>C		p.X2506_splice	ENST00000278616	NM_000051.3	2506			1	2	FACETS	0.924	0.798	1	0.924	0.798	1	CLONAL	1	TRUE	1	0.565839155967208	2		289	199	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604732	48604739	+	frameshift_variant	Frame_Shift_Del	DEL	CAAAGAAA	CAAAGAAA	-	novel	NA	P-0034275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	121	391	0	ENST00000342988.3:c.1556_1563del	p.Lys519ThrfsTer5	p.K519Tfs*5	ENST00000342988	NM_005359.5	518	atCAAAGAAAca/atca	12/12	0.565839155967208	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.565839155967208	1		391	269	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971164	21971164	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	120	430	0	ENST00000304494.5:c.194T>C	p.Leu65Pro	p.L65P	ENST00000304494	NM_000077.4	65	cTc/cCc	2/3	0.565839155967208	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.565839155967208	1		430	272	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817729	3817729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780618828	NA	P-0034277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	58	458	0	ENST00000262367.5:c.3242G>A	p.Arg1081His	p.R1081H	ENST00000262367	NM_004380.2	1081	cGc/cAc	16/31	1	2	FACETS	0.627	0.538	0.723	0.627	0.538	0.723	SUBCLONAL	1	TRUE	1	0.31	2		458	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574030	7574030	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	171	461	0	ENST00000269305.4:c.997del	p.Arg333ValfsTer12	p.R333Vfs*12	ENST00000269305	NM_001126112.2	333	Cgt/gt	10/11	0.153100583312675	0	FACETS	0.905	0.843	0.969			1	CLONAL	5	TRUE	0	0.153100583312675	0		461	418	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543850	212543850	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	32	382	0	ENST00000342788.4:c.1549C>A	p.Pro517Thr	p.P517T	ENST00000342788	NM_005235.2	517	Cca/Aca	13/28	0.123977244934788	4	FACETS	1	0.836	1	0.345	0.279	0.419	CLONAL	1	TRUE	1	0.153100583312675	4		382	466	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71008428	71008428	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	107	288	0	ENST00000318789.4:c.2004del	p.Asp669MetfsTer4	p.D669Mfs*4	ENST00000318789	NM_032682.5	668	gaA/ga	21/21	0.371414985252468	5	FACETS	0.961	0.866	1	0.64	0.577	0.706	CLONAL	2	TRUE	2	0.371414985252468	5		288	467	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	31	460	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.803	0.655	0.967	0.803	0.655	0.967	CLONAL	1	FALSE	1	0.392052722391194	2		460	197	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0034297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	34	438	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.903	0.746	1	0.903	0.746	1	CLONAL	1	FALSE	1	0.392052722391194	2		438	192	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412095	63412095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852217	NA	P-0034297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	135	608	0	ENST00000330258.3:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000330258	NM_152424.3	358	Cga/Tga	2/2	1	1	FACETS	0.873	0.806	0.941	1	0.99	1	CLONAL	2	FALSE	0	0.392052722391194	1		608	317	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593466	48593466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064796102	NA	P-0034297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	71	409	0	ENST00000342988.3:c.1217C>T	p.Ala406Val	p.A406V	ENST00000342988	NM_005359.5	406	gCg/gTg	10/12	0.392052722391194	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	0	0.392052722391194	1		409	238	SUCCESS
APC	324	MSKCC	GRCh37	5	112174430	112174430	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs568149455	NA	P-0034297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	15	307	0	ENST00000257430.4:c.3139G>T	p.Glu1047Ter	p.E1047*	ENST00000257430	NM_000038.5	1047	Gaa/Taa	16/16	1	2	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	FALSE	1	0.392052722391194	2		307	64	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120132	70120133	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0034297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	77	259	0	ENST00000245479.2:c.1137_1138dup	p.His380ArgfsTer4	p.H380Rfs*4	ENST00000245479	NM_000346.3	378	-/GC	3/3	0.392052722391194	1	FACETS	0.818	0.734	0.905	1	0.982	1	CLONAL	2	FALSE	0	0.392052722391194	1		259	193	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214866	36214866	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768047932	NA	P-0034297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	194	945	1	ENST00000222270.7:c.3292G>A	p.Gly1098Arg	p.G1098R	ENST00000222270	NM_014727.1	1098	Ggg/Agg	8/37	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.392052722391194	2		946	733	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528243	157528243	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs797045283	NA	P-0034297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	88	636	1	ENST00000346085.5:c.5968C>T	p.Arg1990Ter	p.R1990*	ENST00000346085	NM_020732.3	1990	Cga/Tga	20/20	0.101657979498661	4	FACETS	1	0.98	1	0.746	0.664	0.832	INDETERMINATE	1	FALSE	2	0.392052722391194	4		637	419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876658468	NA	P-0034298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	173	809	0	ENST00000269305.4:c.577C>G	p.His193Asp	p.H193D	ENST00000269305	NM_001126112.2	193	Cat/Gat	6/11	NA	2	FACETS	0.764	0.711	0.817			1	INDETERMINATE	2	FALSE	NA	0.531830071540984	2		809	426	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11168283	11168283	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	185	886	0	ENST00000361445.4:c.7589A>G	p.Lys2530Arg	p.K2530R	ENST00000361445	NM_004958.3	2530	aAa/aGa	57/58	NA	2	FACETS	1	0.961	1			1	INDETERMINATE	1	FALSE	NA	0.531830071540984	2		886	659	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592644	28592644	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	23	640	0	ENST00000241453.7:c.2501G>C	p.Arg834Pro	p.R834P	ENST00000241453	NM_004119.2	834	cGa/cCa	20/24	0.531830071540984	1	FACETS	0.202	0.157	0.253	0.202	0.157	0.253	SUBCLONAL	1	FALSE	0	0.531830071540984	1		640	315	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0034342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	237	514	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.320576268809974	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	1	0.32362699228884	3		514	840	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0034342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	294	740	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.32362699228884	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.32362699228884	2		740	874	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28644632	28644632	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	93	581	0	ENST00000241453.7:c.161C>A	p.Pro54His	p.P54H	ENST00000241453	NM_004119.2	54	cCc/cAc	2/24	0.282277700071863	3	FACETS	0.873	0.776	0.977	0.436	0.388	0.489	CLONAL	1	TRUE	1	0.32362699228884	3		581	765	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748096	41748096	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	11	83	0	ENST00000226382.2:c.673G>T	p.Gly225Trp	p.G225W	ENST00000226382	NM_003924.3	225	Ggg/Tgg	3/3	1	2	FACETS	0.839	0.588	1	0.839	0.588	1	CLONAL	1	TRUE	1	0.32362699228884	2		83	81	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192432	138192432	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	68	382	0	ENST00000237289.4:c.68A>G	p.Glu23Gly	p.E23G	ENST00000237289	NM_001270507.1	23	gAg/gGg	2/9	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.32362699228884	2		382	399	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0034349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	263	451	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.271055086162106	5	FACETS	1	0.967	1	0.82	0.778	0.861	CLONAL	4	TRUE	0	0.417378663269459	5		451	500	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252994	36252995	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0034349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	178	363	0	ENST00000300305.3:c.367dup	p.Asp123GlyfsTer15	p.D123Gfs*15	ENST00000300305		123	gat/gGat	4/8	0.329474123010853	3	FACETS	0.916	0.849	0.984	0.916	0.849	0.984	CLONAL	2	TRUE	1	0.417378663269459	3		363	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577563	7577563	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	212	676	0	ENST00000269305.4:c.718del	p.Ser240ValfsTer7	p.S240Vfs*7	ENST00000269305	NM_001126112.2	240	Agt/gt	7/11	0.347326068843755	2	FACETS	0.893	0.836	0.951	0.893	0.836	0.951	CLONAL	2	TRUE	0	0.417378663269459	2		676	569	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	105	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.501485406549425	2		148	386	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0034356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	187	458	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	0.501485406549425	2		458	744	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121913370	NA	P-0034356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	21	231	0	ENST00000288602.6:c.1742A>G	p.Asn581Ser	p.N581S	ENST00000288602	NM_004333.4	581	aAt/aGt	15/18	0.501485406549425	2	FACETS	0.219	0.168	0.279	0.11	0.084	0.14	SUBCLONAL	1	TRUE	0	0.501485406549425	2		231	382	SUCCESS
APC	324	MSKCC	GRCh37	5	112174760	112174760	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1554085038	NA	P-0034356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	64	275	0	ENST00000257430.4:c.3469G>C	p.Glu1157Gln	p.E1157Q	ENST00000257430	NM_000038.5	1157	Gag/Cag	16/16	1	2	FACETS	0.798	0.696	0.906	0.798	0.696	0.906	CLONAL	1	TRUE	1	0.501485406549425	2		275	320	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679546	86679546	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554050230	NA	P-0034356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	160	430	0	ENST00000274376.6:c.2707C>T	p.Arg903Ter	p.R903*	ENST00000274376	NM_002890.2	903	Cga/Tga	21/25	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.501485406549425	2		430	600	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205250	46205250	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	86	435	0	ENST00000334344.6:c.334G>A	p.Glu112Lys	p.E112K	ENST00000334344	NM_152641.2	112	Gag/Aag	4/21	1	2	FACETS	0.466	0.412	0.524	0.466	0.412	0.524	SUBCLONAL	1	TRUE	1	0.501485406549425	2		435	736	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	282	625	0	ENST00000267101.3:c.273G>C	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atC	3/28	1	2	FACETS	0.94	0.883	0.999	0.94	0.883	0.999	CLONAL	1	TRUE	1	0.501485406549425	2		625	1196	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822523	72822523	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	83	640	0	ENST00000268489.5:c.9652C>G	p.Pro3218Ala	p.P3218A	ENST00000268489	NM_006885.3	3218	Ccg/Gcg	10/10	1	2	FACETS	0.328	0.288	0.37	0.328	0.288	0.37	SUBCLONAL	1	TRUE	1	0.501485406549425	2		640	1010	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831105	72831105	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200091224	NA	P-0034356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	180	436	1	ENST00000268489.5:c.5476G>A	p.Gly1826Arg	p.G1826R	ENST00000268489	NM_006885.3	1826	Ggg/Agg	9/10	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.501485406549425	2		437	709	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618889	37618889	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	154	446	0	ENST00000447079.4:c.565G>A	p.Glu189Lys	p.E189K	ENST00000447079	NM_015083.1	189	Gag/Aag	1/14	1	2	FACETS	0.869	0.797	0.944	0.869	0.797	0.944	CLONAL	1	TRUE	1	0.501485406549425	2		446	707	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266510	198266510	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	143	380	0	ENST00000335508.6:c.2326G>C	p.Glu776Gln	p.E776Q	ENST00000335508	NM_012433.2	776	Gaa/Caa	16/25	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.501485406549425	2		380	553	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594245	55594245	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	152	444	0	ENST00000288135.5:c.1948C>T	p.His650Tyr	p.H650Y	ENST00000288135	NM_000222.2	650	Cac/Tac	13/21	1	2	FACETS	0.855	0.784	0.929	0.855	0.784	0.929	CLONAL	1	TRUE	1	0.501485406549425	2		444	709	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84384035	84384035	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	236	563	0	ENST00000321945.7:c.817G>C	p.Asp273His	p.D273H	ENST00000321945	NM_139076.2	273	Gac/Cac	9/9	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.501485406549425	2		563	938	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271269	153271269	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	65	242	0	ENST00000281708.4:c.509G>C	p.Arg170Thr	p.R170T	ENST00000281708	NM_033632.3	170	aGa/aCa	3/12	1	2	FACETS	0.836	0.731	0.949	0.836	0.731	0.949	CLONAL	1	TRUE	1	0.501485406549425	2		242	310	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531146	187531146	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	138	323	0	ENST00000441802.2:c.9877C>A	p.Leu3293Met	p.L3293M	ENST00000441802	NM_005245.3	3293	Ctg/Atg	15/27	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.501485406549425	2		323	544	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564474	86564474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	196	464	0	ENST00000274376.6:c.206C>T	p.Ser69Leu	p.S69L	ENST00000274376	NM_002890.2	69	tCa/tTa	1/25	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.501485406549425	2		464	627	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853065	151853065	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	362	371	0	ENST00000262189.6:c.11890C>T	p.Gln3964Ter	p.Q3964*	ENST00000262189	NM_170606.2	3964	Cag/Tag	46/59	0.501485406549425	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.501485406549425	2		371	691	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139794883	139794883	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	130	360	0	ENST00000247668.2:c.277G>T	p.Asp93Tyr	p.D93Y	ENST00000247668	NM_021138.3	93	Gat/Tat	4/11	0.501485406549425	1	FACETS	0.954	0.874	1	0.954	0.874	1	CLONAL	1	TRUE	0	0.501485406549425	1		360	407	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0034358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	403	749	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	0.815239262182537	1	FACETS	0.949	0.922	0.975	0.949	0.922	0.975	CLONAL	1	TRUE	0	0.90206422221063	1		749	517	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699445	117699445	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	356	624	0	ENST00000369458.3:c.196G>A	p.Asp66Asn	p.D66N	ENST00000369458	NM_024626.3	66	Gat/Aat	3/6	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.90206422221063	2		624	718	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0034365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1182	68	583	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	0.311	0.269	0.356	0.311	0.269	0.356	SUBCLONAL	1	TRUE	1	0.35	2		583	1250	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115898	8115899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0034365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1236	152	362	0	ENST00000346208.3:c.1245dup	p.Leu416AlafsTer91	p.L416Afs*91	ENST00000346208		415	atg/atGg	6/6	1	2	FACETS	0.626	0.57	0.684	0.626	0.57	0.684	SUBCLONAL	1	TRUE	1	0.35	2		362	1388	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32968840	32968840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80359194	NA	P-0034365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	12	237	0	ENST00000380152.3:c.9271G>A	p.Val3091Ile	p.V3091I	ENST00000380152		3091	Gtc/Atc	25/27	0.2397049537557	1	FACETS	0.453	0.32	0.613	0.453	0.32	0.613	SUBCLONAL	1	TRUE	0	0.35	1		237	125	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250876	10250876	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	76	412	0	ENST00000340748.4:c.3604G>C	p.Glu1202Gln	p.E1202Q	ENST00000340748		1202	Gag/Cag	32/40	1	2	FACETS	0.372	0.325	0.424	0.372	0.325	0.424	SUBCLONAL	1	TRUE	1	0.35	2		412	1166	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	368	627	0	ENST00000397752.3:c.3028G>A	p.Asp1010Asn	p.D1010N	ENST00000397752	NM_000245.2	1010	Gat/Aat	14/21	0.412687164773734	3	FACETS	0.929	0.887	0.971	0.929	0.887	0.971	CLONAL	3	TRUE	0	0.412687164773734	3		627	772	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827732	72827732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241554729	NA	P-0034368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	170	504	1	ENST00000268489.5:c.8849G>A	p.Arg2950His	p.R2950H	ENST00000268489	NM_006885.3	2950	cGc/cAc	9/10	0.284829751005292	2	FACETS	1	0.977	1	0.577	0.532	0.624	CLONAL	1	TRUE	0	0.412687164773734	2		505	714	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867291	45867291	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199863965	NA	P-0034368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	159	599	1	ENST00000391945.4:c.902C>T	p.Thr301Met	p.T301M	ENST00000391945	NM_000400.3	301	aCg/aTg	10/23	0.216458161367266	5	FACETS	1	0.937	1			1	INDETERMINATE	1	TRUE	NA	0.412687164773734	5		600	1211	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263331	115263331	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	85	501	0	ENST00000438362.2:c.2019G>A	p.Met673Ile	p.M673I	ENST00000438362	NM_001242891.1	673	atG/atA	17/20	1	2	FACETS	0.632	0.559	0.71	0.632	0.559	0.71	SUBCLONAL	1	TRUE	1	0.412687164773734	2		501	652	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172404	7172404	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	81	459	1	ENST00000302850.5:c.1165G>A	p.Glu389Lys	p.E389K	ENST00000302850	NM_000208.2	389	Gaa/Aaa	5/22	1	2	FACETS	0.653	0.576	0.736	0.653	0.576	0.736	SUBCLONAL	1	TRUE	1	0.412687164773734	2		460	601	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645900	215645900	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	138	612	0	ENST00000260947.4:c.698A>C	p.Glu233Ala	p.E233A	ENST00000260947	NM_000465.2	233	gAg/gCg	4/11	0.152229964021455	3	FACETS	1	0.979	1	0.618	0.563	0.674	INDETERMINATE	1	TRUE	1	0.412687164773734	3		612	653	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161825	47161825	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	91	409	0	ENST00000409792.3:c.4301G>A	p.Gly1434Glu	p.G1434E	ENST00000409792	NM_014159.6	1434	gGa/gAa	3/21	1	2	FACETS	0.796	0.708	0.889	0.796	0.708	0.889	SUBCLONAL	1	TRUE	1	0.412687164773734	2		409	554	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240446	98240446	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs975634341	NA	P-0034368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	77	361	0	ENST00000331920.6:c.1238A>G	p.Gln413Arg	p.Q413R	ENST00000331920	NM_000264.3	413	cAg/cGg	9/24	0.112997904962791	5	FACETS	0.931	0.817	1	0.233	0.204	0.264	INDETERMINATE	1	TRUE	1	0.412687164773734	5		361	649	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	102	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.932	0.842	1	0.932	0.842	1	CLONAL	1	TRUE	1	0.61306988496399	2		148	357	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711976	89711978	+	frameshift_variant	Frame_Shift_Ins	INS	GAT	GAT	AAACC	novel	NA	P-0034371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	131	346	3	ENST00000371953.3:c.594_596delinsAAACC	p.Met198IlefsTer24	p.M198Ifs*24	ENST00000371953	NM_000314.4	198	atGATg/atAAACCg	6/9	0.61306988496399	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.61306988496399	1		349	278	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398255	25398255	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913236	NA	P-0034371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	18	497	0	ENST00000311936.3:c.64C>A	p.Gln22Lys	p.Q22K	ENST00000311936	NM_004985.3	22	Cag/Aag	2/5	1	2	FACETS	0.1	0.074	0.13	0.1	0.074	0.13	SUBCLONAL	1	TRUE	1	0.61306988496399	2		497	589	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553486	29553487	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0034371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	576	497	0	ENST00000356175.3:c.2038dup	p.Cys680LeufsTer20	p.C680Lfs*20	ENST00000356175	NM_000267.3	679	att/aTtt	18/57	0.595035453120022	3	FACETS	0.9	0.873	0.927	0.9	0.873	0.927	CLONAL	3	TRUE	0	0.61306988496399	3		497	909	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0034372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	340	880	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.349222794996636	2	FACETS	0.867	0.825	0.908	1	0.994	1	CLONAL	3	TRUE	0	0.349222794996636	2		882	749	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942194	81942194	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs147406608	NA	P-0034372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	61	304	0	ENST00000359376.3:c.1731C>A	p.Phe577Leu	p.F577L	ENST00000359376	NM_002661.3	577	ttC/ttA	17/33	0.184074390088233	3	FACETS	0.846	0.731	0.971	0.423	0.365	0.486	INDETERMINATE	1	TRUE	1	0.349222794996636	3		304	485	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610715	52610715	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0034372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	94	287	0	ENST00000394830.3:c.3459-1G>T		p.X1153_splice	ENST00000394830	NM_018313.4	1153			0.349222794996636	3	FACETS	1	0.975	1	0.661	0.591	0.736	CLONAL	1	TRUE	1	0.349222794996636	3		287	478	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546093	29546093	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	107	375	0	ENST00000356175.3:c.1598T>A	p.Val533Asp	p.V533D	ENST00000356175	NM_000267.3	533	gTc/gAc	14/57	0.231418887492499	3	FACETS	1	0.976	1			1	CLONAL	1	TRUE	NA	0.349222794996636	3		375	556	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52621446	52621446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	267	467	0	ENST00000394830.3:c.2971G>A	p.Glu991Lys	p.E991K	ENST00000394830	NM_018313.4	991	Gaa/Aaa	20/30	0.349222794996636	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.349222794996636	3		467	748	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949074	44949074	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs797045644	NA	P-0034372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	249	237	0	ENST00000377967.4:c.3635A>G	p.Gln1212Arg	p.Q1212R	ENST00000377967	NM_021140.2	1212	cAg/cGg	25/29	0.300913708658697	2	FACETS	1	0.99	1			1	CLONAL	3	TRUE	NA	0.349222794996636	2		237	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0034374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	401	392	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.164490364169427	3	FACETS	1	0.992	1			1	INDETERMINATE	3	TRUE	NA	0.315393876894516	3		392	853	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391103	89391103	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	92	415	0	ENST00000336596.2:c.1169C>A	p.Thr390Asn	p.T390N	ENST00000336596	NM_005233.5	390	aCc/aAc	5/17	1	2	FACETS	0.906	0.806	1	0.906	0.806	1	CLONAL	1	TRUE	1	0.315393876894516	2		415	644	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647949	3647949	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	150	526	0	ENST00000294008.3:c.1215G>C	p.Lys405Asn	p.K405N	ENST00000294008	NM_032444.2	405	aaG/aaC	6/15	0.315393876894516	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.315393876894516	1		526	763	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725482	117725482	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	99	397	0	ENST00000368508.3:c.399G>C	p.Trp133Cys	p.W133C	ENST00000368508	NM_002944.2	133	tgG/tgC	5/43	0.315393876894516	3	FACETS	0.963	0.859	1	0.481	0.429	0.537	CLONAL	1	TRUE	1	0.315393876894516	3		397	755	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578289	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AGATGCTGAGGAGGGGCCAGAC	AGATGCTGAGGAGGGGCCAGAC	GGTCTT	novel	NA	P-0034376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	279	461	1	ENST00000269305.4:c.560_581delinsAAGACC	p.Gly187GlufsTer55	p.G187Efs*55	ENST00000269305	NM_001126112.2	187	gGTCTGGCCCCTCCTCAGCATCTt/gAAGACCt	6/11	0.501032759206969	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.500348152264428	2		462	503	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011192	12011192	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	206	290	1	ENST00000353533.5:c.599T>C	p.Ile200Thr	p.I200T	ENST00000353533	NM_003010.3	200	aTt/aCt	5/11	0.501032759206969	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.500348152264428	2		291	397	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	58	460	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.171838923370442	3	FACETS	1	0.901	1	0.526	0.455	0.604	INDETERMINATE	1	TRUE	1	0.392269979140152	3		460	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0034377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	54	581	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.297586181763912	1	FACETS	0.408	0.349	0.474	0.408	0.349	0.474	SUBCLONAL	1	TRUE	0	0.392269979140152	1		582	542	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0034377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	28	305	3	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.613	0.492	0.749	0.613	0.492	0.749	SUBCLONAL	1	TRUE	1	0.392269979140152	2		308	233	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141493	11141493	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	72	452	3	ENST00000358026.2:c.3470G>A	p.Arg1157Gln	p.R1157Q	ENST00000358026	NM_001128849.1	1157	cGg/cAg	25/36	1	2	FACETS	0.576	0.503	0.655	0.576	0.503	0.655	SUBCLONAL	1	TRUE	1	0.392269979140152	2		455	637	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934190	39934190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146403660	NA	P-0034377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	43	578	6	ENST00000378444.4:c.409G>A	p.Val137Ile	p.V137I	ENST00000378444	NM_001123385.1	137	Gtc/Atc	4/15	1	2	FACETS	0.274	0.229	0.325	0.274	0.229	0.325	SUBCLONAL	1	TRUE	1	0.392269979140152	2		584	799	SUCCESS
APC	324	MSKCC	GRCh37	5	112175672	112175672	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	25	284	0	ENST00000257430.4:c.4381G>T	p.Glu1461Ter	p.E1461*	ENST00000257430	NM_000038.5	1461	Gaa/Taa	16/16	1	2	FACETS	0.502	0.397	0.622	0.502	0.397	0.622	SUBCLONAL	1	TRUE	1	0.392269979140152	2		284	254	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435262	18435262	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	51	304	8	ENST00000266497.5:c.247C>A	p.Gln83Lys	p.Q83K	ENST00000266497		83	Caa/Aaa	1/31	0.171838923370442	3	FACETS	1	0.873	1	0.512	0.437	0.592	INDETERMINATE	1	TRUE	1	0.392269979140152	3		312	304	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245471	46245471	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	71	278	4	ENST00000334344.6:c.3565C>T	p.Gln1189Ter	p.Q1189*	ENST00000334344	NM_152641.2	1189	Cag/Tag	15/21	0.204084051673308	2	FACETS	1	0.883	1	0.503	0.441	0.568	INDETERMINATE	1	TRUE	0	0.392269979140152	2		282	360	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681776	78681776	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	70	450	1	ENST00000306801.3:c.484G>A	p.Gly162Arg	p.G162R	ENST00000306801	NM_020761.2	162	Ggg/Agg	4/34	0.297586181763912	1	FACETS	0.398	0.346	0.454	0.398	0.346	0.454	SUBCLONAL	1	TRUE	0	0.392269979140152	1		451	721	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530115	212530116	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0034377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	37	320	3	ENST00000342788.4:c.1803_1804del	p.Asn601LysfsTer8	p.N601Kfs*8	ENST00000342788	NM_005235.2	601	aaCAgt/aagt	15/28	1	2	FACETS	0.49	0.404	0.586	0.49	0.404	0.586	SUBCLONAL	1	TRUE	1	0.392269979140152	2		323	385	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735457	40735457	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	67	517	9	ENST00000373198.4:c.3416G>T	p.Arg1139Leu	p.R1139L	ENST00000373198	NM_133170.3	1139	cGg/cTg	25/32	1	2	FACETS	0.535	0.464	0.611	0.535	0.464	0.611	SUBCLONAL	1	TRUE	1	0.392269979140152	2		526	639	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046467	69046467	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	46	459	1	ENST00000288368.4:c.3940G>T	p.Ala1314Ser	p.A1314S	ENST00000288368	NM_024870.2	1314	Gca/Tca	32/40	0.36810580586032	3	FACETS	0.481	0.405	0.566	0.241	0.202	0.283	SUBCLONAL	1	TRUE	1	0.392269979140152	3		460	583	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913548	39913548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768510508	NA	P-0034377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	39	396	2	ENST00000378444.4:c.4780G>A	p.Ala1594Thr	p.A1594T	ENST00000378444	NM_001123385.1	1594	Gcc/Acc	13/15	1	2	FACETS	0.354	0.293	0.422	0.354	0.293	0.422	SUBCLONAL	1	TRUE	1	0.392269979140152	2		398	562	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0034385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	232	458	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.514204459071656	6	FACETS	1	0.975	1	1	0.975	1	CLONAL	4	TRUE	2	0.606355796567909	6		458	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	366	643	0	ENST00000269305.4:c.383del	p.Pro128LeufsTer42	p.P128Lfs*42	ENST00000269305	NM_001126112.2	128	cCt/ct	5/11	0.606355796567909	3	FACETS	0.991	0.956	1			1	CLONAL	3	TRUE	NA	0.606355796567909	3		643	529	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220711	1220714	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CACC	CACC	-	novel	NA	P-0034385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	192	529	0	ENST00000326873.7:c.730_733del	p.Thr244SerfsTer42	p.T244Sfs*42	ENST00000326873	NM_000455.4	243	gtCACC/gt	5/10	0.514204459071656	6	FACETS	1	0.981	1	0.577	0.537	0.619	CLONAL	2	TRUE	2	0.606355796567909	6		529	607	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593455	215593455	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881425	NA	P-0034385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	90	286	0	ENST00000260947.4:c.2279C>T	p.Ser760Leu	p.S760L	ENST00000260947	NM_000465.2	760	tCg/tTg	11/11	0.32972557765506	3	FACETS	0.93	0.843	1	0.93	0.843	1	INDETERMINATE	2	TRUE	1	0.606355796567909	3		286	208	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0034387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	99	463	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.44849523766643	2	FACETS	0.964	0.866	1	0.482	0.433	0.533	CLONAL	1	TRUE	0	0.497347590152597	2		463	413	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275813	38275813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs575766741	NA	P-0034387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	135	542	1	ENST00000425967.3:c.1456C>T	p.Pro486Ser	p.P486S	ENST00000425967	NM_001174067.1	486	Ccc/Tcc	11/19	1	2	FACETS	0.934	0.853	1	0.934	0.853	1	CLONAL	1	TRUE	1	0.497347590152597	2		543	581	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466025	69466026	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGA	novel	NA	P-0034387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	98	606	0	ENST00000227507.2:c.863_864insTGA	p.Asp289dup	p.D289dup	ENST00000227507	NM_053056.2	289	acc/acTGAc	5/5	1	2	FACETS	0.715	0.64	0.795	0.715	0.64	0.795	SUBCLONAL	1	TRUE	1	0.497347590152597	2		606	551	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221976	1221976	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs730881984	NA	P-0034387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	112	715	1	ENST00000326873.7:c.891G>T	p.Arg297Ser	p.R297S	ENST00000326873	NM_000455.4	297	agG/agT	7/10	0.497347590152597	1	FACETS	0.734	0.664	0.807	0.734	0.664	0.807	SUBCLONAL	1	TRUE	0	0.497347590152597	1		716	461	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0034392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	15	663	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.815	1	1	0.815	1	CLONAL	1	FALSE	1	0.280075977195662	2		663	95	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0034392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	63	274	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	FALSE	1	0.280075977195662	2		274	450	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944973	31944973	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	57	636	0	ENST00000340398.3:c.128C>T	p.Pro43Leu	p.P43L	ENST00000340398	NM_001013699.2	43	cCt/cTt	1/1	1	2	FACETS	0.844	0.726	0.974	0.844	0.726	0.974	CLONAL	1	FALSE	1	0.280075977195662	2		636	482	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920280	1920280	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1306925576	NA	P-0034392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	30	688	0	ENST00000382891.5:c.1340C>T	p.Ser447Phe	p.S447F	ENST00000382891	NM_133335.3	447	tCc/tTc	5/22	1	2	FACETS	0.908	0.735	1	0.908	0.735	1	CLONAL	1	FALSE	1	0.280075977195662	2		688	236	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503815	149503815	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1389426768	NA	P-0034392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	68	561	0	ENST00000261799.4:c.2021G>A	p.Gly674Glu	p.G674E	ENST00000261799	NM_002609.3	674	gGa/gAa	14/23	1	2	FACETS	0.856	0.746	0.976	0.856	0.746	0.976	CLONAL	1	FALSE	1	0.280075977195662	2		561	567	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041265	47041265	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	75	384	0	ENST00000377604.3:c.1693C>G	p.Pro565Ala	p.P565A	ENST00000377604	NM_001204468.1	565	Cct/Gct	15/24	1	1	FACETS	0.76	0.672	0.852	1	0.978	1	SUBCLONAL	2	FALSE	0	0.280075977195662	1		384	303	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	71	643	0	ENST00000269305.4:c.383del	p.Pro128LeufsTer42	p.P128Lfs*42	ENST00000269305	NM_001126112.2	128	cCt/ct	5/11	1	2	FACETS	0.467	0.406	0.532	0.467	0.406	0.532	SUBCLONAL	1	TRUE	1	0.379360094885257	2		643	802	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0034396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	21	266	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.285	0.219	0.363	0.285	0.219	0.363	SUBCLONAL	1	TRUE	1	0.379360094885257	2		266	388	SUCCESS
APC	324	MSKCC	GRCh37	5	112175751	112175752	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1114167577	NA	P-0034396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	29	301	0	ENST00000257430.4:c.4463dup	p.Leu1488PhefsTer26	p.L1488Ffs*26	ENST00000257430	NM_000038.5	1487	act/acTt	16/16	1	2	FACETS	0.335	0.268	0.411	0.335	0.268	0.411	SUBCLONAL	1	TRUE	1	0.379360094885257	2		301	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034396-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	282	643	0	ENST00000269305.4:c.383del	p.Pro128LeufsTer42	p.P128Lfs*42	ENST00000269305	NM_001126112.2	128	cCt/ct	5/11	0.572814439384678	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.572814439384678	1		643	596	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0034396-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	65	266	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.831	0.728	0.941	0.831	0.728	0.941	CLONAL	1	TRUE	1	0.572814439384678	2		266	273	SUCCESS
APC	324	MSKCC	GRCh37	5	112175751	112175752	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1114167577	NA	P-0034396-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	58	301	0	ENST00000257430.4:c.4463dup	p.Leu1488PhefsTer26	p.L1488Ffs*26	ENST00000257430	NM_000038.5	1487	act/acTt	16/16	1	2	FACETS	0.833	0.724	0.95	0.833	0.724	0.95	CLONAL	1	TRUE	1	0.572814439384678	2		301	243	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557630	95557630	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	227	495	0	ENST00000393063.1:c.5437G>C	p.Glu1813Gln	p.E1813Q	ENST00000393063	NM_030621.3	1813	Gag/Cag	26/28	1	2	FACETS	0.887	0.832	0.944	1	0.994	1	CLONAL	2	TRUE	1	0.41	2		495	624	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560488	95560488	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	204	431	0	ENST00000393063.1:c.5101del	p.Tyr1701ThrfsTer4	p.Y1701Tfs*4	ENST00000393063	NM_030621.3	1701	Tac/ac	25/28	1	2	FACETS	1	0.956	1	1	0.994	1	CLONAL	2	TRUE	1	0.41	2		431	485	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	198	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.742362313552907	2		148	511	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720650	89720650	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0034410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	45	226	0	ENST00000371953.3:c.802-1G>C		p.X268_splice	ENST00000371953	NM_000314.4	268			0.742362313552907	1	FACETS	0.886	0.779	0.994	0.886	0.779	0.994	CLONAL	1	TRUE	0	0.742362313552907	1		226	86	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107042	27107043	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0034410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	90	490	0	ENST00000324856.7:c.6654dup	p.Gln2219AlafsTer6	p.Q2219Afs*6	ENST00000324856	NM_006015.4	2218	atg/atGg	20/20	1	2	FACETS	0.349	0.31	0.392	0.349	0.31	0.392	SUBCLONAL	1	TRUE	1	0.742362313552907	2		490	694	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0034414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	111	463	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.96	0.875	1	0.96	0.875	1	CLONAL	1	TRUE	1	0.75810929238525	2		463	305	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628026	187628026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750746155	NA	P-0034414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	225	589	0	ENST00000441802.2:c.2956G>A	p.Val986Ile	p.V986I	ENST00000441802	NM_005245.3	986	Gtc/Atc	2/27	1	2	FACETS	0.986	0.925	1	0.986	0.925	1	CLONAL	1	TRUE	1	0.75810929238525	2		589	602	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70432654	70432654	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs776044335	NA	P-0034414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	114	361	0	ENST00000373644.4:c.4676G>A	p.Arg1559His	p.R1559H	ENST00000373644	NM_030625.2	1559	cGt/cAt	8/12	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.75810929238525	2		361	299	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868516	117868516	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	140	253	0	ENST00000297338.2:c.826G>C	p.Asp276His	p.D276H	ENST00000297338	NM_006265.2	276	Gat/Cat	8/14	0.75810929238525	5	FACETS	0.759	0.695	0.825	0.506	0.463	0.55	SUBCLONAL	2	TRUE	2	0.75810929238525	5		253	520	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176132125	176132125	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0034414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	102	363	0	ENST00000367669.3:c.643-1G>C		p.X215_splice	ENST00000367669	NM_022457.5	215			0.752597797190622	4	FACETS	1	0.91	1	0.253	0.227	0.28	CLONAL	1	TRUE	0	0.75810929238525	4		363	467	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115716	8115717	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0034414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	89	287	0	ENST00000346208.3:c.1063dup	p.Thr355AsnfsTer16	p.T355Nfs*16	ENST00000346208		354	-/A	6/6	1	2	FACETS	0.845	0.759	0.933	0.845	0.759	0.933	CLONAL	1	TRUE	1	0.75810929238525	2		287	278	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95598882	95598882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	120	471	0	ENST00000393063.1:c.277G>A	p.Gly93Arg	p.G93R	ENST00000393063	NM_030621.3	93	Gga/Aga	4/28	1	2	FACETS	0.795	0.725	0.869	0.795	0.725	0.869	SUBCLONAL	1	TRUE	1	0.75810929238525	2		471	398	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95598887	95598887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878855252	NA	P-0034414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	117	478	0	ENST00000393063.1:c.272G>A	p.Arg91Lys	p.R91K	ENST00000393063	NM_030621.3	91	aGa/aAa	4/28	1	2	FACETS	0.806	0.734	0.881	0.806	0.734	0.881	CLONAL	1	TRUE	1	0.75810929238525	2		478	383	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43730552	43730552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200776719	NA	P-0034414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	160	488	0	ENST00000382044.4:c.3161G>A	p.Arg1054Gln	p.R1054Q	ENST00000382044	NM_001141980.1	1054	cGa/cAa	16/28	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.75810929238525	2		488	422	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063711	67063712	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAATCGT	novel	NA	P-0034414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	91	203	0	ENST00000412916.2:c.163_165+4dup		p.E54fs	ENST00000412916		54	gaa/gAAATCGTaa	2/6	0.75810929238525	1	FACETS	0.926	0.85	1	0.926	0.85	1	CLONAL	1	TRUE	0	0.75810929238525	1		203	161	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022793	31022793	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1167715259	NA	P-0034414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	172	489	0	ENST00000375687.4:c.2278C>T	p.Gln760Ter	p.Q760*	ENST00000375687	NM_015338.5	760	Cag/Tag	13/13	0.606462839438675	3	FACETS	0.99	0.915	1	0.495	0.457	0.534	CLONAL	1	TRUE	1	0.75810929238525	3		489	632	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267836	46267836	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0034414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	216	582	0	ENST00000371998.3:c.2597C>G	p.Ser866Ter	p.S866*	ENST00000371998		866	tCa/tGa	14/23	0.606462839438675	3	FACETS	1	0.948	1	0.51	0.475	0.545	CLONAL	1	TRUE	1	0.75810929238525	3		582	771	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247376	71247376	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	179	384	0	ENST00000318789.4:c.157del	p.His53ThrfsTer29	p.H53Tfs*29	ENST00000318789	NM_032682.5	53	Cac/ac	6/21	1	2	FACETS	0.998	0.929	1	0.998	0.929	1	CLONAL	1	TRUE	1	0.75810929238525	2		384	473	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066471	94066471	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1179484555	NA	P-0034414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	117	300	0	ENST00000369303.4:c.1288C>T	p.Leu430Phe	p.L430F	ENST00000369303	NM_004440.3	430	Ctc/Ttc	5/17	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.75810929238525	2		300	306	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382238	152382238	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	164	416	0	ENST00000206249.3:c.1348T>G	p.Ser450Ala	p.S450A	ENST00000206249	NM_000125.3	450	Tct/Gct	6/8	1	2	FACETS	0.943	0.873	1	0.943	0.873	1	CLONAL	1	TRUE	1	0.75810929238525	2		416	459	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918647	94918647	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	47	322	0	ENST00000536441.1:c.535A>G	p.Lys179Glu	p.K179E	ENST00000536441	NM_144665.3	179	Aaa/Gaa	5/10	1	2	FACETS	0.678	0.573	0.793	0.678	0.573	0.793	SUBCLONAL	1	TRUE	1	0.334256525551151	2		322	415	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0034423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	100	354	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.861	0.781	0.943	0.861	0.781	0.943	CLONAL	1	TRUE	1	0.850664700304406	2		354	273	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519925	NA	P-0034423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	162	554	0	ENST00000263967.3:c.1357G>C	p.Glu453Gln	p.E453Q	ENST00000263967	NM_006218.2	453	Gaa/Caa	8/21	1	2	FACETS	0.959	0.891	1	0.959	0.891	1	CLONAL	1	TRUE	1	0.850664700304406	2		554	397	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970913	21970913	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	244	633	0	ENST00000304494.5:c.445G>T	p.Glu149Ter	p.E149*	ENST00000304494	NM_000077.4	149	Gaa/Taa	2/3	0.850664700304406	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.850664700304406	1		633	307	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112473	115112473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	195	521	1	ENST00000257566.3:c.1267del	p.Arg423GlyfsTer209	p.R423Gfs*209	ENST00000257566	NM_016569.3	423	Cgg/gg	7/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.850664700304406	2		522	432	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572194	64572194	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	183	462	0	ENST00000312049.6:c.1445del	p.Gly482AlafsTer77	p.G482Afs*77	ENST00000312049	NM_130799.2	482	gGc/gc	10/10	0.850664700304406	1	FACETS	0.973	0.927	1	0.973	0.927	1	CLONAL	1	TRUE	0	0.850664700304406	1		462	254	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857112	68857398	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GACCAAATGGAAATAAAGCTTTTTACAGCAAAAAAAAAAAAAAAAAAGTACATACCTAAATAAAACCCAAGCAGCTCTGCTCTCTTCACTCGGCTTGCGGGTGTCTTTAGTTCACTAGCAATTTTATTCTGGAATGAGCTTTTTATTTTCCTCCCCTGGTCTCATCATTTCTTTTTATTGCTTTCTCCAGCCCAAGAATCTATCATTTTGAAGCCAAAGATGGCCTTAGAGGTGGGTGACTACAAAATCAATCTCAAGCTCATGGATAACCAGAATAAAGACCAAGT	GACCAAATGGAAATAAAGCTTTTTACAGCAAAAAAAAAAAAAAAAAAGTACATACCTAAATAAAACCCAAGCAGCTCTGCTCTCTTCACTCGGCTTGCGGGTGTCTTTAGTTCACTAGCAATTTTATTCTGGAATGAGCTTTTTATTTTCCTCCCCTGGTCTCATCATTTCTTTTTATTGCTTTCTCCAGCCCAAGAATCTATCATTTTGAAGCCAAAGATGGCCTTAGAGGTGGGTGACTACAAAATCAATCTCAAGCTCATGGATAACCAGAATAAAGACCAAGT	-	novel	NA	P-0034423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	114	19	0	ENST00000261769.5:c.1937-185_2038del		p.X646_splice	ENST00000261769	NM_004360.3	646		13/16	0.850664700304406	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.850664700304406	1		19	119	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926617	59926617	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	82	451	0	ENST00000259008.2:c.380A>T	p.Asp127Val	p.D127V	ENST00000259008	NM_032043.2	127	gAc/gTc	5/20	NA	2	FACETS	0.699	0.624	0.777			1	INDETERMINATE	1	TRUE	NA	0.850664700304406	2		451	276	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932680	49932680	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	201	622	0	ENST00000296474.3:c.3191C>G	p.Ser1064Cys	p.S1064C	ENST00000296474	NM_002447.2	1064	tCt/tGt	14/20	1	2	FACETS	0.897	0.838	0.956	0.897	0.838	0.956	CLONAL	1	TRUE	1	0.850664700304406	2		622	527	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877810	151877810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	102	312	0	ENST00000262189.6:c.7135G>A	p.Glu2379Lys	p.E2379K	ENST00000262189	NM_170606.2	2379	Gag/Aag	36/59	1	2	FACETS	0.898	0.816	0.982	0.898	0.816	0.982	CLONAL	1	TRUE	1	0.850664700304406	2		312	267	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs786202525	NA	P-0034426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	276	688	0	ENST00000269305.4:c.532del	p.His178ThrfsTer69	p.H178Tfs*69	ENST00000269305	NM_001126112.2	178	Cac/ac	5/11	0.210263206794853	5	FACETS	1	0.977	1	0.855	0.806	0.905	CLONAL	4	TRUE	0	0.210263206794853	5		688	808	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495038	56495038	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	118	591	0	ENST00000267101.3:c.3395A>G	p.Tyr1132Cys	p.Y1132C	ENST00000267101	NM_001982.3	1132	tAc/tGc	27/28	0.210263206794853	2	FACETS	0.876	0.791	0.964	0.876	0.791	0.964	CLONAL	2	TRUE	0	0.210263206794853	2		591	641	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119635015	119635015	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	38	156	0	ENST00000316626.5:c.484A>T	p.Met162Leu	p.M162L	ENST00000316626		162	Atg/Ttg	5/12	0.0643163415212509	4	FACETS	0.875	0.728	1	0.875	0.728	1	INDETERMINATE	2	TRUE	2	0.210263206794853	4		156	250	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0034428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	214	539	1	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	0.269326353161466	3	FACETS	0.848	0.795	0.903	0.848	0.795	0.903	CLONAL	3	TRUE	0	0.347455567441541	3		540	568	SUCCESS
EED	8726	MSKCC	GRCh37	11	85977216	85977216	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	24	321	0	ENST00000263360.6:c.818C>G	p.Ala273Gly	p.A273G	ENST00000263360	NM_003797.3	273	gCa/gGa	8/12	0.347455567441541	3	FACETS	0.421	0.33	0.527	0.211	0.165	0.264	SUBCLONAL	1	TRUE	1	0.347455567441541	3		321	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578540	7578541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGGGC	novel	NA	P-0034429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	32	724	0	ENST00000269305.4:c.385_389dup	p.Asn131ProfsTer41	p.N131Pfs*41	ENST00000269305	NM_001126112.2	130	ctc/ctGCCCTc	5/11	1	2	FACETS	0.623	0.509	0.75	0.623	0.509	0.75	SUBCLONAL	1	TRUE	1	0.454630037019545	2		724	226	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842732	68842732	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	34	472	0	ENST00000261769.5:c.668A>C	p.Glu223Ala	p.E223A	ENST00000261769	NM_004360.3	223	gAa/gCa	5/16	0.264002779341465	1	FACETS	0.722	0.598	0.858	0.722	0.598	0.858	INDETERMINATE	1	TRUE	0	0.454630037019545	1		472	160	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0034430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	344	690	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.508339533371516	1	FACETS	0.778	0.743	0.812	1	0.996	1	SUBCLONAL	2	TRUE	0	0.508339533371516	1		690	649	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440001	56440001	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0034430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	289	557	0	ENST00000407977.2:c.591T>A	p.Tyr197Ter	p.Y197*	ENST00000407977		197	taT/taA	6/10	0.403409422870364	0	FACETS		NA	1			1	NA	2	TRUE	0	0.508339533371516	0		557	513	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208356	5208356	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1257575436	NA	P-0034430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	354	700	0	ENST00000357368.4:c.5534C>T	p.Pro1845Leu	p.P1845L	ENST00000357368	NM_002850.3	1845	cCg/cTg	36/38	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.508339533371516	2		700	936	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942124	81942125	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0034430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	179	642	1	ENST00000359376.3:c.1667dup	p.Lys557GlnfsTer16	p.K557Qfs*16	ENST00000359376	NM_002661.3	554	acg/acGg	17/33	0.373180784372443	1	FACETS	0.712	0.658	0.768	0.712	0.658	0.768	SUBCLONAL	1	TRUE	0	0.508339533371516	1		643	738	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28607287	28607287	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778863205	NA	P-0034430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	203	571	0	ENST00000253063.3:c.1417C>T	p.Arg473Cys	p.R473C	ENST00000253063	NM_031459.4	473	Cgt/Tgt	10/10	0.400473702123862	1	FACETS	0.757	0.703	0.812	0.757	0.703	0.812	SUBCLONAL	1	TRUE	0	0.508339533371516	1		571	787	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467523	66467523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	150	396	0	ENST00000273854.3:c.746G>A	p.Gly249Glu	p.G249E	ENST00000273854	NM_004439.5	249	gGa/gAa	3/18	0.400473702123862	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.508339533371516	1		396	395	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169102	32169102	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	235	653	0	ENST00000375023.3:c.3931C>T	p.Gln1311Ter	p.Q1311*	ENST00000375023	NM_004557.3	1311	Cag/Tag	22/30	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.508339533371516	2		653	852	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349698	70349698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	194	282	0	ENST00000374080.3:c.3860G>A	p.Cys1287Tyr	p.C1287Y	ENST00000374080		1287	tGc/tAc	27/45	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.508339533371516	1		282	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0034431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	581	573	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.678793518023782	3	FACETS	0.995	0.97	1			1	CLONAL	3	TRUE	NA	0.678793518023782	3		574	768	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0034431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	141	240	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.678793518023782	2	FACETS	0.931	0.874	0.987	0.931	0.874	0.987	CLONAL	2	TRUE	0	0.678793518023782	2		240	223	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465600	8465600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1427192894	NA	P-0034431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	686	602	1	ENST00000356435.5:c.3580G>A	p.Ala1194Thr	p.A1194T	ENST00000356435		1194	Gct/Act	21/35	0.678793518023782	6	FACETS	0.954	0.924	0.983	0.954	0.924	0.983	CLONAL	4	TRUE	2	0.678793518023782	6		603	1249	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670674	134670674	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	376	730	0	ENST00000398015.3:c.585G>C	p.Lys195Asn	p.K195N	ENST00000398015	NM_004441.4	195	aaG/aaC	3/16	0.619447332174193	5	FACETS	0.924	0.877	0.971	0.616	0.585	0.648	CLONAL	2	TRUE	2	0.678793518023782	5		730	1210	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593315	67593317	+	inframe_deletion	In_Frame_Del	DEL	GTA	GTA	-	novel	NA	P-0034431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	74	342	0	ENST00000274335.5:c.2061_2063del	p.Leu687_Tyr688delinsPhe	p.L687_Y688delinsF	ENST00000274335		687	ttGTAc/ttc	15/15	0.678793518023782	2	FACETS	0.734	0.649	0.824	0.367	0.324	0.412	SUBCLONAL	1	TRUE	0	0.678793518023782	2		342	297	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68292191	68292191	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs768563592	NA	P-0034434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	232	448	1	ENST00000487270.1:c.95G>T	p.Cys32Phe	p.C32F	ENST00000487270	NM_133509.3	32	tGt/tTt	3/11	1	2	FACETS	0.971	0.915	1	0.971	0.915	1	CLONAL	1	TRUE	1	0.882850287426014	2		449	541	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857616	9857616	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780351	NA	P-0034434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	247	521	0	ENST00000330684.3:c.3785C>T	p.Thr1262Ile	p.T1262I	ENST00000330684	NM_001134407.1	1262	aCc/aTc	13/13	1	2	FACETS	0.973	0.918	1	0.973	0.918	1	CLONAL	1	TRUE	1	0.882850287426014	2		521	575	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306569	41306569	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	77	578	0	ENST00000373198.4:c.1090C>T	p.Arg364Ter	p.R364*	ENST00000373198	NM_133170.3	364	Cga/Tga	7/32	0.226834249343907	3	FACETS	0.984	0.863	1	0.492	0.431	0.558	CLONAL	1	TRUE	1	0.226834249343907	3		578	768	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847399	68847399	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0034443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	71	466	0	ENST00000261769.5:c.1320+1G>T		p.X440_splice	ENST00000261769	NM_004360.3	440			0.226834249343907	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	0	0.226834249343907	1		466	531	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495016	56495016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776728303	NA	P-0034443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	141	498	0	ENST00000267101.3:c.3373C>T	p.Arg1125Trp	p.R1125W	ENST00000267101	NM_001982.3	1125	Cgg/Tgg	27/28	0.158617092318863	3	FACETS	0.914	0.834	0.998	0.914	0.834	0.998	CLONAL	2	TRUE	1	0.226834249343907	3		498	757	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	110	460	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.221300673350702	3	FACETS	1	0.973	1	0.619	0.557	0.685	CLONAL	1	FALSE	1	0.3	3		460	681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0034447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	76	605	14	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	NA	2	FACETS	0.571	0.5	0.648			1	INDETERMINATE	1	FALSE	NA	0.3	2		619	887	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28605681	28605681	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	64	523	0	ENST00000253063.3:c.1285G>A	p.Ala429Thr	p.A429T	ENST00000253063	NM_031459.4	429	Gcc/Acc	9/10	1	2	FACETS	0.594	0.514	0.682	0.594	0.514	0.682	SUBCLONAL	1	FALSE	1	0.3	2		523	718	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27016034	27016034	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	58	559	0	ENST00000335756.4:c.310C>A	p.His104Asn	p.H104N	ENST00000335756	NM_001809.3	104	Cat/Aat	4/5	1	2	FACETS	0.502	0.43	0.581	0.502	0.43	0.581	SUBCLONAL	1	FALSE	1	0.3	2		559	770	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	45	485	3	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.239296113320959	3	FACETS	0.587	0.493	0.691	0.294	0.246	0.346	SUBCLONAL	1	FALSE	1	0.350376216604123	3		488	514	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111499	8111500	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTCC	novel	NA	P-0034449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	45	556	0	ENST00000346208.3:c.986_987insTCCG	p.Arg329SerfsTer24	p.R329Sfs*24	ENST00000346208		329	agg/aGTCCgg	5/6	1	2	FACETS	0.448	0.376	0.528	0.448	0.376	0.528	SUBCLONAL	1	FALSE	1	0.350376216604123	2		556	573	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618667	37618667	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1218924913	NA	P-0034449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	33	421	2	ENST00000447079.4:c.343C>A	p.Gln115Lys	p.Q115K	ENST00000447079	NM_015083.1	115	Cag/Aag	1/14	0.236897053500168	4	FACETS	0.48	0.39	0.582			1	SUBCLONAL	1	FALSE	NA	0.350376216604123	4		423	530	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883587	37883587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	45	710	2	ENST00000269571.5:c.3199G>A	p.Glu1067Lys	p.E1067K	ENST00000269571		1067	Gaa/Aaa	26/27	0.236897053500168	4	FACETS	0.478	0.401	0.565			1	SUBCLONAL	1	FALSE	NA	0.350376216604123	4		712	725	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109308800	109308800	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	30	258	0	ENST00000436639.2:c.1603A>G	p.Met535Val	p.M535V	ENST00000436639	NM_014454.2	535	Atg/Gtg	10/10	0.293881440530333	3	FACETS	0.789	0.639	0.958	0.395	0.319	0.479	CLONAL	1	FALSE	1	0.350376216604123	3		258	255	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345912	152345912	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1356498203	NA	P-0034449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	44	521	2	ENST00000359321.1:c.658G>C	p.Asp220His	p.D220H	ENST00000359321	NM_005431.1	220	Gac/Cac	3/3	1	2	FACETS	0.49	0.41	0.577	0.49	0.41	0.577	SUBCLONAL	1	FALSE	1	0.350376216604123	2		523	513	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187209	38187209	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs957423620	NA	P-0034449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	349	868	11	ENST00000317025.8:c.1268G>C	p.Arg423Thr	p.R423T	ENST00000317025	NM_023034.1	423	aGa/aCa	6/24	0.350376216604123	4	FACETS	0.855	0.811	0.9	1	0.993	1	CLONAL	3	FALSE	2	0.350376216604123	4		879	1049	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579350	7579350	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587781642	NA	P-0034450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	122	551	0	ENST00000269305.4:c.337T>G	p.Phe113Val	p.F113V	ENST00000269305	NM_001126112.2	113	Ttc/Gtc	4/11	0.347979344483219	2	FACETS	0.798	0.729	0.868	0.798	0.729	0.868	SUBCLONAL	2	TRUE	0	0.434577861567667	2		551	352	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465043	120465043	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	45	349	0	ENST00000256646.2:c.5029C>G	p.Gln1677Glu	p.Q1677E	ENST00000256646	NM_024408.3	1677	Cag/Gag	28/34	0.196316959108797	5	FACETS	1	0.961	1	0.498	0.422	0.58	INDETERMINATE	1	TRUE	2	0.434577861567667	5		349	229	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47108559	47108559	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0034450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	67	404	1	ENST00000409792.3:c.6109+1G>A		p.X2037_splice	ENST00000409792	NM_014159.6	2037			0.317881787367643	4	FACETS	1	0.96	1	0.857	0.771	0.943	CLONAL	3	TRUE	0	0.434577861567667	4		405	129	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29497003	29497003	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397514641	NA	P-0034451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	127	277	0	ENST00000356175.3:c.574C>T	p.Arg192Ter	p.R192*	ENST00000356175	NM_000267.3	192	Cga/Tga	5/57	1	2	FACETS	0.763	0.696	0.833	1	0.987	1	SUBCLONAL	2	TRUE	1	0.364910531438902	2		277	456	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527438	29527438	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs878853922	NA	P-0034451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	117	360	0	ENST00000356175.3:c.889-2A>G		p.X297_splice	ENST00000356175	NM_000267.3	297			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.364910531438902	2		360	509	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937477	76937480	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	novel	NA	P-0034451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	118	458	0	ENST00000373344.5:c.3268_3271del	p.Glu1090ArgfsTer27	p.E1090Rfs*27	ENST00000373344	NM_000489.3	1090	GAGAag/ag	9/35	0.260874566990846	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.364910531438902	1		458	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0034464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	248	609	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.219769905942476	3	FACETS	0.889	0.834	0.945	0.593	0.556	0.63	INDETERMINATE	2	FALSE	0	0.422909038530875	3		609	799	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577116	7577122	+	frameshift_variant	Frame_Shift_Del	DEL	AACACGC	AACACGC	-	novel	NA	P-0034465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	1058	527	0	ENST00000269305.4:c.816_822del	p.Arg273ValfsTer70	p.R273Vfs*70	ENST00000269305	NM_001126112.2	272	gtGCGTGTT/gt	8/11	0.642354680475497	4	FACETS	0.88	0.862	0.898			1	CLONAL	4	TRUE	NA	0.642354680475497	4		527	1537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0034469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	69	594	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	NA	2	FACETS	0.564	0.49	0.645			1	INDETERMINATE	1	TRUE	NA	0.25	2		594	979	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0034473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	82	539	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	1	2	FACETS	0.634	0.561	0.712	0.634	0.561	0.712	SUBCLONAL	1	FALSE	1	0.529028943587055	2		539	489	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	308	716	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.529028943587055	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	0	0.529028943587055	1		716	771	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916944	+	inframe_deletion	In_Frame_Del	DEL	GTGAAGAAA	GTGAAGAAA	-	novel	NA	P-0034473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	125	415	0	ENST00000263967.3:c.323_331del	p.Arg108_Lys111delinsGln	p.R108_K111delinsQ	ENST00000263967	NM_006218.2	108	cGTGAAGAAAag/cag	2/21	1	2	FACETS	0.936	0.852	1	0.936	0.852	1	CLONAL	1	FALSE	1	0.529028943587055	2		415	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0034476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	181	745	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.181481637163087	2	FACETS	0.799	0.736	0.863	0.799	0.736	0.863	SUBCLONAL	2	TRUE	0	0.235819334569604	2		745	961	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260094	16260138	+	inframe_deletion	In_Frame_Del	DEL	CATTGAAAGTGACCCGGTGACCCCACCCAGCGATCCAAGCATCCC	CATTGAAAGTGACCCGGTGACCCCACCCAGCGATCCAAGCATCCC	-	novel	NA	P-0034476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	53	531	0	ENST00000375759.3:c.7362_7406del	p.Glu2455_Ile2469del	p.E2455_I2469del	ENST00000375759	NM_015001.2	2453	atCATTGAAAGTGACCCGGTGACCCCACCCAGCGATCCAAGCATCCCc/atc	11/15	1	2	FACETS	0.671	0.571	0.78	0.671	0.571	0.78	SUBCLONAL	1	TRUE	1	0.235819334569604	2		531	670	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797522	45797522	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0034476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	75	615	0	ENST00000450313.1:c.998-1G>A		p.X333_splice	ENST00000450313	NM_012222.2	333			0.198268425726844	3	FACETS	0.77	0.673	0.875	0.385	0.336	0.438	SUBCLONAL	1	TRUE	1	0.235819334569604	3		615	923	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820793	3820820	+	frameshift_variant	Frame_Shift_Del	DEL	AGTGGGAGCTGCTGGCTGGGGAGGAGTC	AGTGGGAGCTGCTGGCTGGGGAGGAGTC	-	novel	NA	P-0034476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1354	76	937	0	ENST00000262367.5:c.2631_2658del	p.Met877IlefsTer41	p.M877Ifs*41	ENST00000262367	NM_004380.2	877	atGACTCCTCCCCAGCCAGCAGCTCCCACT/at	14/31	0.198268425726844	3	FACETS	0.504	0.44	0.573	0.252	0.22	0.287	SUBCLONAL	1	TRUE	1	0.235819334569604	3		937	1430	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152179	11152179	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	53	503	0	ENST00000358026.2:c.4463C>T	p.Pro1488Leu	p.P1488L	ENST00000358026	NM_001128849.1	1488	cCc/cTc	31/36	0.181481637163087	2	FACETS	0.569	0.484	0.663	0.284	0.242	0.332	SUBCLONAL	1	TRUE	0	0.235819334569604	2		503	790	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015107	27015107	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	36	271	2	ENST00000335756.4:c.209T>C	p.Leu70Pro	p.L70P	ENST00000335756	NM_001809.3	70	cTg/cCg	2/5	0.198268425726844	3	FACETS	0.601	0.493	0.722	0.3	0.246	0.361	SUBCLONAL	1	TRUE	1	0.235819334569604	3		273	568	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402489	20402489	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	66	493	0	ENST00000346618.3:c.26T>C	p.Leu9Pro	p.L9P	ENST00000346618	NM_001949.4	9	cTg/cCg	1/7	0.235819334569604	2	FACETS	0.682	0.591	0.781	0.341	0.295	0.391	SUBCLONAL	1	TRUE	0	0.235819334569604	2		493	821	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972921	68972921	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	131	387	0	ENST00000288368.4:c.1246G>T	p.Val416Leu	p.V416L	ENST00000288368	NM_024870.2	416	Gtg/Ttg	11/40	0.235819334569604	2	FACETS	0.844	0.768	0.924	0.844	0.768	0.924	CLONAL	2	TRUE	0	0.235819334569604	2		387	658	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426465	47426465	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs923151586	NA	P-0034476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	77	568	0	ENST00000377045.4:c.808C>G	p.Pro270Ala	p.P270A	ENST00000377045	NM_001654.4	270	Cca/Gca	9/16	1	2	FACETS	0.709	0.621	0.804	0.709	0.621	0.804	SUBCLONAL	1	TRUE	1	0.235819334569604	2		568	921	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0034478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	339	573	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.797061814058025	2	FACETS	0.967	0.94	0.992	0.967	0.94	0.992	CLONAL	2	TRUE	0	0.859205213467652	2		574	408	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0034478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	79	325	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	0.859205213467652	3	FACETS	0.926	0.824	1	0.309	0.274	0.345	CLONAL	1	TRUE	0	0.859205213467652	3		325	284	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115916	8115916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771315353	NA	P-0034478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	217	473	0	ENST00000346208.3:c.1262C>T	p.Pro421Leu	p.P421L	ENST00000346208		421	cCg/cTg	6/6	0.859205213467652	3	FACETS	0.881	0.832	0.929	0.881	0.832	0.929	CLONAL	2	TRUE	1	0.859205213467652	3		473	410	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164779	106164779	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs562667223	NA	P-0034478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	120	507	0	ENST00000380013.4:c.3647G>A	p.Arg1216Gln	p.R1216Q	ENST00000380013	NM_001127208.2	1216	cGa/cAa	6/11	1	2	FACETS	0.87	0.797	0.945	0.87	0.797	0.945	CLONAL	1	TRUE	1	0.859205213467652	2		507	321	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419987	41419987	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376239850	NA	P-0034478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	120	515	1	ENST00000373198.4:c.334C>T	p.Arg112Cys	p.R112C	ENST00000373198	NM_133170.3	112	Cgt/Tgt	3/32	0.660380750093261	4	FACETS	1	0.925	1	0.341	0.309	0.374	CLONAL	1	TRUE	1	0.859205213467652	4		516	508	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420871	49420871	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555185969	NA	P-0034478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	133	656	2	ENST00000301067.7:c.14878C>T	p.Arg4960Ter	p.R4960*	ENST00000301067	NM_003482.3	4960	Cga/Tga	48/54	0.818086672178994	2	FACETS	0.944	0.87	1	0.472	0.435	0.51	CLONAL	1	TRUE	0	0.859205213467652	2		658	328	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375560	15375560	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1296	83	796	0	ENST00000263377.2:c.867G>C	p.Lys289Asn	p.K289N	ENST00000263377	NM_058243.2	289	aaG/aaC	6/20	0.859205213467652	6	FACETS	0.381	0.334	0.431	0.076	0.066	0.087	SUBCLONAL	1	TRUE	1	0.859205213467652	6		796	1379	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023727	31023727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531415735	NA	P-0034478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	205	724	1	ENST00000375687.4:c.3212C>T	p.Ala1071Val	p.A1071V	ENST00000375687	NM_015338.5	1071	gCg/gTg	13/13	0.660380750093261	4	FACETS	1	0.98	1	0.38	0.353	0.408	CLONAL	1	TRUE	1	0.859205213467652	4		725	778	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098490	47098490	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	42	520	0	ENST00000409792.3:c.6784C>G	p.Pro2262Ala	p.P2262A	ENST00000409792	NM_014159.6	2262	Ccc/Gcc	15/21	0.859205213467652	3	FACETS	0.387	0.324	0.457	0.129	0.108	0.153	SUBCLONAL	1	TRUE	0	0.859205213467652	3		520	361	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0034481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	135	236	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	0.805833392881673	2		236	311	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0034481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	145	274	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.805833392881673	2		274	297	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413070	139413072	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0034481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	230	633	0	ENST00000277541.6:c.1070_1072del	p.Phe357del	p.F357del	ENST00000277541	NM_017617.3	357	tTCTac/tac	6/34	1	2	FACETS	0.91	0.854	0.968	0.91	0.854	0.968	CLONAL	1	TRUE	1	0.805833392881673	2		633	627	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525121	157525122	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0034481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	85	268	0	ENST00000346085.5:c.5020_5021del	p.Ser1674ProfsTer14	p.S1674Pfs*14	ENST00000346085	NM_020732.3	1672	aaTCtc/aatc	19/20	1	2	FACETS	0.722	0.646	0.802	0.722	0.646	0.802	SUBCLONAL	1	TRUE	1	0.805833392881673	2		268	292	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397721	139397721	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	58	678	0	ENST00000277541.6:c.5080C>T	p.Gln1694Ter	p.Q1694*	ENST00000277541	NM_017617.3	1694	Cag/Tag	27/34	1	2	FACETS	0.192	0.164	0.222	0.192	0.164	0.222	SUBCLONAL	1	TRUE	1	0.805833392881673	2		678	751	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58711273	58711273	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs771453009	NA	P-0034481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	506	591	0	ENST00000305921.3:c.761A>G	p.Asn254Ser	p.N254S	ENST00000305921	NM_003620.3	254	aAt/aGt	3/6	0.789409359161759	3	FACETS	0.942	0.908	0.976	0.942	0.908	0.976	CLONAL	2	TRUE	1	0.805833392881673	3		591	935	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794556	42794557	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGC	novel	NA	P-0034481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	311	897	0	ENST00000575354.2:c.1639_1642dup	p.Thr548SerfsTer143	p.T548Sfs*143	ENST00000575354	NM_015125.3	546	gca/gCAGCca	10/20	0.805833392881673	1	FACETS	0.871	0.833	0.909	0.871	0.833	0.909	CLONAL	1	TRUE	0	0.805833392881673	1		897	529	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0034499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	129	425	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.792	0.721	0.865	0.792	0.721	0.865	SUBCLONAL	1	TRUE	1	0.608047197290441	2		425	536	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0034499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	120	277	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	0.992	0.904	1	0.992	0.904	1	CLONAL	1	TRUE	1	0.608047197290441	2		277	398	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913237	NA	P-0034499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	48	369	0	ENST00000369535.4:c.35G>C	p.Gly12Ala	p.G12A	ENST00000369535	NM_002524.4	12	gGt/gCt	2/7	1	2	FACETS	0.315	0.266	0.369	0.315	0.266	0.369	SUBCLONAL	1	TRUE	1	0.608047197290441	2		369	501	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	75	388	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	0.649	0.572	0.731	0.649	0.572	0.731	SUBCLONAL	1	TRUE	1	0.608047197290441	2		388	380	SUCCESS
APC	324	MSKCC	GRCh37	5	112174268	112174268	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0034499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	147	286	0	ENST00000257430.4:c.2977A>T	p.Lys993Ter	p.K993*	ENST00000257430	NM_000038.5	993	Aag/Tag	16/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.608047197290441	2		286	441	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995239	15995239	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	228	516	0	ENST00000268712.3:c.2954del	p.Leu985TrpfsTer30	p.L985Wfs*30	ENST00000268712	NM_006311.3	985	tTg/tg	22/46	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.608047197290441	2		516	738	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874334	151874335	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0034499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	107	436	0	ENST00000262189.6:c.8203_8204del	p.Leu2735ArgfsTer2	p.L2735Rfs*2	ENST00000262189	NM_170606.2	2735	TTa/a	38/59	NA	2	FACETS	0.598	0.537	0.661			1	INDETERMINATE	1	TRUE	NA	0.608047197290441	2		436	589	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	48	148	0				ENST00000310581	NM_198253.2	-/1132			0.097359440662818	4	FACETS	1	0.92	1	1	0.92	1	INDETERMINATE	2	TRUE	2	0.732228874690609	4		148	106	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665752	29665755	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1555535032	NA	P-0034501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	99	219	0	ENST00000356175.3:c.6789_6792del	p.Tyr2264ThrfsTer5	p.Y2264Tfs*5	ENST00000356175	NM_000267.3	2263	ACTTac/ac	45/57	0.732228874690609	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.732228874690609	1		219	155	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176543	56176543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	200	410	0	ENST00000399503.3:c.2093C>T	p.Thr698Ile	p.T698I	ENST00000399503	NM_005921.1	698	aCa/aTa	12/20	0.097359440662818	4	FACETS	0.913	0.854	0.974	0.913	0.854	0.974	INDETERMINATE	2	TRUE	2	0.732228874690609	4		410	518	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224316	55224316	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	185	419	0	ENST00000275493.2:c.1097G>T	p.Ser366Ile	p.S366I	ENST00000275493	NM_005228.3	366	aGt/aTt	9/28	0.456076881451507	4	FACETS	1	0.99	1	0.472	0.438	0.507	CLONAL	1	TRUE	1	0.732228874690609	4		419	618	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0034503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	128	463	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.369751536547955	1	FACETS	0.811	0.748	0.873	0.811	0.748	0.873	INDETERMINATE	1	TRUE	0	0.721222853072377	1		463	280	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405955	70405955	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	92	494	1	ENST00000373644.4:c.3469G>C	p.Asp1157His	p.D1157H	ENST00000373644	NM_030625.2	1157	Gat/Cat	4/12	0.369751536547955	1	FACETS	0.5	0.449	0.554	0.5	0.449	0.554	INDETERMINATE	1	TRUE	0	0.721222853072377	1		495	326	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132894	64132894	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	70	609	0	ENST00000334205.4:c.1028C>T	p.Ser343Leu	p.S343L	ENST00000334205	NM_003942.2	343	tCa/tTa	9/17	0.721222853072377	3	FACETS	0.667	0.584	0.755			1	SUBCLONAL	1	TRUE	NA	0.721222853072377	3		609	396	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236220	108236220	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587781711	NA	P-0034503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	105	518	1	ENST00000278616.4:c.9156G>T	p.Trp3052Cys	p.W3052C	ENST00000278616	NM_000051.3	3052	tgG/tgT	63/63	0.721222853072377	1	FACETS	0.996	0.919	1	0.996	0.919	1	CLONAL	1	TRUE	0	0.721222853072377	1		519	187	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248872	133248872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	133	552	2	ENST00000320574.5:c.1723G>A	p.Glu575Lys	p.E575K	ENST00000320574	NM_006231.2	575	Gag/Aag	16/49	0.456132578644896	1	FACETS	0.659	0.606	0.713	0.659	0.606	0.713	SUBCLONAL	1	TRUE	0	0.721222853072377	1		554	358	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41022050	41022050	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0034503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	81	532	0	ENST00000267868.3:c.775-1G>C		p.X259_splice	ENST00000267868	NM_002875.4	259			0.369751536547955	1	FACETS	0.453	0.403	0.506	0.453	0.403	0.506	INDETERMINATE	1	TRUE	0	0.721222853072377	1		532	317	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801803	3801803	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	62	414	0	ENST00000262367.5:c.3703C>G	p.His1235Asp	p.H1235D	ENST00000262367	NM_004380.2	1235	Cat/Gat	20/31	1	2	FACETS	0.445	0.386	0.509	0.445	0.386	0.509	SUBCLONAL	1	TRUE	1	0.721222853072377	2		414	386	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832607	72832607	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0034503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	94	251	0	ENST00000268489.5:c.3974C>G	p.Ser1325Ter	p.S1325*	ENST00000268489	NM_006885.3	1325	tCa/tGa	9/10	0.721222853072377	2	FACETS	0.893	0.826	0.956	0.893	0.826	0.956	CLONAL	2	TRUE	0	0.721222853072377	2		251	146	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805552	46805552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769634543	NA	P-0034503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	72	745	1	ENST00000290295.7:c.404G>A	p.Gly135Glu	p.G135E	ENST00000290295	NM_006361.5	135	gGa/gAa	1/2	1	2	FACETS	0.489	0.429	0.553	0.489	0.429	0.553	SUBCLONAL	1	TRUE	1	0.721222853072377	2		746	408	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770065	56770065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752608224	NA	P-0034503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	61	435	0	ENST00000337432.4:c.61C>T	p.Pro21Ser	p.P21S	ENST00000337432	NM_058216.2	21	Cca/Tca	1/9	1	2	FACETS	0.395	0.342	0.453	0.395	0.342	0.453	SUBCLONAL	1	TRUE	1	0.721222853072377	2		435	428	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926549	59926549	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762701532	NA	P-0034503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	157	594	0	ENST00000259008.2:c.448G>A	p.Glu150Lys	p.E150K	ENST00000259008	NM_032043.2	150	Gaa/Aaa	5/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.721222853072377	2		594	399	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054656	13054656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	59	485	0	ENST00000316448.5:c.1183G>A	p.Glu395Lys	p.E395K	ENST00000316448	NM_004343.3	395	Gag/Aag	9/9	1	2	FACETS	0.445	0.384	0.51	0.445	0.384	0.51	SUBCLONAL	1	TRUE	1	0.721222853072377	2		485	368	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0034503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	46	457	0	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	0.369751536547955	1	FACETS	0.32	0.271	0.373	0.32	0.271	0.373	INDETERMINATE	1	TRUE	0	0.721222853072377	1		457	255	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156122	99156122	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	53	472	0	ENST00000074304.5:c.802G>C	p.Glu268Gln	p.E268Q	ENST00000074304	NM_001134224.1	268	Gag/Cag	10/26	0.369751536547955	1	FACETS	0.41	0.354	0.471	0.41	0.354	0.471	INDETERMINATE	1	TRUE	0	0.721222853072377	1		472	229	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664519	138664519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	18	185	0	ENST00000330315.3:c.1046G>A	p.Arg349Gln	p.R349Q	ENST00000330315	NM_023067.3	349	cGg/cAg	1/1	0.369751536547955	1	FACETS	0.285	0.217	0.363	0.285	0.217	0.363	INDETERMINATE	1	TRUE	0	0.721222853072377	1		185	112	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163533	32163533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370041101	NA	P-0034503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	100	434	1	ENST00000375023.3:c.5693G>A	p.Arg1898Gln	p.R1898Q	ENST00000375023	NM_004557.3	1898	cGg/cAg	30/30	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.721222853072377	2		435	257	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845205	151845205	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	118	468	0	ENST00000262189.6:c.13807G>T	p.Glu4603Ter	p.E4603*	ENST00000262189	NM_170606.2	4603	Gag/Tag	52/59	0.363297122209145	1	FACETS	0.89	0.822	0.959	0.89	0.822	0.959	INDETERMINATE	1	TRUE	0	0.721222853072377	1		468	235	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5557620	5557620	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	94	468	0	ENST00000397747.3:c.634C>T	p.Gln212Ter	p.Q212*	ENST00000397747	NM_025239.3	212	Cag/Tag	5/7	1	2	FACETS	0.938	0.846	1	0.938	0.846	1	CLONAL	1	TRUE	1	0.721222853072377	2		468	278	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626688	100626688	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	36	386	0	ENST00000308731.7:c.242G>A	p.Arg81Lys	p.R81K	ENST00000308731	NM_000061.2	81	aGa/aAa	4/19	0.287349164277981	1	FACETS	0.27	0.224	0.322	0.27	0.224	0.322	INDETERMINATE	1	TRUE	0	0.721222853072377	1		386	236	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195078	123195078	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	95	350	0	ENST00000218089.9:c.1421A>G	p.His474Arg	p.H474R	ENST00000218089	NM_001042749.1	474	cAt/cGt	16/35	0.287349164277981	1	FACETS	0.749	0.68	0.818	0.749	0.68	0.818	INDETERMINATE	1	TRUE	0	0.721222853072377	1		350	225	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37092008	37092009	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	A	novel	NA	P-0034503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	51	457	0	ENST00000231790.2:c.2135_2136delinsA	p.Trp712Ter	p.W712*	ENST00000231790	NM_000249.3	712	tGG/tA	19/19	0.369751536547955	1	FACETS	0.328	0.28	0.379	0.328	0.28	0.379	INDETERMINATE	1	TRUE	0	0.721222853072377	1		457	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780071	NA	P-0034504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	90	490	0	ENST00000269305.4:c.580C>T	p.Leu194Phe	p.L194F	ENST00000269305	NM_001126112.2	194	Ctt/Ttt	6/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.321389064331437	2		490	489	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0034504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	33	463	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.951	0.78	1	0.951	0.78	1	CLONAL	1	FALSE	1	0.321389064331437	2		463	216	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0034504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	15	266	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.392	0.287	0.519	0.392	0.287	0.519	SUBCLONAL	1	FALSE	1	0.321389064331437	2		266	238	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924303	11924303	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs940014479	NA	P-0034504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	12	39	0	ENST00000353533.5:c.100G>T	p.Val34Phe	p.V34F	ENST00000353533	NM_003010.3	34	Gtc/Ttc	1/11	1	2	FACETS	0.545	0.385	0.74	0.545	0.385	0.74	SUBCLONAL	1	FALSE	1	0.321389064331437	2		39	137	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437530	56437531	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0034504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	91	539	0	ENST00000407977.2:c.931dup	p.Leu311ProfsTer132	p.L311Pfs*132	ENST00000407977		311	ctc/cCtc	8/10	0.0315978556650003	3	FACETS	1	0.915	1	0.518	0.46	0.579	INDETERMINATE	1	FALSE	1	0.321389064331437	3		539	635	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151650	55151651	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AATGTAAGTTCAAGGAACACAGACCTTTTTAGACCCAGATTTC	novel	NA	P-0034504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	18	587	0	ENST00000257290.5:c.2438_2439+41dup		p.-812fs	ENST00000257290	NM_006206.4	812	-/AATGTAAGTTCAAGGAACACAGACCTTTTTAGACCCAGATTTC	17/23	0.321389064331437	1	FACETS	0.357	0.269	0.462	0.357	0.269	0.462	SUBCLONAL	1	FALSE	0	0.321389064331437	1		587	263	SUCCESS
APC	324	MSKCC	GRCh37	5	112175895	112176051	+	frameshift_variant	Frame_Shift_Del	DEL	ATGAAACAGAATCAGAGCAGCCTAAAGAATCAAATGAAAACCAAGAGAAAGAGGCAGAAAAAACTATTGATTCTGAAAAGGACCTATTAGATGATTCAGATGATGATGATATTGAAATACTAGAAGAATGTATTATTTCTGCCATGCCAACAAAGTC	ATGAAACAGAATCAGAGCAGCCTAAAGAATCAAATGAAAACCAAGAGAAAGAGGCAGAAAAAACTATTGATTCTGAAAAGGACCTATTAGATGATTCAGATGATGATGATATTGAAATACTAGAAGAATGTATTATTTCTGCCATGCCAACAAAGTC	-	novel	NA	P-0034504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	25	249	0	ENST00000257430.4:c.4606_4762del	p.Glu1536HisfsTer62	p.E1536Hfs*62	ENST00000257430	NM_000038.5	1535	aATGAAACAGAATCAGAGCAGCCTAAAGAATCAAATGAAAACCAAGAGAAAGAGGCAGAAAAAACTATTGATTCTGAAAAGGACCTATTAGATGATTCAGATGATGATGATATTGAAATACTAGAAGAATGTATTATTTCTGCCATGCCAACAAAGTCa/aa	16/16	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	FALSE	1	0.321389064331437	2		249	133	SUCCESS
AR	367	MSKCC	GRCh37	X	66931337	66931337	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	92	249	0	ENST00000374690.3:c.1979T>G	p.Leu660Arg	p.L660R	ENST00000374690	NM_000044.3	660	cTg/cGg	4/8	0.205008591323932	2	FACETS	0.86	0.779	0.941			1	CLONAL	3	FALSE	NA	0.321389064331437	2		249	222	SUCCESS
AR	367	MSKCC	GRCh37	X	66765448	66765450	+	missense_variant	Missense_Mutation	TNP	GAC	GAC	AAA	novel	NA	P-0034504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	24	284	0	ENST00000374690.3:c.460_462delinsAAA	p.Asp154Lys	p.D154K	ENST00000374690	NM_000044.3	154	GAC/AAA	1/8	0.205008591323932	2	FACETS	0.549	0.431	0.684			1	SUBCLONAL	1	FALSE	NA	0.321389064331437	2		284	272	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	47	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.839	0.725	0.958	0.839	0.725	0.958	CLONAL	1	TRUE	1	0.82374872013405	2		148	136	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0034505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	16104	759	2	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.82374872013405	29	FACETS	1	0.999	1			1	CLONAL	28	TRUE	NA	0.82374872013405	29		761	16891	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206943177	206943177	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	177	438	1	ENST00000423557.1:c.441T>A	p.Asn147Lys	p.N147K	ENST00000423557	NM_000572.2	147	aaT/aaA	4/5	1	2	FACETS	0.918	0.854	0.983	0.918	0.854	0.983	CLONAL	1	TRUE	1	0.82374872013405	2		439	468	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561512	9561512	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	283	597	0	ENST00000353224.5:c.270C>G	p.Asp90Glu	p.D90E	ENST00000353224	NM_177990.2	90	gaC/gaG	4/10	0.82374872013405	3	FACETS	0.987	0.929	1	0.493	0.464	0.523	CLONAL	1	TRUE	1	0.82374872013405	3		597	983	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215940	142215940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761331237	NA	P-0034505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	255	587	0	ENST00000350721.4:c.5653G>A	p.Ala1885Thr	p.A1885T	ENST00000350721	NM_001184.3	1885	Gct/Act	33/47	1	2	FACETS	0.973	0.918	1	0.973	0.918	1	CLONAL	1	TRUE	1	0.82374872013405	2		587	636	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	114	460	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.270959817825354	2	FACETS	1	0.98	1	0.675	0.609	0.744	CLONAL	1	TRUE	0	0.272393571066576	2		460	620	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0034515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	370	767	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.102149874066436	6	FACETS	0.907	0.869	0.945			1	INDETERMINATE	5	TRUE	NA	0.445017447412022	6		767	693	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858403	9858403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	156	509	0	ENST00000330684.3:c.2998G>A	p.Val1000Met	p.V1000M	ENST00000330684	NM_001134407.1	1000	Gtg/Atg	13/13	0.380292995200252	2	FACETS	0.835	0.772	0.898	0.835	0.772	0.898	CLONAL	2	TRUE	0	0.445017447412022	2		509	420	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971077	21971077	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	54	227	0	ENST00000304494.5:c.281T>A	p.Leu94Gln	p.L94Q	ENST00000304494	NM_000077.4	94	cTg/cAg	2/3	0.222547834799127	1	FACETS	0.789	0.682	0.905	0.789	0.682	0.905	INDETERMINATE	1	TRUE	0	0.445017447412022	1		227	239	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143010	47143010	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs759274882	NA	P-0034515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	76	491	4	ENST00000409792.3:c.4953del	p.Phe1651LeufsTer12	p.F1651Lfs*12	ENST00000409792	NM_014159.6	1651	ttT/tt	8/21	0.445017447412022	3	FACETS	0.87	0.765	0.982	0.435	0.382	0.491	CLONAL	1	TRUE	1	0.445017447412022	3		495	480	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1940224	1940224	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	49	215	0	ENST00000382891.5:c.1721C>A	p.Ala574Asp	p.A574D	ENST00000382891	NM_133335.3	574	gCc/gAc	8/22	0.445017447412022	2	FACETS	0.91	0.778	1	0.455	0.389	0.526	CLONAL	1	TRUE	0	0.445017447412022	2		215	242	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691039	NA	P-0034542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	609	577	0	ENST00000269305.4:c.919+1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.715742735867376	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.715742735867376	2		577	808	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591925	48591925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660556	NA	P-0034542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	178	414	1	ENST00000342988.3:c.1088G>A	p.Cys363Tyr	p.C363Y	ENST00000342988	NM_005359.5	363	tGt/tAt	9/12	0.715742735867376	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.715742735867376	1		415	310	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432780	432780	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	82	412	0	ENST00000399788.2:c.2136G>C	p.Gln712His	p.Q712H	ENST00000399788	NM_001042603.1	712	caG/caC	15/28	0.715742735867376	3	FACETS	0.578	0.511	0.65	0.289	0.255	0.325	SUBCLONAL	1	TRUE	1	0.715742735867376	3		412	538	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434136	49434136	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	507	505	0	ENST00000301067.7:c.7417C>A	p.Gln2473Lys	p.Q2473K	ENST00000301067	NM_003482.3	2473	Cag/Aag	31/54	0.715742735867376	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.715742735867376	2		505	660	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26970440	26970441	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0034542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	75	86	0	ENST00000381527.3:c.815dup	p.Met273AspfsTer3	p.M273Dfs*3	ENST00000381527	NM_001260.1	270	ata/atAa	8/13	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.715742735867376	2		86	142	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28631552	28631552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	275	295	0	ENST00000241453.7:c.416G>A	p.Gly139Glu	p.G139E	ENST00000241453	NM_004119.2	139	gGa/gAa	4/24	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.715742735867376	2		295	559	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38616972	38616972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764823722	NA	P-0034542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	243	284	0	ENST00000299084.4:c.385G>A	p.Glu129Lys	p.E129K	ENST00000299084	NM_152594.2	129	Gaa/Aaa	4/7	0.461669103571744	3	FACETS	1	0.989	1	0.763	0.726	0.799	CLONAL	2	TRUE	0	0.715742735867376	3		284	403	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951819	2951819	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	83	503	0	ENST00000396946.4:c.3131C>A	p.Ala1044Asp	p.A1044D	ENST00000396946	NM_032415.4	1044	gCt/gAt	23/25	0.473948852623075	2	FACETS	0.267	0.235	0.301	0.133	0.117	0.151	SUBCLONAL	1	TRUE	0	0.715742735867376	2		503	869	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974711	21974716	+	inframe_deletion	In_Frame_Del	DEL	TTGGGC	TTGGGC	-	novel	NA	P-0034542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	252	340	0	ENST00000304494.5:c.111_116del	p.Pro38_Asn39del	p.P38_N39del	ENST00000304494	NM_000077.4	37	ctGCCCAAc/ctc	1/3	0.715742735867376	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.715742735867376	1		340	347	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47088041	47088042	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0034556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	686	430	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	NA	NA	FALSE	1	NA	2		430	746	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	116	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.592759867562943	2		148	306	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057520000	NA	P-0034558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	380	712	0	ENST00000269305.4:c.452C>G	p.Pro151Arg	p.P151R	ENST00000269305	NM_001126112.2	151	cCc/cGc	5/11	0.592759867562943	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.592759867562943	1		712	638	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0034560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	56	425	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.137519998002385	4	FACETS	1	0.95	1	0.818	0.707	0.937	CLONAL	2	FALSE	1	0.197234348081647	4		425	277	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0034560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	149	658	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	0.171872187124678	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	FALSE	2	0.197234348081647	4		658	784	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939279	76939279	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	81	684	0	ENST00000373344.5:c.1469G>T	p.Gly490Val	p.G490V	ENST00000373344	NM_000489.3	490	gGt/gTt	9/35	0.171872187124678	4	FACETS	0.854	0.753	0.961	0.854	0.753	0.961	CLONAL	2	FALSE	2	0.197234348081647	4		684	576	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867469	35867469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs191585195	NA	P-0034560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	19	268	0	ENST00000303115.3:c.283G>A	p.Glu95Lys	p.E95K	ENST00000303115	NM_002185.3	95	Gag/Aag	3/8	0.197234348081647	7	FACETS	1	0.853	1	0.236	0.179	0.302	CLONAL	1	FALSE	2	0.197234348081647	7		268	244	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs878854073	NA	P-0034560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	87	461	0	ENST00000269305.4:c.673-1G>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.171872187124678	4	FACETS	0.95	0.843	1	0.95	0.843	1	CLONAL	2	FALSE	2	0.197234348081647	4		461	556	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100896	27100896	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	96	482	0	ENST00000324856.7:c.4178A>T	p.Tyr1393Phe	p.Y1393F	ENST00000324856	NM_006015.4	1393	tAc/tTc	18/20	0.171872187124678	4	FACETS	1	0.921	1	1	0.921	1	CLONAL	2	FALSE	2	0.197234348081647	4		482	562	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609601	81609601	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs748001659	NA	P-0034560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	98	536	0	ENST00000298171.2:c.1199C>G	p.Pro400Arg	p.P400R	ENST00000298171	NM_000369.2	400	cCc/cGc	10/10	0.130845117246892	3	FACETS	1	0.967	1	0.795	0.712	0.881	CLONAL	2	FALSE	0	0.197234348081647	3		536	458	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472644	88472644	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	43	319	0	ENST00000360948.2:c.1911G>T	p.Met637Ile	p.M637I	ENST00000360948	NM_001012338.2	637	atG/atT	16/19	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	FALSE	1	0.197234348081647	2		319	363	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647510	23647510	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	91	574	0	ENST00000261584.4:c.357A>T	p.Gln119His	p.Q119H	ENST00000261584	NM_024675.3	119	caA/caT	4/13	0.184506488345272	3	FACETS	0.874	0.777	0.976	0.874	0.777	0.976	CLONAL	2	FALSE	1	0.197234348081647	3		574	580	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47684713	47684713	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	63	410	0	ENST00000347630.2:c.736G>T	p.Val246Leu	p.V246L	ENST00000347630	NM_001007230.1	246	Gtg/Ttg	9/11	0.171872187124678	4	FACETS	0.898	0.779	1	0.898	0.779	1	CLONAL	2	FALSE	2	0.197234348081647	4		410	426	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051651	13051651	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	170	511	0	ENST00000316448.5:c.910A>T	p.Ser304Cys	p.S304C	ENST00000316448	NM_004343.3	304	Agt/Tgt	7/9	0.190852012226671	2	FACETS	0.877	0.81	0.947	1	0.986	1	CLONAL	3	FALSE	0	0.197234348081647	2		511	655	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61710148	61710148	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	17	338	0	ENST00000401558.2:c.2756T>G	p.Phe919Cys	p.F919C	ENST00000401558	NM_003400.3	919	tTt/tGt	22/25	0.176766600332166	3	FACETS	0.619	0.461	0.806	0.309	0.23	0.403	SUBCLONAL	1	FALSE	1	0.197234348081647	3		338	306	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57470707	57470707	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	40	314	0	ENST00000371085.3:c.180G>T	p.Met60Ile	p.M60I	ENST00000371085	NM_000516.4	60	atG/atT	2/13	0.197234348081647	5	FACETS	0.821	0.685	0.972	0.548	0.456	0.648	CLONAL	2	FALSE	2	0.197234348081647	5		314	320	SUCCESS
ATR	545	MSKCC	GRCh37	3	142204121	142204121	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	73	396	0	ENST00000350721.4:c.6082G>T	p.Val2028Leu	p.V2028L	ENST00000350721	NM_001184.3	2028	Gtg/Ttg	36/47	0.171872187124678	4	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	FALSE	2	0.197234348081647	4		396	384	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169980	32169980	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	66	682	0	ENST00000375023.3:c.3628C>A	p.Pro1210Thr	p.P1210T	ENST00000375023	NM_004557.3	1210	Ccc/Acc	21/30	0.176766600332166	3	FACETS	1	0.92	1	0.542	0.47	0.62	CLONAL	1	FALSE	1	0.197234348081647	3		682	678	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859649	151859649	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	55	454	0	ENST00000262189.6:c.11013G>T	p.Met3671Ile	p.M3671I	ENST00000262189	NM_170606.2	3671	atG/atT	43/59	0.176766600332166	3	FACETS	1	0.948	1	0.623	0.533	0.72	CLONAL	1	FALSE	1	0.197234348081647	3		454	492	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372223	55372223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	93	290	0	ENST00000297316.4:c.913G>A	p.Ala305Thr	p.A305T	ENST00000297316	NM_022454.3	305	Gcg/Acg	2/2	0.176766600332166	3	FACETS	0.909	0.814	1	1	0.977	1	CLONAL	3	FALSE	1	0.197234348081647	3		290	380	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633315	8633315	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0034560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	53	400	0	ENST00000356435.5:c.352+2T>G		p.X118_splice	ENST00000356435		118			0.176766600332166	3	FACETS	0.827	0.708	0.956	0.827	0.708	0.956	CLONAL	2	FALSE	1	0.197234348081647	3		400	357	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0034560-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	245	425	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.530057713861531	3	FACETS	0.921	0.875	0.966			1	CLONAL	3	TRUE	NA	0.529195107757416	3		425	424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0034560-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	393	658	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	0.446448147347981	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.529195107757416	4		658	1027	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939279	76939279	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034560-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	133	684	0	ENST00000373344.5:c.1469G>T	p.Gly490Val	p.G490V	ENST00000373344	NM_000489.3	490	gGt/gTt	9/35	0.45766081715613	3	FACETS	1	0.927	1	0.51	0.464	0.558	CLONAL	1	TRUE	1	0.529195107757416	3		684	623	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs878854073	NA	P-0034560-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	167	461	0	ENST00000269305.4:c.673-1G>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.446448147347981	4	FACETS	1	0.987	1	0.687	0.633	0.744	CLONAL	1	TRUE	2	0.529195107757416	4		461	702	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100896	27100896	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034560-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	328	482	0	ENST00000324856.7:c.4178A>T	p.Tyr1393Phe	p.Y1393F	ENST00000324856	NM_006015.4	1393	tAc/tTc	18/20	0.530057713861531	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.529195107757416	3		482	729	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609601	81609601	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs748001659	NA	P-0034560-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	286	536	0	ENST00000298171.2:c.1199C>G	p.Pro400Arg	p.P400R	ENST00000298171	NM_000369.2	400	cCc/cGc	10/10	0.441633465160863	3	FACETS	0.886	0.845	0.928	0.886	0.845	0.928	CLONAL	3	TRUE	0	0.529195107757416	3		536	514	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472644	88472644	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034560-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	79	319	0	ENST00000360948.2:c.1911G>T	p.Met637Ile	p.M637I	ENST00000360948	NM_001012338.2	637	atG/atT	16/19	1	2	FACETS	0.827	0.733	0.927	0.827	0.733	0.927	CLONAL	1	TRUE	1	0.529195107757416	2		319	361	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647510	23647510	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034560-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	358	574	0	ENST00000261584.4:c.357A>T	p.Gln119His	p.Q119H	ENST00000261584	NM_024675.3	119	caA/caT	4/13	0.371567192691413	3	FACETS	0.846	0.81	0.883	0.846	0.81	0.883	CLONAL	3	TRUE	0	0.529195107757416	3		574	674	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47684713	47684713	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034560-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	136	410	0	ENST00000347630.2:c.736G>T	p.Val246Leu	p.V246L	ENST00000347630	NM_001007230.1	246	Gtg/Ttg	9/11	0.446448147347981	4	FACETS	1	0.984	1	0.686	0.626	0.748	CLONAL	1	TRUE	2	0.529195107757416	4		410	573	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051651	13051651	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034560-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	92	511	0	ENST00000316448.5:c.910A>T	p.Ser304Cys	p.S304C	ENST00000316448	NM_004343.3	304	Agt/Tgt	7/9	0.458387000734045	3	FACETS	0.713	0.634	0.796	0.238	0.211	0.266	SUBCLONAL	1	TRUE	0	0.529195107757416	3		511	617	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61710148	61710148	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034560-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	83	338	0	ENST00000401558.2:c.2756T>G	p.Phe919Cys	p.F919C	ENST00000401558	NM_003400.3	919	tTt/tGt	22/25	0.530057713861531	3	FACETS	0.906	0.803	1	0.453	0.401	0.508	CLONAL	1	TRUE	1	0.529195107757416	3		338	438	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57470707	57470707	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034560-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	137	314	0	ENST00000371085.3:c.180G>T	p.Met60Ile	p.M60I	ENST00000371085	NM_000516.4	60	atG/atT	2/13	0.530057713861531	4	FACETS	0.813	0.744	0.884	0.813	0.744	0.884	CLONAL	2	TRUE	2	0.529195107757416	4		314	487	SUCCESS
ATR	545	MSKCC	GRCh37	3	142204121	142204121	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034560-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	174	396	0	ENST00000350721.4:c.6082G>T	p.Val2028Leu	p.V2028L	ENST00000350721	NM_001184.3	2028	Gtg/Ttg	36/47	0.328418972218573	3	FACETS	1	0.981	1	0.755	0.706	0.805	CLONAL	2	TRUE	0	0.529195107757416	3		396	367	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169980	32169980	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034560-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	146	682	0	ENST00000375023.3:c.3628C>A	p.Pro1210Thr	p.P1210T	ENST00000375023	NM_004557.3	1210	Ccc/Acc	21/30	0.530057713861531	3	FACETS	0.713	0.65	0.779	0.356	0.325	0.39	SUBCLONAL	1	TRUE	1	0.529195107757416	3		682	979	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859649	151859649	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034560-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	240	454	0	ENST00000262189.6:c.11013G>T	p.Met3671Ile	p.M3671I	ENST00000262189	NM_170606.2	3671	atG/atT	43/59	0.530057713861531	4	FACETS	0.914	0.856	0.972	0.914	0.856	0.972	CLONAL	2	TRUE	2	0.529195107757416	4		454	759	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372223	55372223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034560-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	252	290	0	ENST00000297316.4:c.913G>A	p.Ala305Thr	p.A305T	ENST00000297316	NM_022454.3	305	Gcg/Acg	2/2	0.530057713861531	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.529195107757416	3		290	527	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633315	8633315	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0034560-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	142	400	0	ENST00000356435.5:c.352+2T>G		p.X118_splice	ENST00000356435		118			0.403999246379435	3	FACETS	0.782	0.719	0.847	0.782	0.719	0.847	SUBCLONAL	2	TRUE	1	0.529195107757416	3		400	434	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578124	226578124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034560-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	123	423	0	ENST00000366794.5:c.604G>A	p.Val202Ile	p.V202I	ENST00000366794	NM_001618.3	202	Gtc/Atc	4/23	0.152225655257236	4	FACETS	1	0.977	1	0.619	0.562	0.679	INDETERMINATE	1	TRUE	2	0.529195107757416	4		423	574	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951160	48951160	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034560-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	83	339	0	ENST00000267163.4:c.1323del	p.Ile441MetfsTer16	p.I441Mfs*16	ENST00000267163	NM_000321.2	441	aTt/at	13/27	0.401172133138997	2	FACETS	0.78	0.703	0.859	0.78	0.703	0.859	SUBCLONAL	2	TRUE	0	0.529195107757416	2		339	201	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339076	225339076	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034560-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	46	340	0	ENST00000264414.4:c.2193G>T	p.Lys731Asn	p.K731N	ENST00000264414	NM_003590.4	731	aaG/aaT	16/16	0.530057713861531	3	FACETS	0.777	0.658	0.906	0.388	0.329	0.453	CLONAL	1	TRUE	1	0.529195107757416	3		340	283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576888	7576888	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0034571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	62	611	1	ENST00000269305.4:c.958A>T	p.Lys320Ter	p.K320*	ENST00000269305	NM_001126112.2	320	Aag/Tag	9/11	1	2	FACETS	0.997	0.86	1	0.997	0.86	1	CLONAL	1	TRUE	1	0.16	2		612	777	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856065	111856065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778004604	NA	P-0034571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	47	191	0	ENST00000341259.2:c.116G>A	p.Arg39Gln	p.R39Q	ENST00000341259	NM_005475.2	39	cGg/cAg	2/8	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.16	2		191	562	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943961	71943961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	47	563	0	ENST00000298229.2:c.1894C>T	p.Leu632Phe	p.L632F	ENST00000298229	NM_001567.3	632	Ctc/Ttc	16/28	1	2	FACETS	0.723	0.608	0.85	0.723	0.608	0.85	SUBCLONAL	1	TRUE	1	0.16	2		563	813	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022240	31022240	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	19	190	0	ENST00000375687.4:c.1725A>T	p.Gln575His	p.Q575H	ENST00000375687	NM_015338.5	575	caA/caT	13/13	1	2	FACETS	0.828	0.628	1	0.828	0.628	1	CLONAL	1	TRUE	1	0.16	2		190	287	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643581	52643581	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	35	462	0	ENST00000394830.3:c.2315del	p.Pro772GlnfsTer3	p.P772Qfs*3	ENST00000394830	NM_018313.4	772	cCa/ca	17/30	1	2	FACETS	0.748	0.612	0.901	0.748	0.612	0.901	CLONAL	1	TRUE	1	0.16	2		462	585	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418899	116418899	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	35	329	0	ENST00000397752.3:c.3410C>A	p.Pro1137His	p.P1137H	ENST00000397752	NM_000245.2	1137	cCc/cAc	17/21	1	2	FACETS	0.911	0.747	1	0.911	0.747	1	CLONAL	1	TRUE	1	0.16	2		329	480	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735517	40735517	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	23	536	0	ENST00000373198.4:c.3356T>C	p.Met1119Thr	p.M1119T	ENST00000373198	NM_133170.3	1119	aTg/aCg	25/32	0.3	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		536	458	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24133948	24133948	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	93	202	0	ENST00000263121.7:c.101del	p.Asn34ThrfsTer21	p.N34Tfs*21	ENST00000263121	NM_003073.3	33	ggA/gg	2/9	0.0769170130025284	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		202	232	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0034574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	502	767	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.645672260904558	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.645672260904558	2		767	763	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262639	16262639	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	211	314	0	ENST00000375759.3:c.9904C>G	p.Leu3302Val	p.L3302V	ENST00000375759	NM_015001.2	3302	Ctg/Gtg	11/15	0.243089780412102	2	FACETS	1	0.991	1	0.663	0.622	0.704	INDETERMINATE	1	TRUE	0	0.645672260904558	2		314	493	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142889	7142889	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	223	632	0	ENST00000302850.5:c.2480A>G	p.Gln827Arg	p.Q827R	ENST00000302850	NM_000208.2	827	cAg/cGg	12/22	0.56767702230486	5	FACETS	0.98	0.91	1			1	CLONAL	1	TRUE	NA	0.645672260904558	5		632	1387	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92244459	92244459	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs763800540	NA	P-0034574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	118	322	0	ENST00000265734.4:c.976G>C	p.Ala326Pro	p.A326P	ENST00000265734	NM_001259.6	326	Gcc/Ccc	8/8	0.645672260904558	5	FACETS	0.914	0.825	1	0.229	0.206	0.253	CLONAL	1	TRUE	1	0.645672260904558	5		322	787	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842595	68842595	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0034577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	79	494	0	ENST00000261769.5:c.532-1G>A		p.X178_splice	ENST00000261769	NM_004360.3	178			0.267801088793447	1	FACETS	0.975	0.86	1	0.975	0.86	1	CLONAL	1	TRUE	0	0.267801088793447	1		494	524	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748460	162748460	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	153	453	0	ENST00000367921.3:c.2374C>G	p.Leu792Val	p.L792V	ENST00000367921	NM_006182.2	792	Ctg/Gtg	17/18	0.267801088793447	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.267801088793447	3		453	551	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670447	134670447	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	72	506	0	ENST00000398015.3:c.358G>T	p.Val120Phe	p.V120F	ENST00000398015	NM_004441.4	120	Gtc/Ttc	3/16	1	2	FACETS	0.883	0.772	1	0.883	0.772	1	CLONAL	1	TRUE	1	0.267801088793447	2		506	609	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683415	182683415	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	50	432	0	ENST00000292782.4:c.130T>G	p.Phe44Val	p.F44V	ENST00000292782	NM_020640.2	44	Ttt/Gtt	2/7	1	2	FACETS	0.737	0.625	0.859	0.737	0.625	0.859	SUBCLONAL	1	TRUE	1	0.267801088793447	2		432	507	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0034581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	219	338	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.513245412932553	2	FACETS	0.962	0.909	1	0.962	0.909	1	CLONAL	2	TRUE	0	0.53414986576612	2		338	426	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578214	28578214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778369	NA	P-0034581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1305	111	535	1	ENST00000241453.7:c.2957C>T	p.Pro986Leu	p.P986L	ENST00000241453	NM_004119.2	986	cCg/cTg	24/24	0.463742582580292	5	FACETS	0.529	0.473	0.588			1	SUBCLONAL	1	TRUE	NA	0.53414986576612	5		536	1416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0034581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	458	684	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.53414986576612	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.53414986576612	1		684	996	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39321517	39321517	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	96	492	0	ENST00000373001.3:c.504C>A	p.Asn168Lys	p.N168K	ENST00000373001	NM_022157.3	168	aaC/aaA	3/7	0.17198395988466	0	FACETS	0.304	0.271	0.339			1	INDETERMINATE	1	TRUE	0	0.53414986576612	0		492	551	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0034583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	159	274	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.740463844352803	2		274	410	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685315	89685315	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1554897280	NA	P-0034583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	93	253	0	ENST00000371953.3:c.209+1G>A		p.X70_splice	ENST00000371953	NM_000314.4	70			0.740463844352803	1	FACETS	0.815	0.743	0.888	0.815	0.743	0.888	CLONAL	1	TRUE	0	0.740463844352803	1		253	194	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944842	31944842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	85	659	1	ENST00000340398.3:c.259G>A	p.Ala87Thr	p.A87T	ENST00000340398	NM_001013699.2	87	Gca/Aca	1/1	1	2	FACETS	0.253	0.223	0.286	0.253	0.223	0.286	SUBCLONAL	1	TRUE	1	0.740463844352803	2		660	907	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699430	47699430	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0034583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	44	236	0	ENST00000347630.2:c.79-1G>T		p.X27_splice	ENST00000347630	NM_001007230.1	27			1	2	FACETS	0.353	0.297	0.414	0.353	0.297	0.414	SUBCLONAL	1	TRUE	1	0.740463844352803	2		236	337	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	206	148	0				ENST00000310581	NM_198253.2	-/1132			0.547195246623102	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.586989675084117	3		148	422	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001309	29001309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	76	246	0	ENST00000282397.4:c.1423C>T	p.His475Tyr	p.H475Y	ENST00000282397	NM_002019.4	475	Cat/Tat	10/30	0.23912590947128	5	FACETS	0.801	0.709	0.897	0.534	0.473	0.598	INDETERMINATE	2	TRUE	2	0.586989675084117	5		246	304	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256667	16256667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1387045955	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	400	394	0	ENST00000375759.3:c.3932C>T	p.Pro1311Leu	p.P1311L	ENST00000375759	NM_015001.2	1311	cCt/cTt	11/15	0.344311805729717	6	FACETS	1	0.987	1	0.869	0.841	0.897	INDETERMINATE	5	TRUE	0	0.586989675084117	6		394	568	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261434	16261434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	529	486	0	ENST00000375759.3:c.8699C>T	p.Ser2900Leu	p.S2900L	ENST00000375759	NM_015001.2	2900	tCg/tTg	11/15	0.344311805729717	6	FACETS	0.987	0.957	1	0.823	0.797	0.847	INDETERMINATE	5	TRUE	0	0.586989675084117	6		486	794	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115252203	115252203	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	453	330	0	ENST00000369535.4:c.437C>T	p.Ala146Val	p.A146V	ENST00000369535	NM_002524.4	146	gCc/gTc	4/7	0.326047230182011	6	FACETS	1	0.991	1	0.882	0.855	0.908	INDETERMINATE	5	TRUE	0	0.586989675084117	6		330	634	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246490517	246490517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	110	407	0	ENST00000388985.4:c.517G>A	p.Glu173Lys	p.E173K	ENST00000388985		173	Gaa/Aaa	5/12	0.273453585095654	3	FACETS	0.966	0.885	1	0.644	0.59	0.699	INDETERMINATE	2	TRUE	0	0.586989675084117	3		407	251	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572288	64572289	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AT	novel	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	276	507	0	ENST00000312049.6:c.1351-1_1351delinsAT		p.X451_splice	ENST00000312049	NM_130799.2	451		10/10	0.463640022561321	4	FACETS	0.934	0.88	0.988	0.934	0.88	0.988	CLONAL	2	TRUE	2	0.586989675084117	4		507	799	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149251	119149251	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	265	492	0	ENST00000264033.4:c.1259G>T	p.Arg420Leu	p.R420L	ENST00000264033	NM_005188.3	420	cGa/cTa	9/16	0.586989675084117	2	FACETS	0.965	0.918	1	0.965	0.918	1	CLONAL	2	TRUE	0	0.586989675084117	2		492	468	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793483	18793483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267603405	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	40	257	0	ENST00000266497.5:c.4180G>A	p.Glu1394Lys	p.E1394K	ENST00000266497		1394	Gaa/Aaa	30/31	NA	2	FACETS	1	0.919	1			1	INDETERMINATE	1	TRUE	NA	0.586989675084117	2		257	121	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944740	31944740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	35	70	0	ENST00000340398.3:c.361C>T	p.Pro121Ser	p.P121S	ENST00000340398	NM_001013699.2	121	Ccc/Tcc	1/1	NA	2	FACETS	1	0.944	1			1	INDETERMINATE	1	TRUE	NA	0.586989675084117	2		70	92	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244162	46244163	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	novel	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	171	343	0	ENST00000334344.6:c.2256_2257delinsTT	p.Gln752_Pro753delinsHisSer	p.Q752_P753delinsHS	ENST00000334344	NM_152641.2	752	caACct/caTTct	15/21	0.586989675084117	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	1	0.586989675084117	3		343	364	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133208960	133208960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572252265	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	295	490	0	ENST00000320574.5:c.6271C>T	p.Pro2091Ser	p.P2091S	ENST00000320574	NM_006231.2	2091	Ccc/Tcc	45/49	0.0968913806958827	5	FACETS	0.952	0.903	1			1	INDETERMINATE	3	TRUE	NA	0.586989675084117	5		490	662	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022962	33022962	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	100	311	0	ENST00000300177.4:c.71G>A	p.Gly24Glu	p.G24E	ENST00000300177	NM_001191322.1	24	gGg/gAg	2/2	0.586989675084117	3	FACETS	1	0.962	1	0.572	0.515	0.632	CLONAL	1	TRUE	1	0.586989675084117	3		311	385	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992066	72992066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	265	616	0	ENST00000268489.5:c.1979C>T	p.Thr660Ile	p.T660I	ENST00000268489	NM_006885.3	660	aCc/aTc	2/10	0.463640022561321	4	FACETS	0.892	0.839	0.946	0.892	0.839	0.946	CLONAL	2	TRUE	2	0.586989675084117	4		616	803	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217842	7217842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	364	563	0	ENST00000380728.2:c.169G>A	p.Glu57Lys	p.E57K	ENST00000380728		57	Gaa/Aaa	3/11	0.586989675084117	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.586989675084117	2		563	595	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	363	522	1	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	0.586989675084117	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.586989675084117	2		523	589	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998934	11998934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	88	272	0	ENST00000353533.5:c.436C>T	p.Leu146Phe	p.L146F	ENST00000353533	NM_003010.3	146	Ctt/Ttt	4/11	0.586989675084117	2	FACETS	0.914	0.835	0.992	0.914	0.835	0.992	CLONAL	2	TRUE	0	0.586989675084117	2		272	164	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592305	29592305	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	119	277	1	ENST00000356175.3:c.4720C>T	p.Gln1574Ter	p.Q1574*	ENST00000356175	NM_000267.3	1574	Caa/Taa	35/57	0.586989675084117	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	2	TRUE	0	0.586989675084117	2		278	202	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879655	37879655	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167835335	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	382	663	0	ENST00000269571.5:c.2030G>A	p.Arg677Gln	p.R677Q	ENST00000269571		677	cGa/cAa	17/27	0.586989675084117	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.586989675084117	2		663	635	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756583	756583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	131	316	0	ENST00000314574.4:c.245C>T	p.Pro82Leu	p.P82L	ENST00000314574	NM_005433.3	82	cCa/cTa	2/12	0.464538382332597	4	FACETS	0.849	0.778	0.923	0.849	0.778	0.923	CLONAL	2	TRUE	2	0.586989675084117	4		316	417	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217865	2217865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1464303651	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	446	678	0	ENST00000398665.3:c.2639C>T	p.Pro880Leu	p.P880L	ENST00000398665	NM_032482.2	880	cCg/cTg	22/28	0.23912590947128	5	FACETS	0.894	0.856	0.933	0.894	0.856	0.933	INDETERMINATE	3	TRUE	2	0.586989675084117	5		678	1065	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117281	7117281	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768514435	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	232	594	0	ENST00000302850.5:c.3935C>T	p.Pro1312Leu	p.P1312L	ENST00000302850	NM_000208.2	1312	cCc/cTc	22/22	0.23912590947128	5	FACETS	0.857	0.801	0.915	0.572	0.534	0.61	INDETERMINATE	2	TRUE	2	0.586989675084117	5		594	867	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296145	15296145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	399	662	0	ENST00000263388.2:c.2219C>T	p.Ser740Phe	p.S740F	ENST00000263388	NM_000435.2	740	tCc/tTc	14/33	0.23912590947128	5	FACETS	0.913	0.872	0.955	0.913	0.872	0.955	INDETERMINATE	3	TRUE	2	0.586989675084117	5		662	933	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445417	29445417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769855519	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	356	549	0	ENST00000389048.3:c.3416C>T	p.Pro1139Leu	p.P1139L	ENST00000389048	NM_004304.4	1139	cCc/cTc	21/29	0.23912590947128	5	FACETS	0.861	0.819	0.903	0.861	0.819	0.903	INDETERMINATE	3	TRUE	2	0.586989675084117	5		549	883	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61720085	61720085	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	93	363	0	ENST00000401558.2:c.1349C>T	p.Ser450Phe	p.S450F	ENST00000401558	NM_003400.3	450	tCc/tTc	13/25	0.23912590947128	5	FACETS	0.961	0.864	1	0.641	0.576	0.708	INDETERMINATE	2	TRUE	2	0.586989675084117	5		363	310	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561263	9561263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769939031	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	216	420	1	ENST00000353224.5:c.519G>A	p.Met173Ile	p.M173I	ENST00000353224	NM_177990.2	173	atG/atA	4/10	0.464538382332597	4	FACETS	0.942	0.881	1	0.942	0.881	1	CLONAL	2	TRUE	2	0.586989675084117	4		421	620	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023865	31023865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	284	534	0	ENST00000375687.4:c.3350C>T	p.Pro1117Leu	p.P1117L	ENST00000375687	NM_015338.5	1117	cCc/cTc	13/13	0.464538382332597	4	FACETS	0.92	0.867	0.973	0.92	0.867	0.973	CLONAL	2	TRUE	2	0.586989675084117	4		534	835	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023882	31023882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	268	542	0	ENST00000375687.4:c.3367C>T	p.Pro1123Ser	p.P1123S	ENST00000375687	NM_015338.5	1123	Cca/Tca	13/13	0.464538382332597	4	FACETS	0.906	0.853	0.96	0.906	0.853	0.96	CLONAL	2	TRUE	2	0.586989675084117	4		542	800	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927964	49927964	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	329	548	0	ENST00000296474.3:c.3764C>A	p.Ala1255Glu	p.A1255E	ENST00000296474	NM_002447.2	1255	gCg/gAg	18/20	0.586989675084117	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	1	0.586989675084117	3		548	725	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807513	1807513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	183	633	0	ENST00000260795.2:c.1682G>A	p.Gly561Asp	p.G561D	ENST00000260795		561	gGt/gAt	12/17	1	2	FACETS	0.965	0.895	1	0.965	0.895	1	CLONAL	1	TRUE	1	0.586989675084117	2		633	646	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750570	41750570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	114	437	0	ENST00000226382.2:c.58G>A	p.Gly20Arg	p.G20R	ENST00000226382	NM_003924.3	20	Ggg/Agg	1/3	1	2	FACETS	0.971	0.882	1	0.971	0.882	1	CLONAL	1	TRUE	1	0.586989675084117	2		437	400	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293880	1293880	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778585289	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	216	770	0	ENST00000310581.5:c.1121G>A	p.Gly374Glu	p.G374E	ENST00000310581	NM_198253.2	374	gGg/gAg	2/16	0.547195246623102	3	FACETS	1	0.932	1	0.501	0.466	0.537	CLONAL	1	TRUE	1	0.586989675084117	3		770	950	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686868	117686868	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	31	188	1	ENST00000368508.3:c.2849C>T	p.Ser950Phe	p.S950F	ENST00000368508	NM_002944.2	950	tCt/tTt	19/43	0.586989675084117	3	FACETS	0.768	0.627	0.923	0.384	0.313	0.462	CLONAL	1	TRUE	1	0.586989675084117	3		189	178	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958127	2958127	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs769192567	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	340	580	0	ENST00000396946.4:c.2605C>T	p.Arg869Trp	p.R869W	ENST00000396946	NM_032415.4	869	Cgg/Tgg	19/25	0.23912590947128	5	FACETS	1	0.992	1	0.827	0.785	0.869	INDETERMINATE	2	TRUE	2	0.586989675084117	5		580	878	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979502	2979502	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	306	455	0	ENST00000396946.4:c.745C>T	p.Gln249Ter	p.Q249*	ENST00000396946	NM_032415.4	249	Cag/Tag	6/25	0.23912590947128	5	FACETS	0.848	0.803	0.893	0.848	0.803	0.893	INDETERMINATE	3	TRUE	2	0.586989675084117	5		455	771	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355233	81355233	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	170	305	0	ENST00000222390.5:c.1141C>G	p.Pro381Ala	p.P381A	ENST00000222390	NM_000601.4	381	Cca/Gca	9/18	0.464538382332597	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	2	0.586989675084117	4		305	444	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829281	128829281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	215	595	2	ENST00000249373.3:c.289G>A	p.Asp97Asn	p.D97N	ENST00000249373	NM_005631.4	97	Gac/Aac	1/12	0.464538382332597	4	FACETS	1	0.992	1	0.746	0.695	0.798	CLONAL	1	TRUE	2	0.586989675084117	4		597	779	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104018	69104018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774092508	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	121	414	0	ENST00000288368.4:c.4408G>A	p.Asp1470Asn	p.D1470N	ENST00000288368	NM_024870.2	1470	Gat/Aat	36/40	0.463640022561321	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	2	0.586989675084117	4		414	308	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	225	448	2	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	0.262891749370349	5	FACETS	1	0.938	1	0.668	0.625	0.713	INDETERMINATE	2	TRUE	2	0.586989675084117	5		450	719	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180306	27180306	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	287	476	0	ENST00000380036.4:c.970G>A	p.Asp324Asn	p.D324N	ENST00000380036	NM_000459.3	324	Gat/Aat	7/23	0.262891749370349	5	FACETS	1	0.99	1	0.796	0.752	0.841	INDETERMINATE	2	TRUE	2	0.586989675084117	5		476	770	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223853	53223853	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	512	404	1	ENST00000375401.3:c.3506C>T	p.Ser1169Leu	p.S1169L	ENST00000375401	NM_004187.3	1169	tCg/tTg	23/26	0.534485792776162	2	FACETS	0.859	0.836	0.881			1	CLONAL	3	TRUE	NA	0.586989675084117	2		405	677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780071	NA	P-0034591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	208	490	0	ENST00000269305.4:c.580C>T	p.Leu194Phe	p.L194F	ENST00000269305	NM_001126112.2	194	Ctt/Ttt	6/11	1	2	FACETS	1	0.972	1	1	0.994	1	CLONAL	2	FALSE	1	0.387647756597751	2		490	504	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0034591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	92	236	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.942	0.851	1	1	0.987	1	CLONAL	2	FALSE	1	0.387647756597751	2		236	252	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0034591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	179	569	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	1	2	FACETS	0.88	0.817	0.944	1	0.992	1	CLONAL	2	FALSE	1	0.387647756597751	2		569	525	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813031	76813031	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	212	446	1	ENST00000373344.5:c.6590G>A	p.Arg2197His	p.R2197H	ENST00000373344	NM_000489.3	2197	cGt/cAt	30/35	0.387647756597751	1	FACETS	0.928	0.872	0.985	1	0.994	1	CLONAL	2	FALSE	0	0.387647756597751	1		447	475	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0034593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	152	387	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.539492613454951	6	FACETS	0.946	0.874	1	0.709	0.655	0.764	CLONAL	3	TRUE	2	0.539492613454951	6		387	413	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498000	29498000	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	65	535	1	ENST00000389048.3:c.2006del	p.Asn669IlefsTer42	p.N669Ifs*42	ENST00000389048	NM_004304.4	669	aAt/at	11/29	0.539492613454951	3	FACETS	0.812	0.707	0.924	0.406	0.353	0.462	CLONAL	1	TRUE	1	0.539492613454951	3		536	377	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627238	86627238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	44	318	0	ENST00000274376.6:c.613C>T	p.Leu205Phe	p.L205F	ENST00000274376	NM_002890.2	205	Ctt/Ttt	2/25	0.390124413566879	4	FACETS	0.863	0.728	1	0.288	0.242	0.337	CLONAL	1	TRUE	1	0.539492613454951	4		318	291	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056617	26056617	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs751385999	NA	P-0034593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	36	183	0	ENST00000343677.2:c.40C>G	p.Pro14Ala	p.P14A	ENST00000343677	NM_005319.3	14	Cct/Gct	1/1	0.539492613454951	10	FACETS	1	0.912	1			1	CLONAL	1	TRUE	NA	0.539492613454951	10		183	356	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	177	148	0				ENST00000310581	NM_198253.2	-/1132			0.610239858307911	3	FACETS	1	0.988	1			1	CLONAL	1	FALSE	NA	0.610239858307911	3		148	555	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576898	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0034595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	476	528	0	ENST00000269305.4:c.948_949del	p.Gln317AlafsTer19	p.Q317Afs*19	ENST00000269305	NM_001126112.2	316	ccCCag/ccag	9/11	1	2	FACETS	0.987	0.969	1	1	0.998	1	CLONAL	3	FALSE	1	0.610239858307911	2		528	527	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609786	28609787	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0034595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	140	516	0	ENST00000241453.7:c.1442_1443delinsAT	p.Gly481Asp	p.G481D	ENST00000241453	NM_004119.2	481	gGA/gAT	12/24	0.576868252197726	4	FACETS	1	0.987	1	0.487	0.446	0.529	CLONAL	1	FALSE	1	0.610239858307911	4		516	506	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352388	70352388	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	298	337	0	ENST00000374080.3:c.4415G>A	p.Ser1472Asn	p.S1472N	ENST00000374080		1472	aGc/aAc	31/45	0.446057010434765	5	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	FALSE	2	0.610239858307911	5		337	555	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243481	46243481	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	301	524	0	ENST00000334344.6:c.1834T>G	p.Tyr612Asp	p.Y612D	ENST00000334344	NM_152641.2	612	Tat/Gat	14/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.779510222894931	2		524	740	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578503	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	85	886	0	ENST00000269305.4:c.427del	p.Val143CysfsTer27	p.V143Cfs*27	ENST00000269305	NM_001126112.2	143	Gtg/tg	5/11	1	2	FACETS	0.72	0.635	0.812	0.72	0.635	0.812	SUBCLONAL	1	FALSE	1	0.215943105443066	2		886	1093	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845798	151845798	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	39	729	0	ENST00000262189.6:c.13214G>C	p.Cys4405Ser	p.C4405S	ENST00000262189	NM_170606.2	4405	tGt/tCt	52/59	1	2	FACETS	0.775	0.642	0.923	0.775	0.642	0.923	CLONAL	1	FALSE	1	0.215943105443066	2		729	466	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	175	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.860557026070199	2		148	347	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807289	3807289	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057518844	NA	P-0034608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	200	360	1	ENST00000262367.5:c.3698G>A	p.Arg1233Lys	p.R1233K	ENST00000262367	NM_004380.2	1233	aGg/aAg	19/31	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.860557026070199	2		361	454	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133559	55133559	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3046	4705	451	0	ENST00000257290.5:c.863A>G	p.Tyr288Cys	p.Y288C	ENST00000257290	NM_006206.4	288	tAc/tGc	6/23	0.860557026070199	29	FACETS	0.989	0.978	1	0.636	0.628	0.643	CLONAL	18	TRUE	1	0.860557026070199	29		451	7751	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133750	55133821	+	inframe_deletion	In_Frame_Del	DEL	CAGCCAGTTGGAAGCTGTCAACCTGCATGAAGTCAAACATTTTGTTGTAGAGGTGCGGGCCTACCCACCTCC	CAGCCAGTTGGAAGCTGTCAACCTGCATGAAGTCAAACATTTTGTTGTAGAGGTGCGGGCCTACCCACCTCC	-	novel	NA	P-0034608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6783	927	493	0	ENST00000257290.5:c.966_1037del	p.Ser322_Pro345del	p.S322_P345del	ENST00000257290	NM_006206.4	321	ttCAGCCAGTTGGAAGCTGTCAACCTGCATGAAGTCAAACATTTTGTTGTAGAGGTGCGGGCCTACCCACCTCCc/ttc	7/23	0.860557026070199	29	FACETS	0.881	0.849	0.914	0.126	0.121	0.131	CLONAL	4	TRUE	1	0.860557026070199	29		493	7710	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0034609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	16	328	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.359	0.265	0.473	0.359	0.265	0.473	SUBCLONAL	1	TRUE	1	0.232651526714635	2		328	383	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900116	101900171	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGTACTATTTATTTTTACCTTTAGGTTTACCATTGCTTGTTCAGAGAACAATTGC	GAGTACTATTTATTTTTACCTTTAGGTTTACCATTGCTTGTTCAGAGAACAATTGC	-	novel	NA	P-0034610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	16	202	0	ENST00000374994.4:c.575-22_608del		p.X192_splice	ENST00000374994	NM_004612.2	192		4/9	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		202	141	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0034611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	87	451	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.879	0.786	0.976	0.879	0.786	0.976	CLONAL	1	TRUE	1	0.615075324542212	2		451	322	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063694	67063702	+	inframe_deletion	In_Frame_Del	DEL	GCCGCGACG	GCCGCGACG	-	novel	NA	P-0034611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	117	342	0	ENST00000412916.2:c.148_156del	p.Asp50_Arg52del	p.D50_R52del	ENST00000412916		48	tGCCGCGACGgc/tgc	2/6	0.615075324542212	1	FACETS	0.816	0.745	0.888	0.816	0.745	0.888	CLONAL	1	TRUE	0	0.615075324542212	1		342	323	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857466	68857467	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0034611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	227	734	0	ENST00000261769.5:c.2102dup	p.Glu702ArgfsTer46	p.E702Rfs*46	ENST00000261769	NM_004360.3	701	gtc/gTtc	13/16	0.615075324542212	1	FACETS	0.996	0.938	1	0.996	0.938	1	CLONAL	1	TRUE	0	0.615075324542212	1		734	513	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	149	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.881168404353344	2		148	313	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220274	55220274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	275	774	0	ENST00000275493.2:c.664C>T	p.Arg222Cys	p.R222C	ENST00000275493	NM_005228.3	222	Cgc/Tgc	6/28	0.762985674563583	3	FACETS	0.64	0.599	0.681	0.32	0.299	0.341	SUBCLONAL	1	TRUE	1	0.881168404353344	3		774	1406	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724449	162724449	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	239	537	0	ENST00000367921.3:c.221C>G	p.Pro74Arg	p.P74R	ENST00000367921	NM_006182.2	74	cCt/cGt	5/18	1	2	FACETS	0.935	0.881	0.991	0.935	0.881	0.991	CLONAL	1	TRUE	1	0.881168404353344	2		537	580	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346219	152346219	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	187	667	1	ENST00000359321.1:c.351G>T	p.Leu117Phe	p.L117F	ENST00000359321	NM_005431.1	117	ttG/ttT	3/3	0.865432267824277	3	FACETS	0.698	0.645	0.753	0.349	0.322	0.377	SUBCLONAL	1	TRUE	1	0.881168404353344	3		668	876	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0034617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	160	312	1	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.922	0.856	0.989	1	0.992	1	CLONAL	2	TRUE	1	0.441405862506955	2		313	393	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0034617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	153	435	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	0.441405862506955	2		435	479	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0034617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	163	465	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.824	0.764	0.886	1	0.991	1	CLONAL	2	TRUE	1	0.441405862506955	2		465	448	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0034617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	229	436	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.838	0.786	0.891	1	0.994	1	CLONAL	2	TRUE	1	0.441405862506955	2		436	619	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970927	21970927	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501274	NA	P-0034617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	250	476	0	ENST00000304494.5:c.431G>A	p.Arg144His	p.R144H	ENST00000304494	NM_000077.4	144	cGc/cAc	2/3	1	2	FACETS	0.829	0.78	0.879	1	0.994	1	CLONAL	2	TRUE	1	0.441405862506955	2		476	683	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772951	135772951	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs118203724	NA	P-0034617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	32	409	0	ENST00000298552.3:c.2672del	p.Asn891ThrfsTer40	p.N891Tfs*40	ENST00000298552	NM_001162426.1	891	aAc/ac	21/23	1	2	FACETS	0.34	0.275	0.412	0.34	0.275	0.412	SUBCLONAL	1	TRUE	1	0.441405862506955	2		409	427	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56811512	56811512	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502590	NA	P-0034617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	85	419	0	ENST00000337432.4:c.1060G>A	p.Ala354Thr	p.A354T	ENST00000337432	NM_058216.2	354	Gca/Aca	9/9	1	2	FACETS	0.695	0.616	0.78	0.695	0.616	0.78	SUBCLONAL	1	TRUE	1	0.441405862506955	2		419	554	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992720	68992721	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs764112302	NA	P-0034617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	209	563	9	ENST00000288368.4:c.1693dup	p.Ser565PhefsTer3	p.S565Ffs*3	ENST00000288368	NM_024870.2	562	cgt/cgTt	16/40	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.441405862506955	2		572	656	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056281	27056281	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	153	394	0	ENST00000324856.7:c.1280del	p.Pro427ArgfsTer6	p.P427Rfs*6	ENST00000324856	NM_006015.4	426	aCc/ac	2/20	1	2	FACETS	0.774	0.714	0.835	1	0.99	1	SUBCLONAL	2	TRUE	1	0.441405862506955	2		394	448	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662347	67662348	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0034617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	215	456	0	ENST00000264010.4:c.1593_1594del	p.Phe532ProfsTer27	p.F532Pfs*27	ENST00000264010	NM_006565.3	531	acCTtc/actc	9/12	1	2	FACETS	0.937	0.879	0.995	1	0.994	1	CLONAL	2	TRUE	1	0.441405862506955	2		456	520	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164486	36164486	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	67	300	0	ENST00000300305.3:c.1389del	p.Thr464ProfsTer130	p.T464Pfs*130	ENST00000300305		463	ccC/cc	8/8	1	2	FACETS	0.761	0.664	0.865	0.761	0.664	0.865	SUBCLONAL	1	TRUE	1	0.441405862506955	2		300	399	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928083	178928115	+	inframe_deletion	In_Frame_Del	DEL	ATTTGCTGAACCCTATTGGTGTTACTGGATCAA	ATTTGCTGAACCCTATTGGTGTTACTGGATCAA	-	novel	NA	P-0034617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	152	435	0	ENST00000263967.3:c.1363_1395del	p.Leu455_Asn465del	p.L455_N465del	ENST00000263967	NM_006218.2	454	gATTTGCTGAACCCTATTGGTGTTACTGGATCAAat/gat	8/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.441405862506955	2		435	545	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150449	157150449	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	52	471	0	ENST00000346085.5:c.1631C>A	p.Pro544Gln	p.P544Q	ENST00000346085	NM_020732.3	544	cCg/cAg	2/20	1	2	FACETS	0.421	0.358	0.49	0.421	0.358	0.49	SUBCLONAL	1	TRUE	1	0.441405862506955	2		471	560	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105559	27105560	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0034617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	201	489	0	ENST00000324856.7:c.5170_5171insGT	p.Leu1724ArgfsTer2	p.L1724Rfs*2	ENST00000324856	NM_006015.4	1724	ctg/cGTtg	20/20	1	2	FACETS	0.805	0.751	0.859	1	0.992	1	CLONAL	2	TRUE	1	0.441405862506955	2		489	566	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550586	29550586	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0034622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	47	255	0	ENST00000356175.3:c.1845+1G>T		p.X615_splice	ENST00000356175	NM_000267.3	615			0.3	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.24	1		255	271	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923740	131923740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	34	305	0	ENST00000265335.6:c.1010G>A	p.Arg337Lys	p.R337K	ENST00000265335		337	aGg/aAg	7/25	1	2	FACETS	0.96	0.788	1	0.96	0.788	1	CLONAL	1	TRUE	1	0.24	2		305	295	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78425944	78425944	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	47	365	0	ENST00000370768.2:c.1501C>T	p.Pro501Ser	p.P501S	ENST00000370768	NM_003902.3	501	Cct/Tct	16/20	1	2	FACETS	0.919	0.777	1	0.919	0.777	1	CLONAL	1	TRUE	1	0.24	2		365	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578215	7578221	+	frameshift_variant	Frame_Shift_Del	DEL	AAGTGTT	AAGTGTT	-	novel	NA	P-0034622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	73	667	0	ENST00000269305.4:c.628_634del	p.Asn210PhefsTer35	p.N210Ffs*35	ENST00000269305	NM_001126112.2	210	AACACTTtt/tt	6/11	0.3	1	FACETS	0.843	0.737	0.957	0.843	0.737	0.957	CLONAL	1	TRUE	0	0.24	1		667	635	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17389772	17389772	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769962372	NA	P-0034622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	127	742	0	ENST00000359435.4:c.905C>T	p.Pro302Leu	p.P302L	ENST00000359435	NM_001033549.1	302	cCc/cTc	9/9	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.24	2		742	875	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332868	152332868	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745723014	NA	P-0034625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	163	625	1	ENST00000206249.3:c.1174G>A	p.Val392Ile	p.V392I	ENST00000206249	NM_000125.3	392	Gtc/Atc	5/8	1	2	FACETS	0.865	0.795	0.937	0.865	0.795	0.937	CLONAL	1	TRUE	1	0.492787676988544	2		626	765	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692794	89692794	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121909238	NA	P-0034625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	205	448	0	ENST00000371953.3:c.278A>G	p.His93Arg	p.H93R	ENST00000371953	NM_000314.4	93	cAt/cGt	5/9	0.452021791010523	2	FACETS	0.839	0.786	0.892	0.839	0.786	0.892	CLONAL	2	TRUE	0	0.492787676988544	2		448	496	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788656	3788656	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	330	422	0	ENST00000262367.5:c.4298A>G	p.Tyr1433Cys	p.Y1433C	ENST00000262367	NM_004380.2	1433	tAt/tGt	26/31	0.470164566281018	3	FACETS	0.895	0.854	0.935	0.895	0.854	0.935	CLONAL	3	TRUE	0	0.492787676988544	3		422	622	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579294	7579311	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CCCCTCAGGGCAACTGAC	CCCCTCAGGGCAACTGAC	-	novel	NA	P-0034625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	324	440	0	ENST00000269305.4:c.375+1_375+18del		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.341512271992304	3	FACETS	0.937	0.896	0.978	0.937	0.896	0.978	CLONAL	3	TRUE	0	0.492787676988544	3		440	583	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399807	139399807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	498	723	0	ENST00000277541.6:c.4541G>A	p.Cys1514Tyr	p.C1514Y	ENST00000277541	NM_017617.3	1514	tGc/tAc	25/34	0.492787676988544	2	FACETS	0.971	0.933	1	0.971	0.933	1	CLONAL	2	TRUE	0	0.492787676988544	2		723	1041	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0034627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	147	376	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.898	0.828	0.969	1	0.991	1	CLONAL	2	TRUE	1	0.399367559331254	2		376	410	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	42	217	0	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	1	2	FACETS	0.926	0.786	1	0.926	0.786	1	CLONAL	1	TRUE	1	0.56352081072233	2		217	161	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0034640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	256	658	1	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.56352081072233	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.56352081072233	1		659	520	SUCCESS
APC	324	MSKCC	GRCh37	5	112174998	112174999	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs1554085246	NA	P-0034640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	24	165	0	ENST00000257430.4:c.3709_3710del	p.Gln1237GlufsTer2	p.Q1237Efs*2	ENST00000257430	NM_000038.5	1236	gCA/g	16/16	1	2	FACETS	0.804	0.642	0.982	0.804	0.642	0.982	CLONAL	1	TRUE	1	0.56352081072233	2		165	106	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115415	115115415	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	119	644	0	ENST00000257566.3:c.911G>A	p.Arg304Gln	p.R304Q	ENST00000257566	NM_016569.3	304	cGg/cAg	5/8	0.298205510294402	1	FACETS	0.869	0.794	0.947	0.869	0.794	0.947	INDETERMINATE	1	TRUE	0	0.56352081072233	1		644	349	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480442	57480442	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	92	233	0	ENST00000371085.3:c.437T>C	p.Phe146Ser	p.F146S	ENST00000371085	NM_000516.4	146	tTc/tCc	6/13	0.56352081072233	4	FACETS	1	0.949	1	0.369	0.329	0.411	CLONAL	1	TRUE	1	0.56352081072233	4		233	461	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977891	134977891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	36	435	0	ENST00000398015.3:c.2884C>T	p.Gln962Ter	p.Q962*	ENST00000398015	NM_004441.4	962	Cag/Tag	16/16	1	2	FACETS	0.526	0.435	0.626	0.526	0.435	0.626	SUBCLONAL	1	TRUE	1	0.56352081072233	2		435	243	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231130	53231130	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	183	506	0	ENST00000375401.3:c.1772G>A	p.Gly591Glu	p.G591E	ENST00000375401	NM_004187.3	591	gGa/gAa	13/26	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.56352081072233	2		506	599	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0034646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	112	259	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	0.518638647031379	3	FACETS	0.968	0.885	1	0.968	0.885	1	CLONAL	2	TRUE	1	0.518638647031379	3		259	281	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578446	7578446	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	412	714	0	ENST00000269305.4:c.484A>T	p.Ile162Phe	p.I162F	ENST00000269305	NM_001126112.2	162	Atc/Ttc	5/11	NA	2	FACETS	1	0.968	1			1	INDETERMINATE	2	TRUE	NA	0.518638647031379	2		714	786	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220390	98220390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	197	360	0	ENST00000331920.6:c.3073C>T	p.Arg1025Cys	p.R1025C	ENST00000331920	NM_000264.3	1025	Cgc/Tgc	18/24	0.518638647031379	2	FACETS	0.931	0.874	0.988	0.931	0.874	0.988	CLONAL	2	TRUE	0	0.518638647031379	2		360	408	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986936	36986936	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	3359	518	0	ENST00000354822.5:c.753G>C	p.Lys251Asn	p.K251N	ENST00000354822	NM_001079668.2	251	aaG/aaC	3/3	0.518638647031379	15	FACETS	0.992	0.983	1			1	CLONAL	14	TRUE	NA	0.518638647031379	15		518	4078	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95598885	95598885	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	55	369	0	ENST00000393063.1:c.274A>C	p.Asn92His	p.N92H	ENST00000393063	NM_030621.3	92	Aat/Cat	4/28	0.516675053450945	2	FACETS	0.794	0.686	0.911	0.397	0.343	0.456	CLONAL	1	TRUE	0	0.518638647031379	2		369	267	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66520161	66520161	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	257	520	0	ENST00000358598.2:c.445A>G	p.Ile149Val	p.I149V	ENST00000358598	NM_212471.2	149	Att/Gtt	5/11	0.459082792619107	4	FACETS	0.949	0.892	1	0.949	0.892	1	CLONAL	2	TRUE	2	0.518638647031379	4		520	793	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602758	10602758	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	458	809	1	ENST00000171111.5:c.820del	p.His274ThrfsTer3	p.H274Tfs*3	ENST00000171111	NM_203500.1	274	Cac/ac	3/6	0.516675053450945	2	FACETS	0.989	0.95	1	0.989	0.95	1	CLONAL	2	TRUE	0	0.518638647031379	2		810	893	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710527	40710527	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	281	572	0	ENST00000373198.4:c.4324A>G	p.Thr1442Ala	p.T1442A	ENST00000373198	NM_133170.3	1442	Acc/Gcc	31/32	0.459082792619107	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.518638647031379	4		572	790	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094821	143094821	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	60	367	0	ENST00000262992.4:c.1323C>A	p.Asp441Glu	p.D441E	ENST00000262992	NM_001101669.1	441	gaC/gaA	14/24	0.518638647031379	3	FACETS	0.812	0.703	0.929	0.406	0.351	0.465	CLONAL	1	TRUE	1	0.518638647031379	3		367	359	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	59	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.491934174315201	2		148	226	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0034651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	252	914	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	1	2	FACETS	0.996	0.932	1	0.996	0.932	1	CLONAL	1	TRUE	1	0.491934174315201	2		914	1029	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188136	108188136	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1800060	NA	P-0034651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	127	412	1	ENST00000278616.4:c.6235G>A	p.Val2079Ile	p.V2079I	ENST00000278616	NM_000051.3	2079	Gtc/Atc	43/63	1	2	FACETS	0.906	0.824	0.992	0.906	0.824	0.992	CLONAL	1	TRUE	1	0.491934174315201	2		413	570	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0034651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	417	264	0	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	0.134920538037498	6	FACETS	1	0.983	1			1	INDETERMINATE	4	TRUE	NA	0.491934174315201	6		264	804	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115969	8115970	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0034651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	182	424	0	ENST00000346208.3:c.1316_1317dup	p.Thr440SerfsTer36	p.T440Sfs*36	ENST00000346208		439	gtc/gTCtc	6/6	0.469324099867151	2	FACETS	0.794	0.74	0.849	0.794	0.74	0.849	SUBCLONAL	2	TRUE	0	0.491934174315201	2		424	466	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244933	46244934	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0034651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	179	770	0	ENST00000334344.6:c.3031dup	p.Arg1011LysfsTer46	p.R1011Kfs*46	ENST00000334344	NM_152641.2	1009	-/A	15/21	1	2	FACETS	0.849	0.783	0.917	0.849	0.783	0.917	CLONAL	1	TRUE	1	0.491934174315201	2		770	857	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30047495	30047495	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	126	559	1	ENST00000331968.5:c.2506C>A	p.His836Asn	p.H836N	ENST00000331968	NM_002742.2	836	Cac/Aac	17/18	1	2	FACETS	0.868	0.789	0.951	0.868	0.789	0.951	CLONAL	1	TRUE	1	0.491934174315201	2		560	590	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871839	35871839	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	156	662	0	ENST00000216797.5:c.667C>G	p.Leu223Val	p.L223V	ENST00000216797	NM_020529.2	223	Ctc/Gtc	5/6	1	2	FACETS	0.866	0.795	0.941	0.866	0.795	0.941	CLONAL	1	TRUE	1	0.491934174315201	2		662	732	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839831	27839831	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	154	641	1	ENST00000328488.2:c.263C>T	p.Ser88Leu	p.S88L	ENST00000328488	NM_003533.2	88	tCg/tTg	1/1	1	2	FACETS	0.809	0.741	0.88	0.809	0.741	0.88	CLONAL	1	TRUE	1	0.491934174315201	2		642	774	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652204	36652205	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0034651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	223	787	0	ENST00000244741.5:c.328dup	p.His110ProfsTer19	p.H110Pfs*19	ENST00000244741	NM_000389.4	109	gac/gaCc	2/3	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.491934174315201	2		787	687	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0034652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	61	451	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.2	2		451	571	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0034652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	108	960	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.195449504080596	1	FACETS	0.781	0.699	0.869	0.781	0.699	0.869	SUBCLONAL	1	TRUE	0	0.2	1		960	1244	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853221	68853221	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	85	547	2	ENST00000261769.5:c.1605del	p.Asn536IlefsTer21	p.N536Ifs*21	ENST00000261769	NM_004360.3	535	aTt/at	11/16	0.195449504080596	1	FACETS	0.927	0.819	1	0.927	0.819	1	CLONAL	1	TRUE	0	0.2	1		549	825	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639252	3639252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779970904	NA	P-0034652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	125	846	0	ENST00000294008.3:c.4387G>A	p.Asp1463Asn	p.D1463N	ENST00000294008	NM_032444.2	1463	Gac/Aac	12/15	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.2	2		846	1207	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096625	178096625	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	58	397	0	ENST00000397062.3:c.706G>A	p.Glu236Lys	p.E236K	ENST00000397062	NM_006164.4	236	Gaa/Aaa	5/5	1	2	FACETS	0.934	0.802	1	0.934	0.802	1	CLONAL	1	TRUE	1	0.2	2		397	621	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686247	30686247	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	59	371	0	ENST00000295754.5:c.103G>C	p.Asp35His	p.D35H	ENST00000295754	NM_003242.5	35	Gac/Cac	2/7	1	2	FACETS	0.95	0.817	1	0.95	0.817	1	CLONAL	1	TRUE	1	0.2	2		371	621	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403373	139403373	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	106	773	0	ENST00000277541.6:c.3120C>A	p.Cys1040Ter	p.C1040*	ENST00000277541	NM_017617.3	1040	tgC/tgA	19/34	1	2	FACETS	0.93	0.831	1	0.93	0.831	1	CLONAL	1	TRUE	1	0.2	2		773	1140	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798129	45798129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501346	NA	P-0034663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	93	766	1	ENST00000450313.1:c.722G>A	p.Arg241Gln	p.R241Q	ENST00000450313	NM_012222.2	241	cGg/cAg	9/16	0.258248965860571	3	FACETS	1	0.965	1	0.607	0.54	0.678	CLONAL	1	TRUE	1	0.258248965860571	3		767	670	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004643	16004643	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	81	692	2	ENST00000268712.3:c.2611C>A	p.Pro871Thr	p.P871T	ENST00000268712	NM_006311.3	871	Ccc/Acc	20/46	0.103734692300092	4	FACETS	0.992	0.873	1	0.496	0.436	0.56	INDETERMINATE	1	TRUE	2	0.258248965860571	4		694	796	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798211	42798211	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	65	730	2	ENST00000575354.2:c.4165T>A	p.Ser1389Thr	p.S1389T	ENST00000575354	NM_015125.3	1389	Tct/Act	17/20	0.209657059992453	2	FACETS	0.877	0.761	1	0.438	0.38	0.502	CLONAL	1	TRUE	0	0.258248965860571	2		732	574	SUCCESS
AR	367	MSKCC	GRCh37	X	66931436	66931436	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	69	373	0	ENST00000374690.3:c.2078A>G	p.Asn693Ser	p.N693S	ENST00000374690	NM_000044.3	693	aAc/aGc	4/8	0.258248965860571	2	FACETS	1	0.934	1			1	CLONAL	1	TRUE	NA	0.258248965860571	2		373	481	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	146	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.754839917467504	2		148	341	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21968230	21968240	+	stop_lost,protein_altering_variant,splice_region_variant	Nonstop_Mutation	DEL	AATCGGGGATG	AATCGGGGATG	TGCCC	novel	NA	P-0034666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	84	418	1	ENST00000304494.5:c.459_469delinsGGGCA	p.Asp153_Ter157delinsGluGlyArg	p.D153_*157delinsEGR	ENST00000304494	NM_000077.4	153	gaCATCCCCGATTga/gaGGGCAga	3/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.754839917467504	2		419	182	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21968230	21968238	+	stop_lost,inframe_deletion	Nonstop_Mutation	DEL	AATCGGGGA	AATCGGGGA	-	novel	NA	P-0034666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	85	403	0	ENST00000304494.5:c.461_469del	p.Ile154_Ter157delinsArg	p.I154_*157delinsR	ENST00000304494	NM_000077.4	154	aTCCCCGATTga/aga	3/3	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.754839917467504	2		403	176	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0034667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	78	339	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.138591199892868	4	FACETS	1	0.943	1	1	0.943	1	CLONAL	3	TRUE	1	0.143421696614738	4		339	374	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0034667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	220	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.143479322787925	3	FACETS	0.989	0.925	1	1	0.993	1	CLONAL	5	TRUE	0	0.143421696614738	3		502	665	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0034667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	225	678	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.143479322787925	2	FACETS	1	0.952	1	1	0.994	1	CLONAL	4	TRUE	0	0.143421696614738	2		678	767	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962846	2962846	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	88	726	0	ENST00000396946.4:c.2062C>T	p.Arg688Ter	p.R688*	ENST00000396946	NM_032415.4	688	Cga/Tga	16/25	0.143421696614738	7	FACETS	0.804	0.71	0.904	0.402	0.355	0.452	CLONAL	2	TRUE	3	0.143421696614738	7		726	1037	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750680	128750681	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCC	novel	NA	P-0034667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	126	557	0	ENST00000377970.2:c.219_221dup	p.Pro75dup	p.P75dup	ENST00000377970	NM_002467.4	75	acc/aCCCcc	2/3	0.143421696614738	6	FACETS	0.98	0.89	1	0.784	0.712	0.858	CLONAL	4	TRUE	1	0.143421696614738	6		557	577	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809512	36809512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748294638	NA	P-0034667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	119	733	0	ENST00000373129.3:c.953G>A	p.Arg318His	p.R318H	ENST00000373129	NM_032017.1	318	cGc/cAc	10/12	0.138591199892868	4	FACETS	1	0.965	1	0.767	0.692	0.846	CLONAL	2	TRUE	1	0.143421696614738	4		733	825	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623575	28623575	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	210	570	0	ENST00000241453.7:c.982T>C	p.Tyr328His	p.Y328H	ENST00000241453	NM_004119.2	328	Tac/Cac	8/24	0.138591199892868	4	FACETS	0.965	0.9	1	1	0.992	1	CLONAL	5	TRUE	1	0.143421696614738	4		570	694	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0034669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	286	274	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.930338811592998	2		274	541	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916929	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519931	NA	P-0034669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	26	459	0	ENST00000263967.3:c.316G>C	p.Gly106Arg	p.G106R	ENST00000263967	NM_006218.2	106	Ggc/Cgc	2/21	1	2	FACETS	0.072	0.057	0.09	0.072	0.057	0.09	SUBCLONAL	1	TRUE	1	0.930338811592998	2		459	773	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0034669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16439	1012	432	0	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.930338811592998	30	FACETS	0.874	0.843	0.906	0.06	0.058	0.063	CLONAL	2	TRUE	1	0.930338811592998	30		432	17451	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375235	31375235	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	380	588	0	ENST00000328111.2:c.632A>G	p.Asp211Gly	p.D211G	ENST00000328111	NM_006892.3	211	gAt/gGt	6/23	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.930338811592998	2		588	810	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191784	123191784	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	336	408	0	ENST00000218089.9:c.1374del	p.Asn459ThrfsTer11	p.N459Tfs*11	ENST00000218089	NM_001042749.1	458	gCc/gc	15/35	1	2	FACETS	0.907	0.863	0.952	0.907	0.863	0.952	CLONAL	1	TRUE	1	0.930338811592998	2		408	796	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0034670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	298	425	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.256545608028567	5	FACETS	1	0.985	1	1	0.985	1	CLONAL	4	TRUE	1	0.256545608028567	5		425	727	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0034670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	205	648	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.247944191161531	3	FACETS	0.929	0.866	0.993	0.929	0.866	0.993	CLONAL	3	TRUE	0	0.256545608028567	3		648	647	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843595	156843595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139875058	NA	P-0034670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	165	893	0	ENST00000524377.1:c.1021G>A	p.Val341Met	p.V341M	ENST00000524377	NM_002529.3	341	Gtg/Atg	8/17	0.256545608028567	3	FACETS	0.938	0.862	1			1	CLONAL	2	TRUE	NA	0.256545608028567	3		893	774	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903745	41903746	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0034670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	51	699	0	ENST00000372991.4:c.811dup	p.Arg271ProfsTer53	p.R271Pfs*53	ENST00000372991	NM_001760.3	271	cgg/cCgg	5/5	0.245476586978565	4	FACETS	0.612	0.519	0.715	0.204	0.173	0.239	SUBCLONAL	1	TRUE	1	0.256545608028567	4		699	816	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061679	38061679	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	23	272	0	ENST00000250448.2:c.310A>T	p.Met104Leu	p.M104L	ENST00000250448	NM_004496.3	104	Atg/Ttg	2/2	0.245476586978565	4	FACETS	0.702	0.547	0.881	0.234	0.182	0.294	SUBCLONAL	1	TRUE	1	0.256545608028567	4		272	321	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89345514	89345514	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	60	429	0	ENST00000301030.4:c.7436A>T	p.Asp2479Val	p.D2479V	ENST00000301030	NM_001256183.1	2479	gAc/gTc	9/13	0.105168756797251	4	FACETS	0.869	0.753	0.994	0.869	0.753	0.994	INDETERMINATE	2	TRUE	2	0.256545608028567	4		429	338	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170818	99170825	+	frameshift_variant	Frame_Shift_Del	DEL	GCCTCCAA	GCCTCCAA	-	novel	NA	P-0034670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	60	548	0	ENST00000074304.5:c.1448_1455del	p.Ala483GlyfsTer7	p.A483Gfs*7	ENST00000074304	NM_001134224.1	483	GCCTCCAAg/g	16/26	0.256545608028567	5	FACETS	1	0.938	1	0.291	0.25	0.335	CLONAL	1	TRUE	1	0.256545608028567	5		548	557	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143350324	143350324	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0034670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	66	255	0	ENST00000262992.4:c.136+2T>C		p.X46_splice	ENST00000262992	NM_001101669.1	46			0.256545608028567	2	FACETS	0.878	0.769	0.994	0.878	0.769	0.994	CLONAL	2	TRUE	0	0.256545608028567	2		255	293	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589553	67589585	+	inframe_deletion	In_Frame_Del	DEL	AAGATAATATTGAAGCTGTAGGGAAAAAATTAC	AAGATAATATTGAAGCTGTAGGGAAAAAATTAC	-	novel	NA	P-0034670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	59	206	0	ENST00000274335.5:c.1317_1349del	p.Glu439_His450delinsAsp	p.E439_H450delinsD	ENST00000274335		439	gAAGATAATATTGAAGCTGTAGGGAAAAAATTACat/gat	10/15	0.212293794704167	4	FACETS	1	0.876	1	0.505	0.438	0.577	CLONAL	2	TRUE	0	0.256545608028567	4		206	286	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515237	106515237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	88	364	1	ENST00000359195.3:c.2380G>A	p.Gly794Arg	p.G794R	ENST00000359195	NM_002649.2	794	Gga/Aga	5/11	0.256545608028567	6	FACETS	1	0.915	1	0.517	0.459	0.578	CLONAL	2	TRUE	2	0.256545608028567	6		365	502	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140357	50140357	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	157	491	0	ENST00000246792.3:c.184A>G	p.Ile62Val	p.I62V	ENST00000246792	NM_006270.3	62	Att/Gtt	2/6	1	2	FACETS	0.954	0.879	1	0.954	0.879	1	CLONAL	1	TRUE	1	0.601499811337969	2		491	547	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191646	10191647	+	frameshift_variant,stop_lost	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0034671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	217	537	0	ENST00000256474.2:c.639_640del	p.Asp213GlufsTer42	p.D213Efs*42	ENST00000256474	NM_000551.3	213	gaTTga/gaga	3/3	0.601499811337969	1	FACETS	0.999	0.939	1	0.999	0.939	1	CLONAL	1	TRUE	0	0.601499811337969	1		537	505	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143027	47143027	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	132	409	0	ENST00000409792.3:c.4936del	p.Leu1646Ter	p.L1646*	ENST00000409792	NM_014159.6	1646	Ctg/tg	8/21	0.601499811337969	1	FACETS	0.832	0.764	0.901	0.832	0.764	0.901	CLONAL	1	TRUE	0	0.601499811337969	1		409	369	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52663019	52663019	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	84	354	0	ENST00000394830.3:c.1334del	p.Leu445Ter	p.L445*	ENST00000394830	NM_018313.4	445	tTa/ta	13/30	0.601499811337969	1	FACETS	0.81	0.727	0.896	0.81	0.727	0.896	CLONAL	1	TRUE	0	0.601499811337969	1		354	241	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239954	53239954	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	222	328	0	ENST00000375401.3:c.1487G>C	p.Gly496Ala	p.G496A	ENST00000375401	NM_004187.3	496	gGc/gCc	11/26	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.601499811337969	1		328	370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	464	695	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.905590605480211	2		695	934	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	394	745	0	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	0.905590605480211	2		745	840	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262588	16262588	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	67	383	0	ENST00000375759.3:c.9853C>T	p.Pro3285Ser	p.P3285S	ENST00000375759	NM_015001.2	3285	Cct/Tct	11/15	0.7748600574693	3	FACETS	0.302	0.261	0.345	0.151	0.13	0.173	SUBCLONAL	1	TRUE	1	0.905590605480211	3		383	713	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36826878	36826878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	430	707	0	ENST00000373129.3:c.56C>T	p.Ala19Val	p.A19V	ENST00000373129	NM_032017.1	19	gCt/gTt	3/12	0.7748600574693	3	FACETS	0.996	0.949	1	0.498	0.474	0.522	CLONAL	1	TRUE	1	0.905590605480211	3		707	1385	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	244006446	244006446	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	323	482	0	ENST00000263826.5:c.27A>C	p.Glu9Asp	p.E9D	ENST00000263826	NM_005465.4	9	gaA/gaC	1/13	1	2	FACETS	0.935	0.888	0.982	0.935	0.888	0.982	CLONAL	1	TRUE	1	0.905590605480211	2		482	763	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597975	43597975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057521088	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	423	751	0	ENST00000355710.3:c.523C>T	p.Arg175Cys	p.R175C	ENST00000355710	NM_020975.4	175	Cgc/Tgc	3/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.905590605480211	2		751	879	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112494	115112494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	427	630	0	ENST00000257566.3:c.1246C>T	p.Leu416Phe	p.L416F	ENST00000257566	NM_016569.3	416	Ctt/Ttt	7/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.905590605480211	2		630	885	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120789192	120789192	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	192	353	0	ENST00000257552.2:c.745G>A	p.Glu249Lys	p.E249K	ENST00000257552	NM_002442.3	249	Gag/Aag	11/15	1	2	FACETS	0.91	0.851	0.97	0.91	0.851	0.97	CLONAL	1	TRUE	1	0.905590605480211	2		353	466	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218969	133218969	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	266	722	0	ENST00000320574.5:c.4967C>T	p.Pro1656Leu	p.P1656L	ENST00000320574	NM_006231.2	1656	cCc/cTc	38/49	1	2	FACETS	0.697	0.655	0.739	0.697	0.655	0.739	SUBCLONAL	1	TRUE	1	0.905590605480211	2		722	843	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941739	48941739	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	152	346	0	ENST00000267163.4:c.1049G>A	p.Ser350Asn	p.S350N	ENST00000267163	NM_000321.2	350	aGt/aAt	10/27	0.905590605480211	1	FACETS	0.883	0.838	0.926	0.883	0.838	0.926	CLONAL	1	TRUE	0	0.905590605480211	1		346	208	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	302	776	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	1	2	FACETS	0.935	0.887	0.984	0.935	0.887	0.984	CLONAL	1	TRUE	1	0.905590605480211	2		776	713	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042065	42042066	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	171	484	0	ENST00000219905.7:c.6260_6261delinsAA	p.Arg2087Lys	p.R2087K	ENST00000219905	NM_001164273.1	2087	aGG/aAA	17/24	1	2	FACETS	0.81	0.752	0.87	0.81	0.752	0.87	CLONAL	1	TRUE	1	0.905590605480211	2		484	466	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434613	99434613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253103806	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	311	583	0	ENST00000268035.6:c.700G>A	p.Glu234Lys	p.E234K	ENST00000268035	NM_000875.3	234	Gag/Aag	3/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.905590605480211	2		583	682	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640079	3640079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	470	914	0	ENST00000294008.3:c.3560G>A	p.Arg1187Lys	p.R1187K	ENST00000294008	NM_032444.2	1187	aGg/aAg	12/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.905590605480211	2		914	980	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641455	23641455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881885	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	413	831	0	ENST00000261584.4:c.2020G>A	p.Asp674Asn	p.D674N	ENST00000261584	NM_024675.3	674	Gac/Aac	5/13	0.259651495246765	3	FACETS	1	0.995	1	0.693	0.662	0.724	INDETERMINATE	1	TRUE	1	0.905590605480211	3		831	956	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650756	67650757	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	343	607	0	ENST00000264010.4:c.1061_1062delinsTT	p.Ser354Phe	p.S354F	ENST00000264010	NM_006565.3	354	tCC/tTT	5/12	0.259651495246765	3	FACETS	1	0.994	1	0.679	0.646	0.713	INDETERMINATE	1	TRUE	1	0.905590605480211	3		607	810	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829661	72829661	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	382	729	0	ENST00000268489.5:c.6920G>A	p.Gly2307Asp	p.G2307D	ENST00000268489	NM_006885.3	2307	gGc/gAc	9/10	0.259651495246765	3	FACETS	1	0.994	1	0.635	0.605	0.665	INDETERMINATE	1	TRUE	1	0.905590605480211	3		729	965	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81914514	81914514	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	272	469	0	ENST00000359376.3:c.649-1G>A		p.X217_splice	ENST00000359376	NM_002661.3	217			NA	2	FACETS	0.963	0.911	1			1	INDETERMINATE	1	TRUE	NA	0.905590605480211	2		469	624	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347504	89347504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371567838	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	270	485	0	ENST00000301030.4:c.5446C>T	p.Pro1816Ser	p.P1816S	ENST00000301030	NM_001256183.1	1816	Cct/Tct	9/13	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.905590605480211	2		485	573	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512474	38512474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770732457	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	438	840	1	ENST00000254066.5:c.1385C>T	p.Pro462Leu	p.P462L	ENST00000254066	NM_000964.3	462	cCg/cTg	9/9	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.905590605480211	2		841	955	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40461480	40461480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745362393	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	90	805	0	ENST00000345506.4:c.2200C>T	p.Pro734Ser	p.P734S	ENST00000345506	NM_003152.3	734	Ccc/Tcc	19/20	1	2	FACETS	0.228	0.202	0.257	0.228	0.202	0.257	SUBCLONAL	1	TRUE	1	0.905590605480211	2		805	870	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244858	41244858	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776484	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	101	716	1	ENST00000357654.3:c.2690C>T	p.Pro897Leu	p.P897L	ENST00000357654	NM_007294.3	897	cCa/cTa	10/23	1	2	FACETS	0.298	0.266	0.332	0.298	0.266	0.332	SUBCLONAL	1	TRUE	1	0.905590605480211	2		717	749	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395689	45395689	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	289	399	0	ENST00000262160.6:c.445T>G	p.Cys149Gly	p.C149G	ENST00000262160	NM_005901.5	149	Tgc/Ggc	4/11	0.688518188734007	1	FACETS	0.905	0.872	0.936	0.905	0.872	0.936	CLONAL	1	TRUE	0	0.905590605480211	1		399	386	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210674	2210675	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	552	630	1	ENST00000398665.3:c.1171_1172delinsTT	p.Pro391Phe	p.P391F	ENST00000398665	NM_032482.2	391	CCc/TTc	14/28	0.659875449027011	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.905590605480211	1		631	614	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226935	2226935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1203823093	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	632	405	1	ENST00000398665.3:c.4415C>T	p.Pro1472Leu	p.P1472L	ENST00000398665	NM_032482.2	1472	cCg/cTg	27/28	0.659875449027011	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.905590605480211	1		406	664	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152018	11152019	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	239	468	0	ENST00000358026.2:c.4302_4303delinsAA	p.Glu1435Lys	p.E1435K	ENST00000358026	NM_001128849.1	1434	gaGGag/gaAAag	31/36	1	2	FACETS	0.968	0.913	1	0.968	0.913	1	CLONAL	1	TRUE	1	0.905590605480211	2		468	545	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300222	15300222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	379	677	0	ENST00000263388.2:c.1054G>A	p.Asp352Asn	p.D352N	ENST00000263388	NM_000435.2	352	Gat/Aat	7/33	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.905590605480211	2		677	823	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213593	36213593	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	464	837	0	ENST00000222270.7:c.2695C>G	p.Arg899Gly	p.R899G	ENST00000222270	NM_014727.1	899	Cgg/Ggg	5/37	1	2	FACETS	0.966	0.926	1	0.966	0.926	1	CLONAL	1	TRUE	1	0.905590605480211	2		837	1061	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	144	932	2	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	1	2	FACETS	0.339	0.309	0.371	0.339	0.309	0.371	SUBCLONAL	1	TRUE	1	0.905590605480211	2		934	937	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574104	46574104	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	376	684	0	ENST00000263734.3:c.119A>C	p.Glu40Ala	p.E40A	ENST00000263734	NM_001430.4	40	gAg/gCg	2/16	1	2	FACETS	0.977	0.932	1	0.977	0.932	1	CLONAL	1	TRUE	1	0.905590605480211	2		684	850	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145543	61145543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767519747	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	204	324	0	ENST00000295025.8:c.655C>T	p.Arg219Cys	p.R219C	ENST00000295025	NM_002908.2	219	Cgt/Tgt	7/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.905590605480211	2		324	423	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251647	212251647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	270	489	0	ENST00000342788.4:c.3412G>A	p.Glu1138Lys	p.E1138K	ENST00000342788	NM_005235.2	1138	Gaa/Aaa	27/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.905590605480211	2		489	548	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295755	212295755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	274	606	1	ENST00000342788.4:c.2558C>T	p.Ser853Phe	p.S853F	ENST00000342788	NM_005235.2	853	tCt/tTt	21/28	1	2	FACETS	0.937	0.886	0.988	0.937	0.886	0.988	CLONAL	1	TRUE	1	0.905590605480211	2		607	646	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537975	212537975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267599192	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	156	324	0	ENST00000342788.4:c.1630C>T	p.Arg544Trp	p.R544W	ENST00000342788	NM_005235.2	544	Cgg/Tgg	14/28	1	2	FACETS	0.881	0.817	0.947	0.881	0.817	0.947	CLONAL	1	TRUE	1	0.905590605480211	2		324	391	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656954	45656954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	129	781	1	ENST00000407780.3:c.202C>T	p.Pro68Ser	p.P68S	ENST00000407780	NM_001283052.1	68	Cca/Tca	3/7	1	2	FACETS	0.266	0.24	0.293	0.266	0.24	0.293	SUBCLONAL	1	TRUE	1	0.905590605480211	2		782	1071	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644697	134644697	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	327	500	0	ENST00000398015.3:c.98G>A	p.Gly33Asp	p.G33D	ENST00000398015	NM_004441.4	33	gGc/gAc	2/16	1	2	FACETS	0.949	0.902	0.996	0.949	0.902	0.996	CLONAL	1	TRUE	1	0.905590605480211	2		500	761	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467742	66467742	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	198	422	0	ENST00000273854.3:c.527C>T	p.Thr176Ile	p.T176I	ENST00000273854	NM_004439.5	176	aCc/aTc	3/18	1	2	FACETS	0.98	0.919	1	0.98	0.919	1	CLONAL	1	TRUE	1	0.905590605480211	2		422	446	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627774	187627775	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	223	527	1	ENST00000441802.2:c.3207_3208delinsTT	p.Arg1070Ter	p.R1070*	ENST00000441802	NM_005245.3	1069	atCCga/atTTga	2/27	1	2	FACETS	0.894	0.839	0.949	0.894	0.839	0.949	CLONAL	1	TRUE	1	0.905590605480211	2		528	551	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945667	38945667	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	180	371	0	ENST00000357387.3:c.4559G>T	p.Cys1520Phe	p.C1520F	ENST00000357387	NM_152756.3	1520	tGc/tTc	34/38	NA	2	FACETS	1	0.963	1			1	INDETERMINATE	1	TRUE	NA	0.905590605480211	2		371	382	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962444	38962444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	117	435	0	ENST00000357387.3:c.1688G>A	p.Arg563Lys	p.R563K	ENST00000357387	NM_152756.3	563	aGa/aAa	19/38	NA	2	FACETS	0.751	0.685	0.819			1	INDETERMINATE	1	TRUE	NA	0.905590605480211	2		435	344	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178155	56178155	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	46	313	0	ENST00000399503.3:c.3128C>T	p.Ser1043Phe	p.S1043F	ENST00000399503	NM_005921.1	1043	tCc/tTc	14/20	NA	2	FACETS	0.266	0.224	0.312			1	INDETERMINATE	1	TRUE	NA	0.905590605480211	2		313	382	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513568	149513568	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	91	489	1	ENST00000261799.4:c.635C>T	p.Ser212Leu	p.S212L	ENST00000261799	NM_002609.3	212	tCa/tTa	5/23	1	2	FACETS	0.301	0.267	0.337	0.301	0.267	0.337	SUBCLONAL	1	TRUE	1	0.905590605480211	2		490	668	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176684086	176684086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	319	552	0	ENST00000439151.2:c.4900C>T	p.Arg1634Trp	p.R1634W	ENST00000439151	NM_022455.4	1634	Cgg/Tgg	13/23	1	2	FACETS	0.869	0.824	0.914	0.869	0.824	0.914	CLONAL	1	TRUE	1	0.905590605480211	2		552	811	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401580	401580	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	209	456	2	ENST00000380956.4:c.902G>A	p.Arg301Lys	p.R301K	ENST00000380956	NM_001195286.1	301	aGg/aAg	7/9	1	2	FACETS	0.954	0.895	1	0.954	0.895	1	CLONAL	1	TRUE	1	0.905590605480211	2		458	484	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026915	6026915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782602	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	81	119	0	ENST00000265849.7:c.1481C>T	p.Ser494Leu	p.S494L	ENST00000265849	NM_000535.5	494	tCg/tTg	11/15	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.905590605480211	2		119	174	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042199	6042199	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	423	579	0	ENST00000265849.7:c.422G>A	p.Gly141Glu	p.G141E	ENST00000265849	NM_000535.5	141	gGg/gAg	5/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.905590605480211	2		579	924	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509636	106509636	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs867282260	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	57	436	0	ENST00000359195.3:c.1630C>T	p.Arg544Ter	p.R544*	ENST00000359195	NM_002649.2	544	Cga/Tga	2/11	0.259651495246765	3	FACETS	0.359	0.308	0.414	0.179	0.154	0.207	INDETERMINATE	1	TRUE	1	0.905590605480211	3		436	510	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524300	148524301	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	190	406	0	ENST00000320356.2:c.683_684delinsTT	p.Ser228Phe	p.S228F	ENST00000320356	NM_004456.4	228	tCC/tTT	7/20	0.259651495246765	3	FACETS	1	0.991	1	0.691	0.646	0.736	INDETERMINATE	1	TRUE	1	0.905590605480211	3		406	441	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873563	151873563	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	338	560	0	ENST00000262189.6:c.8975G>C	p.Gly2992Ala	p.G2992A	ENST00000262189	NM_170606.2	2992	gGg/gCg	38/59	0.259651495246765	3	FACETS	0.777	0.741	0.813	0.777	0.741	0.813	INDETERMINATE	2	TRUE	1	0.905590605480211	3		560	698	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878651	151878652	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	232	543	0	ENST00000262189.6:c.6293_6294delinsTT	p.Pro2098Leu	p.P2098L	ENST00000262189	NM_170606.2	2098	cCC/cTT	36/59	0.259651495246765	3	FACETS	1	0.993	1	0.738	0.696	0.781	INDETERMINATE	1	TRUE	1	0.905590605480211	3		543	504	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974714	21974715	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	158	320	1	ENST00000304494.5:c.112_113delinsTT	p.Pro38Phe	p.P38F	ENST00000304494	NM_000077.4	38	CCc/TTc	1/3	0.905590605480211	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.905590605480211	1		321	189	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974715	21974715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	155	318	1	ENST00000304494.5:c.112C>T	p.Pro38Ser	p.P38S	ENST00000304494	NM_000077.4	38	Ccc/Tcc	1/3	0.905590605480211	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.905590605480211	1		319	186	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97897785	97897785	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	346	264	0	ENST00000289081.3:c.687-1G>A		p.X229_splice	ENST00000289081	NM_000136.2	229			0.905590605480211	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.905590605480211	2		264	371	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128321949	128321949	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	189	493	0	ENST00000265960.3:c.811C>T	p.Pro271Ser	p.P271S	ENST00000265960	NM_001006617.1	271	Cct/Tct	6/12	0.905590605480211	2	FACETS	0.627	0.581	0.673	0.313	0.29	0.337	SUBCLONAL	1	TRUE	0	0.905590605480211	2		493	666	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801065	135801065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs118203361	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	42	410	0	ENST00000298552.3:c.272C>T	p.Ser91Leu	p.S91L	ENST00000298552	NM_001162426.1	91	tCg/tTg	5/23	0.905590605480211	2	FACETS	0.174	0.145	0.207	0.087	0.072	0.104	SUBCLONAL	1	TRUE	0	0.905590605480211	2		410	532	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412203	139412204	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	522	582	1	ENST00000277541.6:c.1441_1441+1delinsAA		p.X481_splice	ENST00000277541	NM_017617.3	481		8/34	0.905590605480211	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.905590605480211	2		583	567	SUCCESS
AR	367	MSKCC	GRCh37	X	66765814	66765814	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	473	459	1	ENST00000374690.3:c.826C>T	p.Pro276Ser	p.P276S	ENST00000374690	NM_000044.3	276	Cca/Tca	1/8	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.905590605480211	1		460	502	SUCCESS
AR	367	MSKCC	GRCh37	X	66941766	66941766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	99	256	0	ENST00000374690.3:c.2410G>A	p.Glu804Lys	p.E804K	ENST00000374690	NM_000044.3	804	Gaa/Aaa	6/8	1	1	FACETS	0.335	0.302	0.37	0.335	0.302	0.37	SUBCLONAL	1	TRUE	0	0.905590605480211	1		256	357	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617564	100617564	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	104	384	0	ENST00000308731.7:c.505G>A	p.Glu169Lys	p.E169K	ENST00000308731	NM_000061.2	169	Gag/Aag	6/19	1	1	FACETS	0.31	0.279	0.342	0.31	0.279	0.342	SUBCLONAL	1	TRUE	0	0.905590605480211	1		384	406	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974714	21974714	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1563892591	NA	P-0034671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	158	321	0	ENST00000304494.5:c.113C>T	p.Pro38Leu	p.P38L	ENST00000304494	NM_000077.4	38	cCc/cTc	1/3	0.905590605480211	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.905590605480211	1		321	189	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	63	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.76	0.67	0.853	1	0.976	1	SUBCLONAL	2	TRUE	1	0.460617541243355	2		148	180	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43739599	43739599	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	82	481	0	ENST00000382044.4:c.2801T>A	p.Leu934Gln	p.L934Q	ENST00000382044	NM_001141980.1	934	cTa/cAa	13/28	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.460617541243355	2		481	336	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226874	142226883	+	protein_altering_variant	In_Frame_Del	DEL	CTACTGCCAG	CTACTGCCAG	ACAC	novel	NA	P-0034672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	72	640	3	ENST00000350721.4:c.4921_4930delinsGTGT	p.Leu1641_Ala1644delinsValSer	p.L1641_A1644delinsVS	ENST00000350721	NM_001184.3	1641	CTGGCAGTAGct/GTGTct	28/47	1	2	FACETS	0.732	0.642	0.828	0.732	0.642	0.828	SUBCLONAL	1	TRUE	1	0.460617541243355	2		643	427	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039878	47039878	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	101	470	0	ENST00000377604.3:c.1221T>G	p.Ile407Met	p.I407M	ENST00000377604	NM_001204468.1	407	atT/atG	12/24	1	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.460617541243355	1		470	257	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519985	NA	P-0034679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	113	753	0	ENST00000269305.4:c.857A>C	p.Glu286Ala	p.E286A	ENST00000269305	NM_001126112.2	286	gAa/gCa	8/11	0.287569837615397	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	FALSE	0	0.287569837615397	1		753	669	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483101	29483101	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	115	545	0	ENST00000356175.3:c.162del	p.Ile55Ter	p.I55*	ENST00000356175	NM_000267.3	54	gTt/gt	2/57	1	2	FACETS	0.987	0.889	1	0.987	0.889	1	CLONAL	1	FALSE	1	0.287569837615397	2		545	810	SUCCESS
AR	367	MSKCC	GRCh37	X	66765093	66765093	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	56	310	0	ENST00000374690.3:c.105G>C	p.Gln35His	p.Q35H	ENST00000374690	NM_000044.3	35	caG/caC	1/8	1	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	0	0.287569837615397	1		310	248	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0034682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	67	608	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.85	0.737	0.972	0.85	0.737	0.972	CLONAL	1	TRUE	1	0.207783577981805	2		608	759	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663789	241663790	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTGATCC	novel	NA	P-0034684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	20	531	0	ENST00000366560.3:c.1331_1337dup	p.Asn446LysfsTer8	p.N446Kfs*8	ENST00000366560	NM_000143.3	446	aac/aaGGATCAAc	9/10	NA	2	FACETS	0.147	0.112	0.188			1	INDETERMINATE	1	TRUE	NA	0.700208689972399	2		531	389	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188900	32188900	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	151	962	0	ENST00000375023.3:c.654C>G	p.Phe218Leu	p.F218L	ENST00000375023	NM_004557.3	218	ttC/ttG	4/30	1	2	FACETS	0.414	0.378	0.452	0.414	0.378	0.452	SUBCLONAL	1	TRUE	1	0.700208689972399	2		962	1041	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034695-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	80	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.287764760112929	2		148	381	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106916	27106917	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0034695-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	51	403	0	ENST00000324856.7:c.6527_6528del	p.Gln2176ArgfsTer48	p.Q2176Rfs*48	ENST00000324856	NM_006015.4	2176	cAG/c	20/20	1	2	FACETS	0.846	0.721	0.983	0.846	0.721	0.983	CLONAL	1	TRUE	1	0.287764760112929	2		403	419	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246994	53246994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034695-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	81	518	0	ENST00000375401.3:c.506C>T	p.Ser169Phe	p.S169F	ENST00000375401	NM_004187.3	169	tCt/tTt	4/26	1	2	FACETS	0.984	0.868	1	0.984	0.868	1	CLONAL	1	TRUE	1	0.287764760112929	2		518	572	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0034701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	31	451	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		451	542	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0034701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	35	675	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		675	972	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039374	49039374	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853293	NA	P-0034701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	179	634	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		634	1011	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591085	67591085	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519839	NA	P-0034701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	31	251	0	ENST00000274335.5:c.1678G>T	p.Asp560Tyr	p.D560Y	ENST00000274335		560	Gac/Tac	12/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		251	406	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685307	89685307	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123317	NA	P-0034701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	47	288	0	ENST00000371953.3:c.202T>C	p.Tyr68His	p.Y68H	ENST00000371953	NM_000314.4	68	Tac/Cac	3/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		288	346	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56474143	56474143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs34379766	NA	P-0034701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	77	683	0	ENST00000267101.3:c.59C>T	p.Ser20Phe	p.S20F	ENST00000267101	NM_001982.3	20	tCc/tTc	1/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		683	1013	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338671	70338671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	88	552	1	ENST00000374080.3:c.67G>T	p.Asp23Tyr	p.D23Y	ENST00000374080		23	Gat/Tat	1/45	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		553	738	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101356	27101362	+	frameshift_variant	Frame_Shift_Del	DEL	TTCCCAT	TTCCCAT	CCACA	novel	NA	P-0034701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	62	614	1	ENST00000324856.7:c.4638_4644delinsCCACA	p.Ser1547HisfsTer24	p.S1547Hfs*24	ENST00000324856	NM_006015.4	1546	ccTTCCCAT/ccCCACA	18/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		615	743	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0034702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	617	575	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.544138951328962	4	FACETS	1	0.995	1			1	CLONAL	3	TRUE	NA	0.544138951328962	4		575	1023	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741688	17741688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	160	406	2	ENST00000250003.3:c.359G>A	p.Arg120His	p.R120H	ENST00000250003	NM_002478.4	120	cGc/cAc	1/3	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.544138951328962	2		408	489	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576865	7576865	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0034702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	243	578	0	ENST00000269305.4:c.981T>A	p.Tyr327Ter	p.Y327*	ENST00000269305	NM_001126112.2	327	taT/taA	9/11	0.544138951328962	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.544138951328962	1		578	604	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555610	21555610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756027275	NA	P-0034702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	348	495	1	ENST00000382592.4:c.2660G>A	p.Arg887His	p.R887H	ENST00000382592	NM_014572.2	887	cGc/cAc	6/8	0.544138951328962	2	FACETS	0.99	0.947	1	0.99	0.947	1	CLONAL	2	TRUE	0	0.544138951328962	2		496	646	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937025	48937025	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0034702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	253	279	0	ENST00000267163.4:c.793A>T	p.Lys265Ter	p.K265*	ENST00000267163	NM_000321.2	265	Aaa/Taa	8/27	0.544138951328962	2	FACETS	0.983	0.933	1	0.983	0.933	1	CLONAL	2	TRUE	0	0.544138951328962	2		279	473	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643743	52643743	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	218	570	0	ENST00000394830.3:c.2153A>G	p.Tyr718Cys	p.Y718C	ENST00000394830	NM_018313.4	718	tAc/tGc	17/30	0.544138951328962	1	FACETS	0.881	0.824	0.94	0.881	0.824	0.94	CLONAL	1	TRUE	0	0.544138951328962	1		570	662	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	89	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.382539504414375	2		148	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0034707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	169	477	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.382539504414375	1	FACETS	0.987	0.91	1	0.987	0.91	1	CLONAL	1	TRUE	0	0.382539504414375	1		477	724	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717679	89717679	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554825202	NA	P-0034707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	95	448	0	ENST00000371953.3:c.705del	p.Asp236ThrfsTer20	p.D236Tfs*20	ENST00000371953	NM_000314.4	235	gAa/ga	7/9	0.382539504414375	1	FACETS	0.768	0.686	0.855	0.768	0.686	0.855	SUBCLONAL	1	TRUE	0	0.382539504414375	1		448	523	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664900	29664900	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0034707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	80	388	0	ENST00000356175.3:c.6641+2T>A		p.X2214_splice	ENST00000356175	NM_000267.3	2214			0.382539504414375	1	FACETS	0.942	0.835	1	0.942	0.835	1	CLONAL	1	TRUE	0	0.382539504414375	1		388	359	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55130048	55130048	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	251	634	0	ENST00000257290.5:c.582A>T	p.Lys194Asn	p.K194N	ENST00000257290	NM_006206.4	194	aaA/aaT	4/23	0.382539504414375	7	FACETS	0.866	0.808	0.926			1	CLONAL	2	TRUE	NA	0.382539504414375	7		634	1483	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0034708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	109	558	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.752	0.678	0.829	1	0.984	1	SUBCLONAL	2	TRUE	1	0.29	2		558	500	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244110	5244110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141022401	NA	P-0034708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	148	718	1	ENST00000357368.4:c.1372C>T	p.Arg458Cys	p.R458C	ENST00000357368	NM_002850.3	458	Cgc/Tgc	11/38	1	2	FACETS	0.966	0.881	1	0.966	0.881	1	CLONAL	1	TRUE	1	0.29	2		719	1057	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	104	460	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	0.33	2		460	593	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0034709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	131	614	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.294783771069053	1	FACETS	0.682	0.618	0.75	0.682	0.618	0.75	SUBCLONAL	1	TRUE	0	0.33	1		614	972	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123875214	123875214	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	75	352	1	ENST00000330479.4:c.170A>G	p.Tyr57Cys	p.Y57C	ENST00000330479	NM_020382.3	57	tAc/tGc	3/9	1	2	FACETS	0.905	0.795	1	0.905	0.795	1	CLONAL	1	TRUE	1	0.33	2		353	502	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425218	49425219	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGGCTCTTCCCGAGGTTCCTGCT	novel	NA	P-0034709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1316	105	919	0	ENST00000301067.7:c.13247_13269dup	p.Cys4424SerfsTer16	p.C4424Sfs*16	ENST00000301067	NM_003482.3	4423	-/AGCAGGAACCTCGGGAAGAGCCA	39/54	1	2	FACETS	0.448	0.399	0.5	0.448	0.399	0.5	SUBCLONAL	1	TRUE	1	0.33	2		919	1421	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134885835	134885835	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	43	464	0	ENST00000398015.3:c.1746C>A	p.Tyr582Ter	p.Y582*	ENST00000398015	NM_004441.4	582	taC/taA	9/16	1	2	FACETS	0.419	0.35	0.496	0.419	0.35	0.496	SUBCLONAL	1	TRUE	1	0.33	2		464	622	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0034713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	491	750	1	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.406761088403362	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.523660976978121	3		751	1149	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0034713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	257	312	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.523660976978121	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.523660976978121	1		312	505	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631132	69631132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782507721	NA	P-0034713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	246	623	0	ENST00000334134.2:c.280G>A	p.Gly94Arg	p.G94R	ENST00000334134	NM_005247.2	94	Ggg/Agg	2/3	1	2	FACETS	0.956	0.894	1	0.956	0.894	1	CLONAL	1	TRUE	1	0.523660976978121	2		623	983	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674218	117674218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	51	597	0	ENST00000368508.3:c.4256C>T	p.Ser1419Phe	p.S1419F	ENST00000368508	NM_002944.2	1419	tCc/tTc	26/43	0.205410066763221	3	FACETS	0.773	0.67	0.881	0.515	0.447	0.587	INDETERMINATE	2	TRUE	0	0.523660976978121	3		597	159	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050348	176050348	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	11	421	0	ENST00000367669.3:c.1217G>T	p.Arg406Leu	p.R406L	ENST00000367669	NM_022457.5	406	cGa/cTa	11/20	0.406761088403362	3	FACETS	0.914	0.646	1	0.457	0.323	0.615	CLONAL	1	TRUE	1	0.523660976978121	3		421	58	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946849	17946849	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	130	552	0	ENST00000458235.1:c.1798C>T	p.Gln600Ter	p.Q600*	ENST00000458235	NM_000215.3	600	Cag/Tag	14/24	0.523660976978121	3	FACETS	0.759	0.689	0.834	0.38	0.344	0.417	SUBCLONAL	1	TRUE	1	0.523660976978121	3		552	825	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251982	153251986	+	frameshift_variant	Frame_Shift_Del	DEL	TTACT	TTACT	-	novel	NA	P-0034713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	35	622	0	ENST00000281708.4:c.1020_1024del	p.Lys340AsnfsTer21	p.K340Nfs*21	ENST00000281708	NM_033632.3	340	aaAGTAAta/aata	7/12	0.443622679923674	1	FACETS	0.958	0.807	1	0.958	0.807	1	CLONAL	1	TRUE	0	0.523660976978121	1		622	103	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623266	52623266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749924765	NA	P-0034726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	70	330	0	ENST00000394830.3:c.2785G>A	p.Glu929Lys	p.E929K	ENST00000394830	NM_018313.4	929	Gaa/Aaa	19/30	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.338452748906954	2		330	402	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654711	67654711	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	109	443	0	ENST00000264010.4:c.1198A>C	p.Thr400Pro	p.T400P	ENST00000264010	NM_006565.3	400	Acc/Ccc	6/12	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.338452748906954	2		443	640	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351894	89351894	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149211555	NA	P-0034726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1261	233	1019	0	ENST00000301030.4:c.1056C>G	p.Asp352Glu	p.D352E	ENST00000301030	NM_001256183.1	352	gaC/gaG	9/13	1	2	FACETS	0.922	0.857	0.989	0.922	0.857	0.989	CLONAL	1	TRUE	1	0.338452748906954	2		1019	1494	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189879	66189879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	96	556	0	ENST00000273854.3:c.3067C>T	p.Leu1023Phe	p.L1023F	ENST00000273854	NM_004439.5	1023	Ctt/Ttt	18/18	1	2	FACETS	0.797	0.71	0.889	0.797	0.71	0.889	SUBCLONAL	1	TRUE	1	0.338452748906954	2		556	712	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036002	180036043	+	inframe_deletion	In_Frame_Del	DEL	TCTGCTCAAACTCCTCCGAGGCCAGCACCATCCCACTGTCTG	TCTGCTCAAACTCCTCCGAGGCCAGCACCATCCCACTGTCTG	-	novel	NA	P-0034726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	209	877	0	ENST00000261937.6:c.3818_3859del	p.Thr1273_Gln1286del	p.T1273_Q1286del	ENST00000261937	NM_182925.4	1273	aCAGACAGTGGGATGGTGCTGGCCTCGGAGGAGTTTGAGCAGAta/ata	29/30	1	2	FACETS	0.999	0.926	1	0.999	0.926	1	CLONAL	1	TRUE	1	0.338452748906954	2		877	1236	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046092	180046092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	166	252	0	ENST00000261937.6:c.2779G>A	p.Val927Met	p.V927M	ENST00000261937	NM_182925.4	927	Gtg/Atg	20/30	1	2	FACETS	1	0.927	1	1	0.993	1	CLONAL	2	TRUE	1	0.338452748906954	2		252	490	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046282	180046282	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs372072725	NA	P-0034726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	289	585	0	ENST00000261937.6:c.2732A>G	p.Asn911Ser	p.N911S	ENST00000261937	NM_182925.4	911	aAc/aGc	19/30	1	2	FACETS	0.906	0.854	0.96	1	0.995	1	CLONAL	2	TRUE	1	0.338452748906954	2		585	942	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443617	49443617	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	90	660	0	ENST00000301067.7:c.3754C>G	p.Arg1252Gly	p.R1252G	ENST00000301067	NM_003482.3	1252	Cga/Gga	11/54	0.428971395576033	4	FACETS	0.829	0.735	0.928	0.207	0.183	0.232	CLONAL	1	TRUE	0	0.452848235043699	4		660	697	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857202	9857202	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	37	439	0	ENST00000330684.3:c.4199A>G	p.Tyr1400Cys	p.Y1400C	ENST00000330684	NM_001134407.1	1400	tAt/tGt	13/13	0.452848235043699	2	FACETS	0.376	0.309	0.45	0.188	0.154	0.225	SUBCLONAL	1	TRUE	0	0.452848235043699	2		439	435	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50827550	50827551	+	missense_variant	Missense_Mutation	DNP	AG	AG	TT	novel	NA	P-0034732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	45	433	0	ENST00000398568.2:c.2435_2436delinsTT	p.Gln812Leu	p.Q812L	ENST00000398568	NM_001042412.1	812	cAG/cTT	16/18	0.452848235043699	2	FACETS	0.488	0.411	0.574	0.244	0.205	0.287	SUBCLONAL	1	TRUE	0	0.452848235043699	2		433	407	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579718	7579740	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGTCTGAAAGACAAGAGCAGAA	AAGTCTGAAAGACAAGAGCAGAA	-	novel	NA	P-0034732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	92	559	0	ENST00000269305.4:c.75-19_78del		p.X25_splice	ENST00000269305	NM_001126112.2	25		3/11	0.452848235043699	1	FACETS	0.982	0.882	1	0.982	0.882	1	CLONAL	1	TRUE	0	0.452848235043699	1		559	320	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250049	53250049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	128	248	0	ENST00000375401.3:c.200C>T	p.Pro67Leu	p.P67L	ENST00000375401	NM_004187.3	67	cCc/cTc	2/26	1	1	FACETS	0.798	0.737	0.859	1	0.989	1	SUBCLONAL	2	TRUE	0	0.452848235043699	1		248	274	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0034733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	365	487	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.562267865771287	2	FACETS	0.996	0.954	1	0.996	0.954	1	CLONAL	2	TRUE	0	0.562267865771287	2		487	652	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432480	49432480	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	144	774	0	ENST00000301067.7:c.8659G>T	p.Gly2887Ter	p.G2887*	ENST00000301067	NM_003482.3	2887	Gga/Tga	34/54	0.562267865771287	3	FACETS	0.918	0.839	1	0.459	0.419	0.5	CLONAL	1	TRUE	1	0.562267865771287	3		774	715	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156836734	156836734	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	187	853	0	ENST00000524377.1:c.392C>A	p.Ser131Tyr	p.S131Y	ENST00000524377	NM_002529.3	131	tCc/tAc	4/17	0.311322428834784	4	FACETS	1	0.964	1	0.537	0.496	0.58	INDETERMINATE	1	TRUE	2	0.562267865771287	4		853	968	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762212	43762212	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	191	903	2	ENST00000382044.4:c.1233G>T	p.Gln411His	p.Q411H	ENST00000382044	NM_001141980.1	411	caG/caT	11/28	0.514071296066	3	FACETS	1	0.953	1	0.519	0.481	0.559	CLONAL	1	TRUE	1	0.562267865771287	3		905	838	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791587	42791587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767502801	NA	P-0034733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	372	553	0	ENST00000575354.2:c.568C>T	p.Arg190Cys	p.R190C	ENST00000575354	NM_015125.3	190	Cgc/Tgc	4/20	0.562267865771287	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.562267865771287	2		553	647	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164429	47164429	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	90	429	0	ENST00000409792.3:c.1697C>G	p.Ser566Cys	p.S566C	ENST00000409792	NM_014159.6	566	tCt/tGt	3/21	1	2	FACETS	0.933	0.836	1	0.933	0.836	1	CLONAL	1	TRUE	1	0.562267865771287	2		429	343	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967314	134967314	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	94	491	0	ENST00000398015.3:c.2653C>A	p.Pro885Thr	p.P885T	ENST00000398015	NM_004441.4	885	Ccg/Acg	14/16	0.199770664867012	6	FACETS	1	0.939	1	0.36	0.32	0.402	INDETERMINATE	1	TRUE	3	0.562267865771287	6		491	658	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957453	1957453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	108	604	1	ENST00000382891.5:c.2552C>T	p.Ala851Val	p.A851V	ENST00000382891	NM_133335.3	851	gCg/gTg	14/22	NA	2	FACETS	0.722	0.65	0.797			1	INDETERMINATE	1	TRUE	NA	0.562267865771287	2		605	532	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280052	66280052	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	135	397	0	ENST00000273854.3:c.1637C>A	p.Ala546Glu	p.A546E	ENST00000273854	NM_004439.5	546	gCa/gAa	7/18	0.322867412416883	2	FACETS	0.762	0.704	0.821	0.762	0.704	0.821	INDETERMINATE	2	TRUE	0	0.562267865771287	2		397	315	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443550	49443550	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	42	725	0	ENST00000301067.7:c.3821A>C	p.Asp1274Ala	p.D1274A	ENST00000301067	NM_003482.3	1274	gAt/gCt	11/54	1	2	FACETS	0.971	0.809	1	0.971	0.809	1	CLONAL	1	TRUE	1	0.15	2		725	577	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104425	2104425	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs45444196	NA	P-0034734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	36	770	0	ENST00000219476.3:c.465C>G	p.Tyr155Ter	p.Y155*	ENST00000219476	NM_000548.3	155	taC/taG	5/42	1	2	FACETS	0.767	0.629	0.922	0.767	0.629	0.922	CLONAL	1	TRUE	1	0.15	2		770	626	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92247387	92247387	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	24	232	0	ENST00000265734.4:c.833T>G	p.Leu278Arg	p.L278R	ENST00000265734	NM_001259.6	278	cTg/cGg	7/8	1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	1	0.15	2		232	293	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41001285	41001285	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	53	455	0	ENST00000267868.3:c.406A>G	p.Ile136Val	p.I136V	ENST00000267868	NM_002875.4	136	Atc/Gtc	5/10	1	2	FACETS	0.286	0.243	0.333	0.286	0.243	0.333	SUBCLONAL	1	TRUE	1	0.491267136223988	2		455	755	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577122	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0034736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	184	588	1	ENST00000269305.4:c.816_817delinsTT	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	272	gtGCgt/gtTTgt	8/11	0.491267136223988	1	FACETS	0.7	0.647	0.755	0.7	0.647	0.755	SUBCLONAL	1	TRUE	0	0.491267136223988	1		589	807	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	213	458	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.62815659833286	2		458	649	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039374	49039374	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853293	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	253	634	0	ENST00000267163.4:c.2359C>T	p.Arg787Ter	p.R787*	ENST00000267163	NM_000321.2	787	Cga/Tga	23/27	0.62815659833286	1	FACETS	0.897	0.846	0.949	0.897	0.846	0.949	CLONAL	1	TRUE	0	0.62815659833286	1		634	616	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003808	45003808	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	238	509	0	ENST00000558401.1:c.64C>T	p.Gln22Ter	p.Q22*	ENST00000558401	NM_004048.2	22	Cag/Tag	1/4	0.62815659833286	1	FACETS	0.931	0.877	0.986	0.931	0.877	0.986	CLONAL	1	TRUE	0	0.62815659833286	1		509	558	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163720	32163720	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253487294	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	202	494	0	ENST00000375023.3:c.5506G>A	p.Glu1836Lys	p.E1836K	ENST00000375023	NM_004557.3	1836	Gag/Aag	30/30	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.62815659833286	2		494	629	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371409680	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	491	734	0	ENST00000269305.4:c.848G>C	p.Arg283Pro	p.R283P	ENST00000269305	NM_001126112.2	283	cGc/cCc	8/11	0.62815659833286	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.62815659833286	1		734	1001	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530972	187530972	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1187011117	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	238	467	0	ENST00000441802.2:c.10051G>C	p.Glu3351Gln	p.E3351Q	ENST00000441802	NM_005245.3	3351	Gag/Cag	15/27	1	2	FACETS	0.984	0.922	1	0.984	0.922	1	CLONAL	1	TRUE	1	0.62815659833286	2		467	770	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629110	14629110	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs768130288	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	177	354	0	ENST00000254322.2:c.52G>T	p.Glu18Ter	p.E18*	ENST00000254322	NM_006145.1	18	Gag/Tag	1/3	0.601383869948814	3	FACETS	0.923	0.852	0.997	0.462	0.426	0.499	CLONAL	1	TRUE	1	0.62815659833286	3		354	802	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871149	12871149	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	88	220	0	ENST00000228872.4:c.376G>A	p.Glu126Lys	p.E126K	ENST00000228872	NM_004064.3	126	Gag/Aag	1/3	1	2	FACETS	0.99	0.888	1	0.99	0.888	1	CLONAL	1	TRUE	1	0.62815659833286	2		220	283	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256177	16256177	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	204	510	0	ENST00000375759.3:c.3442G>C	p.Glu1148Gln	p.E1148Q	ENST00000375759	NM_015001.2	1148	Gag/Cag	11/15	1	2	FACETS	0.88	0.819	0.943	0.88	0.819	0.943	CLONAL	1	TRUE	1	0.62815659833286	2		510	738	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149243913	149243913	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	274	456	1	ENST00000360632.3:c.906-1G>T		p.X302_splice	ENST00000360632	NM_015472.4	302			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.62815659833286	2		457	819	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998300	100998300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs900902396	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	67	76	0	ENST00000325455.5:c.1502C>T	p.Ser501Phe	p.S501F	ENST00000325455	NM_001202474.3	501	tCt/tTt	1/8	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.62815659833286	2		76	184	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639900	3639900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs978074181	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	418	798	1	ENST00000294008.3:c.3739G>A	p.Glu1247Lys	p.E1247K	ENST00000294008	NM_032444.2	1247	Gag/Aag	12/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.62815659833286	2		799	1235	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932926	39932926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	325	622	0	ENST00000378444.4:c.1673C>T	p.Ser558Leu	p.S558L	ENST00000378444	NM_001123385.1	558	tCa/tTa	4/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.62815659833286	2		622	951	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772578	135772578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200398750	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	255	503	0	ENST00000298552.3:c.2968G>A	p.Glu990Lys	p.E990K	ENST00000298552	NM_001162426.1	990	Gaa/Aaa	22/23	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.62815659833286	2		503	788	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65304246	65304246	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	215	396	0	ENST00000342505.4:c.2869G>T	p.Glu957Ter	p.E957*	ENST00000342505	NM_002227.2	957	Gaa/Taa	21/25	0.62815659833286	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.62815659833286	1		396	459	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11205069	11205069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	346	611	1	ENST00000361445.4:c.4720G>A	p.Glu1574Lys	p.E1574K	ENST00000361445	NM_004958.3	1574	Gaa/Aaa	33/58	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.62815659833286	2		612	1037	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256159	16256159	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	211	528	0	ENST00000375759.3:c.3424G>A	p.Glu1142Lys	p.E1142K	ENST00000375759	NM_015001.2	1142	Gaa/Aaa	11/15	1	2	FACETS	0.879	0.819	0.941	0.879	0.819	0.941	CLONAL	1	TRUE	1	0.62815659833286	2		528	764	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256282	16256282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	186	505	0	ENST00000375759.3:c.3547G>A	p.Glu1183Lys	p.E1183K	ENST00000375759	NM_015001.2	1183	Gaa/Aaa	11/15	1	2	FACETS	0.862	0.799	0.927	0.862	0.799	0.927	CLONAL	1	TRUE	1	0.62815659833286	2		505	687	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257263	16257263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	216	523	0	ENST00000375759.3:c.4528G>A	p.Asp1510Asn	p.D1510N	ENST00000375759	NM_015001.2	1510	Gat/Aat	11/15	1	2	FACETS	0.878	0.819	0.94	0.878	0.819	0.94	CLONAL	1	TRUE	1	0.62815659833286	2		523	783	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257287	16257287	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	246	606	0	ENST00000375759.3:c.4552G>T	p.Glu1518Ter	p.E1518*	ENST00000375759	NM_015001.2	1518	Gaa/Taa	11/15	1	2	FACETS	0.961	0.901	1	0.961	0.901	1	CLONAL	1	TRUE	1	0.62815659833286	2		606	815	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695839	117695839	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	345	722	0	ENST00000369458.3:c.598G>C	p.Glu200Gln	p.E200Q	ENST00000369458	NM_024626.3	200	Gag/Cag	4/6	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.62815659833286	2		722	1077	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695972	117695974	+	stop_gained	Nonsense_Mutation	TNP	CAC	CAC	TTA	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	188	498	0	ENST00000369458.3:c.463_465delinsTAA	p.Val155Ter	p.V155*	ENST00000369458	NM_024626.3	155	GTG/TAA	4/6	1	2	FACETS	0.815	0.756	0.877	0.815	0.756	0.877	CLONAL	1	TRUE	1	0.62815659833286	2		498	734	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999714	100999714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	81	803	0	ENST00000325455.5:c.88C>T	p.Arg30Cys	p.R30C	ENST00000325455	NM_001202474.3	30	Cgc/Tgc	1/8	1	2	FACETS	0.225	0.197	0.255	0.225	0.197	0.255	SUBCLONAL	1	TRUE	1	0.62815659833286	2		803	1148	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426384	49426384	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1215	592	1136	0	ENST00000301067.7:c.12104C>A	p.Ser4035Ter	p.S4035*	ENST00000301067	NM_003482.3	4035	tCa/tAa	39/54	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.62815659833286	2		1136	1807	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448374	49448374	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	296	654	0	ENST00000301067.7:c.337G>T	p.Glu113Ter	p.E113*	ENST00000301067	NM_003482.3	113	Gag/Tag	3/54	1	2	FACETS	0.913	0.861	0.967	0.913	0.861	0.967	CLONAL	1	TRUE	1	0.62815659833286	2		654	1032	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249755	133249755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755463796	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	182	398	0	ENST00000320574.5:c.1468G>A	p.Asp490Asn	p.D490N	ENST00000320574	NM_006231.2	490	Gac/Aac	14/49	1	2	FACETS	0.967	0.897	1	0.967	0.897	1	CLONAL	1	TRUE	1	0.62815659833286	2		398	599	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041192	29041192	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	387	759	0	ENST00000282397.4:c.236C>G	p.Ser79Cys	p.S79C	ENST00000282397	NM_002019.4	79	tCt/tGt	3/30	0.604241352429526	2	FACETS	1	0.958	1	0.504	0.479	0.53	CLONAL	1	TRUE	0	0.62815659833286	2		759	1222	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911757	32911757	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	241	563	0	ENST00000380152.3:c.3265C>G	p.Gln1089Glu	p.Q1089E	ENST00000380152		1089	Cag/Gag	11/27	0.62815659833286	1	FACETS	0.982	0.926	1	0.982	0.926	1	CLONAL	1	TRUE	0	0.62815659833286	1		563	536	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504525	103504525	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	116	371	0	ENST00000355739.4:c.146C>G	p.Ser49Ter	p.S49*	ENST00000355739	NM_000123.3	49	tCa/tGa	2/15	0.62815659833286	1	FACETS	0.85	0.778	0.924	0.85	0.778	0.924	CLONAL	1	TRUE	0	0.62815659833286	1		371	298	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68934961	68934961	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	186	368	0	ENST00000487270.1:c.1030C>A	p.Leu344Ile	p.L344I	ENST00000487270	NM_133509.3	344	Ctt/Att	10/11	1	2	FACETS	0.961	0.893	1	0.961	0.893	1	CLONAL	1	TRUE	1	0.62815659833286	2		368	616	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609958	81609958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780018604	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	169	334	0	ENST00000298171.2:c.1556G>A	p.Arg519His	p.R519H	ENST00000298171	NM_000369.2	519	cGc/cAc	10/10	1	2	FACETS	0.882	0.815	0.952	0.882	0.815	0.952	CLONAL	1	TRUE	1	0.62815659833286	2		334	610	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720346	43720346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	314	608	0	ENST00000382044.4:c.3696G>A	p.Met1232Ile	p.M1232I	ENST00000382044	NM_001141980.1	1232	atG/atA	18/28	0.62815659833286	1	FACETS	0.985	0.936	1	0.985	0.936	1	CLONAL	1	TRUE	0	0.62815659833286	1		608	696	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720363	43720363	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	259	545	0	ENST00000382044.4:c.3679G>A	p.Glu1227Lys	p.E1227K	ENST00000382044	NM_001141980.1	1227	Gaa/Aaa	18/28	0.62815659833286	1	FACETS	0.936	0.884	0.989	0.936	0.884	0.989	CLONAL	1	TRUE	0	0.62815659833286	1		545	604	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66737015	66737015	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	215	444	0	ENST00000307102.5:c.538C>G	p.Leu180Val	p.L180V	ENST00000307102	NM_002755.3	180	Ctg/Gtg	5/11	1	2	FACETS	0.876	0.817	0.938	0.876	0.817	0.938	CLONAL	1	TRUE	1	0.62815659833286	2		444	781	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2114276	2114276	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs397515297	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	332	612	1	ENST00000219476.3:c.1447G>T	p.Glu483Ter	p.E483*	ENST00000219476	NM_000548.3	483	Gag/Tag	15/42	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.62815659833286	2		613	1015	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661952	29661952	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	197	535	0	ENST00000356175.3:c.5846G>C	p.Arg1949Thr	p.R1949T	ENST00000356175	NM_000267.3	1949	aGa/aCa	39/57	1	2	FACETS	0.883	0.821	0.948	0.883	0.821	0.948	CLONAL	1	TRUE	1	0.62815659833286	2		535	710	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661966	29661966	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	184	509	0	ENST00000356175.3:c.5860C>G	p.Leu1954Val	p.L1954V	ENST00000356175	NM_000267.3	1954	Ctt/Gtt	39/57	1	2	FACETS	0.868	0.804	0.934	0.868	0.804	0.934	CLONAL	1	TRUE	1	0.62815659833286	2		509	675	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40379615	40379615	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	412	716	0	ENST00000293328.3:c.217G>C	p.Glu73Gln	p.E73Q	ENST00000293328	NM_012448.3	73	Gag/Cag	3/19	0.62815659833286	1	FACETS	0.967	0.925	1	0.967	0.925	1	CLONAL	1	TRUE	0	0.62815659833286	1		716	930	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805601	46805601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	451	807	0	ENST00000290295.7:c.355G>A	p.Glu119Lys	p.E119K	ENST00000290295	NM_006361.5	119	Gag/Aag	1/2	0.62815659833286	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.62815659833286	1		807	873	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254570	10254570	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	325	587	0	ENST00000340748.4:c.2940C>G	p.Ile980Met	p.I980M	ENST00000340748		980	atC/atG	28/40	0.601383869948814	3	FACETS	1	0.957	1	0.508	0.479	0.538	CLONAL	1	TRUE	1	0.62815659833286	3		587	1338	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021238	31021238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1272820357	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	272	488	0	ENST00000375687.4:c.1237C>T	p.Arg413Trp	p.R413W	ENST00000375687	NM_015338.5	413	Cgg/Tgg	12/13	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.62815659833286	2		488	845	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206833	36206833	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	146	484	0	ENST00000300305.3:c.679G>A	p.Glu227Lys	p.E227K	ENST00000300305		227	Gaa/Aaa	6/8	0.62815659833286	1	FACETS	0.607	0.557	0.659	0.607	0.557	0.659	SUBCLONAL	1	TRUE	0	0.62815659833286	1		484	525	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281628	142281628	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766837742	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	177	472	0	ENST00000350721.4:c.616G>A	p.Glu206Lys	p.E206K	ENST00000350721	NM_001184.3	206	Gaa/Aaa	4/47	1	2	FACETS	0.924	0.856	0.994	0.924	0.856	0.994	CLONAL	1	TRUE	1	0.62815659833286	2		472	610	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807324	1807324	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	291	682	0	ENST00000260795.2:c.1573G>A	p.Glu525Lys	p.E525K	ENST00000260795		525	Gag/Aag	11/17	1	2	FACETS	0.944	0.889	0.999	0.944	0.889	0.999	CLONAL	1	TRUE	1	0.62815659833286	2		682	982	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968647	55968647	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	284	600	0	ENST00000263923.4:c.2016C>A	p.Asn672Lys	p.N672K	ENST00000263923	NM_002253.2	672	aaC/aaA	14/30	1	2	FACETS	0.941	0.886	0.997	0.941	0.886	0.997	CLONAL	1	TRUE	1	0.62815659833286	2		600	961	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972061	55972061	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1456500122	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	314	501	0	ENST00000263923.4:c.1583A>G	p.Tyr528Cys	p.Y528C	ENST00000263923	NM_002253.2	528	tAc/tGc	12/30	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.62815659833286	2		501	968	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295279	1295279	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	276	480	0				ENST00000310581	NM_198253.2	-/1132			0.601383869948814	3	FACETS	1	0.968	1	0.524	0.492	0.557	CLONAL	1	TRUE	1	0.62815659833286	3		480	1102	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131951743	131951743	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	98	238	0	ENST00000265335.6:c.3085G>C	p.Glu1029Gln	p.E1029Q	ENST00000265335		1029	Gag/Cag	20/25	1	2	FACETS	0.934	0.842	1	0.934	0.842	1	CLONAL	1	TRUE	1	0.62815659833286	2		238	334	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672351	30672351	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	392	766	0	ENST00000376406.3:c.4609C>G	p.Leu1537Val	p.L1537V	ENST00000376406	NM_014641.2	1537	Ctc/Gtc	10/15	1	2	FACETS	0.943	0.896	0.991	0.943	0.896	0.991	CLONAL	1	TRUE	1	0.62815659833286	2		766	1324	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675577	30675577	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1400	290	881	0	ENST00000376406.3:c.2779G>C	p.Glu927Gln	p.E927Q	ENST00000376406	NM_014641.2	927	Gag/Cag	8/15	1	2	FACETS	0.546	0.512	0.582	0.546	0.512	0.582	SUBCLONAL	1	TRUE	1	0.62815659833286	2		881	1690	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527362	157527362	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	187	420	0	ENST00000346085.5:c.5087G>T	p.Gly1696Val	p.G1696V	ENST00000346085	NM_020732.3	1696	gGa/gTa	20/20	1	2	FACETS	0.891	0.827	0.958	0.891	0.827	0.958	CLONAL	1	TRUE	1	0.62815659833286	2		420	668	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852226	128852226	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	406	813	0	ENST00000249373.3:c.2301del	p.Pro768LeufsTer8	p.P768Lfs*8	ENST00000249373	NM_005631.4	766	ctG/ct	12/12	1	2	FACETS	0.944	0.898	0.991	0.944	0.898	0.991	CLONAL	1	TRUE	1	0.62815659833286	2		813	1369	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952107	76952107	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	202	583	2	ENST00000373344.5:c.328G>A	p.Glu110Lys	p.E110K	ENST00000373344	NM_000489.3	110	Gaa/Aaa	5/35	1	2	FACETS	0.877	0.816	0.941	0.877	0.816	0.941	CLONAL	1	TRUE	1	0.62815659833286	2		585	733	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626685	100626685	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56035945	NA	P-0034737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	187	401	1	ENST00000308731.7:c.245G>A	p.Arg82Lys	p.R82K	ENST00000308731	NM_000061.2	82	aGa/aAa	4/19	0.62815659833286	1	FACETS	0.979	0.917	1	0.979	0.917	1	CLONAL	1	TRUE	0	0.62815659833286	1		402	417	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442542	52442542	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1194652468	NA	P-0034738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	143	496	0	ENST00000460680.1:c.203A>G	p.Asp68Gly	p.D68G	ENST00000460680	NM_004656.3	68	gAt/gGt	4/17	0.436708324830327	2	FACETS	0.872	0.806	0.94	0.872	0.806	0.94	CLONAL	2	TRUE	0	0.46303861253257	2		496	354	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481403	140481403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913357	NA	P-0034738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	9	470	0	ENST00000288602.6:c.1405G>A	p.Gly469Arg	p.G469R	ENST00000288602	NM_004333.4	469	Gga/Aga	11/18	0.353955848847898	3	FACETS	0.127	0.084	0.184	0.064	0.042	0.092	SUBCLONAL	1	TRUE	1	0.46303861253257	3		470	376	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115260822	115260822	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	152	666	0	ENST00000438362.2:c.2503A>G	p.Arg835Gly	p.R835G	ENST00000438362	NM_001242891.1	835	Aga/Gga	20/20	0.412079699812322	3	FACETS	0.881	0.812	0.951	0.881	0.812	0.951	CLONAL	2	TRUE	1	0.46303861253257	3		666	459	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874261	155874261	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs483352822	NA	P-0034750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	20	539	0	ENST00000368323.3:c.270G>C	p.Met90Ile	p.M90I	ENST00000368323	NM_006912.5	90	atG/atC	5/6	0.180714887787062	3	FACETS	0.374	0.285	0.48	0.187	0.142	0.24	SUBCLONAL	1	TRUE	1	0.180714887787062	3		539	645	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220706	1220706	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555738475	NA	P-0034750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	50	726	0	ENST00000326873.7:c.727del	p.Val243SerfsTer44	p.V243Sfs*44	ENST00000326873	NM_000455.4	242	Ggg/gg	5/10	0.180714887787062	1	FACETS	0.892	0.757	1	0.892	0.757	1	CLONAL	1	TRUE	0	0.180714887787062	1		726	564	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600408	10600408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1412883238	NA	P-0034750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	85	905	1	ENST00000171111.5:c.1447C>T	p.Arg483Cys	p.R483C	ENST00000171111	NM_203500.1	483	Cgc/Tgc	4/6	0.180714887787062	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.180714887787062	1		906	725	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988724	41988724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	30	490	1	ENST00000219905.7:c.1516G>A	p.Glu506Lys	p.E506K	ENST00000219905	NM_001164273.1	506	Gaa/Aaa	3/24	1	2	FACETS	0.631	0.507	0.772	0.631	0.507	0.772	SUBCLONAL	1	TRUE	1	0.180714887787062	2		491	526	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273269	55273269	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs142188270	NA	P-0034750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	57	518	0	ENST00000275493.2:c.3592C>G	p.Leu1198Val	p.L1198V	ENST00000275493	NM_005228.3	1198	Cta/Gta	28/28	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.180714887787062	2		518	486	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039611	47039611	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	47	600	0	ENST00000377604.3:c.1063G>C	p.Glu355Gln	p.E355Q	ENST00000377604	NM_001204468.1	355	Gag/Cag	11/24	1	2	FACETS	0.96	0.809	1	0.96	0.809	1	CLONAL	1	TRUE	1	0.180714887787062	2		600	542	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0034760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	179	693	0	ENST00000346208.3:c.1220_1221insA	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcAg	6/6	1	2	FACETS	0.969	0.896	1	0.969	0.896	1	CLONAL	1	TRUE	1	0.492558687157892	2		693	750	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945643	71945643	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	153	630	0	ENST00000298229.2:c.2399C>A	p.Ser800Ter	p.S800*	ENST00000298229	NM_001567.3	800	tCa/tAa	21/28	0.49005590668701	1	FACETS	0.973	0.898	1	0.973	0.898	1	CLONAL	1	TRUE	0	0.492558687157892	1		630	481	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420669	49420669	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774403945	NA	P-0034760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	154	702	0	ENST00000301067.7:c.15080G>A	p.Arg5027Gln	p.R5027Q	ENST00000301067	NM_003482.3	5027	cGa/cAa	48/54	1	2	FACETS	0.912	0.836	0.99	0.912	0.836	0.99	CLONAL	1	TRUE	1	0.492558687157892	2		702	686	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349431	73349431	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	38	546	0	ENST00000377767.4:c.905G>A	p.Trp302Ter	p.W302*	ENST00000377767	NM_014953.3	302	tGg/tAg	6/21	1	2	FACETS	0.206	0.17	0.247	0.206	0.17	0.247	SUBCLONAL	1	TRUE	1	0.492558687157892	2		546	748	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753006	57753006	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0034760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	145	416	0	ENST00000274289.3:c.1008+2T>A		p.X336_splice	ENST00000274289	NM_006622.3	336			1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.492558687157892	2		416	564	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874952	151874952	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	135	439	0	ENST00000262189.6:c.7586C>A	p.Ser2529Ter	p.S2529*	ENST00000262189	NM_170606.2	2529	tCa/tAa	38/59	0.462221695288809	1	FACETS	0.979	0.898	1	0.979	0.898	1	CLONAL	1	TRUE	0	0.492558687157892	1		439	422	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932063	39932063	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	192	958	0	ENST00000378444.4:c.2536del	p.Leu846CysfsTer10	p.L846Cfs*10	ENST00000378444	NM_001123385.1	846	Ctg/tg	4/15	1	2	FACETS	0.891	0.825	0.96	0.891	0.825	0.96	CLONAL	1	TRUE	1	0.492558687157892	2		958	875	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577330	64577333	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	rs587776841	NA	P-0034762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	56	693	0	ENST00000312049.6:c.249_252del	p.Ile85SerfsTer33	p.I85Sfs*33	ENST00000312049	NM_130799.2	83	ctGTCT/ct	2/10	0.353602762331258	1	FACETS	0.42	0.359	0.486	0.42	0.359	0.486	SUBCLONAL	1	FALSE	0	0.353602762331258	1		693	621	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43767830	43767830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	151	562	0	ENST00000382044.4:c.1018C>T	p.Pro340Ser	p.P340S	ENST00000382044	NM_001141980.1	340	Cct/Tct	9/28	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.353602762331258	2		562	744	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589821	212589821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	120	461	0	ENST00000342788.4:c.721C>T	p.Pro241Ser	p.P241S	ENST00000342788	NM_005235.2	241	Cct/Tct	6/28	1	2	FACETS	0.982	0.888	1	0.982	0.888	1	CLONAL	1	FALSE	1	0.353602762331258	2		461	691	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0034763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	62	573	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.1	2		574	921	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822033	72822033	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	37	471	0	ENST00000268489.5:c.10142G>C	p.Arg3381Pro	p.R3381P	ENST00000268489	NM_006885.3	3381	cGg/cCg	10/10	1	2	FACETS	0.833	0.687	0.997	1	0.957	1	CLONAL	2	TRUE	1	0.1	2		471	444	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223238	41223238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224762	NA	P-0034763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	47	544	0	ENST00000357654.3:c.4693G>A	p.Glu1565Lys	p.E1565K	ENST00000357654	NM_007294.3	1565	Gaa/Aaa	15/23	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.1	2		544	741	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0034763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	28	340	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.1	2		341	495	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222738	53222738	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	52	514	0	ENST00000375401.3:c.4198G>T	p.Glu1400Ter	p.E1400*	ENST00000375401	NM_004187.3	1400	Gag/Tag	25/26	1	1	FACETS	0.837	0.712	0.974	1	0.969	1	CLONAL	2	TRUE	0	0.1	1		514	590	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	46	460	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.435007646057027	3	FACETS	0.975	0.858	1	0.975	0.858	1	CLONAL	3	TRUE	0	0.435007646057027	3		460	88	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0034773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	9	207	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.2962508605459	4	FACETS	1	0.788	1	0.619	0.42	0.856	CLONAL	1	TRUE	2	0.435007646057027	4		207	48	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578213	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0034773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	77	552	0	ENST00000269305.4:c.636dup	p.Arg213SerfsTer3	p.R213Sfs*3	ENST00000269305	NM_001126112.2	212	-/T	6/11	0.318128131613101	2	FACETS	0.773	0.69	0.859	0.773	0.69	0.859	SUBCLONAL	2	TRUE	0	0.435007646057027	2		552	229	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713582	30713583	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACAT	novel	NA	P-0034773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	43	403	0	ENST00000295754.5:c.910_913dup	p.Leu305HisfsTer8	p.L305Hfs*8	ENST00000295754	NM_003242.5	303	aac/aACATac	4/7	0.435007646057027	1	FACETS	0.949	0.807	1	0.949	0.807	1	CLONAL	1	TRUE	0	0.435007646057027	1		403	163	SUCCESS
AR	367	MSKCC	GRCh37	X	66931306	66931306	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1230215817	NA	P-0034773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	11	236	0	ENST00000374690.3:c.1948A>G	p.Thr650Ala	p.T650A	ENST00000374690	NM_000044.3	650	Acc/Gcc	4/8	0.424800538874202	2	FACETS	0.527	0.368	0.72			1	SUBCLONAL	1	TRUE	NA	0.435007646057027	2		236	96	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0034774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	123	414	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	FALSE	1	0.428958873147473	2		414	549	SUCCESS
APC	324	MSKCC	GRCh37	5	112175529	112175530	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGTAA	novel	NA	P-0034774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	96	344	0	ENST00000257430.4:c.4240_4244dup	p.Ser1415ArgfsTer2	p.S1415Rfs*2	ENST00000257430	NM_000038.5	1413	atg/atGGTAAg	16/16	1	2	FACETS	0.925	0.828	1	0.925	0.828	1	CLONAL	1	FALSE	1	0.428958873147473	2		344	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578532	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28934873	NA	P-0034777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	462	816	0	ENST00000269305.4:c.398T>C	p.Met133Thr	p.M133T	ENST00000269305	NM_001126112.2	133	aTg/aCg	5/11	0.690434583070256	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.690434583070256	2		816	650	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777915	27777915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	39	351	0	ENST00000369163.2:c.64G>A	p.Ala22Thr	p.A22T	ENST00000369163	NM_003536.2	22	Gcc/Acc	1/1	0.690434583070256	5	FACETS	0.372	0.307	0.444	0.124	0.102	0.148	SUBCLONAL	1	TRUE	2	0.690434583070256	5		351	619	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0034782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	104	338	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.550648094790056	4	FACETS	0.965	0.866	1	0.322	0.288	0.357	CLONAL	1	TRUE	1	0.550891116625116	4		338	607	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0034782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	266	238	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.550648094790056	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	3	TRUE	1	0.550891116625116	4		238	493	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664915	138664915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs797044527	NA	P-0034782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	26	252	0	ENST00000330315.3:c.650C>T	p.Ser217Phe	p.S217F	ENST00000330315	NM_023067.3	217	tCc/tTc	1/1	0.550891116625116	3	FACETS	0.268	0.212	0.333	0.134	0.106	0.167	SUBCLONAL	1	TRUE	1	0.550891116625116	3		252	449	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114905857	114905857	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0034782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	314	502	0	ENST00000543371.1:c.875+1G>C		p.X292_splice	ENST00000543371	NM_001198531.1	292			0.550891116625116	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.550891116625116	3		502	694	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748146	41748146	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	21	348	0	ENST00000226382.2:c.623G>T	p.Cys208Phe	p.C208F	ENST00000226382	NM_003924.3	208	tGc/tTc	3/3	1	2	FACETS	0.187	0.143	0.238	0.187	0.143	0.238	SUBCLONAL	1	TRUE	1	0.550891116625116	2		348	408	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0034787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	134	530	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.57544933424956	2		530	415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0034787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	459	494	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.584374348164326	3	FACETS	0.96	0.928	0.992			1	CLONAL	3	TRUE	NA	0.57544933424956	3		495	713	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0034787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	358	575	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.523415283091395	3	FACETS	0.973	0.936	1	0.973	0.936	1	CLONAL	3	TRUE	0	0.57544933424956	3		575	549	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020768	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs926053251	NA	P-0034787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	151	366	0	ENST00000358127.4:c.77T>G	p.Val26Gly	p.V26G	ENST00000358127	NM_001280556.1	26	gTt/gGt	2/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.57544933424956	2		366	448	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89839765	89839765	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs34592408	NA	P-0034787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	236	610	0	ENST00000389301.3:c.1928C>G	p.Pro643Arg	p.P643R	ENST00000389301	NM_000135.2	643	cCc/cGc	22/43	0.584374348164326	3	FACETS	1	0.993	1			1	CLONAL	1	TRUE	NA	0.57544933424956	3		610	710	SUCCESS
APC	324	MSKCC	GRCh37	5	112176030	112176030	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs886039682	NA	P-0034787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	111	302	0	ENST00000257430.4:c.4741del	p.Ser1581LeufsTer69	p.S1581Lfs*69	ENST00000257430	NM_000038.5	1580	aTt/at	16/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.57544933424956	2		302	335	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249399	153249399	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	208	517	0	ENST00000281708.4:c.1379A>G	p.His460Arg	p.H460R	ENST00000281708	NM_033632.3	460	cAt/cGt	9/12	0.334291689240366	1	FACETS	1	0.989	1	1	0.989	1	INDETERMINATE	1	TRUE	0	0.57544933424956	1		517	424	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120571	2120571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45469298	NA	P-0034787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	528	579	1	ENST00000219476.3:c.1831C>T	p.Arg611Trp	p.R611W	ENST00000219476	NM_000548.3	611	Cgg/Tgg	17/42	0.584374348164326	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.57544933424956	3		580	741	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120133	70120145	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCACACGCTGA	GCGCACACGCTGA	-	novel	NA	P-0034787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	89	179	0	ENST00000245479.2:c.1135_1147del	p.Ala379ProfsTer3	p.A379Pfs*3	ENST00000245479	NM_000346.3	379	GCGCACACGCTGAcc/cc	3/3	0.584374348164326	1	FACETS	0.822	0.761	0.881	1	0.988	1	CLONAL	2	TRUE	0	0.57544933424956	1		179	134	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622099	1622099	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	26	615	0	ENST00000344749.5:c.776G>C	p.Ser259Thr	p.S259T	ENST00000344749	NM_001136139.2	259	aGt/aCt	10/19	0.542881824332202	2	FACETS	0.181	0.142	0.225	0.09	0.071	0.113	SUBCLONAL	1	TRUE	0	0.57544933424956	2		615	500	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184736	32184736	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	159	488	1	ENST00000375023.3:c.1847C>A	p.Pro616His	p.P616H	ENST00000375023	NM_004557.3	616	cCc/cAc	11/30	0.158699586558525	4	FACETS	0.82	0.756	0.885	0.82	0.756	0.885	INDETERMINATE	2	TRUE	2	0.57544933424956	4		489	531	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288705	33288705	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	220	426	0	ENST00000374542.5:c.847T>G	p.Phe283Val	p.F283V	ENST00000374542	NM_001141970.1	283	Ttc/Gtc	3/8	0.302869458436969	6	FACETS	0.862	0.807	0.918	0.646	0.605	0.689	INDETERMINATE	3	TRUE	2	0.57544933424956	6		426	636	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396321	139396321	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	198	625	0	ENST00000277541.6:c.5517C>A	p.Asp1839Glu	p.D1839E	ENST00000277541	NM_017617.3	1839	gaC/gaA	30/34	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.57544933424956	NA		625	1005	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938622	76938622	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	204	293	0	ENST00000373344.5:c.2126A>G	p.Asp709Gly	p.D709G	ENST00000373344	NM_000489.3	709	gAt/gGt	9/35	0.584374348164326	2	FACETS	1	0.992	1			1	CLONAL	1	TRUE	NA	0.57544933424956	2		293	490	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127933444	127933444	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	212	385	0	ENST00000373547.4:c.91G>C	p.Val31Leu	p.V31L	ENST00000373547	NM_002721.4	31	Gtt/Ctt	2/7	0.746899886821707	4	FACETS	0.811	0.76	0.863	0.811	0.76	0.863	CLONAL	2	FALSE	2	0.995045671984016	4		385	524	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331724	8331724	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs763525789	NA	P-0034788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	86	354	0	ENST00000356435.5:c.5392C>G	p.Arg1798Gly	p.R1798G	ENST00000356435		1798	Cga/Gga	33/35	0.284379039790638	4	FACETS	1	0.96	1	0.577	0.516	0.64	INDETERMINATE	1	FALSE	2	0.995045671984016	4		354	299	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996861	100996861	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	59	493	0	ENST00000325455.5:c.1666C>A	p.Gln556Lys	p.Q556K	ENST00000325455	NM_001202474.3	556	Caa/Aaa	2/8	0.779754295574359	6	FACETS	0.389	0.334	0.45	0.097	0.083	0.113	SUBCLONAL	1	FALSE	2	0.995045671984016	6		493	911	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536160	41536161	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0034788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	189	480	1	ENST00000263253.7:c.1777_1778delinsTT	p.Pro593Phe	p.P593F	ENST00000263253	NM_001429.3	593	CCt/TTt	9/31	0.651435563879789	4	FACETS	1	0.989	1	0.685	0.638	0.734	CLONAL	1	FALSE	2	0.995045671984016	4		481	553	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974255	2974255	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	81	572	0	ENST00000396946.4:c.1350del	p.Arg451GlyfsTer5	p.R451Gfs*5	ENST00000396946	NM_032415.4	450	ccC/cc	10/25	0.651435563879789	4	FACETS	0.526	0.464	0.593	0.263	0.232	0.297	SUBCLONAL	1	FALSE	2	0.995045671984016	4		572	617	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390827	139390827	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	92	623	0	ENST00000277541.6:c.7364C>T	p.Thr2455Ile	p.T2455I	ENST00000277541	NM_017617.3	2455	aCt/aTt	34/34	0.746899886821707	4	FACETS	0.495	0.439	0.554	0.247	0.219	0.277	SUBCLONAL	1	FALSE	2	0.995045671984016	4		623	746	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169733	32170089	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGTGGAAACTCCCTGGAGCCCAAGGCTGTGGCCACACTGTAACTCAGAGCCATCTACGTCCTTCCTCCTCCTCTCACCCACCCCTCTCCTTCCCTGGCTCCAGTGGATTTCAGGCTCACGTGCAGGCTGGAGGGGTCTCACAGTCGTAGCCATCAAACAGACACTCTTCAGAGTCACACTGTGGGTGGCACTGCCCGTCCCGGAAGAGAAGCCAGCACCGAGAGTGGGAGGGGCAGCCCTTCCAGGGGTCTGGGACTCCCAGAGAGCAGTCCCCTCCATCCCAGTTTCCTCCCGGGCCACTGCAGCCAGCATCGCAGGCCCCATCTCCACTTCTGCCCTCACACCCCTTGGCTCCG	GGGTGGAAACTCCCTGGAGCCCAAGGCTGTGGCCACACTGTAACTCAGAGCCATCTACGTCCTTCCTCCTCCTCTCACCCACCCCTCTCCTTCCCTGGCTCCAGTGGATTTCAGGCTCACGTGCAGGCTGGAGGGGTCTCACAGTCGTAGCCATCAAACAGACACTCTTCAGAGTCACACTGTGGGTGGCACTGCCCGTCCCGGAAGAGAAGCCAGCACCGAGAGTGGGAGGGGCAGCCCTTCCAGGGGTCTGGGACTCCCAGAGAGCAGTCCCCTCCATCCCAGTTTCCTCCCGGGCCACTGCAGCCAGCATCGCAGGCCCCATCTCCACTTCTGCCCTCACACCCCTTGGCTCCG	-	novel	NA	P-0034790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	24	145	0	ENST00000375023.3:c.3519_3755+120del		p.X1173_splice	ENST00000375023	NM_004557.3	1173		21/30	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		145	195	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0034792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	87	463	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.337612489919806	2		463	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	93	544	0	ENST00000269305.4:c.811G>C	p.Glu271Gln	p.E271Q	ENST00000269305	NM_001126112.2	271	Gag/Cag	8/11	NA	3	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.337612489919806	3		544	464	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856020	68856020	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	100	459	1	ENST00000261769.5:c.1828C>T	p.Gln610Ter	p.Q610*	ENST00000261769	NM_004360.3	610	Cag/Tag	12/16	0.337612489919806	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.337612489919806	1		460	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577021	7577021	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1048095040	NA	P-0034792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	95	636	0	ENST00000269305.4:c.917G>A	p.Arg306Gln	p.R306Q	ENST00000269305	NM_001126112.2	306	cGa/cAa	8/11	NA	3	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.337612489919806	3		636	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577154	7577154	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs200579969	NA	P-0034792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	64	465	0	ENST00000269305.4:c.784G>A	p.Gly262Ser	p.G262S	ENST00000269305	NM_001126112.2	262	Ggt/Agt	8/11	NA	3	FACETS	1	0.96	1			1	INDETERMINATE	1	TRUE	NA	0.337612489919806	3		465	349	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102196	27102196	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	62	372	0	ENST00000324856.7:c.5122C>T	p.Gln1708Ter	p.Q1708*	ENST00000324856	NM_006015.4	1708	Cag/Tag	19/20	0.166322418989109	5	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.337612489919806	5		372	405	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059298	42059298	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	70	357	0	ENST00000219905.7:c.9018G>C	p.Gln3006His	p.Q3006H	ENST00000219905	NM_001164273.1	3006	caG/caC	24/24	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.337612489919806	2		357	365	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097733	27097733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	87	528	1	ENST00000324856.7:c.3322G>A	p.Glu1108Lys	p.E1108K	ENST00000324856	NM_006015.4	1108	Gaa/Aaa	12/20	0.166322418989109	5	FACETS	0.763	0.677	0.853			1	INDETERMINATE	2	TRUE	NA	0.337612489919806	5		529	509	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562391	21562391	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	64	486	0	ENST00000382592.4:c.1528G>C	p.Asp510His	p.D510H	ENST00000382592	NM_014572.2	510	Gac/Cac	4/8	0.337612489919806	0	FACETS	0.81	0.707	0.92			1	CLONAL	1	TRUE	0	0.337612489919806	0		486	310	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2111962	2111962	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45457701	NA	P-0034792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	75	529	0	ENST00000219476.3:c.1210C>T	p.Gln404Ter	p.Q404*	ENST00000219476	NM_000548.3	404	Cag/Tag	12/42	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.337612489919806	2		529	432	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632692	3632692	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	73	544	0	ENST00000294008.3:c.5156C>T	p.Ser1719Phe	p.S1719F	ENST00000294008	NM_032444.2	1719	tCt/tTt	15/15	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.337612489919806	2		544	420	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231327	5231327	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	74	431	0	ENST00000357368.4:c.2149G>C	p.Glu717Gln	p.E717Q	ENST00000357368	NM_002850.3	717	Gag/Cag	14/38	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.337612489919806	2		431	341	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	223676	223676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	55	359	0	ENST00000264932.6:c.143C>T	p.Ser48Leu	p.S48L	ENST00000264932	NM_004168.2	48	tCa/tTa	2/15	0.337612489919806	1	FACETS	0.794	0.683	0.915	0.794	0.683	0.915	CLONAL	1	TRUE	0	0.337612489919806	1		359	341	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515100	31515100	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	63	535	0	ENST00000344624.3:c.1285C>G	p.Gln429Glu	p.Q429E	ENST00000344624		429	Cag/Gag	5/33	0.337612489919806	1	FACETS	0.696	0.603	0.795	0.696	0.603	0.795	SUBCLONAL	1	TRUE	0	0.337612489919806	1		535	446	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515125	31515125	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	91	663	0	ENST00000344624.3:c.1260C>G	p.Asn420Lys	p.N420K	ENST00000344624		420	aaC/aaG	5/33	0.337612489919806	1	FACETS	0.813	0.724	0.908	0.813	0.724	0.908	CLONAL	1	TRUE	0	0.337612489919806	1		663	551	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738348	133738348	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1216325712	NA	P-0034793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	90	415	1	ENST00000318560.5:c.748G>A	p.Gly250Arg	p.G250R	ENST00000318560	NM_005157.4	250	Ggg/Agg	4/11	0.182101894950753	2	FACETS	0.703	0.625	0.786	0.352	0.312	0.393	INDETERMINATE	1	TRUE	0	0.465357600529667	2		416	550	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	173	460	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.439050067169819	3	FACETS	0.905	0.839	0.973	0.905	0.839	0.973	CLONAL	2	TRUE	1	0.439050067169819	3		460	531	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0034795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	85	458	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.439050067169819	2		458	329	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0034795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	79	438	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.889	0.786	0.998	0.889	0.786	0.998	CLONAL	1	TRUE	1	0.439050067169819	2		438	405	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0034795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	89	464	1	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.416737782233807	1	FACETS	0.872	0.779	0.969	0.872	0.779	0.969	CLONAL	1	TRUE	0	0.439050067169819	1		465	363	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0034795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	89	266	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.439050067169819	2		266	404	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0034795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	131	236	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.439050067169819	2	FACETS	0.843	0.784	0.901	1	0.986	1	CLONAL	3	TRUE	0	0.439050067169819	2		236	236	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727501	88727501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147992979	NA	P-0034795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	164	482	2	ENST00000360948.2:c.278C>T	p.Thr93Met	p.T93M	ENST00000360948	NM_001012338.2	93	aCg/aTg	3/19	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.439050067169819	2		484	709	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21565541	21565541	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	129	476	0	ENST00000382592.4:c.345G>C	p.Glu115Asp	p.E115D	ENST00000382592	NM_014572.2	115	gaG/gaC	3/8	0.109367512388077	6	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.439050067169819	6		476	806	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444336	50444336	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	86	315	0	ENST00000331340.3:c.266G>C	p.Gly89Ala	p.G89A	ENST00000331340	NM_006060.4	89	gGa/gCa	4/8	0.439050067169819	3	FACETS	0.9	0.798	1	0.45	0.399	0.504	CLONAL	1	TRUE	1	0.439050067169819	3		315	531	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034795-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	50	460	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.273202105449814	1	FACETS	0.571	0.486	0.663	0.571	0.486	0.663	SUBCLONAL	1	TRUE	0	0.398625415155024	1		460	352	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0034795-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	66	458	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.398625415155024	2		458	325	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0034795-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	75	438	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.902	0.794	1	0.902	0.794	1	CLONAL	1	TRUE	1	0.398625415155024	2		438	417	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0034795-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	81	464	1	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.917	0.812	1	0.917	0.812	1	CLONAL	1	TRUE	1	0.398625415155024	2		465	443	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0034795-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	73	266	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.798	0.7	0.903	0.798	0.7	0.903	CLONAL	1	TRUE	1	0.398625415155024	2		266	459	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21565541	21565541	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034795-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	128	476	0	ENST00000382592.4:c.345G>C	p.Glu115Asp	p.E115D	ENST00000382592	NM_014572.2	115	gaG/gaC	3/8	1	2	FACETS	0.935	0.849	1	0.935	0.849	1	CLONAL	1	TRUE	1	0.398625415155024	2		476	687	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849467	68849467	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778170	NA	P-0034795-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	152	619	0	ENST00000261769.5:c.1370C>T	p.Thr457Met	p.T457M	ENST00000261769	NM_004360.3	457	aCg/aTg	10/16	1	2	FACETS	0.945	0.865	1	0.945	0.865	1	CLONAL	1	TRUE	1	0.398625415155024	2		619	807	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685287	89685287	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs398123316	NA	P-0034795-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	41	273	1	ENST00000371953.3:c.182A>T	p.His61Leu	p.H61L	ENST00000371953	NM_000314.4	61	cAt/cTt	3/9	0.398625415155024	1	FACETS	0.969	0.819	1	0.969	0.819	1	CLONAL	1	TRUE	0	0.398625415155024	1		274	170	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0034800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	220	387	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	0.686575732484791	2		387	569	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	284	148	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.686575732484791	2		148	388	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145430	58145430	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894340	NA	P-0034800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	187	334	0	ENST00000257904.6:c.71G>T	p.Arg24Leu	p.R24L	ENST00000257904	NM_000075.3	24	cGt/cTt	2/8	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.686575732484791	2		334	525	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560371	95560371	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	89	412	0	ENST00000393063.1:c.5218G>T	p.Val1740Phe	p.V1740F	ENST00000393063	NM_030621.3	1740	Gtc/Ttc	25/28	NA	2	FACETS	0.439	0.39	0.492			1	INDETERMINATE	1	TRUE	NA	0.686575732484791	2		412	590	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2185916	2185916	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	264	429	0	ENST00000398665.3:c.188A>G	p.Tyr63Cys	p.Y63C	ENST00000398665	NM_032482.2	63	tAt/tGt	3/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.686575732484791	2		429	701	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125278	47125278	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	131	471	1	ENST00000409792.3:c.5992C>T	p.Gln1998Ter	p.Q1998*	ENST00000409792	NM_014159.6	1998	Cag/Tag	12/21	1	2	FACETS	0.465	0.422	0.511	0.465	0.422	0.511	SUBCLONAL	1	TRUE	1	0.686575732484791	2		472	820	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891608	151891608	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	103	367	0	ENST00000262189.6:c.4424A>T	p.Asn1475Ile	p.N1475I	ENST00000262189	NM_170606.2	1475	aAt/aTt	29/59	1	2	FACETS	0.517	0.464	0.574	0.517	0.464	0.574	SUBCLONAL	1	TRUE	1	0.686575732484791	2		367	580	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	68	346	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.797	0.693	0.91	0.797	0.693	0.91	CLONAL	1	TRUE	1	0.26	2		347	656	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	57	313	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	0.3	0	FACETS	1	0.925	1			1	CLONAL	1	TRUE	0	0.26	0		313	293	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584514	48584514	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	50	631	1	ENST00000342988.3:c.692del	p.Gly231AlafsTer10	p.G231Afs*10	ENST00000342988	NM_005359.5	229	ctG/ct	6/12	1	2	FACETS	0.467	0.395	0.546	0.467	0.395	0.546	SUBCLONAL	1	TRUE	1	0.26	2		632	824	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	146	430	0	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	1	2	FACETS	0.944	0.865	1	1	0.991	1	CLONAL	2	TRUE	1	0.26	2		430	595	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806176	1806176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370064407	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	346	773	0	ENST00000260795.2:c.1195C>T	p.Arg399Cys	p.R399C	ENST00000260795		399	Cgc/Tgc	8/17	NA	2	FACETS	0.91	0.864	0.957			1	INDETERMINATE	3	TRUE	NA	0.26	2		773	975	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	40	671	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.295	0.244	0.353	0.295	0.244	0.353	SUBCLONAL	1	TRUE	1	0.26	2		671	1042	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456453	29456453	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1558630501	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	237	667	0	ENST00000389048.3:c.2465del	p.Gly822ValfsTer9	p.G822Vfs*9	ENST00000389048	NM_004304.4	822	gGt/gt	14/29	0.3	1	FACETS	0.989	0.926	1	1	0.994	1	CLONAL	2	TRUE	0	0.26	1		667	802	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871052	12871053	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1555085575	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	64	226	0	ENST00000228872.4:c.285dup	p.Lys96GlnfsTer29	p.K96Qfs*29	ENST00000228872	NM_004064.3	93	-/C	1/3	1	2	FACETS	0.981	0.851	1	0.981	0.851	1	CLONAL	1	TRUE	1	0.26	2		226	502	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744385	41744385	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	185	594	0	ENST00000301178.4:c.1010del	p.Pro337LeufsTer29	p.P337Lfs*29	ENST00000301178	NM_021913.4	335	ggC/gg	8/20	1	2	FACETS	1	0.972	1	1	0.994	1	CLONAL	2	TRUE	1	0.26	2		594	648	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867149	45867149	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1322620921	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	251	714	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	0.995	1	CLONAL	2	TRUE	1	0.26	2		714	846	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586503	189586503	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs143591434	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	124	299	0	ENST00000264731.3:c.1127G>A	p.Arg376His	p.R376H	ENST00000264731	NM_003722.4	376	cGc/cAc	8/14	1	2	FACETS	1	0.969	1	1	0.991	1	CLONAL	2	TRUE	1	0.26	2		299	420	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321390	1321390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769805287	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	41	380	1	ENST00000400841.2:c.365C>T	p.Pro122Leu	p.P122L	ENST00000400841		122	cCg/cTg	4/6	0.3	0	FACETS	0.665	0.555	0.786			1	SUBCLONAL	1	TRUE	NA	0.26	0		381	351	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118895	115118895	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	205	433	0	ENST00000257566.3:c.446A>G	p.Tyr149Cys	p.Y149C	ENST00000257566	NM_016569.3	149	tAc/tGc	2/8	1	2	FACETS	0.897	0.838	0.958	1	0.995	1	CLONAL	3	TRUE	1	0.26	2		433	586	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919007	50919007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1483458869	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	234	619	0	ENST00000440232.2:c.2744C>T	p.Ala915Val	p.A915V	ENST00000440232	NM_002691.3	915	gCg/gTg	22/27	1	2	FACETS	0.853	0.8	0.908	1	0.995	1	CLONAL	3	TRUE	1	0.26	2		619	703	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508856	106508856	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376958957	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	157	424	0	ENST00000359195.3:c.850G>A	p.Glu284Lys	p.E284K	ENST00000359195	NM_002649.2	284	Gaa/Aaa	2/11	1	2	FACETS	1	0.942	1	1	0.992	1	CLONAL	2	TRUE	1	0.26	2		424	587	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905288	50905288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376236497	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	53	861	0	ENST00000440232.2:c.496C>T	p.Arg166Trp	p.R166W	ENST00000440232	NM_002691.3	166	Cgg/Tgg	5/27	1	2	FACETS	0.436	0.37	0.508	0.436	0.37	0.508	SUBCLONAL	1	TRUE	1	0.26	2		861	936	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730074	41730074	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377167564	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	71	551	0	ENST00000242208.4:c.455G>A	p.Arg152His	p.R152H	ENST00000242208	NM_002192.2	152	cGt/cAt	3/3	0.221218149125142	0	FACETS	0.68	0.594	0.773			1	SUBCLONAL	1	TRUE	0	0.26	0		551	594	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783245	9783245	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756497515	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	253	556	0	ENST00000377346.4:c.2489G>A	p.Arg830His	p.R830H	ENST00000377346	NM_005026.3	830	cGt/cAt	20/24	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	2	TRUE	NA	0.26	2		556	826	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259480	16259480	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	181	411	2	ENST00000375759.3:c.6750del	p.Ala2251GlnfsTer102	p.A2251Qfs*102	ENST00000375759	NM_015001.2	2249	Ccc/cc	11/15	0.3	3	FACETS	1	0.985	1			1	CLONAL	2	TRUE	NA	0.26	3		413	635	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346220	152346220	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	237	584	4	ENST00000359321.1:c.350del	p.Leu117TrpfsTer17	p.L117Wfs*17	ENST00000359321	NM_005431.1	117	tTg/tg	3/3	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	1	0.26	2		588	773	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200267	138200267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	62	442	0	ENST00000237289.4:c.1685G>A	p.Arg562His	p.R562H	ENST00000237289	NM_001270507.1	562	cGt/cAt	7/9	0.289902446629799	3	FACETS	0.768	0.662	0.883	0.384	0.331	0.442	SUBCLONAL	1	TRUE	1	0.26	3		442	702	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438211	49438211	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	86	810	1	ENST00000301067.7:c.5058del	p.Lys1686AsnfsTer36	p.K1686Nfs*36	ENST00000301067	NM_003482.3	1686	aaA/aa	20/54	0.107236687862896	4	FACETS	0.752	0.663	0.847	0.376	0.331	0.424	INDETERMINATE	1	TRUE	2	0.26	4		811	1109	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137075	64137075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	241	443	1	ENST00000334205.4:c.1586G>A	p.Arg529His	p.R529H	ENST00000334205	NM_003942.2	529	cGc/cAc	13/17	1	2	FACETS	1	0.949	1	1	0.996	1	CLONAL	3	TRUE	1	0.26	2		444	612	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639245	3639245	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757128699	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	143	870	0	ENST00000294008.3:c.4394G>A	p.Arg1465His	p.R1465H	ENST00000294008	NM_032444.2	1465	cGt/cAt	12/15	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.26	2		870	1032	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383774	15383774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1229253526	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	226	637	0	ENST00000263377.2:c.137C>T	p.Pro46Leu	p.P46L	ENST00000263377	NM_058243.2	46	cCg/cTg	2/20	1	2	FACETS	0.842	0.784	0.902	1	0.993	1	CLONAL	2	TRUE	1	0.26	2		637	1032	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651144	206651144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs533634715	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	338	728	0	ENST00000367120.3:c.754C>T	p.Arg252Trp	p.R252W	ENST00000367120	NM_014002.3	252	Cgg/Tgg	8/22	1	2	FACETS	1	0.991	1	1	0.996	1	CLONAL	2	TRUE	1	0.26	2		728	1062	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100975	41100975	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	193	537	1	ENST00000373198.4:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000373198	NM_133170.3	461	Cga/Tga	8/32	0.3	0	FACETS	0.979	0.912	1			1	CLONAL	2	TRUE	0	0.26	0		538	561	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40498610	40498610	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	231	471	0	ENST00000264657.5:c.250C>T	p.Arg84Ter	p.R84*	ENST00000264657	NM_139276.2	84	Cga/Tga	3/24	1	2	FACETS	1	0.985	1	1	0.995	1	CLONAL	2	TRUE	1	0.26	2		471	757	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793797	89793799	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	189	480	0	ENST00000336032.3:c.868_870del	p.Pro290del	p.P290del	ENST00000336032	NM_006813.2	289	tCTCct/tct	2/2	1	2	FACETS	0.964	0.893	1	1	0.993	1	CLONAL	2	TRUE	1	0.26	2		480	754	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291061	10291061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377146699	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	249	655	1	ENST00000340748.4:c.410C>T	p.Thr137Met	p.T137M	ENST00000340748		137	aCg/aTg	4/40	1	2	FACETS	1	0.98	1	1	0.995	1	CLONAL	2	TRUE	1	0.26	2		656	867	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692783	89692783	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	104	416	0	ENST00000371953.3:c.270del	p.Phe90LeufsTer9	p.F90Lfs*9	ENST00000371953	NM_000314.4	89	ccT/cc	5/9	0.3	0	FACETS	0.638	0.574	0.705			1	SUBCLONAL	2	TRUE	0	0.26	0		416	464	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11269500	11269500	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	144	447	0	ENST00000361445.4:c.3670G>T	p.Asp1224Tyr	p.D1224Y	ENST00000361445	NM_004958.3	1224	Gat/Tat	25/58	NA	2	FACETS	1	0.956	1			1	INDETERMINATE	2	TRUE	NA	0.26	2		447	520	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262237	16262237	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	111	213	0	ENST00000375759.3:c.9502C>T	p.Arg3168Ter	p.R3168*	ENST00000375759	NM_015001.2	3168	Cga/Tga	11/15	0.3	3	FACETS	1	0.953	1			1	CLONAL	3	TRUE	NA	0.26	3		213	301	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325840	65325840	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	185	420	2	ENST00000342505.4:c.1282G>A	p.Ala428Thr	p.A428T	ENST00000342505	NM_002227.2	428	Gcc/Acc	9/25	1	2	FACETS	1	0.985	1	1	0.994	1	CLONAL	2	TRUE	1	0.26	2		422	581	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206667311	206667311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1452780177	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	220	612	0	ENST00000367120.3:c.2104C>T	p.Arg702Cys	p.R702C	ENST00000367120	NM_014002.3	702	Cgc/Tgc	21/22	1	2	FACETS	1	0.969	1	1	0.994	1	CLONAL	2	TRUE	1	0.26	2		612	795	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675280	241675280	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	199	517	0	ENST00000366560.3:c.542T>C	p.Val181Ala	p.V181A	ENST00000366560	NM_000143.3	181	gTt/gCt	4/10	1	2	FACETS	1	0.982	1	1	0.994	1	CLONAL	2	TRUE	1	0.26	2		517	656	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465887	69465887	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	220	548	0	ENST00000227507.2:c.725A>G	p.Asp242Gly	p.D242G	ENST00000227507	NM_053056.2	242	gAc/gGc	5/5	0.3	1	FACETS	1	0.966	1	1	0.994	1	CLONAL	2	TRUE	0	0.26	1		548	699	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518052	69518052	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762243036	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	250	750	3	ENST00000294312.3:c.313G>A	p.Ala105Thr	p.A105T	ENST00000294312	NM_005117.2	105	Gcc/Acc	2/3	0.3	1	FACETS	1	0.982	1	1	0.995	1	CLONAL	2	TRUE	0	0.26	1		753	751	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939788	71939788	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	76	689	0	ENST00000298229.2:c.419del	p.Pro140ArgfsTer39	p.P140Rfs*39	ENST00000298229	NM_001567.3	139	Ccc/cc	4/28	NA	2	FACETS	0.648	0.567	0.736			1	INDETERMINATE	1	TRUE	NA	0.26	2		689	902	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402077	402077	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	147	584	0	ENST00000399788.2:c.4714A>G	p.Lys1572Glu	p.K1572E	ENST00000399788	NM_001042603.1	1572	Aaa/Gaa	27/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.26	2		584	899	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037492	12037492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	137	334	0	ENST00000396373.4:c.1123G>A	p.Gly375Arg	p.G375R	ENST00000396373	NM_001987.4	375	Gga/Aga	6/8	1	2	FACETS	1	0.976	1	1	0.992	1	CLONAL	2	TRUE	1	0.26	2		334	448	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424729	49424729	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370390426	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	342	647	0	ENST00000301067.7:c.13618C>T	p.Arg4540Trp	p.R4540W	ENST00000301067	NM_003482.3	4540	Cgg/Tgg	40/54	0.107236687862896	4	FACETS	1	0.98	1	1	0.995	1	INDETERMINATE	3	TRUE	2	0.26	4		647	1037	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562904	21562904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1390242703	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	284	570	1	ENST00000382592.4:c.1015G>A	p.Ala339Thr	p.A339T	ENST00000382592	NM_014572.2	339	Gcc/Acc	4/8	0.279539337496587	1	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	0	0.26	1		571	788	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994859	73994859	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567610542	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	12	40	0	ENST00000318443.5:c.343G>A	p.Ala115Thr	p.A115T	ENST00000318443	NM_001024736.1	115	Gcg/Acg	3/10	1	2	FACETS	1	0.761	1	1	0.911	1	CLONAL	2	TRUE	1	0.26	2		40	44	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341247	341247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	321	678	0	ENST00000262320.3:c.2237G>A	p.Cys746Tyr	p.C746Y	ENST00000262320	NM_003502.3	746	tGc/tAc	9/11	1	2	FACETS	0.958	0.908	1	1	0.997	1	CLONAL	3	TRUE	1	0.26	2		678	859	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56867129	56867129	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs764428645	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	198	504	0	ENST00000308159.5:c.1348G>A	p.Glu450Lys	p.E450K	ENST00000308159	NM_014669.4	450	Gag/Aag	13/22	1	2	FACETS	1	0.945	1	1	0.994	1	CLONAL	2	TRUE	1	0.26	2		504	746	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821148	72821148	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs923198124	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	279	642	0	ENST00000268489.5:c.11027C>T	p.Ala3676Val	p.A3676V	ENST00000268489	NM_006885.3	3676	gCg/gTg	10/10	1	2	FACETS	0.908	0.856	0.96	1	0.996	1	CLONAL	3	TRUE	1	0.26	2		642	788	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993669	72993669	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762692938	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	94	598	0	ENST00000268489.5:c.376G>A	p.Val126Met	p.V126M	ENST00000268489	NM_006885.3	126	Gtg/Atg	2/10	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.26	2		598	695	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210735	5210735	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	285	752	0	ENST00000357368.4:c.5316T>G	p.Asn1772Lys	p.N1772K	ENST00000357368	NM_002850.3	1772	aaT/aaG	34/38	0.182467394035895	0	FACETS	0.921	0.868	0.975			1	CLONAL	2	TRUE	0	0.26	0		752	881	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260302	10260302	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	184	520	0	ENST00000340748.4:c.2365G>A	p.Gly789Arg	p.G789R	ENST00000340748		789	Ggg/Agg	25/40	1	2	FACETS	1	0.962	1	1	0.993	1	CLONAL	2	TRUE	1	0.26	2		520	668	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11022897	11022897	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	159	867	1	ENST00000327064.4:c.596C>T	p.Ser199Leu	p.S199L	ENST00000327064	NM_199141.1	199	tCg/tTg	5/16	1	2	FACETS	0.947	0.866	1	0.947	0.866	1	CLONAL	1	TRUE	1	0.26	2		868	1291	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130307	11130307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1213692147	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	249	529	1	ENST00000358026.2:c.2546G>A	p.Arg849Gln	p.R849Q	ENST00000358026	NM_001128849.1	849	cGg/cAg	18/36	1	2	FACETS	0.859	0.807	0.913	1	0.996	1	CLONAL	3	TRUE	1	0.26	2		530	743	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797191	42797191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778202	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	146	828	1	ENST00000575354.2:c.3553G>A	p.Ala1185Thr	p.A1185T	ENST00000575354	NM_015125.3	1185	Gcc/Acc	15/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.26	2		829	1041	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714732	52714732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	110	597	0	ENST00000322088.6:c.490G>A	p.Ala164Thr	p.A164T	ENST00000322088	NM_014225.5	164	Gcg/Acg	4/15	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.26	2		597	771	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47709983	47709985	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	148	287	0	ENST00000233146.2:c.2704_2706del	p.Glu902del	p.E902del	ENST00000233146	NM_000251.2	900	tcAGAa/tca	16/16	0.3	0	FACETS	0.854	0.792	0.916			1	CLONAL	3	TRUE	0	0.26	0		287	329	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319093	62319093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786205700	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	266	735	0	ENST00000360203.5:c.1451C>T	p.Pro484Leu	p.P484L	ENST00000360203	NM_001283009.1	484	cCg/cTg	17/35	1	2	FACETS	1	0.976	1	1	0.995	1	CLONAL	2	TRUE	1	0.26	2		735	951	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069292	30069292	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1161410708	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	203	628	2	ENST00000338641.4:c.1160del	p.Lys387ArgfsTer39	p.K387Rfs*39	ENST00000338641	NM_000268.3	386	gAa/ga	12/16	1	2	FACETS	1	0.978	1	1	0.994	1	CLONAL	2	TRUE	1	0.26	2		630	696	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434123	12434123	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	129	373	0	ENST00000287820.6:c.491G>A	p.Arg164Gln	p.R164Q	ENST00000287820	NM_015869.4	164	cGg/cAg	4/7	1	2	FACETS	1	0.918	1	1	0.99	1	CLONAL	2	TRUE	1	0.26	2		373	493	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178943828	178943828	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1365628884	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	80	351	0	ENST00000263967.3:c.2495G>A	p.Arg832Gln	p.R832Q	ENST00000263967	NM_006218.2	832	cGa/cAa	17/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.26	2		351	518	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980598	1980598	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1560826798	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	223	474	0	ENST00000382891.5:c.4060C>T	p.Arg1354Trp	p.R1354W	ENST00000382891	NM_133335.3	1354	Cgg/Tgg	22/22	NA	2	FACETS	0.916	0.858	0.975			1	INDETERMINATE	3	TRUE	NA	0.26	2		474	624	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156519	106156519	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	155	368	0	ENST00000380013.4:c.1420C>A	p.Pro474Thr	p.P474T	ENST00000380013	NM_001127208.2	474	Ccg/Acg	3/11	1	2	FACETS	1	0.983	1	1	0.993	1	CLONAL	2	TRUE	1	0.26	2		368	479	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38960610	38960610	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	95	221	0	ENST00000357387.3:c.1741del	p.Tyr581ThrfsTer24	p.Y581Tfs*24	ENST00000357387	NM_152756.3	581	Tac/ac	20/38	1	2	FACETS	0.942	0.845	1	1	0.986	1	CLONAL	2	TRUE	1	0.26	2		221	388	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450251	50450251	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	53	458	0	ENST00000331340.3:c.435C>G	p.Phe145Leu	p.F145L	ENST00000331340	NM_006060.4	145	ttC/ttG	5/8	0.221218149125142	0	FACETS	0.579	0.494	0.672			1	SUBCLONAL	1	TRUE	0	0.26	0		458	521	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340043	116340043	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	106	281	0	ENST00000397752.3:c.908del	p.Lys303ArgfsTer31	p.K303Rfs*31	ENST00000397752	NM_000245.2	302	gAa/ga	2/21	1	2	FACETS	1	0.93	1	1	0.989	1	CLONAL	2	TRUE	1	0.26	2		281	394	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515092	148515092	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	264	532	0	ENST00000320356.2:c.1117C>A	p.Pro373Thr	p.P373T	ENST00000320356	NM_004456.4	373	Ccc/Acc	10/20	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.26	2		532	823	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162894	38162894	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	98	639	0	ENST00000317025.8:c.2312G>A	p.Gly771Glu	p.G771E	ENST00000317025	NM_023034.1	771	gGg/gAg	13/24	1	2	FACETS	0.736	0.655	0.823	0.736	0.655	0.823	SUBCLONAL	1	TRUE	1	0.26	2		639	1024	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187060	38187060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	222	856	0	ENST00000317025.8:c.1417G>A	p.Ala473Thr	p.A473T	ENST00000317025	NM_023034.1	473	Gcg/Acg	6/24	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.26	2		856	1251	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006101	22006101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1425823622	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	230	549	0	ENST00000276925.6:c.302G>A	p.Arg101Gln	p.R101Q	ENST00000276925	NM_004936.3	101	cGg/cAg	2/2	0.182467394035895	0	FACETS	0.941	0.881	1			1	CLONAL	2	TRUE	0	0.26	0		549	696	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564080	139564080	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537251168	NA	P-0034845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	160	689	0	ENST00000308874.7:c.220C>T	p.Arg74Cys	p.R74C	ENST00000308874		74	Cgc/Tgc	5/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.26	2		689	870	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0034847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	86	463	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.478044175658738	5	FACETS	0.963	0.87	1	0.963	0.87	1	CLONAL	3	TRUE	2	0.497200701222116	5		463	209	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279674	123279674	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs77543610	NA	P-0034847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	25	348	0	ENST00000358487.5:c.758C>G	p.Pro253Arg	p.P253R	ENST00000358487	NM_000141.4	253	cCt/cGt	7/18	0.33347616305721	1	FACETS	0.624	0.5	0.762	0.624	0.5	0.762	SUBCLONAL	1	TRUE	0	0.497200701222116	1		348	121	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575505	64575505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs607969	NA	P-0034847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	10	512	0	ENST00000312049.6:c.512G>A	p.Arg171Gln	p.R171Q	ENST00000312049	NM_130799.2	171	cGg/cAg	3/10	0.332400626500224	2	FACETS	0.226	0.153	0.318	0.113	0.076	0.159	SUBCLONAL	1	TRUE	0	0.497200701222116	2		512	178	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170271	32170271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148269570	NA	P-0034847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	28	749	0	ENST00000375023.3:c.3337C>T	p.Arg1113Cys	p.R1113C	ENST00000375023	NM_004557.3	1113	Cgc/Tgc	21/30	0.398845231414443	4	FACETS	0.677	0.543	0.828	0.226	0.181	0.276	SUBCLONAL	1	TRUE	1	0.497200701222116	4		749	249	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844694	156844697	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CCAG	CCAG	-	novel	NA	P-0034847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	23	845	0	ENST00000524377.1:c.1252-4_1252-1del		p.X418_splice	ENST00000524377	NM_002529.3	418			0.286281555783704	1	FACETS	0.4	0.314	0.497	0.4	0.314	0.497	INDETERMINATE	1	TRUE	0	0.497200701222116	1		845	174	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332900	70332900	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	36	707	0	ENST00000373644.4:c.805C>A	p.Gln269Lys	p.Q269K	ENST00000373644	NM_030625.2	269	Cag/Aag	2/12	NA	2	FACETS	0.75	0.623	0.889			1	INDETERMINATE	1	TRUE	NA	0.497200701222116	2		707	193	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098539	108098539	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	58	366	0	ENST00000278616.4:c.109C>A	p.Pro37Thr	p.P37T	ENST00000278616	NM_000051.3	37	Cct/Act	3/63	NA	2	FACETS	0.773	0.68	0.868			1	INDETERMINATE	2	TRUE	NA	0.497200701222116	2		366	151	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031982	10031982	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	16	667	1	ENST00000330684.3:c.841T>C	p.Tyr281His	p.Y281H	ENST00000330684	NM_001134407.1	281	Tac/Cac	3/13	1	2	FACETS	0.368	0.273	0.48	0.368	0.273	0.48	SUBCLONAL	1	TRUE	1	0.497200701222116	2		668	175	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755675	39755675	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0034847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	14	780	1	ENST00000288319.7:c.1090A>T	p.Lys364Ter	p.K364*	ENST00000288319	NM_182918.3	364	Aag/Tag	10/10	0.367886614169586	2	FACETS	0.359	0.26	0.477	0.179	0.13	0.239	SUBCLONAL	1	TRUE	0	0.497200701222116	2		781	157	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696688	47696688	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519971	NA	P-0034849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	155	541	0	ENST00000347630.2:c.260A>G	p.Tyr87Cys	p.Y87C	ENST00000347630	NM_001007230.1	87	tAc/tGc	5/11	1	2	FACETS	0.885	0.814	0.959	0.885	0.814	0.959	CLONAL	1	TRUE	1	0.593622900426743	2		541	590	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0034850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	172	463	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.25223412769391	1	FACETS	1	0.973	1	1	0.993	1	CLONAL	2	TRUE	0	0.25223412769391	1		463	538	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417910	32417910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	123	528	1	ENST00000332351.3:c.1142C>T	p.Ser381Leu	p.S381L	ENST00000332351	NM_024426.4	381	tCg/tTg	7/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.25223412769391	2		529	811	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223532	2223532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	136	500	0	ENST00000326181.6:c.1063C>T	p.Arg355Trp	p.R355W	ENST00000326181	NM_032271.2	355	Cgg/Tgg	11/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.25223412769391	2		500	949	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632084	1632084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768705868	NA	P-0034850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	131	725	1	ENST00000344749.5:c.251C>T	p.Ser84Leu	p.S84L	ENST00000344749	NM_001136139.2	84	tCg/tTg	5/19	0.25223412769391	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.25223412769391	1		726	858	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340339	116340339	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0034850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	87	262	0	ENST00000397752.3:c.1200+1G>C		p.X400_splice	ENST00000397752	NM_000245.2	400			0.130729253389141	3	FACETS	1	0.95	1	1	0.95	1	INDETERMINATE	2	TRUE	1	0.25223412769391	3		262	349	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0034860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	11	227	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	0.319774985886996	4	FACETS	0.126	0.087	0.176	0.032	0.021	0.044	INDETERMINATE	1	TRUE	0	0.661767302983304	4		227	437	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288486	15288486	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	49	279	0	ENST00000263388.2:c.4253C>G	p.Ser1418Trp	p.S1418W	ENST00000263388	NM_000435.2	1418	tCg/tGg	24/33	0.365258195401779	3	FACETS	0.628	0.534	0.729	0.314	0.267	0.365	INDETERMINATE	1	TRUE	1	0.661767302983304	3		279	314	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713691	30713691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727503473	NA	P-0034860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	53	286	0	ENST00000295754.5:c.1016G>A	p.Arg339Gln	p.R339Q	ENST00000295754	NM_003242.5	339	cGg/cAg	4/7	0.319774985886996	4	FACETS	0.557	0.475	0.646	0.139	0.118	0.162	INDETERMINATE	1	TRUE	0	0.661767302983304	4		286	478	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579349	7579349	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	43	600	0	ENST00000269305.4:c.338T>C	p.Phe113Ser	p.F113S	ENST00000269305	NM_001126112.2	113	tTc/tCc	4/11	0.318801617723444	1	FACETS	0.389	0.325	0.459	0.389	0.325	0.459	SUBCLONAL	1	TRUE	0	0.374661898161642	1		600	480	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412967	49412967	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	59	585	2	ENST00000418115.1:c.56C>A	p.Thr19Lys	p.T19K	ENST00000418115	NM_001664.2	19	aCa/aAa	2/5	0.374661898161642	3	FACETS	0.445	0.382	0.514	0.223	0.191	0.257	SUBCLONAL	1	TRUE	1	0.374661898161642	3		587	840	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	163	148	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		148	460	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0034895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	90	554	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.918	0.82	1	0.918	0.82	1	CLONAL	1	TRUE	1	0.499010302060775	2		554	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0034895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	226	694	1	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.499010302060775	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.499010302060775	1		695	638	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794440	42794441	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0034895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	68	1069	0	ENST00000575354.2:c.1526dup	p.Leu510ThrfsTer4	p.L510Tfs*4	ENST00000575354	NM_015125.3	507	cgc/cgCc	10/20	0.499010302060775	1	FACETS	0.215	0.186	0.246	0.215	0.186	0.246	SUBCLONAL	1	TRUE	0	0.499010302060775	1		1069	953	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223799	2223799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	156	806	0	ENST00000326181.6:c.1097C>T	p.Ser366Phe	p.S366F	ENST00000326181	NM_032271.2	366	tCc/tTc	12/21	1	2	FACETS	0.833	0.764	0.904	0.833	0.764	0.904	CLONAL	1	TRUE	1	0.499010302060775	2		806	751	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458437	12458437	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530007199	NA	P-0034895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	83	721	2	ENST00000287820.6:c.1054G>A	p.Glu352Lys	p.E352K	ENST00000287820	NM_015869.4	352	Gag/Aag	6/7	1	2	FACETS	0.505	0.445	0.568	0.505	0.445	0.568	SUBCLONAL	1	TRUE	1	0.499010302060775	2		723	659	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222756	5222756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374799314	NA	P-0034895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	140	469	1	ENST00000357368.4:c.3047G>A	p.Arg1016Gln	p.R1016Q	ENST00000357368	NM_002850.3	1016	cGg/cAg	18/38	0.499010302060775	1	FACETS	0.856	0.785	0.93	0.856	0.785	0.93	CLONAL	1	TRUE	0	0.499010302060775	1		470	492	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7126648	7126648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866193541	NA	P-0034902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	34	520	0	ENST00000302850.5:c.2960C>T	p.Pro987Leu	p.P987L	ENST00000302850	NM_000208.2	987	cCg/cTg	16/22	1	2	FACETS	0.295	0.24	0.357	0.295	0.24	0.357	SUBCLONAL	1	TRUE	1	0.389029443925424	2		520	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574004	7574005	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	AACATCTCGAAGCGCTCAC	novel	NA	P-0034902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	166	690	0	ENST00000269305.4:c.1004_1022dup	p.Phe341LeufsTer2	p.F341Lfs*2	ENST00000269305	NM_001126112.2	341	ttc/ttGTGAGCGCTTCGAGATGTTc	10/11	0.319286697173875	2	FACETS	0.968	0.889	1	0.484	0.444	0.525	CLONAL	1	TRUE	0	0.389029443925424	2		690	882	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026744	6026744	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	50	404	0	ENST00000265849.7:c.1652G>A	p.Cys551Tyr	p.C551Y	ENST00000265849	NM_000535.5	551	tGc/tAc	11/15	0.389029443925424	1	FACETS	0.577	0.491	0.67	0.577	0.491	0.67	SUBCLONAL	1	TRUE	0	0.389029443925424	1		404	359	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456672	32456672	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	37	422	0	ENST00000332351.3:c.220C>G	p.Arg74Gly	p.R74G	ENST00000332351	NM_024426.4	74	Cgg/Ggg	1/10	1	2	FACETS	0.776	0.64	0.929	0.776	0.64	0.929	CLONAL	1	TRUE	1	0.202426265019875	2		422	471	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527300	157527300	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0034917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	48	266	0	ENST00000346085.5:c.5026-1G>C		p.X1676_splice	ENST00000346085	NM_020732.3	1676			0.188540902686004	3	FACETS	0.819	0.695	0.953	0.819	0.695	0.953	CLONAL	2	TRUE	1	0.202426265019875	3		266	319	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0034918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	72	274	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.65926515046847	2		274	216	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46733272	46733272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs797044888	NA	P-0034918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	153	453	0	ENST00000371975.4:c.1033G>A	p.Gly345Ser	p.G345S	ENST00000371975	NM_003579.3	345	Ggc/Agc	9/18	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.65926515046847	2		453	420	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654553	29654553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876657714	NA	P-0034918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	73	239	0	ENST00000356175.3:c.5242C>T	p.Arg1748Ter	p.R1748*	ENST00000356175	NM_000267.3	1748	Cga/Tga	37/57	1	2	FACETS	0.989	0.879	1	0.989	0.879	1	CLONAL	1	TRUE	1	0.65926515046847	2		239	224	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711874	89711874	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0034918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	235	423	0	ENST00000371953.3:c.493-1G>C		p.X165_splice	ENST00000371953	NM_000314.4	165			0.65926515046847	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.65926515046847	2		423	321	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431955	49431955	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0034918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	238	788	1	ENST00000301067.7:c.9184A>T	p.Lys3062Ter	p.K3062*	ENST00000301067	NM_003482.3	3062	Aag/Tag	34/54	0.327818073884789	6	FACETS	0.968	0.905	1	0.484	0.452	0.516	INDETERMINATE	2	TRUE	2	0.65926515046847	6		789	865	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162278	47162278	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	121	383	0	ENST00000409792.3:c.3848G>T	p.Gly1283Val	p.G1283V	ENST00000409792	NM_014159.6	1283	gGa/gTa	3/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.65926515046847	2		383	313	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554855	106554855	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	105	291	0	ENST00000369096.4:c.1972C>A	p.Pro658Thr	p.P658T	ENST00000369096	NM_001198.3	658	Cca/Aca	7/7	1	2	FACETS	0.971	0.88	1	0.971	0.88	1	CLONAL	1	TRUE	1	0.65926515046847	2		291	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0034919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	376	573	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.45092255214854	2	FACETS	0.979	0.934	1	0.979	0.934	1	CLONAL	2	TRUE	0	0.45092255214854	2		574	852	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0034919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	373	606	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.45092255214854	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.45092255214854	2		606	798	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65349044	65349046	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs1184565600	NA	P-0034919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	118	389	0	ENST00000342505.4:c.119_121del	p.Phe40del	p.F40del	ENST00000342505	NM_002227.2	40	tTCTat/tat	3/25	1	2	FACETS	0.854	0.772	0.939	0.854	0.772	0.939	CLONAL	1	TRUE	1	0.45092255214854	2		389	613	SUCCESS
APC	324	MSKCC	GRCh37	5	112173723	112173723	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0034919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	156	289	0	ENST00000257430.4:c.2432C>G	p.Ser811Ter	p.S811*	ENST00000257430	NM_000038.5	811	tCa/tGa	16/16	0.45092255214854	2	FACETS	0.899	0.833	0.965	0.899	0.833	0.965	CLONAL	2	TRUE	0	0.45092255214854	2		289	385	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0034922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	38	435	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.751283308054909	6	FACETS	0.561	0.464	0.67	0.14	0.116	0.168	SUBCLONAL	1	TRUE	2	0.751283308054909	6		435	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578529	7578529	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs780442292	NA	P-0034922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	375	769	0	ENST00000269305.4:c.401T>G	p.Phe134Cys	p.F134C	ENST00000269305	NM_001126112.2	134	tTt/tGt	5/11	0.636125317896467	2	FACETS	0.965	0.934	0.996	0.965	0.934	0.996	CLONAL	2	TRUE	0	0.751283308054909	2		769	517	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361160	70361160	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs79912241	NA	P-0034922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	17	689	0	ENST00000374080.3:c.6348C>A	p.His2116Gln	p.H2116Q	ENST00000374080		2116	caC/caA	43/45	0.751283308054909	1	FACETS	0.089	0.066	0.116	0.089	0.066	0.116	SUBCLONAL	1	TRUE	0	0.751283308054909	1		689	318	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858334	89858334	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0034922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	129	308	0	ENST00000389301.3:c.1225+1G>A		p.X409_splice	ENST00000389301	NM_000135.2	409			NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.751283308054909	2		308	298	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31020666	31021125	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTTTATTTCTCCCTAGGTGAATTTACTCATGAGATGCAAGTCAGGATACGACAGGAAATGGAGAAGGAAAAGAAGGTGGAACAATGGAAAGAAAAGTTCTTTGAAGACTACTATGGACAGAAGTAAGGCAGTTGGAGCTATGAGTCCTGGTCTGGGGTTTTGAGGGGATAGAGGTAGATGGTCTCAAAATAGCATATACTTATGTGTTGGACAAGAATGTGGAGATTGCAGTGACACTTGGGTCATTTATCTTAATGCCATTCATAGTGAAGCTAACAGAAGTTTTTCCATGGTTAGATTGTGCACCACACAGATTTATTTTGTTCTGAGATATCTGTGTTTCTGGGTCCATATTATTCATAGAAATAAGAGACATGTCCACTCTGGCCTGAAACTGATGGCTGTGATTTTGATTTGCAGGCTGGGTTTGACCAAAGAAGAGTCATTGCAGCAGAACGT	GGTTTATTTCTCCCTAGGTGAATTTACTCATGAGATGCAAGTCAGGATACGACAGGAAATGGAGAAGGAAAAGAAGGTGGAACAATGGAAAGAAAAGTTCTTTGAAGACTACTATGGACAGAAGTAAGGCAGTTGGAGCTATGAGTCCTGGTCTGGGGTTTTGAGGGGATAGAGGTAGATGGTCTCAAAATAGCATATACTTATGTGTTGGACAAGAATGTGGAGATTGCAGTGACACTTGGGTCATTTATCTTAATGCCATTCATAGTGAAGCTAACAGAAGTTTTTCCATGGTTAGATTGTGCACCACACAGATTTATTTTGTTCTGAGATATCTGTGTTTCTGGGTCCATATTATTCATAGAAATAAGAGACATGTCCACTCTGGCCTGAAACTGATGGCTGTGATTTTGATTTGCAGGCTGGGTTTGACCAAAGAAGAGTCATTGCAGCAGAACGT	-	novel	NA	P-0034922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	36	153	0	ENST00000375687.4:c.980-15_1126del		p.X327_splice	ENST00000375687	NM_015338.5	327		11-12/13	0.751283308054909	4	FACETS	0.981	0.817	1	0.491	0.408	0.58	CLONAL	1	TRUE	2	0.751283308054909	4		153	171	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167457	24167457	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	134	669	0	ENST00000263121.7:c.841T>C	p.Trp281Arg	p.W281R	ENST00000263121	NM_003073.3	281	Tgg/Cgg	7/9	1	2	FACETS	0.866	0.794	0.94	0.866	0.794	0.94	CLONAL	1	TRUE	1	0.751283308054909	2		669	412	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49929220	49929220	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs147999292	NA	P-0034922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	183	717	0	ENST00000296474.3:c.3323G>T	p.Arg1108Leu	p.R1108L	ENST00000296474	NM_002447.2	1108	cGa/cTa	15/20	0.534499517871321	3	FACETS	1	0.981	1	0.581	0.539	0.624	CLONAL	1	TRUE	1	0.751283308054909	3		717	577	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249388	153249388	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	33	468	0	ENST00000281708.4:c.1390G>C	p.Val464Leu	p.V464L	ENST00000281708	NM_033632.3	464	Gtg/Ctg	9/12	0.690270895338782	2	FACETS	0.536	0.442	0.639	0.268	0.221	0.32	SUBCLONAL	1	TRUE	0	0.751283308054909	2		468	164	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0034927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	153	236	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.900100523248848	2		236	324	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	207	148	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.900100523248848	2		148	417	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413213	139413213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1311	94	1000	2	ENST00000277541.6:c.929G>A	p.Gly310Glu	p.G310E	ENST00000277541	NM_017617.3	310	gGg/gAg	6/34	1	2	FACETS	0.149	0.131	0.167	0.149	0.131	0.167	SUBCLONAL	1	TRUE	1	0.900100523248848	2		1002	1405	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs770248150	NA	P-0034927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	27	481	0	ENST00000311936.3:c.351A>C	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaC	4/5	0.378754190832731	1	FACETS	0.071	0.056	0.089	0.071	0.056	0.089	INDETERMINATE	1	TRUE	0	0.900100523248848	1		481	463	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097733	27097733	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	61	487	0	ENST00000324856.7:c.3322G>T	p.Glu1108Ter	p.E1108*	ENST00000324856	NM_006015.4	1108	Gaa/Taa	12/20	0.900100523248848	1	FACETS	0.207	0.179	0.237	0.207	0.179	0.237	SUBCLONAL	1	TRUE	0	0.900100523248848	1		487	360	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744482	41744482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752081844	NA	P-0034927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	414	724	1	ENST00000301178.4:c.1102C>T	p.Arg368Trp	p.R368W	ENST00000301178	NM_021913.4	368	Cgg/Tgg	8/20	0.900100523248848	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.900100523248848	1		725	491	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409382	31409382	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1233387563	NA	P-0034927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	156	439	0	ENST00000344624.3:c.3725A>G	p.Asn1242Ser	p.N1242S	ENST00000344624		1242	aAt/aGt	29/33	1	2	FACETS	0.903	0.837	0.969	0.903	0.837	0.969	CLONAL	1	TRUE	1	0.900100523248848	2		439	384	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967782	18967782	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	467	770	1	ENST00000262803.5:c.1921G>A	p.Ala641Thr	p.A641T	ENST00000262803	NM_002911.3	641	Gcc/Acc	14/24	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.900100523248848	2		771	1036	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0034928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	120	425	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.957	1	1	0.99	1	CLONAL	2	TRUE	1	0.3	2		425	370	SUCCESS
ATM	472	MSKCC	GRCh37	11	108126889	108126943	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TATACTAAATTATTTATGAAATATATATATTTTTATTTGTGGTTTACTTTAAGAT	TATACTAAATTATTTATGAAATATATATATTTTTATTTGTGGTTTACTTTAAGAT	-	novel	NA	P-0034928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	31	182	0	ENST00000278616.4:c.2125-51_2128del		p.X709_splice	ENST00000278616	NM_000051.3	709		14/63	1	2	FACETS	0.814	0.67	0.97	1	0.953	1	CLONAL	2	TRUE	1	0.3	2		182	127	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544669	65544674	+	inframe_deletion	In_Frame_Del	DEL	TCAATA	TCAATA	-	novel	NA	P-0034928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	74	680	0	ENST00000358664.4:c.252_257del	p.Ile85_Asp86del	p.I85_D86del	ENST00000358664	NM_002382.4	84	gaTATTGAc/gac	4/5	1	2	FACETS	0.647	0.566	0.735	0.647	0.566	0.735	SUBCLONAL	1	TRUE	1	0.3	2		680	762	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578224	7578224	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	71	556	0	ENST00000269305.4:c.625del	p.Arg209GlufsTer38	p.R209Efs*38	ENST00000269305	NM_001126112.2	209	Aga/ga	6/11	1	2	FACETS	0.668	0.582	0.76	0.668	0.582	0.76	SUBCLONAL	1	TRUE	1	0.3	2		556	709	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176684069	176684069	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs530920626	NA	P-0034928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	46	619	0	ENST00000439151.2:c.4883T>C	p.Met1628Thr	p.M1628T	ENST00000439151	NM_022455.4	1628	aTg/aCg	13/23	1	2	FACETS	0.49	0.412	0.576	0.49	0.412	0.576	SUBCLONAL	1	TRUE	1	0.3	2		619	626	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066503	94066503	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	26	297	0	ENST00000369303.4:c.1256A>T	p.Asn419Ile	p.N419I	ENST00000369303	NM_004440.3	419	aAt/aTt	5/17	0.141718104175998	3	FACETS	0.669	0.531	0.827	0.334	0.265	0.414	INDETERMINATE	1	TRUE	1	0.3	3		297	298	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974775	21974775	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs758455611	NA	P-0034928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	40	230	0	ENST00000304494.5:c.52A>C	p.Thr18Pro	p.T18P	ENST00000304494	NM_000077.4	18	Acg/Ccg	1/3	1	2	FACETS	0.76	0.633	0.9	0.76	0.633	0.9	SUBCLONAL	1	TRUE	1	0.3	2		230	351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0034929-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	45	651	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.2	2		651	371	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655403	45655403	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034929-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	25	576	0	ENST00000407780.3:c.449C>T	p.Ser150Phe	p.S150F	ENST00000407780	NM_001283052.1	150	tCc/tTc	4/7	1	2	FACETS	0.564	0.444	0.703	0.564	0.444	0.703	SUBCLONAL	1	TRUE	1	0.2	2		576	443	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0034933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	72	465	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.0800941471562449	5	FACETS	1	0.894	1	1	0.985	1	CLONAL	5	FALSE	3	0.0800941471562449	5		465	395	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685307	89685307	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123317	NA	P-0034933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	44	288	0	ENST00000371953.3:c.202T>C	p.Tyr68His	p.Y68H	ENST00000371953	NM_000314.4	68	Tac/Cac	3/9	0.0800941471562449	5	FACETS	0.973	0.822	1	1	0.975	1	CLONAL	5	FALSE	3	0.0800941471562449	5		288	253	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888189	112888189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507511	NA	P-0034933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	50	591	1	ENST00000351677.2:c.205G>A	p.Glu69Lys	p.E69K	ENST00000351677	NM_002834.3	69	Gag/Aag	3/16	1	2	FACETS	0.957	0.816	1	1	0.982	1	CLONAL	4	FALSE	1	0.0800941471562449	2		592	326	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101099	27101099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	78	726	0	ENST00000324856.7:c.4381C>T	p.Arg1461Ter	p.R1461*	ENST00000324856	NM_006015.4	1461	Cga/Tga	18/20	0.0800941471562449	4	FACETS	0.982	0.872	1	1	0.982	1	CLONAL	7	FALSE	0	0.0800941471562449	4		726	306	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258036	123258036	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519045	NA	P-0034933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	42	563	0	ENST00000358487.5:c.1645A>C	p.Asn549His	p.N549H	ENST00000358487	NM_000141.4	549	Aat/Cat	12/18	0.0800941471562449	5	FACETS	0.921	0.775	1	1	0.973	1	CLONAL	5	FALSE	3	0.0800941471562449	5		563	255	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169853	32169853	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs751390609	NA	P-0034933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	28	587	0	ENST00000375023.3:c.3755C>T	p.Thr1252Ile	p.T1252I	ENST00000375023	NM_004557.3	1252	aCt/aTt	21/30	0.0800941471562449	8	FACETS	0.951	0.764	1	0.951	0.764	1	CLONAL	4	FALSE	4	0.0800941471562449	8		587	228	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864652	57864652	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141789719	NA	P-0034933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	20	740	0	ENST00000228682.2:c.2129G>A	p.Gly710Glu	p.G710E	ENST00000228682	NM_005269.2	710	gGg/gAg	12/12	0.0800941471562449	9	FACETS	1	0.875	1	0.413	0.316	0.526	CLONAL	2	FALSE	3	0.0800941471562449	9		740	258	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350878	89350878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1336431815	NA	P-0034933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	35	976	0	ENST00000301030.4:c.2072G>A	p.Arg691His	p.R691H	ENST00000301030	NM_001256183.1	691	cGc/cAc	9/13	1	2	FACETS	1	0.879	1	1	0.973	1	CLONAL	3	FALSE	1	0.0800941471562449	2		976	268	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653864	89653870	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGGTAA	AAGGTAA	-	novel	NA	P-0034933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	36	407	0	ENST00000371953.3:c.162_164+4del		p.X54_splice	ENST00000371953	NM_000314.4	54		2/9	0.0800941471562449	5	FACETS	0.976	0.807	1	1	0.964	1	CLONAL	4	FALSE	3	0.0800941471562449	5		407	258	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589591	67589594	+	protein_altering_variant	In_Frame_Del	DEL	TATA	TATA	C	novel	NA	P-0034933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	33	190	0	ENST00000274335.5:c.1354_1357delinsC	p.Tyr452_Asn453delinsHis	p.Y452_N453delinsH	ENST00000274335		452	TATAac/Cac	10/15	0.0800941471562449	10	FACETS	0.991	0.816	1	0.991	0.816	1	CLONAL	6	FALSE	4	0.0800941471562449	10		190	183	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0034937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	173	425	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.15325512504622	3	FACETS	0.849	0.788	0.912	0.566	0.525	0.608	INDETERMINATE	2	TRUE	0	0.499205331754527	3		425	510	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0034937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	391	766	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.437032735285173	2	FACETS	0.913	0.872	0.954	0.913	0.872	0.954	CLONAL	2	TRUE	0	0.499205331754527	2		766	858	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346365	73346365	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	139	396	0	ENST00000377767.4:c.1435G>T	p.Asp479Tyr	p.D479Y	ENST00000377767	NM_014953.3	479	Gac/Tac	10/21	0.481151721340094	3	FACETS	0.956	0.881	1	0.956	0.881	1	CLONAL	2	TRUE	1	0.499205331754527	3		396	364	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013744	12013744	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0034937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	84	274	0	ENST00000353533.5:c.685+1G>T		p.X229_splice	ENST00000353533	NM_003010.3	229			0.437032735285173	2	FACETS	1	0.98	1	0.728	0.654	0.805	CLONAL	1	TRUE	0	0.499205331754527	2		274	231	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511668	38511668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	84	406	0	ENST00000254066.5:c.1166C>T	p.Ala389Val	p.A389V	ENST00000254066	NM_000964.3	389	gCc/gTc	8/9	0.499205331754527	5	FACETS	0.656	0.578	0.74	0.131	0.115	0.148	SUBCLONAL	1	TRUE	0	0.499205331754527	5		406	897	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686391	30686391	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	164	327	0	ENST00000295754.5:c.247G>T	p.Val83Phe	p.V83F	ENST00000295754	NM_003242.5	83	Gtc/Ttc	2/7	0.437032735285173	2	FACETS	0.961	0.897	1	0.961	0.897	1	CLONAL	2	TRUE	0	0.499205331754527	2		327	342	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31401654	31401667	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	ATCTGGGGAAAATT	ATCTGGGGAAAATT	-	novel	NA	P-0034937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	77	410	1	ENST00000344624.3:c.3997_4010del	p.Asn1333GlyfsTer31	p.N1333Gfs*31	ENST00000344624		1333	AATTTTCCCCAGATg/g	33/33	0.219793383935704	5	FACETS	0.777	0.682	0.88	0.259	0.227	0.294	INDETERMINATE	1	TRUE	2	0.499205331754527	5		411	694	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285901	38285901	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	129	516	0	ENST00000425967.3:c.510G>C	p.Glu170Asp	p.E170D	ENST00000425967	NM_001174067.1	170	gaG/gaC	5/19	0.458839111932934	3	FACETS	0.997	0.906	1	0.498	0.453	0.546	CLONAL	1	TRUE	1	0.499205331754527	3		516	648	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5073738	5073738	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	161	367	2	ENST00000381652.3:c.1817A>T	p.His606Leu	p.H606L	ENST00000381652	NM_004972.3	606	cAc/cTc	14/25	0.481151721340094	3	FACETS	0.886	0.82	0.953	0.886	0.82	0.953	CLONAL	2	TRUE	1	0.499205331754527	3		369	455	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436653	52436653	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	125	495	0	ENST00000460680.1:c.2021del	p.Phe674SerfsTer18	p.F674Sfs*18	ENST00000460680	NM_004656.3	674	tTc/tc	16/17	0.3	1	FACETS	0.864	0.784	0.947	0.864	0.784	0.947	CLONAL	1	TRUE	0	0.38	1		495	617	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356739	70356739	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	107	464	0	ENST00000374080.3:c.5411T>A	p.Met1804Lys	p.M1804K	ENST00000374080		1804	aTg/aAg	38/45	0.432271194584826	1	FACETS	0.299	0.269	0.33	0.299	0.269	0.33	INDETERMINATE	1	TRUE	0	0.897312823004894	1		464	440	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0034970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	52	428	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.220346492907678	1	FACETS	0.901	0.768	1	0.901	0.768	1	CLONAL	1	FALSE	0	0.220346492907678	1		428	466	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0034970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	41	507	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.220346492907678	1	FACETS	0.561	0.467	0.667	0.561	0.467	0.667	SUBCLONAL	1	FALSE	0	0.220346492907678	1		507	590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0034970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	104	580	1	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.220346492907678	2		581	824	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604656	48604656	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	42	294	0	ENST00000342988.3:c.1478A>G	p.Asp493Gly	p.D493G	ENST00000342988	NM_005359.5	493	gAt/gGt	12/12	0.220346492907678	1	FACETS	0.831	0.695	0.982	0.831	0.695	0.982	CLONAL	1	FALSE	0	0.220346492907678	1		294	408	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0034974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	10	236	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.719	1	1	0.719	1	CLONAL	1	FALSE	1	0.402857798877499	2		236	48	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0034974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	230	767	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.934	0.877	0.993	1	0.994	1	CLONAL	2	FALSE	1	0.402857798877499	2		767	611	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781371	NA	P-0034974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	149	545	0	ENST00000269305.4:c.328C>T	p.Arg110Cys	p.R110C	ENST00000269305	NM_001126112.2	110	Cgt/Tgt	4/11	1	2	FACETS	0.782	0.72	0.846	1	0.989	1	SUBCLONAL	2	FALSE	1	0.402857798877499	2		545	473	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0034975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	46	704	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.61	0.512	0.72	0.61	0.512	0.72	SUBCLONAL	1	TRUE	1	0.16	2		704	942	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53254021	53254021	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	29	262	0	ENST00000375401.3:c.51C>G	p.Phe17Leu	p.F17L	ENST00000375401	NM_004187.3	17	ttC/ttG	1/26	1	1	FACETS	0.878	0.705	1	0.878	0.705	1	CLONAL	1	TRUE	0	0.16	1		262	380	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	49	460	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.274232698371349	1	FACETS	0.711	0.603	0.829	0.711	0.603	0.829	SUBCLONAL	1	TRUE	0	0.274232698371349	1		460	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0034986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	131	573	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.772	0.702	0.844	1	0.987	1	SUBCLONAL	2	TRUE	1	0.274232698371349	2		574	619	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0034996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	157	435	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.719917565443833	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.719917565443833	3		435	263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578496	7578496	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587782197	NA	P-0034996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	527	732	1	ENST00000269305.4:c.434T>A	p.Leu145Gln	p.L145Q	ENST00000269305	NM_001126112.2	145	cTg/cAg	5/11	0.719917565443833	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.719917565443833	2		733	675	SUCCESS
APC	324	MSKCC	GRCh37	5	112175100	112175101	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0034996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	21	201	0	ENST00000257430.4:c.3814dup	p.Ser1272PhefsTer4	p.S1272Ffs*4	ENST00000257430	NM_000038.5	1270	tgt/tgTt	16/16	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.719917565443833	2		201	48	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206706	36206706	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0034996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	137	630	0	ENST00000300305.3:c.805+1G>A		p.X269_splice	ENST00000300305		269			0.220099693596384	2	FACETS	0.833	0.763	0.904	0.416	0.381	0.453	INDETERMINATE	1	TRUE	0	0.719917565443833	2		630	457	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750456	41750456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774739194	NA	P-0034996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	190	412	0	ENST00000226382.2:c.172C>T	p.Pro58Ser	p.P58S	ENST00000226382	NM_003924.3	58	Cct/Tct	1/3	0.719917565443833	3	FACETS	0.932	0.875	0.989	0.932	0.875	0.989	CLONAL	2	TRUE	1	0.719917565443833	3		412	385	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028137	69028137	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	64	512	0	ENST00000288368.4:c.3296A>T	p.His1099Leu	p.H1099L	ENST00000288368	NM_024870.2	1099	cAt/cTt	26/40	0.412925532602808	4	FACETS	1	0.94	1	0.564	0.493	0.639	INDETERMINATE	1	TRUE	2	0.719917565443833	4		512	271	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099403	157099429	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAGCAGCAACAG	CAGCAGCAGCAGCAGCAGCAGCAACAG	-	rs910569810	NA	P-0034998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	35	240	0	ENST00000346085.5:c.360_386del	p.Gln123_Gln131del	p.Q123_Q131del	ENST00000346085	NM_020732.3	114	CAGCAGCAGCAGCAGCAGCAGCAACAG/-	1/20	0.221990354578747	3	FACETS	1	0.89	1	0.552	0.457	0.657	INDETERMINATE	1	TRUE	1	0.37	3		240	203	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576856	7576856	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	76	573	0	ENST00000269305.4:c.990del	p.Gln331ArgfsTer14	p.Q331Rfs*14	ENST00000269305	NM_001126112.2	330	ctT/ct	9/11	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.37	2		573	405	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021721	71021721	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	41	330	2	ENST00000318789.4:c.1637C>A	p.Pro546Gln	p.P546Q	ENST00000318789	NM_032682.5	546	cCa/cAa	18/21	1	2	FACETS	0.642	0.537	0.759	0.642	0.537	0.759	SUBCLONAL	1	TRUE	1	0.37	2		332	345	SUCCESS
APC	324	MSKCC	GRCh37	5	112173466	112173466	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	24	237	0	ENST00000257430.4:c.2177del	p.Leu726Ter	p.L726*	ENST00000257430	NM_000038.5	725	gcT/gc	16/16	1	2	FACETS	0.786	0.622	0.972	0.786	0.622	0.972	CLONAL	1	TRUE	1	0.37	2		237	165	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913535	NA	P-0035002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	122	401	0	ENST00000311936.3:c.37G>C	p.Gly13Arg	p.G13R	ENST00000311936	NM_004985.3	13	Ggc/Cgc	2/5	0.278966057014199	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.278966057014199	1		401	590	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219336	1219336	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	167	617	0	ENST00000326873.7:c.388G>T	p.Glu130Ter	p.E130*	ENST00000326873	NM_000455.4	130	Gag/Tag	3/10	0.278966057014199	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.278966057014199	1		617	764	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8246235	8246235	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	90	486	0	ENST00000335790.3:c.399C>A	p.Asn133Lys	p.N133K	ENST00000335790	NM_002315.2	133	aaC/aaA	4/4	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.278966057014199	2		486	580	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497701	125497702	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0035002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	103	475	0	ENST00000428830.2:c.265_266delinsTT	p.Gly89Leu	p.G89L	ENST00000428830	NM_001114121.2	89	GGa/TTa	3/14	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.278966057014199	2		475	735	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398267	25398267	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	139	447	0	ENST00000311936.3:c.52G>T	p.Ala18Ser	p.A18S	ENST00000311936	NM_004985.3	18	Gcc/Tcc	2/5	0.278966057014199	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.278966057014199	1		447	652	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437110	110437110	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	25	74	0	ENST00000375856.3:c.1291A>T	p.Met431Leu	p.M431L	ENST00000375856	NM_003749.2	431	Atg/Ttg	1/2	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.278966057014199	2		74	133	SUCCESS
BLM	641	MSKCC	GRCh37	15	91341555	91341555	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs936749145	NA	P-0035002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	126	513	0	ENST00000355112.3:c.3346G>A	p.Asp1116Asn	p.D1116N	ENST00000355112	NM_000057.2	1116	Gac/Aac	17/22	1	2	FACETS	0.94	0.85	1	0.94	0.85	1	CLONAL	1	TRUE	1	0.278966057014199	2		513	961	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602890	10602890	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	198	746	0	ENST00000171111.5:c.688del	p.Thr230ProfsTer8	p.T230Pfs*8	ENST00000171111	NM_203500.1	230	Acc/cc	3/6	0.278966057014199	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.278966057014199	1		746	858	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556727	41556727	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0035002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	72	325	0	ENST00000263253.7:c.3671+1G>T		p.X1224_splice	ENST00000263253	NM_001429.3	1224			1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.278966057014199	2		325	470	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947865	178947865	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776932	NA	P-0035006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	62	384	0	ENST00000263967.3:c.2740G>A	p.Gly914Arg	p.G914R	ENST00000263967	NM_006218.2	914	Gga/Aga	19/21	1	2	FACETS	0.747	0.65	0.851	0.747	0.65	0.851	SUBCLONAL	1	TRUE	1	0.53	2		384	313	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0035006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	108	411	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	1	2	FACETS	0.926	0.837	1	0.926	0.837	1	CLONAL	1	TRUE	1	0.53	2		411	440	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0035006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	14	248	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	0.183	0.132	0.246	0.183	0.132	0.246	SUBCLONAL	1	TRUE	1	0.53	2		248	288	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251907	153251907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	112	504	0	ENST00000281708.4:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000281708	NM_033632.3	367	Cga/Tga	7/12	1	2	FACETS	0.915	0.828	1	0.915	0.828	1	CLONAL	1	TRUE	1	0.53	2		504	462	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161221	56161221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781300314	NA	P-0035006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	156	471	0	ENST00000399503.3:c.1090C>T	p.Arg364Trp	p.R364W	ENST00000399503	NM_005921.1	364	Cgg/Tgg	5/20	0.299694385134262	3	FACETS	1	0.988	1	0.727	0.67	0.786	INDETERMINATE	1	TRUE	1	0.53	3		471	512	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711993	89711993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	101	306	0	ENST00000371953.3:c.611C>T	p.Pro204Leu	p.P204L	ENST00000371953	NM_000314.4	204	cCa/cTa	6/9	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.53	2		306	336	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693000	89693000	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	86	337	0	ENST00000371953.3:c.484G>T	p.Asp162Tyr	p.D162Y	ENST00000371953	NM_000314.4	162	Gac/Tac	5/9	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.53	2		337	322	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023388	27023388	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	118	243	0	ENST00000324856.7:c.494del	p.Ala165GlyfsTer67	p.A165Gfs*67	ENST00000324856	NM_006015.4	165	gCg/gg	1/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.53	2		243	395	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717626	89717626	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	107	303	0	ENST00000371953.3:c.651del	p.Cys218AlafsTer3	p.C218Afs*3	ENST00000371953	NM_000314.4	217	gtC/gt	7/9	1	2	FACETS	0.884	0.797	0.974	0.884	0.797	0.974	CLONAL	1	TRUE	1	0.53	2		303	457	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645196	67645197	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	115	478	0	ENST00000264010.4:c.462dup	p.Cys155MetfsTer8	p.C155Mfs*8	ENST00000264010	NM_006565.3	154	ata/atAa	3/12	1	2	FACETS	0.973	0.882	1	0.973	0.882	1	CLONAL	1	TRUE	1	0.53	2		478	446	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528625	157528625	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	120	552	0	ENST00000346085.5:c.6351del	p.Arg2117SerfsTer28	p.R2117Sfs*28	ENST00000346085	NM_020732.3	2117	aGg/ag	20/20	0.114439880474351	3	FACETS	1	0.968	1	0.574	0.521	0.629	INDETERMINATE	1	TRUE	1	0.53	3		552	499	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087524	27087524	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	271	587	0	ENST00000324856.7:c.2098del	p.Val700LeufsTer42	p.V700Lfs*42	ENST00000324856	NM_006015.4	700	Gtt/tt	5/20	0.465677620976902	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	FALSE	0	0.465677620976902	2		587	574	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982384	201982385	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0035008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	263	563	0	ENST00000359651.3:c.764_765del	p.Lys255ArgfsTer45	p.K255Rfs*45	ENST00000359651		255	AAa/a	6/8	0.465677620976902	7	FACETS	0.973	0.911	1	0.389	0.364	0.415	CLONAL	2	FALSE	2	0.465677620976902	7		563	1256	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394782	394784	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0035008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	95	415	0	ENST00000399788.2:c.4911_4913del	p.His1637del	p.H1637del	ENST00000399788	NM_001042603.1	1637	caTCAa/caa	28/28	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	FALSE	NA	0.465677620976902	2		415	284	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650795	37650795	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	113	415	0	ENST00000447079.4:c.2267A>G	p.Lys756Arg	p.K756R	ENST00000447079	NM_015083.1	756	aAg/aGg	5/14	0.465677620976902	4	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	FALSE	2	0.465677620976902	4		415	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0035010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	113	487	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.26703049845079	2	FACETS	0.93	0.845	1	0.93	0.845	1	CLONAL	2	TRUE	0	0.322145962096804	2		487	377	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222986	1222986	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs864622488	NA	P-0035010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	119	368	1	ENST00000326873.7:c.923G>T	p.Trp308Leu	p.W308L	ENST00000326873	NM_000455.4	308	tGg/tTg	8/10	0.322145962096804	1	FACETS	1	0.962	1	1	0.991	1	CLONAL	2	TRUE	0	0.322145962096804	1		369	286	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988228	36988228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771777676	NA	P-0035010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	81	320	0	ENST00000354822.5:c.425G>A	p.Gly142Glu	p.G142E	ENST00000354822	NM_001079668.2	142	gGa/gAa	2/3	0.0838444336082709	4	FACETS	1	0.955	1	1	0.955	1	INDETERMINATE	2	TRUE	2	0.322145962096804	4		320	291	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129957	55129957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	83	460	0	ENST00000257290.5:c.491G>A	p.Ser164Asn	p.S164N	ENST00000257290	NM_006206.4	164	aGt/aAt	4/23	0.293691017747767	2	FACETS	1	0.968	1	0.633	0.562	0.709	CLONAL	1	TRUE	0	0.322145962096804	2		460	407	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492936	56492937	+	frameshift_variant,start_lost	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	47	173	0	ENST00000407977.2:c.2dup	p.Met1?	p.M1?	ENST00000407977		1	atg/atTg	2/10	0.26703049845079	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.322145962096804	2		173	123	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593443	48593443	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	79	329	0	ENST00000342988.3:c.1194G>A	p.Trp398Ter	p.W398*	ENST00000342988	NM_005359.5	398	tgG/tgA	10/12	0.26703049845079	2	FACETS	1	0.969	1	0.647	0.573	0.726	CLONAL	1	TRUE	0	0.322145962096804	2		329	379	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322277	31322277	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	41	315	0	ENST00000412585.2:c.1072G>T	p.Val358Leu	p.V358L	ENST00000412585	NM_005514.6	358	Gtg/Ttg	7/8	0.0838444336082709	4	FACETS	0.799	0.667	0.947	0.4	0.333	0.474	INDETERMINATE	1	TRUE	2	0.322145962096804	4		315	421	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508836	106508836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	54	305	0	ENST00000359195.3:c.830G>A	p.Arg277Gln	p.R277Q	ENST00000359195	NM_002649.2	277	cGg/cAg	2/11	0.107654478477868	5	FACETS	0.77	0.661	0.887	0.513	0.441	0.592	INDETERMINATE	2	TRUE	2	0.322145962096804	5		305	323	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295216	1295216	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0035016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	88	272	0				ENST00000310581	NM_198253.2	-/1132			0.699580307620986	3	FACETS	0.947	0.848	1			1	CLONAL	1	TRUE	NA	0.814373064318851	3		272	321	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481545	20481545	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	101	256	0	ENST00000346618.3:c.614A>T	p.Asn205Ile	p.N205I	ENST00000346618	NM_001949.4	205	aAc/aTc	3/7	0.811634571988972	2	FACETS	0.98	0.892	1	0.49	0.446	0.536	CLONAL	1	TRUE	0	0.814373064318851	2		256	253	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0035018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	72	506	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	1	2	FACETS	0.778	0.679	0.885	0.778	0.679	0.885	SUBCLONAL	1	TRUE	1	0.26	2		506	712	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101612	27101612	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	50	572	0	ENST00000324856.7:c.4899del	p.Met1634Ter	p.M1634*	ENST00000324856	NM_006015.4	1632	Ccc/cc	18/20	1	2	FACETS	0.437	0.369	0.512	0.437	0.369	0.512	SUBCLONAL	1	TRUE	1	0.26	2		572	880	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100375	27100380	+	inframe_deletion	In_Frame_Del	DEL	CAACAG	CAACAG	-	novel	NA	P-0035018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	58	396	0	ENST00000324856.7:c.4095_4100del	p.Gln1366_Gln1367del	p.Q1366_Q1367del	ENST00000324856	NM_006015.4	1363	CAACAG/-	17/20	1	2	FACETS	0.678	0.582	0.783	0.678	0.582	0.783	SUBCLONAL	1	TRUE	1	0.26	2		396	658	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0035020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	102	288	3				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		291	243	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	125	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.78006626294652	2		148	298	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916614	178916614	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0035023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	226	285	1	ENST00000263967.3:c.1A>G	p.Met1?	p.M1?	ENST00000263967	NM_006218.2	1	Atg/Gtg	2/21	0.78006626294652	3	FACETS	0.932	0.881	0.983	0.932	0.881	0.983	CLONAL	2	TRUE	1	0.78006626294652	3		286	432	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099187	157099195	+	inframe_deletion	In_Frame_Del	DEL	GCGGCGGCA	GCGGCGGCA	-	rs769480864	NA	P-0035023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	124	433	0	ENST00000346085.5:c.133_141del	p.Ala45_Ala47del	p.A45_A47del	ENST00000346085	NM_020732.3	42	GCGGCGGCA/-	1/20	1	2	FACETS	0.594	0.54	0.651	0.594	0.54	0.651	SUBCLONAL	1	TRUE	1	0.78006626294652	2		433	535	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667522	29667522	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0035023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	285	520	0	ENST00000356175.3:c.6859-1G>A		p.X2287_splice	ENST00000356175	NM_000267.3	2287			0.78006626294652	1	FACETS	0.986	0.943	1	0.986	0.943	1	CLONAL	1	TRUE	0	0.78006626294652	1		520	452	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926888	112926888	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397507546	NA	P-0035023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	266	554	0	ENST00000351677.2:c.1508G>C	p.Gly503Ala	p.G503A	ENST00000351677	NM_002834.3	503	gGg/gCg	13/16	1	2	FACETS	0.814	0.765	0.863	0.814	0.765	0.863	CLONAL	1	TRUE	1	0.78006626294652	2		554	838	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725060	89725061	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs797045066	NA	P-0035023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	71	176	0	ENST00000371953.3:c.1048dup	p.Thr350AsnfsTer11	p.T350Nfs*11	ENST00000371953	NM_000314.4	348	aca/acAa	9/9	0.78006626294652	1	FACETS	0.874	0.792	0.955	0.874	0.792	0.955	CLONAL	1	TRUE	0	0.78006626294652	1		176	127	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434646	99434646	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1361565953	NA	P-0035023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	330	590	0	ENST00000268035.6:c.733G>A	p.Asp245Asn	p.D245N	ENST00000268035	NM_000875.3	245	Gac/Aac	3/21	1	2	FACETS	0.917	0.869	0.965	0.917	0.869	0.965	CLONAL	1	TRUE	1	0.78006626294652	2		590	923	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863657	68863657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	311	553	0	ENST00000261769.5:c.2396C>T	p.Pro799Leu	p.P799L	ENST00000261769	NM_004360.3	799	cCc/cTc	15/16	1	2	FACETS	0.992	0.94	1	0.992	0.94	1	CLONAL	1	TRUE	1	0.78006626294652	2		553	804	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275311	115275311	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1307490780	NA	P-0035025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	321	806	0	ENST00000438362.2:c.1102A>G	p.Thr368Ala	p.T368A	ENST00000438362	NM_001242891.1	368	Aca/Gca	10/20	0.710537278280307	2	FACETS	0.998	0.962	1	0.998	0.962	1	CLONAL	2	TRUE	0	0.717990906142375	2		806	448	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577567	64577568	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0035025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	146	308	0	ENST00000312049.6:c.14_15del	p.Ala5GlyfsTer111	p.A5Gfs*111	ENST00000312049	NM_130799.2	5	gCC/g	2/10	0.517551437166865	3	FACETS	1	0.982	1			1	CLONAL	2	TRUE	NA	0.717990906142375	3		308	242	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939458	71939469	+	inframe_deletion	In_Frame_Del	DEL	CCCAACCAGGGC	CCCAACCAGGGC	-	novel	NA	P-0035025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	337	1077	0	ENST00000298229.2:c.314_325del	p.Pro105_Gly108del	p.P105_G108del	ENST00000298229	NM_001567.3	105	CCCAACCAGGGC/-	3/28	0.702330951072096	2	FACETS	0.837	0.802	0.871	0.837	0.802	0.871	CLONAL	2	TRUE	0	0.717990906142375	2		1077	561	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992792	72992792	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	170	662	1	ENST00000268489.5:c.1253del	p.Val418AlafsTer39	p.V418Afs*39	ENST00000268489	NM_006885.3	418	gTc/gc	2/10	0.69752062195443	2	FACETS	0.925	0.875	0.973	0.925	0.875	0.973	CLONAL	2	TRUE	0	0.717990906142375	2		663	256	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912114	76912117	+	frameshift_variant	Frame_Shift_Del	DEL	AATC	AATC	-	novel	NA	P-0035025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	150	478	0	ENST00000373344.5:c.4147_4150del	p.Asp1383PhefsTer106	p.D1383Ffs*106	ENST00000373344	NM_000489.3	1383	GATTtt/tt	13/35	0.69752062195443	2	FACETS	0.972	0.919	1	0.972	0.919	1	CLONAL	2	TRUE	0	0.717990906142375	2		478	215	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112445	115112445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	83	677	1	ENST00000257566.3:c.1295C>T	p.Ser432Leu	p.S432L	ENST00000257566	NM_016569.3	432	tCg/tTg	7/8	0.206175412839467	2	FACETS	1	0.955	1	0.585	0.516	0.659	CLONAL	1	TRUE	0	0.206175412839467	2		678	688	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	192	767	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.206175412839467	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.206175412839467	2		767	834	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	40	298	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.206175412839467	2	FACETS	1	0.919	1	0.59	0.491	0.698	CLONAL	1	TRUE	0	0.206175412839467	2		298	329	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429346	47429346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755229896	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	189	962	0	ENST00000377045.4:c.1474G>A	p.Val492Ile	p.V492I	ENST00000377045	NM_001654.4	492	Gtc/Atc	14/16	0.206175412839467	2	FACETS	0.921	0.851	0.994	0.921	0.851	0.994	CLONAL	2	TRUE	0	0.206175412839467	2		962	995	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427784	72427784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1438865674	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	47	287	0	ENST00000477973.2:c.706C>T	p.Arg236Trp	p.R236W	ENST00000477973	NM_012234.5	236	Cgg/Tgg	4/4	0.206175412839467	3	FACETS	1	0.944	1	0.635	0.537	0.743	CLONAL	1	TRUE	1	0.206175412839467	3		287	396	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313336	65313336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1163622258	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	46	611	0	ENST00000342505.4:c.1778C>T	p.Thr593Met	p.T593M	ENST00000342505	NM_002227.2	593	aCg/aTg	13/25	0.193008631906894	3	FACETS	0.756	0.636	0.89	0.378	0.318	0.445	SUBCLONAL	1	TRUE	1	0.206175412839467	3		611	651	SUCCESS
APC	324	MSKCC	GRCh37	5	112178033	112178033	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs773874693	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	27	381	2	ENST00000257430.4:c.6747del	p.Gly2250AlafsTer29	p.G2250Afs*29	ENST00000257430	NM_000038.5	2248	Aaa/aa	16/16	1	2	FACETS	0.652	0.518	0.804	0.652	0.518	0.804	SUBCLONAL	1	TRUE	1	0.206175412839467	2		383	402	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798142	42798142	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	182	857	1	ENST00000575354.2:c.4096C>T	p.Arg1366Trp	p.R1366W	ENST00000575354	NM_015125.3	1366	Cgg/Tgg	17/20	1	2	FACETS	0.915	0.844	0.989	1	0.992	1	CLONAL	2	TRUE	1	0.206175412839467	2		858	965	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223769	53223769	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376572303	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	94	1159	2	ENST00000375401.3:c.3590C>T	p.Ala1197Val	p.A1197V	ENST00000375401	NM_004187.3	1197	gCg/gTg	23/26	0.206175412839467	2	FACETS	0.869	0.772	0.974	0.435	0.386	0.487	CLONAL	1	TRUE	0	0.206175412839467	2		1161	1049	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379485	225379485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	77	503	2	ENST00000264414.4:c.383G>A	p.Arg128His	p.R128H	ENST00000264414	NM_003590.4	128	cGt/cAt	4/16	0.206175412839467	2	FACETS	0.808	0.712	0.911	0.808	0.712	0.911	CLONAL	2	TRUE	0	0.206175412839467	2		505	462	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201089	108201089	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779865	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	64	547	3	ENST00000278616.4:c.7456C>T	p.Arg2486Ter	p.R2486*	ENST00000278616	NM_000051.3	2486	Cga/Tga	50/63	0.193008631906894	3	FACETS	1	0.95	1	0.605	0.524	0.693	CLONAL	1	TRUE	1	0.206175412839467	3		550	566	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432420	49432420	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	66	888	1	ENST00000301067.7:c.8719del	p.Tyr2907ThrfsTer3	p.Y2907Tfs*3	ENST00000301067	NM_003482.3	2907	Tac/ac	34/54	0.206175412839467	2	FACETS	0.751	0.65	0.86	0.375	0.325	0.43	SUBCLONAL	1	TRUE	0	0.206175412839467	2		889	853	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62323173	62323173	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142877871	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	104	413	0	ENST00000360203.5:c.2635C>T	p.Arg879Trp	p.R879W	ENST00000360203	NM_001283009.1	879	Cgg/Tgg	28/35	0.193008631906894	3	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	1	0.206175412839467	3		413	533	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793286	242793286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757334336	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	210	990	1	ENST00000334409.5:c.791G>A	p.Arg264His	p.R264H	ENST00000334409	NM_005018.2	264	cGc/cAc	5/5	0.206175412839467	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.206175412839467	2		991	920	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702205	47702205	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750047	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	132	570	0	ENST00000233146.2:c.1801C>T	p.Gln601Ter	p.Q601*	ENST00000233146	NM_000251.2	601	Cag/Tag	12/16	0.206175412839467	2	FACETS	0.985	0.896	1	0.985	0.896	1	CLONAL	2	TRUE	0	0.206175412839467	2		570	650	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775779	9775779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1205317546	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	79	933	0	ENST00000377346.4:c.322C>T	p.Arg108Cys	p.R108C	ENST00000377346	NM_005026.3	108	Cgc/Tgc	4/24	0.193008631906894	3	FACETS	0.955	0.839	1	0.478	0.419	0.541	CLONAL	1	TRUE	1	0.206175412839467	3		933	885	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123040881	123040881	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	122	1132	0	ENST00000355640.3:c.1344G>T	p.Lys448Asn	p.K448N	ENST00000355640		448	aaG/aaT	7/7	0.206175412839467	2	FACETS	1	0.942	1	0.532	0.479	0.587	CLONAL	1	TRUE	0	0.206175412839467	2		1132	1113	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645701	12645701	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs397516826	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	24	343	0	ENST00000251849.4:c.768G>T	p.Arg256Ser	p.R256S	ENST00000251849	NM_002880.3	256	agG/agT	7/17	0.206175412839467	3	FACETS	0.563	0.441	0.705	0.282	0.22	0.353	SUBCLONAL	1	TRUE	1	0.206175412839467	3		343	456	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197308	94197308	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	138	516	1	ENST00000323929.3:c.1196del	p.Phe399SerfsTer29	p.F399Sfs*29	ENST00000323929	NM_005591.3	399	tTc/tc	11/20	0.193008631906894	3	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	1	0.206175412839467	3		517	727	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457951	69457951	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	43	524	0	ENST00000227507.2:c.355del	p.Leu119Ter	p.L119*	ENST00000227507	NM_053056.2	117	atC/at	2/5	0.193008631906894	3	FACETS	0.664	0.554	0.786	0.332	0.277	0.393	SUBCLONAL	1	TRUE	1	0.206175412839467	3		524	693	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272513	15272513	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	68	665	0	ENST00000263388.2:c.5926del	p.Leu1976TyrfsTer36	p.L1976Yfs*36	ENST00000263388	NM_000435.2	1976	Cta/ta	33/33	0.193008631906894	3	FACETS	0.969	0.842	1	0.484	0.421	0.554	CLONAL	1	TRUE	1	0.206175412839467	3		665	751	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798271	45798271	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	34	645	1	ENST00000450313.1:c.665C>A	p.Ala222Asp	p.A222D	ENST00000450313	NM_012222.2	222	gCc/gAc	8/16	0.193008631906894	3	FACETS	0.546	0.445	0.661	0.273	0.222	0.331	SUBCLONAL	1	TRUE	1	0.206175412839467	3		646	666	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115260812	115260812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375339756	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	78	652	0	ENST00000438362.2:c.2513G>A	p.Arg838His	p.R838H	ENST00000438362	NM_001242891.1	838	cGt/cAt	20/20	0.193008631906894	3	FACETS	1	0.935	1	0.55	0.482	0.622	CLONAL	1	TRUE	1	0.206175412839467	3		652	759	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261305	115261306	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	128	563	1	ENST00000438362.2:c.2415dup	p.Ile806TyrfsTer5	p.I806Yfs*5	ENST00000438362	NM_001242891.1	805	-/T	19/20	0.193008631906894	3	FACETS	0.934	0.848	1	0.934	0.848	1	CLONAL	2	TRUE	1	0.206175412839467	3		564	733	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749908	162749908	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	44	479	0	ENST00000367921.3:c.2440C>A	p.Leu814Ile	p.L814I	ENST00000367921	NM_006182.2	814	Ctc/Atc	18/18	0.206175412839467	5	FACETS	0.756	0.632	0.894	0.252	0.21	0.298	SUBCLONAL	1	TRUE	2	0.206175412839467	5		479	739	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946996	71946996	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs754591389	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	114	958	2	ENST00000298229.2:c.2845C>T	p.Arg949Ter	p.R949*	ENST00000298229	NM_001567.3	949	Cga/Tga	25/28	0.193008631906894	3	FACETS	1	0.937	1	0.53	0.476	0.588	CLONAL	1	TRUE	1	0.206175412839467	3		960	1151	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134271	41134271	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs138145556	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	47	519	0	ENST00000379561.5:c.1357A>C	p.Ser453Arg	p.S453R	ENST00000379561	NM_002015.3	453	Agt/Cgt	2/3	0.206175412839467	2	FACETS	0.857	0.723	1	0.428	0.361	0.503	CLONAL	1	TRUE	0	0.206175412839467	2		519	532	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518688	103518688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770594395	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	22	336	0	ENST00000355739.4:c.2276G>A	p.Arg759Gln	p.R759Q	ENST00000355739	NM_000123.3	759	cGg/cAg	10/15	0.206175412839467	2	FACETS	0.536	0.415	0.678	0.268	0.207	0.339	SUBCLONAL	1	TRUE	0	0.206175412839467	2		336	398	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396562	396562	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	72	965	0	ENST00000262320.3:c.464T>C	p.Ile155Thr	p.I155T	ENST00000262320	NM_003502.3	155	aTc/aCc	2/11	0.206175412839467	2	FACETS	0.737	0.642	0.84	0.368	0.321	0.42	SUBCLONAL	1	TRUE	0	0.206175412839467	2		965	948	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37672060	37672060	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	112	540	0	ENST00000447079.4:c.2845A>G	p.Ser949Gly	p.S949G	ENST00000447079	NM_015083.1	949	Agc/Ggc	9/14	0.206175412839467	2	FACETS	0.861	0.776	0.951	0.861	0.776	0.951	CLONAL	2	TRUE	0	0.206175412839467	2		540	631	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383885	15383885	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	59	606	1	ENST00000263377.2:c.26C>T	p.Thr9Met	p.T9M	ENST00000263377	NM_058243.2	9	aCg/aTg	2/20	0.193008631906894	3	FACETS	0.911	0.783	1	0.456	0.391	0.526	CLONAL	1	TRUE	1	0.206175412839467	3		607	693	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218848	36218848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774736378	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	49	805	1	ENST00000222270.7:c.4459C>T	p.Arg1487Cys	p.R1487C	ENST00000222270	NM_014727.1	1487	Cgc/Tgc	18/37	0.193008631906894	3	FACETS	0.547	0.462	0.642	0.274	0.231	0.321	SUBCLONAL	1	TRUE	1	0.206175412839467	3		806	958	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99185084	99185084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775014766	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	50	561	0	ENST00000074304.5:c.2486G>A	p.Arg829Gln	p.R829Q	ENST00000074304	NM_001134224.1	829	cGg/cAg	23/26	0.206175412839467	2	FACETS	0.821	0.696	0.958	0.41	0.348	0.479	CLONAL	1	TRUE	0	0.206175412839467	2		561	591	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713651	30713651	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769750420	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	75	509	0	ENST00000295754.5:c.976G>A	p.Ala326Thr	p.A326T	ENST00000295754	NM_003242.5	326	Gcc/Acc	4/7	0.206175412839467	3	FACETS	1	0.973	1	0.723	0.634	0.818	CLONAL	1	TRUE	1	0.206175412839467	3		509	555	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928060	49928060	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	80	684	0	ENST00000296474.3:c.3668A>G	p.Lys1223Arg	p.K1223R	ENST00000296474	NM_002447.2	1223	aAg/aGg	18/20	0.206175412839467	3	FACETS	0.976	0.858	1	0.488	0.429	0.552	CLONAL	1	TRUE	1	0.206175412839467	3		684	877	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356413	66356413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764384268	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	33	413	0	ENST00000273854.3:c.1084C>T	p.Arg362Trp	p.R362W	ENST00000273854	NM_004439.5	362	Cgg/Tgg	5/18	0.193008631906894	3	FACETS	0.761	0.619	0.921	0.381	0.309	0.461	CLONAL	1	TRUE	1	0.206175412839467	3		413	464	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38954955	38954955	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111974076	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	14	259	0	ENST00000357387.3:c.2618G>A	p.Arg873His	p.R873H	ENST00000357387	NM_152756.3	873	cGt/cAt	27/38	1	2	FACETS	0.492	0.355	0.658	0.492	0.355	0.658	SUBCLONAL	1	TRUE	1	0.206175412839467	2		259	276	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38968107	38968107	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	24	377	0	ENST00000357387.3:c.998A>G	p.Asp333Gly	p.D333G	ENST00000357387	NM_152756.3	333	gAt/gGt	12/38	1	2	FACETS	0.669	0.524	0.836	0.669	0.524	0.836	SUBCLONAL	1	TRUE	1	0.206175412839467	2		377	348	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679755	30679756	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	110	683	0	ENST00000376406.3:c.1963_1964del	p.Leu655ArgfsTer30	p.L655Rfs*30	ENST00000376406	NM_014641.2	655	CTa/a	5/15	0.170349791666832	4	FACETS	1	0.976	1	0.432	0.388	0.48	CLONAL	1	TRUE	1	0.206175412839467	4		683	992	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856054	151856054	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	34	594	1	ENST00000262189.6:c.11564A>G	p.Gln3855Arg	p.Q3855R	ENST00000262189	NM_170606.2	3855	cAg/cGg	44/59	1	2	FACETS	0.505	0.411	0.611	0.505	0.411	0.611	SUBCLONAL	1	TRUE	1	0.206175412839467	2		595	653	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917624	151917624	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	45	817	0	ENST00000262189.6:c.3696A>C	p.Glu1232Asp	p.E1232D	ENST00000262189	NM_170606.2	1232	gaA/gaC	23/59	1	2	FACETS	0.511	0.428	0.604	0.511	0.428	0.604	SUBCLONAL	1	TRUE	1	0.206175412839467	2		817	854	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982004	70982004	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	108	821	1	ENST00000276594.2:c.92C>T	p.Thr31Met	p.T31M	ENST00000276594	NM_024504.3	31	aCg/aTg	2/8	0.193008631906894	3	FACETS	0.978	0.875	1	0.489	0.437	0.544	CLONAL	1	TRUE	1	0.206175412839467	3		822	1182	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141568597	141568597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	67	638	0	ENST00000220592.5:c.865G>A	p.Ala289Thr	p.A289T	ENST00000220592	NM_012154.3	289	Gcc/Acc	7/19	0.206175412839467	5	FACETS	0.869	0.753	0.996	0.29	0.251	0.332	CLONAL	1	TRUE	2	0.206175412839467	5		638	979	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786923	135786923	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs535868591	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	31	430	0	ENST00000298552.3:c.946C>T	p.Arg316Trp	p.R316W	ENST00000298552	NM_001162426.1	316	Cgg/Tgg	10/23	0.206175412839467	2	FACETS	0.641	0.518	0.781	0.321	0.259	0.391	SUBCLONAL	1	TRUE	0	0.206175412839467	2		430	469	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391001	139391001	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	135	1107	2	ENST00000277541.6:c.7190T>C	p.Leu2397Pro	p.L2397P	ENST00000277541	NM_017617.3	2397	cTg/cCg	34/34	0.206175412839467	2	FACETS	1	0.967	1	0.572	0.518	0.628	CLONAL	1	TRUE	0	0.206175412839467	2		1109	1145	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401333	139401333	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	221	918	0	ENST00000277541.6:c.3736del	p.Asp1246ThrfsTer199	p.D1246Tfs*199	ENST00000277541	NM_017617.3	1246	Gac/ac	23/34	0.206175412839467	2	FACETS	0.979	0.91	1	0.979	0.91	1	CLONAL	2	TRUE	0	0.206175412839467	2		918	1095	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80646135	80646135	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1264916735	NA	P-0035031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	16	88	0	ENST00000286548.4:c.17T>C	p.Ile6Thr	p.I6T	ENST00000286548	NM_002072.3	6	aTc/aCc	1/7	0.206175412839467	2	FACETS	1	0.886	1	0.699	0.523	0.904	CLONAL	1	TRUE	0	0.206175412839467	2		88	111	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579559	7579559	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	110	584	0	ENST00000269305.4:c.128del	p.Leu43Ter	p.L43*	ENST00000269305	NM_001126112.2	43	tTg/tg	4/11	0.410567944074985	1	FACETS	0.856	0.773	0.943	0.856	0.773	0.943	CLONAL	1	TRUE	0	0.423103729617827	1		584	479	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373461	118373461	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	115	322	0	ENST00000534358.1:c.6854G>T	p.Gly2285Val	p.G2285V	ENST00000534358	NM_005933.3	2285	gGa/gTa	27/36	0.316962649464807	3	FACETS	1	0.977	1	0.801	0.734	0.869	CLONAL	2	TRUE	0	0.423103729617827	3		322	274	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953775	48953807	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATGCTTAAATCAGTAAGTTAAAAACAATATAAA	ATGCTTAAATCAGTAAGTTAAAAACAATATAAA	-	novel	NA	P-0035064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	80	252	1	ENST00000267163.4:c.1379_1389+22del		p.X460_splice	ENST00000267163	NM_000321.2	460		14/27	0.423103729617827	3	FACETS	1	0.963	1	0.406	0.36	0.455	CLONAL	1	TRUE	0	0.423103729617827	3		253	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579559	7579559	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	165	584	0	ENST00000269305.4:c.128del	p.Leu43Ter	p.L43*	ENST00000269305	NM_001126112.2	43	tTg/tg	4/11	0.236464449389176	2	FACETS	1	0.986	1	0.665	0.611	0.721	CLONAL	1	FALSE	0	0.316072722658702	2		584	785	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373461	118373461	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	173	322	0	ENST00000534358.1:c.6854G>T	p.Gly2285Val	p.G2285V	ENST00000534358	NM_005933.3	2285	gGa/gTa	27/36	0.268580720786662	4	FACETS	0.929	0.861	0.998			1	CLONAL	3	FALSE	NA	0.316072722658702	4		322	517	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953775	48953807	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATGCTTAAATCAGTAAGTTAAAAACAATATAAA	ATGCTTAAATCAGTAAGTTAAAAACAATATAAA	-	novel	NA	P-0035064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	72	252	1	ENST00000267163.4:c.1379_1389+22del		p.X460_splice	ENST00000267163	NM_000321.2	460		14/27	0.291281838668366	3	FACETS	1	0.922	1	0.357	0.313	0.405	CLONAL	1	FALSE	0	0.316072722658702	3		253	492	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182681760	182681760	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	49	476	0	ENST00000292782.4:c.298A>C	p.Ile100Leu	p.I100L	ENST00000292782	NM_020640.2	100	Att/Ctt	3/7	0.220263916230654	3	FACETS	0.383	0.323	0.45	0.192	0.161	0.225	SUBCLONAL	1	FALSE	1	0.316072722658702	3		476	937	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965366	68965366	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	114	676	0	ENST00000288368.4:c.978T>A	p.Asn326Lys	p.N326K	ENST00000288368	NM_024870.2	326	aaT/aaA	9/40	0.772827669272186	3	FACETS	1	0.934	1	0.518	0.47	0.567	CLONAL	1	TRUE	1	0.772827669272186	3		676	395	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0035066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	117	207	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.225839994293093	3	FACETS	1	0.963	1	0.553	0.504	0.603	INDETERMINATE	1	TRUE	1	0.839260838234034	3		207	358	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579321	7579322	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs587780067	NA	P-0035066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	297	473	0	ENST00000269305.4:c.365_366del	p.Val122AspfsTer26	p.V122Dfs*26	ENST00000269305	NM_001126112.2	122	gTG/g	4/11	0.839260838234034	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.839260838234034	1		473	354	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696598	47696598	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	289	445	0	ENST00000347630.2:c.350T>C	p.Met117Thr	p.M117T	ENST00000347630	NM_001007230.1	117	aTg/aCg	5/11	0.839260838234034	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.839260838234034	2		445	343	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24129447	24129447	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	32	212	0	ENST00000263121.7:c.91G>A	p.Glu31Lys	p.E31K	ENST00000263121	NM_003073.3	31	Gag/Aag	1/9	0.388089682448296	5	FACETS	0.533	0.434	0.645	0.178	0.144	0.215	INDETERMINATE	1	TRUE	2	0.839260838234034	5		212	323	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845309	76845309	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	121	365	0	ENST00000373344.5:c.6212A>T	p.Tyr2071Phe	p.Y2071F	ENST00000373344	NM_000489.3	2071	tAt/tTt	27/35	0.35700106110802	1	FACETS	0.526	0.482	0.572	0.526	0.482	0.572	INDETERMINATE	1	TRUE	0	0.839260838234034	1		365	318	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0035068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	111	451	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.972	0.878	1	0.972	0.878	1	CLONAL	1	TRUE	1	0.448559820020457	2		451	509	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0035068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	107	313	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.448559820020457	2		313	445	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867298	68867299	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0035068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	156	538	0	ENST00000261769.5:c.2545_2546del	p.Asn849LeufsTer11	p.N849Lfs*11	ENST00000261769	NM_004360.3	849	AAc/c	16/16	0.448559820020457	1	FACETS	0.999	0.921	1	0.999	0.921	1	CLONAL	1	TRUE	0	0.448559820020457	1		538	540	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816483	32816483	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	228	852	0	ENST00000354258.4:c.1692G>T	p.Gln564His	p.Q564H	ENST00000354258	NM_000593.5	564	caG/caT	7/11	1	2	FACETS	0.951	0.886	1	0.951	0.886	1	CLONAL	1	TRUE	1	0.448559820020457	2		852	1069	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008896	152008897	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAGG	novel	NA	P-0035068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	118	411	0	ENST00000262189.6:c.722_725dup	p.Leu242PhefsTer4	p.L242Ffs*4	ENST00000262189	NM_170606.2	242	tta/ttCCTTa	5/59	1	2	FACETS	0.827	0.748	0.911	0.827	0.748	0.911	CLONAL	1	TRUE	1	0.448559820020457	2		411	636	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696601	47696601	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	109	486	0	ENST00000347630.2:c.347C>G	p.Ala116Gly	p.A116G	ENST00000347630	NM_001007230.1	116	gCt/gGt	5/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.717144211217993	2		486	285	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961360	1961360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1047838051	NA	P-0035070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	213	607	1	ENST00000382891.5:c.3148G>A	p.Glu1050Lys	p.E1050K	ENST00000382891	NM_133335.3	1050	Gag/Aag	17/22	1	2	FACETS	0.924	0.863	0.986	0.924	0.863	0.986	CLONAL	1	TRUE	1	0.717144211217993	2		608	643	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114262	143114262	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	84	419	0	ENST00000262992.4:c.1159A>G	p.Arg387Gly	p.R387G	ENST00000262992	NM_001101669.1	387	Aga/Gga	13/24	1	2	FACETS	0.891	0.798	0.987	0.891	0.798	0.987	CLONAL	1	TRUE	1	0.717144211217993	2		419	263	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176618884	176618884	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0035070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	86	441	0	ENST00000439151.2:c.928-1G>A		p.X310_splice	ENST00000439151	NM_022455.4	310			1	2	FACETS	0.808	0.723	0.896	0.808	0.723	0.896	CLONAL	1	TRUE	1	0.717144211217993	2		441	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0035071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	129	732	0	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.303702617855045	1	FACETS	0.903	0.819	0.991	0.903	0.819	0.991	CLONAL	1	TRUE	0	0.303702617855045	1		732	798	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129699	11129699	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	78	687	0	ENST00000358026.2:c.2505G>T	p.Lys835Asn	p.K835N	ENST00000358026	NM_001128849.1	835	aaG/aaT	17/36	0.303702617855045	1	FACETS	0.736	0.647	0.831	0.736	0.647	0.831	SUBCLONAL	1	TRUE	0	0.303702617855045	1		687	592	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678776	52678780	+	frameshift_variant	Frame_Shift_Del	DEL	ATAAA	ATAAA	-	novel	NA	P-0035071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	65	415	0	ENST00000394830.3:c.839_843del	p.Phe280TyrfsTer5	p.F280Yfs*5	ENST00000394830	NM_018313.4	280	tTTTAT/t	9/30	0.303702617855045	1	FACETS	0.873	0.759	0.994	0.873	0.759	0.994	CLONAL	1	TRUE	0	0.303702617855045	1		415	416	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0035072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	538	704	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.692911748793862	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.692911748793862	3		704	1023	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879604	37879604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196929947	NA	P-0035072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	634	899	0	ENST00000269571.5:c.1979G>A	p.Gly660Asp	p.G660D	ENST00000269571		660	gGc/gAc	17/27	0.692911748793862	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.692911748793862	3		899	1202	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578251	7578251	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	246	708	0	ENST00000269305.4:c.598A>T	p.Asn200Tyr	p.N200Y	ENST00000269305	NM_001126112.2	200	Aat/Tat	6/11	0.692911748793862	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.692911748793862	1		708	418	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247174	153247174	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	111	325	0	ENST00000281708.4:c.1628G>C	p.Arg543Thr	p.R543T	ENST00000281708	NM_033632.3	543	aGa/aCa	10/12	1	2	FACETS	0.885	0.804	0.969	0.885	0.804	0.969	CLONAL	1	TRUE	1	0.692911748793862	2		325	362	SUCCESS
APC	324	MSKCC	GRCh37	5	112175389	112175392	+	frameshift_variant	Frame_Shift_Del	DEL	TCAG	TCAG	GC	novel	NA	P-0035072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	88	273	1	ENST00000257430.4:c.4098_4101delinsGC	p.Gln1367HisfsTer7	p.Q1367Hfs*7	ENST00000257430	NM_000038.5	1366	gcTCAG/gcGC	16/16	0.692911748793862	3	FACETS	0.914	0.816	1	0.457	0.408	0.509	CLONAL	1	TRUE	1	0.692911748793862	3		274	374	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323002	31323002	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs41559119	NA	P-0035072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	226	842	0	ENST00000412585.2:c.896-2A>G		p.X299_splice	ENST00000412585	NM_005514.6	299			0.692911748793862	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.692911748793862	1		842	410	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849314	76849314	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	166	410	0	ENST00000373344.5:c.5962G>T	p.Ala1988Ser	p.A1988S	ENST00000373344	NM_000489.3	1988	Gct/Tct	26/35	0.158727129377286	4	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.692911748793862	4		410	652	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0035074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	17	440	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	1	2	FACETS	0.153	0.113	0.2	0.153	0.113	0.2	SUBCLONAL	1	TRUE	1	0.414979521871176	2		440	536	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155491	106155491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	63	315	0	ENST00000380013.4:c.392G>A	p.Arg131Lys	p.R131K	ENST00000380013	NM_001127208.2	131	aGa/aAa	3/11	1	2	FACETS	0.839	0.729	0.956	0.839	0.729	0.956	CLONAL	1	TRUE	1	0.414979521871176	2		315	362	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911254	29911254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41541015	NA	P-0035074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	14	278	0	ENST00000376809.5:c.553G>A	p.Asp185Asn	p.D185N	ENST00000376809	NM_002116.7	185	Gat/Aat	3/8	0.414979521871176	1	FACETS	0.245	0.177	0.328	0.245	0.177	0.328	SUBCLONAL	1	TRUE	0	0.414979521871176	1		278	218	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323093	31323093	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs111351373	NA	P-0035074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	45	756	0	ENST00000412585.2:c.895+1G>T		p.X299_splice	ENST00000412585	NM_005514.6	299			0.414979521871176	1	FACETS	0.302	0.253	0.355	0.302	0.253	0.355	SUBCLONAL	1	TRUE	0	0.414979521871176	1		756	570	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94128989	94128989	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs200143358	NA	P-0035074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	62	323	0	ENST00000369303.4:c.71C>G	p.Thr24Arg	p.T24R	ENST00000369303	NM_004440.3	24	aCa/aGa	1/17	1	2	FACETS	0.766	0.665	0.876	0.766	0.665	0.876	SUBCLONAL	1	TRUE	1	0.414979521871176	2		323	390	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	143	460	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.297893922250187	2	FACETS	0.802	0.745	0.861	0.802	0.745	0.861	INDETERMINATE	2	TRUE	0	0.582361037483896	2		460	306	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0035078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	77	451	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.221631329766876	3	FACETS	1	0.958	1	0.587	0.52	0.656	INDETERMINATE	1	TRUE	1	0.582361037483896	3		451	291	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0035078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	68	240	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.349618244406127	3	FACETS	0.815	0.724	0.909	0.815	0.724	0.909	CLONAL	2	TRUE	1	0.582361037483896	3		240	185	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0035078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	42	238	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.349618244406127	3	FACETS	0.991	0.838	1	0.495	0.419	0.578	CLONAL	1	TRUE	1	0.582361037483896	3		238	188	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0035078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	261	673	0	ENST00000269305.4:c.96+1G>A		p.X32_splice	ENST00000269305	NM_001126112.2	32			0.582361037483896	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.582361037483896	1		673	573	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980343	55980343	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs140419104	NA	P-0035078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	100	514	0	ENST00000263923.4:c.748A>G	p.Thr250Ala	p.T250A	ENST00000263923	NM_002253.2	250	Act/Gct	6/30	0.359844956553089	1	FACETS	0.761	0.687	0.837	0.761	0.687	0.837	SUBCLONAL	1	TRUE	0	0.582361037483896	1		514	320	SUCCESS
APC	324	MSKCC	GRCh37	5	112154723	112154724	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAACTTTGCT	novel	NA	P-0035078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	198	559	1	ENST00000257430.4:c.995_1004dup	p.Ala336AsnfsTer7	p.A336Nfs*7	ENST00000257430	NM_000038.5	332	cga/cGAACTTTGCTga	10/16	0.349618244406127	3	FACETS	1	0.991	1	0.737	0.686	0.788	CLONAL	1	TRUE	1	0.582361037483896	3		560	596	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372698	81372698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371502313	NA	P-0035078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	82	357	2	ENST00000222390.5:c.836G>A	p.Arg279His	p.R279H	ENST00000222390	NM_000601.4	279	cGc/cAc	7/18	0.582361037483896	3	FACETS	0.799	0.707	0.897	0.4	0.353	0.449	SUBCLONAL	1	TRUE	1	0.582361037483896	3		359	455	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	27	460	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.281486173289911	1	FACETS	0.741	0.596	0.905	0.741	0.596	0.905	CLONAL	1	TRUE	0	0.352824465989674	1		460	170	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578467	7578467	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1517	284	724	0	ENST00000269305.4:c.463A>C	p.Thr155Pro	p.T155P	ENST00000269305	NM_001126112.2	155	Acc/Ccc	5/11	0.352824465989674	1	FACETS	0.736	0.689	0.785	0.736	0.689	0.785	SUBCLONAL	1	TRUE	0	0.352824465989674	1		724	1801	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031750	36031750	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879255268	NA	P-0035079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	202	525	1	ENST00000358208.4:c.1579G>A	p.Glu527Lys	p.E527K	ENST00000358208		527	Gag/Aag	12/12	1	2	FACETS	0.877	0.811	0.946	0.877	0.811	0.946	CLONAL	1	TRUE	1	0.352824465989674	2		526	1305	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307414	118307416	+	inframe_deletion	In_Frame_Del	DEL	GCG	GCG	-	rs781936420	NA	P-0035079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	10	17	0	ENST00000534358.1:c.200_202del	p.Ala67del	p.A67del	ENST00000534358	NM_005933.3	63	GCG/-	1/36	1	2	FACETS	0.746	0.512	1	0.746	0.512	1	CLONAL	1	TRUE	1	0.352824465989674	2		17	76	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395698	31395698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	136	356	0	ENST00000328111.2:c.2551G>A	p.Ala851Thr	p.A851T	ENST00000328111	NM_006892.3	851	Gca/Aca	23/23	1	2	FACETS	0.812	0.738	0.891	0.812	0.738	0.891	CLONAL	1	TRUE	1	0.352824465989674	2		356	949	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0035080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	136	425	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.123164089434161	3	FACETS	0.898	0.824	0.975	0.599	0.549	0.65	INDETERMINATE	2	TRUE	0	0.414409982268626	3		425	441	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235935	108235935	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770641163	NA	P-0035080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	114	409	0	ENST00000278616.4:c.8977C>T	p.Arg2993Ter	p.R2993*	ENST00000278616	NM_000051.3	2993	Cga/Tga	62/63	0.414409982268626	2	FACETS	0.852	0.777	0.929	0.852	0.777	0.929	CLONAL	2	TRUE	0	0.414409982268626	2		409	323	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434170	121434170	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	308	692	1	ENST00000257555.6:c.1061C>A	p.Thr354Lys	p.T354K	ENST00000257555		354	aCg/aAg	5/10	0.414542422546745	4	FACETS	0.991	0.941	1	0.991	0.941	1	CLONAL	3	TRUE	1	0.414409982268626	4		693	707	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042345	42042345	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	120	530	0	ENST00000219905.7:c.6543del	p.Leu2182Ter	p.L2182*	ENST00000219905	NM_001164273.1	2180	ggC/gg	17/24	0.382131982465495	2	FACETS	1	0.986	1	0.748	0.682	0.817	CLONAL	1	TRUE	0	0.414409982268626	2		530	387	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679351	29679351	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	139	414	0	ENST00000356175.3:c.7472del	p.Gly2491AlafsTer11	p.G2491Afs*11	ENST00000356175	NM_000267.3	2491	Ggc/gc	50/57	0.414542422546745	3	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	1	0.414409982268626	3		414	388	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428224	47428228	+	missense_variant	Missense_Mutation	ONP	ATGTG	ATGTG	GTGTT	novel	NA	P-0035080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	92	835	0	ENST00000377045.4:c.1184_1188delinsGTGTT	p.His395Arg	p.H395R	ENST00000377045	NM_001654.4	395	cATGTG/cGTGTT	11/16	0.414542422546745	1	FACETS	0.878	0.785	0.975	0.878	0.785	0.975	CLONAL	1	TRUE	0	0.414409982268626	1		835	401	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0035083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	65	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.928	0.805	1	0.928	0.805	1	CLONAL	1	TRUE	1	0.26487757306447	2		502	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0035083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	147	750	1	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.26487757306447	1	FACETS	0.983	0.896	1	0.983	0.896	1	CLONAL	1	TRUE	0	0.26487757306447	1		751	980	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0035093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	502	463	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.592851501739973	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.693689498702888	3		463	965	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141586	202141586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760898260	NA	P-0035093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	207	354	0	ENST00000358485.4:c.874C>T	p.Arg292Trp	p.R292W	ENST00000358485	NM_001080125.1	292	Cgg/Tgg	7/9	1	2	FACETS	0.983	0.918	1	0.983	0.918	1	CLONAL	1	TRUE	1	0.693689498702888	2		354	607	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0035093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	451	490	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.592851501739973	3	FACETS	0.962	0.924	1	0.962	0.924	1	CLONAL	2	TRUE	1	0.693689498702888	3		490	910	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100436	8100436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1220437638	NA	P-0035093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	352	643	1	ENST00000346208.3:c.410C>T	p.Ser137Leu	p.S137L	ENST00000346208		137	tCg/tTg	3/6	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.693689498702888	2		644	931	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740875	58740875	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	206	396	0	ENST00000305921.3:c.1780T>G	p.Leu594Val	p.L594V	ENST00000305921	NM_003620.3	594	Tta/Gta	6/6	1	2	FACETS	0.969	0.904	1	0.969	0.904	1	CLONAL	1	TRUE	1	0.693689498702888	2		396	613	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0035097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	282	451	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.794576341728771	4	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	2	0.79183668772529	4		451	625	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579536	7579536	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	577	761	1	ENST00000269305.4:c.151del	p.Glu51AsnfsTer72	p.E51Nfs*72	ENST00000269305	NM_001126112.2	51	Gaa/aa	4/11	0.794576341728771	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.79183668772529	2		762	716	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349500	73349500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	139	455	0	ENST00000377767.4:c.836G>A	p.Gly279Glu	p.G279E	ENST00000377767	NM_014953.3	279	gGa/gAa	6/21	0.716639503111727	4	FACETS	0.943	0.861	1	0.472	0.43	0.515	CLONAL	1	TRUE	2	0.79183668772529	4		455	667	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630843	187630843	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	256	567	0	ENST00000441802.2:c.139T>A	p.Ser47Thr	p.S47T	ENST00000441802	NM_005245.3	47	Tct/Act	2/27	0.794576341728771	3	FACETS	1	0.98	1	0.55	0.516	0.584	CLONAL	1	TRUE	1	0.79183668772529	3		567	821	SUCCESS
AR	367	MSKCC	GRCh37	X	66905969	66905969	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0035097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	125	377	0	ENST00000374690.3:c.1885+1G>T		p.X629_splice	ENST00000374690	NM_000044.3	629			0.315504408545942	5	FACETS	1	0.938	1			1	INDETERMINATE	1	TRUE	NA	0.79183668772529	5		377	661	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434652	99434652	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1233649195	NA	P-0035098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	271	589	0	ENST00000268035.6:c.739G>A	p.Ala247Thr	p.A247T	ENST00000268035	NM_000875.3	247	Gcc/Acc	3/21	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	FALSE	1	0.568186985961948	2		589	648	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	105	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.616402562369259	2		148	286	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0035099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	307	524	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.616402562369259	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.616402562369259	2		524	498	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578393	7578393	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876660821	NA	P-0035099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	350	661	0	ENST00000269305.4:c.537T>G	p.His179Gln	p.H179Q	ENST00000269305	NM_001126112.2	179	caT/caG	5/11	NA	2	FACETS	0.89	0.852	0.928			1	INDETERMINATE	2	TRUE	NA	0.616402562369259	2		661	638	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419112	419112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778494527	NA	P-0035099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	227	378	1	ENST00000399788.2:c.3235G>A	p.Asp1079Asn	p.D1079N	ENST00000399788	NM_001042603.1	1079	Gac/Aac	22/28	0.522718711044525	3	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	1	0.616402562369259	3		379	481	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555525970	NA	P-0035099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	343	632	0	ENST00000269305.4:c.548C>T	p.Ser183Leu	p.S183L	ENST00000269305	NM_001126112.2	183	tCa/tTa	5/11	NA	2	FACETS	0.931	0.891	0.969			1	INDETERMINATE	2	TRUE	NA	0.616402562369259	2		632	598	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197691	123197699	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTGCAGCA	TTTGCAGCA	-	novel	NA	P-0035099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	93	291	0	ENST00000218089.9:c.1822-3_1827del		p.X608_splice	ENST00000218089	NM_001042749.1	608		20/35	0.182855002517007	4	FACETS	1	0.962	1	0.388	0.347	0.431	INDETERMINATE	1	TRUE	1	0.616402562369259	4		291	419	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	96	460	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.467662711621852	3	FACETS	0.878	0.794	0.964	0.878	0.794	0.964	CLONAL	2	TRUE	1	0.507925544958131	3		460	270	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757274881	NA	P-0035105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	294	932	1	ENST00000269305.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	144	Cag/Tag	5/11	0.507836381070063	1	FACETS	0.926	0.873	0.979	0.926	0.873	0.979	CLONAL	1	TRUE	0	0.507925544958131	1		933	933	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023258	27023265	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCGG	GGCGGCGG	C	novel	NA	P-0035105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	61	160	0	ENST00000324856.7:c.364_371delinsC	p.Gly122ProfsTer108	p.G122Pfs*108	ENST00000324856	NM_006015.4	122	GGCGGCGGc/Cc	1/20	1	2	FACETS	0.677	0.587	0.773	0.677	0.587	0.773	SUBCLONAL	1	TRUE	1	0.507925544958131	2		160	355	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0035106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	336	745	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.441233284672737	2	FACETS	0.907	0.863	0.951	0.907	0.863	0.951	CLONAL	2	TRUE	0	0.485532552209288	2		745	763	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215244	142215244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	131	473	1	ENST00000350721.4:c.5857G>A	p.Ala1953Thr	p.A1953T	ENST00000350721	NM_001184.3	1953	Gct/Act	34/47	1	2	FACETS	0.872	0.793	0.954	0.872	0.793	0.954	CLONAL	1	TRUE	1	0.485532552209288	2		474	619	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959064	2959064	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	334	668	1	ENST00000396946.4:c.2452C>T	p.Arg818Trp	p.R818W	ENST00000396946	NM_032415.4	818	Cgg/Tgg	18/25	0.365005291640403	5	FACETS	0.972	0.919	1	0.648	0.612	0.685	CLONAL	2	TRUE	2	0.485532552209288	5		669	1223	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874945	151874945	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	169	410	1	ENST00000262189.6:c.7593G>T	p.Met2531Ile	p.M2531I	ENST00000262189	NM_170606.2	2531	atG/atT	38/59	0.407964775586742	3	FACETS	0.784	0.725	0.844	0.522	0.483	0.563	SUBCLONAL	2	TRUE	0	0.485532552209288	3		411	552	SUCCESS
APC	324	MSKCC	GRCh37	5	112175189	112175189	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	91	254	0	ENST00000257430.4:c.3899del	p.Asn1300IlefsTer5	p.N1300Ifs*5	ENST00000257430	NM_000038.5	1300	Aat/at	16/16	0.441233284672737	2	FACETS	0.844	0.765	0.925	0.844	0.765	0.925	CLONAL	2	TRUE	0	0.485532552209288	2		254	222	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618689	37618690	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	180	469	0	ENST00000447079.4:c.366dup	p.Leu123ThrfsTer4	p.L123Tfs*4	ENST00000447079	NM_015083.1	122	tta/ttAa	1/14	0.547676268193391	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.547676268193391	1		469	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577537	7577537	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	659	715	0	ENST00000269305.4:c.744del	p.Arg249GlyfsTer96	p.R249Gfs*96	ENST00000269305	NM_001126112.2	248	cgG/cg	7/11	0.547676268193391	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.547676268193391	1		715	1316	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798154	42798154	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1607	165	790	0	ENST00000575354.2:c.4108G>C	p.Val1370Leu	p.V1370L	ENST00000575354	NM_015125.3	1370	Gtg/Ctg	17/20	0.31180373253651	6	FACETS	0.712	0.651	0.777	0.178	0.162	0.195	INDETERMINATE	1	TRUE	2	0.547676268193391	6		790	1772	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962637	38962637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753508286	NA	P-0035118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	18	410	0	ENST00000357387.3:c.1618C>T	p.His540Tyr	p.H540Y	ENST00000357387	NM_152756.3	540	Cat/Tat	18/38	0.267084660185695	1	FACETS	0.3	0.227	0.385	0.3	0.227	0.385	INDETERMINATE	1	TRUE	0	0.547676268193391	1		410	159	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0035137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	20	463	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.564	0.43	0.722	0.564	0.43	0.722	SUBCLONAL	1	TRUE	1	0.15	2		463	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0035137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	44	614	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.15	2		614	482	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100310	8100311	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0035137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	37	686	1	ENST00000346208.3:c.284_285delinsAA	p.Pro95Gln	p.P95Q	ENST00000346208		95	cCC/cAA	3/6	0.133424309718214	3	FACETS	0.891	0.733	1	0.446	0.366	0.535	CLONAL	1	TRUE	1	0.15	3		687	595	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136270	64136270	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0035137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	29	549	0	ENST00000334205.4:c.1428+1G>T		p.X476_splice	ENST00000334205	NM_003942.2	476			1	2	FACETS	0.867	0.695	1	0.867	0.695	1	CLONAL	1	TRUE	1	0.15	2		549	446	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73348124	73348124	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	23	481	0	ENST00000377767.4:c.1061G>T	p.Arg354Ile	p.R354I	ENST00000377767	NM_014953.3	354	aGa/aTa	7/21	0.383716347435465	3	FACETS	0.804	0.626	1	0.402	0.313	0.506	CLONAL	1	TRUE	1	0.15	3		481	410	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515435	103515435	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748923127	NA	P-0035137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	14	255	0	ENST00000355739.4:c.1936G>A	p.Glu646Lys	p.E646K	ENST00000355739	NM_000123.3	646	Gaa/Aaa	8/15	0.383716347435465	3	FACETS	0.92	0.666	1	0.46	0.333	0.614	CLONAL	1	TRUE	1	0.15	3		255	218	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194800	30194800	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs765346110	NA	P-0035137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	38	616	0	ENST00000331968.5:c.345G>C	p.Gln115His	p.Q115H	ENST00000331968	NM_002742.2	115	caG/caC	2/18	0.133424309718214	3	FACETS	0.967	0.799	1	0.484	0.399	0.579	CLONAL	1	TRUE	1	0.15	3		616	563	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220707	1220707	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	34	579	0	ENST00000326873.7:c.725G>T	p.Gly242Val	p.G242V	ENST00000326873	NM_000455.4	242	gGg/gTg	5/10	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.15	2		579	433	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210728	2210728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745700742	NA	P-0035137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	21	569	0	ENST00000398665.3:c.1225C>T	p.Arg409Cys	p.R409C	ENST00000398665	NM_032482.2	409	Cgc/Tgc	14/28	1	2	FACETS	0.683	0.525	0.868	0.683	0.525	0.868	SUBCLONAL	1	TRUE	1	0.15	2		569	410	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911488	134911488	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	27	486	0	ENST00000398015.3:c.1953G>T	p.Lys651Asn	p.K651N	ENST00000398015	NM_004441.4	651	aaG/aaT	11/16	1	2	FACETS	0.678	0.538	0.839	0.678	0.538	0.839	SUBCLONAL	1	TRUE	1	0.15	2		486	531	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217561	142217561	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	29	482	0	ENST00000350721.4:c.5436A>T	p.Lys1812Asn	p.K1812N	ENST00000350721	NM_001184.3	1812	aaA/aaT	32/47	1	2	FACETS	1	0.826	1	1	0.826	1	CLONAL	1	TRUE	1	0.15	2		482	375	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519178	187519178	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	29	465	0	ENST00000441802.2:c.12205G>T	p.Val4069Phe	p.V4069F	ENST00000441802	NM_005245.3	4069	Gtc/Ttc	23/27	0.133424309718214	3	FACETS	0.868	0.695	1	0.434	0.347	0.532	CLONAL	1	TRUE	1	0.15	3		465	479	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271572	26271572	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	25	297	0	ENST00000305910.3:c.41del	p.Gly14AlafsTer23	p.G14Afs*23	ENST00000305910	NM_003534.2	14	gGc/gc	1/1	0.292414472215609	3	FACETS	0.813	0.639	1	0.406	0.319	0.506	CLONAL	1	TRUE	1	0.15	3		297	441	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729515	41729515	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	26	578	0	ENST00000242208.4:c.1014G>C	p.Trp338Cys	p.W338C	ENST00000242208	NM_002192.2	338	tgG/tgC	3/3	0.133424309718214	3	FACETS	0.767	0.606	0.952	0.383	0.303	0.476	CLONAL	1	TRUE	1	0.15	3		578	486	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287319	38287319	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	26	649	1	ENST00000425967.3:c.338G>T	p.Arg113Leu	p.R113L	ENST00000425967	NM_001174067.1	113	cGc/cTc	4/19	1	2	FACETS	0.682	0.539	0.847	0.682	0.539	0.847	SUBCLONAL	1	TRUE	1	0.15	2		650	508	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101895010	101895010	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554699638	NA	P-0035137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	10	208	0	ENST00000374994.4:c.563G>T	p.Gly188Val	p.G188V	ENST00000374994	NM_004612.2	188	gGt/gTt	3/9	0.133424309718214	1	FACETS	0.656	0.445	0.922	0.656	0.445	0.922	SUBCLONAL	1	TRUE	0	0.15	1		208	188	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0035149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	18	554	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.611	0.461	0.789	0.611	0.461	0.789	SUBCLONAL	1	TRUE	1	0.23	2		554	256	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866987936	NA	P-0035150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	87	268	0	ENST00000281708.4:c.1436G>C	p.Arg479Pro	p.R479P	ENST00000281708	NM_033632.3	479	cGa/cCa	10/12	1	2	FACETS	0.991	0.881	1	0.991	0.881	1	CLONAL	1	TRUE	1	0.368126797920685	2		268	477	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254930	16254930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757226572	NA	P-0035150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	110	475	0	ENST00000375759.3:c.2195G>A	p.Arg732Gln	p.R732Q	ENST00000375759	NM_015001.2	732	cGa/cAa	11/15	1	2	FACETS	0.741	0.665	0.821	0.741	0.665	0.821	SUBCLONAL	1	TRUE	1	0.368126797920685	2		475	807	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560263	95560263	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	133	468	0	ENST00000393063.1:c.5326C>G	p.Gln1776Glu	p.Q1776E	ENST00000393063	NM_030621.3	1776	Cag/Gag	25/28	0.368126797920685	3	FACETS	1	0.959	1	0.366	0.332	0.401	CLONAL	1	TRUE	0	0.368126797920685	3		468	779	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540587	187540587	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	84	488	0	ENST00000441802.2:c.7153G>C	p.Asp2385His	p.D2385H	ENST00000441802	NM_005245.3	2385	Gat/Cat	10/27	1	2	FACETS	0.699	0.617	0.786	0.699	0.617	0.786	SUBCLONAL	1	TRUE	1	0.368126797920685	2		488	653	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911302	29911302	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	103	427	0	ENST00000376809.5:c.601G>C	p.Glu201Gln	p.E201Q	ENST00000376809	NM_002116.7	201	Gag/Cag	3/8	1	2	FACETS	0.794	0.711	0.882	0.794	0.711	0.882	SUBCLONAL	1	TRUE	1	0.368126797920685	2		427	705	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912276	29912276	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0035150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	208	700	0	ENST00000376809.5:c.896-1G>A		p.X299_splice	ENST00000376809	NM_002116.7	299			1	2	FACETS	0.817	0.756	0.88	0.817	0.756	0.88	CLONAL	1	TRUE	1	0.368126797920685	2		700	1383	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965846	90965846	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	77	431	0	ENST00000265433.3:c.1471G>C	p.Glu491Gln	p.E491Q	ENST00000265433	NM_002485.4	491	Gaa/Caa	11/16	1	2	FACETS	0.766	0.674	0.865	0.766	0.674	0.865	SUBCLONAL	1	TRUE	1	0.368126797920685	2		431	546	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0035151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	219	514	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.267705472618005	5	FACETS	1	0.987	1	0.832	0.774	0.891	CLONAL	2	TRUE	2	0.267705472618005	5		514	919	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259554	55259554	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs397517134	NA	P-0035151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	190	483	0	ENST00000275493.2:c.2612C>G	p.Ala871Gly	p.A871G	ENST00000275493	NM_005228.3	871	gCa/gGa	21/28	0.267705472618005	5	FACETS	1	0.985	1	0.824	0.763	0.887	CLONAL	2	TRUE	2	0.267705472618005	5		483	805	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985561	2985561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	134	455	0	ENST00000396946.4:c.250G>A	p.Gly84Arg	p.G84R	ENST00000396946	NM_032415.4	84	Ggg/Agg	4/25	0.267705472618005	5	FACETS	0.985	0.897	1	0.657	0.598	0.719	CLONAL	2	TRUE	2	0.267705472618005	5		455	712	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247897	10247897	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	192	693	0	ENST00000340748.4:c.4305C>G	p.Asp1435Glu	p.D1435E	ENST00000340748		1435	gaC/gaG	36/40	0.220462792311831	3	FACETS	0.793	0.733	0.856	0.793	0.733	0.856	SUBCLONAL	2	TRUE	1	0.267705472618005	3		693	1025	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	901	639	0	ENST00000269305.4:c.313G>T	p.Gly105Cys	p.G105C	ENST00000269305	NM_001126112.2	105	Ggc/Tgc	4/11	0.780828109355592	3	FACETS	0.943	0.926	0.96			1	CLONAL	3	TRUE	NA	0.780828109355592	3		639	1134	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267544	198267544	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	167	327	0	ENST00000335508.6:c.1813G>T	p.Gly605Cys	p.G605C	ENST00000335508	NM_012433.2	605	Ggt/Tgt	14/25	0.757332698249438	4	FACETS	1	0.98	1	0.594	0.548	0.642	CLONAL	1	TRUE	2	0.780828109355592	4		327	641	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113384	209113384	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	53	299	0	ENST00000345146.2:c.123C>G	p.Ser41Arg	p.S41R	ENST00000345146	NM_005896.2	41	agC/agG	4/10	0.757332698249438	4	FACETS	0.423	0.36	0.491	0.211	0.18	0.246	SUBCLONAL	1	TRUE	2	0.780828109355592	4		299	572	SUCCESS
APC	324	MSKCC	GRCh37	5	112170648	112170648	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	156	345	0	ENST00000257430.4:c.1744G>A	p.Glu582Lys	p.E582K	ENST00000257430	NM_000038.5	582	Gaa/Aaa	15/16	0.607501062441055	2	FACETS	1	0.989	1	0.68	0.635	0.724	CLONAL	1	TRUE	0	0.780828109355592	2		345	294	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971143	21971143	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	239	380	0	ENST00000304494.5:c.215del	p.Cys72SerfsTer74	p.C72Sfs*74	ENST00000304494	NM_000077.4	72	tGc/tc	2/3	0.620564785201011	2	FACETS	0.969	0.931	1	0.969	0.931	1	CLONAL	2	TRUE	0	0.780828109355592	2		380	316	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578518	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGGCAGGTCTTGGC	CAGGGCAGGTCTTGGC	-	novel	NA	P-0035160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	617	817	0	ENST00000269305.4:c.412_427del	p.Ala138CysfsTer27	p.A138Cfs*27	ENST00000269305	NM_001126112.2	138	GCCAAGACCTGCCCTGtg/tg	5/11	0.173019454990671	5	FACETS	0.915	0.89	0.94			1	INDETERMINATE	5	TRUE	NA	0.526051609673377	5		817	917	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122986	2122986	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0035160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	181	502	0	ENST00000219476.3:c.2355+2T>G		p.X785_splice	ENST00000219476	NM_000548.3	785			0.526051609673377	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.526051609673377	2		502	340	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61713087	61713087	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	106	329	0	ENST00000401558.2:c.2324A>C	p.Asn775Thr	p.N775T	ENST00000401558	NM_003400.3	775	aAt/aCt	20/25	0.168410758499597	6	FACETS	1	0.974	1	0.813	0.737	0.892	INDETERMINATE	2	TRUE	3	0.526051609673377	6		329	339	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874425	151874425	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	177	506	0	ENST00000262189.6:c.8113G>T	p.Glu2705Ter	p.E2705*	ENST00000262189	NM_170606.2	2705	Gag/Tag	38/59	0.168410758499597	6	FACETS	0.86	0.798	0.924	0.86	0.798	0.924	INDETERMINATE	3	TRUE	3	0.526051609673377	6		506	535	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	169	460	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	0.40046457485008	2		460	721	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0035165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	110	438	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.40046457485008	2		438	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578428	7578429	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	79	859	0	ENST00000269305.4:c.501_502insT	p.His168SerfsTer13	p.H168Sfs*13	ENST00000269305	NM_001126112.2	167	-/T	5/11	1	2	FACETS	0.491	0.431	0.556	0.491	0.431	0.556	SUBCLONAL	1	TRUE	1	0.40046457485008	2		859	803	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099405	4099405	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1348137830	NA	P-0035165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	44	724	0	ENST00000262948.5:c.713G>A	p.Arg238Gln	p.R238Q	ENST00000262948	NM_030662.3	238	cGg/cAg	7/11	1	2	FACETS	0.265	0.221	0.314	0.265	0.221	0.314	SUBCLONAL	1	TRUE	1	0.40046457485008	2		724	829	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905462	50905462	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	251	809	0	ENST00000440232.2:c.590G>C	p.Ser197Thr	p.S197T	ENST00000440232	NM_002691.3	197	aGc/aCc	6/27	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.40046457485008	2		809	921	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547970	41547970	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	220	664	0	ENST00000263253.7:c.2951T>A	p.Val984Glu	p.V984E	ENST00000263253	NM_001429.3	984	gTg/gAg	15/31	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.40046457485008	2		664	781	SUCCESS
APC	324	MSKCC	GRCh37	5	112151191	112151191	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0035165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	124	395	0	ENST00000257430.4:c.836del		p.X279_splice	ENST00000257430	NM_000038.5	279			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.40046457485008	2		395	483	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411813	63411813	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	264	454	0	ENST00000330258.3:c.1354del	p.Glu452AsnfsTer3	p.E452Nfs*3	ENST00000330258	NM_152424.3	452	Gaa/aa	2/2	1	1	FACETS	1	0.979	1	1	0.996	1	CLONAL	2	TRUE	0	0.40046457485008	1		454	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0035170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	20	690	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.324711500145058	3	FACETS	0.173	0.131	0.222	0.086	0.065	0.111	SUBCLONAL	1	FALSE	1	0.340173770571097	3		690	796	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030403	49030403	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	159	372	0	ENST00000267163.4:c.1880del	p.Asn627MetfsTer16	p.N627Mfs*16	ENST00000267163	NM_000321.2	626	gcA/gc	19/27	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	2	FALSE	NA	0.340173770571097	2		372	418	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150448	157150448	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	220	497	0	ENST00000346085.5:c.1630C>G	p.Pro544Ala	p.P544A	ENST00000346085	NM_020732.3	544	Ccg/Gcg	2/20	0.211786944246934	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	FALSE	2	0.340173770571097	4		497	780	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390162	89390162	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	67	368	1	ENST00000336596.2:c.911G>T	p.Cys304Phe	p.C304F	ENST00000336596	NM_005233.5	304	tGc/tTc	4/17	1	2	FACETS	0.687	0.598	0.782	0.687	0.598	0.782	SUBCLONAL	1	TRUE	1	0.395854729840078	2		369	493	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188306	10188307	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	130	580	0	ENST00000256474.2:c.450dup	p.Ile151TyrfsTer23	p.I151Yfs*23	ENST00000256474	NM_000551.3	150	aat/aaTt	2/3	0.395854729840078	1	FACETS	0.89	0.81	0.973	0.89	0.81	0.973	CLONAL	1	TRUE	0	0.395854729840078	1		580	592	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5055680	5055680	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1282212623	NA	P-0035171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	37	288	1	ENST00000381652.3:c.948A>T	p.Leu316Phe	p.L316F	ENST00000381652	NM_004972.3	316	ttA/ttT	8/25	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.395854729840078	2		289	180	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914653	39914653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	95	308	0	ENST00000378444.4:c.4709C>T	p.Thr1570Ile	p.T1570I	ENST00000378444	NM_001123385.1	1570	aCc/aTc	12/15	1	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.395854729840078	1		308	321	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0035173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	124	451	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	1	2	FACETS	0.83	0.761	0.901	0.83	0.761	0.901	CLONAL	1	TRUE	1	0.892029869731918	2		451	335	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637689	52637689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	150	535	0	ENST00000394830.3:c.2627G>A	p.Arg876His	p.R876H	ENST00000394830	NM_018313.4	876	cGt/cAt	18/30	0.892029869731918	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.892029869731918	1		535	173	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0035208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	255	482	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	1	2	FACETS	0.86	0.811	0.91	1	0.995	1	CLONAL	2	TRUE	1	0.4736369589672	2		482	626	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0035208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	351	605	14	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.367183945629327	0	FACETS	0.651	0.624	0.678			1	SUBCLONAL	2	TRUE	0	0.4736369589672	0		619	599	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624107	89624283	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	GAGCGAGGGGCATCAGCTACCGCCAAGTCCAGAGCCATTTCCATCCTGCAGAAGAAGCCCCGCCACCAGCAGCTTCTGCCATCTCTCTCCTCCTTTTTCTTCAGCCACAGGCTCCCAGACATGACAGCCATCATCAAAGAGATCGTTAGCAGAAACAAAAGGAGATATCAAGAGGAT	GAGCGAGGGGCATCAGCTACCGCCAAGTCCAGAGCCATTTCCATCCTGCAGAAGAAGCCCCGCCACCAGCAGCTTCTGCCATCTCTCTCCTCCTTTTTCTTCAGCCACAGGCTCCCAGACATGACAGCCATCATCAAAGAGATCGTTAGCAGAAACAAAAGGAGATATCAAGAGGAT	-	novel	NA	P-0035208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	27	99	0	ENST00000371953.3:c.-119_58del		p.*40*	ENST00000371953	NM_000314.4	?-19/403		1/9	0.4736369589672	0	FACETS	0.953	0.792	1			1	CLONAL	1	TRUE	0	0.4736369589672	0		99	63	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061006	38061033	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCCGGGGGCCGGCGCGCCCTCTAGCT	GGCCCGGGGGCCGGCGCGCCCTCTAGCT	-	novel	NA	P-0035208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	174	344	0	ENST00000250448.2:c.956_983del	p.Gln319ProfsTer22	p.Q319Pfs*22	ENST00000250448	NM_004496.3	319	cAGCTAGAGGGCGCGCCGGCCCCCGGGCCc/cc	2/2	1	2	FACETS	0.854	0.795	0.914	1	0.992	1	CLONAL	2	TRUE	1	0.4736369589672	2		344	430	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0035214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	436	880	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.475544564488585	2	FACETS	0.963	0.924	1	0.963	0.924	1	CLONAL	2	TRUE	0	0.490284513336058	2		882	923	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0035214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	32	238	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.470194377095485	1	FACETS	0.601	0.494	0.719	0.601	0.494	0.719	SUBCLONAL	1	TRUE	0	0.490284513336058	1		238	164	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845649	68845649	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	63	557	1	ENST00000261769.5:c.895G>A	p.Ala299Thr	p.A299T	ENST00000261769	NM_004360.3	299	Gcc/Acc	7/16	0.475544564488585	2	FACETS	0.278	0.24	0.321	0.139	0.12	0.161	SUBCLONAL	1	TRUE	0	0.490284513336058	2		558	923	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793418	242793419	+	missense_variant	Missense_Mutation	DNP	GA	GA	TC	novel	NA	P-0035214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	322	637	0	ENST00000334409.5:c.658_659inv	p.Ser220Asp	p.S220D	ENST00000334409	NM_005018.2	220	TCt/GAt	5/5	0.220262859671758	3	FACETS	1	0.95	1	0.667	0.633	0.702	INDETERMINATE	2	TRUE	0	0.490284513336058	3		637	817	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0035220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	58	609	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.213674135639951	1	FACETS	0.929	0.799	1	0.929	0.799	1	CLONAL	1	TRUE	0	0.213674135639951	1		609	522	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919281	48919281	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs587778870	NA	P-0035220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	13	173	0	ENST00000267163.4:c.446C>G	p.Ser149Ter	p.S149*	ENST00000267163	NM_000321.2	149	tCa/tGa	4/27	0.213674135639951	1	FACETS	1	0.801	1	1	0.801	1	CLONAL	1	TRUE	0	0.213674135639951	1		173	95	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0035221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	84	511	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.157075099025229	1	FACETS	0.868	0.769	0.973	0.868	0.769	0.973	INDETERMINATE	1	TRUE	0	0.327085091994369	1		511	495	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0035223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	70	608	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.188784722429819	2	FACETS	0.981	0.856	1	0.491	0.428	0.558	CLONAL	1	TRUE	0	0.255286201277501	2		608	559	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0035223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	50	380	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.255286201277501	12	FACETS	1	0.912	1	0.112	0.094	0.131	CLONAL	1	TRUE	2	0.255286201277501	12		380	799	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115452	115115452	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	56	395	0	ENST00000257566.3:c.874T>G	p.Leu292Val	p.L292V	ENST00000257566	NM_016569.3	292	Tta/Gta	5/8	0.255286201277501	5	FACETS	0.911	0.78	1	0.304	0.26	0.352	CLONAL	1	TRUE	2	0.255286201277501	5		395	666	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	70	274	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.388286190839516	2		274	289	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223532	2223532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	129	500	0	ENST00000326181.6:c.1063C>T	p.Arg355Trp	p.R355W	ENST00000326181	NM_032271.2	355	Cgg/Tgg	11/21	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.388286190839516	2		500	593	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188164	11188164	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587777893	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	120	330	0	ENST00000361445.4:c.5930C>A	p.Thr1977Lys	p.T1977K	ENST00000361445	NM_004958.3	1977	aCa/aAa	43/58	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.388286190839516	2		330	490	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088763	27088763	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	102	434	0	ENST00000324856.7:c.2372A>G	p.Asn791Ser	p.N791S	ENST00000324856	NM_006015.4	791	aAc/aGc	7/20	1	2	FACETS	0.995	0.893	1	0.995	0.893	1	CLONAL	1	TRUE	1	0.388286190839516	2		434	528	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458801	120458801	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	107	483	0	ENST00000256646.2:c.6544C>T	p.Pro2182Ser	p.P2182S	ENST00000256646	NM_024408.3	2182	Cct/Tct	34/34	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.388286190839516	2		483	512	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468187	120468187	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	133	447	0	ENST00000256646.2:c.4252C>T	p.Pro1418Ser	p.P1418S	ENST00000256646	NM_024408.3	1418	Ccc/Tcc	25/34	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.388286190839516	2		447	584	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156848916	156848916	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	113	468	0	ENST00000524377.1:c.1808C>T	p.Ser603Phe	p.S603F	ENST00000524377	NM_002529.3	603	tCc/tTc	15/17	1	2	FACETS	0.959	0.865	1	0.959	0.865	1	CLONAL	1	TRUE	1	0.388286190839516	2		468	607	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741840	162741840	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	76	268	0	ENST00000367921.3:c.1531C>T	p.Gln511Ter	p.Q511*	ENST00000367921	NM_006182.2	511	Cag/Tag	13/18	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.388286190839516	2		268	350	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619213	43619213	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	97	389	0	ENST00000355710.3:c.2896A>G	p.Thr966Ala	p.T966A	ENST00000355710	NM_020975.4	966	Acc/Gcc	17/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.388286190839516	2		389	466	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197330	94197330	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	129	387	0	ENST00000323929.3:c.1174C>T	p.Pro392Ser	p.P392S	ENST00000323929	NM_005591.3	392	Cca/Tca	11/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.388286190839516	2		387	580	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102033294	102033294	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376161041	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	149	342	0	ENST00000282441.5:c.680C>T	p.Ser227Leu	p.S227L	ENST00000282441	NM_001130145.2	227	tCg/tTg	3/9	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.388286190839516	2		342	577	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149235	119149235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756530482	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	147	404	0	ENST00000264033.4:c.1243G>A	p.Gly415Ser	p.G415S	ENST00000264033	NM_005188.3	415	Ggc/Agc	9/16	0.388286190839516	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.388286190839516	1		404	472	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905451	11905451	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	92	283	0	ENST00000396373.4:c.101A>G	p.His34Arg	p.H34R	ENST00000396373	NM_001987.4	34	cAt/cGt	2/8	0.388286190839516	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.388286190839516	1		283	318	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466982	18466982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	151	275	0	ENST00000266497.5:c.1121G>A	p.Gly374Glu	p.G374E	ENST00000266497		374	gGa/gAa	5/31	0.0913477162625322	3	FACETS	1	0.973	1			1	INDETERMINATE	2	TRUE	NA	0.388286190839516	3		275	416	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544088	18544088	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	45	201	0	ENST00000266497.5:c.1905G>A	p.Met635Ile	p.M635I	ENST00000266497		635	atG/atA	13/31	0.0913477162625322	3	FACETS	0.721	0.607	0.846			1	INDETERMINATE	1	TRUE	NA	0.388286190839516	3		201	384	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544120	18544120	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	76	229	0	ENST00000266497.5:c.1937T>C	p.Leu646Pro	p.L646P	ENST00000266497		646	cTt/cCt	13/31	0.0913477162625322	3	FACETS	1	0.906	1			1	INDETERMINATE	1	TRUE	NA	0.388286190839516	3		229	452	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573945	18573945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	63	268	0	ENST00000266497.5:c.2263G>A	p.Glu755Lys	p.E755K	ENST00000266497		755	Gaa/Aaa	15/31	0.0913477162625322	3	FACETS	1	0.927	1			1	INDETERMINATE	1	TRUE	NA	0.388286190839516	3		268	353	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658254	18658254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	126	414	0	ENST00000266497.5:c.3059C>T	p.Ala1020Val	p.A1020V	ENST00000266497		1020	gCt/gTt	22/31	0.371100209300351	5	FACETS	1	0.957	1	0.275	0.249	0.303	CLONAL	1	TRUE	1	0.388286190839516	5		414	933	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691124	18691124	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	91	385	0	ENST00000266497.5:c.3235G>A	p.Glu1079Lys	p.E1079K	ENST00000266497		1079	Gaa/Aaa	23/31	0.371100209300351	5	FACETS	0.965	0.856	1	0.241	0.214	0.271	CLONAL	1	TRUE	1	0.388286190839516	5		385	769	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691166	18691166	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	104	414	0	ENST00000266497.5:c.3277C>T	p.Gln1093Ter	p.Q1093*	ENST00000266497		1093	Caa/Taa	23/31	0.371100209300351	5	FACETS	1	0.943	1	0.27	0.241	0.3	CLONAL	1	TRUE	1	0.388286190839516	5		414	785	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424535	49424535	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	92	482	0	ENST00000301067.7:c.13688C>T	p.Pro4563Leu	p.P4563L	ENST00000301067	NM_003482.3	4563	cCc/cTc	41/54	1	2	FACETS	0.91	0.811	1	0.91	0.811	1	CLONAL	1	TRUE	1	0.388286190839516	2		482	521	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426671	121426671	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	106	405	0	ENST00000257555.6:c.362C>T	p.Ser121Phe	p.S121F	ENST00000257555		121	tCc/tTc	2/10	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.388286190839516	2		405	534	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219468	133219468	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768741587	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	175	593	0	ENST00000320574.5:c.4666C>T	p.Arg1556Trp	p.R1556W	ENST00000320574	NM_006231.2	1556	Cgg/Tgg	36/49	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.388286190839516	2		593	717	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636076	28636076	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	128	397	1	ENST00000241453.7:c.296G>T	p.Gly99Val	p.G99V	ENST00000241453	NM_004119.2	99	gGg/gTg	3/24	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.388286190839516	2		398	625	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281129	49281129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	213	662	0	ENST00000282018.3:c.176C>T	p.Ser59Phe	p.S59F	ENST00000282018	NM_020377.2	59	tCc/tTc	1/1	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.388286190839516	2		662	860	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066913	30066913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	93	310	1	ENST00000331968.5:c.2218C>T	p.Arg740Trp	p.R740W	ENST00000331968	NM_002742.2	740	Cgg/Tgg	16/18	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.388286190839516	2		311	392	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108011	30108011	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	169	440	0	ENST00000331968.5:c.796A>T	p.Lys266Ter	p.K266*	ENST00000331968	NM_002742.2	266	Aaa/Taa	5/18	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.388286190839516	2		440	723	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610632	81610632	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	72	248	0	ENST00000298171.2:c.2230A>T	p.Asn744Tyr	p.N744Y	ENST00000298171	NM_000369.2	744	Aac/Tac	10/10	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.388286190839516	2		248	307	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562404	95562404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377205344	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	117	339	0	ENST00000393063.1:c.4853C>T	p.Ser1618Leu	p.S1618L	ENST00000393063	NM_030621.3	1618	tCa/tTa	24/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.388286190839516	2		339	446	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239605	105239605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	101	458	0	ENST00000349310.3:c.940G>A	p.Glu314Lys	p.E314K	ENST00000349310	NM_001014432.1	314	Gag/Aag	11/15	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.388286190839516	2		458	493	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423503	88423503	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	120	459	1	ENST00000360948.2:c.2332G>A	p.Glu778Lys	p.E778K	ENST00000360948	NM_001012338.2	778	Gag/Aag	18/19	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.388286190839516	2		460	544	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472522	88472522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55890138	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	103	428	0	ENST00000360948.2:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000360948	NM_001012338.2	678	cGa/cAa	16/19	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.388286190839516	2		428	512	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678460	88678460	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	150	556	1	ENST00000360948.2:c.1076C>T	p.Ser359Phe	p.S359F	ENST00000360948	NM_001012338.2	359	tCc/tTc	9/19	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.388286190839516	2		557	624	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679756	88679756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780838684	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	111	415	0	ENST00000360948.2:c.707C>T	p.Ser236Leu	p.S236L	ENST00000360948	NM_001012338.2	236	tCa/tTa	7/19	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.388286190839516	2		415	498	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690570	88690570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	84	291	0	ENST00000360948.2:c.460G>A	p.Glu154Lys	p.E154K	ENST00000360948	NM_001012338.2	154	Gaa/Aaa	5/19	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.388286190839516	2		291	390	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647806	3647806	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	138	548	0	ENST00000294008.3:c.1358C>T	p.Pro453Leu	p.P453L	ENST00000294008	NM_032444.2	453	cCa/cTa	6/15	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.388286190839516	2		548	603	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857313	9857313	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	83	327	0	ENST00000330684.3:c.4088C>T	p.Ser1363Phe	p.S1363F	ENST00000330684	NM_001134407.1	1363	tCc/tTc	13/13	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.388286190839516	2		327	329	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984848	9984848	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	127	382	0	ENST00000330684.3:c.1117G>A	p.Glu373Lys	p.E373K	ENST00000330684	NM_001134407.1	373	Gaa/Aaa	4/13	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.388286190839516	2		382	500	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56871573	56871574	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	97	372	0	ENST00000308159.5:c.1953_1954delinsTT	p.Gln652Ter	p.Q652*	ENST00000308159	NM_014669.4	651	ccCCag/ccTTag	18/22	1	2	FACETS	0.853	0.762	0.949	0.853	0.762	0.949	CLONAL	1	TRUE	1	0.388286190839516	2		372	586	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829710	72829710	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	156	574	2	ENST00000268489.5:c.6871C>A	p.Gln2291Lys	p.Q2291K	ENST00000268489	NM_006885.3	2291	Cag/Aag	9/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.388286190839516	2		576	698	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350486	89350486	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	173	772	2	ENST00000301030.4:c.2464C>T	p.Gln822Ter	p.Q822*	ENST00000301030	NM_001256183.1	822	Cag/Tag	9/13	1	2	FACETS	0.906	0.833	0.981	0.906	0.833	0.981	CLONAL	1	TRUE	1	0.388286190839516	2		774	984	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352512	89352512	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	132	439	0	ENST00000301030.4:c.827C>T	p.Ser276Phe	p.S276F	ENST00000301030	NM_001256183.1	276	tCc/tTc	8/13	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.388286190839516	2		439	602	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352561	89352561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	100	351	0	ENST00000301030.4:c.778C>T	p.Pro260Ser	p.P260S	ENST00000301030	NM_001256183.1	260	Ccg/Tcg	8/13	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.388286190839516	2		351	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	166	632	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.388286190839516	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.388286190839516	1		632	631	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979631	7979631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	72	353	0	ENST00000319144.4:c.1394G>A	p.Gly465Glu	p.G465E	ENST00000319144	NM_001139.2	465	gGg/gAg	11/15	0.388286190839516	1	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	0	0.388286190839516	1		353	293	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682210	37682210	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	141	458	1	ENST00000447079.4:c.3401T>C	p.Met1134Thr	p.M1134T	ENST00000447079	NM_015083.1	1134	aTg/aCg	13/14	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.388286190839516	2		459	613	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436077	56436078	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	101	343	0	ENST00000407977.2:c.1059_1060delinsAT	p.Pro354Ser	p.P354S	ENST00000407977		353	ctCCct/ctATct	9/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.388286190839516	2		343	438	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533763	63533763	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777283610	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	99	433	1	ENST00000307078.5:c.1391C>T	p.Ser464Phe	p.S464F	ENST00000307078	NM_004655.3	464	tCc/tTc	6/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.388286190839516	2		434	446	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170788	11170789	+	missense_variant	Missense_Mutation	DNP	CC	CC	GT	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	122	518	1	ENST00000358026.2:c.4932_4933delinsGT	p.Arg1645Trp	p.R1645W	ENST00000358026	NM_001128849.1	1644	ggCCgg/ggGTgg	35/36	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.388286190839516	2		519	584	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302612	15302612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	143	720	0	ENST00000263388.2:c.746G>A	p.Gly249Glu	p.G249E	ENST00000263388	NM_000435.2	249	gGg/gAg	5/33	1	2	FACETS	0.949	0.866	1	0.949	0.866	1	CLONAL	1	TRUE	1	0.388286190839516	2		720	776	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748841	41748841	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	168	604	0	ENST00000301178.4:c.1366G>T	p.Gly456Ter	p.G456*	ENST00000301178	NM_021913.4	456	Gga/Tga	11/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.388286190839516	2		604	719	SUCCESS
ALK	238	MSKCC	GRCh37	2	29420472	29420472	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	118	399	0	ENST00000389048.3:c.4009G>A	p.Glu1337Lys	p.E1337K	ENST00000389048	NM_004304.4	1337	Gaa/Aaa	27/29	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.388286190839516	2		399	531	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462682	29462682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	175	532	0	ENST00000389048.3:c.2219G>A	p.Gly740Glu	p.G740E	ENST00000389048	NM_004304.4	740	gGa/gAa	13/29	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.388286190839516	2		532	683	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495290	212495290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	79	341	0	ENST00000342788.4:c.1976G>A	p.Gly659Asp	p.G659D	ENST00000342788	NM_005235.2	659	gGt/gAt	17/28	1	2	FACETS	0.978	0.865	1	0.978	0.865	1	CLONAL	1	TRUE	1	0.388286190839516	2		341	416	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661899	227661899	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	147	602	0	ENST00000305123.5:c.1556A>G	p.Asn519Ser	p.N519S	ENST00000305123	NM_005544.2	519	aAt/aGt	1/2	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.388286190839516	2		602	672	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076940	41076940	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	92	392	0	ENST00000373198.4:c.1480C>T	p.Gln494Ter	p.Q494*	ENST00000373198	NM_133170.3	494	Caa/Taa	9/32	0.388286190839516	3	FACETS	1	0.897	1	0.503	0.448	0.562	CLONAL	1	TRUE	1	0.388286190839516	3		392	562	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306554	41306554	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	81	467	0	ENST00000373198.4:c.1105G>C	p.Gly369Arg	p.G369R	ENST00000373198	NM_133170.3	369	Ggt/Cgt	7/32	0.388286190839516	3	FACETS	0.894	0.789	1	0.447	0.394	0.504	CLONAL	1	TRUE	1	0.388286190839516	3		467	557	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262890	46262890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	92	359	0	ENST00000371998.3:c.1063C>T	p.Pro355Ser	p.P355S	ENST00000371998		355	Cct/Tct	10/23	0.388286190839516	3	FACETS	0.974	0.867	1	0.487	0.433	0.544	CLONAL	1	TRUE	1	0.388286190839516	3		359	581	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46275968	46275968	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	97	423	0	ENST00000371998.3:c.3404T>C	p.Phe1135Ser	p.F1135S	ENST00000371998		1135	tTt/tCt	18/23	0.388286190839516	3	FACETS	0.924	0.824	1	0.462	0.412	0.515	CLONAL	1	TRUE	1	0.388286190839516	3		423	646	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458223	12458223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	119	407	0	ENST00000287820.6:c.840G>A	p.Met280Ile	p.M280I	ENST00000287820	NM_015869.4	280	atG/atA	6/7	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.388286190839516	2		407	522	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799683	72799683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	132	425	1	ENST00000325599.8:c.1486C>T	p.Leu496Phe	p.L496F	ENST00000325599	NM_018130.2	496	Ctt/Ttt	11/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.388286190839516	2		426	597	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799851	72799851	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	93	353	0	ENST00000325599.8:c.1318C>T	p.His440Tyr	p.H440Y	ENST00000325599	NM_018130.2	440	Cat/Tat	11/11	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.388286190839516	2		353	466	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259167	89259167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753700696	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	70	275	0	ENST00000336596.2:c.311G>A	p.Arg104Gln	p.R104Q	ENST00000336596	NM_005233.5	104	cGa/cAa	3/17	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.388286190839516	2		275	329	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445067	89445067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	73	265	0	ENST00000336596.2:c.1387C>T	p.Pro463Ser	p.P463S	ENST00000336596	NM_005233.5	463	Cct/Tct	6/17	1	2	FACETS	0.959	0.843	1	0.959	0.843	1	CLONAL	1	TRUE	1	0.388286190839516	2		265	392	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468357	89468357	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs867931903	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	32	157	0	ENST00000336596.2:c.1891G>A	p.Glu631Lys	p.E631K	ENST00000336596	NM_005233.5	631	Gaa/Aaa	11/17	1	2	FACETS	0.947	0.778	1	0.947	0.778	1	CLONAL	1	TRUE	1	0.388286190839516	2		157	174	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498379	89498379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866959883	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	52	182	0	ENST00000336596.2:c.2351G>A	p.Gly784Glu	p.G784E	ENST00000336596	NM_005233.5	784	gGg/gAg	14/17	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.388286190839516	2		182	228	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274940	142274940	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	110	387	0	ENST00000350721.4:c.2120T>C	p.Phe707Ser	p.F707S	ENST00000350721	NM_001184.3	707	tTt/tCt	10/47	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.388286190839516	2		387	504	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612029	189612029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368336834	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	79	342	0	ENST00000264731.3:c.1781G>A	p.Arg594Gln	p.R594Q	ENST00000264731	NM_003722.4	594	cGa/cAa	14/14	1	2	FACETS	0.9	0.795	1	0.9	0.795	1	CLONAL	1	TRUE	1	0.388286190839516	2		342	452	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902604	1902604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	124	511	0	ENST00000382891.5:c.223C>T	p.Pro75Ser	p.P75S	ENST00000382891	NM_133335.3	75	Cca/Tca	2/22	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.388286190839516	2		511	618	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750572	41750572	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	92	405	0	ENST00000226382.2:c.56C>T	p.Ala19Val	p.A19V	ENST00000226382	NM_003924.3	19	gCt/gTt	1/3	1	2	FACETS	0.993	0.887	1	0.993	0.887	1	CLONAL	1	TRUE	1	0.388286190839516	2		405	477	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594221	55594221	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913512	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	218	306	0	ENST00000288135.5:c.1924A>G	p.Lys642Glu	p.K642E	ENST00000288135	NM_000222.2	642	Aaa/Gaa	13/21	1	2	FACETS	0.976	0.915	1	1	0.994	1	CLONAL	2	TRUE	1	0.388286190839516	2		306	575	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156330	106156330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	56	277	0	ENST00000380013.4:c.1231C>T	p.Pro411Ser	p.P411S	ENST00000380013	NM_001127208.2	411	Cct/Tct	3/11	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.388286190839516	2		277	286	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193739	106193739	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	59	157	0	ENST00000380013.4:c.4201G>A	p.Glu1401Lys	p.E1401K	ENST00000380013	NM_001127208.2	1401	Gaa/Aaa	10/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.388286190839516	2		157	224	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538991	187538991	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	115	391	0	ENST00000441802.2:c.8749C>G	p.Arg2917Gly	p.R2917G	ENST00000441802	NM_005245.3	2917	Cga/Gga	10/27	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.388286190839516	2		391	516	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628376	187628376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	167	576	0	ENST00000441802.2:c.2606C>T	p.Ser869Leu	p.S869L	ENST00000441802	NM_005245.3	869	tCa/tTa	2/27	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.388286190839516	2		576	713	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160756	56160756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	61	224	0	ENST00000399503.3:c.1030C>T	p.Pro344Ser	p.P344S	ENST00000399503	NM_005921.1	344	Cct/Tct	4/20	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.388286190839516	2		224	307	SUCCESS
APC	324	MSKCC	GRCh37	5	112177191	112177191	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	83	260	0	ENST00000257430.4:c.5900C>T	p.Ser1967Phe	p.S1967F	ENST00000257430	NM_000038.5	1967	tCc/tTc	16/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.388286190839516	2		260	315	SUCCESS
APC	324	MSKCC	GRCh37	5	112178691	112178691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758713824	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	78	286	0	ENST00000257430.4:c.7400C>T	p.Pro2467Leu	p.P2467L	ENST00000257430	NM_000038.5	2467	cCa/cTa	16/16	1	2	FACETS	0.987	0.872	1	0.987	0.872	1	CLONAL	1	TRUE	1	0.388286190839516	2		286	407	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520190	176520190	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	192	708	0	ENST00000292408.4:c.1109T>C	p.Ile370Thr	p.I370T	ENST00000292408	NM_213647.1	370	aTc/aCc	9/18	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.388286190839516	2		708	783	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056291	180056291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199942873	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	143	677	0	ENST00000261937.6:c.953G>A	p.Arg318Gln	p.R318Q	ENST00000261937	NM_182925.4	318	cGa/cAa	7/30	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.388286190839516	2		677	723	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681111	30681111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377301340	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	60	237	0	ENST00000376406.3:c.608C>T	p.Pro203Leu	p.P203L	ENST00000376406	NM_014641.2	203	cCg/cTg	5/15	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.388286190839516	2		237	254	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956528	93956529	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	83	296	0	ENST00000369303.4:c.2707_2708delinsTT	p.Pro903Phe	p.P903F	ENST00000369303	NM_004440.3	903	CCc/TTc	15/17	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.388286190839516	2		296	376	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536235	106536235	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	106	363	0	ENST00000369096.4:c.202G>A	p.Asp68Asn	p.D68N	ENST00000369096	NM_001198.3	68	Gat/Aat	2/7	1	2	FACETS	0.982	0.883	1	0.982	0.883	1	CLONAL	1	TRUE	1	0.388286190839516	2		363	556	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111995807	111995807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	105	293	1	ENST00000368678.4:c.1291G>A	p.Ala431Thr	p.A431T	ENST00000368678		431	Gcc/Acc	12/13	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.388286190839516	2		294	452	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642495	117642495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs9489124	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	186	539	2	ENST00000368508.3:c.5704G>A	p.Glu1902Lys	p.E1902K	ENST00000368508	NM_002944.2	1902	Gaa/Aaa	35/43	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.388286190839516	2		541	800	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528502	157528502	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1433260222	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	114	487	0	ENST00000346085.5:c.6227T>C	p.Leu2076Pro	p.L2076P	ENST00000346085	NM_020732.3	2076	cTg/cCg	20/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.388286190839516	2		487	556	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528682	157528682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	130	436	1	ENST00000346085.5:c.6407C>T	p.Ser2136Leu	p.S2136L	ENST00000346085	NM_020732.3	2136	tCg/tTg	20/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.388286190839516	2		437	547	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974109	2974109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774299169	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	70	319	0	ENST00000396946.4:c.1496G>A	p.Arg499Lys	p.R499K	ENST00000396946	NM_032415.4	499	aGg/aAg	10/25	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.388286190839516	2		319	348	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729442	41729442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	106	430	0	ENST00000242208.4:c.1087G>A	p.Gly363Arg	p.G363R	ENST00000242208	NM_002192.2	363	Ggg/Agg	3/3	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.388286190839516	2		430	523	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729907	41729907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	124	476	0	ENST00000242208.4:c.622G>A	p.Glu208Lys	p.E208K	ENST00000242208	NM_002192.2	208	Gaa/Aaa	3/3	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.388286190839516	2		476	515	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444390	50444390	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	53	274	0	ENST00000331340.3:c.320T>C	p.Val107Ala	p.V107A	ENST00000331340	NM_006060.4	107	gTt/gCt	4/8	1	2	FACETS	0.812	0.696	0.938	0.812	0.696	0.938	CLONAL	1	TRUE	1	0.388286190839516	2		274	336	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241657	55241657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs549015965	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	111	510	1	ENST00000275493.2:c.2105C>T	p.Ala702Val	p.A702V	ENST00000275493	NM_005228.3	702	gCt/gTt	18/28	0.388286190839516	1	FACETS	0.719	0.647	0.794	0.719	0.647	0.794	SUBCLONAL	1	TRUE	0	0.388286190839516	1		511	641	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187387	38187387	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	158	445	0	ENST00000317025.8:c.1090G>A	p.Glu364Lys	p.E364K	ENST00000317025	NM_023034.1	364	Gaa/Aaa	6/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.388286190839516	2		445	618	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56882326	56882326	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	146	518	0	ENST00000519728.1:c.1024C>T	p.Pro342Ser	p.P342S	ENST00000519728	NM_002350.3	342	Cca/Tca	10/13	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.388286190839516	2		518	684	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950458	68950458	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	120	393	0	ENST00000288368.4:c.770C>T	p.Ser257Phe	p.S257F	ENST00000288368	NM_024870.2	257	tCt/tTt	7/40	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.388286190839516	2		393	531	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981367	68981367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	60	226	0	ENST00000288368.4:c.1439C>T	p.Ser480Leu	p.S480L	ENST00000288368	NM_024870.2	480	tCa/tTa	12/40	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.388286190839516	2		226	287	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009400	69009400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	74	322	0	ENST00000288368.4:c.2517G>A	p.Met839Ile	p.M839I	ENST00000288368	NM_024870.2	839	atG/atA	22/40	1	2	FACETS	0.783	0.687	0.885	0.783	0.687	0.885	SUBCLONAL	1	TRUE	1	0.388286190839516	2		322	487	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033209	69033209	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	101	376	0	ENST00000288368.4:c.3649C>T	p.His1217Tyr	p.H1217Y	ENST00000288368	NM_024870.2	1217	Cat/Tat	30/40	1	2	FACETS	0.995	0.892	1	0.995	0.892	1	CLONAL	1	TRUE	1	0.388286190839516	2		376	523	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964333	70964333	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	74	248	0	ENST00000276594.2:c.1695G>A	p.Met565Ile	p.M565I	ENST00000276594	NM_024504.3	565	atG/atA	8/8	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.388286190839516	2		248	293	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521462	8521462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767340559	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	181	466	1	ENST00000356435.5:c.776C>T	p.Ala259Val	p.A259V	ENST00000356435		259	gCc/gTc	9/35	0.388286190839516	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.388286190839516	1		467	532	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27109591	27109591	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs751496754	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	183	508	0	ENST00000380036.4:c.3G>A	p.Met1?	p.M1?	ENST00000380036	NM_000459.3	1	atG/atA	1/23	0.388286190839516	1	FACETS	0.985	0.911	1	0.985	0.911	1	CLONAL	1	TRUE	0	0.388286190839516	1		508	771	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180309	27180309	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755127644	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	281	447	0	ENST00000380036.4:c.973C>T	p.Arg325Cys	p.R325C	ENST00000380036	NM_000459.3	325	Cgc/Tgc	7/23	0.36828862375323	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.388286190839516	2		447	698	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923450	36923450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1304	194	603	0	ENST00000358127.4:c.812C>T	p.Ala271Val	p.A271V	ENST00000358127	NM_001280556.1	271	gCt/gTt	7/10	1	2	FACETS	0.667	0.615	0.721	0.667	0.615	0.721	SUBCLONAL	1	TRUE	1	0.388286190839516	2		603	1498	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336343	80336343	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	79	315	0	ENST00000286548.4:c.976T>C	p.Ser326Pro	p.S326P	ENST00000286548	NM_002072.3	326	Tcc/Ccc	7/7	1	2	FACETS	0.978	0.865	1	0.978	0.865	1	CLONAL	1	TRUE	1	0.388286190839516	2		315	416	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342859	87342859	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	97	346	0	ENST00000277120.3:c.1144C>T	p.Pro382Ser	p.P382S	ENST00000277120		382	Cct/Tct	9/19	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.388286190839516	2		346	455	SUCCESS
AR	367	MSKCC	GRCh37	X	66942767	66942767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	106	196	0	ENST00000374690.3:c.2548C>T	p.Pro850Ser	p.P850S	ENST00000374690	NM_000044.3	850	Ccc/Tcc	7/8	1	1	FACETS	0.909	0.831	0.988	1	0.989	1	CLONAL	2	TRUE	0	0.388286190839516	1		196	242	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934578	NA	P-0035241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	31	848	0	ENST00000269305.4:c.524G>T	p.Arg175Leu	p.R175L	ENST00000269305	NM_001126112.2	175	cGc/cTc	5/11	1	2	FACETS	0.537	0.436	0.651	0.537	0.436	0.651	SUBCLONAL	1	FALSE	1	0.404848021445115	2		848	285	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417398	139417398	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1317233337	NA	P-0035241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	30	572	0	ENST00000277541.6:c.646G>C	p.Glu216Gln	p.E216Q	ENST00000277541	NM_017617.3	216	Gag/Cag	4/34	0.102463316258048	0	FACETS	0.324	0.262	0.394			1	INDETERMINATE	1	FALSE	0	0.404848021445115	0		572	272	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233120	69233120	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	20	280	1	ENST00000462284.1:c.985T>C	p.Trp329Arg	p.W329R	ENST00000462284	NM_002392.5	329	Tgg/Cgg	11/11	1	2	FACETS	0.629	0.485	0.795	0.629	0.485	0.795	SUBCLONAL	1	FALSE	1	0.404848021445115	2		281	157	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724802	43724809	+	frameshift_variant	Frame_Shift_Del	DEL	TGATTGTA	TGATTGTA	-	novel	NA	P-0035241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	31	643	0	ENST00000382044.4:c.3258_3265del	p.His1086GlnfsTer11	p.H1086Qfs*11	ENST00000382044	NM_001141980.1	1086	caTACAATCAgg/cagg	17/28	1	2	FACETS	0.436	0.353	0.53	0.436	0.353	0.53	SUBCLONAL	1	FALSE	1	0.404848021445115	2		643	351	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032522	12032524	+	inframe_deletion	In_Frame_Del	DEL	GTC	GTC	-	novel	NA	P-0035241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	20	318	0	ENST00000353533.5:c.960_962del	p.Val321del	p.V321del	ENST00000353533	NM_003010.3	320	GTC/-	9/11	1	2	FACETS	0.499	0.383	0.633	0.499	0.383	0.633	SUBCLONAL	1	FALSE	1	0.404848021445115	2		318	198	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589603	67589605	+	inframe_deletion	In_Frame_Del	DEL	TTT	TTT	-	novel	NA	P-0035241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	27	180	0	ENST00000274335.5:c.1366_1368del	p.Phe456del	p.F456del	ENST00000274335		456	TTT/-	10/15	0.333521340771485	4	FACETS	0.679	0.542	0.835	0.339	0.271	0.418	SUBCLONAL	1	FALSE	2	0.404848021445115	4		180	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	31	589	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.142330650141342	4	FACETS	0.823	0.668	0.998	0.411	0.334	0.499	INDETERMINATE	1	FALSE	2	0.34775030210024	4		589	292	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262759	16262759	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	17	214	0	ENST00000375759.3:c.10024C>T	p.Gln3342Ter	p.Q3342*	ENST00000375759	NM_015001.2	3342	Cag/Tag	11/15	0.34775030210024	3	FACETS	0.722	0.542	0.932	0.361	0.271	0.466	CLONAL	1	FALSE	1	0.34775030210024	3		214	159	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654545	29654545	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	17	228	0	ENST00000356175.3:c.5234C>T	p.Ser1745Leu	p.S1745L	ENST00000356175	NM_000267.3	1745	tCa/tTa	37/57	0.26238277227116	3	FACETS	0.7	0.525	0.904	0.35	0.262	0.452	SUBCLONAL	1	FALSE	1	0.34775030210024	3		228	164	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216417	36216417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	40	842	0	ENST00000222270.7:c.3680C>T	p.Pro1227Leu	p.P1227L	ENST00000222270	NM_014727.1	1227	cCa/cTa	12/37	0.26238277227116	3	FACETS	0.621	0.516	0.737	0.31	0.258	0.369	SUBCLONAL	1	FALSE	1	0.34775030210024	3		842	435	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866475	42866475	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	74	767	0	ENST00000398585.3:c.157G>T	p.Glu53Ter	p.E53*	ENST00000398585	NM_001135099.1	53	Gaa/Taa	3/14	0.309957874977131	5	FACETS	1	0.933	1			1	CLONAL	1	FALSE	NA	0.34775030210024	5		767	589	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45658347	45658347	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	38	446	0	ENST00000407780.3:c.39C>A	p.Phe13Leu	p.F13L	ENST00000407780	NM_001283052.1	13	ttC/ttA	2/7	0.34130888033551	3	FACETS	1	0.852	1			1	CLONAL	1	FALSE	NA	0.34775030210024	3		446	250	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0035243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	37	266	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.184318043574755	4	FACETS	1	0.842	1	0.506	0.421	0.599	INDETERMINATE	1	TRUE	2	0.55	4		266	206	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0035243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	81	520	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.55	2		520	239	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711296	114711296	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	92	372	0	ENST00000543371.1:c.311C>T	p.Pro104Leu	p.P104L	ENST00000543371	NM_001198531.1	104	cCc/cTc	3/14	1	2	FACETS	0.914	0.819	1	0.914	0.819	1	CLONAL	1	TRUE	1	0.55	2		372	366	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546137	41546137	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	19	356	2	ENST00000263253.7:c.2752C>T	p.Gln918Ter	p.Q918*	ENST00000263253	NM_001429.3	918	Cag/Tag	14/31	0.3	1	FACETS	0.278	0.212	0.355	0.278	0.212	0.355	INDETERMINATE	1	TRUE	0	0.55	1		358	180	SUCCESS
APC	324	MSKCC	GRCh37	5	112175475	112175476	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	30	257	0	ENST00000257430.4:c.4188dup	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1395	agt/agTt	16/16	0.184318043574755	4	FACETS	0.685	0.554	0.831	0.342	0.277	0.416	INDETERMINATE	1	TRUE	2	0.55	4		257	247	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0035265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	20	735	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		735	240	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845698	68845698	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	36	229	0	ENST00000261769.5:c.944A>G	p.Asn315Ser	p.N315S	ENST00000261769	NM_004360.3	315	aAt/aGt	7/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		229	353	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115111969	115111969	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0035265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	40	208	0	ENST00000257566.3:c.1770+1G>A		p.X590_splice	ENST00000257566	NM_016569.3	590			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		208	453	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100604	67100604	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	33	168	0	ENST00000412916.2:c.302del	p.Met101ArgfsTer3	p.M101Rfs*3	ENST00000412916		101	aTg/ag	4/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		168	167	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753323	42753323	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	118	504	0	ENST00000222329.4:c.941T>A	p.Leu314Gln	p.L314Q	ENST00000222329	NM_006494.2	314	cTg/cAg	4/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		504	900	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0035266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	134	767	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.195370747395357	2	FACETS	0.828	0.753	0.906	0.828	0.753	0.906	CLONAL	2	TRUE	0	0.221165192112145	2		767	732	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028091	69028091	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776025075	NA	P-0035266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	36	397	0	ENST00000288368.4:c.3250C>T	p.Arg1084Trp	p.R1084W	ENST00000288368	NM_024870.2	1084	Cgg/Tgg	26/40	0.221238968406641	3	FACETS	0.66	0.541	0.793	0.33	0.27	0.397	SUBCLONAL	1	TRUE	1	0.221165192112145	3		397	548	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844722	156844722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs986498490	NA	P-0035266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	89	644	2	ENST00000524377.1:c.1276G>A	p.Val426Ile	p.V426I	ENST00000524377	NM_002529.3	426	Gtc/Atc	11/17	0.210241327398664	4	FACETS	0.991	0.877	1	0.495	0.438	0.557	CLONAL	1	TRUE	2	0.221165192112145	4		646	992	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467134	25467134	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	126	463	0	ENST00000264709.3:c.1741T>A	p.Trp581Arg	p.W581R	ENST00000264709	NM_175629.2	581	Tgg/Agg	15/23	0.221238968406641	3	FACETS	0.942	0.854	1	0.942	0.854	1	CLONAL	2	TRUE	1	0.221165192112145	3		463	672	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396919	139396919	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	72	282	0	ENST00000277541.6:c.5189C>G	p.Pro1730Arg	p.P1730R	ENST00000277541	NM_017617.3	1730	cCg/cGg	28/34	1	2	FACETS	0.894	0.786	1	1	0.98	1	CLONAL	2	TRUE	1	0.221165192112145	2		282	364	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0035269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	67	458	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.917	0.8	1	0.917	0.8	1	CLONAL	1	TRUE	1	0.329695654731466	2		458	443	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0035269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	157	680	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.329695654731466	2		680	751	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0035269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	151	606	2	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.329695654731466	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.329695654731466	1		608	655	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937034	48937035	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	33	236	0	ENST00000267163.4:c.806dup	p.Asn269LysfsTer2	p.N269Kfs*2	ENST00000267163	NM_000321.2	268	gaa/gAaa	8/27	0.329695654731466	1	FACETS	0.629	0.514	0.756	0.629	0.514	0.756	SUBCLONAL	1	TRUE	0	0.329695654731466	1		236	266	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61712923	61712923	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	80	396	0	ENST00000401558.2:c.2488del	p.Thr830HisfsTer2	p.T830Hfs*2	ENST00000401558	NM_003400.3	830	Aca/ca	20/25	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.329695654731466	2		396	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0035289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	285	573	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.762639683197201	1	FACETS	0.973	0.93	1	0.973	0.93	1	CLONAL	1	TRUE	0	0.762639683197201	1		574	475	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567782	226567782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763508057	NA	P-0035289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	607	638	0	ENST00000366794.5:c.1384G>A	p.Val462Ile	p.V462I	ENST00000366794	NM_001618.3	462	Gtc/Atc	10/23	0.481193424334024	4	FACETS	0.991	0.955	1	0.991	0.955	1	CLONAL	2	TRUE	2	0.762639683197201	4		638	1416	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29701075	29701075	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	373	312	0	ENST00000356175.3:c.8359T>C	p.Cys2787Arg	p.C2787R	ENST00000356175	NM_000267.3	2787	Tgt/Cgt	57/57	0.762639683197201	2	FACETS	0.99	0.959	1	0.99	0.959	1	CLONAL	2	TRUE	0	0.762639683197201	2		312	494	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170015131	170015131	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	653	639	0	ENST00000295797.4:c.1537T>A	p.Phe513Ile	p.F513I	ENST00000295797	NM_002740.5	513	Ttt/Att	16/18	0.740565775195734	3	FACETS	0.986	0.955	1	0.658	0.637	0.679	CLONAL	2	TRUE	0	0.762639683197201	3		639	1199	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798806	135798806	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	202	248	0	ENST00000298552.3:c.437C>G	p.Ser146Cys	p.S146C	ENST00000298552	NM_001162426.1	146	tCt/tGt	6/23	0.11374725072279	5	FACETS	0.855	0.802	0.907			1	INDETERMINATE	3	TRUE	NA	0.762639683197201	5		248	443	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137323775	137323775	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	10856	824	0	ENST00000481739.1:c.1068G>C	p.Lys356Asn	p.K356N	ENST00000481739	NM_002957.4	356	aaG/aaC	8/10	0.762639683197201	17	FACETS	0.997	0.994	1			1	CLONAL	17	TRUE	NA	0.762639683197201	17		824	11287	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0035290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	22	425	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.699	0.542	0.882	0.699	0.542	0.882	SUBCLONAL	1	TRUE	1	0.19126088390971	2		425	329	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827933	40827933	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	53	463	0	ENST00000373198.4:c.2495C>A	p.Ala832Asp	p.A832D	ENST00000373198	NM_133170.3	832	gCc/gAc	17/32	0.0591605378038418	4	FACETS	0.889	0.756	1	0.444	0.378	0.517	INDETERMINATE	1	TRUE	2	0.19126088390971	4		463	743	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637861	39637861	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	80	270	0	ENST00000262039.4:c.2278A>G	p.Ile760Val	p.I760V	ENST00000262039	NM_002647.2	760	Ata/Gta	22/25	0.447478521377361	1	FACETS	0.374	0.334	0.416	0.374	0.334	0.416	INDETERMINATE	1	TRUE	0	0.904323254835009	1		270	259	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115711	8115712	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCT	novel	NA	P-0035295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	74	293	0	ENST00000346208.3:c.1058_1061dup	p.Thr355ProfsTer17	p.T355Pfs*17	ENST00000346208		353	ccc/cCCCTcc	6/6	0.167533634427843	4	FACETS	0.772	0.679	0.871	0.772	0.679	0.871	INDETERMINATE	2	TRUE	2	0.305975620067327	4		293	409	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870865	12870875	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTCTTCGGC	ACCTCTTCGGC	-	novel	NA	P-0035295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	62	166	0	ENST00000228872.4:c.92_102del	p.Asn31ThrfsTer90	p.N31Tfs*90	ENST00000228872	NM_004064.3	31	aACCTCTTCGGC/a	1/3	0.245867486399304	5	FACETS	1	0.957	1	0.821	0.718	0.93	CLONAL	2	TRUE	2	0.305975620067327	5		166	240	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063666	67063666	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	96	321	0	ENST00000412916.2:c.115G>T	p.Glu39Ter	p.E39*	ENST00000412916		39	Gaa/Taa	2/6	0.207748959244121	2	FACETS	0.767	0.688	0.85	0.767	0.688	0.85	SUBCLONAL	2	TRUE	0	0.305975620067327	2		321	409	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938347	76938347	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	59	656	1	ENST00000373344.5:c.2401T>A	p.Ser801Thr	p.S801T	ENST00000373344	NM_000489.3	801	Tct/Act	9/35	1	2	FACETS	0.39	0.334	0.451	0.39	0.334	0.451	SUBCLONAL	1	TRUE	1	0.305975620067327	2		657	989	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111675	56111675	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	20	166	1	ENST00000399503.3:c.275C>A	p.Ser92Ter	p.S92*	ENST00000399503	NM_005921.1	92	tCg/tAg	1/20	0.321745608894917	2	FACETS	0.499	0.383	0.633	0.249	0.191	0.317	SUBCLONAL	1	TRUE	0	0.409283897348009	2		167	196	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520006	NA	P-0035296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	230	597	0	ENST00000269305.4:c.821T>C	p.Val274Ala	p.V274A	ENST00000269305	NM_001126112.2	274	gTt/gCt	8/11	0.339216067904416	2	FACETS	1	0.992	1	0.714	0.668	0.762	CLONAL	1	TRUE	0	0.409283897348009	2		597	787	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521619	89521619	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0035296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	152	379	0	ENST00000336596.2:c.2696C>G	p.Ser899Ter	p.S899*	ENST00000336596	NM_005233.5	899	tCa/tGa	16/17	0.321745608894917	2	FACETS	0.806	0.743	0.87	0.806	0.743	0.87	CLONAL	2	TRUE	0	0.409283897348009	2		379	461	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81960695	81960695	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	47	386	0	ENST00000359376.3:c.2426G>C	p.Gly809Ala	p.G809A	ENST00000359376	NM_002661.3	809	gGa/gCa	23/33	0.339216067904416	2	FACETS	0.47	0.396	0.551	0.235	0.198	0.276	SUBCLONAL	1	TRUE	0	0.409283897348009	2		386	489	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545099	41545099	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	57	448	0	ENST00000263253.7:c.2299C>G	p.Gln767Glu	p.Q767E	ENST00000263253	NM_001429.3	767	Cag/Gag	13/31	0.339216067904416	2	FACETS	0.418	0.358	0.483	0.209	0.179	0.242	SUBCLONAL	1	TRUE	0	0.409283897348009	2		448	667	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30682823	30682823	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	46	422	0	ENST00000376406.3:c.130G>C	p.Glu44Gln	p.E44Q	ENST00000376406	NM_014641.2	44	Gaa/Caa	2/15	0.371958110499035	3	FACETS	0.382	0.321	0.451	0.191	0.16	0.226	SUBCLONAL	1	TRUE	1	0.409283897348009	3		422	708	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170277	32170337	+	frameshift_variant	Frame_Shift_Del	DEL	GGAAGCCTGGCTTAGGGGAGGGCAGACACAGGCCTCCGTGGTGGCAGTGATGGAAGCCGCA	GGAAGCCTGGCTTAGGGGAGGGCAGACACAGGCCTCCGTGGTGGCAGTGATGGAAGCCGCA	-	novel	NA	P-0035296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	64	666	0	ENST00000375023.3:c.3271_3331del	p.Cys1091HisfsTer16	p.C1091Hfs*16	ENST00000375023	NM_004557.3	1091	TGCGGCTTCCATCACTGCCACCACGGAGGCCTGTGTCTGCCCTCCCCTAAGCCAGGCTTCCca/ca	21/30	0.371958110499035	3	FACETS	0.437	0.377	0.502	0.219	0.188	0.251	SUBCLONAL	1	TRUE	1	0.409283897348009	3		666	862	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198252	138198252	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	28	198	0	ENST00000237289.4:c.845G>T	p.Arg282Ile	p.R282I	ENST00000237289	NM_001270507.1	282	aGa/aTa	6/9	0.371958110499035	3	FACETS	0.397	0.317	0.489	0.199	0.158	0.245	SUBCLONAL	1	TRUE	1	0.409283897348009	3		198	415	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490226	29490226	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs1057521097	NA	P-0035297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	31	336	0	ENST00000356175.3:c.311T>G	p.Leu104Ter	p.L104*	ENST00000356175	NM_000267.3	104	tTa/tGa	4/57	0.254550660932029	3	FACETS	0.848	0.708	0.996	0.848	0.708	0.996	INDETERMINATE	2	TRUE	1	0.52418161106175	3		336	88	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857494	9857494	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	63	386	1	ENST00000330684.3:c.3907G>A	p.Asp1303Asn	p.D1303N	ENST00000330684	NM_001134407.1	1303	Gac/Aac	13/13	0.510869430542049	2	FACETS	0.796	0.706	0.887	0.796	0.706	0.887	SUBCLONAL	2	TRUE	0	0.52418161106175	2		387	151	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587505	29587505	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	21	442	0	ENST00000356175.3:c.4489del	p.Ile1497LeufsTer56	p.I1497Lfs*56	ENST00000356175	NM_000267.3	1496	Aaa/aa	33/57	0.254550660932029	3	FACETS	1	0.924	1	0.722	0.574	0.884	INDETERMINATE	1	TRUE	1	0.52418161106175	3		442	70	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207185	1207208	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGAGGCCAACGTGAAGAAGTAAGT	GGAGGCCAACGTGAAGAAGTAAGT	CTTCCCCA	novel	NA	P-0035297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	99	645	3	ENST00000326873.7:c.273_290+6delinsCTTCCCCA		p.X91_splice	ENST00000326873	NM_000455.4	91		1/10	0.457555908502571	2	FACETS	0.971	0.874	1	0.486	0.437	0.537	CLONAL	1	TRUE	0	0.52418161106175	2		648	389	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191493	10191493	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs5030622	NA	P-0035298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	123	416	0	ENST00000256474.2:c.486C>A	p.Cys162Ter	p.C162*	ENST00000256474	NM_000551.3	162	tgC/tgA	3/3	0.569079324473998	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	FALSE	0	0.569079324473998	1		416	297	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092739	27092740	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0035298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	93	356	0	ENST00000324856.7:c.2765dup	p.Met923HisfsTer13	p.M923Hfs*13	ENST00000324856	NM_006015.4	920	-/G	9/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.569079324473998	2		356	292	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651382	52651382	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	103	582	0	ENST00000394830.3:c.1714G>T	p.Glu572Ter	p.E572*	ENST00000394830	NM_018313.4	572	Gag/Tag	15/30	0.569079324473998	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	0	0.569079324473998	1		582	253	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170714	7170714	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	179	696	0	ENST00000302850.5:c.1317G>A	p.Trp439Ter	p.W439*	ENST00000302850	NM_000208.2	439	tgG/tgA	6/22	1	2	FACETS	0.936	0.866	1	0.936	0.866	1	CLONAL	1	FALSE	1	0.569079324473998	2		696	672	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125836	47125836	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	43	294	0	ENST00000409792.3:c.5434A>G	p.Lys1812Glu	p.K1812E	ENST00000409792	NM_014159.6	1812	Aaa/Gaa	12/21	0.569079324473998	1	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	FALSE	0	0.569079324473998	1		294	102	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043336	6043336	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	39	311	0	ENST00000265849.7:c.338C>T	p.Ser113Leu	p.S113L	ENST00000265849	NM_000535.5	113	tCa/tTa	4/15	0.156113266520709	4	FACETS	1	0.925	1	0.594	0.499	0.698	INDETERMINATE	1	FALSE	2	0.569079324473998	4		311	181	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0035315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	78	354	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.868	0.764	0.98	0.868	0.764	0.98	CLONAL	1	TRUE	1	0.325996433724246	2		354	551	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771367	68771367	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1440280370	NA	P-0035315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	95	251	0	ENST00000261769.5:c.48+1G>A		p.X16_splice	ENST00000261769	NM_004360.3	16			0.325996433724246	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.325996433724246	1		251	406	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864512	56864512	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	162	495	0	ENST00000308159.5:c.1000G>T	p.Ala334Ser	p.A334S	ENST00000308159	NM_014669.4	334	Gct/Tct	10/22	0.325996433724246	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.325996433724246	1		495	783	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913499	NA	P-0035318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	56	323	0	ENST00000345146.2:c.394C>A	p.Arg132Ser	p.R132S	ENST00000345146	NM_005896.2	132	Cgt/Agt	4/10	1	2	FACETS	0.997	0.872	1	0.997	0.872	1	CLONAL	1	TRUE	1	0.672421373413635	2		323	167	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262680	16262680	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	12	422	1	ENST00000375759.3:c.9950del	p.Pro3317ArgfsTer83	p.P3317Rfs*83	ENST00000375759	NM_015001.2	3315	caC/ca	11/15	0.672421373413635	1	FACETS	0.108	0.075	0.148	0.108	0.075	0.148	SUBCLONAL	1	TRUE	0	0.672421373413635	1		423	220	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1976665	1976665	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	126	648	0	ENST00000382891.5:c.3448A>G	p.Thr1150Ala	p.T1150A	ENST00000382891	NM_133335.3	1150	Acc/Gcc	19/22	0.672421373413635	1	FACETS	0.983	0.91	1	0.983	0.91	1	CLONAL	1	TRUE	0	0.672421373413635	1		648	253	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0035319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	96	298	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.938	0.846	1	0.938	0.846	1	CLONAL	1	TRUE	1	0.667006551971365	2		298	307	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	221	539	1	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	1	2	FACETS	0.781	0.728	0.835	0.781	0.728	0.835	SUBCLONAL	1	TRUE	1	0.667006551971365	2		540	849	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0035319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	113	223	2	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.86	0.781	0.942	0.86	0.781	0.942	CLONAL	1	TRUE	1	0.667006551971365	2		225	394	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057936	27057937	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1415146710	NA	P-0035319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	317	643	0	ENST00000324856.7:c.1650dup	p.Tyr551LeufsTer72	p.Y551Lfs*72	ENST00000324856	NM_006015.4	548	-/C	3/20	1	2	FACETS	0.997	0.944	1	0.997	0.944	1	CLONAL	1	TRUE	1	0.667006551971365	2		643	953	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660469	67660469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	262	443	0	ENST00000264010.4:c.1369C>T	p.Arg457Ter	p.R457*	ENST00000264010	NM_006565.3	457	Cga/Tga	8/12	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.667006551971365	2		443	755	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107096	27107096	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	235	523	0	ENST00000324856.7:c.6707G>C	p.Arg2236Pro	p.R2236P	ENST00000324856	NM_006015.4	2236	cGc/cCc	20/20	1	2	FACETS	0.915	0.857	0.975	0.915	0.857	0.975	CLONAL	1	TRUE	1	0.667006551971365	2		523	770	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522353	157522353	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs570186838	NA	P-0035319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	371	686	0	ENST00000346085.5:c.4625C>T	p.Thr1542Met	p.T1542M	ENST00000346085	NM_020732.3	1542	aCg/aTg	18/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.667006551971365	2		686	1055	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434561	49434562	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0035319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	209	657	0	ENST00000301067.7:c.6991dup	p.Leu2331ProfsTer46	p.L2331Pfs*46	ENST00000301067	NM_003482.3	2331	ctg/cCtg	31/54	1	2	FACETS	0.787	0.733	0.844	0.787	0.733	0.844	SUBCLONAL	1	TRUE	1	0.667006551971365	2		657	796	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437224	52437224	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770654975	NA	P-0035319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	356	744	2	ENST00000460680.1:c.1820C>T	p.Thr607Met	p.T607M	ENST00000460680	NM_004656.3	607	aCg/aTg	14/17	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.667006551971365	2		746	1046	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653846	89653846	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762518389	NA	P-0035319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	197	472	0	ENST00000371953.3:c.144C>A	p.Asn48Lys	p.N48K	ENST00000371953	NM_000314.4	48	aaC/aaA	2/9	1	2	FACETS	0.878	0.816	0.941	0.878	0.816	0.941	CLONAL	1	TRUE	1	0.667006551971365	2		472	673	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173614	108173615	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	158	422	0	ENST00000278616.4:c.5358dup	p.Glu1787Ter	p.E1787*	ENST00000278616	NM_000051.3	1785	cct/ccTt	36/63	1	2	FACETS	0.944	0.871	1	0.944	0.871	1	CLONAL	1	TRUE	1	0.667006551971365	2		422	502	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315354	30315354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1480541649	NA	P-0035319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	247	426	0	ENST00000322652.5:c.1039G>A	p.Glu347Lys	p.E347K	ENST00000322652	NM_015355.2	347	Gaa/Aaa	10/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.667006551971365	2		426	718	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41219670	41219670	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	321	585	0	ENST00000357654.3:c.5029A>C	p.Thr1677Pro	p.T1677P	ENST00000357654	NM_007294.3	1677	Act/Cct	16/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.667006551971365	2		585	894	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761459	59761459	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587781417	NA	P-0035319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	269	492	2	ENST00000259008.2:c.2948T>A	p.Ile983Asn	p.I983N	ENST00000259008	NM_032043.2	983	aTt/aAt	20/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.667006551971365	2		494	770	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449609	187449609	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	216	475	0	ENST00000232014.4:c.271T>C	p.Tyr91His	p.Y91H	ENST00000232014	NM_001130845.1	91	Tac/Cac	4/10	1	2	FACETS	0.972	0.909	1	0.972	0.909	1	CLONAL	1	TRUE	1	0.667006551971365	2		475	666	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542420	187542420	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs532008780	NA	P-0035319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	48	508	0	ENST00000441802.2:c.5320A>G	p.Ile1774Val	p.I1774V	ENST00000441802	NM_005245.3	1774	Att/Gtt	10/27	1	2	FACETS	0.193	0.162	0.227	0.193	0.162	0.227	SUBCLONAL	1	TRUE	1	0.667006551971365	2		508	746	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589633	67589663	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TTATATGAAGAATATACCCGCACATCCCAGG	TTATATGAAGAATATACCCGCACATCCCAGG	AAACTCACC	novel	NA	P-0035319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	48	284	1	ENST00000274335.5:c.1396_1425+1delinsAAACTCACC		p.X466_splice	ENST00000274335		466		10/15	1	2	FACETS	0.448	0.381	0.522	0.448	0.381	0.522	SUBCLONAL	1	TRUE	1	0.667006551971365	2		285	321	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505492	157505492	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762153671	NA	P-0035319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	192	362	0	ENST00000346085.5:c.3473G>A	p.Arg1158His	p.R1158H	ENST00000346085	NM_020732.3	1158	cGt/cAt	13/20	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.667006551971365	2		362	568	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523562	106523562	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	135	330	0	ENST00000359195.3:c.2714A>C	p.Glu905Ala	p.E905A	ENST00000359195	NM_002649.2	905	gAa/gCa	8/11	1	2	FACETS	0.856	0.783	0.931	0.856	0.783	0.931	CLONAL	1	TRUE	1	0.667006551971365	2		330	473	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912193	127912193	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	149	326	0	ENST00000373547.4:c.677A>G	p.His226Arg	p.H226R	ENST00000373547	NM_002721.4	226	cAt/cGt	7/7	1	2	FACETS	0.991	0.913	1	0.991	0.913	1	CLONAL	1	TRUE	1	0.667006551971365	2		326	451	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0035320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	177	425	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.12949769146964	3	FACETS	0.854	0.79	0.921	0.569	0.526	0.614	INDETERMINATE	2	TRUE	0	0.354584321172086	3		425	688	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0035320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	63	240	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.354584321172086	3	FACETS	1	0.922	1	0.543	0.472	0.62	CLONAL	1	TRUE	1	0.354584321172086	3		240	385	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593466	48593466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064796102	NA	P-0035320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	110	409	0	ENST00000342988.3:c.1217C>T	p.Ala406Val	p.A406V	ENST00000342988	NM_005359.5	406	gCg/gTg	10/12	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.354584321172086	2		409	603	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604769	48604769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766833269	NA	P-0035320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	78	396	0	ENST00000342988.3:c.1591C>T	p.Arg531Trp	p.R531W	ENST00000342988	NM_005359.5	531	Cgg/Tgg	12/12	1	2	FACETS	0.827	0.728	0.933	0.827	0.728	0.933	CLONAL	1	TRUE	1	0.354584321172086	2		396	532	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533883	63533884	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0035320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	97	462	0	ENST00000307078.5:c.1270_1271del	p.Ser424ProfsTer37	p.S424Pfs*37	ENST00000307078	NM_004655.3	424	TCc/c	6/11	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.354584321172086	2		462	535	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412647	63412648	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	209	584	0	ENST00000330258.3:c.519dup	p.Ser174Ter	p.S174*	ENST00000330258	NM_152424.3	173	-/T	2/2	0.354584321172086	3	FACETS	0.979	0.912	1	0.979	0.912	1	CLONAL	2	TRUE	1	0.354584321172086	3		584	709	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024724	14024724	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	111	453	1	ENST00000311895.7:c.954del	p.Ala319LeufsTer19	p.A319Lfs*19	ENST00000311895	NM_005236.2	317	gAa/ga	5/11	0.354584321172086	3	FACETS	1	0.933	1	0.523	0.471	0.579	CLONAL	1	TRUE	1	0.354584321172086	3		454	704	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349775	89349775	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	334	717	0	ENST00000301030.4:c.3175A>G	p.Lys1059Glu	p.K1059E	ENST00000301030	NM_001256183.1	1059	Aaa/Gaa	9/13	0.354584321172086	3	FACETS	0.949	0.898	1	0.949	0.898	1	CLONAL	2	TRUE	1	0.354584321172086	3		717	1168	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604797	48604797	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	72	351	0	ENST00000342988.3:c.1619T>C	p.Leu540Pro	p.L540P	ENST00000342988	NM_005359.5	540	cTt/cCt	12/12	1	2	FACETS	0.82	0.718	0.93	0.82	0.718	0.93	CLONAL	1	TRUE	1	0.354584321172086	2		351	495	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47724984	47724984	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373478289	NA	P-0035320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	139	661	1	ENST00000449228.1:c.760G>A	p.Ala254Thr	p.A254T	ENST00000449228	NM_001127240.2	254	Gcg/Acg	4/4	0.354584321172086	3	FACETS	1	0.93	1	0.513	0.466	0.562	CLONAL	1	TRUE	1	0.354584321172086	3		662	900	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591117	+	inframe_deletion	In_Frame_Del	DEL	AACAGCATTAAACCAGACCTT	AACAGCATTAAACCAGACCTT	-	novel	NA	P-0035320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	124	241	0	ENST00000274335.5:c.1691_1711del	p.Asn564_Leu570del	p.N564_L570del	ENST00000274335		564	AACAGCATTAAACCAGACCTT/-	12/15	0.354584321172086	3	FACETS	0.962	0.877	1	0.962	0.877	1	CLONAL	2	TRUE	1	0.354584321172086	3		241	428	SUCCESS
APC	324	MSKCC	GRCh37	5	112175554	112175555	+	missense_variant	Missense_Mutation	DNP	TG	TG	CT	novel	NA	P-0035320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	144	332	1	ENST00000257430.4:c.4263_4264delinsCT	p.Asp1422Tyr	p.D1422Y	ENST00000257430	NM_000038.5	1421	agTGat/agCTat	16/16	0.354584321172086	3	FACETS	0.943	0.866	1	0.943	0.866	1	CLONAL	2	TRUE	1	0.354584321172086	3		333	507	SUCCESS
APC	324	MSKCC	GRCh37	5	112175561	112175570	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGATAGCC	CCAGATAGCC	-	novel	NA	P-0035320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	142	325	0	ENST00000257430.4:c.4271_4280del	p.Pro1424LeufsTer46	p.P1424Lfs*46	ENST00000257430	NM_000038.5	1424	CCAGATAGCCct/ct	16/16	0.354584321172086	3	FACETS	0.956	0.877	1	0.956	0.877	1	CLONAL	2	TRUE	1	0.354584321172086	3		325	493	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923090	39923090	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	134	703	0	ENST00000378444.4:c.3618A>T	p.Lys1206Asn	p.K1206N	ENST00000378444	NM_001123385.1	1206	aaA/aaT	8/15	0.354584321172086	3	FACETS	0.91	0.826	0.999	0.455	0.413	0.5	CLONAL	1	TRUE	1	0.354584321172086	3		703	978	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97869361	97869361	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	252	491	1	ENST00000289081.3:c.1520A>T	p.Asp507Val	p.D507V	ENST00000289081	NM_000136.2	507	gAt/gTt	14/15	1	2	FACETS	0.613	0.574	0.652	0.613	0.574	0.652	SUBCLONAL	1	TRUE	1	0.910962481583262	2		492	903	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937001	48937001	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	83	391	0	ENST00000267163.4:c.769C>T	p.Gln257Ter	p.Q257*	ENST00000267163	NM_000321.2	257	Cag/Tag	8/27	0.433846543186942	1	FACETS	0.669	0.594	0.747	0.669	0.594	0.747	SUBCLONAL	1	FALSE	0	0.497447394403267	1		391	375	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692985	89692985	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121909220	NA	P-0035322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	84	379	0	ENST00000371953.3:c.469G>T	p.Glu157Ter	p.E157*	ENST00000371953	NM_000314.4	157	Gaa/Taa	5/9	0.39976300951374	0	FACETS	0.496	0.442	0.553			1	SUBCLONAL	1	FALSE	0	0.497447394403267	0		379	342	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461945	120461945	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	119	493	0	ENST00000256646.2:c.5771G>C	p.Gly1924Ala	p.G1924A	ENST00000256646	NM_024408.3	1924	gGt/gCt	31/34	1	2	FACETS	0.768	0.695	0.845	0.768	0.695	0.845	SUBCLONAL	1	FALSE	1	0.497447394403267	2		493	623	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922574	56922574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	140	472	0	ENST00000519728.1:c.1444G>A	p.Glu482Lys	p.E482K	ENST00000519728	NM_002350.3	482	Gaa/Aaa	13/13	0.31430440933098	1	FACETS	0.499	0.454	0.546	0.499	0.454	0.546	SUBCLONAL	1	FALSE	0	0.497447394403267	1		472	847	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014146	14014146	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	133	505	0	ENST00000311895.7:c.124G>C	p.Asp42His	p.D42H	ENST00000311895	NM_005236.2	42	Gac/Cac	1/11	1	2	FACETS	0.54	0.489	0.593	0.54	0.489	0.593	SUBCLONAL	1	FALSE	1	0.497447394403267	2		505	991	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0035325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	122	745	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.23857756011202	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.23857756011202	1		745	875	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	116	523	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.23857756011202	2		523	868	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591891	48591891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912581	NA	P-0035325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	93	502	0	ENST00000342988.3:c.1054G>A	p.Gly352Arg	p.G352R	ENST00000342988	NM_005359.5	352	Gga/Aga	9/12	0.23857756011202	1	FACETS	0.96	0.854	1	0.96	0.854	1	CLONAL	1	TRUE	0	0.23857756011202	1		502	715	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942752	44942752	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1457797612	NA	P-0035325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	116	284	0	ENST00000377967.4:c.3332G>C	p.Arg1111Pro	p.R1111P	ENST00000377967	NM_021140.2	1111	cGt/cCt	23/29	0.139156691574379	2	FACETS	0.996	0.903	1			1	INDETERMINATE	2	TRUE	NA	0.23857756011202	2		284	488	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371933	55371933	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	33	201	0	ENST00000297316.4:c.623G>T	p.Ser208Ile	p.S208I	ENST00000297316	NM_022454.3	208	aGt/aTt	2/2	1	2	FACETS	0.636	0.518	0.769	0.636	0.518	0.769	SUBCLONAL	1	TRUE	1	0.23857756011202	2		201	435	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0035334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	259	451	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	0.543964039380825	4	FACETS	1	0.99	1	0.779	0.74	0.818	CLONAL	2	TRUE	1	0.848165502065575	4		451	483	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003250	42003250	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0035334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	223	539	0	ENST00000219905.7:c.2787C>G	p.Tyr929Ter	p.Y929*	ENST00000219905	NM_001164273.1	929	taC/taG	8/24	0.848165502065575	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.848165502065575	1		539	266	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0035369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	833	463	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.476884441856849	17	FACETS	0.981	0.963	0.998			1	CLONAL	16	FALSE	NA	0.476884441856849	17		463	1019	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs786203436	NA	P-0035369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	146	975	0	ENST00000269305.4:c.487T>G	p.Tyr163Asp	p.Y163D	ENST00000269305	NM_001126112.2	163	Tac/Gac	5/11	0.453920233794905	3	FACETS	1	0.957	1	0.7	0.648	0.754	CLONAL	2	FALSE	0	0.476884441856849	3		975	361	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508725	106508725	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	36	786	0	ENST00000359195.3:c.719C>A	p.Thr240Asn	p.T240N	ENST00000359195	NM_002649.2	240	aCc/aAc	2/11	0.317579686253168	3	FACETS	0.68	0.562	0.811	0.227	0.187	0.271	SUBCLONAL	1	FALSE	0	0.476884441856849	3		786	275	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354391	40354391	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	36	1310	2	ENST00000293328.3:c.2204G>A	p.Cys735Tyr	p.C735Y	ENST00000293328	NM_012448.3	735	tGt/tAt	18/19	0.453920233794905	3	FACETS	0.511	0.42	0.612	0.17	0.14	0.204	SUBCLONAL	1	FALSE	0	0.476884441856849	3		1312	366	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0035371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	302	463	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.803612017589408	4	FACETS	1	0.941	1	0.333	0.313	0.354	CLONAL	1	TRUE	1	0.803612017589408	4		463	1355	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476811	140476811	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507479	NA	P-0035371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	78	601	0	ENST00000288602.6:c.1595G>A	p.Cys532Tyr	p.C532Y	ENST00000288602	NM_004333.4	532	tGt/tAt	13/18	1	2	FACETS	0.22	0.192	0.249	0.22	0.192	0.249	SUBCLONAL	1	TRUE	1	0.803612017589408	2		601	883	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0035371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	270	332	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	0.803612017589408	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.803612017589408	1		333	402	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0035371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	103	489	4	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	0.803612017589408	1	FACETS	0.307	0.276	0.34	0.307	0.276	0.34	SUBCLONAL	1	TRUE	0	0.803612017589408	1		493	499	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022403	31022425	+	frameshift_variant	Frame_Shift_Del	DEL	CACCACTGCCATAGAGAGGCGGC	CACCACTGCCATAGAGAGGCGGC	-	rs766433101	NA	P-0035371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	129	317	0	ENST00000375687.4:c.1900_1922del	p.Glu635ArgfsTer15	p.E635Rfs*15	ENST00000375687	NM_015338.5	630	CACCACTGCCATAGAGAGGCGGCc/c	13/13	1	2	FACETS	0.743	0.679	0.809	0.743	0.679	0.809	SUBCLONAL	1	TRUE	1	0.803612017589408	2		317	432	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	249	477	0	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	0.803612017589408	1	FACETS	0.668	0.631	0.706	0.668	0.631	0.706	SUBCLONAL	1	TRUE	0	0.803612017589408	1		477	555	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577112	7577112	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1131691029	NA	P-0035371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	466	787	0	ENST00000269305.4:c.826G>C	p.Ala276Pro	p.A276P	ENST00000269305	NM_001126112.2	276	Gcc/Ccc	8/11	0.803612017589408	1	FACETS	0.985	0.953	1	0.985	0.953	1	CLONAL	1	TRUE	0	0.803612017589408	1		787	704	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729888	41729888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1043609570	NA	P-0035371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	89	593	0	ENST00000242208.4:c.641G>A	p.Arg214Gln	p.R214Q	ENST00000242208	NM_002192.2	214	cGg/cAg	3/3	1	2	FACETS	0.264	0.233	0.297	0.264	0.233	0.297	SUBCLONAL	1	TRUE	1	0.803612017589408	2		593	839	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249393	110249393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747114701	NA	P-0035371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1322	251	944	1	ENST00000374672.4:c.1180G>A	p.Ala394Thr	p.A394T	ENST00000374672	NM_004235.4	394	Gcc/Acc	4/5	1	2	FACETS	0.397	0.37	0.425	0.397	0.37	0.425	SUBCLONAL	1	TRUE	1	0.803612017589408	2		945	1573	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738280	145738280	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372205013	NA	P-0035371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1584	161	914	0	ENST00000428558.2:c.2705G>A	p.Arg902Gln	p.R902Q	ENST00000428558	NM_004260.3	902	cGg/cAg	16/22	0.720986571889018	3	FACETS	0.322	0.294	0.352	0.161	0.147	0.176	SUBCLONAL	1	TRUE	1	0.803612017589408	3		914	1745	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225789	26225789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	43	383	0	ENST00000360408.1:c.407C>T	p.Ala136Val	p.A136V	ENST00000360408	NM_003532.2	136	gCg/gTg	1/1	1	2	FACETS	0.151	0.126	0.179	0.151	0.126	0.179	SUBCLONAL	1	TRUE	1	0.803612017589408	2		383	708	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108698	8108698	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs746401290	NA	P-0035371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	263	558	0	ENST00000585124.1:c.697A>G	p.Met233Val	p.M233V	ENST00000585124	NM_004217.3	233	Atg/Gtg	8/9	0.803612017589408	1	FACETS	0.769	0.73	0.808	0.769	0.73	0.808	SUBCLONAL	1	TRUE	0	0.803612017589408	1		558	509	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137321073	137321073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768721235	NA	P-0035371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	36	526	0	ENST00000481739.1:c.1030G>A	p.Ala344Thr	p.A344T	ENST00000481739	NM_002957.4	344	Gcc/Acc	7/10	0.138374631717526	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.803612017589408	0		526	715	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645336	215645336	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	50	622	0	ENST00000260947.4:c.1262C>T	p.Ala421Val	p.A421V	ENST00000260947	NM_000465.2	421	gCt/gTt	4/11	1	2	FACETS	0.147	0.124	0.173	0.147	0.124	0.173	SUBCLONAL	1	TRUE	1	0.803612017589408	2		622	844	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509084	66509085	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	13	335	0	ENST00000273854.3:c.242dup	p.Asn81LysfsTer8	p.N81Kfs*8	ENST00000273854	NM_004439.5	81	aat/aaAt	2/18	0.803612017589408	1	FACETS	0.076	0.053	0.103	0.076	0.053	0.103	SUBCLONAL	1	TRUE	0	0.803612017589408	1		335	256	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827419	72827419	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	433	852	0	ENST00000268489.5:c.9162C>A	p.Asp3054Glu	p.D3054E	ENST00000268489	NM_006885.3	3054	gaC/gaA	9/10	1	2	FACETS	0.973	0.929	1	0.973	0.929	1	CLONAL	1	TRUE	1	0.803612017589408	2		852	1108	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912061	50912061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149569984	NA	P-0035371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	83	793	0	ENST00000440232.2:c.1795G>A	p.Ala599Thr	p.A599T	ENST00000440232	NM_002691.3	599	Gcc/Acc	15/27	1	2	FACETS	0.177	0.155	0.2	0.177	0.155	0.2	SUBCLONAL	1	TRUE	1	0.803612017589408	2		793	1169	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572357	41572357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	75	782	2	ENST00000263253.7:c.4886C>T	p.Ala1629Val	p.A1629V	ENST00000263253	NM_001429.3	1629	gCg/gTg	30/31	0.796906101886267	2	FACETS	0.152	0.132	0.173	0.076	0.066	0.087	SUBCLONAL	1	TRUE	0	0.803612017589408	2		784	1230	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957444	175957444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs201905141	NA	P-0035371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	263	506	0	ENST00000367669.3:c.1952A>G	p.Asn651Ser	p.N651S	ENST00000367669	NM_022457.5	651	aAt/aGt	17/20	1	2	FACETS	0.946	0.892	1	0.946	0.892	1	CLONAL	1	TRUE	1	0.803612017589408	2		506	692	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683168	88683168	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs761612520	NA	P-0035371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	27	467	0	ENST00000372037.3:c.1378A>G	p.Met460Val	p.M460V	ENST00000372037	NM_004329.2	460	Atg/Gtg	12/13	0.803612017589408	1	FACETS	0.094	0.074	0.116	0.094	0.074	0.116	SUBCLONAL	1	TRUE	0	0.803612017589408	1		467	429	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444702	49444702	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	518	816	1	ENST00000301067.7:c.2764del	p.Glu922SerfsTer8	p.E922Sfs*8	ENST00000301067	NM_003482.3	922	Gag/ag	10/54	1	2	FACETS	0.991	0.951	1	0.991	0.951	1	CLONAL	1	TRUE	1	0.803612017589408	2		817	1301	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536623	120536623	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	378	727	0	ENST00000229340.5:c.469G>T	p.Val157Leu	p.V157L	ENST00000229340	NM_006861.6	157	Gtg/Ttg	5/6	1	2	FACETS	0.912	0.867	0.956	0.912	0.867	0.956	CLONAL	1	TRUE	1	0.803612017589408	2		727	1032	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435001	110435001	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0035371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	411	649	0	ENST00000375856.3:c.3400A>T	p.Lys1134Ter	p.K1134*	ENST00000375856	NM_003749.2	1134	Aag/Tag	1/2	1	2	FACETS	0.943	0.899	0.987	0.943	0.899	0.987	CLONAL	1	TRUE	1	0.803612017589408	2		649	1085	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50815298	50815298	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	101	742	0	ENST00000398568.2:c.1651C>G	p.Gln551Glu	p.Q551E	ENST00000398568	NM_001042412.1	551	Cag/Gag	9/18	1	2	FACETS	0.197	0.175	0.22	0.197	0.175	0.22	SUBCLONAL	1	TRUE	1	0.803612017589408	2		742	1279	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991352	72991352	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	84	684	0	ENST00000268489.5:c.2693C>A	p.Pro898His	p.P898H	ENST00000268489	NM_006885.3	898	cCc/cAc	2/10	1	2	FACETS	0.206	0.181	0.233	0.206	0.181	0.233	SUBCLONAL	1	TRUE	1	0.803612017589408	2		684	1016	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602645	10602645	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	448	726	0	ENST00000171111.5:c.933C>G	p.His311Gln	p.H311Q	ENST00000171111	NM_203500.1	311	caC/caG	3/6	1	2	FACETS	0.967	0.925	1	0.967	0.925	1	CLONAL	1	TRUE	1	0.803612017589408	2		726	1153	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61753559	61753559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	310	345	0	ENST00000401558.2:c.224C>T	p.Thr75Met	p.T75M	ENST00000401558	NM_003400.3	75	aCg/aTg	3/25	1	2	FACETS	0.9	0.852	0.949	0.9	0.852	0.949	CLONAL	1	TRUE	1	0.803612017589408	2		345	857	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209108290	209108290	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	70	569	0	ENST00000345146.2:c.559A>G	p.Lys187Glu	p.K187E	ENST00000345146	NM_005896.2	187	Aag/Gag	6/10	1	2	FACETS	0.2	0.173	0.228	0.2	0.173	0.228	SUBCLONAL	1	TRUE	1	0.803612017589408	2		569	873	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37048481	37048481	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs267607744	NA	P-0035371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	259	350	0	ENST00000231790.2:c.381-1G>C		p.X127_splice	ENST00000231790	NM_000249.3	127			0.803612017589408	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.803612017589408	1		350	363	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526376	31526376	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373280782	NA	P-0035371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	553	1023	2	ENST00000344624.3:c.664C>T	p.Pro222Ser	p.P222S	ENST00000344624		222	Cca/Tca	2/33	0.138374631717526	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.803612017589408	0		1025	1413	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755686	57755686	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	474	676	0	ENST00000274289.3:c.101G>C	p.Arg34Pro	p.R34P	ENST00000274289	NM_006622.3	34	cGg/cCg	1/14	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.803612017589408	2		676	1134	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131976493	131976493	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	334	569	0	ENST00000265335.6:c.3748G>C	p.Val1250Leu	p.V1250L	ENST00000265335		1250	Gtt/Ctt	24/25	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.803612017589408	2		569	793	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934046	39934046	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1471719373	NA	P-0035371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	143	405	0	ENST00000378444.4:c.553A>G	p.Ser185Gly	p.S185G	ENST00000378444	NM_001123385.1	185	Agt/Ggt	4/15	1	1	FACETS	0.362	0.331	0.394	0.362	0.331	0.394	SUBCLONAL	1	TRUE	0	0.803612017589408	1		405	588	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793663	NA	P-0035378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	114	555	0	ENST00000263967.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000263967	NM_006218.2	93	cGg/cAg	2/21	1	2	FACETS	0.822	0.743	0.905	0.822	0.743	0.905	CLONAL	1	FALSE	1	0.525274456481575	2		555	528	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245141	46245141	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	22	529	0	ENST00000334344.6:c.3235C>T	p.Leu1079Phe	p.L1079F	ENST00000334344	NM_152641.2	1079	Ctc/Ttc	15/21	0.294911385686418	4	FACETS	0.359	0.278	0.453	0.179	0.139	0.227	INDETERMINATE	1	FALSE	2	0.525274456481575	4		529	356	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374828	149374828	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	71	349	0	ENST00000360632.3:c.266C>G	p.Ser89Trp	p.S89W	ENST00000360632	NM_015472.4	89	tCg/tGg	2/7	1	2	FACETS	0.747	0.656	0.844	0.747	0.656	0.844	SUBCLONAL	1	FALSE	1	0.525274456481575	2		349	362	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41489043	41489043	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758786824	NA	P-0035378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	96	493	0	ENST00000263253.7:c.35C>T	p.Ser12Leu	p.S12L	ENST00000263253	NM_001429.3	12	tCa/tTa	1/31	1	2	FACETS	0.604	0.539	0.673	0.604	0.539	0.673	SUBCLONAL	1	FALSE	1	0.525274456481575	2		493	605	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349308	11349308	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	36	471	1	ENST00000332029.2:c.28G>T	p.Asp10Tyr	p.D10Y	ENST00000332029	NM_003745.1	10	Gac/Tac	2/2	1	2	FACETS	0.207	0.17	0.25	0.207	0.17	0.25	SUBCLONAL	1	FALSE	1	0.525274456481575	2		472	661	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641370	23641373	+	frameshift_variant	Frame_Shift_Del	DEL	ATGG	ATGG	-	novel	NA	P-0035378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	119	879	0	ENST00000261584.4:c.2102_2105del	p.Ser701TyrfsTer7	p.S701Yfs*7	ENST00000261584	NM_024675.3	701	tCCATa/ta	5/13	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.525274456481575	2		879	407	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012162	16012162	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765330083	NA	P-0035378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	66	622	0	ENST00000268712.3:c.2120C>T	p.Ser707Phe	p.S707F	ENST00000268712	NM_006311.3	707	tCt/tTt	19/46	1	2	FACETS	0.504	0.438	0.575	0.504	0.438	0.575	SUBCLONAL	1	FALSE	1	0.525274456481575	2		622	499	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654631	29654631	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	33	353	0	ENST00000356175.3:c.5320G>C	p.Asp1774His	p.D1774H	ENST00000356175	NM_000267.3	1774	Gat/Cat	37/57	1	2	FACETS	0.524	0.429	0.629	0.524	0.429	0.629	SUBCLONAL	1	FALSE	1	0.525274456481575	2		353	240	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40500404	40500405	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	A	novel	NA	P-0035378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	104	456	0	ENST00000264657.5:c.128+2dup		p.X43_splice	ENST00000264657	NM_139276.2	43			1	2	FACETS	0.987	0.891	1	0.987	0.891	1	CLONAL	1	FALSE	1	0.525274456481575	2		456	401	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47685262	47685262	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	25	505	0	ENST00000347630.2:c.688G>T	p.Glu230Ter	p.E230*	ENST00000347630	NM_001007230.1	230	Gaa/Taa	8/11	1	2	FACETS	0.274	0.215	0.34	0.274	0.215	0.34	SUBCLONAL	1	FALSE	1	0.525274456481575	2		505	348	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922365	178922365	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	47	422	0	ENST00000263967.3:c.1134T>G	p.Cys378Trp	p.C378W	ENST00000263967	NM_006218.2	378	tgT/tgG	6/21	1	2	FACETS	0.84	0.717	0.972	0.84	0.717	0.972	CLONAL	1	FALSE	1	0.525274456481575	2		422	213	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671263	30671263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	107	679	1	ENST00000376406.3:c.5614G>A	p.Glu1872Lys	p.E1872K	ENST00000376406	NM_014641.2	1872	Gag/Aag	11/15	0.525274456481575	6	FACETS	1	0.98	1			1	CLONAL	1	FALSE	NA	0.525274456481575	6		680	606	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004410	150004410	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	103	661	0	ENST00000253339.5:c.1815del	p.Glu606LysfsTer42	p.E606Kfs*42	ENST00000253339		605	aaA/aa	3/7	1	2	FACETS	0.959	0.864	1	0.959	0.864	1	CLONAL	1	FALSE	1	0.525274456481575	2		661	409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0035382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	394	605	0	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	0.779233878884094	1	FACETS	0.834	0.802	0.867	0.834	0.802	0.867	CLONAL	1	TRUE	0	0.821757090090238	1		605	677	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100337	8100337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773078501	NA	P-0035382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	336	642	0	ENST00000346208.3:c.311G>A	p.Gly104Asp	p.G104D	ENST00000346208		104	gGc/gAc	3/6	1	2	FACETS	0.712	0.674	0.752	0.712	0.674	0.752	SUBCLONAL	1	TRUE	1	0.821757090090238	2		642	1148	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607738	46607768	+	frameshift_variant	Frame_Shift_Del	DEL	CCACCATTACATTTTGGGCCCACAAAGTGGG	CCACCATTACATTTTGGGCCCACAAAGTGGG	-	novel	NA	P-0035382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	277	656	0	ENST00000263734.3:c.1929_1959del	p.Pro644SerfsTer42	p.P644Sfs*42	ENST00000263734	NM_001430.4	643	CCACCATTACATTTTGGGCCCACAAAGTGGGcc/cc	12/16	0.230094095688732	3	FACETS	0.855	0.803	0.909	0.285	0.267	0.303	INDETERMINATE	1	TRUE	0	0.821757090090238	3		656	1112	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956995	2957009	+	inframe_deletion	In_Frame_Del	DEL	GCGCTTCTTCTGGCT	GCGCTTCTTCTGGCT	-	novel	NA	P-0035382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	208	496	2	ENST00000396946.4:c.2618_2632del	p.Gln873_Ala877del	p.Q873_A877del	ENST00000396946	NM_032415.4	873	cAGCCAGAAGAAGCGCtt/ctt	20/25	0.821757090090238	1	FACETS	0.775	0.731	0.818	0.775	0.731	0.818	SUBCLONAL	1	TRUE	0	0.821757090090238	1		498	385	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098906	47098906	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	238	693	0	ENST00000409792.3:c.6368del	p.Lys2123SerfsTer24	p.K2123Sfs*24	ENST00000409792	NM_014159.6	2123	aAg/ag	15/21	0.622130046185187	2	FACETS	0.905	0.847	0.965	0.453	0.423	0.483	CLONAL	1	TRUE	0	0.628230435704191	2		693	837	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218417	1218417	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	68	466	0	ENST00000326873.7:c.292G>T	p.Glu98Ter	p.E98*	ENST00000326873	NM_000455.4	98	Gaa/Taa	2/10	0.211899104563371	1	FACETS	0.898	0.781	1	0.898	0.781	1	CLONAL	1	TRUE	0	0.211899104563371	1		466	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0035389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	136	541	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	0.347750835799529	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.347750835799529	1		541	557	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610288	10610288	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	260	741	0	ENST00000171111.5:c.422A>G	p.Tyr141Cys	p.Y141C	ENST00000171111	NM_203500.1	141	tAc/tGc	2/6	0.347750835799529	1	FACETS	0.786	0.739	0.834	1	0.994	1	SUBCLONAL	2	TRUE	0	0.347750835799529	1		741	786	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439649	51439649	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs771853517	NA	P-0035389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	80	404	0	ENST00000262662.1:c.214G>T	p.Ala72Ser	p.A72S	ENST00000262662		72	Gct/Tct	4/4	1	2	FACETS	0.917	0.809	1	0.917	0.809	1	CLONAL	1	TRUE	1	0.347750835799529	2		404	502	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446821	49446821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	94	516	1	ENST00000301067.7:c.989C>T	p.Ser330Leu	p.S330L	ENST00000301067	NM_003482.3	330	tCa/tTa	8/54	1	2	FACETS	0.967	0.863	1	0.967	0.863	1	CLONAL	1	TRUE	1	0.347750835799529	2		517	559	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872499	35872499	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	73	504	0	ENST00000216797.5:c.404G>C	p.Cys135Ser	p.C135S	ENST00000216797	NM_020529.2	135	tGt/tCt	3/6	1	2	FACETS	0.776	0.68	0.88	0.776	0.68	0.88	SUBCLONAL	1	TRUE	1	0.347750835799529	2		504	541	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991794	72991794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	46	541	0	ENST00000268489.5:c.2251C>T	p.Leu751Phe	p.L751F	ENST00000268489	NM_006885.3	751	Ctc/Ttc	2/10	1	2	FACETS	0.434	0.365	0.511	0.434	0.365	0.511	SUBCLONAL	1	TRUE	1	0.347750835799529	2		541	609	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119086	70119086	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	49	332	0	ENST00000245479.2:c.658G>A	p.Glu220Lys	p.E220K	ENST00000245479	NM_000346.3	220	Gag/Aag	2/3	1	2	FACETS	0.921	0.784	1	0.921	0.784	1	CLONAL	1	TRUE	1	0.347750835799529	2		332	306	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916882	178916882	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	137	573	0	ENST00000263967.3:c.269G>T	p.Cys90Phe	p.C90F	ENST00000263967	NM_006218.2	90	tGt/tTt	2/21	0.257249439455899	4	FACETS	1	0.977	1	0.411	0.374	0.45	CLONAL	1	TRUE	1	0.347750835799529	4		573	861	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86682643	86682643	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	48	332	1	ENST00000274376.6:c.2848G>A	p.Glu950Lys	p.E950K	ENST00000274376	NM_002890.2	950	Gag/Aag	23/25	0.347750835799529	1	FACETS	0.838	0.714	0.973	0.838	0.714	0.973	CLONAL	1	TRUE	0	0.347750835799529	1		333	272	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	21	272	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.245040118068274	5	FACETS	0.382	0.294	0.486	0.127	0.098	0.162	INDETERMINATE	1	TRUE	2	0.453190899382565	5		272	407	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982004	70982004	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	156	821	1	ENST00000276594.2:c.92C>T	p.Thr31Met	p.T31M	ENST00000276594	NM_024504.3	31	aCg/aTg	2/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.453190899382565	2		822	608	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	321	675	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.453190899382565	2		675	1010	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911514	131911514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143802516	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	180	399	0	ENST00000265335.6:c.259C>T	p.Arg87Cys	p.R87C	ENST00000265335		87	Cgt/Tgt	3/25	0.455215419306148	4	FACETS	0.871	0.806	0.937	0.871	0.806	0.937	CLONAL	2	TRUE	2	0.453190899382565	4		399	663	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	57	496	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.455215419306148	4	FACETS	0.464	0.397	0.538			1	SUBCLONAL	1	TRUE	NA	0.453190899382565	4		496	787	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749415085	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	131	311	0	ENST00000263967.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000263967	NM_006218.2	38	Cgt/Tgt	2/21	0.245040118068274	5	FACETS	1	0.966	1	0.739	0.676	0.804	INDETERMINATE	2	TRUE	2	0.453190899382565	5		311	438	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982356	25982356	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	178	245	0	ENST00000435504.4:c.934C>T	p.Arg312Ter	p.R312*	ENST00000435504		312	Cga/Tga	9/13	0.455215419306148	4	FACETS	0.877	0.817	0.937	1	0.989	1	CLONAL	3	TRUE	2	0.453190899382565	4		245	434	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	192	510	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	0.206543539472855	4	FACETS	1	0.937	1	1	0.937	1	INDETERMINATE	2	TRUE	2	0.453190899382565	4		510	611	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572534	95572534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555370340	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	110	276	0	ENST00000393063.1:c.2831G>A	p.Arg944Gln	p.R944Q	ENST00000393063	NM_030621.3	944	cGa/cAa	19/28	0.339627471189269	4	FACETS	0.966	0.877	1	0.966	0.877	1	CLONAL	2	TRUE	2	0.453190899382565	4		276	365	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237633	16237633	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	190	412	0	ENST00000375759.3:c.1080G>T	p.Lys360Asn	p.K360N	ENST00000375759	NM_015001.2	360	aaG/aaT	5/15	0.453190899382565	6	FACETS	1	0.955	1			1	CLONAL	2	TRUE	NA	0.453190899382565	6		412	767	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706936	117706936	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	167	494	0	ENST00000368508.3:c.2214G>T	p.Glu738Asp	p.E738D	ENST00000368508	NM_002944.2	738	gaG/gaT	15/43	1	2	FACETS	0.76	0.704	0.817	1	0.99	1	SUBCLONAL	2	TRUE	1	0.453190899382565	2		494	485	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	441077	441077	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	172	293	0	ENST00000399788.2:c.1681G>A	p.Glu561Lys	p.E561K	ENST00000399788	NM_001042603.1	561	Gag/Aag	13/28	0.275194409827565	5	FACETS	1	0.985	1			1	CLONAL	2	TRUE	NA	0.453190899382565	5		293	513	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335079	65335079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	138	481	1	ENST00000342505.4:c.562G>A	p.Glu188Lys	p.E188K	ENST00000342505	NM_002227.2	188	Gag/Aag	6/25	NA	2	FACETS	0.982	0.897	1			1	INDETERMINATE	1	TRUE	NA	0.453190899382565	2		482	620	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176118155	176118155	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	106	292	0	ENST00000367669.3:c.818G>T	p.Arg273Ile	p.R273I	ENST00000367669	NM_022457.5	273	aGa/aTa	6/20	0.180918608830005	4	FACETS	0.854	0.772	0.94	0.854	0.772	0.94	INDETERMINATE	2	TRUE	2	0.453190899382565	4		292	398	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25468901	25468901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	207	602	0	ENST00000264709.3:c.1462C>T	p.Arg488Trp	p.R488W	ENST00000264709	NM_175629.2	488	Cgg/Tgg	12/23	0.455215419306148	4	FACETS	0.77	0.716	0.826	0.77	0.716	0.826	SUBCLONAL	2	TRUE	2	0.453190899382565	4		602	862	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976476	25976476	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	46	456	0	ENST00000435504.4:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000435504		357	Cga/Tga	11/13	0.455215419306148	4	FACETS	0.397	0.333	0.467	0.198	0.166	0.234	SUBCLONAL	1	TRUE	2	0.453190899382565	4		456	744	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561352	9561352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773981325	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	80	467	0	ENST00000353224.5:c.430G>A	p.Glu144Lys	p.E144K	ENST00000353224	NM_177990.2	144	Gaa/Aaa	4/10	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.453190899382565	2		467	350	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374881	45374881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	231	490	0	ENST00000262160.6:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000262160	NM_005901.5	321	cGa/cAa	8/11	0.206543539472855	4	FACETS	1	0.976	1	1	0.976	1	INDETERMINATE	2	TRUE	2	0.453190899382565	4		490	685	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32899248	32899248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375125172	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	136	295	0	ENST00000380152.3:c.352C>T	p.Arg118Cys	p.R118C	ENST00000380152		118	Cgc/Tgc	4/27	0.455215419306148	4	FACETS	0.783	0.715	0.853	0.783	0.715	0.853	SUBCLONAL	2	TRUE	2	0.453190899382565	4		295	557	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232138	98232138	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs863224650	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	94	315	0	ENST00000331920.6:c.1804C>T	p.Arg602Ter	p.R602*	ENST00000331920	NM_000264.3	602	Cga/Tga	13/24	0.261222099684035	4	FACETS	0.752	0.673	0.834	0.752	0.673	0.834	INDETERMINATE	2	TRUE	2	0.453190899382565	4		315	401	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216568	108216568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs767845728	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	151	408	0	ENST00000278616.4:c.8517C>A	p.Phe2839Leu	p.F2839L	ENST00000278616	NM_000051.3	2839	ttC/ttA	58/63	0.455215419306148	4	FACETS	0.929	0.855	1			1	CLONAL	2	TRUE	NA	0.453190899382565	4		408	521	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166192	118166192	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	138	321	1	ENST00000369448.3:c.702G>T	p.Lys234Asn	p.K234N	ENST00000369448	NM_017709.3	234	aaG/aaT	2/2	0.177578160335091	5	FACETS	1	0.977	1			1	INDETERMINATE	2	TRUE	NA	0.453190899382565	5		322	433	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131412	202131412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339962485	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	33	419	0	ENST00000358485.4:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000358485	NM_001080125.1	127	cGa/cAa	2/9	0.455215419306148	4	FACETS	0.393	0.32	0.477	0.197	0.16	0.239	SUBCLONAL	1	TRUE	2	0.453190899382565	4		419	538	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495372	149495372	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146614144	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	153	610	2	ENST00000261799.4:c.3275C>T	p.Ser1092Leu	p.S1092L	ENST00000261799	NM_002609.3	1092	tCg/tTg	23/23	0.206543539472855	4	FACETS	0.822	0.755	0.891	0.822	0.755	0.891	INDETERMINATE	2	TRUE	2	0.453190899382565	4		612	597	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280068	66280068	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	26	338	0	ENST00000273854.3:c.1621C>T	p.Arg541Ter	p.R541*	ENST00000273854	NM_004439.5	541	Cga/Tga	7/18	NA	2	FACETS	0.311	0.246	0.385			1	INDETERMINATE	1	TRUE	NA	0.453190899382565	2		338	369	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685281	89685281	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	88	210	0	ENST00000371953.3:c.176C>A	p.Ser59Ter	p.S59*	ENST00000371953	NM_000314.4	59	tCa/tAa	3/9	0.455215419306148	4	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.453190899382565	4		210	384	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480495	57480495	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1422801076	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	75	257	0	ENST00000371085.3:c.490G>A	p.Glu164Lys	p.E164K	ENST00000371085	NM_000516.4	164	Gaa/Aaa	6/13	0.339627471189269	4	FACETS	1	0.964	1	0.628	0.553	0.707	CLONAL	1	TRUE	2	0.453190899382565	4		257	383	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724361	52724361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	161	397	0	ENST00000322088.6:c.1493G>A	p.Arg498His	p.R498H	ENST00000322088	NM_014225.5	498	cGc/cAc	12/15	NA	2	FACETS	0.795	0.736	0.855			1	INDETERMINATE	2	TRUE	NA	0.453190899382565	2		397	447	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812205	43812205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866559375	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	191	476	0	ENST00000372470.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000372470	NM_005373.2	357	cGa/cAa	7/12	0.261222099684035	4	FACETS	0.825	0.765	0.887	0.825	0.765	0.887	INDETERMINATE	2	TRUE	2	0.453190899382565	4		476	742	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911354	32911354	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	155	349	0	ENST00000380152.3:c.2862G>T	p.Glu954Asp	p.E954D	ENST00000380152		954	gaG/gaT	11/27	0.455215419306148	4	FACETS	0.91	0.838	0.985	0.91	0.838	0.985	CLONAL	2	TRUE	2	0.453190899382565	4		349	546	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797910	42797910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367735541	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	280	708	2	ENST00000575354.2:c.3962G>A	p.Arg1321His	p.R1321H	ENST00000575354	NM_015125.3	1321	cGc/cAc	16/20	0.455215419306148	4	FACETS	0.989	0.931	1			1	CLONAL	2	TRUE	NA	0.453190899382565	4		710	908	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576178	88576178	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368708129	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	40	519	1	ENST00000360948.2:c.1495G>A	p.Asp499Asn	p.D499N	ENST00000360948	NM_001012338.2	499	Gac/Aac	13/19	1	2	FACETS	0.447	0.372	0.53	0.447	0.372	0.53	SUBCLONAL	1	TRUE	1	0.453190899382565	2		520	395	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827580	72827580	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	37	682	0	ENST00000268489.5:c.9001G>T	p.Glu3001Ter	p.E3001*	ENST00000268489	NM_006885.3	3001	Gaa/Taa	9/10	0.338938049855908	4	FACETS	0.353	0.29	0.423			1	SUBCLONAL	1	TRUE	NA	0.453190899382565	4		682	673	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788637	3788637	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	146	284	0	ENST00000262367.5:c.4317C>A	p.Phe1439Leu	p.F1439L	ENST00000262367	NM_004380.2	1439	ttC/ttA	26/31	0.245040118068274	5	FACETS	1	0.972	1	0.752	0.691	0.814	INDETERMINATE	2	TRUE	2	0.453190899382565	5		284	480	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81902892	81902892	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	23	468	0	ENST00000359376.3:c.553G>T	p.Asp185Tyr	p.D185Y	ENST00000359376	NM_002661.3	185	Gat/Tat	6/33	1	2	FACETS	0.258	0.2	0.324	0.258	0.2	0.324	SUBCLONAL	1	TRUE	1	0.453190899382565	2		468	394	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39713150	39713150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	95	205	0	ENST00000361337.2:c.556C>T	p.Pro186Ser	p.P186S	ENST00000361337	NM_003286.2	186	Cct/Tct	8/21	0.338938049855908	4	FACETS	0.839	0.754	0.929			1	CLONAL	2	TRUE	NA	0.453190899382565	4		205	363	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164118	47164118	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	143	335	0	ENST00000409792.3:c.2008G>T	p.Glu670Ter	p.E670*	ENST00000409792	NM_014159.6	670	Gaa/Taa	3/21	0.455215419306148	4	FACETS	0.797	0.73	0.867	0.797	0.73	0.867	SUBCLONAL	2	TRUE	2	0.453190899382565	4		335	575	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32920979	32920979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358921	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	153	358	1	ENST00000380152.3:c.6953G>A	p.Arg2318Gln	p.R2318Q	ENST00000380152		2318	cGa/cAa	13/27	0.455215419306148	4	FACETS	0.786	0.722	0.853	0.786	0.722	0.853	SUBCLONAL	2	TRUE	2	0.453190899382565	4		359	624	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872795	136872795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1272938495	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	82	361	0	ENST00000241393.3:c.703C>T	p.Arg235Cys	p.R235C	ENST00000241393	NM_003467.2	235	Cgc/Tgc	2/2	NA	2	FACETS	0.802	0.71	0.9			1	INDETERMINATE	1	TRUE	NA	0.453190899382565	2		361	451	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871196	35871196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773491081	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	94	286	1	ENST00000303115.3:c.418C>T	p.Arg140Trp	p.R140W	ENST00000303115	NM_002185.3	140	Cgg/Tgg	4/8	0.455215419306148	4	FACETS	0.8	0.717	0.886	0.8	0.717	0.886	SUBCLONAL	2	TRUE	2	0.453190899382565	4		287	377	SUCCESS
APC	324	MSKCC	GRCh37	5	112178781	112178781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141010008	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	150	388	1	ENST00000257430.4:c.7490C>T	p.Ser2497Leu	p.S2497L	ENST00000257430	NM_000038.5	2497	tCg/tTg	16/16	0.455215419306148	4	FACETS	0.927	0.852	1	0.927	0.852	1	CLONAL	2	TRUE	2	0.453190899382565	4		389	519	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956771	68956771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774302685	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	114	621	1	ENST00000288368.4:c.889C>T	p.Arg297Cys	p.R297C	ENST00000288368	NM_024870.2	297	Cgt/Tgt	8/40	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.453190899382565	2		622	502	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108091	30108091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80271647	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	92	507	2	ENST00000331968.5:c.716C>T	p.Ser239Leu	p.S239L	ENST00000331968	NM_002742.2	239	tCg/tTg	5/18	0.339627471189269	4	FACETS	0.872	0.775	0.975	0.436	0.387	0.488	CLONAL	1	TRUE	2	0.453190899382565	4		509	677	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199821	138199821	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	154	408	0	ENST00000237289.4:c.1239G>T	p.Lys413Asn	p.K413N	ENST00000237289	NM_001270507.1	413	aaG/aaT	7/9	0.453190899382565	6	FACETS	1	0.957	1			1	CLONAL	2	TRUE	NA	0.453190899382565	6		408	610	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624558	93624558	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867241355	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	79	341	0	ENST00000375746.1:c.649C>T	p.Arg217Cys	p.R217C	ENST00000375746	NM_001174167.1	217	Cgc/Tgc	4/14	0.21907856514256	0	FACETS	0.542	0.48	0.607			1	INDETERMINATE	1	TRUE	0	0.453190899382565	0		341	352	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58711261	58711261	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571290585	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	248	528	0	ENST00000305921.3:c.749G>A	p.Arg250Gln	p.R250Q	ENST00000305921	NM_003620.3	250	cGa/cAa	3/6	0.206543539472855	4	FACETS	0.947	0.888	1	0.947	0.888	1	INDETERMINATE	2	TRUE	2	0.453190899382565	4		528	840	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409422	80409422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	126	342	1	ENST00000286548.4:c.692C>T	p.Ala231Val	p.A231V	ENST00000286548	NM_002072.3	231	gCg/gTg	5/7	0.338938049855908	4	FACETS	0.852	0.777	0.931			1	CLONAL	2	TRUE	NA	0.453190899382565	4		343	474	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515335	103515335	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	68	259	0	ENST00000355739.4:c.1836G>T	p.Glu612Asp	p.E612D	ENST00000355739	NM_000123.3	612	gaG/gaT	8/15	0.187318169377136	3	FACETS	1	0.975	1	0.748	0.659	0.842	INDETERMINATE	1	TRUE	1	0.453190899382565	3		259	246	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638731	176638731	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151165525	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	229	628	1	ENST00000439151.2:c.3331G>A	p.Asp1111Asn	p.D1111N	ENST00000439151	NM_022455.4	1111	Gat/Aat	5/23	0.453190899382565	5	FACETS	0.961	0.897	1			1	CLONAL	2	TRUE	NA	0.453190899382565	5		629	883	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395478	116395478	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45602940	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	98	382	0	ENST00000397752.3:c.1771C>T	p.Arg591Trp	p.R591W	ENST00000397752	NM_000245.2	591	Cgg/Tgg	6/21	0.342388392364024	6	FACETS	0.762	0.682	0.847	0.381	0.341	0.424	SUBCLONAL	2	TRUE	2	0.453190899382565	6		382	541	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395569	116395569	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs375951814	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	108	338	0	ENST00000397752.3:c.1862C>T	p.Thr621Ile	p.T621I	ENST00000397752	NM_000245.2	621	aCa/aTa	6/21	0.342388392364024	6	FACETS	0.901	0.813	0.995	0.451	0.406	0.498	CLONAL	2	TRUE	2	0.453190899382565	6		338	504	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751213	57751213	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	143	299	0	ENST00000274289.3:c.1654C>T	p.Gln552Ter	p.Q552*	ENST00000274289	NM_006622.3	552	Caa/Taa	12/14	0.455215419306148	4	FACETS	0.971	0.892	1	0.971	0.892	1	CLONAL	2	TRUE	2	0.453190899382565	4		299	472	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319939	62319939	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	215	580	0	ENST00000360203.5:c.1781G>A	p.Ser594Asn	p.S594N	ENST00000360203	NM_001283009.1	594	aGc/aAc	21/35	0.339627471189269	4	FACETS	0.875	0.815	0.936	0.875	0.815	0.936	CLONAL	2	TRUE	2	0.453190899382565	4		580	788	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356412	66356412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763166233	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	108	308	0	ENST00000273854.3:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000273854	NM_004439.5	362	cGg/cAg	5/18	NA	2	FACETS	0.833	0.759	0.909			1	INDETERMINATE	2	TRUE	NA	0.453190899382565	2		308	286	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857686	59857686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781321	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	132	356	1	ENST00000259008.2:c.1871C>T	p.Ser624Leu	p.S624L	ENST00000259008	NM_032043.2	624	tCg/tTg	13/20	0.206543539472855	4	FACETS	0.885	0.809	0.965	0.885	0.809	0.965	INDETERMINATE	2	TRUE	2	0.453190899382565	4		357	478	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923133	48923133	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	132	273	0	ENST00000267163.4:c.581C>A	p.Ser194Tyr	p.S194Y	ENST00000267163	NM_000321.2	194	tCt/tAt	6/27	0.455215419306148	4	FACETS	0.8	0.73	0.873	0.8	0.73	0.873	SUBCLONAL	2	TRUE	2	0.453190899382565	4		273	529	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56801452	56801452	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367846829	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	26	402	1	ENST00000337432.4:c.956G>A	p.Arg319Gln	p.R319Q	ENST00000337432	NM_058216.2	319	cGa/cAa	7/9	0.206543539472855	4	FACETS	0.335	0.264	0.416	0.167	0.132	0.208	INDETERMINATE	1	TRUE	2	0.453190899382565	4		403	498	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178943755	178943755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200671228	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	127	273	0	ENST00000263967.3:c.2422C>T	p.Arg808Trp	p.R808W	ENST00000263967	NM_006218.2	808	Cgg/Tgg	17/21	0.245040118068274	5	FACETS	1	0.953	1	0.712	0.65	0.776	INDETERMINATE	2	TRUE	2	0.453190899382565	5		273	441	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105688	27105688	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	126	293	0	ENST00000324856.7:c.5299G>T	p.Glu1767Ter	p.E1767*	ENST00000324856	NM_006015.4	1767	Gaa/Taa	20/20	0.453190899382565	6	FACETS	1	0.934	1			1	CLONAL	2	TRUE	NA	0.453190899382565	6		293	514	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94906445	94906445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766496091	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	150	464	0	ENST00000536441.1:c.1453C>T	p.Arg485Cys	p.R485C	ENST00000536441	NM_144665.3	485	Cgt/Tgt	10/10	0.261222099684035	4	FACETS	0.851	0.782	0.923	0.851	0.782	0.923	INDETERMINATE	2	TRUE	2	0.453190899382565	4		464	565	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40447715	40447715	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	160	591	0	ENST00000345506.4:c.454C>T	p.Arg152Ter	p.R152*	ENST00000345506	NM_003152.3	152	Cga/Tga	6/20	0.455215419306148	4	FACETS	1	0.984	1	0.654	0.6	0.709	CLONAL	1	TRUE	2	0.453190899382565	4		591	785	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865216	57865216	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	185	740	0	ENST00000228682.2:c.2693T>C	p.Val898Ala	p.V898A	ENST00000228682	NM_005269.2	898	gTg/gCg	12/12	0.453190899382565	5	FACETS	1	0.987	1	0.443	0.408	0.479	CLONAL	1	TRUE	2	0.453190899382565	5		740	1032	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707863	43707863	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	264	697	0	ENST00000382044.4:c.5018G>T	p.Arg1673Ile	p.R1673I	ENST00000382044	NM_001141980.1	1673	aGa/aTa	23/28	0.455215419306148	4	FACETS	0.929	0.873	0.987	0.929	0.873	0.987	CLONAL	2	TRUE	2	0.453190899382565	4		697	911	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36808981	36808981	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs534849916	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	212	603	2	ENST00000373129.3:c.1073C>T	p.Ala358Val	p.A358V	ENST00000373129	NM_032017.1	358	gCg/gTg	11/12	0.261222099684035	4	FACETS	0.811	0.755	0.869	0.811	0.755	0.869	INDETERMINATE	2	TRUE	2	0.453190899382565	4		605	838	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518653	103518653	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	75	227	0	ENST00000355739.4:c.2241G>T	p.Gln747His	p.Q747H	ENST00000355739	NM_000123.3	747	caG/caT	10/15	0.187318169377136	3	FACETS	0.829	0.736	0.925	0.829	0.736	0.925	INDETERMINATE	2	TRUE	1	0.453190899382565	3		227	245	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863690	68863690	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1236811420	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	119	339	0	ENST00000261769.5:c.2429T>G	p.Phe810Cys	p.F810C	ENST00000261769	NM_004360.3	810	tTt/tGt	15/16	0.338938049855908	4	FACETS	0.808	0.734	0.886			1	CLONAL	2	TRUE	NA	0.453190899382565	4		339	472	SUCCESS
ATR	545	MSKCC	GRCh37	3	142238616	142238616	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	107	196	0	ENST00000350721.4:c.4277C>A	p.Ser1426Tyr	p.S1426Y	ENST00000350721	NM_001184.3	1426	tCt/tAt	24/47	0.245040118068274	5	FACETS	0.87	0.791	0.951	0.87	0.791	0.951	INDETERMINATE	3	TRUE	2	0.453190899382565	5		196	304	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519596	137519596	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	34	407	0	ENST00000367739.4:c.1042G>T	p.Glu348Ter	p.E348*	ENST00000367739	NM_000416.2	348	Gaa/Taa	7/7	0.453190899382565	6	FACETS	0.432	0.352	0.523			1	SUBCLONAL	1	TRUE	NA	0.453190899382565	6		407	662	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321667	30321667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1213455983	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	220	568	2	ENST00000322652.5:c.1522C>T	p.Arg508Cys	p.R508C	ENST00000322652	NM_015355.2	508	Cgc/Tgc	13/16	0.455215419306148	4	FACETS	0.866	0.807	0.926	0.866	0.807	0.926	CLONAL	2	TRUE	2	0.453190899382565	4		570	815	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383182	42383182	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782657641	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	181	552	1	ENST00000221972.3:c.202C>T	p.Arg68Cys	p.R68C	ENST00000221972	NM_021601.3	68	Cgc/Tgc	2/5	0.261222099684035	4	FACETS	1	0.989	1	0.731	0.675	0.789	INDETERMINATE	1	TRUE	2	0.453190899382565	4		553	794	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510219	187510219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1276553545	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	87	444	0	ENST00000441802.2:c.13294G>A	p.Glu4432Lys	p.E4432K	ENST00000441802	NM_005245.3	4432	Gaa/Aaa	27/27	1	2	FACETS	0.997	0.889	1	0.997	0.889	1	CLONAL	1	TRUE	1	0.453190899382565	2		444	385	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191635	10191635	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774380450	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	62	471	0	ENST00000256474.2:c.628C>T	p.Arg210Trp	p.R210W	ENST00000256474	NM_000551.3	210	Cgg/Tgg	3/3	0.455215419306148	4	FACETS	0.473	0.408	0.545	0.237	0.204	0.273	SUBCLONAL	1	TRUE	2	0.453190899382565	4		471	840	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738302	190738302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	120	307	0	ENST00000441310.2:c.2554G>A	p.Glu852Lys	p.E852K	ENST00000441310	NM_000534.4	852	Gaa/Aaa	12/13	0.455215419306148	4	FACETS	0.974	0.888	1	0.974	0.888	1	CLONAL	2	TRUE	2	0.453190899382565	4		307	395	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573220	64573220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	259	666	0	ENST00000312049.6:c.1072G>A	p.Glu358Lys	p.E358K	ENST00000312049	NM_130799.2	358	Gag/Aag	8/10	0.455215419306148	4	FACETS	0.83	0.778	0.883	0.83	0.778	0.883	CLONAL	2	TRUE	2	0.453190899382565	4		666	1001	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522657	67522657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	143	283	0	ENST00000274335.5:c.154G>T	p.Glu52Ter	p.E52*	ENST00000274335		52	Gaa/Taa	1/15	0.455215419306148	4	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	2	0.453190899382565	4		283	424	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118391571	118391571	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	143	317	1	ENST00000534358.1:c.11484G>T	p.Lys3828Asn	p.K3828N	ENST00000534358	NM_005933.3	3828	aaG/aaT	34/36	0.455215419306148	4	FACETS	0.82	0.751	0.892			1	CLONAL	2	TRUE	NA	0.453190899382565	4		318	559	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22417932	22417932	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	97	228	0	ENST00000344548.3:c.498G>T	p.Lys166Asn	p.K166N	ENST00000344548	NM_001039802.1	166	aaG/aaT	7/7	0.453190899382565	6	FACETS	0.949	0.851	1			1	CLONAL	2	TRUE	NA	0.453190899382565	6		228	430	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100824	27100824	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	104	359	0	ENST00000324856.7:c.4106A>G	p.Tyr1369Cys	p.Y1369C	ENST00000324856	NM_006015.4	1369	tAc/tGc	18/20	0.453190899382565	6	FACETS	0.832	0.747	0.92			1	CLONAL	2	TRUE	NA	0.453190899382565	6		359	526	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599185	28599185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776626676	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	236	832	2	ENST00000253063.3:c.631G>A	p.Val211Met	p.V211M	ENST00000253063	NM_031459.4	211	Gtg/Atg	5/10	0.261222099684035	4	FACETS	0.807	0.754	0.862	0.807	0.754	0.862	INDETERMINATE	2	TRUE	2	0.453190899382565	4		834	938	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309798	65309798	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	150	556	0	ENST00000342505.4:c.2352G>A	p.Trp784Ter	p.W784*	ENST00000342505	NM_002227.2	784	tgG/tgA	17/25	NA	2	FACETS	1	0.96	1			1	INDETERMINATE	1	TRUE	NA	0.453190899382565	2		556	615	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321352	65321352	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	161	549	0	ENST00000342505.4:c.1488G>T	p.Lys496Asn	p.K496N	ENST00000342505	NM_002227.2	496	aaG/aaT	11/25	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.453190899382565	2		549	611	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332642	65332642	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	116	330	0	ENST00000342505.4:c.897G>T	p.Met299Ile	p.M299I	ENST00000342505	NM_002227.2	299	atG/atT	7/25	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.453190899382565	2		330	451	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280642	115280642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	198	604	0	ENST00000438362.2:c.389C>T	p.Ala130Val	p.A130V	ENST00000438362	NM_001242891.1	130	gCt/gTt	4/20	0.177578160335091	5	FACETS	0.88	0.816	0.946			1	INDETERMINATE	2	TRUE	NA	0.453190899382565	5		604	834	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510239	120510239	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1394733490	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	162	357	0	ENST00000256646.2:c.1270A>G	p.Ser424Gly	p.S424G	ENST00000256646	NM_024408.3	424	Agc/Ggc	8/34	0.455215419306148	4	FACETS	0.916	0.845	0.989	0.916	0.845	0.989	CLONAL	2	TRUE	2	0.453190899382565	4		357	567	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737018	162737018	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	147	407	1	ENST00000367921.3:c.1163-1G>T		p.X388_splice	ENST00000367921	NM_006182.2	388			0.180918608830005	4	FACETS	0.972	0.894	1	0.972	0.894	1	INDETERMINATE	2	TRUE	2	0.453190899382565	4		408	485	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737079	162737079	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	187	551	0	ENST00000367921.3:c.1223T>C	p.Ile408Thr	p.I408T	ENST00000367921	NM_006182.2	408	aTc/aCc	11/18	0.180918608830005	4	FACETS	0.898	0.833	0.965	0.898	0.833	0.965	INDETERMINATE	2	TRUE	2	0.453190899382565	4		551	668	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745465	162745465	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	145	331	0	ENST00000367921.3:c.1880A>T	p.Lys627Met	p.K627M	ENST00000367921	NM_006182.2	627	aAg/aTg	15/18	0.180918608830005	4	FACETS	1	0.952	1	1	0.952	1	INDETERMINATE	2	TRUE	2	0.453190899382565	4		331	444	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981197	201981197	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	325	778	0	ENST00000359651.3:c.276C>A	p.Phe92Leu	p.F92L	ENST00000359651		92	ttC/ttA	2/8	0.339627471189269	4	FACETS	0.992	0.938	1	0.992	0.938	1	CLONAL	2	TRUE	2	0.453190899382565	4		778	1051	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204513804	204513804	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	84	196	0	ENST00000367182.3:c.814G>T	p.Asp272Tyr	p.D272Y	ENST00000367182	NM_001278516.1	272	Gac/Tac	9/11	0.339627471189269	4	FACETS	0.814	0.725	0.907	0.814	0.725	0.907	CLONAL	2	TRUE	2	0.453190899382565	4		196	331	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333547	70333547	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs538486517	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	140	485	0	ENST00000373644.4:c.1452G>T	p.Glu484Asp	p.E484D	ENST00000373644	NM_030625.2	484	gaG/gaT	2/12	0.455215419306148	4	FACETS	0.918	0.842	0.997			1	CLONAL	2	TRUE	NA	0.453190899382565	4		485	489	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404659	70404659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	187	394	0	ENST00000373644.4:c.2173G>A	p.Asp725Asn	p.D725N	ENST00000373644	NM_030625.2	725	Gat/Aat	4/12	0.455215419306148	4	FACETS	0.973	0.904	1			1	CLONAL	2	TRUE	NA	0.453190899382565	4		394	616	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123260350	123260350	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	129	507	0	ENST00000358487.5:c.1551G>T	p.Lys517Asn	p.K517N	ENST00000358487	NM_000141.4	517	aaG/aaT	11/18	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.453190899382565	2		507	432	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414253	32414253	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	50	433	0	ENST00000332351.3:c.1298C>A	p.Ser433Tyr	p.S433Y	ENST00000332351	NM_024426.4	433	tCt/tAt	8/10	1	2	FACETS	0.679	0.579	0.788	0.679	0.579	0.788	SUBCLONAL	1	TRUE	1	0.453190899382565	2		433	325	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465963	69465963	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	165	586	0	ENST00000227507.2:c.801C>A	p.Asp267Glu	p.D267E	ENST00000227507	NM_053056.2	267	gaC/gaA	5/5	NA	2	FACETS	1	0.967	1			1	INDETERMINATE	1	TRUE	NA	0.453190899382565	2		586	667	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918635	94918635	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	114	347	0	ENST00000536441.1:c.547A>C	p.Asn183His	p.N183H	ENST00000536441	NM_144665.3	183	Aat/Cat	5/10	0.261222099684035	4	FACETS	0.793	0.718	0.871	0.793	0.718	0.871	INDETERMINATE	2	TRUE	2	0.453190899382565	4		347	461	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998977	100998977	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	22	486	0	ENST00000325455.5:c.825C>A	p.Phe275Leu	p.F275L	ENST00000325455	NM_001202474.3	275	ttC/ttA	1/8	NA	2	FACETS	0.299	0.231	0.377			1	INDETERMINATE	1	TRUE	NA	0.453190899382565	2		486	325	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106420	108106420	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	80	165	0	ENST00000278616.4:c.355G>T	p.Glu119Ter	p.E119*	ENST00000278616	NM_000051.3	119	Gaa/Taa	5/63	0.455215419306148	4	FACETS	0.836	0.743	0.933			1	CLONAL	2	TRUE	NA	0.453190899382565	4		165	307	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199917	108199917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	15	156	0	ENST00000278616.4:c.7259C>T	p.Ala2420Val	p.A2420V	ENST00000278616	NM_000051.3	2420	gCc/gTc	49/63	0.455215419306148	4	FACETS	0.369	0.269	0.488			1	SUBCLONAL	1	TRUE	NA	0.453190899382565	4		156	261	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342500	118342500	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	71	155	0	ENST00000534358.1:c.626A>G	p.Lys209Arg	p.K209R	ENST00000534358	NM_005933.3	209	aAg/aGg	3/36	0.455215419306148	4	FACETS	0.819	0.722	0.921			1	CLONAL	2	TRUE	NA	0.453190899382565	4		155	278	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374685	118374685	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	118	356	0	ENST00000534358.1:c.8078C>A	p.Ser2693Tyr	p.S2693Y	ENST00000534358	NM_005933.3	2693	tCt/tAt	27/36	0.455215419306148	4	FACETS	0.823	0.747	0.901			1	CLONAL	2	TRUE	NA	0.453190899382565	4		356	460	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377244	118377244	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	116	345	0	ENST00000534358.1:c.10637T>C	p.Phe3546Ser	p.F3546S	ENST00000534358	NM_005933.3	3546	tTt/tCt	27/36	0.455215419306148	4	FACETS	0.825	0.748	0.905			1	CLONAL	2	TRUE	NA	0.453190899382565	4		345	451	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497683	125497683	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	183	456	0	ENST00000428830.2:c.247T>G	p.Phe83Val	p.F83V	ENST00000428830	NM_001114121.2	83	Ttt/Gtt	3/14	0.455215419306148	4	FACETS	0.993	0.922	1			1	CLONAL	2	TRUE	NA	0.453190899382565	4		456	591	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	430160	430160	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	76	253	0	ENST00000399788.2:c.2541+1G>A		p.X847_splice	ENST00000399788	NM_001042603.1	847			0.275194409827565	5	FACETS	1	0.976	1			1	CLONAL	1	TRUE	NA	0.453190899382565	5		253	377	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446939	18446939	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	72	344	0	ENST00000266497.5:c.1024T>A	p.Phe342Ile	p.F342I	ENST00000266497		342	Ttt/Att	4/31	NA	2	FACETS	0.951	0.837	1			1	INDETERMINATE	1	TRUE	NA	0.453190899382565	2		344	334	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552725	18552725	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	122	522	0	ENST00000266497.5:c.2136T>G	p.Ile712Met	p.I712M	ENST00000266497		712	atT/atG	14/31	NA	2	FACETS	1	0.925	1			1	INDETERMINATE	1	TRUE	NA	0.453190899382565	2		522	527	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21639514	21639514	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	55	208	0	ENST00000421138.2:c.400A>G	p.Thr134Ala	p.T134A	ENST00000421138		134	Aca/Gca	6/16	0.206543539472855	4	FACETS	1	0.938	1	0.582	0.501	0.669	INDETERMINATE	1	TRUE	2	0.453190899382565	4		208	303	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231397	46231397	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	155	422	0	ENST00000334344.6:c.1237C>G	p.Leu413Val	p.L413V	ENST00000334344	NM_152641.2	413	Ctg/Gtg	10/21	0.453190899382565	5	FACETS	1	0.943	1	0.686	0.632	0.743	CLONAL	2	TRUE	2	0.453190899382565	5		422	558	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246660	46246660	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	67	143	0	ENST00000334344.6:c.4754T>C	p.Val1585Ala	p.V1585A	ENST00000334344	NM_152641.2	1585	gTa/gCa	15/21	0.453190899382565	5	FACETS	1	0.915	1	0.699	0.615	0.786	CLONAL	2	TRUE	2	0.453190899382565	5		143	237	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445802	49445802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	393	949	0	ENST00000301067.7:c.1664C>T	p.Ser555Phe	p.S555F	ENST00000301067	NM_003482.3	555	tCc/tTc	10/54	0.453190899382565	5	FACETS	1	0.96	1	0.675	0.641	0.71	CLONAL	2	TRUE	2	0.453190899382565	5		949	1438	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495835	56495835	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140679673	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	107	292	0	ENST00000267101.3:c.4025C>T	p.Thr1342Met	p.T1342M	ENST00000267101	NM_001982.3	1342	aCg/aTg	28/28	0.453190899382565	5	FACETS	0.83	0.748	0.915	0.553	0.499	0.61	CLONAL	2	TRUE	2	0.453190899382565	5		292	478	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865735	57865735	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	232	622	1	ENST00000228682.2:c.3212C>A	p.Ser1071Tyr	p.S1071Y	ENST00000228682	NM_005269.2	1071	tCt/tAt	12/12	0.453190899382565	5	FACETS	0.925	0.863	0.988	0.616	0.575	0.659	CLONAL	2	TRUE	2	0.453190899382565	5		623	930	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233134	69233134	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs377647994	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	21	326	0	ENST00000462284.1:c.999G>T	p.Glu333Asp	p.E333D	ENST00000462284	NM_002392.5	333	gaG/gaT	11/11	0.206543539472855	4	FACETS	0.364	0.28	0.462	0.182	0.14	0.231	INDETERMINATE	1	TRUE	2	0.453190899382565	4		326	370	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813310	102813310	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	156	417	0	ENST00000307046.8:c.379A>G	p.Thr127Ala	p.T127A	ENST00000307046	NM_001111285.1	127	Acc/Gcc	3/4	0.206543539472855	4	FACETS	1	0.953	1	1	0.953	1	INDETERMINATE	2	TRUE	2	0.453190899382565	4		417	479	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120722	115120722	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	270	650	0	ENST00000257566.3:c.284C>T	p.Pro95Leu	p.P95L	ENST00000257566	NM_016569.3	95	cCc/cTc	1/8	0.206543539472855	4	FACETS	1	0.958	1	1	0.958	1	INDETERMINATE	2	TRUE	2	0.453190899382565	4		650	847	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431327	121431327	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	28	301	0	ENST00000257555.6:c.531C>A	p.Phe177Leu	p.F177L	ENST00000257555		177	ttC/ttA	3/10	0.206543539472855	4	FACETS	0.597	0.478	0.731	0.298	0.239	0.366	INDETERMINATE	1	TRUE	2	0.453190899382565	4		301	301	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202820	133202820	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	180	479	1	ENST00000320574.5:c.6414C>A	p.Phe2138Leu	p.F2138L	ENST00000320574	NM_006231.2	2138	ttC/ttA	46/49	0.206543539472855	4	FACETS	0.968	0.898	1	0.968	0.898	1	INDETERMINATE	2	TRUE	2	0.453190899382565	4		480	596	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620068	21620068	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139154828	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	234	642	0	ENST00000382592.4:c.98C>T	p.Ser33Leu	p.S33L	ENST00000382592	NM_014572.2	33	tCg/tTg	2/8	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.453190899382565	2		642	828	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601304	28601304	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	91	386	0	ENST00000241453.7:c.2128T>A	p.Phe710Ile	p.F710I	ENST00000241453	NM_004119.2	710	Ttt/Att	17/24	NA	2	FACETS	1	0.954	1			1	INDETERMINATE	1	TRUE	NA	0.453190899382565	2		386	358	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005371	29005371	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	95	556	0	ENST00000282397.4:c.890C>A	p.Thr297Asn	p.T297N	ENST00000282397	NM_002019.4	297	aCt/aAt	7/30	NA	2	FACETS	0.93	0.832	1			1	INDETERMINATE	1	TRUE	NA	0.453190899382565	2		556	451	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913900	32913900	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	39	432	0	ENST00000380152.3:c.5408C>A	p.Thr1803Asn	p.T1803N	ENST00000380152		1803	aCt/aAt	11/27	0.455215419306148	4	FACETS	0.416	0.344	0.497	0.208	0.172	0.249	SUBCLONAL	1	TRUE	2	0.453190899382565	4		432	601	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281656	49281656	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	200	791	0	ENST00000282018.3:c.703G>T	p.Glu235Ter	p.E235*	ENST00000282018	NM_020377.2	235	Gaa/Taa	1/1	NA	2	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.453190899382565	2		791	800	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107764	30107764	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	193	514	0	ENST00000331968.5:c.916T>G	p.Phe306Val	p.F306V	ENST00000331968	NM_002742.2	306	Ttc/Gtc	6/18	0.339627471189269	4	FACETS	0.973	0.905	1	0.973	0.905	1	CLONAL	2	TRUE	2	0.453190899382565	4		514	636	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610191	81610191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762013134	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	99	376	1	ENST00000298171.2:c.1789G>A	p.Val597Ile	p.V597I	ENST00000298171	NM_000369.2	597	Gtc/Atc	10/10	0.339627471189269	4	FACETS	0.827	0.744	0.913	0.827	0.744	0.913	CLONAL	2	TRUE	2	0.453190899382565	4		377	384	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643692	38643692	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	153	694	0	ENST00000299084.4:c.1162T>C	p.Ser388Pro	p.S388P	ENST00000299084	NM_152594.2	388	Tct/Cct	7/7	1	2	FACETS	0.963	0.883	1	0.963	0.883	1	CLONAL	1	TRUE	1	0.453190899382565	2		694	701	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43699633	43699633	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	208	561	0	ENST00000382044.4:c.5882G>T	p.Arg1961Ile	p.R1961I	ENST00000382044	NM_001141980.1	1961	aGa/aTa	28/28	0.455215419306148	4	FACETS	0.941	0.877	1	0.941	0.877	1	CLONAL	2	TRUE	2	0.453190899382565	4		561	709	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423571	88423571	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	135	527	0	ENST00000360948.2:c.2264G>A	p.Ser755Asn	p.S755N	ENST00000360948	NM_001012338.2	755	aGc/aAc	18/19	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.453190899382565	2		527	422	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670415	88670415	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	65	285	0	ENST00000360948.2:c.1271A>G	p.Lys424Arg	p.K424R	ENST00000360948	NM_001012338.2	424	aAa/aGa	11/19	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.453190899382565	2		285	226	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819305	3819305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762582037	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	49	586	0	ENST00000262367.5:c.2930C>T	p.Ser977Leu	p.S977L	ENST00000262367	NM_004380.2	977	tCg/tTg	15/31	0.245040118068274	5	FACETS	0.446	0.376	0.523	0.149	0.125	0.175	INDETERMINATE	1	TRUE	2	0.453190899382565	5		586	815	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349099	11349099	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	93	286	0	ENST00000332029.2:c.237C>A	p.Phe79Leu	p.F79L	ENST00000332029	NM_003745.1	79	ttC/ttA	2/2	0.177578160335091	5	FACETS	0.87	0.779	0.966			1	INDETERMINATE	2	TRUE	NA	0.453190899382565	5		286	396	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813766	50813766	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	147	593	1	ENST00000398568.2:c.1320G>T	p.Gln440His	p.Q440H	ENST00000398568	NM_001042412.1	440	caG/caT	8/18	NA	2	FACETS	0.964	0.882	1			1	INDETERMINATE	1	TRUE	NA	0.453190899382565	2		594	673	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828296	72828296	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	160	572	0	ENST00000268489.5:c.8285G>A	p.Gly2762Glu	p.G2762E	ENST00000268489	NM_006885.3	2762	gGa/gAa	9/10	0.338938049855908	4	FACETS	1	0.935	1			1	CLONAL	2	TRUE	NA	0.453190899382565	4		572	506	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830513	72830513	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	160	614	0	ENST00000268489.5:c.6068G>T	p.Arg2023Ile	p.R2023I	ENST00000268489	NM_006885.3	2023	aGa/aTa	9/10	0.338938049855908	4	FACETS	0.867	0.798	0.937			1	CLONAL	2	TRUE	NA	0.453190899382565	4		614	592	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888129	81888129	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	81	437	1	ENST00000359376.3:c.274G>T	p.Glu92Ter	p.E92*	ENST00000359376	NM_002661.3	92	Gaa/Taa	3/33	1	2	FACETS	0.765	0.677	0.86	0.765	0.677	0.86	SUBCLONAL	1	TRUE	1	0.453190899382565	2		438	467	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81973581	81973581	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1481508581	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	106	562	0	ENST00000359376.3:c.3398G>A	p.Arg1133His	p.R1133H	ENST00000359376	NM_002661.3	1133	cGc/cAc	30/33	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.453190899382565	2		562	442	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984028	7984028	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	93	334	1	ENST00000319144.4:c.598C>A	p.Leu200Ile	p.L200I	ENST00000319144	NM_001139.2	200	Ctc/Atc	5/15	0.455215419306148	4	FACETS	1	0.981	1	0.74	0.662	0.822	CLONAL	1	TRUE	2	0.453190899382565	4		335	403	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950311	15950311	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	227	702	1	ENST00000268712.3:c.6633G>T	p.Glu2211Asp	p.E2211D	ENST00000268712	NM_006311.3	2211	gaG/gaT	42/46	0.455215419306148	4	FACETS	0.842	0.786	0.9	0.842	0.786	0.9	CLONAL	2	TRUE	2	0.453190899382565	4		703	864	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687473	37687473	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs757938934	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	20	216	0	ENST00000447079.4:c.4377G>T	p.Trp1459Cys	p.W1459C	ENST00000447079	NM_015083.1	1459	tgG/tgT	14/14	0.455215419306148	4	FACETS	0.353	0.27	0.452	0.177	0.135	0.226	SUBCLONAL	1	TRUE	2	0.453190899382565	4		216	363	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40872306	40872306	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs781642151	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	253	692	0	ENST00000428826.2:c.649C>T	p.Arg217Ter	p.R217*	ENST00000428826		217	Cga/Tga	7/21	0.455215419306148	4	FACETS	0.851	0.798	0.906	0.851	0.798	0.906	CLONAL	2	TRUE	2	0.453190899382565	4		692	953	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59820424	59820424	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768555161	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	162	401	2	ENST00000259008.2:c.2329C>T	p.Arg777Cys	p.R777C	ENST00000259008	NM_032043.2	777	Cgt/Tgt	16/20	0.206543539472855	4	FACETS	1	0.966	1	1	0.966	1	INDETERMINATE	2	TRUE	2	0.453190899382565	4		403	482	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554147	63554147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	167	655	0	ENST00000307078.5:c.592G>A	p.Glu198Lys	p.E198K	ENST00000307078	NM_004655.3	198	Gaa/Aaa	2/11	0.206543539472855	4	FACETS	0.86	0.793	0.928	0.86	0.793	0.928	INDETERMINATE	2	TRUE	2	0.453190899382565	4		655	623	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39567850	39567850	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	57	221	0	ENST00000262039.4:c.606A>C	p.Glu202Asp	p.E202D	ENST00000262039	NM_002647.2	202	gaA/gaC	5/25	0.206543539472855	4	FACETS	1	0.919	1	0.547	0.472	0.628	INDETERMINATE	1	TRUE	2	0.453190899382565	4		221	334	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56412984	56412984	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	171	369	0	ENST00000348428.3:c.1998T>G	p.His666Gln	p.H666Q	ENST00000348428	NM_006785.3	666	caT/caG	16/17	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.453190899382565	NA		369	586	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10283825	10283825	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	189	568	0	ENST00000340748.4:c.661G>T	p.Glu221Ter	p.E221*	ENST00000340748		221	Gaa/Taa	8/40	0.261222099684035	4	FACETS	0.782	0.724	0.842	0.782	0.724	0.842	INDETERMINATE	2	TRUE	2	0.453190899382565	4		568	775	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100009	11100009	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769660597	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	187	501	0	ENST00000358026.2:c.1135G>A	p.Ala379Thr	p.A379T	ENST00000358026	NM_001128849.1	379	Gca/Aca	7/36	0.261222099684035	4	FACETS	0.823	0.762	0.885	0.823	0.762	0.885	INDETERMINATE	2	TRUE	2	0.453190899382565	4		501	729	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19261533	19261533	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	223	566	0	ENST00000162023.5:c.12A>C	p.Lys4Asn	p.K4N	ENST00000162023		4	aaA/aaC	6/13	0.261222099684035	4	FACETS	0.868	0.81	0.928	0.868	0.81	0.928	INDETERMINATE	2	TRUE	2	0.453190899382565	4		566	824	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42790984	42790984	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	232	592	1	ENST00000575354.2:c.129C>A	p.Phe43Leu	p.F43L	ENST00000575354	NM_015125.3	43	ttC/ttA	2/20	0.455215419306148	4	FACETS	0.86	0.803	0.918			1	CLONAL	2	TRUE	NA	0.453190899382565	4		593	865	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551328	29551328	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	69	502	0	ENST00000389048.3:c.1302G>T	p.Lys434Asn	p.K434N	ENST00000389048	NM_004304.4	434	aaG/aaT	6/29	0.21907856514256	0	FACETS	0.512	0.449	0.579			1	INDETERMINATE	1	TRUE	0	0.453190899382565	0		502	325	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224114	39224115	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	260	575	0	ENST00000402219.2:c.3029dup	p.Asn1011GlnfsTer12	p.N1011Qfs*12	ENST00000402219	NM_005633.3	1010	ttc/ttTc	19/23	0.339627471189269	4	FACETS	0.883	0.828	0.939	0.883	0.828	0.939	CLONAL	2	TRUE	2	0.453190899382565	4		575	944	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033448	48033448	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	150	505	1	ENST00000234420.5:c.3752C>A	p.Ser1251Ter	p.S1251*	ENST00000234420	NM_000179.2	1251	tCa/tAa	8/10	0.339627471189269	4	FACETS	1	0.987	1	0.708	0.649	0.77	CLONAL	1	TRUE	2	0.453190899382565	4		506	679	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033789	48033789	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs773763465	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	88	258	0	ENST00000234420.5:c.4000C>T	p.Arg1334Trp	p.R1334W	ENST00000234420	NM_000179.2	1334	Cgg/Tgg	9/10	0.339627471189269	4	FACETS	0.973	0.873	1	0.973	0.873	1	CLONAL	2	TRUE	2	0.453190899382565	4		258	290	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719204	61719204	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	32	364	1	ENST00000401558.2:c.1853T>G	p.Ile618Ser	p.I618S	ENST00000401558	NM_003400.3	618	aTt/aGt	16/25	0.339627471189269	4	FACETS	0.36	0.291	0.438	0.18	0.145	0.219	SUBCLONAL	1	TRUE	2	0.453190899382565	4		365	570	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920736	96920736	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	96	258	0	ENST00000258439.3:c.245-1G>A		p.X82_splice	ENST00000258439	NM_001193304.2	82			0.455215419306148	4	FACETS	0.8	0.718	0.885			1	SUBCLONAL	2	TRUE	NA	0.453190899382565	4		258	385	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872777	136872777	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	98	371	0	ENST00000241393.3:c.721A>G	p.Thr241Ala	p.T241A	ENST00000241393	NM_003467.2	241	Aca/Gca	2/2	NA	2	FACETS	0.934	0.838	1			1	INDETERMINATE	1	TRUE	NA	0.453190899382565	2		371	463	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095913	178095913	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	193	472	0	ENST00000397062.3:c.1418T>G	p.Ile473Ser	p.I473S	ENST00000397062	NM_006164.4	473	aTc/aGc	5/5	0.455215419306148	4	FACETS	0.791	0.734	0.851	0.791	0.734	0.851	SUBCLONAL	2	TRUE	2	0.453190899382565	4		472	782	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719632	190719632	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs757273212	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	74	164	0	ENST00000441310.2:c.1634C>A	p.Ser545Ter	p.S545*	ENST00000441310	NM_000534.4	545	tCa/tAa	9/13	0.455215419306148	4	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	2	0.453190899382565	4		164	200	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422503	225422503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs190453078	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	215	525	0	ENST00000264414.4:c.137G>A	p.Arg46His	p.R46H	ENST00000264414	NM_003590.4	46	cGt/cAt	2/16	0.206543539472855	4	FACETS	0.868	0.809	0.929	0.868	0.809	0.929	INDETERMINATE	2	TRUE	2	0.453190899382565	4		525	794	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877425	40877425	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	118	471	0	ENST00000373198.4:c.2271G>T	p.Glu757Asp	p.E757D	ENST00000373198	NM_133170.3	757	gaG/gaT	15/32	0.31154638902131	0	FACETS	0.853	0.779	0.928			1	CLONAL	1	TRUE	0	0.453190899382565	0		471	334	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161912	47161912	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	177	423	0	ENST00000409792.3:c.4214A>C	p.Lys1405Thr	p.K1405T	ENST00000409792	NM_014159.6	1405	aAa/aCa	3/21	0.455215419306148	4	FACETS	0.879	0.813	0.946	0.879	0.813	0.946	CLONAL	2	TRUE	2	0.453190899382565	4		423	646	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723626	49723626	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	72	202	0	ENST00000449682.2:c.1017-1G>T		p.X339_splice	ENST00000449682	NM_020998.3	339			0.455215419306148	4	FACETS	0.995	0.883	1	0.995	0.883	1	CLONAL	2	TRUE	2	0.453190899382565	4		202	232	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52661288	52661288	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	169	382	0	ENST00000394830.3:c.1541+1G>A		p.X514_splice	ENST00000394830	NM_018313.4	514			0.455215419306148	4	FACETS	0.896	0.827	0.966	0.896	0.827	0.966	CLONAL	2	TRUE	2	0.453190899382565	4		382	605	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920479	134920479	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	103	605	0	ENST00000398015.3:c.2294T>C	p.Leu765Pro	p.L765P	ENST00000398015	NM_004441.4	765	cTc/cCc	12/16	0.455215419306148	1	FACETS	0.937	0.846	1	0.937	0.846	1	CLONAL	1	TRUE	0	0.453190899382565	1		605	375	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189585701	189585701	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	183	490	0	ENST00000264731.3:c.962T>G	p.Ile321Ser	p.I321S	ENST00000264731	NM_003722.4	321	aTt/aGt	7/14	0.245040118068274	5	FACETS	1	0.982	1	0.781	0.725	0.838	INDETERMINATE	2	TRUE	2	0.453190899382565	5		490	579	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902664	1902664	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	234	575	1	ENST00000382891.5:c.283G>T	p.Asp95Tyr	p.D95Y	ENST00000382891	NM_133335.3	95	Gat/Tat	2/22	0.206543539472855	4	FACETS	0.956	0.894	1	0.956	0.894	1	INDETERMINATE	2	TRUE	2	0.453190899382565	4		576	785	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955933	55955933	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	38	399	1	ENST00000263923.4:c.3229A>C	p.Ile1077Leu	p.I1077L	ENST00000263923	NM_002253.2	1077	Att/Ctt	24/30	0.455215419306148	1	FACETS	0.389	0.323	0.464	0.389	0.323	0.464	SUBCLONAL	1	TRUE	0	0.453190899382565	1		400	333	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972865	55972865	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	83	405	1	ENST00000263923.4:c.1525G>T	p.Gly509Ter	p.G509*	ENST00000263923	NM_002253.2	509	Gga/Tga	11/30	0.455215419306148	1	FACETS	0.814	0.724	0.909	0.814	0.724	0.909	CLONAL	1	TRUE	0	0.453190899382565	1		406	348	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361225	66361225	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs150719652	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	21	286	0	ENST00000273854.3:c.947T>C	p.Ile316Thr	p.I316T	ENST00000273854	NM_004439.5	316	aTc/aCc	4/18	NA	2	FACETS	0.298	0.229	0.378			1	INDETERMINATE	1	TRUE	NA	0.453190899382565	2		286	311	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156588	106156588	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	22	275	0	ENST00000380013.4:c.1489A>G	p.Thr497Ala	p.T497A	ENST00000380013	NM_001127208.2	497	Act/Gct	3/11	0.177578160335091	5	FACETS	0.524	0.406	0.661			1	INDETERMINATE	1	TRUE	NA	0.453190899382565	5		275	311	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157856	106157856	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	17	248	0	ENST00000380013.4:c.2757C>A	p.Tyr919Ter	p.Y919*	ENST00000380013	NM_001127208.2	919	taC/taA	3/11	0.177578160335091	5	FACETS	0.435	0.324	0.566			1	INDETERMINATE	1	TRUE	NA	0.453190899382565	5		248	290	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158407	106158407	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	17	278	0	ENST00000380013.4:c.3308A>C	p.Asn1103Thr	p.N1103T	ENST00000380013	NM_001127208.2	1103	aAt/aCt	3/11	0.177578160335091	5	FACETS	0.457	0.341	0.594			1	INDETERMINATE	1	TRUE	NA	0.453190899382565	5		278	276	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532900	187532900	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	21	349	0	ENST00000441802.2:c.9493A>C	p.Ile3165Leu	p.I3165L	ENST00000441802	NM_005245.3	3165	Att/Ctt	14/27	1	2	FACETS	0.32	0.246	0.405	0.32	0.246	0.405	SUBCLONAL	1	TRUE	1	0.453190899382565	2		349	290	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515625	31515625	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	103	398	0	ENST00000344624.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000344624		332	Gaa/Aaa	4/33	1	2	FACETS	0.975	0.878	1	0.975	0.878	1	CLONAL	1	TRUE	1	0.453190899382565	2		398	466	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152446	56152446	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	67	164	0	ENST00000399503.3:c.502G>T	p.Glu168Ter	p.E168*	ENST00000399503	NM_005921.1	168	Gaa/Taa	2/20	0.455215419306148	4	FACETS	0.799	0.701	0.901	0.799	0.701	0.901	CLONAL	2	TRUE	2	0.453190899382565	4		164	269	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155672	56155672	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	115	278	0	ENST00000399503.3:c.764A>T	p.Asn255Ile	p.N255I	ENST00000399503	NM_005921.1	255	aAc/aTc	3/20	0.455215419306148	4	FACETS	0.773	0.7	0.849	0.773	0.7	0.849	SUBCLONAL	2	TRUE	2	0.453190899382565	4		278	477	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754273	57754273	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	41	466	0	ENST00000274289.3:c.578T>G	p.Leu193Arg	p.L193R	ENST00000274289	NM_006622.3	193	cTg/cGg	4/14	0.455215419306148	4	FACETS	0.411	0.342	0.489	0.206	0.171	0.245	SUBCLONAL	1	TRUE	2	0.453190899382565	4		466	639	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149450108	149450108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1415767125	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	196	660	0	ENST00000286301.3:c.1109G>A	p.Arg370His	p.R370H	ENST00000286301	NM_005211.3	370	cGc/cAc	8/22	0.206543539472855	4	FACETS	0.829	0.77	0.891	0.829	0.77	0.891	INDETERMINATE	2	TRUE	2	0.453190899382565	4		660	758	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460453	149460453	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	168	633	0	ENST00000286301.3:c.184T>G	p.Ser62Ala	p.S62A	ENST00000286301	NM_005211.3	62	Tct/Gct	3/22	0.206543539472855	4	FACETS	0.766	0.706	0.829	0.766	0.706	0.829	INDETERMINATE	2	TRUE	2	0.453190899382565	4		633	703	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509454	149509454	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	188	664	0	ENST00000261799.4:c.1445A>G	p.Tyr482Cys	p.Y482C	ENST00000261799	NM_002609.3	482	tAc/tGc	10/23	0.206543539472855	4	FACETS	0.796	0.738	0.857	0.796	0.738	0.857	INDETERMINATE	2	TRUE	2	0.453190899382565	4		664	757	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562133	176562133	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	43	538	1	ENST00000439151.2:c.29G>T	p.Arg10Ile	p.R10I	ENST00000439151	NM_022455.4	10	aGa/aTa	2/23	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.453190899382565	NA		539	764	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638065	176638065	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	170	588	0	ENST00000439151.2:c.2665C>A	p.Leu889Ile	p.L889I	ENST00000439151	NM_022455.4	889	Ctt/Att	5/23	0.453190899382565	5	FACETS	0.84	0.774	0.909			1	CLONAL	2	TRUE	NA	0.453190899382565	5		588	750	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638068	176638068	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	47	591	0	ENST00000439151.2:c.2668T>G	p.Phe890Val	p.F890V	ENST00000439151	NM_022455.4	890	Ttc/Gtc	5/23	0.453190899382565	5	FACETS	0.459	0.386	0.54			1	SUBCLONAL	1	TRUE	NA	0.453190899382565	5		591	759	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675679	30675679	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs758775622	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	381	871	0	ENST00000376406.3:c.2677G>T	p.Glu893Ter	p.E893*	ENST00000376406	NM_014641.2	893	Gaa/Taa	8/15	0.453190899382565	5	FACETS	0.96	0.91	1	0.64	0.607	0.674	CLONAL	2	TRUE	2	0.453190899382565	5		871	1471	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188932	32188932	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	41	741	0	ENST00000375023.3:c.622G>T	p.Gly208Cys	p.G208C	ENST00000375023	NM_004557.3	208	Ggc/Tgc	4/30	NA	2	FACETS	0.281	0.234	0.335			1	INDETERMINATE	1	TRUE	NA	0.453190899382565	2		741	643	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547204	106547204	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	99	235	0	ENST00000369096.4:c.441C>A	p.Phe147Leu	p.F147L	ENST00000369096	NM_001198.3	147	ttC/ttA	4/7	0.453190899382565	5	FACETS	0.895	0.804	0.99			1	CLONAL	2	TRUE	NA	0.453190899382565	5		235	410	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026402	6026402	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	120	419	0	ENST00000265849.7:c.1994G>T	p.Arg665Ile	p.R665I	ENST00000265849	NM_000535.5	665	aGa/aTa	11/15	0.453190899382565	6	FACETS	0.797	0.722	0.877	0.399	0.361	0.439	SUBCLONAL	2	TRUE	2	0.453190899382565	6		419	633	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026547	6026547	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs864622096	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	356	974	1	ENST00000265849.7:c.1849C>T	p.Pro617Ser	p.P617S	ENST00000265849	NM_000535.5	617	Ccc/Tcc	11/15	0.453190899382565	6	FACETS	0.956	0.903	1	0.478	0.451	0.505	CLONAL	2	TRUE	2	0.453190899382565	6		975	1567	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14028674	14028674	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	128	333	0	ENST00000405192.2:c.4G>T	p.Asp2Tyr	p.D2Y	ENST00000405192	NM_001163147.1	2	Gat/Tat	2/12	0.453190899382565	6	FACETS	1	0.951	1	0.532	0.485	0.581	CLONAL	2	TRUE	2	0.453190899382565	6		333	506	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339235	116339235	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	84	342	0	ENST00000397752.3:c.97T>C	p.Ser33Pro	p.S33P	ENST00000397752	NM_000245.2	33	Tcc/Ccc	2/21	0.342388392364024	6	FACETS	0.82	0.728	0.918	0.41	0.364	0.459	CLONAL	2	TRUE	2	0.453190899382565	6		342	431	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482825	140482825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs998233805	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	186	522	1	ENST00000288602.6:c.1310G>A	p.Arg437Gln	p.R437Q	ENST00000288602	NM_004333.4	437	cGa/cAa	10/18	0.453190899382565	6	FACETS	0.816	0.753	0.881	0.408	0.376	0.441	CLONAL	2	TRUE	2	0.453190899382565	6		523	959	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514413	148514413	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	40	482	0	ENST00000320356.2:c.1311G>A	p.Trp437Ter	p.W437*	ENST00000320356	NM_004456.4	437	tgG/tgA	11/20	0.453190899382565	6	FACETS	0.423	0.35	0.505	0.106	0.087	0.127	SUBCLONAL	1	TRUE	2	0.453190899382565	6		482	795	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874046	151874046	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	123	572	0	ENST00000262189.6:c.8492C>A	p.Ser2831Tyr	p.S2831Y	ENST00000262189	NM_170606.2	2831	tCt/tAt	38/59	0.453190899382565	6	FACETS	1	0.972	1	0.299	0.27	0.33	CLONAL	1	TRUE	2	0.453190899382565	6		572	865	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008888	152008888	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	107	312	0	ENST00000262189.6:c.734C>A	p.Ser245Tyr	p.S245Y	ENST00000262189	NM_170606.2	245	tCt/tAt	5/59	0.453190899382565	6	FACETS	0.82	0.738	0.906	0.41	0.369	0.453	CLONAL	2	TRUE	2	0.453190899382565	6		312	549	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345930	152345930	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1200646566	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	51	554	0	ENST00000359321.1:c.640C>T	p.Arg214Ter	p.R214*	ENST00000359321	NM_005431.1	214	Cga/Tga	3/3	0.338938049855908	4	FACETS	0.461	0.391	0.539			1	SUBCLONAL	1	TRUE	NA	0.453190899382565	4		554	709	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346247	152346247	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	150	549	0	ENST00000359321.1:c.323T>G	p.Ile108Ser	p.I108S	ENST00000359321	NM_005431.1	108	aTc/aGc	3/3	0.338938049855908	4	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.453190899382565	4		549	705	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133268	38133268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770152981	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	51	502	1	ENST00000317025.8:c.4205G>A	p.Arg1402His	p.R1402H	ENST00000317025	NM_023034.1	1402	cGc/cAc	24/24	0.455215419306148	4	FACETS	0.397	0.337	0.465			1	SUBCLONAL	1	TRUE	NA	0.453190899382565	4		503	823	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939540	68939540	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	48	307	0	ENST00000288368.4:c.525G>T	p.Lys175Asn	p.K175N	ENST00000288368	NM_024870.2	175	aaG/aaT	5/40	1	2	FACETS	0.776	0.661	0.901	0.776	0.661	0.901	CLONAL	1	TRUE	1	0.453190899382565	2		307	273	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968198	68968198	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	29	570	0	ENST00000288368.4:c.1227C>A	p.Cys409Ter	p.C409*	ENST00000288368	NM_024870.2	409	tgC/tgA	10/40	1	2	FACETS	0.296	0.237	0.363	0.296	0.237	0.363	SUBCLONAL	1	TRUE	1	0.453190899382565	2		570	433	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028055	69028055	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	100	464	0	ENST00000288368.4:c.3214G>T	p.Asp1072Tyr	p.D1072Y	ENST00000288368	NM_024870.2	1072	Gac/Tac	26/40	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.453190899382565	2		464	412	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750813	128750813	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	151	529	0	ENST00000377970.2:c.350T>C	p.Val117Ala	p.V117A	ENST00000377970	NM_002467.4	117	gTg/gCg	2/3	0.339627471189269	4	FACETS	0.866	0.796	0.939	0.866	0.796	0.939	CLONAL	2	TRUE	2	0.453190899382565	4		529	559	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752662	128752662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	67	212	0	ENST00000377970.2:c.823G>A	p.Glu275Lys	p.E275K	ENST00000377970	NM_002467.4	275	Gaa/Aaa	3/3	0.339627471189269	4	FACETS	0.77	0.676	0.87	0.77	0.676	0.87	SUBCLONAL	2	TRUE	2	0.453190899382565	4		212	279	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911481	101911481	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	71	246	0	ENST00000374994.4:c.1406A>C	p.Lys469Thr	p.K469T	ENST00000374994	NM_004612.2	469	aAa/aCa	9/9	0.261222099684035	4	FACETS	0.796	0.702	0.895	0.796	0.702	0.895	INDETERMINATE	2	TRUE	2	0.453190899382565	4		246	286	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127916212	127916212	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	212	517	0	ENST00000373547.4:c.432A>C	p.Lys144Asn	p.K144N	ENST00000373547	NM_002721.4	144	aaA/aaC	5/7	0.261222099684035	4	FACETS	1	0.949	1	1	0.949	1	INDETERMINATE	2	TRUE	2	0.453190899382565	4		517	667	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328356	137328356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	146	693	0	ENST00000481739.1:c.1285G>A	p.Gly429Arg	p.G429R	ENST00000481739	NM_002957.4	429	Ggg/Agg	10/10	0.261222099684035	4	FACETS	1	0.978	1	0.608	0.555	0.663	INDETERMINATE	1	TRUE	2	0.453190899382565	4		693	770	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937668	44937668	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	211	251	0	ENST00000377967.4:c.2856C>A	p.Phe952Leu	p.F952L	ENST00000377967	NM_021140.2	952	ttC/ttA	19/29	0.455215419306148	2	FACETS	1	0.99	1			1	CLONAL	2	TRUE	NA	0.453190899382565	2		251	380	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938995	76938995	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	30	294	0	ENST00000373344.5:c.1753G>A	p.Glu585Lys	p.E585K	ENST00000373344	NM_000489.3	585	Gaa/Aaa	9/35	0.455215419306148	2	FACETS	0.313	0.252	0.382			1	SUBCLONAL	1	TRUE	NA	0.453190899382565	2		294	423	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939158	76939158	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	207	281	0	ENST00000373344.5:c.1590G>T	p.Glu530Asp	p.E530D	ENST00000373344	NM_000489.3	530	gaG/gaT	9/35	0.455215419306148	2	FACETS	1	0.986	1			1	CLONAL	2	TRUE	NA	0.453190899382565	2		281	396	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020327	123020327	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	22	221	0	ENST00000355640.3:c.815T>G	p.Phe272Cys	p.F272C	ENST00000355640		272	tTt/tGt	2/7	0.453190899382565	2	FACETS	0.263	0.203	0.333			1	SUBCLONAL	1	TRUE	NA	0.453190899382565	2		221	369	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182890	123182890	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	23	147	0	ENST00000218089.9:c.855G>T	p.Met285Ile	p.M285I	ENST00000218089	NM_001042749.1	285	atG/atT	10/35	0.453190899382565	2	FACETS	0.379	0.296	0.474			1	SUBCLONAL	1	TRUE	NA	0.453190899382565	2		147	268	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480631	123480631	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0035426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	15	192	0	ENST00000371139.4:c.137+2T>C		p.X46_splice	ENST00000371139	NM_001114937.2	46			1	1	FACETS	0.245	0.179	0.324	0.245	0.179	0.324	SUBCLONAL	1	TRUE	0	0.453190899382565	1		192	209	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136030	64136030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1380280944	NA	P-0035427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	379	707	3	ENST00000334205.4:c.1291C>T	p.Arg431Cys	p.R431C	ENST00000334205	NM_003942.2	431	Cgc/Tgc	11/17	1	2	FACETS	0.978	0.932	1	0.978	0.932	1	CLONAL	1	TRUE	1	0.83863655413848	2		710	924	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0035427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	221	464	0	ENST00000269305.4:c.375+1G>T		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.83863655413848	1	FACETS	0.981	0.938	1	0.981	0.938	1	CLONAL	1	TRUE	0	0.83863655413848	1		464	312	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184186	56184186	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0035427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	114	209	0	ENST00000399503.3:c.4389+2T>A		p.X1463_splice	ENST00000399503	NM_005921.1	1463			1	2	FACETS	0.934	0.854	1	0.934	0.854	1	CLONAL	1	TRUE	1	0.83863655413848	2		209	291	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510194	120510194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199565938	NA	P-0035427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	229	372	2	ENST00000256646.2:c.1315G>A	p.Ala439Thr	p.A439T	ENST00000256646	NM_024408.3	439	Gcc/Acc	8/34	1	2	FACETS	0.934	0.877	0.991	0.934	0.877	0.991	CLONAL	1	TRUE	1	0.83863655413848	2		374	585	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711350	114711350	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	195	224	0	ENST00000543371.1:c.365C>G	p.Ser122Trp	p.S122W	ENST00000543371	NM_001198531.1	122	tCg/tGg	3/14	NA	2	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.83863655413848	2		224	444	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864383	57864383	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	329	631	0	ENST00000228682.2:c.1860G>C	p.Trp620Cys	p.W620C	ENST00000228682	NM_005269.2	620	tgG/tgC	12/12	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.83863655413848	2		631	742	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633146	3633146	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	456	821	0	ENST00000294008.3:c.5105C>G	p.Ser1702Cys	p.S1702C	ENST00000294008	NM_032444.2	1702	tCc/tGc	14/15	0.822222325597459	3	FACETS	1	0.989	1	0.551	0.526	0.577	CLONAL	1	TRUE	1	0.83863655413848	3		821	1400	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279673	18279673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	265	433	0	ENST00000222254.8:c.1946G>A	p.Ser649Asn	p.S649N	ENST00000222254	NM_005027.3	649	aGc/aAc	15/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.83863655413848	2		433	611	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40864899	40864899	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0035427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	174	293	0	ENST00000373198.4:c.2370-1G>C		p.X790_splice	ENST00000373198	NM_133170.3	790			1	2	FACETS	0.967	0.901	1	0.967	0.901	1	CLONAL	1	TRUE	1	0.83863655413848	2		293	429	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927978	178927986	+	inframe_deletion	In_Frame_Del	DEL	ACTGTCCAT	ACTGTCCAT	-	novel	NA	P-0035427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	2361	282	0	ENST00000263967.3:c.1256_1264del	p.His419_Pro421del	p.H419_P421del	ENST00000263967	NM_006218.2	419	cACTGTCCATtg/ctg	8/21	0.83863655413848	17	FACETS	1	0.995	1			1	CLONAL	16	TRUE	NA	0.83863655413848	17		282	2559	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156304	106156304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	156	296	1	ENST00000380013.4:c.1205C>T	p.Ser402Leu	p.S402L	ENST00000380013	NM_001127208.2	402	tCa/tTa	3/11	0.83863655413848	1	FACETS	0.973	0.922	1	0.973	0.922	1	CLONAL	1	TRUE	0	0.83863655413848	1		297	222	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027682	152027687	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAACCT	TAACCT	C	novel	NA	P-0035427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	278	605	1	ENST00000262189.6:c.388_389+4delinsG		p.X130_splice	ENST00000262189	NM_170606.2	130		3/59	0.83863655413848	1	FACETS	0.925	0.887	0.963	0.925	0.887	0.963	CLONAL	1	TRUE	0	0.83863655413848	1		606	416	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0035428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	313	463	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.643029252432801	4	FACETS	0.927	0.886	0.968	0.927	0.886	0.968	CLONAL	3	TRUE	1	0.700822392623505	4		463	546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0035428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	249	750	1	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.587366519045491	2	FACETS	0.797	0.756	0.836	0.797	0.756	0.836	SUBCLONAL	2	TRUE	0	0.700822392623505	2		751	446	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011144	12011144	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	109	397	0	ENST00000353533.5:c.551C>A	p.Ser184Ter	p.S184*	ENST00000353533	NM_003010.3	184	tCg/tAg	5/11	0.587366519045491	2	FACETS	0.755	0.696	0.814	0.755	0.696	0.814	SUBCLONAL	2	TRUE	0	0.700822392623505	2		397	206	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28880890	28880890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	201	442	0	ENST00000282397.4:c.3740G>A	p.Ser1247Asn	p.S1247N	ENST00000282397	NM_002019.4	1247	aGc/aAc	29/30	0.583368464476243	2	FACETS	0.891	0.844	0.936	0.891	0.844	0.936	CLONAL	2	TRUE	0	0.700822392623505	2		442	322	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988285	41988285	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	63	484	0	ENST00000219905.7:c.1077C>A	p.Ser359Arg	p.S359R	ENST00000219905	NM_001164273.1	359	agC/agA	3/24	0.181384106839479	3	FACETS	0.566	0.491	0.647	0.189	0.163	0.216	INDETERMINATE	1	TRUE	0	0.700822392623505	3		484	429	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0035429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	170	583	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	0.951	0.878	1	0.951	0.878	1	CLONAL	1	TRUE	1	0.525603456870557	2		583	680	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934512	9934512	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	117	326	0	ENST00000330684.3:c.1643C>T	p.Ala548Val	p.A548V	ENST00000330684	NM_001134407.1	548	gCt/gTt	7/13	1	2	FACETS	0.782	0.709	0.857	0.782	0.709	0.857	SUBCLONAL	1	TRUE	1	0.659360584945583	2		326	454	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858439	89858439	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	239	579	0	ENST00000389301.3:c.1121A>T	p.His374Leu	p.H374L	ENST00000389301	NM_000135.2	374	cAt/cTt	13/43	0.659360584945583	1	FACETS	0.871	0.82	0.922	0.871	0.82	0.922	CLONAL	1	TRUE	0	0.659360584945583	1		579	558	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905510	50905510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763479070	NA	P-0035430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	368	902	0	ENST00000440232.2:c.638C>T	p.Thr213Ile	p.T213I	ENST00000440232	NM_002691.3	213	aCc/aTc	6/27	0.508243294594775	1	FACETS	0.836	0.796	0.876	0.836	0.796	0.876	CLONAL	1	TRUE	0	0.659360584945583	1		902	895	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518275	187518275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	105	295	0	ENST00000441802.2:c.12419C>T	p.Ala4140Val	p.A4140V	ENST00000441802	NM_005245.3	4140	gCc/gTc	25/27	1	2	FACETS	0.913	0.826	1	0.913	0.826	1	CLONAL	1	TRUE	1	0.659360584945583	2		295	349	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0035434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	90	380	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.855	0.766	0.947	0.855	0.766	0.947	CLONAL	1	TRUE	1	0.636377504999054	2		380	331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577599	7577600	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0035434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	121	558	0	ENST00000269305.4:c.680_681dup	p.Asp228LeufsTer20	p.D228Lfs*20	ENST00000269305	NM_001126112.2	227	-/CT	7/11	0.636377504999054	1	FACETS	0.95	0.874	1	0.95	0.874	1	CLONAL	1	TRUE	0	0.636377504999054	1		558	273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0035435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	226	745	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.308940537240598	3	FACETS	0.991	0.932	1	0.66	0.621	0.7	INDETERMINATE	2	TRUE	0	0.54711192130449	3		745	531	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625249	69625249	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781935233	NA	P-0035435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	186	804	0	ENST00000334134.2:c.544G>A	p.Val182Met	p.V182M	ENST00000334134	NM_005247.2	182	Gtg/Atg	3/3	0.317319687112231	4	FACETS	1	0.99	1	0.722	0.669	0.778	INDETERMINATE	1	TRUE	2	0.54711192130449	4		804	728	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128848674	128848674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1006687669	NA	P-0035435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	46	651	1	ENST00000249373.3:c.1339G>A	p.Glu447Lys	p.E447K	ENST00000249373	NM_005631.4	447	Gag/Aag	7/12	0.286174379920196	3	FACETS	0.406	0.341	0.477	0.203	0.17	0.239	INDETERMINATE	1	TRUE	1	0.54711192130449	3		652	528	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226125	226125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762956849	NA	P-0035435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	84	790	0	ENST00000264932.6:c.584G>A	p.Arg195Gln	p.R195Q	ENST00000264932	NM_004168.2	195	cGg/cAg	5/15	0.420266110487562	2	FACETS	0.498	0.44	0.56	0.249	0.22	0.28	SUBCLONAL	1	TRUE	0	0.54711192130449	2		790	617	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681341	88681341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786202611	NA	P-0035435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	21	243	0	ENST00000372037.3:c.1231G>A	p.Glu411Lys	p.E411K	ENST00000372037	NM_004329.2	411	Gaa/Aaa	11/13	0.317319687112231	4	FACETS	0.555	0.429	0.701	0.277	0.214	0.351	INDETERMINATE	1	TRUE	2	0.54711192130449	4		243	214	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445064	49445064	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	102	626	0	ENST00000301067.7:c.2402C>G	p.Pro801Arg	p.P801R	ENST00000301067	NM_003482.3	801	cCt/cGt	10/54	0.369847227269865	4	FACETS	1	0.908	1	0.507	0.454	0.562	CLONAL	1	TRUE	2	0.54711192130449	4		626	569	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028810	42028810	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	132	646	0	ENST00000219905.7:c.4348C>A	p.Leu1450Met	p.L1450M	ENST00000219905	NM_001164273.1	1450	Ctg/Atg	13/24	0.257787758446411	4	FACETS	1	0.977	1	0.614	0.559	0.671	INDETERMINATE	1	TRUE	2	0.54711192130449	4		646	608	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644820	67644820	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771567232	NA	P-0035435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	29	430	0	ENST00000264010.4:c.85C>T	p.Arg29Trp	p.R29W	ENST00000264010	NM_006565.3	29	Cgg/Tgg	3/12	0.494099930912048	4	FACETS	0.383	0.307	0.47	0.192	0.153	0.235	SUBCLONAL	1	TRUE	2	0.54711192130449	4		430	428	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142943	47142948	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTACC	CTTACC	-	novel	NA	P-0035435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	39	323	0	ENST00000409792.3:c.5015_5015+5del		p.X1672_splice	ENST00000409792	NM_014159.6	1672		8/21	0.494099930912048	4	FACETS	0.603	0.5	0.716	0.301	0.25	0.358	SUBCLONAL	1	TRUE	2	0.54711192130449	4		323	366	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440365	187440365	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	44	588	1	ENST00000232014.4:c.2002C>T	p.Arg668Cys	p.R668C	ENST00000232014	NM_001130845.1	668	Cgt/Tgt	10/10	0.494099930912048	4	FACETS	0.427	0.357	0.504	0.213	0.178	0.252	SUBCLONAL	1	TRUE	2	0.54711192130449	4		589	583	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518121	8518121	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	71	514	0	ENST00000356435.5:c.1270G>T	p.Val424Phe	p.V424F	ENST00000356435		424	Gtc/Ttc	10/35	1	2	FACETS	0.735	0.646	0.83	0.735	0.646	0.83	SUBCLONAL	1	TRUE	1	0.54711192130449	2		514	353	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0035440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	58	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.854	0.735	0.983	0.854	0.735	0.983	CLONAL	1	TRUE	1	0.283072001333269	2		502	480	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0035440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	29	458	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.468	0.375	0.574	0.468	0.375	0.574	SUBCLONAL	1	TRUE	1	0.283072001333269	2		458	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578259	7578259	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	84	468	0	ENST00000269305.4:c.590T>G	p.Val197Gly	p.V197G	ENST00000269305	NM_001126112.2	197	gTg/gGg	6/11	0.268489659413622	1	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	0	0.283072001333269	1		468	509	SUCCESS
APC	324	MSKCC	GRCh37	5	112177659	112177660	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	69	192	0	ENST00000257430.4:c.6371dup	p.Leu2124PhefsTer3	p.L2124Ffs*3	ENST00000257430	NM_000038.5	2123	tgt/tgTt	16/16	0.268489659413622	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.283072001333269	1		192	370	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729925	30729926	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1559472349	NA	P-0035440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	47	261	0	ENST00000295754.5:c.1446_1447del	p.Val484ArgfsTer31	p.V484Rfs*31	ENST00000295754	NM_003242.5	482	ccCTgt/ccgt	6/7	1	2	FACETS	0.854	0.722	0.998	0.854	0.722	0.998	CLONAL	1	TRUE	1	0.283072001333269	2		261	389	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	144	460	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.27213363982165	1	FACETS	0.664	0.615	0.713	0.664	0.615	0.713	INDETERMINATE	1	TRUE	0	0.803240264409479	1		460	323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0035443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	402	581	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.795736142159277	2	FACETS	0.983	0.956	1	0.983	0.956	1	CLONAL	2	TRUE	0	0.803240264409479	2		582	509	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058033	27058033	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	565	486	0	ENST00000324856.7:c.1741C>T	p.Gln581Ter	p.Q581*	ENST00000324856	NM_006015.4	581	Cag/Tag	3/20	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.803240264409479	NA		486	655	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9928043	9928043	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	83	295	0	ENST00000330684.3:c.1696C>T	p.Leu566Phe	p.L566F	ENST00000330684	NM_001134407.1	566	Ctc/Ttc	8/13	1	2	FACETS	0.97	0.873	1	0.97	0.873	1	CLONAL	1	TRUE	1	0.803240264409479	2		295	213	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0035445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	23	298	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.394628075013663	1	FACETS	0.183	0.143	0.23	0.183	0.143	0.23	SUBCLONAL	1	TRUE	0	0.574518126186427	1		298	311	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939029	48939029	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0035445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	96	314	0	ENST00000267163.4:c.862-1G>A		p.X288_splice	ENST00000267163	NM_000321.2	288			1	2	FACETS	0.873	0.783	0.966	0.873	0.783	0.966	CLONAL	1	TRUE	1	0.574518126186427	2		314	383	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420655	49420655	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	33	556	0	ENST00000301067.7:c.15094T>A	p.Cys5032Ser	p.C5032S	ENST00000301067	NM_003482.3	5032	Tgc/Agc	48/54	0.394628075013663	1	FACETS	0.129	0.105	0.157	0.129	0.105	0.157	SUBCLONAL	1	TRUE	0	0.574518126186427	1		556	633	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724415	43724415	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	266	784	1	ENST00000382044.4:c.3652G>A	p.Asp1218Asn	p.D1218N	ENST00000382044	NM_001141980.1	1218	Gat/Aat	17/28	1	2	FACETS	0.911	0.855	0.969	0.911	0.855	0.969	CLONAL	1	TRUE	1	0.574518126186427	2		785	1016	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164995	47164995	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0035445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	159	413	0	ENST00000409792.3:c.1131T>G	p.Tyr377Ter	p.Y377*	ENST00000409792	NM_014159.6	377	taT/taG	3/21	1	2	FACETS	0.916	0.844	0.992	0.916	0.844	0.992	CLONAL	1	TRUE	1	0.574518126186427	2		413	604	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61725860	61725860	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	45	496	0	ENST00000401558.2:c.707T>A	p.Ile236Asn	p.I236N	ENST00000401558	NM_003400.3	236	aTt/aAt	9/25	0.189425743367164	4	FACETS	0.598	0.502	0.704	0.299	0.251	0.352	INDETERMINATE	1	TRUE	2	0.344155233739901	4		496	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0035467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	131	573	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.194868505796807	2	FACETS	1	0.918	1	0.504	0.459	0.551	INDETERMINATE	1	FALSE	0	0.444273607632243	2		574	585	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543850	212543850	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	63	382	0	ENST00000342788.4:c.1549C>A	p.Pro517Thr	p.P517T	ENST00000342788	NM_005235.2	517	Cca/Aca	13/28	0.444273607632243	1	FACETS	0.579	0.503	0.661	0.579	0.503	0.661	SUBCLONAL	1	FALSE	0	0.444273607632243	1		382	381	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041327	42041327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771491619	NA	P-0035467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	28	714	0	ENST00000219905.7:c.5522G>A	p.Arg1841Gln	p.R1841Q	ENST00000219905	NM_001164273.1	1841	cGg/cAg	17/24	0.197826253450871	2	FACETS	0.253	0.201	0.311	0.126	0.1	0.156	INDETERMINATE	1	FALSE	0	0.444273607632243	2		714	499	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984395	201984395	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	236	696	2	ENST00000359651.3:c.1060T>A	p.Phe354Ile	p.F354I	ENST00000359651		354	Ttt/Att	8/8	0.38368182276468	3	FACETS	0.926	0.868	0.985	0.926	0.868	0.985	CLONAL	2	FALSE	1	0.444273607632243	3		698	701	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732926	30732927	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGTGAGACGTTGACTGAGTGCTGGGACCACGACCCAGAGGCCCGTCTC	novel	NA	P-0035467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	31	290	0	ENST00000295754.5:c.1540_1587dup	p.Cys514_Leu529dup	p.C514_L529dup	ENST00000295754	NM_003242.5	514	-/TGTGAGACGTTGACTGAGTGCTGGGACCACGACCCAGAGGCCCGTCTC	7/7	0.126310542500169	5	FACETS	0.898	0.729	1	0.224	0.182	0.272	INDETERMINATE	1	FALSE	1	0.444273607632243	5		290	259	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0035471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	68	581	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.881	0.766	1	0.881	0.766	1	CLONAL	1	TRUE	1	0.23	2		582	671	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0035471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	30	228	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	1	0.818	1	1	0.818	1	CLONAL	1	TRUE	1	0.23	2		228	258	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0035471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	396	415	1	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	0.3	5	FACETS	0.95	0.906	0.994			1	CLONAL	5	TRUE	NA	0.23	5		416	975	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106350	27106363	+	frameshift_variant	Frame_Shift_Del	DEL	CATTCGAAGCCTGT	CATTCGAAGCCTGT	-	novel	NA	P-0035471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	59	585	0	ENST00000324856.7:c.5965_5978del	p.Arg1989CysfsTer5	p.R1989Cfs*5	ENST00000324856	NM_006015.4	1987	acCATTCGAAGCCTGTca/acca	20/20	0.179386176459697	1	FACETS	0.833	0.717	0.959	0.833	0.717	0.959	CLONAL	1	TRUE	0	0.23	1		585	545	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098355	108098355	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	53	367	0	ENST00000278616.4:c.4A>G	p.Ser2Gly	p.S2G	ENST00000278616	NM_000051.3	2	Agt/Ggt	2/63	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.23	2		367	381	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856655	111856655	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1014425313	NA	P-0035471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	32	184	0	ENST00000341259.2:c.706G>A	p.Val236Met	p.V236M	ENST00000341259	NM_005475.2	236	Gtg/Atg	2/8	1	2	FACETS	0.997	0.813	1	0.997	0.813	1	CLONAL	1	TRUE	1	0.23	2		184	279	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791024	42791027	+	frameshift_variant	Frame_Shift_Del	DEL	GAGG	GAGG	-	novel	NA	P-0035471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	29	512	0	ENST00000575354.2:c.169_172del	p.Glu57ProfsTer147	p.E57Pfs*147	ENST00000575354	NM_015125.3	57	GAGGcc/cc	2/20	1	2	FACETS	0.564	0.452	0.692	0.564	0.452	0.692	SUBCLONAL	1	TRUE	1	0.23	2		512	447	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0035485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	92	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.316080249138381	2	FACETS	1	0.892	1	0.501	0.446	0.56	CLONAL	1	TRUE	0	0.316080249138381	2		502	581	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166282	7166282	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	150	581	0	ENST00000302850.5:c.1744G>T	p.Gly582Cys	p.G582C	ENST00000302850	NM_000208.2	582	Ggt/Tgt	8/22	0.295459324069166	2	FACETS	1	0.969	1	0.563	0.515	0.614	CLONAL	1	TRUE	0	0.316080249138381	2		581	843	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435160	56435161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755128667	NA	P-0035485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	223	735	2	ENST00000407977.2:c.1976dup	p.Pro660SerfsTer87	p.P660Sfs*87	ENST00000407977		659	ggt/ggGt	9/10	0.295459324069166	2	FACETS	0.988	0.924	1	0.988	0.924	1	CLONAL	2	TRUE	0	0.316080249138381	2		737	714	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438647	49438647	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	132	656	1	ENST00000301067.7:c.4843C>T	p.Arg1615Ter	p.R1615*	ENST00000301067	NM_003482.3	1615	Cga/Tga	19/54	0.316080249138381	2	FACETS	0.952	0.864	1	0.476	0.432	0.523	CLONAL	1	TRUE	0	0.316080249138381	2		657	877	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034489	47034489	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	118	591	0	ENST00000377604.3:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000377604	NM_001204468.1	192	Cag/Tag	6/24	0.295459324069166	2	FACETS	0.884	0.797	0.975	0.442	0.398	0.488	CLONAL	1	TRUE	0	0.316080249138381	2		591	845	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286197	66286197	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	100	443	0	ENST00000273854.3:c.1489G>A	p.Gly497Arg	p.G497R	ENST00000273854	NM_004439.5	497	Gga/Aga	6/18	0.295459324069166	2	FACETS	1	0.957	1	0.565	0.506	0.627	CLONAL	1	TRUE	0	0.316080249138381	2		443	560	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	23	460	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.623	0.486	0.783	0.623	0.486	0.783	SUBCLONAL	1	TRUE	1	0.2	2		460	369	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952076	178952076	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1064793838	NA	P-0035486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	16	334	0	ENST00000263967.3:c.3131A>G	p.Asn1044Ser	p.N1044S	ENST00000263967	NM_006218.2	1044	aAt/aGt	21/21	1	2	FACETS	0.608	0.45	0.798	0.608	0.45	0.798	SUBCLONAL	1	TRUE	1	0.2	2		334	263	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031750	36031750	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879255268	NA	P-0035486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	29	525	1	ENST00000358208.4:c.1579G>A	p.Glu527Lys	p.E527K	ENST00000358208		527	Gag/Aag	12/12	1	2	FACETS	0.822	0.66	1	0.822	0.66	1	CLONAL	1	TRUE	1	0.2	2		526	353	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971188	21971189	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0035486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	26	366	0	ENST00000304494.5:c.169_170del	p.Ala57ProfsTer62	p.A57Pfs*62	ENST00000304494	NM_000077.4	57	GCc/c	2/3	1	2	FACETS	1	0.824	1	1	0.824	1	CLONAL	1	TRUE	1	0.2	2		366	250	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111012	193111012	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	23	199	0	ENST00000367435.3:c.545T>C	p.Ile182Thr	p.I182T	ENST00000367435	NM_024529.4	182	aTt/aCt	7/17	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.2	2		199	177	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575109	48575109	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	19	387	1	ENST00000342988.3:c.303G>A	p.Trp101Ter	p.W101*	ENST00000342988	NM_005359.5	101	tgG/tgA	3/12	1	2	FACETS	0.674	0.512	0.864	0.674	0.512	0.864	SUBCLONAL	1	TRUE	1	0.2	2		388	282	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	21	460	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.8	0.615	1	0.8	0.615	1	CLONAL	1	TRUE	1	0.13	2		460	404	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453148	140453148	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs397507483	NA	P-0035487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	24	367	0	ENST00000288602.6:c.1787G>T	p.Gly596Val	p.G596V	ENST00000288602	NM_004333.4	596	gGt/gTt	15/18	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.13	2		367	294	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468231	120468231	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	31	660	1	ENST00000256646.2:c.4208C>A	p.Ala1403Asp	p.A1403D	ENST00000256646	NM_024408.3	1403	gCc/gAc	25/34	1	2	FACETS	0.858	0.692	1	0.858	0.692	1	CLONAL	1	TRUE	1	0.13	2		661	556	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984507	72984508	+	missense_variant	Missense_Mutation	DNP	TC	TC	AG	novel	NA	P-0035487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	32	799	2	ENST00000268489.5:c.3076_3077delinsCT	p.Glu1026Leu	p.E1026L	ENST00000268489	NM_006885.3	1026	GAg/CTg	3/10	1	2	FACETS	0.832	0.673	1	0.832	0.673	1	CLONAL	1	TRUE	1	0.13	2		801	592	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163822	47163823	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0035487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	31	578	0	ENST00000409792.3:c.2303_2304del	p.Val768GlyfsTer8	p.V768Gfs*8	ENST00000409792	NM_014159.6	768	gTG/g	3/21	1	2	FACETS	1	0.809	1	1	0.809	1	CLONAL	1	TRUE	1	0.13	2		578	476	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904823	101904823	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	20	387	0	ENST00000374994.4:c.811G>A	p.Gly271Ser	p.G271S	ENST00000374994	NM_004612.2	271	Ggt/Agt	5/9	1	2	FACETS	0.882	0.674	1	0.882	0.674	1	CLONAL	1	TRUE	1	0.13	2		387	349	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0035489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	384	451	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.562146019522313	10	FACETS	0.948	0.914	0.982			1	CLONAL	8	FALSE	NA	0.562146019522313	10		451	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0035489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	275	632	0	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	0.433720787602445	4	FACETS	1	0.962	1	0.76	0.723	0.796	CLONAL	3	FALSE	0	0.562146019522313	4		632	503	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85741985	85741985	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	237	626	0	ENST00000370580.1:c.51G>C	p.Lys17Asn	p.K17N	ENST00000370580	NM_003921.4	17	aaG/aaC	1/3	0.360260144771215	2	FACETS	0.869	0.821	0.917	0.869	0.821	0.917	CLONAL	2	FALSE	0	0.562146019522313	2		626	485	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94923077	94923077	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	68	606	0	ENST00000536441.1:c.391G>A	p.Glu131Lys	p.E131K	ENST00000536441	NM_144665.3	131	Gaa/Aaa	4/10	NA	2	FACETS	0.788	0.691	0.891			1	INDETERMINATE	1	FALSE	NA	0.562146019522313	2		606	307	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334776	81334776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1267493094	NA	P-0035489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	67	508	0	ENST00000222390.5:c.1940G>A	p.Arg647Gln	p.R647Q	ENST00000222390	NM_000601.4	647	cGa/cAa	17/18	0.324841980967255	4	FACETS	0.943	0.823	1			1	INDETERMINATE	1	FALSE	NA	0.562146019522313	4		508	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	589	767	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.740025192484973	3	FACETS	0.979	0.946	1	0.979	0.946	1	CLONAL	2	TRUE	1	0.748564483935493	3		767	1105	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	436	528	2	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.740025192484973	3	FACETS	0.957	0.92	0.995	0.957	0.92	0.995	CLONAL	2	TRUE	1	0.748564483935493	3		530	836	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	159	392	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.848	0.783	0.915	0.848	0.783	0.915	CLONAL	1	TRUE	1	0.748564483935493	2		392	501	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	140	228	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	0.748564483935493	2		228	359	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	507	415	1	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	0.740025192484973	3	FACETS	0.929	0.894	0.964	0.929	0.894	0.964	CLONAL	2	TRUE	1	0.748564483935493	3		416	1002	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073432	8073432	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	273	552	0	ENST00000377482.5:c.1227A>C	p.Lys409Asn	p.K409N	ENST00000377482	NM_018948.3	409	aaA/aaC	4/4	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.748564483935493	2		552	684	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521540	46521540	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	306	653	0	ENST00000262741.5:c.868G>T	p.Glu290Ter	p.E290*	ENST00000262741	NM_003629.3	290	Gaa/Taa	7/10	1	2	FACETS	0.888	0.839	0.937	0.888	0.839	0.937	CLONAL	1	TRUE	1	0.748564483935493	2		653	921	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439657	51439657	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	191	351	0	ENST00000262662.1:c.222T>G	p.Ile74Met	p.I74M	ENST00000262662		74	atT/atG	4/4	1	2	FACETS	0.713	0.661	0.766	0.713	0.661	0.766	SUBCLONAL	1	TRUE	1	0.748564483935493	2		351	716	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307158	65307158	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	238	400	0	ENST00000342505.4:c.2530G>T	p.Asp844Tyr	p.D844Y	ENST00000342505	NM_002227.2	844	Gac/Tac	18/25	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.748564483935493	2		400	615	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745955	162745955	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	159	321	0	ENST00000367921.3:c.2078A>G	p.Gln693Arg	p.Q693R	ENST00000367921	NM_006182.2	693	cAa/cGa	16/18	1	2	FACETS	0.965	0.894	1	0.965	0.894	1	CLONAL	1	TRUE	1	0.748564483935493	2		321	440	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206943235	206943235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760677075	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	184	348	0	ENST00000423557.1:c.383G>A	p.Arg128Gln	p.R128Q	ENST00000423557	NM_000572.2	128	cGa/cAa	4/5	1	2	FACETS	0.936	0.871	1	0.936	0.871	1	CLONAL	1	TRUE	1	0.748564483935493	2		348	525	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716123	243716123	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	322	559	0	ENST00000263826.5:c.1071A>C	p.Leu357Phe	p.L357F	ENST00000263826	NM_005465.4	357	ttA/ttC	10/13	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.748564483935493	2		559	840	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244913	123244913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1224606327	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	340	806	1	ENST00000358487.5:c.2191G>A	p.Glu731Lys	p.E731K	ENST00000358487	NM_000141.4	731	Gaa/Aaa	16/18	1	2	FACETS	0.978	0.928	1	0.978	0.928	1	CLONAL	1	TRUE	1	0.748564483935493	2		807	929	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247533	123247533	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	359	560	0	ENST00000358487.5:c.1958A>C	p.Asn653Thr	p.N653T	ENST00000358487	NM_000141.4	653	aAt/aCt	14/18	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.748564483935493	2		560	953	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103328	119103328	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	219	436	0	ENST00000264033.4:c.366G>T	p.Leu122Phe	p.L122F	ENST00000264033	NM_005188.3	122	ttG/ttT	2/16	1	2	FACETS	0.942	0.882	1	0.942	0.882	1	CLONAL	1	TRUE	1	0.748564483935493	2		436	621	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230691	46230691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424958105	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	220	483	0	ENST00000334344.6:c.940C>T	p.Arg314Cys	p.R314C	ENST00000334344	NM_152641.2	314	Cgt/Tgt	8/21	0.740025192484973	3	FACETS	0.999	0.931	1	0.499	0.465	0.534	CLONAL	1	TRUE	1	0.748564483935493	3		483	809	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864118	57864118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200306754	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	243	518	0	ENST00000228682.2:c.1595G>A	p.Arg532His	p.R532H	ENST00000228682	NM_005269.2	532	cGc/cAc	12/12	0.740025192484973	3	FACETS	0.99	0.927	1	0.495	0.463	0.528	CLONAL	1	TRUE	1	0.748564483935493	3		518	901	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891144	112891144	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	319	640	0	ENST00000351677.2:c.478A>G	p.Ser160Gly	p.S160G	ENST00000351677	NM_002834.3	160	Agc/Ggc	4/16	0.740025192484973	3	FACETS	0.902	0.851	0.955	0.451	0.425	0.478	CLONAL	1	TRUE	1	0.748564483935493	3		640	1298	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250213	133250213	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs864622766	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	228	605	0	ENST00000320574.5:c.1307C>G	p.Pro436Arg	p.P436R	ENST00000320574	NM_006231.2	436	cCc/cGc	13/49	0.722883706912404	3	FACETS	0.925	0.863	0.989			1	CLONAL	1	TRUE	NA	0.748564483935493	3		605	905	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964095	28964095	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1302031800	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	297	562	0	ENST00000282397.4:c.1807A>G	p.Ser603Gly	p.S603G	ENST00000282397	NM_002019.4	603	Agt/Ggt	13/30	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.748564483935493	2		562	753	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893382	32893382	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	200	310	0	ENST00000380152.3:c.236T>C	p.Ile79Thr	p.I79T	ENST00000380152		79	aTa/aCa	3/27	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.748564483935493	2		310	522	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913282	32913282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660146	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	244	440	0	ENST00000380152.3:c.4790C>A	p.Ser1597Tyr	p.S1597Y	ENST00000380152		1597	tCt/tAt	11/27	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.748564483935493	2		440	647	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934254	48934254	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1131690904	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	213	502	0	ENST00000267163.4:c.709G>T	p.Glu237Ter	p.E237*	ENST00000267163	NM_000321.2	237	Gaa/Taa	7/27	1	2	FACETS	0.969	0.907	1	0.969	0.907	1	CLONAL	1	TRUE	1	0.748564483935493	2		502	587	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047519	49047519	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1131690908	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	151	340	0	ENST00000267163.4:c.2513C>A	p.Ser838Ter	p.S838*	ENST00000267163	NM_000321.2	838	tCa/tAa	24/27	1	2	FACETS	0.947	0.875	1	0.947	0.875	1	CLONAL	1	TRUE	1	0.748564483935493	2		340	426	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42050032	42050032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	137	308	0	ENST00000219905.7:c.7186C>T	p.Arg2396Ter	p.R2396*	ENST00000219905	NM_001164273.1	2396	Cga/Tga	19/24	1	2	FACETS	0.941	0.865	1	0.941	0.865	1	CLONAL	1	TRUE	1	0.748564483935493	2		308	389	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678514	88678514	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1337303639	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	217	484	0	ENST00000360948.2:c.1022C>A	p.Pro341His	p.P341H	ENST00000360948	NM_001012338.2	341	cCt/cAt	9/19	1	2	FACETS	0.993	0.93	1	0.993	0.93	1	CLONAL	1	TRUE	1	0.748564483935493	2		484	584	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011200	12011200	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	467	383	0	ENST00000353533.5:c.607G>T	p.Glu203Ter	p.E203*	ENST00000353533	NM_003010.3	203	Gaa/Taa	5/11	0.740025192484973	3	FACETS	0.991	0.966	1	1	0.997	1	CLONAL	3	TRUE	1	0.748564483935493	3		383	577	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215366	41215366	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786203547	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	577	548	0	ENST00000357654.3:c.5177G>T	p.Arg1726Ile	p.R1726I	ENST00000357654	NM_007294.3	1726	aGa/aTa	18/23	0.740025192484973	3	FACETS	0.96	0.926	0.992	0.96	0.926	0.992	CLONAL	2	TRUE	1	0.748564483935493	3		548	1104	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244732	41244732	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555588894	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	769	792	0	ENST00000357654.3:c.2816T>C	p.Val939Ala	p.V939A	ENST00000357654	NM_007294.3	939	gTt/gCt	10/23	0.740025192484973	3	FACETS	0.98	0.951	1	0.98	0.951	1	CLONAL	2	TRUE	1	0.748564483935493	3		792	1440	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245063	41245063	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	954	857	0	ENST00000357654.3:c.2485T>G	p.Phe829Val	p.F829V	ENST00000357654	NM_007294.3	829	Ttt/Gtt	10/23	0.740025192484973	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.748564483935493	3		857	1741	SUCCESS
YES1	7525	MSKCC	GRCh37	18	751726	751726	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1010928891	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	204	423	0	ENST00000314574.4:c.350G>T	p.Arg117Ile	p.R117I	ENST00000314574	NM_005433.3	117	aGa/aTa	3/12	1	2	FACETS	0.908	0.848	0.97	0.908	0.848	0.97	CLONAL	1	TRUE	1	0.748564483935493	2		423	600	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100016	11100016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749059769	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	480	519	2	ENST00000358026.2:c.1142G>A	p.Arg381Gln	p.R381Q	ENST00000358026	NM_001128849.1	381	cGa/cAa	7/36	0.748564483935493	3	FACETS	0.961	0.925	0.997	0.961	0.925	0.997	CLONAL	2	TRUE	1	0.748564483935493	3		521	917	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297788	15297788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748963864	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	710	742	0	ENST00000263388.2:c.1852G>A	p.Glu618Lys	p.E618K	ENST00000263388	NM_000435.2	618	Gaa/Aaa	12/33	0.748564483935493	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.748564483935493	3		742	1274	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966040	25966040	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367562789	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	567	735	1	ENST00000435504.4:c.3166G>A	p.Glu1056Lys	p.E1056K	ENST00000435504		1056	Gaa/Aaa	13/13	0.390340770933912	3	FACETS	0.894	0.862	0.926	0.894	0.862	0.926	INDETERMINATE	2	TRUE	1	0.748564483935493	3		736	1164	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451891	29451891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1381440856	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	275	663	2	ENST00000389048.3:c.2674G>A	p.Ala892Thr	p.A892T	ENST00000389048	NM_004304.4	892	Gcc/Acc	16/29	0.390340770933912	3	FACETS	1	0.98	1	0.546	0.514	0.58	INDETERMINATE	1	TRUE	1	0.748564483935493	3		665	924	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46583316	46583316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367844911	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	312	430	0	ENST00000263734.3:c.244G>A	p.Glu82Lys	p.E82K	ENST00000263734	NM_001430.4	82	Gaa/Aaa	3/16	0.390340770933912	3	FACETS	0.894	0.85	0.937	0.894	0.85	0.937	INDETERMINATE	2	TRUE	1	0.748564483935493	3		430	641	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044542	128044542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764062606	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	338	486	0	ENST00000285398.2:c.1079G>A	p.Arg360His	p.R360H	ENST00000285398	NM_000122.1	360	cGc/cAc	8/15	0.390340770933912	3	FACETS	0.827	0.788	0.867	0.827	0.788	0.867	INDETERMINATE	2	TRUE	1	0.748564483935493	3		486	750	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198260920	198260920	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	319	669	0	ENST00000335508.6:c.3399G>T	p.Met1133Ile	p.M1133I	ENST00000335508	NM_012433.2	1133	atG/atT	23/25	0.390340770933912	3	FACETS	1	0.985	1	0.556	0.525	0.588	INDETERMINATE	1	TRUE	1	0.748564483935493	3		669	1053	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268383	198268383	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1172363633	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	197	384	1	ENST00000335508.6:c.1645C>T	p.Arg549Cys	p.R549C	ENST00000335508	NM_012433.2	549	Cgt/Tgt	12/25	0.390340770933912	3	FACETS	1	0.972	1	0.543	0.505	0.582	INDETERMINATE	1	TRUE	1	0.748564483935493	3		385	666	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137487	202137487	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	314	403	0	ENST00000358485.4:c.715G>T	p.Glu239Ter	p.E239*	ENST00000358485	NM_001080125.1	239	Gaa/Taa	4/9	0.390340770933912	3	FACETS	1	0.99	1	0.599	0.566	0.633	INDETERMINATE	1	TRUE	1	0.748564483935493	3		403	962	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742794	39742794	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	313	324	1	ENST00000361337.2:c.1637G>A	p.Arg546Gln	p.R546Q	ENST00000361337	NM_003286.2	546	cGa/cAa	15/21	0.748564483935493	3	FACETS	0.908	0.864	0.951	0.908	0.864	0.951	CLONAL	2	TRUE	1	0.748564483935493	3		325	633	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29106017	29106017	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs749963436	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	207	440	0	ENST00000328354.6:c.823G>T	p.Glu275Ter	p.E275*	ENST00000328354	NM_007194.3	275	Gaa/Taa	7/15	1	2	FACETS	0.982	0.919	1	0.982	0.919	1	CLONAL	1	TRUE	1	0.748564483935493	2		440	563	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52621440	52621440	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	273	493	0	ENST00000394830.3:c.2977T>G	p.Phe993Val	p.F993V	ENST00000394830	NM_018313.4	993	Ttt/Gtt	20/30	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.748564483935493	2		493	725	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911655	134911655	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	165	315	0	ENST00000398015.3:c.2120C>A	p.Ser707Tyr	p.S707Y	ENST00000398015	NM_004441.4	707	tCt/tAt	11/16	1	2	FACETS	0.988	0.917	1	0.988	0.917	1	CLONAL	1	TRUE	1	0.748564483935493	2		315	446	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170015172	170015172	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	279	571	0	ENST00000295797.4:c.1578T>G	p.Asp526Glu	p.D526E	ENST00000295797	NM_002740.5	526	gaT/gaG	16/18	1	2	FACETS	0.993	0.937	1	0.993	0.937	1	CLONAL	1	TRUE	1	0.748564483935493	2		571	751	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920084	1920084	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	263	553	0	ENST00000382891.5:c.1144G>T	p.Glu382Ter	p.E382*	ENST00000382891	NM_133335.3	382	Gaa/Taa	5/22	1	2	FACETS	0.944	0.889	1	0.944	0.889	1	CLONAL	1	TRUE	1	0.748564483935493	2		553	744	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958820	55958820	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	272	491	0	ENST00000263923.4:c.3033A>C	p.Gln1011His	p.Q1011H	ENST00000263923	NM_002253.2	1011	caA/caC	22/30	1	2	FACETS	0.977	0.921	1	0.977	0.921	1	CLONAL	1	TRUE	1	0.748564483935493	2		491	744	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968548	55968548	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	256	477	0	ENST00000263923.4:c.2115G>T	p.Glu705Asp	p.E705D	ENST00000263923	NM_002253.2	705	gaG/gaT	14/30	1	2	FACETS	0.927	0.872	0.983	0.927	0.872	0.983	CLONAL	1	TRUE	1	0.748564483935493	2		477	738	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245447	153245447	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	258	596	0	ENST00000281708.4:c.1744T>C	p.Ser582Pro	p.S582P	ENST00000281708	NM_033632.3	582	Tcg/Ccg	11/12	1	2	FACETS	0.871	0.819	0.925	0.871	0.819	0.925	CLONAL	1	TRUE	1	0.748564483935493	2		596	791	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517847	187517847	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202133523	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	189	406	1	ENST00000441802.2:c.12847G>A	p.Glu4283Lys	p.E4283K	ENST00000441802	NM_005245.3	4283	Gaa/Aaa	25/27	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.748564483935493	2		407	485	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534269	187534269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1401735284	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	182	376	1	ENST00000441802.2:c.9457G>A	p.Asp3153Asn	p.D3153N	ENST00000441802	NM_005245.3	3153	Gac/Aac	13/27	1	2	FACETS	0.896	0.832	0.96	0.896	0.832	0.96	CLONAL	1	TRUE	1	0.748564483935493	2		377	543	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554893	187554893	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	239	501	0	ENST00000441802.2:c.4268C>G	p.Ser1423Ter	p.S1423*	ENST00000441802	NM_005245.3	1423	tCa/tGa	7/27	1	2	FACETS	0.903	0.847	0.96	0.903	0.847	0.96	CLONAL	1	TRUE	1	0.748564483935493	2		501	707	SUCCESS
APC	324	MSKCC	GRCh37	5	112102033	112102033	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587781587	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	127	295	0	ENST00000257430.4:c.146A>G	p.Lys49Arg	p.K49R	ENST00000257430	NM_000038.5	49	aAa/aGa	3/16	1	2	FACETS	0.917	0.84	0.996	0.917	0.84	0.996	CLONAL	1	TRUE	1	0.748564483935493	2		295	370	SUCCESS
APC	324	MSKCC	GRCh37	5	112174658	112174658	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	167	361	0	ENST00000257430.4:c.3367C>A	p.Gln1123Lys	p.Q1123K	ENST00000257430	NM_000038.5	1123	Caa/Aaa	16/16	1	2	FACETS	0.968	0.898	1	0.968	0.898	1	CLONAL	1	TRUE	1	0.748564483935493	2		361	461	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	124	204	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.748564483935493	2		204	303	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169036	32169036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745902446	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	296	747	0	ENST00000375023.3:c.3997C>T	p.Arg1333Cys	p.R1333C	ENST00000375023	NM_004557.3	1333	Cgt/Tgt	22/30	0.748564483935493	3	FACETS	0.906	0.852	0.961	0.453	0.426	0.481	CLONAL	1	TRUE	1	0.748564483935493	3		747	1200	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93968000	93968000	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	456	387	0	ENST00000369303.4:c.1927G>T	p.Glu643Ter	p.E643*	ENST00000369303	NM_004440.3	643	Gaa/Taa	11/17	0.748564483935493	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.748564483935493	3		387	835	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372752	81372752	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768451705	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	139	319	0	ENST00000222390.5:c.782G>A	p.Arg261His	p.R261H	ENST00000222390	NM_000601.4	261	cGc/cAc	7/18	0.588773969730968	6	FACETS	0.978	0.89	1			1	CLONAL	1	TRUE	NA	0.748564483935493	6		319	948	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508082	106508082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	69	172	0	ENST00000359195.3:c.76C>T	p.Arg26Cys	p.R26C	ENST00000359195	NM_002649.2	26	Cgc/Tgc	2/11	0.740025192484973	3	FACETS	1	0.887	1	0.503	0.443	0.565	CLONAL	1	TRUE	1	0.748564483935493	3		172	252	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843395	128843395	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146797066	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	465	538	0	ENST00000249373.3:c.502C>T	p.Arg168Cys	p.R168C	ENST00000249373	NM_005631.4	168	Cgc/Tgc	2/12	0.740025192484973	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.748564483935493	3		538	834	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945021	151945021	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs756918375	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	57	73	0	ENST00000262189.6:c.2498G>T	p.Arg833Ile	p.R833I	ENST00000262189	NM_170606.2	833	aGa/aTa	14/59	0.740025192484973	3	FACETS	0.854	0.741	0.975	0.427	0.37	0.488	CLONAL	1	TRUE	1	0.748564483935493	3		73	245	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69011978	69011978	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	658	676	0	ENST00000288368.4:c.2615C>A	p.Ser872Tyr	p.S872Y	ENST00000288368	NM_024870.2	872	tCt/tAt	23/40	0.748564483935493	4	FACETS	0.992	0.957	1	0.661	0.638	0.685	CLONAL	2	TRUE	1	0.748564483935493	4		676	1550	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982702	90982702	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs372159380	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	187	341	0	ENST00000265433.3:c.786C>A	p.Phe262Leu	p.F262L	ENST00000265433	NM_002485.4	262	ttC/ttA	7/16	0.748564483935493	4	FACETS	0.953	0.88	1	0.318	0.293	0.343	CLONAL	1	TRUE	1	0.748564483935493	4		341	917	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97897635	97897635	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	366	415	3	ENST00000289081.3:c.836C>A	p.Ser279Ter	p.S279*	ENST00000289081	NM_000136.2	279	tCa/tAa	8/15	0.630440957963065	3	FACETS	0.908	0.868	0.948	0.908	0.868	0.948	CLONAL	2	TRUE	1	0.748564483935493	3		418	740	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135777042	135777042	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	272	595	0	ENST00000298552.3:c.2436A>G	p.Ile812Met	p.I812M	ENST00000298552	NM_001162426.1	812	atA/atG	19/23	0.569564584349852	4	FACETS	0.968	0.907	1	0.323	0.302	0.344	CLONAL	1	TRUE	1	0.748564483935493	4		595	1313	SUCCESS
AR	367	MSKCC	GRCh37	X	66863174	66863174	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	526	285	0	ENST00000374690.3:c.1693G>T	p.Asp565Tyr	p.D565Y	ENST00000374690	NM_000044.3	565	Gat/Tat	2/8	0.704367602852245	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.748564483935493	2		285	653	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920245	76920245	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	273	396	0	ENST00000373344.5:c.3832del	p.Glu1278LysfsTer68	p.E1278Kfs*68	ENST00000373344	NM_000489.3	1278	Gaa/aa	11/35	0.594653960569131	2	FACETS	0.981	0.935	1	0.981	0.935	1	CLONAL	2	TRUE	0	0.594653960569131	2		396	468	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118391576	118391576	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	29	275	0	ENST00000534358.1:c.11489C>G	p.Ser3830Cys	p.S3830C	ENST00000534358	NM_005933.3	3830	tCt/tGt	34/36	1	2	FACETS	0.978	0.783	1	0.978	0.783	1	CLONAL	1	TRUE	1	0.11	2		275	539	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0035504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	161	463	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	0.499894864285599	2		463	574	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273958	10273958	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	176	720	0	ENST00000330684.3:c.311C>T	p.Thr104Met	p.T104M	ENST00000330684	NM_001134407.1	104	aCg/aTg	2/13	0.499894864285599	3	FACETS	0.895	0.824	0.969	0.448	0.412	0.485	CLONAL	1	TRUE	1	0.499894864285599	3		720	983	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170877	56170877	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	170	361	0	ENST00000399503.3:c.1705G>A	p.Val569Ile	p.V569I	ENST00000399503	NM_005921.1	569	Gtt/Att	10/20	0.499894864285599	3	FACETS	0.993	0.924	1	0.993	0.924	1	CLONAL	2	TRUE	1	0.499894864285599	3		361	428	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160706	56160706	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	98	330	0	ENST00000399503.3:c.980T>C	p.Phe327Ser	p.F327S	ENST00000399503	NM_005921.1	327	tTc/tCc	4/20	0.499894864285599	3	FACETS	0.918	0.821	1	0.459	0.41	0.51	CLONAL	1	TRUE	1	0.499894864285599	3		330	534	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578189	7578189	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	26	574	0	ENST00000269305.4:c.660T>G	p.Tyr220Ter	p.Y220*	ENST00000269305	NM_001126112.2	220	taT/taG	6/11	1	2	FACETS	0.37	0.292	0.46	0.37	0.292	0.46	SUBCLONAL	1	FALSE	1	0.216363276638551	2		574	650	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561504	9561504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542553062	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	32	534	0	ENST00000353224.5:c.278C>T	p.Ser93Leu	p.S93L	ENST00000353224	NM_177990.2	93	tCg/tTg	4/10	0.216363276638551	1	FACETS	0.46	0.372	0.559	0.46	0.372	0.559	SUBCLONAL	1	FALSE	0	0.216363276638551	1		534	574	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137800	64137800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771817507	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	54	937	0	ENST00000334205.4:c.1901C>T	p.Ser634Phe	p.S634F	ENST00000334205	NM_003942.2	634	tCc/tTc	15/17	1	2	FACETS	0.557	0.474	0.648	0.557	0.474	0.648	SUBCLONAL	1	FALSE	1	0.216363276638551	2		937	896	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536918	120536918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1367775509	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	52	715	1	ENST00000229340.5:c.268G>A	p.Val90Ile	p.V90I	ENST00000229340	NM_006861.6	90	Gtc/Atc	4/6	1	2	FACETS	0.72	0.612	0.838	0.72	0.612	0.838	SUBCLONAL	1	FALSE	1	0.216363276638551	2		716	668	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300168	15300168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	40	770	0	ENST00000263388.2:c.1108C>T	p.Pro370Ser	p.P370S	ENST00000263388	NM_000435.2	370	Ccg/Tcg	7/33	1	2	FACETS	0.474	0.392	0.565	0.474	0.392	0.565	SUBCLONAL	1	FALSE	1	0.216363276638551	2		770	780	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599332	55599332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	24	498	0	ENST00000288135.5:c.2458G>A	p.Asp820Asn	p.D820N	ENST00000288135	NM_000222.2	820	Gat/Aat	17/21	0.216363276638551	1	FACETS	0.45	0.352	0.563	0.45	0.352	0.563	SUBCLONAL	1	FALSE	0	0.216363276638551	1		498	440	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467410	66467410	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761454685	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	17	266	0	ENST00000273854.3:c.859G>A	p.Gly287Arg	p.G287R	ENST00000273854	NM_004439.5	287	Ggg/Agg	3/18	0.216363276638551	1	FACETS	0.423	0.315	0.552	0.423	0.315	0.552	SUBCLONAL	1	FALSE	0	0.216363276638551	1		266	331	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194766	30194766	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370180862	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	37	559	0	ENST00000331968.5:c.379G>A	p.Asp127Asn	p.D127N	ENST00000331968	NM_002742.2	127	Gat/Aat	2/18	1	2	FACETS	0.531	0.437	0.637	0.531	0.437	0.637	SUBCLONAL	1	FALSE	1	0.216363276638551	2		559	644	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940079	31940079	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	40	727	0	ENST00000375333.2:c.221G>A	p.Gly74Glu	p.G74E	ENST00000375333	NM_032454.1	74	gGa/gAa	2/8	1	2	FACETS	0.607	0.503	0.723	0.607	0.503	0.723	SUBCLONAL	1	FALSE	1	0.216363276638551	2		727	609	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606708	29606708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768680011	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	28	441	0	ENST00000389048.3:c.1172G>A	p.Gly391Glu	p.G391E	ENST00000389048	NM_004304.4	391	gGa/gAa	5/29	1	2	FACETS	0.478	0.381	0.589	0.478	0.381	0.589	SUBCLONAL	1	FALSE	1	0.216363276638551	2		441	542	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775164	73775164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867543814	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	38	647	0	ENST00000254810.4:c.92C>T	p.Pro31Leu	p.P31L	ENST00000254810	NM_005324.3	31	cCc/cTc	2/4	1	2	FACETS	0.547	0.451	0.655	0.547	0.451	0.655	SUBCLONAL	1	FALSE	1	0.216363276638551	2		647	642	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404903	404903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	34	528	0	ENST00000399788.2:c.4291G>A	p.Glu1431Lys	p.E1431K	ENST00000399788	NM_001042603.1	1431	Gaa/Aaa	26/28	0.159487156915471	3	FACETS	0.552	0.45	0.668	0.276	0.225	0.334	SUBCLONAL	1	FALSE	1	0.216363276638551	3		528	631	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9787097	9787098	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	23	364	1	ENST00000377346.4:c.3128_3129delinsAA	p.Arg1043Lys	p.R1043K	ENST00000377346	NM_005026.3	1043	aGG/aAA	24/24	1	2	FACETS	0.611	0.476	0.767	0.611	0.476	0.767	SUBCLONAL	1	FALSE	1	0.216363276638551	2		365	348	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241918	72241918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375352213	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	28	428	0	ENST00000357731.5:c.472C>T	p.Leu158Phe	p.L158F	ENST00000357731	NM_173808.2	158	Ctt/Ttt	3/7	1	2	FACETS	0.621	0.496	0.763	0.621	0.496	0.763	SUBCLONAL	1	FALSE	1	0.216363276638551	2		428	417	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115284216	115284216	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	33	468	0	ENST00000438362.2:c.70C>T	p.Pro24Ser	p.P24S	ENST00000438362	NM_001242891.1	24	Ccc/Tcc	2/20	1	2	FACETS	0.628	0.511	0.76	0.628	0.511	0.76	SUBCLONAL	1	FALSE	1	0.216363276638551	2		468	486	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165677	118165677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	23	359	0	ENST00000369448.3:c.187G>A	p.Gly63Ser	p.G63S	ENST00000369448	NM_017709.3	63	Ggc/Agc	2/2	1	2	FACETS	0.648	0.505	0.813	0.648	0.505	0.813	SUBCLONAL	1	FALSE	1	0.216363276638551	2		359	328	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468259	120468259	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	28	560	0	ENST00000256646.2:c.4180C>T	p.Gln1394Ter	p.Q1394*	ENST00000256646	NM_024408.3	1394	Cag/Tag	25/34	1	2	FACETS	0.486	0.387	0.598	0.486	0.387	0.598	SUBCLONAL	1	FALSE	1	0.216363276638551	2		560	533	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510098	120510098	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	25	415	0	ENST00000256646.2:c.1411T>G	p.Cys471Gly	p.C471G	ENST00000256646	NM_024408.3	471	Tgt/Ggt	8/34	1	2	FACETS	0.503	0.396	0.628	0.503	0.396	0.628	SUBCLONAL	1	FALSE	1	0.216363276638551	2		415	459	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874218	155874218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	40	541	0	ENST00000368323.3:c.313C>T	p.Arg105Cys	p.R105C	ENST00000368323	NM_006912.5	105	Cgt/Tgt	5/6	1	2	FACETS	0.514	0.425	0.612	0.514	0.425	0.612	SUBCLONAL	1	FALSE	1	0.216363276638551	2		541	720	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659787	88659787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564717828	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	33	593	0	ENST00000372037.3:c.434C>T	p.Pro145Leu	p.P145L	ENST00000372037	NM_004329.2	145	cCg/cTg	7/13	1	2	FACETS	0.492	0.399	0.597	0.492	0.399	0.597	SUBCLONAL	1	FALSE	1	0.216363276638551	2		593	620	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631099	69631099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	38	572	0	ENST00000334134.2:c.313C>T	p.Leu105Phe	p.L105F	ENST00000334134	NM_005247.2	105	Ctc/Ttc	2/3	1	2	FACETS	0.66	0.545	0.789	0.66	0.545	0.789	SUBCLONAL	1	FALSE	1	0.216363276638551	2		572	532	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440458	49440458	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	51	783	0	ENST00000301067.7:c.4352G>A	p.Ser1451Asn	p.S1451N	ENST00000301067	NM_003482.3	1451	aGc/aAc	15/54	1	2	FACETS	0.625	0.53	0.73	0.625	0.53	0.73	SUBCLONAL	1	FALSE	1	0.216363276638551	2		783	754	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861279	57861279	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	24	400	0	ENST00000228682.2:c.1076A>T	p.Glu359Val	p.E359V	ENST00000228682	NM_005269.2	359	gAg/gTg	9/12	1	2	FACETS	0.47	0.368	0.589	0.47	0.368	0.589	SUBCLONAL	1	FALSE	1	0.216363276638551	2		400	472	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636193	28636194	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	20	408	0	ENST00000241453.7:c.178_179delinsTT	p.Pro60Leu	p.P60L	ENST00000241453	NM_004119.2	60	CCg/TTg	3/24	0.216363276638551	0	FACETS	0.363	0.277	0.464			1	SUBCLONAL	1	FALSE	0	0.216363276638551	0		408	399	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99451993	99451993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	24	396	0	ENST00000268035.6:c.1327G>A	p.Ala443Thr	p.A443T	ENST00000268035	NM_000875.3	443	Gca/Aca	6/21	1	2	FACETS	0.548	0.429	0.685	0.548	0.429	0.685	SUBCLONAL	1	FALSE	1	0.216363276638551	2		396	405	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858244	9858244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	31	512	0	ENST00000330684.3:c.3157C>T	p.Pro1053Ser	p.P1053S	ENST00000330684	NM_001134407.1	1053	Cca/Tca	13/13	1	2	FACETS	0.614	0.496	0.747	0.614	0.496	0.747	SUBCLONAL	1	FALSE	1	0.216363276638551	2		512	467	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024693	14024693	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	23	464	0	ENST00000311895.7:c.919C>T	p.Leu307Phe	p.L307F	ENST00000311895	NM_005236.2	307	Ctt/Ttt	5/11	1	2	FACETS	0.479	0.372	0.602	0.479	0.372	0.602	SUBCLONAL	1	FALSE	1	0.216363276638551	2		464	444	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885916	59885916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	39	514	0	ENST00000259008.2:c.830C>T	p.Ser277Phe	p.S277F	ENST00000259008	NM_032043.2	277	tCc/tTc	7/20	1	2	FACETS	0.638	0.528	0.761	0.638	0.528	0.761	SUBCLONAL	1	FALSE	1	0.216363276638551	2		514	565	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143226631	143226631	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	22	331	0	ENST00000262992.4:c.483A>T	p.Gln161His	p.Q161H	ENST00000262992	NM_001101669.1	161	caA/caT	7/24	0.216363276638551	1	FACETS	0.433	0.335	0.547	0.433	0.335	0.547	SUBCLONAL	1	FALSE	0	0.216363276638551	1		331	419	SUCCESS
APC	324	MSKCC	GRCh37	5	112179376	112179376	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	22	391	0	ENST00000257430.4:c.8085A>C	p.Lys2695Asn	p.K2695N	ENST00000257430	NM_000038.5	2695	aaA/aaC	16/16	1	2	FACETS	0.534	0.413	0.674	0.534	0.413	0.674	SUBCLONAL	1	FALSE	1	0.216363276638551	2		391	381	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979237	93979237	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	22	336	0	ENST00000369303.4:c.1591G>A	p.Asp531Asn	p.D531N	ENST00000369303	NM_004440.3	531	Gat/Aat	7/17	1	2	FACETS	0.658	0.51	0.83	0.658	0.51	0.83	SUBCLONAL	1	FALSE	1	0.216363276638551	2		336	309	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674236	117674236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	48	632	0	ENST00000368508.3:c.4238G>A	p.Gly1413Glu	p.G1413E	ENST00000368508	NM_002944.2	1413	gGa/gAa	26/43	1	2	FACETS	0.592	0.499	0.695	0.592	0.499	0.695	SUBCLONAL	1	FALSE	1	0.216363276638551	2		632	749	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997732	149997732	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	29	428	0	ENST00000253339.5:c.2735G>A	p.Gly912Glu	p.G912E	ENST00000253339		912	gGg/gAg	5/7	1	2	FACETS	0.497	0.398	0.611	0.497	0.398	0.611	SUBCLONAL	1	FALSE	1	0.216363276638551	2		428	539	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997748	149997748	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	31	452	0	ENST00000253339.5:c.2719G>A	p.Ala907Thr	p.A907T	ENST00000253339		907	Gca/Aca	5/7	1	2	FACETS	0.462	0.373	0.564	0.462	0.373	0.564	SUBCLONAL	1	FALSE	1	0.216363276638551	2		452	620	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099532	157099532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	12	210	2	ENST00000346085.5:c.469C>T	p.Pro157Ser	p.P157S	ENST00000346085	NM_020732.3	157	Ccg/Tcg	1/20	1	2	FACETS	0.507	0.356	0.692	0.507	0.356	0.692	SUBCLONAL	1	FALSE	1	0.216363276638551	2		212	219	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372704	81372704	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	21	331	0	ENST00000222390.5:c.830A>C	p.His277Pro	p.H277P	ENST00000222390	NM_000601.4	277	cAc/cCc	7/18	1	2	FACETS	0.507	0.39	0.644	0.507	0.39	0.644	SUBCLONAL	1	FALSE	1	0.216363276638551	2		331	383	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418932	116418932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761808213	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	21	342	0	ENST00000397752.3:c.3443G>A	p.Arg1148Gln	p.R1148Q	ENST00000397752	NM_000245.2	1148	cGa/cAa	17/21	1	2	FACETS	0.502	0.386	0.637	0.502	0.386	0.637	SUBCLONAL	1	FALSE	1	0.216363276638551	2		342	387	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566110	141566110	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	42	570	0	ENST00000220592.5:c.1154G>A	p.Ser385Asn	p.S385N	ENST00000220592	NM_012154.3	385	aGt/aAt	10/19	1	2	FACETS	0.658	0.548	0.78	0.658	0.548	0.78	SUBCLONAL	1	FALSE	1	0.216363276638551	2		570	590	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482231	87482233	+	missense_variant	Missense_Mutation	TNP	TCC	TCC	GTT	novel	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	71	628	1	ENST00000277120.3:c.1518_1520delinsGTT	p.Pro507Leu	p.P507L	ENST00000277120		506	acTCCa/acGTTa	14/19	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	FALSE	1	0.216363276638551	2		629	649	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128206814	128206814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	76	443	1	ENST00000265960.3:c.1409C>T	p.Ser470Leu	p.S470L	ENST00000265960	NM_001006617.1	470	tCg/tTg	11/12	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.216363276638551	2		444	550	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399926	139399926	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1387664721	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	83	930	0	ENST00000277541.6:c.4422G>A	p.Trp1474Ter	p.W1474*	ENST00000277541	NM_017617.3	1474	tgG/tgA	25/34	1	2	FACETS	0.905	0.797	1	0.905	0.797	1	CLONAL	1	FALSE	1	0.216363276638551	2		930	848	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410285	63410285	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	32	711	0	ENST00000330258.3:c.2882G>A	p.Trp961Ter	p.W961*	ENST00000330258	NM_152424.3	961	tGg/tAg	2/2	0.216363276638551	1	FACETS	0.506	0.41	0.615	0.506	0.41	0.615	SUBCLONAL	1	FALSE	0	0.216363276638551	1		711	521	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938042	76938042	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	37	683	0	ENST00000373344.5:c.2706G>A	p.Met902Ile	p.M902I	ENST00000373344	NM_000489.3	902	atG/atA	9/35	0.216363276638551	1	FACETS	0.414	0.34	0.498	0.414	0.34	0.498	SUBCLONAL	1	FALSE	0	0.216363276638551	1		683	736	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195089	123195089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	27	432	0	ENST00000218089.9:c.1432G>A	p.Ala478Thr	p.A478T	ENST00000218089	NM_001042749.1	478	Gca/Aca	16/35	0.216363276638551	1	FACETS	0.535	0.425	0.661	0.535	0.425	0.661	SUBCLONAL	1	FALSE	0	0.216363276638551	1		432	416	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858105	152858105	+	synonymous_variant	Silent	SNP	G	G	A	novel	NA	P-0035505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	41	754	0	ENST00000406277.2:c.510C>T	p.Ala170=	p.A170=	ENST00000406277	NM_152274.4	170	gcC/gcT	6/7	0.216363276638551	1	FACETS	0.473	0.393	0.562	0.473	0.393	0.562	SUBCLONAL	1	FALSE	0	0.216363276638551	1		754	715	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577064	7577064	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0035514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	271	595	0	ENST00000269305.4:c.874A>T	p.Lys292Ter	p.K292*	ENST00000269305	NM_001126112.2	292	Aaa/Taa	8/11	0.479764041213129	2	FACETS	1	0.994	1	0.741	0.702	0.781	CLONAL	1	TRUE	0	0.615367903736336	2		595	594	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647817	3647817	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	66	577	0	ENST00000294008.3:c.1347G>C	p.Glu449Asp	p.E449D	ENST00000294008	NM_032444.2	449	gaG/gaC	6/15	0.335074202717609	6	FACETS	0.475	0.411	0.545	0.119	0.102	0.137	INDETERMINATE	1	TRUE	2	0.615367903736336	6		577	1008	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527295	187527295	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	305	383	0	ENST00000441802.2:c.10279A>T	p.Asn3427Tyr	p.N3427Y	ENST00000441802	NM_005245.3	3427	Aac/Tac	17/27	NA	2	FACETS	0.993	0.951	1			1	INDETERMINATE	2	TRUE	NA	0.615367903736336	2		383	499	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0035516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	120	387	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.584051656207664	3	FACETS	0.909	0.824	0.999	0.455	0.412	0.5	CLONAL	1	TRUE	1	0.584051656207664	3		387	584	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0035516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	196	458	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	0.584051656207664	2		458	607	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0035516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	79	438	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.793	0.703	0.888	0.793	0.703	0.888	SUBCLONAL	1	TRUE	1	0.584051656207664	2		438	341	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0035516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	130	369	2	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.887	0.809	0.968	0.887	0.809	0.968	CLONAL	1	TRUE	1	0.584051656207664	2		371	502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0035516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	260	605	14	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.566343535430904	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.584051656207664	1		619	587	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189926	66189926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145811811	NA	P-0035516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	93	302	0	ENST00000273854.3:c.3020G>A	p.Arg1007Gln	p.R1007Q	ENST00000273854	NM_004439.5	1007	cGg/cAg	18/18	1	2	FACETS	0.838	0.751	0.93	0.838	0.751	0.93	CLONAL	1	TRUE	1	0.584051656207664	2		302	380	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251754	212251754	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	22	318	0	ENST00000342788.4:c.3305T>G	p.Phe1102Cys	p.F1102C	ENST00000342788	NM_005235.2	1102	tTt/tGt	27/28	0.263899791605808	1	FACETS	0.131	0.101	0.166	0.131	0.101	0.166	INDETERMINATE	1	TRUE	0	0.584051656207664	1		318	407	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699320	18699320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	22	293	0	ENST00000266497.5:c.3421C>A	p.Leu1141Ile	p.L1141I	ENST00000266497		1141	Ctt/Att	24/31	0.263899791605808	1	FACETS	0.137	0.106	0.174	0.137	0.106	0.174	INDETERMINATE	1	TRUE	0	0.584051656207664	1		293	388	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641280	3641280	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140600202	NA	P-0035516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	309	638	2	ENST00000294008.3:c.2359G>A	p.Glu787Lys	p.E787K	ENST00000294008	NM_032444.2	787	Gaa/Aaa	12/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.584051656207664	2		640	995	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134255	41134255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs994659376	NA	P-0035516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	77	387	0	ENST00000379561.5:c.1373C>T	p.Ala458Val	p.A458V	ENST00000379561	NM_002015.3	458	gCg/gTg	2/3	0.283407541583459	5	FACETS	0.666	0.584	0.754	0.222	0.194	0.252	INDETERMINATE	1	TRUE	2	0.584051656207664	5		387	743	SUCCESS
APC	324	MSKCC	GRCh37	5	112174096	112174096	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs398123120	NA	P-0035516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	98	275	3	ENST00000257430.4:c.2805del	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	taC/ta	16/16	1	2	FACETS	0.831	0.746	0.919	0.831	0.746	0.919	CLONAL	1	TRUE	1	0.584051656207664	2		278	404	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526672	106526672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	155	411	0	ENST00000359195.3:c.2965C>T	p.Pro989Ser	p.P989S	ENST00000359195	NM_002649.2	989	Cct/Tct	10/11	0.584051656207664	3	FACETS	0.991	0.91	1	0.496	0.455	0.538	CLONAL	1	TRUE	1	0.584051656207664	3		411	692	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652278	48652278	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781964937	NA	P-0035516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	518	587	13	ENST00000376670.3:c.949C>T	p.Arg317Trp	p.R317W	ENST00000376670	NM_002049.3	317	Cgg/Tgg	6/6	0.584051656207664	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.584051656207664	3		600	1128	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0035520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	405	661	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.842151490443921	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.842151490443921	1		661	526	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243869	41243869	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886040159	NA	P-0035520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	503	626	4	ENST00000357654.3:c.3679C>T	p.Gln1227Ter	p.Q1227*	ENST00000357654	NM_007294.3	1227	Caa/Taa	10/23	0.825168966523906	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.842151490443921	2		630	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0035527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	411	573	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.780472119944841	4	FACETS	0.957	0.937	0.975	1	0.998	1	CLONAL	4	TRUE	2	0.868963883684498	4		574	462	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	194	148	0				ENST00000310581	NM_198253.2	-/1132			0.868963883684498	6	FACETS	0.925	0.859	0.992	0.462	0.429	0.496	CLONAL	2	TRUE	2	0.868963883684498	6		148	661	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844107	68844107	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	127	387	0	ENST00000261769.5:c.695C>T	p.Ser232Phe	p.S232F	ENST00000261769	NM_004360.3	232	tCt/tTt	6/16	0.50233417939749	4	FACETS	1	0.982	1	0.435	0.397	0.474	INDETERMINATE	1	TRUE	1	0.868963883684498	4		387	419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579854	7579854	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	412	585	0	ENST00000269305.4:c.59C>T	p.Ser20Leu	p.S20L	ENST00000269305	NM_001126112.2	20	tCa/tTa	2/11	0.780472119944841	4	FACETS	0.989	0.971	1	1	0.998	1	CLONAL	4	TRUE	2	0.868963883684498	4		585	448	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557389	21557389	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	47	364	0	ENST00000382592.4:c.2456C>G	p.Thr819Ser	p.T819S	ENST00000382592	NM_014572.2	819	aCt/aGt	5/8	0.717960442063348	5	FACETS	0.608	0.514	0.711	0.203	0.171	0.237	SUBCLONAL	1	TRUE	2	0.868963883684498	5		364	410	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557396	21557406	+	frameshift_variant	Frame_Shift_Del	DEL	TGAACCCAGTG	TGAACCCAGTG	-	novel	NA	P-0035527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	53	397	0	ENST00000382592.4:c.2439_2449del	p.Cys813TrpfsTer28	p.C813Wfs*28	ENST00000382592	NM_014572.2	813	tgCACTGGGTTCAgg/tggg	5/8	0.717960442063348	5	FACETS	0.634	0.542	0.735	0.211	0.18	0.245	SUBCLONAL	1	TRUE	2	0.868963883684498	5		397	443	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934729	49934729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	184	484	0	ENST00000296474.3:c.2167G>A	p.Glu723Lys	p.E723K	ENST00000296474	NM_002447.2	723	Gag/Aag	7/20	0.780472119944841	4	FACETS	1	0.943	1	0.511	0.473	0.551	CLONAL	1	TRUE	2	0.868963883684498	4		484	774	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119585447	119585447	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0035527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	30	232	0	ENST00000316626.5:c.938C>G	p.Ser313Ter	p.S313*	ENST00000316626		313	tCa/tGa	9/12	0.780472119944841	4	FACETS	0.777	0.633	0.937	0.389	0.316	0.469	CLONAL	1	TRUE	2	0.868963883684498	4		232	166	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0035528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	79	607	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.221490107810379	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		607	699	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100400	2100400	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0035528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	54	424	0	ENST00000219476.3:c.139-1G>C		p.X47_splice	ENST00000219476	NM_000548.3	47			1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		424	713	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490346	29490346	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	40	565	1	ENST00000356175.3:c.431del	p.Ser144PhefsTer21	p.S144Ffs*21	ENST00000356175	NM_000267.3	144	tCt/tt	4/57	0.221490107810379	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		566	576	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584532	187584532	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	25	522	0	ENST00000441802.2:c.3501T>G	p.Asp1167Glu	p.D1167E	ENST00000441802	NM_005245.3	1167	gaT/gaG	3/27	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		522	383	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0035529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	45	608	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.268	0.225	0.316	0.268	0.225	0.316	SUBCLONAL	1	TRUE	1	0.579165356152936	2		608	579	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843414	3843415	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0035529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	146	379	0	ENST00000262367.5:c.1188dup	p.His397AlafsTer30	p.H397Afs*30	ENST00000262367	NM_004380.2	396	-/G	4/31	0.579165356152936	3	FACETS	1	0.952	1	0.529	0.484	0.575	CLONAL	1	TRUE	1	0.579165356152936	3		379	615	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344081	70344083	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	novel	NA	P-0035529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	269	390	0	ENST00000374080.3:c.1820_1822del	p.Asp607del	p.D607del	ENST00000374080		606	cATGat/cat	13/45	0.305725501023383	2	FACETS	0.948	0.902	0.994			1	INDETERMINATE	2	TRUE	NA	0.579165356152936	2		390	490	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514336	69514354	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTACTGAAGCTGCAGAGAA	GTACTGAAGCTGCAGAGAA	C	novel	NA	P-0035529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	120	366	0	ENST00000294312.3:c.337-10_345delinsG		p.X113_splice	ENST00000294312	NM_005117.2	113		3/3	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.579165356152936	2		366	379	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0035534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	171	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.994	0.92	1	0.994	0.92	1	CLONAL	1	TRUE	1	0.612057906358715	2		502	562	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0035534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	341	573	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.612057906358715	1	FACETS	0.98	0.933	1	0.98	0.933	1	CLONAL	1	TRUE	0	0.612057906358715	1		574	789	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791587	42791587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767502801	NA	P-0035534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	229	553	0	ENST00000575354.2:c.568C>T	p.Arg190Cys	p.R190C	ENST00000575354	NM_015125.3	190	Cgc/Tgc	4/20	1	2	FACETS	0.745	0.695	0.798	0.745	0.695	0.798	SUBCLONAL	1	TRUE	1	0.612057906358715	2		553	1004	SUCCESS
APC	324	MSKCC	GRCh37	5	112163677	112163677	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0035534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	117	330	0	ENST00000257430.4:c.1600A>T	p.Lys534Ter	p.K534*	ENST00000257430	NM_000038.5	534	Aaa/Taa	13/16	0.416674541189886	1	FACETS	0.776	0.708	0.846	0.776	0.708	0.846	SUBCLONAL	1	TRUE	0	0.612057906358715	1		330	342	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0035534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	81	393	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	0.416674541189886	1	FACETS	0.399	0.353	0.449	0.399	0.353	0.449	SUBCLONAL	1	TRUE	0	0.612057906358715	1		393	460	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508824	106508824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226994105	NA	P-0035534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	216	485	0	ENST00000359195.3:c.818G>A	p.Arg273His	p.R273H	ENST00000359195	NM_002649.2	273	cGc/cAc	2/11	0.612057906358715	3	FACETS	0.929	0.864	0.997	0.465	0.432	0.499	CLONAL	1	TRUE	1	0.612057906358715	3		485	992	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111097	193111099	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0035534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	67	298	0	ENST00000367435.3:c.633_635del	p.Arg211del	p.R211del	ENST00000367435	NM_024529.4	210	caGAGg/cag	7/17	1	2	FACETS	0.678	0.593	0.768	0.678	0.593	0.768	SUBCLONAL	1	TRUE	1	0.612057906358715	2		298	323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0035535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	199	581	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.246632442169981	2	FACETS	0.778	0.727	0.829	0.778	0.727	0.829	INDETERMINATE	2	TRUE	0	0.495990562911767	2		582	516	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0035535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	96	387	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.495990562911767	2		387	383	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	133	148	0				ENST00000310581	NM_198253.2	-/1132			0.495969211428702	3	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	1	0.495990562911767	3		148	326	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717661	89717661	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0035535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	108	500	0	ENST00000371953.3:c.686C>G	p.Ser229Ter	p.S229*	ENST00000371953	NM_000314.4	229	tCa/tGa	7/9	0.495990562911767	1	FACETS	0.941	0.854	1	0.941	0.854	1	CLONAL	1	TRUE	0	0.495990562911767	1		500	348	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989514	85989514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	111	464	0	ENST00000263360.6:c.1273C>T	p.Leu425Phe	p.L425F	ENST00000263360	NM_003797.3	425	Ctt/Ttt	12/12	1	2	FACETS	0.897	0.81	0.988	0.897	0.81	0.988	CLONAL	1	TRUE	1	0.495990562911767	2		464	499	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641443	23641443	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs376189676	NA	P-0035535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	212	901	0	ENST00000261584.4:c.2032C>G	p.Leu678Val	p.L678V	ENST00000261584	NM_024675.3	678	Cta/Gta	5/13	1	2	FACETS	0.974	0.906	1	0.974	0.906	1	CLONAL	1	TRUE	1	0.495990562911767	2		901	878	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198260799	198260799	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	111	513	0	ENST00000335508.6:c.3520G>C	p.Glu1174Gln	p.E1174Q	ENST00000335508	NM_012433.2	1174	Gaa/Caa	23/25	NA	2	FACETS	0.934	0.845	1			1	INDETERMINATE	1	TRUE	NA	0.495990562911767	2		513	479	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056634	26056634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145032219	NA	P-0035535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	34	150	0	ENST00000343677.2:c.23C>T	p.Ala8Val	p.A8V	ENST00000343677	NM_005319.3	8	gCt/gTt	1/1	1	2	FACETS	0.857	0.71	1	0.857	0.71	1	CLONAL	1	TRUE	1	0.495990562911767	2		150	160	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109308772	109308772	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	75	297	0	ENST00000436639.2:c.1631G>C	p.Arg544Thr	p.R544T	ENST00000436639	NM_014454.2	544	aGa/aCa	10/10	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.495990562911767	2		297	273	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0035548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	154	554	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.361229464528073	1	FACETS	0.832	0.769	0.896	1	0.991	1	CLONAL	2	TRUE	0	0.361229464528073	1		554	420	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0035548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	17	539	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	1	2	FACETS	0.236	0.176	0.309	0.236	0.176	0.309	SUBCLONAL	1	TRUE	1	0.361229464528073	2		539	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934578	NA	P-0035548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	140	848	0	ENST00000269305.4:c.524G>T	p.Arg175Leu	p.R175L	ENST00000269305	NM_001126112.2	175	cGc/cTc	5/11	0.361229464528073	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.361229464528073	1		848	620	SUCCESS
APC	324	MSKCC	GRCh37	5	112174868	112174868	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085128	NA	P-0035548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	34	338	0	ENST00000257430.4:c.3577C>T	p.Gln1193Ter	p.Q1193*	ENST00000257430	NM_000038.5	1193	Cag/Tag	16/16	1	2	FACETS	0.775	0.637	0.928	0.775	0.637	0.928	CLONAL	1	TRUE	1	0.361229464528073	2		338	243	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992720	68992720	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs182978151	NA	P-0035548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	102	728	0	ENST00000288368.4:c.1685G>A	p.Arg562His	p.R562H	ENST00000288368	NM_024870.2	562	cGt/cAt	16/40	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.361229464528073	2		728	490	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274171	10274171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs960622904	NA	P-0035548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	53	591	0	ENST00000330684.3:c.98C>T	p.Ala33Val	p.A33V	ENST00000330684	NM_001134407.1	33	gCg/gTg	2/13	0.305545349206696	3	FACETS	0.652	0.556	0.758	0.326	0.278	0.379	SUBCLONAL	1	TRUE	1	0.361229464528073	3		591	531	SUCCESS
APC	324	MSKCC	GRCh37	5	112175589	112175592	+	frameshift_variant	Frame_Shift_Del	DEL	CAAG	CAAG	-	novel	NA	P-0035548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	60	355	0	ENST00000257430.4:c.4300_4303del	p.Ser1434GlufsTer38	p.S1434Efs*38	ENST00000257430	NM_000038.5	1433	cCAAGc/cc	16/16	1	2	FACETS	0.986	0.854	1	0.986	0.854	1	CLONAL	1	TRUE	1	0.361229464528073	2		355	337	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0035552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	295	451	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.392496998480315	3	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.392496998480315	3		451	776	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270593	98270595	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	rs756897237	NA	P-0035552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	10	60	0	ENST00000331920.6:c.49_51del	p.Gly17del	p.G17del	ENST00000331920	NM_000264.3	17	GGC/-	1/24	1	2	FACETS	0.579	0.396	0.803	0.579	0.396	0.803	SUBCLONAL	1	TRUE	1	0.392496998480315	2		60	88	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713544	30713546	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0035552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	118	383	0	ENST00000295754.5:c.871_873del	p.Lys291del	p.K291del	ENST00000295754	NM_003242.5	290	gAGAag/gag	4/7	1	2	FACETS	0.921	0.832	1	0.921	0.832	1	CLONAL	1	TRUE	1	0.392496998480315	2		383	653	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249348	110249348	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1181	258	1038	0	ENST00000374672.4:c.1225A>G	p.Lys409Glu	p.K409E	ENST00000374672	NM_004235.4	409	Aag/Gag	4/5	1	2	FACETS	0.914	0.853	0.976	0.914	0.853	0.976	CLONAL	1	TRUE	1	0.392496998480315	2		1038	1439	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784089	120784089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265704785	NA	P-0035552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	232	916	1	ENST00000257552.2:c.896C>T	p.Ser299Leu	p.S299L	ENST00000257552	NM_002442.3	299	tCg/tTg	13/15	0.392496998480315	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.392496998480315	1		917	925	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14303236	14303236	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782047286	NA	P-0035552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	162	673	1	ENST00000256196.4:c.439C>T	p.Arg147Trp	p.R147W	ENST00000256196		147	Cgg/Tgg	5/6	1	2	FACETS	0.881	0.808	0.957	0.881	0.808	0.957	CLONAL	1	TRUE	1	0.392496998480315	2		674	937	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881478	48881478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	66	306	1	ENST00000267163.4:c.200C>T	p.Pro67Leu	p.P67L	ENST00000267163	NM_000321.2	67	cCa/cTa	2/27	1	2	FACETS	0.777	0.676	0.885	0.777	0.676	0.885	SUBCLONAL	1	TRUE	1	0.392496998480315	2		307	433	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492802	56492802	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	327	559	0	ENST00000407977.2:c.137C>G	p.Ala46Gly	p.A46G	ENST00000407977		46	gCt/gGt	2/10	0.392496998480315	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.392496998480315	2		559	825	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0035553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	199	428	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.330349883264834	3	FACETS	0.897	0.834	0.961	0.897	0.834	0.961	CLONAL	2	TRUE	1	0.379937366775636	3		428	695	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591145	67591154	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TACTTGATGT	TACTTGATGT	-	novel	NA	P-0035553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	119	296	0	ENST00000274335.5:c.1738_1745+2del		p.X580_splice	ENST00000274335		580		12/15	0.379937366775636	3	FACETS	0.871	0.792	0.953	0.871	0.792	0.953	CLONAL	2	TRUE	1	0.379937366775636	3		296	428	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259321	36259321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1266842690	NA	P-0035553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	95	425	0	ENST00000300305.3:c.170C>T	p.Pro57Leu	p.P57L	ENST00000300305		57	cCg/cTg	3/8	1	2	FACETS	0.988	0.883	1	0.988	0.883	1	CLONAL	1	TRUE	1	0.379937366775636	2		425	506	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063648	67063663	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGACCGGCCCCACG	AGGGACCGGCCCCACG	-	novel	NA	P-0035553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	68	388	0	ENST00000412916.2:c.100_115del	p.Asp34AsnfsTer50	p.D34Nfs*50	ENST00000412916		33	AGGGACCGGCCCCACGag/ag	2/6	0.379937366775636	1	FACETS	0.585	0.509	0.665	0.585	0.509	0.665	SUBCLONAL	1	TRUE	0	0.379937366775636	1		388	496	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559870	29559870	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs199474764	NA	P-0035553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	56	298	0	ENST00000356175.3:c.3467A>G	p.Asn1156Ser	p.N1156S	ENST00000356175	NM_000267.3	1156	aAc/aGc	26/57	0.330349883264834	3	FACETS	0.831	0.714	0.959	0.416	0.357	0.48	CLONAL	1	TRUE	1	0.379937366775636	3		298	422	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873797	151873797	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	103	460	0	ENST00000262189.6:c.8741C>A	p.Ser2914Ter	p.S2914*	ENST00000262189	NM_170606.2	2914	tCa/tAa	38/59	1	2	FACETS	0.88	0.789	0.976	0.88	0.789	0.976	CLONAL	1	TRUE	1	0.379937366775636	2		460	616	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0035558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	288	514	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.156660139826011	6	FACETS	0.943	0.891	0.996	0.943	0.891	0.996	INDETERMINATE	3	TRUE	3	0.535592894553127	6		514	787	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644490	18644490	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs181773550	NA	P-0035558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	375	507	0	ENST00000266497.5:c.2668G>A	p.Asp890Asn	p.D890N	ENST00000266497		890	Gat/Aat	18/31	0.535592894553127	6	FACETS	0.985	0.948	1			1	CLONAL	5	TRUE	NA	0.535592894553127	6		507	589	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383271	4383271	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	99	530	0	ENST00000261254.3:c.65G>T	p.Arg22Leu	p.R22L	ENST00000261254	NM_001759.3	22	cGa/cTa	1/5	0.535592894553127	2	FACETS	0.931	0.837	1	0.466	0.418	0.515	CLONAL	1	TRUE	0	0.535592894553127	2		530	397	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61711177	61711177	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	74	546	1	ENST00000401558.2:c.2572C>G	p.His858Asp	p.H858D	ENST00000401558	NM_003400.3	858	Cat/Gat	21/25	0.535592894553127	3	FACETS	1	0.905	1	0.515	0.454	0.58	CLONAL	1	TRUE	1	0.535592894553127	3		547	340	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576870	212576870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	107	502	1	ENST00000342788.4:c.1029G>A	p.Met343Ile	p.M343I	ENST00000342788	NM_005235.2	343	atG/atA	9/28	0.130886141516157	6	FACETS	1	0.951	1	0.72	0.652	0.792	INDETERMINATE	2	TRUE	3	0.535592894553127	6		503	383	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0035562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	142	690	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.253630904007345	3	FACETS	0.999	0.919	1	1	0.988	1	CLONAL	3	FALSE	1	0.253630904007345	3		690	421	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820528	44820528	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0035562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	25	199	0	ENST00000377967.4:c.226-1G>C		p.X76_splice	ENST00000377967	NM_021140.2	76			0.253630904007345	2	FACETS	0.842	0.675	1			1	CLONAL	2	FALSE	NA	0.253630904007345	2		199	117	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0035566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	95	735	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.157749095339891	2		735	907	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844127	68844127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780537	NA	P-0035566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	44	595	1	ENST00000261769.5:c.715G>A	p.Gly239Arg	p.G239R	ENST00000261769	NM_004360.3	239	Ggg/Agg	6/16	0.157749095339891	2	FACETS	0.915	0.766	1	0.457	0.383	0.54	CLONAL	1	TRUE	0	0.157749095339891	2		596	610	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572924	41572924	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	79	695	0	ENST00000263253.7:c.5209C>T	p.Arg1737Cys	p.R1737C	ENST00000263253	NM_001429.3	1737	Cgc/Tgc	31/31	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.157749095339891	2		695	838	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120291	70120292	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	219	1008	0	ENST00000245479.2:c.1294dup	p.Tyr432LeufsTer146	p.Y432Lfs*146	ENST00000245479	NM_000346.3	431	-/T	3/3	0.157749095339891	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.157749095339891	2		1008	1157	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103387	77103387	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	54	351	0	ENST00000356341.3:c.179C>G	p.Pro60Arg	p.P60R	ENST00000356341	NM_002576.4	60	cCt/cGt	2/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.157749095339891	2		351	485	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855950	68855952	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1567512205	NA	P-0035566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	58	542	0	ENST00000261769.5:c.1760_1762del	p.Asp587del	p.D587del	ENST00000261769	NM_004360.3	586	tcTGAt/tct	12/16	0.157749095339891	2	FACETS	1	0.945	1	0.607	0.521	0.7	CLONAL	1	TRUE	0	0.157749095339891	2		542	606	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528843	157528843	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	53	526	0	ENST00000346085.5:c.6569del	p.Pro2190LeufsTer3	p.P2190Lfs*3	ENST00000346085	NM_020732.3	2190	Cct/ct	20/20	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.157749095339891	2		526	623	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739639	41739639	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	81	735	0	ENST00000242208.4:c.334G>T	p.Glu112Ter	p.E112*	ENST00000242208	NM_002192.2	112	Gaa/Taa	2/3	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.157749095339891	2		735	922	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339245	87339245	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	83	541	0	ENST00000277120.3:c.827A>T	p.Gln276Leu	p.Q276L	ENST00000277120		276	cAa/cTa	8/19	1	2	FACETS	0.763	0.673	0.859	1	0.978	1	SUBCLONAL	2	TRUE	1	0.157749095339891	2		541	690	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342616	87342616	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	58	569	0	ENST00000277120.3:c.901T>A	p.Trp301Arg	p.W301R	ENST00000277120		301	Tgg/Agg	9/19	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.157749095339891	2		569	651	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	40	148	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.952	0.799	1			1	INDETERMINATE	1	TRUE	NA	0.396286226861098	2		148	212	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249022	55249022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567477136	NA	P-0035567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	146	520	1	ENST00000275493.2:c.2320G>A	p.Val774Met	p.V774M	ENST00000275493	NM_005228.3	774	Gtg/Atg	20/28	0.396286226861098	3	FACETS	0.9	0.821	0.983	0.45	0.41	0.492	CLONAL	1	TRUE	1	0.396286226861098	3		521	981	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690817	89690819	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs1554897864	NA	P-0035567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	91	315	0	ENST00000371953.3:c.226_228del	p.Tyr76del	p.Y76del	ENST00000371953	NM_000314.4	75	cATTat/cat	4/9	0.396286226861098	1	FACETS	0.987	0.883	1	0.987	0.883	1	CLONAL	1	TRUE	0	0.396286226861098	1		315	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7580240	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	CGGGGGGAGCAGCCTCTGGCATTCTGGGAGCTTCATCTGGACCTGGGTCTTCAGTGAACCATTGTTCAATATCGTCCGGGGACAGCATCAAATCATCCATTGCTTGGGACGGCAAGGGGGACTGTAGATGGGTGAAAAGAGCAGTCAGAGGACCAGGTCCTCAGCCCCCCAGCCCCCCAGCCCTCCAGGTCCCCAGCCCTCCAGGTCCCCAGCCCAACCCTTGTCCTTACCAGAACGTTGTTTTCAGGAAGTCTGAAAGACAAGAGCAGAAAGTCAGTCCCATGGAATTTTCGCTTCCCACAGGTCTCTGCTAGGGGGCTGGGGTTGGGGTGGGGGTGGTGGGCCTGCCCTTCCAATGGATCCACTCACAGTTTCCATAGGTCTGAAAATGTTTCCTGACTCAGAGGGGGCTCGACGCTAGGATCTGACTGCGGCTCCTCCATGGCAGTGACCCGGAAGGCAGTCTGGCTGCTGCAAGAGGAAAAGTGGGGATCCAGCATGAGACACTTCCAACCCTGGGTCACCTGGGCCTGCAGAGAAGGAACCCCCTCCCCCAACACCATGCCAGTGTCTGAGACAGCTCGGCTTCCTGTGGAGCAGGAAAAGAATGGCTGCTTCACATTCTCTCTTCCAATGTTTCACCACAACCCAAGCACTCCTGCCCCACCCCTCACCAGCCATGCACTTCTTTGAGGAAAAGACAATCAGAGAGGGACTTCCAACCTTCCCACCACTAAATCCCCAAGACTTCCTAAATGTGCACCCTATTCC	CGGGGGGAGCAGCCTCTGGCATTCTGGGAGCTTCATCTGGACCTGGGTCTTCAGTGAACCATTGTTCAATATCGTCCGGGGACAGCATCAAATCATCCATTGCTTGGGACGGCAAGGGGGACTGTAGATGGGTGAAAAGAGCAGTCAGAGGACCAGGTCCTCAGCCCCCCAGCCCCCCAGCCCTCCAGGTCCCCAGCCCTCCAGGTCCCCAGCCCAACCCTTGTCCTTACCAGAACGTTGTTTTCAGGAAGTCTGAAAGACAAGAGCAGAAAGTCAGTCCCATGGAATTTTCGCTTCCCACAGGTCTCTGCTAGGGGGCTGGGGTTGGGGTGGGGGTGGTGGGCCTGCCCTTCCAATGGATCCACTCACAGTTTCCATAGGTCTGAAAATGTTTCCTGACTCAGAGGGGGCTCGACGCTAGGATCTGACTGCGGCTCCTCCATGGCAGTGACCCGGAAGGCAGTCTGGCTGCTGCAAGAGGAAAAGTGGGGATCCAGCATGAGACACTTCCAACCCTGGGTCACCTGGGCCTGCAGAGAAGGAACCCCCTCCCCCAACACCATGCCAGTGTCTGAGACAGCTCGGCTTCCTGTGGAGCAGGAAAAGAATGGCTGCTTCACATTCTCTCTTCCAATGTTTCACCACAACCCAAGCACTCCTGCCCCACCCCTCACCAGCCATGCACTTCTTTGAGGAAAAGACAATCAGAGAGGGACTTCCAACCTTCCCACCACTAAATCCCCAAGACTTCCTAAATGTGCACCCTATTCC	-	novel	NA	P-0035567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	119	753	0	ENST00000269305.4:c.-28-300_217del		p.X10_splice	ENST00000269305	NM_001126112.2	10		2-4/11	0.381808691574083	2	FACETS	0.759	0.685	0.837	0.38	0.342	0.419	SUBCLONAL	1	TRUE	0	0.396286226861098	2		753	791	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069455	30069455	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	121	510	0	ENST00000338641.4:c.1320G>A	p.Met440Ile	p.M440I	ENST00000338641	NM_000268.3	440	atG/atA	12/16	1	2	FACETS	0.849	0.768	0.935	0.849	0.768	0.935	CLONAL	1	TRUE	1	0.396286226861098	2		510	719	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	254	460	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.762396878539456	2	FACETS	0.917	0.88	0.952	0.917	0.88	0.952	CLONAL	2	TRUE	0	0.787249222200254	2		460	352	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78858829	78858829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769317295	NA	P-0035569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	199	532	0	ENST00000306801.3:c.1864G>A	p.Ala622Thr	p.A622T	ENST00000306801	NM_020761.2	622	Gcc/Acc	17/34	1	2	FACETS	0.728	0.677	0.781	0.728	0.677	0.781	SUBCLONAL	1	TRUE	1	0.787249222200254	2		532	694	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955914	55955914	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	136	429	0	ENST00000263923.4:c.3248C>A	p.Thr1083Lys	p.T1083K	ENST00000263923	NM_002253.2	1083	aCa/aAa	24/30	1	2	FACETS	0.89	0.818	0.964	0.89	0.818	0.964	CLONAL	1	TRUE	1	0.787249222200254	2		429	388	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0035572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	355	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.733324863816334	6	FACETS	1	0.991	1	0.854	0.816	0.892	CLONAL	3	TRUE	2	0.733324863816334	6		502	699	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0035572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	346	573	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.576505796934678	2	FACETS	0.838	0.804	0.871	0.838	0.804	0.871	CLONAL	2	TRUE	0	0.733324863816334	2		574	563	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410675	32410675	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	120	507	0	ENST00000332351.3:c.1483C>T	p.Arg495Trp	p.R495W	ENST00000332351	NM_024426.4	495	Cgg/Tgg	10/10	0.15573492734007	6	FACETS	1	0.953	1	0.363	0.328	0.4	INDETERMINATE	1	TRUE	3	0.733324863816334	6		507	741	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068977	30068977	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	227	549	0	ENST00000331968.5:c.1952C>A	p.Thr651Lys	p.T651K	ENST00000331968	NM_002742.2	651	aCg/aAg	14/18	0.506402598162343	4	FACETS	0.896	0.841	0.952	0.896	0.841	0.952	CLONAL	2	TRUE	2	0.733324863816334	4		549	599	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779742	3779742	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	276	715	0	ENST00000262367.5:c.5306G>A	p.Arg1769Gln	p.R1769Q	ENST00000262367	NM_004380.2	1769	cGg/cAg	31/31	0.612581703390441	3	FACETS	0.802	0.759	0.846	0.802	0.759	0.846	CLONAL	2	TRUE	1	0.733324863816334	3		715	641	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828680	72828680	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	188	719	0	ENST00000268489.5:c.7901G>T	p.Gly2634Val	p.G2634V	ENST00000268489	NM_006885.3	2634	gGa/gTa	9/10	1	2	FACETS	0.852	0.791	0.914	0.852	0.791	0.914	CLONAL	1	TRUE	1	0.733324863816334	2		719	602	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134885803	134885803	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	128	430	0	ENST00000398015.3:c.1714G>T	p.Glu572Ter	p.E572*	ENST00000398015	NM_004441.4	572	Gag/Tag	9/16	0.586901536921865	3	FACETS	0.939	0.856	1	0.47	0.428	0.513	CLONAL	1	TRUE	1	0.733324863816334	3		430	508	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620657	52620657	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	34	349	0	ENST00000394830.3:c.3096del	p.Phe1032LeufsTer102	p.F1032Lfs*102	ENST00000394830	NM_018313.4	1032	ttT/tt	21/30	1	2	FACETS	0.794	0.648	0.957	0.794	0.648	0.957	CLONAL	1	TRUE	1	0.19	2		349	451	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183692	10183693	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs869025615	NA	P-0035582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	42	466	0	ENST00000256474.2:c.163dup	p.Glu55GlyfsTer77	p.E55Gfs*77	ENST00000256474	NM_000551.3	54	atg/atGg	1/3	1	2	FACETS	0.853	0.712	1	0.853	0.712	1	CLONAL	1	TRUE	1	0.19	2		466	518	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188134	108188134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204173	NA	P-0035582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	34	328	0	ENST00000278616.4:c.6233C>T	p.Ser2078Phe	p.S2078F	ENST00000278616	NM_000051.3	2078	tCc/tTc	43/63	1	2	FACETS	0.766	0.626	0.925	0.766	0.626	0.925	CLONAL	1	TRUE	1	0.19	2		328	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576924	7576927	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GTGC	GTGC	AG	novel	NA	P-0035582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	56	587	1	ENST00000269305.4:c.920-1_922delinsCT		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	0.3	1	FACETS	0.859	0.735	0.994	0.859	0.735	0.994	CLONAL	1	TRUE	0	0.19	1		588	621	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189908	66189908	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	48	353	1	ENST00000273854.3:c.3038T>A	p.Val1013Asp	p.V1013D	ENST00000273854	NM_004439.5	1013	gTc/gAc	18/18	1	2	FACETS	0.948	0.801	1	0.948	0.801	1	CLONAL	1	TRUE	1	0.19	2		354	533	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43739025	43739026	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACC	novel	NA	P-0035582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	47	351	0	ENST00000523873.1:c.42_43insACC	p.Leu14_Leu15insThr	p.L14_L15insT	ENST00000523873		14	-/ACC	1/8	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.19	2		351	479	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782187	135782187	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs118203523	NA	P-0035582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	35	375	0	ENST00000298552.3:c.1369del	p.Ser457ValfsTer7	p.S457Vfs*7	ENST00000298552	NM_001162426.1	457	Agt/gt	14/23	0.3	1	FACETS	0.813	0.667	0.977	0.813	0.667	0.977	CLONAL	1	TRUE	0	0.19	1		375	410	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224143	53224144	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0035582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	70	426	0	ENST00000375401.3:c.3407_3408del	p.Ser1136CysfsTer67	p.S1136Cfs*67	ENST00000375401	NM_004187.3	1136	tCT/t	22/26	0.0339325529784968	2	FACETS	0.819	0.716	0.929			1	INDETERMINATE	2	TRUE	NA	0.19	2		426	450	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	70	148	0				ENST00000310581	NM_198253.2	-/1132			0.625692609761604	4	FACETS	0.858	0.753	0.971	0.429	0.376	0.486	CLONAL	1	TRUE	2	0.762359794296368	4		148	377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578532	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28934873	NA	P-0035589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	462	816	0	ENST00000269305.4:c.398T>C	p.Met133Thr	p.M133T	ENST00000269305	NM_001126112.2	133	aTg/aCg	5/11	0.762359794296368	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.762359794296368	2		816	553	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344043	70344043	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	249	419	0	ENST00000374080.3:c.1779C>A	p.Phe593Leu	p.F593L	ENST00000374080		593	ttC/ttA	13/45	0.619509298148867	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.762359794296368	2		419	272	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469999	157469999	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	170	455	0	ENST00000346085.5:c.2796del	p.Pro933ArgfsTer6	p.P933Rfs*6	ENST00000346085	NM_020732.3	931	atG/at	9/20	0.745558098073289	3	FACETS	0.901	0.858	0.941	0.901	0.858	0.941	CLONAL	3	TRUE	0	0.762359794296368	3		455	228	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429407	47429407	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	316	307	0	ENST00000377045.4:c.1535T>C	p.Ile512Thr	p.I512T	ENST00000377045	NM_001654.4	512	aTt/aCt	14/16	0.619509298148867	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.762359794296368	2		307	366	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380295	25380297	+	frameshift_variant	Frame_Shift_Del	DEL	TAT	TAT	A	novel	NA	P-0035589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	190	502	0	ENST00000311936.3:c.161_163delinsT	p.Asp54ValfsTer32	p.D54Vfs*32	ENST00000311936	NM_004985.3	54	gATAtt/gTtt	3/5	0.762359794296368	6	FACETS	1	0.974	1	0.803	0.753	0.852	CLONAL	3	TRUE	2	0.762359794296368	6		502	392	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0035591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	224	428	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.534710873673436	5	FACETS	1	0.987	1			1	CLONAL	2	TRUE	NA	0.651906547860954	5		428	568	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070577	67070577	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	116	254	1	ENST00000412916.2:c.201G>T	p.Gln67His	p.Q67H	ENST00000412916		67	caG/caT	3/6	0.649212217856487	1	FACETS	0.902	0.828	0.977	0.902	0.828	0.977	CLONAL	1	TRUE	0	0.651906547860954	1		255	266	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012172	16012172	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	188	461	0	ENST00000268712.3:c.2110del	p.Ser704ProfsTer64	p.S704Pfs*64	ENST00000268712	NM_006311.3	704	Tcc/cc	19/46	0.61211597222188	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.651906547860954	1		461	339	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485925	40485926	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	225	585	0	ENST00000264657.5:c.939dup	p.Arg314Ter	p.R314*	ENST00000264657	NM_139276.2	313	-/T	9/24	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.651906547860954	2		585	578	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156987	89156987	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0035591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	54	363	0	ENST00000336596.2:c.88+1G>A		p.X30_splice	ENST00000336596	NM_005233.5	30			0.179685887824428	0	FACETS	0.221	0.19	0.254			1	INDETERMINATE	1	TRUE	0	0.651906547860954	0		363	261	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28644632	28644632	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	48	581	0	ENST00000241453.7:c.161C>A	p.Pro54His	p.P54H	ENST00000241453	NM_004119.2	54	cCc/cAc	2/24	0.152339460365053	3	FACETS	0.833	0.702	0.978	0.417	0.351	0.489	CLONAL	1	TRUE	1	0.152339460365053	3		581	814	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578247	7578247	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	104	606	0	ENST00000269305.4:c.602del	p.Leu201CysfsTer46	p.L201Cfs*46	ENST00000269305	NM_001126112.2	201	tTg/tg	6/11	0.152339460365053	3	FACETS	0.913	0.817	1	0.913	0.817	1	CLONAL	2	TRUE	1	0.152339460365053	3		606	805	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641214	3641214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs546657275	NA	P-0035622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	65	908	0	ENST00000294008.3:c.2425G>A	p.Glu809Lys	p.E809K	ENST00000294008	NM_032444.2	809	Gaa/Aaa	12/15	1	2	FACETS	0.809	0.699	0.929	0.809	0.699	0.929	CLONAL	1	TRUE	1	0.152339460365053	2		908	1055	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	25	460	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.654	0.514	0.816	0.654	0.514	0.816	SUBCLONAL	1	TRUE	1	0.13	2		460	588	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196879	108196880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs773570504	NA	P-0035627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	45	395	1	ENST00000278616.4:c.6908dup	p.Glu2304GlyfsTer69	p.E2304Gfs*69	ENST00000278616	NM_000051.3	2301	gca/gcAa	47/63	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.13	2		396	607	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591977	48591977	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs377767354	NA	P-0035627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	26	350	0	ENST00000342988.3:c.1139+1G>A		p.X380_splice	ENST00000342988	NM_005359.5	380			1	2	FACETS	0.932	0.738	1	0.932	0.738	1	CLONAL	1	TRUE	1	0.13	2		350	429	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0035628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	14	463	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.667699689702915	3	FACETS	0.147	0.106	0.198	0.074	0.053	0.099	SUBCLONAL	1	TRUE	1	0.667699689702915	3		463	380	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221995	1221995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201090	NA	P-0035628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	214	559	0	ENST00000326873.7:c.910C>T	p.Arg304Trp	p.R304W	ENST00000326873	NM_000455.4	304	Cgg/Tgg	7/10	0.667699689702915	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.667699689702915	1		559	419	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451365	70451365	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	37	588	0	ENST00000373644.4:c.6205G>C	p.Glu2069Gln	p.E2069Q	ENST00000373644	NM_030625.2	2069	Gag/Cag	12/12	1	2	FACETS	0.204	0.167	0.245	0.204	0.167	0.245	SUBCLONAL	1	TRUE	1	0.667699689702915	2		588	544	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324917	31324917	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs776780353	NA	P-0035628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	63	373	0	ENST00000412585.2:c.19C>T	p.Arg7Ter	p.R7*	ENST00000412585	NM_005514.6	7	Cga/Tga	1/8	1	2	FACETS	0.743	0.65	0.842	0.743	0.65	0.842	SUBCLONAL	1	TRUE	1	0.667699689702915	2		373	254	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874893	151874893	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1473097808	NA	P-0035628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	192	422	0	ENST00000262189.6:c.7645C>T	p.Gln2549Ter	p.Q2549*	ENST00000262189	NM_170606.2	2549	Cag/Tag	38/59	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.667699689702915	2		422	530	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620123	21620123	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	226	685	0	ENST00000382592.4:c.43A>C	p.Ser15Arg	p.S15R	ENST00000382592	NM_014572.2	15	Agc/Cgc	2/8	1	2	FACETS	0.967	0.905	1	0.967	0.905	1	CLONAL	1	TRUE	1	0.667699689702915	2		685	700	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188214	142188214	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	72	451	0	ENST00000350721.4:c.6517C>A	p.Gln2173Lys	p.Q2173K	ENST00000350721	NM_001184.3	2173	Caa/Aaa	38/47	0.667699689702915	3	FACETS	0.975	0.86	1	0.488	0.43	0.548	CLONAL	1	TRUE	1	0.667699689702915	3		451	295	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106058	8106058	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	224	449	0	ENST00000346208.3:c.878T>A	p.Met293Lys	p.M293K	ENST00000346208		293	aTg/aAg	4/6	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.519734188504355	2		449	651	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178685	56178685	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	101	229	0	ENST00000399503.3:c.3658C>T	p.Gln1220Ter	p.Q1220*	ENST00000399503	NM_005921.1	1220	Caa/Taa	14/20	0.487466281324787	3	FACETS	1	0.981	1	0.702	0.633	0.773	CLONAL	1	TRUE	1	0.519734188504355	3		229	349	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793008	33793010	+	inframe_deletion	In_Frame_Del	DEL	CGC	CGC	-	rs780345232	NA	P-0035630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	10	65	1	ENST00000498907.2:c.311_313del	p.Gly104del	p.G104del	ENST00000498907	NM_004364.3	104	gGCGac/gac	1/1	1	2	FACETS	0.35	0.238	0.488	0.35	0.238	0.488	SUBCLONAL	1	TRUE	1	0.519734188504355	2		66	110	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167789	56167790	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATGA	novel	NA	P-0035630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	440	435	0	ENST00000399503.3:c.1356_1359dup	p.Glu454Ter	p.E454*	ENST00000399503	NM_005921.1	452	gat/gATGAat	7/20	0.487466281324787	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.519734188504355	3		435	1022	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0035641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	68	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.215683595977851	2		502	548	SUCCESS
APC	324	MSKCC	GRCh37	5	112178000	112178000	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768922431	NA	P-0035641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	55	332	0	ENST00000257430.4:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000257430	NM_000038.5	2237	Cga/Tga	16/16	0.215683595977851	1	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	0	0.215683595977851	1		332	454	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980527	1980527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760185069	NA	P-0035641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	68	536	1	ENST00000382891.5:c.3989C>T	p.Ala1330Val	p.A1330V	ENST00000382891	NM_133335.3	1330	gCg/gTg	22/22	0.215683595977851	1	FACETS	0.816	0.71	0.932	0.816	0.71	0.932	CLONAL	1	TRUE	0	0.215683595977851	1		537	689	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740543	58740544	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	rs773913732	NA	P-0035642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	91	527	0	ENST00000305921.3:c.1450_1451dup	p.Leu484PhefsTer2	p.L484Ffs*2	ENST00000305921	NM_003620.3	483	act/acTTt	6/6	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.271384446472993	2		527	643	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696425	47696425	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519967	NA	P-0035690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	100	490	0	ENST00000347630.2:c.398T>G	p.Phe133Cys	p.F133C	ENST00000347630	NM_001007230.1	133	tTc/tGc	6/11	1	2	FACETS	0.751	0.674	0.833	0.751	0.674	0.833	SUBCLONAL	1	TRUE	1	0.517785822549776	2		490	514	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259299	16259299	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	59	258	0	ENST00000375759.3:c.6564del	p.Ala2189ProfsTer164	p.A2189Pfs*164	ENST00000375759	NM_015001.2	2188	gcT/gc	11/15	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.517785822549776	2		258	217	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0035695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	308	558	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.677653721089883	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.677653721089883	3		558	570	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594051	55594051	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	127	432	0	ENST00000288135.5:c.1837A>C	p.Lys613Gln	p.K613Q	ENST00000288135	NM_000222.2	613	Aag/Cag	12/21	0.375123947352691	1	FACETS	0.763	0.701	0.826	0.763	0.701	0.826	INDETERMINATE	1	TRUE	0	0.677653721089883	1		432	325	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964358	55964358	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	61	464	2	ENST00000263923.4:c.2455C>T	p.Arg819Ter	p.R819*	ENST00000263923	NM_002253.2	819	Cga/Tga	17/30	0.375123947352691	1	FACETS	0.369	0.32	0.421	0.369	0.32	0.421	INDETERMINATE	1	TRUE	0	0.677653721089883	1		466	323	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99204001	99204001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	77	291	0	ENST00000074304.5:c.2864C>T	p.Ser955Phe	p.S955F	ENST00000074304	NM_001134224.1	955	tCc/tTc	26/26	0.658044410269315	4	FACETS	0.834	0.735	0.94	0.278	0.245	0.314	CLONAL	1	TRUE	1	0.677653721089883	4		291	457	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265901	41266287	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGC	TTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGC	-	novel	NA	P-0035695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	20	52	0	ENST00000349496.5:c.14-116_241+43del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.633720978344001	2	FACETS	0.59	0.459	0.738	0.295	0.229	0.369	SUBCLONAL	1	TRUE	0	0.677653721089883	2		52	100	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170817082	170817082	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	50	422	0	ENST00000296930.5:c.86A>G	p.Tyr29Cys	p.Y29C	ENST00000296930	NM_002520.6	29	tAt/tGt	2/11	0.426484517216292	3	FACETS	0.517	0.44	0.601	0.259	0.22	0.301	SUBCLONAL	1	TRUE	1	0.677653721089883	3		422	382	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636786	176636786	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	110	546	0	ENST00000439151.2:c.1386T>G	p.Asn462Lys	p.N462K	ENST00000439151	NM_022455.4	462	aaT/aaG	5/23	0.426484517216292	3	FACETS	1	0.95	1	0.538	0.487	0.591	CLONAL	1	TRUE	1	0.677653721089883	3		546	404	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069643	69069643	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	47	379	1	ENST00000288368.4:c.4318A>G	p.Lys1440Glu	p.K1440E	ENST00000288368	NM_024870.2	1440	Aag/Gag	35/40	1	2	FACETS	0.417	0.353	0.486	0.417	0.353	0.486	SUBCLONAL	1	TRUE	1	0.677653721089883	2		380	333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0035697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	63	581	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.731	0.632	0.838	0.731	0.632	0.838	SUBCLONAL	1	FALSE	1	0.286815555346308	2		582	601	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0035697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	104	618	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.157603323399956	3	FACETS	1	0.975	1	0.645	0.578	0.715	INDETERMINATE	1	FALSE	1	0.286815555346308	3		618	643	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	72	672	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.286815555346308	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	0	0.286815555346308	1		672	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577095	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519984	NA	P-0035697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	106	843	0	ENST00000269305.4:c.843C>G	p.Asp281Glu	p.D281E	ENST00000269305	NM_001126112.2	281	gaC/gaG	8/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.286815555346308	2		843	621	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316397	14316397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782457908	NA	P-0035697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	40	541	0	ENST00000256196.4:c.208G>A	p.Ala70Thr	p.A70T	ENST00000256196		70	Gca/Aca	3/6	0.286815555346308	1	FACETS	0.409	0.339	0.487	0.409	0.339	0.487	SUBCLONAL	1	FALSE	0	0.286815555346308	1		541	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0035845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	504	573	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.854742311220795	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.854742311220795	1		574	660	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264616	1264616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1189683846	NA	P-0035845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	445	718	1	ENST00000310581.5:c.2746G>A	p.Gly916Ser	p.G916S	ENST00000310581	NM_198253.2	916	Ggc/Agc	11/16	0.79124703799416	3	FACETS	1	0.956	1			1	CLONAL	1	TRUE	NA	0.854742311220795	3		719	1482	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214627	5214627	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	481	795	0	ENST00000357368.4:c.4439G>C	p.Trp1480Ser	p.W1480S	ENST00000357368	NM_002850.3	1480	tGg/tCg	29/38	1	2	FACETS	0.943	0.904	0.983	0.943	0.904	0.983	CLONAL	1	TRUE	1	0.854742311220795	2		795	1193	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0035918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	261	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.483461847596077	2		502	961	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0035918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	177	530	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	0.893	0.824	0.965	0.893	0.824	0.965	CLONAL	1	TRUE	1	0.483461847596077	2		530	820	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0035918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	103	298	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.738	0.662	0.819	0.738	0.662	0.819	SUBCLONAL	1	TRUE	1	0.483461847596077	2		298	577	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473779	67473779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906850	NA	P-0035918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	170	502	0	ENST00000327367.4:c.859C>T	p.Arg287Trp	p.R287W	ENST00000327367	NM_005902.3	287	Cgg/Tgg	6/9	0.483461847596077	1	FACETS	0.892	0.824	0.961	0.892	0.824	0.961	CLONAL	1	TRUE	0	0.483461847596077	1		502	598	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681326	88681326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781332	NA	P-0035918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	136	383	0	ENST00000372037.3:c.1216C>T	p.Arg406Cys	p.R406C	ENST00000372037	NM_004329.2	406	Cgc/Tgc	11/13	0.483461847596077	1	FACETS	0.974	0.893	1	0.974	0.893	1	CLONAL	1	TRUE	0	0.483461847596077	1		383	438	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710590	114710610	+	inframe_deletion	In_Frame_Del	DEL	CGAACAGGAGGAGAAGAGCTC	CGAACAGGAGGAGAAGAGCTC	-	novel	NA	P-0035918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	146	350	0	ENST00000543371.1:c.79_99del	p.Gln27_Glu33del	p.Q27_E33del	ENST00000543371	NM_001198531.1	25	ggCGAACAGGAGGAGAAGAGCTCc/ggc	1/14	1	2	FACETS	0.956	0.875	1	0.956	0.875	1	CLONAL	1	TRUE	1	0.483461847596077	2		350	632	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223356	2223356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1376643409	NA	P-0035918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	234	670	2	ENST00000326181.6:c.968C>T	p.Ser323Leu	p.S323L	ENST00000326181	NM_032271.2	323	tCg/tTg	10/21	1	2	FACETS	0.992	0.926	1	0.992	0.926	1	CLONAL	1	TRUE	1	0.483461847596077	2		672	976	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374935	45374935	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	254	594	0	ENST00000262160.6:c.908C>A	p.Thr303Lys	p.T303K	ENST00000262160	NM_005901.5	303	aCa/aAa	8/11	0.483461847596077	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.483461847596077	1		594	756	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169985763	169985763	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1204274368	NA	P-0035918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	62	591	0	ENST00000295797.4:c.425C>G	p.Thr142Ser	p.T142S	ENST00000295797	NM_002740.5	142	aCt/aGt	5/18	1	2	FACETS	0.248	0.213	0.286	0.248	0.213	0.286	SUBCLONAL	1	TRUE	1	0.483461847596077	2		591	1036	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0036174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	59	387	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.915	0.796	1	1	0.977	1	CLONAL	2	TRUE	1	0.253840232660508	2		387	254	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	111	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.978	0.885	1	1	0.988	1	CLONAL	2	TRUE	1	0.253840232660508	2		148	447	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436071	110436071	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375525958	NA	P-0036174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1503	89	828	2	ENST00000375856.3:c.2330C>T	p.Thr777Met	p.T777M	ENST00000375856	NM_003749.2	777	aCg/aTg	1/2	0.17190792620363	1	FACETS	0.385	0.339	0.433	0.385	0.339	0.433	SUBCLONAL	1	TRUE	0	0.253840232660508	1		830	1592	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123199794	123199795	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	40	534	0	ENST00000218089.9:c.2096dup	p.Asn699LysfsTer4	p.N699Kfs*4	ENST00000218089	NM_001042749.1	698	-/A	21/35	0.17190792620363	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.253840232660508	1		534	189	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123542	108123542	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1057517358	NA	P-0036218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	43	412	0	ENST00000278616.4:c.1803-2A>G		p.X601_splice	ENST00000278616	NM_000051.3	601			1	2	FACETS	0.2	0.167	0.238	0.2	0.167	0.238	SUBCLONAL	1	TRUE	1	0.660046162010272	2		412	650	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180926	32180926	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	34	466	0	ENST00000375023.3:c.2424del	p.Ser809AlafsTer36	p.S809Afs*36	ENST00000375023	NM_004557.3	808	ccC/cc	15/30	1	2	FACETS	0.199	0.162	0.241	0.199	0.162	0.241	SUBCLONAL	1	TRUE	1	0.660046162010272	2		466	517	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0036279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	138	460	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.252831625425796	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.28	3		460	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0036279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	87	573	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.301585544662213	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.28	1		574	514	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637664	23637664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766315705	NA	P-0036279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	31	640	1	ENST00000261584.4:c.2641G>A	p.Gly881Ser	p.G881S	ENST00000261584	NM_024675.3	881	Ggt/Agt	7/13	0.223325491750247	1	FACETS	0.463	0.374	0.564	0.463	0.374	0.564	SUBCLONAL	1	TRUE	0	0.28	1		641	411	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383316	31383316	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	53	580	2	ENST00000328111.2:c.1228C>T	p.Arg410Ter	p.R410*	ENST00000328111	NM_006892.3	410	Cga/Tga	11/23	1	2	FACETS	0.625	0.532	0.726	0.625	0.532	0.726	SUBCLONAL	1	TRUE	1	0.28	2		582	606	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350413	89350413	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	382	834	0	ENST00000301030.4:c.2537C>G	p.Ser846Cys	p.S846C	ENST00000301030	NM_001256183.1	846	tCc/tGc	9/13	1	2	FACETS	0.991	0.945	1	0.991	0.945	1	CLONAL	1	FALSE	1	0.835303868553404	2		834	923	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588742	52588742	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	168	359	0	ENST00000394830.3:c.4286C>G	p.Pro1429Arg	p.P1429R	ENST00000394830	NM_018313.4	1429	cCg/cGg	27/30	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.835303868553404	2		359	364	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0036367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	51	418	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.867	0.736	1	0.867	0.736	1	CLONAL	1	FALSE	1	0.20939450984323	2		418	562	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200209	123200209	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	54	476	0	ENST00000218089.9:c.2188del	p.Val730LeufsTer11	p.V730Lfs*11	ENST00000218089	NM_001042749.1	730	Gtt/tt	23/35	1	2	FACETS	0.931	0.795	1	0.931	0.795	1	CLONAL	1	FALSE	1	0.20939450984323	2		476	554	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0036396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	152	274	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.955	0.884	1	0.955	0.884	1	CLONAL	1	TRUE	1	0.813907651397842	2		274	391	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0036396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	207	453	1	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	0.813907651397842	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.813907651397842	1		454	289	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0036504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	156	274	0				ENST00000310581	NM_198253.2	-/1132			0.479272493700242	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.479272493700242	3		274	363	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926900	112926900	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs886039463	NA	P-0036504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	69	477	0	ENST00000351677.2:c.1520C>A	p.Thr507Lys	p.T507K	ENST00000351677	NM_002834.3	507	aCa/aAa	13/16	0.455483319625279	3	FACETS	0.733	0.64	0.833	0.366	0.32	0.417	SUBCLONAL	1	TRUE	1	0.479272493700242	3		477	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579716	7579716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526933	NA	P-0036504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	168	451	0	ENST00000269305.4:c.80C>T	p.Pro27Leu	p.P27L	ENST00000269305	NM_001126112.2	27	cCt/cTt	3/11	0.302390842230908	2	FACETS	0.823	0.765	0.882	0.823	0.765	0.882	CLONAL	2	TRUE	0	0.479272493700242	2		451	426	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281778	39281778	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519963	NA	P-0036504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	96	271	0	ENST00000402219.2:c.697A>T	p.Asn233Tyr	p.N233Y	ENST00000402219	NM_005633.3	233	Aat/Tat	5/23	0.479272493700242	3	FACETS	0.871	0.787	0.958	0.871	0.787	0.958	CLONAL	2	TRUE	1	0.479272493700242	3		271	285	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590491	67590494	+	frameshift_variant	Frame_Shift_Del	DEL	AGAA	AGAA	-	novel	NA	P-0036504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	71	162	0	ENST00000274335.5:c.1558_1561del	p.Glu520TyrfsTer11	p.E520Yfs*11	ENST00000274335		518	gAGAAa/ga	11/15	0.479272493700242	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.479272493700242	3		162	159	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721123	61721126	+	frameshift_variant	Frame_Shift_Del	DEL	CTCT	CTCT	-	novel	NA	P-0036504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	53	416	0	ENST00000401558.2:c.1148_1151del	p.Glu383ValfsTer36	p.E383Vfs*36	ENST00000401558	NM_003400.3	383	gAGAGt/gt	12/25	0.479272493700242	3	FACETS	0.687	0.588	0.795	0.344	0.294	0.398	SUBCLONAL	1	TRUE	1	0.479272493700242	3		416	399	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0036505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	103	460	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.164400660657888	3	FACETS	1	0.983	1	0.743	0.672	0.818	INDETERMINATE	1	TRUE	1	0.484957627662673	3		460	355	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	77	346	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	0.484957627662673	2	FACETS	0.934	0.826	1	0.467	0.413	0.524	CLONAL	1	TRUE	0	0.484957627662673	2		347	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781371	NA	P-0036505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	129	545	0	ENST00000269305.4:c.328C>T	p.Arg110Cys	p.R110C	ENST00000269305	NM_001126112.2	110	Cgt/Tgt	4/11	1	2	FACETS	0.932	0.848	1	0.932	0.848	1	CLONAL	1	TRUE	1	0.484957627662673	2		545	571	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0036505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	128	475	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	0.484957627662673	2		475	414	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562627	29562627	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0036505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	32	368	0	ENST00000356175.3:c.3709-2A>G		p.X1237_splice	ENST00000356175	NM_000267.3	1237			1	2	FACETS	0.457	0.372	0.552	0.457	0.372	0.552	SUBCLONAL	1	TRUE	1	0.484957627662673	2		368	289	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965666	90965666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	27	361	0	ENST00000265433.3:c.1651del	p.Arg551GlyfsTer8	p.R551Gfs*8	ENST00000265433	NM_002485.4	551	Agg/gg	11/16	1	2	FACETS	0.375	0.299	0.462	0.375	0.299	0.462	SUBCLONAL	1	TRUE	1	0.484957627662673	2		361	297	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101268	27101268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	43	459	2	ENST00000324856.7:c.4555del	p.Gln1519ArgfsTer8	p.Q1519Rfs*8	ENST00000324856	NM_006015.4	1517	gCc/gc	18/20	0.484957627662673	2	FACETS	0.478	0.401	0.563	0.239	0.2	0.282	SUBCLONAL	1	TRUE	0	0.484957627662673	2		461	371	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	143	558	0	ENST00000227507.2:c.859C>T	p.Pro287Ser	p.P287S	ENST00000227507	NM_053056.2	287	Ccc/Tcc	5/5	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.484957627662673	2		558	539	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556463	29556463	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1567849208	NA	P-0036505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	28	344	0	ENST00000356175.3:c.2835del	p.Phe945LeufsTer9	p.F945Lfs*9	ENST00000356175	NM_000267.3	944	Ttt/tt	21/57	1	2	FACETS	0.46	0.369	0.563	0.46	0.369	0.563	SUBCLONAL	1	TRUE	1	0.484957627662673	2		344	251	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717715	89717716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587782341	NA	P-0036505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	72	308	0	ENST00000371953.3:c.741dup	p.Pro248ThrfsTer5	p.P248Tfs*5	ENST00000371953	NM_000314.4	247	tta/ttAa	7/9	0.366402111448114	4	FACETS	1	0.959	1	0.406	0.357	0.458	CLONAL	1	TRUE	1	0.484957627662673	4		308	362	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874553	155874553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	82	421	1	ENST00000368323.3:c.206C>T	p.Ala69Val	p.A69V	ENST00000368323	NM_006912.5	69	gCc/gTc	4/6	0.378531480496727	4	FACETS	0.957	0.846	1	0.319	0.282	0.359	CLONAL	1	TRUE	1	0.484957627662673	4		422	525	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348181	70348181	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	132	540	0	ENST00000374080.3:c.3245C>T	p.Thr1082Ile	p.T1082I	ENST00000374080		1082	aCc/aTc	23/45	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.484957627662673	2		540	483	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156719	20156719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	36	411	0	ENST00000379607.5:c.38G>A	p.Arg13His	p.R13H	ENST00000379607	NM_001412.3	13	cGc/cAc	2/7	1	2	FACETS	0.36	0.296	0.432	0.36	0.296	0.432	SUBCLONAL	1	TRUE	1	0.484957627662673	2		411	412	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303224	15303224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753596637	NA	P-0036505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	49	670	0	ENST00000263388.2:c.304G>A	p.Ala102Thr	p.A102T	ENST00000263388	NM_000435.2	102	Gcc/Acc	3/33	1	2	FACETS	0.351	0.297	0.411	0.351	0.297	0.411	SUBCLONAL	1	TRUE	1	0.484957627662673	2		670	576	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502190	157502190	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs387907144	NA	P-0036505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	32	348	1	ENST00000346085.5:c.3223C>T	p.Arg1075Ter	p.R1075*	ENST00000346085	NM_020732.3	1075	Cga/Tga	12/20	0.164400660657888	3	FACETS	0.42	0.341	0.51	0.21	0.17	0.255	INDETERMINATE	1	TRUE	1	0.484957627662673	3		349	390	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942053	71942053	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	51	537	0	ENST00000298229.2:c.1322del	p.Asn441ThrfsTer2	p.N441Tfs*2	ENST00000298229	NM_001567.3	439	ccA/cc	12/28	1	2	FACETS	0.447	0.38	0.52	0.447	0.38	0.52	SUBCLONAL	1	TRUE	1	0.484957627662673	2		537	471	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0036505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	137	618	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	0.484957627662673	2		619	447	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609673	46609673	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	71	601	0	ENST00000263734.3:c.2402del	p.Pro801HisfsTer39	p.P801Hfs*39	ENST00000263734	NM_001430.4	799	ttC/tt	15/16	1	2	FACETS	0.537	0.469	0.61	0.537	0.469	0.61	SUBCLONAL	1	TRUE	1	0.484957627662673	2		601	545	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185545	27185545	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1564083506	NA	P-0036505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	130	493	0	ENST00000380036.4:c.1250del	p.Pro417LeufsTer10	p.P417Lfs*10	ENST00000380036	NM_000459.3	415	ctC/ct	9/23	1	2	FACETS	0.932	0.849	1	0.932	0.849	1	CLONAL	1	TRUE	1	0.484957627662673	2		493	575	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624301	89624301	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	183	433	0	ENST00000371953.3:c.75del	p.Thr26ProfsTer28	p.T26Pfs*28	ENST00000371953	NM_000314.4	25	ttG/tt	1/9	0.366402111448114	4	FACETS	1	0.97	1	0.718	0.668	0.77	CLONAL	2	TRUE	1	0.484957627662673	4		433	520	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826571	50826571	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1489875475	NA	P-0036505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	27	198	0	ENST00000398568.2:c.2296A>T	p.Ile766Phe	p.I766F	ENST00000398568	NM_001042412.1	766	Att/Ttt	15/18	1	2	FACETS	0.533	0.426	0.653	0.533	0.426	0.653	SUBCLONAL	1	TRUE	1	0.484957627662673	2		198	209	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088771	27088771	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	41	436	1	ENST00000324856.7:c.2380G>T	p.Gly794Trp	p.G794W	ENST00000324856	NM_006015.4	794	Ggg/Tgg	7/20	0.484957627662673	2	FACETS	0.471	0.393	0.557	0.235	0.196	0.279	SUBCLONAL	1	TRUE	0	0.484957627662673	2		437	359	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101174	27101174	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	213	607	0	ENST00000324856.7:c.4456C>T	p.Gln1486Ter	p.Q1486*	ENST00000324856	NM_006015.4	1486	Cag/Tag	18/20	0.484957627662673	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.484957627662673	2		607	416	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532725	46532725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1400804231	NA	P-0036505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	15	300	0	ENST00000262741.5:c.353G>A	p.Arg118Gln	p.R118Q	ENST00000262741	NM_003629.3	118	cGg/cAg	4/10	0.484957627662673	2	FACETS	0.244	0.178	0.323	0.122	0.089	0.162	SUBCLONAL	1	TRUE	0	0.484957627662673	2		300	254	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922300	100922300	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0036505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	17	202	0	ENST00000325455.5:c.2213-1G>T		p.X738_splice	ENST00000325455	NM_001202474.3	738			1	2	FACETS	0.415	0.311	0.537	0.415	0.311	0.537	SUBCLONAL	1	TRUE	1	0.484957627662673	2		202	169	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246644	46246644	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	10	149	0	ENST00000334344.6:c.4738C>G	p.His1580Asp	p.H1580D	ENST00000334344	NM_152641.2	1580	Cat/Gat	15/21	0.164400660657888	3	FACETS	0.324	0.22	0.455	0.162	0.11	0.228	INDETERMINATE	1	TRUE	1	0.484957627662673	3		149	158	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28644741	28644741	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	46	297	0	ENST00000241453.7:c.52del	p.Ser18LeufsTer3	p.S18Lfs*3	ENST00000241453	NM_004119.2	18	Tct/ct	2/24	1	2	FACETS	0.895	0.762	1	0.895	0.762	1	CLONAL	1	TRUE	1	0.484957627662673	2		297	212	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148529800	148529800	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	34	265	0	ENST00000320356.2:c.289C>A	p.Pro97Thr	p.P97T	ENST00000320356	NM_004456.4	97	Cca/Aca	4/20	0.164400660657888	3	FACETS	0.648	0.532	0.777	0.324	0.266	0.389	INDETERMINATE	1	TRUE	1	0.484957627662673	3		265	269	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413141	63413141	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	66	574	0	ENST00000330258.3:c.26C>T	p.Ala9Val	p.A9V	ENST00000330258	NM_152424.3	9	gCt/gTt	2/2	1	2	FACETS	0.492	0.427	0.562	0.492	0.427	0.562	SUBCLONAL	1	TRUE	1	0.484957627662673	2		574	553	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938798	76938798	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	48	505	0	ENST00000373344.5:c.1950A>T	p.Glu650Asp	p.E650D	ENST00000373344	NM_000489.3	650	gaA/gaT	9/35	1	2	FACETS	0.51	0.432	0.596	0.51	0.432	0.596	SUBCLONAL	1	TRUE	1	0.484957627662673	2		505	388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0036508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	149	745	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.406990096546118	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.406990096546118	1		745	530	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028638	12028638	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	83	324	0	ENST00000353533.5:c.841C>T	p.Arg281Ter	p.R281*	ENST00000353533	NM_003010.3	281	Cga/Tga	8/11	0.406990096546118	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.406990096546118	1		324	309	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237715	16237715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	82	401	0	ENST00000375759.3:c.1162G>A	p.Asp388Asn	p.D388N	ENST00000375759	NM_015001.2	388	Gac/Aac	5/15	1	2	FACETS	0.796	0.704	0.895	0.796	0.704	0.895	SUBCLONAL	1	TRUE	1	0.406990096546118	2		401	506	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226799	142226799	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	92	251	0	ENST00000350721.4:c.5005A>G	p.Ile1669Val	p.I1669V	ENST00000350721	NM_001184.3	1669	Att/Gtt	28/47	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.406990096546118	2		251	436	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188208	10188208	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	104	649	0	ENST00000256474.2:c.351G>C	p.Trp117Cys	p.W117C	ENST00000256474	NM_000551.3	117	tgG/tgC	2/3	0.383588224865459	1	FACETS	0.778	0.699	0.862	0.778	0.699	0.862	SUBCLONAL	1	TRUE	0	0.383588224865459	1		649	563	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161671	47161671	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0036524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	26	210	0	ENST00000409792.3:c.4454+1G>A		p.X1485_splice	ENST00000409792	NM_014159.6	1485			0.383588224865459	1	FACETS	0.464	0.369	0.572	0.464	0.369	0.572	SUBCLONAL	1	TRUE	0	0.383588224865459	1		210	236	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39593460	39593460	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs572158415	NA	P-0036526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	112	261	0	ENST00000262039.4:c.1225G>C	p.Asp409His	p.D409H	ENST00000262039	NM_002647.2	409	Gat/Cat	11/25	0.15852541097323	2	FACETS	0.987	0.9	1	0.494	0.45	0.539	INDETERMINATE	1	TRUE	0	0.731797795581157	2		261	310	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524365	187524365	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	147	431	0	ENST00000441802.2:c.11315C>T	p.Pro3772Leu	p.P3772L	ENST00000441802	NM_005245.3	3772	cCc/cTc	19/27	0.731797795581157	1	FACETS	0.565	0.52	0.611	0.565	0.52	0.611	SUBCLONAL	1	TRUE	0	0.731797795581157	1		431	451	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0036527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	217	451	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.992	0.929	1	0.992	0.929	1	CLONAL	1	TRUE	1	0.754381379885268	2		451	580	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0036527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	355	477	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.754381379885268	1	FACETS	0.98	0.94	1	0.98	0.94	1	CLONAL	1	TRUE	0	0.754381379885268	1		477	598	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486112	29486112	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1567816131	NA	P-0036527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	207	365	0	ENST00000356175.3:c.288+1G>T		p.X96_splice	ENST00000356175	NM_000267.3	96			0.754381379885268	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.754381379885268	1		365	331	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037970	49038992	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTAGGTAATTTTCCATAGTAAGTTTTTTTGATAAATCCATATCCATAACATAACATAGGTAATTCATTTGATCTCATTTATTCATTAATGAGATCATATATTCTGTCTGACCTTATTATGTAAATTCACAAATAAAAACTTTTATATTATTTATTTGTAACTTAAATAGAATTGGAAAGATAAGGGTAATTATGAAATTACCCATATTCATAGTTTTTTATAAAGTTAATAAATAATATTTTATCCCTGTAATAAGCAGGTATTTGTAATAAACTTGACATGAGTCATAGAACATTAGATATTCTTTGAAGTTATTTTTATTACTTTATAGGAAAAGCCAGTATAAATGCAGCCTTGCAAATCAATAATACAAATGTTCAGTATAAACACATTTTGTGTTTCCGGTTTACCTTCCCTTTAGAGAAATAGTAGTAGTAAAATATACTTGGTATGACACATTTCATATTGTTCTGTGGAAAGTGAGTTGAGGGGTATTTTTCCCATTTATTATTGGAGTTTTCAAAAGTAATACAAACCAAGTCATTTTTGTTTGTATGTTTGAAGTTATTTTCTAAATTCAATCATTTTAATTGTATATATCAGAGGCATCTGATATAACCTCTGTGTTTTTCCCTAAAATTTGAGTGAAATCTAACTATCACTAAAATATAGTGCTTTTACTAAATGTCTACTTCTTGCAATTGCGTAATGTATACTGAAACCCTTATAGATTGGGGGGGATACCGGGAGGTACAGGCCAGAGAATGTAGTCCAAATATTGGTGGATAATATTATTGGCTTTCGCTCAGCTCTGGCCCTTTGATTCCCATCATGCTTTCCATTCTACCAGTCTATCTACTCCTCTCTTCCCAGTCTATATACTCTTCTCTTCTTGGATGGCCAGCTCTTCCATCTGCTGCTGCCTGGCTATTTCTCTCAATCATTCTGTGACATTTCACTTCTAGAAGAGCAGCTATAATCCAAGCCTAAGAAGTAATTTTATTTATTTATTATTTTTTCC	AGGTAGGTAATTTTCCATAGTAAGTTTTTTTGATAAATCCATATCCATAACATAACATAGGTAATTCATTTGATCTCATTTATTCATTAATGAGATCATATATTCTGTCTGACCTTATTATGTAAATTCACAAATAAAAACTTTTATATTATTTATTTGTAACTTAAATAGAATTGGAAAGATAAGGGTAATTATGAAATTACCCATATTCATAGTTTTTTATAAAGTTAATAAATAATATTTTATCCCTGTAATAAGCAGGTATTTGTAATAAACTTGACATGAGTCATAGAACATTAGATATTCTTTGAAGTTATTTTTATTACTTTATAGGAAAAGCCAGTATAAATGCAGCCTTGCAAATCAATAATACAAATGTTCAGTATAAACACATTTTGTGTTTCCGGTTTACCTTCCCTTTAGAGAAATAGTAGTAGTAAAATATACTTGGTATGACACATTTCATATTGTTCTGTGGAAAGTGAGTTGAGGGGTATTTTTCCCATTTATTATTGGAGTTTTCAAAAGTAATACAAACCAAGTCATTTTTGTTTGTATGTTTGAAGTTATTTTCTAAATTCAATCATTTTAATTGTATATATCAGAGGCATCTGATATAACCTCTGTGTTTTTCCCTAAAATTTGAGTGAAATCTAACTATCACTAAAATATAGTGCTTTTACTAAATGTCTACTTCTTGCAATTGCGTAATGTATACTGAAACCCTTATAGATTGGGGGGGATACCGGGAGGTACAGGCCAGAGAATGTAGTCCAAATATTGGTGGATAATATTATTGGCTTTCGCTCAGCTCTGGCCCTTTGATTCCCATCATGCTTTCCATTCTACCAGTCTATCTACTCCTCTCTTCCCAGTCTATATACTCTTCTCTTCTTGGATGGCCAGCTCTTCCATCTGCTGCTGCCTGGCTATTTCTCTCAATCATTCTGTGACATTTCACTTCTAGAAGAGCAGCTATAATCCAAGCCTAAGAAGTAATTTTATTTATTTATTATTTTTTCC	-	novel	NA	P-0036527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	21	372	1	ENST00000267163.4:c.2210_2212-142del		p.X737_splice	ENST00000267163	NM_000321.2	737		21/27	0.754381379885268	1	FACETS	0.089	0.068	0.114	0.089	0.068	0.114	SUBCLONAL	1	TRUE	0	0.754381379885268	1		373	389	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466807	57466807	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	64	238	0	ENST00000371085.3:c.27del	p.Glu10ArgfsTer48	p.E10Rfs*48	ENST00000371085	NM_000516.4	9	aCc/ac	1/13	0.357390872095938	3	FACETS	0.482	0.418	0.551	0.161	0.139	0.184	INDETERMINATE	1	TRUE	0	0.754381379885268	3		238	485	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591077	67591077	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	148	255	0	ENST00000274335.5:c.1670G>C	p.Arg557Pro	p.R557P	ENST00000274335		557	cGa/cCa	12/15	0.40123187192156	1	FACETS	0.791	0.735	0.847	0.791	0.735	0.847	INDETERMINATE	1	TRUE	0	0.754381379885268	1		255	309	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0036557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	1653	418	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.218695544774499	36	FACETS	1	0.988	1			1	CLONAL	34	TRUE	NA	0.218695544774499	36		418	2092	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0036557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	116	574	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	NA	2	FACETS	1	0.913	1			1	INDETERMINATE	2	TRUE	NA	0.218695544774499	2		574	526	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845939	72845941	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TAA	TAA	-	novel	NA	P-0036557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	48	286	0	ENST00000268489.5:c.3530-4_3530-2del		p.X1177_splice	ENST00000268489	NM_006885.3	1177			1	2	FACETS	0.881	0.752	1	1	0.971	1	CLONAL	2	TRUE	1	0.218695544774499	2		286	249	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619356	1619366	+	frameshift_variant	Frame_Shift_Del	DEL	AACCTGAGGCC	AACCTGAGGCC	-	novel	NA	P-0036557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	115	590	0	ENST00000344749.5:c.1275_1285del	p.Ala426HisfsTer45	p.A426Hfs*45	ENST00000344749	NM_001136139.2	425	ctGGCCTCAGGTTtc/cttc	15/19	1	2	FACETS	0.809	0.73	0.892	1	0.986	1	CLONAL	2	TRUE	1	0.218695544774499	2		590	650	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204864	NA	P-0036565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	151	483	0	ENST00000371953.3:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000371953	NM_000314.4	171	Cag/Tag	6/9	0.478770112723011	1	FACETS	0.968	0.896	1	0.968	0.896	1	CLONAL	1	TRUE	0	0.595613446999447	1		483	368	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221214	1221216	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0036565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	137	550	0	ENST00000326873.7:c.740_742del	p.Asn247del	p.N247del	ENST00000326873	NM_000455.4	246	tACAac/tac	6/10	0.595613446999447	0	FACETS	0.572	0.528	0.617			1	SUBCLONAL	1	TRUE	0	0.595613446999447	0		550	325	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288428	15288428	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	162	493	0	ENST00000263388.2:c.4311del	p.Phe1437LeufsTer141	p.F1437Lfs*141	ENST00000263388	NM_000435.2	1437	ttC/tt	24/33	0.520617827917624	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.595613446999447	1		493	365	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0036616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	71	463	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.818	0.72	0.922	0.818	0.72	0.922	CLONAL	1	TRUE	1	0.545794138722899	2		463	318	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0036616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	193	745	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.523077628151075	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.545794138722899	1		745	489	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0036616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	194	574	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.523077628151075	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.545794138722899	1		574	504	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842334	151842334	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777526116	NA	P-0036616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	56	217	0	ENST00000262189.6:c.14078G>A	p.Arg4693Gln	p.R4693Q	ENST00000262189	NM_170606.2	4693	cGa/cAa	54/59	0.534711323451088	3	FACETS	0.819	0.706	0.941	0.409	0.353	0.471	CLONAL	1	TRUE	1	0.545794138722899	3		217	319	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434581	99434581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1461059080	NA	P-0036616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	109	458	1	ENST00000268035.6:c.668C>T	p.Ala223Val	p.A223V	ENST00000268035	NM_000875.3	223	gCg/gTg	3/21	1	2	FACETS	0.839	0.757	0.925	0.839	0.757	0.925	CLONAL	1	TRUE	1	0.545794138722899	2		459	476	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946820	17946820	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	349	608	0	ENST00000458235.1:c.1827C>A	p.Asp609Glu	p.D609E	ENST00000458235	NM_000215.3	609	gaC/gaA	14/24	0.541668261823125	2	FACETS	0.927	0.885	0.968	0.927	0.885	0.968	CLONAL	2	TRUE	0	0.545794138722899	2		608	690	SUCCESS
APC	324	MSKCC	GRCh37	5	112175764	112175770	+	frameshift_variant	Frame_Shift_Del	DEL	TGCCACG	TGCCACG	CCCACC	novel	NA	P-0036616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	39	265	0	ENST00000257430.4:c.4473_4479delinsCCCACC	p.Ala1492ProfsTer15	p.A1492Pfs*15	ENST00000257430	NM_000038.5	1491	ttTGCCACG/ttCCCACC	16/16	0.546543229802964	1	FACETS	0.615	0.517	0.721	0.615	0.517	0.721	SUBCLONAL	1	TRUE	0	0.545794138722899	1		265	169	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578530	7578530	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	151	644	0	ENST00000269305.4:c.400T>G	p.Phe134Val	p.F134V	ENST00000269305	NM_001126112.2	134	Ttt/Gtt	5/11	0.33972492776702	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.33972492776702	1		644	692	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741762	17741762	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	91	394	0	ENST00000250003.3:c.433C>G	p.Pro145Ala	p.P145A	ENST00000250003	NM_002478.4	145	Ccc/Gcc	1/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.33972492776702	2		394	418	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557371	29557376	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCTC	CCTCTC	A	novel	NA	P-0036623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	48	196	0	ENST00000356175.3:c.3084_3089delinsA	p.Asp1028GlufsTer9	p.D1028Efs*9	ENST00000356175	NM_000267.3	1028	gaCCTCTCa/gaAa	23/57	0.33972492776702	1	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	0	0.33972492776702	1		196	215	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0036639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	73	615	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.309599358840841	1	FACETS	0.89	0.781	1	0.89	0.781	1	CLONAL	1	TRUE	0	0.309599358840841	1		615	448	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508499	106508499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752602335	NA	P-0036639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	28	258	1	ENST00000359195.3:c.493G>A	p.Val165Ile	p.V165I	ENST00000359195	NM_002649.2	165	Gtc/Atc	2/11	0.309599358840841	1	FACETS	0.676	0.544	0.826	0.676	0.544	0.826	SUBCLONAL	1	TRUE	0	0.309599358840841	1		259	226	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3651028	3651028	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372956623	NA	P-0036639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	99	541	0	ENST00000294008.3:c.1115G>A	p.Arg372Gln	p.R372Q	ENST00000294008	NM_032444.2	372	cGg/cAg	5/15	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.309599358840841	2		541	575	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950256	38950256	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs754918290	NA	P-0036639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	89	628	0	ENST00000357387.3:c.3694A>G	p.Met1232Val	p.M1232V	ENST00000357387	NM_152756.3	1232	Atg/Gtg	31/38	0.309599358840841	6	FACETS	0.904	0.799	1	0.181	0.159	0.204	CLONAL	1	TRUE	1	0.309599358840841	6		628	1030	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922644	56922644	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	63	557	0	ENST00000519728.1:c.1514A>C	p.Glu505Ala	p.E505A	ENST00000519728	NM_002350.3	505	gAa/gCa	13/13	0.309599358840841	6	FACETS	0.748	0.645	0.86	0.15	0.129	0.172	SUBCLONAL	1	TRUE	1	0.309599358840841	6		557	881	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411871	116411874	+	intron_variant	Intron	DEL	TTAA	TTAA	G	novel	NA	P-0036639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	60	918	0	ENST00000397752.3:c.2888-32_2888-29delinsG		p.*963*	ENST00000397752	NM_000245.2	-/1390			0.309599358840841	1	FACETS	0.407	0.35	0.47	0.407	0.35	0.47	SUBCLONAL	1	TRUE	0	0.309599358840841	1		918	805	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115904	8115905	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CACG	novel	NA	P-0036663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	26	538	0	ENST00000346208.3:c.1252_1255dup	p.Pro419HisfsTer89	p.P419Hfs*89	ENST00000346208		417	acc/acCACGc	6/6	0.299510014898665	4	FACETS	0.999	0.797	1	0.5	0.398	0.614	CLONAL	1	FALSE	2	0.349257903231638	4		538	201	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0036687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	396	425	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.849	0.81	0.888	1	0.996	1	CLONAL	2	TRUE	1	0.473679505953673	2		425	985	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143521	108143521	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	203	611	0	ENST00000278616.4:c.3226C>T	p.Gln1076Ter	p.Q1076*	ENST00000278616	NM_000051.3	1076	Caa/Taa	22/63	0.473679505953673	1	FACETS	0.903	0.841	0.968	0.903	0.841	0.968	CLONAL	1	TRUE	0	0.473679505953673	1		611	724	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348199	348199	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	166	689	0	ENST00000262320.3:c.1307A>T	p.His436Leu	p.H436L	ENST00000262320	NM_003502.3	436	cAc/cTc	6/11	0.27110130691367	1	FACETS	0.798	0.736	0.863	0.798	0.736	0.863	INDETERMINATE	1	TRUE	0	0.473679505953673	1		689	670	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220702	1220703	+	missense_variant	Missense_Mutation	DNP	GG	GG	TC	novel	NA	P-0036687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	146	554	0	ENST00000326873.7:c.720_721delinsTC	p.Ala241Pro	p.A241P	ENST00000326873	NM_000455.4	240	tcGGct/tcTCct	5/10	0.473679505953673	1	FACETS	0.952	0.875	1	0.952	0.875	1	CLONAL	1	TRUE	0	0.473679505953673	1		554	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0036709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	66	745	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.915	0.794	1	0.915	0.794	1	CLONAL	1	TRUE	1	0.2	2		745	721	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0036709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	63	486	1	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	0.3	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.2	1		487	519	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610349	10610349	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	86	870	0	ENST00000171111.5:c.361G>T	p.Glu121Ter	p.E121*	ENST00000171111	NM_203500.1	121	Gag/Tag	2/6	1	2	FACETS	0.953	0.842	1	0.953	0.842	1	CLONAL	1	TRUE	1	0.2	2		870	902	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564622	55564622	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	32	543	0	ENST00000288135.5:c.510C>G	p.Ile170Met	p.I170M	ENST00000288135	NM_000222.2	170	atC/atG	3/21	0.3	1	FACETS	0.49	0.396	0.596	0.49	0.396	0.596	SUBCLONAL	1	TRUE	0	0.2	1		543	588	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109321766	109321768	+	inframe_deletion	In_Frame_Del	DEL	TTT	TTT	-	novel	NA	P-0036709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	51	694	3	ENST00000436639.2:c.655_657del	p.Lys219del	p.K219del	ENST00000436639	NM_014454.2	219	AAA/-	4/10	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.2	2		697	488	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0036711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	54	236	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.651789085488042	4	FACETS	0.846	0.739	0.957	0.846	0.739	0.957	CLONAL	2	FALSE	2	0.740798979961877	4		236	150	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0036711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	682	917	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.741427454678229	4	FACETS	0.992	0.973	1	0.992	0.973	1	CLONAL	4	FALSE	0	0.740798979961877	4		917	808	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682408	52682410	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0036711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	140	512	0	ENST00000394830.3:c.763_765del	p.Leu255del	p.L255del	ENST00000394830	NM_018313.4	255	CTC/-	8/30	NA	2	FACETS	0.926	0.873	0.977			1	INDETERMINATE	2	FALSE	NA	0.740798979961877	2		512	204	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37141785	37141785	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	180	629	0	ENST00000373509.5:c.860A>G	p.His287Arg	p.H287R	ENST00000373509	NM_002648.3	287	cAt/cGt	6/6	0.741427454678229	4	FACETS	0.972	0.907	1	0.972	0.907	1	CLONAL	2	FALSE	2	0.740798979961877	4		629	435	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829784	76829785	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0036711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	128	320	0	ENST00000373344.5:c.6256_6257del	p.Leu2086ArgfsTer14	p.L2086Rfs*14	ENST00000373344	NM_000489.3	2086	TTa/a	28/35	0.739107732307777	2	FACETS	0.993	0.938	1			1	CLONAL	2	FALSE	NA	0.740798979961877	2		320	174	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0036713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	91	651	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.233499623056529	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.233499623056529	1		651	595	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0036713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	173	380	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.233499623056529	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	3	TRUE	1	0.233499623056529	4		380	577	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152130	11152130	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	57	509	0	ENST00000358026.2:c.4414C>T	p.Gln1472Ter	p.Q1472*	ENST00000358026	NM_001128849.1	1472	Cag/Tag	31/36	0.233499623056529	1	FACETS	0.871	0.748	1	0.871	0.748	1	CLONAL	1	TRUE	0	0.233499623056529	1		509	495	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181372	185181374	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0036713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	53	278	0	ENST00000265026.3:c.1316_1318del	p.Lys439del	p.K439del	ENST00000265026	NM_004721.4	438	gAGAag/gag	8/14	0.103673541772337	3	FACETS	1	0.956	1	0.662	0.566	0.766	INDETERMINATE	1	TRUE	1	0.233499623056529	3		278	383	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251927	153251927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	27	559	0	ENST00000281708.4:c.1079G>A	p.Arg360Lys	p.R360K	ENST00000281708	NM_033632.3	360	aGa/aAa	7/12	0.103673541772337	3	FACETS	0.49	0.389	0.606	0.245	0.194	0.303	INDETERMINATE	1	TRUE	1	0.233499623056529	3		559	527	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0036714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	288	473	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.66531801473028	2		473	797	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021818	71021818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs869025203	NA	P-0036714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	133	216	0	ENST00000318789.4:c.1540C>T	p.Arg514Cys	p.R514C	ENST00000318789	NM_032682.5	514	Cgt/Tgt	18/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.66531801473028	2		216	335	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416663	416663	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	175	356	0	ENST00000399788.2:c.3887T>C	p.Ile1296Thr	p.I1296T	ENST00000399788	NM_001042603.1	1296	aTc/aCc	23/28	NA	2	FACETS	0.98	0.908	1			1	INDETERMINATE	1	TRUE	NA	0.66531801473028	2		356	537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578525	7578525	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	345	942	2	ENST00000269305.4:c.405C>A	p.Cys135Ter	p.C135*	ENST00000269305	NM_001126112.2	135	tgC/tgA	5/11	0.801803629345062	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.801707484397066	1		944	509	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187398	38187398	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	42	484	0	ENST00000317025.8:c.1079G>T	p.Arg360Leu	p.R360L	ENST00000317025	NM_023034.1	360	cGa/cTa	6/24	0.659272125421762	3	FACETS	0.349	0.291	0.412			1	SUBCLONAL	1	TRUE	NA	0.801707484397066	3		484	421	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276898	123276898	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1554928884	NA	P-0036715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	111	357	0	ENST00000358487.5:c.1019A>G	p.Tyr340Cys	p.Y340C	ENST00000358487	NM_000141.4	340	tAt/tGt	8/18	0.788503866698592	1	FACETS	0.965	0.899	1	0.965	0.899	1	CLONAL	1	TRUE	0	0.801707484397066	1		357	172	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14015887	14015887	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0036715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	45	190	0	ENST00000311895.7:c.208-1G>C		p.X70_splice	ENST00000311895	NM_005236.2	70			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.801707484397066	2		190	89	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0036723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	66	463	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	0.420428006157494	2		463	237	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584513	48584514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs377767334	NA	P-0036723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	70	342	0	ENST00000342988.3:c.692dup	p.Ser232GlnfsTer3	p.S232Qfs*3	ENST00000342988	NM_005359.5	229	ctg/ctGg	6/12	0.420428006157494	1	FACETS	0.97	0.856	1	0.97	0.856	1	CLONAL	1	TRUE	0	0.420428006157494	1		342	271	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0036723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	84	199	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	0.420428006157494	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.420428006157494	1		199	227	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0036723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	208	745	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.420428006157494	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.420428006157494	1		745	634	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023141	27023143	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs1015322780	NA	P-0036723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	10	28	0	ENST00000324856.7:c.258_260del	p.Gly87del	p.G87del	ENST00000324856	NM_006015.4	83	GGC/-	1/20	1	2	FACETS	0.587	0.403	0.812	0.587	0.403	0.812	SUBCLONAL	1	TRUE	1	0.420428006157494	2		28	81	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477837	140477851	+	inframe_deletion	In_Frame_Del	DEL	TAGGTGCTGTCACAT	TAGGTGCTGTCACAT	-	novel	NA	P-0036723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	35	523	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	0.833	1	1	0.833	1	CLONAL	1	TRUE	1	0.420428006157494	2		523	166	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0036725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	179	671	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.92	0.851	0.992	0.92	0.851	0.992	CLONAL	1	TRUE	1	0.555721075851368	2		671	700	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058072	27058072	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	70	476	1	ENST00000324856.7:c.1780C>T	p.Gln594Ter	p.Q594*	ENST00000324856	NM_006015.4	594	Cag/Tag	3/20	0.448907084355313	0	FACETS	0.395	0.348	0.446			1	SUBCLONAL	1	TRUE	0	0.555721075851368	0		477	283	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100739	8100739	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1156455762	NA	P-0036725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	222	633	0	ENST00000346208.3:c.713G>C	p.Ser238Thr	p.S238T	ENST00000346208		238	aGc/aCc	3/6	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.555721075851368	2		633	793	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44935940	44935940	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0036725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	53	126	0	ENST00000377967.4:c.2703-2A>T		p.X901_splice	ENST00000377967	NM_021140.2	901			1	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.555721075851368	1		126	97	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1567555907	NA	P-0036727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	450	608	0	ENST00000269305.4:c.314del	p.Gly105AlafsTer18	p.G105Afs*18	ENST00000269305	NM_001126112.2	105	gGc/gc	4/11	0.690496679175913	4	FACETS	0.893	0.869	0.916	0.893	0.869	0.916	CLONAL	4	TRUE	0	0.787305595996958	4		608	572	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213990	36213990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543584446	NA	P-0036727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	71	798	0	ENST00000222270.7:c.2816C>T	p.Thr939Ile	p.T939I	ENST00000222270	NM_014727.1	939	aCa/aTa	6/37	0.787305595996958	3	FACETS	0.443	0.387	0.504	0.222	0.193	0.252	SUBCLONAL	1	TRUE	1	0.787305595996958	3		798	567	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722250	49722250	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	41	445	0	ENST00000449682.2:c.1690C>A	p.Pro564Thr	p.P564T	ENST00000449682	NM_020998.3	564	Cca/Aca	15/18	0.787305595996958	4	FACETS	0.408	0.34	0.484			1	SUBCLONAL	1	TRUE	NA	0.787305595996958	4		445	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0036735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	53	477	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.34659308413313	2		477	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577575	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782289	NA	P-0036735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	38	586	2	ENST00000269305.4:c.706T>C	p.Tyr236His	p.Y236H	ENST00000269305	NM_001126112.2	236	Tac/Cac	7/11	1	2	FACETS	0.834	0.693	0.989	0.834	0.693	0.989	CLONAL	1	TRUE	1	0.34659308413313	2		588	263	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151628	55151628	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	31	609	0	ENST00000257290.5:c.2414G>T	p.Gly805Val	p.G805V	ENST00000257290	NM_006206.4	805	gGa/gTa	17/23	1	2	FACETS	0.608	0.493	0.738	0.608	0.493	0.738	SUBCLONAL	1	TRUE	1	0.34659308413313	2		609	294	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332165	70332165	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	12	211	0	ENST00000373644.4:c.70A>T	p.Asn24Tyr	p.N24Y	ENST00000373644	NM_030625.2	24	Aac/Tac	2/12	0.327704061135404	1	FACETS	0.55	0.39	0.743	0.55	0.39	0.743	SUBCLONAL	1	TRUE	0	0.34659308413313	1		211	104	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934861	9934861	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	44	572	0	ENST00000330684.3:c.1429C>T	p.Leu477Phe	p.L477F	ENST00000330684	NM_001134407.1	477	Ctc/Ttc	6/13	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.34659308413313	2		572	219	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0036743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	70	460	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.171909141741006	2	FACETS	0.83	0.727	0.941	0.415	0.363	0.471	INDETERMINATE	1	FALSE	0	0.408274266224049	2		460	413	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0036743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	166	573	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.34787574997119	2	FACETS	0.924	0.858	0.992	0.924	0.858	0.992	CLONAL	2	FALSE	0	0.408274266224049	2		574	440	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971035	21971035	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	83	540	0	ENST00000304494.5:c.323A>G	p.Asp108Gly	p.D108G	ENST00000304494	NM_000077.4	108	gAt/gGt	2/3	0.379507084624898	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	FALSE	0	0.408274266224049	1		540	303	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998919	11998919	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	56	238	0	ENST00000353533.5:c.421G>T	p.Glu141Ter	p.E141*	ENST00000353533	NM_003010.3	141	Gaa/Taa	4/11	0.34787574997119	2	FACETS	1	0.968	1	0.707	0.615	0.804	CLONAL	1	FALSE	0	0.408274266224049	2		238	194	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584533	48584533	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	57	331	0	ENST00000342988.3:c.706G>T	p.Gly236Ter	p.G236*	ENST00000342988	NM_005359.5	236	Gga/Tga	6/12	0.401428727255023	1	FACETS	0.805	0.697	0.921	0.805	0.697	0.921	CLONAL	1	FALSE	0	0.408274266224049	1		331	276	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0036749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	101	376	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.354374028666428	3	FACETS	1	0.91	1	1	0.91	1	CLONAL	2	TRUE	1	0.354374028666428	3		376	333	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220612	1220612	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201213	NA	P-0036749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	263	675	1	ENST00000326873.7:c.630C>A	p.Cys210Ter	p.C210*	ENST00000326873	NM_000455.4	210	tgC/tgA	5/10	0.354374028666428	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.354374028666428	2		676	669	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230844	53230844	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	58	396	0	ENST00000375401.3:c.1949A>G	p.Lys650Arg	p.K650R	ENST00000375401	NM_004187.3	650	aAg/aGg	14/26	0.0026020267063811	2	FACETS	0.85	0.731	0.98			1	INDETERMINATE	1	FALSE	NA	0.245447614317455	2		396	556	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222144	5222144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1195525448	NA	P-0036757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	153	588	0	ENST00000357368.4:c.3191C>T	p.Thr1064Ile	p.T1064I	ENST00000357368	NM_002850.3	1064	aCa/aTa	19/38	0.510190640055781	1	FACETS	0.991	0.914	1	0.991	0.914	1	CLONAL	1	TRUE	0	0.510190640055781	1		588	451	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624260	89624284	+	frameshift_variant	Frame_Shift_Del	DEL	AACAAAAGGAGATATCAAGAGGATG	AACAAAAGGAGATATCAAGAGGATG	-	novel	NA	P-0036757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	71	301	0	ENST00000371953.3:c.34_58del	p.Asn12AspfsTer4	p.N12Dfs*4	ENST00000371953	NM_000314.4	12	AACAAAAGGAGATATCAAGAGGATGga/ga	1/9	0.383731984803649	1	FACETS	0.703	0.619	0.791	0.703	0.619	0.791	SUBCLONAL	1	TRUE	0	0.510190640055781	1		301	295	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224522	108224523	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	105	289	1	ENST00000278616.4:c.8701_8702delinsTT	p.Pro2901Phe	p.P2901F	ENST00000278616	NM_000051.3	2901	CCt/TTt	60/63	0.510190640055781	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.510190640055781	1		290	299	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005728	150005728	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	34	293	0	ENST00000253339.5:c.497G>C	p.Gly166Ala	p.G166A	ENST00000253339		166	gGg/gCg	3/7	1	2	FACETS	0.356	0.291	0.429	0.356	0.291	0.429	SUBCLONAL	1	TRUE	1	0.510190640055781	2		293	374	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0036760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	201	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.167133044720666	2	FACETS	1	0.991	1	0.722	0.675	0.77	INDETERMINATE	1	TRUE	0	0.536381171432398	2		502	519	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0036760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	112	274	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.875	0.792	0.963	0.875	0.792	0.963	CLONAL	1	TRUE	1	0.536381171432398	2		274	477	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	48	181	0	ENST00000257430.4:c.3919dup	p.Ile1307AsnfsTer8	p.I1307Nfs*8	ENST00000257430	NM_000038.5	1306	gaa/gAaa	16/16	1	2	FACETS	0.817	0.699	0.945	0.817	0.699	0.945	CLONAL	1	TRUE	1	0.536381171432398	2		181	219	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920434	114920434	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	173	431	0	ENST00000543371.1:c.1375T>C	p.Trp459Arg	p.W459R	ENST00000543371	NM_001198531.1	459	Tgg/Cgg	13/14	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.536381171432398	2		431	598	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276456	115276456	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	158	537	0	ENST00000438362.2:c.872T>C	p.Val291Ala	p.V291A	ENST00000438362	NM_001242891.1	291	gTc/gCc	9/20	1	2	FACETS	0.879	0.808	0.953	0.879	0.808	0.953	CLONAL	1	TRUE	1	0.536381171432398	2		537	670	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911621	114911621	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	152	332	0	ENST00000543371.1:c.1139T>A	p.Ile380Asn	p.I380N	ENST00000543371	NM_001198531.1	380	aTc/aAc	10/14	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.536381171432398	2		332	563	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483957	212483957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	23	443	0	ENST00000342788.4:c.2246C>T	p.Ala749Val	p.A749V	ENST00000342788	NM_005235.2	749	gCt/gTt	19/28	1	2	FACETS	0.258	0.201	0.324	0.258	0.201	0.324	SUBCLONAL	1	TRUE	1	0.536381171432398	2		443	332	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871197	35871197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200373233	NA	P-0036760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	93	277	1	ENST00000303115.3:c.419G>A	p.Arg140Gln	p.R140Q	ENST00000303115	NM_002185.3	140	cGg/cAg	4/8	1	2	FACETS	0.873	0.782	0.97	0.873	0.782	0.97	CLONAL	1	TRUE	1	0.536381171432398	2		278	397	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020536	69020536	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	469	469	0	ENST00000288368.4:c.2908C>T	p.His970Tyr	p.H970Y	ENST00000288368	NM_024870.2	970	Cat/Tat	24/40	0.536381171432398	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	0	0.536381171432398	3		469	737	SUCCESS
AR	367	MSKCC	GRCh37	X	66766112	66766112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	61	541	0	ENST00000374690.3:c.1124C>T	p.Pro375Leu	p.P375L	ENST00000374690	NM_000044.3	375	cCg/cTg	1/8	0.338762827227	1	FACETS	0.254	0.218	0.292	0.254	0.218	0.292	SUBCLONAL	1	TRUE	0	0.536381171432398	1		541	656	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578517	7578517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750600586	NA	P-0036762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	1193	633	0	ENST00000269305.4:c.413C>T	p.Ala138Val	p.A138V	ENST00000269305	NM_001126112.2	138	gCc/gTc	5/11	0.0620071362851258	3	FACETS	1	0.989	1			1	INDETERMINATE	3	TRUE	NA	0.841173771750791	3		633	1341	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0036762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	415	462	0	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	0.707474119077078	3	FACETS	0.903	0.867	0.939	0.903	0.867	0.939	CLONAL	2	TRUE	1	0.841173771750791	3		462	776	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587118	189587118	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761885185	NA	P-0036764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	82	272	0	ENST00000264731.3:c.1135C>T	p.Arg379Cys	p.R379C	ENST00000264731	NM_003722.4	379	Cgt/Tgt	9/14	1	2	FACETS	0.798	0.708	0.894	0.798	0.708	0.894	SUBCLONAL	1	TRUE	1	0.516134488378559	2		272	398	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198428	108198428	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1131691162	NA	P-0036764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	108	345	0	ENST00000278616.4:c.7032G>A	p.Trp2344Ter	p.W2344*	ENST00000278616	NM_000051.3	2344	tgG/tgA	48/63	0.516134488378559	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.516134488378559	1		345	308	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0036765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	69	207	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.337717000325239	3	FACETS	0.768	0.673	0.87	0.256	0.224	0.29	INDETERMINATE	1	TRUE	0	0.662136341761258	3		207	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934574	NA	P-0036765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	662	595	0	ENST00000269305.4:c.844C>G	p.Arg282Gly	p.R282G	ENST00000269305	NM_001126112.2	282	Cgg/Ggg	8/11	0.662136341761258	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.662136341761258	3		595	838	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711892	89711892	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	333	476	0	ENST00000371953.3:c.510T>G	p.Ser170Arg	p.S170R	ENST00000371953	NM_000314.4	170	agT/agG	6/9	0.662136341761258	2	FACETS	0.982	0.944	1	0.982	0.944	1	CLONAL	2	TRUE	0	0.662136341761258	2		476	512	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001523	150001523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264217871	NA	P-0036765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	336	467	0	ENST00000253339.5:c.2081G>A	p.Arg694His	p.R694H	ENST00000253339		694	cGt/cAt	4/7	0.431297829062184	3	FACETS	0.958	0.913	1	0.958	0.913	1	CLONAL	2	TRUE	1	0.662136341761258	3		467	705	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707981	43707981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	91	664	0	ENST00000382044.4:c.4900C>T	p.Arg1634Trp	p.R1634W	ENST00000382044	NM_001141980.1	1634	Cgg/Tgg	23/28	1	2	FACETS	0.416	0.37	0.466	0.416	0.37	0.466	SUBCLONAL	1	TRUE	1	0.662136341761258	2		664	660	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78831645	78831645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572833876	NA	P-0036765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	82	555	0	ENST00000306801.3:c.1454G>A	p.Arg485Gln	p.R485Q	ENST00000306801	NM_020761.2	485	cGa/cAa	13/34	0.662136341761258	3	FACETS	0.481	0.424	0.543	0.16	0.141	0.181	SUBCLONAL	1	TRUE	0	0.662136341761258	3		555	685	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645673	12645673	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	22	195	0	ENST00000251849.4:c.796G>A	p.Val266Ile	p.V266I	ENST00000251849	NM_002880.3	266	Gtc/Atc	7/17	0.189828516357044	3	FACETS	0.369	0.286	0.464	0.123	0.095	0.155	INDETERMINATE	1	TRUE	0	0.662136341761258	3		195	240	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	202	586	0	ENST00000269305.4:c.377del	p.Tyr126SerfsTer44	p.Y126Sfs*44	ENST00000269305	NM_001126112.2	126	tAc/tc	5/11	0.31580808846192	1	FACETS	0.775	0.721	0.83	1	0.992	1	SUBCLONAL	2	TRUE	0	0.31580808846192	1		586	695	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439165	52439165	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	148	500	0	ENST00000460680.1:c.1077del	p.Leu361Ter	p.L361*	ENST00000460680	NM_004656.3	359	gcC/gc	11/17	0.2457583774046	4	FACETS	1	0.983	1	0.443	0.404	0.483	CLONAL	1	TRUE	1	0.31580808846192	4		500	929	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793706	89793706	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	97	276	0	ENST00000336032.3:c.775A>G	p.Ile259Val	p.I259V	ENST00000336032	NM_006813.2	259	Att/Gtt	2/2	0.31580808846192	2	FACETS	0.848	0.763	0.938	0.848	0.763	0.938	CLONAL	2	TRUE	0	0.31580808846192	2		276	362	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115947	8115948	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	T	novel	NA	P-0036774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	83	393	0	ENST00000346208.3:c.1293_1294delinsT	p.Pro432HisfsTer43	p.P432Hfs*43	ENST00000346208		431	ggACca/ggTca	6/6	0.305456805440331	4	FACETS	0.896	0.795	1	0.896	0.795	1	CLONAL	2	FALSE	2	0.305456805440331	4		393	396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0036777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	643	581	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.864332287453996	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.864332287453996	1		582	819	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950724	79950725	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCGCAGCGC	rs1554066076	NA	P-0036777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	29	162	5	ENST00000265081.6:c.181_189dup	p.Ala61_Pro63dup	p.A61_P63dup	ENST00000265081	NM_002439.4	61	gcc/gCCGCAGCGCcc	1/24	0.864332287453996	1	FACETS	0.231	0.187	0.28	0.231	0.187	0.28	SUBCLONAL	1	TRUE	0	0.864332287453996	1		167	165	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287212	33287213	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1268651006	NA	P-0036777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	448	676	0	ENST00000374542.5:c.1884dup	p.Cys629LeufsTer29	p.C629Lfs*29	ENST00000374542	NM_001141970.1	628	-/C	6/8	0.864332287453996	1	FACETS	0.901	0.873	0.93	0.901	0.873	0.93	CLONAL	1	TRUE	0	0.864332287453996	1		676	653	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0036786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	239	477	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	NA	3	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.384526238034626	3		477	637	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119495	193119495	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	67	222	0	ENST00000367435.3:c.890G>C	p.Arg297Thr	p.R297T	ENST00000367435	NM_024529.4	297	aGa/aCa	9/17	0.384526238034626	3	FACETS	0.895	0.78	1	0.448	0.39	0.51	CLONAL	1	TRUE	1	0.384526238034626	3		222	464	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413716	138413716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536248537	NA	P-0036786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	85	299	0	ENST00000289153.2:c.1804C>T	p.Pro602Ser	p.P602S	ENST00000289153	NM_006219.2	602	Ccc/Tcc	12/22	0.132902286404243	6	FACETS	1	0.966	1	0.417	0.369	0.469	INDETERMINATE	1	TRUE	3	0.384526238034626	6		299	625	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966654	36966654	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	87	423	0	ENST00000358127.4:c.672G>T	p.Met224Ile	p.M224I	ENST00000358127	NM_001280556.1	224	atG/atT	6/10	0.384526238034626	2	FACETS	0.995	0.884	1	0.497	0.442	0.556	CLONAL	1	TRUE	0	0.384526238034626	2		423	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574002	7574002	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs375338359	NA	P-0036787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	367	614	1	ENST00000269305.4:c.1025G>C	p.Arg342Pro	p.R342P	ENST00000269305	NM_001126112.2	342	cGa/cCa	10/11	1	2	FACETS	1	0.99	1	1	0.997	1	CLONAL	2	TRUE	1	0.763310303231816	2		615	461	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390791	139390794	+	frameshift_variant	Frame_Shift_Del	DEL	GACG	GACG	CCA	novel	NA	P-0036787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	191	734	1	ENST00000277541.6:c.7397_7400delinsTGG	p.Thr2466MetfsTer11	p.T2466Mfs*11	ENST00000277541	NM_017617.3	2466	aCGTCg/aTGGg	34/34	0.170140411783065	2	FACETS	1	0.971	1	0.535	0.499	0.57	INDETERMINATE	1	TRUE	0	0.763310303231816	2		735	468	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060786	38060787	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CATC	novel	NA	P-0036791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	173	743	0	ENST00000250448.2:c.1202_1203insGATG	p.Ile402MetfsTer14	p.I402Mfs*14	ENST00000250448	NM_004496.3	401	tcc/tcGATGc	2/2	1	2	FACETS	0.951	0.874	1	0.951	0.874	1	CLONAL	1	TRUE	1	0.35	2		743	1040	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	307	615	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.948	0.899	0.999	0.948	0.899	0.999	CLONAL	1	TRUE	1	0.826766988492214	2		617	783	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	403	680	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.826766988492214	2		680	939	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	96	223	2	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.835	0.755	0.918	0.835	0.755	0.918	CLONAL	1	TRUE	1	0.826766988492214	2		225	278	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073398	8073398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201286989	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	266	509	1	ENST00000377482.5:c.1261G>A	p.Ala421Thr	p.A421T	ENST00000377482	NM_018948.3	421	Gcc/Acc	4/4	1	2	FACETS	0.904	0.852	0.956	0.904	0.852	0.956	CLONAL	1	TRUE	1	0.826766988492214	2		510	712	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187719	11187719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767904339	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	378	638	0	ENST00000361445.4:c.6178C>T	p.Arg2060Trp	p.R2060W	ENST00000361445	NM_004958.3	2060	Cgg/Tgg	44/58	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.826766988492214	2		638	867	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106726	27106727	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	243	527	2	ENST00000324856.7:c.6341dup	p.Gln2115AlafsTer35	p.Q2115Afs*35	ENST00000324856	NM_006015.4	2113	tcc/tCcc	20/20	1	2	FACETS	0.926	0.871	0.982	0.926	0.871	0.982	CLONAL	1	TRUE	1	0.826766988492214	2		529	635	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748074	72748074	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	270	437	0	ENST00000357731.5:c.104G>T	p.Gly35Val	p.G35V	ENST00000357731	NM_173808.2	35	gGa/gTa	1/7	1	2	FACETS	0.99	0.935	1	0.99	0.935	1	CLONAL	1	TRUE	1	0.826766988492214	2		437	660	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695911	117695911	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	340	594	2	ENST00000369458.3:c.526del	p.Gln176SerfsTer26	p.Q176Sfs*26	ENST00000369458	NM_024626.3	176	Cag/ag	4/6	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.826766988492214	2		596	745	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63760050	63760050	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs201273744	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	155	366	0	ENST00000279873.7:c.703A>T	p.Ile235Leu	p.I235L	ENST00000279873	NM_032199.2	235	Ata/Tta	4/10	1	2	FACETS	0.954	0.884	1	0.954	0.884	1	CLONAL	1	TRUE	1	0.826766988492214	2		366	393	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263973	104263974	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776579	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	120	246	0	ENST00000369902.3:c.71dup	p.Ala25GlyfsTer23	p.A25Gfs*23	ENST00000369902	NM_016169.3	22	gcc/gCcc	1/12	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.826766988492214	2		246	288	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925711	114925711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752060378	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	171	533	2	ENST00000543371.1:c.1789G>A	p.Val597Ile	p.V597I	ENST00000543371	NM_001198531.1	597	Gtc/Atc	14/14	1	2	FACETS	0.71	0.656	0.765	0.71	0.656	0.765	SUBCLONAL	1	TRUE	1	0.826766988492214	2		535	583	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132821	64132821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754458110	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	314	625	0	ENST00000334205.4:c.955C>T	p.Arg319Trp	p.R319W	ENST00000334205	NM_003942.2	319	Cgg/Tgg	9/17	1	2	FACETS	0.955	0.906	1	0.955	0.906	1	CLONAL	1	TRUE	1	0.826766988492214	2		625	795	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	128	296	0	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	0.741	0.677	0.806	0.741	0.677	0.806	SUBCLONAL	1	TRUE	1	0.826766988492214	2		296	418	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514076	69514076	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	66	556	0	ENST00000294312.3:c.605T>C	p.Leu202Pro	p.L202P	ENST00000294312	NM_005117.2	202	cTt/cCt	3/3	1	2	FACETS	0.226	0.195	0.258	0.226	0.195	0.258	SUBCLONAL	1	TRUE	1	0.826766988492214	2		556	708	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922169	100922169	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	97	388	0	ENST00000325455.5:c.2343T>A	p.Asp781Glu	p.D781E	ENST00000325455	NM_001202474.3	781	gaT/gaA	5/8	1	2	FACETS	0.787	0.711	0.866	0.787	0.711	0.866	SUBCLONAL	1	TRUE	1	0.826766988492214	2		388	298	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246567	46246567	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	100	202	0	ENST00000334344.6:c.4661T>C	p.Val1554Ala	p.V1554A	ENST00000334344	NM_152641.2	1554	gTt/gCt	15/21	0.780866519560875	3	FACETS	0.966	0.871	1	0.483	0.435	0.533	CLONAL	1	TRUE	1	0.826766988492214	3		202	354	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416133	49416133	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1422752351	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	72	371	0	ENST00000301067.7:c.16342C>T	p.Arg5448Ter	p.R5448*	ENST00000301067	NM_003482.3	5448	Cga/Tga	52/54	0.780866519560875	3	FACETS	0.374	0.327	0.425	0.187	0.163	0.213	SUBCLONAL	1	TRUE	1	0.826766988492214	3		371	658	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427394	49427395	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs35493001	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	168	671	0	ENST00000301067.7:c.11093dup	p.Phe3699LeufsTer14	p.F3699Lfs*14	ENST00000301067	NM_003482.3	3698	ggc/ggGc	39/54	0.780866519560875	3	FACETS	0.511	0.468	0.555	0.255	0.234	0.278	SUBCLONAL	1	TRUE	1	0.826766988492214	3		671	1125	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857871	57857871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760866050	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	140	445	0	ENST00000228682.2:c.190G>A	p.Glu64Lys	p.E64K	ENST00000228682	NM_005269.2	64	Gag/Aag	3/12	0.780866519560875	3	FACETS	0.553	0.504	0.606	0.277	0.252	0.303	SUBCLONAL	1	TRUE	1	0.826766988492214	3		445	865	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879801	123879801	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	441	394	0	ENST00000330479.4:c.502del	p.Arg168GlufsTer39	p.R168Efs*39	ENST00000330479	NM_020382.3	166	gCc/gc	4/9	0.780866519560875	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.826766988492214	3		394	714	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959048	28959048	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	189	418	0	ENST00000282397.4:c.2090del	p.Asn697ThrfsTer13	p.N697Tfs*13	ENST00000282397	NM_002019.4	697	aAc/ac	14/30	1	2	FACETS	0.927	0.865	0.991	0.927	0.865	0.991	CLONAL	1	TRUE	1	0.826766988492214	2		418	493	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881488	48881489	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	150	358	0	ENST00000267163.4:c.219_220dup	p.Ala74GlufsTer4	p.A74Efs*4	ENST00000267163	NM_000321.2	70	-/AG	2/27	0.826766988492214	1	FACETS	0.851	0.799	0.903	0.851	0.799	0.903	CLONAL	1	TRUE	0	0.826766988492214	1		358	250	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061312	38061312	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1329067081	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	353	596	0	ENST00000250448.2:c.677A>G	p.Asp226Gly	p.D226G	ENST00000250448	NM_004496.3	226	gAc/gGc	2/2	1	2	FACETS	0.921	0.876	0.967	0.921	0.876	0.967	CLONAL	1	TRUE	1	0.826766988492214	2		596	927	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007901	45007901	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	164	405	0	ENST00000558401.1:c.346+2T>C		p.X116_splice	ENST00000558401	NM_004048.2	116			0.826766988492214	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.826766988492214	1		405	229	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339545	339545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761321644	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	373	750	0	ENST00000262320.3:c.2357C>T	p.Ala786Val	p.A786V	ENST00000262320	NM_003502.3	786	gCg/gTg	10/11	1	2	FACETS	0.936	0.891	0.981	0.936	0.891	0.981	CLONAL	1	TRUE	1	0.826766988492214	2		750	964	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225115	2225116	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	414	766	0	ENST00000326181.6:c.1353dup	p.Leu452ThrfsTer28	p.L452Tfs*28	ENST00000326181	NM_032271.2	450	-/A	15/21	1	2	FACETS	0.99	0.945	1	0.99	0.945	1	CLONAL	1	TRUE	1	0.826766988492214	2		766	1012	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	148	287	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.825	0.76	0.891	0.825	0.76	0.891	CLONAL	1	TRUE	1	0.826766988492214	2		287	434	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645878	67645878	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	229	533	0	ENST00000264010.4:c.806A>C	p.Glu269Ala	p.E269A	ENST00000264010	NM_006565.3	269	gAg/gCg	4/12	1	2	FACETS	0.871	0.817	0.926	0.871	0.817	0.926	CLONAL	1	TRUE	1	0.826766988492214	2		533	636	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849662	68849662	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs863224725	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	190	406	0	ENST00000261769.5:c.1565C>T	p.Thr522Ile	p.T522I	ENST00000261769	NM_004360.3	522	aCa/aTa	10/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.826766988492214	2		406	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573943	7573943	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	304	598	0	ENST00000269305.4:c.1084A>C	p.Ser362Arg	p.S362R	ENST00000269305	NM_001126112.2	362	Agc/Cgc	10/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.826766988492214	2		598	712	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	349	649	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.826766988492214	2		649	803	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29686023	29686023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778799019	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	129	352	0	ENST00000356175.3:c.8087C>T	p.Pro2696Leu	p.P2696L	ENST00000356175	NM_000267.3	2696	cCg/cTg	55/57	1	2	FACETS	0.843	0.773	0.915	0.843	0.773	0.915	CLONAL	1	TRUE	1	0.826766988492214	2		352	370	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884001	37884001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	168	747	0	ENST00000269571.5:c.3472C>T	p.Pro1158Ser	p.P1158S	ENST00000269571		1158	Cct/Tct	27/27	1	2	FACETS	0.476	0.437	0.516	0.476	0.437	0.516	SUBCLONAL	1	TRUE	1	0.826766988492214	2		747	854	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696430	47696430	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	274	472	0	ENST00000347630.2:c.393G>C	p.Trp131Cys	p.W131C	ENST00000347630	NM_001007230.1	131	tgG/tgC	6/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.826766988492214	2		472	624	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56339086	56339086	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	30	45	0	ENST00000348428.3:c.209+2T>C		p.X70_splice	ENST00000348428	NM_006785.3	70			1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.826766988492214	2		45	70	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2189768	2189768	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479024523	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	368	638	0	ENST00000398665.3:c.238C>T	p.Arg80Cys	p.R80C	ENST00000398665	NM_032482.2	80	Cgt/Tgt	4/28	0.594427059848145	3	FACETS	0.985	0.934	1			1	CLONAL	1	TRUE	NA	0.826766988492214	3		638	1278	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207618	2207618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	171	626	1	ENST00000398665.3:c.902G>A	p.Gly301Asp	p.G301D	ENST00000398665	NM_032482.2	301	gGc/gAc	11/28	0.594427059848145	3	FACETS	0.483	0.443	0.525			1	SUBCLONAL	1	TRUE	NA	0.826766988492214	3		627	1211	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216596	2216596	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs751006812	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	418	714	0	ENST00000398665.3:c.2240T>C	p.Val747Ala	p.V747A	ENST00000398665	NM_032482.2	747	gTg/gCg	20/28	0.594427059848145	3	FACETS	1	0.966	1			1	CLONAL	1	TRUE	NA	0.826766988492214	3		714	1404	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218539	5218539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374745287	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	419	742	2	ENST00000357368.4:c.3940C>T	p.Arg1314Cys	p.R1314C	ENST00000357368	NM_002850.3	1314	Cgc/Tgc	25/38	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.826766988492214	2		744	971	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308382	15308383	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs749829137	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	120	600	1	ENST00000263388.2:c.125dup	p.Cys43LeufsTer32	p.C43Lfs*32	ENST00000263388	NM_000435.2	42	cct/ccCt	2/33	1	2	FACETS	0.421	0.38	0.463	0.421	0.38	0.463	SUBCLONAL	1	TRUE	1	0.826766988492214	2		601	690	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256769	19256769	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	206	383	2	ENST00000162023.5:c.944del	p.Pro315GlnfsTer?	p.P315Qfs*?	ENST00000162023		315	cCa/ca	13/13	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.826766988492214	2		385	474	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218350	36218350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1454713201	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	385	744	0	ENST00000222270.7:c.4129G>A	p.Glu1377Lys	p.E1377K	ENST00000222270	NM_014727.1	1377	Gag/Aag	16/37	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.826766988492214	2		744	923	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752786	42752786	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762382429	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	402	693	0	ENST00000222329.4:c.1478G>A	p.Arg493His	p.R493H	ENST00000222329	NM_006494.2	493	cGc/cAc	4/4	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.826766988492214	2		693	967	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45873450	45873450	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	136	482	0	ENST00000391945.4:c.46T>C	p.Tyr16His	p.Y16H	ENST00000391945	NM_000400.3	16	Tac/Cac	2/23	1	2	FACETS	0.464	0.422	0.508	0.464	0.422	0.508	SUBCLONAL	1	TRUE	1	0.826766988492214	2		482	709	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905061	50905061	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	290	532	1	ENST00000440232.2:c.347del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	115	Ccc/cc	4/27	1	2	FACETS	0.977	0.925	1	0.977	0.925	1	CLONAL	1	TRUE	1	0.826766988492214	2		533	718	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	275	372	8	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	0.804902968163236	1	FACETS	0.954	0.914	0.993	0.954	0.914	0.993	CLONAL	1	TRUE	0	0.826766988492214	1		380	409	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380578	31380578	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	155	287	0	ENST00000328111.2:c.1066+2T>C		p.X356_splice	ENST00000328111	NM_006892.3	356			1	2	FACETS	0.974	0.903	1	0.974	0.903	1	CLONAL	1	TRUE	1	0.826766988492214	2		287	385	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514831	44514831	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	270	474	1	ENST00000291552.4:c.416C>T	p.Pro139Leu	p.P139L	ENST00000291552	NM_006758.2	139	cCg/cTg	6/8	1	2	FACETS	0.982	0.928	1	0.982	0.928	1	CLONAL	1	TRUE	1	0.826766988492214	2		475	665	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713883	30713883	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143095746	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	247	534	2	ENST00000295754.5:c.1208G>A	p.Arg403His	p.R403H	ENST00000295754	NM_003242.5	403	cGt/cAt	4/7	1	2	FACETS	0.86	0.808	0.912	0.86	0.808	0.912	CLONAL	1	TRUE	1	0.826766988492214	2		536	695	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405934	49405935	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	95	529	1	ENST00000418115.1:c.203_204delinsAA	p.Arg68Gln	p.R68Q	ENST00000418115	NM_001664.2	68	cGC/cAA	3/5	1	2	FACETS	0.32	0.284	0.357	0.32	0.284	0.357	SUBCLONAL	1	TRUE	1	0.826766988492214	2		530	719	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933804	49933804	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369879445	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	308	619	0	ENST00000296474.3:c.2473C>T	p.Arg825Cys	p.R825C	ENST00000296474	NM_002447.2	825	Cgc/Tgc	10/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.826766988492214	2		619	724	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643784	52643784	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	323	671	2	ENST00000394830.3:c.2112G>T	p.Met704Ile	p.M704I	ENST00000394830	NM_018313.4	704	atG/atT	17/30	1	2	FACETS	0.967	0.918	1	0.967	0.918	1	CLONAL	1	TRUE	1	0.826766988492214	2		673	808	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427690	72427690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	217	393	0	ENST00000477973.2:c.800G>A	p.Arg267His	p.R267H	ENST00000477973	NM_012234.5	267	cGc/cAc	4/4	1	2	FACETS	0.923	0.865	0.981	0.923	0.865	0.981	CLONAL	1	TRUE	1	0.826766988492214	2		393	569	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664760	138664761	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs797044528	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	116	172	0	ENST00000330315.3:c.804dup	p.Gly269ArgfsTer265	p.G269Rfs*265	ENST00000330315	NM_023067.3	268	-/C	1/1	1	2	FACETS	0.848	0.774	0.924	0.848	0.774	0.924	CLONAL	1	TRUE	1	0.826766988492214	2		172	331	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539129	187539129	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs893933434	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	325	574	0	ENST00000441802.2:c.8611A>G	p.Thr2871Ala	p.T2871A	ENST00000441802	NM_005245.3	2871	Act/Gct	10/27	0.159260058271163	3	FACETS	0.812	0.773	0.851	0.812	0.773	0.851	INDETERMINATE	2	TRUE	1	0.826766988492214	3		574	684	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564696	86564696	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	117	596	0	ENST00000274376.6:c.428T>C	p.Leu143Pro	p.L143P	ENST00000274376	NM_002890.2	143	cTg/cCg	1/25	1	2	FACETS	0.37	0.333	0.409	0.37	0.333	0.409	SUBCLONAL	1	TRUE	1	0.826766988492214	2		596	765	SUCCESS
APC	324	MSKCC	GRCh37	5	112176653	112176653	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773125634	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	108	283	0	ENST00000257430.4:c.5362C>T	p.Arg1788Cys	p.R1788C	ENST00000257430	NM_000038.5	1788	Cgt/Tgt	16/16	1	2	FACETS	0.913	0.832	0.997	0.913	0.832	0.997	CLONAL	1	TRUE	1	0.826766988492214	2		283	286	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803064	32803064	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	274	572	0	ENST00000374899.4:c.812T>G	p.Leu271Arg	p.L271R	ENST00000374899	NM_018833.2	271	cTc/cGc	5/12	1	2	FACETS	0.93	0.878	0.982	0.93	0.878	0.982	CLONAL	1	TRUE	1	0.826766988492214	2		572	713	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129329	152129329	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	260	462	3	ENST00000206249.3:c.287del	p.Gly96ValfsTer13	p.G96Vfs*13	ENST00000206249	NM_000125.3	94	ctG/ct	1/8	1	2	FACETS	0.913	0.86	0.966	0.913	0.86	0.966	CLONAL	1	TRUE	1	0.826766988492214	2		465	689	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508235	106508235	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1448416221	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	135	243	0	ENST00000359195.3:c.229C>T	p.Arg77Ter	p.R77*	ENST00000359195	NM_002649.2	77	Cga/Tga	2/11	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.826766988492214	2		243	325	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945013	151945013	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	15	82	0	ENST00000262189.6:c.2506del	p.Ser836LeufsTer18	p.S836Lfs*18	ENST00000262189	NM_170606.2	836	Tct/ct	14/59	1	2	FACETS	0.286	0.21	0.374	0.286	0.21	0.374	SUBCLONAL	1	TRUE	1	0.826766988492214	2		82	127	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97933361	97933361	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs755283850	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	148	391	1	ENST00000289081.3:c.521G>A	p.Arg174Gln	p.R174Q	ENST00000289081	NM_000136.2	174	cGa/cAa	6/15	1	2	FACETS	0.878	0.81	0.946	0.878	0.81	0.946	CLONAL	1	TRUE	1	0.826766988492214	2		392	408	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231322	98231322	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746898855	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	312	618	0	ENST00000331920.6:c.1961C>T	p.Thr654Met	p.T654M	ENST00000331920	NM_000264.3	654	aCg/aTg	14/24	1	2	FACETS	0.974	0.923	1	0.974	0.923	1	CLONAL	1	TRUE	1	0.826766988492214	2		618	775	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249318	110249318	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	457	923	0	ENST00000374672.4:c.1255A>G	p.Thr419Ala	p.T419A	ENST00000374672	NM_004235.4	419	Acc/Gcc	4/5	1	2	FACETS	0.958	0.917	1	0.958	0.917	1	CLONAL	1	TRUE	1	0.826766988492214	2		923	1154	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	320	604	5	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	1	2	FACETS	0.934	0.885	0.983	0.934	0.885	0.983	CLONAL	1	TRUE	1	0.826766988492214	2		609	829	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922024	39922024	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	57	369	0	ENST00000378444.4:c.4148A>G	p.Tyr1383Cys	p.Y1383C	ENST00000378444	NM_001123385.1	1383	tAc/tGc	9/15	1	1	FACETS	0.204	0.175	0.235	0.204	0.175	0.235	SUBCLONAL	1	TRUE	0	0.826766988492214	1		369	396	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	257	257	1	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.826766988492214	1		258	349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0036806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	105	520	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.354590587267308	2		520	547	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820014	36820014	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	89	624	0	ENST00000373129.3:c.574A>C	p.Asn192His	p.N192H	ENST00000373129	NM_032017.1	192	Aat/Cat	7/12	1	2	FACETS	0.705	0.625	0.791	0.705	0.625	0.791	SUBCLONAL	1	TRUE	1	0.354590587267308	2		624	712	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81927340	81927340	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	100	606	0	ENST00000359376.3:c.1013G>A	p.Ser338Asn	p.S338N	ENST00000359376	NM_002661.3	338	aGc/aAc	12/33	0.159570404620289	1	FACETS	0.675	0.604	0.752	0.675	0.604	0.752	INDETERMINATE	1	TRUE	0	0.354590587267308	1		606	687	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202704	128202704	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	113	692	0	ENST00000341105.2:c.1016T>A	p.Leu339Gln	p.L339Q	ENST00000341105	NM_032638.4	339	cTg/cAg	4/6	1	2	FACETS	0.889	0.801	0.982	0.889	0.801	0.982	CLONAL	1	TRUE	1	0.354590587267308	2		692	717	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923617	131923617	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	33	243	0	ENST00000265335.6:c.891del	p.Gln298LysfsTer7	p.Q298Kfs*7	ENST00000265335		296	gTt/gt	7/25	1	2	FACETS	0.816	0.669	0.98	0.816	0.669	0.98	CLONAL	1	TRUE	1	0.354590587267308	2		243	228	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0036807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	356	494	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.573350415123671	2	FACETS	0.913	0.876	0.95	0.913	0.876	0.95	CLONAL	2	TRUE	0	0.650950849761681	2		495	599	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941628	48941628	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0036807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	304	217	0	ENST00000267163.4:c.940-2A>G		p.X314_splice	ENST00000267163	NM_000321.2	314			0.650950849761681	5	FACETS	0.947	0.915	0.976	0.947	0.915	0.976	CLONAL	5	TRUE	0	0.650950849761681	5		217	390	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220467	133220467	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146711942	NA	P-0036807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	153	560	1	ENST00000320574.5:c.4246G>A	p.Ala1416Thr	p.A1416T	ENST00000320574	NM_006231.2	1416	Gct/Act	33/49	0.59506354705093	3	FACETS	0.861	0.789	0.935	0.43	0.394	0.468	CLONAL	1	TRUE	1	0.650950849761681	3		561	724	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874542	155874542	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	264	574	0	ENST00000368323.3:c.217A>G	p.Ile73Val	p.I73V	ENST00000368323	NM_006912.5	73	Att/Gtt	4/6	0.539805462537382	5	FACETS	0.851	0.799	0.904	0.567	0.532	0.603	CLONAL	2	TRUE	2	0.650950849761681	5		574	942	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691119	18691119	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	197	437	0	ENST00000266497.5:c.3230A>T	p.Glu1077Val	p.E1077V	ENST00000266497		1077	gAg/gTg	23/31	0.59506354705093	3	FACETS	0.922	0.865	0.98	0.922	0.865	0.98	CLONAL	2	TRUE	1	0.650950849761681	3		437	435	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184963	32184963	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	46	610	0	ENST00000375023.3:c.1705C>A	p.Gln569Lys	p.Q569K	ENST00000375023	NM_004557.3	569	Cag/Aag	10/30	0.59506354705093	3	FACETS	0.276	0.232	0.325	0.138	0.116	0.163	SUBCLONAL	1	TRUE	1	0.650950849761681	3		610	679	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0036808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	186	425	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.989	1	1	0.995	1	CLONAL	2	TRUE	1	0.469690112988478	2		425	325	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0036808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	89	648	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.469690112988478	2		648	271	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0036808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	64	358	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.469690112988478	1	FACETS	0.761	0.679	0.843	1	0.978	1	SUBCLONAL	2	TRUE	0	0.469690112988478	1		358	137	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105748	27105748	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	37	374	0	ENST00000324856.7:c.5359G>T	p.Glu1787Ter	p.E1787*	ENST00000324856	NM_006015.4	1787	Gag/Tag	20/20	0.17289073279169	2	FACETS	0.812	0.691	0.938	0.812	0.691	0.938	INDETERMINATE	2	TRUE	0	0.469690112988478	2		374	97	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110005	115110005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs773785943	NA	P-0036808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	32	637	1	ENST00000257566.3:c.1873C>A	p.Arg625Ser	p.R625S	ENST00000257566	NM_016569.3	625	Cgc/Agc	8/8	1	2	FACETS	1	0.839	1	1	0.839	1	CLONAL	1	TRUE	1	0.469690112988478	2		638	134	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808304	99808304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	17	305	0	ENST00000280892.6:c.385C>T	p.Arg129Trp	p.R129W	ENST00000280892	NM_001130678.1	129	Cgg/Tgg	5/7	1	2	FACETS	0.905	0.69	1	0.905	0.69	1	CLONAL	1	TRUE	1	0.469690112988478	2		305	80	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190656563	190656563	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1367090018	NA	P-0036808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	17	193	0	ENST00000441310.2:c.28C>T	p.Arg10Ter	p.R10*	ENST00000441310	NM_000534.4	10	Cga/Tga	2/13	0.26732215464055	2	FACETS	0.557	0.419	0.717	0.278	0.209	0.359	INDETERMINATE	1	TRUE	0	0.469690112988478	2		193	130	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64288369	64288369	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1420598115	NA	P-0036808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	59	284	0	ENST00000370651.3:c.133A>G	p.Ile45Val	p.I45V	ENST00000370651	NM_003463.4	45	Ata/Gta	3/6	0.305911610510684	3	FACETS	1	0.971	1	0.495	0.432	0.561	CLONAL	1	TRUE	0	0.469690112988478	3		284	209	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106937	27106937	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	22	481	0	ENST00000324856.7:c.6548G>T	p.Arg2183Leu	p.R2183L	ENST00000324856	NM_006015.4	2183	cGt/cTt	20/20	0.17289073279169	2	FACETS	0.568	0.443	0.71	0.284	0.221	0.355	INDETERMINATE	1	TRUE	0	0.469690112988478	2		481	165	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743653	46743653	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1483819603	NA	P-0036808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	51	654	1	ENST00000371975.4:c.2033+1G>A		p.X678_splice	ENST00000371975	NM_003579.3	678			0.17289073279169	2	FACETS	1	0.951	1	0.617	0.533	0.705	INDETERMINATE	1	TRUE	0	0.469690112988478	2		655	176	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619153	43619153	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	57	521	0	ENST00000355710.3:c.2836A>G	p.Thr946Ala	p.T946A	ENST00000355710	NM_020975.4	946	Acc/Gcc	17/20	0.371331245360875	3	FACETS	1	0.971	1	0.749	0.653	0.851	CLONAL	1	TRUE	1	0.469690112988478	3		521	200	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346365	73346365	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	38	366	0	ENST00000377767.4:c.1435G>A	p.Asp479Asn	p.D479N	ENST00000377767	NM_014953.3	479	Gac/Aac	10/21	0.358797838278673	2	FACETS	1	0.955	1	0.71	0.602	0.823	CLONAL	1	TRUE	0	0.469690112988478	2		366	114	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609751	81609751	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	34	471	0	ENST00000298171.2:c.1349G>C	p.Arg450Pro	p.R450P	ENST00000298171	NM_000369.2	450	cGc/cCc	10/10	0.450683182011357	3	FACETS	0.864	0.712	1	0.432	0.356	0.516	CLONAL	1	TRUE	1	0.469690112988478	3		471	207	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868354	56868354	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	25	282	0	ENST00000308159.5:c.1737G>T	p.Glu579Asp	p.E579D	ENST00000308159	NM_014669.4	579	gaG/gaT	15/22	0.23552244105568	1	FACETS	0.627	0.501	0.767	0.627	0.501	0.767	INDETERMINATE	1	TRUE	0	0.469690112988478	1		282	130	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577065	7577065	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	45	739	0	ENST00000269305.4:c.873del	p.Glu294SerfsTer51	p.E294Sfs*51	ENST00000269305	NM_001126112.2	291	aaG/aa	8/11	1	2	FACETS	0.71	0.6	0.829	0.71	0.6	0.829	SUBCLONAL	1	TRUE	1	0.469690112988478	2		739	270	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610177	10610177	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	59	701	0	ENST00000171111.5:c.533A>T	p.Gln178Leu	p.Q178L	ENST00000171111	NM_203500.1	178	cAg/cTg	2/6	0.469690112988478	1	FACETS	0.933	0.815	1	0.933	0.815	1	CLONAL	1	TRUE	0	0.469690112988478	1		701	206	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390919	89390919	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	45	353	0	ENST00000336596.2:c.985C>A	p.Pro329Thr	p.P329T	ENST00000336596	NM_005233.5	329	Cca/Aca	5/17	0.358797838278673	2	FACETS	0.819	0.708	0.934	0.819	0.708	0.934	CLONAL	2	TRUE	0	0.469690112988478	2		353	117	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456563	189456563	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	44	400	0	ENST00000264731.3:c.324G>C	p.Trp108Cys	p.W108C	ENST00000264731	NM_003722.4	108	tgG/tgC	3/14	0.358797838278673	2	FACETS	1	0.958	1	0.684	0.586	0.787	CLONAL	1	TRUE	0	0.469690112988478	2		400	137	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53244010	53244011	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	57	510	0	ENST00000375401.3:c.982_983insT	p.Arg328LeufsTer8	p.R328Lfs*8	ENST00000375401	NM_004187.3	328	cgg/cTgg	8/26	0.469690112988478	1	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	0	0.469690112988478	1		510	181	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0036811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	35	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.25642209610624	1	FACETS	0.433	0.354	0.522	0.433	0.354	0.522	SUBCLONAL	1	TRUE	0	0.25642209610624	1		502	549	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0036811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	48	477	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	0.731	0.618	0.856	0.731	0.618	0.856	SUBCLONAL	1	TRUE	1	0.25642209610624	2		477	512	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467047	25467047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	38	417	1	ENST00000264709.3:c.1828G>A	p.Ala610Thr	p.A610T	ENST00000264709	NM_175629.2	610	Gct/Act	15/23	1	2	FACETS	0.657	0.543	0.784	0.657	0.543	0.784	SUBCLONAL	1	TRUE	1	0.25642209610624	2		418	451	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166815	32166815	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	38	556	0	ENST00000375023.3:c.4423C>T	p.Arg1475Cys	p.R1475C	ENST00000375023	NM_004557.3	1475	Cgc/Tgc	24/30	1	2	FACETS	0.526	0.434	0.63	0.526	0.434	0.63	SUBCLONAL	1	TRUE	1	0.25642209610624	2		556	563	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0036812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	91	298	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.851	0.762	0.946	0.851	0.762	0.946	CLONAL	1	TRUE	1	0.559531798610792	2		298	382	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197365	26197365	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	136	358	0	ENST00000356476.2:c.114G>T	p.Lys38Asn	p.K38N	ENST00000356476		38	aaG/aaT	1/1	0.286847241116161	3	FACETS	1	0.983	1	0.659	0.603	0.717	INDETERMINATE	1	TRUE	1	0.559531798610792	3		358	472	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650864	37650864	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	360	466	0	ENST00000447079.4:c.2336G>A	p.Arg779His	p.R779H	ENST00000447079	NM_015083.1	779	cGt/cAt	5/14	1	2	FACETS	0.956	0.911	1	0.956	0.911	1	CLONAL	1	TRUE	1	0.883775508883315	2		466	852	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861162	57861162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564027387	NA	P-0036825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	144	455	0	ENST00000228682.2:c.959C>T	p.Thr320Met	p.T320M	ENST00000228682	NM_005269.2	320	aCg/aTg	9/12	0.500826493048754	4	FACETS	0.987	0.901	1	0.494	0.45	0.54	CLONAL	1	TRUE	2	0.500826493048754	4		455	874	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094928	11094929	+	missense_variant	Missense_Mutation	DNP	CC	CC	GT	novel	NA	P-0036825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	164	649	1	ENST00000358026.2:c.101_102delinsGT	p.Pro34Arg	p.P34R	ENST00000358026	NM_001128849.1	34	cCC/cGT	2/36	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.500826493048754	2		650	582	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211658	36211658	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	102	452	0	ENST00000222270.7:c.1409G>C	p.Gly470Ala	p.G470A	ENST00000222270	NM_014727.1	470	gGc/gCc	3/37	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.500826493048754	2		452	383	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385100	41385100	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0036825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	107	527	0	ENST00000373198.4:c.859+2T>C		p.X287_splice	ENST00000373198	NM_133170.3	287			0.500826493048754	2	FACETS	0.659	0.592	0.73	0.33	0.296	0.365	SUBCLONAL	1	TRUE	0	0.500826493048754	2		527	648	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057230	180057230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780661773	NA	P-0036827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	81	478	0	ENST00000261937.6:c.508C>T	p.Arg170Cys	p.R170C	ENST00000261937	NM_182925.4	170	Cgc/Tgc	4/30	0.383987302453748	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	0	0.383987302453748	1		478	242	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591825	48591825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767342	NA	P-0036827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	111	407	0	ENST00000342988.3:c.988G>A	p.Glu330Lys	p.E330K	ENST00000342988	NM_005359.5	330	Gaa/Aaa	9/12	0.383987302453748	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	0	0.383987302453748	1		407	354	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620566	52620566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746373271	NA	P-0036827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	161	440	0	ENST00000394830.3:c.3187C>T	p.Arg1063Trp	p.R1063W	ENST00000394830	NM_018313.4	1063	Cgg/Tgg	21/30	0.299705830640133	2	FACETS	0.868	0.803	0.935	0.868	0.803	0.935	CLONAL	2	FALSE	0	0.383987302453748	2		440	483	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724517	43724518	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CA	CA	-	novel	NA	P-0036827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	194	802	0	ENST00000382044.4:c.3549_3550del	p.Cys1183Ter	p.C1183*	ENST00000382044	NM_001141980.1	1183	tgTGag/tgag	17/28	0.325929607905465	2	FACETS	0.839	0.781	0.899	0.839	0.781	0.899	CLONAL	2	FALSE	0	0.383987302453748	2		802	602	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134275	11134275	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	157	472	0	ENST00000358026.2:c.2941A>C	p.Lys981Gln	p.K981Q	ENST00000358026	NM_001128849.1	981	Aag/Cag	20/36	1	2	FACETS	0.873	0.803	0.946	0.873	0.803	0.946	CLONAL	1	TRUE	1	0.562744079999224	2		472	639	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	202	615	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.984	1	1	0.994	1	CLONAL	2	TRUE	1	0.249531051304868	2		617	684	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	36	387	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.746	0.614	0.893	0.746	0.614	0.893	SUBCLONAL	1	TRUE	1	0.249531051304868	2		387	387	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	25	477	0	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	0.249531051304868	1	FACETS	0.351	0.276	0.439	0.351	0.276	0.439	SUBCLONAL	1	TRUE	0	0.249531051304868	1		477	499	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	66	304	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.249531051304868	2		304	493	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465373	120465373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	98	494	0	ENST00000256646.2:c.4888C>T	p.Arg1630Cys	p.R1630C	ENST00000256646	NM_024408.3	1630	Cgc/Tgc	27/34	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.249531051304868	2		494	669	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682399	52682400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	120	494	0	ENST00000394830.3:c.773dup	p.Asn258LysfsTer6	p.N258Kfs*6	ENST00000394830	NM_018313.4	258	aat/aaAt	8/30	1	2	FACETS	0.808	0.732	0.888	1	0.986	1	CLONAL	2	TRUE	1	0.249531051304868	2		494	595	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139831	55139831	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758137485	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	118	375	1	ENST00000257290.5:c.1492G>A	p.Ala498Thr	p.A498T	ENST00000257290	NM_006206.4	498	Gcc/Acc	10/23	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.249531051304868	2		376	657	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092815	27092815	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	49	501	0	ENST00000324856.7:c.2840del	p.Pro947HisfsTer21	p.P947Hfs*21	ENST00000324856	NM_006015.4	946	Ccc/cc	9/20	0.249531051304868	1	FACETS	0.71	0.602	0.829	0.71	0.602	0.829	SUBCLONAL	1	TRUE	0	0.249531051304868	1		501	484	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914070	32914070	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507790	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	29	448	0	ENST00000380152.3:c.5583del	p.Val1862Ter	p.V1862*	ENST00000380152		1860	Aaa/aa	11/27	1	2	FACETS	0.564	0.452	0.691	0.564	0.452	0.691	SUBCLONAL	1	TRUE	1	0.249531051304868	2		448	412	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040630	47040630	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	68	419	0	ENST00000377604.3:c.1265A>G	p.Glu422Gly	p.E422G	ENST00000377604	NM_001204468.1	422	gAg/gGg	13/24	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.249531051304868	2		419	540	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257144	19257144	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	44	485	0	ENST00000162023.5:c.819del	p.Thr274ProfsTer?	p.T274Pfs*?	ENST00000162023		273	ccC/cc	12/13	1	2	FACETS	0.742	0.623	0.875	0.742	0.623	0.875	SUBCLONAL	1	TRUE	1	0.249531051304868	2		485	475	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482926	140482927	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs777474487	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	68	526	0	ENST00000288602.6:c.1208dup	p.Ala404CysfsTer9	p.A404Cfs*9	ENST00000288602	NM_004333.4	403	cct/ccCt	10/18	1	2	FACETS	0.831	0.723	0.948	0.831	0.723	0.948	CLONAL	1	TRUE	1	0.249531051304868	2		526	656	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247894	59247894	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	209	842	0	ENST00000371222.2:c.849del	p.Val284Ter	p.V284*	ENST00000371222	NM_002228.3	283	aaA/aa	1/1	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.249531051304868	2		842	1232	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841231	15841236	+	inframe_deletion	In_Frame_Del	DEL	AGCCGG	AGCCGG	-	rs752736259	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	54	328	0	ENST00000307771.7:c.1338_1343del	p.Ser447_Arg448del	p.S447_R448del	ENST00000307771	NM_005089.3	439	AGCCGG/-	11/11	1	2	FACETS	0.929	0.794	1	0.929	0.794	1	CLONAL	1	TRUE	1	0.249531051304868	2		328	466	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434182	12434182	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776687	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	88	449	0	ENST00000287820.6:c.556del	p.Ser186ValfsTer47	p.S186Vfs*47	ENST00000287820	NM_015869.4	184	Aaa/aa	4/7	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.249531051304868	2		449	520	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196143	108196143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564652222	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	85	501	0	ENST00000278616.4:c.6679C>T	p.Arg2227Cys	p.R2227C	ENST00000278616	NM_000051.3	2227	Cgc/Tgc	46/63	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.249531051304868	2		501	592	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667492	241667492	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766441385	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	18	247	0	ENST00000366560.3:c.958G>A	p.Ala320Thr	p.A320T	ENST00000366560	NM_000143.3	320	Gct/Act	7/10	1	2	FACETS	0.432	0.325	0.559	0.432	0.325	0.559	SUBCLONAL	1	TRUE	1	0.249531051304868	2		247	334	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346270	89346270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764885268	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	57	351	0	ENST00000301030.4:c.6680C>T	p.Pro2227Leu	p.P2227L	ENST00000301030	NM_001256183.1	2227	cCg/cTg	9/13	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.249531051304868	2		351	342	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291084	10291084	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	55	648	0	ENST00000340748.4:c.387del	p.Lys130AsnfsTer129	p.K130Nfs*129	ENST00000340748		129	ccC/cc	4/40	1	2	FACETS	0.609	0.52	0.707	0.609	0.52	0.707	SUBCLONAL	1	TRUE	1	0.249531051304868	2		648	724	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348443	89348443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537684815	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	57	701	1	ENST00000301030.4:c.4507G>A	p.Ala1503Thr	p.A1503T	ENST00000301030	NM_001256183.1	1503	Gcc/Acc	9/13	1	2	FACETS	0.497	0.425	0.576	0.497	0.425	0.576	SUBCLONAL	1	TRUE	1	0.249531051304868	2		702	919	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216189	36216189	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	37	694	0	ENST00000222270.7:c.3602del	p.Pro1201ArgfsTer154	p.P1201Rfs*154	ENST00000222270	NM_014727.1	1199	ggC/gg	11/37	1	2	FACETS	0.405	0.332	0.486	0.405	0.332	0.486	SUBCLONAL	1	TRUE	1	0.249531051304868	2		694	733	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915852	127915852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	73	479	0	ENST00000373547.4:c.629G>A	p.Arg210Gln	p.R210Q	ENST00000373547	NM_002721.4	210	cGa/cAa	6/7	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.249531051304868	2		479	525	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120043	70120043	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	14	39	0	ENST00000245479.2:c.1049del	p.Pro350HisfsTer33	p.P350Hfs*33	ENST00000245479	NM_000346.3	349	Ccc/cc	3/3	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.249531051304868	2		39	85	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424713	47424713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1387037979	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	40	545	1	ENST00000377045.4:c.521G>A	p.Arg174His	p.R174H	ENST00000377045	NM_001654.4	174	cGc/cAc	6/16	1	2	FACETS	0.445	0.369	0.531	0.445	0.369	0.531	SUBCLONAL	1	TRUE	1	0.249531051304868	2		546	720	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55693419	55693419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759162213	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	70	572	0	ENST00000284073.2:c.626C>T	p.Ala209Val	p.A209V	ENST00000284073	NM_138962.2	209	gCg/gTg	9/14	1	2	FACETS	0.684	0.595	0.781	0.684	0.595	0.781	SUBCLONAL	1	TRUE	1	0.249531051304868	2		572	820	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322882	31322882	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1476457470	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	44	535	0	ENST00000412585.2:c.1012+2T>C		p.X338_splice	ENST00000412585	NM_005514.6	338			1	2	FACETS	0.653	0.547	0.77	0.653	0.547	0.77	SUBCLONAL	1	TRUE	1	0.249531051304868	2		535	540	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323268	31323268	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1322740343	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	28	279	1	ENST00000412585.2:c.721T>C	p.Trp241Arg	p.W241R	ENST00000412585	NM_005514.6	241	Tgg/Cgg	4/8	1	2	FACETS	0.733	0.587	0.899	0.733	0.587	0.899	SUBCLONAL	1	TRUE	1	0.249531051304868	2		280	306	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303204	11303204	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs928111290	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	102	514	1	ENST00000361445.4:c.1379G>A	p.Arg460Gln	p.R460Q	ENST00000361445	NM_004958.3	460	cGa/cAa	9/58	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.249531051304868	2		515	641	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22412996	22412996	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	13	174	0	ENST00000344548.3:c.247del	p.Ser83GlnfsTer11	p.S83Qfs*11	ENST00000344548	NM_001039802.1	81	tgT/tg	5/7	1	2	FACETS	0.639	0.457	0.859	0.639	0.457	0.859	SUBCLONAL	1	TRUE	1	0.249531051304868	2		174	163	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161310397	161310397	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1060501392	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	32	514	0	ENST00000367975.2:c.193A>G	p.Met65Val	p.M65V	ENST00000367975	NM_003001.3	65	Atg/Gtg	4/6	1	2	FACETS	0.455	0.368	0.553	0.455	0.368	0.553	SUBCLONAL	1	TRUE	1	0.249531051304868	2		514	564	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625161	69625161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1221660991	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	131	642	0	ENST00000334134.2:c.632G>A	p.Arg211Gln	p.R211Q	ENST00000334134	NM_005247.2	211	cGg/cAg	3/3	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.249531051304868	2		642	802	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1040432	1040432	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	109	663	0	ENST00000358495.3:c.140T>G	p.Leu47Arg	p.L47R	ENST00000358495	NM_134424.2	47	cTg/cGg	3/12	1	2	FACETS	0.97	0.87	1	0.97	0.87	1	CLONAL	1	TRUE	1	0.249531051304868	2		663	901	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445222	49445222	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	51	747	2	ENST00000301067.7:c.2244G>T	p.Glu748Asp	p.E748D	ENST00000301067	NM_003482.3	748	gaG/gaT	10/54	1	2	FACETS	0.432	0.365	0.505	0.432	0.365	0.505	SUBCLONAL	1	TRUE	1	0.249531051304868	2		749	947	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514713	103514713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243423260	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	25	304	1	ENST00000355739.4:c.1214C>T	p.Ala405Val	p.A405V	ENST00000355739	NM_000123.3	405	gCt/gTt	8/15	1	2	FACETS	0.431	0.339	0.537	0.431	0.339	0.537	SUBCLONAL	1	TRUE	1	0.249531051304868	2		305	465	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678367	88678367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	62	814	0	ENST00000360948.2:c.1169C>T	p.Thr390Ile	p.T390I	ENST00000360948	NM_001012338.2	390	aCc/aTc	9/19	1	2	FACETS	0.467	0.402	0.539	0.467	0.402	0.539	SUBCLONAL	1	TRUE	1	0.249531051304868	2		814	1063	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849586	68849586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567508990	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	67	553	1	ENST00000261769.5:c.1489G>A	p.Glu497Lys	p.E497K	ENST00000261769	NM_004360.3	497	Gag/Aag	10/16	1	2	FACETS	0.676	0.587	0.774	0.676	0.587	0.774	SUBCLONAL	1	TRUE	1	0.249531051304868	2		554	794	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822585	72822586	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	57	507	0	ENST00000268489.5:c.9588_9589dup	p.Gln3197ProfsTer45	p.Q3197Pfs*45	ENST00000268489	NM_006885.3	3197	cag/cCCag	10/10	1	2	FACETS	0.696	0.597	0.805	0.696	0.597	0.805	SUBCLONAL	1	TRUE	1	0.249531051304868	2		507	656	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993508	72993509	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	85	596	0	ENST00000268489.5:c.536dup	p.Lys180GlnfsTer30	p.K180Qfs*30	ENST00000268489	NM_006885.3	179	ggc/ggGc	2/10	1	2	FACETS	0.929	0.821	1	0.929	0.821	1	CLONAL	1	TRUE	1	0.249531051304868	2		596	733	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349045	89349045	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	159	838	0	ENST00000301030.4:c.3905A>C	p.Glu1302Ala	p.E1302A	ENST00000301030	NM_001256183.1	1302	gAg/gCg	9/13	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.249531051304868	2		838	1029	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573564	48573564	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs786203560	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	23	276	0	ENST00000342988.3:c.153del	p.Asp52MetfsTer6	p.D52Mfs*6	ENST00000342988	NM_005359.5	50	Aaa/aa	2/12	0.115037344705706	3	FACETS	0.749	0.585	0.938	0.374	0.292	0.469	INDETERMINATE	1	TRUE	1	0.249531051304868	3		276	277	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260057	19260057	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1254581471	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	118	711	2	ENST00000162023.5:c.236G>A	p.Arg79His	p.R79H	ENST00000162023		79	cGc/cAc	7/13	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.249531051304868	2		713	852	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222937	36222938	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1161258635	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	84	799	1	ENST00000222270.7:c.5572dup	p.Arg1858ProfsTer114	p.R1858Pfs*114	ENST00000222270	NM_014727.1	1856	gcc/gCcc	27/37	1	2	FACETS	0.764	0.674	0.861	0.764	0.674	0.861	SUBCLONAL	1	TRUE	1	0.249531051304868	2		800	881	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029096	26029096	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	39	303	0	ENST00000435504.4:c.252+2T>C		p.X84_splice	ENST00000435504		84			1	2	FACETS	0.893	0.742	1	0.893	0.742	1	CLONAL	1	TRUE	1	0.249531051304868	2		303	350	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61706017	61706017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	79	654	1	ENST00000401558.2:c.3154C>T	p.Arg1052Cys	p.R1052C	ENST00000401558	NM_003400.3	1052	Cgt/Tgt	25/25	1	2	FACETS	0.946	0.832	1	0.946	0.832	1	CLONAL	1	TRUE	1	0.249531051304868	2		655	669	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149571	202149571	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	79	423	0	ENST00000358485.4:c.1012T>G	p.Phe338Val	p.F338V	ENST00000358485	NM_001080125.1	338	Ttt/Gtt	8/9	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.249531051304868	2		423	556	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204737525	204737525	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	37	248	1	ENST00000302823.3:c.662C>A	p.Pro221His	p.P221H	ENST00000302823	NM_005214.4	221	cCc/cAc	4/4	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.249531051304868	2		249	256	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46277816	46277816	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	90	358	0	ENST00000371998.3:c.3614T>G	p.Val1205Gly	p.V1205G	ENST00000371998		1205	gTg/gGg	19/23	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.249531051304868	2		358	615	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134885846	134885846	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs770834786	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	56	380	0	ENST00000398015.3:c.1757G>A	p.Arg586Gln	p.R586Q	ENST00000398015	NM_004441.4	586	cGa/cAa	9/16	1	2	FACETS	0.925	0.794	1	0.925	0.794	1	CLONAL	1	TRUE	1	0.249531051304868	2		380	485	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430402	181430402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1007978252	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	156	582	1	ENST00000325404.1:c.254C>T	p.Thr85Met	p.T85M	ENST00000325404	NM_003106.3	85	aCg/aTg	1/1	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.249531051304868	2		583	930	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447010	187447010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	151	705	0	ENST00000232014.4:c.1183C>T	p.Pro395Ser	p.P395S	ENST00000232014	NM_001130845.1	395	Cct/Tct	5/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.249531051304868	2		705	922	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803346	1803346	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	94	616	0	ENST00000260795.2:c.616-1G>A		p.X206_splice	ENST00000260795		206			1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.249531051304868	2		616	752	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524141	187524141	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	111	403	0	ENST00000441802.2:c.11398C>A	p.Pro3800Thr	p.P3800T	ENST00000441802	NM_005245.3	3800	Cct/Act	20/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.249531051304868	2		403	643	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295023	1295023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	33	46	0	ENST00000310581.5:c.82G>A	p.Val28Met	p.V28M	ENST00000310581	NM_198253.2	28	Gtg/Atg	1/16	1	2	FACETS	0.882	0.729	1	1	0.959	1	CLONAL	2	TRUE	1	0.249531051304868	2		46	150	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176618957	176618957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1376422641	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	63	503	1	ENST00000439151.2:c.1000C>T	p.Arg334Cys	p.R334C	ENST00000439151	NM_022455.4	334	Cgc/Tgc	3/23	1	2	FACETS	0.799	0.691	0.917	0.799	0.691	0.917	CLONAL	1	TRUE	1	0.249531051304868	2		504	632	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911080	29911081	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	178	707	0	ENST00000376809.5:c.380dup	p.Ser129ValfsTer48	p.S129Vfs*48	ENST00000376809	NM_002116.7	127	gtg/gTtg	3/8	0.218008954801827	2	FACETS	0.878	0.811	0.949	0.878	0.811	0.949	CLONAL	2	TRUE	0	0.249531051304868	2		707	812	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020438	69020438	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	140	590	0	ENST00000288368.4:c.2810A>G	p.Asn937Ser	p.N937S	ENST00000288368	NM_024870.2	937	aAc/aGc	24/40	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.249531051304868	2		590	761	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331686	8331686	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	58	440	0	ENST00000356435.5:c.5430G>T	p.Glu1810Asp	p.E1810D	ENST00000356435		1810	gaG/gaT	33/35	1	2	FACETS	0.737	0.632	0.851	0.737	0.632	0.851	SUBCLONAL	1	TRUE	1	0.249531051304868	2		440	631	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907095	101907095	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	49	369	0	ENST00000374994.4:c.1055T>C	p.Leu352Ser	p.L352S	ENST00000374994	NM_004612.2	352	tTa/tCa	6/9	1	2	FACETS	0.922	0.782	1	0.922	0.782	1	CLONAL	1	TRUE	1	0.249531051304868	2		369	426	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101910053	101910053	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	37	238	0	ENST00000374994.4:c.1374del	p.Trp458CysfsTer7	p.W458Cfs*7	ENST00000374994	NM_004612.2	458	tGg/tg	8/9	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.249531051304868	2		238	245	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760804	133760804	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs138480160	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	98	585	0	ENST00000318560.5:c.3127A>G	p.Ile1043Val	p.I1043V	ENST00000318560	NM_005157.4	1043	Atc/Gtc	11/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.249531051304868	2		585	667	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820633	44820633	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	34	359	0	ENST00000377967.4:c.333del	p.Ala112HisfsTer68	p.A112Hfs*68	ENST00000377967	NM_021140.2	110	ccA/cc	3/29	1	2	FACETS	0.676	0.553	0.815	0.676	0.553	0.815	SUBCLONAL	1	TRUE	1	0.249531051304868	2		359	403	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045778	47045778	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	138	692	2	ENST00000377604.3:c.2659C>T	p.Pro887Ser	p.P887S	ENST00000377604	NM_001204468.1	887	Cct/Tct	23/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.249531051304868	2		694	793	SUCCESS
AR	367	MSKCC	GRCh37	X	66863117	66863117	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	42	642	1	ENST00000374690.3:c.1636C>A	p.His546Asn	p.H546N	ENST00000374690	NM_000044.3	546	Cat/Aat	2/8	1	2	FACETS	0.406	0.337	0.482	0.406	0.337	0.482	SUBCLONAL	1	TRUE	1	0.249531051304868	2		643	830	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70353058	70353058	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	40	421	0	ENST00000374080.3:c.4613A>G	p.Asn1538Ser	p.N1538S	ENST00000374080		1538	aAc/aGc	33/45	1	2	FACETS	0.623	0.517	0.74	0.623	0.517	0.74	SUBCLONAL	1	TRUE	1	0.249531051304868	2		421	515	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549404	21549404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753026198	NA	P-0036845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	237	504	0	ENST00000382592.4:c.2872C>T	p.Arg958Cys	p.R958C	ENST00000382592	NM_014572.2	958	Cgc/Tgc	8/8	0.837433711725475	1	FACETS	0.904	0.862	0.945	0.904	0.862	0.945	CLONAL	1	FALSE	0	0.837433711725475	1		504	364	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803592	1803592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs949596399	NA	P-0036845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	150	674	1	ENST00000260795.2:c.770C>T	p.Ala257Val	p.A257V	ENST00000260795		257	gCg/gTg	6/17	1	2	FACETS	0.369	0.337	0.403	0.369	0.337	0.403	SUBCLONAL	1	FALSE	1	0.837433711725475	2		675	970	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004742	150004742	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	139	609	0	ENST00000253339.5:c.1483C>T	p.Gln495Ter	p.Q495*	ENST00000253339		495	Caa/Taa	3/7	0.837433711725475	1	FACETS	0.387	0.354	0.421	0.387	0.354	0.421	SUBCLONAL	1	FALSE	0	0.837433711725475	1		609	499	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004877	150004877	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	28	544	0	ENST00000253339.5:c.1348G>C	p.Glu450Gln	p.E450Q	ENST00000253339		450	Gaa/Caa	3/7	0.837433711725475	1	FACETS	0.085	0.068	0.105	0.085	0.068	0.105	SUBCLONAL	1	FALSE	0	0.837433711725475	1		544	456	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005333	150005333	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	31	610	0	ENST00000253339.5:c.892G>T	p.Glu298Ter	p.E298*	ENST00000253339		298	Gag/Tag	3/7	0.837433711725475	1	FACETS	0.087	0.07	0.107	0.087	0.07	0.107	SUBCLONAL	1	FALSE	0	0.837433711725475	1		610	493	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005366	150005366	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	53	656	0	ENST00000253339.5:c.859C>T	p.Arg287Ter	p.R287*	ENST00000253339		287	Cga/Tga	3/7	0.837433711725475	1	FACETS	0.14	0.119	0.163	0.14	0.119	0.163	SUBCLONAL	1	FALSE	0	0.837433711725475	1		656	525	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023009	150023010	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0036845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	35	728	0	ENST00000253339.5:c.253_254del	p.Leu85AlafsTer6	p.L85Afs*6	ENST00000253339		85	CTg/g	1/7	0.837433711725475	1	FACETS	0.082	0.067	0.099	0.082	0.067	0.099	SUBCLONAL	1	FALSE	0	0.837433711725475	1		728	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882019	NA	P-0036848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	201	760	0	ENST00000269305.4:c.455dup	p.Pro153AlafsTer28	p.P153Afs*28	ENST00000269305	NM_001126112.2	152	ccg/ccCg	5/11	0.674082530732385	1	FACETS	0.843	0.79	0.897	0.843	0.79	0.897	CLONAL	1	TRUE	0	0.675996359470891	1		760	467	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0036848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	69	340	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.675996359470891	2		341	201	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584708	48584708	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0036848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	119	417	0	ENST00000342988.3:c.788-2A>T		p.X263_splice	ENST00000342988	NM_005359.5	263			0.675996359470891	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.675996359470891	1		417	230	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023903	27023904	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0036848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	30	111	0	ENST00000324856.7:c.1015dup	p.Ala339GlyfsTer61	p.A339Gfs*61	ENST00000324856	NM_006015.4	337	tgg/tGgg	1/20	1	2	FACETS	0.643	0.526	0.771	0.643	0.526	0.771	SUBCLONAL	1	TRUE	1	0.675996359470891	2		111	138	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245912913	245912913	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	150	459	0	ENST00000388985.4:c.1239T>G	p.Asp413Glu	p.D413E	ENST00000388985		413	gaT/gaG	12/12	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.675996359470891	2		459	416	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623790	28623790	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs200102131	NA	P-0036848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	42	620	0	ENST00000241453.7:c.864A>C	p.Glu288Asp	p.E288D	ENST00000241453	NM_004119.2	288	gaA/gaC	7/24	0.658961081647195	3	FACETS	0.263	0.219	0.313	0.132	0.109	0.157	SUBCLONAL	1	TRUE	1	0.675996359470891	3		620	631	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528147	157528147	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751590307	NA	P-0036848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	143	609	1	ENST00000346085.5:c.5872G>A	p.Val1958Met	p.V1958M	ENST00000346085	NM_020732.3	1958	Gtg/Atg	20/20	1	2	FACETS	0.815	0.748	0.885	0.815	0.748	0.885	CLONAL	1	TRUE	1	0.675996359470891	2		610	519	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945049	151945049	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs755626030	NA	P-0036848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	24	641	1	ENST00000262189.6:c.2470G>T	p.Gly824Cys	p.G824C	ENST00000262189	NM_170606.2	824	Ggc/Tgc	14/59	1	2	FACETS	0.176	0.137	0.22	0.176	0.137	0.22	SUBCLONAL	1	TRUE	1	0.675996359470891	2		642	404	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435160	56435161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755128667	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	57	735	2	ENST00000407977.2:c.1976dup	p.Pro660SerfsTer87	p.P660Sfs*87	ENST00000407977		659	ggt/ggGt	9/10	1	2	FACETS	0.563	0.481	0.653	0.563	0.481	0.653	SUBCLONAL	1	TRUE	1	0.19	2		737	1066	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593437	55593437	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55792975	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	34	569	0	ENST00000288135.5:c.1594G>A	p.Val532Ile	p.V532I	ENST00000288135	NM_000222.2	532	Gta/Ata	10/21	1	2	FACETS	0.539	0.439	0.652	0.539	0.439	0.652	SUBCLONAL	1	TRUE	1	0.19	2		569	664	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	108	655	0	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.19	2		655	1076	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238958	5238958	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	37	426	0	ENST00000357368.4:c.1821del	p.Val608TrpfsTer30	p.V608Wfs*30	ENST00000357368	NM_002850.3	607	ccC/cc	13/38	1	2	FACETS	0.634	0.522	0.761	0.634	0.522	0.761	SUBCLONAL	1	TRUE	1	0.19	2		426	614	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	75	826	2	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.656	0.572	0.746	0.656	0.572	0.746	SUBCLONAL	1	TRUE	1	0.19	2		828	1204	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	44	339	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.889	0.745	1	0.889	0.745	1	CLONAL	1	TRUE	1	0.19	2		339	521	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350090	89350090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745768322	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	114	843	2	ENST00000301030.4:c.2860G>A	p.Ala954Thr	p.A954T	ENST00000301030	NM_001256183.1	954	Gcc/Acc	9/13	1	2	FACETS	0.993	0.891	1	0.993	0.891	1	CLONAL	1	TRUE	1	0.19	2		845	1209	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446270	187446270	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	63	647	0	ENST00000232014.4:c.1418del	p.Pro473ArgfsTer117	p.P473Rfs*117	ENST00000232014	NM_001130845.1	473	cCg/cg	6/10	1	2	FACETS	0.671	0.579	0.772	0.671	0.579	0.772	SUBCLONAL	1	TRUE	1	0.19	2		647	988	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	92	621	1	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.19	2		622	903	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	32	402	0	ENST00000263967.3:c.1034A>G	p.Asn345Ser	p.N345S	ENST00000263967	NM_006218.2	345	aAt/aGt	5/21	1	2	FACETS	0.804	0.652	0.975	0.804	0.652	0.975	CLONAL	1	TRUE	1	0.19	2		402	419	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619172	1619172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374199541	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1204	105	981	2	ENST00000344749.5:c.1388C>T	p.Ala463Val	p.A463V	ENST00000344749	NM_001136139.2	463	gCg/gTg	16/19	1	2	FACETS	0.844	0.754	0.941	0.844	0.754	0.941	CLONAL	1	TRUE	1	0.19	2		983	1309	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	108	708	1	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.19	2		709	1121	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123921	46123921	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	77	300	0	ENST00000334344.6:c.186+1G>A		p.X62_splice	ENST00000334344	NM_152641.2	62			0.325514747429385	3	FACETS	0.836	0.735	0.943	0.836	0.735	0.943	CLONAL	2	TRUE	1	0.19	3		300	531	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141427	11141427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	91	704	0	ENST00000358026.2:c.3404G>A	p.Arg1135Gln	p.R1135Q	ENST00000358026	NM_001128849.1	1135	cGg/cAg	25/36	1	2	FACETS	0.96	0.85	1	0.96	0.85	1	CLONAL	1	TRUE	1	0.19	2		704	998	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126085	2126085	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs999523698	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	105	949	0	ENST00000219476.3:c.2656G>A	p.Val886Met	p.V886M	ENST00000219476	NM_000548.3	886	Gtg/Atg	24/42	1	2	FACETS	0.919	0.821	1	0.919	0.821	1	CLONAL	1	TRUE	1	0.19	2		949	1203	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	87	584	1	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	0.97	0.857	1	0.97	0.857	1	CLONAL	1	TRUE	1	0.19	2		585	944	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	82	797	10	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	0.325514747429385	1	FACETS	0.75	0.659	0.847	0.75	0.659	0.847	SUBCLONAL	1	TRUE	0	0.19	1		807	1042	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1233	112	987	1	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.877	0.786	0.973	0.877	0.786	0.973	CLONAL	1	TRUE	1	0.19	2		988	1345	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274172	10274172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567354612	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	51	510	0	ENST00000330684.3:c.97G>A	p.Ala33Thr	p.A33T	ENST00000330684	NM_001134407.1	33	Gcg/Acg	2/13	1	2	FACETS	0.942	0.8	1	0.942	0.8	1	CLONAL	1	TRUE	1	0.19	2		510	570	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70005612	70005614	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs1553704814	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	24	459	0	ENST00000394351.3:c.649_651del	p.Arg217del	p.R217del	ENST00000394351	NM_000248.3	214	cGAAga/cga	7/9	1	2	FACETS	0.538	0.42	0.673	0.538	0.42	0.673	SUBCLONAL	1	TRUE	1	0.19	2		459	470	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962899	2962899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3735134	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	84	864	1	ENST00000396946.4:c.2009C>T	p.Thr670Met	p.T670M	ENST00000396946	NM_032415.4	670	aCg/aTg	16/25	1	2	FACETS	0.756	0.665	0.853	0.756	0.665	0.853	SUBCLONAL	1	TRUE	1	0.19	2		865	1170	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465639	8465639	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	64	595	0	ENST00000356435.5:c.3541C>T	p.Arg1181Cys	p.R1181C	ENST00000356435		1181	Cgt/Tgt	21/35	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.19	2		595	625	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319354	62319354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748223349	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1157	72	808	1	ENST00000360203.5:c.1546G>A	p.Val516Ile	p.V516I	ENST00000360203	NM_001283009.1	516	Gtc/Atc	18/35	1	2	FACETS	0.617	0.537	0.704	0.617	0.537	0.704	SUBCLONAL	1	TRUE	1	0.19	2		809	1229	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856176	111856176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	123	337	1	ENST00000341259.2:c.227G>A	p.Cys76Tyr	p.C76Y	ENST00000341259	NM_005475.2	76	tGc/tAc	2/8	0.192392330117224	3	FACETS	0.807	0.73	0.89	0.807	0.73	0.89	CLONAL	2	TRUE	1	0.19	3		338	878	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913125	32913126	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs80359462	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	39	558	0	ENST00000380152.3:c.4638dup	p.Asp1547Ter	p.D1547*	ENST00000380152		1545	ctt/cTtt	11/27	1	2	FACETS	0.729	0.603	0.87	0.729	0.603	0.87	SUBCLONAL	1	TRUE	1	0.19	2		558	563	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100466	2100466	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	87	574	0	ENST00000219476.3:c.208del	p.Thr70ProfsTer36	p.T70Pfs*36	ENST00000219476	NM_000548.3	68	gcA/gc	3/42	1	2	FACETS	0.997	0.881	1	0.997	0.881	1	CLONAL	1	TRUE	1	0.19	2		574	919	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641313	3641313	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	89	678	0	ENST00000294008.3:c.2328-2A>C		p.X776_splice	ENST00000294008	NM_032444.2	776			1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.19	2		678	934	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646279	3646279	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749277750	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	112	848	1	ENST00000294008.3:c.1799C>T	p.Pro600Leu	p.P600L	ENST00000294008	NM_032444.2	600	cCg/cTg	8/15	1	2	FACETS	0.987	0.886	1	0.987	0.886	1	CLONAL	1	TRUE	1	0.19	2		849	1194	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984429	72984429	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	68	767	0	ENST00000268489.5:c.3155T>C	p.Leu1052Pro	p.L1052P	ENST00000268489	NM_006885.3	1052	cTg/cCg	3/10	1	2	FACETS	0.787	0.683	0.901	0.787	0.683	0.901	CLONAL	1	TRUE	1	0.19	2		767	909	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664493	29664493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878853908	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	89	692	1	ENST00000356175.3:c.6472C>T	p.Arg2158Cys	p.R2158C	ENST00000356175	NM_000267.3	2158	Cgt/Tgt	42/57	1	2	FACETS	0.852	0.754	0.959	0.852	0.754	0.959	CLONAL	1	TRUE	1	0.19	2		693	1099	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117728	70117728	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	121	769	0	ENST00000245479.2:c.196G>T	p.Glu66Ter	p.E66*	ENST00000245479	NM_000346.3	66	Gag/Tag	1/3	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.19	2		769	1024	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615719	1615720	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTC	novel	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	83	918	0	ENST00000344749.5:c.1549_1551dup	p.Glu517dup	p.E517dup	ENST00000344749	NM_001136139.2	517	-/GAG	17/19	1	2	FACETS	0.724	0.637	0.818	0.724	0.637	0.818	SUBCLONAL	1	TRUE	1	0.19	2		918	1207	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285200	212285200	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	50	571	0	ENST00000342788.4:c.3101T>C	p.Ile1034Thr	p.I1034T	ENST00000342788	NM_005235.2	1034	aTc/aCc	25/28	1	2	FACETS	0.989	0.839	1	0.989	0.839	1	CLONAL	1	TRUE	1	0.19	2		571	532	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143043396	143043396	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs554325579	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	39	398	0	ENST00000262992.4:c.2020G>A	p.Asp674Asn	p.D674N	ENST00000262992	NM_001101669.1	674	Gat/Aat	19/24	1	2	FACETS	0.918	0.761	1	0.918	0.761	1	CLONAL	1	TRUE	1	0.19	2		398	447	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589000	67589000	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	34	328	0	ENST00000274335.5:c.1091T>C	p.Met364Thr	p.M364T	ENST00000274335		364	aTg/aCg	8/15	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.19	2		328	330	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687056	176687056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	92	623	0	ENST00000439151.2:c.5033G>A	p.Gly1678Glu	p.G1678E	ENST00000439151	NM_022455.4	1678	gGg/gAg	14/23	1	2	FACETS	0.909	0.806	1	0.909	0.806	1	CLONAL	1	TRUE	1	0.19	2		623	1065	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680686	30680686	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	77	692	0	ENST00000376406.3:c.1033A>G	p.Ile345Val	p.I345V	ENST00000376406	NM_014641.2	345	Att/Gtt	5/15	1	2	FACETS	0.844	0.739	0.958	0.844	0.739	0.958	CLONAL	1	TRUE	1	0.19	2		692	960	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120606	94120606	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	47	577	0	ENST00000369303.4:c.445A>G	p.Ile149Val	p.I149V	ENST00000369303	NM_004440.3	149	Att/Gtt	3/17	1	2	FACETS	0.743	0.626	0.873	0.743	0.626	0.873	SUBCLONAL	1	TRUE	1	0.19	2		577	666	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380116	116380116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	74	622	1	ENST00000397752.3:c.1505C>T	p.Thr502Ile	p.T502I	ENST00000397752	NM_000245.2	502	aCa/aTa	4/21	1	2	FACETS	0.955	0.834	1	0.955	0.834	1	CLONAL	1	TRUE	1	0.19	2		623	816	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538738	23538739	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	32	344	0	ENST00000380871.4:c.700dup	p.Trp234LeufsTer61	p.W234Lfs*61	ENST00000380871	NM_006167.3	234	tgg/tTgg	2/2	1	2	FACETS	0.868	0.705	1	0.868	0.705	1	CLONAL	1	TRUE	1	0.19	2		344	388	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393622	139393622	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	123	917	0	ENST00000277541.6:c.6024G>T	p.Glu2008Asp	p.E2008D	ENST00000277541	NM_017617.3	2008	gaG/gaT	32/34	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.19	2		917	1225	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356745	70356745	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368093012	NA	P-0036860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	81	655	2	ENST00000374080.3:c.5417C>T	p.Pro1806Leu	p.P1806L	ENST00000374080		1806	cCg/cTg	38/45	0.0808020433059023	0	FACETS	0.768	0.675	0.868			1	INDETERMINATE	1	TRUE	0	0.19	0		657	899	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0036864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	51	617	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		617	800	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0036867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	182	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.921	0.854	0.99	0.921	0.854	0.99	CLONAL	1	TRUE	1	0.629216823908078	2		502	628	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163298694	163298694	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	680	554	0	ENST00000271452.3:c.334C>T	p.Pro112Ser	p.P112S	ENST00000271452	NM_145697.2	112	Cca/Tca	5/14	0.622902967564161	4	FACETS	0.994	0.964	1	0.994	0.964	1	CLONAL	3	TRUE	1	0.629216823908078	4		554	1181	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988334	36988334	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	134	414	1	ENST00000354822.5:c.319C>T	p.Gln107Ter	p.Q107*	ENST00000354822	NM_001079668.2	107	Cag/Tag	2/3	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.629216823908078	2		415	411	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100971	41100971	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	90	551	0	ENST00000373198.4:c.1385T>C	p.Leu462Pro	p.L462P	ENST00000373198	NM_133170.3	462	cTc/cCc	8/32	0.622278167854372	2	FACETS	0.502	0.446	0.561	0.251	0.223	0.281	SUBCLONAL	1	TRUE	0	0.629216823908078	2		551	570	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747970	41747970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	53	135	0	ENST00000226382.2:c.799G>A	p.Gly267Arg	p.G267R	ENST00000226382	NM_003924.3	267	Ggg/Agg	3/3	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.629216823908078	2		135	162	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637362	47637362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	203	738	0	ENST00000233146.2:c.496G>A	p.Val166Met	p.V166M	ENST00000233146	NM_000251.2	166	Gtg/Atg	3/16	1	2	FACETS	0.962	0.892	1	0.962	0.892	1	CLONAL	1	TRUE	1	0.434365540939017	2		738	972	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441324	52441328	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTC	GGCTC	-	novel	NA	P-0036871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	117	545	0	ENST00000460680.1:c.442_446del	p.Glu148ThrfsTer5	p.E148Tfs*5	ENST00000460680	NM_004656.3	148	GAGCCa/a	7/17	0.414087635669769	1	FACETS	0.824	0.746	0.905	0.824	0.746	0.905	CLONAL	1	TRUE	0	0.434365540939017	1		545	512	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0036875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	94	460	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.715	0.636	0.799	0.715	0.636	0.799	SUBCLONAL	1	TRUE	1	0.359113585322047	2		460	732	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0036875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	39	458	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.441	0.365	0.526	0.441	0.365	0.526	SUBCLONAL	1	TRUE	1	0.359113585322047	2		458	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0036875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	173	520	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.359113585322047	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.359113585322047	1		520	716	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393701	139393701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763052700	NA	P-0036875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	158	596	0	ENST00000277541.6:c.5945G>A	p.Arg1982Gln	p.R1982Q	ENST00000277541	NM_017617.3	1982	cGg/cAg	32/34	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.359113585322047	2		596	835	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949056	44949056	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	160	281	0	ENST00000377967.4:c.3617C>T	p.Pro1206Leu	p.P1206L	ENST00000377967	NM_021140.2	1206	cCa/cTa	25/29	1	1	FACETS	0.87	0.807	0.935	1	0.992	1	CLONAL	2	TRUE	0	0.359113585322047	1		281	420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0036876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	285	658	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	0.164782791747826	1	FACETS	1	0.991	1	1	0.991	1	INDETERMINATE	1	TRUE	0	0.407223017612392	1		658	885	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164061	106164061	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	58	358	0	ENST00000380013.4:c.3571C>G	p.Gln1191Glu	p.Q1191E	ENST00000380013	NM_001127208.2	1191	Cag/Gag	5/11	1	2	FACETS	0.611	0.526	0.704	0.611	0.526	0.704	SUBCLONAL	1	TRUE	1	0.407223017612392	2		358	466	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830976	72830976	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	55	558	0	ENST00000268489.5:c.5605C>T	p.Gln1869Ter	p.Q1869*	ENST00000268489	NM_006885.3	1869	Cag/Tag	9/10	0.2060549679767	3	FACETS	0.418	0.356	0.485	0.139	0.118	0.162	INDETERMINATE	1	TRUE	0	0.407223017612392	3		558	778	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629120	187629120	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370787232	NA	P-0036876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	68	570	0	ENST00000441802.2:c.1862C>T	p.Ser621Leu	p.S621L	ENST00000441802	NM_005245.3	621	tCg/tTg	2/27	1	2	FACETS	0.433	0.376	0.495	0.433	0.376	0.495	SUBCLONAL	1	TRUE	1	0.407223017612392	2		570	772	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829754	72829754	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	91	729	0	ENST00000268489.5:c.6827C>G	p.Ser2276Cys	p.S2276C	ENST00000268489	NM_006885.3	2276	tCt/tGt	9/10	0.2060549679767	3	FACETS	0.515	0.456	0.579	0.172	0.152	0.193	INDETERMINATE	1	TRUE	0	0.407223017612392	3		729	1044	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830987	72830987	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	59	561	0	ENST00000268489.5:c.5594C>T	p.Ser1865Phe	p.S1865F	ENST00000268489	NM_006885.3	1865	tCt/tTt	9/10	0.2060549679767	3	FACETS	0.44	0.377	0.508	0.147	0.125	0.17	INDETERMINATE	1	TRUE	0	0.407223017612392	3		561	793	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831842	72831842	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	106	832	0	ENST00000268489.5:c.4739C>A	p.Ser1580Ter	p.S1580*	ENST00000268489	NM_006885.3	1580	tCa/tAa	9/10	0.25195792425582	2	FACETS	0.436	0.39	0.486	0.218	0.195	0.243	SUBCLONAL	1	TRUE	0	0.407223017612392	2		832	1193	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751601	57751601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	36	261	2	ENST00000274289.3:c.1390G>A	p.Glu464Lys	p.E464K	ENST00000274289	NM_006622.3	464	Gaa/Aaa	11/14	0.257441758571762	3	FACETS	0.531	0.436	0.636	0.265	0.218	0.318	SUBCLONAL	1	TRUE	1	0.407223017612392	3		263	401	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041078	180041078	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	78	692	0	ENST00000261937.6:c.3321C>G	p.Ile1107Met	p.I1107M	ENST00000261937	NM_182925.4	1107	atC/atG	24/30	NA	2	FACETS	0.467	0.409	0.529			1	INDETERMINATE	1	TRUE	NA	0.407223017612392	2		692	821	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0036879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	20	451	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.422453921566524	3	FACETS	0.506	0.39	0.64	0.253	0.195	0.32	SUBCLONAL	1	FALSE	1	0.696158862258046	3		451	153	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692910	89692910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	21	623	0	ENST00000371953.3:c.394G>A	p.Gly132Ser	p.G132S	ENST00000371953	NM_000314.4	132	Ggt/Agt	5/9	0.422453921566524	3	FACETS	0.442	0.342	0.557	0.221	0.171	0.279	SUBCLONAL	1	FALSE	1	0.696158862258046	3		623	184	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579488	7579489	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0036879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	50	804	0	ENST00000269305.4:c.198dup	p.Pro67AlafsTer82	p.P67Afs*82	ENST00000269305	NM_001126112.2	66	-/G	4/11	0.422453921566524	3	FACETS	0.629	0.536	0.729	0.314	0.268	0.365	SUBCLONAL	1	FALSE	1	0.696158862258046	3		804	308	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527560	29527560	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs747241884	NA	P-0036879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	30	696	0	ENST00000356175.3:c.1009G>T	p.Glu337Ter	p.E337*	ENST00000356175	NM_000267.3	337	Gaa/Taa	9/57	0.422453921566524	3	FACETS	0.656	0.534	0.792	0.328	0.267	0.396	SUBCLONAL	1	FALSE	1	0.696158862258046	3		696	177	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0036880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	67	350	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.272336133221795	2		350	391	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936096	178936096	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	45	712	0	ENST00000263967.3:c.1638G>C	p.Gln546His	p.Q546H	ENST00000263967	NM_006218.2	546	caG/caC	10/21	0.194992819790968	3	FACETS	1	0.855	1	1	0.855	1	CLONAL	2	TRUE	1	0.272336133221795	3		712	187	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50830331	50830331	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	54	604	1	ENST00000398568.2:c.2775del	p.Arg926GlyfsTer24	p.R926Gfs*24	ENST00000398568	NM_001042412.1	925	tCc/tc	18/18	0.272336133221795	1	FACETS	0.982	0.842	1	0.982	0.842	1	CLONAL	1	TRUE	0	0.272336133221795	1		605	349	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508797	29508797	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	20	511	0	ENST00000356175.3:c.724A>T	p.Met242Leu	p.M242L	ENST00000356175	NM_000267.3	242	Atg/Ttg	7/57	0.126107031641775	3	FACETS	0.888	0.682	1	0.444	0.341	0.563	INDETERMINATE	1	TRUE	1	0.272336133221795	3		511	188	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0036881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	95	438	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.160087531727597	2	FACETS	0.787	0.708	0.871	0.787	0.708	0.871	INDETERMINATE	2	TRUE	0	0.345732874484919	2		438	349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0036881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	104	745	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.302829697900573	1	FACETS	0.807	0.724	0.894	0.807	0.724	0.894	CLONAL	1	TRUE	0	0.345732874484919	1		745	617	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0036881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	148	575	0	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	TRUE	1	0.345732874484919	2		575	724	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990481	69990481	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs201247895	NA	P-0036881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	41	501	0	ENST00000394351.3:c.440C>T	p.Thr147Met	p.T147M	ENST00000394351	NM_000248.3	147	aCg/aTg	4/9	1	2	FACETS	0.494	0.411	0.586	0.494	0.411	0.586	SUBCLONAL	1	TRUE	1	0.345732874484919	2		501	480	SUCCESS
APC	324	MSKCC	GRCh37	5	112090657	112090657	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs145945630	NA	P-0036881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	78	372	1	ENST00000257430.4:c.70C>T	p.Arg24Ter	p.R24*	ENST00000257430	NM_000038.5	24	Cga/Tga	2/16	0.160087531727597	2	FACETS	1	0.964	1	0.616	0.545	0.692	INDETERMINATE	1	TRUE	0	0.345732874484919	2		373	366	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224532	36224532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759167832	NA	P-0036881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	149	965	2	ENST00000222270.7:c.6994C>T	p.Arg2332Cys	p.R2332C	ENST00000222270	NM_014727.1	2332	Cgt/Tgt	29/37	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.345732874484919	2		967	768	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851561	63851561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567464868	NA	P-0036881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	130	683	0	ENST00000279873.7:c.2339G>A	p.Arg780Gln	p.R780Q	ENST00000279873	NM_032199.2	780	cGa/cAa	10/10	0.131423396962772	3	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.345732874484919	3		683	652	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43745205	43745205	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0036881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	111	606	0	ENST00000523873.1:c.119-1G>A		p.X40_splice	ENST00000523873		40			0.16037029070106	3	FACETS	1	0.977	1	0.649	0.585	0.717	INDETERMINATE	1	TRUE	1	0.345732874484919	3		606	580	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856065	111856065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778004604	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	102	191	0	ENST00000341259.2:c.116G>A	p.Arg39Gln	p.R39Q	ENST00000341259	NM_005475.2	39	cGg/cAg	2/8	1	2	FACETS	0.57	0.513	0.63	0.57	0.513	0.63	SUBCLONAL	1	TRUE	1	0.84	2		191	426	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	293	264	0	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.84	2		264	629	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	440	415	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	0.84	2		416	1048	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	196	287	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.807	0.752	0.864	0.807	0.752	0.864	CLONAL	1	TRUE	1	0.84	2		287	578	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	349	372	8	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	0.975	0.928	1	0.975	0.928	1	CLONAL	1	TRUE	1	0.84	2		380	852	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	356	361	3	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	0.84	2		364	806	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	175	368	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.518	0.477	0.56	0.518	0.477	0.56	SUBCLONAL	1	TRUE	1	0.84	2		368	805	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	377	345	1	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	0.969	1	CLONAL	1	TRUE	1	0.84	2		346	880	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144049	11144051	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	352	405	0	ENST00000358026.2:c.3634_3636del	p.Glu1212del	p.E1212del	ENST00000358026	NM_001128849.1	1210	gtGGAg/gtg	26/36	1	2	FACETS	0.91	0.865	0.956	0.91	0.865	0.956	CLONAL	1	TRUE	1	0.84	2		405	921	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	341	421	3	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	0.925	0.878	0.972	0.925	0.878	0.972	CLONAL	1	TRUE	1	0.84	2		424	878	SUCCESS
AR	367	MSKCC	GRCh37	X	66766424	66766424	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	92	46	0	ENST00000374690.3:c.1440del	p.Tyr481ThrfsTer29	p.Y481Tfs*29	ENST00000374690	NM_000044.3	479	gCc/gc	1/8	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.84	1		46	107	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286237	66286238	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	141	322	0	ENST00000273854.3:c.1448dup	p.Asn483LysfsTer21	p.N483Kfs*21	ENST00000273854	NM_004439.5	483	aac/aaAc	6/18	1	2	FACETS	0.454	0.414	0.496	0.454	0.414	0.496	SUBCLONAL	1	TRUE	1	0.84	2		322	740	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472603	88472603	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	257	341	0	ENST00000360948.2:c.1952T>G	p.Leu651Arg	p.L651R	ENST00000360948	NM_001012338.2	651	cTg/cGg	16/19	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.84	2		341	573	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795609	42795609	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	443	465	2	ENST00000575354.2:c.2694del	p.Ala900ProfsTer24	p.A900Pfs*24	ENST00000575354	NM_015125.3	897	Ccc/cc	10/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.84	2		467	1034	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	371	395	0	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.924	0.88	0.969	0.924	0.88	0.969	CLONAL	1	TRUE	1	0.84	2		395	956	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528372	157528372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	422	423	1	ENST00000346085.5:c.6097G>A	p.Gly2033Arg	p.G2033R	ENST00000346085	NM_020732.3	2033	Ggg/Agg	20/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.84	2		424	974	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424178	49424178	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs886040960	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	198	235	0	ENST00000301067.7:c.13884del	p.Thr4629ProfsTer11	p.T4629Pfs*11	ENST00000301067	NM_003482.3	4628	ccC/cc	42/54	1	2	FACETS	0.809	0.754	0.865	0.809	0.754	0.865	CLONAL	1	TRUE	1	0.84	2		235	583	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368388	225368388	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1366667901	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	276	346	0	ENST00000264414.4:c.1358del	p.Asn453ThrfsTer2	p.N453Tfs*2	ENST00000264414	NM_003590.4	453	aAc/ac	9/16	1	2	FACETS	0.876	0.827	0.926	0.876	0.827	0.926	CLONAL	1	TRUE	1	0.84	2		346	750	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	383	470	1	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	1	2	FACETS	0.803	0.764	0.844	0.803	0.764	0.844	CLONAL	1	TRUE	1	0.84	2		471	1135	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	739	382	12	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	1	2	FACETS	0.841	0.821	0.861	1	0.998	1	CLONAL	2	TRUE	1	0.84	2		394	1046	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981903	70981903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747860295	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	375	410	0	ENST00000276594.2:c.193G>A	p.Ala65Thr	p.A65T	ENST00000276594	NM_024504.3	65	Gcc/Acc	2/8	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.84	2		410	885	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43699735	43699735	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137879443	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	305	348	0	ENST00000382044.4:c.5780C>T	p.Thr1927Met	p.T1927M	ENST00000382044	NM_001141980.1	1927	aCg/aTg	28/28	1	2	FACETS	0.958	0.908	1	0.958	0.908	1	CLONAL	1	TRUE	1	0.84	2		348	758	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428542	78428543	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	421	407	0	ENST00000370768.2:c.1256dup	p.Asn419LysfsTer5	p.N419Kfs*5	ENST00000370768	NM_003902.3	419	aat/aaAt	14/20	1	2	FACETS	0.977	0.934	1	0.977	0.934	1	CLONAL	1	TRUE	1	0.84	2		407	1026	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443943	18443943	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1454100925	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	211	292	0	ENST00000266497.5:c.916T>C	p.Cys306Arg	p.C306R	ENST00000266497		306	Tgt/Cgt	3/31	1	2	FACETS	0.904	0.846	0.962	0.904	0.846	0.962	CLONAL	1	TRUE	1	0.84	2		292	556	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434246	49434247	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	501	605	0	ENST00000301067.7:c.7306dup	p.Cys2436LeufsTer13	p.C2436Lfs*13	ENST00000301067	NM_003482.3	2436	tgc/tTgc	31/54	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.84	2		605	1193	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891184	112891184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369155025	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	200	411	0	ENST00000351677.2:c.518G>A	p.Arg173His	p.R173H	ENST00000351677	NM_002834.3	173	cGc/cAc	4/16	1	2	FACETS	0.541	0.501	0.581	0.541	0.501	0.581	SUBCLONAL	1	TRUE	1	0.84	2		411	881	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708473	43708473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	489	470	0	ENST00000382044.4:c.4823G>A	p.Gly1608Asp	p.G1608D	ENST00000382044	NM_001141980.1	1608	gGc/gAc	22/28	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.84	2		470	1106	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346637	89346637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755913170	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	249	290	0	ENST00000301030.4:c.6313G>A	p.Gly2105Ser	p.G2105S	ENST00000301030	NM_001256183.1	2105	Ggc/Agc	9/13	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.84	2		290	576	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864614	37864614	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	198	383	0	ENST00000269571.5:c.266A>G	p.Asn89Ser	p.N89S	ENST00000269571		89	aAc/aGc	3/27	1	2	FACETS	0.556	0.515	0.598	0.556	0.515	0.598	SUBCLONAL	1	TRUE	1	0.84	2		383	848	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763404	59763404	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	199	433	0	ENST00000259008.2:c.2698A>G	p.Thr900Ala	p.T900A	ENST00000259008	NM_032043.2	900	Acc/Gcc	19/20	1	2	FACETS	0.44	0.407	0.475	0.44	0.407	0.475	SUBCLONAL	1	TRUE	1	0.84	2		433	1076	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533066	63533066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776445861	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	368	425	0	ENST00000307078.5:c.1828C>T	p.Arg610Trp	p.R610W	ENST00000307078	NM_004655.3	610	Cgg/Tgg	7/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.84	2		425	836	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732278	74732279	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	110	179	0	ENST00000359995.5:c.630dup	p.Lys211GlnfsTer4	p.K211Qfs*4	ENST00000359995	NM_001195427.1	210	-/C	2/3	1	2	FACETS	0.564	0.51	0.622	0.564	0.51	0.622	SUBCLONAL	1	TRUE	1	0.84	2		179	464	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795607	42795609	+	frameshift_variant	Frame_Shift_Del	DEL	CAC	CAC	GA	novel	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	443	481	3	ENST00000575354.2:c.2687_2689delinsGA	p.Pro896ArgfsTer28	p.P896Rfs*28	ENST00000575354	NM_015125.3	896	cCACcc/cGAcc	10/20	1	2	FACETS	0.995	0.952	1	0.995	0.952	1	CLONAL	1	TRUE	1	0.84	2		484	1060	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634719	158634719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755732603	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	264	312	1	ENST00000263640.3:c.467G>A	p.Arg156His	p.R156H	ENST00000263640	NM_001105.4	156	cGc/cAc	5/11	1	2	FACETS	0.972	0.917	1	0.972	0.917	1	CLONAL	1	TRUE	1	0.84	2		313	647	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437287	220437288	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1190141661	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	182	553	3	ENST00000243786.2:c.197dup	p.Phe67LeufsTer7	p.F67Lfs*7	ENST00000243786	NM_002191.3	64	ctg/ctGg	1/2	1	2	FACETS	0.391	0.36	0.423	0.391	0.36	0.423	SUBCLONAL	1	TRUE	1	0.84	2		556	1108	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37055922	37055922	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs267607784	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	161	177	0	ENST00000231790.2:c.678-1G>A		p.X226_splice	ENST00000231790	NM_000249.3	226			1	2	FACETS	0.921	0.855	0.989	0.921	0.855	0.989	CLONAL	1	TRUE	1	0.84	2		177	416	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131978039	131978039	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	320	348	1	ENST00000265335.6:c.3922G>T	p.Gly1308Ter	p.G1308*	ENST00000265335		1308	Gga/Tga	25/25	1	2	FACETS	0.96	0.911	1	0.96	0.911	1	CLONAL	1	TRUE	1	0.84	2		349	794	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710638	117710638	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs991227380	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	211	269	0	ENST00000368508.3:c.1634T>C	p.Leu545Ser	p.L545S	ENST00000368508	NM_002944.2	545	tTg/tCg	12/43	1	2	FACETS	0.957	0.897	1	0.957	0.897	1	CLONAL	1	TRUE	1	0.84	2		269	525	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845645	151845647	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	382	373	0	ENST00000262189.6:c.13365_13367del	p.Arg4456del	p.R4456del	ENST00000262189	NM_170606.2	4455	agGAGa/aga	52/59	1	2	FACETS	0.996	0.95	1	0.996	0.95	1	CLONAL	1	TRUE	1	0.84	2		373	913	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020373	69020373	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs781779558	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	368	378	0	ENST00000288368.4:c.2745G>A	p.Trp915Ter	p.W915*	ENST00000288368	NM_024870.2	915	tgG/tgA	24/40	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.84	2		378	827	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417562	139417562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	422	457	1	ENST00000277541.6:c.482C>T	p.Ser161Phe	p.S161F	ENST00000277541	NM_017617.3	161	tCc/tTc	4/34	1	2	FACETS	0.98	0.937	1	0.98	0.937	1	CLONAL	1	TRUE	1	0.84	2		458	1025	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	211	388	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.704563003722199	2		388	570	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0036884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	234	376	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.322696994620145	2	FACETS	1	0.955	1	0.511	0.479	0.543	INDETERMINATE	1	TRUE	0	0.704563003722199	2		376	650	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0036884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	250	478	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	0.144037904874071	5	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.704563003722199	5		478	989	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599332	55599332	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519710	NA	P-0036884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	188	556	0	ENST00000288135.5:c.2458G>T	p.Asp820Tyr	p.D820Y	ENST00000288135	NM_000222.2	820	Gat/Tat	17/21	0.704563003722199	3	FACETS	0.569	0.524	0.615			1	SUBCLONAL	1	TRUE	NA	0.704563003722199	3		556	1269	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599333	55599333	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913682	NA	P-0036884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	624	554	2	ENST00000288135.5:c.2459A>T	p.Asp820Val	p.D820V	ENST00000288135	NM_000222.2	820	gAt/gTt	17/21	0.704563003722199	3	FACETS	0.947	0.915	0.979			1	CLONAL	2	TRUE	NA	0.704563003722199	3		556	1265	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835975	151835975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	282	540	1	ENST00000262189.6:c.14549C>T	p.Ser4850Leu	p.S4850L	ENST00000262189	NM_170606.2	4850	tCg/tTg	58/59	0.385811198210434	3	FACETS	1	0.979	1	0.543	0.511	0.576	INDETERMINATE	1	TRUE	1	0.704563003722199	3		541	997	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009294	69009294	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	124	577	1	ENST00000288368.4:c.2411A>T	p.Lys804Met	p.K804M	ENST00000288368	NM_024870.2	804	aAg/aTg	22/40	0.189695946513605	4	FACETS	0.676	0.611	0.744	0.225	0.203	0.248	INDETERMINATE	1	TRUE	1	0.704563003722199	4		578	888	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0036887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	705	484	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.322177172127719	9	FACETS	0.985	0.956	1	1	0.995	1	CLONAL	8	TRUE	2	0.322177172127719	9		484	1182	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578445	7578450	+	inframe_deletion	In_Frame_Del	DEL	ATGGCC	ATGGCC	-	novel	NA	P-0036887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	372	663	0	ENST00000269305.4:c.480_485del	p.Met160_Ala161del	p.M160_A161del	ENST00000269305	NM_001126112.2	160	atGGCCATc/atc	5/11	0.322177172127719	3	FACETS	0.958	0.912	1	0.958	0.912	1	CLONAL	3	TRUE	0	0.322177172127719	3		663	933	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488730	212488730	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	333	579	0	ENST00000342788.4:c.2119C>A	p.Gln707Lys	p.Q707K	ENST00000342788	NM_005235.2	707	Caa/Aaa	18/28	0.322177172127719	5	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	2	0.322177172127719	5		579	927	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421569	32421569	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	208	504	1	ENST00000332351.3:c.1023C>A	p.Ser341Arg	p.S341R	ENST00000332351	NM_024426.4	341	agC/agA	6/10	0.322177172127719	3	FACETS	0.852	0.792	0.914	0.852	0.792	0.914	CLONAL	2	TRUE	1	0.322177172127719	3		505	880	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61727007	61727007	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	63	509	0	ENST00000401558.2:c.431A>C	p.Lys144Thr	p.K144T	ENST00000401558	NM_003400.3	144	aAa/aCa	7/25	0.142993996766554	4	FACETS	0.871	0.753	0.998	0.435	0.376	0.499	INDETERMINATE	1	TRUE	2	0.322177172127719	4		509	594	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593546	215593546	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1559372004	NA	P-0036887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	49	367	0	ENST00000260947.4:c.2188C>G	p.Gln730Glu	p.Q730E	ENST00000260947	NM_000465.2	730	Cag/Gag	11/11	0.322177172127719	5	FACETS	0.748	0.633	0.875	0.249	0.211	0.292	SUBCLONAL	1	TRUE	2	0.322177172127719	5		367	603	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321361	1321361	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763768038	NA	P-0036887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	129	456	0	ENST00000400841.2:c.394G>A	p.Asp132Asn	p.D132N	ENST00000400841		132	Gat/Aat	4/6	0.161603036270591	2	FACETS	1	0.984	1	0.705	0.642	0.771	INDETERMINATE	1	TRUE	0	0.322177172127719	2		456	568	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0036889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	53	236	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.799938377224577	2		236	127	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781504	NA	P-0036889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	490	556	0	ENST00000269305.4:c.314G>T	p.Gly105Val	p.G105V	ENST00000269305	NM_001126112.2	105	gGc/gTc	4/11	0.799938377224577	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.799938377224577	2		556	585	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939666	76939669	+	frameshift_variant	Frame_Shift_Del	DEL	TCAA	TCAA	-	novel	NA	P-0036889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	115	318	0	ENST00000373344.5:c.1079_1082del	p.Ile360ArgfsTer6	p.I360Rfs*6	ENST00000373344	NM_000489.3	360	aTTGAg/ag	9/35	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.799938377224577	1		318	133	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0036907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	120	880	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.312357696013242	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.312357696013242	1		882	633	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	56	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.944	0.812	1	0.944	0.812	1	CLONAL	1	TRUE	1	0.312357696013242	2		148	380	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953730	48953730	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs3092891	NA	P-0036907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	42	293	1	ENST00000267163.4:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000267163	NM_000321.2	445	Cga/Tga	14/27	0.312357696013242	1	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	TRUE	0	0.312357696013242	1		294	224	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245787	46245787	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0036907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	41	490	1	ENST00000334344.6:c.3881T>G	p.Leu1294Ter	p.L1294*	ENST00000334344	NM_152641.2	1294	tTa/tGa	15/21	1	2	FACETS	0.994	0.834	1	0.994	0.834	1	CLONAL	1	TRUE	1	0.312357696013242	2		491	264	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246641	46246641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	12	242	1	ENST00000334344.6:c.4735C>T	p.Gln1579Ter	p.Q1579*	ENST00000334344	NM_152641.2	1579	Cag/Tag	15/21	1	2	FACETS	0.434	0.305	0.592	0.434	0.305	0.592	SUBCLONAL	1	TRUE	1	0.312357696013242	2		243	177	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99491930	99491930	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	110	704	1	ENST00000268035.6:c.3715G>C	p.Asp1239His	p.D1239H	ENST00000268035	NM_000875.3	1239	Gac/Cac	20/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.312357696013242	2		705	520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0036909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	236	767	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.306120556113385	2	FACETS	0.798	0.747	0.85	0.798	0.747	0.85	SUBCLONAL	2	TRUE	0	0.391315926501794	2		767	756	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28929495	NA	P-0036909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	231	610	0	ENST00000275493.2:c.2155G>T	p.Gly719Cys	p.G719C	ENST00000275493	NM_005228.3	719	Ggc/Tgc	18/28	0.271644411105276	4	FACETS	0.899	0.839	0.96	0.899	0.839	0.96	CLONAL	2	TRUE	2	0.391315926501794	4		610	914	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242470	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs397517097	NA	P-0036909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	160	426	0	ENST00000275493.2:c.2240T>C	p.Leu747Ser	p.L747S	ENST00000275493	NM_005228.3	747	tTa/tCa	19/28	0.271644411105276	4	FACETS	0.83	0.764	0.9	0.83	0.764	0.9	CLONAL	2	TRUE	2	0.391315926501794	4		426	685	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510648	38510648	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	238	635	1	ENST00000254066.5:c.902G>T	p.Gly301Val	p.G301V	ENST00000254066	NM_000964.3	301	gGc/gTc	7/9	0.146775068220016	5	FACETS	1	0.962	1	0.695	0.649	0.742	INDETERMINATE	2	TRUE	2	0.391315926501794	5		636	926	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0036910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	152	387	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.9	0.827	0.976	0.9	0.827	0.976	CLONAL	1	TRUE	1	0.569376857945352	2		387	593	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89809209	89809209	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs373998809	NA	P-0036910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	107	603	0	ENST00000389301.3:c.3764A>C	p.Glu1255Ala	p.E1255A	ENST00000389301	NM_000135.2	1255	gAg/gCg	37/43	NA	2	FACETS	0.542	0.487	0.601			1	INDETERMINATE	1	TRUE	NA	0.569376857945352	2		603	693	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743868	41743868	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	198	745	0	ENST00000301178.4:c.803G>T	p.Gly268Val	p.G268V	ENST00000301178	NM_021913.4	268	gGg/gTg	7/20	1	2	FACETS	0.899	0.834	0.965	0.899	0.834	0.965	CLONAL	1	TRUE	1	0.569376857945352	2		745	774	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913534	39913534	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	171	507	1	ENST00000378444.4:c.4794G>A	p.Trp1598Ter	p.W1598*	ENST00000378444	NM_001123385.1	1598	tgG/tgA	13/15	0.569376857945352	1	FACETS	0.922	0.856	0.989	0.922	0.856	0.989	CLONAL	1	TRUE	0	0.569376857945352	1		508	466	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247168	153247168	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1560758208	NA	P-0036911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	130	284	0	ENST00000281708.4:c.1634A>G	p.Tyr545Cys	p.Y545C	ENST00000281708	NM_033632.3	545	tAt/tGt	10/12	0.415609020560853	3	FACETS	0.937	0.859	1	0.937	0.859	1	CLONAL	2	TRUE	1	0.415609020560853	3		284	403	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427438	49427438	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	84	840	0	ENST00000301067.7:c.11050C>T	p.Gln3684Ter	p.Q3684*	ENST00000301067	NM_003482.3	3684	Caa/Taa	39/54	1	2	FACETS	0.888	0.788	0.995	0.888	0.788	0.995	CLONAL	1	TRUE	1	0.415609020560853	2		840	455	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245344	153245345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	117	496	0	ENST00000281708.4:c.1846dup	p.Thr616AsnfsTer28	p.T616Nfs*28	ENST00000281708	NM_033632.3	616	aca/aAca	11/12	0.415609020560853	3	FACETS	0.933	0.842	1	0.466	0.421	0.515	CLONAL	1	TRUE	1	0.415609020560853	3		496	729	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692822	89692823	+	missense_variant	Missense_Mutation	DNP	AC	AC	CT	novel	NA	P-0036912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	51	273	0	ENST00000371953.3:c.306_307delinsCT	p.Lys102_Pro103delinsAsnSer	p.K102_P103delinsNS	ENST00000371953	NM_000314.4	102	aaACcc/aaCTcc	5/9	0.634342024141973	2	FACETS	0.613	0.526	0.706	0.306	0.263	0.353	SUBCLONAL	1	TRUE	0	0.682040646699814	2		273	244	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727855	41727855	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	40	786	0	ENST00000301178.4:c.480C>G	p.Cys160Trp	p.C160W	ENST00000301178	NM_021913.4	160	tgC/tgG	4/20	0.682040646699814	2	FACETS	0.259	0.215	0.308	0.129	0.107	0.154	SUBCLONAL	1	TRUE	0	0.682040646699814	2		786	453	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	99	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.89101800173901	2		148	191	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057520000	NA	P-0036913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	326	523	0	ENST00000269305.4:c.452C>A	p.Pro151His	p.P151H	ENST00000269305	NM_001126112.2	151	cCc/cAc	5/11	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.89101800173901	2		523	690	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0036913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	155	212	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	1	2	FACETS	0.986	0.916	1	0.986	0.916	1	CLONAL	1	TRUE	1	0.89101800173901	2		212	353	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73113168	73113168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	77	94	0	ENST00000356692.5:c.509G>A	p.Gly170Glu	p.G170E	ENST00000356692		170	gGg/gAg	7/9	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.89101800173901	2		94	161	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436149	116436149	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200315561	NA	P-0036913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	213	329	0	ENST00000397752.3:c.4144C>T	p.Arg1382Ter	p.R1382*	ENST00000397752	NM_000245.2	1382	Cga/Tga	21/21	0.882098459599983	3	FACETS	0.931	0.868	0.996	0.466	0.434	0.498	CLONAL	1	TRUE	1	0.89101800173901	3		329	742	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328444	137328444	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	308	487	0	ENST00000481739.1:c.1373C>G	p.Pro458Arg	p.P458R	ENST00000481739	NM_002957.4	458	cCg/cGg	10/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.89101800173901	2		487	644	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76953102	76953102	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	13	439	0	ENST00000373344.5:c.211T>C	p.Ser71Pro	p.S71P	ENST00000373344	NM_000489.3	71	Tcc/Ccc	4/35	0.404684040343929	3	FACETS	0.19	0.135	0.257	0.095	0.067	0.129	INDETERMINATE	1	TRUE	1	0.758921365749232	3		439	249	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0036923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	51	494	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.887	0.756	1	0.887	0.756	1	CLONAL	1	TRUE	1	0.293484828279075	2		495	392	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0036923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	25	380	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.581	0.459	0.722	0.581	0.459	0.722	SUBCLONAL	1	TRUE	1	0.293484828279075	2		380	293	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939409	76939409	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	62	690	0	ENST00000373344.5:c.1339G>A	p.Glu447Lys	p.E447K	ENST00000373344	NM_000489.3	447	Gaa/Aaa	9/35	0.504322278189171	2	FACETS	1	0.922	1	0.537	0.47	0.608	CLONAL	1	TRUE	0	0.504322278189171	2		690	229	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478106	99478106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	205	327	0	ENST00000268035.6:c.3010G>A	p.Glu1004Lys	p.E1004K	ENST00000268035	NM_000875.3	1004	Gaa/Aaa	16/21	0.504322278189171	3	FACETS	0.863	0.814	0.913	1	0.991	1	CLONAL	3	TRUE	1	0.504322278189171	3		327	393	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349717	89349717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753662123	NA	P-0036929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	68	694	0	ENST00000301030.4:c.3233C>T	p.Ala1078Val	p.A1078V	ENST00000301030	NM_001256183.1	1078	gCg/gTg	9/13	0.348265614147625	5	FACETS	1	0.948	1	0.39	0.34	0.443	CLONAL	1	TRUE	2	0.504322278189171	5		694	405	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427929	49427929	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	70	624	1	ENST00000301067.7:c.10661G>C	p.Arg3554Pro	p.R3554P	ENST00000301067	NM_003482.3	3554	cGt/cCt	38/54	0.504322278189171	4	FACETS	0.875	0.765	0.994	0.438	0.382	0.497	CLONAL	1	TRUE	2	0.504322278189171	4		625	477	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456340	99456340	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	99	300	0	ENST00000268035.6:c.1657G>A	p.Asp553Asn	p.D553N	ENST00000268035	NM_000875.3	553	Gac/Aac	8/21	0.504322278189171	3	FACETS	0.991	0.901	1	0.991	0.901	1	CLONAL	2	TRUE	1	0.504322278189171	3		300	248	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462003	120462003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	41	502	0	ENST00000256646.2:c.5713G>A	p.Ala1905Thr	p.A1905T	ENST00000256646	NM_024408.3	1905	Gcc/Acc	31/34	0.48377887104469	5	FACETS	0.85	0.71	1	0.283	0.236	0.335	CLONAL	1	TRUE	2	0.504322278189171	5		502	336	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663824	241663824	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147528200	NA	P-0036929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	17	214	0	ENST00000366560.3:c.1303G>A	p.Val435Met	p.V435M	ENST00000366560	NM_000143.3	435	Gtg/Atg	9/10	0.48377887104469	5	FACETS	1	0.83	1	0.376	0.284	0.481	CLONAL	1	TRUE	2	0.504322278189171	5		214	105	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600434	43600434	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	56	484	0	ENST00000355710.3:c.660C>A	p.Ser220Arg	p.S220R	ENST00000355710	NM_020975.4	220	agC/agA	4/20	0.494695967379689	2	FACETS	1	0.947	1	0.588	0.512	0.667	CLONAL	1	TRUE	0	0.504322278189171	2		484	189	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0036958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	170	608	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	0.64	2		608	400	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504417	186504417	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	62	565	0	ENST00000323963.5:c.754A>G	p.Ile252Val	p.I252V	ENST00000323963		252	Att/Gtt	7/11	1	2	FACETS	0.644	0.56	0.733	0.644	0.56	0.733	SUBCLONAL	1	TRUE	1	0.64	2		565	301	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060728	38060728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	113	892	0	ENST00000250448.2:c.1261G>A	p.Glu421Lys	p.E421K	ENST00000250448	NM_004496.3	421	Gaa/Aaa	2/2	1	2	FACETS	0.665	0.601	0.732	0.665	0.601	0.732	SUBCLONAL	1	TRUE	1	0.64	2		892	531	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467464	66467464	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773032839	NA	P-0036959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	53	340	0	ENST00000273854.3:c.805G>A	p.Asp269Asn	p.D269N	ENST00000273854	NM_004439.5	269	Gat/Aat	3/18	1	2	FACETS	0.801	0.686	0.926	0.801	0.686	0.926	CLONAL	1	TRUE	1	0.360525250127336	2		340	367	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144152	11144152	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	82	594	0	ENST00000358026.2:c.3733G>C	p.Ala1245Pro	p.A1245P	ENST00000358026	NM_001128849.1	1245	Gcc/Ccc	26/36	1	2	FACETS	0.763	0.674	0.859	0.763	0.674	0.859	SUBCLONAL	1	TRUE	1	0.360525250127336	2		594	596	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046092	180046092	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	54	189	0	ENST00000261937.6:c.2779G>C	p.Val927Leu	p.V927L	ENST00000261937	NM_182925.4	927	Gtg/Ctg	20/30	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.360525250127336	2		189	252	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199469669	NA	P-0036962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	227	482	0	ENST00000374080.3:c.130G>T	p.Gly44Cys	p.G44C	ENST00000374080		44	Ggt/Tgt	2/45	1	2	FACETS	0.883	0.829	0.939	0.883	0.829	0.939	CLONAL	1	TRUE	1	0.835631723560996	2		482	615	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0036963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	79	274	0				ENST00000310581	NM_198253.2	-/1132			0.403096330738193	3	FACETS	1	0.889	1	0.503	0.444	0.566	CLONAL	1	TRUE	1	0.435482734990825	3		274	439	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764146326	NA	P-0036963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	175	643	0	ENST00000269305.4:c.841G>T	p.Asp281Tyr	p.D281Y	ENST00000269305	NM_001126112.2	281	Gac/Tac	8/11	0.435482734990825	1	FACETS	0.953	0.881	1	0.953	0.881	1	CLONAL	1	TRUE	0	0.435482734990825	1		643	660	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617740	39617740	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765611552	NA	P-0036963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	48	417	0	ENST00000262039.4:c.1924C>T	p.Arg642Cys	p.R642C	ENST00000262039	NM_002647.2	642	Cgt/Tgt	17/25	0.435482734990825	1	FACETS	0.338	0.286	0.396	0.338	0.286	0.396	SUBCLONAL	1	TRUE	0	0.435482734990825	1		417	510	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0036969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	602	514	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.604559689039163	12	FACETS	1	0.995	1			1	CLONAL	11	TRUE	NA	0.604559689039163	12		514	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0036969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	217	661	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.505156748994991	4	FACETS	1	0.971	1			1	CLONAL	4	TRUE	NA	0.604559689039163	4		661	284	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208016	5208016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1042776388	NA	P-0036969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	11	699	1	ENST00000357368.4:c.5695C>T	p.Arg1899Trp	p.R1899W	ENST00000357368	NM_002850.3	1899	Cgg/Tgg	37/38	0.23097484360055	4	FACETS	0.312	0.216	0.432	0.104	0.072	0.144	INDETERMINATE	1	TRUE	1	0.604559689039163	4		700	187	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143188	30143188	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	20	367	0	ENST00000389048.3:c.338G>T	p.Gly113Val	p.G113V	ENST00000389048	NM_004304.4	113	gGt/gTt	1/29	0.595726879990518	2	FACETS	0.575	0.446	0.722	0.288	0.223	0.361	SUBCLONAL	1	TRUE	0	0.604559689039163	2		367	115	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045469	47045470	+	stop_gained	Nonsense_Mutation	DNP	GA	GA	AT	novel	NA	P-0036969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	64	240	0	ENST00000377604.3:c.2436_2437delinsAT	p.Met812_Lys813delinsIleTer	p.M812_K813delinsI*	ENST00000377604	NM_001204468.1	812	atGAag/atATag	22/24	0.403147334713516	2	FACETS	0.871	0.809	0.927			1	CLONAL	3	TRUE	NA	0.604559689039163	2		240	81	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913399	NA	P-0036970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	74	298	0	ENST00000349496.5:c.100G>C	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Cga	3/15	1	2	FACETS	0.844	0.742	0.953	0.844	0.742	0.953	CLONAL	1	TRUE	1	0.414439045700182	2		298	423	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868124	56868124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	150	487	3	ENST00000308159.5:c.1622C>T	p.Ser541Phe	p.S541F	ENST00000308159	NM_014669.4	541	tCc/tTc	14/22	0.410999269779422	3	FACETS	0.884	0.807	0.964	0.442	0.403	0.482	CLONAL	1	TRUE	1	0.414439045700182	3		490	989	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933192	39933192	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	186	677	4	ENST00000378444.4:c.1407C>A	p.Ser469Arg	p.S469R	ENST00000378444	NM_001123385.1	469	agC/agA	4/15	1	2	FACETS	0.862	0.796	0.932	0.862	0.796	0.932	CLONAL	1	TRUE	1	0.414439045700182	2		681	1041	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0036974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	109	609	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.423930935347757	1	FACETS	0.899	0.812	0.989	0.899	0.812	0.989	CLONAL	1	TRUE	0	0.423930935347757	1		609	451	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144146	11144146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	217	588	1	ENST00000358026.2:c.3727C>T	p.Arg1243Trp	p.R1243W	ENST00000358026	NM_001128849.1	1243	Cgg/Tgg	26/36	0.368008326702893	2	FACETS	0.971	0.912	1	0.971	0.912	1	CLONAL	2	TRUE	0	0.423930935347757	2		589	527	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449727	8449727	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs772305581	NA	P-0036974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	109	479	0	ENST00000356435.5:c.3986C>T	p.Pro1329Leu	p.P1329L	ENST00000356435		1329	cCg/cTg	23/35	1	2	FACETS	0.853	0.768	0.943	0.853	0.768	0.943	CLONAL	1	TRUE	1	0.423930935347757	2		479	603	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25468919	25468919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	93	638	0	ENST00000264709.3:c.1444G>A	p.Glu482Lys	p.E482K	ENST00000264709	NM_175629.2	482	Gag/Aag	12/23	1	2	FACETS	0.737	0.657	0.823	0.737	0.657	0.823	SUBCLONAL	1	TRUE	1	0.423930935347757	2		638	595	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858170	40858170	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	79	690	0	ENST00000428826.2:c.1694C>A	p.Thr565Asn	p.T565N	ENST00000428826		565	aCc/aAc	16/21	0.250028598092441	3	FACETS	0.576	0.506	0.652	0.288	0.253	0.326	INDETERMINATE	1	TRUE	1	0.423930935347757	3		690	784	SUCCESS
AXL	558	MSKCC	GRCh37	19	41749589	41749589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	221	645	0	ENST00000301178.4:c.1514G>A	p.Ser505Asn	p.S505N	ENST00000301178	NM_021913.4	505	aGt/aAt	12/20	0.423930935347757	3	FACETS	0.894	0.835	0.954	0.894	0.835	0.954	CLONAL	2	TRUE	1	0.423930935347757	3		645	707	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0036975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	290	581	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.610888761742383	1	FACETS	0.513	0.485	0.541	0.513	0.485	0.541	SUBCLONAL	1	TRUE	0	0.874036162308373	1		582	728	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	148	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.874036162308373	2		148	298	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341000	70341000	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	65	597	1	ENST00000374080.3:c.733C>A	p.Gln245Lys	p.Q245K	ENST00000374080		245	Cag/Aag	5/45	1	2	FACETS	0.174	0.15	0.2	0.174	0.15	0.2	SUBCLONAL	1	TRUE	1	0.874036162308373	2		598	853	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0036976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	27	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.712	0.565	0.88	0.712	0.565	0.88	SUBCLONAL	1	TRUE	1	0.14	2		502	542	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0036976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	37	690	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.802	0.66	0.962	0.802	0.66	0.962	CLONAL	1	TRUE	1	0.14	2		690	659	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492817	56492817	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	56	570	0	ENST00000407977.2:c.122C>A	p.Ser41Ter	p.S41*	ENST00000407977		41	tCa/tAa	2/10	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.14	2		570	674	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223600	55223600	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	54	412	0	ENST00000275493.2:c.967G>C	p.Val323Leu	p.V323L	ENST00000275493	NM_005228.3	323	Gtc/Ctc	8/28	0.377384911958336	1	FACETS	0.158	0.135	0.184	0.158	0.135	0.184	INDETERMINATE	1	TRUE	0	0.817459252965912	1		412	493	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0036980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	27	458	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.238	0.19	0.293	0.238	0.19	0.293	SUBCLONAL	1	TRUE	1	0.84520688687881	2		458	268	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0036980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	240	509	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	1	2	FACETS	0.998	0.94	1	0.998	0.94	1	CLONAL	1	TRUE	1	0.84520688687881	2		509	569	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438516	52438516	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	rs200156887	NA	P-0036980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	330	527	0	ENST00000460680.1:c.1203T>G	p.Tyr401Ter	p.Y401*	ENST00000460680	NM_004656.3	401	taT/taG	12/17	0.84520688687881	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.84520688687881	1		527	405	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133242000	133242000	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	316	592	0	ENST00000320574.5:c.2356G>T	p.Gly786Cys	p.G786C	ENST00000320574	NM_006231.2	786	Ggc/Tgc	21/49	1	2	FACETS	0.871	0.825	0.918	0.871	0.825	0.918	CLONAL	1	TRUE	1	0.84520688687881	2		592	858	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976245	18976245	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs749947265	NA	P-0036980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	296	646	0	ENST00000262803.5:c.3005A>G	p.Asn1002Ser	p.N1002S	ENST00000262803	NM_002911.3	1002	aAc/aGc	21/24	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.84520688687881	2		646	685	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428190	72428190	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0000815-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	170	278	0	ENST00000477973.2:c.699+1G>A		p.X233_splice	ENST00000477973	NM_012234.5	233			0.585300895243327	1	FACETS	0.624	0.58	0.668	0.624	0.58	0.668	SUBCLONAL	1	TRUE	0	0.787217225344133	1		278	420	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433548	138433548	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000815-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	146	234	0	ENST00000289153.2:c.1064C>G	p.Ala355Gly	p.A355G	ENST00000289153	NM_006219.2	355	gCt/gGt	7/22	1	2	FACETS	0.793	0.729	0.858	0.793	0.729	0.858	SUBCLONAL	1	TRUE	1	0.787217225344133	2		234	468	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508083	106508083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339698935	NA	P-0000815-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	82	134	0	ENST00000359195.3:c.77G>A	p.Arg26His	p.R26H	ENST00000359195	NM_002649.2	26	cGc/cAc	2/11	0.166351445190092	3	FACETS	1	0.964	1	0.593	0.53	0.657	INDETERMINATE	1	TRUE	1	0.787217225344133	3		134	245	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396261	396261	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000815-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	254	506	0	ENST00000262320.3:c.765G>C	p.Glu255Asp	p.E255D	ENST00000262320	NM_003502.3	255	gaG/gaC	2/11	0.787217225344133	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.787217225344133	1		506	327	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363091	40363091	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000845-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	157	305	0	ENST00000397332.2:c.1138del	p.Arg380GlyfsTer17	p.R380Gfs*17	ENST00000397332	NM_001033082.2	380	Cgg/gg	3/3	0.755834476892341	3	FACETS	1	0.931	1	0.506	0.465	0.547	CLONAL	1	TRUE	1	0.755834476892341	3		305	566	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0001111-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	53	604	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.191166007405248	4	FACETS	0.84	0.723	0.966			1	CLONAL	3	TRUE	NA	0.191166007405248	4		605	262	SUCCESS
APC	324	MSKCC	GRCh37	5	112177808	112177808	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1256844270	NA	P-0001111-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	20	346	1	ENST00000257430.4:c.6517A>G	p.Lys2173Glu	p.K2173E	ENST00000257430	NM_000038.5	2173	Aaa/Gaa	16/16	0.191166007405248	3	FACETS	1	0.867	1	0.6	0.461	0.761	CLONAL	1	TRUE	1	0.191166007405248	3		347	191	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579365	7579366	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTA	novel	NA	P-0001111-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	37	356	0	ENST00000269305.4:c.319_321dup	p.Tyr107dup	p.Y107dup	ENST00000269305	NM_001126112.2	107	-/TAC	4/11	0.188854402619102	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	2	TRUE	0	0.191166007405248	2		356	163	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0002240-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	463	296	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.707712334746646	2		296	627	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0003282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	49	344	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.235263258778265	1	FACETS	0.899	0.764	1	0.899	0.764	1	CLONAL	1	TRUE	0	0.246291285676378	1		344	388	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248998	55248999	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCCAGCG	rs727504263	NA	P-0003282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	44	446	0	ENST00000275493.2:c.2300_2308dup	p.Ala767_Val769dup	p.A767_V769dup	ENST00000275493	NM_005228.3	767	atg/aTGGCCAGCGtg	20/28	1	2	FACETS	0.56	0.469	0.662	0.56	0.469	0.662	SUBCLONAL	1	TRUE	1	0.246291285676378	2		446	638	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023769	27023769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	62	212	0	ENST00000324856.7:c.879del	p.Thr294ProfsTer69	p.T294Pfs*69	ENST00000324856	NM_006015.4	292	aCc/ac	1/20	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.246291285676378	2		212	491	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379455	225379455	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	93	516	0	ENST00000264414.4:c.413A>G	p.Asn138Ser	p.N138S	ENST00000264414	NM_003590.4	138	aAc/aGc	4/16	1	2	FACETS	0.968	0.86	1	0.968	0.86	1	CLONAL	1	TRUE	1	0.246291285676378	2		516	780	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250922	153250922	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	51	299	0	ENST00000281708.4:c.1138G>C	p.Asp380His	p.D380H	ENST00000281708	NM_033632.3	380	Gat/Cat	8/12	1	2	FACETS	0.929	0.791	1	0.929	0.791	1	CLONAL	1	TRUE	1	0.246291285676378	2		299	446	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3929856	3929856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1211983012	NA	P-0003282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	49	315	0	ENST00000262367.5:c.62G>A	p.Gly21Asp	p.G21D	ENST00000262367	NM_004380.2	21	gGt/gAt	1/31	0.237967601976517	3	FACETS	0.707	0.598	0.827	0.354	0.299	0.414	SUBCLONAL	1	TRUE	1	0.246291285676378	3		315	632	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31025035	31025035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375101983	NA	P-0003282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	54	472	0	ENST00000375687.4:c.4520C>T	p.Ala1507Val	p.A1507V	ENST00000375687	NM_015338.5	1507	gCg/gTg	13/13	1	2	FACETS	0.68	0.58	0.789	0.68	0.58	0.789	SUBCLONAL	1	TRUE	1	0.246291285676378	2		472	645	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074255	8074255	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	64	429	0	ENST00000377482.5:c.404del	p.Asn135ThrfsTer40	p.N135Tfs*40	ENST00000377482	NM_018948.3	135	aAc/ac	4/4	1	2	FACETS	0.901	0.78	1	0.901	0.78	1	CLONAL	1	TRUE	1	0.246291285676378	2		429	577	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405954	157405954	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	61	421	0	ENST00000346085.5:c.2201del	p.Gly734AlafsTer11	p.G734Afs*11	ENST00000346085	NM_020732.3	732	ccG/cc	6/20	1	2	FACETS	0.761	0.656	0.875	0.761	0.656	0.875	SUBCLONAL	1	TRUE	1	0.246291285676378	2		421	651	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090451	5090451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774355597	NA	P-0003282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	34	191	0	ENST00000381652.3:c.2767C>T	p.Arg923Cys	p.R923C	ENST00000381652	NM_004972.3	923	Cgt/Tgt	21/25	0.226655713535455	1	FACETS	0.917	0.753	1	0.917	0.753	1	CLONAL	1	TRUE	0	0.246291285676378	1		191	264	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274172	10274172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567354612	NA	P-0003282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	67	429	0	ENST00000330684.3:c.97G>A	p.Ala33Thr	p.A33T	ENST00000330684	NM_001134407.1	33	Gcg/Acg	2/13	0.237967601976517	3	FACETS	0.949	0.824	1	0.474	0.412	0.542	CLONAL	1	TRUE	1	0.246291285676378	3		429	644	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660580	67660580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	78	654	0	ENST00000264010.4:c.1480C>T	p.Arg494Cys	p.R494C	ENST00000264010	NM_006565.3	494	Cgc/Tgc	8/12	1	2	FACETS	0.742	0.651	0.84	0.742	0.651	0.84	SUBCLONAL	1	TRUE	1	0.246291285676378	2		654	854	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699526	117699526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	47	391	0	ENST00000369458.3:c.115G>A	p.Val39Ile	p.V39I	ENST00000369458	NM_024626.3	39	Gtc/Atc	3/6	1	2	FACETS	0.826	0.698	0.968	0.826	0.698	0.968	CLONAL	1	TRUE	1	0.246291285676378	2		391	462	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21565434	21565434	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs45453992	NA	P-0003282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	94	599	1	ENST00000382592.4:c.452G>T	p.Arg151Leu	p.R151L	ENST00000382592	NM_014572.2	151	cGg/cTg	3/8	1	2	FACETS	0.881	0.783	0.986	0.881	0.783	0.986	CLONAL	1	TRUE	1	0.246291285676378	2		600	866	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040841	42040841	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	65	554	0	ENST00000219905.7:c.5219C>T	p.Ala1740Val	p.A1740V	ENST00000219905	NM_001164273.1	1740	gCt/gTt	16/24	1	2	FACETS	0.846	0.733	0.968	0.846	0.733	0.968	CLONAL	1	TRUE	1	0.246291285676378	2		554	624	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862766	9862766	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746978701	NA	P-0003282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	78	528	0	ENST00000330684.3:c.2537G>A	p.Arg846His	p.R846H	ENST00000330684	NM_001134407.1	846	cGc/cAc	12/13	0.237967601976517	3	FACETS	0.909	0.797	1	0.454	0.398	0.514	CLONAL	1	TRUE	1	0.246291285676378	3		528	783	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828530	72828530	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	116	704	0	ENST00000268489.5:c.8051T>C	p.Val2684Ala	p.V2684A	ENST00000268489	NM_006885.3	2684	gTg/gCg	9/10	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.246291285676378	2		704	900	SUCCESS
REL	5966	MSKCC	GRCh37	2	61108983	61108983	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	31	299	0	ENST00000295025.8:c.8C>A	p.Ser3Tyr	p.S3Y	ENST00000295025	NM_002908.2	3	tCc/tAc	1/11	1	2	FACETS	0.484	0.391	0.59	0.484	0.391	0.59	SUBCLONAL	1	TRUE	1	0.246291285676378	2		299	520	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050383	37050383	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1248251121	NA	P-0003282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	49	266	0	ENST00000231790.2:c.532G>T	p.Glu178Ter	p.E178*	ENST00000231790	NM_000249.3	178	Gaa/Taa	6/19	0.235263258778265	1	FACETS	0.921	0.782	1	0.921	0.782	1	CLONAL	1	TRUE	0	0.246291285676378	1		266	379	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109309849	109309849	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	92	567	0	ENST00000436639.2:c.1466A>G	p.Asp489Gly	p.D489G	ENST00000436639	NM_014454.2	489	gAt/gGt	9/10	1	2	FACETS	0.958	0.851	1	0.958	0.851	1	CLONAL	1	TRUE	1	0.246291285676378	2		567	780	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0004590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	42	531	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	1	2	FACETS	0.444	0.371	0.525	0.444	0.371	0.525	SUBCLONAL	1	TRUE	1	0.435188784368624	2		531	435	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	71	214	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.729374168135794	2		214	167	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0005141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	95	227	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.729374168135794	2		227	247	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46608752	46608752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	319	578	0	ENST00000263734.3:c.2063G>A	p.Gly688Glu	p.G688E	ENST00000263734	NM_001430.4	688	gGg/gAg	13/16	0.729374168135794	3	FACETS	0.975	0.93	1	0.975	0.93	1	CLONAL	2	TRUE	1	0.729374168135794	3		578	612	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0005813-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	526	396	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.790403559643193	4	FACETS	1	0.996	1	0.83	0.801	0.859	CLONAL	2	TRUE	1	0.790403559643193	4		396	957	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0005813-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	684	619	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.790403559643193	4	FACETS	1	0.979	1	0.679	0.656	0.702	CLONAL	2	TRUE	1	0.790403559643193	4		620	1522	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0005813-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	527	584	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.790403559643193	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.790403559643193	1		584	787	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039377	49039378	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCCTTACAAGTTTCCTAGTTC	novel	NA	P-0005813-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	306	328	0	ENST00000267163.4:c.2363_2384dup	p.Arg798GlnfsTer4	p.R798Qfs*4	ENST00000267163	NM_000321.2	788	agc/aGCCCTTACAAGTTTCCTAGTTCgc	23/27	0.790403559643193	1	FACETS	0.703	0.668	0.738	0.703	0.668	0.738	SUBCLONAL	1	TRUE	0	0.790403559643193	1		328	666	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249092	55249092	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005813-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1372	279	443	0	ENST00000275493.2:c.2390G>C	p.Cys797Ser	p.C797S	ENST00000275493	NM_005228.3	797	tGc/tCc	20/28	0.790403559643193	4	FACETS	0.766	0.717	0.816	0.255	0.239	0.272	SUBCLONAL	1	TRUE	1	0.790403559643193	4		443	1651	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134283	2134283	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005813-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	176	708	0	ENST00000219476.3:c.4060G>T	p.Gly1354Cys	p.G1354C	ENST00000219476	NM_000548.3	1354	Ggc/Tgc	34/42	1	2	FACETS	0.414	0.381	0.449	0.414	0.381	0.449	SUBCLONAL	1	TRUE	1	0.790403559643193	2		708	1076	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247028	53247028	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005813-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	202	545	0	ENST00000375401.3:c.472G>T	p.Glu158Ter	p.E158*	ENST00000375401	NM_004187.3	158	Gaa/Taa	4/26	1	2	FACETS	0.503	0.466	0.542	0.503	0.466	0.542	SUBCLONAL	1	TRUE	1	0.790403559643193	2		545	1016	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0005916-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	67	486	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.185105384522392	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	2	FALSE	0	0.224810692243149	2		486	285	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525099	9525099	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005916-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	24	461	0	ENST00000353224.5:c.1786G>C	p.Glu596Gln	p.E596Q	ENST00000353224	NM_177990.2	596	Gag/Cag	8/10	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	FALSE	1	0.224810692243149	2		461	158	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900206	101900206	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs727503470	NA	P-0005916-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	11	443	1	ENST00000374994.4:c.640G>T	p.Gly214Cys	p.G214C	ENST00000374994	NM_004612.2	214	Ggt/Tgt	4/9	0.185105384522392	2	FACETS	0.487	0.336	0.674	0.243	0.168	0.337	SUBCLONAL	1	FALSE	0	0.224810692243149	2		444	201	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057826	27057826	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005916-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	25	644	0	ENST00000324856.7:c.1534C>T	p.Gln512Ter	p.Q512*	ENST00000324856	NM_006015.4	512	Cag/Tag	3/20	1	2	FACETS	0.66	0.52	0.82	0.66	0.52	0.82	SUBCLONAL	1	FALSE	1	0.224810692243149	2		644	337	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199803	108199803	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005916-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	20	329	0	ENST00000278616.4:c.7145G>T	p.Gly2382Val	p.G2382V	ENST00000278616	NM_000051.3	2382	gGa/gTa	49/63	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	FALSE	1	0.224810692243149	2		329	149	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199922	108199922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1163371592	NA	P-0005916-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	20	255	0	ENST00000278616.4:c.7264G>A	p.Glu2422Lys	p.E2422K	ENST00000278616	NM_000051.3	2422	Gag/Aag	49/63	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	FALSE	1	0.224810692243149	2		255	123	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201074	108201074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005916-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	12	525	0	ENST00000278616.4:c.7441G>A	p.Asp2481Asn	p.D2481N	ENST00000278616	NM_000051.3	2481	Gat/Aat	50/63	1	2	FACETS	0.671	0.473	0.913	0.671	0.473	0.913	SUBCLONAL	1	FALSE	1	0.224810692243149	2		525	159	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201142	108201142	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005916-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	11	436	0	ENST00000278616.4:c.7509G>C	p.Met2503Ile	p.M2503I	ENST00000278616	NM_000051.3	2503	atG/atC	50/63	1	2	FACETS	0.704	0.488	0.969	0.704	0.488	0.969	CLONAL	1	FALSE	1	0.224810692243149	2		436	139	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202172	108202172	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1555123920	NA	P-0005916-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	11	414	0	ENST00000278616.4:c.7517G>A	p.Arg2506Lys	p.R2506K	ENST00000278616	NM_000051.3	2506	aGa/aAa	51/63	1	2	FACETS	0.882	0.614	1	0.882	0.614	1	CLONAL	1	FALSE	1	0.224810692243149	2		414	111	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202232	108202232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659323	NA	P-0005916-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	12	592	0	ENST00000278616.4:c.7577G>A	p.Arg2526Lys	p.R2526K	ENST00000278616	NM_000051.3	2526	aGa/aAa	51/63	1	2	FACETS	0.736	0.52	1	0.736	0.52	1	CLONAL	1	FALSE	1	0.224810692243149	2		592	145	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110704	2110704	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005916-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	21	604	0	ENST00000219476.3:c.1009G>C	p.Glu337Gln	p.E337Q	ENST00000219476	NM_000548.3	337	Gag/Cag	11/42	1	2	FACETS	0.853	0.659	1	0.853	0.659	1	CLONAL	1	FALSE	1	0.224810692243149	2		604	219	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110736	2110736	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005916-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	31	609	0	ENST00000219476.3:c.1041G>C	p.Lys347Asn	p.K347N	ENST00000219476	NM_000548.3	347	aaG/aaC	11/42	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	FALSE	1	0.224810692243149	2		609	194	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40747957	40747957	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005916-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	18	514	0	ENST00000392038.2:c.461A>G	p.Tyr154Cys	p.Y154C	ENST00000392038	NM_001626.4	154	tAt/tGt	6/14	1	2	FACETS	0.817	0.618	1	0.817	0.618	1	CLONAL	1	FALSE	1	0.224810692243149	2		514	196	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797300	135797300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs118203401	NA	P-0005916-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	31	311	0	ENST00000298552.3:c.569del	p.Arg190ProfsTer20	p.R190Pfs*20	ENST00000298552	NM_001162426.1	190	cGc/cc	7/23	0.185105384522392	2	FACETS	1	0.942	1	0.733	0.599	0.883	CLONAL	1	FALSE	0	0.224810692243149	2		311	188	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0005937-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	218	381	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	0.470857075542282	2		381	841	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0005937-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	391	697	3	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	NA	2	FACETS	0.899	0.858	0.94			1	INDETERMINATE	2	TRUE	NA	0.470857075542282	2		700	924	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603023	48603023	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555687378	NA	P-0005937-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	119	399	1	ENST00000342988.3:c.1324C>T	p.Gln442Ter	p.Q442*	ENST00000342988	NM_005359.5	442	Cag/Tag	11/12	0.470857075542282	1	FACETS	0.933	0.85	1	0.933	0.85	1	CLONAL	1	TRUE	0	0.470857075542282	1		400	414	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106364	27106364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005937-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	192	735	0	ENST00000324856.7:c.5975C>T	p.Ser1992Leu	p.S1992L	ENST00000324856	NM_006015.4	1992	tCa/tTa	20/20	0.255482621802093	1	FACETS	0.762	0.706	0.82	0.762	0.706	0.82	INDETERMINATE	1	TRUE	0	0.470857075542282	1		735	818	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443940	18443940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866374517	NA	P-0005937-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	110	342	1	ENST00000266497.5:c.913C>T	p.Pro305Ser	p.P305S	ENST00000266497		305	Cca/Tca	3/31	1	2	FACETS	0.965	0.872	1	0.965	0.872	1	CLONAL	1	TRUE	1	0.470857075542282	2		343	484	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562270	95562270	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555367530	NA	P-0005937-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	166	522	0	ENST00000393063.1:c.4987A>G	p.Ile1663Val	p.I1663V	ENST00000393063	NM_030621.3	1663	Ata/Gta	24/28	0.110470487019492	6	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.470857075542282	6		522	924	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20150381	20150381	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005937-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	60	374	0	ENST00000379607.5:c.256G>A	p.Asp86Asn	p.D86N	ENST00000379607	NM_001412.3	86	Gat/Aat	5/7	0.368267871957265	0	FACETS	0.376	0.325	0.43			1	SUBCLONAL	1	TRUE	0	0.470857075542282	0		374	359	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729821	47729856	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CCGCCGCTCGTACTGTGCGTTGAGGTCGTCCGCCAT	CCGCCGCTCGTACTGTGCGTTGAGGTCGTCCGCCAT	-	novel	NA	P-0005937-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	164	788	0	ENST00000449228.1:c.533_568del	p.Asp178_Ala189del	p.D178_A189del	ENST00000449228	NM_001127240.2	178	gATGGCGGACGACCTCAACGCACAGTACGAGCGGCGGag/gag	3/4	0.470857075542282	1	FACETS	0.793	0.73	0.858	0.793	0.73	0.858	SUBCLONAL	1	TRUE	0	0.470857075542282	1		788	672	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100143	30100143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs191202207	NA	P-0005937-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	229	754	1	ENST00000331968.5:c.1477G>A	p.Glu493Lys	p.E493K	ENST00000331968	NM_002742.2	493	Gaa/Aaa	10/18	1	2	FACETS	0.852	0.793	0.913	0.852	0.793	0.913	CLONAL	1	TRUE	1	0.470857075542282	2		755	1142	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246040	46246040	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005937-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	56	343	0	ENST00000334344.6:c.4134T>A	p.Asn1378Lys	p.N1378K	ENST00000334344	NM_152641.2	1378	aaT/aaA	15/21	1	2	FACETS	0.454	0.389	0.525	0.454	0.389	0.525	SUBCLONAL	1	TRUE	1	0.470857075542282	2		343	524	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239419	105239419	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	310	610	1	ENST00000349310.3:c.968A>G	p.Asp323Gly	p.D323G	ENST00000349310	NM_001014432.1	323	gAc/gGc	12/15	0.670208769996952	3	FACETS	0.999	0.943	1			1	CLONAL	1	TRUE	NA	0.772800048524715	3		611	1113	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662927	227662930	+	frameshift_variant	Frame_Shift_Del	DEL	TGTC	TGTC	-	novel	NA	P-0006829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	348	712	0	ENST00000305123.5:c.525_528del	p.Thr176ArgfsTer3	p.T176Rfs*3	ENST00000305123	NM_005544.2	175	caGACA/ca	1/2	1	2	FACETS	0.932	0.885	0.98	0.932	0.885	0.98	CLONAL	1	TRUE	1	0.772800048524715	2		712	966	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0007082-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	18	485	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.222	0.166	0.289	0.222	0.166	0.289	SUBCLONAL	1	TRUE	1	0.281534442288348	2		485	576	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567300	226567300	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007082-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	63	389	0	ENST00000366794.5:c.1586G>C	p.Gly529Ala	p.G529A	ENST00000366794	NM_001618.3	529	gGa/gCa	11/23	0.281534442288348	5	FACETS	0.819	0.707	0.941	0.273	0.235	0.314	CLONAL	1	TRUE	2	0.281534442288348	5		389	777	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503147	125503148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CATATGTT	novel	NA	P-0007082-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	67	289	0	ENST00000428830.2:c.515_522dup	p.Ala175HisfsTer8	p.A175Hfs*8	ENST00000428830	NM_001114121.2	172	cca/cCATATGTTca	6/14	0.281534442288348	3	FACETS	0.935	0.813	1	0.467	0.406	0.533	CLONAL	1	TRUE	1	0.281534442288348	3		289	581	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	459851	459851	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0007082-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	77	485	0	ENST00000399788.2:c.1244C>G	p.Ser415Ter	p.S415*	ENST00000399788	NM_001042603.1	415	tCa/tGa	10/28	0.281534442288348	3	FACETS	0.656	0.575	0.744	0.328	0.287	0.372	SUBCLONAL	1	TRUE	1	0.281534442288348	3		485	951	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863427	57863427	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007082-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	57	419	0	ENST00000228682.2:c.1522C>G	p.Gln508Glu	p.Q508E	ENST00000228682	NM_005269.2	508	Caa/Gaa	11/12	1	2	FACETS	0.635	0.544	0.734	0.635	0.544	0.734	SUBCLONAL	1	TRUE	1	0.281534442288348	2		419	638	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986803	36986803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007082-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	46	167	0	ENST00000354822.5:c.886G>A	p.Asp296Asn	p.D296N	ENST00000354822	NM_001079668.2	296	Gac/Aac	3/3	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.281534442288348	2		167	233	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708465	43708465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007082-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	109	467	0	ENST00000382044.4:c.4831G>A	p.Glu1611Lys	p.E1611K	ENST00000382044	NM_001141980.1	1611	Gaa/Aaa	22/28	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.281534442288348	2		467	703	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726689	88726689	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007082-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	65	313	0	ENST00000360948.2:c.355C>T	p.Gln119Ter	p.Q119*	ENST00000360948	NM_001012338.2	119	Cag/Tag	4/19	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.281534442288348	2		313	424	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604797	48604797	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007082-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	42	244	0	ENST00000342988.3:c.1619T>G	p.Leu540Arg	p.L540R	ENST00000342988	NM_005359.5	540	cTt/cGt	12/12	0.252138414412297	2	FACETS	1	0.886	1	0.535	0.449	0.629	CLONAL	1	TRUE	0	0.281534442288348	2		244	279	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273836	18273836	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0007082-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	126	527	0	ENST00000222254.8:c.1169C>G	p.Ser390Ter	p.S390*	ENST00000222254	NM_005027.3	390	tCa/tGa	10/16	1	2	FACETS	0.996	0.901	1	0.996	0.901	1	CLONAL	1	TRUE	1	0.281534442288348	2		527	899	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405870	49405870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007082-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	78	333	0	ENST00000418115.1:c.268G>A	p.Asp90Asn	p.D90N	ENST00000418115	NM_001664.2	90	Gat/Aat	3/5	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.281534442288348	2		333	546	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921566	178921566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793349	NA	P-0007082-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	43	207	0	ENST00000263967.3:c.1048G>A	p.Asp350Asn	p.D350N	ENST00000263967	NM_006218.2	350	Gac/Aac	5/21	1	2	FACETS	0.923	0.775	1	0.923	0.775	1	CLONAL	1	TRUE	1	0.281534442288348	2		207	331	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446301	187446301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374228382	NA	P-0007082-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	111	400	0	ENST00000232014.4:c.1387G>A	p.Glu463Lys	p.E463K	ENST00000232014	NM_001130845.1	463	Gag/Aag	6/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.281534442288348	2		400	703	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117684026	117684026	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007082-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	43	316	0	ENST00000368508.3:c.3121C>G	p.Pro1041Ala	p.P1041A	ENST00000368508	NM_002944.2	1041	Cca/Gca	21/43	0.256812043838617	1	FACETS	0.645	0.54	0.76	0.645	0.54	0.76	SUBCLONAL	1	TRUE	0	0.281534442288348	1		316	407	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137540411	137540411	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007082-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	62	308	0	ENST00000367739.4:c.54G>C	p.Glu18Asp	p.E18D	ENST00000367739	NM_000416.2	18	gaG/gaC	1/7	0.281534442288348	3	FACETS	0.711	0.613	0.817	0.355	0.306	0.409	SUBCLONAL	1	TRUE	1	0.281534442288348	3		308	707	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0007082-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	96	396	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.245609666214979	2	FACETS	0.844	0.757	0.935	0.844	0.757	0.935	CLONAL	2	TRUE	0	0.281534442288348	2		396	404	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738796	145738796	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007082-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	127	562	0	ENST00000428558.2:c.2269C>G	p.Gln757Glu	p.Q757E	ENST00000428558	NM_004260.3	757	Cag/Gag	14/22	0.281534442288348	4	FACETS	1	0.971	1	0.594	0.537	0.654	CLONAL	1	TRUE	2	0.281534442288348	4		562	973	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742486	145742486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs62530445	NA	P-0007082-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	116	474	1	ENST00000428558.2:c.302C>T	p.Ser101Leu	p.S101L	ENST00000428558	NM_004260.3	101	tCg/tTg	4/22	0.281534442288348	4	FACETS	1	0.967	1	0.586	0.527	0.648	CLONAL	1	TRUE	2	0.281534442288348	4		475	901	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891190	101891190	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007082-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	36	333	0	ENST00000374994.4:c.151G>C	p.Asp51His	p.D51H	ENST00000374994	NM_004612.2	51	Gat/Cat	2/9	0.281534442288348	3	FACETS	0.546	0.448	0.656	0.273	0.224	0.328	SUBCLONAL	1	TRUE	1	0.281534442288348	3		333	534	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650505	48650505	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007082-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	134	540	2	ENST00000376670.3:c.475C>A	p.Pro159Thr	p.P159T	ENST00000376670	NM_002049.3	159	Ccc/Acc	3/6	0.281534442288348	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.281534442288348	1		542	653	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0010593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	59	870	1	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		871	999	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0011098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	242	631	4	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.455357875930634	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.455357875930634	2		635	447	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	114	726	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.438948636667936	2	FACETS	0.988	0.893	1	0.494	0.446	0.543	CLONAL	1	TRUE	0	0.455357875930634	2		726	507	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0011098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	130	348	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.455357875930634	3	FACETS	0.887	0.813	0.964	0.887	0.813	0.964	CLONAL	2	TRUE	1	0.455357875930634	3		348	395	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111496	8111512	+	frameshift_variant	Frame_Shift_Del	DEL	TGGAGGAGGAATGCCAA	TGGAGGAGGAATGCCAA	-	novel	NA	P-0011321-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	92	566	3	ENST00000346208.3:c.985_1001del	p.Arg329GlyfsTer17	p.R329Gfs*17	ENST00000346208		328	TGGAGGAGGAATGCCAAt/t	5/6	0.188623408312681	5	FACETS	1	0.977	1	0.471	0.419	0.526	INDETERMINATE	1	TRUE	2	0.327735444292069	5		569	593	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15938117	15938117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769360451	NA	P-0011321-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	32	396	0	ENST00000268712.3:c.7097C>T	p.Thr2366Met	p.T2366M	ENST00000268712	NM_006311.3	2366	aCg/aTg	45/46	0.327735444292069	3	FACETS	0.678	0.552	0.821	0.339	0.276	0.411	SUBCLONAL	1	TRUE	1	0.327735444292069	3		396	335	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983104	201983104	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1236669171	NA	P-0011321-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	442	636	12	ENST00000359651.3:c.953A>G	p.Lys318Arg	p.K318R	ENST00000359651		318	aAg/aGg	7/8	0.327735444292069	5	FACETS	0.976	0.934	1	0.976	0.934	1	CLONAL	4	TRUE	1	0.327735444292069	5		648	1031	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983110	201983110	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1195754471	NA	P-0011321-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	430	633	12	ENST00000359651.3:c.959A>G	p.Lys320Arg	p.K320R	ENST00000359651		320	aAg/aGg	7/8	0.327735444292069	5	FACETS	0.951	0.909	0.993	0.951	0.909	0.993	CLONAL	4	TRUE	1	0.327735444292069	5		645	1029	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637295	176637295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201702515	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	98	568	0	ENST00000439151.2:c.1895G>A	p.Arg632Gln	p.R632Q	ENST00000439151	NM_022455.4	632	cGa/cAa	5/23	0.542277265587294	3	FACETS	1	0.909	1	0.338	0.303	0.375	CLONAL	1	TRUE	0	0.548547003945511	3		568	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	286	573	1	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.542277265587294	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	3	TRUE	0	0.548547003945511	3		574	438	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973811	15973811	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	266	457	0	ENST00000268712.3:c.4181C>G	p.Ser1394Ter	p.S1394*	ENST00000268712	NM_006311.3	1394	tCa/tGa	31/46	0.542277265587294	3	FACETS	0.981	0.937	1	0.981	0.937	1	CLONAL	3	TRUE	0	0.548547003945511	3		457	420	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197399	26197399	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	45	323	0	ENST00000356476.2:c.80G>C	p.Arg27Pro	p.R27P	ENST00000356476		27	cGa/cCa	1/1	0.548547003945511	6	FACETS	0.935	0.788	1	0.234	0.197	0.274	CLONAL	1	TRUE	2	0.548547003945511	6		323	368	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024491	31024491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	87	501	0	ENST00000375687.4:c.3976C>T	p.Pro1326Ser	p.P1326S	ENST00000375687	NM_015338.5	1326	Cct/Tct	13/13	0.548547003945511	3	FACETS	1	0.94	1	0.54	0.482	0.602	CLONAL	1	TRUE	1	0.548547003945511	3		501	374	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174379	11174379	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1200645333	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	153	462	0	ENST00000361445.4:c.7296G>A	p.Met2432Ile	p.M2432I	ENST00000361445	NM_004958.3	2432	atG/atA	53/58	0.548547003945511	4	FACETS	0.947	0.874	1	0.474	0.437	0.511	CLONAL	2	TRUE	0	0.548547003945511	4		462	456	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776498	9776498	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	77	439	0	ENST00000377346.4:c.601G>C	p.Glu201Gln	p.E201Q	ENST00000377346	NM_005026.3	201	Gag/Cag	6/24	0.548547003945511	4	FACETS	0.945	0.833	1	0.236	0.208	0.267	CLONAL	1	TRUE	0	0.548547003945511	4		439	460	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784137	9784137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202142608	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	90	534	0	ENST00000377346.4:c.2705G>A	p.Arg902Gln	p.R902Q	ENST00000377346	NM_005026.3	902	cGa/cAa	21/24	0.548547003945511	4	FACETS	1	0.95	1	0.279	0.248	0.311	CLONAL	1	TRUE	0	0.548547003945511	4		534	456	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805735	43805735	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	178	569	0	ENST00000372470.3:c.791C>G	p.Ser264Cys	p.S264C	ENST00000372470	NM_005373.2	264	tCc/tGc	5/12	0.548547003945511	4	FACETS	0.885	0.82	0.951	0.442	0.41	0.476	CLONAL	2	TRUE	0	0.548547003945511	4		569	568	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156848963	156848963	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764022882	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	204	594	0	ENST00000524377.1:c.1855C>G	p.Pro619Ala	p.P619A	ENST00000524377	NM_002529.3	619	Cca/Gca	15/17	0.545759676420893	5	FACETS	1	0.948	1	0.408	0.38	0.437	CLONAL	2	TRUE	0	0.548547003945511	5		594	664	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623634	43623635	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	157	545	0	ENST00000355710.3:c.3262_3263delinsAA	p.Pro1088Lys	p.P1088K	ENST00000355710	NM_020975.4	1088	CCa/AAa	20/20	0.51921881861157	2	FACETS	0.875	0.816	0.935	0.875	0.816	0.935	CLONAL	2	TRUE	0	0.548547003945511	2		545	327	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247602	123247602	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	137	458	0	ENST00000358487.5:c.1889G>C	p.Arg630Thr	p.R630T	ENST00000358487	NM_000141.4	630	aGa/aCa	14/18	0.51921881861157	2	FACETS	0.892	0.827	0.957	0.892	0.827	0.957	CLONAL	2	TRUE	0	0.548547003945511	2		458	280	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518601	69518601	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	57	296	0	ENST00000294312.3:c.44G>C	p.Gly15Ala	p.G15A	ENST00000294312	NM_005117.2	15	gGc/gCc	1/3	0.548547003945511	3	FACETS	1	0.905	1	0.528	0.457	0.603	CLONAL	1	TRUE	1	0.548547003945511	3		296	251	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195243	102195243	+	start_lost	Translation_Start_Site	SNP	G	G	C	novel	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	46	282	0	ENST00000263464.3:c.3G>C	p.Met1?	p.M1?	ENST00000263464	NM_001165.4	1	atG/atC	2/9	0.548547003945511	3	FACETS	0.797	0.676	0.929	0.399	0.338	0.465	CLONAL	1	TRUE	1	0.548547003945511	3		282	268	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865801	57865801	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	168	448	0	ENST00000228682.2:c.3278G>C	p.Arg1093Thr	p.R1093T	ENST00000228682	NM_005269.2	1093	aGa/aCa	12/12	0.530720675618082	2	FACETS	0.917	0.858	0.976	0.917	0.858	0.976	CLONAL	2	TRUE	0	0.548547003945511	2		448	334	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349250	11349250	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	19	139	0	ENST00000332029.2:c.86C>T	p.Ser29Phe	p.S29F	ENST00000332029	NM_003745.1	29	tCc/tTc	2/2	0.359090731434848	5	FACETS	1	0.799	1	0.348	0.267	0.44	CLONAL	1	TRUE	2	0.548547003945511	5		139	121	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56873439	56873439	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	109	518	0	ENST00000308159.5:c.2143G>C	p.Glu715Gln	p.E715Q	ENST00000308159	NM_014669.4	715	Gag/Cag	20/22	0.364007997767126	4	FACETS	1	0.973	1	0.615	0.555	0.679	CLONAL	1	TRUE	2	0.548547003945511	4		518	500	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992774	72992774	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	19	486	0	ENST00000268489.5:c.1271C>A	p.Ala424Asp	p.A424D	ENST00000268489	NM_006885.3	424	gCt/gAt	2/10	0.364007997767126	4	FACETS	0.296	0.224	0.381	0.148	0.112	0.191	SUBCLONAL	1	TRUE	2	0.548547003945511	4		486	362	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075133	16075133	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	52	292	0	ENST00000268712.3:c.419C>G	p.Ser140Cys	p.S140C	ENST00000268712	NM_006311.3	140	tCt/tGt	4/46	0.542277265587294	3	FACETS	0.813	0.697	0.939	0.271	0.232	0.313	CLONAL	1	TRUE	0	0.548547003945511	3		292	297	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223192	41223192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357411	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	234	508	1	ENST00000357654.3:c.4739C>T	p.Ser1580Phe	p.S1580F	ENST00000357654	NM_007294.3	1580	tCt/tTt	15/23	0.540360212873952	5	FACETS	0.897	0.843	0.951	0.897	0.843	0.951	CLONAL	3	TRUE	2	0.548547003945511	5		509	578	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223201	41223201	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	225	486	0	ENST00000357654.3:c.4730C>G	p.Ser1577Cys	p.S1577C	ENST00000357654	NM_007294.3	1577	tCt/tGt	15/23	0.540360212873952	5	FACETS	0.9	0.845	0.955	0.9	0.845	0.955	CLONAL	3	TRUE	2	0.548547003945511	5		486	554	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761499	59761499	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	54	363	0	ENST00000259008.2:c.2908G>T	p.Asp970Tyr	p.D970Y	ENST00000259008	NM_032043.2	970	Gat/Tat	20/20	0.540360212873952	5	FACETS	1	0.88	1	0.343	0.294	0.396	CLONAL	1	TRUE	2	0.548547003945511	5		363	349	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1627384	1627384	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	66	586	0	ENST00000344749.5:c.340G>C	p.Asp114His	p.D114H	ENST00000344749	NM_001136139.2	114	Gac/Cac	6/19	0.548547003945511	3	FACETS	0.705	0.614	0.803	0.352	0.307	0.402	SUBCLONAL	1	TRUE	1	0.548547003945511	3		586	435	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793134	33793134	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	26	228	0	ENST00000498907.2:c.187G>C	p.Asp63His	p.D63H	ENST00000498907	NM_004364.3	63	Gac/Cac	1/1	0.548547003945511	7	FACETS	0.694	0.55	0.858	0.173	0.137	0.215	SUBCLONAL	1	TRUE	3	0.548547003945511	7		228	324	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961366	54961366	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	78	429	0	ENST00000312783.6:c.266C>G	p.Ser89Cys	p.S89C	ENST00000312783	NM_198436.1	89	tCc/tGc	4/10	0.548547003945511	3	FACETS	1	0.932	1	0.538	0.476	0.603	CLONAL	1	TRUE	1	0.548547003945511	3		429	337	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884907	134884907	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	169	516	1	ENST00000398015.3:c.1683C>G	p.Ile561Met	p.I561M	ENST00000398015	NM_004441.4	561	atC/atG	8/16	0.548547003945511	5	FACETS	0.839	0.774	0.907	0.56	0.516	0.605	CLONAL	2	TRUE	2	0.548547003945511	5		517	669	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268415	142268415	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	40	458	0	ENST00000350721.4:c.3077G>C	p.Arg1026Thr	p.R1026T	ENST00000350721	NM_001184.3	1026	aGa/aCa	15/47	0.548547003945511	5	FACETS	0.627	0.521	0.744	0.209	0.173	0.248	SUBCLONAL	1	TRUE	2	0.548547003945511	5		458	424	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217191	66217191	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	89	498	0	ENST00000273854.3:c.2424C>G	p.Ile808Met	p.I808M	ENST00000273854	NM_004439.5	808	atC/atG	14/18	0.530720675618082	2	FACETS	0.986	0.883	1	0.493	0.441	0.547	CLONAL	1	TRUE	0	0.548547003945511	2		498	329	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295098	1295098	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1166646936	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	17	33	0	ENST00000310581.5:c.7C>T	p.Arg3Cys	p.R3C	ENST00000310581	NM_198253.2	3	Cgc/Tgc	1/16	0.548547003945511	14	FACETS	1	0.824	1	0.186	0.14	0.24	CLONAL	2	TRUE	2	0.548547003945511	14		33	119	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197253	26197253	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	82	413	0	ENST00000356476.2:c.226G>C	p.Ala76Pro	p.A76P	ENST00000356476		76	Gcg/Ccg	1/1	0.548547003945511	6	FACETS	1	0.974	1	0.344	0.304	0.386	CLONAL	1	TRUE	2	0.548547003945511	6		413	456	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793641	89793641	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	112	334	0	ENST00000336032.3:c.710A>T	p.Gln237Leu	p.Q237L	ENST00000336032	NM_006813.2	237	cAg/cTg	2/2	0.396079268289745	5	FACETS	1	0.973	1	0.788	0.718	0.859	CLONAL	2	TRUE	2	0.548547003945511	5		334	315	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946340	2946340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1171346123	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	175	941	0	ENST00000396946.4:c.3397C>T	p.Arg1133Cys	p.R1133C	ENST00000396946	NM_032415.4	1133	Cgc/Tgc	25/25	0.548547003945511	3	FACETS	0.95	0.885	1	0.95	0.885	1	CLONAL	2	TRUE	1	0.548547003945511	3		941	428	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355256	81355256	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	69	384	0	ENST00000222390.5:c.1118G>T	p.Arg373Leu	p.R373L	ENST00000222390	NM_000601.4	373	cGa/cTa	9/18	0.548547003945511	3	FACETS	0.954	0.837	1	0.477	0.418	0.54	CLONAL	1	TRUE	1	0.548547003945511	3		384	336	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148513796	148513796	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	171	546	0	ENST00000320356.2:c.1485G>T	p.Arg495Ser	p.R495S	ENST00000320356	NM_004456.4	495	agG/agT	12/20	0.548547003945511	3	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	1	0.548547003945511	3		546	388	SUCCESS
AR	367	MSKCC	GRCh37	X	66905896	66905896	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1266872442	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	164	230	0	ENST00000374690.3:c.1813G>C	p.Asp605His	p.D605H	ENST00000374690	NM_000044.3	605	Gat/Cat	3/8	0.450021834938439	2	FACETS	0.837	0.793	0.88			1	CLONAL	3	TRUE	NA	0.548547003945511	2		230	238	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18943055	18943055	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	78	310	0	ENST00000262803.5:c.37C>G	p.Leu13Val	p.L13V	ENST00000262803	NM_002911.3	13	Ctc/Gtc	1/24	0.548547003945511	3	FACETS	1	0.955	1	0.579	0.513	0.648	CLONAL	1	TRUE	1	0.548547003945511	3		310	313	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18943136	18943136	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	27	231	0	ENST00000262803.5:c.118C>G	p.Leu40Val	p.L40V	ENST00000262803	NM_002911.3	40	Ctt/Gtt	1/24	0.548547003945511	3	FACETS	0.721	0.579	0.88	0.36	0.289	0.44	SUBCLONAL	1	TRUE	1	0.548547003945511	3		231	174	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974385	18974385	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	82	485	0	ENST00000262803.5:c.2739C>G	p.Phe913Leu	p.F913L	ENST00000262803	NM_002911.3	913	ttC/ttG	19/24	0.548547003945511	3	FACETS	0.992	0.88	1	0.496	0.44	0.555	CLONAL	1	TRUE	1	0.548547003945511	3		485	384	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212041	36212041	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	91	697	1	ENST00000222270.7:c.1792G>A	p.Glu598Lys	p.E598K	ENST00000222270	NM_014727.1	598	Gag/Aag	3/37	0.548547003945511	7	FACETS	0.895	0.794	1	0.224	0.198	0.251	CLONAL	1	TRUE	3	0.548547003945511	7		698	879	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133368	38133368	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770031665	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	120	425	0	ENST00000317025.8:c.4105G>A	p.Glu1369Lys	p.E1369K	ENST00000317025	NM_023034.1	1369	Gag/Aag	24/24	0.548547003945511	14	FACETS	0.788	0.71	0.871			1	SUBCLONAL	2	TRUE	NA	0.548547003945511	14		425	1191	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864717	68864717	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	155	334	0	ENST00000288368.4:c.88G>C	p.Glu30Gln	p.E30Q	ENST00000288368	NM_024870.2	30	Gag/Cag	1/40	0.396079268289745	5	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	2	0.548547003945511	5		334	314	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527665	157527668	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs1554237269	NA	P-0014189-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	357	735	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	TRUE	1	NA	2		735	870	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916840	48916841	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs1566186125	NA	P-0014189-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	232	499	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	TRUE	0	NA	0		499	297	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	97	214	0				ENST00000310581	NM_198253.2	-/1132			0.385437024614911	4	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	2	0.386636543547787	4		214	322	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970971	21970971	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	211	472	0	ENST00000304494.5:c.387C>A	p.Tyr129Ter	p.Y129*	ENST00000304494	NM_000077.4	129	taC/taA	2/3	0.386636543547787	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.386636543547787	2		472	500	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412252	139412252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057523819	NA	P-0015747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	616	542	1	ENST00000277541.6:c.1393G>A	p.Ala465Thr	p.A465T	ENST00000277541	NM_017617.3	465	Gcc/Acc	8/34	0.386636543547787	6	FACETS	0.971	0.942	0.999	0.971	0.942	0.999	CLONAL	6	TRUE	0	0.386636543547787	6		543	970	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577102	7577102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793881	NA	P-0015747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	219	544	0	ENST00000269305.4:c.836G>A	p.Gly279Glu	p.G279E	ENST00000269305	NM_001126112.2	279	gGg/gAg	8/11	0.386636543547787	2	FACETS	0.975	0.914	1	0.975	0.914	1	CLONAL	2	TRUE	0	0.386636543547787	2		544	581	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539852	187539852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765674305	NA	P-0015747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	174	311	0	ENST00000441802.2:c.7888G>A	p.Asp2630Asn	p.D2630N	ENST00000441802	NM_005245.3	2630	Gac/Aac	10/27	0.386636543547787	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.386636543547787	3		311	447	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954642	17954643	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	102	505	0	ENST00000458235.1:c.251dup	p.Ser85GlufsTer46	p.S85Efs*46	ENST00000458235	NM_000215.3	84	ccg/ccCg	3/24	0.386636543547787	3	FACETS	0.918	0.822	1	0.459	0.411	0.51	CLONAL	1	TRUE	1	0.386636543547787	3		505	686	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605835	46605835	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765477973	NA	P-0015747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	198	419	0	ENST00000263734.3:c.1483G>A	p.Asp495Asn	p.D495N	ENST00000263734	NM_001430.4	495	Gac/Aac	11/16	0.386636543547787	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.386636543547787	3		419	576	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992720	68992720	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs182978151	NA	P-0015747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	223	481	1	ENST00000288368.4:c.1685G>A	p.Arg562His	p.R562H	ENST00000288368	NM_024870.2	562	cGt/cAt	16/40	0.386636543547787	6	FACETS	1	0.959	1	0.521	0.485	0.558	CLONAL	2	TRUE	2	0.386636543547787	6		482	982	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197163	26197163	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	56	390	0	ENST00000356476.2:c.316G>C	p.Glu106Gln	p.E106Q	ENST00000356476		106	Gag/Cag	1/1	0.385423739067096	3	FACETS	0.76	0.652	0.877	0.253	0.217	0.293	SUBCLONAL	1	TRUE	0	0.386636543547787	3		390	455	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022644	31022644	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	157	393	0	ENST00000375687.4:c.2129G>A	p.Gly710Glu	p.G710E	ENST00000375687	NM_015338.5	710	gGa/gAa	13/13	0.386636543547787	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.386636543547787	3		393	446	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421585	49421585	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0015747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	67	377	0	ENST00000301067.7:c.14643+1G>T		p.X4881_splice	ENST00000301067	NM_003482.3	4881			0.386636543547787	3	FACETS	0.876	0.763	0.998	0.438	0.381	0.499	CLONAL	1	TRUE	1	0.386636543547787	3		377	472	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670302	134670302	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	57	281	0	ENST00000398015.3:c.213G>C	p.Trp71Cys	p.W71C	ENST00000398015	NM_004441.4	71	tgG/tgC	3/16	0.386636543547787	6	FACETS	0.977	0.839	1	0.244	0.209	0.282	CLONAL	1	TRUE	2	0.386636543547787	6		281	535	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159041	24159042	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0016457-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	200	501	0	ENST00000263121.7:c.716_717dup	p.Ala240LeufsTer28	p.A240Lfs*28	ENST00000263121	NM_003073.3	238	gcc/gcCTc	6/9	0.734535162857947	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.734535162857947	1		501	338	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148507458	148507458	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016457-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	170	386	0	ENST00000320356.2:c.1996T>A	p.Tyr666Asn	p.Y666N	ENST00000320356	NM_004456.4	666	Tac/Aac	17/20	0.734535162857947	3	FACETS	1	0.948	1	0.516	0.477	0.557	CLONAL	1	TRUE	1	0.734535162857947	3		386	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0016489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	402	571	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.499338143766443	2	FACETS	0.869	0.832	0.906	0.869	0.832	0.906	CLONAL	2	TRUE	0	0.553444413106615	2		572	836	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524560	187524560	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0016489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	184	589	0	ENST00000441802.2:c.11120C>G	p.Ser3707Ter	p.S3707*	ENST00000441802	NM_005245.3	3707	tCa/tGa	19/27	0.553444413106615	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.553444413106615	1		589	379	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832370	72832370	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	62	411	0	ENST00000268489.5:c.4211A>G	p.Asn1404Ser	p.N1404S	ENST00000268489	NM_006885.3	1404	aAt/aGt	9/10	0.165569617452413	3	FACETS	0.797	0.692	0.909	0.266	0.23	0.303	INDETERMINATE	1	TRUE	0	0.553444413106615	3		411	359	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297751	15297751	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	42	741	0	ENST00000263388.2:c.1889C>A	p.Thr630Asn	p.T630N	ENST00000263388	NM_000435.2	630	aCc/aAc	12/33	0.175430707819873	2	FACETS	0.193	0.161	0.23	0.097	0.08	0.115	INDETERMINATE	1	TRUE	0	0.553444413106615	2		741	785	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016686-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	285	405	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.332572342285749	4	FACETS	1	0.972	1	0.782	0.74	0.825	CLONAL	3	FALSE	0	0.357474515567902	4		405	692	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0016686-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	367	706	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.268772155878827	3	FACETS	1	0.989	1	0.76	0.722	0.798	CLONAL	2	FALSE	0	0.357474515567902	3		706	1062	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0016686-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	343	330	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	0.332572342285749	4	FACETS	1	0.988	1	0.834	0.794	0.874	CLONAL	3	FALSE	0	0.357474515567902	4		330	781	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458085	120458086	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0016686-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1298	265	584	0	ENST00000256646.2:c.7259_7260del	p.Glu2420ValfsTer3	p.E2420Vfs*3	ENST00000256646	NM_024408.3	2420	gAG/g	34/34	0.357474515567902	8	FACETS	0.983	0.919	1			1	CLONAL	2	FALSE	NA	0.357474515567902	8		584	1563	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060782	38060784	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0016686-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	224	917	0	ENST00000250448.2:c.1205_1207del	p.Ile402del	p.I402del	ENST00000250448	NM_004496.3	402	aTCAac/aac	2/2	0.323054558421516	1	FACETS	0.993	0.925	1	0.993	0.925	1	CLONAL	1	FALSE	0	0.357474515567902	1		917	1036	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354375	354375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910854855	NA	P-0016686-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	348	675	2	ENST00000262320.3:c.1183C>T	p.Arg395Cys	p.R395C	ENST00000262320	NM_003502.3	395	Cgc/Tgc	5/11	0.357474515567902	5	FACETS	1	0.967	1	0.688	0.65	0.727	CLONAL	2	FALSE	2	0.357474515567902	5		677	1449	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779598	3779598	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016686-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1468	384	905	2	ENST00000262367.5:c.5450C>T	p.Pro1817Leu	p.P1817L	ENST00000262367	NM_004380.2	1817	cCg/cTg	31/31	0.357474515567902	5	FACETS	0.891	0.844	0.94	0.594	0.562	0.627	CLONAL	2	FALSE	2	0.357474515567902	5		907	1852	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675049	40675049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764271025	NA	P-0016686-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	161	590	2	ENST00000249776.8:c.13G>A	p.Glu5Lys	p.E5K	ENST00000249776	NM_033286.3	5	Gaa/Aaa	1/9	1	2	FACETS	0.983	0.902	1	0.983	0.902	1	CLONAL	1	FALSE	1	0.357474515567902	2		592	916	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946746	71946746	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016686-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	137	608	0	ENST00000298229.2:c.2687C>G	p.Ala896Gly	p.A896G	ENST00000298229	NM_001567.3	896	gCa/gGa	24/28	0.312565683800289	5	FACETS	1	0.926	1	0.256	0.232	0.281	CLONAL	1	FALSE	1	0.357474515567902	5		608	1151	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849335	68849631	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGCAACAGTTAAGGATTTAATTTTATTTTTACTAACACAAAATGTTTCGTTTTGTTTTTAACTTCATTGTTTCTGCTCTCTAGGGCTTGGATTTTGAGGCCAAGCAGCAGTACATTCTACACGTAGCAGTGACGAATGTGGTACCTTTTGAGGTCTCTCTCACCACCTCCACAGCCACCGTCACCGTGGATGTGCTGGATGTGAATGAAGCCCCCATCTTTGTGCCTCCTGAAAAGAGAGTGGAAGTGTCCGAGGACTTTGGCGTGGGCCAGGAAATCACATCCTACACTGCCCAGG	AGCAACAGTTAAGGATTTAATTTTATTTTTACTAACACAAAATGTTTCGTTTTGTTTTTAACTTCATTGTTTCTGCTCTCTAGGGCTTGGATTTTGAGGCCAAGCAGCAGTACATTCTACACGTAGCAGTGACGAATGTGGTACCTTTTGAGGTCTCTCTCACCACCTCCACAGCCACCGTCACCGTGGATGTGCTGGATGTGAATGAAGCCCCCATCTTTGTGCCTCCTGAAAAGAGAGTGGAAGTGTCCGAGGACTTTGGCGTGGGCCAGGAAATCACATCCTACACTGCCCAGG	-	novel	NA	P-0017317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	16	125	0	ENST00000261769.5:c.1321-80_1537del		p.X441_splice	ENST00000261769	NM_004360.3	441		10/16	0.539159703668277	2	FACETS	0.6	0.449	0.773	0.3	0.224	0.387	SUBCLONAL	1	TRUE	0	0.539159703668277	2		125	99	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696659	47696659	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	293	441	0	ENST00000347630.2:c.289G>A	p.Glu97Lys	p.E97K	ENST00000347630	NM_001007230.1	97	Gaa/Aaa	5/11	0.514802762817996	4	FACETS	0.938	0.885	0.992	0.938	0.885	0.992	CLONAL	2	TRUE	2	0.539159703668277	4		441	892	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021631	31021631	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	288	360	0	ENST00000375687.4:c.1630G>A	p.Asp544Asn	p.D544N	ENST00000375687	NM_015338.5	544	Gat/Aat	12/13	0.539159703668277	8	FACETS	1	0.982	1	0.371	0.348	0.394	CLONAL	2	TRUE	2	0.539159703668277	8		360	1256	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023153	31023153	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1266	358	493	0	ENST00000375687.4:c.2638A>G	p.Thr880Ala	p.T880A	ENST00000375687	NM_015338.5	880	Act/Gct	13/13	0.539159703668277	8	FACETS	1	0.979	1	0.357	0.337	0.377	CLONAL	2	TRUE	2	0.539159703668277	8		493	1624	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200038	128200038	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	485	703	0	ENST00000341105.2:c.1267G>T	p.Glu423Ter	p.E423*	ENST00000341105	NM_032638.4	423	Gag/Tag	6/6	0.514802762817996	4	FACETS	0.943	0.901	0.985	0.943	0.901	0.985	CLONAL	2	TRUE	2	0.539159703668277	4		703	1469	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332882	153332882	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0017317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	275	394	0	ENST00000281708.4:c.74C>G	p.Ser25Ter	p.S25*	ENST00000281708	NM_033632.3	25	tCa/tGa	2/12	0.539159703668277	2	FACETS	0.998	0.949	1	0.998	0.949	1	CLONAL	2	TRUE	0	0.539159703668277	2		394	511	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523519	106523519	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	114	168	0	ENST00000359195.3:c.2671A>T	p.Ile891Phe	p.I891F	ENST00000359195	NM_002649.2	891	Att/Ttt	8/11	0.514802762817996	4	FACETS	0.907	0.825	0.991	0.907	0.825	0.991	CLONAL	2	TRUE	2	0.539159703668277	4		168	359	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902229	151902229	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	270	402	0	ENST00000262189.6:c.3923C>A	p.Ser1308Ter	p.S1308*	ENST00000262189	NM_170606.2	1308	tCa/tAa	25/59	0.514802762817996	4	FACETS	0.883	0.83	0.937	0.883	0.83	0.937	CLONAL	2	TRUE	2	0.539159703668277	4		402	873	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128246839	128246839	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	354	527	0	ENST00000265960.3:c.1090G>C	p.Glu364Gln	p.E364Q	ENST00000265960	NM_001006617.1	364	Gag/Cag	9/12	0.486154134993217	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.539159703668277	4		527	996	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	279	491	0	ENST00000397062.3:c.92G>A	p.Gly31Glu	p.G31E	ENST00000397062	NM_006164.4	31	gGa/gAa	2/5	0.424801356049815	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	1	0.424801356049815	4		491	570	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998898	11998898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	28	473	0	ENST00000353533.5:c.400C>T	p.Arg134Trp	p.R134W	ENST00000353533	NM_003010.3	134	Cgg/Tgg	4/11	0.424801356049815	3	FACETS	0.524	0.419	0.643	0.262	0.209	0.322	SUBCLONAL	1	TRUE	1	0.424801356049815	3		473	305	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247367	153247367	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747241612	NA	P-0017682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	131	378	0	ENST00000281708.4:c.1435C>G	p.Arg479Gly	p.R479G	ENST00000281708	NM_033632.3	479	Cga/Gga	10/12	0.424801356049815	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	2	TRUE	0	0.424801356049815	2		378	308	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305403	65305403	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	41	785	0	ENST00000342505.4:c.2725T>C	p.Ser909Pro	p.S909P	ENST00000342505	NM_002227.2	909	Tct/Cct	20/25	0.424801356049815	2	FACETS	0.328	0.273	0.39	0.164	0.136	0.195	SUBCLONAL	1	TRUE	0	0.424801356049815	2		785	588	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163297333	163297333	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	124	798	0	ENST00000271452.3:c.179G>T	p.Arg60Leu	p.R60L	ENST00000271452	NM_145697.2	60	cGa/cTa	3/14	0.40848289256961	5	FACETS	1	0.979	1	0.433	0.392	0.477	CLONAL	1	TRUE	2	0.424801356049815	5		798	735	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211581	46211581	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	56	514	0	ENST00000334344.6:c.547C>G	p.Leu183Val	p.L183V	ENST00000334344	NM_152641.2	183	Cta/Gta	5/21	0.424801356049815	3	FACETS	0.73	0.627	0.842	0.365	0.313	0.421	SUBCLONAL	1	TRUE	1	0.424801356049815	3		514	438	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624812	9624812	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	122	712	1	ENST00000353224.5:c.165C>A	p.Asp55Glu	p.D55E	ENST00000353224	NM_177990.2	55	gaC/gaA	3/10	0.297576699574648	5	FACETS	1	0.975	1	0.412	0.373	0.454	CLONAL	1	TRUE	2	0.424801356049815	5		713	760	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0018403-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	463	707	0	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	0.693340041120242	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.693340041120242	2		707	612	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557642	95557642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018403-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	288	658	0	ENST00000393063.1:c.5425G>A	p.Gly1809Arg	p.G1809R	ENST00000393063	NM_030621.3	1809	Ggg/Agg	26/28	0.338463704038203	3	FACETS	1	0.99	1	0.761	0.726	0.795	INDETERMINATE	2	TRUE	0	0.693340041120242	3		658	490	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784440	9784440	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018403-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	211	668	0	ENST00000377346.4:c.2825T>C	p.Ile942Thr	p.I942T	ENST00000377346	NM_005026.3	942	aTt/aCt	22/24	0.693340041120242	3	FACETS	1	0.973	1	0.542	0.505	0.58	CLONAL	1	TRUE	1	0.693340041120242	3		668	756	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226573273	226573273	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018403-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	442	698	0	ENST00000366794.5:c.943G>T	p.Val315Phe	p.V315F	ENST00000366794	NM_001618.3	315	Gtc/Ttc	7/23	0.693340041120242	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.693340041120242	2		698	581	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104375131	104375131	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018403-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	366	630	0	ENST00000369902.3:c.1129T>C	p.Ser377Pro	p.S377P	ENST00000369902	NM_016169.3	377	Tcc/Ccc	9/12	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.693340041120242	2		630	502	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201860	67201860	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018403-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	310	655	0	ENST00000312629.5:c.1060G>A	p.Asp354Asn	p.D354N	ENST00000312629	NM_003952.2	354	Gac/Aac	13/15	0.443137186260368	3	FACETS	0.951	0.905	0.997	0.951	0.905	0.997	CLONAL	2	TRUE	1	0.693340041120242	3		655	633	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936803	32936803	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018403-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	126	457	0	ENST00000380152.3:c.7949A>G	p.Glu2650Gly	p.E2650G	ENST00000380152		2650	gAa/gGa	17/27	0.693340041120242	3	FACETS	0.932	0.848	1	0.466	0.424	0.51	CLONAL	1	TRUE	1	0.693340041120242	3		457	525	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557538	95557538	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0018403-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	70	424	0	ENST00000393063.1:c.5527+2T>C		p.X1843_splice	ENST00000393063	NM_030621.3	1843			0.338463704038203	3	FACETS	0.77	0.676	0.871	0.257	0.225	0.291	INDETERMINATE	1	TRUE	0	0.693340041120242	3		424	353	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90634864	90634864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018403-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	171	560	0	ENST00000330062.3:c.128G>A	p.Arg43Lys	p.R43K	ENST00000330062	NM_002168.2	43	aGg/aAg	2/11	0.612106232784489	3	FACETS	1	0.971	1	0.551	0.509	0.594	CLONAL	1	TRUE	1	0.693340041120242	3		560	603	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223509	36223509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867769309	NA	P-0018403-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	531	928	0	ENST00000222270.7:c.6059C>T	p.Pro2020Leu	p.P2020L	ENST00000222270	NM_014727.1	2020	cCg/cTg	28/37	0.478996649911492	3	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.693340041120242	3		928	937	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799261	42799261	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018403-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	157	610	0	ENST00000575354.2:c.4745G>A	p.Gly1582Glu	p.G1582E	ENST00000575354	NM_015125.3	1582	gGg/gAg	20/20	0.108368551980061	5	FACETS	0.908	0.837	0.98	0.454	0.418	0.49	INDETERMINATE	2	TRUE	1	0.693340041120242	5		610	509	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191065	185191065	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018403-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	235	760	0	ENST00000265026.3:c.1946C>T	p.Ser649Phe	p.S649F	ENST00000265026	NM_004721.4	649	tCc/tTc	11/14	0.392320552435305	3	FACETS	1	0.988	1	0.616	0.577	0.656	INDETERMINATE	1	TRUE	1	0.693340041120242	3		760	741	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446181	187446181	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1488877472	NA	P-0018403-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	214	819	0	ENST00000232014.4:c.1507G>A	p.Glu503Lys	p.E503K	ENST00000232014	NM_001130845.1	503	Gag/Aag	6/10	0.392320552435305	3	FACETS	1	0.976	1	0.551	0.514	0.59	INDETERMINATE	1	TRUE	1	0.693340041120242	3		819	754	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637423	176637423	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018403-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	287	587	0	ENST00000439151.2:c.2023A>G	p.Met675Val	p.M675V	ENST00000439151	NM_022455.4	675	Atg/Gtg	5/23	0.693340041120242	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.693340041120242	3		587	543	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169251	32169251	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018403-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	198	809	0	ENST00000375023.3:c.3782A>G	p.Asp1261Gly	p.D1261G	ENST00000375023	NM_004557.3	1261	gAt/gGt	22/30	0.693340041120242	3	FACETS	0.936	0.868	1	0.468	0.434	0.503	CLONAL	1	TRUE	1	0.693340041120242	3		809	822	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226039	53226039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018403-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	464	996	1	ENST00000375401.3:c.2810C>T	p.Thr937Ile	p.T937I	ENST00000375401	NM_004187.3	937	aCa/aTa	19/26	0.443137186260368	3	FACETS	0.953	0.915	0.99	0.953	0.915	0.99	CLONAL	2	TRUE	1	0.693340041120242	3		997	946	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107299	193107299	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018403-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	71	263	0	ENST00000367435.3:c.508A>C	p.Ile170Leu	p.I170L	ENST00000367435	NM_024529.4	170	Att/Ctt	6/17	0.693340041120242	2	FACETS	1	0.945	1	0.551	0.491	0.612	CLONAL	1	TRUE	0	0.693340041120242	2		263	186	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0018421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	32	530	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.468	0.379	0.569	0.468	0.379	0.569	SUBCLONAL	1	FALSE	1	0.286503076723192	2		530	477	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0018421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	82	670	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.869	0.766	0.978	0.869	0.766	0.978	CLONAL	1	FALSE	1	0.286503076723192	2		670	659	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0018421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	21	328	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.474	0.365	0.602	0.474	0.365	0.602	SUBCLONAL	1	FALSE	1	0.286503076723192	2		328	309	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259339	11259340	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0018421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	39	427	2	ENST00000361445.4:c.4228_4229delinsTT	p.Pro1410Phe	p.P1410F	ENST00000361445	NM_004958.3	1410	CCt/TTt	28/58	1	2	FACETS	0.453	0.375	0.541	0.453	0.375	0.541	SUBCLONAL	1	FALSE	1	0.286503076723192	2		429	601	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555986	226555986	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	32	309	0	ENST00000366794.5:c.2191G>A	p.Asp731Asn	p.D731N	ENST00000366794	NM_001618.3	731	Gat/Aat	16/23	1	2	FACETS	0.545	0.442	0.661	0.545	0.442	0.661	SUBCLONAL	1	FALSE	1	0.286503076723192	2		309	410	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346472	89346472	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1221986228	NA	P-0018421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	47	498	0	ENST00000301030.4:c.6478C>T	p.Leu2160Phe	p.L2160F	ENST00000301030	NM_001256183.1	2160	Ctt/Ttt	9/13	1	2	FACETS	0.617	0.52	0.723	0.617	0.52	0.723	SUBCLONAL	1	FALSE	1	0.286503076723192	2		498	532	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552264	29552264	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	47	365	1	ENST00000356175.3:c.1997C>T	p.Ser666Phe	p.S666F	ENST00000356175	NM_000267.3	666	tCt/tTt	17/57	1	2	FACETS	0.694	0.586	0.813	0.694	0.586	0.813	SUBCLONAL	1	FALSE	1	0.286503076723192	2		366	473	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591839	48591840	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0018421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	28	300	2	ENST00000342988.3:c.1002_1003delinsAA	p.Val335Ile	p.V335I	ENST00000342988	NM_005359.5	334	caGGta/caAAta	9/12	1	2	FACETS	0.382	0.304	0.47	0.382	0.304	0.47	SUBCLONAL	1	FALSE	1	0.286503076723192	2		302	512	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11015734	11015734	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	37	322	0	ENST00000327064.4:c.328C>T	p.Gln110Ter	p.Q110*	ENST00000327064	NM_199141.1	110	Cag/Tag	2/16	1	2	FACETS	0.573	0.472	0.685	0.573	0.472	0.685	SUBCLONAL	1	FALSE	1	0.286503076723192	2		322	451	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050389	13050389	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs550682309	NA	P-0018421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	28	392	0	ENST00000316448.5:c.341C>G	p.Pro114Arg	p.P114R	ENST00000316448	NM_004343.3	114	cCt/cGt	3/9	1	2	FACETS	0.357	0.284	0.44	0.357	0.284	0.44	SUBCLONAL	1	FALSE	1	0.286503076723192	2		392	548	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627426	14627426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	89	524	0	ENST00000254322.2:c.644G>A	p.Gly215Glu	p.G215E	ENST00000254322	NM_006145.1	215	gGa/gAa	2/3	1	2	FACETS	0.836	0.741	0.938	0.836	0.741	0.938	CLONAL	1	FALSE	1	0.286503076723192	2		524	743	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216718	36216718	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	31	283	0	ENST00000222270.7:c.3884G>A	p.Trp1295Ter	p.W1295*	ENST00000222270	NM_014727.1	1295	tGg/tAg	13/37	1	2	FACETS	0.606	0.491	0.737	0.606	0.491	0.737	SUBCLONAL	1	FALSE	1	0.286503076723192	2		283	357	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733295	40733296	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0018421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	55	320	1	ENST00000373198.4:c.3510_3511delinsTT	p.Pro1171Ser	p.P1171S	ENST00000373198	NM_133170.3	1170	atCCct/atTTct	26/32	1	2	FACETS	0.706	0.604	0.817	0.706	0.604	0.817	SUBCLONAL	1	FALSE	1	0.286503076723192	2		321	544	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696244	52696244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	85	458	1	ENST00000394830.3:c.433C>T	p.Leu145Phe	p.L145F	ENST00000394830	NM_018313.4	145	Ctt/Ttt	5/30	1	2	FACETS	0.799	0.705	0.898	0.799	0.705	0.898	SUBCLONAL	1	FALSE	1	0.286503076723192	2		459	743	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138409894	138409894	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	55	467	0	ENST00000289153.2:c.1984G>A	p.Glu662Lys	p.E662K	ENST00000289153	NM_006219.2	662	Gaa/Aaa	13/22	1	2	FACETS	0.544	0.464	0.631	0.544	0.464	0.631	SUBCLONAL	1	FALSE	1	0.286503076723192	2		467	706	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155369	185155369	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	50	329	0	ENST00000265026.3:c.610G>A	p.Asp204Asn	p.D204N	ENST00000265026	NM_004721.4	204	Gat/Aat	3/14	1	2	FACETS	0.709	0.602	0.827	0.709	0.602	0.827	SUBCLONAL	1	FALSE	1	0.286503076723192	2		329	492	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959914	38959914	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	51	274	0	ENST00000357387.3:c.2018T>G	p.Val673Gly	p.V673G	ENST00000357387	NM_152756.3	673	gTt/gGt	21/38	1	2	FACETS	0.73	0.62	0.849	0.73	0.62	0.849	SUBCLONAL	1	FALSE	1	0.286503076723192	2		274	488	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959927	38959927	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	55	284	0	ENST00000357387.3:c.2005C>A	p.His669Asn	p.H669N	ENST00000357387	NM_152756.3	669	Cac/Aac	21/38	1	2	FACETS	0.741	0.634	0.858	0.741	0.634	0.858	SUBCLONAL	1	FALSE	1	0.286503076723192	2		284	518	SUCCESS
APC	324	MSKCC	GRCh37	5	112151209	112151210	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0018421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	43	346	0	ENST00000257430.4:c.852_853delinsAA	p.Met284_Asp285delinsIleAsn	p.M284_D285delinsIN	ENST00000257430	NM_000038.5	284	atGGac/atAAac	9/16	1	2	FACETS	0.546	0.456	0.645	0.546	0.456	0.645	SUBCLONAL	1	FALSE	1	0.286503076723192	2		346	550	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412297	139412297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	50	441	0	ENST00000277541.6:c.1348G>A	p.Glu450Lys	p.E450K	ENST00000277541	NM_017617.3	450	Gag/Aag	8/34	1	2	FACETS	0.597	0.506	0.697	0.597	0.506	0.697	SUBCLONAL	1	FALSE	1	0.286503076723192	2		441	585	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211873	123211873	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1216415127	NA	P-0018421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	69	429	0	ENST00000218089.9:c.2740C>T	p.Gln914Ter	p.Q914*	ENST00000218089	NM_001042749.1	914	Cag/Tag	27/35	0.286503076723192	1	FACETS	0.6	0.522	0.684	0.6	0.522	0.684	SUBCLONAL	1	FALSE	0	0.286503076723192	1		429	688	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0018771-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	658	833	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.562941898915875	4	FACETS	0.919	0.896	0.941	0.919	0.896	0.941	CLONAL	4	TRUE	0	0.652494586618721	4		833	907	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974727	21974744	+	inframe_deletion	In_Frame_Del	DEL	CCTCCAGCAGCGCCCGCA	CCTCCAGCAGCGCCCGCA	-	novel	NA	P-0018771-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	36	333	0	ENST00000304494.5:c.83_100del	p.Val28_Glu33del	p.V28_E33del	ENST00000304494	NM_000077.4	28	gTGCGGGCGCTGCTGGAGGcg/gcg	1/3	0.323095030278096	1	FACETS	0.31	0.256	0.369	0.31	0.256	0.369	INDETERMINATE	1	TRUE	0	0.652494586618721	1		333	240	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462032	120462032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201996575	NA	P-0018771-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	166	581	0	ENST00000256646.2:c.5684G>A	p.Arg1895His	p.R1895H	ENST00000256646	NM_024408.3	1895	cGt/cAt	31/34	0.288663671929787	1	FACETS	0.671	0.621	0.722	0.671	0.621	0.722	INDETERMINATE	1	TRUE	0	0.652494586618721	1		581	511	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120783942	120783942	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018771-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	263	562	0	ENST00000257552.2:c.1043T>G	p.Leu348Arg	p.L348R	ENST00000257552	NM_002442.3	348	cTt/cGt	13/15	0.638563588360076	2	FACETS	0.993	0.949	1	0.993	0.949	1	CLONAL	2	TRUE	0	0.652494586618721	2		562	406	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437600	56437600	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018771-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	242	399	0	ENST00000407977.2:c.862A>T	p.Ile288Phe	p.I288F	ENST00000407977		288	Att/Ttt	8/10	0.652494586618721	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.652494586618721	2		399	367	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876220	35876220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018771-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	196	474	0	ENST00000303115.3:c.1012C>A	p.Gln338Lys	p.Q338K	ENST00000303115	NM_002185.3	338	Cag/Aag	8/8	0.511775013688681	3	FACETS	1	0.99	1	0.464	0.433	0.497	CLONAL	1	TRUE	0	0.652494586618721	3		474	572	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156731	20156731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	0	101	152	0	ENST00000379607.5:c.26G>A	p.Gly9Asp	p.G9D	ENST00000379607	NM_001412.3	9	gGt/gAt	2/7	0.225740866245207	2	FACETS		NA	1			1	NA	9	FALSE	NA	0.225740866245207	2		152	101	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202351	123202427	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTAAAGAAATGCTGAATTGTTTATACAATATTTTTTAAAAGTTAATGTTAAATTTTTTCAAGGAGGACTTGCTGCG	TTTAAAGAAATGCTGAATTGTTTATACAATATTTTTTAAAAGTTAATGTTAAATTTTTTCAAGGAGGACTTGCTGCG	-	novel	NA	P-0018839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	73	56	0	ENST00000218089.9:c.2266-53_2289del		p.X756_splice	ENST00000218089	NM_001042749.1	756		24/35	0.107638157784946	2	FACETS	1	0.96	1			1	INDETERMINATE	5	FALSE	NA	0.225740866245207	2		56	118	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0018928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	264	724	1	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		725	934	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913492	NA	P-0019174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	341	727	0	ENST00000286548.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000286548	NM_002072.3	209	cAa/cTa	5/7	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		727	836	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402593	139402593	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0019174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	36	710	0	ENST00000277541.6:c.3326-2A>G		p.X1109_splice	ENST00000277541	NM_017617.3	1109			1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		710	553	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019175-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	81	214	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.489516901511795	2		214	244	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782082	NA	P-0019175-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	190	622	0	ENST00000269305.4:c.745A>T	p.Arg249Trp	p.R249W	ENST00000269305	NM_001126112.2	249	Agg/Tgg	7/11	0.489516901511795	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.489516901511795	1		622	490	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712007	89712007	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765433422	NA	P-0019175-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	107	306	0	ENST00000371953.3:c.625G>A	p.Gly209Arg	p.G209R	ENST00000371953	NM_000314.4	209	Gga/Aga	6/9	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.489516901511795	2		306	357	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432522	49432522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019175-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	142	530	0	ENST00000301067.7:c.8617G>A	p.Gly2873Ser	p.G2873S	ENST00000301067	NM_003482.3	2873	Ggt/Agt	34/54	0.489516901511795	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.489516901511795	1		530	416	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457176	25457176	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149095705	NA	P-0019175-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	162	587	0	ENST00000264709.3:c.2711C>T	p.Pro904Leu	p.P904L	ENST00000264709	NM_175629.2	904	cCg/cTg	23/23	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.489516901511795	2		587	568	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470959	25470960	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGACCCCACGGGCTCAG	novel	NA	P-0019175-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	106	716	0	ENST00000264709.3:c.785_801dup	p.Asp268LeufsTer54	p.D268Lfs*54	ENST00000264709	NM_175629.2	267	-/CTGAGCCCGTGGGGTCC	7/23	1	2	FACETS	0.68	0.61	0.753	0.68	0.61	0.753	SUBCLONAL	1	TRUE	1	0.489516901511795	2		716	637	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591069	67591070	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAGTATCGAGAAATTGACAAACGTATGAACAGCATTAAA	novel	NA	P-0019175-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	33	194	0	ENST00000274335.5:c.1663_1701dup	p.Glu555_Lys567dup	p.E555_K567dup	ENST00000274335		555	-/GAGTATCGAGAAATTGACAAACGTATGAACAGCATTAAA	12/15	0.489516901511795	1	FACETS	0.431	0.353	0.518	0.431	0.353	0.518	SUBCLONAL	1	TRUE	0	0.489516901511795	1		194	236	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0019889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	63	331	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.436376995683903	2		331	257	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106805	27106805	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1302295523	NA	P-0019889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	174	616	0	ENST00000324856.7:c.6416C>A	p.Pro2139His	p.P2139H	ENST00000324856	NM_006015.4	2139	cCc/cAc	20/20	1	2	FACETS	0.978	0.902	1	0.978	0.902	1	CLONAL	1	TRUE	1	0.436376995683903	2		616	815	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36826842	36826842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	178	658	0	ENST00000373129.3:c.92G>A	p.Arg31Lys	p.R31K	ENST00000373129	NM_032017.1	31	aGa/aAa	3/12	1	2	FACETS	0.933	0.861	1	0.933	0.861	1	CLONAL	1	TRUE	1	0.436376995683903	2		658	874	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834189	156834189	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	239	913	0	ENST00000524377.1:c.256G>A	p.Asp86Asn	p.D86N	ENST00000524377	NM_002529.3	86	Gat/Aat	2/17	1	2	FACETS	0.97	0.905	1	0.97	0.905	1	CLONAL	1	TRUE	1	0.436376995683903	2		913	1129	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332960	70332960	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751530578	NA	P-0019889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	208	727	0	ENST00000373644.4:c.865C>T	p.Pro289Ser	p.P289S	ENST00000373644	NM_030625.2	289	Ccc/Tcc	2/12	1	2	FACETS	0.924	0.857	0.993	0.924	0.857	0.993	CLONAL	1	TRUE	1	0.436376995683903	2		727	1032	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433072	49433072	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	182	820	0	ENST00000301067.7:c.8299C>T	p.Pro2767Ser	p.P2767S	ENST00000301067	NM_003482.3	2767	Cct/Tct	33/54	1	2	FACETS	0.877	0.809	0.948	0.877	0.809	0.948	CLONAL	1	TRUE	1	0.436376995683903	2		820	951	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95583017	95583017	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886037672	NA	P-0019889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	84	323	0	ENST00000393063.1:c.1525C>T	p.Arg509Ter	p.R509*	ENST00000393063	NM_030621.3	509	Cga/Tga	11/28	1	2	FACETS	0.906	0.804	1	0.906	0.804	1	CLONAL	1	TRUE	1	0.436376995683903	2		323	425	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729086	66729103	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	AATTCATCTGGAGATCAA	AATTCATCTGGAGATCAA	-	novel	NA	P-0019889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	409	571	0	ENST00000307102.5:c.295_312del	p.Ile99_Lys104del	p.I99_K104del	ENST00000307102	NM_002755.3	98	ctAATTCATCTGGAGATCAAa/cta	3/11	0.436376995683903	4	FACETS	0.944	0.902	0.986	0.944	0.902	0.986	CLONAL	3	TRUE	1	0.436376995683903	4		571	951	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396571	396571	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	220	916	0	ENST00000262320.3:c.455A>G	p.Asn152Ser	p.N152S	ENST00000262320	NM_003502.3	152	aAc/aGc	2/11	1	2	FACETS	0.92	0.855	0.987	0.92	0.855	0.987	CLONAL	1	TRUE	1	0.436376995683903	2		916	1096	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857376	9857376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	162	533	0	ENST00000330684.3:c.4025C>T	p.Ser1342Phe	p.S1342F	ENST00000330684	NM_001134407.1	1342	tCc/tTc	13/13	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.436376995683903	2		533	671	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812260	212812260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751175543	NA	P-0019889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	110	410	0	ENST00000342788.4:c.316C>T	p.Arg106Cys	p.R106C	ENST00000342788	NM_005235.2	106	Cgt/Tgt	3/28	1	2	FACETS	0.939	0.847	1	0.939	0.847	1	CLONAL	1	TRUE	1	0.436376995683903	2		410	537	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400190	41400190	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	118	488	0	ENST00000373198.4:c.569G>A	p.Arg190Lys	p.R190K	ENST00000373198	NM_133170.3	190	aGa/aAa	5/32	1	2	FACETS	0.842	0.762	0.927	0.842	0.762	0.927	CLONAL	1	TRUE	1	0.436376995683903	2		488	642	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37622814	37622814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	240	892	1	ENST00000249071.6:c.478C>T	p.Leu160Phe	p.L160F	ENST00000249071	NM_002872.4	160	Ctc/Ttc	6/7	1	2	FACETS	0.945	0.882	1	0.945	0.882	1	CLONAL	1	TRUE	1	0.436376995683903	2		893	1164	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271297	26271297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	125	524	0	ENST00000305910.3:c.316G>A	p.Glu106Lys	p.E106K	ENST00000305910	NM_003534.2	106	Gag/Aag	1/1	0.41881612410539	3	FACETS	0.865	0.783	0.951	0.432	0.391	0.476	CLONAL	1	TRUE	1	0.436376995683903	3		524	807	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673130	30673130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	45	472	0	ENST00000376406.3:c.3830C>T	p.Ser1277Phe	p.S1277F	ENST00000376406	NM_014641.2	1277	tCt/tTt	10/15	0.41881612410539	3	FACETS	0.335	0.28	0.395	0.167	0.14	0.198	SUBCLONAL	1	TRUE	1	0.436376995683903	3		472	751	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56912099	56912099	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	184	721	0	ENST00000519728.1:c.1327C>T	p.Pro443Ser	p.P443S	ENST00000519728	NM_002350.3	443	Ccc/Tcc	12/13	1	2	FACETS	0.983	0.908	1	0.983	0.908	1	CLONAL	1	TRUE	1	0.436376995683903	2		721	858	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931876	68931877	+	stop_gained	Nonsense_Mutation	DNP	AC	AC	TT	novel	NA	P-0019889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	163	684	1	ENST00000288368.4:c.306_307delinsTT	p.Gln102_Gln103delinsHisTer	p.Q102_Q103delinsH*	ENST00000288368	NM_024870.2	102	caACaa/caTTaa	3/40	1	2	FACETS	0.795	0.729	0.863	0.795	0.729	0.863	SUBCLONAL	1	TRUE	1	0.436376995683903	2		685	940	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606544	93606544	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs962420195	NA	P-0019889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	199	719	0	ENST00000375746.1:c.364G>A	p.Asp122Asn	p.D122N	ENST00000375746	NM_001174167.1	122	Gat/Aat	2/14	0.436376995683903	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.436376995683903	1		719	673	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0019889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	117	409	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	1	2	FACETS	0.921	0.833	1	0.921	0.833	1	CLONAL	1	TRUE	1	0.436376995683903	2		409	582	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417575	139417575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	204	934	1	ENST00000277541.6:c.469C>T	p.Pro157Ser	p.P157S	ENST00000277541	NM_017617.3	157	Ccc/Tcc	4/34	1	2	FACETS	0.933	0.865	1	0.933	0.865	1	CLONAL	1	TRUE	1	0.436376995683903	2		935	1002	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021250	31021250	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs375215583	NA	P-0020052-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	190	406	0	ENST00000375687.4:c.1249C>T	p.Arg417Ter	p.R417*	ENST00000375687	NM_015338.5	417	Cga/Tga	12/13	0.840202392730425	7	FACETS	1	0.987	1	0.333	0.307	0.36	CLONAL	1	FALSE	3	0.840202392730425	7		406	1053	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021128	31021128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020052-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	180	465	0	ENST00000375687.4:c.1127G>A	p.Gly376Asp	p.G376D	ENST00000375687	NM_015338.5	376	gGc/gAc	12/13	0.840202392730425	7	FACETS	1	0.97	1	0.277	0.254	0.3	CLONAL	1	FALSE	3	0.840202392730425	7		465	1200	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-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	97	132	0	ENST00000349496.5:c.13+126_153del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.840202392730425	4	FACETS	1	0.983	1	0.74	0.669	0.814	CLONAL	1	FALSE	2	0.840202392730425	4		132	287	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188760	32188760	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020052-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	199	541	2	ENST00000375023.3:c.794C>T	p.Pro265Leu	p.P265L	ENST00000375023	NM_004557.3	265	cCc/cTc	4/30	0.775108307346664	5	FACETS	1	0.955	1	0.348	0.322	0.375	CLONAL	1	FALSE	2	0.840202392730425	5		543	1026	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807987	3807988	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0020052-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	189	570	0	ENST00000262367.5:c.3431_3432del	p.Thr1144ArgfsTer24	p.T1144Rfs*24	ENST00000262367	NM_004380.2	1144	aCA/a	18/31	0.840202392730425	5	FACETS	0.949	0.876	1	0.316	0.292	0.342	CLONAL	1	FALSE	2	0.840202392730425	5		570	1072	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732386	74732386	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020052-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	108	258	0	ENST00000359995.5:c.523T>C	p.Ser175Pro	p.S175P	ENST00000359995	NM_001195427.1	175	Tcg/Ccg	2/3	0.791995206541334	6	FACETS	1	0.951	1	0.219	0.196	0.242	CLONAL	1	FALSE	1	0.840202392730425	6		258	630	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111982964	111982964	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020052-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1236	122	574	0	ENST00000368678.4:c.1583A>G	p.Tyr528Cys	p.Y528C	ENST00000368678		528	tAc/tGc	13/13	0.840202392730425	6	FACETS	0.573	0.516	0.634	0.191	0.172	0.212	SUBCLONAL	1	FALSE	3	0.840202392730425	6		574	1358	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346273	70346273	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020052-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	236	397	0	ENST00000374080.3:c.2624T>C	p.Phe875Ser	p.F875S	ENST00000374080		875	tTc/tCc	19/45	0.840202392730425	3	FACETS	0.871	0.814	0.93			1	CLONAL	1	FALSE	NA	0.840202392730425	3		397	916	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0020290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	268	459	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.829652928678849	3	FACETS	0.894	0.849	0.939	0.894	0.849	0.939	CLONAL	2	TRUE	1	0.829652928678849	3		459	511	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602493	10602493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	553	647	0	ENST00000171111.5:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000171111	NM_203500.1	362	cGg/cAg	3/6	0.829652928678849	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.829652928678849	2		647	655	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578448	7578448	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1064795691	NA	P-0020290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	925	655	0	ENST00000269305.4:c.482C>A	p.Ala161Asp	p.A161D	ENST00000269305	NM_001126112.2	161	gCc/gAc	5/11	0.810318306503804	3	FACETS	0.993	0.978	1	0.993	0.978	1	CLONAL	3	TRUE	0	0.829652928678849	3		655	1059	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30061031	30061031	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0020290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	421	460	0	ENST00000338641.4:c.863C>G	p.Ser288Ter	p.S288*	ENST00000338641	NM_000268.3	288	tCa/tGa	9/16	0.829652928678849	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.829652928678849	2		460	502	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141534	11141534	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	500	580	1	ENST00000358026.2:c.3511G>A	p.Val1171Met	p.V1171M	ENST00000358026	NM_001128849.1	1171	Gtg/Atg	25/36	0.829652928678849	2	FACETS	0.963	0.939	0.985	0.963	0.939	0.985	CLONAL	2	TRUE	0	0.829652928678849	2		581	626	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77070038	77070038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777870573	NA	P-0020290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	205	381	0	ENST00000356341.3:c.502C>T	p.Pro168Ser	p.P168S	ENST00000356341	NM_002576.4	168	Cct/Tct	6/15	0.829652928678849	3	FACETS	0.947	0.882	1	0.474	0.441	0.508	CLONAL	1	TRUE	1	0.829652928678849	3		381	738	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973622	15973622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	415	399	0	ENST00000268712.3:c.4370C>T	p.Ser1457Phe	p.S1457F	ENST00000268712	NM_006311.3	1457	tCc/tTc	31/46	0.810318306503804	3	FACETS	0.982	0.944	1	0.654	0.629	0.679	CLONAL	2	TRUE	0	0.829652928678849	3		399	721	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597494	10597494	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	478	436	0	ENST00000171111.5:c.1709G>C	p.Gly570Ala	p.G570A	ENST00000171111	NM_203500.1	570	gGa/gCa	6/6	0.829652928678849	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.829652928678849	2		436	566	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600000	10600000	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	729	614	0	ENST00000171111.5:c.1576G>C	p.Asp526His	p.D526H	ENST00000171111	NM_203500.1	526	Gat/Cat	5/6	0.829652928678849	2	FACETS	0.973	0.954	0.992	0.973	0.954	0.992	CLONAL	2	TRUE	0	0.829652928678849	2		614	903	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663064	227663064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	238	508	0	ENST00000305123.5:c.391G>A	p.Gly131Ser	p.G131S	ENST00000305123	NM_005544.2	131	Ggt/Agt	1/2	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.829652928678849	2		508	565	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589569	67589610	+	inframe_deletion	In_Frame_Del	DEL	TGTAGGGAAAAAATTACATGAATATAACACTCAGTTTCAAGA	TGTAGGGAAAAAATTACATGAATATAACACTCAGTTTCAAGA	-	novel	NA	P-0020290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	138	125	0	ENST00000274335.5:c.1332_1373del	p.Val445_Glu458del	p.V445_E458del	ENST00000274335		444	gcTGTAGGGAAAAAATTACATGAATATAACACTCAGTTTCAAGAa/gca	10/15	0.827654491265976	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.829652928678849	2		125	158	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518025	8518025	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	525	466	0	ENST00000356435.5:c.1366A>G	p.Thr456Ala	p.T456A	ENST00000356435		456	Aca/Gca	10/35	0.815390285091181	3	FACETS	0.98	0.96	0.999	0.98	0.96	0.999	CLONAL	3	TRUE	0	0.829652928678849	3		466	609	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759875	133759875	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	808	658	0	ENST00000318560.5:c.2198C>T	p.Ser733Leu	p.S733L	ENST00000318560	NM_005157.4	733	tCa/tTa	11/11	0.815390285091181	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.829652928678849	3		658	912	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924213	11924213	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	20	5	0	ENST00000353533.5:c.10C>G	p.Pro4Ala	p.P4A	ENST00000353533	NM_003010.3	4	Ccg/Gcg	1/11	0.810318306503804	3	FACETS	0.91	0.791	1	0.91	0.791	1	CLONAL	3	TRUE	0	0.829652928678849	3		5	25	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11027124	11027124	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	329	697	0	ENST00000327064.4:c.890del	p.Phe297SerfsTer52	p.F297Sfs*52	ENST00000327064	NM_199141.1	297	Ttc/tc	7/16	0.829652928678849	2	FACETS	0.891	0.845	0.938	0.446	0.422	0.469	CLONAL	1	TRUE	0	0.829652928678849	2		697	890	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397167	397168	+	missense_variant	Missense_Mutation	DNP	TC	TC	AG	novel	NA	P-0020290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	94	309	0	ENST00000380956.4:c.552_553delinsAG	p.Asp184_Gln185delinsGluGlu	p.D184_Q185delinsEE	ENST00000380956	NM_001195286.1	184	gaTCag/gaAGag	5/9	0.810318306503804	3	FACETS	0.774	0.693	0.86	0.258	0.231	0.287	SUBCLONAL	1	TRUE	0	0.829652928678849	3		309	414	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786739	3786739	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	354	918	0	ENST00000262367.5:c.4472A>C	p.Gln1491Pro	p.Q1491P	ENST00000262367	NM_004380.2	1491	cAa/cCa	27/31	NA	2	FACETS	0.965	0.919	1			1	INDETERMINATE	1	TRUE	NA	0.873253654903886	2		918	840	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266872	18266872	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	313	656	0	ENST00000222254.8:c.183C>A	p.Asn61Lys	p.N61K	ENST00000222254	NM_005027.3	61	aaC/aaA	2/16	NA	2	FACETS	1	0.962	1			1	INDETERMINATE	1	TRUE	NA	0.873253654903886	2		656	706	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437669	52437669	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	307	836	0	ENST00000460680.1:c.1492del	p.Glu498ArgfsTer73	p.E498Rfs*73	ENST00000460680	NM_004656.3	498	Gag/ag	13/17	0.818923389404754	1	FACETS	0.926	0.891	0.958	0.926	0.891	0.958	CLONAL	1	TRUE	0	0.873253654903886	1		836	428	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349262	70349262	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	332	942	1	ENST00000374080.3:c.3674A>T	p.Lys1225Met	p.K1225M	ENST00000374080		1225	aAg/aTg	26/45	0.205156385728882	1	FACETS	0.537	0.511	0.565	0.537	0.511	0.565	INDETERMINATE	1	TRUE	0	0.873253654903886	1		943	797	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0020685-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	243	625	1	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.198435704322216	2	FACETS	0.985	0.92	1	0.985	0.92	1	CLONAL	2	TRUE	0	0.244586539074906	2		626	1009	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242480	55242503	+	inframe_deletion	In_Frame_Del	DEL	AACATCTCCGAAAGCCAACAAGGA	AACATCTCCGAAAGCCAACAAGGA	-	novel	NA	P-0020685-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	366	316	0	ENST00000275493.2:c.2252_2275del	p.Thr751_Glu758del	p.T751_E758del	ENST00000275493	NM_005228.3	750	gcAACATCTCCGAAAGCCAACAAGGAa/gca	19/28	0.244586539074906	11	FACETS	0.961	0.914	1			1	CLONAL	7	TRUE	NA	0.244586539074906	11		316	935	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687286	117687286	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020685-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	29	382	0	ENST00000368508.3:c.2765G>C	p.Arg922Thr	p.R922T	ENST00000368508	NM_002944.2	922	aGa/aCa	18/43	1	2	FACETS	0.427	0.342	0.525	0.427	0.342	0.525	SUBCLONAL	1	TRUE	1	0.244586539074906	2		382	555	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	516	560	2	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.888	0.852	0.924	0.888	0.852	0.924	CLONAL	1	TRUE	1	0.924134184166672	2		562	1258	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	542	627	6	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.871	0.836	0.905	0.871	0.836	0.905	CLONAL	1	TRUE	1	0.924134184166672	2		633	1347	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736510	85736511	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs387906351	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	83	388	3	ENST00000370580.1:c.136dup	p.Ile46AsnfsTer4	p.I46Nfs*4	ENST00000370580	NM_003921.4	46	ata/aAta	2/3	1	2	FACETS	0.758	0.68	0.839	0.758	0.68	0.839	SUBCLONAL	1	TRUE	1	0.924134184166672	2		391	237	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033352	48033352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750949	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	97	468	0	ENST00000234420.5:c.3656C>T	p.Thr1219Ile	p.T1219I	ENST00000234420	NM_000179.2	1219	aCt/aTt	8/10	1	2	FACETS	0.804	0.729	0.882	0.804	0.729	0.882	CLONAL	1	TRUE	1	0.924134184166672	2		468	261	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	72	275	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.924134184166672	2		275	153	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	335	513	0	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.844	0.801	0.887	0.844	0.801	0.887	CLONAL	1	TRUE	1	0.924134184166672	2		513	859	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	112	271	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.966	0.886	1	0.966	0.886	1	CLONAL	1	TRUE	1	0.924134184166672	2		271	251	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	687	750	2	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.949	0.917	0.982	0.949	0.917	0.982	CLONAL	1	TRUE	1	0.924134184166672	2		752	1566	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	233	317	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.909	0.855	0.963	0.909	0.855	0.963	CLONAL	1	TRUE	1	0.924134184166672	2		317	555	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589168	67589168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	34	259	0	ENST00000274335.5:c.1156C>T	p.Arg386Ter	p.R386*	ENST00000274335		386	Cga/Tga	9/15	1	2	FACETS	0.876	0.742	1	0.876	0.742	1	CLONAL	1	TRUE	1	0.924134184166672	2		259	84	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138642	55138642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143344944	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	419	503	0	ENST00000257290.5:c.1319C>T	p.Thr440Met	p.T440M	ENST00000257290	NM_006206.4	440	aCg/aTg	9/23	1	2	FACETS	0.97	0.928	1	0.97	0.928	1	CLONAL	1	TRUE	1	0.924134184166672	2		503	935	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	544	394	3	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.971	0.934	1	0.971	0.934	1	CLONAL	1	TRUE	1	0.924134184166672	2		397	1213	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024001	27024002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	38	89	0	ENST00000324856.7:c.1113dup	p.Gln372AlafsTer28	p.Q372Afs*28	ENST00000324856	NM_006015.4	369	-/G	1/20	1	2	FACETS	0.623	0.526	0.727	0.623	0.526	0.727	SUBCLONAL	1	TRUE	1	0.924134184166672	2		89	132	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	601	723	9	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.96	0.925	0.995	0.96	0.925	0.995	CLONAL	1	TRUE	1	0.924134184166672	2		732	1355	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	338	510	5	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.924134184166672	2		515	692	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370236	40370236	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs761761205	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	366	738	12	ENST00000293328.3:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000293328	NM_012448.3	368	Cag/ag	9/19	1	2	FACETS	0.606	0.574	0.639	0.606	0.574	0.639	SUBCLONAL	1	TRUE	1	0.924134184166672	2		750	1307	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464896	120464896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	353	487	0	ENST00000256646.2:c.5176C>T	p.Arg1726Cys	p.R1726C	ENST00000256646	NM_024408.3	1726	Cgt/Tgt	28/34	1	2	FACETS	0.955	0.91	1	0.955	0.91	1	CLONAL	1	TRUE	1	0.924134184166672	2		487	800	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794685	42794685	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767618694	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	624	715	0	ENST00000575354.2:c.1765C>T	p.Arg589Trp	p.R589W	ENST00000575354	NM_015125.3	589	Cgg/Tgg	10/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.924134184166672	2		715	1322	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517445	157517445	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs773740590	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	298	351	0	ENST00000346085.5:c.4009C>T	p.Arg1337Ter	p.R1337*	ENST00000346085	NM_020732.3	1337	Cga/Tga	16/20	1	2	FACETS	0.973	0.923	1	0.973	0.923	1	CLONAL	1	TRUE	1	0.924134184166672	2		351	663	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805041	89805041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772505725	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	642	717	0	ENST00000389301.3:c.4336G>A	p.Ala1446Thr	p.A1446T	ENST00000389301	NM_000135.2	1446	Gct/Act	43/43	1	2	FACETS	0.988	0.954	1	0.988	0.954	1	CLONAL	1	TRUE	1	0.924134184166672	2		717	1406	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160663	56160663	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558965285	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	283	336	1	ENST00000399503.3:c.937C>T	p.Arg313Trp	p.R313W	ENST00000399503	NM_005921.1	313	Cgg/Tgg	4/20	1	2	FACETS	0.951	0.901	1	0.951	0.901	1	CLONAL	1	TRUE	1	0.924134184166672	2		337	644	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557570	21557570	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756702960	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	517	635	0	ENST00000382592.4:c.2275C>T	p.Arg759Trp	p.R759W	ENST00000382592	NM_014572.2	759	Cgg/Tgg	5/8	1	2	FACETS	0.966	0.929	1	0.966	0.929	1	CLONAL	1	TRUE	1	0.924134184166672	2		635	1158	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298578	11298578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146049556	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	508	592	0	ENST00000361445.4:c.1883G>A	p.Arg628His	p.R628H	ENST00000361445	NM_004958.3	628	cGc/cAc	12/58	1	2	FACETS	0.923	0.886	0.96	0.923	0.886	0.96	CLONAL	1	TRUE	1	0.924134184166672	2		592	1191	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255020	16255020	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747601086	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	227	334	0	ENST00000375759.3:c.2285G>A	p.Arg762Gln	p.R762Q	ENST00000375759	NM_015001.2	762	cGg/cAg	11/15	1	2	FACETS	0.941	0.886	0.997	0.941	0.886	0.997	CLONAL	1	TRUE	1	0.924134184166672	2		334	522	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	749	773	1	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	1	2	FACETS	0.956	0.925	0.987	0.956	0.925	0.987	CLONAL	1	TRUE	1	0.924134184166672	2		774	1696	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316397	14316397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782457908	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	87	461	0	ENST00000256196.4:c.208G>A	p.Ala70Thr	p.A70T	ENST00000256196		70	Gca/Aca	3/6	1	2	FACETS	0.941	0.852	1	0.941	0.852	1	CLONAL	1	TRUE	1	0.924134184166672	2		461	200	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417910	32417910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	481	547	1	ENST00000332351.3:c.1142C>T	p.Ser381Leu	p.S381L	ENST00000332351	NM_024426.4	381	tCg/tTg	7/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.924134184166672	2		548	1028	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	634	933	3	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	1	2	FACETS	0.764	0.735	0.794	0.764	0.735	0.794	SUBCLONAL	1	TRUE	1	0.924134184166672	2		936	1795	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696345	47696345	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	287	382	0	ENST00000347630.2:c.478G>A	p.Glu160Lys	p.E160K	ENST00000347630	NM_001007230.1	160	Gag/Aag	6/11	1	2	FACETS	0.938	0.889	0.988	0.938	0.889	0.988	CLONAL	1	TRUE	1	0.924134184166672	2		382	662	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056227	27056227	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763630072	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	428	488	0	ENST00000324856.7:c.1223C>T	p.Pro408Leu	p.P408L	ENST00000324856	NM_006015.4	408	cCg/cTg	2/20	1	2	FACETS	0.99	0.948	1	0.99	0.948	1	CLONAL	1	TRUE	1	0.924134184166672	2		488	936	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693008	89693008	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	rs1564830522	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	68	325	2	ENST00000371953.3:c.492+1del		p.K164fs	ENST00000371953	NM_000314.4	164	aaG/aa	5/9	1	2	FACETS	0.827	0.735	0.921	0.827	0.735	0.921	CLONAL	1	TRUE	1	0.924134184166672	2		327	178	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4388026	4388026	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367874736	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	452	400	0	ENST00000261254.3:c.512G>A	p.Arg171Gln	p.R171Q	ENST00000261254	NM_001759.3	171	cGg/cAg	3/5	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.924134184166672	2		400	975	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133236021	133236021	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	545	558	0	ENST00000320574.5:c.3135T>A	p.Asp1045Glu	p.D1045E	ENST00000320574	NM_006231.2	1045	gaT/gaA	26/49	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.924134184166672	2		558	1143	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133236046	133236046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1397985428	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	498	510	3	ENST00000320574.5:c.3110G>A	p.Arg1037His	p.R1037H	ENST00000320574	NM_006231.2	1037	cGt/cAt	26/49	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.924134184166672	2		513	1039	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477167	67477167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	504	510	1	ENST00000327367.4:c.974G>A	p.Gly325Asp	p.G325D	ENST00000327367	NM_005902.3	325	gGc/gAc	7/9	1	2	FACETS	0.993	0.955	1	0.993	0.955	1	CLONAL	1	TRUE	1	0.924134184166672	2		511	1098	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865869	56865869	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761782738	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	223	282	0	ENST00000308159.5:c.1201G>A	p.Asp401Asn	p.D401N	ENST00000308159	NM_014669.4	401	Gac/Aac	11/22	1	2	FACETS	0.889	0.835	0.943	0.889	0.835	0.943	CLONAL	1	TRUE	1	0.924134184166672	2		282	543	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351914	89351914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	743	913	1	ENST00000301030.4:c.1036G>A	p.Glu346Lys	p.E346K	ENST00000301030	NM_001256183.1	346	Gag/Aag	9/13	1	2	FACETS	0.982	0.95	1	0.982	0.95	1	CLONAL	1	TRUE	1	0.924134184166672	2		914	1637	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40498610	40498610	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	266	423	0	ENST00000264657.5:c.250C>T	p.Arg84Ter	p.R84*	ENST00000264657	NM_139276.2	84	Cga/Tga	3/24	1	2	FACETS	0.936	0.885	0.988	0.936	0.885	0.988	CLONAL	1	TRUE	1	0.924134184166672	2		423	615	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492923	56492923	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	255	253	0	ENST00000407977.2:c.16C>T	p.Gln6Ter	p.Q6*	ENST00000407977		6	Cag/Tag	2/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.924134184166672	2		253	475	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78704435	78704435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	481	527	1	ENST00000306801.3:c.583G>A	p.Asp195Asn	p.D195N	ENST00000306801	NM_020761.2	195	Gac/Aac	5/34	1	2	FACETS	0.995	0.956	1	0.995	0.956	1	CLONAL	1	TRUE	1	0.924134184166672	2		528	1046	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7126651	7126651	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	505	558	0	ENST00000302850.5:c.2957G>T	p.Gly986Val	p.G986V	ENST00000302850	NM_000208.2	986	gGg/gTg	16/22	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.924134184166672	2		558	1085	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210925	36210925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531663002	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	720	910	1	ENST00000222270.7:c.676C>T	p.Arg226Trp	p.R226W	ENST00000222270	NM_014727.1	226	Cgg/Tgg	3/37	1	2	FACETS	0.978	0.946	1	0.978	0.946	1	CLONAL	1	TRUE	1	0.924134184166672	2		911	1593	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114292	143114292	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	220	430	0	ENST00000262992.4:c.1129A>G	p.Lys377Glu	p.K377E	ENST00000262992	NM_001101669.1	377	Aag/Gag	13/24	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.924134184166672	2		430	466	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271461	38271461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374473310	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	543	728	4	ENST00000425967.3:c.2360G>A	p.Arg787His	p.R787H	ENST00000425967	NM_001174067.1	787	cGc/cAc	18/19	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.924134184166672	2		732	1163	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922009	39922009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	599	565	0	ENST00000378444.4:c.4163C>T	p.Ala1388Val	p.A1388V	ENST00000378444	NM_001123385.1	1388	gCc/gTc	9/15	1	2	FACETS	0.984	0.949	1	0.984	0.949	1	CLONAL	1	TRUE	1	0.924134184166672	2		565	1317	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341244	70341244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	414	598	0	ENST00000374080.3:c.803G>A	p.Gly268Glu	p.G268E	ENST00000374080		268	gGa/gAa	6/45	1	2	FACETS	0.862	0.823	0.902	0.862	0.823	0.902	CLONAL	1	TRUE	1	0.924134184166672	2		598	1039	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128020	30128020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376745934	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	553	642	0	ENST00000263025.4:c.1109G>A	p.Arg370His	p.R370H	ENST00000263025	NM_002746.2	370	cGc/cAc	8/9	1	2	FACETS	0.917	0.882	0.953	0.917	0.882	0.953	CLONAL	1	TRUE	1	0.924134184166672	2		642	1305	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041214	29041214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758936491	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	262	649	2	ENST00000282397.4:c.214G>A	p.Glu72Lys	p.E72K	ENST00000282397	NM_002019.4	72	Gaa/Aaa	3/30	1	2	FACETS	0.808	0.761	0.855	0.808	0.761	0.855	CLONAL	1	TRUE	1	0.924134184166672	2		651	702	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367885	15367885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753457206	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	727	746	4	ENST00000263377.2:c.1441G>A	p.Ala481Thr	p.A481T	ENST00000263377	NM_058243.2	481	Gcc/Acc	8/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.924134184166672	2		750	1539	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799267	45799267	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	331	354	1	ENST00000450313.1:c.166G>T	p.Gly56Trp	p.G56W	ENST00000450313	NM_012222.2	56	Ggg/Tgg	3/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.924134184166672	2		355	699	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927419	245927419	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	353	491	0	ENST00000388985.4:c.1109G>T	p.Gly370Val	p.G370V	ENST00000388985		370	gGg/gTg	11/12	1	2	FACETS	0.993	0.947	1	0.993	0.947	1	CLONAL	1	TRUE	1	0.924134184166672	2		491	769	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445799	49445799	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	827	928	3	ENST00000301067.7:c.1667del	p.Pro556ArgfsTer374	p.P556Rfs*374	ENST00000301067	NM_003482.3	556	cCg/cg	10/54	1	2	FACETS	0.926	0.897	0.956	0.926	0.897	0.956	CLONAL	1	TRUE	1	0.924134184166672	2		931	1932	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524611	103524612	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs752661599	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	182	239	5	ENST00000355739.4:c.2751dup	p.Leu918IlefsTer12	p.L918Ifs*12	ENST00000355739	NM_000123.3	914	-/A	13/15	1	2	FACETS	0.877	0.818	0.937	0.877	0.818	0.937	CLONAL	1	TRUE	1	0.924134184166672	2		244	449	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347992	89347992	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	714	934	1	ENST00000301030.4:c.4958del	p.Lys1653SerfsTer33	p.K1653Sfs*33	ENST00000301030	NM_001256183.1	1653	aAg/ag	9/13	1	2	FACETS	0.937	0.906	0.969	0.937	0.906	0.969	CLONAL	1	TRUE	1	0.924134184166672	2		935	1649	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007677	62007677	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	486	571	0	ENST00000392795.3:c.190del	p.Met64CysfsTer5	p.M64Cfs*5	ENST00000392795	NM_001039933.1	64	Atg/tg	3/6	1	2	FACETS	0.97	0.931	1	0.97	0.931	1	CLONAL	1	TRUE	1	0.924134184166672	2		571	1084	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249830	39249830	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	181	562	0	ENST00000402219.2:c.1739C>A	p.Pro580His	p.P580H	ENST00000402219	NM_005633.3	580	cCt/cAt	10/23	1	2	FACETS	0.888	0.829	0.949	0.888	0.829	0.949	CLONAL	1	TRUE	1	0.924134184166672	2		562	441	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128018865	128018865	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	350	630	0	ENST00000285398.2:c.2003A>G	p.Gln668Arg	p.Q668R	ENST00000285398	NM_000122.1	668	cAg/cGg	13/15	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.924134184166672	2		630	753	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008503	70008503	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780721280	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	280	317	1	ENST00000394351.3:c.790G>A	p.Ala264Thr	p.A264T	ENST00000394351	NM_000248.3	264	Gca/Aca	8/9	1	2	FACETS	0.956	0.905	1	0.956	0.905	1	CLONAL	1	TRUE	1	0.924134184166672	2		318	634	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096150	71096150	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	302	290	0	ENST00000318789.4:c.607G>T	p.Gly203Cys	p.G203C	ENST00000318789	NM_032682.5	203	Ggc/Tgc	10/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.924134184166672	2		290	626	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1978406	1978406	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	451	504	1	ENST00000382891.5:c.3826G>A	p.Gly1276Arg	p.G1276R	ENST00000382891	NM_133335.3	1276	Ggg/Agg	21/22	1	2	FACETS	0.975	0.935	1	0.975	0.935	1	CLONAL	1	TRUE	1	0.924134184166672	2		505	1001	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931451	131931452	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs397507178	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	154	335	7	ENST00000265335.6:c.2165dup	p.Glu723GlyfsTer5	p.E723Gfs*5	ENST00000265335		719	cta/ctAa	13/25	1	2	FACETS	0.728	0.672	0.785	0.728	0.672	0.785	SUBCLONAL	1	TRUE	1	0.924134184166672	2		342	458	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194593	29194594	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0021117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	722	828	2	ENST00000240100.2:c.1134dup	p.Ser379GlnfsTer71	p.S379Qfs*71	ENST00000240100	NM_001394.6	378	-/C	4/4	1	2	FACETS	0.881	0.851	0.911	0.881	0.851	0.911	CLONAL	1	TRUE	1	0.924134184166672	2		830	1774	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0021172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	179	1381	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		1381	868	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577524	7577524	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022143-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	726	701	1	ENST00000269305.4:c.757A>C	p.Thr253Pro	p.T253P	ENST00000269305	NM_001126112.2	253	Acc/Ccc	7/11	0.854548808449497	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.854548808449497	2		702	816	SUCCESS
APC	324	MSKCC	GRCh37	5	112176863	112176863	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1270783041	NA	P-0022143-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	110	515	0	ENST00000257430.4:c.5572C>T	p.Arg1858Ter	p.R1858*	ENST00000257430	NM_000038.5	1858	Cga/Tga	16/16	0.810531517711538	1	FACETS	0.78	0.723	0.837	0.78	0.723	0.837	SUBCLONAL	1	TRUE	0	0.854548808449497	1		515	189	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556727	41556727	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0022143-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	156	385	0	ENST00000263253.7:c.3671+1G>A		p.X1224_splice	ENST00000263253	NM_001429.3	1224			0.84470686034333	2	FACETS	0.971	0.901	1	0.486	0.45	0.521	CLONAL	1	TRUE	0	0.854548808449497	2		385	376	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335690	81335690	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022143-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	232	511	0	ENST00000222390.5:c.1670G>T	p.Gly557Val	p.G557V	ENST00000222390	NM_000601.4	557	gGa/gTa	15/18	0.814879323375355	5	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.854548808449497	5		511	880	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604648	48604649	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGTGTTG	novel	NA	P-0022143-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	132	310	0	ENST00000342988.3:c.1471_1477dup	p.Asp493GlyfsTer3	p.D493Gfs*3	ENST00000342988	NM_005359.5	490	-/GGTGTTG	12/12	0.825211264912002	1	FACETS	0.819	0.766	0.871	0.819	0.766	0.871	CLONAL	1	TRUE	0	0.854548808449497	1		310	216	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349966	15349966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022143-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	474	807	2	ENST00000263377.2:c.3686G>A	p.Arg1229His	p.R1229H	ENST00000263377	NM_058243.2	1229	cGc/cAc	18/20	0.835803056613589	3	FACETS	1	0.982	1	0.525	0.502	0.55	CLONAL	1	TRUE	1	0.854548808449497	3		809	1507	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192454	138192454	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1324617507	NA	P-0022143-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	101	346	0	ENST00000237289.4:c.90T>A	p.Phe30Leu	p.F30L	ENST00000237289	NM_001270507.1	30	ttT/ttA	2/9	0.835803056613589	3	FACETS	0.953	0.86	1	0.477	0.43	0.525	CLONAL	1	TRUE	1	0.854548808449497	3		346	354	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591085	67591085	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519839	NA	P-0022306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	158	425	0	ENST00000274335.5:c.1678G>T	p.Asp560Tyr	p.D560Y	ENST00000274335		560	Gac/Tac	12/15	0.811236157167183	1	FACETS	0.964	0.911	1	0.964	0.911	1	CLONAL	1	FALSE	0	0.821726211503684	1		425	235	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240314	5240314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777007079	NA	P-0022306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	321	851	1	ENST00000357368.4:c.1600G>A	p.Glu534Lys	p.E534K	ENST00000357368	NM_002850.3	534	Gag/Aag	12/38	1	2	FACETS	0.983	0.933	1	0.983	0.933	1	CLONAL	1	FALSE	1	0.821726211503684	2		852	795	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244157	41244157	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	298	775	0	ENST00000357654.3:c.3391G>C	p.Asp1131His	p.D1131H	ENST00000357654	NM_007294.3	1131	Gat/Cat	10/23	0.823856310371663	4	FACETS	1	0.951	1	0.253	0.238	0.269	CLONAL	1	FALSE	0	0.821726211503684	4		775	1305	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503201	125503201	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	543	545	0	ENST00000428830.2:c.568G>C	p.Asp190His	p.D190H	ENST00000428830	NM_001114121.2	190	Gat/Cat	6/14	0.771391744944535	5	FACETS	0.917	0.884	0.95			1	CLONAL	3	FALSE	NA	0.821726211503684	5		545	1073	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579353	7579363	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGACGGAAA	CCAGACGGAAA	GTTT	novel	NA	P-0022306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	911	812	3	ENST00000269305.4:c.324_334delinsAAAC	p.Phe109AsnfsTer12	p.F109Nfs*12	ENST00000269305	NM_001126112.2	108	ggTTTCCGTCTGGgc/ggAAACgc	4/11	0.823856310371663	4	FACETS	0.887	0.871	0.903	0.887	0.871	0.903	CLONAL	4	FALSE	0	0.821726211503684	4		815	1138	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945472	17945472	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	231	856	0	ENST00000458235.1:c.2258C>G	p.Ala753Gly	p.A753G	ENST00000458235	NM_000215.3	753	gCc/gGc	17/24	0.823856310371663	4	FACETS	0.837	0.78	0.897			1	CLONAL	1	FALSE	NA	0.821726211503684	4		856	1223	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285396	46285691	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTTCATTGAAGGTAGGGAATTATGAATAAGGGATGTTAAAACAATTTACCAAAAGTGTTCAGTACAACTGATGATTCCACTTGGAAATATAAGCAGAGAAATTTTTGAAATAGTTTCAAAATATACTTGAATACATCCAAGTGTCTACTACTTTTATTTTTTATAGGTGGTTTCAGACACCCTCACAGGTTTTCTACCATGCAGCAACTGAACATGGAGGAAAAGATGTATATCCAGGGCAGTGTCTTTGGGAAGGTTGTGAGCCTTTTCAGCGACAGCGGTTTTCTTTTATTAC	CCTTCATTGAAGGTAGGGAATTATGAATAAGGGATGTTAAAACAATTTACCAAAAGTGTTCAGTACAACTGATGATTCCACTTGGAAATATAAGCAGAGAAATTTTTGAAATAGTTTCAAAATATACTTGAATACATCCAAGTGTCTACTACTTTTATTTTTTATAGGTGGTTTCAGACACCCTCACAGGTTTTCTACCATGCAGCAACTGAACATGGAGGAAAAGATGTATATCCAGGGCAGTGTCTTTGGGAAGGTTGTGAGCCTTTTCAGCGACAGCGGTTTTCTTTTATTAC	-	novel	NA	P-0022306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	73	66	0	ENST00000334344.6:c.4923-165_5053del		p.X1641_splice	ENST00000334344	NM_152641.2	1641		17/21	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	1	FALSE	NA	0.821726211503684	2		66	126	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206594	108206594	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022582-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	93	213	0	ENST00000278616.4:c.8174A>T	p.Asp2725Val	p.D2725V	ENST00000278616	NM_000051.3	2725	gAt/gTt	56/63	0.471391670648606	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	0	0.471391670648606	1		213	290	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159754	20159754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022582-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	167	387	0	ENST00000379607.5:c.5C>T	p.Pro2Leu	p.P2L	ENST00000379607	NM_001412.3	2	cCc/cTc	1/7	0.471391670648606	1	FACETS	0.983	0.909	1	0.983	0.909	1	CLONAL	1	FALSE	0	0.471391670648606	1		387	551	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211666	36211666	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022582-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	170	436	0	ENST00000222270.7:c.1417C>G	p.Pro473Ala	p.P473A	ENST00000222270	NM_014727.1	473	Ccc/Gcc	3/37	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	1	0.471391670648606	2		436	695	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339251	70339251	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs199469668	NA	P-0022948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	403	988	0	ENST00000374080.3:c.128A>C	p.Gln43Pro	p.Q43P	ENST00000374080		43	cAa/cCa	2/45	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.578667179546972	2		988	965	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654858	29654858	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0022948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	144	329	0	ENST00000356175.3:c.5546+1G>T		p.X1849_splice	ENST00000356175	NM_000267.3	1849			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.578667179546972	2		329	391	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661898	29661898	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567615766	NA	P-0022948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	311	787	0	ENST00000356175.3:c.5792G>A	p.Trp1931Ter	p.W1931*	ENST00000356175	NM_000267.3	1931	tGg/tAg	39/57	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.578667179546972	2		787	831	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349966	15349966	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	473	1037	0	ENST00000263377.2:c.3686G>C	p.Arg1229Pro	p.R1229P	ENST00000263377	NM_058243.2	1229	cGc/cCc	18/20	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.578667179546972	2		1037	1116	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741212	40741212	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	386	1156	1	ENST00000392038.2:c.1221G>C	p.Arg407Ser	p.R407S	ENST00000392038	NM_001626.4	407	agG/agC	12/14	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.578667179546972	2		1157	1098	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956155	55956155	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	346	939	0	ENST00000263923.4:c.3160T>A	p.Tyr1054Asn	p.Y1054N	ENST00000263923	NM_002253.2	1054	Tat/Aat	23/30	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.578667179546972	2		939	925	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0023825-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	16	348	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.652159460292652	1	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	0	0.652159460292652	1		348	27	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786706	3786706	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023825-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	21	820	0	ENST00000262367.5:c.4505G>T	p.Trp1502Leu	p.W1502L	ENST00000262367	NM_004380.2	1502	tGg/tTg	27/31	0.23090868844695	3	FACETS	1	0.842	1	0.541	0.427	0.665	INDETERMINATE	1	TRUE	1	0.652159460292652	3		820	79	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0023825-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	16	625	0	ENST00000269305.4:c.560-1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.652159460292652	1	FACETS	1	0.793	1	1	0.793	1	CLONAL	1	TRUE	0	0.652159460292652	1		625	33	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70967599	70967599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023825-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	13	524	0	ENST00000276594.2:c.1424G>A	p.Ser475Asn	p.S475N	ENST00000276594	NM_024504.3	475	aGc/aAc	7/8	0.575752481574812	3	FACETS	0.755	0.55	0.994	0.378	0.275	0.497	CLONAL	1	TRUE	1	0.652159460292652	3		524	70	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270149	66270149	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023825-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	14	422	0	ENST00000273854.3:c.1733C>G	p.Ser578Cys	p.S578C	ENST00000273854	NM_004439.5	578	tCt/tGt	8/18	0.560388545505133	1	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	0	0.652159460292652	1		422	26	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176618982	176618982	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023825-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	16	539	0	ENST00000439151.2:c.1025G>T	p.Cys342Phe	p.C342F	ENST00000439151	NM_022455.4	342	tGt/tTt	3/23	1	2	FACETS	0.861	0.657	1	0.861	0.657	1	CLONAL	1	TRUE	1	0.652159460292652	2		539	57	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371000	55371000	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023825-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	34	560	0	ENST00000297316.4:c.302T>C	p.Met101Thr	p.M101T	ENST00000297316	NM_022454.3	101	aTg/aCg	1/2	0.575752481574812	3	FACETS	0.922	0.765	1	0.461	0.382	0.546	CLONAL	1	TRUE	1	0.652159460292652	3		560	150	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0023910-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	111	359	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.576455810526677	3	FACETS	0.894	0.83	0.957	0.894	0.83	0.957	CLONAL	3	TRUE	0	0.576455810526677	3		359	185	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0023910-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	9	619	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.576455810526677	3	FACETS	0.179	0.118	0.257	0.06	0.039	0.086	SUBCLONAL	1	TRUE	0	0.576455810526677	3		620	225	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445007	89445007	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023910-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	45	566	0	ENST00000336596.2:c.1327A>G	p.Ile443Val	p.I443V	ENST00000336596	NM_005233.5	443	Att/Gtt	6/17	0.576455810526677	3	FACETS	1	0.942	1	0.609	0.521	0.704	CLONAL	1	TRUE	1	0.576455810526677	3		566	165	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280314	1280314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561203868	NA	P-0023910-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	208	1123	0	ENST00000310581.5:c.1909G>A	p.Asp637Asn	p.D637N	ENST00000310581	NM_198253.2	637	Gac/Aac	4/16	0.576455810526677	9	FACETS	1	0.967	1			1	CLONAL	5	TRUE	NA	0.576455810526677	9		1123	419	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039380	47039380	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0023910-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	117	880	0	ENST00000377604.3:c.1003A>T	p.Lys335Ter	p.K335*	ENST00000377604	NM_001204468.1	335	Aag/Tag	10/24	0.574771476066713	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.576455810526677	2		880	177	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436431	110436431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023959-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	329	866	1	ENST00000375856.3:c.1970C>T	p.Thr657Met	p.T657M	ENST00000375856	NM_003749.2	657	aCg/aTg	1/2	NA	2	FACETS	0.85	0.807	0.893			1	INDETERMINATE	1	TRUE	NA	0.93189540423419	2		867	831	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255832	16255832	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023959-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	183	337	0	ENST00000375759.3:c.3097G>A	p.Gly1033Arg	p.G1033R	ENST00000375759	NM_015001.2	1033	Gga/Aga	11/15	0.93189540423419	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.93189540423419	1		337	209	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720876	89720876	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs786201041	NA	P-0023959-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	216	327	0	ENST00000371953.3:c.1026+1G>C		p.X342_splice	ENST00000371953	NM_000314.4	342			0.93189540423419	1	FACETS	0.971	0.939	1	0.971	0.939	1	CLONAL	1	TRUE	0	0.93189540423419	1		327	255	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526594	31526594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023959-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	216	586	0	ENST00000344624.3:c.446C>T	p.Pro149Leu	p.P149L	ENST00000344624		149	cCc/cTc	2/33	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.93189540423419	2		586	459	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005491	42005491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023959-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	476	705	3	ENST00000219905.7:c.3227G>A	p.Cys1076Tyr	p.C1076Y	ENST00000219905	NM_001164273.1	1076	tGc/tAc	9/24	0.802455813761378	1	FACETS	0.983	0.962	1	0.983	0.962	1	CLONAL	1	TRUE	0	0.93189540423419	1		708	555	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383847	15383847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024152-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	78	769	1	ENST00000263377.2:c.64G>A	p.Glu22Lys	p.E22K	ENST00000263377	NM_058243.2	22	Gaa/Aaa	2/20	1	2	FACETS	0.874	0.768	0.987	0.874	0.768	0.987	CLONAL	1	TRUE	1	0.271784495737428	2		770	657	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277037	18277037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024686-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	104	476	0	ENST00000222254.8:c.1484G>A	p.Gly495Asp	p.G495D	ENST00000222254	NM_005027.3	495	gGc/gAc	12/16	0.626106171414649	5	FACETS	0.859	0.769	0.954	0.286	0.256	0.318	CLONAL	1	TRUE	2	0.626106171414649	5		476	750	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435104	56435104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024686-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	118	595	0	ENST00000407977.2:c.2033G>A	p.Cys678Tyr	p.C678Y	ENST00000407977		678	tGc/tAc	9/10	0.626106171414649	4	FACETS	0.919	0.83	1	0.459	0.415	0.506	CLONAL	1	TRUE	2	0.626106171414649	4		595	667	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821324	32821324	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024686-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	296	786	2	ENST00000354258.4:c.270del	p.Ala91ProfsTer32	p.A91Pfs*32	ENST00000354258	NM_000593.5	90	ctC/ct	1/11	0.600979408471158	5	FACETS	0.946	0.892	1	0.631	0.595	0.668	CLONAL	2	TRUE	2	0.626106171414649	5		788	969	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6027051	6027051	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs876661256	NA	P-0024686-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	121	545	0	ENST00000265849.7:c.1345C>T	p.Gln449Ter	p.Q449*	ENST00000265849	NM_000535.5	449	Cag/Tag	11/15	0.626106171414649	4	FACETS	1	0.932	1	0.345	0.312	0.379	CLONAL	1	TRUE	1	0.626106171414649	4		545	607	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421541	32421541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025222-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	49	587	0	ENST00000332351.3:c.1051G>A	p.Gly351Arg	p.G351R	ENST00000332351	NM_024426.4	351	Gga/Aga	6/10	0.283984488771079	0	FACETS	0.123	0.104	0.144			1	INDETERMINATE	1	TRUE	0	0.613059843807594	0		587	502	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685311	89685312	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0025222-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	44	271	0	ENST00000371953.3:c.208_209dup	p.Cys71PhefsTer29	p.C71Ffs*29	ENST00000371953	NM_000314.4	69	aat/aaTCt	3/9	0.613059843807594	1	FACETS	0.913	0.79	1	0.913	0.79	1	CLONAL	1	TRUE	0	0.613059843807594	1		271	109	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112892446	112892446	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025222-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	112	377	0	ENST00000351677.2:c.604A>G	p.Met202Val	p.M202V	ENST00000351677	NM_002834.3	202	Atg/Gtg	5/16	1	2	FACETS	0.982	0.892	1	0.982	0.892	1	CLONAL	1	TRUE	1	0.613059843807594	2		377	372	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579372	7579393	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCTGGTAGGTTTTCTGGGAA	GCCCTGGTAGGTTTTCTGGGAA	-	novel	NA	P-0025222-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	173	615	0	ENST00000269305.4:c.294_315del	p.Ser99AlafsTer17	p.S99Afs*17	ENST00000269305	NM_001126112.2	98	ccTTCCCAGAAAACCTACCAGGGC/cc	4/11	0.463698428955954	2	FACETS	1	0.95	1	0.516	0.478	0.555	CLONAL	1	TRUE	0	0.613059843807594	2		615	547	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061853	38061854	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTTCATGGA	rs751854761	NA	P-0025222-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	168	792	0	ENST00000250448.2:c.127_135dup	p.Ser43_Asn45dup	p.S43_N45dup	ENST00000250448	NM_004496.3	43	-/TCCATGAAC	2/2	0.190457237197014	5	FACETS	0.996	0.915	1	0.332	0.305	0.361	INDETERMINATE	1	TRUE	2	0.613059843807594	5		792	1056	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	25	214	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.98	0.772	1	0.98	0.772	1	CLONAL	1	TRUE	1	0.12	2		214	425	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409147	4409147	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587777622	NA	P-0025415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	34	560	0	ENST00000261254.3:c.842C>T	p.Pro281Leu	p.P281L	ENST00000261254	NM_001759.3	281	cCt/cTt	5/5	1	2	FACETS	0.873	0.712	1	0.873	0.712	1	CLONAL	1	TRUE	1	0.12	2		560	649	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911628	39911628	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	62	672	0	ENST00000378444.4:c.5002G>A	p.Asp1668Asn	p.D1668N	ENST00000378444	NM_001123385.1	1668	Gat/Aat	15/15	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.12	2		672	907	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0025681-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	352	863	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.718310581458136	5	FACETS	0.855	0.814	0.895	0.855	0.814	0.895	CLONAL	3	TRUE	2	0.718310581458136	5		863	794	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0025681-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	349	530	2	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	0.634649964291698	3	FACETS	0.913	0.882	0.944	0.913	0.882	0.944	CLONAL	3	TRUE	0	0.718310581458136	3		532	482	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484858	57485003	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTTTGTGGAGTGACCGCCCACCCCCTGCGCTTGCCCAGGAGGCCCTGGTCTGCACTGTTTATAGAGAAGAACCCCGTGCAAGCATTCCAGACCCCTGGCCGAAAGCGCGCTTCTCCCAAGCATTCACACGGCCTCCCTTCTTGT	AGGTTTGTGGAGTGACCGCCCACCCCCTGCGCTTGCCCAGGAGGCCCTGGTCTGCACTGTTTATAGAGAAGAACCCCGTGCAAGCATTCCAGACCCCTGGCCGAAAGCGCGCTTCTCCCAAGCATTCACACGGCCTCCCTTCTTGT	-	novel	NA	P-0025681-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	90	392	0	ENST00000371085.3:c.839+1_840-1del		p.X280_splice	ENST00000371085	NM_000516.4	280		10/13	0.718310581458136	6	FACETS	0.619	0.548	0.696	0.155	0.137	0.174	SUBCLONAL	1	TRUE	2	0.718310581458136	6		392	986	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-0025681-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	69	300	0	ENST00000371085.3:c.970+1_971-1del		p.X324_splice	ENST00000371085	NM_000516.4	324		11/13	0.718310581458136	6	FACETS	0.721	0.628	0.822	0.18	0.157	0.206	SUBCLONAL	1	TRUE	2	0.718310581458136	6		300	649	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380346	14380346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025681-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	251	165	0	ENST00000256196.4:c.71G>A	p.Gly24Asp	p.G24D	ENST00000256196		24	gGc/gAc	1/6	0.499703389058439	4	FACETS	1	0.98	1	1	0.996	1	CLONAL	4	TRUE	2	0.718310581458136	4		165	296	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11193150	11193150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764395301	NA	P-0025681-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	133	457	2	ENST00000361445.4:c.5351G>A	p.Arg1784His	p.R1784H	ENST00000361445	NM_004958.3	1784	cGc/cAc	38/58	0.718310581458136	3	FACETS	0.999	0.912	1	0.499	0.456	0.544	CLONAL	1	TRUE	1	0.718310581458136	3		459	504	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134872996	134872996	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025681-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	237	470	0	ENST00000398015.3:c.1300C>A	p.Pro434Thr	p.P434T	ENST00000398015	NM_004441.4	434	Ccc/Acc	6/16	0.711164507927082	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	2	0.718310581458136	4		470	535	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-0025681-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	75	350	0	ENST00000371085.3:c.1038+1_1039-1del		p.X346_splice	ENST00000371085	NM_000516.4	346		12/13	0.718310581458136	6	FACETS	0.642	0.561	0.728	0.16	0.14	0.182	SUBCLONAL	1	TRUE	2	0.718310581458136	6		350	793	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406567	70406567	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025681-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	134	646	0	ENST00000373644.4:c.4081T>C	p.Ser1361Pro	p.S1361P	ENST00000373644	NM_030625.2	1361	Tca/Cca	4/12	NA	2	FACETS	0.691	0.631	0.754			1	INDETERMINATE	1	TRUE	NA	0.718310581458136	2		646	540	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158594993	158594993	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025681-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	70	444	4	ENST00000263640.3:c.1354C>A	p.Gln452Lys	p.Q452K	ENST00000263640	NM_001105.4	452	Caa/Aaa	10/11	0.655552585508752	3	FACETS	0.564	0.493	0.64	0.282	0.246	0.32	SUBCLONAL	1	TRUE	1	0.718310581458136	3		448	470	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860438	42860438	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025681-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	56	421	0	ENST00000398585.3:c.439G>T	p.Gly147Cys	p.G147C	ENST00000398585	NM_001135099.1	147	Ggc/Tgc	5/14	0.369126352252072	4	FACETS	0.551	0.473	0.637	0.276	0.236	0.319	INDETERMINATE	1	TRUE	2	0.718310581458136	4		421	486	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626628	12626628	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025681-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	75	424	0	ENST00000251849.4:c.1661G>A	p.Arg554Gln	p.R554Q	ENST00000251849	NM_002880.3	554	cGa/cAa	15/17	0.584619587029336	4	FACETS	0.69	0.606	0.78	0.23	0.202	0.26	SUBCLONAL	1	TRUE	1	0.718310581458136	4		424	520	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414895	78414895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	68	539	0	ENST00000370768.2:c.1871C>T	p.Ala624Val	p.A624V	ENST00000370768	NM_003902.3	624	gCc/gTc	19/20	0.526278740902477	5	FACETS	0.559	0.486	0.639	0.186	0.162	0.213	SUBCLONAL	1	TRUE	2	0.740704426157261	5		539	693	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414913	78414913	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	61	535	0	ENST00000370768.2:c.1853A>T	p.Tyr618Phe	p.Y618F	ENST00000370768	NM_003902.3	618	tAt/tTt	19/20	0.526278740902477	5	FACETS	0.499	0.43	0.574	0.166	0.143	0.192	SUBCLONAL	1	TRUE	2	0.740704426157261	5		535	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578415	7578423	+	inframe_deletion	In_Frame_Del	DEL	ACCTCCGTC	ACCTCCGTC	-	novel	NA	P-0026035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	728	834	0	ENST00000269305.4:c.507_515del	p.Met169_Val172delinsIle	p.M169_V172delinsI	ENST00000269305	NM_001126112.2	169	atGACGGAGGTt/att	5/11	0.740704426157261	4	FACETS	0.989	0.971	1	0.989	0.971	1	CLONAL	4	TRUE	0	0.740704426157261	4		834	865	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375447	15375447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	252	889	2	ENST00000263377.2:c.980C>T	p.Pro327Leu	p.P327L	ENST00000263377	NM_058243.2	327	cCt/cTt	6/20	0.734626051935675	3	FACETS	1	0.978	1	0.546	0.512	0.581	CLONAL	1	TRUE	1	0.740704426157261	3		891	854	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920138	76920147	+	frameshift_variant	Frame_Shift_Del	DEL	ATCTCCTGGG	ATCTCCTGGG	-	novel	NA	P-0026035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	224	698	0	ENST00000373344.5:c.3930_3939del	p.Asn1310LysfsTer33	p.N1310Kfs*33	ENST00000373344	NM_000489.3	1310	aaCCCAGGAGAT/aa	11/35	0.313632061563388	6	FACETS	1	0.987	1	0.804	0.754	0.856	INDETERMINATE	2	TRUE	3	0.740704426157261	6		698	622	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	155	645	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.38	2		648	655	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	103	670	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	1	2	FACETS	0.927	0.831	1	0.927	0.831	1	CLONAL	1	TRUE	1	0.38	2		670	585	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	217	567	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.99	0.927	1	1	0.994	1	CLONAL	2	TRUE	1	0.38	2		568	577	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	56	750	0	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	0.485	0.415	0.561	0.485	0.415	0.561	SUBCLONAL	1	TRUE	1	0.38	2		750	608	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106336	27106337	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	125	784	0	ENST00000324856.7:c.5952_5953del	p.Ser1985GlnfsTer13	p.S1985Qfs*13	ENST00000324856	NM_006015.4	1983	TGt/t	20/20	1	2	FACETS	0.88	0.797	0.967	0.88	0.797	0.967	CLONAL	1	TRUE	1	0.38	2		784	748	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798461	45798461	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779997419	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	37	810	0	ENST00000450313.1:c.550C>T	p.Arg184Trp	p.R184W	ENST00000450313	NM_012222.2	184	Cgg/Tgg	7/16	1	2	FACETS	0.266	0.218	0.32	0.266	0.218	0.32	SUBCLONAL	1	TRUE	1	0.38	2		810	732	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263973	104263974	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776579	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	10	204	0	ENST00000369902.3:c.71dup	p.Ala25GlyfsTer23	p.A25Gfs*23	ENST00000369902	NM_016169.3	22	gcc/gCcc	1/12	1	2	FACETS	0.321	0.217	0.45	0.321	0.217	0.45	SUBCLONAL	1	TRUE	1	0.38	2		204	164	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577375	64577375	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1057517902	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	64	764	0	ENST00000312049.6:c.207del	p.Asp70ThrfsTer49	p.D70Tfs*49	ENST00000312049	NM_130799.2	69	ccC/cc	2/10	1	2	FACETS	0.544	0.471	0.624	0.544	0.471	0.624	SUBCLONAL	1	TRUE	1	0.38	2		764	619	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444933	49444933	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767415197	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	88	469	4	ENST00000301067.7:c.2533del	p.Arg845GlyfsTer85	p.R845Gfs*85	ENST00000301067	NM_003482.3	845	Cgg/gg	10/54	1	2	FACETS	0.961	0.855	1	0.961	0.855	1	CLONAL	1	TRUE	1	0.38	2		473	482	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515036	103515036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775996769	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	68	437	1	ENST00000355739.4:c.1537G>A	p.Ala513Thr	p.A513T	ENST00000355739	NM_000123.3	513	Gca/Aca	8/15	1	2	FACETS	0.787	0.686	0.894	0.787	0.686	0.894	SUBCLONAL	1	TRUE	1	0.38	2		438	455	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572555	95572555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	65	343	0	ENST00000393063.1:c.2810G>A	p.Arg937His	p.R937H	ENST00000393063	NM_030621.3	937	cGc/cAc	19/28	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.38	2		343	342	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023006	33023006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	64	531	0	ENST00000300177.4:c.115G>A	p.Ala39Thr	p.A39T	ENST00000300177	NM_001191322.1	39	Gcc/Acc	2/2	1	2	FACETS	0.828	0.719	0.944	0.828	0.719	0.944	CLONAL	1	TRUE	1	0.38	2		531	407	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028815	42028815	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	144	849	1	ENST00000219905.7:c.4357del	p.Tyr1453MetfsTer27	p.Y1453Mfs*27	ENST00000219905	NM_001164273.1	1451	ccT/cc	13/24	1	2	FACETS	0.999	0.912	1	0.999	0.912	1	CLONAL	1	TRUE	1	0.38	2		850	759	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	108	684	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.943	0.848	1	0.943	0.848	1	CLONAL	1	TRUE	1	0.38	2		684	603	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310208	91310208	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs747341586	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	110	476	5	ENST00000355112.3:c.2268del	p.Asp757ThrfsTer4	p.D757Tfs*4	ENST00000355112	NM_000057.2	754	tcA/tc	10/22	1	2	FACETS	0.981	0.884	1	0.981	0.884	1	CLONAL	1	TRUE	1	0.38	2		481	590	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14026116	14026116	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	83	416	0	ENST00000311895.7:c.1081del	p.Met361TrpfsTer15	p.M361Wfs*15	ENST00000311895	NM_005236.2	359	gAa/ga	6/11	1	2	FACETS	0.874	0.773	0.981	0.874	0.773	0.981	CLONAL	1	TRUE	1	0.38	2		416	500	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946216	81946216	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	27	652	0	ENST00000359376.3:c.1949G>A	p.Ser650Asn	p.S650N	ENST00000359376	NM_002661.3	650	aGc/aAc	19/33	1	2	FACETS	0.289	0.229	0.357	0.289	0.229	0.357	SUBCLONAL	1	TRUE	1	0.38	2		652	492	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953259	81953259	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756480279	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	24	444	1	ENST00000359376.3:c.2225G>A	p.Arg742His	p.R742H	ENST00000359376	NM_002661.3	742	cGc/cAc	20/33	1	2	FACETS	0.281	0.219	0.352	0.281	0.219	0.352	SUBCLONAL	1	TRUE	1	0.38	2		445	450	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483121	29483122	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	134	705	0	ENST00000356175.3:c.185dup	p.Leu62PhefsTer5	p.L62Ffs*5	ENST00000356175	NM_000267.3	61	att/aTtt	2/57	1	2	FACETS	0.929	0.845	1	0.929	0.845	1	CLONAL	1	TRUE	1	0.38	2		705	759	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553492	29553492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768638173	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	40	580	0	ENST00000356175.3:c.2041C>T	p.Arg681Ter	p.R681*	ENST00000356175	NM_000267.3	681	Cga/Tga	18/57	1	2	FACETS	0.334	0.276	0.398	0.334	0.276	0.398	SUBCLONAL	1	TRUE	1	0.38	2		580	631	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685584	29685585	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1060500387	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	118	763	0	ENST00000356175.3:c.7996_7997del	p.Ser2666CysfsTer5	p.S2666Cfs*5	ENST00000356175	NM_000267.3	2665	cAG/c	54/57	1	2	FACETS	0.876	0.791	0.965	0.876	0.791	0.965	CLONAL	1	TRUE	1	0.38	2		763	709	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256250	41256251	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs80357604	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	88	565	1	ENST00000357654.3:c.329dup	p.Glu111GlyfsTer3	p.E111Gfs*3	ENST00000357654	NM_007294.3	110	aag/aaAg	6/23	1	2	FACETS	0.705	0.625	0.79	0.705	0.625	0.79	SUBCLONAL	1	TRUE	1	0.38	2		566	657	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7128960	7128960	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139944962	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	103	501	0	ENST00000302850.5:c.2848G>A	p.Val950Ile	p.V950I	ENST00000302850	NM_000208.2	950	Gtc/Atc	15/22	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.38	2		501	541	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281608	15281608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	121	812	0	ENST00000263388.2:c.4765C>T	p.Arg1589Trp	p.R1589W	ENST00000263388	NM_000435.2	1589	Cgg/Tgg	26/33	1	2	FACETS	0.952	0.862	1	0.952	0.862	1	CLONAL	1	TRUE	1	0.38	2		812	669	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216506	36216506	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs956016804	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	132	965	2	ENST00000222270.7:c.3769C>T	p.Arg1257Cys	p.R1257C	ENST00000222270	NM_014727.1	1257	Cgc/Tgc	12/37	1	2	FACETS	0.893	0.811	0.979	0.893	0.811	0.979	CLONAL	1	TRUE	1	0.38	2		967	778	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218411	36218411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368960815	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	43	497	3	ENST00000222270.7:c.4190C>T	p.Ala1397Val	p.A1397V	ENST00000222270	NM_014727.1	1397	gCg/gTg	16/37	1	2	FACETS	0.492	0.412	0.581	0.492	0.412	0.581	SUBCLONAL	1	TRUE	1	0.38	2		500	460	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795608	42795609	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1555770200	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	123	894	0	ENST00000575354.2:c.2694dup	p.Lys899GlnfsTer32	p.K899Qfs*32	ENST00000575354	NM_015125.3	896	-/C	10/20	1	2	FACETS	0.988	0.896	1	0.988	0.896	1	CLONAL	1	TRUE	1	0.38	2		894	655	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273299	198273299	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	73	540	0	ENST00000335508.6:c.911C>T	p.Pro304Leu	p.P304L	ENST00000335508	NM_012433.2	304	cCt/cTt	8/25	1	2	FACETS	0.701	0.614	0.795	0.701	0.614	0.795	SUBCLONAL	1	TRUE	1	0.38	2		540	548	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755570	39755570	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	33	672	0	ENST00000288319.7:c.1195C>A	p.Leu399Ile	p.L399I	ENST00000288319	NM_182918.3	399	Ctc/Atc	10/10	1	2	FACETS	0.315	0.256	0.382	0.315	0.256	0.382	SUBCLONAL	1	TRUE	1	0.38	2		672	551	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050708	30050708	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	27	498	0	ENST00000338641.4:c.514del	p.Arg172GlyfsTer2	p.R172Gfs*2	ENST00000338641	NM_000268.3	170	ccA/cc	5/16	1	2	FACETS	0.279	0.221	0.345	0.279	0.221	0.345	SUBCLONAL	1	TRUE	1	0.38	2		498	510	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37038181	37038181	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1064795693	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	55	322	0	ENST00000231790.2:c.188A>G	p.Asp63Gly	p.D63G	ENST00000231790	NM_000249.3	63	gAc/gGc	2/19	1	2	FACETS	0.72	0.618	0.831	0.72	0.618	0.831	SUBCLONAL	1	TRUE	1	0.38	2		322	402	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067151	37067151	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	83	335	0	ENST00000231790.2:c.1065del	p.Ser356LeufsTer11	p.S356Lfs*11	ENST00000231790	NM_000249.3	354	ggC/gg	12/19	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.38	2		335	426	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266134	41266136	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs587776850	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	33	484	0	ENST00000349496.5:c.133_135del	p.Ser45del	p.S45del	ENST00000349496	NM_001904.3	44	cCTTct/cct	3/15	1	2	FACETS	0.349	0.283	0.423	0.349	0.283	0.423	SUBCLONAL	1	TRUE	1	0.38	2		484	498	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098841	47098841	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	189	1001	0	ENST00000409792.3:c.6433G>A	p.Gly2145Arg	p.G2145R	ENST00000409792	NM_014159.6	2145	Gga/Aga	15/21	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.38	2		1001	942	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645120	86645120	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1210180190	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	96	518	2	ENST00000274376.6:c.1192C>T	p.Arg398Ter	p.R398*	ENST00000274376	NM_002890.2	398	Cga/Tga	8/25	1	2	FACETS	0.909	0.812	1	0.909	0.812	1	CLONAL	1	TRUE	1	0.38	2		520	556	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659245	86659245	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554048066	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	81	459	1	ENST00000274376.6:c.1534C>T	p.Arg512Ter	p.R512*	ENST00000274376	NM_002890.2	512	Cga/Tga	11/25	1	2	FACETS	0.868	0.767	0.976	0.868	0.767	0.976	CLONAL	1	TRUE	1	0.38	2		460	491	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805926	32805927	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	119	923	0	ENST00000374899.4:c.84dup	p.Thr29AspfsTer138	p.T29Dfs*138	ENST00000374899	NM_018833.2	28	-/G	2/12	1	2	FACETS	0.935	0.845	1	0.935	0.845	1	CLONAL	1	TRUE	1	0.38	2		923	670	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710779	117710779	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	80	674	0	ENST00000368508.3:c.1493A>T	p.Asp498Val	p.D498V	ENST00000368508	NM_002944.2	498	gAt/gTt	12/43	1	2	FACETS	0.773	0.681	0.87	0.773	0.681	0.87	SUBCLONAL	1	TRUE	1	0.38	2		674	545	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279390	38279390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs981703846	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	126	864	0	ENST00000425967.3:c.1099G>A	p.Ala367Thr	p.A367T	ENST00000425967	NM_001174067.1	367	Gca/Aca	9/19	1	2	FACETS	0.833	0.755	0.916	0.833	0.755	0.916	CLONAL	1	TRUE	1	0.38	2		864	796	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206636	27206637	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	98	671	0	ENST00000380036.4:c.2426dup	p.Asn809LysfsTer12	p.N809Kfs*12	ENST00000380036	NM_000459.3	807	-/A	15/23	1	2	FACETS	0.836	0.747	0.93	0.836	0.747	0.93	CLONAL	1	TRUE	1	0.38	2		671	617	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	18	427	1	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	1	1	FACETS	0.244	0.184	0.316	0.244	0.184	0.316	SUBCLONAL	1	TRUE	0	0.38	1		428	314	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986987	36986987	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026759-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	30	551	1	ENST00000354822.5:c.702G>T	p.Gln234His	p.Q234H	ENST00000354822	NM_001079668.2	234	caG/caT	3/3	0.351060352727273	1	FACETS	0.276	0.222	0.338	0.276	0.222	0.338	SUBCLONAL	1	TRUE	0	0.359949954422767	1		552	495	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665757	29665757	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs772295894	NA	P-0026759-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	54	322	0	ENST00000356175.3:c.6792C>A	p.Tyr2264Ter	p.Y2264*	ENST00000356175	NM_000267.3	2264	taC/taA	45/57	0.359949954422767	1	FACETS	0.812	0.698	0.935	0.812	0.698	0.935	CLONAL	1	TRUE	0	0.359949954422767	1		322	303	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404603	8404603	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026759-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	20	234	0	ENST00000356435.5:c.4144C>A	p.Pro1382Thr	p.P1382T	ENST00000356435		1382	Cca/Aca	25/35	0.359949954422767	1	FACETS	0.336	0.257	0.429	0.336	0.257	0.429	SUBCLONAL	1	TRUE	0	0.359949954422767	1		234	271	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0027019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	184	674	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.140173237860493	5	FACETS	0.978	0.908	1			1	INDETERMINATE	3	TRUE	NA	0.300723693852305	5		674	605	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964167	28964167	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	41	448	0	ENST00000282397.4:c.1735G>C	p.Val579Leu	p.V579L	ENST00000282397	NM_002019.4	579	Gtt/Ctt	13/30	NA	2	FACETS	0.651	0.543	0.771			1	INDETERMINATE	1	TRUE	NA	0.300723693852305	2		448	419	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878499	151878499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	65	648	0	ENST00000262189.6:c.6446C>T	p.Ser2149Leu	p.S2149L	ENST00000262189	NM_170606.2	2149	tCa/tTa	36/59	0.300723693852305	4	FACETS	0.986	0.856	1	0.329	0.285	0.376	CLONAL	1	TRUE	1	0.300723693852305	4		648	570	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949749	151949749	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	39	485	0	ENST00000262189.6:c.1351C>G	p.His451Asp	p.H451D	ENST00000262189	NM_170606.2	451	Cac/Gac	10/59	0.300723693852305	4	FACETS	0.697	0.577	0.83	0.232	0.192	0.277	SUBCLONAL	1	TRUE	1	0.300723693852305	4		485	484	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0027045-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	39	405	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.287693894812314	3	FACETS	1	0.919	1	0.59	0.491	0.698	CLONAL	1	TRUE	1	0.287693894812314	3		405	263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577527	7577531	+	frameshift_variant	Frame_Shift_Del	DEL	GGATG	GGATG	-	novel	NA	P-0027045-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	113	700	0	ENST00000269305.4:c.750_754del	p.Ile251HisfsTer11	p.I251Hfs*11	ENST00000269305	NM_001126112.2	250	ccCATCCtc/cctc	7/11	0.186301952667346	3	FACETS	1	0.959	1	0.734	0.666	0.805	CLONAL	2	TRUE	0	0.287693894812314	3		700	408	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677209	29677210	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0027045-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	48	416	1	ENST00000356175.3:c.7268_7269del	p.Thr2423SerfsTer3	p.T2423Sfs*3	ENST00000356175	NM_000267.3	2423	ACa/a	49/57	0.186301952667346	3	FACETS	0.918	0.785	1	0.612	0.523	0.706	CLONAL	2	TRUE	0	0.287693894812314	3		417	208	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509665	106509665	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027045-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	50	588	0	ENST00000359195.3:c.1659G>T	p.Lys553Asn	p.K553N	ENST00000359195	NM_002649.2	553	aaG/aaT	2/11	0.214384431753799	4	FACETS	1	0.952	1			1	CLONAL	1	TRUE	NA	0.287693894812314	4		588	341	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0027456-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	523	545	1	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.205810777740687	5	FACETS	1	0.995	1	0.805	0.774	0.836	INDETERMINATE	2	TRUE	2	0.860661599978829	5		546	1153	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579329	7579329	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912658	NA	P-0027456-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	313	480	0	ENST00000269305.4:c.358A>G	p.Lys120Glu	p.K120E	ENST00000269305	NM_001126112.2	120	Aag/Gag	4/11	0.860661599978829	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.860661599978829	1		480	376	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736924	736924	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027456-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	350	426	0	ENST00000314574.4:c.1175A>G	p.Tyr392Cys	p.Y392C	ENST00000314574	NM_005433.3	392	tAt/tGt	10/12	0.413287108103776	4	FACETS	1	0.982	1			1	INDETERMINATE	2	TRUE	NA	0.860661599978829	4		426	717	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56402522	56402522	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027456-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	149	173	0	ENST00000348428.3:c.1564G>T	p.Asp522Tyr	p.D522Y	ENST00000348428	NM_006785.3	522	Gat/Tat	13/17	0.515362714343657	1	FACETS	1	0.985	1	1	0.985	1	INDETERMINATE	1	TRUE	0	0.860661599978829	1		173	183	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261477	142261518	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTTAGCACTCTGGAACTATCACCACTTACCATTTTCTTATC	TCTTAGCACTCTGGAACTATCACCACTTACCATTTTCTTATC	-	novel	NA	P-0027456-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	153	189	0	ENST00000350721.4:c.3439_3450+30del		p.X1147_splice	ENST00000350721	NM_001184.3	1147		17/47	0.783175888036802	4	FACETS	1	0.981	1	0.404	0.371	0.438	CLONAL	1	TRUE	1	0.860661599978829	4		189	546	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245267	41245267	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507198	NA	P-0027456-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	605	610	0	ENST00000357654.3:c.2281G>A	p.Glu761Lys	p.E761K	ENST00000357654	NM_007294.3	761	Gaa/Aaa	10/23	0.860661599978829	2	FACETS	1	0.997	1	0.653	0.631	0.674	CLONAL	1	TRUE	0	0.860661599978829	2		610	1077	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55334497	55334823	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGGTAAGGGAGGGAGGGGGGGACGCCTGGGTCCCCCCCTTCTTGGCTTCTTTATTGCTCTTTGTTATCCCGGTGTAGGAGCCCCCCCCCCCCCGCCATTGGCTCCCCACTTCTCCTGTGCAAGGTTATTTTTTTTAAATAGCAAATCCTTTCTGAGCCCTCTATGCGACCTCTGTTGCCGAATTTCCCCCGCGTGTGCAAAAAATGCAAAAACAAAACAGAATAACAACAGAAAACTACTTTTGGATTTTGTCCTTGATCAAAATTTGCATTGCTTTTTTTTTCCACACCTTCTCTCCCCCCCCCATCTCTCTCTTTCTCTCTCTA	CAGGTAAGGGAGGGAGGGGGGGACGCCTGGGTCCCCCCCTTCTTGGCTTCTTTATTGCTCTTTGTTATCCCGGTGTAGGAGCCCCCCCCCCCCCGCCATTGGCTCCCCACTTCTCCTGTGCAAGGTTATTTTTTTTAAATAGCAAATCCTTTCTGAGCCCTCTATGCGACCTCTGTTGCCGAATTTCCCCCGCGTGTGCAAAAAATGCAAAAACAAAACAGAATAACAACAGAAAACTACTTTTGGATTTTGTCCTTGATCAAAATTTGCATTGCTTTTTTTTTCCACACCTTCTCTCCCCCCCCCATCTCTCTCTTTCTCTCTCTA	-	novel	NA	P-0027456-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	127	316	0	ENST00000284073.2:c.103+1_104-1del		p.X35_splice	ENST00000284073	NM_138962.2	35		2/14	0.860661599978829	2	FACETS	0.346	0.313	0.38	0.173	0.156	0.19	SUBCLONAL	1	TRUE	0	0.860661599978829	2		316	854	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55334906	55335627	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGGTAAACCATTCCCTTCTGGATTTTGTCTTTATTTTAGAACAAAGTTTAAGTTTTATTTTTGGAGGTGTCTTCGGAAGTAGCTAAGCGGATTAGAATGGGGCTCAGGCGCGTGGCTGATCTCGAACGGCGCTCTATACCACCCCCACCGCCCCCTAGTAACCCCAGAGGTTATTGTTAATTGGAGCTGAACTCTGGATACAGAGATACCCATCTCTCTGCTTTTAAGTCATTTTCCCGTCGCTTCTTTTTCTCTGTTTAAAATGACATTCAGCTTCATTTACTTTCGCATAGTTTTTTTTTTTCTTTTGATCTTAATGTGTGTTTCCCCCACACTCCCAGCTCCCCAAACTCTTAAGATCCCTCTTAGAAAGATGGTGGTAAATCTCTTCTAAGTGCCGGGCTTTCTTCGGAATAAAACAAAGCGTTAAGAAAGGGAAGGGGAGGAGGAGAGGAAACTGAGGTGGCCAAAGAGTGGAGGCACCAGCATTTTCCAAGTTACCTCCACCCTCCCTGCCCCCGTTCCACTTCCCCCGTTAACCTTGATGTTTTTTCTTGCGAGGTGGAGGGCTGTAGGCAGGAGGGGAATTGGAGGAGGGGAGTGGGAGGTGGGGGTGCGTGGGGGGCAACTTTTGCTCCTCATTCAGCCTTAGGTCTCACTCCTGGTTGCTTTCAATGGTGTCACATTTTCTTGTTTGTTTTTCTCCCTCTTTGTCTCCTTT	CAGGTAAACCATTCCCTTCTGGATTTTGTCTTTATTTTAGAACAAAGTTTAAGTTTTATTTTTGGAGGTGTCTTCGGAAGTAGCTAAGCGGATTAGAATGGGGCTCAGGCGCGTGGCTGATCTCGAACGGCGCTCTATACCACCCCCACCGCCCCCTAGTAACCCCAGAGGTTATTGTTAATTGGAGCTGAACTCTGGATACAGAGATACCCATCTCTCTGCTTTTAAGTCATTTTCCCGTCGCTTCTTTTTCTCTGTTTAAAATGACATTCAGCTTCATTTACTTTCGCATAGTTTTTTTTTTTCTTTTGATCTTAATGTGTGTTTCCCCCACACTCCCAGCTCCCCAAACTCTTAAGATCCCTCTTAGAAAGATGGTGGTAAATCTCTTCTAAGTGCCGGGCTTTCTTCGGAATAAAACAAAGCGTTAAGAAAGGGAAGGGGAGGAGGAGAGGAAACTGAGGTGGCCAAAGAGTGGAGGCACCAGCATTTTCCAAGTTACCTCCACCCTCCCTGCCCCCGTTCCACTTCCCCCGTTAACCTTGATGTTTTTTCTTGCGAGGTGGAGGGCTGTAGGCAGGAGGGGAATTGGAGGAGGGGAGTGGGAGGTGGGGGTGCGTGGGGGGCAACTTTTGCTCCTCATTCAGCCTTAGGTCTCACTCCTGGTTGCTTTCAATGGTGTCACATTTTCTTGTTTGTTTTTCTCCCTCTTTGTCTCCTTT	-	novel	NA	P-0027456-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	415	431	0	ENST00000284073.2:c.185+1_186-1del		p.X62_splice	ENST00000284073	NM_138962.2	62		3/14	0.860661599978829	2	FACETS	0.733	0.698	0.769	0.366	0.349	0.385	SUBCLONAL	1	TRUE	0	0.860661599978829	2		431	1316	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0027828-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	3475	459	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.411711279387169	31	FACETS	0.994	0.987	1	0.962	0.955	0.969	CLONAL	30	TRUE	0	0.411711279387169	31		459	3945	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0027828-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	183	809	1	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	0.40736339719874	1	FACETS	0.934	0.864	1	0.934	0.864	1	CLONAL	1	TRUE	0	0.411711279387169	1		810	756	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4387998	4387998	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027828-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	126	574	0	ENST00000261254.3:c.484C>T	p.His162Tyr	p.H162Y	ENST00000261254	NM_001759.3	162	Cac/Tac	3/5	0.385550949149575	1	FACETS	0.824	0.748	0.903	0.824	0.748	0.903	CLONAL	1	TRUE	0	0.411711279387169	1		574	590	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218798	66218798	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027828-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	83	304	0	ENST00000273854.3:c.2260G>C	p.Glu754Gln	p.E754Q	ENST00000273854	NM_004439.5	754	Gag/Cag	13/18	0.411711279387169	1	FACETS	0.964	0.859	1	0.964	0.859	1	CLONAL	1	TRUE	0	0.411711279387169	1		304	332	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176085770	176085770	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027944-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	216	335	0	ENST00000367669.3:c.1016G>A	p.Gly339Asp	p.G339D	ENST00000367669	NM_022457.5	339	gGc/gAc	9/20	0.522924272262542	6	FACETS	0.855	0.799	0.912	0.855	0.799	0.912	CLONAL	3	TRUE	3	0.522924272262542	6		335	659	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719971	18719971	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027944-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	172	338	0	ENST00000266497.5:c.3868G>C	p.Val1290Leu	p.V1290L	ENST00000266497		1290	Gta/Cta	27/31	0.522924272262542	6	FACETS	1	0.981	1			1	CLONAL	2	TRUE	NA	0.522924272262542	6		338	567	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425208	49425209	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	G	novel	NA	P-0027944-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	802	437	0	ENST00000301067.7:c.13279_13280delinsC	p.Gly4427GlnfsTer5	p.G4427Qfs*5	ENST00000301067	NM_003482.3	4427	GGa/Ca	39/54	0.522924272262542	9	FACETS	0.981	0.956	1			1	CLONAL	7	TRUE	NA	0.522924272262542	9		437	1264	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9928076	9928076	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027944-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	128	190	2	ENST00000330684.3:c.1663G>T	p.Ala555Ser	p.A555S	ENST00000330684	NM_001134407.1	555	Gcc/Tcc	8/13	0.460016131569453	4	FACETS	0.963	0.882	1	0.963	0.882	1	CLONAL	2	TRUE	2	0.522924272262542	4		192	387	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993684	72993684	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027944-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	82	267	0	ENST00000268489.5:c.361del	p.Asp121ThrfsTer27	p.D121Tfs*27	ENST00000268489	NM_006885.3	121	Gac/ac	2/10	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.522924272262542	2		267	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0027944-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	329	296	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.52382582188981	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	0	0.522924272262542	3		296	523	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541547	29541547	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027944-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	56	233	0	ENST00000356175.3:c.1471T>C	p.Tyr491His	p.Y491H	ENST00000356175	NM_000267.3	491	Tat/Cat	13/57	0.29507203635012	3	FACETS	1	0.908	1	0.355	0.306	0.406	INDETERMINATE	1	TRUE	0	0.522924272262542	3		233	254	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775209	73775209	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027944-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	187	345	0	ENST00000254810.4:c.47C>A	p.Ala16Asp	p.A16D	ENST00000254810	NM_005324.3	16	gCc/gAc	2/4	0.522924272262542	5	FACETS	0.977	0.907	1	0.391	0.362	0.42	CLONAL	2	TRUE	0	0.522924272262542	5		345	653	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17389834	17389834	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027944-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	126	385	0	ENST00000359435.4:c.967A>T	p.Ile323Phe	p.I323F	ENST00000359435	NM_001033549.1	323	Att/Ttt	9/9	0.522924272262542	6	FACETS	1	0.942	1	0.264	0.239	0.291	CLONAL	1	TRUE	2	0.522924272262542	6		385	932	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523701	176523701	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027944-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	89	363	0	ENST00000292408.4:c.2112G>T	p.Glu704Asp	p.E704D	ENST00000292408	NM_213647.1	704	gaG/gaT	16/18	0.52382582188981	3	FACETS	0.842	0.749	0.941	0.421	0.374	0.471	CLONAL	1	TRUE	1	0.522924272262542	3		363	510	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225783	26225783	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027944-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	134	205	0	ENST00000360408.1:c.401A>T	p.Glu134Val	p.E134V	ENST00000360408	NM_003532.2	134	gAg/gTg	1/1	0.52382582188981	3	FACETS	1	0.987	1	0.743	0.681	0.807	CLONAL	1	TRUE	1	0.522924272262542	3		205	435	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017552	112017552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373817482	NA	P-0027944-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	88	334	1	ENST00000368678.4:c.961G>A	p.Asp321Asn	p.D321N	ENST00000368678		321	Gac/Aac	9/13	0.52382582188981	4	FACETS	0.801	0.71	0.898	0.267	0.236	0.3	CLONAL	1	TRUE	1	0.522924272262542	4		335	640	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346570	81346571	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0027944-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	50	230	0	ENST00000222390.5:c.1382_1383delinsAT	p.Trp461Tyr	p.W461Y	ENST00000222390	NM_000601.4	461	tGG/tAT	11/18	0.29507203635012	3	FACETS	0.887	0.758	1	0.296	0.252	0.342	INDETERMINATE	1	TRUE	0	0.522924272262542	3		230	272	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636251	87636251	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027944-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	210	309	0	ENST00000277120.3:c.2416T>A	p.Trp806Arg	p.W806R	ENST00000277120		806	Tgg/Agg	19/19	0.522924272262542	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.522924272262542	2		309	364	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028816	47028816	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027944-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	196	387	0	ENST00000377604.3:c.120C>A	p.Asp40Glu	p.D40E	ENST00000377604	NM_001204468.1	40	gaC/gaA	3/24	0.40210018409518	4	FACETS	0.898	0.835	0.962			1	CLONAL	2	TRUE	NA	0.522924272262542	4		387	636	SUCCESS
AR	367	MSKCC	GRCh37	X	66765686	66765686	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027944-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	92	419	0	ENST00000374690.3:c.698C>A	p.Ser233Tyr	p.S233Y	ENST00000374690	NM_000044.3	233	tCt/tAt	1/8	0.40210018409518	4	FACETS	0.759	0.674	0.849			1	SUBCLONAL	1	TRUE	NA	0.522924272262542	4		419	706	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210181	123210181	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0027944-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	205	308	0	ENST00000218089.9:c.2534-1G>A		p.X845_splice	ENST00000218089	NM_001042749.1	845			NA	2	FACETS	1	0.974	1			1	INDETERMINATE	2	TRUE	NA	0.522924272262542	2		308	372	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971142	21971142	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027944-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	66	182	0	ENST00000304494.5:c.216C>A	p.Cys72Ter	p.C72*	ENST00000304494	NM_000077.4	72	tgC/tgA	2/3	0.522924272262542	2	FACETS	0.784	0.697	0.873	0.784	0.697	0.873	SUBCLONAL	2	TRUE	0	0.522924272262542	2		182	161	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0028391-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	4477	619	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.542379622961504	21	FACETS	1	0.997	1			1	CLONAL	20	TRUE	NA	0.542379622961504	21		620	5039	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0028391-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	4396	645	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.542379622961504	21	FACETS	0.99	0.984	0.997			1	CLONAL	20	TRUE	NA	0.542379622961504	21		645	5035	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577518	7577518	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519995	NA	P-0028391-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	486	701	1	ENST00000269305.4:c.763A>T	p.Ile255Phe	p.I255F	ENST00000269305	NM_001126112.2	255	Atc/Ttc	7/11	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	2	TRUE	NA	0.542379622961504	2		702	886	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0028690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	281	354	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.320705515114858	2	FACETS	0.963	0.92	1	1	0.996	1	CLONAL	4	TRUE	0	0.320705515114858	2		354	455	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0028690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	195	624	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.320705515114858	2	FACETS	1	0.978	1	1	0.993	1	CLONAL	3	TRUE	0	0.320705515114858	2		624	374	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913400	NA	P-0028690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	54	393	0	ENST00000349496.5:c.98C>A	p.Ser33Tyr	p.S33Y	ENST00000349496	NM_001904.3	33	tCt/tAt	3/15	1	2	FACETS	0.85	0.737	0.97	1	0.974	1	CLONAL	2	TRUE	1	0.320705515114858	2		393	198	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	139	719	0	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	0.143461136200255	4	FACETS	1	0.977	1	1	0.977	1	INDETERMINATE	2	TRUE	2	0.320705515114858	4		719	481	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444266	50444266	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	14	374	0	ENST00000331340.3:c.196G>A	p.Glu66Lys	p.E66K	ENST00000331340	NM_006060.4	66	Gag/Aag	4/8	1	2	FACETS	0.353	0.255	0.472	0.353	0.255	0.472	SUBCLONAL	1	TRUE	1	0.320705515114858	2		374	247	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707933	47707933	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1553370397	NA	P-0028690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	30	599	0	ENST00000233146.2:c.2557G>T	p.Glu853Ter	p.E853*	ENST00000233146	NM_000251.2	853	Gag/Tag	15/16	1	2	FACETS	0.742	0.601	0.901	0.742	0.601	0.901	CLONAL	1	TRUE	1	0.320705515114858	2		599	252	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101492	27101492	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	172	934	0	ENST00000324856.7:c.4777del	p.Arg1593GlyfsTer19	p.R1593Gfs*19	ENST00000324856	NM_006015.4	1592	Ccc/cc	18/20	1	2	FACETS	0.885	0.818	0.954	1	0.992	1	CLONAL	2	TRUE	1	0.320705515114858	2		934	606	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101661	27101662	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0028690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	172	1138	0	ENST00000324856.7:c.4948_4949dup	p.Gln1650HisfsTer5	p.Q1650Hfs*5	ENST00000324856	NM_006015.4	1648	gcc/gcCAc	18/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.320705515114858	2		1138	720	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052964	180052971	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCTGGC	GGCCTGGC	-	novel	NA	P-0028690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	80	1210	0	ENST00000261937.6:c.1319_1326del	p.Arg440ProfsTer31	p.R440Pfs*31	ENST00000261937	NM_182925.4	440	cGCCAGGCC/c	10/30	1	2	FACETS	0.752	0.662	0.849	0.752	0.662	0.849	SUBCLONAL	1	TRUE	1	0.320705515114858	2		1210	663	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0028861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	250	331	0				ENST00000310581	NM_198253.2	-/1132			0.529112128132352	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	1	0.529112128132352	3		331	590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0028861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	210	657	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.506454714514801	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.529112128132352	1		657	520	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100006	157100008	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	rs587779748	NA	P-0028861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	12	182	1	ENST00000346085.5:c.954_956del	p.Gly319del	p.G319del	ENST00000346085	NM_020732.3	315	GGA/-	1/20	1	2	FACETS	0.233	0.163	0.318	0.233	0.163	0.318	SUBCLONAL	1	TRUE	1	0.529112128132352	2		183	195	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937001	48937005	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAA	CAGAA	-	rs1566192530	NA	P-0028861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	104	367	0	ENST00000267163.4:c.772_776del	p.Asn258GlufsTer11	p.N258Efs*11	ENST00000267163	NM_000321.2	257	CAGAAc/c	8/27	0.529112128132352	1	FACETS	0.663	0.597	0.732	0.663	0.597	0.732	SUBCLONAL	1	TRUE	0	0.529112128132352	1		367	436	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233037	55233037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1477025000	NA	P-0028861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	82	478	1	ENST00000275493.2:c.1787C>T	p.Pro596Leu	p.P596L	ENST00000275493	NM_005228.3	596	cCg/cTg	15/28	1	2	FACETS	0.574	0.507	0.645	0.574	0.507	0.645	SUBCLONAL	1	TRUE	1	0.529112128132352	2		479	540	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934194	48934194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	123	532	1	ENST00000267163.4:c.649C>T	p.Gln217Ter	p.Q217*	ENST00000267163	NM_000321.2	217	Cag/Tag	7/27	0.529112128132352	1	FACETS	0.563	0.511	0.618	0.563	0.511	0.618	SUBCLONAL	1	TRUE	0	0.529112128132352	1		533	607	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830751	72830751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761415382	NA	P-0028861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	152	641	0	ENST00000268489.5:c.5830G>A	p.Ala1944Thr	p.A1944T	ENST00000268489	NM_006885.3	1944	Gcc/Acc	9/10	0.427928072355509	1	FACETS	0.652	0.598	0.708	0.652	0.598	0.708	SUBCLONAL	1	TRUE	0	0.529112128132352	1		641	648	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711876	89711876	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs786204863	NA	P-0028861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	116	489	1	ENST00000371953.3:c.494G>T	p.Gly165Val	p.G165V	ENST00000371953	NM_000314.4	165	gGa/gTa	6/9	0.529112128132352	1	FACETS	0.733	0.665	0.803	0.733	0.665	0.803	SUBCLONAL	1	TRUE	0	0.529112128132352	1		490	440	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349145	11349145	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	32	293	0	ENST00000332029.2:c.191A>G	p.Tyr64Cys	p.Y64C	ENST00000332029	NM_003745.1	64	tAc/tGc	2/2	0.427928072355509	1	FACETS	0.271	0.22	0.328	0.271	0.22	0.328	SUBCLONAL	1	TRUE	0	0.529112128132352	1		293	328	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32931932	32931933	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs80359672	NA	P-0028861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	45	349	0	ENST00000380152.3:c.7673_7674del	p.Glu2558ValfsTer7	p.E2558Vfs*7	ENST00000380152		2557	gcAGag/gcag	16/27	0.529112128132352	1	FACETS	0.294	0.247	0.346	0.294	0.247	0.346	SUBCLONAL	1	TRUE	0	0.529112128132352	1		349	425	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108863	2108866	+	frameshift_variant	Frame_Shift_Del	DEL	TCAT	TCAT	-	novel	NA	P-0028861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	64	741	0	ENST00000219476.3:c.965_968del	p.Ser322PhefsTer40	p.S322Ffs*40	ENST00000219476	NM_000548.3	322	TCATtt/tt	10/42	0.427928072355509	1	FACETS	0.262	0.226	0.3	0.262	0.226	0.3	SUBCLONAL	1	TRUE	0	0.529112128132352	1		741	680	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129064	2129064	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	122	492	0	ENST00000219476.3:c.2999del	p.Leu1000TrpfsTer16	p.L1000Wfs*16	ENST00000219476	NM_000548.3	1000	Ttg/tg	27/42	0.427928072355509	1	FACETS	0.684	0.621	0.749	0.684	0.621	0.749	SUBCLONAL	1	TRUE	0	0.529112128132352	1		492	496	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029597	14029597	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	39	247	0	ENST00000311895.7:c.1808T>C	p.Leu603Pro	p.L603P	ENST00000311895	NM_005236.2	603	cTg/cCg	8/11	0.427928072355509	1	FACETS	0.359	0.299	0.426	0.359	0.299	0.426	SUBCLONAL	1	TRUE	0	0.529112128132352	1		247	302	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250073	39250073	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs747840148	NA	P-0028861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	88	728	0	ENST00000402219.2:c.1496T>C	p.Val499Ala	p.V499A	ENST00000402219	NM_005633.3	499	gTa/gCa	10/23	0.254936999862555	2	FACETS	0.412	0.365	0.463	0.206	0.182	0.232	INDETERMINATE	1	TRUE	0	0.529112128132352	2		728	807	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0029223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	133	616	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.984	0.905	1	0.984	0.905	1	CLONAL	1	TRUE	1	0.761781362435287	2		616	355	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757274881	NA	P-0029223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	392	743	0	ENST00000269305.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	144	Cag/Tag	5/11	0.761781362435287	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.761781362435287	1		743	556	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797337	135797337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs118203395	NA	P-0029223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	94	220	0	ENST00000298552.3:c.532G>A	p.Val178Ile	p.V178I	ENST00000298552	NM_001162426.1	178	Gtc/Atc	7/23	1	2	FACETS	0.863	0.778	0.951	0.863	0.778	0.951	CLONAL	1	TRUE	1	0.761781362435287	2		220	286	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479299	50479305	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCTCC	CCGCTCC	-	novel	NA	P-0029223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	13	249	0	ENST00000394963.4:c.150_156del	p.Ser51CysfsTer17	p.S51Cfs*17	ENST00000394963	NM_003076.4	49	taCCGCTCC/ta	1/13	0.761781362435287	1	FACETS	0.098	0.07	0.133	0.098	0.07	0.133	SUBCLONAL	1	TRUE	0	0.761781362435287	1		249	215	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912136	114912136	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029619-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	180	386	0	ENST00000543371.1:c.1207del	p.Ala403ProfsTer88	p.A403Pfs*88	ENST00000543371	NM_001198531.1	402	ctG/ct	11/14	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.570625354270042	2		386	465	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541645	120541645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	47	536	0	ENST00000229340.5:c.212G>A	p.Arg71His	p.R71H	ENST00000229340	NM_006861.6	71	cGc/cAc	3/6	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		536	701	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249002	55249003	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCGTGGA	rs397517109	NA	P-0030936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	158	529	0	ENST00000275493.2:c.2303_2311dup	p.Ser768_Asp770dup	p.S768_D770dup	ENST00000275493	NM_005228.3	768	gcc/gcCAGCGTGGAc	20/28	1	2	FACETS	0.856	0.786	0.929	0.856	0.786	0.929	CLONAL	1	TRUE	1	0.51	2		529	724	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031235-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	79	214	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.995	0.891	1	0.995	0.891	1	CLONAL	1	TRUE	1	0.738765564809987	2		214	215	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419897	41419897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs577588058	NA	P-0031235-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	244	501	0	ENST00000373198.4:c.424G>A	p.Val142Ile	p.V142I	ENST00000373198	NM_133170.3	142	Gtc/Atc	3/32	0.738765564809987	4	FACETS	0.999	0.941	1	0.999	0.941	1	CLONAL	2	TRUE	2	0.738765564809987	4		501	575	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11297916	11297916	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031235-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	130	480	0	ENST00000361445.4:c.2192G>A	p.Arg731His	p.R731H	ENST00000361445	NM_004958.3	731	cGc/cAc	13/58	0.738765564809987	2	FACETS	0.994	0.913	1	0.497	0.456	0.539	CLONAL	1	TRUE	0	0.738765564809987	2		480	354	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42385043	42385043	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555844167	NA	P-0031235-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	112	504	0	ENST00000221972.3:c.677C>T	p.Pro226Leu	p.P226L	ENST00000221972	NM_021601.3	226	cCg/cTg	5/5	0.738765564809987	3	FACETS	0.993	0.9	1	0.497	0.45	0.545	CLONAL	1	TRUE	1	0.738765564809987	3		504	418	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38960046	38960046	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031235-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	76	245	0	ENST00000357387.3:c.1886A>G	p.Asp629Gly	p.D629G	ENST00000357387	NM_152756.3	629	gAt/gGt	21/38	0.738765564809987	3	FACETS	1	0.933	1			1	CLONAL	1	TRUE	NA	0.738765564809987	3		245	263	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505129	149505137	+	protein_altering_variant	In_Frame_Del	DEL	GTAACGTGG	GTAACGTGG	CAT	novel	NA	P-0031235-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	119	462	2	ENST00000261799.4:c.1678_1686delinsATG	p.Pro560_Tyr562delinsMet	p.P560_Y562delinsM	ENST00000261799	NM_002609.3	560	CCACGTTAC/ATG	12/23	0.697430870238672	3	FACETS	1	0.975	1	0.599	0.547	0.654	CLONAL	1	TRUE	1	0.738765564809987	3		464	368	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397828	116397828	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031235-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	121	485	0	ENST00000397752.3:c.2102+1del		p.S701fs	ENST00000397752	NM_000245.2	701	aGt/at	8/21	0.738765564809987	4	FACETS	0.938	0.85	1			1	CLONAL	1	TRUE	NA	0.738765564809987	4		485	607	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660569	227660569	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031235-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	102	577	0	ENST00000305123.5:c.2886G>T	p.Met962Ile	p.M962I	ENST00000305123	NM_005544.2	962	atG/atT	1/2	0.738765564809987	4	FACETS	0.788	0.706	0.875	0.394	0.353	0.438	SUBCLONAL	1	TRUE	2	0.738765564809987	4		577	609	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214395	55214395	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031235-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	122	506	0	ENST00000275493.2:c.521G>T	p.Ser174Ile	p.S174I	ENST00000275493	NM_005228.3	174	aGc/aTc	4/28	0.738765564809987	6	FACETS	0.801	0.723	0.884			1	CLONAL	1	TRUE	NA	0.738765564809987	6		506	1021	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0031339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	92	689	3	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	0.207934900641555	2		692	775	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920401	114920401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1422891742	NA	P-0031339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	89	486	1	ENST00000543371.1:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000543371	NM_001198531.1	448	Cgg/Tgg	13/14	1	2	FACETS	0.961	0.85	1	0.961	0.85	1	CLONAL	1	TRUE	1	0.207934900641555	2		487	891	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639543	3639543	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368434737	NA	P-0031339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	60	885	1	ENST00000294008.3:c.4096C>T	p.Arg1366Cys	p.R1366C	ENST00000294008	NM_032444.2	1366	Cgc/Tgc	12/15	1	2	FACETS	0.575	0.494	0.665	0.575	0.494	0.665	SUBCLONAL	1	TRUE	1	0.207934900641555	2		886	1003	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0031395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	175	710	1	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.316819314238552	4	FACETS	1	0.981	1			1	CLONAL	3	FALSE	NA	0.344330301474359	4		711	400	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138176	64138176	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	98	897	0	ENST00000334205.4:c.2099C>T	p.Ser700Leu	p.S700L	ENST00000334205	NM_003942.2	700	tCg/tTg	16/17	0.344330301474359	7	FACETS	1	0.916	1	0.513	0.459	0.57	CLONAL	2	FALSE	3	0.344330301474359	7		897	516	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0031911-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	115	396	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.266525376034566	7	FACETS	1	0.934	1	0.778	0.705	0.854	CLONAL	3	TRUE	3	0.266525376034566	7		396	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0031911-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	150	678	0	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	0.266525376034566	3	FACETS	1	0.954	1	0.705	0.647	0.765	CLONAL	2	TRUE	0	0.266525376034566	3		678	603	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562324	21562324	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031911-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	84	653	0	ENST00000382592.4:c.1595A>G	p.Asp532Gly	p.D532G	ENST00000382592	NM_014572.2	532	gAc/gGc	4/8	0.266525376034566	3	FACETS	1	0.964	1	0.409	0.362	0.46	CLONAL	1	TRUE	0	0.266525376034566	3		653	582	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681102	37681102	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031911-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3748	1126	529	0	ENST00000447079.4:c.3271C>G	p.Pro1091Ala	p.P1091A	ENST00000447079	NM_015083.1	1091	Cct/Gct	12/14	0.266525376034566	55	FACETS	0.998	0.967	1			1	CLONAL	14	TRUE	NA	0.266525376034566	55		529	4874	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051060	13051060	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031911-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	60	460	0	ENST00000316448.5:c.496G>A	p.Asp166Asn	p.D166N	ENST00000316448	NM_004343.3	166	Gat/Aat	5/9	0.266525376034566	3	FACETS	0.86	0.741	0.99	0.287	0.247	0.33	CLONAL	1	TRUE	0	0.266525376034566	3		460	593	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157835	27157835	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs143178677	NA	P-0031911-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	56	467	0	ENST00000380036.4:c.59T>C	p.Val20Ala	p.V20A	ENST00000380036	NM_000459.3	20	gTg/gCg	2/23	0.266525376034566	3	FACETS	1	0.944	1	0.402	0.345	0.463	CLONAL	1	TRUE	0	0.266525376034566	3		467	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578551	7578551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	319	954	1	ENST00000269305.4:c.379T>C	p.Ser127Pro	p.S127P	ENST00000269305	NM_001126112.2	127	Tcc/Ccc	5/11	0.164579098612905	1	FACETS	1	0.977	1	1	0.977	1	INDETERMINATE	1	TRUE	0	0.58	1		955	745	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036017	180036017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	309	854	1	ENST00000261937.6:c.3844G>A	p.Glu1282Lys	p.E1282K	ENST00000261937	NM_182925.4	1282	Gag/Aag	29/30	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.58	2		855	917	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662380	227662380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	108	658	0	ENST00000305123.5:c.1075C>T	p.His359Tyr	p.H359Y	ENST00000305123	NM_005544.2	359	Cat/Tat	1/2	1	2	FACETS	0.517	0.464	0.573	0.517	0.464	0.573	SUBCLONAL	1	TRUE	1	0.58	2		658	721	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540953	187540953	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750839835	NA	P-0031948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	186	490	0	ENST00000441802.2:c.6787G>A	p.Ala2263Thr	p.A2263T	ENST00000441802	NM_005245.3	2263	Gct/Act	10/27	0.300547105936353	1	FACETS	0.941	0.877	1	0.941	0.877	1	INDETERMINATE	1	TRUE	0	0.58	1		490	484	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522619	67522619	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	173	455	1	ENST00000274335.5:c.116C>A	p.Ala39Asp	p.A39D	ENST00000274335		39	gCt/gAt	1/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.58	2		456	523	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406297	70406297	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031997-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	50	322	0	ENST00000373644.4:c.3811G>C	p.Glu1271Gln	p.E1271Q	ENST00000373644	NM_030625.2	1271	Gaa/Caa	4/12	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.413345571168904	2		322	176	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938457	76938457	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031997-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	96	292	0	ENST00000373344.5:c.2291del	p.Leu764CysfsTer4	p.L764Cfs*4	ENST00000373344	NM_000489.3	764	tTg/tg	9/35	0.414118912322101	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	FALSE	0	0.413345571168904	2		292	200	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624472	21624472	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031997-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	13	318	0	ENST00000421138.2:c.1557del	p.Trp519Ter	p.W519*	ENST00000421138		519	tgG/tg	14/16	NA	2	FACETS	0.372	0.266	0.501			1	INDETERMINATE	1	FALSE	NA	0.413345571168904	2		318	169	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857362	9857362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031997-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	10	239	0	ENST00000330684.3:c.4039G>A	p.Gly1347Ser	p.G1347S	ENST00000330684	NM_001134407.1	1347	Ggt/Agt	13/13	0.29755113905467	4	FACETS	0.368	0.249	0.517	0.184	0.124	0.259	SUBCLONAL	1	FALSE	2	0.413345571168904	4		239	186	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420048	152420048	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031997-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	28	286	0	ENST00000206249.3:c.1735T>G	p.Leu579Val	p.L579V	ENST00000206249	NM_000125.3	579	Ttg/Gtg	8/8	0.402050217304456	5	FACETS	0.971	0.781	1	0.324	0.26	0.396	CLONAL	1	FALSE	2	0.413345571168904	5		286	226	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	37	214	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.985	0.818	1	0.985	0.818	1	CLONAL	1	TRUE	1	0.311677453217126	2		214	241	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426123	138426123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217537873	NA	P-0032061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	65	335	0	ENST00000289153.2:c.1408G>A	p.Glu470Lys	p.E470K	ENST00000289153	NM_006219.2	470	Gaa/Aaa	9/22	1	2	FACETS	0.889	0.773	1	0.889	0.773	1	CLONAL	1	TRUE	1	0.311677453217126	2		335	469	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624303	89624303	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs786204853	NA	P-0032061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	55	526	0	ENST00000371953.3:c.77C>T	p.Thr26Ile	p.T26I	ENST00000371953	NM_000314.4	26	aCc/aTc	1/9	0.311677453217126	1	FACETS	0.577	0.494	0.668	0.577	0.494	0.668	SUBCLONAL	1	TRUE	0	0.311677453217126	1		526	516	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0032151-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	27	624	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.0916281260690948	3	FACETS	0.56	0.446	0.691	0.28	0.223	0.346	INDETERMINATE	1	TRUE	1	0.31	3		624	359	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656255	18656255	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033015-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	143	483	0	ENST00000266497.5:c.2934G>T	p.Lys978Asn	p.K978N	ENST00000266497		978	aaG/aaT	21/31	1	2	FACETS	0.954	0.874	1	0.954	0.874	1	CLONAL	1	TRUE	1	0.532362636194482	2		483	563	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439704	51439704	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033015-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	85	439	0	ENST00000262662.1:c.269T>G	p.Leu90Arg	p.L90R	ENST00000262662		90	cTg/cGg	4/4	0.532362636194482	1	FACETS	0.673	0.6	0.75	0.673	0.6	0.75	SUBCLONAL	1	TRUE	0	0.532362636194482	1		439	348	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715678	30715678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039551	NA	P-0033090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	44	402	0	ENST00000295754.5:c.1336G>A	p.Asp446Asn	p.D446N	ENST00000295754	NM_003242.5	446	Gat/Aat	5/7	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.15	2		402	576	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363358	40363358	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	54	685	1	ENST00000397332.2:c.871G>A	p.Glu291Lys	p.E291K	ENST00000397332	NM_001033082.2	291	Gaa/Aaa	3/3	1	2	FACETS	0.773	0.658	0.899	0.773	0.658	0.899	SUBCLONAL	1	TRUE	1	0.15	2		686	932	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183692	10183693	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs869025615	NA	P-0033134-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	19	810	0	ENST00000256474.2:c.163dup	p.Glu55GlyfsTer77	p.E55Gfs*77	ENST00000256474	NM_000551.3	54	atg/atGg	1/3	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		810	534	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41904365	41904365	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033134-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	22	718	0	ENST00000372991.4:c.643C>A	p.Leu215Met	p.L215M	ENST00000372991	NM_001760.3	215	Ctg/Atg	4/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		718	586	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0033420-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	99	667	0	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.278971835018445	2		667	710	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016603	12016603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033420-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	43	473	0	ENST00000353533.5:c.739G>A	p.Asp247Asn	p.D247N	ENST00000353533	NM_003010.3	247	Gac/Aac	7/11	1	2	FACETS	0.566	0.473	0.669	0.566	0.473	0.669	SUBCLONAL	1	TRUE	1	0.278971835018445	2		473	545	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591118	67591150	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	ATCCAGCTGAGAAAGACGAGAGACCAATACTTG	ATCCAGCTGAGAAAGACGAGAGACCAATACTTG	-	novel	NA	P-0033420-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	9	291	0	ENST00000274335.5:c.1713_1745del	p.Ile571_Leu581del	p.I571_L581del	ENST00000274335		571	ATCCAGCTGAGAAAGACGAGAGACCAATACTTG/-	12/15	1	2	FACETS	0.166	0.109	0.239	0.166	0.109	0.239	SUBCLONAL	1	TRUE	1	0.278971835018445	2		291	389	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592170	67592170	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0033420-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	34	192	0	ENST00000274335.5:c.1985+1G>A		p.X662_splice	ENST00000274335		662			1	2	FACETS	0.938	0.77	1	0.938	0.77	1	CLONAL	1	TRUE	1	0.278971835018445	2		192	260	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	84	331	0				ENST00000310581	NM_198253.2	-/1132			0.327550775053737	3	FACETS	1	0.926	1	0.529	0.469	0.593	CLONAL	1	TRUE	1	0.40226082022134	3		331	474	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503148	125503148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	45	453	0	ENST00000428830.2:c.515C>T	p.Pro172Leu	p.P172L	ENST00000428830	NM_001114121.2	172	cCa/cTa	6/14	1	2	FACETS	0.516	0.434	0.606	0.516	0.434	0.606	SUBCLONAL	1	TRUE	1	0.40226082022134	2		453	434	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130436	29130436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555932172	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	134	600	0	ENST00000328354.6:c.274C>T	p.Pro92Ser	p.P92S	ENST00000328354	NM_007194.3	92	Ccc/Tcc	2/15	1	2	FACETS	0.945	0.86	1	0.945	0.86	1	CLONAL	1	TRUE	1	0.40226082022134	2		600	705	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151181	202151181	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	37	258	0	ENST00000358485.4:c.1482-1G>A		p.X494_splice	ENST00000358485	NM_001080125.1	494			1	2	FACETS	0.943	0.786	1	0.943	0.786	1	CLONAL	1	TRUE	1	0.40226082022134	2		258	195	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259262	89259262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770780950	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	57	435	0	ENST00000336596.2:c.406C>T	p.Arg136Ter	p.R136*	ENST00000336596	NM_005233.5	136	Cga/Tga	3/17	0.40226082022134	1	FACETS	0.817	0.707	0.935	0.817	0.707	0.935	CLONAL	1	TRUE	0	0.40226082022134	1		435	277	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750684	128750684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1294281543	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	108	592	0	ENST00000377970.2:c.221C>T	p.Pro74Leu	p.P74L	ENST00000377970	NM_002467.4	74	cCg/cTg	2/3	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.40226082022134	2		592	501	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095680	178095680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	81	572	0	ENST00000397062.3:c.1651C>T	p.His551Tyr	p.H551Y	ENST00000397062	NM_006164.4	551	Cac/Tac	5/5	1	2	FACETS	0.809	0.715	0.909	0.809	0.715	0.909	CLONAL	1	TRUE	1	0.40226082022134	2		572	498	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410343	63410343	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1404477878	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	141	423	1	ENST00000330258.3:c.2824C>T	p.Arg942Ter	p.R942*	ENST00000330258	NM_152424.3	942	Cga/Tga	2/2	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.40226082022134	1		424	421	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830889	72830889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373169704	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	115	583	1	ENST00000268489.5:c.5692G>A	p.Gly1898Arg	p.G1898R	ENST00000268489	NM_006885.3	1898	Ggg/Agg	9/10	1	2	FACETS	0.771	0.694	0.851	0.771	0.694	0.851	SUBCLONAL	1	TRUE	1	0.40226082022134	2		584	742	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272238	142272238	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	40	299	1	ENST00000350721.4:c.2636C>T	p.Ala879Val	p.A879V	ENST00000350721	NM_001184.3	879	gCc/gTc	13/47	0.40226082022134	3	FACETS	0.622	0.518	0.738	0.311	0.259	0.369	SUBCLONAL	1	TRUE	1	0.40226082022134	3		300	384	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984837	72984837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761672999	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	90	440	0	ENST00000268489.5:c.2747G>A	p.Arg916Gln	p.R916Q	ENST00000268489	NM_006885.3	916	cGg/cAg	3/10	1	2	FACETS	0.812	0.722	0.908	0.812	0.722	0.908	CLONAL	1	TRUE	1	0.40226082022134	2		440	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520008	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	269	496	0	ENST00000269305.4:c.613T>G	p.Tyr205Asp	p.Y205D	ENST00000269305	NM_001126112.2	205	Tat/Gat	6/11	0.272191097862325	3	FACETS	1	0.985	1	0.748	0.705	0.791	CLONAL	2	TRUE	0	0.40226082022134	3		496	716	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	153	712	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	1	2	FACETS	0.973	0.891	1	0.973	0.891	1	CLONAL	1	TRUE	1	0.40226082022134	2		712	782	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087515	27087515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866476464	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	151	748	1	ENST00000324856.7:c.2089C>T	p.Pro697Ser	p.P697S	ENST00000324856	NM_006015.4	697	Ccg/Tcg	5/20	1	2	FACETS	0.812	0.742	0.885	0.812	0.742	0.885	CLONAL	1	TRUE	1	0.40226082022134	2		749	925	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441093	149441093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	303	716	0	ENST00000286301.3:c.1819G>A	p.Glu607Lys	p.E607K	ENST00000286301	NM_005211.3	607	Gag/Aag	13/22	0.333860298065721	2	FACETS	0.855	0.808	0.903	0.855	0.808	0.903	CLONAL	2	TRUE	0	0.40226082022134	2		716	881	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17371347	17371347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761180960	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	132	582	0	ENST00000375499.3:c.109C>T	p.Pro37Ser	p.P37S	ENST00000375499	NM_003000.2	37	Ccc/Tcc	2/8	1	2	FACETS	0.851	0.773	0.933	0.851	0.773	0.933	CLONAL	1	TRUE	1	0.40226082022134	2		582	771	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962358	2962358	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1425453938	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	167	713	1	ENST00000396946.4:c.2179C>T	p.Pro727Ser	p.P727S	ENST00000396946	NM_032415.4	727	Ccg/Tcg	17/25	0.327550775053737	3	FACETS	1	0.97	1	0.557	0.512	0.604	CLONAL	1	TRUE	1	0.40226082022134	3		714	895	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93627369	93627369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	95	499	0	ENST00000375746.1:c.836C>T	p.Ser279Phe	p.S279F	ENST00000375746	NM_001174167.1	279	tCc/tTc	6/14	0.333860298065721	2	FACETS	0.896	0.801	0.998	0.448	0.4	0.499	CLONAL	1	TRUE	0	0.40226082022134	2		499	527	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232204	98232204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	91	287	0	ENST00000331920.6:c.1738G>A	p.Val580Ile	p.V580I	ENST00000331920	NM_000264.3	580	Gta/Ata	13/24	0.333860298065721	2	FACETS	1	0.98	1	0.72	0.647	0.797	CLONAL	1	TRUE	0	0.40226082022134	2		287	314	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195632	102195632	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	90	461	0	ENST00000263464.3:c.392G>T	p.Ser131Ile	p.S131I	ENST00000263464	NM_001165.4	131	aGt/aTt	2/9	1	2	FACETS	0.877	0.781	0.98	0.877	0.781	0.98	CLONAL	1	TRUE	1	0.40226082022134	2		461	510	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721394	176721394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201609442	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	170	519	0	ENST00000439151.2:c.7025C>T	p.Ser2342Leu	p.S2342L	ENST00000439151	NM_022455.4	2342	tCa/tTa	23/23	0.333860298065721	2	FACETS	0.797	0.738	0.858	0.797	0.738	0.858	SUBCLONAL	2	TRUE	0	0.40226082022134	2		519	530	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598898	28598898	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1227427377	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	168	740	0	ENST00000253063.3:c.458C>T	p.Pro153Leu	p.P153L	ENST00000253063	NM_031459.4	153	cCc/cTc	4/10	1	2	FACETS	0.909	0.835	0.986	0.909	0.835	0.986	CLONAL	1	TRUE	1	0.40226082022134	2		740	919	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805073	43805073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	101	618	0	ENST00000372470.3:c.523G>A	p.Asp175Asn	p.D175N	ENST00000372470	NM_005373.2	175	Gat/Aat	4/12	1	2	FACETS	0.785	0.702	0.872	0.785	0.702	0.872	SUBCLONAL	1	TRUE	1	0.40226082022134	2		618	640	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115272905	115272905	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs773944665	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	130	728	0	ENST00000438362.2:c.1468A>G	p.Thr490Ala	p.T490A	ENST00000438362	NM_001242891.1	490	Act/Gct	12/20	1	2	FACETS	0.999	0.908	1	0.999	0.908	1	CLONAL	1	TRUE	1	0.40226082022134	2		728	647	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731171	162731172	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	96	462	3	ENST00000367921.3:c.1026_1027delinsAA	p.Met342_Ala343delinsIleThr	p.M342_A343delinsIT	ENST00000367921	NM_006182.2	342	atGGcc/atAAcc	9/18	1	2	FACETS	0.92	0.822	1	0.92	0.822	1	CLONAL	1	TRUE	1	0.40226082022134	2		465	519	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406025	70406026	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	71	610	0	ENST00000373644.4:c.3539_3540delinsTT	p.Ser1180Phe	p.S1180F	ENST00000373644	NM_030625.2	1180	tCC/tTT	4/12	1	2	FACETS	0.65	0.568	0.738	0.65	0.568	0.738	SUBCLONAL	1	TRUE	1	0.40226082022134	2		610	543	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625392	69625392	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	132	642	0	ENST00000334134.2:c.401A>C	p.Tyr134Ser	p.Y134S	ENST00000334134	NM_005247.2	134	tAc/tCc	3/3	1	2	FACETS	0.855	0.776	0.937	0.855	0.776	0.937	CLONAL	1	TRUE	1	0.40226082022134	2		642	768	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366996	118366996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	89	508	0	ENST00000534358.1:c.5578G>A	p.Asp1860Asn	p.D1860N	ENST00000534358	NM_005933.3	1860	Gac/Aac	20/36	1	2	FACETS	0.907	0.807	1	0.907	0.807	1	CLONAL	1	TRUE	1	0.40226082022134	2		508	488	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244215	46244215	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	80	423	0	ENST00000334344.6:c.2309C>G	p.Pro770Arg	p.P770R	ENST00000334344	NM_152641.2	770	cCa/cGa	15/21	0.37404356135525	2	FACETS	1	0.916	1	0.521	0.461	0.584	CLONAL	1	TRUE	0	0.40226082022134	2		423	382	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447899	49447899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	81	523	0	ENST00000301067.7:c.535G>A	p.Gly179Ser	p.G179S	ENST00000301067	NM_003482.3	179	Ggt/Agt	5/54	0.37404356135525	2	FACETS	0.794	0.702	0.893	0.397	0.351	0.447	SUBCLONAL	1	TRUE	0	0.40226082022134	2		523	507	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784083	120784083	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	340	923	0	ENST00000257552.2:c.902C>T	p.Pro301Leu	p.P301L	ENST00000257552	NM_002442.3	301	cCc/cTc	13/15	0.37404356135525	2	FACETS	0.942	0.895	0.99	0.942	0.895	0.99	CLONAL	2	TRUE	0	0.40226082022134	2		923	897	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28599035	28599035	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	82	545	0	ENST00000241453.7:c.2253A>C	p.Gln751His	p.Q751H	ENST00000241453	NM_004119.2	751	caA/caC	18/24	1	2	FACETS	0.708	0.625	0.796	0.708	0.625	0.796	SUBCLONAL	1	TRUE	1	0.40226082022134	2		545	576	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022898	33022898	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768242805	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	62	366	0	ENST00000300177.4:c.7C>T	p.Arg3Cys	p.R3C	ENST00000300177	NM_001191322.1	3	Cgc/Tgc	2/2	1	2	FACETS	0.863	0.75	0.985	0.863	0.75	0.985	CLONAL	1	TRUE	1	0.40226082022134	2		366	357	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67459128	67459128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	112	706	0	ENST00000327367.4:c.544C>T	p.Pro182Ser	p.P182S	ENST00000327367	NM_005902.3	182	Cct/Tct	4/9	1	2	FACETS	0.707	0.635	0.782	0.707	0.635	0.782	SUBCLONAL	1	TRUE	1	0.40226082022134	2		706	788	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2218123	2218123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747417102	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	173	819	0	ENST00000326181.6:c.185C>T	p.Ser62Phe	p.S62F	ENST00000326181	NM_032271.2	62	tCc/tTc	4/21	1	2	FACETS	0.983	0.905	1	0.983	0.905	1	CLONAL	1	TRUE	1	0.40226082022134	2		819	875	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639908	3639908	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	160	679	0	ENST00000294008.3:c.3731G>A	p.Ser1244Asn	p.S1244N	ENST00000294008	NM_032444.2	1244	aGc/aAc	12/15	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.40226082022134	2		679	763	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790520	3790520	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	131	661	0	ENST00000262367.5:c.4013T>G	p.Leu1338Trp	p.L1338W	ENST00000262367	NM_004380.2	1338	tTg/tGg	24/31	1	2	FACETS	0.794	0.721	0.872	0.794	0.721	0.872	SUBCLONAL	1	TRUE	1	0.40226082022134	2		661	820	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857858	9857858	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	134	681	0	ENST00000330684.3:c.3543C>A	p.Asn1181Lys	p.N1181K	ENST00000330684	NM_001134407.1	1181	aaC/aaA	13/13	1	2	FACETS	0.94	0.855	1	0.94	0.855	1	CLONAL	1	TRUE	1	0.40226082022134	2		681	709	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858268	9858268	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	69	524	0	ENST00000330684.3:c.3133T>A	p.Ser1045Thr	p.S1045T	ENST00000330684	NM_001134407.1	1045	Tcc/Acc	13/13	1	2	FACETS	0.67	0.585	0.762	0.67	0.585	0.762	SUBCLONAL	1	TRUE	1	0.40226082022134	2		524	512	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934903	9934903	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	63	522	0	ENST00000330684.3:c.1387A>C	p.Ile463Leu	p.I463L	ENST00000330684	NM_001134407.1	463	Att/Ctt	6/13	1	2	FACETS	0.696	0.604	0.796	0.696	0.604	0.796	SUBCLONAL	1	TRUE	1	0.40226082022134	2		522	450	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984523	72984523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	145	790	0	ENST00000268489.5:c.3061G>A	p.Gly1021Ser	p.G1021S	ENST00000268489	NM_006885.3	1021	Ggc/Agc	3/10	1	2	FACETS	0.819	0.747	0.895	0.819	0.747	0.895	CLONAL	1	TRUE	1	0.40226082022134	2		790	880	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89824989	89824989	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs140823801	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	94	483	0	ENST00000389301.3:c.2977C>T	p.Gln993Ter	p.Q993*	ENST00000389301	NM_000135.2	993	Caa/Taa	30/43	1	2	FACETS	0.887	0.792	0.988	0.887	0.792	0.988	CLONAL	1	TRUE	1	0.40226082022134	2		483	527	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245614	41245614	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	98	762	1	ENST00000357654.3:c.1934C>T	p.Ser645Phe	p.S645F	ENST00000357654	NM_007294.3	645	tCt/tTt	10/23	1	2	FACETS	0.844	0.755	0.939	0.844	0.755	0.939	CLONAL	1	TRUE	1	0.40226082022134	2		763	577	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434936	56434936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1270747984	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	136	653	1	ENST00000407977.2:c.2201C>T	p.Pro734Leu	p.P734L	ENST00000407977		734	cCc/cTc	9/10	1	2	FACETS	0.943	0.859	1	0.943	0.859	1	CLONAL	1	TRUE	1	0.40226082022134	2		654	717	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129673	11129674	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	105	687	0	ENST00000358026.2:c.2479_2480delinsTT	p.Pro827Phe	p.P827F	ENST00000358026	NM_001128849.1	827	CCc/TTc	17/36	1	2	FACETS	0.673	0.603	0.747	0.673	0.603	0.747	SUBCLONAL	1	TRUE	1	0.40226082022134	2		687	776	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213257	39213257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	184	872	0	ENST00000402219.2:c.3710C>T	p.Pro1237Leu	p.P1237L	ENST00000402219	NM_005633.3	1237	cCt/cTt	23/23	1	2	FACETS	0.95	0.877	1	0.95	0.877	1	CLONAL	1	TRUE	1	0.40226082022134	2		872	963	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634843	158634843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	49	301	0	ENST00000263640.3:c.343C>T	p.Pro115Ser	p.P115S	ENST00000263640	NM_001105.4	115	Cct/Tct	5/11	1	2	FACETS	0.837	0.714	0.971	0.837	0.714	0.971	CLONAL	1	TRUE	1	0.40226082022134	2		301	291	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212484000	212484000	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1369649105	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	33	393	0	ENST00000342788.4:c.2203G>A	p.Gly735Ser	p.G735S	ENST00000342788	NM_005235.2	735	Ggt/Agt	19/28	1	2	FACETS	0.621	0.508	0.748	0.621	0.508	0.748	SUBCLONAL	1	TRUE	1	0.40226082022134	2		393	264	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561324	9561324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	75	542	0	ENST00000353224.5:c.458G>A	p.Gly153Glu	p.G153E	ENST00000353224	NM_177990.2	153	gGa/gAa	4/10	1	2	FACETS	0.761	0.669	0.86	0.761	0.669	0.86	SUBCLONAL	1	TRUE	1	0.40226082022134	2		542	490	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31369191	31369191	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	125	538	0	ENST00000328111.2:c.175G>T	p.Glu59Ter	p.E59*	ENST00000328111	NM_006892.3	59	Gag/Tag	3/23	1	2	FACETS	0.833	0.755	0.916	0.833	0.755	0.916	CLONAL	1	TRUE	1	0.40226082022134	2		538	746	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385207	41385207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	129	573	0	ENST00000373198.4:c.754G>A	p.Val252Ile	p.V252I	ENST00000373198	NM_133170.3	252	Gtc/Atc	6/32	1	2	FACETS	0.855	0.776	0.938	0.855	0.776	0.938	CLONAL	1	TRUE	1	0.40226082022134	2		573	750	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62325739	62325739	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324849160	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	102	551	0	ENST00000360203.5:c.3007G>A	p.Asp1003Asn	p.D1003N	ENST00000360203	NM_001283009.1	1003	Gat/Aat	31/35	1	2	FACETS	0.818	0.733	0.908	0.818	0.733	0.908	CLONAL	1	TRUE	1	0.40226082022134	2		551	620	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627401	37627402	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	169	746	2	ENST00000249071.6:c.317_318delinsTT	p.Pro106Leu	p.P106L	ENST00000249071	NM_002872.4	106	cCC/cTT	5/7	1	2	FACETS	0.946	0.87	1	0.946	0.87	1	CLONAL	1	TRUE	1	0.40226082022134	2		748	888	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573296	41573296	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	133	770	0	ENST00000263253.7:c.5581C>T	p.Gln1861Ter	p.Q1861*	ENST00000263253	NM_001429.3	1861	Caa/Taa	31/31	1	2	FACETS	0.847	0.769	0.928	0.847	0.769	0.928	CLONAL	1	TRUE	1	0.40226082022134	2		770	781	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41279561	41279561	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	86	444	0	ENST00000349496.5:c.2131C>T	p.Gln711Ter	p.Q711*	ENST00000349496	NM_001904.3	711	Cag/Tag	14/15	0.40226082022134	1	FACETS	0.858	0.764	0.958	0.858	0.764	0.958	CLONAL	1	TRUE	0	0.40226082022134	1		444	398	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52685817	52685817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	64	503	0	ENST00000394830.3:c.655G>A	p.Asp219Asn	p.D219N	ENST00000394830	NM_018313.4	219	Gat/Aat	7/30	0.40226082022134	1	FACETS	0.807	0.704	0.917	0.807	0.704	0.917	CLONAL	1	TRUE	0	0.40226082022134	1		503	315	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712568	52712568	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	91	508	0	ENST00000394830.3:c.184G>T	p.Asp62Tyr	p.D62Y	ENST00000394830	NM_018313.4	62	Gat/Tat	3/30	0.40226082022134	1	FACETS	0.723	0.644	0.806	0.723	0.644	0.806	SUBCLONAL	1	TRUE	0	0.40226082022134	1		508	500	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119624625	119624625	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	52	437	0	ENST00000316626.5:c.790G>A	p.Asp264Asn	p.D264N	ENST00000316626		264	Gat/Aat	7/12	0.40226082022134	3	FACETS	0.739	0.631	0.858	0.37	0.315	0.429	SUBCLONAL	1	TRUE	1	0.40226082022134	3		437	420	SUCCESS
ATR	545	MSKCC	GRCh37	3	142212057	142212057	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	283	586	0	ENST00000350721.4:c.5995C>T	p.His1999Tyr	p.H1999Y	ENST00000350721	NM_001184.3	1999	Cat/Tat	35/47	0.40226082022134	3	FACETS	0.836	0.791	0.881	1	0.992	1	CLONAL	3	TRUE	1	0.40226082022134	3		586	674	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526178	189526179	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	139	620	0	ENST00000264731.3:c.442_443delinsTT	p.Pro148Phe	p.P148F	ENST00000264731	NM_003722.4	148	CCc/TTc	4/14	0.40226082022134	1	FACETS	0.857	0.783	0.935	0.857	0.783	0.935	CLONAL	1	TRUE	0	0.40226082022134	1		620	644	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1962788	1962789	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	69	433	0	ENST00000382891.5:c.3282_3283delinsAA	p.Glu1095Lys	p.E1095K	ENST00000382891	NM_133335.3	1094	ggGGag/ggAAag	18/22	1	2	FACETS	0.561	0.489	0.64	0.561	0.489	0.64	SUBCLONAL	1	TRUE	1	0.40226082022134	2		433	611	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467644	66467645	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	62	412	1	ENST00000273854.3:c.624_625delinsAA	p.Gly209Arg	p.G209R	ENST00000273854	NM_004439.5	208	aaGGga/aaAAga	3/18	1	2	FACETS	0.829	0.719	0.946	0.829	0.719	0.946	CLONAL	1	TRUE	1	0.40226082022134	2		413	372	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143181674	143181674	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	68	426	0	ENST00000262992.4:c.659G>T	p.Gly220Val	p.G220V	ENST00000262992	NM_001101669.1	220	gGa/gTa	9/24	1	2	FACETS	0.829	0.724	0.941	0.829	0.724	0.941	CLONAL	1	TRUE	1	0.40226082022134	2		426	408	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592132	67592132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1436986737	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	86	201	0	ENST00000274335.5:c.1948G>A	p.Glu650Lys	p.E650K	ENST00000274335		650	Gag/Aag	14/15	0.333860298065721	2	FACETS	0.789	0.707	0.874	0.789	0.707	0.874	SUBCLONAL	2	TRUE	0	0.40226082022134	2		201	271	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052951	180052951	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs954533152	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	338	941	1	ENST00000261937.6:c.1339G>A	p.Ala447Thr	p.A447T	ENST00000261937	NM_182925.4	447	Gcc/Acc	10/30	0.333860298065721	2	FACETS	0.903	0.856	0.949	0.903	0.856	0.949	CLONAL	2	TRUE	0	0.40226082022134	2		942	931	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490599	20490599	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749949370	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	115	597	0	ENST00000346618.3:c.1336G>A	p.Asp446Asn	p.D446N	ENST00000346618	NM_001949.4	446	Gat/Aat	7/7	1	2	FACETS	0.846	0.763	0.933	0.846	0.763	0.933	CLONAL	1	TRUE	1	0.40226082022134	2		597	676	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323001	31323001	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	93	794	0	ENST00000412585.2:c.896-1G>A		p.X299_splice	ENST00000412585	NM_005514.6	299			1	2	FACETS	0.553	0.491	0.619	0.553	0.491	0.619	SUBCLONAL	1	TRUE	1	0.40226082022134	2		794	836	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188337	32188337	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	140	759	0	ENST00000375023.3:c.1004C>T	p.Ser335Phe	p.S335F	ENST00000375023	NM_004557.3	335	tCt/tTt	6/30	1	2	FACETS	0.874	0.797	0.956	0.874	0.797	0.956	CLONAL	1	TRUE	1	0.40226082022134	2		759	796	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798562	32798562	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	79	551	0	ENST00000374899.4:c.1294G>A	p.Asp432Asn	p.D432N	ENST00000374899	NM_018833.2	432	Gat/Aat	8/12	1	2	FACETS	0.613	0.539	0.692	0.613	0.539	0.692	SUBCLONAL	1	TRUE	1	0.40226082022134	2		551	641	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552939	106552939	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777002137	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	128	724	1	ENST00000369096.4:c.904C>T	p.Arg302Trp	p.R302W	ENST00000369096	NM_001198.3	302	Cgg/Tgg	5/7	1	2	FACETS	0.793	0.718	0.871	0.793	0.718	0.871	SUBCLONAL	1	TRUE	1	0.40226082022134	2		725	803	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553180	106553180	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	106	484	0	ENST00000369096.4:c.1145G>A	p.Gly382Asp	p.G382D	ENST00000369096	NM_001198.3	382	gGc/gAc	5/7	1	2	FACETS	0.925	0.831	1	0.925	0.831	1	CLONAL	1	TRUE	1	0.40226082022134	2		484	570	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268016	55268016	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	100	536	0	ENST00000275493.2:c.2856G>A	p.Met952Ile	p.M952I	ENST00000275493	NM_005228.3	952	atG/atA	24/28	0.327550775053737	3	FACETS	0.799	0.714	0.89	0.4	0.357	0.445	SUBCLONAL	1	TRUE	1	0.40226082022134	3		536	747	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268018	55268018	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	104	545	0	ENST00000275493.2:c.2858T>A	p.Ile953Lys	p.I953K	ENST00000275493	NM_005228.3	953	aTa/aAa	24/28	0.327550775053737	3	FACETS	0.814	0.729	0.904	0.407	0.364	0.452	CLONAL	1	TRUE	1	0.40226082022134	3		545	763	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372774	81372775	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	118	335	0	ENST00000222390.5:c.759_760delinsAA	p.Gly254Ser	p.G254S	ENST00000222390	NM_000601.4	253	aaGGgc/aaAAgc	7/18	0.327550775053737	3	FACETS	0.751	0.682	0.824	0.751	0.682	0.824	SUBCLONAL	2	TRUE	1	0.40226082022134	3		335	469	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875096	151875096	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs758221779	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	25	80	0	ENST00000262189.6:c.7443-1G>A		p.X2481_splice	ENST00000262189	NM_170606.2	2481			0.40226082022134	3	FACETS	0.945	0.768	1	0.945	0.768	1	CLONAL	2	TRUE	1	0.40226082022134	3		80	79	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752835	128752836	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	54	292	0	ENST00000377970.2:c.996_997delinsAA	p.Asp333Asn	p.D333N	ENST00000377970	NM_002467.4	332	aaGGac/aaAAac	3/3	1	2	FACETS	0.772	0.662	0.89	0.772	0.662	0.89	SUBCLONAL	1	TRUE	1	0.40226082022134	2		292	348	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739825	145739825	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs760363252	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	164	799	0	ENST00000428558.2:c.1704+1G>A		p.X568_splice	ENST00000428558	NM_004260.3	568			1	2	FACETS	0.981	0.902	1	0.981	0.902	1	CLONAL	1	TRUE	1	0.40226082022134	2		799	831	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650406	48650407	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	129	409	1	ENST00000376670.3:c.376_377delinsAA	p.Gly126Lys	p.G126K	ENST00000376670	NM_002049.3	126	GGa/AAa	3/6	1	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.40226082022134	1		410	426	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033663-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	15	214	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		214	346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747342068	NA	P-0033936-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	234	742	0	ENST00000269305.4:c.394A>G	p.Lys132Glu	p.K132E	ENST00000269305	NM_001126112.2	132	Aag/Gag	5/11	NA	2	FACETS	0.869	0.813	0.926			1	INDETERMINATE	2	TRUE	NA	0.348878637014067	2		742	772	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296171	15296173	+	inframe_deletion	In_Frame_Del	DEL	CTG	CTG	-	novel	NA	P-0033936-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	180	728	0	ENST00000263388.2:c.2191_2193del	p.Gln731del	p.Q731del	ENST00000263388	NM_000435.2	731	CAG/-	14/33	0.236278246487886	5	FACETS	1	0.947	1	0.687	0.634	0.741	CLONAL	2	TRUE	2	0.348878637014067	5		728	763	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0034045-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	59	624	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.685	0.591	0.787	0.685	0.591	0.787	SUBCLONAL	1	TRUE	1	0.401671259009489	2		624	429	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034045-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	77	458	0	ENST00000347630.2:c.397T>C	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	Ttc/Ctc	6/11	1	2	FACETS	0.685	0.602	0.773	0.685	0.602	0.773	SUBCLONAL	1	TRUE	1	0.401671259009489	2		458	560	SUCCESS
APC	324	MSKCC	GRCh37	5	112175977	112175977	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034045-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	27	201	0	ENST00000257430.4:c.4687del	p.Leu1563TyrfsTer2	p.L1563Yfs*2	ENST00000257430	NM_000038.5	1562	gaC/ga	16/16	0.401671259009489	1	FACETS	0.587	0.471	0.717	0.587	0.471	0.717	SUBCLONAL	1	TRUE	0	0.401671259009489	1		201	183	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0034083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	19	627	0	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	1	2	FACETS	0.495	0.374	0.638	0.495	0.374	0.638	SUBCLONAL	1	TRUE	1	0.15	2		627	512	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103382	77103382	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	28	340	0	ENST00000356341.3:c.184G>C	p.Asp62His	p.D62H	ENST00000356341	NM_002576.4	62	Gat/Cat	2/15	1	2	FACETS	0.962	0.769	1	0.962	0.769	1	CLONAL	1	TRUE	1	0.15	2		340	388	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435888	56435888	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	28	664	0	ENST00000407977.2:c.1249G>T	p.Gly417Ter	p.G417*	ENST00000407977		417	Gga/Tga	9/10	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.15	2		664	346	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29497003	29497003	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397514641	NA	P-0034451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	55	305	0	ENST00000356175.3:c.574C>T	p.Arg192Ter	p.R192*	ENST00000356175	NM_000267.3	192	Cga/Tga	5/57	1	2	FACETS	0.878	0.753	1	0.878	0.753	1	CLONAL	1	TRUE	1	0.311000560262386	2		305	403	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527438	29527438	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs878853922	NA	P-0034451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	61	339	0	ENST00000356175.3:c.889-2A>G		p.X297_splice	ENST00000356175	NM_000267.3	297			1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.311000560262386	2		339	377	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937477	76937480	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	novel	NA	P-0034451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	85	518	0	ENST00000373344.5:c.3268_3271del	p.Glu1090ArgfsTer27	p.E1090Rfs*27	ENST00000373344	NM_000489.3	1090	GAGAag/ag	9/35	1	2	FACETS	0.933	0.826	1	0.933	0.826	1	CLONAL	1	TRUE	1	0.311000560262386	2		518	586	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163985	47163985	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	37	398	0	ENST00000409792.3:c.2141G>A	p.Cys714Tyr	p.C714Y	ENST00000409792	NM_014159.6	714	tGc/tAc	3/21	1	2	FACETS	0.576	0.475	0.689	0.576	0.475	0.689	SUBCLONAL	1	TRUE	1	0.311000560262386	2		398	413	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	150	619	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.476138919661634	1	FACETS	0.881	0.81	0.955	0.881	0.81	0.955	CLONAL	1	TRUE	0	0.476138919661634	1		619	545	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210925	36210925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531663002	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	241	910	1	ENST00000222270.7:c.676C>T	p.Arg226Trp	p.R226W	ENST00000222270	NM_014727.1	226	Cgg/Tgg	3/37	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.476138919661634	2		911	935	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	216	750	0	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	0.476138919661634	1	FACETS	0.981	0.915	1	0.981	0.915	1	CLONAL	1	TRUE	0	0.476138919661634	1		750	705	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129671	11129671	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	378	734	0	ENST00000358026.2:c.2481del	p.Ser828ProfsTer3	p.S828Pfs*3	ENST00000358026	NM_001128849.1	826	gCc/gc	17/36	0.474862535861014	2	FACETS	0.953	0.91	0.996	0.953	0.91	0.996	CLONAL	2	TRUE	0	0.476138919661634	2		734	833	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	100	394	3	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	0.476138919661634	1	FACETS	0.947	0.855	1	0.947	0.855	1	CLONAL	1	TRUE	0	0.476138919661634	1		397	338	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795378	42795378	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	137	643	0	ENST00000575354.2:c.2462del	p.Gly821GlufsTer103	p.G821Efs*103	ENST00000575354	NM_015125.3	820	Ggg/gg	10/20	0.476138919661634	1	FACETS	0.87	0.796	0.946	0.87	0.796	0.946	CLONAL	1	TRUE	0	0.476138919661634	1		643	504	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288269	21288269	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	197	793	0	ENST00000354336.3:c.514A>G	p.Met172Val	p.M172V	ENST00000354336	NM_005207.3	172	Atg/Gtg	2/3	1	2	FACETS	0.93	0.862	1	0.93	0.862	1	CLONAL	1	TRUE	1	0.476138919661634	2		793	890	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193202236	193202236	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	139	419	0	ENST00000367435.3:c.1268T>C	p.Val423Ala	p.V423A	ENST00000367435	NM_024529.4	423	gTa/gCa	14/17	0.474862535861014	2	FACETS	1	0.939	1	0.517	0.472	0.563	CLONAL	1	TRUE	0	0.476138919661634	2		419	565	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125635	47125635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	141	467	0	ENST00000409792.3:c.5635C>T	p.Arg1879Cys	p.R1879C	ENST00000409792	NM_014159.6	1879	Cgc/Tgc	12/21	0.476138919661634	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.476138919661634	1		467	441	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998128	169998128	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs753143066	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1181	217	749	5	ENST00000295797.4:c.826del	p.Thr276GlnfsTer7	p.T276Qfs*7	ENST00000295797	NM_002740.5	273	ttA/tt	9/18	0.476138919661634	4	FACETS	0.962	0.893	1	0.321	0.297	0.345	CLONAL	1	TRUE	1	0.476138919661634	4		754	1398	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614463	38614463	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	155	518	0	ENST00000299084.4:c.234del	p.Asp79ThrfsTer42	p.D79Tfs*42	ENST00000299084	NM_152594.2	77	Aaa/aa	3/7	0.476138919661634	1	FACETS	0.924	0.851	0.999	0.924	0.851	0.999	CLONAL	1	TRUE	0	0.476138919661634	1		518	537	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204737476	204737476	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1559592490	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	96	403	0	ENST00000302823.3:c.617del	p.Pro206GlnfsTer23	p.P206Qfs*23	ENST00000302823	NM_005214.4	205	Ccc/cc	4/4	1	2	FACETS	0.969	0.869	1	0.969	0.869	1	CLONAL	1	TRUE	1	0.476138919661634	2		403	416	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560488	65560488	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	140	608	0	ENST00000358664.4:c.109del	p.Asp37ThrfsTer28	p.D37Tfs*28	ENST00000358664	NM_002382.4	37	Gac/ac	3/5	0.476138919661634	1	FACETS	0.838	0.767	0.911	0.838	0.767	0.911	CLONAL	1	TRUE	0	0.476138919661634	1		608	535	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115758	8115758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1218538798	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	143	482	0	ENST00000346208.3:c.1104G>A	p.Met368Ile	p.M368I	ENST00000346208		368	atG/atA	6/6	0.148179305465758	2	FACETS	0.835	0.763	0.911	0.418	0.381	0.456	INDETERMINATE	1	TRUE	0	0.476138919661634	2		482	719	SUCCESS
RET	5979	MSKCC	GRCh37	10	43595934	43595934	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	212	974	0	ENST00000355710.3:c.101A>T	p.Asp34Val	p.D34V	ENST00000355710	NM_020975.4	34	gAt/gTt	2/20	0.148179305465758	2	FACETS	0.941	0.875	1	0.471	0.437	0.505	INDETERMINATE	1	TRUE	0	0.476138919661634	2		974	946	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939492	71939492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	268	1087	1	ENST00000298229.2:c.347C>T	p.Pro116Leu	p.P116L	ENST00000298229	NM_001567.3	116	cCt/cTt	3/28	1	2	FACETS	0.981	0.92	1	0.981	0.92	1	CLONAL	1	TRUE	1	0.476138919661634	2		1088	1147	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949090	71949090	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	173	671	0	ENST00000298229.2:c.3557C>G	p.Pro1186Arg	p.P1186R	ENST00000298229	NM_001567.3	1186	cCg/cGg	27/28	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.476138919661634	2		671	712	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376857	118376857	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	29	420	0	ENST00000534358.1:c.10254del	p.Ser3419LeufsTer5	p.S3419Lfs*5	ENST00000534358	NM_005933.3	3417	aCc/ac	27/36	1	2	FACETS	0.271	0.217	0.332	0.271	0.217	0.332	SUBCLONAL	1	TRUE	1	0.476138919661634	2		420	450	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233964	133233966	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	169	707	0	ENST00000320574.5:c.3428_3430del	p.Lys1143del	p.K1143del	ENST00000320574	NM_006231.2	1143	aAGAtc/atc	28/49	1	2	FACETS	0.929	0.856	1	0.929	0.856	1	CLONAL	1	TRUE	1	0.476138919661634	2		707	764	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436549	110436549	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1002089942	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	227	905	1	ENST00000375856.3:c.1852G>A	p.Ala618Thr	p.A618T	ENST00000375856	NM_003749.2	618	Gcg/Acg	1/2	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.476138919661634	2		906	953	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274098	10274098	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	81	779	0	ENST00000330684.3:c.171del	p.Glu58SerfsTer10	p.E58Sfs*10	ENST00000330684	NM_001134407.1	57	ccC/cc	2/13	0.148179305465758	2	FACETS	0.344	0.302	0.389	0.172	0.151	0.195	INDETERMINATE	1	TRUE	0	0.476138919661634	2		779	990	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641730	23641733	+	frameshift_variant	Frame_Shift_Del	DEL	GATA	GATA	-	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	138	491	0	ENST00000261584.4:c.1742_1745del	p.Leu581SerfsTer17	p.L581Sfs*17	ENST00000261584	NM_024675.3	581	tTATCc/tc	5/13	0.148179305465758	2	FACETS	0.957	0.874	1	0.478	0.437	0.522	INDETERMINATE	1	TRUE	0	0.476138919661634	2		491	606	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924280	11924280	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1294433193	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	27	104	1	ENST00000353533.5:c.80del	p.Pro27ArgfsTer18	p.P27Rfs*18	ENST00000353533	NM_003010.3	26	tCc/tc	1/11	0.476138919661634	1	FACETS	0.873	0.711	1	0.873	0.711	1	CLONAL	1	TRUE	0	0.476138919661634	1		105	99	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41258552	41258552	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	122	404	1	ENST00000357654.3:c.135-2A>T		p.X45_splice	ENST00000357654	NM_007294.3	45			1	2	FACETS	0.989	0.899	1	0.989	0.899	1	CLONAL	1	TRUE	1	0.476138919661634	2		405	518	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007605	62007605	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	245	807	0	ENST00000392795.3:c.262del	p.Gln88SerfsTer3	p.Q88Sfs*3	ENST00000392795	NM_001039933.1	88	Cag/ag	3/6	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.476138919661634	2		807	921	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2180739	2180741	+	inframe_deletion	In_Frame_Del	DEL	ATC	ATC	-	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	373	734	0	ENST00000398665.3:c.112_114del	p.Ile38del	p.I38del	ENST00000398665	NM_032482.2	37	ATC/-	2/28	0.474862535861014	2	FACETS	0.931	0.889	0.974	0.931	0.889	0.974	CLONAL	2	TRUE	0	0.476138919661634	2		734	841	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143979	11143979	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	274	474	0	ENST00000358026.2:c.3560A>C	p.Gln1187Pro	p.Q1187P	ENST00000358026	NM_001128849.1	1187	cAg/cCg	26/36	0.474862535861014	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.476138919661634	2		474	570	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273869	18273869	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	425	773	0	ENST00000222254.8:c.1202T>A	p.Leu401His	p.L401H	ENST00000222254	NM_005027.3	401	cTc/cAc	10/16	0.474862535861014	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.476138919661634	2		773	893	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273952	18273952	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	305	587	1	ENST00000222254.8:c.1285C>A	p.Gln429Lys	p.Q429K	ENST00000222254	NM_005027.3	429	Cag/Aag	10/16	0.474862535861014	2	FACETS	0.948	0.9	0.996	0.948	0.9	0.996	CLONAL	2	TRUE	0	0.476138919661634	2		588	676	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211693	36211693	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1420662989	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	152	597	0	ENST00000222270.7:c.1444C>T	p.Arg482Trp	p.R482W	ENST00000222270	NM_014727.1	482	Cgg/Tgg	3/37	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.476138919661634	2		597	635	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46588161	46588161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1294290798	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	184	707	1	ENST00000263734.3:c.715del	p.Leu239TrpfsTer7	p.L239Wfs*7	ENST00000263734	NM_001430.4	237	atC/at	6/16	1	2	FACETS	0.904	0.835	0.975	0.904	0.835	0.975	CLONAL	1	TRUE	1	0.476138919661634	2		708	855	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46277774	46277774	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	96	447	0	ENST00000371998.3:c.3572T>C	p.Leu1191Pro	p.L1191P	ENST00000371998		1191	cTt/cCt	19/23	1	2	FACETS	0.902	0.808	1	0.902	0.808	1	CLONAL	1	TRUE	1	0.476138919661634	2		447	447	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565548	41565548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138855106	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	119	592	1	ENST00000263253.7:c.4214G>A	p.Arg1405His	p.R1405H	ENST00000263253	NM_001429.3	1405	cGt/cAt	26/31	1	2	FACETS	0.749	0.677	0.825	0.749	0.677	0.825	SUBCLONAL	1	TRUE	1	0.476138919661634	2		593	667	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170011201	170011201	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	152	641	0	ENST00000295797.4:c.1322T>C	p.Val441Ala	p.V441A	ENST00000295797	NM_002740.5	441	gTg/gCg	14/18	0.476138919661634	4	FACETS	0.817	0.746	0.892	0.272	0.248	0.298	CLONAL	1	TRUE	1	0.476138919661634	4		641	1153	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182679103	182679103	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	101	537	0	ENST00000292782.4:c.431T>C	p.Met144Thr	p.M144T	ENST00000292782	NM_020640.2	144	aTg/aCg	4/7	0.476138919661634	4	FACETS	0.684	0.611	0.763	0.228	0.203	0.255	SUBCLONAL	1	TRUE	1	0.476138919661634	4		537	915	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582162	189582162	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	106	495	0	ENST00000264731.3:c.721G>T	p.Val241Leu	p.V241L	ENST00000264731	NM_003722.4	241	Gtg/Ttg	5/14	0.476138919661634	4	FACETS	0.883	0.792	0.98	0.294	0.264	0.327	CLONAL	1	TRUE	1	0.476138919661634	4		495	744	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1955194	1955194	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	192	632	0	ENST00000382891.5:c.2281C>A	p.Leu761Ile	p.L761I	ENST00000382891	NM_133335.3	761	Ctc/Atc	12/22	0.476138919661634	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.476138919661634	1		632	585	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236583	236583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	48	144	0	ENST00000264932.6:c.1301G>A	p.Gly434Asp	p.G434D	ENST00000264932	NM_004168.2	434	gGc/gAc	10/15	0.476138919661634	5	FACETS	1	0.945	1	0.25	0.213	0.291	CLONAL	1	TRUE	0	0.476138919661634	5		144	276	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945799	38945799	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	84	271	0	ENST00000357387.3:c.4427T>A	p.Val1476Glu	p.V1476E	ENST00000357387	NM_152756.3	1476	gTa/gAa	34/38	0.476138919661634	5	FACETS	1	0.951	1	0.227	0.201	0.256	CLONAL	1	TRUE	0	0.476138919661634	5		271	532	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111401	56111401	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	73	307	0	ENST00000399503.3:c.1A>G	p.Met1?	p.M1?	ENST00000399503	NM_005921.1	1	Atg/Gtg	1/20	0.476138919661634	1	FACETS	0.82	0.724	0.92	0.82	0.724	0.92	CLONAL	1	TRUE	0	0.476138919661634	1		307	285	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131930734	131930734	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	87	336	0	ENST00000265335.6:c.1967G>T	p.Arg656Leu	p.R656L	ENST00000265335		656	cGa/cTa	12/25	0.476138919661634	1	FACETS	0.967	0.866	1	0.967	0.866	1	CLONAL	1	TRUE	0	0.476138919661634	1		336	288	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681510	117681510	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	46	292	0	ENST00000368508.3:c.3440C>A	p.Thr1147Lys	p.T1147K	ENST00000368508	NM_002944.2	1147	aCa/aAa	22/43	1	2	FACETS	0.642	0.543	0.749	0.642	0.543	0.749	SUBCLONAL	1	TRUE	1	0.476138919661634	2		292	301	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367243	50367244	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	83	288	0	ENST00000331340.3:c.56dup	p.Val20CysfsTer7	p.V20Cfs*7	ENST00000331340	NM_006060.4	17	agc/agCc	3/8	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.476138919661634	2		288	346	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508334	106508334	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	79	323	0	ENST00000359195.3:c.328T>C	p.Tyr110His	p.Y110H	ENST00000359195	NM_002649.2	110	Tac/Cac	2/11	1	2	FACETS	0.883	0.781	0.99	0.883	0.781	0.99	CLONAL	1	TRUE	1	0.476138919661634	2		323	376	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846353	128846353	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	216	843	0	ENST00000249373.3:c.1189T>C	p.Tyr397His	p.Y397H	ENST00000249373	NM_005631.4	397	Tac/Cac	6/12	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.476138919661634	2		843	886	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852259	128852259	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	207	797	0	ENST00000249373.3:c.2331C>A	p.Asp777Glu	p.D777E	ENST00000249373	NM_005631.4	777	gaC/gaA	12/12	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.476138919661634	2		797	842	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845369	151845369	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	199	736	0	ENST00000262189.6:c.13643T>G	p.Phe4548Cys	p.F4548C	ENST00000262189	NM_170606.2	4548	tTt/tGt	52/59	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.476138919661634	2		736	800	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570246	87570246	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	145	422	0	ENST00000277120.3:c.1987del	p.Glu663AsnfsTer2	p.E663Nfs*2	ENST00000277120		662	acG/ac	17/19	0.464297151961405	2	FACETS	0.773	0.713	0.834	0.773	0.713	0.834	SUBCLONAL	2	TRUE	0	0.476138919661634	2		422	394	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750283	133750283	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	279	588	0	ENST00000318560.5:c.1117del	p.Glu373ArgfsTer5	p.E373Rfs*5	ENST00000318560	NM_005157.4	372	Ggg/gg	7/11	0.464297151961405	2	FACETS	0.911	0.863	0.96	0.911	0.863	0.96	CLONAL	2	TRUE	0	0.476138919661634	2		588	643	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401772	139401772	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	340	853	0	ENST00000277541.6:c.3628C>A	p.Pro1210Thr	p.P1210T	ENST00000277541	NM_017617.3	1210	Cca/Aca	22/34	0.464297151961405	2	FACETS	0.888	0.845	0.932	0.888	0.845	0.932	CLONAL	2	TRUE	0	0.476138919661634	2		853	804	SUCCESS
AR	367	MSKCC	GRCh37	X	66765917	66765917	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	222	950	0	ENST00000374690.3:c.932del	p.Pro311LeufsTer10	p.P311Lfs*10	ENST00000374690	NM_000044.3	310	tCc/tc	1/8	0.476138919661634	1	FACETS	0.886	0.827	0.947	0.886	0.827	0.947	CLONAL	1	TRUE	0	0.476138919661634	1		950	802	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338679	70338679	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034559-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	67	622	0	ENST00000374080.3:c.77del	p.Pro26LeufsTer11	p.P26Lfs*11	ENST00000374080		25	taC/ta	1/45	0.476138919661634	1	FACETS	0.458	0.399	0.522	0.458	0.399	0.522	SUBCLONAL	1	TRUE	0	0.476138919661634	1		622	468	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035084-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	215	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.307217991301919	5	FACETS	0.902	0.848	0.955	0.721	0.679	0.764	CLONAL	4	TRUE	0	0.420969933283233	5		452	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035084-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	114	564	0	ENST00000269305.4:c.380C>A	p.Ser127Tyr	p.S127Y	ENST00000269305	NM_001126112.2	127	tCc/tAc	5/11	0.3994453190891	4	FACETS	0.964	0.868	1	0.482	0.434	0.533	CLONAL	1	TRUE	2	0.420969933283233	4		564	798	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725043	89725043	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1057517809	NA	P-0035084-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	92	131	0	ENST00000371953.3:c.1027-1G>A		p.X343_splice	ENST00000371953	NM_000314.4	343			0.420969933283233	3	FACETS	1	0.975	1	0.82	0.744	0.897	CLONAL	2	TRUE	0	0.420969933283233	3		131	215	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911436	39911436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437936868	NA	P-0035084-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	45	433	0	ENST00000378444.4:c.5194G>A	p.Glu1732Lys	p.E1732K	ENST00000378444	NM_001123385.1	1732	Gaa/Aaa	15/15	0.420969933283233	3	FACETS	0.428	0.359	0.504	0.214	0.179	0.252	SUBCLONAL	1	TRUE	1	0.420969933283233	3		433	605	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934141	39934141	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035084-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	59	472	0	ENST00000378444.4:c.458C>A	p.Pro153His	p.P153H	ENST00000378444	NM_001123385.1	153	cCt/cAt	4/15	0.420969933283233	3	FACETS	0.584	0.502	0.673	0.292	0.251	0.337	SUBCLONAL	1	TRUE	1	0.420969933283233	3		472	581	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056233	27056233	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035084-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	114	424	0	ENST00000324856.7:c.1229G>T	p.Gly410Val	p.G410V	ENST00000324856	NM_006015.4	410	gGa/gTa	2/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.420969933283233	2		424	427	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458168	120458168	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035084-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	162	396	0	ENST00000256646.2:c.7177G>T	p.Ala2393Ser	p.A2393S	ENST00000256646	NM_024408.3	2393	Gct/Tct	34/34	0.318087905112663	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	2	0.420969933283233	4		396	523	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612692	228612692	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035084-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	92	697	0	ENST00000366696.1:c.335T>A	p.Val112Asp	p.V112D	ENST00000366696	NM_003493.2	112	gTc/gAc	1/1	1	2	FACETS	0.7	0.623	0.783	0.7	0.623	0.783	SUBCLONAL	1	TRUE	1	0.420969933283233	2		697	624	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885620	111885620	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035084-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	95	584	0	ENST00000341259.2:c.1397C>G	p.Ser466Cys	p.S466C	ENST00000341259	NM_005475.2	466	tCc/tGc	7/8	0.420969933283233	2	FACETS	0.721	0.643	0.804	0.36	0.321	0.402	SUBCLONAL	1	TRUE	0	0.420969933283233	2		584	626	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991321	41991321	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035084-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	52	372	0	ENST00000219905.7:c.2152C>G	p.Arg718Gly	p.R718G	ENST00000219905	NM_001164273.1	718	Cgg/Ggg	5/24	1	2	FACETS	0.615	0.525	0.713	0.615	0.525	0.713	SUBCLONAL	1	TRUE	1	0.420969933283233	2		372	402	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631599	90631599	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035084-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	61	410	0	ENST00000330062.3:c.670del	p.Thr224ProfsTer25	p.T224Pfs*25	ENST00000330062	NM_002168.2	224	Acc/cc	5/11	1	2	FACETS	0.759	0.657	0.868	0.759	0.657	0.868	SUBCLONAL	1	TRUE	1	0.420969933283233	2		410	382	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576862	7576862	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035084-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	66	450	0	ENST00000269305.4:c.984C>G	p.Phe328Leu	p.F328L	ENST00000269305	NM_001126112.2	328	ttC/ttG	9/11	0.3994453190891	4	FACETS	0.681	0.591	0.779	0.341	0.295	0.39	SUBCLONAL	1	TRUE	2	0.420969933283233	4		450	654	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445020	89445020	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035084-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	48	303	0	ENST00000336596.2:c.1340G>T	p.Arg447Leu	p.R447L	ENST00000336596	NM_005233.5	447	cGg/cTg	6/17	NA	2	FACETS	0.576	0.488	0.672			1	INDETERMINATE	1	TRUE	NA	0.420969933283233	2		303	396	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939738	131939738	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035084-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	57	199	0	ENST00000265335.6:c.2524G>A	p.Val842Ile	p.V842I	ENST00000265335		842	Gtt/Att	15/25	0.420969933283233	3	FACETS	1	0.964	1	0.677	0.587	0.773	CLONAL	1	TRUE	1	0.420969933283233	3		199	242	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032160	26032161	+	missense_variant	Missense_Mutation	DNP	GC	GC	AT	novel	NA	P-0035084-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	77	258	1	ENST00000244661.2:c.128_129delinsAT	p.Arg43His	p.R43H	ENST00000244661	NM_003537.3	43	cGC/cAT	1/1	0.420969933283233	3	FACETS	1	0.972	1	0.449	0.397	0.503	CLONAL	1	TRUE	0	0.420969933283233	3		259	329	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979216	93979216	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035084-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	183	218	0	ENST00000369303.4:c.1612G>A	p.Ala538Thr	p.A538T	ENST00000369303	NM_004440.3	538	Gct/Act	7/17	0.39878340672977	4	FACETS	1	0.967	1	0.788	0.737	0.839	CLONAL	3	TRUE	0	0.420969933283233	4		218	392	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563515	87563515	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035084-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	108	407	0	ENST00000277120.3:c.1903T>A	p.Tyr635Asn	p.Y635N	ENST00000277120		635	Tac/Aac	16/19	0.168668321993151	4	FACETS	0.769	0.694	0.848	0.513	0.462	0.565	INDETERMINATE	2	TRUE	1	0.420969933283233	4		407	474	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295801	212295801	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1423325504	NA	P-0035162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	34	573	1	ENST00000342788.4:c.2512C>T	p.Arg838Ter	p.R838*	ENST00000342788	NM_005235.2	838	Cga/Tga	21/28	0.320826719966451	3	FACETS	0.609	0.498	0.734	0.304	0.249	0.367	SUBCLONAL	1	TRUE	1	0.320826719966451	3		574	404	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443936	18443936	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1195125518	NA	P-0035162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	32	382	0	ENST00000266497.5:c.909T>G	p.Phe303Leu	p.F303L	ENST00000266497		303	ttT/ttG	3/31	0.320826719966451	3	FACETS	0.922	0.752	1	0.461	0.376	0.556	CLONAL	1	TRUE	1	0.320826719966451	3		382	251	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783871	50783871	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	52	670	0	ENST00000398568.2:c.262G>A	p.Asp88Asn	p.D88N	ENST00000398568	NM_001042412.1	88	Gat/Aat	3/18	0.320826719966451	3	FACETS	0.763	0.65	0.887	0.382	0.325	0.444	SUBCLONAL	1	TRUE	1	0.320826719966451	3		670	493	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191029	2191029	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	34	362	0	ENST00000398665.3:c.283C>A	p.Pro95Thr	p.P95T	ENST00000398665	NM_032482.2	95	Ccc/Acc	5/28	1	2	FACETS	0.673	0.551	0.809	0.673	0.551	0.809	SUBCLONAL	1	TRUE	1	0.320826719966451	2		362	315	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120363	94120363	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	42	333	0	ENST00000369303.4:c.688G>T	p.Val230Phe	p.V230F	ENST00000369303	NM_004440.3	230	Gtt/Ttt	3/17	0.320826719966451	3	FACETS	1	0.852	1	0.508	0.426	0.598	CLONAL	1	TRUE	1	0.320826719966451	3		333	299	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411856	116411880	+	intron_variant	Intron	DEL	CCATGATAGCCGTCTTTAACAAGCT	CCATGATAGCCGTCTTTAACAAGCT	-	novel	NA	P-0035162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	1404	966	0	ENST00000397752.3:c.2888-46_2888-22del		p.*963*	ENST00000397752	NM_000245.2	-/1390			0.320826719966451	15	FACETS	0.984	0.968	0.999			1	CLONAL	15	TRUE	NA	0.320826719966451	15		966	1830	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465595	8465595	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	66	608	0	ENST00000356435.5:c.3585C>A	p.His1195Gln	p.H1195Q	ENST00000356435		1195	caC/caA	21/35	0.318157808752168	1	FACETS	0.99	0.865	1	0.99	0.865	1	CLONAL	1	TRUE	0	0.320826719966451	1		608	349	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916438	39916438	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	52	629	0	ENST00000378444.4:c.4565A>G	p.Asp1522Gly	p.D1522G	ENST00000378444	NM_001123385.1	1522	gAt/gGt	11/15	0.196075314162093	4	FACETS	0.823	0.701	0.957	0.412	0.35	0.479	CLONAL	1	TRUE	2	0.320826719966451	4		629	520	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907659	76907659	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	56	706	0	ENST00000373344.5:c.4502A>T	p.Glu1501Val	p.E1501V	ENST00000373344	NM_000489.3	1501	gAa/gTa	15/35	0.196075314162093	4	FACETS	0.84	0.72	0.971	0.42	0.36	0.486	CLONAL	1	TRUE	2	0.320826719966451	4		706	549	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	245	214	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		214	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0035371-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	51	728	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	1	2	FACETS	0.872	0.743	1	0.872	0.743	1	CLONAL	1	FALSE	1	0.3	2		728	390	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358978	81358978	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs374484762	NA	P-0035371-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	34	742	1	ENST00000222390.5:c.983G>T	p.Arg328Leu	p.R328L	ENST00000222390	NM_000601.4	328	cGt/cTt	8/18	1	2	FACETS	0.572	0.468	0.69	0.572	0.468	0.69	SUBCLONAL	1	FALSE	1	0.3	2		743	396	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525133	187525133	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0035371-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	17	373	1	ENST00000441802.2:c.10549-2A>T		p.X3517_splice	ENST00000441802	NM_005245.3	3517			1	2	FACETS	0.606	0.454	0.785	0.606	0.454	0.785	SUBCLONAL	1	FALSE	1	0.3	2		374	187	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099065	27099065	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035371-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	46	620	0	ENST00000324856.7:c.3481A>C	p.Lys1161Gln	p.K1161Q	ENST00000324856	NM_006015.4	1161	Aag/Cag	13/20	1	2	FACETS	0.799	0.674	0.935	0.799	0.674	0.935	CLONAL	1	FALSE	1	0.3	2		620	384	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170813	99170813	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035371-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	46	705	1	ENST00000074304.5:c.1442A>T	p.Tyr481Phe	p.Y481F	ENST00000074304	NM_001134224.1	481	tAc/tTc	16/26	1	2	FACETS	0.743	0.626	0.87	0.743	0.626	0.87	SUBCLONAL	1	FALSE	1	0.3	2		706	413	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911784	32911784	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs690016541	NA	P-0035371-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	32	757	1	ENST00000380152.3:c.3293del	p.Asn1098IlefsTer6	p.N1098Ifs*6	ENST00000380152		1098	Aat/at	11/27	0.180016920582543	3	FACETS	0.683	0.555	0.828	0.342	0.277	0.414	SUBCLONAL	1	FALSE	1	0.3	3		758	359	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375959	118375959	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035371-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	17	608	0	ENST00000534358.1:c.9352A>T	p.Met3118Leu	p.M3118L	ENST00000534358	NM_005933.3	3118	Atg/Ttg	27/36	1	2	FACETS	0.377	0.281	0.491	0.377	0.281	0.491	SUBCLONAL	1	FALSE	1	0.3	2		608	301	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30133010	30133010	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035371-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	65	744	0	ENST00000331968.5:c.591C>A	p.Ser197Arg	p.S197R	ENST00000331968	NM_002742.2	197	agC/agA	4/18	1	2	FACETS	0.736	0.638	0.842	0.736	0.638	0.842	SUBCLONAL	1	FALSE	1	0.3	2		744	589	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933480	100933480	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035371-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	13	313	1	ENST00000325455.5:c.1910G>T	p.Arg637Leu	p.R637L	ENST00000325455	NM_001202474.3	637	cGa/cTa	4/8	1	2	FACETS	0.451	0.322	0.608	0.451	0.322	0.608	SUBCLONAL	1	FALSE	1	0.3	2		314	192	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577064	7577064	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0035514-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	117	748	0	ENST00000269305.4:c.874A>T	p.Lys292Ter	p.K292*	ENST00000269305	NM_001126112.2	292	Aaa/Taa	8/11	0.463407756215477	3	FACETS	0.784	0.713	0.858	0.784	0.713	0.858	SUBCLONAL	2	FALSE	1	0.461307195881396	3		748	398	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527295	187527295	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035514-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	95	598	0	ENST00000441802.2:c.10279A>T	p.Asn3427Tyr	p.N3427Y	ENST00000441802	NM_005245.3	3427	Aac/Tac	17/27	0.445393935820984	1	FACETS	0.773	0.704	0.842	1	0.985	1	SUBCLONAL	2	FALSE	0	0.461307195881396	1		598	205	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061211	38061240	+	inframe_deletion	In_Frame_Del	DEL	AGTAGCAGCCGTTCTCGAACATGTTGCCGG	AGTAGCAGCCGTTCTCGAACATGTTGCCGG	-	novel	NA	P-0035578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	121	443	0	ENST00000250448.2:c.749_778del	p.Ser250_Tyr259del	p.S250_Y259del	ENST00000250448	NM_004496.3	250	tCCGGCAACATGTTCGAGAACGGCTGCTACTtg/ttg	2/2	0.165979209817862	4	FACETS	1	0.984	1	0.69	0.628	0.754	INDETERMINATE	1	TRUE	2	0.73511601214699	4		443	414	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696644	47696644	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	128	537	0	ENST00000347630.2:c.304T>A	p.Phe102Ile	p.F102I	ENST00000347630	NM_001007230.1	102	Ttc/Atc	5/11	1	2	FACETS	0.973	0.892	1	0.973	0.892	1	CLONAL	1	TRUE	1	0.73511601214699	2		537	358	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582349	119582349	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0035578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	308	347	0	ENST00000316626.5:c.1052C>G	p.Ser351Ter	p.S351*	ENST00000316626		351	tCa/tGa	10/12	0.737600367326697	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.73511601214699	3		347	553	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457181	5457181	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	15	336	0	ENST00000381577.3:c.155C>T	p.Ala52Val	p.A52V	ENST00000381577	NM_014143.3	52	gCa/gTa	3/7	0.252392079040016	3	FACETS	0.268	0.196	0.354	0.134	0.098	0.177	INDETERMINATE	1	TRUE	1	0.73511601214699	3		336	208	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988532	41988535	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0035844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	372	648	0	ENST00000219905.7:c.1324_1327del	p.Ser442LeufsTer19	p.S442Lfs*19	ENST00000219905	NM_001164273.1	442	TCTTct/ct	3/24	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.828962221058669	2		648	889	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336102	73336102	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	36	215	0	ENST00000377767.4:c.2301A>T	p.Leu767Phe	p.L767F	ENST00000377767	NM_014953.3	767	ttA/ttT	17/21	1	2	FACETS	0.781	0.645	0.932	0.781	0.645	0.932	CLONAL	1	TRUE	1	0.337589832031419	2		215	273	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347173	89347173	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778991139	NA	P-0035894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	78	395	0	ENST00000301030.4:c.5777C>T	p.Pro1926Leu	p.P1926L	ENST00000301030	NM_001256183.1	1926	cCg/cTg	9/13	1	2	FACETS	0.981	0.865	1	0.981	0.865	1	CLONAL	1	TRUE	1	0.337589832031419	2		395	471	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953729	48953729	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0035896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	25	279	0	ENST00000267163.4:c.1333-1G>A		p.X445_splice	ENST00000267163	NM_000321.2	445			0.245050880712434	1	FACETS	0.558	0.44	0.693	0.558	0.44	0.693	SUBCLONAL	1	TRUE	0	0.245050880712434	1		279	321	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-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	123	890	0	ENST00000397752.3:c.3020_3028+17del		p.X1007_splice	ENST00000397752	NM_000245.2	1007		14/21	0.150958080630489	2	FACETS	1	0.968	1	0.581	0.525	0.64	CLONAL	1	TRUE	0	0.245050880712434	2		890	864	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373870	118373870	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	26	350	0	ENST00000534358.1:c.7263G>A	p.Met2421Ile	p.M2421I	ENST00000534358	NM_005933.3	2421	atG/atA	27/36	1	2	FACETS	0.655	0.519	0.81	0.655	0.519	0.81	SUBCLONAL	1	TRUE	1	0.245050880712434	2		350	324	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441370	149441370	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	108	729	0	ENST00000286301.3:c.1669G>T	p.Glu557Ter	p.E557*	ENST00000286301	NM_005211.3	557	Gag/Tag	12/22	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.245050880712434	2		729	793	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017516	112017516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	31	454	0	ENST00000368678.4:c.997G>A	p.Glu333Lys	p.E333K	ENST00000368678		333	Gag/Aag	9/13	1	2	FACETS	0.534	0.431	0.65	0.534	0.431	0.65	SUBCLONAL	1	TRUE	1	0.245050880712434	2		454	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0035898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	457	631	4	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.810750651978337	3	FACETS	1	0.992	1			1	CLONAL	3	TRUE	NA	0.847053447325601	3		635	502	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874011	123874013	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs780061449	NA	P-0035898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	10	19	0	ENST00000330479.4:c.62_64del	p.Ala21del	p.A21del	ENST00000330479	NM_020382.3	14	gaGGCg/gag	2/9	0.728236676135051	4	FACETS	1	0.852	1	0.703	0.501	0.929	CLONAL	1	TRUE	2	0.847053447325601	4		19	31	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419061	419061	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	103	369	0	ENST00000399788.2:c.3286C>G	p.Leu1096Val	p.L1096V	ENST00000399788	NM_001042603.1	1096	Cta/Gta	22/28	0.831963560968392	3	FACETS	0.708	0.636	0.783	0.354	0.318	0.392	SUBCLONAL	1	TRUE	1	0.847053447325601	3		369	489	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89846290	89846290	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778754162	NA	P-0035898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	90	352	0	ENST00000389301.3:c.1702G>A	p.Val568Ile	p.V568I	ENST00000389301	NM_000135.2	568	Gtc/Atc	18/43	0.617422569492635	2	FACETS	0.631	0.565	0.7	0.315	0.282	0.35	SUBCLONAL	1	TRUE	0	0.847053447325601	2		352	337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	61	690	0	ENST00000269305.4:c.383del	p.Pro128LeufsTer42	p.P128Lfs*42	ENST00000269305	NM_001126112.2	128	cCt/ct	5/11	0.0614260303979726	3	FACETS	0.787	0.678	0.906	0.393	0.339	0.453	INDETERMINATE	1	TRUE	1	0.245161484251483	3		690	710	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207468	29207468	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	14	339	0	ENST00000240100.2:c.328G>C	p.Glu110Gln	p.E110Q	ENST00000240100	NM_001394.6	110	Gag/Cag	1/4	1	2	FACETS	0.476	0.344	0.636	0.476	0.344	0.636	SUBCLONAL	1	TRUE	1	0.245161484251483	2		339	240	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107018	11107018	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	55	432	0	ENST00000358026.2:c.1723C>T	p.Gln575Ter	p.Q575*	ENST00000358026	NM_001128849.1	575	Cag/Tag	10/36	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.245161484251483	2		432	315	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600006	10600006	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	51	644	0	ENST00000171111.5:c.1570G>T	p.Gly524Cys	p.G524C	ENST00000171111	NM_203500.1	524	Ggc/Tgc	5/6	1	2	FACETS	0.811	0.69	0.944	0.811	0.69	0.944	CLONAL	1	TRUE	1	0.245161484251483	2		644	513	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221327	1221327	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	46	496	0	ENST00000326873.7:c.850G>C	p.Asp284His	p.D284H	ENST00000326873	NM_000455.4	284	Gac/Cac	6/10	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.245161484251483	2		496	336	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222152	2222152	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	52	792	1	ENST00000398665.3:c.2984G>T	p.Arg995Leu	p.R995L	ENST00000398665	NM_032482.2	995	cGg/cTg	24/28	1	2	FACETS	0.813	0.692	0.945	0.813	0.692	0.945	CLONAL	1	TRUE	1	0.245161484251483	2		793	522	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950291	17950291	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1346219310	NA	P-0036000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	31	516	1	ENST00000458235.1:c.1436C>A	p.Pro479His	p.P479H	ENST00000458235	NM_000215.3	479	cCc/cAc	10/24	1	2	FACETS	0.556	0.449	0.677	0.556	0.449	0.677	SUBCLONAL	1	TRUE	1	0.245161484251483	2		517	455	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952244	17952244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	45	548	1	ENST00000458235.1:c.1096C>T	p.Pro366Ser	p.P366S	ENST00000458235	NM_000215.3	366	Ccg/Tcg	8/24	1	2	FACETS	0.809	0.68	0.95	0.809	0.68	0.95	CLONAL	1	TRUE	1	0.245161484251483	2		549	454	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211130	36211130	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	87	751	0	ENST00000222270.7:c.881G>T	p.Gly294Val	p.G294V	ENST00000222270	NM_014727.1	294	gGc/gTc	3/37	0.0614260303979726	3	FACETS	0.925	0.818	1	0.463	0.409	0.521	INDETERMINATE	1	TRUE	1	0.245161484251483	3		751	861	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795499	42795499	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	49	573	0	ENST00000575354.2:c.2579C>G	p.Thr860Ser	p.T860S	ENST00000575354	NM_015125.3	860	aCc/aGc	10/20	0.0614260303979726	3	FACETS	0.887	0.751	1	0.443	0.375	0.518	INDETERMINATE	1	TRUE	1	0.245161484251483	3		573	506	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81399266	81399266	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	66	560	0	ENST00000222390.5:c.22C>A	p.Pro8Thr	p.P8T	ENST00000222390	NM_000601.4	8	Cca/Aca	1/18	0.0614260303979726	3	FACETS	1	0.939	1	0.571	0.496	0.652	INDETERMINATE	1	TRUE	1	0.245161484251483	3		560	529	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038524	47038524	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	28	531	1	ENST00000377604.3:c.686G>T	p.Arg229Leu	p.R229L	ENST00000377604	NM_001204468.1	229	cGc/cTc	8/24	1	2	FACETS	0.543	0.433	0.667	0.543	0.433	0.667	SUBCLONAL	1	TRUE	1	0.245161484251483	2		532	421	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795784	42795784	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036036-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	134	650	0	ENST00000575354.2:c.2774del	p.Pro925LeufsTer21	p.P925Lfs*21	ENST00000575354	NM_015125.3	925	Cct/ct	11/20	0.373072291708275	1	FACETS	0.6	0.546	0.657	0.6	0.546	0.657	SUBCLONAL	1	TRUE	0	0.491001647582745	1		650	686	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147573	47147573	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1359363019	NA	P-0036036-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	40	422	0	ENST00000409792.3:c.4753G>A	p.Asp1585Asn	p.D1585N	ENST00000409792	NM_014159.6	1585	Gat/Aat	6/21	NA	2	FACETS	0.385	0.32	0.458			1	INDETERMINATE	1	TRUE	NA	0.491001647582745	2		422	423	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440363	52440364	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036036-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	293	519	0	ENST00000460680.1:c.688_689insA	p.Leu230HisfsTer13	p.L230Hfs*13	ENST00000460680	NM_004656.3	230	ctg/cAtg	9/17	0.491001647582745	1	FACETS	0.834	0.794	0.873	1	0.996	1	CLONAL	2	TRUE	0	0.491001647582745	1		519	540	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253859	153253859	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036036-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	54	386	0	ENST00000281708.4:c.874del	p.Val292CysfsTer50	p.V292Cfs*50	ENST00000281708	NM_033632.3	292	Gtg/tg	6/12	0.491001647582745	1	FACETS	0.948	0.825	1	0.948	0.825	1	CLONAL	1	TRUE	0	0.491001647582745	1		386	175	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922704	44922704	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036036-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	95	427	0	ENST00000377967.4:c.1565G>T	p.Gly522Val	p.G522V	ENST00000377967	NM_021140.2	522	gGa/gTa	16/29	0.285013652693205	1	FACETS	0.704	0.63	0.78	0.704	0.63	0.78	INDETERMINATE	1	TRUE	0	0.491001647582745	1		427	415	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0036051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	116	359	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.891	0.807	0.978	0.891	0.807	0.978	CLONAL	1	TRUE	1	0.540435918760504	2		359	482	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743515	46743516	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AT	novel	NA	P-0036051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	72	337	0	ENST00000371975.4:c.1896_1897delinsAT	p.Phe632_Gln633delinsLeuTer	p.F632_Q633delinsL*	ENST00000371975	NM_003579.3	632	ttCCag/ttATag	17/18	0.319516071237641	1	FACETS	0.715	0.632	0.803	0.715	0.632	0.803	INDETERMINATE	1	TRUE	0	0.540435918760504	1		337	272	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041349	47041349	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0036051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	96	227	0	ENST00000377604.3:c.1694-1G>C		p.X565_splice	ENST00000377604	NM_001204468.1	565			0.101740075929492	2	FACETS	0.94	0.86	1			1	INDETERMINATE	2	TRUE	NA	0.540435918760504	2		227	189	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913517	NA	P-0036052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	40	338	0	ENST00000288135.5:c.1676T>C	p.Val559Ala	p.V559A	ENST00000288135	NM_000222.2	559	gTt/gCt	11/21	0.38590451868431	4	FACETS	0.644	0.536	0.764	0.322	0.268	0.382	SUBCLONAL	1	TRUE	2	0.488973613993394	4		338	378	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549752	187549752	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	181	357	0	ENST00000441802.2:c.4489A>G	p.Arg1497Gly	p.R1497G	ENST00000441802	NM_005245.3	1497	Aga/Gga	8/27	0.488973613993394	4	FACETS	1	0.982	1			1	CLONAL	2	TRUE	NA	0.488973613993394	4		357	475	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578206	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs886039484	NA	P-0036052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	257	535	0	ENST00000269305.4:c.643A>G	p.Ser215Gly	p.S215G	ENST00000269305	NM_001126112.2	215	Agt/Ggt	6/11	0.488973613993394	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.488973613993394	2		535	478	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599320	55599320	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913506	NA	P-0036052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	14	463	0	ENST00000288135.5:c.2446G>T	p.Asp816Tyr	p.D816Y	ENST00000288135	NM_000222.2	816	Gac/Tac	17/21	0.38590451868431	4	FACETS	0.156	0.112	0.21	0.078	0.056	0.105	SUBCLONAL	1	TRUE	2	0.488973613993394	4		463	546	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156439	106156439	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1385026818	NA	P-0036052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	107	252	0	ENST00000380013.4:c.1342del	p.Glu448LysfsTer2	p.E448Kfs*2	ENST00000380013	NM_001127208.2	447	aGg/ag	3/11	0.38590451868431	4	FACETS	0.993	0.902	1	0.993	0.902	1	CLONAL	2	TRUE	2	0.488973613993394	4		252	328	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998386	100998386	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	18	91	0	ENST00000325455.5:c.1416G>T	p.Gln472His	p.Q472H	ENST00000325455	NM_001202474.3	472	caG/caT	1/8	0.420967987909065	3	FACETS	1	0.811	1	0.533	0.409	0.672	CLONAL	1	TRUE	1	0.488973613993394	3		91	86	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216782	7216783	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	96	338	0	ENST00000380728.2:c.640dup	p.Ser214PhefsTer47	p.S214Ffs*47	ENST00000380728		214	tcg/tTcg	8/11	0.488973613993394	2	FACETS	0.88	0.801	0.961	0.88	0.801	0.961	CLONAL	2	TRUE	0	0.488973613993394	2		338	223	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39542515	39542515	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	39	286	0	ENST00000262039.4:c.319G>A	p.Ala107Thr	p.A107T	ENST00000262039	NM_002647.2	107	Gcc/Acc	3/25	0.38590451868431	4	FACETS	0.686	0.57	0.815	0.343	0.285	0.408	SUBCLONAL	1	TRUE	2	0.488973613993394	4		286	346	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176666861	176666861	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	39	225	1	ENST00000439151.2:c.4297A>C	p.Lys1433Gln	p.K1433Q	ENST00000439151	NM_022455.4	1433	Aaa/Caa	8/23	0.488973613993394	3	FACETS	0.741	0.617	0.876	0.37	0.308	0.438	SUBCLONAL	1	TRUE	1	0.488973613993394	3		226	268	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399341	139399342	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCA	novel	NA	P-0036052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	78	643	0	ENST00000277541.6:c.4799_4801dup	p.Leu1600dup	p.L1600dup	ENST00000277541	NM_017617.3	1600	cac/cTGCac	26/34	0.488973613993394	4	FACETS	0.489	0.429	0.555	0.245	0.214	0.278	SUBCLONAL	1	TRUE	2	0.488973613993394	4		643	971	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0036053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	482	381	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.695178086190937	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	1	0.695178086190937	3		381	759	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0036053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	330	411	1	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.554578542584955	3	FACETS	0.879	0.846	0.912	0.879	0.846	0.912	CLONAL	3	TRUE	0	0.695178086190937	3		412	485	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423548	88423548	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	92	472	0	ENST00000360948.2:c.2287A>T	p.Ile763Phe	p.I763F	ENST00000360948	NM_001012338.2	763	Atc/Ttc	18/19	0.563080134227413	1	FACETS	0.496	0.445	0.55	0.496	0.445	0.55	SUBCLONAL	1	TRUE	0	0.695178086190937	1		472	348	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591930	48591930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	116	359	0	ENST00000342988.3:c.1093G>A	p.Gly365Ser	p.G365S	ENST00000342988	NM_005359.5	365	Ggt/Agt	9/12	0.669357916514933	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.695178086190937	1		359	210	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374393	31374393	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	48	337	0	ENST00000328111.2:c.392A>G	p.Asn131Ser	p.N131S	ENST00000328111	NM_006892.3	131	aAc/aGc	5/23	0.695178086190937	3	FACETS	0.411	0.347	0.48	0.205	0.173	0.24	SUBCLONAL	1	TRUE	1	0.695178086190937	3		337	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0036054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	130	535	0	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	0.27999110229843	2	FACETS	1	0.984	1	0.682	0.623	0.744	CLONAL	1	FALSE	0	0.395203300474494	2		535	482	SUCCESS
APC	324	MSKCC	GRCh37	5	112175771	112175771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	45	204	0	ENST00000257430.4:c.4480G>A	p.Glu1494Lys	p.E1494K	ENST00000257430	NM_000038.5	1494	Gaa/Aaa	16/16	0.117623127800425	4	FACETS	1	0.924	1	0.58	0.49	0.677	INDETERMINATE	1	FALSE	2	0.395203300474494	4		204	274	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0036054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	113	391	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	NA	2	FACETS	1	0.912	1			1	INDETERMINATE	1	FALSE	NA	0.395203300474494	2		391	566	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089730	27089730	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	146	431	1	ENST00000324856.7:c.2686G>T	p.Glu896Ter	p.E896*	ENST00000324856	NM_006015.4	896	Gaa/Taa	8/20	0.289557047698795	4	FACETS	0.884	0.81	0.961			1	CLONAL	2	FALSE	NA	0.395203300474494	4		432	583	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912173	114912173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	91	379	0	ENST00000543371.1:c.1243C>T	p.Pro415Ser	p.P415S	ENST00000543371	NM_001198531.1	415	Ccc/Tcc	11/14	1	2	FACETS	0.965	0.861	1	0.965	0.861	1	CLONAL	1	FALSE	1	0.395203300474494	2		379	477	SUCCESS
APC	324	MSKCC	GRCh37	5	112175770	112175770	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	42	207	0	ENST00000257430.4:c.4480del	p.Glu1494LysfsTer13	p.E1494Kfs*13	ENST00000257430	NM_000038.5	1493	acG/ac	16/16	0.117623127800425	4	FACETS	1	0.9	1	0.549	0.461	0.645	INDETERMINATE	1	FALSE	2	0.395203300474494	4		207	270	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237635	16237635	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	140	362	0	ENST00000375759.3:c.1082A>T	p.Lys361Ile	p.K361I	ENST00000375759	NM_015001.2	361	aAa/aTa	5/15	0.289557047698795	4	FACETS	0.777	0.71	0.847			1	SUBCLONAL	2	FALSE	NA	0.395203300474494	4		362	636	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144438	58144438	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0036054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	19	210	0	ENST00000257904.6:c.632+1G>A		p.X211_splice	ENST00000257904	NM_000075.3	211			0.395203300474494	3	FACETS	0.507	0.386	0.649	0.254	0.193	0.325	SUBCLONAL	1	FALSE	1	0.395203300474494	3		210	227	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428225	33428225	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs750621215	NA	P-0036054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	64	341	0	ENST00000345365.6:c.898C>T	p.Arg300Ter	p.R300*	ENST00000345365	NM_002878.3	300	Cga/Tga	9/10	NA	2	FACETS	0.976	0.85	1			1	INDETERMINATE	1	FALSE	NA	0.395203300474494	2		341	332	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763503	59763503	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	109	427	0	ENST00000259008.2:c.2599C>T	p.Gln867Ter	p.Q867*	ENST00000259008	NM_032043.2	867	Cag/Tag	19/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.395203300474494	2		427	466	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285123	15285123	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	60	676	1	ENST00000263388.2:c.4492C>A	p.Leu1498Met	p.L1498M	ENST00000263388	NM_000435.2	1498	Ctg/Atg	25/33	NA	2	FACETS	0.466	0.401	0.537			1	INDETERMINATE	1	FALSE	NA	0.395203300474494	2		677	651	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090611	71090611	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	126	409	0	ENST00000318789.4:c.737G>A	p.Gly246Asp	p.G246D	ENST00000318789	NM_032682.5	246	gGc/gAc	11/21	0.395203300474494	6	FACETS	1	0.984	1			1	CLONAL	1	FALSE	NA	0.395203300474494	6		409	795	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916855	178916855	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	117	555	1	ENST00000263967.3:c.242A>T	p.Glu81Val	p.E81V	ENST00000263967	NM_006218.2	81	gAa/gTa	2/21	0.117623127800425	4	FACETS	1	0.957	1	0.554	0.5	0.612	INDETERMINATE	1	FALSE	2	0.395203300474494	4		556	745	SUCCESS
APC	324	MSKCC	GRCh37	5	112151286	112151286	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	52	239	0	ENST00000257430.4:c.930del	p.Lys311ArgfsTer25	p.K311Rfs*25	ENST00000257430	NM_000038.5	310	aCc/ac	9/16	0.117623127800425	4	FACETS	1	0.944	1	0.608	0.521	0.702	INDETERMINATE	1	FALSE	2	0.395203300474494	4		239	302	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039291	47039291	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	151	587	0	ENST00000377604.3:c.914G>C	p.Arg305Pro	p.R305P	ENST00000377604	NM_001204468.1	305	cGc/cCc	10/24	NA	2	FACETS	1	0.974	1			1	INDETERMINATE	1	FALSE	NA	0.395203300474494	2		587	663	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0036055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	95	331	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.87549680097713	2		331	216	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970971	21970971	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	242	472	0	ENST00000304494.5:c.387C>A	p.Tyr129Ter	p.Y129*	ENST00000304494	NM_000077.4	129	taC/taA	2/3	0.829626149721995	1	FACETS	0.904	0.865	0.941	0.904	0.865	0.941	CLONAL	1	TRUE	0	0.87549680097713	1		472	344	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0036056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	72	303	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.623436342639601	3	FACETS	0.857	0.754	0.966	0.428	0.377	0.483	CLONAL	1	TRUE	1	0.634362210693939	3		303	349	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907630	76907630	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	126	529	0	ENST00000373344.5:c.4531G>T	p.Glu1511Ter	p.E1511*	ENST00000373344	NM_000489.3	1511	Gag/Tag	15/35	0.637416612093118	1	FACETS	0.837	0.769	0.907	0.837	0.769	0.907	CLONAL	1	TRUE	0	0.634362210693939	1		529	324	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541630	187541630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371538987	NA	P-0036057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	21	265	0	ENST00000441802.2:c.6110C>T	p.Thr2037Met	p.T2037M	ENST00000441802	NM_005245.3	2037	aCg/aTg	10/27	1	2	FACETS	0.612	0.472	0.773	0.612	0.472	0.773	SUBCLONAL	1	TRUE	1	0.293486900392153	2		265	234	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143272	108143272	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	52	343	0	ENST00000278616.4:c.3091G>T	p.Glu1031Ter	p.E1031*	ENST00000278616	NM_000051.3	1031	Gag/Tag	21/63	0.178825156306346	2	FACETS	1	0.944	1	0.607	0.52	0.7	CLONAL	1	TRUE	0	0.293486900392153	2		343	292	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922211	39922211	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	41	420	0	ENST00000378444.4:c.3961C>A	p.Gln1321Lys	p.Q1321K	ENST00000378444	NM_001123385.1	1321	Cag/Aag	9/15	0.126783895151749	3	FACETS	0.695	0.579	0.824	0.348	0.289	0.412	INDETERMINATE	1	TRUE	1	0.293486900392153	3		420	461	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0036058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	54	239	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.438	0.375	0.506	0.438	0.375	0.506	SUBCLONAL	1	TRUE	1	0.664716571332548	2		239	371	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087558	27087558	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0036058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	99	431	0	ENST00000324856.7:c.2132C>G	p.Ser711Ter	p.S711*	ENST00000324856	NM_006015.4	711	tCa/tGa	5/20	1	2	FACETS	0.477	0.426	0.53	0.477	0.426	0.53	SUBCLONAL	1	TRUE	1	0.664716571332548	2		431	625	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063717	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0036058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	29	156	0	ENST00000412916.2:c.165+1G>T		p.X55_splice	ENST00000412916		55			0.362334447177557	1	FACETS	0.36	0.292	0.435	0.36	0.292	0.435	INDETERMINATE	1	TRUE	0	0.664716571332548	1		156	162	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879590	37879590	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	101	523	0	ENST00000269571.5:c.1965C>G	p.Ile655Met	p.I655M	ENST00000269571		655	atC/atG	17/27	1	2	FACETS	0.536	0.48	0.595	0.536	0.48	0.595	SUBCLONAL	1	TRUE	1	0.664716571332548	2		523	567	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142927	30142927	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs978946990	NA	P-0036058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	126	563	0	ENST00000389048.3:c.599G>A	p.Arg200Lys	p.R200K	ENST00000389048	NM_004304.4	200	aGa/aAa	1/29	1	2	FACETS	0.516	0.468	0.568	0.516	0.468	0.568	SUBCLONAL	1	TRUE	1	0.664716571332548	2		563	734	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056180	26056180	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	74	414	1	ENST00000343677.2:c.477G>T	p.Lys159Asn	p.K159N	ENST00000343677	NM_005319.3	159	aaG/aaT	1/1	1	2	FACETS	0.467	0.41	0.528	0.467	0.41	0.528	SUBCLONAL	1	TRUE	1	0.664716571332548	2		415	477	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750758	128750758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	74	322	0	ENST00000377970.2:c.295G>A	p.Gly99Arg	p.G99R	ENST00000377970	NM_002467.4	99	Gga/Aga	2/3	1	2	FACETS	0.524	0.46	0.592	0.524	0.46	0.592	SUBCLONAL	1	TRUE	1	0.664716571332548	2		322	425	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907066	101907066	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	62	296	0	ENST00000374994.4:c.1026G>C	p.Lys342Asn	p.K342N	ENST00000374994	NM_004612.2	342	aaG/aaC	6/9	1	2	FACETS	0.469	0.406	0.536	0.469	0.406	0.536	SUBCLONAL	1	TRUE	1	0.664716571332548	2		296	398	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0036059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	746	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.635887839225824	7	FACETS	0.956	0.933	0.979			1	CLONAL	6	TRUE	NA	0.635887839225824	7		452	1059	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057730	27057730	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	234	565	0	ENST00000324856.7:c.1438C>T	p.Gln480Ter	p.Q480*	ENST00000324856	NM_006015.4	480	Cag/Tag	3/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.635887839225824	2		565	694	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006363	12006363	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	114	269	0	ENST00000396373.4:c.331G>A	p.Asp111Asn	p.D111N	ENST00000396373	NM_001987.4	111	Gat/Aat	4/8	0.638203908981278	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.635887839225824	1		269	225	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339607	339607	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	53	359	0	ENST00000262320.3:c.2295G>C	p.Glu765Asp	p.E765D	ENST00000262320	NM_003502.3	765	gaG/gaC	10/11	0.200946967925391	3	FACETS	0.563	0.482	0.652	0.188	0.16	0.218	INDETERMINATE	1	TRUE	0	0.635887839225824	3		359	390	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222997	5222997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	155	462	0	ENST00000357368.4:c.2806G>A	p.Glu936Lys	p.E936K	ENST00000357368	NM_002850.3	936	Gag/Aag	18/38	0.200081331722629	1	FACETS	0.809	0.749	0.87	0.809	0.749	0.87	INDETERMINATE	1	TRUE	0	0.635887839225824	1		462	411	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702235	47702235	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs369385048	NA	P-0036059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	202	384	0	ENST00000233146.2:c.1831G>C	p.Val611Leu	p.V611L	ENST00000233146	NM_000251.2	611	Gtg/Ctg	12/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.635887839225824	2		384	590	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31372595	31372595	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	149	333	0	ENST00000328111.2:c.236G>T	p.Gly79Val	p.G79V	ENST00000328111	NM_006892.3	79	gGg/gTg	4/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.635887839225824	2		333	398	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808301	1808301	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs759229319	NA	P-0036059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	208	616	0	ENST00000260795.2:c.2059A>G	p.Ile687Val	p.I687V	ENST00000260795		687	Atc/Gtc	15/17	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.635887839225824	2		616	635	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729711	41729711	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	128	378	1	ENST00000242208.4:c.818G>T	p.Gly273Val	p.G273V	ENST00000242208	NM_002192.2	273	gGc/gTc	3/3	1	2	FACETS	0.934	0.853	1	0.934	0.853	1	CLONAL	1	TRUE	1	0.635887839225824	2		379	431	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742464	145742470	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCTGC	CCGCTGC	-	novel	NA	P-0036059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	240	581	0	ENST00000428558.2:c.318_324del	p.Gln107SerfsTer5	p.Q107Sfs*5	ENST00000428558	NM_004260.3	106	ggGCAGCGG/gg	4/22	0.638203908981278	3	FACETS	1	0.992	1	0.691	0.648	0.735	CLONAL	1	TRUE	1	0.635887839225824	3		581	720	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224470	53224470	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	191	502	0	ENST00000375401.3:c.3243G>C	p.Trp1081Cys	p.W1081C	ENST00000375401	NM_004187.3	1081	tgG/tgC	21/26	0.638203908981278	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.635887839225824	1		502	375	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226316	2226318	+	missense_variant	Missense_Mutation	TNP	GGG	GGG	TGT	novel	NA	P-0036059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	316	586	0	ENST00000326181.6:c.1929_1931delinsTGT	p.Gln643_Gly644delinsHisVal	p.Q643_G644delinsHV	ENST00000326181	NM_032271.2	643	caGGGc/caTGTc	20/21	0.200946967925391	3	FACETS	1	0.988	1	0.738	0.704	0.771	INDETERMINATE	2	TRUE	0	0.635887839225824	3		586	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0036061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	251	453	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.852152936256952	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.852152936256952	1		453	329	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912716	100912716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1450222910	NA	P-0036061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	32	394	0	ENST00000325455.5:c.2606G>A	p.Arg869His	p.R869H	ENST00000325455	NM_001202474.3	869	cGt/cAt	7/8	1	2	FACETS	0.164	0.133	0.199	0.164	0.133	0.199	SUBCLONAL	1	TRUE	1	0.852152936256952	2		394	458	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428604	49428604	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1439251946	NA	P-0036061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	263	585	0	ENST00000301067.7:c.10346G>C	p.Gly3449Ala	p.G3449A	ENST00000301067	NM_003482.3	3449	gGt/gCt	35/54	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.852152936256952	2		585	575	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81528523	81528523	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	120	280	0	ENST00000298171.2:c.202C>G	p.Pro68Ala	p.P68A	ENST00000298171	NM_000369.2	68	Cca/Gca	2/10	0.844669848529377	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.852152936256952	1		280	158	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457267	89457267	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	24	338	0	ENST00000336596.2:c.1748T>G	p.Phe583Cys	p.F583C	ENST00000336596	NM_005233.5	583	tTt/tGt	9/17	1	2	FACETS	0.147	0.115	0.185	0.147	0.115	0.185	SUBCLONAL	1	TRUE	1	0.852152936256952	2		338	382	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31431719	31431719	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	37	310	0	ENST00000344624.3:c.3109C>T	p.Arg1037Ter	p.R1037*	ENST00000344624		1037	Cga/Tga	23/33	0.841328169585861	3	FACETS	0.196	0.161	0.235	0.098	0.08	0.118	SUBCLONAL	1	TRUE	1	0.852152936256952	3		310	633	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589266	67589267	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	76	169	0	ENST00000274335.5:c.1257dup	p.Leu420IlefsTer22	p.L420Ifs*22	ENST00000274335		418	-/A	9/15	0.852152936256952	1	FACETS	0.77	0.701	0.837	0.77	0.701	0.837	SUBCLONAL	1	TRUE	0	0.852152936256952	1		169	133	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968275	2968275	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1308634122	NA	P-0036061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	42	597	1	ENST00000396946.4:c.1711G>A	p.Asp571Asn	p.D571N	ENST00000396946	NM_032415.4	571	Gac/Aac	13/25	0.852152936256952	1	FACETS	0.138	0.115	0.164	0.138	0.115	0.164	SUBCLONAL	1	TRUE	0	0.852152936256952	1		598	409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs878854073	NA	P-0036062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	68	411	0	ENST00000269305.4:c.673-1G>A		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.303716884152086	1	FACETS	0.939	0.821	1	0.939	0.821	1	CLONAL	1	TRUE	0	0.328900003477937	1		411	368	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089730	27089730	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	75	464	0	ENST00000324856.7:c.2686G>A	p.Glu896Lys	p.E896K	ENST00000324856	NM_006015.4	896	Gaa/Aaa	8/20	0.328900003477937	1	FACETS	0.825	0.725	0.931	0.825	0.725	0.931	CLONAL	1	TRUE	0	0.328900003477937	1		464	462	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134988	41134988	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	57	246	0	ENST00000379561.5:c.640C>A	p.Arg214Ser	p.R214S	ENST00000379561	NM_002015.3	214	Cgt/Agt	2/3	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.328900003477937	2		246	305	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0036065-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	91	530	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.148816216503207	3	FACETS	0.796	0.708	0.889	0.796	0.708	0.889	SUBCLONAL	2	TRUE	1	0.22	3		530	577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0036065-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	78	706	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	1	2	FACETS	0.824	0.722	0.933	0.824	0.722	0.933	CLONAL	1	TRUE	1	0.22	2		706	861	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035169	30035169	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036065-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	40	480	0	ENST00000338641.4:c.331C>T	p.Gln111Ter	p.Q111*	ENST00000338641	NM_000268.3	111	Cag/Tag	3/16	0.252636121333952	1	FACETS	0.591	0.49	0.703	0.591	0.49	0.703	SUBCLONAL	1	TRUE	0	0.22	1		480	548	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453149	140453149	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913361	NA	P-0036065-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	68	324	0	ENST00000288602.6:c.1786G>C	p.Gly596Arg	p.G596R	ENST00000288602	NM_004333.4	596	Ggt/Cgt	15/18	0.148816216503207	3	FACETS	0.945	0.827	1	0.945	0.827	1	CLONAL	2	TRUE	1	0.22	3		324	363	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226551719	226551719	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036065-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	51	513	0	ENST00000366794.5:c.2711G>T	p.Ser904Ile	p.S904I	ENST00000366794	NM_001618.3	904	aGt/aTt	20/23	0.148816216503207	3	FACETS	0.781	0.663	0.911	0.39	0.331	0.456	CLONAL	1	TRUE	1	0.22	3		513	659	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811766	102811766	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036065-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	52	583	0	ENST00000307046.8:c.418A>T	p.Thr140Ser	p.T140S	ENST00000307046	NM_001111285.1	140	Acc/Tcc	4/4	1	2	FACETS	0.723	0.614	0.842	0.723	0.614	0.842	SUBCLONAL	1	TRUE	1	0.22	2		583	654	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279438	1279438	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036065-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	48	782	1	ENST00000310581.5:c.2098C>A	p.Gln700Lys	p.Q700K	ENST00000310581	NM_198253.2	700	Cag/Aag	5/16	1	2	FACETS	0.485	0.408	0.57	0.485	0.408	0.57	SUBCLONAL	1	TRUE	1	0.22	2		783	900	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028894	47028894	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036065-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	30	454	0	ENST00000377604.3:c.199del	p.Glu67ArgfsTer67	p.E67Rfs*67	ENST00000377604	NM_001204468.1	66	gcG/gc	3/24	1	2	FACETS	0.588	0.473	0.718	0.588	0.473	0.718	SUBCLONAL	1	TRUE	1	0.22	2		454	464	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0036084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	198	604	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		605	588	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183868	10183868	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs5030810	NA	P-0036100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	24	436	0	ENST00000256474.2:c.337C>T	p.Arg113Ter	p.R113*	ENST00000256474	NM_000551.3	113	Cga/Tga	1/3	0.240996424048687	1	FACETS	0.534	0.419	0.667	0.534	0.419	0.667	SUBCLONAL	1	TRUE	0	0.240996424048687	1		436	328	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129671	47129677	+	frameshift_variant	Frame_Shift_Del	DEL	TGAGCAC	TGAGCAC	GG	novel	NA	P-0036100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	33	491	1	ENST00000409792.3:c.5203_5209delinsCC	p.Val1735ProfsTer8	p.V1735Pfs*8	ENST00000409792	NM_014159.6	1735	GTGCTCAgc/CCgc	10/21	0.240996424048687	1	FACETS	0.713	0.581	0.86	0.713	0.581	0.86	SUBCLONAL	1	TRUE	0	0.240996424048687	1		492	338	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52663053	52663053	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0036100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	21	240	0	ENST00000394830.3:c.1302-2A>T		p.X434_splice	ENST00000394830	NM_018313.4	434			0.240996424048687	1	FACETS	0.976	0.758	1	0.976	0.758	1	CLONAL	1	TRUE	0	0.240996424048687	1		240	157	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286164	66286164	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	19	324	0	ENST00000273854.3:c.1522del	p.Glu508LysfsTer23	p.E508Kfs*23	ENST00000273854	NM_004439.5	508	Gaa/aa	6/18	1	2	FACETS	0.8	0.61	1	0.8	0.61	1	CLONAL	1	TRUE	1	0.240996424048687	2		324	197	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436161	116436161	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	18	310	0	ENST00000397752.3:c.4156T>C	p.Phe1386Leu	p.F1386L	ENST00000397752	NM_000245.2	1386	Ttc/Ctc	21/21	1	2	FACETS	0.447	0.336	0.579	0.447	0.336	0.579	SUBCLONAL	1	TRUE	1	0.240996424048687	2		310	334	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844241	68844241	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	79	476	0	ENST00000261769.5:c.830del	p.Pro277GlnfsTer5	p.P277Qfs*5	ENST00000261769	NM_004360.3	277	Cca/ca	6/16	0.403880860322333	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.403880860322333	1		476	280	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279766	46279766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	81	539	0	ENST00000371998.3:c.3692G>A	p.Arg1231Lys	p.R1231K	ENST00000371998		1231	aGa/aAa	20/23	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.403880860322333	2		539	371	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881027	37881027	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	110	772	0	ENST00000269571.5:c.2356C>G	p.Leu786Val	p.L786V	ENST00000269571		786	Ctg/Gtg	20/27	0.403880860322333	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.403880860322333	1		772	372	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192615	94192615	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	142	777	0	ENST00000323929.3:c.1459G>C	p.Glu487Gln	p.E487Q	ENST00000323929	NM_005591.3	487	Gaa/Caa	13/20	0.403880860322333	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.403880860322333	1		777	527	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578237	7578239	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0036107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	74	748	0	ENST00000269305.4:c.610_612del	p.Glu204del	p.E204del	ENST00000269305	NM_001126112.2	204	GAG/-	6/11	0.403880860322333	1	FACETS	0.914	0.807	1	0.914	0.807	1	CLONAL	1	TRUE	0	0.403880860322333	1		748	320	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298006	15298006	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	80	857	0	ENST00000263388.2:c.1750G>C	p.Asp584His	p.D584H	ENST00000263388	NM_000435.2	584	Gac/Cac	11/33	1	2	FACETS	0.939	0.83	1	0.939	0.83	1	CLONAL	1	TRUE	1	0.403880860322333	2		857	422	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261535	142261535	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	82	448	0	ENST00000350721.4:c.3422C>G	p.Ser1141Cys	p.S1141C	ENST00000350721	NM_001184.3	1141	tCt/tGt	17/47	1	2	FACETS	0.864	0.765	0.97	0.864	0.765	0.97	CLONAL	1	TRUE	1	0.403880860322333	2		448	470	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278106	142278106	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	24	536	0	ENST00000350721.4:c.1719G>C	p.Leu573Phe	p.L573F	ENST00000350721	NM_001184.3	573	ttG/ttC	7/47	1	2	FACETS	0.299	0.234	0.375	0.299	0.234	0.375	SUBCLONAL	1	TRUE	1	0.403880860322333	2		536	397	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0036108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	73	469	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.77	0.674	0.873	0.77	0.674	0.873	SUBCLONAL	1	TRUE	1	0.348494818001906	2		469	544	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643430	38643434	+	frameshift_variant	Frame_Shift_Del	DEL	TAAGT	TAAGT	-	novel	NA	P-0036108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	82	561	0	ENST00000299084.4:c.906_910del	p.Leu302PhefsTer9	p.L302Ffs*9	ENST00000299084	NM_152594.2	300	acTAAGTta/acta	7/7	1	2	FACETS	0.755	0.667	0.851	0.755	0.667	0.851	SUBCLONAL	1	TRUE	1	0.348494818001906	2		561	623	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	66	597	0	ENST00000269305.4:c.580C>G	p.Leu194Val	p.L194V	ENST00000269305	NM_001126112.2	194	Ctt/Gtt	6/11	0.348494818001906	1	FACETS	0.834	0.728	0.948	0.834	0.728	0.948	CLONAL	1	TRUE	0	0.348494818001906	1		597	375	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163791	47163792	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0036108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	64	519	0	ENST00000409792.3:c.2334_2335del	p.Val779Ter	p.V779*	ENST00000409792	NM_014159.6	778	ccAGtt/cctt	3/21	1	2	FACETS	0.883	0.767	1	0.883	0.767	1	CLONAL	1	TRUE	1	0.348494818001906	2		519	416	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575049	48575083	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTCTAGGTGGCTGGTCGGAAAGGATTTCCTCATG	TTTCTAGGTGGCTGGTCGGAAAGGATTTCCTCATG	-	novel	NA	P-0036108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	21	293	0	ENST00000342988.3:c.250-6_278del		p.X84_splice	ENST00000342988	NM_005359.5	84		3/12	0.348494818001906	1	FACETS	0.359	0.277	0.455	0.359	0.277	0.455	SUBCLONAL	1	TRUE	0	0.348494818001906	1		293	277	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829066	128829066	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs41304185	NA	P-0036109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	31	7	0	ENST00000249373.3:c.74A>G	p.Asp25Gly	p.D25G	ENST00000249373	NM_005631.4	25	gAc/gGc	1/12	0.644289269804688	3	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	1	0.644289269804688	3		7	52	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0036109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	336	665	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.644289269804688	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.644289269804688	1		665	676	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256906	41256906	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886037972	NA	P-0036109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	265	617	1	ENST00000357654.3:c.280C>T	p.Gln94Ter	p.Q94*	ENST00000357654	NM_007294.3	94	Cag/Tag	5/23	0.644289269804688	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.644289269804688	1		618	521	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106543508	106543508	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0036109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	136	285	0	ENST00000369096.4:c.310A>T	p.Lys104Ter	p.K104*	ENST00000369096	NM_001198.3	104	Aaa/Taa	3/7	0.466839860450325	1	FACETS	0.786	0.724	0.85	0.786	0.724	0.85	SUBCLONAL	1	TRUE	0	0.644289269804688	1		285	364	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158099	27158099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	183	528	0	ENST00000380036.4:c.323G>A	p.Gly108Glu	p.G108E	ENST00000380036	NM_000459.3	108	gGa/gAa	2/23	0.173133407932541	0	FACETS	0.325	0.301	0.35			1	INDETERMINATE	1	TRUE	0	0.644289269804688	0		528	621	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060573	38060573	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	27	767	0	ENST00000250448.2:c.1416del	p.Ter473SerfsTer11	p.*473Sfs*11	ENST00000250448	NM_004496.3	472	tcC/tc	2/2	0.0910886841780682	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		767	296	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579350	7579350	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587781642	NA	P-0036112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	40	637	0	ENST00000269305.4:c.337T>G	p.Phe113Val	p.F113V	ENST00000269305	NM_001126112.2	113	Ttc/Gtc	4/11	1	2	FACETS	0.549	0.455	0.653	0.549	0.455	0.653	SUBCLONAL	1	TRUE	1	0.253940244862385	2		637	574	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218500	1218500	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1131690951	NA	P-0036112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	32	414	0	ENST00000326873.7:c.374+1A>G		p.X125_splice	ENST00000326873	NM_000455.4	125			0.253940244862385	1	FACETS	0.604	0.491	0.732	0.604	0.491	0.732	SUBCLONAL	1	TRUE	0	0.253940244862385	1		414	364	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602611	10602611	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	50	683	1	ENST00000171111.5:c.967A>G	p.Lys323Glu	p.K323E	ENST00000171111	NM_203500.1	323	Aag/Gag	3/6	0.253940244862385	1	FACETS	0.633	0.537	0.739	0.633	0.537	0.739	SUBCLONAL	1	TRUE	0	0.253940244862385	1		684	543	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946798	71946798	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0036112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	32	684	0	ENST00000298229.2:c.2738+1G>T		p.X913_splice	ENST00000298229	NM_001567.3	913			0.253940244862385	1	FACETS	0.379	0.307	0.462	0.379	0.307	0.462	SUBCLONAL	1	TRUE	0	0.253940244862385	1		684	580	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481850	56481850	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329534370	NA	P-0036112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	32	659	1	ENST00000267101.3:c.778C>T	p.Pro260Ser	p.P260S	ENST00000267101	NM_001982.3	260	Cca/Tca	7/28	1	2	FACETS	0.415	0.335	0.504	0.415	0.335	0.504	SUBCLONAL	1	TRUE	1	0.253940244862385	2		660	608	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923831	72923831	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	39	521	2	ENST00000268489.5:c.3247G>T	p.Gly1083Cys	p.G1083C	ENST00000268489	NM_006885.3	1083	Ggt/Tgt	4/10	0.196238990995542	1	FACETS	0.568	0.471	0.677	0.568	0.471	0.677	SUBCLONAL	1	TRUE	0	0.253940244862385	1		523	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578281	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0036112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	17	642	1	ENST00000269305.4:c.568_569delinsAT	p.Pro190Ile	p.P190I	ENST00000269305	NM_001126112.2	190	CCt/ATt	6/11	1	2	FACETS	0.264	0.196	0.345	0.264	0.196	0.345	SUBCLONAL	1	TRUE	1	0.253940244862385	2		643	508	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973853	131973853	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	24	346	0	ENST00000265335.6:c.3556G>T	p.Val1186Leu	p.V1186L	ENST00000265335		1186	Gtg/Ttg	23/25	1	2	FACETS	0.545	0.427	0.681	0.545	0.427	0.681	SUBCLONAL	1	TRUE	1	0.253940244862385	2		346	347	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381478	81381478	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	21	353	1	ENST00000222390.5:c.583G>T	p.Glu195Ter	p.E195*	ENST00000222390	NM_000601.4	195	Gag/Tag	5/18	0.253940244862385	1	FACETS	0.36	0.277	0.458	0.36	0.277	0.458	SUBCLONAL	1	TRUE	0	0.253940244862385	1		354	401	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0036115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	145	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.357939609453271	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.357939609453271	1		452	632	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604655	48604655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	69	325	0	ENST00000342988.3:c.1477G>A	p.Asp493Asn	p.D493N	ENST00000342988	NM_005359.5	493	Gat/Aat	12/12	0.357939609453271	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.357939609453271	1		325	302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577128	7577128	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	110	610	0	ENST00000269305.4:c.810T>A	p.Phe270Leu	p.F270L	ENST00000269305	NM_001126112.2	270	ttT/ttA	8/11	0.357939609453271	1	FACETS	0.958	0.864	1	0.958	0.864	1	CLONAL	1	TRUE	0	0.357939609453271	1		610	527	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971024	21971024	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	115	533	0	ENST00000304494.5:c.334del	p.Arg112ValfsTer34	p.R112Vfs*34	ENST00000304494	NM_000077.4	112	Cgt/gt	2/3	1	2	FACETS	0.791	0.719	0.867	1	0.986	1	SUBCLONAL	2	TRUE	1	0.357939609453271	2		533	406	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0036116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	101	469	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.846	0.756	0.941	0.846	0.756	0.941	CLONAL	1	TRUE	1	0.325793891496268	2		469	733	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121912580	NA	P-0036116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	82	419	0	ENST00000342988.3:c.1157G>T	p.Gly386Val	p.G386V	ENST00000342988	NM_005359.5	386	gGt/gTt	10/12	1	2	FACETS	0.915	0.809	1	0.915	0.809	1	CLONAL	1	TRUE	1	0.325793891496268	2		419	550	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805698	89805698	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0036116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	60	553	0	ENST00000389301.3:c.4011-1G>C		p.X1337_splice	ENST00000389301	NM_000135.2	1337			1	2	FACETS	0.794	0.685	0.911	0.794	0.685	0.911	CLONAL	1	TRUE	1	0.325793891496268	2		553	464	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858933	89858933	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	74	574	0	ENST00000389301.3:c.1029G>T	p.Gln343His	p.Q343H	ENST00000389301	NM_000135.2	343	caG/caT	12/43	1	2	FACETS	0.931	0.817	1	0.931	0.817	1	CLONAL	1	TRUE	1	0.325793891496268	2		574	488	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591792	48591792	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0036116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	73	511	0	ENST00000342988.3:c.956-1G>T		p.X319_splice	ENST00000342988	NM_005359.5	319			1	2	FACETS	0.936	0.821	1	0.936	0.821	1	CLONAL	1	TRUE	1	0.325793891496268	2		511	479	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209110121	209110121	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	128	643	2	ENST00000345146.2:c.442G>T	p.Gly148Trp	p.G148W	ENST00000345146	NM_005896.2	148	Ggg/Tgg	5/10	0.283836257853425	3	FACETS	0.991	0.897	1	0.496	0.448	0.545	CLONAL	1	TRUE	1	0.325793891496268	3		645	922	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149440515	149440515	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0036116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	40	692	0	ENST00000286301.3:c.1879A>T	p.Lys627Ter	p.K627*	ENST00000286301	NM_005211.3	627	Aag/Tag	14/22	1	2	FACETS	0.466	0.387	0.554	0.466	0.387	0.554	SUBCLONAL	1	TRUE	1	0.325793891496268	2		692	527	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006883	47006883	+	start_lost	Translation_Start_Site	SNP	G	G	C	novel	NA	P-0036116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	82	435	0	ENST00000377604.3:c.3G>C	p.Met1?	p.M1?	ENST00000377604	NM_001204468.1	1	atG/atC	2/24	0.0302902791852624	2	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.325793891496268	2		435	395	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127164	22127164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057519911	NA	P-0036119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	18	570	0	ENST00000215832.6:c.964G>A	p.Glu322Lys	p.E322K	ENST00000215832	NM_002745.4	322	Gag/Aag	7/9	0.60668989005932	3	FACETS	0.297	0.224	0.384	0.149	0.112	0.192	SUBCLONAL	1	TRUE	1	0.60668989005932	3		570	260	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160227	22160227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	15	391	0	ENST00000215832.6:c.404G>A	p.Arg135Lys	p.R135K	ENST00000215832	NM_002745.4	135	aGa/aAa	3/9	0.60668989005932	3	FACETS	0.256	0.187	0.339	0.128	0.093	0.17	SUBCLONAL	1	TRUE	1	0.60668989005932	3		391	252	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573563	48573564	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs786203560	NA	P-0036119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	50	381	0	ENST00000342988.3:c.153dup	p.Asp52ArgfsTer2	p.D52Rfs*2	ENST00000342988	NM_005359.5	49	-/A	2/12	0.353445957751028	2	FACETS	1	0.967	1	0.698	0.611	0.788	INDETERMINATE	1	TRUE	0	0.60668989005932	2		381	118	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589623	67589634	+	inframe_deletion	In_Frame_Del	DEL	ATATGATAGATT	ATATGATAGATT	-	novel	NA	P-0036119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	119	261	0	ENST00000274335.5:c.1392_1403del	p.Asp464_Tyr467del	p.D464_Y467del	ENST00000274335		462	gaATATGATAGATTa/gaa	10/15	0.442743591211495	5	FACETS	1	0.979	1	0.822	0.753	0.892	CLONAL	2	TRUE	2	0.60668989005932	5		261	304	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923738	72923738	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	23	691	2	ENST00000268489.5:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000268489	NM_006885.3	1114	Cga/Tga	4/10	0.421123356484849	2	FACETS	0.412	0.323	0.513	0.206	0.161	0.257	SUBCLONAL	1	TRUE	0	0.60668989005932	2		693	184	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258590	16258590	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	105	470	1	ENST00000375759.3:c.5855G>A	p.Arg1952Lys	p.R1952K	ENST00000375759	NM_015001.2	1952	aGg/aAg	11/15	0.60668989005932	7	FACETS	1	0.913	1	0.506	0.457	0.559	CLONAL	2	TRUE	3	0.60668989005932	7		471	430	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933742	36933742	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	223	944	2	ENST00000361632.4:c.1657G>A	p.Glu553Lys	p.E553K	ENST00000361632		553	Gag/Aag	12/16	0.470558842789594	6	FACETS	0.931	0.879	0.983	0.931	0.879	0.983	CLONAL	4	TRUE	2	0.60668989005932	6		946	437	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129635	11129635	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	160	734	0	ENST00000358026.2:c.2441C>T	p.Thr814Met	p.T814M	ENST00000358026	NM_001128849.1	814	aCg/aTg	17/36	0.323165458460712	3	FACETS	0.755	0.699	0.813	0.755	0.699	0.813	INDETERMINATE	2	TRUE	1	0.60668989005932	3		734	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0036120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	115	741	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.504055443044675	1	FACETS	0.786	0.727	0.846	1	0.989	1	SUBCLONAL	2	TRUE	0	0.504055443044675	1		741	217	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0036121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	173	485	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.235700718347386	3	FACETS	0.888	0.825	0.952	1	0.992	1	CLONAL	4	FALSE	1	0.235700718347386	3		486	462	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0036121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	189	327	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.235700718347386	3	FACETS	1	0.98	1	1	0.993	1	CLONAL	3	FALSE	1	0.235700718347386	3		327	525	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	178	726	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.86	0.793	0.93	1	0.991	1	CLONAL	2	FALSE	1	0.235700718347386	2		726	878	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0036121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	199	496	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.98	1	1	0.994	1	CLONAL	2	FALSE	1	0.235700718347386	2		496	734	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717737	89717739	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0036121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	90	468	1	ENST00000371953.3:c.764_766del	p.Val255del	p.V255del	ENST00000371953	NM_000314.4	254	aaAGTa/aaa	7/9	0.235700718347386	3	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	FALSE	1	0.235700718347386	3		469	408	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561207	9561207	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	128	540	0	ENST00000353224.5:c.575T>C	p.Phe192Ser	p.F192S	ENST00000353224	NM_177990.2	192	tTt/tCt	4/10	1	2	FACETS	0.815	0.74	0.894	1	0.987	1	CLONAL	2	FALSE	1	0.235700718347386	2		540	666	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077585	30077588	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AAAA	AAAA	-	novel	NA	P-0036121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	108	315	0	ENST00000338641.4:c.1733_1736del	p.Lys578SerfsTer20	p.K578Sfs*20	ENST00000338641	NM_000268.3	578	AAAAag/ag	15/16	1	2	FACETS	0.983	0.887	1	1	0.988	1	CLONAL	2	FALSE	1	0.235700718347386	2		315	466	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591136	67591263	+	splice_donor_variant,splice_acceptor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	AGAGACCAATACTTGATGTAAGTATTTGAAATGGAATCCTATACATGAATAATTGGTGATTGCTACAATTCAGGATGAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGGTTGACTCAAAAA	AGAGACCAATACTTGATGTAAGTATTTGAAATGGAATCCTATACATGAATAATTGGTGATTGCTACAATTCAGGATGAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGGTTGACTCAAAAA	-	novel	NA	P-0036121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	46	249	0	ENST00000274335.5:c.1729_1761del		p.X577_splice	ENST00000274335		577	AGAGACCAATACTTGATGTAAGTATTTGAAATGGAATCCTATACATGAATAATTGGTGATTGCTACAATTCAGGATGAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGGTTGACTCAAAAA/-	12-13/15	1	2	FACETS	0.986	0.841	1	1	0.973	1	CLONAL	2	FALSE	1	0.235700718347386	2		249	198	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0036122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	52	381	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.13	2		381	738	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992217	11992217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	65	532	0	ENST00000396373.4:c.307C>T	p.Arg103Cys	p.R103C	ENST00000396373	NM_001987.4	103	Cgc/Tgc	3/8	0.3	2	FACETS	0.922	0.799	1			1	CLONAL	1	TRUE	NA	0.23	2		532	613	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	115	863	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.957	0.86	1	0.957	0.86	1	CLONAL	1	TRUE	1	0.23	2		863	1045	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	69	586	3	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	0.836	0.727	0.953	0.836	0.727	0.953	CLONAL	1	TRUE	1	0.23	2		589	718	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261326	16261326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760319148	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	39	733	0	ENST00000375759.3:c.8591C>T	p.Ser2864Leu	p.S2864L	ENST00000375759	NM_015001.2	2864	tCg/tTg	11/15	1	2	FACETS	0.539	0.446	0.644	0.539	0.446	0.644	SUBCLONAL	1	TRUE	1	0.23	2		733	629	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22412956	22412956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553196096	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	23	204	0	ENST00000344548.3:c.203G>A	p.Arg68Gln	p.R68Q	ENST00000344548	NM_001039802.1	68	cGa/cAa	5/7	1	2	FACETS	0.738	0.576	0.924	0.738	0.576	0.924	CLONAL	1	TRUE	1	0.23	2		204	271	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106281	27106281	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	71	787	0	ENST00000324856.7:c.5892G>T	p.Glu1964Asp	p.E1964D	ENST00000324856	NM_006015.4	1964	gaG/gaT	20/20	1	2	FACETS	0.76	0.662	0.866	0.76	0.662	0.866	SUBCLONAL	1	TRUE	1	0.23	2		787	812	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	48	741	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.576	0.485	0.676	0.576	0.485	0.676	SUBCLONAL	1	TRUE	1	0.23	2		741	725	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28605706	28605706	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143630873	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	61	716	0	ENST00000253063.3:c.1310G>A	p.Arg437Gln	p.R437Q	ENST00000253063	NM_031459.4	437	cGa/cAa	9/10	1	2	FACETS	0.815	0.702	0.937	0.815	0.702	0.937	CLONAL	1	TRUE	1	0.23	2		716	651	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939086	36939086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372288734	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	95	881	2	ENST00000361632.4:c.623C>T	p.Ala208Val	p.A208V	ENST00000361632		208	gCg/gTg	5/16	1	2	FACETS	0.961	0.854	1	0.961	0.854	1	CLONAL	1	TRUE	1	0.23	2		883	860	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805238	43805238	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	77	819	0	ENST00000372470.3:c.688G>T	p.Glu230Ter	p.E230*	ENST00000372470	NM_005373.2	230	Gaa/Taa	4/12	1	2	FACETS	0.863	0.757	0.977	0.863	0.757	0.977	CLONAL	1	TRUE	1	0.23	2		819	776	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521491	46521491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs942307069	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	82	763	0	ENST00000262741.5:c.917G>A	p.Arg306Gln	p.R306Q	ENST00000262741	NM_003629.3	306	cGa/cAa	7/10	1	2	FACETS	0.791	0.696	0.894	0.791	0.696	0.894	SUBCLONAL	1	TRUE	1	0.23	2		763	901	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46714185	46714185	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	43	609	0	ENST00000371975.4:c.5G>T	p.Arg2Met	p.R2M	ENST00000371975	NM_003579.3	2	aGg/aTg	2/18	1	2	FACETS	0.602	0.503	0.713	0.602	0.503	0.713	SUBCLONAL	1	TRUE	1	0.23	2		609	621	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46715736	46715736	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	66	721	0	ENST00000371975.4:c.155G>A	p.Arg52Gln	p.R52Q	ENST00000371975	NM_003579.3	52	cGg/cAg	3/18	1	2	FACETS	0.672	0.582	0.77	0.672	0.582	0.77	SUBCLONAL	1	TRUE	1	0.23	2		721	854	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439730	51439730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs537858214	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	45	450	0	ENST00000262662.1:c.295G>A	p.Glu99Lys	p.E99K	ENST00000262662		99	Gag/Aag	4/4	1	2	FACETS	0.824	0.693	0.969	0.824	0.693	0.969	CLONAL	1	TRUE	1	0.23	2		450	475	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335121	65335121	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	97	692	0	ENST00000342505.4:c.520C>T	p.Arg174Ter	p.R174*	ENST00000342505	NM_002227.2	174	Cga/Tga	6/25	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.23	2		692	747	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428511	78428511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408536007	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	130	914	0	ENST00000370768.2:c.1288C>T	p.Arg430Cys	p.R430C	ENST00000370768	NM_003902.3	430	Cgt/Tgt	14/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.23	2		914	1020	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273209	115273209	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs990081919	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	82	661	2	ENST00000438362.2:c.1249C>T	p.Arg417Cys	p.R417C	ENST00000438362	NM_001242891.1	417	Cgt/Tgt	11/20	1	2	FACETS	0.977	0.861	1	0.977	0.861	1	CLONAL	1	TRUE	1	0.23	2		663	730	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273218	115273218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	73	637	0	ENST00000438362.2:c.1240C>T	p.Arg414Cys	p.R414C	ENST00000438362	NM_001242891.1	414	Cgt/Tgt	11/20	1	2	FACETS	0.887	0.775	1	0.887	0.775	1	CLONAL	1	TRUE	1	0.23	2		637	716	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729724	162729724	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	76	740	2	ENST00000367921.3:c.810G>T	p.Glu270Asp	p.E270D	ENST00000367921	NM_006182.2	270	gaG/gaT	8/18	1	2	FACETS	0.873	0.765	0.99	0.873	0.765	0.99	CLONAL	1	TRUE	1	0.23	2		742	757	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163297332	163297332	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1292835761	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	55	698	0	ENST00000271452.3:c.178C>T	p.Arg60Ter	p.R60*	ENST00000271452	NM_145697.2	60	Cga/Tga	3/14	1	2	FACETS	0.662	0.566	0.769	0.662	0.566	0.769	SUBCLONAL	1	TRUE	1	0.23	2		698	722	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107291	193107291	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	53	333	0	ENST00000367435.3:c.500C>G	p.Thr167Ser	p.T167S	ENST00000367435	NM_024529.4	167	aCt/aGt	6/17	1	2	FACETS	0.964	0.823	1	0.964	0.823	1	CLONAL	1	TRUE	1	0.23	2		333	478	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800977	243800977	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	58	759	6	ENST00000263826.5:c.497G>A	p.Arg166Gln	p.R166Q	ENST00000263826	NM_005465.4	166	cGa/cAa	5/13	1	2	FACETS	0.535	0.458	0.619	0.535	0.458	0.619	SUBCLONAL	1	TRUE	1	0.23	2		765	943	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692940	89692940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746152219	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	160	733	2	ENST00000371953.3:c.424C>T	p.Arg142Trp	p.R142W	ENST00000371953	NM_000314.4	142	Cgg/Tgg	5/9	1	2	FACETS	0.863	0.792	0.937	1	0.99	1	CLONAL	2	TRUE	1	0.23	2		735	806	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	111	762	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.23	2		762	935	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717644	89717644	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	92	631	1	ENST00000371953.3:c.669G>T	p.Lys223Asn	p.K223N	ENST00000371953	NM_000314.4	223	aaG/aaT	7/9	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.23	2		632	700	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466027	69466027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771951669	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	76	783	0	ENST00000227507.2:c.865G>A	p.Asp289Asn	p.D289N	ENST00000227507	NM_053056.2	289	Gac/Aac	5/5	1	2	FACETS	0.965	0.846	1	0.965	0.846	1	CLONAL	1	TRUE	1	0.23	2		783	685	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939259	71939259	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771645618	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	89	985	0	ENST00000298229.2:c.208C>T	p.Arg70Cys	p.R70C	ENST00000298229	NM_001567.3	70	Cgc/Tgc	2/28	1	2	FACETS	0.896	0.793	1	0.896	0.793	1	CLONAL	1	TRUE	1	0.23	2		985	864	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192611	94192611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145377856	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	134	920	1	ENST00000323929.3:c.1463G>A	p.Arg488His	p.R488H	ENST00000323929	NM_005591.3	488	cGt/cAt	13/20	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.23	2		921	1152	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192615	94192615	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	136	932	0	ENST00000323929.3:c.1459G>T	p.Glu487Ter	p.E487*	ENST00000323929	NM_005591.3	487	Gaa/Taa	13/20	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.23	2		932	1161	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912816	100912816	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs776604342	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	56	515	0	ENST00000325455.5:c.2506C>T	p.Arg836Ter	p.R836*	ENST00000325455	NM_001202474.3	836	Cga/Tga	7/8	1	2	FACETS	0.802	0.687	0.928	0.802	0.687	0.928	CLONAL	1	TRUE	1	0.23	2		515	607	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195313	102195313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370738985	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	80	605	0	ENST00000263464.3:c.73G>A	p.Asp25Asn	p.D25N	ENST00000263464	NM_001165.4	25	Gac/Aac	2/9	1	2	FACETS	0.914	0.804	1	0.914	0.804	1	CLONAL	1	TRUE	1	0.23	2		605	761	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195335	102195335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	88	652	1	ENST00000263464.3:c.95G>A	p.Arg32Gln	p.R32Q	ENST00000263464	NM_001165.4	32	cGa/cAa	2/9	1	2	FACETS	0.96	0.85	1	0.96	0.85	1	CLONAL	1	TRUE	1	0.23	2		653	797	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172385	108172385	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764389018	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	87	685	1	ENST00000278616.4:c.5188C>T	p.Arg1730Ter	p.R1730*	ENST00000278616	NM_000051.3	1730	Cga/Tga	35/63	1	2	FACETS	0.99	0.876	1	0.99	0.876	1	CLONAL	1	TRUE	1	0.23	2		686	764	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216486	108216486	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	53	389	0	ENST00000278616.4:c.8435C>A	p.Ser2812Tyr	p.S2812Y	ENST00000278616	NM_000051.3	2812	tCt/tAt	58/63	1	2	FACETS	0.905	0.773	1	0.905	0.773	1	CLONAL	1	TRUE	1	0.23	2		389	509	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118354927	118354927	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	75	639	2	ENST00000534358.1:c.4116G>T	p.Glu1372Asp	p.E1372D	ENST00000534358	NM_005933.3	1372	gaG/gaT	9/36	1	2	FACETS	0.842	0.736	0.955	0.842	0.736	0.955	CLONAL	1	TRUE	1	0.23	2		641	775	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435524	18435524	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1009436030	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	37	335	0	ENST00000266497.5:c.509G>A	p.Gly170Glu	p.G170E	ENST00000266497		170	gGa/gAa	1/31	1	2	FACETS	0.906	0.749	1	0.906	0.749	1	CLONAL	1	TRUE	1	0.23	2		335	355	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658304	18658304	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	107	721	1	ENST00000266497.5:c.3109G>T	p.Asp1037Tyr	p.D1037Y	ENST00000266497		1037	Gat/Tat	22/31	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.23	2		722	857	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21627900	21627900	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	113	776	0	ENST00000421138.2:c.1230G>T	p.Met410Ile	p.M410I	ENST00000421138		410	atG/atT	12/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.23	2		776	887	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944944	31944944	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144139961	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	44	524	1	ENST00000340398.3:c.157C>T	p.Arg53Cys	p.R53C	ENST00000340398	NM_001013699.2	53	Cgt/Tgt	1/1	1	2	FACETS	0.714	0.598	0.842	0.714	0.598	0.842	SUBCLONAL	1	TRUE	1	0.23	2		525	536	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435035	49435035	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765654409	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	32	618	1	ENST00000301067.7:c.6518C>T	p.Ser2173Leu	p.S2173L	ENST00000301067	NM_003482.3	2173	tCg/tTg	31/54	1	2	FACETS	0.606	0.492	0.736	0.606	0.492	0.736	SUBCLONAL	1	TRUE	1	0.23	2		619	459	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536873	120536873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	92	927	0	ENST00000229340.5:c.313G>A	p.Glu105Lys	p.E105K	ENST00000229340	NM_006861.6	105	Gaa/Aaa	4/6	1	2	FACETS	0.834	0.74	0.935	0.834	0.74	0.935	CLONAL	1	TRUE	1	0.23	2		927	959	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784089	120784089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265704785	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	90	1106	0	ENST00000257552.2:c.896C>T	p.Ser299Leu	p.S299L	ENST00000257552	NM_002442.3	299	tCg/tTg	13/15	1	2	FACETS	0.895	0.793	1	0.895	0.793	1	CLONAL	1	TRUE	1	0.23	2		1106	874	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123888141	123888141	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	22	277	0	ENST00000330479.4:c.619G>T	p.Asp207Tyr	p.D207Y	ENST00000330479	NM_020382.3	207	Gat/Tat	6/9	1	2	FACETS	0.664	0.515	0.837	0.664	0.515	0.837	SUBCLONAL	1	TRUE	1	0.23	2		277	288	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	47	648	0	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	1	2	FACETS	0.747	0.63	0.876	0.747	0.63	0.876	SUBCLONAL	1	TRUE	1	0.23	2		648	547	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28599018	28599018	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	85	694	1	ENST00000241453.7:c.2270G>A	p.Gly757Glu	p.G757E	ENST00000241453	NM_004119.2	757	gGg/gAg	18/24	1	2	FACETS	0.842	0.743	0.948	0.842	0.743	0.948	CLONAL	1	TRUE	1	0.23	2		695	878	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911630	32911630	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	55	656	0	ENST00000380152.3:c.3138A>C	p.Glu1046Asp	p.E1046D	ENST00000380152		1046	gaA/gaC	11/27	1	2	FACETS	0.656	0.56	0.761	0.656	0.56	0.761	SUBCLONAL	1	TRUE	1	0.23	2		656	729	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346942	73346942	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	58	392	0	ENST00000377767.4:c.1275G>T	p.Glu425Asp	p.E425D	ENST00000377767	NM_014953.3	425	gaG/gaT	9/21	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.23	2		392	469	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73350116	73350116	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	103	695	0	ENST00000377767.4:c.769A>C	p.Asn257His	p.N257H	ENST00000377767	NM_014953.3	257	Aat/Cat	5/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.23	2		695	827	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73352369	73352369	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	118	784	0	ENST00000377767.4:c.536G>T	p.Arg179Ile	p.R179I	ENST00000377767	NM_014953.3	179	aGa/aTa	3/21	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.23	2		784	956	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514997	103514997	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137877463	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	34	409	0	ENST00000355739.4:c.1498C>T	p.Arg500Trp	p.R500W	ENST00000355739	NM_000123.3	500	Cgg/Tgg	8/15	1	2	FACETS	0.691	0.564	0.833	0.691	0.564	0.833	SUBCLONAL	1	TRUE	1	0.23	2		409	428	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436170	110436170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1427557055	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	97	887	1	ENST00000375856.3:c.2231G>A	p.Arg744His	p.R744H	ENST00000375856	NM_003749.2	744	cGc/cAc	1/2	1	2	FACETS	0.93	0.828	1	0.93	0.828	1	CLONAL	1	TRUE	1	0.23	2		888	907	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436848	110436848	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	84	781	2	ENST00000375856.3:c.1553G>A	p.Ser518Asn	p.S518N	ENST00000375856	NM_003749.2	518	aGc/aAc	1/2	1	2	FACETS	0.891	0.786	1	0.891	0.786	1	CLONAL	1	TRUE	1	0.23	2		783	820	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046638	30046638	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1419328188	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	58	773	2	ENST00000331968.5:c.2545C>T	p.Arg849Ter	p.R849*	ENST00000331968	NM_002742.2	849	Cga/Tga	18/18	1	2	FACETS	0.624	0.535	0.722	0.624	0.535	0.722	SUBCLONAL	1	TRUE	1	0.23	2		775	808	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060728	38060728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	108	1200	1	ENST00000250448.2:c.1261G>A	p.Glu421Lys	p.E421K	ENST00000250448	NM_004496.3	421	Gaa/Aaa	2/2	1	2	FACETS	0.816	0.73	0.907	0.816	0.73	0.907	CLONAL	1	TRUE	1	0.23	2		1201	1151	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061830	38061830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	138	1065	0	ENST00000250448.2:c.159G>A	p.Met53Ile	p.M53I	ENST00000250448	NM_004496.3	53	atG/atA	2/2	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.23	2		1065	1167	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609450	81609450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374530434	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	66	702	0	ENST00000298171.2:c.1048G>A	p.Ala350Thr	p.A350T	ENST00000298171	NM_000369.2	350	Gct/Act	10/10	1	2	FACETS	0.835	0.725	0.956	0.835	0.725	0.956	CLONAL	1	TRUE	1	0.23	2		702	687	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610328	81610328	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	70	586	0	ENST00000298171.2:c.1926C>A	p.Phe642Leu	p.F642L	ENST00000298171	NM_000369.2	642	ttC/ttA	10/10	1	2	FACETS	0.875	0.762	0.996	0.875	0.762	0.996	CLONAL	1	TRUE	1	0.23	2		586	696	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582911	95582911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143533680	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	86	578	1	ENST00000393063.1:c.1631G>A	p.Arg544Gln	p.R544Q	ENST00000393063	NM_030621.3	544	cGa/cAa	11/28	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.23	2		579	632	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239816	105239816	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	49	868	0	ENST00000349310.3:c.804G>T	p.Lys268Asn	p.K268N	ENST00000349310	NM_001014432.1	268	aaG/aaT	10/15	1	2	FACETS	0.555	0.469	0.65	0.555	0.469	0.65	SUBCLONAL	1	TRUE	1	0.23	2		868	768	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41023302	41023302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	94	756	1	ENST00000267868.3:c.946G>A	p.Asp316Asn	p.D316N	ENST00000267868	NM_002875.4	316	Gac/Aac	10/10	1	2	FACETS	0.978	0.869	1	0.978	0.869	1	CLONAL	1	TRUE	1	0.23	2		757	836	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99452084	99452084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	46	436	1	ENST00000268035.6:c.1418G>A	p.Ser473Asn	p.S473N	ENST00000268035	NM_000875.3	473	aGc/aAc	6/21	1	2	FACETS	0.901	0.76	1	0.901	0.76	1	CLONAL	1	TRUE	1	0.23	2		437	444	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456496	99456496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223089854	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	52	403	0	ENST00000268035.6:c.1813C>T	p.Arg605Cys	p.R605C	ENST00000268035	NM_000875.3	605	Cgc/Tgc	8/21	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.23	2		403	423	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642785	3642785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373178144	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	75	893	3	ENST00000294008.3:c.2242G>A	p.Ala748Thr	p.A748T	ENST00000294008	NM_032444.2	748	Gcc/Acc	11/15	1	2	FACETS	0.722	0.631	0.82	0.722	0.631	0.82	SUBCLONAL	1	TRUE	1	0.23	2		896	903	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862845	9862845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764289741	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	69	807	2	ENST00000330684.3:c.2458G>A	p.Val820Ile	p.V820I	ENST00000330684	NM_001134407.1	820	Gta/Ata	12/13	1	2	FACETS	0.814	0.708	0.929	0.814	0.708	0.929	CLONAL	1	TRUE	1	0.23	2		809	737	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14031629	14031629	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	41	586	0	ENST00000311895.7:c.1818C>A	p.Tyr606Ter	p.Y606*	ENST00000311895	NM_005236.2	606	taC/taA	9/11	1	2	FACETS	0.55	0.457	0.654	0.55	0.457	0.654	SUBCLONAL	1	TRUE	1	0.23	2		586	648	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129830	30129830	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	65	653	2	ENST00000263025.4:c.383A>G	p.Asp128Gly	p.D128G	ENST00000263025	NM_002746.2	128	gAc/gGc	3/9	1	2	FACETS	0.846	0.733	0.969	0.846	0.733	0.969	CLONAL	1	TRUE	1	0.23	2		655	668	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853227	68853227	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881667	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	61	684	0	ENST00000261769.5:c.1610C>T	p.Pro537Leu	p.P537L	ENST00000261769	NM_004360.3	537	cCg/cTg	11/16	1	2	FACETS	0.74	0.637	0.852	0.74	0.637	0.852	SUBCLONAL	1	TRUE	1	0.23	2		684	717	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857469	68857469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149127230	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	76	763	0	ENST00000261769.5:c.2104G>A	p.Glu702Lys	p.E702K	ENST00000261769	NM_004360.3	702	Gaa/Aaa	13/16	1	2	FACETS	0.868	0.761	0.984	0.868	0.761	0.984	CLONAL	1	TRUE	1	0.23	2		763	761	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821437	72821437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371324694	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	63	831	0	ENST00000268489.5:c.10738G>A	p.Asp3580Asn	p.D3580N	ENST00000268489	NM_006885.3	3580	Gat/Aat	10/10	1	2	FACETS	0.621	0.536	0.714	0.621	0.536	0.714	SUBCLONAL	1	TRUE	1	0.23	2		831	882	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984508	72984508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567600485	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	108	1002	0	ENST00000268489.5:c.3076G>A	p.Glu1026Lys	p.E1026K	ENST00000268489	NM_006885.3	1026	Gag/Aag	3/10	1	2	FACETS	0.918	0.822	1	0.918	0.822	1	CLONAL	1	TRUE	1	0.23	2		1002	1023	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888060	81888060	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	33	426	0	ENST00000359376.3:c.205G>A	p.Glu69Lys	p.E69K	ENST00000359376	NM_002661.3	69	Gaa/Aaa	3/33	1	2	FACETS	0.672	0.547	0.813	0.672	0.547	0.813	SUBCLONAL	1	TRUE	1	0.23	2		426	427	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89871709	89871709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144560850	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	50	710	0	ENST00000389301.3:c.688G>A	p.Val230Ile	p.V230I	ENST00000389301	NM_000135.2	230	Gtc/Atc	7/43	1	2	FACETS	0.604	0.511	0.706	0.604	0.511	0.706	SUBCLONAL	1	TRUE	1	0.23	2		710	720	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653011	29653011	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	79	653	0	ENST00000356175.3:c.4946C>T	p.Ala1649Val	p.A1649V	ENST00000356175	NM_000267.3	1649	gCt/gTt	36/57	1	2	FACETS	0.9	0.791	1	0.9	0.791	1	CLONAL	1	TRUE	1	0.23	2		653	763	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664505	29664505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	97	732	1	ENST00000356175.3:c.6484C>T	p.Arg2162Trp	p.R2162W	ENST00000356175	NM_000267.3	2162	Cgg/Tgg	42/57	1	2	FACETS	0.851	0.757	0.952	0.851	0.757	0.952	CLONAL	1	TRUE	1	0.23	2		733	991	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	77	530	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.23	2		530	564	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684061	29684061	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	75	812	3	ENST00000356175.3:c.7759G>T	p.Glu2587Ter	p.E2587*	ENST00000356175	NM_000267.3	2587	Gaa/Taa	52/57	1	2	FACETS	0.811	0.71	0.921	0.811	0.71	0.921	CLONAL	1	TRUE	1	0.23	2		815	804	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37680982	37680982	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	67	563	0	ENST00000447079.4:c.3151C>T	p.Arg1051Ter	p.R1051*	ENST00000447079	NM_015083.1	1051	Cga/Tga	12/14	1	2	FACETS	0.847	0.735	0.968	0.847	0.735	0.968	CLONAL	1	TRUE	1	0.23	2		563	688	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873573	37873573	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	64	825	0	ENST00000269571.5:c.1738G>A	p.Glu580Lys	p.E580K	ENST00000269571		580	Gag/Aag	15/27	1	2	FACETS	0.823	0.712	0.944	0.823	0.712	0.944	CLONAL	1	TRUE	1	0.23	2		825	676	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474351	40474351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780466766	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	64	680	0	ENST00000264657.5:c.2050G>A	p.Gly684Arg	p.G684R	ENST00000264657	NM_139276.2	684	Gga/Aga	21/24	1	2	FACETS	0.757	0.655	0.869	0.757	0.655	0.869	SUBCLONAL	1	TRUE	1	0.23	2		680	735	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870631	40870631	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs751414770	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	55	672	0	ENST00000428826.2:c.772C>T	p.Arg258Ter	p.R258*	ENST00000428826		258	Cga/Tga	9/21	1	2	FACETS	0.686	0.586	0.796	0.686	0.586	0.796	SUBCLONAL	1	TRUE	1	0.23	2		672	697	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696719	47696719	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	60	572	0	ENST00000347630.2:c.229G>T	p.Asp77Tyr	p.D77Y	ENST00000347630	NM_001007230.1	77	Gat/Tat	5/11	1	2	FACETS	0.783	0.674	0.902	0.783	0.674	0.902	CLONAL	1	TRUE	1	0.23	2		572	666	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435317	56435317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200066146	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	71	901	0	ENST00000407977.2:c.1820C>T	p.Ser607Leu	p.S607L	ENST00000407977		607	tCg/tTg	9/10	1	2	FACETS	0.885	0.771	1	0.885	0.771	1	CLONAL	1	TRUE	1	0.23	2		901	698	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56811561	56811561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373170458	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	71	497	1	ENST00000337432.4:c.1109G>A	p.Arg370Gln	p.R370Q	ENST00000337432	NM_058216.2	370	cGa/cAa	9/9	1	2	FACETS	0.98	0.855	1	0.98	0.855	1	CLONAL	1	TRUE	1	0.23	2		498	630	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554344	63554344	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	98	994	0	ENST00000307078.5:c.395A>C	p.Lys132Thr	p.K132T	ENST00000307078	NM_004655.3	132	aAa/aCa	2/11	1	2	FACETS	0.8	0.712	0.894	0.8	0.712	0.894	SUBCLONAL	1	TRUE	1	0.23	2		994	1065	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681713	78681713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1299432885	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	49	688	1	ENST00000306801.3:c.421G>A	p.Ala141Thr	p.A141T	ENST00000306801	NM_020761.2	141	Gcc/Acc	4/34	1	2	FACETS	0.67	0.567	0.784	0.67	0.567	0.784	SUBCLONAL	1	TRUE	1	0.23	2		689	636	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119022	3119022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	64	898	1	ENST00000078429.4:c.706G>A	p.Asp236Asn	p.D236N	ENST00000078429	NM_002067.2	236	Gac/Aac	5/7	1	2	FACETS	0.832	0.72	0.954	0.832	0.72	0.954	CLONAL	1	TRUE	1	0.23	2		899	669	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247890	10247890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	72	940	2	ENST00000340748.4:c.4312G>A	p.Asp1438Asn	p.D1438N	ENST00000340748		1438	Gat/Aat	36/40	1	2	FACETS	0.743	0.648	0.846	0.743	0.648	0.846	SUBCLONAL	1	TRUE	1	0.23	2		942	843	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291206	10291206	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	96	849	0	ENST00000340748.4:c.265G>T	p.Asp89Tyr	p.D89Y	ENST00000340748		89	Gat/Tat	4/40	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.23	2		849	821	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113822	11113822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	45	718	2	ENST00000358026.2:c.1930G>A	p.Glu644Lys	p.E644K	ENST00000358026	NM_001128849.1	644	Gag/Aag	12/36	1	2	FACETS	0.585	0.49	0.69	0.585	0.49	0.69	SUBCLONAL	1	TRUE	1	0.23	2		720	669	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276316	15276316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372834264	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	70	861	2	ENST00000263388.2:c.5678G>A	p.Arg1893Gln	p.R1893Q	ENST00000263388	NM_000435.2	1893	cGa/cAa	31/33	1	2	FACETS	0.793	0.69	0.904	0.793	0.69	0.904	CLONAL	1	TRUE	1	0.23	2		863	768	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379868	17379868	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765555081	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	100	1217	3	ENST00000359435.4:c.253C>T	p.Arg85Trp	p.R85W	ENST00000359435	NM_001033549.1	85	Cgg/Tgg	2/9	1	2	FACETS	0.752	0.669	0.84	0.752	0.669	0.84	SUBCLONAL	1	TRUE	1	0.23	2		1220	1157	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220138	36220138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1201006738	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	86	986	3	ENST00000222270.7:c.4858G>A	p.Glu1620Lys	p.E1620K	ENST00000222270	NM_014727.1	1620	Gag/Aag	22/37	1	2	FACETS	0.819	0.723	0.922	0.819	0.723	0.922	CLONAL	1	TRUE	1	0.23	2		989	913	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753053	42753053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs534018115	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	68	793	0	ENST00000222329.4:c.1211G>A	p.Gly404Asp	p.G404D	ENST00000222329	NM_006494.2	404	gGc/gAc	4/4	1	2	FACETS	0.838	0.728	0.956	0.838	0.728	0.956	CLONAL	1	TRUE	1	0.23	2		793	706	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905725	50905725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs76131127	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	54	1000	3	ENST00000440232.2:c.773C>T	p.Thr258Met	p.T258M	ENST00000440232	NM_002691.3	258	aCg/aTg	7/27	1	2	FACETS	0.571	0.487	0.664	0.571	0.487	0.664	SUBCLONAL	1	TRUE	1	0.23	2		1003	822	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919079	50919079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064795958	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	50	678	0	ENST00000440232.2:c.2816C>T	p.Ser939Leu	p.S939L	ENST00000440232	NM_002691.3	939	tCg/tTg	22/27	1	2	FACETS	0.858	0.728	1	0.858	0.728	1	CLONAL	1	TRUE	1	0.23	2		678	507	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972854	25972854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1005506744	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	62	745	0	ENST00000435504.4:c.1571C>T	p.Ser524Leu	p.S524L	ENST00000435504		524	tCg/tTg	12/13	1	2	FACETS	0.646	0.556	0.743	0.646	0.556	0.743	SUBCLONAL	1	TRUE	1	0.23	2		745	835	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39283896	39283896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs952307464	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	101	832	0	ENST00000402219.2:c.457C>T	p.Arg153Trp	p.R153W	ENST00000402219	NM_005633.3	153	Cgg/Tgg	4/23	1	2	FACETS	0.873	0.779	0.974	0.873	0.779	0.974	CLONAL	1	TRUE	1	0.23	2		832	1006	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046951	128046951	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	74	764	2	ENST00000285398.2:c.784G>T	p.Glu262Ter	p.E262*	ENST00000285398	NM_000122.1	262	Gaa/Taa	6/15	1	2	FACETS	0.766	0.669	0.871	0.766	0.669	0.871	SUBCLONAL	1	TRUE	1	0.23	2		766	840	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095836	178095836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1328262363	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	96	783	2	ENST00000397062.3:c.1495C>T	p.Arg499Trp	p.R499W	ENST00000397062	NM_006164.4	499	Cgg/Tgg	5/5	1	2	FACETS	0.882	0.785	0.987	0.882	0.785	0.987	CLONAL	1	TRUE	1	0.23	2		785	946	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136309	202136309	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	70	731	0	ENST00000358485.4:c.553G>T	p.Glu185Ter	p.E185*	ENST00000358485	NM_001080125.1	185	Gag/Tag	3/9	1	2	FACETS	0.71	0.618	0.81	0.71	0.618	0.81	SUBCLONAL	1	TRUE	1	0.23	2		731	857	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137487	202137487	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	41	610	0	ENST00000358485.4:c.715G>T	p.Glu239Ter	p.E239*	ENST00000358485	NM_001080125.1	239	Gaa/Taa	4/9	1	2	FACETS	0.597	0.496	0.709	0.597	0.496	0.709	SUBCLONAL	1	TRUE	1	0.23	2		610	597	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113200	209113200	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	96	662	2	ENST00000345146.2:c.307C>A	p.Leu103Met	p.L103M	ENST00000345146	NM_005896.2	103	Ctg/Atg	4/10	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.23	2		664	731	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426674	212426674	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs112196222	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	101	712	0	ENST00000342788.4:c.2441A>G	p.Asn814Ser	p.N814S	ENST00000342788	NM_005235.2	814	aAc/aGc	20/28	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.23	2		712	813	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225400312	225400312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768929186	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	63	437	1	ENST00000264414.4:c.311C>T	p.Thr104Met	p.T104M	ENST00000264414	NM_003590.4	104	aCg/aTg	3/16	1	2	FACETS	0.975	0.844	1	0.975	0.844	1	CLONAL	1	TRUE	1	0.23	2		438	562	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662971	227662971	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	89	929	0	ENST00000305123.5:c.484G>T	p.Glu162Ter	p.E162*	ENST00000305123	NM_005544.2	162	Gag/Tag	1/2	1	2	FACETS	0.847	0.749	0.951	0.847	0.749	0.951	CLONAL	1	TRUE	1	0.23	2		929	914	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794919	242794919	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	62	1045	0	ENST00000334409.5:c.290T>C	p.Val97Ala	p.V97A	ENST00000334409	NM_005018.2	97	gTc/gCc	2/5	1	2	FACETS	0.569	0.49	0.655	0.569	0.49	0.655	SUBCLONAL	1	TRUE	1	0.23	2		1045	948	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827892	40827892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs573377632	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	71	669	2	ENST00000373198.4:c.2536G>A	p.Val846Ile	p.V846I	ENST00000373198	NM_133170.3	846	Gtc/Atc	17/32	1	2	FACETS	0.9	0.785	1	0.9	0.785	1	CLONAL	1	TRUE	1	0.23	2		671	686	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447549	12447549	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763106561	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	70	719	0	ENST00000287820.6:c.788C>T	p.Ala263Val	p.A263V	ENST00000287820	NM_015869.4	263	gCg/gTg	5/7	1	2	FACETS	0.68	0.591	0.776	0.68	0.591	0.776	SUBCLONAL	1	TRUE	1	0.23	2		719	895	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267236	41267236	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1323014360	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	91	597	0	ENST00000349496.5:c.820C>T	p.Arg274Cys	p.R274C	ENST00000349496	NM_001904.3	274	Cgt/Tgt	6/15	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.23	2		597	784	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643864	52643864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1422119249	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	96	793	4	ENST00000394830.3:c.2032C>T	p.Arg678Cys	p.R678C	ENST00000394830	NM_018313.4	678	Cgc/Tgc	17/30	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.23	2		797	797	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668765	52668765	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	72	609	0	ENST00000394830.3:c.1154C>A	p.Pro385His	p.P385H	ENST00000394830	NM_018313.4	385	cCt/cAt	12/30	1	2	FACETS	0.872	0.761	0.992	0.872	0.761	0.992	CLONAL	1	TRUE	1	0.23	2		609	718	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713694	52713694	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	62	532	0	ENST00000394830.3:c.34T>C	p.Ser12Pro	p.S12P	ENST00000394830	NM_018313.4	12	Tcc/Ccc	2/30	1	2	FACETS	0.829	0.716	0.953	0.829	0.716	0.953	CLONAL	1	TRUE	1	0.23	2		532	650	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448571	89448571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	88	713	0	ENST00000336596.2:c.1535G>A	p.Arg512Gln	p.R512Q	ENST00000336596	NM_005233.5	512	cGa/cAa	7/17	1	2	FACETS	0.889	0.786	0.999	0.889	0.786	0.999	CLONAL	1	TRUE	1	0.23	2		713	861	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468541	89468541	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	39	349	0	ENST00000336596.2:c.2074+1G>T		p.X692_splice	ENST00000336596	NM_005233.5	692			1	2	FACETS	0.98	0.815	1	0.98	0.815	1	CLONAL	1	TRUE	1	0.23	2		349	346	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480411	89480411	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	42	460	0	ENST00000336596.2:c.2248C>T	p.Arg750Trp	p.R750W	ENST00000336596	NM_005233.5	750	Cgg/Tgg	13/17	1	2	FACETS	0.655	0.546	0.775	0.655	0.546	0.775	SUBCLONAL	1	TRUE	1	0.23	2		460	558	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498456	89498456	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	76	527	0	ENST00000336596.2:c.2428T>G	p.Tyr810Asp	p.Y810D	ENST00000336596	NM_005233.5	810	Tat/Gat	14/17	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.23	2		527	636	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720900	119720900	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	49	586	0	ENST00000316626.5:c.275G>T	p.Arg92Ile	p.R92I	ENST00000316626		92	aGa/aTa	2/12	1	2	FACETS	0.575	0.486	0.674	0.575	0.486	0.674	SUBCLONAL	1	TRUE	1	0.23	2		586	741	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967350	134967350	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs61736108	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	42	482	0	ENST00000398015.3:c.2689G>A	p.Val897Met	p.V897M	ENST00000398015	NM_004441.4	897	Gtg/Atg	14/16	1	2	FACETS	0.797	0.666	0.943	0.797	0.666	0.943	CLONAL	1	TRUE	1	0.23	2		482	458	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149290780	149290780	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	70	698	0	ENST00000360632.3:c.439G>T	p.Glu147Ter	p.E147*	ENST00000360632	NM_015472.4	147	Gaa/Taa	3/7	1	2	FACETS	0.788	0.686	0.899	0.788	0.686	0.899	SUBCLONAL	1	TRUE	1	0.23	2		698	772	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013719	170013719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388201066	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	83	723	2	ENST00000295797.4:c.1438C>T	p.Arg480Cys	p.R480C	ENST00000295797	NM_002740.5	480	Cgc/Tgc	15/18	1	2	FACETS	0.793	0.699	0.895	0.793	0.699	0.895	SUBCLONAL	1	TRUE	1	0.23	2		725	910	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	70	599	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.945	0.824	1	0.945	0.824	1	CLONAL	1	TRUE	1	0.23	2		599	644	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665365	182665365	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	48	402	2	ENST00000292782.4:c.576C>A	p.Phe192Leu	p.F192L	ENST00000292782	NM_020640.2	192	ttC/ttA	5/7	1	2	FACETS	0.716	0.605	0.839	0.716	0.605	0.839	SUBCLONAL	1	TRUE	1	0.23	2		404	583	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185195171	185195171	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	30	383	1	ENST00000265026.3:c.2488C>T	p.Pro830Ser	p.P830S	ENST00000265026	NM_004721.4	830	Cca/Tca	12/14	1	2	FACETS	0.664	0.535	0.81	0.664	0.535	0.81	SUBCLONAL	1	TRUE	1	0.23	2		384	393	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587161	189587161	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173679499	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	63	579	0	ENST00000264731.3:c.1178G>A	p.Arg393Gln	p.R393Q	ENST00000264731	NM_003722.4	393	cGa/cAa	9/14	1	2	FACETS	0.933	0.807	1	0.933	0.807	1	CLONAL	1	TRUE	1	0.23	2		579	587	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808406	1808406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	81	1155	1	ENST00000260795.2:c.2164G>A	p.Asp722Asn	p.D722N	ENST00000260795		722	Gac/Aac	15/17	1	2	FACETS	0.783	0.688	0.884	0.783	0.688	0.884	SUBCLONAL	1	TRUE	1	0.23	2		1156	900	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749389	41749389	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	21	437	0	ENST00000226382.2:c.406G>A	p.Asp136Asn	p.D136N	ENST00000226382	NM_003924.3	136	Gac/Aac	2/3	1	2	FACETS	0.46	0.353	0.585	0.46	0.353	0.585	SUBCLONAL	1	TRUE	1	0.23	2		437	397	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561767	55561767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780349712	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	56	507	0	ENST00000288135.5:c.157G>A	p.Glu53Lys	p.E53K	ENST00000288135	NM_000222.2	53	Gag/Aag	2/21	1	2	FACETS	0.825	0.707	0.955	0.825	0.707	0.955	CLONAL	1	TRUE	1	0.23	2		507	590	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598084	55598084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746503007	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	80	592	0	ENST00000288135.5:c.2281G>A	p.Glu761Lys	p.E761K	ENST00000288135	NM_000222.2	761	Gag/Aag	16/21	1	2	FACETS	0.944	0.83	1	0.944	0.83	1	CLONAL	1	TRUE	1	0.23	2		592	737	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55974004	55974004	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	94	625	1	ENST00000263923.4:c.1312G>T	p.Gly438Cys	p.G438C	ENST00000263923	NM_002253.2	438	Ggc/Tgc	10/30	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.23	2		626	766	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155641	106155641	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	54	447	1	ENST00000380013.4:c.542T>A	p.Ile181Asn	p.I181N	ENST00000380013	NM_001127208.2	181	aTt/aAt	3/11	1	2	FACETS	0.964	0.824	1	0.964	0.824	1	CLONAL	1	TRUE	1	0.23	2		448	487	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193748	106193748	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs974106601	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	42	299	0	ENST00000380013.4:c.4210C>T	p.Arg1404Ter	p.R1404*	ENST00000380013	NM_001127208.2	1404	Cga/Tga	10/11	1	2	FACETS	0.959	0.802	1	0.959	0.802	1	CLONAL	1	TRUE	1	0.23	2		299	381	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193932	106193932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	42	342	0	ENST00000380013.4:c.4394G>A	p.Arg1465Gln	p.R1465Q	ENST00000380013	NM_001127208.2	1465	cGa/cAa	10/11	1	2	FACETS	0.911	0.762	1	0.911	0.762	1	CLONAL	1	TRUE	1	0.23	2		342	401	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516857	187516857	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769928509	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	69	546	0	ENST00000441802.2:c.13124C>T	p.Ser4375Leu	p.S4375L	ENST00000441802	NM_005245.3	4375	tCg/tTg	26/27	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.23	2		546	579	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31466354	31466354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376262500	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	91	1043	1	ENST00000344624.3:c.2401C>T	p.Arg801Cys	p.R801C	ENST00000344624		801	Cgc/Tgc	16/33	1	2	FACETS	0.608	0.538	0.683	0.608	0.538	0.683	SUBCLONAL	1	TRUE	1	0.23	2		1044	1302	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953634	38953634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146765449	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	39	360	0	ENST00000357387.3:c.2719C>T	p.Arg907Cys	p.R907C	ENST00000357387	NM_152756.3	907	Cgt/Tgt	28/38	1	2	FACETS	0.752	0.623	0.895	0.752	0.623	0.895	SUBCLONAL	1	TRUE	1	0.23	2		360	451	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627230	86627230	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	63	542	0	ENST00000274376.6:c.605G>A	p.Gly202Asp	p.G202D	ENST00000274376	NM_002890.2	202	gGc/gAc	2/25	1	2	FACETS	0.987	0.854	1	0.987	0.854	1	CLONAL	1	TRUE	1	0.23	2		542	555	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685313	86685313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886060844	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	28	188	0	ENST00000274376.6:c.3029G>A	p.Arg1010Gln	p.R1010Q	ENST00000274376	NM_002890.2	1010	cGa/cAa	24/25	1	2	FACETS	0.796	0.637	0.976	0.796	0.637	0.976	CLONAL	1	TRUE	1	0.23	2		188	306	SUCCESS
APC	324	MSKCC	GRCh37	5	112178889	112178889	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	62	475	0	ENST00000257430.4:c.7598C>A	p.Ser2533Tyr	p.S2533Y	ENST00000257430	NM_000038.5	2533	tCt/tAt	16/16	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.23	2		475	482	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707828	176707828	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	60	324	0	ENST00000439151.2:c.5885T>G	p.Ile1962Ser	p.I1962S	ENST00000439151	NM_022455.4	1962	aTt/aGt	18/23	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.23	2		324	425	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709529	176709529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777258117	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	60	576	0	ENST00000439151.2:c.5956C>T	p.Arg1986Cys	p.R1986C	ENST00000439151	NM_022455.4	1986	Cgc/Tgc	19/23	1	2	FACETS	0.903	0.778	1	0.903	0.778	1	CLONAL	1	TRUE	1	0.23	2		576	578	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722165	176722165	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	47	562	0	ENST00000439151.2:c.7796C>A	p.Ser2599Tyr	p.S2599Y	ENST00000439151	NM_022455.4	2599	tCt/tAt	23/23	1	2	FACETS	0.758	0.639	0.889	0.758	0.639	0.889	SUBCLONAL	1	TRUE	1	0.23	2		562	539	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047230	180047230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	67	923	2	ENST00000261937.6:c.2485G>A	p.Glu829Lys	p.E829K	ENST00000261937	NM_182925.4	829	Gaa/Aaa	17/30	1	2	FACETS	0.672	0.583	0.769	0.672	0.583	0.769	SUBCLONAL	1	TRUE	1	0.23	2		925	867	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839850	27839850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	81	697	1	ENST00000328488.2:c.244G>A	p.Asp82Asn	p.D82N	ENST00000328488	NM_003533.2	82	Gat/Aat	1/1	1	2	FACETS	0.962	0.847	1	0.962	0.847	1	CLONAL	1	TRUE	1	0.23	2		698	732	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32182015	32182015	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	67	846	0	ENST00000375023.3:c.2039A>G	p.Asp680Gly	p.D680G	ENST00000375023	NM_004557.3	680	gAc/gGc	13/30	1	2	FACETS	0.694	0.602	0.795	0.694	0.602	0.795	SUBCLONAL	1	TRUE	1	0.23	2		846	839	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289545	33289545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1436067809	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	154	1022	0	ENST00000374542.5:c.158C>T	p.Ser53Leu	p.S53L	ENST00000374542	NM_001141970.1	53	tCg/tTg	2/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.23	2		1022	1021	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956553	93956553	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1035177735	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	48	578	1	ENST00000369303.4:c.2683C>T	p.Arg895Ter	p.R895*	ENST00000369303	NM_004440.3	895	Cga/Tga	15/17	1	2	FACETS	0.57	0.481	0.669	0.57	0.481	0.669	SUBCLONAL	1	TRUE	1	0.23	2		579	732	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120701	94120701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	108	664	0	ENST00000369303.4:c.350G>A	p.Gly117Glu	p.G117E	ENST00000369303	NM_004440.3	117	gGa/gAa	3/17	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.23	2		664	787	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552921	106552921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	116	966	0	ENST00000369096.4:c.886C>T	p.Arg296Trp	p.R296W	ENST00000369096	NM_001198.3	296	Cgg/Tgg	5/7	1	2	FACETS	0.963	0.867	1	0.963	0.867	1	CLONAL	1	TRUE	1	0.23	2		966	1047	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683892	117683892	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	107	849	0	ENST00000368508.3:c.3255C>A	p.Phe1085Leu	p.F1085L	ENST00000368508	NM_002944.2	1085	ttC/ttA	21/43	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.23	2		849	897	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683906	117683906	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	120	849	0	ENST00000368508.3:c.3241A>C	p.Lys1081Gln	p.K1081Q	ENST00000368508	NM_002944.2	1081	Aaa/Caa	21/43	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.23	2		849	925	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525060	157525060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1215965074	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	62	525	0	ENST00000346085.5:c.4955C>T	p.Thr1652Met	p.T1652M	ENST00000346085	NM_020732.3	1652	aCg/aTg	19/20	1	2	FACETS	0.8	0.69	0.919	0.8	0.69	0.919	CLONAL	1	TRUE	1	0.23	2		525	674	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14028670	14028670	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	64	494	0	ENST00000405192.2:c.8G>A	p.Gly3Glu	p.G3E	ENST00000405192	NM_001163147.1	3	gGa/gAa	2/12	1	2	FACETS	0.929	0.805	1	0.929	0.805	1	CLONAL	1	TRUE	1	0.23	2		494	599	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259439	55259439	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs397517126	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	52	522	0	ENST00000275493.2:c.2497T>G	p.Leu833Val	p.L833V	ENST00000275493	NM_005228.3	833	Ttg/Gtg	21/28	1	2	FACETS	0.845	0.72	0.983	0.845	0.72	0.983	CLONAL	1	TRUE	1	0.23	2		522	535	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539044	23539044	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754870999	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	66	699	0	ENST00000380871.4:c.395C>T	p.Ser132Phe	p.S132F	ENST00000380871	NM_006167.3	132	tCc/tTc	2/2	1	2	FACETS	0.839	0.728	0.96	0.839	0.728	0.96	CLONAL	1	TRUE	1	0.23	2		699	684	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141570572	141570572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764154303	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	72	640	1	ENST00000220592.5:c.556G>A	p.Glu186Lys	p.E186K	ENST00000220592	NM_012154.3	186	Gaa/Aaa	5/19	1	2	FACETS	0.96	0.839	1	0.96	0.839	1	CLONAL	1	TRUE	1	0.23	2		641	652	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5055672	5055672	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	48	335	0	ENST00000381652.3:c.940T>G	p.Leu314Val	p.L314V	ENST00000381652	NM_004972.3	314	Tta/Gta	8/25	1	2	FACETS	0.96	0.812	1	0.96	0.812	1	CLONAL	1	TRUE	1	0.23	2		335	435	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5066705	5066705	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	67	624	0	ENST00000381652.3:c.1242G>T	p.Lys414Asn	p.K414N	ENST00000381652	NM_004972.3	414	aaG/aaT	10/25	1	2	FACETS	0.777	0.674	0.888	0.777	0.674	0.888	SUBCLONAL	1	TRUE	1	0.23	2		624	750	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341701	8341701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766088715	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	68	782	1	ENST00000356435.5:c.4939G>A	p.Glu1647Lys	p.E1647K	ENST00000356435		1647	Gaa/Aaa	29/35	1	2	FACETS	0.678	0.589	0.775	0.678	0.589	0.775	SUBCLONAL	1	TRUE	1	0.23	2		783	872	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250271	110250271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1406633245	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	51	795	0	ENST00000374672.4:c.404C>T	p.Ser135Leu	p.S135L	ENST00000374672	NM_004235.4	135	tCg/tTg	3/5	1	2	FACETS	0.673	0.571	0.785	0.673	0.571	0.785	SUBCLONAL	1	TRUE	1	0.23	2		795	659	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760592	133760592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2229067	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	88	1094	1	ENST00000318560.5:c.2915C>T	p.Ser972Leu	p.S972L	ENST00000318560	NM_005157.4	972	tCg/tTg	11/11	1	2	FACETS	0.834	0.738	0.938	0.834	0.738	0.938	CLONAL	1	TRUE	1	0.23	2		1095	917	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923083	39923083	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	115	970	1	ENST00000378444.4:c.3625C>T	p.Arg1209Cys	p.R1209C	ENST00000378444	NM_001123385.1	1209	Cgc/Tgc	8/15	1	2	FACETS	0.9	0.809	0.997	0.9	0.809	0.997	CLONAL	1	TRUE	1	0.23	2		971	1111	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932050	39932050	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs923387791	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	55	993	0	ENST00000378444.4:c.2549G>A	p.Arg850His	p.R850H	ENST00000378444	NM_001123385.1	850	cGt/cAt	4/15	1	2	FACETS	0.515	0.439	0.598	0.515	0.439	0.598	SUBCLONAL	1	TRUE	1	0.23	2		993	929	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937723	44937723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	101	725	0	ENST00000377967.4:c.2911C>T	p.Arg971Cys	p.R971C	ENST00000377967	NM_021140.2	971	Cgt/Tgt	19/29	1	2	FACETS	0.859	0.766	0.959	0.859	0.766	0.959	CLONAL	1	TRUE	1	0.23	2		725	1022	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424451	47424451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	70	945	3	ENST00000377045.4:c.371G>A	p.Arg124His	p.R124H	ENST00000377045	NM_001654.4	124	cGt/cAt	5/16	1	2	FACETS	0.659	0.573	0.753	0.659	0.573	0.753	SUBCLONAL	1	TRUE	1	0.23	2		948	923	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225199	53225199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781854324	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	74	841	0	ENST00000375401.3:c.3019C>T	p.Arg1007Cys	p.R1007C	ENST00000375401	NM_004187.3	1007	Cgt/Tgt	20/26	1	2	FACETS	0.803	0.702	0.913	0.803	0.702	0.913	CLONAL	1	TRUE	1	0.23	2		841	801	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53241079	53241079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782110533	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	51	592	2	ENST00000375401.3:c.1132C>T	p.Arg378Trp	p.R378W	ENST00000375401	NM_004187.3	378	Cgg/Tgg	9/26	1	2	FACETS	0.742	0.63	0.865	0.742	0.63	0.865	SUBCLONAL	1	TRUE	1	0.23	2		594	598	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247028	53247028	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	93	828	0	ENST00000375401.3:c.472G>A	p.Glu158Lys	p.E158K	ENST00000375401	NM_004187.3	158	Gaa/Aaa	4/26	1	2	FACETS	0.837	0.743	0.938	0.837	0.743	0.938	CLONAL	1	TRUE	1	0.23	2		828	966	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410597	63410597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758807218	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	91	1004	0	ENST00000330258.3:c.2570G>A	p.Arg857Gln	p.R857Q	ENST00000330258	NM_152424.3	857	cGa/cAa	2/2	1	2	FACETS	0.904	0.802	1	0.904	0.802	1	CLONAL	1	TRUE	1	0.23	2		1004	875	SUCCESS
AR	367	MSKCC	GRCh37	X	66765064	66765064	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	92	825	1	ENST00000374690.3:c.76C>A	p.Leu26Met	p.L26M	ENST00000374690	NM_000044.3	26	Ctg/Atg	1/8	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.23	2		826	796	SUCCESS
AR	367	MSKCC	GRCh37	X	66766474	66766474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	54	652	0	ENST00000374690.3:c.1486G>A	p.Asp496Asn	p.D496N	ENST00000374690	NM_000044.3	496	Gac/Aac	1/8	1	2	FACETS	0.797	0.681	0.925	0.797	0.681	0.925	CLONAL	1	TRUE	1	0.23	2		652	589	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347966	70347966	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770988288	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	61	751	0	ENST00000374080.3:c.3205G>A	p.Asp1069Asn	p.D1069N	ENST00000374080		1069	Gat/Aat	22/45	1	2	FACETS	0.662	0.57	0.763	0.662	0.57	0.763	SUBCLONAL	1	TRUE	1	0.23	2		751	801	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763935	76763935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	85	859	0	ENST00000373344.5:c.7373G>A	p.Gly2458Glu	p.G2458E	ENST00000373344	NM_000489.3	2458	gGa/gAa	35/35	1	2	FACETS	0.861	0.76	0.97	0.861	0.76	0.97	CLONAL	1	TRUE	1	0.23	2		859	858	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874431	76874431	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	88	492	1	ENST00000373344.5:c.5291T>G	p.Phe1764Cys	p.F1764C	ENST00000373344	NM_000489.3	1764	tTt/tGt	21/35	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.23	2		493	681	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939448	76939448	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	140	1021	0	ENST00000373344.5:c.1300G>T	p.Val434Phe	p.V434F	ENST00000373344	NM_000489.3	434	Gtc/Ttc	9/35	1	2	FACETS	0.972	0.883	1	0.972	0.883	1	CLONAL	1	TRUE	1	0.23	2		1021	1252	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176490	123176490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	47	409	0	ENST00000218089.9:c.457G>A	p.Asp153Asn	p.D153N	ENST00000218089	NM_001042749.1	153	Gat/Aat	7/35	1	2	FACETS	0.817	0.69	0.958	0.817	0.69	0.958	CLONAL	1	TRUE	1	0.23	2		409	500	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217381	123217381	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	95	664	0	ENST00000218089.9:c.3035G>A	p.Arg1012Gln	p.R1012Q	ENST00000218089	NM_001042749.1	1012	cGa/cAa	29/35	1	2	FACETS	0.941	0.837	1	0.941	0.837	1	CLONAL	1	TRUE	1	0.23	2		664	878	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913517	NA	P-0036124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	687	441	0	ENST00000288135.5:c.1676T>A	p.Val559Asp	p.V559D	ENST00000288135	NM_000222.2	559	gTt/gAt	11/21	0.883639816139184	4	FACETS	0.989	0.964	1	0.989	0.964	1	CLONAL	3	TRUE	1	0.891866637322257	4		441	982	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162444	47162444	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	338	577	0	ENST00000409792.3:c.3682del	p.Ser1228ValfsTer8	p.S1228Vfs*8	ENST00000409792	NM_014159.6	1228	Agt/gt	3/21	0.866163619656985	2	FACETS	0.952	0.927	0.975	0.952	0.927	0.975	CLONAL	2	TRUE	0	0.891866637322257	2		577	398	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747828	41747828	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	189	411	0	ENST00000226382.2:c.941T>C	p.Phe314Ser	p.F314S	ENST00000226382	NM_003924.3	314	tTc/tCc	3/3	0.276210327904422	1	FACETS	0.475	0.443	0.508	0.475	0.443	0.508	INDETERMINATE	1	TRUE	0	0.891866637322257	1		411	494	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	194	726	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.187271858413363	2	FACETS	0.872	0.814	0.932	0.872	0.814	0.932	INDETERMINATE	2	TRUE	0	0.433472050480975	2		726	513	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115873	8115874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0036125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	332	597	3	ENST00000346208.3:c.1220dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tCcg	6/6	0.42391895527844	4	FACETS	0.977	0.93	1			1	CLONAL	3	TRUE	NA	0.433472050480975	4		600	749	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259348	11259348	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	88	825	0	ENST00000361445.4:c.4220G>A	p.Gly1407Asp	p.G1407D	ENST00000361445	NM_004958.3	1407	gGc/gAc	28/58	0.352231127167123	1	FACETS	0.754	0.671	0.841	0.754	0.671	0.841	SUBCLONAL	1	TRUE	0	0.433472050480975	1		825	422	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115748	8115748	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	98	491	0	ENST00000346208.3:c.1094A>G	p.Asn365Ser	p.N365S	ENST00000346208		365	aAc/aGc	6/6	0.42391895527844	4	FACETS	1	0.944	1			1	CLONAL	1	TRUE	NA	0.433472050480975	4		491	597	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245109	46245109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754489425	NA	P-0036125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	161	617	3	ENST00000334344.6:c.3203G>A	p.Arg1068His	p.R1068H	ENST00000334344	NM_152641.2	1068	cGt/cAt	15/21	0.323293691590107	4	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	2	0.433472050480975	4		620	505	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589223	67589223	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0036125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	100	366	1	ENST00000274335.5:c.1211T>G	p.Leu404Ter	p.L404*	ENST00000274335		404	tTa/tGa	9/15	0.134354969572319	4	FACETS	0.87	0.784	0.961	0.87	0.784	0.961	INDETERMINATE	2	TRUE	2	0.433472050480975	4		367	380	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	159	530	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.319429381316153	2		530	762	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16001793	16001793	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	112	498	0	ENST00000268712.3:c.2708C>G	p.Ser903Ter	p.S903*	ENST00000268712	NM_006311.3	903	tCa/tGa	21/46	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.319429381316153	2		498	688	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	76	310	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.319429381316153	2		310	406	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106058	8106058	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	126	466	0	ENST00000346208.3:c.878T>A	p.Met293Lys	p.M293K	ENST00000346208		293	aTg/aAg	4/6	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.319429381316153	2		466	619	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575671	48575671	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	40	610	0	ENST00000342988.3:c.431C>G	p.Ser144Ter	p.S144*	ENST00000342988	NM_005359.5	144	tCa/tGa	4/12	0.319429381316153	1	FACETS	0.309	0.256	0.369	0.309	0.256	0.369	SUBCLONAL	1	TRUE	0	0.319429381316153	1		610	681	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604787	48604787	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	12	386	0	ENST00000342988.3:c.1609G>C	p.Asp537His	p.D537H	ENST00000342988	NM_005359.5	537	Gac/Cac	12/12	0.319429381316153	1	FACETS	0.134	0.094	0.185	0.134	0.094	0.185	SUBCLONAL	1	TRUE	0	0.319429381316153	1		386	470	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673595	30673595	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	108	772	0	ENST00000376406.3:c.3365C>G	p.Ser1122Cys	p.S1122C	ENST00000376406	NM_014641.2	1122	tCt/tGt	10/15	1	2	FACETS	0.716	0.642	0.796	0.716	0.642	0.796	SUBCLONAL	1	TRUE	1	0.319429381316153	2		772	944	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061264	38061264	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	37	590	1	ENST00000250448.2:c.725C>T	p.Ser242Phe	p.S242F	ENST00000250448	NM_004496.3	242	tCc/tTc	2/2	1	2	FACETS	0.337	0.277	0.404	0.337	0.277	0.404	SUBCLONAL	1	TRUE	1	0.319429381316153	2		591	688	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528086	29528086	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs864622107	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	61	344	0	ENST00000356175.3:c.1094C>G	p.Ser365Ter	p.S365*	ENST00000356175	NM_000267.3	365	tCa/tGa	10/57	1	2	FACETS	0.923	0.799	1	0.923	0.799	1	CLONAL	1	TRUE	1	0.319429381316153	2		344	414	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061226	38061226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	127	505	0	ENST00000250448.2:c.763G>A	p.Glu255Lys	p.E255K	ENST00000250448	NM_004496.3	255	Gag/Aag	2/2	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.319429381316153	2		505	541	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498304	29498304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	103	569	0	ENST00000389048.3:c.1876G>A	p.Asp626Asn	p.D626N	ENST00000389048	NM_004304.4	626	Gac/Aac	10/29	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.319429381316153	2		569	614	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250440	26250440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	95	481	0	ENST00000446824.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000446824	NM_021018.2	132	Cgc/Tgc	1/1	0.319429381316153	5	FACETS	1	0.946	1	0.552	0.491	0.617	CLONAL	1	TRUE	3	0.319429381316153	5		481	797	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180943	32180943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	82	578	0	ENST00000375023.3:c.2407G>A	p.Glu803Lys	p.E803K	ENST00000375023	NM_004557.3	803	Gag/Aag	15/30	1	2	FACETS	0.846	0.747	0.952	0.846	0.747	0.952	CLONAL	1	TRUE	1	0.319429381316153	2		578	607	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342971	118342971	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	51	257	0	ENST00000534358.1:c.1097G>C	p.Arg366Thr	p.R366T	ENST00000534358	NM_005933.3	366	aGg/aCg	3/36	1	2	FACETS	0.847	0.722	0.983	0.847	0.722	0.983	CLONAL	1	TRUE	1	0.319429381316153	2		257	377	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445077	49445077	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057518680	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	132	599	0	ENST00000301067.7:c.2389C>G	p.Leu797Val	p.L797V	ENST00000301067	NM_003482.3	797	Ctg/Gtg	10/54	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.319429381316153	2		599	681	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445343	49445343	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	191	913	0	ENST00000301067.7:c.2123C>T	p.Ser708Phe	p.S708F	ENST00000301067	NM_003482.3	708	tCc/tTc	10/54	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.319429381316153	2		913	1125	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437376	110437376	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776945626	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	26	52	0	ENST00000375856.3:c.1025C>T	p.Ser342Leu	p.S342L	ENST00000375856	NM_003749.2	342	tCg/tTg	1/2	1	2	FACETS	0.875	0.711	1	1	0.95	1	CLONAL	2	TRUE	1	0.319429381316153	2		52	93	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713377	40713377	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1417250081	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	111	662	0	ENST00000373198.4:c.4138G>A	p.Glu1380Lys	p.E1380K	ENST00000373198	NM_133170.3	1380	Gag/Aag	30/32	0.319429381316153	1	FACETS	0.923	0.831	1	0.923	0.831	1	CLONAL	1	TRUE	0	0.319429381316153	1		662	633	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161293444	161293444	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	110	525	0	ENST00000367975.2:c.61C>A	p.Gln21Lys	p.Q21K	ENST00000367975	NM_003001.3	21	Cag/Aag	2/6	0.304942830229275	4	FACETS	0.815	0.73	0.905	0.408	0.365	0.453	CLONAL	1	TRUE	2	0.319429381316153	4		525	1115	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201970	102201970	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	33	197	0	ENST00000263464.3:c.1322C>T	p.Ser441Leu	p.S441L	ENST00000263464	NM_001165.4	441	tCa/tTa	6/9	1	2	FACETS	0.738	0.603	0.888	0.738	0.603	0.888	SUBCLONAL	1	TRUE	1	0.319429381316153	2		197	280	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343074	118343074	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	63	352	0	ENST00000534358.1:c.1200G>C	p.Lys400Asn	p.K400N	ENST00000534358	NM_005933.3	400	aaG/aaC	3/36	1	2	FACETS	0.871	0.755	0.996	0.871	0.755	0.996	CLONAL	1	TRUE	1	0.319429381316153	2		352	453	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443919	49443919	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	165	702	0	ENST00000301067.7:c.3452C>G	p.Ser1151Cys	p.S1151C	ENST00000301067	NM_003482.3	1151	tCc/tGc	11/54	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.319429381316153	2		702	793	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445068	49445068	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	132	597	0	ENST00000301067.7:c.2398C>T	p.Gln800Ter	p.Q800*	ENST00000301067	NM_003482.3	800	Cag/Tag	10/54	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.319429381316153	2		597	683	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061723	38061723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1231025559	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	21	296	0	ENST00000250448.2:c.266C>T	p.Ser89Leu	p.S89L	ENST00000250448	NM_004496.3	89	tCg/tTg	2/2	1	2	FACETS	0.411	0.316	0.521	0.411	0.316	0.521	SUBCLONAL	1	TRUE	1	0.319429381316153	2		296	320	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983772	15983772	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	126	521	0	ENST00000268712.3:c.3350C>G	p.Ser1117Ter	p.S1117*	ENST00000268712	NM_006311.3	1117	tCa/tGa	25/46	1	2	FACETS	0.946	0.856	1	0.946	0.856	1	CLONAL	1	TRUE	1	0.319429381316153	2		521	834	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143004	30143004	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	132	761	0	ENST00000389048.3:c.522C>G	p.Phe174Leu	p.F174L	ENST00000389048	NM_004304.4	174	ttC/ttG	1/29	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.319429381316153	2		761	805	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663163	227663163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	125	723	0	ENST00000305123.5:c.292G>A	p.Asp98Asn	p.D98N	ENST00000305123	NM_005544.2	98	Gac/Aac	1/2	1	2	FACETS	0.984	0.891	1	0.984	0.891	1	CLONAL	1	TRUE	1	0.319429381316153	2		723	795	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794369	242794369	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	115	705	0	ENST00000334409.5:c.573C>G	p.Ile191Met	p.I191M	ENST00000334409	NM_005018.2	191	atC/atG	3/5	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.319429381316153	2		705	675	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24158956	24158956	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	96	609	0	ENST00000263121.7:c.629-1G>C		p.X210_splice	ENST00000263121	NM_003073.3	210			1	2	FACETS	0.926	0.826	1	0.926	0.826	1	CLONAL	1	TRUE	1	0.319429381316153	2		609	649	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427764	72427764	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	72	338	0	ENST00000477973.2:c.726G>C	p.Arg242Ser	p.R242S	ENST00000477973	NM_012234.5	242	agG/agC	4/4	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.319429381316153	2		338	439	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31421411	31421411	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	99	494	0	ENST00000344624.3:c.3493C>T	p.His1165Tyr	p.H1165Y	ENST00000344624		1165	Cat/Tat	27/33	1	2	FACETS	0.831	0.742	0.926	0.831	0.742	0.926	CLONAL	1	TRUE	1	0.319429381316153	2		494	746	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592087	67592087	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	114	258	0	ENST00000274335.5:c.1903G>A	p.Glu635Lys	p.E635K	ENST00000274335		635	Gaa/Aaa	14/15	0.117176648993531	4	FACETS	1	0.95	1	1	0.95	1	INDETERMINATE	2	TRUE	2	0.319429381316153	4		258	439	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908182	41908182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	138	812	1	ENST00000372991.4:c.340C>T	p.Arg114Cys	p.R114C	ENST00000372991	NM_001760.3	114	Cgc/Tgc	2/5	1	2	FACETS	0.923	0.839	1	0.923	0.839	1	CLONAL	1	TRUE	1	0.319429381316153	2		813	936	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877129	151877129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs971788497	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	109	479	0	ENST00000262189.6:c.7232C>T	p.Ser2411Leu	p.S2411L	ENST00000262189	NM_170606.2	2411	tCa/tTa	37/59	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.319429381316153	2		479	615	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15838400	15838400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	113	455	0	ENST00000307771.7:c.898G>A	p.Glu300Lys	p.E300K	ENST00000307771	NM_005089.3	300	Gaa/Aaa	10/11	0.236616601148943	1	FACETS	0.891	0.803	0.984	0.891	0.803	0.984	CLONAL	1	TRUE	0	0.319429381316153	1		455	667	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352707	70352707	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	83	492	0	ENST00000374080.3:c.4428G>T	p.Leu1476Phe	p.L1476F	ENST00000374080		1476	ttG/ttT	32/45	0.236616601148943	1	FACETS	0.776	0.686	0.872	0.776	0.686	0.872	SUBCLONAL	1	TRUE	0	0.319429381316153	1		492	563	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70353006	70353006	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	137	609	0	ENST00000374080.3:c.4561G>C	p.Asp1521His	p.D1521H	ENST00000374080		1521	Gat/Cat	33/45	0.236616601148943	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.319429381316153	1		609	717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0036157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	32	697	3	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.551	0.445	0.671	0.551	0.445	0.671	SUBCLONAL	1	TRUE	1	0.15	2		700	775	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0036157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	49	459	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	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.15	2		459	542	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0036158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	24	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.283865839516314	1	FACETS	0.627	0.494	0.778	0.627	0.494	0.778	SUBCLONAL	1	TRUE	0	0.31082492287879	1		452	208	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882005	NA	P-0036158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	53	663	0	ENST00000269305.4:c.713G>C	p.Cys238Ser	p.C238S	ENST00000269305	NM_001126112.2	238	tGt/tCt	7/11	0.257380728094382	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.31082492287879	1		663	252	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974737	21974838	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	CGCCCGCACCTCCTCTACCCGACCCCGGGCCGCGGCCGTGGCCAGCCAGTCAGCCGAAGGCTCCATGCTGCTCCCCGCCGCCGGCTCCATGCTGCTCCCCGC	CGCCCGCACCTCCTCTACCCGACCCCGGGCCGCGGCCGTGGCCAGCCAGTCAGCCGAAGGCTCCATGCTGCTCCCCGCCGCCGGCTCCATGCTGCTCCCCGC	-	novel	NA	P-0036158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	22	302	0	ENST00000304494.5:c.-12_90del		p.*4*	ENST00000304494	NM_000077.4	?-30/156		1/3	0.282202610667279	0	FACETS	0.617	0.483	0.771			1	SUBCLONAL	1	TRUE	0	0.31082492287879	0		302	158	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	49	214	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.885	0.754	1	0.885	0.754	1	CLONAL	1	TRUE	1	0.366752073600481	2		214	302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1064795203	NA	P-0036161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	134	757	0	ENST00000269305.4:c.532C>G	p.His178Asp	p.H178D	ENST00000269305	NM_001126112.2	178	Cac/Gac	5/11	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.366752073600481	2		757	703	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935107	49935107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370774556	NA	P-0036161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	83	556	0	ENST00000296474.3:c.1892G>A	p.Arg631Gln	p.R631Q	ENST00000296474	NM_002447.2	631	cGg/cAg	6/20	1	2	FACETS	0.875	0.775	0.983	0.875	0.775	0.983	CLONAL	1	TRUE	1	0.366752073600481	2		556	517	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048238	180048238	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	133	845	0	ENST00000261937.6:c.2035C>G	p.Arg679Gly	p.R679G	ENST00000261937	NM_182925.4	679	Cgg/Ggg	14/30	1	2	FACETS	0.898	0.815	0.984	0.898	0.815	0.984	CLONAL	1	TRUE	1	0.366752073600481	2		845	808	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947827	178947827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	40	425	0	ENST00000263967.3:c.2702G>T	p.Cys901Phe	p.C901F	ENST00000263967	NM_006218.2	901	tGt/tTt	19/21	1	2	FACETS	0.96	0.797	1	0.96	0.797	1	CLONAL	1	TRUE	1	0.14	2		425	595	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696644	47696644	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	53	537	0	ENST00000347630.2:c.304T>A	p.Phe102Ile	p.F102I	ENST00000347630	NM_001007230.1	102	Ttc/Atc	5/11	1	2	FACETS	0.889	0.756	1	0.889	0.756	1	CLONAL	1	TRUE	1	0.14	2		537	852	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753681	42753681	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	56	745	0	ENST00000222329.4:c.583G>T	p.Glu195Ter	p.E195*	ENST00000222329	NM_006494.2	195	Gag/Tag	4/4	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.14	2		745	796	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	132	214	0				ENST00000310581	NM_198253.2	-/1132			0.52539686508969	3	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	1	0.52539686508969	3		214	307	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402517	139402517	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	489	835	0	ENST00000277541.6:c.3400C>T	p.Gln1134Ter	p.Q1134*	ENST00000277541	NM_017617.3	1134	Cag/Tag	21/34	0.52539686508969	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.52539686508969	2		835	797	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974318	93974318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	47	424	0	ENST00000369303.4:c.1736G>A	p.Gly579Glu	p.G579E	ENST00000369303	NM_004440.3	579	gGg/gAg	8/17	0.52539686508969	1	FACETS	0.526	0.447	0.611	0.526	0.447	0.611	SUBCLONAL	1	TRUE	0	0.52539686508969	1		424	251	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519130	187519130	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	246	443	0	ENST00000441802.2:c.12253C>T	p.Gln4085Ter	p.Q4085*	ENST00000441802	NM_005245.3	4085	Cag/Tag	23/27	0.52539686508969	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.52539686508969	2		443	442	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217255	66217255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	98	456	0	ENST00000273854.3:c.2360G>T	p.Gly787Val	p.G787V	ENST00000273854	NM_004439.5	787	gGa/gTa	14/18	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.52539686508969	2		456	369	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11210282	11210282	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	139	537	0	ENST00000361445.4:c.4471G>T	p.Gly1491Cys	p.G1491C	ENST00000361445	NM_004958.3	1491	Ggt/Tgt	31/58	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.52539686508969	2		537	476	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276739	115276739	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0036165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	79	359	0	ENST00000438362.2:c.721-1G>T		p.X241_splice	ENST00000438362	NM_001242891.1	241			1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.52539686508969	2		359	271	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699241	117699241	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	108	563	0	ENST00000369458.3:c.400A>T	p.Thr134Ser	p.T134S	ENST00000369458	NM_024626.3	134	Act/Tct	3/6	1	2	FACETS	0.853	0.769	0.941	0.853	0.769	0.941	CLONAL	1	TRUE	1	0.52539686508969	2		563	482	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165779	118165779	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	118	550	1	ENST00000369448.3:c.289G>T	p.Val97Leu	p.V97L	ENST00000369448	NM_017709.3	97	Gtg/Ttg	2/2	1	2	FACETS	0.942	0.855	1	0.942	0.855	1	CLONAL	1	TRUE	1	0.52539686508969	2		551	477	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163307809	163307809	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0036165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	36	309	0	ENST00000271452.3:c.436-1G>T		p.X146_splice	ENST00000271452	NM_145697.2	146			0.280367391088303	2	FACETS	0.573	0.474	0.683	0.287	0.237	0.342	INDETERMINATE	1	TRUE	0	0.52539686508969	2		309	239	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445651	49445652	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs727503989	NA	P-0036165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	179	899	0	ENST00000301067.7:c.1814_1815del	p.Glu605ValfsTer8	p.E605Vfs*8	ENST00000301067	NM_003482.3	605	gAG/g	10/54	1	2	FACETS	0.93	0.859	1	0.93	0.859	1	CLONAL	1	TRUE	1	0.52539686508969	2		899	733	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058788	42058788	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs540985411	NA	P-0036165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	85	396	0	ENST00000219905.7:c.8508A>C	p.Gln2836His	p.Q2836H	ENST00000219905	NM_001164273.1	2836	caA/caC	24/24	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.52539686508969	2		396	322	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472621	88472621	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	110	466	0	ENST00000360948.2:c.1934G>T	p.Arg645Leu	p.R645L	ENST00000360948	NM_001012338.2	645	cGc/cTc	16/19	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.52539686508969	2		466	392	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647725	2647725	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	146	569	0	ENST00000342085.4:c.1628G>A	p.Trp543Ter	p.W543*	ENST00000342085	NM_002613.4	543	tGg/tAg	14/14	1	2	FACETS	0.963	0.883	1	0.963	0.883	1	CLONAL	1	TRUE	1	0.52539686508969	2		569	577	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858605	9858606	+	missense_variant	Missense_Mutation	DNP	CA	CA	AT	novel	NA	P-0036165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	120	659	0	ENST00000330684.3:c.2795_2796delinsAT	p.Met932Asn	p.M932N	ENST00000330684	NM_001134407.1	932	aTG/aAT	13/13	1	2	FACETS	0.974	0.885	1	0.974	0.885	1	CLONAL	1	TRUE	1	0.52539686508969	2		659	469	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351026	89351027	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0036165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	202	915	1	ENST00000301030.4:c.1923_1924delinsTT	p.Lys641_Glu642delinsAsnTer	p.K641_E642delinsN*	ENST00000301030	NM_001256183.1	641	aaGGag/aaTTag	9/13	1	2	FACETS	0.897	0.833	0.964	0.897	0.833	0.964	CLONAL	1	TRUE	1	0.52539686508969	2		916	857	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533023	63533023	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	69	673	0	ENST00000307078.5:c.1871T>G	p.Leu624Arg	p.L624R	ENST00000307078	NM_004655.3	624	cTg/cGg	7/11	1	2	FACETS	0.486	0.423	0.553	0.486	0.423	0.553	SUBCLONAL	1	TRUE	1	0.52539686508969	2		673	541	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353754	15353754	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	108	700	1	ENST00000263377.2:c.3126C>A	p.His1042Gln	p.H1042Q	ENST00000263377	NM_058243.2	1042	caC/caA	14/20	0.367854160849173	1	FACETS	0.507	0.456	0.561	0.507	0.456	0.561	SUBCLONAL	1	TRUE	0	0.52539686508969	1		701	598	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902205	50902205	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	77	789	1	ENST00000440232.2:c.97C>T	p.Gln33Ter	p.Q33*	ENST00000440232	NM_002691.3	33	Caa/Taa	2/27	0.367854160849173	1	FACETS	0.461	0.406	0.52	0.461	0.406	0.52	SUBCLONAL	1	TRUE	0	0.52539686508969	1		790	469	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624898	9624898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	149	530	1	ENST00000353224.5:c.79C>T	p.Pro27Ser	p.P27S	ENST00000353224	NM_177990.2	27	Cca/Tca	3/10	1	2	FACETS	0.98	0.899	1	0.98	0.899	1	CLONAL	1	TRUE	1	0.52539686508969	2		531	579	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509109	66509109	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	61	343	0	ENST00000273854.3:c.218T>A	p.Leu73Gln	p.L73Q	ENST00000273854	NM_004439.5	73	cTg/cAg	2/18	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.52539686508969	2		343	232	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002870	69002870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867044170	NA	P-0036165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	112	417	1	ENST00000288368.4:c.2170G>A	p.Gly724Arg	p.G724R	ENST00000288368	NM_024870.2	724	Gga/Aga	20/40	0.52539686508969	3	FACETS	1	0.941	1	0.529	0.478	0.582	CLONAL	1	TRUE	1	0.52539686508969	3		418	509	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759411	133759412	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0036165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	379	682	0	ENST00000318560.5:c.1739dup	p.Glu581GlyfsTer6	p.E581Gfs*6	ENST00000318560	NM_005157.4	578	-/C	11/11	0.52539686508969	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.52539686508969	2		682	699	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0036166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	209	407	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.404073862357858	3	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	1	0.425311001098661	3		408	587	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0036166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	59	301	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.404073862357858	3	FACETS	0.863	0.745	0.99	0.431	0.372	0.495	CLONAL	1	TRUE	1	0.425311001098661	3		301	390	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117799	108117799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202160435	NA	P-0036166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	144	524	1	ENST00000278616.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000278616	NM_000051.3	337	cGt/cAt	8/63	0.404073862357858	3	FACETS	1	0.914	1	0.501	0.457	0.547	CLONAL	1	TRUE	1	0.425311001098661	3		525	820	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0036166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	269	607	1	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.425311001098661	2	FACETS	0.99	0.936	1	0.99	0.936	1	CLONAL	2	TRUE	0	0.425311001098661	2		608	639	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967059	18967059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	160	747	0	ENST00000262803.5:c.1774G>A	p.Glu592Lys	p.E592K	ENST00000262803	NM_002911.3	592	Gag/Aag	13/24	0.425311001098661	3	FACETS	0.868	0.795	0.945	0.434	0.397	0.473	CLONAL	1	TRUE	1	0.425311001098661	3		747	1051	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376920	118376920	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782425634	NA	P-0036166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	233	459	1	ENST00000534358.1:c.10313C>T	p.Thr3438Met	p.T3438M	ENST00000534358	NM_005933.3	3438	aCg/aTg	27/36	0.404073862357858	3	FACETS	0.986	0.924	1	0.986	0.924	1	CLONAL	2	TRUE	1	0.425311001098661	3		460	674	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090632	71090632	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs755027352	NA	P-0036166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	236	614	0	ENST00000318789.4:c.716A>G	p.His239Arg	p.H239R	ENST00000318789	NM_032682.5	239	cAt/cGt	11/21	0.425311001098661	2	FACETS	0.874	0.821	0.928	0.874	0.821	0.928	CLONAL	2	TRUE	0	0.425311001098661	2		614	635	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578217	7578217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	433	672	1	ENST00000269305.4:c.632C>T	p.Thr211Ile	p.T211I	ENST00000269305	NM_001126112.2	211	aCt/aTt	6/11	0.520469809753827	2	FACETS	0.991	0.953	1	0.991	0.953	1	CLONAL	2	TRUE	0	0.555971053675058	2		673	786	SUCCESS
APC	324	MSKCC	GRCh37	5	112175147	112175147	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	79	289	3	ENST00000257430.4:c.3856G>T	p.Glu1286Ter	p.E1286*	ENST00000257430	NM_000038.5	1286	Gaa/Taa	16/16	0.48110847505675	2	FACETS	0.756	0.68	0.833	0.756	0.68	0.833	SUBCLONAL	2	TRUE	0	0.555971053675058	2		292	188	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445046	49445046	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757089451	NA	P-0036167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	275	508	5	ENST00000301067.7:c.2420C>T	p.Ser807Phe	p.S807F	ENST00000301067	NM_003482.3	807	tCc/tTc	10/54	0.496574672967236	3	FACETS	0.906	0.855	0.956	0.906	0.855	0.956	CLONAL	2	TRUE	1	0.555971053675058	3		513	698	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727865	78727865	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	399	666	1	ENST00000306801.3:c.710T>G	p.Met237Arg	p.M237R	ENST00000306801	NM_020761.2	237	aTg/aGg	6/34	0.496574672967236	3	FACETS	0.98	0.936	1	0.98	0.936	1	CLONAL	2	TRUE	1	0.555971053675058	3		667	936	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	186	214	0				ENST00000310581	NM_198253.2	-/1132			0.331100418180436	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.515022451389133	4		214	468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0036168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	574	766	0	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	0.515022451389133	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.515022451389133	2		766	967	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966881	18966881	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	55	753	0	ENST00000262803.5:c.1692G>C	p.Gln564His	p.Q564H	ENST00000262803	NM_002911.3	564	caG/caC	12/24	1	2	FACETS	0.247	0.211	0.288	0.247	0.211	0.288	SUBCLONAL	1	TRUE	1	0.515022451389133	2		753	863	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64286839	64286839	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	27	533	0	ENST00000370651.3:c.54A>T	p.Arg18Ser	p.R18S	ENST00000370651	NM_003463.4	18	agA/agT	2/6	0.181816530765578	2	FACETS	0.232	0.184	0.287	0.116	0.092	0.144	INDETERMINATE	1	TRUE	0	0.515022451389133	2		533	452	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458591	120458591	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	217	724	0	ENST00000256646.2:c.6754G>C	p.Asp2252His	p.D2252H	ENST00000256646	NM_024408.3	2252	Gat/Cat	34/34	0.301353208163604	1	FACETS	0.939	0.878	1	0.939	0.878	1	INDETERMINATE	1	TRUE	0	0.515022451389133	1		724	666	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518524	204518524	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	22	361	0	ENST00000367182.3:c.1187A>T	p.Asp396Val	p.D396V	ENST00000367182	NM_001278516.1	396	gAt/gTt	11/11	1	2	FACETS	0.225	0.174	0.284	0.225	0.174	0.284	SUBCLONAL	1	TRUE	1	0.515022451389133	2		361	380	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445575	49445575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	120	820	0	ENST00000301067.7:c.1891G>A	p.Glu631Lys	p.E631K	ENST00000301067	NM_003482.3	631	Gag/Aag	10/54	0.181816530765578	2	FACETS	0.653	0.59	0.719	0.326	0.295	0.36	INDETERMINATE	1	TRUE	0	0.515022451389133	2		820	714	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41021761	41021761	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	37	574	0	ENST00000267868.3:c.703C>T	p.Arg235Ter	p.R235*	ENST00000267868	NM_002875.4	235	Cga/Tga	8/10	0.515022451389133	1	FACETS	0.184	0.151	0.221	0.184	0.151	0.221	SUBCLONAL	1	TRUE	0	0.515022451389133	1		574	579	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476394	88476394	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	41	555	1	ENST00000360948.2:c.1738G>T	p.Ala580Ser	p.A580S	ENST00000360948	NM_001012338.2	580	Gct/Tct	15/19	0.515022451389133	1	FACETS	0.276	0.229	0.327	0.276	0.229	0.327	SUBCLONAL	1	TRUE	0	0.515022451389133	1		556	429	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434670	99434670	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	43	706	1	ENST00000268035.6:c.757C>T	p.His253Tyr	p.H253Y	ENST00000268035	NM_000875.3	253	Cac/Tac	3/21	0.515022451389133	1	FACETS	0.178	0.148	0.211	0.178	0.148	0.211	SUBCLONAL	1	TRUE	0	0.515022451389133	1		707	696	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965778	25965778	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	224	766	0	ENST00000435504.4:c.3428C>T	p.Ser1143Phe	p.S1143F	ENST00000435504		1143	tCt/tTt	13/13	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.515022451389133	2		766	834	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966087	25966087	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	188	758	0	ENST00000435504.4:c.3119C>T	p.Ser1040Leu	p.S1040L	ENST00000435504		1040	tCa/tTa	13/13	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.515022451389133	2		758	709	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742524	145742524	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs750999910	NA	P-0036168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	205	740	0	ENST00000428558.2:c.264G>C	p.Lys88Asn	p.K88N	ENST00000428558	NM_004260.3	88	aaG/aaC	4/22	0.515022451389133	3	FACETS	1	0.958	1	0.523	0.485	0.562	CLONAL	1	TRUE	1	0.515022451389133	3		740	957	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519996	NA	P-0036173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	87	921	0	ENST00000269305.4:c.395A>C	p.Lys132Thr	p.K132T	ENST00000269305	NM_001126112.2	132	aAg/aCg	5/11	1	2	FACETS	0.7	0.618	0.788	0.7	0.618	0.788	SUBCLONAL	1	TRUE	1	0.22	2		921	1130	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156381	106156381	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	29	470	0	ENST00000380013.4:c.1282G>C	p.Gly428Arg	p.G428R	ENST00000380013	NM_001127208.2	428	Ggt/Cgt	3/11	1	2	FACETS	0.48	0.384	0.59	0.48	0.384	0.59	SUBCLONAL	1	TRUE	1	0.22	2		470	549	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241614	55241614	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs749554270	NA	P-0036173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	66	930	0	ENST00000275493.2:c.2062C>T	p.Leu688Phe	p.L688F	ENST00000275493	NM_005228.3	688	Ctt/Ttt	18/28	1	2	FACETS	0.529	0.457	0.607	0.529	0.457	0.607	SUBCLONAL	1	TRUE	1	0.22	2		930	1134	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737950	145738056	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCAGGGAAAAAGGGACATGTGGCCAACAGCCCTGATTCTCCAACCTCGTCTCCAACTGGGCAGGGCGTGCTTACCTGTGGGCCAGGGCCTGGAGCTGGGCAGGGCC	CCCAGGGAAAAAGGGACATGTGGCCAACAGCCCTGATTCTCCAACCTCGTCTCCAACTGGGCAGGGCGTGCTTACCTGTGGGCCAGGGCCTGGAGCTGGGCAGGGCC	-	novel	NA	P-0036173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	56	807	0	ENST00000428558.2:c.2854_2886-6del		p.X952_splice	ENST00000428558	NM_004260.3	952		17/22	0.147444413179001	3	FACETS	0.549	0.469	0.638	0.183	0.156	0.213	SUBCLONAL	1	TRUE	0	0.22	3		807	1029	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0036176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	225	571	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.518110331992076	2	FACETS	0.918	0.866	0.971	0.918	0.866	0.971	CLONAL	2	TRUE	0	0.518110331992076	2		572	473	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434522	140434522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	194	474	0	ENST00000288602.6:c.2176C>T	p.Arg726Cys	p.R726C	ENST00000288602	NM_004333.4	726	Cgc/Tgc	18/18	0.518110331992076	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.518110331992076	3		474	439	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463195	25463195	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	293	654	0	ENST00000264709.3:c.2298G>C	p.Lys766Asn	p.K766N	ENST00000264709	NM_175629.2	766	aaG/aaC	19/23	1	2	FACETS	0.948	0.898	0.999	0.948	0.898	0.999	CLONAL	1	TRUE	1	0.871530011868229	2		654	709	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163895	47163898	+	frameshift_variant	Frame_Shift_Del	DEL	CTTT	CTTT	-	novel	NA	P-0036180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	224	726	1	ENST00000409792.3:c.2228_2231del	p.Glu743AlafsTer23	p.E743Afs*23	ENST00000409792	NM_014159.6	743	gAAAGc/gc	3/21	1	2	FACETS	0.82	0.768	0.873	0.82	0.768	0.873	CLONAL	1	TRUE	1	0.871530011868229	2		727	627	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969463	44969463	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	162	303	0	ENST00000377967.4:c.4145del	p.Asp1382AlafsTer2	p.D1382Afs*2	ENST00000377967	NM_021140.2	1382	gAc/gc	28/29	1	1	FACETS	0.953	0.906	0.998	0.953	0.906	0.998	CLONAL	1	TRUE	0	0.871530011868229	1		303	220	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0036181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	260	588	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.629236755078722	1	FACETS	0.915	0.864	0.967	0.915	0.864	0.967	CLONAL	1	TRUE	0	0.629236755078722	1		588	619	SUCCESS
BLM	641	MSKCC	GRCh37	15	91352387	91352387	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	141	418	0	ENST00000355112.3:c.3772G>C	p.Glu1258Gln	p.E1258Q	ENST00000355112	NM_000057.2	1258	Gag/Cag	20/22	1	2	FACETS	0.73	0.667	0.795	0.73	0.667	0.795	SUBCLONAL	1	TRUE	1	0.629236755078722	2		418	614	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16097791	16097791	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	228	627	0	ENST00000268712.3:c.93C>A	p.Asn31Lys	p.N31K	ENST00000268712	NM_006311.3	31	aaC/aaA	2/46	0.629236755078722	1	FACETS	0.842	0.79	0.894	0.842	0.79	0.894	CLONAL	1	TRUE	0	0.629236755078722	1		627	590	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657369	29657369	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764782945	NA	P-0036181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	234	676	0	ENST00000356175.3:c.5602G>A	p.Glu1868Lys	p.E1868K	ENST00000356175	NM_000267.3	1868	Gag/Aag	38/57	0.562458362752268	1	FACETS	0.83	0.78	0.881	0.83	0.78	0.881	CLONAL	1	TRUE	0	0.629236755078722	1		676	614	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792278	33792278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	207	669	2	ENST00000498907.2:c.1043G>A	p.Ser348Asn	p.S348N	ENST00000498907	NM_004364.3	348	aGc/aAc	1/1	1	2	FACETS	0.814	0.757	0.873	0.814	0.757	0.873	CLONAL	1	TRUE	1	0.629236755078722	2		671	808	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222983	1222983	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs398123406	NA	P-0036200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	191	436	0	ENST00000326873.7:c.921-1G>T		p.X307_splice	ENST00000326873	NM_000455.4	307			0.589465682221315	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.589465682221315	1		436	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913343	NA	P-0036200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	300	624	0	ENST00000269305.4:c.817C>G	p.Arg273Gly	p.R273G	ENST00000269305	NM_001126112.2	273	Cgt/Ggt	8/11	0.407352050147041	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.589465682221315	1		624	626	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606708	29606708	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	174	503	0	ENST00000389048.3:c.1172G>T	p.Gly391Val	p.G391V	ENST00000389048	NM_004304.4	391	gGa/gTa	5/29	0.229343500549637	1	FACETS	0.793	0.735	0.852	0.793	0.735	0.852	INDETERMINATE	1	TRUE	0	0.589465682221315	1		503	525	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332595	70332595	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1237626100	NA	P-0036200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	217	531	0	ENST00000373644.4:c.500C>G	p.Pro167Arg	p.P167R	ENST00000373644	NM_030625.2	167	cCt/cGt	2/12	0.368958693358793	1	FACETS	0.844	0.79	0.9	0.844	0.79	0.9	CLONAL	1	TRUE	0	0.589465682221315	1		531	615	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881118	37881118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775394020	NA	P-0036200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	343	615	1	ENST00000269571.5:c.2447G>A	p.Arg816His	p.R816H	ENST00000269571		816	cGc/cAc	20/27	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.589465682221315	2		616	919	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533484	63533484	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	306	625	0	ENST00000307078.5:c.1670G>T	p.Ser557Ile	p.S557I	ENST00000307078	NM_004655.3	557	aGc/aTc	6/11	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.589465682221315	2		625	851	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009117	27009118	+	missense_variant	Missense_Mutation	DNP	CG	CG	AA	novel	NA	P-0036200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	45	128	1	ENST00000335756.4:c.53_54delinsAA	p.Pro18Gln	p.P18Q	ENST00000335756	NM_001809.3	18	cCG/cAA	1/5	0.229343500549637	1	FACETS	0.645	0.551	0.745	0.645	0.551	0.745	INDETERMINATE	1	TRUE	0	0.589465682221315	1		129	167	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197780	66197780	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	192	470	0	ENST00000273854.3:c.2919G>T	p.Trp973Cys	p.W973C	ENST00000273854	NM_004439.5	973	tgG/tgT	17/18	0.368958693358793	1	FACETS	0.897	0.837	0.959	0.897	0.837	0.959	CLONAL	1	TRUE	0	0.589465682221315	1		470	512	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467538	66467539	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0036200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	133	374	0	ENST00000273854.3:c.730_731delinsAA	p.Pro244Asn	p.P244N	ENST00000273854	NM_004439.5	244	CCt/AAt	3/18	0.368958693358793	1	FACETS	0.84	0.771	0.91	0.84	0.771	0.91	CLONAL	1	TRUE	0	0.589465682221315	1		374	379	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532656	187532656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	36	502	0	ENST00000441802.2:c.9737G>A	p.Gly3246Glu	p.G3246E	ENST00000441802	NM_005245.3	3246	gGa/gAa	14/27	0.368958693358793	1	FACETS	0.156	0.128	0.188	0.156	0.128	0.188	SUBCLONAL	1	TRUE	0	0.589465682221315	1		502	552	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021776	69021776	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	214	538	1	ENST00000288368.4:c.3064A>T	p.Thr1022Ser	p.T1022S	ENST00000288368	NM_024870.2	1022	Acc/Tcc	25/40	0.589465682221315	4	FACETS	1	0.975	1	0.369	0.343	0.397	CLONAL	1	TRUE	1	0.589465682221315	4		539	1042	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904830	101904830	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	33	377	0	ENST00000374994.4:c.818G>A	p.Trp273Ter	p.W273*	ENST00000374994	NM_004612.2	273	tGg/tAg	5/9	0.589465682221315	1	FACETS	0.176	0.143	0.214	0.176	0.143	0.214	SUBCLONAL	1	TRUE	0	0.589465682221315	1		377	448	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0036204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	61	331	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.914	0.792	1	0.914	0.792	1	CLONAL	1	TRUE	1	0.367887024081401	2		331	363	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197757	66197757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770802873	NA	P-0036204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	119	483	0	ENST00000273854.3:c.2942G>A	p.Arg981Gln	p.R981Q	ENST00000273854	NM_004439.5	981	cGg/cAg	17/18	1	2	FACETS	0.938	0.847	1	0.938	0.847	1	CLONAL	1	TRUE	1	0.367887024081401	2		483	690	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096480	178096481	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0036204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	86	460	0	ENST00000397062.3:c.850_851delinsAT	p.Glu284Ile	p.E284I	ENST00000397062	NM_006164.4	284	GAa/ATa	5/5	1	2	FACETS	0.796	0.706	0.893	0.796	0.706	0.893	SUBCLONAL	1	TRUE	1	0.367887024081401	2		460	587	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0036206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	69	530	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.815	0.713	0.925	0.815	0.713	0.925	CLONAL	1	FALSE	1	0.410927901304169	2		530	412	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089766	27089767	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	97	366	0	ENST00000324856.7:c.2723dup	p.Gln909ProfsTer27	p.Q909Pfs*27	ENST00000324856	NM_006015.4	908	atc/aTtc	8/20	1	2	FACETS	0.948	0.849	1	0.948	0.849	1	CLONAL	1	FALSE	1	0.410927901304169	2		366	498	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117411	115117412	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	110	368	0	ENST00000257566.3:c.762dup	p.Val255CysfsTer5	p.V255Cfs*5	ENST00000257566	NM_016569.3	254	-/T	4/8	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.410927901304169	2		368	467	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645874	67645874	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	113	441	0	ENST00000264010.4:c.802T>A	p.Cys268Ser	p.C268S	ENST00000264010	NM_006565.3	268	Tgt/Agt	4/12	0.410927901304169	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	FALSE	0	0.410927901304169	1		441	420	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995348	15995349	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	65	385	0	ENST00000268712.3:c.2844dup	p.Pro949ThrfsTer17	p.P949Tfs*17	ENST00000268712	NM_006311.3	948	-/A	22/46	1	2	FACETS	0.691	0.6	0.788	0.691	0.6	0.788	SUBCLONAL	1	FALSE	1	0.410927901304169	2		385	458	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167736	56167736	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0036206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	80	329	0	ENST00000399503.3:c.1302-1G>A		p.X434_splice	ENST00000399503	NM_005921.1	434			0.126109068463897	4	FACETS	1	0.976	1	0.476	0.421	0.533	INDETERMINATE	1	FALSE	1	0.410927901304169	4		329	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0036207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	334	597	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.576360825831955	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.602158104182597	1		597	718	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0036207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	28	228	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	0.510249316369709	1	FACETS	0.23	0.184	0.282	0.23	0.184	0.282	SUBCLONAL	1	TRUE	0	0.602158104182597	1		228	283	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250211	133250211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115047349	NA	P-0036207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	261	473	0	ENST00000320574.5:c.1309G>A	p.Val437Met	p.V437M	ENST00000320574	NM_006231.2	437	Gtg/Atg	13/49	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.602158104182597	2		473	839	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292679	62292679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1044603913	NA	P-0036207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1472	85	457	0	ENST00000360203.5:c.131C>T	p.Thr44Met	p.T44M	ENST00000360203	NM_001283009.1	44	aCg/aTg	3/35	0.602158104182597	6	FACETS	0.4	0.351	0.452	0.08	0.07	0.091	SUBCLONAL	1	TRUE	1	0.602158104182597	6		457	1557	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749407	43749408	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	125	345	0	ENST00000382044.4:c.1398dup	p.Ile467TyrfsTer12	p.I467Yfs*12	ENST00000382044	NM_001141980.1	466	-/T	12/28	1	2	FACETS	0.77	0.7	0.843	0.77	0.7	0.843	SUBCLONAL	1	TRUE	1	0.602158104182597	2		345	539	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448495	89448495	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	147	304	0	ENST00000336596.2:c.1459C>G	p.Leu487Val	p.L487V	ENST00000336596	NM_005233.5	487	Ctg/Gtg	7/17	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.602158104182597	2		304	464	SUCCESS
APC	324	MSKCC	GRCh37	5	112174867	112174868	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs1060503326	NA	P-0036207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	130	264	0	ENST00000257430.4:c.3577_3578del	p.Gln1193ValfsTer14	p.Q1193Vfs*14	ENST00000257430	NM_000038.5	1192	aaACag/aaag	16/16	0.510249316369709	1	FACETS	0.946	0.871	1	0.946	0.871	1	CLONAL	1	TRUE	0	0.602158104182597	1		264	319	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0036210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	18	317	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.592	0.445	0.768	0.592	0.445	0.768	SUBCLONAL	1	TRUE	1	0.14	2		317	434	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692922	89692922	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201044	NA	P-0036210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	38	481	0	ENST00000371953.3:c.406T>C	p.Cys136Arg	p.C136R	ENST00000371953	NM_000314.4	136	Tgt/Cgt	5/9	1	2	FACETS	0.923	0.762	1	0.923	0.762	1	CLONAL	1	TRUE	1	0.14	2		481	588	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589563	67589564	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAAGCTGTA	novel	NA	P-0036210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	17	190	0	ENST00000274335.5:c.1328_1336dup	p.Glu443_Val445dup	p.E443_V445dup	ENST00000274335		443	-/GAAGCTGTA	10/15	1	2	FACETS	0.916	0.684	1	0.916	0.684	1	CLONAL	1	TRUE	1	0.14	2		190	265	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589574	67589574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	21	215	0	ENST00000274335.5:c.1337G>A	p.Gly446Glu	p.G446E	ENST00000274335		446	gGg/gAg	10/15	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.14	2		215	262	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0036211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	250	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.327928998600317	4	FACETS	1	0.987	1			1	CLONAL	3	TRUE	NA	0.327928998600317	4		452	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0036212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	134	591	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.183142554011371	2	FACETS	1	0.986	1	0.743	0.676	0.814	CLONAL	1	TRUE	0	0.227597051092961	2		591	792	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141559	11141559	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	136	614	0	ENST00000358026.2:c.3536A>G	p.Asn1179Ser	p.N1179S	ENST00000358026	NM_001128849.1	1179	aAt/aGt	25/36	0.183142554011371	2	FACETS	0.794	0.722	0.868	0.794	0.722	0.868	SUBCLONAL	2	TRUE	0	0.227597051092961	2		614	753	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231108	46231108	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0036212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	56	515	0	ENST00000334344.6:c.1028T>G	p.Leu343Ter	p.L343*	ENST00000334344	NM_152641.2	343	tTa/tGa	9/21	1	2	FACETS	0.675	0.577	0.782	0.675	0.577	0.782	SUBCLONAL	1	TRUE	1	0.227597051092961	2		515	729	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95596409	95596409	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs763801533	NA	P-0036212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	60	348	0	ENST00000393063.1:c.559C>T	p.Arg187Ter	p.R187*	ENST00000393063	NM_030621.3	187	Cga/Tga	6/28	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.227597051092961	2		348	510	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149894	99149894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368448330	NA	P-0036212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	81	543	0	ENST00000074304.5:c.206C>T	p.Ala69Val	p.A69V	ENST00000074304	NM_001134224.1	69	gCg/gTg	5/26	0.123965608094471	4	FACETS	1	0.93	1	0.541	0.476	0.611	INDETERMINATE	1	TRUE	2	0.227597051092961	4		543	808	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595818	52595818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	69	630	4	ENST00000394830.3:c.4097G>A	p.Arg1366Lys	p.R1366K	ENST00000394830	NM_018313.4	1366	aGa/aAa	26/30	1	2	FACETS	0.781	0.679	0.892	0.781	0.679	0.892	SUBCLONAL	1	TRUE	1	0.227597051092961	2		634	776	SUCCESS
AR	367	MSKCC	GRCh37	X	66863154	66863154	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	153	326	0	ENST00000374690.3:c.1673A>G	p.Lys558Arg	p.K558R	ENST00000374690	NM_000044.3	558	aAg/aGg	2/8	0.227597051092961	2	FACETS	0.838	0.771	0.907			1	CLONAL	3	TRUE	NA	0.227597051092961	2		326	535	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	70	214	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.92	1	1	0.984	1	CLONAL	2	FALSE	1	0.318247893043818	2		214	210	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0036214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	20	533	1	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	1	2	FACETS	0.509	0.39	0.648	0.509	0.39	0.648	SUBCLONAL	1	FALSE	1	0.318247893043818	2		534	247	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104375060	104375060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137880855	NA	P-0036214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	49	471	3	ENST00000369902.3:c.1058C>T	p.Thr353Met	p.T353M	ENST00000369902	NM_016169.3	353	aCg/aTg	9/12	1	2	FACETS	0.577	0.488	0.674	0.577	0.488	0.674	SUBCLONAL	1	FALSE	1	0.318247893043818	2		474	534	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846411	128846412	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0036214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	37	479	1	ENST00000249373.3:c.1247_1248delinsAA	p.Gly416Glu	p.G416E	ENST00000249373	NM_005631.4	416	gGC/gAA	6/12	1	2	FACETS	0.563	0.464	0.673	0.563	0.464	0.673	SUBCLONAL	1	FALSE	1	0.318247893043818	2		480	413	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721018	176721018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	79	418	0	ENST00000439151.2:c.6649G>A	p.Glu2217Lys	p.E2217K	ENST00000439151	NM_022455.4	2217	Gag/Aag	23/23	1	2	FACETS	0.757	0.671	0.847	1	0.978	1	SUBCLONAL	2	FALSE	1	0.318247893043818	2		418	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0036215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	80	571	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.21	2		572	597	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250284	133250284	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	56	482	0	ENST00000320574.5:c.1236G>C	p.Lys412Asn	p.K412N	ENST00000320574	NM_006231.2	412	aaG/aaC	13/49	0.0590378192741441	3	FACETS	0.767	0.66	0.884	0.767	0.66	0.884	INDETERMINATE	2	TRUE	1	0.21	3		482	384	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217849	7217850	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	59	607	0	ENST00000380728.2:c.161dup	p.Glu55GlyfsTer42	p.E55Gfs*42	ENST00000380728		54	aag/aaAg	3/11	1	2	FACETS	0.892	0.767	1	0.892	0.767	1	CLONAL	1	TRUE	1	0.21	2		607	630	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878782	151878782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	66	506	0	ENST00000262189.6:c.6163G>A	p.Asp2055Asn	p.D2055N	ENST00000262189	NM_170606.2	2055	Gat/Aat	36/59	0.0590378192741441	3	FACETS	1	0.972	1	0.747	0.65	0.851	INDETERMINATE	1	TRUE	1	0.21	3		506	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0036216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	365	673	1	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.3	4	FACETS	1	0.972	1	1	0.994	1	CLONAL	4	TRUE	1	0.22	4		674	981	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970901	21970901	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs45476696	NA	P-0036216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	76	515	0	ENST00000304494.5:c.457G>A	p.Asp153Asn	p.D153N	ENST00000304494	NM_000077.4	153	Gac/Aac	2/3	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.22	2		515	463	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058517	72058517	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	53	513	0	ENST00000357731.5:c.923C>G	p.Ala308Gly	p.A308G	ENST00000357731	NM_173808.2	308	gCg/gGg	6/7	0.185758164897537	3	FACETS	1	0.882	1	0.519	0.443	0.603	CLONAL	1	TRUE	1	0.22	3		513	515	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790023	40790023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	52	568	0	ENST00000373198.4:c.2708G>A	p.Gly903Asp	p.G903D	ENST00000373198	NM_133170.3	903	gGc/gAc	18/32	1	2	FACETS	0.884	0.752	1	0.884	0.752	1	CLONAL	1	TRUE	1	0.22	2		568	535	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41542795	41542795	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	52	435	2	ENST00000263253.7:c.2106G>A	p.Met702Ile	p.M702I	ENST00000263253	NM_001429.3	702	atG/atA	11/31	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.22	2		437	438	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0036219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	111	642	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	1	2	FACETS	0.841	0.766	0.918	0.841	0.766	0.918	CLONAL	1	TRUE	1	0.84364013055368	2		642	313	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436737	110436737	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	159	694	0	ENST00000375856.3:c.1664C>G	p.Ser555Cys	p.S555C	ENST00000375856	NM_003749.2	555	tCc/tGc	1/2	0.188421757164059	4	FACETS	0.982	0.913	1	0.982	0.913	1	INDETERMINATE	2	TRUE	2	0.84364013055368	4		694	354	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042214	42042214	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	75	535	0	ENST00000219905.7:c.6409G>T	p.Glu2137Ter	p.E2137*	ENST00000219905	NM_001164273.1	2137	Gaa/Taa	17/24	0.79835002340817	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.84364013055368	1		535	91	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004595	150004595	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	172	687	0	ENST00000253339.5:c.1630C>G	p.Pro544Ala	p.P544A	ENST00000253339		544	Cca/Gca	3/7	0.188421757164059	4	FACETS	0.947	0.883	1	0.947	0.883	1	INDETERMINATE	2	TRUE	2	0.84364013055368	4		687	397	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593582	55593598	+	protein_altering_variant,splice_region_variant	In_Frame_Del	DEL	AAACCCATGTATGAAGT	AAACCCATGTATGAAGT	CA	novel	NA	P-0036220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	77	451	1	ENST00000288135.5:c.1648_1664delinsCA	p.Lys550_Val555delinsGln	p.K550_V555delinsQ	ENST00000288135	NM_000222.2	550	AAACCCATGTATGAAGTa/CAa	11/21	1	2	FACETS	0.889	0.782	1	0.889	0.782	1	CLONAL	1	TRUE	1	0.356619543457034	2		452	486	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380285	25380285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104894364	NA	P-0036220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	18	603	3	ENST00000311936.3:c.173C>T	p.Thr58Ile	p.T58I	ENST00000311936	NM_004985.3	58	aCa/aTa	3/5	1	2	FACETS	0.141	0.106	0.184	0.141	0.106	0.184	SUBCLONAL	1	TRUE	1	0.356619543457034	2		606	714	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564618	55564618	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	76	603	0	ENST00000288135.5:c.506G>C	p.Gly169Ala	p.G169A	ENST00000288135	NM_000222.2	169	gGc/gCc	3/21	1	2	FACETS	0.568	0.498	0.644	0.568	0.498	0.644	SUBCLONAL	1	TRUE	1	0.356619543457034	2		603	750	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564656	55564656	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	70	602	1	ENST00000288135.5:c.544C>A	p.Leu182Ile	p.L182I	ENST00000288135	NM_000222.2	182	Ctc/Atc	3/21	1	2	FACETS	0.55	0.479	0.627	0.55	0.479	0.627	SUBCLONAL	1	TRUE	1	0.356619543457034	2		603	714	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443695	29443695	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs863225281	NA	P-0121595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	22	535	0	ENST00000389048.3:c.3522C>A	p.Phe1174Leu	p.F1174L	ENST00000389048	NM_004304.4	1174	ttC/ttA	23/29	0.334580882287609	5	FACETS	0.186	0.143	0.236	0.037	0.028	0.048	INDETERMINATE	1	NA	0	0.59860342066931	5		535	751	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432664	29432664	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs113994087	NA	P-0121595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	92	456	0	ENST00000389048.3:c.3824G>T	p.Arg1275Leu	p.R1275L	ENST00000389048	NM_004304.4	1275	cGa/cTa	25/29	0.334580882287609	5	FACETS	0.884	0.786	0.988	0.177	0.157	0.198	INDETERMINATE	1	NA	0	0.59860342066931	5		456	660	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0036223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	122	667	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.245212270504517	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.245212270504517	1		667	738	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584534	187584534	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	88	657	0	ENST00000441802.2:c.3499G>T	p.Asp1167Tyr	p.D1167Y	ENST00000441802	NM_005245.3	1167	Gat/Tat	3/27	1	2	FACETS	0.883	0.781	0.992	0.883	0.781	0.992	CLONAL	1	TRUE	1	0.245212270504517	2		657	813	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858281	27858281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	44	655	0	ENST00000359303.2:c.290G>A	p.Cys97Tyr	p.C97Y	ENST00000359303	NM_003535.2	97	tGc/tAc	1/1	1	2	FACETS	0.429	0.358	0.507	0.429	0.358	0.507	SUBCLONAL	1	TRUE	1	0.245212270504517	2		655	837	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721883	49721883	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs532706844	NA	P-0036224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	86	334	0	ENST00000449682.2:c.1880C>T	p.Thr627Met	p.T627M	ENST00000449682	NM_020998.3	627	aCg/aTg	17/18	0.375597292774036	4	FACETS	1	0.926	1	0.529	0.469	0.593	CLONAL	1	TRUE	2	0.461008810385486	4		334	515	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828956	72828956	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	176	709	0	ENST00000268489.5:c.7625T>C	p.Phe2542Ser	p.F2542S	ENST00000268489	NM_006885.3	2542	tTt/tCt	9/10	0.426686365748202	3	FACETS	0.931	0.857	1	0.466	0.428	0.504	CLONAL	1	TRUE	1	0.461008810385486	3		709	1009	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579364	7579371	+	frameshift_variant	Frame_Shift_Del	DEL	CCGTAGCT	CCGTAGCT	-	novel	NA	P-0036224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	352	679	0	ENST00000269305.4:c.316_323del	p.Ser106PhefsTer40	p.S106Ffs*40	ENST00000269305	NM_001126112.2	106	AGCTACGGt/t	4/11	0.461008810385486	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.461008810385486	2		679	727	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678002	117678002	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1008170196	NA	P-0036224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	125	570	0	ENST00000368508.3:c.3931C>T	p.Arg1311Ter	p.R1311*	ENST00000368508	NM_002944.2	1311	Cga/Tga	25/43	0.461008810385486	2	FACETS	0.895	0.812	0.981	0.447	0.406	0.491	CLONAL	1	TRUE	0	0.461008810385486	2		570	606	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737295	145737295	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1336	211	727	0	ENST00000428558.2:c.3392G>C	p.Arg1131Thr	p.R1131T	ENST00000428558	NM_004260.3	1131	aGa/aCa	20/22	0.461008810385486	6	FACETS	1	0.978	1	0.284	0.263	0.307	CLONAL	1	TRUE	2	0.461008810385486	6		727	1547	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390863	139390863	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	424	706	0	ENST00000277541.6:c.7328del	p.Val2443GlyfsTer34	p.V2443Gfs*34	ENST00000277541	NM_017617.3	2443	gTg/gg	34/34	0.461008810385486	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.461008810385486	2		706	910	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101089	26101089	+	start_lost	Translation_Start_Site	SNP	C	C	T	rs1559535727	NA	P-0036231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	99	529	0	ENST00000435504.4:c.3G>A	p.Met1?	p.M1?	ENST00000435504		1	atG/atA	1/13	1	2	FACETS	0.941	0.847	1	0.941	0.847	1	CLONAL	1	TRUE	1	0.554901860709004	2		529	379	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0036231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	83	485	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	0.554901860709004	2		485	280	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0036231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	56	348	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.554901860709004	2		348	191	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330610	65330611	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	84	565	0	ENST00000342505.4:c.1035dup	p.Leu346ThrfsTer4	p.L346Tfs*4	ENST00000342505	NM_002227.2	345	-/A	8/25	0.554901860709004	1	FACETS	0.865	0.775	0.957	0.865	0.775	0.957	CLONAL	1	TRUE	0	0.554901860709004	1		565	253	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894916	101894916	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060502040	NA	P-0036232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	129	431	0	ENST00000374994.4:c.469C>T	p.Arg157Ter	p.R157*	ENST00000374994	NM_004612.2	157	Cga/Tga	3/9	0.323669129279867	2	FACETS	1	0.985	1	0.711	0.648	0.776	CLONAL	1	TRUE	0	0.368893079384477	2		431	492	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910756	29910756	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	48	465	0	ENST00000376809.5:c.296G>C	p.Arg99Pro	p.R99P	ENST00000376809	NM_002116.7	99	cGa/cCa	2/8	1	2	FACETS	0.615	0.521	0.719	0.615	0.521	0.719	SUBCLONAL	1	TRUE	1	0.368893079384477	2		465	423	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042188	42042188	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	118	572	0	ENST00000219905.7:c.6383G>C	p.Ser2128Thr	p.S2128T	ENST00000219905	NM_001164273.1	2128	aGt/aCt	17/24	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.368893079384477	2		572	546	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557276	29557276	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0036232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	61	330	0	ENST00000356175.3:c.2991-2A>G		p.X997_splice	ENST00000356175	NM_000267.3	997			1	2	FACETS	0.961	0.834	1	0.961	0.834	1	CLONAL	1	TRUE	1	0.368893079384477	2		330	344	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415070	116415070	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	131	644	0	ENST00000397752.3:c.3164T>A	p.Leu1055His	p.L1055H	ENST00000397752	NM_000245.2	1055	cTc/cAc	15/21	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.368893079384477	2		644	692	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0036236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	432	728	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.37424536703539	3	FACETS	0.929	0.895	0.964	0.929	0.895	0.964	CLONAL	3	TRUE	0	0.523415629213546	3		728	747	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582168	189582168	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121908835	NA	P-0036236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	79	503	0	ENST00000264731.3:c.727C>T	p.Arg243Trp	p.R243W	ENST00000264731	NM_003722.4	243	Cgg/Tgg	5/14	0.367317982432089	5	FACETS	0.745	0.655	0.842	0.248	0.218	0.281	SUBCLONAL	1	TRUE	2	0.523415629213546	5		503	723	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592672	28592672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	87	653	0	ENST00000241453.7:c.2473G>A	p.Val825Met	p.V825M	ENST00000241453	NM_004119.2	825	Gtg/Atg	20/24	0.240786255707048	2	FACETS	0.508	0.449	0.57	0.254	0.224	0.285	INDETERMINATE	1	TRUE	0	0.523415629213546	2		653	655	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566198	95566198	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	97	590	0	ENST00000393063.1:c.4125del	p.Pro1377LeufsTer2	p.P1377Lfs*2	ENST00000393063	NM_030621.3	1375	gaT/ga	23/28	0.111638367123656	3	FACETS	0.869	0.777	0.966	0.29	0.259	0.322	INDETERMINATE	1	TRUE	0	0.523415629213546	3		590	538	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0036238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	57	331	0				ENST00000310581	NM_198253.2	-/1132			0.220459637426507	2	FACETS	0.983	0.862	1	1	0.972	1	CLONAL	3	TRUE	0	0.24167551245064	2		331	160	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579524	7579527	+	frameshift_variant	Frame_Shift_Del	DEL	TGAA	TGAA	-	novel	NA	P-0036238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	136	840	0	ENST00000269305.4:c.160_163del	p.Phe54LeufsTer68	p.F54Lfs*68	ENST00000269305	NM_001126112.2	54	TTCAct/ct	4/11	0.220459637426507	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	2	TRUE	0	0.24167551245064	2		840	558	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858560	27858560	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	26	409	0	ENST00000359303.2:c.11C>G	p.Thr4Arg	p.T4R	ENST00000359303	NM_003535.2	4	aCg/aGg	1/1	0.24167551245064	2	FACETS	0.794	0.631	0.98	0.397	0.315	0.49	CLONAL	1	TRUE	0	0.24167551245064	2		409	271	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0036242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	115	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.696317823240565	2		452	311	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591247	67591249	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GGT	GGT	-	rs1131692243	NA	P-0036242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	80	349	0	ENST00000274335.5:c.1748_1750del		p.X583_splice	ENST00000274335		583		13/15	1	2	FACETS	0.93	0.831	1	0.93	0.831	1	CLONAL	1	TRUE	1	0.696317823240565	2		349	247	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717699	89717699	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554825210	NA	P-0036242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	301	382	0	ENST00000371953.3:c.724G>T	p.Glu242Ter	p.E242*	ENST00000371953	NM_000314.4	242	Gag/Tag	7/9	0.696317823240565	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.696317823240565	3		382	358	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105972	27105972	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	134	399	0	ENST00000324856.7:c.5583del	p.Ser1861ArgfsTer22	p.S1861Rfs*22	ENST00000324856	NM_006015.4	1861	agC/ag	20/20	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.696317823240565	2		399	383	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980421	201980422	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0036242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	193	517	0	ENST00000359651.3:c.158_159dup	p.Thr54ValfsTer102	p.T54Vfs*102	ENST00000359651		53	ggt/gGTgt	1/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.696317823240565	2		517	525	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924415	112924415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1566185599	NA	P-0036242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	103	357	0	ENST00000351677.2:c.1361C>T	p.Pro454Leu	p.P454L	ENST00000351677	NM_002834.3	454	cCg/cTg	11/16	1	2	FACETS	0.925	0.837	1	0.925	0.837	1	CLONAL	1	TRUE	1	0.696317823240565	2		357	320	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533740	41533741	+	stop_gained,inframe_insertion	Nonsense_Mutation	INS	-	-	ACAGTG	novel	NA	P-0036242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	156	427	0	ENST00000263253.7:c.1707_1712dup	p.Gln570_Trp571insTer	p.Q570_W571ins*	ENST00000263253	NM_001429.3	569	aaa/aaACAGTGa	8/31	1	2	FACETS	0.937	0.865	1	0.937	0.865	1	CLONAL	1	TRUE	1	0.696317823240565	2		427	478	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916856	178916856	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	10	507	0	ENST00000263967.3:c.243A>T	p.Glu81Asp	p.E81D	ENST00000263967	NM_006218.2	81	gaA/gaT	2/21	1	2	FACETS	0.077	0.052	0.11	0.077	0.052	0.11	SUBCLONAL	1	TRUE	1	0.696317823240565	2		507	372	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178215	56178215	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1428148071	NA	P-0036242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	49	269	0	ENST00000399503.3:c.3188C>G	p.Ser1063Cys	p.S1063C	ENST00000399503	NM_005921.1	1063	tCt/tGt	14/20	1	2	FACETS	0.902	0.779	1	0.902	0.779	1	CLONAL	1	TRUE	1	0.696317823240565	2		269	156	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370901	55370901	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	774	371	0	ENST00000297316.4:c.203T>A	p.Ile68Asn	p.I68N	ENST00000297316	NM_022454.3	68	aTc/aAc	1/2	0.696317823240565	6	FACETS	0.971	0.948	0.993	0.971	0.948	0.993	CLONAL	5	TRUE	1	0.696317823240565	6		371	1096	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0036243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	254	545	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.206324668917987	3	FACETS	0.991	0.931	1	0.66	0.62	0.701	INDETERMINATE	2	TRUE	0	0.390997205150311	3		545	784	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0036243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	165	674	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.342458626454337	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.390997205150311	1		674	576	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466019	69466019	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	62	496	0	ENST00000227507.2:c.857C>A	p.Thr286Lys	p.T286K	ENST00000227507	NM_053056.2	286	aCa/aAa	5/5	0.203428885166675	1	FACETS	0.451	0.389	0.517	0.451	0.389	0.517	INDETERMINATE	1	TRUE	0	0.390997205150311	1		496	566	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091424	193091424	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	55	359	0	ENST00000367435.3:c.94T>G	p.Trp32Gly	p.W32G	ENST00000367435	NM_024529.4	32	Tgg/Ggg	1/17	1	2	FACETS	0.474	0.405	0.549	0.474	0.405	0.549	SUBCLONAL	1	TRUE	1	0.390997205150311	2		359	594	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483072	29483072	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	54	405	0	ENST00000356175.3:c.132C>G	p.Ile44Met	p.I44M	ENST00000356175	NM_000267.3	44	atC/atG	2/57	0.206324668917987	3	FACETS	0.531	0.453	0.616	0.177	0.151	0.206	INDETERMINATE	1	TRUE	0	0.390997205150311	3		405	622	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341888	8341888	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	198	494	1	ENST00000356435.5:c.4752T>A	p.His1584Gln	p.H1584Q	ENST00000356435		1584	caT/caA	29/35	0.28191140859008	3	FACETS	0.785	0.729	0.843	0.785	0.729	0.843	SUBCLONAL	2	TRUE	1	0.390997205150311	3		495	771	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53244013	53244013	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	69	423	0	ENST00000375401.3:c.980G>T	p.Cys327Phe	p.C327F	ENST00000375401	NM_004187.3	327	tGc/tTc	8/26	0.202134937220019	0	FACETS	0.4	0.349	0.456			1	INDETERMINATE	1	TRUE	0	0.390997205150311	0		423	537	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0036244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	133	381	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.371364417188665	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.371364417188665	1		381	579	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584560	48584560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	128	549	0	ENST00000342988.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000342988	NM_005359.5	245	Cag/Tag	6/12	0.368472748264652	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.371364417188665	1		549	540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs879253911	NA	P-0036244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	129	658	0	ENST00000269305.4:c.538G>T	p.Glu180Ter	p.E180*	ENST00000269305	NM_001126112.2	180	Gag/Tag	5/11	0.371364417188665	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.371364417188665	1		658	496	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941889	71941889	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	150	692	0	ENST00000298229.2:c.1247C>G	p.Ser416Cys	p.S416C	ENST00000298229	NM_001567.3	416	tCc/tGc	11/28	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.371364417188665	2		692	602	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121480	108121481	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs587781598	NA	P-0036244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	83	414	0	ENST00000278616.4:c.1290_1291del	p.Cys430Ter	p.C430*	ENST00000278616	NM_000051.3	430	TGt/t	10/63	0.371364417188665	1	FACETS	0.847	0.751	0.948	0.847	0.751	0.948	CLONAL	1	TRUE	0	0.371364417188665	1		414	430	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066749	30066749	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	134	560	0	ENST00000331968.5:c.2382G>T	p.Gln794His	p.Q794H	ENST00000331968	NM_002742.2	794	caG/caT	16/18	0.189554089354558	2	FACETS	1	0.976	1	0.601	0.548	0.657	INDETERMINATE	1	TRUE	0	0.371364417188665	2		560	600	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472422	88472422	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	86	474	0	ENST00000360948.2:c.2133G>T	p.Arg711Ser	p.R711S	ENST00000360948	NM_001012338.2	711	agG/agT	16/19	0.371364417188665	1	FACETS	0.952	0.848	1	0.952	0.848	1	CLONAL	1	TRUE	0	0.371364417188665	1		474	396	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59934578	59934578	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	85	363	0	ENST00000259008.2:c.220G>C	p.Glu74Gln	p.E74Q	ENST00000259008	NM_032043.2	74	Gag/Cag	4/20	0.290510917973642	1	FACETS	0.845	0.751	0.946	0.845	0.751	0.946	CLONAL	1	TRUE	0	0.371364417188665	1		363	441	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25990511	25990511	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	110	573	0	ENST00000435504.4:c.716A>C	p.Glu239Ala	p.E239A	ENST00000435504		239	gAa/gCa	8/13	1	2	FACETS	0.9	0.81	0.996	0.9	0.81	0.996	CLONAL	1	TRUE	1	0.371364417188665	2		573	658	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630495	187630495	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763178952	NA	P-0036244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	154	707	1	ENST00000441802.2:c.487G>T	p.Ala163Ser	p.A163S	ENST00000441802	NM_005245.3	163	Gct/Tct	2/27	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.371364417188665	2		708	806	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195185	123195186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	241	418	0	ENST00000218089.9:c.1529dup	p.Glu511GlyfsTer6	p.E511Gfs*6	ENST00000218089	NM_001042749.1	510	gag/gAag	16/35	0.117750260070908	3	FACETS	0.916	0.86	0.974	0.916	0.86	0.974	INDETERMINATE	2	TRUE	1	0.444685724322176	3		418	723	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0036246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	51	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.564	0.478	0.659	0.564	0.478	0.659	SUBCLONAL	1	TRUE	1	0.224309314582523	2		452	806	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0036246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	111	657	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.207098897591671	1	FACETS	0.965	0.866	1	0.965	0.866	1	CLONAL	1	TRUE	0	0.224309314582523	1		657	911	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249360	153249361	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	62	416	0	ENST00000281708.4:c.1417dup	p.Arg473LysfsTer4	p.R473Kfs*4	ENST00000281708	NM_033632.3	473	aga/aAga	9/12	1	2	FACETS	0.74	0.638	0.851	0.74	0.638	0.851	SUBCLONAL	1	TRUE	1	0.224309314582523	2		416	747	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182641	38182641	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs387907272	NA	P-0036246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	12	331	0	ENST00000396334.3:c.794T>C	p.Leu265Pro	p.L265P	ENST00000396334	NM_002468.4	265	cTg/cCg	5/5	1	2	FACETS	0.204	0.142	0.28	0.204	0.142	0.28	SUBCLONAL	1	TRUE	1	0.224309314582523	2		331	525	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591898	48591898	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	74	494	0	ENST00000342988.3:c.1061T>G	p.Val354Gly	p.V354G	ENST00000342988	NM_005359.5	354	gTg/gGg	9/12	0.207098897591671	1	FACETS	0.765	0.669	0.869	0.765	0.669	0.869	SUBCLONAL	1	TRUE	0	0.224309314582523	1		494	766	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390545	139390545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767929506	NA	P-0036246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	86	641	0	ENST00000277541.6:c.7646G>A	p.Arg2549His	p.R2549H	ENST00000277541	NM_017617.3	2549	cGc/cAc	34/34	0.224309314582523	1	FACETS	0.694	0.612	0.782	0.694	0.612	0.782	SUBCLONAL	1	TRUE	0	0.224309314582523	1		641	981	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0036247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	147	603	0	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.682636266743852	1	FACETS	0.979	0.913	1	0.979	0.913	1	CLONAL	1	TRUE	0	0.691488723799567	1		603	284	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0036248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	102	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	1	0.958	1			1	INDETERMINATE	1	TRUE	NA	0.479330363309265	2		452	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578224	7578224	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1429743956	NA	P-0036248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	121	557	0	ENST00000269305.4:c.625A>T	p.Arg209Ter	p.R209*	ENST00000269305	NM_001126112.2	209	Aga/Tga	6/11	0.479330363309265	1	FACETS	0.822	0.747	0.9	0.822	0.747	0.9	CLONAL	1	TRUE	0	0.479330363309265	1		557	467	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737142	145737142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61755067	NA	P-0036248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	146	600	0	ENST00000428558.2:c.3424G>A	p.Asp1142Asn	p.D1142N	ENST00000428558	NM_004260.3	1142	Gac/Aac	21/22	0.467186884725902	4	FACETS	0.947	0.863	1	0.316	0.287	0.345	CLONAL	1	TRUE	1	0.479330363309265	4		600	952	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696187	52696187	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	127	637	0	ENST00000394830.3:c.490G>T	p.Glu164Ter	p.E164*	ENST00000394830	NM_018313.4	164	Gaa/Taa	5/30	0.479330363309265	1	FACETS	0.907	0.828	0.989	0.907	0.828	0.989	CLONAL	1	TRUE	0	0.479330363309265	1		637	444	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218155	69218155	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0036248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	106	426	0	ENST00000462284.1:c.371C>G	p.Ser124Ter	p.S124*	ENST00000462284	NM_002392.5	124	tCa/tGa	6/11	0.479330363309265	1	FACETS	0.986	0.894	1	0.986	0.894	1	CLONAL	1	TRUE	0	0.479330363309265	1		426	341	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540170	23540170	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	27	156	0	ENST00000380871.4:c.233C>G	p.Thr78Ser	p.T78S	ENST00000380871	NM_006167.3	78	aCc/aGc	1/2	0.479330363309265	1	FACETS	0.571	0.46	0.695	0.571	0.46	0.695	SUBCLONAL	1	TRUE	0	0.479330363309265	1		156	150	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411876	116411890	+	intron_variant	Intron	DEL	AAGCTCTTTCTTTCT	AAGCTCTTTCTTTCT	-	novel	NA	P-0036249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	7140	1083	3	ENST00000397752.3:c.2888-27_2888-13del		p.*963*	ENST00000397752	NM_000245.2	-/1390			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		1086	7470	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411876	116411890	+	intron_variant	Intron	DEL	AAGCTCTTTCTTTCT	AAGCTCTTTCTTTCT	-	novel	NA	P-0036249-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	2700	1083	3	ENST00000397752.3:c.2888-27_2888-13del		p.*963*	ENST00000397752	NM_000245.2	-/1390			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		1086	3295	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0036250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	85	303	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.248466025470535	3	FACETS	1	0.971	1	0.643	0.571	0.718	CLONAL	1	TRUE	1	0.386807798043628	3		303	408	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	51	214	0				ENST00000310581	NM_198253.2	-/1132			0.386807798043628	3	FACETS	0.828	0.715	0.949	0.828	0.715	0.949	CLONAL	2	TRUE	1	0.386807798043628	3		214	190	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913783	32913783	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs397507778	NA	P-0036250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	37	416	0	ENST00000380152.3:c.5291C>G	p.Ser1764Ter	p.S1764*	ENST00000380152		1764	tCa/tGa	11/27	1	2	FACETS	0.523	0.431	0.624	0.523	0.431	0.624	SUBCLONAL	1	TRUE	1	0.386807798043628	2		416	366	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436941	110436941	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	13	170	0	ENST00000375856.3:c.1460C>G	p.Ser487Cys	p.S487C	ENST00000375856	NM_003749.2	487	tCc/tGc	1/2	1	2	FACETS	0.407	0.291	0.548	0.407	0.291	0.548	SUBCLONAL	1	TRUE	1	0.386807798043628	2		170	165	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031997	26031997	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	29	341	0	ENST00000244661.2:c.292G>T	p.Glu98Ter	p.E98*	ENST00000244661	NM_003537.3	98	Gag/Tag	1/1	1	2	FACETS	0.467	0.375	0.571	0.467	0.375	0.571	SUBCLONAL	1	TRUE	1	0.386807798043628	2		341	321	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0036259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	153	532	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.315862375551673	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.315862375551673	3		532	519	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279644	123279644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779326224	NA	P-0036259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	49	381	0	ENST00000358487.5:c.788C>T	p.Pro263Leu	p.P263L	ENST00000358487	NM_000141.4	263	cCg/cTg	7/18	0.315862375551673	3	FACETS	0.896	0.761	1	0.448	0.38	0.522	CLONAL	1	TRUE	1	0.315862375551673	3		381	401	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109989	115109989	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	59	486	1	ENST00000257566.3:c.1889A>T	p.Asn630Ile	p.N630I	ENST00000257566	NM_016569.3	630	aAt/aTt	8/8	0.315862375551673	3	FACETS	0.915	0.788	1	0.457	0.394	0.526	CLONAL	1	TRUE	1	0.315862375551673	3		487	473	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118720	115118721	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	65	455	0	ENST00000257566.3:c.620dup	p.Lys208GlufsTer19	p.K208Efs*19	ENST00000257566	NM_016569.3	207	ctg/ctTg	2/8	0.315862375551673	3	FACETS	0.82	0.711	0.938	0.41	0.355	0.469	CLONAL	1	TRUE	1	0.315862375551673	3		455	581	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842404	68842407	+	frameshift_variant	Frame_Shift_Del	DEL	CTGG	CTGG	-	novel	NA	P-0036259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	142	427	0	ENST00000261769.5:c.465_468del	p.Asp155GlufsTer59	p.D155Efs*59	ENST00000261769	NM_004360.3	155	gaCTGG/ga	4/16	0.315862375551673	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.315862375551673	2		427	401	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0036261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	72	588	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.538	0.469	0.613	0.538	0.469	0.613	SUBCLONAL	1	TRUE	1	0.329673461475886	2		588	812	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0036261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	72	303	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.937	0.821	1	0.937	0.821	1	CLONAL	1	TRUE	1	0.329673461475886	2		303	466	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0036261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	169	586	3	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	0.329673461475886	2	FACETS	0.988	0.915	1	0.988	0.915	1	CLONAL	2	TRUE	0	0.329673461475886	2		589	519	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614940	23614940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	97	407	0	ENST00000261584.4:c.3401C>T	p.Ser1134Phe	p.S1134F	ENST00000261584	NM_024675.3	1134	tCt/tTt	13/13	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.329673461475886	2		407	548	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355353	15355353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201062276	NA	P-0036261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	73	346	0	ENST00000263377.2:c.2270C>T	p.Pro757Leu	p.P757L	ENST00000263377	NM_058243.2	757	cCg/cTg	13/20	0.215261925903556	3	FACETS	0.871	0.763	0.988	0.436	0.381	0.494	CLONAL	1	TRUE	1	0.329673461475886	3		346	592	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213962	36213962	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	197	651	0	ENST00000222270.7:c.2788G>T	p.Ala930Ser	p.A930S	ENST00000222270	NM_014727.1	930	Gca/Tca	6/37	0.329673461475886	3	FACETS	1	0.986	1	0.64	0.592	0.69	CLONAL	1	TRUE	1	0.329673461475886	3		651	1087	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499426	89499426	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	85	478	1	ENST00000336596.2:c.2596A>C	p.Asn866His	p.N866H	ENST00000336596	NM_005233.5	866	Aac/Cac	15/17	1	2	FACETS	0.867	0.767	0.973	0.867	0.767	0.973	CLONAL	1	TRUE	1	0.329673461475886	2		479	595	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0036262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	43	490	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.271377392395752	1	FACETS	0.408	0.341	0.483	0.408	0.341	0.483	SUBCLONAL	1	FALSE	0	0.271377392395752	1		490	671	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639102	3639102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550419924	NA	P-0036262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	46	720	1	ENST00000294008.3:c.4537G>A	p.Val1513Ile	p.V1513I	ENST00000294008	NM_032444.2	1513	Gtt/Att	12/15	1	2	FACETS	0.581	0.489	0.684	0.581	0.489	0.684	SUBCLONAL	1	FALSE	1	0.271377392395752	2		721	583	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757274881	NA	P-0036262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	57	743	0	ENST00000269305.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	144	Cag/Tag	5/11	1	2	FACETS	0.608	0.521	0.703	0.608	0.521	0.703	SUBCLONAL	1	FALSE	1	0.271377392395752	2		743	691	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584607	48584607	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	42	485	0	ENST00000342988.3:c.781del	p.His261IlefsTer75	p.H261Ifs*75	ENST00000342988	NM_005359.5	260	taC/ta	6/12	0.271377392395752	1	FACETS	0.575	0.48	0.681	0.575	0.48	0.681	SUBCLONAL	1	FALSE	0	0.271377392395752	1		485	465	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099982	157099982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	25	139	0	ENST00000346085.5:c.919G>A	p.Gly307Ser	p.G307S	ENST00000346085	NM_020732.3	307	Ggc/Agc	1/20	0.271377392395752	1	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	FALSE	0	0.271377392395752	1		139	135	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6029479	6029479	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs141769057	NA	P-0036262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	69	468	0	ENST00000265849.7:c.1096G>C	p.Asp366His	p.D366H	ENST00000265849	NM_000535.5	366	Gat/Cat	10/15	0.271377392395752	3	FACETS	0.655	0.569	0.748	0.327	0.284	0.374	SUBCLONAL	1	FALSE	1	0.271377392395752	3		468	882	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0036263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	69	544	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.941	0.819	1	0.941	0.819	1	CLONAL	1	TRUE	1	0.199486039595392	2		544	735	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0036263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	75	296	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	0.199486039595392	2	FACETS	1	0.972	1	0.703	0.617	0.795	CLONAL	1	TRUE	0	0.199486039595392	2		296	535	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577138	7577138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780075	NA	P-0036263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	69	485	1	ENST00000269305.4:c.800G>A	p.Arg267Gln	p.R267Q	ENST00000269305	NM_001126112.2	267	cGg/cAg	8/11	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.199486039595392	2		486	649	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519896	NA	P-0036263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	62	282	0	ENST00000281708.4:c.1514G>T	p.Arg505Leu	p.R505L	ENST00000281708	NM_033632.3	505	cGc/cTc	10/12	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.199486039595392	2		282	490	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45422959	45422959	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	57	362	2	ENST00000262160.6:c.169C>T	p.Arg57Ter	p.R57*	ENST00000262160	NM_005901.5	57	Cga/Tga	2/11	1	2	FACETS	0.878	0.752	1	0.878	0.752	1	CLONAL	1	TRUE	1	0.199486039595392	2		364	651	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101006	27101006	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	58	552	0	ENST00000324856.7:c.4288C>T	p.Gln1430Ter	p.Q1430*	ENST00000324856	NM_006015.4	1430	Cag/Tag	18/20	1	2	FACETS	0.892	0.766	1	0.892	0.766	1	CLONAL	1	TRUE	1	0.199486039595392	2		552	652	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631271	117631271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	53	365	0	ENST00000368508.3:c.6407G>A	p.Gly2136Glu	p.G2136E	ENST00000368508	NM_002944.2	2136	gGa/gAa	40/43	1	2	FACETS	0.934	0.796	1	0.934	0.796	1	CLONAL	1	TRUE	1	0.199486039595392	2		365	569	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482864	67482864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555414503	NA	P-0036263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	115	370	1	ENST00000327367.4:c.1268G>A	p.Ser423Asn	p.S423N	ENST00000327367	NM_005902.3	423	aGt/aAt	9/9	0.163391428215851	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	0	0.199486039595392	2		371	553	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334828	81334828	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs769585774	NA	P-0036263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	116	370	0	ENST00000222390.5:c.1888C>T	p.Arg630Ter	p.R630*	ENST00000222390	NM_000601.4	630	Cga/Tga	17/18	0.197950758275983	3	FACETS	0.939	0.848	1	0.939	0.848	1	CLONAL	2	TRUE	1	0.199486039595392	3		370	681	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119787	70119788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	68	456	0	ENST00000245479.2:c.790dup	p.Arg264LysfsTer32	p.R264Kfs*32	ENST00000245479	NM_000346.3	263	-/A	3/3	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.199486039595392	2		456	544	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45422986	45422986	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	51	365	0	ENST00000262160.6:c.142C>G	p.Leu48Val	p.L48V	ENST00000262160	NM_005901.5	48	Ctg/Gtg	2/11	1	2	FACETS	0.859	0.73	1	0.859	0.73	1	CLONAL	1	TRUE	1	0.199486039595392	2		365	595	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355321	81355321	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	72	288	0	ENST00000222390.5:c.1053A>C	p.Glu351Asp	p.E351D	ENST00000222390	NM_000601.4	351	gaA/gaC	9/18	0.197950758275983	3	FACETS	0.76	0.665	0.862	0.76	0.665	0.862	SUBCLONAL	2	TRUE	1	0.199486039595392	3		288	522	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841000	15841000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754101239	NA	P-0036264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	177	272	0	ENST00000307771.7:c.1084G>A	p.Glu362Lys	p.E362K	ENST00000307771	NM_005089.3	362	Gaa/Aaa	11/11	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.753224977900918	1		272	252	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123635	108123635	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	130	389	0	ENST00000278616.4:c.1894G>C	p.Glu632Gln	p.E632Q	ENST00000278616	NM_000051.3	632	Gaa/Caa	12/63	1	2	FACETS	0.93	0.854	1	0.93	0.854	1	CLONAL	1	TRUE	1	0.753224977900918	2		389	371	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444206	49444206	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	212	790	0	ENST00000301067.7:c.3165G>C	p.Leu1055Phe	p.L1055F	ENST00000301067	NM_003482.3	1055	ttG/ttC	11/54	1	2	FACETS	0.858	0.801	0.916	0.858	0.801	0.916	CLONAL	1	TRUE	1	0.753224977900918	2		790	656	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176145127	176145127	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	151	401	0	ENST00000367669.3:c.484C>T	p.Gln162Ter	p.Q162*	ENST00000367669	NM_022457.5	162	Cag/Tag	3/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.753224977900918	2		401	378	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982105	201982105	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0036264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	265	634	0	ENST00000359651.3:c.629C>G	p.Ser210Ter	p.S210*	ENST00000359651		210	tCa/tGa	5/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.753224977900918	2		634	650	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982137	201982137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	273	631	0	ENST00000359651.3:c.661C>T	p.Pro221Ser	p.P221S	ENST00000359651		221	Ccc/Tcc	5/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.753224977900918	2		631	645	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120663	115120663	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	208	714	0	ENST00000257566.3:c.343C>G	p.Gln115Glu	p.Q115E	ENST00000257566	NM_016569.3	115	Cag/Gag	1/8	1	2	FACETS	0.947	0.885	1	0.947	0.885	1	CLONAL	1	TRUE	1	0.753224977900918	2		714	583	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123889456	123889456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1289258468	NA	P-0036264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	107	344	0	ENST00000330479.4:c.683G>A	p.Arg228Lys	p.R228K	ENST00000330479	NM_020382.3	228	aGg/aAg	7/9	1	2	FACETS	0.953	0.867	1	0.953	0.867	1	CLONAL	1	TRUE	1	0.753224977900918	2		344	298	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600380	10600380	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	234	702	0	ENST00000171111.5:c.1475C>G	p.Pro492Arg	p.P492R	ENST00000171111	NM_203500.1	492	cCa/cGa	4/6	0.753224977900918	1	FACETS	0.952	0.903	1	0.952	0.903	1	CLONAL	1	TRUE	0	0.753224977900918	1		702	407	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661300	227661300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	243	708	0	ENST00000305123.5:c.2155G>A	p.Glu719Lys	p.E719K	ENST00000305123	NM_005544.2	719	Gag/Aag	1/2	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.753224977900918	2		708	629	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955158	93955158	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	128	476	0	ENST00000369303.4:c.2740C>G	p.Leu914Val	p.L914V	ENST00000369303	NM_004440.3	914	Ctt/Gtt	16/17	1	2	FACETS	0.823	0.752	0.896	0.823	0.752	0.896	CLONAL	1	TRUE	1	0.753224977900918	2		476	413	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040680	47040680	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	240	346	0	ENST00000377604.3:c.1315C>T	p.Gln439Ter	p.Q439*	ENST00000377604	NM_001204468.1	439	Caa/Taa	13/24	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.753224977900918	1		346	315	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0036265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	98	307	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.393277119985595	2		307	360	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954359	48954377	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GTAATGGCCACATATAGCA	GTAATGGCCACATATAGCA	-	novel	NA	P-0036266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	37	400	0	ENST00000267163.4:c.1484_1498+4del		p.VMATYSR494fs	ENST00000267163	NM_000321.2	494	GTAATGGCCACATATAGCAga/ga	16/27	0.411434071383128	1	FACETS	0.412	0.34	0.492	0.412	0.34	0.492	SUBCLONAL	1	TRUE	0	0.411434071383128	1		400	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579329	7579330	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCTGTCCCA	novel	NA	P-0036266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	146	501	0	ENST00000269305.4:c.348_357dup	p.Lys120TrpfsTer32	p.K120Wfs*32	ENST00000269305	NM_001126112.2	119	-/TGGGACAGCC	4/11	0.411434071383128	1	FACETS	0.959	0.879	1	0.959	0.879	1	CLONAL	1	TRUE	0	0.411434071383128	1		501	588	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272196	15272282	+	inframe_deletion	In_Frame_Del	DEL	GCCCCGCCCCCGGGGCCCCTGCGGCCCCAGCCCCGCCTTCCCGGGGGGCCTCCTGCTCTTCTTGGACCCCGACTGTGCCGCTTTGAG	GCCCCGCCCCCGGGGCCCCTGCGGCCCCAGCCCCGCCTTCCCGGGGGGCCTCCTGCTCTTCTTGGACCCCGACTGTGCCGCTTTGAG	-	novel	NA	P-0036266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	19	354	0	ENST00000263388.2:c.6157_6243del	p.Leu2053_Gly2081del	p.L2053_G2081del	ENST00000263388	NM_000435.2	2053	CTCAAAGCGGCACAGTCGGGGTCCAAGAAGAGCAGGAGGCCCCCCGGGAAGGCGGGGCTGGGGCCGCAGGGGCCCCGGGGGCGGGGC/-	33/33	0.411434071383128	1	FACETS	0.231	0.175	0.298	0.231	0.175	0.298	SUBCLONAL	1	TRUE	0	0.411434071383128	1		354	317	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0036267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	28	344	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.129276000713315	0	FACETS	0.145	0.116	0.179			1	INDETERMINATE	1	FALSE	0	0.523209774246451	0		344	351	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0036267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	10	362	1	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	0.129276000713315	0	FACETS	0.051	0.034	0.073			1	INDETERMINATE	1	FALSE	0	0.523209774246451	0		363	355	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0036267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	68	421	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	0.187612711342901	4	FACETS	0.87	0.759	0.989	0.435	0.379	0.495	INDETERMINATE	1	FALSE	2	0.523209774246451	4		421	455	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0036268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	141	448	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.532793148413926	2		448	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0036268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	229	597	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.532793148413926	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.532793148413926	1		597	562	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956956	2956956	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs750486472	NA	P-0036268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	274	491	0	ENST00000396946.4:c.2671C>T	p.Arg891Ter	p.R891*	ENST00000396946	NM_032415.4	891	Cga/Tga	20/25	0.114686784024677	4	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.532793148413926	4		491	682	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120175	70120175	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	114	363	0	ENST00000245479.2:c.1177C>T	p.Gln393Ter	p.Q393*	ENST00000245479	NM_000346.3	393	Cag/Tag	3/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.532793148413926	2		363	365	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272449	11272449	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	146	461	0	ENST00000361445.4:c.3481C>T	p.Arg1161Ter	p.R1161*	ENST00000361445	NM_004958.3	1161	Cga/Tga	23/58	1	2	FACETS	0.956	0.877	1	0.956	0.877	1	CLONAL	1	TRUE	1	0.532793148413926	2		461	573	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289953	15289953	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772172068	NA	P-0036268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	208	685	0	ENST00000263388.2:c.3601C>T	p.Arg1201Cys	p.R1201C	ENST00000263388	NM_000435.2	1201	Cgc/Tgc	22/33	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.532793148413926	2		685	727	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221226	1221226	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876661238	NA	P-0036268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	179	553	2	ENST00000326873.7:c.749C>T	p.Thr250Met	p.T250M	ENST00000326873	NM_000455.4	250	aCg/aTg	6/10	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.532793148413926	2		555	668	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102196203	102196203	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	131	352	0	ENST00000263464.3:c.860G>A	p.Ser287Asn	p.S287N	ENST00000263464	NM_001165.4	287	aGt/aAt	3/9	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.532793148413926	2		352	417	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554681	63554681	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	148	440	0	ENST00000307078.5:c.58G>T	p.Asp20Tyr	p.D20Y	ENST00000307078	NM_004655.3	20	Gat/Tat	2/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.532793148413926	2		440	511	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972106	55972106	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	122	334	0	ENST00000263923.4:c.1538C>G	p.Thr513Ser	p.T513S	ENST00000263923	NM_002253.2	513	aCt/aGt	12/30	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.532793148413926	2		334	428	SUCCESS
APC	324	MSKCC	GRCh37	5	112173531	112173532	+	stop_gained	Nonsense_Mutation	DNP	CA	CA	AG	novel	NA	P-0036268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	101	302	0	ENST00000257430.4:c.2240_2241delinsAG	p.Ser747Ter	p.S747*	ENST00000257430	NM_000038.5	747	tCA/tAG	16/16	1	2	FACETS	0.945	0.851	1	0.945	0.851	1	CLONAL	1	TRUE	1	0.532793148413926	2		302	401	SUCCESS
APC	324	MSKCC	GRCh37	5	112175634	112175634	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	107	301	0	ENST00000257430.4:c.4344del	p.Lys1449SerfsTer24	p.K1449Sfs*24	ENST00000257430	NM_000038.5	1448	aCc/ac	16/16	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.532793148413926	2		301	389	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0036269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	86	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.46798258600485	2		452	337	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591889	48591889	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	127	536	1	ENST00000342988.3:c.1052A>G	p.Asp351Gly	p.D351G	ENST00000342988	NM_005359.5	351	gAt/gGt	9/12	0.46798258600485	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.46798258600485	1		537	363	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741958	145741958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs565903685	NA	P-0036269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	58	641	0	ENST00000428558.2:c.545G>A	p.Arg182Gln	p.R182Q	ENST00000428558	NM_004260.3	182	cGg/cAg	5/22	1	2	FACETS	0.286	0.245	0.331	0.286	0.245	0.331	SUBCLONAL	1	TRUE	1	0.46798258600485	2		641	866	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351803	89351803	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs371142732	NA	P-0036269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	214	852	0	ENST00000301030.4:c.1147A>G	p.Ile383Val	p.I383V	ENST00000301030	NM_001256183.1	383	Ata/Gta	9/13	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.46798258600485	2		852	858	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0036270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	143	490	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.237185346869825	3	FACETS	0.899	0.821	0.981	0.899	0.821	0.981	CLONAL	2	TRUE	1	0.237185346869825	3		490	750	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715678	30715678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039551	NA	P-0036270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	123	402	0	ENST00000295754.5:c.1336G>A	p.Asp446Asn	p.D446N	ENST00000295754	NM_003242.5	446	Gat/Aat	5/7	0.226589333739953	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	2	TRUE	0	0.237185346869825	2		402	513	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210506	5210506	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	75	647	0	ENST00000357368.4:c.5461C>T	p.Arg1821Ter	p.R1821*	ENST00000357368	NM_002850.3	1821	Cga/Tga	35/38	1	2	FACETS	0.971	0.851	1	0.971	0.851	1	CLONAL	1	TRUE	1	0.237185346869825	2		647	651	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0036276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	176	348	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	1	2	FACETS	0.926	0.859	0.995	1	0.994	1	CLONAL	3	TRUE	1	0.23540648012187	2		348	538	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0036276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	58	598	1	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.574	0.492	0.665	0.574	0.492	0.665	SUBCLONAL	1	TRUE	1	0.23540648012187	2		599	858	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127164	22127164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057519911	NA	P-0036276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	24	570	0	ENST00000215832.6:c.964G>A	p.Glu322Lys	p.E322K	ENST00000215832	NM_002745.4	322	Gag/Aag	7/9	1	2	FACETS	0.342	0.267	0.429	0.342	0.267	0.429	SUBCLONAL	1	TRUE	1	0.23540648012187	2		570	596	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0036276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	90	672	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.235480330306523	0	FACETS	0.949	0.843	1			1	CLONAL	1	TRUE	0	0.23540648012187	0		672	616	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835794	68835794	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	212	481	0	ENST00000261769.5:c.385C>T	p.Gln129Ter	p.Q129*	ENST00000261769	NM_004360.3	129	Cag/Tag	3/16	0.235480330306523	0	FACETS	0.939	0.881	0.997			1	CLONAL	3	TRUE	0	0.23540648012187	0		481	489	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031973	26031973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	42	389	0	ENST00000244661.2:c.316G>A	p.Glu106Lys	p.E106K	ENST00000244661	NM_003537.3	106	Gag/Aag	1/1	0.143560002457469	4	FACETS	0.742	0.619	0.88	0.371	0.309	0.44	SUBCLONAL	1	TRUE	2	0.23540648012187	4		389	594	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913495	NA	P-0036276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	241	512	1	ENST00000371085.3:c.602G>T	p.Arg201Leu	p.R201L	ENST00000371085	NM_000516.4	201	cGt/cTt	8/13	1	2	FACETS	0.834	0.781	0.889	1	0.995	1	CLONAL	3	TRUE	1	0.23540648012187	2		513	818	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678735	52678735	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0036276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	43	572	0	ENST00000394830.3:c.884C>G	p.Ser295Ter	p.S295*	ENST00000394830	NM_018313.4	295	tCa/tGa	9/30	0.235480330306523	0	FACETS	0.503	0.421	0.595			1	SUBCLONAL	1	TRUE	0	0.23540648012187	0		572	555	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959097	28959097	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	147	501	0	ENST00000282397.4:c.2041G>C	p.Asp681His	p.D681H	ENST00000282397	NM_002019.4	681	Gac/Cac	14/30	1	2	FACETS	0.892	0.816	0.971	1	0.99	1	CLONAL	2	TRUE	1	0.23540648012187	2		501	700	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106238	27106238	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	199	657	0	ENST00000324856.7:c.5850del	p.Asn1951ThrfsTer5	p.N1951Tfs*5	ENST00000324856	NM_006015.4	1950	cGg/cg	20/20	1	2	FACETS	1	0.977	1	1	0.994	1	CLONAL	2	TRUE	1	0.23540648012187	2		657	753	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061087	38061190	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGCGCCAGAGGGGTCCTTGCGGCTCTCAGGGCCGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTT	GAGGCGCCAGAGGGGTCCTTGCGGCTCTCAGGGCCGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTT	-	novel	NA	P-0036276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	258	211	0	ENST00000250448.2:c.799_902del	p.Lys267Ter	p.K267*	ENST00000250448	NM_004496.3	267	AAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGCGGCGCCAAGGGCGGCCCTGAGAGCCGCAAGGACCCCTCTGGCGCCTCt/t	2/2	1	2	FACETS	0.966	0.918	1	1	0.997	1	CLONAL	5	TRUE	1	0.23540648012187	2		211	454	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041125	42041125	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	214	533	0	ENST00000219905.7:c.5503G>A	p.Gly1835Arg	p.G1835R	ENST00000219905	NM_001164273.1	1835	Ggg/Agg	16/24	1	2	FACETS	1	0.985	1	1	0.995	1	CLONAL	2	TRUE	1	0.23540648012187	2		533	762	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579558	7579558	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs754332870	NA	P-0036276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	85	673	1	ENST00000269305.4:c.129G>C	p.Leu43Phe	p.L43F	ENST00000269305	NM_001126112.2	43	ttG/ttC	4/11	0.235480330306523	0	FACETS	0.883	0.782	0.992			1	CLONAL	1	TRUE	0	0.23540648012187	0		674	625	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004666	16004666	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	91	635	0	ENST00000268712.3:c.2588C>G	p.Ala863Gly	p.A863G	ENST00000268712	NM_006311.3	863	gCt/gGt	20/46	0.235480330306523	1	FACETS	0.973	0.864	1	0.973	0.864	1	CLONAL	1	TRUE	0	0.23540648012187	1		635	701	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16041519	16041519	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	28	323	0	ENST00000268712.3:c.1360C>T	p.Gln454Ter	p.Q454*	ENST00000268712	NM_006311.3	454	Cag/Tag	13/46	0.235480330306523	1	FACETS	0.526	0.42	0.647	0.526	0.42	0.647	SUBCLONAL	1	TRUE	0	0.23540648012187	1		323	399	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121021	3121021	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	37	626	0	ENST00000078429.4:c.924C>A	p.Phe308Leu	p.F308L	ENST00000078429	NM_002067.2	308	ttC/ttA	7/7	1	2	FACETS	0.431	0.354	0.517	0.431	0.354	0.517	SUBCLONAL	1	TRUE	1	0.23540648012187	2		626	730	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281173	15281173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1231	565	775	0	ENST00000263388.2:c.5083G>A	p.Glu1695Lys	p.E1695K	ENST00000263388	NM_000435.2	1695	Gaa/Aaa	27/33	0.23540648012187	9	FACETS	0.975	0.935	1			1	CLONAL	5	TRUE	NA	0.23540648012187	9		775	1796	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022258	26022258	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	71	616	0	ENST00000435504.4:c.399G>C	p.Arg133Ser	p.R133S	ENST00000435504		133	agG/agC	5/13	1	2	FACETS	0.737	0.642	0.84	0.737	0.642	0.84	SUBCLONAL	1	TRUE	1	0.23540648012187	2		616	818	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279555	123279575	+	inframe_deletion	In_Frame_Del	DEL	GCTTGATCCACTGGATGTGGG	GCTTGATCCACTGGATGTGGG	-	novel	NA	P-0036277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	499	644	0	ENST00000358487.5:c.857_877del	p.Pro286_Lys292del	p.P286_K292del	ENST00000358487	NM_000141.4	286	cCCCACATCCAGTGGATCAAGCac/cac	7/18	NA	2	FACETS	0.953	0.925	0.981			1	INDETERMINATE	2	TRUE	NA	0.737103124013251	2		644	710	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267022	41267023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	228	499	1	ENST00000349496.5:c.696dup	p.Lys233Ter	p.K233*	ENST00000349496	NM_001904.3	231	-/T	5/15	0.737103124013251	1	FACETS	0.928	0.878	0.977	0.928	0.878	0.977	CLONAL	1	TRUE	0	0.737103124013251	1		500	421	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442499	52442517	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGAACATGTTATTCACA	AAAGAACATGTTATTCACA	-	novel	NA	P-0036277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	155	467	0	ENST00000460680.1:c.228_246del	p.Ile76MetfsTer5	p.I76Mfs*5	ENST00000460680	NM_004656.3	76	atTGTGAATAACATGTTCTTT/at	4/17	0.737103124013251	1	FACETS	0.885	0.826	0.944	0.885	0.826	0.944	CLONAL	1	TRUE	0	0.737103124013251	1		467	300	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432664	29432664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113994087	NA	P-0121450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	217	556	2	ENST00000389048.3:c.3824G>A	p.Arg1275Gln	p.R1275Q	ENST00000389048	NM_004304.4	1275	cGa/cAa	25/29	1	2	FACETS	0.943	0.883	1	0.943	0.883	1	CLONAL	1	NA	1	0.76956447963393	2		558	598	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	117	214	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.927	0.839	1	0.927	0.839	1	CLONAL	1	TRUE	1	0.458184559774876	2		214	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0036280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	266	801	1	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.428598749029408	1	FACETS	0.934	0.877	0.993	0.934	0.877	0.993	CLONAL	1	TRUE	0	0.458184559774876	1		802	958	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257426	19257426	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	312	887	0	ENST00000162023.5:c.707G>T	p.Cys236Phe	p.C236F	ENST00000162023		236	tGc/tTc	11/13	1	2	FACETS	0.956	0.9	1	0.956	0.9	1	CLONAL	1	TRUE	1	0.458184559774876	2		887	1425	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257442	19257442	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	321	866	1	ENST00000162023.5:c.691G>T	p.Gly231Cys	p.G231C	ENST00000162023		231	Ggc/Tgc	11/13	1	2	FACETS	0.987	0.931	1	0.987	0.931	1	CLONAL	1	TRUE	1	0.458184559774876	2		867	1419	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932688	49932688	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	285	890	3	ENST00000296474.3:c.3183C>A	p.Asp1061Glu	p.D1061E	ENST00000296474	NM_002447.2	1061	gaC/gaA	14/20	1	2	FACETS	0.984	0.924	1	0.984	0.924	1	CLONAL	1	TRUE	1	0.458184559774876	2		893	1264	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485908	8485908	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	172	615	0	ENST00000356435.5:c.2909A>G	p.Gln970Arg	p.Q970R	ENST00000356435		970	cAg/cGg	17/35	1	2	FACETS	0.979	0.902	1	0.979	0.902	1	CLONAL	1	TRUE	1	0.458184559774876	2		615	767	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867546	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGC	GGCGGCGGC	-	rs11466445	NA	P-0036282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	16	31	1	ENST00000374994.4:c.70_78del	p.Ala24_Ala26del	p.A24_A26del	ENST00000374994	NM_004612.2	17	ctGGCGGCGGCg/ctg	1/9	0.209952752101244	4	FACETS	1	0.903	1	0.737	0.561	0.935	INDETERMINATE	1	TRUE	2	0.525261317058579	4		32	63	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061468	38061468	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	92	588	0	ENST00000250448.2:c.521C>A	p.Ser174Ter	p.S174*	ENST00000250448	NM_004496.3	174	tCg/tAg	2/2	0.175010642011911	2	FACETS	0.551	0.49	0.616	0.275	0.245	0.308	INDETERMINATE	1	TRUE	0	0.525261317058579	2		588	636	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129309	2129309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1443030830	NA	P-0036282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1154	113	795	0	ENST00000219476.3:c.3164G>A	p.Gly1055Asp	p.G1055D	ENST00000219476	NM_000548.3	1055	gGc/gAc	28/42	0.435858718085393	5	FACETS	0.607	0.545	0.674	0.152	0.136	0.169	SUBCLONAL	1	TRUE	1	0.525261317058579	5		795	1267	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	117	645	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.855	0.771	0.945	0.855	0.771	0.945	CLONAL	1	TRUE	1	0.33	2		648	829	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	116	627	6	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.912	0.822	1	0.912	0.822	1	CLONAL	1	TRUE	1	0.33	2		633	771	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	99	303	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.262415476933126	3	FACETS	0.857	0.77	0.947	0.857	0.77	0.947	CLONAL	2	TRUE	1	0.33	3		303	408	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	59	863	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.696	0.599	0.801	0.696	0.599	0.801	SUBCLONAL	1	TRUE	1	0.33	2		863	514	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	71	514	8	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.971	0.851	1	0.971	0.851	1	CLONAL	1	TRUE	1	0.33	2		522	443	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	64	460	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.894	0.776	1	0.894	0.776	1	CLONAL	1	TRUE	1	0.33	2		460	434	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	62	448	1	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	1	2	FACETS	0.643	0.556	0.739	0.643	0.556	0.739	SUBCLONAL	1	TRUE	1	0.33	2		449	584	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143440	30143440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	82	356	1	ENST00000389048.3:c.86C>T	p.Ala29Val	p.A29V	ENST00000389048	NM_004304.4	29	gCg/gTg	1/29	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.33	2		357	438	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	78	518	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.33	2		518	456	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	90	517	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.806	0.715	0.902	0.806	0.715	0.902	CLONAL	1	TRUE	1	0.33	2		518	677	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444933	49444933	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767415197	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	97	469	4	ENST00000301067.7:c.2533del	p.Arg845GlyfsTer85	p.R845Gfs*85	ENST00000301067	NM_003482.3	845	Cgg/gg	10/54	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.33	2		473	581	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	120	541	1	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.887	0.801	0.978	0.887	0.801	0.978	CLONAL	1	TRUE	1	0.33	2		542	820	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	50	521	1	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	0.775	0.659	0.901	0.775	0.659	0.901	CLONAL	1	TRUE	1	0.33	2		522	391	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	25	406	0	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS	0.631	0.499	0.782	0.631	0.499	0.782	SUBCLONAL	1	TRUE	1	0.33	2		406	240	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164828	47164828	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764693453	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	73	371	0	ENST00000409792.3:c.1298G>A	p.Arg433His	p.R433H	ENST00000409792	NM_014159.6	433	cGc/cAc	3/21	1	2	FACETS	0.947	0.831	1	0.947	0.831	1	CLONAL	1	TRUE	1	0.33	2		371	467	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	132	654	5	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	1	2	FACETS	0.861	0.781	0.946	0.861	0.781	0.946	CLONAL	1	TRUE	1	0.33	2		659	929	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	23	142	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	0.637	0.498	0.795	0.637	0.498	0.795	SUBCLONAL	1	TRUE	1	0.33	2		142	219	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216546	108216546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529296539	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	48	503	0	ENST00000278616.4:c.8495G>A	p.Arg2832His	p.R2832H	ENST00000278616	NM_000051.3	2832	cGt/cAt	58/63	1	2	FACETS	0.752	0.637	0.877	0.752	0.637	0.877	SUBCLONAL	1	TRUE	1	0.33	2		503	387	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877366	28877366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1392528455	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	75	448	1	ENST00000282397.4:c.3955G>A	p.Ala1319Thr	p.A1319T	ENST00000282397	NM_002019.4	1319	Gcg/Acg	30/30	1	2	FACETS	0.689	0.603	0.781	0.689	0.603	0.781	SUBCLONAL	1	TRUE	1	0.33	2		449	660	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	100	495	6	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.995	0.891	1	0.995	0.891	1	CLONAL	1	TRUE	1	0.33	2		501	609	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898755	134898755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs546798910	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	84	422	0	ENST00000398015.3:c.1813G>A	p.Glu605Lys	p.E605K	ENST00000398015	NM_004441.4	605	Gaa/Aaa	10/16	1	2	FACETS	0.948	0.839	1	0.948	0.839	1	CLONAL	1	TRUE	1	0.33	2		422	537	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602335	10602335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	105	698	1	ENST00000171111.5:c.1243C>T	p.Arg415Cys	p.R415C	ENST00000171111	NM_203500.1	415	Cgc/Tgc	3/6	1	2	FACETS	0.664	0.593	0.738	0.664	0.593	0.738	SUBCLONAL	1	TRUE	1	0.33	2		699	959	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919631	28919631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200840674	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	69	494	1	ENST00000282397.4:c.2306C>T	p.Ala769Val	p.A769V	ENST00000282397	NM_002019.4	769	gCg/gTg	16/30	1	2	FACETS	0.642	0.559	0.732	0.642	0.559	0.732	SUBCLONAL	1	TRUE	1	0.33	2		495	651	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781375	3781375	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	117	633	1	ENST00000262367.5:c.4990C>T	p.Arg1664Cys	p.R1664C	ENST00000262367	NM_004380.2	1664	Cgc/Tgc	30/31	1	2	FACETS	0.909	0.82	1	0.909	0.82	1	CLONAL	1	TRUE	1	0.33	2		634	780	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827201	72827201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138835662	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	87	517	1	ENST00000268489.5:c.9380C>T	p.Pro3127Leu	p.P3127L	ENST00000268489	NM_006885.3	3127	cCg/cTg	9/10	1	2	FACETS	0.774	0.686	0.869	0.774	0.686	0.869	SUBCLONAL	1	TRUE	1	0.33	2		518	681	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799131	42799131	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	140	688	2	ENST00000575354.2:c.4620del	p.Thr1541LeufsTer79	p.T1541Lfs*79	ENST00000575354	NM_015125.3	1539	Ccc/cc	20/20	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.33	2		690	828	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492894	56492894	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	81	345	0	ENST00000407977.2:c.45G>A	p.Trp15Ter	p.W15*	ENST00000407977		15	tgG/tgA	2/10	1	2	FACETS	0.963	0.85	1	0.963	0.85	1	CLONAL	1	TRUE	1	0.33	2		345	510	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413710	138413710	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	98	374	2	ENST00000289153.2:c.1810del	p.Arg604GlyfsTer4	p.R604Gfs*4	ENST00000289153	NM_006219.2	604	Cgg/gg	12/22	1	2	FACETS	0.958	0.856	1	0.958	0.856	1	CLONAL	1	TRUE	1	0.33	2		376	620	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487212	56487212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144549266	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	92	565	0	ENST00000267101.3:c.1358G>A	p.Arg453His	p.R453H	ENST00000267101	NM_001982.3	453	cGt/cAt	12/28	1	2	FACETS	0.805	0.715	0.9	0.805	0.715	0.9	CLONAL	1	TRUE	1	0.33	2		565	693	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481648	56481648	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs774589520	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	146	725	0	ENST00000267101.3:c.683A>G	p.His228Arg	p.H228R	ENST00000267101	NM_001982.3	228	cAt/cGt	6/28	1	2	FACETS	0.908	0.828	0.993	0.908	0.828	0.993	CLONAL	1	TRUE	1	0.33	2		725	974	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119096	70119096	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	56	315	1	ENST00000245479.2:c.672del	p.Gly225AlafsTer28	p.G225Afs*28	ENST00000245479	NM_000346.3	223	tCc/tc	2/3	1	2	FACETS	0.895	0.77	1	0.895	0.77	1	CLONAL	1	TRUE	1	0.33	2		316	379	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324917	31324917	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	109	494	0	ENST00000412585.2:c.19del	p.Arg7GlufsTer13	p.R7Efs*13	ENST00000412585	NM_005514.6	7	Cga/ga	1/8	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.33	2		494	598	SUCCESS
YES1	7525	MSKCC	GRCh37	18	751705	751705	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs374613149	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	47	457	0	ENST00000314574.4:c.371C>T	p.Thr124Met	p.T124M	ENST00000314574	NM_005433.3	124	aCg/aTg	3/12	1	2	FACETS	0.68	0.575	0.795	0.68	0.575	0.795	SUBCLONAL	1	TRUE	1	0.33	2		457	419	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481637	20481637	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	42	257	0	ENST00000346618.3:c.710del	p.Asn237ThrfsTer27	p.N237Tfs*27	ENST00000346618	NM_001949.4	236	Aaa/aa	3/7	0.3	1	FACETS	0.711	0.596	0.837	0.711	0.596	0.837	SUBCLONAL	1	TRUE	0	0.33	1		257	299	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350138	81350138	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	63	461	0	ENST00000222390.5:c.1194T>A	p.Asn398Lys	p.N398K	ENST00000222390	NM_000601.4	398	aaT/aaA	10/18	0.262415476933126	3	FACETS	1	0.966	1	0.684	0.596	0.779	CLONAL	1	TRUE	1	0.33	3		461	325	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456302	32456302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	115	666	0	ENST00000332351.3:c.590C>A	p.Pro197His	p.P197H	ENST00000332351	NM_024426.4	197	cCt/cAt	1/10	1	2	FACETS	0.921	0.83	1	0.921	0.83	1	CLONAL	1	TRUE	1	0.33	2		666	757	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941317	71941317	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	110	558	0	ENST00000298229.2:c.1090+2T>C		p.X364_splice	ENST00000298229	NM_001567.3	364			1	2	FACETS	0.902	0.811	0.999	0.902	0.811	0.999	CLONAL	1	TRUE	1	0.33	2		558	739	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343133	118343133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555035885	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	66	424	0	ENST00000534358.1:c.1259G>A	p.Arg420Gln	p.R420Q	ENST00000534358	NM_005933.3	420	cGg/cAg	3/36	1	2	FACETS	0.763	0.663	0.871	0.763	0.663	0.871	SUBCLONAL	1	TRUE	1	0.33	2		424	524	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628473	21628473	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs760733648	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	61	626	0	ENST00000421138.2:c.1145A>G	p.Asp382Gly	p.D382G	ENST00000421138		382	gAt/gGt	11/16	1	2	FACETS	0.862	0.746	0.987	0.862	0.746	0.987	CLONAL	1	TRUE	1	0.33	2		626	429	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120624	115120624	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	102	649	0	ENST00000257566.3:c.382T>C	p.Ser128Pro	p.S128P	ENST00000257566	NM_016569.3	128	Tcg/Ccg	1/8	1	2	FACETS	0.749	0.67	0.834	0.749	0.67	0.834	SUBCLONAL	1	TRUE	1	0.33	2		649	825	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456316	99456316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376022845	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	71	374	0	ENST00000268035.6:c.1633G>A	p.Gly545Ser	p.G545S	ENST00000268035	NM_000875.3	545	Ggc/Agc	8/21	1	2	FACETS	0.869	0.76	0.986	0.869	0.76	0.986	CLONAL	1	TRUE	1	0.33	2		374	495	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860612	3860612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769798406	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	128	626	2	ENST00000262367.5:c.967C>T	p.Pro323Ser	p.P323S	ENST00000262367	NM_004380.2	323	Cca/Tca	3/31	1	2	FACETS	0.989	0.897	1	0.989	0.897	1	CLONAL	1	TRUE	1	0.33	2		628	784	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274219	10274219	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	61	360	0	ENST00000330684.3:c.50T>C	p.Val17Ala	p.V17A	ENST00000330684	NM_001134407.1	17	gTc/gCc	2/13	1	2	FACETS	0.856	0.74	0.98	0.856	0.74	0.98	CLONAL	1	TRUE	1	0.33	2		360	432	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944228	81944228	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	123	574	0	ENST00000359376.3:c.1837C>A	p.Leu613Ile	p.L613I	ENST00000359376	NM_002661.3	613	Ctc/Atc	18/33	1	2	FACETS	0.92	0.832	1	0.92	0.832	1	CLONAL	1	TRUE	1	0.33	2		574	810	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351769	89351769	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	178	842	4	ENST00000301030.4:c.1181del	p.Asn394IlefsTer33	p.N394Ifs*33	ENST00000301030	NM_001256183.1	394	aAt/at	9/13	1	2	FACETS	0.956	0.88	1	0.956	0.88	1	CLONAL	1	TRUE	1	0.33	2		846	1128	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588766	29588771	+	inframe_deletion	In_Frame_Del	DEL	ATGGCA	ATGGCA	-	novel	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	55	320	0	ENST00000356175.3:c.4553_4558del	p.Met1518_Ala1519del	p.M1518_A1519del	ENST00000356175	NM_000267.3	1518	ATGGCA/-	34/57	1	2	FACETS	0.786	0.674	0.908	0.786	0.674	0.908	CLONAL	1	TRUE	1	0.33	2		320	424	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322711	30322711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	48	497	0	ENST00000322652.5:c.1724G>A	p.Arg575His	p.R575H	ENST00000322652	NM_015355.2	575	cGt/cAt	14/16	1	2	FACETS	0.722	0.612	0.843	0.722	0.612	0.843	SUBCLONAL	1	TRUE	1	0.33	2		497	403	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627360	37627361	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	88	580	0	ENST00000447079.4:c.1280dup	p.Leu427PhefsTer3	p.L427Ffs*3	ENST00000447079	NM_015083.1	425	-/T	2/14	1	2	FACETS	0.717	0.635	0.805	0.717	0.635	0.805	SUBCLONAL	1	TRUE	1	0.33	2		580	744	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883986	37883986	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1364766454	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	137	644	0	ENST00000269571.5:c.3457C>T	p.Arg1153Ter	p.R1153*	ENST00000269571		1153	Cga/Tga	27/27	1	2	FACETS	0.983	0.894	1	0.983	0.894	1	CLONAL	1	TRUE	1	0.33	2		644	845	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25459827	25459827	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	114	525	0	ENST00000264709.3:c.2456T>C	p.Leu819Pro	p.L819P	ENST00000264709	NM_175629.2	819	cTg/cCg	21/23	1	2	FACETS	0.945	0.852	1	0.945	0.852	1	CLONAL	1	TRUE	1	0.33	2		525	731	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149583	202149583	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	84	495	0	ENST00000358485.4:c.1027del	p.His343ThrfsTer6	p.H343Tfs*6	ENST00000358485	NM_001080125.1	342	Ccc/cc	8/9	1	2	FACETS	0.788	0.696	0.886	0.788	0.696	0.886	SUBCLONAL	1	TRUE	1	0.33	2		495	646	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610500	215610500	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1409774815	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	71	491	0	ENST00000260947.4:c.1756A>G	p.Ser586Gly	p.S586G	ENST00000260947	NM_000465.2	586	Agt/Ggt	8/11	1	2	FACETS	0.737	0.643	0.837	0.737	0.643	0.837	SUBCLONAL	1	TRUE	1	0.33	2		491	584	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651200	45651200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	136	561	0	ENST00000407780.3:c.825G>T	p.Trp275Cys	p.W275C	ENST00000407780	NM_001283052.1	275	tgG/tgT	5/7	1	2	FACETS	0.93	0.846	1	0.93	0.846	1	CLONAL	1	TRUE	1	0.33	2		561	886	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434176	12434176	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	77	486	0	ENST00000287820.6:c.544A>G	p.Ile182Val	p.I182V	ENST00000287820	NM_015869.4	182	Atc/Gtc	4/7	1	2	FACETS	0.985	0.867	1	0.985	0.867	1	CLONAL	1	TRUE	1	0.33	2		486	474	SUCCESS
APC	324	MSKCC	GRCh37	5	112176516	112176516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199775075	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	55	302	0	ENST00000257430.4:c.5225G>A	p.Arg1742His	p.R1742H	ENST00000257430	NM_000038.5	1742	cGt/cAt	16/16	1	2	FACETS	0.813	0.697	0.939	0.813	0.697	0.939	CLONAL	1	TRUE	1	0.33	2		302	410	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721924	176721924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	104	566	0	ENST00000439151.2:c.7555G>A	p.Ala2519Thr	p.A2519T	ENST00000439151	NM_022455.4	2519	Gca/Aca	23/23	1	2	FACETS	0.834	0.747	0.926	0.834	0.747	0.926	CLONAL	1	TRUE	1	0.33	2		566	756	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112029224	112029224	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	58	316	0	ENST00000368678.4:c.345-1G>T		p.X115_splice	ENST00000368678		115			1	2	FACETS	0.971	0.838	1	0.971	0.838	1	CLONAL	1	TRUE	1	0.33	2		316	362	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979549	2979549	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	162	503	0	ENST00000396946.4:c.698A>G	p.Lys233Arg	p.K233R	ENST00000396946	NM_032415.4	233	aAg/aGg	6/25	0.262415476933126	3	FACETS	0.804	0.74	0.871	0.804	0.74	0.871	CLONAL	2	TRUE	1	0.33	3		503	711	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566264	141566264	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	103	437	0	ENST00000220592.5:c.1146+2T>C		p.X382_splice	ENST00000220592	NM_012154.3	382			1	2	FACETS	0.923	0.827	1	0.923	0.827	1	CLONAL	1	TRUE	1	0.33	2		437	676	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500816	8500816	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	127	501	1	ENST00000356435.5:c.2066C>T	p.Ala689Val	p.A689V	ENST00000356435		689	gCc/gTc	13/35	0.3	3	FACETS	1	0.93	1	0.516	0.467	0.568	CLONAL	1	TRUE	1	0.33	3		502	869	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793313	139793313	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	174	639	0	ENST00000247668.2:c.121C>A	p.Leu41Ile	p.L41I	ENST00000247668	NM_021138.3	41	Ctc/Atc	2/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.33	2		639	946	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15821895	15821896	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	36	368	0	ENST00000307771.7:c.294dup	p.Arg99ThrfsTer46	p.R99Tfs*46	ENST00000307771	NM_005089.3	96	-/A	4/11	1	2	FACETS	0.579	0.476	0.693	0.579	0.476	0.693	SUBCLONAL	1	TRUE	1	0.33	2		368	377	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006827	47006827	+	5_prime_UTR_variant	5'UTR	SNP	C	C	T	novel	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	122	663	2	ENST00000377604.3:c.-54C>T		p.*18*	ENST00000377604	NM_001204468.1	-/852		2/24	1	2	FACETS	0.896	0.81	0.987	0.896	0.81	0.987	CLONAL	1	TRUE	1	0.33	2		665	825	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040620	47040621	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	77	391	0	ENST00000377604.3:c.1257dup	p.Gly420ArgfsTer23	p.G420Rfs*23	ENST00000377604	NM_001204468.1	419	caa/cAaa	13/24	1	2	FACETS	0.924	0.813	1	0.924	0.813	1	CLONAL	1	TRUE	1	0.33	2		391	505	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652440	48652440	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	142	709	1	ENST00000376670.3:c.1111G>T	p.Val371Leu	p.V371L	ENST00000376670	NM_002049.3	371	Gtg/Ttg	6/6	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.33	2		710	839	SUCCESS
AR	367	MSKCC	GRCh37	X	66905929	66905929	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555990485	NA	P-0036284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	64	523	1	ENST00000374690.3:c.1846C>T	p.Arg616Cys	p.R616C	ENST00000374690	NM_000044.3	616	Cgt/Tgt	3/8	1	2	FACETS	0.785	0.681	0.898	0.785	0.681	0.898	SUBCLONAL	1	TRUE	1	0.33	2		524	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0036285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	310	667	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.574216165529416	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	FALSE	0	0.575262527834444	2		667	537	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039392	49039392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs947540268	NA	P-0036285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	525	661	0	ENST00000267163.4:c.2377C>T	p.Pro793Ser	p.P793S	ENST00000267163	NM_000321.2	793	Cct/Tct	23/27	0.352753132234274	5	FACETS	1	0.994	1			1	CLONAL	3	FALSE	NA	0.575262527834444	5		661	982	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106558	27106558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	274	710	1	ENST00000324856.7:c.6169C>T	p.Arg2057Trp	p.R2057W	ENST00000324856	NM_006015.4	2057	Cgg/Tgg	20/20	0.5837405811076	4	FACETS	0.817	0.769	0.867			1	CLONAL	2	FALSE	NA	0.575262527834444	4		711	918	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8284895	8284895	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	131	450	0	ENST00000335790.3:c.15C>G	p.Asp5Glu	p.D5E	ENST00000335790	NM_002315.2	5	gaC/gaG	1/4	0.575262527834444	7	FACETS	1	0.968	1			1	CLONAL	1	FALSE	NA	0.575262527834444	7		450	962	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243392	46243392	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	93	383	0	ENST00000334344.6:c.1745G>T	p.Arg582Ile	p.R582I	ENST00000334344	NM_152641.2	582	aGa/aTa	14/21	0.342649443034877	6	FACETS	0.78	0.697	0.867	0.39	0.348	0.434	INDETERMINATE	2	FALSE	2	0.575262527834444	6		383	446	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38942461	38942461	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	238	540	0	ENST00000357387.3:c.5072C>G	p.Ala1691Gly	p.A1691G	ENST00000357387	NM_152756.3	1691	gCt/gGt	38/38	0.575262527834444	7	FACETS	0.91	0.849	0.973			1	CLONAL	2	FALSE	NA	0.575262527834444	7		540	1108	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974310	93974310	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0036285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	155	406	0	ENST00000369303.4:c.1742+2T>A		p.X581_splice	ENST00000369303	NM_004440.3	581			0.497262522093485	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	0	0.575262527834444	1		406	314	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0036286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	172	635	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	0.549347295357022	3	FACETS	1	0.966	1	0.543	0.5	0.586	CLONAL	1	TRUE	1	0.548933603289454	3		635	736	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584624	187584624	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1192	114	583	5	ENST00000441802.2:c.3409C>T	p.Pro1137Ser	p.P1137S	ENST00000441802	NM_005245.3	1137	Cca/Tca	3/27	0.548933603289454	7	FACETS	0.754	0.677	0.837	0.151	0.135	0.168	SUBCLONAL	1	TRUE	2	0.548933603289454	7		588	1306	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437122	110437122	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	17	80	0	ENST00000375856.3:c.1279C>A	p.His427Asn	p.H427N	ENST00000375856	NM_003749.2	427	Cac/Aac	1/2	0.549347295357022	3	FACETS	0.626	0.472	0.806	0.313	0.236	0.403	SUBCLONAL	1	TRUE	1	0.548933603289454	3		80	126	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458328	12458329	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGCTC	novel	NA	P-0036286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	374	756	7	ENST00000287820.6:c.948_952dup	p.Val318AlafsTer20	p.V318Afs*20	ENST00000287820	NM_015869.4	315	-/CGCTC	6/7	0.549347295357022	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.548933603289454	3		763	847	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395221	139395221	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756056361	NA	P-0036286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	195	792	3	ENST00000277541.6:c.5717C>T	p.Ala1906Val	p.A1906V	ENST00000277541	NM_017617.3	1906	gCg/gTg	31/34	0.504230383048097	4	FACETS	1	0.959	1	0.527	0.487	0.568	CLONAL	1	TRUE	2	0.548933603289454	4		795	1044	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0036287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	25	408	1	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.696	0.547	0.868	0.696	0.547	0.868	SUBCLONAL	1	TRUE	1	0.13	2		409	553	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	163	214	0				ENST00000310581	NM_198253.2	-/1132			0.652055391483986	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.650656545109871	3		214	303	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0036288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	413	749	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	0.652055391483986	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.650656545109871	2		749	559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0036289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	118	625	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	1	2	FACETS	0.984	0.887	1	0.984	0.887	1	CLONAL	1	TRUE	1	0.267142741625738	2		625	898	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0036289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	123	552	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	1	2	FACETS	0.98	0.885	1	0.98	0.885	1	CLONAL	1	TRUE	1	0.267142741625738	2		552	940	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857047	9857047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568622613	NA	P-0036289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	58	404	0	ENST00000330684.3:c.4354C>T	p.Arg1452Cys	p.R1452C	ENST00000330684	NM_001134407.1	1452	Cgc/Tgc	13/13	1	2	FACETS	0.901	0.775	1	0.901	0.775	1	CLONAL	1	TRUE	1	0.267142741625738	2		404	482	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920401	114920401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1422891742	NA	P-0036289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	90	486	1	ENST00000543371.1:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000543371	NM_001198531.1	448	Cgg/Tgg	13/14	1	2	FACETS	0.838	0.743	0.94	0.838	0.743	0.94	CLONAL	1	TRUE	1	0.267142741625738	2		487	804	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248339	59248351	+	frameshift_variant	Frame_Shift_Del	DEL	TGCGCCGCCGACG	TGCGCCGCCGACG	-	novel	NA	P-0036289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	30	174	0	ENST00000371222.2:c.392_404del	p.Thr131SerfsTer13	p.T131Sfs*13	ENST00000371222	NM_002228.3	131	aCGTCGGCGGCGCAg/ag	1/1	1	2	FACETS	0.72	0.581	0.876	0.72	0.581	0.876	SUBCLONAL	1	TRUE	1	0.267142741625738	2		174	312	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285676	46285676	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	57	491	0	ENST00000334344.6:c.5037del	p.Ser1681LeufsTer20	p.S1681Lfs*20	ENST00000334344	NM_152641.2	1679	cGg/cg	17/21	1	2	FACETS	0.685	0.587	0.792	0.685	0.587	0.792	SUBCLONAL	1	TRUE	1	0.267142741625738	2		491	623	SUCCESS
APC	324	MSKCC	GRCh37	5	112174831	112174831	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	90	330	0	ENST00000257430.4:c.3542del	p.Leu1181Ter	p.L1181*	ENST00000257430	NM_000038.5	1180	agT/ag	16/16	0.203508593952203	2	FACETS	0.906	0.81	1	0.906	0.81	1	CLONAL	2	TRUE	0	0.267142741625738	2		330	372	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288434	21288434	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1404011600	NA	P-0036291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	171	730	1	ENST00000354336.3:c.679A>G	p.Ile227Val	p.I227V	ENST00000354336	NM_005207.3	227	Atc/Gtc	2/3	0.281482558549043	2	FACETS	1	0.953	1	0.526	0.483	0.57	CLONAL	1	FALSE	0	0.345584559453705	2		731	941	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0036293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	794	674	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.797068125780738	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.797068125780738	2		674	967	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390649	139390650	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs763016003	NA	P-0036293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	374	642	0	ENST00000277541.6:c.7541_7542del	p.Pro2514ArgfsTer4	p.P2514Rfs*4	ENST00000277541	NM_017617.3	2514	cCT/c	34/34	0.423785902032043	1	FACETS	0.693	0.661	0.724	0.693	0.661	0.724	INDETERMINATE	1	TRUE	0	0.797068125780738	1		642	815	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121856	2121856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745897413	NA	P-0036293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	181	431	0	ENST00000219476.3:c.2018C>T	p.Ala673Val	p.A673V	ENST00000219476	NM_000548.3	673	gCg/gTg	19/42	0.423785902032043	1	FACETS	0.451	0.418	0.485	0.451	0.418	0.485	INDETERMINATE	1	TRUE	0	0.797068125780738	1		431	606	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742478	145742478	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1508	200	629	0	ENST00000428558.2:c.310G>C	p.Asp104His	p.D104H	ENST00000428558	NM_004260.3	104	Gac/Cac	4/22	0.774148336537251	4	FACETS	0.528	0.487	0.571	0.264	0.243	0.286	SUBCLONAL	1	TRUE	2	0.797068125780738	4		629	1708	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328377	137328379	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0036293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	383	675	0	ENST00000481739.1:c.1306_1308del	p.Leu436del	p.L436del	ENST00000481739	NM_002957.4	436	CTC/-	10/10	0.423785902032043	1	FACETS	0.68	0.649	0.711	0.68	0.649	0.711	INDETERMINATE	1	TRUE	0	0.797068125780738	1		675	850	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711927	89711928	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554900593	NA	P-0036294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	325	500	0	ENST00000371953.3:c.548dup	p.Asn184GlufsTer6	p.N184Efs*6	ENST00000371953	NM_000314.4	182	tta/ttAa	6/9	0.740850629506272	5	FACETS	0.964	0.913	1	0.643	0.608	0.677	CLONAL	2	TRUE	2	0.740850629506272	5		500	961	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210058	55210058	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	187	630	0	ENST00000275493.2:c.168T>G	p.Asn56Lys	p.N56K	ENST00000275493	NM_005228.3	56	aaT/aaG	2/28	0.740850629506272	3	FACETS	0.983	0.911	1	0.491	0.455	0.529	CLONAL	1	TRUE	1	0.740850629506272	3		630	704	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245933	16245933	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	254	411	0	ENST00000375759.3:c.1556T>A	p.Val519Glu	p.V519E	ENST00000375759	NM_015001.2	519	gTg/gAg	8/15	1	2	FACETS	0.986	0.928	1	0.986	0.928	1	CLONAL	1	TRUE	1	0.762361068377725	2		411	676	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0036296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	76	428	0	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.601469699794072	2		428	182	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341238	70341238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754407926	NA	P-0036296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	122	280	0	ENST00000374080.3:c.797G>A	p.Arg266His	p.R266H	ENST00000374080		266	cGc/cAc	6/45	0.476035307191037	2	FACETS	1	0.954	1			1	CLONAL	2	TRUE	NA	0.601469699794072	2		280	197	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128748867	128748867	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	78	407	0	ENST00000377970.2:c.28C>G	p.Gln10Glu	p.Q10E	ENST00000377970	NM_002467.4	10	Cag/Gag	1/3	0.601469699794072	6	FACETS	0.675	0.592	0.765	0.169	0.148	0.192	SUBCLONAL	1	TRUE	2	0.601469699794072	6		407	846	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523540	106523540	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs111306935	NA	P-0036296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	74	293	0	ENST00000359195.3:c.2692A>G	p.Asn898Asp	p.N898D	ENST00000359195	NM_002649.2	898	Aac/Gac	8/11	0.353044985105711	4	FACETS	1	0.976	1	0.724	0.641	0.811	INDETERMINATE	1	TRUE	2	0.601469699794072	4		293	272	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431328	49431328	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	74	449	1	ENST00000301067.7:c.9811C>T	p.Gln3271Ter	p.Q3271*	ENST00000301067	NM_003482.3	3271	Cag/Tag	34/54	0.499059242347016	4	FACETS	0.921	0.82	1	0.921	0.82	1	CLONAL	2	TRUE	2	0.601469699794072	4		450	214	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420774	49420774	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	126	531	0	ENST00000301067.7:c.14975del	p.Leu4992ArgfsTer3	p.L4992Rfs*3	ENST00000301067	NM_003482.3	4992	cTg/cg	48/54	0.499059242347016	4	FACETS	0.89	0.814	0.968	0.89	0.814	0.968	CLONAL	2	TRUE	2	0.601469699794072	4		531	377	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	69	485	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.914	0.796	1	0.914	0.796	1	CLONAL	1	TRUE	1	0.26	2		486	581	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317186	11317186	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763230714	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	57	562	0	ENST00000361445.4:c.308G>A	p.Arg103Gln	p.R103Q	ENST00000361445	NM_004958.3	103	cGa/cAa	4/58	1	2	FACETS	0.658	0.564	0.761	0.658	0.564	0.761	SUBCLONAL	1	TRUE	1	0.26	2		562	666	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257176	16257176	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	37	641	0	ENST00000375759.3:c.4441G>T	p.Glu1481Ter	p.E1481*	ENST00000375759	NM_015001.2	1481	Gaa/Taa	11/15	1	2	FACETS	0.389	0.319	0.467	0.389	0.319	0.467	SUBCLONAL	1	TRUE	1	0.26	2		641	732	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087570	27087570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1387691435	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	94	665	0	ENST00000324856.7:c.2144C>T	p.Ser715Leu	p.S715L	ENST00000324856	NM_006015.4	715	tCg/tTg	5/20	1	2	FACETS	0.818	0.727	0.916	0.818	0.727	0.916	CLONAL	1	TRUE	1	0.26	2		665	884	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28605674	28605674	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	95	642	2	ENST00000253063.3:c.1278G>T	p.Lys426Asn	p.K426N	ENST00000253063	NM_031459.4	426	aaG/aaT	9/10	1	2	FACETS	0.933	0.831	1	0.933	0.831	1	CLONAL	1	TRUE	1	0.26	2		644	783	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812149	43812149	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	70	464	0	ENST00000372470.3:c.1014G>T	p.Glu338Asp	p.E338D	ENST00000372470	NM_005373.2	338	gaG/gaT	7/12	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.26	2		464	531	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78435644	78435644	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	96	685	0	ENST00000370768.2:c.176G>A	p.Gly59Asp	p.G59D	ENST00000370768	NM_003902.3	59	gGt/gAt	2/20	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.26	2		685	684	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176133005	176133005	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	63	540	0	ENST00000367669.3:c.588G>T	p.Gln196His	p.Q196H	ENST00000367669	NM_022457.5	196	caG/caT	4/20	1	2	FACETS	0.747	0.645	0.857	0.747	0.645	0.857	SUBCLONAL	1	TRUE	1	0.26	2		540	649	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608317	43608317	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	116	955	1	ENST00000355710.3:c.1665C>A	p.Phe555Leu	p.F555L	ENST00000355710	NM_020975.4	555	ttC/ttA	9/20	1	2	FACETS	0.959	0.864	1	0.959	0.864	1	CLONAL	1	TRUE	1	0.26	2		956	930	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845627	63845627	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	45	237	0	ENST00000279873.7:c.1366G>T	p.Glu456Ter	p.E456*	ENST00000279873	NM_032199.2	456	Gaa/Taa	9/10	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.26	2		237	337	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333183	70333183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	111	780	0	ENST00000373644.4:c.1088C>T	p.Ser363Phe	p.S363F	ENST00000373644	NM_030625.2	363	tCt/tTt	2/12	1	2	FACETS	0.92	0.826	1	0.92	0.826	1	CLONAL	1	TRUE	1	0.26	2		780	928	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	81	348	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.26	2		348	586	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910882	114910882	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs572431965	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	39	521	0	ENST00000543371.1:c.1001C>T	p.Ser334Leu	p.S334L	ENST00000543371	NM_001198531.1	334	tCa/tTa	9/14	1	2	FACETS	0.449	0.371	0.536	0.449	0.371	0.536	SUBCLONAL	1	TRUE	1	0.26	2		521	668	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625456	69625456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781938977	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	88	675	1	ENST00000334134.2:c.337G>A	p.Ala113Thr	p.A113T	ENST00000334134	NM_005247.2	113	Gcc/Acc	3/3	1	2	FACETS	0.968	0.858	1	0.968	0.858	1	CLONAL	1	TRUE	1	0.26	2		676	699	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94209558	94209558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	42	537	0	ENST00000323929.3:c.556G>A	p.Asp186Asn	p.D186N	ENST00000323929	NM_005591.3	186	Gat/Aat	7/20	1	2	FACETS	0.456	0.379	0.541	0.456	0.379	0.541	SUBCLONAL	1	TRUE	1	0.26	2		537	709	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917635	94917635	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	68	689	0	ENST00000536441.1:c.886G>T	p.Glu296Ter	p.E296*	ENST00000536441	NM_144665.3	296	Gaa/Taa	6/10	1	2	FACETS	0.697	0.606	0.797	0.697	0.606	0.797	SUBCLONAL	1	TRUE	1	0.26	2		689	750	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098519	108098519	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs876658520	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	46	438	0	ENST00000278616.4:c.89T>G	p.Phe30Cys	p.F30C	ENST00000278616	NM_000051.3	30	tTt/tGt	3/63	1	2	FACETS	0.604	0.508	0.71	0.604	0.508	0.71	SUBCLONAL	1	TRUE	1	0.26	2		438	586	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139269	108139269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782298	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	104	836	1	ENST00000278616.4:c.2771G>A	p.Arg924Gln	p.R924Q	ENST00000278616	NM_000051.3	924	cGg/cAg	18/63	1	2	FACETS	0.923	0.825	1	0.923	0.825	1	CLONAL	1	TRUE	1	0.26	2		837	867	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420104	420104	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	103	620	0	ENST00000399788.2:c.3163G>T	p.Glu1055Ter	p.E1055*	ENST00000399788	NM_001042603.1	1055	Gaa/Taa	21/28	1	2	FACETS	0.94	0.84	1	0.94	0.84	1	CLONAL	1	TRUE	1	0.26	2		620	843	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992217	11992217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	86	532	0	ENST00000396373.4:c.307C>T	p.Arg103Cys	p.R103C	ENST00000396373	NM_001987.4	103	Cgc/Tgc	3/8	1	2	FACETS	0.987	0.874	1	0.987	0.874	1	CLONAL	1	TRUE	1	0.26	2		532	670	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49419977	49419977	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762350923	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	81	551	2	ENST00000301067.7:c.15772G>A	p.Ala5258Thr	p.A5258T	ENST00000301067	NM_003482.3	5258	Gcc/Acc	48/54	1	2	FACETS	0.953	0.84	1	0.953	0.84	1	CLONAL	1	TRUE	1	0.26	2		553	654	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865582	57865583	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	68	740	1	ENST00000228682.2:c.3060dup	p.Gly1021ArgfsTer15	p.G1021Rfs*15	ENST00000228682	NM_005269.2	1020	gga/ggAa	12/12	1	2	FACETS	0.643	0.559	0.735	0.643	0.559	0.735	SUBCLONAL	1	TRUE	1	0.26	2		741	813	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112919983	112919983	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	53	549	1	ENST00000351677.2:c.1198G>T	p.Glu400Ter	p.E400*	ENST00000351677	NM_002834.3	400	Gaa/Taa	10/16	1	2	FACETS	0.511	0.434	0.595	0.511	0.434	0.595	SUBCLONAL	1	TRUE	1	0.26	2		550	798	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	88	639	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	0.88	0.779	0.988	0.88	0.779	0.988	CLONAL	1	TRUE	1	0.26	2		639	769	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549161	21549161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1301579203	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	101	812	1	ENST00000382592.4:c.3115G>A	p.Glu1039Lys	p.E1039K	ENST00000382592	NM_014572.2	1039	Gaa/Aaa	8/8	1	2	FACETS	0.796	0.71	0.888	0.796	0.71	0.888	SUBCLONAL	1	TRUE	1	0.26	2		813	976	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959424	26959424	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	56	609	1	ENST00000381527.3:c.591C>A	p.Phe197Leu	p.F197L	ENST00000381527	NM_001260.1	197	ttC/ttA	6/13	1	2	FACETS	0.578	0.494	0.67	0.578	0.494	0.67	SUBCLONAL	1	TRUE	1	0.26	2		610	745	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28931725	28931726	+	missense_variant	Missense_Mutation	DNP	GC	GC	TA	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	97	641	0	ENST00000282397.4:c.2213_2214delinsTA	p.Gly738Val	p.G738V	ENST00000282397	NM_002019.4	738	gGC/gTA	15/30	1	2	FACETS	0.872	0.776	0.973	0.872	0.776	0.973	CLONAL	1	TRUE	1	0.26	2		641	856	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28931726	28931726	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1193193739	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	97	632	0	ENST00000282397.4:c.2213G>T	p.Gly738Val	p.G738V	ENST00000282397	NM_002019.4	738	gGc/gTc	15/30	1	2	FACETS	0.872	0.776	0.973	0.872	0.776	0.973	CLONAL	1	TRUE	1	0.26	2		632	856	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32971092	32971092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659245	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	87	603	0	ENST00000380152.3:c.9559A>G	p.Asn3187Asp	p.N3187D	ENST00000380152		3187	Aat/Gat	26/27	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.26	2		603	649	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972606	32972606	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs778694116	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	98	549	0	ENST00000380152.3:c.9956C>A	p.Ser3319Tyr	p.S3319Y	ENST00000380152		3319	tCt/tAt	27/27	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.26	2		549	680	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050942	49050942	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143105337	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	59	434	0	ENST00000267163.4:c.2626C>T	p.Arg876Cys	p.R876C	ENST00000267163	NM_000321.2	876	Cgc/Tgc	25/27	1	2	FACETS	0.902	0.777	1	0.902	0.777	1	CLONAL	1	TRUE	1	0.26	2		434	503	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527907	103527907	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	67	419	0	ENST00000355739.4:c.3215G>T	p.Arg1072Ile	p.R1072I	ENST00000355739	NM_000123.3	1072	aGa/aTa	15/15	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.26	2		419	506	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060812	38060812	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	84	854	1	ENST00000250448.2:c.1177C>T	p.His393Tyr	p.H393Y	ENST00000250448	NM_004496.3	393	Cac/Tac	2/2	1	2	FACETS	0.847	0.747	0.954	0.847	0.747	0.954	CLONAL	1	TRUE	1	0.26	2		855	763	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243030	105243030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1566818890	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	93	788	1	ENST00000349310.3:c.253G>A	p.Glu85Lys	p.E85K	ENST00000349310	NM_001014432.1	85	Gaa/Aaa	5/15	1	2	FACETS	0.856	0.76	0.958	0.856	0.76	0.958	CLONAL	1	TRUE	1	0.26	2		789	836	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021428	42021428	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	73	749	1	ENST00000219905.7:c.3724C>T	p.Arg1242Ter	p.R1242*	ENST00000219905	NM_001164273.1	1242	Cga/Tga	11/24	1	2	FACETS	0.728	0.636	0.828	0.728	0.636	0.828	SUBCLONAL	1	TRUE	1	0.26	2		750	771	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857434	9857434	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	60	584	0	ENST00000330684.3:c.3967A>C	p.Asn1323His	p.N1323H	ENST00000330684	NM_001134407.1	1323	Aat/Cat	13/13	1	2	FACETS	0.708	0.609	0.815	0.708	0.609	0.815	SUBCLONAL	1	TRUE	1	0.26	2		584	652	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650710	67650710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243010179	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	139	723	1	ENST00000264010.4:c.1015C>T	p.Arg339Trp	p.R339W	ENST00000264010	NM_006565.3	339	Cgg/Tgg	5/12	1	2	FACETS	0.986	0.896	1	0.986	0.896	1	CLONAL	1	TRUE	1	0.26	2		724	1084	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483093	29483093	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	86	724	0	ENST00000356175.3:c.153T>G	p.Phe51Leu	p.F51L	ENST00000356175	NM_000267.3	51	ttT/ttG	2/57	1	2	FACETS	0.764	0.675	0.86	0.764	0.675	0.86	SUBCLONAL	1	TRUE	1	0.26	2		724	866	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483129	29483129	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	88	639	0	ENST00000356175.3:c.189G>T	p.Lys63Asn	p.K63N	ENST00000356175	NM_000267.3	63	aaG/aaT	2/57	1	2	FACETS	0.887	0.786	0.996	0.887	0.786	0.996	CLONAL	1	TRUE	1	0.26	2		639	763	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557387	29557387	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	36	272	0	ENST00000356175.3:c.3100G>T	p.Glu1034Ter	p.E1034*	ENST00000356175	NM_000267.3	1034	Gag/Tag	23/57	1	2	FACETS	0.902	0.744	1	0.902	0.744	1	CLONAL	1	TRUE	1	0.26	2		272	307	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40498592	40498592	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	87	540	0	ENST00000264657.5:c.268C>A	p.Leu90Ile	p.L90I	ENST00000264657	NM_139276.2	90	Ctt/Att	3/24	1	2	FACETS	0.977	0.865	1	0.977	0.865	1	CLONAL	1	TRUE	1	0.26	2		540	685	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245342	41245342	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	146	863	1	ENST00000357654.3:c.2206G>T	p.Glu736Ter	p.E736*	ENST00000357654	NM_007294.3	736	Gaa/Taa	10/23	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.26	2		864	1093	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414754	56414754	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	103	764	0	ENST00000348428.3:c.2155C>T	p.Arg719Ter	p.R719*	ENST00000348428	NM_006785.3	719	Cga/Tga	17/17	1	2	FACETS	0.893	0.798	0.994	0.893	0.798	0.994	CLONAL	1	TRUE	1	0.26	2		764	887	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627677	14627677	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	83	653	1	ENST00000254322.2:c.393C>A	p.Phe131Leu	p.F131L	ENST00000254322	NM_006145.1	131	ttC/ttA	2/3	1	2	FACETS	0.928	0.819	1	0.928	0.819	1	CLONAL	1	TRUE	1	0.26	2		654	688	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220942	36220942	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	64	451	0	ENST00000222270.7:c.4992C>A	p.Phe1664Leu	p.F1664L	ENST00000222270	NM_014727.1	1664	ttC/ttA	23/37	1	2	FACETS	0.918	0.796	1	0.918	0.796	1	CLONAL	1	TRUE	1	0.26	2		451	536	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752781	42752781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772231752	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	92	833	0	ENST00000222329.4:c.1483G>A	p.Glu495Lys	p.E495K	ENST00000222329	NM_006494.2	495	Gaa/Aaa	4/4	1	2	FACETS	0.926	0.823	1	0.926	0.823	1	CLONAL	1	TRUE	1	0.26	2		833	764	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46588054	46588054	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	89	705	0	ENST00000263734.3:c.604T>G	p.Tyr202Asp	p.Y202D	ENST00000263734	NM_001430.4	202	Tac/Gac	6/16	1	2	FACETS	0.869	0.77	0.975	0.869	0.77	0.975	CLONAL	1	TRUE	1	0.26	2		705	788	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607794	46607794	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	95	849	0	ENST00000263734.3:c.1983C>A	p.Phe661Leu	p.F661L	ENST00000263734	NM_001430.4	661	ttC/ttA	12/16	1	2	FACETS	0.846	0.752	0.946	0.846	0.752	0.946	CLONAL	1	TRUE	1	0.26	2		849	864	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641447	47641447	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	111	538	0	ENST00000233146.2:c.832G>T	p.Glu278Ter	p.E278*	ENST00000233146	NM_000251.2	278	Gaa/Taa	5/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.26	2		538	739	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010565	48010565	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	32	344	0	ENST00000234420.5:c.193T>C	p.Ser65Pro	p.S65P	ENST00000234420	NM_000179.2	65	Tca/Cca	1/10	1	2	FACETS	0.644	0.523	0.781	0.644	0.523	0.781	SUBCLONAL	1	TRUE	1	0.26	2		344	382	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026290	48026290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147737737	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	77	555	0	ENST00000234420.5:c.1168G>A	p.Asp390Asn	p.D390N	ENST00000234420	NM_000179.2	390	Gat/Aat	4/10	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.26	2		555	518	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	73	637	0	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	1	2	FACETS	0.77	0.673	0.875	0.77	0.673	0.875	SUBCLONAL	1	TRUE	1	0.26	2		637	729	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	72	637	0	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	1	2	FACETS	0.705	0.615	0.802	0.705	0.615	0.802	SUBCLONAL	1	TRUE	1	0.26	2		637	786	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155420	99155420	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	58	513	0	ENST00000074304.5:c.646C>T	p.Arg216Ter	p.R216*	ENST00000074304	NM_001134224.1	216	Cga/Tga	9/26	1	2	FACETS	0.729	0.626	0.841	0.729	0.626	0.841	SUBCLONAL	1	TRUE	1	0.26	2		513	612	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128036890	128036890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	104	753	1	ENST00000285398.2:c.1589G>A	p.Arg530Gln	p.R530Q	ENST00000285398	NM_000122.1	530	cGa/cAa	10/15	1	2	FACETS	0.834	0.746	0.929	0.834	0.746	0.929	CLONAL	1	TRUE	1	0.26	2		754	959	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137360	202137360	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	39	392	0	ENST00000358485.4:c.589-1G>T		p.X197_splice	ENST00000358485	NM_001080125.1	197			1	2	FACETS	0.625	0.518	0.745	0.625	0.518	0.745	SUBCLONAL	1	TRUE	1	0.26	2		392	480	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209103887	209103887	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	50	534	0	ENST00000345146.2:c.1062C>A	p.Phe354Leu	p.F354L	ENST00000345146	NM_005896.2	354	ttC/ttA	9/10	1	2	FACETS	0.56	0.474	0.655	0.56	0.474	0.655	SUBCLONAL	1	TRUE	1	0.26	2		534	687	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225400355	225400355	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	51	368	0	ENST00000264414.4:c.268C>T	p.Arg90Ter	p.R90*	ENST00000264414	NM_003590.4	90	Cga/Tga	3/16	1	2	FACETS	0.835	0.71	0.971	0.835	0.71	0.971	CLONAL	1	TRUE	1	0.26	2		368	470	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39751841	39751841	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	71	452	1	ENST00000361337.2:c.2202G>T	p.Lys734Asn	p.K734N	ENST00000361337	NM_003286.2	734	aaG/aaT	21/21	1	2	FACETS	0.882	0.77	1	0.882	0.77	1	CLONAL	1	TRUE	1	0.26	2		453	619	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713429	40713429	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	87	681	1	ENST00000373198.4:c.4086C>A	p.Tyr1362Ter	p.Y1362*	ENST00000373198	NM_133170.3	1362	taC/taA	30/32	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.26	NA		682	782	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743943	40743943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs763964405	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	63	579	5	ENST00000373198.4:c.3052C>T	p.Arg1018Ter	p.R1018*	ENST00000373198	NM_133170.3	1018	Cga/Tga	23/32	0.3	1	FACETS	0.663	0.573	0.761	0.663	0.573	0.761	SUBCLONAL	1	TRUE	0	0.26	1		584	636	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944523	40944523	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	60	644	0	ENST00000373198.4:c.1979C>A	p.Ser660Tyr	p.S660Y	ENST00000373198	NM_133170.3	660	tCt/tAt	12/32	0.3	1	FACETS	0.657	0.566	0.757	0.657	0.566	0.757	SUBCLONAL	1	TRUE	0	0.26	1		644	611	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480466	89480466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446890859	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	65	408	0	ENST00000336596.2:c.2303C>T	p.Ser768Leu	p.S768L	ENST00000336596	NM_005233.5	768	tCg/tTg	13/17	1	2	FACETS	0.803	0.696	0.918	0.803	0.696	0.918	CLONAL	1	TRUE	1	0.26	2		408	623	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433416	138433416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1194347036	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	130	717	0	ENST00000289153.2:c.1196G>A	p.Arg399Gln	p.R399Q	ENST00000289153	NM_006219.2	399	cGa/cAa	7/22	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.26	2		717	864	SUCCESS
ATR	545	MSKCC	GRCh37	3	142257364	142257364	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	93	560	1	ENST00000350721.4:c.3685G>T	p.Glu1229Ter	p.E1229*	ENST00000350721	NM_001184.3	1229	Gaa/Taa	19/47	1	2	FACETS	0.985	0.876	1	0.985	0.876	1	CLONAL	1	TRUE	1	0.26	2		561	726	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	80	734	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	0.676	0.593	0.764	0.676	0.593	0.764	SUBCLONAL	1	TRUE	1	0.26	2		734	911	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	70	863	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.581	0.506	0.664	0.581	0.506	0.664	SUBCLONAL	1	TRUE	1	0.26	2		863	926	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182679086	182679086	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	66	712	0	ENST00000292782.4:c.448G>T	p.Glu150Ter	p.E150*	ENST00000292782	NM_020640.2	150	Gaa/Taa	4/7	1	2	FACETS	0.679	0.588	0.777	0.679	0.588	0.777	SUBCLONAL	1	TRUE	1	0.26	2		712	748	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683399	182683399	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	101	583	0	ENST00000292782.4:c.146A>T	p.Glu49Val	p.E49V	ENST00000292782	NM_020640.2	49	gAa/gTa	2/7	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.26	2		583	718	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191026	185191026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	105	817	0	ENST00000265026.3:c.1907C>A	p.Ser636Tyr	p.S636Y	ENST00000265026	NM_004721.4	636	tCt/tAt	11/14	1	2	FACETS	0.899	0.805	1	0.899	0.805	1	CLONAL	1	TRUE	1	0.26	2		817	898	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506931	186506931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	35	307	0	ENST00000323963.5:c.1097G>A	p.Arg366Gln	p.R366Q	ENST00000323963		366	cGa/cAa	11/11	1	2	FACETS	0.623	0.511	0.75	0.623	0.511	0.75	SUBCLONAL	1	TRUE	1	0.26	2		307	432	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447057	187447057	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	130	759	0	ENST00000232014.4:c.1136A>C	p.Lys379Thr	p.K379T	ENST00000232014	NM_001130845.1	379	aAg/aCg	5/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.26	2		759	928	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807537	1807537	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146672976	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	73	770	1	ENST00000260795.2:c.1706C>T	p.Ala569Val	p.A569V	ENST00000260795		569	gCg/gTg	12/17	1	2	FACETS	0.808	0.706	0.918	0.808	0.706	0.918	CLONAL	1	TRUE	1	0.26	2		771	695	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55130090	55130090	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs889394408	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	64	569	0	ENST00000257290.5:c.624A>C	p.Leu208Phe	p.L208F	ENST00000257290	NM_006206.4	208	ttA/ttC	4/23	1	2	FACETS	0.757	0.655	0.868	0.757	0.655	0.868	SUBCLONAL	1	TRUE	1	0.26	2		569	650	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193884	106193884	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	69	422	0	ENST00000380013.4:c.4346C>A	p.Ser1449Tyr	p.S1449Y	ENST00000380013	NM_001127208.2	1449	tCt/tAt	10/11	1	2	FACETS	0.866	0.754	0.986	0.866	0.754	0.986	CLONAL	1	TRUE	1	0.26	2		422	613	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541900	187541900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765843504	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	62	722	0	ENST00000441802.2:c.5840G>A	p.Arg1947His	p.R1947H	ENST00000441802	NM_005245.3	1947	cGc/cAc	10/27	1	2	FACETS	0.539	0.464	0.621	0.539	0.464	0.621	SUBCLONAL	1	TRUE	1	0.26	2		722	885	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541982	187541982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759008415	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	65	678	1	ENST00000441802.2:c.5758G>A	p.Glu1920Lys	p.E1920K	ENST00000441802	NM_005245.3	1920	Gaa/Aaa	10/27	1	2	FACETS	0.691	0.598	0.791	0.691	0.598	0.791	SUBCLONAL	1	TRUE	1	0.26	2		679	724	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409391	31409391	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	77	547	0	ENST00000344624.3:c.3716C>T	p.Thr1239Ile	p.T1239I	ENST00000344624		1239	aCt/aTt	29/33	1	2	FACETS	0.92	0.808	1	0.92	0.808	1	CLONAL	1	TRUE	1	0.26	2		547	644	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86681198	86681198	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	27	410	0	ENST00000274376.6:c.2839G>T	p.Gly947Ter	p.G947*	ENST00000274376	NM_002890.2	947	Gga/Tga	22/25	1	2	FACETS	0.386	0.306	0.478	0.386	0.306	0.478	SUBCLONAL	1	TRUE	1	0.26	2		410	538	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86686647	86686647	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	44	359	1	ENST00000274376.6:c.3091G>T	p.Glu1031Ter	p.E1031*	ENST00000274376	NM_002890.2	1031	Gaa/Taa	25/25	1	2	FACETS	0.812	0.682	0.955	0.812	0.682	0.955	CLONAL	1	TRUE	1	0.26	2		360	417	SUCCESS
APC	324	MSKCC	GRCh37	5	112175166	112175166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371113837	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	33	320	0	ENST00000257430.4:c.3875C>T	p.Thr1292Met	p.T1292M	ENST00000257430	NM_000038.5	1292	aCg/aTg	16/16	1	2	FACETS	0.651	0.53	0.787	0.651	0.53	0.787	SUBCLONAL	1	TRUE	1	0.26	2		320	390	SUCCESS
APC	324	MSKCC	GRCh37	5	112175370	112175370	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	67	358	0	ENST00000257430.4:c.4079C>T	p.Ser1360Phe	p.S1360F	ENST00000257430	NM_000038.5	1360	tCt/tTt	16/16	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.26	2		358	454	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911514	131911514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143802516	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	90	557	0	ENST00000265335.6:c.259C>T	p.Arg87Cys	p.R87C	ENST00000265335		87	Cgt/Tgt	3/25	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.26	2		557	684	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915160	131915160	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	93	678	0	ENST00000265335.6:c.517A>G	p.Lys173Glu	p.K173E	ENST00000265335		173	Aag/Gag	4/25	1	2	FACETS	0.892	0.793	0.998	0.892	0.793	0.998	CLONAL	1	TRUE	1	0.26	2		678	802	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287935	33287935	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs375012684	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	63	553	0	ENST00000374542.5:c.1318G>T	p.Asp440Tyr	p.D440Y	ENST00000374542	NM_001141970.1	440	Gat/Tat	5/8	1	2	FACETS	0.74	0.639	0.849	0.74	0.639	0.849	SUBCLONAL	1	TRUE	1	0.26	2		553	655	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793603	89793603	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	29	406	0	ENST00000336032.3:c.672G>T	p.Lys224Asn	p.K224N	ENST00000336032	NM_006813.2	224	aaG/aaT	2/2	1	2	FACETS	0.391	0.313	0.481	0.391	0.313	0.481	SUBCLONAL	1	TRUE	1	0.26	2		406	570	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555027	106555027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775380311	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	87	505	2	ENST00000369096.4:c.2144C>T	p.Ala715Val	p.A715V	ENST00000369096	NM_001198.3	715	gCg/gTg	7/7	1	2	FACETS	0.913	0.808	1	0.913	0.808	1	CLONAL	1	TRUE	1	0.26	2		507	733	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642538	117642538	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	130	768	0	ENST00000368508.3:c.5661G>T	p.Lys1887Asn	p.K1887N	ENST00000368508	NM_002944.2	1887	aaG/aaT	35/43	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.26	2		768	919	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001305	150001305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568586257	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	55	724	0	ENST00000253339.5:c.2299C>T	p.Arg767Cys	p.R767C	ENST00000253339		767	Cgt/Tgt	4/7	1	2	FACETS	0.515	0.439	0.598	0.515	0.439	0.598	SUBCLONAL	1	TRUE	1	0.26	2		724	822	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023019	150023019	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	66	479	0	ENST00000253339.5:c.244C>T	p.Arg82Ter	p.R82*	ENST00000253339		82	Cga/Tga	1/7	1	2	FACETS	0.5	0.432	0.573	0.5	0.432	0.573	SUBCLONAL	1	TRUE	1	0.26	2		479	1016	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265353	152265353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188957694	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	79	473	0	ENST00000206249.3:c.806G>A	p.Arg269His	p.R269H	ENST00000206249	NM_000125.3	269	cGc/cAc	4/8	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.26	2		473	594	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781201	161781201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55830907	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	70	752	0	ENST00000366898.1:c.1204C>T	p.Arg402Cys	p.R402C	ENST00000366898	NM_004562.2	402	Cgt/Tgt	11/12	1	2	FACETS	0.634	0.552	0.724	0.634	0.552	0.724	SUBCLONAL	1	TRUE	1	0.26	2		752	849	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211050	55211050	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17289589	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	71	682	0	ENST00000275493.2:c.293G>A	p.Arg98Gln	p.R98Q	ENST00000275493	NM_005228.3	98	cGa/cAa	3/28	1	2	FACETS	0.677	0.59	0.771	0.677	0.59	0.771	SUBCLONAL	1	TRUE	1	0.26	2		682	807	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508169	106508169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381484125	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	27	177	0	ENST00000359195.3:c.163G>A	p.Glu55Lys	p.E55K	ENST00000359195	NM_002649.2	55	Gaa/Aaa	2/11	1	2	FACETS	0.75	0.598	0.922	0.75	0.598	0.922	CLONAL	1	TRUE	1	0.26	2		177	277	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340294	116340294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	80	385	1	ENST00000397752.3:c.1156C>T	p.Leu386Phe	p.L386F	ENST00000397752	NM_000245.2	386	Ctc/Ttc	2/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.26	2		386	508	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476884	140476884	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	72	595	0	ENST00000288602.6:c.1522A>G	p.Thr508Ala	p.T508A	ENST00000288602	NM_004333.4	508	Aca/Gca	13/18	1	2	FACETS	0.783	0.684	0.891	0.783	0.684	0.891	SUBCLONAL	1	TRUE	1	0.26	2		595	707	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148526853	148526853	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	85	615	0	ENST00000320356.2:c.451A>T	p.Lys151Ter	p.K151*	ENST00000320356	NM_004456.4	151	Aaa/Taa	5/20	1	2	FACETS	0.955	0.844	1	0.955	0.844	1	CLONAL	1	TRUE	1	0.26	2		615	685	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845367	151845367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	103	758	1	ENST00000262189.6:c.13645C>T	p.Arg4549Cys	p.R4549C	ENST00000262189	NM_170606.2	4549	Cgc/Tgc	52/59	1	2	FACETS	0.955	0.854	1	0.955	0.854	1	CLONAL	1	TRUE	1	0.26	2		759	830	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878061	151878061	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	72	557	0	ENST00000262189.6:c.6884C>T	p.Ala2295Val	p.A2295V	ENST00000262189	NM_170606.2	2295	gCc/gTc	36/59	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.26	2		557	552	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38184373	38184373	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	63	490	0	ENST00000317025.8:c.1583G>A	p.Gly528Glu	p.G528E	ENST00000317025	NM_023034.1	528	gGa/gAa	7/24	1	2	FACETS	0.841	0.728	0.964	0.841	0.728	0.964	CLONAL	1	TRUE	1	0.26	2		490	576	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737101	145737101	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	74	696	1	ENST00000428558.2:c.3465C>A	p.Phe1155Leu	p.F1155L	ENST00000428558	NM_004260.3	1155	ttC/ttA	21/22	1	2	FACETS	0.87	0.762	0.987	0.87	0.762	0.987	CLONAL	1	TRUE	1	0.26	2		697	654	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054643	5054643	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	28	418	0	ENST00000381652.3:c.695G>T	p.Arg232Ile	p.R232I	ENST00000381652	NM_004972.3	232	aGa/aTa	7/25	1	2	FACETS	0.408	0.325	0.503	0.408	0.325	0.503	SUBCLONAL	1	TRUE	1	0.26	2		418	528	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069023	5069023	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs753648225	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	19	307	0	ENST00000381652.3:c.1328G>A	p.Arg443Gln	p.R443Q	ENST00000381652	NM_004972.3	443	cGa/cAa	11/25	1	2	FACETS	0.421	0.319	0.541	0.421	0.319	0.541	SUBCLONAL	1	TRUE	1	0.26	2		307	347	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319965	8319965	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs141403124	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	26	310	0	ENST00000356435.5:c.5536G>A	p.Ala1846Thr	p.A1846T	ENST00000356435		1846	Gcg/Acg	34/35	1	2	FACETS	0.562	0.445	0.696	0.562	0.445	0.696	SUBCLONAL	1	TRUE	1	0.26	2		310	356	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340461	8340461	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	92	514	0	ENST00000356435.5:c.5135A>G	p.Lys1712Arg	p.K1712R	ENST00000356435		1712	aAa/aGa	31/35	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.26	2		514	660	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185512	27185512	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	85	666	0	ENST00000380036.4:c.1212C>A	p.Phe404Leu	p.F404L	ENST00000380036	NM_000459.3	404	ttC/ttA	9/23	1	2	FACETS	0.906	0.8	1	0.906	0.8	1	CLONAL	1	TRUE	1	0.26	2		666	722	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412494	80412494	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	69	242	0	ENST00000286548.4:c.547C>T	p.Arg183Ter	p.R183*	ENST00000286548	NM_002072.3	183	Cga/Tga	4/7	1	2	FACETS	0.777	0.676	0.886	0.777	0.676	0.886	SUBCLONAL	1	TRUE	1	0.26	2		242	683	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891278	101891278	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1368326650	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	102	736	0	ENST00000374994.4:c.239G>A	p.Arg80Gln	p.R80Q	ENST00000374994	NM_004612.2	80	cGa/cAa	2/9	1	2	FACETS	0.962	0.859	1	0.962	0.859	1	CLONAL	1	TRUE	1	0.26	2		736	816	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915951	127915951	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	103	629	0	ENST00000373547.4:c.530G>A	p.Arg177Gln	p.R177Q	ENST00000373547	NM_002721.4	177	cGa/cAa	6/7	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.26	2		629	771	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401004	139401004	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180096756	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	41	644	3	ENST00000277541.6:c.3989G>A	p.Arg1330His	p.R1330H	ENST00000277541	NM_017617.3	1330	cGc/cAc	24/34	1	2	FACETS	0.398	0.33	0.474	0.398	0.33	0.474	SUBCLONAL	1	TRUE	1	0.26	2		647	792	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923634	39923634	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	108	711	3	ENST00000378444.4:c.3457C>A	p.Pro1153Thr	p.P1153T	ENST00000378444	NM_001123385.1	1153	Cca/Aca	7/15	1	2	FACETS	0.973	0.872	1	0.973	0.872	1	CLONAL	1	TRUE	1	0.26	2		714	854	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224247	53224247	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	77	732	0	ENST00000375401.3:c.3304C>A	p.Leu1102Ile	p.L1102I	ENST00000375401	NM_004187.3	1102	Ctc/Atc	22/26	1	2	FACETS	0.787	0.69	0.891	0.787	0.69	0.891	SUBCLONAL	1	TRUE	1	0.26	2		732	753	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226043	53226043	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782308622	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	114	787	0	ENST00000375401.3:c.2806C>T	p.Arg936Cys	p.R936C	ENST00000375401	NM_004187.3	936	Cgc/Tgc	19/26	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.26	2		787	847	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411575	63411575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs904761868	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	67	790	0	ENST00000330258.3:c.1592G>A	p.Arg531Gln	p.R531Q	ENST00000330258	NM_152424.3	531	cGa/cAa	2/2	1	2	FACETS	0.579	0.502	0.663	0.579	0.502	0.663	SUBCLONAL	1	TRUE	1	0.26	2		790	890	SUCCESS
AR	367	MSKCC	GRCh37	X	66765677	66765677	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1315081227	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	126	940	0	ENST00000374690.3:c.689C>T	p.Ser230Leu	p.S230L	ENST00000374690	NM_000044.3	230	tCg/tTg	1/8	1	2	FACETS	0.993	0.898	1	0.993	0.898	1	CLONAL	1	TRUE	1	0.26	2		940	976	SUCCESS
AR	367	MSKCC	GRCh37	X	66942737	66942737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1419690127	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	64	638	0	ENST00000374690.3:c.2518G>A	p.Asp840Asn	p.D840N	ENST00000374690	NM_000044.3	840	Gat/Aat	7/8	1	2	FACETS	0.666	0.576	0.764	0.666	0.576	0.764	SUBCLONAL	1	TRUE	1	0.26	2		638	739	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814238	76814238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	59	496	1	ENST00000373344.5:c.6406G>A	p.Asp2136Asn	p.D2136N	ENST00000373344	NM_000489.3	2136	Gac/Aac	29/35	1	2	FACETS	0.699	0.601	0.806	0.699	0.601	0.806	SUBCLONAL	1	TRUE	1	0.26	2		497	649	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829806	76829806	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	75	601	1	ENST00000373344.5:c.6235C>T	p.Arg2079Ter	p.R2079*	ENST00000373344	NM_000489.3	2079	Cga/Tga	28/35	1	2	FACETS	0.917	0.804	1	0.917	0.804	1	CLONAL	1	TRUE	1	0.26	2		602	629	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854897	76854897	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	56	763	1	ENST00000373344.5:c.5939C>A	p.Ser1980Tyr	p.S1980Y	ENST00000373344	NM_000489.3	1980	tCt/tAt	25/35	1	2	FACETS	0.585	0.5	0.678	0.585	0.5	0.678	SUBCLONAL	1	TRUE	1	0.26	2		764	736	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938029	76938029	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	102	817	0	ENST00000373344.5:c.2719C>T	p.Arg907Ter	p.R907*	ENST00000373344	NM_000489.3	907	Cga/Tga	9/35	1	2	FACETS	0.801	0.715	0.893	0.801	0.715	0.893	CLONAL	1	TRUE	1	0.26	2		817	979	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940445	76940445	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs45572441	NA	P-0036297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	84	650	0	ENST00000373344.5:c.648G>T	p.Met216Ile	p.M216I	ENST00000373344	NM_000489.3	216	atG/atT	8/35	1	2	FACETS	0.842	0.743	0.949	0.842	0.743	0.949	CLONAL	1	TRUE	1	0.26	2		650	767	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183764	10183764	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs5030804	NA	P-0036300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	78	718	0	ENST00000256474.2:c.233A>G	p.Asn78Ser	p.N78S	ENST00000256474	NM_000551.3	78	aAt/aGt	1/3	1	2	FACETS	0.802	0.704	0.907	0.802	0.704	0.907	CLONAL	1	TRUE	1	0.273323117379722	2		718	712	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183800	10183800	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs143985153	NA	P-0036300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	92	716	1	ENST00000256474.2:c.269A>T	p.Asn90Ile	p.N90I	ENST00000256474	NM_000551.3	90	aAc/aTc	1/3	1	2	FACETS	0.98	0.871	1	0.98	0.871	1	CLONAL	1	TRUE	1	0.273323117379722	2		717	687	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829066	128829066	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs41304185	NA	P-0036301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	14	7	0	ENST00000249373.3:c.74A>G	p.Asp25Gly	p.D25G	ENST00000249373	NM_005631.4	25	gAc/gGc	1/12	NA	2	FACETS	1	0.803	1			1	INDETERMINATE	1	TRUE	NA	0.733652510717013	2		7	36	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281359	49281359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764117879	NA	P-0036301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	538	833	2	ENST00000282018.3:c.406C>T	p.Arg136Cys	p.R136C	ENST00000282018	NM_020377.2	136	Cgt/Tgt	1/1	0.709008268931273	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.733652510717013	1		835	902	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46543255	46543255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	334	551	1	ENST00000262741.5:c.246G>T	p.Met82Ile	p.M82I	ENST00000262741	NM_003629.3	82	atG/atT	3/10	NA	2	FACETS	0.943	0.893	0.993			1	INDETERMINATE	1	TRUE	NA	0.733652510717013	2		552	966	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613205	52613207	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs1156298616	NA	P-0036301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	133	606	0	ENST00000394830.3:c.3321_3323del	p.Glu1107del	p.E1107del	ENST00000394830	NM_018313.4	1107	gaAGAt/gat	22/30	1	2	FACETS	0.351	0.318	0.385	0.351	0.318	0.385	SUBCLONAL	1	TRUE	1	0.733652510717013	2		606	1034	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111499	8111522	+	frameshift_variant	Frame_Shift_Del	DEL	AGGAGGAATGCCAATGGGGACCCT	AGGAGGAATGCCAATGGGGACCCT	TCCTCCTCCA	novel	NA	P-0036301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	263	581	2	ENST00000346208.3:c.985_1008delinsTCCTCCTCCA	p.Arg329SerfsTer18	p.R329Sfs*18	ENST00000346208		329	AGGAGGAATGCCAATGGGGACCCT/TCCTCCTCCA	5/6	1	2	FACETS	0.767	0.72	0.815	0.767	0.72	0.815	SUBCLONAL	1	TRUE	1	0.733652510717013	2		583	935	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038189	30038189	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0036304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	78	549	0	ENST00000338641.4:c.364-2A>C		p.X122_splice	ENST00000338641	NM_000268.3	122			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		549	502	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190037	123190037	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	29	319	0	ENST00000218089.9:c.1256C>T	p.Ser419Leu	p.S419L	ENST00000218089	NM_001042749.1	419	tCa/tTa	14/35	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		319	348	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191719	123191722	+	frameshift_variant	Frame_Shift_Ins	INS	CTTC	CTTC	TTTTT	novel	NA	P-0036305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	13	151	0	ENST00000218089.9:c.1308_1311delinsTTTTT	p.Ser438Ter	p.S438*	ENST00000218089	NM_001042749.1	436	ctCTTC/ctTTTTT	15/35	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		151	164	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0036307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	52	331	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.875	0.748	1	0.875	0.748	1	CLONAL	1	TRUE	1	0.331897258024518	2		331	358	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249017	55249018	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCA	rs1554350381	NA	P-0036307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7261	1307	465	0	ENST00000275493.2:c.2317_2319dup	p.His773dup	p.H773dup	ENST00000275493	NM_005228.3	773	ccc/ccCCAc	20/28	0.331897258024518	74	FACETS	0.992	0.962	1	0.161	0.156	0.166	CLONAL	12	TRUE	0	0.331897258024518	74		465	8568	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0036307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5695	6489	838	1	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.331897258024518	74	FACETS	0.989	0.979	1	0.562	0.555	0.568	CLONAL	42	TRUE	0	0.331897258024518	74		839	12184	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0036308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	383	611	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.708857593339168	2	FACETS	0.984	0.951	1	0.984	0.951	1	CLONAL	2	TRUE	0	0.708857593339168	2		611	549	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553402	41553402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	147	370	0	ENST00000263253.7:c.3491G>A	p.Cys1164Tyr	p.C1164Y	ENST00000263253	NM_001429.3	1164	tGt/tAt	18/31	0.708857593339168	3	FACETS	1	0.985	1	0.439	0.404	0.474	CLONAL	1	TRUE	0	0.708857593339168	3		370	427	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528673	157528673	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1226524520	NA	P-0036308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	183	565	0	ENST00000346085.5:c.6398C>T	p.Ala2133Val	p.A2133V	ENST00000346085	NM_020732.3	2133	gCg/gTg	20/20	0.508978152442429	3	FACETS	1	0.976	1	0.559	0.518	0.601	CLONAL	1	TRUE	1	0.708857593339168	3		565	626	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099885	27099885	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	68	467	0	ENST00000324856.7:c.3764G>T	p.Gly1255Val	p.G1255V	ENST00000324856	NM_006015.4	1255	gGg/gTg	15/20	0.266073179564074	6	FACETS	0.688	0.598	0.786	0.172	0.149	0.197	INDETERMINATE	1	TRUE	2	0.708857593339168	6		467	674	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322601	39322601	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	214	494	0	ENST00000373001.3:c.391G>C	p.Glu131Gln	p.E131Q	ENST00000373001	NM_022157.3	131	Gag/Cag	2/7	0.266073179564074	6	FACETS	1	0.956	1	0.516	0.481	0.552	INDETERMINATE	2	TRUE	2	0.708857593339168	6		494	707	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699271	117699271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	177	458	0	ENST00000369458.3:c.370G>A	p.Asp124Asn	p.D124N	ENST00000369458	NM_024626.3	124	Gat/Aat	3/6	0.266073179564074	6	FACETS	0.892	0.825	0.961	0.446	0.412	0.481	INDETERMINATE	2	TRUE	2	0.708857593339168	6		458	677	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600418	43600418	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	104	390	0	ENST00000355710.3:c.644G>C	p.Arg215Pro	p.R215P	ENST00000355710	NM_020975.4	215	cGc/cCc	4/20	0.229121006797996	2	FACETS	0.78	0.705	0.859	0.39	0.352	0.43	INDETERMINATE	1	TRUE	0	0.708857593339168	2		390	376	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435079	18435079	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	69	253	0	ENST00000266497.5:c.64C>A	p.Gln22Lys	p.Q22K	ENST00000266497		22	Caa/Aaa	1/31	0.708857593339168	1	FACETS	0.982	0.887	1	0.982	0.887	1	CLONAL	1	TRUE	0	0.708857593339168	1		253	128	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339575	339575	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	315	703	0	ENST00000262320.3:c.2327G>T	p.Ser776Ile	p.S776I	ENST00000262320	NM_003502.3	776	aGt/aTt	10/11	0.223378403357013	4	FACETS	0.976	0.926	1	0.976	0.926	1	INDETERMINATE	2	TRUE	2	0.708857593339168	4		703	778	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484264	57484264	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	48	369	0	ENST00000371085.3:c.578G>A	p.Ser193Asn	p.S193N	ENST00000371085	NM_000516.4	193	aGc/aAc	7/13	0.229121006797996	2	FACETS	0.354	0.299	0.413	0.177	0.149	0.207	INDETERMINATE	1	TRUE	0	0.708857593339168	2		369	383	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643788	52643788	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	141	577	0	ENST00000394830.3:c.2108C>T	p.Pro703Leu	p.P703L	ENST00000394830	NM_018313.4	703	cCc/cTc	17/30	0.708857593339168	1	FACETS	0.592	0.544	0.641	0.592	0.544	0.641	SUBCLONAL	1	TRUE	0	0.708857593339168	1		577	434	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449466	149449466	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	53	508	0	ENST00000286301.3:c.1480G>C	p.Gly494Arg	p.G494R	ENST00000286301	NM_005211.3	494	Ggc/Cgc	10/22	0.284088309832087	1	FACETS	0.215	0.183	0.249	0.215	0.183	0.249	INDETERMINATE	1	TRUE	0	0.708857593339168	1		508	450	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117645534	117645534	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	268	395	0	ENST00000368508.3:c.5602G>C	p.Val1868Leu	p.V1868L	ENST00000368508	NM_002944.2	1868	Gtt/Ctt	34/43	0.508978152442429	3	FACETS	0.959	0.91	1	0.959	0.91	1	CLONAL	2	TRUE	1	0.708857593339168	3		395	534	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400000	139400000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	459	711	0	ENST00000277541.6:c.4348G>T	p.Glu1450Ter	p.E1450*	ENST00000277541	NM_017617.3	1450	Gag/Tag	25/34	0.26078578571857	3	FACETS	1	0.993	1	0.747	0.72	0.773	INDETERMINATE	2	TRUE	0	0.708857593339168	3		711	783	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227981	53227981	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	480	686	1	ENST00000375401.3:c.2333G>T	p.Arg778Leu	p.R778L	ENST00000375401	NM_004187.3	778	cGa/cTa	16/26	0.708857593339168	3	FACETS	0.987	0.95	1	0.987	0.95	1	CLONAL	2	TRUE	1	0.708857593339168	3		687	929	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410412	63410413	+	missense_variant	Missense_Mutation	DNP	CA	CA	TC	novel	NA	P-0036308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	224	712	1	ENST00000330258.3:c.2754_2755delinsGA	p.Asp919Asn	p.D919N	ENST00000330258	NM_152424.3	918	tcTGat/tcGAat	2/2	0.708857593339168	3	FACETS	1	0.979	1	0.556	0.519	0.594	CLONAL	1	TRUE	1	0.708857593339168	3		713	770	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	213	765	30	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.751	0.698	0.807	1	0.991	1	SUBCLONAL	2	TRUE	1	0.257450348520866	2		795	1101	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	168	395	20	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	0.993	1	CLONAL	2	TRUE	1	0.257450348520866	2		415	573	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946340	2946340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1171346123	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	121	941	0	ENST00000396946.4:c.3397C>T	p.Arg1133Cys	p.R1133C	ENST00000396946	NM_032415.4	1133	Cgc/Tgc	25/25	0.254382812406802	3	FACETS	0.822	0.74	0.909	0.411	0.37	0.455	CLONAL	1	TRUE	1	0.257450348520866	3		941	1291	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	78	534	3	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	0.797	0.7	0.902	0.797	0.7	0.902	CLONAL	1	TRUE	1	0.257450348520866	2		537	760	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	85	397	13	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	0.226368847557963	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.257450348520866	1		410	530	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913837	32913837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359507	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	44	400	1	ENST00000380152.3:c.5351del	p.Asn1784ThrfsTer7	p.N1784Tfs*7	ENST00000380152		1782	cAa/ca	11/27	0.254382812406802	3	FACETS	0.667	0.559	0.788	0.334	0.279	0.394	SUBCLONAL	1	TRUE	1	0.257450348520866	3		401	578	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672323	86672323	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554049422	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	49	360	1	ENST00000274376.6:c.2125C>T	p.Arg709Ter	p.R709*	ENST00000274376	NM_002890.2	709	Cga/Tga	16/25	1	2	FACETS	0.724	0.613	0.846	0.724	0.613	0.846	SUBCLONAL	1	TRUE	1	0.257450348520866	2		361	526	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	135	560	21	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.257450348520866	2		581	763	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	67	493	2	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	0.752	0.653	0.86	0.752	0.653	0.86	SUBCLONAL	1	TRUE	1	0.257450348520866	2		495	692	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	90	388	6	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.257450348520866	2		394	477	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279861	46279866	+	inframe_deletion	In_Frame_Del	DEL	CAGCAA	CAGCAA	-	rs748517056	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	52	475	1	ENST00000371998.3:c.3810_3815del	p.Gln1275_Gln1276del	p.Q1275_Q1276del	ENST00000371998		1263	CAGCAA/-	20/23	0.254382812406802	3	FACETS	0.684	0.581	0.796	0.342	0.29	0.398	SUBCLONAL	1	TRUE	1	0.257450348520866	3		476	667	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012465	29012465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373801409	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	67	485	0	ENST00000282397.4:c.406G>A	p.Val136Ile	p.V136I	ENST00000282397	NM_002019.4	136	Gta/Ata	4/30	0.254382812406802	3	FACETS	0.924	0.803	1	0.462	0.401	0.528	CLONAL	1	TRUE	1	0.257450348520866	3		485	636	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	46	595	4	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	0.463	0.389	0.545	0.463	0.389	0.545	SUBCLONAL	1	TRUE	1	0.257450348520866	2		599	772	SUCCESS
APC	324	MSKCC	GRCh37	5	112174783	112174783	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	76	242	1	ENST00000257430.4:c.3495del	p.Lys1165AsnfsTer17	p.K1165Nfs*17	ENST00000257430	NM_000038.5	1164	atA/at	16/16	1	2	FACETS	0.843	0.745	0.948	1	0.98	1	CLONAL	2	TRUE	1	0.257450348520866	2		243	350	SUCCESS
APC	324	MSKCC	GRCh37	5	112178000	112178000	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768922431	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	61	375	0	ENST00000257430.4:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000257430	NM_000038.5	2237	Cga/Tga	16/16	1	2	FACETS	0.918	0.793	1	0.918	0.793	1	CLONAL	1	TRUE	1	0.257450348520866	2		375	516	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054650	13054658	+	inframe_deletion	In_Frame_Del	DEL	GAGGATGAG	GAGGATGAG	-	rs550353351	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	49	471	0	ENST00000316448.5:c.1191_1199del	p.Glu398_Asp400del	p.E398_D400del	ENST00000316448	NM_004343.3	393	GAGGATGAG/-	9/9	1	2	FACETS	0.561	0.474	0.656	0.561	0.474	0.656	SUBCLONAL	1	TRUE	1	0.257450348520866	2		471	679	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056262	27056262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	122	429	7	ENST00000324856.7:c.1258C>T	p.Gln420Ter	p.Q420*	ENST00000324856	NM_006015.4	420	Cag/Tag	2/20	1	2	FACETS	0.753	0.683	0.828	1	0.985	1	SUBCLONAL	2	TRUE	1	0.257450348520866	2		436	629	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597879	43597879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	123	894	0	ENST00000355710.3:c.427G>A	p.Ala143Thr	p.A143T	ENST00000355710	NM_020975.4	143	Gcc/Acc	3/20	1	2	FACETS	0.756	0.681	0.835	0.756	0.681	0.835	SUBCLONAL	1	TRUE	1	0.257450348520866	2		894	1264	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165282	47165283	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	128	431	1	ENST00000409792.3:c.843dup	p.Glu282ArgfsTer9	p.E282Rfs*9	ENST00000409792	NM_014159.6	281	-/A	3/21	0.257450348520866	2	FACETS	0.797	0.724	0.873	0.797	0.724	0.873	SUBCLONAL	2	TRUE	0	0.257450348520866	2		432	624	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50482355	50482355	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	103	531	3	ENST00000394963.4:c.711del	p.Phe237LeufsTer5	p.F237Lfs*5	ENST00000394963	NM_003076.4	236	Ttt/tt	6/13	1	2	FACETS	0.958	0.857	1	0.958	0.857	1	CLONAL	1	TRUE	1	0.257450348520866	2		534	835	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029072	14029072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763619616	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	46	255	0	ENST00000311895.7:c.1283C>T	p.Ala428Val	p.A428V	ENST00000311895	NM_005236.2	428	gCg/gTg	8/11	1	2	FACETS	0.966	0.816	1	0.966	0.816	1	CLONAL	1	TRUE	1	0.257450348520866	2		255	370	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549116	21549116	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	80	559	0	ENST00000382592.4:c.3160C>T	p.Arg1054Ter	p.R1054*	ENST00000382592	NM_014572.2	1054	Cga/Tga	8/8	0.254382812406802	3	FACETS	0.809	0.711	0.915	0.405	0.355	0.458	CLONAL	1	TRUE	1	0.257450348520866	3		559	867	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303304	15303304	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145069047	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	238	774	22	ENST00000263388.2:c.224G>A	p.Arg75Gln	p.R75Q	ENST00000263388	NM_000435.2	75	cGg/cAg	3/33	1	2	FACETS	0.822	0.767	0.88	1	0.993	1	CLONAL	2	TRUE	1	0.257450348520866	2		796	1124	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070324	37070324	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63749795	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	151	315	18	ENST00000231790.2:c.1459C>T	p.Arg487Ter	p.R487*	ENST00000231790	NM_000249.3	487	Cga/Tga	13/19	0.257450348520866	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.257450348520866	2		333	479	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022295	31022295	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1204364792	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	30	353	0	ENST00000375687.4:c.1780T>C	p.Cys594Arg	p.C594R	ENST00000375687	NM_015338.5	594	Tgc/Cgc	13/13	0.254382812406802	3	FACETS	0.5	0.402	0.612	0.25	0.201	0.306	SUBCLONAL	1	TRUE	1	0.257450348520866	3		353	526	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509084	66509085	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	20	255	3	ENST00000273854.3:c.242dup	p.Asn81LysfsTer8	p.N81Kfs*8	ENST00000273854	NM_004439.5	81	aat/aaAt	2/18	1	2	FACETS	0.5	0.382	0.637	0.5	0.382	0.637	SUBCLONAL	1	TRUE	1	0.257450348520866	2		258	311	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	113	669	10	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.257450348520866	2		679	859	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647657	3647657	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs774532876	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	143	916	2	ENST00000294008.3:c.1406del	p.Pro469HisfsTer4	p.P469Hfs*4	ENST00000294008	NM_032444.2	469	cCa/ca	7/15	1	2	FACETS	0.893	0.812	0.978	0.893	0.812	0.978	CLONAL	1	TRUE	1	0.257450348520866	2		918	1244	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304140	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	40	478	1	ENST00000355112.3:c.1543_1544del	p.Asn515Ter	p.N515*	ENST00000355112	NM_000057.2	512	ggAAaa/ggaa	7/22	1	2	FACETS	0.483	0.401	0.576	0.483	0.401	0.576	SUBCLONAL	1	TRUE	1	0.257450348520866	2		479	643	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899231	78899231	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200514795	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	81	571	0	ENST00000306801.3:c.2870C>T	p.Thr957Met	p.T957M	ENST00000306801	NM_020761.2	957	aCg/aTg	24/34	0.257450348520866	2	FACETS	0.861	0.758	0.971	0.43	0.379	0.486	CLONAL	1	TRUE	0	0.257450348520866	2		571	731	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211779	5211779	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs544687640	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	85	684	0	ENST00000357368.4:c.5056C>T	p.Arg1686Trp	p.R1686W	ENST00000357368	NM_002850.3	1686	Cgg/Tgg	33/38	1	2	FACETS	0.854	0.754	0.961	0.854	0.754	0.961	CLONAL	1	TRUE	1	0.257450348520866	2		684	773	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94908685	94908685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764427282	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	173	665	24	ENST00000536441.1:c.1369C>T	p.Arg457Trp	p.R457W	ENST00000536441	NM_144665.3	457	Cgg/Tgg	9/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.257450348520866	2		689	926	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919194	178919194	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	25	232	2	ENST00000263967.3:c.685del	p.Thr229LeufsTer11	p.T229Lfs*11	ENST00000263967	NM_006218.2	227	Aaa/aa	4/21	1	2	FACETS	0.617	0.486	0.766	0.617	0.486	0.766	SUBCLONAL	1	TRUE	1	0.257450348520866	2		234	315	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117191	7117191	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	63	657	4	ENST00000302850.5:c.4025del	p.Gly1342AlafsTer23	p.G1342Afs*23	ENST00000302850	NM_000208.2	1342	gGc/gc	22/22	1	2	FACETS	0.564	0.487	0.649	0.564	0.487	0.649	SUBCLONAL	1	TRUE	1	0.257450348520866	2		661	867	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30102133	30102133	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	68	610	0	ENST00000331968.5:c.1334G>A	p.Arg445Lys	p.R445K	ENST00000331968	NM_002742.2	445	aGa/aAa	9/18	1	2	FACETS	0.843	0.733	0.961	0.843	0.733	0.961	CLONAL	1	TRUE	1	0.257450348520866	2		610	627	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373548	118373548	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	44	380	0	ENST00000534358.1:c.6941T>C	p.Leu2314Pro	p.L2314P	ENST00000534358	NM_005933.3	2314	cTg/cCg	27/36	1	2	FACETS	0.65	0.545	0.766	0.65	0.545	0.766	SUBCLONAL	1	TRUE	1	0.257450348520866	2		380	526	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480130	50480130	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	51	387	0	ENST00000394963.4:c.364A>G	p.Asn122Asp	p.N122D	ENST00000394963	NM_003076.4	122	Aat/Gat	2/13	1	2	FACETS	0.689	0.585	0.803	0.689	0.585	0.803	SUBCLONAL	1	TRUE	1	0.257450348520866	2		387	575	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218359	133218359	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	107	793	2	ENST00000320574.5:c.5252C>G	p.Ala1751Gly	p.A1751G	ENST00000320574	NM_006231.2	1751	gCc/gGc	39/49	1	2	FACETS	0.765	0.684	0.85	0.765	0.684	0.85	SUBCLONAL	1	TRUE	1	0.257450348520866	2		795	1087	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220501	133220501	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	104	677	0	ENST00000320574.5:c.4212G>T	p.Glu1404Asp	p.E1404D	ENST00000320574	NM_006231.2	1404	gaG/gaT	33/49	1	2	FACETS	0.874	0.782	0.973	0.874	0.782	0.973	CLONAL	1	TRUE	1	0.257450348520866	2		677	924	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778545	3778545	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	155	901	0	ENST00000262367.5:c.6503G>A	p.Gly2168Asp	p.G2168D	ENST00000262367	NM_004380.2	2168	gGc/gAc	31/31	1	2	FACETS	0.944	0.862	1	0.944	0.862	1	CLONAL	1	TRUE	1	0.257450348520866	2		901	1275	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781449	3781449	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	121	393	9	ENST00000262367.5:c.4916C>T	p.Ala1639Val	p.A1639V	ENST00000262367	NM_004380.2	1639	gCt/gTt	30/31	1	2	FACETS	0.835	0.757	0.916	1	0.987	1	CLONAL	2	TRUE	1	0.257450348520866	2		402	563	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992370	72992370	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770958977	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	262	927	34	ENST00000268489.5:c.1675G>A	p.Val559Ile	p.V559I	ENST00000268489	NM_006885.3	559	Gtt/Att	2/10	1	2	FACETS	0.861	0.806	0.918	1	0.994	1	CLONAL	2	TRUE	1	0.257450348520866	2		961	1182	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217036	7217036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754634220	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	79	441	1	ENST00000380728.2:c.485G>A	p.Arg162Gln	p.R162Q	ENST00000380728		162	cGg/cAg	7/11	1	2	FACETS	0.957	0.842	1	0.957	0.842	1	CLONAL	1	TRUE	1	0.257450348520866	2		442	641	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612386	1612386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1359915796	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	142	844	1	ENST00000344749.5:c.1633C>T	p.Arg545Trp	p.R545W	ENST00000344749	NM_001136139.2	545	Cgg/Tgg	18/19	1	2	FACETS	0.951	0.865	1	0.951	0.865	1	CLONAL	1	TRUE	1	0.257450348520866	2		845	1160	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627774	14627774	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs370822819	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	71	635	9	ENST00000254322.2:c.296A>G	p.His99Arg	p.H99R	ENST00000254322	NM_006145.1	99	cAt/cGt	2/3	1	2	FACETS	0.63	0.549	0.719	0.63	0.549	0.719	SUBCLONAL	1	TRUE	1	0.257450348520866	2		644	875	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311647	15311647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	16	47	1	ENST00000263388.2:c.70G>A	p.Val24Met	p.V24M	ENST00000263388	NM_000435.2	24	Gtg/Atg	1/33	1	2	FACETS	0.914	0.693	1	1	0.923	1	CLONAL	2	TRUE	1	0.257450348520866	2		48	68	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224699	36224699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781596697	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1221	124	1056	2	ENST00000222270.7:c.7085C>T	p.Pro2362Leu	p.P2362L	ENST00000222270	NM_014727.1	2362	cCg/cTg	30/37	1	2	FACETS	0.716	0.646	0.791	0.716	0.646	0.791	SUBCLONAL	1	TRUE	1	0.257450348520866	2		1058	1345	SUCCESS
AXL	558	MSKCC	GRCh37	19	41749577	41749577	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774262418	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	104	614	2	ENST00000301178.4:c.1502G>A	p.Arg501His	p.R501H	ENST00000301178	NM_021913.4	501	cGc/cAc	12/20	1	2	FACETS	0.885	0.791	0.985	0.885	0.791	0.985	CLONAL	1	TRUE	1	0.257450348520866	2		616	913	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028240	48028241	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	rs267608042	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	75	428	0	ENST00000234420.5:c.3119_3120del	p.Phe1040Ter	p.F1040*	ENST00000234420	NM_000179.2	1040	TTt/t	4/10	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.257450348520866	2		428	570	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098705	47098705	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408383191	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	257	657	17	ENST00000409792.3:c.6569C>T	p.Pro2190Leu	p.P2190L	ENST00000409792	NM_014159.6	2190	cCc/cTc	15/21	0.257450348520866	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.257450348520866	2		674	845	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880915	134880915	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	84	560	0	ENST00000398015.3:c.1478T>G	p.Ile493Ser	p.I493S	ENST00000398015	NM_004441.4	493	aTt/aGt	7/16	1	2	FACETS	0.943	0.833	1	0.943	0.833	1	CLONAL	1	TRUE	1	0.257450348520866	2		560	692	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535280	66535280	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	70	608	0	ENST00000273854.3:c.181G>T	p.Val61Leu	p.V61L	ENST00000273854	NM_004439.5	61	Gtg/Ttg	1/18	1	2	FACETS	0.693	0.603	0.79	0.693	0.603	0.79	SUBCLONAL	1	TRUE	1	0.257450348520866	2		608	785	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176909	56176909	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	36	266	0	ENST00000399503.3:c.2180-1G>T		p.X727_splice	ENST00000399503	NM_005921.1	727			1	2	FACETS	0.691	0.568	0.828	0.691	0.568	0.828	SUBCLONAL	1	TRUE	1	0.257450348520866	2		266	405	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755669	57755670	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1279983695	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	200	745	14	ENST00000274289.3:c.117dup	p.Glu40ArgfsTer66	p.E40Rfs*66	ENST00000274289	NM_006622.3	39	-/C	1/14	1	2	FACETS	0.803	0.744	0.864	1	0.992	1	CLONAL	2	TRUE	1	0.257450348520866	2		759	968	SUCCESS
APC	324	MSKCC	GRCh37	5	112179589	112179589	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	80	316	9	ENST00000257430.4:c.8298C>A	p.Ser2766Arg	p.S2766R	ENST00000257430	NM_000038.5	2766	agC/agA	16/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.257450348520866	2		325	449	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394891	394891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	66	414	0	ENST00000380956.4:c.287G>A	p.Arg96His	p.R96H	ENST00000380956	NM_001195286.1	96	cGc/cAc	3/9	NA	2	FACETS	0.912	0.793	1			1	INDETERMINATE	1	TRUE	NA	0.257450348520866	2		414	562	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839769	27839769	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	151	537	19	ENST00000328488.2:c.325A>G	p.Asn109Asp	p.N109D	ENST00000328488	NM_003533.2	109	Aac/Gac	1/1	0.226368847557963	1	FACETS	0.758	0.695	0.824	1	0.988	1	SUBCLONAL	2	TRUE	0	0.257450348520866	1		556	674	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968244	2968244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161484391	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	89	784	0	ENST00000396946.4:c.1742C>T	p.Ala581Val	p.A581V	ENST00000396946	NM_032415.4	581	gCg/gTg	13/25	0.254382812406802	3	FACETS	0.631	0.558	0.711	0.316	0.279	0.356	SUBCLONAL	1	TRUE	1	0.257450348520866	3		784	1236	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072538	5072538	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	38	340	0	ENST00000381652.3:c.1688T>C	p.Val563Ala	p.V563A	ENST00000381652	NM_004972.3	563	gTa/gCa	13/25	1	2	FACETS	0.715	0.591	0.852	0.715	0.591	0.852	SUBCLONAL	1	TRUE	1	0.257450348520866	2		340	413	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227670	53227670	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0036309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	68	267	0	ENST00000375401.3:c.2516+2T>C		p.X839_splice	ENST00000375401	NM_004187.3	839			1	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.257450348520866	1		267	362	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934117	39934117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142236686	NA	P-0036310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	33	486	0	ENST00000378444.4:c.482C>T	p.Ala161Val	p.A161V	ENST00000378444	NM_001123385.1	161	gCc/gTc	4/15	0.247786431964796	1	FACETS	0.361	0.294	0.438	0.361	0.294	0.438	SUBCLONAL	1	TRUE	0	0.33	1		486	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0036310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	117	467	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.298226596398339	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.33	1		467	503	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225983	133225983	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs761617609	NA	P-0036310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	89	530	0	ENST00000320574.5:c.3914G>T	p.Gly1305Val	p.G1305V	ENST00000320574	NM_006231.2	1305	gGg/gTg	31/49	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.33	2		530	535	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0036310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	53	329	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.33	2		329	289	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657372	29657372	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	57	449	0	ENST00000356175.3:c.5605G>T	p.Gly1869Cys	p.G1869C	ENST00000356175	NM_000267.3	1869	Ggc/Tgc	38/57	1	2	FACETS	0.916	0.789	1	0.916	0.789	1	CLONAL	1	TRUE	1	0.33	2		449	377	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8246195	8246195	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	29	405	0	ENST00000335790.3:c.439C>A	p.Leu147Ile	p.L147I	ENST00000335790	NM_002315.2	147	Ctc/Atc	4/4	1	2	FACETS	0.404	0.324	0.495	0.404	0.324	0.495	SUBCLONAL	1	TRUE	1	0.33	2		405	435	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933219	100933219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	80	367	1	ENST00000325455.5:c.2171G>A	p.Arg724Lys	p.R724K	ENST00000325455	NM_001202474.3	724	aGg/aAg	4/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.33	2		368	352	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226171	2226171	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	141	561	0	ENST00000326181.6:c.1869del	p.Ser624ProfsTer10	p.S624Pfs*10	ENST00000326181	NM_032271.2	623	cGg/cg	19/21	0.222974379799292	3	FACETS	0.762	0.696	0.831	0.762	0.696	0.831	SUBCLONAL	2	TRUE	1	0.33	3		561	653	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831291	72831291	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	45	324	0	ENST00000268489.5:c.5290G>T	p.Ala1764Ser	p.A1764S	ENST00000268489	NM_006885.3	1764	Gct/Tct	9/10	1	2	FACETS	0.885	0.748	1	0.885	0.748	1	CLONAL	1	TRUE	1	0.33	2		324	308	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760989	59760989	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	48	430	0	ENST00000259008.2:c.3418G>T	p.Glu1140Ter	p.E1140*	ENST00000259008	NM_032043.2	1140	Gaa/Taa	20/20	0.22822827943158	4	FACETS	0.825	0.698	0.965	0.412	0.349	0.483	CLONAL	1	TRUE	2	0.33	4		430	469	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346734	225346734	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	60	334	0	ENST00000264414.4:c.1904C>T	p.Ala635Val	p.A635V	ENST00000264414	NM_003590.4	635	gCc/gTc	14/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.33	2		334	276	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161684	56161684	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	32	369	0	ENST00000399503.3:c.1181G>T	p.Ser394Ile	p.S394I	ENST00000399503	NM_005921.1	394	aGt/aTt	6/20	1	2	FACETS	0.69	0.562	0.834	0.69	0.562	0.834	SUBCLONAL	1	TRUE	1	0.33	2		369	281	SUCCESS
APC	324	MSKCC	GRCh37	5	112162923	112162923	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	38	320	0	ENST00000257430.4:c.1530del	p.Phe510LeufsTer4	p.F510Lfs*4	ENST00000257430	NM_000038.5	509	acT/ac	12/16	0.179192168375761	2	FACETS	1	0.941	1	0.651	0.545	0.766	INDETERMINATE	1	TRUE	0	0.33	2		320	177	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798747	135798747	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	41	191	0	ENST00000298552.3:c.496del	p.Leu166Ter	p.L166*	ENST00000298552	NM_001162426.1	166	Ctg/tg	6/23	0.179192168375761	2	FACETS	1	0.959	1	0.748	0.633	0.872	INDETERMINATE	1	TRUE	0	0.33	2		191	166	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	76	214	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.429027014459222	2		214	305	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711875	89711876	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	GAGTAACTATTCCCAGTCAGAGGCGCTATGTGTATTATTATAGCTACCTGTTAAAGAATCATCTGGAGTATAGACCAGTGGC	novel	NA	P-0036311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	23	430	0	ENST00000371953.3:c.560_561insGTATAGACCAGTGGCGAGTAACTATTCCCAGTCAGAGGCGCTATGTGTATTATTATAGCTACCTGTTAAAGAATCATCTGGA	p.Asp187GlufsTer20	p.D187Efs*20	ENST00000371953	NM_000314.4	165	gga/gGAGTAACTATTCCCAGTCAGAGGCGCTATGTGTATTATTATAGCTACCTGTTAAAGAATCATCTGGAGTATAGACCAGTGGCga	6/9	0.429027014459222	2	FACETS	0.333	0.259	0.418	0.166	0.129	0.209	SUBCLONAL	1	TRUE	0	0.429027014459222	2		430	322	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926887	112926887	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397507545	NA	P-0036311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	21	686	0	ENST00000351677.2:c.1507G>C	p.Gly503Arg	p.G503R	ENST00000351677	NM_002834.3	503	Ggg/Cgg	13/16	0.140760096076639	4	FACETS	0.201	0.154	0.257	0.101	0.077	0.129	INDETERMINATE	1	TRUE	2	0.429027014459222	4		686	696	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572936	7572948	+	frameshift_variant	Frame_Shift_Del	DEL	GTCAGGCCCTTCT	GTCAGGCCCTTCT	-	novel	NA	P-0036312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	40	601	0	ENST00000269305.4:c.1161_1173del	p.Glu388GlnfsTer30	p.E388Qfs*30	ENST00000269305	NM_001126112.2	387	acAGAAGGGCCTGAC/ac	11/11	0.246856382003291	1	FACETS	0.248	0.206	0.296	0.248	0.206	0.296	SUBCLONAL	1	TRUE	0	0.407815149163246	1		601	629	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0036313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	171	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.329145433040466	3	FACETS	0.936	0.87	1	0.936	0.87	1	CLONAL	3	TRUE	0	0.329145433040466	3		452	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0036313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	122	657	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.329145433040466	1	FACETS	0.851	0.77	0.936	0.851	0.77	0.936	CLONAL	1	TRUE	0	0.329145433040466	1		657	728	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663375	227663375	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	120	440	0	ENST00000305123.5:c.80A>G	p.Lys27Arg	p.K27R	ENST00000305123	NM_005544.2	27	aAa/aGa	1/2	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.329145433040466	2		440	676	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs763804037	NA	P-0036313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	116	400	0	ENST00000304494.5:c.143C>G	p.Pro48Arg	p.P48R	ENST00000304494	NM_000077.4	48	cCg/cGg	1/3	0.329145433040466	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.329145433040466	1		400	522	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574024	7574024	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	33	696	1	ENST00000269305.4:c.1003del	p.Arg335ValfsTer10	p.R335Vfs*10	ENST00000269305	NM_001126112.2	335	Cgt/gt	10/11	0.22360172383388	3	FACETS	1	0.896	1	0.574	0.469	0.691	CLONAL	1	TRUE	1	0.22360172383388	3		697	286	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	68	638	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	0.363049023709261	8	FACETS	1	0.896	1	0.411	0.359	0.466	CLONAL	2	FALSE	3	0.363049023709261	8		638	381	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71161692	71161692	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	17	486	0	ENST00000318789.4:c.277C>T	p.Leu93Phe	p.L93F	ENST00000318789	NM_032682.5	93	Ctt/Ttt	7/21	1	2	FACETS	0.66	0.496	0.85	0.66	0.496	0.85	SUBCLONAL	1	FALSE	1	0.363049023709261	2		486	142	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79952294	79952294	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	12	447	0	ENST00000265081.6:c.302del	p.Val101GlufsTer25	p.V101Efs*25	ENST00000265081	NM_002439.4	101	gTa/ga	2/24	0.316982807597337	3	FACETS	0.338	0.237	0.462	0.169	0.118	0.231	SUBCLONAL	1	FALSE	1	0.363049023709261	3		447	231	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366956	118366984	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGAGTCTTTTGGATTTCAAGGTACTGATA	GGAGTCTTTTGGATTTCAAGGTACTGATA	-	novel	NA	P-0036316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	10	420	0	ENST00000534358.1:c.5558-14_5572del		p.X1853_splice	ENST00000534358	NM_005933.3	1853		20/36	0.363049023709261	1	FACETS	0.518	0.355	0.718	0.518	0.355	0.718	SUBCLONAL	1	FALSE	0	0.363049023709261	1		420	87	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40468806	40468850	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CCAAACTGCCCTCCTGCTGAGGGTTCAGCACCTTCACCATTATTT	CCAAACTGCCCTCCTGCTGAGGGTTCAGCACCTTCACCATTATTT	-	novel	NA	P-0036316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	13	515	0	ENST00000264657.5:c.2214_2257+1del		p.X738_splice	ENST00000264657	NM_139276.2	738		23/24	1	2	FACETS	0.305	0.217	0.412	0.305	0.217	0.412	SUBCLONAL	1	FALSE	1	0.363049023709261	2		515	235	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0036319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	304	530	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.580020201292458	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	TRUE	0	0.580020201292458	3		530	445	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482607	56482607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs993665271	NA	P-0036319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	200	910	0	ENST00000267101.3:c.1064C>T	p.Thr355Ile	p.T355I	ENST00000267101	NM_001982.3	355	aCc/aTc	9/28	0.580020201292458	3	FACETS	0.808	0.748	0.871	0.404	0.374	0.436	CLONAL	1	TRUE	1	0.580020201292458	3		910	1101	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	207	772	0	ENST00000206249.3:c.1138G>A	p.Glu380Lys	p.E380K	ENST00000206249	NM_000125.3	380	Gaa/Aaa	5/8	0.549866310166442	2	FACETS	1	0.941	1	0.506	0.471	0.541	CLONAL	1	TRUE	0	0.580020201292458	2		772	706	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257359	16257359	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	268	774	1	ENST00000375759.3:c.4624C>T	p.Arg1542Ter	p.R1542*	ENST00000375759	NM_015001.2	1542	Cga/Tga	11/15	0.278011061362356	3	FACETS	0.835	0.794	0.875	0.835	0.794	0.875	INDETERMINATE	3	TRUE	0	0.580020201292458	3		775	476	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	96	214	0				ENST00000310581	NM_198253.2	-/1132			0.437604403697355	1	FACETS	0.892	0.826	0.955	0.892	0.826	0.955	INDETERMINATE	1	TRUE	0	0.835572877467007	1		214	150	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572942	7572942	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs749817236	NA	P-0036320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	527	698	0	ENST00000269305.4:c.1167del	p.Pro390LeufsTer32	p.P390Lfs*32	ENST00000269305	NM_001126112.2	389	ggG/gg	11/11	0.835572877467007	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.835572877467007	1		698	707	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477842	140477851	+	protein_altering_variant	In_Frame_Del	DEL	GCTGTCACAT	GCTGTCACAT	C	novel	NA	P-0036320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	415	803	0	ENST00000288602.6:c.1457_1466delinsG	p.Asn486_Ala489delinsArg	p.N486_A489delinsR	ENST00000288602	NM_004333.4	486	aATGTGACAGCa/aGa	12/18	1	2	FACETS	0.828	0.789	0.867	0.828	0.789	0.867	CLONAL	1	TRUE	1	0.835572877467007	2		803	1200	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0036322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	345	779	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.616946844100604	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.616946844100604	1		779	693	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs121913468	NA	P-0036322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3137	2014	437	0	ENST00000269571.5:c.2305G>C	p.Asp769His	p.D769H	ENST00000269571		769	Gac/Cac	19/27	0.616946844100604	18	FACETS	0.94	0.921	0.96			1	CLONAL	8	TRUE	NA	0.616946844100604	18		437	5151	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736287	243736287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	176	532	0	ENST00000263826.5:c.760G>A	p.Glu254Lys	p.E254K	ENST00000263826	NM_005465.4	254	Gaa/Aaa	8/13	0.173350013419686	3	FACETS	0.958	0.884	1	0.319	0.294	0.345	INDETERMINATE	1	TRUE	0	0.616946844100604	3		532	779	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0036323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	177	381	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.337114914197552	3	FACETS	0.932	0.863	1	0.932	0.863	1	CLONAL	2	TRUE	1	0.337114914197552	3		381	658	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0036323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	114	318	0	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	0.337114914197552	4	FACETS	1	0.907	1	1	0.907	1	CLONAL	2	TRUE	2	0.337114914197552	4		318	452	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984024	2984024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	125	583	1	ENST00000396946.4:c.506C>T	p.Thr169Met	p.T169M	ENST00000396946	NM_032415.4	169	aCg/aTg	5/25	0.242011385442476	4	FACETS	1	0.959	1	0.555	0.502	0.611	CLONAL	1	TRUE	2	0.337114914197552	4		584	893	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411071	63411071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750971248	NA	P-0036323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	247	636	0	ENST00000330258.3:c.2096G>A	p.Arg699His	p.R699H	ENST00000330258	NM_152424.3	699	cGt/cAt	2/2	0.337114914197552	4	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	2	0.337114914197552	4		636	974	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874751	151874751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149388680	NA	P-0036323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	154	393	0	ENST00000262189.6:c.7787G>A	p.Arg2596Gln	p.R2596Q	ENST00000262189	NM_170606.2	2596	cGg/cAg	38/59	0.337114914197552	4	FACETS	0.996	0.916	1	0.996	0.916	1	CLONAL	2	TRUE	2	0.337114914197552	4		393	613	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114905777	114905777	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	229	475	0	ENST00000543371.1:c.796C>T	p.Gln266Ter	p.Q266*	ENST00000543371	NM_001198531.1	266	Caa/Taa	8/14	0.337114914197552	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.337114914197552	3		475	690	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243378	46243378	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	110	283	0	ENST00000334344.6:c.1731T>A	p.Asn577Lys	p.N577K	ENST00000334344	NM_152641.2	577	aaT/aaA	14/21	0.337114914197552	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	1	0.337114914197552	3		283	347	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435148	49435148	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	173	464	0	ENST00000301067.7:c.6405G>T	p.Leu2135Phe	p.L2135F	ENST00000301067	NM_003482.3	2135	ttG/ttT	31/54	0.337114914197552	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	1	0.337114914197552	3		464	584	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46252684	46252684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	67	309	0	ENST00000371998.3:c.113G>A	p.Arg38Gln	p.R38Q	ENST00000371998		38	cGg/cAg	4/23	0.337114914197552	7	FACETS	1	0.895	1	0.259	0.225	0.296	CLONAL	1	TRUE	3	0.337114914197552	7		309	707	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2972215	2972215	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	231	527	1	ENST00000396946.4:c.1524G>T	p.Gln508His	p.Q508H	ENST00000396946	NM_032415.4	508	caG/caT	11/25	0.242011385442476	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.337114914197552	4		528	840	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355280	81355280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	76	409	1	ENST00000222390.5:c.1094G>A	p.Cys365Tyr	p.C365Y	ENST00000222390	NM_000601.4	365	tGt/tAt	9/18	0.337114914197552	4	FACETS	0.971	0.852	1	0.485	0.426	0.55	CLONAL	1	TRUE	2	0.337114914197552	4		410	621	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0036324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	381	670	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.574773484258874	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.574773484258874	1		670	742	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0036324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	198	674	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.574773484258874	1	FACETS	0.717	0.666	0.768	0.717	0.666	0.768	SUBCLONAL	1	TRUE	0	0.574773484258874	1		674	685	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0036324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	87	260	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.202563767716774	1	FACETS	0.488	0.434	0.545	0.488	0.434	0.545	INDETERMINATE	1	TRUE	0	0.574773484258874	1		261	442	SUCCESS
APC	324	MSKCC	GRCh37	5	112175193	112175193	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1064794042	NA	P-0036324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	90	202	0	ENST00000257430.4:c.3904del	p.Leu1302CysfsTer3	p.L1302Cfs*3	ENST00000257430	NM_000038.5	1301	aCc/ac	16/16	0.202563767716774	1	FACETS	0.879	0.792	0.968	0.879	0.792	0.968	INDETERMINATE	1	TRUE	0	0.574773484258874	1		202	254	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120291	70120292	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	440	934	0	ENST00000245479.2:c.1294dup	p.Tyr432LeufsTer146	p.Y432Lfs*146	ENST00000245479	NM_000346.3	431	-/T	3/3	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.574773484258874	2		934	1328	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911491	114911491	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	79	172	0	ENST00000543371.1:c.1009C>T	p.Gln337Ter	p.Q337*	ENST00000543371	NM_001198531.1	337	Cag/Tag	10/14	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.574773484258874	2		172	234	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5534888	5534888	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	215	400	0	ENST00000397747.3:c.199T>C	p.Ser67Pro	p.S67P	ENST00000397747	NM_025239.3	67	Tcc/Ccc	3/7	0.690492890420937	2	FACETS	1	0.986	1	0.588	0.552	0.625	CLONAL	1	TRUE	0	0.702965752113954	2		400	520	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69012029	69012029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1395087621	NA	P-0036325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1393	134	640	0	ENST00000288368.4:c.2666G>A	p.Cys889Tyr	p.C889Y	ENST00000288368	NM_024870.2	889	tGc/tAc	23/40	0.702965752113954	4	FACETS	0.425	0.385	0.468	0.142	0.128	0.156	SUBCLONAL	1	TRUE	1	0.702965752113954	4		640	1527	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650753	48650753	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776454	NA	P-0036325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	245	643	0	ENST00000376670.3:c.622G>A	p.Gly208Arg	p.G208R	ENST00000376670	NM_002049.3	208	Gga/Aga	4/6	0.702965752113954	1	FACETS	0.985	0.934	1	0.985	0.934	1	CLONAL	1	TRUE	0	0.702965752113954	1		643	459	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0036327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	107	469	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.181117650231251	2		469	797	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181402	38181402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	38	433	0	ENST00000396334.3:c.415G>A	p.Glu139Lys	p.E139K	ENST00000396334	NM_002468.4	139	Gag/Aag	2/5	1	2	FACETS	0.619	0.51	0.741	0.619	0.51	0.741	SUBCLONAL	1	TRUE	1	0.181117650231251	2		433	678	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0036327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	92	738	0	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	1	2	FACETS	0.96	0.851	1	0.96	0.851	1	CLONAL	1	TRUE	1	0.181117650231251	2		738	1058	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119789	70119789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778047936	NA	P-0036327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	47	572	0	ENST00000245479.2:c.791G>A	p.Arg264Lys	p.R264K	ENST00000245479	NM_000346.3	264	aGa/aAa	3/3	0.181117650231251	3	FACETS	0.644	0.541	0.758	0.322	0.27	0.379	SUBCLONAL	1	TRUE	1	0.181117650231251	3		572	879	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190894	185190894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555365583	NA	P-0036327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	56	688	0	ENST00000265026.3:c.1775G>A	p.Arg592Gln	p.R592Q	ENST00000265026	NM_004721.4	592	cGa/cAa	11/14	1	2	FACETS	0.606	0.517	0.703	0.606	0.517	0.703	SUBCLONAL	1	TRUE	1	0.181117650231251	2		688	1021	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521385	187521385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426195084	NA	P-0036327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	37	551	1	ENST00000441802.2:c.11770C>T	p.Arg3924Cys	p.R3924C	ENST00000441802	NM_005245.3	3924	Cgc/Tgc	22/27	1	2	FACETS	0.57	0.468	0.684	0.57	0.468	0.684	SUBCLONAL	1	TRUE	1	0.181117650231251	2		552	717	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874893	151874893	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1473097808	NA	P-0036327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	32	465	0	ENST00000262189.6:c.7645C>T	p.Gln2549Ter	p.Q2549*	ENST00000262189	NM_170606.2	2549	Cag/Tag	38/59	1	2	FACETS	0.558	0.452	0.679	0.558	0.452	0.679	SUBCLONAL	1	TRUE	1	0.181117650231251	2		465	633	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118368699	118368702	+	frameshift_variant	Frame_Shift_Del	DEL	AATT	AATT	-	novel	NA	P-0036327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	78	555	0	ENST00000534358.1:c.5713_5716del	p.Asn1905ValfsTer16	p.N1905Vfs*16	ENST00000534358	NM_005933.3	1905	AATTgt/gt	21/36	1	2	FACETS	0.966	0.847	1	0.966	0.847	1	CLONAL	1	TRUE	1	0.181117650231251	2		555	892	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18762498	18762498	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	47	429	1	ENST00000266497.5:c.3994G>C	p.Val1332Leu	p.V1332L	ENST00000266497		1332	Gtg/Ctg	29/31	1	2	FACETS	0.788	0.663	0.925	0.788	0.663	0.925	CLONAL	1	TRUE	1	0.181117650231251	2		430	659	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585424	29585424	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs137854554	NA	P-0036327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	100	658	0	ENST00000356175.3:c.4173A>T	p.Arg1391Ser	p.R1391S	ENST00000356175	NM_000267.3	1391	agA/agT	31/57	NA	2	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.181117650231251	2		658	912	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643389	52643389	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	68	548	0	ENST00000394830.3:c.2507G>T	p.Arg836Leu	p.R836L	ENST00000394830	NM_018313.4	836	cGg/cTg	17/30	1	2	FACETS	0.955	0.83	1	0.955	0.83	1	CLONAL	1	TRUE	1	0.181117650231251	2		548	786	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0036328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	192	724	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.879	0.813	0.948	0.879	0.813	0.948	CLONAL	1	TRUE	1	0.458387894243904	2		725	953	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578213	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs864309495	NA	P-0036331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	477	610	0	ENST00000269305.4:c.636del	p.Arg213AspfsTer34	p.R213Dfs*34	ENST00000269305	NM_001126112.2	212	ttT/tt	6/11	0.670441682373673	2	FACETS	0.949	0.92	0.978	0.949	0.92	0.978	CLONAL	2	TRUE	0	0.719954929280401	2		610	698	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188404	32188404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763926116	NA	P-0036331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	133	487	0	ENST00000375023.3:c.937G>A	p.Glu313Lys	p.E313K	ENST00000375023	NM_004557.3	313	Gaa/Aaa	6/30	0.646725353304255	5	FACETS	0.772	0.7	0.848	0.154	0.14	0.17	SUBCLONAL	1	TRUE	0	0.719954929280401	5		487	995	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43766936	43766936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778059786	NA	P-0036331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	50	187	0	ENST00000382044.4:c.1115C>T	p.Pro372Leu	p.P372L	ENST00000382044	NM_001141980.1	372	cCt/cTt	10/28	0.719954929280401	3	FACETS	0.592	0.505	0.687	0.296	0.252	0.344	SUBCLONAL	1	TRUE	1	0.719954929280401	3		187	319	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601264	28601264	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	138	425	0	ENST00000241453.7:c.2168T>C	p.Phe723Ser	p.F723S	ENST00000241453	NM_004119.2	723	tTc/tCc	17/24	0.678590471713812	2	FACETS	0.782	0.717	0.85	0.391	0.358	0.425	SUBCLONAL	1	TRUE	0	0.719954929280401	2		425	490	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727130	40727130	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	159	505	0	ENST00000373198.4:c.3834C>A	p.Asp1278Glu	p.D1278E	ENST00000373198	NM_133170.3	1278	gaC/gaA	28/32	0.719954929280401	3	FACETS	0.895	0.823	0.97	0.448	0.411	0.485	CLONAL	1	TRUE	1	0.719954929280401	3		505	671	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32819916	32819916	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	519	661	0	ENST00000354258.4:c.994G>C	p.Glu332Gln	p.E332Q	ENST00000354258	NM_000593.5	332	Gag/Cag	3/11	0.646725353304255	5	FACETS	0.969	0.928	1	0.387	0.371	0.404	CLONAL	2	TRUE	0	0.719954929280401	5		661	1548	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69050669	69050669	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0036331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	344	475	0	ENST00000288368.4:c.4004T>G	p.Leu1335Ter	p.L1335*	ENST00000288368	NM_024870.2	1335	tTa/tGa	33/40	0.676348144723231	5	FACETS	0.995	0.944	1	0.398	0.377	0.419	CLONAL	2	TRUE	0	0.719954929280401	5		475	999	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0036332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	140	710	1	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.236289221888413	2		711	790	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221975	1221975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568710381	NA	P-0036332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	74	679	0	ENST00000326873.7:c.890G>A	p.Arg297Lys	p.R297K	ENST00000326873	NM_000455.4	297	aGg/aAg	7/10	0.236289221888413	1	FACETS	0.76	0.664	0.863	0.76	0.664	0.863	SUBCLONAL	1	TRUE	0	0.236289221888413	1		679	727	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776364	76776364	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	76	256	1	ENST00000373344.5:c.7102C>T	p.Gln2368Ter	p.Q2368*	ENST00000373344	NM_000489.3	2368	Caa/Taa	34/35	1	1	FACETS	0.854	0.755	0.959	1	0.981	1	CLONAL	2	TRUE	0	0.236289221888413	1		257	332	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939630	131939630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	31	221	0	ENST00000265335.6:c.2416G>A	p.Glu806Lys	p.E806K	ENST00000265335		806	Gaa/Aaa	15/25	0.193275537255697	1	FACETS	0.735	0.595	0.891	0.735	0.595	0.891	SUBCLONAL	1	TRUE	0	0.236289221888413	1		221	315	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782404	9782405	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0036332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	47	750	1	ENST00000377346.4:c.2337_2338delinsAT	p.Asn780Tyr	p.N780Y	ENST00000377346	NM_005026.3	779	aaGAac/aaATac	18/24	1	2	FACETS	0.495	0.417	0.583	0.495	0.417	0.583	SUBCLONAL	1	TRUE	1	0.236289221888413	2		751	803	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699313	117699313	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	85	583	0	ENST00000369458.3:c.328G>T	p.Val110Phe	p.V110F	ENST00000369458	NM_024626.3	110	Gtt/Ttt	3/6	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.236289221888413	2		583	710	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590636	95590636	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	67	389	0	ENST00000393063.1:c.1273G>T	p.Glu425Ter	p.E425*	ENST00000393063	NM_030621.3	425	Gaa/Taa	9/28	0.189402002301002	2	FACETS	1	0.933	1	0.558	0.486	0.636	CLONAL	1	TRUE	0	0.236289221888413	2		389	508	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37672036	37672036	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	38	503	0	ENST00000447079.4:c.2821G>T	p.Glu941Ter	p.E941*	ENST00000447079	NM_015083.1	941	Gaa/Taa	9/14	1	2	FACETS	0.436	0.359	0.522	0.436	0.359	0.522	SUBCLONAL	1	TRUE	1	0.236289221888413	2		503	738	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467116	25467116	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	44	598	0	ENST00000264709.3:c.1759G>T	p.Gly587Trp	p.G587W	ENST00000264709	NM_175629.2	587	Ggg/Tgg	15/23	1	2	FACETS	0.563	0.471	0.665	0.563	0.471	0.665	SUBCLONAL	1	TRUE	1	0.236289221888413	2		598	662	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727189	40727189	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	33	479	0	ENST00000373198.4:c.3775C>T	p.His1259Tyr	p.H1259Y	ENST00000373198	NM_133170.3	1259	Cac/Tac	28/32	1	2	FACETS	0.522	0.424	0.633	0.522	0.424	0.633	SUBCLONAL	1	TRUE	1	0.236289221888413	2		479	535	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206141	36206738	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCCCCATGGGCTGGGGGGACCTGCATTCTCTATTGATTTGCAAATAACACCCTTGATGTGATGACATCCATACATTTCAACTATTTCTTAATAATAAAAAAACACTAGATACAAAACCCACAAATAATCTGGCAATAGCGAGAACTTGAAACATCCCATCTTCACTTTGCTTGACGTGTGTGTGTGTGTGTGTCTGCGTGTGTGTCTTCAAGCCTAATGGGTAGGTAAAAAAATAGCATAGCCAAAGCTAACTCTTAAAAAATTCAAGAGAGCTATCTATCCAATATGGATATCCATACCCAGAGCTCCTCGTATCCTCTGTAGCAGTGCTTTTCCTTGTGGGGATCTGGTTACAATGCAGATCTGACTCGGTGGGTCTGGGGTGGGTGGGGCCCAAGACTCTGCATTTCCAACAGCTCCCAGGTGGTGCTGTTGGTTCGAGGCCTTTCTCTGAGCATCAAGGGGAAACCCCAGTTGGTCTGGGAAGGTGTGTGCACATGGGGGCCAGTTGTGGGTGGTGGCCCAGGTGCAGGAGAGGCGGGCAGTGGGCTCCATCTGGTACTTACCCTGCATCTGACTCTGAGGCTGAGGGTTAAAG	GCCCCATGGGCTGGGGGGACCTGCATTCTCTATTGATTTGCAAATAACACCCTTGATGTGATGACATCCATACATTTCAACTATTTCTTAATAATAAAAAAACACTAGATACAAAACCCACAAATAATCTGGCAATAGCGAGAACTTGAAACATCCCATCTTCACTTTGCTTGACGTGTGTGTGTGTGTGTGTCTGCGTGTGTGTCTTCAAGCCTAATGGGTAGGTAAAAAAATAGCATAGCCAAAGCTAACTCTTAAAAAATTCAAGAGAGCTATCTATCCAATATGGATATCCATACCCAGAGCTCCTCGTATCCTCTGTAGCAGTGCTTTTCCTTGTGGGGATCTGGTTACAATGCAGATCTGACTCGGTGGGTCTGGGGTGGGTGGGGCCCAAGACTCTGCATTTCCAACAGCTCCCAGGTGGTGCTGTTGGTTCGAGGCCTTTCTCTGAGCATCAAGGGGAAACCCCAGTTGGTCTGGGAAGGTGTGTGCACATGGGGGCCAGTTGTGGGTGGTGGCCCAGGTGCAGGAGAGGCGGGCAGTGGGCTCCATCTGGTACTTACCCTGCATCTGACTCTGAGGCTGAGGGTTAAAG	-	novel	NA	P-0036332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	10	17	0	ENST00000300305.3:c.774_805+566del		p.X258_splice	ENST00000300305		258		6/8	0.193275537255697	1	FACETS	1	0.796	1	1	0.902	1	CLONAL	2	TRUE	0	0.236289221888413	1		17	32	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602737	55602737	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	92	511	0	ENST00000288135.5:c.2558G>C	p.Trp853Ser	p.W853S	ENST00000288135	NM_000222.2	853	tGg/tCg	18/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.236289221888413	2		511	634	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158469	26158469	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	114	654	0	ENST00000289316.2:c.72G>C	p.Lys24Asn	p.K24N	ENST00000289316	NM_138720.2	24	aaG/aaC	1/2	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.236289221888413	2		654	876	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846362	128846362	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	60	710	1	ENST00000249373.3:c.1198C>A	p.Arg400Ser	p.R400S	ENST00000249373	NM_005631.4	400	Cgt/Agt	6/12	1	2	FACETS	0.75	0.646	0.864	0.75	0.646	0.864	SUBCLONAL	1	TRUE	1	0.236289221888413	2		711	677	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256546	16256546	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	36	546	0	ENST00000375759.3:c.3811G>T	p.Glu1271Ter	p.E1271*	ENST00000375759	NM_015001.2	1271	Gaa/Taa	11/15	0.45826618402027	1	FACETS	0.186	0.152	0.224	0.186	0.152	0.224	SUBCLONAL	1	TRUE	0	0.542169843775665	1		546	520	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922287	100922288	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	124	266	0	ENST00000325455.5:c.2224_2225insA	p.Leu742TyrfsTer4	p.L742Yfs*4	ENST00000325455	NM_001202474.3	742	tta/tAta	5/8	NA	2	FACETS	0.965	0.879	1			1	INDETERMINATE	1	TRUE	NA	0.542169843775665	2		266	474	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150308	108150308	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	37	376	0	ENST00000278616.4:c.3375G>C	p.Leu1125Phe	p.L1125F	ENST00000278616	NM_000051.3	1125	ttG/ttC	23/63	NA	2	FACETS	0.26	0.214	0.312			1	INDETERMINATE	1	TRUE	NA	0.542169843775665	2		376	525	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241901	133241901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	173	562	0	ENST00000320574.5:c.2455G>A	p.Val819Ile	p.V819I	ENST00000320574	NM_006231.2	819	Gtc/Atc	21/49	1	2	FACETS	0.997	0.922	1	0.997	0.922	1	CLONAL	1	TRUE	1	0.542169843775665	2		562	640	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968085	68968085	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	139	494	0	ENST00000288368.4:c.1114C>T	p.Gln372Ter	p.Q372*	ENST00000288368	NM_024870.2	372	Caa/Taa	10/40	0.539027927727791	3	FACETS	0.882	0.804	0.964	0.441	0.402	0.482	CLONAL	1	TRUE	1	0.542169843775665	3		494	739	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	512	765	30	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	0.597767144315202	2	FACETS	0.924	0.892	0.956	0.924	0.892	0.956	CLONAL	2	TRUE	0	0.622580651459564	2		795	890	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	196	443	0	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	0.934	0.868	1	0.934	0.868	1	CLONAL	1	TRUE	1	0.622580651459564	2		443	674	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	152	438	2	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.797	0.731	0.864	0.797	0.731	0.864	SUBCLONAL	1	TRUE	1	0.622580651459564	2		440	613	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992721	68992721	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs764112302	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	189	561	1	ENST00000288368.4:c.1693del	p.Ser565ArgfsTer10	p.S565Rfs*10	ENST00000288368	NM_024870.2	562	cgT/cg	16/40	0.567307910591745	3	FACETS	0.931	0.862	1	0.466	0.431	0.502	CLONAL	1	TRUE	1	0.622580651459564	3		562	855	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	439	514	8	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.839	0.806	0.872	1	0.997	1	CLONAL	2	TRUE	1	0.622580651459564	2		522	840	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376248	15376248	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	153	516	4	ENST00000263377.2:c.766del	p.Gln256SerfsTer27	p.Q256Sfs*27	ENST00000263377	NM_058243.2	256	Cag/ag	5/20	1	2	FACETS	0.786	0.722	0.853	0.786	0.722	0.853	SUBCLONAL	1	TRUE	1	0.622580651459564	2		520	625	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099103	27099103	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	137	363	1	ENST00000324856.7:c.3524del	p.Pro1175HisfsTer5	p.P1175Hfs*5	ENST00000324856	NM_006015.4	1173	atC/at	13/20	1	2	FACETS	0.873	0.799	0.95	0.873	0.799	0.95	CLONAL	1	TRUE	1	0.622580651459564	2		364	504	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	174	517	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.949	0.878	1	0.949	0.878	1	CLONAL	1	TRUE	1	0.622580651459564	2		518	589	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812532	43812532	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	174	438	0	ENST00000372470.3:c.1235A>G	p.His412Arg	p.H412R	ENST00000372470	NM_005373.2	412	cAc/cGc	8/12	1	2	FACETS	0.864	0.799	0.931	0.864	0.799	0.931	CLONAL	1	TRUE	1	0.622580651459564	2		438	647	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248166	59248166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1382928817	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	36	76	0	ENST00000371222.2:c.577G>A	p.Ala193Thr	p.A193T	ENST00000371222	NM_002228.3	193	Gcc/Acc	1/1	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.622580651459564	2		76	93	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567647	226567647	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	197	578	1	ENST00000366794.5:c.1519del	p.Ser507AlafsTer17	p.S507Afs*17	ENST00000366794	NM_001618.3	507	Agc/gc	10/23	1	2	FACETS	0.965	0.897	1	0.965	0.897	1	CLONAL	1	TRUE	1	0.622580651459564	2		579	656	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609122	43609122	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	256	619	0	ENST00000355710.3:c.1878G>T	p.Gln626His	p.Q626H	ENST00000355710	NM_020975.4	626	caG/caT	10/20	1	2	FACETS	0.986	0.926	1	0.986	0.926	1	CLONAL	1	TRUE	1	0.622580651459564	2		619	834	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342917	118342917	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	107	251	0	ENST00000534358.1:c.1043T>C	p.Val348Ala	p.V348A	ENST00000534358	NM_005933.3	348	gTc/gCc	3/36	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.622580651459564	2		251	323	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343502	118343502	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1203844881	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	167	356	0	ENST00000534358.1:c.1628C>T	p.Thr543Met	p.T543M	ENST00000534358	NM_005933.3	543	aCg/aTg	3/36	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.622580651459564	2		356	526	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	245	631	0	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	1	2	FACETS	0.874	0.818	0.931	0.874	0.818	0.931	CLONAL	1	TRUE	1	0.622580651459564	2		631	901	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118367017	118367017	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	207	453	0	ENST00000534358.1:c.5603del	p.Pro1868GlnfsTer3	p.P1868Qfs*3	ENST00000534358	NM_005933.3	1867	Ccc/cc	20/36	1	2	FACETS	0.987	0.92	1	0.987	0.92	1	CLONAL	1	TRUE	1	0.622580651459564	2		453	674	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433394	49433394	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783727	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	424	661	0	ENST00000301067.7:c.8053C>T	p.Arg2685Ter	p.R2685*	ENST00000301067	NM_003482.3	2685	Cga/Tga	32/54	0.597767144315202	2	FACETS	0.882	0.848	0.916	0.882	0.848	0.916	CLONAL	2	TRUE	0	0.622580651459564	2		661	772	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112250	115112250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1345506334	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	86	186	0	ENST00000257566.3:c.1490C>T	p.Pro497Leu	p.P497L	ENST00000257566	NM_016569.3	497	cCc/cTc	7/8	0.567307910591745	3	FACETS	1	0.968	1	0.612	0.547	0.679	CLONAL	1	TRUE	1	0.622580651459564	3		186	296	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008324	29008324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770377283	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	131	367	0	ENST00000282397.4:c.547C>T	p.Arg183Cys	p.R183C	ENST00000282397	NM_002019.4	183	Cgc/Tgc	5/30	1	2	FACETS	0.988	0.904	1	0.988	0.904	1	CLONAL	1	TRUE	1	0.622580651459564	2		367	426	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041210	29041210	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	250	686	1	ENST00000282397.4:c.218G>T	p.Arg73Met	p.R73M	ENST00000282397	NM_002019.4	73	aGg/aTg	3/30	1	2	FACETS	0.901	0.845	0.959	0.901	0.845	0.959	CLONAL	1	TRUE	1	0.622580651459564	2		687	891	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528185	103528185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781355194	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	118	240	1	ENST00000355739.4:c.3493G>A	p.Ala1165Thr	p.A1165T	ENST00000355739	NM_000123.3	1165	Gcc/Acc	15/15	0.359614082555813	3	FACETS	0.996	0.903	1	0.498	0.451	0.547	INDETERMINATE	1	TRUE	1	0.622580651459564	3		241	499	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435333	110435333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196624356	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	119	307	0	ENST00000375856.3:c.3068C>T	p.Ala1023Val	p.A1023V	ENST00000375856	NM_003749.2	1023	gCg/gTg	1/2	0.359614082555813	3	FACETS	1	0.941	1	0.524	0.476	0.575	INDETERMINATE	1	TRUE	1	0.622580651459564	3		307	478	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436297	110436302	+	inframe_deletion	In_Frame_Del	DEL	CGGCGG	CGGCGG	-	rs34412495	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	81	176	0	ENST00000375856.3:c.2099_2104del	p.Ala700_Ala701del	p.A700_A701del	ENST00000375856	NM_003749.2	700	gCCGCCGtg/gtg	1/2	0.359614082555813	3	FACETS	1	0.969	1	0.627	0.559	0.698	INDETERMINATE	1	TRUE	1	0.622580651459564	3		176	272	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437436	110437436	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	271	429	0	ENST00000375856.3:c.965C>T	p.Ala322Val	p.A322V	ENST00000375856	NM_003749.2	322	gCg/gTg	1/2	0.359614082555813	3	FACETS	0.912	0.862	0.962	0.912	0.862	0.962	INDETERMINATE	2	TRUE	1	0.622580651459564	3		429	626	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609984	81609984	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765367813	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	108	268	0	ENST00000298171.2:c.1582C>T	p.Arg528Cys	p.R528C	ENST00000298171	NM_000369.2	528	Cgc/Tgc	10/10	1	2	FACETS	0.918	0.831	1	0.918	0.831	1	CLONAL	1	TRUE	1	0.622580651459564	2		268	378	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41011090	41011090	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	207	491	0	ENST00000267868.3:c.523G>A	p.Ala175Thr	p.A175T	ENST00000267868	NM_002875.4	175	Gct/Act	6/10	1	2	FACETS	0.87	0.81	0.933	0.87	0.81	0.933	CLONAL	1	TRUE	1	0.622580651459564	2		491	764	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712824	43712824	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1201648831	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	241	671	0	ENST00000382044.4:c.4360C>T	p.Arg1454Ter	p.R1454*	ENST00000382044	NM_001141980.1	1454	Cga/Tga	21/28	1	2	FACETS	0.855	0.8	0.912	0.855	0.8	0.912	CLONAL	1	TRUE	1	0.622580651459564	2		671	905	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354374	354374	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	259	634	2	ENST00000262320.3:c.1184G>A	p.Arg395His	p.R395H	ENST00000262320	NM_003502.3	395	cGc/cAc	5/11	1	2	FACETS	0.969	0.91	1	0.969	0.91	1	CLONAL	1	TRUE	1	0.622580651459564	2		636	859	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786719	3786719	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	287	722	0	ENST00000262367.5:c.4492C>T	p.Arg1498Ter	p.R1498*	ENST00000262367	NM_004380.2	1498	Cga/Tga	27/31	1	2	FACETS	0.901	0.848	0.955	0.901	0.848	0.955	CLONAL	1	TRUE	1	0.622580651459564	2		722	1023	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789591	3789591	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	130	320	3	ENST00000262367.5:c.4268del	p.Pro1423LeufsTer36	p.P1423Lfs*36	ENST00000262367	NM_004380.2	1423	cCt/ct	25/31	1	2	FACETS	0.945	0.864	1	0.945	0.864	1	CLONAL	1	TRUE	1	0.622580651459564	2		323	442	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	100	400	1	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.765	0.688	0.846	0.765	0.688	0.846	SUBCLONAL	1	TRUE	1	0.622580651459564	2		401	420	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346157	89346158	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs878855327	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	40	267	1	ENST00000301030.4:c.6792dup	p.Ala2265ArgfsTer8	p.A2265Rfs*8	ENST00000301030	NM_001256183.1	2264	-/C	9/13	1	2	FACETS	0.516	0.432	0.609	0.516	0.432	0.609	SUBCLONAL	1	TRUE	1	0.622580651459564	2		268	249	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961790	15961790	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762874617	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	177	470	0	ENST00000268712.3:c.6005C>T	p.Ala2002Val	p.A2002V	ENST00000268712	NM_006311.3	2002	gCg/gTg	38/46	1	2	FACETS	0.883	0.817	0.951	0.883	0.817	0.951	CLONAL	1	TRUE	1	0.622580651459564	2		470	644	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	263	590	2	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	0.93	0.874	0.989	0.93	0.874	0.989	CLONAL	1	TRUE	1	0.622580651459564	2		592	908	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244970	41244970	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs373207084	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	293	783	0	ENST00000357654.3:c.2578A>G	p.Thr860Ala	p.T860A	ENST00000357654	NM_007294.3	860	Aca/Gca	10/23	1	2	FACETS	0.999	0.942	1	0.999	0.942	1	CLONAL	1	TRUE	1	0.622580651459564	2		783	942	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436026	56436026	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771831816	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	126	376	0	ENST00000407977.2:c.1111C>T	p.Arg371Ter	p.R371*	ENST00000407977		371	Cga/Tga	9/10	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.622580651459564	2		376	391	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448297	56448298	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1567880599	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	192	576	0	ENST00000407977.2:c.349dup	p.Arg117ProfsTer8	p.R117Pfs*8	ENST00000407977		117	cgc/cCgc	3/10	1	2	FACETS	0.794	0.736	0.854	0.794	0.736	0.854	SUBCLONAL	1	TRUE	1	0.622580651459564	2		576	777	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740726	58740726	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	228	496	0	ENST00000305921.3:c.1631G>C	p.Gly544Ala	p.G544A	ENST00000305921	NM_003620.3	544	gGc/gCc	6/6	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.622580651459564	2		496	668	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59820415	59820415	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	147	393	0	ENST00000259008.2:c.2338A>G	p.Ile780Val	p.I780V	ENST00000259008	NM_032043.2	780	Ata/Gta	16/20	1	2	FACETS	0.855	0.785	0.928	0.855	0.785	0.928	CLONAL	1	TRUE	1	0.622580651459564	2		393	552	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732385	74732385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	115	324	0	ENST00000359995.5:c.524C>T	p.Ser175Leu	p.S175L	ENST00000359995	NM_001195427.1	175	tCg/tTg	2/3	1	2	FACETS	0.903	0.82	0.989	0.903	0.82	0.989	CLONAL	1	TRUE	1	0.622580651459564	2		324	409	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612320	1612320	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757572121	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	314	781	0	ENST00000344749.5:c.1699C>T	p.Arg567Trp	p.R567W	ENST00000344749	NM_001136139.2	567	Cgg/Tgg	18/19	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.622580651459564	2		781	976	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244243	5244243	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1390768500	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	227	592	0	ENST00000357368.4:c.1239del	p.Ser414AlafsTer30	p.S414Afs*30	ENST00000357368	NM_002850.3	413	ccC/cc	11/38	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.622580651459564	2		592	728	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223175	36223175	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	271	896	2	ENST00000222270.7:c.5730del	p.Arg1911AspfsTer23	p.R1911Dfs*23	ENST00000222270	NM_014727.1	1909	Ccc/cc	28/37	1	2	FACETS	0.837	0.786	0.89	0.837	0.786	0.89	CLONAL	1	TRUE	1	0.622580651459564	2		898	1040	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224111	36224111	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	255	740	2	ENST00000222270.7:c.6666del	p.Thr2223ProfsTer38	p.T2223Pfs*38	ENST00000222270	NM_014727.1	2221	Ccc/cc	28/37	1	2	FACETS	0.888	0.832	0.944	0.888	0.832	0.944	CLONAL	1	TRUE	1	0.622580651459564	2		742	923	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745212	41745212	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	146	488	0	ENST00000301178.4:c.1278G>T	p.Trp426Cys	p.W426C	ENST00000301178	NM_021913.4	426	tgG/tgT	9/20	1	2	FACETS	0.878	0.806	0.953	0.878	0.806	0.953	CLONAL	1	TRUE	1	0.622580651459564	2		488	534	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797933	42797935	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	256	761	0	ENST00000575354.2:c.3988_3990del	p.Lys1330del	p.K1330del	ENST00000575354	NM_015125.3	1329	AAG/-	16/20	1	2	FACETS	0.915	0.858	0.973	0.915	0.858	0.973	CLONAL	1	TRUE	1	0.622580651459564	2		761	899	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445400	29445400	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	249	727	0	ENST00000389048.3:c.3433del	p.Leu1145CysfsTer5	p.L1145Cfs*5	ENST00000389048	NM_004304.4	1145	Ctg/tg	21/29	1	2	FACETS	0.929	0.871	0.989	0.929	0.871	0.989	CLONAL	1	TRUE	1	0.622580651459564	2		727	861	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142910	30142910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141093002	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	260	705	1	ENST00000389048.3:c.616G>A	p.Ala206Thr	p.A206T	ENST00000389048	NM_004304.4	206	Gcg/Acg	1/29	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.622580651459564	2		706	828	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705459	47705459	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	126	331	0	ENST00000233146.2:c.2260del	p.Thr754LeufsTer9	p.T754Lfs*9	ENST00000233146	NM_000251.2	753	ggA/gg	14/16	1	2	FACETS	0.903	0.824	0.986	0.903	0.824	0.986	CLONAL	1	TRUE	1	0.622580651459564	2		331	448	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	230	424	16	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	0.975	0.912	1	0.975	0.912	1	CLONAL	1	TRUE	1	0.622580651459564	2		440	758	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172161	99172161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs571358585	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	181	448	0	ENST00000074304.5:c.1727C>T	p.Pro576Leu	p.P576L	ENST00000074304	NM_001134224.1	576	cCg/cTg	17/26	1	2	FACETS	0.987	0.916	1	0.987	0.916	1	CLONAL	1	TRUE	1	0.622580651459564	2		448	589	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128028933	128028933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759338358	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	188	580	0	ENST00000285398.2:c.1924C>T	p.Arg642Trp	p.R642W	ENST00000285398	NM_000122.1	642	Cgg/Tgg	12/15	1	2	FACETS	0.798	0.739	0.859	0.798	0.739	0.859	SUBCLONAL	1	TRUE	1	0.622580651459564	2		580	757	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149799	202149799	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	206	579	1	ENST00000358485.4:c.1245del	p.Phe415LeufsTer26	p.F415Lfs*26	ENST00000358485	NM_001080125.1	414	Ttt/tt	8/9	1	2	FACETS	0.875	0.815	0.938	0.875	0.815	0.938	CLONAL	1	TRUE	1	0.622580651459564	2		580	756	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021461	31021461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	160	427	0	ENST00000375687.4:c.1460C>T	p.Ala487Val	p.A487V	ENST00000375687	NM_015338.5	487	gCt/gTt	12/13	1	2	FACETS	0.86	0.792	0.93	0.86	0.792	0.93	CLONAL	1	TRUE	1	0.622580651459564	2		427	598	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31372649	31372649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200902224	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	179	451	0	ENST00000328111.2:c.290G>A	p.Arg97His	p.R97H	ENST00000328111	NM_006892.3	97	cGt/cAt	4/23	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.622580651459564	2		451	520	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376726	31376726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867559860	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	195	474	0	ENST00000328111.2:c.721G>A	p.Ala241Thr	p.A241T	ENST00000328111	NM_006892.3	241	Gcc/Acc	7/23	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.622580651459564	2		474	591	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39744972	39744972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	157	395	0	ENST00000361337.2:c.1762G>A	p.Val588Ile	p.V588I	ENST00000361337	NM_003286.2	588	Gta/Ata	17/21	1	2	FACETS	0.839	0.772	0.909	0.839	0.772	0.909	CLONAL	1	TRUE	1	0.622580651459564	2		395	601	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877391	40877391	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372713520	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	208	578	0	ENST00000373198.4:c.2305G>A	p.Val769Met	p.V769M	ENST00000373198	NM_133170.3	769	Gtg/Atg	15/32	NA	2	FACETS	1	0.934	1			1	INDETERMINATE	1	TRUE	NA	0.622580651459564	2		578	667	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37637694	37637694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1461567991	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	251	578	0	ENST00000249071.6:c.40G>A	p.Val14Met	p.V14M	ENST00000249071	NM_002872.4	14	Gtg/Atg	2/7	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.622580651459564	2		578	794	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573155	41573155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757325753	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	246	614	0	ENST00000263253.7:c.5440C>T	p.Arg1814Trp	p.R1814W	ENST00000263253	NM_001429.3	1814	Cgg/Tgg	31/31	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.622580651459564	2		614	740	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084146	47084146	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	230	485	0	ENST00000409792.3:c.7143del	p.Ser2382LeufsTer29	p.S2382Lfs*29	ENST00000409792	NM_014159.6	2381	ccC/cc	17/21	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.622580651459564	2		485	721	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932636	49932636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780949671	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	208	596	0	ENST00000296474.3:c.3235C>T	p.Arg1079Trp	p.R1079W	ENST00000296474	NM_002447.2	1079	Cgg/Tgg	14/20	1	2	FACETS	0.894	0.833	0.958	0.894	0.833	0.958	CLONAL	1	TRUE	1	0.622580651459564	2		596	747	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1959681	1959681	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553876858	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	82	225	1	ENST00000382891.5:c.2903G>A	p.Arg968His	p.R968H	ENST00000382891	NM_133335.3	968	cGt/cAt	16/22	0.622580651459564	1	FACETS	0.881	0.792	0.971	0.881	0.792	0.971	CLONAL	1	TRUE	0	0.622580651459564	1		226	206	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356229	66356229	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	240	600	0	ENST00000273854.3:c.1268del	p.Asn423ThrfsTer5	p.N423Tfs*5	ENST00000273854	NM_004439.5	423	aAc/ac	5/18	1	2	FACETS	0.963	0.902	1	0.963	0.902	1	CLONAL	1	TRUE	1	0.622580651459564	2		600	801	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224548	224548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751645963	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	205	492	0	ENST00000264932.6:c.224G>A	p.Arg75Gln	p.R75Q	ENST00000264932	NM_004168.2	75	cGa/cAa	3/15	1	2	FACETS	0.915	0.851	0.98	0.915	0.851	0.98	CLONAL	1	TRUE	1	0.622580651459564	2		492	720	SUCCESS
APC	324	MSKCC	GRCh37	5	112170861	112170861	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1114167580	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	160	432	0	ENST00000257430.4:c.1957A>G	p.Arg653Gly	p.R653G	ENST00000257430	NM_000038.5	653	Agg/Ggg	15/16	1	2	FACETS	0.913	0.842	0.986	0.913	0.842	0.986	CLONAL	1	TRUE	1	0.622580651459564	2		432	563	SUCCESS
APC	324	MSKCC	GRCh37	5	112175675	112175676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	105	286	0	ENST00000257430.4:c.4393_4394dup	p.Ser1465ArgfsTer9	p.S1465Rfs*9	ENST00000257430	NM_000038.5	1462	aag/aAGag	16/16	1	2	FACETS	0.978	0.885	1	0.978	0.885	1	CLONAL	1	TRUE	1	0.622580651459564	2		286	345	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931451	131931452	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	72	316	1	ENST00000265335.6:c.2164_2165dup	p.Glu723ArgfsTer14	p.E723Rfs*14	ENST00000265335		719	cta/ctAAa	13/25	1	2	FACETS	0.485	0.425	0.55	0.485	0.425	0.55	SUBCLONAL	1	TRUE	1	0.622580651459564	2		317	477	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944382	131944382	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs748536322	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	65	170	2	ENST00000265335.6:c.2801del	p.Asn934IlefsTer6	p.N934Ifs*6	ENST00000265335		932	Aaa/aa	17/25	1	2	FACETS	0.762	0.667	0.863	0.762	0.667	0.863	SUBCLONAL	1	TRUE	1	0.622580651459564	2		172	274	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459840	149459840	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761316359	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	208	631	2	ENST00000286301.3:c.367G>A	p.Ala123Thr	p.A123T	ENST00000286301	NM_005211.3	123	Gca/Aca	4/22	1	2	FACETS	0.92	0.857	0.985	0.92	0.857	0.985	CLONAL	1	TRUE	1	0.622580651459564	2		633	726	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	138	253	0	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.622580651459564	2		253	433	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839847	27839847	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	204	503	0	ENST00000328488.2:c.247C>A	p.Leu83Met	p.L83M	ENST00000328488	NM_003533.2	83	Ctg/Atg	1/1	1	2	FACETS	0.968	0.902	1	0.968	0.902	1	CLONAL	1	TRUE	1	0.622580651459564	2		503	677	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166206	32166206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773724911	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	279	640	0	ENST00000375023.3:c.4748G>A	p.Arg1583His	p.R1583H	ENST00000375023	NM_004557.3	1583	cGt/cAt	26/30	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.622580651459564	2		640	835	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43742094	43742094	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	280	720	2	ENST00000523873.1:c.83C>A	p.Pro28His	p.P28H	ENST00000523873		28	cCc/cAc	2/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.622580651459564	2		722	852	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631301	117631301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199882276	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	164	441	0	ENST00000368508.3:c.6377G>A	p.Arg2126Gln	p.R2126Q	ENST00000368508	NM_002944.2	2126	cGg/cAg	40/43	1	2	FACETS	0.926	0.855	0.999	0.926	0.855	0.999	CLONAL	1	TRUE	1	0.622580651459564	2		441	569	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718162	117718162	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	253	568	0	ENST00000368508.3:c.695T>C	p.Leu232Pro	p.L232P	ENST00000368508	NM_002944.2	232	cTg/cCg	7/43	1	2	FACETS	0.976	0.916	1	0.976	0.916	1	CLONAL	1	TRUE	1	0.622580651459564	2		568	833	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201873	152201873	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779180038	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	126	341	0	ENST00000206249.3:c.727C>T	p.Arg243Cys	p.R243C	ENST00000206249	NM_000125.3	243	Cgt/Tgt	3/8	1	2	FACETS	0.92	0.839	1	0.92	0.839	1	CLONAL	1	TRUE	1	0.622580651459564	2		341	440	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522598	157522598	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554236040	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	194	507	0	ENST00000346085.5:c.4870C>T	p.Arg1624Ter	p.R1624*	ENST00000346085	NM_020732.3	1624	Cga/Tga	18/20	1	2	FACETS	0.831	0.771	0.893	0.831	0.771	0.893	CLONAL	1	TRUE	1	0.622580651459564	2		507	750	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987423	2987423	+	splice_acceptor_variant	Splice_Site	DEL	T	T	-	rs747113439	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	110	444	0	ENST00000396946.4:c.8-2del		p.X3_splice	ENST00000396946	NM_032415.4	3			NA	2	FACETS	0.501	0.45	0.554			1	INDETERMINATE	1	TRUE	NA	0.622580651459564	2		444	706	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205092	38205092	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	154	736	7	ENST00000317025.8:c.598del	p.Ser200AlafsTer20	p.S200Afs*20	ENST00000317025	NM_023034.1	200	Agc/gc	2/24	0.567307910591745	3	FACETS	0.551	0.503	0.601	0.275	0.251	0.301	SUBCLONAL	1	TRUE	1	0.622580651459564	3		743	1178	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499823	8499823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1273962518	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	162	404	1	ENST00000356435.5:c.2146C>T	p.Arg716Cys	p.R716C	ENST00000356435		716	Cgc/Tgc	14/35	1	2	FACETS	0.931	0.859	1	0.931	0.859	1	CLONAL	1	TRUE	1	0.622580651459564	2		405	559	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27213564	27213564	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	180	531	0	ENST00000380036.4:c.2960G>A	p.Arg987Gln	p.R987Q	ENST00000380036	NM_000459.3	987	cGa/cAa	18/23	1	2	FACETS	0.913	0.846	0.983	0.913	0.846	0.983	CLONAL	1	TRUE	1	0.622580651459564	2		531	633	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223563	53223563	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	180	257	0	ENST00000375401.3:c.3796C>T	p.Gln1266Ter	p.Q1266*	ENST00000375401	NM_004187.3	1266	Cag/Tag	23/26	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.622580651459564	1		257	286	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608310	100608310	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	247	343	2	ENST00000308731.7:c.1780G>T	p.Gly594Trp	p.G594W	ENST00000308731	NM_000061.2	594	Ggg/Tgg	18/19	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.622580651459564	1		345	428	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670339	134670339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1303716587	NA	P-0036335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	61	368	0	ENST00000398015.3:c.250C>T	p.Arg84Cys	p.R84C	ENST00000398015	NM_004441.4	84	Cgc/Tgc	3/16	1	2	FACETS	0.922	0.797	1	0.922	0.797	1	CLONAL	1	TRUE	1	0.27	2		368	490	SUCCESS
ATM	472	MSKCC	GRCh37	11	108183190	108183191	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	35	227	2	ENST00000278616.4:c.5977dup	p.Ser1993LysfsTer2	p.S1993Kfs*2	ENST00000278616	NM_000051.3	1991	gaa/gAaa	40/63	1	2	FACETS	0.853	0.701	1	0.853	0.701	1	CLONAL	1	TRUE	1	0.27	2		229	304	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846132	68846133	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAACGATAATCCTCCGATCTT	novel	NA	P-0036335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	139	617	0	ENST00000261769.5:c.1107_1127dup	p.Asp370_Asn376dup	p.D370_N376dup	ENST00000261769	NM_004360.3	370	acc/acCAACGATAATCCTCCGATCTTc	8/16	0.223870448802542	3	FACETS	1	0.932	1	0.516	0.468	0.566	CLONAL	1	TRUE	1	0.27	3		617	1133	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218665	36218666	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGGATGGCCACTACA	novel	NA	P-0036335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	69	713	1	ENST00000222270.7:c.4372_4386dup	p.Asp1458_Lys1462dup	p.D1458_K1462dup	ENST00000222270	NM_014727.1	1458	gag/gAGGATGGCCACTACAag	17/37	1	2	FACETS	0.573	0.498	0.655	0.573	0.498	0.655	SUBCLONAL	1	TRUE	1	0.27	2		714	892	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416173	29416173	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	146	494	0	ENST00000389048.3:c.4780G>T	p.Glu1594Ter	p.E1594*	ENST00000389048	NM_004304.4	1594	Gaa/Taa	29/29	0.223870448802542	3	FACETS	0.851	0.778	0.927	0.851	0.778	0.927	CLONAL	2	TRUE	1	0.27	3		494	721	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	50	214	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.99	0.847	1	0.99	0.847	1	CLONAL	1	TRUE	1	0.39	2		214	259	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0036336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	77	724	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.791	0.697	0.893	0.791	0.697	0.893	SUBCLONAL	1	TRUE	1	0.39	2		725	499	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507384	8507384	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1419441419	NA	P-0036345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	35	446	0	ENST00000356435.5:c.1594A>G	p.Ile532Val	p.I532V	ENST00000356435		532	Att/Gtt	11/35	0.175783099078793	0	FACETS	0.821	0.687	0.965			1	CLONAL	3	FALSE	0	0.182828149521351	0		446	127	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0036346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	218	906	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	FALSE	NA	0.399792009669233	2		906	978	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0036347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	53	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	0.601	0.816	0.704	0.601	0.816	SUBCLONAL	1	TRUE	1	0.34	2		452	443	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411576	63411576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	101	384	0	ENST00000330258.3:c.1591C>T	p.Arg531Ter	p.R531*	ENST00000330258	NM_152424.3	531	Cga/Tga	2/2	0.0632617103837281	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.34	2		384	438	SUCCESS
APC	324	MSKCC	GRCh37	5	112175720	112175720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	98	314	0	ENST00000257430.4:c.4429C>T	p.Gln1477Ter	p.Q1477*	ENST00000257430	NM_000038.5	1477	Cag/Tag	16/16	0.233115014457813	2	FACETS	1	0.979	1	0.691	0.621	0.765	CLONAL	1	TRUE	0	0.34	2		314	417	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117361	115117368	+	frameshift_variant	Frame_Shift_Del	DEL	GTATGTCC	GTATGTCC	-	novel	NA	P-0036347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	33	380	0	ENST00000257566.3:c.806_813del	p.Arg269LeufsTer6	p.R269Lfs*6	ENST00000257566	NM_016569.3	269	cGGACATAC/c	4/8	1	2	FACETS	0.399	0.325	0.484	0.399	0.325	0.484	SUBCLONAL	1	TRUE	1	0.34	2		380	486	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246826	10246826	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1292341520	NA	P-0036347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	50	720	1	ENST00000340748.4:c.4579G>A	p.Val1527Ile	p.V1527I	ENST00000340748		1527	Gtc/Atc	37/40	1	2	FACETS	0.337	0.285	0.395	0.337	0.285	0.395	SUBCLONAL	1	TRUE	1	0.34	2		721	872	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057520000	NA	P-0036348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	350	821	1	ENST00000269305.4:c.452C>A	p.Pro151His	p.P151H	ENST00000269305	NM_001126112.2	151	cCc/cAc	5/11	0.30969252186659	3	FACETS	0.859	0.821	0.897	0.859	0.821	0.897	CLONAL	3	TRUE	0	0.502781980542665	3		822	676	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085768	16085768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	121	470	0	ENST00000281043.3:c.944C>T	p.Ser315Phe	p.S315F	ENST00000281043	NM_005378.4	315	tCc/tTc	3/3	0.260788812880151	5	FACETS	1	0.946	1	0.702	0.64	0.766	INDETERMINATE	2	TRUE	2	0.502781980542665	5		470	401	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416878	416878	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	135	419	0	ENST00000399788.2:c.3672G>C	p.Glu1224Asp	p.E1224D	ENST00000399788	NM_001042603.1	1224	gaG/gaC	23/28	0.502781980542665	5	FACETS	0.84	0.766	0.916	0.336	0.306	0.367	CLONAL	2	TRUE	0	0.502781980542665	5		419	561	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900388	3900388	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1455123577	NA	P-0036348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	153	712	0	ENST00000262367.5:c.708C>G	p.Ser236Arg	p.S236R	ENST00000262367	NM_004380.2	236	agC/agG	2/31	0.502781980542665	3	FACETS	0.772	0.712	0.835	0.772	0.712	0.835	SUBCLONAL	2	TRUE	1	0.502781980542665	3		712	493	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965080	15965080	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	65	451	0	ENST00000268712.3:c.5516C>G	p.Thr1839Arg	p.T1839R	ENST00000268712	NM_006311.3	1839	aCa/aGa	37/46	0.30969252186659	3	FACETS	1	0.895	1	0.342	0.299	0.389	CLONAL	1	TRUE	0	0.502781980542665	3		451	315	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223227	41223227	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	273	516	0	ENST00000357654.3:c.4704del	p.Ser1569AlafsTer32	p.S1569Afs*32	ENST00000357654	NM_007294.3	1568	atC/at	15/23	0.396360092958362	4	FACETS	0.897	0.855	0.937	0.897	0.855	0.937	CLONAL	4	TRUE	0	0.502781980542665	4		516	455	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602713	55602713	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	69	453	0	ENST00000288135.5:c.2534T>C	p.Val845Ala	p.V845A	ENST00000288135	NM_000222.2	845	gTa/gCa	18/21	0.204823756964267	5	FACETS	0.928	0.809	1	0.309	0.269	0.352	INDETERMINATE	1	TRUE	2	0.502781980542665	5		453	519	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875085	151875085	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	38	126	0	ENST00000262189.6:c.7453C>G	p.Pro2485Ala	p.P2485A	ENST00000262189	NM_170606.2	2485	Cca/Gca	38/59	0.459764801362673	3	FACETS	1	0.95	1	0.83	0.718	0.942	CLONAL	2	TRUE	0	0.502781980542665	3		126	76	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760122	133760122	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	56	551	1	ENST00000318560.5:c.2448del	p.Lys816AsnfsTer27	p.K816Nfs*27	ENST00000318560	NM_005157.4	815	ccA/cc	11/11	0.429787789347569	2	FACETS	0.714	0.616	0.82	0.357	0.308	0.41	SUBCLONAL	1	TRUE	0	0.502781980542665	2		552	312	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0036349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	257	485	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.485678940388564	2		485	813	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033245	69033245	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530869739	NA	P-0036349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	302	541	0	ENST00000288368.4:c.3685G>A	p.Val1229Ile	p.V1229I	ENST00000288368	NM_024870.2	1229	Gtc/Atc	30/40	0.485678940388564	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.485678940388564	4		541	836	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578525	7578525	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519976	NA	P-0036349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	233	951	0	ENST00000269305.4:c.405C>G	p.Cys135Trp	p.C135W	ENST00000269305	NM_001126112.2	135	tgC/tgG	5/11	0.485678940388564	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.485678940388564	1		951	622	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37882870	37882870	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	189	731	0	ENST00000269571.5:c.2928C>A	p.Phe976Leu	p.F976L	ENST00000269571		976	ttC/ttA	24/27	0.485678940388564	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.485678940388564	1		731	500	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437568	56437568	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	37	556	0	ENST00000407977.2:c.894T>G	p.Cys298Trp	p.C298W	ENST00000407977		298	tgT/tgG	8/10	1	2	FACETS	0.289	0.237	0.346	0.289	0.237	0.346	SUBCLONAL	1	TRUE	1	0.485678940388564	2		556	528	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36217174	36217174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	191	813	0	ENST00000222270.7:c.3923C>T	p.Ala1308Val	p.A1308V	ENST00000222270	NM_014727.1	1308	gCa/gTa	14/37	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.485678940388564	2		813	676	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	172	214	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.7	2		214	378	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217312	11217317	+	inframe_deletion	In_Frame_Del	DEL	ACTCGT	ACTCGT	-	novel	NA	P-0036350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	262	850	0	ENST00000361445.4:c.4361_4366del	p.His1454_Trp1456delinsArg	p.H1454_W1456delinsR	ENST00000361445	NM_004958.3	1454	cACGAGTgg/cgg	30/58	1	2	FACETS	0.981	0.923	1	0.981	0.923	1	CLONAL	1	TRUE	1	0.7	2		850	763	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201059	NA	P-0036352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	167	869	1	ENST00000269305.4:c.856G>T	p.Glu286Ter	p.E286*	ENST00000269305	NM_001126112.2	286	Gaa/Taa	8/11	1	2	FACETS	0.993	0.912	1	0.993	0.912	1	CLONAL	1	TRUE	1	0.353322159645904	2		870	952	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720828	89720828	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0036352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	20	395	0	ENST00000371953.3:c.979A>T	p.Lys327Ter	p.K327*	ENST00000371953	NM_000314.4	327	Aaa/Taa	8/9	0.353322159645904	1	FACETS	0.371	0.284	0.473	0.371	0.284	0.473	SUBCLONAL	1	TRUE	0	0.353322159645904	1		395	251	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845119	151845122	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TTTA	TTTA	-	novel	NA	P-0036352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	34	461	0	ENST00000262189.6:c.13890_13893del	p.Lys4631ValfsTer13	p.K4631Vfs*13	ENST00000262189	NM_170606.2	4630	ccTAAA/cc	52/59	1	2	FACETS	0.512	0.418	0.617	0.512	0.418	0.617	SUBCLONAL	1	TRUE	1	0.353322159645904	2		461	376	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	133	214	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.564613295746027	2		214	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	314	772	1	ENST00000269305.4:c.859G>T	p.Glu287Ter	p.E287*	ENST00000269305	NM_001126112.2	287	Gag/Tag	8/11	0.564613295746027	1	FACETS	0.997	0.945	1	0.997	0.945	1	CLONAL	1	TRUE	0	0.564613295746027	1		773	801	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652129	36652129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34916193	NA	P-0036357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	122	602	0	ENST00000244741.5:c.251G>A	p.Arg84Gln	p.R84Q	ENST00000244741	NM_000389.4	84	cGa/cAa	2/3	0.330296061002624	1	FACETS	0.424	0.384	0.467	0.424	0.384	0.467	INDETERMINATE	1	TRUE	0	0.564613295746027	1		602	731	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149440464	149440464	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371692872	NA	P-0036357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	118	622	0	ENST00000286301.3:c.1930G>A	p.Glu644Lys	p.E644K	ENST00000286301	NM_005211.3	644	Gag/Aag	14/22	1	2	FACETS	0.407	0.366	0.45	0.407	0.366	0.45	SUBCLONAL	1	TRUE	1	0.564613295746027	2		622	1028	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045491	47045491	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	170	266	0	ENST00000377604.3:c.2458G>T	p.Glu820Ter	p.E820*	ENST00000377604	NM_001204468.1	820	Gaa/Taa	22/24	0.421193228629009	0	FACETS	0.762	0.713	0.812			1	SUBCLONAL	1	TRUE	NA	0.564613295746027	0		266	344	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933301	100933301	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	112	561	0	ENST00000325455.5:c.2089G>T	p.Asp697Tyr	p.D697Y	ENST00000325455	NM_001202474.3	697	Gat/Tat	4/8	0.370195540409036	1	FACETS	0.404	0.364	0.447	0.404	0.364	0.447	SUBCLONAL	1	TRUE	0	0.564613295746027	1		561	704	SUCCESS
AR	367	MSKCC	GRCh37	X	66863172	66863172	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	151	308	0	ENST00000374690.3:c.1691G>C	p.Gly564Ala	p.G564A	ENST00000374690	NM_000044.3	564	gGa/gCa	2/8	0.421193228629009	0	FACETS	0.64	0.593	0.687			1	SUBCLONAL	1	TRUE	NA	0.564613295746027	0		308	364	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0036360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	23	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.748	0.582	0.941	0.748	0.582	0.941	CLONAL	1	TRUE	1	0.13	2		452	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0036360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	112	687	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.147514461272734	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	2	TRUE	0	0.13	2		688	845	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245040	46245040	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	43	481	0	ENST00000334344.6:c.3134C>A	p.Ser1045Ter	p.S1045*	ENST00000334344	NM_152641.2	1045	tCg/tAg	15/21	1	2	FACETS	0.946	0.79	1	0.946	0.79	1	CLONAL	1	TRUE	1	0.13	2		481	699	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512356	149512356	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	46	571	0	ENST00000261799.4:c.1084G>C	p.Ala362Pro	p.A362P	ENST00000261799	NM_002609.3	362	Gct/Cct	7/23	1	2	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	TRUE	1	0.13	2		571	703	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs864622237	NA	P-0036362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	311	535	0	ENST00000269305.4:c.700T>A	p.Tyr234Asn	p.Y234N	ENST00000269305	NM_001126112.2	234	Tac/Aac	7/11	0.655714653830542	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.672496053029059	2		535	422	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670291	134670291	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	95	340	0	ENST00000398015.3:c.202C>G	p.Gln68Glu	p.Q68E	ENST00000398015	NM_004441.4	68	Cag/Gag	3/16	0.619173077687644	4	FACETS	1	0.939	1	0.535	0.478	0.594	CLONAL	1	TRUE	2	0.672496053029059	4		340	442	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675165	30675165	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	126	453	3	ENST00000376406.3:c.3080C>A	p.Ser1027Tyr	p.S1027Y	ENST00000376406	NM_014641.2	1027	tCc/tAc	9/15	0.646475576788982	3	FACETS	0.999	0.91	1	0.5	0.455	0.546	CLONAL	1	TRUE	1	0.672496053029059	3		456	501	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325484	1325484	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs758423336	NA	P-0036362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	96	424	0	ENST00000400841.2:c.191G>T	p.Gly64Val	p.G64V	ENST00000400841		64	gGt/gTt	3/6	0.64671460075468	2	FACETS	0.86	0.774	0.949	0.43	0.387	0.475	CLONAL	1	TRUE	0	0.672496053029059	2		424	332	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106676	27106755	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCTGAAGCCCAGGACCCCTTTTCCACCCTGGGCCCCAATGCCGTCCTTTCCCCGCAGAGACTGGTCTTGGAAACCCTC	CAGCTGAAGCCCAGGACCCCTTTTCCACCCTGGGCCCCAATGCCGTCCTTTCCCCGCAGAGACTGGTCTTGGAAACCCTC	-	novel	NA	P-0036365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	178	513	0	ENST00000324856.7:c.6287_6366del	p.Ser2096Ter	p.S2096*	ENST00000324856	NM_006015.4	2096	tCAGCTGAAGCCCAGGACCCCTTTTCCACCCTGGGCCCCAATGCCGTCCTTTCCCCGCAGAGACTGGTCTTGGAAACCCTC/t	20/20	0.863913950652229	1	FACETS	0.984	0.938	1	0.984	0.938	1	CLONAL	1	TRUE	0	0.863913950652229	1		513	238	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439734	51439734	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	147	288	0	ENST00000262662.1:c.299A>T	p.Asp100Val	p.D100V	ENST00000262662		100	gAt/gTt	4/4	0.863913950652229	1	FACETS	0.938	0.888	0.986	0.938	0.888	0.986	CLONAL	1	TRUE	0	0.863913950652229	1		288	206	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609933	43609947	+	inframe_deletion	In_Frame_Del	DEL	CTGTGCGACGAGCTG	CTGTGCGACGAGCTG	-	novel	NA	P-0036365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	465	738	0	ENST00000355710.3:c.1885_1899del	p.Leu629_Leu633del	p.L629_L633del	ENST00000355710	NM_020975.4	629	CTGTGCGACGAGCTG/-	11/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.863913950652229	2		738	1003	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0036366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	84	303	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		303	322	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879686	37879686	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	85	577	0	ENST00000269571.5:c.2061G>A	p.Met687Ile	p.M687I	ENST00000269571		687	atG/atA	17/27	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		577	612	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0036368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	134	407	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.402100293399021	3	FACETS	0.848	0.777	0.92	0.848	0.777	0.92	CLONAL	2	TRUE	1	0.466251769036734	3		408	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577587	7577587	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	182	566	0	ENST00000269305.4:c.694A>T	p.Ile232Phe	p.I232F	ENST00000269305	NM_001126112.2	232	Atc/Ttc	7/11	0.466251769036734	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.466251769036734	1		566	561	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0036368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	49	304	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	0.402100293399021	3	FACETS	0.714	0.607	0.831	0.357	0.303	0.416	SUBCLONAL	1	TRUE	1	0.466251769036734	3		304	363	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715979	52715979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786205227	NA	P-0036368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	147	488	1	ENST00000322088.6:c.544C>T	p.Arg182Trp	p.R182W	ENST00000322088	NM_014225.5	182	Cgg/Tgg	5/15	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.466251769036734	2		489	623	SUCCESS
ATM	472	MSKCC	GRCh37	11	108128310	108128310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778065	NA	P-0036368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	88	311	1	ENST00000278616.4:c.2353C>T	p.Arg785Cys	p.R785C	ENST00000278616	NM_000051.3	785	Cgt/Tgt	15/63	1	2	FACETS	0.868	0.773	0.968	0.868	0.773	0.968	CLONAL	1	TRUE	1	0.466251769036734	2		312	435	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21630741	21630741	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs748842496	NA	P-0036368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	77	258	0	ENST00000421138.2:c.863A>T	p.Tyr288Phe	p.Y288F	ENST00000421138		288	tAt/tTt	8/16	0.395366115388785	2	FACETS	0.992	0.878	1	0.496	0.439	0.556	CLONAL	1	TRUE	0	0.466251769036734	2		258	333	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964013	28964013	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	112	461	0	ENST00000282397.4:c.1889A>T	p.Asp630Val	p.D630V	ENST00000282397	NM_002019.4	630	gAt/gTt	13/30	0.402100293399021	3	FACETS	1	0.957	1	0.554	0.5	0.61	CLONAL	1	TRUE	1	0.466251769036734	3		461	535	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37672016	37672016	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	131	554	0	ENST00000447079.4:c.2801C>T	p.Pro934Leu	p.P934L	ENST00000447079	NM_015083.1	934	cCt/cTt	9/14	0.402100293399021	3	FACETS	0.923	0.838	1	0.461	0.419	0.506	CLONAL	1	TRUE	1	0.466251769036734	3		554	751	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	56	375	0	ENST00000263967.3:c.3062A>C	p.Tyr1021Ser	p.Y1021S	ENST00000263967	NM_006218.2	1021	tAc/tCc	21/21	0.402100293399021	3	FACETS	0.634	0.544	0.732	0.317	0.272	0.366	SUBCLONAL	1	TRUE	1	0.466251769036734	3		375	467	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752695	42752695	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1366176199	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	140	558	1	ENST00000222329.4:c.1569del	p.Leu525SerfsTer6	p.L525Sfs*6	ENST00000222329	NM_006494.2	523	ggG/gg	4/4	1	2	FACETS	0.875	0.798	0.956	0.875	0.798	0.956	CLONAL	1	TRUE	1	0.436431955880323	2		559	733	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	323	645	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.932	0.885	0.98	1	0.996	1	CLONAL	2	TRUE	1	0.436431955880323	2		648	794	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	108	395	20	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.436431955880323	2		415	477	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204992	128204992	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	117	591	0	ENST00000341105.2:c.449del	p.Gly150GlufsTer68	p.G150Efs*68	ENST00000341105	NM_032638.4	150	gGa/ga	3/6	1	2	FACETS	0.768	0.693	0.847	0.768	0.693	0.847	SUBCLONAL	1	TRUE	1	0.436431955880323	2		591	698	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	78	303	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.731	0.644	0.824	0.731	0.644	0.824	SUBCLONAL	1	TRUE	1	0.436431955880323	2		303	489	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258976	16258976	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	140	492	0	ENST00000375759.3:c.6241C>T	p.Arg2081Ter	p.R2081*	ENST00000375759	NM_015001.2	2081	Cga/Tga	11/15	1	2	FACETS	0.984	0.899	1	0.984	0.899	1	CLONAL	1	TRUE	1	0.436431955880323	2		492	652	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	93	355	2	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.719	0.64	0.802	0.719	0.64	0.802	SUBCLONAL	1	TRUE	1	0.436431955880323	2		357	593	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	207	567	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.875	0.819	0.932	1	0.993	1	CLONAL	2	TRUE	1	0.436431955880323	2		568	542	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799098	42799098	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	197	816	4	ENST00000575354.2:c.4586del	p.Pro1529LeufsTer91	p.P1529Lfs*91	ENST00000575354	NM_015125.3	1528	Ccc/cc	20/20	1	2	FACETS	0.953	0.883	1	0.953	0.883	1	CLONAL	1	TRUE	1	0.436431955880323	2		820	947	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	282	750	0	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	0.828	0.782	0.876	1	0.995	1	CLONAL	2	TRUE	1	0.436431955880323	2		750	780	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	146	624	3	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.868	0.793	0.946	0.868	0.793	0.946	CLONAL	1	TRUE	1	0.436431955880323	2		627	771	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437565	56437566	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	151	502	0	ENST00000407977.2:c.896_897del	p.Val299GlyfsTer143	p.V299Gfs*143	ENST00000407977		299	gTG/g	8/10	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.436431955880323	2		502	683	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950066	44950066	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs863224886	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	125	262	0	ENST00000377967.4:c.3835C>T	p.Arg1279Ter	p.R1279*	ENST00000377967	NM_021140.2	1279	Cga/Tga	26/29	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.436431955880323	1		262	346	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	83	445	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	NA	2	FACETS	0.594	0.525	0.669			1	INDETERMINATE	1	TRUE	NA	0.436431955880323	2		445	640	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023904	27023904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1232964733	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	14	42	0	ENST00000324856.7:c.1015del	p.Ala339LeufsTer24	p.A339Lfs*24	ENST00000324856	NM_006015.4	337	tGg/tg	1/20	1	2	FACETS	0.867	0.639	1	0.867	0.639	1	CLONAL	1	TRUE	1	0.436431955880323	2		42	74	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612175	189612175	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1560311554	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	109	482	1	ENST00000264731.3:c.1927C>T	p.Arg643Ter	p.R643*	ENST00000264731	NM_003722.4	643	Cga/Tga	14/14	1	2	FACETS	0.787	0.708	0.87	0.787	0.708	0.87	SUBCLONAL	1	TRUE	1	0.436431955880323	2		483	635	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289271	33289271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1303387799	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	111	379	2	ENST00000374542.5:c.281G>A	p.Arg94His	p.R94H	ENST00000374542	NM_001141970.1	94	cGt/cAt	3/8	1	2	FACETS	0.954	0.861	1	0.954	0.861	1	CLONAL	1	TRUE	1	0.436431955880323	2		381	533	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	150	448	1	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	NA	2	FACETS	0.755	0.696	0.816			1	INDETERMINATE	2	TRUE	NA	0.436431955880323	2		449	455	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	75	293	1	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	1	2	FACETS	0.697	0.612	0.788	0.697	0.612	0.788	SUBCLONAL	1	TRUE	1	0.436431955880323	2		294	493	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	105	488	0	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	0.805	0.723	0.891	0.805	0.723	0.891	CLONAL	1	TRUE	1	0.436431955880323	2		488	598	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030692	48030692	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs267608092	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	105	364	1	ENST00000234420.5:c.3312del	p.Phe1104LeufsTer11	p.F1104Lfs*11	ENST00000234420	NM_000179.2	1102	acT/ac	5/10	1	2	FACETS	0.809	0.726	0.896	0.809	0.726	0.896	CLONAL	1	TRUE	1	0.436431955880323	2		365	595	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39629562	39629562	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	78	313	0	ENST00000262039.4:c.2260del	p.Thr754GlnfsTer7	p.T754Qfs*7	ENST00000262039	NM_002647.2	752	acA/ac	21/25	1	2	FACETS	0.905	0.8	1	0.905	0.8	1	CLONAL	1	TRUE	1	0.436431955880323	2		313	395	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337296	89337296	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567537413	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	107	497	0	ENST00000301030.4:c.7735C>T	p.Arg2579Cys	p.R2579C	ENST00000301030	NM_001256183.1	2579	Cgc/Tgc	12/13	1	2	FACETS	0.84	0.755	0.929	0.84	0.755	0.929	CLONAL	1	TRUE	1	0.436431955880323	2		497	584	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630938	187630938	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	86	474	0	ENST00000441802.2:c.44T>G	p.Phe15Cys	p.F15C	ENST00000441802	NM_005245.3	15	tTc/tGc	2/27	0.436431955880323	2	FACETS	0.674	0.597	0.756	0.337	0.298	0.378	SUBCLONAL	1	TRUE	0	0.436431955880323	2		474	585	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158187	106158187	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs780043982	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	79	348	1	ENST00000380013.4:c.3088C>T	p.Gln1030Ter	p.Q1030*	ENST00000380013	NM_001127208.2	1030	Cag/Tag	3/11	1	2	FACETS	0.84	0.742	0.944	0.84	0.742	0.944	CLONAL	1	TRUE	1	0.436431955880323	2		349	431	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143440	30143440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	73	356	1	ENST00000389048.3:c.86C>T	p.Ala29Val	p.A29V	ENST00000389048	NM_004304.4	29	gCg/gTg	1/29	1	2	FACETS	0.996	0.877	1	0.996	0.877	1	CLONAL	1	TRUE	1	0.436431955880323	2		357	336	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262680	16262680	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	74	304	3	ENST00000375759.3:c.9950del	p.Pro3317ArgfsTer83	p.P3317Rfs*83	ENST00000375759	NM_015001.2	3315	caC/ca	11/15	1	2	FACETS	0.774	0.68	0.874	0.774	0.68	0.874	SUBCLONAL	1	TRUE	1	0.436431955880323	2		307	438	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162414	47162414	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	118	461	0	ENST00000409792.3:c.3712del	p.Ser1238LeufsTer21	p.S1238Lfs*21	ENST00000409792	NM_014159.6	1238	Tct/ct	3/21	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.436431955880323	2		461	523	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432117	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	58	591	0	ENST00000257555.6:c.864_865del	p.Pro291ArgfsTer25	p.P291Rfs*25	ENST00000257555		288	ggGCcc/ggcc	4/10	1	2	FACETS	0.368	0.316	0.426	0.368	0.316	0.426	SUBCLONAL	1	TRUE	1	0.436431955880323	2		591	722	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143052	30143052	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1244823020	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	135	614	1	ENST00000389048.3:c.474del	p.Glu160ArgfsTer26	p.E160Rfs*26	ENST00000389048	NM_004304.4	158	ccC/cc	1/29	1	2	FACETS	0.793	0.721	0.868	0.793	0.721	0.868	SUBCLONAL	1	TRUE	1	0.436431955880323	2		615	780	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099468	157099470	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	rs1429292576	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	50	202	0	ENST00000346085.5:c.413_415del	p.Asn138del	p.N138del	ENST00000346085	NM_020732.3	135	tcCAAc/tcc	1/20	1	2	FACETS	0.744	0.635	0.862	0.744	0.635	0.862	SUBCLONAL	1	TRUE	1	0.436431955880323	2		202	308	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905324	50905324	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	181	808	1	ENST00000440232.2:c.537del	p.Arg180GlyfsTer3	p.R180Gfs*3	ENST00000440232	NM_002691.3	178	Ggg/gg	5/27	1	2	FACETS	0.954	0.881	1	0.954	0.881	1	CLONAL	1	TRUE	1	0.436431955880323	2		809	869	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120199	70120199	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	109	597	0	ENST00000245479.2:c.1201C>T	p.Gln401Ter	p.Q401*	ENST00000245479	NM_000346.3	401	Cag/Tag	3/3	1	2	FACETS	0.828	0.746	0.916	0.828	0.746	0.916	CLONAL	1	TRUE	1	0.436431955880323	2		597	603	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508473	106508473	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370328855	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	34	183	0	ENST00000359195.3:c.467C>T	p.Ala156Val	p.A156V	ENST00000359195	NM_002649.2	156	gCg/gTg	2/11	1	2	FACETS	0.649	0.534	0.777	0.649	0.534	0.777	SUBCLONAL	1	TRUE	1	0.436431955880323	2		183	240	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448480	49448480	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	69	505	0	ENST00000301067.7:c.231del	p.His77GlnfsTer53	p.H77Qfs*53	ENST00000301067	NM_003482.3	77	caC/ca	3/54	1	2	FACETS	0.557	0.485	0.634	0.557	0.485	0.634	SUBCLONAL	1	TRUE	1	0.436431955880323	2		505	568	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924618	94924618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1400088899	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	172	600	0	ENST00000536441.1:c.292C>T	p.Arg98Cys	p.R98C	ENST00000536441	NM_144665.3	98	Cgc/Tgc	3/10	1	2	FACETS	0.932	0.858	1	0.932	0.858	1	CLONAL	1	TRUE	1	0.436431955880323	2		600	846	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376683	118376683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149340870	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	42	415	0	ENST00000534358.1:c.10076C>T	p.Ala3359Val	p.A3359V	ENST00000534358	NM_005933.3	3359	gCg/gTg	27/36	1	2	FACETS	0.383	0.319	0.453	0.383	0.319	0.453	SUBCLONAL	1	TRUE	1	0.436431955880323	2		415	503	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223967	36223967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	195	767	0	ENST00000222270.7:c.6517C>T	p.Arg2173Trp	p.R2173W	ENST00000222270	NM_014727.1	2173	Cgg/Tgg	28/37	1	2	FACETS	0.946	0.875	1	0.946	0.875	1	CLONAL	1	TRUE	1	0.436431955880323	2		767	945	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987117	36987117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	125	560	0	ENST00000354822.5:c.572G>A	p.Arg191His	p.R191H	ENST00000354822	NM_001079668.2	191	cGc/cAc	3/3	1	2	FACETS	0.798	0.723	0.877	0.798	0.723	0.877	SUBCLONAL	1	TRUE	1	0.436431955880323	2		560	718	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970916	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	127	492	0	ENST00000265081.6:c.1147_1148del	p.Lys383GlyfsTer20	p.K383Gfs*20	ENST00000265081	NM_002439.4	381	AAa/a	7/24	1	2	FACETS	0.674	0.611	0.742	0.674	0.611	0.742	SUBCLONAL	1	TRUE	1	0.436431955880323	2		492	863	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76764100	76764100	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	32	216	0	ENST00000373344.5:c.7208G>A	p.Ser2403Asn	p.S2403N	ENST00000373344	NM_000489.3	2403	aGc/aAc	35/35	1	1	FACETS	0.377	0.307	0.456	0.377	0.307	0.456	SUBCLONAL	1	TRUE	0	0.436431955880323	1		216	304	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779184	3779184	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	100	503	0	ENST00000262367.5:c.5864C>T	p.Ala1955Val	p.A1955V	ENST00000262367	NM_004380.2	1955	gCg/gTg	31/31	1	2	FACETS	0.814	0.729	0.904	0.814	0.729	0.904	CLONAL	1	TRUE	1	0.436431955880323	2		503	563	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778371	3778371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754601626	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	83	593	2	ENST00000262367.5:c.6677C>T	p.Ala2226Val	p.A2226V	ENST00000262367	NM_004380.2	2226	gCg/gTg	31/31	1	2	FACETS	0.569	0.502	0.641	0.569	0.502	0.641	SUBCLONAL	1	TRUE	1	0.436431955880323	2		595	668	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117578	4117578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1295043645	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	150	575	0	ENST00000262948.5:c.142G>A	p.Glu48Lys	p.E48K	ENST00000262948	NM_030662.3	48	Gag/Aag	2/11	1	2	FACETS	0.921	0.843	1	0.921	0.843	1	CLONAL	1	TRUE	1	0.436431955880323	2		575	746	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11308079	11308079	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	181	728	1	ENST00000361445.4:c.913G>T	p.Gly305Cys	p.G305C	ENST00000361445	NM_004958.3	305	Ggc/Tgc	7/58	1	2	FACETS	0.836	0.771	0.904	0.836	0.771	0.904	CLONAL	1	TRUE	1	0.436431955880323	2		729	992	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932076	36932076	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	120	538	0	ENST00000361632.4:c.2393G>T	p.Gly798Val	p.G798V	ENST00000361632		798	gGg/gTg	16/16	1	2	FACETS	0.946	0.858	1	0.946	0.858	1	CLONAL	1	TRUE	1	0.436431955880323	2		538	581	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054953	176054953	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	147	511	0	ENST00000367669.3:c.1100T>C	p.Leu367Ser	p.L367S	ENST00000367669	NM_022457.5	367	tTg/tCg	10/20	1	2	FACETS	0.891	0.815	0.971	0.891	0.815	0.971	CLONAL	1	TRUE	1	0.436431955880323	2		511	756	SUCCESS
FH	2271	MSKCC	GRCh37	1	241671901	241671901	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1060500901	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	98	368	0	ENST00000366560.3:c.738+2T>C		p.X246_splice	ENST00000366560	NM_000143.3	246			1	2	FACETS	0.865	0.775	0.961	0.865	0.775	0.961	CLONAL	1	TRUE	1	0.436431955880323	2		368	519	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943988	71943988	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	178	594	0	ENST00000298229.2:c.1921C>T	p.Arg641Trp	p.R641W	ENST00000298229	NM_001567.3	641	Cgg/Tgg	16/28	1	2	FACETS	0.96	0.885	1	0.96	0.885	1	CLONAL	1	TRUE	1	0.436431955880323	2		594	850	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209309	133209309	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	143	584	1	ENST00000320574.5:c.6077G>T	p.Arg2026Met	p.R2026M	ENST00000320574	NM_006231.2	2026	aGg/aTg	44/49	1	2	FACETS	0.909	0.83	0.991	0.909	0.83	0.991	CLONAL	1	TRUE	1	0.436431955880323	2		585	721	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563231	21563231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	155	722	0	ENST00000382592.4:c.688C>T	p.His230Tyr	p.H230Y	ENST00000382592	NM_014572.2	230	Cac/Tac	4/8	1	2	FACETS	0.855	0.783	0.93	0.855	0.783	0.93	CLONAL	1	TRUE	1	0.436431955880323	2		722	831	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563345	21563345	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762240840	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	208	931	0	ENST00000382592.4:c.574G>A	p.Glu192Lys	p.E192K	ENST00000382592	NM_014572.2	192	Gag/Aag	4/8	1	2	FACETS	0.893	0.829	0.96	0.893	0.829	0.96	CLONAL	1	TRUE	1	0.436431955880323	2		931	1067	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058859	42058859	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773151185	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	97	353	0	ENST00000219905.7:c.8579G>A	p.Arg2860Gln	p.R2860Q	ENST00000219905	NM_001164273.1	2860	cGg/cAg	24/24	1	2	FACETS	0.889	0.796	0.987	0.889	0.796	0.987	CLONAL	1	TRUE	1	0.436431955880323	2		353	500	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678391	88678391	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	195	855	3	ENST00000360948.2:c.1145del	p.Asn382ThrfsTer32	p.N382Tfs*32	ENST00000360948	NM_001012338.2	382	aAc/ac	9/19	1	2	FACETS	0.923	0.854	0.994	0.923	0.854	0.994	CLONAL	1	TRUE	1	0.436431955880323	2		858	968	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354362	354362	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	164	670	1	ENST00000262320.3:c.1196T>C	p.Val399Ala	p.V399A	ENST00000262320	NM_003502.3	399	gTg/gCg	5/11	1	2	FACETS	0.929	0.854	1	0.929	0.854	1	CLONAL	1	TRUE	1	0.436431955880323	2		671	809	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134963	2134963	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	196	761	0	ENST00000219476.3:c.4505T>C	p.Leu1502Pro	p.L1502P	ENST00000219476	NM_000548.3	1502	cTg/cCg	35/42	1	2	FACETS	0.913	0.845	0.983	0.913	0.845	0.983	CLONAL	1	TRUE	1	0.436431955880323	2		761	984	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15938115	15938115	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	82	276	0	ENST00000268712.3:c.7099C>T	p.Pro2367Ser	p.P2367S	ENST00000268712	NM_006311.3	2367	Cca/Tca	45/46	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.436431955880323	2		276	360	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40364201	40364201	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	211	1000	0	ENST00000293328.3:c.1481T>C	p.Val494Ala	p.V494A	ENST00000293328	NM_012448.3	494	gTg/gCg	13/19	1	2	FACETS	0.883	0.819	0.949	0.883	0.819	0.949	CLONAL	1	TRUE	1	0.436431955880323	2		1000	1095	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40371795	40371795	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	14	233	0	ENST00000293328.3:c.616C>T	p.Gln206Ter	p.Q206*	ENST00000293328	NM_012448.3	206	Cag/Tag	6/19	1	2	FACETS	0.232	0.167	0.311	0.232	0.167	0.311	SUBCLONAL	1	TRUE	1	0.436431955880323	2		233	276	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59924499	59924499	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs533184563	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	127	386	0	ENST00000259008.2:c.590C>A	p.Ser197Tyr	p.S197Y	ENST00000259008	NM_032043.2	197	tCt/tAt	6/20	1	2	FACETS	0.898	0.816	0.985	0.898	0.816	0.985	CLONAL	1	TRUE	1	0.436431955880323	2		386	648	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117927	70117927	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	60	287	0	ENST00000245479.2:c.395A>G	p.Asn132Ser	p.N132S	ENST00000245479	NM_000346.3	132	aAc/aGc	1/3	1	2	FACETS	0.813	0.705	0.93	0.813	0.705	0.93	CLONAL	1	TRUE	1	0.436431955880323	2		287	338	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610562	10610562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752044333	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	193	717	0	ENST00000171111.5:c.148C>T	p.Arg50Cys	p.R50C	ENST00000171111	NM_203500.1	50	Cgc/Tgc	2/6	1	2	FACETS	0.972	0.9	1	0.972	0.9	1	CLONAL	1	TRUE	1	0.436431955880323	2		717	910	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752787	42752787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1397259156	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	175	756	1	ENST00000222329.4:c.1477C>T	p.Arg493Cys	p.R493C	ENST00000222329	NM_006494.2	493	Cgc/Tgc	4/4	1	2	FACETS	0.918	0.846	0.993	0.918	0.846	0.993	CLONAL	1	TRUE	1	0.436431955880323	2		757	874	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419834	41419834	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	56	258	0	ENST00000373198.4:c.486+1G>T		p.X162_splice	ENST00000373198	NM_133170.3	162			NA	2	FACETS	0.817	0.705	0.939			1	INDETERMINATE	1	TRUE	NA	0.436431955880323	2		258	314	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817459	39817459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs993206522	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	124	459	1	ENST00000288319.7:c.104C>T	p.Ala35Val	p.A35V	ENST00000288319	NM_182918.3	35	gCg/gTg	2/10	1	2	FACETS	0.919	0.834	1	0.919	0.834	1	CLONAL	1	TRUE	1	0.436431955880323	2		460	618	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665333	138665333	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	153	781	1	ENST00000330315.3:c.232T>C	p.Ser78Pro	p.S78P	ENST00000330315	NM_023067.3	78	Tcc/Ccc	1/1	1	2	FACETS	0.718	0.657	0.783	0.718	0.657	0.783	SUBCLONAL	1	TRUE	1	0.436431955880323	2		782	976	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919293	178919293	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	55	193	0	ENST00000263967.3:c.778T>C	p.Tyr260His	p.Y260H	ENST00000263967	NM_006218.2	260	Tac/Cac	4/21	1	2	FACETS	0.857	0.739	0.985	0.857	0.739	0.985	CLONAL	1	TRUE	1	0.436431955880323	2		193	294	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629493	187629493	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	117	614	1	ENST00000441802.2:c.1489T>C	p.Tyr497His	p.Y497H	ENST00000441802	NM_005245.3	497	Tac/Cac	2/27	0.436431955880323	2	FACETS	0.69	0.622	0.762	0.345	0.311	0.381	SUBCLONAL	1	TRUE	0	0.436431955880323	2		615	777	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522614	176522614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768792805	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	150	703	0	ENST00000292408.4:c.1711G>A	p.Asp571Asn	p.D571N	ENST00000292408	NM_213647.1	571	Gac/Aac	13/18	1	2	FACETS	0.828	0.757	0.902	0.828	0.757	0.902	CLONAL	1	TRUE	1	0.436431955880323	2		703	830	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523655	176523655	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	151	745	0	ENST00000292408.4:c.2066C>T	p.Pro689Leu	p.P689L	ENST00000292408	NM_213647.1	689	cCg/cTg	16/18	1	2	FACETS	0.796	0.728	0.868	0.796	0.728	0.868	SUBCLONAL	1	TRUE	1	0.436431955880323	2		745	869	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200345	138200345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	119	414	1	ENST00000237289.4:c.1763C>T	p.Ala588Val	p.A588V	ENST00000237289	NM_001270507.1	588	gCt/gTt	7/9	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.436431955880323	2		415	542	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200369	138200369	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs946809001	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	89	444	0	ENST00000237289.4:c.1787G>A	p.Arg596Gln	p.R596Q	ENST00000237289	NM_001270507.1	596	cGg/cAg	7/9	1	2	FACETS	0.679	0.602	0.76	0.679	0.602	0.76	SUBCLONAL	1	TRUE	1	0.436431955880323	2		444	601	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005591	150005591	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	88	312	0	ENST00000253339.5:c.634G>T	p.Gly212Ter	p.G212*	ENST00000253339		212	Gga/Tga	3/7	1	2	FACETS	0.925	0.824	1	0.925	0.824	1	CLONAL	1	TRUE	1	0.436431955880323	2		312	436	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969982	161969983	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs745647746	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	98	518	1	ENST00000366898.1:c.986dup	p.Val330ArgfsTer17	p.V330Rfs*17	ENST00000366898	NM_004562.2	329	ggc/ggGc	9/12	1	2	FACETS	0.77	0.689	0.857	0.77	0.689	0.857	SUBCLONAL	1	TRUE	1	0.436431955880323	2		519	583	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129931	69129931	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	30	270	0	ENST00000288368.4:c.4685C>A	p.Ala1562Asp	p.A1562D	ENST00000288368	NM_024870.2	1562	gCt/gAt	38/40	1	2	FACETS	0.33	0.266	0.404	0.33	0.266	0.404	SUBCLONAL	1	TRUE	1	0.436431955880323	2		270	416	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90995032	90995032	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587781450	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	100	454	0	ENST00000265433.3:c.89A>G	p.Asn30Ser	p.N30S	ENST00000265433	NM_002485.4	30	aAc/aGc	2/16	1	2	FACETS	0.644	0.575	0.717	0.644	0.575	0.717	SUBCLONAL	1	TRUE	1	0.436431955880323	2		454	712	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376641	8376641	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	88	437	0	ENST00000356435.5:c.4472C>T	p.Ala1491Val	p.A1491V	ENST00000356435		1491	gCc/gTc	27/35	1	2	FACETS	0.696	0.618	0.78	0.696	0.618	0.78	SUBCLONAL	1	TRUE	1	0.436431955880323	2		437	579	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412624	139412624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754529382	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	149	652	1	ENST00000277541.6:c.1220C>T	p.Pro407Leu	p.P407L	ENST00000277541	NM_017617.3	407	cCg/cTg	7/34	1	2	FACETS	0.831	0.759	0.905	0.831	0.759	0.905	CLONAL	1	TRUE	1	0.436431955880323	2		653	822	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041612	47041612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	171	303	1	ENST00000377604.3:c.1837C>T	p.Arg613Trp	p.R613W	ENST00000377604	NM_001204468.1	613	Cgg/Tgg	17/24	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.436431955880323	1		304	414	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947827	178947827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	43	425	0	ENST00000263967.3:c.2702G>T	p.Cys901Phe	p.C901F	ENST00000263967	NM_006218.2	901	tGt/tTt	19/21	1	2	FACETS	0.871	0.739	1	0.871	0.739	1	CLONAL	1	TRUE	1	0.539381558090459	2		425	183	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1555525429	NA	P-0036370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	117	493	0	ENST00000269305.4:c.782+1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.539381558090459	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.539381558090459	1		493	259	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111511	8111512	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0036370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	136	475	0	ENST00000346208.3:c.997_998insC	p.Asn333ThrfsTer19	p.N333Tfs*19	ENST00000346208		333	aat/aCat	5/6	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.539381558090459	2		475	445	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0036372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1695	110	485	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.335608763057428	11	FACETS	0.912	0.815	1	0.101	0.09	0.113	CLONAL	1	FALSE	2	0.335608763057428	11		485	1805	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0036372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	45	518	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.26392507653704	0	FACETS	0.312	0.262	0.368			1	SUBCLONAL	1	FALSE	0	0.335608763057428	0		518	571	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602314	10602314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	348	779	0	ENST00000171111.5:c.1264G>A	p.Asp422Asn	p.D422N	ENST00000171111	NM_203500.1	422	Gat/Aat	3/6	1	2	FACETS	1	0.978	1	1	0.996	1	CLONAL	2	FALSE	1	0.335608763057428	2		779	983	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425644	49425644	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057517992	NA	P-0036372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	91	598	0	ENST00000301067.7:c.12844C>T	p.Arg4282Ter	p.R4282*	ENST00000301067	NM_003482.3	4282	Cga/Tga	39/54	0.116514016132732	3	FACETS	1	0.936	1	0.538	0.478	0.601	INDETERMINATE	1	FALSE	1	0.335608763057428	3		598	589	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425896	49425896	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783685	NA	P-0036372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	59	759	0	ENST00000301067.7:c.12592C>T	p.Arg4198Ter	p.R4198*	ENST00000301067	NM_003482.3	4198	Cga/Tga	39/54	0.116514016132732	3	FACETS	0.53	0.455	0.613	0.265	0.227	0.307	INDETERMINATE	1	FALSE	1	0.335608763057428	3		759	774	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215754	133215754	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	55	545	0	ENST00000320574.5:c.5509C>A	p.Leu1837Met	p.L1837M	ENST00000320574	NM_006231.2	1837	Ctg/Atg	40/49	1	2	FACETS	0.458	0.391	0.531	0.458	0.391	0.531	SUBCLONAL	1	FALSE	1	0.335608763057428	2		545	716	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292778	91292778	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	63	497	0	ENST00000355112.3:c.280C>G	p.Pro94Ala	p.P94A	ENST00000355112	NM_000057.2	94	Cca/Gca	3/22	1	2	FACETS	0.551	0.476	0.633	0.551	0.476	0.633	SUBCLONAL	1	FALSE	1	0.335608763057428	2		497	681	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144802	11144802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	56	423	0	ENST00000358026.2:c.3877G>A	p.Glu1293Lys	p.E1293K	ENST00000358026	NM_001128849.1	1293	Gaa/Aaa	28/36	1	2	FACETS	0.588	0.503	0.68	0.588	0.503	0.68	SUBCLONAL	1	FALSE	1	0.335608763057428	2		423	568	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709469	176709469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	49	364	0	ENST00000439151.2:c.5896G>A	p.Glu1966Lys	p.E1966K	ENST00000439151	NM_022455.4	1966	Gaa/Aaa	19/23	1	2	FACETS	0.452	0.382	0.529	0.452	0.382	0.529	SUBCLONAL	1	FALSE	1	0.335608763057428	2		364	646	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777900	27777900	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	34	347	0	ENST00000369163.2:c.49C>T	p.Pro17Ser	p.P17S	ENST00000369163	NM_003536.2	17	Ccg/Tcg	1/1	1	2	FACETS	0.505	0.413	0.609	0.505	0.413	0.609	SUBCLONAL	1	FALSE	1	0.335608763057428	2		347	401	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742031	145742031	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	65	748	0	ENST00000428558.2:c.472G>T	p.Glu158Ter	p.E158*	ENST00000428558	NM_004260.3	158	Gag/Tag	5/22	1	2	FACETS	0.486	0.42	0.557	0.486	0.42	0.557	SUBCLONAL	1	FALSE	1	0.335608763057428	2		748	797	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348247	70348247	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	52	766	0	ENST00000374080.3:c.3311A>G	p.Asn1104Ser	p.N1104S	ENST00000374080		1104	aAc/aGc	23/45	0.335608763057428	1	FACETS	0.329	0.279	0.383	0.329	0.279	0.383	SUBCLONAL	1	FALSE	0	0.335608763057428	1		766	785	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	97	638	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	0.499844566300425	5	FACETS	0.896	0.807	0.989	0.598	0.538	0.66	CLONAL	2	TRUE	2	0.609045667541623	5		638	340	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608062	28608062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	79	702	0	ENST00000241453.7:c.1904C>T	p.Thr635Ile	p.T635I	ENST00000241453	NM_004119.2	635	aCa/aTa	15/24	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.609045667541623	2		702	231	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085824	16085824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763830786	NA	P-0036374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	39	434	1	ENST00000281043.3:c.1000G>A	p.Ala334Thr	p.A334T	ENST00000281043	NM_005378.4	334	Gcc/Acc	3/3	NA	2	FACETS	0.873	0.737	1			1	INDETERMINATE	1	TRUE	NA	0.599424385326843	2		435	149	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188279	10188295	+	frameshift_variant	Frame_Shift_Del	DEL	ATGTTGACGGACAGCCT	ATGTTGACGGACAGCCT	-	novel	NA	P-0036374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	36	814	0	ENST00000256474.2:c.424_440del	p.Val142PhefsTer26	p.V142Ffs*26	ENST00000256474	NM_000551.3	141	aATGTTGACGGACAGCCT/a	2/3	0.599424385326843	1	FACETS	0.662	0.556	0.776	0.662	0.556	0.776	SUBCLONAL	1	TRUE	0	0.599424385326843	1		814	127	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129739	47129739	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0036374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	24	330	0	ENST00000409792.3:c.5143-2A>T		p.X1715_splice	ENST00000409792	NM_014159.6	1715			0.599424385326843	1	FACETS	0.95	0.778	1	0.95	0.778	1	CLONAL	1	TRUE	0	0.599424385326843	1		330	59	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240034	53240034	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0036374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	69	340	2	ENST00000375401.3:c.1407T>A	p.Tyr469Ter	p.Y469*	ENST00000375401	NM_004187.3	469	taT/taA	11/26	1	1	FACETS	0.886	0.821	0.945	1	0.986	1	CLONAL	2	TRUE	0	0.599424385326843	1		342	91	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0036377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	79	485	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.895	0.787	1	0.895	0.787	1	CLONAL	1	TRUE	1	0.27766601176904	2		485	636	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684323	29684323	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs567988442	NA	P-0036377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	40	372	0	ENST00000356175.3:c.7843C>T	p.Gln2615Ter	p.Q2615*	ENST00000356175	NM_000267.3	2615	Caa/Taa	53/57	1	2	FACETS	0.649	0.539	0.771	0.649	0.539	0.771	SUBCLONAL	1	TRUE	1	0.27766601176904	2		372	444	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870927	12870929	+	frameshift_variant	Frame_Shift_Del	DEL	ATG	ATG	CT	novel	NA	P-0036377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	34	197	0	ENST00000228872.4:c.154_156delinsCT	p.Met52LeufsTer19	p.M52Lfs*19	ENST00000228872	NM_004064.3	52	ATG/CT	1/3	0.0399699904578781	3	FACETS	1	0.874	1	0.541	0.444	0.648	INDETERMINATE	1	TRUE	1	0.27766601176904	3		197	258	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874067	151874068	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	62	478	0	ENST00000262189.6:c.8470dup	p.Thr2824AsnfsTer9	p.T2824Nfs*9	ENST00000262189	NM_170606.2	2824	acg/aAcg	38/59	1	2	FACETS	0.746	0.644	0.856	0.746	0.644	0.856	SUBCLONAL	1	TRUE	1	0.27766601176904	2		478	599	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154241	2154242	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755455183	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	79	681	1	ENST00000434045.2:c.686dup	p.Glu230ArgfsTer50	p.E230Rfs*50	ENST00000434045	NM_001127598.1	229	cca/ccCa	5/5	1	2	FACETS	0.863	0.76	0.973	0.863	0.76	0.973	CLONAL	1	TRUE	1	0.324640598908982	2		682	564	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	238	645	3	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	0.324640598908982	2		648	682	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	142	795	3	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.324640598908982	2		798	749	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	53	303	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.963	0.825	1	0.963	0.825	1	CLONAL	1	TRUE	1	0.324640598908982	2		303	339	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	75	567	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.324640598908982	2		568	360	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	140	510	5	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	NA	2	FACETS	0.82	0.751	0.891			1	INDETERMINATE	2	TRUE	NA	0.324640598908982	2		515	526	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120199	70120199	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	106	597	0	ENST00000245479.2:c.1201C>T	p.Gln401Ter	p.Q401*	ENST00000245479	NM_000346.3	401	Cag/Tag	3/3	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.324640598908982	2		597	632	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736166	204736166	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	27	459	0	ENST00000302823.3:c.529del	p.Tyr177IlefsTer10	p.Y177Ifs*10	ENST00000302823	NM_005214.4	175	Ttt/tt	3/4	1	2	FACETS	0.309	0.245	0.383	0.309	0.245	0.383	SUBCLONAL	1	TRUE	1	0.324640598908982	2		459	538	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	96	469	0	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	1	2	FACETS	0.877	0.782	0.979	0.877	0.782	0.979	CLONAL	1	TRUE	1	0.324640598908982	2		469	674	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	46	350	4	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.746	0.63	0.873	0.746	0.63	0.873	SUBCLONAL	1	TRUE	1	0.324640598908982	2		354	380	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417886	32417886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	36	498	2	ENST00000332351.3:c.1166G>A	p.Arg389His	p.R389H	ENST00000332351	NM_024426.4	389	cGc/cAc	7/10	1	2	FACETS	0.415	0.341	0.499	0.415	0.341	0.499	SUBCLONAL	1	TRUE	1	0.324640598908982	2		500	534	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	78	534	3	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	0.939	0.827	1	0.939	0.827	1	CLONAL	1	TRUE	1	0.324640598908982	2		537	512	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151290	202151290	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	82	429	1	ENST00000358485.4:c.1596del	p.Lys532AsnfsTer73	p.K532Nfs*73	ENST00000358485	NM_001080125.1	530	agA/ag	9/9	1	2	FACETS	0.962	0.851	1	0.962	0.851	1	CLONAL	1	TRUE	1	0.324640598908982	2		430	525	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938776	76938776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1557140467	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	90	668	1	ENST00000373344.5:c.1972C>T	p.Arg658Cys	p.R658C	ENST00000373344	NM_000489.3	658	Cgt/Tgt	9/35	0.324640598908982	1	FACETS	0.912	0.812	1	0.912	0.812	1	CLONAL	1	TRUE	0	0.324640598908982	1		669	509	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225408	26225408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	35	172	0	ENST00000360408.1:c.26G>A	p.Arg9His	p.R9H	ENST00000360408	NM_003532.2	9	cGt/cAt	1/1	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.324640598908982	2		172	194	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656846	45656846	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	96	576	0	ENST00000407780.3:c.310A>G	p.Thr104Ala	p.T104A	ENST00000407780	NM_001283052.1	104	Acc/Gcc	3/7	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.324640598908982	2		576	564	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212259	5212259	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	86	633	0	ENST00000357368.4:c.4772C>T	p.Ala1591Val	p.A1591V	ENST00000357368	NM_002850.3	1591	gCc/gTc	32/38	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.324640598908982	2		633	455	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243963	5243963	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761695523	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	109	576	0	ENST00000357368.4:c.1519G>A	p.Val507Ile	p.V507I	ENST00000357368	NM_002850.3	507	Gtc/Atc	11/38	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.324640598908982	2		576	583	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	76	397	13	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.324640598908982	2		410	416	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	359972	359972	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	179	600	2	ENST00000262320.3:c.1116+1G>A		p.X372_splice	ENST00000262320	NM_003502.3	372			NA	2	FACETS	1	0.957	1			1	INDETERMINATE	2	TRUE	NA	0.324640598908982	2		602	529	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432249	432249	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	65	337	0	ENST00000399788.2:c.2274del	p.Asp759IlefsTer2	p.D759Ifs*2	ENST00000399788	NM_001042603.1	758	aaA/aa	16/28	NA	2	FACETS	0.892	0.775	1			1	INDETERMINATE	1	TRUE	NA	0.324640598908982	2		337	449	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428251	33428251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150134822	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	91	532	1	ENST00000345365.6:c.872G>A	p.Arg291His	p.R291H	ENST00000345365	NM_002878.3	291	cGc/cAc	9/10	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.324640598908982	2		533	526	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360679	70360680	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCA	rs786200971	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	18	168	0	ENST00000374080.3:c.6256_6258dup	p.Gln2086dup	p.Q2086dup	ENST00000374080		2086	cgg/cgGCAg	42/45	0.324640598908982	1	FACETS	0.829	0.633	1	0.829	0.633	1	CLONAL	1	TRUE	0	0.324640598908982	1		168	112	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237614	16237614	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	51	408	0	ENST00000375759.3:c.1061G>A	p.Gly354Asp	p.G354D	ENST00000375759	NM_015001.2	354	gGc/gAc	5/15	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.324640598908982	2		408	314	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115748	108115748	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1555067335	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	15	199	1	ENST00000278616.4:c.900del	p.Gly301ValfsTer19	p.G301Vfs*19	ENST00000278616	NM_000051.3	299	gAa/ga	7/63	1	2	FACETS	0.629	0.462	0.825	0.629	0.462	0.825	SUBCLONAL	1	TRUE	1	0.324640598908982	2		200	147	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246312	46246312	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	33	361	0	ENST00000334344.6:c.4406T>G	p.Val1469Gly	p.V1469G	ENST00000334344	NM_152641.2	1469	gTc/gGc	15/21	0.251522941876444	3	FACETS	0.679	0.554	0.82	0.34	0.277	0.41	SUBCLONAL	1	TRUE	1	0.324640598908982	3		361	348	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630484	90630484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	90	575	0	ENST00000330062.3:c.827C>T	p.Thr276Ile	p.T276I	ENST00000330062	NM_002168.2	276	aCc/aTc	7/11	1	2	FACETS	0.879	0.78	0.983	0.879	0.78	0.983	CLONAL	1	TRUE	1	0.324640598908982	2		575	631	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89354977	89354977	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	149	669	0	ENST00000301030.4:c.703G>A	p.Asp235Asn	p.D235N	ENST00000301030	NM_001256183.1	235	Gac/Aac	7/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.324640598908982	2		669	831	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8113500	8113500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs753550850	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	99	674	0	ENST00000585124.1:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000585124	NM_004217.3	15	Cag/Tag	2/9	1	2	FACETS	0.838	0.748	0.933	0.838	0.748	0.933	CLONAL	1	TRUE	1	0.324640598908982	2		674	728	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546030	29546030	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	63	291	0	ENST00000356175.3:c.1535G>T	p.Arg512Ile	p.R512I	ENST00000356175	NM_000267.3	512	aGa/aTa	14/57	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.324640598908982	2		291	371	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664399	29664399	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	67	441	0	ENST00000356175.3:c.6378A>C	p.Gln2126His	p.Q2126H	ENST00000356175	NM_000267.3	2126	caA/caC	42/57	1	2	FACETS	0.962	0.839	1	0.962	0.839	1	CLONAL	1	TRUE	1	0.324640598908982	2		441	429	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435108	56435108	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	31	657	0	ENST00000407977.2:c.2029G>A	p.Ala677Thr	p.A677T	ENST00000407977		677	Gct/Act	9/10	1	2	FACETS	0.315	0.254	0.385	0.315	0.254	0.385	SUBCLONAL	1	TRUE	1	0.324640598908982	2		657	606	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39550304	39550304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	31	219	0	ENST00000262039.4:c.415G>A	p.Gly139Arg	p.G139R	ENST00000262039	NM_002647.2	139	Ggg/Agg	4/25	1	2	FACETS	0.732	0.594	0.886	0.732	0.594	0.886	SUBCLONAL	1	TRUE	1	0.324640598908982	2		219	261	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213574	2213576	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	127	761	0	ENST00000398665.3:c.1597_1599del	p.Leu533del	p.L533del	ENST00000398665	NM_032482.2	532	CTC/-	17/28	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.324640598908982	2		761	754	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260574	10260575	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	72	552	0	ENST00000340748.4:c.2287_2288del	p.Val763LeufsTer6	p.V763Lfs*6	ENST00000340748		763	GTc/c	24/40	1	2	FACETS	0.842	0.737	0.955	0.842	0.737	0.955	CLONAL	1	TRUE	1	0.324640598908982	2		552	527	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47724985	47724985	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs747474100	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	116	807	0	ENST00000449228.1:c.759C>A	p.Ser253Arg	p.S253R	ENST00000449228	NM_001127240.2	253	agC/agA	4/4	1	2	FACETS	0.917	0.827	1	0.917	0.827	1	CLONAL	1	TRUE	1	0.324640598908982	2		807	779	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645634	215645634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786203129	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	60	620	0	ENST00000260947.4:c.964C>T	p.Arg322Cys	p.R322C	ENST00000260947	NM_000465.2	322	Cgt/Tgt	4/11	1	2	FACETS	0.715	0.617	0.822	0.715	0.617	0.822	SUBCLONAL	1	TRUE	1	0.324640598908982	2		620	517	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661341	227661341	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	103	675	0	ENST00000305123.5:c.2114del	p.Gly705AlafsTer29	p.G705Afs*29	ENST00000305123	NM_005544.2	705	gGc/gc	1/2	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.324640598908982	2		675	597	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662351	227662352	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs766624780	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	93	534	0	ENST00000305123.5:c.1103dup	p.Leu369AlafsTer28	p.L369Afs*28	ENST00000305123	NM_005544.2	368	ccg/ccCg	1/2	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.324640598908982	2		534	523	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747062	40747062	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	86	618	0	ENST00000373198.4:c.3020del	p.Asn1007ThrfsTer8	p.N1007Tfs*8	ENST00000373198	NM_133170.3	1007	aAc/ac	22/32	1	2	FACETS	0.917	0.812	1	0.917	0.812	1	CLONAL	1	TRUE	1	0.324640598908982	2		618	578	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526792	31526792	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	101	613	0	ENST00000344624.3:c.248del	p.Pro83HisfsTer25	p.P83Hfs*25	ENST00000344624		83	cCa/ca	2/33	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.324640598908982	2		613	608	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911164	29911164	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs41552413	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	64	318	2	ENST00000376809.5:c.463C>A	p.Arg155Ser	p.R155S	ENST00000376809	NM_002116.7	155	Cgc/Agc	3/8	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.324640598908982	2		320	310	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911183	29911183	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs72555400	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	31	147	0	ENST00000376809.5:c.482A>C	p.Asp161Ala	p.D161A	ENST00000376809	NM_002116.7	161	gAc/gCc	3/8	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.324640598908982	2		147	154	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324534	31324534	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	50	864	0	ENST00000412585.2:c.274A>G	p.Lys92Glu	p.K92E	ENST00000412585	NM_005514.6	92	Aag/Gag	2/8	1	2	FACETS	0.346	0.293	0.406	0.346	0.293	0.406	SUBCLONAL	1	TRUE	1	0.324640598908982	2		864	889	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288359	33288359	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	57	364	0	ENST00000374542.5:c.1049C>A	p.Pro350His	p.P350H	ENST00000374542	NM_001141970.1	350	cCt/cAt	4/8	1	2	FACETS	0.796	0.685	0.917	0.796	0.685	0.917	CLONAL	1	TRUE	1	0.324640598908982	2		364	441	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969107	93969107	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	46	325	0	ENST00000369303.4:c.1889C>T	p.Ala630Val	p.A630V	ENST00000369303	NM_004440.3	630	gCc/gTc	10/17	1	2	FACETS	0.752	0.635	0.88	0.752	0.635	0.88	SUBCLONAL	1	TRUE	1	0.324640598908982	2		325	377	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233129	55233129	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	68	435	0	ENST00000275493.2:c.1879G>T	p.Gly627Ter	p.G627*	ENST00000275493	NM_005228.3	627	Gga/Tga	15/28	1	2	FACETS	0.773	0.673	0.881	0.773	0.673	0.881	SUBCLONAL	1	TRUE	1	0.324640598908982	2		435	542	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273148	55273148	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	125	612	2	ENST00000275493.2:c.3471G>A	p.Trp1157Ter	p.W1157*	ENST00000275493	NM_005228.3	1157	tgG/tgA	28/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.324640598908982	2		614	568	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476752	140476752	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	58	441	0	ENST00000288602.6:c.1654A>C	p.Lys552Gln	p.K552Q	ENST00000288602	NM_004333.4	552	Aaa/Caa	13/18	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.324640598908982	2		441	315	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873309	151873309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145953124	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	43	340	1	ENST00000262189.6:c.9229C>T	p.Arg3077Cys	p.R3077C	ENST00000262189	NM_170606.2	3077	Cgt/Tgt	38/59	1	2	FACETS	0.738	0.619	0.869	0.738	0.619	0.869	SUBCLONAL	1	TRUE	1	0.324640598908982	2		341	359	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908835	101908835	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121918711	NA	P-0036380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	24	569	0	ENST00000374994.4:c.1199A>G	p.Asp400Gly	p.D400G	ENST00000374994	NM_004612.2	400	gAc/gGc	7/9	0.324640598908982	2	FACETS	0.311	0.243	0.389	0.155	0.121	0.195	SUBCLONAL	1	TRUE	0	0.324640598908982	2		569	476	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539726	187539726	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	137	438	0	ENST00000441802.2:c.8014T>C	p.Phe2672Leu	p.F2672L	ENST00000441802	NM_005245.3	2672	Ttt/Ctt	10/27	1	2	FACETS	0.978	0.893	1	0.978	0.893	1	CLONAL	1	TRUE	1	0.461630880722896	2		438	607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0036381-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	108	531	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.571675972808611	1	FACETS	0.859	0.781	0.94	0.859	0.781	0.94	CLONAL	1	TRUE	0	0.571675972808611	1		531	314	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0036381-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	110	545	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.149253265467118	0	FACETS	0.326	0.294	0.359			1	INDETERMINATE	1	TRUE	0	0.571675972808611	0		545	506	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127754	64127754	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036381-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	135	569	0	ENST00000334205.4:c.247C>A	p.Arg83Ser	p.R83S	ENST00000334205	NM_003942.2	83	Cgc/Agc	3/17	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.571675972808611	2		569	357	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877136	151877136	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036381-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	155	373	0	ENST00000262189.6:c.7225C>T	p.Gln2409Ter	p.Q2409*	ENST00000262189	NM_170606.2	2409	Cag/Tag	37/59	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.571675972808611	2		373	523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0036382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	169	667	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.238079583222447	3	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	1	0.33029113015349	3		667	587	SUCCESS
APC	324	MSKCC	GRCh37	5	112157650	112157650	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1060503333	NA	P-0036382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	111	346	4	ENST00000257430.4:c.1370C>A	p.Ser457Ter	p.S457*	ENST00000257430	NM_000038.5	457	tCa/tAa	11/16	0.299495457930737	2	FACETS	0.82	0.743	0.9	0.82	0.743	0.9	CLONAL	2	TRUE	0	0.33029113015349	2		350	410	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416374	29416374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	179	960	4	ENST00000389048.3:c.4579C>T	p.Pro1527Ser	p.P1527S	ENST00000389048	NM_004304.4	1527	Cca/Tca	29/29	0.188914675944656	3	FACETS	0.768	0.709	0.83	0.768	0.709	0.83	INDETERMINATE	2	TRUE	1	0.33029113015349	3		964	822	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289191	33289191	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1260091920	NA	P-0036382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	103	695	2	ENST00000374542.5:c.361G>A	p.Ala121Thr	p.A121T	ENST00000374542	NM_001141970.1	121	Gcc/Acc	3/8	0.194412407229552	5	FACETS	0.853	0.765	0.945	0.568	0.51	0.63	INDETERMINATE	2	TRUE	2	0.33029113015349	5		697	547	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	280	214	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.926007184178682	2		214	522	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199916	108199916	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	97	130	0	ENST00000278616.4:c.7258G>C	p.Ala2420Pro	p.A2420P	ENST00000278616	NM_000051.3	2420	Gcc/Ccc	49/63	1	2	FACETS	0.888	0.807	0.97	0.888	0.807	0.97	CLONAL	1	TRUE	1	0.926007184178682	2		130	236	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156720	20156720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	25	229	0	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		229	282	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412045	116412045	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0036387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	51	703	0	ENST00000397752.3:c.3028+2T>G		p.X1010_splice	ENST00000397752	NM_000245.2	1010			1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		703	802	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0036388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	123	490	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.916	1	1	0.99	1	CLONAL	2	TRUE	1	0.21	2		490	580	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578192	7578192	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	75	458	0	ENST00000269305.4:c.657del	p.Tyr220MetfsTer27	p.Y220Mfs*27	ENST00000269305	NM_001126112.2	219	ccC/cc	6/11	1	2	FACETS	0.965	0.845	1	0.965	0.845	1	CLONAL	1	TRUE	1	0.21	2		458	740	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100049	157100049	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1256773336	NA	P-0036388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	12	65	1	ENST00000346085.5:c.986C>G	p.Ala329Gly	p.A329G	ENST00000346085	NM_020732.3	329	gCa/gGa	1/20	1	2	FACETS	1	0.837	1	1	0.837	1	CLONAL	1	TRUE	1	0.21	2		66	88	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0036390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	8	214	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.108480488088548	3	FACETS	0.196	0.125	0.288	0.098	0.062	0.144	INDETERMINATE	1	FALSE	1	0.3	3		214	313	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106434	27106434	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	75	302	0	ENST00000324856.7:c.6046del	p.Leu2016CysfsTer14	p.L2016Cfs*14	ENST00000324856	NM_006015.4	2015	atC/at	20/20	1	2	FACETS	0.861	0.755	0.974	0.861	0.755	0.974	CLONAL	1	FALSE	1	0.3	2		302	581	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412898	49412898	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519954	NA	P-0036390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	129	489	0	ENST00000418115.1:c.125A>G	p.Tyr42Cys	p.Y42C	ENST00000418115	NM_001664.2	42	tAt/tGt	2/5	0.107621512042931	3	FACETS	1	0.969	1	0.386	0.349	0.424	INDETERMINATE	1	FALSE	0	0.3	3		489	855	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030485	49030485	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs483352690	NA	P-0036391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	53	237	0	ENST00000267163.4:c.1960G>A	p.Val654Met	p.V654M	ENST00000267163	NM_000321.2	654	Gtg/Atg	19/27	1	2	FACETS	0.672	0.576	0.775	0.672	0.576	0.775	SUBCLONAL	1	TRUE	1	0.508980074406612	2		237	310	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199342	16199342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	112	304	0	ENST00000375759.3:c.115C>T	p.Pro39Ser	p.P39S	ENST00000375759	NM_015001.2	39	Ccc/Tcc	2/15	1	2	FACETS	0.982	0.889	1	0.982	0.889	1	CLONAL	1	TRUE	1	0.508980074406612	2		304	448	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231689	66231689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	99	464	0	ENST00000273854.3:c.2011G>A	p.Glu671Lys	p.E671K	ENST00000273854	NM_004439.5	671	Gaa/Aaa	11/18	0.508980074406612	1	FACETS	0.887	0.8	0.977	0.887	0.8	0.977	CLONAL	1	TRUE	0	0.508980074406612	1		464	327	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575194	48575194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555685186	NA	P-0036391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	84	277	0	ENST00000342988.3:c.388C>T	p.Pro130Ser	p.P130S	ENST00000342988	NM_005359.5	130	Cca/Tca	3/12	0.343935320005846	1	FACETS	0.764	0.681	0.851	0.764	0.681	0.851	SUBCLONAL	1	TRUE	0	0.508980074406612	1		277	322	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561701	55561701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	95	264	1	ENST00000288135.5:c.91C>T	p.Pro31Ser	p.P31S	ENST00000288135	NM_000222.2	31	Cca/Tca	2/21	1	2	FACETS	0.822	0.736	0.913	0.822	0.736	0.913	CLONAL	1	TRUE	1	0.508980074406612	2		265	454	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033905	49033906	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0036391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	103	385	0	ENST00000267163.4:c.2042_2043delinsAA	p.Trp681Ter	p.W681*	ENST00000267163	NM_000321.2	681	tGG/tAA	20/27	1	2	FACETS	0.735	0.659	0.814	0.735	0.659	0.814	SUBCLONAL	1	TRUE	1	0.508980074406612	2		385	551	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641116	117641116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	189	522	0	ENST00000368508.3:c.5855G>A	p.Gly1952Glu	p.G1952E	ENST00000368508	NM_002944.2	1952	gGa/gAa	36/43	1	2	FACETS	0.951	0.881	1	0.951	0.881	1	CLONAL	1	TRUE	1	0.508980074406612	2		522	781	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28600012	28600013	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	222	571	0	ENST00000253063.3:c.894_895delinsTT	p.Pro299Ser	p.P299S	ENST00000253063	NM_031459.4	298	acCCcc/acTTcc	6/10	1	2	FACETS	0.996	0.928	1	0.996	0.928	1	CLONAL	1	TRUE	1	0.508980074406612	2		571	876	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206593	108206593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	80	241	0	ENST00000278616.4:c.8173G>A	p.Asp2725Asn	p.D2725N	ENST00000278616	NM_000051.3	2725	Gat/Aat	56/63	0.508980074406612	1	FACETS	0.843	0.751	0.939	0.843	0.751	0.939	CLONAL	1	TRUE	0	0.508980074406612	1		241	278	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434752	110434752	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1787	231	606	0	ENST00000375856.3:c.3649G>C	p.Gly1217Arg	p.G1217R	ENST00000375856	NM_003749.2	1217	Ggc/Cgc	1/2	0.508980074406612	6	FACETS	0.908	0.842	0.976			1	CLONAL	1	TRUE	NA	0.508980074406612	6		606	2018	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436006	110436006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2312	266	759	0	ENST00000375856.3:c.2395C>T	p.Pro799Ser	p.P799S	ENST00000375856	NM_003749.2	799	Ccc/Tcc	1/2	0.508980074406612	6	FACETS	0.818	0.763	0.876			1	CLONAL	1	TRUE	NA	0.508980074406612	6		759	2578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577126	7577145	+	frameshift_variant	Frame_Shift_Del	DEL	TCAAAGCTGTTCCGTCCCAG	TCAAAGCTGTTCCGTCCCAG	-	novel	NA	P-0036391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	219	548	0	ENST00000269305.4:c.793_812del	p.Leu265GlyfsTer34	p.L265Gfs*34	ENST00000269305	NM_001126112.2	265	CTGGGACGGAACAGCTTTGAg/g	8/11	0.508980074406612	1	FACETS	0.974	0.91	1	0.974	0.91	1	CLONAL	1	TRUE	0	0.508980074406612	1		548	659	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244377	41244377	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	216	695	1	ENST00000357654.3:c.3171T>A	p.Ser1057Arg	p.S1057R	ENST00000357654	NM_007294.3	1057	agT/agA	10/23	1	2	FACETS	0.957	0.891	1	0.957	0.891	1	CLONAL	1	TRUE	1	0.508980074406612	2		696	887	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184606	7184607	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	125	327	0	ENST00000302850.5:c.694_695delinsAA	p.Gly232Asn	p.G232N	ENST00000302850	NM_000208.2	232	GGc/AAc	3/22	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.508980074406612	2		327	484	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416599	29416599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	208	457	0	ENST00000389048.3:c.4354G>A	p.Ala1452Thr	p.A1452T	ENST00000389048	NM_004304.4	1452	Gct/Act	29/29	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.508980074406612	2		457	669	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193588	99193589	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	137	420	1	ENST00000074304.5:c.2783_2784delinsTT	p.Ala928Val	p.A928V	ENST00000074304	NM_001134224.1	928	gCC/gTT	25/26	1	2	FACETS	0.878	0.802	0.958	0.878	0.802	0.958	CLONAL	1	TRUE	1	0.508980074406612	2		421	613	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015264	128015264	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	203	431	0	ENST00000285398.2:c.2257G>A	p.Ala753Thr	p.A753T	ENST00000285398	NM_000122.1	753	Gcc/Acc	15/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.508980074406612	2		431	688	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713415	40713415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761334315	NA	P-0036391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	236	574	0	ENST00000373198.4:c.4100C>T	p.Pro1367Leu	p.P1367L	ENST00000373198	NM_133170.3	1367	cCc/cTc	30/32	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.508980074406612	2		574	880	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420079	41420080	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	115	275	1	ENST00000373198.4:c.241_242delinsAA	p.Gly81Lys	p.G81K	ENST00000373198	NM_133170.3	81	GGg/AAg	3/32	1	2	FACETS	0.964	0.873	1	0.964	0.873	1	CLONAL	1	TRUE	1	0.508980074406612	2		276	469	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134959990	134959990	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	162	396	0	ENST00000398015.3:c.2347G>A	p.Gly783Arg	p.G783R	ENST00000398015	NM_004441.4	783	Gga/Aga	13/16	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.508980074406612	2		396	592	SUCCESS
ATR	545	MSKCC	GRCh37	3	142177953	142177954	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0036391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	67	246	0	ENST00000350721.4:c.7350-1_7350delinsAA		p.X2450_splice	ENST00000350721	NM_001184.3	2450		44/47	1	2	FACETS	0.781	0.683	0.885	0.781	0.683	0.885	SUBCLONAL	1	TRUE	1	0.508980074406612	2		246	337	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952019	178952020	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	109	377	0	ENST00000263967.3:c.3074_3075delinsTT	p.Thr1025Ile	p.T1025I	ENST00000263967	NM_006218.2	1025	aCC/aTT	21/21	1	2	FACETS	0.867	0.782	0.956	0.867	0.782	0.956	CLONAL	1	TRUE	1	0.508980074406612	2		377	494	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630081	187630082	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0036391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	191	565	0	ENST00000441802.2:c.900_901delinsTT	p.Gln301Ter	p.Q301*	ENST00000441802	NM_005245.3	300	ctCCag/ctTTag	2/27	0.508980074406612	1	FACETS	0.914	0.85	0.98	0.914	0.85	0.98	CLONAL	1	TRUE	0	0.508980074406612	1		565	612	SUCCESS
APC	324	MSKCC	GRCh37	5	112103006	112103006	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	115	322	1	ENST00000257430.4:c.341C>A	p.Pro114His	p.P114H	ENST00000257430	NM_000038.5	114	cCt/cAt	4/16	1	2	FACETS	0.811	0.733	0.893	0.811	0.733	0.893	CLONAL	1	TRUE	1	0.508980074406612	2		323	557	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149452946	149452946	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	204	489	0	ENST00000286301.3:c.1000T>C	p.Phe334Leu	p.F334L	ENST00000286301	NM_005211.3	334	Ttt/Ctt	7/22	1	2	FACETS	0.986	0.916	1	0.986	0.916	1	CLONAL	1	TRUE	1	0.508980074406612	2		489	813	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224330	55224331	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCCT	novel	NA	P-0036391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	37	354	0	ENST00000275493.2:c.1112_1115dup	p.Val374AlafsTer5	p.V374Afs*5	ENST00000275493	NM_005228.3	371	atc/aTCCTtc	9/28	1	2	FACETS	0.262	0.215	0.314	0.262	0.215	0.314	SUBCLONAL	1	TRUE	1	0.508980074406612	2		354	555	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151947003	151947003	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	93	360	0	ENST00000262189.6:c.1771C>T	p.His591Tyr	p.H591Y	ENST00000262189	NM_170606.2	591	Cat/Tat	13/59	1	2	FACETS	0.86	0.769	0.955	0.86	0.769	0.955	CLONAL	1	TRUE	1	0.508980074406612	2		360	425	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285515	38285515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	290	643	0	ENST00000425967.3:c.638G>A	p.Gly213Glu	p.G213E	ENST00000425967	NM_001174067.1	213	gGg/gAg	6/19	0.508980074406612	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.508980074406612	1		643	836	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900183	101900183	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	120	284	0	ENST00000374994.4:c.617T>A	p.Val206Glu	p.V206E	ENST00000374994	NM_004612.2	206	gTg/gAg	4/9	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.508980074406612	2		284	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0036392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	243	631	4	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.514787089395006	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.514787089395006	1		635	631	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0036392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	102	367	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.514787089395006	1	FACETS	0.843	0.762	0.928	0.843	0.762	0.928	CLONAL	1	TRUE	0	0.514787089395006	1		367	349	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0036392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	45	303	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.166226843914283	2	FACETS	0.486	0.409	0.57	0.243	0.204	0.285	INDETERMINATE	1	TRUE	0	0.514787089395006	2		303	360	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17359612	17359612	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1553178046	NA	P-0036392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	153	392	0	ENST00000375499.3:c.229A>G	p.Ile77Val	p.I77V	ENST00000375499	NM_003000.2	77	Atc/Gtc	3/8	NA	2	FACETS	1	0.961	1			1	INDETERMINATE	1	TRUE	NA	0.514787089395006	2		392	554	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30103665	30103665	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	46	604	0	ENST00000331968.5:c.1273A>G	p.Lys425Glu	p.K425E	ENST00000331968	NM_002742.2	425	Aaa/Gaa	8/18	1	2	FACETS	0.229	0.192	0.27	0.229	0.192	0.27	SUBCLONAL	1	TRUE	1	0.514787089395006	2		604	780	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107749	30107749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760459161	NA	P-0036392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	37	529	0	ENST00000331968.5:c.931C>T	p.Arg311Cys	p.R311C	ENST00000331968	NM_002742.2	311	Cgt/Tgt	6/18	1	2	FACETS	0.209	0.171	0.251	0.209	0.171	0.251	SUBCLONAL	1	TRUE	1	0.514787089395006	2		529	688	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813954	50813954	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	55	408	2	ENST00000398568.2:c.1508T>C	p.Leu503Pro	p.L503P	ENST00000398568	NM_001042412.1	503	cTg/cCg	8/18	0.298907916721825	1	FACETS	0.372	0.319	0.43	0.372	0.319	0.43	INDETERMINATE	1	TRUE	0	0.514787089395006	1		410	426	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822340	72822340	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs754562944	NA	P-0036392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	120	855	0	ENST00000268489.5:c.9835A>G	p.Met3279Val	p.M3279V	ENST00000268489	NM_006885.3	3279	Atg/Gtg	10/10	0.298907916721825	1	FACETS	0.416	0.375	0.459	0.416	0.375	0.459	INDETERMINATE	1	TRUE	0	0.514787089395006	1		855	833	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118398	17118398	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745720578	NA	P-0036392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	221	698	0	ENST00000285071.4:c.1439C>T	p.Pro480Leu	p.P480L	ENST00000285071	NM_144997.5	480	cCc/cTc	13/14	0.514787089395006	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.514787089395006	1		698	606	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436143	56436143	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	188	515	0	ENST00000407977.2:c.994del	p.Tyr332ThrfsTer87	p.Y332Tfs*87	ENST00000407977		332	Tac/ac	9/10	0.514787089395006	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.514787089395006	1		515	484	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478739	57478739	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	121	346	0	ENST00000371085.3:c.325G>T	p.Ala109Ser	p.A109S	ENST00000371085	NM_000516.4	109	Gcc/Tcc	5/13	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.514787089395006	2		346	430	SUCCESS
AR	367	MSKCC	GRCh37	X	66766405	66766405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	10	113	0	ENST00000374690.3:c.1417G>A	p.Gly473Ser	p.G473S	ENST00000374690	NM_000044.3	473	Ggc/Agc	1/8	0.298907916721825	1	FACETS	0.294	0.201	0.409	0.294	0.201	0.409	INDETERMINATE	1	TRUE	0	0.514787089395006	1		113	98	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0036394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	9	269	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.118	0.078	0.17	0.118	0.078	0.17	SUBCLONAL	1	TRUE	1	0.659390135216588	2		269	231	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0036394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	72	405	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.812	0.717	0.911	0.812	0.717	0.911	CLONAL	1	TRUE	1	0.659390135216588	2		405	269	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417050	417050	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199716528	NA	P-0036394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	112	299	1	ENST00000399788.2:c.3500G>A	p.Arg1167His	p.R1167H	ENST00000399788	NM_001042603.1	1167	cGc/cAc	23/28	0.0753014757987727	4	FACETS	1	0.982	1	0.698	0.633	0.765	INDETERMINATE	1	TRUE	2	0.659390135216588	4		300	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0036394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	58	457	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.477036788623055	0	FACETS	0.294	0.256	0.334			1	SUBCLONAL	1	TRUE	0	0.659390135216588	0		457	204	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867305	68867306	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	96	356	0	ENST00000261769.5:c.2553dup	p.Glu852ArgfsTer9	p.E852Rfs*9	ENST00000261769	NM_004360.3	851	tca/tcAa	16/16	0.659390135216588	1	FACETS	0.784	0.71	0.859	0.784	0.71	0.859	SUBCLONAL	1	TRUE	0	0.659390135216588	1		356	249	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922365	178922365	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	74	243	0	ENST00000263967.3:c.1134T>G	p.Cys378Trp	p.C378W	ENST00000263967	NM_006218.2	378	tgT/tgG	6/21	1	2	FACETS	0.79	0.699	0.886	0.79	0.699	0.886	SUBCLONAL	1	TRUE	1	0.659390135216588	2		243	284	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119479	193119480	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0036394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	81	248	0	ENST00000367435.3:c.875_876del	p.Arg292IlefsTer18	p.R292Ifs*18	ENST00000367435	NM_024529.4	292	AGa/a	9/17	1	2	FACETS	0.963	0.861	1	0.963	0.861	1	CLONAL	1	TRUE	1	0.659390135216588	2		248	255	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42053963	42053964	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0036394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	71	184	0	ENST00000219905.7:c.7426_7427del	p.Asp2476SerfsTer29	p.D2476Sfs*29	ENST00000219905	NM_001164273.1	2475	acAGat/acat	21/24	1	2	FACETS	0.825	0.729	0.926	0.825	0.729	0.926	CLONAL	1	TRUE	1	0.659390135216588	2		184	261	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029477	16029478	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0036394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	88	361	0	ENST00000268712.3:c.1552_1553del	p.Glu518ArgfsTer3	p.E518Rfs*3	ENST00000268712	NM_006311.3	518	GAa/a	15/46	0.477036788623055	0	FACETS	0.333	0.299	0.369			1	SUBCLONAL	1	TRUE	0	0.659390135216588	0		361	273	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602635	10602635	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	123	586	0	ENST00000171111.5:c.943C>T	p.Gln315Ter	p.Q315*	ENST00000171111	NM_203500.1	315	Cag/Tag	3/6	0.659390135216588	1	FACETS	0.89	0.819	0.962	0.89	0.819	0.962	CLONAL	1	TRUE	0	0.659390135216588	1		586	281	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881350	111881351	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0036394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	94	291	0	ENST00000393256.3:c.29_30del	p.Ser10Ter	p.S10*	ENST00000393256	NM_006538.4	10	TCt/t	2/4	1	2	FACETS	0.935	0.842	1	0.935	0.842	1	CLONAL	1	TRUE	1	0.659390135216588	2		291	305	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519496	176519496	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	65	657	0	ENST00000292408.4:c.902A>T	p.Tyr301Phe	p.Y301F	ENST00000292408	NM_213647.1	301	tAt/tTt	7/18	1	2	FACETS	0.456	0.397	0.521	0.456	0.397	0.521	SUBCLONAL	1	TRUE	1	0.659390135216588	2		657	432	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202431	123202434	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	novel	NA	P-0036394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	85	308	0	ENST00000218089.9:c.2286_2289del	p.Lys762AsnfsTer3	p.K762Nfs*3	ENST00000218089	NM_001042749.1	761	ttAAAG/tt	24/35	0.38690081886631	1	FACETS	0.549	0.49	0.61	0.549	0.49	0.61	INDETERMINATE	1	TRUE	0	0.659390135216588	1		308	315	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242480	55242503	+	inframe_deletion	In_Frame_Del	DEL	AACATCTCCGAAAGCCAACAAGGA	AACATCTCCGAAAGCCAACAAGGA	-	novel	NA	P-0036397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	13	316	0	ENST00000275493.2:c.2252_2275del	p.Thr751_Glu758del	p.T751_E758del	ENST00000275493	NM_005228.3	750	gcAACATCTCCGAAAGCCAACAAGGAa/gca	19/28	1	2	FACETS	0.267	0.19	0.362	0.267	0.19	0.362	SUBCLONAL	1	FALSE	1	0.3	2		316	324	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	32	214	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		214	390	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675221	40675221	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	57	489	0	ENST00000249776.8:c.185G>T	p.Cys62Phe	p.C62F	ENST00000249776	NM_033286.3	62	tGc/tTc	1/9	1	2	FACETS	0.519	0.445	0.6	0.519	0.445	0.6	SUBCLONAL	1	NA	1	0.392658739568266	2		489	559	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0036401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	503	437	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.264662756088558	9	FACETS	0.962	0.927	0.998			1	CLONAL	8	TRUE	NA	0.264662756088558	9		437	951	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0036401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	231	833	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.231545116916367	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.264662756088558	2		833	797	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841505	156841505	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs145222195	NA	P-0036401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	82	709	0	ENST00000524377.1:c.808G>T	p.Asp270Tyr	p.D270Y	ENST00000524377	NM_002529.3	270	Gat/Tat	7/17	0.264662756088558	6	FACETS	0.813	0.714	0.919	0.203	0.178	0.23	CLONAL	1	TRUE	2	0.264662756088558	6		709	1166	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863677	68863677	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	114	392	0	ENST00000261769.5:c.2416G>T	p.Glu806Ter	p.E806*	ENST00000261769	NM_004360.3	806	Gaa/Taa	15/16	0.264662756088558	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	0	0.264662756088558	2		392	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0036402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	101	678	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.18	2		678	817	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876936	151876936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	39	299	0	ENST00000262189.6:c.7425G>A	p.Met2475Ile	p.M2475I	ENST00000262189	NM_170606.2	2475	atG/atA	37/59	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.18	2		299	403	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28599030	28599030	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	54	652	0	ENST00000241453.7:c.2258C>A	p.Ser753Ter	p.S753*	ENST00000241453	NM_004119.2	753	tCa/tAa	18/24	1	2	FACETS	0.66	0.562	0.768	0.66	0.562	0.768	SUBCLONAL	1	TRUE	1	0.18	2		652	909	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828122	72828122	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1304635065	NA	P-0036402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	80	799	1	ENST00000268489.5:c.8459C>T	p.Ser2820Leu	p.S2820L	ENST00000268489	NM_006885.3	2820	tCa/tTa	9/10	1	2	FACETS	0.778	0.683	0.882	0.778	0.683	0.882	SUBCLONAL	1	TRUE	1	0.18	2		800	1142	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0036405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	647	354	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.725981707429169	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.728512049068158	2		354	812	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0036405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	750	720	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.722785651852993	2	FACETS	0.98	0.957	1	0.98	0.957	1	CLONAL	2	TRUE	0	0.728512049068158	2		720	1050	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0036405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	205	346	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.728512049068158	2		346	547	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717661	89717661	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	226	620	0	ENST00000371953.3:c.686C>A	p.Ser229Ter	p.S229*	ENST00000371953	NM_000314.4	229	tCa/tAa	7/9	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.728512049068158	2		620	583	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056163	27056163	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	199	455	0	ENST00000324856.7:c.1159A>C	p.Met387Leu	p.M387L	ENST00000324856	NM_006015.4	387	Atg/Ctg	2/20	0.709963923931089	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.728512049068158	1		455	335	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056177	27056199	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTCAGCCATATGGCGGGACTA	ACCTCAGCCATATGGCGGGACTA	-	novel	NA	P-0036405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	217	485	0	ENST00000324856.7:c.1176_1198del	p.Gln393IlefsTer222	p.Q393Ifs*222	ENST00000324856	NM_006015.4	391	agACCTCAGCCATATGGCGGGACTAac/agac	2/20	0.709963923931089	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.728512049068158	1		485	377	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663736	241663736	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0036405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	251	785	0	ENST00000366560.3:c.1390+1G>A		p.X464_splice	ENST00000366560	NM_000143.3	464			1	2	FACETS	0.876	0.822	0.93	0.876	0.822	0.93	CLONAL	1	TRUE	1	0.728512049068158	2		785	787	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717682	89717683	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0036405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	201	591	1	ENST00000371953.3:c.708_709del	p.Asp236GlufsTer6	p.D236Efs*6	ENST00000371953	NM_000314.4	236	gAC/g	7/9	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.728512049068158	2		592	547	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590369	67590394	+	frameshift_variant	Frame_Shift_Del	DEL	CCAAATGAAAAGGACAGCTATTGAAG	CCAAATGAAAAGGACAGCTATTGAAG	-	novel	NA	P-0036405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	38	99	0	ENST00000274335.5:c.1432_1457del	p.Gln478IlefsTer2	p.Q478Ifs*2	ENST00000274335		477	atCCAAATGAAAAGGACAGCTATTGAAGca/atca	11/15	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.728512049068158	2		99	102	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591117	67591118	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0036405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	107	277	0	ENST00000274335.5:c.1710_1711insG	p.Ile571AspfsTer31	p.I571Dfs*31	ENST00000274335		570	-/G	12/15	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.728512049068158	2		277	248	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0036406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	117	303	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		303	440	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs760043106	NA	P-0036407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	385	605	0	ENST00000269305.4:c.584T>A	p.Ile195Asn	p.I195N	ENST00000269305	NM_001126112.2	195	aTc/aAc	6/11	0.57498900757835	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.57498900757835	2		605	632	SUCCESS
APC	324	MSKCC	GRCh37	5	112175536	112175536	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	82	327	0	ENST00000257430.4:c.4245del	p.Ser1415ArgfsTer4	p.S1415Rfs*4	ENST00000257430	NM_000038.5	1415	agT/ag	16/16	0.328146853811263	1	FACETS	0.728	0.65	0.81	0.728	0.65	0.81	INDETERMINATE	1	TRUE	0	0.57498900757835	1		327	279	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857020	9857020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555481892	NA	P-0036407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	41	249	0	ENST00000330684.3:c.4381G>A	p.Glu1461Lys	p.E1461K	ENST00000330684	NM_001134407.1	1461	Gaa/Aaa	13/13	0.250023868062312	3	FACETS	0.862	0.725	1	0.431	0.362	0.506	INDETERMINATE	1	TRUE	1	0.57498900757835	3		249	213	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs199469669	NA	P-0036407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	469	249	0	ENST00000374080.3:c.130G>C	p.Gly44Arg	p.G44R	ENST00000374080		44	Ggt/Cgt	2/45	0.567169895101181	2	FACETS	0.869	0.844	0.892			1	CLONAL	3	TRUE	NA	0.57498900757835	2		249	626	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039344	47039344	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	705	352	0	ENST00000377604.3:c.967T>G	p.Tyr323Asp	p.Y323D	ENST00000377604	NM_001204468.1	323	Tac/Gac	10/24	0.57498900757835	4	FACETS	0.979	0.955	1			1	CLONAL	4	TRUE	NA	0.57498900757835	4		352	986	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564575	55564575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777031731	NA	P-0036407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	186	521	1	ENST00000288135.5:c.463C>T	p.Pro155Ser	p.P155S	ENST00000288135	NM_000222.2	155	Cct/Tct	3/21	0.250023868062312	3	FACETS	0.861	0.795	0.93	0.431	0.397	0.465	INDETERMINATE	1	TRUE	1	0.57498900757835	3		522	967	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0036408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	76	331	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.852	0.753	0.957	0.852	0.753	0.957	CLONAL	1	TRUE	1	0.518335809636268	2		331	344	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512309	38512309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	223	652	0	ENST00000254066.5:c.1220C>T	p.Pro407Leu	p.P407L	ENST00000254066	NM_000964.3	407	cCg/cTg	9/9	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.518335809636268	2		652	858	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0036408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	169	643	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	1	2	FACETS	0.855	0.787	0.925	0.855	0.787	0.925	CLONAL	1	TRUE	1	0.518335809636268	2		643	763	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045136	47045136	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	191	283	1	ENST00000377604.3:c.2377C>T	p.Arg793Ter	p.R793*	ENST00000377604	NM_001204468.1	793	Cga/Tga	21/24	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.518335809636268	1		284	389	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100863	27100863	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	102	455	0	ENST00000324856.7:c.4145A>T	p.Lys1382Met	p.K1382M	ENST00000324856	NM_006015.4	1382	aAg/aTg	18/20	1	2	FACETS	0.574	0.513	0.638	0.574	0.513	0.638	SUBCLONAL	1	TRUE	1	0.518335809636268	2		455	686	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105940	27105941	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	172	470	0	ENST00000324856.7:c.5551_5552insT	p.Thr1851IlefsTer3	p.T1851Ifs*3	ENST00000324856	NM_006015.4	1851	acc/aTcc	20/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.518335809636268	2		470	604	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244344	46244344	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	111	428	0	ENST00000334344.6:c.2438C>G	p.Ser813Cys	p.S813C	ENST00000334344	NM_152641.2	813	tCt/tGt	15/21	1	2	FACETS	0.837	0.755	0.922	0.837	0.755	0.922	CLONAL	1	TRUE	1	0.518335809636268	2		428	512	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246315	46246315	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0036408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	127	394	0	ENST00000334344.6:c.4409C>G	p.Ser1470Ter	p.S1470*	ENST00000334344	NM_152641.2	1470	tCa/tGa	15/21	1	2	FACETS	0.984	0.897	1	0.984	0.897	1	CLONAL	1	TRUE	1	0.518335809636268	2		394	498	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942177	81942177	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	138	422	1	ENST00000359376.3:c.1714G>A	p.Asp572Asn	p.D572N	ENST00000359376	NM_002661.3	572	Gac/Aac	17/33	1	2	FACETS	0.995	0.911	1	0.995	0.911	1	CLONAL	1	TRUE	1	0.518335809636268	2		423	535	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66525091	66525091	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1264572252	NA	P-0036408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	94	376	0	ENST00000358598.2:c.850G>T	p.Val284Leu	p.V284L	ENST00000358598	NM_212471.2	284	Gtg/Ttg	9/11	1	2	FACETS	0.617	0.55	0.688	0.617	0.55	0.688	SUBCLONAL	1	TRUE	1	0.518335809636268	2		376	588	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627485	14627485	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	217	514	0	ENST00000254322.2:c.585G>C	p.Lys195Asn	p.K195N	ENST00000254322	NM_006145.1	195	aaG/aaC	2/3	1	2	FACETS	0.987	0.92	1	0.987	0.92	1	CLONAL	1	TRUE	1	0.518335809636268	2		514	848	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24158955	24158955	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0036408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	205	582	0	ENST00000263121.7:c.629-2A>T		p.X210_splice	ENST00000263121	NM_003073.3	210			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.518335809636268	2		582	728	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092938	29092938	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	156	515	0	ENST00000328354.6:c.1046A>T	p.Lys349Met	p.K349M	ENST00000328354	NM_007194.3	349	aAg/aTg	10/15	1	2	FACETS	0.896	0.823	0.972	0.896	0.823	0.972	CLONAL	1	TRUE	1	0.518335809636268	2		515	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519999	NA	P-0036409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	245	551	0	ENST00000269305.4:c.716A>G	p.Asn239Ser	p.N239S	ENST00000269305	NM_001126112.2	239	aAc/aGc	7/11	0.670459776354451	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.670459776354451	1		551	438	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198971	67198971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1279953170	NA	P-0036409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	70	371	0	ENST00000312629.5:c.442C>G	p.Leu148Val	p.L148V	ENST00000312629	NM_003952.2	148	Ctt/Gtt	5/15	1	2	FACETS	0.462	0.404	0.524	0.462	0.404	0.524	SUBCLONAL	1	TRUE	1	0.670459776354451	2		371	452	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489573	40489573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	267	475	0	ENST00000264657.5:c.677C>T	p.Ser226Leu	p.S226L	ENST00000264657	NM_139276.2	226	tCa/tTa	8/24	0.670459776354451	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.670459776354451	1		475	470	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021714	71021714	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	124	387	0	ENST00000318789.4:c.1644G>C	p.Lys548Asn	p.K548N	ENST00000318789	NM_032682.5	548	aaG/aaC	18/21	0.113610969618478	3	FACETS	0.939	0.854	1	0.469	0.427	0.514	INDETERMINATE	1	TRUE	1	0.670459776354451	3		387	526	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104356952	104356994	+	frameshift_variant	Frame_Shift_Del	DEL	CCAAGTGTGCCTGGGATGACCTGAGCCGGCCCCCCGAGGATGA	CCAAGTGTGCCTGGGATGACCTGAGCCGGCCCCCCGAGGATGA	-	novel	NA	P-0036411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	177	520	0	ENST00000369902.3:c.813_855del	p.Lys272ArgfsTer27	p.K272Rfs*27	ENST00000369902	NM_016169.3	271	gCCAAGTGTGCCTGGGATGACCTGAGCCGGCCCCCCGAGGATGAc/gc	7/12	0.617277840346913	1	FACETS	0.949	0.885	1	0.949	0.885	1	CLONAL	1	TRUE	0	0.617277840346913	1		520	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0036412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	149	584	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.176421971682159	3	FACETS	0.879	0.806	0.954	0.879	0.806	0.954	CLONAL	3	TRUE	0	0.204611886921714	3		584	609	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143044529	143044530	+	missense_variant	Missense_Mutation	DNP	TC	TC	AG	novel	NA	P-0036412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	20	358	1	ENST00000262992.4:c.1932_1933delinsCT	p.Gln644_Thr645delinsHisSer	p.Q644_T645delinsHS	ENST00000262992	NM_001101669.1	644	caGAca/caCTca	18/24	0.169562080987327	3	FACETS	1	0.868	1	0.602	0.463	0.762	CLONAL	1	TRUE	1	0.204611886921714	3		359	179	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0036422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	266	571	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.221266118374793	1	FACETS	0.889	0.833	0.948	1	0.994	1	CLONAL	2	TRUE	0	0.221266118374793	1		572	1202	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0036422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	68	286	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.221266118374793	2		286	509	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0036422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	236	616	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.215774683317199	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.221266118374793	4		616	1155	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952138	178952138	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	14	316	0	ENST00000263967.3:c.3193C>T	p.His1065Tyr	p.H1065Y	ENST00000263967	NM_006218.2	1065	Cat/Tat	21/21	1	2	FACETS	0.822	0.597	1	0.822	0.597	1	CLONAL	1	TRUE	1	0.221266118374793	2		316	154	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938932	178938932	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	49	413	0	ENST00000263967.3:c.2174A>G	p.Asp725Gly	p.D725G	ENST00000263967	NM_006218.2	725	gAt/gGt	14/21	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.221266118374793	2		413	411	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0036425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	106	405	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.261251363808992	2	FACETS	0.987	0.892	1	0.987	0.892	1	CLONAL	2	TRUE	0	0.261251363808992	2		405	411	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0036425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	66	407	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.261251363808992	2		408	395	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0036425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	80	391	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.261251363808992	2	FACETS	0.812	0.72	0.91	0.812	0.72	0.91	CLONAL	2	TRUE	0	0.261251363808992	2		391	377	SUCCESS
APC	324	MSKCC	GRCh37	5	112176024	112176024	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	47	350	0	ENST00000257430.4:c.4733del	p.Cys1578LeufsTer72	p.C1578Lfs*72	ENST00000257430	NM_000038.5	1578	tGt/tt	16/16	1	2	FACETS	0.994	0.842	1	0.994	0.842	1	CLONAL	1	TRUE	1	0.261251363808992	2		350	362	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716041	243716041	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	67	640	0	ENST00000263826.5:c.1153C>T	p.Pro385Ser	p.P385S	ENST00000263826	NM_005465.4	385	Cca/Tca	10/13	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.261251363808992	2		640	468	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99154412	99154412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750703654	NA	P-0036425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	75	572	2	ENST00000074304.5:c.554G>A	p.Arg185Gln	p.R185Q	ENST00000074304	NM_001134224.1	185	cGg/cAg	8/26	1	2	FACETS	0.962	0.843	1	0.962	0.843	1	CLONAL	1	TRUE	1	0.261251363808992	2		574	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0036426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	320	588	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.384796565039775	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.384796565039775	2		588	779	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	120	329	0	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	0.384796565039775	2	FACETS	0.948	0.867	1	0.948	0.867	1	CLONAL	2	TRUE	0	0.384796565039775	2		329	329	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402723	20402723	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	68	403	0	ENST00000346618.3:c.260G>A	p.Ser87Asn	p.S87N	ENST00000346618	NM_001949.4	87	aGt/aAt	1/7	0.384796565039775	3	FACETS	0.853	0.744	0.971	0.427	0.372	0.486	CLONAL	1	TRUE	1	0.384796565039775	3		403	494	SUCCESS
AR	367	MSKCC	GRCh37	X	66943570	66943570	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs137852568	NA	P-0036426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	190	290	0	ENST00000374690.3:c.2650A>T	p.Lys884Ter	p.K884*	ENST00000374690	NM_000044.3	884	Aag/Tag	8/8	0.384796565039775	2	FACETS	0.895	0.841	0.948			1	CLONAL	3	TRUE	NA	0.384796565039775	2		290	368	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	172	214	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.487782120592446	2		214	577	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0036428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	41	764	0	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	0.487782120592446	1	FACETS	0.157	0.13	0.187	0.157	0.13	0.187	SUBCLONAL	1	TRUE	0	0.487782120592446	1		764	811	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577543	7577543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1019340046	NA	P-0036428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	166	785	0	ENST00000269305.4:c.738G>A	p.Met246Ile	p.M246I	ENST00000269305	NM_001126112.2	246	atG/atA	7/11	0.359727564199689	0	FACETS	0.499	0.46	0.541			1	SUBCLONAL	1	TRUE	0	0.487782120592446	0		785	698	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762839	40762839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1407888862	NA	P-0036428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	123	514	0	ENST00000392038.2:c.169G>A	p.Val57Ile	p.V57I	ENST00000392038	NM_001626.4	57	Gta/Ata	3/14	1	2	FACETS	0.741	0.671	0.814	0.741	0.671	0.814	SUBCLONAL	1	TRUE	1	0.487782120592446	2		514	681	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665026	138665026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	26	149	0	ENST00000330315.3:c.539G>A	p.Gly180Asp	p.G180D	ENST00000330315	NM_023067.3	180	gGc/gAc	1/1	1	2	FACETS	0.482	0.384	0.594	0.482	0.384	0.594	SUBCLONAL	1	TRUE	1	0.487782120592446	2		149	221	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098949	47098949	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	190	736	0	ENST00000409792.3:c.6325C>T	p.Arg2109Ter	p.R2109*	ENST00000409792	NM_014159.6	2109	Cga/Tga	15/21	1	2	FACETS	0.893	0.834	0.953	0.893	0.834	0.953	CLONAL	1	TRUE	1	0.903253865272855	2		736	471	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562259	21562259	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148138215	NA	P-0036430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	45	1038	4	ENST00000382592.4:c.1660G>A	p.Gly554Ser	p.G554S	ENST00000382592	NM_014572.2	554	Ggc/Agc	4/8	0.195173784831534	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		1042	726	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482342	56482342	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519892	NA	P-0036430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	13	780	1	ENST00000267101.3:c.890A>T	p.Asp297Val	p.D297V	ENST00000267101	NM_001982.3	297	gAt/gTt	8/28	0.424283006259382	4	FACETS		NA	1			1	NA	NA	FALSE	2	NA	4		781	487	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	218473	218473	+	start_lost	Translation_Start_Site	SNP	G	G	T	novel	NA	P-0036430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	16	235	0	ENST00000264932.6:c.3G>T	p.Met1?	p.M1?	ENST00000264932	NM_004168.2	1	atG/atT	1/15	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	NA	NA		235	210	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0036432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	55	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.714	0.611	0.827	0.714	0.611	0.827	SUBCLONAL	1	TRUE	1	0.289613143451196	2		452	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0036432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	103	631	4	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.844	0.754	0.939	0.844	0.754	0.939	CLONAL	1	TRUE	1	0.289613143451196	2		635	843	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0036432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	20	624	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.173	0.131	0.222	0.173	0.131	0.222	SUBCLONAL	1	TRUE	1	0.289613143451196	2		624	799	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087360	27087360	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	67	545	0	ENST00000324856.7:c.1934C>A	p.Ser645Ter	p.S645*	ENST00000324856	NM_006015.4	645	tCa/tAa	5/20	1	2	FACETS	0.697	0.605	0.796	0.697	0.605	0.796	SUBCLONAL	1	TRUE	1	0.289613143451196	2		545	664	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0036433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	40	239	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.707	0.589	0.839	0.707	0.589	0.839	SUBCLONAL	1	TRUE	1	0.29	2		239	390	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0036433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	58	444	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.993	0.856	1	0.993	0.856	1	CLONAL	1	TRUE	1	0.29	2		444	403	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063717	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0036433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	16	156	0	ENST00000412916.2:c.165+1G>T		p.X55_splice	ENST00000412916		55			0.3	1	FACETS	0.46	0.341	0.602	0.46	0.341	0.602	SUBCLONAL	1	TRUE	0	0.29	1		156	205	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896399	151896400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	67	598	0	ENST00000262189.6:c.4237dup	p.Ser1413LysfsTer16	p.S1413Kfs*16	ENST00000262189	NM_170606.2	1413	agt/aAgt	27/59	1	2	FACETS	0.692	0.601	0.79	0.692	0.601	0.79	SUBCLONAL	1	TRUE	1	0.29	2		598	668	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156729	20156729	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs757280897	NA	P-0036434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	300	509	0	ENST00000379607.5:c.28A>G	p.Lys10Glu	p.K10E	ENST00000379607	NM_001412.3	10	Aaa/Gaa	2/7	1	2	FACETS	0.958	0.908	1	0.958	0.908	1	CLONAL	1	TRUE	1	0.86	2		509	728	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0036436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	48	732	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.175258323510484	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.175258323510484	1		732	423	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033245	69033245	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530869739	NA	P-0036437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	17	541	0	ENST00000288368.4:c.3685G>A	p.Val1229Ile	p.V1229I	ENST00000288368	NM_024870.2	1229	Gtc/Atc	30/40	1	2	FACETS	0.611	0.457	0.791	0.611	0.457	0.791	SUBCLONAL	1	TRUE	1	0.289999728756628	2		541	192	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0036439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	93	673	1	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.16	2		674	841	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711874	89711874	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs786204862	NA	P-0036439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	39	457	0	ENST00000371953.3:c.493-1G>A		p.X165_splice	ENST00000371953	NM_000314.4	165			1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.16	2		457	433	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428265	47428265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	29	357	0	ENST00000377045.4:c.1225G>A	p.Val409Met	p.V409M	ENST00000377045	NM_001654.4	409	Gtg/Atg	11/16	1	1	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	0	0.16	1		357	296	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609967	43609967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	95	870	0	ENST00000355710.3:c.1919C>T	p.Ala640Val	p.A640V	ENST00000355710	NM_020975.4	640	gCc/gTc	11/20	0.207316756765837	2	FACETS	1	0.978	1	0.709	0.63	0.792	CLONAL	1	TRUE	0	0.16	2		870	838	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894991	101894991	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	43	344	0	ENST00000374994.4:c.544T>A	p.Tyr182Asn	p.Y182N	ENST00000374994	NM_004612.2	182	Tat/Aat	3/9	1	2	FACETS	0.766	0.643	0.901	1	0.959	1	CLONAL	2	TRUE	1	0.16	2		344	351	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	40	214	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		214	85	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	30	214	0				ENST00000310581	NM_198253.2	-/1132			0.40716151717007	0	FACETS	0.91	0.753	1			1	CLONAL	1	FALSE	0	0.40716151717007	0		214	96	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0036442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	173	670	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.156158979877986	4	FACETS	0.93	0.859	1	0.93	0.859	1	INDETERMINATE	2	FALSE	2	0.40716151717007	4		670	643	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500574	149500574	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0036442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	99	517	0	ENST00000261799.4:c.2464-1G>A		p.X822_splice	ENST00000261799	NM_002609.3	822			0.387850236963247	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	0	0.40716151717007	1		517	349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578476	7578476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767328513	NA	P-0036444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	285	732	0	ENST00000269305.4:c.454C>T	p.Pro152Ser	p.P152S	ENST00000269305	NM_001126112.2	152	Ccg/Tcg	5/11	0.544645122128565	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.564365662355705	1		732	655	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961013	55961013	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	236	602	0	ENST00000263923.4:c.2927G>T	p.Gly976Val	p.G976V	ENST00000263923	NM_002253.2	976	gGa/gTa	21/30	0.560518698149766	2	FACETS	1	0.993	1	0.715	0.672	0.758	CLONAL	1	TRUE	0	0.564365662355705	2		602	585	SUCCESS
APC	324	MSKCC	GRCh37	5	112175486	112175487	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0036444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	158	475	0	ENST00000257430.4:c.4196dup	p.Ser1400PhefsTer9	p.S1400Ffs*9	ENST00000257430	NM_000038.5	1399	cgt/cGgt	16/16	0.549403399985306	2	FACETS	0.962	0.9	1	0.962	0.9	1	CLONAL	2	TRUE	0	0.564365662355705	2		475	291	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	263	690	0	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.312421931927524	2	FACETS	0.995	0.935	1	0.995	0.935	1	CLONAL	2	TRUE	0	0.312421931927524	2		690	846	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0036445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	256	390	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	0.312421931927524	6	FACETS	1	0.978	1	0.856	0.808	0.905	CLONAL	4	TRUE	1	0.312421931927524	6		390	622	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573150	64573150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	75	442	0	ENST00000312049.6:c.1142G>A	p.Ser381Asn	p.S381N	ENST00000312049	NM_130799.2	381	aGc/aAc	8/10	0.312421931927524	5	FACETS	0.855	0.748	0.97	0.285	0.249	0.324	CLONAL	1	TRUE	2	0.312421931927524	5		442	825	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22123507	22123507	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	139	434	2	ENST00000215832.6:c.1069G>A	p.Gly357Arg	p.G357R	ENST00000215832	NM_002745.4	357	Gga/Aga	8/9	0.312421931927524	8	FACETS	1	0.944	1			1	CLONAL	2	TRUE	NA	0.312421931927524	8		436	822	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807569	1807569	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761196249	NA	P-0036445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	122	607	1	ENST00000260795.2:c.1738G>A	p.Asp580Asn	p.D580N	ENST00000260795		580	Gac/Aac	12/17	0.216208333501188	4	FACETS	1	0.952	1	0.363	0.327	0.4	CLONAL	1	TRUE	1	0.312421931927524	4		608	942	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912175	29912175	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs41547331	NA	P-0036445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	57	208	0	ENST00000376809.5:c.895+1G>T		p.X299_splice	ENST00000376809	NM_002116.7	299			0.30339334202763	4	FACETS	0.9	0.78	1	0.9	0.78	1	CLONAL	2	TRUE	2	0.312421931927524	4		208	266	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104025	69104025	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0036445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	142	303	0	ENST00000288368.4:c.4413+2T>C		p.X1471_splice	ENST00000288368	NM_024870.2	1471			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		303	776	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0036449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	336	528	1	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.854351703447708	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.854351703447708	1		529	430	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954315	48954317	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	rs587776788	NA	P-0036449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	169	246	0	ENST00000267163.4:c.1439_1441del	p.Asn480del	p.N480del	ENST00000267163	NM_000321.2	479	gACAac/gac	16/27	0.845266154956402	1	FACETS	0.929	0.881	0.975	0.929	0.881	0.975	CLONAL	1	TRUE	0	0.854351703447708	1		246	244	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398625	116398625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45587940	NA	P-0036449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	231	400	0	ENST00000397752.3:c.2215C>T	p.Arg739Cys	p.R739C	ENST00000397752	NM_000245.2	739	Cgt/Tgt	9/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.854351703447708	2		400	516	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692830	89692830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782343	NA	P-0036449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	85	154	0	ENST00000371953.3:c.314G>A	p.Cys105Tyr	p.C105Y	ENST00000371953	NM_000314.4	105	tGt/tAt	5/9	0.854351703447708	1	FACETS	0.905	0.837	0.969	0.905	0.837	0.969	CLONAL	1	TRUE	0	0.854351703447708	1		154	126	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193202190	193202190	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0036449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	177	231	0	ENST00000367435.3:c.1222A>T	p.Arg408Ter	p.R408*	ENST00000367435	NM_024529.4	408	Aga/Tga	14/17	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.854351703447708	2		231	411	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976606	55976606	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	258	460	0	ENST00000263923.4:c.1219G>T	p.Glu407Ter	p.E407*	ENST00000263923	NM_002253.2	407	Gag/Tag	9/30	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.854351703447708	2		460	590	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032159	26032159	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	159	316	0	ENST00000244661.2:c.130C>G	p.Pro44Ala	p.P44A	ENST00000244661	NM_003537.3	44	Ccg/Gcg	1/1	1	2	FACETS	0.921	0.854	0.989	0.921	0.854	0.989	CLONAL	1	TRUE	1	0.854351703447708	2		316	404	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469872	157469872	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	286	558	0	ENST00000346085.5:c.2666A>T	p.Gln889Leu	p.Q889L	ENST00000346085	NM_020732.3	889	cAg/cTg	9/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.854351703447708	2		558	645	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372536	55372536	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	353	658	0	ENST00000297316.4:c.1226G>T	p.Cys409Phe	p.C409F	ENST00000297316	NM_022454.3	409	tGc/tTc	2/2	1	2	FACETS	0.963	0.917	1	0.963	0.917	1	CLONAL	1	TRUE	1	0.854351703447708	2		658	858	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0036450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	101	395	20	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.823	0.741	0.909	0.823	0.741	0.909	CLONAL	1	TRUE	1	0.592947819655541	2		415	414	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0036450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	105	469	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.688	0.619	0.76	0.688	0.619	0.76	SUBCLONAL	1	TRUE	1	0.592947819655541	2		469	515	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578217	7578217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	190	672	1	ENST00000269305.4:c.632C>T	p.Thr211Ile	p.T211I	ENST00000269305	NM_001126112.2	211	aCt/aTt	6/11	0.583376384908183	1	FACETS	0.836	0.779	0.895	0.836	0.779	0.895	CLONAL	1	TRUE	0	0.592947819655541	1		673	539	SUCCESS
APC	324	MSKCC	GRCh37	5	112175346	112175356	+	frameshift_variant	Frame_Shift_Del	DEL	TTGAATTTTCT	TTGAATTTTCT	-	novel	NA	P-0036450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	129	256	0	ENST00000257430.4:c.4056_4066del	p.Glu1353ArgfsTer18	p.E1353Rfs*18	ENST00000257430	NM_000038.5	1352	gTTGAATTTTCT/g	16/16	0.532415400757555	2	FACETS	0.843	0.781	0.905	0.843	0.781	0.905	CLONAL	2	TRUE	0	0.592947819655541	2		256	258	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0036451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	42	504	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.165253565374882	1	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	FALSE	0	0.203590968320973	1		505	353	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0036451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	47	381	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.752	0.638	0.876	1	0.962	1	SUBCLONAL	2	FALSE	1	0.203590968320973	2		381	307	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394820	45394820	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	14	234	1	ENST00000262160.6:c.529C>T	p.Pro177Ser	p.P177S	ENST00000262160	NM_005901.5	177	Cca/Tca	5/11	0.12509480242776	0	FACETS	0.619	0.449	0.823			1	SUBCLONAL	1	FALSE	0	0.203590968320973	0		235	177	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193172923	193172923	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0036451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	18	209	0	ENST00000367435.3:c.973-2A>T		p.X325_splice	ENST00000367435	NM_024529.4	325			0.165253565374882	1	FACETS	0.691	0.521	0.89	0.691	0.521	0.89	SUBCLONAL	1	FALSE	0	0.203590968320973	1		209	230	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719888	18719888	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	31	260	0	ENST00000266497.5:c.3785C>A	p.Pro1262His	p.P1262H	ENST00000266497		1262	cCt/cAt	27/31	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	1	0.203590968320973	2		260	237	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41525896	41525896	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	17	305	0	ENST00000263253.7:c.1171G>T	p.Ala391Ser	p.A391S	ENST00000263253	NM_001429.3	391	Gca/Tca	5/31	0.16109912914256	1	FACETS	0.708	0.529	0.918	0.708	0.529	0.918	CLONAL	1	FALSE	0	0.203590968320973	1		305	212	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517297	157517297	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0036451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	19	280	0	ENST00000346085.5:c.3863-2A>T		p.X1288_splice	ENST00000346085	NM_020732.3	1288			1	2	FACETS	0.947	0.722	1	0.947	0.722	1	CLONAL	1	FALSE	1	0.203590968320973	2		280	197	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0036452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	219	469	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.808	0.758	0.86	1	0.993	1	CLONAL	2	TRUE	1	0.464626755082962	2		469	583	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0036452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	141	411	1	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.464626755082962	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.464626755082962	1		412	456	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106692	27106692	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	118	507	0	ENST00000324856.7:c.6306del	p.Ser2104ProfsTer31	p.S2104Pfs*31	ENST00000324856	NM_006015.4	2101	gaC/ga	20/20	1	2	FACETS	0.79	0.714	0.87	0.79	0.714	0.87	SUBCLONAL	1	TRUE	1	0.464626755082962	2		507	643	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603007	48603013	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GGTCTTT	GGTCTTT	A	novel	NA	P-0036452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	76	257	0	ENST00000342988.3:c.1309-1_1314delinsA		p.X437_splice	ENST00000342988	NM_005359.5	437		11/12	0.464626755082962	1	FACETS	0.927	0.823	1	0.927	0.823	1	CLONAL	1	TRUE	0	0.464626755082962	1		257	271	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0036454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	87	381	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.3	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	1	0.19	3		381	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579472	7579473	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	C	novel	NA	P-0036454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	56	645	0	ENST00000269305.4:c.214_215delinsG	p.Pro72AlafsTer51	p.P72Afs*51	ENST00000269305	NM_001126112.2	72	CCc/Gc	4/11	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.19	2		645	570	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360862	118360862	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781990391	NA	P-0036454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	26	383	0	ENST00000534358.1:c.4594C>T	p.Arg1532Cys	p.R1532C	ENST00000534358	NM_005933.3	1532	Cgc/Tgc	13/36	1	2	FACETS	0.592	0.468	0.735	0.592	0.468	0.735	SUBCLONAL	1	TRUE	1	0.19	2		383	462	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348536	56348536	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	42	328	0	ENST00000348428.3:c.344A>G	p.His115Arg	p.H115R	ENST00000348428	NM_006785.3	115	cAc/cGc	2/17	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.19	2		328	406	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067004	143067004	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	29	338	0	ENST00000262992.4:c.1709C>T	p.Ser570Phe	p.S570F	ENST00000262992	NM_001101669.1	570	tCt/tTt	16/24	1	2	FACETS	0.877	0.705	1	0.877	0.705	1	CLONAL	1	TRUE	1	0.19	2		338	348	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187405	32187405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	60	611	0	ENST00000375023.3:c.1474G>A	p.Asp492Asn	p.D492N	ENST00000375023	NM_004557.3	492	Gac/Aac	8/30	1	2	FACETS	0.925	0.796	1	0.925	0.796	1	CLONAL	1	TRUE	1	0.19	2		611	683	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289629	33289629	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	39	538	0	ENST00000374542.5:c.74C>T	p.Ser25Phe	p.S25F	ENST00000374542	NM_001141970.1	25	tCc/tTc	2/8	1	2	FACETS	0.642	0.531	0.767	0.642	0.531	0.767	SUBCLONAL	1	TRUE	1	0.19	2		538	639	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92462476	92462476	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	61	478	0	ENST00000265734.4:c.162G>T	p.Met54Ile	p.M54I	ENST00000265734	NM_001259.6	54	atG/atT	2/8	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.19	2		478	511	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401426	139401426	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0036454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	53	539	0	ENST00000277541.6:c.3644-1G>T		p.X1215_splice	ENST00000277541	NM_017617.3	1215			1	2	FACETS	0.969	0.826	1	0.969	0.826	1	CLONAL	1	TRUE	1	0.19	2		539	576	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227821	53227821	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0036454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	66	297	0	ENST00000375401.3:c.2369-2A>T		p.X790_splice	ENST00000375401	NM_004187.3	790			1	1	FACETS	0.825	0.72	0.938	1	0.976	1	CLONAL	2	TRUE	0	0.19	1		297	381	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0036456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	61	407	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.635	0.551	0.726	0.635	0.551	0.726	SUBCLONAL	1	TRUE	1	0.566392451880432	2		408	339	SUCCESS
AR	367	MSKCC	GRCh37	X	66942741	66942741	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs9332969	NA	P-0036456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	25	249	0	ENST00000374690.3:c.2522G>A	p.Arg841His	p.R841H	ENST00000374690	NM_000044.3	841	cGt/cAt	7/8	0.534601708856447	2	FACETS	0.217	0.17	0.27			1	SUBCLONAL	1	TRUE	NA	0.566392451880432	2		249	407	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0036456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	1533	591	2	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.566392451880432	10	FACETS	0.952	0.936	0.966			1	CLONAL	9	TRUE	NA	0.566392451880432	10		593	2064	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	136	500	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.468540467745497	1	FACETS	0.745	0.682	0.81	0.745	0.682	0.81	SUBCLONAL	1	TRUE	0	0.566392451880432	1		500	462	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630190	100630190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs128620185	NA	P-0036456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	111	245	0	ENST00000308731.7:c.83G>A	p.Arg28His	p.R28H	ENST00000308731	NM_000061.2	28	cGc/cAc	2/19	0.534601708856447	2	FACETS	0.839	0.759	0.923			1	CLONAL	1	TRUE	NA	0.566392451880432	2		245	467	SUCCESS
APC	324	MSKCC	GRCh37	5	112175710	112175711	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0036456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	55	338	0	ENST00000257430.4:c.4420dup	p.Ala1474GlyfsTer13	p.A1474Gfs*13	ENST00000257430	NM_000038.5	1473	-/G	16/16	1	2	FACETS	0.539	0.463	0.622	0.539	0.463	0.622	SUBCLONAL	1	TRUE	1	0.566392451880432	2		338	360	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0036457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	254	475	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.727015708303684	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.727015708303684	1		475	405	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281395	49281395	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	278	682	1	ENST00000282018.3:c.442C>A	p.His148Asn	p.H148N	ENST00000282018	NM_020377.2	148	Cat/Aat	1/1	0.727015708303684	1	FACETS	0.991	0.945	1	0.991	0.945	1	CLONAL	1	TRUE	0	0.727015708303684	1		683	491	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101047	41101047	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	177	586	0	ENST00000373198.4:c.1309G>T	p.Ala437Ser	p.A437S	ENST00000373198	NM_133170.3	437	Gcc/Tcc	8/32	1	2	FACETS	0.91	0.845	0.977	0.91	0.845	0.977	CLONAL	1	TRUE	1	0.727015708303684	2		586	535	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535387	66535387	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	83	246	0	ENST00000273854.3:c.74C>A	p.Pro25Gln	p.P25Q	ENST00000273854	NM_004439.5	25	cCa/cAa	1/18	1	2	FACETS	0.932	0.835	1	0.932	0.835	1	CLONAL	1	TRUE	1	0.727015708303684	2		246	245	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	41	214	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.642001704402443	2		214	117	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0036458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	19	485	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.209	0.158	0.269	0.209	0.158	0.269	SUBCLONAL	1	TRUE	1	0.642001704402443	2		485	283	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926888	112926888	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397507546	NA	P-0036458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	86	493	2	ENST00000351677.2:c.1508G>T	p.Gly503Val	p.G503V	ENST00000351677	NM_002834.3	503	gGg/gTg	13/16	1	2	FACETS	0.93	0.833	1	0.93	0.833	1	CLONAL	1	TRUE	1	0.642001704402443	2		495	288	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528496	29528679	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCACCAATGTAAGTCCAAAAGGTATTGCTAAATTACTAAAAAAATTTTTTTCTTTCTTTTCTTTGCGTATTTCTTTTTAAGAAATGCACTCTTGGTTTTCAAAAAGGTTCTGAATTTAGATGTATGAAATAGGAAAATTTCTCCATGGTGATTCTATTTGATAATTGATAAATATTTGTATTTT	TCACCAATGTAAGTCCAAAAGGTATTGCTAAATTACTAAAAAAATTTTTTTCTTTCTTTTCTTTGCGTATTTCTTTTTAAGAAATGCACTCTTGGTTTTCAAAAAGGTTCTGAATTTAGATGTATGAAATAGGAAAATTTCTCCATGGTGATTCTATTTGATAATTGATAAATATTTGTATTTT	-	novel	NA	P-0036458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	31	434	0	ENST00000356175.3:c.1256_1260+179del		p.X419_splice	ENST00000356175	NM_000267.3	419		11/57	1	2	FACETS	0.453	0.369	0.547	0.453	0.369	0.547	SUBCLONAL	1	TRUE	1	0.642001704402443	2		434	213	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502254	157502254	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	125	390	0	ENST00000346085.5:c.3287A>T	p.Lys1096Met	p.K1096M	ENST00000346085	NM_020732.3	1096	aAg/aTg	12/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.642001704402443	2		390	344	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221830	55221830	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	37	660	0	ENST00000275493.2:c.874G>C	p.Val292Leu	p.V292L	ENST00000275493	NM_005228.3	292	Gtg/Ctg	7/28	0.642001704402443	3	FACETS	0.213	0.175	0.256	0.107	0.087	0.128	SUBCLONAL	1	TRUE	1	0.642001704402443	3		660	714	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0036459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	59	571	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.288900292766029	1	FACETS	0.867	0.749	0.995	0.867	0.749	0.995	CLONAL	1	TRUE	0	0.288900292766029	1		572	403	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0036459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	11	624	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.288900292766029	1	FACETS	0.213	0.146	0.296	0.213	0.146	0.296	SUBCLONAL	1	TRUE	0	0.288900292766029	1		624	306	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0036459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	26	449	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	0.568	0.45	0.702	0.568	0.45	0.702	SUBCLONAL	1	TRUE	1	0.288900292766029	2		449	317	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0036459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	140	391	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	1	0.967	1	1	0.992	1	CLONAL	2	TRUE	1	0.288900292766029	2		391	440	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951964	178951964	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	60	496	0	ENST00000263967.3:c.3019G>C	p.Gly1007Arg	p.G1007R	ENST00000263967	NM_006218.2	1007	Ggc/Cgc	21/21	1	2	FACETS	0.946	0.817	1	0.946	0.817	1	CLONAL	1	TRUE	1	0.288900292766029	2		496	439	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142001	108142001	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749471737	NA	P-0036459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	92	387	1	ENST00000278616.4:c.2945G>A	p.Arg982His	p.R982H	ENST00000278616	NM_000051.3	982	cGt/cAt	20/63	1	2	FACETS	0.92	0.825	1	1	0.986	1	CLONAL	2	TRUE	1	0.288900292766029	2		388	346	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012597	36012597	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	46	309	0	ENST00000358208.4:c.41G>A	p.Arg14Gln	p.R14Q	ENST00000358208		14	cGg/cAg	2/12	0.288900292766029	3	FACETS	1	0.952	1	0.67	0.568	0.781	CLONAL	1	TRUE	1	0.288900292766029	3		309	272	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266051	41266631	+	splice_donor_variant,splice_acceptor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	AGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCA	AGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCA	-	novel	NA	P-0036459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	90	244	0	ENST00000349496.5:c.51_431del		p.X17_splice	ENST00000349496	NM_001904.3	17	ccAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCAa/cca	3-4/15	1	2	FACETS	1	0.965	1	1	0.988	1	CLONAL	2	TRUE	1	0.288900292766029	2		244	267	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0036477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	586	569	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.620211111236741	4	FACETS	1	0.981	1			1	CLONAL	4	TRUE	NA	0.620211111236741	4		569	761	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610348	10610349	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0036477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	164	844	0	ENST00000171111.5:c.361dup	p.Glu121GlyfsTer6	p.E121Gfs*6	ENST00000171111	NM_203500.1	121	gag/gGag	2/6	0.620211111236741	1	FACETS	0.958	0.891	1	0.958	0.891	1	CLONAL	1	TRUE	0	0.620211111236741	1		844	381	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861900	57861900	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	159	593	0	ENST00000228682.2:c.1201G>C	p.Gly401Arg	p.G401R	ENST00000228682	NM_005269.2	401	Ggc/Cgc	10/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.620211111236741	2		593	464	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123889498	123889498	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	34	155	0	ENST00000330479.4:c.725T>C	p.Val242Ala	p.V242A	ENST00000330479	NM_020382.3	242	gTg/gCg	7/9	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.620211111236741	2		155	103	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610638	81610638	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	80	428	0	ENST00000298171.2:c.2236C>A	p.His746Asn	p.H746N	ENST00000298171	NM_000369.2	746	Cat/Aat	10/10	1	2	FACETS	0.824	0.733	0.921	0.824	0.733	0.921	CLONAL	1	TRUE	1	0.620211111236741	2		428	313	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736958	736958	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	126	463	0	ENST00000314574.4:c.1141G>T	p.Ala381Ser	p.A381S	ENST00000314574	NM_005433.3	381	Gct/Tct	10/12	0.615918074054893	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.620211111236741	1		463	273	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683689	162683689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770930242	NA	P-0036477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	141	614	0	ENST00000366898.1:c.280G>A	p.Gly94Ser	p.G94S	ENST00000366898	NM_004562.2	94	Ggc/Agc	3/12	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.620211111236741	2		614	430	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739634	41739634	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	119	666	0	ENST00000242208.4:c.339G>C	p.Met113Ile	p.M113I	ENST00000242208	NM_002192.2	113	atG/atC	2/3	1	2	FACETS	0.941	0.856	1	0.941	0.856	1	CLONAL	1	TRUE	1	0.620211111236741	2		666	408	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045022	47045022	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	145	364	0	ENST00000377604.3:c.2348del	p.Leu783ProfsTer19	p.L783Pfs*19	ENST00000377604	NM_001204468.1	783	cTc/cc	20/24	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.620211111236741	1		364	238	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0036478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	319	469	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.624080176108244	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.624080176108244	3		469	626	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0036478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	292	531	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.624080176108244	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.624080176108244	2		531	425	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555687605	NA	P-0036478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	84	311	0	ENST00000342988.3:c.1610A>G	p.Asp537Gly	p.D537G	ENST00000342988	NM_005359.5	537	gAc/gGc	12/12	0.624080176108244	1	FACETS	0.935	0.845	1	0.935	0.845	1	CLONAL	1	TRUE	0	0.624080176108244	1		311	198	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528621	89528621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780470195	NA	P-0036478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	61	142	0	ENST00000336596.2:c.2921C>T	p.Thr974Met	p.T974M	ENST00000336596	NM_005233.5	974	aCg/aTg	17/17	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.624080176108244	2		142	178	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161981	47161981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	98	398	0	ENST00000409792.3:c.4145C>T	p.Ala1382Val	p.A1382V	ENST00000409792	NM_014159.6	1382	gCt/gTt	3/21	1	2	FACETS	0.935	0.843	1	0.935	0.843	1	CLONAL	1	TRUE	1	0.624080176108244	2		398	336	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265433	152265433	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	81	406	0	ENST00000206249.3:c.886C>G	p.Leu296Val	p.L296V	ENST00000206249	NM_000125.3	296	Ctc/Gtc	4/8	1	2	FACETS	0.707	0.627	0.792	0.707	0.627	0.792	SUBCLONAL	1	TRUE	1	0.624080176108244	2		406	367	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711350	114711350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243981730	NA	P-0036479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	24	217	0	ENST00000543371.1:c.365C>T	p.Ser122Leu	p.S122L	ENST00000543371	NM_001198531.1	122	tCg/tTg	3/14	1	2	FACETS	0.742	0.586	0.919	0.742	0.586	0.919	CLONAL	1	TRUE	1	0.347942840642758	2		217	186	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602923	10602923	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	171	670	0	ENST00000171111.5:c.655G>C	p.Glu219Gln	p.E219Q	ENST00000171111	NM_203500.1	219	Gag/Cag	3/6	0.233775164824755	4	FACETS	0.957	0.883	1	0.957	0.883	1	CLONAL	2	TRUE	2	0.347942840642758	4		670	692	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435204	49435204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758476128	NA	P-0036479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	107	497	0	ENST00000301067.7:c.6349C>T	p.Pro2117Ser	p.P2117S	ENST00000301067	NM_003482.3	2117	Ccc/Tcc	31/54	NA	2	FACETS	1	0.948	1			1	INDETERMINATE	2	TRUE	NA	0.347942840642758	2		497	290	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383225	4383225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	21	367	0	ENST00000261254.3:c.19G>A	p.Glu7Lys	p.E7K	ENST00000261254	NM_001759.3	7	Gag/Aag	1/5	0.260218767605523	4	FACETS	0.587	0.453	0.744			1	SUBCLONAL	1	TRUE	NA	0.347942840642758	4		367	277	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858279	27858279	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	69	574	1	ENST00000359303.2:c.292G>C	p.Glu98Gln	p.E98Q	ENST00000359303	NM_003535.2	98	Gag/Cag	1/1	0.215767120672666	3	FACETS	1	0.923	1	0.359	0.314	0.408	CLONAL	1	TRUE	0	0.347942840642758	3		575	432	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864693	68864693	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	55	391	2	ENST00000288368.4:c.64C>T	p.Arg22Cys	p.R22C	ENST00000288368	NM_024870.2	22	Cgc/Tgc	1/40	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.347942840642758	2		393	252	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241863	72241863	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	48	345	0	ENST00000357731.5:c.527C>G	p.Ser176Cys	p.S176C	ENST00000357731	NM_173808.2	176	tCc/tGc	3/7	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.347942840642758	2		345	234	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834174	156834174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	68	732	2	ENST00000524377.1:c.241C>T	p.His81Tyr	p.H81Y	ENST00000524377	NM_002529.3	81	Cat/Tat	2/17	0.31867770006296	3	FACETS	0.956	0.834	1	0.478	0.417	0.544	CLONAL	1	TRUE	1	0.347942840642758	3		734	480	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243827	46243827	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	54	299	0	ENST00000334344.6:c.1921C>G	p.His641Asp	p.H641D	ENST00000334344	NM_152641.2	641	Cat/Gat	15/21	0.347942840642758	11	FACETS	0.926	0.793	1			1	CLONAL	2	TRUE	NA	0.347942840642758	11		299	430	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431339	49431339	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0036479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	54	537	0	ENST00000301067.7:c.9800C>G	p.Ser3267Ter	p.S3267*	ENST00000301067	NM_003482.3	3267	tCa/tGa	34/54	NA	2	FACETS	0.985	0.847	1			1	INDETERMINATE	1	TRUE	NA	0.347942840642758	2		537	315	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118797	115118797	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	70	610	1	ENST00000257566.3:c.544A>C	p.Lys182Gln	p.K182Q	ENST00000257566	NM_016569.3	182	Aag/Cag	2/8	0.347659141344669	3	FACETS	0.98	0.857	1	0.49	0.428	0.557	CLONAL	1	TRUE	1	0.347942840642758	3		611	482	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750891	128750891	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	283	653	1	ENST00000377970.2:c.428T>A	p.Ile143Asn	p.I143N	ENST00000377970	NM_002467.4	143	aTc/aAc	2/3	0.347942840642758	6	FACETS	1	0.977	1	0.844	0.799	0.889	CLONAL	4	TRUE	1	0.347942840642758	6		654	654	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0036480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	34	288	1	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.380032851024512	2	FACETS	1	0.947	1	0.683	0.574	0.798	CLONAL	1	TRUE	0	0.492895139858986	2		289	101	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0036480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	260	631	4	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.291414387261501	3	FACETS	0.923	0.887	0.958	1	0.994	1	INDETERMINATE	4	TRUE	0	0.492895139858986	3		635	356	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287446	46287446	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs774801990	NA	P-0036480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	19	414	0	ENST00000334344.6:c.5305C>T	p.Arg1769Ter	p.R1769*	ENST00000334344	NM_152641.2	1769	Cga/Tga	20/21	0.397849562984078	5	FACETS	0.706	0.538	0.901	0.235	0.179	0.301	CLONAL	1	TRUE	2	0.492895139858986	5		414	190	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532438	63532438	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs762872515	NA	P-0036480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	49	532	0	ENST00000307078.5:c.2141G>A	p.Arg714Gln	p.R714Q	ENST00000307078	NM_004655.3	714	cGg/cAg	8/11	1	2	FACETS	0.695	0.593	0.806	0.695	0.593	0.806	SUBCLONAL	1	TRUE	1	0.492895139858986	2		532	286	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939876	71939876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	80	759	0	ENST00000298229.2:c.503C>T	p.Ala168Val	p.A168V	ENST00000298229	NM_001567.3	168	gCt/gTt	4/28	0.315459302251406	4	FACETS	0.921	0.822	1	0.921	0.822	1	CLONAL	2	TRUE	2	0.492895139858986	4		759	263	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343892	118343892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	90	491	0	ENST00000534358.1:c.2018C>T	p.Ala673Val	p.A673V	ENST00000534358	NM_005933.3	673	gCt/gTt	3/36	0.315459302251406	4	FACETS	0.863	0.774	0.955	0.863	0.774	0.955	CLONAL	2	TRUE	2	0.492895139858986	4		491	316	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246553	41246553	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80357464	NA	P-0036480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	57	767	1	ENST00000357654.3:c.995G>A	p.Arg332Gln	p.R332Q	ENST00000357654	NM_007294.3	332	cGg/cAg	10/23	NA	2	FACETS	0.933	0.809	1			1	INDETERMINATE	1	TRUE	NA	0.492895139858986	2		768	248	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221666	36221666	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1568379151	NA	P-0036480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	45	723	0	ENST00000222270.7:c.5335C>T	p.Arg1779Ter	p.R1779*	ENST00000222270	NM_014727.1	1779	Cga/Tga	26/37	1	2	FACETS	0.609	0.514	0.712	0.609	0.514	0.712	SUBCLONAL	1	TRUE	1	0.492895139858986	2		723	300	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1977089	1977089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	69	741	0	ENST00000382891.5:c.3583G>A	p.Ala1195Thr	p.A1195T	ENST00000382891	NM_133335.3	1195	Gcc/Acc	20/22	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.492895139858986	2		741	216	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866591	117866591	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	19	563	0	ENST00000297338.2:c.1054G>T	p.Asp352Tyr	p.D352Y	ENST00000297338	NM_006265.2	352	Gat/Tat	9/14	0.492895139858986	4	FACETS	0.33	0.25	0.424	0.11	0.083	0.142	SUBCLONAL	1	TRUE	1	0.492895139858986	4		563	349	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933151	39933151	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778096	NA	P-0036482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	342	649	0	ENST00000378444.4:c.1448C>T	p.Pro483Leu	p.P483L	ENST00000378444	NM_001123385.1	483	cCg/cTg	4/15	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.86291671577782	2		649	718	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440372	52440372	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	260	514	0	ENST00000460680.1:c.680G>C	p.Arg227Pro	p.R227P	ENST00000460680	NM_004656.3	227	cGc/cCc	9/17	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.86291671577782	2		514	594	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949152	44949153	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTG	novel	NA	P-0036482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	197	491	0	ENST00000377967.4:c.3714_3716dup	p.Ala1238_Trp1239insCys	p.A1238_W1239insC	ENST00000377967	NM_021140.2	1238	gct/gcTTGt	25/29	1	2	FACETS	0.727	0.677	0.779	0.727	0.677	0.779	SUBCLONAL	1	TRUE	1	0.86291671577782	2		491	628	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274592	198274592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	216	505	0	ENST00000335508.6:c.806G>T	p.Gly269Val	p.G269V	ENST00000335508	NM_012433.2	269	gGa/gTa	7/25	0.489270619985633	1	FACETS	0.437	0.408	0.467	0.437	0.408	0.467	INDETERMINATE	1	TRUE	0	0.86291671577782	1		505	651	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436691	52436691	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1553644634	NA	P-0036482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	264	567	0	ENST00000460680.1:c.1984-1G>A		p.X662_splice	ENST00000460680	NM_004656.3	662			1	2	FACETS	0.99	0.936	1	0.99	0.936	1	CLONAL	1	TRUE	1	0.86291671577782	2		567	618	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436810	52436810	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	244	611	0	ENST00000460680.1:c.1968G>C	p.Lys656Asn	p.K656N	ENST00000460680	NM_004656.3	656	aaG/aaC	15/17	1	2	FACETS	0.901	0.847	0.954	0.901	0.847	0.954	CLONAL	1	TRUE	1	0.86291671577782	2		611	628	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437169	52437169	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	265	452	0	ENST00000460680.1:c.1875G>C	p.Glu625Asp	p.E625D	ENST00000460680	NM_004656.3	625	gaG/gaC	14/17	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.86291671577782	2		452	587	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437246	52437246	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	342	607	0	ENST00000460680.1:c.1798G>C	p.Glu600Gln	p.E600Q	ENST00000460680	NM_004656.3	600	Gag/Cag	14/17	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.86291671577782	2		607	777	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65300293	65300294	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0036483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	30	346	0	ENST00000342505.4:c.3416_3417delinsAT	p.Arg1139His	p.R1139H	ENST00000342505	NM_002227.2	1139	cGG/cAT	25/25	NA	2	FACETS	0.152	0.122	0.187			1	INDETERMINATE	1	TRUE	NA	0.732554890921835	2		346	538	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18762543	18762544	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	126	353	0	ENST00000266497.5:c.4040dup	p.Lys1348GlufsTer19	p.K1348Efs*19	ENST00000266497		1347	gtg/gTtg	29/31	0.732554890921835	4	FACETS	0.816	0.74	0.897	0.272	0.246	0.299	CLONAL	1	TRUE	1	0.732554890921835	4		353	730	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778035	3778035	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	106	824	0	ENST00000262367.5:c.7013C>T	p.Ser2338Phe	p.S2338F	ENST00000262367	NM_004380.2	2338	tCc/tTc	31/31	1	2	FACETS	0.265	0.237	0.296	0.265	0.237	0.296	SUBCLONAL	1	TRUE	1	0.732554890921835	2		824	1091	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579363	7579364	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0036483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	309	611	0	ENST00000269305.4:c.323dup	p.Arg110ProfsTer39	p.R110Pfs*39	ENST00000269305	NM_001126112.2	108	ggt/ggGt	4/11	0.732554890921835	1	FACETS	0.888	0.846	0.93	0.888	0.846	0.93	CLONAL	1	TRUE	0	0.732554890921835	1		611	602	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40856626	40856627	+	missense_variant	Missense_Mutation	DNP	TG	TG	GA	novel	NA	P-0036483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	66	483	0	ENST00000428826.2:c.2010_2011delinsTC	p.Asn671His	p.N671H	ENST00000428826		670	ctCAat/ctTCat	18/21	0.732554890921835	2	FACETS	0.235	0.203	0.269	0.117	0.101	0.135	SUBCLONAL	1	TRUE	0	0.732554890921835	2		483	767	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185200164	185200164	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1268763020	NA	P-0036483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	435	546	0	ENST00000265026.3:c.2821T>C	p.Ser941Pro	p.S941P	ENST00000265026	NM_004721.4	941	Tcg/Ccg	14/14	0.732554890921835	3	FACETS	0.919	0.881	0.956	0.919	0.881	0.956	CLONAL	2	TRUE	1	0.732554890921835	3		546	883	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187377	32187377	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775573404	NA	P-0036483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	319	532	0	ENST00000375023.3:c.1502G>A	p.Cys501Tyr	p.C501Y	ENST00000375023	NM_004557.3	501	tGc/tAc	8/30	0.407254958472227	1	FACETS	0.841	0.801	0.882	0.841	0.801	0.882	INDETERMINATE	1	TRUE	0	0.732554890921835	1		532	656	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271187	38271187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759376422	NA	P-0036483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	62	476	0	ENST00000425967.3:c.2521C>T	p.His841Tyr	p.H841Y	ENST00000425967	NM_001174067.1	841	Cac/Tac	19/19	0.732554890921835	1	FACETS	0.272	0.235	0.311	0.272	0.235	0.311	SUBCLONAL	1	TRUE	0	0.732554890921835	1		476	395	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971163	21971164	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGC	novel	NA	P-0036483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	158	457	0	ENST00000304494.5:c.192_194dup	p.Leu65dup	p.L65dup	ENST00000304494	NM_000077.4	65	ctc/ctGCTc	2/3	0.732554890921835	1	FACETS	0.699	0.649	0.751	0.699	0.649	0.751	SUBCLONAL	1	TRUE	0	0.732554890921835	1		457	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0036485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	188	631	4	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.555628776048054	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.555628776048054	1		635	462	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412029	63412029	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754922124	NA	P-0036485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	145	345	0	ENST00000330258.3:c.1138G>A	p.Glu380Lys	p.E380K	ENST00000330258	NM_152424.3	380	Gag/Aag	2/2	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.555628776048054	1		345	285	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0036485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	88	332	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.555628776048054	1	FACETS	0.826	0.741	0.913	0.826	0.741	0.913	CLONAL	1	TRUE	0	0.555628776048054	1		332	277	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971098	21971098	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs878853647	NA	P-0036485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	146	485	0	ENST00000304494.5:c.260G>C	p.Arg87Pro	p.R87P	ENST00000304494	NM_000077.4	87	cGg/cCg	2/3	1	2	FACETS	0.971	0.891	1	0.971	0.891	1	CLONAL	1	TRUE	1	0.555628776048054	2		485	541	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883212	37883212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs566053951	NA	P-0036485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	202	647	3	ENST00000269571.5:c.3115G>A	p.Ala1039Thr	p.A1039T	ENST00000269571		1039	Gct/Act	25/27	0.257276506989793	3	FACETS	1	0.99	1	0.688	0.641	0.737	INDETERMINATE	1	TRUE	1	0.555628776048054	3		650	675	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023819	27023819	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	247	377	0	ENST00000324856.7:c.925C>T	p.Gln309Ter	p.Q309*	ENST00000324856	NM_006015.4	309	Cag/Tag	1/20	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.555628776048054	2		377	397	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121197	11121197	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	277	512	0	ENST00000358026.2:c.2264A>G	p.Lys755Arg	p.K755R	ENST00000358026	NM_001128849.1	755	aAa/aGa	15/36	0.555628776048054	2	FACETS	0.966	0.919	1	0.966	0.919	1	CLONAL	2	TRUE	0	0.555628776048054	2		512	516	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549823	187549823	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	173	499	0	ENST00000441802.2:c.4418C>T	p.Thr1473Ile	p.T1473I	ENST00000441802	NM_005245.3	1473	aCa/aTa	8/27	1	2	FACETS	0.896	0.827	0.967	0.896	0.827	0.967	CLONAL	1	TRUE	1	0.555628776048054	2		499	695	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636721	8636721	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	91	258	0	ENST00000356435.5:c.188A>C	p.Lys63Thr	p.K63T	ENST00000356435		63	aAa/aCa	2/35	1	2	FACETS	0.993	0.89	1	0.993	0.89	1	CLONAL	1	TRUE	1	0.555628776048054	2		258	330	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212776	27212776	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	220	665	0	ENST00000380036.4:c.2758C>A	p.Leu920Met	p.L920M	ENST00000380036	NM_000459.3	920	Ctg/Atg	17/23	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.555628776048054	2		665	764	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	38	214	0				ENST00000310581	NM_198253.2	-/1132			0.221568223589124	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		214	184	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0036486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	59	485	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.221568223589124	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		485	641	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484153	8484153	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	134	467	0	ENST00000356435.5:c.3379C>T	p.Gln1127Ter	p.Q1127*	ENST00000356435		1127	Caa/Taa	19/35	1	2	FACETS	0.594	0.541	0.649	0.594	0.541	0.649	SUBCLONAL	1	TRUE	1	0.746101460760803	2		467	605	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0036488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	274	657	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.751181554231024	2	FACETS	0.809	0.773	0.845	0.809	0.773	0.845	CLONAL	2	TRUE	0	0.776454627056093	2		657	436	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643734	52643734	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs142097913	NA	P-0036488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	181	736	0	ENST00000394830.3:c.2162T>C	p.Ile721Thr	p.I721T	ENST00000394830	NM_018313.4	721	aTt/aCt	17/30	0.776454627056093	3	FACETS	0.926	0.857	0.997	0.463	0.428	0.499	CLONAL	1	TRUE	1	0.776454627056093	3		736	699	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795354	42795354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	162	622	0	ENST00000575354.2:c.2434C>T	p.Gln812Ter	p.Q812*	ENST00000575354	NM_015125.3	812	Caa/Taa	10/20	0.776454627056093	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.776454627056093	1		622	245	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499342	89499342	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	135	361	0	ENST00000336596.2:c.2512G>C	p.Asp838His	p.D838H	ENST00000336596	NM_005233.5	838	Gat/Cat	15/17	1	2	FACETS	0.999	0.92	1	0.999	0.92	1	CLONAL	1	TRUE	1	0.776454627056093	2		361	348	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230886	66230886	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	75	349	0	ENST00000273854.3:c.2085A>T	p.Lys695Asn	p.K695N	ENST00000273854	NM_004439.5	695	aaA/aaT	12/18	1	2	FACETS	0.755	0.67	0.843	0.755	0.67	0.843	SUBCLONAL	1	TRUE	1	0.776454627056093	2		349	256	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707579	176707579	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	182	570	0	ENST00000439151.2:c.5636T>G	p.Ile1879Ser	p.I1879S	ENST00000439151	NM_022455.4	1879	aTt/aGt	18/23	0.776454627056093	3	FACETS	0.964	0.893	1	0.482	0.446	0.519	CLONAL	1	TRUE	1	0.776454627056093	3		570	675	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0036491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	162	631	4	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.276121056796451	2	FACETS	0.948	0.876	1	0.948	0.876	1	CLONAL	2	TRUE	0	0.326610614765887	2		635	523	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0036491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	51	303	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.305799671354225	3	FACETS	0.922	0.795	1	0.922	0.795	1	CLONAL	2	TRUE	1	0.326610614765887	3		303	197	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197766	66197766	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	25	424	0	ENST00000273854.3:c.2933A>C	p.Lys978Thr	p.K978T	ENST00000273854	NM_004439.5	978	aAg/aCg	17/18	1	2	FACETS	0.582	0.46	0.722	0.582	0.46	0.722	SUBCLONAL	1	TRUE	1	0.326610614765887	2		424	263	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238995	5238995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	87	459	0	ENST00000357368.4:c.1784C>T	p.Ala595Val	p.A595V	ENST00000357368	NM_002850.3	595	gCg/gTg	13/38	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.326610614765887	2		459	461	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928872	44928872	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs755440519	NA	P-0036491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	85	336	0	ENST00000377967.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000377967	NM_021140.2	658	Cga/Tga	17/29	0.178548018084785	5	FACETS	0.934	0.83	1	0.623	0.553	0.696	INDETERMINATE	2	TRUE	2	0.326610614765887	5		336	415	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423598	88423598	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	93	375	0	ENST00000360948.2:c.2237A>C	p.Lys746Thr	p.K746T	ENST00000360948	NM_001012338.2	746	aAg/aCg	18/19	0.304833953271684	3	FACETS	0.893	0.8	0.99	0.893	0.8	0.99	CLONAL	2	TRUE	1	0.326610614765887	3		375	371	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423595	88423595	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	96	376	0	ENST00000360948.2:c.2240T>G	p.Phe747Cys	p.F747C	ENST00000360948	NM_001012338.2	747	tTc/tGc	18/19	0.304833953271684	3	FACETS	0.893	0.802	0.988	0.893	0.802	0.988	CLONAL	2	TRUE	1	0.326610614765887	3		376	383	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732911	30732911	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0036491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	22	159	0	ENST00000295754.5:c.1525-1G>C		p.X509_splice	ENST00000295754	NM_003242.5	509			1	2	FACETS	0.969	0.76	1	0.969	0.76	1	CLONAL	1	TRUE	1	0.326610614765887	2		159	139	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437530	52437530	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	49	520	1	ENST00000460680.1:c.1631T>A	p.Ile544Lys	p.I544K	ENST00000460680	NM_004656.3	544	aTa/aAa	13/17	0.326610614765887	1	FACETS	0.743	0.632	0.864	0.743	0.632	0.864	SUBCLONAL	1	TRUE	0	0.326610614765887	1		521	338	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934294	68934294	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	49	361	0	ENST00000288368.4:c.360T>G	p.Asp120Glu	p.D120E	ENST00000288368	NM_024870.2	120	gaT/gaG	4/40	0.305799671354225	3	FACETS	1	0.862	1	0.507	0.431	0.59	CLONAL	1	TRUE	1	0.326610614765887	3		361	344	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90994973	90994973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	27	318	0	ENST00000265433.3:c.148G>A	p.Ala50Thr	p.A50T	ENST00000265433	NM_002485.4	50	Gct/Act	2/16	0.305799671354225	3	FACETS	0.766	0.612	0.941	0.383	0.306	0.471	CLONAL	1	TRUE	1	0.326610614765887	3		318	251	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0036492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	222	667	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.618743198534494	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.618743198534494	1		667	457	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804305	43804305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28928907	NA	P-0036492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	180	397	0	ENST00000372470.3:c.305G>A	p.Arg102His	p.R102H	ENST00000372470	NM_005373.2	102	cGt/cAt	3/12	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.618743198534494	2		397	514	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356256	66356256	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	73	442	0	ENST00000273854.3:c.1241A>G	p.Tyr414Cys	p.Y414C	ENST00000273854	NM_004439.5	414	tAc/tGc	5/18	1	2	FACETS	0.449	0.393	0.508	0.449	0.393	0.508	SUBCLONAL	1	TRUE	1	0.618743198534494	2		442	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519990	NA	P-0036493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	235	271	0	ENST00000269305.4:c.796G>C	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Cga	8/11	0.318461397964294	6	FACETS	0.95	0.904	0.995	0.95	0.904	0.995	INDETERMINATE	4	TRUE	2	0.939154687062853	6		271	379	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380350	14380350	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	394	145	0	ENST00000256196.4:c.67G>T	p.Gly23Cys	p.G23C	ENST00000256196		23	Ggc/Tgc	1/6	0.939154687062853	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.939154687062853	3		145	407	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657658	37657658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	270	204	0	ENST00000447079.4:c.2575G>A	p.Asp859Asn	p.D859N	ENST00000447079	NM_015083.1	859	Gat/Aat	6/14	0.851977427072855	4	FACETS	0.963	0.924	1	0.963	0.924	1	CLONAL	3	TRUE	1	0.939154687062853	4		204	386	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439637	51439637	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	95	178	0	ENST00000262662.1:c.202C>G	p.Arg68Gly	p.R68G	ENST00000262662		68	Cga/Gga	4/4	0.561418294362945	4	FACETS	1	0.976	1	0.427	0.385	0.471	INDETERMINATE	1	TRUE	1	0.939154687062853	4		178	306	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748748	43748751	+	frameshift_variant	Frame_Shift_Del	DEL	TTCT	TTCT	-	novel	NA	P-0036493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	137	357	0	ENST00000382044.4:c.2055_2058del	p.Glu686LysfsTer12	p.E686Kfs*12	ENST00000382044	NM_001141980.1	685	aaAGAA/aa	12/28	1	2	FACETS	0.889	0.821	0.959	0.889	0.821	0.959	CLONAL	1	TRUE	1	0.939154687062853	2		357	328	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839773	27839773	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	369	289	0	ENST00000328488.2:c.321T>A	p.Asp107Glu	p.D107E	ENST00000328488	NM_003533.2	107	gaT/gaA	1/1	0.939154687062853	6	FACETS	0.935	0.898	0.971			1	CLONAL	4	TRUE	NA	0.939154687062853	6		289	605	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001149	150001149	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	28	255	0	ENST00000253339.5:c.2455G>T	p.Val819Phe	p.V819F	ENST00000253339		819	Gtt/Ttt	4/7	1	2	FACETS	0.295	0.237	0.36	0.295	0.237	0.36	SUBCLONAL	1	TRUE	1	0.939154687062853	2		255	202	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370786	55370786	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	288	268	0	ENST00000297316.4:c.88T>C	p.Cys30Arg	p.C30R	ENST00000297316	NM_022454.3	30	Tgc/Cgc	1/2	0.342436874713767	6	FACETS	0.959	0.918	1	0.959	0.918	1	INDETERMINATE	4	TRUE	2	0.939154687062853	6		268	460	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061191	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs879499034	NA	P-0036494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	164	429	0	ENST00000250448.2:c.798C>A	p.Phe266Leu	p.F266L	ENST00000250448	NM_004496.3	266	ttC/ttA	2/2	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.682920705216131	2		429	339	SUCCESS
APC	324	MSKCC	GRCh37	5	112175780	112175780	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	54	266	0	ENST00000257430.4:c.4490del	p.Pro1497GlnfsTer10	p.P1497Qfs*10	ENST00000257430	NM_000038.5	1497	Cca/ca	16/16	0.619299111666016	1	FACETS	0.89	0.786	0.996	0.89	0.786	0.996	CLONAL	1	TRUE	0	0.682920705216131	1		266	117	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813023	89813023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142833057	NA	P-0036494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	110	574	0	ENST00000389301.3:c.3482C>T	p.Thr1161Met	p.T1161M	ENST00000389301	NM_000135.2	1161	aCg/aTg	35/43	0.621120753478768	1	FACETS	0.774	0.707	0.843	0.774	0.707	0.843	SUBCLONAL	1	TRUE	0	0.682920705216131	1		574	274	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747075	40747075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199637632	NA	P-0036494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	65	539	0	ENST00000373198.4:c.3007G>A	p.Val1003Ile	p.V1003I	ENST00000373198	NM_133170.3	1003	Gtc/Atc	22/32	0.49450322906889	0	FACETS		NA	1			1	NA	1	TRUE	0	0.682920705216131	0		539	202	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276378	115276482	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATAACTTTGGTTACAGTTCCTTCAAAATGTTCAATGCTGATATCTTCAAAAATGACTGTTCCTTGAGGCAATAGTCTGACATCTGTTGCAACTTCTTTACCCTAA	ATAACTTTGGTTACAGTTCCTTCAAAATGTTCAATGCTGATATCTTCAAAAATGACTGTTCCTTGAGGCAATAGTCTGACATCTGTTGCAACTTCTTTACCCTAA	-	novel	NA	P-0036494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	87	570	0	ENST00000438362.2:c.850-4_950del		p.X284_splice	ENST00000438362	NM_001242891.1	284		9/20	1	2	FACETS	0.758	0.677	0.843	0.758	0.677	0.843	SUBCLONAL	1	TRUE	1	0.682920705216131	2		570	336	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874194	151874194	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	93	428	2	ENST00000262189.6:c.8344G>T	p.Asp2782Tyr	p.D2782Y	ENST00000262189	NM_170606.2	2782	Gat/Tat	38/59	0.478339299506613	4	FACETS	0.93	0.83	1	0.31	0.276	0.345	CLONAL	1	TRUE	1	0.682920705216131	4		430	493	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0036495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	37	303	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.2	2		303	346	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	23	214	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.782	0.611	0.98	0.782	0.611	0.98	CLONAL	1	TRUE	1	0.2	2		214	294	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0036496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	396	485	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.674422630524863	5	FACETS	0.996	0.954	1	0.747	0.715	0.778	CLONAL	3	TRUE	1	0.679279849169661	5		485	788	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212522512	212522512	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs747144499	NA	P-0036496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	96	270	0	ENST00000342788.4:c.1913G>A	p.Trp638Ter	p.W638*	ENST00000342788	NM_005235.2	638	tGg/tAg	16/28	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.679279849169661	2		270	268	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247782	10247782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	24	601	1	ENST00000340748.4:c.4420G>A	p.Gly1474Arg	p.G1474R	ENST00000340748		1474	Ggg/Agg	36/40	0.112424571301994	1	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	FALSE	0	0.112424571301994	1		602	336	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50916765	50916765	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	12	362	2	ENST00000440232.2:c.2237G>T	p.Ser746Ile	p.S746I	ENST00000440232	NM_002691.3	746	aGc/aTc	18/27	0.112424571301994	1	FACETS	1	0.719	1	1	0.719	1	CLONAL	1	FALSE	0	0.112424571301994	1		364	197	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710580	40710580	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	35	650	0	ENST00000373198.4:c.4271A>G	p.Asp1424Gly	p.D1424G	ENST00000373198	NM_133170.3	1424	gAc/gGc	31/32	0.112424571301994	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	0	0.112424571301994	1		650	449	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127920529	127920529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	196	340	0	ENST00000373547.4:c.370G>A	p.Gly124Arg	p.G124R	ENST00000373547	NM_002721.4	124	Gga/Aga	4/7	0.626228957222709	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.700485288387908	1		340	341	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202465	123202465	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	189	171	0	ENST00000218089.9:c.2317C>T	p.Gln773Ter	p.Q773*	ENST00000218089	NM_001042749.1	773	Caa/Taa	24/35	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.700485288387908	1		171	306	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321345	65321345	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	213	463	0	ENST00000342505.4:c.1495C>T	p.Gln499Ter	p.Q499*	ENST00000342505	NM_002227.2	499	Cag/Tag	11/25	0.700485288387908	1	FACETS	0.969	0.914	1	0.969	0.914	1	CLONAL	1	TRUE	0	0.700485288387908	1		463	408	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102196221	102196221	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	219	293	0	ENST00000263464.3:c.878T>G	p.Phe293Cys	p.F293C	ENST00000263464	NM_001165.4	293	tTt/tGt	3/9	0.700485288387908	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.700485288387908	1		293	365	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424398	49424398	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	268	363	0	ENST00000301067.7:c.13825C>T	p.Gln4609Ter	p.Q4609*	ENST00000301067	NM_003482.3	4609	Cag/Tag	41/54	0.664861029989902	2	FACETS	0.942	0.902	0.982	0.942	0.902	0.982	CLONAL	2	TRUE	0	0.700485288387908	2		363	406	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765736	41765736	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	125	363	0	ENST00000301178.4:c.2612C>G	p.Ser871Cys	p.S871C	ENST00000301178	NM_021913.4	871	tCc/tGc	20/20	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.700485288387908	2		363	295	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200359	138200359	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	132	367	0	ENST00000237289.4:c.1777C>G	p.Gln593Glu	p.Q593E	ENST00000237289	NM_001270507.1	593	Caa/Gaa	7/9	NA	2	FACETS	0.805	0.736	0.877			1	INDETERMINATE	1	TRUE	NA	0.700485288387908	2		367	468	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	120	569	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	0.8	2		569	331	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	247	645	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.951	0.895	1	0.951	0.895	1	CLONAL	1	TRUE	1	0.8	2		648	649	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	333	395	20	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.977	0.946	1	1	0.997	1	CLONAL	2	TRUE	1	0.8	2		415	426	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202968	16202968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781049707	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	189	339	1	ENST00000375759.3:c.676C>T	p.Arg226Trp	p.R226W	ENST00000375759	NM_015001.2	226	Cgg/Tgg	3/15	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.8	2		340	464	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255718	16255718	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	26	229	0	ENST00000375759.3:c.2983G>A	p.Ala995Thr	p.A995T	ENST00000375759	NM_015001.2	995	Gca/Aca	11/15	1	2	FACETS	0.204	0.161	0.252	0.204	0.161	0.252	SUBCLONAL	1	TRUE	1	0.8	2		229	319	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260395	16260395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	163	357	0	ENST00000375759.3:c.7660G>A	p.Val2554Ile	p.V2554I	ENST00000375759	NM_015001.2	2554	Gtc/Atc	11/15	1	2	FACETS	0.837	0.774	0.901	0.837	0.774	0.901	CLONAL	1	TRUE	1	0.8	2		357	487	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938264	36938264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150616658	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	263	523	0	ENST00000361632.4:c.697C>T	p.Arg233Trp	p.R233W	ENST00000361632		233	Cgg/Tgg	6/16	1	2	FACETS	0.95	0.896	1	0.95	0.896	1	CLONAL	1	TRUE	1	0.8	2		523	692	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736510	85736511	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs387906351	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	109	388	3	ENST00000370580.1:c.136dup	p.Ile46AsnfsTer4	p.I46Nfs*4	ENST00000370580	NM_003921.4	46	ata/aAta	2/3	1	2	FACETS	0.836	0.76	0.914	0.836	0.76	0.914	CLONAL	1	TRUE	1	0.8	2		391	326	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849069	156849069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750168062	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	302	566	0	ENST00000524377.1:c.1961G>A	p.Arg654His	p.R654H	ENST00000524377	NM_002529.3	654	cGc/cAc	15/17	1	2	FACETS	0.965	0.914	1	0.965	0.914	1	CLONAL	1	TRUE	1	0.8	2		566	782	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633626	69633626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781923153	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	52	51	0	ENST00000334134.2:c.76C>T	p.Arg26Trp	p.R26W	ENST00000334134	NM_005247.2	26	Cgg/Tgg	1/3	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.8	2		51	95	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196879	108196880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs773570504	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	125	259	0	ENST00000278616.4:c.6908dup	p.Glu2304GlyfsTer69	p.E2304Gfs*69	ENST00000278616	NM_000051.3	2301	gca/gcAa	47/63	1	2	FACETS	0.956	0.877	1	0.956	0.877	1	CLONAL	1	TRUE	1	0.8	2		259	327	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307394	118307394	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	18	23	0	ENST00000534358.1:c.173del	p.Pro58ArgfsTer92	p.P58Rfs*92	ENST00000534358	NM_005933.3	56	tCc/tc	1/36	1	2	FACETS	0.726	0.564	0.903	0.726	0.564	0.903	CLONAL	1	TRUE	1	0.8	2		23	62	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871044	12871044	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	126	183	0	ENST00000228872.4:c.275del	p.Pro92ArgfsTer27	p.P92Rfs*27	ENST00000228872	NM_004064.3	91	Ccc/cc	1/3	0.214764047418495	4	FACETS	0.995	0.917	1	0.995	0.917	1	INDETERMINATE	2	TRUE	2	0.8	4		183	285	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432375	49432375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751964761	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	283	522	0	ENST00000301067.7:c.8764C>T	p.Arg2922Trp	p.R2922W	ENST00000301067	NM_003482.3	2922	Cgg/Tgg	34/54	0.114227346340961	3	FACETS	1	0.994	1	0.723	0.684	0.762	INDETERMINATE	1	TRUE	1	0.8	3		522	685	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	285	512	1	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.114227346340961	3	FACETS	1	0.994	1	0.701	0.663	0.74	INDETERMINATE	1	TRUE	1	0.8	3		513	711	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482363	56482363	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	218	420	0	ENST00000267101.3:c.911C>T	p.Ala304Val	p.A304V	ENST00000267101	NM_001982.3	304	gCc/gTc	8/28	0.114227346340961	3	FACETS	1	0.991	1	0.694	0.65	0.737	INDETERMINATE	1	TRUE	1	0.8	3		420	550	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233793	133233794	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1555225149	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	246	526	0	ENST00000320574.5:c.3510dup	p.Leu1171ThrfsTer6	p.L1171Tfs*6	ENST00000320574	NM_006231.2	1170	-/A	29/49	1	2	FACETS	0.917	0.862	0.972	0.917	0.862	0.972	CLONAL	1	TRUE	1	0.8	2		526	671	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253208	133253208	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764254754	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	176	373	0	ENST00000320574.5:c.833C>T	p.Thr278Met	p.T278M	ENST00000320574	NM_006231.2	278	aCg/aTg	9/49	1	2	FACETS	0.88	0.817	0.944	0.88	0.817	0.944	CLONAL	1	TRUE	1	0.8	2		373	500	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609958	81609958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780018604	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	100	261	0	ENST00000298171.2:c.1556G>A	p.Arg519His	p.R519H	ENST00000298171	NM_000369.2	519	cGc/cAc	10/10	1	2	FACETS	0.916	0.831	1	0.916	0.831	1	CLONAL	1	TRUE	1	0.8	2		261	273	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570459	95570459	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	17	197	0	ENST00000393063.1:c.3274C>A	p.Pro1092Thr	p.P1092T	ENST00000393063	NM_030621.3	1092	Cct/Act	22/28	1	2	FACETS	0.17	0.127	0.221	0.17	0.127	0.221	SUBCLONAL	1	TRUE	1	0.8	2		197	250	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	101	438	2	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.775	0.7	0.852	0.775	0.7	0.852	SUBCLONAL	1	TRUE	1	0.8	2		440	326	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2221325	2221325	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371097636	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	270	496	0	ENST00000326181.6:c.409G>A	p.Val137Ile	p.V137I	ENST00000326181	NM_032271.2	137	Gtc/Atc	6/21	1	2	FACETS	0.938	0.884	0.991	0.938	0.884	0.991	CLONAL	1	TRUE	1	0.8	2		496	720	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779727	3779727	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	207	439	0	ENST00000262367.5:c.5321G>A	p.Arg1774His	p.R1774H	ENST00000262367	NM_004380.2	1774	cGc/cAc	31/31	1	2	FACETS	0.913	0.853	0.973	0.913	0.853	0.973	CLONAL	1	TRUE	1	0.8	2		439	567	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134428	30134428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	288	455	0	ENST00000263025.4:c.103C>T	p.Pro35Ser	p.P35S	ENST00000263025	NM_002746.2	35	Ccg/Tcg	1/9	1	2	FACETS	0.956	0.904	1	0.956	0.904	1	CLONAL	1	TRUE	1	0.8	2		455	753	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782295	56782295	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs557498689	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	170	309	0	ENST00000308159.5:c.136C>T	p.Arg46Cys	p.R46C	ENST00000308159	NM_014669.4	46	Cgt/Tgt	2/22	1	2	FACETS	0.932	0.866	1	0.932	0.866	1	CLONAL	1	TRUE	1	0.8	2		309	456	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	133	269	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.945	0.869	1	0.945	0.869	1	CLONAL	1	TRUE	1	0.8	2		270	352	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832557	72832557	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141100730	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	180	301	0	ENST00000268489.5:c.4024G>A	p.Gly1342Arg	p.G1342R	ENST00000268489	NM_006885.3	1342	Gga/Aga	9/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.8	2		301	426	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845477	72845477	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1395722106	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	175	346	0	ENST00000268489.5:c.3863C>T	p.Thr1288Met	p.T1288M	ENST00000268489	NM_006885.3	1288	aCg/aTg	7/10	1	2	FACETS	0.99	0.921	1	0.99	0.921	1	CLONAL	1	TRUE	1	0.8	2		346	442	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81979857	81979857	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764693069	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	178	305	0	ENST00000359376.3:c.3559C>T	p.Arg1187Trp	p.R1187W	ENST00000359376	NM_002661.3	1187	Cgg/Tgg	31/33	1	2	FACETS	0.989	0.921	1	0.989	0.921	1	CLONAL	1	TRUE	1	0.8	2		305	450	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350411	89350411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs565590201	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	276	573	0	ENST00000301030.4:c.2539G>A	p.Asp847Asn	p.D847N	ENST00000301030	NM_001256183.1	847	Gat/Aat	9/13	1	2	FACETS	0.999	0.944	1	0.999	0.944	1	CLONAL	1	TRUE	1	0.8	2		573	691	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351703	89351703	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773132293	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	349	522	0	ENST00000301030.4:c.1247C>T	p.Ala416Val	p.A416V	ENST00000301030	NM_001256183.1	416	gCg/gTg	9/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.8	2		522	857	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805104	89805104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778321	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	213	338	0	ENST00000389301.3:c.4273C>T	p.Arg1425Cys	p.R1425C	ENST00000389301	NM_000135.2	1425	Cgt/Tgt	43/43	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.8	2		338	518	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110597	8110597	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	257	404	0	ENST00000585124.1:c.295A>G	p.Ser99Gly	p.S99G	ENST00000585124	NM_004217.3	99	Agc/Ggc	5/9	1	2	FACETS	0.968	0.912	1	0.968	0.912	1	CLONAL	1	TRUE	1	0.8	2		404	664	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41251830	41251830	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80357264	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	214	478	0	ENST00000357654.3:c.509G>A	p.Arg170Gln	p.R170Q	ENST00000357654	NM_007294.3	170	cGg/cAg	7/23	1	2	FACETS	0.89	0.833	0.949	0.89	0.833	0.949	CLONAL	1	TRUE	1	0.8	2		478	601	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677762	47677762	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1380705599	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	119	266	0	ENST00000347630.2:c.1103G>A	p.Arg368His	p.R368H	ENST00000347630	NM_001007230.1	368	cGc/cAc	11/11	1	2	FACETS	0.924	0.845	1	0.924	0.845	1	CLONAL	1	TRUE	1	0.8	2		266	322	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440904	56440904	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1458799446	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	290	464	1	ENST00000407977.2:c.433C>T	p.Arg145Ter	p.R145*	ENST00000407977		145	Cga/Tga	4/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.8	2		465	703	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58725428	58725429	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	23	362	0	ENST00000305921.3:c.1008dup	p.Tyr337IlefsTer5	p.Y337Ifs*5	ENST00000305921	NM_003620.3	334	-/A	4/6	1	2	FACETS	0.136	0.105	0.171	0.136	0.105	0.171	SUBCLONAL	1	TRUE	1	0.8	2		362	423	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	273	795	3	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.867	0.817	0.918	0.867	0.817	0.918	CLONAL	1	TRUE	1	0.8	2		798	787	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	149	669	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	0.95	0.878	1	0.95	0.878	1	CLONAL	1	TRUE	1	0.8	2		669	392	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	175	367	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.8	2		367	391	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117245	7117245	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	255	520	0	ENST00000302850.5:c.3971T>C	p.Met1324Thr	p.M1324T	ENST00000302850	NM_000208.2	1324	aTg/aCg	22/22	1	2	FACETS	0.949	0.894	1	0.949	0.894	1	CLONAL	1	TRUE	1	0.8	2		520	672	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610591	10610591	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173824866	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	266	477	0	ENST00000171111.5:c.119C>T	p.Ala40Val	p.A40V	ENST00000171111	NM_203500.1	40	gCg/gTg	2/6	1	2	FACETS	0.942	0.888	0.996	0.942	0.888	0.996	CLONAL	1	TRUE	1	0.8	2		477	706	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955118	17955118	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs955716335	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	332	548	0	ENST00000458235.1:c.109C>G	p.Pro37Ala	p.P37A	ENST00000458235	NM_000215.3	37	Ccc/Gcc	2/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.8	2		548	764	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213945	36213945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747264846	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	270	579	0	ENST00000222270.7:c.2771G>A	p.Arg924Gln	p.R924Q	ENST00000222270	NM_014727.1	924	cGg/cAg	6/37	1	2	FACETS	0.912	0.86	0.965	0.912	0.86	0.965	CLONAL	1	TRUE	1	0.8	2		579	740	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40740960	40740960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	264	572	0	ENST00000392038.2:c.1358del	p.Pro453LeufsTer122	p.P453Lfs*122	ENST00000392038	NM_001626.4	453	cCt/ct	13/14	1	2	FACETS	0.964	0.909	1	0.964	0.909	1	CLONAL	1	TRUE	1	0.8	2		572	685	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743883	41743883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374699228	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	314	511	0	ENST00000301178.4:c.818C>T	p.Ala273Val	p.A273V	ENST00000301178	NM_021913.4	273	gCg/gTg	7/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.8	2		511	768	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383692	42383692	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202097187	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	248	393	0	ENST00000221972.3:c.467C>T	p.Ala156Val	p.A156V	ENST00000221972	NM_021601.3	156	gCg/gTg	3/5	1	2	FACETS	0.932	0.877	0.988	0.932	0.877	0.988	CLONAL	1	TRUE	1	0.8	2		393	665	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794686	42794686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202152564	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	209	543	0	ENST00000575354.2:c.1766G>A	p.Arg589Gln	p.R589Q	ENST00000575354	NM_015125.3	589	cGg/cAg	10/20	1	2	FACETS	0.895	0.836	0.954	0.895	0.836	0.954	CLONAL	1	TRUE	1	0.8	2		543	584	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918992	50918992	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568638496	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	214	417	1	ENST00000440232.2:c.2729G>A	p.Arg910Gln	p.R910Q	ENST00000440232	NM_002691.3	910	cGg/cAg	22/27	0.3	1	FACETS	0.57	0.534	0.607	0.57	0.534	0.607	INDETERMINATE	1	TRUE	0	0.8	1		418	563	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965131	25965131	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	211	407	0	ENST00000435504.4:c.4075T>C	p.Ser1359Pro	p.S1359P	ENST00000435504		1359	Tca/Cca	13/13	1	2	FACETS	0.94	0.88	1	0.94	0.88	1	CLONAL	1	TRUE	1	0.8	2		407	561	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966872	25966873	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	191	460	0	ENST00000435504.4:c.2333dup	p.Val779SerfsTer25	p.V779Sfs*25	ENST00000435504		778	cca/ccCa	13/13	1	2	FACETS	0.796	0.74	0.853	0.796	0.74	0.853	SUBCLONAL	1	TRUE	1	0.8	2		460	600	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	rs267608078	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	110	343	0	ENST00000234420.5:c.3260_3261dup	p.Phe1088ProfsTer3	p.F1088Pfs*3	ENST00000234420	NM_000179.2	1085	acc/aCCcc	5/10	1	2	FACETS	0.516	0.465	0.569	0.516	0.465	0.569	SUBCLONAL	1	TRUE	1	0.8	2		343	533	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033352	48033352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750949	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	117	468	0	ENST00000234420.5:c.3656C>T	p.Thr1219Ile	p.T1219I	ENST00000234420	NM_000179.2	1219	aCt/aTt	8/10	1	2	FACETS	0.911	0.833	0.992	0.911	0.833	0.992	CLONAL	1	TRUE	1	0.8	2		468	321	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137461	202137461	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	125	280	0	ENST00000358485.4:c.689T>C	p.Leu230Pro	p.L230P	ENST00000358485	NM_001080125.1	230	cTg/cCg	4/9	1	2	FACETS	0.936	0.858	1	0.936	0.858	1	CLONAL	1	TRUE	1	0.8	2		280	334	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021181	31021181	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs534065676	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	188	356	0	ENST00000375687.4:c.1180C>T	p.Arg394Cys	p.R394C	ENST00000375687	NM_015338.5	394	Cgt/Tgt	12/13	1	2	FACETS	0.944	0.88	1	0.944	0.88	1	CLONAL	1	TRUE	1	0.8	2		356	498	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21304065	21304065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1375676692	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	215	333	0	ENST00000354336.3:c.844C>T	p.Arg282Cys	p.R282C	ENST00000354336	NM_005207.3	282	Cgc/Tgc	3/3	1	2	FACETS	0.908	0.85	0.967	0.908	0.85	0.967	CLONAL	1	TRUE	1	0.8	2		333	592	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163376	47163377	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	117	275	0	ENST00000409792.3:c.2749dup	p.Ser917LysfsTer18	p.S917Kfs*18	ENST00000409792	NM_014159.6	917	agt/aAgt	3/21	1	2	FACETS	0.897	0.82	0.977	0.897	0.82	0.977	CLONAL	1	TRUE	1	0.8	2		275	326	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204992	128204992	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	114	591	0	ENST00000341105.2:c.449del	p.Gly150GlufsTer68	p.G150Efs*68	ENST00000341105	NM_032638.4	150	gGa/ga	3/6	0.114227346340961	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.8	0		591	570	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403608	138403608	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1266528244	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	42	402	0	ENST00000289153.2:c.2174T>C	p.Leu725Ser	p.L725S	ENST00000289153	NM_006219.2	725	tTa/tCa	15/22	1	2	FACETS	0.198	0.165	0.235	0.198	0.165	0.235	SUBCLONAL	1	TRUE	1	0.8	2		402	530	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517762	187517762	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	71	160	0	ENST00000441802.2:c.12932del	p.Pro4311HisfsTer38	p.P4311Hfs*38	ENST00000441802	NM_005245.3	4311	cCa/ca	25/27	0.114227346340961	3	FACETS	1	0.909	1	0.516	0.456	0.578	INDETERMINATE	1	TRUE	1	0.8	3		160	241	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254582	1254582	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	66	452	0	ENST00000310581.5:c.3196C>T	p.Pro1066Ser	p.P1066S	ENST00000310581	NM_198253.2	1066	Ccc/Tcc	15/16	1	2	FACETS	0.319	0.277	0.364	0.319	0.277	0.364	SUBCLONAL	1	TRUE	1	0.8	2		452	517	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048238	180048238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324497116	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	251	558	1	ENST00000261937.6:c.2035C>T	p.Arg679Trp	p.R679W	ENST00000261937	NM_182925.4	679	Cgg/Tgg	14/30	0.114227346340961	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.8	0		559	719	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053143	180053143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1245699281	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	250	541	0	ENST00000261937.6:c.1226G>A	p.Arg409Lys	p.R409K	ENST00000261937	NM_182925.4	409	aGg/aAg	9/30	0.114227346340961	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.8	0		541	643	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405042	405042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	146	300	0	ENST00000380956.4:c.1124G>A	p.Gly375Asp	p.G375D	ENST00000380956	NM_001195286.1	375	gGc/gAc	8/9	0.114227346340961	3	FACETS	1	0.97	1	0.557	0.512	0.603	INDETERMINATE	1	TRUE	1	0.8	3		300	459	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185819	32185819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145916093	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	257	520	2	ENST00000375023.3:c.1577C>T	p.Ala526Val	p.A526V	ENST00000375023	NM_004557.3	526	gCg/gTg	9/30	0.114227346340961	3	FACETS	1	0.992	1	0.674	0.635	0.714	INDETERMINATE	1	TRUE	1	0.8	3		522	667	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964394	93964394	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	101	301	0	ENST00000369303.4:c.2503A>G	p.Arg835Gly	p.R835G	ENST00000369303	NM_004440.3	835	Aga/Gga	14/17	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.8	2		301	231	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068121	94068121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149408123	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	55	154	1	ENST00000369303.4:c.841C>T	p.Arg281Cys	p.R281C	ENST00000369303	NM_004440.3	281	Cgt/Tgt	4/17	1	2	FACETS	0.881	0.771	0.996	0.881	0.771	0.996	CLONAL	1	TRUE	1	0.8	2		155	156	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137524803	137524803	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55881171	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	91	286	0	ENST00000367739.4:c.566C>T	p.Thr189Met	p.T189M	ENST00000367739	NM_000416.2	189	aCg/aTg	5/7	0.114227346340961	3	FACETS	1	0.954	1	0.553	0.497	0.611	INDETERMINATE	1	TRUE	1	0.8	3		286	288	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150533	157150533	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	168	300	0	ENST00000346085.5:c.1715G>A	p.Gly572Glu	p.G572E	ENST00000346085	NM_020732.3	572	gGa/gAa	2/20	0.114227346340961	3	FACETS	1	0.984	1	0.607	0.563	0.653	INDETERMINATE	1	TRUE	1	0.8	3		300	484	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528715	157528715	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	35	353	0	ENST00000346085.5:c.6440G>T	p.Arg2147Met	p.R2147M	ENST00000346085	NM_020732.3	2147	aGg/aTg	20/20	0.114227346340961	3	FACETS	0.247	0.202	0.298	0.124	0.101	0.149	INDETERMINATE	1	TRUE	1	0.8	3		353	495	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508860	106508860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1251220989	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	176	318	0	ENST00000359195.3:c.854C>T	p.Thr285Met	p.T285M	ENST00000359195	NM_002649.2	285	aCg/aTg	2/11	1	2	FACETS	0.948	0.882	1	0.948	0.882	1	CLONAL	1	TRUE	1	0.8	2		318	464	SUCCESS
MET	4233	MSKCC	GRCh37	7	116414203	116414203	+	intron_variant	Intron	SNP	T	T	A	rs1405799810	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	159	433	0	ENST00000397752.3:c.3029-732T>A		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.743	0.685	0.802	0.743	0.685	0.802	SUBCLONAL	1	TRUE	1	0.8	2		433	535	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992721	68992721	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs764112302	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	13	561	1	ENST00000288368.4:c.1693del	p.Ser565ArgfsTer10	p.S565Rfs*10	ENST00000288368	NM_024870.2	562	cgT/cg	16/40	0.3	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.8	0		562	215	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128268598	128268598	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749606853	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	277	528	1	ENST00000265960.3:c.1057C>T	p.Arg353Cys	p.R353C	ENST00000265960	NM_001006617.1	353	Cgc/Tgc	8/12	1	2	FACETS	0.989	0.935	1	0.989	0.935	1	CLONAL	1	TRUE	1	0.8	2		529	700	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759781	133759781	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764106779	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	169	373	0	ENST00000318560.5:c.2104G>A	p.Glu702Lys	p.E702K	ENST00000318560	NM_005157.4	702	Gag/Aag	11/11	1	2	FACETS	0.992	0.922	1	0.992	0.922	1	CLONAL	1	TRUE	1	0.8	2		373	426	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931673	39931673	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121434619	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	274	274	0	ENST00000378444.4:c.2926C>T	p.Arg976Ter	p.R976*	ENST00000378444	NM_001123385.1	976	Cga/Tga	4/15	0.3	2	FACETS	0.984	0.95	1	0.984	0.95	1	INDETERMINATE	2	TRUE	0	0.8	2		274	348	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436297	110436297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1178312245	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	160	225	0	ENST00000375856.3:c.2104G>A	p.Val702Met	p.V702M	ENST00000375856	NM_003749.2	702	Gtg/Atg	1/2	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.8	2		225	356	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902312	151902312	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	13	184	0	ENST00000262189.6:c.3842-2A>T		p.X1281_splice	ENST00000262189	NM_170606.2	1281			1	2	FACETS	0.197	0.141	0.265	0.197	0.141	0.265	SUBCLONAL	1	TRUE	1	0.8	2		184	165	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656483	3656483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201117707	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	244	580	1	ENST00000294008.3:c.752C>T	p.Ala251Val	p.A251V	ENST00000294008	NM_032444.2	251	gCg/gTg	3/15	1	2	FACETS	0.853	0.801	0.906	0.853	0.801	0.906	CLONAL	1	TRUE	1	0.8	2		581	715	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162660	47162660	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs975806896	NA	P-0036500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	141	312	0	ENST00000409792.3:c.3466C>T	p.Arg1156Cys	p.R1156C	ENST00000409792	NM_014159.6	1156	Cgc/Tgc	3/21	1	2	FACETS	0.974	0.899	1	0.974	0.899	1	CLONAL	1	TRUE	1	0.8	2		312	362	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880882	134880882	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs936404830	NA	P-0036501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	57	383	0	ENST00000398015.3:c.1445C>T	p.Ser482Phe	p.S482F	ENST00000398015	NM_004441.4	482	tCc/tTc	7/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.581213310158058	2		383	168	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948780	55948780	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs763426023	NA	P-0036501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	86	346	1	ENST00000263923.4:c.3685C>T	p.Arg1229Ter	p.R1229*	ENST00000263923	NM_002253.2	1229	Cga/Tga	28/30	0.101987026358824	4	FACETS	0.907	0.814	1	0.907	0.814	1	INDETERMINATE	2	TRUE	2	0.581213310158058	4		347	258	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911194	29911201	+	frameshift_variant	Frame_Shift_Del	DEL	CAGATCAC	CAGATCAC	-	novel	NA	P-0036501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	766	443	0	ENST00000376809.5:c.495_502del	p.Ile166AlafsTer8	p.I166Afs*8	ENST00000376809	NM_002116.7	165	CAGATCACc/c	3/8	0.581213310158058	8	FACETS	0.959	0.94	0.976	0.959	0.94	0.976	CLONAL	8	TRUE	0	0.581213310158058	8		443	943	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	23	588	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.163	0.126	0.205	0.163	0.126	0.205	SUBCLONAL	1	TRUE	1	0.48	2		588	589	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	46	367	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.545	0.46	0.637	0.545	0.46	0.637	SUBCLONAL	1	TRUE	1	0.48	2		367	352	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	21	348	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.326	0.251	0.414	0.326	0.251	0.414	SUBCLONAL	1	TRUE	1	0.48	2		348	268	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023019	150023019	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	142	479	0	ENST00000253339.5:c.244C>T	p.Arg82Ter	p.R82*	ENST00000253339		82	Cga/Tga	1/7	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.48	2		479	542	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412494	80412494	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	16	242	0	ENST00000286548.4:c.547C>T	p.Arg183Ter	p.R183*	ENST00000286548	NM_002072.3	183	Cga/Tga	4/7	1	2	FACETS	0.18	0.132	0.237	0.18	0.132	0.237	SUBCLONAL	1	TRUE	1	0.48	2		242	370	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	68	407	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.48	2		408	276	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398279	25398279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894365	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	25	360	0	ENST00000311936.3:c.40G>A	p.Val14Ile	p.V14I	ENST00000311936	NM_004985.3	14	Gta/Ata	2/5	1	2	FACETS	0.441	0.349	0.547	0.441	0.349	0.547	SUBCLONAL	1	TRUE	1	0.48	2		360	236	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190826	11190826	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	44	316	0	ENST00000361445.4:c.5373T>G	p.His1791Gln	p.H1791Q	ENST00000361445	NM_004958.3	1791	caT/caG	39/58	1	2	FACETS	0.508	0.427	0.597	0.508	0.427	0.597	SUBCLONAL	1	TRUE	1	0.48	2		316	361	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255338	16255338	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200134542	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	32	325	1	ENST00000375759.3:c.2603C>T	p.Ala868Val	p.A868V	ENST00000375759	NM_015001.2	868	gCg/gTg	11/15	1	2	FACETS	0.361	0.293	0.438	0.361	0.293	0.438	SUBCLONAL	1	TRUE	1	0.48	2		326	369	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599988	28599988	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	35	537	0	ENST00000253063.3:c.870G>T	p.Glu290Asp	p.E290D	ENST00000253063	NM_031459.4	290	gaG/gaT	6/10	1	2	FACETS	0.248	0.202	0.299	0.248	0.202	0.299	SUBCLONAL	1	TRUE	1	0.48	2		537	589	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932400	36932400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764345289	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	52	541	0	ENST00000361632.4:c.2069C>T	p.Thr690Met	p.T690M	ENST00000361632		690	aCg/aTg	16/16	1	2	FACETS	0.346	0.294	0.403	0.346	0.294	0.403	SUBCLONAL	1	TRUE	1	0.48	2		541	627	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748102	72748102	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	118	382	0	ENST00000357731.5:c.76T>G	p.Cys26Gly	p.C26G	ENST00000357731	NM_173808.2	26	Tgc/Ggc	1/7	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.48	2		382	387	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880485	155880485	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	30	392	0	ENST00000368323.3:c.68A>C	p.Lys23Thr	p.K23T	ENST00000368323	NM_006912.5	23	aAa/aCa	2/6	1	2	FACETS	0.3	0.241	0.366	0.3	0.241	0.366	SUBCLONAL	1	TRUE	1	0.48	2		392	417	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740212	162740212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219740609	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	56	387	0	ENST00000367921.3:c.1414G>A	p.Asp472Asn	p.D472N	ENST00000367921	NM_006182.2	472	Gat/Aat	12/18	1	2	FACETS	0.557	0.478	0.642	0.557	0.478	0.642	SUBCLONAL	1	TRUE	1	0.48	2		387	419	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743288	162743288	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	12	167	0	ENST00000367921.3:c.1758A>C	p.Glu586Asp	p.E586D	ENST00000367921	NM_006182.2	586	gaA/gaC	14/18	1	2	FACETS	0.217	0.152	0.297	0.217	0.152	0.297	SUBCLONAL	1	TRUE	1	0.48	2		167	230	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099338	193099338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	67	326	0	ENST00000367435.3:c.272G>A	p.Arg91Gln	p.R91Q	ENST00000367435	NM_024529.4	91	cGa/cAa	3/17	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.48	2		326	268	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206942067	206942067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	89	291	0	ENST00000423557.1:c.451G>A	p.Glu151Lys	p.E151K	ENST00000423557	NM_000572.2	151	Gag/Aag	5/5	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.48	2		291	284	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606911	43606911	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	62	647	0	ENST00000355710.3:c.1520C>A	p.Ser507Ter	p.S507*	ENST00000355710	NM_020975.4	507	tCa/tAa	7/20	1	2	FACETS	0.364	0.314	0.419	0.364	0.314	0.419	SUBCLONAL	1	TRUE	1	0.48	2		647	710	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607663	43607663	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	191	685	1	ENST00000355710.3:c.1639G>T	p.Asp547Tyr	p.D547Y	ENST00000355710	NM_020975.4	547	Gat/Tat	8/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.48	2		686	726	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332565	70332565	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs185830524	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	96	393	0	ENST00000373644.4:c.470C>T	p.Ser157Leu	p.S157L	ENST00000373644	NM_030625.2	157	tCg/tTg	2/12	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.48	2		393	356	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450904	70450904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	38	379	0	ENST00000373644.4:c.5744C>T	p.Ala1915Val	p.A1915V	ENST00000373644	NM_030625.2	1915	gCt/gTt	12/12	1	2	FACETS	0.341	0.281	0.407	0.341	0.281	0.407	SUBCLONAL	1	TRUE	1	0.48	2		379	465	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683424	88683424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	51	181	0	ENST00000372037.3:c.1547G>T	p.Arg516Ile	p.R516I	ENST00000372037	NM_004329.2	516	aGa/aTa	13/13	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.48	2		181	180	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920404	114920404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	42	398	0	ENST00000543371.1:c.1345G>A	p.Ala449Thr	p.A449T	ENST00000543371	NM_001198531.1	449	Gca/Aca	13/14	1	2	FACETS	0.337	0.281	0.4	0.337	0.281	0.4	SUBCLONAL	1	TRUE	1	0.48	2		398	519	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251853	8251853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748397251	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	152	474	0	ENST00000335790.3:c.224G>A	p.Arg75Gln	p.R75Q	ENST00000335790	NM_002315.2	75	cGa/cAa	2/4	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.48	2		474	503	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94170371	94170371	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745614941	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	23	292	0	ENST00000323929.3:c.1898G>A	p.Arg633Gln	p.R633Q	ENST00000323929	NM_005591.3	633	cGa/cAa	17/20	1	2	FACETS	0.351	0.274	0.44	0.351	0.274	0.44	SUBCLONAL	1	TRUE	1	0.48	2		292	273	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180586	94180586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780018393	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	75	314	0	ENST00000323929.3:c.1582G>A	p.Ala528Thr	p.A528T	ENST00000323929	NM_005591.3	528	Gca/Aca	15/20	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.48	2		314	294	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94908780	94908780	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	88	419	0	ENST00000536441.1:c.1274T>G	p.Val425Gly	p.V425G	ENST00000536441	NM_144665.3	425	gTt/gGt	9/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.48	2		419	313	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142026	108142026	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	71	392	0	ENST00000278616.4:c.2970T>G	p.Ile990Met	p.I990M	ENST00000278616	NM_000051.3	990	atT/atG	20/63	1	2	FACETS	0.948	0.835	1	0.948	0.835	1	CLONAL	1	TRUE	1	0.48	2		392	312	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149251	119149251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267606708	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	12	455	1	ENST00000264033.4:c.1259G>A	p.Arg420Gln	p.R420Q	ENST00000264033	NM_005188.3	420	cGa/cAa	9/16	1	2	FACETS	0.099	0.069	0.137	0.099	0.069	0.137	SUBCLONAL	1	TRUE	1	0.48	2		456	503	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419112	419112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778494527	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	27	243	0	ENST00000399788.2:c.3235G>A	p.Asp1079Asn	p.D1079N	ENST00000399788	NM_001042603.1	1079	Gac/Aac	22/28	1	2	FACETS	0.538	0.431	0.659	0.538	0.431	0.659	SUBCLONAL	1	TRUE	1	0.48	2		243	209	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793390	18793390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	17	361	1	ENST00000266497.5:c.4087G>A	p.Ala1363Thr	p.A1363T	ENST00000266497		1363	Gca/Aca	30/31	1	2	FACETS	0.261	0.195	0.34	0.261	0.195	0.34	SUBCLONAL	1	TRUE	1	0.48	2		362	271	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378649	25378649	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	75	346	0	ENST00000311936.3:c.349A>C	p.Lys117Gln	p.K117Q	ENST00000311936	NM_004985.3	117	Aaa/Caa	4/5	1	2	FACETS	0.933	0.824	1	0.933	0.824	1	CLONAL	1	TRUE	1	0.48	2		346	335	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230691	46230691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424958105	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	12	388	0	ENST00000334344.6:c.940C>T	p.Arg314Cys	p.R314C	ENST00000334344	NM_152641.2	314	Cgt/Tgt	8/21	1	2	FACETS	0.143	0.1	0.197	0.143	0.1	0.197	SUBCLONAL	1	TRUE	1	0.48	2		388	349	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436643	49436643	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	141	475	0	ENST00000301067.7:c.5663C>T	p.Ser1888Phe	p.S1888F	ENST00000301067	NM_003482.3	1888	tCc/tTc	26/54	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.48	2		475	557	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487277	56487277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035001455	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	95	407	0	ENST00000267101.3:c.1423C>T	p.Arg475Trp	p.R475W	ENST00000267101	NM_001982.3	475	Cgg/Tgg	12/28	1	2	FACETS	0.927	0.83	1	0.927	0.83	1	CLONAL	1	TRUE	1	0.48	2		407	427	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864148	57864148	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766159479	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	40	389	0	ENST00000228682.2:c.1625G>A	p.Arg542His	p.R542H	ENST00000228682	NM_005269.2	542	cGc/cAc	12/12	1	2	FACETS	0.31	0.257	0.369	0.31	0.257	0.369	SUBCLONAL	1	TRUE	1	0.48	2		389	538	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118902	115118903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	69	260	0	ENST00000257566.3:c.438dup	p.Ala147SerfsTer13	p.A147Sfs*13	ENST00000257566	NM_016569.3	146	-/A	2/8	1	2	FACETS	0.995	0.875	1	0.995	0.875	1	CLONAL	1	TRUE	1	0.48	2		260	289	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	109	395	0	ENST00000320574.5:c.1231G>C	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ctg	13/49	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.48	2		395	394	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257249	133257249	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500889	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	32	389	2	ENST00000320574.5:c.229C>T	p.Arg77Cys	p.R77C	ENST00000320574	NM_006231.2	77	Cgc/Tgc	3/49	1	2	FACETS	0.348	0.282	0.422	0.348	0.282	0.422	SUBCLONAL	1	TRUE	1	0.48	2		391	383	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26911760	26911760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	15	309	0	ENST00000381527.3:c.185C>T	p.Ser62Leu	p.S62L	ENST00000381527	NM_001260.1	62	tCg/tTg	2/13	1	2	FACETS	0.259	0.189	0.343	0.259	0.189	0.343	SUBCLONAL	1	TRUE	1	0.48	2		309	241	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967528	26967528	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	13	244	0	ENST00000381527.3:c.671T>G	p.Phe224Cys	p.F224C	ENST00000381527	NM_001260.1	224	tTt/tGt	7/13	1	2	FACETS	0.267	0.19	0.36	0.267	0.19	0.36	SUBCLONAL	1	TRUE	1	0.48	2		244	203	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602426	28602426	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	37	340	0	ENST00000241453.7:c.1943-1G>A		p.X648_splice	ENST00000241453	NM_004119.2	648			1	2	FACETS	0.444	0.367	0.53	0.444	0.367	0.53	SUBCLONAL	1	TRUE	1	0.48	2		340	347	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28979966	28979966	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs61763181	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	19	508	0	ENST00000282397.4:c.1502G>T	p.Arg501Ile	p.R501I	ENST00000282397	NM_002019.4	501	aGa/aTa	11/30	1	2	FACETS	0.224	0.169	0.288	0.224	0.169	0.288	SUBCLONAL	1	TRUE	1	0.48	2		508	354	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910615	32910615	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	14	298	0	ENST00000380152.3:c.2123C>A	p.Ser708Tyr	p.S708Y	ENST00000380152		708	tCt/tAt	11/27	1	2	FACETS	0.287	0.208	0.383	0.287	0.208	0.383	SUBCLONAL	1	TRUE	1	0.48	2		298	203	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913065	32913065	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	66	340	0	ENST00000380152.3:c.4573C>A	p.His1525Asn	p.H1525N	ENST00000380152		1525	Cat/Aat	11/27	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.48	2		340	261	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944627	32944627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55763607	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	98	441	0	ENST00000380152.3:c.8420C>T	p.Ser2807Leu	p.S2807L	ENST00000380152		2807	tCg/tTg	19/27	1	2	FACETS	0.947	0.85	1	0.947	0.85	1	CLONAL	1	TRUE	1	0.48	2		441	431	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972596	32972596	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs758051959	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	68	327	0	ENST00000380152.3:c.9946G>T	p.Glu3316Ter	p.E3316*	ENST00000380152		3316	Gaa/Taa	27/27	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.48	2		327	270	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335850	73335850	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	37	337	0	ENST00000377767.4:c.2445A>C	p.Lys815Asn	p.K815N	ENST00000377767	NM_014953.3	815	aaA/aaC	18/21	1	2	FACETS	0.471	0.39	0.562	0.471	0.39	0.562	SUBCLONAL	1	TRUE	1	0.48	2		337	327	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353761	68353761	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	15	248	0	ENST00000487270.1:c.596T>G	p.Ile199Ser	p.I199S	ENST00000487270	NM_133509.3	199	aTt/aGt	7/11	1	2	FACETS	0.316	0.231	0.417	0.316	0.231	0.417	SUBCLONAL	1	TRUE	1	0.48	2		248	198	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562587	95562587	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	75	245	0	ENST00000393063.1:c.4670A>C	p.Lys1557Thr	p.K1557T	ENST00000393063	NM_030621.3	1557	aAa/aCa	24/28	1	2	FACETS	0.989	0.874	1	0.989	0.874	1	CLONAL	1	TRUE	1	0.48	2		245	316	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571510	95571510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	42	298	0	ENST00000393063.1:c.3167G>A	p.Ser1056Asn	p.S1056N	ENST00000393063	NM_030621.3	1056	aGc/aAc	21/28	1	2	FACETS	0.444	0.371	0.525	0.444	0.371	0.525	SUBCLONAL	1	TRUE	1	0.48	2		298	394	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95584041	95584041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	23	394	0	ENST00000393063.1:c.1427G>A	p.Ser476Asn	p.S476N	ENST00000393063	NM_030621.3	476	aGc/aAc	10/28	1	2	FACETS	0.358	0.279	0.448	0.358	0.279	0.448	SUBCLONAL	1	TRUE	1	0.48	2		394	268	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023066	33023066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1230965844	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	71	267	0	ENST00000300177.4:c.175G>A	p.Gly59Arg	p.G59R	ENST00000300177	NM_001191322.1	59	Ggg/Agg	2/2	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.48	2		267	293	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670452	88670452	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143617169	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	64	221	0	ENST00000360948.2:c.1234G>A	p.Glu412Lys	p.E412K	ENST00000360948	NM_001012338.2	412	Gaa/Aaa	11/19	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.48	2		221	248	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641249	3641249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	224	646	2	ENST00000294008.3:c.2390G>A	p.Gly797Asp	p.G797D	ENST00000294008	NM_032444.2	797	gGc/gAc	12/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.48	2		648	827	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778758	3778758	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	72	745	0	ENST00000262367.5:c.6290T>C	p.Met2097Thr	p.M2097T	ENST00000262367	NM_004380.2	2097	aTg/aCg	31/31	1	2	FACETS	0.379	0.331	0.432	0.379	0.331	0.432	SUBCLONAL	1	TRUE	1	0.48	2		745	791	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349000	11349000	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	35	408	0	ENST00000332029.2:c.336T>G	p.Phe112Leu	p.F112L	ENST00000332029	NM_003745.1	112	ttT/ttG	2/2	1	2	FACETS	0.275	0.224	0.331	0.275	0.224	0.331	SUBCLONAL	1	TRUE	1	0.48	2		408	531	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133307	30133307	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	41	481	0	ENST00000263025.4:c.191G>A	p.Arg64His	p.R64H	ENST00000263025	NM_002746.2	64	cGc/cAc	2/9	1	2	FACETS	0.327	0.272	0.389	0.327	0.272	0.389	SUBCLONAL	1	TRUE	1	0.48	2		481	522	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888076	81888076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1353659689	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	31	291	0	ENST00000359376.3:c.221G>A	p.Arg74His	p.R74H	ENST00000359376	NM_002661.3	74	cGc/cAc	3/33	1	2	FACETS	0.389	0.315	0.473	0.389	0.315	0.473	SUBCLONAL	1	TRUE	1	0.48	2		291	332	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81957097	81957097	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	82	314	0	ENST00000359376.3:c.2315G>T	p.Arg772Ile	p.R772I	ENST00000359376	NM_002661.3	772	aGa/aTa	22/33	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.48	2		314	321	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81968055	81968055	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	31	259	0	ENST00000359376.3:c.2761G>A	p.Glu921Lys	p.E921K	ENST00000359376	NM_002661.3	921	Gag/Aag	26/33	1	2	FACETS	0.409	0.331	0.496	0.409	0.331	0.496	SUBCLONAL	1	TRUE	1	0.48	2		259	316	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371746	89371746	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	28	401	0	ENST00000301030.4:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000301030	NM_001256183.1	32	Gat/Tat	4/13	1	2	FACETS	0.302	0.241	0.372	0.302	0.241	0.372	SUBCLONAL	1	TRUE	1	0.48	2		401	386	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983112	7983112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	42	423	1	ENST00000319144.4:c.902G>A	p.Gly301Glu	p.G301E	ENST00000319144	NM_001139.2	301	gGa/gAa	7/15	1	2	FACETS	0.412	0.344	0.487	0.412	0.344	0.487	SUBCLONAL	1	TRUE	1	0.48	2		424	425	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110655	8110655	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	48	409	0	ENST00000585124.1:c.237T>G	p.Ile79Met	p.I79M	ENST00000585124	NM_004217.3	79	atT/atG	5/9	1	2	FACETS	0.402	0.34	0.471	0.402	0.34	0.471	SUBCLONAL	1	TRUE	1	0.48	2		409	497	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533316	29533316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1466678870	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	17	189	0	ENST00000356175.3:c.1319G>A	p.Arg440Gln	p.R440Q	ENST00000356175	NM_000267.3	440	cGa/cAa	12/57	1	2	FACETS	0.283	0.211	0.369	0.283	0.211	0.369	SUBCLONAL	1	TRUE	1	0.48	2		189	250	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663484	29663484	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	32	336	0	ENST00000356175.3:c.6077C>A	p.Ser2026Ter	p.S2026*	ENST00000356175	NM_000267.3	2026	tCa/tAa	40/57	1	2	FACETS	0.436	0.354	0.527	0.436	0.354	0.527	SUBCLONAL	1	TRUE	1	0.48	2		336	306	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320971	30320971	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	23	461	0	ENST00000322652.5:c.1381T>C	p.Tyr461His	p.Y461H	ENST00000322652	NM_015355.2	461	Tat/Cat	12/16	1	2	FACETS	0.245	0.191	0.308	0.245	0.191	0.308	SUBCLONAL	1	TRUE	1	0.48	2		461	391	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245303	41245303	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs80357114	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	32	603	0	ENST00000357654.3:c.2245G>T	p.Asp749Tyr	p.D749Y	ENST00000357654	NM_007294.3	749	Gat/Tat	10/23	1	2	FACETS	0.256	0.207	0.312	0.256	0.207	0.312	SUBCLONAL	1	TRUE	1	0.48	2		603	520	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58701094	58701094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	31	403	0	ENST00000305921.3:c.685G>A	p.Glu229Lys	p.E229K	ENST00000305921	NM_003620.3	229	Gaa/Aaa	2/6	1	2	FACETS	0.331	0.268	0.403	0.331	0.268	0.403	SUBCLONAL	1	TRUE	1	0.48	2		403	390	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736915	736915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs910562293	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	94	430	0	ENST00000314574.4:c.1184G>A	p.Arg395Gln	p.R395Q	ENST00000314574	NM_005433.3	395	cGa/cAa	10/12	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.48	2		430	351	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604736	48604736	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	22	308	0	ENST00000342988.3:c.1558G>T	p.Glu520Ter	p.E520*	ENST00000342988	NM_005359.5	520	Gaa/Taa	12/12	1	2	FACETS	0.255	0.197	0.323	0.255	0.197	0.323	SUBCLONAL	1	TRUE	1	0.48	2		308	359	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604755	48604755	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	91	301	0	ENST00000342988.3:c.1577A>C	p.Glu526Ala	p.E526A	ENST00000342988	NM_005359.5	526	gAa/gCa	12/12	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.48	2		301	348	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244223	5244223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199851847	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	58	477	0	ENST00000357368.4:c.1259G>A	p.Arg420His	p.R420H	ENST00000357368	NM_002850.3	420	cGc/cAc	11/38	1	2	FACETS	0.425	0.365	0.491	0.425	0.365	0.491	SUBCLONAL	1	TRUE	1	0.48	2		477	568	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265724	10265724	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	45	356	0	ENST00000340748.4:c.1453G>A	p.Glu485Lys	p.E485K	ENST00000340748		485	Gaa/Aaa	19/40	1	2	FACETS	0.478	0.403	0.562	0.478	0.403	0.562	SUBCLONAL	1	TRUE	1	0.48	2		356	392	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19261504	19261504	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	84	473	0	ENST00000162023.5:c.41A>G	p.Gln14Arg	p.Q14R	ENST00000162023		14	cAa/cGa	6/13	1	2	FACETS	0.487	0.43	0.549	0.487	0.43	0.549	SUBCLONAL	1	TRUE	1	0.48	2		473	718	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765576	41765576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763066660	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	55	473	0	ENST00000301178.4:c.2452G>A	p.Glu818Lys	p.E818K	ENST00000301178	NM_021913.4	818	Gaa/Aaa	20/20	1	2	FACETS	0.445	0.381	0.515	0.445	0.381	0.515	SUBCLONAL	1	TRUE	1	0.48	2		473	515	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972919	25972919	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	21	340	0	ENST00000435504.4:c.1506G>T	p.Glu502Asp	p.E502D	ENST00000435504		502	gaG/gaT	12/13	1	2	FACETS	0.227	0.174	0.288	0.227	0.174	0.288	SUBCLONAL	1	TRUE	1	0.48	2		340	386	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029109	26029109	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	19	255	0	ENST00000435504.4:c.241T>C	p.Tyr81His	p.Y81H	ENST00000435504		81	Tat/Cat	4/13	1	2	FACETS	0.382	0.291	0.489	0.382	0.291	0.489	SUBCLONAL	1	TRUE	1	0.48	2		255	207	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068357	26068357	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	43	396	0	ENST00000435504.4:c.133G>T	p.Glu45Ter	p.E45*	ENST00000435504		45	Gaa/Taa	2/13	1	2	FACETS	0.759	0.641	0.888	0.759	0.641	0.888	SUBCLONAL	1	TRUE	1	0.48	2		396	236	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025841	48025841	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542848931	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	15	186	0	ENST00000234420.5:c.719G>A	p.Arg240Gln	p.R240Q	ENST00000234420	NM_000179.2	240	cGa/cAa	4/10	1	2	FACETS	0.396	0.291	0.52	0.396	0.291	0.52	SUBCLONAL	1	TRUE	1	0.48	2		186	158	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99136593	99136593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770686205	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	38	397	0	ENST00000074304.5:c.82G>A	p.Asp28Asn	p.D28N	ENST00000074304	NM_001134224.1	28	Gac/Aac	3/26	1	2	FACETS	0.337	0.278	0.403	0.337	0.278	0.403	SUBCLONAL	1	TRUE	1	0.48	2		397	470	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266478	198266478	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	38	261	0	ENST00000335508.6:c.2358A>C	p.Lys786Asn	p.K786N	ENST00000335508	NM_012433.2	786	aaA/aaC	16/25	1	2	FACETS	0.965	0.81	1	0.965	0.81	1	CLONAL	1	TRUE	1	0.48	2		261	164	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131357	202131357	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	40	337	0	ENST00000358485.4:c.325G>A	p.Glu109Lys	p.E109K	ENST00000358485	NM_001080125.1	109	Gaa/Aaa	2/9	1	2	FACETS	0.446	0.371	0.529	0.446	0.371	0.529	SUBCLONAL	1	TRUE	1	0.48	2		337	374	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209108194	209108194	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	80	347	0	ENST00000345146.2:c.655T>G	p.Tyr219Asp	p.Y219D	ENST00000345146	NM_005896.2	219	Tat/Gat	6/10	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.48	2		347	299	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645637	215645637	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	28	462	0	ENST00000260947.4:c.961A>C	p.Lys321Gln	p.K321Q	ENST00000260947	NM_000465.2	321	Aaa/Caa	4/11	1	2	FACETS	0.286	0.228	0.352	0.286	0.228	0.352	SUBCLONAL	1	TRUE	1	0.48	2		462	408	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730910	40730910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370873414	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	35	401	1	ENST00000373198.4:c.3625C>T	p.Arg1209Trp	p.R1209W	ENST00000373198	NM_133170.3	1209	Cgg/Tgg	27/32	1	2	FACETS	0.277	0.226	0.334	0.277	0.226	0.334	SUBCLONAL	1	TRUE	1	0.48	2		402	527	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54959339	54959339	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	26	328	0	ENST00000312783.6:c.361G>T	p.Glu121Ter	p.E121*	ENST00000312783	NM_198436.1	121	Gaa/Taa	5/10	1	2	FACETS	0.395	0.314	0.488	0.395	0.314	0.488	SUBCLONAL	1	TRUE	1	0.48	2		328	274	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42843742	42843742	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	139	387	0	ENST00000398585.3:c.1177A>C	p.Thr393Pro	p.T393P	ENST00000398585	NM_001135099.1	393	Act/Cct	10/14	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.48	2		387	541	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	34	219	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	1	2	FACETS	0.541	0.444	0.648	0.541	0.444	0.648	SUBCLONAL	1	TRUE	1	0.48	2		219	262	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268823	41268823	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	74	395	0	ENST00000349496.5:c.1061A>C	p.Lys354Thr	p.K354T	ENST00000349496	NM_001904.3	354	aAg/aCg	7/15	1	2	FACETS	0.964	0.851	1	0.964	0.851	1	CLONAL	1	TRUE	1	0.48	2		395	320	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275123	41275123	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	69	288	0	ENST00000349496.5:c.1289A>C	p.Asn430Thr	p.N430T	ENST00000349496	NM_001904.3	430	aAt/aCt	9/15	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.48	2		288	284	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163731	47163731	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367547253	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	24	341	0	ENST00000409792.3:c.2395G>A	p.Asp799Asn	p.D799N	ENST00000409792	NM_014159.6	799	Gat/Aat	3/21	1	2	FACETS	0.395	0.311	0.492	0.395	0.311	0.492	SUBCLONAL	1	TRUE	1	0.48	2		341	253	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164855	47164855	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424607930	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	72	249	0	ENST00000409792.3:c.1271G>A	p.Arg424Gln	p.R424Q	ENST00000409792	NM_014159.6	424	cGa/cAa	3/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.48	2		249	231	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164922	47164922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779483918	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	50	218	2	ENST00000409792.3:c.1204C>T	p.Arg402Trp	p.R402W	ENST00000409792	NM_014159.6	402	Cgg/Tgg	3/21	1	2	FACETS	0.934	0.802	1	0.934	0.802	1	CLONAL	1	TRUE	1	0.48	2		220	223	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164999	47164999	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	26	291	0	ENST00000409792.3:c.1127A>C	p.Lys376Thr	p.K376T	ENST00000409792	NM_014159.6	376	aAa/aCa	3/21	1	2	FACETS	0.43	0.341	0.53	0.43	0.341	0.53	SUBCLONAL	1	TRUE	1	0.48	2		291	252	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720928	119720928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	28	387	0	ENST00000316626.5:c.247G>A	p.Ala83Thr	p.A83T	ENST00000316626		83	Gcc/Acc	2/12	1	2	FACETS	0.296	0.236	0.364	0.296	0.236	0.364	SUBCLONAL	1	TRUE	1	0.48	2		387	394	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670327	134670327	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373140258	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	88	294	0	ENST00000398015.3:c.238C>T	p.Arg80Trp	p.R80W	ENST00000398015	NM_004441.4	80	Cgg/Tgg	3/16	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.48	2		294	364	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242880	142242880	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	108	387	0	ENST00000350721.4:c.4107A>C	p.Leu1369Phe	p.L1369F	ENST00000350721	NM_001184.3	1369	ttA/ttC	22/47	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.48	2		387	429	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281484	142281484	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	104	489	0	ENST00000350721.4:c.760G>T	p.Glu254Ter	p.E254*	ENST00000350721	NM_001184.3	254	Gaa/Taa	4/47	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.48	2		489	408	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191328	185191328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	127	438	0	ENST00000265026.3:c.2209C>T	p.Pro737Ser	p.P737S	ENST00000265026	NM_004721.4	737	Cca/Tca	11/14	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.48	2		438	493	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506987	186506987	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	23	223	0	ENST00000323963.5:c.1153C>A	p.Leu385Ile	p.L385I	ENST00000323963		385	Ctt/Att	11/11	1	2	FACETS	0.432	0.338	0.539	0.432	0.338	0.539	SUBCLONAL	1	TRUE	1	0.48	2		223	222	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981522	55981522	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	38	352	0	ENST00000263923.4:c.415A>C	p.Thr139Pro	p.T139P	ENST00000263923	NM_002253.2	139	Act/Cct	4/30	1	2	FACETS	0.521	0.432	0.619	0.521	0.432	0.619	SUBCLONAL	1	TRUE	1	0.48	2		352	304	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196213	106196213	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs370735654	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	15	173	0	ENST00000380013.4:c.4546C>T	p.Arg1516Ter	p.R1516*	ENST00000380013	NM_001127208.2	1516	Cga/Tga	11/11	1	2	FACETS	0.338	0.248	0.445	0.338	0.248	0.445	SUBCLONAL	1	TRUE	1	0.48	2		173	185	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332915	153332915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200698994	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	87	334	0	ENST00000281708.4:c.41G>A	p.Arg14Gln	p.R14Q	ENST00000281708	NM_033632.3	14	cGa/cAa	2/12	1	2	FACETS	0.951	0.848	1	0.951	0.848	1	CLONAL	1	TRUE	1	0.48	2		334	381	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524651	187524651	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754963553	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	172	505	1	ENST00000441802.2:c.11029G>A	p.Asp3677Asn	p.D3677N	ENST00000441802	NM_005245.3	3677	Gac/Aac	19/27	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.48	2		506	699	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524834	187524834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771664786	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	80	525	1	ENST00000441802.2:c.10846G>A	p.Val3616Ile	p.V3616I	ENST00000441802	NM_005245.3	3616	Gta/Ata	19/27	1	2	FACETS	0.533	0.47	0.602	0.533	0.47	0.602	SUBCLONAL	1	TRUE	1	0.48	2		526	625	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282547	1282547	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	36	332	0	ENST00000310581.5:c.1766T>G	p.Ile589Ser	p.I589S	ENST00000310581	NM_198253.2	589	aTc/aGc	3/16	1	2	FACETS	0.363	0.298	0.436	0.363	0.298	0.436	SUBCLONAL	1	TRUE	1	0.48	2		332	413	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176913	56176913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	56	251	1	ENST00000399503.3:c.2183C>T	p.Ser728Phe	p.S728F	ENST00000399503	NM_005921.1	728	tCc/tTc	13/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.48	2		252	158	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591085	67591085	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519839	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	18	425	0	ENST00000274335.5:c.1678G>T	p.Asp560Tyr	p.D560Y	ENST00000274335		560	Gac/Tac	12/15	1	2	FACETS	0.475	0.36	0.608	0.475	0.36	0.608	SUBCLONAL	1	TRUE	1	0.48	2		425	158	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591303	67591303	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	20	209	0	ENST00000274335.5:c.1801G>T	p.Glu601Ter	p.E601*	ENST00000274335		601	Gaa/Taa	13/15	1	2	FACETS	0.375	0.288	0.477	0.375	0.288	0.477	SUBCLONAL	1	TRUE	1	0.48	2		209	222	SUCCESS
APC	324	MSKCC	GRCh37	5	112151211	112151211	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs201093383	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	84	304	0	ENST00000257430.4:c.854A>G	p.Asp285Gly	p.D285G	ENST00000257430	NM_000038.5	285	gAc/gGc	9/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.48	2		304	280	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	51	204	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.979	0.842	1	0.979	0.842	1	CLONAL	1	TRUE	1	0.48	2		204	217	SUCCESS
APC	324	MSKCC	GRCh37	5	112176873	112176873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	17	269	0	ENST00000257430.4:c.5582C>A	p.Ser1861Tyr	p.S1861Y	ENST00000257430	NM_000038.5	1861	tCt/tAt	16/16	1	2	FACETS	0.262	0.196	0.342	0.262	0.196	0.342	SUBCLONAL	1	TRUE	1	0.48	2		269	270	SUCCESS
APC	324	MSKCC	GRCh37	5	112179452	112179452	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782312	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	74	303	0	ENST00000257430.4:c.8161C>T	p.Arg2721Cys	p.R2721C	ENST00000257430	NM_000038.5	2721	Cgc/Tgc	16/16	1	2	FACETS	0.923	0.814	1	0.923	0.814	1	CLONAL	1	TRUE	1	0.48	2		303	334	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931321	131931321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773761143	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	28	381	0	ENST00000265335.6:c.2026G>A	p.Glu676Lys	p.E676K	ENST00000265335		676	Gaa/Aaa	13/25	1	2	FACETS	0.282	0.225	0.347	0.282	0.225	0.347	SUBCLONAL	1	TRUE	1	0.48	2		381	414	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515193	149515193	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	36	493	0	ENST00000261799.4:c.289G>T	p.Glu97Ter	p.E97*	ENST00000261799	NM_002609.3	97	Gaa/Taa	3/23	1	2	FACETS	0.231	0.189	0.278	0.231	0.189	0.278	SUBCLONAL	1	TRUE	1	0.48	2		493	649	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057663	180057663	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	78	721	0	ENST00000261937.6:c.292C>A	p.Leu98Met	p.L98M	ENST00000261937	NM_182925.4	98	Ctg/Atg	3/30	1	2	FACETS	0.415	0.364	0.47	0.415	0.364	0.47	SUBCLONAL	1	TRUE	1	0.48	2		721	783	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271393	26271393	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	25	325	0	ENST00000305910.3:c.220G>T	p.Glu74Ter	p.E74*	ENST00000305910	NM_003534.2	74	Gaa/Taa	1/1	1	2	FACETS	0.242	0.19	0.301	0.242	0.19	0.301	SUBCLONAL	1	TRUE	1	0.48	2		325	431	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803500	32803500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550712305	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	210	452	1	ENST00000374899.4:c.659G>A	p.Arg220Gln	p.R220Q	ENST00000374899	NM_018833.2	220	cGa/cAa	4/12	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.48	2		453	686	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288569	33288569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1266548613	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	33	323	1	ENST00000374542.5:c.983G>A	p.Arg328His	p.R328H	ENST00000374542	NM_001141970.1	328	cGt/cAt	3/8	1	2	FACETS	0.357	0.291	0.432	0.357	0.291	0.432	SUBCLONAL	1	TRUE	1	0.48	2		324	385	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120505	94120505	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	54	287	0	ENST00000369303.4:c.546C>A	p.Phe182Leu	p.F182L	ENST00000369303	NM_004440.3	182	ttC/ttA	3/17	1	2	FACETS	0.962	0.831	1	0.962	0.831	1	CLONAL	1	TRUE	1	0.48	2		287	234	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710904	117710904	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	40	301	0	ENST00000368508.3:c.1368G>T	p.Lys456Asn	p.K456N	ENST00000368508	NM_002944.2	456	aaG/aaT	12/43	1	2	FACETS	0.434	0.361	0.515	0.434	0.361	0.515	SUBCLONAL	1	TRUE	1	0.48	2		301	384	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997454	149997454	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	107	405	0	ENST00000253339.5:c.2825A>G	p.Glu942Gly	p.E942G	ENST00000253339		942	gAa/gGa	6/7	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.48	2		405	382	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683734	162683734	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs770994041	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	38	413	0	ENST00000366898.1:c.235G>T	p.Glu79Ter	p.E79*	ENST00000366898	NM_004562.2	79	Gaa/Taa	3/12	1	2	FACETS	0.287	0.237	0.344	0.287	0.237	0.344	SUBCLONAL	1	TRUE	1	0.48	2		413	551	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739875	41739875	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	43	308	0	ENST00000242208.4:c.98C>A	p.Pro33His	p.P33H	ENST00000242208	NM_002192.2	33	cCc/cAc	2/3	1	2	FACETS	0.5	0.42	0.589	0.5	0.42	0.589	SUBCLONAL	1	TRUE	1	0.48	2		308	358	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350062	81350062	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs759145490	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	15	253	0	ENST00000222390.5:c.1270C>T	p.Arg424Cys	p.R424C	ENST00000222390	NM_000601.4	424	Cgt/Tgt	10/18	1	2	FACETS	0.329	0.241	0.434	0.329	0.241	0.434	SUBCLONAL	1	TRUE	1	0.48	2		253	190	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403225	116403225	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	120	437	0	ENST00000397752.3:c.2486A>C	p.Lys829Thr	p.K829T	ENST00000397752	NM_000245.2	829	aAa/aCa	11/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.48	2		437	403	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128848686	128848686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763192441	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	164	432	0	ENST00000249373.3:c.1351C>T	p.Arg451Cys	p.R451C	ENST00000249373	NM_005631.4	451	Cgc/Tgc	7/12	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.48	2		432	555	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506185	148506185	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747933788	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	39	297	0	ENST00000320356.2:c.2173G>A	p.Glu725Lys	p.E725K	ENST00000320356	NM_004456.4	725	Gaa/Aaa	19/20	1	2	FACETS	0.44	0.365	0.523	0.44	0.365	0.523	SUBCLONAL	1	TRUE	1	0.48	2		297	369	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148526853	148526853	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	75	346	0	ENST00000320356.2:c.451A>C	p.Lys151Gln	p.K151Q	ENST00000320356	NM_004456.4	151	Aaa/Caa	5/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.48	2		346	270	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980570	70980570	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	60	472	0	ENST00000276594.2:c.807C>A	p.Phe269Leu	p.F269L	ENST00000276594	NM_024504.3	269	ttC/ttA	4/8	1	2	FACETS	0.484	0.417	0.556	0.484	0.417	0.556	SUBCLONAL	1	TRUE	1	0.48	2		472	517	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212815	27212815	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1307510192	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	161	490	1	ENST00000380036.4:c.2797G>A	p.Ala933Thr	p.A933T	ENST00000380036	NM_000459.3	933	Gcg/Acg	17/23	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.48	2		491	588	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239929	98239929	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	27	332	0	ENST00000331920.6:c.1403C>G	p.Ala468Gly	p.A468G	ENST00000331920	NM_000264.3	468	gCc/gGc	10/24	1	2	FACETS	0.33	0.262	0.407	0.33	0.262	0.407	SUBCLONAL	1	TRUE	1	0.48	2		332	341	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128201272	128201272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779657195	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	111	399	1	ENST00000265960.3:c.1463C>T	p.Ser488Leu	p.S488L	ENST00000265960	NM_001006617.1	488	tCg/tTg	12/12	1	2	FACETS	0.896	0.809	0.988	0.896	0.809	0.988	CLONAL	1	TRUE	1	0.48	2		400	516	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802643	135802643	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	84	290	0	ENST00000298552.3:c.155C>G	p.Thr52Ser	p.T52S	ENST00000298552	NM_001162426.1	52	aCc/aGc	4/23	1	2	FACETS	0.986	0.878	1	0.986	0.878	1	CLONAL	1	TRUE	1	0.48	2		290	355	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034472	47034472	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1267331723	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	17	262	0	ENST00000377604.3:c.557G>A	p.Arg186Gln	p.R186Q	ENST00000377604	NM_001204468.1	186	cGa/cAa	6/24	1	1	FACETS	0.166	0.123	0.217	0.166	0.123	0.217	SUBCLONAL	1	TRUE	0	0.48	1		262	324	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412029	63412029	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754922124	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	26	345	0	ENST00000330258.3:c.1138G>A	p.Glu380Lys	p.E380K	ENST00000330258	NM_152424.3	380	Gag/Aag	2/2	1	1	FACETS	0.344	0.274	0.425	0.344	0.274	0.425	SUBCLONAL	1	TRUE	0	0.48	1		345	239	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907795	76907795	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782646619	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	61	124	0	ENST00000373344.5:c.4366G>A	p.Glu1456Lys	p.E1456K	ENST00000373344	NM_000489.3	1456	Gag/Aag	15/35	1	1	FACETS	0.878	0.789	0.966	1	0.982	1	CLONAL	2	TRUE	0	0.48	1		124	110	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76953080	76953080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	25	210	0	ENST00000373344.5:c.233G>A	p.Arg78Gln	p.R78Q	ENST00000373344	NM_000489.3	78	cGa/cAa	4/35	1	1	FACETS	0.531	0.423	0.652	0.531	0.423	0.652	SUBCLONAL	1	TRUE	0	0.48	1		210	149	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215244	123215244	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	45	143	0	ENST00000218089.9:c.2790G>T	p.Met930Ile	p.M930I	ENST00000218089	NM_001042749.1	930	atG/atT	28/35	1	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.48	1		143	111	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161392	55161392	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767697835	NA	P-0036503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	32	311	0	ENST00000257290.5:c.3223G>A	p.Asp1075Asn	p.D1075N	ENST00000257290	NM_006206.4	1075	Gac/Aac	23/23	1	2	FACETS	0.338	0.274	0.411	0.338	0.274	0.411	SUBCLONAL	1	TRUE	1	0.48	2		311	394	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508169	106508169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381484125	NA	P-0036507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	18	177	0	ENST00000359195.3:c.163G>A	p.Glu55Lys	p.E55K	ENST00000359195	NM_002649.2	55	Gaa/Aaa	2/11	0.211590822922243	3	FACETS	1	0.802	1	0.534	0.404	0.686	CLONAL	1	TRUE	1	0.211590822922243	3		177	176	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45649954	45649954	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs186459476	NA	P-0036507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	27	407	2	ENST00000407780.3:c.881C>T	p.Pro294Leu	p.P294L	ENST00000407780	NM_001283052.1	294	cCg/cTg	6/7	1	2	FACETS	0.727	0.579	0.896	0.727	0.579	0.896	SUBCLONAL	1	TRUE	1	0.211590822922243	2		409	351	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266510	198266510	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	39	322	0	ENST00000335508.6:c.2326G>C	p.Glu776Gln	p.E776Q	ENST00000335508	NM_012433.2	776	Gaa/Caa	16/25	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.211590822922243	2		322	340	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117601	70117602	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	38	557	0	ENST00000245479.2:c.69_70insT	p.Pro24SerfsTer228	p.P24Sfs*228	ENST00000245479	NM_000346.3	23	-/T	1/3	1	2	FACETS	0.813	0.672	0.97	0.813	0.672	0.97	CLONAL	1	TRUE	1	0.211590822922243	2		557	442	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201777	66201777	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	49	435	0	ENST00000273854.3:c.2725C>T	p.Gln909Ter	p.Q909*	ENST00000273854	NM_004439.5	909	Cag/Tag	16/18	0.211590822922243	1	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	0	0.211590822922243	1		435	389	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540238	187540238	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	47	414	0	ENST00000441802.2:c.7502T>G	p.Leu2501Arg	p.L2501R	ENST00000441802	NM_005245.3	2501	cTa/cGa	10/27	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.211590822922243	2		414	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0036509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	515	504	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.546856282221058	3	FACETS	0.931	0.908	0.952			1	CLONAL	3	FALSE	NA	0.815292626650684	3		505	637	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107170	27107170	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs750806872	NA	P-0036509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	249	499	1	ENST00000324856.7:c.6781A>G	p.Ile2261Val	p.I2261V	ENST00000324856	NM_006015.4	2261	Atc/Gtc	20/20	1	2	FACETS	0.924	0.87	0.979	0.924	0.87	0.979	CLONAL	1	FALSE	1	0.815292626650684	2		500	661	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437926	110437987	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCGGCGGCGGGGGGCGCGTCTCCGGCGGCCGCGCGGCCCTCGCTGACCAGGTCGGTGAGC	GCGCGGCGGCGGGGGGCGCGTCTCCGGCGGCCGCGCGGCCCTCGCTGACCAGGTCGGTGAGC	-	novel	NA	P-0036509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	100	4	0	ENST00000375856.3:c.414_475del	p.Leu139ArgfsTer37	p.L139Rfs*37	ENST00000375856	NM_003749.2	138	gcGCTCACCGACCTGGTCAGCGAGGGCCGCGCGGCCGCCGGAGACGCGCCCCCCGCCGCCGCGCcc/gccc	1/2	0.800862347936298	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	FALSE	0	0.815292626650684	2		4	105	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0036510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	239	485	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	0.899788261898425	2		485	514	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0036510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	111	227	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.953	0.872	1	0.953	0.872	1	CLONAL	1	TRUE	1	0.899788261898425	2		227	259	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0036510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	694	946	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	1	0.996	1	1	0.998	1	CLONAL	2	TRUE	1	0.899788261898425	2		947	751	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579506	7579506	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	349	627	0	ENST00000269305.4:c.181G>C	p.Asp61His	p.D61H	ENST00000269305	NM_001126112.2	61	Gat/Cat	4/11	1	2	FACETS	0.987	0.94	1	0.987	0.94	1	CLONAL	1	TRUE	1	0.899788261898425	2		627	786	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649272	23649272	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs202194596	NA	P-0036510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	192	322	0	ENST00000261584.4:c.110G>A	p.Arg37His	p.R37H	ENST00000261584	NM_024675.3	37	cGt/cAt	3/13	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.899788261898425	2		322	407	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579503	7579503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	355	630	0	ENST00000269305.4:c.184G>A	p.Glu62Lys	p.E62K	ENST00000269305	NM_001126112.2	62	Gaa/Aaa	4/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.899788261898425	2		630	783	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874710	151874710	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	190	372	0	ENST00000262189.6:c.7828C>T	p.Arg2610Ter	p.R2610*	ENST00000262189	NM_170606.2	2610	Cga/Tga	38/59	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.899788261898425	2		372	417	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222519	157222519	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554265250	NA	P-0036510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	247	393	0	ENST00000346085.5:c.1786C>T	p.Gln596Ter	p.Q596*	ENST00000346085	NM_020732.3	596	Cag/Tag	4/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.899788261898425	2		393	542	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579882	7579882	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201382018	NA	P-0036510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	281	520	1	ENST00000269305.4:c.31G>A	p.Glu11Lys	p.E11K	ENST00000269305	NM_001126112.2	11	Gag/Aag	2/11	1	2	FACETS	0.967	0.916	1	0.967	0.916	1	CLONAL	1	TRUE	1	0.899788261898425	2		521	646	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425704	49425704	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	275	553	0	ENST00000301067.7:c.12784C>T	p.Gln4262Ter	p.Q4262*	ENST00000301067	NM_003482.3	4262	Caa/Taa	39/54	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.899788261898425	2		553	601	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427414	49427415	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0036510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	295	643	1	ENST00000301067.7:c.11073_11074del	p.Leu3692GlyfsTer20	p.L3692Gfs*20	ENST00000301067	NM_003482.3	3691	tcCCtg/tctg	39/54	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.899788261898425	2		644	654	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786701	3786701	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0036510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	329	552	0	ENST00000262367.5:c.4510A>T	p.Lys1504Ter	p.K1504*	ENST00000262367	NM_004380.2	1504	Aaa/Taa	27/31	1	2	FACETS	0.928	0.882	0.975	0.928	0.882	0.975	CLONAL	1	TRUE	1	0.899788261898425	2		552	788	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579485	7579485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	333	591	0	ENST00000269305.4:c.202G>A	p.Glu68Lys	p.E68K	ENST00000269305	NM_001126112.2	68	Gag/Aag	4/11	1	2	FACETS	0.986	0.938	1	0.986	0.938	1	CLONAL	1	TRUE	1	0.899788261898425	2		591	751	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518162	8518162	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	153	386	0	ENST00000356435.5:c.1229C>A	p.Thr410Lys	p.T410K	ENST00000356435		410	aCa/aAa	10/35	1	2	FACETS	0.827	0.765	0.891	0.827	0.765	0.891	CLONAL	1	TRUE	1	0.899788261898425	2		386	411	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137320984	137320984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	336	673	2	ENST00000481739.1:c.941C>T	p.Ser314Phe	p.S314F	ENST00000481739	NM_002957.4	314	tCc/tTc	7/10	1	2	FACETS	0.967	0.92	1	0.967	0.92	1	CLONAL	1	TRUE	1	0.899788261898425	2		675	772	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939919	76939924	+	inframe_deletion	In_Frame_Del	DEL	CCAAGT	CCAAGT	-	novel	NA	P-0036510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	280	503	0	ENST00000373344.5:c.824_829del	p.Asp275_Leu276del	p.D275_L276del	ENST00000373344	NM_000489.3	275	gACTTGGtc/gtc	9/35	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.899788261898425	2		503	620	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287234	46287234	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	26	345	0	ENST00000334344.6:c.5179C>A	p.Pro1727Thr	p.P1727T	ENST00000334344	NM_152641.2	1727	Cct/Act	19/21	0.208786197820839	3	FACETS	0.969	0.768	1	0.484	0.384	0.599	CLONAL	1	TRUE	1	0.18	3		345	325	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061212	38061232	+	inframe_deletion	In_Frame_Del	DEL	GTAGCAGCCGTTCTCGAACAT	GTAGCAGCCGTTCTCGAACAT	-	novel	NA	P-0036511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	29	447	0	ENST00000250448.2:c.757_777del	p.Met253_Tyr259del	p.M253_Y259del	ENST00000250448	NM_004496.3	253	ATGTTCGAGAACGGCTGCTAC/-	2/2	1	2	FACETS	0.806	0.646	0.987	0.806	0.646	0.987	CLONAL	1	TRUE	1	0.18	2		447	400	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871865	12871865	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	23	124	0	ENST00000228872.4:c.583del	p.Arg195AspfsTer30	p.R195Dfs*30	ENST00000228872	NM_004064.3	194	agA/ag	2/3	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.18	2		124	173	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978967	25978967	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0036511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	22	335	0	ENST00000435504.4:c.956T>A	p.Leu319Ter	p.L319*	ENST00000435504		319	tTa/tAa	10/13	1	2	FACETS	0.998	0.775	1	0.998	0.775	1	CLONAL	1	TRUE	1	0.18	2		335	245	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922294	178922294	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	18	276	0	ENST00000263967.3:c.1063T>C	p.Tyr355His	p.Y355H	ENST00000263967	NM_006218.2	355	Tat/Cat	6/21	1	2	FACETS	0.901	0.68	1	0.901	0.68	1	CLONAL	1	TRUE	1	0.18	2		276	222	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0036513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	11	359	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.185	0.127	0.258	0.185	0.127	0.258	SUBCLONAL	1	TRUE	1	0.262023632498035	2		359	454	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0036513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	66	532	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.933	0.811	1	0.933	0.811	1	CLONAL	1	TRUE	1	0.262023632498035	2		532	540	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313149	30313149	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	38	543	0	ENST00000262643.3:c.843del	p.Leu282TrpfsTer31	p.L282Wfs*31	ENST00000262643	NM_001238.2	281	ctG/ct	10/12	1	2	FACETS	0.537	0.443	0.642	0.537	0.443	0.642	SUBCLONAL	1	TRUE	1	0.262023632498035	2		543	540	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	186	726	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.601057775470062	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.601057775470062	1		726	420	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372098	55372098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs62642516	NA	P-0036514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	102	390	0	ENST00000297316.4:c.788C>T	p.Pro263Leu	p.P263L	ENST00000297316	NM_022454.3	263	cCg/cTg	2/2	0.558058958721471	4	FACETS	0.652	0.583	0.726	0.217	0.194	0.242	SUBCLONAL	1	TRUE	1	0.601057775470062	4		390	833	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157256708	157256708	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	84	148	0	ENST00000346085.5:c.2035C>T	p.Pro679Ser	p.P679S	ENST00000346085	NM_020732.3	679	Cca/Tca	5/20	0.601057775470062	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.601057775470062	1		148	176	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177395	56177399	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	ONP	AGGTA	AGGTA	CGGTG	novel	NA	P-0036514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	93	266	0	ENST00000399503.3:c.2370-2_2372delinsCGGTG		p.X790_splice	ENST00000399503	NM_005921.1	790		14/20	0.190850870633475	4	FACETS	0.765	0.687	0.845	0.765	0.687	0.845	INDETERMINATE	2	TRUE	2	0.601057775470062	4		266	324	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0036515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	314	513	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.686752328773398	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.697951384372609	2		513	438	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40491369	40491369	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	199	497	0	ENST00000264657.5:c.431T>C	p.Leu144Pro	p.L144P	ENST00000264657	NM_139276.2	144	cTg/cCg	5/24	0.686752328773398	2	FACETS	1	0.97	1	0.534	0.498	0.57	CLONAL	1	TRUE	0	0.697951384372609	2		497	534	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380522	31380522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1013448701	NA	P-0036515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	105	418	0	ENST00000328111.2:c.1012G>A	p.Gly338Arg	p.G338R	ENST00000328111	NM_006892.3	338	Ggg/Agg	9/23	0.617899023244422	4	FACETS	1	0.917	1	0.511	0.46	0.565	CLONAL	1	TRUE	2	0.697951384372609	4		418	500	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0036522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	53	303	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.194058476681302	3	FACETS	1	0.86	1	0.505	0.43	0.587	CLONAL	1	TRUE	1	0.193989821215241	3		303	594	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317461	1317461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781459586	NA	P-0036522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	56	658	1	ENST00000400841.2:c.604G>A	p.Asp202Asn	p.D202N	ENST00000400841		202	Gac/Aac	5/6	0.168982439839006	0	FACETS	0.447	0.382	0.52			1	SUBCLONAL	1	TRUE	NA	0.193989821215241	0		659	1040	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735510	204735510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759232662	NA	P-0036522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	56	406	0	ENST00000302823.3:c.311C>T	p.Thr104Met	p.T104M	ENST00000302823	NM_005214.4	104	aCg/aTg	2/4	1	2	FACETS	0.891	0.763	1	0.891	0.763	1	CLONAL	1	TRUE	1	0.193989821215241	2		406	648	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968233	134968233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753895808	NA	P-0036522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	221	562	0	ENST00000398015.3:c.2746G>A	p.Val916Met	p.V916M	ENST00000398015	NM_004441.4	916	Gtg/Atg	15/16	0.165221962304171	3	FACETS	0.951	0.886	1	0.951	0.886	1	CLONAL	3	TRUE	0	0.193989821215241	3		562	876	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575068	48575068	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0036522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	63	367	0	ENST00000342988.3:c.262A>T	p.Lys88Ter	p.K88*	ENST00000342988	NM_005359.5	88	Aaa/Taa	3/12	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.193989821215241	2		367	547	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339554	81339554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs571102402	NA	P-0036522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	44	448	0	ENST00000222390.5:c.1450G>A	p.Val484Ile	p.V484I	ENST00000222390	NM_000601.4	484	Gta/Ata	13/18	0.194058476681302	3	FACETS	0.677	0.566	0.8	0.339	0.283	0.4	SUBCLONAL	1	TRUE	1	0.193989821215241	3		448	735	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406637	70406637	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	68	595	0	ENST00000373644.4:c.4152del	p.Glu1384AspfsTer17	p.E1384Dfs*17	ENST00000373644	NM_030625.2	1384	gAa/ga	4/12	1	2	FACETS	0.789	0.685	0.903	0.789	0.685	0.903	CLONAL	1	TRUE	1	0.193989821215241	2		595	888	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881350	37881350	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	101	654	2	ENST00000269571.5:c.2542G>A	p.Ala848Thr	p.A848T	ENST00000269571		848	Gct/Act	21/27	1	2	FACETS	0.973	0.868	1	0.973	0.868	1	CLONAL	1	TRUE	1	0.193989821215241	2		656	1070	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562645	29562645	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	163	517	0	ENST00000356175.3:c.3725T>G	p.Val1242Gly	p.V1242G	ENST00000356175	NM_000267.3	1242	gTt/gGt	28/57	0.717089244684105	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.725285170522619	2		517	214	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912144	76912144	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0036523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	67	321	0	ENST00000373344.5:c.4121-1G>A		p.X1374_splice	ENST00000373344	NM_000489.3	1374			0.725285170522619	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.725285170522619	2		321	87	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894229	NA	P-0036529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	299	422	0	ENST00000451590.1:c.34G>T	p.Gly12Cys	p.G12C	ENST00000451590	NM_001130442.1	12	Ggc/Tgc	2/5	0.216764067759299	1	FACETS	0.968	0.916	1	1	0.996	1	CLONAL	2	TRUE	0	0.31462873640787	1		422	827	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057979	27057979	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	180	512	0	ENST00000324856.7:c.1687C>T	p.Gln563Ter	p.Q563*	ENST00000324856	NM_006015.4	563	Cag/Tag	3/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.31462873640787	2		512	854	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027168	49027168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913305	NA	P-0036529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	116	343	0	ENST00000267163.4:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	579	Cga/Tga	18/27	0.31462873640787	1	FACETS	0.969	0.875	1	0.969	0.875	1	CLONAL	1	TRUE	0	0.31462873640787	1		343	641	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717607	89717614	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGATCCT	CAGATCCT	-	novel	NA	P-0036529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	87	298	0	ENST00000371953.3:c.635_642del		p.X212_splice	ENST00000371953	NM_000314.4	212		7/9	0.31462873640787	1	FACETS	0.947	0.842	1	0.947	0.842	1	CLONAL	1	TRUE	0	0.31462873640787	1		298	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577090	+	inframe_deletion	In_Frame_Del	DEL	CCTCTGTGC	CCTCTGTGC	-	novel	NA	P-0036529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	178	620	0	ENST00000269305.4:c.848_856del	p.Arg283_Glu286delinsGln	p.R283_E286delinsQ	ENST00000269305	NM_001126112.2	283	cGCACAGAGGaa/caa	8/11	0.31462873640787	1	FACETS	0.991	0.913	1	0.991	0.913	1	CLONAL	1	TRUE	0	0.31462873640787	1		620	962	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645944	215645945	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0036529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	103	484	0	ENST00000260947.4:c.653_654delinsCT	p.Trp218Ser	p.W218S	ENST00000260947	NM_000465.2	218	tGG/tCT	4/11	1	2	FACETS	0.734	0.656	0.817	0.734	0.656	0.817	SUBCLONAL	1	TRUE	1	0.31462873640787	2		484	892	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661789	227661789	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	160	573	0	ENST00000305123.5:c.1666C>A	p.Pro556Thr	p.P556T	ENST00000305123	NM_005544.2	556	Cct/Act	1/2	1	2	FACETS	0.988	0.905	1	0.988	0.905	1	CLONAL	1	TRUE	1	0.31462873640787	2		573	1029	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671451	30671451	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	150	655	0	ENST00000376406.3:c.5509G>C	p.Val1837Leu	p.V1837L	ENST00000376406	NM_014641.2	1837	Gtg/Ctg	10/15	1	2	FACETS	0.838	0.764	0.915	0.838	0.764	0.915	CLONAL	1	TRUE	1	0.31462873640787	2		655	1138	SUCCESS
AR	367	MSKCC	GRCh37	X	66766305	66766305	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	57	299	0	ENST00000374690.3:c.1317C>A	p.Phe439Leu	p.F439L	ENST00000374690	NM_000044.3	439	ttC/ttA	1/8	1	2	FACETS	0.677	0.581	0.782	0.677	0.581	0.782	SUBCLONAL	1	TRUE	1	0.31462873640787	2		299	535	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855227	76855227	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	105	432	0	ENST00000373344.5:c.5760G>T	p.Met1920Ile	p.M1920I	ENST00000373344	NM_000489.3	1920	atG/atT	24/35	1	2	FACETS	0.811	0.726	0.901	0.811	0.726	0.901	CLONAL	1	TRUE	1	0.31462873640787	2		432	823	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227882	123227882	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	90	301	0	ENST00000218089.9:c.3593G>C	p.Ser1198Thr	p.S1198T	ENST00000218089	NM_001042749.1	1198	aGc/aCc	33/35	1	2	FACETS	0.988	0.878	1	0.988	0.878	1	CLONAL	1	TRUE	1	0.31462873640787	2		301	579	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726612	46726612	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	71	442	0	ENST00000371975.4:c.693del	p.Lys232AsnfsTer20	p.K232Nfs*20	ENST00000371975	NM_003579.3	231	Ggg/gg	7/18	1	2	FACETS	0.897	0.784	1	0.897	0.784	1	CLONAL	1	TRUE	1	0.270040018453772	2		442	586	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968563	55968563	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	96	533	0	ENST00000263923.4:c.2100G>T	p.Trp700Cys	p.W700C	ENST00000263923	NM_002253.2	700	tgG/tgT	14/30	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.270040018453772	2		533	705	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526298	31526298	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	144	752	2	ENST00000344624.3:c.742G>A	p.Asp248Asn	p.D248N	ENST00000344624		248	Gat/Aat	2/33	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.270040018453772	2		754	1048	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0036531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	122	485	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.553959187178002	5	FACETS	0.701	0.632	0.773	0.175	0.158	0.194	SUBCLONAL	1	TRUE	1	0.626980762580236	5		485	1078	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434618	49434618	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	277	696	4	ENST00000301067.7:c.6935C>A	p.Ser2312Ter	p.S2312*	ENST00000301067	NM_003482.3	2312	tCa/tAa	31/54	1	2	FACETS	0.918	0.863	0.973	0.918	0.863	0.973	CLONAL	1	TRUE	1	0.626980762580236	2		700	963	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434654	49434654	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs757251259	NA	P-0036531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	305	743	3	ENST00000301067.7:c.6899G>T	p.Gly2300Val	p.G2300V	ENST00000301067	NM_003482.3	2300	gGg/gTg	31/54	1	2	FACETS	0.924	0.872	0.978	0.924	0.872	0.978	CLONAL	1	TRUE	1	0.626980762580236	2		746	1053	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444775	49444779	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTC	CTCTC	-	novel	NA	P-0036531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	284	734	5	ENST00000301067.7:c.2687_2691del	p.Gly896AlafsTer5	p.G896Afs*5	ENST00000301067	NM_003482.3	896	gGAGAG/g	10/54	1	2	FACETS	0.88	0.828	0.934	0.88	0.828	0.934	CLONAL	1	TRUE	1	0.626980762580236	2		739	1029	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0036532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	83	359	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.21	2		359	718	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123788	11123788	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1064795105	NA	P-0036532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	51	494	0	ENST00000358026.2:c.2438C>T	p.Ser813Leu	p.S813L	ENST00000358026	NM_001128849.1	813	tCa/tTa	16/36	1	2	FACETS	0.661	0.56	0.772	0.661	0.56	0.772	SUBCLONAL	1	TRUE	1	0.21	2		494	735	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589557	67589562	+	inframe_deletion	In_Frame_Del	DEL	TAATAT	TAATAT	-	novel	NA	P-0036532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	14	140	0	ENST00000274335.5:c.1321_1326del	p.Asn441_Ile442del	p.N441_I442del	ENST00000274335		440	gaTAATATt/gat	10/15	1	2	FACETS	0.601	0.434	0.801	0.601	0.434	0.801	SUBCLONAL	1	TRUE	1	0.21	2		140	222	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0036533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	53	469	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.609	0.519	0.709	0.609	0.519	0.709	SUBCLONAL	1	TRUE	1	0.26	2		469	669	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971170	21971170	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	40	309	0	ENST00000304494.5:c.188T>A	p.Leu63Gln	p.L63Q	ENST00000304494	NM_000077.4	63	cTg/cAg	2/3	1	2	FACETS	0.993	0.828	1	0.993	0.828	1	CLONAL	1	TRUE	1	0.26	2		309	310	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233744	133233744	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	60	495	0	ENST00000320574.5:c.3560T>G	p.Phe1187Cys	p.F1187C	ENST00000320574	NM_006231.2	1187	tTc/tGc	29/49	1	2	FACETS	0.8	0.689	0.92	0.8	0.689	0.92	CLONAL	1	TRUE	1	0.26	2		495	577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578374	7578375	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0036533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	55	594	0	ENST00000269305.4:c.555dup	p.Asp186ArgfsTer23	p.D186Rfs*23	ENST00000269305	NM_001126112.2	185	-/C	5/11	1	2	FACETS	0.794	0.679	0.919	0.794	0.679	0.919	CLONAL	1	TRUE	1	0.26	2		594	533	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0036535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	105	485	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.569273141161373	3	FACETS	0.894	0.815	0.975	0.894	0.815	0.975	CLONAL	2	TRUE	1	0.569273141161373	3		485	265	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412303	139412303	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs869025494	NA	P-0036535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	201	655	0	ENST00000277541.6:c.1342C>T	p.Arg448Ter	p.R448*	ENST00000277541	NM_017617.3	448	Cga/Tga	8/34	0.569273141161373	2	FACETS	0.903	0.839	0.969	0.452	0.419	0.485	CLONAL	1	TRUE	0	0.569273141161373	2		655	782	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150039	202150039	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1368296717	NA	P-0036535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	161	479	0	ENST00000358485.4:c.1480C>T	p.Arg494Ter	p.R494*	ENST00000358485	NM_001080125.1	494	Cga/Tga	8/9	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.569273141161373	2		479	564	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632477	3632477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371875095	NA	P-0036535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	218	738	0	ENST00000294008.3:c.5371C>T	p.Arg1791Cys	p.R1791C	ENST00000294008	NM_032444.2	1791	Cgt/Tgt	15/15	0.11198714230631	6	FACETS	0.776	0.722	0.833			1	INDETERMINATE	2	TRUE	NA	0.569273141161373	6		738	1055	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512239	120512239	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1557826752	NA	P-0036535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	139	479	0	ENST00000256646.2:c.1003T>C	p.Cys335Arg	p.C335R	ENST00000256646	NM_024408.3	335	Tgc/Cgc	6/34	1	2	FACETS	0.885	0.809	0.963	0.885	0.809	0.963	CLONAL	1	TRUE	1	0.569273141161373	2		479	552	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685275	89685275	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	52	213	0	ENST00000371953.3:c.170T>C	p.Leu57Ser	p.L57S	ENST00000371953	NM_000314.4	57	tTg/tCg	3/9	0.569273141161373	1	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	0	0.569273141161373	1		213	126	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448682	49448682	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0036535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	117	362	0	ENST00000301067.7:c.176+1G>A		p.X59_splice	ENST00000301067	NM_003482.3	59			1	2	FACETS	0.89	0.807	0.976	0.89	0.807	0.976	CLONAL	1	TRUE	1	0.569273141161373	2		362	462	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871819	35871820	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	182	506	0	ENST00000216797.5:c.686dup	p.Asn229LysfsTer3	p.N229Kfs*3	ENST00000216797	NM_020529.2	229	aat/aaAt	5/6	1	2	FACETS	0.966	0.895	1	0.966	0.895	1	CLONAL	1	TRUE	1	0.569273141161373	2		506	662	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991274	41991274	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	111	375	0	ENST00000219905.7:c.2105G>C	p.Arg702Thr	p.R702T	ENST00000219905	NM_001164273.1	702	aGa/aCa	5/24	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.569273141161373	2		375	367	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413167	139413167	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	224	737	0	ENST00000277541.6:c.975C>G	p.Asn325Lys	p.N325K	ENST00000277541	NM_017617.3	325	aaC/aaG	6/34	0.569273141161373	2	FACETS	0.978	0.913	1	0.489	0.456	0.522	CLONAL	1	TRUE	0	0.569273141161373	2		737	805	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161757	47161757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761450181	NA	P-0036545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	44	313	0	ENST00000409792.3:c.4369C>T	p.Pro1457Ser	p.P1457S	ENST00000409792	NM_014159.6	1457	Cca/Tca	3/21	0.266349251343866	1	FACETS	0.131	0.11	0.155	0.131	0.11	0.155	INDETERMINATE	1	TRUE	0	0.890715927781094	1		313	417	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413650	138413650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs78077615	NA	P-0036545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	107	388	0	ENST00000289153.2:c.1870G>A	p.Val624Ile	p.V624I	ENST00000289153	NM_006219.2	624	Gta/Ata	12/22	1	2	FACETS	0.438	0.394	0.485	0.438	0.394	0.485	SUBCLONAL	1	TRUE	1	0.890715927781094	2		388	548	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752961	128752962	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAA	novel	NA	P-0036545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	234	347	0	ENST00000377970.2:c.1124_1125insAAA	p.His374_Asn375insLys	p.H374_N375insK	ENST00000377970	NM_002467.4	374	-/AAA	3/3	0.202800681862385	5	FACETS	0.849	0.802	0.896			1	INDETERMINATE	3	TRUE	NA	0.890715927781094	5		347	482	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969321	44969337	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGGTGGAGGTTTTTGA	CAGGTGGAGGTTTTTGA	AC	novel	NA	P-0036545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	341	165	1	ENST00000377967.4:c.4006-3_4019delinsAC		p.X1336_splice	ENST00000377967	NM_021140.2	1336		28/29	0.843476893986745	2	FACETS	1	0.99	1			1	CLONAL	2	TRUE	NA	0.890715927781094	2		166	375	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0036547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	86	569	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.46821378893879	3	FACETS	1	0.959	1	0.57	0.511	0.631	CLONAL	1	TRUE	1	0.764231177512672	3		569	273	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0036547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	36	405	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.504	0.419	0.597	0.504	0.419	0.597	SUBCLONAL	1	TRUE	1	0.764231177512672	2		405	187	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0036547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	47	530	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.591	0.505	0.684	0.591	0.505	0.684	SUBCLONAL	1	TRUE	1	0.764231177512672	2		530	208	SUCCESS
APC	324	MSKCC	GRCh37	5	112175761	112175761	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	55	293	0	ENST00000257430.4:c.4473del	p.Phe1491LeufsTer16	p.F1491Lfs*16	ENST00000257430	NM_000038.5	1490	caT/ca	16/16	1	2	FACETS	0.523	0.451	0.601	0.523	0.451	0.601	SUBCLONAL	1	TRUE	1	0.764231177512672	2		293	275	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436553	49436553	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778461	NA	P-0036547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	286	731	0	ENST00000301067.7:c.5753G>A	p.Arg1918His	p.R1918H	ENST00000301067	NM_003482.3	1918	cGt/cAt	26/54	0.46821378893879	3	FACETS	1	0.993	1	0.681	0.644	0.72	CLONAL	1	TRUE	1	0.764231177512672	3		731	759	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11264751	11264751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1384864432	NA	P-0036547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	135	560	0	ENST00000361445.4:c.3811G>A	p.Ala1271Thr	p.A1271T	ENST00000361445	NM_004958.3	1271	Gct/Act	26/58	1	2	FACETS	0.594	0.542	0.648	0.594	0.542	0.648	SUBCLONAL	1	TRUE	1	0.764231177512672	2		560	595	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934229	48934229	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	43	420	0	ENST00000267163.4:c.684A>C	p.Lys228Asn	p.K228N	ENST00000267163	NM_000321.2	228	aaA/aaC	7/27	1	2	FACETS	0.469	0.395	0.549	0.469	0.395	0.549	SUBCLONAL	1	TRUE	1	0.764231177512672	2		420	240	SUCCESS
APC	324	MSKCC	GRCh37	5	112175399	112175399	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	45	280	0	ENST00000257430.4:c.4111del	p.Ser1371ValfsTer44	p.S1371Vfs*44	ENST00000257430	NM_000038.5	1370	Aaa/aa	16/16	1	2	FACETS	0.548	0.465	0.637	0.548	0.465	0.637	SUBCLONAL	1	TRUE	1	0.764231177512672	2		280	215	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044425	5044425	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	91	469	0	ENST00000381652.3:c.373T>C	p.Cys125Arg	p.C125R	ENST00000381652	NM_004972.3	125	Tgc/Cgc	5/25	1	2	FACETS	0.608	0.543	0.675	0.608	0.543	0.675	SUBCLONAL	1	TRUE	1	0.764231177512672	2		469	392	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900180	101900180	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	44	294	0	ENST00000374994.4:c.614T>G	p.Ile205Ser	p.I205S	ENST00000374994	NM_004612.2	205	aTt/aGt	4/9	1	2	FACETS	0.582	0.494	0.676	0.582	0.494	0.676	SUBCLONAL	1	TRUE	1	0.764231177512672	2		294	198	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911492	101911492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	35	279	0	ENST00000374994.4:c.1417G>A	p.Glu473Lys	p.E473K	ENST00000374994	NM_004612.2	473	Gaa/Aaa	9/9	1	2	FACETS	0.523	0.434	0.621	0.523	0.434	0.621	SUBCLONAL	1	TRUE	1	0.764231177512672	2		279	175	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0036548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	76	212	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.985	0.874	1	0.985	0.874	1	CLONAL	1	TRUE	1	0.561337057950947	2		212	275	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579361	7579361	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1064796722	NA	P-0036548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	419	500	0	ENST00000269305.4:c.326T>C	p.Phe109Ser	p.F109S	ENST00000269305	NM_001126112.2	109	tTc/tCc	4/11	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.561337057950947	2		500	679	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52676048	52676048	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	52	316	0	ENST00000394830.3:c.1009G>T	p.Val337Leu	p.V337L	ENST00000394830	NM_018313.4	337	Gta/Tta	11/30	0.554349474460803	1	FACETS	0.427	0.366	0.494	0.427	0.366	0.494	SUBCLONAL	1	TRUE	0	0.561337057950947	1		316	312	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0036549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	292	531	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	0.639382683596972	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.702288184518388	4		531	660	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222982	1222982	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs727504172	NA	P-0036549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	195	448	0	ENST00000326873.7:c.921-2A>T		p.X307_splice	ENST00000326873	NM_000455.4	307			0.511560043871824	4	FACETS	0.894	0.834	0.954	0.894	0.834	0.954	CLONAL	2	TRUE	2	0.702288184518388	4		448	529	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165701	185165701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	98	341	1	ENST00000265026.3:c.976C>T	p.Arg326Trp	p.R326W	ENST00000265026	NM_004721.4	326	Cgg/Tgg	5/14	0.700668136484831	3	FACETS	0.891	0.8	0.987	0.446	0.4	0.494	CLONAL	1	TRUE	1	0.702288184518388	3		342	423	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020177	123020177	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	142	684	0	ENST00000355640.3:c.665G>T	p.Arg222Leu	p.R222L	ENST00000355640		222	cGa/cTa	2/7	0.706819078092842	3	FACETS	0.822	0.751	0.896	0.411	0.375	0.448	CLONAL	1	TRUE	1	0.702288184518388	3		684	665	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699474	117699474	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	105	442	0	ENST00000369458.3:c.167G>T	p.Cys56Phe	p.C56F	ENST00000369458	NM_024626.3	56	tGc/tTc	3/6	0.241478172620947	3	FACETS	1	0.971	1	0.594	0.538	0.652	INDETERMINATE	1	TRUE	1	0.702288184518388	3		442	340	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572565	64572565	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	132	533	1	ENST00000312049.6:c.1291G>T	p.Val431Leu	p.V431L	ENST00000312049	NM_130799.2	431	Gtg/Ttg	9/10	0.706819078092842	3	FACETS	1	0.942	1	0.52	0.475	0.567	CLONAL	1	TRUE	1	0.702288184518388	3		534	488	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575073	64575073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	300	566	0	ENST00000312049.6:c.734C>T	p.Pro245Leu	p.P245L	ENST00000312049	NM_130799.2	245	cCt/cTt	4/10	0.706819078092842	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.702288184518388	3		566	546	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206683	108206683	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	66	264	0	ENST00000278616.4:c.8263T>G	p.Tyr2755Asp	p.Y2755D	ENST00000278616	NM_000051.3	2755	Tat/Gat	56/63	0.613328673369023	1	FACETS	0.96	0.863	1	0.96	0.863	1	CLONAL	1	TRUE	0	0.702288184518388	1		264	127	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349400	73349400	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	177	423	0	ENST00000377767.4:c.936T>G	p.Asp312Glu	p.D312E	ENST00000377767	NM_014953.3	312	gaT/gaG	6/21	0.706819078092842	3	FACETS	0.938	0.878	0.998	0.938	0.878	0.998	CLONAL	2	TRUE	1	0.702288184518388	3		423	363	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042061	14042061	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	194	313	0	ENST00000311895.7:c.2608G>T	p.Val870Phe	p.V870F	ENST00000311895	NM_005236.2	870	Gtt/Ttt	11/11	0.639382683596972	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.702288184518388	4		313	453	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207033	1207033	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0036549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	279	648	1	ENST00000326873.7:c.121A>T	p.Lys41Ter	p.K41*	ENST00000326873	NM_000455.4	41	Aag/Tag	1/10	0.511560043871824	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.702288184518388	4		649	643	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795243	42795243	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367942692	NA	P-0036549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	288	627	0	ENST00000575354.2:c.2323C>T	p.Pro775Ser	p.P775S	ENST00000575354	NM_015125.3	775	Ccc/Tcc	10/20	0.511560043871824	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.702288184518388	4		627	656	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645858	215645858	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	122	615	0	ENST00000260947.4:c.740C>G	p.Ser247Cys	p.S247C	ENST00000260947	NM_000465.2	247	tCt/tGt	4/11	0.700668136484831	3	FACETS	0.891	0.809	0.976	0.445	0.404	0.488	CLONAL	1	TRUE	1	0.702288184518388	3		615	527	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627232	12627232	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	205	390	0	ENST00000251849.4:c.1484G>T	p.Arg495Leu	p.R495L	ENST00000251849	NM_002880.3	495	cGc/cTc	14/17	0.1864686227865	5	FACETS	0.927	0.872	0.983			1	INDETERMINATE	3	TRUE	NA	0.702288184518388	5		390	431	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094865	143094865	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs561832739	NA	P-0036549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	111	540	0	ENST00000262992.4:c.1279C>A	p.His427Asn	p.H427N	ENST00000262992	NM_001101669.1	427	Cat/Aat	14/24	0.706819078092842	3	FACETS	0.96	0.868	1	0.48	0.434	0.528	CLONAL	1	TRUE	1	0.702288184518388	3		540	445	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952462	38952462	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs775622112	NA	P-0036549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	25	332	0	ENST00000357387.3:c.2963A>G	p.His988Arg	p.H988R	ENST00000357387	NM_152756.3	988	cAc/cGc	30/38	0.639382683596972	4	FACETS	0.291	0.229	0.363	0.146	0.114	0.182	SUBCLONAL	1	TRUE	2	0.702288184518388	4		332	416	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146121	38146121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	375	716	1	ENST00000317025.8:c.3385C>T	p.Pro1129Ser	p.P1129S	ENST00000317025	NM_023034.1	1129	Cca/Tca	19/24	0.639382683596972	4	FACETS	0.991	0.945	1	0.991	0.945	1	CLONAL	2	TRUE	2	0.702288184518388	4		717	917	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74868151	74868151	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	64	187	0	ENST00000284811.8:c.143G>T	p.Gly48Val	p.G48V	ENST00000284811		48	gGc/gTc	3/4	0.639382683596972	4	FACETS	0.976	0.866	1	0.976	0.866	1	CLONAL	2	TRUE	2	0.702288184518388	4		187	159	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045527	47045527	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	244	518	0	ENST00000377604.3:c.2494G>T	p.Glu832Ter	p.E832*	ENST00000377604	NM_001204468.1	832	Gag/Tag	22/24	0.639382683596972	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	2	0.702288184518388	4		518	577	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338665	70338665	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	149	503	1	ENST00000374080.3:c.61C>T	p.Pro21Ser	p.P21S	ENST00000374080		21	Cct/Tct	1/45	0.706819078092842	3	FACETS	1	0.963	1	0.541	0.497	0.586	CLONAL	1	TRUE	1	0.702288184518388	3		504	530	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0036552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	27	286	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.768	0.61	0.95	0.768	0.61	0.95	CLONAL	1	TRUE	1	0.14	2		286	502	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922364	178922364	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	28	318	0	ENST00000263967.3:c.1133G>T	p.Cys378Phe	p.C378F	ENST00000263967	NM_006218.2	378	tGt/tTt	6/21	1	2	FACETS	0.758	0.604	0.933	0.758	0.604	0.933	CLONAL	1	TRUE	1	0.14	2		318	528	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936093	178936093	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913275	NA	P-0036552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	35	571	0	ENST00000263967.3:c.1635G>T	p.Glu545Asp	p.E545D	ENST00000263967	NM_006218.2	545	gaG/gaT	10/21	1	2	FACETS	0.726	0.593	0.876	0.726	0.593	0.876	SUBCLONAL	1	TRUE	1	0.14	2		571	689	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717715	89717716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587782341	NA	P-0036552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	75	375	0	ENST00000371953.3:c.741dup	p.Pro248ThrfsTer5	p.P248Tfs*5	ENST00000371953	NM_000314.4	247	tta/ttAa	7/9	1	2	FACETS	0.917	0.805	1	1	0.981	1	CLONAL	2	TRUE	1	0.14	2		375	584	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082316	16082317	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	66	835	0	ENST00000281043.3:c.130_131delinsTT	p.Pro44Phe	p.P44F	ENST00000281043	NM_005378.4	44	CCc/TTc	2/3	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.14	2		835	921	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0036553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	143	321	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.335754509103066	3	FACETS	0.939	0.864	1	0.626	0.576	0.678	CLONAL	2	TRUE	0	0.431418675425411	3		321	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs17849781	NA	P-0036553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	206	621	0	ENST00000269305.4:c.832C>G	p.Pro278Ala	p.P278A	ENST00000269305	NM_001126112.2	278	Cct/Gct	8/11	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.431418675425411	2		621	783	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979319	40979319	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1217327426	NA	P-0036553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	170	533	1	ENST00000373198.4:c.1814C>T	p.Thr605Met	p.T605M	ENST00000373198	NM_133170.3	605	aCg/aTg	11/32	0.431418675425411	4	FACETS	0.987	0.906	1			1	CLONAL	1	TRUE	NA	0.431418675425411	4		534	1143	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792016	42792017	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAAA	novel	NA	P-0036553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	51	534	0	ENST00000575354.2:c.824_827dup	p.Ser277GlufsTer39	p.S277Efs*39	ENST00000575354	NM_015125.3	274	cga/cGAAAga	6/20	0.280427399568639	3	FACETS	0.374	0.317	0.437	0.125	0.105	0.146	SUBCLONAL	1	TRUE	0	0.431418675425411	3		534	769	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383490	31383490	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	59	486	0	ENST00000328111.2:c.1287C>A	p.Ser429Arg	p.S429R	ENST00000328111	NM_006892.3	429	agC/agA	12/23	0.431418675425411	6	FACETS	0.474	0.407	0.549			1	SUBCLONAL	1	TRUE	NA	0.431418675425411	6		486	1074	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755554	39755554	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	33	407	1	ENST00000288319.7:c.1211C>A	p.Pro404Gln	p.P404Q	ENST00000288319	NM_182918.3	404	cCg/cAg	10/10	1	2	FACETS	0.313	0.255	0.38	0.313	0.255	0.38	SUBCLONAL	1	TRUE	1	0.431418675425411	2		408	488	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900135	151900171	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTGCTCACTCCAGCCTGAAACAACAGTCACATTTAT	ACTGCTCACTCCAGCCTGAAACAACAGTCACATTTAT	-	novel	NA	P-0036553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	41	279	0	ENST00000262189.6:c.3962-22_3976del		p.X1321_splice	ENST00000262189	NM_170606.2	1321		26/59	0.348705999296233	4	FACETS	0.55	0.458	0.652	0.275	0.229	0.326	SUBCLONAL	1	TRUE	2	0.431418675425411	4		279	495	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0036554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	116	303	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.876	0.793	0.963	0.876	0.793	0.963	CLONAL	1	TRUE	1	0.509058344629217	2		303	520	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	65	214	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.793	0.693	0.9	0.793	0.693	0.9	SUBCLONAL	1	TRUE	1	0.509058344629217	2		214	322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0036554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	235	544	0	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	0.509058344629217	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.509058344629217	1		544	560	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661861	29661861	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	117	404	0	ENST00000356175.3:c.5755G>C	p.Glu1919Gln	p.E1919Q	ENST00000356175	NM_000267.3	1919	Gaa/Caa	39/57	1	2	FACETS	0.819	0.741	0.901	0.819	0.741	0.901	CLONAL	1	TRUE	1	0.509058344629217	2		404	561	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350558	15350558	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747411770	NA	P-0036554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	165	627	0	ENST00000263377.2:c.3357C>G	p.Ile1119Met	p.I1119M	ENST00000263377	NM_058243.2	1119	atC/atG	16/20	1	2	FACETS	0.976	0.9	1	0.976	0.9	1	CLONAL	1	TRUE	1	0.509058344629217	2		627	664	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0036555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	119	452	0	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.27	2		452	662	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2194565	2194565	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	30	305	0	ENST00000398665.3:c.640G>T	p.Ala214Ser	p.A214S	ENST00000398665	NM_032482.2	214	Gca/Tca	7/28	1	2	FACETS	0.506	0.407	0.618	0.506	0.407	0.618	SUBCLONAL	1	TRUE	1	0.27	2		305	439	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197139	26197139	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	98	379	0	ENST00000356476.2:c.340C>G	p.His114Asp	p.H114D	ENST00000356476		114	Cac/Gac	1/1	0.163168486512543	4	FACETS	1	0.971	1	0.422	0.376	0.471	CLONAL	1	TRUE	1	0.27	4		379	728	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0036556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	70	381	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.928	0.814	1	0.928	0.814	1	CLONAL	1	TRUE	1	0.425086685183877	2		381	355	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0036556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	188	485	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.425086685183877	4	FACETS	0.984	0.921	1	0.984	0.921	1	CLONAL	3	TRUE	1	0.425086685183877	4		485	427	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087558	27087558	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0036556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	126	431	0	ENST00000324856.7:c.2132C>G	p.Ser711Ter	p.S711*	ENST00000324856	NM_006015.4	711	tCa/tGa	5/20	1	2	FACETS	0.86	0.78	0.944	0.86	0.78	0.944	CLONAL	1	TRUE	1	0.425086685183877	2		431	689	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106771	27106771	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	133	484	0	ENST00000324856.7:c.6382C>T	p.Gln2128Ter	p.Q2128*	ENST00000324856	NM_006015.4	2128	Cag/Tag	20/20	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.425086685183877	2		484	621	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124280	2124280	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	166	788	0	ENST00000219476.3:c.2435G>T	p.Ser812Ile	p.S812I	ENST00000219476	NM_000548.3	812	aGc/aTc	22/42	1	2	FACETS	0.883	0.811	0.957	0.883	0.811	0.957	CLONAL	1	TRUE	1	0.425086685183877	2		788	885	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425776	49425776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123714	NA	P-0036558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	12	480	1	ENST00000301067.7:c.12712C>T	p.Arg4238Cys	p.R4238C	ENST00000301067	NM_003482.3	4238	Cgc/Tgc	39/54	1	2	FACETS	0.182	0.128	0.249	0.182	0.128	0.249	SUBCLONAL	1	TRUE	1	0.7	2		481	188	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428192	49428202	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CTGATCACTCC	CTGATCACTCC	-	novel	NA	P-0036558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	70	574	0	ENST00000301067.7:c.10498_10507+1del		p.X3500_splice	ENST00000301067	NM_003482.3	3500		37/54	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.7	2		574	187	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86668013	86668013	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0036559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	39	177	0	ENST00000274376.6:c.1776+1G>A		p.X592_splice	ENST00000274376	NM_002890.2	592			0.360204429331684	1	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	0	0.360204429331684	1		177	164	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17117043	17117043	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	126	480	0	ENST00000285071.4:c.1666G>C	p.Gly556Arg	p.G556R	ENST00000285071	NM_144997.5	556	Ggc/Cgc	14/14	0.360204429331684	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.360204429331684	1		480	559	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437487	52437494	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGATGA	GCTGATGA	-	novel	NA	P-0036559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	75	411	0	ENST00000460680.1:c.1667_1674del	p.Val556AspfsTer8	p.V556Dfs*8	ENST00000460680	NM_004656.3	556	gTCATCAGC/g	13/17	0.360204429331684	1	FACETS	0.894	0.788	1	0.894	0.788	1	CLONAL	1	TRUE	0	0.360204429331684	1		411	382	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023150	31023150	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	112	499	0	ENST00000375687.4:c.2635G>A	p.Asp879Asn	p.D879N	ENST00000375687	NM_015338.5	879	Gat/Aat	13/13	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.394406488174278	2		499	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934571	NA	P-0036561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	133	466	0	ENST00000269305.4:c.747G>C	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agC	7/11	0.394406488174278	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.394406488174278	1		466	476	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252884	36252885	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	60	290	0	ENST00000300305.3:c.477dup	p.Asp160Ter	p.D160*	ENST00000300305		159	-/T	4/8	1	2	FACETS	0.988	0.857	1	0.988	0.857	1	CLONAL	1	TRUE	1	0.394406488174278	2		290	308	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881414	37881414	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1131692237	NA	P-0036561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	530	574	0	ENST00000269571.5:c.2606T>G	p.Leu869Arg	p.L869R	ENST00000269571		869	cTg/cGg	21/27	0.394406488174278	7	FACETS	1	0.991	1			1	CLONAL	5	TRUE	NA	0.394406488174278	7		574	990	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350006	89350006	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779463117	NA	P-0036561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	56	598	0	ENST00000301030.4:c.2944G>A	p.Glu982Lys	p.E982K	ENST00000301030	NM_001256183.1	982	Gag/Aag	9/13	1	2	FACETS	0.493	0.422	0.57	0.493	0.422	0.57	SUBCLONAL	1	TRUE	1	0.394406488174278	2		598	576	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518532	204518532	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	62	218	0	ENST00000367182.3:c.1195C>G	p.His399Asp	p.H399D	ENST00000367182	NM_001278516.1	399	Cac/Gac	11/11	0.222570092548211	3	FACETS	1	0.965	1	0.448	0.39	0.51	INDETERMINATE	1	TRUE	0	0.394406488174278	3		218	280	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112474	115112478	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCC	GGGCC	-	novel	NA	P-0036561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	145	544	0	ENST00000257566.3:c.1262_1266del	p.Arg421ProfsTer16	p.R421Pfs*16	ENST00000257566	NM_016569.3	421	cGGCCC/c	7/8	0.274708492806457	2	FACETS	0.855	0.787	0.924	0.855	0.787	0.924	CLONAL	2	TRUE	0	0.394406488174278	2		544	430	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022484	31022484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	45	241	0	ENST00000375687.4:c.1969G>A	p.Glu657Lys	p.E657K	ENST00000375687	NM_015338.5	657	Gag/Aag	13/13	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.394406488174278	2		241	212	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912283	97912283	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	77	338	0	ENST00000289081.3:c.608T>A	p.Leu203His	p.L203H	ENST00000289081	NM_000136.2	203	cTc/cAc	7/15	0.394406488174278	1	FACETS	0.917	0.811	1	0.917	0.811	1	CLONAL	1	TRUE	0	0.394406488174278	1		338	342	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128321983	128321988	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGCC	GAAGCC	A	novel	NA	P-0036561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	81	486	0	ENST00000265960.3:c.772_777delinsT	p.Gly258Ter	p.G258*	ENST00000265960	NM_001006617.1	258	GGCTTC/T	6/12	0.37091829220381	4	FACETS	0.819	0.722	0.924			1	CLONAL	1	TRUE	NA	0.394406488174278	4		486	699	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102198835	102198835	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	63	354	0	ENST00000263464.3:c.1006G>T	p.Ala336Ser	p.A336S	ENST00000263464	NM_001165.4	336	Gcc/Tcc	4/9	0.711663923050188	4	FACETS	0.858	0.747	0.978	0.429	0.373	0.489	CLONAL	1	FALSE	2	0.711663923050188	4		354	353	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961970	41961970	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	132	408	1	ENST00000219905.7:c.878G>T	p.Arg293Leu	p.R293L	ENST00000219905	NM_001164273.1	293	cGt/cTt	2/24	0.675933534753457	3	FACETS	0.852	0.787	0.918	0.852	0.787	0.918	CLONAL	2	FALSE	1	0.711663923050188	3		409	295	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0036563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	391	684	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.483554939273941	3	FACETS	0.987	0.958	1			1	CLONAL	3	FALSE	NA	0.711663923050188	3		684	503	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098806	178098806	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	378	617	0	ENST00000397062.3:c.239C>G	p.Thr80Arg	p.T80R	ENST00000397062	NM_006164.4	80	aCa/aGa	2/5	0.711663923050188	5	FACETS	0.984	0.942	1	0.984	0.942	1	CLONAL	3	FALSE	2	0.711663923050188	5		617	744	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430393	181430393	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	245	575	0	ENST00000325404.1:c.245T>C	p.Leu82Ser	p.L82S	ENST00000325404	NM_003106.3	82	tTg/tCg	1/1	0.711663923050188	6	FACETS	0.949	0.889	1	0.475	0.444	0.506	CLONAL	2	FALSE	2	0.711663923050188	6		575	879	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158118	106158118	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	166	268	0	ENST00000380013.4:c.3019A>G	p.Thr1007Ala	p.T1007A	ENST00000380013	NM_001127208.2	1007	Act/Gct	3/11	0.711663923050188	3	FACETS	0.954	0.909	0.997	0.954	0.909	0.997	CLONAL	3	FALSE	0	0.711663923050188	3		268	221	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917664	151917664	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	110	392	1	ENST00000262189.6:c.3656C>T	p.Thr1219Ile	p.T1219I	ENST00000262189	NM_170606.2	1219	aCc/aTc	23/59	0.551579057517809	4	FACETS	0.938	0.856	1			1	CLONAL	2	FALSE	NA	0.711663923050188	4		393	282	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409031	139409031	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	290	778	0	ENST00000277541.6:c.2138G>T	p.Cys713Phe	p.C713F	ENST00000277541	NM_017617.3	713	tGc/tTc	13/34	0.695240126262777	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	FALSE	0	0.711663923050188	2		778	400	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938567	44938567	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	78	386	0	ENST00000377967.4:c.3115C>T	p.Gln1039Ter	p.Q1039*	ENST00000377967	NM_021140.2	1039	Cag/Tag	20/29	NA	2	FACETS	1	0.917	1			1	INDETERMINATE	1	FALSE	NA	0.711663923050188	2		386	213	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020163	123020163	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	118	691	0	ENST00000355640.3:c.651G>T	p.Trp217Cys	p.W217C	ENST00000355640		217	tgG/tgT	2/7	0.711663923050188	3	FACETS	0.951	0.863	1	0.475	0.431	0.521	CLONAL	1	FALSE	1	0.711663923050188	3		691	473	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0036566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	129	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.263732175813232	3	FACETS	0.847	0.771	0.926	0.847	0.771	0.926	CLONAL	2	TRUE	1	0.32	3		452	552	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0036566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	36	227	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.257686663103152	3	FACETS	0.837	0.69	1	0.418	0.345	0.5	CLONAL	1	TRUE	1	0.32	3		227	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0036566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	217	584	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.247196427387384	2	FACETS	0.862	0.803	0.922	0.862	0.803	0.922	CLONAL	2	TRUE	0	0.32	2		584	787	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451406	187451406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779268890	NA	P-0036566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	38	402	1	ENST00000232014.4:c.76C>T	p.Arg26Trp	p.R26W	ENST00000232014	NM_001130845.1	26	Cgg/Tgg	3/10	0.250972319016481	4	FACETS	0.593	0.489	0.708	0.296	0.244	0.354	SUBCLONAL	1	TRUE	2	0.32	4		403	529	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729560	41729560	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	167	528	0	ENST00000242208.4:c.969G>T	p.Lys323Asn	p.K323N	ENST00000242208	NM_002192.2	323	aaG/aaT	3/3	0.250972319016481	4	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	2	0.32	4		528	683	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945097	31945097	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	66	550	0	ENST00000340398.3:c.4G>T	p.Ala2Ser	p.A2S	ENST00000340398	NM_001013699.2	2	Gcc/Tcc	1/1	0.263732175813232	3	FACETS	0.725	0.629	0.829	0.363	0.314	0.415	SUBCLONAL	1	TRUE	1	0.32	3		550	660	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431339	49431339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	49	528	0	ENST00000301067.7:c.9800C>T	p.Ser3267Leu	p.S3267L	ENST00000301067	NM_003482.3	3267	tCa/tTa	34/54	0.263732175813232	3	FACETS	0.637	0.539	0.744	0.318	0.269	0.372	SUBCLONAL	1	TRUE	1	0.32	3		528	558	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28963990	28963990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	54	403	0	ENST00000282397.4:c.1912G>A	p.Ala638Thr	p.A638T	ENST00000282397	NM_002019.4	638	Gcc/Acc	13/30	1	2	FACETS	0.752	0.643	0.87	0.752	0.643	0.87	SUBCLONAL	1	TRUE	1	0.32	2		403	449	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500316	99500316	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	90	623	1	ENST00000268035.6:c.3749A>T	p.Gln1250Leu	p.Q1250L	ENST00000268035	NM_000875.3	1250	cAg/cTg	21/21	1	2	FACETS	0.887	0.788	0.993	0.887	0.788	0.993	CLONAL	1	TRUE	1	0.32	2		624	634	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182174	99182174	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	153	490	0	ENST00000074304.5:c.2239A>T	p.Thr747Ser	p.T747S	ENST00000074304	NM_001134224.1	747	Act/Tct	21/26	0.263732175813232	3	FACETS	0.903	0.83	0.98	0.903	0.83	0.98	CLONAL	2	TRUE	1	0.32	3		490	614	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098786	47098786	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	189	650	1	ENST00000409792.3:c.6488C>A	p.Pro2163His	p.P2163H	ENST00000409792	NM_014159.6	2163	cCc/cAc	15/21	0.263732175813232	3	FACETS	0.846	0.783	0.911	0.846	0.783	0.911	CLONAL	2	TRUE	1	0.32	3		651	810	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127579	55127579	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	45	238	0	ENST00000257290.5:c.367G>T	p.Asp123Tyr	p.D123Y	ENST00000257290	NM_006206.4	123	Gac/Tac	3/23	0.257686663103152	3	FACETS	1	0.92	1	0.572	0.484	0.669	CLONAL	1	TRUE	1	0.32	3		238	285	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230763	66230763	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	55	341	0	ENST00000273854.3:c.2208C>G	p.Ile736Met	p.I736M	ENST00000273854	NM_004439.5	736	atC/atG	12/18	NA	2	FACETS	0.974	0.837	1			1	INDETERMINATE	1	TRUE	NA	0.32	2		341	353	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142949992	142949992	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	152	523	0	ENST00000262992.4:c.2718G>T	p.Met906Ile	p.M906I	ENST00000262992	NM_001101669.1	906	atG/atT	24/24	0.257686663103152	3	FACETS	0.942	0.865	1	0.942	0.865	1	CLONAL	2	TRUE	1	0.32	3		523	585	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630275	187630275	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	98	559	0	ENST00000441802.2:c.707G>T	p.Gly236Val	p.G236V	ENST00000441802	NM_005245.3	236	gGc/gTc	2/27	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.32	2		559	596	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225630	225630	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	140	458	2	ENST00000264932.6:c.409G>T	p.Asp137Tyr	p.D137Y	ENST00000264932	NM_004168.2	137	Gat/Tat	4/15	0.242497382367821	4	FACETS	0.964	0.881	1			1	CLONAL	2	TRUE	NA	0.32	4		460	599	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183043	32183043	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	249	665	0	ENST00000375023.3:c.1981C>A	p.Pro661Thr	p.P661T	ENST00000375023	NM_004557.3	661	Cct/Act	12/30	0.303910766673003	4	FACETS	1	0.986	1	0.789	0.739	0.84	CLONAL	2	TRUE	1	0.32	4		665	868	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971329	13971329	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	111	371	1	ENST00000405192.2:c.600G>T	p.Leu200Phe	p.L200F	ENST00000405192	NM_001163147.1	200	ttG/ttT	8/12	0.250972319016481	4	FACETS	1	0.906	1	1	0.906	1	CLONAL	2	TRUE	2	0.32	4		372	457	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334710	81334710	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	136	504	0	ENST00000222390.5:c.2006G>C	p.Cys669Ser	p.C669S	ENST00000222390	NM_000601.4	669	tGt/tCt	17/18	0.250972319016481	4	FACETS	0.841	0.767	0.919	0.841	0.767	0.919	CLONAL	2	TRUE	2	0.32	4		504	667	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486232	8486232	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs142397137	NA	P-0036566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	51	337	0	ENST00000356435.5:c.2585G>T	p.Arg862Leu	p.R862L	ENST00000356435		862	cGc/cTc	17/35	0.152461709453629	3	FACETS	0.968	0.825	1			1	INDETERMINATE	1	TRUE	NA	0.32	3		337	382	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934310	39934310	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	175	590	0	ENST00000378444.4:c.289G>T	p.Gly97Cys	p.G97C	ENST00000378444	NM_001123385.1	97	Ggc/Tgc	4/15	0.303910766673003	2	FACETS	0.907	0.839	0.976	0.907	0.839	0.976	CLONAL	2	TRUE	0	0.32	2		590	603	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	105	645	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.797	0.717	0.881	0.797	0.717	0.881	SUBCLONAL	1	TRUE	1	0.5	2		648	527	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	146	795	3	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.911	0.834	0.991	0.911	0.834	0.991	CLONAL	1	TRUE	1	0.5	2		798	641	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021785	71021785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs112795301	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	71	341	0	ENST00000318789.4:c.1573C>T	p.Arg525Ter	p.R525*	ENST00000318789	NM_032682.5	525	Cga/Tga	18/21	1	2	FACETS	0.863	0.759	0.974	0.863	0.759	0.974	CLONAL	1	TRUE	1	0.5	2		341	329	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	159	514	8	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.924	0.85	1	0.924	0.85	1	CLONAL	1	TRUE	1	0.5	2		522	688	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	24	260	3	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.632	0.5	0.779	0.632	0.5	0.779	SUBCLONAL	1	TRUE	1	0.5	2		263	152	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	106	723	9	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.872	0.786	0.963	0.872	0.786	0.963	CLONAL	1	TRUE	1	0.5	2		732	486	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101267	27101268	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	111	619	1	ENST00000324856.7:c.4555dup	p.Gln1519ProfsTer13	p.Q1519Pfs*13	ENST00000324856	NM_006015.4	1517	gcc/gCcc	18/20	1	2	FACETS	0.972	0.879	1	0.972	0.879	1	CLONAL	1	TRUE	1	0.5	2		620	457	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	84	483	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	1	2	FACETS	0.836	0.743	0.934	0.836	0.743	0.934	CLONAL	1	TRUE	1	0.5	2		483	402	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398279	25398279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894365	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	114	360	0	ENST00000311936.3:c.40G>A	p.Val14Ile	p.V14I	ENST00000311936	NM_004985.3	14	Gta/Ata	2/5	1	2	FACETS	0.919	0.832	1	0.919	0.832	1	CLONAL	1	TRUE	1	0.5	2		360	496	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486063	29486064	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs771115661	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	76	427	0	ENST00000356175.3:c.246_247del	p.Gln83ValfsTer23	p.Q83Vfs*23	ENST00000356175	NM_000267.3	80	taTCtc/tatc	3/57	1	2	FACETS	0.704	0.62	0.793	0.704	0.62	0.793	SUBCLONAL	1	TRUE	1	0.5	2		427	432	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119562107	119562107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139402886	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	82	357	0	ENST00000316626.5:c.1229C>T	p.Ala410Val	p.A410V	ENST00000316626		410	gCg/gTg	11/12	1	2	FACETS	0.916	0.814	1	0.916	0.814	1	CLONAL	1	TRUE	1	0.5	2		357	358	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553478	29553478	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781807	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	129	654	1	ENST00000356175.3:c.2033del	p.Pro678ArgfsTer10	p.P678Rfs*10	ENST00000356175	NM_000267.3	676	aCc/ac	18/57	1	2	FACETS	0.787	0.715	0.862	0.787	0.715	0.862	SUBCLONAL	1	TRUE	1	0.5	2		655	656	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	81	553	5	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	1	2	FACETS	0.876	0.777	0.98	0.876	0.777	0.98	CLONAL	1	TRUE	1	0.5	2		558	370	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900984	114900984	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778855667	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	110	530	0	ENST00000543371.1:c.598del	p.Leu200SerfsTer25	p.L200Sfs*25	ENST00000543371	NM_001198531.1	198	caC/ca	6/14	1	2	FACETS	0.926	0.837	1	0.926	0.837	1	CLONAL	1	TRUE	1	0.5	2		530	475	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262326	46262326	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	145	619	1	ENST00000371998.3:c.915del	p.Phe305LeufsTer3	p.F305Lfs*3	ENST00000371998		304	Ttt/tt	9/23	1	2	FACETS	0.895	0.819	0.974	0.895	0.819	0.974	CLONAL	1	TRUE	1	0.5	2		620	648	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835781	68835781	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060501215	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	133	544	0	ENST00000261769.5:c.377del	p.Pro126ArgfsTer89	p.P126Rfs*89	ENST00000261769	NM_004360.3	124	cgC/cg	3/16	1	2	FACETS	0.998	0.911	1	0.998	0.911	1	CLONAL	1	TRUE	1	0.5	2		544	533	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	83	347	2	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.933	0.829	1	0.933	0.829	1	CLONAL	1	TRUE	1	0.5	2		349	356	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123837	46123837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	61	293	3	ENST00000334344.6:c.109del	p.Ile37SerfsTer21	p.I37Sfs*21	ENST00000334344	NM_152641.2	35	Aaa/aa	2/21	1	2	FACETS	0.961	0.838	1	0.961	0.838	1	CLONAL	1	TRUE	1	0.5	2		296	254	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793677	89793677	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	98	342	2	ENST00000336032.3:c.752del	p.Lys251SerfsTer14	p.K251Sfs*14	ENST00000336032	NM_006813.2	249	gAa/ga	2/2	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.5	2		344	375	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856097	111856097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1013978345	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	125	593	1	ENST00000341259.2:c.148C>T	p.Arg50Trp	p.R50W	ENST00000341259	NM_005475.2	50	Cgg/Tgg	2/8	1	2	FACETS	0.963	0.876	1	0.963	0.876	1	CLONAL	1	TRUE	1	0.5	2		594	519	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950727	79950727	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1574197	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	23	197	0	ENST00000265081.6:c.181G>C	p.Ala61Pro	p.A61P	ENST00000265081	NM_002439.4	61	Gca/Cca	1/24	1	2	FACETS	0.754	0.597	0.93	0.754	0.597	0.93	CLONAL	1	TRUE	1	0.5	2		197	122	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426774	49426774	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1334139538	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	69	426	3	ENST00000301067.7:c.11714A>T	p.Gln3905Leu	p.Q3905L	ENST00000301067	NM_003482.3	3905	cAg/cTg	39/54	1	2	FACETS	0.952	0.837	1	0.952	0.837	1	CLONAL	1	TRUE	1	0.5	2		429	290	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438018	49438018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs111266743	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	131	753	1	ENST00000301067.7:c.5153C>T	p.Ala1718Val	p.A1718V	ENST00000301067	NM_003482.3	1718	gCg/gTg	21/54	1	2	FACETS	0.887	0.807	0.969	0.887	0.807	0.969	CLONAL	1	TRUE	1	0.5	2		754	591	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879673	151879673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	55	230	0	ENST00000262189.6:c.5272C>T	p.Arg1758Cys	p.R1758C	ENST00000262189	NM_170606.2	1758	Cgt/Tgt	36/59	1	2	FACETS	0.965	0.835	1	0.965	0.835	1	CLONAL	1	TRUE	1	0.5	2		230	228	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113790	11113790	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	105	667	2	ENST00000358026.2:c.1902del	p.Ala636ProfsTer10	p.A636Pfs*10	ENST00000358026	NM_001128849.1	633	gCc/gc	12/36	1	2	FACETS	0.789	0.71	0.873	0.789	0.71	0.873	SUBCLONAL	1	TRUE	1	0.5	2		669	532	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376248	15376248	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	72	516	4	ENST00000263377.2:c.766del	p.Gln256SerfsTer27	p.Q256Sfs*27	ENST00000263377	NM_058243.2	256	Cag/ag	5/20	1	2	FACETS	0.709	0.623	0.802	0.709	0.623	0.802	SUBCLONAL	1	TRUE	1	0.5	2		520	406	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099403	157099408	+	inframe_deletion	In_Frame_Del	DEL	CAGCAG	CAGCAG	-	rs587779743	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	30	299	0	ENST00000346085.5:c.357_362del	p.Gln130_Gln131del	p.Q130_Q131del	ENST00000346085	NM_020732.3	114	CAGCAG/-	1/20	1	2	FACETS	0.71	0.578	0.856	0.71	0.578	0.856	SUBCLONAL	1	TRUE	1	0.5	2		299	169	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842405	68842405	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	122	619	0	ENST00000261769.5:c.466T>C	p.Trp156Arg	p.W156R	ENST00000261769	NM_004360.3	156	Tgg/Cgg	4/16	1	2	FACETS	0.978	0.889	1	0.978	0.889	1	CLONAL	1	TRUE	1	0.5	2		619	499	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346972	89346972	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1251064433	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	75	438	0	ENST00000301030.4:c.5978G>A	p.Arg1993His	p.R1993H	ENST00000301030	NM_001256183.1	1993	cGt/cAt	9/13	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.5	2		438	291	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	115	838	0	ENST00000222270.7:c.520_521dup	p.Lys175GlnfsTer20	p.K175Qfs*20	ENST00000222270	NM_014727.1	172	acc/aCCcc	3/37	1	2	FACETS	0.707	0.638	0.779	0.707	0.638	0.779	SUBCLONAL	1	TRUE	1	0.5	2		838	651	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347432	91347433	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	86	365	0	ENST00000355112.3:c.3600dup	p.Gln1201ThrfsTer16	p.Q1201Tfs*16	ENST00000355112	NM_000057.2	1198	-/A	19/22	1	2	FACETS	0.953	0.85	1	0.953	0.85	1	CLONAL	1	TRUE	1	0.5	2		365	361	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218893	193218893	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774557338	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	66	324	0	ENST00000367435.3:c.1451G>A	p.Arg484His	p.R484H	ENST00000367435	NM_024529.4	484	cGt/cAt	16/17	1	2	FACETS	0.989	0.868	1	0.989	0.868	1	CLONAL	1	TRUE	1	0.5	2		324	267	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226574028	226574028	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs201777393	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	33	456	0	ENST00000366794.5:c.833C>T	p.Ala278Val	p.A278V	ENST00000366794	NM_001618.3	278	gCg/gTg	6/23	1	2	FACETS	0.378	0.308	0.457	0.378	0.308	0.457	SUBCLONAL	1	TRUE	1	0.5	2		456	349	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424467	49424467	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	111	686	0	ENST00000301067.7:c.13756A>G	p.Asn4586Asp	p.N4586D	ENST00000301067	NM_003482.3	4586	Aat/Gat	41/54	1	2	FACETS	0.908	0.82	1	0.908	0.82	1	CLONAL	1	TRUE	1	0.5	2		686	489	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440055	49440055	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886049483	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	122	727	2	ENST00000301067.7:c.4571G>A	p.Arg1524His	p.R1524H	ENST00000301067	NM_003482.3	1524	cGc/cAc	16/54	1	2	FACETS	0.856	0.777	0.939	0.856	0.777	0.939	CLONAL	1	TRUE	1	0.5	2		729	570	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643454	38643455	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	122	601	0	ENST00000299084.4:c.926_927del	p.Val309GlyfsTer3	p.V309Gfs*3	ENST00000299084	NM_152594.2	308	tcTGtg/tctg	7/7	1	2	FACETS	0.963	0.875	1	0.963	0.875	1	CLONAL	1	TRUE	1	0.5	2		601	507	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858335	89858335	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	83	425	0	ENST00000389301.3:c.1225G>T	p.Asp409Tyr	p.D409Y	ENST00000389301	NM_000135.2	409	Gac/Tac	13/43	1	2	FACETS	0.895	0.795	1	0.895	0.795	1	CLONAL	1	TRUE	1	0.5	2		425	371	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989451	7989452	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	121	748	0	ENST00000319144.4:c.234dup	p.Lys79GlnfsTer46	p.K79Qfs*46	ENST00000319144	NM_001139.2	78	-/C	2/15	1	2	FACETS	0.815	0.738	0.895	0.815	0.738	0.895	CLONAL	1	TRUE	1	0.5	2		748	594	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971336	15971336	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	153	546	0	ENST00000268712.3:c.4613T>C	p.Val1538Ala	p.V1538A	ENST00000268712	NM_006311.3	1538	gTg/gCg	32/46	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.5	2		546	579	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436142	56436143	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	102	621	0	ENST00000407977.2:c.994dup	p.Tyr332LeufsTer111	p.Y332Lfs*111	ENST00000407977		332	tac/tTac	9/10	1	2	FACETS	0.818	0.734	0.905	0.818	0.734	0.905	CLONAL	1	TRUE	1	0.5	2		621	499	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117860	70117860	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	96	453	0	ENST00000245479.2:c.328A>G	p.Asn110Asp	p.N110D	ENST00000245479	NM_000346.3	110	Aac/Gac	1/3	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.5	2		453	366	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170652	7170652	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	162	814	0	ENST00000302850.5:c.1379A>G	p.Lys460Arg	p.K460R	ENST00000302850	NM_000208.2	460	aAa/aGa	6/22	1	2	FACETS	0.864	0.794	0.937	0.864	0.794	0.937	CLONAL	1	TRUE	1	0.5	2		814	750	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224208	36224208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568382188	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	124	749	0	ENST00000222270.7:c.6758C>T	p.Pro2253Leu	p.P2253L	ENST00000222270	NM_014727.1	2253	cCg/cTg	28/37	1	2	FACETS	0.98	0.892	1	0.98	0.892	1	CLONAL	1	TRUE	1	0.5	2		749	506	SUCCESS
ALK	238	MSKCC	GRCh37	2	29450476	29450476	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	177	990	0	ENST00000389048.3:c.2878A>G	p.Ser960Gly	p.S960G	ENST00000389048	NM_004304.4	960	Agt/Ggt	17/29	1	2	FACETS	0.912	0.842	0.985	0.912	0.842	0.985	CLONAL	1	TRUE	1	0.5	2		990	776	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332660	153332660	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	103	528	0	ENST00000281708.4:c.296A>G	p.Glu99Gly	p.E99G	ENST00000281708	NM_033632.3	99	gAg/gGg	2/12	1	2	FACETS	0.932	0.839	1	0.932	0.839	1	CLONAL	1	TRUE	1	0.5	2		528	442	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675871	30675872	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	156	920	1	ENST00000376406.3:c.2484_2485del	p.Gly829AlafsTer7	p.G829Afs*7	ENST00000376406	NM_014641.2	828	agAGgg/aggg	8/15	1	2	FACETS	0.826	0.758	0.898	0.826	0.758	0.898	CLONAL	1	TRUE	1	0.5	2		921	755	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527327	137527327	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	173	726	0	ENST00000367739.4:c.319G>T	p.Gly107Ter	p.G107*	ENST00000367739	NM_000416.2	107	Gga/Tga	3/7	1	2	FACETS	0.969	0.895	1	0.969	0.895	1	CLONAL	1	TRUE	1	0.5	2		726	714	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508037	106508037	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	33	184	0	ENST00000359195.3:c.31G>T	p.Val11Leu	p.V11L	ENST00000359195	NM_002649.2	11	Gtg/Ttg	2/11	1	2	FACETS	0.898	0.743	1	0.898	0.743	1	CLONAL	1	TRUE	1	0.5	2		184	147	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842334	151842334	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777526116	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	19	250	0	ENST00000262189.6:c.14078G>A	p.Arg4693Gln	p.R4693Q	ENST00000262189	NM_170606.2	4693	cGa/cAa	54/59	1	2	FACETS	0.278	0.211	0.357	0.278	0.211	0.357	SUBCLONAL	1	TRUE	1	0.5	2		250	273	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879593	151879594	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGC	rs749417254	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	61	425	0	ENST00000262189.6:c.5349_5351dup	p.Gln1787dup	p.Q1787dup	ENST00000262189	NM_170606.2	1787	caa/caGCAa	36/59	1	2	FACETS	0.649	0.562	0.742	0.649	0.562	0.742	SUBCLONAL	1	TRUE	1	0.5	2		425	376	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15833886	15833886	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	36	97	0	ENST00000307771.7:c.644G>T	p.Arg215Met	p.R215M	ENST00000307771	NM_005089.3	215	aGg/aTg	8/11	1	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.5	1		97	89	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32921012	32921031	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CGATTACCTGTGTACCCTTT	CGATTACCTGTGTACCCTTT	-	novel	NA	P-0036572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	95	430	0	ENST00000380152.3:c.6988_7007del	p.Ile2330HisfsTer3	p.I2330Hfs*3	ENST00000380152		2329	cCGATTACCTGTGTACCCTTT/c	13/27	0.783465579080342	1	FACETS	0.699	0.636	0.762	0.699	0.636	0.762	SUBCLONAL	1	TRUE	0	0.783465579080342	1		430	211	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518083	103518083	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	63	264	0	ENST00000355739.4:c.2021C>G	p.Ser674Cys	p.S674C	ENST00000355739	NM_000123.3	674	tCc/tGc	9/15	1	2	FACETS	0.619	0.541	0.701	0.619	0.541	0.701	SUBCLONAL	1	TRUE	1	0.783465579080342	2		264	260	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40469203	40469220	+	inframe_deletion	In_Frame_Del	DEL	GTCACACAGATAAACTTG	GTCACACAGATAAACTTG	-	novel	NA	P-0036572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	185	271	0	ENST00000264657.5:c.2124_2141del	p.Lys709_Thr714del	p.K709_T714del	ENST00000264657	NM_139276.2	708	acCAAGTTTATCTGTGTGACa/aca	22/24	0.783465579080342	3	FACETS	0.817	0.765	0.87	0.817	0.765	0.87	CLONAL	2	TRUE	1	0.783465579080342	3		271	402	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468390	89468390	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	92	212	0	ENST00000336596.2:c.1924C>A	p.Leu642Ile	p.L642I	ENST00000336596	NM_005233.5	642	Ctt/Att	11/17	NA	2	FACETS	0.886	0.799	0.976			1	INDETERMINATE	1	TRUE	NA	0.783465579080342	2		212	265	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066525	94066525	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	172	346	0	ENST00000369303.4:c.1234A>C	p.Thr412Pro	p.T412P	ENST00000369303	NM_004440.3	412	Act/Cct	5/17	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.783465579080342	2		346	437	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998264	100998264	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	58	244	0	ENST00000325455.5:c.1538C>A	p.Pro513His	p.P513H	ENST00000325455	NM_001202474.3	513	cCt/cAt	1/8	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.333847244642037	2		244	305	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027728	152027728	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	237	735	0	ENST00000262189.6:c.347C>A	p.Ser116Ter	p.S116*	ENST00000262189	NM_170606.2	116	tCg/tAg	3/59	0.236021813850488	3	FACETS	1	0.992	1	0.738	0.689	0.79	CLONAL	1	TRUE	1	0.333847244642037	3		735	1122	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0036574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	109	474	0	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	0.451921109130327	2	FACETS	0.603	0.543	0.665	0.301	0.271	0.333	SUBCLONAL	1	TRUE	0	0.67497524013976	2		474	536	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233551	69233551	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5364	1147	301	0	ENST00000462284.1:c.1416G>C	p.Lys472Asn	p.K472N	ENST00000462284	NM_002392.5	472	aaG/aaC	11/11	0.67497524013976	39	FACETS	1	0.973	1			1	CLONAL	7	TRUE	NA	0.67497524013976	39		301	6511	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732430	74732441	+	missense_variant	Missense_Mutation	ONP	GTCGACCGAGAT	GTCGACCGAGAT	ATGGTCCAAGTC	novel	NA	P-0036574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	35	305	1	ENST00000359995.5:c.468_479delinsGACTTGGACCAT	p.Ser157_Thr160delinsThrTrpThrIle	p.S157_T160delinsTWTI	ENST00000359995	NM_001195427.1	156	cgATCTCGGTCGACc/cgGACTTGGACCATc	2/3	1	2	FACETS	0.372	0.306	0.445	0.372	0.306	0.445	SUBCLONAL	1	TRUE	1	0.67497524013976	2		306	279	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732418	74732428	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGACTTGGA	CTGGACTTGGA	-	novel	NA	P-0036574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	38	327	0	ENST00000359995.5:c.481_491del	p.Ser161IlefsTer50	p.S161Ifs*50	ENST00000359995	NM_001195427.1	161	TCCAAGTCCAGa/a	2/3	1	2	FACETS	0.375	0.311	0.446	0.375	0.311	0.446	SUBCLONAL	1	TRUE	1	0.67497524013976	2		327	300	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732396	74732414	+	frameshift_variant	Frame_Shift_Del	DEL	GGACTTGGACCTTCGTGCG	GGACTTGGACCTTCGTGCG	-	novel	NA	P-0036574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	39	359	0	ENST00000359995.5:c.495_513del	p.Ala166SerfsTer60	p.A166Sfs*60	ENST00000359995	NM_001195427.1	165	tcCGCACGAAGGTCCAAGTCC/tc	2/3	1	2	FACETS	0.356	0.295	0.422	0.356	0.295	0.422	SUBCLONAL	1	TRUE	1	0.67497524013976	2		359	325	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390779	139390779	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	230	872	0	ENST00000277541.6:c.7412C>A	p.Ser2471Ter	p.S2471*	ENST00000277541	NM_017617.3	2471	tCg/tAg	34/34	0.763161303157295	2	FACETS	0.753	0.704	0.804	0.377	0.352	0.402	SUBCLONAL	1	TRUE	0	0.763161303157295	2		872	800	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399422	139399422	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	279	818	0	ENST00000277541.6:c.4721T>C	p.Leu1574Pro	p.L1574P	ENST00000277541	NM_017617.3	1574	cTg/cCg	26/34	0.763161303157295	2	FACETS	0.86	0.811	0.911	0.43	0.405	0.456	CLONAL	1	TRUE	0	0.763161303157295	2		818	850	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397762	139397762	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	34	633	0	ENST00000277541.6:c.5039T>G	p.Ile1680Ser	p.I1680S	ENST00000277541	NM_017617.3	1680	aTt/aGt	27/34	0.763161303157295	2	FACETS	0.132	0.107	0.16	0.066	0.053	0.08	SUBCLONAL	1	TRUE	0	0.763161303157295	2		633	674	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390793	139390793	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	47	859	0	ENST00000277541.6:c.7398del	p.Ser2467ArgfsTer10	p.S2467Rfs*10	ENST00000277541	NM_017617.3	2466	acG/ac	34/34	0.763161303157295	2	FACETS	0.161	0.135	0.19	0.081	0.067	0.095	SUBCLONAL	1	TRUE	0	0.763161303157295	2		859	764	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0036578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	36	331	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.984	0.81	1	0.984	0.81	1	CLONAL	1	TRUE	1	0.2	2		331	366	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0036578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	87	303	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.87	0.773	0.973	1	0.983	1	CLONAL	2	TRUE	1	0.2	2		303	500	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252155	226252155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553260624	NA	P-0036578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	10	140	0	ENST00000366813.1:c.103G>A	p.Gly35Arg	p.G35R	ENST00000366813		35	Ggg/Agg	1/3	1	2	FACETS	0.719	0.489	1	0.719	0.489	1	CLONAL	1	TRUE	1	0.2	2		140	139	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984163	2984163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387907352	NA	P-0036578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	55	414	0	ENST00000396946.4:c.367G>A	p.Gly123Ser	p.G123S	ENST00000396946	NM_032415.4	123	Ggc/Agc	5/25	0.3	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.2	1		414	431	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147534	47147534	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	80	423	1	ENST00000409792.3:c.4792C>T	p.Arg1598Ter	p.R1598*	ENST00000409792	NM_014159.6	1598	Cga/Tga	6/21	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.425361074663052	2		424	308	SUCCESS
AR	367	MSKCC	GRCh37	X	66765163	66765163	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	23	260	0	ENST00000374690.3:c.175C>T	p.Gln59Ter	p.Q59*	ENST00000374690	NM_000044.3	59	Cag/Tag	1/8	1	2	FACETS	0.819	0.647	1	0.819	0.647	1	CLONAL	1	TRUE	1	0.425361074663052	2		260	132	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435758	49435758	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	118	657	1	ENST00000301067.7:c.6125G>C	p.Cys2042Ser	p.C2042S	ENST00000301067	NM_003482.3	2042	tGc/tCc	29/54	0.425361074663052	3	FACETS	1	0.974	1	0.607	0.55	0.667	CLONAL	1	TRUE	1	0.425361074663052	3		658	554	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225449723	225449723	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	189	297	0	ENST00000264414.4:c.4T>A	p.Ser2Thr	p.S2T	ENST00000264414	NM_003590.4	2	Tcg/Acg	1/16	0.425361074663052	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.425361074663052	1		297	487	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46277748	46277748	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0036579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	59	302	0	ENST00000371998.3:c.3547-1G>A		p.X1183_splice	ENST00000371998		1183			1	2	FACETS	0.878	0.76	1	0.878	0.76	1	CLONAL	1	TRUE	1	0.425361074663052	2		302	316	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98222044	98222044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	66	341	1	ENST00000331920.6:c.2725G>A	p.Asp909Asn	p.D909N	ENST00000331920	NM_000264.3	909	Gat/Aat	17/24	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.425361074663052	2		342	305	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786415	135786415	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	64	467	0	ENST00000298552.3:c.1115del	p.Pro372LeufsTer68	p.P372Lfs*68	ENST00000298552	NM_001162426.1	372	cCt/ct	11/23	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.425361074663052	2		467	296	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0036581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	154	542	1	ENST00000311936.3:c.180_181delinsAA	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggAAaa	3/5	0.618737391034249	4	FACETS	1	0.986	1	0.673	0.619	0.728	CLONAL	1	TRUE	2	0.738319429966219	4		543	539	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781783	3781783	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	84	539	0	ENST00000262367.5:c.4884del	p.His1628GlnfsTer7	p.H1628Qfs*7	ENST00000262367	NM_004380.2	1628	caC/ca	29/31	0.738319429966219	3	FACETS	0.771	0.696	0.848	0.771	0.696	0.848	SUBCLONAL	2	TRUE	1	0.738319429966219	3		539	202	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0036582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	273	490	0	ENST00000269305.4:c.97-1G>A		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.528763564790717	2	FACETS	0.989	0.942	1	0.989	0.942	1	CLONAL	2	TRUE	0	0.565600860309446	2		490	488	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355177	15355177	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760576705	NA	P-0036582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	826	941	2	ENST00000263377.2:c.2446G>A	p.Val816Ile	p.V816I	ENST00000263377	NM_058243.2	816	Gtc/Atc	13/20	0.565600860309446	5	FACETS	0.897	0.872	0.922			1	CLONAL	4	TRUE	NA	0.565600860309446	5		943	1505	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774134	56774134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35151472	NA	P-0036582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	270	619	0	ENST00000337432.4:c.485G>A	p.Gly162Glu	p.G162E	ENST00000337432	NM_058216.2	162	gGa/gAa	3/9	0.547935152690007	3	FACETS	1	0.973	1	0.695	0.658	0.733	CLONAL	2	TRUE	0	0.565600860309446	3		619	587	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278382	39278382	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	43	674	0	ENST00000402219.2:c.767G>C	p.Ser256Thr	p.S256T	ENST00000402219	NM_005633.3	256	aGt/aCt	6/23	0.527147046150822	3	FACETS	0.424	0.355	0.501	0.212	0.177	0.251	SUBCLONAL	1	TRUE	1	0.565600860309446	3		674	460	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045758	143045758	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1311150586	NA	P-0036582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	133	401	0	ENST00000262992.4:c.1876A>G	p.Ile626Val	p.I626V	ENST00000262992	NM_001101669.1	626	Atc/Gtc	17/24	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.565600860309446	2		401	458	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30668375	30668375	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	97	470	0	ENST00000376406.3:c.6137T>G	p.Phe2046Cys	p.F2046C	ENST00000376406	NM_014641.2	2046	tTc/tGc	15/15	0.519910557586073	4	FACETS	0.838	0.748	0.933	0.209	0.187	0.234	CLONAL	1	TRUE	0	0.565600860309446	4		470	641	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715903	117715903	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0036582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	52	314	0	ENST00000368508.3:c.857-2A>T		p.X286_splice	ENST00000368508	NM_002944.2	286			0.527147046150822	3	FACETS	0.907	0.779	1	0.454	0.389	0.523	CLONAL	1	TRUE	1	0.565600860309446	3		314	260	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151871199	151871238	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCAGCCACTCCACCTACCTGCTCATCACCATTGGTGGCAT	GCAGCCACTCCACCTACCTGCTCATCACCATTGGTGGCAT	-	novel	NA	P-0036582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	59	412	0	ENST00000262189.6:c.9352_9374+17del		p.X3118_splice	ENST00000262189	NM_170606.2	3118		39/59	0.527147046150822	3	FACETS	0.567	0.489	0.652	0.284	0.244	0.326	SUBCLONAL	1	TRUE	1	0.565600860309446	3		412	472	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774134	56774134	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	121	619	0	ENST00000337432.4:c.485G>C	p.Gly162Ala	p.G162A	ENST00000337432	NM_058216.2	162	gGa/gCa	3/9	0.547935152690007	3	FACETS	0.935	0.847	1	0.312	0.282	0.343	CLONAL	1	TRUE	0	0.565600860309446	3		619	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0036583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	194	571	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.365851710664993	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.37692987288152	2		572	489	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938089	76938092	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	novel	NA	P-0036583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	154	737	0	ENST00000373344.5:c.2656_2659del	p.Glu886LeufsTer18	p.E886Lfs*18	ENST00000373344	NM_000489.3	886	GAGAct/ct	9/35	0.37692987288152	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.37692987288152	1		737	545	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252155	226252155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553260624	NA	P-0036583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	19	140	0	ENST00000366813.1:c.103G>A	p.Gly35Arg	p.G35R	ENST00000366813		35	Ggg/Agg	1/3	1	2	FACETS	0.775	0.607	0.959	1	0.924	1	CLONAL	2	TRUE	1	0.37692987288152	2		140	65	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388677	31388677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	70	611	0	ENST00000328111.2:c.1942G>A	p.Gly648Arg	p.G648R	ENST00000328111	NM_006892.3	648	Gga/Aga	18/23	0.133598519440943	3	FACETS	0.774	0.676	0.881	0.387	0.338	0.441	INDETERMINATE	1	TRUE	1	0.37692987288152	3		611	570	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139738	55139741	+	missense_variant	Missense_Mutation	ONP	AACA	AACA	TGTT	novel	NA	P-0036583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	59	543	1	ENST00000257290.5:c.1399_1402inv	p.Asn467_Asn468delinsCysTyr	p.N467_N468delinsCY	ENST00000257290	NM_006206.4	467	AACAat/TGTTat	10/23	0.133598519440943	3	FACETS	0.72	0.62	0.828	0.36	0.31	0.414	INDETERMINATE	1	TRUE	1	0.37692987288152	3		544	517	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0036590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	103	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.168220603962075	3	FACETS	1	0.967	1	0.787	0.708	0.871	CLONAL	2	TRUE	0	0.197632785059987	3		452	485	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720663	89720663	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	28	239	0	ENST00000371953.3:c.814del	p.His272ThrfsTer4	p.H272Tfs*4	ENST00000371953	NM_000314.4	272	Cac/ac	8/9	1	2	FACETS	0.81	0.653	0.984	1	0.945	1	CLONAL	2	TRUE	1	0.197632785059987	2		239	175	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484596	57484596	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913494	NA	P-0036590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	845	644	2	ENST00000371085.3:c.680A>G	p.Gln227Arg	p.Q227R	ENST00000371085	NM_000516.4	227	cAg/cGg	9/13	0.197632785059987	12	FACETS	1	0.983	1			1	CLONAL	12	TRUE	NA	0.197632785059987	12		646	1399	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0036591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	114	669	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.314903809918348	2	FACETS	1	0.983	1	0.7	0.636	0.766	CLONAL	1	FALSE	0	0.415561264533626	2		669	392	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0036591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	220	490	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.415561264533626	6	FACETS	1	0.938	1	1	0.938	1	CLONAL	3	FALSE	3	0.415561264533626	6		490	645	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0036591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	261	946	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.267957990246352	3	FACETS	1	0.965	1	0.69	0.649	0.731	CLONAL	2	FALSE	0	0.415561264533626	3		947	733	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127726	47127726	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	66	550	1	ENST00000409792.3:c.5356C>G	p.Leu1786Val	p.L1786V	ENST00000409792	NM_014159.6	1786	Cta/Gta	11/21	0.419098142216861	4	FACETS	0.766	0.665	0.875	0.255	0.221	0.292	SUBCLONAL	1	FALSE	1	0.415561264533626	4		551	587	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0036592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	10	797	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.324	0.218	0.458	0.324	0.218	0.458	SUBCLONAL	1	TRUE	1	0.13	2		797	475	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	15	931	0	ENST00000267101.3:c.310G>C	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ctg	3/28	1	2	FACETS	0.32	0.232	0.426	0.32	0.232	0.426	SUBCLONAL	1	TRUE	1	0.13	2		931	722	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16097870	16097870	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs76145228	NA	P-0036592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	20	302	1	ENST00000268712.3:c.14G>T	p.Gly5Val	p.G5V	ENST00000268712	NM_006311.3	5	gGt/gTt	2/46	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.13	2		303	208	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	189	726	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.689552628031424	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.689552628031424	1		726	299	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0036593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	171	613	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.125932623473684	4	FACETS	0.855	0.793	0.918	0.855	0.793	0.918	INDETERMINATE	2	TRUE	2	0.689552628031424	4		613	490	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115973	8115973	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	100	448	0	ENST00000346208.3:c.1320del	p.Ala441ProfsTer34	p.A441Pfs*34	ENST00000346208		440	aCc/ac	6/6	0.187428376304605	4	FACETS	0.857	0.776	0.94	0.857	0.776	0.94	INDETERMINATE	2	TRUE	2	0.689552628031424	4		448	286	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696644	47696644	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519964	NA	P-0036594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	231	532	0	ENST00000347630.2:c.304T>G	p.Phe102Val	p.F102V	ENST00000347630	NM_001007230.1	102	Ttc/Gtc	5/11	0.238647176286709	3	FACETS	0.782	0.735	0.829	0.782	0.735	0.829	INDETERMINATE	2	TRUE	1	0.702946006347465	3		532	568	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913396	NA	P-0036594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	11	297	0	ENST00000349496.5:c.95A>G	p.Asp32Gly	p.D32G	ENST00000349496	NM_001904.3	32	gAc/gGc	3/15	1	2	FACETS	0.082	0.056	0.114	0.082	0.056	0.114	SUBCLONAL	1	TRUE	1	0.702946006347465	2		297	382	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619219	37619241	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAGATCTGTCAGTCCCTATAG	CAGAGATCTGTCAGTCCCTATAG	-	novel	NA	P-0036594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	152	460	0	ENST00000447079.4:c.898_920del	p.Arg300GlufsTer43	p.R300Efs*43	ENST00000447079	NM_015083.1	299	CAGAGATCTGTCAGTCCCTATAGc/c	1/14	0.238647176286709	3	FACETS	1	0.989	1	0.725	0.671	0.781	INDETERMINATE	1	TRUE	1	0.702946006347465	3		460	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0036595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	221	631	4	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.419145033035564	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.419145033035564	1		635	819	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0036595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	121	303	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.86	0.779	0.946	0.86	0.779	0.946	CLONAL	1	TRUE	1	0.419145033035564	2		303	671	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495040	56495040	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	117	733	0	ENST00000267101.3:c.3397C>T	p.His1133Tyr	p.H1133Y	ENST00000267101	NM_001982.3	1133	Cat/Tat	27/28	0.255245200299647	1	FACETS	0.473	0.426	0.523	0.473	0.426	0.523	SUBCLONAL	1	TRUE	0	0.419145033035564	1		733	933	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805049	43805049	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	117	725	0	ENST00000372470.3:c.499T>C	p.Tyr167His	p.Y167H	ENST00000372470	NM_005373.2	167	Tac/Cac	4/12	0.255245200299647	1	FACETS	0.512	0.461	0.566	0.512	0.461	0.566	SUBCLONAL	1	TRUE	0	0.419145033035564	1		725	862	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120789170	120789170	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	167	508	1	ENST00000257552.2:c.767C>T	p.Ala256Val	p.A256V	ENST00000257552	NM_002442.3	256	gCc/gTc	11/15	0.255245200299647	1	FACETS	0.959	0.884	1	0.959	0.884	1	CLONAL	1	TRUE	0	0.419145033035564	1		509	657	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610504	81610504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758957398	NA	P-0036595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	173	520	0	ENST00000298171.2:c.2102G>A	p.Arg701His	p.R701H	ENST00000298171	NM_000369.2	701	cGc/cAc	10/10	0.261904713129838	1	FACETS	0.996	0.92	1	0.996	0.92	1	CLONAL	1	TRUE	0	0.419145033035564	1		520	655	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370186	40370186	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	273	945	0	ENST00000293328.3:c.1152G>T	p.Lys384Asn	p.K384N	ENST00000293328	NM_012448.3	384	aaG/aaT	9/19	0.419145033035564	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.419145033035564	1		945	992	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0036597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	93	693	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.115969723640768	3	FACETS	1	0.939	1	0.543	0.482	0.607	INDETERMINATE	1	TRUE	1	0.25	3		693	771	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579463	7579463	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	48	787	0	ENST00000269305.4:c.224del	p.Pro75LeufsTer48	p.P75Lfs*48	ENST00000269305	NM_001126112.2	75	cCt/ct	4/11	1	2	FACETS	0.61	0.514	0.715	0.61	0.514	0.715	SUBCLONAL	1	TRUE	1	0.25	2		787	630	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367348	50367348	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	23	362	0	ENST00000331340.3:c.155T>G	p.Val52Gly	p.V52G	ENST00000331340	NM_006060.4	52	gTc/gGc	3/8	1	2	FACETS	0.428	0.333	0.538	0.428	0.333	0.538	SUBCLONAL	1	TRUE	1	0.25	2		362	430	SUCCESS
APC	324	MSKCC	GRCh37	5	112175378	112175378	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0036598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	75	238	0	ENST00000257430.4:c.4087A>T	p.Lys1363Ter	p.K1363*	ENST00000257430	NM_000038.5	1363	Aaa/Taa	16/16	1	2	FACETS	0.985	0.871	1	0.985	0.871	1	CLONAL	1	TRUE	1	0.481969066747014	2		238	316	SUCCESS
APC	324	MSKCC	GRCh37	5	112174793	112174793	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	80	229	0	ENST00000257430.4:c.3502G>T	p.Glu1168Ter	p.E1168*	ENST00000257430	NM_000038.5	1168	Gaa/Taa	16/16	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.481969066747014	2		229	296	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087448	27087448	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	520	641	5	ENST00000324856.7:c.2022del	p.Ser674ArgfsTer68	p.S674Rfs*68	ENST00000324856	NM_006015.4	674	agT/ag	5/20	0.481969066747014	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.481969066747014	2		646	975	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857323	9857323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	124	397	1	ENST00000330684.3:c.4078G>T	p.Asp1360Tyr	p.D1360Y	ENST00000330684	NM_001134407.1	1360	Gac/Tac	13/13	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.481969066747014	2		398	489	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118922	70118922	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	236	611	0	ENST00000245479.2:c.494A>G	p.His165Arg	p.H165R	ENST00000245479	NM_000346.3	165	cAc/cGc	2/3	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.481969066747014	2		611	862	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119798	70119799	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	215	522	2	ENST00000245479.2:c.801dup	p.Ile268TyrfsTer28	p.I268Yfs*28	ENST00000245479	NM_000346.3	267	cct/ccTt	3/3	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.481969066747014	2		524	775	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908830	101908841	+	inframe_deletion	In_Frame_Del	DEL	TGCTGACATCTA	TGCTGACATCTA	-	novel	NA	P-0036598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	203	570	5	ENST00000374994.4:c.1197_1208del	p.Asp400_Ala403del	p.D400_A403del	ENST00000374994	NM_004612.2	398	cgTGCTGACATCTAt/cgt	7/9	0.443613436775275	2	FACETS	0.786	0.735	0.838	0.786	0.735	0.838	SUBCLONAL	2	TRUE	0	0.481969066747014	2		575	536	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058736	47058737	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	66	475	0	ENST00000409792.3:c.7541dup	p.His2514GlnfsTer6	p.H2514Qfs*6	ENST00000409792	NM_014159.6	2514	cac/caAc	21/21	0.320141749128614	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.320141749128614	1		475	296	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378590	25378590	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	187	734	0	ENST00000311936.3:c.408T>G	p.Ser136Arg	p.S136R	ENST00000311936	NM_004985.3	136	agT/agG	4/5	0.320141749128614	5	FACETS	0.877	0.814	0.943	0.877	0.814	0.943	CLONAL	3	TRUE	2	0.320141749128614	5		734	657	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620510	52620510	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	95	621	0	ENST00000394830.3:c.3243del	p.Gly1082ValfsTer52	p.G1082Vfs*52	ENST00000394830	NM_018313.4	1081	aaA/aa	21/30	0.320141749128614	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.320141749128614	1		621	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579580	7579580	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	240	541	0	ENST00000269305.4:c.107del	p.Pro36ArgfsTer8	p.P36Rfs*8	ENST00000269305	NM_001126112.2	36	cCg/cg	4/11	0.789614350728382	1	FACETS	0.973	0.934	1	0.973	0.934	1	CLONAL	1	TRUE	0	0.867658724983559	1		541	322	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909656	76909656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1557118764	NA	P-0036609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	198	379	0	ENST00000373344.5:c.4249C>T	p.Arg1417Trp	p.R1417W	ENST00000373344	NM_000489.3	1417	Cgg/Tgg	14/35	1	2	FACETS	0.863	0.806	0.921	0.863	0.806	0.921	CLONAL	1	TRUE	1	0.867658724983559	2		379	529	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575469	64575469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs794728650	NA	P-0036609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	267	510	3	ENST00000312049.6:c.548G>A	p.Trp183Ter	p.W183*	ENST00000312049	NM_130799.2	183	tGg/tAg	3/10	0.867441640705211	1	FACETS	0.976	0.939	1	0.976	0.939	1	CLONAL	1	TRUE	0	0.867658724983559	1		513	357	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923158	39923158	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	233	495	0	ENST00000378444.4:c.3550G>A	p.Glu1184Lys	p.E1184K	ENST00000378444	NM_001123385.1	1184	Gaa/Aaa	8/15	1	2	FACETS	0.814	0.763	0.865	0.814	0.763	0.865	CLONAL	1	TRUE	1	0.867658724983559	2		495	660	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937918	76937918	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	316	546	0	ENST00000373344.5:c.2830G>T	p.Glu944Ter	p.E944*	ENST00000373344	NM_000489.3	944	Gaa/Taa	9/35	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.867658724983559	2		546	622	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201693	66201693	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0121487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	247	401	0	ENST00000273854.3:c.2809C>G	p.Arg937Gly	p.R937G	ENST00000273854	NM_004439.5	937	Cgt/Ggt	16/18	1	2	FACETS	0.962	0.908	1	0.962	0.908	1	CLONAL	1	NA	1	0.923450861210053	2		401	556	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0036612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	78	625	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.298674108247013	1	FACETS	0.983	0.868	1	0.983	0.868	1	CLONAL	1	TRUE	0	0.311515448197177	1		625	430	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0036615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	117	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.26109984545116	3	FACETS	0.995	0.902	1	0.995	0.902	1	CLONAL	2	TRUE	1	0.26109984545116	3		452	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057520005	NA	P-0036615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	112	485	0	ENST00000269305.4:c.820G>T	p.Val274Phe	p.V274F	ENST00000269305	NM_001126112.2	274	Gtt/Ttt	8/11	0.26109984545116	3	FACETS	0.879	0.793	0.968	0.879	0.793	0.968	CLONAL	2	TRUE	1	0.26109984545116	3		485	552	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031269	36031269	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	55	439	0	ENST00000358208.4:c.1388G>T	p.Arg463Leu	p.R463L	ENST00000358208		463	cGg/cTg	11/12	0.26109984545116	3	FACETS	1	0.941	1			1	CLONAL	1	TRUE	NA	0.26109984545116	3		439	399	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830534	72830534	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	35	610	0	ENST00000268489.5:c.6047A>T	p.Glu2016Val	p.E2016V	ENST00000268489	NM_006885.3	2016	gAg/gTg	9/10	1	2	FACETS	0.523	0.428	0.629	0.523	0.428	0.629	SUBCLONAL	1	TRUE	1	0.26109984545116	2		610	513	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610389	10610389	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	112	602	0	ENST00000171111.5:c.321del	p.Phe107LeufsTer50	p.F107Lfs*50	ENST00000171111	NM_203500.1	107	ttC/tt	2/6	0.219540298613844	2	FACETS	0.814	0.735	0.897	0.814	0.735	0.897	CLONAL	2	TRUE	0	0.26109984545116	2		602	527	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0036617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	76	469	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.911	0.802	1	0.911	0.802	1	CLONAL	1	TRUE	1	0.380183337821371	2		469	439	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682980	241682980	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1463008959	NA	P-0036617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	92	336	0	ENST00000366560.3:c.43G>T	p.Val15Leu	p.V15L	ENST00000366560	NM_000143.3	15	Gtg/Ttg	1/10	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.380183337821371	2		336	452	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793489	18793489	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0036617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	66	248	0	ENST00000266497.5:c.4185+1G>T		p.X1395_splice	ENST00000266497		1395			1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.380183337821371	2		248	302	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845410	156845410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	150	739	0	ENST00000524377.1:c.1453G>A	p.Gly485Arg	p.G485R	ENST00000524377	NM_002529.3	485	Ggg/Agg	12/17	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.380183337821371	2		739	720	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436425	110436425	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	193	571	0	ENST00000375856.3:c.1976G>T	p.Gly659Val	p.G659V	ENST00000375856	NM_003749.2	659	gGc/gTc	1/2	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.380183337821371	2		571	847	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647549	23647549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	102	567	0	ENST00000261584.4:c.318del	p.Phe107LeufsTer70	p.F107Lfs*70	ENST00000261584	NM_024675.3	106	tcC/tc	4/13	1	2	FACETS	0.865	0.775	0.961	0.865	0.775	0.961	CLONAL	1	TRUE	1	0.380183337821371	2		567	620	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602443	10602445	+	frameshift_variant	Frame_Shift_Del	DEL	CGC	CGC	GG	novel	NA	P-0036617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	155	597	1	ENST00000171111.5:c.1133_1135delinsCC	p.Gly378AlafsTer22	p.G378Afs*22	ENST00000171111	NM_203500.1	378	gGCGgc/gCCgc	3/6	0.380183337821371	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.380183337821371	1		598	562	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123760	11123864	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGCCCTTCCTCATCATCGTGCCTCTCTCGTGAGTACCCGCTGCCAGCAACATCCCACACGCCGCTCACACGCTCCTGTGTTTGTTTCCTAAGTTTGCCGCAGTA	GGGCCCTTCCTCATCATCGTGCCTCTCTCGTGAGTACCCGCTGCCAGCAACATCCCACACGCCGCTCACACGCTCCTGTGTTTGTTTCCTAAGTTTGCCGCAGTA	-	novel	NA	P-0036617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	55	513	0	ENST00000358026.2:c.2411_2438+77del		p.X804_splice	ENST00000358026	NM_001128849.1	804		16/36	0.380183337821371	1	FACETS	0.542	0.465	0.627	0.542	0.465	0.627	SUBCLONAL	1	TRUE	0	0.380183337821371	1		513	432	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646111	215646111	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	74	511	0	ENST00000260947.4:c.487G>T	p.Val163Leu	p.V163L	ENST00000260947	NM_000465.2	163	Gtg/Ttg	4/11	1	2	FACETS	0.7	0.614	0.793	0.7	0.614	0.793	SUBCLONAL	1	TRUE	1	0.380183337821371	2		511	556	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569241	67569241	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	59	432	0	ENST00000274335.5:c.358G>A	p.Glu120Lys	p.E120K	ENST00000274335		120	Gag/Aag	2/15	1	2	FACETS	0.633	0.546	0.729	0.633	0.546	0.729	SUBCLONAL	1	TRUE	1	0.380183337821371	2		432	490	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367336	50367336	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	85	304	0	ENST00000331340.3:c.143A>T	p.Lys48Met	p.K48M	ENST00000331340	NM_006060.4	48	aAg/aTg	3/8	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.380183337821371	2		304	392	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843259	128843259	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	129	641	0	ENST00000249373.3:c.366C>G	p.Ile122Met	p.I122M	ENST00000249373	NM_005631.4	122	atC/atG	2/12	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.380183337821371	2		641	602	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054828	5054828	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	56	280	0	ENST00000381652.3:c.880G>T	p.Gly294Cys	p.G294C	ENST00000381652	NM_004972.3	294	Ggt/Tgt	7/25	0.380183337821371	1	FACETS	0.795	0.686	0.913	0.795	0.686	0.913	CLONAL	1	TRUE	0	0.380183337821371	1		280	300	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221976	98221976	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	84	389	0	ENST00000331920.6:c.2793del	p.Val932SerfsTer30	p.V932Sfs*30	ENST00000331920	NM_000264.3	931	ccC/cc	17/24	0.380183337821371	1	FACETS	0.86	0.764	0.962	0.86	0.764	0.962	CLONAL	1	TRUE	0	0.380183337821371	1		389	416	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039633	47039644	+	inframe_deletion	In_Frame_Del	DEL	TCCTGCAGGCCC	TCCTGCAGGCCC	-	novel	NA	P-0036617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	122	586	0	ENST00000377604.3:c.1086_1097del	p.Ile362_Leu366delinsMet	p.I362_L366delinsM	ENST00000377604	NM_001204468.1	362	aTCCTGCAGGCCCtg/atg	11/24	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.380183337821371	2		586	602	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412141	63412141	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	128	845	1	ENST00000330258.3:c.1026C>A	p.Asp342Glu	p.D342E	ENST00000330258	NM_152424.3	342	gaC/gaA	2/2	1	2	FACETS	0.899	0.815	0.987	0.899	0.815	0.987	CLONAL	1	TRUE	1	0.380183337821371	2		846	749	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76949391	76949391	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	57	390	0	ENST00000373344.5:c.406G>A	p.Glu136Lys	p.E136K	ENST00000373344	NM_000489.3	136	Gaa/Aaa	6/35	1	2	FACETS	0.623	0.535	0.719	0.623	0.535	0.719	SUBCLONAL	1	TRUE	1	0.380183337821371	2		390	481	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020374	123020374	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	33	328	0	ENST00000355640.3:c.862G>T	p.Gly288Ter	p.G288*	ENST00000355640		288	Gga/Tga	2/7	1	2	FACETS	0.573	0.468	0.691	0.573	0.468	0.691	SUBCLONAL	1	TRUE	1	0.380183337821371	2		328	303	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0036618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	98	571	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.3	3	FACETS	1	0.972	1	0.64	0.571	0.712	CLONAL	1	TRUE	1	0.26	3		572	666	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228613023	228613023	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs759975640	NA	P-0036618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	28	298	0	ENST00000366696.1:c.4G>T	p.Ala2Ser	p.A2S	ENST00000366696	NM_003493.2	2	Gcc/Tcc	1/1	1	2	FACETS	0.841	0.675	1	0.841	0.675	1	CLONAL	1	TRUE	1	0.26	2		298	256	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618598	37618605	+	frameshift_variant	Frame_Shift_Del	DEL	GACCGAAG	GACCGAAG	-	novel	NA	P-0036618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	87	424	0	ENST00000447079.4:c.275_282del	p.Asp92GlyfsTer32	p.D92Gfs*32	ENST00000447079	NM_015083.1	92	GACCGAAGg/g	1/14	0.3	3	FACETS	0.857	0.763	0.958	0.857	0.763	0.958	CLONAL	2	TRUE	1	0.26	3		424	441	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940451	13940451	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	21	320	0	ENST00000405192.2:c.1055G>T	p.Trp352Leu	p.W352L	ENST00000405192	NM_001163147.1	352	tGg/tTg	11/12	1	2	FACETS	0.42	0.322	0.533	0.42	0.322	0.533	SUBCLONAL	1	TRUE	1	0.26	2		320	385	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054415	42054415	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	101	194	0	ENST00000219905.7:c.7601del	p.Gly2534AspfsTer23	p.G2534Dfs*23	ENST00000219905	NM_001164273.1	2533	atG/at	22/24	0.764862614682855	1	FACETS	0.954	0.881	1	0.954	0.881	1	CLONAL	1	TRUE	0	0.764862614682855	1		194	171	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593598	55593660	+	inframe_deletion	In_Frame_Del	DEL	TACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAAC	TACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAAC	-	novel	NA	P-0036620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	110	272	0	ENST00000288135.5:c.1665_1727del	p.Gln556_Leu576del	p.Q556_L576del	ENST00000288135	NM_000222.2	555	gTACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAACtt/gtt	11/21	1	2	FACETS	0.846	0.769	0.926	0.846	0.769	0.926	CLONAL	1	TRUE	1	0.764862614682855	2		272	340	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0036621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	40	201	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.319684753436163	2		201	235	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0036621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	41	275	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.319684753436163	2		275	216	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0036621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	36	214	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	1	2	FACETS	0.785	0.648	0.937	0.785	0.648	0.937	CLONAL	1	TRUE	1	0.319684753436163	2		214	287	SUCCESS
APC	324	MSKCC	GRCh37	5	112175524	112175524	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	58	255	0	ENST00000257430.4:c.4233del	p.Ser1411ArgfsTer4	p.S1411Rfs*4	ENST00000257430	NM_000038.5	1411	agT/ag	16/16	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.319684753436163	2		255	362	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593466	48593466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064796102	NA	P-0036621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	68	285	0	ENST00000342988.3:c.1217C>T	p.Ala406Val	p.A406V	ENST00000342988	NM_005359.5	406	gCg/gTg	10/12	0.319684753436163	1	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	0	0.319684753436163	1		285	357	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448601	89448601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775665893	NA	P-0036621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	72	387	0	ENST00000336596.2:c.1565G>A	p.Arg522His	p.R522H	ENST00000336596	NM_005233.5	522	cGc/cAc	7/17	NA	2	FACETS	0.946	0.829	1			1	INDETERMINATE	1	TRUE	NA	0.319684753436163	2		387	476	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655378	67655378	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1319839645	NA	P-0036621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	82	364	0	ENST00000264010.4:c.1241C>T	p.Ala414Val	p.A414V	ENST00000264010	NM_006565.3	414	gCt/gTt	7/12	1	2	FACETS	0.957	0.846	1	0.957	0.846	1	CLONAL	1	TRUE	1	0.319684753436163	2		364	536	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266816	18266816	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750768114	NA	P-0036625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	136	816	1	ENST00000222254.8:c.127G>A	p.Val43Met	p.V43M	ENST00000222254	NM_005027.3	43	Gtg/Atg	2/16	1	2	FACETS	0.566	0.515	0.62	0.566	0.515	0.62	SUBCLONAL	1	TRUE	1	0.623820777544067	2		817	770	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419867	41419867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1569159161	NA	P-0036625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	164	522	0	ENST00000373198.4:c.454G>A	p.Ala152Thr	p.A152T	ENST00000373198	NM_133170.3	152	Gcc/Acc	3/32	1	2	FACETS	0.866	0.799	0.936	0.866	0.799	0.936	CLONAL	1	TRUE	1	0.623820777544067	2		522	607	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531806	46531806	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	105	555	0	ENST00000262741.5:c.541C>G	p.Leu181Val	p.L181V	ENST00000262741	NM_003629.3	181	Ctg/Gtg	5/10	1	2	FACETS	0.453	0.406	0.503	0.453	0.406	0.503	SUBCLONAL	1	TRUE	1	0.623820777544067	2		555	743	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323180	31323180	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	530	874	0	ENST00000412585.2:c.809C>A	p.Ala270Asp	p.A270D	ENST00000412585	NM_005514.6	270	gCt/gAt	4/8	0.623820777544067	3	FACETS	0.986	0.949	1	0.986	0.949	1	CLONAL	2	TRUE	1	0.623820777544067	3		874	1130	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0036627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	847	775	2	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.812056972056825	2	FACETS	0.966	0.948	0.982	0.966	0.948	0.982	CLONAL	2	TRUE	0	0.848349347706636	2		777	1034	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598140	52598140	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	67	734	0	ENST00000394830.3:c.3726G>T	p.Gln1242His	p.Q1242H	ENST00000394830	NM_018313.4	1242	caG/caT	24/30	0.814219273204698	2	FACETS	0.189	0.164	0.217	0.095	0.082	0.109	SUBCLONAL	1	TRUE	0	0.848349347706636	2		734	834	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614980	23614980	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	71	417	0	ENST00000261584.4:c.3361G>C	p.Gly1121Arg	p.G1121R	ENST00000261584	NM_024675.3	1121	Ggt/Cgt	13/13	0.593219191297961	3	FACETS	0.357	0.312	0.407			1	SUBCLONAL	1	TRUE	NA	0.848349347706636	3		417	667	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598159	52598159	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs560772391	NA	P-0036627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	68	712	0	ENST00000394830.3:c.3707A>G	p.Tyr1236Cys	p.Y1236C	ENST00000394830	NM_018313.4	1236	tAc/tGc	24/30	0.814219273204698	2	FACETS	0.197	0.17	0.225	0.098	0.085	0.113	SUBCLONAL	1	TRUE	0	0.848349347706636	2		712	815	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0036628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	62	631	4	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.337045660811651	1	FACETS	0.82	0.712	0.937	0.82	0.712	0.937	CLONAL	1	TRUE	0	0.337045660811651	1		635	373	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301078	65301078	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0036628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	22	303	0	ENST00000342505.4:c.3369+1G>A		p.X1123_splice	ENST00000342505	NM_002227.2	1123			0.337045660811651	1	FACETS	0.537	0.418	0.674	0.537	0.418	0.674	SUBCLONAL	1	TRUE	0	0.337045660811651	1		303	202	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424736	49424736	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	65	817	0	ENST00000301067.7:c.13611G>C	p.Lys4537Asn	p.K4537N	ENST00000301067	NM_003482.3	4537	aaG/aaC	40/54	0.337045660811651	3	FACETS	0.784	0.68	0.896	0.392	0.34	0.448	SUBCLONAL	1	TRUE	1	0.337045660811651	3		817	575	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215617263	215617263	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375515606	NA	P-0036628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	30	420	0	ENST00000260947.4:c.1585C>T	p.Arg529Trp	p.R529W	ENST00000260947	NM_000465.2	529	Cgg/Tgg	7/11	1	2	FACETS	0.664	0.537	0.807	0.664	0.537	0.807	SUBCLONAL	1	TRUE	1	0.337045660811651	2		420	268	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268205	153268208	+	frameshift_variant	Frame_Shift_Del	DEL	TGGT	TGGT	-	novel	NA	P-0036628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	35	324	0	ENST00000281708.4:c.600_603del	p.Pro201ValfsTer37	p.P201Vfs*37	ENST00000281708	NM_033632.3	200	gtACCA/gt	4/12	1	2	FACETS	0.724	0.595	0.866	0.724	0.595	0.866	SUBCLONAL	1	TRUE	1	0.337045660811651	2		324	287	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589153	67589155	+	inframe_deletion	In_Frame_Del	DEL	ATC	ATC	-	novel	NA	P-0036628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	28	312	0	ENST00000274335.5:c.1142_1144del	p.Ile381del	p.I381del	ENST00000274335		381	ATC/-	9/15	1	2	FACETS	1	0.836	1	1	0.836	1	CLONAL	1	TRUE	1	0.337045660811651	2		312	160	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277050	38277050	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0036628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	42	645	0	ENST00000425967.3:c.1377+1G>C		p.X459_splice	ENST00000425967	NM_001174067.1	459			1	2	FACETS	0.784	0.657	0.923	0.784	0.657	0.923	CLONAL	1	TRUE	1	0.337045660811651	2		645	318	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577508	7577508	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060501201	NA	P-0036629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	324	735	1	ENST00000269305.4:c.773A>G	p.Glu258Gly	p.E258G	ENST00000269305	NM_001126112.2	258	gAa/gGa	7/11	0.78303714229192	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.787723653833451	1		736	482	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631305	117631305	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	222	510	0	ENST00000368508.3:c.6373G>T	p.Val2125Phe	p.V2125F	ENST00000368508	NM_002944.2	2125	Gtt/Ttt	40/43	1	2	FACETS	0.829	0.775	0.884	0.829	0.775	0.884	CLONAL	1	TRUE	1	0.787723653833451	2		510	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0036630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	496	535	0	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	0.841989485218288	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.841989485218288	1		535	669	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446166	49446166	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs398123715	NA	P-0036630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	432	843	0	ENST00000301067.7:c.1300del	p.Leu434Ter	p.L434*	ENST00000301067	NM_003482.3	434	Cta/ta	10/54	1	2	FACETS	0.915	0.874	0.957	0.915	0.874	0.957	CLONAL	1	TRUE	1	0.841989485218288	2		843	1121	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988577	41988577	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	262	555	1	ENST00000219905.7:c.1369A>G	p.Lys457Glu	p.K457E	ENST00000219905	NM_001164273.1	457	Aaa/Gaa	3/24	1	2	FACETS	0.906	0.854	0.959	0.906	0.854	0.959	CLONAL	1	TRUE	1	0.841989485218288	2		556	687	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420250	88420250	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	332	618	0	ENST00000360948.2:c.2436G>C	p.Gln812His	p.Q812H	ENST00000360948	NM_001012338.2	812	caG/caC	19/19	1	2	FACETS	0.929	0.882	0.976	0.929	0.882	0.976	CLONAL	1	TRUE	1	0.841989485218288	2		618	849	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129638	2129638	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	599	1004	1	ENST00000219476.3:c.3365G>T	p.Arg1122Leu	p.R1122L	ENST00000219476	NM_000548.3	1122	cGt/cTt	29/42	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.841989485218288	2		1005	1415	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551260	29551260	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	421	765	0	ENST00000389048.3:c.1370T>A	p.Phe457Tyr	p.F457Y	ENST00000389048	NM_004304.4	457	tTc/tAc	6/29	1	2	FACETS	0.968	0.925	1	0.968	0.925	1	CLONAL	1	TRUE	1	0.841989485218288	2		765	1033	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99181130	99181130	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1322380161	NA	P-0036630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	428	756	0	ENST00000074304.5:c.2071A>G	p.Ile691Val	p.I691V	ENST00000074304	NM_001134224.1	691	Att/Gtt	20/26	1	2	FACETS	0.971	0.928	1	0.971	0.928	1	CLONAL	1	TRUE	1	0.841989485218288	2		756	1047	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376762	31376762	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	139	652	0	ENST00000328111.2:c.757C>A	p.Gln253Lys	p.Q253K	ENST00000328111	NM_006892.3	253	Cag/Aag	7/23	1	2	FACETS	0.358	0.325	0.392	0.358	0.325	0.392	SUBCLONAL	1	TRUE	1	0.841989485218288	2		652	922	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647535	117647535	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	255	722	0	ENST00000368508.3:c.5409G>C	p.Trp1803Cys	p.W1803C	ENST00000368508	NM_002944.2	1803	tgG/tgC	33/43	1	2	FACETS	0.948	0.894	1	0.948	0.894	1	CLONAL	1	TRUE	1	0.841989485218288	2		722	639	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940428	13940428	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	236	507	0	ENST00000405192.2:c.1078G>T	p.Ala360Ser	p.A360S	ENST00000405192	NM_001163147.1	360	Gct/Tct	11/12	1	2	FACETS	0.941	0.884	0.997	0.941	0.884	0.997	CLONAL	1	TRUE	1	0.841989485218288	2		507	596	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508563	106508563	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	215	364	0	ENST00000359195.3:c.557C>A	p.Ala186Glu	p.A186E	ENST00000359195	NM_002649.2	186	gCg/gAg	2/11	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.841989485218288	2		364	506	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371758	116371758	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201980687	NA	P-0036630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	303	517	0	ENST00000397752.3:c.1237C>T	p.Arg413Cys	p.R413C	ENST00000397752	NM_000245.2	413	Cgt/Tgt	3/21	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.841989485218288	2		517	655	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852220	128852220	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	554	996	1	ENST00000249373.3:c.2292G>T	p.Gln764His	p.Q764H	ENST00000249373	NM_005631.4	764	caG/caT	12/12	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.841989485218288	2		997	1253	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409045	139409045	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0036630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	663	1204	0	ENST00000277541.6:c.2124C>G	p.Tyr708Ter	p.Y708*	ENST00000277541	NM_017617.3	708	taC/taG	13/34	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.841989485218288	2		1204	1501	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325431	1325431	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	352	645	0	ENST00000400841.2:c.244T>A	p.Ser82Thr	p.S82T	ENST00000400841		82	Tcg/Acg	3/6	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.841989485218288	2		645	827	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650837	48650837	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	410	887	0	ENST00000376670.3:c.706G>C	p.Gly236Arg	p.G236R	ENST00000376670	NM_002049.3	236	Ggg/Cgg	4/6	1	2	FACETS	0.916	0.874	0.959	0.916	0.874	0.959	CLONAL	1	TRUE	1	0.841989485218288	2		887	1063	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410903	63410903	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	437	855	0	ENST00000330258.3:c.2264A>T	p.Glu755Val	p.E755V	ENST00000330258	NM_152424.3	755	gAg/gTg	2/2	1	2	FACETS	0.959	0.917	1	0.959	0.917	1	CLONAL	1	TRUE	1	0.841989485218288	2		855	1082	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227930	123227930	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	254	618	0	ENST00000218089.9:c.3641C>A	p.Ser1214Tyr	p.S1214Y	ENST00000218089	NM_001042749.1	1214	tCc/tAc	33/35	1	2	FACETS	0.973	0.918	1	0.973	0.918	1	CLONAL	1	TRUE	1	0.841989485218288	2		618	620	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181402	38181402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	326	433	0	ENST00000396334.3:c.415G>A	p.Glu139Lys	p.E139K	ENST00000396334	NM_002468.4	139	Gag/Aag	2/5	0.442584990726909	1	FACETS	0.753	0.72	0.785	0.753	0.72	0.785	INDETERMINATE	1	TRUE	0	0.873937886183481	1		433	558	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258070	123258070	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519799	NA	P-0036631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	118	660	0	ENST00000358487.5:c.1611G>A	p.Met537Ile	p.M537I	ENST00000358487	NM_000141.4	537	atG/atA	12/18	0.873937886183481	1	FACETS	0.753	0.699	0.805	0.753	0.699	0.805	SUBCLONAL	1	TRUE	0	0.873937886183481	1		660	202	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271969	18271969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1418268495	NA	P-0036631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	438	497	1	ENST00000222254.8:c.572C>T	p.Ser191Leu	p.S191L	ENST00000222254	NM_005027.3	191	tCg/tTg	5/16	0.445640794740959	1	FACETS	0.831	0.803	0.859	0.831	0.803	0.859	INDETERMINATE	1	TRUE	0	0.873937886183481	1		498	679	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412639	139412639	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1037236860	NA	P-0036631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	317	949	1	ENST00000277541.6:c.1205C>T	p.Ser402Leu	p.S402L	ENST00000277541	NM_017617.3	402	tCg/tTg	7/34	0.873937886183481	2	FACETS	0.502	0.473	0.533	0.251	0.236	0.267	SUBCLONAL	1	TRUE	0	0.873937886183481	2		950	1444	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890145	76890145	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	54	655	0	ENST00000373344.5:c.4749G>C	p.Lys1583Asn	p.K1583N	ENST00000373344	NM_000489.3	1583	aaG/aaC	17/35	0.445640794740959	1	FACETS	0.273	0.235	0.313	0.273	0.235	0.313	INDETERMINATE	1	TRUE	0	0.873937886183481	1		655	255	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056533	26056533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1332170864	NA	P-0036631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	167	287	0	ENST00000343677.2:c.124G>A	p.Glu42Lys	p.E42K	ENST00000343677	NM_005319.3	42	Gag/Aag	1/1	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.873937886183481	2		287	360	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045930	26045930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	244	528	1	ENST00000540144.1:c.292G>A	p.Glu98Lys	p.E98K	ENST00000540144	NM_003531.2	98	Gag/Aag	1/1	1	2	FACETS	0.969	0.914	1	0.969	0.914	1	CLONAL	1	TRUE	1	0.873937886183481	2		529	576	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332632	65332632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	68	496	0	ENST00000342505.4:c.907C>T	p.His303Tyr	p.H303Y	ENST00000342505	NM_002227.2	303	Cat/Tat	7/25	0.624299106966244	3	FACETS	0.465	0.405	0.529	0.155	0.135	0.177	SUBCLONAL	1	TRUE	0	0.873937886183481	3		496	481	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858343	59858343	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375246789	NA	P-0036631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	54	434	0	ENST00000259008.2:c.1652C>T	p.Ala551Val	p.A551V	ENST00000259008	NM_032043.2	551	gCg/gTg	12/20	0.873937886183481	1	FACETS	0.295	0.254	0.338	0.295	0.254	0.338	SUBCLONAL	1	TRUE	0	0.873937886183481	1		434	236	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438509	52438509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035262201	NA	P-0036631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	507	819	0	ENST00000460680.1:c.1210G>A	p.Asp404Asn	p.D404N	ENST00000460680	NM_004656.3	404	Gac/Aac	12/17	0.442584990726909	1	FACETS	0.769	0.743	0.795	0.769	0.743	0.795	INDETERMINATE	1	TRUE	0	0.873937886183481	1		819	849	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042169	14042169	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	70	352	3	ENST00000311895.7:c.2716G>A	p.Ala906Thr	p.A906T	ENST00000311895	NM_005236.2	906	Gca/Aca	11/11	0.445640794740959	1	FACETS	0.333	0.293	0.375	0.333	0.293	0.375	INDETERMINATE	1	TRUE	0	0.873937886183481	1		355	271	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942786	15942786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	162	698	0	ENST00000268712.3:c.6916G>A	p.Glu2306Lys	p.E2306K	ENST00000268712	NM_006311.3	2306	Gag/Aag	44/46	0.441602857214257	1	FACETS	0.321	0.295	0.348	0.321	0.295	0.348	INDETERMINATE	1	TRUE	0	0.873937886183481	1		698	650	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758775	41758775	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	709	924	1	ENST00000301178.4:c.1829G>C	p.Arg610Pro	p.R610P	ENST00000301178	NM_021913.4	610	cGa/cCa	16/20	0.621520461991489	3	FACETS	0.871	0.844	0.898	0.871	0.844	0.898	CLONAL	2	TRUE	1	0.873937886183481	3		925	1338	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422561	225422561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	66	228	0	ENST00000264414.4:c.79G>A	p.Glu27Lys	p.E27K	ENST00000264414	NM_003590.4	27	Gaa/Aaa	2/16	0.873937886183481	1	FACETS	0.868	0.794	0.938	0.868	0.794	0.938	CLONAL	1	TRUE	0	0.873937886183481	1		228	98	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655198	45655198	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	804	715	1	ENST00000407780.3:c.654G>C	p.Glu218Asp	p.E218D	ENST00000407780	NM_001283052.1	218	gaG/gaC	4/7	0.873937886183481	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.873937886183481	2		716	864	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656984	45656984	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	874	917	1	ENST00000407780.3:c.172G>C	p.Glu58Gln	p.E58Q	ENST00000407780	NM_001283052.1	58	Gag/Cag	3/7	0.873937886183481	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.873937886183481	2		918	976	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272139	142272139	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	51	530	2	ENST00000350721.4:c.2735G>T	p.Arg912Ile	p.R912I	ENST00000350721	NM_001184.3	912	aGa/aTa	13/47	0.651059857246986	4	FACETS	0.385	0.327	0.449	0.128	0.109	0.15	SUBCLONAL	1	TRUE	1	0.873937886183481	4		532	568	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272693	142272693	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	71	558	0	ENST00000350721.4:c.2506G>A	p.Asp836Asn	p.D836N	ENST00000350721	NM_001184.3	836	Gac/Aac	11/47	0.651059857246986	4	FACETS	0.502	0.438	0.571	0.167	0.146	0.191	SUBCLONAL	1	TRUE	1	0.873937886183481	4		558	606	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272756	142272756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	68	532	0	ENST00000350721.4:c.2443G>A	p.Asp815Asn	p.D815N	ENST00000350721	NM_001184.3	815	Gat/Aat	11/47	0.651059857246986	4	FACETS	0.449	0.391	0.513	0.15	0.13	0.171	SUBCLONAL	1	TRUE	1	0.873937886183481	4		532	649	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272812	142272812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	56	410	0	ENST00000350721.4:c.2387G>A	p.Arg796Lys	p.R796K	ENST00000350721	NM_001184.3	796	aGa/aAa	11/47	0.651059857246986	4	FACETS	0.482	0.413	0.557	0.161	0.137	0.186	SUBCLONAL	1	TRUE	1	0.873937886183481	4		410	498	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61197647	61197647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	62	444	0	ENST00000301761.2:c.29C>T	p.Ser10Leu	p.S10L	ENST00000301761	NM_017841.2	10	tCg/tTg	1/4	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.271893376640953	2		444	325	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696644	47696644	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519964	NA	P-0036632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	46	532	0	ENST00000347630.2:c.304T>G	p.Phe102Val	p.F102V	ENST00000347630	NM_001007230.1	102	Ttc/Gtc	5/11	0.159357260793949	1	FACETS	1	0.915	1	1	0.915	1	INDETERMINATE	1	FALSE	0	0.271893376640953	1		532	261	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	24	331	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.836	1	1	0.836	1	CLONAL	1	TRUE	1	0.626341386998035	2		331	74	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	72	498	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.626341386998035	2		498	228	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231707	66231707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1211795184	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	47	416	0	ENST00000273854.3:c.1993G>A	p.Glu665Lys	p.E665K	ENST00000273854	NM_004439.5	665	Gaa/Aaa	11/18	1	2	FACETS	0.739	0.632	0.855	0.739	0.632	0.855	SUBCLONAL	1	TRUE	1	0.626341386998035	2		416	203	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941633	48941633	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	17	207	0	ENST00000267163.4:c.943G>T	p.Glu315Ter	p.E315*	ENST00000267163	NM_000321.2	315	Gaa/Taa	10/27	0.605424427144751	1	FACETS	0.313	0.236	0.403	0.313	0.236	0.403	SUBCLONAL	1	TRUE	0	0.626341386998035	1		207	119	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163783	72163783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	32	428	2	ENST00000357731.5:c.575G>A	p.Gly192Glu	p.G192E	ENST00000357731	NM_173808.2	192	gGa/gAa	4/7	1	2	FACETS	0.587	0.482	0.703	0.587	0.482	0.703	SUBCLONAL	1	TRUE	1	0.626341386998035	2		430	174	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530405	187530405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	75	383	2	ENST00000441802.2:c.10138G>A	p.Gly3380Arg	p.G3380R	ENST00000441802	NM_005245.3	3380	Gga/Aga	16/27	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.626341386998035	2		385	183	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602286	10602286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	17	527	1	ENST00000171111.5:c.1292C>T	p.Ser431Phe	p.S431F	ENST00000171111	NM_203500.1	431	tCc/tTc	3/6	1	2	FACETS	0.305	0.228	0.395	0.305	0.228	0.395	SUBCLONAL	1	TRUE	1	0.626341386998035	2		528	178	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52725428	52725428	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1194775389	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	107	573	0	ENST00000322088.6:c.1595C>T	p.Pro532Leu	p.P532L	ENST00000322088	NM_014225.5	532	cCg/cTg	13/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.626341386998035	2		573	236	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812205	43812205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866559375	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	113	540	3	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	0.626341386998035	2		543	262	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067398	37067398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782273	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	54	382	3	ENST00000231790.2:c.1309C>T	p.Pro437Ser	p.P437S	ENST00000231790	NM_000249.3	437	Cct/Tct	12/19	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.626341386998035	2		385	154	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349733	15349733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754054879	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	62	583	0	ENST00000263377.2:c.3841C>T	p.Arg1281Trp	p.R1281W	ENST00000263377	NM_058243.2	1281	Cgg/Tgg	19/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.626341386998035	2		583	140	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726927	61726927	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	100	507	2	ENST00000401558.2:c.511C>T	p.Leu171Phe	p.L171F	ENST00000401558	NM_003400.3	171	Ctt/Ttt	7/25	0.185883899394701	3	FACETS	0.822	0.747	0.899	0.822	0.747	0.899	INDETERMINATE	2	TRUE	1	0.626341386998035	3		509	255	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582897	95582897	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	22	393	0	ENST00000393063.1:c.1645T>C	p.Ser549Pro	p.S549P	ENST00000393063	NM_030621.3	549	Tct/Cct	11/28	0.289427792552176	1	FACETS	0.207	0.161	0.261	0.207	0.161	0.261	INDETERMINATE	1	TRUE	0	0.626341386998035	1		393	233	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	62	457	1	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.626341386998035	2		458	193	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411137	63411137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	79	266	3	ENST00000330258.3:c.2030C>T	p.Ser677Phe	p.S677F	ENST00000330258	NM_152424.3	677	tCc/tTc	2/2	0.309456723970721	2	FACETS	1	0.973	1			1	INDETERMINATE	2	TRUE	NA	0.626341386998035	2		269	112	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031678	69031678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	62	389	2	ENST00000288368.4:c.3433C>T	p.Pro1145Ser	p.P1145S	ENST00000288368	NM_024870.2	1145	Ccc/Tcc	28/40	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.626341386998035	2		391	146	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216515	36216515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372953726	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	61	624	2	ENST00000222270.7:c.3778C>T	p.Arg1260Cys	p.R1260C	ENST00000222270	NM_014727.1	1260	Cgt/Tgt	12/37	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.626341386998035	2		626	192	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453400	40453400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	42	701	0	ENST00000345506.4:c.1097C>T	p.Pro366Leu	p.P366L	ENST00000345506	NM_003152.3	366	cCc/cTc	10/20	1	2	FACETS	0.888	0.755	1	0.888	0.755	1	CLONAL	1	TRUE	1	0.626341386998035	2		701	151	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292591	15292591	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758913191	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	51	593	0	ENST00000263388.2:c.2588C>T	p.Ser863Leu	p.S863L	ENST00000263388	NM_000435.2	863	tCg/tTg	17/33	1	2	FACETS	0.831	0.716	0.953	0.831	0.716	0.953	CLONAL	1	TRUE	1	0.626341386998035	2		593	196	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462975	120462975	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1435723160	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	59	381	1	ENST00000256646.2:c.5356C>T	p.Arg1786Ter	p.R1786*	ENST00000256646	NM_024408.3	1786	Cga/Tga	30/34	1	2	FACETS	0.951	0.832	1	0.951	0.832	1	CLONAL	1	TRUE	1	0.626341386998035	2		382	198	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500591	99500591	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1442885994	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	47	369	4	ENST00000268035.6:c.4024G>A	p.Glu1342Lys	p.E1342K	ENST00000268035	NM_000875.3	1342	Gag/Aag	21/21	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.626341386998035	2		373	131	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187069	11187069	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	65	427	0	ENST00000361445.4:c.6349C>T	p.Gln2117Ter	p.Q2117*	ENST00000361445	NM_004958.3	2117	Cag/Tag	45/58	0.309456723970721	3	FACETS	1	0.948	1			1	INDETERMINATE	1	TRUE	NA	0.626341386998035	3		427	236	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17354356	17354356	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	41	335	2	ENST00000375499.3:c.428T>A	p.Leu143Ter	p.L143*	ENST00000375499	NM_003000.2	143	tTg/tAg	5/8	0.332952480249495	5	FACETS	1	0.953	1	0.465	0.392	0.544	INDETERMINATE	1	TRUE	2	0.626341386998035	5		337	182	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22405021	22405021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	25	85	1	ENST00000344548.3:c.50C>T	p.Thr17Ile	p.T17I	ENST00000344548	NM_001039802.1	17	aCa/aTa	3/7	0.332952480249495	5	FACETS	0.806	0.65	0.977	0.538	0.433	0.651	INDETERMINATE	2	TRUE	2	0.626341386998035	5		86	96	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28586441	28586441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	59	353	3	ENST00000253063.3:c.83C>T	p.Pro28Leu	p.P28L	ENST00000253063	NM_031459.4	28	cCc/cTc	1/10	0.332952480249495	5	FACETS	1	0.962	1	0.829	0.731	0.928	INDETERMINATE	2	TRUE	2	0.626341386998035	5		356	147	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598974	28598975	+	stop_gained,splice_region_variant	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	50	593	3	ENST00000253063.3:c.534_535delinsTT	p.Gln179Ter	p.Q179*	ENST00000253063	NM_031459.4	178	atCCag/atTTag	4/10	0.332952480249495	5	FACETS	0.819	0.705	0.94	0.546	0.47	0.627	INDETERMINATE	2	TRUE	2	0.626341386998035	5		596	189	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46527632	46527632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569257270	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	90	481	2	ENST00000262741.5:c.733C>T	p.Arg245Cys	p.R245C	ENST00000262741	NM_003629.3	245	Cgc/Tgc	6/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.626341386998035	2		483	250	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466355	120466355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	22	495	1	ENST00000256646.2:c.4764G>A	p.Met1588Ile	p.M1588I	ENST00000256646	NM_024408.3	1588	atG/atA	26/34	1	2	FACETS	0.353	0.275	0.443	0.353	0.275	0.443	SUBCLONAL	1	TRUE	1	0.626341386998035	2		496	199	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849022	156849023	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	54	595	2	ENST00000524377.1:c.1914_1915delinsAA	p.Met638_Val639delinsIleMet	p.M638_V639delinsIM	ENST00000524377	NM_002529.3	638	atGGtg/atAAtg	15/17	1	2	FACETS	0.953	0.828	1	0.953	0.828	1	CLONAL	1	TRUE	1	0.626341386998035	2		597	181	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107266	193107267	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	89	248	2	ENST00000367435.3:c.475_476delinsAA	p.Gly159Asn	p.G159N	ENST00000367435	NM_024529.4	159	GGt/AAt	6/17	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.626341386998035	2		250	238	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239498	123239498	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	66	637	1	ENST00000358487.5:c.2339C>A	p.Ser780Ter	p.S780*	ENST00000358487	NM_000141.4	780	tCa/tAa	18/18	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.626341386998035	2		638	194	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186830	108186830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866290641	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	41	368	0	ENST00000278616.4:c.6188G>A	p.Gly2063Glu	p.G2063E	ENST00000278616	NM_000051.3	2063	gGa/gAa	42/63	1	2	FACETS	0.748	0.632	0.873	0.748	0.632	0.873	SUBCLONAL	1	TRUE	1	0.626341386998035	2		368	175	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192063	108192063	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs779742477	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	65	432	1	ENST00000278616.4:c.6488T>G	p.Leu2163Arg	p.L2163R	ENST00000278616	NM_000051.3	2163	cTt/cGt	45/63	1	2	FACETS	0.939	0.826	1	0.939	0.826	1	CLONAL	1	TRUE	1	0.626341386998035	2		433	221	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514045	125514045	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	46	462	0	ENST00000428830.2:c.983G>A	p.Trp328Ter	p.W328*	ENST00000428830	NM_001114121.2	328	tGg/tAg	10/14	1	2	FACETS	0.69	0.587	0.8	0.69	0.587	0.8	SUBCLONAL	1	TRUE	1	0.626341386998035	2		462	213	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433077	49433077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	129	617	6	ENST00000301067.7:c.8294C>T	p.Ser2765Phe	p.S2765F	ENST00000301067	NM_003482.3	2765	tCc/tTc	33/54	0.626341386998035	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.626341386998035	2		623	175	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443875	49443875	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	53	542	1	ENST00000301067.7:c.3496A>G	p.Met1166Val	p.M1166V	ENST00000301067	NM_003482.3	1166	Atg/Gtg	11/54	0.626341386998035	2	FACETS	1	0.89	1	0.513	0.446	0.583	CLONAL	1	TRUE	0	0.626341386998035	2		543	165	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856451	111856451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	17	205	0	ENST00000341259.2:c.502G>A	p.Glu168Lys	p.E168K	ENST00000341259	NM_005475.2	168	Gag/Aag	2/8	0.626341386998035	2	FACETS	0.724	0.553	0.916	0.362	0.276	0.458	CLONAL	1	TRUE	0	0.626341386998035	2		205	75	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549380	21549380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	10	479	0	ENST00000382592.4:c.2896G>A	p.Asp966Asn	p.D966N	ENST00000382592	NM_014572.2	966	Gac/Aac	8/8	0.605424427144751	1	FACETS	0.194	0.132	0.271	0.194	0.132	0.271	SUBCLONAL	1	TRUE	0	0.626341386998035	1		479	113	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562963	95562963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	93	351	0	ENST00000393063.1:c.4294C>T	p.Pro1432Ser	p.P1432S	ENST00000393063	NM_030621.3	1432	Ccg/Tcg	24/28	0.289427792552176	1	FACETS	1	0.973	1	1	0.973	1	INDETERMINATE	1	TRUE	0	0.626341386998035	1		351	175	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961514	41961514	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	84	568	0	ENST00000219905.7:c.422G>A	p.Trp141Ter	p.W141*	ENST00000219905	NM_001164273.1	141	tGg/tAg	2/24	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.626341386998035	2		568	225	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640511	3640511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	55	664	0	ENST00000294008.3:c.3128G>A	p.Gly1043Glu	p.G1043E	ENST00000294008	NM_032444.2	1043	gGg/gAg	12/15	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.626341386998035	2		664	161	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900915	3900915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	64	610	0	ENST00000262367.5:c.181C>T	p.Pro61Ser	p.P61S	ENST00000262367	NM_004380.2	61	Cca/Tca	2/31	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.626341386998035	2		610	199	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350107	89350108	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	49	656	7	ENST00000301030.4:c.2842_2843delinsAA	p.Gly948Lys	p.G948K	ENST00000301030	NM_001256183.1	948	GGg/AAg	9/13	1	2	FACETS	0.794	0.682	0.914	0.794	0.682	0.914	CLONAL	1	TRUE	1	0.626341386998035	2		663	197	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627547	37627547	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774921821	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	50	445	0	ENST00000447079.4:c.1462G>A	p.Glu488Lys	p.E488K	ENST00000447079	NM_015083.1	488	Gag/Aag	2/14	1	2	FACETS	0.912	0.787	1	0.912	0.787	1	CLONAL	1	TRUE	1	0.626341386998035	2		445	175	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602430	10602430	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1319802890	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	18	584	1	ENST00000171111.5:c.1148C>T	p.Ser383Leu	p.S383L	ENST00000171111	NM_203500.1	383	tCg/tTg	3/6	1	2	FACETS	0.432	0.328	0.552	0.432	0.328	0.552	SUBCLONAL	1	TRUE	1	0.626341386998035	2		585	133	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974351	18974351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1249690376	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	60	517	5	ENST00000262803.5:c.2705C>T	p.Pro902Leu	p.P902L	ENST00000262803	NM_002911.3	902	cCg/cTg	19/24	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.626341386998035	2		522	187	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029126	26029127	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	68	354	0	ENST00000435504.4:c.223_224delinsTT	p.Pro75Leu	p.P75L	ENST00000435504		75	CCa/TTa	4/13	0.185883899394701	3	FACETS	1	0.95	1	0.577	0.508	0.65	INDETERMINATE	1	TRUE	1	0.626341386998035	3		354	247	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068349	26068350	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	42	331	3	ENST00000435504.4:c.140_140+1delinsAA		p.X47_splice	ENST00000435504		47		2/13	0.185883899394701	3	FACETS	1	0.896	1	0.537	0.455	0.624	INDETERMINATE	1	TRUE	1	0.626341386998035	3		334	164	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131399	202131399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	54	429	0	ENST00000358485.4:c.367G>A	p.Glu123Lys	p.E123K	ENST00000358485	NM_001080125.1	123	Gag/Aag	2/9	0.185883899394701	3	FACETS	1	0.905	1	0.529	0.458	0.605	INDETERMINATE	1	TRUE	1	0.626341386998035	3		429	214	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267814	46267814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	88	497	1	ENST00000371998.3:c.2575G>A	p.Asp859Asn	p.D859N	ENST00000371998		859	Gat/Aat	14/23	1	2	FACETS	0.983	0.881	1	0.983	0.881	1	CLONAL	1	TRUE	1	0.626341386998035	2		498	286	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69998236	69998236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	66	409	0	ENST00000394351.3:c.476G>A	p.Gly159Glu	p.G159E	ENST00000394351	NM_000248.3	159	gGa/gAa	5/9	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.626341386998035	2		409	202	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198297	185198297	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	45	451	2	ENST00000265026.3:c.2779G>A	p.Val927Met	p.V927M	ENST00000265026	NM_004721.4	927	Gtg/Atg	13/14	1	2	FACETS	0.752	0.641	0.872	0.752	0.641	0.872	SUBCLONAL	1	TRUE	1	0.626341386998035	2		453	191	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139762	55139762	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	82	454	1	ENST00000257290.5:c.1423G>A	p.Glu475Lys	p.E475K	ENST00000257290	NM_006206.4	475	Gag/Aag	10/23	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.626341386998035	2		455	190	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391390	84391390	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1046873224	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	76	610	4	ENST00000321945.7:c.442C>T	p.Arg148Ter	p.R148*	ENST00000321945	NM_139076.2	148	Cga/Tga	5/9	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.626341386998035	2		614	230	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196986	106196986	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	24	303	0	ENST00000380013.4:c.5319C>G	p.Phe1773Leu	p.F1773L	ENST00000380013	NM_001127208.2	1773	ttC/ttG	11/11	1	2	FACETS	0.644	0.513	0.79	0.644	0.513	0.79	SUBCLONAL	1	TRUE	1	0.626341386998035	2		303	119	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249468	153249468	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	43	479	0	ENST00000281708.4:c.1310G>A	p.Gly437Glu	p.G437E	ENST00000281708	NM_033632.3	437	gGa/gAa	9/12	1	2	FACETS	0.53	0.447	0.621	0.53	0.447	0.621	SUBCLONAL	1	TRUE	1	0.626341386998035	2		479	259	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541866	187541867	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	87	451	0	ENST00000441802.2:c.5873_5874del	p.Arg1958IlefsTer10	p.R1958Ifs*10	ENST00000441802	NM_005245.3	1958	aGA/a	10/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.626341386998035	2		451	202	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542746	187542746	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761417017	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	71	472	0	ENST00000441802.2:c.4994C>T	p.Pro1665Leu	p.P1665L	ENST00000441802	NM_005245.3	1665	cCg/cTg	10/27	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.626341386998035	2		472	194	SUCCESS
APC	324	MSKCC	GRCh37	5	112175561	112175561	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554085700	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	66	273	0	ENST00000257430.4:c.4270C>T	p.Pro1424Ser	p.P1424S	ENST00000257430	NM_000038.5	1424	Cca/Tca	16/16	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.626341386998035	2		273	181	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402473	20402474	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	16	398	2	ENST00000346618.3:c.10_11delinsAA	p.Gly4Lys	p.G4K	ENST00000346618	NM_001949.4	4	GGa/AAa	1/7	0.218624931632411	4	FACETS	0.422	0.312	0.551	0.211	0.156	0.276	INDETERMINATE	1	TRUE	2	0.626341386998035	4		400	197	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816545	32816545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778774698	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	82	618	0	ENST00000354258.4:c.1630C>T	p.Arg544Cys	p.R544C	ENST00000354258	NM_000593.5	544	Cgc/Tgc	7/11	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.626341386998035	2		618	243	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980767	70980768	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	43	375	2	ENST00000276594.2:c.701-1_701delinsAA		p.X234_splice	ENST00000276594	NM_024504.3	234		3/8	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.626341386998035	2		377	132	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650854	93650855	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	55	420	1	ENST00000375746.1:c.1780_1781delinsTT	p.Pro594Phe	p.P594F	ENST00000375746	NM_001174167.1	594	CCt/TTt	13/14	0.289427792552176	1	FACETS	0.569	0.493	0.649	0.569	0.493	0.649	INDETERMINATE	1	TRUE	0	0.626341386998035	1		421	212	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779145	135779145	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	20	400	1	ENST00000298552.3:c.2101C>A	p.Gln701Lys	p.Q701K	ENST00000298552	NM_001162426.1	701	Cag/Aag	17/23	0.289427792552176	1	FACETS	0.249	0.191	0.316	0.249	0.191	0.316	INDETERMINATE	1	TRUE	0	0.626341386998035	1		401	176	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400150	139400150	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	43	600	0	ENST00000277541.6:c.4198C>T	p.Gln1400Ter	p.Q1400*	ENST00000277541	NM_017617.3	1400	Cag/Tag	25/34	0.289427792552176	1	FACETS	0.704	0.602	0.811	0.704	0.602	0.811	INDETERMINATE	1	TRUE	0	0.626341386998035	1		600	134	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412375	139412375	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	50	502	4	ENST00000277541.6:c.1270G>C	p.Glu424Gln	p.E424Q	ENST00000277541	NM_017617.3	424	Gag/Cag	8/34	0.289427792552176	1	FACETS	0.736	0.638	0.838	0.736	0.638	0.838	INDETERMINATE	1	TRUE	0	0.626341386998035	1		506	149	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938803	76938803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	89	285	2	ENST00000373344.5:c.1945G>A	p.Glu649Lys	p.E649K	ENST00000373344	NM_000489.3	649	Gag/Aag	9/35	0.309456723970721	2	FACETS	1	0.982	1			1	INDETERMINATE	2	TRUE	NA	0.626341386998035	2		287	119	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575044	64575044	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	88	501	0	ENST00000312049.6:c.763G>T	p.Glu255Ter	p.E255*	ENST00000312049	NM_130799.2	255	Gag/Tag	4/10	0.903924307017495	1	FACETS	0.306	0.273	0.34	0.306	0.273	0.34	SUBCLONAL	1	TRUE	0	0.903924307017495	1		501	349	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472453	88472453	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	290	615	0	ENST00000360948.2:c.2102C>T	p.Ser701Phe	p.S701F	ENST00000360948	NM_001012338.2	701	tCc/tTc	16/19	0.903924307017495	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.903924307017495	1		615	336	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348789	11348789	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	21	334	0	ENST00000332029.2:c.547G>C	p.Val183Leu	p.V183L	ENST00000332029	NM_003745.1	183	Gtg/Ctg	2/2	0.27749107922212	1	FACETS	0.08	0.061	0.102	0.08	0.061	0.102	INDETERMINATE	1	TRUE	0	0.903924307017495	1		334	317	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216533	7216557	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AGTCGGAGAAGCCAGTCTGCTGGTT	AGTCGGAGAAGCCAGTCTGCTGGTT	-	novel	NA	P-0036640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	19	600	0	ENST00000380728.2:c.778_802del	p.Asn260HisfsTer77	p.N260Hfs*77	ENST00000380728		260	AACCAGCAGACTGGCTTCTCCGACTca/ca	9/11	0.903924307017495	1	FACETS	0.064	0.048	0.082	0.064	0.048	0.082	SUBCLONAL	1	TRUE	0	0.903924307017495	1		600	361	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0036643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	98	274	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	0.262746177566807	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.262746177566807	2		274	347	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018151	48018151	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502871	NA	P-0036643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	92	590	0	ENST00000234420.5:c.346G>A	p.Asp116Asn	p.D116N	ENST00000234420	NM_000179.2	116	Gat/Aat	2/10	0.262746177566807	3	FACETS	0.928	0.823	1	0.464	0.411	0.52	CLONAL	1	TRUE	1	0.262746177566807	3		590	854	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984856	9984856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	54	484	0	ENST00000330684.3:c.1109G>A	p.Arg370Gln	p.R370Q	ENST00000330684	NM_001134407.1	370	cGg/cAg	4/13	0.262746177566807	3	FACETS	0.737	0.629	0.856	0.368	0.314	0.428	SUBCLONAL	1	TRUE	1	0.262746177566807	3		484	631	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348083	348083	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1168676445	NA	P-0036643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	108	659	1	ENST00000262320.3:c.1423G>A	p.Val475Ile	p.V475I	ENST00000262320	NM_003502.3	475	Gta/Ata	6/11	0.262746177566807	3	FACETS	1	0.928	1	0.522	0.468	0.58	CLONAL	1	TRUE	1	0.262746177566807	3		660	891	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912102	114912102	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	58	345	0	ENST00000543371.1:c.1172T>G	p.Leu391Arg	p.L391R	ENST00000543371	NM_001198531.1	391	cTg/cGg	11/14	0.262746177566807	3	FACETS	1	0.876	1	0.51	0.438	0.587	CLONAL	1	TRUE	1	0.262746177566807	3		345	490	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212365	36212365	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	99	666	2	ENST00000222270.7:c.2116C>T	p.Arg706Ter	p.R706*	ENST00000222270	NM_014727.1	706	Cga/Tga	3/37	0.262746177566807	3	FACETS	0.977	0.871	1	0.488	0.435	0.545	CLONAL	1	TRUE	1	0.262746177566807	3		668	873	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0036644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	415	697	3	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.825924668766916	2	FACETS	0.933	0.907	0.957	0.933	0.907	0.957	CLONAL	2	TRUE	0	0.84277302786992	2		700	528	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0036644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	298	354	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.840464870307434	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.84277302786992	2		354	350	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249348	110249348	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	256	860	0	ENST00000374672.4:c.1225A>C	p.Lys409Gln	p.K409Q	ENST00000374672	NM_004235.4	409	Aag/Cag	4/5	0.606448949210633	4	FACETS	0.901	0.843	0.962	0.451	0.421	0.481	CLONAL	1	TRUE	2	0.84277302786992	4		860	1242	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11554273	NA	P-0036644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	320	603	0	ENST00000371085.3:c.601C>A	p.Arg201Ser	p.R201S	ENST00000371085	NM_000516.4	201	Cgt/Agt	8/13	0.667933125224838	4	FACETS	0.919	0.873	0.966	0.919	0.873	0.966	CLONAL	2	TRUE	2	0.84277302786992	4		603	761	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584709	48584709	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0036644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	113	426	0	ENST00000342988.3:c.788-1G>T		p.X263_splice	ENST00000342988	NM_005359.5	263			0.84277302786992	1	FACETS	0.929	0.869	0.987	0.929	0.869	0.987	CLONAL	1	TRUE	0	0.84277302786992	1		426	167	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377330	118377330	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	100	289	0	ENST00000534358.1:c.10723C>T	p.Gln3575Ter	p.Q3575*	ENST00000534358	NM_005933.3	3575	Caa/Taa	27/36	0.807245288997631	3	FACETS	0.899	0.81	0.993	0.45	0.405	0.497	CLONAL	1	TRUE	1	0.84277302786992	3		289	375	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983059	201983060	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0036644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	396	785	0	ENST00000359651.3:c.909dup	p.Lys304GlnfsTer167	p.K304Qfs*167	ENST00000359651		303	ttc/ttCc	7/8	0.825924668766916	2	FACETS	0.967	0.941	0.991	0.967	0.941	0.991	CLONAL	2	TRUE	0	0.84277302786992	2		785	486	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355131	15355131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1322882125	NA	P-0036644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	501	854	1	ENST00000263377.2:c.2492C>T	p.Pro831Leu	p.P831L	ENST00000263377	NM_058243.2	831	cCg/cTg	13/20	0.807245288997631	3	FACETS	0.978	0.944	1	0.978	0.944	1	CLONAL	2	TRUE	1	0.84277302786992	3		855	864	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84390305	84390305	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0036644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	338	444	0	ENST00000321945.7:c.477-1G>A		p.X159_splice	ENST00000321945	NM_139076.2	159			0.667933125224838	4	FACETS	0.993	0.946	1	0.993	0.946	1	CLONAL	2	TRUE	2	0.84277302786992	4		444	744	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938654	76938655	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	230	778	1	ENST00000373344.5:c.2093dup	p.Asp699GlyfsTer2	p.D699Gfs*2	ENST00000373344	NM_000489.3	698	aag/aaAg	9/35	0.807245288997631	3	FACETS	0.863	0.806	0.922	0.431	0.403	0.461	CLONAL	1	TRUE	1	0.84277302786992	3		779	899	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984233	7984233	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	326	550	1	ENST00000319144.4:c.496G>A	p.Val166Met	p.V166M	ENST00000319144	NM_001139.2	166	Gtg/Atg	4/15	0.717723293799446	4	FACETS	1	0.992	1	0.793	0.756	0.83	CLONAL	2	TRUE	1	0.717723293799446	4		551	656	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163779	47163779	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	169	604	1	ENST00000409792.3:c.2347G>T	p.Val783Phe	p.V783F	ENST00000409792	NM_014159.6	783	Gtt/Ttt	3/21	0.707240460412578	1	FACETS	0.784	0.731	0.838	0.784	0.731	0.838	SUBCLONAL	1	TRUE	0	0.717723293799446	1		605	385	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0036661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	74	569	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.853	0.747	0.967	1	0.979	1	CLONAL	2	TRUE	1	0.14	2		569	620	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425385	49425386	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	50	846	0	ENST00000301067.7:c.13102dup	p.Thr4368AsnfsTer4	p.T4368Nfs*4	ENST00000301067	NM_003482.3	4368	acc/aAcc	39/54	1	2	FACETS	0.874	0.74	1	0.874	0.74	1	CLONAL	1	TRUE	1	0.14	2		846	817	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346341	73346341	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	29	490	0	ENST00000377767.4:c.1459G>C	p.Asp487His	p.D487H	ENST00000377767	NM_014953.3	487	Gac/Cac	10/21	1	2	FACETS	0.751	0.601	0.922	0.751	0.601	0.922	CLONAL	1	TRUE	1	0.14	2		490	552	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680758	88680758	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	104	552	0	ENST00000360948.2:c.499G>C	p.Asp167His	p.D167H	ENST00000360948	NM_001012338.2	167	Gac/Cac	6/19	1	2	FACETS	0.542	0.486	0.601	0.542	0.486	0.601	SUBCLONAL	1	TRUE	1	0.577320342056982	2		552	665	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216194	36216194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1414381689	NA	P-0036662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	187	592	0	ENST00000222270.7:c.3602C>T	p.Pro1201Leu	p.P1201L	ENST00000222270	NM_014727.1	1201	cCg/cTg	11/37	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.577320342056982	2		592	647	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158626952	158626952	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	143	454	1	ENST00000263640.3:c.718C>G	p.Arg240Gly	p.R240G	ENST00000263640	NM_001105.4	240	Cgt/Ggt	7/11	1	2	FACETS	0.822	0.752	0.894	0.822	0.752	0.894	CLONAL	1	TRUE	1	0.577320342056982	2		455	603	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325661	87325661	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	170	438	0	ENST00000277120.3:c.538A>G	p.Ser180Gly	p.S180G	ENST00000277120		180	Agc/Ggc	6/19	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	1	TRUE	NA	0.577320342056982	2		438	525	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0036664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	113	560	2	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.83	0.75	0.914	0.83	0.75	0.914	CLONAL	1	TRUE	1	0.51776986250813	2		562	526	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0036664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	167	765	30	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.872	0.803	0.943	0.872	0.803	0.943	CLONAL	1	TRUE	1	0.51776986250813	2		795	740	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0036664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	112	513	0	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.702	0.633	0.775	0.702	0.633	0.775	SUBCLONAL	1	TRUE	1	0.51776986250813	2		513	616	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	37	347	2	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.384	0.317	0.459	0.384	0.317	0.459	SUBCLONAL	1	TRUE	1	0.51776986250813	2		349	372	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591145	67591145	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	90	281	0	ENST00000274335.5:c.1738T>A	p.Tyr580Asn	p.Y580N	ENST00000274335		580	Tac/Aac	12/15	1	2	FACETS	0.91	0.813	1	0.91	0.813	1	CLONAL	1	TRUE	1	0.51776986250813	2		281	382	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299832	15299832	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465285176	NA	P-0036664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	144	694	2	ENST00000263388.2:c.1346G>A	p.Arg449His	p.R449H	ENST00000263388	NM_000435.2	449	cGc/cAc	8/33	1	2	FACETS	0.79	0.722	0.861	0.79	0.722	0.861	SUBCLONAL	1	TRUE	1	0.51776986250813	2		696	704	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	96	719	0	ENST00000397062.3:c.246A>T	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaT	2/5	1	2	FACETS	0.449	0.4	0.502	0.449	0.4	0.502	SUBCLONAL	1	TRUE	1	0.51776986250813	2		719	825	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799098	42799098	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	102	816	4	ENST00000575354.2:c.4586del	p.Pro1529LeufsTer91	p.P1529Lfs*91	ENST00000575354	NM_015125.3	1528	Ccc/cc	20/20	1	2	FACETS	0.579	0.518	0.643	0.579	0.518	0.643	SUBCLONAL	1	TRUE	1	0.51776986250813	2		820	681	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720712	89720712	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	49	130	0	ENST00000371953.3:c.867del	p.Val290Ter	p.V290*	ENST00000371953	NM_000314.4	288	gAa/ga	8/9	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.51776986250813	2		130	175	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	146	750	0	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	0.995	0.912	1	0.995	0.912	1	CLONAL	1	TRUE	1	0.51776986250813	2		750	567	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214592	5214592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369295620	NA	P-0036664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	63	658	0	ENST00000357368.4:c.4474C>T	p.Arg1492Trp	p.R1492W	ENST00000357368	NM_002850.3	1492	Cgg/Tgg	29/38	1	2	FACETS	0.393	0.34	0.451	0.393	0.34	0.451	SUBCLONAL	1	TRUE	1	0.51776986250813	2		658	619	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70412277	70412277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	98	246	0	ENST00000373644.4:c.4387G>A	p.Ala1463Thr	p.A1463T	ENST00000373644	NM_030625.2	1463	Gca/Aca	6/12	1	2	FACETS	0.887	0.796	0.982	0.887	0.796	0.982	CLONAL	1	TRUE	1	0.51776986250813	2		246	427	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877407	28877407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759739030	NA	P-0036664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	82	420	1	ENST00000282397.4:c.3914G>A	p.Arg1305His	p.R1305H	ENST00000282397	NM_002019.4	1305	cGc/cAc	30/30	1	2	FACETS	0.523	0.461	0.589	0.523	0.461	0.589	SUBCLONAL	1	TRUE	1	0.51776986250813	2		421	606	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246021942	246021942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1320812485	NA	P-0036664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	139	680	1	ENST00000388985.4:c.932C>T	p.Ala311Val	p.A311V	ENST00000388985		311	gCa/gTa	10/12	0.51776986250813	3	FACETS	0.677	0.615	0.741	0.338	0.307	0.371	SUBCLONAL	1	TRUE	1	0.51776986250813	3		681	999	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0036664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	265	795	1	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.826	0.78	0.871	1	0.995	1	CLONAL	2	TRUE	1	0.51776986250813	2		796	620	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591246	67591246	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0036664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	139	411	2	ENST00000274335.5:c.1746-2A>G		p.X582_splice	ENST00000274335		582			1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.51776986250813	2		413	530	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644874	67644874	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	91	471	0	ENST00000264010.4:c.143del	p.Gly48ValfsTer14	p.G48Vfs*14	ENST00000264010	NM_006565.3	47	Ggg/gg	3/12	1	2	FACETS	0.745	0.664	0.83	0.745	0.664	0.83	SUBCLONAL	1	TRUE	1	0.51776986250813	2		471	472	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419987	41419987	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376239850	NA	P-0036664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	132	468	0	ENST00000373198.4:c.334C>T	p.Arg112Cys	p.R112C	ENST00000373198	NM_133170.3	112	Cgt/Tgt	3/32	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.51776986250813	2		468	504	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272238	15272238	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs760917811	NA	P-0036664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	37	607	0	ENST00000263388.2:c.6201del	p.Lys2069ArgfsTer16	p.K2069Rfs*16	ENST00000263388	NM_000435.2	2067	ccC/cc	33/33	1	2	FACETS	0.322	0.265	0.385	0.322	0.265	0.385	SUBCLONAL	1	TRUE	1	0.51776986250813	2		607	444	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099312	157099313	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAC	rs752012879	NA	P-0036664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	43	284	0	ENST00000346085.5:c.264_266dup	p.His89dup	p.H89dup	ENST00000346085	NM_020732.3	89	-/CAC	1/20	1	2	FACETS	0.539	0.453	0.634	0.539	0.453	0.634	SUBCLONAL	1	TRUE	1	0.51776986250813	2		284	308	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090446	37090446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750217	NA	P-0036664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	115	417	0	ENST00000231790.2:c.2041G>A	p.Ala681Thr	p.A681T	ENST00000231790	NM_000249.3	681	Gct/Act	18/19	1	2	FACETS	0.837	0.757	0.92	0.837	0.757	0.92	CLONAL	1	TRUE	1	0.51776986250813	2		417	531	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11206767	11206767	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	42	523	1	ENST00000361445.4:c.4652C>T	p.Ala1551Val	p.A1551V	ENST00000361445	NM_004958.3	1551	gCa/gTa	32/58	1	2	FACETS	0.239	0.198	0.283	0.239	0.198	0.283	SUBCLONAL	1	TRUE	1	0.51776986250813	2		524	680	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400766	72400767	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0036664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	92	296	0	ENST00000357731.5:c.404_405del	p.Val135AlafsTer5	p.V135Afs*5	ENST00000357731	NM_173808.2	135	gTG/g	2/7	1	2	FACETS	0.96	0.86	1	0.96	0.86	1	CLONAL	1	TRUE	1	0.51776986250813	2		296	370	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653815	89653815	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1064796886	NA	P-0036664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	140	463	0	ENST00000371953.3:c.113C>G	p.Pro38Arg	p.P38R	ENST00000371953	NM_000314.4	38	cCt/cGt	2/9	1	2	FACETS	0.874	0.798	0.952	0.874	0.798	0.952	CLONAL	1	TRUE	1	0.51776986250813	2		463	619	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779301	3779301	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs559294915	NA	P-0036664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	110	518	0	ENST00000262367.5:c.5747T>C	p.Met1916Thr	p.M1916T	ENST00000262367	NM_004380.2	1916	aTg/aCg	31/31	1	2	FACETS	0.852	0.769	0.938	0.852	0.769	0.938	CLONAL	1	TRUE	1	0.51776986250813	2		518	499	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825480	50825480	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	105	391	0	ENST00000398568.2:c.2114del	p.Lys705ArgfsTer27	p.K705Rfs*27	ENST00000398568	NM_001042412.1	704	cAa/ca	14/18	1	2	FACETS	0.859	0.774	0.949	0.859	0.774	0.949	CLONAL	1	TRUE	1	0.51776986250813	2		391	472	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791339	42791339	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	113	599	1	ENST00000575354.2:c.404del	p.Pro135GlnfsTer70	p.P135Qfs*70	ENST00000575354	NM_015125.3	133	ggC/gg	3/20	1	2	FACETS	0.819	0.74	0.902	0.819	0.74	0.902	CLONAL	1	TRUE	1	0.51776986250813	2		600	533	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919963	50919963	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	109	666	0	ENST00000440232.2:c.3050C>A	p.Thr1017Lys	p.T1017K	ENST00000440232	NM_002691.3	1017	aCa/aAa	24/27	1	2	FACETS	0.805	0.726	0.888	0.805	0.726	0.888	CLONAL	1	TRUE	1	0.51776986250813	2		666	523	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607756	46607756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	167	687	2	ENST00000263734.3:c.1945C>T	p.Pro649Ser	p.P649S	ENST00000263734	NM_001430.4	649	Ccc/Tcc	12/16	1	2	FACETS	0.989	0.913	1	0.989	0.913	1	CLONAL	1	TRUE	1	0.51776986250813	2		689	652	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182662954	182662954	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	28	381	0	ENST00000292782.4:c.708G>A	p.Trp236Ter	p.W236*	ENST00000292782	NM_020640.2	236	tgG/tgA	7/7	1	2	FACETS	0.23	0.183	0.284	0.23	0.183	0.284	SUBCLONAL	1	TRUE	1	0.51776986250813	2		381	470	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197560	106197560	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	98	364	0	ENST00000380013.4:c.5893C>A	p.Leu1965Met	p.L1965M	ENST00000380013	NM_001127208.2	1965	Ctg/Atg	11/11	1	2	FACETS	0.901	0.809	0.998	0.901	0.809	0.998	CLONAL	1	TRUE	1	0.51776986250813	2		364	420	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052878	180052878	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1301490674	NA	P-0036664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	49	704	0	ENST00000261937.6:c.1412A>G	p.Gln471Arg	p.Q471R	ENST00000261937	NM_182925.4	471	cAg/cGg	10/30	1	2	FACETS	0.306	0.258	0.358	0.306	0.258	0.358	SUBCLONAL	1	TRUE	1	0.51776986250813	2		704	619	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169852	32169852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs758030641	NA	P-0036664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	46	602	0	ENST00000375023.3:c.3755+1G>A		p.X1252_splice	ENST00000375023	NM_004557.3	1252			1	2	FACETS	0.322	0.271	0.379	0.322	0.271	0.379	SUBCLONAL	1	TRUE	1	0.51776986250813	2		602	552	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171979	32171979	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	118	475	0	ENST00000375023.3:c.3053C>T	p.Thr1018Ile	p.T1018I	ENST00000375023	NM_004557.3	1018	aCa/aTa	19/30	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.51776986250813	2		475	456	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553507	106553507	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775366457	NA	P-0036664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	28	349	0	ENST00000369096.4:c.1472C>T	p.Ala491Val	p.A491V	ENST00000369096	NM_001198.3	491	gCg/gTg	5/7	1	2	FACETS	0.358	0.287	0.439	0.358	0.287	0.439	SUBCLONAL	1	TRUE	1	0.51776986250813	2		349	302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0036665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	204	697	3	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.441287793608869	1	FACETS	0.971	0.903	1	0.971	0.903	1	CLONAL	1	TRUE	0	0.441287793608869	1		700	742	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0036665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	160	469	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.976	0.897	1	0.976	0.897	1	CLONAL	1	TRUE	1	0.441287793608869	2		469	743	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457288	25457288	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	118	404	1	ENST00000264709.3:c.2599G>T	p.Val867Leu	p.V867L	ENST00000264709	NM_175629.2	867	Gta/Tta	23/23	1	2	FACETS	0.88	0.796	0.968	0.88	0.796	0.968	CLONAL	1	TRUE	1	0.441287793608869	2		405	608	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0036666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	63	569	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.847	0.731	0.972	0.847	0.731	0.972	CLONAL	1	TRUE	1	0.206112491319687	2		569	722	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0036666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	34	631	4	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.432	0.351	0.523	0.432	0.351	0.523	SUBCLONAL	1	TRUE	1	0.206112491319687	2		635	764	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0036666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	43	321	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.206112491319687	1	FACETS	0.826	0.692	0.975	0.826	0.692	0.975	CLONAL	1	TRUE	0	0.206112491319687	1		321	453	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730876	40730876	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372862828	NA	P-0036666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	60	682	0	ENST00000373198.4:c.3659G>A	p.Arg1220Gln	p.R1220Q	ENST00000373198	NM_133170.3	1220	cGg/cAg	27/32	NA	2	FACETS	0.704	0.605	0.812			1	INDETERMINATE	1	TRUE	NA	0.206112491319687	2		682	827	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117614	70117614	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	122	623	0	ENST00000245479.2:c.82G>T	p.Glu28Ter	p.E28*	ENST00000245479	NM_000346.3	28	Gag/Tag	1/3	1	2	FACETS	0.89	0.806	0.978	1	0.988	1	CLONAL	2	TRUE	1	0.206112491319687	2		623	665	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577497	7577497	+	splice_donor_variant	Splice_Site	SNP	A	A	C	rs876659076	NA	P-0036666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	59	649	0	ENST00000269305.4:c.782+2T>G		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	0.796	0.684	0.919	0.796	0.684	0.919	CLONAL	1	TRUE	1	0.206112491319687	2		649	719	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911573	134911573	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs368515643	NA	P-0036666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	64	574	0	ENST00000398015.3:c.2038A>G	p.Ile680Val	p.I680V	ENST00000398015	NM_004441.4	680	Atc/Gtc	11/16	0.206112491319687	1	FACETS	0.886	0.767	1	0.886	0.767	1	CLONAL	1	TRUE	0	0.206112491319687	1		574	629	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0036668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	18	303	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.98	0.739	1	0.98	0.739	1	CLONAL	1	TRUE	1	0.15	2		303	245	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054238	30054242	+	frameshift_variant	Frame_Shift_Del	DEL	CTACT	CTACT	-	novel	NA	P-0036668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	68	499	0	ENST00000338641.4:c.660_664del	p.Tyr221CysfsTer5	p.Y221Cfs*5	ENST00000338641	NM_000268.3	220	aaCTACTtt/aatt	7/16	1	2	FACETS	0.978	0.849	1	0.978	0.849	1	CLONAL	1	TRUE	1	0.15	2		499	927	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0036669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	428	405	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.822328481969708	2		405	729	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	308	483	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.822328481969708	2		483	708	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333123	70333123	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	393	711	0	ENST00000373644.4:c.1028C>G	p.Pro343Arg	p.P343R	ENST00000373644	NM_030625.2	343	cCa/cGa	2/12	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.822328481969708	2		711	883	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608503	28608503	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	342	556	0	ENST00000241453.7:c.1639A>G	p.Thr547Ala	p.T547A	ENST00000241453	NM_004119.2	547	Aca/Gca	13/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.822328481969708	2		556	768	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042341	16042341	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0036669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	255	476	0	ENST00000268712.3:c.1333A>T	p.Lys445Ter	p.K445*	ENST00000268712	NM_006311.3	445	Aag/Tag	12/46	1	2	FACETS	0.992	0.936	1	0.992	0.936	1	CLONAL	1	TRUE	1	0.822328481969708	2		476	625	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417487	139417487	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	441	729	0	ENST00000277541.6:c.557C>A	p.Pro186His	p.P186H	ENST00000277541	NM_017617.3	186	cCc/cAc	4/34	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.822328481969708	2		729	1036	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65300295	65300295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	31	384	0	ENST00000342505.4:c.3415C>T	p.Arg1139Trp	p.R1139W	ENST00000342505	NM_002227.2	1139	Cgg/Tgg	25/25	0.358899997649119	1	FACETS	0.762	0.622	0.917	0.762	0.622	0.917	CLONAL	1	FALSE	0	0.358899997649119	1		384	186	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096132	2096133	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs763525759	NA	P-0036675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	10	563	2	ENST00000219066.1:c.374dup	p.Val127GlyfsTer43	p.V127Gfs*43	ENST00000219066	NM_002528.5	125	cca/ccCa	2/6	1	2	FACETS	0.284	0.192	0.4	0.284	0.192	0.4	SUBCLONAL	1	FALSE	1	0.358899997649119	2		565	196	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577586	7577586	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587781589	NA	P-0036675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	39	531	0	ENST00000269305.4:c.695T>C	p.Ile232Thr	p.I232T	ENST00000269305	NM_001126112.2	232	aTc/aCc	7/11	0.199218183024108	1	FACETS	0.98	0.822	1	0.98	0.822	1	INDETERMINATE	1	FALSE	0	0.358899997649119	1		531	182	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060751	38060760	+	frameshift_variant	Frame_Shift_Del	DEL	TGCTGCTGCT	TGCTGCTGCT	-	novel	NA	P-0036675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	102	878	0	ENST00000250448.2:c.1229_1238del	p.Glu410ValfsTer27	p.E410Vfs*27	ENST00000250448	NM_004496.3	410	gAGCAGCAGCAt/gt	2/2	0.276005455373417	4	FACETS	0.9	0.81	0.994	0.9	0.81	0.994	CLONAL	2	FALSE	2	0.358899997649119	4		878	429	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039374	49039374	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853293	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	374	692	0	ENST00000267163.4:c.2359C>T	p.Arg787Ter	p.R787*	ENST00000267163	NM_000321.2	787	Cga/Tga	23/27	0.816393499324648	1	FACETS	0.975	0.943	1	0.975	0.943	1	CLONAL	1	TRUE	0	0.859465110590787	1		692	509	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285327	212285327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143134749	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	194	478	0	ENST00000342788.4:c.2974C>T	p.Arg992Cys	p.R992C	ENST00000342788	NM_005235.2	992	Cgt/Tgt	25/28	1	2	FACETS	0.992	0.929	1	0.992	0.929	1	CLONAL	1	TRUE	1	0.859465110590787	2		478	455	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307212	65307212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150021823	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	288	666	0	ENST00000342505.4:c.2476C>T	p.Arg826Cys	p.R826C	ENST00000342505	NM_002227.2	826	Cgc/Tgc	18/25	1	2	FACETS	0.951	0.9	1	0.951	0.9	1	CLONAL	1	TRUE	1	0.859465110590787	2		666	705	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578177	7578177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs267605076	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	333	723	0	ENST00000269305.4:c.672G>T	p.Glu224Asp	p.E224D	ENST00000269305	NM_001126112.2	224	gaG/gaT	6/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.859465110590787	2		723	754	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574004	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	325	758	1	ENST00000269305.4:c.1023_1024delinsTT	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	341	ttCCga/ttTTga	10/11	1	2	FACETS	0.921	0.874	0.969	0.921	0.874	0.969	CLONAL	1	TRUE	1	0.859465110590787	2		759	821	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144026	11144026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	309	623	0	ENST00000358026.2:c.3607C>T	p.Arg1203Cys	p.R1203C	ENST00000358026	NM_001128849.1	1203	Cgc/Tgc	26/36	1	2	FACETS	0.981	0.931	1	0.981	0.931	1	CLONAL	1	TRUE	1	0.859465110590787	2		623	733	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903719	41903719	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	354	645	0	ENST00000372991.4:c.838C>T	p.Gln280Ter	p.Q280*	ENST00000372991	NM_001760.3	280	Cag/Tag	5/5	1	2	FACETS	0.967	0.92	1	0.967	0.92	1	CLONAL	1	TRUE	1	0.859465110590787	2		645	852	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609349	39609349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201418439	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	152	432	0	ENST00000262039.4:c.1651C>T	p.Arg551Trp	p.R551W	ENST00000262039	NM_002647.2	551	Cgg/Tgg	15/25	1	2	FACETS	0.619	0.569	0.671	0.619	0.569	0.671	SUBCLONAL	1	TRUE	1	0.859465110590787	2		432	571	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317926	8317926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	151	407	0	ENST00000356435.5:c.5687C>T	p.Ser1896Phe	p.S1896F	ENST00000356435		1896	tCc/tTc	35/35	1	2	FACETS	0.648	0.596	0.702	0.648	0.596	0.702	SUBCLONAL	1	TRUE	1	0.859465110590787	2		407	542	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855565	45855565	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555775416	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	328	728	1	ENST00000391945.4:c.2092C>T	p.Gln698Ter	p.Q698*	ENST00000391945	NM_000400.3	698	Cag/Tag	22/23	1	2	FACETS	0.937	0.889	0.984	0.937	0.889	0.984	CLONAL	1	TRUE	1	0.859465110590787	2		729	815	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692800	89692800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204856	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	138	406	0	ENST00000371953.3:c.284C>T	p.Pro95Leu	p.P95L	ENST00000371953	NM_000314.4	95	cCa/cTa	5/9	1	2	FACETS	0.834	0.767	0.902	0.834	0.767	0.902	CLONAL	1	TRUE	1	0.859465110590787	2		406	385	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7174684	7174684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1188187072	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	327	637	0	ENST00000302850.5:c.1033G>A	p.Glu345Lys	p.E345K	ENST00000302850	NM_000208.2	345	Gag/Aag	4/22	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.859465110590787	2		637	761	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40476813	40476813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	347	670	2	ENST00000264657.5:c.1516G>A	p.Glu506Lys	p.E506K	ENST00000264657	NM_139276.2	506	Gag/Aag	17/24	1	2	FACETS	0.978	0.93	1	0.978	0.93	1	CLONAL	1	TRUE	1	0.859465110590787	2		672	826	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041084	29041084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	292	716	0	ENST00000282397.4:c.344C>T	p.Ser115Leu	p.S115L	ENST00000282397	NM_002019.4	115	tCa/tTa	3/30	0.859465110590787	1	FACETS	0.92	0.884	0.955	0.92	0.884	0.955	CLONAL	1	TRUE	0	0.859465110590787	1		716	421	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911973	32911973	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555283261	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	297	664	0	ENST00000380152.3:c.3481G>A	p.Asp1161Asn	p.D1161N	ENST00000380152		1161	Gat/Aat	11/27	0.816393499324648	1	FACETS	0.952	0.916	0.986	0.952	0.916	0.986	CLONAL	1	TRUE	0	0.859465110590787	1		664	414	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120702	94120702	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	263	594	0	ENST00000369303.4:c.349G>A	p.Gly117Arg	p.G117R	ENST00000369303	NM_004440.3	117	Gga/Aga	3/17	1	2	FACETS	0.984	0.929	1	0.984	0.929	1	CLONAL	1	TRUE	1	0.859465110590787	2		594	622	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513239	149513239	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs34586048	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	331	713	0	ENST00000261799.4:c.844G>A	p.Glu282Lys	p.E282K	ENST00000261799	NM_002609.3	282	Gag/Aag	6/23	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.859465110590787	2		713	744	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257725	16257725	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	279	528	0	ENST00000375759.3:c.4990G>A	p.Glu1664Lys	p.E1664K	ENST00000375759	NM_015001.2	1664	Gag/Aag	11/15	1	2	FACETS	0.991	0.938	1	0.991	0.938	1	CLONAL	1	TRUE	1	0.859465110590787	2		528	655	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458735	120458735	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	276	587	0	ENST00000256646.2:c.6610C>A	p.Leu2204Ile	p.L2204I	ENST00000256646	NM_024408.3	2204	Ctt/Att	34/34	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.859465110590787	2		587	634	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462168	120462168	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	302	637	1	ENST00000256646.2:c.5548G>T	p.Asp1850Tyr	p.D1850Y	ENST00000256646	NM_024408.3	1850	Gat/Tat	31/34	1	2	FACETS	0.947	0.897	0.997	0.947	0.897	0.997	CLONAL	1	TRUE	1	0.859465110590787	2		638	742	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163325176	163325176	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	155	441	0	ENST00000271452.3:c.1312G>T	p.Glu438Ter	p.E438*	ENST00000271452	NM_145697.2	438	Gaa/Taa	14/14	1	2	FACETS	0.888	0.823	0.956	0.888	0.823	0.956	CLONAL	1	TRUE	1	0.859465110590787	2		441	406	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578207	226578208	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	263	584	0	ENST00000366794.5:c.520_521delinsTT	p.Pro174Phe	p.P174F	ENST00000366794	NM_001618.3	174	CCc/TTc	4/23	1	2	FACETS	0.93	0.878	0.983	0.93	0.878	0.983	CLONAL	1	TRUE	1	0.859465110590787	2		584	658	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307564	118307564	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	331	588	0	ENST00000534358.1:c.337G>A	p.Asp113Asn	p.D113N	ENST00000534358	NM_005933.3	113	Gac/Aac	1/36	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.859465110590787	2		588	720	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257762	133257762	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	374	656	1	ENST00000320574.5:c.166C>T	p.Pro56Ser	p.P56S	ENST00000320574	NM_006231.2	56	Cct/Tct	2/49	1	2	FACETS	0.983	0.938	1	0.983	0.938	1	CLONAL	1	TRUE	1	0.859465110590787	2		657	885	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514523	103514523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372910916	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	255	311	0	ENST00000355739.4:c.1024C>T	p.Pro342Ser	p.P342S	ENST00000355739	NM_000123.3	342	Cca/Tca	8/15	0.699919475084388	3	FACETS	0.966	0.919	1	0.966	0.919	1	CLONAL	2	TRUE	1	0.859465110590787	3		311	439	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705404	43705404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	396	809	0	ENST00000382044.4:c.5218C>T	p.Leu1740Phe	p.L1740F	ENST00000382044	NM_001141980.1	1740	Ctc/Ttc	24/28	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.859465110590787	2		809	921	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312408	91312408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	304	658	0	ENST00000355112.3:c.2353G>A	p.Glu785Lys	p.E785K	ENST00000355112	NM_000057.2	785	Gag/Aag	11/22	1	2	FACETS	0.9	0.852	0.948	0.9	0.852	0.948	CLONAL	1	TRUE	1	0.859465110590787	2		658	786	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778907	3778908	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	211	594	2	ENST00000262367.5:c.6140_6141delinsAT	p.Ala2047Asp	p.A2047D	ENST00000262367	NM_004380.2	2047	gCC/gAT	31/31	1	2	FACETS	0.933	0.875	0.993	0.933	0.875	0.993	CLONAL	1	TRUE	1	0.859465110590787	2		596	526	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900608	3900608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	333	716	3	ENST00000262367.5:c.488C>T	p.Thr163Ile	p.T163I	ENST00000262367	NM_004380.2	163	aCt/aTt	2/31	1	2	FACETS	0.878	0.833	0.923	0.878	0.833	0.923	CLONAL	1	TRUE	1	0.859465110590787	2		719	883	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785700	50785701	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	269	690	2	ENST00000398568.2:c.690_691delinsAA	p.Glu231Lys	p.E231K	ENST00000398568	NM_001042412.1	230	ttGGaa/ttAAaa	4/18	1	2	FACETS	0.865	0.815	0.915	0.865	0.815	0.915	CLONAL	1	TRUE	1	0.859465110590787	2		692	724	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662390	67662390	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	226	763	0	ENST00000264010.4:c.1636C>T	p.His546Tyr	p.H546Y	ENST00000264010	NM_006565.3	546	Cac/Tac	9/12	1	2	FACETS	0.568	0.529	0.608	0.568	0.529	0.608	SUBCLONAL	1	TRUE	1	0.859465110590787	2		763	926	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830128	72830129	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	305	705	1	ENST00000268489.5:c.6452_6453delinsAA	p.Arg2151Lys	p.R2151K	ENST00000268489	NM_006885.3	2151	aGG/aAA	9/10	1	2	FACETS	0.881	0.834	0.928	0.881	0.834	0.928	CLONAL	1	TRUE	1	0.859465110590787	2		706	806	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349727	89349727	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	395	1102	1	ENST00000301030.4:c.3223G>A	p.Glu1075Lys	p.E1075K	ENST00000301030	NM_001256183.1	1075	Gaa/Aaa	9/13	1	2	FACETS	0.904	0.862	0.946	0.904	0.862	0.946	CLONAL	1	TRUE	1	0.859465110590787	2		1103	1017	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973610	15973610	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	274	516	0	ENST00000268712.3:c.4382C>T	p.Ser1461Phe	p.S1461F	ENST00000268712	NM_006311.3	1461	tCc/tTc	31/46	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.859465110590787	2		516	598	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428329	33428330	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	306	678	2	ENST00000345365.6:c.793_794delinsAA	p.Gly265Lys	p.G265K	ENST00000345365	NM_002878.3	265	GGa/AAa	9/10	1	2	FACETS	0.901	0.854	0.95	0.901	0.854	0.95	CLONAL	1	TRUE	1	0.859465110590787	2		680	790	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676333	37676333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1302109388	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	280	567	0	ENST00000447079.4:c.3088C>T	p.Pro1030Ser	p.P1030S	ENST00000447079	NM_015083.1	1030	Cct/Tct	11/14	1	2	FACETS	0.967	0.915	1	0.967	0.915	1	CLONAL	1	TRUE	1	0.859465110590787	2		567	674	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246387	41246388	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	295	871	1	ENST00000357654.3:c.1160_1161delinsTT	p.Ser387Phe	p.S387F	ENST00000357654	NM_007294.3	387	tCC/tTT	10/23	1	2	FACETS	0.882	0.835	0.931	0.882	0.835	0.931	CLONAL	1	TRUE	1	0.859465110590787	2		872	778	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272083	15272084	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	213	587	0	ENST00000263388.2:c.6355_6356delinsAA	p.Gly2119Asn	p.G2119N	ENST00000263388	NM_000435.2	2119	GGt/AAt	33/33	1	2	FACETS	0.853	0.798	0.909	0.853	0.798	0.909	CLONAL	1	TRUE	1	0.859465110590787	2		587	581	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797930	42797931	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	303	789	2	ENST00000575354.2:c.3982_3983delinsAA	p.Gly1328Asn	p.G1328N	ENST00000575354	NM_015125.3	1328	GGc/AAc	16/20	1	2	FACETS	0.912	0.864	0.961	0.912	0.864	0.961	CLONAL	1	TRUE	1	0.859465110590787	2		791	773	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213351	39213351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	405	874	0	ENST00000402219.2:c.3616G>A	p.Asp1206Asn	p.D1206N	ENST00000402219	NM_005633.3	1206	Gac/Aac	23/23	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.859465110590787	2		874	942	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873011	136873011	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	204	456	0	ENST00000241393.3:c.487C>T	p.Pro163Ser	p.P163S	ENST00000241393	NM_003467.2	163	Cct/Tct	2/2	1	2	FACETS	0.942	0.882	1	0.942	0.882	1	CLONAL	1	TRUE	1	0.859465110590787	2		456	504	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573596	41573597	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	299	747	1	ENST00000263253.7:c.5881_5882delinsTT	p.Pro1961Phe	p.P1961F	ENST00000263253	NM_001429.3	1961	CCc/TTc	31/31	1	2	FACETS	0.926	0.877	0.976	0.926	0.877	0.976	CLONAL	1	TRUE	1	0.859465110590787	2		748	751	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266559	41266560	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	284	650	1	ENST00000349496.5:c.356_357delinsTT	p.Pro119Leu	p.P119L	ENST00000349496	NM_001904.3	119	cCC/cTT	4/15	1	2	FACETS	0.981	0.928	1	0.981	0.928	1	CLONAL	1	TRUE	1	0.859465110590787	2		651	674	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595857	52595857	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	402	727	0	ENST00000394830.3:c.4058C>T	p.Ser1353Phe	p.S1353F	ENST00000394830	NM_018313.4	1353	tCt/tTt	26/30	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.859465110590787	2		727	918	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205098	128205099	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	330	676	1	ENST00000341105.2:c.342_343delinsTT	p.Pro115Ser	p.P115S	ENST00000341105	NM_032638.4	114	aaCCcc/aaTTcc	3/6	1	2	FACETS	0.962	0.914	1	0.962	0.914	1	CLONAL	1	TRUE	1	0.859465110590787	2		677	798	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515663	31515664	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	133	458	0	ENST00000344624.3:c.955_956delinsAA	p.Gly319Asn	p.G319N	ENST00000344624		319	GGt/AAt	4/33	1	2	FACETS	0.667	0.61	0.726	0.667	0.61	0.726	SUBCLONAL	1	TRUE	1	0.859465110590787	2		458	464	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526636	31526636	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	281	564	1	ENST00000344624.3:c.404C>A	p.Ala135Glu	p.A135E	ENST00000344624		135	gCa/gAa	2/33	1	2	FACETS	0.963	0.911	1	0.963	0.911	1	CLONAL	1	TRUE	1	0.859465110590787	2		565	679	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155583	56155583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	112	364	0	ENST00000399503.3:c.675G>A	p.Met225Ile	p.M225I	ENST00000399503	NM_005921.1	225	atG/atA	3/20	1	2	FACETS	0.574	0.519	0.631	0.574	0.519	0.631	SUBCLONAL	1	TRUE	1	0.859465110590787	2		364	454	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751236	57751236	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	26	457	0	ENST00000274289.3:c.1631T>C	p.Val544Ala	p.V544A	ENST00000274289	NM_006622.3	544	gTt/gCt	12/14	1	2	FACETS	0.133	0.105	0.166	0.133	0.105	0.166	SUBCLONAL	1	TRUE	1	0.859465110590787	2		457	454	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80109403	80109403	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	179	446	0	ENST00000265081.6:c.2656G>A	p.Glu886Lys	p.E886K	ENST00000265081	NM_002439.4	886	Gag/Aag	20/24	1	2	FACETS	0.966	0.901	1	0.966	0.901	1	CLONAL	1	TRUE	1	0.859465110590787	2		446	431	SUCCESS
APC	324	MSKCC	GRCh37	5	112174817	112174818	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	127	394	0	ENST00000257430.4:c.3526_3527delinsTT	p.Pro1176Phe	p.P1176F	ENST00000257430	NM_000038.5	1176	CCt/TTt	16/16	1	2	FACETS	0.932	0.857	1	0.932	0.857	1	CLONAL	1	TRUE	1	0.859465110590787	2		394	317	SUCCESS
APC	324	MSKCC	GRCh37	5	112177601	112177601	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	191	526	0	ENST00000257430.4:c.6310A>T	p.Ile2104Phe	p.I2104F	ENST00000257430	NM_000038.5	2104	Att/Ttt	16/16	1	2	FACETS	0.885	0.826	0.946	0.885	0.826	0.946	CLONAL	1	TRUE	1	0.859465110590787	2		526	502	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636916	176636917	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	236	582	0	ENST00000439151.2:c.1516_1517delinsTT	p.Pro506Leu	p.P506L	ENST00000439151	NM_022455.4	506	CCa/TTa	5/23	1	2	FACETS	0.873	0.82	0.927	0.873	0.82	0.927	CLONAL	1	TRUE	1	0.859465110590787	2		582	629	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910657	29910657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	291	897	0	ENST00000376809.5:c.197G>A	p.Ser66Asn	p.S66N	ENST00000376809	NM_002116.7	66	aGc/aAc	2/8	1	2	FACETS	0.654	0.615	0.693	0.654	0.615	0.693	SUBCLONAL	1	TRUE	1	0.859465110590787	2		897	1036	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035208	6035208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060503122	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	270	567	0	ENST00000265849.7:c.860G>A	p.Arg287Lys	p.R287K	ENST00000265849	NM_000535.5	287	aGa/aAa	8/15	1	2	FACETS	0.929	0.878	0.982	0.929	0.878	0.982	CLONAL	1	TRUE	1	0.859465110590787	2		567	676	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367315	50367315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751092583	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	203	450	0	ENST00000331340.3:c.122C>T	p.Ser41Leu	p.S41L	ENST00000331340	NM_006060.4	41	tCg/tTg	3/8	1	2	FACETS	0.956	0.896	1	0.956	0.896	1	CLONAL	1	TRUE	1	0.859465110590787	2		450	494	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849801	151849801	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1417315920	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	146	317	0	ENST00000262189.6:c.12515C>T	p.Pro4172Leu	p.P4172L	ENST00000262189	NM_170606.2	4172	cCa/cTa	49/59	0.845022420653459	2	FACETS	0.858	0.792	0.926	0.429	0.396	0.463	CLONAL	1	TRUE	0	0.859465110590787	2		317	396	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873435	151873435	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	516	614	0	ENST00000262189.6:c.9103C>T	p.Gln3035Ter	p.Q3035*	ENST00000262189	NM_170606.2	3035	Caa/Taa	38/59	0.845022420653459	2	FACETS	0.959	0.937	0.98	0.959	0.937	0.98	CLONAL	2	TRUE	0	0.859465110590787	2		614	626	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5465556	5465556	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	167	423	0	ENST00000381577.3:c.740T>A	p.Ile247Asn	p.I247N	ENST00000381577	NM_014143.3	247	aTc/aAc	5/7	1	2	FACETS	0.825	0.765	0.887	0.825	0.765	0.887	CLONAL	1	TRUE	1	0.859465110590787	2		423	471	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133748334	133748334	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs560686582	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	325	618	0	ENST00000318560.5:c.995G>A	p.Arg332Gln	p.R332Q	ENST00000318560	NM_005157.4	332	cGg/cAg	6/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.859465110590787	2		618	756	SUCCESS
BTK	695	MSKCC	GRCh37	X	100612514	100612514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	237	314	0	ENST00000308731.7:c.1160C>T	p.Thr387Ile	p.T387I	ENST00000308731	NM_000061.2	387	aCt/aTt	13/19	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.859465110590787	1		314	294	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0036679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	132	381	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.0974968489163957	4	FACETS	1	0.971	1	1	0.971	1	INDETERMINATE	2	TRUE	2	0.188706613637829	4		381	712	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578530	7578533	+	frameshift_variant	Frame_Shift_Del	DEL	ACAT	ACAT	-	novel	NA	P-0036679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	115	803	0	ENST00000269305.4:c.397_400del	p.Met133PhefsTer36	p.M133Ffs*36	ENST00000269305	NM_001126112.2	133	ATGTtt/tt	5/11	0.146971477159343	3	FACETS	1	0.978	1	0.664	0.597	0.735	CLONAL	1	TRUE	1	0.188706613637829	3		803	1004	SUCCESS
CBL	867	MSKCC	GRCh37	11	119167680	119167680	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1414663764	NA	P-0036679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	57	530	2	ENST00000264033.4:c.2089G>T	p.Asp697Tyr	p.D697Y	ENST00000264033	NM_005188.3	697	Gac/Tac	13/16	1	2	FACETS	0.862	0.738	0.997	0.862	0.738	0.997	CLONAL	1	TRUE	1	0.188706613637829	2		532	701	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670503	134670503	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	39	685	0	ENST00000398015.3:c.414C>G	p.Asp138Glu	p.D138E	ENST00000398015	NM_004441.4	138	gaC/gaG	3/16	0.146971477159343	3	FACETS	0.621	0.513	0.742	0.311	0.256	0.371	SUBCLONAL	1	TRUE	1	0.188706613637829	3		685	728	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045818	143045818	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	64	540	0	ENST00000262992.4:c.1816C>A	p.Leu606Ile	p.L606I	ENST00000262992	NM_001101669.1	606	Ctc/Atc	17/24	1	2	FACETS	0.797	0.689	0.915	0.797	0.689	0.915	CLONAL	1	TRUE	1	0.188706613637829	2		540	851	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081638	143081638	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	51	478	0	ENST00000262992.4:c.1436G>T	p.Gly479Val	p.G479V	ENST00000262992	NM_001101669.1	479	gGa/gTa	15/24	1	2	FACETS	0.918	0.779	1	0.918	0.779	1	CLONAL	1	TRUE	1	0.188706613637829	2		478	589	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527943	157527943	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	47	540	0	ENST00000346085.5:c.5668G>C	p.Glu1890Gln	p.E1890Q	ENST00000346085	NM_020732.3	1890	Gaa/Caa	20/20	0.119687513894866	3	FACETS	0.787	0.662	0.924	0.393	0.331	0.462	CLONAL	1	TRUE	1	0.188706613637829	3		540	693	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0036681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	330	697	3	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.330667143881559	1	FACETS	0.964	0.923	1	1	0.997	1	CLONAL	3	FALSE	0	0.330667143881559	1		700	576	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0036681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	216	448	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.317959099565342	2	FACETS	0.909	0.855	0.964	1	0.992	1	CLONAL	3	FALSE	0	0.330667143881559	2		448	479	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0036681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	49	233	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.330667143881559	0	FACETS	0.616	0.532	0.705			1	SUBCLONAL	2	FALSE	0	0.330667143881559	0		233	161	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0036681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	53	393	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	0.289586188716097	1	FACETS	0.839	0.719	0.968	0.839	0.719	0.968	CLONAL	1	FALSE	0	0.330667143881559	1		393	319	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541630	187541630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371538987	NA	P-0036681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	27	265	0	ENST00000441802.2:c.6110C>T	p.Thr2037Met	p.T2037M	ENST00000441802	NM_005245.3	2037	aCg/aTg	10/27	0.330667143881559	1	FACETS	0.326	0.259	0.403	0.326	0.259	0.403	SUBCLONAL	1	FALSE	0	0.330667143881559	1		265	418	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156674	2156674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1356855570	NA	P-0036681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	225	562	0	ENST00000434045.2:c.248G>A	p.Arg83His	p.R83H	ENST00000434045	NM_001127598.1	83	cGc/cAc	3/5	1	2	FACETS	1	0.948	1	1	0.994	1	CLONAL	2	FALSE	1	0.330667143881559	2		562	671	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911217	32911217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660858	NA	P-0036681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	66	551	0	ENST00000380152.3:c.2725C>T	p.Leu909Phe	p.L909F	ENST00000380152		909	Ctt/Ttt	11/27	0.290393639111865	3	FACETS	0.765	0.664	0.874	0.383	0.332	0.437	SUBCLONAL	1	FALSE	1	0.330667143881559	3		551	608	SUCCESS
APC	324	MSKCC	GRCh37	5	112175755	112175759	+	frameshift_variant	Frame_Shift_Del	DEL	ATTAC	ATTAC	GTT	novel	NA	P-0036681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	109	351	1	ENST00000257430.4:c.4464_4468delinsGTT	p.His1490PhefsTer23	p.H1490Ffs*23	ENST00000257430	NM_000038.5	1488	ttATTACat/ttGTTat	16/16	0.289586188716097	1	FACETS	0.92	0.838	1	1	0.988	1	CLONAL	2	FALSE	0	0.330667143881559	1		352	299	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854960	76854960	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	371	703	2	ENST00000373344.5:c.5876A>T	p.Asn1959Ile	p.N1959I	ENST00000373344	NM_000489.3	1959	aAt/aTt	25/35	0.118005899662885	6	FACETS	0.991	0.944	1	1	0.994	1	INDETERMINATE	4	FALSE	3	0.330667143881559	6		705	940	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7174684	7174684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1188187072	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	372	637	0	ENST00000302850.5:c.1033G>A	p.Glu345Lys	p.E345K	ENST00000302850	NM_000208.2	345	Gag/Aag	4/22	0.904396975896219	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.904396975896219	1		637	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	383	741	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.904396975896219	1	FACETS	0.996	0.969	1	0.996	0.969	1	CLONAL	1	TRUE	0	0.904396975896219	1		741	466	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983037	149983037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	314	699	0	ENST00000253339.5:c.3221C>T	p.Ala1074Val	p.A1074V	ENST00000253339		1074	gCa/gTa	7/7	0.904396975896219	1	FACETS	0.98	0.951	1	0.98	0.951	1	CLONAL	1	TRUE	0	0.904396975896219	1		699	388	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705472	47705472	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658254	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	207	414	1	ENST00000233146.2:c.2272G>A	p.Asp758Asn	p.D758N	ENST00000233146	NM_000251.2	758	Gat/Aat	14/16	1	2	FACETS	0.974	0.914	1	0.974	0.914	1	CLONAL	1	TRUE	1	0.904396975896219	2		415	470	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414921	78414921	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	269	491	0	ENST00000370768.2:c.1845G>T	p.Trp615Cys	p.W615C	ENST00000370768	NM_003902.3	615	tgG/tgT	19/20	1	2	FACETS	0.982	0.929	1	0.982	0.929	1	CLONAL	1	TRUE	1	0.904396975896219	2		491	606	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027133	49027133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853292	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	292	350	0	ENST00000267163.4:c.1700C>T	p.Ser567Leu	p.S567L	ENST00000267163	NM_000321.2	567	tCa/tTa	18/27	0.901366965981688	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.904396975896219	2		350	317	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649216	23649216	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	269	561	0	ENST00000261584.4:c.166G>T	p.Asp56Tyr	p.D56Y	ENST00000261584	NM_024675.3	56	Gat/Tat	3/13	1	2	FACETS	0.915	0.865	0.966	0.915	0.865	0.966	CLONAL	1	TRUE	1	0.904396975896219	2		561	650	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916505	39916505	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	445	399	0	ENST00000378444.4:c.4498G>T	p.Ala1500Ser	p.A1500S	ENST00000378444	NM_001123385.1	1500	Gcc/Tcc	11/15	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.904396975896219	1		399	479	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020386	69020386	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	283	562	2	ENST00000288368.4:c.2758C>T	p.Gln920Ter	p.Q920*	ENST00000288368	NM_024870.2	920	Cag/Tag	24/40	1	2	FACETS	0.919	0.87	0.969	0.919	0.87	0.969	CLONAL	1	TRUE	1	0.904396975896219	2		564	681	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11206806	11206806	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	335	575	0	ENST00000361445.4:c.4613G>T	p.Arg1538Leu	p.R1538L	ENST00000361445	NM_004958.3	1538	cGg/cTg	32/58	0.891521155559192	3	FACETS	1	0.972	1	0.52	0.492	0.548	CLONAL	1	TRUE	1	0.904396975896219	3		575	1034	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100940	27100940	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	643	573	0	ENST00000324856.7:c.4222G>T	p.Ala1408Ser	p.A1408S	ENST00000324856	NM_006015.4	1408	Gcc/Tcc	18/20	0.891521155559192	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.904396975896219	3		573	1021	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939375	36939375	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	350	657	0	ENST00000361632.4:c.475A>T	p.Lys159Ter	p.K159*	ENST00000361632		159	Aag/Tag	4/16	1	2	FACETS	0.981	0.935	1	0.981	0.935	1	CLONAL	1	TRUE	1	0.904396975896219	2		657	789	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162722942	162722942	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	295	702	0	ENST00000367921.3:c.140C>T	p.Thr47Ile	p.T47I	ENST00000367921	NM_006182.2	47	aCa/aTa	4/18	1	2	FACETS	0.902	0.854	0.951	0.902	0.854	0.951	CLONAL	1	TRUE	1	0.904396975896219	2		702	723	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138055	64138055	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	373	727	0	ENST00000334205.4:c.1978G>T	p.Ala660Ser	p.A660S	ENST00000334205	NM_003942.2	660	Gcc/Tcc	16/17	1	2	FACETS	0.996	0.951	1	0.996	0.951	1	CLONAL	1	TRUE	1	0.904396975896219	2		727	828	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172516	108172516	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	96	251	0	ENST00000278616.4:c.5319G>C	p.Lys1773Asn	p.K1773N	ENST00000278616	NM_000051.3	1773	aaG/aaC	35/63	1	2	FACETS	0.944	0.858	1	0.944	0.858	1	CLONAL	1	TRUE	1	0.904396975896219	2		251	225	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359425	118359425	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	256	548	1	ENST00000534358.1:c.4429C>T	p.Arg1477Cys	p.R1477C	ENST00000534358	NM_005933.3	1477	Cgt/Tgt	11/36	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.904396975896219	2		549	561	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435110	18435110	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	190	456	0	ENST00000266497.5:c.95C>A	p.Ser32Tyr	p.S32Y	ENST00000266497		32	tCt/tAt	1/31	1	2	FACETS	0.87	0.812	0.929	0.87	0.812	0.929	CLONAL	1	TRUE	1	0.904396975896219	2		456	483	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435658	18435658	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	101	275	0	ENST00000266497.5:c.643G>T	p.Gly215Ter	p.G215*	ENST00000266497		215	Gga/Tga	1/31	1	2	FACETS	0.833	0.757	0.912	0.833	0.757	0.912	CLONAL	1	TRUE	1	0.904396975896219	2		275	268	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650679	18650679	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1374460535	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	150	418	1	ENST00000266497.5:c.2890C>A	p.Gln964Lys	p.Q964K	ENST00000266497		964	Caa/Aaa	20/31	1	2	FACETS	0.945	0.876	1	0.945	0.876	1	CLONAL	1	TRUE	1	0.904396975896219	2		419	351	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487681	56487681	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	313	574	0	ENST00000267101.3:c.1613+1G>T		p.X538_splice	ENST00000267101	NM_001982.3	538			0.22719371429181	3	FACETS	0.791	0.754	0.829	0.791	0.754	0.829	INDETERMINATE	2	TRUE	1	0.904396975896219	3		574	635	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864565	57864565	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	395	725	0	ENST00000228682.2:c.2042C>A	p.Pro681Gln	p.P681Q	ENST00000228682	NM_005269.2	681	cCa/cAa	12/12	0.22719371429181	3	FACETS	1	0.994	1	0.651	0.621	0.682	INDETERMINATE	1	TRUE	1	0.904396975896219	3		725	974	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557368	21557368	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	445	389	0	ENST00000382592.4:c.2477A>G	p.Gln826Arg	p.Q826R	ENST00000382592	NM_014572.2	826	cAg/cGg	5/8	0.901366965981688	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.904396975896219	2		389	490	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437110	110437110	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	112	102	0	ENST00000375856.3:c.1291A>G	p.Met431Val	p.M431V	ENST00000375856	NM_003749.2	431	Atg/Gtg	1/2	0.891521155559192	3	FACETS	0.932	0.864	0.999	0.932	0.864	0.999	CLONAL	2	TRUE	1	0.904396975896219	3		102	193	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108091	30108091	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	259	562	0	ENST00000331968.5:c.716C>A	p.Ser239Ter	p.S239*	ENST00000331968	NM_002742.2	239	tCg/tAg	5/18	1	2	FACETS	0.889	0.839	0.94	0.889	0.839	0.94	CLONAL	1	TRUE	1	0.904396975896219	2		562	644	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647732	2647732	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	330	524	0	ENST00000342085.4:c.1635G>T	p.Gln545His	p.Q545H	ENST00000342085	NM_002613.4	545	caG/caT	14/14	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.904396975896219	2		524	672	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857854	9857854	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	370	675	0	ENST00000330684.3:c.3547C>A	p.Gln1183Lys	p.Q1183K	ENST00000330684	NM_001134407.1	1183	Cag/Aag	13/13	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.904396975896219	2		675	787	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772198	68772198	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1060501226	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	273	594	0	ENST00000261769.5:c.49-2A>G		p.X17_splice	ENST00000261769	NM_004360.3	17			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.904396975896219	2		594	601	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095967	11095967	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	345	705	1	ENST00000358026.2:c.241G>T	p.Glu81Ter	p.E81*	ENST00000358026	NM_001128849.1	81	Gag/Tag	3/36	0.904396975896219	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.904396975896219	1		706	402	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466797	25466797	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	312	544	0	ENST00000264709.3:c.1906G>C	p.Val636Leu	p.V636L	ENST00000264709	NM_175629.2	636	Gtg/Ctg	16/23	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.904396975896219	2		544	689	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873442	136873442	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	266	451	0	ENST00000241393.3:c.56G>T	p.Gly19Val	p.G19V	ENST00000241393	NM_003467.2	19	gGg/gTg	2/2	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.904396975896219	2		451	577	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634699	158634699	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	244	403	0	ENST00000263640.3:c.487G>T	p.Glu163Ter	p.E163*	ENST00000263640	NM_001105.4	163	Gag/Tag	5/11	1	2	FACETS	0.922	0.869	0.976	0.922	0.869	0.976	CLONAL	1	TRUE	1	0.904396975896219	2		403	585	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560914	9560914	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	357	567	0	ENST00000353224.5:c.868T>A	p.Ser290Thr	p.S290T	ENST00000353224	NM_177990.2	290	Tcg/Acg	4/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.904396975896219	2		567	734	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31015979	31015979	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	292	508	0	ENST00000375687.4:c.301G>T	p.Glu101Ter	p.E101*	ENST00000375687	NM_015338.5	101	Gag/Tag	5/13	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.904396975896219	2		508	626	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279950	46279950	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	462	758	0	ENST00000371998.3:c.3876G>T	p.Met1292Ile	p.M1292I	ENST00000371998		1292	atG/atT	20/23	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.904396975896219	2		758	950	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101776	71101776	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	144	263	1	ENST00000318789.4:c.422A>T	p.Gln141Leu	p.Q141L	ENST00000318789	NM_032682.5	141	cAg/cTg	9/21	1	2	FACETS	0.918	0.849	0.988	0.918	0.849	0.988	CLONAL	1	TRUE	1	0.904396975896219	2		264	347	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73113260	73113260	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1249439927	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	74	157	0	ENST00000356692.5:c.601G>C	p.Glu201Gln	p.E201Q	ENST00000356692		201	Gag/Cag	7/9	1	2	FACETS	0.914	0.819	1	0.914	0.819	1	CLONAL	1	TRUE	1	0.904396975896219	2		157	179	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631613	119631613	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	149	355	0	ENST00000316626.5:c.653G>T	p.Cys218Phe	p.C218F	ENST00000316626		218	tGt/tTt	6/12	1	2	FACETS	0.812	0.75	0.875	0.812	0.75	0.875	CLONAL	1	TRUE	1	0.904396975896219	2		355	406	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138382830	138382830	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs991602361	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	273	484	0	ENST00000289153.2:c.2714G>T	p.Cys905Phe	p.C905F	ENST00000289153	NM_006219.2	905	tGt/tTt	19/22	1	2	FACETS	0.964	0.913	1	0.964	0.913	1	CLONAL	1	TRUE	1	0.904396975896219	2		484	626	SUCCESS
ATR	545	MSKCC	GRCh37	3	142218561	142218561	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	192	390	0	ENST00000350721.4:c.5289-1G>A		p.X1763_splice	ENST00000350721	NM_001184.3	1763			1	2	FACETS	0.974	0.912	1	0.974	0.912	1	CLONAL	1	TRUE	1	0.904396975896219	2		390	436	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504914	186504914	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	160	333	0	ENST00000323963.5:c.772-2A>T		p.X258_splice	ENST00000323963		258			1	2	FACETS	0.912	0.847	0.978	0.912	0.847	0.978	CLONAL	1	TRUE	1	0.904396975896219	2		333	388	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	240505	240505	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	45	87	0	ENST00000264932.6:c.1465G>T	p.Gly489Trp	p.G489W	ENST00000264932	NM_004168.2	489	Ggg/Tgg	11/15	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.904396975896219	2		87	95	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31504727	31504727	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	371	677	0	ENST00000344624.3:c.1603C>T	p.Leu535Phe	p.L535F	ENST00000344624		535	Ctc/Ttc	8/33	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.904396975896219	2		677	760	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155651	56155651	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	222	344	0	ENST00000399503.3:c.743G>T	p.Arg248Leu	p.R248L	ENST00000399503	NM_005921.1	248	cGa/cTa	3/20	1	2	FACETS	0.994	0.935	1	0.994	0.935	1	CLONAL	1	TRUE	1	0.904396975896219	2		344	494	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449821	149449821	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	405	780	0	ENST00000286301.3:c.1243G>T	p.Gly415Cys	p.G415C	ENST00000286301	NM_005211.3	415	Ggc/Tgc	9/22	0.904396975896219	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.904396975896219	1		780	471	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997499	149997499	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	239	445	0	ENST00000253339.5:c.2780A>T	p.Tyr927Phe	p.Y927F	ENST00000253339		927	tAc/tTc	6/7	0.904396975896219	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.904396975896219	1		445	280	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527698	157527698	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	367	648	0	ENST00000346085.5:c.5423G>T	p.Arg1808Leu	p.R1808L	ENST00000346085	NM_020732.3	1808	cGt/cTt	20/20	0.904396975896219	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.904396975896219	1		648	422	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372741	81372741	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	225	428	0	ENST00000222390.5:c.793G>T	p.Gly265Cys	p.G265C	ENST00000222390	NM_000601.4	265	Ggc/Tgc	7/18	1	2	FACETS	0.995	0.937	1	0.995	0.937	1	CLONAL	1	TRUE	1	0.904396975896219	2		428	500	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376023	8376023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1256692385	NA	P-0036682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	214	332	0	ENST00000356435.5:c.4574C>T	p.Pro1525Leu	p.P1525L	ENST00000356435		1525	cCa/cTa	28/35	0.904396975896219	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.904396975896219	1		332	253	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	51	690	0	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	1	2	FACETS	0.839	0.714	0.976	1	0.969	1	CLONAL	2	TRUE	1	0.134443143857582	2		690	452	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221309	1221310	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs587776659	NA	P-0036684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	28	674	0	ENST00000326873.7:c.834_835del	p.Cys278TrpfsTer6	p.C278Wfs*6	ENST00000326873	NM_000455.4	278	TGt/t	6/10	0.134443143857582	1	FACETS	1	0.806	1	1	0.806	1	CLONAL	1	TRUE	0	0.134443143857582	1		674	385	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578290	212578290	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	210	588	0	ENST00000342788.4:c.967T>C	p.Cys323Arg	p.C323R	ENST00000342788	NM_005235.2	323	Tgt/Cgt	8/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.615603816340133	2		588	616	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159106	24159106	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	332	465	0	ENST00000263121.7:c.778C>T	p.Gln260Ter	p.Q260*	ENST00000263121	NM_003073.3	260	Cag/Tag	6/9	0.615603816340133	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.615603816340133	2		465	459	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0036686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	13	327	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.501	0.356	0.678	0.501	0.356	0.678	SUBCLONAL	1	TRUE	1	0.14	2		327	371	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0036686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	28	485	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.709	0.565	0.874	0.709	0.565	0.874	SUBCLONAL	1	TRUE	1	0.14	2		485	564	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100152	27100152	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	45	614	0	ENST00000324856.7:c.3951del	p.Met1318CysfsTer163	p.M1318Cfs*163	ENST00000324856	NM_006015.4	1316	tcG/tc	16/20	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.14	2		614	562	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563357	21563357	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs185326327	NA	P-0036686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	55	936	2	ENST00000382592.4:c.562G>A	p.Gly188Ser	p.G188S	ENST00000382592	NM_014572.2	188	Ggt/Agt	4/8	1	2	FACETS	0.987	0.843	1	0.987	0.843	1	CLONAL	1	TRUE	1	0.14	2		938	796	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0036687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	272	381	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA	2	FACETS	0.79	0.749	0.833			1	INDETERMINATE	2	TRUE	NA	0.581234808867112	2		381	592	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143521	108143521	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	120	553	0	ENST00000278616.4:c.3226C>T	p.Gln1076Ter	p.Q1076*	ENST00000278616	NM_000051.3	1076	Caa/Taa	22/63	0.581234808867112	1	FACETS	0.951	0.872	1	0.951	0.872	1	CLONAL	1	TRUE	0	0.581234808867112	1		553	308	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348199	348199	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	152	685	0	ENST00000262320.3:c.1307A>T	p.His436Leu	p.H436L	ENST00000262320	NM_003502.3	436	cAc/cTc	6/11	1	2	FACETS	0.863	0.793	0.936	0.863	0.793	0.936	CLONAL	1	TRUE	1	0.581234808867112	2		685	606	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220702	1220703	+	missense_variant	Missense_Mutation	DNP	GG	GG	TC	novel	NA	P-0036687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	136	666	1	ENST00000326873.7:c.720_721delinsTC	p.Ala241Pro	p.A241P	ENST00000326873	NM_000455.4	240	tcGGct/tcTCct	5/10	0.581234808867112	1	FACETS	0.783	0.718	0.849	0.783	0.718	0.849	SUBCLONAL	1	TRUE	0	0.581234808867112	1		667	424	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141493	11141493	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	29	672	0	ENST00000358026.2:c.3470G>A	p.Arg1157Gln	p.R1157Q	ENST00000358026	NM_001128849.1	1157	cGg/cAg	25/36	1	2	FACETS	0.187	0.15	0.23	0.187	0.15	0.23	SUBCLONAL	1	TRUE	1	0.763904877316802	2		672	405	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587385	29587385	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0036698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	176	224	0	ENST00000356175.3:c.4368-2A>C		p.X1456_splice	ENST00000356175	NM_000267.3	1456			0.636278399564515	1	FACETS	0.968	0.907	1	0.968	0.907	1	CLONAL	1	TRUE	0	0.680008889950039	1		224	353	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136101	11136101	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	217	624	0	ENST00000358026.2:c.3085A>C	p.Lys1029Gln	p.K1029Q	ENST00000358026	NM_001128849.1	1029	Aaa/Caa	22/36	1	2	FACETS	0.951	0.889	1	0.951	0.889	1	CLONAL	1	TRUE	1	0.680008889950039	2		624	671	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0036702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	455	405	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.534219772101754	5	FACETS	0.999	0.965	1			1	CLONAL	4	TRUE	NA	0.590448212270953	5		405	727	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142542	119142542	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	138	395	0	ENST00000264033.4:c.541A>T	p.Ile181Phe	p.I181F	ENST00000264033	NM_005188.3	181	Att/Ttt	3/16	1	2	FACETS	0.946	0.867	1	0.946	0.867	1	CLONAL	1	TRUE	1	0.590448212270953	2		395	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579574	7579575	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0036702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	183	643	0	ENST00000269305.4:c.112dup	p.Gln38ProfsTer5	p.Q38Pfs*5	ENST00000269305	NM_001126112.2	38	caa/cCaa	4/11	0.590448212270953	1	FACETS	0.933	0.87	0.998	0.933	0.87	0.998	CLONAL	1	TRUE	0	0.590448212270953	1		643	468	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15943758	15943758	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	165	369	0	ENST00000268712.3:c.6730del	p.Ser2244GlnfsTer49	p.S2244Qfs*49	ENST00000268712	NM_006311.3	2244	Tca/ca	43/46	0.590448212270953	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.590448212270953	1		369	372	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741455	39741455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	96	350	0	ENST00000361337.2:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000361337	NM_003286.2	448	Cgg/Tgg	14/21	1	2	FACETS	0.821	0.737	0.91	0.821	0.737	0.91	CLONAL	1	TRUE	1	0.590448212270953	2		350	396	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93607878	93607878	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0036702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	101	347	0	ENST00000375746.1:c.578+2T>A		p.X193_splice	ENST00000375746	NM_001174167.1	193			1	2	FACETS	0.992	0.895	1	0.992	0.895	1	CLONAL	1	TRUE	1	0.590448212270953	2		347	345	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0036704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	131	331	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.605552575635188	2		331	401	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0036704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	142	576	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.911	0.835	0.989	0.911	0.835	0.989	CLONAL	1	TRUE	1	0.605552575635188	2		576	515	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568656	41568656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	82	293	0	ENST00000263253.7:c.4606G>A	p.Glu1536Lys	p.E1536K	ENST00000263253	NM_001429.3	1536	Gaa/Aaa	28/31	1	2	FACETS	0.86	0.766	0.959	0.86	0.766	0.959	CLONAL	1	TRUE	1	0.605552575635188	2		293	315	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101089	26101089	+	start_lost	Translation_Start_Site	SNP	C	C	T	rs1559535727	NA	P-0036704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	117	529	0	ENST00000435504.4:c.3G>A	p.Met1?	p.M1?	ENST00000435504		1	atG/atA	1/13	0.605552575635188	1	FACETS	0.824	0.753	0.897	0.824	0.753	0.897	CLONAL	1	TRUE	0	0.605552575635188	1		529	327	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119483	193119483	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	80	314	0	ENST00000367435.3:c.878A>G	p.Tyr293Cys	p.Y293C	ENST00000367435	NM_024529.4	293	tAc/tGc	9/17	1	2	FACETS	0.803	0.713	0.898	0.803	0.713	0.898	CLONAL	1	TRUE	1	0.605552575635188	2		314	329	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912435	50912435	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	235	749	1	ENST00000440232.2:c.1949C>T	p.Ser650Leu	p.S650L	ENST00000440232	NM_002691.3	650	tCa/tTa	16/27	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.605552575635188	2		750	697	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537076	41537076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	93	264	0	ENST00000263253.7:c.1903G>A	p.Glu635Lys	p.E635K	ENST00000263253	NM_001429.3	635	Gag/Aag	10/31	1	2	FACETS	0.931	0.836	1	0.931	0.836	1	CLONAL	1	TRUE	1	0.605552575635188	2		264	330	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197187	26197187	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	152	481	0	ENST00000356476.2:c.292G>T	p.Glu98Ter	p.E98*	ENST00000356476		98	Gag/Tag	1/1	1	2	FACETS	0.998	0.919	1	0.998	0.919	1	CLONAL	1	TRUE	1	0.605552575635188	2		481	503	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797313	135797313	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	85	213	0	ENST00000298552.3:c.556G>C	p.Ala186Pro	p.A186P	ENST00000298552	NM_001162426.1	186	Gca/Cca	7/23	0.605552575635188	1	FACETS	0.989	0.894	1	0.989	0.894	1	CLONAL	1	TRUE	0	0.605552575635188	1		213	198	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981516	201981516	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	239	815	0	ENST00000359651.3:c.430G>C	p.Glu144Gln	p.E144Q	ENST00000359651		144	Gag/Cag	3/8	1	2	FACETS	0.985	0.923	1	0.985	0.923	1	CLONAL	1	TRUE	1	0.605552575635188	2		815	801	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948187	71948187	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	263	928	0	ENST00000298229.2:c.2899C>G	p.Pro967Ala	p.P967A	ENST00000298229	NM_001567.3	967	Cct/Gct	26/28	1	2	FACETS	0.961	0.902	1	0.961	0.902	1	CLONAL	1	TRUE	1	0.605552575635188	2		928	904	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448455	49448455	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	179	509	0	ENST00000301067.7:c.256G>C	p.Glu86Gln	p.E86Q	ENST00000301067	NM_003482.3	86	Gag/Cag	3/54	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.605552575635188	2		509	557	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495696	56495696	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	131	452	0	ENST00000267101.3:c.3886C>T	p.Gln1296Ter	p.Q1296*	ENST00000267101	NM_001982.3	1296	Cag/Tag	28/28	1	2	FACETS	0.966	0.883	1	0.966	0.883	1	CLONAL	1	TRUE	1	0.605552575635188	2		452	448	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112538	2112538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397515187	NA	P-0036704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	256	766	0	ENST00000219476.3:c.1298C>T	p.Ser433Phe	p.S433F	ENST00000219476	NM_000548.3	433	tCc/tTc	13/42	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.605552575635188	2		766	813	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038605	14038605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	85	242	0	ENST00000311895.7:c.1930G>A	p.Glu644Lys	p.E644K	ENST00000311895	NM_005236.2	644	Gaa/Aaa	10/11	1	2	FACETS	0.791	0.705	0.882	0.791	0.705	0.882	SUBCLONAL	1	TRUE	1	0.605552575635188	2		242	355	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568593	41568593	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	148	514	0	ENST00000263253.7:c.4543G>T	p.Glu1515Ter	p.E1515*	ENST00000263253	NM_001429.3	1515	Gaa/Taa	28/31	1	2	FACETS	0.887	0.815	0.962	0.887	0.815	0.962	CLONAL	1	TRUE	1	0.605552575635188	2		514	551	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129701	47129701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	125	444	0	ENST00000409792.3:c.5179G>A	p.Glu1727Lys	p.E1727K	ENST00000409792	NM_014159.6	1727	Gag/Aag	10/21	1	2	FACETS	0.786	0.715	0.861	0.786	0.715	0.861	SUBCLONAL	1	TRUE	1	0.605552575635188	2		444	525	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198296	138198296	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	104	279	0	ENST00000237289.4:c.889G>C	p.Glu297Gln	p.E297Q	ENST00000237289	NM_001270507.1	297	Gag/Cag	6/9	1	2	FACETS	0.918	0.83	1	0.918	0.83	1	CLONAL	1	TRUE	1	0.605552575635188	2		279	374	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	40	214	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		214	335	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413042	139413042	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0036706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	39	449	0	ENST00000277541.6:c.1099+1G>C		p.X367_splice	ENST00000277541	NM_017617.3	367			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		449	334	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970897	21970914	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	INS	TCACCTGAGGGACCTTCC	TCACCTGAGGGACCTTCC	AGATCATCAGTCCAGACCTTT	novel	NA	P-0036706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	37	797	0	ENST00000304494.5:c.444_457+4delinsAAAGGTCTGGACTGATGATCT		p.X148_splice	ENST00000304494	NM_000077.4	148		2/3	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		797	578	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028669	12028669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	52	471	0	ENST00000353533.5:c.872G>T	p.Trp291Leu	p.W291L	ENST00000353533	NM_003010.3	291	tGg/tTg	8/11	0.298646452263204	3	FACETS	0.78	0.671	0.898	0.26	0.223	0.3	INDETERMINATE	1	TRUE	0	0.76	3		471	242	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0036710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	40	239	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.290973220041556	4	FACETS	1	0.957	1	0.713	0.605	0.826	INDETERMINATE	1	TRUE	2	0.76	4		239	130	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562493	21562493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1417916199	NA	P-0036710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	12	88	0	ENST00000382592.4:c.1426G>A	p.Ala476Thr	p.A476T	ENST00000382592	NM_014572.2	476	Gcc/Acc	4/8	0.216239529616081	6	FACETS	1	0.816	1			1	CLONAL	1	TRUE	NA	0.216239529616081	6		88	129	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028669	12028669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	129	471	0	ENST00000353533.5:c.872G>T	p.Trp291Leu	p.W291L	ENST00000353533	NM_003010.3	291	tGg/tTg	8/11	0.216239529616081	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	3	TRUE	0	0.216239529616081	3		471	399	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0036710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	66	239	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.191776293952215	4	FACETS	1	0.952	1	0.793	0.694	0.899	CLONAL	2	TRUE	1	0.216239529616081	4		239	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0036716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	130	631	4	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.363443699177766	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.363443699177766	1		635	495	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0036716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	78	490	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.862	0.759	0.971	0.862	0.759	0.971	CLONAL	1	TRUE	1	0.363443699177766	2		490	498	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244155	153244156	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0036716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	45	441	0	ENST00000281708.4:c.2001dup	p.Ser668GlufsTer26	p.S668Efs*26	ENST00000281708	NM_033632.3	667	-/G	12/12	1	2	FACETS	0.479	0.402	0.564	0.479	0.402	0.564	SUBCLONAL	1	TRUE	1	0.363443699177766	2		441	517	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907161	101907161	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	55	267	0	ENST00000374994.4:c.1121G>C	p.Gly374Ala	p.G374A	ENST00000374994	NM_004612.2	374	gGa/gCa	6/9	0.163154957231662	2	FACETS	0.931	0.801	1	0.466	0.4	0.536	INDETERMINATE	1	TRUE	0	0.363443699177766	2		267	325	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822099	72822099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	34	483	0	ENST00000268489.5:c.10076C>T	p.Ser3359Phe	p.S3359F	ENST00000268489	NM_006885.3	3359	tCc/tTc	10/10	1	2	FACETS	0.481	0.393	0.58	0.481	0.393	0.58	SUBCLONAL	1	TRUE	1	0.363443699177766	2		483	389	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435734	56435734	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1399776234	NA	P-0036716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	58	466	0	ENST00000407977.2:c.1403C>G	p.Ser468Ter	p.S468*	ENST00000407977		468	tCa/tGa	9/10	0.363443699177766	1	FACETS	0.678	0.585	0.779	0.678	0.585	0.779	SUBCLONAL	1	TRUE	0	0.363443699177766	1		466	385	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436137	56436137	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	45	450	0	ENST00000407977.2:c.1000G>T	p.Glu334Ter	p.E334*	ENST00000407977		334	Gaa/Taa	9/10	0.363443699177766	1	FACETS	0.529	0.446	0.621	0.529	0.446	0.621	SUBCLONAL	1	TRUE	0	0.363443699177766	1		450	383	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215633977	215633977	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1553619701	NA	P-0036716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	41	318	0	ENST00000260947.4:c.1374C>A	p.Asp458Glu	p.D458E	ENST00000260947	NM_000465.2	458	gaC/gaA	5/11	1	2	FACETS	0.49	0.408	0.582	0.49	0.408	0.582	SUBCLONAL	1	TRUE	1	0.363443699177766	2		318	460	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713129	30713129	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0036716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	21	243	0	ENST00000295754.5:c.455-1G>A		p.X152_splice	ENST00000295754	NM_003242.5	152			1	2	FACETS	0.366	0.281	0.464	0.366	0.281	0.464	SUBCLONAL	1	TRUE	1	0.363443699177766	2		243	316	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713408	30713408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	39	410	0	ENST00000295754.5:c.733G>A	p.Glu245Lys	p.E245K	ENST00000295754	NM_003242.5	245	Gag/Aag	4/7	1	2	FACETS	0.48	0.398	0.572	0.48	0.398	0.572	SUBCLONAL	1	TRUE	1	0.363443699177766	2		410	447	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715713	30715713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	44	296	0	ENST00000295754.5:c.1371G>A	p.Met457Ile	p.M457I	ENST00000295754	NM_003242.5	457	atG/atA	5/7	1	2	FACETS	0.503	0.422	0.593	0.503	0.422	0.593	SUBCLONAL	1	TRUE	1	0.363443699177766	2		296	481	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732961	30732961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	20	284	1	ENST00000295754.5:c.1574C>T	p.Pro525Leu	p.P525L	ENST00000295754	NM_003242.5	525	cCa/cTa	7/7	1	2	FACETS	0.361	0.276	0.46	0.361	0.276	0.46	SUBCLONAL	1	TRUE	1	0.363443699177766	2		285	305	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641147	93641147	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	155	506	0	ENST00000375746.1:c.1493G>A	p.Arg498Lys	p.R498K	ENST00000375746	NM_001174167.1	498	aGa/aAa	11/14	0.163154957231662	2	FACETS	1	0.984	1	0.642	0.59	0.697	INDETERMINATE	1	TRUE	0	0.363443699177766	2		506	664	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517201	NA	P-0036718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	263	671	0	ENST00000263967.3:c.1637A>C	p.Gln546Pro	p.Q546P	ENST00000263967	NM_006218.2	546	cAg/cCg	10/21	1	2	FACETS	0.928	0.876	0.981	0.928	0.876	0.981	CLONAL	1	TRUE	1	0.892381242743871	2		671	635	SUCCESS
APC	324	MSKCC	GRCh37	5	112164663	112164664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	125	216	0	ENST00000257430.4:c.1742dup	p.Glu582GlyfsTer20	p.E582Gfs*20	ENST00000257430	NM_000038.5	579	-/A	14/16	0.892381242743871	1	FACETS	0.804	0.752	0.854	0.804	0.752	0.854	CLONAL	1	TRUE	0	0.892381242743871	1		216	193	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348880	89348880	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1306	75	1055	0	ENST00000301030.4:c.4070C>G	p.Ser1357Cys	p.S1357C	ENST00000301030	NM_001256183.1	1357	tCc/tGc	9/13	1	2	FACETS	0.122	0.106	0.139	0.122	0.106	0.139	SUBCLONAL	1	TRUE	1	0.892381242743871	2		1055	1381	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796964	78796964	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	399	640	1	ENST00000306801.3:c.1077del	p.Tyr360IlefsTer54	p.Y360Ifs*54	ENST00000306801	NM_020761.2	359	tcG/tc	9/34	1	2	FACETS	0.983	0.939	1	0.983	0.939	1	CLONAL	1	TRUE	1	0.892381242743871	2		641	910	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145729	11145731	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0036718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	348	678	0	ENST00000358026.2:c.4094_4096del	p.Lys1365del	p.K1365del	ENST00000358026	NM_001128849.1	1364	gAGAag/gag	29/36	0.892381242743871	1	FACETS	0.891	0.86	0.92	0.891	0.86	0.92	CLONAL	1	TRUE	0	0.892381242743871	1		678	485	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176671252	176671252	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0036718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	256	485	0	ENST00000439151.2:c.4359T>A	p.Tyr1453Ter	p.Y1453*	ENST00000439151	NM_022455.4	1453	taT/taA	9/23	0.892381242743871	1	FACETS	0.99	0.956	1	0.99	0.956	1	CLONAL	1	TRUE	0	0.892381242743871	1		485	321	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0036719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	512	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.891437471066579	2	FACETS	0.977	0.96	0.994	0.977	0.96	0.994	CLONAL	2	TRUE	0	0.912585928681448	2		452	574	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	214	357	0	ENST00000263967.3:c.1034A>G	p.Asn345Ser	p.N345S	ENST00000263967	NM_006218.2	345	aAt/aGt	5/21	1	2	FACETS	0.981	0.922	1	0.981	0.922	1	CLONAL	1	TRUE	1	0.912585928681448	2		357	478	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107017	27107017	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	383	518	0	ENST00000324856.7:c.6628C>T	p.Gln2210Ter	p.Q2210*	ENST00000324856	NM_006015.4	2210	Cag/Tag	20/20	0.895835159742138	2	FACETS	0.992	0.972	1	0.992	0.972	1	CLONAL	2	TRUE	0	0.912585928681448	2		518	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0036720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	67	710	1	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.212885115265963	1	FACETS	0.722	0.627	0.824	0.722	0.627	0.824	SUBCLONAL	1	TRUE	0	0.262730663460394	1		711	614	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342407	118342407	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	15	227	0	ENST00000534358.1:c.533G>A	p.Arg178Lys	p.R178K	ENST00000534358	NM_005933.3	178	aGa/aAa	3/36	1	2	FACETS	0.546	0.4	0.721	0.546	0.4	0.721	SUBCLONAL	1	TRUE	1	0.262730663460394	2		227	209	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954622	17954622	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	74	858	0	ENST00000458235.1:c.272A>G	p.Glu91Gly	p.E91G	ENST00000458235	NM_000215.3	91	gAg/gGg	3/24	1	2	FACETS	0.863	0.755	0.978	0.863	0.755	0.978	CLONAL	1	TRUE	1	0.262730663460394	2		858	653	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0036726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	395	697	3	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	NA	2	FACETS	0.884	0.856	0.912			1	INDETERMINATE	2	TRUE	NA	0.819434841227176	2		700	545	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2239	58	456	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.819434841227176	11	FACETS	0.289	0.246	0.336			1	SUBCLONAL	1	TRUE	NA	0.819434841227176	11		456	2297	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0036726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	228	444	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			0.347749875318788	5	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.819434841227176	5		444	498	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990417	81990417	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	72	406	0	ENST00000359376.3:c.3688G>T	p.Ala1230Ser	p.A1230S	ENST00000359376	NM_002661.3	1230	Gcc/Tcc	32/33	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.819434841227176	NA		406	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0036729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	173	611	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.751729902142297	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.751729902142297	1		611	246	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562746	29562746	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs199474742	NA	P-0036729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	93	571	1	ENST00000356175.3:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000356175	NM_000267.3	1276	Cga/Tga	28/57	0.751729902142297	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.751729902142297	1		572	144	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203792	94203792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753958669	NA	P-0036729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	23	189	0	ENST00000323929.3:c.862C>T	p.Arg288Cys	p.R288C	ENST00000323929	NM_005591.3	288	Cgt/Tgt	9/20	0.287762877014055	3	FACETS	0.886	0.706	1	0.295	0.235	0.362	INDETERMINATE	1	TRUE	0	0.751729902142297	3		189	95	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845689	68845689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	176	537	0	ENST00000261769.5:c.935C>T	p.Pro312Leu	p.P312L	ENST00000261769	NM_004360.3	312	cCt/cTt	7/16	0.225435040698407	3	FACETS	0.828	0.773	0.883	0.828	0.773	0.883	INDETERMINATE	2	TRUE	1	0.751729902142297	3		537	389	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982419	25982419	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	106	332	0	ENST00000435504.4:c.871A>G	p.Thr291Ala	p.T291A	ENST00000435504		291	Aca/Gca	9/13	0.248512702795077	2	FACETS	0.969	0.882	1	0.485	0.441	0.53	INDETERMINATE	1	TRUE	0	0.751729902142297	2		332	291	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723603	49723620	+	inframe_deletion	In_Frame_Del	DEL	GGCAGAAGTTCTCCCGAA	GGCAGAAGTTCTCCCGAA	-	novel	NA	P-0036729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	35	121	0	ENST00000449682.2:c.1022_1039del	p.Leu341_Cys346del	p.L341_C346del	ENST00000449682	NM_020998.3	341	cTTCGGGAGAACTTCTGCCgg/cgg	9/18	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.751729902142297	2		121	64	SUCCESS
APC	324	MSKCC	GRCh37	5	112173394	112173394	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783030	NA	P-0036729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	24	258	1	ENST00000257430.4:c.2107del	p.Ala703GlnfsTer15	p.A703Qfs*15	ENST00000257430	NM_000038.5	701	atG/at	16/16	0.179892978312919	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.751729902142297	0		259	49	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335062	81335062	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	83	281	0	ENST00000222390.5:c.1765G>T	p.Val589Phe	p.V589F	ENST00000222390	NM_000601.4	589	Gtc/Ttc	16/18	0.745510760834119	3	FACETS	0.808	0.73	0.887	0.808	0.73	0.887	CLONAL	2	TRUE	1	0.751729902142297	3		281	188	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034465	47034465	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	203	615	2	ENST00000377604.3:c.550G>A	p.Ala184Thr	p.A184T	ENST00000377604	NM_001204468.1	184	Gct/Act	6/24	0.248512702795077	2	FACETS	1	0.993	1	0.722	0.681	0.763	INDETERMINATE	1	TRUE	0	0.751729902142297	2		617	374	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0036730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	98	391	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.746171551043893	NA		391	847	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500886	8500886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	69	581	0	ENST00000356435.5:c.1996C>T	p.Pro666Ser	p.P666S	ENST00000356435		666	Cct/Tct	13/35	0.718783007396265	2	FACETS	0.287	0.25	0.328	0.144	0.125	0.164	SUBCLONAL	1	TRUE	0	0.746171551043893	2		581	644	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916933	178916933	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	232	495	0	ENST00000263967.3:c.320A>G	p.Asn107Ser	p.N107S	ENST00000263967	NM_006218.2	107	aAc/aGc	2/21	0.746171551043893	3	FACETS	1	0.966	1	0.526	0.491	0.561	CLONAL	1	TRUE	1	0.746171551043893	3		495	812	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805675	43805675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	129	550	0	ENST00000372470.3:c.731C>T	p.Ser244Leu	p.S244L	ENST00000372470	NM_005373.2	244	tCa/tTa	5/12	0.385151847968759	1	FACETS	0.348	0.316	0.381	0.348	0.316	0.381	INDETERMINATE	1	TRUE	0	0.746171551043893	1		550	623	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944121	71944121	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	143	627	0	ENST00000298229.2:c.1954G>A	p.Glu652Lys	p.E652K	ENST00000298229	NM_001567.3	652	Gag/Aag	17/28	0.385151847968759	1	FACETS	0.337	0.308	0.368	0.337	0.308	0.368	INDETERMINATE	1	TRUE	0	0.746171551043893	1		627	712	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790476	3790476	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	76	631	0	ENST00000262367.5:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000262367	NM_004380.2	1353	Gaa/Taa	24/31	1	2	FACETS	0.217	0.189	0.247	0.217	0.189	0.247	SUBCLONAL	1	TRUE	1	0.746171551043893	2		631	939	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14022042	14022042	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	87	569	0	ENST00000311895.7:c.742G>C	p.Glu248Gln	p.E248Q	ENST00000311895	NM_005236.2	248	Gaa/Caa	4/11	1	2	FACETS	0.341	0.302	0.384	0.341	0.302	0.384	SUBCLONAL	1	TRUE	1	0.746171551043893	2		569	683	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288841	15288841	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	31	180	0	ENST00000263388.2:c.3898G>C	p.Val1300Leu	p.V1300L	ENST00000263388	NM_000435.2	1300	Gtg/Ctg	24/33	0.418546588119284	1	FACETS	0.273	0.222	0.329	0.273	0.222	0.329	INDETERMINATE	1	TRUE	0	0.746171551043893	1		180	191	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972626	25972626	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	238	468	0	ENST00000435504.4:c.1799C>T	p.Ser600Leu	p.S600L	ENST00000435504		600	tCa/tTa	12/13	1	2	FACETS	0.987	0.928	1	0.987	0.928	1	CLONAL	1	TRUE	1	0.746171551043893	2		468	646	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972713	25972713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	254	521	0	ENST00000435504.4:c.1712C>T	p.Ser571Phe	p.S571F	ENST00000435504		571	tCc/tTc	12/13	1	2	FACETS	0.998	0.94	1	0.998	0.94	1	CLONAL	1	TRUE	1	0.746171551043893	2		521	682	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281685	142281685	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	168	584	0	ENST00000350721.4:c.559G>A	p.Gly187Arg	p.G187R	ENST00000350721	NM_001184.3	187	Gga/Aga	4/47	0.746171551043893	3	FACETS	0.544	0.499	0.591	0.272	0.249	0.296	SUBCLONAL	1	TRUE	1	0.746171551043893	3		584	1137	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582020	189582020	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0036730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	400	325	0	ENST00000264731.3:c.580-1G>T		p.X194_splice	ENST00000264731	NM_003722.4	194			0.423051485127593	4	FACETS	0.854	0.819	0.888	1	0.995	1	INDETERMINATE	3	TRUE	2	0.746171551043893	4		325	731	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332724	153332724	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	501	574	0	ENST00000281708.4:c.232G>T	p.Glu78Ter	p.E78*	ENST00000281708	NM_033632.3	78	Gaa/Taa	2/12	0.707206589958996	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.746171551043893	2		574	665	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939083	131939083	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	111	372	0	ENST00000265335.6:c.2299G>T	p.Asp767Tyr	p.D767Y	ENST00000265335		767	Gac/Tac	14/25	0.746171551043893	1	FACETS	0.57	0.519	0.623	0.57	0.519	0.623	SUBCLONAL	1	TRUE	0	0.746171551043893	1		372	327	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903783	41903784	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0036730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	354	651	0	ENST00000372991.4:c.772_773dup	p.Ser259ProfsTer46	p.S259Pfs*46	ENST00000372991	NM_001760.3	258	gcc/gcGCc	5/5	0.746171551043893	1	FACETS	0.953	0.913	0.993	0.953	0.913	0.993	CLONAL	1	TRUE	0	0.746171551043893	1		651	624	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880121	151880121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	308	533	0	ENST00000262189.6:c.5203C>T	p.Leu1735Phe	p.L1735F	ENST00000262189	NM_170606.2	1735	Ctt/Ttt	35/59	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.746171551043893	2		533	768	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945568	151945568	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	126	246	0	ENST00000262189.6:c.1951G>T	p.Glu651Ter	p.E651*	ENST00000262189	NM_170606.2	651	Gaa/Taa	14/59	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.746171551043893	2		246	306	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430665	80430665	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1425322060	NA	P-0036730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	93	566	0	ENST00000286548.4:c.343G>A	p.Glu115Lys	p.E115K	ENST00000286548	NM_002072.3	115	Gaa/Aaa	3/7	0.718783007396265	2	FACETS	0.5	0.446	0.557	0.25	0.223	0.279	SUBCLONAL	1	TRUE	0	0.746171551043893	2		566	499	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270457	98270457	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs781768965	NA	P-0036730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	191	599	0	ENST00000331920.6:c.187G>C	p.Glu63Gln	p.E63Q	ENST00000331920	NM_000264.3	63	Gag/Cag	1/24	0.746171551043893	2	FACETS	0.568	0.525	0.612	0.284	0.262	0.306	SUBCLONAL	1	TRUE	0	0.746171551043893	2		599	902	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578505	+	inframe_deletion	In_Frame_Del	DEL	GCACAG	GCACAG	-	novel	NA	P-0036730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	493	890	0	ENST00000269305.4:c.425_430del	p.Pro142_Val143del	p.P142_V143del	ENST00000269305	NM_001126112.2	142	cCTGTGCag/cag	5/11	0.746171551043893	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.746171551043893	1		890	783	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777747	3777747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367899910	NA	P-0036732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	82	934	0	ENST00000262367.5:c.7301C>T	p.Thr2434Met	p.T2434M	ENST00000262367	NM_004380.2	2434	aCg/aTg	31/31	0.599089402511237	3	FACETS	0.289	0.254	0.327	0.145	0.127	0.164	SUBCLONAL	1	TRUE	1	0.629596993270251	3		934	1185	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0036732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	385	667	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.616722330626783	2	FACETS	0.936	0.9	0.973	0.936	0.9	0.973	CLONAL	2	TRUE	0	0.629596993270251	2		667	653	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605102	46605102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540130771	NA	P-0036732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	63	694	0	ENST00000263734.3:c.1319C>T	p.Thr440Met	p.T440M	ENST00000263734	NM_001430.4	440	aCg/aTg	10/16	0.629596993270251	4	FACETS	0.279	0.24	0.322	0.093	0.08	0.108	SUBCLONAL	1	TRUE	1	0.629596993270251	4		694	1167	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719504	61719504	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	376	555	0	ENST00000401558.2:c.1679A>G	p.Lys560Arg	p.K560R	ENST00000401558	NM_003400.3	560	aAa/aGa	15/25	0.629596993270251	4	FACETS	0.897	0.859	0.936	0.897	0.859	0.936	CLONAL	3	TRUE	1	0.629596993270251	4		555	723	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0036732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	184	485	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.599089402511237	3	FACETS	1	0.986	1	0.63	0.584	0.677	CLONAL	1	TRUE	1	0.629596993270251	3		485	610	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573291	55573291	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	24	345	0	ENST00000288135.5:c.953T>C	p.Met318Thr	p.M318T	ENST00000288135	NM_000222.2	318	aTg/aCg	6/21	1	2	FACETS	0.268	0.211	0.335	0.268	0.211	0.335	SUBCLONAL	1	TRUE	1	0.629596993270251	2		345	284	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84388636	84388636	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	66	506	0	ENST00000321945.7:c.652A>G	p.Met218Val	p.M218V	ENST00000321945	NM_139076.2	218	Atg/Gtg	7/9	0.465690155393804	4	FACETS	0.38	0.329	0.436	0.19	0.164	0.218	SUBCLONAL	1	TRUE	2	0.629596993270251	4		506	898	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0036732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	141	487	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.961	0.882	1	0.961	0.882	1	CLONAL	1	TRUE	1	0.629596993270251	2		487	466	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538178	187538178	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	171	553	0	ENST00000441802.2:c.9056A>G	p.Asn3019Ser	p.N3019S	ENST00000441802	NM_005245.3	3019	aAc/aGc	11/27	1	2	FACETS	0.929	0.859	1	0.929	0.859	1	CLONAL	1	TRUE	1	0.629596993270251	2		553	585	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39074230	39074230	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	66	386	0	ENST00000357387.3:c.80C>G	p.Pro27Arg	p.P27R	ENST00000357387	NM_152756.3	27	cCg/cGg	2/38	0.629596993270251	3	FACETS	0.402	0.349	0.461	0.134	0.116	0.154	SUBCLONAL	1	TRUE	0	0.629596993270251	3		386	685	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0036732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	212	321	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.581413828159273	3	FACETS	1	0.987	1	0.765	0.722	0.806	CLONAL	2	TRUE	0	0.629596993270251	3		321	386	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057599	180057599	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751885535	NA	P-0036732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	493	860	0	ENST00000261937.6:c.356G>A	p.Arg119His	p.R119H	ENST00000261937	NM_182925.4	119	cGc/cAc	3/30	NA	2	FACETS	0.979	0.946	1			1	INDETERMINATE	2	TRUE	NA	0.629596993270251	2		860	800	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061191	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs879499034	NA	P-0036734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	47	429	0	ENST00000250448.2:c.798C>A	p.Phe266Leu	p.F266L	ENST00000250448	NM_004496.3	266	ttC/ttA	2/2	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.22	2		429	292	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618629	37618629	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	26	405	0	ENST00000447079.4:c.305C>A	p.Ser102Ter	p.S102*	ENST00000447079	NM_015083.1	102	tCa/tAa	1/14	0.129780411352541	1	FACETS	0.683	0.542	0.844	0.683	0.542	0.844	INDETERMINATE	1	TRUE	0	0.22	1		405	308	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572456	95572458	+	missense_variant	Missense_Mutation	TNP	TCT	TCT	AAG	novel	NA	P-0036734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	16	407	0	ENST00000393063.1:c.2907_2909delinsCTT	p.Glu970Leu	p.E970L	ENST00000393063	NM_030621.3	969	gcAGAa/gcCTTa	19/28	1	2	FACETS	0.713	0.528	0.932	0.713	0.528	0.932	CLONAL	1	TRUE	1	0.22	2		407	204	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657673	37657673	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	26	427	0	ENST00000447079.4:c.2590A>G	p.Asn864Asp	p.N864D	ENST00000447079	NM_015083.1	864	Aac/Gac	6/14	0.129780411352541	1	FACETS	0.935	0.744	1	0.935	0.744	1	INDETERMINATE	1	TRUE	0	0.22	1		427	225	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0036742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	124	380	1	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	0.41003727440092	2	FACETS	1	0.985	1	0.72	0.657	0.785	CLONAL	1	TRUE	0	0.411072928823939	2		381	419	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976745	2976745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748839211	NA	P-0036742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	98	639	0	ENST00000396946.4:c.1267C>T	p.Arg423Trp	p.R423W	ENST00000396946	NM_032415.4	423	Cgg/Tgg	9/25	0.350296951171432	3	FACETS	0.92	0.822	1	0.46	0.411	0.512	CLONAL	1	TRUE	1	0.411072928823939	3		639	625	SUCCESS
APC	324	MSKCC	GRCh37	5	112175771	112175771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	38	204	0	ENST00000257430.4:c.4480G>A	p.Glu1494Lys	p.E1494K	ENST00000257430	NM_000038.5	1494	Gaa/Aaa	16/16	0.411072928823939	1	FACETS	0.89	0.747	1	0.89	0.747	1	CLONAL	1	TRUE	0	0.411072928823939	1		204	165	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153542	108153542	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	143	341	0	ENST00000278616.4:c.3682G>T	p.Glu1228Ter	p.E1228*	ENST00000278616	NM_000051.3	1228	Gaa/Taa	25/63	0.411072928823939	2	FACETS	0.899	0.829	0.97	0.899	0.829	0.97	CLONAL	2	TRUE	0	0.411072928823939	2		341	387	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39745032	39745032	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	76	381	0	ENST00000361337.2:c.1822C>G	p.Pro608Ala	p.P608A	ENST00000361337	NM_003286.2	608	Ccg/Gcg	17/21	0.350296951171432	3	FACETS	0.993	0.874	1	0.496	0.437	0.56	CLONAL	1	TRUE	1	0.411072928823939	3		381	449	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169999732	169999732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	75	343	0	ENST00000295797.4:c.1043G>A	p.Arg348Lys	p.R348K	ENST00000295797	NM_002740.5	348	aGa/aAa	11/18	1	2	FACETS	0.948	0.835	1	0.948	0.835	1	CLONAL	1	TRUE	1	0.411072928823939	2		343	385	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228235	53228235	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	206	563	0	ENST00000375401.3:c.2167G>T	p.Asp723Tyr	p.D723Y	ENST00000375401	NM_004187.3	723	Gac/Tac	15/26	0.0852084505327033	3	FACETS	1	0.948	1			1	INDETERMINATE	2	TRUE	NA	0.411072928823939	3		563	594	SUCCESS
APC	324	MSKCC	GRCh37	5	112175769	112175770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	38	285	0	ENST00000257430.4:c.4478_4479insA	p.Glu1494GlyfsTer20	p.E1494Gfs*20	ENST00000257430	NM_000038.5	1493	acg/acAg	16/16	0.411072928823939	1	FACETS	0.874	0.733	1	0.874	0.733	1	CLONAL	1	TRUE	0	0.411072928823939	1		285	168	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0036744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	19	381	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.442	0.334	0.569	0.442	0.334	0.569	SUBCLONAL	1	TRUE	1	0.182286049264426	2		381	472	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220400	1220400	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1359582062	NA	P-0036744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	42	638	1	ENST00000326873.7:c.493G>T	p.Glu165Ter	p.E165*	ENST00000326873	NM_000455.4	165	Gag/Tag	4/10	1	2	FACETS	0.711	0.592	0.843	0.711	0.592	0.843	SUBCLONAL	1	TRUE	1	0.182286049264426	2		639	648	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044472	47044472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556781457	NA	P-0036744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	39	266	0	ENST00000377604.3:c.1969C>T	p.Arg657Cys	p.R657C	ENST00000377604	NM_001204468.1	657	Cgc/Tgc	18/24	1	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.182286049264426	1		266	296	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301158	65301158	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	42	193	0	ENST00000342505.4:c.3290G>T	p.Gly1097Val	p.G1097V	ENST00000342505	NM_002227.2	1097	gGc/gTc	24/25	0.182286049264426	2	FACETS	0.866	0.728	1	0.866	0.728	1	CLONAL	2	TRUE	0	0.182286049264426	2		193	266	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313328	65313328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	93	416	0	ENST00000342505.4:c.1786C>T	p.His596Tyr	p.H596Y	ENST00000342505	NM_002227.2	596	Cac/Tac	13/25	0.182286049264426	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	2	TRUE	0	0.182286049264426	2		416	494	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098759	47098759	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	67	564	0	ENST00000409792.3:c.6515C>G	p.Pro2172Arg	p.P2172R	ENST00000409792	NM_014159.6	2172	cCc/cGc	15/21	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.182286049264426	2		564	658	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411877	116411899	+	splice_region_variant,intron_variant	Splice_Region	DEL	AGCTCTTTCTTTCTCTCTGTTTT	AGCTCTTTCTTTCTCTCTGTTTT	-	novel	NA	P-0036746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	122	869	0	ENST00000397752.3:c.2888-25_2888-3del		p.X963_splice	ENST00000397752	NM_000245.2	963			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		869	972	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0036747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	72	344	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.854	0.756	0.956	0.854	0.756	0.956	CLONAL	1	TRUE	1	0.68	2		344	248	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685307	89685307	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123317	NA	P-0036747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	81	288	0	ENST00000371953.3:c.202T>C	p.Tyr68His	p.Y68H	ENST00000371953	NM_000314.4	68	Tac/Cac	3/9	1	2	FACETS	0.822	0.732	0.915	0.822	0.732	0.915	CLONAL	1	TRUE	1	0.68	2		288	290	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624275	89624275	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204910	NA	P-0036747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	141	331	0	ENST00000371953.3:c.49C>T	p.Gln17Ter	p.Q17*	ENST00000371953	NM_000314.4	17	Caa/Taa	1/9	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.68	2		331	370	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696713	47696713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	31	367	0	ENST00000347630.2:c.235G>A	p.Glu79Lys	p.E79K	ENST00000347630	NM_001007230.1	79	Gaa/Aaa	5/11	1	2	FACETS	0.234	0.189	0.285	0.234	0.189	0.285	SUBCLONAL	1	TRUE	1	0.68	2		367	390	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519938	NA	P-0036747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	103	281	0	ENST00000263967.3:c.1034A>C	p.Asn345Thr	p.N345T	ENST00000263967	NM_006218.2	345	aAt/aCt	5/21	1	2	FACETS	0.993	0.901	1	0.993	0.901	1	CLONAL	1	TRUE	1	0.68	2		281	305	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264490	16264490	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	103	431	0	ENST00000375759.3:c.10693C>T	p.Arg3565Ter	p.R3565*	ENST00000375759	NM_015001.2	3565	Cga/Tga	13/15	1	2	FACETS	0.935	0.847	1	0.935	0.847	1	CLONAL	1	TRUE	1	0.68	2		431	324	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105586	27105587	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	107	422	0	ENST00000324856.7:c.5198dup	p.Tyr1734ValfsTer2	p.Y1734Vfs*2	ENST00000324856	NM_006015.4	1733	gag/gAag	20/20	1	2	FACETS	0.787	0.711	0.865	0.787	0.711	0.865	SUBCLONAL	1	TRUE	1	0.68	2		422	400	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105967	27105967	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	106	405	0	ENST00000324856.7:c.5578G>T	p.Glu1860Ter	p.E1860*	ENST00000324856	NM_006015.4	1860	Gag/Tag	20/20	1	2	FACETS	0.956	0.868	1	0.956	0.868	1	CLONAL	1	TRUE	1	0.68	2		405	326	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466017	69466017	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	167	579	2	ENST00000227507.2:c.855C>A	p.Cys285Ter	p.C285*	ENST00000227507	NM_053056.2	285	tgC/tgA	5/5	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.68	2		581	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578191	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs530941076	NA	P-0036750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	440	497	0	ENST00000269305.4:c.658T>A	p.Tyr220Asn	p.Y220N	ENST00000269305	NM_001126112.2	220	Tat/Aat	6/11	0.903348237948689	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.903348237948689	2		497	477	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922364	178922364	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397514565	NA	P-0036752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	116	233	0	ENST00000263967.3:c.1133G>A	p.Cys378Tyr	p.C378Y	ENST00000263967	NM_006218.2	378	tGt/tAt	6/21	0.517566245464024	3	FACETS	0.841	0.767	0.916	0.841	0.767	0.916	CLONAL	2	TRUE	1	0.534732970842238	3		233	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578412	+	inframe_deletion	In_Frame_Del	DEL	CATGGTGGGGGCAGCGCCTCA	CATGGTGGGGGCAGCGCCTCA	-	novel	NA	P-0036752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	187	555	1	ENST00000269305.4:c.518_538del	p.Val173_His179del	p.V173_H179del	ENST00000269305	NM_001126112.2	173	gTGAGGCGCTGCCCCCACCATGag/gag	5/11	0.534732970842238	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.534732970842238	1		556	499	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0036753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	81	407	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.287227959814226	2	FACETS	0.966	0.86	1	0.966	0.86	1	CLONAL	2	TRUE	0	0.287227959814226	2		408	292	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578224	7578224	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1429743956	NA	P-0036753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	133	557	0	ENST00000269305.4:c.625A>T	p.Arg209Ter	p.R209*	ENST00000269305	NM_001126112.2	209	Aga/Tga	6/11	0.287227959814226	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.287227959814226	1		557	587	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105682	27105682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1164908440	NA	P-0036753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	80	310	0	ENST00000324856.7:c.5293G>A	p.Glu1765Lys	p.E1765K	ENST00000324856	NM_006015.4	1765	Gaa/Aaa	20/20	1	2	FACETS	0.819	0.727	0.916	1	0.981	1	CLONAL	2	TRUE	1	0.287227959814226	2		310	340	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650052	206650052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540205249	NA	P-0036753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	34	506	1	ENST00000367120.3:c.572G>A	p.Arg191Gln	p.R191Q	ENST00000367120	NM_014002.3	191	cGa/cAa	7/22	1	2	FACETS	0.391	0.319	0.473	0.391	0.319	0.473	SUBCLONAL	1	TRUE	1	0.287227959814226	2		507	605	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457707	67457707	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	130	434	1	ENST00000327367.4:c.517C>T	p.Gln173Ter	p.Q173*	ENST00000327367	NM_005902.3	173	Cag/Tag	3/9	0.287227959814226	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	2	TRUE	0	0.287227959814226	2		435	442	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0036754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	62	448	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.957	0.827	1	0.957	0.827	1	CLONAL	1	TRUE	1	0.231081774909629	2		448	561	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132542	11132542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	68	607	2	ENST00000358026.2:c.2758G>A	p.Glu920Lys	p.E920K	ENST00000358026	NM_001128849.1	920	Gag/Aag	19/36	0.231081774909629	1	FACETS	0.695	0.604	0.794	0.695	0.604	0.794	SUBCLONAL	1	TRUE	0	0.231081774909629	1		609	749	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514631	103514631	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	41	272	0	ENST00000355739.4:c.1132G>T	p.Val378Leu	p.V378L	ENST00000355739	NM_000123.3	378	Gta/Tta	8/15	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.231081774909629	2		272	310	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560409	95560409	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1262583273	NA	P-0036754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	55	465	0	ENST00000393063.1:c.5180A>G	p.His1727Arg	p.H1727R	ENST00000393063	NM_030621.3	1727	cAc/cGc	25/28	1	2	FACETS	0.814	0.696	0.943	0.814	0.696	0.943	CLONAL	1	TRUE	1	0.231081774909629	2		465	585	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222992	1222993	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0036754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	76	451	0	ENST00000326873.7:c.929_930del	p.Arg310GlnfsTer7	p.R310Qfs*7	ENST00000326873	NM_000455.4	310	cGG/c	8/10	0.231081774909629	1	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	0	0.231081774909629	1		451	578	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602292	10602292	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	74	621	0	ENST00000171111.5:c.1286G>A	p.Gly429Asp	p.G429D	ENST00000171111	NM_203500.1	429	gGc/gAc	3/6	0.231081774909629	1	FACETS	0.682	0.596	0.775	0.682	0.596	0.775	SUBCLONAL	1	TRUE	0	0.231081774909629	1		621	831	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412508	63412508	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202069335	NA	P-0036754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	92	308	0	ENST00000330258.3:c.659C>T	p.Thr220Ile	p.T220I	ENST00000330258	NM_152424.3	220	aCc/aTc	2/2	1	1	FACETS	0.898	0.804	0.998	1	0.985	1	CLONAL	2	TRUE	0	0.231081774909629	1		308	392	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0036755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	132	469	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	0.453205486648153	2		469	535	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972412	81972412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779506592	NA	P-0036755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	104	381	0	ENST00000359376.3:c.3205G>A	p.Gly1069Ser	p.G1069S	ENST00000359376	NM_002661.3	1069	Ggt/Agt	29/33	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.453205486648153	2		381	441	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175212	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	106	194	0	ENST00000257430.4:c.3924del	p.Glu1309LysfsTer12	p.E1309Kfs*12	ENST00000257430	NM_000038.5	1307	atA/at	16/16	0.453205486648153	2	FACETS	0.947	0.865	1	0.947	0.865	1	CLONAL	2	TRUE	0	0.453205486648153	2		194	247	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400299	139400299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150343794	NA	P-0036755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	162	638	0	ENST00000277541.6:c.4049G>A	p.Arg1350His	p.R1350H	ENST00000277541	NM_017617.3	1350	cGt/cAt	25/34	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.453205486648153	2		638	662	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662551	227662551	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	109	506	0	ENST00000305123.5:c.904C>T	p.Arg302Ter	p.R302*	ENST00000305123	NM_005544.2	302	Cga/Tga	1/2	1	2	FACETS	0.892	0.804	0.985	0.892	0.804	0.985	CLONAL	1	TRUE	1	0.453205486648153	2		506	539	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959350	26959350	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	91	292	0	ENST00000381527.3:c.517G>A	p.Asp173Asn	p.D173N	ENST00000381527	NM_001260.1	173	Gac/Aac	6/13	0.453205486648153	3	FACETS	1	0.945	1	0.547	0.488	0.61	CLONAL	1	TRUE	1	0.453205486648153	3		292	450	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554306	63554306	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	196	758	0	ENST00000307078.5:c.433G>T	p.Val145Phe	p.V145F	ENST00000307078	NM_004655.3	145	Gtc/Ttc	2/11	1	2	FACETS	0.998	0.925	1	0.998	0.925	1	CLONAL	1	TRUE	1	0.453205486648153	2		758	867	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950048	38950048	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	119	379	0	ENST00000357387.3:c.3902A>T	p.Gln1301Leu	p.Q1301L	ENST00000357387	NM_152756.3	1301	cAg/cTg	31/38	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.453205486648153	2		379	481	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438379	110438379	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	14	75	0	ENST00000375856.3:c.22G>T	p.Gly8Trp	p.G8W	ENST00000375856	NM_003749.2	8	Ggg/Tgg	1/2	1	2	FACETS	1	0.8	1	1	0.8	1	CLONAL	1	TRUE	1	0.250489273724983	2		75	100	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39542573	39542573	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs778669649	NA	P-0036759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	70	364	0	ENST00000262039.4:c.377C>A	p.Thr126Lys	p.T126K	ENST00000262039	NM_002647.2	126	aCg/aAg	3/25	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.250489273724983	2		364	440	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630914	187630915	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0036759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	67	460	0	ENST00000441802.2:c.67_68delinsAT	p.Gly23Ile	p.G23I	ENST00000441802	NM_005245.3	23	GGc/ATc	2/27	0.250489273724983	2	FACETS	1	0.903	1	0.522	0.455	0.596	CLONAL	1	TRUE	0	0.250489273724983	2		460	512	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021785	71021785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs112795301	NA	P-0036763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	188	341	0	ENST00000318789.4:c.1573C>T	p.Arg525Ter	p.R525*	ENST00000318789	NM_032682.5	525	Cga/Tga	18/21	0.902412757249833	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.902412757249833	1		341	221	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137244	64137244	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774562817	NA	P-0036763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	554	657	0	ENST00000334205.4:c.1676C>T	p.Pro559Leu	p.P559L	ENST00000334205	NM_003942.2	559	cCg/cTg	14/17	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.902412757249833	2		657	1093	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941675	48941675	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	162	264	0	ENST00000267163.4:c.987del	p.Asp330IlefsTer2	p.D330Ifs*2	ENST00000267163	NM_000321.2	329	Aaa/aa	10/27	0.902412757249833	1	FACETS	0.99	0.948	1	0.99	0.948	1	CLONAL	1	TRUE	0	0.902412757249833	1		264	199	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577143	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0036763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	370	541	2	ENST00000269305.4:c.795_796delinsTT	p.Gly266Ter	p.G266*	ENST00000269305	NM_001126112.2	265	ctGGga/ctTTga	8/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.902412757249833	2		543	772	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579709	7579709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	314	513	0	ENST00000269305.4:c.87del	p.Asn29LysfsTer15	p.N29Kfs*15	ENST00000269305	NM_001126112.2	29	aaC/aa	3/11	1	2	FACETS	0.979	0.93	1	0.979	0.93	1	CLONAL	1	TRUE	1	0.902412757249833	2		513	711	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774802	73774802	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	483	719	3	ENST00000254810.4:c.285G>T	p.Glu95Asp	p.E95D	ENST00000254810	NM_005324.3	95	gaG/gaT	4/4	1	2	FACETS	0.988	0.949	1	0.988	0.949	1	CLONAL	1	TRUE	1	0.902412757249833	2		722	1083	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589771	55589773	+	inframe_deletion	In_Frame_Del	DEL	ACG	ACG	-	novel	NA	P-0036763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	250	368	0	ENST00000288135.5:c.1255_1257del	p.Asp419del	p.D419del	ENST00000288135	NM_000222.2	418	tACGac/tac	8/21	1	2	FACETS	0.988	0.933	1	0.988	0.933	1	CLONAL	1	TRUE	1	0.902412757249833	2		368	561	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671474	30671474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	441	762	0	ENST00000376406.3:c.5486G>A	p.Arg1829Lys	p.R1829K	ENST00000376406	NM_014641.2	1829	aGa/aAa	10/15	0.902412757249833	2	FACETS	0.986	0.945	1	0.493	0.472	0.514	CLONAL	1	TRUE	0	0.902412757249833	2		762	991	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0036766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	223	678	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.361558589241265	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.371816738041715	2		678	557	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81892752	81892752	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	58	365	0	ENST00000359376.3:c.463C>G	p.Gln155Glu	p.Q155E	ENST00000359376	NM_002661.3	155	Caa/Gaa	5/33	0.361558589241265	2	FACETS	0.91	0.786	1	0.455	0.393	0.522	CLONAL	1	TRUE	0	0.371816738041715	2		365	343	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161326550	161326550	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	12	134	0	ENST00000367975.2:c.325G>C	p.Gly109Arg	p.G109R	ENST00000367975	NM_003001.3	109	Ggg/Cgg	5/6	0.371816738041715	3	FACETS	0.475	0.335	0.647	0.238	0.167	0.324	SUBCLONAL	1	TRUE	1	0.371816738041715	3		134	161	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893262	32893262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398122724	NA	P-0036766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	82	275	0	ENST00000380152.3:c.116C>T	p.Ala39Val	p.A39V	ENST00000380152		39	gCt/gTt	3/27	0.269714466509674	3	FACETS	0.785	0.699	0.877			1	SUBCLONAL	2	TRUE	NA	0.371816738041715	3		275	333	SUCCESS
ATR	545	MSKCC	GRCh37	3	142276536	142277487	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCAATCTTGGCTCACTGAAACCTCTGCCTCCTGGGTTCAAGAGATTCTTGTATCTCAGCCTCCCTAGTAGCTGGGACTACAGGCGTGAGCCACCATGCCTGGCTAATTTTTGTATTTTTAGAAGAGATGAGGTTTTGCCATGTTGGCCAGGCTGGTCTCAAGCTCCTGACCTCAAGAGATCCGCATGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGTGCCTGGCCTAATGTTTCTATTTCTTAAACTGAGAAGTTGGTATAAGAATTTTTGGTATATTGTTCTTCTTTTTAAAATATTTCTCAAATACTTCCTAATTTTATTAAATGAAGATAATGATATGTAAGGACACATTGCAAATGTTTTACAAAAAGAAAGGAAATGGGATATGTGGGGCAGGCTTTTATGTGTTACTTTTTATGTATCTAACCCCCTTCTGAACTATTAAAAATGTACCTGCTCTTTTAATTATTGAAAAAAATATAAATAAGTCTTAGAAGTCCTATATAGAGATGAGTTAAAACAAACCACACAAGGCCAGGCATGGTGGCTCACGCCTGTAATCCTAGCACTTTAGAAGGCTGGGGCAGGTGGATCACTTGAGGTCAGGAGTTCGAGACCAGCCTGGCTAACATGGTGAAACCCCGCCTCTACTAAAAATATAAGAATTAGCTGGGTATGGTGGTGCGCACCTGTAATCCTAGCTACTCAGGAGGCTGAGGCAGGAAAATTGCTTGAACCTGAAGACGGAGGTTGCAGCAAGCCGAGATTGCGCCACTGCACTCCAGCATGGGCGACAGAGTAAGACTCCGTCTCAAAAATAAATAAATAAATAAATAAATAAATAAATAAATAGATAGATAGATAGATAGATAGATAAATAAAACAAACCACACACACATTCTTGTGAGCACTTACAATAGCTATCTGAAATCCTACA	GCAATCTTGGCTCACTGAAACCTCTGCCTCCTGGGTTCAAGAGATTCTTGTATCTCAGCCTCCCTAGTAGCTGGGACTACAGGCGTGAGCCACCATGCCTGGCTAATTTTTGTATTTTTAGAAGAGATGAGGTTTTGCCATGTTGGCCAGGCTGGTCTCAAGCTCCTGACCTCAAGAGATCCGCATGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGTGCCTGGCCTAATGTTTCTATTTCTTAAACTGAGAAGTTGGTATAAGAATTTTTGGTATATTGTTCTTCTTTTTAAAATATTTCTCAAATACTTCCTAATTTTATTAAATGAAGATAATGATATGTAAGGACACATTGCAAATGTTTTACAAAAAGAAAGGAAATGGGATATGTGGGGCAGGCTTTTATGTGTTACTTTTTATGTATCTAACCCCCTTCTGAACTATTAAAAATGTACCTGCTCTTTTAATTATTGAAAAAAATATAAATAAGTCTTAGAAGTCCTATATAGAGATGAGTTAAAACAAACCACACAAGGCCAGGCATGGTGGCTCACGCCTGTAATCCTAGCACTTTAGAAGGCTGGGGCAGGTGGATCACTTGAGGTCAGGAGTTCGAGACCAGCCTGGCTAACATGGTGAAACCCCGCCTCTACTAAAAATATAAGAATTAGCTGGGTATGGTGGTGCGCACCTGTAATCCTAGCTACTCAGGAGGCTGAGGCAGGAAAATTGCTTGAACCTGAAGACGGAGGTTGCAGCAAGCCGAGATTGCGCCACTGCACTCCAGCATGGGCGACAGAGTAAGACTCCGTCTCAAAAATAAATAAATAAATAAATAAATAAATAAATAAATAGATAGATAGATAGATAGATAGATAAATAAAACAAACCACACACACATTCTTGTGAGCACTTACAATAGCTATCTGAAATCCTACA	-	novel	NA	P-0036766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	39	0	0	ENST00000350721.4:c.1864_1885+930del		p.X622_splice	ENST00000350721	NM_001184.3	622		8/47	0.236257963154022	5	FACETS	0.834	0.692	0.991	0.278	0.23	0.331	CLONAL	1	TRUE	2	0.371816738041715	5		0	392	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970981	55970981	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	96	591	0	ENST00000263923.4:c.1816T>G	p.Leu606Val	p.L606V	ENST00000263923	NM_002253.2	606	Ttg/Gtg	13/30	0.199312679471422	5	FACETS	1	0.958	1	0.385	0.343	0.429	INDETERMINATE	1	TRUE	2	0.371816738041715	5		591	697	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528014	157528014	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	86	458	0	ENST00000346085.5:c.5739C>A	p.His1913Gln	p.H1913Q	ENST00000346085	NM_020732.3	1913	caC/caA	20/20	0.371816738041715	2	FACETS	1	0.95	1	0.56	0.498	0.626	CLONAL	1	TRUE	0	0.371816738041715	2		458	413	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567546196	NA	P-0036769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	248	683	0	ENST00000269305.4:c.949del	p.Gln317SerfsTer28	p.Q317Sfs*28	ENST00000269305	NM_001126112.2	317	Cag/ag	9/11	0.652999141241815	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.652999141241815	1		683	464	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0036769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	38	301	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.475494153972514	1	FACETS	0.417	0.348	0.491	0.417	0.348	0.491	SUBCLONAL	1	TRUE	0	0.652999141241815	1		301	188	SUCCESS
APC	324	MSKCC	GRCh37	5	112174872	112174872	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	89	241	0	ENST00000257430.4:c.3581C>A	p.Ser1194Ter	p.S1194*	ENST00000257430	NM_000038.5	1194	tCa/tAa	16/16	0.475494153972514	1	FACETS	0.72	0.648	0.794	0.72	0.648	0.794	SUBCLONAL	1	TRUE	0	0.652999141241815	1		241	255	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782006	NA	P-0036778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	33	838	1	ENST00000269305.4:c.859G>A	p.Glu287Lys	p.E287K	ENST00000269305	NM_001126112.2	287	Gag/Aag	8/11	1	2	FACETS	0.469	0.38	0.571	0.469	0.38	0.571	SUBCLONAL	1	TRUE	1	0.13	2		839	1082	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	17	447	0	ENST00000263967.3:c.3129G>C	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atC	21/21	1	2	FACETS	0.527	0.392	0.689	0.527	0.392	0.689	SUBCLONAL	1	TRUE	1	0.13	2		447	496	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0036782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	247	303	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.530264873933928	3	FACETS	0.94	0.885	0.996	0.94	0.885	0.996	CLONAL	2	TRUE	1	0.530264873933928	3		303	627	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	166	214	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.530264873933928	2		214	462	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298006	11298006	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	227	728	0	ENST00000361445.4:c.2102A>G	p.Asn701Ser	p.N701S	ENST00000361445	NM_004958.3	701	aAt/aGt	13/58	1	2	FACETS	0.916	0.854	0.979	0.916	0.854	0.979	CLONAL	1	TRUE	1	0.530264873933928	2		728	935	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374038	118374038	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	176	542	0	ENST00000534358.1:c.7431G>A	p.Met2477Ile	p.M2477I	ENST00000534358	NM_005933.3	2477	atG/atA	27/36	1	2	FACETS	0.957	0.884	1	0.957	0.884	1	CLONAL	1	TRUE	1	0.530264873933928	2		542	694	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196276	106196276	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	100	296	0	ENST00000380013.4:c.4609C>T	p.Gln1537Ter	p.Q1537*	ENST00000380013	NM_001127208.2	1537	Cag/Tag	11/11	1	2	FACETS	0.967	0.871	1	0.967	0.871	1	CLONAL	1	TRUE	1	0.530264873933928	2		296	390	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28897068	28897068	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs35549791	NA	P-0036789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	58	416	0	ENST00000282397.4:c.2812A>G	p.Met938Val	p.M938V	ENST00000282397	NM_002019.4	938	Atg/Gtg	21/30	0.660738473137131	2	FACETS	0.642	0.557	0.733	0.321	0.278	0.367	SUBCLONAL	1	TRUE	0	0.678962837046914	2		416	266	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775676	9775676	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	269	714	0	ENST00000377346.4:c.219C>G	p.Ile73Met	p.I73M	ENST00000377346	NM_005026.3	73	atC/atG	4/24	0.678962837046914	3	FACETS	0.873	0.826	0.92			1	CLONAL	2	TRUE	NA	0.678962837046914	3		714	608	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909631	76909632	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	72	591	0	ENST00000373344.5:c.4273dup	p.Arg1425LysfsTer5	p.R1425Kfs*5	ENST00000373344	NM_000489.3	1425	agg/aAgg	14/35	0.660311676196269	2	FACETS	0.545	0.479	0.616	0.273	0.239	0.308	SUBCLONAL	1	TRUE	0	0.678962837046914	2		591	389	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231295	46231295	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	361	501	0	ENST00000334344.6:c.1135G>T	p.Gly379Ter	p.G379*	ENST00000334344	NM_152641.2	379	Gga/Tga	10/21	0.659352786242713	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	0	0.678962837046914	3		501	468	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609889	81609889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769777295	NA	P-0036789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	248	401	1	ENST00000298171.2:c.1487C>T	p.Thr496Met	p.T496M	ENST00000298171	NM_000369.2	496	aCg/aTg	10/10	0.678962837046914	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.678962837046914	3		402	300	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121829	2121829	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs991714565	NA	P-0036789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	111	670	0	ENST00000219476.3:c.1991C>G	p.Ser664Cys	p.S664C	ENST00000219476	NM_000548.3	664	tCt/tGt	19/42	0.273460155060931	4	FACETS	1	0.904	1			1	INDETERMINATE	1	TRUE	NA	0.678962837046914	4		670	548	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577604	7577610	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	CCAACCT	CCAACCT	-	novel	NA	P-0036789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	377	500	0	ENST00000269305.4:c.673-2_677del		p.X225_splice	ENST00000269305	NM_001126112.2	225		7/11	0.646689188688481	4	FACETS	0.977	0.949	1	0.977	0.949	1	CLONAL	4	TRUE	0	0.678962837046914	4		500	477	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36022395	36022395	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	83	608	1	ENST00000358208.4:c.448G>A	p.Glu150Lys	p.E150K	ENST00000358208		150	Gag/Aag	4/12	0.523346842252607	4	FACETS	0.636	0.562	0.716	0.212	0.187	0.239	SUBCLONAL	1	TRUE	1	0.678962837046914	4		609	645	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89176380	89176380	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	58	375	0	ENST00000336596.2:c.110C>A	p.Thr37Lys	p.T37K	ENST00000336596	NM_005233.5	37	aCa/aAa	2/17	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.678962837046914	NA		375	265	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259389	89259389	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	219	524	0	ENST00000336596.2:c.533G>T	p.Gly178Val	p.G178V	ENST00000336596	NM_005233.5	178	gGa/gTa	3/17	0.446417848171336	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.678962837046914	1		524	335	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048734	180048734	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	100	772	0	ENST00000261937.6:c.1828T>C	p.Cys610Arg	p.C610R	ENST00000261937	NM_182925.4	610	Tgc/Cgc	13/30	0.340203348541693	3	FACETS	0.774	0.694	0.858	0.258	0.231	0.286	INDETERMINATE	1	TRUE	0	0.678962837046914	3		772	510	SUCCESS
ATM	472	MSKCC	GRCh37	11	108128233	108128234	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	20	338	0	ENST00000278616.4:c.2277dup	p.Ile760TyrfsTer5	p.I760Yfs*5	ENST00000278616	NM_000051.3	759	agt/agTt	15/63	0.284115955819152	1	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	0	0.284115955819152	1		338	104	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	56	214	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.938	1			1	INDETERMINATE	2	TRUE	NA	0.327482104303084	2		214	153	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316062	11316062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	41	434	0	ENST00000361445.4:c.692C>T	p.Pro231Leu	p.P231L	ENST00000361445	NM_004958.3	231	cCt/cTt	5/58	0.327482104303084	3	FACETS	1	0.952	1	0.697	0.587	0.817	CLONAL	1	TRUE	1	0.327482104303084	3		434	209	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258976	16258976	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	73	492	0	ENST00000375759.3:c.6241C>T	p.Arg2081Ter	p.R2081*	ENST00000375759	NM_015001.2	2081	Cga/Tga	11/15	0.327482104303084	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.327482104303084	3		492	214	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259787	16259787	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	32	470	0	ENST00000375759.3:c.7052C>T	p.Pro2351Leu	p.P2351L	ENST00000375759	NM_015001.2	2351	cCt/cTt	11/15	0.327482104303084	3	FACETS	0.952	0.777	1	0.476	0.388	0.573	CLONAL	1	TRUE	1	0.327482104303084	3		470	239	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797482	45797482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778538	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	86	774	1	ENST00000450313.1:c.1037C>T	p.Ser346Leu	p.S346L	ENST00000450313	NM_012222.2	346	tCg/tTg	12/16	0.19635922879235	3	FACETS	1	0.963	1	1	0.963	1	INDETERMINATE	2	TRUE	1	0.327482104303084	3		775	262	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459013	120459013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	30	777	0	ENST00000256646.2:c.6332C>T	p.Thr2111Ile	p.T2111I	ENST00000256646	NM_024408.3	2111	aCc/aTc	34/34	0.327482104303084	3	FACETS	0.867	0.702	1	0.433	0.351	0.526	CLONAL	1	TRUE	1	0.327482104303084	3		777	246	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309776	104309776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202247756	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	28	638	2	ENST00000369902.3:c.367C>T	p.Arg123Cys	p.R123C	ENST00000369902	NM_016169.3	123	Cgt/Tgt	3/12	0.19635922879235	3	FACETS	0.896	0.721	1	0.448	0.36	0.547	INDETERMINATE	1	TRUE	1	0.327482104303084	3		640	222	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724348	112724349	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	22	518	1	ENST00000369452.4:c.232_233delinsTT	p.Ala78Leu	p.A78L	ENST00000369452	NM_007373.3	78	GCa/TTa	2/9	0.19635922879235	3	FACETS	0.85	0.663	1	0.425	0.331	0.532	INDETERMINATE	1	TRUE	1	0.327482104303084	3		519	184	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244913	123244913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1224606327	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	22	827	1	ENST00000358487.5:c.2191G>A	p.Glu731Lys	p.E731K	ENST00000358487	NM_000141.4	731	Gaa/Aaa	16/18	0.19635922879235	3	FACETS	0.649	0.504	0.816	0.324	0.252	0.408	INDETERMINATE	1	TRUE	1	0.327482104303084	3		828	241	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123260410	123260410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	25	601	0	ENST00000358487.5:c.1491G>A	p.Met497Ile	p.M497I	ENST00000358487	NM_000141.4	497	atG/atA	11/18	0.19635922879235	3	FACETS	0.756	0.598	0.936	0.378	0.299	0.468	INDETERMINATE	1	TRUE	1	0.327482104303084	3		601	235	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154345	2154345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	38	809	0	ENST00000434045.2:c.583G>A	p.Gly195Ser	p.G195S	ENST00000434045	NM_001127598.1	195	Ggt/Agt	5/5	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.327482104303084	2		809	222	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588223	69588223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	29	590	0	ENST00000168712.1:c.475G>A	p.Glu159Lys	p.E159K	ENST00000168712	NM_002007.2	159	Gag/Aag	3/3	0.212508937359283	1	FACETS	0.737	0.596	0.895	0.737	0.596	0.895	SUBCLONAL	1	TRUE	0	0.327482104303084	1		590	201	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933481	100933481	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	20	263	0	ENST00000325455.5:c.1909C>G	p.Arg637Gly	p.R637G	ENST00000325455	NM_001202474.3	637	Cga/Gga	4/8	1	2	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	TRUE	1	0.327482104303084	2		263	109	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121493	108121493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	35	401	0	ENST00000278616.4:c.1301C>T	p.Pro434Leu	p.P434L	ENST00000278616	NM_000051.3	434	cCa/cTa	10/63	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.327482104303084	2		401	171	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544065	18544065	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	21	298	0	ENST00000266497.5:c.1882C>T	p.Pro628Ser	p.P628S	ENST00000266497		628	Cca/Tca	13/31	0.279433163048527	4	FACETS	0.906	0.712	1			1	CLONAL	2	TRUE	NA	0.327482104303084	4		298	94	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641411	18641411	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	16	293	0	ENST00000266497.5:c.2410T>C	p.Tyr804His	p.Y804H	ENST00000266497		804	Tat/Cat	17/31	0.279433163048527	4	FACETS	0.947	0.706	1			1	CLONAL	1	TRUE	NA	0.327482104303084	4		293	137	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628639	21628639	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377215617	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	14	665	0	ENST00000421138.2:c.1069C>T	p.His357Tyr	p.H357Y	ENST00000421138		357	Cat/Tat	10/16	0.279433163048527	4	FACETS	0.624	0.452	0.83			1	SUBCLONAL	1	TRUE	NA	0.327482104303084	4		665	182	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442998	49442998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375144626	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	67	479	0	ENST00000301067.7:c.3910C>T	p.Arg1304Cys	p.R1304C	ENST00000301067	NM_003482.3	1304	Cgc/Tgc	12/54	0.306588018675825	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.327482104303084	2		479	184	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858477	57858477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760192848	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	75	632	0	ENST00000228682.2:c.215G>A	p.Arg72Gln	p.R72Q	ENST00000228682	NM_005269.2	72	cGg/cAg	4/12	0.306588018675825	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.327482104303084	2		632	193	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254193	133254193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146592584	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	26	585	0	ENST00000320574.5:c.691C>T	p.Arg231Cys	p.R231C	ENST00000320574	NM_006231.2	231	Cgc/Tgc	7/49	0.293500407785535	3	FACETS	0.757	0.602	0.934	0.379	0.301	0.467	CLONAL	1	TRUE	1	0.327482104303084	3		585	244	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578193	28578193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs968020606	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	28	517	0	ENST00000241453.7:c.2978C>T	p.Ser993Leu	p.S993L	ENST00000241453	NM_004119.2	993	tCg/tTg	24/24	0.306588018675825	2	FACETS	0.838	0.675	1	0.419	0.337	0.511	CLONAL	1	TRUE	0	0.327482104303084	2		517	204	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893595	28893595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	58	458	0	ENST00000282397.4:c.3251C>T	p.Ser1084Phe	p.S1084F	ENST00000282397	NM_002019.4	1084	tCt/tTt	24/30	0.306588018675825	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	2	TRUE	0	0.327482104303084	2		458	167	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28903809	28903809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	82	642	0	ENST00000282397.4:c.2650C>T	p.His884Tyr	p.H884Y	ENST00000282397	NM_002019.4	884	Cac/Tac	19/30	0.306588018675825	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.327482104303084	2		642	218	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133781	41133781	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	37	396	0	ENST00000379561.5:c.1847C>T	p.Ser616Phe	p.S616F	ENST00000379561	NM_002015.3	616	tCc/tTc	2/3	0.306588018675825	2	FACETS	1	0.941	1	0.657	0.549	0.775	CLONAL	1	TRUE	0	0.327482104303084	2		396	172	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987076	36987076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	33	765	0	ENST00000354822.5:c.613G>A	p.Glu205Lys	p.E205K	ENST00000354822	NM_001079668.2	205	Gag/Aag	3/3	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.327482104303084	2		765	193	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610228	81610228	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139352934	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	32	448	0	ENST00000298171.2:c.1826G>A	p.Arg609Gln	p.R609Q	ENST00000298171	NM_000369.2	609	cGa/cAa	10/10	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.327482104303084	2		448	168	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569888	95569888	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	30	396	0	ENST00000393063.1:c.3845C>T	p.Ser1282Phe	p.S1282F	ENST00000393063	NM_030621.3	1282	tCt/tTt	22/28	1	2	FACETS	0.99	0.805	1	0.99	0.805	1	CLONAL	1	TRUE	1	0.327482104303084	2		396	185	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43783949	43783949	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs753287025	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	30	445	0	ENST00000382044.4:c.289C>T	p.Pro97Ser	p.P97S	ENST00000382044	NM_001141980.1	97	Cct/Tct	4/28	0.327482104303084	1	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	0	0.327482104303084	1		445	143	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774207	66774207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	33	879	0	ENST00000307102.5:c.683C>T	p.Ser228Phe	p.S228F	ENST00000307102	NM_002755.3	228	tCc/tTc	6/11	0.19635922879235	3	FACETS	1	0.887	1	0.556	0.456	0.666	INDETERMINATE	1	TRUE	1	0.327482104303084	3		879	211	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423503	88423503	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	31	605	1	ENST00000360948.2:c.2332G>A	p.Glu778Lys	p.E778K	ENST00000360948	NM_001012338.2	778	Gag/Aag	18/19	0.19635922879235	3	FACETS	1	0.915	1	0.612	0.5	0.736	INDETERMINATE	1	TRUE	1	0.327482104303084	3		606	180	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293001	91293001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	24	643	0	ENST00000355112.3:c.503C>T	p.Ser168Leu	p.S168L	ENST00000355112	NM_000057.2	168	tCa/tTa	3/22	0.19635922879235	3	FACETS	0.797	0.628	0.99	0.399	0.314	0.495	INDETERMINATE	1	TRUE	1	0.327482104303084	3		643	214	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303447	91303447	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	20	466	0	ENST00000355112.3:c.1158T>G	p.Ile386Met	p.I386M	ENST00000355112	NM_000057.2	386	atT/atG	6/22	0.19635922879235	3	FACETS	0.836	0.644	1	0.418	0.322	0.529	INDETERMINATE	1	TRUE	1	0.327482104303084	3		466	170	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358397	91358397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1277229461	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	32	646	0	ENST00000355112.3:c.4142C>T	p.Ser1381Leu	p.S1381L	ENST00000355112	NM_000057.2	1381	tCa/tTa	22/22	0.19635922879235	3	FACETS	1	0.869	1	0.539	0.441	0.648	INDETERMINATE	1	TRUE	1	0.327482104303084	3		646	211	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121909	2121909	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760489473	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	32	885	1	ENST00000219476.3:c.2071C>T	p.Arg691Cys	p.R691C	ENST00000219476	NM_000548.3	691	Cgc/Tgc	19/42	1	2	FACETS	0.884	0.723	1	0.884	0.723	1	CLONAL	1	TRUE	1	0.327482104303084	2		886	221	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900491	3900491	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1298871021	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	31	885	0	ENST00000262367.5:c.605C>T	p.Ser202Leu	p.S202L	ENST00000262367	NM_004380.2	202	tCa/tTa	2/31	1	2	FACETS	0.745	0.606	0.902	0.745	0.606	0.902	CLONAL	1	TRUE	1	0.327482104303084	2		885	254	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858019	9858019	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	32	574	0	ENST00000330684.3:c.3382T>A	p.Phe1128Ile	p.F1128I	ENST00000330684	NM_001134407.1	1128	Ttc/Atc	13/13	1	2	FACETS	0.972	0.796	1	0.972	0.796	1	CLONAL	1	TRUE	1	0.327482104303084	2		574	201	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858028	9858028	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1200593226	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	31	579	0	ENST00000330684.3:c.3373G>A	p.Glu1125Lys	p.E1125K	ENST00000330684	NM_001134407.1	1125	Gag/Aag	13/13	1	2	FACETS	0.976	0.796	1	0.976	0.796	1	CLONAL	1	TRUE	1	0.327482104303084	2		579	194	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128033	30128033	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	38	720	0	ENST00000263025.4:c.1096C>T	p.Gln366Ter	p.Q366*	ENST00000263025	NM_002746.2	366	Cag/Tag	8/9	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.327482104303084	2		720	210	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813723	50813723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	32	679	0	ENST00000398568.2:c.1277C>T	p.Thr426Ile	p.T426I	ENST00000398568	NM_001042412.1	426	aCc/aTc	8/18	1	2	FACETS	0.963	0.788	1	0.963	0.788	1	CLONAL	1	TRUE	1	0.327482104303084	2		679	203	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832591	72832592	+	missense_variant	Missense_Mutation	DNP	CT	CT	TA	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	16	347	0	ENST00000268489.5:c.3989_3990delinsTA	p.Lys1330Ile	p.K1330I	ENST00000268489	NM_006885.3	1330	aAG/aTA	9/10	1	2	FACETS	0.808	0.603	1	0.808	0.603	1	CLONAL	1	TRUE	1	0.327482104303084	2		347	121	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923722	72923722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1169589589	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	47	692	0	ENST00000268489.5:c.3356G>A	p.Arg1119Gln	p.R1119Q	ENST00000268489	NM_006885.3	1119	cGa/cAa	4/10	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.327482104303084	2		692	228	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89815176	89815176	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	32	495	0	ENST00000389301.3:c.3240-1G>A		p.X1080_splice	ENST00000389301	NM_000135.2	1080			1	2	FACETS	0.931	0.761	1	0.931	0.761	1	CLONAL	1	TRUE	1	0.327482104303084	2		495	210	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89862377	89862377	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757389865	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	31	698	1	ENST00000389301.3:c.943C>T	p.Pro315Ser	p.P315S	ENST00000389301	NM_000135.2	315	Cct/Tct	11/43	1	2	FACETS	1	0.842	1	1	0.842	1	CLONAL	1	TRUE	1	0.327482104303084	2		699	183	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	65	619	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.327482104303084	3	FACETS	0.947	0.831	1	0.947	0.831	1	CLONAL	2	TRUE	1	0.327482104303084	3		619	244	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	51	697	3	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.327482104303084	3	FACETS	1	0.954	1	0.652	0.558	0.753	CLONAL	1	TRUE	1	0.327482104303084	3		700	278	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528489	29528489	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764079291	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	34	503	0	ENST00000356175.3:c.1246C>T	p.Arg416Ter	p.R416*	ENST00000356175	NM_000267.3	416	Cga/Tga	11/57	0.306588018675825	2	FACETS	0.989	0.829	1	0.989	0.829	1	CLONAL	2	TRUE	0	0.327482104303084	2		503	105	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821940	59821940	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	31	421	0	ENST00000259008.2:c.2110T>G	p.Leu704Val	p.L704V	ENST00000259008	NM_032043.2	704	Tta/Gta	15/20	0.303976613316032	5	FACETS	1	0.922	1	0.818	0.676	0.972	CLONAL	2	TRUE	2	0.327482104303084	5		421	115	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59937198	59937198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	65	484	0	ENST00000259008.2:c.164C>T	p.Ala55Val	p.A55V	ENST00000259008	NM_032043.2	55	gCc/gTc	3/20	0.303976613316032	5	FACETS	0.963	0.849	1	0.963	0.849	1	CLONAL	3	TRUE	2	0.327482104303084	5		484	205	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732329	74732329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770775763	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	43	308	0	ENST00000359995.5:c.580C>T	p.Pro194Ser	p.P194S	ENST00000359995	NM_001195427.1	194	Cca/Tca	2/3	0.327482104303084	6	FACETS	0.79	0.665	0.927	0.527	0.443	0.618	CLONAL	2	TRUE	3	0.327482104303084	6		308	275	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400676	56400676	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	42	348	0	ENST00000348428.3:c.1270T>C	p.Phe424Leu	p.F424L	ENST00000348428	NM_006785.3	424	Ttc/Ctc	11/17	0.277251119829994	4	FACETS	0.93	0.787	1	0.93	0.787	1	CLONAL	2	TRUE	2	0.327482104303084	4		348	183	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110201	3110201	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	63	746	0	ENST00000078429.4:c.191G>A	p.Gly64Asp	p.G64D	ENST00000078429	NM_002067.2	64	gGc/gAc	2/7	0.327482104303084	3	FACETS	0.881	0.771	0.998	0.881	0.771	0.998	CLONAL	2	TRUE	1	0.327482104303084	3		746	254	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117551	4117551	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121434498	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	37	422	0	ENST00000262948.5:c.169T>G	p.Phe57Val	p.F57V	ENST00000262948	NM_030662.3	57	Ttt/Gtt	2/11	0.327482104303084	3	FACETS	0.894	0.75	1	0.894	0.75	1	CLONAL	2	TRUE	1	0.327482104303084	3		422	147	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247910	10247910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	55	689	0	ENST00000340748.4:c.4292C>T	p.Ala1431Val	p.A1431V	ENST00000340748		1431	gCc/gTc	36/40	0.327482104303084	3	FACETS	1	0.964	1	0.701	0.604	0.804	CLONAL	1	TRUE	1	0.327482104303084	3		689	279	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054707	13054707	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	45	324	0	ENST00000316448.5:c.1234C>T	p.Gln412Ter	p.Q412*	ENST00000316448	NM_004343.3	412	Cag/Tag	9/9	0.225251552746141	2	FACETS	0.928	0.796	1	0.928	0.796	1	CLONAL	2	TRUE	0	0.327482104303084	2		324	148	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271633	15271633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	23	992	1	ENST00000263388.2:c.6806C>T	p.Ser2269Phe	p.S2269F	ENST00000263388	NM_000435.2	2269	tCc/tTc	33/33	0.225251552746141	2	FACETS	0.56	0.437	0.7	0.28	0.218	0.35	SUBCLONAL	1	TRUE	0	0.327482104303084	2		993	251	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387305	17387305	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	65	690	0	ENST00000359435.4:c.571C>T	p.Gln191Ter	p.Q191*	ENST00000359435	NM_001033549.1	191	Cag/Tag	7/9	0.225251552746141	2	FACETS	0.945	0.833	1	0.945	0.833	1	CLONAL	2	TRUE	0	0.327482104303084	2		690	210	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18975030	18975030	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	37	376	0	ENST00000262803.5:c.2827C>T	p.Pro943Ser	p.P943S	ENST00000262803	NM_002911.3	943	Cca/Tca	20/24	0.327482104303084	3	FACETS	1	0.953	1	0.743	0.62	0.876	CLONAL	1	TRUE	1	0.327482104303084	3		376	177	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227722	36227724	+	missense_variant	Missense_Mutation	TNP	TTG	TTG	CCC	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	28	623	0	ENST00000222270.7:c.7291_7293delinsCCC	p.Leu2431Pro	p.L2431P	ENST00000222270	NM_014727.1	2431	TTG/CCC	31/37	0.327482104303084	3	FACETS	0.793	0.636	0.97	0.396	0.318	0.485	CLONAL	1	TRUE	1	0.327482104303084	3		623	251	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765640	41765640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	80	715	0	ENST00000301178.4:c.2516G>A	p.Gly839Glu	p.G839E	ENST00000301178	NM_021913.4	839	gGa/gAa	20/20	0.327482104303084	3	FACETS	0.991	0.882	1	0.991	0.882	1	CLONAL	2	TRUE	1	0.327482104303084	3		715	287	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793475	42793475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	65	789	0	ENST00000575354.2:c.1277C>T	p.Ser426Phe	p.S426F	ENST00000575354	NM_015125.3	426	tCt/tTt	8/20	0.327482104303084	3	FACETS	0.859	0.752	0.971	0.859	0.752	0.971	CLONAL	2	TRUE	1	0.327482104303084	3		789	269	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796505	42796505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	65	934	0	ENST00000575354.2:c.3062C>T	p.Pro1021Leu	p.P1021L	ENST00000575354	NM_015125.3	1021	cCt/cTt	13/20	0.327482104303084	3	FACETS	1	0.972	1	0.74	0.647	0.84	CLONAL	1	TRUE	1	0.327482104303084	3		934	312	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917081	50917082	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	62	839	0	ENST00000440232.2:c.2333_2334delinsTT	p.Ala778Val	p.A778V	ENST00000440232	NM_002691.3	778	gCC/gTT	19/27	0.327482104303084	3	FACETS	0.77	0.671	0.876	0.77	0.671	0.876	SUBCLONAL	2	TRUE	1	0.327482104303084	3		839	286	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714679	52714679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	82	756	1	ENST00000322088.6:c.437C>T	p.Ser146Leu	p.S146L	ENST00000322088	NM_014225.5	146	tCg/tTg	4/15	0.327482104303084	3	FACETS	0.94	0.837	1	0.94	0.837	1	CLONAL	2	TRUE	1	0.327482104303084	3		757	310	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991692	25991692	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	52	488	0	ENST00000435504.4:c.550C>T	p.Pro184Ser	p.P184S	ENST00000435504		184	Cca/Tca	7/13	0.327482104303084	2	FACETS	0.877	0.759	1	0.877	0.759	1	CLONAL	2	TRUE	0	0.327482104303084	2		488	181	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449834	29449835	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	42	979	2	ENST00000389048.3:c.3020_3021delinsAT	p.Phe1007Tyr	p.F1007Y	ENST00000389048	NM_004304.4	1007	tTC/tAT	18/29	0.327482104303084	2	FACETS	0.913	0.767	1	0.456	0.383	0.537	CLONAL	1	TRUE	0	0.327482104303084	2		981	281	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606929	47606929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	37	458	0	ENST00000263735.4:c.679C>T	p.His227Tyr	p.H227Y	ENST00000263735	NM_002354.2	227	Cat/Tat	7/9	0.327482104303084	2	FACETS	0.949	0.801	1	0.949	0.801	1	CLONAL	2	TRUE	0	0.327482104303084	2		458	119	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248423	212248423	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771634130	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	27	350	0	ENST00000342788.4:c.3844C>T	p.Pro1282Ser	p.P1282S	ENST00000342788	NM_005235.2	1282	Cct/Tct	28/28	0.327482104303084	3	FACETS	1	0.826	1	0.516	0.414	0.631	CLONAL	1	TRUE	1	0.327482104303084	3		350	186	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710637	40710637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1161104430	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	53	532	0	ENST00000373198.4:c.4214G>A	p.Gly1405Glu	p.G1405E	ENST00000373198	NM_133170.3	1405	gGa/gAa	31/32	0.206497749700308	3	FACETS	1	0.929	1	0.739	0.642	0.84	CLONAL	2	TRUE	0	0.327482104303084	3		532	170	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730938	40730938	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	15	450	0	ENST00000373198.4:c.3598-1G>A		p.X1200_splice	ENST00000373198	NM_133170.3	1200			0.206497749700308	3	FACETS	0.501	0.366	0.661	0.167	0.122	0.221	SUBCLONAL	1	TRUE	0	0.327482104303084	3		450	213	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770576	40770576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	65	544	2	ENST00000373198.4:c.2806C>T	p.Arg936Ter	p.R936*	ENST00000373198	NM_133170.3	936	Cga/Tga	19/32	0.206497749700308	3	FACETS	1	0.918	1	0.703	0.619	0.792	CLONAL	2	TRUE	0	0.327482104303084	3		546	219	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076862	41076862	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs750249800	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	17	450	0	ENST00000373198.4:c.1558G>A	p.Glu520Lys	p.E520K	ENST00000373198	NM_133170.3	520	Gag/Aag	9/32	0.206497749700308	3	FACETS	0.664	0.498	0.859	0.221	0.166	0.287	SUBCLONAL	1	TRUE	0	0.327482104303084	3		450	182	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076967	41076967	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	41	445	0	ENST00000373198.4:c.1453C>T	p.Pro485Ser	p.P485S	ENST00000373198	NM_133170.3	485	Cca/Tca	9/32	0.206497749700308	3	FACETS	0.934	0.791	1	0.623	0.527	0.725	CLONAL	2	TRUE	0	0.327482104303084	3		445	156	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306755	41306755	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	69	459	0	ENST00000373198.4:c.904G>A	p.Ala302Thr	p.A302T	ENST00000373198	NM_133170.3	302	Gcc/Acc	7/32	0.206497749700308	3	FACETS	0.843	0.748	0.94	0.843	0.748	0.94	CLONAL	3	TRUE	0	0.327482104303084	3		459	194	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39772529	39772529	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	34	537	0	ENST00000288319.7:c.712C>T	p.Pro238Ser	p.P238S	ENST00000288319	NM_182918.3	238	Cct/Tct	6/10	0.303976613316032	5	FACETS	1	0.935	1	0.443	0.364	0.53	CLONAL	1	TRUE	2	0.327482104303084	5		537	233	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866331	42866331	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs574582815	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	71	677	0	ENST00000398585.3:c.301G>C	p.Val101Leu	p.V101L	ENST00000398585	NM_001135099.1	101	Gtc/Ctc	3/14	0.303976613316032	5	FACETS	1	0.93	1	0.721	0.635	0.812	CLONAL	2	TRUE	2	0.327482104303084	5		677	299	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866385	42866385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	36	688	1	ENST00000398585.3:c.247C>T	p.Pro83Ser	p.P83S	ENST00000398585	NM_001135099.1	83	Ccg/Tcg	3/14	0.303976613316032	5	FACETS	1	0.874	1	0.358	0.295	0.428	CLONAL	1	TRUE	2	0.327482104303084	5		689	305	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421265	12421265	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777067241	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	30	654	0	ENST00000287820.6:c.145G>A	p.Asp49Asn	p.D49N	ENST00000287820	NM_015869.4	49	Gat/Aat	2/7	0.327482104303084	3	FACETS	0.853	0.69	1	0.426	0.345	0.518	CLONAL	1	TRUE	1	0.327482104303084	3		654	250	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162039	47162039	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	20	514	0	ENST00000409792.3:c.4087G>C	p.Asp1363His	p.D1363H	ENST00000409792	NM_014159.6	1363	Gac/Cac	3/21	0.327482104303084	3	FACETS	0.768	0.591	0.974	0.384	0.295	0.487	CLONAL	1	TRUE	1	0.327482104303084	3		514	185	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162323	47162323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773098323	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	17	498	0	ENST00000409792.3:c.3803C>T	p.Ser1268Phe	p.S1268F	ENST00000409792	NM_014159.6	1268	tCt/tTt	3/21	0.327482104303084	3	FACETS	0.623	0.466	0.807	0.311	0.233	0.404	SUBCLONAL	1	TRUE	1	0.327482104303084	3		498	194	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163830	47163830	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs755560393	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	27	540	0	ENST00000409792.3:c.2296A>G	p.Met766Val	p.M766V	ENST00000409792	NM_014159.6	766	Atg/Gtg	3/21	0.327482104303084	3	FACETS	0.864	0.692	1	0.432	0.346	0.53	CLONAL	1	TRUE	1	0.327482104303084	3		540	222	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164165	47164165	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	47	406	0	ENST00000409792.3:c.1961C>A	p.Ser654Tyr	p.S654Y	ENST00000409792	NM_014159.6	654	tCt/tAt	3/21	0.327482104303084	3	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	1	0.327482104303084	3		406	149	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164362	47164362	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	33	419	0	ENST00000409792.3:c.1764del	p.Phe588LeufsTer13	p.F588Lfs*13	ENST00000409792	NM_014159.6	588	ttT/tt	3/21	0.327482104303084	3	FACETS	0.923	0.767	1	0.923	0.767	1	CLONAL	2	TRUE	1	0.327482104303084	3		419	127	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49724707	49724707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	48	687	0	ENST00000449682.2:c.482C>T	p.Thr161Ile	p.T161I	ENST00000449682	NM_020998.3	161	aCt/aTt	5/18	0.327482104303084	3	FACETS	0.992	0.853	1	0.992	0.853	1	CLONAL	2	TRUE	1	0.327482104303084	3		687	172	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453544	138453545	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	21	491	1	ENST00000289153.2:c.903_904delinsAA	p.Ala302Thr	p.A302T	ENST00000289153	NM_006219.2	301	gaGGct/gaAAct	5/22	1	2	FACETS	0.838	0.651	1	0.838	0.651	1	CLONAL	1	TRUE	1	0.327482104303084	2		492	153	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590717	189590717	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1361527608	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	34	548	0	ENST00000264731.3:c.1282C>T	p.Pro428Ser	p.P428S	ENST00000264731	NM_003722.4	428	Cct/Tct	10/14	0.327482104303084	3	FACETS	1	0.869	1	0.535	0.44	0.64	CLONAL	1	TRUE	1	0.327482104303084	3		548	226	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807660	1807660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1176295260	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	30	807	0	ENST00000260795.2:c.1829C>T	p.Ser610Phe	p.S610F	ENST00000260795		610	tCc/tTc	12/17	0.212508937359283	1	FACETS	0.774	0.629	0.936	0.774	0.629	0.936	CLONAL	1	TRUE	0	0.327482104303084	1		807	198	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155278	55155278	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	31	403	0	ENST00000257290.5:c.2877A>T	p.Lys959Asn	p.K959N	ENST00000257290	NM_006206.4	959	aaA/aaT	21/23	0.19635922879235	3	FACETS	1	0.939	1	0.702	0.575	0.841	INDETERMINATE	1	TRUE	1	0.327482104303084	3		403	157	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594013	55594013	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	32	515	0	ENST00000288135.5:c.1799T>A	p.Phe600Tyr	p.F600Y	ENST00000288135	NM_000222.2	600	tTc/tAc	12/21	0.19635922879235	3	FACETS	1	0.912	1	0.602	0.493	0.722	INDETERMINATE	1	TRUE	1	0.327482104303084	3		515	189	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956220	55956220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190050670	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	33	538	3	ENST00000263923.4:c.3095G>A	p.Arg1032Gln	p.R1032Q	ENST00000263923	NM_002253.2	1032	cGa/cAa	23/30	0.19635922879235	3	FACETS	1	0.909	1	0.589	0.484	0.705	INDETERMINATE	1	TRUE	1	0.327482104303084	3		541	199	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961077	55961077	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs201830601	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	29	737	0	ENST00000263923.4:c.2863A>G	p.Ile955Val	p.I955V	ENST00000263923	NM_002253.2	955	Atc/Gtc	21/30	0.19635922879235	3	FACETS	0.977	0.789	1	0.488	0.394	0.594	INDETERMINATE	1	TRUE	1	0.327482104303084	3		737	211	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961812	55961812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	32	480	0	ENST00000263923.4:c.2749G>A	p.Glu917Lys	p.E917K	ENST00000263923	NM_002253.2	917	Gaa/Aaa	20/30	0.19635922879235	3	FACETS	1	0.947	1	0.743	0.612	0.887	INDETERMINATE	1	TRUE	1	0.327482104303084	3		480	153	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972883	55972883	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	15	553	0	ENST00000263923.4:c.1507C>T	p.Gln503Ter	p.Q503*	ENST00000263923	NM_002253.2	503	Caa/Taa	11/30	0.19635922879235	3	FACETS	0.814	0.6	1	0.407	0.3	0.533	INDETERMINATE	1	TRUE	1	0.327482104303084	3		553	131	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157521	106157521	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	22	300	0	ENST00000380013.4:c.2422G>T	p.Glu808Ter	p.E808*	ENST00000380013	NM_001127208.2	808	Gaa/Taa	3/11	0.19635922879235	3	FACETS	1	0.92	1	0.717	0.565	0.887	INDETERMINATE	1	TRUE	1	0.327482104303084	3		300	109	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332477	153332477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147025249	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	26	454	0	ENST00000281708.4:c.479C>T	p.Pro160Leu	p.P160L	ENST00000281708	NM_033632.3	160	cCa/cTa	2/12	0.19635922879235	3	FACETS	1	0.891	1	0.592	0.474	0.724	INDETERMINATE	1	TRUE	1	0.327482104303084	3		454	156	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524168	187524168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	25	429	0	ENST00000441802.2:c.11371C>T	p.His3791Tyr	p.H3791Y	ENST00000441802	NM_005245.3	3791	Cac/Tac	20/27	0.19635922879235	3	FACETS	1	0.859	1	0.552	0.439	0.679	INDETERMINATE	1	TRUE	1	0.327482104303084	3		429	161	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628376	187628376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	35	767	0	ENST00000441802.2:c.2606C>T	p.Ser869Leu	p.S869L	ENST00000441802	NM_005245.3	869	tCa/tTa	2/27	0.296821344135243	1	FACETS	0.761	0.628	0.908	0.761	0.628	0.908	CLONAL	1	TRUE	0	0.327482104303084	1		767	235	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515325	31515325	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs369352228	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	27	575	0	ENST00000344624.3:c.1060C>T	p.Arg354Cys	p.R354C	ENST00000344624		354	Cgc/Tgc	5/33	0.327482104303084	3	FACETS	1	0.871	1			1	CLONAL	1	TRUE	NA	0.327482104303084	3		575	172	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871203	35871203	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	27	389	0	ENST00000303115.3:c.425G>A	p.Gly142Glu	p.G142E	ENST00000303115	NM_002185.3	142	gGa/gAa	4/8	0.225251552746141	2	FACETS	1	0.917	1	0.639	0.516	0.774	CLONAL	1	TRUE	0	0.327482104303084	2		389	129	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80063881	80063881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	19	519	0	ENST00000265081.6:c.2026C>T	p.Pro676Ser	p.P676S	ENST00000265081	NM_002439.4	676	Cct/Tct	14/24	0.225251552746141	2	FACETS	1	0.807	1	0.527	0.406	0.666	CLONAL	1	TRUE	0	0.327482104303084	2		519	110	SUCCESS
APC	324	MSKCC	GRCh37	5	112154801	112154801	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs863224455	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	33	588	0	ENST00000257430.4:c.1072C>T	p.Gln358Ter	p.Q358*	ENST00000257430	NM_000038.5	358	Cag/Tag	10/16	0.327482104303084	3	FACETS	1	0.842	1			1	CLONAL	1	TRUE	NA	0.327482104303084	3		588	228	SUCCESS
APC	324	MSKCC	GRCh37	5	112177169	112177170	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	13	368	0	ENST00000257430.4:c.5878_5879delinsTT	p.Pro1960Leu	p.P1960L	ENST00000257430	NM_000038.5	1960	CCg/TTg	16/16	0.327482104303084	3	FACETS	0.62	0.444	0.832			1	SUBCLONAL	1	TRUE	NA	0.327482104303084	3		368	149	SUCCESS
APC	324	MSKCC	GRCh37	5	112178042	112178042	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777206261	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	22	386	0	ENST00000257430.4:c.6751C>T	p.Pro2251Ser	p.P2251S	ENST00000257430	NM_000038.5	2251	Cca/Tca	16/16	0.327482104303084	3	FACETS	0.909	0.71	1			1	CLONAL	1	TRUE	NA	0.327482104303084	3		386	172	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441389	149441389	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	29	664	0	ENST00000286301.3:c.1650G>A	p.Trp550Ter	p.W550*	ENST00000286301	NM_005211.3	550	tgG/tgA	12/22	1	2	FACETS	0.798	0.644	0.97	0.798	0.644	0.97	CLONAL	1	TRUE	1	0.327482104303084	2		664	222	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505103	149505103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	29	635	0	ENST00000261799.4:c.1712C>T	p.Ser571Phe	p.S571F	ENST00000261799	NM_002609.3	571	tCt/tTt	12/23	1	2	FACETS	0.824	0.665	1	0.824	0.665	1	CLONAL	1	TRUE	1	0.327482104303084	2		635	215	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043921	180043921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	51	755	0	ENST00000261937.6:c.3075G>A	p.Met1025Ile	p.M1025I	ENST00000261937	NM_182925.4	1025	atG/atA	22/30	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.327482104303084	2		755	217	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048652	180048652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772355537	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	39	693	0	ENST00000261937.6:c.1910G>A	p.Ser637Asn	p.S637N	ENST00000261937	NM_182925.4	637	aGc/aAc	13/30	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.327482104303084	2		693	208	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057783	180057783	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	12	515	0	ENST00000261937.6:c.172G>T	p.Glu58Ter	p.E58*	ENST00000261937	NM_182925.4	58	Gag/Tag	3/30	1	2	FACETS	0.473	0.333	0.643	0.473	0.333	0.643	SUBCLONAL	1	TRUE	1	0.327482104303084	2		515	155	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673565	30673565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	44	780	0	ENST00000376406.3:c.3395C>T	p.Ser1132Phe	p.S1132F	ENST00000376406	NM_014641.2	1132	tCc/tTc	10/15	0.216558472457699	3	FACETS	1	0.896	1			1	CLONAL	1	TRUE	NA	0.327482104303084	3		780	289	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324867	31324867	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	38	459	0	ENST00000412585.2:c.69G>A	p.Trp23Ter	p.W23*	ENST00000412585	NM_005514.6	23	tgG/tgA	1/8	0.303976613316032	5	FACETS	0.892	0.745	1	0.595	0.497	0.701	CLONAL	2	TRUE	2	0.327482104303084	5		459	194	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169973	32169973	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	47	837	0	ENST00000375023.3:c.3635A>G	p.Lys1212Arg	p.K1212R	ENST00000375023	NM_004557.3	1212	aAg/aGg	21/30	0.293500407785535	3	FACETS	1	0.922	1	0.57	0.484	0.664	CLONAL	1	TRUE	1	0.327482104303084	3		837	293	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170150	32170151	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	40	772	1	ENST00000375023.3:c.3457_3458delinsAA	p.Gly1153Lys	p.G1153K	ENST00000375023	NM_004557.3	1153	GGg/AAg	21/30	0.293500407785535	3	FACETS	1	0.899	1	0.553	0.462	0.653	CLONAL	1	TRUE	1	0.327482104303084	3		773	257	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184781	32184781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762081312	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	33	598	0	ENST00000375023.3:c.1802G>A	p.Gly601Glu	p.G601E	ENST00000375023	NM_004557.3	601	gGa/gAa	11/30	0.293500407785535	3	FACETS	1	0.829	1	0.505	0.414	0.607	CLONAL	1	TRUE	1	0.327482104303084	3		598	232	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190348	32190349	+	missense_variant	Missense_Mutation	DNP	CC	CC	GT	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	38	656	1	ENST00000375023.3:c.390_391delinsAC	p.Gly131Arg	p.G131R	ENST00000375023	NM_004557.3	130	agGGgc/agACgc	3/30	0.293500407785535	3	FACETS	1	0.89	1	0.547	0.455	0.648	CLONAL	1	TRUE	1	0.327482104303084	3		657	247	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32790084	32790084	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1434083106	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	16	227	0	ENST00000374899.4:c.1944G>A	p.Trp648Ter	p.W648*	ENST00000374899	NM_018833.2	648	tgG/tgA	12/12	0.293500407785535	3	FACETS	1	0.822	1	0.563	0.422	0.726	CLONAL	1	TRUE	1	0.327482104303084	3		227	101	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287355	33287355	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	35	571	0	ENST00000374542.5:c.1742C>T	p.Ser581Phe	p.S581F	ENST00000374542	NM_001141970.1	581	tCt/tTt	6/8	0.293500407785535	3	FACETS	1	0.846	1	0.514	0.424	0.614	CLONAL	1	TRUE	1	0.327482104303084	3		571	242	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287982	33287982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	28	509	0	ENST00000374542.5:c.1271C>T	p.Ser424Phe	p.S424F	ENST00000374542	NM_001141970.1	424	tCc/tTc	5/8	0.293500407785535	3	FACETS	0.913	0.734	1	0.456	0.367	0.557	CLONAL	1	TRUE	1	0.327482104303084	3		509	218	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955105	93955105	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	16	467	0	ENST00000369303.4:c.2793G>A	p.Trp931Ter	p.W931*	ENST00000369303	NM_004440.3	931	tgG/tgA	16/17	0.19635922879235	3	FACETS	0.94	0.702	1	0.47	0.351	0.609	INDETERMINATE	1	TRUE	1	0.327482104303084	3		467	121	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956704	93956704	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	22	320	0	ENST00000369303.4:c.2533-1G>A		p.X845_splice	ENST00000369303	NM_004440.3	845			0.19635922879235	3	FACETS	1	0.905	1	0.657	0.517	0.815	INDETERMINATE	1	TRUE	1	0.327482104303084	3		320	119	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553249	106553249	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1415765117	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	43	534	0	ENST00000369096.4:c.1214C>T	p.Ser405Leu	p.S405L	ENST00000369096	NM_001198.3	405	tCg/tTg	5/7	0.19635922879235	3	FACETS	0.776	0.657	0.904	0.776	0.657	0.904	INDETERMINATE	2	TRUE	1	0.327482104303084	3		534	197	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553360	106553360	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	17	457	0	ENST00000369096.4:c.1325G>A	p.Arg442Lys	p.R442K	ENST00000369096	NM_001198.3	442	aGg/aAg	5/7	0.19635922879235	3	FACETS	0.779	0.586	1	0.39	0.293	0.503	INDETERMINATE	1	TRUE	1	0.327482104303084	3		457	155	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112035643	112035643	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	31	398	0	ENST00000368678.4:c.251T>A	p.Val84Glu	p.V84E	ENST00000368678		84	gTg/gAg	4/13	0.19635922879235	3	FACETS	1	0.921	1	0.629	0.514	0.757	INDETERMINATE	1	TRUE	1	0.327482104303084	3		398	175	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117645530	117645530	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	38	584	0	ENST00000368508.3:c.5606G>A	p.Gly1869Glu	p.G1869E	ENST00000368508	NM_002944.2	1869	gGa/gAa	34/43	0.32320328912007	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.327482104303084	1		584	155	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715509	117715509	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	16	331	0	ENST00000368508.3:c.980G>A	p.Gly327Glu	p.G327E	ENST00000368508	NM_002944.2	327	gGa/gAa	10/43	1	2	FACETS	0.782	0.583	1	0.782	0.583	1	CLONAL	1	TRUE	1	0.327482104303084	2		331	125	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415675	152415675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	44	478	0	ENST00000206249.3:c.1525C>T	p.Leu509Phe	p.L509F	ENST00000206249	NM_000125.3	509	Ctc/Ttc	7/8	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.327482104303084	2		478	193	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157470057	157470057	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554226145	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	28	325	1	ENST00000346085.5:c.2851C>T	p.Gln951Ter	p.Q951*	ENST00000346085	NM_020732.3	951	Cag/Tag	9/20	1	2	FACETS	1	0.812	1	1	0.812	1	CLONAL	1	TRUE	1	0.327482104303084	2		326	170	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683565	162683565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	30	498	0	ENST00000366898.1:c.404G>A	p.Gly135Glu	p.G135E	ENST00000366898	NM_004562.2	135	gGa/gAa	3/12	0.279433163048527	4	FACETS	1	0.932	1			1	CLONAL	1	TRUE	NA	0.327482104303084	4		498	179	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683629	162683629	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	38	523	0	ENST00000366898.1:c.340G>T	p.Gly114Ter	p.G114*	ENST00000366898	NM_004562.2	114	Gga/Tga	3/12	0.279433163048527	4	FACETS	0.798	0.667	0.941			1	CLONAL	2	TRUE	NA	0.327482104303084	4		523	193	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954927	2954927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	139	726	0	ENST00000396946.4:c.2783G>A	p.Gly928Glu	p.G928E	ENST00000396946	NM_032415.4	928	gGg/gAg	21/25	0.327482104303084	5	FACETS	0.891	0.822	0.962	1	0.98	1	CLONAL	4	TRUE	2	0.327482104303084	5		726	355	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979559	2979559	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	61	460	0	ENST00000396946.4:c.688G>A	p.Asp230Asn	p.D230N	ENST00000396946	NM_032415.4	230	Gat/Aat	6/25	0.327482104303084	5	FACETS	1	0.947	1	0.778	0.679	0.882	CLONAL	2	TRUE	2	0.327482104303084	5		460	238	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729505	41729505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	52	572	0	ENST00000242208.4:c.1024C>T	p.Pro342Ser	p.P342S	ENST00000242208	NM_002192.2	342	Ccc/Tcc	3/3	0.327482104303084	8	FACETS	0.999	0.856	1	0.4	0.342	0.462	CLONAL	2	TRUE	3	0.327482104303084	8		572	315	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223550	55223550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	53	637	0	ENST00000275493.2:c.917C>T	p.Ser306Leu	p.S306L	ENST00000275493	NM_005228.3	306	tCg/tTg	8/28	0.327482104303084	5	FACETS	0.757	0.649	0.873	0.504	0.432	0.582	SUBCLONAL	2	TRUE	2	0.327482104303084	5		637	319	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397692	116397692	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	60	562	0	ENST00000397752.3:c.1966G>A	p.Asp656Asn	p.D656N	ENST00000397752	NM_000245.2	656	Gat/Aat	8/21	0.318448924754553	5	FACETS	0.964	0.845	1			1	CLONAL	3	TRUE	NA	0.327482104303084	5		562	189	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436101	116436101	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	62	481	2	ENST00000397752.3:c.4096C>T	p.Pro1366Ser	p.P1366S	ENST00000397752	NM_000245.2	1366	Cct/Tct	21/21	0.321451124312482	5	FACETS	0.984	0.857	1	0.492	0.428	0.559	CLONAL	2	TRUE	1	0.327482104303084	5		483	287	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439617	140439617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	25	671	0	ENST00000288602.6:c.2122C>T	p.Pro708Ser	p.P708S	ENST00000288602	NM_004333.4	708	Ccc/Tcc	17/18	0.321451124312482	5	FACETS	1	0.854	1	0.275	0.218	0.34	CLONAL	1	TRUE	1	0.327482104303084	5		671	207	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873285	151873285	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	28	289	0	ENST00000262189.6:c.9253C>T	p.Pro3085Ser	p.P3085S	ENST00000262189	NM_170606.2	3085	Cct/Tct	38/59	0.327482104303084	5	FACETS	1	0.921	1			1	CLONAL	1	TRUE	NA	0.327482104303084	5		289	194	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956771	68956771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774302685	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	27	597	1	ENST00000288368.4:c.889C>T	p.Arg297Cys	p.R297C	ENST00000288368	NM_024870.2	297	Cgt/Tgt	8/40	1	2	FACETS	0.837	0.671	1	0.837	0.671	1	CLONAL	1	TRUE	1	0.327482104303084	2		598	197	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002813	69002813	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	15	254	0	ENST00000288368.4:c.2114-1G>A		p.X705_splice	ENST00000288368	NM_024870.2	705			1	2	FACETS	1	0.756	1	1	0.756	1	CLONAL	1	TRUE	1	0.327482104303084	2		254	90	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69011986	69011986	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	23	638	0	ENST00000288368.4:c.2623G>A	p.Glu875Lys	p.E875K	ENST00000288368	NM_024870.2	875	Gaa/Aaa	23/40	1	2	FACETS	0.789	0.62	0.982	0.789	0.62	0.982	CLONAL	1	TRUE	1	0.327482104303084	2		638	178	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030817	69030817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	37	370	0	ENST00000288368.4:c.3359C>T	p.Ser1120Phe	p.S1120F	ENST00000288368	NM_024870.2	1120	tCc/tTc	27/40	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.327482104303084	2		370	182	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457207	5457207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	28	351	0	ENST00000381577.3:c.181G>A	p.Asp61Asn	p.D61N	ENST00000381577	NM_014143.3	61	Gat/Aat	3/7	0.212508937359283	1	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	0	0.327482104303084	1		351	121	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341196	8341196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	23	452	0	ENST00000356435.5:c.5020C>T	p.Arg1674Cys	p.R1674C	ENST00000356435		1674	Cgc/Tgc	30/35	0.212508937359283	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.327482104303084	1		452	88	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484342	8484342	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1338134782	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	21	481	0	ENST00000356435.5:c.3190G>A	p.Asp1064Asn	p.D1064N	ENST00000356435		1064	Gat/Aat	19/35	0.212508937359283	1	FACETS	0.851	0.664	1	0.851	0.664	1	CLONAL	1	TRUE	0	0.327482104303084	1		481	126	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528755	8528755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	26	377	0	ENST00000356435.5:c.377C>T	p.Pro126Leu	p.P126L	ENST00000356435		126	cCt/cTt	4/35	0.212508937359283	1	FACETS	1	0.82	1	1	0.82	1	CLONAL	1	TRUE	0	0.327482104303084	1		377	130	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633430	8633430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	23	430	1	ENST00000356435.5:c.239C>T	p.Ser80Leu	p.S80L	ENST00000356435		80	tCa/tTa	3/35	0.212508937359283	1	FACETS	0.87	0.687	1	0.87	0.687	1	CLONAL	1	TRUE	0	0.327482104303084	1		431	135	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	36	470	0	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	0.212508937359283	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.327482104303084	1		470	123	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637113	93637113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	21	431	0	ENST00000375746.1:c.1163G>A	p.Gly388Asp	p.G388D	ENST00000375746	NM_001174167.1	388	gGc/gAc	9/14	1	2	FACETS	0.884	0.688	1	0.884	0.688	1	CLONAL	1	TRUE	1	0.327482104303084	2		431	145	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98011548	98011548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767124692	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	37	432	0	ENST00000289081.3:c.26C>T	p.Ser9Phe	p.S9F	ENST00000289081	NM_000136.2	9	tCt/tTt	2/15	1	2	FACETS	0.785	0.658	0.92	1	0.959	1	CLONAL	2	TRUE	1	0.327482104303084	2		432	144	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209616	98209616	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	31	636	0	ENST00000331920.6:c.3922A>G	p.Arg1308Gly	p.R1308G	ENST00000331920	NM_000264.3	1308	Aga/Gga	23/24	1	2	FACETS	0.981	0.801	1	0.981	0.801	1	CLONAL	1	TRUE	1	0.327482104303084	2		636	193	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240380	98240380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	21	465	0	ENST00000331920.6:c.1304C>T	p.Ser435Phe	p.S435F	ENST00000331920	NM_000264.3	435	tCt/tTt	9/24	1	2	FACETS	0.705	0.546	0.887	0.705	0.546	0.887	SUBCLONAL	1	TRUE	1	0.327482104303084	2		465	182	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412689	63412689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760337524	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	77	355	0	ENST00000330258.3:c.478C>T	p.Pro160Ser	p.P160S	ENST00000330258	NM_152424.3	160	Ccc/Tcc	2/2	0.327482104303084	2	FACETS	0.897	0.819	0.974			1	CLONAL	4	TRUE	NA	0.327482104303084	2		355	131	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342969	70342969	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	62	280	0	ENST00000374080.3:c.1510G>A	p.Val504Met	p.V504M	ENST00000374080		504	Gtg/Atg	11/45	0.327482104303084	2	FACETS	1	0.961	1			1	CLONAL	2	TRUE	NA	0.327482104303084	2		280	156	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0036810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	130	381	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.992	0.906	1	0.992	0.906	1	CLONAL	1	TRUE	1	0.54494253333797	2		381	481	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528104	29528105	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGATGTGGATCTAATGATTGACTGCCTTGTTT	novel	NA	P-0036810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	65	453	1	ENST00000356175.3:c.1113_1144dup	p.Ser382Ter	p.S382*	ENST00000356175	NM_000267.3	371	gca/gcAGATGTGGATCTAATGATTGACTGCCTTGTTTa	10/57	0.54494253333797	1	FACETS	0.47	0.41	0.535	0.47	0.41	0.535	SUBCLONAL	1	TRUE	0	0.54494253333797	1		454	369	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510569	38510569	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	116	452	0	ENST00000254066.5:c.823A>C	p.Thr275Pro	p.T275P	ENST00000254066	NM_000964.3	275	Acg/Ccg	7/9	0.54494253333797	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.54494253333797	1		452	289	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602619	10602619	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	190	626	0	ENST00000171111.5:c.959G>C	p.Arg320Pro	p.R320P	ENST00000171111	NM_203500.1	320	cGg/cCg	3/6	0.54494253333797	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.54494253333797	1		626	472	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247453	71247453	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	113	522	0	ENST00000318789.4:c.80T>C	p.Leu27Pro	p.L27P	ENST00000318789	NM_032682.5	27	cTa/cCa	6/21	1	2	FACETS	0.728	0.657	0.802	0.728	0.657	0.802	SUBCLONAL	1	TRUE	1	0.54494253333797	2		522	570	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345750	152345750	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	87	249	1	ENST00000359321.1:c.820G>T	p.Glu274Ter	p.E274*	ENST00000359321	NM_005431.1	274	Gaa/Taa	3/3	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.54494253333797	2		250	288	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0036810-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	51	469	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.722	0.615	0.84	0.722	0.615	0.84	SUBCLONAL	1	TRUE	1	0.330650344525369	2		469	427	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220649	1220649	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036810-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	70	708	0	ENST00000326873.7:c.667G>T	p.Glu223Ter	p.E223*	ENST00000326873	NM_000455.4	223	Gag/Tag	5/10	0.330650344525369	1	FACETS	0.826	0.723	0.936	0.826	0.723	0.936	CLONAL	1	TRUE	0	0.330650344525369	1		708	428	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356205	66356205	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036810-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	110	579	0	ENST00000273854.3:c.1292T>C	p.Leu431Pro	p.L431P	ENST00000273854	NM_004439.5	431	cTa/cCa	5/18	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.330650344525369	2		579	539	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573933	18573933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036810-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	53	341	0	ENST00000266497.5:c.2251G>A	p.Asp751Asn	p.D751N	ENST00000266497		751	Gat/Aat	15/31	1	2	FACETS	0.855	0.732	0.989	0.855	0.732	0.989	CLONAL	1	TRUE	1	0.330650344525369	2		341	375	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819174	3819174	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0036810-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	53	483	0	ENST00000262367.5:c.3060+1G>A		p.X1020_splice	ENST00000262367	NM_004380.2	1020			0.294331473756162	3	FACETS	0.896	0.766	1	0.448	0.383	0.519	CLONAL	1	TRUE	1	0.330650344525369	3		483	417	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644415	18644415	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036810-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	49	382	0	ENST00000266497.5:c.2593G>T	p.Glu865Ter	p.E865*	ENST00000266497		865	Gaa/Taa	18/31	1	2	FACETS	0.83	0.706	0.966	0.83	0.706	0.966	CLONAL	1	TRUE	1	0.330650344525369	2		382	357	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47685245	47685245	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036810-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	56	366	0	ENST00000347630.2:c.705G>T	p.Glu235Asp	p.E235D	ENST00000347630	NM_001007230.1	235	gaG/gaT	8/11	1	2	FACETS	0.918	0.79	1	0.918	0.79	1	CLONAL	1	TRUE	1	0.330650344525369	2		366	369	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713696	30713696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036810-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	40	373	0	ENST00000295754.5:c.1021G>A	p.Val341Ile	p.V341I	ENST00000295754	NM_003242.5	341	Gtc/Atc	4/7	1	2	FACETS	0.82	0.685	0.969	0.82	0.685	0.969	CLONAL	1	TRUE	1	0.330650344525369	2		373	295	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0036824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	86	569	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.766	0.684	0.851	0.766	0.684	0.851	SUBCLONAL	1	TRUE	1	0.689210478697555	2		569	326	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562746	29562746	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs199474742	NA	P-0036824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	143	571	1	ENST00000356175.3:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000356175	NM_000267.3	1276	Cga/Tga	28/57	0.689210478697555	1	FACETS	0.913	0.848	0.978	0.913	0.848	0.978	CLONAL	1	TRUE	0	0.689210478697555	1		572	298	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0036824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	304	687	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.689210478697555	1	FACETS	0.948	0.902	0.994	0.948	0.902	0.994	CLONAL	1	TRUE	0	0.689210478697555	1		688	610	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0036824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	53	268	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.884	0.767	1	0.884	0.767	1	CLONAL	1	TRUE	1	0.689210478697555	2		268	174	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0036824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	132	407	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.689210478697555	2		408	372	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412110	63412110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852216	NA	P-0036824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	350	909	0	ENST00000330258.3:c.1057C>T	p.Arg353Ter	p.R353*	ENST00000330258	NM_152424.3	353	Cga/Tga	2/2	0.639288387941403	4	FACETS	1	0.994	1	0.471	0.445	0.496	CLONAL	1	TRUE	1	0.689210478697555	4		909	1215	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49941021	49941021	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	76	419	0	ENST00000296474.3:c.22C>A	p.Pro8Thr	p.P8T	ENST00000296474	NM_002447.2	8	Cct/Act	1/20	1	2	FACETS	0.453	0.398	0.511	0.453	0.398	0.511	SUBCLONAL	1	TRUE	1	0.689210478697555	2		419	487	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243047	105243048	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCAGGCAGCGGATGATGAAGGTGTTGGGCCGGGGCC	novel	NA	P-0036833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	65	865	0	ENST00000349310.3:c.200_235dup	p.Arg67_Leu78dup	p.R67_L78dup	ENST00000349310	NM_001014432.1	67	cag/cGGCCCCGGCCCAACACCTTCATCATCCGCTGCCTGCag	5/15	0.10821179630701	4	FACETS	1	0.963	1	0.663	0.575	0.759	INDETERMINATE	1	TRUE	2	0.210229080569379	4		865	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	241	564	0	ENST00000269305.4:c.380C>A	p.Ser127Tyr	p.S127Y	ENST00000269305	NM_001126112.2	127	tCc/tAc	5/11	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.313257326350343	2		564	1136	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003260	143003260	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	99	469	0	ENST00000262992.4:c.2566G>C	p.Glu856Gln	p.E856Q	ENST00000262992	NM_001101669.1	856	Gaa/Caa	23/24	1	2	FACETS	0.807	0.72	0.9	0.807	0.72	0.9	CLONAL	1	TRUE	1	0.313257326350343	2		469	783	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261523	16261523	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0036850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	351	487	0	ENST00000375759.3:c.8788A>T	p.Lys2930Ter	p.K2930*	ENST00000375759	NM_015001.2	2930	Aag/Tag	11/15	0.806027724778744	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.806027724778744	1		487	519	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346965	70346965	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	289	429	0	ENST00000374080.3:c.2832G>C	p.Met944Ile	p.M944I	ENST00000374080		944	atG/atC	20/45	1	2	FACETS	0.873	0.825	0.923	0.873	0.825	0.923	CLONAL	1	TRUE	1	0.806027724778744	2		429	821	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482926	140482927	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs777474487	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	87	885	6	ENST00000288602.6:c.1208dup	p.Ala404CysfsTer9	p.A404Cfs*9	ENST00000288602	NM_004333.4	403	cct/ccCt	10/18	0.404703541093452	3	FACETS	0.66	0.584	0.742	0.33	0.292	0.371	SUBCLONAL	1	TRUE	1	0.404703541093452	3		891	783	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	168	763	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.791	0.726	0.858	0.791	0.726	0.858	SUBCLONAL	1	TRUE	1	0.404703541093452	2		765	1050	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	277	645	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.404703541093452	2		648	952	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661663	227661664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	45	782	0	ENST00000305123.5:c.1790_1791dup	p.His598GlyfsTer39	p.H598Gfs*39	ENST00000305123	NM_005544.2	597	-/GG	1/2	1	2	FACETS	0.308	0.258	0.364	0.308	0.258	0.364	SUBCLONAL	1	TRUE	1	0.404703541093452	2		782	722	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	125	303	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.404703541093452	3	FACETS	0.79	0.72	0.863	0.79	0.72	0.863	SUBCLONAL	2	TRUE	1	0.404703541093452	3		303	470	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	43	513	0	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.295	0.246	0.349	0.295	0.246	0.349	SUBCLONAL	1	TRUE	1	0.404703541093452	2		513	721	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	53	355	2	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.421	0.358	0.49	0.421	0.358	0.49	SUBCLONAL	1	TRUE	1	0.404703541093452	2		357	622	SUCCESS
APC	324	MSKCC	GRCh37	5	112175600	112175600	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	68	454	0	ENST00000257430.4:c.4312del	p.Thr1438HisfsTer35	p.T1438Hfs*35	ENST00000257430	NM_000038.5	1437	Aaa/aa	16/16	1	2	FACETS	0.891	0.78	1	0.891	0.78	1	CLONAL	1	TRUE	1	0.404703541093452	2		454	377	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748272	41748272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774521395	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	179	993	0	ENST00000226382.2:c.497C>T	p.Ala166Val	p.A166V	ENST00000226382	NM_003924.3	166	gCg/gTg	3/3	0.125480887842461	0	FACETS	0.49	0.451	0.531			1	INDETERMINATE	1	TRUE	0	0.404703541093452	0		993	1075	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	76	670	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	1	2	FACETS	0.403	0.353	0.458	0.403	0.353	0.458	SUBCLONAL	1	TRUE	1	0.404703541093452	2		670	931	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	70	567	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.674	0.589	0.766	0.674	0.589	0.766	SUBCLONAL	1	TRUE	1	0.404703541093452	2		568	513	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	126	550	2	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	0.34048231387271	3	FACETS	0.817	0.745	0.892	0.817	0.745	0.892	CLONAL	2	TRUE	1	0.404703541093452	3		552	458	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	154	782	9	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.855	0.783	0.931	0.855	0.783	0.931	CLONAL	1	TRUE	1	0.404703541093452	2		791	890	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451784	29451784	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs772809305	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	124	916	0	ENST00000389048.3:c.2781del	p.Cys928AlafsTer11	p.C928Afs*11	ENST00000389048	NM_004304.4	927	ggG/gg	16/29	1	2	FACETS	0.75	0.678	0.826	0.75	0.678	0.826	SUBCLONAL	1	TRUE	1	0.404703541093452	2		916	817	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	164	924	2	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.831	0.763	0.903	0.831	0.763	0.903	CLONAL	1	TRUE	1	0.404703541093452	2		926	975	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088788	27088788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	95	710	3	ENST00000324856.7:c.2402del	p.Gly801ValfsTer32	p.G801Vfs*32	ENST00000324856	NM_006015.4	799	caG/ca	7/20	1	2	FACETS	0.686	0.611	0.766	0.686	0.611	0.766	SUBCLONAL	1	TRUE	1	0.404703541093452	2		713	684	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456467	99456467	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56248469	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	75	529	1	ENST00000268035.6:c.1784G>A	p.Arg595His	p.R595H	ENST00000268035	NM_000875.3	595	cGt/cAt	8/21	1	2	FACETS	0.709	0.622	0.801	0.709	0.622	0.801	SUBCLONAL	1	TRUE	1	0.404703541093452	2		530	523	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19261529	19261529	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	166	904	1	ENST00000162023.5:c.16del	p.Ile6SerfsTer14	p.I6Sfs*14	ENST00000162023		6	Atc/tc	6/13	1	2	FACETS	0.775	0.711	0.842	0.775	0.711	0.842	SUBCLONAL	1	TRUE	1	0.404703541093452	2		905	1058	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937104	39937104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	166	490	0	ENST00000378444.4:c.79G>A	p.Glu27Lys	p.E27K	ENST00000378444	NM_001123385.1	27	Gaa/Aaa	2/15	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.404703541093452	1		490	534	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871053	12871053	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	70	346	1	ENST00000228872.4:c.285del	p.Gly97ValfsTer22	p.G97Vfs*22	ENST00000228872	NM_004064.3	94	Ccc/cc	1/3	0.404703541093452	3	FACETS	0.829	0.724	0.941	0.414	0.362	0.471	CLONAL	1	TRUE	1	0.404703541093452	3		347	502	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245586	41245587	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs80357522	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	165	1193	9	ENST00000357654.3:c.1961dup	p.Tyr655ValfsTer18	p.Y655Vfs*18	ENST00000357654	NM_007294.3	654	aag/aaAg	10/23	1	2	FACETS	0.867	0.796	0.941	0.867	0.796	0.941	CLONAL	1	TRUE	1	0.404703541093452	2		1202	941	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259729	16259729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758740337	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	69	628	0	ENST00000375759.3:c.6994C>T	p.Arg2332Cys	p.R2332C	ENST00000375759	NM_015001.2	2332	Cgc/Tgc	11/15	1	2	FACETS	0.546	0.476	0.623	0.546	0.476	0.623	SUBCLONAL	1	TRUE	1	0.404703541093452	2		628	624	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117861247	117861247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	101	670	0	ENST00000297338.2:c.1642G>A	p.Asp548Asn	p.D548N	ENST00000297338	NM_006265.2	548	Gat/Aat	13/14	0.34048231387271	3	FACETS	0.834	0.745	0.927	0.417	0.372	0.464	CLONAL	1	TRUE	1	0.404703541093452	3		670	720	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966873	25966873	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1271466699	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	147	891	5	ENST00000435504.4:c.2333del	p.Pro778GlnfsTer21	p.P778Qfs*21	ENST00000435504		778	cCa/ca	13/13	1	2	FACETS	0.782	0.714	0.854	0.782	0.714	0.854	SUBCLONAL	1	TRUE	1	0.404703541093452	2		896	929	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368387	225368388	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	73	722	0	ENST00000264414.4:c.1358dup	p.Asn453LysfsTer5	p.N453Kfs*5	ENST00000264414	NM_003590.4	453	aac/aaAc	9/16	1	2	FACETS	0.652	0.571	0.74	0.652	0.571	0.74	SUBCLONAL	1	TRUE	1	0.404703541093452	2		722	553	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	119	514	8	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.761	0.687	0.839	0.761	0.687	0.839	SUBCLONAL	1	TRUE	1	0.404703541093452	2		522	773	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112347	115112347	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1291364957	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	37	508	1	ENST00000257566.3:c.1393G>A	p.Ala465Thr	p.A465T	ENST00000257566	NM_016569.3	465	Gcc/Acc	7/8	0.34048231387271	3	FACETS	0.358	0.294	0.43	0.179	0.147	0.215	SUBCLONAL	1	TRUE	1	0.404703541093452	3		509	614	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434959	49434959	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555192751	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	116	676	1	ENST00000301067.7:c.6594del	p.Tyr2199IlefsTer65	p.Y2199Ifs*65	ENST00000301067	NM_003482.3	2198	ccC/cc	31/54	0.404703541093452	3	FACETS	0.846	0.762	0.934	0.423	0.381	0.467	CLONAL	1	TRUE	1	0.404703541093452	3		677	815	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291084	10291084	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	162	995	4	ENST00000340748.4:c.387del	p.Lys130AsnfsTer129	p.K130Nfs*129	ENST00000340748		129	ccC/cc	4/40	1	2	FACETS	0.857	0.786	0.931	0.857	0.786	0.931	CLONAL	1	TRUE	1	0.404703541093452	2		999	934	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554345	141554345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748399150	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1287	177	1195	4	ENST00000220592.5:c.1806del	p.Ala603ProfsTer92	p.A603Pfs*92	ENST00000220592	NM_012154.3	602	ccC/cc	14/19	0.34048231387271	3	FACETS	0.718	0.66	0.78	0.359	0.33	0.39	SUBCLONAL	1	TRUE	1	0.404703541093452	3		1199	1464	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849914	156849914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763122825	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	183	958	2	ENST00000524377.1:c.2170G>A	p.Gly724Ser	p.G724S	ENST00000524377	NM_002529.3	724	Ggc/Agc	16/17	1	2	FACETS	0.83	0.765	0.897	0.83	0.765	0.897	CLONAL	1	TRUE	1	0.404703541093452	2		960	1090	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527886	157527886	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	112	644	1	ENST00000346085.5:c.5614del	p.Ser1872AlafsTer3	p.S1872Afs*3	ENST00000346085	NM_020732.3	1871	Aaa/aa	20/20	1	2	FACETS	0.943	0.85	1	0.943	0.85	1	CLONAL	1	TRUE	1	0.404703541093452	2		645	587	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731149	162731149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147483979	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	126	709	1	ENST00000367921.3:c.1004C>T	p.Thr335Met	p.T335M	ENST00000367921	NM_006182.2	335	aCg/aTg	9/18	1	2	FACETS	0.931	0.844	1	0.931	0.844	1	CLONAL	1	TRUE	1	0.404703541093452	2		710	669	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41562637	41562637	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555910814	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	161	637	0	ENST00000263253.7:c.3841C>T	p.Arg1281Ter	p.R1281*	ENST00000263253	NM_001429.3	1281	Cga/Tga	23/31	0.352555313367437	2	FACETS	1	0.989	1	0.746	0.689	0.806	CLONAL	1	TRUE	0	0.404703541093452	2		637	533	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100727	8100727	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	108	832	0	ENST00000346208.3:c.701T>C	p.Phe234Ser	p.F234S	ENST00000346208		234	tTc/tCc	3/6	1	2	FACETS	0.632	0.566	0.701	0.632	0.566	0.701	SUBCLONAL	1	TRUE	1	0.404703541093452	2		832	845	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117423	115117423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	181	571	1	ENST00000257566.3:c.751C>T	p.Arg251Trp	p.R251W	ENST00000257566	NM_016569.3	251	Cgg/Tgg	4/8	0.34048231387271	3	FACETS	0.804	0.744	0.865	0.804	0.744	0.865	CLONAL	2	TRUE	1	0.404703541093452	3		572	669	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741825	17741825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs548800810	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	104	385	0	ENST00000250003.3:c.496G>A	p.Asp166Asn	p.D166N	ENST00000250003	NM_002478.4	166	Gac/Aac	1/3	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.404703541093452	2		385	491	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456619	32456621	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	rs770519620	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	82	380	0	ENST00000332351.3:c.271_273del	p.Gly91del	p.G91del	ENST00000332351	NM_024426.4	91	GGC/-	1/10	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.404703541093452	2		380	379	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976896	18976896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1333445130	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	57	805	1	ENST00000262803.5:c.3281C>T	p.Ala1094Val	p.A1094V	ENST00000262803	NM_002911.3	1094	gCg/gTg	23/24	1	2	FACETS	0.341	0.291	0.395	0.341	0.291	0.395	SUBCLONAL	1	TRUE	1	0.404703541093452	2		806	827	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797191	42797191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778202	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	215	1135	2	ENST00000575354.2:c.3553G>A	p.Ala1185Thr	p.A1185T	ENST00000575354	NM_015125.3	1185	Gcc/Acc	15/20	1	2	FACETS	0.888	0.825	0.955	0.888	0.825	0.955	CLONAL	1	TRUE	1	0.404703541093452	2		1137	1196	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639102	3639102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550419924	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	183	720	1	ENST00000294008.3:c.4537G>A	p.Val1513Ile	p.V1513I	ENST00000294008	NM_032444.2	1513	Gtt/Att	12/15	1	2	FACETS	0.841	0.775	0.91	0.841	0.775	0.91	CLONAL	1	TRUE	1	0.404703541093452	2		721	1075	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22412941	22412941	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	22	256	0	ENST00000344548.3:c.188A>T	p.Asp63Val	p.D63V	ENST00000344548	NM_001039802.1	63	gAt/gTt	5/7	1	2	FACETS	0.457	0.355	0.574	0.457	0.355	0.574	SUBCLONAL	1	TRUE	1	0.404703541093452	2		256	238	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551550	150551550	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	202	1002	0	ENST00000369026.2:c.457A>G	p.Asn153Asp	p.N153D	ENST00000369026	NM_021960.4	153	Aac/Gac	1/3	1	2	FACETS	0.782	0.724	0.844	0.782	0.724	0.844	SUBCLONAL	1	TRUE	1	0.404703541093452	2		1002	1276	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870410	155870410	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	78	523	1	ENST00000368323.3:c.430-1G>T		p.X144_splice	ENST00000368323	NM_006912.5	144			1	2	FACETS	0.73	0.643	0.823	0.73	0.643	0.823	SUBCLONAL	1	TRUE	1	0.404703541093452	2		524	528	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666684	206666684	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	147	907	0	ENST00000367120.3:c.2018G>T	p.Ser673Ile	p.S673I	ENST00000367120	NM_014002.3	673	aGc/aTc	20/22	1	2	FACETS	0.749	0.683	0.818	0.749	0.683	0.818	SUBCLONAL	1	TRUE	1	0.404703541093452	2		907	970	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446283	70446284	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	102	688	0	ENST00000373644.4:c.5229_5230dup	p.Arg1744LysfsTer19	p.R1744Kfs*19	ENST00000373644	NM_030625.2	1741	-/AA	11/12	1	2	FACETS	0.675	0.603	0.751	0.675	0.603	0.751	SUBCLONAL	1	TRUE	1	0.404703541093452	2		688	747	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137238	64137238	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	199	1052	0	ENST00000334205.4:c.1670T>C	p.Leu557Ser	p.L557S	ENST00000334205	NM_003942.2	557	tTg/tCg	14/17	1	2	FACETS	0.906	0.838	0.976	0.906	0.838	0.976	CLONAL	1	TRUE	1	0.404703541093452	2		1052	1086	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129797	108129797	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	83	627	0	ENST00000278616.4:c.2461A>G	p.Ser821Gly	p.S821G	ENST00000278616	NM_000051.3	821	Agt/Ggt	16/63	1	2	FACETS	0.82	0.726	0.921	0.82	0.726	0.921	CLONAL	1	TRUE	1	0.404703541093452	2		627	500	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199814	108199814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	38	381	0	ENST00000278616.4:c.7156G>A	p.Ala2386Thr	p.A2386T	ENST00000278616	NM_000051.3	2386	Gca/Aca	49/63	1	2	FACETS	0.671	0.557	0.796	0.671	0.557	0.796	SUBCLONAL	1	TRUE	1	0.404703541093452	2		381	280	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392702	118392702	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	108	834	0	ENST00000534358.1:c.11734T>G	p.Cys3912Gly	p.C3912G	ENST00000534358	NM_005933.3	3912	Tgt/Ggt	36/36	1	2	FACETS	0.718	0.645	0.796	0.718	0.645	0.796	SUBCLONAL	1	TRUE	1	0.404703541093452	2		834	743	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125076	46125076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	42	366	0	ENST00000334344.6:c.263C>T	p.Ala88Val	p.A88V	ENST00000334344	NM_152641.2	88	gCt/gTt	3/21	0.404703541093452	3	FACETS	0.658	0.551	0.777	0.329	0.275	0.389	SUBCLONAL	1	TRUE	1	0.404703541093452	3		366	379	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123892084	123892084	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	133	392	0	ENST00000330479.4:c.893A>T	p.Asn298Ile	p.N298I	ENST00000330479	NM_020382.3	298	aAt/aTt	8/9	0.34048231387271	3	FACETS	0.925	0.848	1	0.925	0.848	1	CLONAL	2	TRUE	1	0.404703541093452	3		392	427	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858133	9858133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1320797353	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	157	1065	1	ENST00000330684.3:c.3268G>A	p.Val1090Met	p.V1090M	ENST00000330684	NM_001134407.1	1090	Gtg/Atg	13/13	1	2	FACETS	0.817	0.748	0.889	0.817	0.748	0.889	CLONAL	1	TRUE	1	0.404703541093452	2		1066	950	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348059	89348059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1402377065	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1229	209	1516	3	ENST00000301030.4:c.4891C>T	p.Arg1631Trp	p.R1631W	ENST00000301030	NM_001256183.1	1631	Cgg/Tgg	9/13	1	2	FACETS	0.718	0.665	0.774	0.718	0.665	0.774	SUBCLONAL	1	TRUE	1	0.404703541093452	2		1519	1438	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550542	29550542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500288	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	40	555	0	ENST00000356175.3:c.1802G>A	p.Arg601Gln	p.R601Q	ENST00000356175	NM_000267.3	601	cGg/cAg	16/57	1	2	FACETS	0.477	0.397	0.567	0.477	0.397	0.567	SUBCLONAL	1	TRUE	1	0.404703541093452	2		555	414	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40860057	40860057	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	159	924	0	ENST00000428826.2:c.1579C>T	p.Pro527Ser	p.P527S	ENST00000428826		527	Cca/Tca	15/21	1	2	FACETS	0.826	0.757	0.899	0.826	0.757	0.899	CLONAL	1	TRUE	1	0.404703541093452	2		924	951	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119011	70119011	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	150	874	1	ENST00000245479.2:c.583C>T	p.Gln195Ter	p.Q195*	ENST00000245479	NM_000346.3	195	Cag/Tag	2/3	1	2	FACETS	0.782	0.714	0.853	0.782	0.714	0.853	SUBCLONAL	1	TRUE	1	0.404703541093452	2		875	948	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169536	11169536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	143	800	3	ENST00000358026.2:c.4702G>A	p.Ala1568Thr	p.A1568T	ENST00000358026	NM_001128849.1	1568	Gca/Aca	33/36	1	2	FACETS	0.78	0.711	0.853	0.78	0.711	0.853	SUBCLONAL	1	TRUE	1	0.404703541093452	2		803	906	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948759	17948759	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	173	1179	0	ENST00000458235.1:c.1683G>T	p.Lys561Asn	p.K561N	ENST00000458235	NM_000215.3	561	aaG/aaT	12/24	1	2	FACETS	0.733	0.673	0.795	0.733	0.673	0.795	SUBCLONAL	1	TRUE	1	0.404703541093452	2		1179	1167	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753887	42753887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778205341	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	109	1046	0	ENST00000222329.4:c.377G>A	p.Gly126Asp	p.G126D	ENST00000222329	NM_006494.2	126	gGt/gAt	4/4	1	2	FACETS	0.474	0.424	0.527	0.474	0.424	0.527	SUBCLONAL	1	TRUE	1	0.404703541093452	2		1046	1137	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791254	42791254	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs756450250	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	102	876	1	ENST00000575354.2:c.314G>T	p.Ser105Ile	p.S105I	ENST00000575354	NM_015125.3	105	aGc/aTc	3/20	1	2	FACETS	0.504	0.449	0.562	0.504	0.449	0.562	SUBCLONAL	1	TRUE	1	0.404703541093452	2		877	1001	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912160	50912160	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	156	929	2	ENST00000440232.2:c.1892+2T>C		p.X631_splice	ENST00000440232	NM_002691.3	631			1	2	FACETS	0.792	0.725	0.863	0.792	0.725	0.863	SUBCLONAL	1	TRUE	1	0.404703541093452	2		931	973	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966879	25966879	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs755787643	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	162	892	0	ENST00000435504.4:c.2327C>A	p.Thr776Asn	p.T776N	ENST00000435504		776	aCc/aAc	13/13	1	2	FACETS	0.863	0.791	0.937	0.863	0.791	0.937	CLONAL	1	TRUE	1	0.404703541093452	2		892	928	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416399	29416400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	169	1151	0	ENST00000389048.3:c.4553dup	p.Asn1519GlufsTer2	p.N1519Efs*2	ENST00000389048	NM_004304.4	1518	aag/aaAg	29/29	1	2	FACETS	0.727	0.667	0.79	0.727	0.667	0.79	SUBCLONAL	1	TRUE	1	0.404703541093452	2		1151	1149	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266464	198266464	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	62	524	0	ENST00000335508.6:c.2370+2T>C		p.X790_splice	ENST00000335508	NM_012433.2	790			1	2	FACETS	0.868	0.754	0.99	0.868	0.754	0.99	CLONAL	1	TRUE	1	0.404703541093452	2		524	353	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137452	202137452	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	84	603	1	ENST00000358485.4:c.680A>T	p.Asn227Ile	p.N227I	ENST00000358485	NM_001080125.1	227	aAc/aTc	4/9	1	2	FACETS	0.863	0.765	0.967	0.863	0.765	0.967	CLONAL	1	TRUE	1	0.404703541093452	2		604	481	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215609814	215609814	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	77	542	0	ENST00000260947.4:c.1880G>A	p.Gly627Glu	p.G627E	ENST00000260947	NM_000465.2	627	gGa/gAa	9/11	1	2	FACETS	0.793	0.698	0.894	0.793	0.698	0.894	SUBCLONAL	1	TRUE	1	0.404703541093452	2		542	480	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714369	40714369	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs775489787	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	107	643	1	ENST00000373198.4:c.4028G>A	p.Arg1343Gln	p.R1343Q	ENST00000373198	NM_133170.3	1343	cGg/cAg	29/32	1	2	FACETS	0.929	0.836	1	0.929	0.836	1	CLONAL	1	TRUE	1	0.404703541093452	2		644	569	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400095	41400095	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	97	692	1	ENST00000373198.4:c.664C>A	p.His222Asn	p.H222N	ENST00000373198	NM_133170.3	222	Cat/Aat	5/32	1	2	FACETS	0.817	0.73	0.909	0.817	0.73	0.909	CLONAL	1	TRUE	1	0.404703541093452	2		693	587	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267848	46267849	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	137	880	0	ENST00000371998.3:c.2615dup	p.Asn872LysfsTer23	p.N872Kfs*23	ENST00000371998		870	gta/gtAa	14/23	1	2	FACETS	0.864	0.786	0.945	0.864	0.786	0.945	CLONAL	1	TRUE	1	0.404703541093452	2		880	784	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52661365	52661365	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs145261114	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	107	542	0	ENST00000394830.3:c.1465A>G	p.Arg489Gly	p.R489G	ENST00000394830	NM_018313.4	489	Agg/Ggg	14/30	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.404703541093452	2		542	490	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430506	181430506	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	166	914	0	ENST00000325404.1:c.358A>G	p.Met120Val	p.M120V	ENST00000325404	NM_003106.3	120	Atg/Gtg	1/1	1	2	FACETS	0.896	0.823	0.972	0.896	0.823	0.972	CLONAL	1	TRUE	1	0.404703541093452	2		914	916	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503835	186503835	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	97	709	0	ENST00000323963.5:c.512A>G	p.Tyr171Cys	p.Y171C	ENST00000323963		171	tAc/tGc	5/11	1	2	FACETS	0.773	0.69	0.861	0.773	0.69	0.861	SUBCLONAL	1	TRUE	1	0.404703541093452	2		709	620	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447652	187447652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1473954844	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	117	760	1	ENST00000232014.4:c.541G>A	p.Ala181Thr	p.A181T	ENST00000232014	NM_001130845.1	181	Gcc/Acc	5/10	1	2	FACETS	0.715	0.644	0.789	0.715	0.644	0.789	SUBCLONAL	1	TRUE	1	0.404703541093452	2		761	809	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607174	189607174	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1478677560	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	147	1038	0	ENST00000264731.3:c.1553G>A	p.Gly518Glu	p.G518E	ENST00000264731	NM_003722.4	518	gGa/gAa	12/14	1	2	FACETS	0.747	0.681	0.816	0.747	0.681	0.816	SUBCLONAL	1	TRUE	1	0.404703541093452	2		1038	973	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549491	187549491	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs888946039	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	86	648	0	ENST00000441802.2:c.4627C>T	p.Arg1543Cys	p.R1543C	ENST00000441802	NM_005245.3	1543	Cgc/Tgc	9/27	1	2	FACETS	0.777	0.689	0.871	0.777	0.689	0.871	SUBCLONAL	1	TRUE	1	0.404703541093452	2		648	547	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149498364	149498364	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	144	963	2	ENST00000261799.4:c.2850del	p.Phe951SerfsTer28	p.F951Sfs*28	ENST00000261799	NM_002609.3	950	ccC/cc	21/23	1	2	FACETS	0.733	0.668	0.801	0.733	0.668	0.801	SUBCLONAL	1	TRUE	1	0.404703541093452	2		965	971	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158400	26158400	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs140899305	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	154	1055	2	ENST00000289316.2:c.3G>A	p.Met1?	p.M1?	ENST00000289316	NM_138720.2	1	atG/atA	1/2	1	2	FACETS	0.641	0.585	0.7	0.641	0.585	0.7	SUBCLONAL	1	TRUE	1	0.404703541093452	2		1057	1187	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815835	32815835	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs192572056	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	144	797	4	ENST00000354258.4:c.1781C>T	p.Thr594Met	p.T594M	ENST00000354258	NM_000593.5	594	aCg/aTg	8/11	1	2	FACETS	0.788	0.718	0.861	0.788	0.718	0.861	SUBCLONAL	1	TRUE	1	0.404703541093452	2		801	903	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528267	157528267	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554237811	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	164	876	0	ENST00000346085.5:c.5992G>T	p.Glu1998Ter	p.E1998*	ENST00000346085	NM_020732.3	1998	Gag/Tag	20/20	1	2	FACETS	0.944	0.867	1	0.944	0.867	1	CLONAL	1	TRUE	1	0.404703541093452	2		876	859	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2969704	2969705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	149	916	0	ENST00000396946.4:c.1574dup	p.His527AlafsTer11	p.H527Afs*11	ENST00000396946	NM_032415.4	525	aag/aaAg	12/25	1	2	FACETS	0.76	0.694	0.829	0.76	0.694	0.829	SUBCLONAL	1	TRUE	1	0.404703541093452	2		916	969	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845997	151845997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	242	843	0	ENST00000262189.6:c.13015C>T	p.His4339Tyr	p.H4339Y	ENST00000262189	NM_170606.2	4339	Cat/Tat	52/59	0.404703541093452	3	FACETS	0.809	0.757	0.862	0.809	0.757	0.862	CLONAL	2	TRUE	1	0.404703541093452	3		843	889	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859731	151859731	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	204	592	5	ENST00000262189.6:c.10931C>A	p.Pro3644His	p.P3644H	ENST00000262189	NM_170606.2	3644	cCt/cAt	43/59	0.404703541093452	3	FACETS	0.928	0.865	0.993	0.928	0.865	0.993	CLONAL	2	TRUE	1	0.404703541093452	3		597	653	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931783	68931783	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	145	641	0	ENST00000288368.4:c.214-1G>T		p.X72_splice	ENST00000288368	NM_024870.2	72			0.34048231387271	3	FACETS	0.848	0.779	0.92	0.848	0.779	0.92	CLONAL	2	TRUE	1	0.404703541093452	3		641	508	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989665	68989665	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	260	868	0	ENST00000288368.4:c.1603T>C	p.Phe535Leu	p.F535L	ENST00000288368	NM_024870.2	535	Ttt/Ctt	15/40	0.34048231387271	3	FACETS	0.821	0.77	0.873	0.821	0.77	0.873	CLONAL	2	TRUE	1	0.404703541093452	3		868	941	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981407	70981407	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs751042462	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	306	1026	1	ENST00000276594.2:c.689del	p.Pro230GlnfsTer64	p.P230Qfs*64	ENST00000276594	NM_024504.3	230	cCa/ca	2/8	0.34048231387271	3	FACETS	0.791	0.745	0.837	0.791	0.745	0.837	SUBCLONAL	2	TRUE	1	0.404703541093452	3		1027	1150	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97863996	97863996	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1351542759	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	110	729	1	ENST00000289081.3:c.1670A>G	p.Gln557Arg	p.Q557R	ENST00000289081	NM_000136.2	557	cAa/cGa	15/15	1	2	FACETS	0.78	0.701	0.863	0.78	0.701	0.863	SUBCLONAL	1	TRUE	1	0.404703541093452	2		730	697	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969436	44969436	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	101	384	0	ENST00000377967.4:c.4118T>C	p.Val1373Ala	p.V1373A	ENST00000377967	NM_021140.2	1373	gTg/gCg	28/29	1	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.404703541093452	1		384	327	SUCCESS
AR	367	MSKCC	GRCh37	X	66765299	66765299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781422644	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	135	433	0	ENST00000374690.3:c.311C>T	p.Pro104Leu	p.P104L	ENST00000374690	NM_000044.3	104	cCc/cTc	1/8	1	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.404703541093452	1		433	448	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534374	187534374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756482497	NA	P-0036852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	102	877	0	ENST00000441802.2:c.9352G>A	p.Val3118Met	p.V3118M	ENST00000441802	NM_005245.3	3118	Gtg/Atg	13/27	1	2	FACETS	0.749	0.67	0.832	0.749	0.67	0.832	SUBCLONAL	1	TRUE	1	0.404703541093452	2		877	673	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0036853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	247	738	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	0.858	0.808	0.909	1	0.996	1	CLONAL	3	TRUE	1	0.312993376393208	2		738	613	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864648	68864648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	61	244	0	ENST00000288368.4:c.19G>A	p.Gly7Arg	p.G7R	ENST00000288368	NM_024870.2	7	Gga/Aga	1/40	1	2	FACETS	1	0.898	1	1	0.981	1	CLONAL	2	TRUE	1	0.312993376393208	2		244	190	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	134	726	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.947	0.865	1	0.947	0.865	1	CLONAL	1	TRUE	1	0.535924649088839	2		726	528	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0036855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	308	624	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.535924649088839	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.535924649088839	3		624	675	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0036855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	221	876	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.535924649088839	2		876	772	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0036855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	109	362	1	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.535924649088839	2		363	363	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647124	2647124	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	109	482	0	ENST00000342085.4:c.1402G>C	p.Gly468Arg	p.G468R	ENST00000342085	NM_002613.4	468	Ggt/Cgt	13/14	1	2	FACETS	0.853	0.77	0.94	0.853	0.77	0.94	CLONAL	1	TRUE	1	0.535924649088839	2		482	477	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0036857-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	81	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.274842927565714	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.274842927565714	1		452	377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0036857-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	88	561	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.274842927565714	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.274842927565714	1		561	516	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0036857-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	130	354	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.274842927565714	2	FACETS	0.919	0.845	0.995	1	0.986	1	CLONAL	3	TRUE	0	0.274842927565714	2		354	343	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948044	178948044	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036857-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	56	290	0	ENST00000263967.3:c.2816A>G	p.Asp939Gly	p.D939G	ENST00000263967	NM_006218.2	939	gAt/gGt	20/21	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.274842927565714	2		290	356	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919820	96919820	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036857-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	49	432	0	ENST00000258439.3:c.443A>G	p.Tyr148Cys	p.Y148C	ENST00000258439	NM_001193304.2	148	tAt/tGt	4/4	1	2	FACETS	0.67	0.567	0.783	0.67	0.567	0.783	SUBCLONAL	1	TRUE	1	0.274842927565714	2		432	532	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	103	393	0	ENST00000397062.3:c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	NM_006164.4	34	Cga/Gga	2/5	0.175604691742987	2	FACETS	1	0.911	1	0.503	0.455	0.552	INDETERMINATE	1	TRUE	0	0.652414465337471	2		393	314	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412969	49412969	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	144	753	0	ENST00000418115.1:c.54G>C	p.Lys18Asn	p.K18N	ENST00000418115	NM_001664.2	18	aaG/aaC	2/5	0.175604691742987	2	FACETS	1	0.942	1	0.514	0.473	0.557	INDETERMINATE	1	TRUE	0	0.652414465337471	2		753	429	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445170	49445170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	36	795	0	ENST00000301067.7:c.2296G>A	p.Glu766Lys	p.E766K	ENST00000301067	NM_003482.3	766	Gag/Aag	10/54	0.268542410612665	3	FACETS	0.369	0.303	0.442	0.184	0.151	0.221	INDETERMINATE	1	TRUE	1	0.652414465337471	3		795	397	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445521	49445521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	30	833	0	ENST00000301067.7:c.1945G>A	p.Glu649Lys	p.E649K	ENST00000301067	NM_003482.3	649	Gag/Aag	10/54	0.268542410612665	3	FACETS	0.356	0.287	0.434	0.178	0.143	0.217	INDETERMINATE	1	TRUE	1	0.652414465337471	3		833	343	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271978	15271978	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	101	699	1	ENST00000263388.2:c.6461G>T	p.Gly2154Val	p.G2154V	ENST00000263388	NM_000435.2	2154	gGa/gTa	33/33	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.652414465337471	2		700	294	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933647	49933647	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	88	908	0	ENST00000296474.3:c.2630A>G	p.Glu877Gly	p.E877G	ENST00000296474	NM_002447.2	877	gAg/gGg	10/20	0.175604691742987	2	FACETS	0.798	0.714	0.887	0.399	0.357	0.444	INDETERMINATE	1	TRUE	0	0.652414465337471	2		908	338	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916938	+	inframe_deletion	In_Frame_Del	DEL	GTG	GTG	-	novel	NA	P-0036863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	81	479	0	ENST00000263967.3:c.323_325del	p.Arg108_Glu109delinsGln	p.R108_E109delinsQ	ENST00000263967	NM_006218.2	108	cGTGaa/caa	2/21	0.175604691742987	2	FACETS	0.845	0.752	0.941	0.422	0.376	0.471	INDETERMINATE	1	TRUE	0	0.652414465337471	2		479	294	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864390	151864390	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0036863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	149	595	1	ENST00000262189.6:c.9591T>A	p.Tyr3197Ter	p.Y3197*	ENST00000262189	NM_170606.2	3197	taT/taA	42/59	0.268542410612665	3	FACETS	0.759	0.701	0.818	0.759	0.701	0.818	INDETERMINATE	2	TRUE	1	0.652414465337471	3		596	399	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0036868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	206	763	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.858	0.801	0.917	0.858	0.801	0.917	CLONAL	1	TRUE	1	0.763149778780504	2		765	629	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602493	10602493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	200	647	0	ENST00000171111.5:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000171111	NM_203500.1	362	cGg/cAg	3/6	1	2	FACETS	0.878	0.819	0.939	0.878	0.819	0.939	CLONAL	1	TRUE	1	0.763149778780504	2		647	597	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0036868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	47	278	0	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	2	FACETS	0.589	0.503	0.682	0.589	0.503	0.682	SUBCLONAL	1	TRUE	1	0.763149778780504	2		278	209	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0036868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	47	260	3	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.607	0.518	0.702	0.607	0.518	0.702	SUBCLONAL	1	TRUE	1	0.763149778780504	2		263	203	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772037	135772037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs796053461	NA	P-0036868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	203	452	2	ENST00000298552.3:c.3080G>A	p.Arg1027Gln	p.R1027Q	ENST00000298552	NM_001162426.1	1027	cGg/cAg	23/23	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.763149778780504	2		454	500	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0036868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	316	430	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.763149778780504	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.763149778780504	2		430	403	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099312	157099312	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	45	306	0	ENST00000346085.5:c.249G>C	p.Gln83His	p.Q83H	ENST00000346085	NM_020732.3	83	caG/caC	1/20	1	2	FACETS	0.279	0.235	0.329	0.279	0.235	0.329	SUBCLONAL	1	TRUE	1	0.763149778780504	2		306	422	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602619	10602619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	231	679	0	ENST00000171111.5:c.959G>A	p.Arg320Gln	p.R320Q	ENST00000171111	NM_203500.1	320	cGg/cAg	3/6	1	2	FACETS	0.856	0.802	0.912	0.856	0.802	0.912	CLONAL	1	TRUE	1	0.763149778780504	2		679	707	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560464	95560464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	195	522	0	ENST00000393063.1:c.5125G>A	p.Asp1709Asn	p.D1709N	ENST00000393063	NM_030621.3	1709	Gat/Aat	25/28	1	2	FACETS	0.875	0.815	0.936	0.875	0.815	0.936	CLONAL	1	TRUE	1	0.763149778780504	2		522	584	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0036868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	19	406	4	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	1	2	FACETS	0.15	0.113	0.193	0.15	0.113	0.193	SUBCLONAL	1	TRUE	1	0.763149778780504	2		410	332	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347484	91347484	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	161	530	2	ENST00000355112.3:c.3651del	p.Lys1217AsnfsTer62	p.K1217Nfs*62	ENST00000355112	NM_000057.2	1216	Aaa/aa	19/22	1	2	FACETS	0.787	0.727	0.85	0.787	0.727	0.85	SUBCLONAL	1	TRUE	1	0.763149778780504	2		532	536	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630626	158630626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912678	NA	P-0036868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	69	210	0	ENST00000263640.3:c.617G>A	p.Arg206His	p.R206H	ENST00000263640	NM_001105.4	206	cGc/cAc	6/11	1	2	FACETS	0.857	0.759	0.959	0.857	0.759	0.959	CLONAL	1	TRUE	1	0.763149778780504	2		210	211	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	292	883	4	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.886	0.836	0.936	0.886	0.836	0.936	CLONAL	1	TRUE	1	0.763149778780504	2		887	864	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466022	69466024	+	inframe_deletion	In_Frame_Del	DEL	CCA	CCA	-	novel	NA	P-0036868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	254	675	0	ENST00000227507.2:c.862_864del	p.Thr288del	p.T288del	ENST00000227507	NM_053056.2	287	cCCAcc/ccc	5/5	1	2	FACETS	0.946	0.89	1	0.946	0.89	1	CLONAL	1	TRUE	1	0.763149778780504	2		675	704	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101181	27101181	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0036868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	223	638	0	ENST00000324856.7:c.4463C>G	p.Ser1488Ter	p.S1488*	ENST00000324856	NM_006015.4	1488	tCa/tGa	18/20	1	2	FACETS	0.969	0.909	1	0.969	0.909	1	CLONAL	1	TRUE	1	0.763149778780504	2		638	603	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274749	123274750	+	protein_altering_variant	In_Frame_Ins	INS	-	-	TAT	novel	NA	P-0036868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	245	602	0	ENST00000358487.5:c.1168_1169insATA	p.Cys390delinsTyrSer	p.C390delinsYS	ENST00000358487	NM_000141.4	390	tgt/tATAgt	9/18	0.763149778780504	2	FACETS	0.943	0.886	1	0.471	0.443	0.501	CLONAL	1	TRUE	0	0.763149778780504	2		602	681	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505399	125505399	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	17	355	0	ENST00000428830.2:c.689C>A	p.Pro230His	p.P230H	ENST00000428830	NM_001114121.2	230	cCt/cAt	7/14	1	2	FACETS	0.15	0.111	0.195	0.15	0.111	0.195	SUBCLONAL	1	TRUE	1	0.763149778780504	2		355	298	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271630	15271630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148716935	NA	P-0036868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	319	936	0	ENST00000263388.2:c.6809C>T	p.Thr2270Met	p.T2270M	ENST00000263388	NM_000435.2	2270	aCg/aTg	33/33	1	2	FACETS	0.886	0.838	0.934	0.886	0.838	0.934	CLONAL	1	TRUE	1	0.763149778780504	2		936	944	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229205	36229205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	234	632	0	ENST00000222270.7:c.7895G>A	p.Arg2632His	p.R2632H	ENST00000222270	NM_014727.1	2632	cGc/cAc	37/37	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.763149778780504	2		632	600	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951933	178951933	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	33	517	0	ENST00000263967.3:c.2988T>A	p.Asn996Lys	p.N996K	ENST00000263967	NM_006218.2	996	aaT/aaA	21/21	1	2	FACETS	0.221	0.179	0.267	0.221	0.179	0.267	SUBCLONAL	1	TRUE	1	0.763149778780504	2		517	392	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182679091	182679091	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs200237071	NA	P-0036868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	95	562	0	ENST00000292782.4:c.443T>C	p.Leu148Ser	p.L148S	ENST00000292782	NM_020640.2	148	tTg/tCg	4/7	1	2	FACETS	0.609	0.545	0.675	0.609	0.545	0.675	SUBCLONAL	1	TRUE	1	0.763149778780504	2		562	409	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539966	187539966	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs770591336	NA	P-0036868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	57	471	0	ENST00000441802.2:c.7774A>G	p.Asn2592Asp	p.N2592D	ENST00000441802	NM_005245.3	2592	Aat/Gat	10/27	1	2	FACETS	0.288	0.247	0.333	0.288	0.247	0.333	SUBCLONAL	1	TRUE	1	0.763149778780504	2		471	518	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591064	67591092	+	protein_altering_variant	In_Frame_Del	DEL	GCAGCTGAGTATCGAGAAATTGACAAACG	GCAGCTGAGTATCGAGAAATTGACAAACG	CT	novel	NA	P-0036868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	72	271	1	ENST00000274335.5:c.1657_1685delinsCT	p.Ala553_Arg562delinsLeu	p.A553_R562delinsL	ENST00000274335		553	GCAGCTGAGTATCGAGAAATTGACAAACGt/CTt	12/15	1	2	FACETS	0.943	0.84	1	0.943	0.84	1	CLONAL	1	TRUE	1	0.763149778780504	2		272	200	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8338930	8338930	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	136	495	0	ENST00000356435.5:c.5371G>A	p.Asp1791Asn	p.D1791N	ENST00000356435		1791	Gat/Aat	32/35	1	2	FACETS	0.9	0.827	0.975	0.9	0.827	0.975	CLONAL	1	TRUE	1	0.763149778780504	2		495	396	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410036	63410036	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	61	639	0	ENST00000330258.3:c.3131T>C	p.Met1044Thr	p.M1044T	ENST00000330258	NM_152424.3	1044	aTg/aCg	2/2	1	2	FACETS	0.288	0.248	0.331	0.288	0.248	0.331	SUBCLONAL	1	TRUE	1	0.763149778780504	2		639	556	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0036874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	155	469	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.67079501201294	3	FACETS	0.95	0.885	1	0.95	0.885	1	CLONAL	2	TRUE	1	0.672820754886311	3		469	324	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610436	215610449	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAATCCTCACCTGT	AAATCCTCACCTGT	-	novel	NA	P-0036874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	60	377	0	ENST00000260947.4:c.1807_1810+10del		p.X603_splice	ENST00000260947	NM_000465.2	603		8/11	1	2	FACETS	0.991	0.87	1	0.991	0.87	1	CLONAL	1	TRUE	1	0.672820754886311	2		377	180	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0036879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	21	405	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.757	0.582	0.961	0.757	0.582	0.961	CLONAL	1	TRUE	1	0.15	2		405	370	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692910	89692910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	34	465	1	ENST00000371953.3:c.394G>A	p.Gly132Ser	p.G132S	ENST00000371953	NM_000314.4	132	Ggt/Agt	5/9	1	2	FACETS	0.867	0.707	1	0.867	0.707	1	CLONAL	1	TRUE	1	0.15	2		466	523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579488	7579489	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0036879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	63	644	0	ENST00000269305.4:c.198dup	p.Pro67AlafsTer82	p.P67Afs*82	ENST00000269305	NM_001126112.2	66	-/G	4/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.15	2		644	712	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0036890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	73	359	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.218389586621293	5	FACETS	0.951	0.84	1	0.634	0.56	0.712	INDETERMINATE	2	TRUE	2	0.428973021967629	5		359	294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579433	7579433	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1064793279	NA	P-0036890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	60	626	0	ENST00000269305.4:c.254del	p.Pro85LeufsTer38	p.P85Lfs*38	ENST00000269305	NM_001126112.2	85	cCt/ct	4/11	0.428973021967629	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.428973021967629	1		626	171	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198246	138198246	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200840068	NA	P-0036890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	75	369	0	ENST00000237289.4:c.839G>A	p.Arg280Gln	p.R280Q	ENST00000237289	NM_001270507.1	280	cGg/cAg	6/9	0.428973021967629	6	FACETS	0.892	0.787	1			1	CLONAL	2	TRUE	NA	0.428973021967629	6		369	364	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574314	95574314	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	43	434	0	ENST00000393063.1:c.2553G>C	p.Gln851His	p.Q851H	ENST00000393063	NM_030621.3	851	caG/caC	17/28	0.286419677645135	6	FACETS	0.927	0.777	1	0.232	0.194	0.273	CLONAL	1	TRUE	2	0.428973021967629	6		434	402	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198240	138198240	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173687713	NA	P-0036890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	77	361	1	ENST00000237289.4:c.833G>A	p.Arg278Lys	p.R278K	ENST00000237289	NM_001270507.1	278	aGa/aAa	6/9	0.428973021967629	6	FACETS	0.926	0.819	1			1	CLONAL	2	TRUE	NA	0.428973021967629	6		362	360	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412727	63412727	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	14	584	0	ENST00000330258.3:c.440T>C	p.Val147Ala	p.V147A	ENST00000330258	NM_152424.3	147	gTg/gCg	2/2	0.251383187024462	1	FACETS	0.248	0.179	0.331	0.248	0.179	0.331	INDETERMINATE	1	TRUE	0	0.428973021967629	1		584	207	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0036891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	36	359	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.139319821948026	3	FACETS	0.859	0.707	1	0.43	0.353	0.515	INDETERMINATE	1	TRUE	1	0.24	3		359	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0036891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	31	278	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	1	2	FACETS	0.82	0.665	0.995	0.82	0.665	0.995	CLONAL	1	TRUE	1	0.24	2		278	315	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732946	30732946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	21	183	0	ENST00000295754.5:c.1559G>T	p.Cys520Phe	p.C520F	ENST00000295754	NM_003242.5	520	tGc/tTc	7/7	1	2	FACETS	0.641	0.494	0.812	0.641	0.494	0.812	SUBCLONAL	1	TRUE	1	0.24	2		183	273	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0036892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	86	321	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.922	0.822	1	0.922	0.822	1	CLONAL	1	TRUE	1	0.532986571088322	2		321	350	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0036892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	32	469	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.305	0.247	0.37	0.305	0.247	0.37	SUBCLONAL	1	TRUE	1	0.532986571088322	2		469	394	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0036892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	18	490	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.17	0.127	0.221	0.17	0.127	0.221	SUBCLONAL	1	TRUE	1	0.532986571088322	2		490	397	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0036892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	66	530	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.532986571088322	2		530	229	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554630	63554630	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555583747	NA	P-0036892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	110	367	0	ENST00000307078.5:c.109C>T	p.Gln37Ter	p.Q37*	ENST00000307078	NM_004655.3	37	Cag/Tag	2/11	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.532986571088322	2		367	403	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589527	69589527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	15	52	0	ENST00000168712.1:c.326C>T	p.Ala109Val	p.A109V	ENST00000168712	NM_002007.2	109	gCg/gTg	1/3	1	2	FACETS	0.97	0.732	1	0.97	0.732	1	CLONAL	1	TRUE	1	0.532986571088322	2		52	58	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755506	39755506	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	22	355	0	ENST00000288319.7:c.1259C>T	p.Ser420Phe	p.S420F	ENST00000288319	NM_182918.3	420	tCc/tTc	10/10	1	2	FACETS	0.267	0.207	0.337	0.267	0.207	0.337	SUBCLONAL	1	TRUE	1	0.532986571088322	2		355	309	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808938	3808938	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	138	441	0	ENST00000262367.5:c.3286C>T	p.Pro1096Ser	p.P1096S	ENST00000262367	NM_004380.2	1096	Cca/Tca	17/31	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.532986571088322	2		441	502	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028656	12028656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	85	383	0	ENST00000353533.5:c.859C>T	p.Arg287Cys	p.R287C	ENST00000353533	NM_003010.3	287	Cgc/Tgc	8/11	0.532986571088322	1	FACETS	0.845	0.756	0.937	0.845	0.756	0.937	CLONAL	1	TRUE	0	0.532986571088322	1		383	277	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707606	176707606	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	115	408	0	ENST00000439151.2:c.5663A>G	p.Asp1888Gly	p.D1888G	ENST00000439151	NM_022455.4	1888	gAc/gGc	18/23	1	2	FACETS	0.974	0.884	1	0.974	0.884	1	CLONAL	1	TRUE	1	0.532986571088322	2		408	443	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722132	176722132	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	41	370	0	ENST00000439151.2:c.7763A>T	p.Gln2588Leu	p.Q2588L	ENST00000439151	NM_022455.4	2588	cAa/cTa	23/23	1	2	FACETS	0.42	0.351	0.497	0.42	0.351	0.497	SUBCLONAL	1	TRUE	1	0.532986571088322	2		370	366	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0036893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	167	381	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.453440523638196	2	FACETS	1	0.988	1	0.674	0.624	0.726	CLONAL	1	TRUE	0	0.48384083830478	2		381	512	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16001793	16001793	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0036893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	31	498	0	ENST00000268712.3:c.2708C>G	p.Ser903Ter	p.S903*	ENST00000268712	NM_006311.3	903	tCa/tGa	21/46	1	2	FACETS	0.304	0.246	0.371	0.304	0.246	0.371	SUBCLONAL	1	TRUE	1	0.48384083830478	2		498	421	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348849	89348849	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	56	399	0	ENST00000301030.4:c.4101G>C	p.Lys1367Asn	p.K1367N	ENST00000301030	NM_001256183.1	1367	aaG/aaC	9/13	0.28007647993643	1	FACETS	0.469	0.403	0.54	0.469	0.403	0.54	INDETERMINATE	1	TRUE	0	0.48384083830478	1		399	374	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	495101	495101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201821956	NA	P-0036893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	34	309	0	ENST00000399788.2:c.205C>T	p.Arg69Cys	p.R69C	ENST00000399788	NM_001042603.1	69	Cgt/Tgt	2/28	0.453440523638196	2	FACETS	0.378	0.309	0.455	0.189	0.154	0.228	SUBCLONAL	1	TRUE	0	0.48384083830478	2		309	372	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483100	29483100	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1060500330	NA	P-0036893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	124	334	0	ENST00000356175.3:c.160G>T	p.Val54Phe	p.V54F	ENST00000356175	NM_000267.3	54	Gtt/Ttt	2/57	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.48384083830478	2		334	455	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187803	11187804	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0036893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	91	354	0	ENST00000361445.4:c.6093_6094delinsTT	p.Glu2032Ter	p.E2032*	ENST00000361445	NM_004958.3	2031	ctGGaa/ctTTaa	44/58	1	2	FACETS	0.995	0.89	1	0.995	0.89	1	CLONAL	1	TRUE	1	0.48384083830478	2		354	378	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468423	120468423	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	95	333	0	ENST00000256646.2:c.4016G>T	p.Gly1339Val	p.G1339V	ENST00000256646	NM_024408.3	1339	gGg/gTg	25/34	1	2	FACETS	0.944	0.846	1	0.944	0.846	1	CLONAL	1	TRUE	1	0.48384083830478	2		333	416	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226590028	226590028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	34	359	0	ENST00000366794.5:c.173G>A	p.Trp58Ter	p.W58*	ENST00000366794	NM_001618.3	58	tGg/tAg	2/23	1	2	FACETS	0.329	0.269	0.397	0.329	0.269	0.397	SUBCLONAL	1	TRUE	1	0.48384083830478	2		359	427	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534803	18534803	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	138	264	0	ENST00000266497.5:c.1861G>T	p.Val621Leu	p.V621L	ENST00000266497		621	Gtg/Ttg	12/31	0.453440523638196	2	FACETS	0.905	0.837	0.974	0.905	0.837	0.974	CLONAL	2	TRUE	0	0.48384083830478	2		264	315	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32903615	32903615	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	46	372	0	ENST00000380152.3:c.667C>G	p.His223Asp	p.H223D	ENST00000380152		223	Cat/Gat	8/27	0.48384083830478	1	FACETS	0.432	0.365	0.505	0.432	0.365	0.505	SUBCLONAL	1	TRUE	0	0.48384083830478	1		372	334	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572824	41572825	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	45	370	0	ENST00000263253.7:c.5113dup	p.Met1705AsnfsTer10	p.M1705Nfs*10	ENST00000263253	NM_001429.3	1703	-/A	31/31	1	2	FACETS	0.454	0.382	0.533	0.454	0.382	0.533	SUBCLONAL	1	TRUE	1	0.48384083830478	2		370	410	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0036894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	19	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.649	0.493	0.832	0.649	0.493	0.832	SUBCLONAL	1	FALSE	1	0.217003576133385	2		452	270	SUCCESS
APC	324	MSKCC	GRCh37	5	112175162	112175162	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561588104	NA	P-0036894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	37	137	0	ENST00000257430.4:c.3871C>T	p.Gln1291Ter	p.Q1291*	ENST00000257430	NM_000038.5	1291	Cag/Tag	16/16	0.217003576133385	3	FACETS	0.788	0.654	0.935	0.525	0.436	0.623	CLONAL	2	FALSE	0	0.217003576133385	3		137	240	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577049	7577049	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	209	640	1	ENST00000269305.4:c.889del	p.His297ThrfsTer48	p.H297Tfs*48	ENST00000269305	NM_001126112.2	297	Cac/ac	8/11	0.161787068056589	3	FACETS	0.959	0.912	1			1	INDETERMINATE	3	TRUE	NA	0.587027386615468	3		641	320	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120479955	120479955	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	100	514	0	ENST00000256646.2:c.3472T>C	p.Cys1158Arg	p.C1158R	ENST00000256646	NM_024408.3	1158	Tgc/Cgc	21/34	0.593004719587282	4	FACETS	1	0.95	1			1	CLONAL	1	TRUE	NA	0.587027386615468	4		514	493	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248527	8248527	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	76	490	0	ENST00000335790.3:c.360C>G	p.Asn120Lys	p.N120K	ENST00000335790	NM_002315.2	120	aaC/aaG	3/4	0.593004719587282	3	FACETS	0.974	0.86	1	0.487	0.43	0.547	CLONAL	1	TRUE	1	0.587027386615468	3		490	344	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89354962	89354962	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	88	551	1	ENST00000301030.4:c.718G>T	p.Asp240Tyr	p.D240Y	ENST00000301030	NM_001256183.1	240	Gac/Tac	7/13	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.587027386615468	2		552	293	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257898	19257898	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	99	637	0	ENST00000162023.5:c.488C>G	p.Ala163Gly	p.A163G	ENST00000162023		163	gCc/gGc	9/13	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.587027386615468	2		637	296	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593540	215593545	+	inframe_deletion	In_Frame_Del	DEL	AGCGCT	AGCGCT	-	novel	NA	P-0036895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	80	345	0	ENST00000260947.4:c.2189_2194del	p.Gln730_Phe732delinsLeu	p.Q730_F732delinsL	ENST00000260947	NM_000465.2	730	cAGCGCTtc/ctc	11/11	0.587027386615468	6	FACETS	1	0.924	1			1	CLONAL	1	TRUE	NA	0.587027386615468	6		345	557	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155184	106155184	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	94	329	0	ENST00000380013.4:c.85C>G	p.Pro29Ala	p.P29A	ENST00000380013	NM_001127208.2	29	Cct/Gct	3/11	0.531990199250191	3	FACETS	0.809	0.732	0.889	0.539	0.488	0.593	CLONAL	2	TRUE	0	0.587027386615468	3		329	256	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149447890	149447890	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	93	509	0	ENST00000286301.3:c.1514C>A	p.Ala505Asp	p.A505D	ENST00000286301	NM_005211.3	505	gCc/gAc	11/22	0.302443185231163	4	FACETS	1	0.973	1	0.423	0.379	0.47	INDETERMINATE	1	TRUE	1	0.587027386615468	4		509	396	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0036902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	42	530	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.649	0.543	0.767	0.649	0.543	0.767	SUBCLONAL	1	TRUE	1	0.317820469971666	2		530	407	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578538	7578538	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1131691037	NA	P-0036902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	191	861	1	ENST00000269305.4:c.392A>T	p.Asn131Ile	p.N131I	ENST00000269305	NM_001126112.2	131	aAc/aTc	5/11	0.317820469971666	1	FACETS	0.844	0.779	0.912	0.844	0.779	0.912	CLONAL	1	TRUE	0	0.317820469971666	1		862	1198	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0036904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	98	327	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.434706805364414	2	FACETS	1	0.944	1	0.538	0.483	0.596	CLONAL	1	TRUE	0	0.434706805364414	2		327	419	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0036904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	174	876	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	1	2	FACETS	0.867	0.799	0.939	0.867	0.799	0.939	CLONAL	1	TRUE	1	0.434706805364414	2		876	923	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0036904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	161	460	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.434706805364414	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.434706805364414	2		460	347	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0036904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	59	563	0	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	0.434706805364414	2	FACETS	0.406	0.349	0.469	0.203	0.174	0.235	SUBCLONAL	1	TRUE	0	0.434706805364414	2		563	668	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0036904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	31	449	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	0.366	0.296	0.445	0.366	0.296	0.445	SUBCLONAL	1	TRUE	1	0.434706805364414	2		449	390	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105586	27105586	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	158	488	0	ENST00000324856.7:c.5197G>T	p.Glu1733Ter	p.E1733*	ENST00000324856	NM_006015.4	1733	Gag/Tag	20/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.434706805364414	2		488	687	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023401	27023401	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	120	445	0	ENST00000324856.7:c.508del	p.His170ThrfsTer62	p.H170Tfs*62	ENST00000324856	NM_006015.4	169	ttC/tt	1/20	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.434706805364414	2		445	517	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338671	70338671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	113	556	0	ENST00000374080.3:c.67G>T	p.Asp23Tyr	p.D23Y	ENST00000374080		23	Gat/Tat	1/45	1	2	FACETS	0.809	0.729	0.892	0.809	0.729	0.892	CLONAL	1	TRUE	1	0.434706805364414	2		556	643	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981816	101981827	+	inframe_deletion	In_Frame_Del	DEL	CGTGCCCCAGAC	CGTGCCCCAGAC	-	novel	NA	P-0036904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	86	615	0	ENST00000282441.5:c.244_255del	p.Gln82_Pro85del	p.Q82_P85del	ENST00000282441	NM_001130145.2	79	aaCGTGCCCCAGACc/aac	1/9	1	2	FACETS	0.503	0.445	0.566	0.503	0.445	0.566	SUBCLONAL	1	TRUE	1	0.434706805364414	2		615	786	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466025	69466028	+	protein_altering_variant	In_Frame_Del	DEL	CCGA	CCGA	G	novel	NA	P-0036904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	136	698	0	ENST00000227507.2:c.863_866delinsG	p.Thr288_Asp289delinsSer	p.T288_D289delinsS	ENST00000227507	NM_053056.2	288	aCCGAc/aGc	5/5	1	2	FACETS	0.822	0.748	0.9	0.822	0.748	0.9	CLONAL	1	TRUE	1	0.434706805364414	2		698	761	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573738	64573738	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	31	632	2	ENST00000312049.6:c.1015C>T	p.Gln339Ter	p.Q339*	ENST00000312049	NM_130799.2	339	Cag/Tag	7/10	0.642612480203812	2	FACETS	0.211	0.17	0.257	0.106	0.085	0.129	SUBCLONAL	1	TRUE	0	0.642612480203812	2		634	457	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289016	33289016	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	271	685	0	ENST00000374542.5:c.536del	p.Pro179GlnfsTer50	p.P179Qfs*50	ENST00000374542	NM_001141970.1	179	cCa/ca	3/8	0.636096377333294	2	FACETS	0.948	0.904	0.99	0.948	0.904	0.99	CLONAL	2	TRUE	0	0.642612480203812	2		685	445	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574514	64574534	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGGGGTGGGCTCCAGCTCC	CCAGGGGTGGGCTCCAGCTCC	A	novel	NA	P-0036906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	169	695	0	ENST00000312049.6:c.861_881delinsT	p.Glu287AspfsTer23	p.E287Dfs*23	ENST00000312049	NM_130799.2	287	gaGGAGCTGGAGCCCACCCCTGGc/gaTc	6/10	0.642612480203812	2	FACETS	1	0.988	1	0.651	0.606	0.697	CLONAL	1	TRUE	0	0.642612480203812	2		695	404	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0036908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	33	669	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	0.69	0.56	0.838	0.69	0.56	0.838	SUBCLONAL	1	TRUE	1	0.14	2		669	683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0036908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	41	906	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	1	2	FACETS	0.58	0.481	0.692	0.58	0.481	0.692	SUBCLONAL	1	TRUE	1	0.14	2		906	1009	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059206	27059207	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0036908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	37	445	0	ENST00000324856.7:c.1848dup	p.Ser617LeufsTer6	p.S617Lfs*6	ENST00000324856	NM_006015.4	615	gcc/gCcc	4/20	1	2	FACETS	0.768	0.632	0.922	0.768	0.632	0.922	CLONAL	1	TRUE	1	0.14	2		445	688	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0036916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	8	530	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.205	0.132	0.301	0.205	0.132	0.301	SUBCLONAL	1	TRUE	1	0.355705023251698	2		530	219	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0036916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	70	693	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	1	2	FACETS	0.967	0.847	1	0.967	0.847	1	CLONAL	1	TRUE	1	0.355705023251698	2		693	407	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0036916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	86	222	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.355705023251698	2	FACETS	0.822	0.736	0.912	0.822	0.736	0.912	CLONAL	2	TRUE	0	0.355705023251698	2		222	294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0036916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	73	301	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.355705023251698	2		301	347	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435907	49435907	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	35	333	0	ENST00000301067.7:c.6074A>G	p.Asn2025Ser	p.N2025S	ENST00000301067	NM_003482.3	2025	aAc/aGc	28/54	1	2	FACETS	0.459	0.376	0.552	0.459	0.376	0.552	SUBCLONAL	1	TRUE	1	0.355705023251698	2		333	429	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247224	153247224	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	43	253	0	ENST00000281708.4:c.1578G>T	p.Trp526Cys	p.W526C	ENST00000281708	NM_033632.3	526	tgG/tgT	10/12	1	2	FACETS	0.751	0.631	0.883	0.751	0.631	0.883	SUBCLONAL	1	TRUE	1	0.355705023251698	2		253	322	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718145	117718145	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	24	349	0	ENST00000368508.3:c.712A>C	p.Lys238Gln	p.K238Q	ENST00000368508	NM_002944.2	238	Aaa/Caa	7/43	1	2	FACETS	0.301	0.235	0.377	0.301	0.235	0.377	SUBCLONAL	1	TRUE	1	0.355705023251698	2		349	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0036917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	27	689	3	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	1	2	FACETS	0.551	0.439	0.679	0.551	0.439	0.679	SUBCLONAL	1	TRUE	1	0.29	2		692	338	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242483	55242506	+	inframe_deletion	In_Frame_Del	DEL	ATCTCCGAAAGCCAACAAGGAAAT	ATCTCCGAAAGCCAACAAGGAAAT	-	rs727504232	NA	P-0036917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	12	372	0	ENST00000275493.2:c.2253_2276del	p.Ser752_Ile759del	p.S752_I759del	ENST00000275493	NM_005228.3	751	acATCTCCGAAAGCCAACAAGGAAATc/acc	19/28	0.217679437238405	3	FACETS	0.337	0.236	0.462	0.169	0.118	0.231	SUBCLONAL	1	TRUE	1	0.29	3		372	281	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057911	27057911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs892173376	NA	P-0036917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	21	461	2	ENST00000324856.7:c.1619C>T	p.Thr540Met	p.T540M	ENST00000324856	NM_006015.4	540	aCg/aTg	3/20	1	2	FACETS	0.442	0.34	0.56	0.442	0.34	0.56	SUBCLONAL	1	TRUE	1	0.29	2		463	328	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0036918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	82	569	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.313389215609869	3	FACETS	1	0.966	1	0.801	0.716	0.888	CLONAL	2	FALSE	0	0.313389215609869	3		569	252	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352008	70352008	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	51	243	0	ENST00000374080.3:c.4205G>A	p.Ser1402Asn	p.S1402N	ENST00000374080		1402	aGt/aAt	30/45	0.313389215609869	2	FACETS	1	0.954	1			1	CLONAL	2	FALSE	NA	0.313389215609869	2		243	133	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243315	123243315	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	67	674	0	ENST00000358487.5:c.2198A>G	p.Tyr733Cys	p.Y733C	ENST00000358487	NM_000141.4	733	tAc/tGc	17/18	0.313389215609869	4	FACETS	0.968	0.849	1	0.968	0.849	1	CLONAL	2	FALSE	2	0.313389215609869	4		674	290	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857572	9857572	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	22	499	0	ENST00000330684.3:c.3829C>A	p.Leu1277Ile	p.L1277I	ENST00000330684	NM_001134407.1	1277	Ctt/Att	13/13	0.313389215609869	3	FACETS	0.855	0.666	1	0.427	0.333	0.536	CLONAL	1	FALSE	1	0.313389215609869	3		499	190	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481434	40481434	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	23	477	1	ENST00000264657.5:c.1275T>A	p.Asn425Lys	p.N425K	ENST00000264657	NM_139276.2	425	aaT/aaA	14/24	0.313389215609869	3	FACETS	0.738	0.578	0.922	0.369	0.289	0.461	CLONAL	1	FALSE	1	0.313389215609869	3		478	230	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597453	10597453	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	77	562	0	ENST00000171111.5:c.1750T>A	p.Tyr584Asn	p.Y584N	ENST00000171111	NM_203500.1	584	Tac/Aac	6/6	0.298182924801935	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	FALSE	0	0.313389215609869	2		562	230	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971024	21971024	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876660436	NA	P-0036918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	36	200	0	ENST00000304494.5:c.334C>G	p.Arg112Gly	p.R112G	ENST00000304494	NM_000077.4	112	Cgt/Ggt	2/3	0.298182924801935	2	FACETS	1	0.903	1	1	0.965	1	CLONAL	3	FALSE	0	0.313389215609869	2		200	72	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0036921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	85	569	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.952	0.847	1	0.952	0.847	1	CLONAL	1	TRUE	1	0.455755954587736	2		569	392	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0036921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	84	321	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.347778080071359	3	FACETS	1	0.974	1	0.664	0.591	0.74	CLONAL	1	TRUE	1	0.455755954587736	3		321	341	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0036921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	78	619	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.455755954587736	1	FACETS	0.864	0.766	0.966	0.864	0.766	0.966	CLONAL	1	TRUE	0	0.455755954587736	1		619	306	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0036921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	11	286	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.411870577478227	0	FACETS	0.148	0.102	0.205			1	SUBCLONAL	1	TRUE	0	0.455755954587736	0		286	177	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175481	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0036921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	67	354	0	ENST00000257430.4:c.4192_4193del	p.Arg1399PhefsTer9	p.R1399Ffs*9	ENST00000257430	NM_000038.5	1397	GAg/g	16/16	0.347778080071359	3	FACETS	1	0.913	1	0.528	0.461	0.599	CLONAL	1	TRUE	1	0.455755954587736	3		354	342	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535309	66535309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	54	382	0	ENST00000273854.3:c.152G>A	p.Arg51Gln	p.R51Q	ENST00000273854	NM_004439.5	51	cGg/cAg	1/18	1	2	FACETS	0.926	0.798	1	0.926	0.798	1	CLONAL	1	TRUE	1	0.455755954587736	2		382	256	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040640	47040640	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	82	490	0	ENST00000377604.3:c.1275G>A	p.Trp425Ter	p.W425*	ENST00000377604	NM_001204468.1	425	tgG/tgA	13/24	0.192375306187994	1	FACETS	0.86	0.766	0.96	0.86	0.766	0.96	INDETERMINATE	1	TRUE	0	0.455755954587736	1		490	323	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479838	67479838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779602560	NA	P-0036921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	71	457	2	ENST00000327367.4:c.1145C>T	p.Ala382Val	p.A382V	ENST00000327367	NM_005902.3	382	gCg/gTg	8/9	0.455755954587736	1	FACETS	0.962	0.851	1	0.962	0.851	1	CLONAL	1	TRUE	0	0.455755954587736	1		459	250	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273029	55273029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770749711	NA	P-0036921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	82	540	1	ENST00000275493.2:c.3352G>A	p.Ala1118Thr	p.A1118T	ENST00000275493	NM_005228.3	1118	Gcg/Acg	28/28	0.400813394537047	3	FACETS	0.98	0.868	1	0.49	0.434	0.55	CLONAL	1	TRUE	1	0.455755954587736	3		541	451	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717690	89717691	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTACTT	novel	NA	P-0036921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	51	447	0	ENST00000371953.3:c.718_724dup	p.Glu242ValfsTer3	p.E242Vfs*3	ENST00000371953	NM_000314.4	239	atg/aTGTACTTtg	7/9	0.455755954587736	1	FACETS	0.726	0.623	0.836	0.726	0.623	0.836	SUBCLONAL	1	TRUE	0	0.455755954587736	1		447	238	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390719	118390719	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	87	410	0	ENST00000534358.1:c.11369A>C	p.Gln3790Pro	p.Q3790P	ENST00000534358	NM_005933.3	3790	cAg/cCg	33/36	1	2	FACETS	0.992	0.884	1	0.992	0.884	1	CLONAL	1	TRUE	1	0.455755954587736	2		410	385	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663896	29663896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	92	483	0	ENST00000356175.3:c.6328C>T	p.His2110Tyr	p.H2110Y	ENST00000356175	NM_000267.3	2110	Cac/Tac	41/57	NA	2	FACETS	1	0.916	1			1	INDETERMINATE	1	TRUE	NA	0.455755954587736	2		483	393	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0036922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	53	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.971	0.828	1	0.971	0.828	1	CLONAL	1	FALSE	1	0.202149090408882	2		452	540	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246227	46246227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	53	305	0	ENST00000334344.6:c.4321C>T	p.Gln1441Ter	p.Q1441*	ENST00000334344	NM_152641.2	1441	Caa/Taa	15/21	1	2	FACETS	0.986	0.841	1	0.986	0.841	1	CLONAL	1	FALSE	1	0.202149090408882	2		305	532	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219349	1219353	+	frameshift_variant	Frame_Shift_Del	DEL	GTGGC	GTGGC	-	novel	NA	P-0036922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	70	310	0	ENST00000326873.7:c.401_405del	p.Cys134TyrfsTer27	p.C134Yfs*27	ENST00000326873	NM_000455.4	134	tGTGGC/t	3/10	0.202149090408882	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	0	0.202149090408882	1		310	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	88	611	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.887497063959439	3	FACETS	0.878	0.786	0.975			1	CLONAL	1	TRUE	NA	0.887497063959439	3		611	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579529	7579529	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658483	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	185	398	0	ENST00000269305.4:c.158G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tGg/tAg	4/11	0.887497063959439	3	FACETS	0.929	0.875	0.982			1	CLONAL	2	TRUE	NA	0.887497063959439	3		398	324	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434791	99434791	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	85	345	0	ENST00000268035.6:c.878C>T	p.Ser293Phe	p.S293F	ENST00000268035	NM_000875.3	293	tCc/tTc	3/21	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.887497063959439	2		345	174	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653865	89653865	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	57	326	0	ENST00000371953.3:c.163A>T	p.Arg55Trp	p.R55W	ENST00000371953	NM_000314.4	55	Agg/Tgg	2/9	1	2	FACETS	0.973	0.86	1	0.973	0.86	1	CLONAL	1	TRUE	1	0.887497063959439	2		326	132	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120478170	120478170	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	109	368	0	ENST00000256646.2:c.3580C>T	p.Gln1194Ter	p.Q1194*	ENST00000256646	NM_024408.3	1194	Cag/Tag	22/34	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.887497063959439	2		368	237	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259389	89259389	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	78	394	0	ENST00000336596.2:c.533G>A	p.Gly178Glu	p.G178E	ENST00000336596	NM_005233.5	178	gGa/gAa	3/17	0.879508130646498	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.887497063959439	1		394	86	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708063	117708063	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868430526	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	60	295	0	ENST00000368508.3:c.2114G>A	p.Gly705Glu	p.G705E	ENST00000368508	NM_002944.2	705	gGa/gAa	14/43	NA	2	FACETS	1	0.927	1			1	INDETERMINATE	1	TRUE	NA	0.887497063959439	2		295	128	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857547	9857547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367543132	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	71	395	0	ENST00000330684.3:c.3854G>A	p.Arg1285Lys	p.R1285K	ENST00000330684	NM_001134407.1	1285	aGg/aAg	13/13	1	2	FACETS	0.894	0.798	0.992	0.894	0.798	0.992	CLONAL	1	TRUE	1	0.887497063959439	2		395	179	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947540	48947540	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	85	390	0	ENST00000267163.4:c.1128-1G>A		p.X376_splice	ENST00000267163	NM_000321.2	376			0.887497063959439	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.887497063959439	1		390	97	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437115	110437115	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1450781846	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	20	41	0	ENST00000375856.3:c.1286G>T	p.Arg429Leu	p.R429L	ENST00000375856	NM_003749.2	429	cGc/cTc	1/2	1	2	FACETS	0.98	0.79	1	0.98	0.79	1	CLONAL	1	TRUE	1	0.887497063959439	2		41	46	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675047	40675047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	89	315	1	ENST00000249776.8:c.11C>T	p.Pro4Leu	p.P4L	ENST00000249776	NM_033286.3	4	cCc/cTc	1/9	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.887497063959439	2		316	181	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980352	201980352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	84	412	0	ENST00000359651.3:c.88C>T	p.Pro30Ser	p.P30S	ENST00000359651		30	Ccc/Tcc	1/8	0.887497063959439	3	FACETS	0.905	0.808	1	0.452	0.404	0.503	CLONAL	1	TRUE	1	0.887497063959439	3		412	302	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395129	139395129	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	79	389	0	ENST00000277541.6:c.5809C>G	p.Arg1937Gly	p.R1937G	ENST00000277541	NM_017617.3	1937	Cgc/Ggc	31/34	1	2	FACETS	0.927	0.834	1	0.927	0.834	1	CLONAL	1	TRUE	1	0.887497063959439	2		389	192	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246567	46246567	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	79	209	0	ENST00000334344.6:c.4661T>C	p.Val1554Ala	p.V1554A	ENST00000334344	NM_152641.2	1554	gTt/gCt	15/21	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.887497063959439	2		209	176	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776089	9776089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	93	408	0	ENST00000377346.4:c.553C>T	p.Leu185Phe	p.L185F	ENST00000377346	NM_005026.3	185	Ctc/Ttc	5/24	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.887497063959439	2		408	202	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175952	176175952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1358618553	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	27	47	0	ENST00000367669.3:c.163G>A	p.Ala55Thr	p.A55T	ENST00000367669	NM_022457.5	55	Gcc/Acc	1/20	0.887497063959439	3	FACETS	1	0.949	1	0.744	0.622	0.87	CLONAL	1	TRUE	1	0.887497063959439	3		47	59	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607564	43607564	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	87	375	0	ENST00000355710.3:c.1540G>A	p.Gly514Ser	p.G514S	ENST00000355710	NM_020975.4	514	Ggc/Agc	8/20	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.887497063959439	2		375	195	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444933	49444934	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	109	310	2	ENST00000301067.7:c.2532_2533delinsTT	p.Arg845Trp	p.R845W	ENST00000301067	NM_003482.3	844	ccCCgg/ccTTgg	10/54	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.887497063959439	2		312	219	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2221290	2221291	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	91	385	1	ENST00000326181.6:c.374_375delinsTT	p.Pro125Leu	p.P125L	ENST00000326181	NM_032271.2	125	cCC/cTT	6/21	1	2	FACETS	0.945	0.857	1	0.945	0.857	1	CLONAL	1	TRUE	1	0.887497063959439	2		386	217	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786141	3786179	+	inframe_deletion	In_Frame_Del	DEL	CTTCAAAATAGGGCAGTTCCTTGGCACTGGTGAGCCTGT	CTTCAAAATAGGGCAGTTCCTTGGCACTGGTGAGCCTGT	-	novel	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	82	420	0	ENST00000262367.5:c.4586_4624del	p.Asp1529_Glu1541del	p.D1529_E1541del	ENST00000262367	NM_004380.2	1529	gACAGGCTCACCAGTGCCAAGGAACTGCCCTATTTTGAAGgt/ggt	28/31	1	2	FACETS	0.948	0.854	1	0.948	0.854	1	CLONAL	1	TRUE	1	0.887497063959439	2		420	195	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992788	72992789	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	93	326	1	ENST00000268489.5:c.1256_1257delinsTT	p.Pro419Leu	p.P419L	ENST00000268489	NM_006885.3	419	cCC/cTT	2/10	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.887497063959439	2		327	182	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357057	89357057	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	105	338	0	ENST00000301030.4:c.577G>T	p.Asp193Tyr	p.D193Y	ENST00000301030	NM_001256183.1	193	Gac/Tac	6/13	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.887497063959439	2		338	224	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770113	56770113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	97	345	3	ENST00000337432.4:c.109G>A	p.Glu37Lys	p.E37K	ENST00000337432	NM_058216.2	37	Gaa/Aaa	1/9	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.887497063959439	2		348	193	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222098	2222099	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	180	379	1	ENST00000398665.3:c.2930_2931delinsTT	p.Thr977Ile	p.T977I	ENST00000398665	NM_032482.2	977	aCC/aTT	24/28	0.524805970116612	4	FACETS	0.902	0.853	0.949			1	INDETERMINATE	3	TRUE	NA	0.887497063959439	4		380	283	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122898	7122898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	69	362	0	ENST00000302850.5:c.3361G>A	p.Glu1121Lys	p.E1121K	ENST00000302850	NM_000208.2	1121	Gag/Aag	18/22	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.887497063959439	2		362	145	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098392	11098392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745462998	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	83	257	0	ENST00000358026.2:c.910C>T	p.Pro304Ser	p.P304S	ENST00000358026	NM_001128849.1	304	Ccc/Tcc	6/36	1	2	FACETS	0.995	0.899	1	0.995	0.899	1	CLONAL	1	TRUE	1	0.887497063959439	2		257	188	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50138992	50138992	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs199540462	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	88	413	0	ENST00000246792.3:c.571C>T	p.Arg191Trp	p.R191W	ENST00000246792	NM_006270.3	191	Cgg/Tgg	5/6	1	2	FACETS	0.803	0.723	0.885	0.803	0.723	0.885	CLONAL	1	TRUE	1	0.887497063959439	2		413	247	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965284	25965284	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61745460	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	96	329	0	ENST00000435504.4:c.3922C>T	p.Leu1308Phe	p.L1308F	ENST00000435504		1308	Ctt/Ttt	13/13	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.887497063959439	2		329	193	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978897	25978904	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTTCCT	TCTTTCCT	-	novel	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	68	276	0	ENST00000435504.4:c.1019_1026del	p.Lys340ThrfsTer5	p.K340Tfs*5	ENST00000435504		340	aAGGAAAGA/a	10/13	1	2	FACETS	0.815	0.723	0.91	0.815	0.723	0.91	CLONAL	1	TRUE	1	0.887497063959439	2		276	188	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225449667	225449668	+	missense_variant	Missense_Mutation	DNP	GG	GG	CA	novel	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	38	171	1	ENST00000264414.4:c.59_60delinsTG	p.Ala20Val	p.A20V	ENST00000264414	NM_003590.4	20	gCC/gTG	1/16	1	2	FACETS	0.8	0.68	0.926	0.8	0.68	0.926	CLONAL	1	TRUE	1	0.887497063959439	2		172	107	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561309	9561310	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	51	331	0	ENST00000353224.5:c.472_473delinsTT	p.Pro158Leu	p.P158L	ENST00000353224	NM_177990.2	158	CCg/TTg	4/10	0.887497063959439	3	FACETS	0.783	0.674	0.899	0.391	0.337	0.45	SUBCLONAL	1	TRUE	1	0.887497063959439	3		331	212	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171709	36171709	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	84	304	1	ENST00000300305.3:c.856C>T	p.Gln286Ter	p.Q286*	ENST00000300305		286	Caa/Taa	7/8	1	2	FACETS	0.976	0.882	1	0.976	0.882	1	CLONAL	1	TRUE	1	0.887497063959439	2		305	194	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610605	52610605	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	96	382	0	ENST00000394830.3:c.3568G>T	p.Val1190Leu	p.V1190L	ENST00000394830	NM_018313.4	1190	Gta/Tta	23/30	0.879508130646498	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.887497063959439	1		382	112	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73108268	73108268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748641752	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	41	176	0	ENST00000356692.5:c.368G>A	p.Arg123Lys	p.R123K	ENST00000356692		123	aGa/aAa	4/9	0.879508130646498	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.887497063959439	1		176	50	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644721	134644721	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs759393707	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	173	355	0	ENST00000398015.3:c.122G>A	p.Gly41Glu	p.G41E	ENST00000398015	NM_004441.4	41	gGg/gAg	2/16	0.887497063959439	3	FACETS	0.932	0.877	0.986	0.932	0.877	0.986	CLONAL	2	TRUE	1	0.887497063959439	3		355	302	SUCCESS
ATR	545	MSKCC	GRCh37	3	142183937	142183937	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	66	298	0	ENST00000350721.4:c.7041+2T>C		p.X2347_splice	ENST00000350721	NM_001184.3	2347			0.887497063959439	3	FACETS	1	0.916	1	0.524	0.462	0.588	CLONAL	1	TRUE	1	0.887497063959439	3		298	205	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522632	176522632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	90	418	0	ENST00000292408.4:c.1729C>T	p.Pro577Ser	p.P577S	ENST00000292408	NM_213647.1	577	Cct/Tct	13/18	1	2	FACETS	0.943	0.854	1	0.943	0.854	1	CLONAL	1	TRUE	1	0.887497063959439	2		418	215	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030248	180030248	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	103	411	0	ENST00000261937.6:c.4036G>A	p.Glu1346Lys	p.E1346K	ENST00000261937	NM_182925.4	1346	Gag/Aag	30/30	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.887497063959439	2		411	212	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032021	26032022	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	63	251	1	ENST00000244661.2:c.267_268delinsAA	p.Val90Met	p.V90M	ENST00000244661	NM_003537.3	89	gcGGtg/gcAAtg	1/1	0.283396209330293	4	FACETS	1	0.974	1	0.732	0.646	0.822	INDETERMINATE	1	TRUE	2	0.887497063959439	4		252	183	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124438	94124438	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	51	361	0	ENST00000369303.4:c.145T>A	p.Ser49Thr	p.S49T	ENST00000369303	NM_004440.3	49	Tcc/Acc	2/17	1	2	FACETS	0.898	0.785	1	0.898	0.785	1	CLONAL	1	TRUE	1	0.887497063959439	2		361	128	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231056	98231056	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	98	381	0	ENST00000331920.6:c.2227T>G	p.Phe743Val	p.F743V	ENST00000331920	NM_000264.3	743	Ttc/Gtc	14/24	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.887497063959439	2		381	205	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128347856	128347856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	76	389	0	ENST00000265960.3:c.649G>A	p.Glu217Lys	p.E217K	ENST00000265960	NM_001006617.1	217	Gaa/Aaa	5/12	1	2	FACETS	0.979	0.88	1	0.979	0.88	1	CLONAL	1	TRUE	1	0.887497063959439	2		389	175	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760588	133760589	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	87	413	1	ENST00000318560.5:c.2911_2912delinsTT	p.Pro971Leu	p.P971L	ENST00000318560	NM_005157.4	971	CCg/TTg	11/11	1	2	FACETS	0.966	0.874	1	0.966	0.874	1	CLONAL	1	TRUE	1	0.887497063959439	2		414	203	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225449668	225449668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	38	172	0	ENST00000264414.4:c.59C>T	p.Ala20Val	p.A20V	ENST00000264414	NM_003590.4	20	gCc/gTc	1/16	1	2	FACETS	0.8	0.68	0.926	0.8	0.68	0.926	CLONAL	1	TRUE	1	0.887497063959439	2		172	107	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	171	726	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.792763630972514	1	FACETS	0.901	0.848	0.953	0.901	0.848	0.953	CLONAL	1	TRUE	0	0.794485603346862	1		726	288	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654642	67654642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	30	319	2	ENST00000264010.4:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000264010	NM_006565.3	377	Cgt/Tgt	6/12	0.794485603346862	1	FACETS	0.159	0.128	0.193	0.159	0.128	0.193	SUBCLONAL	1	TRUE	0	0.794485603346862	1		321	287	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	28	354	0	ENST00000206249.3:c.1607T>C	p.Leu536Pro	p.L536P	ENST00000206249	NM_000125.3	536	cTc/cCc	8/8	0.792763630972514	1	FACETS	0.143	0.114	0.176	0.143	0.114	0.176	SUBCLONAL	1	TRUE	0	0.794485603346862	1		354	297	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796080	78796080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	132	258	0	ENST00000306801.3:c.970G>A	p.Ala324Thr	p.A324T	ENST00000306801	NM_020761.2	324	Gcg/Acg	8/34	1	2	FACETS	0.884	0.811	0.958	0.884	0.811	0.958	CLONAL	1	TRUE	1	0.794485603346862	2		258	376	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874601	35874601	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	27	359	0	ENST00000303115.3:c.757G>C	p.Val253Leu	p.V253L	ENST00000303115	NM_002185.3	253	Gtc/Ctc	6/8	1	2	FACETS	0.142	0.113	0.176	0.142	0.113	0.176	SUBCLONAL	1	TRUE	1	0.794485603346862	2		359	478	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771903	135771903	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	30	327	0	ENST00000298552.3:c.3214G>T	p.Ala1072Ser	p.A1072S	ENST00000298552	NM_001162426.1	1072	Gcc/Tcc	23/23	1	2	FACETS	0.162	0.13	0.198	0.162	0.13	0.198	SUBCLONAL	1	TRUE	1	0.794485603346862	2		327	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0036936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	108	404	0	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	0.42118472830033	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.42118472830033	2		404	230	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120181	70120182	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CG	novel	NA	P-0036936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	68	202	0	ENST00000245479.2:c.1185_1186dup	p.His396ArgfsTer8	p.H396Rfs*8	ENST00000245479	NM_000346.3	395	acg/aCGcg	3/3	0.42118472830033	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.42118472830033	3		202	161	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591888	48591888	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519739	NA	P-0036936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	33	371	0	ENST00000342988.3:c.1051G>C	p.Asp351His	p.D351H	ENST00000342988	NM_005359.5	351	Gat/Cat	9/12	0.42118472830033	1	FACETS	0.847	0.701	1	0.847	0.701	1	CLONAL	1	TRUE	0	0.42118472830033	1		371	146	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184830	32184830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150609093	NA	P-0036936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	33	316	0	ENST00000375023.3:c.1753C>T	p.Arg585Cys	p.R585C	ENST00000375023	NM_004557.3	585	Cgc/Tgc	11/30	0.42118472830033	3	FACETS	0.878	0.721	1	0.439	0.36	0.527	CLONAL	1	TRUE	1	0.42118472830033	3		316	216	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114724367	114724368	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0036936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	53	307	0	ENST00000543371.1:c.436dup	p.Gln146ProfsTer15	p.Q146Pfs*15	ENST00000543371	NM_001198531.1	145	cac/caCc	4/14	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.42118472830033	2		307	241	SUCCESS
APC	324	MSKCC	GRCh37	5	112154977	112154977	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0036936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	102	389	0	ENST00000257430.4:c.1248C>G	p.Tyr416Ter	p.Y416*	ENST00000257430	NM_000038.5	416	taC/taG	10/16	0.42118472830033	2	FACETS	0.984	0.897	1	0.984	0.897	1	CLONAL	2	TRUE	0	0.42118472830033	2		389	246	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528648	157528648	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	35	363	0	ENST00000346085.5:c.6373C>A	p.Pro2125Thr	p.P2125T	ENST00000346085	NM_020732.3	2125	Cca/Aca	20/20	0.42118472830033	3	FACETS	0.732	0.602	0.875	0.366	0.301	0.438	SUBCLONAL	1	TRUE	1	0.42118472830033	3		363	275	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114724370	114724370	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	53	303	0	ENST00000543371.1:c.437A>G	p.Gln146Arg	p.Q146R	ENST00000543371	NM_001198531.1	146	cAg/cGg	4/14	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.42118472830033	2		303	232	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0036937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	111	331	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.998	0.908	1	0.998	0.908	1	CLONAL	1	TRUE	1	0.66	2		331	337	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856060	45856060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913024	NA	P-0036937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	147	483	0	ENST00000391945.4:c.1846C>T	p.Arg616Trp	p.R616W	ENST00000391945	NM_000400.3	616	Cgg/Tgg	20/23	1	2	FACETS	0.831	0.763	0.901	0.831	0.763	0.901	CLONAL	1	TRUE	1	0.66	2		483	536	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931992	39931993	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	TT	novel	NA	P-0036937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	124	326	0	ENST00000378444.4:c.2606_2607insAA	p.Tyr869Ter	p.Y869*	ENST00000378444	NM_001123385.1	869	tat/taAAt	4/15	0.188351836295804	2	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.66	2		326	313	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144906	47144906	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1064794751	NA	P-0036937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	14	352	0	ENST00000409792.3:c.4847A>T	p.Asp1616Val	p.D1616V	ENST00000409792	NM_014159.6	1616	gAt/gTt	7/21	1	2	FACETS	0.18	0.13	0.24	0.18	0.13	0.24	SUBCLONAL	1	TRUE	1	0.66	2		352	236	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948284	71948284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs569099732	NA	P-0036938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	206	586	0	ENST00000298229.2:c.2996C>T	p.Pro999Leu	p.P999L	ENST00000298229	NM_001567.3	999	cCg/cTg	26/28	0.685394309131251	4	FACETS	1	0.949	1			1	CLONAL	1	TRUE	NA	0.813257070692165	4		586	895	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436354	110436354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	82	210	1	ENST00000375856.3:c.2047G>A	p.Val683Met	p.V683M	ENST00000375856	NM_003749.2	683	Gtg/Atg	1/2	0.813257070692165	1	FACETS	0.973	0.898	1	0.973	0.898	1	CLONAL	1	TRUE	0	0.813257070692165	1		211	123	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0036939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	95	357	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.355222328885583	2		357	468	SUCCESS
APC	324	MSKCC	GRCh37	5	112175925	112175925	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs863225356	NA	P-0036939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	43	176	0	ENST00000257430.4:c.4634C>A	p.Ser1545Ter	p.S1545*	ENST00000257430	NM_000038.5	1545	tCa/tAa	16/16	0.355222328885583	1	FACETS	0.986	0.834	1	0.986	0.834	1	CLONAL	1	TRUE	0	0.355222328885583	1		176	202	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099968	27099968	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	105	387	0	ENST00000324856.7:c.3847G>C	p.Gly1283Arg	p.G1283R	ENST00000324856	NM_006015.4	1283	Ggt/Cgt	15/20	1	2	FACETS	0.968	0.869	1	0.968	0.869	1	CLONAL	1	TRUE	1	0.355222328885583	2		387	611	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682571	37682593	+	splice_donor_variant,intron_variant	Splice_Site	DEL	TAAACAGACCGGTCATGAATCTC	TAAACAGACCGGTCATGAATCTC	-	novel	NA	P-0036939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	54	144	0	ENST00000447079.4:c.3760+2_3760+24del		p.X1254_splice	ENST00000447079	NM_015083.1	1254			1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.355222328885583	2		144	252	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216321	2216321	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	139	549	0	ENST00000398665.3:c.1965G>T	p.Glu655Asp	p.E655D	ENST00000398665	NM_032482.2	655	gaG/gaT	20/28	1	2	FACETS	0.956	0.87	1	0.956	0.87	1	CLONAL	1	TRUE	1	0.355222328885583	2		549	819	SUCCESS
APC	324	MSKCC	GRCh37	5	112170810	112170810	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	110	463	0	ENST00000257430.4:c.1906G>C	p.Gly636Arg	p.G636R	ENST00000257430	NM_000038.5	636	Ggt/Cgt	15/16	0.355222328885583	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.355222328885583	1		463	474	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218849	36218849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753899619	NA	P-0036989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	114	638	1	ENST00000222270.7:c.4460G>A	p.Arg1487His	p.R1487H	ENST00000222270	NM_014727.1	1487	cGc/cAc	18/37	1	2	FACETS	0.678	0.613	0.747	0.678	0.613	0.747	SUBCLONAL	1	TRUE	1	0.596115430788532	2		639	564	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222163	2222163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	164	749	0	ENST00000398665.3:c.2995C>T	p.Pro999Ser	p.P999S	ENST00000398665	NM_032482.2	999	Cct/Tct	24/28	1	2	FACETS	0.72	0.662	0.781	0.72	0.662	0.781	SUBCLONAL	1	TRUE	1	0.596115430788532	2		749	764	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40739804	40739804	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	203	773	0	ENST00000392038.2:c.1421C>T	p.Ser474Phe	p.S474F	ENST00000392038	NM_001626.4	474	tCc/tTc	14/14	1	2	FACETS	0.945	0.879	1	0.945	0.879	1	CLONAL	1	TRUE	1	0.596115430788532	2		773	721	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47600707	47600707	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	54	337	0	ENST00000263735.4:c.182A>C	p.Lys61Thr	p.K61T	ENST00000263735	NM_002354.2	61	aAg/aCg	2/9	1	2	FACETS	0.365	0.312	0.423	0.365	0.312	0.423	SUBCLONAL	1	TRUE	1	0.596115430788532	2		337	496	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158094	106158094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	38	229	0	ENST00000380013.4:c.2995G>A	p.Glu999Lys	p.E999K	ENST00000380013	NM_001127208.2	999	Gaa/Aaa	3/11	1	2	FACETS	0.455	0.378	0.541	0.455	0.378	0.541	SUBCLONAL	1	TRUE	1	0.596115430788532	2		229	280	SUCCESS
APC	324	MSKCC	GRCh37	5	112175141	112175141	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	31	205	0	ENST00000257430.4:c.3850G>A	p.Glu1284Lys	p.E1284K	ENST00000257430	NM_000038.5	1284	Gaa/Aaa	16/16	1	2	FACETS	0.562	0.459	0.677	0.562	0.459	0.677	SUBCLONAL	1	TRUE	1	0.596115430788532	2		205	185	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271357	26271357	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	45	417	0	ENST00000305910.3:c.256C>T	p.Gln86Ter	p.Q86*	ENST00000305910	NM_003534.2	86	Cag/Tag	1/1	0.415894461988522	1	FACETS	0.282	0.237	0.331	0.282	0.237	0.331	SUBCLONAL	1	TRUE	0	0.596115430788532	1		417	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0036990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	264	504	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.479441746038807	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.479441746038807	2		505	534	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0036990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	98	631	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	0.165539384532553	5	FACETS	0.976	0.879	1	0.651	0.586	0.719	INDETERMINATE	2	TRUE	2	0.479441746038807	5		631	360	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14015969	14015969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760327512	NA	P-0036990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	76	300	0	ENST00000311895.7:c.289C>T	p.Arg97Cys	p.R97C	ENST00000311895	NM_005236.2	97	Cgc/Tgc	2/11	0.341471038694229	5	FACETS	1	0.941	1	0.727	0.646	0.811	CLONAL	2	TRUE	2	0.479441746038807	5		300	250	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692907	89692907	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	116	447	0	ENST00000371953.3:c.391A>C	p.Thr131Pro	p.T131P	ENST00000371953	NM_000314.4	131	Act/Cct	5/9	0.479441746038807	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.479441746038807	2		447	217	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163759	47163763	+	frameshift_variant	Frame_Shift_Del	DEL	TTTGG	TTTGG	-	novel	NA	P-0036991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	119	490	0	ENST00000409792.3:c.2363_2367del	p.Thr788ArgfsTer11	p.T788Rfs*11	ENST00000409792	NM_014159.6	788	aCCAAA/a	3/21	1	2	FACETS	0.889	0.812	0.967	0.889	0.812	0.967	CLONAL	1	TRUE	1	0.792260108821389	2		490	338	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136853	55136853	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	7738	397	0	ENST00000257290.5:c.1175A>G	p.Tyr392Cys	p.Y392C	ENST00000257290	NM_006206.4	392	tAt/tGt	8/23	0.792260108821389	60	FACETS	0.996	0.993	0.999			1	CLONAL	58	TRUE	NA	0.792260108821389	60		397	8108	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20488446	20488446	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	92	325	1	ENST00000346618.3:c.1102C>A	p.His368Asn	p.H368N	ENST00000346618	NM_001949.4	368	Cac/Aac	6/7	1	2	FACETS	0.88	0.794	0.969	0.88	0.794	0.969	CLONAL	1	TRUE	1	0.792260108821389	2		326	264	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180305	32180305	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs941106697	NA	P-0036991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	178	581	1	ENST00000375023.3:c.2626G>A	p.Gly876Arg	p.G876R	ENST00000375023	NM_004557.3	876	Ggg/Agg	17/30	0.285525146847551	1	FACETS	0.596	0.555	0.638	0.596	0.555	0.638	INDETERMINATE	1	TRUE	0	0.792260108821389	1		582	455	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0036998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	48	263	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.827	0.704	0.96	1	0.968	1	CLONAL	2	FALSE	1	0.214977785621607	2		263	270	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0036998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	54	259	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.214977785621607	2		259	335	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0036998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	77	327	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	0.986	1	CLONAL	2	FALSE	1	0.214977785621607	2		327	295	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717704	89717704	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	120	364	0	ENST00000371953.3:c.731del	p.Pro244LeufsTer12	p.P244Lfs*12	ENST00000371953	NM_000314.4	243	ttC/tt	7/9	1	2	FACETS	1	0.962	1	1	0.99	1	CLONAL	2	FALSE	1	0.214977785621607	2		364	501	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101750	71101751	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	89	241	0	ENST00000318789.4:c.447dup	p.Gln150ThrfsTer20	p.Q150Tfs*20	ENST00000318789	NM_032682.5	149	-/A	9/21	1	2	FACETS	0.988	0.881	1	1	0.986	1	CLONAL	2	FALSE	1	0.214977785621607	2		241	419	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720858	89720858	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1564568660	NA	P-0036998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	123	267	0	ENST00000371953.3:c.1012del	p.Ser338LeufsTer6	p.S338Lfs*6	ENST00000371953	NM_000314.4	337	Ttt/tt	8/9	1	2	FACETS	1	0.97	1	1	0.991	1	CLONAL	2	FALSE	1	0.214977785621607	2		267	496	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235819	108235819	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs767507047	NA	P-0036998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	84	341	0	ENST00000278616.4:c.8861A>G	p.Tyr2954Cys	p.Y2954C	ENST00000278616	NM_000051.3	2954	tAt/tGt	62/63	1	2	FACETS	0.965	0.857	1	1	0.984	1	CLONAL	2	FALSE	1	0.214977785621607	2		341	405	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972794	25972794	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761581753	NA	P-0036998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	73	427	0	ENST00000435504.4:c.1631C>T	p.Ala544Val	p.A544V	ENST00000435504		544	gCg/gTg	12/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.214977785621607	2		427	561	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178541	56178541	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	67	221	0	ENST00000399503.3:c.3514A>C	p.Asn1172His	p.N1172H	ENST00000399503	NM_005921.1	1172	Aat/Cat	14/20	1	2	FACETS	1	0.944	1	1	0.983	1	CLONAL	2	FALSE	1	0.214977785621607	2		221	275	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946779	71946779	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs933270129	NA	P-0037000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	121	568	1	ENST00000298229.2:c.2720G>A	p.Arg907Gln	p.R907Q	ENST00000298229	NM_001567.3	907	cGa/cAa	24/28	1	2	FACETS	0.428	0.386	0.472	0.428	0.386	0.472	SUBCLONAL	1	TRUE	1	0.722259862220397	2		569	783	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0037000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	79	569	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.42454853528418	1	FACETS	0.336	0.297	0.378	0.336	0.297	0.378	INDETERMINATE	1	TRUE	0	0.722259862220397	1		569	416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0037000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	262	588	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.719237188978204	1	FACETS	0.978	0.93	1	0.978	0.93	1	CLONAL	1	TRUE	0	0.722259862220397	1		588	474	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610575	215610575	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	155	409	0	ENST00000260947.4:c.1681A>G	p.Asn561Asp	p.N561D	ENST00000260947	NM_000465.2	561	Aac/Gac	8/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.722259862220397	2		409	390	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182662920	182662920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	203	513	1	ENST00000292782.4:c.742C>T	p.Arg248Cys	p.R248C	ENST00000292782	NM_020640.2	248	Cgc/Tgc	7/7	0.42454853528418	1	FACETS	0.796	0.747	0.846	0.796	0.747	0.846	INDETERMINATE	1	TRUE	0	0.722259862220397	1		514	451	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532678	187532678	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777770871	NA	P-0037000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	202	470	0	ENST00000441802.2:c.9715G>A	p.Val3239Met	p.V3239M	ENST00000441802	NM_005245.3	3239	Gtg/Atg	14/27	0.722259862220397	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.722259862220397	1		470	333	SUCCESS
APC	324	MSKCC	GRCh37	5	112137082	112137082	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0037000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	64	246	0	ENST00000257430.4:c.834+2T>G		p.X278_splice	ENST00000257430	NM_000038.5	278			0.357467693068447	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.722259862220397	0		246	215	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0037000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	66	288	1	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.357467693068447	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.722259862220397	0		289	191	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777993	27777993	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	98	366	0	ENST00000369163.2:c.142G>T	p.Ala48Ser	p.A48S	ENST00000369163	NM_003536.2	48	Gct/Tct	1/1	1	2	FACETS	0.533	0.477	0.592	0.533	0.477	0.592	SUBCLONAL	1	TRUE	1	0.722259862220397	2		366	509	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	70	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.915	0.801	1	0.915	0.801	1	CLONAL	1	TRUE	1	0.357549247063213	2		452	428	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	81	431	2	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.852	0.752	0.958	0.852	0.752	0.958	CLONAL	1	TRUE	1	0.357549247063213	2		433	532	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	13	381	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.17	0.12	0.23	0.17	0.12	0.23	SUBCLONAL	1	TRUE	1	0.357549247063213	2		381	429	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	52	485	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.357549247063213	1	FACETS	0.763	0.653	0.882	0.763	0.653	0.882	SUBCLONAL	1	TRUE	0	0.357549247063213	1		486	313	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024505	16024505	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	100	492	3	ENST00000268712.3:c.1713del	p.Arg572GlufsTer18	p.R572Efs*18	ENST00000268712	NM_006311.3	571	ggG/gg	16/46	1	2	FACETS	0.966	0.865	1	0.966	0.865	1	CLONAL	1	TRUE	1	0.357549247063213	2		495	579	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738669	145738669	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs34293591	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	159	699	2	ENST00000428558.2:c.2395G>A	p.Val799Met	p.V799M	ENST00000428558	NM_004260.3	799	Gtg/Atg	15/22	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.357549247063213	2		701	806	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654820	29654820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786203416	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	61	354	0	ENST00000356175.3:c.5509G>A	p.Ala1837Thr	p.A1837T	ENST00000356175	NM_000267.3	1837	Gca/Aca	37/57	1	2	FACETS	0.812	0.703	0.93	0.812	0.703	0.93	CLONAL	1	TRUE	1	0.357549247063213	2		354	420	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980849	40980849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs548511212	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	93	511	1	ENST00000373198.4:c.1637G>A	p.Arg546Gln	p.R546Q	ENST00000373198	NM_133170.3	546	cGg/cAg	10/32	1	2	FACETS	0.842	0.749	0.94	0.842	0.749	0.94	CLONAL	1	TRUE	1	0.357549247063213	2		512	618	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727483	66727483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504317	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	77	416	0	ENST00000307102.5:c.199G>A	p.Asp67Asn	p.D67N	ENST00000307102	NM_002755.3	67	Gac/Aac	2/11	0.357549247063213	1	FACETS	0.9	0.795	1	0.9	0.795	1	CLONAL	1	TRUE	0	0.357549247063213	1		416	393	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821959	72821960	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs762108866	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	52	380	1	ENST00000268489.5:c.10215dup	p.Gly3406ArgfsTer25	p.G3406Rfs*25	ENST00000268489	NM_006885.3	3405	-/C	10/10	1	2	FACETS	0.725	0.619	0.841	0.725	0.619	0.841	SUBCLONAL	1	TRUE	1	0.357549247063213	2		381	401	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287889	33287891	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs749346133	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	66	599	1	ENST00000374542.5:c.1362_1364del	p.Glu457del	p.E457del	ENST00000374542	NM_001141970.1	454	gaAGAg/gag	5/8	1	2	FACETS	0.568	0.493	0.65	0.568	0.493	0.65	SUBCLONAL	1	TRUE	1	0.357549247063213	2		600	650	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482926	140482927	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs777474487	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	107	885	6	ENST00000288602.6:c.1208dup	p.Ala404CysfsTer9	p.A404Cfs*9	ENST00000288602	NM_004333.4	403	cct/ccCt	10/18	1	2	FACETS	0.97	0.872	1	0.97	0.872	1	CLONAL	1	TRUE	1	0.357549247063213	2		891	617	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154241	2154242	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755455183	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	90	681	1	ENST00000434045.2:c.686dup	p.Glu230ArgfsTer50	p.E230Rfs*50	ENST00000434045	NM_001127598.1	229	cca/ccCa	5/5	1	2	FACETS	0.737	0.654	0.826	0.737	0.654	0.826	SUBCLONAL	1	TRUE	1	0.357549247063213	2		682	683	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591135	67591136	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	35	252	0	ENST00000274335.5:c.1732_1733del	p.Asp578ProfsTer23	p.D578Pfs*23	ENST00000274335		576	acGAga/acga	12/15	1	2	FACETS	0.739	0.609	0.883	0.739	0.609	0.883	SUBCLONAL	1	TRUE	1	0.357549247063213	2		252	265	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851941	128851943	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs767361434	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	91	632	0	ENST00000249373.3:c.2021_2023del	p.Lys674del	p.K674del	ENST00000249373	NM_005631.4	671	cgGAAg/cgg	12/12	1	2	FACETS	0.742	0.659	0.831	0.742	0.659	0.831	SUBCLONAL	1	TRUE	1	0.357549247063213	2		632	686	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40460234	40460234	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	99	503	0	ENST00000345506.4:c.1945C>T	p.Arg649Trp	p.R649W	ENST00000345506	NM_003152.3	649	Cgg/Tgg	17/20	1	2	FACETS	0.817	0.73	0.909	0.817	0.73	0.909	CLONAL	1	TRUE	1	0.357549247063213	2		503	678	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727501	88727501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147992979	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	126	546	2	ENST00000360948.2:c.278C>T	p.Thr93Met	p.T93M	ENST00000360948	NM_001012338.2	93	aCg/aTg	3/19	0.357549247063213	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.357549247063213	1		548	485	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512370	38512370	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567767560	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	72	648	1	ENST00000254066.5:c.1286del	p.Gly429ValfsTer214	p.G429Vfs*214	ENST00000254066	NM_000964.3	427	ccG/cc	9/9	1	2	FACETS	0.594	0.519	0.675	0.594	0.519	0.675	SUBCLONAL	1	TRUE	1	0.357549247063213	2		649	678	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	111	763	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.929	0.837	1	0.929	0.837	1	CLONAL	1	TRUE	1	0.357549247063213	2		765	668	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752695	42752695	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1366176199	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	118	558	1	ENST00000222329.4:c.1569del	p.Leu525SerfsTer6	p.L525Sfs*6	ENST00000222329	NM_006494.2	523	ggG/gg	4/4	1	2	FACETS	0.966	0.873	1	0.966	0.873	1	CLONAL	1	TRUE	1	0.357549247063213	2		559	683	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939674	76939674	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	95	357	1	ENST00000373344.5:c.1074del	p.Lys358AsnfsTer2	p.K358Nfs*2	ENST00000373344	NM_000489.3	358	aaA/aa	9/35	1	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.357549247063213	1		358	354	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	149	560	2	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.357549247063213	2		562	773	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695815	117695815	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1443124633	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	106	475	0	ENST00000369458.3:c.622A>G	p.Met208Val	p.M208V	ENST00000369458	NM_024626.3	208	Atg/Gtg	4/6	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.357549247063213	2		475	585	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555611	21555611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573724179	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	119	531	0	ENST00000382592.4:c.2659C>T	p.Arg887Cys	p.R887C	ENST00000382592	NM_014572.2	887	Cgc/Tgc	6/8	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.357549247063213	2		531	647	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777114	9777114	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs754116182	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	141	666	1	ENST00000377346.4:c.883del	p.Gln295ArgfsTer39	p.Q295Rfs*39	ENST00000377346	NM_005026.3	293	gCc/gc	7/24	1	2	FACETS	0.983	0.897	1	0.983	0.897	1	CLONAL	1	TRUE	1	0.357549247063213	2		667	802	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800427	32800427	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111303994	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	162	846	0	ENST00000374899.4:c.1120G>A	p.Ala374Thr	p.A374T	ENST00000374899	NM_018833.2	374	Gcc/Acc	6/12	1	2	FACETS	0.896	0.822	0.975	0.896	0.822	0.975	CLONAL	1	TRUE	1	0.357549247063213	2		846	1011	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60795958	60795958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369294037	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	86	418	0	ENST00000333681.4:c.620G>A	p.Arg207Gln	p.R207Q	ENST00000333681		207	cGg/cAg	3/3	1	2	FACETS	0.864	0.766	0.968	0.864	0.766	0.968	CLONAL	1	TRUE	1	0.357549247063213	2		418	557	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129646	2129646	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747420910	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	145	687	2	ENST00000219476.3:c.3373C>T	p.Arg1125Trp	p.R1125W	ENST00000219476	NM_000548.3	1125	Cgg/Tgg	29/42	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.357549247063213	2		689	765	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593351	67593352	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	53	287	0	ENST00000274335.5:c.2101_2102del	p.Thr701LeufsTer39	p.T701Lfs*39	ENST00000274335		699	caACac/caac	15/15	1	2	FACETS	0.847	0.726	0.979	0.847	0.726	0.979	CLONAL	1	TRUE	1	0.357549247063213	2		287	350	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797404	42797404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748515698	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	154	676	1	ENST00000575354.2:c.3766C>T	p.Arg1256Trp	p.R1256W	ENST00000575354	NM_015125.3	1256	Cgg/Tgg	15/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.357549247063213	2		677	803	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800429	32800429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750440758	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	163	847	0	ENST00000374899.4:c.1118G>A	p.Arg373His	p.R373H	ENST00000374899	NM_018833.2	373	cGc/cAc	6/12	1	2	FACETS	0.89	0.816	0.968	0.89	0.816	0.968	CLONAL	1	TRUE	1	0.357549247063213	2		847	1024	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749975	162749975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147604927	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	95	518	1	ENST00000367921.3:c.2507C>T	p.Thr836Met	p.T836M	ENST00000367921	NM_006182.2	836	aCg/aTg	18/18	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.357549247063213	2		519	514	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998292	100998292	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	36	164	0	ENST00000325455.5:c.1510G>A	p.Ala504Thr	p.A504T	ENST00000325455	NM_001202474.3	504	Gcc/Acc	1/8	1	2	FACETS	0.92	0.762	1	0.92	0.762	1	CLONAL	1	TRUE	1	0.357549247063213	2		164	219	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497837	120497837	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1553198267	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	96	460	0	ENST00000256646.2:c.2045A>G	p.Asp682Gly	p.D682G	ENST00000256646	NM_024408.3	682	gAc/gGc	13/34	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.357549247063213	2		460	504	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615005	43615005	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760012685	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	86	538	1	ENST00000355710.3:c.2419G>A	p.Ala807Thr	p.A807T	ENST00000355710	NM_020975.4	807	Gcc/Acc	14/20	1	2	FACETS	0.808	0.716	0.907	0.808	0.716	0.907	CLONAL	1	TRUE	1	0.357549247063213	2		539	595	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946931	71946931	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1375254938	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	163	773	1	ENST00000298229.2:c.2780C>T	p.Pro927Leu	p.P927L	ENST00000298229	NM_001567.3	927	cCg/cTg	25/28	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.357549247063213	2		774	861	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194167	94194167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398359004	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	26	519	1	ENST00000323929.3:c.1261C>T	p.Pro421Ser	p.P421S	ENST00000323929	NM_005591.3	421	Cct/Tct	12/20	1	2	FACETS	0.341	0.269	0.423	0.341	0.269	0.423	SUBCLONAL	1	TRUE	1	0.357549247063213	2		520	427	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433113	49433113	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	124	657	1	ENST00000301067.7:c.8258del	p.Pro2753GlnfsTer4	p.P2753Qfs*4	ENST00000301067	NM_003482.3	2753	cCa/ca	33/54	1	2	FACETS	0.987	0.894	1	0.987	0.894	1	CLONAL	1	TRUE	1	0.357549247063213	2		658	703	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111886044	111886044	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769682050	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	92	475	0	ENST00000341259.2:c.1666G>A	p.Glu556Lys	p.E556K	ENST00000341259	NM_005475.2	556	Gaa/Aaa	8/8	1	2	FACETS	0.967	0.862	1	0.967	0.862	1	CLONAL	1	TRUE	1	0.357549247063213	2		475	532	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879626	123879626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376869233	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	59	296	0	ENST00000330479.4:c.322G>A	p.Ala108Thr	p.A108T	ENST00000330479	NM_020382.3	108	Gcc/Acc	4/9	1	2	FACETS	0.927	0.802	1	0.927	0.802	1	CLONAL	1	TRUE	1	0.357549247063213	2		296	356	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881529	48881532	+	frameshift_variant	Frame_Shift_Del	DEL	TGGA	TGGA	-	novel	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	34	303	0	ENST00000267163.4:c.255_258del	p.Asp85GlufsTer25	p.D85Efs*25	ENST00000267163	NM_000321.2	84	gTGGAt/gt	2/27	1	2	FACETS	0.799	0.657	0.957	0.799	0.657	0.957	CLONAL	1	TRUE	1	0.357549247063213	2		303	238	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590680	95590680	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	65	425	0	ENST00000393063.1:c.1229T>C	p.Val410Ala	p.V410A	ENST00000393063	NM_030621.3	410	gTg/gCg	9/28	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.357549247063213	2		425	352	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094671	2094671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	186	750	0	ENST00000219066.1:c.509C>T	p.Ala170Val	p.A170V	ENST00000219066	NM_002528.5	170	gCc/gTc	3/6	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.357549247063213	2		750	812	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3634840	3634841	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs752736478	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	135	687	0	ENST00000294008.3:c.4668dup	p.Lys1557GlnfsTer24	p.K1557Qfs*24	ENST00000294008	NM_032444.2	1556	-/C	13/15	1	2	FACETS	0.904	0.822	0.991	0.904	0.822	0.991	CLONAL	1	TRUE	1	0.357549247063213	2		687	835	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647562	3647562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1336212611	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	152	794	0	ENST00000294008.3:c.1501C>T	p.Pro501Ser	p.P501S	ENST00000294008	NM_032444.2	501	Cca/Tca	7/15	1	2	FACETS	0.962	0.88	1	0.962	0.88	1	CLONAL	1	TRUE	1	0.357549247063213	2		794	884	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883131	37883131	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	178	757	0	ENST00000269571.5:c.3034G>T	p.Asp1012Tyr	p.D1012Y	ENST00000269571		1012	Gat/Tat	25/27	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.357549247063213	2		757	772	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252720	10252720	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377078524	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	117	532	2	ENST00000340748.4:c.3245G>A	p.Arg1082His	p.R1082H	ENST00000340748		1082	cGc/cAc	29/40	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.357549247063213	2		534	627	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794847	42794847	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778199	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	112	535	0	ENST00000575354.2:c.1927G>A	p.Gly643Ser	p.G643S	ENST00000575354	NM_015125.3	643	Ggc/Agc	10/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.357549247063213	2		535	558	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030716	48030718	+	inframe_deletion	In_Frame_Del	DEL	TAA	TAA	-	novel	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	62	367	0	ENST00000234420.5:c.3331_3333del	p.Asn1111del	p.N1111del	ENST00000234420	NM_000179.2	1110	ccTAAt/cct	5/10	1	2	FACETS	0.905	0.786	1	0.905	0.786	1	CLONAL	1	TRUE	1	0.357549247063213	2		367	383	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095645	178095646	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	78	525	0	ENST00000397062.3:c.1685_1686del	p.Leu562ArgfsTer8	p.L562Rfs*8	ENST00000397062	NM_006164.4	562	cTC/c	5/5	1	2	FACETS	0.901	0.795	1	0.901	0.795	1	CLONAL	1	TRUE	1	0.357549247063213	2		525	484	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265547	198265547	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	82	639	0	ENST00000335508.6:c.2610G>T	p.Glu870Asp	p.E870D	ENST00000335508	NM_012433.2	870	gaG/gaT	18/25	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.357549247063213	2		639	445	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024038	31024038	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	130	549	0	ENST00000375687.4:c.3523G>T	p.Glu1175Ter	p.E1175*	ENST00000375687	NM_015338.5	1175	Gag/Tag	13/13	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.357549247063213	2		549	622	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089076	37089076	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	95	438	0	ENST00000231790.2:c.1798G>T	p.Glu600Ter	p.E600*	ENST00000231790	NM_000249.3	600	Gaa/Taa	16/19	0.357549247063213	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.357549247063213	1		438	388	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968294	134968294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	111	512	2	ENST00000398015.3:c.2807G>A	p.Gly936Asp	p.G936D	ENST00000398015	NM_004441.4	936	gGc/gAc	15/16	1	2	FACETS	0.964	0.868	1	0.964	0.868	1	CLONAL	1	TRUE	1	0.357549247063213	2		514	644	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007411	143007411	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	40	207	0	ENST00000262992.4:c.2375-2A>G		p.X792_splice	ENST00000262992	NM_001101669.1	792			1	2	FACETS	0.956	0.801	1	0.956	0.801	1	CLONAL	1	TRUE	1	0.357549247063213	2		207	234	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143226671	143226671	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	58	304	0	ENST00000262992.4:c.443C>G	p.Ala148Gly	p.A148G	ENST00000262992	NM_001101669.1	148	gCc/gGc	7/24	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.357549247063213	2		304	309	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754595	57754595	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	68	388	0	ENST00000274289.3:c.452A>G	p.Asp151Gly	p.D151G	ENST00000274289	NM_006622.3	151	gAc/gGc	3/14	1	2	FACETS	0.921	0.805	1	0.921	0.805	1	CLONAL	1	TRUE	1	0.357549247063213	2		388	413	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323205	31323205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	122	625	0	ENST00000412585.2:c.784G>A	p.Asp262Asn	p.D262N	ENST00000412585	NM_005514.6	262	Gat/Aat	4/8	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.357549247063213	2		625	682	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172159	32172159	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	99	525	0	ENST00000375023.3:c.2873del	p.Pro958GlnfsTer90	p.P958Qfs*90	ENST00000375023	NM_004557.3	958	cCa/ca	19/30	1	2	FACETS	0.743	0.663	0.828	0.743	0.663	0.828	SUBCLONAL	1	TRUE	1	0.357549247063213	2		525	745	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109321829	109321830	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	79	565	0	ENST00000436639.2:c.593dup	p.Asn198LysfsTer2	p.N198Kfs*2	ENST00000436639	NM_014454.2	198	aat/aaAt	4/10	1	2	FACETS	0.865	0.762	0.974	0.865	0.762	0.974	CLONAL	1	TRUE	1	0.357549247063213	2		565	511	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372338	55372338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	180	751	0	ENST00000297316.4:c.1028G>A	p.Arg343Gln	p.R343Q	ENST00000297316	NM_022454.3	343	cGg/cAg	2/2	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.357549247063213	2		751	825	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90947814	90947814	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	31	392	0	ENST00000265433.3:c.2261G>T	p.Arg754Ile	p.R754I	ENST00000265433	NM_002485.4	754	aGa/aTa	16/16	1	2	FACETS	0.604	0.49	0.732	0.604	0.49	0.732	SUBCLONAL	1	TRUE	1	0.357549247063213	2		392	287	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399382	139399383	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	179	791	0	ENST00000277541.6:c.4760dup	p.Asn1587LysfsTer23	p.N1587Kfs*23	ENST00000277541	NM_017617.3	1587	aac/aaAc	26/34	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.357549247063213	2		791	938	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413124	139413125	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0037001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	150	735	0	ENST00000277541.6:c.1017_1018del	p.Ala340GlnfsTer12	p.A340Qfs*12	ENST00000277541	NM_017617.3	339	tgTGcc/tgcc	6/34	1	2	FACETS	0.89	0.813	0.971	0.89	0.813	0.971	CLONAL	1	TRUE	1	0.357549247063213	2		735	943	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593662	55593663	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCTTATGATCACAAATGGGAGTTTCCCAGAAACAGG	novel	NA	P-0037004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	158	391	0	ENST00000288135.5:c.1730_1765dup	p.Pro577_Arg588dup	p.P577_R588dup	ENST00000288135	NM_000222.2	577	-/CCTTATGATCACAAATGGGAGTTTCCCAGAAACAGG	11/21	1	2	FACETS	0.49	0.45	0.532	0.49	0.45	0.532	SUBCLONAL	1	TRUE	1	0.88260514768988	2		391	730	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919228	48919228	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs749495284	NA	P-0037005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	87	148	0	ENST00000267163.4:c.393C>G	p.Phe131Leu	p.F131L	ENST00000267163	NM_000321.2	131	ttC/ttG	4/27	0.673622096848007	1	FACETS	0.861	0.78	0.943	0.861	0.78	0.943	CLONAL	1	TRUE	0	0.673622096848007	1		148	199	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	79	597	3	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	2	FACETS	0.803	0.707	0.906	0.803	0.707	0.906	CLONAL	1	TRUE	1	0.327799988426369	2		600	600	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	23	269	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.31	0.241	0.39	0.31	0.241	0.39	SUBCLONAL	1	TRUE	1	0.327799988426369	2		269	453	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	167	645	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.824	0.761	0.89	1	0.991	1	CLONAL	2	TRUE	1	0.327799988426369	2		648	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	124	571	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.327799988426369	2		572	726	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	105	627	6	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.327799988426369	2		633	610	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	90	765	30	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.725	0.643	0.813	0.725	0.643	0.813	SUBCLONAL	1	TRUE	1	0.327799988426369	2		795	757	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913253	39913253	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	106	508	0	ENST00000378444.4:c.4862del	p.Pro1621GlnfsTer53	p.P1621Qfs*53	ENST00000378444	NM_001123385.1	1621	cCa/ca	14/15	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.327799988426369	2		508	631	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	64	443	0	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	0.665	0.576	0.762	0.665	0.576	0.762	SUBCLONAL	1	TRUE	1	0.327799988426369	2		443	587	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	85	395	20	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	0.327799988426369	2		415	417	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796882	42796883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761345552	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	143	859	3	ENST00000575354.2:c.3347dup	p.Ser1117LysfsTer34	p.S1117Kfs*34	ENST00000575354	NM_015125.3	1114	gcc/gCcc	14/20	1	2	FACETS	0.922	0.84	1	0.922	0.84	1	CLONAL	1	TRUE	1	0.327799988426369	2		862	946	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851848	134851848	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	100	592	0	ENST00000398015.3:c.1259del	p.Pro420HisfsTer28	p.P420Hfs*28	ENST00000398015	NM_004441.4	418	ttC/tt	5/16	1	2	FACETS	0.955	0.854	1	0.955	0.854	1	CLONAL	1	TRUE	1	0.327799988426369	2		592	639	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435128	110435129	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs772322568	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	73	713	1	ENST00000375856.3:c.3272dup	p.Lys1092GlufsTer233	p.K1092Efs*233	ENST00000375856	NM_003749.2	1091	ccg/ccCg	1/2	1	2	FACETS	0.555	0.485	0.632	0.555	0.485	0.632	SUBCLONAL	1	TRUE	1	0.327799988426369	2		714	802	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266112	41266112	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913228	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	10	256	0	ENST00000349496.5:c.109T>G	p.Ser37Ala	p.S37A	ENST00000349496	NM_001904.3	37	Tct/Gct	3/15	1	2	FACETS	0.161	0.108	0.228	0.161	0.108	0.228	SUBCLONAL	1	TRUE	1	0.327799988426369	2		256	379	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716329	52716329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863225094	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	17	529	0	ENST00000322088.6:c.773G>A	p.Arg258His	p.R258H	ENST00000322088	NM_014225.5	258	cGc/cAc	6/15	1	2	FACETS	0.173	0.128	0.227	0.173	0.128	0.227	SUBCLONAL	1	TRUE	1	0.327799988426369	2		529	598	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151254	202151254	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	77	423	0	ENST00000358485.4:c.1557del	p.Lys520AsnfsTer10	p.K520Nfs*10	ENST00000358485	NM_001080125.1	518	atG/at	9/9	1	2	FACETS	0.938	0.825	1	0.938	0.825	1	CLONAL	1	TRUE	1	0.327799988426369	2		423	501	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790819	89790819	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	110	621	1	ENST00000336032.3:c.211del	p.Gln71SerfsTer112	p.Q71Sfs*112	ENST00000336032	NM_006813.2	69	aCc/ac	1/2	1	2	FACETS	0.87	0.782	0.964	0.87	0.782	0.964	CLONAL	1	TRUE	1	0.327799988426369	2		622	771	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420040	152420040	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201118302	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	81	425	0	ENST00000206249.3:c.1727C>T	p.Ser576Leu	p.S576L	ENST00000206249	NM_000125.3	576	tCg/tTg	8/8	1	2	FACETS	0.846	0.747	0.953	0.846	0.747	0.953	CLONAL	1	TRUE	1	0.327799988426369	2		425	584	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508628	106508628	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	85	396	0	ENST00000359195.3:c.622C>T	p.Pro208Ser	p.P208S	ENST00000359195	NM_002649.2	208	Ccg/Tcg	2/11	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.327799988426369	2		396	495	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176710863	176710863	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1220317485	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	66	441	0	ENST00000439151.2:c.6085A>G	p.Thr2029Ala	p.T2029A	ENST00000439151	NM_022455.4	2029	Aca/Gca	20/23	1	2	FACETS	0.698	0.606	0.797	0.698	0.606	0.797	SUBCLONAL	1	TRUE	1	0.327799988426369	2		441	577	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	86	698	2	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	1	2	FACETS	0.683	0.604	0.768	0.683	0.604	0.768	SUBCLONAL	1	TRUE	1	0.327799988426369	2		700	768	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749442	41749442	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1476963248	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	63	391	2	ENST00000226382.2:c.353C>T	p.Ala118Val	p.A118V	ENST00000226382	NM_003924.3	118	gCg/gTg	2/3	1	2	FACETS	0.814	0.706	0.932	0.814	0.706	0.932	CLONAL	1	TRUE	1	0.327799988426369	2		393	472	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661663	227661664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	50	782	0	ENST00000305123.5:c.1790_1791dup	p.His598GlyfsTer39	p.H598Gfs*39	ENST00000305123	NM_005544.2	597	-/GG	1/2	1	2	FACETS	0.599	0.509	0.699	0.599	0.509	0.699	SUBCLONAL	1	TRUE	1	0.327799988426369	2		782	509	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32189104	32189104	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	61	344	0	ENST00000375023.3:c.452-2A>G		p.X151_splice	ENST00000375023	NM_004557.3	151			1	2	FACETS	0.933	0.808	1	0.933	0.808	1	CLONAL	1	TRUE	1	0.327799988426369	2		344	399	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127704	64127704	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	71	693	0	ENST00000334205.4:c.197T>C	p.Val66Ala	p.V66A	ENST00000334205	NM_003942.2	66	gTg/gCg	3/17	1	2	FACETS	0.579	0.505	0.66	0.579	0.505	0.66	SUBCLONAL	1	TRUE	1	0.327799988426369	2		693	748	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138933	64138933	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	93	452	0	ENST00000334205.4:c.2300G>C	p.Gly767Ala	p.G767A	ENST00000334205	NM_003942.2	767	gGc/gCc	17/17	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.327799988426369	2		452	479	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440199	49440200	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	77	460	0	ENST00000301067.7:c.4425_4426dup	p.Ser1476CysfsTer31	p.S1476Cfs*31	ENST00000301067	NM_003482.3	1476	tcc/tGTcc	16/54	1	2	FACETS	0.967	0.851	1	0.967	0.851	1	CLONAL	1	TRUE	1	0.327799988426369	2		460	486	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835665	68835665	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	121	542	0	ENST00000261769.5:c.259del	p.Arg87GlyfsTer30	p.R87Gfs*30	ENST00000261769	NM_004360.3	86	Aaa/aa	3/16	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.327799988426369	2		542	714	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853272	68853273	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	111	464	0	ENST00000261769.5:c.1659dup	p.Glu554Ter	p.E554*	ENST00000261769	NM_004360.3	552	gat/gaTt	11/16	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.327799988426369	2		464	618	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822144	72822144	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs187184056	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	96	463	0	ENST00000268489.5:c.10031A>G	p.Tyr3344Cys	p.Y3344C	ENST00000268489	NM_006885.3	3344	tAc/tGc	10/10	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.327799988426369	2		463	545	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654769	29654770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	34	306	0	ENST00000356175.3:c.5460dup	p.His1821ThrfsTer20	p.H1821Tfs*20	ENST00000356175	NM_000267.3	1820	caa/cAaa	37/57	1	2	FACETS	0.467	0.381	0.564	0.467	0.381	0.564	SUBCLONAL	1	TRUE	1	0.327799988426369	2		306	444	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243649	41243649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	120	593	0	ENST00000357654.3:c.3899G>A	p.Cys1300Tyr	p.C1300Y	ENST00000357654	NM_007294.3	1300	tGc/tAc	10/23	1	2	FACETS	0.926	0.836	1	0.926	0.836	1	CLONAL	1	TRUE	1	0.327799988426369	2		593	791	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797375	42797376	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	112	695	0	ENST00000575354.2:c.3743dup	p.Leu1249ThrfsTer6	p.L1249Tfs*6	ENST00000575354	NM_015125.3	1246	agc/agCc	15/20	1	2	FACETS	0.911	0.82	1	0.911	0.82	1	CLONAL	1	TRUE	1	0.327799988426369	2		695	750	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436306	52436306	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	novel	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	75	483	0	ENST00000460680.1:c.2188T>C	p.Ter730ArgextTer205	p.*730Rext*205	ENST00000460680	NM_004656.3	730	Tga/Cga	17/17	1	2	FACETS	0.877	0.77	0.991	0.877	0.77	0.991	CLONAL	1	TRUE	1	0.327799988426369	2		483	522	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027152	71027153	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	69	361	0	ENST00000318789.4:c.1174_1175del	p.Ser392GlnfsTer68	p.S392Qfs*68	ENST00000318789	NM_032682.5	392	TCc/c	15/21	1	2	FACETS	0.919	0.803	1	0.919	0.803	1	CLONAL	1	TRUE	1	0.327799988426369	2		361	458	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729658	41729658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1159649174	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	97	498	0	ENST00000242208.4:c.871C>T	p.Pro291Ser	p.P291S	ENST00000242208	NM_002192.2	291	Cct/Tct	3/3	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.327799988426369	2		498	573	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220256	55220256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1190573231	NA	P-0037006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	132	749	0	ENST00000275493.2:c.646G>A	p.Ala216Thr	p.A216T	ENST00000275493	NM_005228.3	216	Gcc/Acc	6/28	1	2	FACETS	0.954	0.866	1	0.954	0.866	1	CLONAL	1	TRUE	1	0.327799988426369	2		749	844	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312627	30312627	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0037008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	51	432	0	ENST00000262643.3:c.610-2A>T		p.X204_splice	ENST00000262643	NM_001238.2	204			1	2	FACETS	0.937	0.801	1	0.937	0.801	1	CLONAL	1	TRUE	1	0.32872084340616	2		432	331	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183752	10183754	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	rs794729660	NA	P-0037008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	87	669	0	ENST00000256474.2:c.223_225del	p.Ile75del	p.I75del	ENST00000256474	NM_000551.3	74	gTCAtc/gtc	1/3	0.32872084340616	1	FACETS	0.945	0.84	1	0.945	0.84	1	CLONAL	1	TRUE	0	0.32872084340616	1		669	468	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103652	47103652	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0037008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	37	339	0	ENST00000409792.3:c.6293+1G>T		p.X2098_splice	ENST00000409792	NM_014159.6	2098			0.32872084340616	1	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	TRUE	0	0.32872084340616	1		339	185	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439856	52439857	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1553645486	NA	P-0037008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	63	541	0	ENST00000460680.1:c.855dup	p.Lys286GlnfsTer21	p.K286Qfs*21	ENST00000460680	NM_004656.3	285	-/C	10/17	0.32872084340616	1	FACETS	0.977	0.85	1	0.977	0.85	1	CLONAL	1	TRUE	0	0.32872084340616	1		541	328	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469852	157469852	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	78	578	0	ENST00000346085.5:c.2646G>A	p.Met882Ile	p.M882I	ENST00000346085	NM_020732.3	882	atG/atA	9/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.32872084340616	2		578	430	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0037009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	16	381	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.445445088018718	3	FACETS	1	0.902	1	0.732	0.558	0.926	CLONAL	1	FALSE	1	0.445445088018718	3		381	60	SUCCESS
APC	324	MSKCC	GRCh37	5	112173387	112173387	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1060503336	NA	P-0037009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	38	286	0	ENST00000257430.4:c.2096G>A	p.Trp699Ter	p.W699*	ENST00000257430	NM_000038.5	699	tGg/tAg	16/16	0.443930868913756	3	FACETS	1	0.947	1	1	0.947	1	CLONAL	3	FALSE	0	0.445445088018718	3		286	60	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610119	81610119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	55	417	0	ENST00000298171.2:c.1717G>A	p.Asp573Asn	p.D573N	ENST00000298171	NM_000369.2	573	Gac/Aac	10/10	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	FALSE	1	0.445445088018718	2		417	216	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0037010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	12	303	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.591	0.414	0.811	0.591	0.414	0.811	SUBCLONAL	1	TRUE	1	0.11	2		303	369	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0037010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	14	166	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.727	0.524	0.974	0.727	0.524	0.974	CLONAL	1	TRUE	1	0.11	2		166	350	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608325	100608325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	22	192	0	ENST00000308731.7:c.1765G>A	p.Glu589Lys	p.E589K	ENST00000308731	NM_000061.2	589	Gaa/Aaa	18/19	1	1	FACETS	1	0.776	1	1	0.776	1	CLONAL	1	TRUE	0	0.11	1		192	377	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519922	NA	P-0037169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	186	731	0	ENST00000397062.3:c.235G>A	p.Glu79Lys	p.E79K	ENST00000397062	NM_006164.4	79	Gag/Aag	2/5	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.274769346251377	2		731	1209	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0037169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	158	535	0	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	0.274769346251377	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.274769346251377	1		535	888	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098816	178098816	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	180	743	0	ENST00000397062.3:c.229G>C	p.Asp77His	p.D77H	ENST00000397062	NM_006164.4	77	Gat/Cat	2/5	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.274769346251377	2		743	1189	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076785	72076785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576347795	NA	P-0037169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	124	475	0	ENST00000357731.5:c.712G>A	p.Gly238Arg	p.G238R	ENST00000357731	NM_173808.2	238	Gga/Aga	5/7	1	2	FACETS	0.997	0.902	1	0.997	0.902	1	CLONAL	1	TRUE	1	0.274769346251377	2		475	905	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266749	198266749	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0037169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	91	555	0	ENST00000335508.6:c.2183T>G	p.Leu728Ter	p.L728*	ENST00000335508	NM_012433.2	728	tTa/tGa	15/25	1	2	FACETS	0.843	0.748	0.944	0.843	0.748	0.944	CLONAL	1	TRUE	1	0.274769346251377	2		555	786	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196483	106196483	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs763874158	NA	P-0037169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	85	468	0	ENST00000380013.4:c.4816G>C	p.Gly1606Arg	p.G1606R	ENST00000380013	NM_001127208.2	1606	Ggt/Cgt	11/11	1	2	FACETS	0.911	0.806	1	0.911	0.806	1	CLONAL	1	TRUE	1	0.274769346251377	2		468	679	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001216-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	19	709	0	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	0.681303817055039	2	FACETS	0.152	0.115	0.196	0.076	0.057	0.098	SUBCLONAL	1	TRUE	0	0.686652369426664	2		709	364	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0001216-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	139	823	5	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	0.485516182039022	4	FACETS	0.955	0.871	1			1	CLONAL	1	TRUE	NA	0.686652369426664	4		828	715	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0001216-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	167	1091	1	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	0.678169540948471	2	FACETS	0.997	0.924	1	0.498	0.462	0.536	CLONAL	1	TRUE	0	0.686652369426664	2		1092	488	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643348	52643348	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001216-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	92	459	0	ENST00000394830.3:c.2548C>T	p.Arg850Ter	p.R850*	ENST00000394830	NM_018313.4	850	Cga/Tga	17/30	0.678169540948471	2	FACETS	0.918	0.826	1	0.459	0.413	0.507	CLONAL	1	TRUE	0	0.686652369426664	2		459	292	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087503	27087503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001216-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	390	564	4	ENST00000324856.7:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000324856	NM_006015.4	693	Cga/Tga	5/20	0.681303817055039	2	FACETS	0.998	0.964	1	0.998	0.964	1	CLONAL	2	TRUE	0	0.686652369426664	2		568	569	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552152	29552152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199474738	NA	P-0001216-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	125	347	0	ENST00000356175.3:c.1885G>A	p.Gly629Arg	p.G629R	ENST00000356175	NM_000267.3	629	Ggg/Agg	17/57	0.678169540948471	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.686652369426664	2		347	179	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222373	2222373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001216-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	254	541	1	ENST00000398665.3:c.3205G>A	p.Ala1069Thr	p.A1069T	ENST00000398665	NM_032482.2	1069	Gcc/Acc	24/28	0.657136054048986	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.686652369426664	3		542	451	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541324	187541324	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001216-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	195	529	1	ENST00000441802.2:c.6416del	p.Lys2139SerfsTer8	p.K2139Sfs*8	ENST00000441802	NM_005245.3	2139	aAg/ag	10/27	NA	2	FACETS	1	0.966	1			1	INDETERMINATE	2	TRUE	NA	0.686652369426664	2		530	279	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0001216-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	114	293	7	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	0.686652369426664	3	FACETS	0.892	0.819	0.965	0.892	0.819	0.965	CLONAL	2	TRUE	1	0.686652369426664	3		300	250	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0001216-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	195	569	7	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	0.678169540948471	2	FACETS	0.887	0.84	0.934	0.887	0.84	0.934	CLONAL	2	TRUE	0	0.686652369426664	2		576	320	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467855	99467856	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0001216-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	29	426	0	ENST00000268035.6:c.2732_2733dup	p.Gly912LeufsTer26	p.G912Lfs*26	ENST00000268035	NM_000875.3	908	-/TC	13/21	0.681303817055039	2	FACETS	0.283	0.227	0.345	0.141	0.113	0.173	SUBCLONAL	1	TRUE	0	0.686652369426664	2		426	299	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14026116	14026116	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001216-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	57	315	0	ENST00000311895.7:c.1081del	p.Met361TrpfsTer15	p.M361Wfs*15	ENST00000311895	NM_005236.2	359	gAa/ga	6/11	0.686652369426664	4	FACETS	0.819	0.706	0.94			1	CLONAL	1	TRUE	NA	0.686652369426664	4		315	342	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005513	42005517	+	frameshift_variant	Frame_Shift_Del	DEL	GAAAA	GAAAA	-	novel	NA	P-0001216-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	321	757	1	ENST00000219905.7:c.3255_3259del	p.Arg1085SerfsTer5	p.R1085Sfs*5	ENST00000219905	NM_001164273.1	1083	ttGAAAAga/ttga	9/24	0.678169540948471	2	FACETS	0.929	0.892	0.966	0.929	0.892	0.966	CLONAL	2	TRUE	0	0.686652369426664	2		758	503	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778363	3778363	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139688311	NA	P-0001216-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	159	782	1	ENST00000262367.5:c.6685G>A	p.Gly2229Ser	p.G2229S	ENST00000262367	NM_004380.2	2229	Ggc/Agc	31/31	0.592355854154786	4	FACETS	0.993	0.911	1	0.496	0.455	0.539	CLONAL	1	TRUE	2	0.686652369426664	4		783	787	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572519	64572519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555164143	NA	P-0001216-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	149	683	0	ENST00000312049.6:c.1337G>A	p.Arg446His	p.R446H	ENST00000312049	NM_130799.2	446	cGt/cAt	9/10	0.686652369426664	2	FACETS	0.96	0.885	1	0.48	0.442	0.519	CLONAL	1	TRUE	0	0.686652369426664	2		683	452	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420213	49420213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267607237	NA	P-0001216-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	289	822	2	ENST00000301067.7:c.15536G>A	p.Arg5179His	p.R5179H	ENST00000301067	NM_003482.3	5179	cGt/cAt	48/54	0.686652369426664	4	FACETS	0.9	0.85	0.95			1	CLONAL	2	TRUE	NA	0.686652369426664	4		824	789	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085897	16085897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775092426	NA	P-0001216-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	21	520	1	ENST00000281043.3:c.1073C>T	p.Pro358Leu	p.P358L	ENST00000281043	NM_005378.4	358	cCg/cTg	3/3	0.686652369426664	2	FACETS	0.208	0.16	0.264	0.104	0.08	0.132	SUBCLONAL	1	TRUE	0	0.686652369426664	2		521	294	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864062	97864062	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779902	NA	P-0001216-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	142	770	0	ENST00000289081.3:c.1604G>A	p.Arg535His	p.R535H	ENST00000289081	NM_000136.2	535	cGt/cAt	15/15	0.681303817055039	2	FACETS	0.951	0.874	1	0.475	0.437	0.515	CLONAL	1	TRUE	0	0.686652369426664	2		770	435	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912139	50912139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501836	NA	P-0001216-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	197	887	2	ENST00000440232.2:c.1873G>A	p.Gly625Arg	p.G625R	ENST00000440232	NM_002691.3	625	Ggg/Agg	15/27	0.662754257121629	3	FACETS	1	0.964	1	0.53	0.492	0.569	CLONAL	1	TRUE	1	0.686652369426664	3		889	727	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114901004	114901004	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001216-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	135	572	0	ENST00000543371.1:c.614C>T	p.Thr205Met	p.T205M	ENST00000543371	NM_001198531.1	205	aCg/aTg	6/14	0.681303817055039	2	FACETS	0.971	0.891	1	0.485	0.445	0.527	CLONAL	1	TRUE	0	0.686652369426664	2		572	405	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256586	133256586	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001216-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	123	549	0	ENST00000320574.5:c.377G>T	p.Gly126Val	p.G126V	ENST00000320574	NM_006231.2	126	gGc/gTc	5/49	0.577055586431588	4	FACETS	0.994	0.901	1			1	CLONAL	1	TRUE	NA	0.686652369426664	4		549	608	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260150	10260150	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001216-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	137	741	0	ENST00000340748.4:c.2517del	p.Ser840ProfsTer55	p.S840Pfs*55	ENST00000340748		839	ccC/cc	25/40	0.662754257121629	3	FACETS	0.831	0.758	0.907	0.416	0.379	0.454	CLONAL	1	TRUE	1	0.686652369426664	3		741	645	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249602	110249602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001216-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	221	1094	1	ENST00000374672.4:c.1073C>T	p.Pro358Leu	p.P358L	ENST00000374672	NM_004235.4	358	cCg/cTg	3/5	0.681303817055039	2	FACETS	1	0.944	1	0.504	0.472	0.538	CLONAL	1	TRUE	0	0.686652369426664	2		1095	638	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70350044	70350044	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762692180	NA	P-0001216-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	17	248	0	ENST00000374080.3:c.4027C>T	p.Arg1343Cys	p.R1343C	ENST00000374080		1343	Cgc/Tgc	28/45	0.652909455695108	2	FACETS	0.18	0.134	0.235			1	SUBCLONAL	1	TRUE	NA	0.686652369426664	2		248	275	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0001631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	401	673	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.430339824559882	4	FACETS	1	0.966	1			1	CLONAL	3	TRUE	NA	0.430339824559882	4		673	878	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519936	NA	P-0001631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	340	520	1	ENST00000263967.3:c.3127A>T	p.Met1043Leu	p.M1043L	ENST00000263967	NM_006218.2	1043	Atg/Ttg	21/21	0.430339824559882	4	FACETS	1	0.968	1			1	CLONAL	3	TRUE	NA	0.430339824559882	4		521	738	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849662	68849663	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0001631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	202	488	0	ENST00000261769.5:c.1565+1_1565+2dup		p.T522fs	ENST00000261769	NM_004360.3	522	aca/acGTa		0.430339824559882	2	FACETS	0.904	0.846	0.964	0.904	0.846	0.964	CLONAL	2	TRUE	0	0.430339824559882	2		488	519	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845412	151845412	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	322	801	0	ENST00000262189.6:c.13600C>T	p.Gln4534Ter	p.Q4534*	ENST00000262189	NM_170606.2	4534	Cag/Tag	52/59	0.421656102338072	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.430339824559882	4		801	1014	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579341	7579345	+	frameshift_variant	Frame_Shift_Del	DEL	AATGC	AATGC	-	novel	NA	P-0001768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	303	679	0	ENST00000269305.4:c.342_346del	p.Leu114PhefsTer33	p.L114Ffs*33	ENST00000269305	NM_001126112.2	114	ttGCATTct/ttct	4/11	0.511170106296937	2	FACETS	0.874	0.83	0.919	0.874	0.83	0.919	CLONAL	2	TRUE	0	0.511170106296937	2		679	678	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111886062	111886062	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs183875955	NA	P-0001768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	53	581	0	ENST00000341259.2:c.1684C>T	p.Arg562Trp	p.R562W	ENST00000341259	NM_005475.2	562	Cgg/Tgg	8/8	0.511170106296937	3	FACETS	0.316	0.269	0.369	0.158	0.134	0.185	SUBCLONAL	1	TRUE	1	0.511170106296937	3		581	823	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111965617	111965617	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	13	16	0	ENST00000375549.3:c.403A>G	p.Thr135Ala	p.T135A	ENST00000375549	NM_003002.3	135	Acc/Gcc	4/4	0.473495385778354	6	FACETS	0.989	0.728	1	0.495	0.364	0.643	CLONAL	2	TRUE	2	0.511170106296937	6		16	52	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206898	36206898	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	137	328	0	ENST00000300305.3:c.614G>C	p.Arg205Thr	p.R205T	ENST00000300305		205	aGa/aCa	6/8	0.511170106296937	5	FACETS	1	0.959	1			1	CLONAL	1	TRUE	NA	0.511170106296937	5		328	866	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003295	143003295	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	142	781	2	ENST00000262992.4:c.2531G>A	p.Ser844Asn	p.S844N	ENST00000262992	NM_001101669.1	844	aGt/aAt	23/24	0.264595528535079	2	FACETS	0.672	0.612	0.734	0.336	0.306	0.367	INDETERMINATE	1	TRUE	0	0.511170106296937	2		783	827	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170832326	170832326	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	54	612	0	ENST00000296930.5:c.690A>T	p.Lys230Asn	p.K230N	ENST00000296930	NM_002520.6	230	aaA/aaT	9/11	0.270091399019804	5	FACETS	0.472	0.402	0.549	0.157	0.134	0.183	INDETERMINATE	1	TRUE	2	0.511170106296937	5		612	791	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399916	139399916	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	275	783	0	ENST00000277541.6:c.4432G>C	p.Asp1478His	p.D1478H	ENST00000277541	NM_017617.3	1478	Gac/Cac	25/34	0.244263337134894	4	FACETS	0.813	0.764	0.863	0.813	0.764	0.863	INDETERMINATE	2	TRUE	2	0.511170106296937	4		783	1000	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430341	47430341	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	89	408	0	ENST00000377045.4:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000377045	NM_001654.4	539	cCc/cGc	15/16	0.4994190820789	2	FACETS	0.64	0.569	0.716			1	SUBCLONAL	1	TRUE	NA	0.511170106296937	2		408	544	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0001776-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	104	526	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.273331122454957	2	FACETS	0.815	0.734	0.9	0.815	0.734	0.9	CLONAL	2	TRUE	0	0.281137663046423	2		526	454	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0001776-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	90	577	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	0.974	1	CLONAL	1	TRUE	1	0.281137663046423	2		577	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0001776-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	138	863	7	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.240534072871446	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.281137663046423	1		870	830	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59878678	59878679	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0001776-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	61	546	0	ENST00000259008.2:c.1075dup	p.Ile359AsnfsTer5	p.I359Nfs*5	ENST00000259008	NM_032043.2	359	ata/aAta	8/20	1	2	FACETS	0.736	0.634	0.845	0.736	0.634	0.845	SUBCLONAL	1	TRUE	1	0.281137663046423	2		546	590	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163632	32163632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001776-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	94	405	0	ENST00000375023.3:c.5594C>T	p.Ser1865Leu	p.S1865L	ENST00000375023	NM_004557.3	1865	tCa/tTa	30/30	0.281137663046423	3	FACETS	0.718	0.637	0.805	0.359	0.318	0.403	SUBCLONAL	1	TRUE	1	0.281137663046423	3		405	1062	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0002372-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	195	255	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.995	0.928	1	0.995	0.928	1	CLONAL	1	TRUE	1	0.690985919428231	2		255	567	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0002372-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	63	242	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.690985919428231	1	FACETS	0.796	0.706	0.887	0.796	0.706	0.887	SUBCLONAL	1	TRUE	0	0.690985919428231	1		242	150	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742679	39742679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002372-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	166	355	0	ENST00000361337.2:c.1522C>T	p.Arg508Cys	p.R508C	ENST00000361337	NM_003286.2	508	Cgt/Tgt	15/21	1	2	FACETS	0.959	0.888	1	0.959	0.888	1	CLONAL	1	TRUE	1	0.690985919428231	2		355	501	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428573	72428573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002372-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	151	335	0	ENST00000477973.2:c.431C>T	p.Pro144Leu	p.P144L	ENST00000477973	NM_012234.5	144	cCt/cTt	2/4	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.690985919428231	2		335	422	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211626	46211626	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0004752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	69	574	2	ENST00000334344.6:c.592A>T	p.Lys198Ter	p.K198*	ENST00000334344	NM_152641.2	198	Aaa/Taa	5/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.2	2		576	600	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211626	46211626	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0004752-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	48	574	2	ENST00000334344.6:c.592A>T	p.Lys198Ter	p.K198*	ENST00000334344	NM_152641.2	198	Aaa/Taa	5/21	1	2	FACETS	0.783	0.66	0.92	0.783	0.66	0.92	CLONAL	1	TRUE	1	0.13	2		576	943	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211626	46211626	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0004752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	79	574	2	ENST00000334344.6:c.592A>T	p.Lys198Ter	p.K198*	ENST00000334344	NM_152641.2	198	Aaa/Taa	5/21	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.257529189610391	2		576	610	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509743	106509744	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	TACGAAAGCCTTGCTCTGGCATTTTAGATACGAAAGCC	novel	NA	P-0004752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	59	753	0	ENST00000359195.3:c.1749_1750insGCTCTGGCATTTTAGATACGAAAGCCTACGAAAGCCTT	p.Lys584AlafsTer5	p.K584Afs*5	ENST00000359195	NM_002649.2	579	-/TACGAAAGCCTTGCTCTGGCATTTTAGATACGAAAGCC	2/11	1	2	FACETS	0.544	0.466	0.628	0.544	0.466	0.628	SUBCLONAL	1	TRUE	1	0.257529189610391	2		753	843	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509773	106509787	+	inframe_deletion	In_Frame_Del	DEL	TCCTAAGCTATTTAG	TCCTAAGCTATTTAG	-	novel	NA	P-0004752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	95	904	0	ENST00000359195.3:c.1768_1782del	p.Pro590_Ser594del	p.P590_S594del	ENST00000359195	NM_002649.2	589	taTCCTAAGCTATTTAGt/tat	2/11	1	2	FACETS	0.804	0.714	0.899	0.804	0.714	0.899	CLONAL	1	TRUE	1	0.257529189610391	2		904	918	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0005813-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	353	673	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.249491650217474	11	FACETS	0.979	0.935	1			1	CLONAL	9	FALSE	NA	0.249491650217474	11		673	682	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571448	95571448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373412959	NA	P-0005813-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	42	120	0	ENST00000393063.1:c.3229G>A	p.Asp1077Asn	p.D1077N	ENST00000393063	NM_030621.3	1077	Gat/Aat	21/28	0.105900678521787	5	FACETS	1	0.94	1	0.427	0.357	0.504	INDETERMINATE	1	FALSE	2	0.249491650217474	5		120	361	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467380	66467380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005813-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	35	76	0	ENST00000273854.3:c.889G>A	p.Glu297Lys	p.E297K	ENST00000273854	NM_004439.5	297	Gag/Aag	3/18	0.239377946399048	3	FACETS	1	0.941	1	0.689	0.569	0.822	CLONAL	1	FALSE	1	0.249491650217474	3		76	229	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115701	8115701	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0005813-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	38	80	1	ENST00000346208.3:c.1048-1G>A		p.X350_splice	ENST00000346208		350			0.220001890019648	3	FACETS	0.834	0.703	0.974	1	0.938	1	CLONAL	3	FALSE	1	0.249491650217474	3		81	137	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578541	+	inframe_deletion	In_Frame_Del	DEL	GGCAAAACATCTTGTTGA	GGCAAAACATCTTGTTGA	-	novel	NA	P-0005813-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	49	424	0	ENST00000269305.4:c.389_406del	p.Leu130_Cys135del	p.L130_C135del	ENST00000269305	NM_001126112.2	130	cTCAACAAGATGTTTTGCCaa/caa	5/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.249491650217474	NA		424	600	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	129	272	0				ENST00000310581	NM_198253.2	-/1132			0.214745864219445	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.283214631737293	1		272	722	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0006097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	121	561	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.172864946669861	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.283214631737293	1		561	720	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916929	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519931	NA	P-0006097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	122	692	0	ENST00000263967.3:c.316G>C	p.Gly106Arg	p.G106R	ENST00000263967	NM_006218.2	106	Ggc/Cgc	2/21	0.220853673502361	3	FACETS	1	0.919	1	0.51	0.46	0.563	CLONAL	1	TRUE	1	0.283214631737293	3		692	964	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	50	710	0	ENST00000335508.6:c.2704G>A	p.Glu902Lys	p.E902K	ENST00000335508	NM_012433.2	902	Gaa/Aaa	18/25	0.172864946669861	1	FACETS	0.361	0.305	0.423	0.361	0.305	0.423	SUBCLONAL	1	TRUE	0	0.283214631737293	1		710	840	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900371	101900371	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1564162124	NA	P-0006097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	89	326	0	ENST00000374994.4:c.805G>A	p.Asp269Asn	p.D269N	ENST00000374994	NM_004612.2	269	Gac/Aac	4/9	0.283214631737293	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.283214631737293	1		326	458	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941858	44941858	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0006097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	56	276	0	ENST00000377967.4:c.3182C>G	p.Ser1061Ter	p.S1061*	ENST00000377967	NM_021140.2	1061	tCa/tGa	21/29	0.283214631737293	0	FACETS	0.702	0.603	0.809			1	SUBCLONAL	1	TRUE	NA	0.283214631737293	0		276	404	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202503	123202504	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0006097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	81	241	0	ENST00000218089.9:c.2356dup	p.Gln786ProfsTer8	p.Q786Pfs*8	ENST00000218089	NM_001042749.1	785	-/C	24/35	1	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.283214631737293	1		241	328	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986637	36986637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1191023334	NA	P-0006097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	36	212	1	ENST00000354822.5:c.1052C>T	p.Pro351Leu	p.P351L	ENST00000354822	NM_001079668.2	351	cCa/cTa	3/3	0.214745864219445	1	FACETS	0.704	0.581	0.841	0.704	0.581	0.841	SUBCLONAL	1	TRUE	0	0.283214631737293	1		213	310	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422922	12422922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	293	816	0	ENST00000287820.6:c.412G>A	p.Glu138Lys	p.E138K	ENST00000287820	NM_015869.4	138	Gaa/Aaa	3/7	0.235178229547496	2	FACETS	0.86	0.809	0.913	0.86	0.809	0.913	CLONAL	2	TRUE	0	0.283214631737293	2		816	1203	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754569	57754569	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	63	624	0	ENST00000274289.3:c.478G>C	p.Glu160Gln	p.E160Q	ENST00000274289	NM_006622.3	160	Gaa/Caa	3/14	1	2	FACETS	0.546	0.471	0.628	0.546	0.471	0.628	SUBCLONAL	1	TRUE	1	0.283214631737293	2		624	815	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139411760	139411760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1269	115	970	1	ENST00000277541.6:c.1519G>A	p.Asp507Asn	p.D507N	ENST00000277541	NM_017617.3	507	Gac/Aac	9/34	0.283214631737293	1	FACETS	0.504	0.452	0.559	0.504	0.452	0.559	SUBCLONAL	1	TRUE	0	0.283214631737293	1		971	1384	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0006237-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	96	364	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.646	0.581	0.715	0.646	0.581	0.715	SUBCLONAL	1	TRUE	1	0.836710017902587	2		364	355	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	2208	488	2	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.340274749399602	23	FACETS	1	0.993	1			1	CLONAL	22	TRUE	NA	0.340274749399602	23		490	2682	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14017064	14017064	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	84	405	0	ENST00000405192.2:c.223C>G	p.Gln75Glu	p.Q75E	ENST00000405192	NM_001163147.1	75	Cag/Gag	5/12	0.340274749399602	3	FACETS	0.969	0.857	1	0.485	0.428	0.545	CLONAL	1	TRUE	1	0.340274749399602	3		405	596	SUCCESS
APC	324	MSKCC	GRCh37	5	112176893	112176893	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	85	416	0	ENST00000257430.4:c.5602G>C	p.Asp1868His	p.D1868H	ENST00000257430	NM_000038.5	1868	Gat/Cat	16/16	0.340274749399602	4	FACETS	0.951	0.841	1	0.476	0.42	0.535	CLONAL	1	TRUE	2	0.340274749399602	4		416	704	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528895	157528895	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs763772159	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	96	572	0	ENST00000346085.5:c.6620G>C	p.Arg2207Thr	p.R2207T	ENST00000346085	NM_020732.3	2207	aGa/aCa	20/20	0.340274749399602	5	FACETS	0.917	0.816	1	0.306	0.272	0.342	CLONAL	1	TRUE	2	0.340274749399602	5		572	929	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510333	187510333	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	76	287	0	ENST00000441802.2:c.13180C>G	p.Leu4394Val	p.L4394V	ENST00000441802	NM_005245.3	4394	Ctg/Gtg	27/27	0.340274749399602	3	FACETS	1	0.943	1	0.562	0.494	0.634	CLONAL	1	TRUE	1	0.340274749399602	3		287	465	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250442	110250444	+	inframe_deletion	In_Frame_Del	DEL	CCG	CCG	-	novel	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	100	521	0	ENST00000374672.4:c.231_233del	p.Gly78del	p.G78del	ENST00000374672	NM_004235.4	77	ggCGGa/gga	3/5	0.340274749399602	3	FACETS	0.909	0.811	1	0.454	0.405	0.506	CLONAL	1	TRUE	1	0.340274749399602	3		521	757	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574014	7574014	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	293	591	0	ENST00000269305.4:c.1013del	p.Phe338SerfsTer7	p.F338Sfs*7	ENST00000269305	NM_001126112.2	338	tTc/tc	10/11	0.31079873053259	2	FACETS	0.997	0.941	1	0.997	0.941	1	CLONAL	2	TRUE	0	0.340274749399602	2		591	864	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877338	89877338	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs756995764	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	101	464	0	ENST00000389301.3:c.425G>C	p.Arg142Thr	p.R142T	ENST00000389301	NM_000135.2	142	aGa/aCa	4/43	0.340274749399602	3	FACETS	0.948	0.847	1	0.316	0.282	0.352	CLONAL	1	TRUE	0	0.340274749399602	3		464	733	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1962801	1962801	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772470710	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	110	457	0	ENST00000382891.5:c.3295G>A	p.Glu1099Lys	p.E1099K	ENST00000382891	NM_133335.3	1099	Gag/Aag	18/22	0.340274749399602	3	FACETS	1	0.912	1			1	CLONAL	1	TRUE	NA	0.340274749399602	3		457	745	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2220106	2220106	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	100	539	2	ENST00000398665.3:c.2692-1G>T		p.X898_splice	ENST00000398665	NM_032482.2	898			1	2	FACETS	0.833	0.744	0.927	0.833	0.744	0.927	CLONAL	1	TRUE	1	0.340274749399602	2		541	706	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919113	178919113	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1821	136	256	0	ENST00000263967.3:c.598C>T	p.Pro200Ser	p.P200S	ENST00000263967	NM_006218.2	200	Cca/Tca	4/21	0.340274749399602	23	FACETS	0.934	0.845	1			1	CLONAL	2	TRUE	NA	0.340274749399602	23		256	1957	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430877	78430877	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	91	550	0	ENST00000370768.2:c.512G>T	p.Gly171Val	p.G171V	ENST00000370768	NM_003902.3	171	gGa/gTa	8/20	1	2	FACETS	0.713	0.633	0.799	0.713	0.633	0.799	SUBCLONAL	1	TRUE	1	0.340274749399602	2		550	750	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69229762	69229762	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	65	276	0	ENST00000462284.1:c.838G>A	p.Glu280Lys	p.E280K	ENST00000462284	NM_002392.5	280	Gag/Aag	9/11	0.340274749399602	4	FACETS	1	0.883	1			1	CLONAL	1	TRUE	NA	0.340274749399602	4		276	503	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112910775	112910775	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	89	382	0	ENST00000351677.2:c.784C>G	p.Leu262Val	p.L262V	ENST00000351677	NM_002834.3	262	Ctc/Gtc	7/16	0.340274749399602	3	FACETS	0.901	0.8	1			1	CLONAL	1	TRUE	NA	0.340274749399602	3		382	679	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536692	120536692	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	168	757	0	ENST00000229340.5:c.400G>C	p.Asp134His	p.D134H	ENST00000229340	NM_006861.6	134	Gat/Cat	5/6	0.340274749399602	3	FACETS	0.973	0.892	1			1	CLONAL	1	TRUE	NA	0.340274749399602	3		757	1188	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210883	133210883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	151	721	0	ENST00000320574.5:c.5893G>A	p.Glu1965Lys	p.E1965K	ENST00000320574	NM_006231.2	1965	Gaa/Aaa	43/49	0.313649805185908	4	FACETS	0.951	0.867	1	0.317	0.289	0.347	CLONAL	1	TRUE	1	0.340274749399602	4		721	1251	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034772	42034772	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	106	508	0	ENST00000219905.7:c.4614C>G	p.Phe1538Leu	p.F1538L	ENST00000219905	NM_001164273.1	1538	ttC/ttG	15/24	0.31079873053259	2	FACETS	0.95	0.853	1	0.475	0.426	0.526	CLONAL	1	TRUE	0	0.340274749399602	2		508	656	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640038	3640038	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs758163209	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1463	191	813	0	ENST00000294008.3:c.3601C>G	p.Gln1201Glu	p.Q1201E	ENST00000294008	NM_032444.2	1201	Cag/Gag	12/15	0.340274749399602	5	FACETS	1	0.941	1	0.342	0.314	0.37	CLONAL	1	TRUE	2	0.340274749399602	5		813	1654	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614968	23614968	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs146444298	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	85	344	0	ENST00000261584.4:c.3373G>C	p.Asp1125His	p.D1125H	ENST00000261584	NM_024675.3	1125	Gat/Cat	13/13	0.340274749399602	3	FACETS	1	0.912	1	0.345	0.305	0.387	CLONAL	1	TRUE	0	0.340274749399602	3		344	565	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346418	89346418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	129	558	0	ENST00000301030.4:c.6532G>A	p.Asp2178Asn	p.D2178N	ENST00000301030	NM_001256183.1	2178	Gat/Aat	9/13	0.340274749399602	3	FACETS	1	0.952	1	0.359	0.326	0.395	CLONAL	1	TRUE	0	0.340274749399602	3		558	823	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665730	29665730	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	53	200	0	ENST00000356175.3:c.6765G>C	p.Glu2255Asp	p.E2255D	ENST00000356175	NM_000267.3	2255	gaG/gaC	45/57	NA	2	FACETS	1	0.882	1			1	INDETERMINATE	1	TRUE	NA	0.340274749399602	2		200	302	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926523	59926523	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1567	156	737	0	ENST00000259008.2:c.474G>C	p.Lys158Asn	p.K158N	ENST00000259008	NM_032043.2	158	aaG/aaC	5/20	0.340274749399602	7	FACETS	0.985	0.898	1	0.246	0.224	0.269	CLONAL	1	TRUE	3	0.340274749399602	7		737	1723	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78914319	78914319	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	93	563	0	ENST00000306801.3:c.2943G>C	p.Glu981Asp	p.E981D	ENST00000306801	NM_020761.2	981	gaG/gaC	25/34	0.340274749399602	3	FACETS	0.754	0.67	0.845	0.377	0.335	0.423	SUBCLONAL	1	TRUE	1	0.340274749399602	3		563	848	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793299	33793299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	26	146	0	ENST00000498907.2:c.22G>A	p.Glu8Lys	p.E8K	ENST00000498907	NM_004364.3	8	Gag/Aag	1/1	0.313649805185908	4	FACETS	0.989	0.789	1	0.33	0.263	0.406	CLONAL	1	TRUE	1	0.340274749399602	4		146	207	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872331	45872331	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1248	165	751	0	ENST00000391945.4:c.180G>C	p.Gln60His	p.Q60H	ENST00000391945	NM_000400.3	60	caG/caC	3/23	0.313649805185908	4	FACETS	0.92	0.842	1	0.307	0.28	0.334	CLONAL	1	TRUE	1	0.340274749399602	4		751	1413	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222353	39222353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881028	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1292	158	666	0	ENST00000402219.2:c.3257C>T	p.Pro1086Leu	p.P1086L	ENST00000402219	NM_005633.3	1086	cCg/cTg	20/23	0.340274749399602	5	FACETS	0.967	0.884	1	0.242	0.221	0.264	CLONAL	1	TRUE	1	0.340274749399602	5		666	1450	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190717486	190717486	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	79	268	0	ENST00000441310.2:c.805C>T	p.Gln269Ter	p.Q269*	ENST00000441310	NM_000534.4	269	Caa/Taa	7/13	0.340274749399602	3	FACETS	1	0.953	1	0.58	0.512	0.653	CLONAL	1	TRUE	1	0.340274749399602	3		268	468	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231107	142231107	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	80	405	0	ENST00000350721.4:c.4847C>G	p.Ser1616Ter	p.S1616*	ENST00000350721	NM_001184.3	1616	tCa/tGa	27/47	0.340274749399602	3	FACETS	0.878	0.773	0.99	0.439	0.386	0.495	CLONAL	1	TRUE	1	0.340274749399602	3		405	627	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157050	106157050	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	90	387	0	ENST00000380013.4:c.1951C>G	p.Leu651Val	p.L651V	ENST00000380013	NM_001127208.2	651	Ctc/Gtc	3/11	0.325820438277497	4	FACETS	1	0.89	1	0.501	0.445	0.562	CLONAL	1	TRUE	2	0.340274749399602	4		387	707	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032111	26032111	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs753823527	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	82	377	0	ENST00000244661.2:c.178G>T	p.Glu60Ter	p.E60*	ENST00000244661	NM_003537.3	60	Gag/Tag	1/1	0.340274749399602	6	FACETS	0.94	0.827	1			1	CLONAL	1	TRUE	NA	0.340274749399602	6		377	862	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528159	157528159	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	110	562	0	ENST00000346085.5:c.5884G>C	p.Asp1962His	p.D1962H	ENST00000346085	NM_020732.3	1962	Gat/Cat	20/20	0.340274749399602	5	FACETS	0.916	0.821	1	0.305	0.273	0.339	CLONAL	1	TRUE	2	0.340274749399602	5		562	1066	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528254	157528254	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	124	583	2	ENST00000346085.5:c.5979G>T	p.Gln1993His	p.Q1993H	ENST00000346085	NM_020732.3	1993	caG/caT	20/20	0.340274749399602	5	FACETS	1	0.914	1	0.338	0.305	0.373	CLONAL	1	TRUE	2	0.340274749399602	5		585	1086	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528552	157528552	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	139	672	0	ENST00000346085.5:c.6277G>C	p.Asp2093His	p.D2093H	ENST00000346085	NM_020732.3	2093	Gac/Cac	20/20	0.340274749399602	5	FACETS	0.994	0.902	1	0.331	0.3	0.364	CLONAL	1	TRUE	2	0.340274749399602	5		672	1242	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161990430	161990430	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	132	390	0	ENST00000366898.1:c.890T>G	p.Leu297Trp	p.L297W	ENST00000366898	NM_004562.2	297	tTg/tGg	8/12	0.340274749399602	5	FACETS	0.77	0.699	0.844	0.513	0.466	0.563	SUBCLONAL	2	TRUE	2	0.340274749399602	5		390	761	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740736	145740736	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1595	114	671	0	ENST00000428558.2:c.1364C>G	p.Ser455Cys	p.S455C	ENST00000428558	NM_004260.3	455	tCc/tGc	7/22	0.340274749399602	8	FACETS	0.792	0.71	0.88	0.132	0.118	0.147	SUBCLONAL	1	TRUE	2	0.340274749399602	8		671	1709	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608291	100608291	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	154	762	0	ENST00000308731.7:c.1799G>C	p.Arg600Thr	p.R600T	ENST00000308731	NM_000061.2	600	aGa/aCa	18/19	0.325820438277497	4	FACETS	0.961	0.877	1	0.48	0.438	0.525	CLONAL	1	TRUE	2	0.340274749399602	4		762	1263	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020249	123020249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	148	689	1	ENST00000355640.3:c.737C>T	p.Ser246Phe	p.S246F	ENST00000355640		246	tCt/tTt	2/7	0.325820438277497	4	FACETS	1	0.93	1	0.511	0.466	0.559	CLONAL	1	TRUE	2	0.340274749399602	4		690	1140	SUCCESS
APC	324	MSKCC	GRCh37	5	112116485	112116485	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs752152148	NA	P-0006766-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	197	242	0	ENST00000257430.4:c.532-2A>T		p.X178_splice	ENST00000257430	NM_000038.5	178			0.737918127346941	3	FACETS	0.925	0.891	0.957	0.925	0.891	0.957	CLONAL	3	TRUE	0	0.839695121692672	3		242	240	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691039	NA	P-0006766-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	466	659	0	ENST00000269305.4:c.919+1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			NA	2	FACETS	0.911	0.886	0.935			1	INDETERMINATE	2	TRUE	NA	0.839695121692672	2		659	609	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219175	94219175	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs779269083	NA	P-0006766-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	92	493	0	ENST00000323929.3:c.229G>T	p.Glu77Ter	p.E77*	ENST00000323929	NM_005591.3	77	Gag/Tag	4/20	0.693385863962453	4	FACETS	0.495	0.439	0.555	0.165	0.146	0.185	SUBCLONAL	1	TRUE	1	0.839695121692672	4		493	814	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444617	187444617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs545063119	NA	P-0006766-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	282	534	0	ENST00000232014.4:c.1610C>T	p.Thr537Met	p.T537M	ENST00000232014	NM_001130845.1	537	aCg/aTg	7/10	0.693385863962453	4	FACETS	0.851	0.804	0.898	0.567	0.536	0.599	CLONAL	2	TRUE	1	0.839695121692672	4		534	726	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023008	27023010	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs587779737	NA	P-0007119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	11	37	0	ENST00000324856.7:c.126_128del	p.Ala45del	p.A45del	ENST00000324856	NM_006015.4	38	gaGGCg/gag	1/20	0.235906166699957	3	FACETS	0.848	0.589	1	0.424	0.294	0.582	CLONAL	1	TRUE	1	0.235906166699957	3		37	123	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0007119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	47	597	0	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.228518982428215	1	FACETS	0.523	0.44	0.615	0.523	0.44	0.615	SUBCLONAL	1	TRUE	0	0.235906166699957	1		597	672	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721187	61721187	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	45	370	0	ENST00000401558.2:c.1087A>G	p.Thr363Ala	p.T363A	ENST00000401558	NM_003400.3	363	Act/Gct	12/25	0.167498146831542	4	FACETS	0.873	0.733	1	0.291	0.244	0.343	CLONAL	1	TRUE	1	0.235906166699957	4		370	540	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652820	212652820	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	52	493	1	ENST00000342788.4:c.486T>A	p.His162Gln	p.H162Q	ENST00000342788	NM_005235.2	162	caT/caA	4/28	0.235906166699957	1	FACETS	0.683	0.581	0.795	0.683	0.581	0.795	SUBCLONAL	1	TRUE	0	0.235906166699957	1		494	569	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439886	220439886	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs758448367	NA	P-0007119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	74	613	1	ENST00000243786.2:c.739C>A	p.Arg247Ser	p.R247S	ENST00000243786	NM_002191.3	247	Cgc/Agc	2/2	0.109217903520114	3	FACETS	1	0.895	1			1	INDETERMINATE	1	TRUE	NA	0.235906166699957	3		614	684	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468494	89468494	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	104	487	0	ENST00000336596.2:c.2028G>T	p.Gln676His	p.Q676H	ENST00000336596	NM_005233.5	676	caG/caT	11/17	0.235906166699957	3	FACETS	0.869	0.781	0.963	0.869	0.781	0.963	CLONAL	2	TRUE	1	0.235906166699957	3		487	567	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133578	55133578	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	24	383	0	ENST00000257290.5:c.882G>T	p.Gln294His	p.Q294H	ENST00000257290	NM_006206.4	294	caG/caT	6/23	0.235906166699957	0	FACETS	0.353	0.276	0.443			1	SUBCLONAL	1	TRUE	0	0.235906166699957	0		383	440	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197202	26197202	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs930112338	NA	P-0007119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	105	950	0	ENST00000356476.2:c.277C>G	p.Leu93Val	p.L93V	ENST00000356476		93	Ctg/Gtg	1/1	0.161902458531332	5	FACETS	0.985	0.88	1	0.328	0.293	0.366	CLONAL	1	TRUE	2	0.235906166699957	5		950	1223	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359019	81359019	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	42	589	0	ENST00000222390.5:c.942G>T	p.Arg314Ser	p.R314S	ENST00000222390	NM_000601.4	314	agG/agT	8/18	0.235906166699957	3	FACETS	0.557	0.463	0.661	0.278	0.231	0.331	SUBCLONAL	1	TRUE	1	0.235906166699957	3		589	715	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92404082	92404082	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	83	414	0	ENST00000265734.4:c.297A>T	p.Glu99Asp	p.E99D	ENST00000265734	NM_001259.6	99	gaA/gaT	3/8	0.235906166699957	3	FACETS	1	0.967	1	0.639	0.564	0.718	CLONAL	1	TRUE	1	0.235906166699957	3		414	616	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509528	106509528	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	73	384	0	ENST00000359195.3:c.1522C>A	p.Pro508Thr	p.P508T	ENST00000359195	NM_002649.2	508	Cca/Aca	2/11	0.235906166699957	3	FACETS	1	0.961	1	0.627	0.549	0.711	CLONAL	1	TRUE	1	0.235906166699957	3		384	552	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453075	140453075	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	102	303	0	ENST00000288602.6:c.1860G>T	p.Met620Ile	p.M620I	ENST00000288602	NM_004333.4	620	atG/atT	15/18	0.235906166699957	3	FACETS	1	0.899	1	1	0.899	1	CLONAL	2	TRUE	1	0.235906166699957	3		303	483	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94178979	94178979	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	55	380	0	ENST00000323929.3:c.1864G>T	p.Asp622Tyr	p.D622Y	ENST00000323929	NM_005591.3	622	Gat/Tat	16/20	0.097402363032016	4	FACETS	1	0.946	1	0.614	0.526	0.71	INDETERMINATE	1	TRUE	2	0.235906166699957	4		380	469	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998288	100998288	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	23	161	1	ENST00000325455.5:c.1514C>T	p.Ala505Val	p.A505V	ENST00000325455	NM_001202474.3	505	gCc/gTc	1/8	0.097402363032016	4	FACETS	0.927	0.724	1	0.463	0.362	0.58	INDETERMINATE	1	TRUE	2	0.235906166699957	4		162	260	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991608	72991608	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	50	591	0	ENST00000268489.5:c.2437A>T	p.Thr813Ser	p.T813S	ENST00000268489	NM_006885.3	813	Acc/Tcc	2/10	0.228518982428215	1	FACETS	0.521	0.441	0.609	0.521	0.441	0.609	SUBCLONAL	1	TRUE	0	0.235906166699957	1		591	718	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438279	56438279	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	99	421	0	ENST00000407977.2:c.714G>T	p.Trp238Cys	p.W238C	ENST00000407977		238	tgG/tgT	7/10	0.235906166699957	3	FACETS	0.798	0.714	0.887	0.798	0.714	0.887	SUBCLONAL	2	TRUE	1	0.235906166699957	3		421	588	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59934592	59934592	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	40	270	2	ENST00000259008.2:c.206G>T	p.Gly69Val	p.G69V	ENST00000259008	NM_032043.2	69	gGg/gTg	4/20	0.235906166699957	3	FACETS	0.83	0.689	0.985	0.415	0.344	0.493	CLONAL	1	TRUE	1	0.235906166699957	3		272	457	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39567792	39567792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1185331367	NA	P-0007119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	30	360	0	ENST00000262039.4:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000262039	NM_002647.2	183	cGa/cAa	5/25	1	2	FACETS	0.573	0.461	0.7	0.573	0.461	0.7	SUBCLONAL	1	TRUE	1	0.235906166699957	2		360	444	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210472	2210472	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	72	374	2	ENST00000398665.3:c.1079C>A	p.Pro360Gln	p.P360Q	ENST00000398665	NM_032482.2	360	cCa/cAa	13/28	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.235906166699957	2		376	513	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096009	11096009	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	129	556	1	ENST00000358026.2:c.283G>T	p.Gly95Ter	p.G95*	ENST00000358026	NM_001128849.1	95	Gga/Tga	3/36	1	2	FACETS	0.788	0.716	0.864	1	0.987	1	SUBCLONAL	2	TRUE	1	0.235906166699957	2		557	694	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520212	9520212	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	65	488	0	ENST00000353224.5:c.2057C>A	p.Ser686Tyr	p.S686Y	ENST00000353224	NM_177990.2	686	tCt/tAt	10/10	0.235906166699957	3	FACETS	1	0.924	1	0.548	0.475	0.627	CLONAL	1	TRUE	1	0.235906166699957	3		488	562	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064329	30064329	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	116	494	0	ENST00000338641.4:c.893A>T	p.Gln298Leu	p.Q298L	ENST00000338641	NM_000268.3	298	cAg/cTg	10/16	0.161902458531332	5	FACETS	0.927	0.836	1	0.618	0.557	0.682	CLONAL	2	TRUE	2	0.235906166699957	5		494	718	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480571	123480571	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1227385786	NA	P-0007119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	32	225	0	ENST00000371139.4:c.79G>T	p.Gly27Cys	p.G27C	ENST00000371139	NM_001114937.2	27	Ggc/Tgc	1/4	0.186633716010789	0	FACETS	0.693	0.564	0.838			1	SUBCLONAL	1	TRUE	NA	0.235906166699957	0		225	299	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0007136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	443	675	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.794303171713094	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.794303171713094	2		675	552	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0007136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	329	441	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.794303171713094	3	FACETS	0.984	0.941	1	0.984	0.941	1	CLONAL	2	TRUE	1	0.794303171713094	3		441	588	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0007136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	97	205	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	0.794303171713094	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.794303171713094	1		205	131	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672519	30672519	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	427	593	0	ENST00000376406.3:c.4441T>A	p.Ser1481Thr	p.S1481T	ENST00000376406	NM_014641.2	1481	Tcc/Acc	10/15	0.794303171713094	3	FACETS	0.983	0.945	1	0.983	0.945	1	CLONAL	2	TRUE	1	0.794303171713094	3		593	764	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981660	101981660	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	12	10	0	ENST00000282441.5:c.81G>C	p.Gln27His	p.Q27H	ENST00000282441	NM_001130145.2	27	caG/caC	1/9	0.794303171713094	3	FACETS	0.959	0.699	1	0.48	0.349	0.627	CLONAL	1	TRUE	1	0.794303171713094	3		10	44	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218347	133218347	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760235113	NA	P-0007136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	459	577	0	ENST00000320574.5:c.5264G>A	p.Gly1755Glu	p.G1755E	ENST00000320574	NM_006231.2	1755	gGg/gAg	39/49	0.794303171713094	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.794303171713094	3		577	767	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792869	33792869	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	141	73	0	ENST00000498907.2:c.452G>C	p.Gly151Ala	p.G151A	ENST00000498907	NM_004364.3	151	gGg/gCg	1/1	0.661856260469232	4	FACETS	0.974	0.901	1	0.974	0.901	1	CLONAL	2	TRUE	2	0.794303171713094	4		73	327	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412109	63412109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1157288902	NA	P-0007136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	527	781	0	ENST00000330258.3:c.1058G>A	p.Arg353Gln	p.R353Q	ENST00000330258	NM_152424.3	353	cGa/cAa	2/2	0.661856260469232	4	FACETS	0.934	0.897	0.972	0.934	0.897	0.972	CLONAL	2	TRUE	2	0.794303171713094	4		781	1274	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911340	32911340	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	115	426	0	ENST00000380152.3:c.2848G>T	p.Val950Phe	p.V950F	ENST00000380152		950	Gtt/Ttt	11/27	0.794303171713094	6	FACETS	0.879	0.791	0.972			1	CLONAL	1	TRUE	NA	0.794303171713094	6		426	853	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39239288	39239288	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs139859866	NA	P-0007136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	191	477	0	ENST00000402219.2:c.2369T>C	p.Leu790Ser	p.L790S	ENST00000402219	NM_005633.3	790	tTa/tCa	14/23	0.794303171713094	3	FACETS	0.833	0.771	0.896	0.416	0.385	0.448	CLONAL	1	TRUE	1	0.794303171713094	3		477	807	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0007788-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	45	620	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	0.695	0.586	0.813	0.695	0.586	0.813	SUBCLONAL	1	TRUE	1	0.411356487282266	2		620	315	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0007788-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	52	587	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	1	2	FACETS	0.632	0.539	0.733	0.632	0.539	0.733	SUBCLONAL	1	TRUE	1	0.411356487282266	2		587	400	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489207	2489207	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007788-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	36	1056	2	ENST00000355716.4:c.112G>C	p.Ala38Pro	p.A38P	ENST00000355716	NM_003820.2	38	Gct/Cct	2/8	0.288978745528201	4	FACETS	0.652	0.536	0.781			1	SUBCLONAL	1	TRUE	NA	0.411356487282266	4		1058	379	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932152	36932152	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007788-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	31	824	0	ENST00000361632.4:c.2317A>G	p.Thr773Ala	p.T773A	ENST00000361632		773	Act/Gct	16/16	0.3940035886366	1	FACETS	0.374	0.303	0.454	0.374	0.303	0.454	SUBCLONAL	1	TRUE	0	0.411356487282266	1		824	320	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282336	115282336	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007788-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	61	576	0	ENST00000438362.2:c.314A>T	p.Asn105Ile	p.N105I	ENST00000438362	NM_001242891.1	105	aAc/aTc	3/20	0.3940035886366	1	FACETS	0.876	0.763	0.996	0.876	0.763	0.996	CLONAL	1	TRUE	0	0.411356487282266	1		576	269	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577562	7577563	+	missense_variant	Missense_Mutation	DNP	CT	CT	AA	novel	NA	P-0007788-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	116	908	1	ENST00000269305.4:c.718_719delinsTT	p.Ser240Phe	p.S240F	ENST00000269305	NM_001126112.2	240	AGt/TTt	7/11	0.284664238322045	2	FACETS	0.815	0.743	0.889	0.815	0.743	0.889	CLONAL	2	TRUE	0	0.411356487282266	2		909	346	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096065	11096068	+	frameshift_variant	Frame_Shift_Del	DEL	GGAC	GGAC	-	novel	NA	P-0007788-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	47	969	0	ENST00000358026.2:c.339_342del	p.Met113IlefsTer189	p.M113Ifs*189	ENST00000358026	NM_001128849.1	113	atGGAC/at	3/36	0.241553626300025	0	FACETS	0.405	0.343	0.473			1	INDETERMINATE	1	TRUE	0	0.411356487282266	0		969	332	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467197	25467197	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007788-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	24	678	0	ENST00000264709.3:c.1678G>T	p.Val560Leu	p.V560L	ENST00000264709	NM_175629.2	560	Gtg/Ttg	15/23	0.197419969028303	1	FACETS	0.328	0.257	0.409	0.328	0.257	0.409	INDETERMINATE	1	TRUE	0	0.411356487282266	1		678	283	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46266444	46266444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007788-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	24	777	1	ENST00000371998.3:c.2429C>T	p.Ser810Phe	p.S810F	ENST00000371998		810	tCt/tTt	13/23	1	2	FACETS	0.407	0.319	0.507	0.407	0.319	0.507	SUBCLONAL	1	TRUE	1	0.411356487282266	2		778	287	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0007788-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	30	329	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.3940035886366	1	FACETS	0.686	0.558	0.826	0.686	0.558	0.826	SUBCLONAL	1	TRUE	0	0.411356487282266	1		329	169	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539493	187539493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007788-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	36	690	0	ENST00000441802.2:c.8247G>T	p.Glu2749Asp	p.E2749D	ENST00000441802	NM_005245.3	2749	gaG/gaT	10/27	1	2	FACETS	0.712	0.589	0.847	0.712	0.589	0.847	SUBCLONAL	1	TRUE	1	0.411356487282266	2		690	246	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344679	70344679	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007788-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	63	977	0	ENST00000374080.3:c.2040del	p.Lys681SerfsTer30	p.K681Sfs*30	ENST00000374080		680	gaG/ga	14/45	1	2	FACETS	0.868	0.755	0.989	0.868	0.755	0.989	CLONAL	1	TRUE	1	0.411356487282266	2		977	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0007901-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	83	675	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		675	1048	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0007901-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	66	604	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		604	951	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17116982	17116982	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007901-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	200	584	1	ENST00000285071.4:c.1727A>G	p.Glu576Gly	p.E576G	ENST00000285071	NM_144997.5	576	gAg/gGg	14/14	0.3	4	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	4		585	1096	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0008077-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	291	701	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.276171365550608	3	FACETS	1	0.961	1	0.682	0.643	0.721	CLONAL	2	TRUE	0	0.398203254093693	3		701	857	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243484	46243484	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008077-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	190	483	0	ENST00000334344.6:c.1837C>T	p.Gln613Ter	p.Q613*	ENST00000334344	NM_152641.2	613	Cag/Tag	14/21	0.276171365550608	3	FACETS	1	0.944	1	0.677	0.63	0.726	CLONAL	2	TRUE	0	0.398203254093693	3		483	563	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741454	145741454	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008077-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	501	1039	2	ENST00000428558.2:c.1049G>T	p.Arg350Met	p.R350M	ENST00000428558	NM_004260.3	350	aGg/aTg	5/22	0.37294616673964	3	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.398203254093693	3		1041	1329	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667601	29667601	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008077-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	298	769	0	ENST00000356175.3:c.6937G>C	p.Gly2313Arg	p.G2313R	ENST00000356175	NM_000267.3	2313	Ggt/Cgt	46/57	0.276171365550608	3	FACETS	1	0.98	1	0.718	0.679	0.758	CLONAL	2	TRUE	0	0.398203254093693	3		769	833	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868166	45868166	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1463343405	NA	P-0008077-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	438	1028	1	ENST00000391945.4:c.524A>G	p.Tyr175Cys	p.Y175C	ENST00000391945	NM_000400.3	175	tAc/tGc	7/23	0.301699075229242	4	FACETS	1	0.994	1	0.819	0.782	0.857	CLONAL	2	TRUE	1	0.398203254093693	4		1029	1252	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21627866	21627866	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008077-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	80	862	0	ENST00000421138.2:c.1264G>A	p.Asp422Asn	p.D422N	ENST00000421138		422	Gat/Aat	12/16	0.276171365550608	3	FACETS	0.572	0.502	0.646	0.191	0.167	0.216	SUBCLONAL	1	TRUE	0	0.398203254093693	3		862	843	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578498	7578499	+	missense_variant	Missense_Mutation	DNP	CT	CT	GG	novel	NA	P-0009450-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	367	919	1	ENST00000269305.4:c.431_432delinsCC	p.Gln144Pro	p.Q144P	ENST00000269305	NM_001126112.2	144	cAG/cCC	5/11	0.717723303375014	2	FACETS	0.985	0.952	1	0.985	0.952	1	CLONAL	2	TRUE	0	0.745454921449805	2		920	500	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48921906	48921975	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TATGACTTCTAAATTACGAAAAAATGTTAAAAAGTCATAATGTTTTTCTTTTCAGGACATGTGAACTTAT	TATGACTTCTAAATTACGAAAAAATGTTAAAAAGTCATAATGTTTTTCTTTTCAGGACATGTGAACTTAT	-	novel	NA	P-0009450-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	111	115	0	ENST00000267163.4:c.501-55_515del		p.X167_splice	ENST00000267163	NM_000321.2	167		5/27	0.743007708195742	3	FACETS	1	0.985	1	0.826	0.771	0.878	CLONAL	2	TRUE	0	0.745454921449805	3		115	165	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145289	58145289	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009450-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	37	521	0	ENST00000257904.6:c.212T>C	p.Val71Ala	p.V71A	ENST00000257904	NM_000075.3	71	gTt/gCt	2/8	0.716333384636615	2	FACETS	0.293	0.242	0.35	0.146	0.121	0.175	SUBCLONAL	1	TRUE	0	0.745454921449805	2		521	339	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626737	28626737	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009450-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	33	561	0	ENST00000241453.7:c.559G>C	p.Glu187Gln	p.E187Q	ENST00000241453	NM_004119.2	187	Gag/Cag	5/24	0.743007708195742	3	FACETS	0.205	0.166	0.249	0.068	0.055	0.083	SUBCLONAL	1	TRUE	0	0.745454921449805	3		561	593	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845344	42845344	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009450-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	195	793	0	ENST00000398585.3:c.918G>A	p.Trp306Ter	p.W306*	ENST00000398585	NM_001135099.1	306	tgG/tgA	9/14	0.666695102501535	3	FACETS	1	0.94	1	0.506	0.47	0.544	CLONAL	1	TRUE	1	0.745454921449805	3		793	709	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590726	189590726	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009450-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	42	632	0	ENST00000264731.3:c.1291A>G	p.Thr431Ala	p.T431A	ENST00000264731	NM_003722.4	431	Aca/Gca	10/14	0.743007708195742	3	FACETS	0.277	0.23	0.328	0.092	0.076	0.11	SUBCLONAL	1	TRUE	0	0.745454921449805	3		632	559	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0010847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	94	436	1	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	0.380834386559515	1	FACETS	0.779	0.696	0.867	0.779	0.696	0.867	SUBCLONAL	1	TRUE	0	0.380834386559515	1		437	513	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222201	2222201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	143	556	0	ENST00000326181.6:c.485C>T	p.Pro162Leu	p.P162L	ENST00000326181	NM_032271.2	162	cCc/cTc	8/21	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.380834386559515	2		556	717	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0010847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	187	382	1	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	0.195511058595413	2	FACETS	0.797	0.74	0.856	0.797	0.74	0.856	INDETERMINATE	2	TRUE	0	0.380834386559515	2		383	616	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325105	123325105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	153	666	0	ENST00000358487.5:c.223G>A	p.Asp75Asn	p.D75N	ENST00000358487	NM_000141.4	75	Gat/Aat	3/18	0.298016969940693	1	FACETS	0.824	0.755	0.897	0.824	0.755	0.897	CLONAL	1	TRUE	0	0.380834386559515	1		666	789	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729934	41729934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146325702	NA	P-0010847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	220	678	0	ENST00000242208.4:c.595G>A	p.Gly199Arg	p.G199R	ENST00000242208	NM_002192.2	199	Ggg/Agg	3/3	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.380834386559515	2		678	878	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129869	55129869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	159	605	0	ENST00000257290.5:c.403G>A	p.Asp135Asn	p.D135N	ENST00000257290	NM_006206.4	135	Gat/Aat	4/23	0.380834386559515	3	FACETS	1	0.93	1	0.508	0.465	0.553	CLONAL	1	TRUE	1	0.380834386559515	3		605	978	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562641	29562641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854562	NA	P-0010847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	71	502	0	ENST00000356175.3:c.3721C>T	p.Arg1241Ter	p.R1241*	ENST00000356175	NM_000267.3	1241	Cga/Tga	28/57	0.195511058595413	2	FACETS	0.436	0.38	0.497	0.218	0.19	0.249	INDETERMINATE	1	TRUE	0	0.380834386559515	2		502	855	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176666786	176666786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	72	314	0	ENST00000439151.2:c.4222C>T	p.Pro1408Ser	p.P1408S	ENST00000439151	NM_022455.4	1408	Cca/Tca	8/23	1	2	FACETS	0.846	0.742	0.958	0.846	0.742	0.958	CLONAL	1	TRUE	1	0.380834386559515	2		314	447	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458690	120458690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1386606005	NA	P-0010847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	174	574	0	ENST00000256646.2:c.6655C>T	p.Pro2219Ser	p.P2219S	ENST00000256646	NM_024408.3	2219	Ccc/Tcc	34/34	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.380834386559515	2		574	739	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470977	25470977	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	83	636	0	ENST00000264709.3:c.784C>T	p.Pro262Ser	p.P262S	ENST00000264709	NM_175629.2	262	Cct/Tct	7/23	0.298016969940693	1	FACETS	0.494	0.436	0.557	0.494	0.436	0.557	SUBCLONAL	1	TRUE	0	0.380834386559515	1		636	714	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439769	220439769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111982983	NA	P-0010847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	106	709	0	ENST00000243786.2:c.622C>T	p.Arg208Trp	p.R208W	ENST00000243786	NM_002191.3	208	Cgg/Tgg	2/2	1	2	FACETS	0.733	0.657	0.814	0.733	0.657	0.814	SUBCLONAL	1	TRUE	1	0.380834386559515	2		709	759	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55974004	55974004	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754979123	NA	P-0010847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	174	517	1	ENST00000263923.4:c.1312G>A	p.Gly438Ser	p.G438S	ENST00000263923	NM_002253.2	438	Ggc/Agc	10/30	0.380834386559515	3	FACETS	1	0.979	1	0.591	0.544	0.64	CLONAL	1	TRUE	1	0.380834386559515	3		518	920	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38954953	38954953	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	90	282	0	ENST00000357387.3:c.2620C>T	p.Pro874Ser	p.P874S	ENST00000357387	NM_152756.3	874	Cct/Tct	27/38	0.380834386559515	3	FACETS	1	0.934	1	0.535	0.476	0.598	CLONAL	1	TRUE	1	0.380834386559515	3		282	526	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197396	26197396	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	92	360	0	ENST00000356476.2:c.83A>T	p.Lys28Met	p.K28M	ENST00000356476		28	aAg/aTg	1/1	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.380834386559515	2		360	424	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956991	2956991	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	200	503	0	ENST00000396946.4:c.2636C>T	p.Ser879Leu	p.S879L	ENST00000396946	NM_032415.4	879	tCa/tTa	20/25	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.380834386559515	2		503	822	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367239	50367239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1045233686	NA	P-0010847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	81	259	0	ENST00000331340.3:c.46G>A	p.Glu16Lys	p.E16K	ENST00000331340	NM_006060.4	16	Gaa/Aaa	3/8	1	2	FACETS	0.886	0.783	0.996	0.886	0.783	0.996	CLONAL	1	TRUE	1	0.380834386559515	2		259	480	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372059	55372059	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	26	224	0	ENST00000297316.4:c.749C>A	p.Thr250Asn	p.T250N	ENST00000297316	NM_022454.3	250	aCc/aAc	2/2	1	2	FACETS	0.488	0.387	0.602	0.488	0.387	0.602	SUBCLONAL	1	TRUE	1	0.380834386559515	2		224	280	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325128	123325128	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	136	639	0	ENST00000358487.5:c.200C>A	p.Ala67Asp	p.A67D	ENST00000358487	NM_000141.4	67	gCc/gAc	3/18	0.298016969940693	1	FACETS	0.735	0.668	0.804	0.735	0.668	0.804	SUBCLONAL	1	TRUE	0	0.380834386559515	1		639	787	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925096	81925096	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867804190	NA	P-0010847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	139	472	3	ENST00000359376.3:c.887C>T	p.Ser296Leu	p.S296L	ENST00000359376	NM_002661.3	296	tCa/tTa	11/33	0.380834386559515	1	FACETS	0.947	0.865	1	0.947	0.865	1	CLONAL	1	TRUE	0	0.380834386559515	1		475	624	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739007	40739007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	121	443	0	ENST00000373198.4:c.3277C>T	p.Pro1093Ser	p.P1093S	ENST00000373198	NM_133170.3	1093	Ccc/Tcc	24/32	1	2	FACETS	0.947	0.857	1	0.947	0.857	1	CLONAL	1	TRUE	1	0.380834386559515	2		443	671	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123880935	123880935	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010920-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	174	555	0	ENST00000330479.4:c.553T>G	p.Tyr185Asp	p.Y185D	ENST00000330479	NM_020382.3	185	Tac/Gac	5/9	0.331692897278442	3	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	1	0.460867185031058	3		555	458	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266501	198266501	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010920-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	103	541	0	ENST00000335508.6:c.2335T>G	p.Ser779Ala	p.S779A	ENST00000335508	NM_012433.2	779	Tct/Gct	16/25	0.470575323691481	4	FACETS	0.816	0.73	0.908			1	CLONAL	1	TRUE	NA	0.460867185031058	4		541	800	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52661328	52661328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010920-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	143	675	0	ENST00000394830.3:c.1502C>T	p.Ser501Phe	p.S501F	ENST00000394830	NM_018313.4	501	tCt/tTt	14/30	0.401531627701235	4	FACETS	1	0.958	1			1	CLONAL	1	TRUE	NA	0.460867185031058	4		675	837	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859301	151859319	+	frameshift_variant	Frame_Shift_Del	DEL	AGATGACTTTTTATTTTTC	AGATGACTTTTTATTTTTC	-	novel	NA	P-0010920-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	159	523	0	ENST00000262189.6:c.11343_11361del	p.Leu3781PhefsTer4	p.L3781Ffs*4	ENST00000262189	NM_170606.2	3781	ttGAAAAATAAAAAGTCATCT/tt	43/59	0.115608355053339	5	FACETS	1	0.96	1			1	INDETERMINATE	2	TRUE	NA	0.460867185031058	5		523	548	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841271	15841271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768133914	NA	P-0010920-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	339	352	1	ENST00000307771.7:c.1355G>A	p.Arg452His	p.R452H	ENST00000307771	NM_005089.3	452	cGc/cAc	11/11	1	1	FACETS	1	0.994	1	1	0.997	1	CLONAL	3	TRUE	0	0.460867185031058	1		353	364	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561764	55561764	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913505	NA	P-0011037-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	121	412	1	ENST00000288135.5:c.154G>A	p.Asp52Asn	p.D52N	ENST00000288135	NM_000222.2	52	Gac/Aac	2/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.537992458501339	2		413	389	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0012897-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	227	255	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.364319057938955	4	FACETS	0.949	0.885	1	0.633	0.59	0.676	CLONAL	2	TRUE	1	0.364319057938955	4		255	896	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012897-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	157	312	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.345935360027706	3	FACETS	1	0.982	1	0.625	0.573	0.679	CLONAL	1	TRUE	1	0.364319057938955	3		312	815	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0012897-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	224	425	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	0.345935360027706	3	FACETS	1	0.983	1	0.589	0.547	0.632	CLONAL	1	TRUE	1	0.364319057938955	3		425	1235	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531765	46531765	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012897-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1299	140	371	1	ENST00000262741.5:c.582G>T	p.Glu194Asp	p.E194D	ENST00000262741	NM_003629.3	194	gaG/gaT	5/10	0.345935360027706	3	FACETS	0.631	0.573	0.693	0.316	0.286	0.347	SUBCLONAL	1	TRUE	1	0.364319057938955	3		372	1439	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225561	26225561	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012897-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1741	680	895	1	ENST00000360408.1:c.179A>T	p.Glu60Val	p.E60V	ENST00000360408	NM_003532.2	60	gAg/gTg	1/1	0.313349352709505	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.364319057938955	4		896	2421	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602484	10602485	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0012897-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	227	347	0	ENST00000171111.5:c.1093dup	p.Leu365ProfsTer50	p.L365Pfs*50	ENST00000171111	NM_203500.1	365	ctg/cCtg	3/6	0.364319057938955	2	FACETS	0.992	0.93	1	0.992	0.93	1	CLONAL	2	TRUE	0	0.364319057938955	2		347	628	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374293	138374293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013032-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	303	697	0	ENST00000289153.2:c.3151G>A	p.Glu1051Lys	p.E1051K	ENST00000289153	NM_006219.2	1051	Gaa/Aaa	22/22	0.349127071289554	1	FACETS	0.728	0.69	0.765	0.728	0.69	0.765	INDETERMINATE	1	TRUE	0	0.740738221943205	1		697	708	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013032-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	360	604	0	ENST00000269305.4:c.376T>C	p.Tyr126His	p.Y126H	ENST00000269305	NM_001126112.2	126	Tac/Cac	5/11	0.737771616911086	1	FACETS	0.975	0.934	1	0.975	0.934	1	CLONAL	1	TRUE	0	0.740738221943205	1		604	628	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860080	57860080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs563340967	NA	P-0013032-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	174	549	0	ENST00000228682.2:c.820G>A	p.Gly274Ser	p.G274S	ENST00000228682	NM_005269.2	274	Ggc/Agc	8/12	0.396428593158701	1	FACETS	0.383	0.353	0.414	0.383	0.353	0.414	INDETERMINATE	1	TRUE	0	0.740738221943205	1		549	773	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278062	18278062	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013032-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	371	515	0	ENST00000222254.8:c.1682A>C	p.Asn561Thr	p.N561T	ENST00000222254	NM_005027.3	561	aAc/aCc	13/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.740738221943205	2		515	975	SUCCESS
APC	324	MSKCC	GRCh37	5	112175866	112175867	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCTCCAGTTCAGGAAAATGACAATGGGAATGAAA	novel	NA	P-0013032-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	65	164	0	ENST00000257430.4:c.4577_4610dup	p.Glu1538SerfsTer6	p.E1538Sfs*6	ENST00000257430	NM_000038.5	1525	-/CCTCCAGTTCAGGAAAATGACAATGGGAATGAAA	16/16	0.740738221943205	1	FACETS	0.472	0.415	0.533	0.472	0.415	0.533	SUBCLONAL	1	TRUE	0	0.740738221943205	1		164	234	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866452	42866506	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	TTCCGGTTGGTATCCATGGTTTTCATAGTAAGGTCCAATAGCTGGTGGTGACCCC	TTCCGGTTGGTATCCATGGTTTTCATAGTAAGGTCCAATAGCTGGTGGTGACCCC	-	novel	NA	P-0013032-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	171	687	0	ENST00000398585.3:c.127-1_180del		p.X43_splice	ENST00000398585	NM_001135099.1	43		3/14	0.396428593158701	1	FACETS	0.276	0.253	0.3	0.276	0.253	0.3	INDETERMINATE	1	TRUE	0	0.740738221943205	1		687	1054	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060573	38060573	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013032-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	403	547	0	ENST00000250448.2:c.1416del	p.Ter473SerfsTer11	p.*473Sfs*11	ENST00000250448	NM_004496.3	472	tcC/tc	2/2	1	2	FACETS	0.965	0.919	1	0.965	0.919	1	CLONAL	1	TRUE	1	0.740738221943205	2		547	1128	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433010	49433028	+	frameshift_variant	Frame_Shift_Del	DEL	GTTCACATCCATAGAGGAA	GTTCACATCCATAGAGGAA	-	novel	NA	P-0013032-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	273	422	0	ENST00000301067.7:c.8343_8361del	p.Ser2782AlafsTer5	p.S2782Afs*5	ENST00000301067	NM_003482.3	2781	ccTTCCTCTATGGATGTGAAC/cc	33/54	NA	2	FACETS	0.904	0.852	0.958			1	INDETERMINATE	1	TRUE	NA	0.740738221943205	2		422	815	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913400	NA	P-0014519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	112	335	0	ENST00000349496.5:c.98C>A	p.Ser33Tyr	p.S33Y	ENST00000349496	NM_001904.3	33	tCt/tAt	3/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.666554286842768	2		335	297	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0014519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	274	436	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	0.666554286842768	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.666554286842768	1		436	386	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089590	27089591	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0014519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	338	574	0	ENST00000324856.7:c.2547_2548dup	p.Tyr850PhefsTer10	p.Y850Ffs*10	ENST00000324856	NM_006015.4	849	cct/ccTTt	8/20	0.666554286842768	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.666554286842768	1		574	504	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271534	26271534	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	17	379	0	ENST00000305910.3:c.79C>T	p.Arg27Trp	p.R27W	ENST00000305910	NM_003534.2	27	Cgg/Tgg	1/1	1	2	FACETS	0.16	0.119	0.209	0.16	0.119	0.209	SUBCLONAL	1	TRUE	1	0.666554286842768	2		379	319	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568563	41568563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555911574	NA	P-0015127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	91	557	0	ENST00000263253.7:c.4513G>A	p.Glu1505Lys	p.E1505K	ENST00000263253	NM_001429.3	1505	Gag/Aag	28/31	1	2	FACETS	0.581	0.516	0.65	0.581	0.516	0.65	SUBCLONAL	1	TRUE	1	0.494105807227549	2		557	634	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805882	46805882	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780165	NA	P-0015127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	94	360	0	ENST00000290295.7:c.74G>A	p.Arg25Gln	p.R25Q	ENST00000290295	NM_006361.5	25	cGg/cAg	1/2	0.494105807227549	3	FACETS	0.754	0.672	0.842	0.377	0.336	0.421	SUBCLONAL	1	TRUE	1	0.494105807227549	3		360	629	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875876	76875876	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	232	469	0	ENST00000373344.5:c.5259del	p.Asn1753LysfsTer3	p.N1753Kfs*3	ENST00000373344	NM_000489.3	1753	aaT/aa	20/35	0.320271338892923	5	FACETS	0.958	0.901	1	0.958	0.901	1	CLONAL	3	TRUE	2	0.494105807227549	5		469	569	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	856	812	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.886136072628712	7	FACETS	0.938	0.919	0.956	0.938	0.919	0.956	CLONAL	6	TRUE	1	0.886136072628712	7		812	1104	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0015210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	295	359	2	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.769417335438643	4	FACETS	0.905	0.857	0.952	0.905	0.857	0.952	CLONAL	2	TRUE	2	0.886136072628712	4		361	694	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439674	51439674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1258626034	NA	P-0015210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	164	299	0	ENST00000262662.1:c.239C>T	p.Ala80Val	p.A80V	ENST00000262662		80	gCa/gTa	4/4	0.871747974370219	3	FACETS	1	0.937	1	0.508	0.469	0.547	CLONAL	1	TRUE	1	0.886136072628712	3		299	526	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278091	41278111	+	inframe_deletion	In_Frame_Del	DEL	CTGCTGTTTTGTTCCGAATGT	CTGCTGTTTTGTTCCGAATGT	-	novel	NA	P-0015210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	110	306	0	ENST00000349496.5:c.1970_1990del	p.Ala657_Ser663del	p.A657_S663del	ENST00000349496	NM_001904.3	656	gCTGCTGTTTTGTTCCGAATGTct/gct	13/15	0.871747974370219	3	FACETS	0.784	0.709	0.863	0.392	0.354	0.432	SUBCLONAL	1	TRUE	1	0.886136072628712	3		306	457	SUCCESS
APC	324	MSKCC	GRCh37	5	112173668	112173668	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	238	290	0	ENST00000257430.4:c.2377C>T	p.Gln793Ter	p.Q793*	ENST00000257430	NM_000038.5	793	Caa/Taa	16/16	0.769417335438643	4	FACETS	0.919	0.866	0.973	0.919	0.866	0.973	CLONAL	2	TRUE	2	0.886136072628712	4		290	551	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0015218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	25	526	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.437	0.343	0.547	0.437	0.343	0.547	SUBCLONAL	1	TRUE	1	0.13	2		526	880	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0015218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1298	52	863	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	1	2	FACETS	0.593	0.502	0.693	0.593	0.502	0.693	SUBCLONAL	1	TRUE	1	0.13	2		863	1350	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637598	52637601	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	novel	NA	P-0015218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	42	348	0	ENST00000394830.3:c.2715_2718del	p.Glu908AsnfsTer6	p.E908Nfs*6	ENST00000394830	NM_018313.4	905	gaGAGA/ga	18/30	1	2	FACETS	0.901	0.751	1	0.901	0.751	1	CLONAL	1	TRUE	1	0.13	2		348	717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0015323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	232	863	7	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.290029526300823	2	FACETS	0.842	0.786	0.9	0.842	0.786	0.9	CLONAL	2	TRUE	0	0.290029526300823	2		870	950	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0015323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	210	328	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.215459019766789	4	FACETS	0.9	0.835	0.967	0.9	0.835	0.967	CLONAL	2	TRUE	2	0.290029526300823	4		328	1038	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057520000	NA	P-0015376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	94	469	2	ENST00000269305.4:c.452C>A	p.Pro151His	p.P151H	ENST00000269305	NM_001126112.2	151	cCc/cAc	5/11	NA	2	FACETS	0.889	0.797	0.986			1	INDETERMINATE	2	TRUE	NA	0.271710072312724	2		471	389	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587777894	NA	P-0015376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	67	401	0	ENST00000361445.4:c.6644C>A	p.Ser2215Tyr	p.S2215Y	ENST00000361445	NM_004958.3	2215	tCt/tAt	47/58	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.271710072312724	2		401	429	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31947215	31947215	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	119	368	0	ENST00000375333.2:c.700C>T	p.Pro234Ser	p.P234S	ENST00000375333	NM_032454.1	234	Ccg/Tcg	5/8	0.239871676683553	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.271710072312724	2		368	396	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0015380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	84	291	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.277463195212711	2	FACETS	0.858	0.768	0.953	0.858	0.768	0.953	CLONAL	2	TRUE	0	0.354588818452054	2		291	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0015380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	155	571	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.354588818452054	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.354588818452054	2		571	371	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0015380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	126	605	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.267918748282116	2	FACETS	0.963	0.882	1	0.963	0.882	1	CLONAL	2	TRUE	0	0.354588818452054	2		605	369	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213872	66213872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772452750	NA	P-0015380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	64	427	1	ENST00000273854.3:c.2558G>A	p.Arg853Gln	p.R853Q	ENST00000273854	NM_004439.5	853	cGa/cAa	15/18	1	2	FACETS	0.952	0.829	1	0.952	0.829	1	CLONAL	1	TRUE	1	0.354588818452054	2		428	379	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101274	27101275	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	87	480	0	ENST00000324856.7:c.4559dup	p.Ala1522ArgfsTer10	p.A1522Rfs*10	ENST00000324856	NM_006015.4	1519	cag/caGg	18/20	0.267918748282116	2	FACETS	0.829	0.742	0.919	0.829	0.742	0.919	CLONAL	2	TRUE	0	0.354588818452054	2		480	296	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	443560	443560	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	114	343	0	ENST00000399788.2:c.1337A>G	p.Asn446Ser	p.N446S	ENST00000399788	NM_001042603.1	446	aAt/aGt	11/28	0.207665481333103	4	FACETS	1	0.92	1	1	0.92	1	INDETERMINATE	2	TRUE	2	0.354588818452054	4		343	429	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591894	48591894	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	73	357	0	ENST00000342988.3:c.1057T>C	p.Tyr353His	p.Y353H	ENST00000342988	NM_005359.5	353	Tac/Cac	9/12	0.354588818452054	2	FACETS	0.884	0.784	0.987	0.884	0.784	0.987	CLONAL	2	TRUE	0	0.354588818452054	2		357	233	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729713	41729713	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	66	414	1	ENST00000242208.4:c.816G>T	p.Lys272Asn	p.K272N	ENST00000242208	NM_002192.2	272	aaG/aaT	3/3	0.238470329810182	4	FACETS	1	0.963	1	0.648	0.565	0.737	CLONAL	1	TRUE	2	0.354588818452054	4		415	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0015548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	541	660	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.551651776612034	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	FALSE	0	0.554257290065104	2		661	913	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130439	29130439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	508	714	1	ENST00000328354.6:c.271G>A	p.Ala91Thr	p.A91T	ENST00000328354	NM_007194.3	91	Gcc/Acc	2/15	0.554257290065104	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	FALSE	0	0.554257290065104	2		715	823	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275139	41275139	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	199	334	2	ENST00000349496.5:c.1305G>T	p.Lys435Asn	p.K435N	ENST00000349496	NM_001904.3	435	aaG/aaT	9/15	0.554257290065104	4	FACETS	0.976	0.91	1	0.976	0.91	1	CLONAL	2	FALSE	2	0.554257290065104	4		336	572	SUCCESS
APC	324	MSKCC	GRCh37	5	112111351	112111352	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0015548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	187	462	0	ENST00000257430.4:c.449_450del	p.Lys150ArgfsTer17	p.K150Rfs*17	ENST00000257430	NM_000038.5	150	AAa/a	5/16	0.554257290065104	3	FACETS	0.868	0.818	0.917	0.868	0.818	0.917	CLONAL	3	FALSE	0	0.554257290065104	3		462	331	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495472	149495472	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	666	977	1	ENST00000261799.4:c.3175T>A	p.Ser1059Thr	p.S1059T	ENST00000261799	NM_002609.3	1059	Tcc/Acc	23/23	0.554257290065104	3	FACETS	1	0.978	1	0.678	0.654	0.701	CLONAL	2	FALSE	0	0.554257290065104	3		978	1510	SUCCESS
AR	367	MSKCC	GRCh37	X	66766237	66766237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	203	247	0	ENST00000374690.3:c.1249G>A	p.Ala417Thr	p.A417T	ENST00000374690	NM_000044.3	417	Gcg/Acg	1/8	0.554257290065104	6	FACETS	1	0.987	1	0.83	0.774	0.888	CLONAL	2	FALSE	3	0.554257290065104	6		247	620	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0015567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	150	790	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.260239235249546	4	FACETS	1	0.964	1	0.534	0.494	0.575	INDETERMINATE	2	TRUE	0	0.598655759225794	4		790	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747342068	NA	P-0015567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	443	1110	0	ENST00000269305.4:c.394A>G	p.Lys132Glu	p.K132E	ENST00000269305	NM_001126112.2	132	Aag/Gag	5/11	0.532572698546862	2	FACETS	0.925	0.89	0.96	0.925	0.89	0.96	CLONAL	2	TRUE	0	0.598655759225794	2		1110	800	SUCCESS
APC	324	MSKCC	GRCh37	5	112175215	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0015567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	31	244	0	ENST00000257430.4:c.3925_3926del	p.Glu1309LysfsTer5	p.E1309Kfs*5	ENST00000257430	NM_000038.5	1308	aaAGaa/aaaa	16/16	0.179940279427211	2	FACETS	0.785	0.645	0.936	0.392	0.322	0.468	INDETERMINATE	1	TRUE	0	0.598655759225794	2		244	132	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498424	89498424	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1176464192	NA	P-0015567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	79	377	2	ENST00000336596.2:c.2396G>A	p.Arg799His	p.R799H	ENST00000336596	NM_005233.5	799	cGc/cAc	14/17	0.260239235249546	4	FACETS	1	0.97	1	0.606	0.547	0.666	INDETERMINATE	2	TRUE	0	0.598655759225794	4		379	174	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392144	81392145	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	14	330	0	ENST00000222390.5:c.132dup	p.Ser45IlefsTer28	p.S45Ifs*28	ENST00000222390	NM_000601.4	44	-/A	2/18	0.598655759225794	3	FACETS	0.411	0.298	0.545	0.205	0.149	0.273	SUBCLONAL	1	TRUE	1	0.598655759225794	3		330	148	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563108	21563108	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746991718	NA	P-0015567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1256	200	820	0	ENST00000382592.4:c.811C>T	p.Arg271Cys	p.R271C	ENST00000382592	NM_014572.2	271	Cgc/Tgc	4/8	0.281735219662033	6	FACETS	1	0.931	1	0.168	0.155	0.182	INDETERMINATE	1	TRUE	0	0.598655759225794	6		820	1456	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944250	81944250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147396004	NA	P-0015567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	419	808	0	ENST00000359376.3:c.1859C>T	p.Thr620Met	p.T620M	ENST00000359376	NM_002661.3	620	aCg/aTg	18/33	0.273287307667633	5	FACETS	0.956	0.91	1	0.637	0.606	0.669	INDETERMINATE	2	TRUE	2	0.598655759225794	5		808	1390	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117861	70117862	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGTT	novel	NA	P-0015567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	151	421	0	ENST00000245479.2:c.331_332insTTCG	p.Ala111ValfsTer142	p.A111Vfs*142	ENST00000245479	NM_000346.3	110	aac/aaCGTTc	1/3	0.201207714342318	4	FACETS	1	0.987	1	0.709	0.651	0.768	INDETERMINATE	1	TRUE	2	0.598655759225794	4		421	569	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196432	106196432	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	47	460	0	ENST00000380013.4:c.4765T>C	p.Tyr1589His	p.Y1589H	ENST00000380013	NM_001127208.2	1589	Tat/Cat	11/11	0.179940279427211	2	FACETS	1	0.922	1	0.553	0.477	0.633	INDETERMINATE	1	TRUE	0	0.598655759225794	2		460	142	SUCCESS
APC	324	MSKCC	GRCh37	5	112173968	112173968	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	69	407	0	ENST00000257430.4:c.2677del	p.Glu893LysfsTer23	p.E893Kfs*23	ENST00000257430	NM_000038.5	893	Gaa/aa	16/16	0.179940279427211	2	FACETS	0.918	0.81	1	0.459	0.405	0.516	INDETERMINATE	1	TRUE	0	0.598655759225794	2		407	251	SUCCESS
APC	324	MSKCC	GRCh37	5	112175365	112175366	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	145	272	0	ENST00000257430.4:c.4077dup	p.Ser1360IlefsTer15	p.S1360Ifs*15	ENST00000257430	NM_000038.5	1358	-/A	16/16	0.555917644709602	1	FACETS	0.89	0.827	0.954	0.89	0.827	0.954	CLONAL	1	TRUE	0	0.693235757534575	1		272	307	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573563	48573564	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs786203560	NA	P-0015961-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	27	333	0	ENST00000342988.3:c.153dup	p.Asp52ArgfsTer2	p.D52Rfs*2	ENST00000342988	NM_005359.5	49	-/A	2/12	1	2	FACETS	0.579	0.461	0.716	0.579	0.461	0.716	SUBCLONAL	1	TRUE	1	0.225650860556378	2		333	413	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775719	9775719	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015961-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	127	855	0	ENST00000377346.4:c.262C>A	p.Arg88Ser	p.R88S	ENST00000377346	NM_005026.3	88	Cgt/Agt	4/24	0.225650860556378	3	FACETS	1	0.97	1	0.589	0.533	0.649	CLONAL	1	TRUE	1	0.225650860556378	3		855	1063	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78831605	78831605	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015961-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	42	618	0	ENST00000306801.3:c.1414A>G	p.Ile472Val	p.I472V	ENST00000306801	NM_020761.2	472	Atc/Gtc	13/34	0.225650860556378	3	FACETS	0.522	0.435	0.62	0.261	0.217	0.31	SUBCLONAL	1	TRUE	1	0.225650860556378	3		618	793	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916926	178916937	+	inframe_deletion	In_Frame_Del	DEL	GTAGGCAACCGT	GTAGGCAACCGT	-	novel	NA	P-0016441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	120	664	0	ENST00000263967.3:c.314_325del	p.Val105_Arg108del	p.V105_R108del	ENST00000263967	NM_006218.2	105	GTAGGCAACCGT/-	2/21	1	2	FACETS	0.918	0.827	1	0.918	0.827	1	CLONAL	1	TRUE	1	0.245115184584713	2		664	1067	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0016441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	111	420	0	ENST00000269305.4:c.782+1G>C		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.245115184584713	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.245115184584713	1		420	722	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246695	41246695	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	121	479	0	ENST00000357654.3:c.853C>T	p.His285Tyr	p.H285Y	ENST00000357654	NM_007294.3	285	Cat/Tat	10/23	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.245115184584713	2		479	893	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440695	56440696	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0016441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	127	678	0	ENST00000407977.2:c.522dup	p.Phe175ValfsTer13	p.F175Vfs*13	ENST00000407977		174	-/G	5/10	0.245115184584713	1	FACETS	0.968	0.876	1	0.968	0.876	1	CLONAL	1	TRUE	0	0.245115184584713	1		678	939	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581343	48581344	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CATT	novel	NA	P-0016441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	95	474	0	ENST00000342988.3:c.649_652dup	p.Pro218HisfsTer18	p.P218Hfs*18	ENST00000342988	NM_005359.5	216	aac/aaCATTc	5/12	0.245115184584713	1	FACETS	0.879	0.782	0.982	0.879	0.782	0.982	CLONAL	1	TRUE	0	0.245115184584713	1		474	774	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918712	44918712	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0016441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	106	230	0	ENST00000377967.4:c.1194+1G>C		p.X398_splice	ENST00000377967	NM_021140.2	398			1	1	FACETS	0.906	0.818	0.998	1	0.987	1	CLONAL	2	TRUE	0	0.245115184584713	1		230	419	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692911	89692911	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121909241	NA	P-0016721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	36	619	1	ENST00000371953.3:c.395G>T	p.Gly132Val	p.G132V	ENST00000371953	NM_000314.4	132	gGt/gTt	5/9	1	2	FACETS	0.119	0.097	0.144	0.119	0.097	0.144	SUBCLONAL	1	FALSE	1	0.918384917091245	2		620	657	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303175	11303175	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	38	550	0	ENST00000361445.4:c.1408C>T	p.His470Tyr	p.H470Y	ENST00000361445	NM_004958.3	470	Cat/Tat	9/58	1	2	FACETS	0.115	0.094	0.138	0.115	0.094	0.138	SUBCLONAL	1	FALSE	1	0.918384917091245	2		550	719	SUCCESS
APC	324	MSKCC	GRCh37	5	112175030	112175030	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	27	297	0	ENST00000257430.4:c.3739G>T	p.Ala1247Ser	p.A1247S	ENST00000257430	NM_000038.5	1247	Gcc/Tcc	16/16	NA	2	FACETS	0.131	0.104	0.163			1	INDETERMINATE	1	FALSE	NA	0.918384917091245	2		297	448	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659176	86659176	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	15	212	1	ENST00000274376.6:c.1465C>T	p.Arg489Cys	p.R489C	ENST00000274376	NM_002890.2	489	Cgt/Tgt	11/25	1	2	FACETS	0.116	0.084	0.154	0.116	0.084	0.154	SUBCLONAL	1	FALSE	1	0.918384917091245	2		213	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0016809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	103	753	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	NA	2	FACETS	0.984	0.899	1			1	INDETERMINATE	2	TRUE	NA	0.44522108061162	2		753	235	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249810	39249810	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1458063607	NA	P-0016809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	112	371	0	ENST00000402219.2:c.1759A>G	p.Ile587Val	p.I587V	ENST00000402219	NM_005633.3	587	Ata/Gta	10/23	0.419054527480764	3	FACETS	0.915	0.843	0.988	1	0.985	1	CLONAL	3	TRUE	1	0.44522108061162	3		371	224	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945675	54945675	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	67	319	0	ENST00000312783.6:c.895G>C	p.Glu299Gln	p.E299Q	ENST00000312783	NM_198436.1	299	Gaa/Caa	9/10	0.44522108061162	5	FACETS	0.962	0.854	1	0.962	0.854	1	CLONAL	3	TRUE	2	0.44522108061162	5		319	174	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888844	76888844	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	75	436	0	ENST00000373344.5:c.4985C>A	p.Pro1662His	p.P1662H	ENST00000373344	NM_000489.3	1662	cCt/cAt	19/35	1	2	FACETS	0.941	0.844	1	1	0.984	1	CLONAL	2	TRUE	1	0.44522108061162	2		436	179	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115905	8115906	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016952-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	70	390	0	ENST00000346208.3:c.1252dup	p.Thr418AsnfsTer89	p.T418Nfs*89	ENST00000346208		417	-/A	6/6	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.287397701552136	2		390	458	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106122	27106147	+	frameshift_variant	Frame_Shift_Del	DEL	GGATGACATGTTGTCTACTCGGTCTA	GGATGACATGTTGTCTACTCGGTCTA	-	novel	NA	P-0016952-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	81	458	0	ENST00000324856.7:c.5734_5759del	p.Asp1912HisfsTer8	p.D1912Hfs*8	ENST00000324856	NM_006015.4	1911	atGGATGACATGTTGTCTACTCGGTCTAgc/atgc	20/20	0.287397701552136	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.287397701552136	1		458	415	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419919	152419924	+	inframe_deletion	In_Frame_Del	DEL	CTCTAT	CTCTAT	-	novel	NA	P-0016952-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	86	480	0	ENST00000206249.3:c.1606_1611del	p.Leu536_Tyr537del	p.L536_Y537del	ENST00000206249	NM_000125.3	536	CTCTAT/-	8/8	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.287397701552136	2		480	508	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522551	176522551	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774571806	NA	P-0016986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	11	644	1	ENST00000292408.4:c.1648G>A	p.Val550Met	p.V550M	ENST00000292408	NM_213647.1	550	Gtg/Atg	13/18	0.431156279818778	3	FACETS	0.107	0.073	0.15	0.054	0.036	0.075	SUBCLONAL	1	FALSE	1	0.475091808389082	3		645	535	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200939	108200939	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0016986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	79	265	0	ENST00000278616.4:c.7308-2A>G		p.X2436_splice	ENST00000278616	NM_000051.3	2436			0.475091808389082	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	FALSE	0	0.475091808389082	1		265	236	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752938	42752941	+	frameshift_variant	Frame_Shift_Del	DEL	GTCA	GTCA	-	novel	NA	P-0016986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	218	982	0	ENST00000222329.4:c.1323_1326del	p.Asp442SerfsTer88	p.D442Sfs*88	ENST00000222329	NM_006494.2	441	acTGAC/ac	4/4	1	2	FACETS	0.911	0.848	0.977	0.911	0.848	0.977	CLONAL	1	FALSE	1	0.475091808389082	2		982	1007	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347553	118347553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555037629	NA	P-0017019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	56	349	0	ENST00000534358.1:c.3190C>T	p.Arg1064Ter	p.R1064*	ENST00000534358	NM_005933.3	1064	Cga/Tga	4/36	1	2	FACETS	0.407	0.348	0.472	0.407	0.348	0.472	SUBCLONAL	1	TRUE	1	0.37	2		349	743	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944842	31944842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1344	164	708	0	ENST00000340398.3:c.259G>A	p.Ala87Thr	p.A87T	ENST00000340398	NM_001013699.2	87	Gca/Aca	1/1	1	2	FACETS	0.588	0.538	0.641	0.588	0.538	0.641	SUBCLONAL	1	TRUE	1	0.37	2		708	1508	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231289	98231289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139705799	NA	P-0017019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	66	424	2	ENST00000331920.6:c.1994G>A	p.Arg665His	p.R665H	ENST00000331920	NM_000264.3	665	cGc/cAc	14/24	1	2	FACETS	0.363	0.314	0.417	0.363	0.314	0.417	SUBCLONAL	1	TRUE	1	0.37	2		426	982	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0017058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	557	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.332765097603741	5	FACETS	0.889	0.854	0.924			1	CLONAL	4	TRUE	NA	0.332765097603741	5		502	1412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0017058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	176	660	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.307764914535472	1	FACETS	0.923	0.85	0.999	0.923	0.85	0.999	CLONAL	1	TRUE	0	0.332765097603741	1		661	955	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439907	56439907	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	264	463	0	ENST00000407977.2:c.685C>T	p.Pro229Ser	p.P229S	ENST00000407977		229	Ccg/Tcg	6/10	0.332717499103982	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.332765097603741	2		463	725	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603132	48603133	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0017058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	108	432	0	ENST00000342988.3:c.1434_1435dup	p.Ala479GlufsTer26	p.A479Efs*26	ENST00000342988	NM_005359.5	478	ata/atAGa	11/12	0.280596278753001	1	FACETS	0.784	0.704	0.869	0.784	0.704	0.869	SUBCLONAL	1	TRUE	0	0.332765097603741	1		432	690	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0017063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	333	571	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.454974172494887	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.454974172494887	1		571	768	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1620991	1620991	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762619225	NA	P-0017063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	175	661	4	ENST00000344749.5:c.1069G>A	p.Val357Met	p.V357M	ENST00000344749	NM_001136139.2	357	Gtg/Atg	13/19	0.440515094748136	3	FACETS	0.941	0.866	1	0.47	0.433	0.51	CLONAL	1	TRUE	1	0.454974172494887	3		665	1004	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948009	17948009	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	50	571	0	ENST00000458235.1:c.1715C>G	p.Ala572Gly	p.A572G	ENST00000458235	NM_000215.3	572	gCa/gGa	13/24	1	2	FACETS	0.246	0.208	0.288	0.246	0.208	0.288	SUBCLONAL	1	TRUE	1	0.454974172494887	2		571	893	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953142	38953142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs569163921	NA	P-0017063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	85	352	0	ENST00000357387.3:c.2842G>A	p.Val948Met	p.V948M	ENST00000357387	NM_152756.3	948	Gtg/Atg	29/38	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.454974172494887	2		352	351	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519459	176519459	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1216312811	NA	P-0017063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	421	618	0	ENST00000292408.4:c.865A>G	p.Ile289Val	p.I289V	ENST00000292408	NM_213647.1	289	Atc/Gtc	7/18	1	2	FACETS	0.834	0.796	0.873	1	0.996	1	CLONAL	2	TRUE	1	0.454974172494887	2		618	1109	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0017270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	69	268	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.61563279121443	1	FACETS	0.952	0.85	1	0.952	0.85	1	CLONAL	1	TRUE	0	0.61563279121443	1		268	163	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0017270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	223	804	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.61563279121443	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.61563279121443	1		804	460	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17947965	17947965	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	264	512	0	ENST00000458235.1:c.1759C>T	p.Leu587Phe	p.L587F	ENST00000458235	NM_000215.3	587	Ctc/Ttc	13/24	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.61563279121443	2		512	828	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309879	30309879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	204	382	0	ENST00000307677.4:c.143C>T	p.Pro48Leu	p.P48L	ENST00000307677	NM_138578.1	48	cCc/cTc	2/3	0.61563279121443	3	FACETS	1	0.928	1	0.5	0.464	0.537	CLONAL	1	TRUE	1	0.61563279121443	3		382	867	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	201	272	0				ENST00000310581	NM_198253.2	-/1132			0.343892795345599	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	2	0.459332771532969	4		272	611	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920402	114920402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs927089403	NA	P-0017489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	468	552	0	ENST00000543371.1:c.1343G>A	p.Arg448Gln	p.R448Q	ENST00000543371	NM_001198531.1	448	cGg/cAg	13/14	0.459332771532969	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	0	0.459332771532969	3		552	816	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030223	180030223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200835339	NA	P-0017489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	331	621	3	ENST00000261937.6:c.4061G>A	p.Arg1354His	p.R1354H	ENST00000261937	NM_182925.4	1354	cGc/cAc	30/30	0.459332771532969	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.459332771532969	2		624	686	SUCCESS
APC	324	MSKCC	GRCh37	5	112175350	112175351	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	156	260	0	ENST00000257430.4:c.4063dup	p.Ser1355PhefsTer20	p.S1355Ffs*20	ENST00000257430	NM_000038.5	1353	-/T	16/16	0.459332771532969	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.459332771532969	2		260	323	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28601376	28601376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	147	544	1	ENST00000253063.3:c.1061G>A	p.Arg354Gln	p.R354Q	ENST00000253063	NM_031459.4	354	cGg/cAg	8/10	0.459332771532969	3	FACETS	0.938	0.857	1	0.469	0.428	0.512	CLONAL	1	TRUE	1	0.459332771532969	3		545	839	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576862	7576863	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041285	NA	P-0017489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	339	596	0	ENST00000269305.4:c.983dup	p.Thr329HisfsTer8	p.T329Hfs*8	ENST00000269305	NM_001126112.2	328	ttc/ttTc	9/11	0.459332771532969	2	FACETS	0.962	0.916	1	0.962	0.916	1	CLONAL	2	TRUE	0	0.459332771532969	2		596	767	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829887	72829887	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017703-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	156	758	1	ENST00000268489.5:c.6694G>T	p.Glu2232Ter	p.E2232*	ENST00000268489	NM_006885.3	2232	Gaa/Taa	9/10	NA	2	FACETS	0.963	0.882	1			1	INDETERMINATE	1	FALSE	NA	0.3549249990481	2		759	913	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618837	37618837	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017703-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	113	556	0	ENST00000447079.4:c.513del	p.Ser171ArgfsTer20	p.S171Rfs*20	ENST00000447079	NM_015083.1	171	agC/ag	1/14	1	2	FACETS	0.783	0.705	0.867	0.783	0.705	0.867	SUBCLONAL	1	FALSE	1	0.3549249990481	2		556	813	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673701	37673701	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017703-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	126	632	0	ENST00000447079.4:c.2855G>C	p.Cys952Ser	p.C952S	ENST00000447079	NM_015083.1	952	tGt/tCt	10/14	1	2	FACETS	0.873	0.791	0.96	0.873	0.791	0.96	CLONAL	1	FALSE	1	0.3549249990481	2		632	813	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259012	153259013	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0017808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	75	373	0	ENST00000281708.4:c.802_803del	p.Met268AspfsTer18	p.M268Dfs*18	ENST00000281708	NM_033632.3	268	ATg/g	5/12	0.516294569934861	2	FACETS	1	0.978	1	0.719	0.643	0.798	CLONAL	1	TRUE	0	0.5292380549054	2		373	197	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0017808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	360	733	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	0.515291689053332	1	FACETS	0.995	0.946	1	0.995	0.946	1	CLONAL	1	TRUE	0	0.5292380549054	1		733	1005	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604790	48604790	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1568211615	NA	P-0017808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	196	494	0	ENST00000342988.3:c.1612G>T	p.Glu538Ter	p.E538*	ENST00000342988	NM_005359.5	538	Gaa/Taa	12/12	0.5292380549054	1	FACETS	0.897	0.836	0.961	0.897	0.836	0.961	CLONAL	1	TRUE	0	0.5292380549054	1		494	607	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776541	9776541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779226622	NA	P-0017808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	295	710	0	ENST00000377346.4:c.644C>T	p.Ala215Val	p.A215V	ENST00000377346	NM_005026.3	215	gCg/gTg	6/24	1	2	FACETS	0.956	0.9	1	0.956	0.9	1	CLONAL	1	TRUE	1	0.5292380549054	2		710	1166	SUCCESS
APC	324	MSKCC	GRCh37	5	112175371	112175372	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0017808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	209	256	0	ENST00000257430.4:c.4083dup	p.Ser1362LeufsTer13	p.S1362Lfs*13	ENST00000257430	NM_000038.5	1360	-/C	16/16	0.527167266892948	2	FACETS	0.831	0.78	0.883	0.831	0.78	0.883	CLONAL	2	TRUE	0	0.5292380549054	2		256	475	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0018070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	32	625	3	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.5	0.405	0.607	0.5	0.405	0.607	SUBCLONAL	1	TRUE	1	0.28	2		628	457	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169374	11169374	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	68	966	0	ENST00000361445.4:c.7501A>T	p.Ile2501Phe	p.I2501F	ENST00000361445	NM_004958.3	2501	Att/Ttt	56/58	0.299683768556326	1	FACETS	0.663	0.577	0.756	0.663	0.577	0.756	SUBCLONAL	1	TRUE	0	0.28	1		966	630	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953258	81953258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776768909	NA	P-0018070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	45	389	0	ENST00000359376.3:c.2224C>T	p.Arg742Cys	p.R742C	ENST00000359376	NM_002661.3	742	Cgc/Tgc	20/33	1	2	FACETS	0.855	0.72	1	0.855	0.72	1	CLONAL	1	TRUE	1	0.28	2		389	376	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795356	39795356	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	55	695	0	ENST00000288319.7:c.364G>T	p.Glu122Ter	p.E122*	ENST00000288319	NM_182918.3	122	Gag/Tag	3/10	1	2	FACETS	0.677	0.579	0.785	0.677	0.579	0.785	SUBCLONAL	1	TRUE	1	0.28	2		695	580	SUCCESS
APC	324	MSKCC	GRCh37	5	112173210	112173308	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTGTGACCTTAATTTTGTGATCTCTTGATTTTATTTCAGGCAAATCCTAAGAGAGAACAACTGTCTACAAACTTTATTACAACACTTAAAATCTCATA	ATTGTGACCTTAATTTTGTGATCTCTTGATTTTATTTCAGGCAAATCCTAAGAGAGAACAACTGTCTACAAACTTTATTACAACACTTAAAATCTCATA	-	novel	NA	P-0018070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	23	177	0	ENST00000257430.4:c.1959-40_2017del		p.X653_splice	ENST00000257430	NM_000038.5	653		16/16	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.28	2		177	117	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92244481	92244481	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	76	410	0	ENST00000265734.4:c.954G>T	p.Gln318His	p.Q318H	ENST00000265734	NM_001259.6	318	caG/caT	8/8	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.28	2		410	413	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018156-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	350	812	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.47821907066479	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.47821907066479	3		812	561	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0018156-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	357	753	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.458537598322041	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.47821907066479	2		753	726	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019077-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	409	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.458948804130425	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.458948804130425	3		502	1058	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0019077-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	273	683	0	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	0.420728887563913	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.458948804130425	1		683	763	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939186	36939186	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019077-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	116	735	1	ENST00000361632.4:c.523C>A	p.Leu175Met	p.L175M	ENST00000361632		175	Ctg/Atg	5/16	1	2	FACETS	0.471	0.423	0.522	0.471	0.423	0.522	SUBCLONAL	1	TRUE	1	0.458948804130425	2		736	1073	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554353	81554353	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019077-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	154	459	16	ENST00000298171.2:c.373C>A	p.Leu125Ile	p.L125I	ENST00000298171	NM_000369.2	125	Ctc/Atc	4/10	1	2	FACETS	0.973	0.892	1	0.973	0.892	1	CLONAL	1	TRUE	1	0.458948804130425	2		475	690	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117746744	117746744	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019077-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	119	427	11	ENST00000368508.3:c.76C>T	p.Gln26Ter	p.Q26*	ENST00000368508	NM_002944.2	26	Cag/Tag	1/43	0.450317375788627	2	FACETS	0.885	0.801	0.973	0.442	0.4	0.487	CLONAL	1	TRUE	0	0.458948804130425	2		438	586	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501351	140501351	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs387906661	NA	P-0019077-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	98	288	0	ENST00000288602.6:c.721A>C	p.Thr241Pro	p.T241P	ENST00000288602	NM_004333.4	241	Acg/Ccg	6/18	1	2	FACETS	0.998	0.896	1	0.998	0.896	1	CLONAL	1	TRUE	1	0.458948804130425	2		288	428	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974740	21974765	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCACCTCCTCTACCCGACCCCGGG	CCGCACCTCCTCTACCCGACCCCGGG	-	novel	NA	P-0019077-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	96	322	2	ENST00000304494.5:c.62_87del	p.Ala21GlyfsTer14	p.A21Gfs*14	ENST00000304494	NM_000077.4	21	gCCCGGGGTCGGGTAGAGGAGGTGCGG/g	1/3	0.458948804130425	1	FACETS	0.983	0.885	1	0.983	0.885	1	CLONAL	1	TRUE	0	0.458948804130425	1		324	328	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	156	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.141323924193365	3	FACETS	0.876	0.804	0.95			1	INDETERMINATE	2	TRUE	NA	0.307193039116839	3		502	669	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0019267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	106	876	1	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	1	2	FACETS	0.948	0.85	1	0.948	0.85	1	CLONAL	1	TRUE	1	0.307193039116839	2		877	728	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047314	77047314	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	96	468	0	ENST00000356341.3:c.1230C>A	p.Phe410Leu	p.F410L	ENST00000356341	NM_002576.4	410	ttC/ttA	13/15	0.307193039116839	3	FACETS	0.879	0.789	0.974	0.879	0.789	0.974	CLONAL	2	TRUE	1	0.307193039116839	3		468	410	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652204	3652204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	92	917	3	ENST00000294008.3:c.865G>A	p.Glu289Lys	p.E289K	ENST00000294008	NM_032444.2	289	Gag/Aag	4/15	0.307193039116839	6	FACETS	0.998	0.885	1	0.333	0.295	0.373	CLONAL	1	TRUE	3	0.307193039116839	6		920	969	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117878	70117888	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCAGGCGGC	GCGCAGGCGGC	-	novel	NA	P-0019267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	92	479	1	ENST00000245479.2:c.353_363del	p.Ala118GlufsTer130	p.A118Efs*130	ENST00000245479	NM_000346.3	116	GCGCAGGCGGCg/g	1/3	0.307193039116839	3	FACETS	0.909	0.814	1	0.909	0.814	1	CLONAL	2	TRUE	1	0.307193039116839	3		480	380	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225669	225669	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542980860	NA	P-0019267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	66	865	1	ENST00000264932.6:c.448G>A	p.Val150Met	p.V150M	ENST00000264932	NM_004168.2	150	Gtg/Atg	4/15	0.116913936020549	5	FACETS	0.693	0.6	0.794	0.231	0.2	0.265	INDETERMINATE	1	TRUE	2	0.307193039116839	5		866	906	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	200	812	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.309324853618861	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.309324853618861	3		812	716	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0019587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	94	290	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.309324853618861	2		290	451	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0019587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	15	535	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.17	0.123	0.226	0.17	0.123	0.226	SUBCLONAL	1	TRUE	1	0.309324853618861	2		535	572	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0019587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	30	845	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	0.347	0.279	0.425	0.347	0.279	0.425	SUBCLONAL	1	TRUE	1	0.309324853618861	2		845	559	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261272	115261273	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TAGGCGA	novel	NA	P-0019587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	99	831	0	ENST00000438362.2:c.2442_2448dup	p.Met817SerfsTer13	p.M817Sfs*13	ENST00000438362	NM_001242891.1	816	-/TCGCCTA	19/20	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.309324853618861	2		831	639	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115446	115115446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	279	680	0	ENST00000257566.3:c.880del	p.Ile294Ter	p.I294*	ENST00000257566	NM_016569.3	294	Ata/ta	5/8	0.309324853618861	3	FACETS	0.942	0.89	0.995	0.942	0.89	0.995	CLONAL	3	TRUE	0	0.309324853618861	3		680	737	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877386	89877386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139160837	NA	P-0019587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	103	845	0	ENST00000389301.3:c.377C>T	p.Thr126Met	p.T126M	ENST00000389301	NM_000135.2	126	aCg/aTg	4/43	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.309324853618861	2		845	660	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221060	5221060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140049694	NA	P-0019587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	111	809	0	ENST00000357368.4:c.3406G>A	p.Gly1136Ser	p.G1136S	ENST00000357368	NM_002850.3	1136	Ggc/Agc	20/38	0.309324853618861	3	FACETS	1	0.957	1	0.56	0.503	0.62	CLONAL	1	TRUE	1	0.309324853618861	3		809	740	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793100	42793100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762179630	NA	P-0019587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	146	1018	3	ENST00000575354.2:c.992C>T	p.Pro331Leu	p.P331L	ENST00000575354	NM_015125.3	331	cCg/cTg	7/20	0.309324853618861	3	FACETS	1	0.932	1	0.513	0.467	0.561	CLONAL	1	TRUE	1	0.309324853618861	3		1021	1062	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543845	212543845	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	78	621	0	ENST00000342788.4:c.1554C>A	p.Asp518Glu	p.D518E	ENST00000342788	NM_005235.2	518	gaC/gaA	13/28	1	2	FACETS	0.924	0.813	1	0.924	0.813	1	CLONAL	1	TRUE	1	0.309324853618861	2		621	546	SUCCESS
APC	324	MSKCC	GRCh37	5	112174374	112174374	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1114167617	NA	P-0019587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	74	483	0	ENST00000257430.4:c.3083G>A	p.Ser1028Asn	p.S1028N	ENST00000257430	NM_000038.5	1028	aGt/aAt	16/16	NA	2	FACETS	1	0.972	1			1	INDETERMINATE	1	TRUE	NA	0.309324853618861	2		483	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0019594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	450	812	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.745305596383072	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.745305596383072	1		812	670	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0019594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	176	540	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.732	0.677	0.789	0.732	0.677	0.789	SUBCLONAL	1	TRUE	1	0.745305596383072	2		540	645	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0019594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	248	528	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	NA	2	FACETS	0.899	0.845	0.955			1	INDETERMINATE	1	TRUE	NA	0.745305596383072	2		529	740	SUCCESS
APC	324	MSKCC	GRCh37	5	112174094	112174095	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs863225332	NA	P-0019594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	175	361	0	ENST00000257430.4:c.2804dup	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	tac/tAac	16/16	0.745305596383072	1	FACETS	0.982	0.925	1	0.982	0.925	1	CLONAL	1	TRUE	0	0.745305596383072	1		361	300	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35860962	35860962	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	61	330	0	ENST00000303115.3:c.91G>A	p.Glu31Lys	p.E31K	ENST00000303115	NM_002185.3	31	Gaa/Aaa	2/8	0.412246728202232	1	FACETS	0.346	0.3	0.394	0.346	0.3	0.394	INDETERMINATE	1	TRUE	0	0.745305596383072	1		330	297	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423497	116423497	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	157	381	0	ENST00000397752.3:c.3772C>T	p.Gln1258Ter	p.Q1258*	ENST00000397752	NM_000245.2	1258	Caa/Taa	19/21	1	2	FACETS	0.824	0.76	0.89	0.824	0.76	0.89	CLONAL	1	TRUE	1	0.745305596383072	2		381	511	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0019699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	273	364	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.258873170916207	5	FACETS	1	0.975	1	0.712	0.669	0.756	CLONAL	2	TRUE	2	0.430470026958701	5		364	977	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807914	3807914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	200	660	3	ENST00000262367.5:c.3505C>T	p.Arg1169Cys	p.R1169C	ENST00000262367	NM_004380.2	1169	Cgc/Tgc	18/31	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.430470026958701	2		663	890	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045902	180045902	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	183	610	0	ENST00000261937.6:c.2869C>T	p.Arg957Cys	p.R957C	ENST00000261937	NM_182925.4	957	Cgc/Tgc	21/30	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.430470026958701	2		610	805	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577123	+	missense_variant	Missense_Mutation	ONP	CGCA	CGCA	AGCG	novel	NA	P-0019699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	444	967	2	ENST00000269305.4:c.815_818delinsCGCT	p.Val272_Arg273delinsAlaLeu	p.V272_R273delinsAL	ENST00000269305	NM_001126112.2	272	gTGCGt/gCGCTt	8/11	0.430470026958701	2	FACETS	0.843	0.805	0.882	0.843	0.805	0.882	CLONAL	2	TRUE	0	0.430470026958701	2		969	1223	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0019780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	233	432	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.312173176593111	1	FACETS	0.833	0.784	0.883	0.833	0.784	0.883	INDETERMINATE	1	TRUE	0	0.667916661610071	1		438	558	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0019780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	159	328	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.753	0.693	0.816	0.753	0.693	0.816	SUBCLONAL	1	TRUE	1	0.667916661610071	2		328	632	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0019780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	155	580	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.312173176593111	1	FACETS	0.631	0.582	0.681	0.631	0.582	0.681	INDETERMINATE	1	TRUE	0	0.667916661610071	1		580	490	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562282	21562282	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs543513326	NA	P-0019780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	792	1008	1	ENST00000382592.4:c.1637C>T	p.Ala546Val	p.A546V	ENST00000382592	NM_014572.2	546	gCg/gTg	4/8	0.311567597018682	5	FACETS	0.929	0.9	0.958	0.929	0.9	0.958	INDETERMINATE	3	TRUE	2	0.667916661610071	5		1009	1704	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691003	NA	P-0019780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	377	550	0	ENST00000269305.4:c.96+1G>T		p.X32_splice	ENST00000269305	NM_001126112.2	32			0.600457130698443	2	FACETS	0.905	0.869	0.939	0.905	0.869	0.939	CLONAL	2	TRUE	0	0.667916661610071	2		550	624	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430363	181430363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	590	760	0	ENST00000325404.1:c.215G>A	p.Ser72Asn	p.S72N	ENST00000325404	NM_003106.3	72	aGc/aAc	1/1	0.619758527870757	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.667916661610071	2		760	815	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0019841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	334	812	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.397548009637736	2	FACETS	0.856	0.812	0.901	0.856	0.812	0.901	CLONAL	2	FALSE	0	0.435789966141612	2		812	895	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102056750	102056755	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TCCTCT	TCCTCT	-	novel	NA	P-0019841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	34	549	0	ENST00000282441.5:c.694_699del	p.Leu232_Pro233del	p.L232_P233del	ENST00000282441	NM_001130145.2	230	ggTCCTCTt/ggt	4/9	0.239951182394632	3	FACETS	0.492	0.402	0.593	0.246	0.201	0.297	INDETERMINATE	1	FALSE	1	0.435789966141612	3		549	386	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585371	29585371	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555618494	NA	P-0019841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	165	661	0	ENST00000356175.3:c.4120C>T	p.Gln1374Ter	p.Q1374*	ENST00000356175	NM_000267.3	1374	Cag/Tag	31/57	0.257632475492868	2	FACETS	1	0.99	1	0.747	0.691	0.804	INDETERMINATE	1	FALSE	0	0.435789966141612	2		661	507	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672531	30672531	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	62	647	1	ENST00000376406.3:c.4429A>G	p.Arg1477Gly	p.R1477G	ENST00000376406	NM_014641.2	1477	Aga/Gga	10/15	0.435789966141612	5	FACETS	0.691	0.596	0.794			1	SUBCLONAL	1	FALSE	NA	0.435789966141612	5		648	681	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	341	687	2	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.572960417302252	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.577554786130901	2		689	575	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685271	89685271	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	133	676	2	ENST00000371953.3:c.170del	p.Leu57TrpfsTer42	p.L57Wfs*42	ENST00000371953	NM_000314.4	56	Ttt/tt	3/9	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.577554786130901	2		678	400	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	182	551	1	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.78	0.721	0.841	0.78	0.721	0.841	SUBCLONAL	1	TRUE	1	0.577554786130901	2		552	808	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	173	730	12	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.577554786130901	2		742	513	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	206	432	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.577554786130901	2		438	652	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	116	622	5	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.577554786130901	2		627	379	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012386	152012386	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	117	740	1	ENST00000262189.6:c.427del	p.Ser143ValfsTer3	p.S143Vfs*3	ENST00000262189	NM_170606.2	143	Agt/gt	4/59	1	2	FACETS	0.956	0.868	1	0.956	0.868	1	CLONAL	1	TRUE	1	0.577554786130901	2		741	424	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053590	37053590	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs63751711	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	31	837	2	ENST00000231790.2:c.677G>A	p.Arg226Gln	p.R226Q	ENST00000231790	NM_000249.3	226	cGa/cAa	8/19	0.572960417302252	2	FACETS	0.19	0.153	0.233	0.095	0.076	0.117	SUBCLONAL	1	TRUE	0	0.577554786130901	2		839	564	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	191	352	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.577554786130901	2		352	615	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952006	178952006	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	167	931	0	ENST00000263967.3:c.3061T>C	p.Tyr1021His	p.Y1021H	ENST00000263967	NM_006218.2	1021	Tac/Cac	21/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.577554786130901	2		931	536	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749415085	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	106	763	1	ENST00000263967.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000263967	NM_006218.2	38	Cgt/Tgt	2/21	1	2	FACETS	0.911	0.823	1	0.911	0.823	1	CLONAL	1	TRUE	1	0.577554786130901	2		764	403	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913527	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	119	1072	0	ENST00000311936.3:c.436G>C	p.Ala146Pro	p.A146P	ENST00000311936	NM_004985.3	146	Gca/Cca	4/5	0.15743037511564	0	FACETS	0.385	0.35	0.422			1	INDETERMINATE	1	TRUE	0	0.577554786130901	0		1072	452	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475061	40475063	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	237	717	0	ENST00000264657.5:c.1847_1849del	p.Glu616del	p.E616del	ENST00000264657	NM_139276.2	616	gAAGga/gga	20/24	1	2	FACETS	0.975	0.912	1	0.975	0.912	1	CLONAL	1	TRUE	1	0.577554786130901	2		717	842	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054984	176054984	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	190	1144	1	ENST00000367669.3:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000367669	NM_022457.5	357	Cga/Tga	10/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.577554786130901	2		1145	638	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310208	91310208	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs747341586	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	160	889	0	ENST00000355112.3:c.2268del	p.Asp757ThrfsTer4	p.D757Tfs*4	ENST00000355112	NM_000057.2	754	tcA/tc	10/22	1	2	FACETS	0.916	0.843	0.991	0.916	0.843	0.991	CLONAL	1	TRUE	1	0.577554786130901	2		889	605	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029445	16029446	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	177	1150	9	ENST00000268712.3:c.1584dup	p.Glu529ArgfsTer7	p.E529Rfs*7	ENST00000268712	NM_006311.3	528	-/A	15/46	1	2	FACETS	0.862	0.797	0.93	0.862	0.797	0.93	CLONAL	1	TRUE	1	0.577554786130901	2		1159	711	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870961	12870962	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	155	682	0	ENST00000228872.4:c.192dup	p.Gln65SerfsTer60	p.Q65Sfs*60	ENST00000228872	NM_004064.3	63	gat/gaTt	1/3	0.0996067009774699	4	FACETS	0.864	0.797	0.933	0.864	0.797	0.933	INDETERMINATE	2	TRUE	2	0.577554786130901	4		682	490	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218979	193218979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500011	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	83	667	0	ENST00000367435.3:c.1537C>T	p.Arg513Trp	p.R513W	ENST00000367435	NM_024529.4	513	Cgg/Tgg	16/17	1	2	FACETS	0.871	0.776	0.971	0.871	0.776	0.971	CLONAL	1	TRUE	1	0.577554786130901	2		667	330	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	234	898	2	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	1	2	FACETS	0.851	0.795	0.909	0.851	0.795	0.909	CLONAL	1	TRUE	1	0.577554786130901	2		900	952	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815757	32815757	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	229	1069	0	ENST00000354258.4:c.1859del	p.Gly620AspfsTer44	p.G620Dfs*44	ENST00000354258	NM_000593.5	620	gGa/ga	8/11	1	2	FACETS	0.877	0.819	0.938	0.877	0.819	0.938	CLONAL	1	TRUE	1	0.577554786130901	2		1069	904	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39317348	39317348	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	190	1156	2	ENST00000373001.3:c.838C>T	p.Gln280Ter	p.Q280*	ENST00000373001	NM_022157.3	280	Caa/Taa	5/7	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.577554786130901	2		1158	649	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466512	120466512	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	157	1138	5	ENST00000256646.2:c.4607C>T	p.Ala1536Val	p.A1536V	ENST00000256646	NM_024408.3	1536	gCt/gTt	26/34	1	2	FACETS	0.603	0.552	0.656	0.603	0.552	0.656	SUBCLONAL	1	TRUE	1	0.577554786130901	2		1143	902	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910819	114910819	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	253	1114	1	ENST00000543371.1:c.938C>T	p.Ala313Val	p.A313V	ENST00000543371	NM_001198531.1	313	gCc/gTc	9/14	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.577554786130901	2		1115	862	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390460	118390461	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	196	957	0	ENST00000534358.1:c.11280dup	p.Asn3762GlufsTer9	p.N3762Efs*9	ENST00000534358	NM_005933.3	3758	-/C	32/36	1	2	FACETS	0.931	0.865	0.999	0.931	0.865	0.999	CLONAL	1	TRUE	1	0.577554786130901	2		957	729	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252326	133252326	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1488526952	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	172	862	0	ENST00000320574.5:c.1101del	p.Phe367LeufsTer15	p.F367Lfs*15	ENST00000320574	NM_006231.2	367	ttT/tt	11/49	NA	2	FACETS	0.95	0.878	1			1	INDETERMINATE	1	TRUE	NA	0.577554786130901	2		862	627	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434962	110434964	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs1183676528	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	257	1150	8	ENST00000375856.3:c.3437_3439del	p.Arg1146del	p.R1146del	ENST00000375856	NM_003749.2	1146	cGCCac/cac	1/2	1	2	FACETS	0.955	0.895	1	0.955	0.895	1	CLONAL	1	TRUE	1	0.577554786130901	2		1158	932	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042041	42042041	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	177	1049	0	ENST00000219905.7:c.6240del	p.Val2081TrpfsTer21	p.V2081Wfs*21	ENST00000219905	NM_001164273.1	2079	gAa/ga	17/24	1	2	FACETS	0.897	0.83	0.967	0.897	0.83	0.967	CLONAL	1	TRUE	1	0.577554786130901	2		1049	683	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14015969	14015969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760327512	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	143	700	0	ENST00000311895.7:c.289C>T	p.Arg97Cys	p.R97C	ENST00000311895	NM_005236.2	97	Cgc/Tgc	2/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.577554786130901	2		700	472	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829902	72829902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756354750	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	243	1053	3	ENST00000268489.5:c.6679C>T	p.Arg2227Trp	p.R2227W	ENST00000268489	NM_006885.3	2227	Cgg/Tgg	9/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.577554786130901	2		1056	818	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122374	17122374	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1060502368	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	63	940	1	ENST00000285071.4:c.1021del	p.Arg341GlyfsTer12	p.R341Gfs*12	ENST00000285071	NM_144997.5	341	Cgg/gg	9/14	1	2	FACETS	0.345	0.298	0.396	0.345	0.298	0.396	SUBCLONAL	1	TRUE	1	0.577554786130901	2		941	632	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285179	198285179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	165	1002	1	ENST00000335508.6:c.388C>T	p.Pro130Ser	p.P130S	ENST00000335508	NM_012433.2	130	Cca/Tca	4/25	1	2	FACETS	0.962	0.888	1	0.962	0.888	1	CLONAL	1	TRUE	1	0.577554786130901	2		1003	594	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645975	215645975	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs587780033	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	151	900	0	ENST00000260947.4:c.623del	p.Lys208ArgfsTer4	p.K208Rfs*4	ENST00000260947	NM_000465.2	208	aAg/ag	4/11	1	2	FACETS	0.979	0.901	1	0.979	0.901	1	CLONAL	1	TRUE	1	0.577554786130901	2		900	534	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661664	227661665	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	162	784	0	ENST00000305123.5:c.1790_1791del	p.Gly597AlafsTer13	p.G597Afs*13	ENST00000305123	NM_005544.2	597	gGG/g	1/2	1	2	FACETS	0.993	0.916	1	0.993	0.916	1	CLONAL	1	TRUE	1	0.577554786130901	2		784	565	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077552	30077552	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757586383	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	208	1035	0	ENST00000338641.4:c.1699G>A	p.Asp567Asn	p.D567N	ENST00000338641	NM_000268.3	567	Gac/Aac	15/16	1	2	FACETS	0.907	0.844	0.972	0.907	0.844	0.972	CLONAL	1	TRUE	1	0.577554786130901	2		1035	794	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042537	37042537	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	283	926	0	ENST00000231790.2:c.299del	p.Arg100GlnfsTer8	p.R100Qfs*8	ENST00000231790	NM_000249.3	100	cGa/ca	3/19	0.572960417302252	2	FACETS	0.94	0.895	0.985	0.94	0.895	0.985	CLONAL	2	TRUE	0	0.577554786130901	2		926	521	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815453	32815453	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	99	848	0	ENST00000354258.4:c.1921-1G>A		p.X641_splice	ENST00000354258	NM_000593.5	641			1	2	FACETS	0.524	0.468	0.584	0.524	0.468	0.584	SUBCLONAL	1	TRUE	1	0.577554786130901	2		848	654	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815802	32815802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	230	1016	0	ENST00000354258.4:c.1814G>A	p.Ser605Asn	p.S605N	ENST00000354258	NM_000593.5	605	aGc/aAc	8/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.577554786130901	2		1016	753	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821048	32821048	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	82	1262	4	ENST00000354258.4:c.546del	p.Ser184ProfsTer54	p.S184Pfs*54	ENST00000354258	NM_000593.5	182	ccC/cc	1/11	1	2	FACETS	0.308	0.27	0.348	0.308	0.27	0.348	SUBCLONAL	1	TRUE	1	0.577554786130901	2		1266	923	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211166	55211166	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs754854319	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	89	788	0	ENST00000275493.2:c.409A>G	p.Met137Val	p.M137V	ENST00000275493	NM_005228.3	137	Atg/Gtg	3/28	1	2	FACETS	0.452	0.401	0.507	0.452	0.401	0.507	SUBCLONAL	1	TRUE	1	0.577554786130901	2		788	682	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100463	157100477	+	frameshift_variant	Frame_Shift_Del	DEL	AGCAGGCGGCCGCGG	AGCAGGCGGCCGCGG	T	novel	NA	P-0020144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	14	59	0	ENST00000346085.5:c.1400_1414delinsT	p.Gln467LeufsTer63	p.Q467Lfs*63	ENST00000346085	NM_020732.3	467	cAGCAGGCGGCCGCGGgc/cTgc	1/20	1	2	FACETS	0.898	0.67	1	0.898	0.67	1	CLONAL	1	TRUE	1	0.577554786130901	2		59	54	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0020315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	517	562	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.189069060636977	9	FACETS	0.999	0.974	1			1	CLONAL	14	TRUE	NA	0.189069060636977	9		562	650	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640527	3640527	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	241	1032	0	ENST00000294008.3:c.3112G>C	p.Gly1038Arg	p.G1038R	ENST00000294008	NM_032444.2	1038	Ggg/Cgg	12/15	0.189069060636977	9	FACETS	1	0.973	1	0.91	0.855	0.966	CLONAL	6	TRUE	2	0.189069060636977	9		1032	665	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208380	5208380	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	144	909	0	ENST00000357368.4:c.5510G>C	p.Arg1837Pro	p.R1837P	ENST00000357368	NM_002850.3	1837	cGg/cCg	36/38	0.189069060636977	1	FACETS	1	0.974	1	1	0.993	1	CLONAL	3	TRUE	0	0.189069060636977	1		909	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587781702	NA	P-0020525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	356	622	0	ENST00000269305.4:c.920-1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.74670594536729	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.74670594536729	1		622	558	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355045	73355045	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	267	864	0	ENST00000377767.4:c.325A>G	p.Ile109Val	p.I109V	ENST00000377767	NM_014953.3	109	Atc/Gtc	2/21	0.269924797757736	5	FACETS	0.957	0.901	1	0.383	0.36	0.406	INDETERMINATE	2	TRUE	0	0.74670594536729	5		864	792	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0020634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	189	804	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.137141482065962	2	FACETS	0.945	0.872	1	0.945	0.872	1	CLONAL	2	FALSE	0	0.163461351619448	2		804	1223	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63700048	63700048	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	42	287	0	ENST00000279873.7:c.383C>T	p.Pro128Leu	p.P128L	ENST00000279873	NM_032199.2	128	cCa/cTa	3/10	1	2	FACETS	0.906	0.756	1	0.906	0.756	1	CLONAL	1	FALSE	1	0.163461351619448	2		287	567	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885339	111885452	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GATAGCCAAGGTATGGGGTGGGGTGGGGTGGGGTGGGGCAGGCAGGACCGTGCCACCCCTCTCCACTGGAGTTCAGGGTCCTAGAGGGACAGCCCGAGCCCACCATCCTCTCCT	GATAGCCAAGGTATGGGGTGGGGTGGGGTGGGGTGGGGCAGGCAGGACCGTGCCACCCCTCTCCACTGGAGTTCAGGGTCCTAGAGGGACAGCCCGAGCCCACCATCCTCTCCT	-	novel	NA	P-0020634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	42	369	0	ENST00000341259.2:c.1227_1237-8del		p.X409_splice	ENST00000341259	NM_005475.2	409		6/8	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	FALSE	1	0.163461351619448	2		369	479	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134980	2134980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1535	94	1243	2	ENST00000219476.3:c.4522C>T	p.Pro1508Ser	p.P1508S	ENST00000219476	NM_000548.3	1508	Ccc/Tcc	35/42	0.163461351619448	0	FACETS	0.591	0.523	0.663			1	SUBCLONAL	1	FALSE	0	0.163461351619448	0		1245	1629	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900954	3900954	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1404	159	1009	0	ENST00000262367.5:c.142G>A	p.Gly48Arg	p.G48R	ENST00000262367	NM_004380.2	48	Gga/Aga	2/31	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.163461351619448	2		1009	1563	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852056	128852056	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1448	110	1214	0	ENST00000249373.3:c.2128C>A	p.Gln710Lys	p.Q710K	ENST00000249373	NM_005631.4	710	Cag/Aag	12/12	0.163461351619448	2	FACETS	0.864	0.773	0.961	0.432	0.386	0.481	CLONAL	1	FALSE	0	0.163461351619448	2		1214	1558	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637029	93637029	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	40	464	0	ENST00000375746.1:c.1079C>T	p.Pro360Leu	p.P360L	ENST00000375746	NM_001174167.1	360	cCc/cTc	9/14	0.151856129994012	2	FACETS	0.664	0.55	0.792	0.332	0.275	0.396	SUBCLONAL	1	FALSE	0	0.163461351619448	2		464	737	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148678	20148678	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	63	948	0	ENST00000379607.5:c.385A>C	p.Ile129Leu	p.I129L	ENST00000379607	NM_001412.3	129	Att/Ctt	6/7	0.163461351619448	1	FACETS	0.6	0.517	0.691	0.6	0.517	0.691	SUBCLONAL	1	FALSE	0	0.163461351619448	1		948	1180	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	230	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.926	0.862	0.992	0.926	0.862	0.992	CLONAL	1	FALSE	1	0.435390376588398	2		502	1141	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0020642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	322	755	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.435390376588398	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	0	0.435390376588398	1		755	1008	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575209	48575209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767326	NA	P-0020642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	115	306	0	ENST00000342988.3:c.403C>T	p.Arg135Ter	p.R135*	ENST00000342988	NM_005359.5	135	Cga/Tga	3/12	0.435390376588398	1	FACETS	0.914	0.829	1	0.914	0.829	1	CLONAL	1	FALSE	0	0.435390376588398	1		306	452	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624184	89624232	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	GCCATCTCTCTCCTCCTTTTTCTTCAGCCACAGGCTCCCAGACATGACA	GCCATCTCTCTCCTCCTTTTTCTTCAGCCACAGGCTCCCAGACATGACA	-	novel	NA	P-0020642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	80	106	0	ENST00000371953.3:c.-37_12del		p.*13*	ENST00000371953	NM_000314.4	?-2/403		1/9	1	2	FACETS	0.892	0.801	0.985	1	0.984	1	CLONAL	2	FALSE	1	0.435390376588398	2		106	206	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472460	88472460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	144	664	0	ENST00000360948.2:c.2095G>A	p.Gly699Ser	p.G699S	ENST00000360948	NM_001012338.2	699	Ggc/Agc	16/19	1	2	FACETS	0.683	0.623	0.747	0.683	0.623	0.747	SUBCLONAL	1	FALSE	1	0.435390376588398	2		664	968	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266074	41266266	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTG	ACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTG	-	novel	NA	P-0020642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	99	316	0	ENST00000349496.5:c.71_241+22del		p.X24_splice	ENST00000349496	NM_001904.3	24		3/15	0.435390376588398	1	FACETS	0.814	0.731	0.901	0.814	0.731	0.901	CLONAL	1	FALSE	0	0.435390376588398	1		316	437	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0020823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	52	417	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.921	0.784	1	0.921	0.784	1	CLONAL	1	TRUE	1	0.18	2		417	627	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913315	NA	P-0020823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	79	817	2	ENST00000326873.7:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000326873	NM_000455.4	194	Gac/Tac	4/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.18	2		819	595	SUCCESS
ATM	472	MSKCC	GRCh37	11	108213987	108213987	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs778269655	NA	P-0020823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	28	436	0	ENST00000278616.4:c.8307G>A	p.Trp2769Ter	p.W2769*	ENST00000278616	NM_000051.3	2769	tgG/tgA	57/63	1	2	FACETS	0.782	0.625	0.961	0.782	0.625	0.961	CLONAL	1	TRUE	1	0.18	2		436	398	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424552	49424552	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0020823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	30	625	0	ENST00000301067.7:c.13672-1G>T		p.X4558_splice	ENST00000301067	NM_003482.3	4558			1	2	FACETS	0.664	0.534	0.812	0.664	0.534	0.812	SUBCLONAL	1	TRUE	1	0.18	2		625	502	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588677	28588677	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	27	533	2	ENST00000241453.7:c.2771C>A	p.Ser924Tyr	p.S924Y	ENST00000241453	NM_004119.2	924	tCc/tAc	23/24	1	2	FACETS	0.626	0.497	0.774	0.626	0.497	0.774	SUBCLONAL	1	TRUE	1	0.18	2		535	479	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66468023	66468023	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0020823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	15	280	0	ENST00000273854.3:c.247-1G>T		p.X83_splice	ENST00000273854	NM_004439.5	83			1	2	FACETS	0.809	0.593	1	0.809	0.593	1	CLONAL	1	TRUE	1	0.18	2		280	206	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2969661	2969661	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	51	861	2	ENST00000396946.4:c.1618G>T	p.Gly540Ter	p.G540*	ENST00000396946	NM_032415.4	540	Gga/Tga	12/25	1	2	FACETS	0.917	0.779	1	0.917	0.779	1	CLONAL	1	TRUE	1	0.18	2		863	618	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633319	8633319	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs778130827	NA	P-0020823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	74	614	0	ENST00000356435.5:c.350G>T	p.Arg117Leu	p.R117L	ENST00000356435		117	cGg/cTg	3/35	1	2	FACETS	0.816	0.716	0.923	1	0.978	1	CLONAL	2	TRUE	1	0.18	2		614	504	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858038	152858039	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0020823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	32	478	1	ENST00000406277.2:c.576_577delinsCT	p.Val193Leu	p.V193L	ENST00000406277	NM_152274.4	192	gcGGtg/gcCTtg	6/7	1	2	FACETS	0.979	0.796	1	0.979	0.796	1	CLONAL	1	TRUE	1	0.18	2		479	363	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579361	7579361	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1064796722	NA	P-0020927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	138	1060	0	ENST00000269305.4:c.326T>C	p.Phe109Ser	p.F109S	ENST00000269305	NM_001126112.2	109	tTc/tCc	4/11	0.189887173471447	2	FACETS	0.922	0.84	1	0.922	0.84	1	CLONAL	2	TRUE	0	0.189887173471447	2		1060	788	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156263	119156263	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1311047726	NA	P-0020927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	71	571	0	ENST00000264033.4:c.1928T>C	p.Leu643Pro	p.L643P	ENST00000264033	NM_005188.3	643	cTg/cCg	11/16	0.189887173471447	3	FACETS	0.792	0.692	0.899	0.792	0.692	0.899	SUBCLONAL	2	TRUE	1	0.189887173471447	3		571	517	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349681	15349686	+	inframe_deletion	In_Frame_Del	DEL	TGCTGC	TGCTGC	-	rs745340727	NA	P-0020927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	39	868	0	ENST00000263377.2:c.3888_3893del	p.Gln1299_Gln1300del	p.Q1299_Q1300del	ENST00000263377	NM_058243.2	1296	caGCAGCAa/caa	19/20	0.131362635491217	4	FACETS	0.894	0.74	1	0.447	0.37	0.533	CLONAL	1	TRUE	2	0.189887173471447	4		868	547	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	80	366	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.345094658999392	4	FACETS	0.796	0.7	0.899	0.265	0.233	0.3	SUBCLONAL	1	TRUE	1	0.392605031935059	4		366	713	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691003	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	310	550	0	ENST00000269305.4:c.96+1G>T		p.X32_splice	ENST00000269305	NM_001126112.2	32			0.353105442630935	2	FACETS	0.843	0.797	0.89	0.843	0.797	0.89	CLONAL	2	TRUE	0	0.392605031935059	2		550	937	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796616	42796616	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	462	541	0	ENST00000575354.2:c.3173C>G	p.Ser1058Ter	p.S1058*	ENST00000575354	NM_015125.3	1058	tCa/tGa	13/20	0.357712136522943	3	FACETS	0.917	0.88	0.955	0.917	0.88	0.955	CLONAL	3	TRUE	0	0.392605031935059	3		541	1023	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389380	8389380	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	193	518	1	ENST00000356435.5:c.4238C>A	p.Ala1413Asp	p.A1413D	ENST00000356435		1413	gCc/gAc	26/35	0.354173253342579	3	FACETS	0.789	0.732	0.848	0.789	0.732	0.848	SUBCLONAL	2	TRUE	1	0.392605031935059	3		519	745	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256958	16256958	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	329	664	0	ENST00000375759.3:c.4223T>G	p.Leu1408Trp	p.L1408W	ENST00000375759	NM_015001.2	1408	tTg/tGg	11/15	0.354173253342579	3	FACETS	0.95	0.899	1	0.95	0.899	1	CLONAL	2	TRUE	1	0.392605031935059	3		664	1055	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937882	36937882	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1188	510	827	0	ENST00000361632.4:c.954G>C	p.Trp318Cys	p.W318C	ENST00000361632		318	tgG/tgC	7/16	0.354173253342579	3	FACETS	0.915	0.875	0.956	0.915	0.875	0.956	CLONAL	2	TRUE	1	0.392605031935059	3		827	1698	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301112	65301112	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	70	313	1	ENST00000342505.4:c.3336A>T	p.Lys1112Asn	p.K1112N	ENST00000342505	NM_002227.2	1112	aaA/aaT	24/25	0.377544259792418	3	FACETS	0.654	0.57	0.745	0.327	0.285	0.373	SUBCLONAL	1	TRUE	1	0.392605031935059	3		314	652	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77034348	77034348	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	342	612	0	ENST00000356341.3:c.1609G>A	p.Ala537Thr	p.A537T	ENST00000356341	NM_002576.4	537	Gct/Act	15/15	0.297606723077937	3	FACETS	0.917	0.868	0.966			1	CLONAL	2	TRUE	NA	0.392605031935059	3		612	1137	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428426	49428426	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	347	632	2	ENST00000301067.7:c.10379A>T	p.Gln3460Leu	p.Q3460L	ENST00000301067	NM_003482.3	3460	cAg/cTg	36/54	0.331404800808844	4	FACETS	0.888	0.84	0.938	0.888	0.84	0.938	CLONAL	2	TRUE	2	0.392605031935059	4		634	1386	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248806	133248806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768396766	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	302	599	2	ENST00000320574.5:c.1789G>A	p.Glu597Lys	p.E597K	ENST00000320574	NM_006231.2	597	Gaa/Aaa	16/49	0.354173253342579	3	FACETS	0.82	0.773	0.869	0.82	0.773	0.869	CLONAL	2	TRUE	1	0.392605031935059	3		601	1122	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134809	41134809	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	212	415	0	ENST00000379561.5:c.819G>C	p.Lys273Asn	p.K273N	ENST00000379561	NM_002015.3	273	aaG/aaC	2/3	0.353105442630935	2	FACETS	0.901	0.843	0.961	0.901	0.843	0.961	CLONAL	2	TRUE	0	0.392605031935059	2		415	599	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961903	41961903	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	186	375	0	ENST00000219905.7:c.811G>T	p.Gly271Ter	p.G271*	ENST00000219905	NM_001164273.1	271	Gga/Tga	2/24	0.331404800808844	4	FACETS	0.951	0.881	1	0.951	0.881	1	CLONAL	2	TRUE	2	0.392605031935059	4		375	694	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712698	43712698	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	402	794	1	ENST00000382044.4:c.4486G>T	p.Val1496Phe	p.V1496F	ENST00000382044	NM_001141980.1	1496	Gtt/Ttt	21/28	0.331404800808844	4	FACETS	0.886	0.841	0.932	0.886	0.841	0.932	CLONAL	2	TRUE	2	0.392605031935059	4		795	1609	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43783894	43783894	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	352	659	0	ENST00000382044.4:c.344A>T	p.Gln115Leu	p.Q115L	ENST00000382044	NM_001141980.1	115	cAg/cTg	4/28	0.331404800808844	4	FACETS	0.949	0.898	1	0.949	0.898	1	CLONAL	2	TRUE	2	0.392605031935059	4		659	1316	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423526	88423526	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	311	772	0	ENST00000360948.2:c.2309C>A	p.Pro770Gln	p.P770Q	ENST00000360948	NM_001012338.2	770	cCa/cAa	18/19	0.331404800808844	4	FACETS	0.832	0.784	0.882	0.832	0.784	0.882	CLONAL	2	TRUE	2	0.392605031935059	4		772	1326	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118562	17118562	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	348	607	0	ENST00000285071.4:c.1369G>A	p.Asp457Asn	p.D457N	ENST00000285071	NM_144997.5	457	Gac/Aac	12/14	0.252510338093465	2	FACETS	0.893	0.847	0.939	0.893	0.847	0.939	CLONAL	2	TRUE	0	0.392605031935059	2		607	993	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207093	1207093	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	462	760	0	ENST00000326873.7:c.181G>C	p.Gly61Arg	p.G61R	ENST00000326873	NM_000455.4	61	Ggc/Cgc	1/10	0.353105442630935	2	FACETS	0.912	0.872	0.953	0.912	0.872	0.953	CLONAL	2	TRUE	0	0.392605031935059	2		760	1290	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1627399	1627399	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs538284851	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	406	702	0	ENST00000344749.5:c.325G>C	p.Ala109Pro	p.A109P	ENST00000344749	NM_001136139.2	109	Gcc/Ccc	6/19	0.353105442630935	2	FACETS	0.918	0.875	0.961	0.918	0.875	0.961	CLONAL	2	TRUE	0	0.392605031935059	2		702	1127	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105555	11105555	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	378	761	0	ENST00000358026.2:c.1471A>T	p.Arg491Ter	p.R491*	ENST00000358026	NM_001128849.1	491	Aga/Tga	9/36	0.353105442630935	2	FACETS	0.851	0.809	0.894	0.851	0.809	0.894	CLONAL	2	TRUE	0	0.392605031935059	2		761	1131	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050034	13050034	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	237	483	0	ENST00000316448.5:c.178G>T	p.Glu60Ter	p.E60*	ENST00000316448	NM_004343.3	60	Gag/Tag	2/9	0.353105442630935	2	FACETS	0.843	0.79	0.897	0.843	0.79	0.897	CLONAL	2	TRUE	0	0.392605031935059	2		483	716	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229351	36229351	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	494	519	0	ENST00000222270.7:c.8041C>G	p.Leu2681Val	p.L2681V	ENST00000222270	NM_014727.1	2681	Ctg/Gtg	37/37	0.357712136522943	3	FACETS	0.891	0.855	0.927	0.891	0.855	0.927	CLONAL	3	TRUE	0	0.392605031935059	3		519	1126	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607819	46607819	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1304	449	737	0	ENST00000263734.3:c.2008C>T	p.Pro670Ser	p.P670S	ENST00000263734	NM_001430.4	670	Cct/Tct	12/16	0.331404800808844	4	FACETS	0.909	0.865	0.953	0.909	0.865	0.953	CLONAL	2	TRUE	2	0.392605031935059	4		737	1753	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61724037	61724037	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	201	549	0	ENST00000401558.2:c.865C>G	p.Leu289Val	p.L289V	ENST00000401558	NM_003400.3	289	Ctg/Gtg	10/25	0.331404800808844	4	FACETS	0.753	0.698	0.81	0.753	0.698	0.81	SUBCLONAL	2	TRUE	2	0.392605031935059	4		549	947	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248352	212248352	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	57	224	0	ENST00000342788.4:c.3915T>A	p.Asn1305Lys	p.N1305K	ENST00000342788	NM_005235.2	1305	aaT/aaA	28/28	0.354173253342579	3	FACETS	0.9	0.775	1	0.45	0.387	0.518	CLONAL	1	TRUE	1	0.392605031935059	3		224	386	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251712	212251712	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	85	386	0	ENST00000342788.4:c.3347C>A	p.Ala1116Glu	p.A1116E	ENST00000342788	NM_005235.2	1116	gCa/gAa	27/28	0.354173253342579	3	FACETS	0.736	0.65	0.827	0.368	0.325	0.414	SUBCLONAL	1	TRUE	1	0.392605031935059	3		386	704	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389096	31389096	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	803	476	0	ENST00000328111.2:c.2009G>C	p.Arg670Pro	p.R670P	ENST00000328111	NM_006892.3	670	cGg/cCg	19/23	0.392605031935059	5	FACETS	0.966	0.94	0.992			1	CLONAL	5	TRUE	NA	0.392605031935059	5		476	1346	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165045	47165045	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	98	447	0	ENST00000409792.3:c.1081G>C	p.Glu361Gln	p.E361Q	ENST00000409792	NM_014159.6	361	Gag/Cag	3/21	0.343058757717815	1	FACETS	0.867	0.777	0.961	0.867	0.777	0.961	CLONAL	1	TRUE	0	0.392605031935059	1		447	463	SUCCESS
APC	324	MSKCC	GRCh37	5	112177611	112177611	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	182	382	0	ENST00000257430.4:c.6320G>T	p.Gly2107Val	p.G2107V	ENST00000257430	NM_000038.5	2107	gGt/gTt	16/16	0.392605031935059	2	FACETS	0.972	0.905	1	0.972	0.905	1	CLONAL	2	TRUE	0	0.392605031935059	2		382	477	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138974	37138974	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1286	400	735	0	ENST00000373509.5:c.314G>A	p.Arg105Lys	p.R105K	ENST00000373509	NM_002648.3	105	aGg/aAg	4/6	0.326573235817553	4	FACETS	0.842	0.798	0.886			1	CLONAL	2	TRUE	NA	0.392605031935059	4		735	1686	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793876	89793876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	99	403	1	ENST00000336032.3:c.945G>A	p.Met315Ile	p.M315I	ENST00000336032	NM_006813.2	315	atG/atA	2/2	1	2	FACETS	0.831	0.743	0.924	0.831	0.743	0.924	CLONAL	1	TRUE	1	0.392605031935059	2		404	607	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450250	50450250	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	260	506	0	ENST00000331340.3:c.434T>A	p.Phe145Tyr	p.F145Y	ENST00000331340	NM_006060.4	145	tTc/tAc	5/8	0.331404800808844	4	FACETS	0.9	0.843	0.958	0.9	0.843	0.958	CLONAL	2	TRUE	2	0.392605031935059	4		506	1025	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848645	151848645	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	127	335	0	ENST00000262189.6:c.12548C>G	p.Ser4183Cys	p.S4183C	ENST00000262189	NM_170606.2	4183	tCt/tGt	50/59	0.331404800808844	4	FACETS	1	0.985	1	0.732	0.665	0.803	CLONAL	1	TRUE	2	0.392605031935059	4		335	615	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009358	69009358	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	462	528	0	ENST00000288368.4:c.2475C>A	p.Tyr825Ter	p.Y825*	ENST00000288368	NM_024870.2	825	taC/taA	22/40	0.357712136522943	3	FACETS	0.931	0.893	0.969	0.931	0.893	0.969	CLONAL	3	TRUE	0	0.392605031935059	3		528	1008	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340384	8340384	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	121	561	0	ENST00000356435.5:c.5212A>G	p.Thr1738Ala	p.T1738A	ENST00000356435		1738	Acc/Gcc	31/35	0.354173253342579	3	FACETS	0.747	0.674	0.825	0.374	0.337	0.413	SUBCLONAL	1	TRUE	1	0.392605031935059	3		561	987	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471047	8471047	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	106	546	0	ENST00000356435.5:c.3452G>C	p.Arg1151Pro	p.R1151P	ENST00000356435		1151	cGc/cCc	20/35	0.354173253342579	3	FACETS	0.892	0.8	0.99	0.446	0.4	0.495	CLONAL	1	TRUE	1	0.392605031935059	3		546	724	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485782	8485782	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	149	300	0	ENST00000356435.5:c.3035G>C	p.Arg1012Thr	p.R1012T	ENST00000356435		1012	aGg/aCg	17/35	0.354173253342579	3	FACETS	0.985	0.907	1	0.985	0.907	1	CLONAL	2	TRUE	1	0.392605031935059	3		300	461	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966683	36966683	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	233	453	3	ENST00000358127.4:c.643C>A	p.Pro215Thr	p.P215T	ENST00000358127	NM_001280556.1	215	Ccg/Acg	6/10	0.326573235817553	4	FACETS	0.897	0.838	0.959			1	CLONAL	2	TRUE	NA	0.392605031935059	4		456	921	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76777759	76777759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	264	277	1	ENST00000373344.5:c.6957G>A	p.Met2319Ile	p.M2319I	ENST00000373344	NM_000489.3	2319	atG/atA	32/35	0.326573235817553	2	FACETS	0.909	0.864	0.955			1	CLONAL	3	TRUE	NA	0.392605031935059	2		278	493	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99440101	99440103	+	missense_variant	Missense_Mutation	TNP	AAG	AAG	CAT	novel	NA	P-0020945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	275	613	0	ENST00000268035.6:c.1069_1071delinsCAT	p.Lys357His	p.K357H	ENST00000268035	NM_000875.3	357	AAG/CAT	4/21	0.331404800808844	4	FACETS	0.866	0.812	0.92	0.866	0.812	0.92	CLONAL	2	TRUE	2	0.392605031935059	4		613	1127	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220717	1220717	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587782018	NA	P-0020955-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	517	577	0	ENST00000326873.7:c.734+1G>T		p.X245_splice	ENST00000326873	NM_000455.4	245			0.398339912942749	4	FACETS	0.993	0.958	1	0.993	0.958	1	CLONAL	4	TRUE	0	0.398339912942749	4		577	914	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657313	29657313	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0020955-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	206	569	1	ENST00000356175.3:c.5547-1G>T		p.X1849_splice	ENST00000356175	NM_000267.3	1849			0.398339912942749	4	FACETS	0.929	0.865	0.996			1	CLONAL	2	TRUE	NA	0.398339912942749	4		570	778	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143289	108143291	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0020955-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	250	462	0	ENST00000278616.4:c.3108_3110del	p.Ser1037del	p.S1037del	ENST00000278616	NM_000051.3	1036	ttCTCt/ttt	21/63	0.398339912942749	3	FACETS	0.941	0.89	0.993	0.941	0.89	0.993	CLONAL	3	TRUE	0	0.398339912942749	3		462	533	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335623	73335623	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020955-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	76	274	0	ENST00000377767.4:c.2548G>T	p.Ala850Ser	p.A850S	ENST00000377767	NM_014953.3	850	Gcc/Tcc	19/21	0.398339912942749	6	FACETS	0.951	0.833	1			1	CLONAL	1	TRUE	NA	0.398339912942749	6		274	721	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349420	73349420	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020955-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	107	477	0	ENST00000377767.4:c.916T>C	p.Ser306Pro	p.S306P	ENST00000377767	NM_014953.3	306	Tct/Cct	6/21	0.398339912942749	6	FACETS	0.891	0.798	0.991			1	CLONAL	1	TRUE	NA	0.398339912942749	6		477	1083	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483016	29483016	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020955-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	168	315	0	ENST00000356175.3:c.76G>T	p.Gly26Ter	p.G26*	ENST00000356175	NM_000267.3	26	Gga/Tga	2/57	0.398339912942749	4	FACETS	1	0.966	1			1	CLONAL	2	TRUE	NA	0.398339912942749	4		315	547	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339481	81339481	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020955-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	181	508	0	ENST00000222390.5:c.1523T>A	p.Met508Lys	p.M508K	ENST00000222390	NM_000601.4	508	aTg/aAg	13/18	0.398339912942749	2	FACETS	0.874	0.812	0.937	0.874	0.812	0.937	CLONAL	2	TRUE	0	0.398339912942749	2		508	520	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044925	47044925	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020955-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	383	416	0	ENST00000377604.3:c.2251G>T	p.Glu751Ter	p.E751*	ENST00000377604	NM_001204468.1	751	Gag/Tag	20/24	0.362774779659204	2	FACETS	0.938	0.9	0.976			1	CLONAL	3	TRUE	NA	0.398339912942749	2		416	683	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	102	272	0				ENST00000310581	NM_198253.2	-/1132			0.170286265656225	1	FACETS	0.671	0.6	0.747	0.671	0.6	0.747	INDETERMINATE	1	TRUE	0	0.339904820023071	1		272	742	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0020995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	583	561	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.339904820023071	4	FACETS	0.947	0.913	0.98			1	CLONAL	4	TRUE	NA	0.339904820023071	4		561	1214	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806555	1806555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1189213092	NA	P-0020995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	674	729	0	ENST00000260795.2:c.1271C>T	p.Ser424Phe	p.S424F	ENST00000260795		424	tCc/tTc	9/17	0.339904820023071	4	FACETS	1	0.986	1			1	CLONAL	4	TRUE	NA	0.339904820023071	4		729	1288	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983121	201983122	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	163	800	0	ENST00000359651.3:c.971dup	p.Met324IlefsTer147	p.M324Ifs*147	ENST00000359651		324	atg/aTtg	7/8	1	2	FACETS	0.998	0.916	1	0.998	0.916	1	CLONAL	1	TRUE	1	0.339904820023071	2		800	961	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806582	1806582	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	852	868	0	ENST00000260795.2:c.1298C>G	p.Ser433Cys	p.S433C	ENST00000260795		433	tCc/tGc	9/17	0.339904820023071	4	FACETS	1	0.993	1			1	CLONAL	4	TRUE	NA	0.339904820023071	4		868	1588	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806683	1806683	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	853	814	0	ENST00000260795.2:c.1399C>G	p.Leu467Val	p.L467V	ENST00000260795		467	Ctg/Gtg	9/17	0.339904820023071	4	FACETS	1	0.992	1			1	CLONAL	4	TRUE	NA	0.339904820023071	4		814	1600	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651979	36651980	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	154	703	0	ENST00000244741.5:c.102dup	p.Asp35Ter	p.D35*	ENST00000244741	NM_000389.4	34	tgt/tgTt	2/3	1	2	FACETS	0.972	0.889	1	0.972	0.889	1	CLONAL	1	TRUE	1	0.339904820023071	2		703	932	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609684	117609684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	285	608	0	ENST00000368508.3:c.7015C>T	p.His2339Tyr	p.H2339Y	ENST00000368508	NM_002944.2	2339	Cac/Tac	43/43	0.672881114638769	5	FACETS	1	0.99	1	0.314	0.294	0.334	CLONAL	1	TRUE	1	0.684736717034915	5		608	1344	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0021325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	283	812	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	0.736794638797167	2		812	765	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	220	374	1	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	0.736794638797167	2	FACETS	0.976	0.933	1	0.976	0.933	1	CLONAL	2	TRUE	0	0.736794638797167	2		375	306	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578493	7578493	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1206165503	NA	P-0021325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	456	488	2	ENST00000269305.4:c.437G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tGg/tAg	5/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.736794638797167	2		490	1236	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456756	32456756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	363	925	4	ENST00000332351.3:c.136G>A	p.Ala46Thr	p.A46T	ENST00000332351	NM_024426.4	46	Gcc/Acc	1/10	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.736794638797167	2		929	839	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222886	5222886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372440262	NA	P-0021325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	98	917	1	ENST00000357368.4:c.2917G>A	p.Gly973Ser	p.G973S	ENST00000357368	NM_002850.3	973	Ggt/Agt	18/38	1	2	FACETS	0.328	0.292	0.367	0.328	0.292	0.367	SUBCLONAL	1	TRUE	1	0.736794638797167	2		918	810	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640512	3640512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776060270	NA	P-0021325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	372	980	0	ENST00000294008.3:c.3127G>A	p.Gly1043Arg	p.G1043R	ENST00000294008	NM_032444.2	1043	Ggg/Agg	12/15	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.736794638797167	2		980	902	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579576	7579640	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGACGGCAAGGGGGACTGTAGATGGGTGAAAAGAGCAGTCAGAGGACCAGGTCCTCAGCCCCCCA	GGACGGCAAGGGGGACTGTAGATGGGTGAAAAGAGCAGTCAGAGGACCAGGTCCTCAGCCCCCCA	-	novel	NA	P-0021325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	218	870	0	ENST00000269305.4:c.97-50_111del		p.X33_splice	ENST00000269305	NM_001126112.2	33		4/11	1	2	FACETS	0.829	0.774	0.885	0.829	0.774	0.885	CLONAL	1	TRUE	1	0.736794638797167	2		870	714	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584781	48584782	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATCTTCA	novel	NA	P-0021325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	212	727	0	ENST00000342988.3:c.860_866dup	p.His290SerfsTer20	p.H290Sfs*20	ENST00000342988	NM_005359.5	287	cat/cATCTTCAat	7/12	0.736794638797167	1	FACETS	0.631	0.59	0.672	0.631	0.59	0.672	SUBCLONAL	1	TRUE	0	0.736794638797167	1		727	576	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0021448-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	717	742	1	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	0.252824388046573	6	FACETS	1	0.987	1			1	INDETERMINATE	4	TRUE	NA	0.841465832925568	6		743	1118	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0021448-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	245	673	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	0.841465832925568	2		673	525	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266134	41266136	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs587776850	NA	P-0021448-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	114	323	0	ENST00000349496.5:c.133_135del	p.Ser45del	p.S45del	ENST00000349496	NM_001904.3	44	cCTTct/cct	3/15	1	2	FACETS	0.724	0.659	0.793	0.724	0.659	0.793	SUBCLONAL	1	TRUE	1	0.841465832925568	2		323	374	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348857	89348857	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021448-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	339	891	0	ENST00000301030.4:c.4093C>T	p.Arg1365Ter	p.R1365*	ENST00000301030	NM_001256183.1	1365	Cga/Tga	9/13	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.841465832925568	2		891	796	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416133	49416133	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1422752351	NA	P-0021448-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	142	326	0	ENST00000301067.7:c.16342C>T	p.Arg5448Ter	p.R5448*	ENST00000301067	NM_003482.3	5448	Cga/Tga	52/54	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.841465832925568	2		326	317	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22412956	22412956	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021448-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	80	157	0	ENST00000344548.3:c.203G>T	p.Arg68Leu	p.R68L	ENST00000344548	NM_001039802.1	68	cGa/cTa	5/7	0.516179224848006	1	FACETS	0.706	0.641	0.771	0.706	0.641	0.771	SUBCLONAL	1	TRUE	0	0.841465832925568	1		157	156	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422670	49422671	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021448-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	257	623	1	ENST00000301067.7:c.14322_14323delinsAA	p.Trp4774_Glu4775delinsTer	p.W4774_E4775delins*	ENST00000301067	NM_003482.3	4774	tgGGaa/tgAAaa	45/54	1	2	FACETS	0.951	0.897	1	0.951	0.897	1	CLONAL	1	TRUE	1	0.841465832925568	2		624	642	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933037	39933038	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTTCTCTTC	novel	NA	P-0021448-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	349	335	0	ENST00000378444.4:c.1552_1561dup	p.Asn521ArgfsTer39	p.N521Rfs*39	ENST00000378444	NM_001123385.1	521	aat/aGAAGAGAACAat	4/15	1	1	FACETS	0.975	0.94	1	0.975	0.94	1	CLONAL	1	TRUE	0	0.841465832925568	1		335	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0021497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	172	786	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.325659867875709	1	FACETS	0.996	0.917	1	0.996	0.917	1	CLONAL	1	TRUE	0	0.325659867875709	1		787	888	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0021497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	76	571	1	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.879	0.772	0.993	0.879	0.772	0.993	CLONAL	1	TRUE	1	0.325659867875709	2		572	531	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857449	9857449	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774419037	NA	P-0021497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	59	606	0	ENST00000330684.3:c.3952C>T	p.Arg1318Trp	p.R1318W	ENST00000330684	NM_001134407.1	1318	Cgg/Tgg	13/13	0.301360144938766	3	FACETS	0.478	0.41	0.553	0.239	0.205	0.277	SUBCLONAL	1	TRUE	1	0.325659867875709	3		606	881	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933367	39933367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754579483	NA	P-0021497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	186	400	2	ENST00000378444.4:c.1232G>A	p.Arg411Gln	p.R411Q	ENST00000378444	NM_001123385.1	411	cGg/cAg	4/15	1	1	FACETS	0.793	0.736	0.851	1	0.991	1	SUBCLONAL	2	TRUE	0	0.325659867875709	1		402	603	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436576	110436576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	168	817	3	ENST00000375856.3:c.1825G>A	p.Ala609Thr	p.A609T	ENST00000375856	NM_003749.2	609	Gcg/Acg	1/2	1	2	FACETS	0.989	0.908	1	0.989	0.908	1	CLONAL	1	TRUE	1	0.325659867875709	2		820	1043	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711311	114711311	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	106	512	0	ENST00000543371.1:c.326C>T	p.Pro109Leu	p.P109L	ENST00000543371	NM_001198531.1	109	cCc/cTc	3/14	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.325659867875709	2		512	634	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591921	48591921	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	118	556	0	ENST00000342988.3:c.1084T>G	p.Phe362Val	p.F362V	ENST00000342988	NM_005359.5	362	Ttt/Gtt	9/12	0.325659867875709	1	FACETS	0.985	0.891	1	0.985	0.891	1	CLONAL	1	TRUE	0	0.325659867875709	1		556	616	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210477	5210478	+	splice_donor_variant,intron_variant	Splice_Site	DNP	CA	CA	TC	novel	NA	P-0021497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	51	642	1	ENST00000357368.4:c.5487+2_5487+3delinsGA		p.X1829_splice	ENST00000357368	NM_002850.3	1829			1	2	FACETS	0.358	0.303	0.418	0.358	0.303	0.418	SUBCLONAL	1	TRUE	1	0.325659867875709	2		643	876	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214624	5214624	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	151	917	0	ENST00000357368.4:c.4442A>C	p.Glu1481Ala	p.E1481A	ENST00000357368	NM_002850.3	1481	gAg/gCg	29/38	1	2	FACETS	0.909	0.83	0.992	0.909	0.83	0.992	CLONAL	1	TRUE	1	0.325659867875709	2		917	1020	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514500	41514501	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0021497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	74	746	1	ENST00000373198.4:c.160_161delinsCT	p.Trp54Leu	p.W54L	ENST00000373198	NM_133170.3	54	TGg/CTg	2/32	0.325659867875709	5	FACETS	0.55	0.48	0.627	0.138	0.12	0.157	SUBCLONAL	1	TRUE	1	0.325659867875709	5		747	1229	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650279	12650279	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	133	762	0	ENST00000251849.4:c.567C>A	p.Asn189Lys	p.N189K	ENST00000251849	NM_002880.3	189	aaC/aaA	5/17	1	2	FACETS	0.946	0.859	1	0.946	0.859	1	CLONAL	1	TRUE	1	0.325659867875709	2		762	863	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670699	134670699	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1559768997	NA	P-0021497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	105	660	0	ENST00000398015.3:c.610G>T	p.Ala204Ser	p.A204S	ENST00000398015	NM_004441.4	204	Gca/Tca	3/16	1	2	FACETS	0.786	0.704	0.874	0.786	0.704	0.874	SUBCLONAL	1	TRUE	1	0.325659867875709	2		660	820	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162950	38162951	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0021497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	133	620	0	ENST00000317025.8:c.2255dup	p.Cys752TrpfsTer5	p.C752Wfs*5	ENST00000317025	NM_023034.1	752	tgt/tgGt	13/24	0.325659867875709	4	FACETS	0.994	0.901	1	0.331	0.3	0.365	CLONAL	1	TRUE	1	0.325659867875709	4		620	1089	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117870674	117870674	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	334	620	1	ENST00000297338.2:c.398T>A	p.Phe133Tyr	p.F133Y	ENST00000297338	NM_006265.2	133	tTc/tAc	5/14	0.325659867875709	4	FACETS	1	0.95	1	1	0.95	1	CLONAL	3	TRUE	1	0.325659867875709	4		621	905	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738385	145738386	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0021497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	147	753	0	ENST00000428558.2:c.2599dup	p.Ala867GlyfsTer17	p.A867Gfs*17	ENST00000428558	NM_004260.3	867	gcc/gGcc	16/22	0.325659867875709	4	FACETS	0.954	0.869	1	0.318	0.289	0.348	CLONAL	1	TRUE	1	0.325659867875709	4		753	1254	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0021593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	114	752	2	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.3	3	FACETS	1	0.98	1	0.676	0.61	0.746	CLONAL	1	FALSE	1	0.3	3		754	646	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579336	7579351	+	frameshift_variant	Frame_Shift_Del	DEL	CCCAGAATGCAAGAAG	CCCAGAATGCAAGAAG	-	novel	NA	P-0021593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	53	633	0	ENST00000269305.4:c.336_351del	p.Phe113GlnfsTer5	p.F113Qfs*5	ENST00000269305	NM_001126112.2	112	ggCTTCTTGCATTCTGGG/gg	4/11	0.00108864424317945	1	FACETS	0.707	0.604	0.819	0.707	0.604	0.819	INDETERMINATE	1	FALSE	0	0.3	1		633	425	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919252	48919252	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	18	214	0	ENST00000267163.4:c.417del	p.Asp139GlufsTer14	p.D139Efs*14	ENST00000267163	NM_000321.2	139	gaT/ga	4/27	0.228268005681601	1	FACETS	0.634	0.48	0.812	0.634	0.48	0.812	SUBCLONAL	1	FALSE	0	0.3	1		214	161	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863611	68863611	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	203	845	0	ENST00000261769.5:c.2350C>G	p.Arg784Gly	p.R784G	ENST00000261769	NM_004360.3	784	Cgt/Ggt	15/16	0.143186866082388	9	FACETS	1	0.939	1			1	CLONAL	6	TRUE	NA	0.143186866082388	9		845	703	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164571	36164571	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	163	644	1	ENST00000300305.3:c.1304C>A	p.Ala435Asp	p.A435D	ENST00000300305		435	gCc/gAc	8/8	1	2	FACETS	0.932	0.866	1	1	0.995	1	CLONAL	6	TRUE	1	0.143186866082388	2		645	407	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31421465	31421465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021655-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	204	656	0	ENST00000344624.3:c.3439G>A	p.Glu1147Lys	p.E1147K	ENST00000344624		1147	Gaa/Aaa	27/33	1	2	FACETS	0.931	0.87	0.994	0.931	0.87	0.994	CLONAL	1	TRUE	1	0.778179370155692	2		656	563	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220716	1220716	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021655-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	70	678	0	ENST00000326873.7:c.734T>A	p.Leu245His	p.L245H	ENST00000326873	NM_000455.4	245	cTc/cAc	5/10	1	2	FACETS	0.203	0.176	0.232	0.203	0.176	0.232	SUBCLONAL	1	TRUE	1	0.778179370155692	2		678	885	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0021843-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	190	596	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.18654305889346	2	FACETS	0.877	0.81	0.946	0.877	0.81	0.946	CLONAL	2	TRUE	0	0.221828067851187	2		597	977	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221782	55221786	+	missense_variant	Missense_Mutation	ONP	CAGAT	CAGAT	AGAGA	novel	NA	P-0021843-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	164	616	3	ENST00000275493.2:c.826_830delinsAGAGA	p.Gln276_Met277delinsArgGlu	p.Q276_M277delinsRE	ENST00000275493	NM_005228.3	276	CAGATg/AGAGAg	7/28	0.181063444733707	3	FACETS	0.82	0.752	0.891	0.82	0.752	0.891	CLONAL	2	TRUE	1	0.221828067851187	3		619	1002	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143298	108143310	+	frameshift_variant	Frame_Shift_Del	DEL	AATGGCCCTAGTA	AATGGCCCTAGTA	-	novel	NA	P-0021843-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	103	462	0	ENST00000278616.4:c.3120_3132del	p.Met1040IlefsTer20	p.M1040Ifs*20	ENST00000278616	NM_000051.3	1039	agAATGGCCCTAGTA/ag	21/63	0.213053473890357	2	FACETS	1	0.977	1	0.671	0.601	0.745	CLONAL	1	TRUE	0	0.221828067851187	2		462	692	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988916	41988916	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0021843-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	118	436	1	ENST00000219905.7:c.1708A>T	p.Lys570Ter	p.K570*	ENST00000219905	NM_001164273.1	570	Aag/Tag	3/24	0.18654305889346	2	FACETS	0.816	0.737	0.898	0.816	0.737	0.898	CLONAL	2	TRUE	0	0.221828067851187	2		437	652	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857925	9857925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs534440095	NA	P-0021894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	28	783	0	ENST00000330684.3:c.3476G>A	p.Arg1159His	p.R1159H	ENST00000330684	NM_001134407.1	1159	cGc/cAc	13/13	1	2	FACETS	0.518	0.413	0.639	0.518	0.413	0.639	SUBCLONAL	1	FALSE	1	0.223632777730047	2		783	483	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024614	31024614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147456014	NA	P-0021894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	30	765	1	ENST00000375687.4:c.4099G>A	p.Val1367Ile	p.V1367I	ENST00000375687	NM_015338.5	1367	Gtc/Atc	13/13	1	2	FACETS	0.554	0.446	0.678	0.554	0.446	0.678	SUBCLONAL	1	FALSE	1	0.223632777730047	2		766	484	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061168	38061195	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCCCGGCTGCTTCTCGCACTTGAAGC	GCCCCCGGCTGCTTCTCGCACTTGAAGC	-	novel	NA	P-0021894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	27	331	0	ENST00000250448.2:c.794_821del	p.Arg265ProfsTer47	p.R265Pfs*47	ENST00000250448	NM_004496.3	265	cGCTTCAAGTGCGAGAAGCAGCCGGGGGCc/cc	2/2	1	2	FACETS	0.936	0.747	1	0.936	0.747	1	CLONAL	1	FALSE	1	0.223632777730047	2		331	258	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705557	47705561	+	frameshift_variant	Frame_Shift_Del	DEL	AACTT	AACTT	-	novel	NA	P-0021894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	24	629	0	ENST00000233146.2:c.2358_2362del	p.Glu786AspfsTer11	p.E786Dfs*11	ENST00000233146	NM_000251.2	786	gAACTT/g	14/16	1	2	FACETS	0.869	0.684	1	0.869	0.684	1	CLONAL	1	FALSE	1	0.223632777730047	2		629	247	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0021940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	137	502	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	0.586222439087031	2		502	463	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612120	43612120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773256580	NA	P-0021940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	71	611	1	ENST00000355710.3:c.2225C>T	p.Thr742Met	p.T742M	ENST00000355710	NM_020975.4	742	aCg/aTg	12/20	0.568170014614048	3	FACETS	0.898	0.789	1	0.449	0.394	0.507	CLONAL	1	TRUE	1	0.586222439087031	3		612	349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1555525585	NA	P-0021940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	166	621	0	ENST00000269305.4:c.673-2A>G		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.535106046180181	1	FACETS	0.988	0.919	1	0.988	0.919	1	CLONAL	1	TRUE	0	0.586222439087031	1		621	405	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998606	100998606	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs369578132	NA	P-0021940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	114	662	0	ENST00000325455.5:c.1196G>T	p.Arg399Leu	p.R399L	ENST00000325455	NM_001202474.3	399	cGc/cTc	1/8	0.566389126394363	3	FACETS	0.876	0.791	0.965	0.438	0.395	0.483	CLONAL	1	TRUE	1	0.586222439087031	3		662	574	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907383	32907383	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	78	615	0	ENST00000380152.3:c.1768T>G	p.Phe590Val	p.F590V	ENST00000380152		590	Ttt/Gtt	10/27	0.139695162691316	0	FACETS	0.377	0.335	0.422			1	INDETERMINATE	1	TRUE	0	0.586222439087031	0		615	292	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933270	39933271	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	236	700	0	ENST00000378444.4:c.1328dup	p.Leu443PhefsTer4	p.L443Ffs*4	ENST00000378444	NM_001123385.1	443	ttg/ttTg	4/15	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.586222439087031	1		700	421	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933275	39933275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	244	688	1	ENST00000378444.4:c.1324G>A	p.Asp442Asn	p.D442N	ENST00000378444	NM_001123385.1	442	Gac/Aac	4/15	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.586222439087031	1		689	417	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0021967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	388	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.284627422415848	1	FACETS	1	0.994	1	1	0.997	1	CLONAL	2	TRUE	0	0.284627422415848	1		502	938	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024001	27024002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0021967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	32	110	0	ENST00000324856.7:c.1113dup	p.Gln372AlafsTer28	p.Q372Afs*28	ENST00000324856	NM_006015.4	369	-/G	1/20	0.284627422415848	1	FACETS	1	0.839	1	1	0.839	1	CLONAL	1	TRUE	0	0.284627422415848	1		110	188	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579558	7579559	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAAT	novel	NA	P-0021967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	200	666	0	ENST00000269305.4:c.125_128dup	p.Met44PhefsTer9	p.M44Ffs*9	ENST00000269305	NM_001126112.2	43	ttg/ttATTTg	4/11	0.284627422415848	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.284627422415848	1		666	1171	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	223	368	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.187593530701982	5	FACETS	1	0.945	1	1	0.945	1	INDETERMINATE	3	TRUE	2	0.700564203152733	5		368	435	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0022090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	192	478	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.270845401555437	5	FACETS	1	0.969	1	0.712	0.664	0.762	INDETERMINATE	2	TRUE	2	0.700564203152733	5		478	526	SUCCESS
APC	324	MSKCC	GRCh37	5	112154942	112154942	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779780	NA	P-0022090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	1070	727	1	ENST00000257430.4:c.1213C>T	p.Arg405Ter	p.R405*	ENST00000257430	NM_000038.5	405	Cga/Tga	10/16	0.700564203152733	4	FACETS	1	0.995	1	1	0.995	1	CLONAL	4	TRUE	0	0.700564203152733	4		728	1267	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085971	16085971	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	283	617	1	ENST00000281043.3:c.1147C>T	p.Arg383Cys	p.R383C	ENST00000281043	NM_005378.4	383	Cgc/Tgc	3/3	0.677238759726047	3	FACETS	1	0.992	1	0.664	0.627	0.703	CLONAL	1	TRUE	1	0.700564203152733	3		618	821	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46733230	46733230	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	177	725	0	ENST00000371975.4:c.991G>C	p.Asp331His	p.D331H	ENST00000371975	NM_003579.3	331	Gat/Cat	9/18	0.199180047847749	5	FACETS	1	0.954	1	0.35	0.322	0.379	INDETERMINATE	1	TRUE	2	0.700564203152733	5		725	987	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209061	133209061	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	216	542	0	ENST00000320574.5:c.6170A>C	p.Asn2057Thr	p.N2057T	ENST00000320574	NM_006231.2	2057	aAt/aCt	45/49	0.270845401555437	5	FACETS	1	0.966	1	0.699	0.654	0.745	INDETERMINATE	2	TRUE	2	0.700564203152733	5		542	603	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170760	11170760	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	360	786	0	ENST00000358026.2:c.4904A>G	p.Glu1635Gly	p.E1635G	ENST00000358026	NM_001128849.1	1635	gAg/gGg	35/36	0.270845401555437	5	FACETS	1	0.991	1	0.788	0.75	0.826	INDETERMINATE	2	TRUE	2	0.700564203152733	5		786	892	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143443	30143443	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	259	465	0	ENST00000389048.3:c.83G>A	p.Arg28His	p.R28H	ENST00000389048	NM_004304.4	28	cGc/cAc	1/29	0.677238759726047	3	FACETS	1	0.992	1	0.682	0.642	0.723	CLONAL	1	TRUE	1	0.700564203152733	3		465	732	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921546	178921546	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	88	402	0	ENST00000263967.3:c.1028A>T	p.Tyr343Phe	p.Y343F	ENST00000263967	NM_006218.2	343	tAc/tTc	5/21	0.270845401555437	5	FACETS	0.927	0.832	1	0.618	0.554	0.683	INDETERMINATE	2	TRUE	2	0.700564203152733	5		402	278	SUCCESS
APC	324	MSKCC	GRCh37	5	112175793	112175794	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0022090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	442	351	0	ENST00000257430.4:c.4503_4504dup	p.Cys1502PhefsTer6	p.C1502Ffs*6	ENST00000257430	NM_000038.5	1501	tct/tcTTt	16/16	0.700564203152733	4	FACETS	0.941	0.915	0.966	0.941	0.915	0.966	CLONAL	4	TRUE	0	0.700564203152733	4		351	570	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965639	93965639	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	113	641	0	ENST00000369303.4:c.2289T>G	p.Asn763Lys	p.N763K	ENST00000369303	NM_004440.3	763	aaT/aaG	13/17	1	2	FACETS	0.703	0.636	0.772	0.703	0.636	0.772	SUBCLONAL	1	TRUE	1	0.700564203152733	2		641	459	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370918	55370918	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	50	780	0	ENST00000297316.4:c.220G>C	p.Ala74Pro	p.A74P	ENST00000297316	NM_022454.3	74	Gct/Cct	1/2	0.493204772908611	1	FACETS	0.129	0.109	0.151	0.129	0.109	0.151	SUBCLONAL	1	TRUE	0	0.700564203152733	1		780	720	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	486	812	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.604093863738514	2		812	1418	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023769	27023769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	405	722	0	ENST00000324856.7:c.879del	p.Thr294ProfsTer69	p.T294Pfs*69	ENST00000324856	NM_006015.4	292	aCc/ac	1/20	0.281377937528828	1	FACETS	0.855	0.815	0.896	0.855	0.815	0.896	INDETERMINATE	1	TRUE	0	0.604093863738514	1		722	1094	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0022102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	357	851	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.587663700261698	1	FACETS	0.99	0.943	1	0.99	0.943	1	CLONAL	1	TRUE	0	0.604093863738514	1		851	833	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358343	91358343	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500649	NA	P-0022102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	132	539	0	ENST00000355112.3:c.4088C>T	p.Thr1363Ile	p.T1363I	ENST00000355112	NM_000057.2	1363	aCa/aTa	22/22	0.312411137199684	1	FACETS	0.42	0.382	0.461	0.42	0.382	0.461	INDETERMINATE	1	TRUE	0	0.604093863738514	1		539	726	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30954186	30954186	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0022102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	174	364	0	ENST00000375687.4:c.58-1G>A		p.X20_splice	ENST00000375687	NM_015338.5	20			1	2	FACETS	0.971	0.899	1	0.971	0.899	1	CLONAL	1	TRUE	1	0.604093863738514	2		364	593	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76931760	76931760	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	345	343	0	ENST00000373344.5:c.3770C>G	p.Thr1257Arg	p.T1257R	ENST00000373344	NM_000489.3	1257	aCa/aGa	10/35	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.604093863738514	1		343	614	SUCCESS
APC	324	MSKCC	GRCh37	5	112175858	112175858	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0022114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	169	297	1	ENST00000257430.4:c.4567A>T	p.Arg1523Ter	p.R1523*	ENST00000257430	NM_000038.5	1523	Aga/Tga	16/16	0.575549165216782	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.622087686816997	1		298	334	SUCCESS
APC	324	MSKCC	GRCh37	5	112175875	112175905	+	frameshift_variant	Frame_Shift_Del	DEL	TCAGGAAAATGACAATGGGAATGAAACAGAA	TCAGGAAAATGACAATGGGAATGAAACAGAA	-	novel	NA	P-0022114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	133	282	0	ENST00000257430.4:c.4588_4618del	p.Glu1530SerfsTer25	p.E1530Sfs*25	ENST00000257430	NM_000038.5	1528	gtTCAGGAAAATGACAATGGGAATGAAACAGAA/gt	16/16	0.575549165216782	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.622087686816997	1		282	292	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671946	30671946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	415	764	0	ENST00000376406.3:c.5014C>A	p.Pro1672Thr	p.P1672T	ENST00000376406	NM_014641.2	1672	Cct/Act	10/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.622087686816997	2		764	1232	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523534	106523534	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	33	348	0	ENST00000359195.3:c.2686G>T	p.Val896Leu	p.V896L	ENST00000359195	NM_002649.2	896	Gtg/Ttg	8/11	1	2	FACETS	0.19	0.154	0.231	0.19	0.154	0.231	SUBCLONAL	1	TRUE	1	0.622087686816997	2		348	557	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0022148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	220	794	0	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.642843026155336	2		794	583	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562953	29562953	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0022148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	161	777	0	ENST00000356175.3:c.3888T>G	p.Tyr1296Ter	p.Y1296*	ENST00000356175	NM_000267.3	1296	taT/taG	29/57	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.642843026155336	2		777	488	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	464350	464350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs975911125	NA	P-0022272-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	346	724	3	ENST00000399788.2:c.844C>T	p.Arg282Trp	p.R282W	ENST00000399788	NM_001042603.1	282	Cgg/Tgg	7/28	0.92678976802364	2	FACETS	0.655	0.62	0.69	0.327	0.31	0.345	SUBCLONAL	1	TRUE	0	0.937972965909012	2		727	1127	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888714	76888714	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022272-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	248	620	0	ENST00000373344.5:c.5115C>A	p.Asn1705Lys	p.N1705K	ENST00000373344	NM_000489.3	1705	aaC/aaA	19/35	1	2	FACETS	0.413	0.385	0.441	0.413	0.385	0.441	SUBCLONAL	1	TRUE	1	0.937972965909012	2		620	1281	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0022329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	163	622	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.196283339041193	5	FACETS	0.903	0.829	0.979			1	CLONAL	3	TRUE	NA	0.196283339041193	5		622	794	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577525	7577527	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0022329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	130	790	0	ENST00000269305.4:c.754_756del	p.Leu252del	p.L252del	ENST00000269305	NM_001126112.2	252	CTC/-	7/11	0.196283339041193	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	2	TRUE	0	0.196283339041193	2		790	658	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914723	39914723	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	89	325	1	ENST00000378444.4:c.4639C>T	p.Arg1547Ter	p.R1547*	ENST00000378444	NM_001123385.1	1547	Cga/Tga	12/15	0.196283339041193	2	FACETS	1	0.912	1			1	CLONAL	3	TRUE	NA	0.196283339041193	2		326	297	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944172	71944172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	78	724	1	ENST00000298229.2:c.2005G>A	p.Asp669Asn	p.D669N	ENST00000298229	NM_001567.3	669	Gac/Aac	17/28	0.103950633210256	4	FACETS	1	0.975	1	0.74	0.651	0.837	INDETERMINATE	1	TRUE	2	0.196283339041193	4		725	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578270	7578270	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	13	739	0	ENST00000269305.4:c.579T>G	p.His193Gln	p.H193Q	ENST00000269305	NM_001126112.2	193	caT/caG	6/11	0.196283339041193	2	FACETS	0.24	0.17	0.327	0.12	0.085	0.164	SUBCLONAL	1	TRUE	0	0.196283339041193	2		739	551	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167448	24167448	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	34	889	0	ENST00000263121.7:c.832C>T	p.Gln278Ter	p.Q278*	ENST00000263121	NM_003073.3	278	Cag/Tag	7/9	1	2	FACETS	0.511	0.416	0.618	0.511	0.416	0.618	SUBCLONAL	1	TRUE	1	0.196283339041193	2		889	678	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430210	181430226	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGCGGCAACTCCACC	GCGGCGGCAACTCCACC	-	rs1553862927	NA	P-0022329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	33	417	0	ENST00000325404.1:c.70_86del	p.Asn24GlyfsTer66	p.N24Gfs*66	ENST00000325404	NM_003106.3	21	gGCGGCGGCAACTCCACC/g	1/1	0.196283339041193	4	FACETS	0.996	0.811	1	0.332	0.27	0.401	CLONAL	1	TRUE	1	0.196283339041193	4		417	404	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509763	106509763	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	54	583	0	ENST00000359195.3:c.1757C>T	p.Pro586Leu	p.P586L	ENST00000359195	NM_002649.2	586	cCa/cTa	2/11	0.163270641441814	4	FACETS	1	0.917	1	0.556	0.474	0.645	CLONAL	1	TRUE	2	0.196283339041193	4		583	592	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407844	139407844	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs764191723	NA	P-0022329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	66	626	1	ENST00000277541.6:c.2353G>A	p.Gly785Ser	p.G785S	ENST00000277541	NM_017617.3	785	Ggt/Agt	14/34	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.196283339041193	2		627	469	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	351	812	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.522838270151442	4	FACETS	0.975	0.925	1	0.975	0.925	1	CLONAL	2	TRUE	2	0.539020018387411	4		812	1028	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0022333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	480	863	7	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.539020018387411	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.539020018387411	2		870	800	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165212	47165213	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	122	463	1	ENST00000409792.3:c.913dup	p.Thr305AsnfsTer4	p.T305Nfs*4	ENST00000409792	NM_014159.6	305	aca/aAca	3/21	0.539020018387411	3	FACETS	0.953	0.864	1	0.477	0.432	0.523	CLONAL	1	TRUE	1	0.539020018387411	3		464	603	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506328	120506328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	161	644	0	ENST00000256646.2:c.1784G>A	p.Cys595Tyr	p.C595Y	ENST00000256646	NM_024408.3	595	tGc/tAc	11/34	0.522838270151442	4	FACETS	0.881	0.808	0.959	0.441	0.404	0.48	CLONAL	1	TRUE	2	0.539020018387411	4		644	1043	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610498	81610498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	114	511	0	ENST00000298171.2:c.2096G>A	p.Cys699Tyr	p.C699Y	ENST00000298171	NM_000369.2	699	tGt/tAt	10/10	0.539020018387411	3	FACETS	0.932	0.842	1	0.466	0.421	0.514	CLONAL	1	TRUE	1	0.539020018387411	3		511	576	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462643	29462643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs187200776	NA	P-0022340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	230	1056	2	ENST00000389048.3:c.2258G>A	p.Arg753Gln	p.R753Q	ENST00000389048	NM_004304.4	753	cGg/cAg	13/29	1	2	FACETS	0.973	0.913	1	0.973	0.913	1	CLONAL	1	TRUE	1	0.723813893022376	2		1058	653	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384932	17384932	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	222	1013	1	ENST00000359435.4:c.483del	p.Asp162ThrfsTer67	p.D162Tfs*67	ENST00000359435	NM_001033549.1	161	tCc/tc	5/9	0.709384640103475	3	FACETS	0.961	0.896	1	0.481	0.448	0.514	CLONAL	1	TRUE	1	0.723813893022376	3		1014	869	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239957	98239957	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	163	607	0	ENST00000331920.6:c.1375C>G	p.Arg459Gly	p.R459G	ENST00000331920	NM_000264.3	459	Cgc/Ggc	10/24	0.723813893022376	3	FACETS	1	0.979	1	0.583	0.539	0.629	CLONAL	1	TRUE	1	0.723813893022376	3		607	526	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0022344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	13	291	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.431	0.306	0.585	0.431	0.306	0.585	SUBCLONAL	1	TRUE	1	0.15	2		291	402	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	162	812	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	0.319871567695278	2		812	953	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0022387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	95	641	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.874	0.778	0.975	0.874	0.778	0.975	CLONAL	1	TRUE	1	0.319871567695278	2		642	680	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777966	3777966	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	184	1243	2	ENST00000262367.5:c.7082C>T	p.Ser2361Phe	p.S2361F	ENST00000262367	NM_004380.2	2361	tCc/tTc	31/31	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.319871567695278	2		1245	1116	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437593	56437593	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	165	611	1	ENST00000407977.2:c.869G>A	p.Cys290Tyr	p.C290Y	ENST00000407977		290	tGc/tAc	8/10	0.319871567695278	2	FACETS	0.994	0.919	1	0.994	0.919	1	CLONAL	2	TRUE	0	0.319871567695278	2		612	519	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673479	30673479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	114	833	1	ENST00000376406.3:c.3481G>A	p.Val1161Ile	p.V1161I	ENST00000376406	NM_014641.2	1161	Gtt/Att	10/15	1	2	FACETS	0.937	0.844	1	0.937	0.844	1	CLONAL	1	TRUE	1	0.319871567695278	2		834	761	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	630	812	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.579183611372342	6	FACETS	0.941	0.909	0.972			1	CLONAL	4	TRUE	NA	0.579183611372342	6		812	1248	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873161	71873161	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	115	648	0	ENST00000357731.5:c.1033A>G	p.Ile345Val	p.I345V	ENST00000357731	NM_173808.2	345	Ata/Gta	7/7	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.579183611372342	2		648	381	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245035	133245036	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0022402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	150	1174	0	ENST00000320574.5:c.2079_2080insCT	p.Lys694LeufsTer99	p.K694Lfs*99	ENST00000320574	NM_006231.2	693	-/CT	19/49	0.579183611372342	3	FACETS	0.846	0.774	0.921	0.423	0.387	0.461	CLONAL	1	TRUE	1	0.579183611372342	3		1174	790	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56867201	56867201	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	323	863	0	ENST00000308159.5:c.1420G>A	p.Ala474Thr	p.A474T	ENST00000308159	NM_014669.4	474	Gca/Aca	13/22	0.579183611372342	3	FACETS	0.94	0.893	0.988	0.94	0.893	0.988	CLONAL	2	TRUE	1	0.579183611372342	3		863	765	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230918	66230918	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	47	586	0	ENST00000273854.3:c.2053G>A	p.Glu685Lys	p.E685K	ENST00000273854	NM_004439.5	685	Gaa/Aaa	12/18	1	2	FACETS	0.741	0.632	0.858	0.741	0.632	0.858	SUBCLONAL	1	TRUE	1	0.579183611372342	2		586	219	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578409	+	frameshift_variant	Frame_Shift_Del	DEL	TGGTGGGGGCAGCGCC	TGGTGGGGGCAGCGCC	-	novel	NA	P-0022402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	327	913	0	ENST00000269305.4:c.521_536del	p.Arg174MetfsTer68	p.R174Mfs*68	ENST00000269305	NM_001126112.2	174	aGGCGCTGCCCCCACCAt/at	5/11	0.579183611372342	2	FACETS	0.985	0.943	1	0.985	0.943	1	CLONAL	2	TRUE	0	0.579183611372342	2		913	573	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47724981	47724981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754077264	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	192	760	2	ENST00000449228.1:c.763G>A	p.Gly255Arg	p.G255R	ENST00000449228	NM_001127240.2	255	Ggg/Agg	4/4	1	2	FACETS	0.529	0.489	0.571	0.529	0.489	0.571	SUBCLONAL	1	TRUE	1	0.738144543394212	2		762	983	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584607	52584607	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	64	602	2	ENST00000394830.3:c.4406C>T	p.Pro1469Leu	p.P1469L	ENST00000394830	NM_018313.4	1469	cCc/cTc	29/30	0.738144543394212	1	FACETS	0.185	0.16	0.212	0.185	0.16	0.212	SUBCLONAL	1	TRUE	0	0.738144543394212	1		604	591	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984957	55984957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776989013	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	41	494	0	ENST00000263923.4:c.172G>A	p.Asp58Asn	p.D58N	ENST00000263923	NM_002253.2	58	Gac/Aac	3/30	0.738144543394212	1	FACETS	0.166	0.138	0.197	0.166	0.138	0.197	SUBCLONAL	1	TRUE	0	0.738144543394212	1		494	422	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805484	46805484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	188	823	2	ENST00000290295.7:c.472C>T	p.Pro158Ser	p.P158S	ENST00000290295	NM_006361.5	158	Ccg/Tcg	1/2	0.738144543394212	1	FACETS	0.501	0.464	0.538	0.501	0.464	0.538	SUBCLONAL	1	TRUE	0	0.738144543394212	1		825	642	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828324	72828324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	121	639	0	ENST00000268489.5:c.8257G>A	p.Asp2753Asn	p.D2753N	ENST00000268489	NM_006885.3	2753	Gac/Aac	9/10	0.738144543394212	1	FACETS	0.464	0.422	0.507	0.464	0.422	0.507	SUBCLONAL	1	TRUE	0	0.738144543394212	1		639	446	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633256	12633256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	58	677	1	ENST00000251849.4:c.1144C>T	p.Pro382Ser	p.P382S	ENST00000251849	NM_002880.3	382	Cca/Tca	11/17	0.738144543394212	1	FACETS	0.202	0.173	0.233	0.202	0.173	0.233	SUBCLONAL	1	TRUE	0	0.738144543394212	1		678	492	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961097	55961097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	49	715	0	ENST00000263923.4:c.2843G>A	p.Gly948Glu	p.G948E	ENST00000263923	NM_002253.2	948	gGg/gAg	21/30	0.738144543394212	1	FACETS	0.156	0.131	0.182	0.156	0.131	0.182	SUBCLONAL	1	TRUE	0	0.738144543394212	1		715	538	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067863	30067863	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778412102	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	49	547	1	ENST00000338641.4:c.1048G>A	p.Glu350Lys	p.E350K	ENST00000338641	NM_000268.3	350	Gaa/Aaa	11/16	0.738144543394212	1	FACETS	0.175	0.148	0.204	0.175	0.148	0.204	SUBCLONAL	1	TRUE	0	0.738144543394212	1		548	480	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613678	100613678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	46	550	0	ENST00000308731.7:c.901G>A	p.Glu301Lys	p.E301K	ENST00000308731	NM_000061.2	301	Gaa/Aaa	11/19	0.738144543394212	1	FACETS	0.163	0.137	0.192	0.163	0.137	0.192	SUBCLONAL	1	TRUE	0	0.738144543394212	1		550	482	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574482	64574482	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs398124437	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	68	701	0	ENST00000312049.6:c.912+1G>A		p.X304_splice	ENST00000312049	NM_130799.2	304			0.738144543394212	1	FACETS	0.227	0.197	0.259	0.227	0.197	0.259	SUBCLONAL	1	TRUE	0	0.738144543394212	1		701	512	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391710	139391710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201518848	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	44	816	2	ENST00000277541.6:c.6481C>T	p.Pro2161Ser	p.P2161S	ENST00000277541	NM_017617.3	2161	Ccc/Tcc	34/34	0.738144543394212	1	FACETS	0.106	0.088	0.126	0.106	0.088	0.126	SUBCLONAL	1	TRUE	0	0.738144543394212	1		818	708	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189882	11189882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751960147	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	47	491	0	ENST00000361445.4:c.5627C>T	p.Thr1876Ile	p.T1876I	ENST00000361445	NM_004958.3	1876	aCc/aTc	40/58	0.738144543394212	1	FACETS	0.206	0.174	0.241	0.206	0.174	0.241	SUBCLONAL	1	TRUE	0	0.738144543394212	1		491	390	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781575	9781575	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	44	662	1	ENST00000377346.4:c.1885C>A	p.Leu629Met	p.L629M	ENST00000377346	NM_005026.3	629	Ctg/Atg	15/24	0.738144543394212	1	FACETS	0.144	0.12	0.17	0.144	0.12	0.17	SUBCLONAL	1	TRUE	0	0.738144543394212	1		663	522	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188950	11188950	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	152	691	1	ENST00000361445.4:c.5773G>A	p.Glu1925Lys	p.E1925K	ENST00000361445	NM_004958.3	1925	Gag/Aag	41/58	0.738144543394212	1	FACETS	0.534	0.491	0.577	0.534	0.491	0.577	SUBCLONAL	1	TRUE	0	0.738144543394212	1		692	487	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261811	16261811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	59	641	0	ENST00000375759.3:c.9076C>T	p.Pro3026Ser	p.P3026S	ENST00000375759	NM_015001.2	3026	Cct/Tct	11/15	0.738144543394212	1	FACETS	0.214	0.184	0.247	0.214	0.184	0.247	SUBCLONAL	1	TRUE	0	0.738144543394212	1		641	471	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726609	46726609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771270089	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	81	598	0	ENST00000371975.4:c.688G>A	p.Val230Ile	p.V230I	ENST00000371975	NM_003579.3	230	Gtt/Att	7/18	0.738144543394212	1	FACETS	0.267	0.235	0.3	0.267	0.235	0.3	SUBCLONAL	1	TRUE	0	0.738144543394212	1		598	519	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414907	78414907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	39	540	1	ENST00000370768.2:c.1859G>A	p.Arg620Lys	p.R620K	ENST00000370768	NM_003902.3	620	aGa/aAa	19/20	0.738144543394212	1	FACETS	0.152	0.126	0.182	0.152	0.126	0.182	SUBCLONAL	1	TRUE	0	0.738144543394212	1		541	438	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268940	115268940	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	132	676	2	ENST00000438362.2:c.1670G>A	p.Gly557Asp	p.G557D	ENST00000438362	NM_001242891.1	557	gGt/gAt	14/20	0.738144543394212	1	FACETS	0.536	0.491	0.583	0.536	0.491	0.583	SUBCLONAL	1	TRUE	0	0.738144543394212	1		678	421	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612951	228612951	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	43	455	1	ENST00000366696.1:c.76G>A	p.Ala26Thr	p.A26T	ENST00000366696	NM_003493.2	26	Gct/Act	1/1	0.738144543394212	1	FACETS	0.158	0.132	0.187	0.158	0.132	0.187	SUBCLONAL	1	TRUE	0	0.738144543394212	1		456	464	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451026	70451026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	54	639	0	ENST00000373644.4:c.5866C>T	p.Pro1956Ser	p.P1956S	ENST00000373644	NM_030625.2	1956	Cca/Tca	12/12	0.738144543394212	1	FACETS	0.149	0.127	0.174	0.149	0.127	0.174	SUBCLONAL	1	TRUE	0	0.738144543394212	1		639	619	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154429	2154429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	83	606	0	ENST00000434045.2:c.499G>A	p.Gly167Ser	p.G167S	ENST00000434045	NM_001127598.1	167	Ggc/Agc	5/5	0.738144543394212	1	FACETS	0.233	0.205	0.262	0.233	0.205	0.262	SUBCLONAL	1	TRUE	0	0.738144543394212	1		606	609	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200070	67200070	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	136	615	0	ENST00000312629.5:c.458-1G>A		p.X153_splice	ENST00000312629	NM_003952.2	153			0.738144543394212	1	FACETS	0.488	0.447	0.531	0.488	0.447	0.531	SUBCLONAL	1	TRUE	0	0.738144543394212	1		615	476	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94926687	94926687	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	82	543	0	ENST00000536441.1:c.79-1G>A		p.X27_splice	ENST00000536441	NM_144665.3	27			0.738144543394212	1	FACETS	0.434	0.386	0.484	0.434	0.386	0.484	SUBCLONAL	1	TRUE	0	0.738144543394212	1		543	323	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999345	100999345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	34	878	1	ENST00000325455.5:c.457G>A	p.Ala153Thr	p.A153T	ENST00000325455	NM_001202474.3	153	Gct/Act	1/8	0.738144543394212	1	FACETS	0.091	0.074	0.111	0.091	0.074	0.111	SUBCLONAL	1	TRUE	0	0.738144543394212	1		879	636	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497533	125497533	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	37	424	0	ENST00000428830.2:c.97G>A	p.Glu33Lys	p.E33K	ENST00000428830	NM_001114121.2	33	Gaa/Aaa	3/14	0.738144543394212	1	FACETS	0.258	0.214	0.307	0.258	0.214	0.307	SUBCLONAL	1	TRUE	0	0.738144543394212	1		424	245	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800813	18800813	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	51	446	0	ENST00000266497.5:c.4189G>A	p.Val1397Ile	p.V1397I	ENST00000266497		1397	Gta/Ata	31/31	1	2	FACETS	0.455	0.388	0.526	0.455	0.388	0.526	SUBCLONAL	1	TRUE	1	0.738144543394212	2		446	304	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123650	46123650	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	59	439	1	ENST00000334344.6:c.31G>A	p.Asp11Asn	p.D11N	ENST00000334344	NM_152641.2	11	Gac/Aac	1/21	1	2	FACETS	0.226	0.194	0.262	0.226	0.194	0.262	SUBCLONAL	1	TRUE	1	0.738144543394212	2		440	706	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420990	49420990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	41	461	0	ENST00000301067.7:c.14759C>T	p.Pro4920Leu	p.P4920L	ENST00000301067	NM_003482.3	4920	cCc/cTc	48/54	1	2	FACETS	0.169	0.14	0.201	0.169	0.14	0.201	SUBCLONAL	1	TRUE	1	0.738144543394212	2		461	658	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481399	56481399	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565857178	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	61	786	1	ENST00000267101.3:c.586G>A	p.Gly196Ser	p.G196S	ENST00000267101	NM_001982.3	196	Ggt/Agt	5/28	1	2	FACETS	0.176	0.151	0.204	0.176	0.151	0.204	SUBCLONAL	1	TRUE	1	0.738144543394212	2		787	938	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493739	56493739	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	148	596	0	ENST00000267101.3:c.3055G>A	p.Glu1019Lys	p.E1019K	ENST00000267101	NM_001982.3	1019	Gag/Aag	25/28	1	2	FACETS	0.521	0.477	0.568	0.521	0.477	0.568	SUBCLONAL	1	TRUE	1	0.738144543394212	2		596	769	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864117	57864117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749783306	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	53	611	0	ENST00000228682.2:c.1594C>T	p.Arg532Cys	p.R532C	ENST00000228682	NM_005269.2	532	Cgc/Tgc	12/12	1	2	FACETS	0.17	0.144	0.198	0.17	0.144	0.198	SUBCLONAL	1	TRUE	1	0.738144543394212	2		611	847	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864733	57864733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	173	780	0	ENST00000228682.2:c.2210G>A	p.Gly737Glu	p.G737E	ENST00000228682	NM_005269.2	737	gGg/gAg	12/12	1	2	FACETS	0.512	0.471	0.555	0.512	0.471	0.555	SUBCLONAL	1	TRUE	1	0.738144543394212	2		780	915	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437619	110437619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	57	792	2	ENST00000375856.3:c.782G>A	p.Arg261His	p.R261H	ENST00000375856	NM_003749.2	261	cGc/cAc	1/2	0.738144543394212	1	FACETS	0.125	0.106	0.145	0.125	0.106	0.145	SUBCLONAL	1	TRUE	0	0.738144543394212	1		794	782	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060848	38060848	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1274348196	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	85	702	0	ENST00000250448.2:c.1141C>T	p.Pro381Ser	p.P381S	ENST00000250448	NM_004496.3	381	Ccc/Tcc	2/2	1	2	FACETS	0.204	0.179	0.23	0.204	0.179	0.23	SUBCLONAL	1	TRUE	1	0.738144543394212	2		702	1129	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570333	95570333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	44	487	0	ENST00000393063.1:c.3400C>T	p.His1134Tyr	p.H1134Y	ENST00000393063	NM_030621.3	1134	Cat/Tat	22/28	1	2	FACETS	0.235	0.196	0.277	0.235	0.196	0.277	SUBCLONAL	1	TRUE	1	0.738144543394212	2		487	508	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95577716	95577716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	73	483	0	ENST00000393063.1:c.2194G>A	p.Glu732Lys	p.E732K	ENST00000393063	NM_030621.3	732	Gaa/Aaa	15/28	1	2	FACETS	0.38	0.333	0.431	0.38	0.333	0.431	SUBCLONAL	1	TRUE	1	0.738144543394212	2		483	520	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95595897	95595897	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	71	606	0	ENST00000393063.1:c.646C>T	p.Pro216Ser	p.P216S	ENST00000393063	NM_030621.3	216	Cca/Tca	7/28	1	2	FACETS	0.44	0.385	0.499	0.44	0.385	0.499	SUBCLONAL	1	TRUE	1	0.738144543394212	2		606	437	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239707	105239707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	59	648	0	ENST00000349310.3:c.838C>T	p.Leu280Phe	p.L280F	ENST00000349310	NM_001014432.1	280	Ctc/Ttc	11/15	1	2	FACETS	0.212	0.182	0.245	0.212	0.182	0.245	SUBCLONAL	1	TRUE	1	0.738144543394212	2		648	754	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035053	42035053	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	73	640	0	ENST00000219905.7:c.4895C>T	p.Ala1632Val	p.A1632V	ENST00000219905	NM_001164273.1	1632	gCc/gTc	15/24	0.738144543394212	1	FACETS	0.234	0.205	0.266	0.234	0.205	0.266	SUBCLONAL	1	TRUE	0	0.738144543394212	1		640	533	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90633734	90633734	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	251	634	0	ENST00000330062.3:c.350C>T	p.Thr117Ile	p.T117I	ENST00000330062	NM_002168.2	117	aCc/aTc	3/11	0.738144543394212	1	FACETS	0.954	0.906	1	0.954	0.906	1	CLONAL	1	TRUE	0	0.738144543394212	1		634	450	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	338184	338184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1431827864	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	33	763	1	ENST00000262320.3:c.2527G>A	p.Asp843Asn	p.D843N	ENST00000262320	NM_003502.3	843	Gac/Aac	11/11	0.738144543394212	1	FACETS	0.1	0.081	0.121	0.1	0.081	0.121	SUBCLONAL	1	TRUE	0	0.738144543394212	1		764	565	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108803	2108803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	97	832	1	ENST00000219476.3:c.904G>A	p.Ala302Thr	p.A302T	ENST00000219476	NM_000548.3	302	Gct/Act	10/42	0.738144543394212	1	FACETS	0.255	0.227	0.284	0.255	0.227	0.284	SUBCLONAL	1	TRUE	0	0.738144543394212	1		833	651	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349029	11349029	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769403369	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	41	458	0	ENST00000332029.2:c.307G>A	p.Val103Met	p.V103M	ENST00000332029	NM_003745.1	103	Gtg/Atg	2/2	0.738144543394212	1	FACETS	0.111	0.092	0.133	0.111	0.092	0.133	SUBCLONAL	1	TRUE	0	0.738144543394212	1		458	629	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81968122	81968122	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771302628	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	34	544	0	ENST00000359376.3:c.2828C>T	p.Thr943Ile	p.T943I	ENST00000359376	NM_002661.3	943	aCc/aTc	26/33	0.738144543394212	1	FACETS	0.151	0.123	0.182	0.151	0.123	0.182	SUBCLONAL	1	TRUE	0	0.738144543394212	1		544	385	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217848	7217848	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	44	736	0	ENST00000380728.2:c.163G>A	p.Glu55Lys	p.E55K	ENST00000380728		55	Gag/Aag	3/11	0.738144543394212	1	FACETS	0.142	0.119	0.168	0.142	0.119	0.168	SUBCLONAL	1	TRUE	0	0.738144543394212	1		736	530	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508245	38508245	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	71	559	0	ENST00000254066.5:c.553G>A	p.Gly185Arg	p.G185R	ENST00000254066	NM_000964.3	185	Ggg/Agg	5/9	0.738144543394212	1	FACETS	0.282	0.246	0.319	0.282	0.246	0.319	SUBCLONAL	1	TRUE	0	0.738144543394212	1		559	431	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489469	40489469	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	46	531	0	ENST00000264657.5:c.781G>A	p.Asp261Asn	p.D261N	ENST00000264657	NM_139276.2	261	Gat/Aat	8/24	0.738144543394212	1	FACETS	0.155	0.13	0.183	0.155	0.13	0.183	SUBCLONAL	1	TRUE	0	0.738144543394212	1		531	506	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246511	41246511	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	96	806	0	ENST00000357654.3:c.1037C>T	p.Pro346Leu	p.P346L	ENST00000357654	NM_007294.3	346	cCc/cTc	10/23	0.738144543394212	1	FACETS	0.281	0.251	0.313	0.281	0.251	0.313	SUBCLONAL	1	TRUE	0	0.738144543394212	1		806	584	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619133	1619133	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	288	680	0	ENST00000344749.5:c.1427C>G	p.Ser476Cys	p.S476C	ENST00000344749	NM_001136139.2	476	tCt/tGt	16/19	0.738144543394212	1	FACETS	0.977	0.932	1	0.977	0.932	1	CLONAL	1	TRUE	0	0.738144543394212	1		680	504	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262465	10262465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	179	733	1	ENST00000340748.4:c.2030G>A	p.Gly677Asp	p.G677D	ENST00000340748		677	gGt/gAt	22/40	0.738144543394212	1	FACETS	0.526	0.487	0.565	0.526	0.487	0.565	SUBCLONAL	1	TRUE	0	0.738144543394212	1		734	582	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18958600	18958600	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	281	720	1	ENST00000262803.5:c.419G>A	p.Ser140Asn	p.S140N	ENST00000262803	NM_002911.3	140	aGc/aAc	3/24	0.738144543394212	1	FACETS	0.968	0.923	1	0.968	0.923	1	CLONAL	1	TRUE	0	0.738144543394212	1		721	496	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257913	19257913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748383473	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	420	843	0	ENST00000162023.5:c.473G>A	p.Gly158Glu	p.G158E	ENST00000162023		158	gGg/gAg	9/13	0.738144543394212	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.738144543394212	1		843	667	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214770	36214770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	49	604	0	ENST00000222270.7:c.3196G>A	p.Glu1066Lys	p.E1066K	ENST00000222270	NM_014727.1	1066	Gag/Aag	8/37	1	2	FACETS	0.177	0.149	0.207	0.177	0.149	0.207	SUBCLONAL	1	TRUE	1	0.738144543394212	2		604	752	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223491	36223491	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746768623	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	58	803	0	ENST00000222270.7:c.6041G>A	p.Gly2014Glu	p.G2014E	ENST00000222270	NM_014727.1	2014	gGg/gAg	28/37	1	2	FACETS	0.183	0.157	0.213	0.183	0.157	0.213	SUBCLONAL	1	TRUE	1	0.738144543394212	2		803	857	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752649	42752649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	135	604	0	ENST00000222329.4:c.1615G>A	p.Ala539Thr	p.A539T	ENST00000222329	NM_006494.2	539	Gcc/Acc	4/4	1	2	FACETS	0.439	0.398	0.481	0.439	0.398	0.481	SUBCLONAL	1	TRUE	1	0.738144543394212	2		604	834	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753482	42753482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	57	804	0	ENST00000222329.4:c.782C>T	p.Pro261Leu	p.P261L	ENST00000222329	NM_006494.2	261	cCc/cTc	4/4	1	2	FACETS	0.163	0.139	0.19	0.163	0.139	0.19	SUBCLONAL	1	TRUE	1	0.738144543394212	2		804	946	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796311	42796311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs966402205	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	210	859	0	ENST00000575354.2:c.2960C>T	p.Pro987Leu	p.P987L	ENST00000575354	NM_015125.3	987	cCt/cTt	12/20	1	2	FACETS	0.566	0.525	0.608	0.566	0.525	0.608	SUBCLONAL	1	TRUE	1	0.738144543394212	2		859	1006	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796750	42796750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	58	739	0	ENST00000575354.2:c.3208G>A	p.Val1070Met	p.V1070M	ENST00000575354	NM_015125.3	1070	Gtg/Atg	14/20	1	2	FACETS	0.183	0.156	0.212	0.183	0.156	0.212	SUBCLONAL	1	TRUE	1	0.738144543394212	2		739	861	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729866	47729866	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	415	644	0	ENST00000449228.1:c.523G>C	p.Ala175Pro	p.A175P	ENST00000449228	NM_001127240.2	175	Gct/Cct	3/4	1	2	FACETS	0.95	0.906	0.996	0.95	0.906	0.996	CLONAL	1	TRUE	1	0.738144543394212	2		644	1183	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023104	48023104	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	202	461	0	ENST00000234420.5:c.529C>T	p.Gln177Ter	p.Q177*	ENST00000234420	NM_000179.2	177	Caa/Taa	3/10	0.738144543394212	1	FACETS	0.959	0.906	1	0.959	0.906	1	CLONAL	1	TRUE	0	0.738144543394212	1		461	360	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735428	204735428	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1378866958	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	44	519	0	ENST00000302823.3:c.229G>A	p.Ala77Thr	p.A77T	ENST00000302823	NM_005214.4	77	Gct/Act	2/4	0.738144543394212	1	FACETS	0.162	0.135	0.191	0.162	0.135	0.191	SUBCLONAL	1	TRUE	0	0.738144543394212	1		519	465	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645841	215645841	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	80	821	0	ENST00000260947.4:c.757C>T	p.Gln253Ter	p.Q253*	ENST00000260947	NM_000465.2	253	Cag/Tag	4/11	0.738144543394212	1	FACETS	0.27	0.238	0.304	0.27	0.238	0.304	SUBCLONAL	1	TRUE	0	0.738144543394212	1		821	507	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30956927	30956927	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	39	499	0	ENST00000375687.4:c.252+1G>A		p.X84_splice	ENST00000375687	NM_015338.5	84			1	2	FACETS	0.17	0.141	0.204	0.17	0.141	0.204	SUBCLONAL	1	TRUE	1	0.738144543394212	2		499	620	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022890	31022890	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	54	595	0	ENST00000375687.4:c.2375G>A	p.Gly792Asp	p.G792D	ENST00000375687	NM_015338.5	792	gGc/gAc	13/13	1	2	FACETS	0.197	0.168	0.23	0.197	0.168	0.23	SUBCLONAL	1	TRUE	1	0.738144543394212	2		595	741	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288467	21288467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	43	787	0	ENST00000354336.3:c.712G>A	p.Val238Ile	p.V238I	ENST00000354336	NM_005207.3	238	Gtc/Atc	2/3	0.738144543394212	1	FACETS	0.139	0.116	0.165	0.139	0.116	0.165	SUBCLONAL	1	TRUE	0	0.738144543394212	1		787	528	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37640181	37640181	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	206	879	0	ENST00000249071.6:c.8C>T	p.Ala3Val	p.A3V	ENST00000249071	NM_002872.4	3	gCc/gTc	1/7	0.738144543394212	1	FACETS	0.486	0.452	0.52	0.486	0.452	0.52	SUBCLONAL	1	TRUE	0	0.738144543394212	1		879	725	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546191	41546191	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	62	441	0	ENST00000263253.7:c.2806C>T	p.Pro936Ser	p.P936S	ENST00000263253	NM_001429.3	936	Cct/Tct	14/31	0.738144543394212	1	FACETS	0.342	0.297	0.39	0.342	0.297	0.39	SUBCLONAL	1	TRUE	0	0.738144543394212	1		441	310	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572344	41572344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	150	769	0	ENST00000263253.7:c.4873G>A	p.Asp1625Asn	p.D1625N	ENST00000263253	NM_001429.3	1625	Gat/Aat	30/31	0.738144543394212	1	FACETS	0.487	0.448	0.528	0.487	0.448	0.528	SUBCLONAL	1	TRUE	0	0.738144543394212	1		769	526	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933663	49933663	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746415001	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	65	823	1	ENST00000296474.3:c.2614C>T	p.Pro872Ser	p.P872S	ENST00000296474	NM_002447.2	872	Cca/Tca	10/20	0.738144543394212	1	FACETS	0.176	0.152	0.201	0.176	0.152	0.201	SUBCLONAL	1	TRUE	0	0.738144543394212	1		824	633	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101732	71101732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	41	385	0	ENST00000318789.4:c.466C>T	p.Leu156Phe	p.L156F	ENST00000318789	NM_032682.5	156	Ctt/Ttt	9/21	0.738144543394212	1	FACETS	0.229	0.191	0.271	0.229	0.191	0.271	SUBCLONAL	1	TRUE	0	0.738144543394212	1		385	306	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260193	149260194	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTGCTG	rs748784098	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	166	620	0	ENST00000360632.3:c.694_699dup	p.Gln232_Gln233dup	p.Q232_Q233dup	ENST00000360632	NM_015472.4	232	-/CAGCAG	4/7	0.738144543394212	1	FACETS	0.654	0.607	0.702	0.654	0.607	0.702	SUBCLONAL	1	TRUE	0	0.738144543394212	1		620	434	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952094	178952094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	33	466	1	ENST00000263967.3:c.3149G>A	p.Gly1050Asp	p.G1050D	ENST00000263967	NM_006218.2	1050	gGc/gAc	21/21	0.738144543394212	1	FACETS	0.168	0.137	0.203	0.168	0.137	0.203	SUBCLONAL	1	TRUE	0	0.738144543394212	1		467	336	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683330	182683330	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	178	671	0	ENST00000292782.4:c.215A>T	p.Tyr72Phe	p.Y72F	ENST00000292782	NM_020640.2	72	tAc/tTc	2/7	0.738144543394212	1	FACETS	0.933	0.877	0.989	0.933	0.877	0.989	CLONAL	1	TRUE	0	0.738144543394212	1		671	326	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557750	187557750	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749093377	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	33	434	0	ENST00000441802.2:c.3961G>A	p.Asp1321Asn	p.D1321N	ENST00000441802	NM_005245.3	1321	Gat/Aat	5/27	0.738144543394212	1	FACETS	0.175	0.143	0.212	0.175	0.143	0.212	SUBCLONAL	1	TRUE	0	0.738144543394212	1		434	322	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627839	187627839	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201722651	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	170	711	1	ENST00000441802.2:c.3143C>T	p.Pro1048Leu	p.P1048L	ENST00000441802	NM_005245.3	1048	cCt/cTt	2/27	0.738144543394212	1	FACETS	0.526	0.486	0.566	0.526	0.486	0.566	SUBCLONAL	1	TRUE	0	0.738144543394212	1		712	553	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35857093	35857093	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	92	423	0	ENST00000303115.3:c.14G>A	p.Gly5Asp	p.G5D	ENST00000303115	NM_002185.3	5	gGt/gAt	1/8	1	2	FACETS	0.508	0.453	0.566	0.508	0.453	0.566	SUBCLONAL	1	TRUE	1	0.738144543394212	2		423	491	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152437	56152437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	39	241	0	ENST00000399503.3:c.493G>A	p.Glu165Lys	p.E165K	ENST00000399503	NM_005921.1	165	Gag/Aag	2/20	1	2	FACETS	0.361	0.3	0.428	0.361	0.3	0.428	SUBCLONAL	1	TRUE	1	0.738144543394212	2		241	293	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672362	86672362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	26	390	0	ENST00000274376.6:c.2164G>A	p.Glu722Lys	p.E722K	ENST00000274376	NM_002890.2	722	Gag/Aag	16/25	1	2	FACETS	0.174	0.137	0.216	0.174	0.137	0.216	SUBCLONAL	1	TRUE	1	0.738144543394212	2		390	405	SUCCESS
APC	324	MSKCC	GRCh37	5	112174008	112174008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554084407	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	38	469	0	ENST00000257430.4:c.2717C>T	p.Ser906Phe	p.S906F	ENST00000257430	NM_000038.5	906	tCt/tTt	16/16	1	2	FACETS	0.184	0.151	0.22	0.184	0.151	0.22	SUBCLONAL	1	TRUE	1	0.738144543394212	2		469	560	SUCCESS
APC	324	MSKCC	GRCh37	5	112176941	112176941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	92	483	0	ENST00000257430.4:c.5650G>A	p.Ala1884Thr	p.A1884T	ENST00000257430	NM_000038.5	1884	Gca/Aca	16/16	1	2	FACETS	0.475	0.423	0.53	0.475	0.423	0.53	SUBCLONAL	1	TRUE	1	0.738144543394212	2		483	525	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722321	176722321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	55	491	0	ENST00000439151.2:c.7952C>T	p.Ser2651Phe	p.S2651F	ENST00000439151	NM_022455.4	2651	tCt/tTt	23/23	0.382382834254952	1	FACETS	0.171	0.146	0.198	0.171	0.146	0.198	INDETERMINATE	1	TRUE	0	0.738144543394212	1		491	550	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393211	393211	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	75	563	2	ENST00000380956.4:c.59G>A	p.Gly20Asp	p.G20D	ENST00000380956	NM_001195286.1	20	gGc/gAc	2/9	0.738144543394212	1	FACETS	0.234	0.205	0.266	0.234	0.205	0.266	SUBCLONAL	1	TRUE	0	0.738144543394212	1		565	547	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170244	32170244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	38	785	0	ENST00000375023.3:c.3364G>A	p.Gly1122Ser	p.G1122S	ENST00000375023	NM_004557.3	1122	Ggt/Agt	21/30	0.738144543394212	1	FACETS	0.109	0.09	0.131	0.109	0.09	0.131	SUBCLONAL	1	TRUE	0	0.738144543394212	1		785	595	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171992	32171992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	50	603	0	ENST00000375023.3:c.3040C>T	p.Pro1014Ser	p.P1014S	ENST00000375023	NM_004557.3	1014	Ccc/Tcc	19/30	0.738144543394212	1	FACETS	0.19	0.161	0.222	0.19	0.161	0.222	SUBCLONAL	1	TRUE	0	0.738144543394212	1		603	450	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188299	32188299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780149009	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	63	819	0	ENST00000375023.3:c.1042G>A	p.Gly348Ser	p.G348S	ENST00000375023	NM_004557.3	348	Ggc/Agc	6/30	0.738144543394212	1	FACETS	0.168	0.145	0.193	0.168	0.145	0.193	SUBCLONAL	1	TRUE	0	0.738144543394212	1		819	641	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288690	33288690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	34	436	0	ENST00000374542.5:c.862G>A	p.Asp288Asn	p.D288N	ENST00000374542	NM_001141970.1	288	Gat/Aat	3/8	0.738144543394212	1	FACETS	0.123	0.1	0.148	0.123	0.1	0.148	SUBCLONAL	1	TRUE	0	0.738144543394212	1		436	474	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652114	36652114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	80	691	1	ENST00000244741.5:c.236C>T	p.Pro79Leu	p.P79L	ENST00000244741	NM_000389.4	79	cCc/cTc	2/3	0.738144543394212	1	FACETS	0.205	0.18	0.232	0.205	0.18	0.232	SUBCLONAL	1	TRUE	0	0.738144543394212	1		692	667	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706859	117706859	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	44	447	0	ENST00000368508.3:c.2291G>A	p.Gly764Glu	p.G764E	ENST00000368508	NM_002944.2	764	gGa/gAa	15/43	0.738144543394212	1	FACETS	0.203	0.17	0.239	0.203	0.17	0.239	SUBCLONAL	1	TRUE	0	0.738144543394212	1		447	371	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2952963	2952963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	66	785	1	ENST00000396946.4:c.2977C>T	p.Leu993Phe	p.L993F	ENST00000396946	NM_032415.4	993	Ctc/Ttc	22/25	1	2	FACETS	0.165	0.142	0.189	0.165	0.142	0.189	SUBCLONAL	1	TRUE	1	0.738144543394212	2		786	1086	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956944	2956944	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	50	635	0	ENST00000396946.4:c.2683C>T	p.Leu895Phe	p.L895F	ENST00000396946	NM_032415.4	895	Ctt/Ttt	20/25	1	2	FACETS	0.141	0.119	0.166	0.141	0.119	0.166	SUBCLONAL	1	TRUE	1	0.738144543394212	2		635	959	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403179	116403179	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	90	749	0	ENST00000397752.3:c.2440C>T	p.Pro814Ser	p.P814S	ENST00000397752	NM_000245.2	814	Ccc/Tcc	11/21	1	2	FACETS	0.414	0.368	0.463	0.414	0.368	0.463	SUBCLONAL	1	TRUE	1	0.738144543394212	2		749	589	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501299	140501299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	156	443	2	ENST00000288602.6:c.773G>A	p.Gly258Asp	p.G258D	ENST00000288602	NM_004333.4	258	gGt/gAt	6/18	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.738144543394212	2		445	358	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843752	151843752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	163	578	0	ENST00000262189.6:c.13963C>T	p.Pro4655Ser	p.P4655S	ENST00000262189	NM_170606.2	4655	Cca/Tca	53/59	1	2	FACETS	0.631	0.58	0.683	0.631	0.58	0.683	SUBCLONAL	1	TRUE	1	0.738144543394212	2		578	700	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848013	151848013	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1231682758	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	40	502	0	ENST00000262189.6:c.12746C>T	p.Thr4249Ile	p.T4249I	ENST00000262189	NM_170606.2	4249	aCt/aTt	51/59	1	2	FACETS	0.198	0.164	0.237	0.198	0.164	0.237	SUBCLONAL	1	TRUE	1	0.738144543394212	2		502	546	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274823	38274823	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	40	487	0	ENST00000425967.3:c.1756+1G>A		p.X586_splice	ENST00000425967	NM_001174067.1	586			0.738144543394212	1	FACETS	0.203	0.169	0.241	0.203	0.169	0.241	SUBCLONAL	1	TRUE	0	0.738144543394212	1		487	337	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958367	90958367	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1554556454	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	23	481	0	ENST00000265433.3:c.2070+1G>A		p.X690_splice	ENST00000265433	NM_002485.4	690			0.738144543394212	1	FACETS	0.202	0.158	0.252	0.202	0.158	0.252	SUBCLONAL	1	TRUE	0	0.738144543394212	1		481	195	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741905	145741905	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779547501	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	79	821	0	ENST00000428558.2:c.598G>A	p.Asp200Asn	p.D200N	ENST00000428558	NM_004260.3	200	Gat/Aat	5/22	0.738144543394212	1	FACETS	0.219	0.192	0.247	0.219	0.192	0.247	SUBCLONAL	1	TRUE	0	0.738144543394212	1		821	617	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27203075	27203075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747400050	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	308	667	1	ENST00000380036.4:c.2167C>T	p.Pro723Ser	p.P723S	ENST00000380036	NM_000459.3	723	Cca/Tca	13/23	0.738144543394212	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.738144543394212	1		668	512	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27229211	27229211	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	26	639	0	ENST00000380036.4:c.3356C>T	p.Ser1119Phe	p.S1119F	ENST00000380036	NM_000459.3	1119	tCt/tTt	23/23	0.738144543394212	1	FACETS	0.091	0.071	0.113	0.091	0.071	0.113	SUBCLONAL	1	TRUE	0	0.738144543394212	1		639	491	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37033997	37033997	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759944754	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	30	564	0	ENST00000358127.4:c.32G>A	p.Arg11Gln	p.R11Q	ENST00000358127	NM_001280556.1	11	cGg/cAg	1/10	0.738144543394212	1	FACETS	0.099	0.079	0.121	0.099	0.079	0.121	SUBCLONAL	1	TRUE	0	0.738144543394212	1		564	520	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93640037	93640037	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	39	372	0	ENST00000375746.1:c.1366C>T	p.Leu456Phe	p.L456F	ENST00000375746	NM_001174167.1	456	Ctc/Ttc	10/14	0.738144543394212	1	FACETS	0.212	0.176	0.252	0.212	0.176	0.252	SUBCLONAL	1	TRUE	0	0.738144543394212	1		372	314	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759578	133759578	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1284103223	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	30	778	2	ENST00000318560.5:c.1901G>A	p.Gly634Asp	p.G634D	ENST00000318560	NM_005157.4	634	gGc/gAc	11/11	0.738144543394212	1	FACETS	0.089	0.071	0.109	0.089	0.071	0.109	SUBCLONAL	1	TRUE	0	0.738144543394212	1		780	579	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227012	53227012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	75	688	0	ENST00000375401.3:c.2563G>A	p.Ala855Thr	p.A855T	ENST00000375401	NM_004187.3	855	Gcc/Acc	18/26	0.738144543394212	1	FACETS	0.219	0.192	0.248	0.219	0.192	0.248	SUBCLONAL	1	TRUE	0	0.738144543394212	1		688	585	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861508	152861508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	161	528	0	ENST00000406277.2:c.244G>A	p.Glu82Lys	p.E82K	ENST00000406277	NM_152274.4	82	Gaa/Aaa	4/7	0.738144543394212		FACETS		0.581	0.674				SUBCLONAL	1	TRUE	0	0.738144543394212	1		528	439	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937034	36937036	+	missense_variant,splice_region_variant	Missense_Mutation	TNP	CTC	CTC	TTT	novel	NA	P-0022440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	48	484	0	ENST00000361632.4:c.1283_1285delinsAAA	p.Arg428_Gly429delinsLysSer	p.R428_G429delinsKS	ENST00000361632		428	aGAGgc/aAAAgc	9/16	0.738144543394212	1	FACETS	0.176	0.149	0.207	0.176	0.149	0.207	SUBCLONAL	1	TRUE	0	0.738144543394212	1		484	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0022458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	74	681	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	0.769	0.672	0.873	0.769	0.672	0.873	SUBCLONAL	1	TRUE	1	0.251610499435597	2		681	765	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242478	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAG	AATTAAGAGAAG	CAC	rs727503015	NA	P-0022458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	833	675	2	ENST00000275493.2:c.2237_2248delinsCAC	p.Glu746_Ala750delinsAlaPro	p.E746_A750delinsAP	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGca/gCACca	19/28	0.251610499435597	13	FACETS	0.959	0.932	0.985	0.879	0.854	0.903	CLONAL	11	TRUE	1	0.251610499435597	13		677	1497	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955585	90955585	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	62	499	0	ENST00000265433.3:c.2080C>T	p.Pro694Ser	p.P694S	ENST00000265433	NM_002485.4	694	Cct/Tct	14/16	1	2	FACETS	0.868	0.75	0.996	0.868	0.75	0.996	CLONAL	1	TRUE	1	0.251610499435597	2		499	568	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90995077	90995077	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	47	479	0	ENST00000265433.3:c.44C>A	p.Pro15Gln	p.P15Q	ENST00000265433	NM_002485.4	15	cCa/cAa	2/16	0.251610499435597	3	FACETS	0.831	0.701	0.974	0.277	0.233	0.325	CLONAL	1	TRUE	0	0.251610499435597	3		479	506	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440334	52440334	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0022543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	266	658	1	ENST00000460680.1:c.718A>T	p.Lys240Ter	p.K240*	ENST00000460680	NM_004656.3	240	Aag/Tag	9/17	0.270734320655478	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.31	1		659	1003	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256561	16256561	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	125	545	0	ENST00000375759.3:c.3826del	p.Ile1276Ter	p.I1276*	ENST00000375759	NM_015001.2	1276	Ata/ta	11/15	0.300183815525321	1	FACETS	0.826	0.748	0.909	0.826	0.748	0.909	CLONAL	1	TRUE	0	0.31	1		545	825	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427190	49427190	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1216	170	673	0	ENST00000301067.7:c.11298C>G	p.Asn3766Lys	p.N3766K	ENST00000301067	NM_003482.3	3766	aaC/aaG	39/54	1	2	FACETS	0.791	0.726	0.86	0.791	0.726	0.86	SUBCLONAL	1	TRUE	1	0.31	2		673	1386	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489543	40489543	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs371541785	NA	P-0022543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	451	542	0	ENST00000264657.5:c.707C>G	p.Thr236Arg	p.T236R	ENST00000264657	NM_139276.2	236	aCg/aGg	8/24	0.29309901532478	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.31	3		542	1513	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565562	41565562	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	77	488	0	ENST00000263253.7:c.4228A>G	p.Arg1410Gly	p.R1410G	ENST00000263253	NM_001429.3	1410	Agg/Ggg	26/31	1	2	FACETS	0.729	0.64	0.826	0.729	0.64	0.826	SUBCLONAL	1	TRUE	1	0.31	2		488	681	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0022555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	91	364	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.210780721731387	4	FACETS	0.778	0.696	0.864	0.778	0.696	0.864	INDETERMINATE	2	TRUE	2	0.456460182371329	4		364	373	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0022555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	233	255	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.389783464750908	2	FACETS	0.913	0.859	0.968	0.913	0.859	0.968	CLONAL	2	TRUE	0	0.456460182371329	2		255	559	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0022555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	68	290	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.142765751101263	5	FACETS	1	0.921	1	0.269	0.235	0.307	INDETERMINATE	1	TRUE	1	0.456460182371329	5		290	466	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0022555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	164	753	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.335482752215843	3	FACETS	1	0.934	1	0.672	0.623	0.721	CLONAL	2	TRUE	0	0.456460182371329	3		753	438	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735467	40735467	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776642212	NA	P-0022555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	188	1030	1	ENST00000373198.4:c.3406C>T	p.Arg1136Cys	p.R1136C	ENST00000373198	NM_133170.3	1136	Cgt/Tgt	25/32	0.126168701150965	4	FACETS	1	0.989	1	0.718	0.665	0.774	INDETERMINATE	1	TRUE	2	0.456460182371329	4		1031	835	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257751	133257751	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	176	935	1	ENST00000320574.5:c.177G>T	p.Lys59Asn	p.K59N	ENST00000320574	NM_006231.2	59	aaG/aaT	2/49	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.456460182371329	2		936	665	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437908	110437908	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	11	36	0	ENST00000375856.3:c.493G>A	p.Ala165Thr	p.A165T	ENST00000375856	NM_003749.2	165	Gcc/Acc	1/2	0.431903941760742	3	FACETS	1	0.82	1	0.617	0.439	0.822	CLONAL	1	TRUE	1	0.456460182371329	3		36	48	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632618	3632618	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	96	1203	1	ENST00000294008.3:c.5230C>T	p.Gln1744Ter	p.Q1744*	ENST00000294008	NM_032444.2	1744	Cag/Tag	15/15	1	2	FACETS	0.453	0.402	0.507	0.453	0.402	0.507	SUBCLONAL	1	TRUE	1	0.456460182371329	2		1204	929	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646641	23646641	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	35	702	0	ENST00000261584.4:c.1226A>C	p.Tyr409Ser	p.Y409S	ENST00000261584	NM_024675.3	409	tAt/tCt	4/13	1	2	FACETS	0.331	0.27	0.398	0.331	0.27	0.398	SUBCLONAL	1	TRUE	1	0.456460182371329	2		702	464	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538254	9538254	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0022555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	130	868	2	ENST00000353224.5:c.1743+1del		p.X581_splice	ENST00000353224	NM_177990.2	581			0.126168701150965	4	FACETS	1	0.981	1	0.652	0.593	0.714	INDETERMINATE	1	TRUE	2	0.456460182371329	4		870	636	SUCCESS
APC	324	MSKCC	GRCh37	5	112175944	112175945	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0022555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	77	322	0	ENST00000257430.4:c.4655_4656del	p.Glu1552GlyfsTer6	p.E1552Gfs*6	ENST00000257430	NM_000038.5	1551	aaAGag/aaag	16/16	0.142765751101263	5	FACETS	0.963	0.855	1	0.482	0.427	0.539	INDETERMINATE	2	TRUE	1	0.456460182371329	5		322	295	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0022639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	526	660	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.843748383859779	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.843748383859779	1		661	646	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11291084	11291085	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0022639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	101	614	0	ENST00000361445.4:c.2676_2677delinsTT	p.Ala893Ser	p.A893S	ENST00000361445	NM_004958.3	892	ggGGct/ggTTct	18/58	1	2	FACETS	0.26	0.232	0.29	0.26	0.232	0.29	SUBCLONAL	1	TRUE	1	0.843748383859779	2		614	920	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425860	49425860	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	420	706	1	ENST00000301067.7:c.12628C>T	p.Gln4210Ter	p.Q4210*	ENST00000301067	NM_003482.3	4210	Cag/Tag	39/54	1	2	FACETS	0.996	0.952	1	0.996	0.952	1	CLONAL	1	TRUE	1	0.843748383859779	2		707	1000	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233988	133233988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs531475854	NA	P-0022639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	429	657	3	ENST00000320574.5:c.3406C>T	p.Arg1136Trp	p.R1136W	ENST00000320574	NM_006231.2	1136	Cgg/Tgg	28/49	1	2	FACETS	0.983	0.939	1	0.983	0.939	1	CLONAL	1	TRUE	1	0.843748383859779	2		660	1035	SUCCESS
APC	324	MSKCC	GRCh37	5	112174532	112174574	+	frameshift_variant	Frame_Shift_Del	DEL	AGCACTGATGATAAACACCTCAAGTTCCAACCACATTTTGGAC	AGCACTGATGATAAACACCTCAAGTTCCAACCACATTTTGGAC	-	novel	NA	P-0022639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	201	417	0	ENST00000257430.4:c.3245_3287del	p.Thr1082ArgfsTer30	p.T1082Rfs*30	ENST00000257430	NM_000038.5	1081	AGCACTGATGATAAACACCTCAAGTTCCAACCACATTTTGGACag/ag	16/16	0.843748383859779	1	FACETS	0.998	0.953	1	0.998	0.953	1	CLONAL	1	TRUE	0	0.843748383859779	1		417	276	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046421	69046421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	116	736	2	ENST00000288368.4:c.3894G>A	p.Met1298Ile	p.M1298I	ENST00000288368	NM_024870.2	1298	atG/atA	32/40	0.390724244772062	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.390724244772062	1		738	474	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31486629	31486629	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756470214	NA	P-0022663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	86	696	1	ENST00000344624.3:c.1883C>T	p.Thr628Met	p.T628M	ENST00000344624		628	aCg/aTg	11/33	1	2	FACETS	0.84	0.745	0.941	0.84	0.745	0.941	CLONAL	1	TRUE	1	0.390724244772062	2		697	524	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939156	76939156	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1557141276	NA	P-0022663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	62	773	2	ENST00000373344.5:c.1592A>T	p.Asn531Ile	p.N531I	ENST00000373344	NM_000489.3	531	aAt/aTt	9/35	0.388888730160966	1	FACETS	0.863	0.751	0.982	0.863	0.751	0.982	CLONAL	1	TRUE	0	0.390724244772062	1		775	296	SUCCESS
BTK	695	MSKCC	GRCh37	X	100609634	100609634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	84	689	2	ENST00000308731.7:c.1615G>A	p.Asp539Asn	p.D539N	ENST00000308731	NM_000061.2	539	Gat/Aat	16/19	1	2	FACETS	0.838	0.742	0.94	0.838	0.742	0.94	CLONAL	1	TRUE	1	0.390724244772062	2		691	513	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0022668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	455	932	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.508566907289787	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	0	0.508566907289787	3		932	732	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602583	10602583	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	223	761	0	ENST00000171111.5:c.995del	p.Gly332AlafsTer68	p.G332Afs*68	ENST00000171111	NM_203500.1	332	gGc/gc	3/6	0.508566907289787	2	FACETS	0.953	0.899	1	0.953	0.899	1	CLONAL	2	TRUE	0	0.508566907289787	2		761	460	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123695	11123695	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	283	854	2	ENST00000358026.2:c.2345G>A	p.Gly782Asp	p.G782D	ENST00000358026	NM_001128849.1	782	gGc/gAc	16/36	0.508566907289787	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.508566907289787	2		856	526	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101249	27101249	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	137	711	1	ENST00000324856.7:c.4531A>G	p.Arg1511Gly	p.R1511G	ENST00000324856	NM_006015.4	1511	Agg/Ggg	18/20	0.508566907289787	2	FACETS	1	0.974	1	0.579	0.531	0.63	CLONAL	1	TRUE	0	0.508566907289787	2		712	465	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102056763	102056763	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	70	425	0	ENST00000282441.5:c.703G>A	p.Gly235Arg	p.G235R	ENST00000282441	NM_001130145.2	235	Gga/Aga	4/9	0.508566907289787	3	FACETS	0.857	0.75	0.971	0.428	0.375	0.486	CLONAL	1	TRUE	1	0.508566907289787	3		425	403	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135264	2135264	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs45517353	NA	P-0022668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	175	1013	1	ENST00000219476.3:c.4603G>T	p.Asp1535Tyr	p.D1535Y	ENST00000219476	NM_000548.3	1535	Gac/Tac	36/42	0.505710473104826	4	FACETS	1	0.981	1	0.401	0.37	0.434	CLONAL	1	TRUE	1	0.508566907289787	4		1014	862	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521177	187521177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778434346	NA	P-0022668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	85	784	0	ENST00000441802.2:c.11978C>T	p.Pro3993Leu	p.P3993L	ENST00000441802	NM_005245.3	3993	cCc/cTc	22/27	1	2	FACETS	0.743	0.659	0.831	0.743	0.659	0.831	SUBCLONAL	1	TRUE	1	0.508566907289787	2		784	450	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187560939	187560939	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0022668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	79	468	0	ENST00000441802.2:c.3581-2A>T		p.X1194_splice	ENST00000441802	NM_005245.3	1194			1	2	FACETS	0.962	0.854	1	0.962	0.854	1	CLONAL	1	TRUE	1	0.508566907289787	2		468	323	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564456	86564490	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGAGCCGCTTTGGGGTCAGAGTTCCTAGGAGCC	GCGGAGCCGCTTTGGGGTCAGAGTTCCTAGGAGCC	-	novel	NA	P-0022668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	183	601	0	ENST00000274376.6:c.189_223del	p.Gly64ValfsTer36	p.G64Vfs*36	ENST00000274376	NM_002890.2	63	gGCGGAGCCGCTTTGGGGTCAGAGTTCCTAGGAGCC/g	1/25	0.506749160774703	2	FACETS	0.98	0.92	1	0.98	0.92	1	CLONAL	2	TRUE	0	0.508566907289787	2		601	367	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675325	176675325	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	72	445	0	ENST00000439151.2:c.4641G>C	p.Gln1547His	p.Q1547H	ENST00000439151	NM_022455.4	1547	caG/caC	11/23	0.506749160774703	2	FACETS	0.893	0.787	1	0.447	0.393	0.503	CLONAL	1	TRUE	0	0.508566907289787	2		445	317	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69011919	69011919	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	118	748	0	ENST00000288368.4:c.2556T>G	p.Ile852Met	p.I852M	ENST00000288368	NM_024870.2	852	atT/atG	23/40	0.47823105500907	3	FACETS	1	0.956	1	0.547	0.495	0.601	CLONAL	1	TRUE	1	0.508566907289787	3		748	532	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374580	118374580	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	28	451	0	ENST00000534358.1:c.7973A>C	p.Lys2658Thr	p.K2658T	ENST00000534358	NM_005933.3	2658	aAg/aCg	27/36	1	2	FACETS	0.988	0.789	1	0.988	0.789	1	CLONAL	1	TRUE	1	0.13	2		451	436	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32971045	32971045	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	33	437	0	ENST00000380152.3:c.9512T>G	p.Ile3171Arg	p.I3171R	ENST00000380152		3171	aTa/aGa	26/27	1	2	FACETS	0.992	0.807	1	0.992	0.807	1	CLONAL	1	TRUE	1	0.13	2		437	512	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221228	1221228	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	42	937	0	ENST00000326873.7:c.751G>C	p.Gly251Arg	p.G251R	ENST00000326873	NM_000455.4	251	Ggt/Cgt	6/10	0.211404596449458	1	FACETS	0.807	0.672	0.957	0.807	0.672	0.957	CLONAL	1	TRUE	0	0.13	1		937	749	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0022703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	117	577	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.3	4	FACETS	0.858	0.783	0.935	0.572	0.522	0.623	INDETERMINATE	2	TRUE	1	0.69	4		577	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0022703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	60	681	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	0.519	0.45	0.594	0.519	0.45	0.594	SUBCLONAL	1	TRUE	1	0.69	2		681	335	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226566897	226566897	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	52	628	0	ENST00000366794.5:c.1691A>G	p.Lys564Arg	p.K564R	ENST00000366794	NM_001618.3	564	aAa/aGa	12/23	1	2	FACETS	0.369	0.314	0.428	0.369	0.314	0.428	SUBCLONAL	1	TRUE	1	0.69	2		628	409	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628435	21628435	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	39	680	0	ENST00000421138.2:c.1183A>G	p.Met395Val	p.M395V	ENST00000421138		395	Atg/Gtg	11/16	1	2	FACETS	0.236	0.195	0.281	0.236	0.195	0.281	SUBCLONAL	1	TRUE	1	0.69	2		680	479	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864619	57864619	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	39	789	0	ENST00000228682.2:c.2096A>G	p.Asp699Gly	p.D699G	ENST00000228682	NM_005269.2	699	gAt/gGt	12/12	0.279320974509874	3	FACETS	0.342	0.283	0.407	0.171	0.141	0.204	INDETERMINATE	1	TRUE	1	0.69	3		789	445	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16055293	16055293	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0022714-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	433	511	0	ENST00000268712.3:c.809C>G	p.Ser270Ter	p.S270*	ENST00000268712	NM_006311.3	270	tCa/tGa	8/46	0.834835156509204	2	FACETS	0.99	0.965	1	0.99	0.965	1	CLONAL	2	TRUE	0	0.834835156509204	2		511	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578509	7578509	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519978	NA	P-0022714-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	694	763	0	ENST00000269305.4:c.421T>C	p.Cys141Arg	p.C141R	ENST00000269305	NM_001126112.2	141	Tgc/Cgc	5/11	0.834835156509204	2	FACETS	0.984	0.964	1	0.984	0.964	1	CLONAL	2	TRUE	0	0.834835156509204	2		763	845	SUCCESS
CBL	867	MSKCC	GRCh37	11	119146705	119146705	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0022714-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	195	388	0	ENST00000264033.4:c.870-2A>T		p.X290_splice	ENST00000264033	NM_005188.3	290			0.834835156509204	2	FACETS	1	0.968	1	0.526	0.493	0.56	CLONAL	1	TRUE	0	0.834835156509204	2		388	444	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633155	3633155	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022714-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	318	772	0	ENST00000294008.3:c.5096C>G	p.Ser1699Cys	p.S1699C	ENST00000294008	NM_032444.2	1699	tCt/tGt	14/15	1	2	FACETS	0.993	0.943	1	0.993	0.943	1	CLONAL	1	TRUE	1	0.834835156509204	2		772	767	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858473	27858473	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022714-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	161	384	0	ENST00000359303.2:c.98C>T	p.Thr33Ile	p.T33I	ENST00000359303	NM_003535.2	33	aCt/aTt	1/1	0.834835156509204	2	FACETS	1	0.94	1	0.506	0.47	0.543	CLONAL	1	TRUE	0	0.834835156509204	2		384	381	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0022730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	190	373	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.994	0.929	1	0.994	0.929	1	CLONAL	1	TRUE	1	0.838530484471614	2		373	456	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831357	72831358	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTG	rs34918837	NA	P-0022730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	97	335	2	ENST00000268489.5:c.5221_5223dup	p.Gln1741dup	p.Q1741dup	ENST00000268489	NM_006885.3	1741	-/CAA	9/10	1	2	FACETS	0.532	0.477	0.59	0.532	0.477	0.59	SUBCLONAL	1	TRUE	1	0.838530484471614	2		337	435	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434229	49434235	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTAAC	GGGTAAC	-	novel	NA	P-0022730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	601	1153	0	ENST00000301067.7:c.7318_7324del	p.Val2440LeufsTer43	p.V2440Lfs*43	ENST00000301067	NM_003482.3	2440	GTTACCCct/ct	31/54	1	2	FACETS	0.949	0.913	0.985	0.949	0.913	0.985	CLONAL	1	TRUE	1	0.838530484471614	2		1153	1511	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749050	43749050	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	508	914	0	ENST00000382044.4:c.1756C>T	p.Gln586Ter	p.Q586*	ENST00000382044	NM_001141980.1	586	Cag/Tag	12/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.838530484471614	2		914	1175	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816564	32816564	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	433	884	1	ENST00000354258.4:c.1611A>T	p.Lys537Asn	p.K537N	ENST00000354258	NM_000593.5	537	aaA/aaT	7/11	1	2	FACETS	0.934	0.892	0.976	0.934	0.892	0.976	CLONAL	1	TRUE	1	0.838530484471614	2		885	1106	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433060	49433060	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1251778848	NA	P-0022744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	269	1015	7	ENST00000301067.7:c.8311C>T	p.Arg2771Ter	p.R2771*	ENST00000301067	NM_003482.3	2771	Cga/Tga	33/54	0.162703685123863	5	FACETS	1	0.974	1	0.714	0.669	0.76	INDETERMINATE	2	TRUE	2	0.306393316841222	5		1022	1197	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576862	7576862	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	191	815	2	ENST00000269305.4:c.984del	p.Phe328LeufsTer17	p.F328Lfs*17	ENST00000269305	NM_001126112.2	328	ttC/tt	9/11	0.251937681418256	2	FACETS	0.816	0.756	0.878	0.816	0.756	0.878	CLONAL	2	TRUE	0	0.306393316841222	2		817	764	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427861	49427861	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	217	907	8	ENST00000301067.7:c.10729C>T	p.Gln3577Ter	p.Q3577*	ENST00000301067	NM_003482.3	3577	Caa/Taa	38/54	0.162703685123863	5	FACETS	0.954	0.886	1	0.636	0.591	0.683	INDETERMINATE	2	TRUE	2	0.306393316841222	5		915	1084	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222966	36222966	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1412	139	1175	1	ENST00000222270.7:c.5595C>G	p.Ile1865Met	p.I1865M	ENST00000222270	NM_014727.1	1865	atC/atG	27/37	0.306393316841222	5	FACETS	0.854	0.774	0.938			1	CLONAL	1	TRUE	NA	0.306393316841222	5		1176	1551	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223296	36223296	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1701	172	1209	3	ENST00000222270.7:c.5846C>G	p.Thr1949Arg	p.T1949R	ENST00000222270	NM_014727.1	1949	aCa/aGa	28/37	0.306393316841222	5	FACETS	0.875	0.801	0.952			1	CLONAL	1	TRUE	NA	0.306393316841222	5		1212	1873	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223489	36223489	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1409	101	1090	3	ENST00000222270.7:c.6042del	p.Ser2015AlafsTer25	p.S2015Afs*25	ENST00000222270	NM_014727.1	2013	atG/at	28/37	0.306393316841222	5	FACETS	0.637	0.567	0.712			1	SUBCLONAL	1	TRUE	NA	0.306393316841222	5		1093	1510	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324690	31324690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1399078190	NA	P-0022746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	44	255	12	ENST00000412585.2:c.118G>A	p.Gly40Ser	p.G40S	ENST00000412585	NM_005514.6	40	Ggc/Agc	2/8	0.665476718357518	1	FACETS	0.573	0.489	0.662	0.573	0.489	0.662	SUBCLONAL	1	TRUE	0	0.665476718357518	1		267	154	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324674	31324674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11546719	NA	P-0022746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	24	220	2	ENST00000412585.2:c.134G>A	p.Arg45His	p.R45H	ENST00000412585	NM_005514.6	45	cGc/cAc	2/8	0.665476718357518	1	FACETS	0.339	0.269	0.418	0.339	0.269	0.418	SUBCLONAL	1	TRUE	0	0.665476718357518	1		222	142	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122251	2122251	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	277	720	0	ENST00000219476.3:c.2107T>A	p.Trp703Arg	p.W703R	ENST00000219476	NM_000548.3	703	Tgg/Agg	20/42	0.665476718357518	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.665476718357518	1		720	536	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541699	187541699	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	107	546	0	ENST00000441802.2:c.6041A>C	p.Tyr2014Ser	p.Y2014S	ENST00000441802	NM_005245.3	2014	tAt/tCt	10/27	1	2	FACETS	0.954	0.866	1	0.954	0.866	1	CLONAL	1	TRUE	1	0.665476718357518	2		546	337	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031885	26031885	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	52	313	0	ENST00000244661.2:c.404G>T	p.Arg135Ile	p.R135I	ENST00000244661	NM_003537.3	135	aGa/aTa	1/1	0.665476718357518	1	FACETS	0.509	0.439	0.583	0.509	0.439	0.583	SUBCLONAL	1	TRUE	0	0.665476718357518	1		313	205	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323286	31323286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146555925	NA	P-0022746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	13	168	0	ENST00000412585.2:c.703G>A	p.Ala235Thr	p.A235T	ENST00000412585	NM_005514.6	235	Gcg/Acg	4/8	0.665476718357518	1	FACETS	0.146	0.104	0.197	0.146	0.104	0.197	SUBCLONAL	1	TRUE	0	0.665476718357518	1		168	178	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289323	33289323	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	105	467	0	ENST00000374542.5:c.229C>T	p.Gln77Ter	p.Q77*	ENST00000374542	NM_001141970.1	77	Cag/Tag	3/8	0.665476718357518	1	FACETS	0.932	0.853	1	0.932	0.853	1	CLONAL	1	TRUE	0	0.665476718357518	1		467	226	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0022781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	67	828	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	NA	2	FACETS	0.895	0.777	1			1	INDETERMINATE	1	TRUE	NA	0.202516826121628	2		828	739	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973156	25973156	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	23	548	0	ENST00000435504.4:c.1269del	p.Pro424GlnfsTer2	p.P424Qfs*2	ENST00000435504		423	gtT/gt	12/13	1	2	FACETS	0.559	0.435	0.703	0.559	0.435	0.703	SUBCLONAL	1	TRUE	1	0.202516826121628	2		548	406	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0022815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	94	417	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.169501682030909	2	FACETS	1	0.961	1	0.588	0.523	0.656	CLONAL	1	TRUE	0	0.246090611693276	2		417	650	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0022815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	49	353	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.96	0.814	1	0.96	0.814	1	CLONAL	1	TRUE	1	0.246090611693276	2		353	415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0022815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	96	660	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.167270539785811	2	FACETS	1	0.964	1	0.596	0.532	0.665	CLONAL	1	TRUE	0	0.246090611693276	2		661	654	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651643	48651643	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	63	867	1	ENST00000376670.3:c.809G>A	p.Arg270Gln	p.R270Q	ENST00000376670	NM_002049.3	270	cGg/cAg	5/6	NA	2	FACETS	0.874	0.756	1			1	INDETERMINATE	1	TRUE	NA	0.246090611693276	2		868	586	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858384	9858384	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200526162	NA	P-0022815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	26	573	0	ENST00000330684.3:c.3017C>T	p.Ala1006Val	p.A1006V	ENST00000330684	NM_001134407.1	1006	gCg/gTg	13/13	1	2	FACETS	0.563	0.446	0.698	0.563	0.446	0.698	SUBCLONAL	1	TRUE	1	0.246090611693276	2		573	375	SUCCESS
APC	324	MSKCC	GRCh37	5	112176030	112176030	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs886039682	NA	P-0022815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	23	458	0	ENST00000257430.4:c.4741del	p.Ser1581LeufsTer69	p.S1581Lfs*69	ENST00000257430	NM_000038.5	1580	aTt/at	16/16	1	2	FACETS	0.483	0.376	0.607	0.483	0.376	0.607	SUBCLONAL	1	TRUE	1	0.246090611693276	2		458	387	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	114	812	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	0.343983893413622	2		812	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577508	7577508	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060501201	NA	P-0022841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	83	835	0	ENST00000269305.4:c.773A>G	p.Glu258Gly	p.E258G	ENST00000269305	NM_001126112.2	258	gAa/gGa	7/11	0.343983893413622	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.343983893413622	1		835	355	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40854573	40854573	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866623552	NA	P-0022841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	78	716	1	ENST00000428826.2:c.2221G>A	p.Glu741Lys	p.E741K	ENST00000428826		741	Gag/Aag	21/21	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.343983893413622	2		717	447	SUCCESS
ATR	545	MSKCC	GRCh37	3	142254980	142254981	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	48	466	0	ENST00000350721.4:c.3788dup	p.Ile1264AspfsTer14	p.I1264Dfs*14	ENST00000350721	NM_001184.3	1263	aag/aaAg	20/47	0.343983893413622	3	FACETS	0.752	0.637	0.879	0.376	0.318	0.44	SUBCLONAL	1	TRUE	1	0.343983893413622	3		466	435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587781525	NA	P-0022871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	2025	872	2	ENST00000269305.4:c.842A>T	p.Asp281Val	p.D281V	ENST00000269305	NM_001126112.2	281	gAc/gTc	8/11	0.293801964619749	4	FACETS	1	0.998	1			1	INDETERMINATE	4	TRUE	NA	0.731400096950954	4		874	2312	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221765	55221765	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1328	1262	721	0	ENST00000275493.2:c.809A>G	p.Tyr270Cys	p.Y270C	ENST00000275493	NM_005228.3	270	tAc/tGc	7/28	0.483411099613385	6	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	3	0.731400096950954	6		721	2590	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878186	48878186	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0022871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	517	223	1	ENST00000267163.4:c.137+1G>A		p.X46_splice	ENST00000267163	NM_000321.2	46			0.731400096950954	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.731400096950954	2		224	621	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101633	27101633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1655	679	929	0	ENST00000324856.7:c.4915A>G	p.Ile1639Val	p.I1639V	ENST00000324856	NM_006015.4	1639	Atc/Gtc	18/20	0.731400096950954	3	FACETS	1	0.991	1	0.543	0.522	0.565	CLONAL	1	TRUE	1	0.731400096950954	3		929	2334	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176055021	176055021	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	95	664	0	ENST00000367669.3:c.1032G>C	p.Lys344Asn	p.K344N	ENST00000367669	NM_022457.5	344	aaG/aaC	10/20	0.731400096950954	3	FACETS	0.857	0.781	0.934	0.857	0.781	0.934	CLONAL	2	TRUE	1	0.731400096950954	3		664	207	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252059	226252059	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	381	268	0	ENST00000366813.1:c.7C>G	p.Arg3Gly	p.R3G	ENST00000366813		3	Cgt/Ggt	1/3	0.731400096950954	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.731400096950954	3		268	645	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111957665	111957665	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	687	567	0	ENST00000375549.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000375549	NM_003002.3	12	Ggt/Cgt	1/4	0.525911175262988	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.731400096950954	4		567	1605	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636323	21636323	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	69	610	0	ENST00000421138.2:c.687T>A	p.His229Gln	p.H229Q	ENST00000421138		229	caT/caA	7/16	0.301736878913662	5	FACETS	1	0.927	1	0.361	0.316	0.409	INDETERMINATE	1	TRUE	2	0.731400096950954	5		610	365	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562756	21562757	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0022871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	1348	672	0	ENST00000382592.4:c.1162_1163delinsTT	p.Ala388Leu	p.A388L	ENST00000382592	NM_014572.2	388	GCg/TTg	4/8	0.731400096950954	2	FACETS	1	0.999	1	1	0.999	1	CLONAL	2	TRUE	0	0.731400096950954	2		672	1560	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819303	3819303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2698	1170	744	0	ENST00000262367.5:c.2932G>A	p.Val978Met	p.V978M	ENST00000262367	NM_004380.2	978	Gtg/Atg	15/31	0.731400096950954	5	FACETS	0.867	0.842	0.893	0.578	0.561	0.595	CLONAL	2	TRUE	2	0.731400096950954	5		744	3868	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943775	9943775	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2264	436	584	2	ENST00000330684.3:c.1166T>C	p.Val389Ala	p.V389A	ENST00000330684	NM_001134407.1	389	gTg/gCg	5/13	0.731400096950954	5	FACETS	0.926	0.878	0.975	0.309	0.292	0.325	CLONAL	1	TRUE	2	0.731400096950954	5		586	2700	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641642	23641642	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	185	742	0	ENST00000261584.4:c.1833C>G	p.Asp611Glu	p.D611E	ENST00000261584	NM_024675.3	611	gaC/gaG	5/13	0.731400096950954	5	FACETS	0.778	0.721	0.837	0.519	0.48	0.558	SUBCLONAL	2	TRUE	2	0.731400096950954	5		742	682	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618788	37618788	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	298	572	0	ENST00000447079.4:c.464A>C	p.Asn155Thr	p.N155T	ENST00000447079	NM_015083.1	155	aAt/aCt	1/14	0.525911175262988	4	FACETS	1	0.965	1	0.519	0.488	0.551	CLONAL	1	TRUE	2	0.731400096950954	4		572	1359	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119971	70119971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	689	382	0	ENST00000245479.2:c.973G>A	p.Ala325Thr	p.A325T	ENST00000245479	NM_000346.3	325	Gcg/Acg	3/3	0.525911175262988	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	2	0.731400096950954	4		382	1479	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662783	227662783	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1317	521	802	2	ENST00000305123.5:c.672G>T	p.Glu224Asp	p.E224D	ENST00000305123	NM_005544.2	224	gaG/gaT	1/2	0.729199141546042	3	FACETS	1	0.984	1	0.529	0.506	0.553	CLONAL	1	TRUE	1	0.731400096950954	3		804	1838	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678720	52678720	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	497	688	3	ENST00000394830.3:c.899G>A	p.Arg300Lys	p.R300K	ENST00000394830	NM_018313.4	300	aGg/aAg	9/30	0.731400096950954	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.731400096950954	2		691	666	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582192	189582192	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2206	608	522	4	ENST00000264731.3:c.751C>A	p.Arg251Ser	p.R251S	ENST00000264731	NM_003722.4	251	Cgt/Agt	5/14	0.731400096950954	8	FACETS	0.944	0.904	0.984	0.315	0.301	0.328	CLONAL	2	TRUE	2	0.731400096950954	8		526	2814	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0022873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	156	268	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.335461979875582	3	FACETS	0.89	0.825	0.955	0.89	0.825	0.955	CLONAL	3	TRUE	0	0.35692138082248	3		268	386	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374293	138374293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	148	697	0	ENST00000289153.2:c.3151G>A	p.Glu1051Lys	p.E1051K	ENST00000289153	NM_006219.2	1051	Gaa/Aaa	22/22	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.35692138082248	2		697	823	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0022873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	160	863	7	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.35692138082248	2		870	853	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138382756	138382756	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0022873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	104	495	1	ENST00000289153.2:c.2788del	p.Thr930LeufsTer62	p.T930Lfs*62	ENST00000289153	NM_006219.2	930	Act/ct	19/22	1	2	FACETS	0.97	0.87	1	0.97	0.87	1	CLONAL	1	TRUE	1	0.35692138082248	2		496	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578408	7578434	+	inframe_deletion	In_Frame_Del	DEL	CCTCACAACCTCCGTCATGTGCTGTGA	CCTCACAACCTCCGTCATGTGCTGTGA	-	novel	NA	P-0022873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	120	669	0	ENST00000269305.4:c.496_522del	p.Ser166_Arg174del	p.S166_R174del	ENST00000269305	NM_001126112.2	166	TCACAGCACATGACGGAGGTTGTGAGG/-	5/11	1	2	FACETS	0.825	0.745	0.91	0.825	0.745	0.91	CLONAL	1	TRUE	1	0.35692138082248	2		669	815	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10284577	10284577	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1474694064	NA	P-0022873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	52	506	0	ENST00000340748.4:c.605A>G	p.Glu202Gly	p.E202G	ENST00000340748		202	gAg/gGg	7/40	0.193783847427787	2	FACETS	0.452	0.384	0.526	0.226	0.192	0.263	INDETERMINATE	1	TRUE	0	0.35692138082248	2		506	645	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31451736	31451736	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	65	359	0	ENST00000344624.3:c.2586G>T	p.Met862Ile	p.M862I	ENST00000344624		862	atG/atT	18/33	0.335461979875582	3	FACETS	0.891	0.774	1	0.297	0.258	0.339	CLONAL	1	TRUE	0	0.35692138082248	3		359	482	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992762	68992762	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	266	579	0	ENST00000288368.4:c.1727A>T	p.His576Leu	p.H576L	ENST00000288368	NM_024870.2	576	cAt/cTt	16/40	0.343943368842574	4	FACETS	0.955	0.896	1	0.637	0.597	0.677	CLONAL	2	TRUE	1	0.35692138082248	4		579	1059	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249857	110249857	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	107	517	0	ENST00000374672.4:c.818C>T	p.Thr273Met	p.T273M	ENST00000374672	NM_004235.4	273	aCg/aTg	3/5	1	2	FACETS	0.924	0.83	1	0.924	0.83	1	CLONAL	1	TRUE	1	0.35692138082248	2		517	649	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281623	15281623	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	170	696	0	ENST00000263388.2:c.4750C>G	p.Leu1584Val	p.L1584V	ENST00000263388	NM_000435.2	1584	Ctg/Gtg	26/33	0.193783847427787	2	FACETS	0.965	0.887	1	0.483	0.443	0.524	INDETERMINATE	1	TRUE	0	0.35692138082248	2		696	987	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213272	36213273	+	missense_variant	Missense_Mutation	DNP	AG	AG	GA	novel	NA	P-0022873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	134	673	0	ENST00000222270.7:c.2469_2470delinsGA	p.Gly824Arg	p.G824R	ENST00000222270	NM_014727.1	823	ggAGgg/ggGAgg	4/37	0.35692138082248	3	FACETS	0.912	0.828	1	0.456	0.414	0.501	CLONAL	1	TRUE	1	0.35692138082248	3		673	970	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156205	106156205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144422103	NA	P-0022873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	83	343	0	ENST00000380013.4:c.1106G>A	p.Arg369Gln	p.R369Q	ENST00000380013	NM_001127208.2	369	cGg/cAg	3/11	0.35692138082248	2	FACETS	1	0.892	1	0.503	0.446	0.565	CLONAL	1	TRUE	0	0.35692138082248	2		343	462	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411759	63411760	+	missense_variant	Missense_Mutation	DNP	CT	CT	AC	novel	NA	P-0022873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	35	422	1	ENST00000330258.3:c.1407_1408delinsGT	p.Gly470Cys	p.G470C	ENST00000330258	NM_152424.3	469	gaAGgt/gaGTgt	2/2	0.294092641881913	2	FACETS	0.291	0.238	0.351			1	SUBCLONAL	1	TRUE	NA	0.35692138082248	2		423	674	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912655	NA	P-0022889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	434	969	0	ENST00000269305.4:c.725G>C	p.Cys242Ser	p.C242S	ENST00000269305	NM_001126112.2	242	tGc/tCc	7/11	0.547996811895662	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.547996811895662	2		969	696	SUCCESS
APC	324	MSKCC	GRCh37	5	112175531	112175532	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1554085654	NA	P-0022889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	75	303	0	ENST00000257430.4:c.4241dup	p.Ser1415LysfsTer8	p.S1415Kfs*8	ENST00000257430	NM_000038.5	1414	gta/gTta	16/16	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.547996811895662	2		303	263	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497638	125497638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	108	704	0	ENST00000428830.2:c.202G>A	p.Val68Ile	p.V68I	ENST00000428830	NM_001114121.2	68	Gta/Ata	3/14	0.547996811895662	3	FACETS	0.887	0.799	0.98	0.444	0.399	0.49	CLONAL	1	TRUE	1	0.547996811895662	3		704	566	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253747	153253747	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0022889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	49	509	0	ENST00000281708.4:c.985+1G>T		p.X329_splice	ENST00000281708	NM_033632.3	329			0.547996811895662	3	FACETS	0.626	0.532	0.729	0.313	0.266	0.365	SUBCLONAL	1	TRUE	1	0.547996811895662	3		509	364	SUCCESS
APC	324	MSKCC	GRCh37	5	112111417	112111417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1242594500	NA	P-0022889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	39	406	0	ENST00000257430.4:c.514C>T	p.Leu172Phe	p.L172F	ENST00000257430	NM_000038.5	172	Ctt/Ttt	5/16	1	2	FACETS	0.572	0.477	0.676	0.572	0.477	0.676	SUBCLONAL	1	TRUE	1	0.547996811895662	2		406	249	SUCCESS
APC	324	MSKCC	GRCh37	5	112174188	112174189	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	76	561	0	ENST00000257430.4:c.2898dup	p.Val967CysfsTer3	p.V967Cfs*3	ENST00000257430	NM_000038.5	966	agt/agTt	16/16	1	2	FACETS	0.828	0.732	0.929	0.828	0.732	0.929	CLONAL	1	TRUE	1	0.547996811895662	2		561	335	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371888	116371888	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	108	648	3	ENST00000397752.3:c.1367G>A	p.Gly456Glu	p.G456E	ENST00000397752	NM_000245.2	456	gGg/gAg	3/21	0.526282411300845	4	FACETS	1	0.904	1	0.335	0.301	0.371	CLONAL	1	TRUE	1	0.547996811895662	4		651	607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0022893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	662	755	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.434527814435011	3	FACETS	0.886	0.858	0.913	0.886	0.858	0.913	CLONAL	3	TRUE	0	0.525740714528358	3		755	1197	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427453	427453	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780617531	NA	P-0022893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	474	988	1	ENST00000399788.2:c.2716G>A	p.Glu906Lys	p.E906K	ENST00000399788	NM_001042603.1	906	Gaa/Aaa	19/28	0.390867441255708	3	FACETS	1	0.989	1	0.724	0.695	0.754	CLONAL	2	TRUE	0	0.525740714528358	3		989	1048	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435228	49435228	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	262	988	0	ENST00000301067.7:c.6325C>T	p.Gln2109Ter	p.Q2109*	ENST00000301067	NM_003482.3	2109	Cag/Tag	31/54	0.525740714528358	3	FACETS	1	0.988	1	0.401	0.376	0.428	CLONAL	1	TRUE	0	0.525740714528358	3		988	1045	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821595	72821618	+	inframe_deletion	In_Frame_Del	DEL	CCGCCGCCGCCGCCGCCGCCGCCA	CCGCCGCCGCCGCCGCCGCCGCCA	-	rs765152994	NA	P-0022893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	47	179	0	ENST00000268489.5:c.10557_10580del	p.Gly3520_Gly3527del	p.G3520_G3527del	ENST00000268489	NM_006885.3	3519	ggTGGCGGCGGCGGCGGCGGCGGCGGc/ggc	10/10	0.389958366950496	2	FACETS	0.946	0.81	1	0.473	0.405	0.546	CLONAL	1	TRUE	0	0.525740714528358	2		179	189	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499486	89499486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373736475	NA	P-0022893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	126	691	1	ENST00000336596.2:c.2656G>A	p.Gly886Ser	p.G886S	ENST00000336596	NM_005233.5	886	Ggc/Agc	15/17	NA	2	FACETS	0.81	0.736	0.887			1	INDETERMINATE	1	TRUE	NA	0.525740714528358	2		692	592	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679061	117679061	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	333	887	0	ENST00000368508.3:c.3760G>T	p.Val1254Phe	p.V1254F	ENST00000368508	NM_002944.2	1254	Gtt/Ttt	24/43	0.119926376244891	5	FACETS	1	0.989	1	0.574	0.544	0.605	INDETERMINATE	2	TRUE	1	0.525740714528358	5		887	987	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467908	50467908	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	85	514	0	ENST00000331340.3:c.1143G>T	p.Leu381Phe	p.L381F	ENST00000331340	NM_006060.4	381	ttG/ttT	8/8	0.139328914710446	3	FACETS	0.828	0.735	0.928	0.276	0.245	0.31	INDETERMINATE	1	TRUE	0	0.525740714528358	3		514	493	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486128	8486128	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	210	731	1	ENST00000356435.5:c.2689G>C	p.Ala897Pro	p.A897P	ENST00000356435		897	Gcc/Ccc	17/35	0.436959798184828	4	FACETS	1	0.987	1	0.321	0.298	0.345	CLONAL	1	TRUE	0	0.525740714528358	4		732	950	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971073	21971101	+	frameshift_variant	Frame_Shift_Del	DEL	CACCAGCGTGTCCAGGAAGCCCTCCCGGG	CACCAGCGTGTCCAGGAAGCCCTCCCGGG	-	novel	NA	P-0022893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	394	806	0	ENST00000304494.5:c.257_285del	p.Ala86GlyfsTer24	p.A86Gfs*24	ENST00000304494	NM_000077.4	86	gCCCGGGAGGGCTTCCTGGACACGCTGGTG/g	2/3	0.436959798184828	4	FACETS	0.84	0.802	0.878	0.63	0.601	0.658	CLONAL	3	TRUE	0	0.525740714528358	4		806	908	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	303	312	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.639604973997489	2		312	918	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432651	49432651	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs727503983	NA	P-0022909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	478	1357	5	ENST00000301067.7:c.8488C>T	p.Arg2830Ter	p.R2830*	ENST00000301067	NM_003482.3	2830	Cga/Tga	34/54	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.639604973997489	2		1362	1413	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115852	8115853	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	358	1011	1	ENST00000346208.3:c.1199dup	p.Met400IlefsTer107	p.M400Ifs*107	ENST00000346208		400	atg/aTtg	6/6	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.639604973997489	2		1012	1066	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99440018	99440018	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	196	688	0	ENST00000268035.6:c.986C>G	p.Pro329Arg	p.P329R	ENST00000268035	NM_000875.3	329	cCg/cGg	4/21	0.639604973997489	3	FACETS	0.868	0.804	0.934	0.434	0.402	0.467	CLONAL	1	TRUE	1	0.639604973997489	3		688	932	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0022936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	558	919	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.654953452337549	3	FACETS	1	0.992	1	1	0.998	1	CLONAL	3	TRUE	1	0.654953452337549	3		919	726	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589623	67589634	+	inframe_deletion	In_Frame_Del	DEL	ATATGATAGATT	ATATGATAGATT	-	novel	NA	P-0022936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	133	460	0	ENST00000274335.5:c.1392_1403del	p.Asp464_Tyr467del	p.D464_Y467del	ENST00000274335		462	gaATATGATAGATTa/gaa	10/15	0.654953452337549	2	FACETS	0.839	0.781	0.897	0.839	0.781	0.897	CLONAL	2	TRUE	0	0.654953452337549	2		460	242	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932065	39932065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1009877078	NA	P-0022936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	364	438	1	ENST00000378444.4:c.2534C>T	p.Ala845Val	p.A845V	ENST00000378444	NM_001123385.1	845	gCc/gTc	4/15	0.628757399158434	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.654953452337549	2		439	462	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	200	502	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	0.434336907311175	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.433791852647827	4		502	538	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577085	+	missense_variant	Missense_Mutation	ONP	CCTC	CCTC	TCTT	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	346	932	1	ENST00000269305.4:c.853_856delinsAAGA	p.Glu285_Glu286delinsLysLys	p.E285_E286delinsKK	ENST00000269305	NM_001126112.2	285	GAGGaa/AAGAaa	8/11	0.433791852647827	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.433791852647827	2		933	769	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334803	81334803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	203	672	1	ENST00000222390.5:c.1913G>A	p.Gly638Glu	p.G638E	ENST00000222390	NM_000601.4	638	gGa/gAa	17/18	0.433791852647827	5	FACETS	0.844	0.783	0.907	0.563	0.522	0.605	CLONAL	2	TRUE	2	0.433791852647827	5		673	915	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939417	76939417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781932965	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	161	540	0	ENST00000373344.5:c.1331G>A	p.Arg444Gln	p.R444Q	ENST00000373344	NM_000489.3	444	cGa/cAa	9/35	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.433791852647827	1		540	402	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341914	8341914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	192	633	0	ENST00000356435.5:c.4726G>A	p.Glu1576Lys	p.E1576K	ENST00000356435		1576	Gaa/Aaa	29/35	0.433791852647827	2	FACETS	0.868	0.81	0.927	0.868	0.81	0.927	CLONAL	2	TRUE	0	0.433791852647827	2		633	510	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361213	66361213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1410955850	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	72	520	0	ENST00000273854.3:c.959G>A	p.Gly320Asp	p.G320D	ENST00000273854	NM_004439.5	320	gGc/gAc	4/18	1	2	FACETS	0.895	0.786	1	0.895	0.786	1	CLONAL	1	TRUE	1	0.433791852647827	2		520	371	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001124	150001124	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	96	714	0	ENST00000253339.5:c.2480G>C	p.Arg827Thr	p.R827T	ENST00000253339		827	aGa/aCa	4/7	0.423260836161794	2	FACETS	0.785	0.701	0.874	0.392	0.35	0.437	SUBCLONAL	1	TRUE	0	0.433791852647827	2		714	564	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468381	89468381	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754102338	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	124	319	0	ENST00000336596.2:c.1915C>T	p.Arg639Cys	p.R639C	ENST00000336596	NM_005233.5	639	Cgc/Tgc	11/17	0.425646409210912	3	FACETS	0.837	0.771	0.904	1	0.982	1	CLONAL	3	TRUE	1	0.433791852647827	3		319	277	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724696	112724696	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	132	817	0	ENST00000369452.4:c.580C>G	p.Leu194Val	p.L194V	ENST00000369452	NM_007373.3	194	Ctc/Gtc	2/9	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.433791852647827	2		817	592	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40476813	40476813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	253	844	1	ENST00000264657.5:c.1516G>A	p.Glu506Lys	p.E506K	ENST00000264657	NM_139276.2	506	Gag/Aag	17/24	0.433791852647827	2	FACETS	0.92	0.867	0.974	0.92	0.867	0.974	CLONAL	2	TRUE	0	0.433791852647827	2		845	634	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877822	151877822	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	150	494	0	ENST00000262189.6:c.7123C>T	p.Gln2375Ter	p.Q2375*	ENST00000262189	NM_170606.2	2375	Caa/Taa	36/59	0.433791852647827	5	FACETS	0.961	0.882	1	0.641	0.588	0.695	CLONAL	2	TRUE	2	0.433791852647827	5		494	594	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925427	114925427	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs760036701	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	156	906	0	ENST00000543371.1:c.1505C>G	p.Ser502Cys	p.S502C	ENST00000543371	NM_001198531.1	502	tCc/tGc	14/14	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.433791852647827	2		906	704	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575434	64575434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	177	993	1	ENST00000312049.6:c.583G>A	p.Glu195Lys	p.E195K	ENST00000312049	NM_130799.2	195	Gag/Aag	3/10	1	2	FACETS	0.943	0.87	1	0.943	0.87	1	CLONAL	1	TRUE	1	0.433791852647827	2		994	865	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575441	64575441	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs142862945	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	181	980	0	ENST00000312049.6:c.576G>C	p.Gln192His	p.Q192H	ENST00000312049	NM_130799.2	192	caG/caC	3/10	1	2	FACETS	0.964	0.89	1	0.964	0.89	1	CLONAL	1	TRUE	1	0.433791852647827	2		980	866	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204867	94204867	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	112	739	0	ENST00000323929.3:c.718C>A	p.Leu240Ile	p.L240I	ENST00000323929	NM_005591.3	240	Ctt/Att	8/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.433791852647827	2		739	471	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245613	46245613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	175	483	0	ENST00000334344.6:c.3707C>T	p.Pro1236Leu	p.P1236L	ENST00000334344	NM_152641.2	1236	cCa/cTa	15/21	0.434336907311175	3	FACETS	1	0.933	1	1	0.933	1	CLONAL	2	TRUE	1	0.433791852647827	3		483	489	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434390	49434408	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGGCCGAGGAGTCAATG	TGGGGCCGAGGAGTCAATG	-	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	308	989	0	ENST00000301067.7:c.7145_7163del	p.Pro2382HisfsTer38	p.P2382Hfs*38	ENST00000301067	NM_003482.3	2382	cCATTGACTCCTCGGCCCCAa/ca	31/54	0.434336907311175	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.433791852647827	3		989	838	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495346	56495346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	155	739	0	ENST00000267101.3:c.3536C>T	p.Ser1179Leu	p.S1179L	ENST00000267101	NM_001982.3	1179	tCa/tTa	28/28	0.434336907311175	3	FACETS	1	0.958	1	0.537	0.492	0.584	CLONAL	1	TRUE	1	0.433791852647827	3		739	810	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865696	57865696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	155	1079	0	ENST00000228682.2:c.3173G>A	p.Gly1058Glu	p.G1058E	ENST00000228682	NM_005269.2	1058	gGg/gAg	12/12	0.434336907311175	3	FACETS	0.92	0.842	1	0.46	0.421	0.501	CLONAL	1	TRUE	1	0.433791852647827	3		1079	945	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226340	133226340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113594027	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	343	1029	1	ENST00000320574.5:c.3718G>A	p.Glu1240Lys	p.E1240K	ENST00000320574	NM_006231.2	1240	Gag/Aag	30/49	0.434336907311175	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.433791852647827	3		1030	918	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134642	41134642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	173	570	0	ENST00000379561.5:c.986C>T	p.Ser329Leu	p.S329L	ENST00000379561	NM_002015.3	329	tCa/tTa	2/3	0.430386728238681	2	FACETS	0.906	0.843	0.971	0.906	0.843	0.971	CLONAL	2	TRUE	0	0.433791852647827	2		570	440	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039464	49039464	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	216	774	1	ENST00000267163.4:c.2449G>T	p.Glu817Ter	p.E817*	ENST00000267163	NM_000321.2	817	Gaa/Taa	23/27	0.430386728238681	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.433791852647827	2		775	486	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105641	30105641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	170	1127	0	ENST00000331968.5:c.1045G>A	p.Asp349Asn	p.D349N	ENST00000331968	NM_002742.2	349	Gat/Aat	7/18	0.434336907311175	3	FACETS	1	0.974	1	0.569	0.524	0.616	CLONAL	1	TRUE	1	0.433791852647827	3		1127	838	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239878	105239878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	116	804	0	ENST00000349310.3:c.742G>A	p.Asp248Asn	p.D248N	ENST00000349310	NM_001014432.1	248	Gac/Aac	10/15	0.434336907311175	3	FACETS	0.951	0.859	1	0.476	0.429	0.525	CLONAL	1	TRUE	1	0.433791852647827	3		804	684	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74003508	74003508	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	133	900	0	ENST00000318443.5:c.1579G>C	p.Glu527Gln	p.E527Q	ENST00000318443	NM_001024736.1	527	Gaa/Caa	9/10	1	2	FACETS	0.939	0.855	1	0.939	0.855	1	CLONAL	1	TRUE	1	0.433791852647827	2		900	653	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304238	91304238	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	112	693	0	ENST00000355112.3:c.1635A>T	p.Arg545Ser	p.R545S	ENST00000355112	NM_000057.2	545	agA/agT	7/22	1	2	FACETS	0.953	0.86	1	0.953	0.86	1	CLONAL	1	TRUE	1	0.433791852647827	2		693	542	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828039	3828039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	134	794	0	ENST00000262367.5:c.2086C>T	p.Pro696Ser	p.P696S	ENST00000262367	NM_004380.2	696	Cca/Tca	10/31	1	2	FACETS	0.995	0.907	1	0.995	0.907	1	CLONAL	1	TRUE	1	0.433791852647827	2		794	621	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435981	56435981	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	93	515	0	ENST00000407977.2:c.1156C>G	p.Arg386Gly	p.R386G	ENST00000407977		386	Cgg/Ggg	9/10	0.433791852647827	2	FACETS	1	0.913	1	0.512	0.458	0.569	CLONAL	1	TRUE	0	0.433791852647827	2		515	419	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211644	5211644	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	414	808	0	ENST00000357368.4:c.5191G>T	p.Glu1731Ter	p.E1731*	ENST00000357368	NM_002850.3	1731	Gag/Tag	33/38	0.434336907311175	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	0	0.433791852647827	3		808	752	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262085	10262085	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	341	848	0	ENST00000340748.4:c.2206G>C	p.Glu736Gln	p.E736Q	ENST00000340748		736	Gaa/Caa	23/40	0.434336907311175	3	FACETS	0.911	0.869	0.953	0.911	0.869	0.953	CLONAL	3	TRUE	0	0.433791852647827	3		848	700	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599907	10599907	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	424	998	0	ENST00000171111.5:c.1669del	p.Leu557TrpfsTer38	p.L557Wfs*38	ENST00000171111	NM_203500.1	557	Ctg/tg	5/6	0.434336907311175	3	FACETS	0.943	0.904	0.981	0.943	0.904	0.981	CLONAL	3	TRUE	0	0.433791852647827	3		998	841	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994397	25994397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757065305	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	270	505	1	ENST00000435504.4:c.416C>T	p.Ser139Phe	p.S139F	ENST00000435504		139	tCc/tTc	6/13	0.434336907311175	4	FACETS	1	0.963	1	1	0.963	1	CLONAL	3	TRUE	1	0.433791852647827	4		506	583	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663155	227663155	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	122	774	0	ENST00000305123.5:c.300G>C	p.Glu100Asp	p.E100D	ENST00000305123	NM_005544.2	100	gaG/gaC	1/2	0.434336907311175	3	FACETS	0.875	0.791	0.964	0.438	0.395	0.482	CLONAL	1	TRUE	1	0.433791852647827	3		774	782	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019162	31019162	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	236	846	0	ENST00000375687.4:c.757G>C	p.Glu253Gln	p.E253Q	ENST00000375687	NM_015338.5	253	Gag/Cag	9/13	0.434336907311175	3	FACETS	0.954	0.895	1	0.954	0.895	1	CLONAL	2	TRUE	1	0.433791852647827	3		846	694	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021263	31021263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	230	684	1	ENST00000375687.4:c.1262G>A	p.Arg421Lys	p.R421K	ENST00000375687	NM_015338.5	421	aGa/aAa	12/13	0.434336907311175	3	FACETS	0.967	0.907	1	0.967	0.907	1	CLONAL	2	TRUE	1	0.433791852647827	3		685	667	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948024	178948024	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	82	425	0	ENST00000263967.3:c.2796A>G	p.Ile932Met	p.I932M	ENST00000263967	NM_006218.2	932	atA/atG	20/21	0.434336907311175	4	FACETS	1	0.927	1	0.532	0.471	0.598	CLONAL	1	TRUE	2	0.433791852647827	4		425	509	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66468007	66468007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868264524	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	71	404	0	ENST00000273854.3:c.262G>A	p.Glu88Lys	p.E88K	ENST00000273854	NM_004439.5	88	Gaa/Aaa	3/18	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.433791852647827	2		404	303	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383771	84383771	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1345611154	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	148	998	0	ENST00000321945.7:c.1081C>T	p.Arg361Trp	p.R361W	ENST00000321945	NM_139076.2	361	Cgg/Tgg	9/9	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.433791852647827	2		998	673	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541990	187541990	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs767036657	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	103	643	0	ENST00000441802.2:c.5750C>G	p.Ser1917Cys	p.S1917C	ENST00000441802	NM_005245.3	1917	tCc/tGc	10/27	1	2	FACETS	0.954	0.857	1	0.954	0.857	1	CLONAL	1	TRUE	1	0.433791852647827	2		643	498	SUCCESS
APC	324	MSKCC	GRCh37	5	112111357	112111357	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	71	343	2	ENST00000257430.4:c.454G>T	p.Glu152Ter	p.E152*	ENST00000257430	NM_000038.5	152	Gaa/Taa	5/16	0.433791852647827	2	FACETS	1	0.977	1	0.747	0.663	0.835	CLONAL	1	TRUE	0	0.433791852647827	2		345	219	SUCCESS
APC	324	MSKCC	GRCh37	5	112111406	112111406	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	94	439	0	ENST00000257430.4:c.503G>C	p.Arg168Thr	p.R168T	ENST00000257430	NM_000038.5	168	aGa/aCa	5/16	0.433791852647827	2	FACETS	0.863	0.781	0.948	0.863	0.781	0.948	CLONAL	2	TRUE	0	0.433791852647827	2		439	251	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197454	26197454	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	84	429	0	ENST00000356476.2:c.25C>T	p.Arg9Cys	p.R9C	ENST00000356476		9	Cgc/Tgc	1/1	0.427238516533324	4	FACETS	1	0.956	1	0.582	0.516	0.652	CLONAL	1	TRUE	2	0.433791852647827	4		429	477	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670552	30670553	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	137	683	1	ENST00000376406.3:c.5967_5968delinsAA	p.Ala1990Thr	p.A1990T	ENST00000376406	NM_014641.2	1989	agGGct/agAAct	13/15	0.427238516533324	4	FACETS	1	0.98	1	0.63	0.574	0.689	CLONAL	1	TRUE	2	0.433791852647827	4		684	719	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971375	13971375	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	72	431	0	ENST00000405192.2:c.555-1G>A		p.X185_splice	ENST00000405192	NM_001163147.1	185			0.408407192667205	1	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	0	0.433791852647827	1		431	256	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151947033	151947033	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	251	638	0	ENST00000262189.6:c.1741C>T	p.Gln581Ter	p.Q581*	ENST00000262189	NM_170606.2	581	Caa/Taa	13/59	0.433791852647827	5	FACETS	0.989	0.931	1	0.989	0.931	1	CLONAL	3	TRUE	2	0.433791852647827	5		638	644	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771866	135771866	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	136	837	0	ENST00000298552.3:c.3251C>G	p.Ser1084Ter	p.S1084*	ENST00000298552	NM_001162426.1	1084	tCa/tGa	23/23	0.434336907311175	4	FACETS	0.916	0.831	1	0.458	0.415	0.502	CLONAL	1	TRUE	2	0.433791852647827	4		837	982	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936027	44936027	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	98	419	0	ENST00000377967.4:c.2788C>T	p.Pro930Ser	p.P930S	ENST00000377967	NM_021140.2	930	Ccc/Tcc	18/29	1	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.433791852647827	1		419	286	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0022989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	474	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.669023332873264	3	FACETS	0.931	0.894	0.969	0.621	0.596	0.646	CLONAL	2	TRUE	0	0.671761009217902	3		502	1012	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0022989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	228	673	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	0.671761009217902	2		673	661	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0022989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	338	298	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	0.669023332873264	3	FACETS	0.983	0.95	1	0.983	0.95	1	CLONAL	3	TRUE	0	0.671761009217902	3		298	456	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864471	57864471	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	292	754	1	ENST00000228682.2:c.1948G>T	p.Ala650Ser	p.A650S	ENST00000228682	NM_005269.2	650	Gct/Tct	12/12	0.669023332873264	3	FACETS	0.964	0.906	1	0.321	0.302	0.341	CLONAL	1	TRUE	0	0.671761009217902	3		755	1205	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959408	26959408	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	447	683	0	ENST00000381527.3:c.575C>T	p.Pro192Leu	p.P192L	ENST00000381527	NM_001260.1	192	cCa/cTa	6/13	0.671761009217902	3	FACETS	0.963	0.924	1	0.963	0.924	1	CLONAL	2	TRUE	1	0.671761009217902	3		683	923	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29701168	29701168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368149035	NA	P-0022989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	128	391	0	ENST00000356175.3:c.8452G>A	p.Val2818Met	p.V2818M	ENST00000356175	NM_000267.3	2818	Gtg/Atg	57/57	1	2	FACETS	0.864	0.789	0.942	0.864	0.789	0.942	CLONAL	1	TRUE	1	0.671761009217902	2		391	441	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526558	31526558	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760078843	NA	P-0022989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	263	860	0	ENST00000344624.3:c.482C>T	p.Pro161Leu	p.P161L	ENST00000344624		161	cCg/cTg	2/33	0.671761009217902	3	FACETS	0.793	0.742	0.846	0.397	0.371	0.423	SUBCLONAL	1	TRUE	1	0.671761009217902	3		860	1319	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206739	27206739	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147231791	NA	P-0022989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	245	728	0	ENST00000380036.4:c.2524C>T	p.Arg842Cys	p.R842C	ENST00000380036	NM_000459.3	842	Cgc/Tgc	15/23	1	2	FACETS	0.96	0.901	1	0.96	0.901	1	CLONAL	1	TRUE	1	0.671761009217902	2		728	760	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579480	7579480	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	226	813	0	ENST00000269305.4:c.207del	p.Ala70LeufsTer53	p.A70Lfs*53	ENST00000269305	NM_001126112.2	69	gcT/gc	4/11	0.244668123762677	3	FACETS	0.985	0.923	1	0.657	0.615	0.699	INDETERMINATE	2	TRUE	0	0.431612324299562	3		813	646	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432750	78432750	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	78	480	0	ENST00000370768.2:c.326A>C	p.Asp109Ala	p.D109A	ENST00000370768	NM_003902.3	109	gAt/gCt	5/20	0.259930800129415	5	FACETS	1	0.936	1	0.366	0.321	0.413	CLONAL	1	TRUE	2	0.431612324299562	5		480	543	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451462	70451462	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	101	677	0	ENST00000373644.4:c.6302T>G	p.Leu2101Trp	p.L2101W	ENST00000373644	NM_030625.2	2101	tTg/tGg	12/12	0.244668123762677	3	FACETS	1	0.911	1	0.339	0.304	0.377	INDETERMINATE	1	TRUE	0	0.431612324299562	3		677	559	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022453	12022453	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	145	999	0	ENST00000396373.4:c.559A>G	p.Thr187Ala	p.T187A	ENST00000396373	NM_001987.4	187	Acg/Gcg	5/8	0.324868767796522	1	FACETS	0.801	0.733	0.872	0.801	0.733	0.872	CLONAL	1	TRUE	0	0.431612324299562	1		999	658	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986535	36986535	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	128	872	0	ENST00000354822.5:c.1154C>G	p.Ser385Trp	p.S385W	ENST00000354822	NM_001079668.2	385	tCg/tGg	3/3	0.25843911464476	4	FACETS	1	0.96	1	0.553	0.501	0.607	INDETERMINATE	1	TRUE	2	0.431612324299562	4		872	768	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572477	41572477	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	105	874	1	ENST00000263253.7:c.5006C>T	p.Thr1669Ile	p.T1669I	ENST00000263253	NM_001429.3	1669	aCc/aTc	30/31	0.244668123762677	3	FACETS	0.752	0.673	0.835	0.251	0.224	0.279	INDETERMINATE	1	TRUE	0	0.431612324299562	3		875	787	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978476	70978476	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	49	376	0	ENST00000276594.2:c.1177T>A	p.Ser393Thr	p.S393T	ENST00000276594	NM_024504.3	393	Tct/Act	5/8	0.431612324299562	4	FACETS	0.768	0.652	0.896	0.384	0.326	0.448	SUBCLONAL	1	TRUE	2	0.431612324299562	4		376	423	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554290	29554291	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	234	756	0	ENST00000356175.3:c.2306_2307insT	p.Thr770HisfsTer6	p.T770Hfs*6	ENST00000356175	NM_000267.3	769	ccc/ccTc	19/57	0.574532836958747	1	FACETS	0.986	0.927	1	0.986	0.927	1	CLONAL	1	TRUE	0	0.574532836958747	1		756	589	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439947	56440258	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGCCAGGATGATCACAAAGATGGTGCCCACCACTGTCATTAGGATCCACACATCATAATCTGGCTGGGGAGTGAGCAGAGAGGGAAAGGGTCATACTTCCGGGATGAGCTGGGTCAATTCGGGAGGAAACACAGGAGCCCGGGAGGCACATAGCTAACTGGAGGTTCCCTTGAGTCCTCCATCTGAGGGGATGGAGAGGAACCTGCAAGTGGGATTAGGTGGGCCCTCCCTGCCCAAGGGCACTCAGAGAGGATCTTCCAGATGTCACTGGGAGAAGTACTATCTCAAAACCCATGTGCTTGGGGAAAAAAG	AGCCAGGATGATCACAAAGATGGTGCCCACCACTGTCATTAGGATCCACACATCATAATCTGGCTGGGGAGTGAGCAGAGAGGGAAAGGGTCATACTTCCGGGATGAGCTGGGTCAATTCGGGAGGAAACACAGGAGCCCGGGAGGCACATAGCTAACTGGAGGTTCCCTTGAGTCCTCCATCTGAGGGGATGGAGAGGAACCTGCAAGTGGGATTAGGTGGGCCCTCCCTGCCCAAGGGCACTCAGAGAGGATCTTCCAGATGTCACTGGGAGAAGTACTATCTCAAAACCCATGTGCTTGGGGAAAAAAG	-	novel	NA	P-0023116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	88	985	0	ENST00000407977.2:c.583-249_645del		p.X195_splice	ENST00000407977		195		6/10	0.574532836958747	1	FACETS	0.458	0.407	0.512	0.458	0.407	0.512	SUBCLONAL	1	TRUE	0	0.574532836958747	1		985	477	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591900	48591900	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	209	739	1	ENST00000342988.3:c.1063G>T	p.Asp355Tyr	p.D355Y	ENST00000342988	NM_005359.5	355	Gac/Tac	9/12	0.574532836958747	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.574532836958747	1		740	509	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950676	79950676	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	169	565	0	ENST00000265081.6:c.130G>A	p.Ala44Thr	p.A44T	ENST00000265081	NM_002439.4	44	Gcc/Acc	1/24	0.574532836958747	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.574532836958747	1		565	374	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528335	157528335	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	41	900	0	ENST00000346085.5:c.6060G>C	p.Leu2020Phe	p.L2020F	ENST00000346085	NM_020732.3	2020	ttG/ttC	20/20	1	2	FACETS	0.741	0.616	0.882	0.741	0.616	0.882	SUBCLONAL	1	TRUE	1	0.14	2		900	790	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602767	10602767	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	42	930	3	ENST00000171111.5:c.811G>T	p.Val271Leu	p.V271L	ENST00000171111	NM_203500.1	271	Gtg/Ttg	3/6	1	2	FACETS	0.786	0.655	0.933	0.786	0.655	0.933	CLONAL	1	TRUE	1	0.14	2		933	763	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728616	190728616	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	57	743	0	ENST00000441310.2:c.2004A>C	p.Leu668Phe	p.L668F	ENST00000441310	NM_000534.4	668	ttA/ttC	10/13	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.14	2		743	780	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279214	142279214	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	47	841	0	ENST00000350721.4:c.1432G>T	p.Glu478Ter	p.E478*	ENST00000350721	NM_001184.3	478	Gaa/Taa	6/47	1	2	FACETS	0.893	0.752	1	0.893	0.752	1	CLONAL	1	TRUE	1	0.14	2		841	752	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453118	140453118	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	43	687	0	ENST00000288602.6:c.1817G>T	p.Gly606Val	p.G606V	ENST00000288602	NM_004333.4	606	gGg/gTg	15/18	1	2	FACETS	0.986	0.824	1	0.986	0.824	1	CLONAL	1	TRUE	1	0.14	2		687	623	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020414	69020414	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	66	893	0	ENST00000288368.4:c.2786A>C	p.His929Pro	p.H929P	ENST00000288368	NM_024870.2	929	cAc/cCc	24/40	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.14	2		893	804	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0023215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	67	453	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.522325890515116	1	FACETS	0.962	0.852	1	0.962	0.852	1	CLONAL	1	TRUE	0	0.522325890515116	1		453	197	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944547	71944547	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	116	1019	1	ENST00000298229.2:c.2103del	p.His701GlnfsTer57	p.H701Qfs*57	ENST00000298229	NM_001567.3	701	caC/ca	18/28	0.522325890515116	1	FACETS	0.894	0.814	0.977	0.894	0.814	0.977	CLONAL	1	TRUE	0	0.522325890515116	1		1020	367	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25368383	25368383	+	intron_variant	Intron	SNP	T	T	G	novel	NA	P-0023215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	85	537	0	ENST00000311936.3:c.451-5538A>C		p.*151*	ENST00000311936	NM_004985.3	188/189			1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.522325890515116	2		537	316	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016600	12016600	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	98	623	0	ENST00000353533.5:c.736T>C	p.Cys246Arg	p.C246R	ENST00000353533	NM_003010.3	246	Tgt/Cgt	7/11	0.522325890515116	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.522325890515116	1		623	266	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210769	5210769	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770699501	NA	P-0023215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	157	1073	1	ENST00000357368.4:c.5282C>T	p.Thr1761Met	p.T1761M	ENST00000357368	NM_002850.3	1761	aCg/aTg	34/38	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.522325890515116	2		1074	481	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748899	41748899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750167315	NA	P-0023215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	65	877	1	ENST00000301178.4:c.1424G>A	p.Arg475Gln	p.R475Q	ENST00000301178	NM_021913.4	475	cGa/cAa	11/20	1	2	FACETS	0.525	0.456	0.599	0.525	0.456	0.599	SUBCLONAL	1	TRUE	1	0.522325890515116	2		878	474	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721038	61721038	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	82	633	0	ENST00000401558.2:c.1236G>A	p.Met412Ile	p.M412I	ENST00000401558	NM_003400.3	412	atG/atA	12/25	1	2	FACETS	0.918	0.816	1	0.918	0.816	1	CLONAL	1	TRUE	1	0.522325890515116	2		633	342	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934578	NA	P-0023220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	237	743	0	ENST00000269305.4:c.524G>T	p.Arg175Leu	p.R175L	ENST00000269305	NM_001126112.2	175	cGc/cTc	5/11	0.474110490831499	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.474110490831499	1		743	705	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714388	40714388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760880188	NA	P-0023220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	86	694	0	ENST00000373198.4:c.4009C>T	p.Arg1337Cys	p.R1337C	ENST00000373198	NM_133170.3	1337	Cgc/Tgc	29/32	0.452935751853464	1	FACETS	0.415	0.367	0.466	0.415	0.367	0.466	SUBCLONAL	1	TRUE	0	0.474110490831499	1		694	667	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028660	12028660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	70	586	0	ENST00000353533.5:c.863C>T	p.Ser288Phe	p.S288F	ENST00000353533	NM_003010.3	288	tCt/tTt	8/11	0.474110490831499	1	FACETS	0.424	0.37	0.482	0.424	0.37	0.482	SUBCLONAL	1	TRUE	0	0.474110490831499	1		586	531	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46738425	46738425	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	84	808	0	ENST00000371975.4:c.1326G>C	p.Met442Ile	p.M442I	ENST00000371975	NM_003579.3	442	atG/atC	12/18	0.221271704322955	1	FACETS	0.356	0.314	0.401	0.356	0.314	0.401	INDETERMINATE	1	TRUE	0	0.474110490831499	1		808	759	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420540	49420540	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	377	686	1	ENST00000301067.7:c.15209A>G	p.Tyr5070Cys	p.Y5070C	ENST00000301067	NM_003482.3	5070	tAt/tGt	48/54	0.465881059245153	2	FACETS	0.999	0.955	1	0.999	0.955	1	CLONAL	2	TRUE	0	0.474110490831499	2		687	796	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590663	95590663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	61	486	1	ENST00000393063.1:c.1246G>A	p.Glu416Lys	p.E416K	ENST00000393063	NM_030621.3	416	Gag/Aag	9/28	0.221271704322955	1	FACETS	0.421	0.364	0.483	0.421	0.364	0.483	INDETERMINATE	1	TRUE	0	0.474110490831499	1		487	466	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647436	3647436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377148341	NA	P-0023220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	127	827	1	ENST00000294008.3:c.1627G>A	p.Glu543Lys	p.E543K	ENST00000294008	NM_032444.2	543	Gag/Aag	7/15	1	2	FACETS	0.563	0.509	0.619	0.563	0.509	0.619	SUBCLONAL	1	TRUE	1	0.474110490831499	2		828	952	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740390	58740390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs900497056	NA	P-0023220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	97	716	0	ENST00000305921.3:c.1295C>T	p.Ser432Phe	p.S432F	ENST00000305921	NM_003620.3	432	tCt/tTt	6/6	0.24450679419558	2	FACETS	0.534	0.476	0.596	0.267	0.238	0.298	INDETERMINATE	1	TRUE	0	0.474110490831499	2		716	766	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221227	1221227	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131690948	NA	P-0023220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	246	847	0	ENST00000326873.7:c.752del	p.Gly251ValfsTer36	p.G251Vfs*36	ENST00000326873	NM_000455.4	250	acG/ac	6/10	0.474110490831499	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.474110490831499	1		847	753	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2185928	2185928	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	149	607	0	ENST00000398665.3:c.200G>A	p.Ser67Asn	p.S67N	ENST00000398665	NM_032482.2	67	aGc/aAc	3/28	0.474110490831499	1	FACETS	0.856	0.786	0.929	0.856	0.786	0.929	CLONAL	1	TRUE	0	0.474110490831499	1		607	560	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600365	10600365	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	255	1003	1	ENST00000171111.5:c.1490G>T	p.Trp497Leu	p.W497L	ENST00000171111	NM_203500.1	497	tGg/tTg	4/6	0.474110490831499	1	FACETS	0.991	0.931	1	0.991	0.931	1	CLONAL	1	TRUE	0	0.474110490831499	1		1004	828	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346615	225346615	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	132	580	0	ENST00000264414.4:c.2023C>T	p.Gln675Ter	p.Q675*	ENST00000264414	NM_003590.4	675	Caa/Taa	14/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.474110490831499	2		580	509	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103674	47103674	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	60	464	0	ENST00000409792.3:c.6272G>A	p.Gly2091Glu	p.G2091E	ENST00000409792	NM_014159.6	2091	gGa/gAa	14/21	0.221271704322955	1	FACETS	0.436	0.376	0.5	0.436	0.376	0.5	INDETERMINATE	1	TRUE	0	0.474110490831499	1		464	443	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71050182	71050182	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1477164140	NA	P-0023220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	69	452	1	ENST00000318789.4:c.1003G>A	p.Asp335Asn	p.D335N	ENST00000318789	NM_032682.5	335	Gat/Aat	13/21	0.221271704322955	1	FACETS	0.46	0.401	0.523	0.46	0.401	0.523	INDETERMINATE	1	TRUE	0	0.474110490831499	1		453	483	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403564	138403564	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	109	952	0	ENST00000289153.2:c.2218G>A	p.Glu740Lys	p.E740K	ENST00000289153	NM_006219.2	740	Gag/Aag	15/22	0.221271704322955	1	FACETS	0.452	0.406	0.501	0.452	0.406	0.501	INDETERMINATE	1	TRUE	0	0.474110490831499	1		952	776	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146723	185146723	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	109	802	0	ENST00000265026.3:c.354T>G	p.Ile118Met	p.I118M	ENST00000265026	NM_004721.4	118	atT/atG	2/14	0.221271704322955	1	FACETS	0.483	0.433	0.535	0.483	0.433	0.535	INDETERMINATE	1	TRUE	0	0.474110490831499	1		802	727	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442817	187442817	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	139	606	0	ENST00000232014.4:c.1889A>G	p.Tyr630Cys	p.Y630C	ENST00000232014	NM_001130845.1	630	tAt/tGt	9/10	0.221271704322955	1	FACETS	0.786	0.719	0.856	0.786	0.719	0.856	INDETERMINATE	1	TRUE	0	0.474110490831499	1		606	569	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405069	405069	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	180	670	0	ENST00000380956.4:c.1151C>G	p.Thr384Ser	p.T384S	ENST00000380956	NM_001195286.1	384	aCt/aGt	8/9	0.330827988788933	3	FACETS	1	0.964	1	0.537	0.496	0.581	CLONAL	1	TRUE	1	0.474110490831499	3		670	874	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490522	20490522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	164	690	2	ENST00000346618.3:c.1259G>A	p.Gly420Glu	p.G420E	ENST00000346618	NM_001949.4	420	gGa/gAa	7/7	0.330827988788933	3	FACETS	0.952	0.874	1	0.476	0.437	0.517	CLONAL	1	TRUE	1	0.474110490831499	3		692	899	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350154	81350154	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs745919057	NA	P-0023220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	120	469	0	ENST00000222390.5:c.1178G>T	p.Arg393Leu	p.R393L	ENST00000222390	NM_000601.4	393	cGt/cTt	10/18	0.474110490831499	1	FACETS	0.993	0.905	1	0.993	0.905	1	CLONAL	1	TRUE	0	0.474110490831499	1		469	389	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117875414	117875414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	55	628	0	ENST00000297338.2:c.229G>A	p.Asp77Asn	p.D77N	ENST00000297338	NM_006265.2	77	Gac/Aac	3/14	0.24450679419558	2	FACETS	0.371	0.316	0.43	0.185	0.158	0.215	INDETERMINATE	1	TRUE	0	0.474110490831499	2		628	626	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401856	139401856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	118	942	0	ENST00000277541.6:c.3544G>A	p.Glu1182Lys	p.E1182K	ENST00000277541	NM_017617.3	1182	Gag/Aag	22/34	0.474110490831499	1	FACETS	0.451	0.406	0.498	0.451	0.406	0.498	SUBCLONAL	1	TRUE	0	0.474110490831499	1		942	842	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019912	123019912	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	211	360	0	ENST00000355640.3:c.400G>A	p.Glu134Lys	p.E134K	ENST00000355640		134	Gag/Aag	2/7	1	1	FACETS	0.766	0.721	0.812	1	0.993	1	SUBCLONAL	2	TRUE	0	0.474110490831499	1		360	443	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0023221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	425	433	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.353661217557157	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	0	0.353661217557157	3		433	893	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0023221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	191	596	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.244017777645506	2	FACETS	1	0.985	1	0.623	0.576	0.671	CLONAL	1	TRUE	0	0.353661217557157	2		597	867	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484312	120484312	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	92	470	0	ENST00000256646.2:c.2818G>T	p.Gly940Cys	p.G940C	ENST00000256646	NM_024408.3	940	Ggt/Tgt	18/34	1	2	FACETS	0.999	0.89	1	0.999	0.89	1	CLONAL	1	TRUE	1	0.353661217557157	2		470	521	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170817115	170817115	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	37	465	0	ENST00000296930.5:c.119A>G	p.His40Arg	p.H40R	ENST00000296930	NM_002520.6	40	cAc/cGc	2/11	0.296326374611384	5	FACETS	0.475	0.39	0.57	0.158	0.13	0.19	SUBCLONAL	1	TRUE	2	0.353661217557157	5		465	674	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272959	11272959	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	27	356	0	ENST00000361445.4:c.3292G>T	p.Ala1098Ser	p.A1098S	ENST00000361445	NM_004958.3	1098	Gct/Tct	22/58	0.353661217557157	3	FACETS	0.379	0.301	0.469	0.19	0.15	0.235	SUBCLONAL	1	TRUE	1	0.353661217557157	3		356	474	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	574	812	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.466707856164564	5	FACETS	0.865	0.833	0.899			1	CLONAL	3	TRUE	NA	0.609170356476941	5		812	1389	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095625	178095625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765321668	NA	P-0023225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	234	505	0	ENST00000397062.3:c.1706G>A	p.Arg569His	p.R569H	ENST00000397062	NM_006164.4	569	cGt/cAt	5/5	0.178406878737361	4	FACETS	1	0.99	1	0.664	0.62	0.709	INDETERMINATE	1	TRUE	2	0.609170356476941	4		505	931	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916954	178916954	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs746860750	NA	P-0023225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	126	420	0	ENST00000263967.3:c.341A>G	p.Asn114Ser	p.N114S	ENST00000263967	NM_006218.2	114	aAt/aGt	2/21	0.491499248501893	4	FACETS	0.936	0.849	1	0.312	0.283	0.343	CLONAL	1	TRUE	1	0.609170356476941	4		420	711	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	212	812	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.262341773055831	1	FACETS	0.868	0.809	0.928	0.868	0.809	0.928	INDETERMINATE	1	TRUE	0	0.500351502659851	1		812	732	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577575	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782289	NA	P-0023266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	187	862	0	ENST00000269305.4:c.706T>C	p.Tyr236His	p.Y236H	ENST00000269305	NM_001126112.2	236	Tac/Cac	7/11	0.500351502659851	1	FACETS	0.999	0.929	1	0.999	0.929	1	CLONAL	1	TRUE	0	0.500351502659851	1		862	561	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948826	71948826	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	104	937	0	ENST00000298229.2:c.3538G>C	p.Asp1180His	p.D1180H	ENST00000298229	NM_001567.3	1180	Gac/Cac	26/28	1	2	FACETS	0.478	0.428	0.532	0.478	0.428	0.532	SUBCLONAL	1	TRUE	1	0.500351502659851	2		937	869	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579529	7579529	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658483	NA	P-0023267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	206	1040	0	ENST00000269305.4:c.158G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tGg/tAg	4/11	0.198534302475244	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.198534302475244	2		1040	956	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0023296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	503	794	1	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.804426553007803	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.804426553007803	1		795	739	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950905	32950915	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGCAGACCC	GCAGCAGACCC	-	novel	NA	P-0023296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	459	778	0	ENST00000380152.3:c.8731_8741del	p.Ala2911SerfsTer4	p.A2911Sfs*4	ENST00000380152		2911	GCAGCAGACCCa/a	21/27	0.804426553007803	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.804426553007803	1		778	681	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916752	48916753	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	447	690	0	ENST00000267163.4:c.287dup	p.Glu97GlyfsTer13	p.E97Gfs*13	ENST00000267163	NM_000321.2	94	-/A	3/27	0.804426553007803	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.804426553007803	1		690	628	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349157	89349157	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	835	1238	0	ENST00000301030.4:c.3793T>G	p.Ser1265Ala	p.S1265A	ENST00000301030	NM_001256183.1	1265	Tcc/Gcc	9/13	0.804426553007803	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.804426553007803	1		1238	1196	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183637	10183637	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	902	794	0	ENST00000256474.2:c.106G>T	p.Glu36Ter	p.E36*	ENST00000256474	NM_000551.3	36	Gag/Tag	1/3	NA	2	FACETS	0.993	0.975	1			1	INDETERMINATE	2	TRUE	NA	0.804426553007803	2		794	1129	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680772	30680772	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	752	636	0	ENST00000376406.3:c.947T>A	p.Val316Asp	p.V316D	ENST00000376406	NM_014641.2	316	gTc/gAc	5/15	0.804426553007803	3	FACETS	0.979	0.951	1	0.979	0.951	1	CLONAL	2	TRUE	1	0.804426553007803	3		636	1339	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137528107	137528107	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	265	377	0	ENST00000367739.4:c.193A>G	p.Asn65Asp	p.N65D	ENST00000367739	NM_000416.2	65	Aac/Gac	2/7	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.804426553007803	2		377	609	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035235	6035238	+	frameshift_variant	Frame_Shift_Del	DEL	TGCG	TGCG	-	novel	NA	P-0023296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	420	680	0	ENST00000265849.7:c.830_833del	p.Thr277MetfsTer29	p.T277Mfs*29	ENST00000265849	NM_000535.5	277	aCGCAt/at	8/15	0.804426553007803	3	FACETS	0.935	0.889	0.982	0.468	0.444	0.491	CLONAL	1	TRUE	1	0.804426553007803	3		680	1566	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282097	38282097	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	593	1103	1	ENST00000425967.3:c.959G>T	p.Trp320Leu	p.W320L	ENST00000425967	NM_001174067.1	320	tGg/tTg	8/19	1	2	FACETS	0.978	0.941	1	0.978	0.941	1	CLONAL	1	TRUE	1	0.804426553007803	2		1104	1507	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391092	139391092	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs988059037	NA	P-0023296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	571	939	2	ENST00000277541.6:c.7099G>A	p.Gly2367Ser	p.G2367S	ENST00000277541	NM_017617.3	2367	Ggc/Agc	34/34	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.804426553007803	2		941	1310	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0023310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	472	620	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.853120235141265	5	FACETS	1	0.977	1	1	0.977	1	CLONAL	4	TRUE	1	0.853120235141265	5		620	627	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204864	NA	P-0023310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	374	475	1	ENST00000371953.3:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000371953	NM_000314.4	171	Cag/Tag	6/9	0.853120235141265	3	FACETS	0.924	0.9	0.947	1	0.997	1	CLONAL	3	TRUE	1	0.853120235141265	3		476	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0023310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	499	439	0	ENST00000269305.4:c.375+1G>T		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.853120235141265	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.853120235141265	3		439	537	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27217701	27217701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772600804	NA	P-0023310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	300	542	0	ENST00000380036.4:c.3007C>T	p.Arg1003Cys	p.R1003C	ENST00000380036	NM_000459.3	1003	Cgc/Tgc	19/23	0.853120235141265	3	FACETS	1	0.991	1	0.405	0.383	0.428	CLONAL	1	TRUE	0	0.853120235141265	3		542	825	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215349	142215349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	45	392	0	ENST00000350721.4:c.5752G>A	p.Glu1918Lys	p.E1918K	ENST00000350721	NM_001184.3	1918	Gaa/Aaa	34/47	0.833982599663597	4	FACETS	0.283	0.237	0.333	0.141	0.118	0.167	SUBCLONAL	1	TRUE	2	0.853120235141265	4		392	692	SUCCESS
ATR	545	MSKCC	GRCh37	3	142216018	142216018	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	78	420	0	ENST00000350721.4:c.5575G>C	p.Glu1859Gln	p.E1859Q	ENST00000350721	NM_001184.3	1859	Gag/Cag	33/47	0.833982599663597	4	FACETS	0.483	0.424	0.546	0.241	0.212	0.273	SUBCLONAL	1	TRUE	2	0.853120235141265	4		420	702	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540016	187540016	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	48	469	0	ENST00000441802.2:c.7724G>A	p.Gly2575Glu	p.G2575E	ENST00000441802	NM_005245.3	2575	gGa/gAa	10/27	0.317953559480836	3	FACETS	0.361	0.305	0.422	0.18	0.152	0.211	INDETERMINATE	1	TRUE	1	0.853120235141265	3		469	445	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0023345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	331	255	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.491526632731213	3	FACETS	0.916	0.868	0.964	0.916	0.868	0.964	CLONAL	2	TRUE	1	0.491526632731213	3		255	916	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902696	1902696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	241	832	0	ENST00000382891.5:c.315G>A	p.Met105Ile	p.M105I	ENST00000382891	NM_133335.3	105	atG/atA	2/22	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.491526632731213	2		832	934	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0023345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	248	660	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.491526632731213	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.491526632731213	1		661	704	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0023345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	68	553	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	1	2	FACETS	0.849	0.744	0.96	0.849	0.744	0.96	CLONAL	1	TRUE	1	0.491526632731213	2		553	326	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061317	38061317	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	197	888	1	ENST00000250448.2:c.672C>A	p.Phe224Leu	p.F224L	ENST00000250448	NM_004496.3	224	ttC/ttA	2/2	0.491526632731213	3	FACETS	0.967	0.895	1	0.483	0.447	0.521	CLONAL	1	TRUE	1	0.491526632731213	3		889	1033	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131490	202131490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	46	543	1	ENST00000358485.4:c.458G>A	p.Gly153Asp	p.G153D	ENST00000358485	NM_001080125.1	153	gGc/gAc	2/9	1	2	FACETS	0.39	0.328	0.458	0.39	0.328	0.458	SUBCLONAL	1	TRUE	1	0.491526632731213	2		544	480	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589753	69589753	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	74	212	0	ENST00000168712.1:c.100G>A	p.Ala34Thr	p.A34T	ENST00000168712	NM_002007.2	34	Gca/Aca	1/3	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.491526632731213	2		212	247	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885919	111885934	+	frameshift_variant	Frame_Shift_Del	DEL	GTCTCCCAGGGCGATC	GTCTCCCAGGGCGATC	AT	novel	NA	P-0023345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	153	671	3	ENST00000341259.2:c.1541_1556delinsAT	p.Gly514AspfsTer27	p.G514Dfs*27	ENST00000341259	NM_005475.2	514	gGTCTCCCAGGGCGATCc/gATc	8/8	1	2	FACETS	0.863	0.792	0.938	0.863	0.792	0.938	CLONAL	1	TRUE	1	0.491526632731213	2		674	721	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107727	30107727	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867845509	NA	P-0023345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	237	700	0	ENST00000331968.5:c.953A>G	p.Asn318Ser	p.N318S	ENST00000331968	NM_002742.2	318	aAc/aGc	6/18	0.491526632731213	3	FACETS	0.928	0.872	0.986	0.928	0.872	0.986	CLONAL	2	TRUE	1	0.491526632731213	3		700	647	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560425	65560425	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0023345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	101	380	1	ENST00000358664.4:c.171+1G>A		p.X57_splice	ENST00000358664	NM_002382.4	57			0.491526632731213	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.491526632731213	1		381	280	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122332	17122332	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131690832	NA	P-0023345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	108	446	1	ENST00000285071.4:c.1062+1G>A		p.X354_splice	ENST00000285071	NM_144997.5	354			0.491526632731213	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.491526632731213	1		447	311	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955129	17955129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768370832	NA	P-0023345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	235	883	2	ENST00000458235.1:c.98G>A	p.Arg33Gln	p.R33Q	ENST00000458235	NM_000215.3	33	cGg/cAg	2/24	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.491526632731213	2		885	921	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18972915	18972915	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	236	844	1	ENST00000262803.5:c.2558del	p.Leu853Ter	p.L853*	ENST00000262803	NM_002911.3	852	Ttt/tt	18/24	1	2	FACETS	0.937	0.874	1	0.937	0.874	1	CLONAL	1	TRUE	1	0.491526632731213	2		845	1025	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022405	26022405	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0023345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	134	499	0	ENST00000435504.4:c.253-1G>T		p.X85_splice	ENST00000435504		85			0.491526632731213	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.491526632731213	1		499	382	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662116	227662116	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	180	643	0	ENST00000305123.5:c.1339C>T	p.Pro447Ser	p.P447S	ENST00000305123	NM_005544.2	447	Ccg/Tcg	1/2	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.491526632731213	2		643	678	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013713	170013713	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	123	668	0	ENST00000295797.4:c.1432C>T	p.Gln478Ter	p.Q478*	ENST00000295797	NM_002740.5	478	Caa/Taa	15/18	1	2	FACETS	0.941	0.855	1	0.941	0.855	1	CLONAL	1	TRUE	1	0.491526632731213	2		668	532	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777891	27777891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	79	461	1	ENST00000369163.2:c.40G>A	p.Gly14Ser	p.G14S	ENST00000369163	NM_003536.2	14	Ggc/Agc	1/1	1	2	FACETS	0.846	0.749	0.949	0.846	0.749	0.949	CLONAL	1	TRUE	1	0.491526632731213	2		462	380	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	425	812	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.548064104701902	3	FACETS	0.998	0.955	1	0.998	0.955	1	CLONAL	2	TRUE	1	0.569474385813278	3		812	961	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0023385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	218	863	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.569474385813278	1	FACETS	0.997	0.936	1	0.997	0.936	1	CLONAL	1	TRUE	0	0.569474385813278	1		863	549	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372025	55372025	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	163	821	4	ENST00000297316.4:c.715G>A	p.Ala239Thr	p.A239T	ENST00000297316	NM_022454.3	239	Gcc/Acc	2/2	0.389813332230256	5	FACETS	1	0.955	1			1	CLONAL	1	TRUE	NA	0.569474385813278	5		825	1000	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873885	151873885	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	208	627	1	ENST00000262189.6:c.8653G>T	p.Glu2885Ter	p.E2885*	ENST00000262189	NM_170606.2	2885	Gaa/Taa	38/59	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.569474385813278	2		628	636	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971023	21971024	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0023385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	152	724	0	ENST00000304494.5:c.334dup	p.Arg112ProfsTer8	p.R112Pfs*8	ENST00000304494	NM_000077.4	112	cgt/cCgt	2/3	0.569474385813278	1	FACETS	0.984	0.911	1	0.984	0.911	1	CLONAL	1	TRUE	0	0.569474385813278	1		724	388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576870	7576870	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs876659384	NA	P-0023529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	154	685	0	ENST00000269305.4:c.976G>T	p.Glu326Ter	p.E326*	ENST00000269305	NM_001126112.2	326	Gaa/Taa	9/11	0.368750435013592	3	FACETS	1	0.986	1	0.819	0.764	0.874	CLONAL	2	FALSE	0	0.523668973312592	3		685	302	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0023529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	180	567	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	NA	2	FACETS	0.902	0.858	0.944			1	INDETERMINATE	3	FALSE	NA	0.523668973312592	2		567	254	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630876	187630876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767601213	NA	P-0023529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	53	535	0	ENST00000441802.2:c.106C>T	p.His36Tyr	p.H36Y	ENST00000441802	NM_005245.3	36	Cac/Tac	2/27	1	2	FACETS	0.969	0.837	1	0.969	0.837	1	CLONAL	1	FALSE	1	0.523668973312592	2		535	209	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332645	153332645	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	25	600	0	ENST00000281708.4:c.311A>T	p.His104Leu	p.H104L	ENST00000281708	NM_033632.3	104	cAt/cTt	2/12	1	2	FACETS	0.612	0.487	0.752	0.612	0.487	0.752	SUBCLONAL	1	FALSE	1	0.523668973312592	2		600	156	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679018	117679018	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	36	553	0	ENST00000368508.3:c.3803T>C	p.Ile1268Thr	p.I1268T	ENST00000368508	NM_002944.2	1268	aTt/aCt	24/43	0.523668973312592	2	FACETS	0.755	0.642	0.873	0.755	0.642	0.873	SUBCLONAL	2	FALSE	0	0.523668973312592	2		553	91	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971098	+	stop_gained	Nonsense_Mutation	TNP	CCC	CCC	ACA	novel	NA	P-0023529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	245	536	0	ENST00000304494.5:c.260_262delinsTGT	p.Arg87_Glu88delinsLeuTer	p.R87_E88delinsL*	ENST00000304494	NM_000077.4	87	cGGGag/cTGTag	2/3	0.492654557982758	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	FALSE	0	0.523668973312592	3		536	382	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250354	110250354	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	TCT	novel	NA	P-0023529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	459	768	0	ENST00000374672.4:c.321delinsAGA	p.Phe107LeufsTer8	p.F107Lfs*8	ENST00000374672	NM_004235.4	107	ttT/ttAGA	3/5	0.523668973312592	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	FALSE	0	0.523668973312592	3		768	712	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054372	13054372	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	139	660	2	ENST00000316448.5:c.982G>T	p.Asp328Tyr	p.D328Y	ENST00000316448	NM_004343.3	328	Gac/Tac	8/9	1	2	FACETS	0.429	0.391	0.47	0.429	0.391	0.47	SUBCLONAL	1	TRUE	1	0.834319523734302	2		662	776	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791248	42791248	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	340	845	0	ENST00000575354.2:c.308C>T	p.Pro103Leu	p.P103L	ENST00000575354	NM_015125.3	103	cCt/cTt	3/20	1	2	FACETS	0.933	0.886	0.98	0.933	0.886	0.98	CLONAL	1	TRUE	1	0.834319523734302	2		845	874	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201059	NA	P-0023600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	98	715	0	ENST00000269305.4:c.856G>T	p.Glu286Ter	p.E286*	ENST00000269305	NM_001126112.2	286	Gaa/Taa	8/11	0.272720761843452	1	FACETS	0.857	0.765	0.955	0.857	0.765	0.955	CLONAL	1	TRUE	0	0.29	1		715	674	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213891	66213891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	81	561	0	ENST00000273854.3:c.2539C>A	p.Pro847Thr	p.P847T	ENST00000273854	NM_004439.5	847	Cca/Aca	15/18	1	2	FACETS	0.873	0.769	0.984	0.873	0.769	0.984	CLONAL	1	TRUE	1	0.29	2		561	640	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207176	1207176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	111	803	1	ENST00000326873.7:c.267del	p.Asn90ThrfsTer6	p.N90Tfs*6	ENST00000326873	NM_000455.4	88	atC/at	1/10	0.3	1	FACETS	0.935	0.841	1	0.935	0.841	1	CLONAL	1	TRUE	0	0.29	1		804	700	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841491	156841491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	99	762	1	ENST00000524377.1:c.794G>A	p.Cys265Tyr	p.C265Y	ENST00000524377	NM_002529.3	265	tGc/tAc	7/17	0.145391467295178	3	FACETS	1	0.941	1	0.36	0.321	0.401	INDETERMINATE	1	TRUE	0	0.29	3		763	724	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307583	118307583	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	92	651	0	ENST00000534358.1:c.356C>T	p.Ser119Leu	p.S119L	ENST00000534358	NM_005933.3	119	tCg/tTg	1/36	0.3	3	FACETS	0.912	0.809	1	0.456	0.404	0.511	CLONAL	1	TRUE	1	0.29	3		651	797	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555685	21555685	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	88	649	0	ENST00000382592.4:c.2585G>T	p.Arg862Leu	p.R862L	ENST00000382592	NM_014572.2	862	cGg/cTg	6/8	1	2	FACETS	0.857	0.759	0.962	0.857	0.759	0.962	CLONAL	1	TRUE	1	0.29	2		649	708	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40462560	40462560	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	96	590	0	ENST00000345506.4:c.2258A>G	p.Asp753Gly	p.D753G	ENST00000345506	NM_003152.3	753	gAc/gGc	20/20	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.29	2		590	662	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794791	42794791	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	82	541	0	ENST00000575354.2:c.1871G>T	p.Gly624Val	p.G624V	ENST00000575354	NM_015125.3	624	gGa/gTa	10/20	0.3	1	FACETS	0.987	0.873	1	0.987	0.873	1	CLONAL	1	TRUE	0	0.29	1		541	490	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119634948	119634948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334056340	NA	P-0023600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	61	393	0	ENST00000316626.5:c.551C>T	p.Pro184Leu	p.P184L	ENST00000316626		184	cCg/cTg	5/12	1	2	FACETS	0.891	0.77	1	0.891	0.77	1	CLONAL	1	TRUE	1	0.29	2		393	472	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526334	31526334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	117	915	0	ENST00000344624.3:c.706C>T	p.His236Tyr	p.H236Y	ENST00000344624		236	Cac/Tac	2/33	0.145391467295178	3	FACETS	0.79	0.711	0.875	0.263	0.237	0.292	INDETERMINATE	1	TRUE	0	0.29	3		915	1169	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983052	111983053	+	missense_variant	Missense_Mutation	DNP	AG	AG	GC	novel	NA	P-0023600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	68	699	1	ENST00000368678.4:c.1494_1495delinsGC	p.His498_Cys499delinsGlnArg	p.H498_C499delinsQR	ENST00000368678		498	caCTgc/caGCgc	13/13	1	2	FACETS	0.671	0.583	0.766	0.671	0.583	0.766	SUBCLONAL	1	TRUE	1	0.29	2		700	699	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426081	47426081	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	72	367	0	ENST00000377045.4:c.601G>C	p.Ala201Pro	p.A201P	ENST00000377045	NM_001654.4	201	Gcc/Ccc	7/16	1	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.29	1		367	366	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411813	63411813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	87	430	1	ENST00000330258.3:c.1354G>A	p.Glu452Lys	p.E452K	ENST00000330258	NM_152424.3	452	Gaa/Aaa	2/2	1	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.29	1		431	387	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0023635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	404	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.483073479625183	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.483073479625183	2		502	805	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591888	48591888	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	156	664	0	ENST00000342988.3:c.1051G>T	p.Asp351Tyr	p.D351Y	ENST00000342988	NM_005359.5	351	Gat/Tat	9/12	0.483073479625183	1	FACETS	0.928	0.855	1	0.928	0.855	1	CLONAL	1	TRUE	0	0.483073479625183	1		664	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0023635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	206	754	0	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	0.483073479625183	1	FACETS	0.955	0.89	1	0.955	0.89	1	CLONAL	1	TRUE	0	0.483073479625183	1		754	677	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970969	21970969	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	199	623	0	ENST00000304494.5:c.389T>A	p.Leu130Gln	p.L130Q	ENST00000304494	NM_000077.4	130	cTg/cAg	2/3	0.483073479625183	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.483073479625183	1		623	570	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160492	108160492	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	196	693	1	ENST00000278616.4:c.4400A>T	p.Asp1467Val	p.D1467V	ENST00000278616	NM_000051.3	1467	gAc/gTc	29/63	1	2	FACETS	0.999	0.927	1	0.999	0.927	1	CLONAL	1	TRUE	1	0.483073479625183	2		694	812	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502167	157502203	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAGAGAAAGCTCTGGGTCGACCGATACCTCACCTT	CAGAGAGAAAGCTCTGGGTCGACCGATACCTCACCTT	-	novel	NA	P-0023635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	139	517	0	ENST00000346085.5:c.3202_3238del	p.Glu1068TrpfsTer50	p.E1068Wfs*50	ENST00000346085	NM_020732.3	1067	cCAGAGAGAAAGCTCTGGGTCGACCGATACCTCACCTTc/cc	12/20	0.255439503822421	1	FACETS	0.844	0.773	0.918	0.844	0.773	0.918	INDETERMINATE	1	TRUE	0	0.483073479625183	1		517	517	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0023677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	810	567	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.754843948970917	3	FACETS	0.997	0.979	1	0.997	0.979	1	CLONAL	3	TRUE	0	0.754843948970917	3		567	988	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0023677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	254	641	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.754843948970917	2		642	617	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0023677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	435	1162	3	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.754843948970917	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.754843948970917	1		1165	678	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683523	182683523	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	264	724	3	ENST00000292782.4:c.22C>T	p.Gln8Ter	p.Q8*	ENST00000292782	NM_020640.2	8	Cag/Tag	2/7	1	2	FACETS	0.911	0.857	0.965	0.911	0.857	0.965	CLONAL	1	TRUE	1	0.754843948970917	2		727	768	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957550	1957550	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3738	287	1125	0	ENST00000382891.5:c.2649C>G	p.Ile883Met	p.I883M	ENST00000382891	NM_133335.3	883	atC/atG	14/22	0.754843948970917	9	FACETS	0.688	0.642	0.736			1	SUBCLONAL	1	TRUE	NA	0.754843948970917	9		1125	4025	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970984	21970985	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0023677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	332	989	3	ENST00000304494.5:c.373dup	p.Asp125GlyfsTer17	p.D125Gfs*17	ENST00000304494	NM_000077.4	125	gat/gGat	2/3	0.754843948970917	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.754843948970917	1		992	490	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	145	812	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.426034805077556	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.466026666750567	4		812	417	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0023914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	49	291	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.422850769530772	3	FACETS	1	0.874	1	0.512	0.438	0.593	CLONAL	1	TRUE	1	0.466026666750567	3		291	253	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0023914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	158	641	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.441986691512708	5	FACETS	0.98	0.909	1	0.98	0.909	1	CLONAL	3	TRUE	2	0.466026666750567	5		642	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577552	7577553	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATGCAGGA	novel	NA	P-0023914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	143	449	0	ENST00000269305.4:c.721_728dup	p.Met243IlefsTer7	p.M243Ifs*7	ENST00000269305	NM_001126112.2	243	atg/atTCCTGCATg	7/11	0.238200620668443	4	FACETS	1	0.97	1			1	INDETERMINATE	3	TRUE	NA	0.466026666750567	4		449	278	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69032509	69032509	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1248374672	NA	P-0023914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	122	495	0	ENST00000288368.4:c.3583C>T	p.Arg1195Ter	p.R1195*	ENST00000288368	NM_024870.2	1195	Cga/Tga	29/40	0.426034805077556	4	FACETS	0.897	0.817	0.979	0.897	0.817	0.979	CLONAL	2	TRUE	2	0.466026666750567	4		495	428	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0023946-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	276	255	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.901	0.848	0.954	0.901	0.848	0.954	CLONAL	1	TRUE	1	0.736666179487843	2		255	832	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518660	204518660	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023946-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	280	438	0	ENST00000367182.3:c.1323G>C	p.Glu441Asp	p.E441D	ENST00000367182	NM_001278516.1	441	gaG/gaC	11/11	0.733664043557802	4	FACETS	1	0.942	1	0.335	0.314	0.356	CLONAL	1	TRUE	1	0.736666179487843	4		438	1315	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943946	71943946	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023946-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	432	714	0	ENST00000298229.2:c.1879G>A	p.Glu627Lys	p.E627K	ENST00000298229	NM_001567.3	627	Gag/Aag	16/28	1	2	FACETS	0.893	0.851	0.935	0.893	0.851	0.935	CLONAL	1	TRUE	1	0.736666179487843	2		714	1314	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944526	71944526	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023946-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	426	656	2	ENST00000298229.2:c.2082G>C	p.Trp694Cys	p.W694C	ENST00000298229	NM_001567.3	694	tgG/tgC	18/28	1	2	FACETS	0.988	0.943	1	0.988	0.943	1	CLONAL	1	TRUE	1	0.736666179487843	2		658	1171	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119687	108119687	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023946-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	198	283	1	ENST00000278616.4:c.1093G>C	p.Glu365Gln	p.E365Q	ENST00000278616	NM_000051.3	365	Gag/Cag	9/63	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.736666179487843	2		284	471	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49419971	49419971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023946-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	227	500	3	ENST00000301067.7:c.15778C>T	p.Pro5260Ser	p.P5260S	ENST00000301067	NM_003482.3	5260	Ccc/Tcc	48/54	1	2	FACETS	0.795	0.743	0.849	0.795	0.743	0.849	SUBCLONAL	1	TRUE	1	0.736666179487843	2		503	775	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420020	49420020	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023946-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	326	614	2	ENST00000301067.7:c.15729C>G	p.Ile5243Met	p.I5243M	ENST00000301067	NM_003482.3	5243	atC/atG	48/54	1	2	FACETS	0.897	0.849	0.945	0.897	0.849	0.945	CLONAL	1	TRUE	1	0.736666179487843	2		616	987	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061839	38061839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752132466	NA	P-0023946-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1287	532	677	1	ENST00000250448.2:c.150G>A	p.Met50Ile	p.M50I	ENST00000250448	NM_004496.3	50	atG/atA	2/2	1	2	FACETS	0.794	0.76	0.829	0.794	0.76	0.829	SUBCLONAL	1	TRUE	1	0.736666179487843	2		678	1819	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354402	354402	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023946-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	466	657	0	ENST00000262320.3:c.1156C>T	p.Gln386Ter	p.Q386*	ENST00000262320	NM_003502.3	386	Cag/Tag	5/11	0.701439199350611	3	FACETS	1	0.99	1	0.561	0.535	0.588	CLONAL	1	TRUE	1	0.736666179487843	3		657	1542	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023946-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	393	641	1	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.736666179487843	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.736666179487843	1		642	622	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821842	72821842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023946-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	312	529	1	ENST00000268489.5:c.10333G>A	p.Glu3445Lys	p.E3445K	ENST00000268489	NM_006885.3	3445	Gaa/Aaa	10/10	0.736666179487843	1	FACETS	0.892	0.85	0.933	0.892	0.85	0.933	CLONAL	1	TRUE	0	0.736666179487843	1		530	600	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0023946-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	385	612	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	0.707300823048186	1	FACETS	0.942	0.903	0.98	0.942	0.903	0.98	CLONAL	1	TRUE	0	0.736666179487843	1		612	701	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961849	15961860	+	frameshift_variant	Frame_Shift_Del	DEL	AGGTGAGCTGGC	AGGTGAGCTGGC	TG	novel	NA	P-0023946-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	307	593	2	ENST00000268712.3:c.5935_5946delinsCA	p.Ala1979GlnfsTer67	p.A1979Qfs*67	ENST00000268712	NM_006311.3	1979	GCCAGCTCACCT/CA	38/46	0.707300823048186	1	FACETS	0.9	0.858	0.942	0.9	0.858	0.942	CLONAL	1	TRUE	0	0.736666179487843	1		595	585	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657486	29657486	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs786203896	NA	P-0023946-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	23	444	0	ENST00000356175.3:c.5719G>T	p.Glu1907Ter	p.E1907*	ENST00000356175	NM_000267.3	1907	Gaa/Taa	38/57	0.707300823048186	1	FACETS	0.094	0.073	0.119	0.094	0.073	0.119	SUBCLONAL	1	TRUE	0	0.736666179487843	1		444	420	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667571	29667571	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691073	NA	P-0023946-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	53	674	2	ENST00000356175.3:c.6907C>T	p.Gln2303Ter	p.Q2303*	ENST00000356175	NM_000267.3	2303	Cag/Tag	46/57	0.707300823048186	1	FACETS	0.117	0.099	0.137	0.117	0.099	0.137	SUBCLONAL	1	TRUE	0	0.736666179487843	1		676	775	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47679226	47679226	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0023946-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	182	439	0	ENST00000347630.2:c.980+1G>T		p.X327_splice	ENST00000347630	NM_001007230.1	327			0.707300823048186	1	FACETS	0.59	0.548	0.633	0.59	0.548	0.633	SUBCLONAL	1	TRUE	0	0.736666179487843	1		439	529	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368223	45368223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023946-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	286	477	1	ENST00000262160.6:c.1379C>T	p.Ser460Leu	p.S460L	ENST00000262160	NM_005901.5	460	tCa/tTa	11/11	0.736666179487843	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.736666179487843	1		478	481	SUCCESS
REL	5966	MSKCC	GRCh37	2	61121620	61121620	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023946-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	362	573	0	ENST00000295025.8:c.242G>C	p.Gly81Ala	p.G81A	ENST00000295025	NM_002908.2	81	gGa/gCa	3/11	NA	2	FACETS	0.975	0.927	1			1	INDETERMINATE	1	TRUE	NA	0.736666179487843	2		573	1008	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252947	36252948	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0023946-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	330	506	0	ENST00000300305.3:c.414_415insC	p.Asn139GlnfsTer5	p.N139Qfs*5	ENST00000300305		138	-/C	4/8	1	2	FACETS	0.943	0.894	0.993	0.943	0.894	0.993	CLONAL	1	TRUE	1	0.736666179487843	2		506	950	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252987	36252993	+	frameshift_variant	Frame_Shift_Del	DEL	TGGAACA	TGGAACA	-	novel	NA	P-0023946-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	288	526	1	ENST00000300305.3:c.369_375del	p.Asp123GlufsTer8	p.D123Efs*8	ENST00000300305		123	gaTGTTCCA/ga	4/8	1	2	FACETS	0.857	0.808	0.908	0.857	0.808	0.908	CLONAL	1	TRUE	1	0.736666179487843	2		527	912	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722761	49722761	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs62262682	NA	P-0023946-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	16	25	0	ENST00000449682.2:c.1478G>T	p.Arg493Leu	p.R493L	ENST00000449682	NM_020998.3	493	cGt/cTt	13/18	1	2	FACETS	0.658	0.5	0.836	0.658	0.5	0.836	SUBCLONAL	1	TRUE	1	0.736666179487843	2		25	66	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825328	134825328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023946-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	255	453	0	ENST00000398015.3:c.844G>A	p.Glu282Lys	p.E282K	ENST00000398015	NM_004441.4	282	Gaa/Aaa	4/16	NA	2	FACETS	1	0.956	1			1	INDETERMINATE	1	TRUE	NA	0.736666179487843	2		453	680	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294240	1294240	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023946-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	51	410	0	ENST00000310581.5:c.761G>T	p.Gly254Val	p.G254V	ENST00000310581	NM_198253.2	254	gGg/gTg	2/16	1	2	FACETS	0.194	0.164	0.227	0.194	0.164	0.227	SUBCLONAL	1	TRUE	1	0.736666179487843	2		410	713	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6048638	6048638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023946-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1310	81	559	0	ENST00000265849.7:c.13G>A	p.Glu5Lys	p.E5K	ENST00000265849	NM_000535.5	5	Gag/Aag	1/15	0.701439199350611	3	FACETS	0.216	0.189	0.245	0.108	0.094	0.123	SUBCLONAL	1	TRUE	1	0.736666179487843	3		559	1391	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873626	151873626	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023946-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	339	449	0	ENST00000262189.6:c.8912C>G	p.Ser2971Cys	p.S2971C	ENST00000262189	NM_170606.2	2971	tCt/tGt	38/59	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.736666179487843	2		449	916	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949162	151949162	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023946-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	286	597	0	ENST00000262189.6:c.1483G>C	p.Glu495Gln	p.E495Q	ENST00000262189	NM_170606.2	495	Gag/Cag	11/59	1	2	FACETS	0.86	0.81	0.91	0.86	0.81	0.91	CLONAL	1	TRUE	1	0.736666179487843	2		597	903	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046476	69046476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023946-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	194	643	1	ENST00000288368.4:c.3949C>T	p.Leu1317Phe	p.L1317F	ENST00000288368	NM_024870.2	1317	Ctt/Ttt	32/40	0.132618186241326	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.736666179487843	0		644	944	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537088	80537088	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023946-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	66	591	0	ENST00000286548.4:c.310G>T	p.Glu104Ter	p.E104*	ENST00000286548	NM_002072.3	104	Gag/Tag	2/7	0.523443249928013	1	FACETS	0.148	0.128	0.17	0.148	0.128	0.17	SUBCLONAL	1	TRUE	0	0.736666179487843	1		591	766	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128201179	128201179	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023946-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	77	585	1	ENST00000265960.3:c.1556C>G	p.Ser519Cys	p.S519C	ENST00000265960	NM_001006617.1	519	tCc/tGc	12/12	0.421874244690854	3	FACETS	0.237	0.207	0.27	0.119	0.103	0.135	INDETERMINATE	1	TRUE	1	0.736666179487843	3		586	1206	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223591	53223591	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023946-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	224	464	0	ENST00000375401.3:c.3768G>T	p.Glu1256Asp	p.E1256D	ENST00000375401	NM_004187.3	1256	gaG/gaT	23/26	0.132618186241326	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.736666179487843	0		464	712	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0024025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	327	675	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.447820398050228	3	FACETS	1	0.989	1	0.759	0.721	0.797	CLONAL	2	TRUE	0	0.447820398050228	3		675	785	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0024025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	66	373	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	0.41280679214066	3	FACETS	1	0.938	1	0.373	0.326	0.424	CLONAL	1	TRUE	0	0.447820398050228	3		373	322	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241722	55241722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1051753269	NA	P-0024025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	168	642	2	ENST00000275493.2:c.2170G>A	p.Gly724Ser	p.G724S	ENST00000275493	NM_005228.3	724	Ggc/Agc	18/28	0.447820398050228	4	FACETS	1	0.982	1	0.308	0.282	0.334	CLONAL	1	TRUE	0	0.447820398050228	4		644	883	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528711	8528711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774617096	NA	P-0024025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	64	482	1	ENST00000356435.5:c.421C>T	p.Arg141Cys	p.R141C	ENST00000356435		141	Cgc/Tgc	4/35	0.41280679214066	3	FACETS	0.767	0.666	0.876	0.256	0.222	0.292	SUBCLONAL	1	TRUE	0	0.447820398050228	3		483	456	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242486	+	inframe_deletion	In_Frame_Del	DEL	TTAAGAGAAGCAACATCT	TTAAGAGAAGCAACATCT	-	rs121913440	NA	P-0024025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	278	487	0	ENST00000275493.2:c.2239_2256del	p.Leu747_Ser752del	p.L747_S752del	ENST00000275493	NM_005228.3	747	TTAAGAGAAGCAACATCT/-	19/28	0.447820398050228	4	FACETS	1	0.988	1	0.842	0.8	0.883	CLONAL	3	TRUE	0	0.447820398050228	4		487	534	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242713	16242713	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	86	487	0	ENST00000375759.3:c.1334T>A	p.Leu445His	p.L445H	ENST00000375759	NM_015001.2	445	cTt/cAt	6/15	0.447820398050228	3	FACETS	0.72	0.637	0.808			1	SUBCLONAL	1	TRUE	NA	0.447820398050228	3		487	653	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743346	162743346	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	110	413	0	ENST00000367921.3:c.1816G>T	p.Ala606Ser	p.A606S	ENST00000367921	NM_006182.2	606	Gct/Tct	14/18	0.447820398050228	7	FACETS	1	0.98	1	0.28	0.252	0.311	CLONAL	1	TRUE	2	0.447820398050228	7		413	743	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28901634	28901634	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	73	459	0	ENST00000282397.4:c.2761C>G	p.Leu921Val	p.L921V	ENST00000282397	NM_002019.4	921	Ctc/Gtc	20/30	0.41280679214066	3	FACETS	0.811	0.711	0.918	0.27	0.237	0.306	CLONAL	1	TRUE	0	0.447820398050228	3		459	492	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170827161	170827161	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	106	191	1	ENST00000296930.5:c.529G>T	p.Asp177Tyr	p.D177Y	ENST00000296930	NM_002520.6	177	Gat/Tat	7/11	0.447820398050228	4	FACETS	1	0.911	1	0.502	0.455	0.551	CLONAL	2	TRUE	0	0.447820398050228	4		192	341	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209600	98209600	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	92	738	1	ENST00000331920.6:c.3938C>G	p.Pro1313Arg	p.P1313R	ENST00000331920	NM_000264.3	1313	cCa/cGa	23/24	0.353400404704569	2	FACETS	0.731	0.651	0.816	0.366	0.325	0.408	SUBCLONAL	1	TRUE	0	0.447820398050228	2		739	562	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140487374	140487374	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	105	434	0	ENST00000288602.6:c.1151G>C	p.Arg384Thr	p.R384T	ENST00000288602	NM_004333.4	384	aGa/aCa	9/18	0.41280679214066	3	FACETS	0.938	0.842	1	0.313	0.28	0.347	CLONAL	1	TRUE	0	0.447820398050228	3		434	612	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428229	49428229	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs902898516	NA	P-0024025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	105	787	1	ENST00000301067.7:c.10471C>T	p.Arg3491Cys	p.R3491C	ENST00000301067	NM_003482.3	3491	Cgt/Tgt	37/54	0.447820398050228	4	FACETS	0.728	0.651	0.809	0.182	0.162	0.203	SUBCLONAL	1	TRUE	0	0.447820398050228	4		788	933	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197161	26197161	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	87	648	1	ENST00000356476.2:c.318G>T	p.Glu106Asp	p.E106D	ENST00000356476		106	gaG/gaT	1/1	0.447820398050228	4	FACETS	0.679	0.601	0.764	0.17	0.15	0.191	SUBCLONAL	1	TRUE	0	0.447820398050228	4		649	828	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0024048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	170	660	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.28834065842021	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	0	0.321757926559643	2		661	522	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133238258	133238258	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	56	392	0	ENST00000320574.5:c.2719A>G	p.Asn907Asp	p.N907D	ENST00000320574	NM_006231.2	907	Aat/Gat	24/49	0.321757926559643	3	FACETS	0.978	0.841	1	0.489	0.42	0.564	CLONAL	1	TRUE	1	0.321757926559643	3		392	413	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26978183	26978183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	61	524	0	ENST00000381527.3:c.1360C>T	p.Pro454Ser	p.P454S	ENST00000381527	NM_001260.1	454	Cct/Tct	13/13	0.321757926559643	1	FACETS	0.994	0.864	1	0.994	0.864	1	CLONAL	1	TRUE	0	0.321757926559643	1		524	320	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003747	45003747	+	start_lost	Translation_Start_Site	SNP	G	G	C	novel	NA	P-0024048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	32	404	0	ENST00000558401.1:c.3G>C	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	atG/atC	1/4	0.28834065842021	2	FACETS	0.663	0.54	0.801	0.332	0.27	0.401	SUBCLONAL	1	TRUE	0	0.321757926559643	2		404	300	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348247	348247	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	173	728	0	ENST00000262320.3:c.1259A>C	p.Glu420Ala	p.E420A	ENST00000262320	NM_003502.3	420	gAg/gCg	6/11	0.298468933386434	3	FACETS	1	0.94	1	0.679	0.628	0.732	CLONAL	2	TRUE	0	0.321757926559643	3		728	613	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2220061	2220141	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTGGGGCACCTGCTGCCCCTGACACACAGGGTTTTCTCTCTGCAGAGGAGCACCCCCAGTCCCGTGCTGCAGCCCCGTGA	CCTGGGGCACCTGCTGCCCCTGACACACAGGGTTTTCTCTCTGCAGAGGAGCACCCCCAGTCCCGTGCTGCAGCCCCGTGA	-	novel	NA	P-0024048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	35	277	1	ENST00000398665.3:c.2692-44_2728del		p.X898_splice	ENST00000398665	NM_032482.2	898		23/28	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.321757926559643	2		278	190	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285858	39285858	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	55	564	0	ENST00000402219.2:c.301A>G	p.Asn101Asp	p.N101D	ENST00000402219	NM_005633.3	101	Aac/Gac	3/23	0.287950220432311	3	FACETS	0.794	0.68	0.918	0.397	0.34	0.459	CLONAL	1	TRUE	1	0.321757926559643	3		564	500	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397222	397222	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	45	290	0	ENST00000380956.4:c.607C>A	p.His203Asn	p.H203N	ENST00000380956	NM_001195286.1	203	Cac/Aac	5/9	0.223749776767878	4	FACETS	0.927	0.78	1	0.463	0.39	0.544	CLONAL	1	TRUE	2	0.321757926559643	4		290	399	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1555525585	NA	P-0024117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	243	621	0	ENST00000269305.4:c.673-2A>G		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.387243225711022	2	FACETS	0.996	0.937	1	0.996	0.937	1	CLONAL	2	TRUE	0	0.387243225711022	2		621	630	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061221	38061232	+	inframe_deletion	In_Frame_Del	DEL	GTTCTCGAACAT	GTTCTCGAACAT	-	novel	NA	P-0024117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	236	585	0	ENST00000250448.2:c.757_768del	p.Met253_Asn256del	p.M253_N256del	ENST00000250448	NM_004496.3	253	ATGTTCGAGAAC/-	2/2	0.353253725085147	4	FACETS	1	0.981	1			1	CLONAL	2	TRUE	NA	0.387243225711022	4		585	759	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841843	151841843	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	99	584	0	ENST00000262189.6:c.14298A>C	p.Lys4766Asn	p.K4766N	ENST00000262189	NM_170606.2	4766	aaA/aaC	55/59	0.336672270076863	4	FACETS	1	0.901	1	0.336	0.3	0.375	CLONAL	1	TRUE	1	0.387243225711022	4		584	703	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0024184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	62	552	1	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	1	2	FACETS	0.929	0.803	1	0.929	0.803	1	CLONAL	1	TRUE	1	0.238684051312402	2		553	559	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0024184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	96	652	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	0.982	0.874	1	0.982	0.874	1	CLONAL	1	TRUE	1	0.238684051312402	2		652	819	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030479	49030479	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	88	480	0	ENST00000267163.4:c.1959del	p.Val654CysfsTer4	p.V654Cfs*4	ENST00000267163	NM_000321.2	652	Aaa/aa	19/27	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.238684051312402	2		480	638	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272337	15272337	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs771517374	NA	P-0024184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	98	740	5	ENST00000263388.2:c.6102del	p.Gly2035ValfsTer50	p.G2035Vfs*50	ENST00000263388	NM_000435.2	2034	ccC/cc	33/33	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.238684051312402	2		745	755	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070577	67070578	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	61	398	1	ENST00000412916.2:c.207dup	p.Pro70SerfsTer13	p.P70Sfs*13	ENST00000412916		67	-/T	3/6	0.238684051312402	1	FACETS	0.864	0.746	0.992	0.864	0.746	0.992	CLONAL	1	TRUE	0	0.238684051312402	1		399	521	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630605	187630605	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	104	820	0	ENST00000441802.2:c.377del	p.Asn126IlefsTer20	p.N126Ifs*20	ENST00000441802	NM_005245.3	126	aAt/at	2/27	1	2	FACETS	0.871	0.779	0.97	0.871	0.779	0.97	CLONAL	1	TRUE	1	0.238684051312402	2		820	1000	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355347	15355347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767979123	NA	P-0024184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	76	468	0	ENST00000263377.2:c.2276C>T	p.Pro759Leu	p.P759L	ENST00000263377	NM_058243.2	759	cCg/cTg	13/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.238684051312402	2		468	470	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216419	7216419	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	93	701	0	ENST00000380728.2:c.829del	p.Gln277ArgfsTer68	p.Q277Rfs*68	ENST00000380728		277	Cag/ag	10/11	0.238684051312402	1	FACETS	0.935	0.831	1	0.935	0.831	1	CLONAL	1	TRUE	0	0.238684051312402	1		701	734	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900138	151900138	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	93	419	0	ENST00000262189.6:c.3973C>T	p.Gln1325Ter	p.Q1325*	ENST00000262189	NM_170606.2	1325	Cag/Tag	26/59	0.238684051312402	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.238684051312402	1		419	622	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210893	36210893	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	95	660	2	ENST00000222270.7:c.649del	p.Arg217GlyfsTer22	p.R217Gfs*22	ENST00000222270	NM_014727.1	215	aCc/ac	3/37	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.238684051312402	2		662	716	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258607	16258607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753287056	NA	P-0024184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	69	557	1	ENST00000375759.3:c.5872C>T	p.Arg1958Trp	p.R1958W	ENST00000375759	NM_015001.2	1958	Cgg/Tgg	11/15	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.238684051312402	2		558	540	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946376	71946376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	113	752	0	ENST00000298229.2:c.2540G>A	p.Ser847Asn	p.S847N	ENST00000298229	NM_001567.3	847	aGc/aAc	23/28	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.238684051312402	2		752	847	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172415	108172415	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1358200819	NA	P-0024184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	117	616	0	ENST00000278616.4:c.5218A>G	p.Ile1740Val	p.I1740V	ENST00000278616	NM_000051.3	1740	Att/Gtt	35/63	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.238684051312402	2		616	928	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344392	118344393	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0024184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	46	367	0	ENST00000534358.1:c.2522dup	p.Gly842ArgfsTer5	p.G842Rfs*5	ENST00000534358	NM_005933.3	840	acc/aCcc	3/36	1	2	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	TRUE	1	0.238684051312402	2		367	384	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492628	56492628	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	97	593	1	ENST00000267101.3:c.2782del	p.Glu928SerfsTer16	p.E928Sfs*16	ENST00000267101	NM_001982.3	926	aaG/aa	23/28	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.238684051312402	2		594	790	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2097749	2097749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567376138	NA	P-0024184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	67	570	1	ENST00000219066.1:c.100G>A	p.Glu34Lys	p.E34K	ENST00000219066	NM_002528.5	34	Gag/Aag	1/6	1	2	FACETS	0.84	0.73	0.96	0.84	0.73	0.96	CLONAL	1	TRUE	1	0.238684051312402	2		571	668	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351149	89351149	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs772229371	NA	P-0024184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	38	602	0	ENST00000301030.4:c.1801C>T	p.Arg601Ter	p.R601*	ENST00000301030	NM_001256183.1	601	Cga/Tga	9/13	0.238684051312402	1	FACETS	0.469	0.387	0.561	0.469	0.387	0.561	SUBCLONAL	1	TRUE	0	0.238684051312402	1		602	598	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246806	41246806	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs879255288	NA	P-0024184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	91	613	0	ENST00000357654.3:c.742A>G	p.Thr248Ala	p.T248A	ENST00000357654	NM_007294.3	248	Acc/Gcc	10/23	1	2	FACETS	0.876	0.777	0.983	0.876	0.777	0.983	CLONAL	1	TRUE	1	0.238684051312402	2		613	870	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526547	66526547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	74	478	1	ENST00000358598.2:c.1103G>A	p.Arg368Gln	p.R368Q	ENST00000358598	NM_212471.2	368	cGa/cAa	11/11	1	2	FACETS	0.92	0.805	1	0.92	0.805	1	CLONAL	1	TRUE	1	0.238684051312402	2		479	674	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56401610	56401610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866923273	NA	P-0024184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	109	562	0	ENST00000348428.3:c.1472C>T	p.Ala491Val	p.A491V	ENST00000348428	NM_006785.3	491	gCc/gTc	12/17	1	2	FACETS	0.999	0.896	1	0.999	0.896	1	CLONAL	1	TRUE	1	0.238684051312402	2		562	914	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748595	40748595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750813623	NA	P-0024184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	78	507	0	ENST00000373198.4:c.2921G>A	p.Arg974Gln	p.R974Q	ENST00000373198	NM_133170.3	974	cGg/cAg	21/32	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.238684051312402	2		507	619	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936113	49936113	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	82	557	0	ENST00000296474.3:c.1557G>T	p.Gln519His	p.Q519H	ENST00000296474	NM_002447.2	519	caG/caT	4/20	0.238684051312402	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.238684051312402	1		557	510	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613086	52613086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780124443	NA	P-0024184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	65	452	1	ENST00000394830.3:c.3442C>T	p.Arg1148Cys	p.R1148C	ENST00000394830	NM_018313.4	1148	Cgt/Tgt	22/30	0.238684051312402	1	FACETS	0.922	0.801	1	0.922	0.801	1	CLONAL	1	TRUE	0	0.238684051312402	1		453	520	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803443	1803443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766423062	NA	P-0024184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	104	819	0	ENST00000260795.2:c.712C>T	p.Arg238Trp	p.R238W	ENST00000260795		238	Cgg/Tgg	5/17	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.238684051312402	2		819	784	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133821	55133821	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	66	519	0	ENST00000257290.5:c.1034C>T	p.Pro345Leu	p.P345L	ENST00000257290	NM_006206.4	345	cCc/cTc	7/23	1	2	FACETS	0.882	0.766	1	0.882	0.766	1	CLONAL	1	TRUE	1	0.238684051312402	2		519	627	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638352	176638353	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs587784092	NA	P-0024184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	97	682	0	ENST00000439151.2:c.2954_2955del	p.Ser985CysfsTer25	p.S985Cfs*25	ENST00000439151	NM_022455.4	984	gaCTct/gact	5/23	1	2	FACETS	0.914	0.814	1	0.914	0.814	1	CLONAL	1	TRUE	1	0.238684051312402	2		682	889	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137320974	137320974	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	78	768	1	ENST00000481739.1:c.931G>A	p.Ala311Thr	p.A311T	ENST00000481739	NM_002957.4	311	Gcc/Acc	7/10	1	2	FACETS	0.785	0.688	0.888	0.785	0.688	0.888	SUBCLONAL	1	TRUE	1	0.238684051312402	2		769	833	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0024204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	186	675	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.295324141684165	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.29	1		675	917	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0024204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	126	478	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.29	2		478	828	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0024204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	55	329	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.93	0.798	1	0.93	0.798	1	CLONAL	1	TRUE	1	0.29	2		329	408	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265579	198265579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	157	792	2	ENST00000335508.6:c.2578G>A	p.Glu860Lys	p.E860K	ENST00000335508	NM_012433.2	860	Gaa/Aaa	18/25	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.29	2		794	908	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354055	15354055	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765227557	NA	P-0024204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	103	638	0	ENST00000263377.2:c.2825C>T	p.Thr942Met	p.T942M	ENST00000263377	NM_058243.2	942	aCg/aTg	14/20	1	2	FACETS	0.996	0.892	1	0.996	0.892	1	CLONAL	1	TRUE	1	0.29	2		638	713	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900395	32900395	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	51	579	0	ENST00000380152.3:c.492G>C	p.Leu164Phe	p.L164F	ENST00000380152		164	ttG/ttC	6/27	0.265827616502706	3	FACETS	0.513	0.435	0.599	0.257	0.217	0.3	SUBCLONAL	1	TRUE	1	0.29	3		579	785	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120135	70120136	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0024204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	48	258	0	ENST00000245479.2:c.1138dup	p.His380ProfsTer198	p.H380Pfs*198	ENST00000245479	NM_000346.3	379	-/C	3/3	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.29	2		258	244	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266074	41266112	+	inframe_deletion	In_Frame_Del	DEL	ACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATT	ACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATT	-	novel	NA	P-0024204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	94	390	0	ENST00000349496.5:c.71_109del	p.His24_Ser37delinsPro	p.H24_S37delinsP	ENST00000349496	NM_001904.3	24	cACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTct/cct	3/15	0.295324141684165	2	FACETS	0.752	0.673	0.835	0.752	0.673	0.835	SUBCLONAL	2	TRUE	0	0.29	2		390	431	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138277	2138277	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	TCT	novel	NA	P-0024204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	175	978	0	ENST00000219476.3:c.5210delinsTCT	p.Pro1737LeufsTer90	p.P1737Lfs*90	ENST00000219476	NM_000548.3	1737	cCc/cTCTc	41/42	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.29	2		978	1101	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	58	673	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.182286086427513	3	FACETS	0.974	0.836	1	0.487	0.418	0.563	CLONAL	1	FALSE	1	0.183866539884224	3		673	707	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717678	89717678	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554825200	NA	P-0024324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	48	681	3	ENST00000371953.3:c.703G>T	p.Glu235Ter	p.E235*	ENST00000371953	NM_000314.4	235	Gaa/Taa	7/9	0.183866539884224	3	FACETS	0.866	0.731	1	0.433	0.365	0.508	CLONAL	1	FALSE	1	0.183866539884224	3		684	658	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678584	88678584	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	18	438	0	ENST00000360948.2:c.952G>A	p.Glu318Lys	p.E318K	ENST00000360948	NM_001012338.2	318	Gag/Aag	9/19	0.183866539884224	3	FACETS	0.742	0.559	0.959	0.371	0.279	0.48	CLONAL	1	FALSE	1	0.183866539884224	3		438	288	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725540	162725540	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	49	578	0	ENST00000367921.3:c.652G>C	p.Asp218His	p.D218H	ENST00000367921	NM_006182.2	218	Gat/Cat	7/18	0.183866539884224	5	FACETS	1	0.909	1	0.277	0.234	0.324	CLONAL	1	FALSE	1	0.183866539884224	5		578	614	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984417	201984417	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	46	756	1	ENST00000359651.3:c.1082G>A	p.Trp361Ter	p.W361*	ENST00000359651		361	tGg/tAg	8/8	0.183866539884224	5	FACETS	0.754	0.633	0.888	0.188	0.158	0.222	SUBCLONAL	1	FALSE	1	0.183866539884224	5		757	847	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845537	63845537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	58	539	0	ENST00000279873.7:c.1276G>A	p.Glu426Lys	p.E426K	ENST00000279873	NM_032199.2	426	Gag/Aag	9/10	0.183866539884224	3	FACETS	1	0.88	1	0.514	0.441	0.594	CLONAL	1	FALSE	1	0.183866539884224	3		539	670	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41228538	41228538	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	79	880	0	ENST00000357654.3:c.4451C>G	p.Ser1484Cys	p.S1484C	ENST00000357654	NM_007294.3	1484	tCt/tGt	13/23	0.183866539884224	2	FACETS	0.941	0.826	1	0.471	0.413	0.533	CLONAL	1	FALSE	0	0.183866539884224	2		880	913	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42385046	42385046	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0024324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	33	771	0	ENST00000221972.3:c.680G>C	p.Ter227SerextTer36	p.*227Sext*36	ENST00000221972	NM_021601.3	227	tGa/tCa	5/5	0.183866539884224	3	FACETS	0.741	0.602	0.898	0.37	0.301	0.449	SUBCLONAL	1	FALSE	1	0.183866539884224	3		771	529	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038434	180038434	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	46	811	0	ENST00000261937.6:c.3583G>C	p.Glu1195Gln	p.E1195Q	ENST00000261937	NM_182925.4	1195	Gaa/Caa	27/30	0.183866539884224	3	FACETS	0.92	0.774	1	0.46	0.387	0.541	CLONAL	1	FALSE	1	0.183866539884224	3		811	594	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979485	2979485	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	61	903	0	ENST00000396946.4:c.762G>C	p.Lys254Asn	p.K254N	ENST00000396946	NM_032415.4	254	aaG/aaC	6/25	0.081526736171373	3	FACETS	0.762	0.655	0.879			1	INDETERMINATE	1	FALSE	NA	0.183866539884224	3		903	951	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975423	13975423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	44	613	1	ENST00000405192.2:c.464C>T	p.Ser155Leu	p.S155L	ENST00000405192	NM_001163147.1	155	tCa/tTa	7/12	0.183866539884224	7	FACETS	1	0.906	1	0.28	0.234	0.331	CLONAL	1	FALSE	3	0.183866539884224	7		614	623	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0024350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	114	319	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.577539989895326	3	FACETS	1	0.971	1	0.734	0.679	0.788	CLONAL	2	TRUE	0	0.671110005738423	3		319	206	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0024350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	334	1044	1	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.596707098543266	2	FACETS	0.791	0.756	0.827	0.791	0.756	0.827	SUBCLONAL	2	TRUE	0	0.671110005738423	2		1045	629	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268704	98268704	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774822170	NA	P-0024350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	57	540	1	ENST00000331920.6:c.379G>A	p.Glu127Lys	p.E127K	ENST00000331920	NM_000264.3	127	Gag/Aag	2/24	0.671110005738423	3	FACETS	0.528	0.454	0.608	0.176	0.151	0.203	SUBCLONAL	1	TRUE	0	0.671110005738423	3		541	430	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11276208	11276208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	121	706	1	ENST00000361445.4:c.3114G>A	p.Met1038Ile	p.M1038I	ENST00000361445	NM_004958.3	1038	atG/atA	20/58	0.596707098543266	2	FACETS	0.827	0.753	0.904	0.414	0.376	0.452	CLONAL	1	TRUE	0	0.671110005738423	2		707	436	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844702	156844702	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765681685	NA	P-0024350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1319	216	1333	0	ENST00000524377.1:c.1256C>T	p.Ser419Leu	p.S419L	ENST00000524377	NM_002529.3	419	tCg/tTg	11/17	0.671110005738423	6	FACETS	0.982	0.91	1	0.164	0.151	0.177	CLONAL	1	TRUE	0	0.671110005738423	6		1333	1535	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518485	204518485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	122	608	0	ENST00000367182.3:c.1148C>T	p.Ser383Phe	p.S383F	ENST00000367182	NM_001278516.1	383	tCc/tTc	11/11	0.671110005738423	6	FACETS	0.942	0.851	1	0.157	0.141	0.173	CLONAL	1	TRUE	0	0.671110005738423	6		608	904	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923143	48923144	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0024350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	304	761	0	ENST00000267163.4:c.591_592del	p.Leu199IlefsTer3	p.L199Ifs*3	ENST00000267163	NM_000321.2	197	acATtt/actt	6/27	0.577353303116263	3	FACETS	0.886	0.851	0.921	0.886	0.851	0.921	CLONAL	3	TRUE	0	0.671110005738423	3		761	455	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342651	70342651	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1373901177	NA	P-0024350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	203	1011	0	ENST00000374080.3:c.1412C>G	p.Ser471Cys	p.S471C	ENST00000374080		471	tCt/tGt	10/45	NA	2	FACETS	0.888	0.827	0.951			1	INDETERMINATE	1	TRUE	NA	0.671110005738423	2		1011	681	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	645	812	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.539517850804	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	TRUE	1	0.539517850804	4		812	1223	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0024358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	343	924	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.408230370767866	2	FACETS	0.772	0.735	0.811	0.772	0.735	0.811	SUBCLONAL	2	TRUE	0	0.539517850804	2		924	823	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923329	131923329	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs766315644	NA	P-0024358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	29	459	1	ENST00000265335.6:c.832C>T	p.Arg278Ter	p.R278*	ENST00000265335		278	Cga/Tga	6/25	1	2	FACETS	0.224	0.179	0.275	0.224	0.179	0.275	SUBCLONAL	1	TRUE	1	0.539517850804	2		460	480	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0024443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	138	242	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.626326914548223	3	FACETS	0.968	0.896	1	0.968	0.896	1	CLONAL	2	TRUE	1	0.626326914548223	3		242	299	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0024443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	158	567	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.185350363869106	5	FACETS	0.849	0.782	0.919			1	INDETERMINATE	2	TRUE	NA	0.626326914548223	5		567	576	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581243	48581243	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	277	571	0	ENST00000342988.3:c.547C>T	p.Gln183Ter	p.Q183*	ENST00000342988	NM_005359.5	183	Cag/Tag	5/12	0.626326914548223	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.626326914548223	2		571	427	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411576	63411576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	332	802	1	ENST00000330258.3:c.1591C>T	p.Arg531Ter	p.R531*	ENST00000330258	NM_152424.3	531	Cga/Tga	2/2	0.558710589248793	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	2	0.626326914548223	4		803	822	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579394	7579394	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	375	757	1	ENST00000269305.4:c.293del	p.Pro98LeufsTer25	p.P98Lfs*25	ENST00000269305	NM_001126112.2	98	cCt/ct	4/11	0.626326914548223	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.626326914548223	2		758	589	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36814310	36814310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773276972	NA	P-0024443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	140	499	0	ENST00000373129.3:c.730G>A	p.Val244Met	p.V244M	ENST00000373129	NM_032017.1	244	Gtg/Atg	8/12	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.626326914548223	2		499	409	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727105	40727105	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	260	576	0	ENST00000373198.4:c.3859A>G	p.Asn1287Asp	p.N1287D	ENST00000373198	NM_133170.3	1287	Aac/Gac	28/32	0.602726238801005	4	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	2	0.626326914548223	4		576	668	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015123	71015123	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	234	396	1	ENST00000318789.4:c.1807C>T	p.Arg603Trp	p.R603W	ENST00000318789	NM_032682.5	603	Cgg/Tgg	20/21	0.626326914548223	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.626326914548223	3		397	474	SUCCESS
APC	324	MSKCC	GRCh37	5	112173971	112173972	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0024443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	94	384	0	ENST00000257430.4:c.2682_2683del	p.Ala896HisfsTer15	p.A896Hfs*15	ENST00000257430	NM_000038.5	894	GTg/g	16/16	0.626326914548223	3	FACETS	0.915	0.818	1	0.457	0.409	0.508	CLONAL	1	TRUE	1	0.626326914548223	3		384	431	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069031	5069031	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	56	287	1	ENST00000381652.3:c.1336G>T	p.Val446Phe	p.V446F	ENST00000381652	NM_004972.3	446	Gtc/Ttc	11/25	0.626326914548223	3	FACETS	1	0.887	1	0.513	0.444	0.585	CLONAL	1	TRUE	1	0.626326914548223	3		288	229	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577520	64577520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760629445	NA	P-0024444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	391	459	0	ENST00000312049.6:c.62G>A	p.Arg21His	p.R21H	ENST00000312049	NM_130799.2	21	cGc/cAc	2/10	0.887145893048939	3	FACETS	0.985	0.947	1	0.985	0.947	1	CLONAL	2	TRUE	1	0.887145893048939	3		459	646	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579323	7579329	+	frameshift_variant	Frame_Shift_Del	DEL	CAGACTT	CAGACTT	-	novel	NA	P-0024444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	494	552	0	ENST00000269305.4:c.358_364del	p.Lys120Ter	p.K120*	ENST00000269305	NM_001126112.2	120	AAGTCTGtg/tg	4/11	0.882447288416837	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.887145893048939	2		552	557	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577375	64577375	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1057517902	NA	P-0024508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	310	726	0	ENST00000312049.6:c.207del	p.Asp70ThrfsTer49	p.D70Tfs*49	ENST00000312049	NM_130799.2	69	ccC/cc	2/10	0.310157448925175	1	FACETS	0.903	0.854	0.954	1	0.995	1	CLONAL	2	TRUE	0	0.310157448925175	1		726	935	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196789	108196789	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	165	308	0	ENST00000278616.4:c.6812C>G	p.Pro2271Arg	p.P2271R	ENST00000278616	NM_000051.3	2271	cCt/cGt	47/63	0.310157448925175	1	FACETS	1	0.964	1	1	0.993	1	CLONAL	2	TRUE	0	0.310157448925175	1		308	424	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562477	21562477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757658067	NA	P-0024575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	18	235	1	ENST00000382592.4:c.1442C>T	p.Ala481Val	p.A481V	ENST00000382592	NM_014572.2	481	gCg/gTg	4/8	0.391114766465021	5	FACETS	0.936	0.71	1	0.234	0.177	0.3	CLONAL	1	TRUE	1	0.391114766465021	5		236	156	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0024575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	140	737	0	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.391114766465021	2	FACETS	0.849	0.789	0.91	1	0.986	1	CLONAL	3	TRUE	0	0.391114766465021	2		737	281	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604778	48604778	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767383	NA	P-0024575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	44	683	0	ENST00000342988.3:c.1600C>T	p.Gln534Ter	p.Q534*	ENST00000342988	NM_005359.5	534	Cag/Tag	12/12	0.391114766465021	1	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	0	0.391114766465021	1		683	170	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281516	142281516	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	65	946	0	ENST00000350721.4:c.728A>T	p.Lys243Ile	p.K243I	ENST00000350721	NM_001184.3	243	aAa/aTa	4/47	0.340710816509323	3	FACETS	1	0.943	1	0.574	0.501	0.653	CLONAL	1	TRUE	1	0.391114766465021	3		946	346	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0024575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	65	608	1	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	0.391114766465021	2	FACETS	0.913	0.808	1	0.913	0.808	1	CLONAL	2	TRUE	0	0.391114766465021	2		609	182	SUCCESS
APC	324	MSKCC	GRCh37	5	112175516	112175516	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	69	597	0	ENST00000257430.4:c.4225C>G	p.Pro1409Ala	p.P1409A	ENST00000257430	NM_000038.5	1409	Cca/Gca	16/16	0.391114766465021	2	FACETS	0.964	0.857	1	0.964	0.857	1	CLONAL	2	TRUE	0	0.391114766465021	2		597	183	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940177	31940177	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0024575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	76	1130	1	ENST00000375333.2:c.319A>T	p.Lys107Ter	p.K107*	ENST00000375333	NM_032454.1	107	Aaa/Taa	2/8	1	2	FACETS	0.869	0.765	0.98	0.869	0.765	0.98	CLONAL	1	TRUE	1	0.391114766465021	2		1131	447	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183098	32183098	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	84	1231	0	ENST00000375023.3:c.1926C>G	p.Asp642Glu	p.D642E	ENST00000375023	NM_004557.3	642	gaC/gaG	12/30	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.391114766465021	2		1231	390	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850951	128850951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767352128	NA	P-0024575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	75	753	1	ENST00000249373.3:c.1798G>A	p.Val600Met	p.V600M	ENST00000249373	NM_005631.4	600	Gtg/Atg	10/12	0.28982693357933	5	FACETS	1	0.964	1	0.423	0.371	0.478	CLONAL	1	TRUE	2	0.391114766465021	5		754	480	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930087	68930087	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	25	671	0	ENST00000288368.4:c.148T>G	p.Leu50Val	p.L50V	ENST00000288368	NM_024870.2	50	Tta/Gta	2/40	0.391114766465021	4	FACETS	0.565	0.445	0.701	0.188	0.148	0.234	SUBCLONAL	1	TRUE	1	0.391114766465021	4		671	315	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	186	812	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.433606882744471	2		812	733	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579369	7579369	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555526581	NA	P-0024640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	160	835	0	ENST00000269305.4:c.318C>G	p.Ser106Arg	p.S106R	ENST00000269305	NM_001126112.2	106	agC/agG	4/11	0.433606882744471	1	FACETS	0.919	0.846	0.995	0.919	0.846	0.995	CLONAL	1	TRUE	0	0.433606882744471	1		835	629	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441771	49441771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	111	581	0	ENST00000301067.7:c.4213C>T	p.His1405Tyr	p.H1405Y	ENST00000301067	NM_003482.3	1405	Cac/Tac	14/54	1	2	FACETS	0.832	0.75	0.919	0.832	0.75	0.919	CLONAL	1	TRUE	1	0.433606882744471	2		581	615	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0024728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1320	24	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.052	0.04	0.066	0.052	0.04	0.066	SUBCLONAL	1	TRUE	1	0.689850511780494	2		502	1344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0024728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	273	812	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.689850511780494	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.689850511780494	1		812	474	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000100	30000100	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	339	665	0	ENST00000338641.4:c.113A>T	p.Glu38Val	p.E38V	ENST00000338641	NM_000268.3	38	gAg/gTg	1/16	0.689850511780494	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.689850511780494	1		665	644	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	66	812	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	0.14	2		812	812	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066776	77066776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750826465	NA	P-0024770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	32	492	0	ENST00000356341.3:c.709C>T	p.Arg237Trp	p.R237W	ENST00000356341	NM_002576.4	237	Cgg/Tgg	7/15	1	2	FACETS	0.799	0.647	0.972	0.799	0.647	0.972	CLONAL	1	TRUE	1	0.14	2		492	572	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163450	108163450	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	38	608	0	ENST00000278616.4:c.4544del	p.Asn1515ThrfsTer28	p.N1515Tfs*28	ENST00000278616	NM_000051.3	1514	gAa/ga	30/63	1	2	FACETS	0.715	0.589	0.857	0.715	0.589	0.857	SUBCLONAL	1	TRUE	1	0.14	2		608	759	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533833	63533833	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555577991	NA	P-0024770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	29	497	1	ENST00000307078.5:c.1321G>A	p.Asp441Asn	p.D441N	ENST00000307078	NM_004655.3	441	Gat/Aat	6/11	1	2	FACETS	1	0.814	1	1	0.814	1	CLONAL	1	TRUE	1	0.14	2		498	408	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967912	93967912	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	44	553	0	ENST00000369303.4:c.2015C>G	p.Thr672Arg	p.T672R	ENST00000369303	NM_004440.3	672	aCa/aGa	11/17	1	2	FACETS	0.774	0.647	0.916	0.774	0.647	0.916	CLONAL	1	TRUE	1	0.14	2		553	812	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119660	108119660	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	95	161	0	ENST00000278616.4:c.1066G>A	p.Val356Ile	p.V356I	ENST00000278616	NM_000051.3	356	Gtt/Att	9/63	0.391849659919742	3	FACETS	0.884	0.805	0.964	0.884	0.805	0.964	CLONAL	3	TRUE	0	0.406634089131107	3		161	212	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562490	95562490	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	122	500	0	ENST00000393063.1:c.4767G>T	p.Lys1589Asn	p.K1589N	ENST00000393063	NM_030621.3	1589	aaG/aaT	24/28	0.341721108362016	4	FACETS	1	0.977	1	0.629	0.569	0.692	CLONAL	1	TRUE	2	0.406634089131107	4		500	671	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129318	2129318	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	233	732	0	ENST00000219476.3:c.3173A>G	p.Lys1058Arg	p.K1058R	ENST00000219476	NM_000548.3	1058	aAa/aGa	28/42	0.333222549689521	2	FACETS	0.773	0.724	0.824	0.773	0.724	0.824	SUBCLONAL	2	TRUE	0	0.406634089131107	2		732	741	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934347	81934347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	198	591	1	ENST00000359376.3:c.1324C>T	p.Pro442Ser	p.P442S	ENST00000359376	NM_002661.3	442	Ccc/Tcc	14/33	0.333222549689521	2	FACETS	0.758	0.706	0.812	0.758	0.706	0.812	SUBCLONAL	2	TRUE	0	0.406634089131107	2		592	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863224683	NA	P-0024844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	280	755	0	ENST00000269305.4:c.388C>T	p.Leu130Phe	p.L130F	ENST00000269305	NM_001126112.2	130	Ctc/Ttc	5/11	0.333222549689521	2	FACETS	0.824	0.776	0.872	0.824	0.776	0.872	CLONAL	2	TRUE	0	0.406634089131107	2		755	836	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585361	29585361	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0024844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	242	571	0	ENST00000356175.3:c.4111-1G>T		p.X1371_splice	ENST00000356175	NM_000267.3	1371			0.333222549689521	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.406634089131107	2		571	589	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511574	66511574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	101	415	0	ENST00000358598.2:c.34G>A	p.Ala12Thr	p.A12T	ENST00000358598	NM_212471.2	12	Gca/Aca	2/11	0.406634089131107	12	FACETS	1	0.966	1			1	CLONAL	1	TRUE	NA	0.406634089131107	12		415	1247	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221966	1221966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	230	620	1	ENST00000326873.7:c.881C>T	p.Pro294Leu	p.P294L	ENST00000326873	NM_000455.4	294	cCg/cTg	7/10	0.311447858183956	2	FACETS	0.821	0.769	0.874	0.821	0.769	0.874	CLONAL	2	TRUE	0	0.406634089131107	2		621	689	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600393	10600393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	237	773	0	ENST00000171111.5:c.1462G>A	p.Glu488Lys	p.E488K	ENST00000171111	NM_203500.1	488	Gag/Aag	4/6	0.311447858183956	2	FACETS	1	0.99	1	0.656	0.613	0.7	CLONAL	1	TRUE	0	0.406634089131107	2		773	888	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170510	11170510	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	184	618	0	ENST00000358026.2:c.4813G>T	p.Glu1605Ter	p.E1605*	ENST00000358026	NM_001128849.1	1605	Gag/Tag	34/36	0.311447858183956	2	FACETS	1	0.988	1	0.666	0.617	0.717	CLONAL	1	TRUE	0	0.406634089131107	2		618	679	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966872	25966873	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0024844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	88	683	1	ENST00000435504.4:c.2333dup	p.Val779SerfsTer25	p.V779Sfs*25	ENST00000435504		778	cca/ccCa	13/13	0.32142006855265	3	FACETS	0.657	0.581	0.738	0.328	0.29	0.369	SUBCLONAL	1	TRUE	1	0.406634089131107	3		684	793	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664919	138664919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	45	147	0	ENST00000330315.3:c.646G>A	p.Ala216Thr	p.A216T	ENST00000330315	NM_023067.3	216	Gcc/Acc	1/1	0.341721108362016	4	FACETS	0.935	0.789	1	0.467	0.394	0.548	CLONAL	1	TRUE	2	0.406634089131107	4		147	333	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138644	55138644	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	187	597	0	ENST00000257290.5:c.1321C>A	p.Pro441Thr	p.P441T	ENST00000257290	NM_006206.4	441	Ccg/Acg	9/23	0.21511648932695	3	FACETS	0.775	0.718	0.834	0.775	0.718	0.834	INDETERMINATE	2	TRUE	1	0.406634089131107	3		597	714	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139810	55139810	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	92	521	0	ENST00000257290.5:c.1471G>T	p.Ala491Ser	p.A491S	ENST00000257290	NM_006206.4	491	Gcc/Tcc	10/23	0.21511648932695	3	FACETS	0.772	0.686	0.864	0.386	0.343	0.432	INDETERMINATE	1	TRUE	1	0.406634089131107	3		521	705	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630977	187630977	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	93	437	0	ENST00000441802.2:c.5G>T	p.Gly2Val	p.G2V	ENST00000441802	NM_005245.3	2	gGg/gTg	2/27	0.21511648932695	3	FACETS	1	0.911	1	0.512	0.457	0.572	INDETERMINATE	1	TRUE	1	0.406634089131107	3		437	537	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679595	86679595	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0024844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	351	580	0	ENST00000274376.6:c.2756C>G	p.Ser919Ter	p.S919*	ENST00000274376	NM_002890.2	919	tCa/tGa	21/25	0.349592717242347	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.406634089131107	3		580	655	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038374	180038384	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCGTCAGCC	CAGCGTCAGCC	-	novel	NA	P-0024844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	317	588	0	ENST00000261937.6:c.3633_3643del	p.Ala1212GlyfsTer30	p.A1212Gfs*30	ENST00000261937	NM_182925.4	1211	caGGCTGACGCTGag/caag	27/30	0.349592717242347	3	FACETS	1	0.992	1	0.823	0.781	0.865	CLONAL	2	TRUE	0	0.406634089131107	3		588	760	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818875	32818875	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	216	583	0	ENST00000354258.4:c.1076del	p.Leu359ArgfsTer5	p.L359Rfs*5	ENST00000354258	NM_000593.5	359	cTg/cg	4/11	0.178651053885107	4	FACETS	1	0.975	1			1	INDETERMINATE	2	TRUE	NA	0.406634089131107	4		583	688	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129295	152129295	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	229	505	1	ENST00000206249.3:c.248G>T	p.Gly83Val	p.G83V	ENST00000206249	NM_000125.3	83	gGg/gTg	1/8	0.333222549689521	2	FACETS	0.961	0.903	1	0.961	0.903	1	CLONAL	2	TRUE	0	0.406634089131107	2		506	586	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388023	81388023	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	116	628	1	ENST00000222390.5:c.352C>A	p.Leu118Ile	p.L118I	ENST00000222390	NM_000601.4	118	Ctc/Atc	3/18	0.409042356429907	3	FACETS	1	0.944	1	0.533	0.481	0.588	CLONAL	1	TRUE	1	0.406634089131107	3		629	644	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128322075	128322075	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	184	516	0	ENST00000265960.3:c.685G>T	p.Ala229Ser	p.A229S	ENST00000265960	NM_001006617.1	229	Gcc/Tcc	6/12	0.341721108362016	4	FACETS	0.873	0.808	0.94	0.873	0.808	0.94	CLONAL	2	TRUE	2	0.406634089131107	4		516	729	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781186	135781186	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	230	610	0	ENST00000298552.3:c.1779A>T	p.Arg593Ser	p.R593S	ENST00000298552	NM_001162426.1	593	agA/agT	15/23	0.341721108362016	4	FACETS	0.883	0.824	0.944	0.883	0.824	0.944	CLONAL	2	TRUE	2	0.406634089131107	4		610	901	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0024898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	143	755	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.363361334166328	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.363361334166328	1		755	541	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0024898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	42	790	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.288	0.239	0.342	0.288	0.239	0.342	SUBCLONAL	1	TRUE	1	0.363361334166328	2		790	803	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0024913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	226	463	1	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.912994678330627	2		464	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0024913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	1208	867	1	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	0.901209294491969	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.912994678330627	3		868	1285	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985571	60985571	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	89	352	0	ENST00000333681.4:c.329G>A	p.Arg110His	p.R110H	ENST00000333681		110	cGc/cAc	2/3	0.30729561561192	3	FACETS	1	0.976	1	0.687	0.612	0.768	CLONAL	1	TRUE	1	0.30729561561192	3		352	486	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227784	53227784	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	168	702	0	ENST00000375401.3:c.2404del	p.Arg802ValfsTer14	p.R802Vfs*14	ENST00000375401	NM_004187.3	802	Cgt/gt	17/26	0.236462215326249	2	FACETS	1	0.987	1	0.694	0.638	0.751	CLONAL	1	TRUE	0	0.30729561561192	2		702	788	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023501	27023501	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1251950978	NA	P-0025100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	81	529	0	ENST00000324856.7:c.607C>T	p.His203Tyr	p.H203Y	ENST00000324856	NM_006015.4	203	Cac/Tac	1/20	0.304373026771217	3	FACETS	0.67	0.589	0.757	0.335	0.294	0.379	SUBCLONAL	1	TRUE	1	0.30729561561192	3		529	908	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913878	32913878	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	75	485	0	ENST00000380152.3:c.5386G>C	p.Asp1796His	p.D1796H	ENST00000380152		1796	Gat/Cat	11/27	0.234618793984518	2	FACETS	0.756	0.668	0.849	0.756	0.668	0.849	SUBCLONAL	2	TRUE	0	0.30729561561192	2		485	323	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841123	15841124	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0025100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	114	481	0	ENST00000307771.7:c.1212dup	p.Lys405GlufsTer23	p.K405Efs*23	ENST00000307771	NM_005089.3	403	agg/aGgg	11/11	0.236462215326249	2	FACETS	1	0.977	1	0.641	0.579	0.706	CLONAL	1	TRUE	0	0.30729561561192	2		481	579	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869496	102869496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	104	413	0	ENST00000307046.8:c.145G>A	p.Gly49Arg	p.G49R	ENST00000307046	NM_001111285.1	49	Gga/Aga	2/4	0.304373026771217	3	FACETS	1	0.976	1	0.649	0.582	0.719	CLONAL	1	TRUE	1	0.30729561561192	3		413	602	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508977	106508977	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760224981	NA	P-0025100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	59	424	0	ENST00000359195.3:c.971C>T	p.Pro324Leu	p.P324L	ENST00000359195	NM_002649.2	324	cCa/cTa	2/11	0.30729561561192	7	FACETS	0.725	0.622	0.838	0.121	0.103	0.14	SUBCLONAL	1	TRUE	1	0.30729561561192	7		424	937	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0025135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	47	761	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.34	2		761	227	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846296	156846296	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	30	931	0	ENST00000524377.1:c.1737C>A	p.Cys579Ter	p.C579*	ENST00000524377	NM_002529.3	579	tgC/tgA	14/17	1	2	FACETS	0.754	0.611	0.915	0.754	0.611	0.915	CLONAL	1	TRUE	1	0.34	2		931	234	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219393	1219393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	20	754	0	ENST00000326873.7:c.445C>T	p.Pro149Ser	p.P149S	ENST00000326873	NM_000455.4	149	Cca/Tca	3/10	0.3	1	FACETS	0.491	0.377	0.623	0.491	0.377	0.623	SUBCLONAL	1	TRUE	0	0.34	1		754	199	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957431	1957431	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	11	424	0	ENST00000382891.5:c.2530C>A	p.Leu844Met	p.L844M	ENST00000382891	NM_133335.3	844	Ctg/Atg	14/22	0.28088498844702	0	FACETS	0.27	0.187	0.373			1	SUBCLONAL	1	TRUE	0	0.34	0		424	158	SUCCESS
EED	8726	MSKCC	GRCh37	11	85977249	85977256	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AAACTAAC	AAACTAAC	-	novel	NA	P-0025135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	16	348	0	ENST00000263360.6:c.852_859del	p.Thr285AlafsTer11	p.T285Afs*11	ENST00000263360	NM_003797.3	284	aAAACTAAC/a	8/12	0.22979065254142	3	FACETS	0.406	0.3	0.533	0.203	0.15	0.267	SUBCLONAL	1	TRUE	1	0.34	3		348	271	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390649	139390650	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs763016003	NA	P-0025186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	81	529	0	ENST00000277541.6:c.7541_7542del	p.Pro2514ArgfsTer4	p.P2514Rfs*4	ENST00000277541	NM_017617.3	2514	cCT/c	34/34	1	2	FACETS	0.905	0.797	1	0.905	0.797	1	CLONAL	1	TRUE	1	0.24	2		529	746	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261740	16261740	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs547140333	NA	P-0025186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	35	365	0	ENST00000375759.3:c.9005C>T	p.Pro3002Leu	p.P3002L	ENST00000375759	NM_015001.2	3002	cCc/cTc	11/15	0.10347466130661	0	FACETS	0.392	0.321	0.473			1	INDETERMINATE	1	TRUE	0	0.24	0		365	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574013	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1567542146	NA	P-0025186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	77	457	0	ENST00000269305.4:c.1014_1015insT	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	338	-/T	10/11	1	2	FACETS	0.881	0.773	0.998	0.881	0.773	0.998	CLONAL	1	TRUE	1	0.24	2		457	728	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157470038	157470048	+	stop_gained	Nonsense_Mutation	ONP	GGCAGCCGCAG	GGCAGCCGCAG	ACCGTAAGGCA	novel	NA	P-0025186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	32	284	1	ENST00000346085.5:c.2832_2842delinsACCGTAAGGCA	p.Ala945_Ala948delinsProTer	p.A945_A948delinsP*	ENST00000346085	NM_020732.3	944	gaGGCAGCCGCAGca/gaACCGTAAGGCAca	9/20	1	2	FACETS	0.57	0.462	0.692	0.57	0.462	0.692	SUBCLONAL	1	TRUE	1	0.24	2		285	468	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950073	44950073	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	60	391	1	ENST00000377967.4:c.3842T>A	p.Ile1281Asn	p.I1281N	ENST00000377967	NM_021140.2	1281	aTc/aAc	26/29	1	2	FACETS	0.681	0.586	0.785	0.681	0.586	0.785	SUBCLONAL	1	TRUE	1	0.24	2		392	734	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061215	38061235	+	inframe_deletion	In_Frame_Del	DEL	GCAGCCGTTCTCGAACATGTT	GCAGCCGTTCTCGAACATGTT	-	novel	NA	P-0025276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	132	507	0	ENST00000250448.2:c.754_774del	p.Asn252_Cys258del	p.N252_C258del	ENST00000250448	NM_004496.3	252	AACATGTTCGAGAACGGCTGC/-	2/2	1	2	FACETS	0.847	0.769	0.93	0.847	0.769	0.93	CLONAL	1	TRUE	1	0.369116947156799	2		507	844	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922293	100922293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149186732	NA	P-0025276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	132	370	0	ENST00000325455.5:c.2219G>A	p.Arg740Gln	p.R740Q	ENST00000325455	NM_001202474.3	740	cGa/cAa	5/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.369116947156799	2		370	600	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912277	32912277	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	168	519	0	ENST00000380152.3:c.3785C>A	p.Ser1262Ter	p.S1262*	ENST00000380152		1262	tCa/tAa	11/27	0.366890970254348	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.369116947156799	1		519	741	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685997	29685997	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	157	452	0	ENST00000356175.3:c.8061T>G	p.Phe2687Leu	p.F2687L	ENST00000356175	NM_000267.3	2687	ttT/ttG	55/57	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.369116947156799	2		452	712	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971046	55971046	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	174	554	0	ENST00000263923.4:c.1751A>G	p.Tyr584Cys	p.Y584C	ENST00000263923	NM_002253.2	584	tAc/tGc	13/30	1	2	FACETS	0.955	0.879	1	0.955	0.879	1	CLONAL	1	TRUE	1	0.369116947156799	2		554	987	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964454	70964454	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	373	625	0	ENST00000276594.2:c.1574C>G	p.Ser525Cys	p.S525C	ENST00000276594	NM_024504.3	525	tCt/tGt	8/8	0.369116947156799	4	FACETS	0.956	0.906	1	0.956	0.906	1	CLONAL	2	TRUE	2	0.369116947156799	4		625	1447	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964534	70964534	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	347	535	0	ENST00000276594.2:c.1494C>A	p.Phe498Leu	p.F498L	ENST00000276594	NM_024504.3	498	ttC/ttA	8/8	0.369116947156799	4	FACETS	0.944	0.892	0.996	0.944	0.892	0.996	CLONAL	2	TRUE	2	0.369116947156799	4		535	1364	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	85	272	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.801	0.707	0.902	0.801	0.707	0.902	CLONAL	1	TRUE	1	0.254748245398416	2		272	833	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0025313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	91	561	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.154601304321437	2	FACETS	0.861	0.763	0.965	0.43	0.381	0.483	CLONAL	1	TRUE	0	0.254748245398416	2		561	830	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253911	NA	P-0025313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	116	572	0	ENST00000269305.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000269305	NM_001126112.2	180	Gag/Aag	5/11	0.19803622898061	1	FACETS	0.953	0.858	1	0.953	0.858	1	CLONAL	1	TRUE	0	0.254748245398416	1		572	834	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482552	56482552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	98	573	0	ENST00000267101.3:c.1009G>A	p.Gly337Arg	p.G337R	ENST00000267101	NM_001982.3	337	Ggg/Agg	9/28	1	2	FACETS	0.832	0.741	0.929	0.832	0.741	0.929	CLONAL	1	TRUE	1	0.254748245398416	2		573	925	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028697	42028697	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	120	600	2	ENST00000219905.7:c.4235C>T	p.Ser1412Phe	p.S1412F	ENST00000219905	NM_001164273.1	1412	tCt/tTt	13/24	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.254748245398416	2		602	914	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753155	42753155	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	105	684	0	ENST00000222329.4:c.1109C>G	p.Ser370Cys	p.S370C	ENST00000222329	NM_006494.2	370	tCt/tGt	4/4	1	2	FACETS	0.737	0.658	0.82	0.737	0.658	0.82	SUBCLONAL	1	TRUE	1	0.254748245398416	2		684	1119	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0025475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	159	812	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.3	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	0	0.3	1		812	858	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217037	7217037	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	75	471	0	ENST00000380728.2:c.484del	p.Arg162GlyfsTer183	p.R162Gfs*183	ENST00000380728		162	Cgg/gg	7/11	0.3	1	FACETS	0.777	0.682	0.879	0.777	0.682	0.879	SUBCLONAL	1	FALSE	0	0.3	1		471	547	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874197	151874197	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs571899020	NA	P-0025475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	72	413	0	ENST00000262189.6:c.8341A>G	p.Ile2781Val	p.I2781V	ENST00000262189	NM_170606.2	2781	Att/Gtt	38/59	1	2	FACETS	0.751	0.656	0.854	0.751	0.656	0.854	SUBCLONAL	1	FALSE	1	0.3	2		413	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0025551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	385	596	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.773042825900527	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.773042825900527	1		597	575	SUCCESS
ATM	472	MSKCC	GRCh37	11	108213949	108213949	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs761625350	NA	P-0025551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	199	331	0	ENST00000278616.4:c.8269G>A	p.Val2757Met	p.V2757M	ENST00000278616	NM_000051.3	2757	Gtg/Atg	57/63	1	2	FACETS	0.968	0.904	1	0.968	0.904	1	CLONAL	1	TRUE	1	0.773042825900527	2		331	532	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016634	12016635	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	303	440	0	ENST00000353533.5:c.771dup	p.Ile258TyrfsTer10	p.I258Yfs*10	ENST00000353533	NM_003010.3	257	tct/tcTt	7/11	0.773042825900527	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.773042825900527	1		440	475	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613358	100613358	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	282	580	0	ENST00000308731.7:c.1042G>C	p.Glu348Gln	p.E348Q	ENST00000308731	NM_000061.2	348	Gag/Cag	12/19	1	2	FACETS	0.868	0.818	0.918	0.868	0.818	0.918	CLONAL	1	TRUE	1	0.773042825900527	2		580	841	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615086	100615086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868983143	NA	P-0025551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	349	587	0	ENST00000308731.7:c.829G>A	p.Glu277Lys	p.E277K	ENST00000308731	NM_000061.2	277	Gaa/Aaa	9/19	1	2	FACETS	0.924	0.877	0.972	0.924	0.877	0.972	CLONAL	1	TRUE	1	0.773042825900527	2		587	977	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207076	1207077	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs121913319	NA	P-0025764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	222	358	0	ENST00000326873.7:c.169dup	p.Glu57GlyfsTer106	p.E57Gfs*106	ENST00000326873	NM_000455.4	55	ctg/ctGg	1/10	0.675348497190808	1	FACETS	0.999	0.943	1	0.999	0.943	1	CLONAL	1	TRUE	0	0.675348497190808	1		358	436	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602329	10602329	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	271	372	0	ENST00000171111.5:c.1249G>T	p.Gly417Trp	p.G417W	ENST00000171111	NM_203500.1	417	Ggg/Tgg	3/6	0.675348497190808	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.675348497190808	1		372	519	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794734	120794734	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	248	344	0	ENST00000257552.2:c.623A>G	p.Asp208Gly	p.D208G	ENST00000257552	NM_002442.3	208	gAc/gGc	9/15	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.675348497190808	2		344	732	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490395	29490395	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1555606137	NA	P-0025764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	427	338	0	ENST00000356175.3:c.479+1G>T		p.X160_splice	ENST00000356175	NM_000267.3	160			NA	2	FACETS	0.945	0.912	0.978			1	INDETERMINATE	2	TRUE	NA	0.675348497190808	2		338	669	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028472	42028472	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	177	380	0	ENST00000219905.7:c.4010A>T	p.Glu1337Val	p.E1337V	ENST00000219905	NM_001164273.1	1337	gAg/gTg	13/24	1	2	FACETS	0.769	0.711	0.829	0.769	0.711	0.829	SUBCLONAL	1	TRUE	1	0.675348497190808	2		380	682	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028461	42028471	+	frameshift_variant	Frame_Shift_Del	DEL	CAAACTGATTG	CAAACTGATTG	-	novel	NA	P-0025764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	164	368	0	ENST00000219905.7:c.3999_4009del	p.Lys1334AspfsTer24	p.K1334Dfs*24	ENST00000219905	NM_001164273.1	1333	acCAAACTGATTGag/acag	13/24	1	2	FACETS	0.734	0.676	0.794	0.734	0.676	0.794	SUBCLONAL	1	TRUE	1	0.675348497190808	2		368	662	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025791-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	492	604	0	ENST00000269305.4:c.376T>C	p.Tyr126His	p.Y126H	ENST00000269305	NM_001126112.2	126	Tac/Cac	5/11	NA	2	FACETS	0.89	0.859	0.92			1	INDETERMINATE	2	TRUE	NA	0.678521979649218	2		604	815	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961884	15961884	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs970987519	NA	P-0025791-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	69	454	0	ENST00000268712.3:c.5911G>A	p.Asp1971Asn	p.D1971N	ENST00000268712	NM_006311.3	1971	Gat/Aat	38/46	0.560710178499487	3	FACETS	0.635	0.555	0.721	0.212	0.185	0.241	SUBCLONAL	1	TRUE	0	0.678521979649218	3		454	429	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612157	189612157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025791-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	150	568	1	ENST00000264731.3:c.1909C>T	p.Arg637Cys	p.R637C	ENST00000264731	NM_003722.4	637	Cgt/Tgt	14/14	0.578785508683964	3	FACETS	0.817	0.748	0.889	0.408	0.374	0.445	CLONAL	1	TRUE	1	0.678521979649218	3		569	725	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910605	32910605	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025791-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	150	438	0	ENST00000380152.3:c.2113G>C	p.Glu705Gln	p.E705Q	ENST00000380152		705	Gaa/Caa	11/27	0.266388094515789	3	FACETS	0.781	0.723	0.841			1	INDETERMINATE	2	TRUE	NA	0.678521979649218	3		438	379	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337604	73337604	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025791-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	56	315	0	ENST00000377767.4:c.2112G>C	p.Lys704Asn	p.K704N	ENST00000377767	NM_014953.3	704	aaG/aaC	16/21	0.6603545540516	4	FACETS	0.696	0.598	0.802	0.232	0.199	0.268	SUBCLONAL	1	TRUE	1	0.678521979649218	4		315	398	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437961	110437961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025791-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	58	66	0	ENST00000375856.3:c.440G>A	p.Arg147His	p.R147H	ENST00000375856	NM_003749.2	147	cGc/cAc	1/2	0.6603545540516	4	FACETS	1	0.971	1	0.491	0.428	0.556	CLONAL	1	TRUE	1	0.678521979649218	4		66	195	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023301	31023301	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025791-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1179	175	569	1	ENST00000375687.4:c.2786A>T	p.Glu929Val	p.E929V	ENST00000375687	NM_015338.5	929	gAg/gTg	13/13	0.50306489749267	6	FACETS	0.898	0.825	0.975	0.299	0.275	0.325	CLONAL	1	TRUE	3	0.678521979649218	6		570	1354	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38176442	38176442	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025791-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	94	458	0	ENST00000317025.8:c.1826A>C	p.Gln609Pro	p.Q609P	ENST00000317025	NM_023034.1	609	cAg/cCg	9/24	1	2	FACETS	0.689	0.617	0.765	0.689	0.617	0.765	SUBCLONAL	1	TRUE	1	0.678521979649218	2		458	402	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0025909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	232	368	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	0.871167697493943	2		368	531	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489545	40489546	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0025909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	403	558	1	ENST00000264657.5:c.704_705del	p.Leu235HisfsTer7	p.L235Hfs*7	ENST00000264657	NM_139276.2	235	cTC/c	8/24	1	2	FACETS	0.978	0.934	1	0.978	0.934	1	CLONAL	1	TRUE	1	0.871167697493943	2		559	946	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602788	10602788	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	576	783	0	ENST00000171111.5:c.790G>T	p.Val264Phe	p.V264F	ENST00000171111	NM_203500.1	264	Gtc/Ttc	3/6	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.871167697493943	2		783	1289	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0025948-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	111	417	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.34	2		417	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579575	7579575	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025948-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	116	549	0	ENST00000269305.4:c.112C>T	p.Gln38Ter	p.Q38*	ENST00000269305	NM_001126112.2	38	Caa/Taa	4/11	1	2	FACETS	0.985	0.889	1	0.985	0.889	1	CLONAL	1	TRUE	1	0.34	2		549	693	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851763	134851763	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201125634	NA	P-0025948-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	65	502	0	ENST00000398015.3:c.1169G>A	p.Arg390His	p.R390H	ENST00000398015	NM_004441.4	390	cGc/cAc	5/16	0.171274797881598	3	FACETS	0.654	0.566	0.749	0.327	0.283	0.375	INDETERMINATE	1	TRUE	1	0.34	3		502	684	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913499	NA	P-0026227-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	46	339	0	ENST00000345146.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000345146	NM_005896.2	132	Cgt/Ggt	4/10	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.383555449581082	2		339	196	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0026227-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	16	742	1	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	1	2	FACETS	0.221	0.162	0.291	0.221	0.162	0.291	SUBCLONAL	1	TRUE	1	0.383555449581082	2		743	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0026227-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	242	668	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	3	TRUE	NA	0.383555449581082	2		668	378	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413070	139413072	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0026227-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	29	586	0	ENST00000277541.6:c.1070_1072del	p.Phe357del	p.F357del	ENST00000277541	NM_017617.3	357	tTCTac/tac	6/34	0.313462632498689	0	FACETS	0.63	0.512	0.76			1	SUBCLONAL	1	TRUE	0	0.383555449581082	0		586	148	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938752	76938752	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026227-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	74	419	1	ENST00000373344.5:c.1996C>T	p.Arg666Ter	p.R666*	ENST00000373344	NM_000489.3	666	Cga/Tga	9/35	1	1	FACETS	0.917	0.823	1	1	0.984	1	CLONAL	2	TRUE	0	0.383555449581082	1		420	170	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576365	67576365	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026227-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	25	255	0	ENST00000274335.5:c.644G>A	p.Ser215Asn	p.S215N	ENST00000274335		215	aGc/aAc	5/15	1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	1	0.383555449581082	2		255	126	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589621	67589621	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026227-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	21	275	0	ENST00000274335.5:c.1384G>T	p.Glu462Ter	p.E462*	ENST00000274335		462	Gaa/Taa	10/15	1	2	FACETS	0.793	0.618	0.994	0.793	0.618	0.994	CLONAL	1	TRUE	1	0.383555449581082	2		275	138	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0026253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	51	368	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.316030881478657	2	FACETS	0.901	0.77	1	0.451	0.385	0.523	CLONAL	1	TRUE	0	0.327045057232363	2		368	346	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0026253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	205	337	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.327045057232363	3	FACETS	0.937	0.877	0.998	0.937	0.877	0.998	CLONAL	3	TRUE	0	0.327045057232363	3		337	519	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578493	7578493	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1206165503	NA	P-0026253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	220	488	2	ENST00000269305.4:c.437G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tGg/tAg	5/11	NA	2	FACETS	0.958	0.895	1			1	INDETERMINATE	2	TRUE	NA	0.327045057232363	2		490	702	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255092	16255093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	71	297	0	ENST00000375759.3:c.2363dup	p.Asn788LysfsTer2	p.N788Kfs*2	ENST00000375759	NM_015001.2	786	aca/acAa	11/15	NA	2	FACETS	0.974	0.853	1			1	INDETERMINATE	1	TRUE	NA	0.327045057232363	2		297	446	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245183	46245183	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	65	266	0	ENST00000334344.6:c.3277C>G	p.Pro1093Ala	p.P1093A	ENST00000334344	NM_152641.2	1093	Cct/Gct	15/21	0.316030881478657	2	FACETS	0.967	0.842	1	0.484	0.421	0.551	CLONAL	1	TRUE	0	0.327045057232363	2		266	411	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843806	151843807	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0026253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	39	210	0	ENST00000262189.6:c.13908_13909del	p.Lys4636AsnfsTer13	p.K4636Nfs*13	ENST00000262189	NM_170606.2	4636	aaGAtt/aatt	53/59	0.318841828407958	2	FACETS	0.782	0.651	0.927	0.391	0.325	0.464	CLONAL	1	TRUE	0	0.327045057232363	2		210	305	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0026502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	320	786	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.198946469871337	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.198946469871337	2		787	1488	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543826	212543826	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775988789	NA	P-0026502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	70	524	2	ENST00000342788.4:c.1573C>T	p.Arg525Cys	p.R525C	ENST00000342788	NM_005235.2	525	Cgc/Tgc	13/28	0.198946469871337	3	FACETS	0.809	0.704	0.924	0.405	0.352	0.462	CLONAL	1	TRUE	1	0.198946469871337	3		526	956	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925195	81925195	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	73	429	0	ENST00000359376.3:c.986C>T	p.Thr329Met	p.T329M	ENST00000359376	NM_002661.3	329	aCg/aTg	11/33	0.198946469871337	3	FACETS	0.84	0.732	0.956	0.42	0.366	0.478	CLONAL	1	TRUE	1	0.198946469871337	3		429	961	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484058	50484058	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1442501952	NA	P-0026502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	133	628	0	ENST00000394963.4:c.908G>A	p.Arg303Gln	p.R303Q	ENST00000394963	NM_003076.4	303	cGa/cAa	8/13	0.198946469871337	2	FACETS	1	0.937	1	0.522	0.473	0.575	CLONAL	1	TRUE	0	0.198946469871337	2		628	1280	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473616	67473616	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs778356642	NA	P-0026502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	90	621	1	ENST00000327367.4:c.696G>A	p.Trp232Ter	p.W232*	ENST00000327367	NM_005902.3	232	tgG/tgA	6/9	1	2	FACETS	0.796	0.705	0.895	0.796	0.705	0.895	SUBCLONAL	1	TRUE	1	0.198946469871337	2		622	1136	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0026810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	156	611	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.570796301158761	1	FACETS	0.943	0.874	1	0.943	0.874	1	CLONAL	1	TRUE	0	0.570796301158761	1		611	414	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950727	79950728	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCGCCCC	rs60484572	NA	P-0026810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	14	245	1	ENST00000265081.6:c.195_203dup	p.Pro67_Pro69dup	p.P67_P69dup	ENST00000265081	NM_002439.4	67	gca/gCAGCGCCCCca	1/24	0.570796301158761	1	FACETS	0.28	0.204	0.371	0.28	0.204	0.371	SUBCLONAL	1	TRUE	0	0.570796301158761	1		246	125	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164010	47164010	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	34	374	0	ENST00000409792.3:c.2116G>A	p.Glu706Lys	p.E706K	ENST00000409792	NM_014159.6	706	Gaa/Aaa	3/21	1	2	FACETS	0.505	0.415	0.604	0.505	0.415	0.604	SUBCLONAL	1	TRUE	1	0.570796301158761	2		374	236	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344860	70344860	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	127	554	0	ENST00000374080.3:c.2090G>T	p.Gly697Val	p.G697V	ENST00000374080		697	gGc/gTc	15/45	1	2	FACETS	0.931	0.849	1	0.931	0.849	1	CLONAL	1	TRUE	1	0.570796301158761	2		554	478	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0027309-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	108	433	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.433817993709316	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	0	0.433817993709316	1		433	389	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0027309-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	150	368	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.433817993709316	3	FACETS	0.901	0.83	0.974	0.901	0.83	0.974	CLONAL	2	TRUE	1	0.433817993709316	3		368	467	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346115	152346115	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027309-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	108	478	0	ENST00000359321.1:c.455C>T	p.Ser152Leu	p.S152L	ENST00000359321	NM_005431.1	152	tCa/tTa	3/3	0.433817993709316	1	FACETS	0.942	0.852	1	0.942	0.852	1	CLONAL	1	TRUE	0	0.433817993709316	1		478	414	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104530	193104530	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027309-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	96	371	0	ENST00000367435.3:c.317C>T	p.Ala106Val	p.A106V	ENST00000367435	NM_024529.4	106	gCa/gTa	4/17	1	2	FACETS	0.909	0.813	1	0.909	0.813	1	CLONAL	1	TRUE	1	0.433817993709316	2		371	487	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858921	243858924	+	frameshift_variant	Frame_Shift_Del	DEL	AGGT	AGGT	-	novel	NA	P-0027309-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	83	350	0	ENST00000263826.5:c.141_144del	p.Leu47PhefsTer14	p.L47Ffs*14	ENST00000263826	NM_005465.4	47	ttACCT/tt	2/13	1	2	FACETS	0.781	0.691	0.876	0.781	0.691	0.876	SUBCLONAL	1	TRUE	1	0.433817993709316	2		350	490	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205110	61205110	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0027309-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	120	443	0	ENST00000301761.2:c.50C>G	p.Ser17Ter	p.S17*	ENST00000301761	NM_017841.2	17	tCa/tGa	2/4	1	2	FACETS	0.897	0.812	0.986	0.897	0.812	0.986	CLONAL	1	TRUE	1	0.433817993709316	2		443	617	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028810	42028810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371316400	NA	P-0027309-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	154	558	0	ENST00000219905.7:c.4348C>G	p.Leu1450Val	p.L1450V	ENST00000219905	NM_001164273.1	1450	Ctg/Gtg	13/24	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.433817993709316	2		558	674	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0028196-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	108	433	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	0.989	1	CLONAL	2	TRUE	1	0.14	2		433	704	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578400	7578400	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs751477326	NA	P-0028196-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	43	645	1	ENST00000269305.4:c.530C>G	p.Pro177Arg	p.P177R	ENST00000269305	NM_001126112.2	177	cCc/cGc	5/11	1	2	FACETS	0.777	0.648	0.92	0.777	0.648	0.92	CLONAL	1	TRUE	1	0.14	2		646	791	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430042	78430042	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0028196-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	23	274	0	ENST00000370768.2:c.838-1G>T		p.X280_splice	ENST00000370768	NM_003902.3	280			1	2	FACETS	0.745	0.58	0.937	0.745	0.58	0.937	CLONAL	1	TRUE	1	0.14	2		274	441	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285871	46285871	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028196-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	23	294	0	ENST00000334344.6:c.5140del	p.Ser1714LeufsTer7	p.S1714Lfs*7	ENST00000334344	NM_152641.2	1713	tcT/tc	18/21	1	2	FACETS	0.721	0.561	0.907	0.721	0.561	0.907	CLONAL	1	TRUE	1	0.14	2		294	456	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0028288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	25	687	2	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	0.109	0.085	0.137	0.109	0.085	0.137	SUBCLONAL	1	TRUE	1	0.886724796112528	2		689	516	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371799	55371820	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCCGCGCTGGGCCCCGAG	GGCGGCCGCGCTGGGCCCCGAG	-	novel	NA	P-0028288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	96	222	0	ENST00000297316.4:c.499_520del	p.Leu167TrpfsTer213	p.L167Wfs*213	ENST00000297316	NM_022454.3	163	caGGCGGCCGCGCTGGGCCCCGAG/ca	2/2	1	2	FACETS	0.773	0.699	0.85	0.773	0.699	0.85	SUBCLONAL	1	TRUE	1	0.886724796112528	2		222	280	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685271	89685271	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	231	676	2	ENST00000371953.3:c.170del	p.Leu57TrpfsTer42	p.L57Wfs*42	ENST00000371953	NM_000314.4	56	Ttt/tt	3/9	0.495782889042592	3	FACETS	0.969	0.921	1	0.646	0.614	0.678	INDETERMINATE	2	TRUE	0	0.886724796112528	3		678	388	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279674	123279675	+	missense_variant	Missense_Mutation	DNP	GG	GG	CA	novel	NA	P-0028288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	333	418	0	ENST00000358487.5:c.757_758delinsTG	p.Pro253Cys	p.P253C	ENST00000358487	NM_000141.4	253	CCt/TGt	7/18	0.495782889042592	3	FACETS	0.86	0.822	0.899	0.574	0.548	0.599	INDETERMINATE	2	TRUE	0	0.886724796112528	3		418	630	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416243	416243	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs200449935	NA	P-0028288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	135	367	0	ENST00000399788.2:c.3943A>G	p.Ser1315Gly	p.S1315G	ENST00000399788	NM_001042603.1	1315	Agt/Ggt	24/28	NA	2	FACETS	0.537	0.49	0.586			1	INDETERMINATE	1	TRUE	NA	0.886724796112528	2		367	567	SUCCESS
AXL	558	MSKCC	GRCh37	19	41749570	41749570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747576071	NA	P-0028288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	197	658	1	ENST00000301178.4:c.1495C>T	p.Arg499Cys	p.R499C	ENST00000301178	NM_021913.4	499	Cgc/Tgc	12/20	1	2	FACETS	0.469	0.434	0.505	0.469	0.434	0.505	SUBCLONAL	1	TRUE	1	0.886724796112528	2		659	947	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589620	67589622	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0028288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	55	303	0	ENST00000274335.5:c.1384_1386del	p.Glu462del	p.E462del	ENST00000274335		461	cgAGAa/cga	10/15	1	2	FACETS	0.388	0.333	0.446	0.388	0.333	0.446	SUBCLONAL	1	TRUE	1	0.886724796112528	2		303	320	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940473	76940474	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0028288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	140	609	1	ENST00000373344.5:c.619_620delinsTT	p.Asp207Phe	p.D207F	ENST00000373344	NM_000489.3	207	GAt/TTt	8/35	1	2	FACETS	0.529	0.483	0.576	0.529	0.483	0.576	SUBCLONAL	1	TRUE	1	0.886724796112528	2		610	597	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953918	131953918	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028467-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	182	318	0	ENST00000265335.6:c.3321G>A	p.Met1107Ile	p.M1107I	ENST00000265335		1107	atG/atA	21/25	0.684459262705453	3	FACETS	0.798	0.745	0.853	0.798	0.745	0.853	SUBCLONAL	2	TRUE	1	0.69496447737215	3		318	442	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953940	131953940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028467-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	189	312	0	ENST00000265335.6:c.3343G>A	p.Glu1115Lys	p.E1115K	ENST00000265335		1115	Gaa/Aaa	21/25	0.684459262705453	3	FACETS	0.837	0.782	0.891	0.837	0.782	0.891	CLONAL	2	TRUE	1	0.69496447737215	3		312	438	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953930	131953930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028467-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	192	313	0	ENST00000265335.6:c.3333G>A	p.Met1111Ile	p.M1111I	ENST00000265335		1111	atG/atA	21/25	0.684459262705453	3	FACETS	0.838	0.785	0.893	0.838	0.785	0.893	CLONAL	2	TRUE	1	0.69496447737215	3		313	444	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003749	45003749	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs368160918	NA	P-0028467-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	137	373	0	ENST00000558401.1:c.5C>G	p.Ser2Cys	p.S2C	ENST00000558401	NM_004048.2	2	tCt/tGt	1/4	0.558341130310022	2	FACETS	0.971	0.892	1	0.486	0.446	0.526	CLONAL	1	TRUE	0	0.69496447737215	2		373	406	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842338	151842338	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028467-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	72	201	0	ENST00000262189.6:c.14074G>T	p.Gly4692Cys	p.G4692C	ENST00000262189	NM_170606.2	4692	Ggc/Tgc	54/59	0.682463467540304	4	FACETS	0.922	0.81	1	0.461	0.405	0.521	CLONAL	1	TRUE	2	0.69496447737215	4		201	381	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141545629	141545629	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028467-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1392	199	701	0	ENST00000220592.5:c.2209G>T	p.Asp737Tyr	p.D737Y	ENST00000220592	NM_012154.3	737	Gac/Tac	17/19	0.69496447737215	6	FACETS	0.86	0.794	0.929	0.172	0.158	0.186	CLONAL	1	TRUE	1	0.69496447737215	6		701	1591	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514038	69514038	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028467-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	130	413	0	ENST00000294312.3:c.643G>C	p.Glu215Gln	p.E215Q	ENST00000294312	NM_005117.2	215	Gag/Cag	3/3	0.682463467540304	4	FACETS	1	0.922	1	0.507	0.461	0.555	CLONAL	1	TRUE	2	0.69496447737215	4		413	625	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578742	7579554	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGCTCTGTCACTCAGGCTGGAGCACAGTGGTGTGATCACAGCTCACTGCAGCCTCCATCTCCTGGCCTCAAGTGATCTTCCCACCTCAGCCTCCTAAGTGGCTGGGACTATAGGTGTGCACCACCATGCCTGGCTAATTTTTTGTATTTTTTTGTAGAGACGAGGTTTCATCATGTTACCCAGGCTGGTCTTGAACTCCTGGGCTCAGGTGATCTGCCTGCCTTGGCCTCTTTGAGAGTGCTGGGATTGCAGGTGTGAGCCACCAAGCCTGGTCAGGAGCTTATTTTCAAAAGCCAAGGAATACACGTGGATGAAGAAAAAGAAAAGTTCTGCATCCCCAGGAGAGATGCTGAGGGTGTGATGGGATGGATAAAAGCCCAAATTCAAGGGGGGAATATTCAACTTTGGGACAGGAGTCAGAGATCACACATTAAGTGGGTAAACTATAAAAAAACACTGACAGGAAGCCAAAGGGTGAAGAGGAATCCCAAAGTTCCAAACAAAAGAAATGCAGGGGGATACGGCCAGGCATTGAAGTCTCATGGAAGCCAGCCCCTCAGGGCAACTGACCGTGCAAGTCACAGACTTGGCTGTCCCAGAATGCAAGAAGCCCAGACGGAAACCGTAGCTGCCCTGGTAGGTTTTCTGGGAAGGGACAGAAGATGACAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTGCAGGGGCCACGGGGGGAGCAGCCTCTGGCATTCTGGGAGCTTCATCTGGACCTGGGTCTTCAGTGAACCATTGTTCAATATCGTCCGGGGACAG	TGCTCTGTCACTCAGGCTGGAGCACAGTGGTGTGATCACAGCTCACTGCAGCCTCCATCTCCTGGCCTCAAGTGATCTTCCCACCTCAGCCTCCTAAGTGGCTGGGACTATAGGTGTGCACCACCATGCCTGGCTAATTTTTTGTATTTTTTTGTAGAGACGAGGTTTCATCATGTTACCCAGGCTGGTCTTGAACTCCTGGGCTCAGGTGATCTGCCTGCCTTGGCCTCTTTGAGAGTGCTGGGATTGCAGGTGTGAGCCACCAAGCCTGGTCAGGAGCTTATTTTCAAAAGCCAAGGAATACACGTGGATGAAGAAAAAGAAAAGTTCTGCATCCCCAGGAGAGATGCTGAGGGTGTGATGGGATGGATAAAAGCCCAAATTCAAGGGGGGAATATTCAACTTTGGGACAGGAGTCAGAGATCACACATTAAGTGGGTAAACTATAAAAAAACACTGACAGGAAGCCAAAGGGTGAAGAGGAATCCCAAAGTTCCAAACAAAAGAAATGCAGGGGGATACGGCCAGGCATTGAAGTCTCATGGAAGCCAGCCCCTCAGGGCAACTGACCGTGCAAGTCACAGACTTGGCTGTCCCAGAATGCAAGAAGCCCAGACGGAAACCGTAGCTGCCCTGGTAGGTTTTCTGGGAAGGGACAGAAGATGACAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTGCAGGGGCCACGGGGGGAGCAGCCTCTGGCATTCTGGGAGCTTCATCTGGACCTGGGTCTTCAGTGAACCATTGTTCAATATCGTCCGGGGACAG	-	novel	NA	P-0028467-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	167	56	0	ENST00000269305.4:c.133_376-188del		p.X45_splice	ENST00000269305	NM_001126112.2	45		4/11	0.681966469910386	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	4	TRUE	0	0.69496447737215	4		56	195	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681071	37681071	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028467-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	117	402	0	ENST00000447079.4:c.3240G>T	p.Lys1080Asn	p.K1080N	ENST00000447079	NM_015083.1	1080	aaG/aaT	12/14	0.682463467540304	4	FACETS	0.907	0.82	0.999	0.454	0.41	0.5	CLONAL	1	TRUE	2	0.69496447737215	4		402	629	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025559	1025559	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1882	210	704	3	ENST00000358495.3:c.816G>A	p.Met272Ile	p.M272I	ENST00000358495	NM_134424.2	272	atG/atA	9/12	0.490022551020892	8	FACETS	1	0.934	1			1	CLONAL	1	TRUE	NA	0.490022551020892	8		707	2092	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285250	212285250	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	110	514	1	ENST00000342788.4:c.3051G>T	p.Met1017Ile	p.M1017I	ENST00000342788	NM_005235.2	1017	atG/atT	25/28	0.491286741978646	3	FACETS	0.907	0.817	1	0.454	0.408	0.502	CLONAL	1	TRUE	1	0.490022551020892	3		515	616	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578532	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	597	953	0	ENST00000269305.4:c.398T>A	p.Met133Lys	p.M133K	ENST00000269305	NM_001126112.2	133	aTg/aAg	5/11	0.427124086313205	3	FACETS	0.986	0.958	1			1	CLONAL	3	TRUE	NA	0.604212943815656	3		953	870	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945129	32945129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80359104	NA	P-0028706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	46	255	0	ENST00000380152.3:c.8524C>T	p.Arg2842Cys	p.R2842C	ENST00000380152		2842	Cgc/Tgc	20/27	0.474047351974447	5	FACETS	0.836	0.707	0.978			1	CLONAL	1	TRUE	NA	0.604212943815656	5		255	347	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266063	41266316	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATA	GGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATA	-	novel	NA	P-0028706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	37	297	0	ENST00000349496.5:c.60_241+72del		p.X20_splice	ENST00000349496	NM_001904.3	20		3/15	0.601771459338871	2	FACETS	0.765	0.64	0.901	0.383	0.32	0.451	CLONAL	1	TRUE	0	0.604212943815656	2		297	160	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0028718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	150	488	2	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.464406194552438	2		490	590	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0028718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	139	418	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.464406194552438	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.464406194552438	1		418	449	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845757	68845757	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587780784	NA	P-0028718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	99	332	0	ENST00000261769.5:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000261769	NM_004360.3	335	Cga/Tga	7/16	0.464406194552438	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.464406194552438	1		332	305	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120827	115120842	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGCGCCCGGCAGCG	AGGGCGCCCGGCAGCG	-	novel	NA	P-0028718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	116	432	0	ENST00000257566.3:c.164_179del	p.Ser55TrpfsTer28	p.S55Wfs*28	ENST00000257566	NM_016569.3	55	tCGCTGCCGGGCGCCCTg/tg	1/8	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.464406194552438	2		432	464	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39240599	39240601	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ACC	ACC	-	novel	NA	P-0028718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	81	236	0	ENST00000402219.2:c.2167_2167+2del		p.X723_splice	ENST00000402219	NM_005633.3	723		13/23	1	2	FACETS	0.883	0.783	0.99	0.883	0.783	0.99	CLONAL	1	TRUE	1	0.464406194552438	2		236	395	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413710	138413711	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0028718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	89	406	0	ENST00000289153.2:c.1809_1810del	p.Arg604GlyfsTer28	p.R604Gfs*28	ENST00000289153	NM_006219.2	603	ccCCgg/ccgg	12/22	1	2	FACETS	0.841	0.749	0.938	0.841	0.749	0.938	CLONAL	1	TRUE	1	0.464406194552438	2		406	456	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843356	128843369	+	frameshift_variant	Frame_Shift_Del	DEL	GCCATCGTGGAGAG	GCCATCGTGGAGAG	-	novel	NA	P-0028718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	130	569	0	ENST00000249373.3:c.464_477del	p.Ala155GlyfsTer6	p.A155Gfs*6	ENST00000249373	NM_005631.4	155	GCCATCGTGGAGAGg/g	2/12	1	2	FACETS	0.836	0.759	0.915	0.836	0.759	0.915	CLONAL	1	TRUE	1	0.464406194552438	2		569	670	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873831	151873831	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	113	370	0	ENST00000262189.6:c.8707C>T	p.Gln2903Ter	p.Q2903*	ENST00000262189	NM_170606.2	2903	Caa/Taa	38/59	1	2	FACETS	0.895	0.808	0.985	0.895	0.808	0.985	CLONAL	1	TRUE	1	0.464406194552438	2		370	544	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412585	63412585	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	121	478	0	ENST00000330258.3:c.582del	p.Lys195ArgfsTer14	p.K195Rfs*14	ENST00000330258	NM_152424.3	194	gcC/gc	2/2	NA	2	FACETS	0.978	0.887	1			1	INDETERMINATE	1	TRUE	NA	0.464406194552438	2		478	533	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0029112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	343	433	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.216510769209921	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.323710817434474	4		433	1318	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0029112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	89	681	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.323710817434474	1	FACETS	0.677	0.6	0.759	0.677	0.6	0.759	SUBCLONAL	1	TRUE	0	0.323710817434474	1		681	681	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241654	55241654	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	347	857	0	ENST00000275493.2:c.2102A>T	p.Gln701Leu	p.Q701L	ENST00000275493	NM_005228.3	701	cAa/cTa	18/28	0.216510769209921	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.323710817434474	4		857	1316	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814930	139814930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371121908	NA	P-0029161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	215	585	0	ENST00000247668.2:c.923G>A	p.Arg308Gln	p.R308Q	ENST00000247668	NM_021138.3	308	cGg/cAg	8/11	1	2	FACETS	0.597	0.554	0.641	0.597	0.554	0.641	SUBCLONAL	1	TRUE	1	0.617388181083436	2		585	1167	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849851	156849851	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	189	620	0	ENST00000524377.1:c.2107A>G	p.Lys703Glu	p.K703E	ENST00000524377	NM_002529.3	703	Aag/Gag	16/17	0.333076116572895	2	FACETS	0.523	0.483	0.566	0.262	0.241	0.283	INDETERMINATE	1	TRUE	0	0.617388181083436	2		620	1170	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101197	41101197	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568910629	NA	P-0029161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1197	168	496	0	ENST00000373198.4:c.1159G>A	p.Val387Ile	p.V387I	ENST00000373198	NM_133170.3	387	Gta/Ata	8/32	0.361668302883829	4	FACETS	0.645	0.591	0.702	0.322	0.295	0.351	INDETERMINATE	1	TRUE	2	0.617388181083436	4		496	1365	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214407	55214407	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	144	550	0	ENST00000275493.2:c.533T>A	p.Met178Lys	p.M178K	ENST00000275493	NM_005228.3	178	aTg/aAg	4/28	0.334736761427017	1	FACETS	0.358	0.326	0.391	0.358	0.326	0.391	INDETERMINATE	1	TRUE	0	0.617388181083436	1		550	902	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0029362-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	150	804	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.194658644942954	2	FACETS	0.918	0.842	0.996	0.918	0.842	0.996	CLONAL	2	TRUE	0	0.269712960296205	2		804	606	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591136	67591144	+	inframe_deletion	In_Frame_Del	DEL	AGAGACCAA	AGAGACCAA	-	novel	NA	P-0029362-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	30	292	0	ENST00000274335.5:c.1729_1737del	p.Arg577_Gln579del	p.R577_Q579del	ENST00000274335		577	AGAGACCAA/-	12/15	0.175794316246043	2	FACETS	0.809	0.654	0.983	0.404	0.327	0.492	CLONAL	1	TRUE	0	0.269712960296205	2		292	275	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115284258	115284258	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029362-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	64	515	0	ENST00000438362.2:c.28G>C	p.Asp10His	p.D10H	ENST00000438362	NM_001242891.1	10	Gat/Cat	2/20	0.199575020124116	4	FACETS	1	0.97	1	0.731	0.636	0.834	CLONAL	1	TRUE	2	0.269712960296205	4		515	412	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387692	17387692	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029362-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	165	695	0	ENST00000359435.4:c.760G>T	p.Glu254Ter	p.E254*	ENST00000359435	NM_001033549.1	254	Gag/Tag	8/9	0.194658644942954	2	FACETS	0.888	0.818	0.961	0.888	0.818	0.961	CLONAL	2	TRUE	0	0.269712960296205	2		695	689	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447358	187447358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764799764	NA	P-0029362-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	111	754	0	ENST00000232014.4:c.835G>C	p.Glu279Gln	p.E279Q	ENST00000232014	NM_001130845.1	279	Gag/Cag	5/10	0.269712960296205	5	FACETS	1	0.978	1	0.448	0.402	0.496	CLONAL	1	TRUE	2	0.269712960296205	5		754	861	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447660	187447660	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029362-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	120	700	0	ENST00000232014.4:c.533G>C	p.Arg178Thr	p.R178T	ENST00000232014	NM_001130845.1	178	aGa/aCa	5/10	0.269712960296205	5	FACETS	0.842	0.761	0.928	0.561	0.507	0.619	CLONAL	2	TRUE	2	0.269712960296205	5		700	742	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207203	1207203	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0029599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	494	615	0	ENST00000326873.7:c.290+1G>T		p.X97_splice	ENST00000326873	NM_000455.4	97			0.845130542144027	4	FACETS	0.999	0.983	1	0.999	0.983	1	CLONAL	4	FALSE	0	0.853078676887095	4		615	537	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0029599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	194	436	1	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	0.826203102474838	3	FACETS	0.992	0.962	1	0.992	0.962	1	CLONAL	3	FALSE	0	0.853078676887095	3		437	218	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423407	116423407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913671	NA	P-0029892-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3033	2829	283	0	ENST00000397752.3:c.3682G>A	p.Asp1228Asn	p.D1228N	ENST00000397752	NM_000245.2	1228	Gac/Aac	19/21	0.642391629149344	45	FACETS	1	0.991	1			1	CLONAL	22	FALSE	NA	0.642391629149344	45		283	5862	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423407	116423407	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913671	NA	P-0029892-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5313	549	283	0	ENST00000397752.3:c.3682G>C	p.Asp1228His	p.D1228H	ENST00000397752	NM_000245.2	1228	Gac/Cac	19/21	0.642391629149344	45	FACETS	1	0.985	1			1	CLONAL	4	FALSE	NA	0.642391629149344	45		283	5862	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533259	29533259	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1353527088	NA	P-0029892-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	119	294	1	ENST00000356175.3:c.1262C>T	p.Ser421Phe	p.S421F	ENST00000356175	NM_000267.3	421	tCc/tTc	12/57	0.477746678890363	5	FACETS	1	0.983	1	0.467	0.423	0.513	CLONAL	1	FALSE	2	0.642391629149344	5		295	519	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010592	48010592	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1553408388	NA	P-0029892-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	109	520	0	ENST00000234420.5:c.220G>T	p.Gly74Ter	p.G74*	ENST00000234420	NM_000179.2	74	Gga/Tga	1/10	0.296037333737613	5	FACETS	0.789	0.708	0.875	0.263	0.236	0.292	INDETERMINATE	1	FALSE	2	0.642391629149344	5		520	845	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5462959	5462959	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029892-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	112	241	1	ENST00000381577.3:c.520G>A	p.Val174Ile	p.V174I	ENST00000381577	NM_014143.3	174	Gtc/Atc	4/7	0.654975933621808	1	FACETS	0.759	0.712	0.803	1	0.99	1	SUBCLONAL	2	FALSE	0	0.642391629149344	1		242	156	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989165	41989165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029892-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	154	579	0	ENST00000219905.7:c.1957G>A	p.Val653Met	p.V653M	ENST00000219905	NM_001164273.1	653	Gtg/Atg	3/24	0.531142967791325	4	FACETS	0.953	0.873	1	0.477	0.436	0.519	CLONAL	1	FALSE	2	0.642391629149344	4		579	826	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78820294	78820294	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029892-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	116	702	1	ENST00000306801.3:c.1234C>A	p.Gln412Lys	p.Q412K	ENST00000306801	NM_020761.2	412	Cag/Aag	11/34	0.654975933621808	3	FACETS	0.668	0.603	0.737	0.223	0.201	0.246	SUBCLONAL	1	FALSE	0	0.642391629149344	3		703	714	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574662	41574662	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778302414	NA	P-0029892-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	338	798	0	ENST00000263253.7:c.6947C>T	p.Pro2316Leu	p.P2316L	ENST00000263253	NM_001429.3	2316	cCa/cTa	31/31	0.31432539940546	3	FACETS	0.826	0.784	0.867	0.826	0.784	0.867	INDETERMINATE	2	FALSE	1	0.642391629149344	3		798	842	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31464390	31464390	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029892-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1643	263	839	0	ENST00000344624.3:c.2527A>C	p.Ser843Arg	p.S843R	ENST00000344624		843	Agt/Cgt	17/33	0.642391629149344	6	FACETS	0.982	0.916	1	0.245	0.229	0.263	CLONAL	1	FALSE	2	0.642391629149344	6		839	1906	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157256711	157256711	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0029892-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	54	185	0	ENST00000346085.5:c.2037+1G>T		p.X679_splice	ENST00000346085	NM_020732.3	679			0.654975933621808	3	FACETS	0.864	0.745	0.992	0.432	0.372	0.496	CLONAL	1	FALSE	1	0.642391629149344	3		185	257	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0029922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	292	555	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		555	647	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0029928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	472	700	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	0.99	0.955	1			1	INDETERMINATE	2	TRUE	NA	0.596578902030197	2		700	799	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748309	41748309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs894529129	NA	P-0029928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	129	631	0	ENST00000226382.2:c.460C>T	p.Arg154Cys	p.R154C	ENST00000226382	NM_003924.3	154	Cgc/Tgc	3/3	0.596578902030197	1	FACETS	0.486	0.441	0.532	0.486	0.441	0.532	SUBCLONAL	1	TRUE	0	0.596578902030197	1		631	625	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755554	39755554	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	113	439	1	ENST00000288319.7:c.1211del	p.Pro404ArgfsTer25	p.P404Rfs*25	ENST00000288319	NM_182918.3	404	cCg/cg	10/10	0.305841145958636	1	FACETS	0.44	0.397	0.486	0.44	0.397	0.486	INDETERMINATE	1	TRUE	0	0.596578902030197	1		440	604	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188183	11188183	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057524049	NA	P-0029928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	116	429	0	ENST00000361445.4:c.5911G>A	p.Ala1971Thr	p.A1971T	ENST00000361445	NM_004958.3	1971	Gcc/Acc	43/58	0.596578902030197	1	FACETS	0.597	0.541	0.655	0.597	0.541	0.655	SUBCLONAL	1	TRUE	0	0.596578902030197	1		429	457	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2090156	2090156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148474733	NA	P-0029928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	357	847	3	ENST00000219066.1:c.793G>A	p.Ala265Thr	p.A265T	ENST00000219066	NM_002528.5	265	Gcc/Acc	5/6	0.305841145958636	1	FACETS	0.96	0.914	1	0.96	0.914	1	INDETERMINATE	1	TRUE	0	0.596578902030197	1		850	875	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288999	33288999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766610163	NA	P-0029928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	131	516	0	ENST00000374542.5:c.553C>T	p.Arg185Trp	p.R185W	ENST00000374542	NM_001141970.1	185	Cgg/Tgg	3/8	0.305841145958636	1	FACETS	0.458	0.416	0.502	0.458	0.416	0.502	INDETERMINATE	1	TRUE	0	0.596578902030197	1		516	673	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436331	110436331	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	106	280	0	ENST00000375856.3:c.2070G>T	p.Leu690Phe	p.L690F	ENST00000375856	NM_003749.2	690	ttG/ttT	1/2	0.594824818878001	2	FACETS	1	0.938	1	0.523	0.473	0.573	CLONAL	1	TRUE	0	0.596578902030197	2		280	340	SUCCESS
APC	324	MSKCC	GRCh37	5	112173625	112173625	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	117	409	0	ENST00000257430.4:c.2336del	p.Leu779Ter	p.L779*	ENST00000257430	NM_000038.5	778	aaT/aa	16/16	0.305841145958636	1	FACETS	0.693	0.631	0.758	0.693	0.631	0.758	INDETERMINATE	1	TRUE	0	0.596578902030197	1		409	397	SUCCESS
APC	324	MSKCC	GRCh37	5	112175329	112175534	+	frameshift_variant	Frame_Shift_Del	DEL	AGCCAGGCACAAAGCTGTTGAATTTTCTTCAGGAGCGAAATCTCCCTCCAAAAGTGGTGCTCAGACACCCAAAAGTCCACCTGAACACTATGTTCAGGAGACCCCACTCATGTTTAGCAGATGTACTTCTGTCAGTTCACTTGATAGTTTTGAGAGTCGTTCGATTGCCAGCTCCGTTCAGAGTGAACCATGCAGTGGAATGGTAA	AGCCAGGCACAAAGCTGTTGAATTTTCTTCAGGAGCGAAATCTCCCTCCAAAAGTGGTGCTCAGACACCCAAAAGTCCACCTGAACACTATGTTCAGGAGACCCCACTCATGTTTAGCAGATGTACTTCTGTCAGTTCACTTGATAGTTTTGAGAGTCGTTCGATTGCCAGCTCCGTTCAGAGTGAACCATGCAGTGGAATGGTAA	-	novel	NA	P-0029928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	44	298	0	ENST00000257430.4:c.4038_4243del	p.Ala1347TrpfsTer7	p.A1347Wfs*7	ENST00000257430	NM_000038.5	1346	tcAGCCAGGCACAAAGCTGTTGAATTTTCTTCAGGAGCGAAATCTCCCTCCAAAAGTGGTGCTCAGACACCCAAAAGTCCACCTGAACACTATGTTCAGGAGACCCCACTCATGTTTAGCAGATGTACTTCTGTCAGTTCACTTGATAGTTTTGAGAGTCGTTCGATTGCCAGCTCCGTTCAGAGTGAACCATGCAGTGGAATGGTAAgt/tcgt	16/16	0.305841145958636	1	FACETS	0.363	0.306	0.426	0.363	0.306	0.426	INDETERMINATE	1	TRUE	0	0.596578902030197	1		298	285	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0030293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	179	502	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	0.50356067339691	2		502	621	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087503	27087503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	48	564	4	ENST00000324856.7:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000324856	NM_006015.4	693	Cga/Tga	5/20	0.492655962741728	1	FACETS	0.201	0.169	0.236	0.201	0.169	0.236	SUBCLONAL	1	TRUE	0	0.50356067339691	1		568	711	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217330	11217330	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	133	560	0	ENST00000361445.4:c.4348T>G	p.Tyr1450Asp	p.Y1450D	ENST00000361445	NM_004958.3	1450	Tat/Gat	30/58	0.492655962741728	1	FACETS	0.731	0.667	0.797	0.731	0.667	0.797	SUBCLONAL	1	TRUE	0	0.50356067339691	1		560	541	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910883	114910883	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1477809102	NA	P-0030293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	185	484	1	ENST00000543371.1:c.1001+1G>A		p.X334_splice	ENST00000543371	NM_001198531.1	334			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.50356067339691	2		485	625	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602404	10602404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1432914621	NA	P-0030293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	224	684	0	ENST00000171111.5:c.1174G>A	p.Ala392Thr	p.A392T	ENST00000171111	NM_203500.1	392	Gcc/Acc	3/6	1	2	FACETS	0.917	0.854	0.982	0.917	0.854	0.982	CLONAL	1	TRUE	1	0.50356067339691	2		684	970	SUCCESS
APC	324	MSKCC	GRCh37	5	112174265	112174275	+	frameshift_variant	Frame_Shift_Del	DEL	AGTAAGTTTTG	AGTAAGTTTTG	-	novel	NA	P-0030293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	149	485	0	ENST00000257430.4:c.2974_2984del	p.Ser992GlnfsTer12	p.S992Qfs*12	ENST00000257430	NM_000038.5	992	AGTAAGTTTTGc/c	16/16	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.50356067339691	2		485	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0030526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	336	675	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.573230161645805	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.573230161645805	1		675	755	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0030526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	71	451	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.440029872007166	1	FACETS	0.39	0.341	0.442	0.39	0.341	0.442	SUBCLONAL	1	TRUE	0	0.573230161645805	1		451	453	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	83	559	0	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	0.440029872007166	1	FACETS	0.401	0.355	0.451	0.401	0.355	0.451	SUBCLONAL	1	TRUE	0	0.573230161645805	1		559	515	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120139	70120140	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CG	novel	NA	P-0030526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	82	228	0	ENST00000245479.2:c.1143_1144dup	p.Leu382ArgfsTer2	p.L382Rfs*2	ENST00000245479	NM_000346.3	381	acg/aCGcg	3/3	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.573230161645805	2		228	271	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588868	69588868	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	132	588	0	ENST00000168712.1:c.368G>A	p.Arg123Gln	p.R123Q	ENST00000168712	NM_002007.2	123	cGg/cAg	2/3	0.440029872007166	1	FACETS	0.505	0.46	0.553	0.505	0.46	0.553	SUBCLONAL	1	TRUE	0	0.573230161645805	1		588	650	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031634	36031634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750108303	NA	P-0030526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	116	689	1	ENST00000358208.4:c.1463C>T	p.Pro488Leu	p.P488L	ENST00000358208		488	cCg/cTg	12/12	0.312218126731366	3	FACETS	0.442	0.397	0.49	0.221	0.198	0.245	INDETERMINATE	1	TRUE	1	0.573230161645805	3		690	1178	SUCCESS
AR	367	MSKCC	GRCh37	X	66863201	66863201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057521121	NA	P-0030526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	91	503	0	ENST00000374690.3:c.1720G>A	p.Ala574Thr	p.A574T	ENST00000374690	NM_000044.3	574	Gct/Act	2/8	0.512451616782821	1	FACETS	0.378	0.336	0.423	0.378	0.336	0.423	SUBCLONAL	1	TRUE	0	0.573230161645805	1		503	599	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0030702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	289	526	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.366156894380425	3	FACETS	0.844	0.793	0.895	0.844	0.793	0.895	CLONAL	2	TRUE	1	0.366156894380425	3		526	1107	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381513	81381514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0030702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	61	430	0	ENST00000222390.5:c.547dup	p.Glu183GlyfsTer20	p.E183Gfs*20	ENST00000222390	NM_000601.4	183	gaa/gGaa	5/18	0.123023091330778	3	FACETS	0.564	0.486	0.649			1	INDETERMINATE	1	TRUE	NA	0.366156894380425	3		430	699	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0031083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	28	364	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.681	0.543	0.839	0.681	0.543	0.839	SUBCLONAL	1	TRUE	1	0.16	2		364	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs786202525	NA	P-0031083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	36	514	0	ENST00000269305.4:c.532del	p.His178ThrfsTer69	p.H178Tfs*69	ENST00000269305	NM_001126112.2	178	Cac/ac	5/11	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.16	2		514	412	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509060	106509060	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	25	433	0	ENST00000359195.3:c.1054G>A	p.Val352Met	p.V352M	ENST00000359195	NM_002649.2	352	Gtg/Atg	2/11	1	2	FACETS	0.654	0.514	0.815	0.654	0.514	0.815	SUBCLONAL	1	TRUE	1	0.16	2		433	478	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661671	227661671	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369611716	NA	P-0031083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	23	402	0	ENST00000305123.5:c.1784G>A	p.Arg595Gln	p.R595Q	ENST00000305123	NM_005544.2	595	cGg/cAg	1/2	1	2	FACETS	0.685	0.533	0.861	0.685	0.533	0.861	SUBCLONAL	1	TRUE	1	0.16	2		402	420	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440764	56440764	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	26	346	0	ENST00000407977.2:c.454C>T	p.Gln152Ter	p.Q152*	ENST00000407977		152	Cag/Tag	5/10	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.16	2		346	276	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591855	48591855	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0031083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	28	326	0	ENST00000342988.3:c.1018A>T	p.Lys340Ter	p.K340*	ENST00000342988	NM_005359.5	340	Aag/Tag	9/12	1	2	FACETS	0.888	0.71	1	0.888	0.71	1	CLONAL	1	TRUE	1	0.16	2		326	394	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974691	21974691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1563892516	NA	P-0031083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	23	309	0	ENST00000304494.5:c.136C>T	p.Arg46Trp	p.R46W	ENST00000304494	NM_000077.4	46	Cgg/Tgg	1/3	1	2	FACETS	0.94	0.733	1	0.94	0.733	1	CLONAL	1	TRUE	1	0.16	2		309	306	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426151	47426151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	31	581	0	ENST00000377045.4:c.671C>T	p.Thr224Met	p.T224M	ENST00000377045	NM_001654.4	224	aCg/aTg	7/16	1	2	FACETS	0.773	0.625	0.943	0.773	0.625	0.943	CLONAL	1	TRUE	1	0.16	2		581	501	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435155	56435155	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	115	687	0	ENST00000407977.2:c.1982C>T	p.Ser661Phe	p.S661F	ENST00000407977		661	tCc/tTc	9/10	0.294483144402311	3	FACETS	0.525	0.472	0.581			1	INDETERMINATE	1	TRUE	NA	0.581957618441353	3		687	972	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508741	29508741	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567826110	NA	P-0031357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	283	548	0	ENST00000356175.3:c.668G>A	p.Trp223Ter	p.W223*	ENST00000356175	NM_000267.3	223	tGg/tAg	7/57	0.532214004240775	2	FACETS	0.896	0.852	0.939	0.896	0.852	0.939	CLONAL	2	TRUE	0	0.581957618441353	2		548	543	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858570	57858570	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	492	637	0	ENST00000228682.2:c.308C>A	p.Pro103His	p.P103H	ENST00000228682	NM_005269.2	103	cCc/cAc	4/12	0.581957618441353	2	FACETS	0.996	0.961	1	0.996	0.961	1	CLONAL	2	TRUE	0	0.581957618441353	2		637	849	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233736	133233736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	284	391	0	ENST00000320574.5:c.3568G>A	p.Glu1190Lys	p.E1190K	ENST00000320574	NM_006231.2	1190	Gag/Aag	29/49	0.581957618441353	2	FACETS	0.992	0.946	1	0.992	0.946	1	CLONAL	2	TRUE	0	0.581957618441353	2		391	492	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233839	133233839	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1449239461	NA	P-0031357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	346	478	1	ENST00000320574.5:c.3465G>T	p.Lys1155Asn	p.K1155N	ENST00000320574	NM_006231.2	1155	aaG/aaT	29/49	0.581957618441353	2	FACETS	0.975	0.933	1	0.975	0.933	1	CLONAL	2	TRUE	0	0.581957618441353	2		479	610	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133234009	133234009	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	338	514	0	ENST00000320574.5:c.3385G>A	p.Asp1129Asn	p.D1129N	ENST00000320574	NM_006231.2	1129	Gat/Aat	28/49	0.581957618441353	2	FACETS	0.944	0.903	0.985	0.944	0.903	0.985	CLONAL	2	TRUE	0	0.581957618441353	2		514	615	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037880	49037880	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	125	375	0	ENST00000267163.4:c.2120C>G	p.Ser707Cys	p.S707C	ENST00000267163	NM_000321.2	707	tCc/tGc	21/27	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.581957618441353	NA		375	363	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732891	74732891	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	60	162	0	ENST00000359995.5:c.352C>G	p.Arg118Gly	p.R118G	ENST00000359995	NM_001195427.1	118	Cgg/Ggg	1/3	0.581957618441353	3	FACETS	0.944	0.82	1	0.315	0.273	0.359	CLONAL	1	TRUE	0	0.581957618441353	3		162	282	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56411677	56411677	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	288	458	0	ENST00000348428.3:c.1861A>C	p.Lys621Gln	p.K621Q	ENST00000348428	NM_006785.3	621	Aaa/Caa	15/17	0.556534384007975	2	FACETS	0.934	0.889	0.978	0.934	0.889	0.978	CLONAL	2	TRUE	0	0.581957618441353	2		458	530	SUCCESS
APC	324	MSKCC	GRCh37	5	112173835	112173835	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs764867930	NA	P-0031357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	179	354	1	ENST00000257430.4:c.2544A>T	p.Lys848Asn	p.K848N	ENST00000257430	NM_000038.5	848	aaA/aaT	16/16	0.302464826129045	2	FACETS	1	0.988	1	0.66	0.614	0.706	INDETERMINATE	1	TRUE	0	0.581957618441353	2		355	466	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120834	94120835	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTG	novel	NA	P-0031357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	235	539	0	ENST00000369303.4:c.214_216dup	p.Gln72dup	p.Q72dup	ENST00000369303	NM_004440.3	72	-/CAG	3/17	0.532214004240775	2	FACETS	0.795	0.75	0.84	0.795	0.75	0.84	SUBCLONAL	2	TRUE	0	0.581957618441353	2		539	508	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0031621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	129	368	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.436528891568261	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	0	0.436528891568261	2		368	295	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263213	115263213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	121	496	1	ENST00000438362.2:c.2137G>A	p.Ala713Thr	p.A713T	ENST00000438362	NM_001242891.1	713	Gct/Act	17/20	0.262038199981129	4	FACETS	1	0.981	1	0.338	0.306	0.372	CLONAL	1	TRUE	0	0.436528891568261	4		497	589	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176153806	176153806	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	50	312	0	ENST00000367669.3:c.430G>C	p.Glu144Gln	p.E144Q	ENST00000367669	NM_022457.5	144	Gaa/Caa	2/20	1	2	FACETS	0.672	0.572	0.78	0.672	0.572	0.78	SUBCLONAL	1	TRUE	1	0.436528891568261	2		312	341	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099299	193099354	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTAGACTGAAAATATTCCTGTGGTTAGAAGACCTGATCGAAAAGATCTACTTGGA	TTTAGACTGAAAATATTCCTGTGGTTAGAAGACCTGATCGAAAAGATCTACTTGGA	GGAAATACAAATTCTCTTCCCTCTAATCAT	novel	NA	P-0031621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	35	416	2	ENST00000367435.3:c.238-5_288delinsGGAAATACAAATTCTCTTCCCTCTAATCAT		p.X80_splice	ENST00000367435	NM_024529.4	80		3/17	1	2	FACETS	0.54	0.444	0.647	0.54	0.444	0.647	SUBCLONAL	1	TRUE	1	0.436528891568261	2		418	297	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711241	114711241	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0031621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	34	243	0	ENST00000543371.1:c.257-1G>C		p.X86_splice	ENST00000543371	NM_001198531.1	86			0.206643666116882	3	FACETS	0.756	0.621	0.906	0.252	0.207	0.302	INDETERMINATE	1	TRUE	0	0.436528891568261	3		243	251	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343868	118343868	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	67	422	1	ENST00000534358.1:c.1994C>T	p.Ser665Phe	p.S665F	ENST00000534358	NM_005933.3	665	tCt/tTt	3/36	0.170760313793758	0	FACETS	0.526	0.46	0.596			1	INDETERMINATE	1	TRUE	0	0.436528891568261	0		423	329	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712767	43712767	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	88	590	0	ENST00000382044.4:c.4417C>T	p.Gln1473Ter	p.Q1473*	ENST00000382044	NM_001141980.1	1473	Cag/Tag	21/28	0.436528891568261	2	FACETS	0.828	0.736	0.925	0.414	0.368	0.463	CLONAL	1	TRUE	0	0.436528891568261	2		590	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0031621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	215	427	1	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.436528891568261	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.436528891568261	2		428	425	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266745	18266745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754693011	NA	P-0031621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	68	404	0	ENST00000222254.8:c.56G>A	p.Arg19Gln	p.R19Q	ENST00000222254	NM_005027.3	19	cGg/cAg	2/16	0.436528891568261	4	FACETS	0.673	0.585	0.768			1	SUBCLONAL	1	TRUE	NA	0.436528891568261	4		404	665	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258560	19258560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372543417	NA	P-0031621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	76	557	2	ENST00000162023.5:c.340C>T	p.Arg114Trp	p.R114W	ENST00000162023		114	Cgg/Tgg	8/13	0.436528891568261	4	FACETS	0.52	0.455	0.591			1	SUBCLONAL	1	TRUE	NA	0.436528891568261	4		559	962	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035106	30035106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	45	384	2	ENST00000338641.4:c.268G>A	p.Glu90Lys	p.E90K	ENST00000338641	NM_000268.3	90	Gaa/Aaa	3/16	0.436528891568261	3	FACETS	0.528	0.443	0.621	0.264	0.221	0.311	SUBCLONAL	1	TRUE	1	0.436528891568261	3		386	476	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665360	138665360	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906920	NA	P-0031621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	66	500	0	ENST00000330315.3:c.205G>A	p.Glu69Lys	p.E69K	ENST00000330315	NM_023067.3	69	Gag/Aag	1/1	0.436528891568261	2	FACETS	0.686	0.597	0.781	0.343	0.298	0.391	SUBCLONAL	1	TRUE	0	0.436528891568261	2		500	441	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540874	187540874	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs562612394	NA	P-0031621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	51	351	2	ENST00000441802.2:c.6866C>T	p.Ala2289Val	p.A2289V	ENST00000441802	NM_005245.3	2289	gCg/gTg	10/27	0.206643666116882	3	FACETS	0.85	0.726	0.984	0.283	0.242	0.328	INDETERMINATE	1	TRUE	0	0.436528891568261	3		353	335	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041083	112041083	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	48	366	2	ENST00000368678.4:c.172G>A	p.Gly58Ser	p.G58S	ENST00000368678		58	Ggc/Agc	3/13	0.166605649875722	2	FACETS	0.709	0.603	0.825	0.355	0.301	0.413	INDETERMINATE	1	TRUE	0	0.436528891568261	2		368	310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0031660-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	19	571	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.392	0.296	0.507	0.392	0.296	0.507	SUBCLONAL	1	TRUE	1	0.13	2		571	745	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0032013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	19	291	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.23708209744432	3	FACETS	0.719	0.547	0.92	0.359	0.273	0.46	CLONAL	1	TRUE	1	0.252195205715096	3		291	236	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0032013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	82	478	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.886	0.787	0.991	1	0.983	1	CLONAL	2	TRUE	1	0.252195205715096	2		478	367	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	78	357	0	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	0.23708209744432	3	FACETS	0.769	0.678	0.866	0.769	0.678	0.866	SUBCLONAL	2	TRUE	1	0.252195205715096	3		357	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0032013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	288	593	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.252195205715096	2	FACETS	0.874	0.824	0.925	1	0.992	1	CLONAL	3	TRUE	0	0.252195205715096	2		593	871	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2193766	2193766	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	69	526	1	ENST00000398665.3:c.572C>T	p.Pro191Leu	p.P191L	ENST00000398665	NM_032482.2	191	cCg/cTg	6/28	1	2	FACETS	0.805	0.7	0.918	0.805	0.7	0.918	CLONAL	1	TRUE	1	0.252195205715096	2		527	680	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919312	178919313	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0032013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	18	218	0	ENST00000263967.3:c.799_800del	p.Leu267GlufsTer4	p.L267Efs*4	ENST00000263967	NM_006218.2	266	cCT/c	4/21	0.23708209744432	3	FACETS	0.765	0.578	0.985	0.383	0.289	0.493	CLONAL	1	TRUE	1	0.252195205715096	3		218	210	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	158	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.916	0.841	0.994	0.916	0.841	0.994	CLONAL	1	TRUE	1	0.464917745676374	2		502	742	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0032020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	422	753	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.461030255778949	2	FACETS	0.916	0.876	0.956	0.916	0.876	0.956	CLONAL	2	TRUE	0	0.464917745676374	2		753	991	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0032020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	98	347	0	ENST00000262160.6:c.1391C>G	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tGa	11/11	0.414858090192588	1	FACETS	0.828	0.744	0.915	0.828	0.744	0.915	CLONAL	1	TRUE	0	0.464917745676374	1		347	391	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223251	5223251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199604489	NA	P-0032020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	184	615	0	ENST00000357368.4:c.2552G>A	p.Arg851His	p.R851H	ENST00000357368	NM_002850.3	851	cGc/cAc	18/38	0.241419990941262	1	FACETS	0.8	0.741	0.862	0.8	0.741	0.862	INDETERMINATE	1	TRUE	0	0.464917745676374	1		615	759	SUCCESS
APC	324	MSKCC	GRCh37	5	112175530	112175530	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	70	330	0	ENST00000257430.4:c.4240del	p.Val1414Ter	p.V1414*	ENST00000257430	NM_000038.5	1413	atG/at	16/16	1	2	FACETS	0.692	0.606	0.785	0.692	0.606	0.785	SUBCLONAL	1	TRUE	1	0.464917745676374	2		330	435	SUCCESS
APC	324	MSKCC	GRCh37	5	112173607	112173607	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	86	324	13	ENST00000257430.4:c.2319del	p.Phe773LeufsTer4	p.F773Lfs*4	ENST00000257430	NM_000038.5	772	acT/ac	16/16	1	2	FACETS	0.916	0.815	1	0.916	0.815	1	CLONAL	1	TRUE	1	0.464917745676374	2		337	404	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457304	67457304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223765	NA	P-0032020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	272	590	1	ENST00000327367.4:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000327367	NM_005902.3	93	cGa/cAa	2/9	0.464917745676374	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.464917745676374	1		591	689	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106869	27106871	+	frameshift_variant	Frame_Shift_Del	DEL	CCC	CCC	AG	novel	NA	P-0032020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	164	486	2	ENST00000324856.7:c.6480_6482delinsAG	p.Asn2160LysfsTer40	p.N2160Kfs*40	ENST00000324856	NM_006015.4	2160	aaCCCg/aaAGg	20/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.464917745676374	2		488	652	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983018	201983019	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0032020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	204	742	0	ENST00000359651.3:c.869_870dup	p.Gly291ArgfsTer4	p.G291Rfs*4	ENST00000359651		289	-/GA	7/8	1	2	FACETS	0.914	0.848	0.983	0.914	0.848	0.983	CLONAL	1	TRUE	1	0.464917745676374	2		742	960	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870825	12870825	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	13	133	0	ENST00000228872.4:c.52G>T	p.Ala18Ser	p.A18S	ENST00000228872	NM_004064.3	18	Gcc/Tcc	1/3	1	2	FACETS	0.245	0.175	0.331	0.245	0.175	0.331	SUBCLONAL	1	TRUE	1	0.464917745676374	2		133	228	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119806	70119806	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	346	560	0	ENST00000245479.2:c.809del	p.Phe270SerfsTer9	p.F270Sfs*9	ENST00000245479	NM_000346.3	270	Ttc/tc	3/3	0.461030255778949	2	FACETS	0.933	0.888	0.978	0.933	0.888	0.978	CLONAL	2	TRUE	0	0.464917745676374	2		560	798	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368200	45368200	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	novel	NA	P-0032020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	91	363	0	ENST00000262160.6:c.1402T>C	p.Ter468GlnextTer8	p.*468Qext*8	ENST00000262160	NM_005901.5	468	Taa/Caa	11/11	0.414858090192588	1	FACETS	0.821	0.735	0.911	0.821	0.735	0.911	CLONAL	1	TRUE	0	0.464917745676374	1		363	366	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249382	153249382	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	143	510	0	ENST00000281708.4:c.1396T>C	p.Cys466Arg	p.C466R	ENST00000281708	NM_033632.3	466	Tgt/Cgt	9/12	1	2	FACETS	0.836	0.763	0.912	0.836	0.763	0.912	CLONAL	1	TRUE	1	0.464917745676374	2		510	736	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	349	272	0				ENST00000310581	NM_198253.2	-/1132			0.914519483945067	4	FACETS	0.94	0.906	0.973	0.94	0.906	0.973	CLONAL	3	TRUE	1	0.953098367163032	4		272	507	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555604	21555604	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1231018689	NA	P-0032023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	234	588	0	ENST00000382592.4:c.2665+1G>T		p.X889_splice	ENST00000382592	NM_014572.2	889			0.936536919056745	3	FACETS	0.856	0.8	0.913	0.428	0.4	0.457	CLONAL	1	TRUE	1	0.953098367163032	3		588	847	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577538	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCTCC	GGCCTCC	-	novel	NA	P-0032023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	746	745	0	ENST00000269305.4:c.743_749del	p.Arg248ProfsTer95	p.R248Pfs*95	ENST00000269305	NM_001126112.2	248	cGGAGGCCc/cc	7/11	0.953098367163032	2	FACETS	0.981	0.969	0.992	0.981	0.969	0.992	CLONAL	2	TRUE	0	0.953098367163032	2		745	798	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255143	16255143	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	197	350	0	ENST00000375759.3:c.2408A>G	p.Glu803Gly	p.E803G	ENST00000375759	NM_015001.2	803	gAg/gGg	11/15	0.809303354208816	2	FACETS	0.951	0.888	1	0.475	0.444	0.507	CLONAL	1	TRUE	0	0.809303354208816	2		350	512	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279693	18279693	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs751033999	NA	P-0032041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	261	524	0	ENST00000222254.8:c.1966G>C	p.Ala656Pro	p.A656P	ENST00000222254	NM_005027.3	656	Gcc/Ccc	15/16	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.809303354208816	2		524	643	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176055021	176055021	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	135	510	0	ENST00000367669.3:c.1032G>T	p.Lys344Asn	p.K344N	ENST00000367669	NM_022457.5	344	aaG/aaT	10/20	0.447123053310186	1	FACETS	0.393	0.359	0.429	0.393	0.359	0.429	INDETERMINATE	1	TRUE	0	0.785952774777513	1		510	530	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115763	8115836	+	frameshift_variant	Frame_Shift_Del	DEL	GCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAGAACAGCTCGTTTAACCCGGCC	GCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAGAACAGCTCGTTTAACCCGGCC	-	novel	NA	P-0032047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	196	510	0	ENST00000346208.3:c.1111_1184del	p.Lys371ProfsTer111	p.K371Pfs*111	ENST00000346208		370	aGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAGAACAGCTCGTTTAACCCGGCC/a	6/6	1	2	FACETS	0.778	0.724	0.834	0.778	0.724	0.834	SUBCLONAL	1	TRUE	1	0.785952774777513	2		510	641	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609096	43609096	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs76262710	NA	P-0032047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	1873	831	0	ENST00000355710.3:c.1852T>G	p.Cys618Gly	p.C618G	ENST00000355710	NM_020975.4	618	Tgc/Ggc	10/20	0.579478146201811	6	FACETS	0.96	0.945	0.973			1	CLONAL	5	TRUE	NA	0.785952774777513	6		831	2555	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7163211	7163211	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0032047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	138	444	0	ENST00000302850.5:c.1862-1G>T		p.X621_splice	ENST00000302850	NM_000208.2	621			1	2	FACETS	0.484	0.441	0.53	0.484	0.441	0.53	SUBCLONAL	1	TRUE	1	0.785952774777513	2		444	725	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164627	36164627	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	130	435	0	ENST00000300305.3:c.1248del	p.Ser417ProfsTer177	p.S417Pfs*177	ENST00000300305		416	ttC/tt	8/8	0.785952774777513	1	FACETS	0.507	0.464	0.551	0.507	0.464	0.551	SUBCLONAL	1	TRUE	0	0.785952774777513	1		435	396	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0032126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	58	417	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.336	0.288	0.389	0.336	0.288	0.389	SUBCLONAL	1	TRUE	1	0.413300436322644	2		417	835	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000307	42000307	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	38	635	0	ENST00000219905.7:c.2326G>T	p.Gly776Ter	p.G776*	ENST00000219905	NM_001164273.1	776	Gga/Tga	7/24	1	2	FACETS	0.262	0.216	0.314	0.262	0.216	0.314	SUBCLONAL	1	TRUE	1	0.413300436322644	2		635	701	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220673	1220673	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	61	876	0	ENST00000326873.7:c.692del	p.Phe231SerfsTer56	p.F231Sfs*56	ENST00000326873	NM_000455.4	231	Ttc/tc	5/10	1	2	FACETS	0.305	0.262	0.352	0.305	0.262	0.352	SUBCLONAL	1	TRUE	1	0.413300436322644	2		876	967	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11114073	11114073	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	62	584	0	ENST00000358026.2:c.2001+1del		p.E667fs	ENST00000358026	NM_001128849.1	667	gaG/ga	13/36	1	2	FACETS	0.434	0.374	0.499	0.434	0.374	0.499	SUBCLONAL	1	TRUE	1	0.413300436322644	2		584	692	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623152	52623152	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	67	726	1	ENST00000394830.3:c.2899G>T	p.Glu967Ter	p.E967*	ENST00000394830	NM_018313.4	967	Gaa/Taa	19/30	1	2	FACETS	0.369	0.32	0.423	0.369	0.32	0.423	SUBCLONAL	1	TRUE	1	0.413300436322644	2		727	879	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280394	1280394	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs776763536	NA	P-0032126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	67	784	0	ENST00000310581.5:c.1829G>T	p.Arg610Leu	p.R610L	ENST00000310581	NM_198253.2	610	cGg/cTg	4/16	1	2	FACETS	0.352	0.305	0.403	0.352	0.305	0.403	SUBCLONAL	1	TRUE	1	0.413300436322644	2		784	922	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211050	55211050	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs17289589	NA	P-0032126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	51	680	0	ENST00000275493.2:c.293G>T	p.Arg98Leu	p.R98L	ENST00000275493	NM_005228.3	98	cGa/cTa	3/28	1	2	FACETS	0.293	0.248	0.342	0.293	0.248	0.342	SUBCLONAL	1	TRUE	1	0.413300436322644	2		680	843	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041045	47041046	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	TT	novel	NA	P-0032126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	57	799	2	ENST00000377604.3:c.1575_1575+1delinsTT		p.X525_splice	ENST00000377604	NM_001204468.1	525		14/24	1	2	FACETS	0.356	0.304	0.412	0.356	0.304	0.412	SUBCLONAL	1	TRUE	1	0.413300436322644	2		801	775	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940008	76940008	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs797044865	NA	P-0032171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	88	669	0	ENST00000373344.5:c.740A>G	p.Asn247Ser	p.N247S	ENST00000373344	NM_000489.3	247	aAc/aGc	9/35	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		669	723	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120239	70120239	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772647517	NA	P-0032171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	61	835	1	ENST00000245479.2:c.1241C>T	p.Ser414Leu	p.S414L	ENST00000245479	NM_000346.3	414	tCg/tTg	3/3	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		836	814	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156713	20156713	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	75	627	2	ENST00000379607.5:c.44G>T	p.Gly15Val	p.G15V	ENST00000379607	NM_001412.3	15	gGt/gTt	2/7	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		629	715	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032313-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	54	272	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		272	341	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0032378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	169	660	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.356534033875628	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.356534033875628	1		661	629	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729106	66729106	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	123	487	0	ENST00000307102.5:c.314C>G	p.Pro105Arg	p.P105R	ENST00000307102	NM_002755.3	105	cCc/cGc	3/11	0.356534033875628	3	FACETS	1	0.955	1	0.365	0.33	0.402	CLONAL	1	TRUE	0	0.356534033875628	3		487	743	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42788883	42788883	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs918165496	NA	P-0032378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	95	362	0	ENST00000575354.2:c.27G>T	p.Met9Ile	p.M9I	ENST00000575354	NM_015125.3	9	atG/atT	1/20	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.356534033875628	2		362	498	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727441	66727441	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519728	NA	P-0032387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	108	350	0	ENST00000307102.5:c.157T>C	p.Phe53Leu	p.F53L	ENST00000307102	NM_002755.3	53	Ttt/Ctt	2/11	1	2	FACETS	0.8	0.721	0.883	0.8	0.721	0.883	SUBCLONAL	1	TRUE	1	0.528434193410032	2		350	511	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145662	11145662	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770839933	NA	P-0032387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	218	479	0	ENST00000358026.2:c.4024G>A	p.Glu1342Lys	p.E1342K	ENST00000358026	NM_001128849.1	1342	Gag/Aag	29/36	0.528434193410032	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.528434193410032	1		479	590	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843699	156843699	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	334	653	0	ENST00000524377.1:c.1125G>C	p.Met375Ile	p.M375I	ENST00000524377	NM_002529.3	375	atG/atC	8/17	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.528434193410032	2		653	1194	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488220	56488220	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	176	383	1	ENST00000267101.3:c.1739G>T	p.Arg580Leu	p.R580L	ENST00000267101	NM_001982.3	580	cGa/cTa	15/28	1	2	FACETS	0.97	0.896	1	0.97	0.896	1	CLONAL	1	TRUE	1	0.528434193410032	2		384	687	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106676	2106676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45517122	NA	P-0032387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	270	594	0	ENST00000219476.3:c.680G>A	p.Cys227Tyr	p.C227Y	ENST00000219476	NM_000548.3	227	tGc/tAc	8/42	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.528434193410032	2		594	912	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600448	10600448	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	102	542	0	ENST00000171111.5:c.1407T>A	p.Asn469Lys	p.N469K	ENST00000171111	NM_203500.1	469	aaT/aaA	4/6	0.528434193410032	1	FACETS	0.422	0.378	0.469	0.422	0.378	0.469	SUBCLONAL	1	TRUE	0	0.528434193410032	1		542	673	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133803	55133804	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0032387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	141	310	0	ENST00000257290.5:c.1017dup	p.Arg340AlafsTer19	p.R340Afs*19	ENST00000257290	NM_006206.4	339	gtg/gtGg	7/23	0.528434193410032	1	FACETS	0.894	0.822	0.969	0.894	0.822	0.969	CLONAL	1	TRUE	0	0.528434193410032	1		310	439	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444424	50444424	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	141	274	0	ENST00000331340.3:c.354G>C	p.Lys118Asn	p.K118N	ENST00000331340	NM_006060.4	118	aaG/aaC	4/8	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.528434193410032	2		274	506	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737166	145737166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1220462752	NA	P-0032387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1474	217	464	0	ENST00000428558.2:c.3400G>A	p.Asp1134Asn	p.D1134N	ENST00000428558	NM_004260.3	1134	Gat/Aat	21/22	0.528434193410032	6	FACETS	0.999	0.926	1			1	CLONAL	1	TRUE	NA	0.528434193410032	6		464	1691	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410145	63410145	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	228	550	0	ENST00000330258.3:c.3022C>A	p.Pro1008Thr	p.P1008T	ENST00000330258	NM_152424.3	1008	Cca/Aca	2/2	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.528434193410032	2		550	807	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920402	114920402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs927089403	NA	P-0032391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	80	552	0	ENST00000543371.1:c.1343G>A	p.Arg448Gln	p.R448Q	ENST00000543371	NM_001198531.1	448	cGg/cAg	13/14	1	2	FACETS	0.661	0.582	0.746	0.661	0.582	0.746	SUBCLONAL	1	TRUE	1	0.38	2		552	637	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0032391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	90	478	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	NA	3	FACETS	0.782	0.694	0.876	0.391	0.347	0.438	INDETERMINATE	1	TRUE	1	0.38	3		478	721	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0032391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	25	352	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.312	0.245	0.389	0.312	0.245	0.389	SUBCLONAL	1	TRUE	1	0.38	2		352	422	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497347	149497347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140261309	NA	P-0032391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	69	580	1	ENST00000261799.4:c.2971C>T	p.Arg991Cys	p.R991C	ENST00000261799	NM_002609.3	991	Cgc/Tgc	22/23	1	2	FACETS	0.716	0.625	0.815	0.716	0.625	0.815	SUBCLONAL	1	TRUE	1	0.38	2		581	507	SUCCESS
APC	324	MSKCC	GRCh37	5	112175608	112175608	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	34	353	0	ENST00000257430.4:c.4317del	p.Pro1440HisfsTer33	p.P1440Hfs*33	ENST00000257430	NM_000038.5	1439	ccT/cc	16/16	0.14349896105933	3	FACETS	0.614	0.502	0.739	0.307	0.251	0.37	INDETERMINATE	1	TRUE	1	0.38	3		353	347	SUCCESS
APC	324	MSKCC	GRCh37	5	112173560	112173560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	40	349	0	ENST00000257430.4:c.2269C>T	p.Gln757Ter	p.Q757*	ENST00000257430	NM_000038.5	757	Caa/Taa	16/16	0.14349896105933	3	FACETS	0.663	0.552	0.786	0.331	0.276	0.393	INDETERMINATE	1	TRUE	1	0.38	3		349	378	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88676898	88676900	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0032391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	73	634	0	ENST00000372037.3:c.683_685del	p.Arg228_Thr229delinsPro	p.R228_T229delinsP	ENST00000372037	NM_004329.2	228	cGAAct/cct	9/13	1	2	FACETS	0.587	0.514	0.667	0.587	0.514	0.667	SUBCLONAL	1	TRUE	1	0.38	2		634	654	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578514	7578550	+	frameshift_variant	Frame_Shift_Del	DEL	TTGGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGGG	TTGGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGGG	-	novel	NA	P-0032391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	42	928	0	ENST00000269305.4:c.380_416del	p.Ser127Ter	p.S127*	ENST00000269305	NM_001126112.2	127	tCCCCTGCCCTCAACAAGATGTTTTGCCAACTGGCCAAg/tg	5/11	1	2	FACETS	0.379	0.315	0.449	0.379	0.315	0.449	SUBCLONAL	1	TRUE	1	0.38	2		928	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578234	7578234	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs786202222	NA	P-0032410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	191	525	0	ENST00000269305.4:c.615T>A	p.Tyr205Ter	p.Y205*	ENST00000269305	NM_001126112.2	205	taT/taA	6/11	0.217611440141464	3	FACETS	1	0.977	1	0.752	0.697	0.809	CLONAL	2	TRUE	0	0.259935703010504	3		525	736	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612665	228612665	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	195	612	0	ENST00000366696.1:c.362T>C	p.Met121Thr	p.M121T	ENST00000366696	NM_003493.2	121	aTg/aCg	1/1	0.246808596497135	3	FACETS	1	0.951	1	0.688	0.638	0.74	CLONAL	2	TRUE	0	0.259935703010504	3		612	821	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578229	7578229	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	186	515	0	ENST00000269305.4:c.620A>G	p.Asp207Gly	p.D207G	ENST00000269305	NM_001126112.2	207	gAt/gGt	6/11	0.217611440141464	3	FACETS	1	0.97	1	0.727	0.674	0.783	CLONAL	2	TRUE	0	0.259935703010504	3		515	741	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267723	198267723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	47	267	0	ENST00000335508.6:c.1756G>A	p.Asp586Asn	p.D586N	ENST00000335508	NM_012433.2	586	Gat/Aat	13/25	1	2	FACETS	0.737	0.622	0.863	0.737	0.622	0.863	SUBCLONAL	1	TRUE	1	0.259935703010504	2		267	491	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43752288	43752288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	53	390	0	ENST00000523873.1:c.689del	p.Pro230ArgfsTer?	p.P230Rfs*?	ENST00000523873		230	Ccg/cg	8/8	1	2	FACETS	0.853	0.728	0.989	0.853	0.728	0.989	CLONAL	1	TRUE	1	0.259935703010504	2		390	478	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0032447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	346	804	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.313748239656851	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	0	0.313748239656851	3		804	813	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959063	2959063	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41497250	NA	P-0032447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	59	658	0	ENST00000396946.4:c.2453G>A	p.Arg818Gln	p.R818Q	ENST00000396946	NM_032415.4	818	cGg/cAg	18/25	0.271153680648085	4	FACETS	0.737	0.634	0.851	0.246	0.211	0.284	SUBCLONAL	1	TRUE	1	0.313748239656851	4		658	670	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945081	31945081	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	252	532	0	ENST00000340398.3:c.20C>A	p.Thr7Asn	p.T7N	ENST00000340398	NM_001013699.2	7	aCt/aAt	1/1	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.764891266966396	2		532	649	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64290015	64290015	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs563964139	NA	P-0032459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	263	449	1	ENST00000370651.3:c.458G>A	p.Arg153His	p.R153H	ENST00000370651	NM_003463.4	153	cGt/cAt	6/6	1	2	FACETS	0.914	0.861	0.969	0.914	0.861	0.969	CLONAL	1	TRUE	1	0.764891266966396	2		450	752	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821640	72821640	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	91	65	0	ENST00000268489.5:c.10535G>T	p.Gly3512Val	p.G3512V	ENST00000268489	NM_006885.3	3512	gGc/gTc	10/10	0.883083210925854	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.883083210925854	1		65	106	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024616	11024616	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	251	513	0	ENST00000327064.4:c.733G>C	p.Val245Leu	p.V245L	ENST00000327064	NM_199141.1	245	Gtg/Ctg	6/16	1	2	FACETS	0.929	0.876	0.983	0.929	0.876	0.983	CLONAL	1	TRUE	1	0.883083210925854	2		513	612	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665399	182665399	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	195	297	0	ENST00000292782.4:c.542A>G	p.Tyr181Cys	p.Y181C	ENST00000292782	NM_020640.2	181	tAc/tGc	5/7	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.883083210925854	2		297	438	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045710	26045710	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	157	277	0	ENST00000540144.1:c.72A>T	p.Lys24Asn	p.K24N	ENST00000540144	NM_003531.2	24	aaA/aaT	1/1	0.839401953369371	3	FACETS	1	0.973	1	0.556	0.514	0.599	CLONAL	1	TRUE	1	0.883083210925854	3		277	461	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0032484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	22	761	2	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.672	0.519	0.852	0.672	0.519	0.852	SUBCLONAL	1	TRUE	1	0.11	2		763	595	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0032484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	17	291	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.761	0.567	0.994	0.761	0.567	0.994	CLONAL	1	TRUE	1	0.11	2		291	406	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981851	201981852	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0032484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	44	748	1	ENST00000359651.3:c.567dup	p.Ser190LeufsTer6	p.S190Lfs*6	ENST00000359651		188	gcc/gCcc	4/8	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.11	2		749	644	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0032530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	338	622	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.465780268897269	2		622	994	SUCCESS
APC	324	MSKCC	GRCh37	5	112175531	112175532	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1554085654	NA	P-0032530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	99	303	0	ENST00000257430.4:c.4241dup	p.Ser1415LysfsTer8	p.S1415Kfs*8	ENST00000257430	NM_000038.5	1414	gta/gTta	16/16	1	2	FACETS	0.771	0.691	0.857	0.771	0.691	0.857	SUBCLONAL	1	TRUE	1	0.465780268897269	2		303	551	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0032530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	256	381	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	0.465780268897269	3	FACETS	0.832	0.782	0.884	0.832	0.782	0.884	CLONAL	2	TRUE	1	0.465780268897269	3		381	814	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268084	153268084	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	134	266	0	ENST00000281708.4:c.724C>T	p.Gln242Ter	p.Q242*	ENST00000281708	NM_033632.3	242	Cag/Tag	4/12	1	2	FACETS	0.997	0.91	1	0.997	0.91	1	CLONAL	1	TRUE	1	0.465780268897269	2		266	577	SUCCESS
APC	324	MSKCC	GRCh37	5	112174405	112174406	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0032530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	81	280	0	ENST00000257430.4:c.3116dup	p.Arg1040LysfsTer8	p.R1040Kfs*8	ENST00000257430	NM_000038.5	1038	-/G	16/16	1	2	FACETS	0.935	0.829	1	0.935	0.829	1	CLONAL	1	TRUE	1	0.465780268897269	2		280	372	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740243	162740243	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	275	375	0	ENST00000367921.3:c.1445A>G	p.Gln482Arg	p.Q482R	ENST00000367921	NM_006182.2	482	cAg/cGg	12/18	0.465780268897269	3	FACETS	0.984	0.928	1	0.984	0.928	1	CLONAL	2	TRUE	1	0.465780268897269	3		375	740	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236086	108236086	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782292	NA	P-0032530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	168	494	0	ENST00000278616.4:c.9022C>G	p.Arg3008Gly	p.R3008G	ENST00000278616	NM_000051.3	3008	Cgt/Ggt	63/63	1	2	FACETS	0.846	0.778	0.916	0.846	0.778	0.916	CLONAL	1	TRUE	1	0.465780268897269	2		494	853	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562213	21562213	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	242	612	2	ENST00000382592.4:c.1706A>T	p.Asp569Val	p.D569V	ENST00000382592	NM_014572.2	569	gAt/gTt	4/8	1	2	FACETS	0.954	0.891	1	0.954	0.891	1	CLONAL	1	TRUE	1	0.465780268897269	2		614	1089	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955557	48955567	+	frameshift_variant	Frame_Shift_Del	DEL	TGGAATCCCTT	TGGAATCCCTT	-	novel	NA	P-0032530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	58	361	0	ENST00000267163.4:c.1673_1683del	p.Met558SerfsTer10	p.M558Sfs*10	ENST00000267163	NM_000321.2	558	aTGGAATCCCTT/a	17/27	0.465780268897269	1	FACETS	0.418	0.36	0.481	0.418	0.36	0.481	SUBCLONAL	1	TRUE	0	0.465780268897269	1		361	457	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0032538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	192	353	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.982	0.914	1	0.982	0.914	1	CLONAL	1	TRUE	1	0.666018505958647	2		353	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0032538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	437	571	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	NA	2	FACETS	1	0.967	1			1	INDETERMINATE	2	TRUE	NA	0.666018505958647	2		571	656	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584560	48584560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	273	523	0	ENST00000342988.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000342988	NM_005359.5	245	Cag/Tag	6/12	0.666018505958647	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.666018505958647	1		523	469	SUCCESS
APC	324	MSKCC	GRCh37	5	112175175	112175175	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	113	276	0	ENST00000257430.4:c.3885del	p.Ala1296GlnfsTer9	p.A1296Qfs*9	ENST00000257430	NM_000038.5	1295	gAa/ga	16/16	1	2	FACETS	0.917	0.833	1	0.917	0.833	1	CLONAL	1	TRUE	1	0.666018505958647	2		276	370	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120502	70120503	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	369	639	0	ENST00000245479.2:c.1505dup	p.Tyr503LeufsTer75	p.Y503Lfs*75	ENST00000245479	NM_000346.3	502	gtc/gTtc	3/3	0.470308110239541	1	FACETS	0.868	0.828	0.909	0.868	0.828	0.909	CLONAL	1	TRUE	0	0.666018505958647	1		639	851	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978935	25978935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	55	432	0	ENST00000435504.4:c.988G>A	p.Glu330Lys	p.E330K	ENST00000435504		330	Gaa/Aaa	10/13	1	2	FACETS	0.533	0.455	0.618	0.533	0.455	0.618	SUBCLONAL	1	TRUE	1	0.309910952181551	2		432	666	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111494	8111495	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTGGAGG	novel	NA	P-0032553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	88	414	0	ENST00000346208.3:c.981_987dup	p.Arg330LeufsTer24	p.R330Lfs*24	ENST00000346208		327	ctc/ctCTGGAGGc	5/6	0.309910952181551	3	FACETS	0.805	0.712	0.904	0.402	0.356	0.452	CLONAL	1	TRUE	1	0.309910952181551	3		414	815	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057945	27057958	+	frameshift_variant	Frame_Shift_Del	DEL	CTCACAGCCACAGG	CTCACAGCCACAGG	-	novel	NA	P-0032553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	123	475	0	ENST00000324856.7:c.1657_1670del	p.Gln553ValfsTer65	p.Q553Vfs*65	ENST00000324856	NM_006015.4	551	taCTCACAGCCACAGGct/tact	3/20	0.309910952181551	2	FACETS	0.951	0.859	1	0.475	0.429	0.524	CLONAL	1	TRUE	0	0.309910952181551	2		475	835	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032567	12032567	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	186	390	0	ENST00000353533.5:c.1003G>T	p.Glu335Ter	p.E335*	ENST00000353533	NM_003010.3	335	Gaa/Taa	9/11	0.301053395203911	3	FACETS	0.923	0.855	0.994	0.615	0.57	0.663	CLONAL	2	TRUE	0	0.309910952181551	3		390	751	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004980	150004980	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	69	478	0	ENST00000253339.5:c.1245del	p.Asn415LysfsTer46	p.N415Kfs*46	ENST00000253339		415	aaT/aa	3/7	0.281116382868401	3	FACETS	0.706	0.615	0.806	0.235	0.204	0.269	SUBCLONAL	1	TRUE	0	0.309910952181551	3		478	728	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0032849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	121	622	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.218743993053244	3	FACETS	0.897	0.816	0.982	0.897	0.816	0.982	CLONAL	3	TRUE	0	0.218743993053244	3		622	456	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0032849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	49	535	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.218743993053244	3	FACETS	0.948	0.803	1	0.474	0.401	0.554	CLONAL	1	TRUE	1	0.218743993053244	3		535	524	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457303	67457303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768713596	NA	P-0032849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	136	615	1	ENST00000327367.4:c.277C>T	p.Arg93Ter	p.R93*	ENST00000327367	NM_005902.3	93	Cga/Tga	2/9	0.218743993053244	3	FACETS	1	0.976	1	0.797	0.728	0.869	CLONAL	2	TRUE	0	0.218743993053244	3		616	577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576865	7576865	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	rs879254077	NA	P-0032849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	121	714	0	ENST00000269305.4:c.981T>G	p.Tyr327Ter	p.Y327*	ENST00000269305	NM_001126112.2	327	taT/taG	9/11	0.174295192533272	2	FACETS	0.934	0.847	1	0.934	0.847	1	CLONAL	2	TRUE	0	0.218743993053244	2		714	592	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	100	485	2	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	0.218743993053244	3	FACETS	0.983	0.881	1	0.983	0.881	1	CLONAL	2	TRUE	1	0.218743993053244	3		487	516	SUCCESS
APC	324	MSKCC	GRCh37	5	112175907	112175907	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0032849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	38	266	0	ENST00000257430.4:c.4616C>G	p.Ser1539Ter	p.S1539*	ENST00000257430	NM_000038.5	1539	tCa/tGa	16/16	NA	2	FACETS	1	0.919	1			1	INDETERMINATE	1	TRUE	NA	0.218743993053244	2		266	292	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711033	114711033	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0032849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	33	149	0	ENST00000543371.1:c.256+1G>C		p.X86_splice	ENST00000543371	NM_001198531.1	86			0.218743993053244	4	FACETS	0.897	0.737	1	0.897	0.737	1	CLONAL	2	TRUE	2	0.218743993053244	4		149	205	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226576454	226576454	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	100	463	0	ENST00000366794.5:c.620A>C	p.Lys207Thr	p.K207T	ENST00000366794	NM_001618.3	207	aAg/aCg	5/23	0.218743993053244	3	FACETS	1	0.907	1	1	0.907	1	CLONAL	2	TRUE	1	0.218743993053244	3		463	501	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679823	88679823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777599584	NA	P-0032849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	83	450	1	ENST00000360948.2:c.640G>A	p.Val214Met	p.V214M	ENST00000360948	NM_001012338.2	214	Gtg/Atg	7/19	0.218743993053244	3	FACETS	1	0.955	1	0.765	0.68	0.854	CLONAL	2	TRUE	0	0.218743993053244	3		451	367	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860747	3860747	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	70	434	0	ENST00000262367.5:c.832C>T	p.Gln278Ter	p.Q278*	ENST00000262367	NM_004380.2	278	Cag/Tag	3/31	0.218743993053244	3	FACETS	0.814	0.712	0.923	0.814	0.712	0.923	CLONAL	2	TRUE	1	0.218743993053244	3		434	436	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663437	67663437	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0032849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	23	212	0	ENST00000264010.4:c.1837+1G>T		p.X613_splice	ENST00000264010	NM_006565.3	613			0.218743993053244	3	FACETS	0.952	0.745	1	0.476	0.372	0.596	CLONAL	1	TRUE	1	0.218743993053244	3		212	245	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981449	55981449	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	59	407	0	ENST00000263923.4:c.488C>A	p.Ala163Glu	p.A163E	ENST00000263923	NM_002253.2	163	gCa/gAa	4/30	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.218743993053244	2		407	410	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345769	152345769	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1433853429	NA	P-0032849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	58	346	0	ENST00000359321.1:c.801A>C	p.Lys267Asn	p.K267N	ENST00000359321	NM_005431.1	267	aaA/aaC	3/3	0.218743993053244	4	FACETS	0.79	0.681	0.908	0.79	0.681	0.908	CLONAL	2	TRUE	2	0.218743993053244	4		346	409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576857	7576857	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032859-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	107	668	0	ENST00000269305.4:c.989T>G	p.Leu330Arg	p.L330R	ENST00000269305	NM_001126112.2	330	cTt/cGt	9/11	0.202527133263851	2	FACETS	1	0.98	1	0.709	0.636	0.787	CLONAL	1	TRUE	0	0.20550614215103	2		668	734	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89335055	89335055	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1213853388	NA	P-0032859-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	41	406	0	ENST00000301030.4:c.7823G>A	p.Arg2608Gln	p.R2608Q	ENST00000301030	NM_001256183.1	2608	cGg/cAg	13/13	1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	1	0.20550614215103	2		406	395	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132776	64132776	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032859-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	51	582	0	ENST00000334205.4:c.910C>A	p.Leu304Ile	p.L304I	ENST00000334205	NM_003942.2	304	Ctc/Atc	9/17	0.173107118080183	2	FACETS	0.729	0.618	0.851	0.364	0.309	0.426	SUBCLONAL	1	TRUE	0	0.20550614215103	2		582	681	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441813	49441813	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032859-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	52	535	0	ENST00000301067.7:c.4171G>C	p.Glu1391Gln	p.E1391Q	ENST00000301067	NM_003482.3	1391	Gag/Cag	14/54	1	2	FACETS	0.775	0.659	0.903	0.775	0.659	0.903	CLONAL	1	TRUE	1	0.20550614215103	2		535	653	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100050	30100050	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369255115	NA	P-0032859-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	86	807	0	ENST00000331968.5:c.1570G>A	p.Val524Ile	p.V524I	ENST00000331968	NM_002742.2	524	Gtt/Att	10/18	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.20550614215103	2		807	771	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106922	11106922	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032859-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	70	771	0	ENST00000358026.2:c.1627G>C	p.Asp543His	p.D543H	ENST00000358026	NM_001128849.1	543	Gac/Cac	10/36	1	2	FACETS	0.881	0.767	1	0.881	0.767	1	CLONAL	1	TRUE	1	0.20550614215103	2		771	773	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004475	150004475	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032859-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	44	652	0	ENST00000253339.5:c.1750C>T	p.Gln584Ter	p.Q584*	ENST00000253339		584	Cag/Tag	3/7	0.161264359003628	1	FACETS	0.547	0.457	0.646	0.547	0.457	0.646	SUBCLONAL	1	TRUE	0	0.20550614215103	1		652	703	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522305	157522305	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0032859-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	83	776	1	ENST00000346085.5:c.4577C>G	p.Ser1526Ter	p.S1526*	ENST00000346085	NM_020732.3	1526	tCa/tGa	18/20	0.161264359003628	1	FACETS	0.847	0.746	0.955	0.847	0.746	0.955	CLONAL	1	TRUE	0	0.20550614215103	1		777	856	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259448	55259448	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032859-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	41	433	0	ENST00000275493.2:c.2506C>G	p.Arg836Gly	p.R836G	ENST00000275493	NM_005228.3	836	Cgc/Ggc	21/28	1	2	FACETS	0.767	0.639	0.911	0.767	0.639	0.911	CLONAL	1	TRUE	1	0.20550614215103	2		433	520	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401047	139401047	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032859-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	158	934	0	ENST00000277541.6:c.3946T>G	p.Cys1316Gly	p.C1316G	ENST00000277541	NM_017617.3	1316	Tgc/Ggc	24/34	1	2	FACETS	0.779	0.713	0.848	1	0.989	1	SUBCLONAL	2	TRUE	1	0.20550614215103	2		934	987	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42057117	42057117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	112	552	0	ENST00000219905.7:c.7778C>T	p.Ser2593Phe	p.S2593F	ENST00000219905	NM_001164273.1	2593	tCt/tTt	23/24	1	2	FACETS	0.945	0.857	1	0.945	0.857	1	CLONAL	1	TRUE	1	0.582177113086073	2		552	407	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874286	155874286	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs868208063	NA	P-0033020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	338	525	0	ENST00000368323.3:c.245T>G	p.Phe82Cys	p.F82C	ENST00000368323	NM_006912.5	82	tTt/tGt	5/6	0.663901033456951	4	FACETS	1	0.992	1			1	CLONAL	3	TRUE	NA	0.663901033456951	4		525	501	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376106	225376106	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	138	694	0	ENST00000264414.4:c.848G>T	p.Gly283Val	p.G283V	ENST00000264414	NM_003590.4	283	gGg/gTg	6/16	0.370675069214135	1	FACETS	0.798	0.736	0.861	0.798	0.736	0.861	INDETERMINATE	1	TRUE	0	0.663901033456951	1		694	348	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597987	43597987	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	117	831	0	ENST00000355710.3:c.535A>T	p.Asn179Tyr	p.N179Y	ENST00000355710	NM_020975.4	179	Aac/Tac	3/20	1	2	FACETS	0.935	0.851	1	0.935	0.851	1	CLONAL	1	TRUE	1	0.663901033456951	2		831	377	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591669	38591669	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	124	644	1	ENST00000299084.4:c.128C>G	p.Thr43Ser	p.T43S	ENST00000299084	NM_152594.2	43	aCt/aGt	2/7	1	2	FACETS	0.98	0.896	1	0.98	0.896	1	CLONAL	1	TRUE	1	0.663901033456951	2		645	381	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602613	10602613	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	122	638	0	ENST00000171111.5:c.965C>G	p.Pro322Arg	p.P322R	ENST00000171111	NM_203500.1	322	cCc/cGc	3/6	0.663901033456951	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.663901033456951	1		638	228	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221250	1221250	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	GT	novel	NA	P-0033020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	153	744	0	ENST00000326873.7:c.773delinsGT	p.Asp258GlyfsTer8	p.D258Gfs*8	ENST00000326873	NM_000455.4	258	gAc/gGTc	6/10	0.663901033456951	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.663901033456951	1		744	279	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727441	66727441	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519728	NA	P-0033021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	124	350	0	ENST00000307102.5:c.157T>C	p.Phe53Leu	p.F53L	ENST00000307102	NM_002755.3	53	Ttt/Ctt	2/11	0.371545109737174	2	FACETS	1	0.951	1	0.537	0.487	0.589	CLONAL	1	TRUE	0	0.371545109737174	2		350	622	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225603	2225603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	152	610	2	ENST00000326181.6:c.1606G>A	p.Gly536Ser	p.G536S	ENST00000326181	NM_032271.2	536	Ggc/Agc	17/21	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.371545109737174	2		612	812	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386428	31386432	+	protein_altering_variant	In_Frame_Del	DEL	CAGTG	CAGTG	AT	novel	NA	P-0033021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	119	571	2	ENST00000328111.2:c.1653_1657delinsAT	p.Ser552_Asp553delinsTyr	p.S552_D553delinsY	ENST00000328111	NM_006892.3	551	acCAGTGac/acATac	15/23	0.315118918200287	3	FACETS	0.854	0.771	0.943			1	CLONAL	1	TRUE	NA	0.371545109737174	3		573	889	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0033326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	680	562	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.569965483207252	3	FACETS	0.978	0.952	1	0.978	0.952	1	CLONAL	3	TRUE	0	0.585792471268994	3		562	1023	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0033326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	417	538	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.434843127497739	4	FACETS	0.943	0.905	0.981			1	CLONAL	3	TRUE	NA	0.585792471268994	4		538	798	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589540	69589540	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1174143141	NA	P-0033326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	57	105	0	ENST00000168712.1:c.313G>A	p.Gly105Ser	p.G105S	ENST00000168712	NM_002007.2	105	Ggc/Agc	1/3	0.585792471268994	3	FACETS	0.88	0.761	1	0.44	0.38	0.504	CLONAL	1	TRUE	1	0.585792471268994	3		105	286	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919556	78919556	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368881284	NA	P-0033326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	134	337	0	ENST00000306801.3:c.3115G>A	p.Ala1039Thr	p.A1039T	ENST00000306801	NM_020761.2	1039	Gcc/Acc	26/34	0.528746737987104	4	FACETS	0.978	0.889	1	0.326	0.296	0.357	CLONAL	1	TRUE	1	0.585792471268994	4		337	742	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468358	120468358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138567855	NA	P-0033326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	255	591	1	ENST00000256646.2:c.4081G>A	p.Ala1361Thr	p.A1361T	ENST00000256646	NM_024408.3	1361	Gcc/Acc	25/34	0.434843127497739	4	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.585792471268994	4		592	1224	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103378	119103378	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	101	347	0	ENST00000264033.4:c.416G>T	p.Arg139Ile	p.R139I	ENST00000264033	NM_005188.3	139	aGa/aTa	2/16	0.585792471268994	3	FACETS	0.856	0.768	0.949	0.428	0.384	0.475	CLONAL	1	TRUE	1	0.585792471268994	3		347	521	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265144	5265144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769916725	NA	P-0033326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	301	848	2	ENST00000357368.4:c.443G>A	p.Arg148Gln	p.R148Q	ENST00000357368	NM_002850.3	148	cGg/cAg	5/38	1	2	FACETS	0.998	0.941	1	0.998	0.941	1	CLONAL	1	TRUE	1	0.585792471268994	2		850	1030	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718761	190718761	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	91	324	0	ENST00000441310.2:c.919G>C	p.Asp307His	p.D307H	ENST00000441310	NM_000534.4	307	Gat/Cat	8/13	0.569965483207252	3	FACETS	0.816	0.728	0.91	0.272	0.242	0.304	CLONAL	1	TRUE	0	0.585792471268994	3		324	492	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974725	21974742	+	inframe_deletion	In_Frame_Del	DEL	CGCCTCCAGCAGCGCCCG	CGCCTCCAGCAGCGCCCG	-	novel	NA	P-0033326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	207	318	0	ENST00000304494.5:c.85_102del	p.Arg29_Ala34del	p.R29_A34del	ENST00000304494	NM_000077.4	29	CGGGCGCTGCTGGAGGCG/-	1/3	0.569280037646913	2	FACETS	0.883	0.833	0.934	0.883	0.833	0.934	CLONAL	2	TRUE	0	0.585792471268994	2		318	400	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974726	21974726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554656344	NA	P-0033326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	20	316	0	ENST00000304494.5:c.101C>T	p.Ala34Val	p.A34V	ENST00000304494	NM_000077.4	34	gCg/gTg	1/3	0.569280037646913	2	FACETS	0.176	0.134	0.226	0.088	0.067	0.113	SUBCLONAL	1	TRUE	0	0.585792471268994	2		316	387	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	120	272	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.326997611772754	2		272	577	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942817	44942817	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	209	328	0	ENST00000377967.4:c.3397C>T	p.Gln1133Ter	p.Q1133*	ENST00000377967	NM_021140.2	1133	Caa/Taa	23/29	1	1	FACETS	0.837	0.781	0.894	1	0.993	1	CLONAL	2	TRUE	0	0.326997611772754	1		328	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579406	7579406	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0033360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	261	826	0	ENST00000269305.4:c.281C>G	p.Ser94Ter	p.S94*	ENST00000269305	NM_001126112.2	94	tCa/tGa	4/11	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.326997611772754	2		826	1085	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0033360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	317	965	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.326997611772754	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.326997611772754	1		965	1229	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2492114	2492114	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	95	764	0	ENST00000355716.4:c.512C>G	p.Ser171Cys	p.S171C	ENST00000355716	NM_003820.2	171	tCt/tGt	5/8	1	2	FACETS	0.514	0.456	0.576	0.514	0.456	0.576	SUBCLONAL	1	TRUE	1	0.326997611772754	2		764	1131	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988533	41988533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	138	483	0	ENST00000219905.7:c.1325C>T	p.Ser442Phe	p.S442F	ENST00000219905	NM_001164273.1	442	tCt/tTt	3/24	0.147489314523866	2	FACETS	1	0.955	1	0.538	0.49	0.589	INDETERMINATE	1	TRUE	0	0.326997611772754	2		483	784	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988785	41988785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770212789	NA	P-0033360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	115	441	0	ENST00000219905.7:c.1577C>T	p.Ser526Leu	p.S526L	ENST00000219905	NM_001164273.1	526	tCa/tTa	3/24	0.147489314523866	2	FACETS	1	0.936	1	0.524	0.473	0.578	INDETERMINATE	1	TRUE	0	0.326997611772754	2		441	671	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786792	3786800	+	inframe_deletion	In_Frame_Del	DEL	GGCCCAGAT	GGCCCAGAT	-	novel	NA	P-0033360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	111	588	0	ENST00000262367.5:c.4411_4419del	p.Ile1471_Ala1473del	p.I1471_A1473del	ENST00000262367	NM_004380.2	1471	ATCTGGGCC/-	27/31	0.295264496473231	1	FACETS	0.766	0.689	0.848	0.766	0.689	0.848	SUBCLONAL	1	TRUE	0	0.326997611772754	1		588	741	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921193	50921193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	193	824	0	ENST00000440232.2:c.3313G>A	p.Glu1105Lys	p.E1105K	ENST00000440232	NM_002691.3	1105	Gag/Aag	27/27	0.277523090435433	1	FACETS	0.841	0.777	0.908	0.841	0.777	0.908	CLONAL	1	TRUE	0	0.326997611772754	1		824	1174	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12632314	12632314	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	159	540	0	ENST00000251849.4:c.1353G>C	p.Gln451His	p.Q451H	ENST00000251849	NM_002880.3	451	caG/caC	12/17	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.326997611772754	2		540	910	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158149	47158150	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0033360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	69	569	0	ENST00000409792.3:c.4549_4550delinsTT	p.Gly1517Leu	p.G1517L	ENST00000409792	NM_014159.6	1517	GGg/TTg	4/21	1	2	FACETS	0.425	0.368	0.486	0.425	0.368	0.486	SUBCLONAL	1	TRUE	1	0.326997611772754	2		569	994	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109319829	109319829	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	85	569	0	ENST00000436639.2:c.859G>C	p.Asp287His	p.D287H	ENST00000436639	NM_014454.2	287	Gat/Cat	5/10	0.295264496473231	1	FACETS	0.505	0.445	0.568	0.505	0.445	0.568	SUBCLONAL	1	TRUE	0	0.326997611772754	1		569	862	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941653	48941653	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0033384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	38	224	0	ENST00000267163.4:c.963C>G	p.Tyr321Ter	p.Y321*	ENST00000267163	NM_000321.2	321	taC/taG	10/27	0.601475925436401	2	FACETS	1	0.962	1	0.735	0.631	0.841	CLONAL	1	TRUE	0	0.601475925436401	2		224	86	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587780070	NA	P-0033384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	278	916	0	ENST00000269305.4:c.535C>G	p.His179Asp	p.H179D	ENST00000269305	NM_001126112.2	179	Cat/Gat	5/11	0.601475925436401	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.601475925436401	2		916	436	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	121	657	0	ENST00000346208.3:c.1220_1221insA	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcAg	6/6	0.276316588877166	6	FACETS	1	0.979	1	0.323	0.292	0.356	INDETERMINATE	1	TRUE	2	0.601475925436401	6		657	686	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110073	115110073	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	223	1145	0	ENST00000257566.3:c.1805del	p.Pro602LeufsTer30	p.P602Lfs*30	ENST00000257566	NM_016569.3	602	cCt/ct	8/8	0.584990067134443	3	FACETS	1	0.984	1	0.583	0.544	0.623	CLONAL	1	TRUE	1	0.601475925436401	3		1145	827	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806242	1806242	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	140	986	0	ENST00000260795.2:c.1261C>T	p.Arg421Ter	p.R421*	ENST00000260795		421	Cga/Tga	8/17	0.285483447604173	1	FACETS	0.796	0.732	0.861	0.796	0.732	0.861	INDETERMINATE	1	TRUE	0	0.601475925436401	1		986	409	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73047240	73047246	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGGAA	GGGGGAA	AG	novel	NA	P-0033384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	59	541	2	ENST00000356692.5:c.47_53delinsAG	p.Arg16LysfsTer29	p.R16Kfs*29	ENST00000356692		16	aGGGGGAAa/aAGa	2/9	0.601475925436401	3	FACETS	0.599	0.517	0.688	0.3	0.258	0.344	SUBCLONAL	1	TRUE	1	0.601475925436401	3		543	426	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	290	272	0				ENST00000310581	NM_198253.2	-/1132			0.164469761310632	4	FACETS	0.96	0.907	1	0.96	0.907	1	INDETERMINATE	2	TRUE	2	0.574244268450982	4		272	828	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0033407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	554	755	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.574244268450982	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.574244268450982	1		755	1028	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262117	10262119	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	novel	NA	P-0033407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	475	761	1	ENST00000340748.4:c.2172_2174del	p.Lys725del	p.K725del	ENST00000340748		724	aaGAAa/aaa	23/40	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.574244268450982	2		762	1172	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025941	1025941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	283	616	0	ENST00000358495.3:c.589G>A	p.Glu197Lys	p.E197K	ENST00000358495	NM_134424.2	197	Gaa/Aaa	8/12	1	2	FACETS	0.913	0.858	0.969	0.913	0.858	0.969	CLONAL	1	TRUE	1	0.574244268450982	2		616	1080	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50788308	50788308	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	82	825	0	ENST00000398568.2:c.886C>G	p.Leu296Val	p.L296V	ENST00000398568	NM_001042412.1	296	Cta/Gta	5/18	0.564089071322844	2	FACETS	0.35	0.308	0.395	0.175	0.154	0.198	SUBCLONAL	1	TRUE	0	0.574244268450982	2		825	817	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	149	812	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.436959095565244	3	FACETS	1	0.947	1	0.525	0.48	0.572	CLONAL	1	TRUE	1	0.436959095565244	3		812	792	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0033563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	298	641	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.423596560671537	2	FACETS	0.929	0.88	0.979	0.929	0.88	0.979	CLONAL	2	TRUE	0	0.436959095565244	2		642	734	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0033563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	194	347	0	ENST00000262160.6:c.1391C>G	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tGa	11/11	0.436959095565244	2	FACETS	0.879	0.821	0.938	0.879	0.821	0.938	CLONAL	2	TRUE	0	0.436959095565244	2		347	505	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750677	128750677	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	306	622	0	ENST00000377970.2:c.214C>A	p.Pro72Thr	p.P72T	ENST00000377970	NM_002467.4	72	Ccc/Acc	2/3	1	2	FACETS	0.778	0.735	0.822	1	0.995	1	SUBCLONAL	2	TRUE	1	0.436959095565244	2		622	900	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051652	30051652	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	61	343	0	ENST00000338641.4:c.586C>G	p.Arg196Gly	p.R196G	ENST00000338641	NM_000268.3	196	Cga/Gga	6/16	1	2	FACETS	0.481	0.414	0.552	0.481	0.414	0.552	SUBCLONAL	1	TRUE	1	0.436959095565244	2		343	581	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	184	272	0				ENST00000310581	NM_198253.2	-/1132			0.39434122380315	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.394777958096943	3		272	532	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	352	555	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.39434122380315	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.394777958096943	3		555	996	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	187	497	1	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.114441564914985	5	FACETS	1	0.944	1	0.681	0.631	0.733	INDETERMINATE	2	TRUE	2	0.394777958096943	5		498	738	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806225	1806225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	216	705	0	ENST00000260795.2:c.1244C>T	p.Ser415Phe	p.S415F	ENST00000260795		415	tCc/tTc	8/17	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.394777958096943	2		705	944	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979280	40979280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	305	501	0	ENST00000373198.4:c.1853G>A	p.Gly618Glu	p.G618E	ENST00000373198	NM_133170.3	618	gGa/gAa	11/32	0.130730181183013	6	FACETS	1	0.991	1	0.831	0.784	0.88	INDETERMINATE	2	TRUE	3	0.394777958096943	6		501	1109	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636727	8636727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159852	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	146	305	0	ENST00000356435.5:c.182G>A	p.Gly61Glu	p.G61E	ENST00000356435		61	gGa/gAa	2/35	0.114441564914985	5	FACETS	1	0.96	1	0.718	0.658	0.779	INDETERMINATE	2	TRUE	2	0.394777958096943	5		305	547	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804298	43804298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760631916	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	339	527	1	ENST00000372470.3:c.298G>A	p.Glu100Lys	p.E100K	ENST00000372470	NM_005373.2	100	Gaa/Aaa	3/12	0.39434122380315	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.394777958096943	3		528	980	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521768	89521768	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	103	257	0	ENST00000336596.2:c.2845G>A	p.Asp949Asn	p.D949N	ENST00000336596	NM_005233.5	949	Gat/Aat	16/17	0.130730181183013	6	FACETS	1	0.966	1	0.774	0.698	0.854	INDETERMINATE	2	TRUE	3	0.394777958096943	6		257	402	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858097	9858097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770546037	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	183	643	0	ENST00000330684.3:c.3304G>A	p.Glu1102Lys	p.E1102K	ENST00000330684	NM_001134407.1	1102	Gag/Aag	13/13	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.394777958096943	2		643	874	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32920978	32920978	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs80358920	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	48	381	0	ENST00000380152.3:c.6952C>T	p.Arg2318Ter	p.R2318*	ENST00000380152		2318	Cga/Tga	13/27	1	2	FACETS	0.637	0.54	0.743	0.637	0.54	0.743	SUBCLONAL	1	TRUE	1	0.394777958096943	2		381	382	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552660	18552660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758604951	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	91	562	0	ENST00000266497.5:c.2071C>T	p.Leu691Phe	p.L691F	ENST00000266497		691	Ctt/Ttt	14/31	1	2	FACETS	0.871	0.776	0.973	0.871	0.776	0.973	CLONAL	1	TRUE	1	0.394777958096943	2		562	529	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120810	115120810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1469975580	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	111	394	2	ENST00000257566.3:c.196G>A	p.Asp66Asn	p.D66N	ENST00000257566	NM_016569.3	66	Gat/Aat	1/8	0.377258724636525	3	FACETS	1	0.961	1	0.567	0.511	0.626	CLONAL	1	TRUE	1	0.394777958096943	3		396	594	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031699	69031699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	95	541	0	ENST00000288368.4:c.3454C>T	p.His1152Tyr	p.H1152Y	ENST00000288368	NM_024870.2	1152	Cat/Tat	28/40	1	2	FACETS	0.866	0.773	0.964	0.866	0.773	0.964	CLONAL	1	TRUE	1	0.394777958096943	2		541	556	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770576	40770576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	226	468	1	ENST00000373198.4:c.2806C>T	p.Arg936Ter	p.R936*	ENST00000373198	NM_133170.3	936	Cga/Tga	19/32	0.130730181183013	6	FACETS	0.841	0.785	0.898	0.841	0.785	0.898	INDETERMINATE	3	TRUE	3	0.394777958096943	6		469	812	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27204924	27204924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	211	396	0	ENST00000380036.4:c.2225G>A	p.Gly742Glu	p.G742E	ENST00000380036	NM_000459.3	742	gGa/gAa	14/23	0.114441564914985	5	FACETS	1	0.987	1	0.833	0.777	0.89	INDETERMINATE	2	TRUE	2	0.394777958096943	5		396	681	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184761	32184761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	150	532	0	ENST00000375023.3:c.1822C>T	p.Pro608Ser	p.P608S	ENST00000375023	NM_004557.3	608	Cca/Tca	11/30	0.130730181183013	6	FACETS	1	0.978	1	0.409	0.373	0.447	INDETERMINATE	1	TRUE	3	0.394777958096943	6		532	1109	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21630868	21630868	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	104	497	0	ENST00000421138.2:c.736C>T	p.Pro246Ser	p.P246S	ENST00000421138		246	Cct/Tct	8/16	1	2	FACETS	0.878	0.788	0.973	0.878	0.788	0.973	CLONAL	1	TRUE	1	0.394777958096943	2		497	600	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198965	67198965	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs529074150	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	109	389	0	ENST00000312629.5:c.436C>T	p.Leu146Phe	p.L146F	ENST00000312629	NM_003952.2	146	Ctc/Ttc	5/15	0.39434122380315		FACETS		0.805	0.992				CLONAL	1	TRUE	1	0.394777958096943	3		389	738	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012423	29012423	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	96	551	0	ENST00000282397.4:c.448G>A	p.Glu150Lys	p.E150K	ENST00000282397	NM_002019.4	150	Gaa/Aaa	4/30	1	2	FACETS	0.803	0.716	0.894	0.803	0.716	0.894	CLONAL	1	TRUE	1	0.394777958096943	2		551	606	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38632018	38632018	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	212	563	1	ENST00000299084.4:c.504T>A	p.Tyr168Ter	p.Y168*	ENST00000299084	NM_152594.2	168	taT/taA	5/7	0.191067644354227	3	FACETS	0.954	0.89	1	0.954	0.89	1	INDETERMINATE	2	TRUE	1	0.394777958096943	3		564	674	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43699598	43699598	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766550469	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	181	569	0	ENST00000382044.4:c.5917G>A	p.Asp1973Asn	p.D1973N	ENST00000382044	NM_001141980.1	1973	Gat/Aat	28/28	0.191067644354227	3	FACETS	1	0.99	1	0.735	0.679	0.792	INDETERMINATE	1	TRUE	1	0.394777958096943	3		569	747	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679714	88679714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	166	381	0	ENST00000360948.2:c.749C>T	p.Ser250Phe	p.S250F	ENST00000360948	NM_001012338.2	250	tCc/tTc	7/19	0.191067644354227	3	FACETS	0.825	0.762	0.891	0.825	0.762	0.891	INDETERMINATE	2	TRUE	1	0.394777958096943	3		381	610	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858448	9858448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	141	520	1	ENST00000330684.3:c.2953C>T	p.Pro985Ser	p.P985S	ENST00000330684	NM_001134407.1	985	Cct/Tct	13/13	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.394777958096943	2		521	658	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650744	67650744	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	184	561	0	ENST00000264010.4:c.1049C>T	p.Pro350Leu	p.P350L	ENST00000264010	NM_006565.3	350	cCa/cTa	5/12	1	2	FACETS	0.972	0.897	1	0.972	0.897	1	CLONAL	1	TRUE	1	0.394777958096943	2		561	959	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867383	68867383	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	89	349	0	ENST00000261769.5:c.2630G>A	p.Gly877Glu	p.G877E	ENST00000261769	NM_004360.3	877	gGa/gAa	16/16	1	2	FACETS	0.97	0.863	1	0.97	0.863	1	CLONAL	1	TRUE	1	0.394777958096943	2		349	465	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974733	15974733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	205	395	0	ENST00000268712.3:c.4142C>T	p.Ser1381Phe	p.S1381F	ENST00000268712	NM_006311.3	1381	tCc/tTc	30/46	0.389171168937157	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.394777958096943	2		395	489	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40371803	40371803	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139065819	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	113	341	0	ENST00000293328.3:c.608C>T	p.Ala203Val	p.A203V	ENST00000293328	NM_012448.3	203	gCc/gTc	6/19	0.39434122380315	3	FACETS	1	0.956	1	0.554	0.499	0.611	CLONAL	1	TRUE	1	0.394777958096943	3		341	619	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245867	41245867	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	253	675	0	ENST00000357654.3:c.1681T>A	p.Ser561Thr	p.S561T	ENST00000357654	NM_007294.3	561	Tct/Act	10/23	0.39434122380315	3	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	1	0.394777958096943	3		675	767	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797903	42797903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	212	741	0	ENST00000575354.2:c.3955C>T	p.Pro1319Ser	p.P1319S	ENST00000575354	NM_015125.3	1319	Ccg/Tcg	16/20	0.39434122380315	3	FACETS	1	0.962	1	0.528	0.49	0.568	CLONAL	1	TRUE	1	0.394777958096943	3		741	1217	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155364	99155364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	113	327	0	ENST00000074304.5:c.590C>T	p.Pro197Leu	p.P197L	ENST00000074304	NM_001134224.1	197	cCt/cTt	9/26	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.394777958096943	2		327	503	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458559	12458559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	367	705	0	ENST00000287820.6:c.1176G>A	p.Met392Ile	p.M392I	ENST00000287820	NM_015869.4	392	atG/atA	6/7	0.130730181183013	6	FACETS	1	0.991	1	0.801	0.759	0.844	INDETERMINATE	2	TRUE	3	0.394777958096943	6		705	1385	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427594	72427594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1453644601	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	207	321	0	ENST00000477973.2:c.896C>T	p.Ser299Phe	p.S299F	ENST00000477973	NM_012234.5	299	tCc/tTc	4/4	0.130730181183013	6	FACETS	0.988	0.922	1	0.988	0.922	1	INDETERMINATE	3	TRUE	3	0.394777958096943	6		321	633	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955032	93955032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	71	251	0	ENST00000369303.4:c.2866G>A	p.Ala956Thr	p.A956T	ENST00000369303	NM_004440.3	956	Gcc/Acc	16/17	0.394777958096943	2	FACETS	0.952	0.848	1	0.952	0.848	1	CLONAL	2	TRUE	0	0.394777958096943	2		251	189	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683864	117683864	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs765131630	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	200	581	0	ENST00000368508.3:c.3283A>T	p.Asn1095Tyr	p.N1095Y	ENST00000368508	NM_002944.2	1095	Aac/Tac	21/43	0.394777958096943	2	FACETS	0.971	0.907	1	0.971	0.907	1	CLONAL	2	TRUE	0	0.394777958096943	2		581	522	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148513775	148513776	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	190	572	2	ENST00000320356.2:c.1505_1505+1delinsAA		p.X502_splice	ENST00000320356	NM_004456.4	502		12/20	0.114441564914985	5	FACETS	0.903	0.835	0.972	0.602	0.557	0.648	INDETERMINATE	2	TRUE	2	0.394777958096943	5		574	849	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934353	68934353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	89	481	1	ENST00000288368.4:c.419G>A	p.Arg140Lys	p.R140K	ENST00000288368	NM_024870.2	140	aGa/aAa	4/40	1	2	FACETS	0.896	0.797	1	0.896	0.797	1	CLONAL	1	TRUE	1	0.394777958096943	2		482	503	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950505	68950505	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs967932513	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	98	392	0	ENST00000288368.4:c.817G>A	p.Val273Met	p.V273M	ENST00000288368	NM_024870.2	273	Gtg/Atg	7/40	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.394777958096943	2		392	462	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030817	69030817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	90	320	0	ENST00000288368.4:c.3359C>T	p.Ser1120Phe	p.S1120F	ENST00000288368	NM_024870.2	1120	tCc/tTc	27/40	1	2	FACETS	0.846	0.753	0.945	0.846	0.753	0.945	CLONAL	1	TRUE	1	0.394777958096943	2		320	539	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033172	69033172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1002113584	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	82	370	0	ENST00000288368.4:c.3612G>A	p.Met1204Ile	p.M1204I	ENST00000288368	NM_024870.2	1204	atG/atA	30/40	1	2	FACETS	0.869	0.769	0.976	0.869	0.769	0.976	CLONAL	1	TRUE	1	0.394777958096943	2		370	478	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072529	5072529	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	93	309	0	ENST00000381652.3:c.1679T>C	p.Phe560Ser	p.F560S	ENST00000381652	NM_004972.3	560	tTt/tCt	13/25	0.114441564914985	5	FACETS	1	0.955	1	0.744	0.668	0.824	INDETERMINATE	2	TRUE	2	0.394777958096943	5		309	336	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336335	80336335	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	172	378	0	ENST00000286548.4:c.984C>A	p.Phe328Leu	p.F328L	ENST00000286548	NM_002072.3	328	ttC/ttA	7/7	0.114441564914985	5	FACETS	0.981	0.905	1	0.654	0.603	0.707	INDETERMINATE	2	TRUE	2	0.394777958096943	5		378	707	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121913370	NA	P-0033746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	138	220	2	ENST00000288602.6:c.1742A>G	p.Asn581Ser	p.N581S	ENST00000288602	NM_004333.4	581	aAt/aGt	15/18	0.486507300711807	5	FACETS	0.953	0.873	1	0.635	0.582	0.69	CLONAL	2	TRUE	2	0.559764049069129	5		222	476	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996840	100996840	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	154	590	0	ENST00000325455.5:c.1687C>A	p.Pro563Thr	p.P563T	ENST00000325455	NM_001202474.3	563	Cct/Act	2/8	0.526910405969552	3	FACETS	0.986	0.905	1	0.493	0.452	0.536	CLONAL	1	TRUE	1	0.559764049069129	3		590	714	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828231	72828231	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	157	543	1	ENST00000268489.5:c.8350C>A	p.Pro2784Thr	p.P2784T	ENST00000268489	NM_006885.3	2784	Ccc/Acc	9/10	0.526910405969552	3	FACETS	1	0.931	1	0.508	0.466	0.551	CLONAL	1	TRUE	1	0.559764049069129	3		544	707	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340184	116340184	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	100	306	3	ENST00000397752.3:c.1046G>A	p.Ser349Asn	p.S349N	ENST00000397752	NM_000245.2	349	aGc/aAc	2/21	0.486507300711807	5	FACETS	1	0.93	1	0.351	0.313	0.39	CLONAL	1	TRUE	2	0.559764049069129	5		309	625	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	38	622	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.589568360988745	3	FACETS	0.611	0.508	0.726	0.306	0.254	0.363	SUBCLONAL	1	TRUE	1	0.589568360988745	3		622	273	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	219	551	1	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.851	0.793	0.911	0.851	0.793	0.911	CLONAL	1	TRUE	1	0.589568360988745	2		552	873	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	322	612	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.892	0.842	0.944	0.892	0.842	0.944	CLONAL	1	TRUE	1	0.589568360988745	2		616	1224	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	400	675	1	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.589568360988745	2		676	1292	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151290	202151290	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	112	468	0	ENST00000358485.4:c.1596del	p.Lys532AsnfsTer73	p.K532Nfs*73	ENST00000358485	NM_001080125.1	530	agA/ag	9/9	1	2	FACETS	0.871	0.789	0.957	0.871	0.789	0.957	CLONAL	1	TRUE	1	0.589568360988745	2		468	436	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	85	746	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.788	0.702	0.879	0.788	0.702	0.879	SUBCLONAL	1	TRUE	1	0.589568360988745	2		751	366	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1215	381	678	1	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.589568360988745	3	FACETS	1	0.975	1	0.524	0.497	0.553	CLONAL	1	TRUE	1	0.589568360988745	3		679	1596	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1445	449	753	5	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	0.589568360988745	3	FACETS	1	0.976	1	0.521	0.495	0.547	CLONAL	1	TRUE	1	0.589568360988745	3		758	1894	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	47	329	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.589568360988745	3	FACETS	0.918	0.782	1	0.459	0.391	0.532	CLONAL	1	TRUE	1	0.589568360988745	3		329	225	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722761	49722761	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs62262682	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	11	25	0	ENST00000449682.2:c.1478G>T	p.Arg493Leu	p.R493L	ENST00000449682	NM_020998.3	493	cGt/cTt	13/18	0.589568360988745	2	FACETS	0.811	0.607	1	0.811	0.607	1	CLONAL	2	TRUE	0	0.589568360988745	2		25	23	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630605	187630605	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	186	820	0	ENST00000441802.2:c.377del	p.Asn126IlefsTer20	p.N126Ifs*20	ENST00000441802	NM_005245.3	126	aAt/at	2/27	0.49524751448078	1	FACETS	0.851	0.792	0.911	0.851	0.792	0.911	CLONAL	1	TRUE	0	0.589568360988745	1		820	523	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	124	468	2	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	1	2	FACETS	0.882	0.803	0.964	0.882	0.803	0.964	CLONAL	1	TRUE	1	0.589568360988745	2		470	477	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	75	622	0	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	1	2	FACETS	0.729	0.643	0.82	0.729	0.643	0.82	SUBCLONAL	1	TRUE	1	0.589568360988745	2		622	349	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303199	15303199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769955930	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	444	805	0	ENST00000263388.2:c.329G>A	p.Arg110His	p.R110H	ENST00000263388	NM_000435.2	110	cGt/cAt	3/33	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.589568360988745	2		805	1497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	391	785	0	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	1	2	FACETS	0.907	0.86	0.954	0.907	0.86	0.954	CLONAL	1	TRUE	1	0.589568360988745	2		785	1463	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	48	376	5	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.693	0.591	0.802	0.693	0.591	0.802	SUBCLONAL	1	TRUE	1	0.589568360988745	2		381	235	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15960949	15960949	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199804512	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	218	510	0	ENST00000268712.3:c.6271A>G	p.Thr2091Ala	p.T2091A	ENST00000268712	NM_006311.3	2091	Aca/Gca	40/46	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.589568360988745	2		510	691	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482927	140482927	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	197	628	4	ENST00000288602.6:c.1208del	p.Pro403LeufsTer8	p.P403Lfs*8	ENST00000288602	NM_004333.4	403	cCt/ct	10/18	0.553247668069197	3	FACETS	0.951	0.881	1	0.475	0.44	0.512	CLONAL	1	TRUE	1	0.589568360988745	3		632	910	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1336	407	674	4	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	0.437640984135249	3	FACETS	1	0.968	1			1	CLONAL	1	TRUE	NA	0.589568360988745	3		678	1743	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540230	23540235	+	inframe_deletion	In_Frame_Del	DEL	GGCTCC	GGCTCC	-	rs753037741	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	154	357	2	ENST00000380871.4:c.168_173del	p.Pro62_Glu63del	p.P62_E63del	ENST00000380871	NM_006167.3	56	ccGGAGCCa/cca	1/2	1	2	FACETS	0.693	0.635	0.753	0.693	0.635	0.753	SUBCLONAL	1	TRUE	1	0.589568360988745	2		359	754	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129338	152129338	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1361952517	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	317	477	0	ENST00000206249.3:c.296del	p.Pro99HisfsTer10	p.P99Hfs*10	ENST00000206249	NM_000125.3	97	ttC/tt	1/8	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.589568360988745	2		477	1065	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903745	41903746	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	345	702	1	ENST00000372991.4:c.811dup	p.Arg271ProfsTer53	p.R271Pfs*53	ENST00000372991	NM_001760.3	271	cgg/cCgg	5/5	1	2	FACETS	0.844	0.798	0.891	0.844	0.798	0.891	CLONAL	1	TRUE	1	0.589568360988745	2		703	1387	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003747	45003747	+	start_lost	Translation_Start_Site	SNP	G	G	T	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	457	457	0	ENST00000558401.1:c.3G>T	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	atG/atT	1/4	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.589568360988745	2		457	1536	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521721	89521721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372594677	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	207	465	0	ENST00000336596.2:c.2798C>T	p.Thr933Met	p.T933M	ENST00000336596	NM_005233.5	933	aCg/aTg	16/17	0.589568360988745	3	FACETS	1	0.966	1	0.532	0.494	0.571	CLONAL	1	TRUE	1	0.589568360988745	3		465	855	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258889	16258889	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	298	601	7	ENST00000375759.3:c.6158del	p.Asn2053ThrfsTer11	p.N2053Tfs*11	ENST00000375759	NM_015001.2	2052	Aaa/aa	11/15	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.589568360988745	2		608	997	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090474	37090474	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	436	405	0	ENST00000231790.2:c.2069A>G	p.Tyr690Cys	p.Y690C	ENST00000231790	NM_000249.3	690	tAc/tGc	18/19	0.589568360988745	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.589568360988745	2		405	686	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589582	67589582	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	15	252	0	ENST00000274335.5:c.1345T>A	p.Leu449Ile	p.L449I	ENST00000274335		449	Tta/Ata	10/15	1	2	FACETS	0.485	0.359	0.632	0.485	0.359	0.632	SUBCLONAL	1	TRUE	1	0.589568360988745	2		252	105	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655413	45655413	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	425	758	2	ENST00000407780.3:c.439del	p.His147ThrfsTer15	p.H147Tfs*15	ENST00000407780	NM_001283052.1	147	Cac/ac	4/7	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.589568360988745	2		760	1360	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257899	19257899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374422850	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	587	913	4	ENST00000162023.5:c.487G>A	p.Ala163Thr	p.A163T	ENST00000162023		163	Gcc/Acc	9/13	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.589568360988745	2		917	1714	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986760	36986760	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	86	67	0	ENST00000354822.5:c.929C>T	p.Ala310Val	p.A310V	ENST00000354822	NM_001079668.2	310	gCc/gTc	3/3	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.589568360988745	2		67	214	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655479	67655479	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs769948988	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	66	474	2	ENST00000264010.4:c.1342C>T	p.Arg448Ter	p.R448*	ENST00000264010	NM_006565.3	448	Cga/Tga	7/12	1	2	FACETS	0.718	0.628	0.813	0.718	0.628	0.813	SUBCLONAL	1	TRUE	1	0.589568360988745	2		476	312	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727981	78727981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1481790013	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	200	356	0	ENST00000306801.3:c.826C>T	p.Arg276Cys	p.R276C	ENST00000306801	NM_020761.2	276	Cgc/Tgc	6/34	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.589568360988745	2		356	634	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527742	157527742	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	284	526	0	ENST00000346085.5:c.5471del	p.Gly1824ValfsTer27	p.G1824Vfs*27	ENST00000346085	NM_020732.3	1823	Ggg/gg	20/20	1	2	FACETS	0.995	0.937	1	0.995	0.937	1	CLONAL	1	TRUE	1	0.589568360988745	2		526	968	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980402	201980402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	870	767	4	ENST00000359651.3:c.142del	p.Gln48ArgfsTer107	p.Q48Rfs*107	ENST00000359651		46	aaC/aa	1/8	0.589568360988745	3	FACETS	0.967	0.938	0.997	0.967	0.938	0.997	CLONAL	2	TRUE	1	0.589568360988745	3		771	1975	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156811	106156811	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146049881	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	181	450	0	ENST00000380013.4:c.1712G>A	p.Arg571His	p.R571H	ENST00000380013	NM_001127208.2	571	cGt/cAt	3/11	1	2	FACETS	0.973	0.902	1	0.973	0.902	1	CLONAL	1	TRUE	1	0.589568360988745	2		450	631	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247354	71247354	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs374060287	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	259	425	0	ENST00000318789.4:c.179A>G	p.Gln60Arg	p.Q60R	ENST00000318789	NM_032682.5	60	cAg/cGg	6/21	0.589568360988745	3	FACETS	0.958	0.897	1	0.479	0.448	0.511	CLONAL	1	TRUE	1	0.589568360988745	3		425	1187	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242935	142242935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	67	632	2	ENST00000350721.4:c.4052G>A	p.Arg1351Gln	p.R1351Q	ENST00000350721	NM_001184.3	1351	cGg/cAg	22/47	0.589568360988745	3	FACETS	0.316	0.274	0.363	0.158	0.137	0.182	SUBCLONAL	1	TRUE	1	0.589568360988745	3		634	930	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434180	49434180	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1493	421	776	0	ENST00000301067.7:c.7373A>G	p.Gln2458Arg	p.Q2458R	ENST00000301067	NM_003482.3	2458	cAg/cGg	31/54	0.589568360988745	3	FACETS	0.966	0.917	1	0.483	0.458	0.508	CLONAL	1	TRUE	1	0.589568360988745	3		776	1914	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200228	67200228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770979132	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	323	690	2	ENST00000312629.5:c.536C>T	p.Thr179Met	p.T179M	ENST00000312629	NM_003952.2	179	aCg/aTg	7/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.589568360988745	2		692	1080	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685596	29685596	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	105	620	0	ENST00000356175.3:c.8006A>G	p.Tyr2669Cys	p.Y2669C	ENST00000356175	NM_000267.3	2669	tAc/tGc	54/57	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.589568360988745	2		620	347	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25468913	25468913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	360	677	2	ENST00000264709.3:c.1450C>T	p.Arg484Trp	p.R484W	ENST00000264709	NM_175629.2	484	Cgg/Tgg	12/23	1	2	FACETS	0.974	0.923	1	0.974	0.923	1	CLONAL	1	TRUE	1	0.589568360988745	2		679	1254	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741598	145741598	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1242395636	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	406	851	0	ENST00000428558.2:c.905C>A	p.Pro302His	p.P302H	ENST00000428558	NM_004260.3	302	cCt/cAt	5/22	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.589568360988745	2		851	1375	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106246	27106246	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	320	585	0	ENST00000324856.7:c.5857A>T	p.Lys1953Ter	p.K1953*	ENST00000324856	NM_006015.4	1953	Aag/Tag	20/20	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.589568360988745	2		585	1075	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344435	118344435	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	117	288	0	ENST00000534358.1:c.2565del	p.Glu856ArgfsTer93	p.E856Rfs*93	ENST00000534358	NM_005933.3	854	gCc/gc	3/36	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.589568360988745	2		288	397	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156232	119156232	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	189	457	1	ENST00000264033.4:c.1897G>A	p.Asp633Asn	p.D633N	ENST00000264033	NM_005188.3	633	Gat/Aat	11/16	1	2	FACETS	0.831	0.769	0.894	0.831	0.769	0.894	CLONAL	1	TRUE	1	0.589568360988745	2		458	772	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21629843	21629843	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	126	699	0	ENST00000421138.2:c.949+2T>C		p.X317_splice	ENST00000421138		317			0.589568360988745	3	FACETS	0.782	0.716	0.849	0.782	0.716	0.849	SUBCLONAL	2	TRUE	1	0.589568360988745	3		699	354	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246681	46246681	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	52	142	0	ENST00000334344.6:c.4773+2T>C		p.X1591_splice	ENST00000334344	NM_152641.2	1591			0.589568360988745	3	FACETS	0.944	0.812	1	0.472	0.406	0.543	CLONAL	1	TRUE	1	0.589568360988745	3		142	242	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434610	49434610	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	751	721	1	ENST00000301067.7:c.6943del	p.His2315ThrfsTer7	p.H2315Tfs*7	ENST00000301067	NM_003482.3	2315	Cac/ac	31/54	0.589568360988745	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.589568360988745	3		722	1623	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491654	56491654	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	550	541	0	ENST00000267101.3:c.2546A>G	p.Gln849Arg	p.Q849R	ENST00000267101	NM_001982.3	849	cAg/cGg	21/28	0.589568360988745	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.589568360988745	3		541	1167	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033874	49033874	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	168	481	0	ENST00000267163.4:c.2011T>A	p.Ser671Thr	p.S671T	ENST00000267163	NM_000321.2	671	Tct/Act	20/27	0.566036815533211	3	FACETS	1	0.952	1	0.523	0.481	0.565	CLONAL	1	TRUE	1	0.589568360988745	3		481	706	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675041	40675041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	58	537	1	ENST00000249776.8:c.5C>T	p.Ala2Val	p.A2V	ENST00000249776	NM_033286.3	2	gCg/gTg	1/9	1	2	FACETS	0.25	0.214	0.29	0.25	0.214	0.29	SUBCLONAL	1	TRUE	1	0.589568360988745	2		538	786	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43699703	43699703	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	354	592	0	ENST00000382044.4:c.5812T>C	p.Cys1938Arg	p.C1938R	ENST00000382044	NM_001141980.1	1938	Tgt/Cgt	28/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.589568360988745	2		592	1117	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817865	3817865	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	143	755	0	ENST00000262367.5:c.3106A>G	p.Thr1036Ala	p.T1036A	ENST00000262367	NM_004380.2	1036	Aca/Gca	16/31	1	2	FACETS	0.866	0.794	0.942	0.866	0.794	0.942	CLONAL	1	TRUE	1	0.589568360988745	2		755	560	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832823	3832823	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	375	660	0	ENST00000262367.5:c.1435A>C	p.Ser479Arg	p.S479R	ENST00000262367	NM_004380.2	479	Agc/Cgc	6/31	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.589568360988745	2		660	1103	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129779	30129779	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	398	647	0	ENST00000263025.4:c.434A>G	p.Tyr145Cys	p.Y145C	ENST00000263025	NM_002746.2	145	tAc/tGc	3/9	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.589568360988745	2		647	1216	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821365	72821365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745550429	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	199	283	1	ENST00000268489.5:c.10810G>A	p.Ala3604Thr	p.A3604T	ENST00000268489	NM_006885.3	3604	Gcc/Acc	10/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.589568360988745	2		284	619	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830476	72830476	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	364	599	2	ENST00000268489.5:c.6105G>T	p.Gln2035His	p.Q2035H	ENST00000268489	NM_006885.3	2035	caG/caT	9/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.589568360988745	2		601	1095	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320295	30320299	+	frameshift_variant	Frame_Shift_Del	DEL	AAGAA	AAGAA	-	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	38	322	0	ENST00000322652.5:c.1244_1248del	p.Glu415GlyfsTer5	p.E415Gfs*5	ENST00000322652	NM_015355.2	412	acAAGAAaa/acaa	11/16	1	2	FACETS	0.908	0.764	1	0.908	0.764	1	CLONAL	1	TRUE	1	0.589568360988745	2		322	142	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40880888	40880888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	119	889	1	ENST00000428826.2:c.72G>A	p.Met24Ile	p.M24I	ENST00000428826		24	atG/atA	3/21	1	2	FACETS	0.781	0.708	0.857	0.781	0.708	0.857	SUBCLONAL	1	TRUE	1	0.589568360988745	2		890	517	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60795965	60795965	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1335816980	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	275	458	0	ENST00000333681.4:c.613A>G	p.Ser205Gly	p.S205G	ENST00000333681		205	Agc/Ggc	3/3	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.589568360988745	2		458	909	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214046	36214046	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	444	749	0	ENST00000222270.7:c.2872G>A	p.Gly958Ser	p.G958S	ENST00000222270	NM_014727.1	958	Ggc/Agc	6/37	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.589568360988745	2		749	1481	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220949	36220949	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	186	411	0	ENST00000222270.7:c.4999G>A	p.Ala1667Thr	p.A1667T	ENST00000222270	NM_014727.1	1667	Gcc/Acc	23/37	1	2	FACETS	0.962	0.892	1	0.962	0.892	1	CLONAL	1	TRUE	1	0.589568360988745	2		411	656	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795235	42795235	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	317	655	0	ENST00000575354.2:c.2318del	p.Pro773LeufsTer151	p.P773Lfs*151	ENST00000575354	NM_015125.3	772	gCc/gc	10/20	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.589568360988745	2		655	1071	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50916701	50916701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878854532	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	237	422	0	ENST00000440232.2:c.2173C>T	p.Arg725Cys	p.R725C	ENST00000440232	NM_002691.3	725	Cgt/Tgt	18/27	1	2	FACETS	0.979	0.916	1	0.979	0.916	1	CLONAL	1	TRUE	1	0.589568360988745	2		422	821	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028024	48028024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	108	342	0	ENST00000234420.5:c.2902G>A	p.Val968Ile	p.V968I	ENST00000234420	NM_000179.2	968	Gtc/Atc	4/10	1	2	FACETS	0.942	0.852	1	0.942	0.852	1	CLONAL	1	TRUE	1	0.589568360988745	2		342	389	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028207	48028207	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	119	438	0	ENST00000234420.5:c.3085T>G	p.Leu1029Val	p.L1029V	ENST00000234420	NM_000179.2	1029	Ttg/Gtg	4/10	1	2	FACETS	0.973	0.885	1	0.973	0.885	1	CLONAL	1	TRUE	1	0.589568360988745	2		438	415	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158637085	158637085	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	282	593	1	ENST00000263640.3:c.95T>G	p.Leu32Arg	p.L32R	ENST00000263640	NM_001105.4	32	cTc/cGc	4/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.589568360988745	2		594	884	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661036	227661036	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	74	553	0	ENST00000305123.5:c.2419T>A	p.Ser807Thr	p.S807T	ENST00000305123	NM_005544.2	807	Tct/Act	1/2	1	2	FACETS	0.271	0.236	0.308	0.271	0.236	0.308	SUBCLONAL	1	TRUE	1	0.589568360988745	2		553	928	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262879	46262879	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	184	515	0	ENST00000371998.3:c.1052T>G	p.Leu351Arg	p.L351R	ENST00000371998		351	cTc/cGc	10/23	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.589568360988745	2		515	493	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12653540	12653540	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	297	507	0	ENST00000251849.4:c.229A>G	p.Ser77Gly	p.S77G	ENST00000251849	NM_002880.3	77	Agc/Ggc	3/17	0.437640984135249	3	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.589568360988745	3		507	1161	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37045929	37045929	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	254	581	0	ENST00000231790.2:c.344T>G	p.Ile115Ser	p.I115S	ENST00000231790	NM_000249.3	115	aTt/aGt	4/19	0.589568360988745	2	FACETS	0.949	0.902	0.996	0.949	0.902	0.996	CLONAL	2	TRUE	0	0.589568360988745	2		581	454	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441286	52441286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	637	513	2	ENST00000460680.1:c.484G>A	p.Val162Met	p.V162M	ENST00000460680	NM_004656.3	162	Gtg/Atg	7/17	0.589568360988745	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.589568360988745	2		515	1029	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651419	52651421	+	inframe_deletion	In_Frame_Del	DEL	ATA	ATA	-	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	219	719	0	ENST00000394830.3:c.1675_1677del	p.Tyr559del	p.Y559del	ENST00000394830	NM_018313.4	559	TAT/-	15/30	0.589568360988745	2	FACETS	0.78	0.734	0.827	0.78	0.734	0.827	SUBCLONAL	2	TRUE	0	0.589568360988745	2		719	476	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021729	71021729	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	124	569	0	ENST00000318789.4:c.1629del	p.Lys543AsnfsTer56	p.K543Nfs*56	ENST00000318789	NM_032682.5	543	aaA/aa	18/21	0.589568360988745	3	FACETS	0.838	0.76	0.92	0.419	0.38	0.46	CLONAL	1	TRUE	1	0.589568360988745	3		569	650	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645064	86645064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	55	409	0	ENST00000274376.6:c.1136C>T	p.Ser379Leu	p.S379L	ENST00000274376	NM_002890.2	379	tCa/tTa	8/25	1	2	FACETS	0.804	0.696	0.92	0.804	0.696	0.92	CLONAL	1	TRUE	1	0.589568360988745	2		409	232	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721925	176721925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223692368	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	278	568	0	ENST00000439151.2:c.7556C>T	p.Ala2519Val	p.A2519V	ENST00000439151	NM_022455.4	2519	gCa/gTa	23/23	1	2	FACETS	0.925	0.869	0.981	0.925	0.869	0.981	CLONAL	1	TRUE	1	0.589568360988745	2		568	1020	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048110	180048110	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	137	705	0	ENST00000261937.6:c.2163G>C	p.Lys721Asn	p.K721N	ENST00000261937	NM_182925.4	721	aaG/aaC	14/30	1	2	FACETS	0.359	0.325	0.394	0.359	0.325	0.394	SUBCLONAL	1	TRUE	1	0.589568360988745	2		705	1295	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163839	152163839	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	316	536	0	ENST00000206249.3:c.560T>C	p.Val187Ala	p.V187A	ENST00000206249	NM_000125.3	187	gTg/gCg	2/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.589568360988745	2		536	965	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206872	162206872	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	198	394	1	ENST00000366898.1:c.803G>T	p.Cys268Phe	p.C268F	ENST00000366898	NM_004562.2	268	tGt/tTt	7/12	1	2	FACETS	0.991	0.921	1	0.991	0.921	1	CLONAL	1	TRUE	1	0.589568360988745	2		395	678	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211091	55211091	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	311	539	2	ENST00000275493.2:c.334T>C	p.Tyr112His	p.Y112H	ENST00000275493	NM_005228.3	112	Tac/Cac	3/28	0.553247668069197	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.589568360988745	3		541	675	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540176	23540176	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	206	284	1	ENST00000380871.4:c.227T>C	p.Leu76Pro	p.L76P	ENST00000380871	NM_006167.3	76	cTg/cCg	1/2	1	2	FACETS	0.916	0.852	0.981	0.916	0.852	0.981	CLONAL	1	TRUE	1	0.589568360988745	2		285	763	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141557580	141557580	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	426	805	2	ENST00000220592.5:c.1735C>A	p.Leu579Met	p.L579M	ENST00000220592	NM_012154.3	579	Ctg/Atg	13/19	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.589568360988745	2		807	1354	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209602	98209602	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	283	516	0	ENST00000331920.6:c.3936G>A	p.Trp1312Ter	p.W1312*	ENST00000331920	NM_000264.3	1312	tgG/tgA	23/24	0.589568360988745	3	FACETS	0.952	0.893	1	0.476	0.446	0.506	CLONAL	1	TRUE	1	0.589568360988745	3		516	1306	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229464	98229464	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253407915	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	152	454	1	ENST00000331920.6:c.2494G>A	p.Val832Ile	p.V832I	ENST00000331920	NM_000264.3	832	Gtc/Atc	15/24	0.589568360988745	3	FACETS	0.944	0.866	1	0.472	0.433	0.513	CLONAL	1	TRUE	1	0.589568360988745	3		455	707	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300062	137300062	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1456	446	694	0	ENST00000481739.1:c.347T>A	p.Val116Asp	p.V116D	ENST00000481739	NM_002957.4	116	gTc/gAc	3/10	0.589568360988745	3	FACETS	1	0.972	1	0.515	0.49	0.541	CLONAL	1	TRUE	1	0.589568360988745	3		694	1902	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599988	10599988	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	223	653	0	ENST00000171111.5:c.1588C>T	p.Gln530Ter	p.Q530*	ENST00000171111	NM_203500.1	530	Cag/Tag	5/6	0.558696728596452	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.558696728596452	1		653	492	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121151	11121152	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0033844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	185	642	0	ENST00000358026.2:c.2223_2224del	p.Arg741SerfsTer82	p.R741Sfs*82	ENST00000358026	NM_001128849.1	740	GAg/g	15/36	0.558696728596452	1	FACETS	0.92	0.856	0.985	0.92	0.856	0.985	CLONAL	1	TRUE	0	0.558696728596452	1		642	519	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023736	27023736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	90	309	0	ENST00000324856.7:c.842C>T	p.Ala281Val	p.A281V	ENST00000324856	NM_006015.4	281	gCg/gTg	1/20	1	2	FACETS	0.934	0.836	1	0.934	0.836	1	CLONAL	1	TRUE	1	0.558696728596452	2		309	345	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058550	72058550	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	151	467	0	ENST00000357731.5:c.890G>T	p.Cys297Phe	p.C297F	ENST00000357731	NM_173808.2	297	tGt/tTt	6/7	1	2	FACETS	0.943	0.867	1	0.943	0.867	1	CLONAL	1	TRUE	1	0.558696728596452	2		467	573	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984386	201984390	+	frameshift_variant	Frame_Shift_Del	DEL	GTCTA	GTCTA	-	novel	NA	P-0033844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	150	519	0	ENST00000359651.3:c.1051_1055del	p.Val351GlnfsTer118	p.V351Qfs*118	ENST00000359651		351	GTCTAc/c	8/8	NA	2	FACETS	1	0.931	1			1	INDETERMINATE	1	TRUE	NA	0.558696728596452	2		519	530	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446810	49446810	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	147	459	0	ENST00000301067.7:c.1000A>T	p.Asn334Tyr	p.N334Y	ENST00000301067	NM_003482.3	334	Aat/Tat	8/54	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.558696728596452	2		459	507	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913248	32913248	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	153	472	0	ENST00000380152.3:c.4756A>G	p.Thr1586Ala	p.T1586A	ENST00000380152		1586	Aca/Gca	11/27	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.558696728596452	2		472	514	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220450	1220461	+	inframe_deletion	In_Frame_Del	DEL	CCTGCTGCTCAC	CCTGCTGCTCAC	-	novel	NA	P-0033844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	150	746	0	ENST00000326873.7:c.544_555del	p.Leu182_Thr185del	p.L182_T185del	ENST00000326873	NM_000455.4	181	aaCCTGCTGCTCACc/aac	4/10	0.558696728596452	1	FACETS	0.896	0.827	0.967	0.896	0.827	0.967	CLONAL	1	TRUE	0	0.558696728596452	1		746	432	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220451	1220466	+	protein_altering_variant	In_Frame_Del	DEL	CTGCTGCTCACCACCG	CTGCTGCTCACCACCG	ACCC	novel	NA	P-0033844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	150	743	5	ENST00000326873.7:c.544_559delinsACCC	p.Leu182_Gly187delinsThrArg	p.L182_G187delinsTR	ENST00000326873	NM_000455.4	182	CTGCTGCTCACCACCGgt/ACCCgt	4/10	0.558696728596452	1	FACETS	0.9	0.83	0.971	0.9	0.83	0.971	CLONAL	1	TRUE	0	0.558696728596452	1		748	430	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207577	2207582	+	inframe_deletion	In_Frame_Del	DEL	CGGCAC	CGGCAC	-	novel	NA	P-0033844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	117	383	0	ENST00000398665.3:c.862_867del	p.Gly288_Thr289del	p.G288_T289del	ENST00000398665	NM_032482.2	287	atCGGCACc/atc	11/28	0.558696728596452	1	FACETS	0.983	0.899	1	0.983	0.899	1	CLONAL	1	TRUE	0	0.558696728596452	1		383	307	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980883	40980883	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	127	425	1	ENST00000373198.4:c.1603C>A	p.Leu535Ile	p.L535I	ENST00000373198	NM_133170.3	535	Ctc/Atc	10/32	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.558696728596452	2		426	444	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908876	101908876	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs387906697	NA	P-0033844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	194	599	0	ENST00000374994.4:c.1240C>T	p.Arg414Ter	p.R414*	ENST00000374994	NM_004612.2	414	Cga/Tga	7/9	0.558696728596452	1	FACETS	0.989	0.924	1	0.989	0.924	1	CLONAL	1	TRUE	0	0.558696728596452	1		599	506	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750311	133750311	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	173	522	0	ENST00000318560.5:c.1142A>T	p.Asp381Val	p.D381V	ENST00000318560	NM_005157.4	381	gAt/gTt	7/11	0.558696728596452	1	FACETS	0.97	0.902	1	0.97	0.902	1	CLONAL	1	TRUE	0	0.558696728596452	1		522	460	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983088	201983098	+	frameshift_variant	Frame_Shift_Del	DEL	CAACTATGGGG	CAACTATGGGG	A	novel	NA	P-0033844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	165	525	0	ENST00000359651.3:c.937_947delinsA	p.Gln313ThrfsTer9	p.Q313Tfs*9	ENST00000359651		313	CAACTATGGGGc/Ac	7/8	NA	2	FACETS	1	0.952	1			1	INDETERMINATE	1	TRUE	NA	0.558696728596452	2		525	567	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0033858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	391	417	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.4252713092035	4	FACETS	0.979	0.941	1	0.979	0.941	1	CLONAL	4	TRUE	0	0.431066461120311	4		417	663	SUCCESS
APC	324	MSKCC	GRCh37	5	112175350	112175351	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	169	260	0	ENST00000257430.4:c.4063dup	p.Ser1355PhefsTer20	p.S1355Ffs*20	ENST00000257430	NM_000038.5	1353	-/T	16/16	0.428559895293466	3	FACETS	0.859	0.801	0.917	0.859	0.801	0.917	CLONAL	3	TRUE	0	0.431066461120311	3		260	370	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124767	108124767	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0033858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	76	281	0	ENST00000278616.4:c.2124+1G>A		p.X708_splice	ENST00000278616	NM_000051.3	708			0.431066461120311	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.431066461120311	1		281	243	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59820385	59820385	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	36	449	0	ENST00000259008.2:c.2368A>G	p.Lys790Glu	p.K790E	ENST00000259008	NM_032043.2	790	Aaa/Gaa	16/20	0.429971268576891	3	FACETS	0.329	0.269	0.395	0.164	0.134	0.198	SUBCLONAL	1	TRUE	1	0.431066461120311	3		449	618	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500337	8500815	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCATCAATGTCTCTGAAATATGTAAGACAAAAAGGCAACAAAAAGGTAAGAAGGTAGTTTTGAAAAGTTAACTTCAAAATGTAAAAGAAGTGACTACAAAAAGCCAAGAAAAACACAGAAGACTTTAGATGGAGGCACAGAGACGGGCTGGACTGCAAGACCATAGGAGCCAACAGTTCTTTTAAAGAGAAGCAAATTACTGCATTGAGATTGAAAAAAATGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGCCAGGCTGTAGCAAAGACAAGTCTTTGGCAAAAATACTAAAGTAACAGCAATGCTGGGTAAAAAGATGAGCAGAGAAAAAAGATTACTGTGAGCCTATTGAAAGACAGCAGATCAAGACTGTGTCAGAAGGGTGCAAACTGACGTAGCGGAGGCAACATACCATCTTCATTGGTTCGAATCAACACGGACAAGCTCTCAGGGCCAGGGCCGACATCTGTATGG	GCATCAATGTCTCTGAAATATGTAAGACAAAAAGGCAACAAAAAGGTAAGAAGGTAGTTTTGAAAAGTTAACTTCAAAATGTAAAAGAAGTGACTACAAAAAGCCAAGAAAAACACAGAAGACTTTAGATGGAGGCACAGAGACGGGCTGGACTGCAAGACCATAGGAGCCAACAGTTCTTTTAAAGAGAAGCAAATTACTGCATTGAGATTGAAAAAAATGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGCCAGGCTGTAGCAAAGACAAGTCTTTGGCAAAAATACTAAAGTAACAGCAATGCTGGGTAAAAAGATGAGCAGAGAAAAAAGATTACTGTGAGCCTATTGAAAGACAGCAGATCAAGACTGTGTCAGAAGGGTGCAAACTGACGTAGCGGAGGCAACATACCATCTTCATTGGTTCGAATCAACACGGACAAGCTCTCAGGGCCAGGGCCGACATCTGTATGG	-	novel	NA	P-0033858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	76	1	0	ENST00000356435.5:c.2067_2128+417del		p.X689_splice	ENST00000356435		689		13/35	1	2	FACETS	0.659	0.579	0.745	0.659	0.579	0.745	SUBCLONAL	1	TRUE	1	0.431066461120311	2		1	535	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0034038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	522	675	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.6550590161885	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.6550590161885	3		675	694	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910399	50910399	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	186	532	1	ENST00000440232.2:c.1654C>T	p.Gln552Ter	p.Q552*	ENST00000440232	NM_002691.3	552	Cag/Tag	13/27	0.492984825135819	3	FACETS	1	0.97	1			1	CLONAL	1	TRUE	NA	0.6550590161885	3		533	694	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533661	41533661	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs142823793	NA	P-0034038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	129	383	0	ENST00000263253.7:c.1627A>G	p.Met543Val	p.M543V	ENST00000263253	NM_001429.3	543	Atg/Gtg	8/31	0.6550590161885	3	FACETS	1	0.967	1			1	CLONAL	1	TRUE	NA	0.6550590161885	3		383	465	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73096435	73096435	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	21	67	0	ENST00000356692.5:c.215A>C	p.Asn72Thr	p.N72T	ENST00000356692		72	aAc/aCc	3/9	0.6550590161885	3	FACETS	0.905	0.712	1	0.453	0.356	0.561	CLONAL	1	TRUE	1	0.6550590161885	3		67	94	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0034093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	372	700	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.518332988809706	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.543600556072658	2		700	616	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0034093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	58	290	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.498587479754152	3	FACETS	0.92	0.797	1	0.46	0.398	0.526	CLONAL	1	TRUE	1	0.543600556072658	3		290	295	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56875738	56875738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147381896	NA	P-0034093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	187	407	0	ENST00000308159.5:c.2342G>A	p.Arg781His	p.R781H	ENST00000308159	NM_014669.4	781	cGc/cAc	21/22	0.268522901931455	4	FACETS	1	0.951	1	1	0.951	1	INDETERMINATE	2	TRUE	2	0.543600556072658	4		407	518	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480306	89480306	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	71	276	0	ENST00000336596.2:c.2143G>T	p.Asp715Tyr	p.D715Y	ENST00000336596	NM_005233.5	715	Gat/Tat	13/17	0.498587479754152	3	FACETS	1	0.921	1	0.531	0.467	0.598	CLONAL	1	TRUE	1	0.543600556072658	3		276	313	SUCCESS
APC	324	MSKCC	GRCh37	5	112111364	112111364	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554071529	NA	P-0034093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	87	195	1	ENST00000257430.4:c.465del	p.Asp156ThrfsTer14	p.D156Tfs*14	ENST00000257430	NM_000038.5	154	gAa/ga	5/16	0.498587479754152	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.543600556072658	3		196	178	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0034143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	287	503	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.356486861689507	3	FACETS	0.989	0.939	1	0.989	0.939	1	CLONAL	3	TRUE	0	0.389811327701026	3		503	593	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169741	11169741	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1228569453	NA	P-0034143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	65	438	1	ENST00000361445.4:c.7412C>T	p.Thr2471Met	p.T2471M	ENST00000361445	NM_004958.3	2471	aCg/aTg	55/58	0.389811327701026	1	FACETS	0.63	0.548	0.719	0.63	0.548	0.719	SUBCLONAL	1	TRUE	0	0.389811327701026	1		439	426	SUCCESS
APC	324	MSKCC	GRCh37	5	112176027	112176030	+	frameshift_variant	Frame_Shift_Del	DEL	TTAT	TTAT	-	novel	NA	P-0034143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	56	247	0	ENST00000257430.4:c.4738_4741del	p.Ile1580LeufsTer69	p.I1580Lfs*69	ENST00000257430	NM_000038.5	1579	aTTATt/at	16/16	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.389811327701026	2		247	270	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710592	114710592	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	115	310	0	ENST00000543371.1:c.78del	p.Glu26AspfsTer16	p.E26Dfs*16	ENST00000543371	NM_001198531.1	26	gAa/ga	1/14	0.300078718817741	3	FACETS	0.974	0.886	1	0.974	0.886	1	CLONAL	2	TRUE	1	0.389811327701026	3		310	362	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295726	15295726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	48	532	1	ENST00000263388.2:c.2401G>A	p.Gly801Ser	p.G801S	ENST00000263388	NM_000435.2	801	Ggc/Agc	15/33	0.151961741442756	2	FACETS	0.579	0.491	0.677	0.29	0.245	0.339	INDETERMINATE	1	TRUE	0	0.389811327701026	2		533	425	SUCCESS
APC	324	MSKCC	GRCh37	5	112174079	112174080	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0034143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	48	317	0	ENST00000257430.4:c.2791_2792del	p.His931PhefsTer8	p.H931Ffs*8	ENST00000257430	NM_000038.5	930	ACa/a	16/16	1	2	FACETS	0.886	0.754	1	0.886	0.754	1	CLONAL	1	TRUE	1	0.389811327701026	2		317	278	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782329	NA	P-0034321-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	60	537	0	ENST00000269305.4:c.746G>A	p.Arg249Lys	p.R249K	ENST00000269305	NM_001126112.2	249	aGg/aAg	7/11	1	2	FACETS	0.211	0.181	0.243	0.211	0.181	0.243	SUBCLONAL	1	TRUE	1	0.761839083065676	2		537	748	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778249	3778249	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034321-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	278	524	0	ENST00000262367.5:c.6799C>T	p.Gln2267Ter	p.Q2267*	ENST00000262367	NM_004380.2	2267	Cag/Tag	31/31	1	2	FACETS	0.997	0.941	1	0.997	0.941	1	CLONAL	1	TRUE	1	0.761839083065676	2		524	732	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245336	53245336	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034321-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	276	557	0	ENST00000375401.3:c.701A>C	p.Lys234Thr	p.K234T	ENST00000375401	NM_004187.3	234	aAa/aCa	6/26	NA	2	FACETS	0.936	0.883	0.99			1	INDETERMINATE	1	TRUE	NA	0.761839083065676	2		557	774	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181287	123181287	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034321-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	69	229	0	ENST00000218089.9:c.751G>T	p.Glu251Ter	p.E251*	ENST00000218089	NM_001042749.1	251	Gaa/Taa	9/35	0.761839083065676	1	FACETS	0.992	0.903	1	0.992	0.903	1	CLONAL	1	TRUE	0	0.761839083065676	1		229	113	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0034361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	295	538	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.527714490134043	4	FACETS	0.951	0.898	1	0.951	0.898	1	CLONAL	2	TRUE	2	0.574047652806962	4		538	851	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0034361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	362	583	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.527714490134043	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	2	0.574047652806962	4		583	857	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	373	681	1	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.568099505420368	2	FACETS	0.986	0.946	1	0.986	0.946	1	CLONAL	2	TRUE	0	0.574047652806962	2		682	659	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871842	35871842	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	71	454	0	ENST00000216797.5:c.664C>A	p.His222Asn	p.H222N	ENST00000216797	NM_020529.2	222	Cac/Aac	5/6	0.160411074138275	2	FACETS	1	0.906	1	0.523	0.456	0.595	CLONAL	1	TRUE	0	0.212020849526821	2		454	640	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615758	1615758	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769351563	NA	P-0034388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	52	746	0	ENST00000344749.5:c.1513G>A	p.Glu505Lys	p.E505K	ENST00000344749	NM_001136139.2	505	Gag/Aag	17/19	1	2	FACETS	0.501	0.425	0.585	0.501	0.425	0.585	SUBCLONAL	1	TRUE	1	0.212020849526821	2		746	979	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191199	2191199	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	49	585	0	ENST00000398665.3:c.453C>G	p.Ile151Met	p.I151M	ENST00000398665	NM_032482.2	151	atC/atG	5/28	1	2	FACETS	0.531	0.448	0.623	0.531	0.448	0.623	SUBCLONAL	1	TRUE	1	0.212020849526821	2		585	870	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469562	25469562	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	44	715	0	ENST00000264709.3:c.1206G>C	p.Gln402His	p.Q402H	ENST00000264709	NM_175629.2	402	caG/caC	10/23	0.160411074138275	2	FACETS	0.557	0.466	0.659	0.279	0.233	0.33	SUBCLONAL	1	TRUE	0	0.212020849526821	2		715	745	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702630	52702630	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	95	397	0	ENST00000394830.3:c.268C>T	p.Gln90Ter	p.Q90*	ENST00000394830	NM_018313.4	90	Cag/Tag	4/30	0.160411074138275	2	FACETS	1	0.978	1	0.712	0.635	0.795	CLONAL	1	TRUE	0	0.212020849526821	2		397	629	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970900	21970900	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0034388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	107	637	0	ENST00000304494.5:c.457+1del		p.X153_splice	ENST00000304494	NM_000077.4	153			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.212020849526821	2		637	810	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578642	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAAGCAACTGGAAGACGGCAGCAAAGAAACAAACA	TACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAAGCAACTGGAAGACGGCAGCAAAGAAACAAACA	-	novel	NA	P-0034388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	70	658	0	ENST00000269305.4:c.376-88_377del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	0.212020849526821	1	FACETS	0.751	0.654	0.856	0.751	0.654	0.856	SUBCLONAL	1	TRUE	0	0.212020849526821	1		658	786	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0034677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	125	368	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	0.533028121061607	2		368	457	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0034677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	335	398	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.498097832669296	5	FACETS	1	0.991	1	0.809	0.767	0.851	CLONAL	2	TRUE	2	0.533028121061607	5		398	932	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0034677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	381	587	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.498097832669296	5	FACETS	0.969	0.92	1	0.646	0.613	0.68	CLONAL	2	TRUE	2	0.533028121061607	5		587	1327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519980	NA	P-0034677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	248	589	0	ENST00000269305.4:c.528C>G	p.Cys176Trp	p.C176W	ENST00000269305	NM_001126112.2	176	tgC/tgG	5/11	0.533028121061607	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.533028121061607	1		589	605	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0034677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	145	351	3	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	0.533028121061607	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.533028121061607	1		354	369	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249091	55249091	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519861	NA	P-0034677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1255	228	625	0	ENST00000275493.2:c.2389T>A	p.Cys797Ser	p.C797S	ENST00000275493	NM_005228.3	797	Tgc/Agc	20/28	0.498097832669296	5	FACETS	1	0.956	1	0.346	0.321	0.372	CLONAL	1	TRUE	2	0.533028121061607	5		625	1483	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221107	5221107	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs372506721	NA	P-0034677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	206	586	0	ENST00000357368.4:c.3359A>G	p.Asn1120Ser	p.N1120S	ENST00000357368	NM_002850.3	1120	aAc/aGc	20/38	1	2	FACETS	0.937	0.871	1	0.937	0.871	1	CLONAL	1	TRUE	1	0.533028121061607	2		586	825	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920322	1920322	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	264	667	1	ENST00000382891.5:c.1382T>C	p.Leu461Ser	p.L461S	ENST00000382891	NM_133335.3	461	tTg/tCg	5/22	0.497843092449666	3	FACETS	1	0.955	1	0.512	0.479	0.546	CLONAL	1	TRUE	1	0.533028121061607	3		668	1225	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115928	8115929	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0034764-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	177	413	0	ENST00000346208.3:c.1275dup	p.Ser426IlefsTer81	p.S426Ifs*81	ENST00000346208		425	cca/ccAa	6/6	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.79328894714515	2		413	375	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841488	156841488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1023556915	NA	P-0034764-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	12	700	2	ENST00000524377.1:c.791C>T	p.Thr264Met	p.T264M	ENST00000524377	NM_002529.3	264	aCg/aTg	7/17	1	2	FACETS	0.055	0.038	0.076	0.055	0.038	0.076	SUBCLONAL	1	TRUE	1	0.79328894714515	2		702	551	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085885	16085885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs185639773	NA	P-0034764-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	10	466	1	ENST00000281043.3:c.1061C>T	p.Ala354Val	p.A354V	ENST00000281043	NM_005378.4	354	gCg/gTg	3/3	0.374341583454237	1	FACETS	0.078	0.052	0.11	0.078	0.052	0.11	INDETERMINATE	1	TRUE	0	0.79328894714515	1		467	196	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371594	225371594	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034764-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	17	519	1	ENST00000264414.4:c.1010A>G	p.Asn337Ser	p.N337S	ENST00000264414	NM_003590.4	337	aAt/aGt	7/16	0.374341583454237	1	FACETS	0.168	0.126	0.217	0.168	0.126	0.217	INDETERMINATE	1	TRUE	0	0.79328894714515	1		520	154	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145588	24145588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762962010	NA	P-0034842-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	55	405	1	ENST00000263121.7:c.607G>A	p.Ala203Thr	p.A203T	ENST00000263121	NM_003073.3	203	Gcc/Acc	5/9	0.301559078267106	5	FACETS	0.899	0.771	1	0.18	0.154	0.208	INDETERMINATE	1	TRUE	0	0.515251594332138	5		406	421	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478632	99478632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1351130675	NA	P-0034842-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	33	370	0	ENST00000268035.6:c.3274C>T	p.Arg1092Trp	p.R1092W	ENST00000268035	NM_000875.3	1092	Cgg/Tgg	17/21	0.390072108606183	1	FACETS	0.498	0.409	0.596	0.498	0.409	0.596	SUBCLONAL	1	TRUE	0	0.515251594332138	1		370	191	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374828	149374828	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034842-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	235	190	0	ENST00000360632.3:c.266C>G	p.Ser89Trp	p.S89W	ENST00000360632	NM_015472.4	89	tCg/tGg	2/7	0.515251594332138	8	FACETS	0.991	0.955	1			1	CLONAL	8	TRUE	NA	0.515251594332138	8		190	293	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112745394	112745394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1038605223	NA	P-0034842-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	32	317	0	ENST00000369452.4:c.712T>C	p.Cys238Arg	p.C238R	ENST00000369452	NM_007373.3	238	Tgt/Cgt	3/9	0.474030438007592	3	FACETS	0.509	0.414	0.615	0.254	0.207	0.308	SUBCLONAL	1	TRUE	1	0.515251594332138	3		317	307	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779700	3779701	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0034842-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	45	521	0	ENST00000262367.5:c.5347dup	p.Cys1783LeufsTer183	p.C1783Lfs*183	ENST00000262367	NM_004380.2	1783	tgc/tTgc	31/31	0.389602692632414	3	FACETS	0.793	0.671	0.926	0.264	0.223	0.309	CLONAL	1	TRUE	0	0.515251594332138	3		521	277	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86676324	86676324	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0034842-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	82	197	0	ENST00000274376.6:c.2604-2A>T		p.X868_splice	ENST00000274376	NM_002890.2	868			0.515251594332138	3	FACETS	1	0.906	1	1	0.906	1	CLONAL	2	TRUE	1	0.515251594332138	3		197	199	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426879	6426880	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACC	novel	NA	P-0034842-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	303	395	0	ENST00000356142.4:c.74_76dup	p.Thr25dup	p.T25dup	ENST00000356142	NM_018890.3	25	-/ACC	2/7	0.467585027973831	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	TRUE	0	0.515251594332138	3		395	484	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220502	1220502	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	rs121913317	NA	P-0034908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	500	688	0	ENST00000326873.7:c.595G>T	p.Glu199Ter	p.E199*	ENST00000326873	NM_000455.4	199	Gag/Tag	4/10	0.726667772361056	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.726667772361056	1		688	805	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	597	835	1	ENST00000269305.4:c.383del	p.Pro128LeufsTer42	p.P128Lfs*42	ENST00000269305	NM_001126112.2	128	cCt/ct	5/11	0.726667772361056	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.726667772361056	1		836	998	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578548	7578548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	598	823	1	ENST00000269305.4:c.382C>T	p.Pro128Ser	p.P128S	ENST00000269305	NM_001126112.2	128	Cct/Tct	5/11	0.726667772361056	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.726667772361056	1		824	996	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088799	27088799	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	293	398	0	ENST00000324856.7:c.2408A>G	p.Tyr803Cys	p.Y803C	ENST00000324856	NM_006015.4	803	tAt/tGt	7/20	0.726667772361056	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.726667772361056	1		398	450	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843498	3843498	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0034908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	444	586	0	ENST00000262367.5:c.1105A>T	p.Arg369Ter	p.R369*	ENST00000262367	NM_004380.2	369	Aga/Tga	4/31	0.726667772361056	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.726667772361056	1		586	679	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62305393	62305393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	438	668	0	ENST00000360203.5:c.866C>T	p.Ala289Val	p.A289V	ENST00000360203	NM_001283009.1	289	gCa/gTa	10/35	0.306796902033172	1	FACETS	0.723	0.691	0.754	0.723	0.691	0.754	INDETERMINATE	1	TRUE	0	0.726667772361056	1		668	1062	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182670	38182670	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1445122296	NA	P-0034908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	583	432	0	ENST00000396334.3:c.823A>G	p.Lys275Glu	p.K275E	ENST00000396334	NM_002468.4	275	Aaa/Gaa	5/5	0.726667772361056	2	FACETS	0.989	0.963	1	0.989	0.963	1	CLONAL	2	TRUE	0	0.726667772361056	2		432	811	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0034988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	116	478	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.886	0.801	0.976	0.886	0.801	0.976	CLONAL	1	TRUE	1	0.442879270508635	2		478	591	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0034988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	99	436	1	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.442879270508635	2		437	438	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248648	10248648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	128	549	0	ENST00000340748.4:c.4105G>A	p.Asp1369Asn	p.D1369N	ENST00000340748		1369	Gac/Aac	35/40	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.442879270508635	2		549	487	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114905777	114905777	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	119	505	0	ENST00000543371.1:c.796C>T	p.Gln266Ter	p.Q266*	ENST00000543371	NM_001198531.1	266	Caa/Taa	8/14	1	2	FACETS	0.946	0.857	1	0.946	0.857	1	CLONAL	1	TRUE	1	0.442879270508635	2		505	568	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131244	17131244	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	190	907	0	ENST00000285071.4:c.208G>T	p.Glu70Ter	p.E70*	ENST00000285071	NM_144997.5	70	Gag/Tag	4/14	0.442879270508635	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.442879270508635	1		907	653	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86676359	86676359	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	71	317	0	ENST00000274376.6:c.2637A>C	p.Lys879Asn	p.K879N	ENST00000274376	NM_002890.2	879	aaA/aaC	20/25	0.41071653167799	2	FACETS	1	0.892	1	0.507	0.446	0.572	CLONAL	1	TRUE	0	0.442879270508635	2		317	316	SUCCESS
APC	324	MSKCC	GRCh37	5	112175249	112175249	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	134	294	0	ENST00000257430.4:c.3958del	p.Val1320Ter	p.V1320*	ENST00000257430	NM_000038.5	1320	Gtg/tg	16/16	0.41071653167799	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.442879270508635	2		294	278	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309090	137309090	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	185	1037	0	ENST00000481739.1:c.697G>C	p.Glu233Gln	p.E233Q	ENST00000481739	NM_002957.4	233	Gag/Cag	5/10	1	2	FACETS	0.885	0.817	0.956	0.885	0.817	0.956	CLONAL	1	TRUE	1	0.442879270508635	2		1037	944	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0035026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	122	433	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.237377012282221	4	FACETS	1	0.984	1	0.729	0.66	0.803	CLONAL	1	TRUE	2	0.275639041830955	4		433	774	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210075	55210075	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	158	614	0	ENST00000275493.2:c.185T>G	p.Leu62Arg	p.L62R	ENST00000275493	NM_005228.3	62	cTt/cGt	2/28	0.237377012282221	4	FACETS	0.775	0.709	0.843	0.775	0.709	0.843	SUBCLONAL	2	TRUE	2	0.275639041830955	4		614	944	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627249	86627249	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	53	371	0	ENST00000274376.6:c.624G>C	p.Glu208Asp	p.E208D	ENST00000274376	NM_002890.2	208	gaG/gaC	2/25	0.270789378735953	3	FACETS	0.908	0.775	1	0.454	0.387	0.527	CLONAL	1	TRUE	1	0.275639041830955	3		371	482	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0035033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	101	432	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.409629146424809	2	FACETS	0.939	0.844	1	0.47	0.422	0.52	CLONAL	1	TRUE	0	0.469549758761766	2		438	458	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0035033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	70	328	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.712	0.623	0.807	0.712	0.623	0.807	SUBCLONAL	1	TRUE	1	0.469549758761766	2		328	419	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885511	23885512	+	splice_acceptor_variant	Splice_Site	INS	-	-	TGAT	novel	NA	P-0035033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	98	383	0	ENST00000374561.5:c.301-5_301-2dup		p.X101_splice	ENST00000374561	NM_002167.4	101			1	2	FACETS	0.975	0.875	1	0.975	0.875	1	CLONAL	1	TRUE	1	0.469549758761766	2		383	428	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261356	115261357	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0035033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	92	330	0	ENST00000438362.2:c.2364dup	p.Lys789GlnfsTer9	p.K789Qfs*9	ENST00000438362	NM_001242891.1	788	-/C	19/20	1	2	FACETS	0.893	0.797	0.993	0.893	0.797	0.993	CLONAL	1	TRUE	1	0.469549758761766	2		330	439	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0035033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	77	290	1	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	0.409629146424809	2	FACETS	0.808	0.713	0.909	0.404	0.356	0.455	CLONAL	1	TRUE	0	0.469549758761766	2		291	406	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244913	46244913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	136	563	0	ENST00000334344.6:c.3007G>A	p.Val1003Ile	p.V1003I	ENST00000334344	NM_152641.2	1003	Gtc/Atc	15/21	1	2	FACETS	0.924	0.843	1	0.924	0.843	1	CLONAL	1	TRUE	1	0.469549758761766	2		563	627	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58142976	58142976	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	165	684	0	ENST00000257904.6:c.808C>T	p.Gln270Ter	p.Q270*	ENST00000257904	NM_000075.3	270	Cag/Tag	7/8	1	2	FACETS	0.854	0.785	0.926	0.854	0.785	0.926	CLONAL	1	TRUE	1	0.469549758761766	2		684	823	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856094	111856094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs895574020	NA	P-0035033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	125	304	0	ENST00000341259.2:c.145G>A	p.Ala49Thr	p.A49T	ENST00000341259	NM_005475.2	49	Gcc/Acc	2/8	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.469549758761766	2		304	524	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954273	32954273	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359752	NA	P-0035033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	68	464	3	ENST00000380152.3:c.9253del	p.Thr3085GlnfsTer19	p.T3085Qfs*19	ENST00000380152		3083	Aaa/aa	24/27	0.469549758761766	6	FACETS	0.638	0.554	0.73	0.128	0.11	0.146	SUBCLONAL	1	TRUE	1	0.469549758761766	6		467	880	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135029	2135029	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0035033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	168	698	0	ENST00000219476.3:c.4569+2T>C		p.X1523_splice	ENST00000219476	NM_000548.3	1523			0.434289417946237	3	FACETS	0.959	0.882	1	0.48	0.441	0.52	CLONAL	1	TRUE	1	0.469549758761766	3		698	921	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579370	7579376	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCCCT	CTGCCCT	-	novel	NA	P-0035033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	311	665	0	ENST00000269305.4:c.311_317del	p.Gln104ProfsTer17	p.Q104Pfs*17	ENST00000269305	NM_001126112.2	104	cAGGGCAGc/cc	4/11	0.469549758761766	2	FACETS	0.884	0.839	0.93	0.884	0.839	0.93	CLONAL	2	TRUE	0	0.469549758761766	2		665	749	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229009	36229009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	209	805	2	ENST00000222270.7:c.7789G>A	p.Ala2597Thr	p.A2597T	ENST00000222270	NM_014727.1	2597	Gcg/Acg	36/37	0.434289417946237	3	FACETS	0.938	0.87	1	0.469	0.435	0.505	CLONAL	1	TRUE	1	0.469549758761766	3		807	1172	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967065	25967071	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCCTC	CTGCCTC	-	novel	NA	P-0035033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	170	578	0	ENST00000435504.4:c.2135_2141del	p.Gly712ValfsTer85	p.G712Vfs*85	ENST00000435504		712	gGAGGCAGt/gt	13/13	0.286649026379889	3	FACETS	1	0.966	1	0.544	0.5	0.589	CLONAL	1	TRUE	1	0.469549758761766	3		578	822	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158637068	158637069	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CA	CA	-	rs141073095	NA	P-0035033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	126	567	5	ENST00000263640.3:c.111_112del	p.Cys37Ter	p.C37*	ENST00000263640	NM_001105.4	37	tgTGaa/tgaa	4/11	0.286649026379889	3	FACETS	0.78	0.706	0.858	0.39	0.353	0.429	SUBCLONAL	1	TRUE	1	0.469549758761766	3		572	850	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572924	41572924	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	91	651	1	ENST00000263253.7:c.5209C>T	p.Arg1737Cys	p.R1737C	ENST00000263253	NM_001429.3	1737	Cgc/Tgc	31/31	0.434289417946237	3	FACETS	0.616	0.546	0.69	0.308	0.273	0.345	SUBCLONAL	1	TRUE	1	0.469549758761766	3		652	777	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37056036	37056036	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs267607789	NA	P-0035033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	164	242	0	ENST00000231790.2:c.790+1G>A		p.X264_splice	ENST00000231790	NM_000249.3	264			0.439799274907348	3	FACETS	0.924	0.865	0.983	0.924	0.865	0.983	CLONAL	3	TRUE	0	0.469549758761766	3		242	311	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163377	47163377	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	62	344	0	ENST00000409792.3:c.2749del	p.Ser917ValfsTer5	p.S917Vfs*5	ENST00000409792	NM_014159.6	917	Agt/gt	3/21	0.439799274907348	3	FACETS	0.725	0.627	0.83	0.242	0.209	0.277	SUBCLONAL	1	TRUE	0	0.469549758761766	3		344	450	SUCCESS
APC	324	MSKCC	GRCh37	5	112174775	112174776	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0035033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	46	215	0	ENST00000257430.4:c.3485dup	p.Tyr1162Ter	p.Y1162*	ENST00000257430	NM_000038.5	1162	tat/tAat	16/16	1	2	FACETS	0.867	0.737	1	0.867	0.737	1	CLONAL	1	TRUE	1	0.469549758761766	2		215	226	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704481	117704481	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs36029166	NA	P-0035033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	80	276	2	ENST00000368508.3:c.2495del	p.Lys832ArgfsTer2	p.K832Rfs*2	ENST00000368508	NM_002944.2	832	aAg/ag	16/43	0.434289417946237	3	FACETS	1	0.894	1	0.506	0.447	0.568	CLONAL	1	TRUE	1	0.469549758761766	3		278	416	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978602	70978602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	136	633	0	ENST00000276594.2:c.1051G>A	p.Glu351Lys	p.E351K	ENST00000276594	NM_024504.3	351	Gag/Aag	5/8	0.434289417946237	3	FACETS	0.818	0.744	0.897	0.409	0.372	0.449	CLONAL	1	TRUE	1	0.469549758761766	3		633	874	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776976	135776977	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	rs118203701	NA	P-0035033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	116	411	0	ENST00000298552.3:c.2501dup	p.Leu835AlafsTer5	p.L835Afs*5	ENST00000298552	NM_001162426.1	834	aag/aaAg	19/23	0.469549758761766	3	FACETS	1	0.946	1	0.534	0.483	0.588	CLONAL	1	TRUE	1	0.469549758761766	3		411	571	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409904	63409904	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1359607854	NA	P-0035033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	105	201	0	ENST00000330258.3:c.3263C>T	p.Pro1088Leu	p.P1088L	ENST00000330258	NM_152424.3	1088	cCc/cTc	2/2	0.469549758761766	2	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.469549758761766	2		201	326	SUCCESS
AR	367	MSKCC	GRCh37	X	66765796	66765797	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0035033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	192	482	0	ENST00000374690.3:c.812dup	p.Leu272ThrfsTer33	p.L272Tfs*33	ENST00000374690	NM_000044.3	270	gcc/gCcc	1/8	0.469549758761766	2	FACETS	1	0.96	1			1	CLONAL	1	TRUE	NA	0.469549758761766	2		482	776	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0035035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	107	552	1	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	1	2	FACETS	0.976	0.877	1	0.976	0.877	1	CLONAL	1	TRUE	1	0.349291767429331	2		553	628	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426801	47426806	+	inframe_deletion	In_Frame_Del	DEL	AGGCTT	AGGCTT	-	novel	NA	P-0035035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	94	602	0	ENST00000377045.4:c.1046_1051del	p.Gln349_Phe351delinsLeu	p.Q349_F351delinsL	ENST00000377045	NM_001654.4	349	cAGGCTTtc/ctc	10/16	0.3275066298104	1	FACETS	0.814	0.726	0.907	0.814	0.726	0.907	CLONAL	1	TRUE	0	0.349291767429331	1		602	546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579419	7579420	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0035035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	124	812	1	ENST00000269305.4:c.266_267dup	p.Ser90ProfsTer34	p.S90Pfs*34	ENST00000269305	NM_001126112.2	89	-/CC	4/11	0.301266654177305	1	FACETS	0.797	0.722	0.877	0.797	0.722	0.877	SUBCLONAL	1	TRUE	0	0.349291767429331	1		813	735	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141545625	141545625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750084158	NA	P-0035035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	105	931	2	ENST00000220592.5:c.2213C>T	p.Thr738Met	p.T738M	ENST00000220592	NM_012154.3	738	aCg/aTg	17/19	1	2	FACETS	0.601	0.537	0.669	0.601	0.537	0.669	SUBCLONAL	1	TRUE	1	0.349291767429331	2		933	1000	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs967461896	NA	P-0035090-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	404	737	0	ENST00000269305.4:c.526T>A	p.Cys176Ser	p.C176S	ENST00000269305	NM_001126112.2	176	Tgc/Agc	5/11	0.729453298106904	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.729453298106904	2		737	530	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240308	41240308	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035090-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	59	406	0	ENST00000379561.5:c.42C>G	p.Phe14Leu	p.F14L	ENST00000379561	NM_002015.3	14	ttC/ttG	1/3	0.595651893018913	4	FACETS	0.552	0.475	0.635	0.276	0.237	0.318	SUBCLONAL	1	TRUE	2	0.729453298106904	4		406	507	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26956975	26956975	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035090-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	98	366	0	ENST00000381527.3:c.481G>T	p.Gly161Cys	p.G161C	ENST00000381527	NM_001260.1	161	Ggt/Tgt	5/13	0.595651893018913	4	FACETS	1	0.947	1	0.544	0.488	0.603	CLONAL	1	TRUE	2	0.729453298106904	4		366	427	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110204	3110204	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035090-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	137	753	0	ENST00000078429.4:c.194C>G	p.Ala65Gly	p.A65G	ENST00000078429	NM_002067.2	65	gCc/gGc	2/7	0.729453298106904	3	FACETS	0.73	0.665	0.798	0.365	0.332	0.399	SUBCLONAL	1	TRUE	1	0.729453298106904	3		753	702	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652142	36652142	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035090-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	160	737	0	ENST00000244741.5:c.264G>C	p.Glu88Asp	p.E88D	ENST00000244741	NM_000389.4	88	gaG/gaC	2/3	0.65492337795901	4	FACETS	0.922	0.846	1	0.461	0.423	0.501	CLONAL	1	TRUE	2	0.729453298106904	4		737	823	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	298	700	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.388555334859745	3	FACETS	0.931	0.879	0.984	0.931	0.879	0.984	CLONAL	2	TRUE	1	0.438543663239995	3		700	890	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	157	368	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.398009114570724	3	FACETS	0.923	0.852	0.995	0.615	0.568	0.664	CLONAL	2	TRUE	0	0.438543663239995	3		368	473	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	92	432	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.388555334859745	3	FACETS	1	0.925	1	0.523	0.466	0.583	CLONAL	1	TRUE	1	0.438543663239995	3		438	489	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	302	675	1	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	0.297388499019738	4	FACETS	0.948	0.894	1	0.948	0.894	1	CLONAL	2	TRUE	2	0.438543663239995	4		676	1045	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132617	11132617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1445478818	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	352	843	2	ENST00000358026.2:c.2833G>A	p.Ala945Thr	p.A945T	ENST00000358026	NM_001128849.1	945	Gca/Aca	19/36	0.388555334859745	3	FACETS	0.945	0.896	0.994	0.945	0.896	0.994	CLONAL	2	TRUE	1	0.438543663239995	3		845	1036	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475061	40475063	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	290	717	0	ENST00000264657.5:c.1847_1849del	p.Glu616del	p.E616del	ENST00000264657	NM_139276.2	616	gAAGga/gga	20/24	0.297388499019738	4	FACETS	0.877	0.825	0.93	0.877	0.825	0.93	CLONAL	2	TRUE	2	0.438543663239995	4		717	1085	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	145	898	2	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	0.388555334859745	3	FACETS	0.785	0.715	0.859	0.393	0.357	0.43	SUBCLONAL	1	TRUE	1	0.438543663239995	3		900	1027	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515025	148515025	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	131	604	0	ENST00000320356.2:c.1184del	p.Gly395GlufsTer29	p.G395Efs*29	ENST00000320356	NM_004456.4	395	gGa/ga	10/20	0.438543663239995	4	FACETS	0.86	0.78	0.946	0.287	0.26	0.316	CLONAL	1	TRUE	1	0.438543663239995	4		604	999	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	154	679	2	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	0.388555334859745	3	FACETS	1	0.925	1	0.506	0.463	0.55	CLONAL	1	TRUE	1	0.438543663239995	3		681	847	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258744	115258744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434596	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	19	418	0	ENST00000369535.4:c.38G>A	p.Gly13Asp	p.G13D	ENST00000369535	NM_002524.4	13	gGt/gAt	2/7	0.388555334859745	3	FACETS	0.149	0.112	0.193	0.075	0.056	0.097	SUBCLONAL	1	TRUE	1	0.438543663239995	3		418	707	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678727	52678727	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	357	539	0	ENST00000394830.3:c.892C>T	p.Arg298Ter	p.R298*	ENST00000394830	NM_018313.4	298	Cga/Tga	9/30	0.413051311877057	3	FACETS	1	0.993	1	0.827	0.788	0.866	CLONAL	2	TRUE	0	0.438543663239995	3		539	800	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	231	572	1	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	0.388555334859745	3	FACETS	0.908	0.851	0.967	0.908	0.851	0.967	CLONAL	2	TRUE	1	0.438543663239995	3		573	707	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	122	534	2	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	0.297388499019738	4	FACETS	0.975	0.881	1	0.487	0.44	0.537	CLONAL	1	TRUE	2	0.438543663239995	4		536	821	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667635	29667638	+	frameshift_variant	Frame_Shift_Del	DEL	TAGA	TAGA	-	novel	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	255	577	0	ENST00000356175.3:c.6974_6977del	p.Asp2325ValfsTer49	p.D2325Vfs*49	ENST00000356175	NM_000267.3	2324	tTAGAt/tt	46/57	0.297388499019738	4	FACETS	0.796	0.745	0.848	0.796	0.745	0.848	SUBCLONAL	2	TRUE	2	0.438543663239995	4		577	1051	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971058	21971058	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660818	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	244	446	0	ENST00000579755.1:c.343C>T	p.Arg115Trp	p.R115W	ENST00000579755		115	Cgg/Tgg	2/3	0.39932507951965	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.438543663239995	2		446	492	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405953	157405954	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1554294674	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	76	531	0	ENST00000346085.5:c.2201dup	p.Ser736IlefsTer27	p.S736Ifs*27	ENST00000346085	NM_020732.3	732	ccg/ccGg	6/20	0.388555334859745	3	FACETS	0.621	0.545	0.704	0.311	0.272	0.352	SUBCLONAL	1	TRUE	1	0.438543663239995	3		531	680	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639588	47639588	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63749897	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	155	345	0	ENST00000233146.2:c.687del	p.Ala230LeufsTer16	p.A230Lfs*16	ENST00000233146	NM_000251.2	227	agA/ag	4/16	0.39962862523542	3	FACETS	0.842	0.776	0.91	0.842	0.776	0.91	CLONAL	2	TRUE	1	0.438543663239995	3		345	512	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023831	27023831	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1415214478	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	134	256	1	ENST00000324856.7:c.941del	p.Gly314AlafsTer49	p.G314Afs*49	ENST00000324856	NM_006015.4	313	Ggg/gg	1/20	0.388555334859745	3	FACETS	0.927	0.85	1	0.927	0.85	1	CLONAL	2	TRUE	1	0.438543663239995	3		257	402	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486050	29486050	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1438566555	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	199	377	0	ENST00000356175.3:c.233del	p.Asn78IlefsTer7	p.N78Ifs*7	ENST00000356175	NM_000267.3	76	gAa/ga	3/57	0.297388499019738	4	FACETS	0.979	0.911	1	0.979	0.911	1	CLONAL	2	TRUE	2	0.438543663239995	4		377	667	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209282	98209282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372686352	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	129	729	0	ENST00000331920.6:c.4256G>A	p.Arg1419Gln	p.R1419Q	ENST00000331920	NM_000264.3	1419	cGg/cAg	23/24	0.39932507951965	2	FACETS	0.86	0.781	0.943	0.43	0.39	0.472	CLONAL	1	TRUE	0	0.438543663239995	2		729	684	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77069989	77069990	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAT	rs149665907	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	85	558	0	ENST00000356341.3:c.548_550dup	p.Asp183dup	p.D183dup	ENST00000356341	NM_002576.4	183	gct/gATGct	6/15	0.388555334859745	3	FACETS	0.666	0.588	0.749	0.333	0.294	0.375	SUBCLONAL	1	TRUE	1	0.438543663239995	3		558	710	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	334	757	1	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	0.388555334859745	3	FACETS	0.909	0.861	0.958	0.909	0.861	0.958	CLONAL	2	TRUE	1	0.438543663239995	3		758	1022	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	178	920	7	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	0.388555334859745	3	FACETS	0.858	0.79	0.93	0.429	0.395	0.465	CLONAL	1	TRUE	1	0.438543663239995	3		927	1153	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900060	151900060	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	136	488	1	ENST00000262189.6:c.4051del	p.Arg1351GlyfsTer23	p.R1351Gfs*23	ENST00000262189	NM_170606.2	1351	Agg/gg	26/59	0.438543663239995	4	FACETS	0.84	0.763	0.922	0.28	0.254	0.308	CLONAL	1	TRUE	1	0.438543663239995	4		489	1062	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	174	693	2	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	0.39962862523542	3	FACETS	1	0.983	1	0.614	0.566	0.664	CLONAL	1	TRUE	1	0.438543663239995	3		695	788	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350822	15350822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200902225	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	213	560	0	ENST00000263377.2:c.3181G>A	p.Glu1061Lys	p.E1061K	ENST00000263377	NM_058243.2	1061	Gaa/Aaa	15/20	0.388555334859745	3	FACETS	0.848	0.792	0.907	0.848	0.792	0.907	CLONAL	2	TRUE	1	0.438543663239995	3		560	698	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059207	27059207	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	96	514	0	ENST00000324856.7:c.1848del	p.Ser617GlnfsTer2	p.S617Qfs*2	ENST00000324856	NM_006015.4	615	gCc/gc	4/20	0.388555334859745	3	FACETS	0.754	0.672	0.841	0.377	0.336	0.421	SUBCLONAL	1	TRUE	1	0.438543663239995	3		514	708	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134473	30134473	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	79	498	0	ENST00000263025.4:c.58del	p.Val20SerfsTer12	p.V20Sfs*12	ENST00000263025	NM_002746.2	20	Gtc/tc	1/9	0.388555334859745	3	FACETS	0.851	0.751	0.959	0.426	0.375	0.48	CLONAL	1	TRUE	1	0.438543663239995	3		498	516	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225770	26225770	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs966515186	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	100	517	0	ENST00000360408.1:c.388C>T	p.Arg130Cys	p.R130C	ENST00000360408	NM_003532.2	130	Cgc/Tgc	1/1	0.413051311877057	3	FACETS	0.798	0.713	0.888	0.266	0.237	0.296	SUBCLONAL	1	TRUE	0	0.438543663239995	3		517	697	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007585	62007585	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs377108188	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	181	870	0	ENST00000392795.3:c.282G>T	p.Lys94Asn	p.K94N	ENST00000392795	NM_001039933.1	94	aaG/aaT	3/6	0.297388499019738	4	FACETS	0.977	0.899	1	0.488	0.449	0.529	CLONAL	1	TRUE	2	0.438543663239995	4		870	1216	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211521	98211521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559827048	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	216	506	2	ENST00000331920.6:c.3634G>A	p.Gly1212Ser	p.G1212S	ENST00000331920	NM_000264.3	1212	Ggc/Agc	22/24	0.39932507951965	2	FACETS	0.973	0.914	1	0.973	0.914	1	CLONAL	2	TRUE	0	0.438543663239995	2		508	506	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260144	16260144	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	127	561	0	ENST00000375759.3:c.7409C>A	p.Pro2470His	p.P2470H	ENST00000375759	NM_015001.2	2470	cCc/cAc	11/15	0.388555334859745	3	FACETS	1	0.945	1	0.529	0.48	0.58	CLONAL	1	TRUE	1	0.438543663239995	3		561	668	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318805	163318806	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1557956181	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	70	428	0	ENST00000271452.3:c.1201dup	p.Ile401AsnfsTer2	p.I401Nfs*2	ENST00000271452	NM_145697.2	399	caa/cAaa	13/14	0.388555334859745	3	FACETS	0.684	0.597	0.778	0.342	0.298	0.389	SUBCLONAL	1	TRUE	1	0.438543663239995	3		428	569	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925622	114925622	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1189031682	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	264	704	0	ENST00000543371.1:c.1704del	p.Ser569ProfsTer33	p.S569Pfs*33	ENST00000543371	NM_001198531.1	567	gCc/gc	14/14	0.388555334859745	3	FACETS	0.937	0.882	0.994	0.937	0.882	0.994	CLONAL	2	TRUE	1	0.438543663239995	3		704	783	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912755	100912755	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1228592262	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	113	547	1	ENST00000325455.5:c.2567T>C	p.Ile856Thr	p.I856T	ENST00000325455	NM_001202474.3	856	aTt/aCt	7/8	0.388555334859745	3	FACETS	0.824	0.741	0.911	0.412	0.37	0.456	CLONAL	1	TRUE	1	0.438543663239995	3		548	763	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427395	49427395	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs35493001	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	155	699	0	ENST00000301067.7:c.11093del	p.Gly3698AlafsTer51	p.G3698Afs*51	ENST00000301067	NM_003482.3	3698	gGc/gc	39/54	0.39962862523542	3	FACETS	0.998	0.914	1	0.499	0.457	0.543	CLONAL	1	TRUE	1	0.438543663239995	3		699	864	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856186	111856187	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	189	326	1	ENST00000341259.2:c.240_241del	p.Asp81ArgfsTer41	p.D81Rfs*41	ENST00000341259	NM_005475.2	79	gtGCgc/gtgc	2/8	0.438543663239995	3	FACETS	0.765	0.709	0.822	0.765	0.709	0.822	SUBCLONAL	2	TRUE	1	0.438543663239995	3		327	687	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72994013	72994013	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	135	640	0	ENST00000268489.5:c.32G>T	p.Gly11Val	p.G11V	ENST00000268489	NM_006885.3	11	gGg/gTg	2/10	0.388555334859745	3	FACETS	0.941	0.855	1	0.47	0.427	0.515	CLONAL	1	TRUE	1	0.438543663239995	3		640	798	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007194	62007194	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	81	729	0	ENST00000392795.3:c.488T>C	p.Ile163Thr	p.I163T	ENST00000392795	NM_001039933.1	163	aTc/aCc	4/6	0.297388499019738	4	FACETS	0.477	0.419	0.54	0.239	0.209	0.27	SUBCLONAL	1	TRUE	2	0.438543663239995	4		729	1113	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867354	45867354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755174338	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	122	738	0	ENST00000391945.4:c.839G>A	p.Arg280His	p.R280H	ENST00000391945	NM_000400.3	280	cGc/cAc	10/23	0.388555334859745	3	FACETS	0.791	0.714	0.871	0.395	0.357	0.436	SUBCLONAL	1	TRUE	1	0.438543663239995	3		738	858	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42851109	42851110	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	85	479	0	ENST00000398585.3:c.783dup	p.Leu262ThrfsTer5	p.L262Tfs*5	ENST00000398585	NM_001135099.1	261	-/A	7/14	0.126691076795775	3	FACETS	0.676	0.598	0.76	0.225	0.199	0.254	INDETERMINATE	1	TRUE	0	0.438543663239995	3		479	699	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050303	37050303	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	237	254	0	ENST00000231790.2:c.454-2A>T		p.X152_splice	ENST00000231790	NM_000249.3	152			0.413051311877057	3	FACETS	0.976	0.924	1	0.976	0.924	1	CLONAL	3	TRUE	0	0.438543663239995	3		254	450	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935640	49935640	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	231	543	0	ENST00000296474.3:c.1724A>G	p.His575Arg	p.H575R	ENST00000296474	NM_002447.2	575	cAc/cGc	5/20	0.413051311877057	3	FACETS	1	0.956	1	0.682	0.64	0.725	CLONAL	2	TRUE	0	0.438543663239995	3		543	628	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356274	66356274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	115	613	0	ENST00000273854.3:c.1223G>A	p.Cys408Tyr	p.C408Y	ENST00000273854	NM_004439.5	408	tGt/tAt	5/18	0.39932507951965	2	FACETS	0.84	0.759	0.926	0.42	0.379	0.463	CLONAL	1	TRUE	0	0.438543663239995	2		613	624	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056240	26056240	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs547786942	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	462	634	0	ENST00000343677.2:c.417G>C	p.Lys139Asn	p.K139N	ENST00000343677	NM_005319.3	139	aaG/aaC	1/1	0.413051311877057	3	FACETS	0.997	0.959	1	0.997	0.959	1	CLONAL	3	TRUE	0	0.438543663239995	3		634	859	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441971	6441971	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	194	709	0	ENST00000356142.4:c.530C>T	p.Ser177Leu	p.S177L	ENST00000356142	NM_018890.3	177	tCg/tTg	7/7	0.438543663239995	4	FACETS	1	0.963	1	0.357	0.329	0.385	CLONAL	1	TRUE	1	0.438543663239995	4		709	1189	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975492	13975492	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	63	328	0	ENST00000405192.2:c.395T>C	p.Met132Thr	p.M132T	ENST00000405192	NM_001163147.1	132	aTg/aCg	7/12	0.438543663239995	4	FACETS	0.818	0.709	0.937	0.273	0.236	0.313	CLONAL	1	TRUE	1	0.438543663239995	4		328	505	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508623	106508623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	85	425	0	ENST00000359195.3:c.617C>T	p.Pro206Leu	p.P206L	ENST00000359195	NM_002649.2	206	cCc/cTc	2/11	0.438543663239995	4	FACETS	0.797	0.704	0.896	0.266	0.234	0.299	SUBCLONAL	1	TRUE	1	0.438543663239995	4		425	700	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140507808	140507810	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	novel	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	311	485	0	ENST00000288602.6:c.661_663del	p.Glu221del	p.E221del	ENST00000288602	NM_004333.4	221	GAA/-	5/18	0.438543663239995	4	FACETS	0.863	0.818	0.909	0.863	0.818	0.909	CLONAL	3	TRUE	1	0.438543663239995	4		485	788	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845394	151845394	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	538	712	3	ENST00000262189.6:c.13618C>T	p.Gln4540Ter	p.Q4540*	ENST00000262189	NM_170606.2	4540	Caa/Taa	52/59	0.438543663239995	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	1	0.438543663239995	4		715	1148	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874826	151874826	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142788583	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	177	368	0	ENST00000262189.6:c.7712G>A	p.Arg2571Gln	p.R2571Q	ENST00000262189	NM_170606.2	2571	cGg/cAg	38/59	0.438543663239995	4	FACETS	0.907	0.84	0.977	0.605	0.56	0.652	CLONAL	2	TRUE	1	0.438543663239995	4		368	640	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551310	141551310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	195	933	1	ENST00000220592.5:c.1987C>T	p.Arg663Cys	p.R663C	ENST00000220592	NM_012154.3	663	Cgc/Tgc	15/19	0.388555334859745	3	FACETS	0.904	0.835	0.975	0.452	0.417	0.488	CLONAL	1	TRUE	1	0.438543663239995	3		934	1200	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145736855	145736855	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	163	697	0	ENST00000428558.2:c.3586del	p.Val1196TrpfsTer23	p.V1196Wfs*23	ENST00000428558	NM_004260.3	1196	Gtg/tg	22/22	0.388555334859745	3	FACETS	0.984	0.903	1	0.492	0.451	0.535	CLONAL	1	TRUE	1	0.438543663239995	3		697	921	SUCCESS
AR	367	MSKCC	GRCh37	X	66765267	66765267	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	91	570	0	ENST00000374690.3:c.279G>T	p.Glu93Asp	p.E93D	ENST00000374690	NM_000044.3	93	gaG/gaT	1/8	0.438543663239995	2	FACETS	0.804	0.716	0.897	0.402	0.358	0.449	CLONAL	1	TRUE	0	0.438543663239995	2		570	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578260	7578260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204041	NA	P-0035127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	209	714	0	ENST00000269305.4:c.589G>A	p.Val197Met	p.V197M	ENST00000269305	NM_001126112.2	197	Gtg/Atg	6/11	0.378622904623198	2	FACETS	0.928	0.869	0.988	0.928	0.869	0.988	CLONAL	2	TRUE	0	0.420178297431845	2		714	536	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0035127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	141	568	2	ENST00000311936.3:c.180_181delinsAA	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggAAaa	3/5	0.328231030769109	4	FACETS	1	0.976	1			1	CLONAL	2	TRUE	NA	0.420178297431845	4		570	411	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259578	89259578	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	95	449	0	ENST00000336596.2:c.722G>A	p.Arg241Lys	p.R241K	ENST00000336596	NM_005233.5	241	aGg/aAg	3/17	0.378622904623198	2	FACETS	0.788	0.711	0.867	0.788	0.711	0.867	SUBCLONAL	2	TRUE	0	0.420178297431845	2		449	287	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448297	56448298	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1567880599	NA	P-0035127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	432	724	2	ENST00000407977.2:c.349dup	p.Arg117ProfsTer8	p.R117Pfs*8	ENST00000407977		117	cgc/cCgc	3/10	0.420178297431845	1	FACETS	0.803	0.768	0.838	1	0.996	1	CLONAL	2	TRUE	0	0.420178297431845	1		726	1012	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087587	27087587	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	134	567	0	ENST00000324856.7:c.2161G>T	p.Gly721Cys	p.G721C	ENST00000324856	NM_006015.4	721	Ggc/Tgc	5/20	1	2	FACETS	0.941	0.857	1	0.941	0.857	1	CLONAL	1	TRUE	1	0.420178297431845	2		567	678	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251805	212251805	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	87	402	0	ENST00000342788.4:c.3254C>G	p.Thr1085Ser	p.T1085S	ENST00000342788	NM_005235.2	1085	aCt/aGt	27/28	0.420178297431845	5	FACETS	0.867	0.767	0.974	0.289	0.255	0.325	CLONAL	1	TRUE	2	0.420178297431845	5		402	779	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55231434	55231434	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	162	628	0	ENST00000275493.2:c.1640G>A	p.Arg547Lys	p.R547K	ENST00000275493	NM_005228.3	547	aGg/aAg	14/28	1	2	FACETS	0.862	0.791	0.936	0.862	0.791	0.936	CLONAL	1	TRUE	1	0.420178297431845	2		628	895	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566379	139566379	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	154	652	0	ENST00000308874.7:c.638A>C	p.Lys213Thr	p.K213T	ENST00000308874		213	aAg/aCg	9/10	0.378622904623198	2	FACETS	1	0.959	1	0.536	0.491	0.582	CLONAL	1	TRUE	0	0.420178297431845	2		652	684	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0035140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	118	567	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.202932098319738	2		567	1131	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221315	1221316	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	45	565	1	ENST00000326873.7:c.838_839insT	p.Pro280LeufsTer5	p.P280Lfs*5	ENST00000326873	NM_000455.4	280	ccc/cTcc	6/10	0.202932098319738	0	FACETS	0.888	0.748	1			1	CLONAL	1	TRUE	0	0.202932098319738	0		566	398	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039440	47039440	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0035140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	50	259	0	ENST00000377604.3:c.1062+1G>T		p.X354_splice	ENST00000377604	NM_001204468.1	354			0.0603904368439712	2	FACETS	1	0.927	1			1	INDETERMINATE	2	TRUE	NA	0.202932098319738	2		259	218	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	231	734	0	ENST00000269305.4:c.772G>C	p.Glu258Gln	p.E258Q	ENST00000269305	NM_001126112.2	258	Gaa/Caa	7/11	0.563390630676489	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.563390630676489	1		734	562	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593491	48593494	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	rs80338965	NA	P-0035154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	75	384	0	ENST00000342988.3:c.1245_1248del	p.Asp415GlufsTer20	p.D415Efs*20	ENST00000342988	NM_005359.5	414	ttAGAC/tt	10/12	0.563390630676489	1	FACETS	0.637	0.564	0.715	0.637	0.564	0.715	SUBCLONAL	1	TRUE	0	0.563390630676489	1		384	300	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520087	106520087	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774448553	NA	P-0035154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	52	331	1	ENST00000359195.3:c.2515C>T	p.Arg839Cys	p.R839C	ENST00000359195	NM_002649.2	839	Cgc/Tgc	6/11	1	2	FACETS	0.82	0.707	0.942	0.82	0.707	0.942	CLONAL	1	TRUE	1	0.563390630676489	2		332	225	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324509	31324509	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs41553715	NA	P-0035154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	20	433	6	ENST00000412585.2:c.299A>T	p.Glu100Val	p.E100V	ENST00000412585	NM_005514.6	100	gAg/gTg	2/8	0.447670006249441	2	FACETS	0.258	0.197	0.329	0.129	0.098	0.165	SUBCLONAL	1	TRUE	0	0.563390630676489	2		439	275	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971150	21971173	+	inframe_deletion	In_Frame_Del	DEL	GCTCCGCGCCGTGGAGCAGCAGCA	GCTCCGCGCCGTGGAGCAGCAGCA	-	novel	NA	P-0035154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	88	429	0	ENST00000304494.5:c.185_208del	p.Leu62_Glu69del	p.L62_E69del	ENST00000304494	NM_000077.4	62	cTGCTGCTGCTCCACGGCGCGGAGCcc/ccc	2/3	0.284403361918316	1	FACETS	0.658	0.588	0.731	0.658	0.588	0.731	INDETERMINATE	1	TRUE	0	0.563390630676489	1		429	341	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619810	1619810	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1302173832	NA	P-0035154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	154	717	1	ENST00000344749.5:c.1136C>T	p.Ser379Leu	p.S379L	ENST00000344749	NM_001136139.2	379	tCg/tTg	14/19	1	2	FACETS	0.823	0.756	0.894	0.823	0.756	0.894	CLONAL	1	TRUE	1	0.563390630676489	2		718	664	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120740	115120740	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	168	672	0	ENST00000257566.3:c.266C>A	p.Pro89His	p.P89H	ENST00000257566	NM_016569.3	89	cCt/cAt	1/8	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.563390630676489	2		672	590	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266058	41266274	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTG	AAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTG	-	novel	NA	P-0035154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	60	348	0	ENST00000349496.5:c.59_241+34del		p.X20_splice	ENST00000349496	NM_001904.3	20		3/15	0.556281013899841	2	FACETS	0.906	0.791	1	0.453	0.395	0.515	CLONAL	1	TRUE	0	0.563390630676489	2		348	235	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142950045	142950045	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	96	553	0	ENST00000262992.4:c.2665G>C	p.Val889Leu	p.V889L	ENST00000262992	NM_001101669.1	889	Gta/Cta	24/24	1	2	FACETS	0.881	0.791	0.975	0.881	0.791	0.975	CLONAL	1	TRUE	1	0.563390630676489	2		553	387	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589547	67589582	+	inframe_deletion	In_Frame_Del	DEL	TCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAAT	TCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAAT	-	novel	NA	P-0035154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	45	229	0	ENST00000274335.5:c.1311_1346del	p.Lys438_Leu449del	p.K438_L449del	ENST00000274335		437	gTCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAATta/gta	10/15	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.563390630676489	2		229	154	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0035156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	211	433	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.3	4	FACETS	1	0.975	1			1	CLONAL	4	TRUE	NA	0.13	4		433	834	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578420	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AG	novel	NA	P-0035156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	31	685	1	ENST00000269305.4:c.510_511delinsCT	p.Glu171Ter	p.E171*	ENST00000269305	NM_001126112.2	170	acGGag/acCTag	5/11	1	2	FACETS	0.506	0.407	0.619	0.506	0.407	0.619	SUBCLONAL	1	TRUE	1	0.13	2		686	943	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513346	44513346	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	42	442	0	ENST00000291552.4:c.589T>G	p.Ser197Ala	p.S197A	ENST00000291552	NM_006758.2	197	Tcc/Gcc	8/8	1	2	FACETS	0.856	0.713	1	0.856	0.713	1	CLONAL	1	TRUE	1	0.13	2		442	755	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790122	40790122	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372056802	NA	P-0035172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	228	487	0	ENST00000373198.4:c.2609G>A	p.Arg870His	p.R870H	ENST00000373198	NM_133170.3	870	cGc/cAc	18/32	0.252698784864683	3	FACETS	0.907	0.848	0.967	0.907	0.848	0.967	CLONAL	3	TRUE	0	0.252698784864683	3		487	747	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577507	7577507	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	137	587	0	ENST00000269305.4:c.774A>C	p.Glu258Asp	p.E258D	ENST00000269305	NM_001126112.2	258	gaA/gaC	7/11	1	2	FACETS	0.756	0.689	0.827	1	0.987	1	SUBCLONAL	2	TRUE	1	0.252698784864683	2		587	717	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404619	8404619	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	32	276	0	ENST00000356435.5:c.4128C>A	p.Asn1376Lys	p.N1376K	ENST00000356435		1376	aaC/aaA	25/35	0.251182052220664	2	FACETS	0.688	0.559	0.834	0.344	0.279	0.417	SUBCLONAL	1	TRUE	0	0.252698784864683	2		276	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0035175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	245	675	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.770636623661868	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.772346944861305	1		675	371	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0035175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	193	568	2	ENST00000311936.3:c.180_181delinsAA	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggAAaa	3/5	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.772346944861305	2		570	487	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411216	63411216	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778026	NA	P-0035175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	101	668	2	ENST00000330258.3:c.1951G>A	p.Val651Ile	p.V651I	ENST00000330258	NM_152424.3	651	Gtc/Atc	2/2	NA	2	FACETS	0.6	0.539	0.663			1	INDETERMINATE	1	TRUE	NA	0.772346944861305	2		670	436	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782071	9782071	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	118	700	4	ENST00000377346.4:c.2094C>A	p.Phe698Leu	p.F698L	ENST00000377346	NM_005026.3	698	ttC/ttA	17/24	NA	2	FACETS	0.749	0.681	0.819			1	INDETERMINATE	1	TRUE	NA	0.772346944861305	2		704	408	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999732	100999732	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	223	685	4	ENST00000325455.5:c.70G>A	p.Gly24Arg	p.G24R	ENST00000325455	NM_001202474.3	24	Gga/Aga	1/8	1	2	FACETS	0.996	0.934	1	0.996	0.934	1	CLONAL	1	TRUE	1	0.772346944861305	2		689	580	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492904	56492905	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0035175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	187	328	2	ENST00000407977.2:c.33_34dup	p.Leu12ProfsTer7	p.L12Pfs*7	ENST00000407977		12	ctc/cCCtc	2/10	0.772346944861305	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.772346944861305	1		330	257	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17389843	17389843	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	26	816	0	ENST00000359435.4:c.976G>C	p.Glu326Gln	p.E326Q	ENST00000359435	NM_001033549.1	326	Gag/Cag	9/9	0.772346944861305	1	FACETS	0.105	0.083	0.13	0.105	0.083	0.13	SUBCLONAL	1	TRUE	0	0.772346944861305	1		816	394	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165684	47165684	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	60	659	0	ENST00000409792.3:c.442C>G	p.Leu148Val	p.L148V	ENST00000409792	NM_014159.6	148	Ctg/Gtg	3/21	0.577057493771099	1	FACETS	0.252	0.218	0.289	0.252	0.218	0.289	SUBCLONAL	1	TRUE	0	0.772346944861305	1		659	378	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851565	134851565	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0035175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	37	501	0	ENST00000398015.3:c.971C>G	p.Ser324Ter	p.S324*	ENST00000398015	NM_004441.4	324	tCa/tGa	5/16	NA	2	FACETS	0.282	0.233	0.337			1	INDETERMINATE	1	TRUE	NA	0.772346944861305	2		501	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0035180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	20	700	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.957	0.743	1	0.957	0.743	1	CLONAL	1	TRUE	1	0.38	2		700	110	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0035180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	15	596	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.731	0.541	0.954	0.731	0.541	0.954	CLONAL	1	TRUE	1	0.38	2		597	108	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0035180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	23	436	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.487879610302356	1	FACETS	0.883	0.701	1	0.883	0.701	1	CLONAL	1	TRUE	0	0.38	1		436	111	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562657	29562660	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs1064794276	NA	P-0035180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	29	446	0	ENST00000356175.3:c.3739_3742del	p.Phe1247IlefsTer18	p.F1247Ifs*18	ENST00000356175	NM_000267.3	1246	cTGTTt/ct	28/57	0.402779182303906	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.38	1		446	98	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851717	134851717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150028142	NA	P-0035180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	30	427	0	ENST00000398015.3:c.1123G>A	p.Asp375Asn	p.D375N	ENST00000398015	NM_004441.4	375	Gac/Aac	5/16	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.38	2		427	119	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245759	41245759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55650082	NA	P-0035180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	20	616	0	ENST00000357654.3:c.1789G>A	p.Glu597Lys	p.E597K	ENST00000357654	NM_007294.3	597	Gaa/Aaa	10/23	0.0839839724769605	0	FACETS	0.653	0.508	0.815			1	INDETERMINATE	1	TRUE	0	0.38	0		616	100	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846291	156846291	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760764097	NA	P-0035180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	23	690	0	ENST00000524377.1:c.1732G>A	p.Val578Ile	p.V578I	ENST00000524377	NM_002529.3	578	Gtc/Atc	14/17	1	2	FACETS	1	0.817	1	1	0.817	1	CLONAL	1	TRUE	1	0.38	2		690	117	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56871587	56871587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758034157	NA	P-0035180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	30	403	0	ENST00000308159.5:c.1967C>T	p.Pro656Leu	p.P656L	ENST00000308159	NM_014669.4	656	cCg/cTg	18/22	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.38	2		403	108	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209630	98209630	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779365332	NA	P-0035180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	13	503	2	ENST00000331920.6:c.3908G>A	p.Arg1303His	p.R1303H	ENST00000331920	NM_000264.3	1303	cGc/cAc	23/24	1	2	FACETS	0.522	0.375	0.699	0.522	0.375	0.699	SUBCLONAL	1	TRUE	1	0.38	2		505	131	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470498	25470498	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747448117	NA	P-0035180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	19	532	2	ENST00000264709.3:c.976C>T	p.Arg326Cys	p.R326C	ENST00000264709	NM_175629.2	326	Cgc/Tgc	8/23	0.487879610302356	1	FACETS	0.976	0.758	1	0.976	0.758	1	CLONAL	1	TRUE	0	0.38	1		534	83	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371797	116371797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774779741	NA	P-0035180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	11	463	0	ENST00000397752.3:c.1276C>T	p.Arg426Cys	p.R426C	ENST00000397752	NM_000245.2	426	Cgc/Tgc	3/21	1	2	FACETS	0.517	0.36	0.709	0.517	0.36	0.709	SUBCLONAL	1	TRUE	1	0.38	2		463	112	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579365	7579365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782461	NA	P-0035180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	36	518	0	ENST00000269305.4:c.322G>A	p.Gly108Ser	p.G108S	ENST00000269305	NM_001126112.2	108	Ggt/Agt	4/11	1	2	FACETS	0.777	0.652	0.909	1	0.958	1	CLONAL	2	TRUE	1	0.38	2		518	122	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858201	9858201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	22	497	0	ENST00000330684.3:c.3200G>A	p.Arg1067Gln	p.R1067Q	ENST00000330684	NM_001134407.1	1067	cGg/cAg	13/13	1	2	FACETS	0.949	0.746	1	0.949	0.746	1	CLONAL	1	TRUE	1	0.38	2		497	122	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041026	112041026	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746134687	NA	P-0035180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	26	331	0	ENST00000368678.4:c.229C>T	p.Arg77Cys	p.R77C	ENST00000368678		77	Cgt/Tgt	3/13	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.38	2		331	107	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198888	67198888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751194292	NA	P-0035180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	22	403	0	ENST00000312629.5:c.359G>A	p.Arg120Gln	p.R120Q	ENST00000312629	NM_003952.2	120	cGg/cAg	5/15	1	2	FACETS	1	0.836	1	1	0.836	1	CLONAL	1	TRUE	1	0.38	2		403	108	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568636	41568636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	28	294	0	ENST00000263253.7:c.4586G>A	p.Arg1529Gln	p.R1529Q	ENST00000263253	NM_001429.3	1529	cGa/cAa	28/31	0.144467008233851	0	FACETS	0.923	0.756	1			1	INDETERMINATE	1	TRUE	0	0.38	0		294	99	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306549	163306549	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753469318	NA	P-0035180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	24	312	0	ENST00000271452.3:c.346C>T	p.Arg116Trp	p.R116W	ENST00000271452	NM_145697.2	116	Cgg/Tgg	6/14	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.38	2		312	112	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478756	57478757	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0035180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	13	339	1	ENST00000371085.3:c.348dup	p.Val117ArgfsTer23	p.V117Rfs*23	ENST00000371085	NM_000516.4	114	-/C	5/13	1	2	FACETS	0.664	0.479	0.885	0.664	0.479	0.885	SUBCLONAL	1	TRUE	1	0.38	2		340	103	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277291	41277291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	17	323	1	ENST00000349496.5:c.1760G>A	p.Arg587Gln	p.R587Q	ENST00000349496	NM_001904.3	587	cGa/cAa	11/15	1	2	FACETS	0.973	0.739	1	0.973	0.739	1	CLONAL	1	TRUE	1	0.38	2		324	92	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860908	151860908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	20	267	0	ENST00000262189.6:c.9754C>T	p.Arg3252Cys	p.R3252C	ENST00000262189	NM_170606.2	3252	Cgt/Tgt	43/59	1	2	FACETS	0.993	0.772	1	0.993	0.772	1	CLONAL	1	TRUE	1	0.38	2		267	106	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420190	49420190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775954885	NA	P-0035180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	17	564	0	ENST00000301067.7:c.15559G>A	p.Ala5187Thr	p.A5187T	ENST00000301067	NM_003482.3	5187	Gcc/Acc	48/54	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.38	2		564	72	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039222	49039223	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0035180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	28	386	0	ENST00000267163.4:c.2302_2303del	p.Ile768PhefsTer26	p.I768Ffs*26	ENST00000267163	NM_000321.2	767	aAT/a	22/27	0.402779182303906	1	FACETS	0.785	0.65	0.927	1	0.95	1	CLONAL	2	TRUE	0	0.38	1		386	76	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134658	2134658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777529733	NA	P-0035180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	10	564	0	ENST00000219476.3:c.4435G>A	p.Ala1479Thr	p.A1479T	ENST00000219476	NM_000548.3	1479	Gcc/Acc	34/42	1	2	FACETS	0.492	0.335	0.685	0.492	0.335	0.685	SUBCLONAL	1	TRUE	1	0.38	2		564	107	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346348	89346348	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371524118	NA	P-0035180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	25	382	0	ENST00000301030.4:c.6602C>T	p.Ala2201Val	p.A2201V	ENST00000301030	NM_001256183.1	2201	gCa/gTa	9/13	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.38	2		382	93	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212224	5212224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151279682	NA	P-0035180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	13	546	0	ENST00000357368.4:c.4807G>A	p.Asp1603Asn	p.D1603N	ENST00000357368	NM_002850.3	1603	Gac/Aac	32/38	0.0839839724769605	0	FACETS	0.404	0.291	0.539			1	INDETERMINATE	1	TRUE	0	0.38	0		546	105	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254461	10254461	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144533539	NA	P-0035180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	34	441	2	ENST00000340748.4:c.3049C>T	p.Arg1017Trp	p.R1017W	ENST00000340748		1017	Cgg/Tgg	28/40	0.0839839724769605	0	FACETS	0.917	0.765	1			1	INDETERMINATE	1	TRUE	0	0.38	0		443	121	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943480	17943480	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	33	575	0	ENST00000458235.1:c.2528C>T	p.Pro843Leu	p.P843L	ENST00000458235	NM_000215.3	843	cCg/cTg	19/24	0.0839839724769605	0	FACETS	0.97	0.809	1			1	INDETERMINATE	1	TRUE	0	0.38	0		575	111	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288140	21288140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	23	454	0	ENST00000354336.3:c.385C>T	p.Arg129Trp	p.R129W	ENST00000354336	NM_005207.3	129	Cgg/Tgg	2/3	0.402779182303906	3	FACETS	0.98	0.772	1			1	CLONAL	1	TRUE	NA	0.38	3		454	147	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293643	1293643	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	26	805	2	ENST00000310581.5:c.1358G>A	p.Arg453His	p.R453H	ENST00000310581	NM_198253.2	453	cGc/cAc	2/16	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.38	2		807	120	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638210	176638210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1023599621	NA	P-0035180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	20	557	0	ENST00000439151.2:c.2810G>A	p.Arg937Gln	p.R937Q	ENST00000439151	NM_022455.4	937	cGg/cAg	5/23	1	2	FACETS	0.993	0.772	1	0.993	0.772	1	CLONAL	1	TRUE	1	0.38	2		557	106	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76812968	76812968	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	29	263	0	ENST00000373344.5:c.6653del	p.Pro2218LeufsTer32	p.P2218Lfs*32	ENST00000373344	NM_000489.3	2218	cCt/ct	30/35	1	1	FACETS	1	0.907	1	1	0.967	1	CLONAL	2	TRUE	0	0.38	1		263	56	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0035180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	94	700	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	0.238146645805989	2		700	747	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0035180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	88	596	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.979	0.867	1	0.979	0.867	1	CLONAL	1	TRUE	1	0.238146645805989	2		597	755	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562657	29562660	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs1064794276	NA	P-0035180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	51	446	0	ENST00000356175.3:c.3739_3742del	p.Phe1247IlefsTer18	p.F1247Ifs*18	ENST00000356175	NM_000267.3	1246	cTGTTt/ct	28/57	1	2	FACETS	0.825	0.702	0.961	0.825	0.702	0.961	CLONAL	1	TRUE	1	0.238146645805989	2		446	519	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851717	134851717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150028142	NA	P-0035180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	60	427	0	ENST00000398015.3:c.1123G>A	p.Asp375Asn	p.D375N	ENST00000398015	NM_004441.4	375	Gac/Aac	5/16	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.238146645805989	2		427	467	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245759	41245759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55650082	NA	P-0035180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	85	616	0	ENST00000357654.3:c.1789G>A	p.Glu597Lys	p.E597K	ENST00000357654	NM_007294.3	597	Gaa/Aaa	10/23	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.238146645805989	2		616	704	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846291	156846291	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760764097	NA	P-0035180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	77	690	0	ENST00000524377.1:c.1732G>A	p.Val578Ile	p.V578I	ENST00000524377	NM_002529.3	578	Gtc/Atc	14/17	1	2	FACETS	0.867	0.76	0.982	0.867	0.76	0.982	CLONAL	1	TRUE	1	0.238146645805989	2		690	746	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56871587	56871587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758034157	NA	P-0035180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	56	403	0	ENST00000308159.5:c.1967C>T	p.Pro656Leu	p.P656L	ENST00000308159	NM_014669.4	656	cCg/cTg	18/22	1	2	FACETS	0.97	0.832	1	0.97	0.832	1	CLONAL	1	TRUE	1	0.238146645805989	2		403	485	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470498	25470498	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747448117	NA	P-0035180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	80	532	2	ENST00000264709.3:c.976C>T	p.Arg326Cys	p.R326C	ENST00000264709	NM_175629.2	326	Cgc/Tgc	8/23	0.238146645805989	1	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	0	0.238146645805989	1		534	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579365	7579365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782461	NA	P-0035180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	83	518	0	ENST00000269305.4:c.322G>A	p.Gly108Ser	p.G108S	ENST00000269305	NM_001126112.2	108	Ggt/Agt	4/11	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.238146645805989	2		518	684	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858201	9858201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	60	497	0	ENST00000330684.3:c.3200G>A	p.Arg1067Gln	p.R1067Q	ENST00000330684	NM_001134407.1	1067	cGg/cAg	13/13	1	2	FACETS	0.818	0.704	0.942	0.818	0.704	0.942	CLONAL	1	TRUE	1	0.238146645805989	2		497	616	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041026	112041026	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746134687	NA	P-0035180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	68	331	0	ENST00000368678.4:c.229C>T	p.Arg77Cys	p.R77C	ENST00000368678		77	Cgt/Tgt	3/13	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.238146645805989	2		331	480	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198888	67198888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751194292	NA	P-0035180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	65	403	0	ENST00000312629.5:c.359G>A	p.Arg120Gln	p.R120Q	ENST00000312629	NM_003952.2	120	cGg/cAg	5/15	1	2	FACETS	0.885	0.767	1	0.885	0.767	1	CLONAL	1	TRUE	1	0.238146645805989	2		403	617	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568636	41568636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	24	294	0	ENST00000263253.7:c.4586G>A	p.Arg1529Gln	p.R1529Q	ENST00000263253	NM_001429.3	1529	cGa/cAa	28/31	1	2	FACETS	0.588	0.461	0.734	0.588	0.461	0.734	SUBCLONAL	1	TRUE	1	0.238146645805989	2		294	343	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306549	163306549	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753469318	NA	P-0035180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	37	312	0	ENST00000271452.3:c.346C>T	p.Arg116Trp	p.R116W	ENST00000271452	NM_145697.2	116	Cgg/Tgg	6/14	1	2	FACETS	0.888	0.734	1	0.888	0.734	1	CLONAL	1	TRUE	1	0.238146645805989	2		312	350	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277291	41277291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	32	323	1	ENST00000349496.5:c.1760G>A	p.Arg587Gln	p.R587Q	ENST00000349496	NM_001904.3	587	cGa/cAa	11/15	1	2	FACETS	0.64	0.519	0.776	0.64	0.519	0.776	SUBCLONAL	1	TRUE	1	0.238146645805989	2		324	420	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860908	151860908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	37	267	0	ENST00000262189.6:c.9754C>T	p.Arg3252Cys	p.R3252C	ENST00000262189	NM_170606.2	3252	Cgt/Tgt	43/59	1	2	FACETS	0.842	0.695	1	0.842	0.695	1	CLONAL	1	TRUE	1	0.238146645805989	2		267	369	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420190	49420190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775954885	NA	P-0035180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	66	564	0	ENST00000301067.7:c.15559G>A	p.Ala5187Thr	p.A5187T	ENST00000301067	NM_003482.3	5187	Gcc/Acc	48/54	1	2	FACETS	0.836	0.725	0.956	0.836	0.725	0.956	CLONAL	1	TRUE	1	0.238146645805989	2		564	663	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039222	49039223	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0035180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	45	386	0	ENST00000267163.4:c.2302_2303del	p.Ile768PhefsTer26	p.I768Ffs*26	ENST00000267163	NM_000321.2	767	aAT/a	22/27	1	2	FACETS	0.818	0.688	0.962	0.818	0.688	0.962	CLONAL	1	TRUE	1	0.238146645805989	2		386	462	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346348	89346348	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371524118	NA	P-0035180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	37	382	0	ENST00000301030.4:c.6602C>T	p.Ala2201Val	p.A2201V	ENST00000301030	NM_001256183.1	2201	gCa/gTa	9/13	1	2	FACETS	0.752	0.621	0.9	0.752	0.621	0.9	SUBCLONAL	1	TRUE	1	0.238146645805989	2		382	413	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254461	10254461	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144533539	NA	P-0035180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	55	441	2	ENST00000340748.4:c.3049C>T	p.Arg1017Trp	p.R1017W	ENST00000340748		1017	Cgg/Tgg	28/40	1	2	FACETS	0.769	0.657	0.891	0.769	0.657	0.891	SUBCLONAL	1	TRUE	1	0.238146645805989	2		443	601	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943480	17943480	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	69	575	0	ENST00000458235.1:c.2528C>T	p.Pro843Leu	p.P843L	ENST00000458235	NM_000215.3	843	cCg/cTg	19/24	1	2	FACETS	0.881	0.767	1	0.881	0.767	1	CLONAL	1	TRUE	1	0.238146645805989	2		575	658	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293643	1293643	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	64	805	2	ENST00000310581.5:c.1358G>A	p.Arg453His	p.R453H	ENST00000310581	NM_198253.2	453	cGc/cAc	2/16	1	2	FACETS	0.796	0.689	0.913	0.796	0.689	0.913	CLONAL	1	TRUE	1	0.238146645805989	2		807	675	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76812968	76812968	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	54	263	0	ENST00000373344.5:c.6653del	p.Pro2218LeufsTer32	p.P2218Lfs*32	ENST00000373344	NM_000489.3	2218	cCt/ct	30/35	1	1	FACETS	0.762	0.657	0.875	1	0.969	1	SUBCLONAL	2	TRUE	0	0.238146645805989	1		263	262	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0035209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	58	804	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	0.541	0.464	0.626	0.541	0.464	0.626	SUBCLONAL	1	TRUE	1	0.288099526454424	2		804	744	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795019	242795019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1319637878	NA	P-0035209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	52	1045	1	ENST00000334409.5:c.190G>A	p.Val64Met	p.V64M	ENST00000334409	NM_005018.2	64	Gtg/Atg	2/5	0.116544601637574	3	FACETS	0.406	0.344	0.474	0.203	0.172	0.237	INDETERMINATE	1	TRUE	1	0.288099526454424	3		1046	1017	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476388	88476388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374759890	NA	P-0035209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	36	538	0	ENST00000360948.2:c.1744C>T	p.Arg582Trp	p.R582W	ENST00000360948	NM_001012338.2	582	Cgg/Tgg	15/19	1	2	FACETS	0.41	0.336	0.493	0.41	0.336	0.493	SUBCLONAL	1	TRUE	1	0.288099526454424	2		538	610	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188187	32188187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754712190	NA	P-0035209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	63	612	3	ENST00000375023.3:c.1154G>A	p.Arg385His	p.R385H	ENST00000375023	NM_004557.3	385	cGc/cAc	6/30	0.116544601637574	3	FACETS	0.879	0.761	1	0.44	0.38	0.504	INDETERMINATE	1	TRUE	1	0.288099526454424	3		615	569	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472558	88472558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	29	599	1	ENST00000360948.2:c.1997G>A	p.Gly666Asp	p.G666D	ENST00000360948	NM_001012338.2	666	gGt/gAt	16/19	1	2	FACETS	0.369	0.296	0.454	0.369	0.296	0.454	SUBCLONAL	1	TRUE	1	0.288099526454424	2		600	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574035	7574035	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0035209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	90	625	0	ENST00000269305.4:c.994-2A>C		p.X332_splice	ENST00000269305	NM_001126112.2	332			1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.288099526454424	2		625	554	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0035244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	92	433	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.758	0.674	0.847	1	0.98	1	SUBCLONAL	2	TRUE	1	0.2	2		433	607	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0035244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	121	397	0	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.2	2		397	823	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861786	57861786	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	33	330	0	ENST00000228682.2:c.1087G>T	p.Val363Leu	p.V363L	ENST00000228682	NM_005269.2	363	Gta/Tta	10/12	0.100952978923824	0	FACETS	0.49	0.398	0.594			1	INDETERMINATE	1	TRUE	0	0.2	0		330	539	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923264	26923264	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	33	304	0	ENST00000381527.3:c.260C>T	p.Ser87Phe	p.S87F	ENST00000381527	NM_001260.1	87	tCt/tTt	3/13	0.204169703700824	1	FACETS	0.681	0.555	0.824	0.681	0.555	0.824	SUBCLONAL	1	TRUE	0	0.2	1		304	436	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858095	152858095	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	103	412	0	ENST00000406277.2:c.520G>C	p.Asp174His	p.D174H	ENST00000406277	NM_152274.4	174	Gac/Cac	6/7	1	2	FACETS	0.779	0.698	0.865	1	0.983	1	SUBCLONAL	2	TRUE	1	0.2	2		412	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0035300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	106	707	1	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	1	2	FACETS	1	0.915	1	1	0.988	1	CLONAL	2	TRUE	1	0.162036175052964	2		708	641	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0035340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	147	761	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.24	2		761	929	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221322	1221322	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	74	637	0	ENST00000326873.7:c.845T>G	p.Leu282Arg	p.L282R	ENST00000326873	NM_000455.4	282	cTc/cGc	6/10	1	2	FACETS	0.962	0.842	1	0.962	0.842	1	CLONAL	1	TRUE	1	0.24	2		637	641	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494637	2494637	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	76	661	1	ENST00000355716.4:c.777G>T	p.Gln259His	p.Q259H	ENST00000355716	NM_003820.2	259	caG/caT	8/8	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.24	2		662	619	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431922	49431922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	70	780	0	ENST00000301067.7:c.9217G>A	p.Val3073Ile	p.V3073I	ENST00000301067	NM_003482.3	3073	Gta/Ata	34/54	0.268181900980584	3	FACETS	0.737	0.641	0.842			1	SUBCLONAL	1	TRUE	NA	0.24	3		780	886	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112464	115112464	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	71	542	1	ENST00000257566.3:c.1276G>T	p.Gly426Trp	p.G426W	ENST00000257566	NM_016569.3	426	Ggg/Tgg	7/8	1	2	FACETS	0.879	0.767	1	0.879	0.767	1	CLONAL	1	TRUE	1	0.24	2		543	673	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251135	251135	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	22	176	0	ENST00000264932.6:c.1580G>T	p.Arg527Leu	p.R527L	ENST00000264932	NM_004168.2	527	cGt/cTt	12/15	0.139827952780521	3	FACETS	0.838	0.651	1	0.419	0.325	0.527	INDETERMINATE	1	TRUE	1	0.24	3		176	245	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141568600	141568600	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	45	569	0	ENST00000220592.5:c.862C>T	p.Pro288Ser	p.P288S	ENST00000220592	NM_012154.3	288	Ccc/Tcc	7/19	1	2	FACETS	0.501	0.42	0.592	0.501	0.42	0.592	SUBCLONAL	1	TRUE	1	0.24	2		569	748	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0035368-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	63	417	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.972	0.84	1	0.972	0.84	1	CLONAL	1	TRUE	1	0.19	2		417	682	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035368-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	51	328	4	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.902	0.766	1	0.902	0.766	1	CLONAL	1	TRUE	1	0.19	2		332	595	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986988	36986988	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035368-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	71	501	1	ENST00000354822.5:c.701A>T	p.Gln234Leu	p.Q234L	ENST00000354822	NM_001079668.2	234	cAg/cTg	3/3	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.19	2		502	638	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683183	88683183	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035368-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	31	342	0	ENST00000372037.3:c.1393C>G	p.Pro465Ala	p.P465A	ENST00000372037	NM_004329.2	465	Ccg/Gcg	12/13	1	2	FACETS	0.688	0.556	0.839	0.688	0.556	0.839	SUBCLONAL	1	TRUE	1	0.19	2		342	474	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	39	272	0				ENST00000310581	NM_198253.2	-/1132			0.3272228234811	0	FACETS	0.92	0.782	1			1	CLONAL	1	FALSE	0	0.418007648808011	0		272	118	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164509	36164509	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	159	380	0	ENST00000300305.3:c.1366G>A	p.Glu456Lys	p.E456K	ENST00000300305		456	Gag/Aag	8/8	0.258163735136553	0	FACETS	1	0.964	1			1	CLONAL	1	FALSE	0	0.418007648808011	0		380	416	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097737	27097737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	190	421	0	ENST00000324856.7:c.3326G>A	p.Arg1109Gln	p.R1109Q	ENST00000324856	NM_006015.4	1109	cGg/cAg	12/20	0.242310245864227	4	FACETS	1	0.986	1	1	0.986	1	INDETERMINATE	2	FALSE	2	0.418007648808011	4		421	523	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590888	95590888	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	54	339	0	ENST00000393063.1:c.1021C>T	p.His341Tyr	p.H341Y	ENST00000393063	NM_030621.3	341	Cac/Tac	9/28	0.11446481034595	0	FACETS	0.699	0.605	0.8			1	INDETERMINATE	1	FALSE	0	0.418007648808011	0		339	215	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157256700	157256700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	70	201	0	ENST00000346085.5:c.2027C>T	p.Ser676Leu	p.S676L	ENST00000346085	NM_020732.3	676	tCa/tTa	5/20	0.212318499374842	4	FACETS	0.994	0.878	1	0.994	0.878	1	INDETERMINATE	2	FALSE	2	0.418007648808011	4		201	239	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0035469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	88	417	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA	3	FACETS	1	0.971	1	0.648	0.575	0.724	INDETERMINATE	1	TRUE	1	0.305995823904832	3		417	512	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602354	10602354	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	220	1063	1	ENST00000171111.5:c.1224del	p.Met409Ter	p.M409*	ENST00000171111	NM_203500.1	408	ccC/cc	3/6	0.305995823904832	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.305995823904832	1		1064	1082	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041266	47041266	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0035469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	216	507	0	ENST00000377604.3:c.1693+1G>A		p.X565_splice	ENST00000377604	NM_001204468.1	565			NA	2	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.305995823904832	2		507	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0035469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	128	575	0	ENST00000269305.4:c.375+1del		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.305995823904832	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.305995823904832	1		575	642	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112197	115112197	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	98	550	0	ENST00000257566.3:c.1543G>T	p.Gly515Trp	p.G515W	ENST00000257566	NM_016569.3	515	Ggg/Tgg	7/8	NA	3	FACETS	1	0.921	1	0.519	0.463	0.579	INDETERMINATE	1	TRUE	1	0.305995823904832	3		550	711	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46583304	46583304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370125133	NA	P-0035469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	127	402	1	ENST00000263734.3:c.232G>A	p.Glu78Lys	p.E78K	ENST00000263734	NM_001430.4	78	Gag/Aag	3/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.305995823904832	2		403	609	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942049	81942049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	79	560	0	ENST00000359376.3:c.1586G>A	p.Gly529Glu	p.G529E	ENST00000359376	NM_002661.3	529	gGg/gAg	17/33	1	2	FACETS	0.816	0.718	0.921	0.816	0.718	0.921	CLONAL	1	TRUE	1	0.305995823904832	2		560	633	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971206	21971206	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	94	375	0	ENST00000304494.5:c.152T>A	p.Val51Asp	p.V51D	ENST00000304494	NM_000077.4	51	gTc/gAc	2/3	0.305995823904832	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.305995823904832	1		375	446	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752341	57752341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	45	573	0	ENST00000274289.3:c.1232C>T	p.Pro411Leu	p.P411L	ENST00000274289	NM_006622.3	411	cCc/cTc	9/14	1	2	FACETS	0.642	0.54	0.755	0.642	0.54	0.755	SUBCLONAL	1	TRUE	1	0.305995823904832	2		573	458	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636186	28636186	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs147453280	NA	P-0035469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	135	578	0	ENST00000241453.7:c.186C>A	p.Asp62Glu	p.D62E	ENST00000241453	NM_004119.2	62	gaC/gaA	3/24	0.305995823904832	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.305995823904832	1		578	666	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014070	70014070	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	126	641	0	ENST00000394351.3:c.931G>T	p.Val311Leu	p.V311L	ENST00000394351	NM_000248.3	311	Gtg/Ttg	9/9	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.305995823904832	2		641	743	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138680	55138680	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	100	482	0	ENST00000257290.5:c.1357A>C	p.Ile453Leu	p.I453L	ENST00000257290	NM_006206.4	453	Att/Ctt	9/23	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.305995823904832	2		482	630	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709571	176709571	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	71	457	0	ENST00000439151.2:c.5998A>T	p.Thr2000Ser	p.T2000S	ENST00000439151	NM_022455.4	2000	Acc/Tcc	19/23	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.305995823904832	2		457	385	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738155	133738155	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	50	493	0	ENST00000318560.5:c.555C>A	p.Tyr185Ter	p.Y185*	ENST00000318560	NM_005157.4	185	taC/taA	4/11	1	2	FACETS	0.507	0.43	0.593	0.507	0.43	0.593	SUBCLONAL	1	TRUE	1	0.305995823904832	2		493	644	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0035475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	87	598	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.952	0.847	1	0.952	0.847	1	CLONAL	1	TRUE	1	0.425934977431364	2		598	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579463	7579463	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	289	1036	1	ENST00000269305.4:c.224del	p.Pro75LeufsTer48	p.P75Lfs*48	ENST00000269305	NM_001126112.2	75	cCt/ct	4/11	NA	2	FACETS	0.906	0.857	0.956			1	INDETERMINATE	2	TRUE	NA	0.425934977431364	2		1037	749	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407554	139407555	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0035475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	321	1193	0	ENST00000277541.6:c.2385_2386del	p.Ala796ValfsTer12	p.A796Vfs*12	ENST00000277541	NM_017617.3	795	tgTGcg/tgcg	15/34	0.425934977431364	2	FACETS	0.939	0.891	0.987	0.939	0.891	0.987	CLONAL	2	TRUE	0	0.425934977431364	2		1193	803	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0035476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	263	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.218430502596515	3	FACETS	1	0.984	1	1	0.994	1	CLONAL	3	TRUE	1	0.218430502596515	3		502	793	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	89	799	0	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.218430502596515	2		799	654	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0035476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	96	481	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	0.218430502596515	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	0	0.218430502596515	2		481	414	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	27	272	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.924	0.753	1	0.924	0.753	1	CLONAL	1	TRUE	1	0.59	2		272	99	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0035478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	69	364	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.100767698446708	3	FACETS	1	0.926	1	0.537	0.472	0.605	INDETERMINATE	1	TRUE	1	0.59	3		364	282	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0035478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	73	513	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	0.100767698446708	0	FACETS	0.284	0.25	0.321			1	INDETERMINATE	1	TRUE	0	0.59	0		513	357	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244286	46244286	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	41	468	0	ENST00000334344.6:c.2380C>T	p.Gln794Ter	p.Q794*	ENST00000334344	NM_152641.2	794	Caa/Taa	15/21	0.275128643895131	4	FACETS	1	0.916	1	0.57	0.48	0.667	INDETERMINATE	1	TRUE	2	0.59	4		468	194	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178710	32178710	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	61	663	0	ENST00000375023.3:c.2684T>A	p.Ile895Lys	p.I895K	ENST00000375023	NM_004557.3	895	aTa/aAa	18/30	0.275128643895131	3	FACETS	1	0.932	1	0.553	0.483	0.628	INDETERMINATE	1	TRUE	1	0.59	3		663	242	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0035479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	322	558	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	0.952	0.905	0.999	0.952	0.905	0.999	CLONAL	1	TRUE	1	0.932133263500957	2		558	726	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156742	20156742	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0035479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	283	209	0	ENST00000379607.5:c.17-2A>G		p.X6_splice	ENST00000379607	NM_001412.3	6			1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.932133263500957	1		209	299	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0035480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	35	674	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.17	2		674	362	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0035480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	23	290	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.190210086063254	4	FACETS	1	0.82	1	0.529	0.413	0.664	CLONAL	1	TRUE	2	0.17	4		290	299	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0035480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	51	830	1	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	0.111755562867197	3	FACETS	0.788	0.671	0.916	0.788	0.671	0.916	CLONAL	2	TRUE	1	0.17	3		831	413	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370709	55370709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	30	572	1	ENST00000297316.4:c.11C>T	p.Pro4Leu	p.P4L	ENST00000297316	NM_022454.3	4	cCg/cTg	1/2	0.111755562867197	3	FACETS	1	0.934	1	0.704	0.569	0.856	CLONAL	1	TRUE	1	0.17	3		573	272	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969932	81969932	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024473204	NA	P-0035480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	48	524	0	ENST00000359376.3:c.3001C>T	p.Arg1001Cys	p.R1001C	ENST00000359376	NM_002661.3	1001	Cgc/Tgc	27/33	0.190210086063254	0	FACETS	1	0.943	1			1	CLONAL	1	TRUE	0	0.17	0		524	375	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692902	89692902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909218	NA	P-0035480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	33	482	0	ENST00000371953.3:c.386G>A	p.Gly129Glu	p.G129E	ENST00000371953	NM_000314.4	129	gGa/gAa	5/9	0.190210086063254	4	FACETS	1	0.906	1	0.595	0.484	0.718	CLONAL	1	TRUE	2	0.17	4		482	382	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720805	89720805	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	15	374	0	ENST00000371953.3:c.956del	p.Thr319IlefsTer2	p.T319Ifs*2	ENST00000371953	NM_000314.4	319	aCt/at	8/9	0.190210086063254	4	FACETS	0.965	0.707	1	0.482	0.353	0.637	CLONAL	1	TRUE	2	0.17	4		374	214	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106496	27106496	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	39	733	0	ENST00000324856.7:c.6108del	p.Glu2036AspfsTer6	p.E2036Dfs*6	ENST00000324856	NM_006015.4	2036	gAa/ga	20/20	0.190210086063254	3	FACETS	1	0.844	1	0.51	0.422	0.608	CLONAL	1	TRUE	1	0.17	3		733	488	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962497	100962497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	50	588	0	ENST00000325455.5:c.1900C>T	p.Leu634Phe	p.L634F	ENST00000325455	NM_001202474.3	634	Ctt/Ttt	3/8	0.190210086063254	3	FACETS	0.955	0.809	1	0.478	0.404	0.558	CLONAL	1	TRUE	1	0.17	3		588	668	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591135	67591135	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	17	337	0	ENST00000274335.5:c.1728del	p.Arg577GlufsTer5	p.R577Efs*5	ENST00000274335		576	acG/ac	12/15	0.190210086063254	4	FACETS	0.807	0.602	1	0.403	0.301	0.525	CLONAL	1	TRUE	2	0.17	4		337	290	SUCCESS
APC	324	MSKCC	GRCh37	5	112173838	112173838	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	21	365	0	ENST00000257430.4:c.2547del	p.Asp849GlufsTer12	p.D849Efs*12	ENST00000257430	NM_000038.5	849	gaT/ga	16/16	0.190210086063254	4	FACETS	1	0.838	1	0.556	0.429	0.704	CLONAL	1	TRUE	2	0.17	4		365	260	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411384	63411384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149055969	NA	P-0035480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	27	808	0	ENST00000330258.3:c.1783G>A	p.Ala595Thr	p.A595T	ENST00000330258	NM_152424.3	595	Gcc/Acc	2/2	1	2	FACETS	0.999	0.796	1	0.999	0.796	1	CLONAL	1	TRUE	1	0.17	2		808	318	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0035481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	109	368	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.241644937602764	3	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	1	0.241644937602764	3		368	486	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651631	48651631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	84	671	1	ENST00000376670.3:c.797C>T	p.Thr266Met	p.T266M	ENST00000376670	NM_002049.3	266	aCg/aTg	5/6	1	2	FACETS	0.979	0.865	1	0.979	0.865	1	CLONAL	1	TRUE	1	0.241644937602764	2		672	710	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510805	157510806	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1289067120	NA	P-0035481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	67	520	0	ENST00000346085.5:c.3586dup	p.Gln1196ProfsTer14	p.Q1196Pfs*14	ENST00000346085	NM_020732.3	1194	acc/aCcc	14/20	0.241644937602764	3	FACETS	0.884	0.768	1	0.442	0.384	0.505	CLONAL	1	TRUE	1	0.241644937602764	3		520	703	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600447	10600447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	102	732	3	ENST00000171111.5:c.1408C>T	p.Arg470Cys	p.R470C	ENST00000171111	NM_203500.1	470	Cgt/Tgt	4/6	1	2	FACETS	0.953	0.851	1	0.953	0.851	1	CLONAL	1	TRUE	1	0.241644937602764	2		735	886	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522416	176522416	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519792	NA	P-0035481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	214	747	0	ENST00000292408.4:c.1605C>G	p.Asn535Lys	p.N535K	ENST00000292408	NM_213647.1	535	aaC/aaG	12/18	0.241644937602764	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	1	0.241644937602764	3		747	970	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127167	22127167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	74	510	0	ENST00000215832.6:c.961G>A	p.Asp321Asn	p.D321N	ENST00000215832	NM_002745.4	321	Gac/Aac	7/9	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.241644937602764	2		510	599	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197187	26197187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	65	545	0	ENST00000356476.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000356476		98	Gag/Aag	1/1	0.241644937602764	3	FACETS	0.828	0.717	0.949	0.414	0.358	0.475	CLONAL	1	TRUE	1	0.241644937602764	3		545	728	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844139	68844139	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	86	636	0	ENST00000261769.5:c.727G>A	p.Glu243Lys	p.E243K	ENST00000261769	NM_004360.3	243	Gag/Aag	6/16	0.240036421507071	1	FACETS	0.933	0.825	1	0.933	0.825	1	CLONAL	1	TRUE	0	0.241644937602764	1		636	671	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440114	220440114	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	110	859	0	ENST00000243786.2:c.967G>A	p.Gly323Arg	p.G323R	ENST00000243786	NM_002191.3	323	Ggg/Agg	2/2	0.191780517169127	3	FACETS	1	0.934	1	0.528	0.473	0.586	CLONAL	1	TRUE	1	0.241644937602764	3		859	967	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504433	186504433	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	72	413	0	ENST00000323963.5:c.770A>G	p.Glu257Gly	p.E257G	ENST00000323963		257	gAg/gGg	7/11	0.241644937602764	3	FACETS	0.857	0.748	0.976	0.429	0.374	0.488	CLONAL	1	TRUE	1	0.241644937602764	3		413	779	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435793	116435793	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	101	632	0	ENST00000397752.3:c.3883T>C	p.Tyr1295His	p.Y1295H	ENST00000397752	NM_000245.2	1295	Tac/Cac	20/21	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.241644937602764	2		632	778	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0035482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	72	753	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.688278824446283	1	FACETS	0.251	0.219	0.285	0.251	0.219	0.285	SUBCLONAL	1	TRUE	0	0.688278824446283	1		753	547	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0035482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	192	377	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.684393274376719	1	FACETS	0.984	0.925	1	0.984	0.925	1	CLONAL	1	TRUE	0	0.688278824446283	1		377	372	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006641	62006641	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149266494	NA	P-0035482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	55	782	0	ENST00000392795.3:c.638C>T	p.Thr213Met	p.T213M	ENST00000392795	NM_001039933.1	213	aCg/aTg	6/6	0.53101503320065	3	FACETS	0.199	0.169	0.232	0.1	0.084	0.116	SUBCLONAL	1	TRUE	1	0.688278824446283	3		782	1079	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114794	108114794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	171	703	0	ENST00000278616.4:c.611G>A	p.Gly204Glu	p.G204E	ENST00000278616	NM_000051.3	204	gGa/gAa	6/63	1	2	FACETS	0.656	0.605	0.71	0.656	0.605	0.71	SUBCLONAL	1	TRUE	1	0.688278824446283	2		703	757	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860544	45860544	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1049046025	NA	P-0035482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	295	892	0	ENST00000391945.4:c.1463T>C	p.Val488Ala	p.V488A	ENST00000391945	NM_000400.3	488	gTc/gCc	15/23	1	2	FACETS	0.914	0.862	0.967	0.914	0.862	0.967	CLONAL	1	TRUE	1	0.688278824446283	2		892	938	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142964	47142964	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	31	480	0	ENST00000409792.3:c.4999C>G	p.Gln1667Glu	p.Q1667E	ENST00000409792	NM_014159.6	1667	Cag/Gag	8/21	1	2	FACETS	0.828	0.668	1	0.828	0.668	1	CLONAL	1	TRUE	1	0.13	2		480	576	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843724	156843724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035483-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	89	685	0	ENST00000524377.1:c.1150G>A	p.Glu384Lys	p.E384K	ENST00000524377	NM_002529.3	384	Gag/Aag	8/17	1	2	FACETS	0.958	0.85	1	0.958	0.85	1	CLONAL	1	TRUE	1	0.29	2		685	641	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0035483-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	42	610	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.186084626226934	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.29	1		610	207	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578374	7578374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501206	NA	P-0035483-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	8	539	0	ENST00000269305.4:c.556G>A	p.Asp186Asn	p.D186N	ENST00000269305	NM_001126112.2	186	Gat/Aat	5/11	0.186084626226934	1	FACETS	0.129	0.082	0.189	0.129	0.082	0.189	SUBCLONAL	1	TRUE	0	0.29	1		539	367	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152038	55152038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370600501	NA	P-0035483-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	22	536	0	ENST00000257290.5:c.2470G>A	p.Val824Ile	p.V824I	ENST00000257290	NM_006206.4	824	Gtc/Atc	18/23	0.149823867825191	4	FACETS	0.493	0.381	0.623	0.247	0.19	0.312	INDETERMINATE	1	TRUE	2	0.29	4		536	397	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0035488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	63	433	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.48	0.415	0.552	0.48	0.415	0.552	SUBCLONAL	1	TRUE	1	0.38523503565138	2		433	681	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034492	47034492	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0035488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	178	529	1	ENST00000377604.3:c.576+1G>A		p.X192_splice	ENST00000377604	NM_001204468.1	192			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.38523503565138	2		530	838	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74000805	74000805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775466357	NA	P-0035488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	109	456	0	ENST00000318443.5:c.1495G>A	p.Glu499Lys	p.E499K	ENST00000318443	NM_001024736.1	499	Gag/Aag	7/10	1	2	FACETS	0.805	0.723	0.891	0.805	0.723	0.891	CLONAL	1	TRUE	1	0.38523503565138	2		456	703	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0035491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	131	364	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.922	0.844	1	0.922	0.844	1	CLONAL	1	TRUE	1	0.641115169197919	2		364	443	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246390	53246390	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	233	688	0	ENST00000375401.3:c.592C>T	p.Arg198Ter	p.R198*	ENST00000375401	NM_004187.3	198	Cga/Tga	5/26	0.641115169197919	1	FACETS	0.915	0.861	0.968	0.915	0.861	0.968	CLONAL	1	TRUE	0	0.641115169197919	1		688	540	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136366	2136366	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	256	588	0	ENST00000219476.3:c.4835A>T	p.Asp1612Val	p.D1612V	ENST00000219476	NM_000548.3	1612	gAt/gTt	37/42	0.641115169197919	1	FACETS	0.95	0.898	1	0.95	0.898	1	CLONAL	1	TRUE	0	0.641115169197919	1		588	571	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145748	11145780	+	inframe_deletion	In_Frame_Del	DEL	CTCCCGCCACCGCAAGGAGGTGGACTACAGCGA	CTCCCGCCACCGCAAGGAGGTGGACTACAGCGA	-	novel	NA	P-0035491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	65	571	0	ENST00000358026.2:c.4113_4145del	p.Arg1372_Ser1382del	p.R1372_S1382del	ENST00000358026	NM_001128849.1	1370	ggCTCCCGCCACCGCAAGGAGGTGGACTACAGCGAc/ggc	29/36	0.283572391652825	1	FACETS	0.279	0.242	0.319	0.279	0.242	0.319	INDETERMINATE	1	TRUE	0	0.641115169197919	1		571	494	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718717	190718717	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	148	437	0	ENST00000441310.2:c.875A>C	p.Tyr292Ser	p.Y292S	ENST00000441310	NM_000534.4	292	tAt/tCt	8/13	1	2	FACETS	0.857	0.787	0.929	0.857	0.787	0.929	CLONAL	1	TRUE	1	0.641115169197919	2		437	539	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692902	89692902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909218	NA	P-0035493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	88	482	0	ENST00000371953.3:c.386G>A	p.Gly129Glu	p.G129E	ENST00000371953	NM_000314.4	129	gGa/gAa	5/9	0.216227968362141	1	FACETS	0.693	0.613	0.779	0.693	0.613	0.779	SUBCLONAL	1	TRUE	0	0.253868675273397	1		482	873	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579368	7579368	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	304	641	0	ENST00000269305.4:c.319del	p.Tyr107ThrfsTer16	p.Y107Tfs*16	ENST00000269305	NM_001126112.2	107	Tac/ac	4/11	0.253868675273397	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.253868675273397	2		641	1124	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042149	6042149	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1554303942	NA	P-0035493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	60	439	0	ENST00000265849.7:c.472A>T	p.Ser158Cys	p.S158C	ENST00000265849	NM_000535.5	158	Agc/Tgc	5/15	1	2	FACETS	0.699	0.602	0.806	0.699	0.602	0.806	SUBCLONAL	1	TRUE	1	0.253868675273397	2		439	676	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849801	156849801	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	99	436	0	ENST00000524377.1:c.2057G>T	p.Arg686Leu	p.R686L	ENST00000524377	NM_002529.3	686	cGc/cTc	16/17	1	2	FACETS	0.932	0.831	1	0.932	0.831	1	CLONAL	1	TRUE	1	0.253868675273397	2		436	837	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599910	10599910	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	220	627	0	ENST00000171111.5:c.1666G>T	p.Ala556Ser	p.A556S	ENST00000171111	NM_203500.1	556	Gcc/Tcc	5/6	0.253868675273397	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.253868675273397	1		627	1009	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0035494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	182	417	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.229609708409532	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	0	0.229609708409532	2		417	770	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592251	29592251	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs797044942	NA	P-0035494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	20	160	0	ENST00000356175.3:c.4666C>T	p.Gln1556Ter	p.Q1556*	ENST00000356175	NM_000267.3	1556	Cag/Tag	35/57	1	2	FACETS	0.583	0.446	0.743	0.583	0.446	0.743	SUBCLONAL	1	TRUE	1	0.229609708409532	2		160	299	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578197	7578197	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878854072	NA	P-0035494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	117	605	1	ENST00000269305.4:c.652G>A	p.Val218Met	p.V218M	ENST00000269305	NM_001126112.2	218	Gtg/Atg	6/11	0.229609708409532	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.229609708409532	1		606	822	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163733	72163733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	112	553	0	ENST00000357731.5:c.625G>A	p.Val209Met	p.V209M	ENST00000357731	NM_173808.2	209	Gtg/Atg	4/7	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.229609708409532	2		553	939	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573730	64573730	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	151	505	0	ENST00000312049.6:c.1023G>A	p.Trp341Ter	p.W341*	ENST00000312049	NM_130799.2	341	tgG/tgA	7/10	0.202351931747338	2	FACETS	0.967	0.887	1	0.967	0.887	1	CLONAL	2	TRUE	0	0.229609708409532	2		505	680	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591749	38591749	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0035494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	73	314	0	ENST00000299084.4:c.207+1G>T		p.X69_splice	ENST00000299084	NM_152594.2	69			1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.229609708409532	2		314	544	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777819	3777819	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	181	930	0	ENST00000262367.5:c.7229C>G	p.Pro2410Arg	p.P2410R	ENST00000262367	NM_004380.2	2410	cCc/cGc	31/31	0.205131154557563	3	FACETS	1	0.985	1	0.656	0.604	0.711	CLONAL	1	TRUE	1	0.229609708409532	3		930	1339	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9928000	9928000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	66	368	0	ENST00000330684.3:c.1739G>A	p.Ser580Asn	p.S580N	ENST00000330684	NM_001134407.1	580	aGc/aAc	8/13	0.205131154557563	3	FACETS	0.98	0.85	1	0.49	0.425	0.561	CLONAL	1	TRUE	1	0.229609708409532	3		368	654	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17129578	17129578	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs777336970	NA	P-0035494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	141	717	2	ENST00000285071.4:c.308C>A	p.Ser103Tyr	p.S103Y	ENST00000285071	NM_144997.5	103	tCc/tAc	5/14	0.229609708409532	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.229609708409532	1		719	879	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603033	48603033	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	68	373	0	ENST00000342988.3:c.1334G>T	p.Arg445Leu	p.R445L	ENST00000342988	NM_005359.5	445	cGa/cTa	11/12	1	2	FACETS	0.969	0.844	1	0.969	0.844	1	CLONAL	1	TRUE	1	0.229609708409532	2		373	611	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096100	178096100	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	97	439	0	ENST00000397062.3:c.1231C>T	p.Gln411Ter	p.Q411*	ENST00000397062	NM_006164.4	411	Cag/Tag	5/5	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.229609708409532	2		439	652	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89176402	89176402	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	62	259	0	ENST00000336596.2:c.132G>C	p.Trp44Cys	p.W44C	ENST00000336596	NM_005233.5	44	tgG/tgC	2/17	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.229609708409532	2		259	450	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200041	128200041	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	131	740	1	ENST00000341105.2:c.1264C>A	p.Gln422Lys	p.Q422K	ENST00000341105	NM_032638.4	422	Cag/Aag	6/6	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.229609708409532	2		741	1000	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169953120	169953120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	104	365	0	ENST00000295797.4:c.204G>A	p.Met68Ile	p.M68I	ENST00000295797	NM_002740.5	68	atG/atA	2/18	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.229609708409532	2		365	797	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630533	187630533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753323036	NA	P-0035494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	150	648	0	ENST00000441802.2:c.449C>T	p.Ser150Leu	p.S150L	ENST00000441802	NM_005245.3	150	tCa/tTa	2/27	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.229609708409532	2		648	1057	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109312026	109312026	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	81	367	0	ENST00000436639.2:c.1246G>T	p.Glu416Ter	p.E416*	ENST00000436639	NM_014454.2	416	Gaa/Taa	8/10	1	2	FACETS	0.98	0.863	1	0.98	0.863	1	CLONAL	1	TRUE	1	0.229609708409532	2		367	720	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864827	117864827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	57	485	0	ENST00000297338.2:c.1282G>A	p.Glu428Lys	p.E428K	ENST00000297338	NM_006265.2	428	Gag/Aag	10/14	0.205131154557563	3	FACETS	0.559	0.478	0.648	0.28	0.239	0.324	SUBCLONAL	1	TRUE	1	0.229609708409532	3		485	990	SUCCESS
AR	367	MSKCC	GRCh37	X	66766086	66766086	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	117	693	0	ENST00000374690.3:c.1098C>G	p.Asn366Lys	p.N366K	ENST00000374690	NM_000044.3	366	aaC/aaG	1/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.229609708409532	2		693	800	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357054	70357054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	89	659	0	ENST00000374080.3:c.5569C>T	p.Pro1857Ser	p.P1857S	ENST00000374080		1857	Cca/Tca	39/45	1	2	FACETS	0.975	0.864	1	0.975	0.864	1	CLONAL	1	TRUE	1	0.229609708409532	2		659	795	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0035499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	30	473	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	0.506	0.406	0.621	0.506	0.406	0.621	SUBCLONAL	1	TRUE	1	0.11	2		473	1078	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266713	198266713	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	43	432	0	ENST00000335508.6:c.2219G>T	p.Gly740Val	p.G740V	ENST00000335508	NM_012433.2	740	gGa/gTa	15/25	1	2	FACETS	0.953	0.795	1	0.953	0.795	1	CLONAL	1	TRUE	1	0.11	2		432	820	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0035501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	432	675	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.672590255404939	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	FALSE	0	0.672590255404939	2		675	637	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0035501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	170	204	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	0.256332226501705	5	FACETS	0.903	0.861	0.942	0.903	0.861	0.942	INDETERMINATE	5	FALSE	0	0.672590255404939	5		204	225	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073547	8073547	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	58	377	0	ENST00000377482.5:c.1112del	p.Gly371AspfsTer81	p.G371Dfs*81	ENST00000377482	NM_018948.3	371	gGa/ga	4/4	0.552494494206558	3	FACETS	0.835	0.724	0.954	0.418	0.362	0.477	CLONAL	1	FALSE	1	0.672590255404939	3		377	276	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114799801	114799801	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	102	372	0	ENST00000543371.1:c.468G>C	p.Trp156Cys	p.W156C	ENST00000543371	NM_001198531.1	156	tgG/tgC	5/14	0.672590255404939	3	FACETS	0.778	0.698	0.862	0.259	0.232	0.288	SUBCLONAL	1	FALSE	0	0.672590255404939	3		372	521	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417946	32417946	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	94	421	0	ENST00000332351.3:c.1106G>C	p.Arg369Pro	p.R369P	ENST00000332351	NM_024426.4	369	cGa/cCa	7/10	0.554249175955312	3	FACETS	0.629	0.56	0.701	0.314	0.28	0.351	SUBCLONAL	1	FALSE	1	0.672590255404939	3		421	594	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81557418	81557418	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	51	408	0	ENST00000298171.2:c.398T>G	p.Ile133Ser	p.I133S	ENST00000298171	NM_000369.2	133	aTt/aGt	5/10	0.672590255404939	4	FACETS	0.707	0.603	0.819	0.353	0.301	0.41	SUBCLONAL	1	FALSE	2	0.672590255404939	4		408	359	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245831	41245831	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	56	626	0	ENST00000357654.3:c.1717T>G	p.Ser573Ala	p.S573A	ENST00000357654	NM_007294.3	573	Tca/Gca	10/23	0.666976312810442	2	FACETS	0.572	0.494	0.656	0.286	0.247	0.328	SUBCLONAL	1	FALSE	0	0.672590255404939	2		626	291	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245795	5245795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368461283	NA	P-0035501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	326	697	2	ENST00000357368.4:c.980C>T	p.Thr327Met	p.T327M	ENST00000357368	NM_002850.3	327	aCg/aTg	10/38	0.660357296235217	2	FACETS	0.971	0.933	1	0.971	0.933	1	CLONAL	2	FALSE	0	0.672590255404939	2		699	499	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213312	36213327	+	frameshift_variant	Frame_Shift_Del	DEL	TCCGACAGAGGCCCTG	TCCGACAGAGGCCCTG	-	novel	NA	P-0035501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	119	724	0	ENST00000222270.7:c.2513_2528del	p.Asp838GlyfsTer143	p.D838Gfs*143	ENST00000222270	NM_014727.1	837	TCCGACAGAGGCCCTGtc/tc	4/37	0.566468103272278	5	FACETS	0.774	0.698	0.855	0.258	0.232	0.285	SUBCLONAL	1	FALSE	2	0.672590255404939	5		724	918	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024326	31024327	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CACCTCGTTCACTAGCCCGGCCTGGGAGCCTAACACTTTGCTTC	novel	NA	P-0035501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	91	570	0	ENST00000375687.4:c.3820_3821insCACTAGCCCGGCCTGGGAGCCTAACACTTTGCTTCCACCTCGTT	p.Phe1274SerfsTer21	p.F1274Sfs*21	ENST00000375687	NM_015338.5	1271	aca/aCACCTCGTTCACTAGCCCGGCCTGGGAGCCTAACACTTTGCTTCca	13/13	0.672590255404939	4	FACETS	0.442	0.392	0.497	0.221	0.196	0.249	SUBCLONAL	1	FALSE	2	0.672590255404939	4		570	1023	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101070	41101070	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	161	600	0	ENST00000373198.4:c.1286T>A	p.Val429Glu	p.V429E	ENST00000373198	NM_133170.3	429	gTg/gAg	8/32	0.672590255404939	4	FACETS	1	0.972	1	0.562	0.516	0.609	CLONAL	1	FALSE	2	0.672590255404939	4		600	713	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39003684	39003684	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	32	297	0	ENST00000357387.3:c.236T>G	p.Phe79Cys	p.F79C	ENST00000357387	NM_152756.3	79	tTt/tGt	4/38	0.609096243844928	5	FACETS	0.82	0.67	0.988	0.273	0.223	0.33	CLONAL	1	FALSE	2	0.672590255404939	5		297	233	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249166	55249166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397517125	NA	P-0035501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	96	538	1	ENST00000275493.2:c.2464G>A	p.Ala822Thr	p.A822T	ENST00000275493	NM_005228.3	822	Gca/Aca	20/28	0.401329302368961	5	FACETS	1	0.915	1	0.343	0.306	0.382	INDETERMINATE	1	FALSE	2	0.672590255404939	5		539	558	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499682	8499682	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	82	507	1	ENST00000356435.5:c.2287C>G	p.Pro763Ala	p.P763A	ENST00000356435		763	Ccc/Gcc	14/35	0.401329302368961	5	FACETS	0.798	0.704	0.898	0.266	0.234	0.3	INDETERMINATE	1	FALSE	2	0.672590255404939	5		508	614	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602488	10602488	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1397945617	NA	P-0035502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	66	628	0	ENST00000171111.5:c.1090G>T	p.Gly364Cys	p.G364C	ENST00000171111	NM_203500.1	364	Ggc/Tgc	3/6	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.17	2		628	741	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0035502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	81	682	1	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.17	2		683	930	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467207	25467207	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	39	399	0	ENST00000264709.3:c.1668G>T	p.Arg556Ser	p.R556S	ENST00000264709	NM_175629.2	556	agG/agT	15/23	1	2	FACETS	0.886	0.734	1	0.886	0.734	1	CLONAL	1	TRUE	1	0.17	2		399	518	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537945	212537945	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	78	364	0	ENST00000342788.4:c.1660G>T	p.Glu554Ter	p.E554*	ENST00000342788	NM_005235.2	554	Gag/Tag	14/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.17	2		364	662	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140165	50140165	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	50	582	1	ENST00000246792.3:c.260A>T	p.Gln87Leu	p.Q87L	ENST00000246792	NM_006270.3	87	cAg/cTg	3/6	1	2	FACETS	0.915	0.775	1	0.915	0.775	1	CLONAL	1	TRUE	1	0.17	2		583	643	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961321	54961321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs2230743	NA	P-0035502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	58	601	0	ENST00000312783.6:c.311C>T	p.Ser104Leu	p.S104L	ENST00000312783	NM_198436.1	104	tCg/tTg	4/10	1	2	FACETS	0.706	0.605	0.818	0.706	0.605	0.818	SUBCLONAL	1	TRUE	1	0.17	2		601	966	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047245	180047245	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs796052104	NA	P-0035502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	96	773	1	ENST00000261937.6:c.2470C>A	p.Leu824Met	p.L824M	ENST00000261937	NM_182925.4	824	Ctg/Atg	17/30	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.17	2		774	994	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18473912	18473912	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	30	453	0	ENST00000266497.5:c.1154G>T	p.Ser385Ile	p.S385I	ENST00000266497		385	aGt/aTt	6/31	1	2	FACETS	1	0.816	1	1	0.816	1	CLONAL	1	TRUE	1	0.17	2		453	349	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433349	49433349	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	45	634	0	ENST00000301067.7:c.8098C>G	p.Leu2700Val	p.L2700V	ENST00000301067	NM_003482.3	2700	Ctg/Gtg	32/54	1	2	FACETS	0.674	0.564	0.795	0.674	0.564	0.795	SUBCLONAL	1	TRUE	1	0.17	2		634	786	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828902	26828908	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	GATGGGT	GATGGGT	-	novel	NA	P-0035502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	37	257	0	ENST00000381527.3:c.126_128+4del		p.X42_splice	ENST00000381527	NM_001260.1	42		1/13	0.3	1	FACETS	0.998	0.824	1	0.998	0.824	1	CLONAL	1	TRUE	0	0.17	1		257	399	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436935	110436935	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	39	344	0	ENST00000375856.3:c.1466C>T	p.Ser489Leu	p.S489L	ENST00000375856	NM_003749.2	489	tCg/tTg	1/2	NA	3	FACETS	1	0.847	1	0.512	0.424	0.61	INDETERMINATE	1	TRUE	1	0.17	3		344	486	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724866	43724866	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	39	505	0	ENST00000382044.4:c.3201G>T	p.Leu1067Phe	p.L1067F	ENST00000382044	NM_001141980.1	1067	ttG/ttT	17/28	1	2	FACETS	0.858	0.71	1	0.858	0.71	1	CLONAL	1	TRUE	1	0.17	2		505	535	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476377	88476377	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	62	584	0	ENST00000360948.2:c.1755C>A	p.Phe585Leu	p.F585L	ENST00000360948	NM_001012338.2	585	ttC/ttA	15/19	1	2	FACETS	0.947	0.817	1	0.947	0.817	1	CLONAL	1	TRUE	1	0.17	2		584	770	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044488	12044488	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1168805084	NA	P-0035502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	37	406	0	ENST00000353533.5:c.1111G>A	p.Glu371Lys	p.E371K	ENST00000353533	NM_003010.3	371	Gaa/Aaa	11/11	1	2	FACETS	0.749	0.617	0.898	0.749	0.617	0.898	SUBCLONAL	1	TRUE	1	0.17	2		406	581	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615755	1615755	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	91	739	0	ENST00000344749.5:c.1516G>A	p.Glu506Lys	p.E506K	ENST00000344749	NM_001136139.2	506	Gag/Aag	17/19	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.17	2		739	895	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214046	36214046	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	74	823	1	ENST00000222270.7:c.2872G>T	p.Gly958Cys	p.G958C	ENST00000222270	NM_014727.1	958	Ggc/Tgc	6/37	1	2	FACETS	0.767	0.669	0.873	0.767	0.669	0.873	SUBCLONAL	1	TRUE	1	0.17	2		824	1135	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216516	36216516	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	95	814	0	ENST00000222270.7:c.3779G>T	p.Arg1260Leu	p.R1260L	ENST00000222270	NM_014727.1	1260	cGt/cTt	12/37	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.17	2		814	1039	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182666	38182666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	67	444	0	ENST00000396334.3:c.819G>A	p.Met273Ile	p.M273I	ENST00000396334	NM_002468.4	273	atG/atA	5/5	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.17	2		444	608	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916803	178916803	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	48	578	0	ENST00000263967.3:c.190G>C	p.Asp64His	p.D64H	ENST00000263967	NM_006218.2	64	Gat/Cat	2/21	0.114880116207362	3	FACETS	0.933	0.787	1	0.311	0.262	0.365	CLONAL	1	TRUE	0	0.17	3		578	657	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922297	178922297	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	40	349	0	ENST00000263967.3:c.1066G>C	p.Val356Leu	p.V356L	ENST00000263967	NM_006218.2	356	Gtt/Ctt	6/21	0.114880116207362	3	FACETS	0.98	0.814	1	0.327	0.271	0.389	CLONAL	1	TRUE	0	0.17	3		349	521	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430672	181430672	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	159	664	0	ENST00000325404.1:c.524A>T	p.Gln175Leu	p.Q175L	ENST00000325404	NM_003106.3	175	cAg/cTg	1/1	0.114880116207362	3	FACETS	1	0.981	1	0.819	0.751	0.89	CLONAL	2	TRUE	0	0.17	3		664	826	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970988	55970988	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	76	591	0	ENST00000263923.4:c.1809C>A	p.Cys603Ter	p.C603*	ENST00000263923	NM_002253.2	603	tgC/tgA	13/30	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.17	2		591	755	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094828	143094828	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	39	472	0	ENST00000262992.4:c.1316C>G	p.Ser439Cys	p.S439C	ENST00000262992	NM_001101669.1	439	tCt/tGt	14/24	1	2	FACETS	0.79	0.653	0.942	0.79	0.653	0.942	CLONAL	1	TRUE	1	0.17	2		472	581	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64288384	64288384	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	15	346	0	ENST00000370651.3:c.148G>A	p.Glu50Lys	p.E50K	ENST00000370651	NM_003463.4	50	Gaa/Aaa	3/6	1	2	FACETS	0.621	0.454	0.823	0.621	0.454	0.823	SUBCLONAL	1	TRUE	1	0.17	2		346	284	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622183	162622184	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0035502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	53	422	0	ENST00000366898.1:c.513_514delinsAT	p.Ala172Ser	p.A172S	ENST00000366898	NM_004562.2	171	caGGca/caATca	4/12	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.17	2		422	619	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388121	81388121	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0035502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	25	334	0	ENST00000222390.5:c.255-1G>T		p.X85_splice	ENST00000222390	NM_000601.4	85			1	2	FACETS	0.94	0.741	1	0.94	0.741	1	CLONAL	1	TRUE	1	0.17	2		334	313	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864534	56864534	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	119	567	0	ENST00000519728.1:c.497C>G	p.Ser166Cys	p.S166C	ENST00000519728	NM_002350.3	166	tCt/tGt	7/13	1	2	FACETS	0.821	0.74	0.906	1	0.986	1	CLONAL	2	TRUE	1	0.17	2		567	853	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434627	128434627	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	50	597	0	ENST00000265960.3:c.227G>T	p.Trp76Leu	p.W76L	ENST00000265960	NM_001006617.1	76	tGg/tTg	2/12	1	2	FACETS	0.784	0.664	0.917	0.784	0.664	0.917	CLONAL	1	TRUE	1	0.17	2		597	750	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410642	63410642	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	63	411	0	ENST00000330258.3:c.2525A>T	p.Glu842Val	p.E842V	ENST00000330258	NM_152424.3	842	gAg/gTg	2/2	NA	2	FACETS	1	0.963	1			1	INDETERMINATE	1	TRUE	NA	0.17	2		411	553	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345304	70345304	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	76	315	0	ENST00000374080.3:c.2330A>G	p.Asp777Gly	p.D777G	ENST00000374080		777	gAt/gGt	16/45	NA	2	FACETS	0.951	0.837	1			1	INDETERMINATE	2	TRUE	NA	0.17	2		315	470	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0035503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	20	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.647	0.504	0.808	0.647	0.504	0.808	SUBCLONAL	1	TRUE	1	0.618190256323037	2		502	100	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420108	49420108	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs398123729	NA	P-0035505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	26	550	0	ENST00000301067.7:c.15641G>C	p.Arg5214Pro	p.R5214P	ENST00000301067	NM_003482.3	5214	cGc/cCc	48/54	1	2	FACETS	0.608	0.481	0.755	0.608	0.481	0.755	SUBCLONAL	1	TRUE	1	0.18	2		550	475	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937440	178937440	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs768646872	NA	P-0035505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	21	365	0	ENST00000263967.3:c.1828A>G	p.Met610Val	p.M610V	ENST00000263967	NM_006218.2	610	Atg/Gtg	12/21	0.161898189028103	3	FACETS	0.687	0.529	0.873	0.344	0.264	0.437	SUBCLONAL	1	TRUE	1	0.18	3		365	370	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86676338	86676338	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0035505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	11	173	0	ENST00000274376.6:c.2616T>A	p.Tyr872Ter	p.Y872*	ENST00000274376	NM_002890.2	872	taT/taA	20/25	1	2	FACETS	0.711	0.492	0.981	0.711	0.492	0.981	CLONAL	1	TRUE	1	0.18	2		173	172	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120338	94120338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	23	306	0	ENST00000369303.4:c.713C>T	p.Ala238Val	p.A238V	ENST00000369303	NM_004440.3	238	gCa/gTa	3/17	1	2	FACETS	0.858	0.669	1	0.858	0.669	1	CLONAL	1	TRUE	1	0.18	2		306	298	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324674	31324674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11546719	NA	P-0035506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	10	220	2	ENST00000412585.2:c.134G>A	p.Arg45His	p.R45H	ENST00000412585	NM_005514.6	45	cGc/cAc	2/8	0.143411166846622	4	FACETS	1	0.813	1	0.644	0.445	0.884	INDETERMINATE	1	FALSE	2	0.333900915931397	4		222	62	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851512	63851512	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	23	516	0	ENST00000279873.7:c.2290G>A	p.Glu764Lys	p.E764K	ENST00000279873	NM_032199.2	764	Gaa/Aaa	10/10	1	2	FACETS	0.9	0.709	1	0.9	0.709	1	CLONAL	1	FALSE	1	0.333900915931397	2		516	153	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0035508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	215	673	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.947	0.884	1	0.947	0.884	1	CLONAL	1	TRUE	1	0.687266739106542	2		673	661	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0035508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	130	261	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	1	2	FACETS	0.968	0.887	1	0.968	0.887	1	CLONAL	1	TRUE	1	0.687266739106542	2		261	391	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	203	498	0	ENST00000263967.3:c.3012G>A	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atA	21/21	1	2	FACETS	0.899	0.838	0.962	0.899	0.838	0.962	CLONAL	1	TRUE	1	0.687266739106542	2		498	657	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248409	59248409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184098204	NA	P-0035508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	197	419	0	ENST00000371222.2:c.334G>A	p.Glu112Lys	p.E112K	ENST00000371222	NM_002228.3	112	Gag/Aag	1/1	0.687266739106542	1	FACETS	0.98	0.922	1	0.98	0.922	1	CLONAL	1	TRUE	0	0.687266739106542	1		419	384	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023380	27023389	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCGCCGCG	CGCCGCCGCG	-	novel	NA	P-0035508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	36	325	0	ENST00000324856.7:c.486_495del	p.Ala163ProfsTer66	p.A163Pfs*66	ENST00000324856	NM_006015.4	162	gcCGCCGCCGCG/gc	1/20	0.687266739106542	1	FACETS	0.222	0.183	0.265	0.222	0.183	0.265	SUBCLONAL	1	TRUE	0	0.687266739106542	1		325	310	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023452	27023452	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	121	538	1	ENST00000324856.7:c.558del	p.Ser186ArgfsTer46	p.S186Rfs*46	ENST00000324856	NM_006015.4	186	agC/ag	1/20	0.687266739106542	1	FACETS	0.491	0.446	0.537	0.491	0.446	0.537	SUBCLONAL	1	TRUE	0	0.687266739106542	1		539	471	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577348	64577349	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0035508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	259	575	0	ENST00000312049.6:c.233_234del	p.Phe78SerfsTer38	p.F78Sfs*38	ENST00000312049	NM_130799.2	78	tTT/t	2/10	0.687266739106542	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.687266739106542	1		575	461	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43767812	43767812	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	183	443	0	ENST00000382044.4:c.1036C>G	p.Leu346Val	p.L346V	ENST00000382044	NM_001141980.1	346	Ctc/Gtc	9/28	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.687266739106542	2		443	526	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805489	46805489	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	318	788	0	ENST00000290295.7:c.467G>C	p.Gly156Ala	p.G156A	ENST00000290295	NM_006361.5	156	gGa/gCa	1/2	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.687266739106542	2		788	878	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403474	138403474	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	181	422	0	ENST00000289153.2:c.2308G>C	p.Glu770Gln	p.E770Q	ENST00000289153	NM_006219.2	770	Gaa/Caa	15/22	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.687266739106542	2		422	522	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177654	56177655	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0035508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	147	366	0	ENST00000399503.3:c.2629_2630dup	p.Leu877PhefsTer33	p.L877Ffs*33	ENST00000399503	NM_005921.1	876	act/acTTt	14/20	1	2	FACETS	0.918	0.845	0.993	0.918	0.845	0.993	CLONAL	1	TRUE	1	0.687266739106542	2		366	466	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036979	180036979	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	266	610	0	ENST00000261937.6:c.3733G>C	p.Glu1245Gln	p.E1245Q	ENST00000261937	NM_182925.4	1245	Gag/Cag	28/30	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.687266739106542	2		610	723	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001099	150001099	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	188	470	0	ENST00000253339.5:c.2505G>C	p.Leu835Phe	p.L835F	ENST00000253339		835	ttG/ttC	4/7	1	2	FACETS	0.932	0.866	0.999	0.932	0.866	0.999	CLONAL	1	TRUE	1	0.687266739106542	2		470	587	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	248	563	0	ENST00000206249.3:c.1138G>A	p.Glu380Lys	p.E380K	ENST00000206249	NM_000125.3	380	Gaa/Aaa	5/8	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.687266739106542	2		563	710	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0035510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	69	757	0	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	0.3	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.16	1		757	640	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0035510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	17	641	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.284	0.211	0.372	0.284	0.211	0.372	SUBCLONAL	1	TRUE	1	0.16	2		642	748	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775782	9775782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767750196	NA	P-0035510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	50	758	0	ENST00000377346.4:c.325G>A	p.Val109Met	p.V109M	ENST00000377346	NM_005026.3	109	Gtg/Atg	4/24	1	2	FACETS	0.866	0.733	1	0.866	0.733	1	CLONAL	1	TRUE	1	0.16	2		758	722	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217247	7217248	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	67	738	0	ENST00000380728.2:c.457dup	p.Met153AsnfsTer53	p.M153Nfs*53	ENST00000380728		153	atg/aAtg	6/11	0.3	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.16	1		738	608	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011212	12011212	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	26	403	0	ENST00000353533.5:c.622del	p.Ile208SerfsTer3	p.I208Sfs*3	ENST00000353533	NM_003010.3	207	Aaa/aa	5/11	0.3	1	FACETS	0.724	0.573	0.898	0.724	0.573	0.898	SUBCLONAL	1	TRUE	0	0.16	1		403	413	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46275994	46275994	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	38	663	0	ENST00000371998.3:c.3430C>T	p.Gln1144Ter	p.Q1144*	ENST00000371998		1144	Cag/Tag	18/23	1	2	FACETS	0.771	0.636	0.923	0.771	0.636	0.923	CLONAL	1	TRUE	1	0.16	2		663	616	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026853	71026853	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	29	427	0	ENST00000318789.4:c.1369G>T	p.Glu457Ter	p.E457*	ENST00000318789	NM_032682.5	457	Gaa/Taa	16/21	1	2	FACETS	0.833	0.668	1	0.833	0.668	1	CLONAL	1	TRUE	1	0.16	2		427	435	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0035510-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	35	374	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.819	0.676	0.976	1	0.956	1	CLONAL	2	TRUE	1	0.19	2		374	225	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383891	15383891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035510-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	31	540	3	ENST00000263377.2:c.20C>T	p.Pro7Leu	p.P7L	ENST00000263377	NM_058243.2	7	cCt/cTt	2/20	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.19	2		543	271	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534630	140534630	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035510-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	58	523	0	ENST00000288602.6:c.283A>G	p.Arg95Gly	p.R95G	ENST00000288602	NM_004333.4	95	Aga/Gga	3/18	1	2	FACETS	1	0.927	1	1	0.98	1	CLONAL	2	TRUE	1	0.19	2		523	276	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035510-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	61	381	0	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	1	2	FACETS	0.845	0.744	0.949	0.845	0.744	0.949	CLONAL	1	FALSE	1	0.844637758896362	2		381	171	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435626	18435626	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035510-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	39	275	0	ENST00000266497.5:c.611C>G	p.Ser204Cys	p.S204C	ENST00000266497		204	tCt/tGt	1/31	0.13721787189507	4	FACETS	1	0.952	1	0.681	0.578	0.791	INDETERMINATE	1	FALSE	2	0.844637758896362	4		275	125	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576437	67576437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141981005	NA	P-0035510-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	62	487	2	ENST00000274335.5:c.716C>T	p.Thr239Met	p.T239M	ENST00000274335		239	aCg/aTg	5/15	1	2	FACETS	0.426	0.369	0.486	0.426	0.369	0.486	SUBCLONAL	1	FALSE	1	0.844637758896362	2		489	345	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004998	150004998	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035510-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	98	553	0	ENST00000253339.5:c.1227G>T	p.Met409Ile	p.M409I	ENST00000253339		409	atG/atT	3/7	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	FALSE	1	0.844637758896362	2		553	232	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0035511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	538	376	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	0.236850975912227	4	FACETS	0.99	0.96	1			1	INDETERMINATE	3	TRUE	NA	0.793305849629997	4		376	819	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733280	40733280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370508724	NA	P-0035511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	446	508	1	ENST00000373198.4:c.3526C>T	p.Arg1176Cys	p.R1176C	ENST00000373198	NM_133170.3	1176	Cgt/Tgt	26/32	0.621502472587412	5	FACETS	1	0.994	1	0.805	0.771	0.84	CLONAL	2	TRUE	2	0.793305849629997	5		509	1019	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348011	89348011	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	348	939	1	ENST00000301030.4:c.4939C>T	p.Pro1647Ser	p.P1647S	ENST00000301030	NM_001256183.1	1647	Cct/Tct	9/13	0.793305849629997	1	FACETS	0.743	0.709	0.778	0.743	0.709	0.778	SUBCLONAL	1	TRUE	0	0.793305849629997	1		940	712	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0035511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	104	397	2				ENST00000310581	NM_198253.2	-/1132			0.793305849629997	1	FACETS	0.461	0.417	0.507	0.461	0.417	0.507	SUBCLONAL	1	TRUE	0	0.793305849629997	1		399	343	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740573	145740573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573164516	NA	P-0035511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	351	713	0	ENST00000428558.2:c.1444C>T	p.Arg482Cys	p.R482C	ENST00000428558	NM_004260.3	482	Cgc/Tgc	8/22	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.793305849629997	2		713	805	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796963	78796963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	541	609	0	ENST00000306801.3:c.1076C>T	p.Ser359Leu	p.S359L	ENST00000306801	NM_020761.2	359	tCg/tTg	9/34	0.793305849629997	2	FACETS	0.981	0.957	1	0.981	0.957	1	CLONAL	2	TRUE	0	0.793305849629997	2		609	695	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818366	43818366	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	153	642	0	ENST00000372470.3:c.1831G>A	p.Ala611Thr	p.A611T	ENST00000372470	NM_005373.2	611	Gct/Act	12/12	0.571563693069519	1	FACETS	0.389	0.357	0.422	0.389	0.357	0.422	SUBCLONAL	1	TRUE	0	0.793305849629997	1		642	599	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175945	176175945	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370981350	NA	P-0035511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	94	92	0	ENST00000367669.3:c.170G>A	p.Gly57Asp	p.G57D	ENST00000367669	NM_022457.5	57	gGc/gAc	1/20	0.793305849629997	3	FACETS	1	0.966	1	0.583	0.525	0.642	CLONAL	1	TRUE	1	0.793305849629997	3		92	284	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574565	64574565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060499973	NA	P-0035511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	250	602	0	ENST00000312049.6:c.830C>T	p.Pro277Leu	p.P277L	ENST00000312049	NM_130799.2	277	cCc/cTc	6/10	0.793305849629997	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.793305849629997	1		602	378	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180535	94180535	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	185	419	0	ENST00000323929.3:c.1633C>T	p.Leu545Phe	p.L545F	ENST00000323929	NM_005591.3	545	Ctt/Ttt	15/20	0.793305849629997	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.793305849629997	1		419	276	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122902	2122902	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	124	672	0	ENST00000219476.3:c.2273C>A	p.Ser758Tyr	p.S758Y	ENST00000219476	NM_000548.3	758	tCc/tAc	21/42	0.793305849629997	1	FACETS	0.358	0.325	0.392	0.358	0.325	0.392	SUBCLONAL	1	TRUE	0	0.793305849629997	1		672	527	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158636966	158636967	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AT	novel	NA	P-0035511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	224	486	0	ENST00000263640.3:c.213_214delinsAT	p.Phe71_Gln72delinsLeuTer	p.F71_Q72delinsL*	ENST00000263640	NM_001105.4	71	ttCCag/ttATag	4/11	1	2	FACETS	0.905	0.848	0.963	0.905	0.848	0.963	CLONAL	1	TRUE	1	0.793305849629997	2		486	624	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197387	26197387	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1344624542	NA	P-0035511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	270	362	1	ENST00000356476.2:c.92C>T	p.Pro31Leu	p.P31L	ENST00000356476		31	cCa/cTa	1/1	0.620141724670795	5	FACETS	1	0.982	1	0.731	0.69	0.772	CLONAL	2	TRUE	2	0.793305849629997	5		363	680	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188355	32188355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	366	594	0	ENST00000375023.3:c.986G>A	p.Gly329Glu	p.G329E	ENST00000375023	NM_004557.3	329	gGg/gAg	6/30	0.382859281302087	3	FACETS	0.85	0.812	0.888	0.85	0.812	0.888	INDETERMINATE	2	TRUE	1	0.793305849629997	3		594	758	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55229226	55229227	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0035511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	277	359	0	ENST00000275493.2:c.1533_1534delinsTT	p.Pro512Ser	p.P512S	ENST00000275493	NM_005228.3	511	tcCCcc/tcTTcc	13/28	0.793305849629997	3	FACETS	0.987	0.94	1	0.987	0.94	1	CLONAL	2	TRUE	1	0.793305849629997	3		359	494	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126432	5126432	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	120	344	0	ENST00000381652.3:c.3277G>A	p.Gly1093Arg	p.G1093R	ENST00000381652	NM_004972.3	1093	Gga/Aga	24/25	0.793305849629997	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.793305849629997	1		344	171	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841274	15841274	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	249	381	0	ENST00000307771.7:c.1358G>A	p.Ser453Asn	p.S453N	ENST00000307771	NM_005089.3	453	aGc/aAc	11/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.793305849629997	2		381	593	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763848	76763848	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1242884944	NA	P-0035511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	253	643	0	ENST00000373344.5:c.7460C>T	p.Ser2487Phe	p.S2487F	ENST00000373344	NM_000489.3	2487	tCc/tTc	35/35	1	2	FACETS	0.924	0.87	0.98	0.924	0.87	0.98	CLONAL	1	TRUE	1	0.793305849629997	2		643	690	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0035512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	167	610	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.547408011010465	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.625875953122176	2		610	239	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102117	27102357	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCAGAGAGCACATGGGCATTAGATACCATCAACATCCTGCTGTATGATGACAACAGCATCATGACCTTCAACCTCAGTCAGGTGAGTATCAGTGCCTGGGGAAGATTGAGAGGGTTTGGGATCTTCTTAGTGTAGACAATGGGAATGTCTCATCTTTAGCCACCTTGGTCTTTCTCTTTCTCTCTTGTAGATATCTTCCATGCCAGTACTTTGCTTCCTTTGCCTCTGGGCACGGGCCCA	GGCAGAGAGCACATGGGCATTAGATACCATCAACATCCTGCTGTATGATGACAACAGCATCATGACCTTCAACCTCAGTCAGGTGAGTATCAGTGCCTGGGGAAGATTGAGAGGGTTTGGGATCTTCTTAGTGTAGACAATGGGAATGTCTCATCTTTAGCCACCTTGGTCTTTCTCTTTCTCTCTTGTAGATATCTTCCATGCCAGTACTTTGCTTCCTTTGCCTCTGGGCACGGGCCCA	-	novel	NA	P-0035512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	66	617	0	ENST00000324856.7:c.5045_5124+161del		p.X1682_splice	ENST00000324856	NM_006015.4	1682		19/20	NA	2	FACETS	1	0.935	1			1	INDETERMINATE	1	TRUE	NA	0.625875953122176	2		617	194	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912734	32912734	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	136	392	0	ENST00000380152.3:c.4243del	p.Glu1415SerfsTer4	p.E1415Sfs*4	ENST00000380152		1414	acG/ac	11/27	0.625875953122176	4	FACETS	0.92	0.868	0.969			1	CLONAL	4	TRUE	NA	0.625875953122176	4		392	192	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341349	89341353	+	frameshift_variant	Frame_Shift_Del	DEL	GATAC	GATAC	-	novel	NA	P-0035512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	22	583	0	ENST00000301030.4:c.7582_7586del	p.Val2528LeufsTer2	p.V2528Lfs*2	ENST00000301030	NM_001256183.1	2528	GTATCc/c	11/13	0.545703264674489	2	FACETS	0.276	0.214	0.347	0.138	0.107	0.174	SUBCLONAL	1	TRUE	0	0.625875953122176	2		583	255	SUCCESS
APC	324	MSKCC	GRCh37	5	112175708	112175708	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	39	304	0	ENST00000257430.4:c.4417A>T	p.Asn1473Tyr	p.N1473Y	ENST00000257430	NM_000038.5	1473	Aat/Tat	16/16	0.55857885313596	3	FACETS	0.986	0.829	1	0.493	0.414	0.578	CLONAL	1	TRUE	1	0.625875953122176	3		304	166	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846065	68846065	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	217	676	1	ENST00000261769.5:c.1036C>T	p.Gln346Ter	p.Q346*	ENST00000261769	NM_004360.3	346	Caa/Taa	8/16	0.560781194531273	1	FACETS	0.924	0.865	0.984	0.924	0.865	0.984	CLONAL	1	TRUE	0	0.560781194531273	1		677	603	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692818	89692818	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1339631701	NA	P-0035513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	85	252	0	ENST00000371953.3:c.302T>C	p.Ile101Thr	p.I101T	ENST00000371953	NM_000314.4	101	aTc/aCc	5/9	0.560781194531273	1	FACETS	0.814	0.729	0.902	0.814	0.729	0.902	CLONAL	1	TRUE	0	0.560781194531273	1		252	268	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589607	67589612	+	inframe_deletion	In_Frame_Del	DEL	AAGAAA	AAGAAA	-	novel	NA	P-0035513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	96	211	0	ENST00000274335.5:c.1372_1377del	p.Glu458_Lys459del	p.E458_K459del	ENST00000274335		457	cAAGAAAaa/caa	10/15	1	2	FACETS	0.943	0.848	1	0.943	0.848	1	CLONAL	1	TRUE	1	0.560781194531273	2		211	363	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230576	46230577	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0035513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	177	517	0	ENST00000334344.6:c.826dup	p.Leu276ProfsTer4	p.L276Pfs*4	ENST00000334344	NM_152641.2	275	-/C	8/21	1	2	FACETS	0.976	0.903	1	0.976	0.903	1	CLONAL	1	TRUE	1	0.560781194531273	2		517	647	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576828	7576874	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GATAAGAGGTCCCAAGACTTAGTACCTGAAGGGTGAAATATTCTCCA	GATAAGAGGTCCCAAGACTTAGTACCTGAAGGGTGAAATATTCTCCA	-	novel	NA	P-0035513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	161	539	0	ENST00000269305.4:c.972_993+25del		p.X324_splice	ENST00000269305	NM_001126112.2	324		9/11	0.560781194531273	1	FACETS	0.887	0.82	0.954	0.887	0.82	0.954	CLONAL	1	TRUE	0	0.560781194531273	1		539	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0035522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	272	539	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.507346321183325	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.507346321183325	1		539	747	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520168	9520168	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0035522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	149	354	0	ENST00000353224.5:c.2101A>T	p.Lys701Ter	p.K701*	ENST00000353224	NM_177990.2	701	Aaa/Taa	10/10	1	2	FACETS	0.963	0.883	1	0.963	0.883	1	CLONAL	1	TRUE	1	0.507346321183325	2		354	610	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684301	29684302	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	219	416	0	ENST00000356175.3:c.7822dup	p.Tyr2608LeufsTer5	p.Y2608Lfs*5	ENST00000356175	NM_000267.3	2607	-/T	53/57	0.507346321183325	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.507346321183325	1		416	635	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591899	48591911	+	frameshift_variant	Frame_Shift_Del	DEL	GGACCCTTCTGGA	GGACCCTTCTGGA	-	novel	NA	P-0035522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	142	367	0	ENST00000342988.3:c.1065_1077del	p.Asp355GlufsTer25	p.D355Efs*25	ENST00000342988	NM_005359.5	354	gtGGACCCTTCTGGA/gt	9/12	0.507346321183325	1	FACETS	0.853	0.782	0.925	0.853	0.782	0.925	CLONAL	1	TRUE	0	0.507346321183325	1		367	490	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504430	186504430	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	176	450	0	ENST00000323963.5:c.767G>C	p.Arg256Thr	p.R256T	ENST00000323963		256	aGa/aCa	7/11	1	2	FACETS	0.772	0.711	0.835	0.772	0.711	0.835	SUBCLONAL	1	TRUE	1	0.507346321183325	2		450	899	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231062	53231062	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	208	441	0	ENST00000375401.3:c.1840G>T	p.Ala614Ser	p.A614S	ENST00000375401	NM_004187.3	614	Gct/Tct	13/26	0.507346321183325	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.507346321183325	1		441	559	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936094	+	missense_variant	Missense_Mutation	TNP	AGC	AGC	GGA	novel	NA	P-0035522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	338	452	0	ENST00000263967.3:c.1634_1636delinsGGA	p.Glu545_Gln546delinsGlyLys	p.E545_Q546delinsGK	ENST00000263967	NM_006218.2	545	gAGCag/gGGAag	10/21	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.507346321183325	2		452	938	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0035524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	66	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.219234144997867	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.219234144997867	1		502	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0035524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	81	660	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.219234144997867	1	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	0	0.219234144997867	1		661	636	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0035524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	46	495	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.906	0.764	1	0.906	0.764	1	CLONAL	1	TRUE	1	0.219234144997867	2		495	463	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11999013	11999013	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0035524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	46	289	0	ENST00000353533.5:c.513+2T>C		p.X171_splice	ENST00000353533	NM_003010.3	171			0.219234144997867	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.219234144997867	1		289	315	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226556023	226556023	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0035524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	37	289	0	ENST00000366794.5:c.2155-1G>A		p.X719_splice	ENST00000366794	NM_001618.3	719			1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.219234144997867	2		289	302	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971140	21971159	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCAGTTGGGCTCCGCGCC	GCGCAGTTGGGCTCCGCGCC	-	novel	NA	P-0035524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	37	429	0	ENST00000304494.5:c.199_218del	p.Gly67ArgfsTer46	p.G67Rfs*46	ENST00000304494	NM_000077.4	67	GGCGCGGAGCCCAACTGCGCc/c	2/3	1	2	FACETS	0.945	0.781	1	0.945	0.781	1	CLONAL	1	TRUE	1	0.219234144997867	2		429	357	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0035526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	73	673	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.547	0.478	0.62	0.547	0.478	0.62	SUBCLONAL	1	TRUE	1	0.478738436422491	2		673	558	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs770248150	NA	P-0121442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	349	558	7	ENST00000311936.3:c.351A>T	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaT	4/5	0.669196537987775	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	3	NA	1	0.669196537987775	4		565	580	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720833	89720836	+	frameshift_variant	Frame_Shift_Del	DEL	AAAT	AAAT	-	rs587782304	NA	P-0035533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	73	315	0	ENST00000371953.3:c.987_990del	p.Asn329LysfsTer14	p.N329Kfs*14	ENST00000371953	NM_000314.4	328	gcAAAT/gc	8/9	0.334407773818699	1	FACETS	0.782	0.686	0.885	0.782	0.686	0.885	SUBCLONAL	1	TRUE	0	0.334407773818699	1		315	465	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	103	494	1	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	1	2	FACETS	0.933	0.836	1	0.933	0.836	1	CLONAL	1	TRUE	1	0.334407773818699	2		495	660	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307173	65307173	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs181919006	NA	P-0035533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	78	411	0	ENST00000342505.4:c.2515C>T	p.Arg839Ter	p.R839*	ENST00000342505	NM_002227.2	839	Cga/Tga	18/25	1	2	FACETS	0.714	0.628	0.807	0.714	0.628	0.807	SUBCLONAL	1	TRUE	1	0.334407773818699	2		411	653	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221279	36221279	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555731976	NA	P-0035533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	197	793	0	ENST00000222270.7:c.5113C>T	p.Arg1705Ter	p.R1705*	ENST00000222270	NM_014727.1	1705	Cga/Tga	24/37	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.334407773818699	2		793	1135	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929036	44929037	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0035533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	115	414	0	ENST00000377967.4:c.2136_2137insG	p.Thr713AspfsTer17	p.T713Dfs*17	ENST00000377967	NM_021140.2	712	-/G	17/29	0.15458233595552	3	FACETS	1	0.947	1	0.539	0.485	0.595	INDETERMINATE	1	TRUE	1	0.334407773818699	3		414	745	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0035537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	59	502	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	0.18	2		502	639	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034475	47034475	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	109	675	0	ENST00000377604.3:c.560G>A	p.Trp187Ter	p.W187*	ENST00000377604	NM_001204468.1	187	tGg/tAg	6/24	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.18	2		675	860	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509915	106509915	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	76	649	0	ENST00000359195.3:c.1909G>T	p.Asp637Tyr	p.D637Y	ENST00000359195	NM_002649.2	637	Gat/Tat	2/11	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.18	2		649	829	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363090	40363090	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	62	574	1	ENST00000397332.2:c.1139G>T	p.Arg380Leu	p.R380L	ENST00000397332	NM_001033082.2	380	cGg/cTg	3/3	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.18	2		575	671	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743859	40743859	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	63	506	0	ENST00000373198.4:c.3136del	p.Arg1046AlafsTer54	p.R1046Afs*54	ENST00000373198	NM_133170.3	1046	Cgc/gc	23/32	0.3	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.18	1		506	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0035549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	235	753	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.475486787516719	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.475486787516719	1		753	644	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0035549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	39	323	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.239701053678945	1	FACETS	0.344	0.285	0.408	0.344	0.285	0.408	INDETERMINATE	1	TRUE	0	0.475486787516719	1		323	364	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	105	419	0	ENST00000257430.4:c.4199C>A	p.Ser1400Ter	p.S1400*	ENST00000257430	NM_000038.5	1400	tCg/tAg	16/16	0.239701053678945	1	FACETS	0.84	0.758	0.925	0.84	0.758	0.925	INDETERMINATE	1	TRUE	0	0.475486787516719	1		419	401	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332607	153332607	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	257	467	0	ENST00000281708.4:c.349G>T	p.Glu117Ter	p.E117*	ENST00000281708	NM_033632.3	117	Gag/Tag	2/12	0.461636191254414	2	FACETS	0.908	0.858	0.959	0.908	0.858	0.959	CLONAL	2	TRUE	0	0.475486787516719	2		467	595	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967567	26967567	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	821	530	1	ENST00000381527.3:c.710G>A	p.Arg237Gln	p.R237Q	ENST00000381527	NM_001260.1	237	cGa/cAa	7/13	0.475486787516719	6	FACETS	0.984	0.958	1	0.984	0.958	1	CLONAL	5	TRUE	1	0.475486787516719	6		531	1369	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633551	69633551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	38	335	1	ENST00000334134.2:c.151G>A	p.Ala51Thr	p.A51T	ENST00000334134	NM_005247.2	51	Gcc/Acc	1/3	0.239701053678945	1	FACETS	0.375	0.311	0.446	0.375	0.311	0.446	INDETERMINATE	1	TRUE	0	0.475486787516719	1		336	325	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857779	9857779	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs78544202	NA	P-0035549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	126	633	0	ENST00000330684.3:c.3622C>T	p.Arg1208Trp	p.R1208W	ENST00000330684	NM_001134407.1	1208	Cgg/Tgg	13/13	1	2	FACETS	0.845	0.767	0.927	0.845	0.767	0.927	CLONAL	1	TRUE	1	0.475486787516719	2		633	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0035550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	296	746	1	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.777543216434869	1	FACETS	0.934	0.893	0.975	0.934	0.893	0.975	CLONAL	1	TRUE	0	0.777543216434869	1		747	498	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712007	89712007	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs765433422	NA	P-0035550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	212	348	0	ENST00000371953.3:c.625G>T	p.Gly209Ter	p.G209*	ENST00000371953	NM_000314.4	209	Gga/Tga	6/9	0.777543216434869	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.777543216434869	1		348	309	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954379	48954379	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0035550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	219	406	0	ENST00000267163.4:c.1498+2T>G		p.X500_splice	ENST00000267163	NM_000321.2	500			0.777543216434869	1	FACETS	0.975	0.927	1	0.975	0.927	1	CLONAL	1	TRUE	0	0.777543216434869	1		406	353	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431178	49431178	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs793888512	NA	P-0035550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	363	767	0	ENST00000301067.7:c.9961C>T	p.Arg3321Ter	p.R3321*	ENST00000301067	NM_003482.3	3321	Cga/Tga	34/54	0.777543216434869	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.777543216434869	1		767	541	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95583026	95583026	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	161	293	0	ENST00000393063.1:c.1516A>T	p.Arg506Trp	p.R506W	ENST00000393063	NM_030621.3	506	Agg/Tgg	11/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.777543216434869	2		293	371	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346808	91346808	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	232	500	0	ENST00000355112.3:c.3416G>T	p.Arg1139Leu	p.R1139L	ENST00000355112	NM_000057.2	1139	cGa/cTa	18/22	1	2	FACETS	0.95	0.892	1	0.95	0.892	1	CLONAL	1	TRUE	1	0.777543216434869	2		500	628	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285149	15285149	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	468	1017	1	ENST00000263388.2:c.4466A>T	p.Asn1489Ile	p.N1489I	ENST00000263388	NM_000435.2	1489	aAc/aTc	25/33	1	2	FACETS	0.968	0.927	1	0.968	0.927	1	CLONAL	1	TRUE	1	0.777543216434869	2		1018	1243	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55960990	55960990	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	302	531	0	ENST00000263923.4:c.2950A>T	p.Ser984Cys	p.S984C	ENST00000263923	NM_002253.2	984	Agt/Tgt	21/30	0.777543216434869	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.777543216434869	1		531	419	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099395	27099395	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	96	688	0	ENST00000324856.7:c.3632A>G	p.Tyr1211Cys	p.Y1211C	ENST00000324856	NM_006015.4	1211	tAt/tGt	14/20	1	2	FACETS	0.814	0.726	0.908	0.814	0.726	0.908	CLONAL	1	TRUE	1	0.354497955623496	2		688	665	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8105995	8105995	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	42	520	1	ENST00000346208.3:c.815C>T	p.Pro272Leu	p.P272L	ENST00000346208		272	cCa/cTa	4/6	1	2	FACETS	0.418	0.348	0.495	0.418	0.348	0.495	SUBCLONAL	1	TRUE	1	0.354497955623496	2		521	567	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348710	89348710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749292180	NA	P-0035551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	83	1217	0	ENST00000301030.4:c.4240G>A	p.Asp1414Asn	p.D1414N	ENST00000301030	NM_001256183.1	1414	Gat/Aat	9/13	1	2	FACETS	0.379	0.333	0.428	0.379	0.333	0.428	SUBCLONAL	1	TRUE	1	0.354497955623496	2		1217	1236	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0035560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	140	538	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.243733487129925	3	FACETS	0.849	0.775	0.927	0.849	0.775	0.927	CLONAL	2	TRUE	1	0.28	3		538	671	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383252	4383252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	54	355	3	ENST00000261254.3:c.46C>T	p.Arg16Trp	p.R16W	ENST00000261254	NM_001759.3	16	Cgg/Tgg	1/5	NA	2	FACETS	1	0.869	1			1	INDETERMINATE	1	TRUE	NA	0.28	2		358	380	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30061031	30061031	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0035560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	164	442	0	ENST00000338641.4:c.863C>G	p.Ser288Ter	p.S288*	ENST00000338641	NM_000268.3	288	tCa/tGa	9/16	NA	2	FACETS	0.931	0.858	1			1	INDETERMINATE	2	TRUE	NA	0.28	2		442	629	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098380	11098380	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	76	573	1	ENST00000358026.2:c.898C>T	p.Gln300Ter	p.Q300*	ENST00000358026	NM_001128849.1	300	Cag/Tag	6/36	0.3	1	FACETS	0.85	0.747	0.961	0.85	0.747	0.961	CLONAL	1	TRUE	0	0.28	1		574	549	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274166	18274166	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	56	433	0	ENST00000222254.8:c.1384C>T	p.Gln462Ter	p.Q462*	ENST00000222254	NM_005027.3	462	Cag/Tag	11/16	1	2	FACETS	0.709	0.608	0.82	0.709	0.608	0.82	SUBCLONAL	1	TRUE	1	0.28	2		433	564	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259540	16259540	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1378062212	NA	P-0035560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	67	417	0	ENST00000375759.3:c.6805G>A	p.Val2269Ile	p.V2269I	ENST00000375759	NM_015001.2	2269	Gta/Ata	11/15	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.28	2		417	463	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125006	46125006	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	50	274	0	ENST00000334344.6:c.193G>C	p.Glu65Gln	p.E65Q	ENST00000334344	NM_152641.2	65	Gag/Cag	3/21	0.243733487129925	3	FACETS	0.755	0.641	0.881	0.378	0.32	0.441	SUBCLONAL	1	TRUE	1	0.28	3		274	539	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121912	2121912	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs201769220	NA	P-0035560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	99	827	2	ENST00000219476.3:c.2074G>T	p.Val692Phe	p.V692F	ENST00000219476	NM_000548.3	692	Gtc/Ttc	19/42	1	2	FACETS	0.989	0.883	1	0.989	0.883	1	CLONAL	1	TRUE	1	0.28	2		829	715	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225924	2225927	+	frameshift_variant	Frame_Shift_Del	DEL	TGTC	TGTC	-	novel	NA	P-0035560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	73	731	0	ENST00000326181.6:c.1719_1722del	p.Cys574AlafsTer59	p.C574Afs*59	ENST00000326181	NM_032271.2	572	atTGTC/at	18/21	1	2	FACETS	0.771	0.674	0.876	0.771	0.674	0.876	SUBCLONAL	1	TRUE	1	0.28	2		731	676	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273900	10273901	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0035560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	92	700	2	ENST00000330684.3:c.368_369delinsAA	p.Pro123Gln	p.P123Q	ENST00000330684	NM_001134407.1	123	cCC/cAA	2/13	1	2	FACETS	0.82	0.728	0.919	0.82	0.728	0.919	CLONAL	1	TRUE	1	0.28	2		702	801	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207131	1207131	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	104	752	0	ENST00000326873.7:c.219del	p.Cys73Ter	p.C73*	ENST00000326873	NM_000455.4	73	tgC/tg	1/10	0.3	1	FACETS	0.799	0.715	0.888	0.799	0.715	0.888	SUBCLONAL	1	TRUE	0	0.28	1		752	800	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602562	10602562	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	69	657	0	ENST00000171111.5:c.1016T>C	p.Leu339Pro	p.L339P	ENST00000171111	NM_203500.1	339	cTc/cCc	3/6	0.3	1	FACETS	0.792	0.691	0.901	0.792	0.691	0.901	CLONAL	1	TRUE	0	0.28	1		657	535	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098392	11098392	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	72	545	0	ENST00000358026.2:c.910C>G	p.Pro304Ala	p.P304A	ENST00000358026	NM_001128849.1	304	Ccc/Gcc	6/36	0.3	1	FACETS	0.838	0.733	0.95	0.838	0.733	0.95	CLONAL	1	TRUE	0	0.28	1		545	528	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287202	33287202	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	81	530	0	ENST00000374542.5:c.1895C>G	p.Ser632Cys	p.S632C	ENST00000374542	NM_001141970.1	632	tCt/tGt	6/8	1	2	FACETS	0.834	0.734	0.94	0.834	0.734	0.94	CLONAL	1	TRUE	1	0.28	2		530	694	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289085	33289085	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	104	645	0	ENST00000374542.5:c.467C>G	p.Ser156Cys	p.S156C	ENST00000374542	NM_001141970.1	156	tCt/tGt	3/8	1	2	FACETS	0.856	0.766	0.952	0.856	0.766	0.952	CLONAL	1	TRUE	1	0.28	2		645	868	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932895	39932896	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0035560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	63	619	3	ENST00000378444.4:c.1703_1704delinsTT	p.Ala568Val	p.A568V	ENST00000378444	NM_001123385.1	568	gCC/gTT	4/15	NA	2	FACETS	0.785	0.679	0.9			1	INDETERMINATE	1	TRUE	NA	0.28	2		622	573	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039323	47039350	+	frameshift_variant	Frame_Shift_Del	DEL	ATCCTGGGGGCCCTGGCACCCTACGCGG	ATCCTGGGGGCCCTGGCACCCTACGCGG	-	novel	NA	P-0035560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	102	709	0	ENST00000377604.3:c.946_973del	p.Ile316CysfsTer10	p.I316Cfs*10	ENST00000377604	NM_001204468.1	316	ATCCTGGGGGCCCTGGCACCCTACGCGGtg/tg	10/24	0.3	1	FACETS	0.912	0.816	1	0.912	0.816	1	CLONAL	1	TRUE	0	0.28	1		709	687	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410546	63410546	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	88	722	1	ENST00000330258.3:c.2621del	p.Gly874AspfsTer102	p.G874Dfs*102	ENST00000330258	NM_152424.3	874	gGa/ga	2/2	1	2	FACETS	0.822	0.727	0.922	0.822	0.727	0.922	CLONAL	1	TRUE	1	0.28	2		723	765	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	59	272	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.924	0.809	1	0.924	0.809	1	CLONAL	1	TRUE	1	0.668475932081979	2		272	191	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0035564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	464	605	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.665499619384866	2	FACETS	0.916	0.884	0.947	0.916	0.884	0.947	CLONAL	2	TRUE	0	0.668475932081979	2		605	758	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720650	89720650	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0035564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	60	302	0	ENST00000371953.3:c.802-1G>T		p.X268_splice	ENST00000371953	NM_000314.4	268			0.668475932081979	1	FACETS	0.616	0.54	0.696	0.616	0.54	0.696	SUBCLONAL	1	TRUE	0	0.668475932081979	1		302	194	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456864	32456864	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	142	339	0	ENST00000332351.3:c.28C>T	p.Pro10Ser	p.P10S	ENST00000332351	NM_024426.4	10	Ccg/Tcg	1/10	1	2	FACETS	0.955	0.878	1	0.955	0.878	1	CLONAL	1	TRUE	1	0.668475932081979	2		339	445	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170256	119170256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374672276	NA	P-0035564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	118	287	0	ENST00000264033.4:c.2486G>A	p.Arg829Gln	p.R829Q	ENST00000264033	NM_005188.3	829	cGg/cAg	16/16	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.668475932081979	2		287	326	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435434	18435434	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	118	275	0	ENST00000266497.5:c.419G>A	p.Arg140Lys	p.R140K	ENST00000266497		140	aGa/aAa	1/31	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.668475932081979	2		275	351	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877393	28877393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs991429591	NA	P-0035564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	205	442	1	ENST00000282397.4:c.3928G>A	p.Asp1310Asn	p.D1310N	ENST00000282397	NM_002019.4	1310	Gac/Aac	30/30	1	2	FACETS	0.911	0.849	0.975	0.911	0.849	0.975	CLONAL	1	TRUE	1	0.668475932081979	2		443	673	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527723	103527723	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0035564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	88	290	0	ENST00000355739.4:c.3031A>T	p.Lys1011Ter	p.K1011*	ENST00000355739	NM_000123.3	1011	Aag/Tag	15/15	1	2	FACETS	0.808	0.723	0.897	0.808	0.723	0.897	CLONAL	1	TRUE	1	0.668475932081979	2		290	326	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858390	9858390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	215	522	0	ENST00000330684.3:c.3011C>T	p.Ser1004Phe	p.S1004F	ENST00000330684	NM_001134407.1	1004	tCc/tTc	13/13	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.668475932081979	2		522	584	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042182	14042182	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765582513	NA	P-0035564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	113	264	0	ENST00000311895.7:c.2729C>T	p.Ser910Leu	p.S910L	ENST00000311895	NM_005236.2	910	tCa/tTa	11/11	1	2	FACETS	0.989	0.9	1	0.989	0.9	1	CLONAL	1	TRUE	1	0.668475932081979	2		264	342	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615725	1615725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1470356277	NA	P-0035564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	270	802	0	ENST00000344749.5:c.1546G>A	p.Glu516Lys	p.E516K	ENST00000344749	NM_001136139.2	516	Gag/Aag	17/19	1	2	FACETS	0.913	0.858	0.968	0.913	0.858	0.968	CLONAL	1	TRUE	1	0.668475932081979	2		802	885	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400109	41400109	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	190	540	0	ENST00000373198.4:c.650G>A	p.Gly217Glu	p.G217E	ENST00000373198	NM_133170.3	217	gGg/gAg	5/32	1	2	FACETS	0.972	0.904	1	0.972	0.904	1	CLONAL	1	TRUE	1	0.668475932081979	2		540	585	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720906	119720906	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	202	459	0	ENST00000316626.5:c.269A>G	p.Asp90Gly	p.D90G	ENST00000316626		90	gAc/gGc	2/12	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.668475932081979	2		459	597	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512446	149512446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1291265658	NA	P-0035564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	217	562	1	ENST00000261799.4:c.994C>T	p.Arg332Trp	p.R332W	ENST00000261799	NM_002609.3	332	Cgg/Tgg	7/23	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.668475932081979	2		563	648	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0035564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	301	682	0	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	0.635553703379575	3	FACETS	0.982	0.924	1	0.491	0.462	0.521	CLONAL	1	TRUE	1	0.668475932081979	3		682	1224	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874913	151874913	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1432874243	NA	P-0035564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	182	372	0	ENST00000262189.6:c.7625C>T	p.Ser2542Leu	p.S2542L	ENST00000262189	NM_170606.2	2542	tCa/tTa	38/59	1	2	FACETS	0.99	0.92	1	0.99	0.92	1	CLONAL	1	TRUE	1	0.668475932081979	2		372	550	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978530	70978530	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	374	507	0	ENST00000276594.2:c.1123G>A	p.Asp375Asn	p.D375N	ENST00000276594	NM_024504.3	375	Gat/Aat	5/8	0.635553703379575	3	FACETS	0.977	0.934	1	0.977	0.934	1	CLONAL	2	TRUE	1	0.668475932081979	3		507	764	SUCCESS
AR	367	MSKCC	GRCh37	X	66765350	66765350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749864595	NA	P-0035564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	212	709	1	ENST00000374690.3:c.362C>T	p.Ser121Leu	p.S121L	ENST00000374690	NM_000044.3	121	tCg/tTg	1/8	1	2	FACETS	0.901	0.84	0.963	0.901	0.84	0.963	CLONAL	1	TRUE	1	0.668475932081979	2		710	704	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0035565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	158	436	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.274008628350013	2	FACETS	1	0.988	1	0.739	0.679	0.801	CLONAL	1	TRUE	0	0.32	2		436	668	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142051	108142051	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	71	438	0	ENST00000278616.4:c.2999del	p.Asn1000ThrfsTer2	p.N1000Tfs*2	ENST00000278616	NM_000051.3	999	Aaa/aa	20/63	1	2	FACETS	0.593	0.517	0.676	0.593	0.517	0.676	SUBCLONAL	1	TRUE	1	0.32	2		438	748	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338671	70338671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	64	447	0	ENST00000374080.3:c.67G>T	p.Asp23Tyr	p.D23Y	ENST00000374080		23	Gat/Tat	1/45	1	2	FACETS	0.643	0.557	0.737	0.643	0.557	0.737	SUBCLONAL	1	TRUE	1	0.32	2		447	622	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216487	108216488	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	rs991405942	NA	P-0035565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	58	266	0	ENST00000278616.4:c.8438_8439del	p.Phe2813Ter	p.F2813*	ENST00000278616	NM_000051.3	2812	tcTTtt/tctt	58/63	1	2	FACETS	0.88	0.758	1	0.88	0.758	1	CLONAL	1	TRUE	1	0.32	2		266	412	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246416	46246416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140500006	NA	P-0035565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	57	266	0	ENST00000334344.6:c.4510C>T	p.Arg1504Trp	p.R1504W	ENST00000334344	NM_152641.2	1504	Cgg/Tgg	15/21	1	2	FACETS	0.942	0.812	1	0.942	0.812	1	CLONAL	1	TRUE	1	0.32	2		266	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0035570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	321	679	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.485266249939244	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.484930120292164	2		679	534	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380346	14380346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	362	216	0	ENST00000256196.4:c.71G>A	p.Gly24Asp	p.G24D	ENST00000256196		24	gGc/gAc	1/6	0.484930120292164	8	FACETS	0.954	0.918	0.988			1	CLONAL	7	TRUE	NA	0.484930120292164	8		216	549	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593364	67593365	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGC	novel	NA	P-0035570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	66	347	0	ENST00000274335.5:c.2111_2113dup	p.Val704_Gln705insLeu	p.V704_Q705insL	ENST00000274335		704	gtg/gTGCtg	15/15	0.485266249939244	3	FACETS	0.895	0.781	1	0.447	0.39	0.509	CLONAL	1	TRUE	1	0.484930120292164	3		347	378	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0035571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	74	368	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.984	0.865	1	0.984	0.865	1	CLONAL	1	TRUE	1	0.331952330358813	2		368	453	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222198	5222198	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	122	580	0	ENST00000357368.4:c.3137T>A	p.Met1046Lys	p.M1046K	ENST00000357368	NM_002850.3	1046	aTg/aAg	19/38	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.331952330358813	2		580	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0035573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	253	700	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.211733075077456	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	TRUE	0	0.268662155097704	3		700	684	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0035573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	183	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.268662155097704	4	FACETS	1	0.982	1	0.796	0.736	0.857	CLONAL	2	TRUE	1	0.268662155097704	4		502	724	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615035	43615035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142318626	NA	P-0035573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	72	664	1	ENST00000355710.3:c.2449C>T	p.Arg817Cys	p.R817C	ENST00000355710	NM_020975.4	817	Cgc/Tgc	14/20	0.219030365124251	4	FACETS	0.991	0.866	1	0.496	0.433	0.564	CLONAL	1	TRUE	2	0.268662155097704	4		665	686	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913920	32913920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358766	NA	P-0035573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	174	516	0	ENST00000380152.3:c.5428G>A	p.Val1810Ile	p.V1810I	ENST00000380152		1810	Gtt/Att	11/27	0.268662155097704	3	FACETS	1	0.983	1	0.812	0.752	0.875	CLONAL	2	TRUE	0	0.268662155097704	3		516	603	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670664	134670664	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1180432163	NA	P-0035573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	163	752	1	ENST00000398015.3:c.575T>C	p.Phe192Ser	p.F192S	ENST00000398015	NM_004441.4	192	tTc/tCc	3/16	0.219030365124251	4	FACETS	0.82	0.752	0.89	0.82	0.752	0.89	CLONAL	2	TRUE	2	0.268662155097704	4		753	939	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0035575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	390	417	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.261443418028852	5	FACETS	1	0.987	1	1	0.987	1	CLONAL	4	TRUE	1	0.261443418028852	5		417	950	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858956	243858957	+	stop_gained	Nonsense_Mutation	DNP	CT	CT	AC	novel	NA	P-0035575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	69	396	1	ENST00000263826.5:c.108_109delinsGT	p.Ile36_Gly37delinsMetTer	p.I36_G37delinsM*	ENST00000263826	NM_005465.4	36	atAGga/atGTga	2/13	0.261443418028852	5	FACETS	0.885	0.77	1	0.295	0.256	0.337	CLONAL	1	TRUE	2	0.261443418028852	5		397	830	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137199	64137199	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	168	367	0	ENST00000334205.4:c.1631G>T	p.Gly544Val	p.G544V	ENST00000334205	NM_003942.2	544	gGg/gTg	14/17	0.237049709305441	4	FACETS	0.987	0.908	1	0.987	0.908	1	CLONAL	2	TRUE	2	0.261443418028852	4		367	821	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204637	108204637	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	98	189	0	ENST00000278616.4:c.7952A>G	p.Gln2651Arg	p.Q2651R	ENST00000278616	NM_000051.3	2651	cAg/cGg	54/63	0.261443418028852	2	FACETS	0.966	0.869	1	0.966	0.869	1	CLONAL	2	TRUE	0	0.261443418028852	2		189	388	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123888	46123909	+	frameshift_variant	Frame_Shift_Del	DEL	ACCAGAGTCACTACTTTAGGCG	ACCAGAGTCACTACTTTAGGCG	-	novel	NA	P-0035575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	37	210	0	ENST00000334344.6:c.154_175del	p.Thr52AspfsTer31	p.T52Dfs*31	ENST00000334344	NM_152641.2	52	ACCAGAGTCACTACTTTAGGCGga/ga	2/21	0.261443418028852	3	FACETS	0.93	0.769	1	0.465	0.384	0.555	CLONAL	1	TRUE	1	0.261443418028852	3		210	344	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868668	37868668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1303	103	417	0	ENST00000269571.5:c.1115G>A	p.Gly372Glu	p.G372E	ENST00000269571		372	gGg/gAg	9/27	0.261443418028852	7	FACETS	0.927	0.826	1	0.185	0.165	0.207	CLONAL	1	TRUE	2	0.261443418028852	7		417	1406	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921571	178921571	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	56	256	0	ENST00000263967.3:c.1053T>G	p.Ile351Met	p.I351M	ENST00000263967	NM_006218.2	351	atT/atG	5/21	0.261443418028852	3	FACETS	1	0.91	1	0.541	0.464	0.624	CLONAL	1	TRUE	1	0.261443418028852	3		256	448	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955043	55955043	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	73	327	0	ENST00000263923.4:c.3502G>A	p.Ala1168Thr	p.A1168T	ENST00000263923	NM_002253.2	1168	Gct/Act	26/30	0.261443418028852	3	FACETS	1	0.909	1	0.524	0.458	0.594	CLONAL	1	TRUE	1	0.261443418028852	3		327	603	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188754	32188754	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0035575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	73	364	0	ENST00000375023.3:c.799+1G>T		p.X267_splice	ENST00000375023	NM_004557.3	267			0.261443418028852	3	FACETS	0.775	0.676	0.881	0.387	0.338	0.441	SUBCLONAL	1	TRUE	1	0.261443418028852	3		364	815	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821139	32821139	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	266	457	1	ENST00000354258.4:c.455G>A	p.Trp152Ter	p.W152*	ENST00000354258	NM_000593.5	152	tGg/tAg	1/11	0.261443418028852	3	FACETS	0.956	0.895	1	0.956	0.895	1	CLONAL	2	TRUE	1	0.261443418028852	3		458	1204	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932735	39932735	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	129	652	0	ENST00000378444.4:c.1864C>A	p.Pro622Thr	p.P622T	ENST00000378444	NM_001123385.1	622	Cca/Aca	4/15	1	2	FACETS	0.889	0.804	0.979	0.889	0.804	0.979	CLONAL	1	TRUE	1	0.261443418028852	2		652	1110	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913514	NA	P-0035576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	343	439	0	ENST00000288135.5:c.2466T>G	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaG	17/21	0.452487749582386	4	FACETS	0.978	0.932	1			1	INDETERMINATE	2	TRUE	NA	0.900898625793959	4		439	740	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971184	21971184	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs201208890	NA	P-0035576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	24	312	0	ENST00000579755.1:c.217A>C	p.Ser73Arg	p.S73R	ENST00000579755		73	Agt/Cgt	2/3	0.113657282297323	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.900898625793959	0		312	81	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041041	42041041	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	496	559	0	ENST00000219905.7:c.5419C>T	p.Gln1807Ter	p.Q1807*	ENST00000219905	NM_001164273.1	1807	Cag/Tag	16/24	0.900898625793959	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.900898625793959	1		559	573	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593607	55593627	+	inframe_deletion	In_Frame_Del	DEL	AGGTTGTTGAGGAGATAAATG	AGGTTGTTGAGGAGATAAATG	-	novel	NA	P-0035576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	290	384	0	ENST00000288135.5:c.1673_1693del	p.Lys558_Gly565delinsArg	p.K558_G565delinsR	ENST00000288135	NM_000222.2	558	aAGGTTGTTGAGGAGATAAATGga/aga	11/21	0.452487749582386	4	FACETS	0.852	0.807	0.898			1	INDETERMINATE	2	TRUE	NA	0.900898625793959	4		384	718	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	8	812	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.8	1	1	0.8	1	CLONAL	1	FALSE	1	0.341295333104187	2		812	35	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0035579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	37	683	0	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	1	2	FACETS	0.892	0.741	1	0.892	0.741	1	CLONAL	1	FALSE	1	0.341295333104187	2		683	243	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0035579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	217	330	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	0.935	0.874	0.998	1	0.994	1	CLONAL	2	FALSE	1	0.341295333104187	2		330	680	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170827907	170827909	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	rs761817600	NA	P-0035579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	10	572	0	ENST00000296930.5:c.652_654del	p.Ser218del	p.S218del	ENST00000296930	NM_002520.6	216	cCATca/cca	8/11	1	2	FACETS	0.313	0.212	0.44	0.313	0.212	0.44	SUBCLONAL	1	FALSE	1	0.341295333104187	2		572	187	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420314	88420314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767941638	NA	P-0035579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	12	431	3	ENST00000360948.2:c.2372G>A	p.Arg791Gln	p.R791Q	ENST00000360948	NM_001012338.2	791	cGg/cAg	19/19	1	2	FACETS	1	0.73	1	1	0.73	1	CLONAL	1	FALSE	1	0.341295333104187	2		434	69	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118613	17118613	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	13	430	0	ENST00000285071.4:c.1318G>C	p.Glu440Gln	p.E440Q	ENST00000285071	NM_144997.5	440	Gag/Cag	12/14	1	2	FACETS	0.577	0.414	0.773	0.577	0.414	0.773	SUBCLONAL	1	FALSE	1	0.341295333104187	2		430	132	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639354	3639355	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0035579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	11	770	0	ENST00000294008.3:c.4284_4285insTG	p.His1429CysfsTer22	p.H1429Cfs*22	ENST00000294008	NM_032444.2	1428	-/TG	12/15	1	2	FACETS	0.457	0.317	0.63	0.457	0.317	0.63	SUBCLONAL	1	FALSE	1	0.341295333104187	2		770	141	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	40	272	0				ENST00000310581	NM_198253.2	-/1132			0.166715713434098	3	FACETS	0.884	0.738	1	0.884	0.738	1	CLONAL	2	TRUE	1	0.166715713434098	3		272	294	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0035580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	122	903	3	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.166715713434098	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	2	TRUE	0	0.166715713434098	2		906	718	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0035580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	206	724	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	1	2	FACETS	1	0.976	1	1	0.994	1	CLONAL	2	TRUE	1	0.166715713434098	2		724	1102	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829321	128829321	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs945428238	NA	P-0035580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	118	493	0	ENST00000249373.3:c.329C>T	p.Ser110Leu	p.S110L	ENST00000249373	NM_005631.4	110	tCg/tTg	1/12	0.166715713434098	3	FACETS	0.986	0.889	1	0.986	0.889	1	CLONAL	2	TRUE	1	0.166715713434098	3		493	778	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197163	26197163	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	41	473	0	ENST00000356476.2:c.316G>C	p.Glu106Gln	p.E106Q	ENST00000356476		106	Gag/Cag	1/1	0.166715713434098	5	FACETS	0.852	0.707	1	0.284	0.235	0.338	CLONAL	1	TRUE	2	0.166715713434098	5		473	722	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106182988	106182988	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	19	252	0	ENST00000380013.4:c.4027G>C	p.Asp1343His	p.D1343H	ENST00000380013	NM_001127208.2	1343	Gat/Cat	8/11	0.152609048579715	3	FACETS	0.921	0.7	1	0.307	0.233	0.394	CLONAL	1	TRUE	0	0.166715713434098	3		252	268	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430381	78430381	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	78	477	0	ENST00000370768.2:c.787G>A	p.Glu263Lys	p.E263K	ENST00000370768	NM_003902.3	263	Gaa/Aaa	10/20	0.152609048579715	3	FACETS	0.83	0.729	0.937	0.553	0.486	0.625	CLONAL	2	TRUE	0	0.166715713434098	3		477	611	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858938	243858938	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	96	443	0	ENST00000263826.5:c.127C>G	p.Gln43Glu	p.Q43E	ENST00000263826	NM_005465.4	43	Caa/Gaa	2/13	0.166715713434098	3	FACETS	0.952	0.849	1	0.952	0.849	1	CLONAL	2	TRUE	1	0.166715713434098	3		443	655	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201875	67201875	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	41	554	0	ENST00000312629.5:c.1075G>C	p.Asp359His	p.D359H	ENST00000312629	NM_003952.2	359	Gat/Cat	13/15	NA	4	FACETS	0.721	0.599	0.858	0.36	0.299	0.429	INDETERMINATE	1	TRUE	2	0.166715713434098	4		554	796	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998944	100998944	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	77	451	1	ENST00000325455.5:c.858C>A	p.Asp286Glu	p.D286E	ENST00000325455	NM_001202474.3	286	gaC/gaA	1/8	NA	4	FACETS	1	0.921	1	1	0.921	1	INDETERMINATE	2	TRUE	2	0.166715713434098	4		452	508	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998958	100998958	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	71	456	0	ENST00000325455.5:c.844C>A	p.Leu282Met	p.L282M	ENST00000325455	NM_001202474.3	282	Ctg/Atg	1/8	NA	4	FACETS	0.99	0.866	1	0.99	0.866	1	INDETERMINATE	2	TRUE	2	0.166715713434098	4		456	502	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374313	118374313	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	28	355	0	ENST00000534358.1:c.7706G>T	p.Gly2569Val	p.G2569V	ENST00000534358	NM_005933.3	2569	gGa/gTa	27/36	NA	4	FACETS	0.782	0.624	0.963	0.391	0.312	0.482	INDETERMINATE	1	TRUE	2	0.166715713434098	4		355	501	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100212	30100212	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	55	391	0	ENST00000331968.5:c.1408G>A	p.Glu470Lys	p.E470K	ENST00000331968	NM_002742.2	470	Gaa/Aaa	10/18	0.166715713434098	3	FACETS	1	0.943	1	0.608	0.52	0.704	CLONAL	1	TRUE	1	0.166715713434098	3		391	588	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872976	35872976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388058525	NA	P-0035580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	89	417	0	ENST00000216797.5:c.256G>A	p.Glu86Lys	p.E86K	ENST00000216797	NM_020529.2	86	Gaa/Aaa	2/6	0.166715713434098	3	FACETS	0.76	0.673	0.853	0.76	0.673	0.853	SUBCLONAL	2	TRUE	1	0.166715713434098	3		417	761	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004922	16004922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	56	642	0	ENST00000268712.3:c.2332G>A	p.Glu778Lys	p.E778K	ENST00000268712	NM_006311.3	778	Gaa/Aaa	20/46	1	2	FACETS	0.716	0.612	0.831	0.716	0.612	0.831	SUBCLONAL	1	TRUE	1	0.166715713434098	2		642	938	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858074	40858074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	55	652	1	ENST00000428826.2:c.1790G>A	p.Cys597Tyr	p.C597Y	ENST00000428826		597	tGc/tAc	16/21	1	2	FACETS	0.66	0.563	0.768	0.66	0.563	0.768	SUBCLONAL	1	TRUE	1	0.166715713434098	2		653	999	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440936	56440936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	47	542	0	ENST00000407977.2:c.401C>T	p.Ala134Val	p.A134V	ENST00000407977		134	gCc/gTc	4/10	1	2	FACETS	0.751	0.632	0.883	0.751	0.632	0.883	SUBCLONAL	1	TRUE	1	0.166715713434098	2		542	751	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191170	2191170	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	184	636	0	ENST00000398665.3:c.424G>C	p.Asp142His	p.D142H	ENST00000398665	NM_032482.2	142	Gac/Cac	5/28	0.166715713434098	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.166715713434098	2		636	968	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965178	25965178	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	38	595	0	ENST00000435504.4:c.4028C>G	p.Ser1343Cys	p.S1343C	ENST00000435504		1343	tCt/tGt	13/13	0.166715713434098	3	FACETS	0.806	0.665	0.964	0.403	0.332	0.482	CLONAL	1	TRUE	1	0.166715713434098	3		595	613	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551243	29551243	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	127	516	1	ENST00000389048.3:c.1387C>A	p.Gln463Lys	p.Q463K	ENST00000389048	NM_004304.4	463	Cag/Aag	6/29	0.166715713434098	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.166715713434098	3		517	746	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872950	136872950	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	53	317	1	ENST00000241393.3:c.548G>A	p.Arg183Lys	p.R183K	ENST00000241393	NM_003467.2	183	aGa/aAa	2/2	0.166715713434098	3	FACETS	0.859	0.735	0.994	0.859	0.735	0.994	CLONAL	2	TRUE	1	0.166715713434098	3		318	401	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149751	202149751	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1227299223	NA	P-0035580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	49	634	0	ENST00000358485.4:c.1192C>G	p.Gln398Glu	p.Q398E	ENST00000358485	NM_001080125.1	398	Cag/Gag	8/9	0.166715713434098	3	FACETS	0.709	0.599	0.832	0.355	0.299	0.416	SUBCLONAL	1	TRUE	1	0.166715713434098	3		634	898	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741503	39741503	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	30	281	0	ENST00000361337.2:c.1390G>T	p.Asp464Tyr	p.D464Y	ENST00000361337	NM_003286.2	464	Gac/Tac	14/21	0.166715713434098	5	FACETS	0.811	0.652	0.992	0.203	0.163	0.248	CLONAL	1	TRUE	1	0.166715713434098	5		281	555	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89444986	89444986	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0035580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	52	325	0	ENST00000336596.2:c.1307-1G>T		p.X436_splice	ENST00000336596	NM_005233.5	436			0.166715713434098	3	FACETS	1	0.959	1	0.695	0.592	0.808	CLONAL	1	TRUE	1	0.166715713434098	3		325	486	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575593	55575593	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	28	353	0	ENST00000288135.5:c.1119C>A	p.Tyr373Ter	p.Y373*	ENST00000288135	NM_000222.2	373	taC/taA	7/21	0.152609048579715	3	FACETS	0.866	0.692	1	0.289	0.23	0.356	CLONAL	1	TRUE	0	0.166715713434098	3		353	420	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517753	176517753	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	48	620	0	ENST00000292408.4:c.363G>C	p.Leu121Phe	p.L121F	ENST00000292408	NM_213647.1	121	ttG/ttC	4/18	0.166715713434098	3	FACETS	0.762	0.642	0.894	0.381	0.321	0.447	SUBCLONAL	1	TRUE	1	0.166715713434098	3		620	819	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896531	151896531	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	20	255	0	ENST00000262189.6:c.4106G>T	p.Gly1369Val	p.G1369V	ENST00000262189	NM_170606.2	1369	gGa/gTa	27/59	0.166715713434098	3	FACETS	0.833	0.637	1	0.417	0.318	0.532	CLONAL	1	TRUE	1	0.166715713434098	3		255	312	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206652	27206652	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	51	480	0	ENST00000380036.4:c.2437C>G	p.Pro813Ala	p.P813A	ENST00000380036	NM_000459.3	813	Cct/Gct	15/23	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.166715713434098	2		480	611	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409911	63409911	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1296222452	NA	P-0035580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	18	207	0	ENST00000330258.3:c.3256C>T	p.Gln1086Ter	p.Q1086*	ENST00000330258	NM_152424.3	1086	Cag/Tag	2/2	0.0810050932834132	2	FACETS	0.854	0.643	1			1	INDETERMINATE	1	TRUE	NA	0.166715713434098	2		207	253	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0035583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	485	802	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.664811874785814	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.664811874785814	2		802	705	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45423069	45423069	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	22	336	0	ENST00000262160.6:c.59A>T	p.Lys20Met	p.K20M	ENST00000262160	NM_005901.5	20	aAg/aTg	2/11	0.664811874785814	2	FACETS	0.216	0.167	0.273	0.108	0.083	0.137	SUBCLONAL	1	TRUE	0	0.664811874785814	2		336	306	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561502	9561502	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	154	538	0	ENST00000353224.5:c.280G>T	p.Val94Leu	p.V94L	ENST00000353224	NM_177990.2	94	Gtg/Ttg	4/10	0.549645442546105	5	FACETS	0.851	0.778	0.928	0.284	0.259	0.31	CLONAL	1	TRUE	2	0.664811874785814	5		538	1087	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117739647	117739647	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	214	333	0	ENST00000368508.3:c.146C>A	p.Thr49Lys	p.T49K	ENST00000368508	NM_002944.2	49	aCa/aAa	2/43	0.547802481363072	4	FACETS	0.939	0.879	0.999	0.939	0.879	0.999	CLONAL	2	TRUE	2	0.664811874785814	4		333	571	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971279	13971279	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	305	533	0	ENST00000405192.2:c.650A>T	p.Glu217Val	p.E217V	ENST00000405192	NM_001163147.1	217	gAg/gTg	8/12	0.664811874785814	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.664811874785814	3		533	609	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs985033810	NA	P-0035584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	129	620	0	ENST00000269305.4:c.731G>T	p.Gly244Val	p.G244V	ENST00000269305	NM_001126112.2	244	gGc/gTc	7/11	0.242701478068535	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	0	0.258231814633645	2		620	489	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226550800	226550800	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	98	535	0	ENST00000366794.5:c.2848G>C	p.Gly950Arg	p.G950R	ENST00000366794	NM_001618.3	950	Ggt/Cgt	21/23	0.258231814633645	3	FACETS	0.75	0.671	0.834			1	SUBCLONAL	2	TRUE	NA	0.258231814633645	3		535	571	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437083	110437083	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	24	66	0	ENST00000375856.3:c.1318C>G	p.Pro440Ala	p.P440A	ENST00000375856	NM_003749.2	440	Ccc/Gcc	1/2	0.258231814633645	4	FACETS	0.939	0.757	1	0.939	0.757	1	CLONAL	3	TRUE	1	0.258231814633645	4		66	83	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39644711	39644711	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	74	283	0	ENST00000262039.4:c.2440A>G	p.Asn814Asp	p.N814D	ENST00000262039	NM_002647.2	814	Aat/Gat	23/25	0.118535010298185	5	FACETS	0.974	0.857	1			1	INDETERMINATE	2	TRUE	NA	0.258231814633645	5		283	408	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523747	41523747	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	86	587	0	ENST00000263253.7:c.1163G>C	p.Cys388Ser	p.C388S	ENST00000263253	NM_001429.3	388	tGc/tCc	4/31	0.0854431681055263	3	FACETS	1	0.959	1	0.591	0.523	0.664	INDETERMINATE	1	TRUE	1	0.258231814633645	3		587	636	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs863224499	NA	P-0035586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	83	623	0	ENST00000269305.4:c.672+1G>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.229529597374098	1	FACETS	0.899	0.794	1	0.899	0.794	1	CLONAL	1	TRUE	0	0.243164056005802	1		623	667	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989600	15989600	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	37	272	0	ENST00000268712.3:c.3173C>T	p.Ser1058Leu	p.S1058L	ENST00000268712	NM_006311.3	1058	tCa/tTa	23/46	1	2	FACETS	0.713	0.588	0.852	0.713	0.588	0.852	SUBCLONAL	1	TRUE	1	0.243164056005802	2		272	427	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120255	70120278	+	inframe_deletion	In_Frame_Del	DEL	CTACAGCCCCTTCAACCTCCCACA	CTACAGCCCCTTCAACCTCCCACA	-	novel	NA	P-0035586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	108	838	0	ENST00000245479.2:c.1268_1291del	p.Phe423_Pro430del	p.F423_P430del	ENST00000245479	NM_000346.3	419	gcCTACAGCCCCTTCAACCTCCCACAc/gcc	3/3	1	2	FACETS	0.83	0.743	0.923	0.83	0.743	0.923	CLONAL	1	TRUE	1	0.243164056005802	2		838	1070	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379622	17379622	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1267028244	NA	P-0035586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	21	334	0	ENST00000359435.4:c.7G>A	p.Val3Met	p.V3M	ENST00000359435	NM_001033549.1	3	Gtg/Atg	2/9	1	2	FACETS	0.414	0.318	0.527	0.414	0.318	0.527	SUBCLONAL	1	TRUE	1	0.243164056005802	2		334	417	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143113	30143113	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	71	620	0	ENST00000389048.3:c.413C>A	p.Ala138Asp	p.A138D	ENST00000389048	NM_004304.4	138	gCc/gAc	1/29	1	2	FACETS	0.808	0.704	0.92	0.808	0.704	0.92	CLONAL	1	TRUE	1	0.243164056005802	2		620	723	SUCCESS
APC	324	MSKCC	GRCh37	5	112174201	112174201	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	59	329	0	ENST00000257430.4:c.2910del	p.Ser970ArgfsTer10	p.S970Rfs*10	ENST00000257430	NM_000038.5	970	agT/ag	16/16	0.243164056005802	1	FACETS	0.839	0.723	0.966	0.839	0.723	0.966	CLONAL	1	TRUE	0	0.243164056005802	1		329	508	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522328	157522328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542516057	NA	P-0035586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	83	763	0	ENST00000346085.5:c.4600C>T	p.Arg1534Cys	p.R1534C	ENST00000346085	NM_020732.3	1534	Cgc/Tgc	18/20	1	2	FACETS	0.704	0.62	0.795	0.704	0.62	0.795	SUBCLONAL	1	TRUE	1	0.243164056005802	2		763	970	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0035587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	401	488	2	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.718697157757209	4	FACETS	0.914	0.878	0.95	0.914	0.878	0.95	CLONAL	3	TRUE	1	0.717569198828705	4		490	700	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779746	3779747	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	220	698	2	ENST00000262367.5:c.5301dup	p.Arg1768ThrfsTer198	p.R1768Tfs*198	ENST00000262367	NM_004380.2	1767	-/A	31/31	1	2	FACETS	0.791	0.738	0.846	0.791	0.738	0.846	SUBCLONAL	1	TRUE	1	0.717569198828705	2		700	775	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692889	89692889	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	209	380	0	ENST00000371953.3:c.373A>G	p.Lys125Glu	p.K125E	ENST00000371953	NM_000314.4	125	Aaa/Gaa	5/9	0.691540418331075	2	FACETS	0.937	0.892	0.98	0.937	0.892	0.98	CLONAL	2	TRUE	0	0.717569198828705	2		380	311	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943737	71943737	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	145	824	0	ENST00000298229.2:c.1780G>T	p.Asp594Tyr	p.D594Y	ENST00000298229	NM_001567.3	594	Gac/Tac	15/28	0.33090999620792	1	FACETS	0.876	0.799	0.955	0.876	0.799	0.955	CLONAL	1	TRUE	0	0.347703094434864	1		824	787	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0035590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	93	417	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.756	0.674	0.843	0.756	0.674	0.843	SUBCLONAL	1	TRUE	1	0.444217163270708	2		417	554	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0035590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	61	291	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.78	0.677	0.891	0.78	0.677	0.891	SUBCLONAL	1	TRUE	1	0.444217163270708	2		291	352	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578446	7578446	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	66	643	0	ENST00000269305.4:c.484A>T	p.Ile162Phe	p.I162F	ENST00000269305	NM_001126112.2	162	Atc/Ttc	5/11	1	2	FACETS	0.344	0.298	0.394	0.344	0.298	0.394	SUBCLONAL	1	TRUE	1	0.444217163270708	2		643	864	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544682	65544682	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	138	647	0	ENST00000358664.4:c.244C>T	p.Gln82Ter	p.Q82*	ENST00000358664	NM_002382.4	82	Cag/Tag	4/5	0.444217163270708	1	FACETS	0.721	0.658	0.788	0.721	0.658	0.788	SUBCLONAL	1	TRUE	0	0.444217163270708	1		647	670	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109908	115109908	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	69	235	0	ENST00000257566.3:c.1970C>A	p.Thr657Asn	p.T657N	ENST00000257566	NM_016569.3	657	aCc/aAc	8/8	1	2	FACETS	0.9	0.789	1	0.9	0.789	1	CLONAL	1	TRUE	1	0.444217163270708	2		235	345	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39746901	39746901	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	24	266	0	ENST00000361337.2:c.1915A>T	p.Thr639Ser	p.T639S	ENST00000361337	NM_003286.2	639	Act/Tct	18/21	1	2	FACETS	0.277	0.217	0.347	0.277	0.217	0.347	SUBCLONAL	1	TRUE	1	0.444217163270708	2		266	390	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256341	46256341	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	24	343	0	ENST00000371998.3:c.569A>T	p.Gln190Leu	p.Q190L	ENST00000371998		190	cAa/cTa	7/23	1	2	FACETS	0.246	0.192	0.308	0.246	0.192	0.308	SUBCLONAL	1	TRUE	1	0.444217163270708	2		343	439	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890317	72890317	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	116	376	0	ENST00000325599.8:c.365A>T	p.Asp122Val	p.D122V	ENST00000325599	NM_018130.2	122	gAt/gTt	4/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.444217163270708	2		376	487	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277521	142277521	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	42	355	0	ENST00000350721.4:c.1830G>C	p.Leu610Phe	p.L610F	ENST00000350721	NM_001184.3	610	ttG/ttC	8/47	1	2	FACETS	0.459	0.383	0.542	0.459	0.383	0.542	SUBCLONAL	1	TRUE	1	0.444217163270708	2		355	412	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280253	142280253	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	59	320	0	ENST00000350721.4:c.1181G>A	p.Gly394Asp	p.G394D	ENST00000350721	NM_001184.3	394	gGc/gAc	5/47	1	2	FACETS	0.716	0.619	0.821	0.716	0.619	0.821	SUBCLONAL	1	TRUE	1	0.444217163270708	2		320	371	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056364	26056364	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	42	362	0	ENST00000343677.2:c.293G>T	p.Gly98Val	p.G98V	ENST00000343677	NM_005319.3	98	gGc/gTc	1/1	1	2	FACETS	0.328	0.273	0.389	0.328	0.273	0.389	SUBCLONAL	1	TRUE	1	0.444217163270708	2		362	576	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0035592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	130	544	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.131860305862427	3	FACETS	1	0.984	1	0.679	0.621	0.738	INDETERMINATE	1	FALSE	1	0.607760362238993	3		544	411	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28631508	28631508	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	89	464	0	ENST00000241453.7:c.460A>G	p.Ile154Val	p.I154V	ENST00000241453	NM_004119.2	154	Ata/Gta	4/24	0.329977026765755	1	FACETS	0.857	0.773	0.943	0.857	0.773	0.943	INDETERMINATE	1	FALSE	0	0.607760362238993	1		464	238	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061197	38061235	+	inframe_deletion	In_Frame_Del	DEL	CTTCTGGCGGCGCAAGTAGCAGCCGTTCTCGAACATGTT	CTTCTGGCGGCGCAAGTAGCAGCCGTTCTCGAACATGTT	-	novel	NA	P-0035592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	202	383	0	ENST00000250448.2:c.754_792del	p.Asn252_Lys264del	p.N252_K264del	ENST00000250448	NM_004496.3	252	AACATGTTCGAGAACGGCTGCTACTTGCGCCGCCAGAAG/-	2/2	0.331870013487139	5	FACETS	1	0.985	1			1	INDETERMINATE	3	FALSE	NA	0.607760362238993	5		383	374	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505516	25505516	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	145	763	1	ENST00000264709.3:c.242A>G	p.Asp81Gly	p.D81G	ENST00000264709	NM_175629.2	81	gAc/gGc	4/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.607760362238993	2		764	425	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0035596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	32	488	2	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.227120221159129	0	FACETS	0.506	0.43	0.584			1	INDETERMINATE	1	TRUE	0	0.646849864314862	0		490	69	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115750	8115750	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs104894164	NA	P-0035596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	83	396	0	ENST00000346208.3:c.1096C>T	p.Arg366Ter	p.R366*	ENST00000346208		366	Cga/Tga	6/6	0.203232346297452	1	FACETS	0.839	0.755	0.924	0.839	0.755	0.924	INDETERMINATE	1	TRUE	0	0.646849864314862	1		396	207	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047495	49047495	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0035596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	11	128	0	ENST00000267163.4:c.2490-1G>T		p.X830_splice	ENST00000267163	NM_000321.2	830			0.646849864314862	1	FACETS	0.959	0.715	1	0.959	0.715	1	CLONAL	1	TRUE	0	0.646849864314862	1		128	24	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063312	67063312	+	start_lost	Translation_Start_Site	SNP	T	T	A	novel	NA	P-0035596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	81	122	0	ENST00000412916.2:c.2T>A	p.Met1?	p.M1?	ENST00000412916		1	aTg/aAg	1/6	0.646849864314862	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.646849864314862	1		122	125	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112527	2112527	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs45493394	NA	P-0035604-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	365	888	0	ENST00000219476.3:c.1287T>G	p.Tyr429Ter	p.Y429*	ENST00000219476	NM_000548.3	429	taT/taG	13/42	0.423936349429696	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.423936349429696	1		888	1070	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136255	2136255	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035604-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	493	731	0	ENST00000219476.3:c.4724T>C	p.Leu1575Pro	p.L1575P	ENST00000219476	NM_000548.3	1575	cTg/cCg	37/42	0.423936349429696	1	FACETS	1	0.984	1	1	0.998	1	CLONAL	2	TRUE	0	0.423936349429696	1		731	886	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677237	29677238	+	missense_variant	Missense_Mutation	DNP	GC	GC	AT	novel	NA	P-0035604-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	50	415	0	ENST00000356175.3:c.7295_7296delinsAT	p.Cys2432Tyr	p.C2432Y	ENST00000356175	NM_000267.3	2432	tGC/tAT	49/57	0.423936349429696	0	FACETS	0.34	0.289	0.395			1	SUBCLONAL	1	TRUE	0	0.423936349429696	0		415	400	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314571	30314571	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035604-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	230	604	1	ENST00000262643.3:c.1120C>T	p.Arg374Ter	p.R374*	ENST00000262643	NM_001238.2	374	Cga/Tga	12/12	0.423936349429696	0	FACETS	1	0.974	1			1	CLONAL	1	TRUE	0	0.423936349429696	0		605	586	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524896	187524896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035604-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	91	768	1	ENST00000441802.2:c.10784C>T	p.Thr3595Ile	p.T3595I	ENST00000441802	NM_005245.3	3595	aCa/aTa	19/27	0.423936349429696	0	FACETS	0.325	0.288	0.364			1	SUBCLONAL	1	TRUE	0	0.423936349429696	0		769	761	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248528	212248528	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	184	650	1	ENST00000342788.4:c.3739C>A	p.Leu1247Met	p.L1247M	ENST00000342788	NM_005235.2	1247	Ctg/Atg	28/28	0.298457443133316	3	FACETS	1	0.989	1	0.704	0.651	0.759	CLONAL	1	TRUE	1	0.393417666020845	3		651	795	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434426	110434426	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	49	485	0	ENST00000375856.3:c.3975C>G	p.Phe1325Leu	p.F1325L	ENST00000375856	NM_003749.2	1325	ttC/ttG	1/2	1	2	FACETS	0.44	0.372	0.515	0.44	0.372	0.515	SUBCLONAL	1	TRUE	1	0.393417666020845	2		485	566	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949198	71949198	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	58	766	0	ENST00000298229.2:c.3665G>A	p.Trp1222Ter	p.W1222*	ENST00000298229	NM_001567.3	1222	tGg/tAg	27/28	1	2	FACETS	0.434	0.372	0.501	0.434	0.372	0.501	SUBCLONAL	1	TRUE	1	0.393417666020845	2		766	680	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793433	18793433	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	115	518	0	ENST00000266497.5:c.4130G>C	p.Arg1377Pro	p.R1377P	ENST00000266497		1377	cGt/cCt	30/31	0.393417666020845	3	FACETS	1	0.904	1	0.501	0.452	0.553	CLONAL	1	TRUE	1	0.393417666020845	3		518	698	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577087	7577114	+	frameshift_variant	Frame_Shift_Del	DEL	GTGCGCCGGTCTCTCCCAGGACAGGCAC	GTGCGCCGGTCTCTCCCAGGACAGGCAC	-	novel	NA	P-0035615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	99	743	1	ENST00000269305.4:c.824_851del	p.Cys275Ter	p.C275*	ENST00000269305	NM_001126112.2	275	tGTGCCTGTCCTGGGAGAGACCGGCGCACa/ta	8/11	0.393417666020845	1	FACETS	0.707	0.632	0.785	0.707	0.632	0.785	SUBCLONAL	1	TRUE	0	0.393417666020845	1		744	572	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379742	17379742	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	91	752	0	ENST00000359435.4:c.127G>T	p.Ala43Ser	p.A43S	ENST00000359435	NM_001033549.1	43	Gcc/Tcc	2/9	1	2	FACETS	0.532	0.472	0.597	0.532	0.472	0.597	SUBCLONAL	1	TRUE	1	0.393417666020845	2		752	869	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466830	25466830	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	112	539	0	ENST00000264709.3:c.1873C>G	p.Pro625Ala	p.P625A	ENST00000264709	NM_175629.2	625	Cct/Gct	16/23	0.206103393181321	3	FACETS	0.962	0.866	1	0.481	0.433	0.532	INDETERMINATE	1	TRUE	1	0.393417666020845	3		539	708	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221657	22221657	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	40	134	0	ENST00000215832.6:c.74A>T	p.Tyr25Phe	p.Y25F	ENST00000215832	NM_002745.4	25	tAc/tTc	1/9	0.189740581206571	2	FACETS	1	0.96	1	0.748	0.634	0.868	INDETERMINATE	1	TRUE	0	0.393417666020845	2		134	136	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182679134	182679134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs922979204	NA	P-0035615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	145	565	0	ENST00000292782.4:c.400A>G	p.Ile134Val	p.I134V	ENST00000292782	NM_020640.2	134	Ata/Gta	4/7	0.298457443133316	3	FACETS	1	0.984	1	0.667	0.61	0.727	CLONAL	1	TRUE	1	0.393417666020845	3		565	661	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056602	26056602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200705328	NA	P-0035615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	52	255	0	ENST00000343677.2:c.55C>T	p.Pro19Ser	p.P19S	ENST00000343677	NM_005319.3	19	Cct/Tct	1/1	1	2	FACETS	0.924	0.793	1	0.924	0.793	1	CLONAL	1	TRUE	1	0.393417666020845	2		255	286	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5078442	5078442	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	73	431	0	ENST00000381652.3:c.2129A>T	p.Asp710Val	p.D710V	ENST00000381652	NM_004972.3	710	gAc/gTc	16/25	0.393417666020845	1	FACETS	0.787	0.692	0.887	0.787	0.692	0.887	SUBCLONAL	1	TRUE	0	0.393417666020845	1		431	379	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521355	8521355	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs200703886	NA	P-0035615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	123	647	1	ENST00000356435.5:c.883A>G	p.Arg295Gly	p.R295G	ENST00000356435		295	Aga/Gga	9/35	0.393417666020845	1	FACETS	0.895	0.813	0.982	0.895	0.813	0.982	CLONAL	1	TRUE	0	0.393417666020845	1		648	561	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352801	70352801	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	70	328	0	ENST00000374080.3:c.4522C>T	p.His1508Tyr	p.H1508Y	ENST00000374080		1508	Cac/Tac	32/45	1	1	FACETS	0.922	0.811	1	0.922	0.811	1	CLONAL	1	TRUE	0	0.393417666020845	1		328	310	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000057	30000058	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0035617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	128	483	0	ENST00000338641.4:c.71_72del	p.Val24GlufsTer24	p.V24Efs*24	ENST00000338641	NM_000268.3	24	GTg/g	1/16	0.555598689125198	1	FACETS	0.883	0.809	0.959	0.883	0.809	0.959	CLONAL	1	TRUE	0	0.555598689125198	1		483	377	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000103	30000103	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0035618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	180	567	0	ENST00000338641.4:c.114+2T>C		p.X38_splice	ENST00000338641	NM_000268.3	38			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		567	302	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0035620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	145	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.881	0.809	0.957	0.881	0.809	0.957	CLONAL	1	TRUE	1	0.607027180385345	2		502	542	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0035620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	173	368	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.607027180385345	2		368	481	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477807	140477807	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs180177038	NA	P-0035620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	193	530	0	ENST00000288602.6:c.1501G>A	p.Glu501Lys	p.E501K	ENST00000288602	NM_004333.4	501	Gaa/Aaa	12/18	0.607027180385345	1	FACETS	0.978	0.915	1	0.978	0.915	1	CLONAL	1	TRUE	0	0.607027180385345	1		530	453	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480335	56480335	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	156	483	0	ENST00000267101.3:c.442T>C	p.Tyr148His	p.Y148H	ENST00000267101	NM_001982.3	148	Tat/Cat	4/28	1	2	FACETS	0.897	0.826	0.971	0.897	0.826	0.971	CLONAL	1	TRUE	1	0.607027180385345	2		483	573	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180321	27180327	+	frameshift_variant	Frame_Shift_Ins	INS	TGTCTCT	TGTCTCT	AGCGATCACAGGATGGCAGGG	novel	NA	P-0035620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	154	541	0	ENST00000380036.4:c.985_991delinsAGCGATCACAGGATGGCAGGG	p.Cys329SerfsTer25	p.C329Sfs*25	ENST00000380036	NM_000459.3	329	TGTCTCTgc/AGCGATCACAGGATGGCAGGGgc	7/23	0.607027180385345	1	FACETS	0.92	0.853	0.989	0.92	0.853	0.989	CLONAL	1	TRUE	0	0.607027180385345	1		541	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0035624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	582	675	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.758533599832459	2	FACETS	0.999	0.974	1	0.999	0.974	1	CLONAL	2	TRUE	0	0.771897161866989	2		675	755	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	451	812	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	0.995	0.968	1			1	INDETERMINATE	2	TRUE	NA	0.771897161866989	2		812	587	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106862	27106863	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	400	526	0	ENST00000324856.7:c.6476dup	p.Asn2160GlufsTer65	p.N2160Efs*65	ENST00000324856	NM_006015.4	2158	cga/cgAa	20/20	0.729772874254118	2	FACETS	0.912	0.882	0.942	0.912	0.882	0.942	CLONAL	2	TRUE	0	0.771897161866989	2		526	568	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853864	59853864	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	58	383	0	ENST00000259008.2:c.1995G>C	p.Gln665His	p.Q665H	ENST00000259008	NM_032043.2	665	caG/caC	14/20	0.758533599832459	2	FACETS	0.305	0.262	0.351	0.152	0.131	0.176	SUBCLONAL	1	TRUE	0	0.771897161866989	2		383	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0035631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	200	786	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.312669863661891	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.312669863661891	1		787	908	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0035632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	340	417	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.315535626870165	4	FACETS	0.982	0.937	1	0.982	0.937	1	CLONAL	4	TRUE	0	0.331600320782027	4		417	695	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	38	272	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.756	0.628	0.899	0.756	0.628	0.899	SUBCLONAL	1	TRUE	1	0.331600320782027	2		272	303	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428017	33428017	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	109	518	0	ENST00000345365.6:c.942G>T	p.Trp314Cys	p.W314C	ENST00000345365	NM_002878.3	314	tgG/tgT	10/10	1	2	FACETS	0.839	0.753	0.929	0.839	0.753	0.929	CLONAL	1	TRUE	1	0.331600320782027	2		518	784	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678029	58678029	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567962294	NA	P-0035632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	66	157	0	ENST00000305921.3:c.254C>T	p.Ser85Leu	p.S85L	ENST00000305921	NM_003620.3	85	tCg/tTg	1/6	0.3182982702498	3	FACETS	1	0.952	1	0.6	0.523	0.682	CLONAL	1	TRUE	1	0.331600320782027	3		157	387	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247959	59247959	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	191	619	0	ENST00000371222.2:c.784A>C	p.Asn262His	p.N262H	ENST00000371222	NM_002228.3	262	Aac/Cac	1/1	1	2	FACETS	0.888	0.819	0.959	0.888	0.819	0.959	CLONAL	1	TRUE	1	0.331600320782027	2		619	1298	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432592	78432592	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	112	521	0	ENST00000370768.2:c.391G>T	p.Gly131Ter	p.G131*	ENST00000370768	NM_003902.3	131	Gga/Tga	6/20	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.331600320782027	2		521	632	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550761	150550761	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs150698207	NA	P-0035632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	157	439	0	ENST00000369026.2:c.895G>T	p.Val299Leu	p.V299L	ENST00000369026	NM_021960.4	299	Gta/Tta	2/3	1	2	FACETS	0.914	0.836	0.995	0.914	0.836	0.995	CLONAL	1	TRUE	1	0.331600320782027	2		439	1036	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487278	56487278	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	231	499	0	ENST00000267101.3:c.1424G>T	p.Arg475Leu	p.R475L	ENST00000267101	NM_001982.3	475	cGg/cTg	12/28	0.311688244046454	2	FACETS	0.943	0.882	1	0.943	0.882	1	CLONAL	2	TRUE	0	0.331600320782027	2		499	739	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434348	121434348	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	284	515	0	ENST00000257555.6:c.1112C>T	p.Ser371Leu	p.S371L	ENST00000257555		371	tCa/tTa	6/10	0.291148832037315	3	FACETS	1	0.99	1	0.818	0.772	0.865	CLONAL	2	TRUE	0	0.331600320782027	3		515	814	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133234556	133234556	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	240	341	0	ENST00000320574.5:c.3276G>T	p.Arg1092Ser	p.R1092S	ENST00000320574	NM_006231.2	1092	agG/agT	27/49	0.291148832037315	3	FACETS	0.98	0.923	1	0.98	0.923	1	CLONAL	3	TRUE	0	0.331600320782027	3		341	574	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483899	88483899	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	124	604	0	ENST00000360948.2:c.1671C>G	p.Cys557Trp	p.C557W	ENST00000360948	NM_001012338.2	557	tgC/tgG	14/19	1	2	FACETS	0.82	0.741	0.903	0.82	0.741	0.903	CLONAL	1	TRUE	1	0.331600320782027	2		604	912	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817898	3817898	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	88	445	0	ENST00000262367.5:c.3073G>T	p.Asp1025Tyr	p.D1025Y	ENST00000262367	NM_004380.2	1025	Gat/Tat	16/31	0.313307939013434	3	FACETS	0.796	0.705	0.894	0.398	0.352	0.447	SUBCLONAL	1	TRUE	1	0.331600320782027	3		445	777	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244058	41244058	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	131	636	0	ENST00000357654.3:c.3490A>T	p.Ser1164Cys	p.S1164C	ENST00000357654	NM_007294.3	1164	Agt/Tgt	10/23	0.130606304805516	3	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.331600320782027	3		636	803	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143044506	143044506	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	93	418	0	ENST00000262992.4:c.1956C>A	p.Phe652Leu	p.F652L	ENST00000262992	NM_001101669.1	652	ttC/ttA	18/24	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.331600320782027	2		418	534	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197302	26197302	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	114	371	0	ENST00000356476.2:c.177del	p.Glu60SerfsTer3	p.E60Sfs*3	ENST00000356476		59	acC/ac	1/1	1	2	FACETS	0.911	0.82	1	0.911	0.82	1	CLONAL	1	TRUE	1	0.331600320782027	2		371	755	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021710	69021710	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	80	434	0	ENST00000288368.4:c.2998G>T	p.Gly1000Cys	p.G1000C	ENST00000288368	NM_024870.2	1000	Ggt/Tgt	25/40	0.311447374025889	3	FACETS	0.792	0.697	0.895	0.396	0.348	0.448	SUBCLONAL	1	TRUE	1	0.331600320782027	3		434	710	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593604	55593609	+	inframe_deletion	In_Frame_Del	DEL	GGAAGG	GGAAGG	-	novel	NA	P-0035634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	221	360	0	ENST00000288135.5:c.1670_1675del	p.Trp557_Val559delinsPhe	p.W557_V559delinsF	ENST00000288135	NM_000222.2	557	tGGAAGGtt/ttt	11/21	0.78753238799855	1	FACETS	0.972	0.924	1	0.972	0.924	1	CLONAL	1	TRUE	0	0.78753238799855	1		360	350	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217285	11217285	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	393	537	0	ENST00000361445.4:c.4393A>G	p.Lys1465Glu	p.K1465E	ENST00000361445	NM_004958.3	1465	Aag/Gag	30/58	0.78753238799855	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.78753238799855	1		537	580	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265343	152265343	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0035634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	126	338	0	ENST00000206249.3:c.796A>T	p.Lys266Ter	p.K266*	ENST00000206249	NM_000125.3	266	Aaa/Taa	4/8	0.78753238799855	1	FACETS	0.53	0.485	0.576	0.53	0.485	0.576	SUBCLONAL	1	TRUE	0	0.78753238799855	1		338	366	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0035635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	161	516	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.602061781680434	2		516	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0035635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	376	660	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.592413182866885	2	FACETS	0.958	0.919	0.996	0.958	0.919	0.996	CLONAL	2	TRUE	0	0.602061781680434	2		661	652	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727453	66727453	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397516790	NA	P-0035635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	259	437	0	ENST00000307102.5:c.169A>G	p.Lys57Glu	p.K57E	ENST00000307102	NM_002755.3	57	Aag/Gag	2/11	0.588787166385708	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.602061781680434	4		437	671	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554408	63554408	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	453	641	1	ENST00000307078.5:c.331T>C	p.Trp111Arg	p.W111R	ENST00000307078	NM_004655.3	111	Tgg/Cgg	2/11	0.592413182866885	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.602061781680434	2		642	744	SUCCESS
APC	324	MSKCC	GRCh37	5	112175219	112175219	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0035635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	208	246	1	ENST00000257430.4:c.3928A>T	p.Lys1310Ter	p.K1310*	ENST00000257430	NM_000038.5	1310	Aag/Tag	16/16	0.594078401753665	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	TRUE	0	0.602061781680434	3		247	293	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047963	180047963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	413	626	0	ENST00000261937.6:c.2212G>A	p.Val738Met	p.V738M	ENST00000261937	NM_182925.4	738	Gtg/Atg	15/30	0.594078401753665	3	FACETS	1	0.973	1	0.682	0.652	0.711	CLONAL	2	TRUE	0	0.602061781680434	3		626	873	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0035638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	334	605	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.755312241567055	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.755312241567055	2		605	393	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600378	10600378	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	380	738	1	ENST00000171111.5:c.1477G>A	p.Glu493Lys	p.E493K	ENST00000171111	NM_203500.1	493	Gag/Aag	4/6	0.557611587766554	4	FACETS	1	0.984	1			1	CLONAL	2	TRUE	NA	0.755312241567055	4		739	830	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250862	153250862	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	136	397	0	ENST00000281708.4:c.1198G>A	p.Asp400Asn	p.D400N	ENST00000281708	NM_033632.3	400	Gac/Aac	8/12	0.755312241567055	3	FACETS	0.922	0.856	0.988	0.922	0.856	0.988	CLONAL	2	TRUE	1	0.755312241567055	3		397	269	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246078861	246078861	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	175	620	0	ENST00000388985.4:c.784G>C	p.Asp262His	p.D262H	ENST00000388985		262	Gac/Cac	8/12	0.712106259792532	5	FACETS	1	0.926	1			1	CLONAL	1	TRUE	NA	0.755312241567055	5		620	982	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4388040	4388040	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	459	408	0	ENST00000261254.3:c.526C>G	p.Leu176Val	p.L176V	ENST00000261254	NM_001759.3	176	Ctg/Gtg	3/5	0.755312241567055	5	FACETS	1	0.992	1	1	0.992	1	CLONAL	5	TRUE	0	0.755312241567055	5		408	508	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346289	89346289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	33	347	2	ENST00000301030.4:c.6661G>A	p.Val2221Met	p.V2221M	ENST00000301030	NM_001256183.1	2221	Gtg/Atg	9/13	0.219848713299287	6	FACETS	0.822	0.672	0.988	0.274	0.224	0.33	INDETERMINATE	1	TRUE	3	0.755312241567055	6		349	267	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661995	29661995	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	103	422	0	ENST00000356175.3:c.5889T>A	p.Asn1963Lys	p.N1963K	ENST00000356175	NM_000267.3	1963	aaT/aaA	39/57	0.214064565458896	4	FACETS	1	0.977	1	0.32	0.289	0.353	INDETERMINATE	1	TRUE	0	0.755312241567055	4		422	374	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873714	37873714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1173337736	NA	P-0035638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	129	537	0	ENST00000269571.5:c.1879C>T	p.Pro627Ser	p.P627S	ENST00000269571		627	Ccc/Tcc	15/27	0.214064565458896	4	FACETS	1	0.979	1	0.312	0.284	0.34	INDETERMINATE	1	TRUE	0	0.755312241567055	4		537	481	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56367740	56367740	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	251	457	0	ENST00000348428.3:c.566T>G	p.Val189Gly	p.V189G	ENST00000348428	NM_006785.3	189	gTc/gGc	4/17	0.755312241567055	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.755312241567055	2		457	311	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24135778	24135778	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	221	418	0	ENST00000263121.7:c.265A>T	p.Thr89Ser	p.T89S	ENST00000263121	NM_003073.3	89	Acc/Tcc	3/9	0.5393668763673	4	FACETS	0.934	0.877	0.992	0.934	0.877	0.992	CLONAL	2	TRUE	2	0.755312241567055	4		418	550	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259546	89259546	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	221	418	0	ENST00000336596.2:c.690T>G	p.Cys230Trp	p.C230W	ENST00000336596	NM_005233.5	230	tgT/tgG	3/17	0.544803660080762	3	FACETS	1	0.99	1			1	CLONAL	2	TRUE	NA	0.755312241567055	3		418	347	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449709	187449709	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1415288002	NA	P-0035638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	343	357	0	ENST00000232014.4:c.171C>G	p.Phe57Leu	p.F57L	ENST00000232014	NM_001130845.1	57	ttC/ttG	4/10	0.755312241567055	11	FACETS	1	0.981	1	0.71	0.674	0.747	CLONAL	4	TRUE	5	0.755312241567055	11		357	938	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541607	187541608	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0035638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	212	380	0	ENST00000441802.2:c.6132_6133delinsTT	p.Gln2044_Glu2045delinsHisTer	p.Q2044_E2045delinsH*	ENST00000441802	NM_005245.3	2044	caGGag/caTTag	10/27	0.755312241567055	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.755312241567055	3		380	335	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043125	6043328	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTATTTGCTTCATTTCATTCATTTATTGCTCACATTTCAGAAGTACTATGACTTAGATTGGCAGCGAGACAAAACAGAATTCAGAAGCTAGAAGTTGAGATGTTGAGATAGAAAACTGAAAATAATAATGATTCCAATTAATTTTCAGAGAGGTTTCTCTAAGGGGTCAAGTGAGTGGATAAAAATATTGTATCACCTCAGTGC	CTATTTGCTTCATTTCATTCATTTATTGCTCACATTTCAGAAGTACTATGACTTAGATTGGCAGCGAGACAAAACAGAATTCAGAAGCTAGAAGTTGAGATGTTGAGATAGAAAACTGAAAATAATAATGATTCCAATTAATTTTCAGAGAGGTTTCTCTAAGGGGTCAAGTGAGTGGATAAAAATATTGTATCACCTCAGTGC	-	novel	NA	P-0035638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	69	33	0	ENST00000265849.7:c.346_353+196del		p.X116_splice	ENST00000265849	NM_000535.5	116		4/15	0.755312241567055	6	FACETS	0.956	0.866	1	0.956	0.866	1	CLONAL	4	TRUE	2	0.755312241567055	6		33	120	SUCCESS
AR	367	MSKCC	GRCh37	X	66931447	66931447	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	279	238	0	ENST00000374690.3:c.2089T>A	p.Ser697Thr	p.S697T	ENST00000374690	NM_000044.3	697	Tcc/Acc	4/8	0.476408014720197	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.755312241567055	2		238	314	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0035640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	24	673	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.43	0.336	0.538	0.43	0.336	0.538	SUBCLONAL	1	TRUE	1	0.273763575704275	2		673	408	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692790	89692790	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	90	351	0	ENST00000371953.3:c.274G>C	p.Asp92His	p.D92H	ENST00000371953	NM_000314.4	92	Gac/Cac	5/9	0.224063366011653	2	FACETS	0.814	0.727	0.906	0.814	0.727	0.906	CLONAL	2	TRUE	0	0.273763575704275	2		351	404	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981315	68981315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866864487	NA	P-0035640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	22	330	0	ENST00000288368.4:c.1387C>T	p.Arg463Cys	p.R463C	ENST00000288368	NM_024870.2	463	Cgc/Tgc	12/40	1	2	FACETS	0.407	0.315	0.514	0.407	0.315	0.514	SUBCLONAL	1	TRUE	1	0.273763575704275	2		330	395	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424706	47424706	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	79	581	0	ENST00000377045.4:c.514T>A	p.Ser172Thr	p.S172T	ENST00000377045	NM_001654.4	172	Tcg/Acg	6/16	1	2	FACETS	0.902	0.793	1	0.902	0.793	1	CLONAL	1	TRUE	1	0.273763575704275	2		581	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0035643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	484	755	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.41454528626108	3	FACETS	1	0.983	1	1	0.997	1	CLONAL	3	TRUE	1	0.41454528626108	3		755	908	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0035643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	94	298	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	0.41454528626108	2		298	402	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123721	11123721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	142	496	0	ENST00000358026.2:c.2371G>A	p.Ala791Thr	p.A791T	ENST00000358026	NM_001128849.1	791	Gcg/Acg	16/36	0.153786518994696	3	FACETS	1	0.978	1	0.605	0.553	0.66	INDETERMINATE	1	TRUE	1	0.41454528626108	3		496	683	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121756	108121756	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	51	453	0	ENST00000278616.4:c.1564G>A	p.Glu522Lys	p.E522K	ENST00000278616	NM_000051.3	522	Gaa/Aaa	10/63	1	2	FACETS	0.387	0.328	0.451	0.387	0.328	0.451	SUBCLONAL	1	TRUE	1	0.41454528626108	2		453	636	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435066	56435066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	39	585	0	ENST00000407977.2:c.2071C>T	p.Pro691Ser	p.P691S	ENST00000407977		691	Cct/Tct	9/10	1	2	FACETS	0.305	0.252	0.364	0.305	0.252	0.364	SUBCLONAL	1	TRUE	1	0.41454528626108	2		585	617	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499841	8499841	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0035644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	48	306	0	ENST00000356435.5:c.2129-1G>T		p.X710_splice	ENST00000356435		710			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		306	209	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578533	7578539	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTGTT	TCTTGTT	-	novel	NA	P-0035645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	403	659	6	ENST00000269305.4:c.391_397del	p.Asn131CysfsTer37	p.N131Cfs*37	ENST00000269305	NM_001126112.2	131	AACAAGAtg/tg	5/11	0.672033654112271	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.672033654112271	1		665	684	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696718	47696718	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	202	393	4	ENST00000347630.2:c.230A>G	p.Asp77Gly	p.D77G	ENST00000347630	NM_001007230.1	77	gAt/gGt	5/11	0.153015754210622	4	FACETS	0.894	0.835	0.955	0.894	0.835	0.955	INDETERMINATE	2	TRUE	2	0.672033654112271	4		397	562	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0035646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	503	516	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.56904977941405	4	FACETS	0.971	0.943	0.998	0.971	0.943	0.998	CLONAL	4	TRUE	0	0.584749632909398	4		516	702	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254631	10254631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750276897	NA	P-0035646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	207	412	0	ENST00000340748.4:c.2879G>A	p.Arg960Gln	p.R960Q	ENST00000340748		960	cGg/cAg	28/40	0.584749632909398	3	FACETS	0.999	0.938	1	0.999	0.938	1	CLONAL	2	TRUE	1	0.584749632909398	3		412	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0035647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	220	753	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.34885421197057	2	FACETS	0.878	0.822	0.934	0.878	0.822	0.934	CLONAL	2	TRUE	0	0.417649160450957	2		753	600	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	106	374	1	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	0.417649160450957	2	FACETS	0.884	0.805	0.966	0.884	0.805	0.966	CLONAL	2	TRUE	0	0.417649160450957	2		375	287	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163313598	163313598	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	96	211	1	ENST00000271452.3:c.745G>A	p.Glu249Lys	p.E249K	ENST00000271452	NM_145697.2	249	Gag/Aag	10/14	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.417649160450957	2		212	344	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965427	18965427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	159	373	1	ENST00000262803.5:c.1174G>A	p.Ala392Thr	p.A392T	ENST00000262803	NM_002911.3	392	Gcc/Acc	9/24	0.284130063142765	3	FACETS	1	0.953	1			1	CLONAL	2	TRUE	NA	0.417649160450957	3		374	443	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021674	31021674	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	53	381	1	ENST00000375687.4:c.1673A>G	p.Glu558Gly	p.E558G	ENST00000375687	NM_015338.5	558	gAa/gGa	12/13	0.417649160450957	5	FACETS	0.46	0.391	0.536	0.153	0.13	0.179	SUBCLONAL	1	TRUE	2	0.417649160450957	5		382	897	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147565	47147566	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0035647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	101	382	0	ENST00000409792.3:c.4760_4761del	p.Lys1587ArgfsTer3	p.K1587Rfs*3	ENST00000409792	NM_014159.6	1587	aAA/a	6/21	0.417649160450957	1	FACETS	0.94	0.846	1	0.94	0.846	1	CLONAL	1	TRUE	0	0.417649160450957	1		382	407	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725088	49725088	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	127	580	0	ENST00000449682.2:c.256A>G	p.Asn86Asp	p.N86D	ENST00000449682	NM_020998.3	86	Aac/Gac	3/18	0.417649160450957	1	FACETS	0.726	0.659	0.796	0.726	0.659	0.796	SUBCLONAL	1	TRUE	0	0.417649160450957	1		580	663	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123245042	123245042	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	118	397	0	ENST00000358487.5:c.2062T>G	p.Ser688Ala	p.S688A	ENST00000358487	NM_000141.4	688	Tcc/Gcc	16/18	1	2	FACETS	1	0.974	1	1	0.991	1	CLONAL	2	TRUE	1	0.29152575929393	2		397	344	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0035660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	234	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.926	0.869	0.985	0.926	0.869	0.985	CLONAL	1	TRUE	1	0.736418026844266	2		502	686	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0035660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	337	812	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.716522010306882	1	FACETS	0.99	0.948	1	0.99	0.948	1	CLONAL	1	TRUE	0	0.736418026844266	1		812	584	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321666	62321666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759789479	NA	P-0035660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	301	777	0	ENST00000360203.5:c.2285G>A	p.Arg762Gln	p.R762Q	ENST00000360203	NM_001283009.1	762	cGg/cAg	26/35	0.263504169435116	1	FACETS	0.684	0.648	0.721	0.684	0.648	0.721	INDETERMINATE	1	TRUE	0	0.736418026844266	1		777	755	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0035661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	300	368	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.42132709097174	3	FACETS	0.924	0.879	0.97	0.924	0.879	0.97	INDETERMINATE	2	TRUE	1	0.705843000965457	3		368	622	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038951	12038951	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	155	251	0	ENST00000396373.4:c.1244T>A	p.Leu415His	p.L415H	ENST00000396373	NM_001987.4	415	cTt/cAt	7/8	1	2	FACETS	0.894	0.825	0.966	0.894	0.825	0.966	CLONAL	1	TRUE	1	0.705843000965457	2		251	491	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961807	55961807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	52	417	0	ENST00000263923.4:c.2754C>A	p.Phe918Leu	p.F918L	ENST00000263923	NM_002253.2	918	ttC/ttA	20/30	0.225981908031372	3	FACETS	0.262	0.222	0.306	0.131	0.111	0.153	INDETERMINATE	1	TRUE	1	0.705843000965457	3		417	761	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27228238	27228238	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	270	636	0	ENST00000380036.4:c.3235C>A	p.Pro1079Thr	p.P1079T	ENST00000380036	NM_000459.3	1079	Cct/Act	22/23	1	2	FACETS	0.965	0.909	1	0.965	0.909	1	CLONAL	1	TRUE	1	0.705843000965457	2		636	793	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0035662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	225	673	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.824	0.77	0.879	0.824	0.77	0.879	CLONAL	1	FALSE	1	0.712257332988283	2		673	767	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0035662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	180	353	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.945	0.878	1	0.945	0.878	1	CLONAL	1	FALSE	1	0.712257332988283	2		353	535	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0035662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	347	696	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.672475249196334	1	FACETS	0.938	0.896	0.979	0.938	0.896	0.979	CLONAL	1	FALSE	0	0.712257332988283	1		696	669	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584560	48584560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	227	523	0	ENST00000342988.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000342988	NM_005359.5	245	Cag/Tag	6/12	0.712257332988283	1	FACETS	0.868	0.818	0.917	0.868	0.818	0.917	CLONAL	1	FALSE	0	0.712257332988283	1		523	473	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923684	39923684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1231642126	NA	P-0035662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	331	629	0	ENST00000378444.4:c.3407G>A	p.Arg1136His	p.R1136H	ENST00000378444	NM_001123385.1	1136	cGc/cAc	7/15	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	FALSE	NA	0.712257332988283	2		629	728	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151882717	151882717	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0035662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	147	218	0	ENST00000262189.6:c.5009-1G>A		p.X1670_splice	ENST00000262189	NM_170606.2	1670			0.143644840783241	3	FACETS	0.833	0.772	0.894	0.833	0.772	0.894	INDETERMINATE	2	FALSE	1	0.712257332988283	3		218	336	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38632026	38632026	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0035662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	197	601	0	ENST00000299084.4:c.512C>G	p.Ser171Ter	p.S171*	ENST00000299084	NM_152594.2	171	tCa/tGa	5/7	1	2	FACETS	0.81	0.753	0.869	0.81	0.753	0.869	CLONAL	1	FALSE	1	0.712257332988283	2		601	683	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551889	150551889	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs755460962	NA	P-0035662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	142	251	0	ENST00000369026.2:c.118A>G	p.Lys40Glu	p.K40E	ENST00000369026	NM_021960.4	40	Aag/Gag	1/3	0.712257332988283	4	FACETS	1	0.962	1			1	CLONAL	1	FALSE	NA	0.712257332988283	4		251	624	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26927934	26927934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	185	397	0	ENST00000381527.3:c.373C>T	p.Arg125Trp	p.R125W	ENST00000381527	NM_001260.1	125	Cgg/Tgg	4/13	0.712257332988283	1	FACETS	0.984	0.926	1	0.984	0.926	1	CLONAL	1	FALSE	0	0.712257332988283	1		397	340	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846043	68846043	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	332	568	2	ENST00000261769.5:c.1016del	p.Pro339LeufsTer17	p.P339Lfs*17	ENST00000261769	NM_004360.3	338	ttC/tt	8/16	0.697978248845795	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	0	0.712257332988283	1		570	574	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496932	29496932	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1131691994	NA	P-0035662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	180	359	0	ENST00000356175.3:c.503C>G	p.Ser168Ter	p.S168*	ENST00000356175	NM_000267.3	168	tCa/tGa	5/57	0.672475249196334	1	FACETS	0.875	0.819	0.931	0.875	0.819	0.931	CLONAL	1	FALSE	0	0.712257332988283	1		359	372	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453318	40453318	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	293	739	0	ENST00000345506.4:c.1015C>A	p.Pro339Thr	p.P339T	ENST00000345506	NM_003152.3	339	Cct/Act	10/20	0.672475249196334	1	FACETS	0.904	0.86	0.948	0.904	0.86	0.948	CLONAL	1	FALSE	0	0.712257332988283	1		739	586	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245802	5245802	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	377	671	0	ENST00000357368.4:c.973C>T	p.Gln325Ter	p.Q325*	ENST00000357368	NM_002850.3	325	Cag/Tag	10/38	0.332078158516433	1	FACETS	0.796	0.76	0.833	0.796	0.76	0.833	INDETERMINATE	1	FALSE	0	0.712257332988283	1		671	856	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627325	14627328	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0035662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	430	819	1	ENST00000254322.2:c.742_745del	p.Lys248GlufsTer23	p.K248Efs*23	ENST00000254322	NM_006145.1	248	AAGAga/ga	2/3	NA	2	FACETS	0.969	0.924	1			1	INDETERMINATE	1	FALSE	NA	0.712257332988283	2		820	1246	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627477	14627477	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	327	538	0	ENST00000254322.2:c.593G>T	p.Arg198Leu	p.R198L	ENST00000254322	NM_006145.1	198	cGa/cTa	2/3	NA	2	FACETS	0.994	0.942	1			1	INDETERMINATE	1	FALSE	NA	0.712257332988283	2		538	924	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189388	99189388	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	163	481	1	ENST00000074304.5:c.2644G>A	p.Glu882Lys	p.E882K	ENST00000074304	NM_001134224.1	882	Gag/Aag	24/26	0.271734219075527	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.712257332988283	0		482	584	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164621	36164633	+	frameshift_variant	Frame_Shift_Del	DEL	CATGGAGAACTGG	CATGGAGAACTGG	-	novel	NA	P-0035662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	217	474	1	ENST00000300305.3:c.1242_1254del	p.Tyr414Ter	p.Y414*	ENST00000300305		414	taCCAGTTCTCCATG/ta	8/8	1	2	FACETS	0.785	0.732	0.84	0.785	0.732	0.84	SUBCLONAL	1	FALSE	1	0.712257332988283	2		475	776	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900291	101900291	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	177	359	0	ENST00000374994.4:c.725G>A	p.Trp242Ter	p.W242*	ENST00000374994	NM_004612.2	242	tGg/tAg	4/9	0.332078158516433	1	FACETS	0.623	0.578	0.668	0.623	0.578	0.668	INDETERMINATE	1	FALSE	0	0.712257332988283	1		359	514	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133803	41133803	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768488321	NA	P-0035663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	159	415	1	ENST00000379561.5:c.1825C>T	p.Arg609Cys	p.R609C	ENST00000379561	NM_002015.3	609	Cgc/Tgc	2/3	0.815508540518094	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.815508540518094	1		416	221	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032803	30032804	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0035663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	188	391	0	ENST00000338641.4:c.179_180dup	p.Phe61GlyfsTer63	p.F61Gfs*63	ENST00000338641	NM_000268.3	60	tgg/tGGgg	2/16	0.815508540518094	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.815508540518094	1		391	261	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0035664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	48	685	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	1	2	FACETS	0.819	0.691	0.96	0.819	0.691	0.96	CLONAL	1	TRUE	1	0.18	2		685	651	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138521	11138521	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	44	676	0	ENST00000358026.2:c.3277C>T	p.Arg1093Ter	p.R1093*	ENST00000358026	NM_001128849.1	1093	Cga/Tga	24/36	1	2	FACETS	0.745	0.624	0.88	0.745	0.624	0.88	SUBCLONAL	1	TRUE	1	0.18	2		676	656	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881427	48881430	+	frameshift_variant	Frame_Shift_Del	DEL	AAGA	AAGA	-	novel	NA	P-0035664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	28	223	0	ENST00000267163.4:c.151_154del	p.Glu51GlnfsTer13	p.E51Qfs*13	ENST00000267163	NM_000321.2	50	gAAGAa/ga	2/27	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.18	2		223	214	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249522	153249522	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	42	565	0	ENST00000281708.4:c.1256G>T	p.Gly419Val	p.G419V	ENST00000281708	NM_033632.3	419	gGa/gTa	9/12	1	2	FACETS	0.919	0.767	1	0.919	0.767	1	CLONAL	1	TRUE	1	0.18	2		565	508	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710794	117710794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146130970	NA	P-0035664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	43	383	0	ENST00000368508.3:c.1478G>A	p.Arg493His	p.R493H	ENST00000368508	NM_002944.2	493	cGc/cAc	12/43	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.18	2		383	461	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84393376	84393377	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	TTAA	novel	NA	P-0035665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	10	264	0	ENST00000321945.7:c.280_281insTTAA	p.Lys94IlefsTer21	p.K94Ifs*21	ENST00000321945	NM_139076.2	94	aag/aTTAAag	4/9	1	2	FACETS	0.441	0.3	0.616	0.441	0.3	0.616	SUBCLONAL	1	TRUE	1	0.368370699171248	2		264	123	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0035666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	147	673	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.395824139091344	3	FACETS	1	0.976	1	0.593	0.542	0.646	CLONAL	1	TRUE	1	0.395824139091344	3		673	750	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098975	178098975	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1328994103	NA	P-0035666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	90	327	0	ENST00000397062.3:c.70T>C	p.Trp24Arg	p.W24R	ENST00000397062	NM_006164.4	24	Tgg/Cgg	2/5	0.395824139091344	2	FACETS	1	0.954	1	0.563	0.502	0.626	CLONAL	1	TRUE	0	0.395824139091344	2		327	404	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864315	57864315	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs758888293	NA	P-0035666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	126	727	0	ENST00000228682.2:c.1796del	p.Gly599ValfsTer14	p.G599Vfs*14	ENST00000228682	NM_005269.2	598	Ggg/gg	12/12	0.392803142314873	2	FACETS	0.99	0.899	1	0.495	0.449	0.543	CLONAL	1	TRUE	0	0.395824139091344	2		727	643	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246757	41246757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397509322	NA	P-0035666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	161	683	0	ENST00000357654.3:c.791G>A	p.Ser264Asn	p.S264N	ENST00000357654	NM_007294.3	264	aGt/aAt	10/23	0.388009185897878	2	FACETS	1	0.947	1	0.521	0.478	0.565	CLONAL	1	TRUE	0	0.395824139091344	2		683	781	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953781	131953781	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	48	321	0	ENST00000265335.6:c.3184G>C	p.Glu1062Gln	p.E1062Q	ENST00000265335		1062	Gag/Cag	21/25	1	2	FACETS	0.848	0.722	0.985	0.848	0.722	0.985	CLONAL	1	TRUE	1	0.395824139091344	2		321	286	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056446	26056446	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	80	348	0	ENST00000343677.2:c.211T>A	p.Tyr71Asn	p.Y71N	ENST00000343677	NM_005319.3	71	Tat/Aat	1/1	0.362284193126409	2	FACETS	1	0.935	1	0.54	0.479	0.606	CLONAL	1	TRUE	0	0.395824139091344	2		348	374	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894800	101894800	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	86	405	0	ENST00000374994.4:c.353C>A	p.Ser118Ter	p.S118*	ENST00000374994	NM_004612.2	118	tCa/tAa	3/9	0.395824139091344	3	FACETS	1	0.903	1	0.509	0.452	0.571	CLONAL	1	TRUE	1	0.395824139091344	3		405	511	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	49	812	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.836	0.714	0.967	1	0.97	1	CLONAL	2	FALSE	1	0.23636537721351	2		812	248	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0035692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	61	291	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.23636537721351	3	FACETS	1	0.951	1	1	0.979	1	CLONAL	3	FALSE	1	0.23636537721351	3		291	166	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0035692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	169	468	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.23636537721351	2	FACETS	0.951	0.887	1	1	0.993	1	CLONAL	4	FALSE	0	0.23636537721351	2		468	376	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0035692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	28	290	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.23636537721351	3	FACETS	1	0.898	1	0.599	0.482	0.732	CLONAL	1	FALSE	1	0.23636537721351	3		290	221	SUCCESS
RET	5979	MSKCC	GRCh37	10	43598018	43598018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753707182	NA	P-0035692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	76	440	1	ENST00000355710.3:c.566G>A	p.Arg189His	p.R189H	ENST00000355710	NM_020975.4	189	cGc/cAc	3/20	0.23636537721351	3	FACETS	0.821	0.723	0.925	0.821	0.723	0.925	CLONAL	2	FALSE	1	0.23636537721351	3		441	438	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0035692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	114	338	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.23636537721351	5	FACETS	0.959	0.869	1	0.959	0.869	1	CLONAL	3	FALSE	2	0.23636537721351	5		339	454	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920412	134920412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746798014	NA	P-0035692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	140	437	1	ENST00000398015.3:c.2227C>T	p.Arg743Trp	p.R743W	ENST00000398015	NM_004441.4	743	Cgg/Tgg	12/16	0.23636537721351	5	FACETS	1	0.962	1	1	0.989	1	CLONAL	3	FALSE	3	0.23636537721351	5		438	492	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485280	8485280	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329600473	NA	P-0035692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	34	228	0	ENST00000356435.5:c.3100G>A	p.Val1034Met	p.V1034M	ENST00000356435		1034	Gtg/Atg	18/35	0.23636537721351	5	FACETS	1	0.936	1	0.451	0.37	0.542	CLONAL	1	FALSE	2	0.23636537721351	5		228	288	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196768	123196770	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0035692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	49	139	0	ENST00000218089.9:c.1661_1663del	p.Lys554del	p.K554del	ENST00000218089	NM_001042749.1	552	gAGAag/gag	18/35	0.23636537721351	3	FACETS	1	0.915	1	1	0.915	1	CLONAL	2	FALSE	1	0.23636537721351	3		139	211	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437515	49437515	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	138	390	0	ENST00000301067.7:c.5370del	p.Phe1790LeufsTer12	p.F1790Lfs*12	ENST00000301067	NM_003482.3	1790	ttT/tt	23/54	0.23636537721351	5	FACETS	1	0.955	1	1	0.989	1	CLONAL	3	FALSE	3	0.23636537721351	5		390	495	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041576	47041576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	117	456	0	ENST00000377604.3:c.1801C>T	p.Gln601Ter	p.Q601*	ENST00000377604	NM_001204468.1	601	Cag/Tag	17/24	0.23636537721351	3	FACETS	0.953	0.868	1	1	0.984	1	CLONAL	3	FALSE	1	0.23636537721351	3		456	387	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0035693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	55	290	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.3	1	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	0	0.39	1		290	217	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257167	16257167	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	97	600	0	ENST00000375759.3:c.4432A>G	p.Lys1478Glu	p.K1478E	ENST00000375759	NM_015001.2	1478	Aaa/Gaa	11/15	1	2	FACETS	0.895	0.8	0.995	0.895	0.8	0.995	CLONAL	1	TRUE	1	0.39	2		600	556	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0035693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	44	275	0	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.39	2		275	210	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243246	123243246	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	160	1055	0	ENST00000358487.5:c.2267A>G	p.Asp756Gly	p.D756G	ENST00000358487	NM_000141.4	756	gAc/gGc	17/18	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.39	2		1055	815	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	150	678	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	0.39	2		679	667	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912023	32912023	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	98	776	0	ENST00000380152.3:c.3531C>G	p.Asp1177Glu	p.D1177E	ENST00000380152		1177	gaC/gaG	11/27	1	2	FACETS	0.861	0.769	0.957	0.861	0.769	0.957	CLONAL	1	TRUE	1	0.39	2		776	584	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354604	91354604	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	84	535	1	ENST00000355112.3:c.4048del	p.Thr1350LeufsTer56	p.T1350Lfs*56	ENST00000355112	NM_000057.2	1348	agA/ag	21/22	1	2	FACETS	0.936	0.831	1	0.936	0.831	1	CLONAL	1	TRUE	1	0.39	2		536	460	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274211	10274211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779149309	NA	P-0035693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	55	475	0	ENST00000330684.3:c.58G>A	p.Gly20Ser	p.G20S	ENST00000330684	NM_001134407.1	20	Ggt/Agt	2/13	1	2	FACETS	0.969	0.835	1	0.969	0.835	1	CLONAL	1	TRUE	1	0.39	2		475	291	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822586	72822586	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	95	601	5	ENST00000268489.5:c.9589del	p.Gln3197SerfsTer44	p.Q3197Sfs*44	ENST00000268489	NM_006885.3	3197	Cag/ag	10/10	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.39	2		606	469	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998898	11998898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	42	225	0	ENST00000353533.5:c.400C>T	p.Arg134Trp	p.R134W	ENST00000353533	NM_003010.3	134	Cgg/Tgg	4/11	1	2	FACETS	0.962	0.81	1	0.962	0.81	1	CLONAL	1	TRUE	1	0.39	2		225	224	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687471	37687472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs760014508	NA	P-0035693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	31	353	0	ENST00000447079.4:c.4382dup	p.Thr1463AsnfsTer50	p.T1463Nfs*50	ENST00000447079	NM_015083.1	1459	tgg/tGgg	14/14	1	2	FACETS	0.799	0.651	0.963	0.799	0.651	0.963	CLONAL	1	TRUE	1	0.39	2		353	199	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40456401	40456401	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	96	781	0	ENST00000345506.4:c.1211A>C	p.Glu404Ala	p.E404A	ENST00000345506	NM_003152.3	404	gAg/gCg	11/20	1	2	FACETS	0.797	0.711	0.888	0.797	0.711	0.888	SUBCLONAL	1	TRUE	1	0.39	2		781	618	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437569	56437569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	92	750	0	ENST00000407977.2:c.893G>A	p.Cys298Tyr	p.C298Y	ENST00000407977		298	tGt/tAt	8/10	1	2	FACETS	0.834	0.742	0.93	0.834	0.742	0.93	CLONAL	1	TRUE	1	0.39	2		750	566	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662571	227662571	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	44	634	0	ENST00000305123.5:c.884G>A	p.Ser295Asn	p.S295N	ENST00000305123	NM_005544.2	295	aGc/aAc	1/2	1	2	FACETS	0.508	0.426	0.599	0.508	0.426	0.599	SUBCLONAL	1	TRUE	1	0.39	2		634	444	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022443	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	rs750318549	NA	P-0035693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	35	321	0	ENST00000375687.4:c.1933_1934del	p.Gly645TrpfsTer12	p.G645Wfs*12	ENST00000375687	NM_015338.5	643	GGg/g	13/13	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.39	2		321	172	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265049	46265049	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	76	605	0	ENST00000371998.3:c.1924del	p.Leu642Ter	p.L642*	ENST00000371998		640	tCc/tc	12/23	1	2	FACETS	0.831	0.731	0.938	0.831	0.731	0.938	CLONAL	1	TRUE	1	0.39	2		605	469	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042540	37042540	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs267607727	NA	P-0035693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	79	483	0	ENST00000231790.2:c.302G>T	p.Gly101Val	p.G101V	ENST00000231790	NM_000249.3	101	gGt/gTt	3/19	1	2	FACETS	0.842	0.743	0.948	0.842	0.743	0.948	CLONAL	1	TRUE	1	0.39	2		483	481	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125635	47125635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	95	549	0	ENST00000409792.3:c.5635C>T	p.Arg1879Cys	p.R1879C	ENST00000409792	NM_014159.6	1879	Cgc/Tgc	12/21	1	2	FACETS	0.978	0.874	1	0.978	0.874	1	CLONAL	1	TRUE	1	0.39	2		549	498	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439783	52439783	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	92	694	0	ENST00000460680.1:c.929C>T	p.Thr310Ile	p.T310I	ENST00000460680	NM_004656.3	310	aCa/aTa	10/17	1	2	FACETS	0.906	0.807	1	0.906	0.807	1	CLONAL	1	TRUE	1	0.39	2		694	521	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801064	1801064	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	150	1275	3	ENST00000260795.2:c.197del	p.Gly66ValfsTer32	p.G66Vfs*32	ENST00000260795		65	Ggg/gg	2/17	NA	2	FACETS	0.971	0.889	1			1	INDETERMINATE	1	TRUE	NA	0.39	2		1278	792	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803444	1803444	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199944818	NA	P-0035693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	92	799	1	ENST00000260795.2:c.713G>A	p.Arg238Gln	p.R238Q	ENST00000260795		238	cGg/cAg	5/17	NA	2	FACETS	0.837	0.745	0.934			1	INDETERMINATE	1	TRUE	NA	0.39	2		800	564	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0035693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	29	204	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.551	0.443	0.672	0.551	0.443	0.672	SUBCLONAL	1	TRUE	1	0.39	2		204	270	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	45	318	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	0.836	0.707	0.977	0.836	0.707	0.977	CLONAL	1	TRUE	1	0.39	2		318	276	SUCCESS
APC	324	MSKCC	GRCh37	5	112178781	112178781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141010008	NA	P-0035693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	83	549	0	ENST00000257430.4:c.7490C>T	p.Ser2497Leu	p.S2497L	ENST00000257430	NM_000038.5	2497	tCg/tTg	16/16	0.3	1	FACETS	0.936	0.832	1	0.936	0.832	1	CLONAL	1	TRUE	0	0.39	1		549	366	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26021082	26021082	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	76	508	0	ENST00000357647.3:c.365C>A	p.Pro122His	p.P122H	ENST00000357647	NM_003529.2	122	cCc/cAc	1/1	1	2	FACETS	0.967	0.853	1	0.967	0.853	1	CLONAL	1	TRUE	1	0.39	2		508	403	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527697	157527697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745372243	NA	P-0035693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	91	771	1	ENST00000346085.5:c.5422C>T	p.Arg1808Cys	p.R1808C	ENST00000346085	NM_020732.3	1808	Cgt/Tgt	20/20	1	2	FACETS	0.794	0.706	0.887	0.794	0.706	0.887	SUBCLONAL	1	TRUE	1	0.39	2		772	588	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769886672	NA	P-0035693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	26	361	1	ENST00000405192.2:c.414dup	p.Thr139HisfsTer24	p.T139Hfs*24	ENST00000405192	NM_001163147.1	138	-/C	7/12	1	2	FACETS	0.463	0.367	0.572	0.463	0.367	0.572	SUBCLONAL	1	TRUE	1	0.39	2		362	288	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949775	151949775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	79	479	0	ENST00000262189.6:c.1325G>A	p.Gly442Asp	p.G442D	ENST00000262189	NM_170606.2	442	gGc/gAc	10/59	1	2	FACETS	0.904	0.799	1	0.904	0.799	1	CLONAL	1	TRUE	1	0.39	2		479	448	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390656	139390656	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	136	1075	0	ENST00000277541.6:c.7535del	p.Pro2512ArgfsTer77	p.P2512Rfs*77	ENST00000277541	NM_017617.3	2512	cCg/cg	34/34	1	2	FACETS	0.937	0.853	1	0.937	0.853	1	CLONAL	1	TRUE	1	0.39	2		1075	744	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417349	139417349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs869025493	NA	P-0035693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	123	867	0	ENST00000277541.6:c.695C>T	p.Thr232Ile	p.T232I	ENST00000277541	NM_017617.3	232	aCc/aTc	4/34	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.39	2		867	614	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	79	873	1	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	1	2	FACETS	0.659	0.58	0.744	0.659	0.58	0.744	SUBCLONAL	1	TRUE	1	0.39	2		874	615	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937362	76937362	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	50	430	0	ENST00000373344.5:c.3386T>G	p.Leu1129Arg	p.L1129R	ENST00000373344	NM_000489.3	1129	cTg/cGg	9/35	1	2	FACETS	0.77	0.656	0.894	0.77	0.656	0.894	SUBCLONAL	1	TRUE	1	0.39	2		430	333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0035696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	60	746	1	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.618508776753733	1	FACETS	0.38	0.329	0.435	0.38	0.329	0.435	SUBCLONAL	1	TRUE	0	0.618508776753733	1		747	353	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0035696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	76	598	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.999	0.889	1	0.999	0.889	1	CLONAL	1	TRUE	1	0.618508776753733	2		598	246	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0035696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	59	812	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.618508776753733	1	FACETS	0.321	0.276	0.368	0.321	0.276	0.368	SUBCLONAL	1	TRUE	0	0.618508776753733	1		812	411	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684326	29684326	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201367	NA	P-0035696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	209	515	1	ENST00000356175.3:c.7846C>T	p.Arg2616Ter	p.R2616*	ENST00000356175	NM_000267.3	2616	Cga/Tga	53/57	0.618508776753733	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.618508776753733	1		516	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577557	7577557	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519982	NA	P-0035696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	18	612	0	ENST00000269305.4:c.724T>C	p.Cys242Arg	p.C242R	ENST00000269305	NM_001126112.2	242	Tgc/Cgc	7/11	0.618508776753733	1	FACETS	0.088	0.066	0.115	0.088	0.066	0.115	SUBCLONAL	1	TRUE	0	0.618508776753733	1		612	455	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219934	36219934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	135	578	2	ENST00000222270.7:c.4736G>A	p.Arg1579His	p.R1579H	ENST00000222270	NM_014727.1	1579	cGt/cAt	21/37	1	2	FACETS	0.917	0.839	0.998	0.917	0.839	0.998	CLONAL	1	TRUE	1	0.618508776753733	2		580	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs878854073	NA	P-0035696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	37	454	0	ENST00000269305.4:c.673-1G>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.618508776753733	1	FACETS	0.262	0.217	0.313	0.262	0.217	0.313	SUBCLONAL	1	TRUE	0	0.618508776753733	1		454	315	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750382	133750382	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1005779892	NA	P-0035696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	142	482	0	ENST00000318560.5:c.1213T>C	p.Trp405Arg	p.W405R	ENST00000318560	NM_005157.4	405	Tgg/Cgg	7/11	0.618508776753733	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.618508776753733	1		482	310	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	18	272	0				ENST00000310581	NM_198253.2	-/1132			0.233758461788579	3	FACETS	0.878	0.663	1	0.439	0.331	0.564	CLONAL	1	TRUE	1	0.233758461788579	3		272	196	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0035699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	116	761	0	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	1	2	FACETS	0.998	0.905	1	1	0.989	1	CLONAL	2	TRUE	1	0.233758461788579	2		761	497	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912416	32912416	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	40	275	0	ENST00000380152.3:c.3924A>C	p.Glu1308Asp	p.E1308D	ENST00000380152		1308	gaA/gaC	11/27	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.233758461788579	2		275	286	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281419	49281419	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	56	880	0	ENST00000282018.3:c.466T>C	p.Trp156Arg	p.W156R	ENST00000282018	NM_020377.2	156	Tgg/Cgg	1/1	1	2	FACETS	0.818	0.7	0.946	0.818	0.7	0.946	CLONAL	1	TRUE	1	0.233758461788579	2		880	586	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222904	5222904	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	21	477	0	ENST00000357368.4:c.2899G>T	p.Val967Leu	p.V967L	ENST00000357368	NM_002850.3	967	Gtg/Ttg	18/38	1	2	FACETS	0.691	0.533	0.875	0.691	0.533	0.875	SUBCLONAL	1	TRUE	1	0.233758461788579	2		477	260	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609911	117609911	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	51	507	0	ENST00000368508.3:c.6788T>C	p.Leu2263Ser	p.L2263S	ENST00000368508	NM_002944.2	2263	tTa/tCa	43/43	1	2	FACETS	0.242	0.206	0.283	0.242	0.206	0.283	SUBCLONAL	1	TRUE	1	0.785281388808919	2		507	536	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786795	3786795	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	353	435	0	ENST00000262367.5:c.4416G>T	p.Trp1472Cys	p.W1472C	ENST00000262367	NM_004380.2	1472	tgG/tgT	27/31	0.785281388808919	2	FACETS	0.853	0.821	0.884	0.853	0.821	0.884	CLONAL	2	TRUE	0	0.785281388808919	2		435	527	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553420	106553420	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	72	337	0	ENST00000369096.4:c.1385A>G	p.Asn462Ser	p.N462S	ENST00000369096	NM_001198.3	462	aAc/aGc	5/7	1	2	FACETS	0.443	0.389	0.5	0.443	0.389	0.5	SUBCLONAL	1	TRUE	1	0.865431871157616	2		337	376	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0035706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	135	673	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.677	0.616	0.74	0.677	0.616	0.74	SUBCLONAL	1	TRUE	1	0.592033668607918	2		673	674	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0035706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	98	366	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.761	0.683	0.843	0.761	0.683	0.843	SUBCLONAL	1	TRUE	1	0.592033668607918	2		366	435	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717618	89717635	+	frameshift_variant	Frame_Shift_Del	DEL	TTTGTGGTCTGCCAGCTA	TTTGTGGTCTGCCAGCTA	C	novel	NA	P-0035706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	111	389	0	ENST00000371953.3:c.643_660delinsC	p.Phe215GlnfsTer22	p.F215Qfs*22	ENST00000371953	NM_000314.4	215	TTTGTGGTCTGCCAGCTA/C	7/9	1	2	FACETS	0.694	0.626	0.766	0.694	0.626	0.766	SUBCLONAL	1	TRUE	1	0.592033668607918	2		389	540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0035707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	276	571	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.306544984665285	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.306544984665285	2		571	859	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0035707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	187	478	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.306544984665285	3	FACETS	0.882	0.816	0.95	0.882	0.816	0.95	CLONAL	2	TRUE	1	0.306544984665285	3		478	798	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0035707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	111	359	2	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.306544984665285	2	FACETS	0.894	0.81	0.981	0.894	0.81	0.981	CLONAL	2	TRUE	0	0.306544984665285	2		361	405	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924344	112924344	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1178602062	NA	P-0035707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	130	442	0	ENST00000351677.2:c.1290C>A	p.Ser430Arg	p.S430R	ENST00000351677	NM_002834.3	430	agC/agA	11/16	0.306544984665285	3	FACETS	1	0.969	1	0.578	0.524	0.635	CLONAL	1	TRUE	1	0.306544984665285	3		442	846	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482864	67482864	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	198	474	0	ENST00000327367.4:c.1268G>C	p.Ser423Thr	p.S423T	ENST00000327367	NM_005902.3	423	aGt/aCt	9/9	0.306544984665285	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.306544984665285	2		474	627	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358405	91358405	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	153	583	0	ENST00000355112.3:c.4150C>G	p.His1384Asp	p.H1384D	ENST00000355112	NM_000057.2	1384	Cat/Gat	22/22	0.306544984665285	2	FACETS	1	0.948	1	0.525	0.48	0.573	CLONAL	1	TRUE	0	0.306544984665285	2		583	950	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372034	45372034	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	298	442	0	ENST00000262160.6:c.1135G>A	p.Gly379Ser	p.G379S	ENST00000262160	NM_005901.5	379	Ggc/Agc	9/11	0.182129736714645	3	FACETS	1	0.959	1			1	INDETERMINATE	3	TRUE	NA	0.306544984665285	3		442	737	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256820	19256820	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	50	250	0	ENST00000162023.5:c.893G>A	p.Ser298Asn	p.S298N	ENST00000162023		298	aGc/aAc	13/13	0.306544984665285	3	FACETS	0.842	0.715	0.98	0.421	0.357	0.49	CLONAL	1	TRUE	1	0.306544984665285	3		250	447	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214710	36214710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	202	464	0	ENST00000222270.7:c.3136C>T	p.Arg1046Cys	p.R1046C	ENST00000222270	NM_014727.1	1046	Cgc/Tgc	8/37	0.306544984665285	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.306544984665285	3		464	726	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510127	187510127	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	100	419	0	ENST00000441802.2:c.13386C>G	p.Ile4462Met	p.I4462M	ENST00000441802	NM_005245.3	4462	atC/atG	27/27	0.306544984665285	2	FACETS	0.972	0.869	1	0.486	0.434	0.541	CLONAL	1	TRUE	0	0.306544984665285	2		419	671	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271388	26271388	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	177	441	0	ENST00000305910.3:c.225C>G	p.Ile75Met	p.I75M	ENST00000305910	NM_003534.2	75	atC/atG	1/1	0.306544984665285	2	FACETS	0.925	0.857	0.996	0.925	0.857	0.996	CLONAL	2	TRUE	0	0.306544984665285	2		441	624	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412196	63412196	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	295	418	0	ENST00000330258.3:c.971C>A	p.Ser324Ter	p.S324*	ENST00000330258	NM_152424.3	324	tCa/tAa	2/2	0.285235304151221	2	FACETS	0.918	0.87	0.966			1	CLONAL	3	TRUE	NA	0.306544984665285	2		418	699	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587781702	NA	P-0035709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	157	622	0	ENST00000269305.4:c.920-1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			NA	2	FACETS	0.939	0.87	1			1	INDETERMINATE	2	TRUE	NA	0.412954332053776	2		622	405	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638122	176638122	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	143	598	0	ENST00000439151.2:c.2722A>T	p.Ser908Cys	p.S908C	ENST00000439151	NM_022455.4	908	Agt/Tgt	5/23	0.412954332053776	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.412954332053776	2		598	300	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972939	68972939	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	66	424	0	ENST00000288368.4:c.1264A>T	p.Ile422Phe	p.I422F	ENST00000288368	NM_024870.2	422	Att/Ttt	11/40	0.412954332053776	5	FACETS	0.882	0.766	1	0.294	0.255	0.336	CLONAL	1	TRUE	2	0.412954332053776	5		424	587	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	221	488	2	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.326394367789581	7	FACETS	1	0.944	1	0.76	0.709	0.812	CLONAL	3	FALSE	3	0.326394367789581	7		490	809	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231437	46231437	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	91	435	0	ENST00000334344.6:c.1277C>T	p.Thr426Met	p.T426M	ENST00000334344	NM_152641.2	426	aCg/aTg	10/21	0.200560273627558	3	FACETS	1	0.972	1			1	CLONAL	1	FALSE	NA	0.326394367789581	3		435	505	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847333	68847333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	287	506	0	ENST00000261769.5:c.1255G>A	p.Asp419Asn	p.D419N	ENST00000261769	NM_004360.3	419	Gat/Aat	9/16	0.326394367789581	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	FALSE	1	0.326394367789581	4		506	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	379	539	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.324050198783761	3	FACETS	0.925	0.881	0.97	0.925	0.881	0.97	CLONAL	3	FALSE	0	0.326394367789581	3		539	973	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970901	21970901	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs45476696	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	369	689	0	ENST00000304494.5:c.457G>T	p.Asp153Tyr	p.D153Y	ENST00000304494	NM_000077.4	153	Gac/Tac	2/3	0.301704365062057	3	FACETS	0.941	0.896	0.986	0.941	0.896	0.986	CLONAL	3	FALSE	0	0.326394367789581	3		689	932	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949125	71949125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745724027	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	151	745	1	ENST00000298229.2:c.3592G>A	p.Glu1198Lys	p.E1198K	ENST00000298229	NM_001567.3	1198	Gag/Aag	27/28	0.198472744713474	5	FACETS	0.837	0.766	0.912	0.558	0.51	0.608	CLONAL	2	FALSE	2	0.326394367789581	5		746	823	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469629	25469629	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750837407	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	67	591	2	ENST00000264709.3:c.1139C>T	p.Ala380Val	p.A380V	ENST00000264709	NM_175629.2	380	gCg/gTg	10/23	0.326394367789581	5	FACETS	0.771	0.669	0.882	0.257	0.223	0.294	SUBCLONAL	1	FALSE	2	0.326394367789581	5		593	793	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212581	36212581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	212	865	1	ENST00000222270.7:c.2332G>A	p.Ala778Thr	p.A778T	ENST00000222270	NM_014727.1	778	Gcg/Acg	3/37	0.326394367789581	3	FACETS	0.862	0.802	0.925	0.862	0.802	0.925	CLONAL	2	FALSE	1	0.326394367789581	3		866	876	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11168242	11168242	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	199	552	0	ENST00000361445.4:c.7630G>T	p.Gly2544Cys	p.G2544C	ENST00000361445	NM_004958.3	2544	Ggc/Tgc	57/58	0.326394367789581	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	FALSE	1	0.326394367789581	3		552	612	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511672	46511672	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	82	643	0	ENST00000262741.5:c.1105G>T	p.Glu369Ter	p.E369*	ENST00000262741	NM_003629.3	369	Gag/Tag	9/10	0.326394367789581	3	FACETS	0.664	0.584	0.75	0.332	0.292	0.375	SUBCLONAL	1	FALSE	1	0.326394367789581	3		643	880	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615613	43615613	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	44	474	0	ENST00000355710.3:c.2692G>A	p.Asp898Asn	p.D898N	ENST00000355710	NM_020975.4	898	Gat/Aat	15/20	0.326394367789581	4	FACETS	0.577	0.483	0.681	0.192	0.161	0.227	SUBCLONAL	1	FALSE	1	0.326394367789581	4		474	620	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342983	118342983	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	27	239	0	ENST00000534358.1:c.1109C>A	p.Thr370Asn	p.T370N	ENST00000534358	NM_005933.3	370	aCc/aAc	3/36	0.198472744713474	5	FACETS	0.775	0.617	0.954	0.258	0.205	0.318	CLONAL	1	FALSE	2	0.326394367789581	5		239	318	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148501	119148501	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	168	442	0	ENST00000264033.4:c.1042G>T	p.Asp348Tyr	p.D348Y	ENST00000264033	NM_005188.3	348	Gat/Tat	7/16	0.198472744713474	5	FACETS	0.846	0.782	0.913	0.846	0.782	0.913	CLONAL	3	FALSE	2	0.326394367789581	5		442	604	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18762537	18762537	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	151	373	0	ENST00000266497.5:c.4033A>C	p.Ile1345Leu	p.I1345L	ENST00000266497		1345	Ata/Cta	29/31	0.326394367789581	5	FACETS	1	0.98	1	0.806	0.74	0.874	CLONAL	2	FALSE	2	0.326394367789581	5		373	570	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415566	49415566	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	74	365	0	ENST00000301067.7:c.16611C>A	p.Asn5537Lys	p.N5537K	ENST00000301067	NM_003482.3	5537	aaC/aaA	54/54	0.176888336814118	5	FACETS	0.775	0.681	0.875	0.516	0.454	0.583	INDETERMINATE	2	FALSE	2	0.326394367789581	5		365	436	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424113	49424114	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	78	769	0	ENST00000301067.7:c.13948_13949insT	p.Glu4650ValfsTer12	p.E4650Vfs*12	ENST00000301067	NM_003482.3	4650	gag/gTag	42/54	0.176888336814118	5	FACETS	0.783	0.687	0.887	0.261	0.229	0.296	INDETERMINATE	1	FALSE	2	0.326394367789581	5		769	909	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435483	49435483	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	139	634	0	ENST00000301067.7:c.6189G>T	p.Lys2063Asn	p.K2063N	ENST00000301067	NM_003482.3	2063	aaG/aaT	30/54	0.176888336814118	5	FACETS	0.845	0.77	0.923	0.563	0.513	0.616	INDETERMINATE	2	FALSE	2	0.326394367789581	5		634	751	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432048	121432048	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	95	768	0	ENST00000257555.6:c.795C>A	p.Tyr265Ter	p.Y265*	ENST00000257555		265	taC/taA	4/10	0.326394367789581	3	FACETS	0.766	0.681	0.857	0.383	0.34	0.429	SUBCLONAL	1	FALSE	1	0.326394367789581	3		768	884	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133208923	133208924	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	115	520	2	ENST00000320574.5:c.6307_6308delinsAT	p.Glu2103Met	p.E2103M	ENST00000320574	NM_006231.2	2103	GAg/ATg	45/49	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.326394367789581	2		522	557	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30102088	30102088	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	132	492	0	ENST00000331968.5:c.1379G>T	p.Ser460Ile	p.S460I	ENST00000331968	NM_002742.2	460	aGc/aTc	9/18	0.326394367789581	5	FACETS	0.844	0.767	0.924	0.562	0.511	0.616	CLONAL	2	FALSE	2	0.326394367789581	5		492	714	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566220	95566220	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs767112987	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	63	528	1	ENST00000393063.1:c.4103G>T	p.Arg1368Leu	p.R1368L	ENST00000393063	NM_030621.3	1368	cGc/cTc	23/28	0.326394367789581	5	FACETS	0.706	0.61	0.812	0.235	0.203	0.271	SUBCLONAL	1	FALSE	2	0.326394367789581	5		529	814	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827169	72827169	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	63	461	0	ENST00000268489.5:c.9412A>C	p.Thr3138Pro	p.T3138P	ENST00000268489	NM_006885.3	3138	Act/Cct	9/10	0.326394367789581	4	FACETS	0.968	0.838	1	0.323	0.279	0.37	CLONAL	1	FALSE	1	0.326394367789581	4		461	529	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604707	48604707	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs377767371	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	50	389	0	ENST00000342988.3:c.1529G>T	p.Gly510Val	p.G510V	ENST00000342988	NM_005359.5	510	gGa/gTa	12/12	NA	2	FACETS	0.745	0.634	0.867			1	INDETERMINATE	1	FALSE	NA	0.326394367789581	2		389	411	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110507	4110507	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	67	401	0	ENST00000262948.5:c.450G>T	p.Met150Ile	p.M150I	ENST00000262948	NM_030662.3	150	atG/atT	3/11	0.326394367789581	3	FACETS	1	0.937	1	0.562	0.49	0.639	CLONAL	1	FALSE	1	0.326394367789581	3		401	425	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256700	19256700	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	137	537	0	ENST00000162023.5:c.1013C>T	p.Pro338Leu	p.P338L	ENST00000162023		338	cCc/cTc	13/13	0.326394367789581	3	FACETS	0.916	0.838	0.997	0.916	0.838	0.997	CLONAL	2	FALSE	1	0.326394367789581	3		537	533	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127780	47127780	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	167	420	0	ENST00000409792.3:c.5302A>G	p.Lys1768Glu	p.K1768E	ENST00000409792	NM_014159.6	1768	Aag/Gag	11/21	0.326394367789581	2	FACETS	0.993	0.92	1	0.993	0.92	1	CLONAL	2	FALSE	0	0.326394367789581	2		420	515	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720921	119720921	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	53	491	0	ENST00000316626.5:c.254A>T	p.Lys85Met	p.K85M	ENST00000316626		85	aAg/aTg	2/12	0.326394367789581	6	FACETS	0.57	0.485	0.665	0.19	0.161	0.222	SUBCLONAL	1	FALSE	3	0.326394367789581	6		491	941	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200005	128200005	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	53	627	1	ENST00000341105.2:c.1300G>T	p.Ala434Ser	p.A434S	ENST00000341105	NM_032638.4	434	Gct/Tct	6/6	0.326394367789581	6	FACETS	0.529	0.449	0.617	0.176	0.149	0.206	SUBCLONAL	1	FALSE	3	0.326394367789581	6		628	1015	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433508	138433508	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	54	441	0	ENST00000289153.2:c.1104C>G	p.Ile368Met	p.I368M	ENST00000289153	NM_006219.2	368	atC/atG	7/22	0.326394367789581	6	FACETS	0.721	0.614	0.838	0.24	0.204	0.28	SUBCLONAL	1	FALSE	3	0.326394367789581	6		441	759	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955922	55955922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	106	508	0	ENST00000263923.4:c.3240A>T	p.Arg1080Ser	p.R1080S	ENST00000263923	NM_002253.2	1080	agA/agT	24/30	0.111904583617606	4	FACETS	1	0.981	1	0.72	0.647	0.798	INDETERMINATE	1	FALSE	2	0.326394367789581	4		508	598	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467454	66467455	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	49	297	0	ENST00000273854.3:c.814_815delinsAA	p.Pro272Asn	p.P272N	ENST00000273854	NM_004439.5	272	CCc/AAc	3/18	0.111904583617606	4	FACETS	1	0.947	1	0.632	0.538	0.734	INDETERMINATE	1	FALSE	2	0.326394367789581	4		297	315	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510059	187510059	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	44	422	0	ENST00000441802.2:c.13454A>C	p.Asn4485Thr	p.N4485T	ENST00000441802	NM_005245.3	4485	aAc/aCc	27/27	1	2	FACETS	0.585	0.491	0.689	0.585	0.491	0.689	SUBCLONAL	1	FALSE	1	0.326394367789581	2		422	461	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530997	187530997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	83	492	0	ENST00000441802.2:c.10026del	p.Val3343SerfsTer33	p.V3343Sfs*33	ENST00000441802	NM_005245.3	3342	acA/ac	15/27	1	2	FACETS	0.982	0.869	1	0.982	0.869	1	CLONAL	1	FALSE	1	0.326394367789581	2		492	518	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952498	38952498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	29	301	1	ENST00000357387.3:c.2927C>T	p.Ala976Val	p.A976V	ENST00000357387	NM_152756.3	976	gCt/gTt	30/38	0.326394367789581	3	FACETS	0.505	0.405	0.619	0.253	0.202	0.31	SUBCLONAL	1	FALSE	1	0.326394367789581	3		302	409	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665508	176665508	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	159	381	0	ENST00000439151.2:c.4192G>T	p.Gly1398Ter	p.G1398*	ENST00000439151	NM_022455.4	1398	Gga/Tga	7/23	0.258718588300861	3	FACETS	1	0.982	1	0.805	0.745	0.868	CLONAL	2	FALSE	0	0.326394367789581	3		381	469	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696808	176696808	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	18	217	0	ENST00000439151.2:c.5509G>C	p.Ala1837Pro	p.A1837P	ENST00000439151	NM_022455.4	1837	Gct/Cct	16/23	0.258718588300861	3	FACETS	0.629	0.475	0.809	0.21	0.158	0.27	SUBCLONAL	1	FALSE	0	0.326394367789581	3		217	204	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004544	150004544	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	305	698	0	ENST00000253339.5:c.1681A>T	p.Lys561Ter	p.K561*	ENST00000253339		561	Aaa/Taa	3/7	0.225824517026233	4	FACETS	1	0.991	1			1	CLONAL	2	FALSE	NA	0.326394367789581	4		698	997	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419904	152419904	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	63	508	0	ENST00000206249.3:c.1591A>C	p.Lys531Gln	p.K531Q	ENST00000206249	NM_000125.3	531	Aag/Cag	8/8	0.326394367789581	3	FACETS	0.713	0.616	0.818	0.356	0.308	0.409	SUBCLONAL	1	FALSE	1	0.326394367789581	3		508	630	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729960	41729960	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	138	589	1	ENST00000242208.4:c.569A>C	p.Glu190Ala	p.E190A	ENST00000242208	NM_002192.2	190	gAa/gCa	3/3	0.326394367789581	5	FACETS	1	0.98	1	0.319	0.29	0.35	CLONAL	1	FALSE	1	0.326394367789581	5		590	987	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467850	50467850	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	182	338	0	ENST00000331340.3:c.1085A>G	p.Asn362Ser	p.N362S	ENST00000331340	NM_006060.4	362	aAc/aGc	8/8	0.326394367789581	5	FACETS	1	0.981	1	0.863	0.804	0.924	CLONAL	3	FALSE	1	0.326394367789581	5		338	481	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467988	50467988	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	124	352	0	ENST00000331340.3:c.1223G>C	p.Arg408Pro	p.R408P	ENST00000331340	NM_006060.4	408	cGc/cCc	8/8	0.326394367789581	5	FACETS	0.925	0.839	1	0.462	0.419	0.508	CLONAL	2	FALSE	1	0.326394367789581	5		352	612	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355239	81355239	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	104	323	0	ENST00000222390.5:c.1135C>G	p.Gln379Glu	p.Q379E	ENST00000222390	NM_000601.4	379	Caa/Gaa	9/18	0.326394367789581	6	FACETS	0.973	0.875	1	0.487	0.437	0.539	CLONAL	2	FALSE	2	0.326394367789581	6		323	541	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508883	106508883	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	37	384	0	ENST00000359195.3:c.877G>C	p.Val293Leu	p.V293L	ENST00000359195	NM_002649.2	293	Gtg/Ctg	2/11	0.326394367789581	6	FACETS	0.607	0.499	0.729	0.152	0.124	0.183	SUBCLONAL	1	FALSE	2	0.326394367789581	6		384	617	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880087	151880087	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	77	546	0	ENST00000262189.6:c.5237A>T	p.Glu1746Val	p.E1746V	ENST00000262189	NM_170606.2	1746	gAa/gTa	35/59	0.326394367789581	6	FACETS	0.875	0.767	0.992	0.219	0.191	0.248	CLONAL	1	FALSE	2	0.326394367789581	6		546	891	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549436	5549436	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	76	623	1	ENST00000397747.3:c.463T>C	p.Trp155Arg	p.W155R	ENST00000397747	NM_025239.3	155	Tgg/Cgg	4/7	0.301704365062057	3	FACETS	0.753	0.66	0.854	0.251	0.22	0.285	SUBCLONAL	1	FALSE	0	0.326394367789581	3		624	719	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916937	+	inframe_deletion	In_Frame_Del	DEL	GGCAACCGT	GGCAACCGT	-	novel	NA	P-0035714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	75	462	0	ENST00000263967.3:c.317_325del	p.Gly106_Arg108del	p.G106_R108del	ENST00000263967	NM_006218.2	106	GGCAACCGT/-	2/21	1	2	FACETS	0.659	0.579	0.744	0.659	0.579	0.744	SUBCLONAL	1	TRUE	1	0.50478976584294	2		462	451	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063669	67063669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	152	348	0	ENST00000412916.2:c.118C>T	p.Arg40Cys	p.R40C	ENST00000412916		40	Cgc/Tgc	2/6	0.50478976584294	2	FACETS	0.959	0.893	1	0.959	0.893	1	CLONAL	2	TRUE	0	0.50478976584294	2		348	314	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859690	151859690	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	79	403	0	ENST00000262189.6:c.10972C>T	p.Gln3658Ter	p.Q3658*	ENST00000262189	NM_170606.2	3658	Caa/Taa	43/59	0.50478976584294	4	FACETS	0.831	0.732	0.937	0.277	0.244	0.313	CLONAL	1	TRUE	1	0.50478976584294	4		403	567	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864343	151864344	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	433	606	0	ENST00000262189.6:c.9637dup	p.Ser3213PhefsTer3	p.S3213Ffs*3	ENST00000262189	NM_170606.2	3213	tca/tTca	42/59	0.50478976584294	4	FACETS	0.95	0.911	0.989	0.95	0.911	0.989	CLONAL	3	TRUE	1	0.50478976584294	4		606	906	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	43	272	0				ENST00000310581	NM_198253.2	-/1132			0.128420386809908	4	FACETS	1	0.937	1			1	INDETERMINATE	2	TRUE	NA	0.275449590526485	4		272	165	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0035717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9709	1539	351	1	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.275449590526485	126	FACETS	0.998	0.97	1	0.143	0.138	0.147	CLONAL	18	TRUE	0	0.275449590526485	126		352	11248	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357138	70357138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762659794	NA	P-0035717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	83	573	0	ENST00000374080.3:c.5653G>A	p.Val1885Ile	p.V1885I	ENST00000374080		1885	Gtc/Atc	39/45	0.275449590526485	0	FACETS	0.668	0.595	0.744			1	SUBCLONAL	2	TRUE	0	0.275449590526485	0		573	327	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0035717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	101	212	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	0.275449590526485	5	FACETS	1	0.946	1	0.802	0.725	0.882	CLONAL	3	TRUE	1	0.275449590526485	5		212	323	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420246	88420246	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746738110	NA	P-0035717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	96	425	0	ENST00000360948.2:c.2440C>T	p.Arg814Trp	p.R814W	ENST00000360948	NM_001012338.2	814	Cgg/Tgg	19/19	0.275449590526485	1	FACETS	0.767	0.688	0.849	1	0.982	1	SUBCLONAL	2	TRUE	0	0.275449590526485	1		425	392	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653129	29653130	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0035717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	127	315	0	ENST00000356175.3:c.5065_5066del	p.Asp1689LeufsTer7	p.D1689Lfs*7	ENST00000356175	NM_000267.3	1688	atAGac/atac	36/57	1	2	FACETS	0.835	0.765	0.907	1	0.992	1	CLONAL	3	TRUE	1	0.275449590526485	2		315	368	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663934	29663934	+	splice_donor_variant	Splice_Site	SNP	T	T	G	rs1567617158	NA	P-0035717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	110	295	0	ENST00000356175.3:c.6364+2T>G		p.X2122_splice	ENST00000356175	NM_000267.3	2122			1	2	FACETS	1	0.976	1	1	0.99	1	CLONAL	2	TRUE	1	0.275449590526485	2		295	325	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	88	812	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.76	0.677	0.847	0.76	0.677	0.847	SUBCLONAL	1	TRUE	1	0.573308392379361	2		812	404	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143548	108143548	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	83	342	0	ENST00000278616.4:c.3253G>C	p.Val1085Leu	p.V1085L	ENST00000278616	NM_000051.3	1085	Gtt/Ctt	22/63	1	2	FACETS	0.795	0.707	0.889	0.795	0.707	0.889	SUBCLONAL	1	TRUE	1	0.573308392379361	2		342	364	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582953	95582953	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	97	290	0	ENST00000393063.1:c.1589A>C	p.Lys530Thr	p.K530T	ENST00000393063	NM_030621.3	530	aAa/aCa	11/28	0.226017445687062	1	FACETS	0.764	0.689	0.842	0.764	0.689	0.842	INDETERMINATE	1	TRUE	0	0.573308392379361	1		290	316	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675094	40675094	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1340669131	NA	P-0035718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	196	561	0	ENST00000249776.8:c.58A>G	p.Thr20Ala	p.T20A	ENST00000249776	NM_033286.3	20	Aca/Gca	1/9	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.573308392379361	2		561	655	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578318	7578884	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTGGGGACCCTGGGCAACCAGCCCTGTCGTCTCTCCAGCCCCAGCTGCTCACCATCGCTATCTGAGCAGCGCTCATGGTGGGGGCAGCGCCTCACAACCTCCGTCATGTGCTGTGACTGCTTGTAGATGGCCATGGCGCGGACGCGGGTGCCGGGCGGGGGTGTGGAATCAACCCACAGCTGCACAGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAAGCAACTGGAAGACGGCAGCAAAGAAACAAACATGCGTAAGCACCTCCTGCAACCCACTAGCGAGCTAGAGAGAGTTGGCGTCTACACCTCAGGAGCTTTTCTTTTTTTTTTTTTTTTTTGAGATAGGGTCTTGCTCTGTCACTCAGGCTGGAGCACAGTGGTGTGATCACAGCTCACTGCAGCCTCCATCTCCTGGCCTCAAGTGATCTTCCCACCTCAGCCTCCTAAGTGGCTGGGACTATAGGTGTGCACCACCATGCCTGGCTAATTTTTT	CCTGGGGACCCTGGGCAACCAGCCCTGTCGTCTCTCCAGCCCCAGCTGCTCACCATCGCTATCTGAGCAGCGCTCATGGTGGGGGCAGCGCCTCACAACCTCCGTCATGTGCTGTGACTGCTTGTAGATGGCCATGGCGCGGACGCGGGTGCCGGGCGGGGGTGTGGAATCAACCCACAGCTGCACAGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAAGCAACTGGAAGACGGCAGCAAAGAAACAAACATGCGTAAGCACCTCCTGCAACCCACTAGCGAGCTAGAGAGAGTTGGCGTCTACACCTCAGGAGCTTTTCTTTTTTTTTTTTTTTTTTGAGATAGGGTCTTGCTCTGTCACTCAGGCTGGAGCACAGTGGTGTGATCACAGCTCACTGCAGCCTCCATCTCCTGGCCTCAAGTGATCTTCCCACCTCAGCCTCCTAAGTGGCTGGGACTATAGGTGTGCACCACCATGCCTGGCTAATTTTTT	-	novel	NA	P-0035718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	77	388	0	ENST00000269305.4:c.376-330_560-29del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	0.573308392379361	1	FACETS	0.731	0.65	0.816	0.731	0.65	0.816	SUBCLONAL	1	TRUE	0	0.573308392379361	1		388	262	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786421	135786421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs796053457	NA	P-0035718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	114	379	0	ENST00000298552.3:c.1109C>T	p.Ser370Leu	p.S370L	ENST00000298552	NM_001162426.1	370	tCa/tTa	11/23	1	2	FACETS	0.859	0.778	0.943	0.859	0.778	0.943	CLONAL	1	TRUE	1	0.573308392379361	2		379	463	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405630	139405630	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	182	647	0	ENST00000277541.6:c.2561C>G	p.Ser854Cys	p.S854C	ENST00000277541	NM_017617.3	854	tCc/tGc	16/34	1	2	FACETS	0.911	0.843	0.981	0.911	0.843	0.981	CLONAL	1	TRUE	1	0.573308392379361	2		647	697	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314912	1314912	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1401505455	NA	P-0035718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	90	314	0	ENST00000400841.2:c.749C>G	p.Ser250Cys	p.S250C	ENST00000400841		250	tCt/tGt	6/6	1	1	FACETS	0.833	0.749	0.919	0.833	0.749	0.919	CLONAL	1	TRUE	0	0.573308392379361	1		314	269	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0035721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	283	675	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.439657380447277	2	FACETS	0.862	0.818	0.907	0.862	0.818	0.907	CLONAL	2	TRUE	0	0.549673463217076	2		675	597	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0035721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	2074	265	0	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	0.549673463217076	24	FACETS	0.997	0.986	1			1	CLONAL	22	TRUE	NA	0.549673463217076	24		265	2425	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842450	68842450	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	142	423	0	ENST00000261769.5:c.513del	p.Pro172LeufsTer43	p.P172Lfs*43	ENST00000261769	NM_004360.3	171	Ttt/tt	4/16	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.549673463217076	2		423	512	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986994	36986994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	37	413	1	ENST00000354822.5:c.695C>T	p.Pro232Leu	p.P232L	ENST00000354822	NM_001079668.2	232	cCc/cTc	3/3	0.460212789023897	3	FACETS	0.846	0.703	1	0.423	0.351	0.502	CLONAL	1	FALSE	1	0.482868693958201	3		414	225	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56911060	56911060	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0035722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	18	487	0	ENST00000519728.1:c.1204+2T>C		p.X402_splice	ENST00000519728	NM_002350.3	402			0.284346503108545	3	FACETS	0.765	0.583	0.975	0.382	0.291	0.488	INDETERMINATE	1	FALSE	1	0.482868693958201	3		487	121	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	138	812	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	0.558356216201515	2		812	474	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113272	209113272	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	200	375	0	ENST00000345146.2:c.235G>A	p.Asp79Asn	p.D79N	ENST00000345146	NM_005896.2	79	Gat/Aat	4/10	0.314954002160822	1	FACETS	0.848	0.79	0.907	0.848	0.79	0.907	INDETERMINATE	1	TRUE	0	0.558356216201515	1		375	609	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45423008	45423008	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	145	362	0	ENST00000262160.6:c.120G>A	p.Trp40Ter	p.W40*	ENST00000262160	NM_005901.5	40	tgG/tgA	2/11	0.558356216201515	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.558356216201515	1		362	370	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238969	5238969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144851217	NA	P-0035723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	19	299	0	ENST00000357368.4:c.1810G>A	p.Ala604Thr	p.A604T	ENST00000357368	NM_002850.3	604	Gcc/Acc	13/38	0.558356216201515	1	FACETS	0.14	0.106	0.18	0.14	0.106	0.18	SUBCLONAL	1	TRUE	0	0.558356216201515	1		299	351	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5239055	5239055	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs185326821	NA	P-0035723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	264	452	0	ENST00000357368.4:c.1724C>T	p.Pro575Leu	p.P575L	ENST00000357368	NM_002850.3	575	cCg/cTg	13/38	0.558356216201515	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.558356216201515	1		452	610	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960062	134960062	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774372100	NA	P-0035723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	130	476	0	ENST00000398015.3:c.2419G>A	p.Val807Ile	p.V807I	ENST00000398015	NM_004441.4	807	Gtt/Att	13/16	0.314954002160822	1	FACETS	0.452	0.41	0.496	0.452	0.41	0.496	INDETERMINATE	1	TRUE	0	0.558356216201515	1		476	743	SUCCESS
APC	324	MSKCC	GRCh37	5	112175172	112175172	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	133	179	0	ENST00000257430.4:c.3881del	p.Gln1294ArgfsTer11	p.Q1294Rfs*11	ENST00000257430	NM_000038.5	1294	cAg/cg	16/16	0.551707439002926	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.558356216201515	2		179	231	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	175	812	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.276282819202045	4	FACETS	0.843	0.78	0.908	1	0.985	1	CLONAL	3	TRUE	2	0.290926290209919	4		812	614	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0035724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	98	289	0	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	0.267033590220471	3	FACETS	0.841	0.759	0.925	1	0.975	1	CLONAL	3	TRUE	1	0.290926290209919	3		289	306	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143462	108143462	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0035724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	109	443	0	ENST00000278616.4:c.3167C>G	p.Ser1056Ter	p.S1056*	ENST00000278616	NM_000051.3	1056	tCa/tGa	22/63	0.267033590220471	3	FACETS	0.768	0.692	0.848	0.768	0.692	0.848	SUBCLONAL	2	TRUE	1	0.290926290209919	3		443	559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0035725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	26	611	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	1	2	FACETS	0.465	0.368	0.576	0.465	0.368	0.576	SUBCLONAL	1	TRUE	1	0.29	2		611	386	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247190	153247190	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	22	303	0	ENST00000281708.4:c.1612C>T	p.Gln538Ter	p.Q538*	ENST00000281708	NM_033632.3	538	Cag/Tag	10/12	1	2	FACETS	0.584	0.453	0.734	0.584	0.453	0.734	SUBCLONAL	1	TRUE	1	0.29	2		303	260	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49054168	49054168	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	15	272	0	ENST00000267163.4:c.2748G>C	p.Met916Ile	p.M916I	ENST00000267163	NM_000321.2	916	atG/atC	27/27	1	2	FACETS	0.442	0.323	0.585	0.442	0.323	0.585	SUBCLONAL	1	TRUE	1	0.29	2		272	234	SUCCESS
AR	367	MSKCC	GRCh37	X	66765265	66765265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	14	248	0	ENST00000374690.3:c.277G>A	p.Glu93Lys	p.E93K	ENST00000374690	NM_000044.3	93	Gag/Aag	1/8	1	1	FACETS	0.513	0.372	0.681	0.513	0.372	0.681	SUBCLONAL	1	TRUE	0	0.29	1		248	161	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0035727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	184	368	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.987	0.921	1	0.987	0.921	1	CLONAL	1	TRUE	1	0.830194720005565	2		368	449	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845608	68845610	+	inframe_deletion	In_Frame_Del	DEL	CAG	CAG	-	novel	NA	P-0035727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	482	408	0	ENST00000261769.5:c.855_857del	p.Ala286del	p.A286del	ENST00000261769	NM_004360.3	285	aCAGcc/acc	7/16	NA	2	FACETS	0.968	0.944	0.991			1	INDETERMINATE	2	TRUE	NA	0.830194720005565	2		408	600	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613307	100613307	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	68	385	0	ENST00000308731.7:c.1093A>T	p.Asn365Tyr	p.N365Y	ENST00000308731	NM_000061.2	365	Aac/Tac	12/19	1	2	FACETS	0.26	0.226	0.297	0.26	0.226	0.297	SUBCLONAL	1	TRUE	1	0.830194720005565	2		385	629	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0035728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	246	755	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.763116735470314	1	FACETS	0.999	0.953	1	0.999	0.953	1	CLONAL	1	TRUE	0	0.780208381329644	1		755	385	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991706	72991706	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540253425	NA	P-0035728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	116	146	1	ENST00000268489.5:c.2339C>T	p.Ala780Val	p.A780V	ENST00000268489	NM_006885.3	780	gCg/gTg	2/10	0.780208381329644	4	FACETS	0.865	0.791	0.941	0.577	0.527	0.627	CLONAL	2	TRUE	1	0.780208381329644	4		147	306	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675668	86675668	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs983011713	NA	P-0035728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	36	226	1	ENST00000274376.6:c.2603+1G>A		p.X868_splice	ENST00000274376	NM_002890.2	868			0.763116735470314	1	FACETS	0.304	0.253	0.361	0.304	0.253	0.361	SUBCLONAL	1	TRUE	0	0.780208381329644	1		227	185	SUCCESS
APC	324	MSKCC	GRCh37	5	112175331	112175332	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGG	novel	NA	P-0035728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	76	200	0	ENST00000257430.4:c.4043_4046dup	p.His1349GlnfsTer6	p.H1349Qfs*6	ENST00000257430	NM_000038.5	1347	gcc/gcCAGGc	16/16	0.763116735470314	1	FACETS	0.808	0.732	0.884	0.808	0.732	0.884	CLONAL	1	TRUE	0	0.780208381329644	1		200	147	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	124	812	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	FALSE	1	0.300896897004169	2		812	611	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0035733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	96	433	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.114244257633603	3	FACETS	1	0.964	1	0.597	0.532	0.667	INDETERMINATE	1	TRUE	1	0.23	3		433	779	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0035733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	84	761	0	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	0.3	1	FACETS	0.691	0.609	0.78	0.691	0.609	0.78	SUBCLONAL	1	TRUE	0	0.23	1		761	935	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041657	47041657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	96	329	0	ENST00000377604.3:c.1882G>T	p.Glu628Ter	p.E628*	ENST00000377604	NM_001204468.1	628	Gag/Tag	17/24	0.15885833776819	2	FACETS	0.814	0.727	0.905			1	CLONAL	2	TRUE	NA	0.23	2		329	513	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0035734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	422	761	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.91253806327026	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.91253806327026	1		761	493	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960072	134960072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs371334171	NA	P-0035734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	688	834	0	ENST00000398015.3:c.2429A>G	p.Tyr810Cys	p.Y810C	ENST00000398015	NM_004441.4	810	tAt/tGt	13/16	0.8421234906265	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.91253806327026	3		834	1088	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796916	45796916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758262369	NA	P-0035734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	324	711	0	ENST00000450313.1:c.1414G>A	p.Gly472Ser	p.G472S	ENST00000450313	NM_012222.2	472	Ggt/Agt	14/16	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.91253806327026	2		711	655	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946211	71946211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393227840	NA	P-0035734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	341	979	0	ENST00000298229.2:c.2467C>T	p.Leu823Phe	p.L823F	ENST00000298229	NM_001567.3	823	Ctc/Ttc	22/28	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.91253806327026	2		979	746	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038934	12038934	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	202	340	0	ENST00000396373.4:c.1227G>C	p.Lys409Asn	p.K409N	ENST00000396373	NM_001987.4	409	aaG/aaC	7/8	1	2	FACETS	0.913	0.855	0.971	0.913	0.855	0.971	CLONAL	1	TRUE	1	0.91253806327026	2		340	485	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027162	49027162	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0035734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	209	384	0	ENST00000267163.4:c.1729A>T	p.Lys577Ter	p.K577*	ENST00000267163	NM_000321.2	577	Aag/Tag	18/27	0.91253806327026	1	FACETS	0.992	0.957	1	0.992	0.957	1	CLONAL	1	TRUE	0	0.91253806327026	1		384	251	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936038	178936038	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1302938521	NA	P-0035734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	46	71	0	ENST00000263967.3:c.1580A>G	p.Asp527Gly	p.D527G	ENST00000263967	NM_006218.2	527	gAc/gGc	10/21	0.8421234906265	3	FACETS	1	0.939	1	0.583	0.503	0.665	CLONAL	1	TRUE	1	0.91253806327026	3		71	126	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521460	8521460	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	335	824	0	ENST00000356435.5:c.778G>T	p.Val260Leu	p.V260L	ENST00000356435		260	Gtg/Ttg	9/35	1	2	FACETS	0.915	0.87	0.961	0.915	0.87	0.961	CLONAL	1	TRUE	1	0.91253806327026	2		824	802	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0035735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	100	368	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.387160437081773	2		368	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0035735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	181	503	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.387160437081773	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.387160437081773	1		503	677	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508439	29508439	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0035735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	17	243	0	ENST00000356175.3:c.587-1G>C		p.X196_splice	ENST00000356175	NM_000267.3	196			0.387160437081773	1	FACETS	0.216	0.161	0.282	0.216	0.161	0.282	SUBCLONAL	1	TRUE	0	0.387160437081773	1		243	328	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29115464	29115464	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555924525	NA	P-0035735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	112	349	0	ENST00000328354.6:c.602T>G	p.Phe201Cys	p.F201C	ENST00000328354	NM_007194.3	201	tTt/tGt	5/15	0.387160437081773	1	FACETS	0.968	0.875	1	0.968	0.875	1	CLONAL	1	TRUE	0	0.387160437081773	1		349	482	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620464	52620464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	127	491	1	ENST00000394830.3:c.3289G>A	p.Glu1097Lys	p.E1097K	ENST00000394830	NM_018313.4	1097	Gaa/Aaa	21/30	1	2	FACETS	0.814	0.737	0.895	0.814	0.737	0.895	CLONAL	1	TRUE	1	0.387160437081773	2		492	806	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157132	106157132	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	113	409	0	ENST00000380013.4:c.2033G>T	p.Gly678Val	p.G678V	ENST00000380013	NM_001127208.2	678	gGc/gTc	3/11	0.387160437081773	1	FACETS	0.961	0.869	1	0.961	0.869	1	CLONAL	1	TRUE	0	0.387160437081773	1		409	490	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754604	57754604	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs779187630	NA	P-0035735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	140	458	0	ENST00000274289.3:c.443A>G	p.Tyr148Cys	p.Y148C	ENST00000274289	NM_006622.3	148	tAc/tGc	3/14	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.387160437081773	2		458	692	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207132	1207134	+	frameshift_variant	Frame_Shift_Ins	INS	AGG	AGG	CTCC	novel	NA	P-0035735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	163	751	0	ENST00000326873.7:c.220_222delinsCTCC	p.Arg74LeufsTer89	p.R74Lfs*89	ENST00000326873	NM_000455.4	74	AGG/CTCC	1/10	0.387160437081773	1	FACETS	0.861	0.791	0.933	0.861	0.791	0.933	CLONAL	1	TRUE	0	0.387160437081773	1		751	789	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0035736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	85	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.274995108282118	3	FACETS	0.711	0.628	0.799	0.355	0.314	0.4	SUBCLONAL	1	TRUE	1	0.43	3		502	676	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0035736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	18	291	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.204	0.153	0.264	0.204	0.153	0.264	SUBCLONAL	1	TRUE	1	0.43	2		291	411	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0035737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	616	526	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.53451153195203	5	FACETS	1	0.987	1	1	0.987	1	CLONAL	4	TRUE	1	0.53941681478452	5		526	1002	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0035737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	378	660	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.53941681478452	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.53941681478452	2		661	655	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673671	30673671	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	174	772	0	ENST00000376406.3:c.3289G>A	p.Glu1097Lys	p.E1097K	ENST00000376406	NM_014641.2	1097	Gag/Aag	10/15	0.249584407054611	5	FACETS	1	0.974	1	0.379	0.348	0.411	INDETERMINATE	1	TRUE	2	0.53941681478452	5		772	1027	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0035739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	320	700	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.299444358064195	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.309094694331249	2		700	952	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0035739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	96	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.948	0.846	1	0.948	0.846	1	CLONAL	1	TRUE	1	0.309094694331249	2		502	655	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0035739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	62	368	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	0.309094694331249	2		368	491	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0035739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	63	353	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.994	0.863	1	0.994	0.863	1	CLONAL	1	TRUE	1	0.309094694331249	2		353	410	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453150	140453150	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913341	NA	P-0035739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	73	406	0	ENST00000288602.6:c.1785T>G	p.Phe595Leu	p.F595L	ENST00000288602	NM_004333.4	595	ttT/ttG	15/18	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.309094694331249	2		406	439	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262339	115262339	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	107	412	0	ENST00000438362.2:c.2215G>A	p.Gly739Arg	p.G739R	ENST00000438362	NM_001242891.1	739	Gga/Aga	18/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.309094694331249	2		412	601	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	495130	495130	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	95	452	0	ENST00000399788.2:c.176C>G	p.Pro59Arg	p.P59R	ENST00000399788	NM_001042603.1	59	cCt/cGt	2/28	NA	2	FACETS	1	0.916	1			1	INDETERMINATE	1	TRUE	NA	0.309094694331249	2		452	596	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281935	49281935	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	338	817	0	ENST00000282018.3:c.982G>A	p.Ala328Thr	p.A328T	ENST00000282018	NM_020377.2	328	Gca/Aca	1/1	0.243479803040752	4	FACETS	1	0.991	1	0.818	0.774	0.863	CLONAL	2	TRUE	1	0.309094694331249	4		817	1167	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805772	46805772	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	299	672	0	ENST00000290295.7:c.184C>T	p.Gln62Ter	p.Q62*	ENST00000290295	NM_006361.5	62	Caa/Taa	1/2	0.299444358064195	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.309094694331249	2		672	835	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0035742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	84	675	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.13	2		675	868	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0035742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	28	478	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.698	0.556	0.861	0.698	0.556	0.861	SUBCLONAL	1	TRUE	1	0.13	2		478	617	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673359	30673359	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs143258964	NA	P-0035742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	62	973	0	ENST00000376406.3:c.3601A>C	p.Thr1201Pro	p.T1201P	ENST00000376406	NM_014641.2	1201	Aca/Cca	10/15	1	2	FACETS	0.857	0.738	0.988	0.857	0.738	0.988	CLONAL	1	TRUE	1	0.13	2		973	1113	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068357	26068357	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	53	556	0	ENST00000435504.4:c.133G>T	p.Glu45Ter	p.E45*	ENST00000435504		45	Gaa/Taa	2/13	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.13	2		556	567	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606679	29606679	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs865931787	NA	P-0035742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	32	651	0	ENST00000389048.3:c.1201C>T	p.Arg401Ter	p.R401*	ENST00000389048	NM_004304.4	401	Cga/Tga	5/29	1	2	FACETS	0.778	0.63	0.946	0.778	0.63	0.946	CLONAL	1	TRUE	1	0.13	2		651	633	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418997	116418997	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200754673	NA	P-0035742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	21	316	0	ENST00000397752.3:c.3508C>T	p.Arg1170Ter	p.R1170*	ENST00000397752	NM_000245.2	1170	Cga/Tga	17/21	1	2	FACETS	0.923	0.71	1	0.923	0.71	1	CLONAL	1	TRUE	1	0.13	2		316	350	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007824	45007825	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0035742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	77	570	0	ENST00000558401.1:c.276dup	p.Thr93HisfsTer2	p.T93Hfs*2	ENST00000558401	NM_004048.2	91	acc/aCcc	2/4	1	2	FACETS	0.862	0.757	0.976	1	0.98	1	CLONAL	2	TRUE	1	0.13	2		570	687	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374881	45374881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	38	802	0	ENST00000262160.6:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000262160	NM_005901.5	321	cGa/cAa	8/11	1	2	FACETS	0.799	0.658	0.956	0.799	0.658	0.956	CLONAL	1	TRUE	1	0.13	2		802	732	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0035742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	39	608	0	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.13	2		608	582	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473635	67473635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906853	NA	P-0035742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	84	721	0	ENST00000327367.4:c.715G>A	p.Glu239Lys	p.E239K	ENST00000327367	NM_005902.3	239	Gag/Aag	6/9	1	2	FACETS	0.826	0.729	0.931	1	0.98	1	CLONAL	2	TRUE	1	0.13	2		721	782	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680780	88680780	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	57	768	0	ENST00000360948.2:c.477G>T	p.Gln159His	p.Q159H	ENST00000360948	NM_001012338.2	159	caG/caT	6/19	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.13	2		768	787	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615593	43615593	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	39	687	1	ENST00000355710.3:c.2672C>T	p.Ser891Leu	p.S891L	ENST00000355710	NM_020975.4	891	tCg/tTg	15/20	1	2	FACETS	0.783	0.647	0.936	0.783	0.647	0.936	CLONAL	1	TRUE	1	0.13	2		688	766	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149447833	149447833	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	45	792	0	ENST00000286301.3:c.1571C>T	p.Ser524Phe	p.S524F	ENST00000286301	NM_005211.3	524	tCc/tTc	11/22	1	2	FACETS	0.842	0.706	0.994	0.842	0.706	0.994	CLONAL	1	TRUE	1	0.13	2		792	822	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281952	142281952	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0035742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	32	390	0	ENST00000350721.4:c.293-1G>T		p.X98_splice	ENST00000350721	NM_001184.3	98			1	2	FACETS	0.954	0.773	1	0.954	0.773	1	CLONAL	1	TRUE	1	0.13	2		390	516	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670340	134670340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415689583	NA	P-0035742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	30	512	2	ENST00000398015.3:c.251G>A	p.Arg84His	p.R84H	ENST00000398015	NM_004441.4	84	cGc/cAc	3/16	1	2	FACETS	0.855	0.687	1	0.855	0.687	1	CLONAL	1	TRUE	1	0.13	2		514	540	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054649	5054649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373174105	NA	P-0035742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	32	384	0	ENST00000381652.3:c.701G>A	p.Arg234His	p.R234H	ENST00000381652	NM_004972.3	234	cGc/cAc	7/25	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.13	2		384	448	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371711	45371711	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	41	481	0	ENST00000262160.6:c.1280G>A	p.Arg427Gln	p.R427Q	ENST00000262160	NM_005901.5	427	cGa/cAa	10/11	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.13	2		481	512	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437463	110437463	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	49	775	2	ENST00000375856.3:c.938C>T	p.Ala313Val	p.A313V	ENST00000375856	NM_003749.2	313	gCc/gTc	1/2	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.13	2		777	727	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81968046	81968046	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	23	382	0	ENST00000359376.3:c.2752A>C	p.Lys918Gln	p.K918Q	ENST00000359376	NM_002661.3	918	Aag/Cag	26/33	1	2	FACETS	0.823	0.64	1	0.823	0.64	1	CLONAL	1	TRUE	1	0.13	2		382	430	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40458326	40458326	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	12	256	0	ENST00000345506.4:c.1541A>C	p.Lys514Thr	p.K514T	ENST00000345506	NM_003152.3	514	aAa/aCa	14/20	1	2	FACETS	0.81	0.569	1	0.81	0.569	1	CLONAL	1	TRUE	1	0.13	2		256	228	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761400	59761400	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	39	596	0	ENST00000259008.2:c.3007T>C	p.Ser1003Pro	p.S1003P	ENST00000259008	NM_032043.2	1003	Tca/Cca	20/20	1	2	FACETS	0.906	0.749	1	0.906	0.749	1	CLONAL	1	TRUE	1	0.13	2		596	662	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245519	153245519	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	31	488	0	ENST00000281708.4:c.1672T>C	p.Ser558Pro	p.S558P	ENST00000281708	NM_033632.3	558	Tct/Cct	11/12	1	2	FACETS	0.93	0.751	1	0.93	0.751	1	CLONAL	1	TRUE	1	0.13	2		488	513	SUCCESS
APC	324	MSKCC	GRCh37	5	112178904	112178904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	27	388	0	ENST00000257430.4:c.7613G>A	p.Arg2538Lys	p.R2538K	ENST00000257430	NM_000038.5	2538	aGa/aAa	16/16	1	2	FACETS	0.873	0.693	1	0.873	0.693	1	CLONAL	1	TRUE	1	0.13	2		388	476	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140508700	140508700	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	40	625	0	ENST00000288602.6:c.600T>G	p.Ile200Met	p.I200M	ENST00000288602	NM_004333.4	200	atT/atG	4/18	1	2	FACETS	0.893	0.74	1	0.893	0.74	1	CLONAL	1	TRUE	1	0.13	2		625	689	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913237	NA	P-0035743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	16	340	0	ENST00000369535.4:c.35G>C	p.Gly12Ala	p.G12A	ENST00000369535	NM_002524.4	12	gGt/gCt	2/7	1	2	FACETS	0.058	0.042	0.077	0.058	0.042	0.077	SUBCLONAL	1	TRUE	1	0.83667997894546	2		340	658	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892272	9892272	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	182	359	0	ENST00000330684.3:c.2218G>T	p.Gly740Trp	p.G740W	ENST00000330684	NM_001134407.1	740	Ggg/Tgg	11/13	0.202436046663999	1	FACETS	0.482	0.448	0.517	0.482	0.448	0.517	INDETERMINATE	1	TRUE	0	0.83667997894546	1		359	525	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55335700	55335700	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	319	601	0	ENST00000284073.2:c.255G>C	p.Glu85Asp	p.E85D	ENST00000284073	NM_138962.2	85	gaG/gaC	4/14	0.338361403624865	3	FACETS	0.826	0.779	0.875			1	INDETERMINATE	1	TRUE	NA	0.83667997894546	3		601	1309	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724450	724450	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1219050353	NA	P-0035743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	265	750	0	ENST00000314574.4:c.1606C>T	p.Gln536Ter	p.Q536*	ENST00000314574	NM_005433.3	536	Cag/Tag	12/12	1	2	FACETS	0.596	0.559	0.634	0.596	0.559	0.634	SUBCLONAL	1	TRUE	1	0.83667997894546	2		750	1063	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099982	157099993	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGCGGC	GGCGGCGGCGGC	-	rs587779747	NA	P-0035743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	155	196	0	ENST00000346085.5:c.933_944del	p.Gly316_Gly319del	p.G316_G319del	ENST00000346085	NM_020732.3	307	GGCGGCGGCGGC/-	1/20	0.83667997894546	1	FACETS	0.813	0.763	0.863	0.813	0.763	0.863	CLONAL	1	TRUE	0	0.83667997894546	1		196	265	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595395	141595395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150671066	NA	P-0035743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1719	291	441	1	ENST00000220592.5:c.38C>T	p.Ala13Val	p.A13V	ENST00000220592	NM_012154.3	13	gCg/gTg	2/19	0.83667997894546	7	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.83667997894546	7		442	2010	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448571	89448571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	196	485	2	ENST00000336596.2:c.1535G>A	p.Arg512Gln	p.R512Q	ENST00000336596	NM_005233.5	512	cGa/cAa	7/17	1	2	FACETS	0.896	0.831	0.962	1	0.993	1	CLONAL	2	FALSE	1	0.280175181824718	2		487	781	SUCCESS
APC	324	MSKCC	GRCh37	5	112175720	112175720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	154	316	0	ENST00000257430.4:c.4429C>T	p.Gln1477Ter	p.Q1477*	ENST00000257430	NM_000038.5	1477	Cag/Tag	16/16	0.265960750071168	0	FACETS	0.723	0.67	0.776			1	SUBCLONAL	3	FALSE	0	0.280175181824718	0		316	365	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061228	38061228	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	210	553	0	ENST00000250448.2:c.761del	p.Phe254SerfsTer67	p.F254Sfs*67	ENST00000250448	NM_004496.3	254	tTc/tc	2/2	1	2	FACETS	0.86	0.799	0.922	1	0.993	1	CLONAL	2	FALSE	1	0.280175181824718	2		553	872	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456351	32456351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	279	719	1	ENST00000332351.3:c.541G>A	p.Gly181Ser	p.G181S	ENST00000332351	NM_024426.4	181	Ggt/Agt	1/10	1	2	FACETS	1	0.978	1	1	0.996	1	CLONAL	2	FALSE	1	0.280175181824718	2		720	925	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911544	32911544	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0035746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	86	338	0	ENST00000380152.3:c.3052A>T	p.Lys1018Ter	p.K1018*	ENST00000380152		1018	Aag/Tag	11/27	0.280175181824718	0	FACETS	0.658	0.587	0.732			1	SUBCLONAL	2	FALSE	0	0.280175181824718	0		338	336	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0035748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	455	368	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.261085817112364	7	FACETS	1	0.989	1	1	0.996	1	CLONAL	8	TRUE	0	0.261085817112364	7		368	684	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0035748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	135	596	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.261085817112364	3	FACETS	0.835	0.76	0.913	0.835	0.76	0.913	CLONAL	2	TRUE	1	0.261085817112364	3		597	700	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496924	29496927	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs786201874	NA	P-0035748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	107	410	0	ENST00000356175.3:c.499_502del	p.Cys167GlnfsTer10	p.C167Qfs*10	ENST00000356175	NM_000267.3	165	acTGTT/ac	5/57	0.261085817112364	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.261085817112364	3		410	389	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827956	72827956	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	68	979	0	ENST00000268489.5:c.8625G>C	p.Leu2875Phe	p.L2875F	ENST00000268489	NM_006885.3	2875	ttG/ttC	9/10	0.253611139325603	2	FACETS	0.776	0.675	0.886	0.388	0.337	0.443	SUBCLONAL	1	TRUE	0	0.261085817112364	2		979	671	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828038	72828038	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	89	1009	0	ENST00000268489.5:c.8543G>C	p.Gly2848Ala	p.G2848A	ENST00000268489	NM_006885.3	2848	gGa/gCa	9/10	0.253611139325603	2	FACETS	0.903	0.8	1	0.452	0.4	0.507	CLONAL	1	TRUE	0	0.261085817112364	2		1009	755	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	47	391	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	0.252562013796542	1	FACETS	0.772	0.653	0.904	0.772	0.653	0.904	CLONAL	1	TRUE	0	0.252562013796542	1		392	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	70	660	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.726	0.632	0.827	0.726	0.632	0.827	SUBCLONAL	1	TRUE	1	0.252562013796542	2		661	764	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	64	431	0	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.252562013796542	2		431	423	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857910	9857910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	94	621	0	ENST00000330684.3:c.3491C>T	p.Thr1164Met	p.T1164M	ENST00000330684	NM_001134407.1	1164	aCg/aTg	13/13	0.252562013796542	3	FACETS	1	0.926	1	0.527	0.468	0.589	CLONAL	1	TRUE	1	0.252562013796542	3		621	796	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279325	18279325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	51	475	0	ENST00000222254.8:c.1777G>A	p.Glu593Lys	p.E593K	ENST00000222254	NM_005027.3	593	Gag/Aag	14/16	1	2	FACETS	0.784	0.667	0.913	0.784	0.667	0.913	CLONAL	1	TRUE	1	0.252562013796542	2		475	515	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032062	26032062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	111	388	0	ENST00000244661.2:c.227C>T	p.Ala76Val	p.A76V	ENST00000244661	NM_003537.3	76	gCc/gTc	1/1	0.234634647414697	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.252562013796542	2		388	415	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273974	10273974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773569899	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	116	788	1	ENST00000330684.3:c.295G>A	p.Val99Met	p.V99M	ENST00000330684	NM_001134407.1	99	Gtg/Atg	2/13	0.252562013796542	3	FACETS	1	0.965	1	0.58	0.522	0.641	CLONAL	1	TRUE	1	0.252562013796542	3		789	892	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759406	133759406	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1371645607	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	105	629	0	ENST00000318560.5:c.1729C>T	p.Arg577Ter	p.R577*	ENST00000318560	NM_005157.4	577	Cga/Tga	11/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.252562013796542	2		629	699	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683508	182683508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	51	536	0	ENST00000292782.4:c.37C>T	p.Arg13Cys	p.R13C	ENST00000292782	NM_020640.2	13	Cgt/Tgt	2/7	0.252562013796542	3	FACETS	0.55	0.466	0.643	0.275	0.233	0.322	SUBCLONAL	1	TRUE	1	0.252562013796542	3		536	827	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138382756	138382756	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	162	495	1	ENST00000289153.2:c.2788del	p.Thr930LeufsTer62	p.T930Lfs*62	ENST00000289153	NM_006219.2	930	Act/ct	19/22	0.252562013796542	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.252562013796542	3		496	665	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614463	38614463	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	58	480	0	ENST00000299084.4:c.234del	p.Asp79ThrfsTer42	p.D79Tfs*42	ENST00000299084	NM_152594.2	77	Aaa/aa	3/7	1	2	FACETS	0.776	0.666	0.895	0.776	0.666	0.895	SUBCLONAL	1	TRUE	1	0.252562013796542	2		480	592	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214398	36214398	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs868041281	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	61	495	1	ENST00000222270.7:c.3057del	p.Gly1020AlafsTer4	p.G1020Afs*4	ENST00000222270	NM_014727.1	1018	Aaa/aa	7/37	1	2	FACETS	0.775	0.669	0.892	0.775	0.669	0.892	SUBCLONAL	1	TRUE	1	0.252562013796542	2		496	623	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438211	49438211	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	105	756	1	ENST00000301067.7:c.5058del	p.Lys1686AsnfsTer36	p.K1686Nfs*36	ENST00000301067	NM_003482.3	1686	aaA/aa	20/54	1	2	FACETS	0.892	0.798	0.992	0.892	0.798	0.992	CLONAL	1	TRUE	1	0.252562013796542	2		757	932	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643348	52643348	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	57	459	0	ENST00000394830.3:c.2548C>T	p.Arg850Ter	p.R850*	ENST00000394830	NM_018313.4	850	Cga/Tga	17/30	0.252562013796542	1	FACETS	0.876	0.754	1	0.876	0.754	1	CLONAL	1	TRUE	0	0.252562013796542	1		459	450	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437711	49437713	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs886049482	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	62	774	0	ENST00000301067.7:c.5257_5259del	p.Lys1753del	p.K1753del	ENST00000301067	NM_003482.3	1753	AAG/-	22/54	1	2	FACETS	0.603	0.52	0.694	0.603	0.52	0.694	SUBCLONAL	1	TRUE	1	0.252562013796542	2		774	814	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814964	43814964	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	46	478	0	ENST00000372470.3:c.1499T>C	p.Leu500Pro	p.L500P	ENST00000372470	NM_005373.2	500	cTa/cCa	10/12	1	2	FACETS	0.689	0.58	0.809	0.689	0.58	0.809	SUBCLONAL	1	TRUE	1	0.252562013796542	2		478	529	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562930	95562930	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	36	374	0	ENST00000393063.1:c.4327C>A	p.Leu1443Met	p.L1443M	ENST00000393063	NM_030621.3	1443	Ctg/Atg	24/28	1	2	FACETS	0.685	0.564	0.822	0.685	0.564	0.822	SUBCLONAL	1	TRUE	1	0.252562013796542	2		374	416	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341217	341217	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	87	685	0	ENST00000262320.3:c.2267T>C	p.Val756Ala	p.V756A	ENST00000262320	NM_003502.3	756	gTg/gCg	9/11	0.252562013796542	3	FACETS	0.943	0.834	1	0.471	0.417	0.53	CLONAL	1	TRUE	1	0.252562013796542	3		685	823	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858087	9858087	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	91	722	0	ENST00000330684.3:c.3314A>G	p.Tyr1105Cys	p.Y1105C	ENST00000330684	NM_001134407.1	1105	tAc/tGc	13/13	0.252562013796542	3	FACETS	1	0.906	1	0.512	0.454	0.574	CLONAL	1	TRUE	1	0.252562013796542	3		722	793	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992063	72992063	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1464416233	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	71	627	0	ENST00000268489.5:c.1982T>C	p.Met661Thr	p.M661T	ENST00000268489	NM_006885.3	661	aTg/aCg	2/10	0.252562013796542	3	FACETS	0.945	0.825	1	0.473	0.412	0.538	CLONAL	1	TRUE	1	0.252562013796542	3		627	670	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347676	89347676	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	66	575	0	ENST00000301030.4:c.5274del	p.Ser1759ProfsTer204	p.S1759Pfs*204	ENST00000301030	NM_001256183.1	1758	ccC/cc	9/13	0.252562013796542	3	FACETS	1	0.882	1	0.508	0.441	0.581	CLONAL	1	TRUE	1	0.252562013796542	3		575	579	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359635	40359635	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776285574	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	98	641	1	ENST00000293328.3:c.2018G>A	p.Arg673Gln	p.R673Q	ENST00000293328	NM_012448.3	673	cGg/cAg	16/19	1	2	FACETS	0.91	0.811	1	0.91	0.811	1	CLONAL	1	TRUE	1	0.252562013796542	2		642	853	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265365	10265365	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	64	683	0	ENST00000340748.4:c.1681G>A	p.Val561Met	p.V561M	ENST00000340748		561	Gtg/Atg	20/40	1	2	FACETS	0.728	0.63	0.835	0.728	0.63	0.835	SUBCLONAL	1	TRUE	1	0.252562013796542	2		683	696	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313364	30313364	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	74	628	0	ENST00000262643.3:c.964T>C	p.Cys322Arg	p.C322R	ENST00000262643	NM_001238.2	322	Tgc/Cgc	11/12	1	2	FACETS	0.811	0.709	0.92	0.811	0.709	0.92	CLONAL	1	TRUE	1	0.252562013796542	2		628	723	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727934	41727934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748904765	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	78	619	1	ENST00000301178.4:c.559G>A	p.Gly187Ser	p.G187S	ENST00000301178	NM_021913.4	187	Ggc/Agc	4/20	1	2	FACETS	0.993	0.873	1	0.993	0.873	1	CLONAL	1	TRUE	1	0.252562013796542	2		620	622	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383609	42383610	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	58	397	1	ENST00000221972.3:c.390dup	p.Arg131GlnfsTer51	p.R131Qfs*51	ENST00000221972	NM_021601.3	128	-/C	3/5	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.252562013796542	2		398	357	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99136527	99136527	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	72	626	0	ENST00000074304.5:c.16C>T	p.His6Tyr	p.H6Y	ENST00000074304	NM_001134224.1	6	Cac/Tac	3/26	1	2	FACETS	0.912	0.797	1	0.912	0.797	1	CLONAL	1	TRUE	1	0.252562013796542	2		626	625	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215274	142215274	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	49	550	0	ENST00000350721.4:c.5827G>C	p.Ala1943Pro	p.A1943P	ENST00000350721	NM_001184.3	1943	Gct/Cct	34/47	0.252562013796542	3	FACETS	0.606	0.512	0.71	0.303	0.256	0.355	SUBCLONAL	1	TRUE	1	0.252562013796542	3		550	721	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808588	1808588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs555257146	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	79	793	3	ENST00000260795.2:c.2201C>T	p.Ala734Val	p.A734V	ENST00000260795		734	gCg/gTg	16/17	1	2	FACETS	0.876	0.77	0.99	0.876	0.77	0.99	CLONAL	1	TRUE	1	0.252562013796542	2		796	714	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685290	86685290	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	38	222	0	ENST00000274376.6:c.3006C>A	p.Cys1002Ter	p.C1002*	ENST00000274376	NM_002890.2	1002	tgC/tgA	24/25	1	2	FACETS	0.958	0.795	1	0.958	0.795	1	CLONAL	1	TRUE	1	0.252562013796542	2		222	314	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358966	81358966	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	78	550	0	ENST00000222390.5:c.995A>G	p.Gln332Arg	p.Q332R	ENST00000222390	NM_000601.4	332	cAg/cGg	8/18	1	2	FACETS	0.934	0.821	1	0.934	0.821	1	CLONAL	1	TRUE	1	0.252562013796542	2		550	661	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509226	106509226	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	70	550	0	ENST00000359195.3:c.1220A>T	p.Glu407Val	p.E407V	ENST00000359195	NM_002649.2	407	gAg/gTg	2/11	1	2	FACETS	0.883	0.77	1	0.883	0.77	1	CLONAL	1	TRUE	1	0.252562013796542	2		550	628	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511214	148511214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	77	470	0	ENST00000320356.2:c.1688C>T	p.Pro563Leu	p.P563L	ENST00000320356	NM_004456.4	563	cCg/cTg	15/20	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.252562013796542	2		470	579	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859800	151859800	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	49	389	0	ENST00000262189.6:c.10862C>T	p.Ala3621Val	p.A3621V	ENST00000262189	NM_170606.2	3621	gCt/gTt	43/59	1	2	FACETS	0.956	0.811	1	0.956	0.811	1	CLONAL	1	TRUE	1	0.252562013796542	2		389	406	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864557	56864557	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	97	720	0	ENST00000519728.1:c.520C>T	p.Pro174Ser	p.P174S	ENST00000519728	NM_002350.3	174	Cct/Tct	7/13	0.252562013796542	3	FACETS	0.96	0.855	1	0.48	0.427	0.537	CLONAL	1	TRUE	1	0.252562013796542	3		720	901	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949093	44949094	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGATAAATGCAGGCACTGTT	novel	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	30	332	0	ENST00000377967.4:c.3655_3675dup	p.Trp1219_Val1225dup	p.W1219_V1225dup	ENST00000377967	NM_021140.2	1219	-/TGGATAAATGCAGGCACTGTT	25/29	1	1	FACETS	0.485	0.39	0.592	0.485	0.39	0.592	SUBCLONAL	1	TRUE	0	0.252562013796542	1		332	428	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035901	47035904	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CTCC	CTCC	-	novel	NA	P-0035750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	79	384	0	ENST00000377604.3:c.582_585del	p.Leu195ThrfsTer70	p.L195Tfs*70	ENST00000377604	NM_001204468.1	193	caCTCC/ca	7/24	1	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.252562013796542	1		384	393	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994410	25994410	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0035752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	14	323	0	ENST00000435504.4:c.404-1G>T		p.X135_splice	ENST00000435504		135			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		323	242	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099332	193099332	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	73	355	0	ENST00000367435.3:c.266C>T	p.Pro89Leu	p.P89L	ENST00000367435	NM_024529.4	89	cCt/cTt	3/17	0.613940566133044	5	FACETS	0.649	0.567	0.737	0.13	0.113	0.148	SUBCLONAL	1	TRUE	0	0.613940566133044	5		355	704	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578463	7578463	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371524413	NA	P-0035753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	365	733	0	ENST00000269305.4:c.467G>C	p.Arg156Pro	p.R156P	ENST00000269305	NM_001126112.2	156	cGc/cCc	5/11	0.613940566133044	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.613940566133044	2		733	585	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099346	193099346	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	80	372	0	ENST00000367435.3:c.280C>A	p.Leu94Ile	p.L94I	ENST00000367435	NM_024529.4	94	Cta/Ata	3/17	0.613940566133044	5	FACETS	0.68	0.598	0.768	0.136	0.119	0.154	SUBCLONAL	1	TRUE	0	0.613940566133044	5		372	736	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523043	25523043	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	151	709	0	ENST00000264709.3:c.142G>T	p.Val48Leu	p.V48L	ENST00000264709	NM_175629.2	48	Gtg/Ttg	3/23	0.613940566133044	6	FACETS	1	0.924	1	0.253	0.231	0.277	CLONAL	1	TRUE	2	0.613940566133044	6		709	1082	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696738	176696738	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	138	390	0	ENST00000439151.2:c.5441del	p.Pro1814LeufsTer7	p.P1814Lfs*7	ENST00000439151	NM_022455.4	1813	ttC/tt	16/23	0.613940566133044	5	FACETS	1	0.975	1	0.297	0.271	0.325	CLONAL	1	TRUE	1	0.613940566133044	5		390	726	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854906	76854906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	52	602	0	ENST00000373344.5:c.5930C>T	p.Pro1977Leu	p.P1977L	ENST00000373344	NM_000489.3	1977	cCt/cTt	25/35	0.613940566133044	1	FACETS	0.291	0.248	0.337	0.291	0.248	0.337	SUBCLONAL	1	TRUE	0	0.613940566133044	1		602	404	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0035754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	99	673	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.786	0.703	0.873	0.786	0.703	0.873	SUBCLONAL	1	TRUE	1	0.455708820497206	2		673	553	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0035754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	63	319	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.455708820497206	1	FACETS	0.893	0.782	1	0.893	0.782	1	CLONAL	1	TRUE	0	0.455708820497206	1		319	239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0035754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	275	824	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.455708820497206	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.455708820497206	1		824	786	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0035756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	161	903	3	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.804924627411141	1	FACETS	0.916	0.862	0.968	0.916	0.862	0.968	CLONAL	1	FALSE	0	0.804924627411141	1		906	261	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860345	42860345	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1385130606	NA	P-0035756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	201	721	0	ENST00000398585.3:c.532G>A	p.Gly178Ser	p.G178S	ENST00000398585	NM_001135099.1	178	Ggc/Agc	5/14	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.804924627411141	2		721	475	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333041	70333041	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	225	799	0	ENST00000373644.4:c.946G>T	p.Ala316Ser	p.A316S	ENST00000373644	NM_030625.2	316	Gct/Tct	2/12	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.804924627411141	2		799	527	SUCCESS
ATM	472	MSKCC	GRCh37	11	108127041	108127041	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0035756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	164	555	0	ENST00000278616.4:c.2224A>T	p.Lys742Ter	p.K742*	ENST00000278616	NM_000051.3	742	Aag/Tag	14/63	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.804924627411141	2		555	367	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434584	99434585	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0035756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	130	563	2	ENST00000268035.6:c.671_672delinsTT	p.Cys224Phe	p.C224F	ENST00000268035	NM_000875.3	224	tGC/tTT	3/21	1	2	FACETS	0.861	0.79	0.935	0.861	0.79	0.935	CLONAL	1	FALSE	1	0.804924627411141	2		565	375	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973220	25973220	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	151	488	0	ENST00000435504.4:c.1205A>G	p.Lys402Arg	p.K402R	ENST00000435504		402	aAg/aGg	12/13	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.804924627411141	2		488	354	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520257	9520257	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	118	420	0	ENST00000353224.5:c.2012C>A	p.Ser671Ter	p.S671*	ENST00000353224	NM_177990.2	671	tCa/tAa	10/10	1	2	FACETS	0.878	0.802	0.956	0.878	0.802	0.956	CLONAL	1	FALSE	1	0.804924627411141	2		420	334	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829791	76829791	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	202	555	0	ENST00000373344.5:c.6250T>G	p.Tyr2084Asp	p.Y2084D	ENST00000373344	NM_000489.3	2084	Tac/Gac	28/35	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.671838806828516	2		555	572	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829791	76829791	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035760-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	55	555	0	ENST00000373344.5:c.6250T>G	p.Tyr2084Asp	p.Y2084D	ENST00000373344	NM_000489.3	2084	Tac/Gac	28/35	1	2	FACETS	1	0.951	1	1	0.98	1	CLONAL	2	FALSE	1	0.166462633103826	2		555	267	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0035761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	61	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	224	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0035762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	138	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.371569333477071	5	FACETS	0.954	0.884	1			1	CLONAL	4	TRUE	NA	0.371569333477071	5		502	303	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0035762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	44	673	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.371569333477071	2		673	231	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731140	162731140	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752360996	NA	P-0035762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	48	404	0	ENST00000367921.3:c.995G>A	p.Arg332Gln	p.R332Q	ENST00000367921	NM_006182.2	332	cGg/cAg	9/18	0.371569333477071	3	FACETS	0.744	0.63	0.868	0.372	0.315	0.434	SUBCLONAL	1	TRUE	1	0.371569333477071	3		404	412	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717726	89717726	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	41	316	0	ENST00000371953.3:c.751G>A	p.Gly251Ser	p.G251S	ENST00000371953	NM_000314.4	251	Ggt/Agt	7/9	1	2	FACETS	0.897	0.753	1	0.897	0.753	1	CLONAL	1	TRUE	1	0.371569333477071	2		316	246	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771314	68771331	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	CAGCCATGGGCCCTTGGA	CAGCCATGGGCCCTTGGA	GG	novel	NA	P-0035762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	13	172	2	ENST00000261769.5:c.-5_13delinsGG		p.*2*	ENST00000261769	NM_004360.3	?-5/882		1/16	0.324983398624271	1	FACETS	0.564	0.407	0.751	0.564	0.407	0.751	SUBCLONAL	1	TRUE	0	0.371569333477071	1		174	101	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838030	156838030	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	291	710	39	ENST00000524377.1:c.563A>T	p.Asn188Ile	p.N188I	ENST00000524377	NM_002529.3	188	aAt/aTt	5/17	1	2	FACETS	0.946	0.9	0.993	1	0.996	1	CLONAL	3	TRUE	1	0.35407341378002	2		749	579	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169401	11169401	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	109	491	0	ENST00000361445.4:c.7474G>T	p.Ala2492Ser	p.A2492S	ENST00000361445	NM_004958.3	2492	Gcc/Tcc	56/58	0.190900709944084	4	FACETS	1	0.971	1	0.805	0.725	0.889	CLONAL	2	TRUE	1	0.190900709944084	4		491	563	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0035765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	311	519	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	0.907092910532538	2		519	669	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831201	72831201	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	229	441	0	ENST00000268489.5:c.5380C>T	p.Gln1794Ter	p.Q1794*	ENST00000268489	NM_006885.3	1794	Cag/Tag	9/10	1	2	FACETS	0.965	0.909	1	0.965	0.909	1	CLONAL	1	TRUE	1	0.907092910532538	2		441	523	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061211	38061211	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	806	496	0	ENST00000250448.2:c.778T>G	p.Leu260Val	p.L260V	ENST00000250448	NM_004496.3	260	Ttg/Gtg	2/2	0.907092910532538	4	FACETS	1	0.983	1			1	CLONAL	3	TRUE	NA	0.907092910532538	4		496	1122	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76954101	76954122	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGAACCACTGATTTTATCTAAA	AGAACCACTGATTTTATCTAAA	-	novel	NA	P-0035765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	401	224	0	ENST00000373344.5:c.134-5_150del		p.X45_splice	ENST00000373344	NM_000489.3	45		3/35	0.907092910532538	2	FACETS	0.98	0.96	0.999			1	CLONAL	2	TRUE	NA	0.907092910532538	2		224	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0035769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	119	675	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.386946761626284	2	FACETS	1	0.966	1	0.56	0.511	0.61	CLONAL	1	TRUE	0	0.595397676524458	2		675	357	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0035769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	625	652	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.595397676524458	12	FACETS	1	0.994	1			1	CLONAL	11	TRUE	NA	0.595397676524458	12		652	734	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949157	71949157	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	114	822	0	ENST00000298229.2:c.3624C>G	p.Ile1208Met	p.I1208M	ENST00000298229	NM_001567.3	1208	atC/atG	27/28	0.544092716029263	1	FACETS	0.409	0.368	0.451	0.409	0.368	0.451	SUBCLONAL	1	TRUE	0	0.595397676524458	1		822	658	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291097	10291097	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	40	758	0	ENST00000340748.4:c.374C>G	p.Ala125Gly	p.A125G	ENST00000340748		125	gCc/gGc	4/40	0.507376711116249	1	FACETS	0.254	0.211	0.301	0.254	0.211	0.301	SUBCLONAL	1	TRUE	0	0.595397676524458	1		758	372	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375213	15375213	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0035769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	56	511	0	ENST00000263377.2:c.1212+2T>G		p.X404_splice	ENST00000263377	NM_058243.2	404			0.507376711116249	1	FACETS	0.47	0.406	0.539	0.47	0.406	0.539	SUBCLONAL	1	TRUE	0	0.595397676524458	1		511	281	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319707	62319707	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	111	856	0	ENST00000360203.5:c.1690C>A	p.Pro564Thr	p.P564T	ENST00000360203	NM_001283009.1	564	Cct/Act	20/35	0.396431418597786	1	FACETS	0.321	0.288	0.356	0.321	0.288	0.356	SUBCLONAL	1	TRUE	0	0.595397676524458	1		856	816	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692922	89692922	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201044	NA	P-0035771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	332	463	0	ENST00000371953.3:c.406T>C	p.Cys136Arg	p.C136R	ENST00000371953	NM_000314.4	136	Tgt/Cgt	5/9	0.776760335455021	3	FACETS	0.946	0.904	0.988	0.631	0.602	0.659	CLONAL	2	TRUE	0	0.787792563618362	3		463	621	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0035771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	238	581	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.839	0.787	0.893	0.839	0.787	0.893	CLONAL	1	TRUE	1	0.787792563618362	2		581	720	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	169	363	0	ENST00000397062.3:c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	NM_006164.4	34	Cga/Gga	2/5	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.787792563618362	2		363	409	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675268	176675269	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	139	445	0	ENST00000439151.2:c.4591dup	p.Met1531AsnfsTer4	p.M1531Nfs*4	ENST00000439151	NM_022455.4	1528	-/A	11/23	1	2	FACETS	0.824	0.757	0.894	0.824	0.757	0.894	CLONAL	1	TRUE	1	0.787792563618362	2		445	428	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519886	NA	P-0035771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	84	316	0	ENST00000349496.5:c.97T>C	p.Ser33Pro	p.S33P	ENST00000349496	NM_001904.3	33	Tct/Cct	3/15	1	2	FACETS	0.485	0.43	0.543	0.485	0.43	0.543	SUBCLONAL	1	TRUE	1	0.787792563618362	2		316	440	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0035771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	895	570	0	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	0.776760335455021	3	FACETS	0.977	0.96	0.993	0.977	0.96	0.993	CLONAL	3	TRUE	0	0.787792563618362	3		570	1081	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121909229	NA	P-0035771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	137	426	0	ENST00000371953.3:c.389G>T	p.Arg130Leu	p.R130L	ENST00000371953	NM_000314.4	130	cGa/cTa	5/9	0.776760335455021	3	FACETS	0.805	0.735	0.878	0.268	0.245	0.293	CLONAL	1	TRUE	0	0.787792563618362	3		426	602	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149516594	149516594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150173975	NA	P-0035771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	78	736	4	ENST00000261799.4:c.17C>T	p.Ala6Val	p.A6V	ENST00000261799	NM_002609.3	6	gCg/gTg	2/23	1	2	FACETS	0.232	0.203	0.263	0.232	0.203	0.263	SUBCLONAL	1	TRUE	1	0.787792563618362	2		740	855	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303288	11303288	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199646229	NA	P-0035771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	265	647	3	ENST00000361445.4:c.1295C>T	p.Ala432Val	p.A432V	ENST00000361445	NM_004958.3	432	gCg/gTg	9/58	1	2	FACETS	0.835	0.785	0.885	0.835	0.785	0.885	CLONAL	1	TRUE	1	0.787792563618362	2		650	806	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436066	56436066	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	37	513	0	ENST00000407977.2:c.1071C>A	p.Tyr357Ter	p.Y357*	ENST00000407977		357	taC/taA	9/10	1	2	FACETS	0.168	0.138	0.202	0.168	0.138	0.202	SUBCLONAL	1	TRUE	1	0.787792563618362	2		513	559	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610258	10610258	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	181	761	3	ENST00000171111.5:c.452G>A	p.Cys151Tyr	p.C151Y	ENST00000171111	NM_203500.1	151	tGt/tAt	2/6	1	2	FACETS	0.455	0.42	0.493	0.455	0.42	0.493	SUBCLONAL	1	TRUE	1	0.787792563618362	2		764	1009	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858221	27858221	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	202	569	0	ENST00000359303.2:c.350G>T	p.Arg117Leu	p.R117L	ENST00000359303	NM_003535.2	117	cGt/cTt	1/1	1	2	FACETS	0.85	0.793	0.909	0.85	0.793	0.909	CLONAL	1	TRUE	1	0.787792563618362	2		569	603	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023864	27023865	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	T	novel	NA	P-0035771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	34	174	1	ENST00000324856.7:c.970_971delinsT	p.Gly324SerfsTer39	p.G324Sfs*39	ENST00000324856	NM_006015.4	324	GGc/Tc	1/20	1	2	FACETS	0.258	0.211	0.311	0.258	0.211	0.311	SUBCLONAL	1	TRUE	1	0.787792563618362	2		175	334	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593315	67593318	+	protein_altering_variant	In_Frame_Del	DEL	GTAC	GTAC	A	novel	NA	P-0035771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	172	334	0	ENST00000274335.5:c.2061_2064delinsA	p.Tyr688del	p.Y688del	ENST00000274335		687	ttGTAC/ttA	15/15	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.787792563618362	2		334	431	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	63	812	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	0.19	2		812	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0035776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	74	755	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.798	0.697	0.908	0.798	0.697	0.908	CLONAL	1	TRUE	1	0.19	2		755	976	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0035776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	20	761	2	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.438	0.334	0.56	0.438	0.334	0.56	SUBCLONAL	1	TRUE	1	0.19	2		763	481	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	115	612	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.595	0.537	0.656	0.595	0.537	0.656	SUBCLONAL	1	TRUE	1	0.613430846077856	2		616	630	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	164	673	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.906	0.836	0.979	0.906	0.836	0.979	CLONAL	1	TRUE	1	0.613430846077856	2		673	590	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	100	363	0	ENST00000397062.3:c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	NM_006164.4	34	Cga/Gga	2/5	0.613430846077856	3	FACETS	0.852	0.764	0.945	0.426	0.382	0.473	CLONAL	1	TRUE	1	0.613430846077856	3		363	500	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	98	621	3	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.436	0.389	0.486	0.436	0.389	0.486	SUBCLONAL	1	TRUE	1	0.613430846077856	2		624	733	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	132	365	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.873	0.797	0.951	0.873	0.797	0.951	CLONAL	1	TRUE	1	0.613430846077856	2		366	493	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	100	342	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.613430846077856	3	FACETS	0.973	0.874	1	0.486	0.437	0.538	CLONAL	1	TRUE	1	0.613430846077856	3		342	438	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289665	15289665	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	106	788	0	ENST00000263388.2:c.3806del	p.Gly1269ValfsTer3	p.G1269Vfs*3	ENST00000263388	NM_000435.2	1269	gGt/gt	23/33	1	2	FACETS	0.407	0.364	0.452	0.407	0.364	0.452	SUBCLONAL	1	TRUE	1	0.613430846077856	2		788	849	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954272	32954273	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359752	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	151	477	2	ENST00000380152.3:c.9253dup	p.Thr3085AsnfsTer26	p.T3085Nfs*26	ENST00000380152		3082	-/A	24/27	1	2	FACETS	0.975	0.897	1	0.975	0.897	1	CLONAL	1	TRUE	1	0.613430846077856	2		479	505	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	104	366	6	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.963	0.871	1	0.963	0.871	1	CLONAL	1	TRUE	1	0.613430846077856	2		372	352	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222475	2222475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200919682	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	92	698	1	ENST00000398665.3:c.3307G>A	p.Val1103Met	p.V1103M	ENST00000398665	NM_032482.2	1103	Gtg/Atg	24/28	1	2	FACETS	0.383	0.339	0.429	0.383	0.339	0.429	SUBCLONAL	1	TRUE	1	0.613430846077856	2		699	784	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444659	78444659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs908264837	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	63	418	1	ENST00000370768.2:c.30del	p.Ser11LeufsTer43	p.S11Lfs*43	ENST00000370768	NM_003902.3	10	ccC/cc	1/20	1	2	FACETS	0.393	0.34	0.451	0.393	0.34	0.451	SUBCLONAL	1	TRUE	1	0.613430846077856	2		419	522	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276861	15276861	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	36	656	5	ENST00000263388.2:c.5404del	p.Ala1802LeufsTer23	p.A1802Lfs*23	ENST00000263388	NM_000435.2	1802	Gct/ct	30/33	1	2	FACETS	0.176	0.144	0.212	0.176	0.144	0.212	SUBCLONAL	1	TRUE	1	0.613430846077856	2		661	667	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309887	65309887	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1304838920	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	127	397	1	ENST00000342505.4:c.2263C>T	p.Arg755Ter	p.R755*	ENST00000342505	NM_002227.2	755	Cga/Tga	17/25	1	2	FACETS	0.904	0.825	0.986	0.904	0.825	0.986	CLONAL	1	TRUE	1	0.613430846077856	2		398	458	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200073	128200073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374457534	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	263	869	3	ENST00000341105.2:c.1232C>T	p.Ala411Val	p.A411V	ENST00000341105	NM_032638.4	411	gCg/gTg	6/6	1	2	FACETS	0.883	0.829	0.939	0.883	0.829	0.939	CLONAL	1	TRUE	1	0.613430846077856	2		872	971	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686961	37686962	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	59	430	1	ENST00000447079.4:c.3871dup	p.Gln1291ProfsTer19	p.Q1291Pfs*19	ENST00000447079	NM_015083.1	1289	gcc/gCcc	14/14	1	2	FACETS	0.39	0.336	0.449	0.39	0.336	0.449	SUBCLONAL	1	TRUE	1	0.613430846077856	2		431	493	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	207	703	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.923	0.86	0.989	0.923	0.86	0.989	CLONAL	1	TRUE	1	0.613430846077856	2		704	731	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527259	187527259	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201982861	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	161	477	0	ENST00000441802.2:c.10315G>A	p.Val3439Ile	p.V3439I	ENST00000441802	NM_005245.3	3439	Gtc/Atc	17/27	1	2	FACETS	0.821	0.756	0.889	0.821	0.756	0.889	CLONAL	1	TRUE	1	0.613430846077856	2		477	639	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430231	181430231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	43	350	0	ENST00000325404.1:c.83C>T	p.Ala28Val	p.A28V	ENST00000325404	NM_003106.3	28	gCg/gTg	1/1	1	2	FACETS	0.298	0.249	0.352	0.298	0.249	0.352	SUBCLONAL	1	TRUE	1	0.613430846077856	2		350	471	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	180	638	6	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.844	0.781	0.91	0.844	0.781	0.91	CLONAL	1	TRUE	1	0.613430846077856	2		644	695	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948208	71948209	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs749079348	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	193	909	5	ENST00000298229.2:c.2927dup	p.Pro977ThrfsTer7	p.P977Tfs*7	ENST00000298229	NM_001567.3	974	gcc/gCcc	26/28	1	2	FACETS	0.651	0.602	0.701	0.651	0.602	0.701	SUBCLONAL	1	TRUE	1	0.613430846077856	2		914	967	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223858	36223858	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	232	883	1	ENST00000222270.7:c.6413del	p.Pro2138ArgfsTer15	p.P2138Rfs*15	ENST00000222270	NM_014727.1	2136	ctC/ct	28/37	1	2	FACETS	0.853	0.796	0.911	0.853	0.796	0.911	CLONAL	1	TRUE	1	0.613430846077856	2		884	887	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012386	152012386	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	33	740	1	ENST00000262189.6:c.427del	p.Ser143ValfsTer3	p.S143Vfs*3	ENST00000262189	NM_170606.2	143	Agt/gt	4/59	1	2	FACETS	0.254	0.207	0.308	0.254	0.207	0.308	SUBCLONAL	1	TRUE	1	0.613430846077856	2		741	423	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821381	72821382	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	33	446	0	ENST00000268489.5:c.10793dup	p.Pro3599SerfsTer67	p.P3599Sfs*67	ENST00000268489	NM_006885.3	3598	cct/ccCt	10/10	1	2	FACETS	0.233	0.189	0.282	0.233	0.189	0.282	SUBCLONAL	1	TRUE	1	0.613430846077856	2		446	462	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976372	18976372	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	197	770	1	ENST00000262803.5:c.3022C>T	p.Arg1008Ter	p.R1008*	ENST00000262803	NM_002911.3	1008	Cga/Tga	22/24	1	2	FACETS	0.973	0.905	1	0.973	0.905	1	CLONAL	1	TRUE	1	0.613430846077856	2		771	660	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807167	1807167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751635116	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	187	739	5	ENST00000260795.2:c.1498G>A	p.Ala500Thr	p.A500T	ENST00000260795		500	Gcc/Acc	10/17	1	2	FACETS	0.852	0.789	0.916	0.852	0.789	0.916	CLONAL	1	TRUE	1	0.613430846077856	2		744	716	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599915	10599915	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	201	663	1	ENST00000171111.5:c.1661G>A	p.Arg554Gln	p.R554Q	ENST00000171111	NM_203500.1	554	cGa/cAa	5/6	1	2	FACETS	0.847	0.787	0.909	0.847	0.787	0.909	CLONAL	1	TRUE	1	0.613430846077856	2		664	774	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330470	65330470	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	143	440	0	ENST00000342505.4:c.1176G>A	p.Met392Ile	p.M392I	ENST00000342505	NM_002227.2	392	atG/atA	8/25	1	2	FACETS	0.878	0.805	0.954	0.878	0.805	0.954	CLONAL	1	TRUE	1	0.613430846077856	2		440	531	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670368	246670368	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	113	368	0	ENST00000388985.4:c.152G>A	p.Arg51His	p.R51H	ENST00000388985		51	cGc/cAc	1/12	0.546790956791533	4	FACETS	0.882	0.795	0.974	0.294	0.265	0.325	CLONAL	1	TRUE	1	0.613430846077856	4		368	674	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711988	89711989	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	rs1085308054	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	158	400	0	ENST00000371953.3:c.607_608del	p.Ile203SerfsTer39	p.I203Sfs*39	ENST00000371953	NM_000314.4	202	acTAtt/actt	6/9	0.613430846077856	3	FACETS	1	0.979	1	0.594	0.547	0.642	CLONAL	1	TRUE	1	0.613430846077856	3		400	567	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720770	89720771	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	11	180	0	ENST00000371953.3:c.922dup	p.Arg308ProfsTer4	p.R308Pfs*4	ENST00000371953	NM_000314.4	307	-/C	8/9	0.613430846077856	3	FACETS	0.321	0.222	0.443	0.16	0.111	0.222	SUBCLONAL	1	TRUE	1	0.613430846077856	3		180	146	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123353274	123353274	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	41	522	0	ENST00000358487.5:c.58C>A	p.Leu20Met	p.L20M	ENST00000358487	NM_000141.4	20	Ctg/Atg	2/18	0.613430846077856	3	FACETS	0.22	0.182	0.262	0.11	0.091	0.131	SUBCLONAL	1	TRUE	1	0.613430846077856	3		522	795	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414289	32414289	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	116	450	0	ENST00000332351.3:c.1262A>T	p.Tyr421Phe	p.Y421F	ENST00000332351	NM_024426.4	421	tAc/tTc	8/10	1	2	FACETS	0.873	0.793	0.957	0.873	0.793	0.957	CLONAL	1	TRUE	1	0.613430846077856	2		450	433	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645992	67645995	+	frameshift_variant	Frame_Shift_Del	DEL	CCCT	CCCT	-	novel	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	145	474	0	ENST00000264010.4:c.922_925del	p.Leu308Ter	p.L308*	ENST00000264010	NM_006565.3	307	aCCCTc/ac	4/12	1	2	FACETS	0.874	0.802	0.949	0.874	0.802	0.949	CLONAL	1	TRUE	1	0.613430846077856	2		474	541	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552216	29552216	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1135402826	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	132	464	0	ENST00000356175.3:c.1949T>A	p.Leu650Ter	p.L650*	ENST00000356175	NM_000267.3	650	tTa/tAa	17/57	1	2	FACETS	0.971	0.889	1	0.971	0.889	1	CLONAL	1	TRUE	1	0.613430846077856	2		464	443	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664869	29664869	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	114	356	0	ENST00000356175.3:c.6612G>A	p.Trp2204Ter	p.W2204*	ENST00000356175	NM_000267.3	2204	tgG/tgA	43/57	1	2	FACETS	0.847	0.768	0.929	0.847	0.768	0.929	CLONAL	1	TRUE	1	0.613430846077856	2		356	439	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214890	36214890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	194	761	0	ENST00000222270.7:c.3316C>T	p.Arg1106Trp	p.R1106W	ENST00000222270	NM_014727.1	1106	Cgg/Tgg	8/37	1	2	FACETS	0.871	0.809	0.936	0.871	0.809	0.936	CLONAL	1	TRUE	1	0.613430846077856	2		761	726	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50143282	50143282	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	67	227	0	ENST00000246792.3:c.74del	p.Pro25ArgfsTer21	p.P25Rfs*21	ENST00000246792	NM_006270.3	25	cCg/cg	1/6	1	2	FACETS	0.756	0.663	0.854	0.756	0.663	0.854	SUBCLONAL	1	TRUE	1	0.613430846077856	2		227	289	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032065	48032065	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	119	374	0	ENST00000234420.5:c.3455T>C	p.Val1152Ala	p.V1152A	ENST00000234420	NM_000179.2	1152	gTa/gCa	6/10	0.613430846077856	3	FACETS	0.912	0.826	1	0.456	0.413	0.501	CLONAL	1	TRUE	1	0.613430846077856	3		374	556	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728671	190728672	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	118	338	0	ENST00000441310.2:c.2065dup	p.Arg689LysfsTer7	p.R689Kfs*7	ENST00000441310	NM_000534.4	687	gaa/gAaa	10/13	0.613430846077856	3	FACETS	0.911	0.825	1	0.455	0.412	0.501	CLONAL	1	TRUE	1	0.613430846077856	3		338	552	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39658070	39658070	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	139	519	0	ENST00000361337.2:c.34-1G>T		p.X12_splice	ENST00000361337	NM_003286.2	12			1	2	FACETS	0.804	0.735	0.875	0.804	0.735	0.875	CLONAL	1	TRUE	1	0.613430846077856	2		519	564	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645685	12645685	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	72	259	0	ENST00000251849.4:c.784A>G	p.Asn262Asp	p.N262D	ENST00000251849	NM_002880.3	262	Aat/Gat	7/17	1	2	FACETS	0.765	0.674	0.86	0.765	0.674	0.86	SUBCLONAL	1	TRUE	1	0.613430846077856	2		259	307	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109314035	109314035	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	143	449	0	ENST00000436639.2:c.1188A>C	p.Lys396Asn	p.K396N	ENST00000436639	NM_014454.2	396	aaA/aaC	7/10	1	2	FACETS	0.967	0.888	1	0.967	0.888	1	CLONAL	1	TRUE	1	0.613430846077856	2		449	482	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522246	157522246	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	162	593	0	ENST00000346085.5:c.4520del	p.Asn1507IlefsTer72	p.N1507Ifs*72	ENST00000346085	NM_020732.3	1506	atA/at	18/20	1	2	FACETS	0.864	0.797	0.935	0.864	0.797	0.935	CLONAL	1	TRUE	1	0.613430846077856	2		593	611	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859653	151859653	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs879219321	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	90	440	0	ENST00000262189.6:c.11009A>G	p.Asn3670Ser	p.N3670S	ENST00000262189	NM_170606.2	3670	aAt/aGt	43/59	1	2	FACETS	0.562	0.5	0.628	0.562	0.5	0.628	SUBCLONAL	1	TRUE	1	0.613430846077856	2		440	522	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5463000	5463000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1347840317	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	102	314	0	ENST00000381577.3:c.561G>T	p.Glu187Asp	p.E187D	ENST00000381577	NM_014143.3	187	gaG/gaT	4/7	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.613430846077856	2		314	312	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418253	139418253	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	261	882	0	ENST00000277541.6:c.319C>A	p.Leu107Ile	p.L107I	ENST00000277541	NM_017617.3	107	Ctc/Atc	3/34	1	2	FACETS	0.89	0.835	0.947	0.89	0.835	0.947	CLONAL	1	TRUE	1	0.613430846077856	2		882	956	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0035778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	143	794	0	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.387606499944204	2		794	731	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920172	76920173	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	122	340	0	ENST00000373344.5:c.3904dup	p.Arg1302LysfsTer7	p.R1302Kfs*7	ENST00000373344	NM_000489.3	1302	aga/aAga	11/35	1	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.387606499944204	1		340	415	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589550	67589552	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs1131692242	NA	P-0035778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	31	188	0	ENST00000274335.5:c.1317_1319del	p.Glu439del	p.E439del	ENST00000274335		438	aAAGaa/aaa	10/15	1	2	FACETS	0.93	0.761	1	0.93	0.761	1	CLONAL	1	TRUE	1	0.387606499944204	2		188	172	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346860	91346860	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	153	492	0	ENST00000355112.3:c.3468T>G	p.Asp1156Glu	p.D1156E	ENST00000355112	NM_000057.2	1156	gaT/gaG	18/22	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.387606499944204	2		492	750	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670021	29670028	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAATAGAG	TAATAGAG	-	novel	NA	P-0035778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	108	393	0	ENST00000356175.3:c.7000-5_7002del		p.X2334_splice	ENST00000356175	NM_000267.3	2334		47/57	0.25177750552344	1	FACETS	0.99	0.893	1	0.99	0.893	1	CLONAL	1	TRUE	0	0.387606499944204	1		393	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs786201057	NA	P-0035779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	318	630	0	ENST00000269305.4:c.374C>G	p.Thr125Arg	p.T125R	ENST00000269305	NM_001126112.2	125	aCg/aGg	4/11	0.629699964765468	3	FACETS	0.847	0.816	0.876	0.847	0.816	0.876	CLONAL	3	TRUE	0	0.795281448311346	3		630	440	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458418	120458452	+	frameshift_variant	Frame_Shift_Del	DEL	GAGCTGGAAAGTCACAATGGGGGGCAAGGGCTCCC	GAGCTGGAAAGTCACAATGGGGGGCAAGGGCTCCC	-	novel	NA	P-0035779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	808	699	0	ENST00000256646.2:c.6893_6927del	p.Arg2298HisfsTer3	p.R2298Hfs*3	ENST00000256646	NM_024408.3	2298	cGGGAGCCCTTGCCCCCCATTGTGACTTTCCAGCTC/c	34/34	0.795281448311346	11	FACETS	1	0.995	1			1	CLONAL	8	TRUE	NA	0.795281448311346	11		699	1096	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589744	69589744	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	15	120	0	ENST00000168712.1:c.109G>T	p.Gly37Cys	p.G37C	ENST00000168712	NM_002007.2	37	Ggc/Tgc	1/3	0.795281448311346	6	FACETS	0.455	0.333	0.6			1	SUBCLONAL	1	TRUE	NA	0.795281448311346	6		120	215	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	60	812	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.651	0.56	0.751	0.651	0.56	0.751	SUBCLONAL	1	TRUE	1	0.24	2		812	768	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330522	65330522	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	52	517	0	ENST00000342505.4:c.1124T>G	p.Ile375Ser	p.I375S	ENST00000342505	NM_002227.2	375	aTt/aGt	8/25	1	2	FACETS	0.473	0.401	0.552	0.473	0.401	0.552	SUBCLONAL	1	TRUE	1	0.24	2		517	917	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577134	7577134	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	84	608	0	ENST00000269305.4:c.804del	p.Asn268LysfsTer77	p.N268Kfs*77	ENST00000269305	NM_001126112.2	268	aaC/aa	8/11	1	2	FACETS	0.98	0.866	1	0.98	0.866	1	CLONAL	1	TRUE	1	0.24	2		608	714	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852394	63852394	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	173	561	0	ENST00000279873.7:c.3172C>A	p.His1058Asn	p.H1058N	ENST00000279873	NM_032199.2	1058	Cac/Aac	10/10	1	2	FACETS	0.966	0.896	1	0.966	0.896	1	CLONAL	1	TRUE	1	0.689807522191676	2		561	519	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444003	49444003	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	199	663	0	ENST00000301067.7:c.3368C>G	p.Ala1123Gly	p.A1123G	ENST00000301067	NM_003482.3	1123	gCc/gGc	11/54	0.689807522191676	3	FACETS	0.927	0.86	0.996	0.464	0.43	0.498	CLONAL	1	TRUE	1	0.689807522191676	3		663	837	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181311	123181311	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs774761933	NA	P-0035783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	38	137	1	ENST00000218089.9:c.775C>T	p.Arg259Ter	p.R259*	ENST00000218089	NM_001042749.1	259	Cga/Tga	9/35	1	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.878524346958062	1		138	43	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0035785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	66	555	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.16	2		555	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579350	7579350	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587781642	NA	P-0035785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	41	723	0	ENST00000269305.4:c.337T>G	p.Phe113Val	p.F113V	ENST00000269305	NM_001126112.2	113	Ttc/Gtc	4/11	1	2	FACETS	0.935	0.778	1	0.935	0.778	1	CLONAL	1	TRUE	1	0.16	2		723	548	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625159	69625159	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554980306	NA	P-0035785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	43	846	1	ENST00000334134.2:c.634C>T	p.Arg212Trp	p.R212W	ENST00000334134	NM_005247.2	212	Cgg/Tgg	3/3	1	2	FACETS	0.69	0.576	0.818	0.69	0.576	0.818	SUBCLONAL	1	TRUE	1	0.16	2		847	779	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492794	56492794	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1480969068	NA	P-0035785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	48	701	0	ENST00000407977.2:c.145A>G	p.Arg49Gly	p.R49G	ENST00000407977		49	Aga/Gga	2/10	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.16	2		701	531	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974744	21974770	+	inframe_deletion	In_Frame_Del	DEL	ACCTCCTCTACCCGACCCCGGGCCGCG	ACCTCCTCTACCCGACCCCGGGCCGCG	-	novel	NA	P-0035785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	14	383	0	ENST00000304494.5:c.57_83del	p.Ala20_Val28del	p.A20_V28del	ENST00000304494	NM_000077.4	19	gcCGCGGCCCGGGGTCGGGTAGAGGAGGTg/gcg	1/3	1	2	FACETS	0.643	0.464	0.86	0.643	0.464	0.86	SUBCLONAL	1	TRUE	1	0.16	2		383	272	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	326	761	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.655639486647147	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.655639486647147	1		761	618	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602488	10602488	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1397945617	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	197	628	0	ENST00000171111.5:c.1090G>T	p.Gly364Cys	p.G364C	ENST00000171111	NM_203500.1	364	Ggc/Tgc	3/6	0.655639486647147	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.655639486647147	1		628	371	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085656	16085656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201115523	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	179	723	0	ENST00000281043.3:c.832G>A	p.Asp278Asn	p.D278N	ENST00000281043	NM_005378.4	278	Gac/Aac	3/3	0.248995077411959	1	FACETS	0.606	0.561	0.652	0.606	0.561	0.652	INDETERMINATE	1	TRUE	0	0.655639486647147	1		723	606	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916788	178916788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1266632047	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	184	487	0	ENST00000263967.3:c.175C>T	p.His59Tyr	p.H59Y	ENST00000263967	NM_006218.2	59	Cat/Tat	2/21	1	2	FACETS	0.86	0.797	0.924	0.86	0.797	0.924	CLONAL	1	TRUE	1	0.655639486647147	2		487	653	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081573	143081573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	224	744	0	ENST00000262992.4:c.1501C>T	p.Pro501Ser	p.P501S	ENST00000262992	NM_001101669.1	501	Ccc/Tcc	15/24	0.654885916106321	1	FACETS	0.878	0.826	0.931	0.878	0.826	0.931	CLONAL	1	TRUE	0	0.655639486647147	1		744	523	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142964	47142964	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	168	480	0	ENST00000409792.3:c.4999C>G	p.Gln1667Glu	p.Q1667E	ENST00000409792	NM_014159.6	1667	Cag/Gag	8/21	0.655639486647147	1	FACETS	0.886	0.825	0.947	0.886	0.825	0.947	CLONAL	1	TRUE	0	0.655639486647147	1		480	389	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430557	78430557	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	151	452	1	ENST00000370768.2:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000370768	NM_003902.3	245	Caa/Taa	9/20	0.655639486647147	3	FACETS	0.725	0.663	0.789	0.362	0.331	0.395	SUBCLONAL	1	TRUE	1	0.655639486647147	3		453	844	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425664	49425664	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	212	810	0	ENST00000301067.7:c.12824A>G	p.Gln4275Arg	p.Q4275R	ENST00000301067	NM_003482.3	4275	cAg/cGg	39/54	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.655639486647147	2		810	646	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434378	49434378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	307	976	1	ENST00000301067.7:c.7175C>T	p.Pro2392Leu	p.P2392L	ENST00000301067	NM_003482.3	2392	cCt/cTt	31/54	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.655639486647147	2		977	780	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240963	133240963	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	208	800	0	ENST00000320574.5:c.2554C>T	p.Gln852Ter	p.Q852*	ENST00000320574	NM_006231.2	852	Cag/Tag	22/49	0.487896042141317	1	FACETS	0.729	0.681	0.778	0.729	0.681	0.778	SUBCLONAL	1	TRUE	0	0.655639486647147	1		800	585	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001934	29001934	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	218	596	1	ENST00000282397.4:c.1231C>A	p.Gln411Lys	p.Q411K	ENST00000282397	NM_002019.4	411	Cag/Aag	9/30	0.654885916106321	1	FACETS	0.949	0.893	1	0.949	0.893	1	CLONAL	1	TRUE	0	0.655639486647147	1		597	471	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571433	95571433	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	124	291	0	ENST00000393063.1:c.3244G>T	p.Val1082Phe	p.V1082F	ENST00000393063	NM_030621.3	1082	Gtc/Ttc	21/28	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.655639486647147	2		291	369	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679173	88679173	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	217	695	2	ENST00000360948.2:c.864C>A	p.Asn288Lys	p.N288K	ENST00000360948	NM_001012338.2	288	aaC/aaA	8/19	0.655639486647147	3	FACETS	0.825	0.766	0.885	0.412	0.383	0.443	CLONAL	1	TRUE	1	0.655639486647147	3		697	1066	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647264	2647264	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1291358013	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	200	717	0	ENST00000342085.4:c.1542C>G	p.Phe514Leu	p.F514L	ENST00000342085	NM_002613.4	514	ttC/ttG	13/14	0.152157275785743	0	FACETS	0.344	0.32	0.368			1	INDETERMINATE	1	TRUE	0	0.655639486647147	0		717	611	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858417	9858417	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	216	680	1	ENST00000330684.3:c.2984C>A	p.Thr995Lys	p.T995K	ENST00000330684	NM_001134407.1	995	aCg/aAg	13/13	0.152157275785743	0	FACETS	0.358	0.335	0.382			1	INDETERMINATE	1	TRUE	0	0.655639486647147	0		681	633	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827301	72827301	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	240	938	0	ENST00000268489.5:c.9280G>T	p.Ala3094Ser	p.A3094S	ENST00000268489	NM_006885.3	3094	Gca/Tca	9/10	0.152157275785743	0	FACETS	0.297	0.278	0.317			1	INDETERMINATE	1	TRUE	0	0.655639486647147	0		938	849	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068447	16068447	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	16	136	0	ENST00000268712.3:c.464C>A	p.Ala155Asp	p.A155D	ENST00000268712	NM_006311.3	155	gCt/gAt	5/46	0.655639486647147	1	FACETS	0.234	0.174	0.305	0.234	0.174	0.305	SUBCLONAL	1	TRUE	0	0.655639486647147	1		136	140	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804307	46804307	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	59	967	0	ENST00000290295.7:c.700G>C	p.Glu234Gln	p.E234Q	ENST00000290295	NM_006361.5	234	Gag/Cag	2/2	0.655639486647147	1	FACETS	0.154	0.132	0.178	0.154	0.132	0.178	SUBCLONAL	1	TRUE	0	0.655639486647147	1		967	785	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438235	56438235	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	52	897	0	ENST00000407977.2:c.758G>A	p.Arg253Lys	p.R253K	ENST00000407977		253	aGg/aAg	7/10	0.655639486647147	1	FACETS	0.165	0.14	0.192	0.165	0.14	0.192	SUBCLONAL	1	TRUE	0	0.655639486647147	1		897	647	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59861731	59861731	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	238	458	0	ENST00000259008.2:c.1528A>T	p.Lys510Ter	p.K510*	ENST00000259008	NM_032043.2	510	Aaa/Taa	11/20	0.655639486647147	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.655639486647147	1		458	463	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220378	1220378	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	296	966	0	ENST00000326873.7:c.471C>G	p.Phe157Leu	p.F157L	ENST00000326873	NM_000455.4	157	ttC/ttG	4/10	0.655639486647147	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.655639486647147	1		966	517	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27016119	27016119	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	217	613	0	ENST00000335756.4:c.395T>A	p.Ile132Asn	p.I132N	ENST00000335756	NM_001809.3	132	aTc/aAc	4/5	0.248995077411959	1	FACETS	0.792	0.742	0.842	0.792	0.742	0.842	INDETERMINATE	1	TRUE	0	0.655639486647147	1		613	562	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27016121	27016122	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	180	597	0	ENST00000335756.4:c.401dup	p.Leu135ProfsTer2	p.L135Pfs*2	ENST00000335756	NM_001809.3	133	cgg/cGgg	4/5	0.248995077411959	1	FACETS	0.671	0.623	0.72	0.671	0.623	0.72	INDETERMINATE	1	TRUE	0	0.655639486647147	1		597	550	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044330	128044330	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	213	768	0	ENST00000285398.2:c.1291A>G	p.Lys431Glu	p.K431E	ENST00000285398	NM_000122.1	431	Aag/Gag	8/15	1	2	FACETS	0.965	0.901	1	0.965	0.901	1	CLONAL	1	TRUE	1	0.655639486647147	2		768	673	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248579	212248579	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	281	759	0	ENST00000342788.4:c.3688C>A	p.Pro1230Thr	p.P1230T	ENST00000342788	NM_005235.2	1230	Cca/Aca	28/28	1	2	FACETS	0.899	0.847	0.954	0.899	0.847	0.954	CLONAL	1	TRUE	1	0.655639486647147	2		759	953	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212252683	212252683	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs766441342	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	88	170	0	ENST00000342788.4:c.3170C>A	p.Thr1057Asn	p.T1057N	ENST00000342788	NM_005235.2	1057	aCc/aAc	26/28	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.655639486647147	2		170	265	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368461	225368462	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	185	464	0	ENST00000264414.4:c.1284dup	p.Glu429Ter	p.E429*	ENST00000264414	NM_003590.4	428	-/T	9/16	1	2	FACETS	0.86	0.798	0.925	0.86	0.798	0.925	CLONAL	1	TRUE	1	0.655639486647147	2		464	656	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867502	35867502	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	95	293	0	ENST00000303115.3:c.316A>T	p.Asn106Tyr	p.N106Y	ENST00000303115	NM_002185.3	106	Aat/Tat	3/8	1	2	FACETS	0.816	0.733	0.903	0.816	0.733	0.903	CLONAL	1	TRUE	1	0.655639486647147	2		293	355	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867560	35867560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	70	205	0	ENST00000303115.3:c.374C>T	p.Thr125Ile	p.T125I	ENST00000303115	NM_002185.3	125	aCt/aTt	3/8	1	2	FACETS	0.841	0.742	0.944	0.841	0.742	0.944	CLONAL	1	TRUE	1	0.655639486647147	2		205	254	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131895004	131895004	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	45	265	0	ENST00000265335.6:c.158G>T	p.Cys53Phe	p.C53F	ENST00000265335		53	tGt/tTt	2/25	1	2	FACETS	0.467	0.394	0.546	0.467	0.394	0.546	SUBCLONAL	1	TRUE	1	0.655639486647147	2		265	294	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024205	112024205	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	131	470	0	ENST00000368678.4:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000368678		194	Gat/Tat	7/13	0.654885916106321	1	FACETS	0.98	0.907	1	0.98	0.907	1	CLONAL	1	TRUE	0	0.655639486647147	1		470	274	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024214	112024214	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	119	447	0	ENST00000368678.4:c.571G>C	p.Asp191His	p.D191H	ENST00000368678		191	Gat/Cat	7/13	0.654885916106321	1	FACETS	0.949	0.874	1	0.949	0.874	1	CLONAL	1	TRUE	0	0.655639486647147	1		447	257	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117684019	117684019	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	207	450	0	ENST00000368508.3:c.3128C>T	p.Ala1043Val	p.A1043V	ENST00000368508	NM_002944.2	1043	gCa/gTa	21/43	0.654885916106321	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.655639486647147	1		450	404	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005306	150005306	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	232	714	0	ENST00000253339.5:c.919A>T	p.Thr307Ser	p.T307S	ENST00000253339		307	Act/Tct	3/7	0.654885916106321	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.655639486647147	1		714	449	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90971075	90971075	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	272	336	0	ENST00000265433.3:c.1002G>C	p.Lys334Asn	p.K334N	ENST00000265433	NM_002485.4	334	aaG/aaC	9/16	0.580993313322704	3	FACETS	0.929	0.88	0.978	0.619	0.586	0.652	CLONAL	2	TRUE	0	0.655639486647147	3		336	593	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517947	8517947	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	194	542	0	ENST00000356435.5:c.1444T>G	p.Leu482Val	p.L482V	ENST00000356435		482	Tta/Gta	10/35	NA	2	FACETS	0.902	0.839	0.967			1	INDETERMINATE	1	TRUE	NA	0.655639486647147	2		542	656	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226186	53226186	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs375850872	NA	P-0035786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	227	438	0	ENST00000375401.3:c.2663G>T	p.Arg888Leu	p.R888L	ENST00000375401	NM_004187.3	888	cGt/cTt	19/26	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.655639486647147	1		438	313	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	82	622	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.801	0.709	0.9	0.801	0.709	0.9	CLONAL	1	TRUE	1	0.413506118687786	2		622	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	20	675	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.106	0.08	0.136	0.106	0.08	0.136	SUBCLONAL	1	TRUE	1	0.413506118687786	2		675	915	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	175	687	2	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.413506118687786	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	0	0.413506118687786	2		689	421	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	135	622	5	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.766	0.703	0.832	1	0.988	1	SUBCLONAL	2	TRUE	1	0.413506118687786	2		627	426	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	93	365	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.766	0.683	0.855	0.766	0.683	0.855	SUBCLONAL	1	TRUE	1	0.413506118687786	2		366	587	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11181381	11181381	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	189	666	0	ENST00000361445.4:c.6855G>T	p.Glu2285Asp	p.E2285D	ENST00000361445	NM_004958.3	2285	gaG/gaT	49/58	1	2	FACETS	0.94	0.868	1	0.94	0.868	1	CLONAL	1	TRUE	1	0.413506118687786	2		666	973	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260612	16260612	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	106	565	0	ENST00000375759.3:c.7877C>A	p.Pro2626His	p.P2626H	ENST00000375759	NM_015001.2	2626	cCt/cAt	11/15	1	2	FACETS	0.656	0.587	0.728	0.656	0.587	0.728	SUBCLONAL	1	TRUE	1	0.413506118687786	2		565	782	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101153	27101154	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	153	645	0	ENST00000324856.7:c.4438dup	p.Met1480AsnfsTer11	p.M1480Nfs*11	ENST00000324856	NM_006015.4	1479	caa/cAaa	18/20	1	2	FACETS	0.855	0.782	0.93	0.855	0.782	0.93	CLONAL	1	TRUE	1	0.413506118687786	2		645	866	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599271	28599271	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs770146088	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	184	778	0	ENST00000253063.3:c.722del	p.Pro241GlnfsTer6	p.P241Qfs*6	ENST00000253063	NM_031459.4	239	agC/ag	5/10	1	2	FACETS	0.863	0.796	0.933	0.863	0.796	0.933	CLONAL	1	TRUE	1	0.413506118687786	2		778	1031	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812297	43812297	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	141	456	0	ENST00000372470.3:c.1162G>A	p.Ala388Thr	p.A388T	ENST00000372470	NM_005373.2	388	Gct/Act	7/12	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.413506118687786	2		456	658	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226566892	226566892	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	112	491	0	ENST00000366794.5:c.1696A>G	p.Thr566Ala	p.T566A	ENST00000366794	NM_001618.3	566	Acc/Gcc	12/23	1	2	FACETS	0.65	0.584	0.719	0.65	0.584	0.719	SUBCLONAL	1	TRUE	1	0.413506118687786	2		491	834	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136178	64136178	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	122	555	0	ENST00000334205.4:c.1337T>C	p.Leu446Pro	p.L446P	ENST00000334205	NM_003942.2	446	cTg/cCg	12/17	1	2	FACETS	0.761	0.688	0.838	0.761	0.688	0.838	SUBCLONAL	1	TRUE	1	0.413506118687786	2		555	775	SUCCESS
ATM	472	MSKCC	GRCh37	11	108128263	108128263	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1377126475	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	33	401	1	ENST00000278616.4:c.2306A>G	p.Glu769Gly	p.E769G	ENST00000278616	NM_000051.3	769	gAg/gGg	15/63	1	2	FACETS	0.278	0.225	0.337	0.278	0.225	0.337	SUBCLONAL	1	TRUE	1	0.413506118687786	2		402	575	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514413	125514413	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	106	298	0	ENST00000428830.2:c.1108T>C	p.Trp370Arg	p.W370R	ENST00000428830	NM_001114121.2	370	Tgg/Cgg	11/14	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.413506118687786	2		298	472	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18576963	18576963	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778117246	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	117	460	0	ENST00000266497.5:c.2371C>T	p.Arg791Cys	p.R791C	ENST00000266497		791	Cgt/Tgt	16/31	1	2	FACETS	0.865	0.782	0.953	0.865	0.782	0.953	CLONAL	1	TRUE	1	0.413506118687786	2		460	654	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424178	49424178	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs886040960	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	77	426	1	ENST00000301067.7:c.13884del	p.Thr4629ProfsTer11	p.T4629Pfs*11	ENST00000301067	NM_003482.3	4628	ccC/cc	42/54	1	2	FACETS	0.662	0.581	0.747	0.662	0.581	0.747	SUBCLONAL	1	TRUE	1	0.413506118687786	2		427	563	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426973	49426973	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1565778024	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	132	533	1	ENST00000301067.7:c.11515del	p.Gln3839SerfsTer42	p.Q3839Sfs*42	ENST00000301067	NM_003482.3	3839	Cag/ag	39/54	1	2	FACETS	0.982	0.894	1	0.982	0.894	1	CLONAL	1	TRUE	1	0.413506118687786	2		534	650	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434175	49434175	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs570260017	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	199	806	0	ENST00000301067.7:c.7378C>T	p.Arg2460Cys	p.R2460C	ENST00000301067	NM_003482.3	2460	Cgt/Tgt	31/54	1	2	FACETS	0.933	0.864	1	0.933	0.864	1	CLONAL	1	TRUE	1	0.413506118687786	2		806	1032	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434417	49434417	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	156	623	1	ENST00000301067.7:c.7136C>A	p.Ala2379Asp	p.A2379D	ENST00000301067	NM_003482.3	2379	gCt/gAt	31/54	1	2	FACETS	0.974	0.893	1	0.974	0.893	1	CLONAL	1	TRUE	1	0.413506118687786	2		624	775	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484318	50484318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141728974	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	203	553	1	ENST00000394963.4:c.1078C>T	p.Arg360Trp	p.R360W	ENST00000394963	NM_003076.4	360	Cgg/Tgg	9/13	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.413506118687786	2		554	915	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	258	753	5	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.413506118687786	2		758	941	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437358	110437358	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	45	143	0	ENST00000375856.3:c.1043C>T	p.Ala348Val	p.A348V	ENST00000375856	NM_003749.2	348	gCc/gTc	1/2	1	2	FACETS	0.98	0.832	1	0.98	0.832	1	CLONAL	1	TRUE	1	0.413506118687786	2		143	222	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30047521	30047521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	72	370	0	ENST00000331968.5:c.2480G>A	p.Arg827His	p.R827H	ENST00000331968	NM_002742.2	827	cGc/cAc	17/18	1	2	FACETS	0.687	0.601	0.779	0.687	0.601	0.779	SUBCLONAL	1	TRUE	1	0.413506118687786	2		370	507	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061207	38061207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	154	506	0	ENST00000250448.2:c.782G>A	p.Arg261His	p.R261H	ENST00000250448	NM_004496.3	261	cGc/cAc	2/2	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.413506118687786	2		506	712	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610314	81610314	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	32	399	0	ENST00000298171.2:c.1912G>C	p.Ala638Pro	p.A638P	ENST00000298171	NM_000369.2	638	Gcc/Ccc	10/10	1	2	FACETS	0.278	0.225	0.339	0.278	0.225	0.339	SUBCLONAL	1	TRUE	1	0.413506118687786	2		399	556	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007825	45007825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	232	384	2	ENST00000558401.1:c.276del	p.Thr93LeufsTer10	p.T93Lfs*10	ENST00000558401	NM_004048.2	91	aCc/ac	2/4	1	2	FACETS	0.898	0.843	0.954	1	0.994	1	CLONAL	2	TRUE	1	0.413506118687786	2		386	625	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774184	66774185	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	424	806	0	ENST00000307102.5:c.662dup	p.Asn221LysfsTer65	p.N221Kfs*65	ENST00000307102	NM_002755.3	220	-/A	6/11	0.413506118687786	2	FACETS	0.87	0.83	0.911	0.87	0.83	0.911	CLONAL	2	TRUE	0	0.413506118687786	2		806	1178	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844229	68844229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	47	435	0	ENST00000261769.5:c.817G>A	p.Glu273Lys	p.E273K	ENST00000261769	NM_004360.3	273	Gaa/Aaa	6/16	1	2	FACETS	0.365	0.308	0.429	0.365	0.308	0.429	SUBCLONAL	1	TRUE	1	0.413506118687786	2		435	622	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844245	68844245	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs878854697	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	116	361	1	ENST00000261769.5:c.832+1G>T		p.X278_splice	ENST00000261769	NM_004360.3	278			1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.413506118687786	2		362	555	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	98	576	2	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	0.649	0.579	0.724	0.649	0.579	0.724	SUBCLONAL	1	TRUE	1	0.413506118687786	2		578	730	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346158	89346158	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs878855327	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	55	269	1	ENST00000301030.4:c.6792del	p.Ala2265ProfsTer72	p.A2265Pfs*72	ENST00000301030	NM_001256183.1	2264	ccC/cc	9/13	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.413506118687786	2		270	264	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574023	7574023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771939956	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	150	579	0	ENST00000269305.4:c.1004G>A	p.Arg335His	p.R335H	ENST00000269305	NM_001126112.2	335	cGt/cAt	10/11	1	2	FACETS	0.876	0.801	0.955	0.876	0.801	0.955	CLONAL	1	TRUE	1	0.413506118687786	2		579	828	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512370	38512370	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567767560	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	47	643	2	ENST00000254066.5:c.1286del	p.Gly429ValfsTer214	p.G429Vfs*214	ENST00000254066	NM_000964.3	427	ccG/cc	9/9	1	2	FACETS	0.279	0.234	0.328	0.279	0.234	0.328	SUBCLONAL	1	TRUE	1	0.413506118687786	2		645	816	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436112	56436112	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	125	474	0	ENST00000407977.2:c.1025T>C	p.Ile342Thr	p.I342T	ENST00000407977		342	aTt/aCt	9/10	1	2	FACETS	0.871	0.79	0.957	0.871	0.79	0.957	CLONAL	1	TRUE	1	0.413506118687786	2		474	694	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	143	468	0	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	0.958	0.875	1	0.958	0.875	1	CLONAL	1	TRUE	1	0.413506118687786	2		468	722	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118901	70118901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	180	496	1	ENST00000245479.2:c.473C>T	p.Ala158Val	p.A158V	ENST00000245479	NM_000346.3	158	gCg/gTg	2/3	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.413506118687786	2		497	774	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244357	5244357	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	265	802	0	ENST00000357368.4:c.1125del	p.Tyr376IlefsTer17	p.Y376Ifs*17	ENST00000357368	NM_002850.3	375	ccG/cc	11/38	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.413506118687786	2		802	1072	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10283797	10283797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771381056	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	133	651	0	ENST00000340748.4:c.689G>A	p.Arg230His	p.R230H	ENST00000340748		230	cGc/cAc	8/40	1	2	FACETS	0.716	0.65	0.786	0.716	0.65	0.786	SUBCLONAL	1	TRUE	1	0.413506118687786	2		651	898	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132617	11132617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1445478818	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	193	843	2	ENST00000358026.2:c.2833G>A	p.Ala945Thr	p.A945T	ENST00000358026	NM_001128849.1	945	Gca/Aca	19/36	1	2	FACETS	0.923	0.854	0.996	0.923	0.854	0.996	CLONAL	1	TRUE	1	0.413506118687786	2		845	1011	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209221	36209221	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs774099554	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	23	311	0	ENST00000222270.7:c.301T>C	p.Trp101Arg	p.W101R	ENST00000222270	NM_014727.1	101	Tgg/Cgg	1/37	1	2	FACETS	0.306	0.238	0.385	0.306	0.238	0.385	SUBCLONAL	1	TRUE	1	0.413506118687786	2		311	363	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216506	36216506	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs956016804	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	198	797	0	ENST00000222270.7:c.3769C>T	p.Arg1257Cys	p.R1257C	ENST00000222270	NM_014727.1	1257	Cgc/Tgc	12/37	1	2	FACETS	0.966	0.895	1	0.966	0.895	1	CLONAL	1	TRUE	1	0.413506118687786	2		797	991	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752873	42752873	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	67	823	0	ENST00000222329.4:c.1391del	p.Pro464LeufsTer67	p.P464Lfs*67	ENST00000222329	NM_006494.2	464	cCt/ct	4/4	1	2	FACETS	0.312	0.27	0.358	0.312	0.27	0.358	SUBCLONAL	1	TRUE	1	0.413506118687786	2		823	1039	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799283	42799283	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	107	420	0	ENST00000575354.2:c.4771del	p.Ala1591LeufsTer29	p.A1591Lfs*29	ENST00000575354	NM_015125.3	1589	gaG/ga	20/20	1	2	FACETS	0.855	0.769	0.947	0.855	0.769	0.947	CLONAL	1	TRUE	1	0.413506118687786	2		420	605	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919865	50919866	+	splice_acceptor_variant	Splice_Site	INS	-	-	G	rs756872503	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	132	631	1	ENST00000440232.2:c.2959dup		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	0.807	0.733	0.885	0.807	0.733	0.885	CLONAL	1	TRUE	1	0.413506118687786	2		632	791	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907653	111907653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	114	347	0	ENST00000393256.3:c.427C>T	p.Arg143Cys	p.R143C	ENST00000393256	NM_006538.4	143	Cgc/Tgc	3/4	1	2	FACETS	0.927	0.837	1	0.927	0.837	1	CLONAL	1	TRUE	1	0.413506118687786	2		347	595	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921764	111921764	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	124	348	0	ENST00000393256.3:c.553C>T	p.Arg185Ter	p.R185*	ENST00000393256	NM_006538.4	185	Cga/Tga	4/4	1	2	FACETS	0.91	0.825	0.999	0.91	0.825	0.999	CLONAL	1	TRUE	1	0.413506118687786	2		348	659	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044404	128044404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	177	640	0	ENST00000285398.2:c.1217C>T	p.Ala406Val	p.A406V	ENST00000285398	NM_000122.1	406	gCc/gTc	8/15	1	2	FACETS	0.929	0.856	1	0.929	0.856	1	CLONAL	1	TRUE	1	0.413506118687786	2		640	922	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046999	128046999	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs760816658	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	49	485	0	ENST00000285398.2:c.736A>G	p.Met246Val	p.M246V	ENST00000285398	NM_000122.1	246	Atg/Gtg	6/15	1	2	FACETS	0.297	0.251	0.348	0.297	0.251	0.348	SUBCLONAL	1	TRUE	1	0.413506118687786	2		485	798	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248737	212248737	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	38	348	0	ENST00000342788.4:c.3530del	p.Asn1177MetfsTer27	p.N1177Mfs*27	ENST00000342788	NM_005235.2	1177	aAt/at	28/28	1	2	FACETS	0.373	0.308	0.446	0.373	0.308	0.446	SUBCLONAL	1	TRUE	1	0.413506118687786	2		348	493	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212615384	212615384	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	116	382	0	ENST00000342788.4:c.602C>T	p.Thr201Ile	p.T201I	ENST00000342788	NM_005235.2	201	aCa/aTa	5/28	1	2	FACETS	0.945	0.854	1	0.945	0.854	1	CLONAL	1	TRUE	1	0.413506118687786	2		382	594	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206809	36206809	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	142	483	0	ENST00000300305.3:c.703G>A	p.Ala235Thr	p.A235T	ENST00000300305		235	Gcc/Acc	6/8	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.413506118687786	2		483	577	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288424	21288425	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	188	601	0	ENST00000354336.3:c.673dup	p.Ala225GlyfsTer28	p.A225Gfs*28	ENST00000354336	NM_005207.3	223	-/G	2/3	1	2	FACETS	0.971	0.898	1	0.971	0.898	1	CLONAL	1	TRUE	1	0.413506118687786	2		601	936	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091792	29091793	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758677815	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	177	562	0	ENST00000328354.6:c.1164dup	p.Thr389HisfsTer6	p.T389Hfs*6	ENST00000328354	NM_007194.3	388	-/C	11/15	1	2	FACETS	0.958	0.883	1	0.958	0.883	1	CLONAL	1	TRUE	1	0.413506118687786	2		562	894	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053590	37053590	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs63751711	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	231	837	2	ENST00000231790.2:c.677G>A	p.Arg226Gln	p.R226Q	ENST00000231790	NM_000249.3	226	cGa/cAa	8/19	0.413506118687786	2	FACETS	0.897	0.842	0.953	0.897	0.842	0.953	CLONAL	2	TRUE	0	0.413506118687786	2		839	623	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412922	49412922	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	166	624	0	ENST00000418115.1:c.101A>G	p.Tyr34Cys	p.Y34C	ENST00000418115	NM_001664.2	34	tAt/tGt	2/5	0.413506118687786	2	FACETS	0.782	0.717	0.849	0.391	0.358	0.425	SUBCLONAL	1	TRUE	0	0.413506118687786	2		624	1027	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468386	89468386	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	44	172	0	ENST00000336596.2:c.1923del	p.Lys641AsnfsTer15	p.K641Nfs*15	ENST00000336596	NM_005233.5	640	ttA/tt	11/17	1	2	FACETS	0.887	0.75	1	0.887	0.75	1	CLONAL	1	TRUE	1	0.413506118687786	2		172	240	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149245627	149245627	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	171	543	0	ENST00000360632.3:c.901A>G	p.Asn301Asp	p.N301D	ENST00000360632	NM_015472.4	301	Aat/Gat	5/7	1	2	FACETS	0.999	0.92	1	0.999	0.92	1	CLONAL	1	TRUE	1	0.413506118687786	2		543	828	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998128	169998128	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs753143066	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	164	598	7	ENST00000295797.4:c.826del	p.Thr276GlnfsTer7	p.T276Qfs*7	ENST00000295797	NM_002740.5	273	ttA/tt	9/18	1	2	FACETS	0.821	0.753	0.892	0.821	0.753	0.892	CLONAL	1	TRUE	1	0.413506118687786	2		605	966	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998165	169998165	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	165	619	1	ENST00000295797.4:c.861del	p.Glu288SerfsTer45	p.E288Sfs*45	ENST00000295797	NM_002740.5	286	Aaa/aa	9/18	1	2	FACETS	0.863	0.792	0.936	0.863	0.792	0.936	CLONAL	1	TRUE	1	0.413506118687786	2		620	925	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	85	436	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	0.916	0.813	1	0.916	0.813	1	CLONAL	1	TRUE	1	0.413506118687786	2		436	449	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921337	178921337	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	124	430	0	ENST00000263967.3:c.819A>G	p.Ile273Met	p.I273M	ENST00000263967	NM_006218.2	273	atA/atG	5/21	1	2	FACETS	0.898	0.814	0.986	0.898	0.814	0.986	CLONAL	1	TRUE	1	0.413506118687786	2		430	668	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506996	186506996	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	42	218	0	ENST00000323963.5:c.1162A>G	p.Ile388Val	p.I388V	ENST00000323963		388	Att/Gtt	11/11	1	2	FACETS	0.555	0.464	0.655	0.555	0.464	0.655	SUBCLONAL	1	TRUE	1	0.413506118687786	2		218	366	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1936921	1936921	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	96	381	1	ENST00000382891.5:c.1606A>T	p.Thr536Ser	p.T536S	ENST00000382891	NM_133335.3	536	Aca/Tca	7/22	1	2	FACETS	0.792	0.707	0.882	0.792	0.707	0.882	SUBCLONAL	1	TRUE	1	0.413506118687786	2		382	586	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244148	153244148	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	155	468	2	ENST00000281708.4:c.2009del	p.Gly670GlufsTer37	p.G670Efs*37	ENST00000281708	NM_033632.3	670	gGa/ga	12/12	1	2	FACETS	0.981	0.9	1	0.981	0.9	1	CLONAL	1	TRUE	1	0.413506118687786	2		470	764	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249478	153249478	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	172	538	0	ENST00000281708.4:c.1300A>G	p.Ile434Val	p.I434V	ENST00000281708	NM_033632.3	434	Atc/Gtc	9/12	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.413506118687786	2		538	775	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867541	35867541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	77	186	1	ENST00000303115.3:c.361del	p.Ile121Ter	p.I121*	ENST00000303115	NM_002185.3	119	Aaa/aa	3/8	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.413506118687786	2		187	362	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874637	35874637	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	93	350	4	ENST00000303115.3:c.799del	p.Arg267GlyfsTer28	p.R267Gfs*28	ENST00000303115	NM_002185.3	265	Aaa/aa	6/8	1	2	FACETS	0.722	0.643	0.806	0.722	0.643	0.806	SUBCLONAL	1	TRUE	1	0.413506118687786	2		354	623	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958620	38958620	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	40	195	0	ENST00000357387.3:c.2345C>T	p.Ala782Val	p.A782V	ENST00000357387	NM_152756.3	782	gCc/gTc	24/38	1	2	FACETS	0.711	0.594	0.84	0.711	0.594	0.84	SUBCLONAL	1	TRUE	1	0.413506118687786	2		195	272	SUCCESS
APC	324	MSKCC	GRCh37	5	112102932	112102932	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554069710	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	90	323	0	ENST00000257430.4:c.271del	p.Met91CysfsTer34	p.M91Cfs*34	ENST00000257430	NM_000038.5	89	tcA/tc	4/16	1	2	FACETS	0.946	0.843	1	0.946	0.843	1	CLONAL	1	TRUE	1	0.413506118687786	2		323	460	SUCCESS
APC	324	MSKCC	GRCh37	5	112137021	112137021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762117133	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	114	321	0	ENST00000257430.4:c.775C>T	p.Arg259Trp	p.R259W	ENST00000257430	NM_000038.5	259	Cgg/Tgg	8/16	1	2	FACETS	0.993	0.898	1	0.993	0.898	1	CLONAL	1	TRUE	1	0.413506118687786	2		321	555	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052980	180052980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	200	781	0	ENST00000261937.6:c.1310G>A	p.Arg437His	p.R437H	ENST00000261937	NM_182925.4	437	cGt/cAt	10/30	1	2	FACETS	0.832	0.77	0.897	0.832	0.77	0.897	CLONAL	1	TRUE	1	0.413506118687786	2		781	1162	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671772	30671772	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1237536606	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	170	631	0	ENST00000376406.3:c.5188C>A	p.Pro1730Thr	p.P1730T	ENST00000376406	NM_014641.2	1730	Cct/Act	10/15	1	2	FACETS	0.992	0.913	1	0.992	0.913	1	CLONAL	1	TRUE	1	0.413506118687786	2		631	829	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166924	32166924	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	164	657	0	ENST00000375023.3:c.4316-2A>C		p.X1439_splice	ENST00000375023	NM_004557.3	1439			1	2	FACETS	0.853	0.783	0.926	0.853	0.783	0.926	CLONAL	1	TRUE	1	0.413506118687786	2		657	930	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678985	117678986	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	74	322	0	ENST00000368508.3:c.3835dup	p.Ser1279PhefsTer52	p.S1279Ffs*52	ENST00000368508	NM_002944.2	1279	tct/tTct	24/43	1	2	FACETS	0.899	0.791	1	0.899	0.791	1	CLONAL	1	TRUE	1	0.413506118687786	2		322	398	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724328	117724328	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	157	485	0	ENST00000368508.3:c.551C>A	p.Pro184His	p.P184H	ENST00000368508	NM_002944.2	184	cCc/cAc	6/43	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.413506118687786	2		485	709	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151833975	151833975	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	49	441	0	ENST00000262189.6:c.14678A>G	p.Asp4893Gly	p.D4893G	ENST00000262189	NM_170606.2	4893	gAc/gGc	59/59	0.413506118687786	2	FACETS	0.309	0.26	0.362	0.154	0.13	0.181	SUBCLONAL	1	TRUE	0	0.413506118687786	2		441	768	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012371	152012371	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	245	398	0	ENST00000262189.6:c.442G>T	p.Gly148Ter	p.G148*	ENST00000262189	NM_170606.2	148	Gga/Tga	4/59	NA	2	FACETS	0.974	0.918	1			1	INDETERMINATE	2	TRUE	NA	0.413506118687786	2		398	608	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133935	38133935	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	287	799	1	ENST00000317025.8:c.3951G>T	p.Lys1317Asn	p.K1317N	ENST00000317025	NM_023034.1	1317	aaG/aaT	23/24	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.413506118687786	2		800	1266	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372376	55372376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	211	775	0	ENST00000297316.4:c.1066G>A	p.Gly356Arg	p.G356R	ENST00000297316	NM_022454.3	356	Ggg/Agg	2/2	1	2	FACETS	0.902	0.837	0.97	0.902	0.837	0.97	CLONAL	1	TRUE	1	0.413506118687786	2		775	1131	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542163	141542163	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324425100	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	137	471	1	ENST00000220592.5:c.2560C>T	p.Arg854Cys	p.R854C	ENST00000220592	NM_012154.3	854	Cgc/Tgc	19/19	1	2	FACETS	0.858	0.781	0.939	0.858	0.781	0.939	CLONAL	1	TRUE	1	0.413506118687786	2		472	772	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561427	141561427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	110	360	0	ENST00000220592.5:c.1378C>T	p.Arg460Cys	p.R460C	ENST00000220592	NM_012154.3	460	Cgc/Tgc	11/19	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.413506118687786	2		360	482	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738154	145738154	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1430844611	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	51	652	2	ENST00000428558.2:c.2756C>T	p.Ala919Val	p.A919V	ENST00000428558	NM_004260.3	919	gCc/gTc	17/22	1	2	FACETS	0.275	0.233	0.322	0.275	0.233	0.322	SUBCLONAL	1	TRUE	1	0.413506118687786	2		654	896	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507414	8507414	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	71	263	0	ENST00000356435.5:c.1564T>G	p.Phe522Val	p.F522V	ENST00000356435		522	Ttc/Gtc	11/35	0.413506118687786	2	FACETS	0.735	0.644	0.834	0.368	0.322	0.417	SUBCLONAL	1	TRUE	0	0.413506118687786	2		263	467	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524955	8524955	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	62	332	1	ENST00000356435.5:c.649T>C	p.Tyr217His	p.Y217H	ENST00000356435		217	Tat/Cat	7/35	0.413506118687786	2	FACETS	0.568	0.491	0.651	0.284	0.245	0.326	SUBCLONAL	1	TRUE	0	0.413506118687786	2		333	528	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209616	98209617	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761353734	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	81	432	3	ENST00000331920.6:c.3921dup	p.Arg1308GlnfsTer17	p.R1308Qfs*17	ENST00000331920	NM_000264.3	1307	-/C	23/24	1	2	FACETS	0.748	0.66	0.841	0.748	0.66	0.841	SUBCLONAL	1	TRUE	1	0.413506118687786	2		435	524	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128420047	128420047	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	164	658	1	ENST00000265960.3:c.381del	p.Lys127AsnfsTer20	p.K127Nfs*20	ENST00000265960	NM_001006617.1	127	aaA/aa	4/12	1	2	FACETS	0.821	0.753	0.892	0.821	0.753	0.892	CLONAL	1	TRUE	1	0.413506118687786	2		659	966	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760827	133760827	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	150	722	0	ENST00000318560.5:c.3150G>A	p.Met1050Ile	p.M1050I	ENST00000318560	NM_005157.4	1050	atG/atA	11/11	1	2	FACETS	0.87	0.795	0.948	0.87	0.795	0.948	CLONAL	1	TRUE	1	0.413506118687786	2		722	834	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424466	47424466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	182	357	0	ENST00000377045.4:c.386G>A	p.Gly129Asp	p.G129D	ENST00000377045	NM_001654.4	129	gGc/gAc	5/16	1	1	FACETS	0.774	0.722	0.827	1	0.992	1	SUBCLONAL	2	TRUE	0	0.413506118687786	1		357	451	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038262	30038277	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGTCCAGGCCAAGGTA	CGTCCAGGCCAAGGTA	TG	novel	NA	P-0035788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	44	484	2	ENST00000338641.4:c.435_447+3delinsTG		p.X145_splice	ENST00000338641	NM_000268.3	145		4/16	0.344891548115098	2	FACETS	1	0.916	1	0.564	0.478	0.658	CLONAL	1	TRUE	0	0.344891548115098	2		486	226	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575625	55575625	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	28	488	0	ENST00000288135.5:c.1151G>A	p.Gly384Asp	p.G384D	ENST00000288135	NM_000222.2	384	gGc/gAc	7/21	0.176189704426909	4	FACETS	0.84	0.674	1	0.42	0.337	0.514	INDETERMINATE	1	TRUE	2	0.344891548115098	4		488	260	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175549	108175549	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204433	NA	P-0035789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	132	440	0	ENST00000278616.4:c.5644C>T	p.Arg1882Ter	p.R1882*	ENST00000278616	NM_000051.3	1882	Cga/Tga	37/63	0.141203220241833	6	FACETS	1	0.97	1	0.765	0.697	0.836	INDETERMINATE	2	TRUE	3	0.324327608668621	6		440	585	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124282	2124282	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375030314	NA	P-0035789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	245	1018	1	ENST00000219476.3:c.2437G>A	p.Val813Met	p.V813M	ENST00000219476	NM_000548.3	813	Gtg/Atg	22/42	0.299311176514679	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.324327608668621	3		1019	802	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	205	938	0	ENST00000269305.4:c.166G>T	p.Glu56Ter	p.E56*	ENST00000269305	NM_001126112.2	56	Gaa/Taa	4/11	0.324327608668621	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.324327608668621	2		938	611	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101026	41101026	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	72	757	0	ENST00000373198.4:c.1330T>G	p.Ser444Ala	p.S444A	ENST00000373198	NM_133170.3	444	Tcc/Gcc	8/32	0.324327608668621	5	FACETS	0.794	0.693	0.904	0.265	0.231	0.302	CLONAL	1	TRUE	2	0.324327608668621	5		757	831	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0035789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	101	328	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.324327608668621	2	FACETS	0.998	0.903	1	0.998	0.903	1	CLONAL	2	TRUE	0	0.324327608668621	2		328	312	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099762	157099762	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0035789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	63	418	0	ENST00000346085.5:c.699C>G	p.Tyr233Ter	p.Y233*	ENST00000346085	NM_020732.3	233	taC/taG	1/20	0.131043171202945	4	FACETS	0.817	0.711	0.929	0.817	0.711	0.929	INDETERMINATE	2	TRUE	2	0.324327608668621	4		418	315	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172206	38172206	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0035789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	386	522	0	ENST00000317025.8:c.2201C>G	p.Ser734Ter	p.S734*	ENST00000317025	NM_023034.1	734	tCa/tGa	12/24	0.324327608668621	11	FACETS	0.942	0.899	0.985			1	CLONAL	7	TRUE	NA	0.324327608668621	11		522	888	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399222	139399222	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs535702482	NA	P-0035789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	95	950	0	ENST00000277541.6:c.4921C>T	p.Pro1641Ser	p.P1641S	ENST00000277541	NM_017617.3	1641	Cct/Tct	26/34	0.32286583469191	3	FACETS	1	0.915	1	0.516	0.459	0.576	CLONAL	1	TRUE	1	0.324327608668621	3		950	660	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0035791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	481	753	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.395116874495829	3	FACETS	0.838	0.804	0.872	0.838	0.804	0.872	CLONAL	3	TRUE	0	0.440621422990257	3		753	1060	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136840	69136840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746734356	NA	P-0035791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	24	336	0	ENST00000288368.4:c.4754G>A	p.Arg1585Gln	p.R1585Q	ENST00000288368	NM_024870.2	1585	cGg/cAg	39/40	0.238466923725717	2	FACETS	0.252	0.197	0.315	0.126	0.098	0.158	INDETERMINATE	1	TRUE	0	0.440621422990257	2		336	433	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510778	120510778	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	299	580	0	ENST00000256646.2:c.1186A>T	p.Asn396Tyr	p.N396Y	ENST00000256646	NM_024408.3	396	Aat/Tat	7/34	0.440621422990257	3	FACETS	0.86	0.811	0.91	0.86	0.811	0.91	CLONAL	2	TRUE	1	0.440621422990257	3		580	963	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974676	21974676	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0035791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	123	556	0	ENST00000304494.5:c.150+1G>A		p.X50_splice	ENST00000304494	NM_000077.4	50			0.258534268479693	1	FACETS	0.829	0.753	0.908	0.829	0.753	0.908	INDETERMINATE	1	TRUE	0	0.440621422990257	1		556	525	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413145	63413145	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	283	342	0	ENST00000330258.3:c.22G>A	p.Ala8Thr	p.A8T	ENST00000330258	NM_152424.3	8	Gct/Act	2/2	0.401018690965681	2	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.440621422990257	2		342	569	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	175	272	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.746596162657739	2		272	406	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101712	27101712	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1195567104	NA	P-0035793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	404	816	0	ENST00000324856.7:c.4993+1G>T		p.X1665_splice	ENST00000324856	NM_006015.4	1665			1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.746596162657739	2		816	976	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913233	NA	P-0035793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	461	794	1	ENST00000451590.1:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000451590	NM_001130442.1	61	cAg/cTg	3/5	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.746596162657739	2		795	1008	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89839754	89839754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	375	846	0	ENST00000389301.3:c.1939G>A	p.Glu647Lys	p.E647K	ENST00000389301	NM_000135.2	647	Gag/Aag	22/43	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.746596162657739	2		846	986	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855786	45855786	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	265	608	0	ENST00000391945.4:c.2024G>T	p.Gly675Val	p.G675V	ENST00000391945	NM_000400.3	675	gGc/gTc	21/23	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.746596162657739	2		608	622	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545883	41545883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	450	854	0	ENST00000263253.7:c.2498C>T	p.Ser833Leu	p.S833L	ENST00000263253	NM_001429.3	833	tCg/tTg	14/31	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.746596162657739	2		854	974	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405939	49405939	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	292	567	0	ENST00000418115.1:c.199G>C	p.Asp67His	p.D67H	ENST00000418115	NM_001664.2	67	Gat/Cat	3/5	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.746596162657739	2		567	679	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916810	178916810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	384	540	0	ENST00000263967.3:c.197C>T	p.Ser66Phe	p.S66F	ENST00000263967	NM_006218.2	66	tCt/tTt	2/21	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.746596162657739	2		540	845	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0035793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	229	453	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.746596162657739	2		453	484	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430698	181430698	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1454294338	NA	P-0035793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	378	752	0	ENST00000325404.1:c.550C>A	p.Pro184Thr	p.P184T	ENST00000325404	NM_003106.3	184	Ccg/Acg	1/1	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.746596162657739	2		752	821	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651893	36651894	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0035793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	49	586	0	ENST00000244741.5:c.19dup	p.Asp7GlyfsTer29	p.D7Gfs*29	ENST00000244741	NM_000389.4	5	-/G	2/3	0.640292893340478	3	FACETS	0.26	0.22	0.305	0.087	0.073	0.102	SUBCLONAL	1	TRUE	0	0.746596162657739	3		586	693	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652070	36652087	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGGAGCGTGTGCGGGG	CTGGGAGCGTGTGCGGGG	ACACGCTC	novel	NA	P-0035793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	199	913	4	ENST00000244741.5:c.192_209delinsACACGCTC	p.Trp65HisfsTer80	p.W65Hfs*80	ENST00000244741	NM_000389.4	64	gcCTGGGAGCGTGTGCGGGGc/gcACACGCTCc	2/3	0.640292893340478	3	FACETS	1	0.986	1	0.409	0.381	0.437	CLONAL	1	TRUE	0	0.746596162657739	3		917	597	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0035793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	296	398	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.746596162657739	2		398	637	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	277	222	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.746596162657739	1		222	312	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053590	37053590	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs63751711	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	133	837	2	ENST00000231790.2:c.677G>A	p.Arg226Gln	p.R226Q	ENST00000231790	NM_000249.3	226	cGa/cAa	8/19	0.3	0	FACETS	0.58	0.532	0.629			1	INDETERMINATE	1	TRUE	0	0.54	0		839	391	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	137	568	3	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.963	0.881	1	0.963	0.881	1	CLONAL	1	TRUE	1	0.54	2		571	527	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	384	372	1	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	1	2	FACETS	0.99	0.949	1	1	0.997	1	CLONAL	2	TRUE	1	0.54	2		373	718	SUCCESS
APC	324	MSKCC	GRCh37	5	112176064	112176064	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554086185	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	60	382	1	ENST00000257430.4:c.4778del	p.Lys1593SerfsTer57	p.K1593Sfs*57	ENST00000257430	NM_000038.5	1591	gcA/gc	16/16	1	2	FACETS	0.661	0.573	0.756	0.661	0.573	0.756	SUBCLONAL	1	TRUE	1	0.54	2		383	336	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911519	134911519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752762812	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	224	611	4	ENST00000398015.3:c.1984C>T	p.Arg662Cys	p.R662C	ENST00000398015	NM_004441.4	662	Cgt/Tgt	11/16	0.3	3	FACETS	0.888	0.833	0.944	0.888	0.833	0.944	INDETERMINATE	2	TRUE	1	0.54	3		615	593	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023769	27023769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	148	722	0	ENST00000324856.7:c.879del	p.Thr294ProfsTer69	p.T294Pfs*69	ENST00000324856	NM_006015.4	292	aCc/ac	1/20	1	2	FACETS	0.845	0.774	0.918	0.845	0.774	0.918	CLONAL	1	TRUE	1	0.54	2		722	649	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	65	478	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.414	0.359	0.473	0.414	0.359	0.473	SUBCLONAL	1	TRUE	1	0.54	2		478	582	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530956	187530956	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs760734038	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	124	447	0	ENST00000441802.2:c.10067C>T	p.Thr3356Met	p.T3356M	ENST00000441802	NM_005245.3	3356	aCg/aTg	15/27	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.54	2		447	409	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835781	68835781	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060501215	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	317	603	4	ENST00000261769.5:c.377del	p.Pro126ArgfsTer89	p.P126Rfs*89	ENST00000261769	NM_004360.3	124	cgC/cg	3/16	1	2	FACETS	0.91	0.867	0.954	1	0.996	1	CLONAL	2	TRUE	1	0.54	2		607	645	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029193	26029195	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	118	415	0	ENST00000435504.4:c.155_157del	p.Pro52del	p.P52del	ENST00000435504		52	cCTCtt/ctt	4/13	0.3	1	FACETS	0.674	0.612	0.74	0.674	0.612	0.74	INDETERMINATE	1	TRUE	0	0.54	1		415	473	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740840	58740840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149137187	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	146	538	0	ENST00000305921.3:c.1745G>A	p.Arg582His	p.R582H	ENST00000305921	NM_003620.3	582	cGc/cAc	6/6	1	2	FACETS	0.952	0.873	1	0.952	0.873	1	CLONAL	1	TRUE	1	0.54	2		538	568	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099103	27099103	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	129	500	0	ENST00000324856.7:c.3524del	p.Pro1175HisfsTer5	p.P1175Hfs*5	ENST00000324856	NM_006015.4	1173	atC/at	13/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.54	2		500	461	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003812	45003812	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	184	585	1	ENST00000558401.1:c.67+1G>A		p.X23_splice	ENST00000558401	NM_004048.2	23			1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.54	2		586	662	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36821030	36821030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1171838543	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	152	713	0	ENST00000373129.3:c.347G>A	p.Arg116His	p.R116H	ENST00000373129	NM_032017.1	116	cGc/cAc	6/12	1	2	FACETS	0.935	0.859	1	0.935	0.859	1	CLONAL	1	TRUE	1	0.54	2		713	602	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357060	89357060	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	145	673	0	ENST00000301030.4:c.574del	p.Ala192GlnfsTer36	p.A192Qfs*36	ENST00000301030	NM_001256183.1	192	Gca/ca	6/13	1	2	FACETS	0.858	0.785	0.933	0.858	0.785	0.933	CLONAL	1	TRUE	1	0.54	2		673	626	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	244	1208	4	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.854	0.798	0.912	0.854	0.798	0.912	CLONAL	1	TRUE	1	0.54	2		1212	1058	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	139	714	2	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.646	0.588	0.706	0.646	0.588	0.706	SUBCLONAL	1	TRUE	1	0.54	2		716	797	SUCCESS
APC	324	MSKCC	GRCh37	5	112116517	112116517	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs869312753	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	56	304	0	ENST00000257430.4:c.562C>T	p.Gln188Ter	p.Q188*	ENST00000257430	NM_000038.5	188	Caa/Taa	6/16	1	2	FACETS	0.705	0.609	0.809	0.705	0.609	0.809	SUBCLONAL	1	TRUE	1	0.54	2		304	294	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68290283	68290283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867530891	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	114	468	0	ENST00000487270.1:c.23G>A	p.Arg8Gln	p.R8Q	ENST00000487270	NM_133509.3	8	cGa/cAa	2/11	1	2	FACETS	0.809	0.731	0.89	0.809	0.731	0.89	CLONAL	1	TRUE	1	0.54	2		468	522	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244967	46244967	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	131	635	0	ENST00000334344.6:c.3065del	p.Pro1022HisfsTer38	p.P1022Hfs*38	ENST00000334344	NM_152641.2	1021	Ccc/cc	15/21	1	2	FACETS	0.834	0.759	0.911	0.834	0.759	0.911	CLONAL	1	TRUE	1	0.54	2		635	582	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223175	36223175	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	274	1391	6	ENST00000222270.7:c.5730del	p.Arg1911AspfsTer23	p.R1911Dfs*23	ENST00000222270	NM_014727.1	1909	Ccc/cc	28/37	1	2	FACETS	0.843	0.79	0.897	0.843	0.79	0.897	CLONAL	1	TRUE	1	0.54	2		1397	1204	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451801	29451801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745317944	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	88	765	0	ENST00000389048.3:c.2764G>A	p.Gly922Arg	p.G922R	ENST00000389048	NM_004304.4	922	Gga/Aga	16/29	0.3	1	FACETS	0.487	0.432	0.544	0.487	0.432	0.544	INDETERMINATE	1	TRUE	0	0.54	1		765	489	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244859	46244859	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	159	732	1	ENST00000334344.6:c.2953C>T	p.Pro985Ser	p.P985S	ENST00000334344	NM_152641.2	985	Cct/Tct	15/21	1	2	FACETS	0.895	0.823	0.97	0.895	0.823	0.97	CLONAL	1	TRUE	1	0.54	2		733	658	SUCCESS
APC	324	MSKCC	GRCh37	5	112178970	112178970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759069096	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	61	392	0	ENST00000257430.4:c.7679G>A	p.Arg2560Gln	p.R2560Q	ENST00000257430	NM_000038.5	2560	cGa/cAa	16/16	1	2	FACETS	0.751	0.653	0.855	0.751	0.653	0.855	SUBCLONAL	1	TRUE	1	0.54	2		392	301	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137323779	137323779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368400425	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	224	1028	0	ENST00000481739.1:c.1072C>T	p.Arg358Trp	p.R358W	ENST00000481739	NM_002957.4	358	Cgg/Tgg	8/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.54	2		1028	809	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968579	55968579	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	200	691	0	ENST00000263923.4:c.2084del	p.Pro695LeufsTer14	p.P695Lfs*14	ENST00000263923	NM_002253.2	695	cCt/ct	14/30	1	2	FACETS	0.982	0.913	1	0.982	0.913	1	CLONAL	1	TRUE	1	0.54	2		691	754	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607627	43607627	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	210	1189	0	ENST00000355710.3:c.1603G>T	p.Gly535Cys	p.G535C	ENST00000355710	NM_020975.4	535	Ggc/Tgc	8/20	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.54	2		1189	777	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444471	49444471	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	126	770	1	ENST00000301067.7:c.2900G>A	p.Ser967Asn	p.S967N	ENST00000301067	NM_003482.3	967	aGt/aAt	11/54	1	2	FACETS	0.806	0.732	0.883	0.806	0.732	0.883	CLONAL	1	TRUE	1	0.54	2		771	579	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034903	42034903	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	164	711	0	ENST00000219905.7:c.4745T>C	p.Val1582Ala	p.V1582A	ENST00000219905	NM_001164273.1	1582	gTt/gCt	15/24	1	2	FACETS	0.926	0.853	1	0.926	0.853	1	CLONAL	1	TRUE	1	0.54	2		711	656	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007798	45007799	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	147	506	1	ENST00000558401.1:c.246_247del	p.Phe82LeufsTer7	p.F82Lfs*7	ENST00000558401	NM_004048.2	82	tTC/t	2/4	1	2	FACETS	0.939	0.861	1	0.939	0.861	1	CLONAL	1	TRUE	1	0.54	2		507	580	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647490	3647490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143831403	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	145	1069	0	ENST00000294008.3:c.1573C>T	p.Arg525Cys	p.R525C	ENST00000294008	NM_032444.2	525	Cgc/Tgc	7/15	1	2	FACETS	0.617	0.562	0.673	0.617	0.562	0.673	SUBCLONAL	1	TRUE	1	0.54	2		1069	871	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808913	3808913	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	186	767	0	ENST00000262367.5:c.3311A>G	p.Gln1104Arg	p.Q1104R	ENST00000262367	NM_004380.2	1104	cAg/cGg	17/31	1	2	FACETS	0.892	0.826	0.961	0.892	0.826	0.961	CLONAL	1	TRUE	1	0.54	2		767	772	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646865	37646865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749022057	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	209	635	1	ENST00000447079.4:c.1987C>T	p.Arg663Cys	p.R663C	ENST00000447079	NM_015083.1	663	Cgt/Tgt	3/14	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.54	2		636	754	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37665956	37665956	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	103	507	0	ENST00000447079.4:c.2610-2A>C		p.X870_splice	ENST00000447079	NM_015083.1	870			1	2	FACETS	0.727	0.653	0.805	0.727	0.653	0.805	SUBCLONAL	1	TRUE	1	0.54	2		507	525	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804384	46804384	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	126	635	0	ENST00000290295.7:c.623C>T	p.Pro208Leu	p.P208L	ENST00000290295	NM_006361.5	208	cCt/cTt	2/2	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.54	2		635	458	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581231	48581231	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs542392980	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	169	570	0	ENST00000342988.3:c.535A>G	p.Ile179Val	p.I179V	ENST00000342988	NM_005359.5	179	Att/Gtt	5/12	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.54	2		570	619	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2189793	2189793	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	251	882	0	ENST00000398665.3:c.263T>G	p.Leu88Arg	p.L88R	ENST00000398665	NM_032482.2	88	cTg/cGg	4/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.54	2		882	864	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221610	36221610	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	253	933	1	ENST00000222270.7:c.5279G>T	p.Cys1760Phe	p.C1760F	ENST00000222270	NM_014727.1	1760	tGc/tTc	26/37	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.54	2		934	825	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793555	42793555	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	212	1031	1	ENST00000575354.2:c.1357A>T	p.Ile453Phe	p.I453F	ENST00000575354	NM_015125.3	453	Att/Ttt	8/20	1	2	FACETS	0.877	0.816	0.941	0.877	0.816	0.941	CLONAL	1	TRUE	1	0.54	2		1032	895	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546134	41546134	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	130	514	0	ENST00000263253.7:c.2749C>T	p.Gln917Ter	p.Q917*	ENST00000263253	NM_001429.3	917	Cag/Tag	14/31	1	2	FACETS	0.94	0.858	1	0.94	0.858	1	CLONAL	1	TRUE	1	0.54	2		514	512	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039532	180039532	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	225	1078	3	ENST00000261937.6:c.3511del	p.Asp1171ThrfsTer82	p.D1171Tfs*82	ENST00000261937	NM_182925.4	1171	Gac/ac	26/30	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.54	2		1081	803	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800460	32800460	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573005983	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	276	1230	2	ENST00000374899.4:c.1087C>T	p.Arg363Trp	p.R363W	ENST00000374899	NM_018833.2	363	Cgg/Tgg	6/12	1	2	FACETS	0.91	0.855	0.968	0.91	0.855	0.968	CLONAL	1	TRUE	1	0.54	2		1232	1123	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117639372	117639372	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	159	585	1	ENST00000368508.3:c.5984T>C	p.Leu1995Pro	p.L1995P	ENST00000368508	NM_002944.2	1995	cTg/cCg	37/43	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.54	2		586	512	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129084	152129084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761420991	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	166	869	1	ENST00000206249.3:c.37G>A	p.Ala13Thr	p.A13T	ENST00000206249	NM_000125.3	13	Gcc/Acc	1/8	1	2	FACETS	0.899	0.828	0.972	0.899	0.828	0.972	CLONAL	1	TRUE	1	0.54	2		870	684	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523549	148523549	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	33	181	0	ENST00000320356.2:c.904T>C	p.Tyr302His	p.Y302H	ENST00000320356	NM_004456.4	302	Tat/Cat	8/20	1	2	FACETS	0.574	0.471	0.688	0.574	0.471	0.688	SUBCLONAL	1	TRUE	1	0.54	2		181	213	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27220102	27220102	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	179	712	0	ENST00000380036.4:c.3159G>T	p.Gln1053His	p.Q1053H	ENST00000380036	NM_000459.3	1053	caG/caT	21/23	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.54	2		712	652	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128419995	128419995	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1238730432	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	267	906	0	ENST00000265960.3:c.433C>T	p.Arg145Cys	p.R145C	ENST00000265960	NM_001006617.1	145	Cgc/Tgc	4/12	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.54	2		906	931	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354291	70354291	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1218546722	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	121	562	1	ENST00000374080.3:c.4702G>A	p.Gly1568Ser	p.G1568S	ENST00000374080		1568	Ggc/Agc	34/45	0.0532080873119423	2	FACETS	0.846	0.767	0.927			1	INDETERMINATE	1	TRUE	NA	0.54	2		563	530	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220499	123220501	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0035794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	157	383	1	ENST00000218089.9:c.3162_3164del	p.Asp1055del	p.D1055del	ENST00000218089	NM_001042749.1	1052	ggTGAt/ggt	30/35	0.0532080873119423	2	FACETS	0.831	0.773	0.889			1	INDETERMINATE	2	TRUE	NA	0.54	2		384	350	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0035809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	27	158	1	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	FALSE	0	0.377671862220499	1		159	96	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578507	7578507	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519977	NA	P-0035812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	203	798	0	ENST00000269305.4:c.423C>G	p.Cys141Trp	p.C141W	ENST00000269305	NM_001126112.2	141	tgC/tgG	5/11	0.191772963935474	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.29	2		798	619	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545817	41545817	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs750026216	NA	P-0035812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	54	612	0	ENST00000263253.7:c.2432G>T	p.Gly811Val	p.G811V	ENST00000263253	NM_001429.3	811	gGg/gTg	14/31	0.247409372307208	4	FACETS	0.757	0.645	0.878	0.378	0.322	0.439	SUBCLONAL	1	TRUE	2	0.29	4		612	635	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302238	15302238	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	63	548	0	ENST00000263388.2:c.1033A>C	p.Thr345Pro	p.T345P	ENST00000263388	NM_000435.2	345	Act/Cct	6/33	1	2	FACETS	0.398	0.344	0.457	0.398	0.344	0.457	SUBCLONAL	1	TRUE	1	0.514829138642855	2		548	615	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0035815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	35	577	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.189277245821278	1	FACETS	0.933	0.766	1	0.933	0.766	1	CLONAL	1	TRUE	0	0.189277245821278	1		577	359	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268761	41268761	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs778624338	NA	P-0035815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	67	417	0	ENST00000349496.5:c.999C>A	p.Tyr333Ter	p.Y333*	ENST00000349496	NM_001904.3	333	taC/taA	7/15	0.173311622822063	2	FACETS	0.849	0.741	0.965	0.849	0.741	0.965	CLONAL	2	TRUE	0	0.189277245821278	2		417	417	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437783	52437789	+	frameshift_variant	Frame_Shift_Del	DEL	AGAGGTC	AGAGGTC	-	novel	NA	P-0035815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	100	595	0	ENST00000460680.1:c.1372_1378del	p.Asp458GlnfsTer111	p.D458Qfs*111	ENST00000460680	NM_004656.3	458	GACCTCTca/ca	13/17	0.173311622822063	2	FACETS	0.815	0.729	0.907	0.815	0.729	0.907	CLONAL	2	TRUE	0	0.189277245821278	2		595	648	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0035816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	106	625	3	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.427611090562039	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.45188507866323	1		628	298	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0035816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	34	790	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.147806913195187	2	FACETS	0.187	0.152	0.227	0.093	0.076	0.114	INDETERMINATE	1	TRUE	0	0.45188507866323	2		790	805	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121601	108121601	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0035816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	144	400	0	ENST00000278616.4:c.1409C>G	p.Ser470Ter	p.S470*	ENST00000278616	NM_000051.3	470	tCa/tGa	10/63	0.45188507866323	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.45188507866323	1		400	440	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0035820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	108	673	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	0.225319283434237	2		673	840	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0035820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	122	570	0	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.225319283434237	2		570	762	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097802	27097802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	44	336	0	ENST00000324856.7:c.3391C>T	p.Gln1131Ter	p.Q1131*	ENST00000324856	NM_006015.4	1131	Cag/Tag	12/20	1	2	FACETS	0.955	0.802	1	0.955	0.802	1	CLONAL	1	TRUE	1	0.225319283434237	2		336	409	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623566	43623566	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0035820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	35	360	0	ENST00000355710.3:c.3194C>G	p.Ser1065Ter	p.S1065*	ENST00000355710	NM_020975.4	1065	tCa/tGa	20/20	1	2	FACETS	0.62	0.508	0.747	0.62	0.508	0.747	SUBCLONAL	1	TRUE	1	0.225319283434237	2		360	501	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493770	56493770	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	89	381	1	ENST00000267101.3:c.3086C>A	p.Ser1029Tyr	p.S1029Y	ENST00000267101	NM_001982.3	1029	tCc/tAc	25/28	1	2	FACETS	0.764	0.679	0.854	1	0.98	1	SUBCLONAL	2	TRUE	1	0.225319283434237	2		382	517	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845577	128845577	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	98	556	0	ENST00000249373.3:c.874G>C	p.Glu292Gln	p.E292Q	ENST00000249373	NM_005631.4	292	Gag/Cag	4/12	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.225319283434237	2		556	743	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	38	272	0				ENST00000310581	NM_198253.2	-/1132			0.13410211140048	4	FACETS	0.872	0.756	0.986	1	0.956	1	INDETERMINATE	3	TRUE	2	0.661565449914614	4		272	73	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720650	89720650	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1257124719	NA	P-0035821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	28	121	0	ENST00000371953.3:c.802-1G>A		p.X268_splice	ENST00000371953	NM_000314.4	268			0.661565449914614	2	FACETS	0.941	0.809	1	0.941	0.809	1	CLONAL	2	TRUE	0	0.661565449914614	2		121	45	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641489	18641489	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	22	378	0	ENST00000266497.5:c.2488A>C	p.Lys830Gln	p.K830Q	ENST00000266497		830	Aag/Cag	17/31	0.13410211140048	4	FACETS	0.891	0.717	1	0.891	0.717	1	INDETERMINATE	2	TRUE	2	0.661565449914614	4		378	62	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600491	10600491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	42	592	0	ENST00000171111.5:c.1364C>T	p.Pro455Leu	p.P455L	ENST00000171111	NM_203500.1	455	cCa/cTa	4/6	0.369975660745937	3	FACETS	0.928	0.805	1	0.928	0.805	1	INDETERMINATE	2	TRUE	1	0.661565449914614	3		592	91	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241955	39241955	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	22	101	0	ENST00000402219.2:c.1891T>G	p.Tyr631Asp	p.Y631D	ENST00000402219	NM_005633.3	631	Tac/Gac	11/23	0.369975660745937	3	FACETS	1	0.895	1	0.606	0.484	0.738	INDETERMINATE	1	TRUE	1	0.661565449914614	3		101	73	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447116	187447125	+	frameshift_variant	Frame_Shift_Del	DEL	AGAAGCCTGG	AGAAGCCTGG	-	novel	NA	P-0035821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	53	791	0	ENST00000232014.4:c.1068_1077del	p.Gln357AlafsTer72	p.Q357Afs*72	ENST00000232014	NM_001130845.1	356	ctCCAGGCTTCT/ct	5/10	0.662890598475552	3	FACETS	1	0.913	1	1	0.913	1	CLONAL	2	TRUE	1	0.661565449914614	3		791	103	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591116	67591116	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	35	260	0	ENST00000274335.5:c.1709T>C	p.Leu570Pro	p.L570P	ENST00000274335		570	cTt/cCt	12/15	0.13410211140048	4	FACETS	1	0.929	1	1	0.929	1	INDETERMINATE	2	TRUE	2	0.661565449914614	4		260	76	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0035822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	95	398	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.279804234808197	3	FACETS	0.973	0.89	1			1	INDETERMINATE	2	TRUE	NA	0.706851910776786	3		398	187	SUCCESS
APC	324	MSKCC	GRCh37	5	112174096	112174096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs137854575	NA	P-0035822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	57	333	0	ENST00000257430.4:c.2805C>A	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	taC/taA	16/16	0.706851910776786	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.706851910776786	1		333	88	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0035822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	60	863	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.706851910776786	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.706851910776786	1		863	107	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391481	139391481	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	32	860	0	ENST00000277541.6:c.6710T>G	p.Met2237Arg	p.M2237R	ENST00000277541	NM_017617.3	2237	aTg/aGg	34/34	0.312528379692143	1	FACETS	0.412	0.34	0.491	0.412	0.34	0.491	INDETERMINATE	1	TRUE	0	0.706851910776786	1		860	142	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589610	67589612	+	inframe_deletion	In_Frame_Del	DEL	AAA	AAA	-	novel	NA	P-0035823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	175	262	0	ENST00000274335.5:c.1376_1378del	p.Lys459del	p.K459del	ENST00000274335		458	gAAAaa/gaa	10/15	0.165952004330778	11	FACETS	1	0.957	1	1	0.991	1	CLONAL	12	FALSE	2	0.165952004330778	11		262	301	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913400	NA	P-0035823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	66	335	0	ENST00000349496.5:c.98C>A	p.Ser33Tyr	p.S33Y	ENST00000349496	NM_001904.3	33	tCt/tAt	3/15	0.165952004330778	7	FACETS	0.935	0.83	1	1	0.979	1	CLONAL	7	FALSE	3	0.165952004330778	7		335	172	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0035823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	81	622	5	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	0.124632573661616	4	FACETS	0.998	0.9	1	1	0.989	1	CLONAL	6	FALSE	2	0.165952004330778	4		627	190	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624301	89624301	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	33	534	0	ENST00000371953.3:c.75G>C	p.Leu25Phe	p.L25F	ENST00000371953	NM_000314.4	25	ttG/ttC	1/9	0.124632573661616	4	FACETS	1	0.856	1	0.531	0.432	0.642	CLONAL	1	FALSE	2	0.165952004330778	4		534	437	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655389	67655389	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	27	568	0	ENST00000264010.4:c.1252C>A	p.Gln418Lys	p.Q418K	ENST00000264010	NM_006565.3	418	Caa/Aaa	7/12	1	2	FACETS	1	0.817	1	1	0.817	1	CLONAL	1	FALSE	1	0.165952004330778	2		568	317	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118997	70118998	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0035823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	126	608	0	ENST00000245479.2:c.571dup	p.Glu191GlyfsTer61	p.E191Gfs*61	ENST00000245479	NM_000346.3	190	gag/gaGg	2/3	0.163893068111532	4	FACETS	0.942	0.862	1	1	0.991	1	CLONAL	5	FALSE	2	0.165952004330778	4		608	376	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599937	10599937	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369083385	NA	P-0035823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	128	596	0	ENST00000171111.5:c.1639G>A	p.Val547Ile	p.V547I	ENST00000171111	NM_203500.1	547	Gta/Ata	5/6	0.165952004330778	7	FACETS	0.934	0.858	1	1	0.989	1	CLONAL	7	FALSE	3	0.165952004330778	7		596	334	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106940	27106940	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	81	417	0	ENST00000324856.7:c.6551C>A	p.Ala2184Asp	p.A2184D	ENST00000324856	NM_006015.4	2184	gCc/gAc	20/20	0.165952004330778	8	FACETS	1	0.924	1	1	0.987	1	CLONAL	8	FALSE	4	0.165952004330778	8		417	178	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106920	27106938	+	frameshift_variant	Frame_Shift_Del	DEL	GGACAGCCTGGCAGCTCGT	GGACAGCCTGGCAGCTCGT	-	novel	NA	P-0035823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	75	439	0	ENST00000324856.7:c.6532_6550del	p.Asp2178ProfsTer16	p.D2178Pfs*16	ENST00000324856	NM_006015.4	2177	ggGGACAGCCTGGCAGCTCGT/gg	20/20	0.165952004330778	8	FACETS	1	0.921	1	1	0.984	1	CLONAL	7	FALSE	4	0.165952004330778	8		439	187	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37665978	37665978	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	58	458	0	ENST00000447079.4:c.2630A>G	p.Asp877Gly	p.D877G	ENST00000447079	NM_015083.1	877	gAt/gGt	7/14	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.274209643886631	2		458	288	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37672062	37672062	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0035824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	57	416	0	ENST00000447079.4:c.2846+1G>T		p.X949_splice	ENST00000447079	NM_015083.1	949			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.274209643886631	2		416	299	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180374	38180374	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1318941505	NA	P-0035824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	132	639	0	ENST00000396334.3:c.222C>G	p.Ile74Met	p.I74M	ENST00000396334	NM_002468.4	74	atC/atG	1/5	0.19888346095396	4	FACETS	1	0.98	1	0.651	0.59	0.715	CLONAL	1	FALSE	2	0.274209643886631	4		639	942	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576853	7576853	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs11575996	NA	P-0035827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	154	598	0	ENST00000269305.4:c.993G>T	p.Gln331His	p.Q331H	ENST00000269305	NM_001126112.2	331	caG/caT	9/11	0.206791058753465	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	3	TRUE	1	0.206791058753465	4		598	547	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691186	18691186	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	18	427	0	ENST00000266497.5:c.3297C>A	p.Cys1099Ter	p.C1099*	ENST00000266497		1099	tgC/tgA	23/31	0.206791058753465	0	FACETS	1	0.828	1			1	CLONAL	1	TRUE	0	0.206791058753465	0		427	124	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7123001	7123001	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0035827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	53	670	1	ENST00000302850.5:c.3259-1G>T		p.X1087_splice	ENST00000302850	NM_000208.2	1087			0.206791058753465	1	FACETS	0.999	0.853	1	0.999	0.853	1	CLONAL	1	TRUE	0	0.206791058753465	1		671	460	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290009	15290009	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	53	847	0	ENST00000263388.2:c.3545G>A	p.Cys1182Tyr	p.C1182Y	ENST00000263388	NM_000435.2	1182	tGc/tAc	22/33	1	2	FACETS	0.811	0.691	0.943	0.811	0.691	0.943	CLONAL	1	TRUE	1	0.206791058753465	2		847	632	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889108	76889108	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	10	317	0	ENST00000373344.5:c.4902G>C	p.Trp1634Cys	p.W1634C	ENST00000373344	NM_000489.3	1634	tgG/tgC	18/35	0.206791058753465	0	FACETS	0.544	0.37	0.761			1	SUBCLONAL	1	TRUE	0	0.206791058753465	0		317	141	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52621447	52621447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	95	464	0	ENST00000394830.3:c.2970del	p.Glu991LysfsTer17	p.E991Kfs*17	ENST00000394830	NM_018313.4	990	aaA/aa	20/30	0.3532722458353	1	FACETS	0.952	0.852	1	0.952	0.852	1	CLONAL	1	TRUE	0	0.3532722458353	1		464	465	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902696	1902696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	95	832	0	ENST00000382891.5:c.315G>A	p.Met105Ile	p.M105I	ENST00000382891	NM_133335.3	105	atG/atA	2/22	0.330887600715543	0	FACETS	0.75	0.671	0.833			1	SUBCLONAL	1	TRUE	0	0.3532722458353	0		832	464	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991107	41991107	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	74	422	0	ENST00000219905.7:c.2060C>G	p.Ser687Cys	p.S687C	ENST00000219905	NM_001164273.1	687	tCt/tGt	4/24	1	2	FACETS	0.825	0.724	0.933	0.825	0.724	0.933	CLONAL	1	TRUE	1	0.3532722458353	2		422	508	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058642	47058647	+	inframe_deletion	In_Frame_Del	DEL	TCTTAA	TCTTAA	-	novel	NA	P-0035831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	117	636	0	ENST00000409792.3:c.7631_7636del	p.Ile2544_Lys2545del	p.I2544_K2545del	ENST00000409792	NM_014159.6	2544	aTTAAGAag/aag	21/21	0.3532722458353	1	FACETS	0.953	0.863	1	0.953	0.863	1	CLONAL	1	TRUE	0	0.3532722458353	1		636	572	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717777	89717777	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0035832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	247	322	0	ENST00000371953.3:c.801+1G>T		p.X267_splice	ENST00000371953	NM_000314.4	267			0.822728245593923	2	FACETS	0.918	0.883	0.951	0.918	0.883	0.951	CLONAL	2	TRUE	0	0.827936359661009	2		322	325	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371409680	NA	P-0035832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	616	657	0	ENST00000269305.4:c.848G>C	p.Arg283Pro	p.R283P	ENST00000269305	NM_001126112.2	283	cGc/cCc	8/11	0.803075457981814	2	FACETS	0.974	0.953	0.994	0.974	0.953	0.994	CLONAL	2	TRUE	0	0.827936359661009	2		657	764	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937055	48937055	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	515	315	0	ENST00000267163.4:c.823G>T	p.Glu275Ter	p.E275*	ENST00000267163	NM_000321.2	275	Gaa/Taa	8/27	0.799656474749591	4	FACETS	0.962	0.943	0.98	0.962	0.943	0.98	CLONAL	4	TRUE	0	0.827936359661009	4		315	591	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427890	49427890	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	648	755	0	ENST00000301067.7:c.10700T>A	p.Val3567Asp	p.V3567D	ENST00000301067	NM_003482.3	3567	gTt/gAt	38/54	0.827936359661009	3	FACETS	0.992	0.961	1	0.992	0.961	1	CLONAL	2	TRUE	1	0.827936359661009	3		755	1116	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0035833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	48	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.942	0.795	1	0.942	0.795	1	CLONAL	1	TRUE	1	0.148979769590895	2		502	684	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0035833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	86	604	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	1	2	FACETS	0.802	0.709	0.901	1	0.98	1	CLONAL	2	TRUE	1	0.148979769590895	2		604	720	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981550	201981551	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0035833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	100	743	0	ENST00000359651.3:c.466_467dup	p.Gly157GlnfsTer98	p.G157Qfs*98	ENST00000359651		155	gac/gaCCc	3/8	1	2	FACETS	0.826	0.737	0.92	1	0.984	1	CLONAL	2	TRUE	1	0.148979769590895	2		743	813	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974766	21974766	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	14	124	0	ENST00000304494.5:c.61G>C	p.Ala21Pro	p.A21P	ENST00000304494	NM_000077.4	21	Gcc/Ccc	1/3	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.148979769590895	2		124	138	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0035834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	227	673	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.324476632826947	3	FACETS	0.944	0.886	1	0.944	0.886	1	CLONAL	3	TRUE	0	0.329428807388702	3		673	567	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0035834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	79	516	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.78	0.686	0.88	0.78	0.686	0.88	SUBCLONAL	1	TRUE	1	0.329428807388702	2		516	615	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764146326	NA	P-0035834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	142	739	0	ENST00000269305.4:c.841G>A	p.Asp281Asn	p.D281N	ENST00000269305	NM_001126112.2	281	Gac/Aac	8/11	0.329428807388702	1	FACETS	0.927	0.845	1	0.927	0.845	1	CLONAL	1	TRUE	0	0.329428807388702	1		739	777	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177395	56177395	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0035834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	59	350	0	ENST00000399503.3:c.2370-2A>T		p.X790_splice	ENST00000399503	NM_005921.1	790			1	2	FACETS	0.992	0.858	1	0.992	0.858	1	CLONAL	1	TRUE	1	0.329428807388702	2		350	361	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856623	111856623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	85	96	0	ENST00000341259.2:c.674G>A	p.Arg225His	p.R225H	ENST00000341259	NM_005475.2	225	cGc/cAc	2/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.707003006856911	2		96	181	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587782272	NA	P-0035835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	1108	533	0	ENST00000269305.4:c.994-1G>C		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.707003006856911	4	FACETS	0.984	0.969	0.999	0.984	0.969	0.999	CLONAL	4	TRUE	0	0.707003006856911	4		533	1359	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060709	38060709	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	507	796	1	ENST00000250448.2:c.1280C>T	p.Ser427Leu	p.S427L	ENST00000250448	NM_004496.3	427	tCg/tTg	2/2	0.707003006856911	2	FACETS	1	0.989	1	0.545	0.523	0.568	CLONAL	1	TRUE	0	0.707003006856911	2		797	1315	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549203	21549203	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773354669	NA	P-0035835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	400	794	2	ENST00000382592.4:c.3073C>T	p.Leu1025Phe	p.L1025F	ENST00000382592	NM_014572.2	1025	Ctc/Ttc	8/8	0.707003006856911	2	FACETS	1	0.966	1	0.509	0.484	0.533	CLONAL	1	TRUE	0	0.707003006856911	2		796	1112	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217838	7217841	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0035835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	1314	666	0	ENST00000380728.2:c.170_173del	p.Glu57GlyfsTer5	p.E57Gfs*5	ENST00000380728		57	gAAGAg/gg	3/11	0.707003006856911	4	FACETS	0.957	0.942	0.971	0.957	0.942	0.971	CLONAL	4	TRUE	0	0.707003006856911	4		666	1658	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505607	186505607	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	547	463	0	ENST00000323963.5:c.1015G>A	p.Val339Met	p.V339M	ENST00000323963		339	Gtg/Atg	10/11	0.516055881164892	4	FACETS	0.903	0.872	0.934	0.903	0.872	0.934	CLONAL	3	TRUE	1	0.707003006856911	4		463	975	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0035836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	173	488	2	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.26291961377335	9	FACETS	0.93	0.859	1	0.532	0.491	0.574	CLONAL	4	TRUE	2	0.26291961377335	9		490	679	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0035836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	337	757	0	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	0.259995232672146	3	FACETS	0.835	0.79	0.881	0.835	0.79	0.881	CLONAL	3	TRUE	0	0.26291961377335	3		757	1158	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610099	43610099	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	255	581	0	ENST00000355710.3:c.2051C>A	p.Pro684Gln	p.P684Q	ENST00000355710	NM_020975.4	684	cCg/cAg	11/20	0.238022433197938	3	FACETS	0.925	0.865	0.987	0.925	0.865	0.987	CLONAL	2	TRUE	1	0.26291961377335	3		581	1186	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589785	69589785	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	160	16	0	ENST00000168712.1:c.68G>T	p.Trp23Leu	p.W23L	ENST00000168712	NM_002007.2	23	tGg/tTg	1/3	0.26291961377335	21	FACETS	0.984	0.939	1			1	CLONAL	21	TRUE	NA	0.26291961377335	21		16	206	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459646	40459646	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	137	575	0	ENST00000345506.4:c.1811A>T	p.His604Leu	p.H604L	ENST00000345506	NM_003152.3	604	cAc/cTc	16/20	0.254098073947577	3	FACETS	0.979	0.889	1	0.49	0.444	0.538	CLONAL	1	TRUE	1	0.26291961377335	3		575	1204	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546700	9546700	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	124	376	0	ENST00000353224.5:c.1322G>T	p.Ser441Ile	p.S441I	ENST00000353224	NM_177990.2	441	aGc/aTc	5/10	0.15763290181224	4	FACETS	0.861	0.78	0.946	0.861	0.78	0.946	INDETERMINATE	2	TRUE	2	0.26291961377335	4		376	692	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045768	47045768	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	146	314	0	ENST00000377604.3:c.2649del	p.Ile884LeufsTer2	p.I884Lfs*2	ENST00000377604	NM_001204468.1	883	ggC/gg	23/24	0.102494686227364	2	FACETS	0.866	0.793	0.942			1	INDETERMINATE	2	TRUE	NA	0.26291961377335	2		314	641	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	200	812	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.119199726571903	3	FACETS	1	0.988	1	0.644	0.6	0.689	INDETERMINATE	1	TRUE	1	0.690094167505596	3		812	605	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0035839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	206	433	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	0.690094167505596	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.690094167505596	1		433	368	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3634780	3634780	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1296	311	679	0	ENST00000294008.3:c.4729G>T	p.Glu1577Ter	p.E1577*	ENST00000294008	NM_032444.2	1577	Gaa/Taa	13/15	0.690094167505596	4	FACETS	0.948	0.891	1	0.316	0.297	0.336	CLONAL	1	TRUE	1	0.690094167505596	4		679	1607	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061462	38061462	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	82	489	0	ENST00000250448.2:c.527T>C	p.Ile176Thr	p.I176T	ENST00000250448	NM_004496.3	176	aTc/aCc	2/2	1	2	FACETS	0.721	0.637	0.811	0.721	0.637	0.811	SUBCLONAL	1	TRUE	1	0.411046533705192	2		489	553	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506330	120506330	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	78	554	0	ENST00000256646.2:c.1782C>G	p.Ile594Met	p.I594M	ENST00000256646	NM_024408.3	594	atC/atG	11/34	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.411046533705192	NA		554	687	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506380	120506380	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	77	565	0	ENST00000256646.2:c.1732C>A	p.Pro578Thr	p.P578T	ENST00000256646	NM_024408.3	578	Cct/Act	11/34	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.411046533705192	NA		565	707	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842720	68842727	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTGGAT	CTCTGGAT	-	novel	NA	P-0035842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	157	584	0	ENST00000261769.5:c.656_663del	p.Pro219GlnfsTer22	p.P219Qfs*22	ENST00000261769	NM_004360.3	219	cCTCTGGAT/c	5/16	0.411046533705192	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.411046533705192	1		584	563	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804379	46804379	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1467916908	NA	P-0035842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	91	490	0	ENST00000290295.7:c.628G>A	p.Ala210Thr	p.A210T	ENST00000290295	NM_006361.5	210	Gcc/Acc	2/2	0.411046533705192	1	FACETS	0.718	0.64	0.801	0.718	0.64	0.801	SUBCLONAL	1	TRUE	0	0.411046533705192	1		490	490	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115405	115115429	+	protein_altering_variant	In_Frame_Del	DEL	TCCAGTGTCCCGGAAACCTTTTGCA	TCCAGTGTCCCGGAAACCTTTTGCA	C	novel	NA	P-0035842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	66	629	0	ENST00000257566.3:c.897_921delinsG	p.Phe299_Gly307delinsLeu	p.F299_G307delinsL	ENST00000257566	NM_016569.3	299	ttTGCAAAAGGTTTCCGGGACACTGGA/ttG	5/8	1	2	FACETS	0.458	0.397	0.524	0.458	0.397	0.524	SUBCLONAL	1	TRUE	1	0.411046533705192	2		629	701	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579321	7579322	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs587780067	NA	P-0035847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	289	594	0	ENST00000269305.4:c.365_366del	p.Val122AspfsTer26	p.V122Dfs*26	ENST00000269305	NM_001126112.2	122	gTG/g	4/11	0.689369983846872	1	FACETS	0.922	0.876	0.968	0.922	0.876	0.968	CLONAL	1	TRUE	0	0.689369983846872	1		594	596	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631837	90631837	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519736	NA	P-0035847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	202	622	0	ENST00000330062.3:c.516G>C	p.Arg172Ser	p.R172S	ENST00000330062	NM_002168.2	172	agG/agC	4/11	0.346375728611902	1	FACETS	0.384	0.356	0.413	0.384	0.356	0.413	INDETERMINATE	1	TRUE	0	0.689369983846872	1		622	1000	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0035848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	637	812	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	NA	2	FACETS	0.971	0.947	0.994			1	INDETERMINATE	2	TRUE	NA	0.761012044991544	2		812	862	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591925	48591925	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	87	521	2	ENST00000342988.3:c.1088G>T	p.Cys363Phe	p.C363F	ENST00000342988	NM_005359.5	363	tGt/tTt	9/12	0.406175078165779	1	FACETS	0.779	0.693	0.87	0.779	0.693	0.87	SUBCLONAL	1	TRUE	0	0.406175078165779	1		523	438	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023855	27023855	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	39	139	0	ENST00000324856.7:c.961C>T	p.Gln321Ter	p.Q321*	ENST00000324856	NM_006015.4	321	Cag/Tag	1/20	0.406175078165779	1	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	0	0.406175078165779	1		139	150	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0035850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	139	298	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.961	0.878	1	0.961	0.878	1	CLONAL	1	TRUE	1	0.48877432748414	2		298	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781504	NA	P-0035850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	230	701	1	ENST00000269305.4:c.314G>A	p.Gly105Asp	p.G105D	ENST00000269305	NM_001126112.2	105	gGc/gAc	4/11	1	2	FACETS	0.989	0.922	1	0.989	0.922	1	CLONAL	1	TRUE	1	0.48877432748414	2		702	952	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0035850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	249	660	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.48877432748414	2		661	1014	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075570	8075570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1289050189	NA	P-0035850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	52	609	0	ENST00000377482.5:c.110G>A	p.Arg37His	p.R37H	ENST00000377482	NM_018948.3	37	cGc/cAc	2/4	1	2	FACETS	0.217	0.184	0.254	0.217	0.184	0.254	SUBCLONAL	1	TRUE	1	0.48877432748414	2		609	979	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845336	42845336	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	229	771	1	ENST00000398585.3:c.926G>T	p.Ser309Ile	p.S309I	ENST00000398585	NM_001135099.1	309	aGc/aTc	9/14	1	2	FACETS	0.982	0.916	1	0.982	0.916	1	CLONAL	1	TRUE	1	0.48877432748414	2		772	954	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053354	37053354	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0035850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	38	632	0	ENST00000231790.2:c.588+1G>A		p.X196_splice	ENST00000231790	NM_000249.3	196			0.48877432748414	1	FACETS	0.156	0.129	0.188	0.156	0.129	0.188	SUBCLONAL	1	TRUE	0	0.48877432748414	1		632	751	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912116	76912116	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	190	259	0	ENST00000373344.5:c.4148A>G	p.Asp1383Gly	p.D1383G	ENST00000373344	NM_000489.3	1383	gAt/gGt	13/35	1	1	FACETS	0.803	0.754	0.85	1	0.993	1	CLONAL	2	TRUE	0	0.48877432748414	1		259	366	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0035851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	2017	433	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.254816991175983	19	FACETS	1	0.989	1	0.95	0.936	0.964	CLONAL	17	TRUE	1	0.254816991175983	19		433	2931	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0035851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	2171	587	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.254816991175983	19	FACETS	1	0.989	1	1	0.989	1	CLONAL	18	TRUE	1	0.254816991175983	19		587	2986	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246002	41246002	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	204	834	0	ENST00000357654.3:c.1546G>T	p.Asp516Tyr	p.D516Y	ENST00000357654	NM_007294.3	516	Gat/Tat	10/23	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.254816991175983	2		834	1215	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31521249	31521250	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0035851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	151	666	0	ENST00000344624.3:c.926_927dup	p.Glu310LysfsTer43	p.E310Kfs*43	ENST00000344624		309	-/AA	3/33	0.254816991175983	3	FACETS	1	0.972	1	0.577	0.527	0.631	CLONAL	1	TRUE	1	0.254816991175983	3		666	1157	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447715	187447715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778509539	NA	P-0035851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	69	603	1	ENST00000232014.4:c.478C>T	p.Arg160Cys	p.R160C	ENST00000232014	NM_001130845.1	160	Cgt/Tgt	5/10	1	2	FACETS	0.586	0.509	0.67	0.586	0.509	0.67	SUBCLONAL	1	TRUE	1	0.254816991175983	2		604	924	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0035851-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	1201	433	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.365485723301867	23	FACETS	1	0.995	1	1	0.998	1	CLONAL	23	FALSE	1	0.365485723301867	23		433	1361	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0035851-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	1309	587	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.365485723301867	23	FACETS	1	0.991	1	1	0.991	1	CLONAL	22	FALSE	1	0.365485723301867	23		587	1564	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246002	41246002	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035851-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	107	834	0	ENST00000357654.3:c.1546G>T	p.Asp516Tyr	p.D516Y	ENST00000357654	NM_007294.3	516	Gat/Tat	10/23	0.185546166603381	1	FACETS	0.755	0.685	0.826	1	0.985	1	INDETERMINATE	2	FALSE	0	0.365485723301867	1		834	317	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31521249	31521250	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0035851-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	91	666	0	ENST00000344624.3:c.926_927dup	p.Glu310LysfsTer43	p.E310Kfs*43	ENST00000344624		309	-/AA	3/33	1	2	FACETS	0.865	0.777	0.955	1	0.985	1	CLONAL	2	FALSE	1	0.365485723301867	2		666	288	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631934	90631934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913502	NA	P-0035851-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	14	672	1	ENST00000330062.3:c.419G>A	p.Arg140Gln	p.R140Q	ENST00000330062	NM_002168.2	140	cGg/cAg	4/11	1	2	FACETS	0.173	0.124	0.232	0.173	0.124	0.232	SUBCLONAL	1	FALSE	1	0.365485723301867	2		673	443	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793663	NA	P-0035851-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	8	622	0	ENST00000263967.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000263967	NM_006218.2	93	cGg/cAg	2/21	0.317363425584885	1	FACETS	0.114	0.073	0.168	0.114	0.073	0.168	SUBCLONAL	1	FALSE	0	0.365485723301867	1		622	314	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533093	63533093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750354919	NA	P-0035851-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	41	577	3	ENST00000307078.5:c.1801G>A	p.Gly601Ser	p.G601S	ENST00000307078	NM_004655.3	601	Ggc/Agc	7/11	0.185546166603381	1	FACETS	0.672	0.563	0.791	0.672	0.563	0.791	INDETERMINATE	1	FALSE	0	0.365485723301867	1		580	273	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259172	36259172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035851-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	197	514	1	ENST00000300305.3:c.319C>T	p.Arg107Cys	p.R107C	ENST00000300305		107	Cgc/Tgc	3/8	0.270077647611359	4	FACETS	0.914	0.853	0.976	1	0.99	1	CLONAL	3	FALSE	2	0.365485723301867	4		515	537	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879228	151879228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200152380	NA	P-0035851-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	12	588	1	ENST00000262189.6:c.5717G>A	p.Arg1906Gln	p.R1906Q	ENST00000262189	NM_170606.2	1906	cGa/cAa	36/59	0.198036778670533	2	FACETS	0.344	0.242	0.469	0.172	0.121	0.235	INDETERMINATE	1	FALSE	0	0.365485723301867	2		589	191	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0035853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	123	628	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	TRUE	1	0.293647090238822	2		628	754	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0035855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	142	353	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.42302199318087	2	FACETS	0.907	0.836	0.981	0.454	0.418	0.491	INDETERMINATE	1	TRUE	0	0.786393797098254	2		353	398	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916946	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0035855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	194	375	0	ENST00000263967.3:c.332_334del	p.Lys111del	p.K111del	ENST00000263967	NM_006218.2	111	AAG/-	2/21	0.42302199318087	2	FACETS	1	0.95	1	0.51	0.476	0.544	INDETERMINATE	1	TRUE	0	0.786393797098254	2		375	484	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063717	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs924551538	NA	P-0035855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	39	169	1	ENST00000412916.2:c.165+1G>A		p.X55_splice	ENST00000412916		55			0.452169336900176	1	FACETS	0.409	0.345	0.478	0.409	0.345	0.478	INDETERMINATE	1	TRUE	0	0.786393797098254	1		170	147	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115450	115115451	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAA	novel	NA	P-0035855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	146	554	0	ENST00000257566.3:c.875_876insTTT	p.Gln291_Leu292insPhe	p.Q291_L292insF	ENST00000257566	NM_016569.3	292	tta/ttTTTa	5/8	1	2	FACETS	0.489	0.446	0.533	0.489	0.446	0.533	SUBCLONAL	1	TRUE	1	0.786393797098254	2		554	760	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177727	56177727	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	83	404	0	ENST00000399503.3:c.2701del	p.Ser901ProfsTer8	p.S901Pfs*8	ENST00000399503	NM_005921.1	900	agT/ag	14/20	1	2	FACETS	0.509	0.451	0.57	0.509	0.451	0.57	SUBCLONAL	1	TRUE	1	0.786393797098254	2		404	415	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188297	10188297	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs869025653	NA	P-0035857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	420	711	0	ENST00000256474.2:c.444del	p.Phe148LeufsTer11	p.F148Lfs*11	ENST00000256474	NM_000551.3	147	aTt/at	2/3	0.610304347329646	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.610304347329646	1		711	850	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176496	123176496	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0035857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	62	195	0	ENST00000218089.9:c.462+1G>C		p.X154_splice	ENST00000218089	NM_001042749.1	154			0.610304347329646	0	FACETS	0.495	0.437	0.554			1	SUBCLONAL	1	TRUE	NA	0.610304347329646	0		195	160	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442539	52442539	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	328	574	0	ENST00000460680.1:c.206del	p.Thr69SerfsTer3	p.T69Sfs*3	ENST00000460680	NM_004656.3	69	aCg/ag	4/17	0.610304347329646	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.610304347329646	1		574	682	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163325201	163325201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	30	310	0	ENST00000271452.3:c.1337C>T	p.Ala446Val	p.A446V	ENST00000271452	NM_145697.2	446	gCt/gTt	14/14	0.164317442949057	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		310	378	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	141	812	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.207326700248906	3	FACETS	0.922	0.84	1	0.922	0.84	1	CLONAL	2	TRUE	1	0.207326700248906	3		812	814	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578477	+	inframe_deletion	In_Frame_Del	DEL	GGG	GGG	-	novel	NA	P-0035865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	253	806	0	ENST00000269305.4:c.453_455del	p.Pro153del	p.P153del	ENST00000269305	NM_001126112.2	151	ccCCCg/ccg	5/11	0.207326700248906	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.207326700248906	2		806	1016	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683417	182683417	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	67	607	0	ENST00000292782.4:c.128A>G	p.Asn43Ser	p.N43S	ENST00000292782	NM_020640.2	43	aAt/aGt	2/7	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.207326700248906	2		607	622	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0035866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	835	468	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.611893191874204	4	FACETS	0.961	0.939	0.981	0.961	0.939	0.981	CLONAL	4	TRUE	0	0.611893191874204	4		468	1145	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602619	10602619	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1239985410	NA	P-0035866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	432	732	0	ENST00000171111.5:c.959G>T	p.Arg320Leu	p.R320L	ENST00000171111	NM_203500.1	320	cGg/cTg	3/6	0.581103270411735	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.611893191874204	2		732	685	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278061	18278061	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519801	NA	P-0035866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	187	632	0	ENST00000222254.8:c.1681A>G	p.Asn561Asp	p.N561D	ENST00000222254	NM_005027.3	561	Aac/Gac	13/16	0.581103270411735	2	FACETS	0.857	0.794	0.922	0.429	0.397	0.461	CLONAL	1	TRUE	0	0.611893191874204	2		632	713	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789646	3789646	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	157	511	0	ENST00000262367.5:c.4213G>T	p.Val1405Leu	p.V1405L	ENST00000262367	NM_004380.2	1405	Gtg/Ttg	25/31	0.611893191874204	3	FACETS	0.937	0.861	1	0.469	0.43	0.509	CLONAL	1	TRUE	1	0.611893191874204	3		511	715	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248649	59248650	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0035866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	208	858	0	ENST00000371222.2:c.93dup	p.Lys32GlnfsTer75	p.K32Qfs*75	ENST00000371222	NM_002228.3	31	-/C	1/1	0.611893191874204	2	FACETS	0.79	0.734	0.847	0.395	0.367	0.424	SUBCLONAL	1	TRUE	0	0.611893191874204	2		858	861	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076794	72076794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145840571	NA	P-0035866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	285	538	0	ENST00000357731.5:c.703G>A	p.Val235Met	p.V235M	ENST00000357731	NM_173808.2	235	Gtg/Atg	5/7	0.611893191874204	2	FACETS	0.951	0.907	0.994	0.951	0.907	0.994	CLONAL	2	TRUE	0	0.611893191874204	2		538	490	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439703	49439703	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	371	636	0	ENST00000301067.7:c.4741G>T	p.Glu1581Ter	p.E1581*	ENST00000301067	NM_003482.3	1581	Gag/Tag	18/54	0.611893191874204	3	FACETS	0.936	0.893	0.979	0.936	0.893	0.979	CLONAL	2	TRUE	1	0.611893191874204	3		636	846	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288885	15288885	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	57	176	0	ENST00000263388.2:c.3854G>C	p.Arg1285Pro	p.R1285P	ENST00000263388	NM_000435.2	1285	cGt/cCt	24/33	0.581103270411735	2	FACETS	0.927	0.807	1	0.463	0.403	0.527	CLONAL	1	TRUE	0	0.611893191874204	2		176	201	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488750	212488750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	151	532	0	ENST00000342788.4:c.2099C>A	p.Pro700His	p.P700H	ENST00000342788	NM_005235.2	700	cCc/cAc	18/28	0.602893390867553	3	FACETS	0.987	0.905	1	0.329	0.301	0.358	CLONAL	1	TRUE	0	0.611893191874204	3		532	653	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79974863	79974863	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	284	564	1	ENST00000265081.6:c.1291G>T	p.Ala431Ser	p.A431S	ENST00000265081	NM_002439.4	431	Gcc/Tcc	8/24	0.611893191874204	2	FACETS	0.936	0.892	0.979	0.936	0.892	0.979	CLONAL	2	TRUE	0	0.611893191874204	2		565	496	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64289996	64289996	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	279	468	0	ENST00000370651.3:c.439C>G	p.Leu147Val	p.L147V	ENST00000370651	NM_003463.4	147	Ctg/Gtg	6/6	0.611893191874204	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.611893191874204	2		468	454	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523609	106523609	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0035866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	75	287	0	ENST00000359195.3:c.2760+1G>T		p.X920_splice	ENST00000359195	NM_002649.2	920			0.38808651486588	6	FACETS	1	0.963	1	0.416	0.366	0.469	CLONAL	1	TRUE	3	0.611893191874204	6		287	437	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751191	128751191	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	149	434	0	ENST00000377970.2:c.728A>G	p.Glu243Gly	p.E243G	ENST00000377970	NM_002467.4	243	gAg/gGg	2/3	0.611893191874204	3	FACETS	0.955	0.875	1	0.477	0.437	0.519	CLONAL	1	TRUE	1	0.611893191874204	3		434	666	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482437	56482437	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	107	564	0	ENST00000267101.3:c.985A>G	p.Lys329Glu	p.K329E	ENST00000267101	NM_001982.3	329	Aaa/Gaa	8/28	1	2	FACETS	0.893	0.802	0.989	0.893	0.802	0.989	CLONAL	1	TRUE	1	0.363271592769157	2		564	660	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637689	52637689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	54	547	0	ENST00000394830.3:c.2627G>A	p.Arg876His	p.R876H	ENST00000394830	NM_018313.4	876	cGt/cAt	18/30	0.363271592769157	1	FACETS	0.701	0.602	0.809	0.701	0.602	0.809	SUBCLONAL	1	TRUE	0	0.363271592769157	1		547	347	SUCCESS
APC	324	MSKCC	GRCh37	5	112175372	112175372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	102	278	0	ENST00000257430.4:c.4081C>T	p.Pro1361Ser	p.P1361S	ENST00000257430	NM_000038.5	1361	Ccc/Tcc	16/16	0.32423741386344	2	FACETS	1	0.983	1	0.739	0.666	0.815	CLONAL	1	TRUE	0	0.363271592769157	2		278	380	SUCCESS
APC	324	MSKCC	GRCh37	5	112175093	112175093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	84	244	0	ENST00000257430.4:c.3802C>T	p.Pro1268Ser	p.P1268S	ENST00000257430	NM_000038.5	1268	Cca/Tca	16/16	0.32423741386344	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	0	0.363271592769157	2		244	222	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661120	227661120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	143	659	1	ENST00000305123.5:c.2335G>A	p.Glu779Lys	p.E779K	ENST00000305123	NM_005544.2	779	Gag/Aag	1/2	1	2	FACETS	0.99	0.904	1	0.99	0.904	1	CLONAL	1	TRUE	1	0.363271592769157	2		660	795	SUCCESS
APC	324	MSKCC	GRCh37	5	112174053	112174053	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	125	375	0	ENST00000257430.4:c.2762C>T	p.Ala921Val	p.A921V	ENST00000257430	NM_000038.5	921	gCa/gTa	16/16	0.32423741386344	2	FACETS	0.964	0.883	1	0.964	0.883	1	CLONAL	2	TRUE	0	0.363271592769157	2		375	357	SUCCESS
APC	324	MSKCC	GRCh37	5	112174558	112174558	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs757020768	NA	P-0035867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	152	383	0	ENST00000257430.4:c.3267C>G	p.Phe1089Leu	p.F1089L	ENST00000257430	NM_000038.5	1089	ttC/ttG	16/16	0.32423741386344	2	FACETS	0.94	0.868	1	0.94	0.868	1	CLONAL	2	TRUE	0	0.363271592769157	2		383	445	SUCCESS
APC	324	MSKCC	GRCh37	5	112174973	112174973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	83	264	0	ENST00000257430.4:c.3682C>G	p.Gln1228Glu	p.Q1228E	ENST00000257430	NM_000038.5	1228	Cag/Gag	16/16	0.32423741386344	2	FACETS	0.802	0.716	0.891	0.802	0.716	0.891	CLONAL	2	TRUE	0	0.363271592769157	2		264	285	SUCCESS
APC	324	MSKCC	GRCh37	5	112175046	112175046	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	81	226	0	ENST00000257430.4:c.3755C>G	p.Ser1252Cys	p.S1252C	ENST00000257430	NM_000038.5	1252	tCt/tGt	16/16	0.32423741386344	2	FACETS	0.895	0.801	0.994	0.895	0.801	0.994	CLONAL	2	TRUE	0	0.363271592769157	2		226	249	SUCCESS
APC	324	MSKCC	GRCh37	5	112175370	112175370	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	104	273	0	ENST00000257430.4:c.4079C>T	p.Ser1360Phe	p.S1360F	ENST00000257430	NM_000038.5	1360	tCt/tTt	16/16	0.32423741386344	2	FACETS	1	0.983	1	0.73	0.659	0.805	CLONAL	1	TRUE	0	0.363271592769157	2		273	392	SUCCESS
APC	324	MSKCC	GRCh37	5	112175466	112175466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	186	407	0	ENST00000257430.4:c.4175C>T	p.Ser1392Leu	p.S1392L	ENST00000257430	NM_000038.5	1392	tCa/tTa	16/16	0.32423741386344	2	FACETS	0.889	0.826	0.953	0.889	0.826	0.953	CLONAL	2	TRUE	0	0.363271592769157	2		407	576	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035183	30035184	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0035868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	299	605	0	ENST00000338641.4:c.346dup	p.His116ProfsTer14	p.H116Pfs*14	ENST00000338641	NM_000268.3	115	-/C	3/16	0.723111039135745	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.723111039135745	1		605	503	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246445	105246445	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	152	658	0	ENST00000349310.3:c.155T>G	p.Leu52Arg	p.L52R	ENST00000349310	NM_001014432.1	52	cTc/cGc	4/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.196931218817916	2		658	1093	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226561959	226561959	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1479237968	NA	P-0035870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	37	603	0	ENST00000366794.5:c.2038G>C	p.Glu680Gln	p.E680Q	ENST00000366794	NM_001618.3	680	Gaa/Caa	14/23	1	2	FACETS	0.535	0.439	0.642	0.535	0.439	0.642	SUBCLONAL	1	TRUE	1	0.196931218817916	2		603	703	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154776	2154776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750845881	NA	P-0035870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	63	777	1	ENST00000434045.2:c.445G>A	p.Asp149Asn	p.D149N	ENST00000434045	NM_001127598.1	149	Gac/Aac	4/5	1	2	FACETS	0.568	0.489	0.654	0.568	0.489	0.654	SUBCLONAL	1	TRUE	1	0.196931218817916	2		778	1127	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	152	644	0	ENST00000397062.3:c.246A>T	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaT	2/5	1	2	FACETS	0.892	0.816	0.972	0.892	0.816	0.972	CLONAL	1	TRUE	1	0.38951197157032	2		644	875	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519016	103519016	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	112	463	0	ENST00000355739.4:c.2354A>G	p.Gln785Arg	p.Q785R	ENST00000355739	NM_000123.3	785	cAg/cGg	11/15	1	2	FACETS	0.981	0.885	1	0.981	0.885	1	CLONAL	1	TRUE	1	0.38951197157032	2		463	586	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804198	46804198	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	218	756	0	ENST00000290295.7:c.809A>T	p.Lys270Ile	p.K270I	ENST00000290295	NM_006361.5	270	aAa/aTa	2/2	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.38951197157032	2		756	965	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637981	39637981	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0035872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	125	600	0	ENST00000262039.4:c.2398A>T	p.Lys800Ter	p.K800*	ENST00000262039	NM_002647.2	800	Aaa/Taa	22/25	0.200377941865763	1	FACETS	0.7	0.634	0.77	0.7	0.634	0.77	INDETERMINATE	1	TRUE	0	0.38951197157032	1		600	738	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249943	39249943	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs746798986	NA	P-0035872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	99	646	0	ENST00000402219.2:c.1626A>G	p.Ile542Met	p.I542M	ENST00000402219	NM_005633.3	542	atA/atG	10/23	1	2	FACETS	0.881	0.788	0.979	0.881	0.788	0.979	CLONAL	1	TRUE	1	0.38951197157032	2		646	577	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180799	106180799	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1560563453	NA	P-0035872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	40	408	0	ENST00000380013.4:c.3827T>C	p.Leu1276Pro	p.L1276P	ENST00000380013	NM_001127208.2	1276	cTg/cCg	7/11	1	2	FACETS	0.412	0.342	0.49	0.412	0.342	0.49	SUBCLONAL	1	TRUE	1	0.38951197157032	2		408	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0035875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	92	789	0	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	0.268422630488014	1	FACETS	0.586	0.52	0.658	0.586	0.52	0.658	SUBCLONAL	1	TRUE	0	0.268422630488014	1		789	1012	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974727	21974744	+	inframe_deletion	In_Frame_Del	DEL	CCTCCAGCAGCGCCCGCA	CCTCCAGCAGCGCCCGCA	-	novel	NA	P-0035875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	34	287	0	ENST00000304494.5:c.83_100del	p.Val28_Glu33del	p.V28_E33del	ENST00000304494	NM_000077.4	28	gTGCGGGCGCTGCTGGAGGcg/gcg	1/3	0.268422630488014	1	FACETS	0.494	0.403	0.596	0.494	0.403	0.596	SUBCLONAL	1	TRUE	0	0.268422630488014	1		287	444	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120535170	120535170	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs761499454	NA	P-0035875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	152	520	0	ENST00000229340.5:c.485A>G	p.Asn162Ser	p.N162S	ENST00000229340	NM_006861.6	162	aAc/aGc	6/6	0.268422630488014	1	FACETS	0.761	0.698	0.827	1	0.988	1	SUBCLONAL	2	TRUE	0	0.268422630488014	1		520	644	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016571	12016571	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	57	393	0	ENST00000353533.5:c.707T>G	p.Leu236Arg	p.L236R	ENST00000353533	NM_003010.3	236	cTt/cGt	7/11	0.268422630488014	1	FACETS	0.717	0.615	0.827	0.717	0.615	0.827	SUBCLONAL	1	TRUE	0	0.268422630488014	1		393	513	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340408	8340408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775122610	NA	P-0035875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	74	532	0	ENST00000356435.5:c.5188C>T	p.Arg1730Trp	p.R1730W	ENST00000356435		1730	Cgg/Tgg	31/35	0.268422630488014	1	FACETS	0.648	0.566	0.736	0.648	0.566	0.736	SUBCLONAL	1	TRUE	0	0.268422630488014	1		532	737	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	69	272	0				ENST00000310581	NM_198253.2	-/1132			0.159400759535349	6	FACETS	1	0.952	1	0.397	0.347	0.452	INDETERMINATE	1	TRUE	3	0.502151433351002	6		272	462	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0035908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	105	561	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.159400759535349	6	FACETS	1	0.982	1	0.495	0.444	0.548	INDETERMINATE	1	TRUE	3	0.502151433351002	6		561	565	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045016	47045016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556782040	NA	P-0035908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	127	383	0	ENST00000377604.3:c.2342C>T	p.Ser781Leu	p.S781L	ENST00000377604	NM_001204468.1	781	tCa/tTa	20/24	0.474976224323168	2	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.502151433351002	2		383	414	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023943	27023943	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	24	81	0	ENST00000324856.7:c.1049C>A	p.Ser350Ter	p.S350*	ENST00000324856	NM_006015.4	350	tCg/tAg	1/20	0.191748590813461	6	FACETS	1	0.865	1	0.734	0.59	0.89	INDETERMINATE	2	TRUE	3	0.502151433351002	6		81	87	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228998	36228998	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	138	791	0	ENST00000222270.7:c.7778G>A	p.Arg2593His	p.R2593H	ENST00000222270	NM_014727.1	2593	cGc/cAc	36/37	0.502151433351002	6	FACETS	0.999	0.907	1	0.25	0.226	0.274	CLONAL	1	TRUE	2	0.502151433351002	6		791	1103	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984364	201984365	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CG	novel	NA	P-0035908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	360	539	0	ENST00000359651.3:c.1030_1031dup	p.Val345GlyfsTer103	p.V345Gfs*103	ENST00000359651		343	-/CG	8/8	0.502151433351002	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.502151433351002	3		539	569	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118382717	118382717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs907814598	NA	P-0035908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	51	419	0	ENST00000534358.1:c.11123G>A	p.Arg3708His	p.R3708H	ENST00000534358	NM_005933.3	3708	cGc/cAc	31/36	0.502151433351002	3	FACETS	0.555	0.472	0.645	0.277	0.236	0.323	SUBCLONAL	1	TRUE	1	0.502151433351002	3		419	458	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987025	36987025	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	132	607	0	ENST00000354822.5:c.664G>A	p.Glu222Lys	p.E222K	ENST00000354822	NM_001079668.2	222	Gag/Aag	3/3	0.502151433351002	3	FACETS	1	0.969	1	0.569	0.518	0.622	CLONAL	1	TRUE	1	0.502151433351002	3		607	578	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47724999	47724999	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs772912619	NA	P-0035908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	303	782	0	ENST00000449228.1:c.745G>C	p.Asp249His	p.D249H	ENST00000449228	NM_001127240.2	249	Gac/Cac	4/4	0.502151433351002	6	FACETS	1	0.972	1	0.525	0.494	0.556	CLONAL	2	TRUE	2	0.502151433351002	6		782	1152	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735342	204735342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	50	236	0	ENST00000302823.3:c.143C>T	p.Ala48Val	p.A48V	ENST00000302823	NM_005214.4	48	gCc/gTc	2/4	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.502151433351002	2		236	168	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434140	12434140	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	2581	368	0	ENST00000287820.6:c.508A>G	p.Lys170Glu	p.K170E	ENST00000287820	NM_015869.4	170	Aag/Gag	4/7	0.502151433351002	31	FACETS	1	0.996	1			1	CLONAL	29	TRUE	NA	0.502151433351002	31		368	2909	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650324	48650324	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	119	338	0	ENST00000376670.3:c.294C>A	p.Tyr98Ter	p.Y98*	ENST00000376670	NM_002049.3	98	taC/taA	3/6	0.474976224323168	2	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.502151433351002	2		338	344	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0035909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	141	374	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.730917929010915	3	FACETS	0.954	0.874	1	0.477	0.437	0.519	CLONAL	1	TRUE	1	0.730917929010915	3		374	552	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023405	27023405	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	276	464	0	ENST00000324856.7:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000324856	NM_006015.4	171	Caa/Taa	1/20	0.705571582858664	1	FACETS	0.992	0.945	1	0.992	0.945	1	CLONAL	1	TRUE	0	0.730917929010915	1		464	483	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199862	108199862	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	126	203	0	ENST00000278616.4:c.7204G>T	p.Glu2402Ter	p.E2402*	ENST00000278616	NM_000051.3	2402	Gaa/Taa	49/63	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.730917929010915	2		203	297	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5258138	5258138	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	291	576	1	ENST00000357368.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000357368	NM_002850.3	199	gGa/gTa	8/38	1	2	FACETS	0.999	0.944	1	0.999	0.944	1	CLONAL	1	TRUE	1	0.730917929010915	2		577	797	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177688	56177704	+	frameshift_variant	Frame_Shift_Del	DEL	ATCTGTTCCCAACAACT	ATCTGTTCCCAACAACT	-	novel	NA	P-0035909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	141	287	0	ENST00000399503.3:c.2666_2682del	p.Val889GlyfsTer9	p.V889Gfs*9	ENST00000399503	NM_005921.1	887	gcATCTGTTCCCAACAACTat/gcat	14/20	0.705571582858664	1	FACETS	0.85	0.789	0.911	0.85	0.789	0.911	CLONAL	1	TRUE	0	0.730917929010915	1		287	288	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577563	7577563	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1567549584	NA	P-0035911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	334	555	0	ENST00000269305.4:c.718A>G	p.Ser240Gly	p.S240G	ENST00000269305	NM_001126112.2	240	Agt/Ggt	7/11	0.595793535546689	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.595793535546689	3		555	670	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923045	44923048	+	frameshift_variant	Frame_Shift_Del	DEL	CTAT	CTAT	-	rs398122969	NA	P-0035911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	437	216	0	ENST00000377967.4:c.1909_1912del	p.Ser637ThrfsTer53	p.S637Tfs*53	ENST00000377967	NM_021140.2	636	CTATct/ct	16/29	0.595793535546689	4	FACETS	1	0.994	1			1	CLONAL	4	TRUE	NA	0.595793535546689	4		216	541	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218408	133218408	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	176	660	2	ENST00000320574.5:c.5203G>A	p.Ala1735Thr	p.A1735T	ENST00000320574	NM_006231.2	1735	Gcc/Acc	39/49	0.595793535546689	4	FACETS	1	0.97	1	0.553	0.509	0.598	CLONAL	1	TRUE	2	0.595793535546689	4		662	853	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061200	38061201	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCGGCGCAAG	novel	NA	P-0035912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	171	455	0	ENST00000250448.2:c.777_788dup	p.Arg262_Gln263insHisLeuArgArg	p.R262_Q263insHLRR	ENST00000250448	NM_004496.3	263	cag/caCTTGCGCCGCCAg	2/2	0.306247576569016	3	FACETS	1	0.988	1	0.695	0.642	0.75	CLONAL	1	TRUE	1	0.487045956638865	3		455	628	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578266	7578266	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs942158624	NA	P-0035913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	271	594	0	ENST00000269305.4:c.583A>T	p.Ile195Phe	p.I195F	ENST00000269305	NM_001126112.2	195	Atc/Ttc	6/11	0.47945106457242	2	FACETS	0.787	0.746	0.828	0.787	0.746	0.828	SUBCLONAL	2	TRUE	0	0.6085923871158	2		594	566	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440707	56440707	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0035913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	313	624	0	ENST00000407977.2:c.511A>T	p.Lys171Ter	p.K171*	ENST00000407977		171	Aag/Tag	5/10	0.47945106457242	2	FACETS	0.881	0.84	0.921	0.881	0.84	0.921	CLONAL	2	TRUE	0	0.6085923871158	2		624	584	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795592	42795593	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	91	812	0	ENST00000575354.2:c.2673dup	p.Val892CysfsTer39	p.V892Cfs*39	ENST00000575354	NM_015125.3	891	tct/tcTt	10/20	0.586706183362687	4	FACETS	0.536	0.475	0.602	0.179	0.158	0.201	SUBCLONAL	1	TRUE	1	0.6085923871158	4		812	897	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349247	70349247	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	138	371	0	ENST00000374080.3:c.3659T>A	p.Val1220Glu	p.V1220E	ENST00000374080		1220	gTg/gAg	26/45	1	1	FACETS	0.915	0.844	0.987	0.915	0.844	0.987	CLONAL	1	TRUE	0	0.6085923871158	1		371	345	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945058	151945058	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs748010370	NA	P-0035914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	55	669	0	ENST00000262189.6:c.2461C>G	p.Pro821Ala	p.P821A	ENST00000262189	NM_170606.2	821	Cca/Gca	14/59	1	2	FACETS	0.288	0.245	0.334	0.288	0.245	0.334	SUBCLONAL	1	TRUE	1	0.58291164195827	2		669	656	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820601	44820601	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	27	261	0	ENST00000377967.4:c.298G>C	p.Gly100Arg	p.G100R	ENST00000377967	NM_021140.2	100	Ggt/Cgt	3/29	1	1	FACETS	0.201	0.16	0.248	0.201	0.16	0.248	SUBCLONAL	1	TRUE	0	0.58291164195827	1		261	327	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046534	30046534	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	226	623	0	ENST00000331968.5:c.2649C>G	p.His883Gln	p.H883Q	ENST00000331968	NM_002742.2	883	caC/caG	18/18	1	2	FACETS	0.98	0.916	1	0.98	0.916	1	CLONAL	1	TRUE	1	0.58291164195827	2		623	791	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041855	42041855	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0035914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	211	451	0	ENST00000219905.7:c.6050C>G	p.Ser2017Ter	p.S2017*	ENST00000219905	NM_001164273.1	2017	tCa/tGa	17/24	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.58291164195827	2		451	708	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66679749	66679749	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	145	363	0	ENST00000307102.5:c.64G>A	p.Gly22Arg	p.G22R	ENST00000307102	NM_002755.3	22	Ggg/Agg	1/11	1	2	FACETS	0.861	0.789	0.935	0.861	0.789	0.935	CLONAL	1	TRUE	1	0.58291164195827	2		363	578	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778383	3778383	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	254	673	0	ENST00000262367.5:c.6665C>A	p.Ala2222Asp	p.A2222D	ENST00000262367	NM_004380.2	2222	gCt/gAt	31/31	0.577450791374525	1	FACETS	0.941	0.887	0.997	0.941	0.887	0.997	CLONAL	1	TRUE	0	0.58291164195827	1		673	656	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647536	23647536	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	265	625	0	ENST00000261584.4:c.331G>A	p.Asp111Asn	p.D111N	ENST00000261584	NM_024675.3	111	Gat/Aat	4/13	0.134404176236107	0	FACETS	0.448	0.421	0.476			1	INDETERMINATE	1	TRUE	0	0.58291164195827	0		625	846	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579375	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0035914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	230	675	0	ENST00000269305.4:c.312_313delinsTT	p.Gln104_Gly105delinsHisCys	p.Q104_G105delinsHC	ENST00000269305	NM_001126112.2	104	caGGgc/caTTgc	4/11	0.577450791374525	1	FACETS	0.828	0.776	0.882	0.828	0.776	0.882	CLONAL	1	TRUE	0	0.58291164195827	1		675	675	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553624	29553624	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	207	493	0	ENST00000356175.3:c.2173G>T	p.Glu725Ter	p.E725*	ENST00000356175	NM_000267.3	725	Gaa/Taa	18/57	0.577450791374525	1	FACETS	0.985	0.923	1	0.985	0.923	1	CLONAL	1	TRUE	0	0.58291164195827	1		493	511	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110280	3110280	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	243	731	0	ENST00000078429.4:c.270G>C	p.Met90Ile	p.M90I	ENST00000078429	NM_002067.2	90	atG/atC	2/7	1	2	FACETS	0.748	0.698	0.799	0.748	0.698	0.799	SUBCLONAL	1	TRUE	1	0.58291164195827	2		731	1115	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209098	36209098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	29	88	0	ENST00000222270.7:c.178G>A	p.Glu60Lys	p.E60K	ENST00000222270	NM_014727.1	60	Gag/Aag	1/37	1	2	FACETS	0.701	0.57	0.844	0.701	0.57	0.844	SUBCLONAL	1	TRUE	1	0.58291164195827	2		88	142	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796616	42796616	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	211	632	0	ENST00000575354.2:c.3173C>A	p.Ser1058Ter	p.S1058*	ENST00000575354	NM_015125.3	1058	tCa/tAa	13/20	1	2	FACETS	0.893	0.831	0.956	0.893	0.831	0.956	CLONAL	1	TRUE	1	0.58291164195827	2		632	811	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086164	16086164	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	349	434	0	ENST00000281043.3:c.1340T>C	p.Leu447Ser	p.L447S	ENST00000281043	NM_005378.4	447	tTg/tCg	3/3	0.54851359309453	2	FACETS	0.963	0.922	1	0.963	0.922	1	CLONAL	2	TRUE	0	0.58291164195827	2		434	622	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685282	86685282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	71	202	0	ENST00000274376.6:c.2998G>A	p.Glu1000Lys	p.E1000K	ENST00000274376	NM_002890.2	1000	Gag/Aag	24/25	0.577450791374525	1	FACETS	0.846	0.752	0.944	0.846	0.752	0.944	CLONAL	1	TRUE	0	0.58291164195827	1		202	204	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981728	70981728	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	282	796	0	ENST00000276594.2:c.368G>T	p.Gly123Val	p.G123V	ENST00000276594	NM_024504.3	123	gGt/gTt	2/8	1	2	FACETS	0.906	0.852	0.962	0.906	0.852	0.962	CLONAL	1	TRUE	1	0.58291164195827	2		796	1068	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559373	141559373	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	243	629	0	ENST00000220592.5:c.1428G>T	p.Lys476Asn	p.K476N	ENST00000220592	NM_012154.3	476	aaG/aaT	12/19	1	2	FACETS	0.952	0.891	1	0.952	0.891	1	CLONAL	1	TRUE	1	0.58291164195827	2		629	876	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5563174	5563174	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	175	399	0	ENST00000397747.3:c.779G>C	p.Arg260Thr	p.R260T	ENST00000397747	NM_025239.3	260	aGa/aCa	6/7	0.58291164195827	1	FACETS	0.929	0.864	0.995	0.929	0.864	0.995	CLONAL	1	TRUE	0	0.58291164195827	1		399	458	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485863	8485863	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	151	365	0	ENST00000356435.5:c.2954A>T	p.Lys985Ile	p.K985I	ENST00000356435		985	aAa/aTa	17/35	0.58291164195827	1	FACETS	0.932	0.862	1	0.932	0.862	1	CLONAL	1	TRUE	0	0.58291164195827	1		365	394	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	57	368	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.755	0.652	0.865	0.755	0.652	0.865	SUBCLONAL	1	TRUE	1	0.5	2		368	302	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	122	364	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.5	2		364	389	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	30	709	0	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.233	0.187	0.286	0.233	0.187	0.286	SUBCLONAL	1	TRUE	1	0.5	2		709	514	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	197	612	4	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	0.5	2		616	578	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	38	453	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.227	0.186	0.272	0.227	0.186	0.272	SUBCLONAL	1	TRUE	1	0.5	2		453	671	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	43	823	5	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.273	0.227	0.323	0.273	0.227	0.323	SUBCLONAL	1	TRUE	1	0.5	2		828	631	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209593	98209593	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	87	529	0	ENST00000331920.6:c.3945del	p.Tyr1316ThrfsTer56	p.Y1316Tfs*56	ENST00000331920	NM_000264.3	1315	ccC/cc	23/24	1	2	FACETS	0.928	0.828	1	0.928	0.828	1	CLONAL	1	TRUE	1	0.5	2		529	375	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056317	27056317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776238347	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	32	405	2	ENST00000324856.7:c.1313C>T	p.Ala438Val	p.A438V	ENST00000324856	NM_006015.4	438	gCg/gTg	2/20	1	2	FACETS	0.355	0.288	0.43	0.355	0.288	0.43	SUBCLONAL	1	TRUE	1	0.5	2		407	361	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	52	792	1	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	1	2	FACETS	0.277	0.235	0.324	0.277	0.235	0.324	SUBCLONAL	1	TRUE	1	0.5	2		793	750	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	95	539	4	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.682	0.609	0.76	0.682	0.609	0.76	SUBCLONAL	1	TRUE	1	0.5	2		543	557	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820004	36820004	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	38	742	0	ENST00000373129.3:c.584A>G	p.His195Arg	p.H195R	ENST00000373129	NM_032017.1	195	cAc/cGc	7/12	1	2	FACETS	0.205	0.168	0.245	0.205	0.168	0.245	SUBCLONAL	1	TRUE	1	0.5	2		742	743	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058574	72058574	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	129	620	0	ENST00000357731.5:c.866A>G	p.Gln289Arg	p.Q289R	ENST00000357731	NM_173808.2	289	cAg/cGg	6/7	1	2	FACETS	0.754	0.685	0.827	0.754	0.685	0.827	SUBCLONAL	1	TRUE	1	0.5	2		620	684	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913250	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	22	449	0	ENST00000369535.4:c.34G>A	p.Gly12Ser	p.G12S	ENST00000369535	NM_002524.4	12	Ggt/Agt	2/7	1	2	FACETS	0.154	0.119	0.196	0.154	0.119	0.196	SUBCLONAL	1	TRUE	1	0.5	2		449	570	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318800	163318800	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	96	428	0	ENST00000271452.3:c.1190A>G	p.Glu397Gly	p.E397G	ENST00000271452	NM_145697.2	397	gAa/gGa	13/14	1	2	FACETS	0.885	0.793	0.981	0.885	0.793	0.981	CLONAL	1	TRUE	1	0.5	2		428	434	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263974	104263974	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776579	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	58	267	0	ENST00000369902.3:c.71del	p.Pro24ArgfsTer72	p.P24Rfs*72	ENST00000369902	NM_016169.3	22	gCc/gc	1/12	1	2	FACETS	0.82	0.71	0.937	0.82	0.71	0.937	CLONAL	1	TRUE	1	0.5	2		267	283	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104269048	104269049	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	151	617	0	ENST00000369902.3:c.306_307del	p.Asn102LysfsTer4	p.N102Kfs*4	ENST00000369902	NM_016169.3	102	aAC/a	2/12	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.5	2		617	602	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	95	432	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.854	0.764	0.948	0.854	0.764	0.948	CLONAL	1	TRUE	1	0.5	2		438	445	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154241	2154242	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755455183	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	94	705	1	ENST00000434045.2:c.686dup	p.Glu230ArgfsTer50	p.E230Rfs*50	ENST00000434045	NM_001127598.1	229	cca/ccCa	5/5	1	2	FACETS	0.749	0.669	0.834	0.749	0.669	0.834	SUBCLONAL	1	TRUE	1	0.5	2		706	502	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625281	69625281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35983315	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	141	789	1	ENST00000334134.2:c.512G>A	p.Arg171His	p.R171H	ENST00000334134	NM_005247.2	171	cGc/cAc	3/3	1	2	FACETS	0.984	0.901	1	0.984	0.901	1	CLONAL	1	TRUE	1	0.5	2		790	573	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	183	554	11	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	0.3	2	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.5	2		565	562	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18576957	18576957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	91	595	0	ENST00000266497.5:c.2365G>A	p.Ala789Thr	p.A789T	ENST00000266497		789	Gcc/Acc	16/31	0.120509689143351	0	FACETS	0.315	0.28	0.352			1	INDETERMINATE	1	TRUE	0	0.5	0		595	578	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50482355	50482355	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	41	638	3	ENST00000394963.4:c.711del	p.Phe237LeufsTer5	p.F237Lfs*5	ENST00000394963	NM_003076.4	236	Ttt/tt	6/13	0.120509689143351	3	FACETS	0.286	0.238	0.341	0.143	0.119	0.171	INDETERMINATE	1	TRUE	1	0.5	3		641	716	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	129	719	4	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.859	0.781	0.94	0.859	0.781	0.94	CLONAL	1	TRUE	1	0.5	2		723	601	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210891	133210891	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs764022756	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	143	768	0	ENST00000320574.5:c.5885A>G	p.Glu1962Gly	p.E1962G	ENST00000320574	NM_006231.2	1962	gAg/gGg	43/49	1	2	FACETS	0.844	0.771	0.919	0.844	0.771	0.919	CLONAL	1	TRUE	1	0.5	2		768	678	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912301	32912301	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1555283405	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	91	588	0	ENST00000380152.3:c.3811del	p.Ser1271GlnfsTer5	p.S1271Qfs*5	ENST00000380152		1270	gTt/gt	11/27	1	2	FACETS	0.743	0.662	0.828	0.743	0.662	0.828	SUBCLONAL	1	TRUE	1	0.5	2		588	490	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950876	32950876	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	161	579	0	ENST00000380152.3:c.8702G>C	p.Gly2901Ala	p.G2901A	ENST00000380152		2901	gGt/gCt	21/27	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.5	2		579	631	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103525620	103525620	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149859074	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	23	404	0	ENST00000355739.4:c.2891G>A	p.Arg964Gln	p.R964Q	ENST00000355739	NM_000123.3	964	cGg/cAg	14/15	1	2	FACETS	0.212	0.165	0.268	0.212	0.165	0.268	SUBCLONAL	1	TRUE	1	0.5	2		404	433	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019469	42019469	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	103	745	1	ENST00000219905.7:c.3525del	p.Thr1176ArgfsTer8	p.T1176Rfs*8	ENST00000219905	NM_001164273.1	1174	atC/at	10/24	1	2	FACETS	0.791	0.71	0.876	0.791	0.71	0.876	SUBCLONAL	1	TRUE	1	0.5	2		746	521	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	103	568	3	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.871	0.783	0.963	0.871	0.783	0.963	CLONAL	1	TRUE	1	0.5	2		571	473	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639398	3639398	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748691881	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	83	795	1	ENST00000294008.3:c.4241del	p.Pro1414HisfsTer36	p.P1414Hfs*36	ENST00000294008	NM_032444.2	1414	cCa/ca	12/15	1	2	FACETS	0.673	0.596	0.756	0.673	0.596	0.756	SUBCLONAL	1	TRUE	1	0.5	2		796	493	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785567	50785567	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	152	796	0	ENST00000398568.2:c.557T>C	p.Leu186Pro	p.L186P	ENST00000398568	NM_001042412.1	186	cTt/cCt	4/18	1	2	FACETS	0.741	0.678	0.807	0.741	0.678	0.807	SUBCLONAL	1	TRUE	1	0.5	2		796	820	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33446128	33446128	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	91	452	0	ENST00000345365.6:c.144+2T>C		p.X48_splice	ENST00000345365	NM_002878.3	48			1	2	FACETS	0.805	0.718	0.897	0.805	0.718	0.897	CLONAL	1	TRUE	1	0.5	2		452	452	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	336	675	1	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	1	2	FACETS	0.977	0.931	1	1	0.996	1	CLONAL	2	TRUE	1	0.5	2		676	688	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772462	56772462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	154	676	1	ENST00000337432.4:c.316G>A	p.Ala106Thr	p.A106T	ENST00000337432	NM_058216.2	106	Gca/Aca	2/9	1	2	FACETS	0.987	0.907	1	0.987	0.907	1	CLONAL	1	TRUE	1	0.5	2		677	624	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	44	1091	1	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.281	0.235	0.332	0.281	0.235	0.332	SUBCLONAL	1	TRUE	1	0.5	2		1092	627	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985776	60985776	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1184260603	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	19	291	1	ENST00000333681.4:c.124del	p.Ala42ProfsTer54	p.A42Pfs*54	ENST00000333681		42	Gcc/cc	2/3	1	2	FACETS	0.276	0.21	0.355	0.276	0.21	0.355	SUBCLONAL	1	TRUE	1	0.5	2		292	275	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221294	1221294	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782199	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	44	721	1	ENST00000326873.7:c.817G>A	p.Ala273Thr	p.A273T	ENST00000326873	NM_000455.4	273	Gcc/Acc	6/10	1	2	FACETS	0.249	0.208	0.294	0.249	0.208	0.294	SUBCLONAL	1	TRUE	1	0.5	2		722	708	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612392	1612392	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	139	880	0	ENST00000344749.5:c.1627A>G	p.Arg543Gly	p.R543G	ENST00000344749	NM_001136139.2	543	Agg/Ggg	18/19	1	2	FACETS	0.694	0.632	0.759	0.694	0.632	0.759	SUBCLONAL	1	TRUE	1	0.5	2		880	801	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4090693	4090693	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	136	817	0	ENST00000262948.5:c.1106T>C	p.Ile369Thr	p.I369T	ENST00000262948	NM_030662.3	369	aTc/aCc	11/11	1	2	FACETS	0.774	0.705	0.846	0.774	0.705	0.846	SUBCLONAL	1	TRUE	1	0.5	2		817	703	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231328	5231328	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs775268583	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	72	490	0	ENST00000357368.4:c.2148C>G	p.Asp716Glu	p.D716E	ENST00000357368	NM_002850.3	716	gaC/gaG	14/38	1	2	FACETS	0.83	0.73	0.936	0.83	0.73	0.936	CLONAL	1	TRUE	1	0.5	2		490	347	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11151994	11151994	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	47	426	0	ENST00000358026.2:c.4278G>T	p.Glu1426Asp	p.E1426D	ENST00000358026	NM_001128849.1	1426	gaG/gaT	31/36	1	2	FACETS	0.478	0.404	0.56	0.478	0.404	0.56	SUBCLONAL	1	TRUE	1	0.5	2		426	393	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303086	15303086	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	129	997	0	ENST00000263388.2:c.364C>T	p.Pro122Ser	p.P122S	ENST00000263388	NM_000435.2	122	Ccc/Tcc	4/33	1	2	FACETS	0.759	0.689	0.832	0.759	0.689	0.832	SUBCLONAL	1	TRUE	1	0.5	2		997	680	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213971	36213971	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	133	949	2	ENST00000222270.7:c.2801del	p.Gly934GlufsTer52	p.G934Efs*52	ENST00000222270	NM_014727.1	933	Ggg/gg	6/37	1	2	FACETS	0.79	0.719	0.865	0.79	0.719	0.865	SUBCLONAL	1	TRUE	1	0.5	2		951	673	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794440	42794441	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	157	1028	1	ENST00000575354.2:c.1526dup	p.Leu510ThrfsTer4	p.L510Tfs*4	ENST00000575354	NM_015125.3	507	cgc/cgCc	10/20	1	2	FACETS	0.757	0.694	0.823	0.757	0.694	0.823	SUBCLONAL	1	TRUE	1	0.5	2		1029	830	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	13	367	3	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	1	2	FACETS	0.231	0.165	0.312	0.231	0.165	0.312	SUBCLONAL	1	TRUE	1	0.5	2		370	225	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467164	25467164	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	86	540	1	ENST00000264709.3:c.1711del	p.Ala571LeufsTer80	p.A571Lfs*80	ENST00000264709	NM_175629.2	571	Gct/ct	15/23	1	2	FACETS	0.878	0.781	0.979	0.878	0.781	0.979	CLONAL	1	TRUE	1	0.5	2		541	392	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151290	202151290	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	111	468	0	ENST00000358485.4:c.1596del	p.Lys532AsnfsTer73	p.K532Nfs*73	ENST00000358485	NM_001080125.1	530	agA/ag	9/9	1	2	FACETS	0.796	0.718	0.878	0.796	0.718	0.878	SUBCLONAL	1	TRUE	1	0.5	2		468	558	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735376	204735376	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	48	306	0	ENST00000302823.3:c.177G>C	p.Glu59Asp	p.E59D	ENST00000302823	NM_005214.4	59	gaG/gaC	2/4	1	2	FACETS	0.727	0.62	0.844	0.727	0.62	0.844	SUBCLONAL	1	TRUE	1	0.5	2		306	264	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116262	209116263	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs754375602	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	45	325	1	ENST00000345146.2:c.13dup	p.Ile5AsnfsTer13	p.I5Nfs*13	ENST00000345146	NM_005896.2	5	atc/aAtc	3/10	1	2	FACETS	0.497	0.419	0.583	0.497	0.419	0.583	SUBCLONAL	1	TRUE	1	0.5	2		326	362	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793431	242793431	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376257658	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	37	725	1	ENST00000334409.5:c.646G>A	p.Val216Met	p.V216M	ENST00000334409	NM_005018.2	216	Gtg/Atg	5/5	1	2	FACETS	0.285	0.235	0.342	0.285	0.235	0.342	SUBCLONAL	1	TRUE	1	0.5	2		726	519	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026137	36026137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1464185975	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	35	883	3	ENST00000358208.4:c.739G>A	p.Val247Met	p.V247M	ENST00000358208		247	Gtg/Atg	7/12	1	2	FACETS	0.207	0.169	0.25	0.207	0.169	0.25	SUBCLONAL	1	TRUE	1	0.5	2		886	676	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306638	41306638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	137	822	0	ENST00000373198.4:c.1021G>A	p.Asp341Asn	p.D341N	ENST00000373198	NM_133170.3	341	Gac/Aac	7/32	1	2	FACETS	0.919	0.84	1	0.919	0.84	1	CLONAL	1	TRUE	1	0.5	2		822	596	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268332	46268332	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs763186106	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	22	392	1	ENST00000371998.3:c.2719C>T	p.Arg907Ter	p.R907*	ENST00000371998		907	Cga/Tga	15/23	1	2	FACETS	0.204	0.158	0.258	0.204	0.158	0.258	SUBCLONAL	1	TRUE	1	0.5	2		393	431	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	193	391	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.806	0.753	0.859	1	0.992	1	CLONAL	2	TRUE	1	0.5	2		392	479	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067242	37067242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750760	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	126	353	0	ENST00000231790.2:c.1153C>T	p.Arg385Cys	p.R385C	ENST00000231790	NM_000249.3	385	Cgt/Tgt	12/19	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.5	2		353	503	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535430	66535430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	31	396	0	ENST00000273854.3:c.31C>T	p.Arg11Cys	p.R11C	ENST00000273854	NM_004439.5	11	Cgc/Tgc	1/18	1	2	FACETS	0.369	0.299	0.448	0.369	0.299	0.448	SUBCLONAL	1	TRUE	1	0.5	2		396	336	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106162508	106162508	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	55	270	0	ENST00000380013.4:c.3426del	p.Asp1143MetfsTer9	p.D1143Mfs*9	ENST00000380013	NM_001127208.2	1141	gAa/ga	4/11	1	2	FACETS	0.849	0.733	0.974	0.849	0.733	0.974	CLONAL	1	TRUE	1	0.5	2		270	259	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081569	143081569	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	104	631	0	ENST00000262992.4:c.1505del	p.Pro502GlnfsTer2	p.P502Qfs*2	ENST00000262992	NM_001101669.1	502	cCa/ca	15/24	1	2	FACETS	0.73	0.655	0.809	0.73	0.655	0.809	SUBCLONAL	1	TRUE	1	0.5	2		631	570	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294328	1294328	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	26	604	0	ENST00000310581.5:c.673G>T	p.Gly225Trp	p.G225W	ENST00000310581	NM_198253.2	225	Ggg/Tgg	2/16	1	2	FACETS	0.245	0.193	0.304	0.245	0.193	0.304	SUBCLONAL	1	TRUE	1	0.5	2		604	425	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294665	1294665	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	106	485	4	ENST00000310581.5:c.336del	p.Glu113ArgfsTer15	p.E113Rfs*15	ENST00000310581	NM_198253.2	112	ccC/cc	2/16	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.5	2		489	375	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31424571	31424571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1186040397	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	139	663	0	ENST00000344624.3:c.3224G>A	p.Arg1075His	p.R1075H	ENST00000344624		1075	cGc/cAc	25/33	1	2	FACETS	0.762	0.694	0.832	0.762	0.694	0.832	SUBCLONAL	1	TRUE	1	0.5	2		663	730	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	178	746	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.934	0.863	1	0.934	0.863	1	CLONAL	1	TRUE	1	0.5	2		751	762	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131972877	131972877	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	93	330	0	ENST00000265335.6:c.3460A>G	p.Thr1154Ala	p.T1154A	ENST00000265335		1154	Acc/Gcc	22/25	1	2	FACETS	0.901	0.806	1	0.901	0.806	1	CLONAL	1	TRUE	1	0.5	2		330	413	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509368	149509368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765383598	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	94	633	1	ENST00000261799.4:c.1531C>T	p.Arg511Cys	p.R511C	ENST00000261799	NM_002609.3	511	Cgc/Tgc	10/23	1	2	FACETS	0.724	0.647	0.807	0.724	0.647	0.807	SUBCLONAL	1	TRUE	1	0.5	2		634	519	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047181	180047181	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	102	683	0	ENST00000261937.6:c.2534T>C	p.Leu845Pro	p.L845P	ENST00000261937	NM_182925.4	845	cTg/cCg	17/30	1	2	FACETS	0.826	0.742	0.914	0.826	0.742	0.914	CLONAL	1	TRUE	1	0.5	2		683	494	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047947	180047947	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	194	819	1	ENST00000261937.6:c.2228C>T	p.Ala743Val	p.A743V	ENST00000261937	NM_182925.4	743	gCg/gTg	15/30	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.5	2		820	625	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057557	180057557	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	119	685	0	ENST00000261937.6:c.398G>T	p.Arg133Ile	p.R133I	ENST00000261937	NM_182925.4	133	aGa/aTa	3/30	1	2	FACETS	0.917	0.832	1	0.917	0.832	1	CLONAL	1	TRUE	1	0.5	2		685	519	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680818	30680818	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	31	633	0	ENST00000376406.3:c.901A>G	p.Thr301Ala	p.T301A	ENST00000376406	NM_014641.2	301	Aca/Gca	5/15	1	2	FACETS	0.215	0.173	0.262	0.215	0.173	0.262	SUBCLONAL	1	TRUE	1	0.5	2		633	578	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324935	31324935	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	55	384	0	ENST00000412585.2:c.1A>G	p.Met1?	p.M1?	ENST00000412585	NM_005514.6	1	Atg/Gtg	1/8	1	2	FACETS	0.692	0.595	0.796	0.692	0.595	0.796	SUBCLONAL	1	TRUE	1	0.5	2		384	318	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31947330	31947330	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1179338180	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	78	447	0	ENST00000375333.2:c.815C>T	p.Thr272Met	p.T272M	ENST00000375333	NM_032454.1	272	aCg/aTg	5/8	1	2	FACETS	0.707	0.624	0.796	0.707	0.624	0.796	SUBCLONAL	1	TRUE	1	0.5	2		447	441	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508169	106508169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381484125	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	32	213	0	ENST00000359195.3:c.163G>A	p.Glu55Lys	p.E55K	ENST00000359195	NM_002649.2	55	Gaa/Aaa	2/11	1	2	FACETS	0.696	0.57	0.834	0.696	0.57	0.834	SUBCLONAL	1	TRUE	1	0.5	2		213	184	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485975	8485975	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	90	488	1	ENST00000356435.5:c.2842A>G	p.Asn948Asp	p.N948D	ENST00000356435		948	Aat/Gat	17/35	1	2	FACETS	0.73	0.65	0.815	0.73	0.65	0.815	SUBCLONAL	1	TRUE	1	0.5	2		489	493	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1327757	1327757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1178003047	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	175	779	0	ENST00000400841.2:c.124G>A	p.Val42Met	p.V42M	ENST00000400841		42	Gtg/Atg	2/6	1	1	FACETS	0.762	0.704	0.822	0.762	0.704	0.822	SUBCLONAL	1	TRUE	0	0.5	1		779	689	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045477	47045477	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	27	288	0	ENST00000377604.3:c.2444G>A	p.Arg815Gln	p.R815Q	ENST00000377604	NM_001204468.1	815	cGg/cAg	22/24	1	1	FACETS	0.325	0.26	0.4	0.325	0.26	0.4	SUBCLONAL	1	TRUE	0	0.5	1		288	249	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0035917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	341	622	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.715836688896685	3	FACETS	0.91	0.878	0.94	0.91	0.878	0.94	CLONAL	3	TRUE	0	0.715836688896685	3		622	474	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0035917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	151	291	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.715836688896685	3	FACETS	0.821	0.761	0.881	0.821	0.761	0.881	CLONAL	2	TRUE	1	0.715836688896685	3		291	349	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188164	11188164	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	124	515	0	ENST00000361445.4:c.5930C>G	p.Thr1977Arg	p.T1977R	ENST00000361445	NM_004958.3	1977	aCa/aGa	43/58	1	2	FACETS	0.758	0.691	0.828	0.758	0.691	0.828	SUBCLONAL	1	TRUE	1	0.715836688896685	2		515	457	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245380	153245380	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	304	638	0	ENST00000281708.4:c.1811A>C	p.Lys604Thr	p.K604T	ENST00000281708	NM_033632.3	604	aAa/aCa	11/12	0.665012311938979	2	FACETS	0.89	0.853	0.927	0.89	0.853	0.927	CLONAL	2	TRUE	0	0.715836688896685	2		638	477	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119791	70119791	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	141	643	0	ENST00000245479.2:c.793C>T	p.Gln265Ter	p.Q265*	ENST00000245479	NM_000346.3	265	Cag/Tag	3/3	1	2	FACETS	0.897	0.825	0.972	0.897	0.825	0.972	CLONAL	1	TRUE	1	0.715836688896685	2		643	439	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795334	42795334	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	87	630	0	ENST00000575354.2:c.2414C>T	p.Pro805Leu	p.P805L	ENST00000575354	NM_015125.3	805	cCa/cTa	10/20	1	2	FACETS	0.821	0.735	0.91	0.821	0.735	0.91	CLONAL	1	TRUE	1	0.715836688896685	2		630	296	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723366	49723366	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	92	490	0	ENST00000449682.2:c.1177C>T	p.Arg393Cys	p.R393C	ENST00000449682	NM_020998.3	393	Cgc/Tgc	10/18	1	2	FACETS	0.857	0.77	0.946	0.857	0.77	0.946	CLONAL	1	TRUE	1	0.715836688896685	2		490	300	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860314	151860314	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	101	513	0	ENST00000262189.6:c.10348C>A	p.Gln3450Lys	p.Q3450K	ENST00000262189	NM_170606.2	3450	Cag/Aag	43/59	1	2	FACETS	0.737	0.664	0.813	0.737	0.664	0.813	SUBCLONAL	1	TRUE	1	0.715836688896685	2		513	383	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	168	272	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.958668781596012	2		272	317	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0035919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	198	298	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.954	0.895	1	0.954	0.895	1	CLONAL	1	TRUE	1	0.958668781596012	2		298	433	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426111	47426111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	388	841	0	ENST00000377045.4:c.631C>T	p.Arg211Cys	p.R211C	ENST00000377045	NM_001654.4	211	Cgc/Tgc	7/16	1	2	FACETS	0.851	0.812	0.891	0.851	0.812	0.891	CLONAL	1	TRUE	1	0.958668781596012	2		841	951	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429848	78429848	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0035919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	387	402	0	ENST00000370768.2:c.941-1G>A		p.X314_splice	ENST00000370768	NM_003902.3	314			0.958668781596012	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.958668781596012	1		402	412	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795219	42795219	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	CC	novel	NA	P-0035919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	385	809	0	ENST00000575354.2:c.2299delinsCC	p.Thr767ProfsTer164	p.T767Pfs*164	ENST00000575354	NM_015125.3	767	Acc/CCcc	10/20	0.958668781596012	1	FACETS	0.986	0.967	1	0.986	0.967	1	CLONAL	1	TRUE	0	0.958668781596012	1		809	424	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842642	68842642	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	367	538	0	ENST00000261769.5:c.578C>G	p.Thr193Ser	p.T193S	ENST00000261769	NM_004360.3	193	aCt/aGt	5/16	0.508794665722967	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.518417721243871	2		538	697	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054652	5054652	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	104	271	0	ENST00000381652.3:c.704G>C	p.Arg235Thr	p.R235T	ENST00000381652	NM_004972.3	235	aGa/aCa	7/25	1	2	FACETS	0.996	0.898	1	0.996	0.898	1	CLONAL	1	TRUE	1	0.518417721243871	2		271	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0035921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	257	571	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.242639539967732	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.267742750593657	2		571	952	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206818	36206818	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	188	534	0	ENST00000300305.3:c.694C>T	p.Arg232Trp	p.R232W	ENST00000300305		232	Cgg/Tgg	6/8	0.242639539967732	2	FACETS	0.955	0.885	1	0.955	0.885	1	CLONAL	2	TRUE	0	0.267742750593657	2		534	735	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744449	41744449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143593613	NA	P-0035921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	268	754	1	ENST00000301178.4:c.1069C>T	p.Arg357Trp	p.R357W	ENST00000301178	NM_021913.4	357	Cgg/Tgg	8/20	0.267742750593657	3	FACETS	0.863	0.808	0.92	0.863	0.808	0.92	CLONAL	2	TRUE	1	0.267742750593657	3		755	1315	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670405	88670405	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	104	403	0	ENST00000360948.2:c.1281A>C	p.Glu427Asp	p.E427D	ENST00000360948	NM_001012338.2	427	gaA/gaC	11/19	1	2	FACETS	0.751	0.675	0.831	1	0.983	1	SUBCLONAL	2	TRUE	1	0.267742750593657	2		403	517	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204904	128204904	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1347	136	939	1	ENST00000341105.2:c.537A>C	p.Lys179Asn	p.K179N	ENST00000341105	NM_032638.4	179	aaA/aaC	3/6	0.249642454561249	4	FACETS	0.868	0.787	0.955	0.289	0.262	0.319	CLONAL	1	TRUE	1	0.267742750593657	4		940	1483	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508750	31508750	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	105	728	0	ENST00000344624.3:c.1565T>G	p.Leu522Arg	p.L522R	ENST00000344624		522	cTt/cGt	7/33	0.249642454561249	4	FACETS	0.807	0.721	0.899	0.269	0.24	0.3	CLONAL	1	TRUE	1	0.267742750593657	4		728	1232	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981997	70981997	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	288	956	2	ENST00000276594.2:c.99C>A	p.Phe33Leu	p.F33L	ENST00000276594	NM_024504.3	33	ttC/ttA	2/8	0.211827816204898	3	FACETS	0.888	0.833	0.944	0.888	0.833	0.944	CLONAL	2	TRUE	1	0.267742750593657	3		958	1374	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375994	8375994	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	101	335	0	ENST00000356435.5:c.4603T>G	p.Leu1535Val	p.L1535V	ENST00000356435		1535	Tta/Gta	28/35	0.240695031133912	2	FACETS	0.855	0.769	0.946	0.855	0.769	0.946	CLONAL	2	TRUE	0	0.267742750593657	2		335	441	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0035922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	85	433	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.139964240513866	3	FACETS	0.914	0.808	1	0.457	0.404	0.514	INDETERMINATE	1	TRUE	1	0.334465313372994	3		433	649	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0035922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	101	642	1	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.333563960643841	1	FACETS	0.835	0.748	0.928	0.835	0.748	0.928	CLONAL	1	TRUE	0	0.334465313372994	1		643	602	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47612306	47612309	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TTAT	TTAT	-	novel	NA	P-0035922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	46	417	0	ENST00000263735.4:c.862_865del	p.Ile288ProfsTer14	p.I288Pfs*14	ENST00000263735	NM_002354.2	287	gTTATt/gt	8/9	1	2	FACETS	0.527	0.443	0.619	0.527	0.443	0.619	SUBCLONAL	1	TRUE	1	0.334465313372994	2		417	522	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598124	52598125	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	153	760	0	ENST00000394830.3:c.3741dup	p.Gly1248ArgfsTer10	p.G1248Rfs*10	ENST00000394830	NM_018313.4	1247	-/A	24/30	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.334465313372994	2		760	902	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040940	47040941	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs1556779417	NA	P-0035922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	97	1050	0	ENST00000377604.3:c.1473_1474del	p.Ser492AspfsTer25	p.S492Dfs*25	ENST00000377604	NM_001204468.1	490	tcTGtg/tctg	14/24	0.278956880114123	1	FACETS	0.662	0.59	0.738	0.662	0.59	0.738	SUBCLONAL	1	TRUE	0	0.334465313372994	1		1050	730	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0035923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	124	790	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.81	0.733	0.892	0.81	0.733	0.892	CLONAL	1	TRUE	1	0.363915361419366	2		790	841	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0035923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	101	319	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.361206264134872	3	FACETS	0.758	0.681	0.838	0.758	0.681	0.838	SUBCLONAL	2	TRUE	1	0.363915361419366	3		319	433	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692980	89692980	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1060500126	NA	P-0035923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	92	554	0	ENST00000371953.3:c.464A>G	p.Tyr155Cys	p.Y155C	ENST00000371953	NM_000314.4	155	tAt/tGt	5/9	0.361206264134872	3	FACETS	0.919	0.818	1	0.46	0.409	0.514	CLONAL	1	TRUE	1	0.363915361419366	3		554	650	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916924	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	93	549	0	ENST00000263967.3:c.311C>G	p.Pro104Arg	p.P104R	ENST00000263967	NM_006218.2	104	cCa/cGa	2/21	1	2	FACETS	0.73	0.649	0.816	0.73	0.649	0.816	SUBCLONAL	1	TRUE	1	0.363915361419366	2		549	700	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266112	41266112	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913228	NA	P-0035923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	69	324	0	ENST00000349496.5:c.109T>G	p.Ser37Ala	p.S37A	ENST00000349496	NM_001904.3	37	Tct/Gct	3/15	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.363915361419366	2		324	366	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466019	69466019	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	90	823	0	ENST00000227507.2:c.857C>G	p.Thr286Arg	p.T286R	ENST00000227507	NM_053056.2	286	aCa/aGa	5/5	1	2	FACETS	0.67	0.594	0.751	0.67	0.594	0.751	SUBCLONAL	1	TRUE	1	0.363915361419366	2		823	738	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752420	55752420	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	54	847	0	ENST00000284073.2:c.878C>A	p.Ser293Tyr	p.S293Y	ENST00000284073	NM_138962.2	293	tCc/tAc	12/14	1	2	FACETS	0.309	0.263	0.36	0.309	0.263	0.36	SUBCLONAL	1	TRUE	1	0.363915361419366	2		847	960	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158626896	158626896	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	110	595	2	ENST00000263640.3:c.774G>T	p.Arg258Ser	p.R258S	ENST00000263640	NM_001105.4	258	agG/agT	7/11	0.361206264134872	3	FACETS	0.933	0.838	1	0.466	0.419	0.517	CLONAL	1	TRUE	1	0.363915361419366	3		597	766	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670404	246670404	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1258460062	NA	P-0035924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	58	653	0	ENST00000388985.4:c.116C>G	p.Thr39Arg	p.T39R	ENST00000388985		39	aCg/aGg	1/12	0.209228184812825	4	FACETS	1	0.922	1	0.81	0.706	0.92	CLONAL	3	FALSE	0	0.209086545492896	4		653	207	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636121	28636121	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs778119340	NA	P-0035924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	78	729	0	ENST00000241453.7:c.251A>T	p.Asp84Val	p.D84V	ENST00000241453	NM_004119.2	84	gAt/gTt	3/24	0.209086545492896	0	FACETS	0.878	0.811	0.941			1	CLONAL	6	FALSE	0	0.209086545492896	0		729	112	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011109	12011109	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	150	472	0	ENST00000353533.5:c.516del	p.Asp173ThrfsTer24	p.D173Tfs*24	ENST00000353533	NM_003010.3	172	ggT/gg	5/11	0.209228184812825	0	FACETS	0.906	0.868	0.939			1	CLONAL	7	FALSE	0	0.209086545492896	0		472	179	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322768	30322768	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	87	362	0	ENST00000322652.5:c.1786del	p.Thr596ProfsTer18	p.T596Pfs*18	ENST00000322652	NM_015355.2	594	gAa/ga	14/16	NA	2	FACETS	0.962	0.876	1			1	INDETERMINATE	5	FALSE	NA	0.209086545492896	2		362	173	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0035925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	379	865	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.453552794852121	0	FACETS		NA	1			1	NA	2	TRUE	0	0.513497031670295	0		865	501	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0035925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5172	1758	886	4	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.513497031670295	26	FACETS	1	0.984	1			1	CLONAL	7	TRUE	NA	0.513497031670295	26		890	6930	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0035925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3244	1519	351	1	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.513497031670295	26	FACETS	0.988	0.963	1			1	CLONAL	9	TRUE	NA	0.513497031670295	26		352	4763	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0035925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	204	598	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.988	0.931	1	1	0.994	1	CLONAL	2	TRUE	1	0.513497031670295	2		598	402	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133533	55133550	+	inframe_deletion	In_Frame_Del	DEL	GGCCACGGTGAAAGACAG	GGCCACGGTGAAAGACAG	-	novel	NA	P-0035925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5165	397	567	0	ENST00000257290.5:c.837_854del	p.Glu279_Ser285delinsAsp	p.E279_S285delinsD	ENST00000257290	NM_006206.4	279	gaGGCCACGGTGAAAGACAGt/gat	6/23	0.513497031670295	30	FACETS	1	0.987	1			1	CLONAL	2	TRUE	NA	0.513497031670295	30		567	5562	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133565	55133565	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4633	754	551	0	ENST00000257290.5:c.869G>C	p.Cys290Ser	p.C290S	ENST00000257290	NM_006206.4	290	tGt/tCt	6/23	0.513497031670295	30	FACETS	1	0.992	1			1	CLONAL	4	TRUE	NA	0.513497031670295	30		551	5387	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268882	55268882	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	6234	840	1	ENST00000275493.2:c.2948G>A	p.Gly983Glu	p.G983E	ENST00000275493	NM_005228.3	983	gGg/gAg	25/28	0.513497031670295	26	FACETS	0.996	0.992	1			1	CLONAL	26	TRUE	NA	0.513497031670295	26		841	6714	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873513	151873513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	175	722	0	ENST00000262189.6:c.9025C>T	p.Pro3009Ser	p.P3009S	ENST00000262189	NM_170606.2	3009	Cct/Tct	38/59	0.513497031670295	3	FACETS	0.879	0.809	0.951	0.439	0.404	0.476	CLONAL	1	TRUE	1	0.513497031670295	3		722	975	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0035926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	107	488	2	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.461150058694905	3	FACETS	0.97	0.872	1	0.485	0.436	0.536	CLONAL	1	TRUE	1	0.461150058694905	3		490	589	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0035926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	337	642	1	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.461150058694905	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.461150058694905	2		643	594	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884864	134884864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257672576	NA	P-0035926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	135	564	0	ENST00000398015.3:c.1640C>T	p.Ala547Val	p.A547V	ENST00000398015	NM_004441.4	547	gCg/gTg	8/16	0.461150058694905	3	FACETS	1	0.955	1	0.538	0.49	0.589	CLONAL	1	TRUE	1	0.461150058694905	3		564	669	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502244	157502244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370283707	NA	P-0035926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	255	469	2	ENST00000346085.5:c.3277G>A	p.Val1093Met	p.V1093M	ENST00000346085	NM_020732.3	1093	Gtg/Atg	12/20	0.449938281093638	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.461150058694905	4		471	737	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911641	114911642	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0035926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	35	392	0	ENST00000543371.1:c.1161_1161+1dup		p.R387fs	ENST00000543371	NM_001198531.1	387	agg/aGGgg	10/14	0.461150058694905	3	FACETS	0.38	0.311	0.458	0.127	0.103	0.153	SUBCLONAL	1	TRUE	0	0.461150058694905	3		392	491	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652947	29652947	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770124316	NA	P-0035926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	105	524	0	ENST00000356175.3:c.4882G>A	p.Gly1628Arg	p.G1628R	ENST00000356175	NM_000267.3	1628	Ggg/Agg	36/57	0.461150058694905	4	FACETS	0.857	0.768	0.952	0.429	0.384	0.476	CLONAL	1	TRUE	2	0.461150058694905	4		524	776	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0035927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	62	822	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.462481020822992	4	FACETS	0.286	0.246	0.33	0.143	0.123	0.165	SUBCLONAL	1	TRUE	2	0.624654187872753	4		822	1128	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0035927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	536	753	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.624654187872753	2	FACETS	0.975	0.943	1	0.975	0.943	1	CLONAL	2	TRUE	0	0.624654187872753	2		753	880	SUCCESS
APC	324	MSKCC	GRCh37	5	112175246	112175246	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1057517558	NA	P-0035927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	242	291	0	ENST00000257430.4:c.3956del	p.Pro1319LeufsTer2	p.P1319Lfs*2	ENST00000257430	NM_000038.5	1319	Cct/ct	16/16	0.624654187872753	3	FACETS	0.977	0.935	1	0.977	0.935	1	CLONAL	3	TRUE	0	0.624654187872753	3		291	347	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790156	40790156	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1238	124	583	0	ENST00000373198.4:c.2575C>A	p.Gln859Lys	p.Q859K	ENST00000373198	NM_133170.3	859	Cag/Aag	18/32	0.624654187872753	7	FACETS	0.747	0.673	0.825	0.149	0.134	0.165	SUBCLONAL	1	TRUE	2	0.624654187872753	7		583	1362	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435658	18435658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143896492	NA	P-0035927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	59	289	0	ENST00000266497.5:c.643G>A	p.Gly215Arg	p.G215R	ENST00000266497		215	Gga/Aga	1/31	0.579755861634365	4	FACETS	0.616	0.531	0.709	0.308	0.265	0.355	SUBCLONAL	1	TRUE	2	0.624654187872753	4		289	498	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62325812	62325812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141782041	NA	P-0035927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1309	191	580	0	ENST00000360203.5:c.3080C>T	p.Pro1027Leu	p.P1027L	ENST00000360203	NM_001283009.1	1027	cCc/cTc	31/35	0.624654187872753	7	FACETS	1	0.952	1	0.209	0.192	0.226	CLONAL	1	TRUE	2	0.624654187872753	7		580	1500	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416769	416769	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773466573	NA	P-0035927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	94	400	0	ENST00000399788.2:c.3781C>T	p.Arg1261Trp	p.R1261W	ENST00000399788	NM_001042603.1	1261	Cgg/Tgg	23/28	0.579755861634365	4	FACETS	0.803	0.715	0.896	0.401	0.357	0.448	CLONAL	1	TRUE	2	0.624654187872753	4		400	609	SUCCESS
AR	367	MSKCC	GRCh37	X	66765653	66765653	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1731	113	961	0	ENST00000374690.3:c.665A>T	p.Lys222Met	p.K222M	ENST00000374690	NM_000044.3	222	aAg/aTg	1/8	0.624654187872753	5	FACETS	0.38	0.34	0.423	0.127	0.113	0.141	SUBCLONAL	1	TRUE	2	0.624654187872753	5		961	1844	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21553919	21553919	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	258	422	0	ENST00000382592.4:c.2683G>T	p.Asp895Tyr	p.D895Y	ENST00000382592	NM_014572.2	895	Gac/Tac	7/8	0.444588879978396	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.444588879978396	1		422	675	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440870	52440870	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	467	599	0	ENST00000460680.1:c.634G>T	p.Glu212Ter	p.E212*	ENST00000460680	NM_004656.3	212	Gag/Tag	8/17	0.444588879978396	2	FACETS	0.93	0.891	0.97	0.93	0.891	0.97	CLONAL	2	TRUE	0	0.444588879978396	2		599	1129	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70967605	70967605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	257	554	0	ENST00000276594.2:c.1418C>T	p.Ser473Phe	p.S473F	ENST00000276594	NM_024504.3	473	tCt/tTt	7/8	0.157805792371776	4	FACETS	0.861	0.807	0.916	0.861	0.807	0.916	INDETERMINATE	2	TRUE	2	0.444588879978396	4		554	970	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0035962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	165	675	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.451417538868778	1	FACETS	0.94	0.868	1	0.94	0.868	1	CLONAL	1	TRUE	0	0.451417538868778	1		675	602	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	92	812	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.801	0.714	0.893	0.801	0.714	0.893	CLONAL	1	TRUE	1	0.451417538868778	2		812	509	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0035962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	92	539	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	1	2	FACETS	0.926	0.828	1	0.926	0.828	1	CLONAL	1	TRUE	1	0.451417538868778	2		539	440	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0035962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	159	625	3	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.995	0.926	1	1	0.993	1	CLONAL	2	TRUE	1	0.451417538868778	2		628	354	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045136	47045136	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	317	360	0	ENST00000377604.3:c.2377C>T	p.Arg793Ter	p.R793*	ENST00000377604	NM_001204468.1	793	Cga/Tga	21/24	0.402703496652721	2	FACETS	0.922	0.883	0.959			1	CLONAL	3	TRUE	NA	0.451417538868778	2		360	508	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850900	63850900	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	94	371	0	ENST00000279873.7:c.1678A>C	p.Ser560Arg	p.S560R	ENST00000279873	NM_032199.2	560	Agc/Cgc	10/10	0.385890013083984	4	FACETS	1	0.969	1			1	CLONAL	1	FALSE	NA	0.472411415706028	4		371	474	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	31	272	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.633	0.514	0.767	0.633	0.514	0.767	SUBCLONAL	1	TRUE	1	0.36	2		272	272	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0035968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	68	364	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.295022774058102	3	FACETS	0.946	0.826	1	0.473	0.413	0.538	CLONAL	1	TRUE	1	0.36	3		364	471	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562220	21562220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	47	1091	0	ENST00000382592.4:c.1699G>A	p.Gly567Arg	p.G567R	ENST00000382592	NM_014572.2	567	Gga/Aga	4/8	0.00926197899798886	3	FACETS	0.353	0.296	0.415			1	INDETERMINATE	1	TRUE	NA	0.36	3		1091	874	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281176	49281176	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758137158	NA	P-0035968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	149	979	0	ENST00000282018.3:c.223G>A	p.Val75Ile	p.V75I	ENST00000282018	NM_020377.2	75	Gtt/Att	1/1	1	2	FACETS	0.808	0.737	0.882	0.808	0.737	0.882	CLONAL	1	TRUE	1	0.36	2		979	1025	SUCCESS
AR	367	MSKCC	GRCh37	X	66942672	66942672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	23	228	0	ENST00000374690.3:c.2453C>T	p.Pro818Leu	p.P818L	ENST00000374690	NM_000044.3	818	cCa/cTa	7/8	1	1	FACETS	0.431	0.337	0.539	0.431	0.337	0.539	SUBCLONAL	1	TRUE	0	0.36	1		228	243	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562888	21562888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759368766	NA	P-0035969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	93	765	2	ENST00000382592.4:c.1031C>T	p.Pro344Leu	p.P344L	ENST00000382592	NM_014572.2	344	cCg/cTg	4/8	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.212970847395537	2		767	857	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0035973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	1011	488	2	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.508256848800416	4	FACETS	0.944	0.922	0.965			1	CLONAL	4	TRUE	NA	0.508256848800416	4		490	1589	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653824	89653824	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	195	545	0	ENST00000371953.3:c.122G>C	p.Arg41Thr	p.R41T	ENST00000371953	NM_000314.4	41	aGa/aCa	2/9	1	2	FACETS	0.875	0.811	0.942	0.875	0.811	0.942	CLONAL	1	TRUE	1	0.508256848800416	2		545	877	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-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	152	497	0	ENST00000269305.4:c.365_375+8del		p.X122_splice	ENST00000269305	NM_001126112.2	122		4/11	0.508256848800416	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.508256848800416	1		497	418	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0035998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	17	488	2	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.254	0.189	0.33	0.254	0.189	0.33	SUBCLONAL	1	TRUE	1	0.549070047155105	2		490	244	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0035998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	68	364	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.549070047155105	2		364	232	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0035998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	151	616	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.549070047155105	2		616	530	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0035998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	64	340	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	0.147088682777629	0	FACETS	0.696	0.619	0.775			1	INDETERMINATE	1	TRUE	0	0.549070047155105	0		340	151	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235839	108235845	+	frameshift_variant	Frame_Shift_Del	DEL	ACCATGA	ACCATGA	-	novel	NA	P-0035998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	64	383	0	ENST00000278616.4:c.8882_8888del	p.Thr2961IlefsTer3	p.T2961Ifs*3	ENST00000278616	NM_000051.3	2961	ACCATGAat/at	62/63	1	2	FACETS	0.959	0.841	1	0.959	0.841	1	CLONAL	1	TRUE	1	0.549070047155105	2		383	243	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445089	49445089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	36	502	0	ENST00000301067.7:c.2377G>A	p.Glu793Lys	p.E793K	ENST00000301067	NM_003482.3	793	Gag/Aag	10/54	0.14123457883172	4	FACETS	0.545	0.448	0.652	0.272	0.224	0.326	INDETERMINATE	1	TRUE	2	0.549070047155105	4		502	373	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459506	40459506	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	21	420	0	ENST00000345506.4:c.1767G>C	p.Trp589Cys	p.W589C	ENST00000345506	NM_003152.3	589	tgG/tgC	15/20	1	2	FACETS	0.209	0.16	0.266	0.209	0.16	0.266	SUBCLONAL	1	TRUE	1	0.549070047155105	2		420	366	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17941316	17941316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749169776	NA	P-0035998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	54	477	0	ENST00000458235.1:c.3092C>T	p.Ser1031Leu	p.S1031L	ENST00000458235	NM_000215.3	1031	tCg/tTg	22/24	1	2	FACETS	0.637	0.547	0.733	0.637	0.547	0.733	SUBCLONAL	1	TRUE	1	0.549070047155105	2		477	309	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295192	1295193	+	upstream_gene_variant	5'Flank	INS	-	-	GCGGAAAGGAAGGGGAGGGGCTA	novel	NA	P-0035998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	19	190	0				ENST00000310581	NM_198253.2	-/1132			0.375281917637411	3	FACETS	0.684	0.525	0.866	0.342	0.262	0.433	SUBCLONAL	1	TRUE	1	0.549070047155105	3		190	129	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779192	135779192	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0035998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	20	333	0	ENST00000298552.3:c.2054C>G	p.Ser685Ter	p.S685*	ENST00000298552	NM_001162426.1	685	tCa/tGa	17/23	0.549070047155105	1	FACETS	0.262	0.201	0.332	0.262	0.201	0.332	SUBCLONAL	1	TRUE	0	0.549070047155105	1		333	202	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922061	39922061	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs863224850	NA	P-0035998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	57	676	0	ENST00000378444.4:c.4111C>T	p.Gln1371Ter	p.Q1371*	ENST00000378444	NM_001123385.1	1371	Cag/Tag	9/15	0.401306491516992	1	FACETS	0.327	0.281	0.377	0.327	0.281	0.377	SUBCLONAL	1	TRUE	0	0.549070047155105	1		676	461	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53244001	53244001	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	33	533	0	ENST00000375401.3:c.992C>T	p.Ser331Phe	p.S331F	ENST00000375401	NM_004187.3	331	tCt/tTt	8/26	0.401306491516992	1	FACETS	0.247	0.201	0.299	0.247	0.201	0.299	SUBCLONAL	1	TRUE	0	0.549070047155105	1		533	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0036001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	177	675	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.514102890800558	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	0	0.514102890800558	1		675	487	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511750	46511750	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	168	490	0	ENST00000262741.5:c.1027A>G	p.Ile343Val	p.I343V	ENST00000262741	NM_003629.3	343	Atc/Gtc	9/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.514102890800558	2		490	526	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739902	145739902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	47	521	1	ENST00000428558.2:c.1628G>A	p.Gly543Asp	p.G543D	ENST00000428558	NM_004260.3	543	gGc/gAc	10/22	0.514102890800558	4	FACETS	0.329	0.277	0.388	0.11	0.092	0.13	SUBCLONAL	1	FALSE	1	0.514102890800558	4		522	841	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520006	NA	P-0036003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	208	612	0	ENST00000269305.4:c.821T>C	p.Val274Ala	p.V274A	ENST00000269305	NM_001126112.2	274	gTt/gCt	8/11	0.15460656696292	2	FACETS	1	0.975	1	1	0.994	1	CLONAL	4	TRUE	0	0.15460656696292	2		612	618	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008501	70008501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147148433	NA	P-0036003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	20	287	0	ENST00000394351.3:c.788G>A	p.Arg263His	p.R263H	ENST00000394351	NM_000248.3	263	cGc/cAc	8/9	0.145643119521124	3	FACETS	0.757	0.578	0.968	0.379	0.289	0.484	CLONAL	1	TRUE	1	0.15460656696292	3		287	368	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805133	43805133	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	36	534	1	ENST00000372470.3:c.583C>A	p.Pro195Thr	p.P195T	ENST00000372470	NM_005373.2	195	Cct/Act	4/12	0.145643119521124	3	FACETS	1	0.835	1	0.509	0.418	0.611	CLONAL	1	TRUE	1	0.15460656696292	3		535	493	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839778	27839778	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	86	500	0	ENST00000328488.2:c.316G>C	p.Glu106Gln	p.E106Q	ENST00000328488	NM_003533.2	106	Gag/Cag	1/1	0.15460656696292	6	FACETS	1	0.894	1	0.755	0.671	0.845	CLONAL	3	TRUE	2	0.15460656696292	6		500	482	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431575	6431575	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1562466717	NA	P-0036003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	49	181	0	ENST00000356142.4:c.128A>G	p.Asn43Ser	p.N43S	ENST00000356142	NM_018890.3	43	aAt/aGt	3/7	0.149497350336829	3	FACETS	0.969	0.84	1	1	0.979	1	CLONAL	5	TRUE	1	0.15460656696292	3		181	141	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918592	44918593	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0036003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	130	482	0	ENST00000377967.4:c.1076_1077dup	p.Thr360AlafsTer18	p.T360Afs*18	ENST00000377967	NM_021140.2	359	ggc/gGCgc	12/29	0.15460656696292	1	FACETS	0.951	0.871	1	1	0.993	1	CLONAL	4	TRUE	0	0.15460656696292	1		482	408	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0036004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	612	368	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.568710279076928	10	FACETS	1	0.99	1			1	CLONAL	9	TRUE	NA	0.568710279076928	10		368	767	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579378	7579378	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0036004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	148	537	0	ENST00000269305.4:c.309C>G	p.Tyr103Ter	p.Y103*	ENST00000269305	NM_001126112.2	103	taC/taG	4/11	0.568710279076928	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.568710279076928	1		537	325	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62309633	62309633	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113684274	NA	P-0036004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	76	457	0	ENST00000360203.5:c.971G>A	p.Arg324His	p.R324H	ENST00000360203	NM_001283009.1	324	cGc/cAc	12/35	0.291516714501857	5	FACETS	0.962	0.845	1			1	INDETERMINATE	1	TRUE	NA	0.568710279076928	5		457	515	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140130	50140130	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1488434625	NA	P-0036004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	48	520	1	ENST00000246792.3:c.295C>T	p.Arg99Cys	p.R99C	ENST00000246792	NM_006270.3	99	Cgt/Tgt	3/6	1	2	FACETS	0.477	0.404	0.556	0.477	0.404	0.556	SUBCLONAL	1	TRUE	1	0.568710279076928	2		521	354	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845627	63845627	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1198909219	NA	P-0036004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	10	146	0	ENST00000279873.7:c.1366G>C	p.Glu456Gln	p.E456Q	ENST00000279873	NM_032199.2	456	Gaa/Caa	9/10	0.256875519574077	4	FACETS	0.301	0.204	0.424	0.151	0.102	0.212	INDETERMINATE	1	TRUE	2	0.568710279076928	4		146	183	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153582	108153582	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	47	295	0	ENST00000278616.4:c.3722A>G	p.Tyr1241Cys	p.Y1241C	ENST00000278616	NM_000051.3	1241	tAc/tGc	25/63	0.2437199119838	4	FACETS	0.864	0.733	1			1	INDETERMINATE	1	TRUE	NA	0.568710279076928	4		295	300	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155309	185155309	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	329	339	0	ENST00000265026.3:c.550T>G	p.Leu184Val	p.L184V	ENST00000265026	NM_004721.4	184	Ttg/Gtg	3/14	0.568710279076928	5	FACETS	1	0.974	1	1	0.974	1	CLONAL	4	TRUE	1	0.568710279076928	5		339	525	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0036006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	161	675	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.35702359231887	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.35702359231887	1		675	726	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0036006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	208	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.344125859522889	2	FACETS	0.991	0.926	1	0.991	0.926	1	CLONAL	2	TRUE	0	0.35702359231887	2		502	588	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920402	114920402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs927089403	NA	P-0036006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	101	552	0	ENST00000543371.1:c.1343G>A	p.Arg448Gln	p.R448Q	ENST00000543371	NM_001198531.1	448	cGg/cAg	13/14	1	2	FACETS	0.809	0.724	0.9	0.809	0.724	0.9	CLONAL	1	TRUE	1	0.35702359231887	2		552	699	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879794	37879794	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	97	478	0	ENST00000269571.5:c.2089G>T	p.Val697Leu	p.V697L	ENST00000269571		697	Gtg/Ttg	18/27	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.35702359231887	2		478	505	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs748696421	NA	P-0036006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	25	403	0	ENST00000397062.3:c.100C>T	p.Arg34Ter	p.R34*	ENST00000397062	NM_006164.4	34	Cga/Tga	2/5	1	2	FACETS	0.318	0.25	0.396	0.318	0.25	0.396	SUBCLONAL	1	TRUE	1	0.35702359231887	2		403	441	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591102	67591113	+	inframe_deletion	In_Frame_Del	DEL	CATTAAACCAGA	CATTAAACCAGA	-	novel	NA	P-0036006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	48	300	0	ENST00000274335.5:c.1696_1707del	p.Ile566_Asp569del	p.I566_D569del	ENST00000274335		565	agCATTAAACCAGAc/agc	12/15	0.35702359231887	1	FACETS	0.856	0.73	0.993	0.856	0.73	0.993	CLONAL	1	TRUE	0	0.35702359231887	1		300	258	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241872	72241872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752419911	NA	P-0036006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	87	314	0	ENST00000357731.5:c.518G>A	p.Arg173Gln	p.R173Q	ENST00000357731	NM_173808.2	173	cGa/cAa	3/7	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.35702359231887	2		314	487	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257169	19257169	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	119	541	0	ENST00000162023.5:c.794C>A	p.Pro265Gln	p.P265Q	ENST00000162023		265	cCg/cAg	12/13	0.35702359231887	3	FACETS	1	0.939	1	0.527	0.475	0.581	CLONAL	1	TRUE	1	0.35702359231887	3		541	746	SUCCESS
APC	324	MSKCC	GRCh37	5	112175411	112175412	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AACA	novel	NA	P-0036006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	53	280	0	ENST00000257430.4:c.4121_4124dup	p.His1375GlnfsTer12	p.H1375Qfs*12	ENST00000257430	NM_000038.5	1374	gaa/gAACAaa	16/16	0.35702359231887	1	FACETS	0.816	0.7	0.94	0.816	0.7	0.94	CLONAL	1	TRUE	0	0.35702359231887	1		280	299	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0036008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	198	417	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.12201911501169	3	FACETS	1	0.981	1	1	0.981	1	INDETERMINATE	2	FALSE	1	0.233002880533107	3		417	814	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514129	125514129	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	72	639	0	ENST00000428830.2:c.1067A>G	p.Asn356Ser	p.N356S	ENST00000428830	NM_001114121.2	356	aAt/aGt	10/14	NA	2	FACETS	0.976	0.853	1			1	INDETERMINATE	1	FALSE	NA	0.233002880533107	2		639	633	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563033	21563033	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	98	1024	0	ENST00000382592.4:c.886G>A	p.Gly296Arg	p.G296R	ENST00000382592	NM_014572.2	296	Gga/Aga	4/8	1	2	FACETS	0.755	0.672	0.844	0.755	0.672	0.844	SUBCLONAL	1	FALSE	1	0.233002880533107	2		1024	1114	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828222	72828222	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	41	804	0	ENST00000268489.5:c.8359C>A	p.Pro2787Thr	p.P2787T	ENST00000268489	NM_006885.3	2787	Cct/Act	9/10	1	2	FACETS	0.467	0.388	0.556	0.467	0.388	0.556	SUBCLONAL	1	FALSE	1	0.233002880533107	2		804	753	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41276086	41276086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	51	666	0	ENST00000357654.3:c.28G>A	p.Glu10Lys	p.E10K	ENST00000357654	NM_007294.3	10	Gaa/Aaa	2/23	0.188760724835336	3	FACETS	0.85	0.722	0.991	0.425	0.361	0.496	CLONAL	1	FALSE	1	0.233002880533107	3		666	575	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038274	30038274	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	30	495	0	ENST00000338641.4:c.447G>C	p.Lys149Asn	p.K149N	ENST00000338641	NM_000268.3	149	aaG/aaC	4/16	1	2	FACETS	0.544	0.438	0.666	0.544	0.438	0.666	SUBCLONAL	1	FALSE	1	0.233002880533107	2		495	473	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161283	185161283	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	64	913	0	ENST00000265026.3:c.710C>G	p.Ala237Gly	p.A237G	ENST00000265026	NM_004721.4	237	gCc/gGc	4/14	1	2	FACETS	0.675	0.583	0.775	0.675	0.583	0.775	SUBCLONAL	1	FALSE	1	0.233002880533107	2		913	814	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748173	41748173	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	51	753	0	ENST00000226382.2:c.596G>T	p.Gly199Val	p.G199V	ENST00000226382	NM_003924.3	199	gGt/gTt	3/3	1	2	FACETS	0.58	0.492	0.677	0.58	0.492	0.677	SUBCLONAL	1	FALSE	1	0.233002880533107	2		753	755	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508092	106508092	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	28	254	0	ENST00000359195.3:c.86C>G	p.Ala29Gly	p.A29G	ENST00000359195	NM_002649.2	29	gCg/gGg	2/11	0.188760724835336	3	FACETS	0.852	0.682	1	0.426	0.341	0.523	CLONAL	1	FALSE	1	0.233002880533107	3		254	315	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209643	98209643	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	55	669	0	ENST00000331920.6:c.3895G>T	p.Gly1299Cys	p.G1299C	ENST00000331920	NM_000264.3	1299	Ggc/Tgc	23/24	1	2	FACETS	0.623	0.532	0.723	0.623	0.532	0.723	SUBCLONAL	1	FALSE	1	0.233002880533107	2		669	758	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279595	123279595	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	108	660	0	ENST00000358487.5:c.837G>T	p.Lys279Asn	p.K279N	ENST00000358487	NM_000141.4	279	aaG/aaT	7/18	0.302986224522917	3	FACETS	0.59	0.528	0.656	0.295	0.264	0.328	SUBCLONAL	1	TRUE	1	0.451895712807909	3		660	993	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0036009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	495	733	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.451895712807909	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.451895712807909	3		733	793	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976482	7976482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	139	661	1	ENST00000319144.4:c.1910G>A	p.Arg637Gln	p.R637Q	ENST00000319144	NM_001139.2	637	cGa/cAa	14/15	0.451895712807909	3	FACETS	1	0.973	1	0.387	0.353	0.423	CLONAL	1	TRUE	0	0.451895712807909	3		662	649	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603007	48603007	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0036009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	77	318	0	ENST00000342988.3:c.1309-1G>C		p.X437_splice	ENST00000342988	NM_005359.5	437			0.400638875983625	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.451895712807909	1		318	249	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280017	66280017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	54	240	0	ENST00000273854.3:c.1672G>A	p.Glu558Lys	p.E558K	ENST00000273854	NM_004439.5	558	Gaa/Aaa	7/18	0.34026836213955	3	FACETS	0.961	0.826	1	0.48	0.413	0.553	CLONAL	1	TRUE	1	0.451895712807909	3		240	305	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392110	81392110	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs932514859	NA	P-0036009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	205	476	1	ENST00000222390.5:c.167C>A	p.Ala56Glu	p.A56E	ENST00000222390	NM_000601.4	56	gCa/gAa	2/18	0.451895712807909	4	FACETS	1	0.983	1	0.575	0.537	0.613	CLONAL	2	TRUE	0	0.451895712807909	4		477	573	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0036010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	23	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.47	0.365	0.591	0.47	0.365	0.591	SUBCLONAL	1	FALSE	1	0.204493082926825	2		502	479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0036010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	55	753	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.204493082926825	1	FACETS	0.764	0.653	0.886	0.764	0.653	0.886	SUBCLONAL	1	FALSE	0	0.204493082926825	1		753	632	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891035	112891035	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs755619262	NA	P-0036010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	23	372	0	ENST00000351677.2:c.369G>T	p.Glu123Asp	p.E123D	ENST00000351677	NM_002834.3	123	gaG/gaT	4/16	1	2	FACETS	0.703	0.548	0.882	0.703	0.548	0.882	SUBCLONAL	1	FALSE	1	0.204493082926825	2		372	320	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186757	108186757	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs864622251	NA	P-0036010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	31	460	0	ENST00000278616.4:c.6115G>T	p.Glu2039Ter	p.E2039*	ENST00000278616	NM_000051.3	2039	Gaa/Taa	42/63	1	2	FACETS	0.731	0.591	0.889	0.731	0.591	0.889	SUBCLONAL	1	FALSE	1	0.204493082926825	2		460	415	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0036011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	172	417	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.982	0.905	1	0.982	0.905	1	CLONAL	1	TRUE	1	0.441756818257497	2		417	793	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653796	89653798	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs1554893765	NA	P-0036011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	153	479	0	ENST00000371953.3:c.97_99del	p.Ile33del	p.I33del	ENST00000371953	NM_000314.4	32	ATT/-	2/9	0.441756818257497	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.441756818257497	1		479	450	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216624	108216626	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs786203976	NA	P-0036011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	109	449	1	ENST00000278616.4:c.8578_8580del	p.Ser2860del	p.S2860del	ENST00000278616	NM_000051.3	2858	aCTTct/act	58/63	0.441756818257497	1	FACETS	0.988	0.895	1	0.988	0.895	1	CLONAL	1	TRUE	0	0.441756818257497	1		450	389	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38283756	38283756	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	169	745	0	ENST00000425967.3:c.722A>T	p.Tyr241Phe	p.Y241F	ENST00000425967	NM_001174067.1	241	tAt/tTt	7/19	0.441756818257497	1	FACETS	0.837	0.772	0.905	0.837	0.772	0.905	CLONAL	1	TRUE	0	0.441756818257497	1		745	712	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	144	272	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.819359950215629	2		272	342	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0036017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	143	336	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.819359950215629	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.819359950215629	1		336	199	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875685	35875685	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	141	322	0	ENST00000303115.3:c.872G>T	p.Arg291Ile	p.R291I	ENST00000303115	NM_002185.3	291	aGa/aTa	7/8	1	2	FACETS	0.983	0.908	1	0.983	0.908	1	CLONAL	1	TRUE	1	0.819359950215629	2		322	350	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717615	89717615	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909227	NA	P-0036020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	125	420	0	ENST00000371953.3:c.640C>T	p.Gln214Ter	p.Q214*	ENST00000371953	NM_000314.4	214	Cag/Tag	7/9	0.312617417634717	1	FACETS	0.992	0.9	1	0.992	0.9	1	CLONAL	1	TRUE	0	0.327649543440578	1		420	643	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245513	153245513	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	156	511	0	ENST00000281708.4:c.1678G>C	p.Asp560His	p.D560H	ENST00000281708	NM_033632.3	560	Gat/Cat	11/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.327649543440578	2		511	834	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0036020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	111	326	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.327649543440578	2		326	669	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0036020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	143	552	1	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	0.196271126489313	3	FACETS	1	0.964	1	0.555	0.506	0.607	INDETERMINATE	1	TRUE	1	0.327649543440578	3		553	915	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138955	37138955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1650	176	874	0	ENST00000373509.5:c.295G>A	p.Gly99Ser	p.G99S	ENST00000373509	NM_002648.3	99	Ggt/Agt	4/6	1	2	FACETS	0.588	0.539	0.64	0.588	0.539	0.64	SUBCLONAL	1	TRUE	1	0.327649543440578	2		874	1826	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813630	50813630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	171	688	1	ENST00000398568.2:c.1184C>T	p.Ser395Phe	p.S395F	ENST00000398568	NM_001042412.1	395	tCt/tTt	8/18	1	2	FACETS	0.916	0.841	0.994	0.916	0.841	0.994	CLONAL	1	TRUE	1	0.327649543440578	2		689	1140	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677894	58677894	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	41	479	1	ENST00000305921.3:c.119C>A	p.Ser40Ter	p.S40*	ENST00000305921	NM_003620.3	40	tCg/tAg	1/6	0.253185969156842	2	FACETS	0.313	0.259	0.373	0.156	0.129	0.187	SUBCLONAL	1	TRUE	0	0.327649543440578	2		480	800	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520123	9520123	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	56	435	0	ENST00000353224.5:c.2146T>C	p.Tyr716His	p.Y716H	ENST00000353224	NM_177990.2	716	Tac/Cac	10/10	0.196271126489313	3	FACETS	0.469	0.401	0.544	0.235	0.2	0.272	INDETERMINATE	1	TRUE	1	0.327649543440578	3		435	848	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058685	47058685	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	87	697	0	ENST00000409792.3:c.7593G>C	p.Glu2531Asp	p.E2531D	ENST00000409792	NM_014159.6	2531	gaG/gaC	21/21	0.315142918068325	2	FACETS	0.438	0.386	0.494	0.219	0.193	0.247	SUBCLONAL	1	TRUE	0	0.327649543440578	2		697	1213	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439302	52439302	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56238158	NA	P-0036020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	61	616	0	ENST00000460680.1:c.940G>A	p.Glu314Lys	p.E314K	ENST00000460680	NM_004656.3	314	Gag/Aag	11/17	0.315142918068325	2	FACETS	0.333	0.286	0.385	0.167	0.143	0.193	SUBCLONAL	1	TRUE	0	0.327649543440578	2		616	1117	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170011255	170011255	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	189	685	0	ENST00000295797.4:c.1376C>G	p.Ser459Cys	p.S459C	ENST00000295797	NM_002740.5	459	tCc/tGc	14/18	0.327649543440578	3	FACETS	0.967	0.892	1	0.322	0.297	0.349	CLONAL	1	TRUE	0	0.327649543440578	3		685	1388	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265418	152265418	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs746807379	NA	P-0036020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	110	531	0	ENST00000206249.3:c.871C>A	p.Leu291Ile	p.L291I	ENST00000206249	NM_000125.3	291	Ctt/Att	4/8	1	2	FACETS	0.836	0.751	0.926	0.836	0.751	0.926	CLONAL	1	TRUE	1	0.327649543440578	2		531	803	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370763	55370763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757830070	NA	P-0036020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	170	539	2	ENST00000297316.4:c.65C>T	p.Ala22Val	p.A22V	ENST00000297316	NM_022454.3	22	gCg/gTg	1/2	0.249829200217266	1	FACETS	0.984	0.905	1	0.984	0.905	1	CLONAL	1	TRUE	0	0.327649543440578	1		541	882	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0036023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	471	622	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.280946260126143	6	FACETS	1	0.98	1			1	INDETERMINATE	4	TRUE	NA	0.615078699266205	6		622	833	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0036023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	591	804	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.478518767522637	4	FACETS	1	0.996	1	0.86	0.835	0.885	CLONAL	3	TRUE	0	0.615078699266205	4		804	902	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0036023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	162	353	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.473187730673047	3	FACETS	1	0.986	1	0.794	0.745	0.843	CLONAL	2	TRUE	0	0.615078699266205	3		353	289	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411678	63411678	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	477	480	0	ENST00000330258.3:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000330258	NM_152424.3	497	Cga/Tga	2/2	0.615078699266205	3	FACETS	1	0.994	1			1	CLONAL	3	TRUE	NA	0.615078699266205	3		480	622	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906331	50906331	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371120096	NA	P-0036023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	349	807	0	ENST00000440232.2:c.992G>A	p.Arg331Gln	p.R331Q	ENST00000440232	NM_002691.3	331	cGg/cAg	9/27	0.615078699266205	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.615078699266205	3		807	702	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	90	551	1	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.368	0.327	0.413	0.368	0.327	0.413	SUBCLONAL	1	TRUE	1	0.690288477243321	2		552	708	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	91	623	1	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	0.291	0.258	0.327	0.291	0.258	0.327	SUBCLONAL	1	TRUE	1	0.690288477243321	2		624	905	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	219	709	0	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.84	0.784	0.898	0.84	0.784	0.898	CLONAL	1	TRUE	1	0.690288477243321	2		709	755	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	38	865	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	1	2	FACETS	0.095	0.078	0.115	0.095	0.078	0.115	SUBCLONAL	1	TRUE	1	0.690288477243321	2		865	1156	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332337	70332337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761821309	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	193	528	0	ENST00000373644.4:c.242G>A	p.Arg81His	p.R81H	ENST00000373644	NM_030625.2	81	cGc/cAc	2/12	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.690288477243321	2		528	555	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	453	612	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.931	0.899	0.962	1	0.997	1	CLONAL	2	TRUE	1	0.690288477243321	2		616	705	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589610	67589612	+	inframe_deletion	In_Frame_Del	DEL	AAA	AAA	-	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	54	262	0	ENST00000274335.5:c.1376_1378del	p.Lys459del	p.K459del	ENST00000274335		458	gAAAaa/gaa	10/15	1	2	FACETS	0.689	0.596	0.789	0.689	0.596	0.789	SUBCLONAL	1	TRUE	1	0.690288477243321	2		262	227	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	105	453	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.415	0.372	0.461	0.415	0.372	0.461	SUBCLONAL	1	TRUE	1	0.690288477243321	2		453	733	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143383	30143383	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1558550140	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	89	692	0	ENST00000389048.3:c.143G>A	p.Arg48His	p.R48H	ENST00000389048	NM_004304.4	48	cGc/cAc	1/29	1	2	FACETS	0.381	0.338	0.428	0.381	0.338	0.428	SUBCLONAL	1	TRUE	1	0.690288477243321	2		692	676	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	121	434	5	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	1	2	FACETS	0.859	0.783	0.938	0.859	0.783	0.938	CLONAL	1	TRUE	1	0.690288477243321	2		439	408	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	79	670	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	1	2	FACETS	0.392	0.345	0.442	0.392	0.345	0.442	SUBCLONAL	1	TRUE	1	0.690288477243321	2		670	584	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	136	823	5	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	0.690288477243321	3	FACETS	0.437	0.396	0.48	0.218	0.198	0.24	SUBCLONAL	1	TRUE	1	0.690288477243321	3		828	1214	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661664	227661664	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs761880048	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	187	673	8	ENST00000305123.5:c.1791del	p.His598ThrfsTer38	p.H598Tfs*38	ENST00000305123	NM_005544.2	597	ggG/gg	1/2	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.690288477243321	2		681	530	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245587	41245587	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357522	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	141	987	4	ENST00000357654.3:c.1961del	p.Lys654SerfsTer47	p.K654Sfs*47	ENST00000357654	NM_007294.3	654	aAg/ag	10/23	1	2	FACETS	0.476	0.434	0.521	0.476	0.434	0.521	SUBCLONAL	1	TRUE	1	0.690288477243321	2		991	858	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468185	120468185	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	260	739	3	ENST00000256646.2:c.4254del	p.Ser1419AlafsTer8	p.S1419Afs*8	ENST00000256646	NM_024408.3	1418	ccC/cc	25/34	1	2	FACETS	0.996	0.938	1	0.996	0.938	1	CLONAL	1	TRUE	1	0.690288477243321	2		742	756	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	204	730	12	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	0.690288477243321	2		742	540	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907421	32907421	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359306	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	71	339	5	ENST00000380152.3:c.1813del	p.Ile605TyrfsTer9	p.I605Yfs*9	ENST00000380152		602	ggA/gg	10/27	1	2	FACETS	0.85	0.752	0.953	0.85	0.752	0.953	CLONAL	1	TRUE	1	0.690288477243321	2		344	242	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994854	73994854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770650860	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	33	126	0	ENST00000318443.5:c.338G>A	p.Arg113His	p.R113H	ENST00000318443	NM_001024736.1	113	cGt/cAt	3/10	1	2	FACETS	0.831	0.692	0.98	0.831	0.692	0.98	CLONAL	1	TRUE	1	0.690288477243321	2		126	115	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508725	106508725	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	228	607	0	ENST00000359195.3:c.723del	p.Gly242AlafsTer17	p.G242Afs*17	ENST00000359195	NM_002649.2	240	aCc/ac	2/11	0.690288477243321	3	FACETS	0.925	0.862	0.989	0.462	0.431	0.495	CLONAL	1	TRUE	1	0.690288477243321	3		607	961	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962854	2962854	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	89	884	2	ENST00000396946.4:c.2054del	p.Gly685AlafsTer31	p.G685Afs*31	ENST00000396946	NM_032415.4	685	gGc/gc	16/25	0.690288477243321	3	FACETS	0.295	0.26	0.332	0.147	0.13	0.166	SUBCLONAL	1	TRUE	1	0.690288477243321	3		886	1177	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199945	138199945	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	136	480	0	ENST00000237289.4:c.1368del	p.Pro457LeufsTer20	p.P457Lfs*20	ENST00000237289	NM_001270507.1	455	Ggg/gg	7/9	1	2	FACETS	0.968	0.889	1	0.968	0.889	1	CLONAL	1	TRUE	1	0.690288477243321	2		480	407	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725018	47725019	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs762488821	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	355	967	0	ENST00000449228.1:c.725dup	p.Arg243GlnfsTer7	p.R243Qfs*7	ENST00000449228	NM_001127240.2	242	ggc/ggGc	4/4	1	2	FACETS	0.998	0.947	1	0.998	0.947	1	CLONAL	1	TRUE	1	0.690288477243321	2		967	1031	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100312	27100312	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	295	847	2	ENST00000324856.7:c.4024C>T	p.Gln1342Ter	p.Q1342*	ENST00000324856	NM_006015.4	1342	Cag/Tag	17/20	1	2	FACETS	0.933	0.88	0.987	0.933	0.88	0.987	CLONAL	1	TRUE	1	0.690288477243321	2		849	916	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007741	45007742	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	61	497	0	ENST00000558401.1:c.194_195del	p.Arg65AsnfsTer2	p.R65Nfs*2	ENST00000558401	NM_004048.2	63	gGA/g	2/4	1	2	FACETS	0.422	0.365	0.483	0.422	0.365	0.483	SUBCLONAL	1	TRUE	1	0.690288477243321	2		497	419	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800902	120800903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs748469666	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	360	880	5	ENST00000257552.2:c.345dup	p.Leu116AlafsTer15	p.L116Afs*15	ENST00000257552	NM_002442.3	115	-/G	6/15	1	2	FACETS	0.911	0.864	0.959	0.911	0.864	0.959	CLONAL	1	TRUE	1	0.690288477243321	2		885	1145	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209593	98209593	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	184	529	0	ENST00000331920.6:c.3945del	p.Tyr1316ThrfsTer56	p.Y1316Tfs*56	ENST00000331920	NM_000264.3	1315	ccC/cc	23/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.690288477243321	2		529	500	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739691	145739691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747307935	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	263	799	1	ENST00000428558.2:c.1760C>T	p.Ala587Val	p.A587V	ENST00000428558	NM_004260.3	587	gCg/gTg	11/22	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.690288477243321	2		800	719	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509927	187509927	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555931755	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	63	451	1	ENST00000441802.2:c.13586C>T	p.Ala4529Val	p.A4529V	ENST00000441802	NM_005245.3	4529	gCg/gTg	27/27	1	2	FACETS	0.396	0.343	0.453	0.396	0.343	0.453	SUBCLONAL	1	TRUE	1	0.690288477243321	2		452	461	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851591	134851591	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748976557	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	210	659	0	ENST00000398015.3:c.997G>A	p.Val333Ile	p.V333I	ENST00000398015	NM_004441.4	333	Gtc/Atc	5/16	1	2	FACETS	0.967	0.903	1	0.967	0.903	1	CLONAL	1	TRUE	1	0.690288477243321	2		659	629	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250244	110250244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1471124290	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	239	832	0	ENST00000374672.4:c.431C>T	p.Ala144Val	p.A144V	ENST00000374672	NM_004235.4	144	gCg/gTg	3/5	1	2	FACETS	0.991	0.93	1	0.991	0.93	1	CLONAL	1	TRUE	1	0.690288477243321	2		832	699	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176560	142176560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151162347	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	129	560	0	ENST00000350721.4:c.7541G>A	p.Arg2514His	p.R2514H	ENST00000350721	NM_001184.3	2514	cGc/cAc	45/47	1	2	FACETS	0.797	0.727	0.869	0.797	0.727	0.869	SUBCLONAL	1	TRUE	1	0.690288477243321	2		560	469	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857228	78857228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	125	801	0	ENST00000306801.3:c.1594C>T	p.Arg532Trp	p.R532W	ENST00000306801	NM_020761.2	532	Cgg/Tgg	15/34	1	2	FACETS	0.338	0.305	0.373	0.338	0.305	0.373	SUBCLONAL	1	TRUE	1	0.690288477243321	2		801	1072	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133981	38133981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	287	859	0	ENST00000317025.8:c.3905del	p.Asn1302MetfsTer4	p.N1302Mfs*4	ENST00000317025	NM_023034.1	1302	aAt/at	23/24	1	2	FACETS	0.964	0.909	1	0.964	0.909	1	CLONAL	1	TRUE	1	0.690288477243321	2		859	863	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376248	15376248	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	144	613	2	ENST00000263377.2:c.766del	p.Gln256SerfsTer27	p.Q256Sfs*27	ENST00000263377	NM_058243.2	256	Cag/ag	5/20	1	2	FACETS	0.75	0.688	0.815	0.75	0.688	0.815	SUBCLONAL	1	TRUE	1	0.690288477243321	2		615	556	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78519468	78519468	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	67	555	0	ENST00000306801.3:c.43del	p.Glu15ArgfsTer17	p.E15Rfs*17	ENST00000306801	NM_020761.2	13	ctG/ct	1/34	1	2	FACETS	0.268	0.233	0.307	0.268	0.233	0.307	SUBCLONAL	1	TRUE	1	0.690288477243321	2		555	723	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517474	176517474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200344385	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	172	936	1	ENST00000292408.4:c.175C>T	p.Arg59Trp	p.R59W	ENST00000292408	NM_213647.1	59	Cgg/Tgg	3/18	1	2	FACETS	0.521	0.479	0.564	0.521	0.479	0.564	SUBCLONAL	1	TRUE	1	0.690288477243321	2		937	957	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228761	36228761	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	273	881	1	ENST00000222270.7:c.7660C>T	p.Arg2554Cys	p.R2554C	ENST00000222270	NM_014727.1	2554	Cgt/Tgt	35/37	1	2	FACETS	0.999	0.941	1	0.999	0.941	1	CLONAL	1	TRUE	1	0.690288477243321	2		882	792	SUCCESS
FH	2271	MSKCC	GRCh37	1	241661204	241661204	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	98	847	1	ENST00000366560.3:c.1457C>T	p.Ala486Val	p.A486V	ENST00000366560	NM_000143.3	486	gCt/gTt	10/10	1	2	FACETS	0.368	0.328	0.411	0.368	0.328	0.411	SUBCLONAL	1	TRUE	1	0.690288477243321	2		848	771	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199861	138199861	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	106	522	0	ENST00000237289.4:c.1279C>A	p.Pro427Thr	p.P427T	ENST00000237289	NM_001270507.1	427	Cct/Act	7/9	1	2	FACETS	0.636	0.573	0.702	0.636	0.573	0.702	SUBCLONAL	1	TRUE	1	0.690288477243321	2		522	483	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099117	27099117	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	162	411	0	ENST00000324856.7:c.3533G>T	p.Gly1178Val	p.G1178V	ENST00000324856	NM_006015.4	1178	gGc/gTc	13/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.690288477243321	2		411	449	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845423	156845423	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	367	1027	0	ENST00000524377.1:c.1466A>G	p.His489Arg	p.H489R	ENST00000524377	NM_002529.3	489	cAc/cGc	12/17	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.690288477243321	2		1027	968	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405043	70405043	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	163	645	2	ENST00000373644.4:c.2557G>T	p.Gly853Cys	p.G853C	ENST00000373644	NM_030625.2	853	Ggt/Tgt	4/12	1	2	FACETS	0.99	0.916	1	0.99	0.916	1	CLONAL	1	TRUE	1	0.690288477243321	2		647	477	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451534	70451535	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	307	813	2	ENST00000373644.4:c.6380_6381dup	p.Val2128ThrfsTer53	p.V2128Tfs*53	ENST00000373644	NM_030625.2	2125	ctc/ctCAc	12/12	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.690288477243321	2		815	885	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420067	49420067	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	60	742	0	ENST00000301067.7:c.15682T>C	p.Tyr5228His	p.Y5228H	ENST00000301067	NM_003482.3	5228	Tat/Cat	48/54	1	2	FACETS	0.22	0.189	0.254	0.22	0.189	0.254	SUBCLONAL	1	TRUE	1	0.690288477243321	2		742	791	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422959	49422959	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	287	845	0	ENST00000301067.7:c.14136G>T	p.Glu4712Asp	p.E4712D	ENST00000301067	NM_003482.3	4712	gaG/gaT	44/54	1	2	FACETS	0.999	0.943	1	0.999	0.943	1	CLONAL	1	TRUE	1	0.690288477243321	2		845	832	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427680	49427682	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	rs762392663	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	164	722	0	ENST00000301067.7:c.10806_10808del	p.Gln3612del	p.Q3612del	ENST00000301067	NM_003482.3	3602	caACAg/cag	39/54	1	2	FACETS	0.74	0.682	0.8	0.74	0.682	0.8	SUBCLONAL	1	TRUE	1	0.690288477243321	2		722	642	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120806636	120806636	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	164	282	0	ENST00000257552.2:c.100G>T	p.Glu34Ter	p.E34*	ENST00000257552	NM_002442.3	34	Gaa/Taa	2/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.690288477243321	2		282	436	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353790	68353790	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1189894184	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	76	491	0	ENST00000487270.1:c.625C>A	p.Leu209Ile	p.L209I	ENST00000487270	NM_133509.3	209	Ctt/Att	7/11	1	2	FACETS	0.512	0.451	0.577	0.512	0.451	0.577	SUBCLONAL	1	TRUE	1	0.690288477243321	2		491	430	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705382	43705382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	95	1072	0	ENST00000382044.4:c.5240G>A	p.Ser1747Asn	p.S1747N	ENST00000382044	NM_001141980.1	1747	aGt/aAt	24/28	1	2	FACETS	0.244	0.216	0.273	0.244	0.216	0.273	SUBCLONAL	1	TRUE	1	0.690288477243321	2		1072	1129	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131672	2131672	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	137	964	0	ENST00000219476.3:c.3687G>T	p.Gln1229His	p.Q1229H	ENST00000219476	NM_000548.3	1229	caG/caT	31/42	1	2	FACETS	0.454	0.412	0.497	0.454	0.412	0.497	SUBCLONAL	1	TRUE	1	0.690288477243321	2		964	875	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632378	3632378	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1037474114	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	137	1068	0	ENST00000294008.3:c.5470C>T	p.Gln1824Ter	p.Q1824*	ENST00000294008	NM_032444.2	1824	Cag/Tag	15/15	1	2	FACETS	0.395	0.359	0.433	0.395	0.359	0.433	SUBCLONAL	1	TRUE	1	0.690288477243321	2		1068	1005	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641113	3641113	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	498	1337	1	ENST00000294008.3:c.2526T>G	p.Asp842Glu	p.D842E	ENST00000294008	NM_032444.2	842	gaT/gaG	12/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.690288477243321	2		1338	1403	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349260	11349260	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	140	339	0	ENST00000332029.2:c.76T>C	p.Ser26Pro	p.S26P	ENST00000332029	NM_003745.1	26	Tcc/Ccc	2/2	1	2	FACETS	0.882	0.809	0.957	0.882	0.809	0.957	CLONAL	1	TRUE	1	0.690288477243321	2		339	460	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853308	68853308	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	243	623	0	ENST00000261769.5:c.1691T>C	p.Leu564Pro	p.L564P	ENST00000261769	NM_004360.3	564	cTa/cCa	11/16	1	2	FACETS	0.931	0.874	0.99	0.931	0.874	0.99	CLONAL	1	TRUE	1	0.690288477243321	2		623	756	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217874	2217874	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	120	1045	0	ENST00000398665.3:c.2648T>C	p.Ile883Thr	p.I883T	ENST00000398665	NM_032482.2	883	aTt/aCt	22/28	1	2	FACETS	0.315	0.283	0.348	0.315	0.283	0.348	SUBCLONAL	1	TRUE	1	0.690288477243321	2		1045	1104	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184573	7184573	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs911809758	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	137	511	0	ENST00000302850.5:c.728G>A	p.Cys243Tyr	p.C243Y	ENST00000302850	NM_000208.2	243	tGt/tAt	3/22	1	2	FACETS	0.539	0.49	0.589	0.539	0.49	0.589	SUBCLONAL	1	TRUE	1	0.690288477243321	2		511	737	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295228	15295228	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	421	1134	3	ENST00000263388.2:c.2444C>T	p.Ala815Val	p.A815V	ENST00000263388	NM_000435.2	815	gCt/gTt	16/33	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.690288477243321	2		1137	1165	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311605	15311605	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1445073298	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	42	111	0	ENST00000263388.2:c.112del	p.Ala38LeufsTer198	p.A38Lfs*198	ENST00000263388	NM_000435.2	38	Gct/ct	1/33	1	2	FACETS	0.951	0.813	1	0.951	0.813	1	CLONAL	1	TRUE	1	0.690288477243321	2		111	128	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214812	36214812	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1014637026	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	239	793	0	ENST00000222270.7:c.3238G>A	p.Val1080Ile	p.V1080I	ENST00000222270	NM_014727.1	1080	Gtc/Atc	8/37	1	2	FACETS	0.889	0.833	0.946	0.889	0.833	0.946	CLONAL	1	TRUE	1	0.690288477243321	2		793	779	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31511249	31511249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	316	967	1	ENST00000344624.3:c.1325G>A	p.Arg442His	p.R442H	ENST00000344624		442	cGt/cAt	6/33	1	2	FACETS	0.928	0.877	0.979	0.928	0.877	0.979	CLONAL	1	TRUE	1	0.690288477243321	2		968	987	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515636	31515636	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	160	564	0	ENST00000344624.3:c.983G>A	p.Gly328Glu	p.G328E	ENST00000344624		328	gGa/gAa	4/33	1	2	FACETS	0.958	0.885	1	0.958	0.885	1	CLONAL	1	TRUE	1	0.690288477243321	2		564	484	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80063767	80063769	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	rs758193305	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	135	495	0	ENST00000265081.6:c.1917_1919del	p.Phe639del	p.F639del	ENST00000265081	NM_002439.4	638	TTC/-	14/24	1	2	FACETS	0.856	0.784	0.93	0.856	0.784	0.93	CLONAL	1	TRUE	1	0.690288477243321	2		495	457	SUCCESS
APC	324	MSKCC	GRCh37	5	112162856	112162856	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	145	562	0	ENST00000257430.4:c.1460G>T	p.Gly487Val	p.G487V	ENST00000257430	NM_000038.5	487	gGg/gTg	12/16	1	2	FACETS	0.927	0.853	1	0.927	0.853	1	CLONAL	1	TRUE	1	0.690288477243321	2		562	453	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671699	30671699	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	274	823	0	ENST00000376406.3:c.5261G>T	p.Arg1754Met	p.R1754M	ENST00000376406	NM_014641.2	1754	aGg/aTg	10/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.690288477243321	2		823	776	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324073	31324073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1192086647	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	43	306	0	ENST00000412585.2:c.490G>A	p.Ala164Thr	p.A164T	ENST00000412585	NM_005514.6	164	Gct/Act	3/8	1	2	FACETS	0.399	0.335	0.469	0.399	0.335	0.469	SUBCLONAL	1	TRUE	1	0.690288477243321	2		306	312	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31947212	31947212	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775212501	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	328	760	0	ENST00000375333.2:c.697C>T	p.Arg233Ter	p.R233*	ENST00000375333	NM_032454.1	233	Cga/Tga	5/8	1	2	FACETS	0.969	0.917	1	0.969	0.917	1	CLONAL	1	TRUE	1	0.690288477243321	2		760	981	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434521	140434521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777533608	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	103	384	0	ENST00000288602.6:c.2177G>A	p.Arg726His	p.R726H	ENST00000288602	NM_004333.4	726	cGc/cAc	18/18	0.690288477243321	3	FACETS	0.749	0.672	0.83	0.374	0.336	0.415	SUBCLONAL	1	TRUE	1	0.690288477243321	3		384	536	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945103	151945103	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	48	742	0	ENST00000262189.6:c.2416T>C	p.Ser806Pro	p.S806P	ENST00000262189	NM_170606.2	806	Tcc/Ccc	14/59	0.690288477243321	3	FACETS	0.296	0.249	0.347	0.148	0.124	0.174	SUBCLONAL	1	TRUE	1	0.690288477243321	3		742	633	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005900	69005900	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	203	677	0	ENST00000288368.4:c.2311T>C	p.Ser771Pro	p.S771P	ENST00000288368	NM_024870.2	771	Tct/Cct	21/40	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.690288477243321	2		677	538	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739319	145739319	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs911017899	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	45	848	0	ENST00000428558.2:c.2051C>T	p.Thr684Ile	p.T684I	ENST00000428558	NM_004260.3	684	aCa/aTa	12/22	1	2	FACETS	0.15	0.126	0.178	0.15	0.126	0.178	SUBCLONAL	1	TRUE	1	0.690288477243321	2		848	867	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27220097	27220097	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	320	740	0	ENST00000380036.4:c.3157del	p.Gln1053ArgfsTer9	p.Q1053Rfs*9	ENST00000380036	NM_000459.3	1052	Ccc/cc	21/23	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.690288477243321	2		740	849	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402544	139402544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767963898	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	363	945	2	ENST00000277541.6:c.3373G>A	p.Ala1125Thr	p.A1125T	ENST00000277541	NM_017617.3	1125	Gcg/Acg	21/34	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.690288477243321	2		947	992	SUCCESS
AR	367	MSKCC	GRCh37	X	66931346	66931346	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	109	651	0	ENST00000374690.3:c.1988C>A	p.Ser663Ter	p.S663*	ENST00000374690	NM_000044.3	663	tCa/tAa	4/8	1	2	FACETS	0.452	0.406	0.501	0.452	0.406	0.501	SUBCLONAL	1	TRUE	1	0.690288477243321	2		651	698	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763976	76763976	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	306	865	0	ENST00000373344.5:c.7332G>C	p.Leu2444Phe	p.L2444F	ENST00000373344	NM_000489.3	2444	ttG/ttC	35/35	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.690288477243321	2		865	885	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266714	198266714	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	43	495	0	ENST00000335508.6:c.2218G>C	p.Gly740Arg	p.G740R	ENST00000335508	NM_012433.2	740	Gga/Cga	15/25	0.363391493368173	3	FACETS	0.415	0.347	0.49	0.207	0.173	0.245	SUBCLONAL	1	FALSE	1	0.493256008468309	3		495	524	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476833	140476833	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs766837571	NA	P-0036029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	30	673	0	ENST00000288602.6:c.1573C>G	p.Leu525Val	p.L525V	ENST00000288602	NM_004333.4	525	Ctg/Gtg	13/18	1	2	FACETS	0.225	0.181	0.276	0.225	0.181	0.276	SUBCLONAL	1	FALSE	1	0.493256008468309	2		673	540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0036030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	483	755	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.815860788153436	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.815860788153436	2		755	538	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244091	153244091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	530	558	0	ENST00000281708.4:c.2066G>A	p.Arg689Gln	p.R689Q	ENST00000281708	NM_033632.3	689	cGg/cAg	12/12	0.815860788153436	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	1	0.815860788153436	3		558	809	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579426	7579426	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	618	738	1	ENST00000269305.4:c.261del	p.Ala88ProfsTer35	p.A88Pfs*35	ENST00000269305	NM_001126112.2	87	ccA/cc	4/11	0.606586303903399	2	FACETS	0.979	0.948	1	0.979	0.948	1	CLONAL	2	TRUE	0	0.607195758435528	2		739	1040	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653846	89653846	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762518389	NA	P-0036031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	200	416	0	ENST00000371953.3:c.144C>A	p.Asn48Lys	p.N48K	ENST00000371953	NM_000314.4	48	aaC/aaA	2/9	0.607195758435528	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.607195758435528	1		416	425	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397594	116397594	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0036031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	238	677	0	ENST00000397752.3:c.1965+1G>A		p.X655_splice	ENST00000397752	NM_000245.2	655			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.607195758435528	2		677	753	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0036032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	68	433	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.18	2		433	614	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78820364	78820364	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	56	748	0	ENST00000306801.3:c.1304T>C	p.Ile435Thr	p.I435T	ENST00000306801	NM_020761.2	435	aTc/aCc	11/34	1	2	FACETS	0.922	0.789	1	0.922	0.789	1	CLONAL	1	TRUE	1	0.18	2		748	675	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142948	47142948	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	40	401	0	ENST00000409792.3:c.5015G>A	p.Gly1672Glu	p.G1672E	ENST00000409792	NM_014159.6	1672	gGa/gAa	8/21	1	2	FACETS	0.952	0.791	1	0.952	0.791	1	CLONAL	1	TRUE	1	0.18	2		401	467	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045540	47045581	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGAAGTACGGCGGCATATCCACAGCCTCTGTGTGAGTGGCTG	GGAAGTACGGCGGCATATCCACAGCCTCTGTGTGAGTGGCTG	-	novel	NA	P-0036032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	37	733	0	ENST00000377604.3:c.2509_2537+13del		p.X837_splice	ENST00000377604	NM_001204468.1	837		22/24	1	2	FACETS	0.867	0.715	1	0.867	0.715	1	CLONAL	1	TRUE	1	0.18	2		733	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0036033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	239	700	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.263256293283416	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.31	2		700	747	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0036033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	190	453	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.263256293283416	2	FACETS	0.918	0.852	0.985	0.918	0.852	0.985	CLONAL	2	TRUE	0	0.31	2		453	668	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007711	45007711	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	69	508	0	ENST00000558401.1:c.158C>A	p.Ser53Tyr	p.S53Y	ENST00000558401	NM_004048.2	53	tCc/tAc	2/4	0.263256293283416	2	FACETS	0.809	0.706	0.921	0.405	0.353	0.461	CLONAL	1	TRUE	0	0.31	2		508	550	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22153321	22153321	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	173	524	0	ENST00000215832.6:c.589G>C	p.Glu197Gln	p.E197Q	ENST00000215832	NM_002745.4	197	Gaa/Caa	4/9	0.300127867787324	2	FACETS	0.907	0.839	0.978	0.907	0.839	0.978	CLONAL	2	TRUE	0	0.31	2		524	615	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645789	12645789	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0036033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	47	373	0	ENST00000251849.4:c.681-1G>C		p.X227_splice	ENST00000251849	NM_002880.3	227			0.29859941155789	3	FACETS	0.84	0.71	0.983	0.42	0.355	0.492	CLONAL	1	TRUE	1	0.31	3		373	417	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38955776	38955776	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	44	430	0	ENST00000357387.3:c.2530G>A	p.Glu844Lys	p.E844K	ENST00000357387	NM_152756.3	844	Gag/Aag	26/38	0.301909650970416	6	FACETS	0.674	0.564	0.797	0.169	0.141	0.2	SUBCLONAL	1	TRUE	2	0.31	6		430	682	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73113186	73113186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	10	102	0	ENST00000356692.5:c.527C>T	p.Pro176Leu	p.P176L	ENST00000356692		176	cCa/cTa	7/9	0.29859941155789	3	FACETS	0.569	0.387	0.795	0.284	0.193	0.398	SUBCLONAL	1	TRUE	1	0.31	3		102	131	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450366	50450366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	212	457	0	ENST00000331340.3:c.550C>T	p.Arg184Trp	p.R184W	ENST00000331340	NM_006060.4	184	Cgg/Tgg	5/8	0.523484179643229	5	FACETS	0.96	0.896	1	0.64	0.597	0.683	CLONAL	2	TRUE	2	0.660363088132067	5		457	666	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678795	52678795	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0036034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	161	325	0	ENST00000394830.3:c.824C>G	p.Ser275Ter	p.S275*	ENST00000394830	NM_018313.4	275	tCa/tGa	9/30	0.660363088132067	2	FACETS	0.991	0.936	1	0.991	0.936	1	CLONAL	2	TRUE	0	0.660363088132067	2		325	246	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038958	12038958	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	156	284	0	ENST00000396373.4:c.1251del	p.Phe417LeufsTer4	p.F417Lfs*4	ENST00000396373	NM_001987.4	417	ttC/tt	7/8	0.619639758558268	5	FACETS	1	0.96	1			1	CLONAL	2	TRUE	NA	0.660363088132067	5		284	444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577513	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0036034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	365	783	0	ENST00000269305.4:c.768_770del	p.Leu257del	p.L257del	ENST00000269305	NM_001126112.2	256	acACTg/acg	7/11	0.660363088132067	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.660363088132067	2		783	523	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594235	55594235	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0036034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	90	512	0	ENST00000288135.5:c.1938C>G	p.Tyr646Ter	p.Y646*	ENST00000288135	NM_000222.2	646	taC/taG	13/21	0.660363088132067	3	FACETS	0.927	0.828	1	0.464	0.414	0.516	CLONAL	1	TRUE	1	0.660363088132067	3		512	391	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859371	151859371	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	104	511	1	ENST00000262189.6:c.11291G>T	p.Gly3764Val	p.G3764V	ENST00000262189	NM_170606.2	3764	gGg/gTg	43/59	0.631862486636013	4	FACETS	0.987	0.887	1	0.329	0.295	0.364	CLONAL	1	TRUE	1	0.660363088132067	4		512	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579349	7579349	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1567555667	NA	P-0036035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	253	714	0	ENST00000269305.4:c.338T>G	p.Phe113Cys	p.F113C	ENST00000269305	NM_001126112.2	113	tTc/tGc	4/11	0.497714149551615	1	FACETS	0.958	0.9	1	0.958	0.9	1	CLONAL	1	TRUE	0	0.497714149551615	1		714	797	SUCCESS
APC	324	MSKCC	GRCh37	5	112175419	112175419	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0036035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	100	303	0	ENST00000257430.4:c.4128T>A	p.Tyr1376Ter	p.Y1376*	ENST00000257430	NM_000038.5	1376	taT/taA	16/16	1	2	FACETS	0.948	0.852	1	0.948	0.852	1	CLONAL	1	TRUE	1	0.497714149551615	2		303	424	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870778	12870778	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	46	106	0	ENST00000228872.4:c.5C>A	p.Ser2Ter	p.S2*	ENST00000228872	NM_004064.3	2	tCa/tAa	1/3	0.371363110443219	3	FACETS	1	0.93	1	0.58	0.494	0.672	CLONAL	1	TRUE	1	0.497714149551615	3		106	199	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906957	32906957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80358422	NA	P-0036035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	317	403	0	ENST00000380152.3:c.1342C>T	p.Arg448Cys	p.R448C	ENST00000380152		448	Cgt/Tgt	10/27	0.497714149551615	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.497714149551615	3		403	782	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838148	89838148	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	242	685	0	ENST00000389301.3:c.2089G>T	p.Val697Phe	p.V697F	ENST00000389301	NM_000135.2	697	Gtt/Ttt	23/43	1	2	FACETS	0.87	0.812	0.93	0.87	0.812	0.93	CLONAL	1	TRUE	1	0.497714149551615	2		685	1118	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219479	5219479	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0036035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	196	635	0	ENST00000357368.4:c.3766-1G>C		p.X1256_splice	ENST00000357368	NM_002850.3	1256			0.497714149551615	3	FACETS	0.982	0.909	1	0.491	0.454	0.529	CLONAL	1	TRUE	1	0.497714149551615	3		635	1002	SUCCESS
APC	324	MSKCC	GRCh37	5	112173696	112173696	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	172	341	0	ENST00000257430.4:c.2405del	p.Asp802AlafsTer18	p.D802Afs*18	ENST00000257430	NM_000038.5	802	gAc/gc	16/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.497714149551615	2		341	632	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0036085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	155	417	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.312577628619092	2	FACETS	0.865	0.802	0.929	1	0.986	1	CLONAL	3	TRUE	0	0.312577628619092	2		417	382	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882025	NA	P-0036085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	52	630	0	ENST00000269305.4:c.646G>T	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ttg	6/11	0.312577628619092	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.312577628619092	1		630	258	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856506	111856506	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs183913232	NA	P-0036085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	11	221	1	ENST00000341259.2:c.557G>T	p.Ser186Ile	p.S186I	ENST00000341259	NM_005475.2	186	aGc/aTc	2/8	0.205448214487008	3	FACETS	0.375	0.259	0.52	0.188	0.129	0.26	SUBCLONAL	1	TRUE	1	0.312577628619092	3		222	217	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628707	187628707	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	47	712	0	ENST00000441802.2:c.2275G>T	p.Gly759Ter	p.G759*	ENST00000441802	NM_005245.3	759	Gga/Tga	2/27	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.312577628619092	2		712	287	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876425	35876425	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	41	601	2	ENST00000303115.3:c.1217T>G	p.Leu406Arg	p.L406R	ENST00000303115	NM_002185.3	406	cTt/cGt	8/8	0.312577628619092	4	FACETS	0.859	0.716	1	0.286	0.238	0.339	CLONAL	1	TRUE	1	0.312577628619092	4		603	401	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317085	11317085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	51	590	1	ENST00000361445.4:c.409G>A	p.Gly137Arg	p.G137R	ENST00000361445	NM_004958.3	137	Ggg/Agg	4/58	0.228843671211905	2	FACETS	1	0.955	1	0.653	0.56	0.753	CLONAL	1	TRUE	0	0.312577628619092	2		591	250	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599954	28599954	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	25	697	0	ENST00000253063.3:c.836C>G	p.Ser279Cys	p.S279C	ENST00000253063	NM_031459.4	279	tCc/tGc	6/10	0.228843671211905	2	FACETS	0.555	0.438	0.689	0.278	0.219	0.345	SUBCLONAL	1	TRUE	0	0.312577628619092	2		697	288	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241857	72241857	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	25	294	0	ENST00000357731.5:c.533C>A	p.Ser178Ter	p.S178*	ENST00000357731	NM_173808.2	178	tCa/tAa	3/7	0.120244943913642	4	FACETS	1	0.821	1	0.52	0.412	0.642	INDETERMINATE	1	TRUE	2	0.312577628619092	4		294	202	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828121	243828122	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	16	537	1	ENST00000263826.5:c.236_237delinsAA	p.Trp79Ter	p.W79*	ENST00000263826	NM_005465.4	79	tGG/tAA	3/13	0.228843671211905	2	FACETS	0.376	0.278	0.494	0.188	0.139	0.247	SUBCLONAL	1	TRUE	0	0.312577628619092	2		538	272	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933385	100933385	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	44	544	0	ENST00000325455.5:c.2005C>A	p.Leu669Ile	p.L669I	ENST00000325455	NM_001202474.3	669	Cta/Ata	4/8	1	2	FACETS	0.858	0.723	1	0.858	0.723	1	CLONAL	1	TRUE	1	0.312577628619092	2		544	328	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336187	73336187	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	27	222	0	ENST00000377767.4:c.2216T>C	p.Leu739Pro	p.L739P	ENST00000377767	NM_014953.3	739	cTg/cCg	17/21	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.312577628619092	2		222	149	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920391	134920391	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	50	540	0	ENST00000398015.3:c.2206G>T	p.Ala736Ser	p.A736S	ENST00000398015	NM_004441.4	736	Gct/Tct	12/16	0.312577628619092	1	FACETS	0.967	0.827	1	0.967	0.827	1	CLONAL	1	TRUE	0	0.312577628619092	1		540	279	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980508	70980508	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	81	728	1	ENST00000276594.2:c.869C>A	p.Ala290Asp	p.A290D	ENST00000276594	NM_024504.3	290	gCc/gAc	4/8	1	2	FACETS	0.802	0.713	0.896	1	0.981	1	CLONAL	2	TRUE	1	0.312577628619092	2		729	323	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53253992	53253992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	21	625	0	ENST00000375401.3:c.80C>T	p.Pro27Leu	p.P27L	ENST00000375401	NM_004187.3	27	cCt/cTt	1/26	0.312577628619092	0	FACETS	0.351	0.271	0.445			1	SUBCLONAL	1	TRUE	0	0.312577628619092	0		625	263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0036086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	291	700	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.547319716531069	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.547319716531069	1		700	706	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0036086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	344	622	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.460495269418528	3	FACETS	0.983	0.944	1			1	CLONAL	3	TRUE	NA	0.547319716531069	3		622	543	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0036086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	116	488	2	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	0.547319716531069	2		490	379	SUCCESS
APC	324	MSKCC	GRCh37	5	112175789	112175789	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	124	273	0	ENST00000257430.4:c.4501del	p.Ser1501LeufsTer6	p.S1501Lfs*6	ENST00000257430	NM_000038.5	1500	Ttt/tt	16/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.547319716531069	2		273	348	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288650	198288650	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	249	604	1	ENST00000335508.6:c.77A>T	p.Asp26Val	p.D26V	ENST00000335508	NM_012433.2	26	gAt/gTt	2/25	0.308382516803016	1	FACETS	0.87	0.816	0.924	0.87	0.816	0.924	INDETERMINATE	1	TRUE	0	0.547319716531069	1		605	760	SUCCESS
APC	324	MSKCC	GRCh37	5	112174372	112174372	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0036086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	56	220	0	ENST00000257430.4:c.3081T>A	p.Tyr1027Ter	p.Y1027*	ENST00000257430	NM_000038.5	1027	taT/taA	16/16	1	2	FACETS	0.97	0.842	1	0.97	0.842	1	CLONAL	1	TRUE	1	0.547319716531069	2		220	211	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687294	117687294	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	39	338	0	ENST00000368508.3:c.2757A>T	p.Glu919Asp	p.E919D	ENST00000368508	NM_002944.2	919	gaA/gaT	18/43	1	2	FACETS	0.282	0.233	0.337	0.282	0.233	0.337	SUBCLONAL	1	TRUE	1	0.547319716531069	2		338	505	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0036087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	51	488	2	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.242280574701309	1	FACETS	0.441	0.375	0.513	0.441	0.375	0.513	INDETERMINATE	1	TRUE	0	0.423147643252792	1		490	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0036087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	266	675	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.423147643252792	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.423147643252792	1		675	902	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0036087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	62	502	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.423147643252792	1	FACETS	0.57	0.494	0.652	0.57	0.494	0.652	SUBCLONAL	1	TRUE	0	0.423147643252792	1		502	405	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251907	153251907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	86	619	1	ENST00000281708.4:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000281708	NM_033632.3	367	Cga/Tga	7/12	0.242280574701309	1	FACETS	0.924	0.824	1	0.924	0.824	1	INDETERMINATE	1	TRUE	0	0.423147643252792	1		620	347	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637539	52637540	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	34	491	0	ENST00000394830.3:c.2776dup	p.Arg926LysfsTer4	p.R926Kfs*4	ENST00000394830	NM_018313.4	926	aga/aAga	18/30	0.242280574701309	1	FACETS	0.297	0.242	0.358	0.297	0.242	0.358	INDETERMINATE	1	TRUE	0	0.423147643252792	1		491	427	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099108	27099109	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	145	413	0	ENST00000324856.7:c.3525dup	p.Leu1176IlefsTer17	p.L1176Ifs*17	ENST00000324856	NM_006015.4	1175	cca/ccAa	13/20	0.242280574701309	1	FACETS	0.961	0.882	1	0.961	0.882	1	INDETERMINATE	1	TRUE	0	0.423147643252792	1		413	562	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2185874	2185874	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	81	664	1	ENST00000398665.3:c.146C>A	p.Pro49Gln	p.P49Q	ENST00000398665	NM_032482.2	49	cCg/cAg	3/28	0.242280574701309	1	FACETS	0.374	0.329	0.423	0.374	0.329	0.423	INDETERMINATE	1	TRUE	0	0.423147643252792	1		665	806	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40747910	40747910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572670425	NA	P-0036087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	228	726	0	ENST00000392038.2:c.508C>T	p.Arg170Trp	p.R170W	ENST00000392038	NM_001626.4	170	Cgg/Tgg	6/14	0.242280574701309	1	FACETS	0.884	0.824	0.946	0.884	0.824	0.946	INDETERMINATE	1	TRUE	0	0.423147643252792	1		726	961	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966088	25966088	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	94	708	0	ENST00000435504.4:c.3118T>C	p.Ser1040Pro	p.S1040P	ENST00000435504		1040	Tca/Cca	13/13	0.196162088739833	2	FACETS	0.498	0.442	0.557	0.249	0.221	0.279	INDETERMINATE	1	TRUE	0	0.423147643252792	2		708	893	SUCCESS
APC	324	MSKCC	GRCh37	5	112173848	112173849	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	rs794727160	NA	P-0036087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	92	337	0	ENST00000257430.4:c.2563_2564del	p.Glu855ThrfsTer56	p.E855Tfs*56	ENST00000257430	NM_000038.5	853	GAg/g	16/16	0.402019656927712	2	FACETS	1	0.98	1	0.718	0.645	0.793	CLONAL	1	TRUE	0	0.423147643252792	2		337	303	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0036088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	34	700	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.704	0.574	0.851	0.704	0.574	0.851	SUBCLONAL	1	TRUE	1	0.17	2		700	568	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0036088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	38	812	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	0.17	2		812	402	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0036093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	70	526	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.177324555906328	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.177324555906328	1		526	504	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0036093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	28	291	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.177324555906328	1	FACETS	0.55	0.439	0.678	0.55	0.439	0.678	SUBCLONAL	1	TRUE	0	0.177324555906328	1		291	523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578429	7578430	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0036093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	77	851	0	ENST00000269305.4:c.499_500dup	p.Gln167HisfsTer4	p.Q167Hfs*4	ENST00000269305	NM_001126112.2	167	cag/caCAg	5/11	0.177324555906328	1	FACETS	0.875	0.766	0.992	0.875	0.766	0.992	CLONAL	1	TRUE	0	0.177324555906328	1		851	905	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738074	145738074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763161407	NA	P-0036093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	43	865	3	ENST00000428558.2:c.2836C>T	p.Arg946Cys	p.R946C	ENST00000428558	NM_004260.3	946	Cgt/Tgt	17/22	0.121558239711217	1	FACETS	0.526	0.438	0.623	0.526	0.438	0.623	SUBCLONAL	1	TRUE	0	0.177324555906328	1		868	841	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852482	63852483	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	43	584	0	ENST00000279873.7:c.3261dup	p.Asn1088Ter	p.N1088*	ENST00000279873	NM_032199.2	1087	tgt/tgTt	10/10	1	2	FACETS	0.774	0.646	0.915	0.774	0.646	0.915	CLONAL	1	TRUE	1	0.177324555906328	2		584	627	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864144	57864144	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	72	674	0	ENST00000228682.2:c.1621C>A	p.Arg541Ser	p.R541S	ENST00000228682	NM_005269.2	541	Cgc/Agc	12/12	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.177324555906328	2		674	743	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370874	55370874	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	85	685	0	ENST00000297316.4:c.176C>T	p.Ala59Val	p.A59V	ENST00000297316	NM_022454.3	59	gCg/gTg	1/2	0.177324555906328	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.177324555906328	1		685	681	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0036094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	9	526	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.722	0.481	1	0.722	0.481	1	CLONAL	1	TRUE	1	0.228615216999846	2		526	109	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0036094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	44	605	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.228615216999846	2		605	262	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861886	57861886	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754780184	NA	P-0036094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	35	536	1	ENST00000228682.2:c.1187G>A	p.Arg396Gln	p.R396Q	ENST00000228682	NM_005269.2	396	cGg/cAg	10/12	0.105182592923805	3	FACETS	1	0.883	1	0.55	0.452	0.66	INDETERMINATE	1	TRUE	1	0.228615216999846	3		537	310	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0036096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	57	812	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.16693331831403	0	FACETS	0.611	0.525	0.704			1	INDETERMINATE	1	TRUE	0	0.293143774630808	0		812	450	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0036096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	21	268	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.702	0.543	0.886	0.702	0.543	0.886	SUBCLONAL	1	TRUE	1	0.293143774630808	2		268	204	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745588	162745588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754868982	NA	P-0036096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	56	446	1	ENST00000367921.3:c.2003G>A	p.Arg668His	p.R668H	ENST00000367921	NM_006182.2	668	cGc/cAc	15/18	1	2	FACETS	0.675	0.578	0.781	0.675	0.578	0.781	SUBCLONAL	1	TRUE	1	0.293143774630808	2		447	566	SUCCESS
APC	324	MSKCC	GRCh37	5	112173964	112173968	+	frameshift_variant	Frame_Shift_Del	DEL	GGAAG	GGAAG	-	novel	NA	P-0036096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	38	293	2	ENST00000257430.4:c.2673_2677del	p.Met891IlefsTer19	p.M891Ifs*19	ENST00000257430	NM_000038.5	891	atGGAAGaa/ataa	16/16	1	2	FACETS	0.767	0.636	0.913	0.767	0.636	0.913	CLONAL	1	TRUE	1	0.293143774630808	2		295	338	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635201	87635201	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	79	475	0	ENST00000277120.3:c.2253C>A	p.Asp751Glu	p.D751E	ENST00000277120		751	gaC/gaA	18/19	1	2	FACETS	0.851	0.749	0.961	0.851	0.749	0.961	CLONAL	1	TRUE	1	0.293143774630808	2		475	633	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120527	70120527	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0036126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	56	714	0	ENST00000245479.2:c.1529G>C	p.Ter510SerextTer49	p.*510Sext*49	ENST00000245479	NM_000346.3	510	tGa/tCa	3/3	0.354805028104011	2	FACETS	0.292	0.249	0.339	0.146	0.124	0.17	SUBCLONAL	1	TRUE	0	0.429815299456813	2		714	892	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	388	755	0	ENST00000269305.4:c.470T>G	p.Val157Gly	p.V157G	ENST00000269305	NM_001126112.2	157	gTc/gGc	5/11	0.354805028104011	2	FACETS	0.958	0.914	1	0.958	0.914	1	CLONAL	2	TRUE	0	0.429815299456813	2		755	942	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955538	48955538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913303	NA	P-0036126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	89	391	0	ENST00000267163.4:c.1654C>T	p.Arg552Ter	p.R552*	ENST00000267163	NM_000321.2	552	Cga/Tga	17/27	0.354805028104011	2	FACETS	1	0.964	1	0.592	0.529	0.657	CLONAL	1	TRUE	0	0.429815299456813	2		391	350	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692793	89692793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	97	374	0	ENST00000371953.3:c.277C>T	p.His93Tyr	p.H93Y	ENST00000371953	NM_000314.4	93	Cat/Tat	5/9	0.350467699341622	2	FACETS	1	0.981	1	0.714	0.644	0.787	CLONAL	1	TRUE	0	0.429815299456813	2		374	316	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233341	69233343	+	frameshift_variant	Frame_Shift_Del	DEL	GCC	GCC	A	novel	NA	P-0036126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	17	283	0	ENST00000462284.1:c.1206_1208delinsA	p.Pro403IlefsTer4	p.P403Ifs*4	ENST00000462284	NM_002392.5	402	caGCCa/caAa	11/11	0.413819040281656	1	FACETS	0.284	0.212	0.368	0.284	0.212	0.368	SUBCLONAL	1	TRUE	0	0.429815299456813	1		283	219	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727482	88727482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368510978	NA	P-0036129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	28	681	0	ENST00000360948.2:c.297G>A	p.Met99Ile	p.M99I	ENST00000360948	NM_001012338.2	99	atG/atA	3/19	0.241223519301669	1	FACETS	0.199	0.158	0.245	0.199	0.158	0.245	INDETERMINATE	1	FALSE	0	0.427867908428213	1		681	518	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3794916	3794916	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	42	623	0	ENST00000262367.5:c.3961G>C	p.Glu1321Gln	p.E1321Q	ENST00000262367	NM_004380.2	1321	Gaa/Caa	23/31	0.254295064616452	3	FACETS	1	0.878	1	0.525	0.442	0.615	INDETERMINATE	1	FALSE	1	0.427867908428213	3		623	227	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916214	9916214	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	18	564	0	ENST00000330684.3:c.2075G>C	p.Arg692Thr	p.R692T	ENST00000330684	NM_001134407.1	692	aGa/aCa	10/13	0.254295064616452	3	FACETS	0.63	0.478	0.808	0.315	0.239	0.404	INDETERMINATE	1	FALSE	1	0.427867908428213	3		564	162	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271535	38271535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	24	759	0	ENST00000425967.3:c.2286G>A	p.Met762Ile	p.M762I	ENST00000425967	NM_001174067.1	762	atG/atA	18/19	0.427867908428213	1	FACETS	0.215	0.168	0.269	0.215	0.168	0.269	SUBCLONAL	1	FALSE	0	0.427867908428213	1		759	410	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0036130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	88	812	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.966	0.857	1	0.966	0.857	1	CLONAL	1	TRUE	1	0.326651944003037	2		812	558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0036130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	131	746	1	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.326651944003037	1	FACETS	0.99	0.9	1	0.99	0.9	1	CLONAL	1	TRUE	0	0.326651944003037	1		747	678	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs80338963	NA	P-0036130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	101	602	0	ENST00000342988.3:c.1081C>A	p.Arg361Ser	p.R361S	ENST00000342988	NM_005359.5	361	Cgc/Agc	9/12	0.326651944003037	1	FACETS	0.974	0.874	1	0.974	0.874	1	CLONAL	1	TRUE	0	0.326651944003037	1		602	531	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438169	56438169	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	136	884	0	ENST00000407977.2:c.824G>C	p.Cys275Ser	p.C275S	ENST00000407977		275	tGt/tCt	7/10	0.326651944003037	1	FACETS	0.913	0.831	0.999	0.913	0.831	0.999	CLONAL	1	TRUE	0	0.326651944003037	1		884	763	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401499	401499	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	30	359	0	ENST00000380956.4:c.821G>C	p.Cys274Ser	p.C274S	ENST00000380956	NM_001195286.1	274	tGc/tCc	7/9	1	2	FACETS	0.45	0.362	0.55	0.45	0.362	0.55	SUBCLONAL	1	TRUE	1	0.326651944003037	2		359	408	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753175	57753175	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	239	441	0	ENST00000274289.3:c.841G>A	p.Glu281Lys	p.E281K	ENST00000274289	NM_006622.3	281	Gaa/Aaa	7/14	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.918754231818996	2		441	464	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0036134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	144	291	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.622285729746642	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.622285729746642	1		291	275	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0036134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	85	822	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.230938427954645	1	FACETS	0.84	0.756	0.926	0.84	0.756	0.926	INDETERMINATE	1	TRUE	0	0.622285729746642	1		822	224	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0036134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	394	1019	0	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	0.584573257015134	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.622285729746642	1		1019	785	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020768	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs926053251	NA	P-0036134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	200	625	1	ENST00000358127.4:c.77T>G	p.Val26Gly	p.V26G	ENST00000358127	NM_001280556.1	26	gTt/gGt	2/10	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.622285729746642	NA		626	406	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439778	220439778	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	291	968	0	ENST00000243786.2:c.631G>A	p.Ala211Thr	p.A211T	ENST00000243786	NM_002191.3	211	Gcc/Acc	2/2	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.622285729746642	2		968	740	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0000041-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	229	313	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.411126615825412	5	FACETS	0.928	0.876	0.981	0.928	0.876	0.981	CLONAL	4	FALSE	1	0.411126615825412	5		313	485	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051003	180051003	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs307826	NA	P-0000041-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	14	897	0	ENST00000261937.6:c.1480A>G	p.Thr494Ala	p.T494A	ENST00000261937	NM_182925.4	494	Acg/Gcg	11/30	NA	2	FACETS	0.267	0.193	0.357			1	INDETERMINATE	1	FALSE	NA	0.411126615825412	2		897	255	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178570	32178570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs17604492	NA	P-0000041-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	23	767	0	ENST00000375023.3:c.2824G>A	p.Gly942Arg	p.G942R	ENST00000375023	NM_004557.3	942	Ggg/Agg	18/30	NA	2	FACETS	0.33	0.257	0.415			1	INDETERMINATE	1	FALSE	NA	0.411126615825412	2		767	339	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576777	212576777	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	rs76603692	NA	P-0000041-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	26	901	0	ENST00000342788.4:c.1122T>G	p.His374Gln	p.H374Q	ENST00000342788	NM_005235.2	374	caT/caG	9/28	0.348299036084631	3	FACETS	0.461	0.365	0.57	0.23	0.182	0.285	SUBCLONAL	1	FALSE	1	0.411126615825412	3		901	331	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067053	143067053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61733152	NA	P-0000041-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	26	1067	0	ENST00000262992.4:c.1660G>A	p.Gly554Ser	p.G554S	ENST00000262992	NM_001101669.1	554	Ggc/Agc	16/24	0.379409589198344	3	FACETS	0.462	0.366	0.572	0.154	0.122	0.191	SUBCLONAL	1	FALSE	0	0.411126615825412	3		1067	330	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359051	81359051	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs5745687	NA	P-0000041-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	28	1063	0	ENST00000222390.5:c.910G>A	p.Glu304Lys	p.E304K	ENST00000222390	NM_000601.4	304	Gaa/Aaa	8/18	0.335950202319832	3	FACETS	0.549	0.44	0.673	0.183	0.146	0.225	SUBCLONAL	1	FALSE	0	0.411126615825412	3		1063	299	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435220	18435220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201018498	NA	P-0000041-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	39	1005	0	ENST00000266497.5:c.205C>T	p.Pro69Ser	p.P69S	ENST00000266497		69	Cca/Tca	1/31	0.411126615825412	13	FACETS	0.915	0.757	1	0.131	0.108	0.157	CLONAL	1	FALSE	6	0.411126615825412	13		1005	676	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201381	133201381	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs73155056	NA	P-0000041-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	17	846	0	ENST00000320574.5:c.6763A>T	p.Ile2255Phe	p.I2255F	ENST00000320574	NM_006231.2	2255	Atc/Ttc	49/49	NA	2	FACETS	0.282	0.21	0.368			1	INDETERMINATE	1	FALSE	NA	0.411126615825412	2		846	293	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579300	7579313	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGGCAACTGACCG	AGGGCAACTGACCG	-	novel	NA	P-0000041-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	109	577	0	ENST00000269305.4:c.374_375+12del		p.X125_splice	ENST00000269305	NM_001126112.2	125		4/11	0.208250420974557	6	FACETS	0.998	0.915	1			1	INDETERMINATE	4	FALSE	NA	0.411126615825412	6		577	242	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038229	30038229	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000041-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	24	1165	0	ENST00000338641.4:c.402del	p.Pro135LeufsTer39	p.P135Lfs*39	ENST00000338641	NM_000268.3	134	ccT/cc	4/16	0.350879763787218	4	FACETS	0.421	0.33	0.527	0.211	0.165	0.264	SUBCLONAL	1	FALSE	2	0.411126615825412	4		1165	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579369	7579369	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555526581	NA	P-0000969-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	200	1029	0	ENST00000269305.4:c.318C>G	p.Ser106Arg	p.S106R	ENST00000269305	NM_001126112.2	106	agC/agG	4/11	0.703014403572529	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.703014403572529	2		1029	270	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030323	180030323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745546499	NA	P-0000969-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	120	2007	0	ENST00000261937.6:c.3961C>T	p.Arg1321Trp	p.R1321W	ENST00000261937	NM_182925.4	1321	Cgg/Tgg	30/30	0.671759227439141	2	FACETS	0.843	0.768	0.921	0.421	0.384	0.461	CLONAL	1	TRUE	0	0.703014403572529	2		2007	405	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287461	33287461	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000969-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	97	950	0	ENST00000374542.5:c.1636G>C	p.Glu546Gln	p.E546Q	ENST00000374542	NM_001141970.1	546	Gaa/Caa	6/8	0.651813722863074	3	FACETS	0.935	0.839	1	0.467	0.419	0.518	CLONAL	1	TRUE	1	0.703014403572529	3		950	399	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259012	153259013	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0000969-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	220	1540	0	ENST00000281708.4:c.802_803del	p.Met268AspfsTer18	p.M268Dfs*18	ENST00000281708	NM_033632.3	268	ATg/g	5/12	0.650797333508781	2	FACETS	0.788	0.746	0.83	0.788	0.746	0.83	SUBCLONAL	2	TRUE	0	0.703014403572529	2		1540	397	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0000991-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	237	851	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.344443342346058	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	FALSE	0	0.376921681821206	3		851	456	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175996804	175996804	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000991-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	117	272	0	ENST00000367669.3:c.1633C>G	p.Leu545Val	p.L545V	ENST00000367669	NM_022457.5	545	Cta/Gta	15/20	0.376921681821206	3	FACETS	1	0.983	1	0.474	0.429	0.521	CLONAL	1	FALSE	0	0.376921681821206	3		272	519	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239927	98239927	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1438523462	NA	P-0000991-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	60	123	2	ENST00000331920.6:c.1405G>A	p.Val469Met	p.V469M	ENST00000331920	NM_000264.3	469	Gtg/Atg	10/24	0.348231230426617	2	FACETS	0.948	0.834	1	0.948	0.834	1	CLONAL	2	FALSE	0	0.376921681821206	2		125	168	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596014	43596014	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000991-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	77	255	0	ENST00000355710.3:c.181G>A	p.Glu61Lys	p.E61K	ENST00000355710	NM_020975.4	61	Gag/Aag	2/20	0.376921681821206	5	FACETS	0.848	0.749	0.953	0.565	0.499	0.636	CLONAL	2	FALSE	2	0.376921681821206	5		255	377	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250908	99250908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780055504	NA	P-0000991-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	277	356	0	ENST00000268035.6:c.212G>A	p.Arg71His	p.R71H	ENST00000268035	NM_000875.3	71	cGc/cAc	2/21	0.376921681821206	5	FACETS	1	0.985	1			1	CLONAL	3	FALSE	NA	0.376921681821206	5		356	687	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973802	15973802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000991-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	30	186	0	ENST00000268712.3:c.4190C>T	p.Ser1397Phe	p.S1397F	ENST00000268712	NM_006311.3	1397	tCt/tTt	31/46	0.344443342346058	3	FACETS	0.498	0.401	0.608	0.166	0.133	0.203	SUBCLONAL	1	FALSE	0	0.376921681821206	3		186	380	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602493	10602493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000991-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	123	256	0	ENST00000171111.5:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000171111	NM_203500.1	362	cGg/cAg	3/6	0.376921681821206	2	FACETS	0.926	0.857	0.994	1	0.987	1	CLONAL	3	FALSE	0	0.376921681821206	2		256	235	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19261496	19261496	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763146191	NA	P-0000991-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	113	496	0	ENST00000162023.5:c.49C>T	p.Arg17Trp	p.R17W	ENST00000162023		17	Cgg/Tgg	6/13	NA	2	FACETS	1	0.978	1			1	INDETERMINATE	1	FALSE	NA	0.376921681821206	2		496	469	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439881	52439882	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	rs1327490224	NA	P-0000991-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	97	261	0	ENST00000460680.1:c.830_831del	p.Gln277ArgfsTer6	p.Q277Rfs*6	ENST00000460680	NM_004656.3	277	cAA/c	10/17	0.265467114273028	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	0	0.376921681821206	1		261	285	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120479954	120479954	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002354-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	90	727	0	ENST00000256646.2:c.3473G>A	p.Cys1158Tyr	p.C1158Y	ENST00000256646	NM_024408.3	1158	tGc/tAc	21/34	0.2113872211744	1	FACETS	0.968	0.858	1	0.968	0.858	1	CLONAL	1	TRUE	0	0.2113872211744	1		727	787	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0002845-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7418	850	438	1	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.454	0.436	0.472	0.454	0.436	0.472	SUBCLONAL	1	TRUE	1	0.452848307725203	2		439	8268	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0002845-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	261	623	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.414960754226849	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.452848307725203	2		623	560	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378552	25378552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002845-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7059	810	343	0	ENST00000311936.3:c.446G>A	p.Arg149Lys	p.R149K	ENST00000311936	NM_004985.3	149	aGa/aAa	4/5	1	2	FACETS	0.455	0.437	0.473	0.455	0.437	0.473	SUBCLONAL	1	TRUE	1	0.452848307725203	2		343	7869	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210399	2210399	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002845-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	30	239	0	ENST00000398665.3:c.1006G>A	p.Glu336Lys	p.E336K	ENST00000398665	NM_032482.2	336	Gag/Aag	13/28	0.452848307725203	1	FACETS	0.346	0.279	0.422	0.346	0.279	0.422	SUBCLONAL	1	TRUE	0	0.452848307725203	1		239	296	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546557	9546557	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002845-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	171	433	0	ENST00000353224.5:c.1465G>T	p.Glu489Ter	p.E489*	ENST00000353224	NM_177990.2	489	Gaa/Taa	5/10	0.356685116824411	3	FACETS	1	0.984	1	0.625	0.576	0.676	CLONAL	1	TRUE	1	0.452848307725203	3		433	741	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241677	55241677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504256	NA	P-0003107-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	169	702	0	ENST00000275493.2:c.2125G>A	p.Glu709Lys	p.E709K	ENST00000275493	NM_005228.3	709	Gaa/Aaa	18/28	0.134438092287719	4	FACETS	0.963	0.887	1	0.963	0.887	1	INDETERMINATE	2	FALSE	2	0.28283355468252	4		702	796	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0003107-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	151	593	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.134438092287719	4	FACETS	0.931	0.852	1	0.931	0.852	1	INDETERMINATE	2	FALSE	2	0.28283355468252	4		593	736	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604699	48604699	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003107-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	74	375	0	ENST00000342988.3:c.1521A>C	p.Lys507Asn	p.K507N	ENST00000342988	NM_005359.5	507	aaA/aaC	12/12	0.160021929253015	2	FACETS	1	0.975	1	0.737	0.65	0.83	INDETERMINATE	1	FALSE	0	0.28283355468252	2		375	355	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420094	152420112	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	CGGTCTGAGAGCTCCCTGG	CGGTCTGAGAGCTCCCTGG	-	novel	NA	P-0003107-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	58	377	0	ENST00000206249.3:c.1782_*12del		p.*594*	ENST00000206249	NM_000125.3	594		8/8	0.157512325953613	3	FACETS	1	0.967	1	0.483	0.417	0.554	INDETERMINATE	1	FALSE	0	0.28283355468252	3		377	323	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953974	32953974	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs80359156	NA	P-0003107-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	27	425	0	ENST00000380152.3:c.9041C>G	p.Ser3014Ter	p.S3014*	ENST00000380152		3014	tCa/tGa	23/27	1	2	FACETS	0.432	0.343	0.534	0.432	0.343	0.534	SUBCLONAL	1	FALSE	1	0.28283355468252	2		425	442	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394867	394867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202124383	NA	P-0121452-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	60	508	0	ENST00000380956.4:c.263C>T	p.Pro88Leu	p.P88L	ENST00000380956	NM_001195286.1	88	cCg/cTg	3/9	0.587938465654449	3	FACETS	0.474	0.409	0.543	0.237	0.204	0.272	SUBCLONAL	1	NA	1	0.884902510882419	3		508	413	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870802	12870802	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121452-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	50	197	0	ENST00000228872.4:c.29G>T	p.Ser10Ile	p.S10I	ENST00000228872	NM_004064.3	10	aGc/aTc	1/3	0.584066376760131	4	FACETS	1	0.928	1	0.376	0.323	0.431	CLONAL	1	NA	1	0.884902510882419	4		197	189	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643742	38643742	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121452-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	361	929	0	ENST00000299084.4:c.1212G>T	p.Trp404Cys	p.W404C	ENST00000299084	NM_152594.2	404	tgG/tgT	7/7	0.880455990180125	3	FACETS	1	0.954	1	0.503	0.477	0.53	CLONAL	1	NA	1	0.884902510882419	3		929	1170	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401722	401722	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121452-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	169	661	0	ENST00000380956.4:c.1044C>A	p.Asn348Lys	p.N348K	ENST00000380956	NM_001195286.1	348	aaC/aaA	7/9	0.587938465654449	3	FACETS	1	0.959	1	0.527	0.488	0.567	CLONAL	1	NA	1	0.884902510882419	3		661	523	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98009720	98009720	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121452-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	140	475	0	ENST00000289081.3:c.244G>T	p.Ala82Ser	p.A82S	ENST00000289081	NM_000136.2	82	Gca/Tca	3/15	1	2	FACETS	0.884	0.815	0.954	0.884	0.815	0.954	CLONAL	1	NA	1	0.884902510882419	2		475	358	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	100	349	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.902	0.817	0.99	0.902	0.817	0.99	CLONAL	1	TRUE	1	0.767085269321797	2		349	289	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0005284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	179	567	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.904	0.84	0.97	0.904	0.84	0.97	CLONAL	1	TRUE	1	0.767085269321797	2		567	516	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412884	49412884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	230	666	1	ENST00000418115.1:c.139G>A	p.Glu47Lys	p.E47K	ENST00000418115	NM_001664.2	47	Gag/Aag	2/5	1	2	FACETS	0.97	0.911	1	0.97	0.911	1	CLONAL	1	TRUE	1	0.767085269321797	2		667	618	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004922	150004922	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	35	545	0	ENST00000253339.5:c.1303C>T	p.Gln435Ter	p.Q435*	ENST00000253339		435	Cag/Tag	3/7	1	2	FACETS	0.174	0.142	0.21	0.174	0.142	0.21	SUBCLONAL	1	TRUE	1	0.767085269321797	2		545	524	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652070	36652071	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGG	novel	NA	P-0005284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	212	714	0	ENST00000244741.5:c.193_195dup	p.Trp65dup	p.W65dup	ENST00000244741	NM_000389.4	65	-/TGG	2/3	1	2	FACETS	0.932	0.872	0.994	0.932	0.872	0.994	CLONAL	1	TRUE	1	0.767085269321797	2		714	593	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984365	201984366	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	191	591	0	ENST00000359651.3:c.1033dup	p.Val345GlyfsTer126	p.V345Gfs*126	ENST00000359651		344	cgg/cGgg	8/8	1	2	FACETS	0.954	0.889	1	0.954	0.889	1	CLONAL	1	TRUE	1	0.767085269321797	2		591	522	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244079	46244079	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	146	492	0	ENST00000334344.6:c.2173C>T	p.Gln725Ter	p.Q725*	ENST00000334344	NM_152641.2	725	Cag/Tag	15/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.433232985736976	2		492	550	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295699	212295699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776347334	NA	P-0005729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	123	519	0	ENST00000342788.4:c.2614G>A	p.Glu872Lys	p.E872K	ENST00000342788	NM_005235.2	872	Gaa/Aaa	21/28	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.433232985736976	2		519	531	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935426	36935426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	41	697	0	ENST00000361632.4:c.1301G>A	p.Arg434Lys	p.R434K	ENST00000361632		434	aGa/aAa	10/16	1	2	FACETS	0.308	0.256	0.366	0.308	0.256	0.366	SUBCLONAL	1	TRUE	1	0.433232985736976	2		697	615	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164781	36164781	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	172	757	0	ENST00000300305.3:c.1094G>A	p.Gly365Asp	p.G365D	ENST00000300305		365	gGc/gAc	8/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.433232985736976	2		757	646	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319902	8319902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	129	423	0	ENST00000356435.5:c.5599G>A	p.Glu1867Lys	p.E1867K	ENST00000356435		1867	Gaa/Aaa	34/35	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.433232985736976	2		423	461	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472433	88472433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	116	493	0	ENST00000360948.2:c.2122G>A	p.Asp708Asn	p.D708N	ENST00000360948	NM_001012338.2	708	Gat/Aat	16/19	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.433232985736976	2		493	426	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056500	26056500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	58	211	0	ENST00000343677.2:c.157G>A	p.Glu53Lys	p.E53K	ENST00000343677	NM_005319.3	53	Gag/Aag	1/1	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.433232985736976	2		211	219	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117730789	117730789	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	160	492	0	ENST00000368508.3:c.245T>C	p.Val82Ala	p.V82A	ENST00000368508	NM_002944.2	82	gTt/gCt	4/43	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.433232985736976	2		492	541	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023956	27023957	+	stop_gained	Nonsense_Mutation	DNP	AC	AC	TT	novel	NA	P-0005729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	21	92	0	ENST00000324856.7:c.1062_1063delinsTT	p.Gln354_Gln355delinsHisTer	p.Q354_Q355delinsH*	ENST00000324856	NM_006015.4	354	caACaa/caTTaa	1/20	1	2	FACETS	1	0.83	1	1	0.83	1	CLONAL	1	TRUE	1	0.433232985736976	2		92	91	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512368	120512368	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0005729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	86	355	0	ENST00000256646.2:c.875-1G>A		p.X292_splice	ENST00000256646	NM_024408.3	292			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.433232985736976	2		355	350	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828236	72828236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	144	578	0	ENST00000268489.5:c.8345G>A	p.Gly2782Asp	p.G2782D	ENST00000268489	NM_006885.3	2782	gGt/gAt	9/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.433232985736976	2		578	542	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41247907	41247907	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	145	506	0	ENST00000357654.3:c.626C>G	p.Pro209Arg	p.P209R	ENST00000357654	NM_007294.3	209	cCt/cGt	9/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.433232985736976	2		506	564	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2180711	2180711	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0005729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	136	650	0	ENST00000398665.3:c.82-1G>A		p.X28_splice	ENST00000398665	NM_032482.2	28			1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.433232985736976	2		650	616	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662934	227662935	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0005729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	144	743	2	ENST00000305123.5:c.520_521delinsAA	p.Gly174Asn	p.G174N	ENST00000305123	NM_005544.2	174	GGt/AAt	1/2	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.433232985736976	2		745	608	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62322295	62322295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1215899054	NA	P-0005729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	216	705	0	ENST00000360203.5:c.2551G>A	p.Glu851Lys	p.E851K	ENST00000360203	NM_001283009.1	851	Gag/Aag	27/35	1	2	FACETS	0.775	0.725	0.827	1	0.992	1	SUBCLONAL	2	TRUE	1	0.433232985736976	2		705	643	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103777	47103777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146911485	NA	P-0005729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	163	509	0	ENST00000409792.3:c.6169C>T	p.Pro2057Ser	p.P2057S	ENST00000409792	NM_014159.6	2057	Cct/Tct	14/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.433232985736976	2		509	631	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322421	31322421	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs147623692	NA	P-0005729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	112	403	0	ENST00000412585.2:c.1034C>A	p.Ser345Tyr	p.S345Y	ENST00000412585	NM_005514.6	345	tCt/tAt	6/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.433232985736976	2		403	386	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790784	89790785	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0005729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	161	849	0	ENST00000336032.3:c.171_172delinsTT	p.Pro58Ser	p.P58S	ENST00000336032	NM_006813.2	57	ctCCct/ctTTct	1/2	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.433232985736976	2		849	609	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401037	139401037	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	177	825	0	ENST00000277541.6:c.3956G>A	p.Gly1319Glu	p.G1319E	ENST00000277541	NM_017617.3	1319	gGg/gAg	24/34	0.434565250692788	2	FACETS	1	0.984	1	0.621	0.574	0.669	CLONAL	1	TRUE	0	0.433232985736976	2		825	658	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412233	139412233	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	357	737	0	ENST00000277541.6:c.1412T>A	p.Ile471Asn	p.I471N	ENST00000277541	NM_017617.3	471	aTt/aAt	8/34	0.434565250692788	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.433232985736976	2		737	701	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0006116-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	95	562	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.21043947644179	3	FACETS	1	0.975	1	0.673	0.599	0.751	CLONAL	1	TRUE	1	0.24	3		562	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0006116-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	83	801	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	1	2	FACETS	0.835	0.736	0.942	0.835	0.736	0.942	CLONAL	1	TRUE	1	0.24	2		802	828	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348785	11348785	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006116-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	21	454	0	ENST00000332029.2:c.551C>T	p.Ala184Val	p.A184V	ENST00000332029	NM_003745.1	184	gCc/gTc	2/2	1	2	FACETS	0.335	0.257	0.426	0.335	0.257	0.426	SUBCLONAL	1	TRUE	1	0.24	2		454	523	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251992	8251992	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006116-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	54	882	0	ENST00000335790.3:c.85C>A	p.Arg29Ser	p.R29S	ENST00000335790	NM_002315.2	29	Cgc/Agc	2/4	0.0871298412984709	3	FACETS	0.521	0.443	0.606	0.26	0.221	0.303	INDETERMINATE	1	TRUE	1	0.24	3		882	968	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524719	187524719	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006116-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	56	889	0	ENST00000441802.2:c.10961A>T	p.Glu3654Val	p.E3654V	ENST00000441802	NM_005245.3	3654	gAa/gTa	19/27	1	2	FACETS	0.444	0.379	0.516	0.444	0.379	0.516	SUBCLONAL	1	TRUE	1	0.24	2		889	1050	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169706	11169706	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	180	396	0	ENST00000361445.4:c.7447A>C	p.Ile2483Leu	p.I2483L	ENST00000361445	NM_004958.3	2483	Att/Ctt	55/58	1	2	FACETS	0.798	0.74	0.857	0.798	0.74	0.857	SUBCLONAL	1	TRUE	1	0.797494624915714	2		396	566	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578142	226578142	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	202	308	0	ENST00000366794.5:c.586A>C	p.Lys196Gln	p.K196Q	ENST00000366794	NM_001618.3	196	Aag/Cag	4/23	1	2	FACETS	0.967	0.904	1	0.967	0.904	1	CLONAL	1	TRUE	1	0.797494624915714	2		308	524	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151947966	151947966	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	602	409	0	ENST00000262189.6:c.1707G>C	p.Gln569His	p.Q569H	ENST00000262189	NM_170606.2	569	caG/caC	12/59	0.761693623284351	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.797494624915714	4		409	1328	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5029879	5029879	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	224	355	0	ENST00000381652.3:c.323C>G	p.Thr108Ser	p.T108S	ENST00000381652	NM_004972.3	108	aCc/aGc	4/25	1	2	FACETS	0.955	0.896	1	0.955	0.896	1	CLONAL	1	TRUE	1	0.797494624915714	2		355	588	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527858	103527858	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	338	471	0	ENST00000355739.4:c.3166C>G	p.Gln1056Glu	p.Q1056E	ENST00000355739	NM_000123.3	1056	Cag/Gag	15/15	1	2	FACETS	0.998	0.949	1	0.998	0.949	1	CLONAL	1	TRUE	1	0.797494624915714	2		471	849	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038265	30038269	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGG	CCAGG	-	novel	NA	P-0006126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	266	456	0	ENST00000338641.4:c.441_445del	p.Ala148ValfsTer3	p.A148Vfs*3	ENST00000338641	NM_000268.3	146	gtCCAGGcc/gtcc	4/16	1	2	FACETS	0.964	0.909	1	0.964	0.909	1	CLONAL	1	TRUE	1	0.797494624915714	2		456	692	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188078	11188078	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006263-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	83	484	0	ENST00000361445.4:c.6016G>T	p.Val2006Phe	p.V2006F	ENST00000361445	NM_004958.3	2006	Gtc/Ttc	43/58	0.183357368269085	1	FACETS	0.858	0.759	0.963	0.858	0.759	0.963	INDETERMINATE	1	TRUE	0	0.317341404195347	1		484	513	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183703	10183703	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006263-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	121	539	0	ENST00000256474.2:c.172del	p.Arg58GlyfsTer9	p.R58Gfs*9	ENST00000256474	NM_000551.3	58	Cgg/gg	1/3	0.317341404195347	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.317341404195347	1		539	602	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164441	47164441	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006263-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	61	400	0	ENST00000409792.3:c.1685del	p.Pro562LeufsTer17	p.P562Lfs*17	ENST00000409792	NM_014159.6	562	cCt/ct	3/21	0.317341404195347	1	FACETS	0.874	0.758	0.999	0.874	0.758	0.999	CLONAL	1	TRUE	0	0.317341404195347	1		400	370	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584627	52584628	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006263-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	118	568	0	ENST00000394830.3:c.4385dup	p.Gln1463AlafsTer46	p.Q1463Afs*46	ENST00000394830	NM_018313.4	1462	cag/caAg	29/30	0.317341404195347	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.317341404195347	1		568	612	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097625	11097625	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	412	362	3	ENST00000358026.2:c.810del	p.Met272CysfsTer31	p.M272Cfs*31	ENST00000358026	NM_001128849.1	269	Ccc/cc	5/36	0.709128291921044	2	FACETS	0.988	0.956	1	0.988	0.956	1	CLONAL	2	TRUE	0	0.709128291921044	2		365	588	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0006724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	304	384	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.688185949028525	4	FACETS	0.901	0.853	0.95	0.901	0.853	0.95	CLONAL	2	TRUE	2	0.709128291921044	4		384	813	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057520005	NA	P-0006724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	492	392	0	ENST00000269305.4:c.820G>T	p.Val274Phe	p.V274F	ENST00000269305	NM_001126112.2	274	Gtt/Ttt	8/11	0.709128291921044	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.709128291921044	2		392	688	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106833	27106833	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0006724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	404	278	0	ENST00000324856.7:c.6444T>A	p.Tyr2148Ter	p.Y2148*	ENST00000324856	NM_006015.4	2148	taT/taA	20/20	0.70700420743794	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.709128291921044	2		278	548	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967051	25967051	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	326	255	0	ENST00000435504.4:c.2155A>G	p.Arg719Gly	p.R719G	ENST00000435504		719	Aga/Gga	13/13	NA	2	FACETS	0.98	0.944	1			1	INDETERMINATE	2	TRUE	NA	0.709128291921044	2		255	469	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873212	136873212	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	617	597	0	ENST00000241393.3:c.286G>C	p.Val96Leu	p.V96L	ENST00000241393	NM_003467.2	96	Gtt/Ctt	2/2	0.709128291921044	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.709128291921044	3		597	1112	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198263186	198263186	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	140	284	0	ENST00000335508.6:c.3133A>T	p.Arg1045Trp	p.R1045W	ENST00000335508	NM_012433.2	1045	Agg/Tgg	21/25	0.709128291921044	3	FACETS	0.707	0.645	0.773	0.354	0.322	0.387	SUBCLONAL	1	TRUE	1	0.709128291921044	3		284	756	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576902	212576902	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0006724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	129	251	0	ENST00000342788.4:c.998-1G>T		p.X333_splice	ENST00000342788	NM_005235.2	333			0.709128291921044	3	FACETS	0.97	0.885	1	0.485	0.442	0.53	CLONAL	1	TRUE	1	0.709128291921044	3		251	508	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499435	89499435	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	398	334	0	ENST00000336596.2:c.2605C>A	p.Pro869Thr	p.P869T	ENST00000336596	NM_005233.5	869	Ccc/Acc	15/17	0.685082036294874	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.709128291921044	2		334	561	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671946	30671946	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	454	408	0	ENST00000376406.3:c.5014C>T	p.Pro1672Ser	p.P1672S	ENST00000376406	NM_014641.2	1672	Cct/Tct	10/15	0.709128291921044	4	FACETS	0.981	0.939	1	0.981	0.939	1	CLONAL	2	TRUE	2	0.709128291921044	4		408	1115	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673274	30673274	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1348049159	NA	P-0006724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	445	424	0	ENST00000376406.3:c.3686G>T	p.Arg1229Met	p.R1229M	ENST00000376406	NM_014641.2	1229	aGg/aTg	10/15	0.709128291921044	4	FACETS	0.825	0.787	0.863	0.825	0.787	0.863	CLONAL	2	TRUE	2	0.709128291921044	4		424	1300	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974325	93974325	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1562053469	NA	P-0006724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	426	461	0	ENST00000369303.4:c.1729A>G	p.Ile577Val	p.I577V	ENST00000369303	NM_004440.3	577	Atc/Gtc	8/17	0.696621724382804	2	FACETS	0.92	0.888	0.951	0.92	0.888	0.951	CLONAL	2	TRUE	0	0.709128291921044	2		461	653	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508682	106508682	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs760803722	NA	P-0006724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	313	282	0	ENST00000359195.3:c.676C>G	p.Arg226Gly	p.R226G	ENST00000359195	NM_002649.2	226	Cgc/Ggc	2/11	0.607427417552584	4	FACETS	0.934	0.885	0.983	0.934	0.885	0.983	CLONAL	2	TRUE	2	0.709128291921044	4		282	808	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395458	116395458	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	376	389	1	ENST00000397752.3:c.1751G>T	p.Cys584Phe	p.C584F	ENST00000397752	NM_000245.2	584	tGt/tTt	6/21	0.607427417552584	4	FACETS	0.954	0.909	1	0.954	0.909	1	CLONAL	2	TRUE	2	0.709128291921044	4		390	950	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625197	69625197	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	358	325	0	ENST00000334134.2:c.596C>A	p.Pro199His	p.P199H	ENST00000334134	NM_005247.2	199	cCc/cAc	3/3	0.367677718095124	3	FACETS	1	0.975	1			1	INDETERMINATE	2	TRUE	NA	0.709128291921044	3		325	666	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998526	100998526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	326	259	0	ENST00000325455.5:c.1276C>T	p.Pro426Ser	p.P426S	ENST00000325455	NM_001202474.3	426	Ccg/Tcg	1/8	0.709128291921044	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.709128291921044	3		259	597	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061775	38061775	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs755762174	NA	P-0006724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	375	290	0	ENST00000250448.2:c.214G>T	p.Gly72Cys	p.G72C	ENST00000250448	NM_004496.3	72	Ggc/Tgc	2/2	0.709128291921044	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.709128291921044	3		290	670	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609339	81609339	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	403	453	0	ENST00000298171.2:c.937A>C	p.Lys313Gln	p.K313Q	ENST00000298171	NM_000369.2	313	Aaa/Caa	10/10	0.709128291921044	3	FACETS	0.907	0.868	0.946	0.907	0.868	0.946	CLONAL	2	TRUE	1	0.709128291921044	3		453	849	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992901	72992901	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	539	486	0	ENST00000268489.5:c.1144G>T	p.Gly382Cys	p.G382C	ENST00000268489	NM_006885.3	382	Ggc/Tgc	2/10	0.709128291921044	3	FACETS	0.956	0.921	0.991	0.956	0.921	0.991	CLONAL	2	TRUE	1	0.709128291921044	3		486	1077	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677950	58677950	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	422	175	0	ENST00000305921.3:c.175C>T	p.Pro59Ser	p.P59S	ENST00000305921	NM_003620.3	59	Ccc/Tcc	1/6	0.709128291921044	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.709128291921044	3		175	719	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107057	11107057	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0006724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	265	207	0	ENST00000358026.2:c.1761+1G>C		p.X587_splice	ENST00000358026	NM_001128849.1	587			0.709128291921044	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.709128291921044	2		207	346	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791838	42791838	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	322	287	0	ENST00000575354.2:c.724G>C	p.Gly242Arg	p.G242R	ENST00000575354	NM_015125.3	242	Ggg/Cgg	5/20	0.709128291921044	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.709128291921044	2		287	450	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077459	30077459	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	408	285	2	ENST00000338641.4:c.1606C>T	p.Gln536Ter	p.Q536*	ENST00000338641	NM_000268.3	536	Cag/Tag	15/16	0.696621724382804	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.709128291921044	2		287	554	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423602	88423602	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	335	322	0	ENST00000360948.2:c.2233del	p.Arg745GlyfsTer14	p.R745Gfs*14	ENST00000360948	NM_001012338.2	745	Cgg/gg	18/19	0.709128291921044	2	FACETS	0.992	0.957	1	0.992	0.957	1	CLONAL	2	TRUE	0	0.709128291921044	2		322	476	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732285	74732285	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006803-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	189	250	0	ENST00000359995.5:c.624T>G	p.Ser208Arg	p.S208R	ENST00000359995	NM_001195427.1	208	agT/agG	2/3	1	2	FACETS	0.905	0.846	0.965	0.905	0.846	0.965	CLONAL	1	TRUE	1	0.923914651757522	2		250	452	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211069	36211069	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006803-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	615	793	0	ENST00000222270.7:c.820C>G	p.Pro274Ala	p.P274A	ENST00000222270	NM_014727.1	274	Cca/Gca	3/37	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.923914651757522	2		793	1315	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133173	38133173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006803-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	439	568	0	ENST00000317025.8:c.4300G>A	p.Glu1434Lys	p.E1434K	ENST00000317025	NM_023034.1	1434	Gaa/Aaa	24/24	1	2	FACETS	0.946	0.905	0.986	0.946	0.905	0.986	CLONAL	1	TRUE	1	0.923914651757522	2		568	1005	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265518	198265518	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006803-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	558	627	1	ENST00000335508.6:c.2639G>A	p.Gly880Glu	p.G880E	ENST00000335508	NM_012433.2	880	gGa/gAa	18/25	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.923914651757522	2		628	1163	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954221	48954221	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0006803-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	225	265	0	ENST00000267163.4:c.1421+1G>A		p.X474_splice	ENST00000267163	NM_000321.2	474			0.923914651757522	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.923914651757522	1		265	262	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041591	14041591	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006803-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	65	472	0	ENST00000311895.7:c.2138T>G	p.Val713Gly	p.V713G	ENST00000311895	NM_005236.2	713	gTt/gGt	11/11	1	2	FACETS	0.176	0.152	0.202	0.176	0.152	0.202	SUBCLONAL	1	TRUE	1	0.923914651757522	2		472	799	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577541	7577542	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0006803-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	475	632	0	ENST00000269305.4:c.739_740del	p.Asn247ProfsTer16	p.N247Pfs*16	ENST00000269305	NM_001126112.2	247	AAc/c	7/11	0.923914651757522	1	FACETS	0.991	0.97	1	0.991	0.97	1	CLONAL	1	TRUE	0	0.923914651757522	1		632	558	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147726	61147727	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0006803-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	37	266	0	ENST00000295025.8:c.1036_1037delinsAT	p.Pro346Ile	p.P346I	ENST00000295025	NM_002908.2	346	CCa/ATa	10/11	1	2	FACETS	0.157	0.129	0.189	0.157	0.129	0.189	SUBCLONAL	1	TRUE	1	0.923914651757522	2		266	510	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671434	30671442	+	inframe_deletion	In_Frame_Del	DEL	CTCTTCCTT	CTCTTCCTT	-	novel	NA	P-0006803-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	315	700	2	ENST00000376406.3:c.5518_5526del	p.Lys1840_Glu1842del	p.K1840_E1842del	ENST00000376406	NM_014641.2	1840	AAGGAAGAG/-	10/15	1	2	FACETS	0.595	0.561	0.63	0.595	0.561	0.63	SUBCLONAL	1	TRUE	1	0.923914651757522	2		702	1146	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0007629-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	269	328	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	0.640173724298277	4	FACETS	0.951	0.897	1	0.951	0.897	1	CLONAL	2	TRUE	2	0.666609449941491	4		328	707	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204864	NA	P-0007629-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	278	339	0	ENST00000371953.3:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000371953	NM_000314.4	171	Cag/Tag	6/9	0.6428213056962	2	FACETS	0.944	0.902	0.984	0.944	0.902	0.984	CLONAL	2	TRUE	0	0.666609449941491	2		339	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0007629-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	401	436	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.6428213056962	2	FACETS	0.998	0.963	1	0.998	0.963	1	CLONAL	2	TRUE	0	0.666609449941491	2		436	603	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11293481	11293481	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007629-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	181	429	0	ENST00000361445.4:c.2395C>G	p.Leu799Val	p.L799V	ENST00000361445	NM_004958.3	799	Ctg/Gtg	15/58	0.635210226994821	3	FACETS	1	0.974	1	0.555	0.514	0.598	CLONAL	1	TRUE	1	0.666609449941491	3		429	652	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39239301	39239301	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007629-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	276	414	0	ENST00000402219.2:c.2356C>T	p.Arg786Ter	p.R786*	ENST00000402219	NM_005633.3	786	Cga/Tga	14/23	0.635210226994821	3	FACETS	0.848	0.802	0.894	0.848	0.802	0.894	CLONAL	2	TRUE	1	0.666609449941491	3		414	651	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008179-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	224	489	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.208216460590942	5	FACETS	0.993	0.94	1			1	INDETERMINATE	3	TRUE	NA	0.834207184292363	5		489	406	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233024	55233024	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144943614	NA	P-0008179-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	264	319	0	ENST00000275493.2:c.1774G>A	p.Val592Ile	p.V592I	ENST00000275493	NM_005228.3	592	Gtc/Atc	15/28	0.834207184292363	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	2	0.834207184292363	4		319	574	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	463304	463304	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008179-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	124	546	0	ENST00000399788.2:c.967C>G	p.Leu323Val	p.L323V	ENST00000399788	NM_001042603.1	323	Cta/Gta	8/28	0.11318315735395	6	FACETS	1	0.968	1			1	INDETERMINATE	2	TRUE	NA	0.834207184292363	6		546	354	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120554439	120554439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008179-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	13	59	0	ENST00000229340.5:c.16G>A	p.Asp6Asn	p.D6N	ENST00000229340	NM_006861.6	6	Gac/Aac	1/6	0.754126565744155	5	FACETS	0.797	0.577	1	0.266	0.192	0.353	CLONAL	1	TRUE	2	0.834207184292363	5		59	88	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647834	3647834	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008695-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	80	656	1	ENST00000294008.3:c.1330G>A	p.Glu444Lys	p.E444K	ENST00000294008	NM_032444.2	444	Gaa/Aaa	6/15	1	2	FACETS	0.326	0.286	0.368	0.326	0.286	0.368	SUBCLONAL	1	TRUE	1	0.686806161811684	2		657	715	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010974-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	75	349	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.798	0.7	0.903	1	0.977	1	CLONAL	2	TRUE	1	0.17	2		349	553	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010974-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	29	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.424	0.339	0.522	0.424	0.339	0.522	SUBCLONAL	1	TRUE	1	0.17	2		539	805	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0010974-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	21	256	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.396	0.303	0.505	0.396	0.303	0.505	SUBCLONAL	1	TRUE	1	0.17	2		256	624	SUCCESS
APC	324	MSKCC	GRCh37	5	112103020	112103020	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010974-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	57	470	0	ENST00000257430.4:c.355C>G	p.Pro119Ala	p.P119A	ENST00000257430	NM_000038.5	119	Cca/Gca	4/16	1	2	FACETS	0.875	0.75	1	0.875	0.75	1	CLONAL	1	TRUE	1	0.17	2		470	766	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149987	202149987	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	143	607	1	ENST00000358485.4:c.1428G>T	p.Glu476Asp	p.E476D	ENST00000358485	NM_001080125.1	476	gaG/gaT	8/9	0.248707364179238	3	FACETS	0.803	0.733	0.877	0.803	0.733	0.877	CLONAL	2	TRUE	1	0.248707364179238	3		608	805	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61197647	61197647	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	46	533	0	ENST00000301761.2:c.29C>A	p.Ser10Ter	p.S10*	ENST00000301761	NM_017841.2	10	tCg/tAg	1/4	0.188691984836598	3	FACETS	0.721	0.606	0.847	0.36	0.303	0.424	SUBCLONAL	1	TRUE	1	0.248707364179238	3		533	577	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201019	108201019	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	66	476	0	ENST00000278616.4:c.7386C>G	p.Phe2462Leu	p.F2462L	ENST00000278616	NM_000051.3	2462	ttC/ttG	50/63	0.248707364179238	4	FACETS	1	0.894	1	0.517	0.448	0.591	CLONAL	1	TRUE	2	0.248707364179238	4		476	641	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909626	76909626	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	54	592	0	ENST00000373344.5:c.4279C>T	p.Arg1427Cys	p.R1427C	ENST00000373344	NM_000489.3	1427	Cgt/Tgt	14/35	0.189669579606319	4	FACETS	0.707	0.602	0.822	0.353	0.301	0.411	SUBCLONAL	1	TRUE	2	0.248707364179238	4		592	767	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	218	558	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.794034588626555	2		558	543	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973911	55973911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs941528100	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	232	404	0	ENST00000263923.4:c.1405G>A	p.Glu469Lys	p.E469K	ENST00000263923	NM_002253.2	469	Gag/Aag	10/30	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.794034588626555	2		404	544	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056966	180056966	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	380	624	0	ENST00000261937.6:c.653A>G	p.Asn218Ser	p.N218S	ENST00000261937	NM_182925.4	218	aAc/aGc	5/30	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.794034588626555	2		624	884	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	258	405	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.794034588626555	2		405	634	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525104	9525104	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	213	388	0	ENST00000353224.5:c.1781C>T	p.Ser594Phe	p.S594F	ENST00000353224	NM_177990.2	594	tCc/tTc	8/10	1	2	FACETS	0.986	0.924	1	0.986	0.924	1	CLONAL	1	TRUE	1	0.794034588626555	2		388	544	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743362	162743362	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372362070	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	368	331	0	ENST00000367921.3:c.1832G>A	p.Arg611Gln	p.R611Q	ENST00000367921	NM_006182.2	611	cGa/cAa	14/18	0.794034588626555	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.794034588626555	3		331	647	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462691	29462691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368581969	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	356	520	1	ENST00000389048.3:c.2210C>T	p.Ser737Leu	p.S737L	ENST00000389048	NM_004304.4	737	tCg/tTg	13/29	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.794034588626555	2		521	803	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858735	9858735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	212	370	0	ENST00000330684.3:c.2666G>A	p.Gly889Glu	p.G889E	ENST00000330684	NM_001134407.1	889	gGa/gAa	13/13	1	2	FACETS	0.976	0.914	1	0.976	0.914	1	CLONAL	1	TRUE	1	0.794034588626555	2		370	547	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499393	89499393	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	226	424	0	ENST00000336596.2:c.2563C>T	p.Gln855Ter	p.Q855*	ENST00000336596	NM_005233.5	855	Cag/Tag	15/17	1	2	FACETS	0.942	0.884	1	0.942	0.884	1	CLONAL	1	TRUE	1	0.794034588626555	2		424	604	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265492	198265492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	265	602	0	ENST00000335508.6:c.2665G>A	p.Glu889Lys	p.E889K	ENST00000335508	NM_012433.2	889	Gaa/Aaa	18/25	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.794034588626555	2		602	632	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201798	152201798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761613029	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	144	299	0	ENST00000206249.3:c.652G>A	p.Asp218Asn	p.D218N	ENST00000206249	NM_000125.3	218	Gac/Aac	3/8	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.794034588626555	2		299	347	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587133	189587133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	178	413	0	ENST00000264731.3:c.1150G>A	p.Gly384Ser	p.G384S	ENST00000264731	NM_003722.4	384	Ggt/Agt	9/14	1	2	FACETS	0.977	0.909	1	0.977	0.909	1	CLONAL	1	TRUE	1	0.794034588626555	2		413	459	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032027	10032027	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	268	544	0	ENST00000330684.3:c.796G>A	p.Glu266Lys	p.E266K	ENST00000330684	NM_001134407.1	266	Gag/Aag	3/13	1	2	FACETS	0.978	0.923	1	0.978	0.923	1	CLONAL	1	TRUE	1	0.794034588626555	2		544	690	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644448	18644448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751457593	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	184	418	0	ENST00000266497.5:c.2626C>T	p.Leu876Phe	p.L876F	ENST00000266497		876	Ctt/Ttt	18/31	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.794034588626555	2		418	453	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961492	41961492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	286	518	0	ENST00000219905.7:c.400C>T	p.Arg134Cys	p.R134C	ENST00000219905	NM_001164273.1	134	Cgt/Tgt	2/24	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.794034588626555	2		518	689	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351149	89351149	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs772229371	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	349	550	1	ENST00000301030.4:c.1801C>T	p.Arg601Ter	p.R601*	ENST00000301030	NM_001256183.1	601	Cga/Tga	9/13	0.794034588626555	1	FACETS	0.974	0.937	1	0.974	0.937	1	CLONAL	1	TRUE	0	0.794034588626555	1		551	544	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206647765	206647765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782640857	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	322	439	1	ENST00000367120.3:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000367120	NM_014002.3	60	cGg/cAg	4/22	0.794034588626555	3	FACETS	0.976	0.922	1	0.488	0.461	0.516	CLONAL	1	TRUE	1	0.794034588626555	3		440	1161	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737108	162737108	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	580	471	0	ENST00000367921.3:c.1252A>G	p.Ile418Val	p.I418V	ENST00000367921	NM_006182.2	418	Atc/Gtc	11/18	0.794034588626555	3	FACETS	0.999	0.967	1	0.999	0.967	1	CLONAL	2	TRUE	1	0.794034588626555	3		471	1021	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310974	123310974	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	211	368	0	ENST00000358487.5:c.455-1G>A		p.X152_splice	ENST00000358487	NM_000141.4	152			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.794034588626555	2		368	498	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933195	100933195	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	139	368	0	ENST00000325455.5:c.2195G>A	p.Trp732Ter	p.W732*	ENST00000325455	NM_001202474.3	732	tGg/tAg	4/8	0.794034588626555	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.794034588626555	1		368	206	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230729	46230729	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	189	407	0	ENST00000334344.6:c.980del	p.Leu327Ter	p.L327*	ENST00000334344	NM_152641.2	326	tcT/tc	8/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.794034588626555	2		407	458	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231189	46231189	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	154	386	0	ENST00000334344.6:c.1109T>C	p.Leu370Ser	p.L370S	ENST00000334344	NM_152641.2	370	tTa/tCa	9/21	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.794034588626555	2		386	381	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231201	46231201	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	146	371	0	ENST00000334344.6:c.1120+1G>T		p.X374_splice	ENST00000334344	NM_152641.2	374			1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.794034588626555	2		371	367	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436420	49436420	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	284	488	0	ENST00000301067.7:c.5791C>T	p.Pro1931Ser	p.P1931S	ENST00000301067	NM_003482.3	1931	Cct/Tct	27/54	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.794034588626555	2		488	668	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986541	36986541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs548436641	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	385	449	0	ENST00000354822.5:c.1148C>T	p.Ser383Leu	p.S383L	ENST00000354822	NM_001079668.2	383	tCg/tTg	3/3	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.794034588626555	2		449	883	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574292	95574292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144649926	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	269	315	0	ENST00000393063.1:c.2575C>T	p.Arg859Trp	p.R859W	ENST00000393063	NM_030621.3	859	Cgg/Tgg	17/28	0.191767370620278	6	FACETS	1	0.99	1			1	INDETERMINATE	3	TRUE	NA	0.794034588626555	6		315	503	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647229	2647229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	372	504	0	ENST00000342085.4:c.1507G>A	p.Glu503Lys	p.E503K	ENST00000342085	NM_002613.4	503	Gaa/Aaa	13/14	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.794034588626555	2		504	873	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639096	3639096	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	367	569	0	ENST00000294008.3:c.4543G>A	p.Asp1515Asn	p.D1515N	ENST00000294008	NM_032444.2	1515	Gac/Aac	12/15	1	2	FACETS	0.942	0.896	0.989	0.942	0.896	0.989	CLONAL	1	TRUE	1	0.794034588626555	2		569	981	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614887	23614887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	282	480	0	ENST00000261584.4:c.3454C>T	p.Pro1152Ser	p.P1152S	ENST00000261584	NM_024675.3	1152	Cca/Tca	13/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.794034588626555	2		480	663	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783650	50783650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	227	471	0	ENST00000398568.2:c.41C>T	p.Pro14Leu	p.P14L	ENST00000398568	NM_001042412.1	14	cCc/cTc	3/18	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.794034588626555	2		471	528	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827286	72827286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	396	602	0	ENST00000268489.5:c.9295G>A	p.Gly3099Arg	p.G3099R	ENST00000268489	NM_006885.3	3099	Ggg/Agg	9/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.794034588626555	2		602	942	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830138	72830138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1355338329	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	399	520	0	ENST00000268489.5:c.6443C>T	p.Pro2148Leu	p.P2148L	ENST00000268489	NM_006885.3	2148	cCt/cTt	9/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.794034588626555	2		520	917	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15952262	15952262	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	272	504	0	ENST00000268712.3:c.6433G>T	p.Glu2145Ter	p.E2145*	ENST00000268712	NM_006311.3	2145	Gag/Tag	41/46	1	2	FACETS	0.873	0.822	0.924	0.873	0.822	0.924	CLONAL	1	TRUE	1	0.794034588626555	2		504	785	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684338	29684338	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	254	548	0	ENST00000356175.3:c.7858G>T	p.Glu2620Ter	p.E2620*	ENST00000356175	NM_000267.3	2620	Gaa/Taa	53/57	0.794034588626555	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.794034588626555	1		548	338	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41247929	41247929	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	200	407	1	ENST00000357654.3:c.604C>T	p.Gln202Ter	p.Q202*	ENST00000357654	NM_007294.3	202	Caa/Taa	9/23	1	2	FACETS	0.942	0.88	1	0.942	0.88	1	CLONAL	1	TRUE	1	0.794034588626555	2		408	535	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760800	59760800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1285317687	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	266	568	0	ENST00000259008.2:c.3607G>A	p.Glu1203Lys	p.E1203K	ENST00000259008	NM_032043.2	1203	Gaa/Aaa	20/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.794034588626555	2		568	617	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7168037	7168037	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866529817	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	258	500	0	ENST00000302850.5:c.1552C>T	p.Pro518Ser	p.P518S	ENST00000302850	NM_000208.2	518	Ccg/Tcg	7/22	1	2	FACETS	0.934	0.879	0.989	0.934	0.879	0.989	CLONAL	1	TRUE	1	0.794034588626555	2		500	696	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46271013	46271013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	358	442	0	ENST00000371998.3:c.3137G>A	p.Gly1046Asp	p.G1046D	ENST00000371998		1046	gGc/gAc	17/23	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.794034588626555	2		442	813	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127717	47127717	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759310174	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	283	397	0	ENST00000409792.3:c.5365G>A	p.Gly1789Ser	p.G1789S	ENST00000409792	NM_014159.6	1789	Ggc/Agc	11/21	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.794034588626555	2		397	700	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027101	71027101	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	303	473	1	ENST00000318789.4:c.1226C>T	p.Thr409Ile	p.T409I	ENST00000318789	NM_032682.5	409	aCc/aTc	15/21	1	2	FACETS	0.95	0.9	1	0.95	0.9	1	CLONAL	1	TRUE	1	0.794034588626555	2		474	803	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225542	26225542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755226121	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	238	360	0	ENST00000360408.1:c.160C>T	p.Arg54Cys	p.R54C	ENST00000360408	NM_003532.2	54	Cgc/Tgc	1/1	1	2	FACETS	0.927	0.87	0.984	0.927	0.87	0.984	CLONAL	1	TRUE	1	0.794034588626555	2		360	647	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974414	93974414	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1380030438	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	125	298	1	ENST00000369303.4:c.1640C>T	p.Ala547Val	p.A547V	ENST00000369303	NM_004440.3	547	gCt/gTt	8/17	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.794034588626555	2		299	308	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845228	151845228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	737	440	0	ENST00000262189.6:c.13784G>A	p.Arg4595His	p.R4595H	ENST00000262189	NM_170606.2	4595	cGc/cAc	52/59	0.74501578891869	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	1	0.794034588626555	4		440	1078	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874299	151874299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	689	459	0	ENST00000262189.6:c.8239G>A	p.Asp2747Asn	p.D2747N	ENST00000262189	NM_170606.2	2747	Gac/Aac	38/59	0.74501578891869	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	1	0.794034588626555	4		459	975	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69103965	69103965	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	221	485	0	ENST00000288368.4:c.4355A>G	p.Tyr1452Cys	p.Y1452C	ENST00000288368	NM_024870.2	1452	tAc/tGc	36/40	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.794034588626555	2		485	521	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916439	39916439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	389	226	0	ENST00000378444.4:c.4564G>A	p.Asp1522Asn	p.D1522N	ENST00000378444	NM_001123385.1	1522	Gat/Aat	11/15	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.794034588626555	1		226	464	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242484	+	inframe_deletion	In_Frame_Del	DEL	AATTAAGAGAAGCAACAT	AATTAAGAGAAGCAACAT	-	rs121913422	NA	P-0013189-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	19	390	0	ENST00000275493.2:c.2237_2254del	p.Glu746_Ser752delinsAla	p.E746_S752delinsA	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATct/gct	19/28	1	2	FACETS	0.3	0.227	0.387	0.3	0.227	0.387	SUBCLONAL	1	TRUE	1	0.2	2		390	633	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0013189-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	96	588	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	1	2	FACETS	0.895	0.795	1	0.895	0.795	1	CLONAL	1	TRUE	1	0.2	2		588	1073	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518704	204518704	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	117	360	0	ENST00000367182.3:c.1367A>G	p.His456Arg	p.H456R	ENST00000367182	NM_001278516.1	456	cAt/cGt	11/11	0.507087810318166	3	FACETS	0.908	0.821	1	0.454	0.41	0.5	CLONAL	1	TRUE	1	0.507087810318166	3		360	637	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971147	21971147	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1554654153	NA	P-0014545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	102	419	0	ENST00000304494.5:c.211A>T	p.Asn71Tyr	p.N71Y	ENST00000304494	NM_000077.4	71	Aac/Tac	2/3	0.411571475868384	1	FACETS	0.694	0.624	0.766	0.694	0.624	0.766	SUBCLONAL	1	TRUE	0	0.507087810318166	1		419	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782177	NA	P-0015099-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	353	590	0	ENST00000269305.4:c.644G>C	p.Ser215Thr	p.S215T	ENST00000269305	NM_001126112.2	215	aGt/aCt	6/11	0.938434598704059	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.946340543982934	2		590	365	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015099-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	353	471	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	0.946340543982934	5	FACETS	1	0.991	1	0.768	0.732	0.805	CLONAL	2	TRUE	2	0.946340543982934	5		471	783	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653849	89653859	+	frameshift_variant	Frame_Shift_Del	DEL	TATTGATGATG	TATTGATGATG	-	novel	NA	P-0015099-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	122	413	0	ENST00000371953.3:c.149_159del	p.Ile50SerfsTer9	p.I50Sfs*9	ENST00000371953	NM_000314.4	49	aaTATTGATGATGta/aata	2/9	0.930499263116913	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.946340543982934	1		413	134	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437350	110437350	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015099-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	36	47	0	ENST00000375856.3:c.1051C>G	p.Pro351Ala	p.P351A	ENST00000375856	NM_003749.2	351	Ccg/Gcg	1/2	0.946340543982934	5	FACETS	0.807	0.68	0.942	0.538	0.453	0.628	CLONAL	2	TRUE	2	0.946340543982934	5		47	114	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042320	16042320	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0015099-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	210	320	0	ENST00000268712.3:c.1352+2T>C		p.X451_splice	ENST00000268712	NM_006311.3	451			0.938434598704059	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.946340543982934	2		320	221	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672836	86672836	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015099-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	102	252	0	ENST00000274376.6:c.2323G>C	p.Asp775His	p.D775H	ENST00000274376	NM_002890.2	775	Gac/Cac	17/25	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.946340543982934	2		252	200	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953040	2953040	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141751925	NA	P-0015099-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	147	643	0	ENST00000396946.4:c.2900G>A	p.Arg967His	p.R967H	ENST00000396946	NM_032415.4	967	cGc/cAc	22/25	0.545191270058835	4	FACETS	1	0.982	1	0.417	0.384	0.452	INDETERMINATE	1	TRUE	1	0.946340543982934	4		643	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0015350-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	151	527	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.382661220861827	2	FACETS	0.903	0.837	0.971	0.903	0.837	0.971	CLONAL	2	TRUE	0	0.445740577676704	2		527	375	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0015350-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	413	523	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.445740577676704	12	FACETS	1	0.977	1			1	CLONAL	4	TRUE	NA	0.445740577676704	12		523	1430	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0015350-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	620	478	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.445740577676704	12	FACETS	1	0.991	1			1	CLONAL	11	TRUE	NA	0.445740577676704	12		478	792	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132428	11132428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	367	709	1	ENST00000358026.2:c.2644G>A	p.Glu882Lys	p.E882K	ENST00000358026	NM_001128849.1	882	Gaa/Aaa	19/36	0.891802419729373	3	FACETS	1	0.986	1	0.55	0.523	0.579	CLONAL	1	TRUE	1	0.891802419729373	3		710	1081	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095002	11095002	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1315494799	NA	P-0015648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	577	754	1	ENST00000358026.2:c.175C>T	p.Gln59Ter	p.Q59*	ENST00000358026	NM_001128849.1	59	Cag/Tag	2/36	0.891802419729373	3	FACETS	0.969	0.939	1	0.969	0.939	1	CLONAL	2	TRUE	1	0.891802419729373	3		755	965	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579312	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0015648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	391	479	0	ENST00000269305.4:c.375_375+1delinsTT		p.X125_splice	ENST00000269305	NM_001126112.2	125		4/11	0.891802419729373	2	FACETS	0.992	0.97	1	0.992	0.97	1	CLONAL	2	TRUE	0	0.891802419729373	2		479	442	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637567	176637567	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1388213942	NA	P-0015648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	283	588	1	ENST00000439151.2:c.2167A>G	p.Thr723Ala	p.T723A	ENST00000439151	NM_022455.4	723	Acc/Gcc	5/23	1	2	FACETS	0.998	0.946	1	0.998	0.946	1	CLONAL	1	TRUE	1	0.891802419729373	2		589	636	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0015964-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	148	384	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.617251548483491	3	FACETS	0.634	0.58	0.691	0.317	0.29	0.346	SUBCLONAL	1	TRUE	1	0.883485274624504	3		384	762	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0015964-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	255	460	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.805484249337803	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.883485274624504	1		460	308	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015964-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	309	378	0	ENST00000263967.3:c.3012G>A	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atA	21/21	0.617251548483491	3	FACETS	1	0.989	1	0.582	0.551	0.614	CLONAL	1	TRUE	1	0.883485274624504	3		378	866	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175891	176175891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1227884588	NA	P-0015964-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	23	78	0	ENST00000367669.3:c.224C>T	p.Ser75Leu	p.S75L	ENST00000367669	NM_022457.5	75	tCg/tTg	1/20	0.444974152234498	1	FACETS	0.33	0.263	0.403	0.33	0.263	0.403	INDETERMINATE	1	TRUE	0	0.883485274624504	1		78	88	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114901023	114901023	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs979684293	NA	P-0015964-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	241	388	0	ENST00000543371.1:c.633C>A	p.Phe211Leu	p.F211L	ENST00000543371	NM_001198531.1	211	ttC/ttA	6/14	0.644069027423672	1	FACETS	0.785	0.747	0.822	0.785	0.747	0.822	SUBCLONAL	1	TRUE	0	0.883485274624504	1		388	388	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494962	56494962	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015964-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	319	369	0	ENST00000267101.3:c.3319G>C	p.Glu1107Gln	p.E1107Q	ENST00000267101	NM_001982.3	1107	Gag/Cag	27/28	0.475411428402474	4	FACETS	0.833	0.79	0.877	0.833	0.79	0.877	INDETERMINATE	2	TRUE	2	0.883485274624504	4		369	816	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987165	36987165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015964-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	137	470	0	ENST00000354822.5:c.524C>T	p.Ser175Leu	p.S175L	ENST00000354822	NM_001079668.2	175	tCg/tTg	3/3	0.431586307038048	1	FACETS	0.366	0.335	0.398	0.366	0.335	0.398	INDETERMINATE	1	TRUE	0	0.883485274624504	1		470	473	SUCCESS
BLM	641	MSKCC	GRCh37	15	91298064	91298064	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015964-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	56	264	0	ENST00000355112.3:c.983C>G	p.Ser328Cys	p.S328C	ENST00000355112	NM_000057.2	328	tCt/tGt	5/22	0.192994238007649	5	FACETS	0.583	0.499	0.673			1	INDETERMINATE	1	TRUE	NA	0.883485274624504	5		264	506	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770065	56770065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752608224	NA	P-0015964-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	115	398	1	ENST00000337432.4:c.61C>T	p.Pro21Ser	p.P21S	ENST00000337432	NM_058216.2	21	Cca/Tca	1/9	0.883485274624504	1	FACETS	0.512	0.468	0.556	0.512	0.468	0.556	SUBCLONAL	1	TRUE	0	0.883485274624504	1		399	284	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39595513	39595513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746929631	NA	P-0015964-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	97	208	0	ENST00000262039.4:c.1399G>A	p.Asp467Asn	p.D467N	ENST00000262039	NM_002647.2	467	Gat/Aat	12/25	NA	2	FACETS	0.841	0.762	0.922			1	INDETERMINATE	1	TRUE	NA	0.883485274624504	2		208	261	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3094724	3094724	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015964-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	152	192	0	ENST00000078429.4:c.75C>G	p.Ile25Met	p.I25M	ENST00000078429	NM_002067.2	25	atC/atG	1/7	0.883485274624504	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.883485274624504	1		192	181	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660992	227660992	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015964-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	203	407	0	ENST00000305123.5:c.2463C>A	p.Cys821Ter	p.C821*	ENST00000305123	NM_005544.2	821	tgC/tgA	1/2	NA	2	FACETS	0.813	0.76	0.868			1	INDETERMINATE	1	TRUE	NA	0.883485274624504	2		407	565	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662172	227662172	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015964-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	238	440	0	ENST00000305123.5:c.1283C>A	p.Ser428Ter	p.S428*	ENST00000305123	NM_005544.2	428	tCg/tAg	1/2	NA	2	FACETS	0.811	0.762	0.862			1	INDETERMINATE	1	TRUE	NA	0.883485274624504	2		440	664	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911510	134911510	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015964-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	62	448	0	ENST00000398015.3:c.1975G>A	p.Glu659Lys	p.E659K	ENST00000398015	NM_004441.4	659	Gag/Aag	11/16	0.617251548483491	3	FACETS	0.291	0.251	0.335	0.145	0.125	0.168	SUBCLONAL	1	TRUE	1	0.883485274624504	3		448	696	SUCCESS
ATR	545	MSKCC	GRCh37	3	142218544	142218544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015964-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	146	299	0	ENST00000350721.4:c.5305G>A	p.Glu1769Lys	p.E1769K	ENST00000350721	NM_001184.3	1769	Gaa/Aaa	31/47	0.617251548483491	3	FACETS	0.643	0.588	0.701	0.322	0.294	0.351	SUBCLONAL	1	TRUE	1	0.883485274624504	3		299	741	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952478	38952478	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015964-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	105	243	0	ENST00000357387.3:c.2947G>C	p.Asp983His	p.D983H	ENST00000357387	NM_152756.3	983	Gat/Cat	30/38	0.319001077771111	3	FACETS	0.679	0.61	0.75	0.339	0.305	0.375	INDETERMINATE	1	TRUE	1	0.883485274624504	3		243	505	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176561	56176561	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1561198459	NA	P-0015964-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	313	339	0	ENST00000399503.3:c.2111C>G	p.Ser704Ter	p.S704*	ENST00000399503	NM_005921.1	704	tCa/tGa	12/20	0.668127188793007	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.883485274624504	1		339	382	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031939	26031939	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015964-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	164	254	0	ENST00000244661.2:c.350G>A	p.Arg117Gln	p.R117Q	ENST00000244661	NM_003537.3	117	cGa/cAa	1/1	0.319001077771111	3	FACETS	1	0.984	1	0.61	0.565	0.655	INDETERMINATE	1	TRUE	1	0.883485274624504	3		254	439	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679733	30679733	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015964-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	268	492	0	ENST00000376406.3:c.1986G>T	p.Gln662His	p.Q662H	ENST00000376406	NM_014641.2	662	caG/caT	5/15	1	2	FACETS	0.933	0.882	0.986	0.933	0.882	0.986	CLONAL	1	TRUE	1	0.883485274624504	2		492	650	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965690	93965690	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015964-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	270	332	0	ENST00000369303.4:c.2238G>C	p.Met746Ile	p.M746I	ENST00000369303	NM_004440.3	746	atG/atC	13/17	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.883485274624504	2		332	556	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975403	13975403	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015964-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	137	319	0	ENST00000405192.2:c.484G>T	p.Asp162Tyr	p.D162Y	ENST00000405192	NM_001163147.1	162	Gac/Tac	7/12	0.432008858712641	1	FACETS	0.334	0.305	0.364	0.334	0.305	0.364	INDETERMINATE	1	TRUE	0	0.883485274624504	1		319	518	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862873	117862875	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0015964-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	256	375	0	ENST00000297338.2:c.1602_1604del	p.Glu534del	p.E534del	ENST00000297338	NM_006265.2	534	gaAGAt/gat	12/14	0.883485274624504	3	FACETS	0.88	0.825	0.937	0.44	0.412	0.469	CLONAL	1	TRUE	1	0.883485274624504	3		375	949	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016240-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	60	349	0				ENST00000310581	NM_198253.2	-/1132			0.186991318816931	1	FACETS	1	0.934	1	1	0.934	1	INDETERMINATE	1	TRUE	0	0.346161133632772	1		349	256	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428415	47428415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1183909266	NA	P-0016240-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	124	625	1	ENST00000377045.4:c.1283G>A	p.Arg428Gln	p.R428Q	ENST00000377045	NM_001654.4	428	cGa/cAa	12/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.346161133632772	2		626	598	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845312	76845312	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016240-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	77	403	0	ENST00000373344.5:c.6209T>C	p.Ile2070Thr	p.I2070T	ENST00000373344	NM_000489.3	2070	aTt/aCt	27/35	1	2	FACETS	0.967	0.852	1	0.967	0.852	1	CLONAL	1	TRUE	1	0.346161133632772	2		403	460	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933433	100933433	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016240-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	87	361	0	ENST00000325455.5:c.1957G>T	p.Ala653Ser	p.A653S	ENST00000325455	NM_001202474.3	653	Gct/Tct	4/8	0.346161133632772	1	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	0	0.346161133632772	1		361	405	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858372	9858372	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016240-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	80	438	0	ENST00000330684.3:c.3029C>A	p.Pro1010His	p.P1010H	ENST00000330684	NM_001134407.1	1010	cCc/cAc	13/13	1	2	FACETS	0.998	0.882	1	0.998	0.882	1	CLONAL	1	TRUE	1	0.346161133632772	2		438	463	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641282	23641282	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016240-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	135	534	1	ENST00000261584.4:c.2193del	p.Gly732ValfsTer32	p.G732Vfs*32	ENST00000261584	NM_024675.3	731	ttA/tt	5/13	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.346161133632772	2		535	678	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573997	7574017	+	inframe_deletion	In_Frame_Del	DEL	GCTCTCGGAACATCTCGAAGC	GCTCTCGGAACATCTCGAAGC	-	novel	NA	P-0016240-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	99	548	0	ENST00000269305.4:c.1010_1030del	p.Arg337_Glu343del	p.R337_E343del	ENST00000269305	NM_001126112.2	337	cGCTTCGAGATGTTCCGAGAGCtg/ctg	10/11	1	2	FACETS	0.99	0.886	1	0.99	0.886	1	CLONAL	1	TRUE	1	0.346161133632772	2		548	578	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731493	47731493	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016240-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	12	36	0	ENST00000449228.1:c.299C>T	p.Thr100Ile	p.T100I	ENST00000449228	NM_001127240.2	100	aCc/aTc	2/4	0.346161133632772	1	FACETS	0.925	0.689	1	1	0.908	1	CLONAL	2	TRUE	0	0.346161133632772	1		36	31	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133854	55133854	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016240-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	72	360	0	ENST00000257290.5:c.1067T>G	p.Leu356Arg	p.L356R	ENST00000257290	NM_006206.4	356	cTg/cGg	7/23	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.346161133632772	2		360	386	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710986	117710986	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016240-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	55	222	0	ENST00000368508.3:c.1286A>G	p.Asp429Gly	p.D429G	ENST00000368508	NM_002944.2	429	gAt/gGt	12/43	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.346161133632772	2		222	257	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635250	87635250	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016240-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	120	507	0	ENST00000277120.3:c.2302C>T	p.Gln768Ter	p.Q768*	ENST00000277120		768	Cag/Tag	18/19	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.346161133632772	2		507	555	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877429	89877429	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759763556	NA	P-0017625-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	63	488	0	ENST00000389301.3:c.334C>T	p.Leu112Phe	p.L112F	ENST00000389301	NM_000135.2	112	Ctc/Ttc	4/43	1	2	FACETS	0.841	0.727	0.965	0.841	0.727	0.965	CLONAL	1	TRUE	1	0.22	2		488	681	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051638	30051638	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017625-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	55	323	0	ENST00000338641.4:c.572G>A	p.Trp191Ter	p.W191*	ENST00000338641	NM_000268.3	191	tGg/tAg	6/16	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.22	2		323	468	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440359	52440366	+	protein_altering_variant	In_Frame_Del	DEL	CATCAGGT	CATCAGGT	TA	novel	NA	P-0017625-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	76	517	1	ENST00000460680.1:c.686_693delinsTA	p.Asn229_Met231delinsIle	p.N229_M231delinsI	ENST00000460680	NM_004656.3	229	aACCTGATG/aTA	9/17	1	2	FACETS	0.996	0.873	1	0.996	0.873	1	CLONAL	1	TRUE	1	0.22	2		518	694	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441465	52441465	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0017625-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	46	379	0	ENST00000460680.1:c.387T>A	p.Tyr129Ter	p.Y129*	ENST00000460680	NM_004656.3	129	taT/taA	6/17	1	2	FACETS	0.738	0.62	0.867	0.738	0.62	0.867	SUBCLONAL	1	TRUE	1	0.22	2		379	567	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223607	36223607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs943288736	NA	P-0017625-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	98	773	0	ENST00000222270.7:c.6157C>T	p.Pro2053Ser	p.P2053S	ENST00000222270	NM_014727.1	2053	Cct/Tct	28/37	1	2	FACETS	0.917	0.816	1	0.917	0.816	1	CLONAL	1	TRUE	1	0.22	2		773	972	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168524	56168524	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs906919457	NA	P-0017625-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	40	261	0	ENST00000399503.3:c.1480A>C	p.Lys494Gln	p.K494Q	ENST00000399503	NM_005921.1	494	Aag/Cag	8/20	1	2	FACETS	0.713	0.592	0.848	0.713	0.592	0.848	SUBCLONAL	1	TRUE	1	0.22	2		261	510	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017690-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	56	349	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.362244041276758	2		349	263	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0017690-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	31	426	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.362244041276758	1	FACETS	0.289	0.233	0.352	0.289	0.233	0.352	SUBCLONAL	1	TRUE	0	0.362244041276758	1		426	485	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0017690-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	212	751	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	0.362244041276758	2		751	901	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70412313	70412313	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017690-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	93	387	0	ENST00000373644.4:c.4423G>A	p.Glu1475Lys	p.E1475K	ENST00000373644	NM_030625.2	1475	Gaa/Aaa	6/12	1	2	FACETS	0.843	0.751	0.941	0.843	0.751	0.941	CLONAL	1	TRUE	1	0.362244041276758	2		387	609	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102094471	102094471	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017690-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	55	493	0	ENST00000282441.5:c.1151C>T	p.Pro384Leu	p.P384L	ENST00000282441	NM_001130145.2	384	cCt/cTt	7/9	1	2	FACETS	0.522	0.446	0.605	0.522	0.446	0.605	SUBCLONAL	1	TRUE	1	0.362244041276758	2		493	582	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164889	36164889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1358657401	NA	P-0017690-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	45	573	1	ENST00000300305.3:c.986C>T	p.Ala329Val	p.A329V	ENST00000300305		329	gCg/gTg	8/8	1	2	FACETS	0.35	0.293	0.413	0.35	0.293	0.413	SUBCLONAL	1	TRUE	1	0.362244041276758	2		574	710	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436681	52436681	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017690-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	154	594	1	ENST00000460680.1:c.1993C>T	p.Gln665Ter	p.Q665*	ENST00000460680	NM_004656.3	665	Cag/Tag	16/17	0.362244041276758	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.362244041276758	1		595	687	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874562	35874562	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017690-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	113	596	0	ENST00000303115.3:c.718C>T	p.Pro240Ser	p.P240S	ENST00000303115	NM_002185.3	240	Cct/Tct	6/8	1	2	FACETS	0.787	0.708	0.87	0.787	0.708	0.87	SUBCLONAL	1	TRUE	1	0.362244041276758	2		596	793	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868900	117868900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1444200944	NA	P-0017690-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	126	425	2	ENST00000297338.2:c.799G>A	p.Asp267Asn	p.D267N	ENST00000297338	NM_006265.2	267	Gat/Aat	7/14	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.362244041276758	2		427	646	SUCCESS
AR	367	MSKCC	GRCh37	X	66931514	66931514	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017690-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	35	262	2	ENST00000374690.3:c.2156G>A	p.Trp719Ter	p.W719*	ENST00000374690	NM_000044.3	719	tGg/tAg	4/8	1	1	FACETS	0.424	0.348	0.51	0.424	0.348	0.51	SUBCLONAL	1	TRUE	0	0.362244041276758	1		264	373	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50811826	50811826	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs886040872	NA	P-0018198-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	190	426	0	ENST00000398568.2:c.1103C>A	p.Ser368Ter	p.S368*	ENST00000398568	NM_001042412.1	368	tCa/tAa	7/18	0.779575930087868	1	FACETS	0.991	0.939	1	0.991	0.939	1	CLONAL	1	TRUE	0	0.787819252176581	1		426	295	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144879	47144879	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018198-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	273	460	0	ENST00000409792.3:c.4874G>C	p.Arg1625Pro	p.R1625P	ENST00000409792	NM_014159.6	1625	cGt/cCt	7/21	1	2	FACETS	0.991	0.936	1	0.991	0.936	1	CLONAL	1	TRUE	1	0.787819252176581	2		460	699	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864391	151864392	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018198-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	250	459	0	ENST00000262189.6:c.9589dup	p.Tyr3197LeufsTer3	p.Y3197Lfs*3	ENST00000262189	NM_170606.2	3197	tat/tTat	42/59	0.763217292962598	2	FACETS	0.9	0.846	0.955	0.45	0.423	0.478	CLONAL	1	TRUE	0	0.787819252176581	2		459	705	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445467	49445467	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018198-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	298	577	0	ENST00000301067.7:c.1999G>T	p.Glu667Ter	p.E667*	ENST00000301067	NM_003482.3	667	Gag/Tag	10/54	0.787819252176581	3	FACETS	0.942	0.888	0.999	0.471	0.444	0.5	CLONAL	1	TRUE	1	0.787819252176581	3		577	1119	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	280	611	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.563465746533714	3	FACETS	0.941	0.89	0.992	0.941	0.89	0.992	CLONAL	2	TRUE	1	0.563465746533714	3		617	677	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	343	506	13	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.484924097692241	4	FACETS	0.952	0.903	1	0.952	0.903	1	CLONAL	2	TRUE	2	0.563465746533714	4		519	1000	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	160	614	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.563465746533714	1	FACETS	0.981	0.909	1	0.981	0.909	1	CLONAL	1	TRUE	0	0.563465746533714	1		615	416	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	168	776	3	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	0.563465746533714	3	FACETS	0.932	0.858	1	0.466	0.429	0.505	CLONAL	1	TRUE	1	0.563465746533714	3		779	820	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	50	201	6	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	0.484924097692241	4	FACETS	1	0.862	1	0.504	0.431	0.584	CLONAL	1	TRUE	2	0.563465746533714	4		207	275	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	110	575	1	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	0.563465746533714	2	FACETS	0.86	0.777	0.946	0.43	0.388	0.473	CLONAL	1	TRUE	0	0.563465746533714	2		576	454	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	28	325	4	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	1	2	FACETS	0.245	0.195	0.301	0.245	0.195	0.301	SUBCLONAL	1	TRUE	1	0.563465746533714	2		329	406	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686901	37686901	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	98	415	2	ENST00000447079.4:c.3810del	p.Gly1271AspfsTer23	p.G1271Dfs*23	ENST00000447079	NM_015083.1	1269	Ccc/cc	14/14	0.563465746533714	3	FACETS	0.931	0.834	1	0.465	0.417	0.517	CLONAL	1	TRUE	1	0.563465746533714	3		417	479	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636203	87636203	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	96	392	1	ENST00000277120.3:c.2368C>T	p.Arg790Ter	p.R790*	ENST00000277120		790	Cga/Tga	19/19	0.563465746533714	4	FACETS	0.983	0.878	1	0.491	0.439	0.547	CLONAL	1	TRUE	2	0.563465746533714	4		393	542	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500579	99500579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34102392	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	109	427	2	ENST00000268035.6:c.4012G>A	p.Ala1338Thr	p.A1338T	ENST00000268035	NM_000875.3	1338	Gcc/Acc	21/21	1	2	FACETS	0.953	0.862	1	0.953	0.862	1	CLONAL	1	TRUE	1	0.563465746533714	2		429	406	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909689	50909689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	204	721	0	ENST00000440232.2:c.1409G>A	p.Arg470His	p.R470H	ENST00000440232	NM_002691.3	470	cGc/cAc	12/27	0.563465746533714	4	FACETS	1	0.982	1	0.393	0.364	0.422	CLONAL	1	TRUE	1	0.563465746533714	4		721	961	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464537	25464537	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752434188	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	137	679	1	ENST00000264709.3:c.1976G>A	p.Arg659His	p.R659H	ENST00000264709	NM_175629.2	659	cGc/cAc	17/23	0.563465746533714	3	FACETS	0.86	0.783	0.94	0.43	0.391	0.47	CLONAL	1	TRUE	1	0.563465746533714	3		680	725	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222730	5222731	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs756013055	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	95	491	7	ENST00000357368.4:c.3072dup	p.Val1025ArgfsTer34	p.V1025Rfs*34	ENST00000357368	NM_002850.3	1024	-/C	18/38	1	2	FACETS	0.793	0.711	0.88	0.793	0.711	0.88	SUBCLONAL	1	TRUE	1	0.563465746533714	2		498	425	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111517	8111517	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	131	548	0	ENST00000346208.3:c.1003G>A	p.Asp335Asn	p.D335N	ENST00000346208		335	Gac/Aac	5/6	0.484924097692241	4	FACETS	0.972	0.883	1	0.486	0.441	0.533	CLONAL	1	TRUE	2	0.563465746533714	4		548	748	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	332	1027	2	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.526977726560868	4	FACETS	0.968	0.917	1	0.968	0.917	1	CLONAL	2	TRUE	2	0.563465746533714	4		1029	952	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188143	11188143	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772288758	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	128	506	1	ENST00000361445.4:c.5951C>T	p.Thr1984Met	p.T1984M	ENST00000361445	NM_004958.3	1984	aCg/aTg	43/58	0.563465746533714	3	FACETS	0.972	0.884	1	0.486	0.442	0.532	CLONAL	1	TRUE	1	0.563465746533714	3		507	599	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716229	243716229	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	116	454	0	ENST00000263826.5:c.965A>G	p.Asp322Gly	p.D322G	ENST00000263826	NM_005465.4	322	gAc/gGc	10/13	0.563465746533714	4	FACETS	0.92	0.83	1	0.46	0.415	0.507	CLONAL	1	TRUE	2	0.563465746533714	4		454	700	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360844	118360844	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	153	337	0	ENST00000534358.1:c.4576A>C	p.Ile1526Leu	p.I1526L	ENST00000534358	NM_005933.3	1526	Atc/Ctc	13/36	0.526977726560868	4	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	2	0.563465746533714	4		337	419	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366515	118366515	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	203	393	0	ENST00000534358.1:c.5464T>G	p.Leu1822Val	p.L1822V	ENST00000534358	NM_005933.3	1822	Tta/Gta	19/36	0.526977726560868	4	FACETS	0.992	0.926	1	0.992	0.926	1	CLONAL	2	TRUE	2	0.563465746533714	4		393	568	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628427	21628427	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	164	533	0	ENST00000421138.2:c.1191T>A	p.Asn397Lys	p.N397K	ENST00000421138		397	aaT/aaA	11/16	0.526977726560868	4	FACETS	0.951	0.873	1	0.476	0.436	0.517	CLONAL	1	TRUE	2	0.563465746533714	4		533	957	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218390	133218390	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs781481160	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	141	718	1	ENST00000320574.5:c.5221C>T	p.Gln1741Ter	p.Q1741*	ENST00000320574	NM_006231.2	1741	Cag/Tag	39/49	0.526977726560868	4	FACETS	0.893	0.814	0.977	0.447	0.407	0.489	CLONAL	1	TRUE	2	0.563465746533714	4		719	876	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919682	28919682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs115085855	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	89	345	0	ENST00000282397.4:c.2255C>T	p.Ser752Leu	p.S752L	ENST00000282397	NM_002019.4	752	tCg/tTg	16/30	1	2	FACETS	0.895	0.8	0.994	0.895	0.8	0.994	CLONAL	1	TRUE	1	0.563465746533714	2		345	353	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873751	35873751	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	137	471	1	ENST00000216797.5:c.100C>A	p.Leu34Met	p.L34M	ENST00000216797	NM_020529.2	34	Ctg/Atg	1/6	0.563465746533714	4	FACETS	1	0.911	1	0.5	0.455	0.547	CLONAL	1	TRUE	2	0.563465746533714	4		472	760	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95579430	95579430	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	86	230	0	ENST00000393063.1:c.2039T>C	p.Val680Ala	p.V680A	ENST00000393063	NM_030621.3	680	gTt/gCt	13/28	0.563465746533714	4	FACETS	1	0.963	1	0.597	0.531	0.666	CLONAL	1	TRUE	2	0.563465746533714	4		230	400	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682249	37682249	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	143	492	1	ENST00000447079.4:c.3440A>T	p.Gln1147Leu	p.Q1147L	ENST00000447079	NM_015083.1	1147	cAg/cTg	13/14	0.563465746533714	3	FACETS	1	0.957	1	0.536	0.49	0.583	CLONAL	1	TRUE	1	0.563465746533714	3		493	607	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212173	36212173	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1237717780	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	375	523	2	ENST00000222270.7:c.1924C>T	p.Arg642Trp	p.R642W	ENST00000222270	NM_014727.1	642	Cgg/Tgg	3/37	0.563465746533714	4	FACETS	0.988	0.947	1	0.988	0.947	1	CLONAL	3	TRUE	1	0.563465746533714	4		525	702	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752817	42752817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	513	811	0	ENST00000222329.4:c.1447C>T	p.Arg483Cys	p.R483C	ENST00000222329	NM_006494.2	483	Cgc/Tgc	4/4	0.563465746533714	4	FACETS	0.959	0.923	0.994	0.959	0.923	0.994	CLONAL	3	TRUE	1	0.563465746533714	4		811	990	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912486	50912486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	184	661	0	ENST00000440232.2:c.2000G>A	p.Arg667Gln	p.R667Q	ENST00000440232	NM_002691.3	667	cGg/cAg	16/27	0.563465746533714	4	FACETS	1	0.983	1	0.409	0.377	0.441	CLONAL	1	TRUE	1	0.563465746533714	4		661	833	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560946	9560946	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	117	453	0	ENST00000353224.5:c.836A>G	p.Gln279Arg	p.Q279R	ENST00000353224	NM_177990.2	279	cAg/cGg	4/10	0.526977726560868	4	FACETS	0.984	0.889	1	0.492	0.444	0.542	CLONAL	1	TRUE	2	0.563465746533714	4		453	660	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521688	89521688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1410875132	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	201	421	0	ENST00000336596.2:c.2765G>A	p.Gly922Asp	p.G922D	ENST00000336596	NM_005233.5	922	gGt/gAt	16/17	0.563465746533714	4	FACETS	0.923	0.861	0.987	0.923	0.861	0.987	CLONAL	2	TRUE	2	0.563465746533714	4		421	604	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523731	176523731	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	117	560	2	ENST00000292408.4:c.2147del	p.Pro716GlnfsTer6	p.P716Qfs*6	ENST00000292408	NM_213647.1	714	tgC/tg	16/18	0.484924097692241	4	FACETS	0.845	0.763	0.933	0.423	0.381	0.467	CLONAL	1	TRUE	2	0.563465746533714	4		562	768	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112035595	112035595	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	126	442	1	ENST00000368678.4:c.299A>G	p.Asp100Gly	p.D100G	ENST00000368678		100	gAc/gGc	4/13	0.563465746533714	3	FACETS	0.988	0.898	1	0.494	0.449	0.542	CLONAL	1	TRUE	1	0.563465746533714	3		443	580	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	420	588	18	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	0.526977726560868	4	FACETS	0.858	0.822	0.895	1	0.995	1	CLONAL	3	TRUE	2	0.563465746533714	4		606	905	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291170	10291170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369196079	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	38	703	0	ENST00000340748.4:c.301C>T	p.Arg101Trp	p.R101W	ENST00000340748		101	Cgg/Tgg	4/40	1	2	FACETS	0.208	0.171	0.249	0.208	0.171	0.249	SUBCLONAL	1	TRUE	1	0.563465746533714	2		703	649	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031586	36031586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774838914	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	122	549	0	ENST00000358208.4:c.1415G>A	p.Arg472His	p.R472H	ENST00000358208		472	cGc/cAc	12/12	0.526977726560868	4	FACETS	1	0.955	1	0.545	0.494	0.599	CLONAL	1	TRUE	2	0.563465746533714	4		549	621	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446849	18446849	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	82	277	0	ENST00000266497.5:c.934A>G	p.Lys312Glu	p.K312E	ENST00000266497		312	Aaa/Gaa	4/31	0.526977726560868	4	FACETS	0.994	0.88	1	0.497	0.44	0.558	CLONAL	1	TRUE	2	0.563465746533714	4		277	458	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427714	49427714	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs372758101	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	135	709	0	ENST00000301067.7:c.10774A>G	p.Met3592Val	p.M3592V	ENST00000301067	NM_003482.3	3592	Atg/Gtg	39/54	0.526977726560868	4	FACETS	0.776	0.705	0.852	0.388	0.352	0.426	SUBCLONAL	1	TRUE	2	0.563465746533714	4		709	965	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68290297	68290297	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	139	370	0	ENST00000487270.1:c.37del	p.Gln13LysfsTer7	p.Q13Kfs*7	ENST00000487270	NM_133509.3	13	Caa/aa	2/11	0.563465746533714	4	FACETS	1	0.948	1	0.528	0.481	0.577	CLONAL	1	TRUE	2	0.563465746533714	4		370	730	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867035	45867035	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	122	533	0	ENST00000391945.4:c.1084G>C	p.Ala362Pro	p.A362P	ENST00000391945	NM_000400.3	362	Gcc/Ccc	11/23	0.563465746533714	4	FACETS	1	0.918	1	0.338	0.306	0.372	CLONAL	1	TRUE	1	0.563465746533714	4		533	667	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39239472	39239473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	31	505	0	ENST00000402219.2:c.2184dup	p.Trp729MetfsTer3	p.W729Mfs*3	ENST00000402219	NM_005633.3	728	-/A	14/23	NA	2	FACETS	0.217	0.175	0.265			1	INDETERMINATE	1	TRUE	NA	0.563465746533714	2		505	506	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156050	99156050	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866440781	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	137	565	0	ENST00000074304.5:c.730C>T	p.Arg244Trp	p.R244W	ENST00000074304	NM_001134224.1	244	Cgg/Tgg	10/26	0.526977726560868	4	FACETS	1	0.911	1	0.5	0.455	0.547	CLONAL	1	TRUE	2	0.563465746533714	4		565	760	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719028	190719028	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1386650528	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	84	251	0	ENST00000441310.2:c.1030A>G	p.Asn344Asp	p.N344D	ENST00000441310	NM_000534.4	344	Aat/Gat	9/13	0.526977726560868	4	FACETS	1	0.931	1	0.535	0.474	0.599	CLONAL	1	TRUE	2	0.563465746533714	4		251	436	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37045904	37045904	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs572906317	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	136	510	0	ENST00000231790.2:c.319A>G	p.Ile107Val	p.I107V	ENST00000231790	NM_000249.3	107	Ata/Gta	4/19	0.563465746533714	4	FACETS	0.997	0.908	1	0.498	0.454	0.546	CLONAL	1	TRUE	2	0.563465746533714	4		510	757	SUCCESS
ATR	545	MSKCC	GRCh37	3	142241574	142241574	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	110	388	0	ENST00000350721.4:c.4262T>A	p.Ile1421Asn	p.I1421N	ENST00000350721	NM_001184.3	1421	aTt/aAt	23/47	0.563465746533714	4	FACETS	0.929	0.836	1	0.465	0.418	0.514	CLONAL	1	TRUE	2	0.563465746533714	4		388	657	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209427	98209427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	48	574	0	ENST00000331920.6:c.4111G>A	p.Val1371Met	p.V1371M	ENST00000331920	NM_000264.3	1371	Gtg/Atg	23/24	0.563465746533714	4	FACETS	0.35	0.294	0.411	0.175	0.147	0.206	SUBCLONAL	1	TRUE	2	0.563465746533714	4		574	762	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	168	222	0	ENST00000256196.4:c.68G>A	p.Gly23Asp	p.G23D	ENST00000256196		23	gGc/gAc	1/6	0.194979066228596	2	FACETS	0.832	0.766	0.902	0.416	0.383	0.451	INDETERMINATE	1	TRUE	0	0.479443693673098	2		222	842	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17941354	17941354	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0019747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	332	564	0	ENST00000458235.1:c.3054C>G	p.Tyr1018Ter	p.Y1018*	ENST00000458235	NM_000215.3	1018	taC/taG	22/24	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.479443693673098	2		564	1306	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226556001	226556001	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	78	312	0	ENST00000366794.5:c.2176G>T	p.Asp726Tyr	p.D726Y	ENST00000366794	NM_001618.3	726	Gac/Tac	16/23	0.479443693673098	3	FACETS	0.607	0.533	0.686	0.303	0.266	0.343	SUBCLONAL	1	TRUE	1	0.479443693673098	3		312	665	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499123	149499123	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200865355	NA	P-0019747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	139	500	0	ENST00000261799.4:c.2705C>A	p.Thr902Asn	p.T902N	ENST00000261799	NM_002609.3	902	aCc/aAc	20/23	0.479443693673098	4	FACETS	0.848	0.771	0.929	0.212	0.192	0.233	CLONAL	1	TRUE	0	0.479443693673098	4		500	1012	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133308	38133308	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	156	436	0	ENST00000317025.8:c.4165C>A	p.His1389Asn	p.H1389N	ENST00000317025	NM_023034.1	1389	Cat/Aat	24/24	1	2	FACETS	0.887	0.813	0.963	0.887	0.813	0.963	CLONAL	1	TRUE	1	0.479443693673098	2		436	734	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507363	8507363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	76	354	0	ENST00000356435.5:c.1615C>T	p.Pro539Ser	p.P539S	ENST00000356435		539	Cca/Tca	11/35	0.388641661821158	2	FACETS	0.638	0.561	0.72	0.319	0.28	0.36	SUBCLONAL	1	TRUE	0	0.479443693673098	2		354	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587781525	NA	P-0019831-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	142	690	0	ENST00000269305.4:c.842A>G	p.Asp281Gly	p.D281G	ENST00000269305	NM_001126112.2	281	gAc/gGc	8/11	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.32	2		690	872	SUCCESS
APC	324	MSKCC	GRCh37	5	112174835	112174835	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0019831-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	62	256	0	ENST00000257430.4:c.3544A>T	p.Lys1182Ter	p.K1182*	ENST00000257430	NM_000038.5	1182	Aaa/Taa	16/16	1	2	FACETS	0.969	0.84	1	0.969	0.84	1	CLONAL	1	TRUE	1	0.32	2		256	400	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122518	17122518	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019831-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	108	650	0	ENST00000285071.4:c.877G>T	p.Glu293Ter	p.E293*	ENST00000285071	NM_144997.5	293	Gaa/Taa	9/14	1	2	FACETS	0.875	0.786	0.971	0.875	0.786	0.971	CLONAL	1	TRUE	1	0.32	2		650	771	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221909	98221909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019831-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	116	583	0	ENST00000331920.6:c.2860G>T	p.Asp954Tyr	p.D954Y	ENST00000331920	NM_000264.3	954	Gac/Tac	17/24	1	2	FACETS	0.877	0.79	0.969	0.877	0.79	0.969	CLONAL	1	TRUE	1	0.32	2		583	827	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882025	NA	P-0019978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	286	666	1	ENST00000269305.4:c.646G>T	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ttg	6/11	0.336142471747157	3	FACETS	1	0.993	1			1	CLONAL	1	TRUE	NA	0.480603065297063	3		667	1054	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400147	139400147	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	412	790	1	ENST00000277541.6:c.4201G>T	p.Gly1401Trp	p.G1401W	ENST00000277541	NM_017617.3	1401	Ggg/Tgg	25/34	0.441261513543588	3	FACETS	0.824	0.784	0.864	0.824	0.784	0.864	CLONAL	2	TRUE	1	0.480603065297063	3		791	1291	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219381	1219381	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	343	665	1	ENST00000326873.7:c.433G>T	p.Glu145Ter	p.E145*	ENST00000326873	NM_000455.4	145	Gag/Tag	3/10	0.352938667239225	2	FACETS	0.778	0.739	0.818	0.778	0.739	0.818	SUBCLONAL	2	TRUE	0	0.480603065297063	2		666	917	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426876	70426877	+	missense_variant	Missense_Mutation	DNP	TG	TG	CT	novel	NA	P-0019978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	171	379	0	ENST00000373644.4:c.4536_4537delinsCT	p.Ala1513Ser	p.A1513S	ENST00000373644	NM_030625.2	1512	acTGct/acCTct	7/12	0.356718526796065	3	FACETS	1	0.988	1	0.702	0.648	0.757	CLONAL	1	TRUE	1	0.480603065297063	3		379	629	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129804	108129804	+	splice_donor_variant	Splice_Site	SNP	T	T	G	rs878853495	NA	P-0019978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	141	374	0	ENST00000278616.4:c.2466+2T>G		p.X822_splice	ENST00000278616	NM_000051.3	822			0.359052867820256	3	FACETS	1	0.984	1	0.658	0.602	0.716	CLONAL	1	TRUE	1	0.480603065297063	3		374	553	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896966	28896966	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	112	518	1	ENST00000282397.4:c.2914C>A	p.Gln972Lys	p.Q972K	ENST00000282397	NM_002019.4	972	Cag/Aag	21/30	1	2	FACETS	0.689	0.621	0.762	0.689	0.621	0.762	SUBCLONAL	1	TRUE	1	0.480603065297063	2		519	676	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29002027	29002027	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	98	427	0	ENST00000282397.4:c.1138T>C	p.Ser380Pro	p.S380P	ENST00000282397	NM_002019.4	380	Tct/Cct	9/30	1	2	FACETS	0.679	0.606	0.755	0.679	0.606	0.755	SUBCLONAL	1	TRUE	1	0.480603065297063	2		427	601	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347853	73347853	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1310582067	NA	P-0019978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	76	268	0	ENST00000377767.4:c.1208A>T	p.Asp403Val	p.D403V	ENST00000377767	NM_014953.3	403	gAt/gTt	8/21	0.480603065297063	1	FACETS	0.749	0.662	0.84	0.749	0.662	0.84	SUBCLONAL	1	TRUE	0	0.480603065297063	1		268	321	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129797	30129797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	309	522	0	ENST00000263025.4:c.416G>A	p.Ser139Asn	p.S139N	ENST00000263025	NM_002746.2	139	aGc/aAc	3/9	0.364252311824637	2	FACETS	1	0.994	1	0.737	0.697	0.778	CLONAL	1	TRUE	0	0.480603065297063	2		522	872	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553570	29553570	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	84	269	0	ENST00000356175.3:c.2119A>T	p.Met707Leu	p.M707L	ENST00000356175	NM_000267.3	707	Atg/Ttg	18/57	1	2	FACETS	0.865	0.769	0.967	0.865	0.769	0.967	CLONAL	1	TRUE	1	0.480603065297063	2		269	404	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78921128	78921128	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	184	498	0	ENST00000306801.3:c.3242G>T	p.Cys1081Phe	p.C1081F	ENST00000306801	NM_020761.2	1081	tGc/tTc	27/34	0.359052867820256	3	FACETS	1	0.975	1	0.562	0.519	0.606	CLONAL	1	TRUE	1	0.480603065297063	3		498	845	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279691	18279691	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	168	451	0	ENST00000222254.8:c.1964A>T	p.Tyr655Phe	p.Y655F	ENST00000222254	NM_005027.3	655	tAc/tTc	15/16	0.352938667239225	2	FACETS	1	0.972	1	0.555	0.512	0.599	CLONAL	1	TRUE	0	0.480603065297063	2		451	630	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825326	134825326	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	301	405	0	ENST00000398015.3:c.842C>G	p.Ala281Gly	p.A281G	ENST00000398015	NM_004441.4	281	gCt/gGt	4/16	0.382184478120728	3	FACETS	1	0.992	1	0.826	0.785	0.867	CLONAL	2	TRUE	0	0.480603065297063	3		405	627	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982115	38982115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1303	143	332	0	ENST00000357387.3:c.607G>A	p.Ala203Thr	p.A203T	ENST00000357387	NM_152756.3	203	Gcc/Acc	8/38	0.480603065297063	11	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.480603065297063	11		332	1446	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982018	93982018	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0019978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	158	329	0	ENST00000369303.4:c.1447A>T	p.Lys483Ter	p.K483*	ENST00000369303	NM_004440.3	483	Aaa/Taa	6/17	0.350066085066859	2	FACETS	1	0.988	1	0.701	0.648	0.756	CLONAL	1	TRUE	0	0.480603065297063	2		329	469	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5029906	5029906	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	100	324	0	ENST00000381652.3:c.350G>A	p.Arg117Lys	p.R117K	ENST00000381652	NM_004972.3	117	aGa/aAa	4/25	0.350066085066859	2	FACETS	1	0.957	1	0.558	0.502	0.616	CLONAL	1	TRUE	0	0.480603065297063	2		324	373	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549130	87549130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	204	499	0	ENST00000277120.3:c.1687G>A	p.Gly563Arg	p.G563R	ENST00000277120		563	Gga/Aga	15/19	0.441261513543588	3	FACETS	1	0.991	1	0.726	0.676	0.778	CLONAL	1	TRUE	1	0.480603065297063	3		499	725	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209591	98209591	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs147067171	NA	P-0019978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	126	436	0	ENST00000331920.6:c.3947A>G	p.Tyr1316Cys	p.Y1316C	ENST00000331920	NM_000264.3	1316	tAc/tGc	23/24	0.441261513543588	3	FACETS	0.925	0.839	1	0.463	0.419	0.508	CLONAL	1	TRUE	1	0.480603065297063	3		436	703	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858125	152858125	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	437	430	0	ENST00000406277.2:c.490G>C	p.Val164Leu	p.V164L	ENST00000406277	NM_152274.4	164	Gtt/Ctt	6/7	0.480603065297063	2	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.480603065297063	2		430	810	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389363	8389363	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	163	532	0	ENST00000356435.5:c.4255T>C	p.Tyr1419His	p.Y1419H	ENST00000356435		1419	Tat/Cat	26/35	0.350066085066859	2	FACETS	1	0.971	1	0.554	0.511	0.599	CLONAL	1	TRUE	0	0.480603065297063	2		532	612	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69229763	69230449	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTAGTATTTTTTTTCCCCTCTAATTATATTGGAAAATTATTAAATATTTTCTATGTTCATTGACTTTGAGATTGAAATAATATTATTCAGATTTCACTTGAAATCTTTACCTCTTGATTTGTTTAAACTAACACATTGGTTTGTGGACTTGAGGATTTCATAGTTCTTTATCATCTGATTTATATTATTATATTACTACTAATTGCCAAGAAGTCAATAGACCTCAATGAACATGCTTATTATAATGGTCTGTTCACTTTTAAAAACATATAATTCAACTACTGTTTTAATATTAACTTACTTTCTATAAAAGTAAAACATGCATACAGTTAAAGTCAAGTAGTACCCTTAGAGATCTGTTTCCCAGAAGTGACTGCCTTTAACATTTCTAGCTATTTCCCTATTATTTAATATCTCCATATTAGTTATTTATGAAGTAAAACCACCTAGCTGAATGTTTTGTTTTATTCATCCTAAACATCCTTTGTATTGACTTTTACCATTGTGGGTAAGGATTTCTCTCTCCTCCATTTTTTCCCCCTTTACACTCACTTACTCTATTTGATATTGTCTAAGGCTTTCTCATATATTGTAGTACATGATATTTGTTTAGGACTTATTACTAGGAAGCCTTCTGATTGAAGGAAATAGGGCGATGAATTGATGCTAATGAATGTGTTTTATT	AGGTAGTATTTTTTTTCCCCTCTAATTATATTGGAAAATTATTAAATATTTTCTATGTTCATTGACTTTGAGATTGAAATAATATTATTCAGATTTCACTTGAAATCTTTACCTCTTGATTTGTTTAAACTAACACATTGGTTTGTGGACTTGAGGATTTCATAGTTCTTTATCATCTGATTTATATTATTATATTACTACTAATTGCCAAGAAGTCAATAGACCTCAATGAACATGCTTATTATAATGGTCTGTTCACTTTTAAAAACATATAATTCAACTACTGTTTTAATATTAACTTACTTTCTATAAAAGTAAAACATGCATACAGTTAAAGTCAAGTAGTACCCTTAGAGATCTGTTTCCCAGAAGTGACTGCCTTTAACATTTCTAGCTATTTCCCTATTATTTAATATCTCCATATTAGTTATTTATGAAGTAAAACCACCTAGCTGAATGTTTTGTTTTATTCATCCTAAACATCCTTTGTATTGACTTTTACCATTGTGGGTAAGGATTTCTCTCTCCTCCATTTTTTCCCCCTTTACACTCACTTACTCTATTTGATATTGTCTAAGGCTTTCTCATATATTGTAGTACATGATATTTGTTTAGGACTTATTACTAGGAAGCCTTCTGATTGAAGGAAATAGGGCGATGAATTGATGCTAATGAATGTGTTTTATT	-	novel	NA	P-0019978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	22	279	0	ENST00000462284.1:c.840+4_843del		p.X280_splice	ENST00000462284	NM_002392.5	280		9/11	0.350066085066859	2	FACETS	0.251	0.194	0.317	0.125	0.097	0.159	SUBCLONAL	1	TRUE	0	0.480603065297063	2		279	365	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38960598	38960598	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1450418574	NA	P-0019978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	79	239	0	ENST00000357387.3:c.1753A>G	p.Ser585Gly	p.S585G	ENST00000357387	NM_152756.3	585	Agt/Ggt	20/38	0.480603065297063	11	FACETS	1	0.917	1			1	CLONAL	1	TRUE	NA	0.480603065297063	11		239	982	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41904360	41904415	+	frameshift_variant	Frame_Shift_Del	DEL	ACCCAGGCCTTGCACTGCAGCCCCAATGCTGCCCGTGGCGATCATGGATGGCGGGT	ACCCAGGCCTTGCACTGCAGCCCCAATGCTGCCCGTGGCGATCATGGATGGCGGGT	-	novel	NA	P-0019978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	45	539	0	ENST00000372991.4:c.593_648del	p.Tyr198CysfsTer8	p.Y198Cfs*8	ENST00000372991	NM_001760.3	198	tACCCGCCATCCATGATCGCCACGGGCAGCATTGGGGCTGCAGTGCAAGGCCTGGGT/t	4/5	0.359052867820256	3	FACETS	0.272	0.227	0.321	0.136	0.113	0.161	SUBCLONAL	1	TRUE	1	0.480603065297063	3		539	855	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020830-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	53	349	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		349	127	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0022066-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	2493	560	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.641010853397905	13	FACETS	1	0.991	1			1	CLONAL	12	TRUE	NA	0.641010853397905	13		560	2931	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061250	38061250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1459219194	NA	P-0022066-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	252	627	1	ENST00000250448.2:c.739C>T	p.His247Tyr	p.H247Y	ENST00000250448	NM_004496.3	247	Cac/Tac	2/2	1	2	FACETS	0.984	0.924	1	0.984	0.924	1	CLONAL	1	TRUE	1	0.641010853397905	2		628	799	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842468	68842468	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1555515232	NA	P-0022066-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	210	615	0	ENST00000261769.5:c.529C>T	p.Gln177Ter	p.Q177*	ENST00000261769	NM_004360.3	177	Cag/Tag	4/16	0.631281227989661	1	FACETS	0.974	0.916	1	0.974	0.916	1	CLONAL	1	TRUE	0	0.641010853397905	1		615	457	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326690	62326690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375593361	NA	P-0022066-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	308	746	0	ENST00000360203.5:c.3509G>A	p.Arg1170Gln	p.R1170Q	ENST00000360203	NM_001283009.1	1170	cGg/cAg	34/35	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.641010853397905	2		746	931	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808247	99808247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022066-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	212	579	0	ENST00000280892.6:c.442C>T	p.Arg148Cys	p.R148C	ENST00000280892	NM_001130678.1	148	Cgc/Tgc	5/7	1	2	FACETS	0.92	0.858	0.984	0.92	0.858	0.984	CLONAL	1	TRUE	1	0.641010853397905	2		579	719	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986817	36986817	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519223	NA	P-0022066-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	27	210	0	ENST00000354822.5:c.872C>T	p.Pro291Leu	p.P291L	ENST00000354822	NM_001079668.2	291	cCg/cTg	3/3	1	2	FACETS	0.337	0.269	0.414	0.337	0.269	0.414	SUBCLONAL	1	TRUE	1	0.641010853397905	2		210	250	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457304	67457304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223765	NA	P-0022087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	242	803	1	ENST00000327367.4:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000327367	NM_005902.3	93	cGa/cAa	2/9	0.224940130495961	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.227526333757915	2		804	1043	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181006	32181006	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	99	802	0	ENST00000375023.3:c.2344T>G	p.Cys782Gly	p.C782G	ENST00000375023	NM_004557.3	782	Tgt/Ggt	15/30	0.227526333757915	4	FACETS	0.845	0.752	0.945	0.423	0.376	0.473	CLONAL	1	TRUE	2	0.227526333757915	4		802	1264	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0022146-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	243	256	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.618429882552311	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	FALSE	2	0.618429882552311	4		256	579	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0022146-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	169	558	0				ENST00000310581	NM_198253.2	-/1132			0.186280088837261	5	FACETS	1	0.985	1	0.819	0.761	0.877	INDETERMINATE	2	FALSE	2	0.618429882552311	5		558	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0022146-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	316	654	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.618429882552311	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	FALSE	0	0.618429882552311	2		654	480	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518437	204518437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201947927	NA	P-0022146-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	111	557	2	ENST00000367182.3:c.1100C>T	p.Ser367Leu	p.S367L	ENST00000367182	NM_001278516.1	367	tCg/tTg	11/11	0.618429882552311	3	FACETS	0.957	0.865	1	0.479	0.432	0.527	CLONAL	1	FALSE	1	0.618429882552311	3		559	491	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0022146-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	184	839	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	0.618429882552311	3	FACETS	0.924	0.854	0.997	0.462	0.427	0.499	CLONAL	1	FALSE	1	0.618429882552311	3		839	843	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434062	49434063	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0022146-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	119	620	0	ENST00000301067.7:c.7490_7491delinsAT	p.Ala2497Asp	p.A2497D	ENST00000301067	NM_003482.3	2497	gCC/gAT	31/54	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.618429882552311	2		620	363	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78866553	78866553	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145440027	NA	P-0022146-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	313	720	2	ENST00000306801.3:c.2126G>A	p.Arg709Gln	p.R709Q	ENST00000306801	NM_020761.2	709	cGa/cAa	19/34	0.618429882552311	2	FACETS	0.959	0.917	0.999	0.959	0.917	0.999	CLONAL	2	FALSE	0	0.618429882552311	2		722	528	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262932	46262932	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs6094756	NA	P-0022146-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	245	569	0	ENST00000371998.3:c.1105C>T	p.Leu369Phe	p.L369F	ENST00000371998		369	Ctt/Ttt	10/23	0.473258680190428	4	FACETS	0.999	0.94	1	0.999	0.94	1	CLONAL	2	FALSE	2	0.618429882552311	4		569	642	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158175	106158175	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022146-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	222	434	0	ENST00000380013.4:c.3076G>A	p.Glu1026Lys	p.E1026K	ENST00000380013	NM_001127208.2	1026	Gag/Aag	3/11	0.615454949425109	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	FALSE	0	0.618429882552311	2		434	350	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93973581	93973581	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1179394255	NA	P-0022146-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	199	465	0	ENST00000369303.4:c.1795C>T	p.His599Tyr	p.H599Y	ENST00000369303	NM_004440.3	599	Cat/Tat	9/17	0.618429882552311	3	FACETS	0.865	0.809	0.921	0.865	0.809	0.921	CLONAL	2	FALSE	1	0.618429882552311	3		465	487	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686904	117686904	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022146-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	43	277	0	ENST00000368508.3:c.2813G>A	p.Gly938Glu	p.G938E	ENST00000368508	NM_002944.2	938	gGg/gAg	19/43	0.618429882552311	3	FACETS	0.855	0.723	0.998	0.427	0.361	0.499	CLONAL	1	FALSE	1	0.618429882552311	3		277	213	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500990	8500990	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022146-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	127	601	0	ENST00000356435.5:c.1892A>C	p.Gln631Pro	p.Q631P	ENST00000356435		631	cAa/cCa	13/35	0.618429882552311	1	FACETS	0.892	0.82	0.966	0.892	0.82	0.966	CLONAL	1	FALSE	0	0.618429882552311	1		601	318	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971170	21971170	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022146-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	169	199	0	ENST00000304494.5:c.188T>C	p.Leu63Pro	p.L63P	ENST00000304494	NM_000077.4	63	cTg/cCg	2/3	0.618429882552311	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	0	0.618429882552311	1		199	296	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	374	609	0	ENST00000206249.3:c.1609T>G	p.Tyr537Asp	p.Y537D	ENST00000206249	NM_000125.3	537	Tat/Gat	8/8	0.812996520702184	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.836832256737734	1		609	482	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245586	41245587	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs80357522	NA	P-0022166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1519	410	1035	4	ENST00000357654.3:c.1961dup	p.Tyr655ValfsTer18	p.Y655Vfs*18	ENST00000357654	NM_007294.3	654	aag/aaAg	10/23	0.80539916988264	4	FACETS	0.933	0.885	0.982	0.467	0.442	0.491	CLONAL	1	TRUE	2	0.836832256737734	4		1039	1929	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27204960	27204960	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	311	580	0	ENST00000380036.4:c.2261C>T	p.Ser754Phe	p.S754F	ENST00000380036	NM_000459.3	754	tCt/tTt	14/23	1	2	FACETS	0.982	0.931	1	0.982	0.931	1	CLONAL	1	TRUE	1	0.836832256737734	2		580	757	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216703	7216704	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	558	475	0	ENST00000380728.2:c.719dup	p.Thr241AspfsTer20	p.T241Dfs*20	ENST00000380728		240	cag/caAg	8/11	NA	2	FACETS	0.998	0.977	1			1	INDETERMINATE	2	TRUE	NA	0.836832256737734	2		475	668	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798830	42798830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	465	897	0	ENST00000575354.2:c.4402G>A	p.Asp1468Asn	p.D1468N	ENST00000575354	NM_015125.3	1468	Gac/Aac	19/20	0.78281474072117	3	FACETS	0.969	0.925	1	0.485	0.462	0.508	CLONAL	1	TRUE	1	0.836832256737734	3		897	1626	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591247	67591247	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0022166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	235	390	0	ENST00000274335.5:c.1746-1G>T		p.X582_splice	ENST00000274335		582			0.837102579675503	3	FACETS	1	0.958	1	0.515	0.482	0.549	CLONAL	1	TRUE	1	0.836832256737734	3		390	773	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426492	49426492	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1392	548	1129	3	ENST00000301067.7:c.11996C>G	p.Pro3999Arg	p.P3999R	ENST00000301067	NM_003482.3	3999	cCt/cGt	39/54	0.599107442638085	3	FACETS	0.958	0.917	0.999			1	CLONAL	1	TRUE	NA	0.836832256737734	3		1132	1940	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570832	226570832	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746522692	NA	P-0022166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	311	613	1	ENST00000366794.5:c.1064G>A	p.Arg355His	p.R355H	ENST00000366794	NM_001618.3	355	cGt/cAt	8/23	0.837102579675503	3	FACETS	0.93	0.877	0.984			1	CLONAL	1	TRUE	NA	0.836832256737734	3		614	1134	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245415	41245600	+	inframe_deletion	In_Frame_Del	DEL	CTTAGTAAAAGAACCAGGTGCATTTGTTAACTTCAGCTCTGGGAAAGTATCGCTGTCATGTCTTTTACTTGTCTGTTCATTTGGCTTGTTACTCTTCTTGGCTCCAGTTGCAGGTTCTTTACCTTCCATGAGTTGTAGGTTTCTGCTGTGCCTGACTGGCATTTGGTTGTACTTTTTTTTCTTTAT	CTTAGTAAAAGAACCAGGTGCATTTGTTAACTTCAGCTCTGGGAAAGTATCGCTGTCATGTCTTTTACTTGTCTGTTCATTTGGCTTGTTACTCTTCTTGGCTCCAGTTGCAGGTTCTTTACCTTCCATGAGTTGTAGGTTTCTGCTGTGCCTGACTGGCATTTGGTTGTACTTTTTTTTCTTTAT	-	novel	NA	P-0022166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1546	365	926	0	ENST00000357654.3:c.1948_2133del	p.Ile650_Lys711del	p.I650_K711del	ENST00000357654	NM_007294.3	650	ATAAAGAAAAAAAAGTACAACCAAATGCCAGTCAGGCACAGCAGAAACCTACAACTCATGGAAGGTAAAGAACCTGCAACTGGAGCCAAGAAGAGTAACAAGCCAAATGAACAGACAAGTAAAAGACATGACAGCGATACTTTCCCAGAGCTGAAGTTAACAAATGCACCTGGTTCTTTTACTAAG/-	10/23	0.80539916988264	4	FACETS	0.838	0.792	0.886	0.419	0.396	0.443	CLONAL	1	TRUE	2	0.836832256737734	4		926	1911	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656835	45656835	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	356	630	0	ENST00000407780.3:c.321C>G	p.Asp107Glu	p.D107E	ENST00000407780	NM_001283052.1	107	gaC/gaG	3/7	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.836832256737734	2		630	795	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127530	55127530	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1448	225	399	0	ENST00000257290.5:c.318G>T	p.Gln106His	p.Q106H	ENST00000257290	NM_006206.4	106	caG/caT	3/23	0.836832256737734	7	FACETS	0.994	0.922	1	0.248	0.23	0.267	CLONAL	1	TRUE	3	0.836832256737734	7		399	1673	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044859	47044859	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	396	888	1	ENST00000377604.3:c.2185G>T	p.Val729Leu	p.V729L	ENST00000377604	NM_001204468.1	729	Gtg/Ttg	20/24	0.78281474072117	3	FACETS	0.935	0.888	0.983	0.467	0.444	0.492	CLONAL	1	TRUE	1	0.836832256737734	3		889	1436	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443695	29443695	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs863225281	NA	P-0121444-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	366	544	0	ENST00000389048.3:c.3522C>G	p.Phe1174Leu	p.F1174L	ENST00000389048	NM_004304.4	1174	ttC/ttG	23/29	0.72466955027136	3	FACETS	1	0.96	1	0.669	0.64	0.697	CLONAL	2	NA	0	0.72466955027136	3		544	686	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224189	36224189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376011791	NA	P-0121444-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	116	704	0	ENST00000222270.7:c.6739G>A	p.Gly2247Arg	p.G2247R	ENST00000222270	NM_014727.1	2247	Gga/Aga	28/37	0.72466955027136	3	FACETS	0.598	0.539	0.66	0.299	0.269	0.33	SUBCLONAL	1	NA	1	0.72466955027136	3		704	729	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914127	32914127	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs55996097	NA	P-0121444-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	246	472	1	ENST00000380152.3:c.5635G>T	p.Glu1879Ter	p.E1879*	ENST00000380152		1879	Gag/Tag	11/27	0.474948044413499	4	FACETS	1	0.976	1	0.531	0.501	0.562	CLONAL	2	NA	0	0.72466955027136	4		473	551	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363415	40363415	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121444-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	93	800	0	ENST00000397332.2:c.814G>T	p.Ala272Ser	p.A272S	ENST00000397332	NM_001033082.2	272	Gct/Tct	3/3	0.72466955027136	3	FACETS	0.36	0.32	0.404	0.18	0.16	0.202	SUBCLONAL	1	NA	1	0.72466955027136	3		800	970	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444390	50444390	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0121444-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	54	363	0	ENST00000331340.3:c.320T>G	p.Val107Gly	p.V107G	ENST00000331340	NM_006060.4	107	gTt/gGt	4/8	0.72466955027136	4	FACETS	0.288	0.245	0.335	0.096	0.081	0.112	SUBCLONAL	1	NA	1	0.72466955027136	4		363	893	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0022651-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	305	622	0	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	0.445844346967286	2	FACETS	0.915	0.868	0.963	0.915	0.868	0.963	CLONAL	2	TRUE	0	0.452298260146224	2		622	737	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166763	32166763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761314959	NA	P-0022651-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	371	676	0	ENST00000375023.3:c.4475G>A	p.Arg1492Gln	p.R1492Q	ENST00000375023	NM_004557.3	1492	cGg/cAg	24/30	0.452298260146224	5	FACETS	0.99	0.939	1	0.66	0.626	0.696	CLONAL	2	TRUE	2	0.452298260146224	5		676	1390	SUCCESS
AR	367	MSKCC	GRCh37	X	66765533	66765533	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022651-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	145	620	0	ENST00000374690.3:c.545A>G	p.Lys182Arg	p.K182R	ENST00000374690	NM_000044.3	182	aAa/aGa	1/8	0.377517495408126	4	FACETS	0.781	0.711	0.855	0.391	0.355	0.428	SUBCLONAL	1	TRUE	2	0.452298260146224	4		620	1192	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349257	15349257	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0022861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	368	462	0	ENST00000263377.2:c.4021-1G>C		p.X1341_splice	ENST00000263377	NM_058243.2	1341			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		462	531	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391803	139391803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022960-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	34	526	0	ENST00000277541.6:c.6388G>A	p.Gly2130Arg	p.G2130R	ENST00000277541	NM_017617.3	2130	Ggg/Agg	34/34	1	2	FACETS	0.267	0.218	0.323	0.267	0.218	0.323	SUBCLONAL	1	TRUE	1	0.61	2		526	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578189	7578189	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1567551150	NA	P-0023401-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	358	720	1	ENST00000269305.4:c.660T>A	p.Tyr220Ter	p.Y220*	ENST00000269305	NM_001126112.2	220	taT/taA	6/11	0.5233993727224	2	FACETS	0.955	0.913	0.996	0.955	0.913	0.996	CLONAL	2	TRUE	0	0.549716054556368	2		721	682	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981495	55981495	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023401-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	124	414	0	ENST00000263923.4:c.442del	p.Ile148PhefsTer44	p.I148Ffs*44	ENST00000263923	NM_002253.2	148	Att/tt	4/30	0.549716054556368	3	FACETS	0.904	0.82	0.993	0.452	0.41	0.497	CLONAL	1	TRUE	1	0.549716054556368	3		414	636	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795373	39795373	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs760655364	NA	P-0023401-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	128	566	0	ENST00000288319.7:c.347C>A	p.Pro116Gln	p.P116Q	ENST00000288319	NM_182918.3	116	cCa/cAa	3/10	0.549716054556368	2	FACETS	0.856	0.779	0.936	0.428	0.389	0.468	CLONAL	1	TRUE	0	0.549716054556368	2		566	544	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	23	349	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.81	0.632	1	0.81	0.632	1	CLONAL	1	TRUE	1	0.2	2		349	284	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0023450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	81	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.241424996461867	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.2	2		539	348	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101195	27101195	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	43	783	0	ENST00000324856.7:c.4477C>T	p.Gln1493Ter	p.Q1493*	ENST00000324856	NM_006015.4	1493	Cag/Tag	18/20	1	2	FACETS	0.927	0.776	1	0.927	0.776	1	CLONAL	1	TRUE	1	0.2	2		783	464	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107180	27107180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1308037041	NA	P-0023450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	74	709	0	ENST00000324856.7:c.6791C>T	p.Ser2264Leu	p.S2264L	ENST00000324856	NM_006015.4	2264	tCa/tTa	20/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.2	2		709	633	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519874	NA	P-0023450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	44	600	0	ENST00000356142.4:c.85C>A	p.Pro29Thr	p.P29T	ENST00000356142	NM_018890.3	29	Cct/Act	2/7	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.2	2		600	415	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828180	3828180	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	26	338	1	ENST00000262367.5:c.1945G>T	p.Glu649Ter	p.E649*	ENST00000262367	NM_004380.2	649	Gaa/Taa	10/31	0.170172189933522	3	FACETS	1	0.848	1	0.542	0.43	0.669	CLONAL	1	TRUE	1	0.2	3		339	264	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101360	27101360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	60	648	1	ENST00000324856.7:c.4642C>T	p.His1548Tyr	p.H1548Y	ENST00000324856	NM_006015.4	1548	Cat/Tat	18/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.2	2		649	511	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981809	201981809	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	146	667	1	ENST00000359651.3:c.520C>T	p.Gln174Ter	p.Q174*	ENST00000359651		174	Cag/Tag	4/8	0.125401093977444	3	FACETS	1	0.972	1	0.764	0.698	0.832	CLONAL	2	TRUE	0	0.2	3		668	701	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983105	201983105	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	99	653	0	ENST00000359651.3:c.954G>C	p.Lys318Asn	p.K318N	ENST00000359651		318	aaG/aaC	7/8	0.125401093977444	3	FACETS	0.929	0.831	1	0.619	0.554	0.689	CLONAL	2	TRUE	0	0.2	3		653	586	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274824	123274824	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	122	493	0	ENST00000358487.5:c.1094G>C	p.Arg365Thr	p.R365T	ENST00000358487	NM_000141.4	365	aGa/aCa	9/18	0.2345800764419	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	TRUE	0	0.2	3		493	385	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118350916	118350916	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	56	536	0	ENST00000534358.1:c.3597G>C	p.Trp1199Cys	p.W1199C	ENST00000534358	NM_005933.3	1199	tgG/tgC	6/36	1	2	FACETS	0.816	0.703	0.939	1	0.972	1	CLONAL	2	TRUE	1	0.2	2		536	343	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373813	118373814	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	35	366	0	ENST00000534358.1:c.7210dup	p.Thr2404AsnfsTer21	p.T2404Nfs*21	ENST00000534358	NM_005933.3	2402	-/A	27/36	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.2	2		366	242	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869472	102869472	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	98	524	1	ENST00000307046.8:c.169G>A	p.Glu57Lys	p.E57K	ENST00000307046	NM_001111285.1	57	Gag/Aag	2/4	0.241424996461867	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.2	2		525	430	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061334	38061334	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	65	600	1	ENST00000250448.2:c.655del	p.Arg219AlafsTer102	p.R219Afs*102	ENST00000250448	NM_004496.3	219	Cgc/gc	2/2	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.2	2		601	565	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124285	2124285	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	64	798	0	ENST00000219476.3:c.2440G>C	p.Glu814Gln	p.E814Q	ENST00000219476	NM_000548.3	814	Gag/Cag	22/42	0.170172189933522	3	FACETS	0.932	0.806	1	0.466	0.403	0.535	CLONAL	1	TRUE	1	0.2	3		798	755	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804406	46804406	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0023450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	35	460	0	ENST00000290295.7:c.602-1G>C		p.X201_splice	ENST00000290295	NM_006361.5	201			1	2	FACETS	0.877	0.719	1	0.877	0.719	1	CLONAL	1	TRUE	1	0.2	2		460	399	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017232	31017232	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0023450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	126	309	0	ENST00000375687.4:c.563C>G	p.Ser188Ter	p.S188*	ENST00000375687	NM_015338.5	188	tCa/tGa	7/13	0.245308265121467	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	3	TRUE	0	0.2	3		309	413	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39713173	39713173	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	96	294	0	ENST00000361337.2:c.579G>C	p.Lys193Asn	p.K193N	ENST00000361337	NM_003286.2	193	aaG/aaC	8/21	0.245308265121467	3	FACETS	0.898	0.811	0.988	1	0.97	1	CLONAL	4	TRUE	0	0.2	3		294	294	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119562146	119562146	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	37	512	0	ENST00000316626.5:c.1190T>A	p.Ile397Asn	p.I397N	ENST00000316626		397	aTt/aAt	11/12	0.112060757612993	3	FACETS	0.705	0.58	0.846	0.353	0.29	0.423	INDETERMINATE	1	TRUE	1	0.2	3		512	577	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0023695-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	123	435	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	0.956	0.867	1	0.956	0.867	1	CLONAL	1	TRUE	1	0.41351465795058	2		435	622	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039427	49039427	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023695-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	145	436	0	ENST00000267163.4:c.2412C>G	p.Ile804Met	p.I804M	ENST00000267163	NM_000321.2	804	atC/atG	23/27	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.41351465795058	2		436	692	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923789	72923790	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0023695-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	140	542	0	ENST00000268489.5:c.3288dup	p.Thr1097HisfsTer58	p.T1097Hfs*58	ENST00000268489	NM_006885.3	1096	-/C	4/10	1	2	FACETS	0.923	0.841	1	0.923	0.841	1	CLONAL	1	TRUE	1	0.41351465795058	2		542	734	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143968	11143968	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023742-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	281	75	0	ENST00000358026.2:c.3550del	p.Leu1184CysfsTer32	p.L1184Cfs*32	ENST00000358026	NM_001128849.1	1183	gaC/ga	26/36	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.665296631464985	2		75	804	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0023910-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	85	562	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.476563177153229	3	FACETS	0.962	0.88	1	0.962	0.88	1	CLONAL	3	TRUE	0	0.476563177153229	3		562	153	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0023910-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	13	523	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.476563177153229	3	FACETS	0.341	0.243	0.46	0.114	0.081	0.154	SUBCLONAL	1	TRUE	0	0.476563177153229	3		523	198	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280314	1280314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561203868	NA	P-0023910-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	187	671	0	ENST00000310581.5:c.1909G>A	p.Asp637Asn	p.D637N	ENST00000310581	NM_198253.2	637	Gac/Aac	4/16	0.476563177153229	9	FACETS	1	0.969	1			1	CLONAL	5	TRUE	NA	0.476563177153229	9		671	397	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445007	89445007	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023910-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	53	390	0	ENST00000336596.2:c.1327A>G	p.Ile443Val	p.I443V	ENST00000336596	NM_005233.5	443	Att/Gtt	6/17	0.476563177153229	3	FACETS	0.81	0.704	0.922	0.81	0.704	0.922	CLONAL	2	TRUE	1	0.476563177153229	3		390	170	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039380	47039380	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0023910-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	99	576	1	ENST00000377604.3:c.1003A>T	p.Lys335Ter	p.K335*	ENST00000377604	NM_001204468.1	335	Aag/Tag	10/24	0.476563177153229	2	FACETS	0.955	0.889	1	1	0.988	1	CLONAL	3	TRUE	0	0.476563177153229	2		577	145	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207064	1207065	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1131690917	NA	P-0025031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	241	561	0	ENST00000326873.7:c.157dup	p.Asp53GlyfsTer110	p.D53Gfs*110	ENST00000326873	NM_000455.4	51	atg/atGg	1/10	0.483826666684296	1	FACETS	0.83	0.777	0.885	0.83	0.777	0.885	CLONAL	1	TRUE	0	0.499891779739075	1		561	871	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968200	134968200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143309901	NA	P-0025031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	184	385	0	ENST00000398015.3:c.2713C>T	p.Arg905Cys	p.R905C	ENST00000398015	NM_004441.4	905	Cgc/Tgc	15/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.499891779739075	2		385	690	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434122	12434122	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1170672782	NA	P-0025031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	126	244	1	ENST00000287820.6:c.490C>T	p.Arg164Trp	p.R164W	ENST00000287820	NM_015869.4	164	Cgg/Tgg	4/7	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.499891779739075	2		245	501	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519792	29519792	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	161	449	0	ENST00000389048.3:c.1779G>T	p.Trp593Cys	p.W593C	ENST00000389048	NM_004304.4	593	tgG/tgT	9/29	0.468524586311431	1	FACETS	0.913	0.843	0.985	0.913	0.843	0.985	CLONAL	1	TRUE	0	0.499891779739075	1		449	529	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061145	38061145	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	71	255	0	ENST00000250448.2:c.844A>C	p.Ser282Arg	p.S282R	ENST00000250448	NM_004496.3	282	Agc/Cgc	2/2	1	2	FACETS	0.721	0.632	0.816	0.721	0.632	0.816	SUBCLONAL	1	TRUE	1	0.499891779739075	2		255	394	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619222	43619222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	140	384	1	ENST00000355710.3:c.2905C>T	p.Arg969Trp	p.R969W	ENST00000355710	NM_020975.4	969	Cgg/Tgg	17/20	1	2	FACETS	0.888	0.811	0.968	0.888	0.811	0.968	CLONAL	1	TRUE	1	0.499891779739075	2		385	631	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982980	201982981	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGTTC	novel	NA	P-0025031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	241	533	0	ENST00000359651.3:c.831_835dup	p.Ile279SerfsTer17	p.I279Sfs*17	ENST00000359651		277	gag/gAGTTCag	7/8	1	2	FACETS	0.974	0.91	1	0.974	0.91	1	CLONAL	1	TRUE	1	0.499891779739075	2		533	990	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577270	64577271	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GACA	novel	NA	P-0025031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	210	510	1	ENST00000312049.6:c.308_311dup	p.Leu105ValfsTer13	p.L105Vfs*13	ENST00000312049	NM_130799.2	104	tcc/tcTGTCc	2/10	0.424450573641859	1	FACETS	0.854	0.796	0.914	0.854	0.796	0.914	CLONAL	1	TRUE	0	0.499891779739075	1		511	738	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245598	46245599	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TACT	novel	NA	P-0025031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	106	200	0	ENST00000334344.6:c.3693_3696dup	p.Ala1233TyrfsTer9	p.A1233Yfs*9	ENST00000334344	NM_152641.2	1231	act/acTACTt	15/21	1	2	FACETS	0.964	0.87	1	0.964	0.87	1	CLONAL	1	TRUE	1	0.499891779739075	2		200	440	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820922	3820925	+	frameshift_variant	Frame_Shift_Del	DEL	TAGC	TAGC	-	novel	NA	P-0025031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	189	547	0	ENST00000262367.5:c.2526_2529del	p.Gln842HisfsTer6	p.Q842Hfs*6	ENST00000262367	NM_004380.2	842	caGCTA/ca	14/31	1	2	FACETS	0.815	0.753	0.879	0.815	0.753	0.879	CLONAL	1	TRUE	1	0.499891779739075	2		547	928	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577563	7577571	+	inframe_deletion	In_Frame_Del	DEL	TGTTACACA	TGTTACACA	-	novel	NA	P-0025031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	205	524	0	ENST00000269305.4:c.710_718del	p.Met237_Asn239del	p.M237_N239del	ENST00000269305	NM_001126112.2	237	aTGTGTAACAgt/agt	7/11	0.483826666684296	1	FACETS	0.903	0.842	0.967	0.903	0.842	0.967	CLONAL	1	TRUE	0	0.499891779739075	1		524	681	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795383	42795386	+	frameshift_variant	Frame_Shift_Del	DEL	AATC	AATC	-	novel	NA	P-0025031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	162	396	0	ENST00000575354.2:c.2464_2467del	p.Ile822ProfsTer101	p.I822Pfs*101	ENST00000575354	NM_015125.3	821	ggAATC/gg	10/20	0.483826666684296	1	FACETS	0.93	0.859	1	0.93	0.859	1	CLONAL	1	TRUE	0	0.499891779739075	1		396	523	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024905	31024906	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0025031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	206	446	0	ENST00000375687.4:c.4391_4392del	p.Pro1464GlnfsTer31	p.P1464Qfs*31	ENST00000375687	NM_015338.5	1464	CCc/c	13/13	1	2	FACETS	0.992	0.922	1	0.992	0.922	1	CLONAL	1	TRUE	1	0.499891779739075	2		446	831	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163623	47163623	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	121	279	0	ENST00000409792.3:c.2503del	p.Ile835TyrfsTer7	p.I835Yfs*7	ENST00000409792	NM_014159.6	835	Ata/ta	3/21	1	2	FACETS	0.874	0.793	0.959	0.874	0.793	0.959	CLONAL	1	TRUE	1	0.499891779739075	2		279	554	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524954	187524955	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0025031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	211	548	0	ENST00000441802.2:c.10725_10726insTT	p.Asp3576LeufsTer4	p.D3576Lfs*4	ENST00000441802	NM_005245.3	3575	-/TT	19/27	0.499891779739075	1	FACETS	0.796	0.741	0.853	0.796	0.741	0.853	SUBCLONAL	1	TRUE	0	0.499891779739075	1		548	795	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402572	20402573	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CACT	novel	NA	P-0025031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	196	463	0	ENST00000346618.3:c.110_113dup	p.Leu39ThrfsTer129	p.L39Tfs*129	ENST00000346618	NM_001949.4	37	gca/gCACTca	1/7	1	2	FACETS	0.932	0.864	1	0.932	0.864	1	CLONAL	1	TRUE	1	0.499891779739075	2		463	841	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518270	8518270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556357771	NA	P-0025071-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	54	369	1	ENST00000356435.5:c.1121C>T	p.Ala374Val	p.A374V	ENST00000356435		374	gCg/gTg	10/35	0.326430588252461	1	FACETS	0.679	0.581	0.785	0.679	0.581	0.785	SUBCLONAL	1	TRUE	0	0.326430588252461	1		370	408	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421614	49421614	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025071-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	77	788	0	ENST00000301067.7:c.14615A>G	p.Gln4872Arg	p.Q4872R	ENST00000301067	NM_003482.3	4872	cAa/cGa	47/54	0.200962249561158	3	FACETS	0.659	0.577	0.747	0.22	0.192	0.249	SUBCLONAL	1	TRUE	0	0.326430588252461	3		788	833	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923159	48923159	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025071-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	215	403	0	ENST00000267163.4:c.607+1del		p.G203fs	ENST00000267163	NM_000321.2	203	Ggg/gg	6/27	0.326430588252461	3	FACETS	0.969	0.909	1			1	CLONAL	3	TRUE	NA	0.326430588252461	3		403	527	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831080	72831080	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025071-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	68	509	0	ENST00000268489.5:c.5501A>G	p.Asp1834Gly	p.D1834G	ENST00000268489	NM_006885.3	1834	gAt/gGt	9/10	0.200962249561158	3	FACETS	0.934	0.814	1	0.311	0.271	0.355	CLONAL	1	TRUE	0	0.326430588252461	3		509	519	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125305	47125305	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025071-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	79	682	0	ENST00000409792.3:c.5965G>C	p.Asp1989His	p.D1989H	ENST00000409792	NM_014159.6	1989	Gat/Cat	12/21	1	2	FACETS	0.642	0.564	0.726	0.642	0.564	0.726	SUBCLONAL	1	TRUE	1	0.326430588252461	2		682	754	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738104	145738105	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCCAGTGGTGTGGGTGCAGCTCCAGGTAGCA	novel	NA	P-0025071-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	71	902	0	ENST00000428558.2:c.2773_2805dup	p.Cys925_Leu935dup	p.C925_L935dup	ENST00000428558	NM_004260.3	925	-/TGCTACCTGGAGCTGCACCCACACCACTGGCTG	17/22	0.297078343642805	3	FACETS	0.552	0.48	0.629			1	SUBCLONAL	1	TRUE	NA	0.326430588252461	3		902	917	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117629979	117629979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767792683	NA	P-0025071-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	59	500	0	ENST00000368508.3:c.6547C>T	p.Pro2183Ser	p.P2183S	ENST00000368508	NM_002944.2	2183	Cca/Tca	41/43	0.326430588252461	2	FACETS	0.638	0.549	0.734	0.319	0.274	0.367	SUBCLONAL	1	TRUE	0	0.326430588252461	2		500	567	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117630059	117630059	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025071-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	41	423	0	ENST00000368508.3:c.6467C>G	p.Thr2156Ser	p.T2156S	ENST00000368508	NM_002944.2	2156	aCt/aGt	41/43	0.326430588252461	2	FACETS	0.501	0.417	0.595	0.251	0.208	0.298	SUBCLONAL	1	TRUE	0	0.326430588252461	2		423	501	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196162	138196162	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025071-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	45	396	0	ENST00000237289.4:c.476A>C	p.Tyr159Ser	p.Y159S	ENST00000237289	NM_001270507.1	159	tAt/tCt	3/9	0.326430588252461	3	FACETS	0.519	0.435	0.612	0.259	0.217	0.306	SUBCLONAL	1	TRUE	1	0.326430588252461	3		396	618	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0025881-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	250	313	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.388606991541118	6	FACETS	0.909	0.856	0.962			1	CLONAL	4	TRUE	NA	0.388606991541118	6		313	629	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0025881-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	283	776	4	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.378896451259859	2	FACETS	0.949	0.897	1	0.949	0.897	1	CLONAL	2	TRUE	0	0.388606991541118	2		780	767	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555267	106555267	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025881-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3008	167	399	0	ENST00000369096.4:c.2384C>A	p.Ser795Ter	p.S795*	ENST00000369096	NM_001198.3	795	tCa/tAa	7/7	0.388606991541118	25	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.388606991541118	25		399	3175	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026464-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	145	349	0				ENST00000310581	NM_198253.2	-/1132			0.454859830311488	4	FACETS	1	0.949	1	0.691	0.638	0.746	CLONAL	2	TRUE	1	0.57029304839329	4		349	385	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0026464-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	115	256	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.915	0.83	1	0.915	0.83	1	CLONAL	1	TRUE	1	0.57029304839329	2		256	441	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73046198	73046198	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026464-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	93	279	0	ENST00000356692.5:c.10G>C	p.Glu4Gln	p.E4Q	ENST00000356692		4	Gag/Cag	1/9	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.57029304839329	2		279	293	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70350003	70350003	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026515-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	248	433	0	ENST00000374080.3:c.3986G>A	p.Arg1329Gln	p.R1329Q	ENST00000374080		1329	cGa/cAa	28/45	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.704915625646837	2		433	666	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187558044	187558044	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026515-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	156	292	0	ENST00000441802.2:c.3667C>G	p.Pro1223Ala	p.P1223A	ENST00000441802	NM_005245.3	1223	Ccc/Gcc	5/27	1	2	FACETS	0.975	0.901	1	0.975	0.901	1	CLONAL	1	TRUE	1	0.704915625646837	2		292	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579426	7579454	+	frameshift_variant	Frame_Shift_Del	DEL	TGGTGCAGGGGCCGCCGGTGTAGGAGCTG	TGGTGCAGGGGCCGCCGGTGTAGGAGCTG	GGCC	novel	NA	P-0026533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	292	750	3	ENST00000269305.4:c.233_261delinsGGCC	p.Ala78GlyfsTer37	p.A78Gfs*37	ENST00000269305	NM_001126112.2	78	gCAGCTCCTACACCGGCGGCCCCTGCACCA/gGGCC	4/11	0.516480256203047	2	FACETS	0.982	0.934	1	0.982	0.934	1	CLONAL	2	TRUE	0	0.516480256203047	2		753	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577519	7577519	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026552-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	145	412	2	ENST00000269305.4:c.762del	p.Ile255SerfsTer90	p.I255Sfs*90	ENST00000269305	NM_001126112.2	254	atC/at	7/11	0.164441429250023	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	2	TRUE	0	0.164441429250023	2		414	876	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278782	1278782	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026552-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	269	536	0	ENST00000310581.5:c.2260C>A	p.His754Asn	p.H754N	ENST00000310581	NM_198253.2	754	Cac/Aac	6/16	0.164441429250023	3	FACETS	0.915	0.86	0.972			1	CLONAL	4	TRUE	NA	0.164441429250023	3		536	967	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876364	35876364	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026552-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	193	497	0	ENST00000303115.3:c.1156A>T	p.Arg386Trp	p.R386W	ENST00000303115	NM_002185.3	386	Agg/Tgg	8/8	0.164441429250023	4	FACETS	1	0.978	1	0.854	0.792	0.919	CLONAL	3	TRUE	0	0.164441429250023	4		497	800	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570404	87570404	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026552-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	52	565	0	ENST00000277120.3:c.2144G>C	p.Arg715Pro	p.R715P	ENST00000277120		715	cGg/cCg	17/19	1	2	FACETS	0.81	0.688	0.944	0.81	0.688	0.944	CLONAL	1	TRUE	1	0.164441429250023	2		565	781	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410603	63410603	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1237782051	NA	P-0026552-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	133	602	0	ENST00000330258.3:c.2564A>G	p.His855Arg	p.H855R	ENST00000330258	NM_152424.3	855	cAt/cGt	2/2	0.133568588990735	3	FACETS	0.89	0.807	0.977	0.89	0.807	0.977	CLONAL	2	TRUE	1	0.164441429250023	3		602	984	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148875	119148876	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GG	GG	T	novel	NA	P-0026552-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	57	268	1	ENST00000264033.4:c.1096-1_1096delinsT		p.X366_splice	ENST00000264033	NM_005188.3	366		8/16	0.164441429250023	5	FACETS	0.829	0.712	0.957			1	CLONAL	2	TRUE	NA	0.164441429250023	5		269	521	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0027351-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	152	562	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.839	0.766	0.915	0.839	0.766	0.915	CLONAL	1	TRUE	1	0.348885333353614	2		562	1039	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087528	27087528	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027351-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	209	791	0	ENST00000324856.7:c.2102G>T	p.Gly701Val	p.G701V	ENST00000324856	NM_006015.4	701	gGc/gTc	5/20	1	2	FACETS	0.949	0.879	1	0.949	0.879	1	CLONAL	1	TRUE	1	0.348885333353614	2		791	1263	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039344	47039344	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027351-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	205	740	0	ENST00000377604.3:c.967T>G	p.Tyr323Asp	p.Y323D	ENST00000377604	NM_001204468.1	323	Tac/Gac	10/24	1	2	FACETS	0.928	0.859	1	0.928	0.859	1	CLONAL	1	TRUE	1	0.348885333353614	2		740	1266	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267359	198267359	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs377023736	NA	P-0027975-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	12	399	2	ENST00000335508.6:c.1998G>T	p.Lys666Asn	p.K666N	ENST00000335508	NM_012433.2	666	aaG/aaT	14/25	1	2	FACETS	0.098	0.068	0.134	0.098	0.068	0.134	SUBCLONAL	1	TRUE	1	0.614149090643817	2		401	400	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425424	49425424	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027975-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	98	592	1	ENST00000301067.7:c.13064C>T	p.Pro4355Leu	p.P4355L	ENST00000301067	NM_003482.3	4355	cCt/cTt	39/54	1	2	FACETS	0.847	0.761	0.935	0.847	0.761	0.935	CLONAL	1	TRUE	1	0.614149090643817	2		593	377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0028702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	363	879	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.836304258143844	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.836304258143844	1		879	499	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243941	41243941	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs62625308	NA	P-0028702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	398	662	0	ENST00000357654.3:c.3607C>T	p.Arg1203Ter	p.R1203*	ENST00000357654	NM_007294.3	1203	Cga/Tga	10/23	0.836304258143844	1	FACETS	0.992	0.96	1	0.992	0.96	1	CLONAL	1	TRUE	0	0.836304258143844	1		662	558	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533577	63533577	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs778137043	NA	P-0028702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	359	684	0	ENST00000307078.5:c.1577A>G	p.Lys526Arg	p.K526R	ENST00000307078	NM_004655.3	526	aAg/aGg	6/11	0.836304258143844	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.836304258143844	1		684	482	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347857	70347857	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	321	649	0	ENST00000374080.3:c.3096C>G	p.His1032Gln	p.H1032Q	ENST00000374080		1032	caC/caG	22/45	0.631517754932474	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.631517754932474	2		649	489	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	38	349	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.345908443157562	2		349	184	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0029592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	109	777	0	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.345908443157562	3	FACETS	0.638	0.572	0.71	0.319	0.286	0.355	SUBCLONAL	1	TRUE	1	0.345908443157562	3		777	1158	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941094	36941094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760367363	NA	P-0029592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	108	634	0	ENST00000361632.4:c.245C>T	p.Thr82Ile	p.T82I	ENST00000361632		82	aCc/aTc	3/16	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.345908443157562	2		634	593	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133559	55133559	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1206	2316	446	1	ENST00000257290.5:c.863A>G	p.Tyr288Cys	p.Y288C	ENST00000257290	NM_006206.4	288	tAc/tGc	6/23	0.345908443157562	31	FACETS	0.994	0.98	1			1	CLONAL	23	TRUE	NA	0.345908443157562	31		447	3522	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515208	106515208	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	70	405	0	ENST00000359195.3:c.2351G>T	p.Arg784Ile	p.R784I	ENST00000359195	NM_002649.2	784	aGa/aTa	5/11	0.32678526655583	3	FACETS	0.761	0.663	0.866	0.38	0.331	0.433	SUBCLONAL	1	TRUE	1	0.345908443157562	3		405	624	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92247520	92247520	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs902137115	NA	P-0030398-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	63	209	0	ENST00000265734.4:c.700G>A	p.Val234Met	p.V234M	ENST00000265734	NM_001259.6	234	Gtg/Atg	7/8	1	2	FACETS	0.773	0.679	0.872	0.773	0.679	0.872	SUBCLONAL	1	TRUE	1	0.775853384971913	2		209	210	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420097	41420097	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030398-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	76	298	0	ENST00000373198.4:c.224T>A	p.Met75Lys	p.M75K	ENST00000373198	NM_133170.3	75	aTg/aAg	3/32	1	2	FACETS	0.907	0.81	1	0.907	0.81	1	CLONAL	1	TRUE	1	0.775853384971913	2		298	216	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520006	NA	P-0030503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	308	581	0	ENST00000269305.4:c.821T>G	p.Val274Gly	p.V274G	ENST00000269305	NM_001126112.2	274	gTt/gGt	8/11	0.424720241696365	2	FACETS	0.845	0.802	0.89	0.845	0.802	0.89	CLONAL	2	TRUE	0	0.483789606479205	2		581	753	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121565	108121566	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0031268-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	168	534	0	ENST00000278616.4:c.1375dup	p.Leu459ProfsTer28	p.L459Pfs*28	ENST00000278616	NM_000051.3	458	tgc/tgCc	10/63	0.205427761209891	1	FACETS	0.994	0.916	1	1	0.992	1	CLONAL	2	TRUE	0	0.205427761209891	1		534	738	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645415	215645415	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs756647439	NA	P-0031268-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	273	777	0	ENST00000260947.4:c.1183C>A	p.Pro395Thr	p.P395T	ENST00000260947	NM_000465.2	395	Cca/Aca	4/11	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.205427761209891	2		777	1107	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577530	7577530	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs730882007	NA	P-0031325-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	54	666	0	ENST00000269305.4:c.751A>C	p.Ile251Leu	p.I251L	ENST00000269305	NM_001126112.2	251	Atc/Ctc	7/11	0.201637662589054	2	FACETS	0.989	0.846	1	0.494	0.423	0.572	CLONAL	1	TRUE	0	0.252878226131392	2		666	432	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81927400	81927400	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0031325-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	130	507	1	ENST00000359376.3:c.1072+1G>A		p.X358_splice	ENST00000359376	NM_002661.3	358			0.218175189181436	5	FACETS	1	0.946	1	0.706	0.641	0.773	CLONAL	2	TRUE	2	0.252878226131392	5		508	670	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662984	52662984	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031325-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	23	267	0	ENST00000394830.3:c.1369G>C	p.Glu457Gln	p.E457Q	ENST00000394830	NM_018313.4	457	Gaa/Caa	13/30	1	2	FACETS	0.669	0.522	0.838	0.669	0.522	0.838	SUBCLONAL	1	TRUE	1	0.252878226131392	2		267	272	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138197138	138197138	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031325-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	21	255	0	ENST00000237289.4:c.640A>T	p.Met214Leu	p.M214L	ENST00000237289	NM_001270507.1	214	Atg/Ttg	5/9	0.223168192003964	2	FACETS	0.589	0.454	0.746	0.294	0.227	0.373	SUBCLONAL	1	TRUE	0	0.252878226131392	2		255	282	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291519	15291519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031325-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	24	575	0	ENST00000263388.2:c.3115C>T	p.Pro1039Ser	p.P1039S	ENST00000263388	NM_000435.2	1039	Ccc/Tcc	19/33	0.0820769952566689	3	FACETS	0.469	0.367	0.587			1	INDETERMINATE	1	TRUE	NA	0.252878226131392	3		575	456	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	225	493	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	FALSE	1	0.478279136200306	2		493	728	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0031335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	49	879	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.291521140123847	0	FACETS	0.155	0.131	0.182			1	SUBCLONAL	1	FALSE	0	0.478279136200306	0		879	689	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0031335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	63	407	1	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.627	0.544	0.717	0.627	0.544	0.717	SUBCLONAL	1	FALSE	1	0.478279136200306	2		408	420	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0031335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	169	488	3	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.478279136200306	2		491	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	175	697	0	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.291521140123847	0	FACETS	0.434	0.399	0.47			1	SUBCLONAL	1	FALSE	0	0.478279136200306	0		697	880	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937104	39937104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	311	534	2	ENST00000378444.4:c.79G>A	p.Glu27Lys	p.E27K	ENST00000378444	NM_001123385.1	27	Gaa/Aaa	2/15	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	FALSE	1	0.478279136200306	2		536	911	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411576	63411576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	316	728	2	ENST00000330258.3:c.1591C>T	p.Arg531Ter	p.R531*	ENST00000330258	NM_152424.3	531	Cga/Tga	2/2	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.478279136200306	2		730	1109	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981241	201981241	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	280	747	0	ENST00000359651.3:c.320T>G	p.Leu107Arg	p.L107R	ENST00000359651		107	cTt/cGt	2/8	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.478279136200306	2		747	1000	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813715	50813715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	144	742	0	ENST00000398568.2:c.1269G>A	p.Met423Ile	p.M423I	ENST00000398568	NM_001042412.1	423	atG/atA	8/18	1	2	FACETS	0.57	0.519	0.624	0.57	0.519	0.624	SUBCLONAL	1	FALSE	1	0.478279136200306	2		742	1056	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113747	11113747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	112	581	0	ENST00000358026.2:c.1855G>A	p.Val619Met	p.V619M	ENST00000358026	NM_001128849.1	619	Gtg/Atg	12/36	1	2	FACETS	0.414	0.371	0.46	0.414	0.371	0.46	SUBCLONAL	1	FALSE	1	0.478279136200306	2		581	1131	SUCCESS
APC	324	MSKCC	GRCh37	5	112175656	112175656	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	127	392	0	ENST00000257430.4:c.4365del	p.Asn1455LysfsTer18	p.N1455Kfs*18	ENST00000257430	NM_000038.5	1455	aaT/aa	16/16	1	2	FACETS	0.865	0.786	0.948	0.865	0.786	0.948	CLONAL	1	FALSE	1	0.478279136200306	2		392	614	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0031338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	274	256	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.642176858281824	1	FACETS	0.736	0.7	0.77	0.736	0.7	0.77	SUBCLONAL	1	TRUE	0	0.869845752203286	1		256	484	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0031341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	394	527	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.574826181334822	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.760613474708412	3		527	700	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578383	7578383	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	357	514	0	ENST00000269305.4:c.547del	p.Ser183GlnfsTer64	p.S183Qfs*64	ENST00000269305	NM_001126112.2	183	Tca/ca	5/11	0.760613474708412	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.760613474708412	1		514	520	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139562760	139562760	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	332	750	0	ENST00000308874.7:c.26T>A	p.Leu9Gln	p.L9Q	ENST00000308874		9	cTg/cAg	3/10	1	2	FACETS	0.976	0.926	1	0.976	0.926	1	CLONAL	1	TRUE	1	0.760613474708412	2		750	894	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	177	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.221761761130952	7	FACETS	0.929	0.862	0.998			1	CLONAL	5	TRUE	NA	0.221761761130952	7		493	534	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579419	7579420	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs587783062	NA	P-0031352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	89	734	0	ENST00000269305.4:c.267dup	p.Ser90LeufsTer59	p.S90Lfs*59	ENST00000269305	NM_001126112.2	89	-/C	4/11	0.221761761130952	2	FACETS	0.876	0.78	0.978	0.876	0.78	0.978	CLONAL	2	TRUE	0	0.221761761130952	2		734	458	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543825	212543825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770003740	NA	P-0031352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	54	432	0	ENST00000342788.4:c.1574G>A	p.Arg525His	p.R525H	ENST00000342788	NM_005235.2	525	cGc/cAc	13/28	0.214328926439325	3	FACETS	0.8	0.687	0.923	0.8	0.687	0.923	CLONAL	2	TRUE	1	0.221761761130952	3		432	338	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449745	8449745	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1172700321	NA	P-0031352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	45	491	2	ENST00000356435.5:c.3968G>A	p.Arg1323His	p.R1323H	ENST00000356435		1323	cGc/cAc	23/35	0.153672802744682	0	FACETS	1	0.913	1			1	CLONAL	1	TRUE	0	0.221761761130952	0		493	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0031359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	344	765	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.831431162228473	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.831431162228473	1		765	441	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865050	57865050	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	452	948	0	ENST00000228682.2:c.2527C>A	p.His843Asn	p.H843N	ENST00000228682	NM_005269.2	843	Cat/Aat	12/12	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.831431162228473	2		948	996	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033919	49033929	+	frameshift_variant	Frame_Shift_Del	DEL	CACACCCTGCA	CACACCCTGCA	-	novel	NA	P-0031359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	256	543	0	ENST00000267163.4:c.2056_2066del	p.His686GlufsTer2	p.H686Efs*2	ENST00000267163	NM_000321.2	686	CACACCCTGCAg/g	20/27	0.831431162228473	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.831431162228473	1		543	351	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506708	103506708	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	154	286	0	ENST00000355739.4:c.451G>A	p.Glu151Lys	p.E151K	ENST00000355739	NM_000123.3	151	Gag/Aag	4/15	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.831431162228473	2		286	369	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331790	68331790	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	314	565	0	ENST00000487270.1:c.386C>A	p.Thr129Asn	p.T129N	ENST00000487270	NM_133509.3	129	aCc/aAc	5/11	1	2	FACETS	0.976	0.926	1	0.976	0.926	1	CLONAL	1	TRUE	1	0.831431162228473	2		565	774	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678541	88678541	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	417	462	0	ENST00000360948.2:c.995C>A	p.Thr332Lys	p.T332K	ENST00000360948	NM_001012338.2	332	aCg/aAg	9/19	0.831431162228473	3	FACETS	0.99	0.953	1	0.99	0.953	1	CLONAL	2	TRUE	1	0.831431162228473	3		462	717	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905710	50905710	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0031359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	366	956	2	ENST00000440232.2:c.759-1G>T		p.X253_splice	ENST00000440232	NM_002691.3	253			1	2	FACETS	0.951	0.905	0.997	0.951	0.905	0.997	CLONAL	1	TRUE	1	0.831431162228473	2		958	926	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934190	39934190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146403660	NA	P-0031359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	342	781	0	ENST00000378444.4:c.409G>A	p.Val137Ile	p.V137I	ENST00000378444	NM_001123385.1	137	Gtc/Atc	4/15	NA	2	FACETS	0.92	0.874	0.967			1	INDETERMINATE	1	TRUE	NA	0.831431162228473	2		781	894	SUCCESS
AR	367	MSKCC	GRCh37	X	66943561	66943561	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	199	514	0	ENST00000374690.3:c.2641C>G	p.Leu881Val	p.L881V	ENST00000374690	NM_000044.3	881	Ctg/Gtg	8/8	0.221386139323173	1	FACETS	0.547	0.511	0.584	0.547	0.511	0.584	INDETERMINATE	1	TRUE	0	0.831431162228473	1		514	511	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860098	151860098	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs571653303	NA	P-0031374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	104	504	0	ENST00000262189.6:c.10564A>G	p.Ile3522Val	p.I3522V	ENST00000262189	NM_170606.2	3522	Atc/Gtc	43/59	1	2	FACETS	0.769	0.689	0.853	0.769	0.689	0.853	SUBCLONAL	1	TRUE	1	0.408030132750179	2		504	663	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	99	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.3	1	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	0	0.27	1		493	627	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0031393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	61	445	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.25528715748278	0	FACETS	0.875	0.758	1			1	CLONAL	1	TRUE	0	0.27	0		445	377	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099479	27099479	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0031393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	91	401	0	ENST00000324856.7:c.3715+1G>A		p.X1239_splice	ENST00000324856	NM_006015.4	1239			0.243465263719684	2	FACETS	0.889	0.796	0.988	0.889	0.796	0.988	CLONAL	2	TRUE	0	0.27	2		401	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578232	7578232	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	108	619	0	ENST00000269305.4:c.617del	p.Leu206TrpfsTer41	p.L206Wfs*41	ENST00000269305	NM_001126112.2	206	tTg/tg	6/11	0.3	1	FACETS	0.987	0.887	1	0.987	0.887	1	CLONAL	1	TRUE	0	0.27	1		619	701	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440207	49440207	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs767466146	NA	P-0031393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	50	529	0	ENST00000301067.7:c.4419G>T	p.Trp1473Cys	p.W1473C	ENST00000301067	NM_003482.3	1473	tgG/tgT	16/54	1	2	FACETS	0.676	0.573	0.789	0.676	0.573	0.789	SUBCLONAL	1	TRUE	1	0.27	2		529	548	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867355	45867365	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGCTCGTCT	GCTGCTCGTCT	-	novel	NA	P-0031393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	65	582	0	ENST00000391945.4:c.828_838del	p.Asp277ProfsTer97	p.D277Pfs*97	ENST00000391945	NM_000400.3	276	acAGACGAGCAGCgc/acgc	10/23	0.235580267348932	2	FACETS	0.765	0.663	0.876	0.383	0.331	0.438	SUBCLONAL	1	TRUE	0	0.27	2		582	629	SUCCESS
APC	324	MSKCC	GRCh37	5	112116500	112116500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	49	337	0	ENST00000257430.4:c.545C>T	p.Thr182Ile	p.T182I	ENST00000257430	NM_000038.5	182	aCa/aTa	6/16	1	2	FACETS	0.724	0.614	0.846	0.724	0.614	0.846	SUBCLONAL	1	TRUE	1	0.27	2		337	501	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	332	648	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.623944553264297	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.623944553264297	1		648	716	SUCCESS
AR	367	MSKCC	GRCh37	X	66765159	66765185	+	inframe_deletion	In_Frame_Del	DEL	GCAGCAGCAGCAGCAGCAGCAGCAGCA	GCAGCAGCAGCAGCAGCAGCAGCAGCA	-	rs3032358	NA	P-0031403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	37	122	0	ENST00000374690.3:c.213_239del	p.Gln72_Gln80del	p.Q72_Q80del	ENST00000374690	NM_000044.3	57	ctGCAGCAGCAGCAGCAGCAGCAGCAGCAg/ctg	1/8	1	2	FACETS	0.303	0.249	0.362	0.303	0.249	0.362	SUBCLONAL	1	TRUE	1	0.623944553264297	2		122	392	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874163	155874163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs977405637	NA	P-0031403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	128	610	1	ENST00000368323.3:c.368G>A	p.Arg123His	p.R123H	ENST00000368323	NM_006912.5	123	cGt/cAt	5/6	0.295588284881612	3	FACETS	0.522	0.472	0.575	0.261	0.236	0.288	INDETERMINATE	1	TRUE	1	0.623944553264297	3		611	1031	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874893	151874893	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1473097808	NA	P-0031403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	133	339	0	ENST00000262189.6:c.7645C>T	p.Gln2549Ter	p.Q2549*	ENST00000262189	NM_170606.2	2549	Cag/Tag	38/59	1	2	FACETS	0.925	0.846	1	0.925	0.846	1	CLONAL	1	TRUE	1	0.623944553264297	2		339	461	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42870101	42870102	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0031403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	139	626	0	ENST00000398585.3:c.70dup	p.Ser24PhefsTer11	p.S24Ffs*11	ENST00000398585	NM_001135099.1	24	tcc/tTcc	2/14	1	2	FACETS	0.554	0.505	0.606	0.554	0.505	0.606	SUBCLONAL	1	TRUE	1	0.623944553264297	2		626	804	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0031413-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	151	851	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.3	3	FACETS	1	0.986	1			1	CLONAL	1	FALSE	NA	0.3	3		851	832	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0031413-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	66	459	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	0.841	0.731	0.96	0.841	0.731	0.96	CLONAL	1	FALSE	1	0.3	2		459	523	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732907	74732908	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0031413-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	16	205	0	ENST00000359995.5:c.335dup	p.Gly113ArgfsTer11	p.G113Rfs*11	ENST00000359995	NM_001195427.1	112	ggc/ggGc	1/3	0.3	3	FACETS	0.507	0.375	0.664	0.253	0.187	0.332	SUBCLONAL	1	FALSE	1	0.3	3		205	242	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728602	190728602	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031413-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	37	298	0	ENST00000441310.2:c.1990C>T	p.Gln664Ter	p.Q664*	ENST00000441310	NM_000534.4	664	Cag/Tag	10/13	0.158995577775633	3	FACETS	0.527	0.434	0.632	0.264	0.217	0.316	INDETERMINATE	1	FALSE	1	0.3	3		298	538	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467919	66467919	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031413-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	35	371	0	ENST00000273854.3:c.350G>T	p.Trp117Leu	p.W117L	ENST00000273854	NM_004439.5	117	tGg/tTg	3/18	1	2	FACETS	0.423	0.346	0.51	0.423	0.346	0.51	SUBCLONAL	1	FALSE	1	0.3	2		371	552	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	231	349	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.993	0.933	1	0.993	0.933	1	CLONAL	1	TRUE	1	0.780264290454302	2		349	596	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0031416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	183	567	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.791	0.734	0.849	0.791	0.734	0.849	SUBCLONAL	1	TRUE	1	0.780264290454302	2		567	593	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0031416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	65	407	1	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.958	0.848	1	0.958	0.848	1	CLONAL	1	TRUE	1	0.780264290454302	2		408	174	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651970	36651971	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0031416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	254	646	0	ENST00000244741.5:c.94dup	p.Arg32ProfsTer4	p.R32Pfs*4	ENST00000244741	NM_000389.4	31	agc/agCc	2/3	1	2	FACETS	0.851	0.8	0.903	0.851	0.8	0.903	CLONAL	1	TRUE	1	0.780264290454302	2		646	765	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857538	9857538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778951185	NA	P-0031416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	167	457	0	ENST00000330684.3:c.3863G>A	p.Arg1288His	p.R1288H	ENST00000330684	NM_001134407.1	1288	cGt/cAt	13/13	1	2	FACETS	0.962	0.893	1	0.962	0.893	1	CLONAL	1	TRUE	1	0.780264290454302	2		457	445	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741919	17741919	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	102	214	0	ENST00000250003.3:c.590C>G	p.Ser197Cys	p.S197C	ENST00000250003	NM_002478.4	197	tCc/tGc	1/3	1	2	FACETS	0.76	0.687	0.836	0.76	0.687	0.836	SUBCLONAL	1	TRUE	1	0.780264290454302	2		214	344	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790476	3790476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	318	627	0	ENST00000262367.5:c.4057G>A	p.Glu1353Lys	p.E1353K	ENST00000262367	NM_004380.2	1353	Gaa/Aaa	24/31	0.780264290454302	1	FACETS	0.894	0.855	0.933	0.894	0.855	0.933	CLONAL	1	TRUE	0	0.780264290454302	1		627	556	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420273	49420273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1205083140	NA	P-0031416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	346	709	0	ENST00000301067.7:c.15476G>A	p.Arg5159Gln	p.R5159Q	ENST00000301067	NM_003482.3	5159	cGg/cAg	48/54	0.326813944670834	3	FACETS	1	0.994	1	0.681	0.647	0.716	INDETERMINATE	1	TRUE	1	0.780264290454302	3		709	905	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436527	49436527	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	244	676	0	ENST00000301067.7:c.5779C>T	p.Gln1927Ter	p.Q1927*	ENST00000301067	NM_003482.3	1927	Caa/Taa	26/54	0.326813944670834	3	FACETS	1	0.986	1	0.588	0.552	0.625	INDETERMINATE	1	TRUE	1	0.780264290454302	3		676	739	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139013	50139013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	416	908	0	ENST00000246792.3:c.550G>A	p.Glu184Lys	p.E184K	ENST00000246792	NM_006270.3	184	Gag/Aag	5/6	1	2	FACETS	0.952	0.908	0.996	0.952	0.908	0.996	CLONAL	1	TRUE	1	0.780264290454302	2		908	1120	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281837	142281837	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	81	579	0	ENST00000350721.4:c.407G>A	p.Ser136Asn	p.S136N	ENST00000350721	NM_001184.3	136	aGc/aAc	4/47	1	2	FACETS	0.827	0.739	0.918	0.827	0.739	0.918	CLONAL	1	TRUE	1	0.780264290454302	2		579	251	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948160	178948160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	77	247	0	ENST00000263967.3:c.2932G>A	p.Glu978Lys	p.E978K	ENST00000263967	NM_006218.2	978	Gag/Aag	20/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.780264290454302	2		247	180	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630953	187630953	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs202138193	NA	P-0031416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	198	536	0	ENST00000441802.2:c.29T>C	p.Leu10Pro	p.L10P	ENST00000441802	NM_005245.3	10	cTt/cCt	2/27	1	2	FACETS	0.943	0.881	1	0.943	0.881	1	CLONAL	1	TRUE	1	0.780264290454302	2		536	538	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969378	44969379	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACATAGTACATTGCCAAGATTGTGCACGAAAAACAAGCGGAAACTTGGAAAACTTTGTGGTGCTAGAACAGTACAAAATG	novel	NA	P-0031416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	45	308	0	ENST00000377967.4:c.4061_4140dup	p.Glu1381ThrfsTer2	p.E1381Tfs*2	ENST00000377967	NM_021140.2	1354	tac/tACATAGTACATTGCCAAGATTGTGCACGAAAAACAAGCGGAAACTTGGAAAACTTTGTGGTGCTAGAACAGTACAAAATGac	28/29	1	1	FACETS	0.157	0.131	0.185	0.157	0.131	0.185	SUBCLONAL	1	TRUE	0	0.780264290454302	1		308	449	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0031432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	31	308	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	0.168247493625307	4	FACETS	1	0.824	1	0.509	0.412	0.618	CLONAL	1	TRUE	2	0.231700310011289	4		308	324	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0031432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	70	532	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.227854540419235	0	FACETS	0.917	0.802	1			1	CLONAL	1	TRUE	0	0.231700310011289	0		532	506	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371799	55371820	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCCGCGCTGGGCCCCGAG	GGCGGCCGCGCTGGGCCCCGAG	-	novel	NA	P-0031432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	59	185	0	ENST00000297316.4:c.499_520del	p.Leu167TrpfsTer213	p.L167Wfs*213	ENST00000297316	NM_022454.3	163	caGGCGGCCGCGCTGGGCCCCGAG/ca	2/2	1	2	FACETS	0.762	0.66	0.873	1	0.971	1	SUBCLONAL	2	TRUE	1	0.231700310011289	2		185	334	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631671	90631671	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	79	440	0	ENST00000330062.3:c.598G>C	p.Asp200His	p.D200H	ENST00000330062	NM_002168.2	200	Gat/Cat	5/11	0.152585920165916	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.231700310011289	1		440	551	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597451	10597451	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0031432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	91	538	0	ENST00000171111.5:c.1752C>G	p.Tyr584Ter	p.Y584*	ENST00000171111	NM_203500.1	584	taC/taG	6/6	0.227854540419235	0	FACETS	1	0.933	1			1	CLONAL	1	TRUE	0	0.231700310011289	0		538	565	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383649	15383649	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	51	304	1	ENST00000263377.2:c.262G>T	p.Asp88Tyr	p.D88Y	ENST00000263377	NM_058243.2	88	Gat/Tat	2/20	1	2	FACETS	0.974	0.829	1	0.974	0.829	1	CLONAL	1	TRUE	1	0.231700310011289	2		305	452	SUCCESS
AR	367	MSKCC	GRCh37	X	66765040	66765040	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	132	578	0	ENST00000374690.3:c.52A>G	p.Thr18Ala	p.T18A	ENST00000374690	NM_000044.3	18	Acc/Gcc	1/8	0.168247493625307	4	FACETS	0.785	0.712	0.862	0.785	0.712	0.862	SUBCLONAL	2	TRUE	2	0.231700310011289	4		578	894	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0031440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	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	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.253325623882693	2		539	482	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0031440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	59	303	1	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.253325623882693	1	FACETS	0.879	0.757	1	0.879	0.757	1	CLONAL	1	TRUE	0	0.253325623882693	1		304	463	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0031447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	201	459	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.641587733561287	4	FACETS	0.778	0.724	0.833	0.778	0.724	0.833	SUBCLONAL	2	TRUE	2	0.651517590130362	4		459	655	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161284198	161284198	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs587776652	NA	P-0031447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	104	355	0	ENST00000367975.2:c.3G>A	p.Met1?	p.M1?	ENST00000367975	NM_003001.3	1	atG/atA	1/6	0.651517590130362	4	FACETS	1	0.907	1	0.337	0.302	0.373	CLONAL	1	TRUE	1	0.651517590130362	4		355	522	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31424569	31424569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773151368	NA	P-0031447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1810	183	659	1	ENST00000344624.3:c.3226G>A	p.Glu1076Lys	p.E1076K	ENST00000344624		1076	Gaa/Aaa	25/33	0.651517590130362	10	FACETS	1	0.932	1	0.145	0.133	0.158	CLONAL	1	TRUE	3	0.651517590130362	10		660	1993	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0031451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	362	508	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.656720868061098	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.702269362345033	2		508	514	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747993	41748031	+	inframe_deletion	In_Frame_Del	DEL	GCCGCCGCTGCCGCTGCCGCCGCCGCCGCTGCCGCGGCC	GCCGCCGCTGCCGCTGCCGCCGCCGCCGCTGCCGCGGCC	-	rs757020181	NA	P-0031451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	17	92	0	ENST00000226382.2:c.738_776del	p.Ala248_Ala260del	p.A248_A260del	ENST00000226382	NM_003924.3	246	gcGGCCGCGGCAGCGGCGGCGGCGGCAGCGGCAGCGGCGGCa/gca	3/3	0.702269362345033	3	FACETS	0.327	0.245	0.424	0.164	0.122	0.212	SUBCLONAL	1	TRUE	1	0.702269362345033	3		92	200	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	81	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.41258745281642	3	FACETS	0.771	0.686	0.86	0.771	0.686	0.86	SUBCLONAL	2	TRUE	1	0.41258745281642	3		493	307	SUCCESS
APC	324	MSKCC	GRCh37	5	112175240	112175240	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	25	243	0	ENST00000257430.4:c.3949G>T	p.Glu1317Ter	p.E1317*	ENST00000257430	NM_000038.5	1317	Gaa/Taa	16/16	1	2	FACETS	0.673	0.535	0.83	0.673	0.535	0.83	SUBCLONAL	1	TRUE	1	0.41258745281642	2		243	180	SUCCESS
APC	324	MSKCC	GRCh37	5	112136975	112136975	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0031454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	54	355	0	ENST00000257430.4:c.730-1G>A		p.X244_splice	ENST00000257430	NM_000038.5	244			1	2	FACETS	0.948	0.817	1	0.948	0.817	1	CLONAL	1	TRUE	1	0.41258745281642	2		355	276	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206809	36206809	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	42	422	0	ENST00000300305.3:c.703G>A	p.Ala235Thr	p.A235T	ENST00000300305		235	Gcc/Acc	6/8	1	2	FACETS	0.44	0.367	0.52	0.44	0.367	0.52	SUBCLONAL	1	TRUE	1	0.41258745281642	2		422	463	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119794	70119794	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	104	634	0	ENST00000245479.2:c.800del	p.Pro267LeufsTer12	p.P267Lfs*12	ENST00000245479	NM_000346.3	266	Ccc/cc	3/3	1	2	FACETS	0.8	0.718	0.887	0.8	0.718	0.887	SUBCLONAL	1	TRUE	1	0.41258745281642	2		634	630	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633319	8633319	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs778130827	NA	P-0031454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	38	442	0	ENST00000356435.5:c.350G>A	p.Arg117Gln	p.R117Q	ENST00000356435		117	cGg/cAg	3/35	1	2	FACETS	0.493	0.408	0.587	0.493	0.408	0.587	SUBCLONAL	1	TRUE	1	0.41258745281642	2		442	374	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129868	69129868	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776942401	NA	P-0031454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	58	245	1	ENST00000288368.4:c.4622C>T	p.Thr1541Met	p.T1541M	ENST00000288368	NM_024870.2	1541	aCg/aTg	38/40	1	2	FACETS	0.887	0.767	1	0.887	0.767	1	CLONAL	1	TRUE	1	0.41258745281642	2		246	317	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048590	180048590	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	120	672	1	ENST00000261937.6:c.1972C>T	p.Arg658Trp	p.R658W	ENST00000261937	NM_182925.4	658	Cgg/Tgg	13/30	1	2	FACETS	0.841	0.76	0.925	0.841	0.76	0.925	CLONAL	1	TRUE	1	0.41258745281642	2		673	692	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923021	44923021	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	184	554	0	ENST00000377967.4:c.1882G>T	p.Ala628Ser	p.A628S	ENST00000377967	NM_021140.2	628	Gca/Tca	16/29	0.41258745281642	7	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.41258745281642	7		554	1271	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0031465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	203	557	1	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	0.552575386106669	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.569032919702618	1		558	456	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555687605	NA	P-0031465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	118	346	0	ENST00000342988.3:c.1610A>G	p.Asp537Gly	p.D537G	ENST00000342988	NM_005359.5	537	gAc/gGc	12/12	0.569032919702618	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.569032919702618	1		346	278	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508682	106508682	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760803722	NA	P-0031465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	129	469	1	ENST00000359195.3:c.676C>T	p.Arg226Cys	p.R226C	ENST00000359195	NM_002649.2	226	Cgc/Tgc	2/11	0.569032919702618	3	FACETS	0.955	0.868	1	0.477	0.434	0.523	CLONAL	1	TRUE	1	0.569032919702618	3		470	610	SUCCESS
APC	324	MSKCC	GRCh37	5	112175256	112175265	+	frameshift_variant	Frame_Shift_Del	DEL	AAGTTCCAGC	AAGTTCCAGC	TTT	novel	NA	P-0031465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	119	305	0	ENST00000257430.4:c.3965_3974delinsTTT	p.Glu1322ValfsTer2	p.E1322Vfs*2	ENST00000257430	NM_000038.5	1322	gAAGTTCCAGCa/gTTTa	16/16	0.539128714318227	2	FACETS	1	0.986	1	0.729	0.669	0.79	CLONAL	1	TRUE	0	0.569032919702618	2		305	287	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0031467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	183	756	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	1	2	FACETS	1	0.971	1	1	0.994	1	CLONAL	2	TRUE	1	0.495162923931469	2		756	350	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0031467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	44	512	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.440600409684724	3	FACETS	0.798	0.673	0.934	0.399	0.336	0.467	CLONAL	1	TRUE	1	0.495162923931469	3		512	278	SUCCESS
APC	324	MSKCC	GRCh37	5	112175273	112175273	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123121	NA	P-0031467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	67	285	0	ENST00000257430.4:c.3982C>T	p.Gln1328Ter	p.Q1328*	ENST00000257430	NM_000038.5	1328	Cag/Tag	16/16	0.440600409684724	3	FACETS	0.938	0.832	1	0.938	0.832	1	CLONAL	2	TRUE	1	0.495162923931469	3		285	180	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120003	70120003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	86	177	0	ENST00000245479.2:c.1005G>A	p.Trp335Ter	p.W335*	ENST00000245479	NM_000346.3	335	tgG/tgA	3/3	0.488514110487361	4	FACETS	0.956	0.868	1	1	0.982	1	CLONAL	3	TRUE	2	0.495162923931469	4		177	181	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633500	69633500	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	77	302	1	ENST00000334134.2:c.202C>A	p.Leu68Met	p.L68M	ENST00000334134	NM_005247.2	68	Ctg/Atg	1/3	0.495162923931469	3	FACETS	0.902	0.807	1	0.902	0.807	1	CLONAL	2	TRUE	1	0.495162923931469	3		303	215	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191523	185191523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	306	624	0	ENST00000265026.3:c.2404C>T	p.Pro802Ser	p.P802S	ENST00000265026	NM_004721.4	802	Cct/Tct	11/14	0.423334147462223	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.495162923931469	3		624	674	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249390	153249390	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	120	574	0	ENST00000281708.4:c.1388C>G	p.Thr463Ser	p.T463S	ENST00000281708	NM_033632.3	463	aCt/aGt	9/12	0.495162923931469	2	FACETS	0.997	0.921	1	0.997	0.921	1	CLONAL	2	TRUE	0	0.495162923931469	2		574	243	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437782	52437782	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0031574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	58	560	0	ENST00000460680.1:c.1379C>G	p.Ser460Ter	p.S460*	ENST00000460680	NM_004656.3	460	tCa/tGa	13/17	0.727186561039553	1	FACETS	0.194	0.167	0.225	0.194	0.167	0.225	SUBCLONAL	1	TRUE	0	0.727186561039553	1		560	522	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0031574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	455	616	0	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	0.713531970916288	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.727186561039553	1		616	795	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441252	52441252	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	179	523	0	ENST00000460680.1:c.518A>G	p.Tyr173Cys	p.Y173C	ENST00000460680	NM_004656.3	173	tAt/tGt	7/17	0.727186561039553	1	FACETS	0.537	0.498	0.578	0.537	0.498	0.578	SUBCLONAL	1	TRUE	0	0.727186561039553	1		523	583	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938229	76938230	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0031574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	85	287	0	ENST00000373344.5:c.2518dup	p.Arg840LysfsTer9	p.R840Kfs*9	ENST00000373344	NM_000489.3	840	aga/aAga	9/35	1	1	FACETS	0.767	0.694	0.841	0.767	0.694	0.841	SUBCLONAL	1	TRUE	0	0.727186561039553	1		287	194	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426778	49426778	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555188537	NA	P-0031574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	17	254	0	ENST00000301067.7:c.11710C>T	p.Gln3904Ter	p.Q3904*	ENST00000301067	NM_003482.3	3904	Cag/Tag	39/54	1	2	FACETS	0.138	0.102	0.18	0.138	0.102	0.18	SUBCLONAL	1	TRUE	1	0.727186561039553	2		254	339	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255619	16255631	+	frameshift_variant	Frame_Shift_Del	DEL	AAGCACCTCAAGC	AAGCACCTCAAGC	-	novel	NA	P-0031574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	345	506	0	ENST00000375759.3:c.2884_2896del	p.Lys962LeufsTer8	p.K962Lfs*8	ENST00000375759	NM_015001.2	962	AAGCACCTCAAGCct/ct	11/15	0.347069772368358	2	FACETS	0.995	0.96	1	0.995	0.96	1	INDETERMINATE	2	TRUE	0	0.727186561039553	2		506	477	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608510	28608510	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	46	748	0	ENST00000241453.7:c.1632C>A	p.Phe544Leu	p.F544L	ENST00000241453	NM_004119.2	544	ttC/ttA	13/24	0.727186561039553	1	FACETS	0.292	0.247	0.34	0.292	0.247	0.34	SUBCLONAL	1	TRUE	0	0.727186561039553	1		748	276	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805555	89805555	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1301606691	NA	P-0031574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	92	555	1	ENST00000389301.3:c.4153G>C	p.Glu1385Gln	p.E1385Q	ENST00000389301	NM_000135.2	1385	Gag/Cag	41/43	0.713596094019375	2	FACETS	0.453	0.404	0.506	0.227	0.202	0.253	SUBCLONAL	1	TRUE	0	0.727186561039553	2		556	558	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559192	29559192	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0031574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	77	441	0	ENST00000356175.3:c.3299C>G	p.Ser1100Ter	p.S1100*	ENST00000356175	NM_000267.3	1100	tCa/tGa	25/57	0.727186561039553	1	FACETS	0.511	0.454	0.57	0.511	0.454	0.57	SUBCLONAL	1	TRUE	0	0.727186561039553	1		441	264	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654740	29654740	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	27	366	0	ENST00000356175.3:c.5431del	p.Glu1811AsnfsTer31	p.E1811Nfs*31	ENST00000356175	NM_000267.3	1810	tGg/tg	37/57	0.727186561039553	1	FACETS	0.095	0.075	0.118	0.095	0.075	0.118	SUBCLONAL	1	TRUE	0	0.727186561039553	1		366	495	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023183	31023183	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	85	649	0	ENST00000375687.4:c.2668C>G	p.Leu890Val	p.L890V	ENST00000375687	NM_015338.5	890	Ctc/Gtc	13/13	0.254971157043397	3	FACETS	0.418	0.369	0.47	0.209	0.184	0.235	INDETERMINATE	1	TRUE	1	0.727186561039553	3		649	763	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109311931	109311942	+	inframe_deletion	In_Frame_Del	DEL	ATTATAAGTAAG	ATTATAAGTAAG	-	novel	NA	P-0031574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	29	565	0	ENST00000436639.2:c.1330_1341del	p.Leu444_Asn447del	p.L444_N447del	ENST00000436639	NM_014454.2	444	CTTACTTATAAT/-	8/10	0.727186561039553	1	FACETS	0.15	0.12	0.184	0.15	0.12	0.184	SUBCLONAL	1	TRUE	0	0.727186561039553	1		565	338	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932303	39932303	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	113	363	0	ENST00000378444.4:c.2296G>T	p.Glu766Ter	p.E766*	ENST00000378444	NM_001123385.1	766	Gag/Tag	4/15	1	1	FACETS	0.343	0.309	0.378	0.343	0.309	0.378	SUBCLONAL	1	TRUE	0	0.727186561039553	1		363	577	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0031577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	277	308	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	0.714133645764793	1	FACETS	0.978	0.931	1	0.978	0.931	1	CLONAL	1	TRUE	0	0.714133645764793	1		308	510	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593478	215593478	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	189	297	0	ENST00000260947.4:c.2256G>T	p.Gln752His	p.Q752H	ENST00000260947	NM_000465.2	752	caG/caT	11/11	0.382456044247949	1	FACETS	0.745	0.696	0.794	0.745	0.696	0.794	INDETERMINATE	1	TRUE	0	0.714133645764793	1		297	457	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021757	71021757	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	298	382	0	ENST00000318789.4:c.1601G>T	p.Trp534Leu	p.W534L	ENST00000318789	NM_032682.5	534	tGg/tTg	18/21	0.714133645764793	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.714133645764793	1		382	497	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258832	16258832	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	326	556	2	ENST00000375759.3:c.6097G>A	p.Ala2033Thr	p.A2033T	ENST00000375759	NM_015001.2	2033	Gct/Act	11/15	1	2	FACETS	0.883	0.835	0.932	0.883	0.835	0.932	CLONAL	1	TRUE	1	0.714133645764793	2		558	1034	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259153	16259153	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	345	550	0	ENST00000375759.3:c.6418G>C	p.Asp2140His	p.D2140H	ENST00000375759	NM_015001.2	2140	Gat/Cat	11/15	1	2	FACETS	0.958	0.908	1	0.958	0.908	1	CLONAL	1	TRUE	1	0.714133645764793	2		550	1009	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405171	70405171	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	345	507	0	ENST00000373644.4:c.2685G>T	p.Glu895Asp	p.E895D	ENST00000373644	NM_030625.2	895	gaG/gaT	4/12	0.714133645764793	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.714133645764793	1		507	594	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94211952	94211952	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs763298588	NA	P-0031577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	254	534	1	ENST00000323929.3:c.493A>T	p.Ser165Cys	p.S165C	ENST00000323929	NM_005591.3	165	Agt/Tgt	6/20	1	2	FACETS	0.984	0.925	1	0.984	0.925	1	CLONAL	1	TRUE	1	0.714133645764793	2		535	723	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434055	49434055	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	322	552	0	ENST00000301067.7:c.7498G>T	p.Ala2500Ser	p.A2500S	ENST00000301067	NM_003482.3	2500	Gcg/Tcg	31/54	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.714133645764793	2		552	902	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893213	32893213	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs1060502376	NA	P-0031577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	101	262	0	ENST00000380152.3:c.68-1G>C		p.X23_splice	ENST00000380152		23			1	2	FACETS	0.76	0.685	0.838	0.76	0.685	0.838	SUBCLONAL	1	TRUE	1	0.714133645764793	2		262	372	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632627	3632627	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs755353749	NA	P-0031577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	227	727	0	ENST00000294008.3:c.5221A>G	p.Ser1741Gly	p.S1741G	ENST00000294008	NM_032444.2	1741	Agt/Ggt	15/15	0.347433737262018	1	FACETS	0.398	0.37	0.426	0.398	0.37	0.426	INDETERMINATE	1	TRUE	0	0.714133645764793	1		727	1028	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521516	187521516	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0031577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	196	316	0	ENST00000441802.2:c.11641-2A>G		p.X3881_splice	ENST00000441802	NM_005245.3	3881			NA	2	FACETS	0.909	0.846	0.973			1	INDETERMINATE	1	TRUE	NA	0.714133645764793	2		316	604	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295204	1295204	+	upstream_gene_variant	5'Flank	DEL	G	G	-	novel	NA	P-0031577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	231	348	0				ENST00000310581	NM_198253.2	-/1132			0.714133645764793	3	FACETS	0.99	0.924	1	0.495	0.462	0.529	CLONAL	1	TRUE	1	0.714133645764793	3		348	887	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721585	176721585	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	375	503	0	ENST00000439151.2:c.7216C>A	p.Pro2406Thr	p.P2406T	ENST00000439151	NM_022455.4	2406	Cct/Act	23/23	0.714133645764793	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.714133645764793	1		503	653	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0031600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	146	400	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.978	0.903	1	0.978	0.903	1	CLONAL	1	TRUE	1	0.769419571278847	2		400	388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0031600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	439	685	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	NA	2	FACETS	0.925	0.896	0.953			1	INDETERMINATE	2	TRUE	NA	0.769419571278847	2		685	617	SUCCESS
APC	324	MSKCC	GRCh37	5	112175282	112175282	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0031600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	86	215	0	ENST00000257430.4:c.3991A>T	p.Arg1331Ter	p.R1331*	ENST00000257430	NM_000038.5	1331	Aga/Tga	16/16	1	2	FACETS	0.853	0.766	0.944	0.853	0.766	0.944	CLONAL	1	TRUE	1	0.769419571278847	2		215	262	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976744	2976744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs577877958	NA	P-0031600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	241	516	0	ENST00000396946.4:c.1268G>A	p.Arg423Gln	p.R423Q	ENST00000396946	NM_032415.4	423	cGg/cAg	9/25	1	2	FACETS	0.996	0.937	1	0.996	0.937	1	CLONAL	1	TRUE	1	0.769419571278847	2		516	629	SUCCESS
APC	324	MSKCC	GRCh37	5	112137030	112137030	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	172	476	0	ENST00000257430.4:c.784G>T	p.Glu262Ter	p.E262*	ENST00000257430	NM_000038.5	262	Gaa/Taa	8/16	1	2	FACETS	0.84	0.779	0.904	0.84	0.779	0.904	CLONAL	1	TRUE	1	0.769419571278847	2		476	532	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133234534	133234534	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	194	355	0	ENST00000320574.5:c.3298C>G	p.Gln1100Glu	p.Q1100E	ENST00000320574	NM_006231.2	1100	Caa/Gaa	27/49	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.769419571278847	2		355	492	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514655	103514655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758046666	NA	P-0031600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	303	343	0	ENST00000355739.4:c.1156C>T	p.Arg386Trp	p.R386W	ENST00000355739	NM_000123.3	386	Cgg/Tgg	8/15	0.633721654754963	3	FACETS	0.984	0.939	1	0.984	0.939	1	CLONAL	2	TRUE	1	0.769419571278847	3		343	554	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0031603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	386	868	1	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.582658032782834	2	FACETS	0.982	0.943	1	0.982	0.943	1	CLONAL	2	TRUE	0	0.602236673923185	2		869	653	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959120	28959121	+	missense_variant	Missense_Mutation	DNP	GC	GC	AG	novel	NA	P-0031603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	90	341	0	ENST00000282397.4:c.2017_2018delinsCT	p.Ala673Leu	p.A673L	ENST00000282397	NM_002019.4	673	GCc/CTc	14/30	0.577091837436807	2	FACETS	0.687	0.613	0.766	0.344	0.306	0.383	SUBCLONAL	1	TRUE	0	0.602236673923185	2		341	435	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	164	557	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.596276702900608	4	FACETS	1	0.963	1	0.541	0.497	0.587	CLONAL	1	FALSE	2	0.596276702900608	4		557	811	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998934	11998934	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	269	282	0	ENST00000353533.5:c.436del	p.Met147TrpfsTer5	p.M147Wfs*5	ENST00000353533	NM_003010.3	146	Ctt/tt	4/11	0.596276702900608	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	FALSE	0	0.596276702900608	3		282	381	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55260478	55260478	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	130	417	0	ENST00000275493.2:c.2645C>A	p.Ala882Glu	p.A882E	ENST00000275493	NM_005228.3	882	gCa/gAa	22/28	0.596276702900608	3	FACETS	0.769	0.698	0.843	0.385	0.349	0.422	SUBCLONAL	1	FALSE	1	0.596276702900608	3		417	736	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0031615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	132	460	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.875	0.796	0.959	1	0.989	1	CLONAL	2	FALSE	1	0.202939586367015	2		460	743	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0031615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	50	313	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.916	0.777	1	0.916	0.777	1	CLONAL	1	FALSE	1	0.202939586367015	2		313	538	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0031615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	20	488	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.349	0.266	0.448	0.349	0.266	0.448	SUBCLONAL	1	FALSE	1	0.202939586367015	2		488	564	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0031615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	53	382	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	1	2	FACETS	0.971	0.828	1	0.971	0.828	1	CLONAL	1	FALSE	1	0.202939586367015	2		382	538	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459896	149459896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	88	517	0	ENST00000286301.3:c.311C>T	p.Pro104Leu	p.P104L	ENST00000286301	NM_005211.3	104	cCt/cTt	4/22	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.202939586367015	2		517	734	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058589	42058589	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0031615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	53	350	0	ENST00000219905.7:c.8309C>G	p.Ser2770Ter	p.S2770*	ENST00000219905	NM_001164273.1	2770	tCa/tGa	24/24	0.105753459427609	3	FACETS	1	0.941	1	0.606	0.517	0.702	INDETERMINATE	1	FALSE	1	0.202939586367015	3		350	475	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059075	42059075	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	66	398	0	ENST00000219905.7:c.8795C>G	p.Ser2932Cys	p.S2932C	ENST00000219905	NM_001164273.1	2932	tCt/tGt	24/24	0.105753459427609	3	FACETS	1	0.961	1	0.65	0.565	0.742	INDETERMINATE	1	FALSE	1	0.202939586367015	3		398	551	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820993	32820993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	58	635	0	ENST00000354258.4:c.601G>A	p.Val201Ile	p.V201I	ENST00000354258	NM_000593.5	201	Gtt/Att	1/11	1	2	FACETS	0.611	0.523	0.707	0.611	0.523	0.707	SUBCLONAL	1	FALSE	1	0.202939586367015	2		635	936	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059242	27059244	+	frameshift_variant	Frame_Shift_Del	DEL	GAT	GAT	A	novel	NA	P-0031615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	34	510	0	ENST00000324856.7:c.1879_1881delinsA	p.Asp627AsnfsTer14	p.D627Nfs*14	ENST00000324856	NM_006015.4	627	GAT/A	4/20	1	2	FACETS	0.512	0.417	0.619	0.512	0.417	0.619	SUBCLONAL	1	FALSE	1	0.202939586367015	2		510	655	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425694	49425694	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	105	672	0	ENST00000301067.7:c.12794G>A	p.Gly4265Asp	p.G4265D	ENST00000301067	NM_003482.3	4265	gGc/gAc	39/54	0.340700564672778	1	FACETS	0.567	0.508	0.629	0.567	0.508	0.629	SUBCLONAL	1	TRUE	0	0.404967023104749	1		672	730	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112939993	112939993	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	244	539	0	ENST00000351677.2:c.1645C>G	p.Leu549Val	p.L549V	ENST00000351677	NM_002834.3	549	Cta/Gta	14/16	0.356641266204591	2	FACETS	0.924	0.869	0.98	0.924	0.869	0.98	CLONAL	2	TRUE	0	0.404967023104749	2		539	652	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578206	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs886039484	NA	P-0031643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	194	682	0	ENST00000269305.4:c.643A>G	p.Ser215Gly	p.S215G	ENST00000269305	NM_001126112.2	215	Agt/Ggt	6/11	0.404967023104749	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.404967023104749	1		682	728	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578467	7578467	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	257	767	0	ENST00000269305.4:c.463A>C	p.Thr155Pro	p.T155P	ENST00000269305	NM_001126112.2	155	Acc/Ccc	5/11	0.498419605214929	1	FACETS	0.936	0.879	0.994	0.936	0.879	0.994	CLONAL	1	TRUE	0	0.498419605214929	1		767	827	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047888	180047888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	287	844	0	ENST00000261937.6:c.2287G>A	p.Val763Met	p.V763M	ENST00000261937	NM_182925.4	763	Gtg/Atg	15/30	0.498419605214929	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.498419605214929	1		844	841	SUCCESS
FH	2271	MSKCC	GRCh37	1	241671940	241671940	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	190	570	0	ENST00000366560.3:c.701C>G	p.Thr234Ser	p.T234S	ENST00000366560	NM_000143.3	234	aCt/aGt	5/10	1	2	FACETS	0.986	0.914	1	0.986	0.914	1	CLONAL	1	TRUE	1	0.498419605214929	2		570	773	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80088574	80088574	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	170	517	0	ENST00000265081.6:c.2566A>G	p.Lys856Glu	p.K856E	ENST00000265081	NM_002439.4	856	Aaa/Gaa	19/24	0.498419605214929	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.498419605214929	1		517	458	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026705	6026705	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1152	303	944	1	ENST00000265849.7:c.1691T>G	p.Val564Gly	p.V564G	ENST00000265849	NM_000535.5	564	gTt/gGt	11/15	0.439150634447479	3	FACETS	1	0.968	1	0.522	0.49	0.554	CLONAL	1	TRUE	1	0.498419605214929	3		945	1455	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55225394	55225394	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	407	582	1	ENST00000275493.2:c.1246G>T	p.Asp416Tyr	p.D416Y	ENST00000275493	NM_005228.3	416	Gac/Tac	11/28	0.439150634447479	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.498419605214929	3		583	1012	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81399202	81399202	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	338	603	0	ENST00000222390.5:c.86C>A	p.Ala29Glu	p.A29E	ENST00000222390	NM_000601.4	29	gCa/gAa	1/18	0.439150634447479	3	FACETS	0.896	0.849	0.942	0.896	0.849	0.942	CLONAL	2	TRUE	1	0.498419605214929	3		603	946	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526738	106526738	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0031665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	135	381	0	ENST00000359195.3:c.3030+1G>A		p.X1010_splice	ENST00000359195	NM_002649.2	1010			0.439150634447479	3	FACETS	0.957	0.871	1	0.479	0.435	0.524	CLONAL	1	TRUE	1	0.498419605214929	3		381	707	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873361	151873361	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	142	381	0	ENST00000262189.6:c.9177G>C	p.Leu3059Phe	p.L3059F	ENST00000262189	NM_170606.2	3059	ttG/ttC	38/59	0.439150634447479	3	FACETS	1	0.925	1	0.507	0.463	0.553	CLONAL	1	TRUE	1	0.498419605214929	3		381	702	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0031721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	210	522	1	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.668153759852098	3	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.858117580139287	3		523	599	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0031721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	404	622	0	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	0.668153759852098	3	FACETS	0.967	0.929	1			1	CLONAL	2	TRUE	NA	0.858117580139287	3		622	696	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102199	27102199	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0031721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	152	530	0	ENST00000324856.7:c.5124+1G>C		p.X1708_splice	ENST00000324856	NM_006015.4	1708			1	2	FACETS	0.911	0.843	0.98	0.911	0.843	0.98	CLONAL	1	TRUE	1	0.858117580139287	2		530	389	SUCCESS
AR	367	MSKCC	GRCh37	X	66943642	66943642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	234	394	0	ENST00000374690.3:c.2722C>T	p.Leu908Phe	p.L908F	ENST00000374690	NM_000044.3	908	Ctt/Ttt	8/8	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.858117580139287	1		394	273	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953258	81953258	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	142	375	0	ENST00000359376.3:c.2224C>A	p.Arg742Ser	p.R742S	ENST00000359376	NM_002661.3	742	Cgc/Agc	20/33	1	2	FACETS	0.844	0.778	0.912	0.844	0.778	0.912	CLONAL	1	TRUE	1	0.858117580139287	2		375	392	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710984	117710984	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	122	370	0	ENST00000368508.3:c.1288G>T	p.Gly430Cys	p.G430C	ENST00000368508	NM_002944.2	430	Ggc/Tgc	12/43	1	2	FACETS	0.906	0.83	0.982	0.906	0.83	0.982	CLONAL	1	TRUE	1	0.858117580139287	2		370	314	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	207	296	0	ENST00000304494.5:c.341C>G	p.Pro114Arg	p.P114R	ENST00000304494	NM_000077.4	114	cCc/cGc	2/3	0.85880415972684	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.858117580139287	1		296	247	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928834	49928834	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs878910700	NA	P-0031721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	33	717	0	ENST00000296474.3:c.3532C>T	p.Arg1178Trp	p.R1178W	ENST00000296474	NM_002447.2	1178	Cgg/Tgg	16/20	0.858117580139287	1	FACETS	0.176	0.144	0.212	0.176	0.144	0.212	SUBCLONAL	1	TRUE	0	0.858117580139287	1		717	249	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100495	8100495	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	191	767	0	ENST00000346208.3:c.469C>A	p.Pro157Thr	p.P157T	ENST00000346208		157	Ccg/Acg	3/6	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.858117580139287	2		767	421	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633488	69633488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1419524448	NA	P-0031721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	50	208	0	ENST00000334134.2:c.214G>A	p.Ala72Thr	p.A72T	ENST00000334134	NM_005247.2	72	Gcc/Acc	1/3	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.858117580139287	NA		208	114	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205253	46205253	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	373	585	0	ENST00000334344.6:c.337G>T	p.Val113Leu	p.V113L	ENST00000334344	NM_152641.2	113	Gta/Tta	4/21	0.374169208900868	5	FACETS	0.962	0.922	1			1	INDETERMINATE	3	TRUE	NA	0.858117580139287	5		585	689	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292847	91292847	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	237	736	0	ENST00000355112.3:c.349G>T	p.Glu117Ter	p.E117*	ENST00000355112	NM_000057.2	117	Gaa/Taa	3/22	1	2	FACETS	0.972	0.916	1	0.972	0.916	1	CLONAL	1	TRUE	1	0.858117580139287	2		736	568	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992205	72992205	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	191	718	0	ENST00000268489.5:c.1840G>T	p.Gly614Trp	p.G614W	ENST00000268489	NM_006885.3	614	Ggg/Tgg	2/10	1	2	FACETS	0.925	0.864	0.988	0.925	0.864	0.988	CLONAL	1	TRUE	1	0.858117580139287	2		718	481	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357162	89357162	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0031721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	209	700	0	ENST00000301030.4:c.472A>T	p.Lys158Ter	p.K158*	ENST00000301030	NM_001256183.1	158	Aaa/Taa	6/13	1	2	FACETS	0.984	0.923	1	0.984	0.923	1	CLONAL	1	TRUE	1	0.858117580139287	2		700	495	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995262	15995263	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0031721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	179	580	1	ENST00000268712.3:c.2930_2931delinsTT	p.Arg977Leu	p.R977L	ENST00000268712	NM_006311.3	977	cGG/cTT	22/46	1	2	FACETS	0.895	0.834	0.958	0.895	0.834	0.958	CLONAL	1	TRUE	1	0.858117580139287	2		581	466	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554251	29554251	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	176	413	0	ENST00000356175.3:c.2267A>C	p.Gln756Pro	p.Q756P	ENST00000356175	NM_000267.3	756	cAg/cCg	19/57	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.858117580139287	2		413	329	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296394	15296394	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	210	816	0	ENST00000263388.2:c.2048G>T	p.Cys683Phe	p.C683F	ENST00000263388	NM_000435.2	683	tGc/tTc	13/33	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.858117580139287	2		816	442	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657020	215657020	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0031721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	191	405	0	ENST00000260947.4:c.364+1G>A		p.X122_splice	ENST00000260947	NM_000465.2	122			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.858117580139287	2		405	434	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022306	31022306	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	132	491	0	ENST00000375687.4:c.1791C>G	p.Ile597Met	p.I597M	ENST00000375687	NM_015338.5	597	atC/atG	13/13	1	2	FACETS	0.684	0.625	0.744	0.684	0.625	0.744	SUBCLONAL	1	TRUE	1	0.858117580139287	2		491	450	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944485	40944485	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	188	694	0	ENST00000373198.4:c.2017C>A	p.Leu673Met	p.L673M	ENST00000373198	NM_133170.3	673	Ctg/Atg	12/32	1	2	FACETS	0.864	0.805	0.924	0.864	0.805	0.924	CLONAL	1	TRUE	1	0.858117580139287	2		694	507	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71064723	71064723	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	217	604	1	ENST00000318789.4:c.951C>G	p.Cys317Trp	p.C317W	ENST00000318789	NM_032682.5	317	tgC/tgG	12/21	0.858117580139287	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.858117580139287	1		605	288	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138407760	138407760	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	392	669	0	ENST00000289153.2:c.2093A>T	p.Tyr698Phe	p.Y698F	ENST00000289153	NM_006219.2	698	tAc/tTc	14/22	0.85880415972684	3	FACETS	0.9	0.864	0.937	0.9	0.864	0.937	CLONAL	2	TRUE	1	0.858117580139287	3		669	725	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665334	176665334	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	237	493	0	ENST00000439151.2:c.4018G>T	p.Glu1340Ter	p.E1340*	ENST00000439151	NM_022455.4	1340	Gaa/Taa	7/23	0.85880415972684	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.858117580139287	1		493	293	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522039	157522039	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	183	590	0	ENST00000346085.5:c.4311G>C	p.Gln1437His	p.Q1437H	ENST00000346085	NM_020732.3	1437	caG/caC	18/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.858117580139287	2		590	377	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028025	69028025	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs200550325	NA	P-0031721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	167	628	0	ENST00000288368.4:c.3184C>G	p.Arg1062Gly	p.R1062G	ENST00000288368	NM_024870.2	1062	Cgt/Ggt	26/40	1	2	FACETS	0.863	0.801	0.926	0.863	0.801	0.926	CLONAL	1	TRUE	1	0.858117580139287	2		628	451	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518418	8518418	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	118	293	0	ENST00000356435.5:c.973C>A	p.Pro325Thr	p.P325T	ENST00000356435		325	Cct/Act	10/35	0.85880415972684	1	FACETS	0.994	0.937	1	0.994	0.937	1	CLONAL	1	TRUE	0	0.858117580139287	1		293	158	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409880	63409880	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	128	258	0	ENST00000330258.3:c.3287A>T	p.Gln1096Leu	p.Q1096L	ENST00000330258	NM_152424.3	1096	cAg/cTg	2/2	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.858117580139287	1		258	152	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0031735-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	63	432	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	0.236184093341174	2		432	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577563	7577563	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1567549584	NA	P-0031735-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	156	650	0	ENST00000269305.4:c.718A>G	p.Ser240Gly	p.S240G	ENST00000269305	NM_001126112.2	240	Agt/Ggt	7/11	0.236184093341174	2	FACETS	0.926	0.85	1	0.926	0.85	1	CLONAL	2	TRUE	0	0.236184093341174	2		650	713	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799221	45799221	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031735-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	40	484	0	ENST00000450313.1:c.212A>C	p.Gln71Pro	p.Q71P	ENST00000450313	NM_012222.2	71	cAg/cCg	3/16	1	2	FACETS	0.743	0.617	0.882	0.743	0.617	0.882	SUBCLONAL	1	TRUE	1	0.236184093341174	2		484	456	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435601	18435602	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0031735-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	32	314	0	ENST00000266497.5:c.586_587delinsTT	p.Gly196Leu	p.G196L	ENST00000266497		196	GGa/TTa	1/31	1	2	FACETS	0.816	0.664	0.988	0.816	0.664	0.988	CLONAL	1	TRUE	1	0.236184093341174	2		314	332	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525111	9525111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031735-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	47	365	0	ENST00000353224.5:c.1774C>A	p.Gln592Lys	p.Q592K	ENST00000353224	NM_177990.2	592	Caa/Aaa	8/10	1	2	FACETS	0.9	0.761	1	0.9	0.761	1	CLONAL	1	TRUE	1	0.236184093341174	2		365	442	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430434	181430434	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031735-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	53	610	0	ENST00000325404.1:c.286del	p.Arg96GlyfsTer7	p.R96Gfs*7	ENST00000325404	NM_003106.3	96	Cgg/gg	1/1	0.227638645773002	1	FACETS	0.823	0.702	0.954	0.823	0.702	0.954	CLONAL	1	TRUE	0	0.236184093341174	1		610	481	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430648	181430648	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031735-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	63	541	2	ENST00000325404.1:c.500G>T	p.Ser167Ile	p.S167I	ENST00000325404	NM_003106.3	167	aGc/aTc	1/1	0.227638645773002	1	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	0	0.236184093341174	1		543	444	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535363	66535363	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031735-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	91	531	1	ENST00000273854.3:c.98C>A	p.Ser33Tyr	p.S33Y	ENST00000273854	NM_004439.5	33	tCt/tAt	1/18	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.236184093341174	2		532	572	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515189	31515189	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031735-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	95	782	0	ENST00000344624.3:c.1196A>G	p.Lys399Arg	p.K399R	ENST00000344624		399	aAg/aGg	5/33	1	2	FACETS	0.825	0.733	0.923	0.825	0.733	0.923	CLONAL	1	TRUE	1	0.236184093341174	2		782	975	SUCCESS
APC	324	MSKCC	GRCh37	5	112177543	112177543	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031735-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	34	340	0	ENST00000257430.4:c.6252G>T	p.Gln2084His	p.Q2084H	ENST00000257430	NM_000038.5	2084	caG/caT	16/16	1	2	FACETS	0.859	0.704	1	0.859	0.704	1	CLONAL	1	TRUE	1	0.236184093341174	2		340	335	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341104	8341104	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031735-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	46	449	0	ENST00000356435.5:c.5112T>A	p.Phe1704Leu	p.F1704L	ENST00000356435		1704	ttT/ttA	30/35	1	2	FACETS	0.843	0.711	0.989	0.843	0.711	0.989	CLONAL	1	TRUE	1	0.236184093341174	2		449	462	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465578	8465578	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031735-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	51	642	0	ENST00000356435.5:c.3602C>A	p.Thr1201Asn	p.T1201N	ENST00000356435		1201	aCt/aAt	21/35	1	2	FACETS	0.71	0.603	0.828	0.71	0.603	0.828	SUBCLONAL	1	TRUE	1	0.236184093341174	2		642	608	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499740	8499740	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031735-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	77	571	0	ENST00000356435.5:c.2229G>T	p.Gln743His	p.Q743H	ENST00000356435		743	caG/caT	14/35	1	2	FACETS	0.937	0.822	1	0.937	0.822	1	CLONAL	1	TRUE	1	0.236184093341174	2		571	696	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0031741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	150	432	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.209469218032684	3	FACETS	0.828	0.756	0.903	0.828	0.756	0.903	CLONAL	2	TRUE	1	0.209469218032684	3		432	956	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207077	1207077	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs121913319	NA	P-0031741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	193	1135	3	ENST00000326873.7:c.169del	p.Glu57LysfsTer7	p.E57Kfs*7	ENST00000326873	NM_000455.4	55	ctG/ct	1/10	1	2	FACETS	0.801	0.739	0.864	1	0.991	1	CLONAL	2	TRUE	1	0.209469218032684	2		1138	1151	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259166	89259166	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	71	582	0	ENST00000336596.2:c.310C>T	p.Arg104Ter	p.R104*	ENST00000336596	NM_005233.5	104	Cga/Tga	3/17	1	2	FACETS	0.943	0.822	1	0.943	0.822	1	CLONAL	1	TRUE	1	0.209469218032684	2		582	719	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56811507	56811507	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	59	727	2	ENST00000337432.4:c.1055C>G	p.Thr352Ser	p.T352S	ENST00000337432	NM_058216.2	352	aCt/aGt	9/9	1	2	FACETS	0.652	0.559	0.753	0.652	0.559	0.753	SUBCLONAL	1	TRUE	1	0.209469218032684	2		729	864	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727127	40727127	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	85	887	0	ENST00000373198.4:c.3837C>G	p.Phe1279Leu	p.F1279L	ENST00000373198	NM_133170.3	1279	ttC/ttG	28/32	1	2	FACETS	0.877	0.774	0.989	0.877	0.774	0.989	CLONAL	1	TRUE	1	0.209469218032684	2		887	925	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620479	52620479	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	53	690	0	ENST00000394830.3:c.3274G>T	p.Glu1092Ter	p.E1092*	ENST00000394830	NM_018313.4	1092	Gag/Tag	21/30	1	2	FACETS	0.611	0.52	0.712	0.611	0.52	0.712	SUBCLONAL	1	TRUE	1	0.209469218032684	2		690	828	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857304	68857304	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	72	429	0	ENST00000261769.5:c.1939C>T	p.Gln647Ter	p.Q647*	ENST00000261769	NM_004360.3	647	Caa/Taa	13/16	0.317757833010868	1	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	0	0.317757833010868	1		429	371	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085897	16085897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775092426	NA	P-0031743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	119	673	2	ENST00000281043.3:c.1073C>T	p.Pro358Leu	p.P358L	ENST00000281043	NM_005378.4	358	cCg/cTg	3/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.317757833010868	2		675	625	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191119	185191119	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	138	666	0	ENST00000265026.3:c.2000C>T	p.Ala667Val	p.A667V	ENST00000265026	NM_004721.4	667	gCc/gTc	11/14	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.317757833010868	2		666	701	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517394	176517394	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	31	461	0	ENST00000292408.4:c.95C>T	p.Pro32Leu	p.P32L	ENST00000292408	NM_213647.1	32	cCc/cTc	3/18	0.211827704944704	4	FACETS	0.483	0.39	0.589	0.242	0.195	0.295	SUBCLONAL	1	TRUE	2	0.317757833010868	4		461	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578419	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587781845	NA	P-0031790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	711	553	1	ENST00000269305.4:c.511G>T	p.Glu171Ter	p.E171*	ENST00000269305	NM_001126112.2	171	Gag/Tag	5/11	0.684199193567253	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.684199193567253	3		554	890	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272209	15272209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	363	445	1	ENST00000263388.2:c.6230C>T	p.Pro2077Leu	p.P2077L	ENST00000263388	NM_000435.2	2077	cCc/cTc	33/33	0.641356493421702	4	FACETS	0.923	0.878	0.969	0.923	0.878	0.969	CLONAL	2	TRUE	2	0.684199193567253	4		446	968	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658300	18658300	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	220	366	0	ENST00000266497.5:c.3105C>A	p.His1035Gln	p.H1035Q	ENST00000266497		1035	caC/caA	22/31	0.60565957971893	5	FACETS	0.929	0.869	0.992	0.62	0.579	0.661	CLONAL	2	TRUE	2	0.684199193567253	5		366	701	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662793	117662793	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	148	176	0	ENST00000368508.3:c.4672C>A	p.Pro1558Thr	p.P1558T	ENST00000368508	NM_002944.2	1558	Cca/Aca	29/43	0.60565957971893	5	FACETS	0.949	0.882	1	0.949	0.882	1	CLONAL	3	TRUE	2	0.684199193567253	5		176	308	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467748	50467748	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs758496021	NA	P-0031790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	433	444	0	ENST00000331340.3:c.983G>T	p.Arg328Leu	p.R328L	ENST00000331340	NM_006060.4	328	cGc/cTc	8/8	0.641356493421702	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	2	0.684199193567253	4		444	1032	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396362	139396362	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	666	499	0	ENST00000277541.6:c.5476G>T	p.Glu1826Ter	p.E1826*	ENST00000277541	NM_017617.3	1826	Gag/Tag	30/34	0.684199193567253	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.684199193567253	3		499	825	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	86	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.280247620956962	5	FACETS	0.887	0.797	0.981	0.887	0.797	0.981	CLONAL	3	TRUE	2	0.411562564768577	5		493	254	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0031792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	51	378	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.411562564768577	3	FACETS	1	0.891	1	0.524	0.449	0.606	CLONAL	1	TRUE	1	0.411562564768577	3		378	285	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247910	59247910	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	302	667	0	ENST00000371222.2:c.833C>G	p.Ala278Gly	p.A278G	ENST00000371222	NM_002228.3	278	gCc/gGc	1/1	0.352907376764908	2	FACETS	0.954	0.904	1	0.954	0.904	1	CLONAL	2	TRUE	0	0.411562564768577	2		667	769	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913082	44913082	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	62	225	0	ENST00000377967.4:c.757C>A	p.His253Asn	p.H253N	ENST00000377967	NM_021140.2	253	Cat/Aat	10/29	0.404965176676066	2	FACETS	0.913	0.822	1			1	CLONAL	3	TRUE	NA	0.411562564768577	2		225	110	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0031802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	156	460	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.441405860342494	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.441405860342494	1		460	526	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0031802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	73	367	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.271146911521653	1	FACETS	0.464	0.406	0.526	0.464	0.406	0.526	SUBCLONAL	1	TRUE	0	0.441405860342494	1		367	556	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119781	70119781	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1274036689	NA	P-0031802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	191	544	0	ENST00000245479.2:c.788del	p.Gly263AlafsTer16	p.G263Afs*16	ENST00000245479	NM_000346.3	261	gaG/ga	3/3	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.441405860342494	2		544	827	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0031802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	99	303	1	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.441405860342494	1	FACETS	0.836	0.751	0.925	0.836	0.751	0.925	CLONAL	1	TRUE	0	0.441405860342494	1		304	418	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522416	176522416	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519792	NA	P-0031802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	272	650	0	ENST00000292408.4:c.1605C>G	p.Asn535Lys	p.N535K	ENST00000292408	NM_213647.1	535	aaC/aaG	12/18	0.214250250581032	2	FACETS	1	0.993	1	0.708	0.666	0.751	INDETERMINATE	1	TRUE	0	0.441405860342494	2		650	870	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888189	112888189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507511	NA	P-0031802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	148	495	0	ENST00000351677.2:c.205G>A	p.Glu69Lys	p.E69K	ENST00000351677	NM_002834.3	69	Gag/Aag	3/16	1	2	FACETS	0.891	0.815	0.97	0.891	0.815	0.97	CLONAL	1	TRUE	1	0.441405860342494	2		495	753	SUCCESS
APC	324	MSKCC	GRCh37	5	112175411	112175411	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	83	219	0	ENST00000257430.4:c.4120G>T	p.Glu1374Ter	p.E1374*	ENST00000257430	NM_000038.5	1374	Gaa/Taa	16/16	0.271146911521653	1	FACETS	0.967	0.863	1	0.967	0.863	1	CLONAL	1	TRUE	0	0.441405860342494	1		219	303	SUCCESS
APC	324	MSKCC	GRCh37	5	112175351	112175352	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0031802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	25	205	0	ENST00000257430.4:c.4062_4063del	p.Ser1355PhefsTer19	p.S1355Ffs*19	ENST00000257430	NM_000038.5	1354	TTt/t	16/16	0.271146911521653	1	FACETS	0.343	0.271	0.426	0.343	0.271	0.426	SUBCLONAL	1	TRUE	0	0.441405860342494	1		205	257	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	151	820	2	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	0.271146911521653	1	FACETS	0.864	0.793	0.938	0.864	0.793	0.938	CLONAL	1	TRUE	0	0.441405860342494	1		822	617	SUCCESS
APC	324	MSKCC	GRCh37	5	112175072	112175072	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	58	170	0	ENST00000257430.4:c.3781A>C	p.Thr1261Pro	p.T1261P	ENST00000257430	NM_000038.5	1261	Act/Cct	16/16	0.271146911521653	1	FACETS	0.894	0.778	1	0.894	0.778	1	CLONAL	1	TRUE	0	0.441405860342494	1		170	229	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0031803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	133	851	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.31	2		851	739	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398255	25398255	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913236	NA	P-0031803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	21	396	0	ENST00000311936.3:c.64C>A	p.Gln22Lys	p.Q22K	ENST00000311936	NM_004985.3	22	Cag/Aag	2/5	0.30076422776175	1	FACETS	0.806	0.627	1	0.806	0.627	1	CLONAL	1	TRUE	0	0.31	1		396	142	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277230	41277230	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	38	246	0	ENST00000349496.5:c.1699G>A	p.Glu567Lys	p.E567K	ENST00000349496	NM_001904.3	567	Gaa/Aaa	11/15	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.31	2		246	191	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0031803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	30	359	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	0.30076422776175	1	FACETS	0.94	0.765	1	0.94	0.765	1	CLONAL	1	TRUE	0	0.31	1		359	174	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699324	18699324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369934938	NA	P-0031803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	15	303	0	ENST00000266497.5:c.3425G>A	p.Arg1142His	p.R1142H	ENST00000266497		1142	cGt/cAt	24/31	0.30076422776175	1	FACETS	0.687	0.507	0.898	0.687	0.507	0.898	SUBCLONAL	1	TRUE	0	0.31	1		303	119	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436108	51436108	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	55	350	0	ENST00000262662.1:c.68G>C	p.Ser23Thr	p.S23T	ENST00000262662		23	aGt/aCt	3/4	1	2	FACETS	0.98	0.842	1	0.98	0.842	1	CLONAL	1	TRUE	1	0.31	2		350	362	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865611	57865611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1027428919	NA	P-0031803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	113	633	0	ENST00000228682.2:c.3088G>A	p.Glu1030Lys	p.E1030K	ENST00000228682	NM_005269.2	1030	Gaa/Aaa	12/12	0.30076422776175	1	FACETS	0.878	0.79	0.969	0.878	0.79	0.969	CLONAL	1	TRUE	0	0.31	1		633	702	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241496	105241496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	99	555	0	ENST00000349310.3:c.484G>A	p.Gly162Ser	p.G162S	ENST00000349310	NM_001014432.1	162	Ggc/Agc	7/15	0.30076422776175	1	FACETS	0.843	0.754	0.938	0.843	0.754	0.938	CLONAL	1	TRUE	0	0.31	1		555	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0031832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	154	503	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.387765388094286	1	FACETS	0.956	0.877	1	0.956	0.877	1	CLONAL	1	TRUE	0	0.387765388094286	1		504	670	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	85	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.855	0.758	0.958	0.855	0.758	0.958	CLONAL	1	TRUE	1	0.387765388094286	2		493	513	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	88	328	0	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	0.270737914380978	1	FACETS	0.841	0.749	0.938	0.841	0.749	0.938	CLONAL	1	TRUE	0	0.387765388094286	1		328	435	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114917829	114917829	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0031832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	106	456	0	ENST00000543371.1:c.1318+1G>A		p.X440_splice	ENST00000543371	NM_001198531.1	440			0.270737914380978	1	FACETS	0.776	0.698	0.859	0.776	0.698	0.859	SUBCLONAL	1	TRUE	0	0.387765388094286	1		456	568	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949133	71949141	+	inframe_deletion	In_Frame_Del	DEL	CATGAGTGC	CATGAGTGC	-	novel	NA	P-0031832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	213	711	0	ENST00000298229.2:c.3601_3609del	p.Met1201_Ala1203del	p.M1201_A1203del	ENST00000298229	NM_001567.3	1200	ggCATGAGTGCc/ggc	27/28	0.387765388094286	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.387765388094286	1		711	794	SUCCESS
APC	324	MSKCC	GRCh37	5	112173860	112173860	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	42	268	0	ENST00000257430.4:c.2569G>T	p.Gly857Ter	p.G857*	ENST00000257430	NM_000038.5	857	Gga/Tga	16/16	0.270737914380978	1	FACETS	0.468	0.392	0.553	0.468	0.392	0.553	SUBCLONAL	1	TRUE	0	0.387765388094286	1		268	373	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967972	93967972	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	49	450	0	ENST00000369303.4:c.1955T>G	p.Leu652Trp	p.L652W	ENST00000369303	NM_004440.3	652	tTg/tGg	11/17	0.387765388094286	1	FACETS	0.435	0.369	0.508	0.435	0.369	0.508	SUBCLONAL	1	TRUE	0	0.387765388094286	1		450	468	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0031833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	85	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.289425114050812	0	FACETS	0.306	0.273	0.341			1	INDETERMINATE	1	TRUE	0	0.624541397303976	0		539	334	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0031833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	46	312	0	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	1	2	FACETS	0.921	0.789	1	0.921	0.789	1	CLONAL	1	TRUE	1	0.624541397303976	2		312	160	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519980	NA	P-0031833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	67	610	0	ENST00000269305.4:c.528C>G	p.Cys176Trp	p.C176W	ENST00000269305	NM_001126112.2	176	tgC/tgG	5/11	0.624541397303976	1	FACETS	0.69	0.609	0.774	0.69	0.609	0.774	SUBCLONAL	1	TRUE	0	0.624541397303976	1		610	214	SUCCESS
APC	324	MSKCC	GRCh37	5	112175213	112175213	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0031833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	45	207	0	ENST00000257430.4:c.3922A>T	p.Lys1308Ter	p.K1308*	ENST00000257430	NM_000038.5	1308	Aaa/Taa	16/16	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.624541397303976	2		207	123	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237659	133237659	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	105	590	0	ENST00000320574.5:c.2956C>T	p.Gln986Ter	p.Q986*	ENST00000320574	NM_006231.2	986	Caa/Taa	25/49	0.17990583336627	0	FACETS	0.353	0.319	0.388			1	INDETERMINATE	1	TRUE	0	0.624541397303976	0		590	358	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468368	89468368	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	35	211	1	ENST00000336596.2:c.1902G>T	p.Glu634Asp	p.E634D	ENST00000336596	NM_005233.5	634	gaG/gaT	11/17	1	2	FACETS	0.83	0.693	0.978	0.83	0.693	0.978	CLONAL	1	TRUE	1	0.624541397303976	2		212	135	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0031890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	84	313	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.350204028441628	6	FACETS	0.946	0.843	1	0.473	0.421	0.527	CLONAL	2	TRUE	2	0.564010893245746	6		313	335	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415537	152415537	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519714	NA	P-0031890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	132	666	0	ENST00000206249.3:c.1387T>C	p.Ser463Pro	p.S463P	ENST00000206249	NM_000125.3	463	Tcc/Ccc	7/8	0.346174677706085	4	FACETS	0.979	0.899	1	0.979	0.899	1	CLONAL	2	TRUE	2	0.564010893245746	4		666	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0031913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	49	624	2	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.14	2		626	686	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983294	15983294	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567882136	NA	P-0031913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	36	471	0	ENST00000268712.3:c.3485G>A	p.Arg1162Gln	p.R1162Q	ENST00000268712	NM_006311.3	1162	cGg/cAg	26/46	1	2	FACETS	0.763	0.626	0.918	0.763	0.626	0.918	CLONAL	1	TRUE	1	0.14	2		471	674	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7978975	7978975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769562383	NA	P-0031936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	667	638	1	ENST00000319144.4:c.1592C>T	p.Pro531Leu	p.P531L	ENST00000319144	NM_001139.2	531	cCg/cTg	12/15	0.732165317500898	3	FACETS	0.957	0.937	0.977	0.957	0.937	0.977	CLONAL	3	TRUE	0	0.773472001981643	3		639	833	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	790	685	0	ENST00000269305.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	336	Gag/Tag	10/11	0.732165317500898	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.773472001981643	3		685	942	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502163	157502163	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554231195	NA	P-0031936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	162	527	0	ENST00000346085.5:c.3196G>T	p.Glu1066Ter	p.E1066*	ENST00000346085	NM_020732.3	1066	Gag/Tag	12/20	0.773472001981643	3	FACETS	0.954	0.879	1	0.477	0.439	0.516	CLONAL	1	TRUE	1	0.773472001981643	3		527	609	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390861	139390861	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	664	788	1	ENST00000277541.6:c.7330C>T	p.Gln2444Ter	p.Q2444*	ENST00000277541	NM_017617.3	2444	Cag/Tag	34/34	0.773472001981643	4	FACETS	0.99	0.963	1	0.99	0.963	1	CLONAL	3	TRUE	1	0.773472001981643	4		789	1025	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100406	8100406	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	118	782	0	ENST00000346208.3:c.380C>A	p.Pro127Gln	p.P127Q	ENST00000346208		127	cCg/cAg	3/6	0.773472001981643	3	FACETS	0.438	0.394	0.484	0.219	0.197	0.242	SUBCLONAL	1	TRUE	1	0.773472001981643	3		782	967	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376221	118376221	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	144	470	0	ENST00000534358.1:c.9614del	p.Ser3205ThrfsTer10	p.S3205Tfs*10	ENST00000534358	NM_005933.3	3205	aGc/ac	27/36	0.368629470342942	1	FACETS	0.676	0.625	0.727	0.676	0.625	0.727	INDETERMINATE	1	TRUE	0	0.773472001981643	1		470	338	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244852	46244852	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	98	718	0	ENST00000334344.6:c.2946C>A	p.Asn982Lys	p.N982K	ENST00000334344	NM_152641.2	982	aaC/aaA	15/21	0.599530624327881	5	FACETS	0.472	0.42	0.528	0.157	0.14	0.176	SUBCLONAL	1	TRUE	2	0.773472001981643	5		718	1160	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29497016	29497016	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1555607126	NA	P-0031936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	236	368	0	ENST00000356175.3:c.586+1G>T		p.X196_splice	ENST00000356175	NM_000267.3	196			0.720239832798588	5	FACETS	0.865	0.81	0.921	0.346	0.324	0.369	CLONAL	2	TRUE	0	0.773472001981643	5		368	762	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435483	56435483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746033324	NA	P-0031936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	97	795	1	ENST00000407977.2:c.1654C>T	p.Arg552Cys	p.R552C	ENST00000407977		552	Cgc/Tgc	9/10	0.229334504737141	3	FACETS	0.433	0.385	0.483			1	INDETERMINATE	1	TRUE	NA	0.773472001981643	3		796	804	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793397	42793397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767293276	NA	P-0031936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	51	630	1	ENST00000575354.2:c.1199C>T	p.Pro400Leu	p.P400L	ENST00000575354	NM_015125.3	400	cCc/cTc	8/20	0.44260137357516	5	FACETS	0.345	0.292	0.403	0.115	0.097	0.135	INDETERMINATE	1	TRUE	2	0.773472001981643	5		631	826	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803356	1803356	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	78	668	0	ENST00000260795.2:c.625C>G	p.Gln209Glu	p.Q209E	ENST00000260795		209	Cag/Gag	5/17	0.368629470342942	1	FACETS	0.275	0.242	0.31	0.275	0.242	0.31	INDETERMINATE	1	TRUE	0	0.773472001981643	1		668	450	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912331	97912331	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	170	430	0	ENST00000289081.3:c.560G>C	p.Cys187Ser	p.C187S	ENST00000289081	NM_000136.2	187	tGt/tCt	7/15	0.740834846986578	2	FACETS	0.931	0.864	1	0.466	0.432	0.5	CLONAL	1	TRUE	0	0.773472001981643	2		430	472	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692896	89692896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123322	NA	P-0031951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	228	464	0	ENST00000371953.3:c.380G>A	p.Gly127Glu	p.G127E	ENST00000371953	NM_000314.4	127	gGa/gAa	5/9	0.597221373296511	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.597221373296511	1		464	481	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576857	7576857	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	560	675	1	ENST00000269305.4:c.989T>C	p.Leu330Pro	p.L330P	ENST00000269305	NM_001126112.2	330	cTt/cCt	9/11	0.594017510739381	2	FACETS	0.944	0.913	0.976	0.944	0.913	0.976	CLONAL	2	TRUE	0	0.597221373296511	2		676	993	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976402	18976402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748251529	NA	P-0031951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	354	750	0	ENST00000262803.5:c.3052G>A	p.Gly1018Arg	p.G1018R	ENST00000262803	NM_002911.3	1018	Ggg/Agg	22/24	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.597221373296511	2		750	1129	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591121	67591135	+	inframe_deletion	In_Frame_Del	DEL	CAGCTGAGAAAGACG	CAGCTGAGAAAGACG	-	novel	NA	P-0031951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	54	276	0	ENST00000274335.5:c.1714_1728del	p.Gln572_Thr576del	p.Q572_T576del	ENST00000274335		572	CAGCTGAGAAAGACG/-	12/15	0.597221373296511	1	FACETS	0.366	0.313	0.422	0.366	0.313	0.422	SUBCLONAL	1	TRUE	0	0.597221373296511	1		276	347	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188061	32188061	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	168	622	1	ENST00000375023.3:c.1160G>T	p.Gly387Val	p.G387V	ENST00000375023	NM_004557.3	387	gGa/gTa	7/30	0.154815370765265	2	FACETS	0.667	0.613	0.722	0.333	0.306	0.361	INDETERMINATE	1	TRUE	0	0.597221373296511	2		623	844	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033853	49033855	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0031951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	252	432	0	ENST00000267163.4:c.1990_1992del	p.Thr664del	p.T664del	ENST00000267163	NM_000321.2	664	ACA/-	20/27	0.597221373296511	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.597221373296511	1		432	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0031963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	284	879	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.305154502994676	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.305154502994676	2		879	799	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907082	32907082	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	117	474	0	ENST00000380152.3:c.1467del	p.Gly490GlufsTer19	p.G490Efs*19	ENST00000380152		489	tcT/tc	10/27	0.305154502994676	3	FACETS	0.94	0.853	1	0.94	0.853	1	CLONAL	2	TRUE	1	0.305154502994676	3		474	470	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0031965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	47	565	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.93	0.785	1	0.93	0.785	1	CLONAL	1	TRUE	1	0.201033551336376	2		565	503	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0031965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	47	455	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.201033551336376	2		455	413	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295133	1295163	+	5_prime_UTR_variant	5'UTR	DEL	CACGTGCGCAGCAGGACGCAGCGCTGCCTGA	CACGTGCGCAGCAGGACGCAGCGCTGCCTGA	TGT	novel	NA	P-0031965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	21	172	0				ENST00000310581	NM_198253.2	-/1132		1/16	1	2	FACETS	0.901	0.696	1	0.901	0.696	1	CLONAL	1	TRUE	1	0.201033551336376	2		172	232	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589585	67589605	+	inframe_deletion	In_Frame_Del	DEL	CATGAATATAACACTCAGTTT	CATGAATATAACACTCAGTTT	-	novel	NA	P-0031965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	11	206	0	ENST00000274335.5:c.1350_1370del	p.His450_Phe456del	p.H450_F456del	ENST00000274335		450	CATGAATATAACACTCAGTTT/-	10/15	1	2	FACETS	0.601	0.416	0.831	0.601	0.416	0.831	SUBCLONAL	1	TRUE	1	0.201033551336376	2		206	182	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176662828	176662828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368706736	NA	P-0031965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	27	354	0	ENST00000439151.2:c.3803G>A	p.Arg1268Gln	p.R1268Q	ENST00000439151	NM_022455.4	1268	cGg/cAg	6/23	1	2	FACETS	0.917	0.731	1	0.917	0.731	1	CLONAL	1	TRUE	1	0.201033551336376	2		354	293	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406297	70406297	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	48	684	0	ENST00000373644.4:c.3811G>C	p.Glu1271Gln	p.E1271Q	ENST00000373644	NM_030625.2	1271	Gaa/Caa	4/12	0.172742236320681	3	FACETS	0.707	0.597	0.829	0.354	0.298	0.415	SUBCLONAL	1	TRUE	1	0.242239983600579	3		684	628	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938457	76938457	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	101	777	0	ENST00000373344.5:c.2291del	p.Leu764CysfsTer4	p.L764Cfs*4	ENST00000373344	NM_000489.3	764	tTg/tg	9/35	0.19816605858922	2	FACETS	0.771	0.691	0.855	0.771	0.691	0.855	SUBCLONAL	2	TRUE	0	0.242239983600579	2		777	541	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0031999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	170	619	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.204658891601685	3	FACETS	0.888	0.816	0.964	0.888	0.816	0.964	CLONAL	2	TRUE	1	0.204658891601685	3		619	1031	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183540	185183540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	43	395	1	ENST00000265026.3:c.1394C>T	p.Ala465Val	p.A465V	ENST00000265026	NM_004721.4	465	gCg/gTg	9/14	1	2	FACETS	0.783	0.654	0.925	0.783	0.654	0.925	CLONAL	1	TRUE	1	0.204658891601685	2		396	537	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246116	46246116	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	94	399	0	ENST00000334344.6:c.4210C>T	p.Gln1404Ter	p.Q1404*	ENST00000334344	NM_152641.2	1404	Caa/Taa	15/21	0.204658891601685	2	FACETS	0.834	0.744	0.929	0.834	0.744	0.929	CLONAL	2	TRUE	0	0.204658891601685	2		399	551	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161310416	161310416	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	73	567	0	ENST00000367975.2:c.212A>G	p.His71Arg	p.H71R	ENST00000367975	NM_003001.3	71	cAc/cGc	4/6	0.188637362991003	4	FACETS	0.782	0.682	0.891	0.261	0.227	0.297	SUBCLONAL	1	TRUE	1	0.204658891601685	4		567	1099	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350040	15350040	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1231	121	1050	0	ENST00000263377.2:c.3612C>G	p.Ser1204Arg	p.S1204R	ENST00000263377	NM_058243.2	1204	agC/agG	18/20	1	2	FACETS	0.875	0.788	0.967	0.875	0.788	0.967	CLONAL	1	TRUE	1	0.204658891601685	2		1050	1352	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891328	101891328	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	115	702	0	ENST00000374994.4:c.289A>C	p.Thr97Pro	p.T97P	ENST00000374994	NM_004612.2	97	Aca/Cca	2/9	0.204658891601685	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.204658891601685	1		702	919	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	97	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.2	2		539	785	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778914	9778914	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	48	653	0	ENST00000377346.4:c.1183T>A	p.Tyr395Asn	p.Y395N	ENST00000377346	NM_005026.3	395	Tac/Aac	9/24	0.538717203210003	2	FACETS	0.305	0.257	0.357	0.153	0.128	0.179	SUBCLONAL	1	TRUE	0	0.586131956115738	2		653	537	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894228	NA	P-0032009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	240	627	0	ENST00000451590.1:c.37G>C	p.Gly13Arg	p.G13R	ENST00000451590	NM_001130442.1	13	Ggt/Cgt	2/5	0.541959563264556	2	FACETS	0.973	0.923	1	0.973	0.923	1	CLONAL	2	TRUE	0	0.586131956115738	2		627	421	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94209459	94209459	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	111	396	0	ENST00000323929.3:c.655A>T	p.Asn219Tyr	p.N219Y	ENST00000323929	NM_005591.3	219	Aac/Tac	7/20	0.541959563264556	2	FACETS	1	0.95	1	0.535	0.486	0.586	CLONAL	1	TRUE	0	0.586131956115738	2		396	354	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217867	7217868	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0032009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	314	705	0	ENST00000380728.2:c.143_144del	p.Gln48ArgfsTer48	p.Q48Rfs*48	ENST00000380728		48	cAG/c	3/11	0.571464995619255	2	FACETS	0.905	0.863	0.947	0.905	0.863	0.947	CLONAL	2	TRUE	0	0.586131956115738	2		705	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0032009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	226	739	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.571464995619255	2	FACETS	0.774	0.729	0.82	0.774	0.729	0.82	SUBCLONAL	2	TRUE	0	0.586131956115738	2		739	498	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526081	66526082	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0032009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	279	469	0	ENST00000358598.2:c.913dup	p.Arg305ProfsTer6	p.R305Pfs*6	ENST00000358598	NM_212471.2	304	-/C	10/11	0.582820241540579	2	FACETS	0.903	0.859	0.947	0.903	0.859	0.947	CLONAL	2	TRUE	0	0.586131956115738	2		469	527	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5239008	5239008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138765579	NA	P-0032009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	184	627	2	ENST00000357368.4:c.1771G>A	p.Ala591Thr	p.A591T	ENST00000357368	NM_002850.3	591	Gcc/Acc	13/38	0.304088720046165	3	FACETS	1	0.985	1	0.413	0.382	0.444	INDETERMINATE	1	TRUE	0	0.586131956115738	3		629	656	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366336	15366336	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	138	623	0	ENST00000263377.2:c.1819T>G	p.Cys607Gly	p.C607G	ENST00000263377	NM_058243.2	607	Tgc/Ggc	10/20	0.304088720046165	3	FACETS	1	0.97	1	0.378	0.345	0.412	INDETERMINATE	1	TRUE	0	0.586131956115738	3		623	537	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743881	40743882	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0032009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	89	635	0	ENST00000373198.4:c.3113_3114del	p.Glu1038AlafsTer19	p.E1038Afs*19	ENST00000373198	NM_133170.3	1038	gAG/g	23/32	0.300426392078676	3	FACETS	0.596	0.528	0.668	0.298	0.264	0.334	INDETERMINATE	1	TRUE	1	0.586131956115738	3		635	659	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665353	117665353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	140	429	0	ENST00000368508.3:c.4394C>T	p.Thr1465Ile	p.T1465I	ENST00000368508	NM_002944.2	1465	aCa/aTa	27/43	0.174321127420335	2	FACETS	1	0.961	1	0.538	0.494	0.583	INDETERMINATE	1	TRUE	0	0.586131956115738	2		429	444	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0032042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	66	526	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.931	0.808	1	0.931	0.808	1	CLONAL	1	TRUE	1	0.21	2		527	675	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	61	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.0660068831980336	4	FACETS	1	0.93	1	0.564	0.486	0.649	INDETERMINATE	1	TRUE	2	0.21	4		493	623	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0032042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	112	776	4	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.295404963993702	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.21	1		780	844	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732969	30732969	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	98	372	0	ENST00000295754.5:c.1582C>G	p.Arg528Gly	p.R528G	ENST00000295754	NM_003242.5	528	Cgt/Ggt	7/7	0.231493304751275	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.21	2		372	399	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912139	50912139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501836	NA	P-0032042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	116	880	1	ENST00000440232.2:c.1873G>A	p.Gly625Arg	p.G625R	ENST00000440232	NM_002691.3	625	Ggg/Agg	15/27	0.3	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.21	1		881	896	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950500	68950500	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	55	243	0	ENST00000288368.4:c.812T>A	p.Leu271His	p.L271H	ENST00000288368	NM_024870.2	271	cTt/cAt	7/40	1	2	FACETS	0.895	0.766	1	0.895	0.766	1	CLONAL	1	TRUE	1	0.21	2		243	585	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341631	70341631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	114	895	1	ENST00000374080.3:c.1066C>T	p.Arg356Trp	p.R356W	ENST00000374080		356	Cgg/Tgg	7/45	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.21	2		896	974	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216967	7216967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	144	301	0	ENST00000380728.2:c.554G>A	p.Gly185Asp	p.G185D	ENST00000380728		185	gGt/gAt	7/11	1	2	FACETS	0.998	0.917	1	1	0.991	1	CLONAL	2	TRUE	1	0.3	2		301	481	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0032048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	368	851	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.726085000600566	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.726085000600566	2		851	504	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0032048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	184	256	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.726085000600566	4	FACETS	0.935	0.871	0.999	0.935	0.871	0.999	CLONAL	2	TRUE	2	0.726085000600566	4		256	468	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423539	88423539	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	253	634	0	ENST00000360948.2:c.2296T>A	p.Tyr766Asn	p.Y766N	ENST00000360948	NM_001012338.2	766	Tat/Aat	18/19	0.578927696159268	4	FACETS	0.928	0.874	0.983	0.928	0.874	0.983	CLONAL	2	TRUE	2	0.726085000600566	4		634	648	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2220147	2220147	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200507664	NA	P-0032048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	200	768	1	ENST00000398665.3:c.2732C>T	p.Ser911Leu	p.S911L	ENST00000398665	NM_032482.2	911	tCg/tTg	23/28	0.726085000600566	3	FACETS	1	0.982	1	0.577	0.537	0.618	CLONAL	1	TRUE	1	0.726085000600566	3		769	651	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219026	36219026	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1026487026	NA	P-0032048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	176	735	1	ENST00000222270.7:c.4525G>A	p.Asp1509Asn	p.D1509N	ENST00000222270	NM_014727.1	1509	Gac/Aac	19/37	0.726085000600566	3	FACETS	1	0.936	1	0.507	0.468	0.546	CLONAL	1	TRUE	1	0.726085000600566	3		736	652	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956703	93956703	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	134	314	0	ENST00000369303.4:c.2533G>T	p.Val845Phe	p.V845F	ENST00000369303	NM_004440.3	845	Gtt/Ttt	15/17	0.616114645417011	4	FACETS	0.87	0.8	0.942	0.87	0.8	0.942	CLONAL	2	TRUE	2	0.726085000600566	4		314	366	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	161	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.308135717874223	3	FACETS	0.919	0.846	0.995	0.919	0.846	0.995	CLONAL	2	TRUE	1	0.308135717874223	3		539	656	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0032056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	271	851	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.308135717874223	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.308135717874223	2		851	809	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106182928	106182928	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	105	258	0	ENST00000380013.4:c.3967G>T	p.Glu1323Ter	p.E1323*	ENST00000380013	NM_001127208.2	1323	Gag/Tag	8/11	0.308135717874223	2	FACETS	0.811	0.732	0.894	0.811	0.732	0.894	CLONAL	2	TRUE	0	0.308135717874223	2		258	420	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593478	48593479	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs730881952	NA	P-0032056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	114	313	0	ENST00000342988.3:c.1231_1232del	p.Ser411LeufsTer17	p.S411Lfs*17	ENST00000342988	NM_005359.5	410	cAG/c	10/12	0.308135717874223	2	FACETS	0.913	0.829	1	0.913	0.829	1	CLONAL	2	TRUE	0	0.308135717874223	2		313	405	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123885	46123885	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	152	244	0	ENST00000334344.6:c.151del	p.Tyr51ThrfsTer7	p.Y51Tfs*7	ENST00000334344	NM_152641.2	51	Tac/ac	2/21	1	2	FACETS	0.98	0.908	1	0.98	0.908	1	CLONAL	1	TRUE	1	0.85	2		244	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764146326	NA	P-0032057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	223	558	0	ENST00000269305.4:c.841G>A	p.Asp281Asn	p.D281N	ENST00000269305	NM_001126112.2	281	Gac/Aac	8/11	1	2	FACETS	0.959	0.901	1	0.959	0.901	1	CLONAL	1	TRUE	1	0.85	2		558	547	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	57	349	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.368752324239595	2		349	290	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0032071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	133	384	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	0.368752324239595	2		384	633	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	166	319	1	ENST00000397062.3:c.92G>A	p.Gly31Glu	p.G31E	ENST00000397062	NM_006164.4	31	gGa/gAa	2/5	0.368752324239595	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.368752324239595	2		320	436	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119679	108119679	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	45	147	0	ENST00000278616.4:c.1085G>A	p.Arg362Lys	p.R362K	ENST00000278616	NM_000051.3	362	aGa/aAa	9/63	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.368752324239595	2		147	223	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41247926	41247926	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	87	442	0	ENST00000357654.3:c.607G>C	p.Glu203Gln	p.E203Q	ENST00000357654	NM_007294.3	203	Gaa/Caa	9/23	1	2	FACETS	0.889	0.789	0.995	0.889	0.789	0.995	CLONAL	1	TRUE	1	0.368752324239595	2		442	531	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084112	47084112	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	153	607	1	ENST00000409792.3:c.7177C>T	p.Pro2393Ser	p.P2393S	ENST00000409792	NM_014159.6	2393	Ccc/Tcc	17/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.368752324239595	2		608	735	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0032073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	149	614	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.416669211004667	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.416669211004667	1		615	501	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29002008	29002008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141378173	NA	P-0032073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	92	445	0	ENST00000282397.4:c.1157G>A	p.Arg386His	p.R386H	ENST00000282397	NM_002019.4	386	cGt/cAt	9/30	1	2	FACETS	0.878	0.783	0.979	0.878	0.783	0.979	CLONAL	1	TRUE	1	0.416669211004667	2		445	503	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285139	15285141	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs1365002420	NA	P-0032073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	1176	794	0	ENST00000263388.2:c.4474_4476del	p.Glu1492del	p.E1492del	ENST00000263388	NM_000435.2	1492	GAG/-	25/33	0.416669211004667	8	FACETS	1	0.991	1			1	CLONAL	7	TRUE	NA	0.416669211004667	8		794	1778	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638467	176638467	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784095	NA	P-0032073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	54	663	2	ENST00000439151.2:c.3067C>T	p.Arg1023Ter	p.R1023*	ENST00000439151	NM_022455.4	1023	Cga/Tga	5/23	1	2	FACETS	0.396	0.338	0.46	0.396	0.338	0.46	SUBCLONAL	1	TRUE	1	0.416669211004667	2		665	654	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0032124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	156	562	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.21022998391018	4	FACETS	1	0.987	1	0.705	0.646	0.766	INDETERMINATE	1	TRUE	2	0.401909162695859	4		562	772	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99454561	99454561	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1201603650	NA	P-0032124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	43	570	1	ENST00000268035.6:c.1480C>T	p.His494Tyr	p.H494Y	ENST00000268035	NM_000875.3	494	Cat/Tat	7/21	1	2	FACETS	0.284	0.236	0.336	0.284	0.236	0.336	SUBCLONAL	1	TRUE	1	0.401909162695859	2		571	754	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032542	47032542	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886044718	NA	P-0032124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	178	643	0	ENST00000377604.3:c.448C>T	p.Gln150Ter	p.Q150*	ENST00000377604	NM_001204468.1	150	Cag/Tag	5/24	0.2413722370625	3	FACETS	1	0.988	1	0.694	0.641	0.75	CLONAL	1	TRUE	1	0.401909162695859	3		643	766	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422649	47422649	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	41	636	0	ENST00000377045.4:c.121G>T	p.Val41Phe	p.V41F	ENST00000377045	NM_001654.4	41	Gtc/Ttc	3/16	0.2413722370625	3	FACETS	0.315	0.261	0.375	0.157	0.13	0.188	SUBCLONAL	1	TRUE	1	0.401909162695859	3		636	779	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	41	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.796	0.662	0.946	0.796	0.662	0.946	CLONAL	1	TRUE	1	0.18	2		539	572	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940008	76940008	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs797044865	NA	P-0032171-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	374	679	0	ENST00000373344.5:c.740A>G	p.Asn247Ser	p.N247S	ENST00000373344	NM_000489.3	247	aAc/aGc	9/35	0.634959008333308	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.634959008333308	3		679	750	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120239	70120239	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772647517	NA	P-0032171-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	216	778	1	ENST00000245479.2:c.1241C>T	p.Ser414Leu	p.S414L	ENST00000245479	NM_000346.3	414	tCg/tTg	3/3	0.634959008333308	3	FACETS	1	0.958	1	0.52	0.484	0.557	CLONAL	1	TRUE	1	0.634959008333308	3		779	862	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156713	20156713	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032171-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	412	643	0	ENST00000379607.5:c.44G>T	p.Gly15Val	p.G15V	ENST00000379607	NM_001412.3	15	gGt/gTt	2/7	0.634959008333308	3	FACETS	0.959	0.918	1	0.959	0.918	1	CLONAL	2	TRUE	1	0.634959008333308	3		643	891	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0032172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	384	547	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.492882428967152	6	FACETS	0.979	0.932	1	0.979	0.932	1	CLONAL	3	TRUE	3	0.492882428967152	6		547	1053	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578507	7578507	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	417	895	0	ENST00000269305.4:c.423C>A	p.Cys141Ter	p.C141*	ENST00000269305	NM_001126112.2	141	tgC/tgA	5/11	0.492882428967152	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.492882428967152	2		895	813	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922694	44922694	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397514628	NA	P-0032172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	102	191	0	ENST00000377967.4:c.1555C>T	p.Arg519Ter	p.R519*	ENST00000377967	NM_021140.2	519	Cga/Tga	16/29	0.432506365966687	2	FACETS	1	0.977	1			1	CLONAL	2	TRUE	NA	0.492882428967152	2		191	178	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9770559	9770559	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	148	714	0	ENST00000377346.4:c.46G>C	p.Glu16Gln	p.E16Q	ENST00000377346	NM_005026.3	16	Gag/Cag	3/24	0.471965300986394	3	FACETS	1	0.937	1	0.515	0.471	0.561	CLONAL	1	TRUE	1	0.492882428967152	3		714	727	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120529586	120529586	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	170	432	0	ENST00000256646.2:c.871A>G	p.Thr291Ala	p.T291A	ENST00000256646	NM_024408.3	291	Aca/Gca	5/34	0.471965300986394	3	FACETS	0.941	0.874	1	0.941	0.874	1	CLONAL	2	TRUE	1	0.492882428967152	3		432	457	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94923050	94923050	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	159	674	0	ENST00000536441.1:c.418G>T	p.Glu140Ter	p.E140*	ENST00000536441	NM_144665.3	140	Gag/Tag	4/10	0.471965300986394	3	FACETS	0.965	0.886	1	0.483	0.443	0.525	CLONAL	1	TRUE	1	0.492882428967152	3		674	833	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505337	125505337	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	73	393	0	ENST00000428830.2:c.627C>G	p.Asp209Glu	p.D209E	ENST00000428830	NM_001114121.2	209	gaC/gaG	7/14	1	2	FACETS	0.733	0.644	0.828	0.733	0.644	0.828	SUBCLONAL	1	TRUE	1	0.492882428967152	2		393	404	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650562	18650562	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	193	512	0	ENST00000266497.5:c.2773G>T	p.Asp925Tyr	p.D925Y	ENST00000266497		925	Gat/Tat	20/31	0.492882428967152	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.492882428967152	1		512	452	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937062	48937066	+	frameshift_variant	Frame_Shift_Del	DEL	TCTGT	TCTGT	-	novel	NA	P-0032172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	147	240	0	ENST00000267163.4:c.830_834del	p.Leu277GlnfsTer4	p.L277Qfs*4	ENST00000267163	NM_000321.2	277	cTCTGT/c	8/27	0.398862205328115	3	FACETS	0.873	0.813	0.932	0.873	0.813	0.932	CLONAL	3	TRUE	0	0.492882428967152	3		240	284	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807835	3807835	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	78	480	0	ENST00000262367.5:c.3584C>G	p.Ser1195Cys	p.S1195C	ENST00000262367	NM_004380.2	1195	tCc/tGc	18/31	0.147650513303174	6	FACETS	1	0.889	1	0.337	0.296	0.381	INDETERMINATE	1	TRUE	3	0.492882428967152	6		480	621	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733053	74733053	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	77	418	0	ENST00000359995.5:c.190G>C	p.Asp64His	p.D64H	ENST00000359995	NM_001195427.1	64	Gac/Cac	1/3	0.106223093981142	6	FACETS	1	0.923	1	0.356	0.313	0.403	INDETERMINATE	1	TRUE	3	0.492882428967152	6		418	581	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754516	42754516	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	353	916	0	ENST00000222329.4:c.224A>T	p.Gln75Leu	p.Q75L	ENST00000222329	NM_006494.2	75	cAg/cTg	2/4	0.471965300986394	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.492882428967152	3		916	807	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917813	29917813	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	117	672	0	ENST00000389048.3:c.855C>A	p.Asn285Lys	p.N285K	ENST00000389048	NM_004304.4	285	aaC/aaA	3/29	1	2	FACETS	0.915	0.829	1	0.915	0.829	1	CLONAL	1	TRUE	1	0.492882428967152	2		672	519	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921470	178921470	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	104	520	0	ENST00000263967.3:c.952A>G	p.Met318Val	p.M318V	ENST00000263967	NM_006218.2	318	Atg/Gtg	5/21	0.492882428967152	6	FACETS	0.868	0.776	0.967	0.289	0.258	0.323	CLONAL	1	TRUE	3	0.492882428967152	6		520	965	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540779	187540779	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	55	406	0	ENST00000441802.2:c.6961C>T	p.Gln2321Ter	p.Q2321*	ENST00000441802	NM_005245.3	2321	Cag/Tag	10/27	0.492882428967152	1	FACETS	0.833	0.723	0.949	0.833	0.723	0.949	CLONAL	1	TRUE	0	0.492882428967152	1		406	202	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569790	67569790	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	184	325	0	ENST00000274335.5:c.451A>G	p.Arg151Gly	p.R151G	ENST00000274335		151	Aga/Gga	3/15	0.354539729685935	4	FACETS	0.979	0.91	1	0.979	0.91	1	CLONAL	2	TRUE	2	0.492882428967152	4		325	569	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176516656	176516656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	275	684	0	ENST00000292408.4:c.53C>T	p.Pro18Leu	p.P18L	ENST00000292408	NM_213647.1	18	cCa/cTa	2/18	0.106223093981142	6	FACETS	0.899	0.847	0.952	0.899	0.847	0.952	INDETERMINATE	3	TRUE	3	0.492882428967152	6		684	822	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030221	180030221	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	251	681	0	ENST00000261937.6:c.4063G>T	p.Val1355Leu	p.V1355L	ENST00000261937	NM_182925.4	1355	Gtg/Ttg	30/30	0.106223093981142	6	FACETS	0.891	0.837	0.946	0.891	0.837	0.946	INDETERMINATE	3	TRUE	3	0.492882428967152	6		681	757	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401323	139401323	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	310	965	0	ENST00000277541.6:c.3746del	p.Gly1249AlafsTer196	p.G1249Afs*196	ENST00000277541	NM_017617.3	1249	gGc/gc	23/34	0.492882428967152	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.492882428967152	1		965	640	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	101	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.552	0.494	0.614	0.552	0.494	0.614	SUBCLONAL	1	TRUE	1	0.582613862355109	2		539	628	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0032182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	984	432	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.466034816301995	9	FACETS	0.971	0.948	0.995			1	CLONAL	7	TRUE	NA	0.466034816301995	9		432	1634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0032182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	220	621	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.421024834408667	2	FACETS	0.858	0.805	0.912	0.858	0.805	0.912	CLONAL	2	TRUE	0	0.466034816301995	2		621	550	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5239059	5239059	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	155	634	0	ENST00000357368.4:c.1720G>C	p.Asp574His	p.D574H	ENST00000357368	NM_002850.3	574	Gac/Cac	13/38	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.466034816301995	2		634	583	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508725	106508725	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	72	520	0	ENST00000359195.3:c.719C>A	p.Thr240Asn	p.T240N	ENST00000359195	NM_002649.2	240	aCc/aAc	2/11	1	2	FACETS	0.54	0.472	0.613	0.54	0.472	0.613	SUBCLONAL	1	TRUE	1	0.466034816301995	2		520	572	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	171	349	0				ENST00000310581	NM_198253.2	-/1132			0.552582100089566	3	FACETS	0.98	0.913	1	0.98	0.913	1	CLONAL	2	TRUE	1	0.552582100089566	3		349	403	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0032184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	281	567	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.552582100089566	3	FACETS	0.959	0.907	1			1	CLONAL	2	TRUE	NA	0.552582100089566	3		567	677	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0032184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	191	384	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	0.523442585601002	5	FACETS	0.88	0.817	0.946	0.587	0.544	0.631	CLONAL	2	TRUE	2	0.552582100089566	5		384	718	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	326	492	0	ENST00000335508.6:c.2704G>C	p.Glu902Gln	p.E902Q	ENST00000335508	NM_012433.2	902	Gaa/Caa	18/25	0.542383951296173	5	FACETS	0.854	0.81	0.899			1	CLONAL	3	TRUE	NA	0.552582100089566	5		492	842	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858308	59858308	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	322	494	0	ENST00000259008.2:c.1687G>C	p.Asp563His	p.D563H	ENST00000259008	NM_032043.2	563	Gat/Cat	12/20	0.405651176740878	5	FACETS	1	0.99	1	0.789	0.747	0.831	CLONAL	2	TRUE	2	0.552582100089566	5		494	901	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74859031	74859031	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	296	362	0	ENST00000284811.8:c.173A>G	p.Asn58Ser	p.N58S	ENST00000284811		58	aAt/aGt	4/4	0.344426852344549	4	FACETS	1	0.99	1	0.84	0.803	0.877	CLONAL	3	TRUE	0	0.552582100089566	4		362	495	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265441	198265441	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	308	459	0	ENST00000335508.6:c.2716G>C	p.Glu906Gln	p.E906Q	ENST00000335508	NM_012433.2	906	Gag/Cag	18/25	0.542383951296173	5	FACETS	0.851	0.806	0.896			1	CLONAL	3	TRUE	NA	0.552582100089566	5		459	799	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265489	198265489	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1332070905	NA	P-0032184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	438	619	0	ENST00000335508.6:c.2668G>A	p.Glu890Lys	p.E890K	ENST00000335508	NM_012433.2	890	Gaa/Aaa	18/25	0.542383951296173	5	FACETS	0.925	0.885	0.965			1	CLONAL	3	TRUE	NA	0.552582100089566	5		619	1045	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539826	187539826	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	260	417	0	ENST00000441802.2:c.7914C>A	p.Asp2638Glu	p.D2638E	ENST00000441802	NM_005245.3	2638	gaC/gaA	10/27	0.552582100089566	3	FACETS	0.967	0.913	1	0.967	0.913	1	CLONAL	2	TRUE	1	0.552582100089566	3		417	621	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0032209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	312	685	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.688027516204157	1	FACETS	0.946	0.902	0.989	0.946	0.902	0.989	CLONAL	1	TRUE	0	0.725162086702994	1		685	580	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0032209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	118	382	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	0.18952808341517	2	FACETS	1	0.987	1	0.704	0.651	0.758	INDETERMINATE	1	TRUE	0	0.725162086702994	2		382	231	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727455	66727455	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs869025608	NA	P-0032209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	214	438	1	ENST00000307102.5:c.171G>T	p.Lys57Asn	p.K57N	ENST00000307102	NM_002755.3	57	aaG/aaT	2/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.725162086702994	2		439	566	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222475	2222475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200919682	NA	P-0032209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	337	611	0	ENST00000398665.3:c.3307G>A	p.Val1103Met	p.V1103M	ENST00000398665	NM_032482.2	1103	Gtg/Atg	24/28	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.725162086702994	2		611	927	SUCCESS
APC	324	MSKCC	GRCh37	5	112128142	112128142	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0032209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	58	302	0	ENST00000257430.4:c.646-1G>A		p.X216_splice	ENST00000257430	NM_000038.5	216			1	2	FACETS	0.69	0.6	0.785	0.69	0.6	0.785	SUBCLONAL	1	TRUE	1	0.725162086702994	2		302	232	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814946	139814946	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	203	506	0	ENST00000247668.2:c.939G>C	p.Lys313Asn	p.K313N	ENST00000247668	NM_021138.3	313	aaG/aaC	8/11	0.312712354683037	1	FACETS	0.623	0.581	0.665	0.623	0.581	0.665	INDETERMINATE	1	TRUE	0	0.725162086702994	1		506	573	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285869	46285869	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	114	352	0	ENST00000334344.6:c.5137T>A	p.Ser1713Thr	p.S1713T	ENST00000334344	NM_152641.2	1713	Tct/Act	18/21	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.725162086702994	2		352	299	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218452	5218452	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753143589	NA	P-0032209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	267	606	0	ENST00000357368.4:c.4027C>T	p.Arg1343Cys	p.R1343C	ENST00000357368	NM_002850.3	1343	Cgc/Tgc	25/38	1	2	FACETS	0.924	0.87	0.979	0.924	0.87	0.979	CLONAL	1	TRUE	1	0.725162086702994	2		606	797	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37048528	37048528	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	70	414	0	ENST00000231790.2:c.427G>T	p.Ala143Ser	p.A143S	ENST00000231790	NM_000249.3	143	Gct/Tct	5/19	0.18952808341517	2	FACETS	0.565	0.495	0.638	0.282	0.247	0.319	INDETERMINATE	1	TRUE	0	0.725162086702994	2		414	342	SUCCESS
APC	324	MSKCC	GRCh37	5	112116537	112116538	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAAAT	novel	NA	P-0032209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	96	355	0	ENST00000257430.4:c.585_589dup	p.Arg197LysfsTer10	p.R197Kfs*10	ENST00000257430	NM_000038.5	194	-/CAAAT	6/16	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.725162086702994	2		355	254	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0032213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	163	364	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	0.174119639113838	3	FACETS	1	0.989	1	0.695	0.646	0.745	INDETERMINATE	1	TRUE	1	0.872167333717347	3		364	386	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772958	135772958	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	173	372	0	ENST00000298552.3:c.2665G>T	p.Glu889Ter	p.E889*	ENST00000298552	NM_001162426.1	889	Gaa/Taa	21/23	0.872167333717347	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.872167333717347	1		372	205	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0032213-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	138	364	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	1	2	FACETS	0.884	0.816	0.954	0.884	0.816	0.954	CLONAL	1	TRUE	1	0.89416277114469	2		364	349	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772958	135772958	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032213-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	198	372	0	ENST00000298552.3:c.2665G>T	p.Glu889Ter	p.E889*	ENST00000298552	NM_001162426.1	889	Gaa/Taa	21/23	0.89416277114469	1	FACETS	0.987	0.948	1	0.987	0.948	1	CLONAL	1	TRUE	0	0.89416277114469	1		372	248	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175440	108175440	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032213-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	47	409	0	ENST00000278616.4:c.5535G>T	p.Leu1845Phe	p.L1845F	ENST00000278616	NM_000051.3	1845	ttG/ttT	37/63	1	2	FACETS	0.259	0.219	0.303	0.259	0.219	0.303	SUBCLONAL	1	TRUE	1	0.89416277114469	2		409	406	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0032216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	421	655	0	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.798550068663397	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.798550068663397	1		655	603	SUCCESS
AR	367	MSKCC	GRCh37	X	66765715	66765715	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	483	990	0	ENST00000374690.3:c.727G>C	p.Val243Leu	p.V243L	ENST00000374690	NM_000044.3	243	Gtg/Ctg	1/8	1	2	FACETS	0.921	0.881	0.961	0.921	0.881	0.961	CLONAL	1	TRUE	1	0.798550068663397	2		990	1314	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418643	49418643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs936142615	NA	P-0032216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	383	642	0	ENST00000301067.7:c.15871G>A	p.Glu5291Lys	p.E5291K	ENST00000301067	NM_003482.3	5291	Gag/Aag	49/54	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.798550068663397	2		642	959	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878115	48878115	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	48	72	0	ENST00000267163.4:c.68del	p.Pro23ArgfsTer42	p.P23Rfs*42	ENST00000267163	NM_000321.2	23	Ccg/cg	1/27	0.798550068663397	1	FACETS	0.989	0.888	1	0.989	0.888	1	CLONAL	1	TRUE	0	0.798550068663397	1		72	73	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052650	42052650	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	378	583	0	ENST00000219905.7:c.7321G>T	p.Asp2441Tyr	p.D2441Y	ENST00000219905	NM_001164273.1	2441	Gat/Tat	20/24	0.798550068663397	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.798550068663397	1		583	542	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879699	37879699	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	363	546	0	ENST00000269571.5:c.2074C>T	p.Gln692Ter	p.Q692*	ENST00000269571		692	Cag/Tag	17/27	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.798550068663397	2		546	855	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259304	36259304	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	369	329	0	ENST00000300305.3:c.187G>T	p.Ala63Ser	p.A63S	ENST00000300305		63	Gcc/Tcc	3/8	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.798550068663397	2		329	703	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215907	142215907	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	262	530	0	ENST00000350721.4:c.5686G>C	p.Ala1896Pro	p.A1896P	ENST00000350721	NM_001184.3	1896	Gcc/Ccc	33/47	1	2	FACETS	0.958	0.903	1	0.958	0.903	1	CLONAL	1	TRUE	1	0.798550068663397	2		530	685	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152129	55152129	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	406	664	1	ENST00000257290.5:c.2561G>T	p.Ser854Ile	p.S854I	ENST00000257290	NM_006206.4	854	aGt/aTt	18/23	1	2	FACETS	0.948	0.904	0.992	0.948	0.904	0.992	CLONAL	1	TRUE	1	0.798550068663397	2		665	1073	SUCCESS
AR	367	MSKCC	GRCh37	X	66931246	66931246	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1085307962	NA	P-0032216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	185	368	0	ENST00000374690.3:c.1888C>T	p.Arg630Trp	p.R630W	ENST00000374690	NM_000044.3	630	Cgg/Tgg	4/8	1	2	FACETS	0.984	0.917	1	0.984	0.917	1	CLONAL	1	TRUE	1	0.798550068663397	2		368	471	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939645	76939645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	204	819	0	ENST00000373344.5:c.1103C>A	p.Ser368Tyr	p.S368Y	ENST00000373344	NM_000489.3	368	tCc/tAc	9/35	1	2	FACETS	0.747	0.696	0.8	0.747	0.696	0.8	SUBCLONAL	1	TRUE	1	0.798550068663397	2		819	684	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0032233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	210	384	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.763718061354487	2		384	506	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189387	56189387	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	346	520	0	ENST00000399503.3:c.4421del	p.Pro1474LeufsTer16	p.P1474Lfs*16	ENST00000399503	NM_005921.1	1473	atC/at	20/20	0.516664340686124	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	0	0.763718061354487	1		520	550	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	216	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.50075620782348	4	FACETS	0.958	0.895	1	0.958	0.895	1	CLONAL	2	TRUE	2	0.50075620782348	4		539	676	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0032234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	124	297	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	0.44948210652246	4	FACETS	0.943	0.862	1	0.943	0.862	1	CLONAL	2	TRUE	2	0.50075620782348	4		297	394	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427687	49427687	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	105	670	0	ENST00000301067.7:c.10801C>T	p.Gln3601Ter	p.Q3601*	ENST00000301067	NM_003482.3	3601	Caa/Taa	39/54	0.50075620782348	4	FACETS	0.824	0.738	0.915	0.412	0.369	0.458	CLONAL	1	TRUE	2	0.50075620782348	4		670	764	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78866624	78866624	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	239	565	0	ENST00000306801.3:c.2197A>G	p.Arg733Gly	p.R733G	ENST00000306801	NM_020761.2	733	Agg/Ggg	19/34	0.44948210652246	4	FACETS	0.977	0.916	1	0.977	0.916	1	CLONAL	2	TRUE	2	0.50075620782348	4		565	733	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639671	47639671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	31	382	0	ENST00000233146.2:c.764G>T	p.Ser255Ile	p.S255I	ENST00000233146	NM_000251.2	255	aGt/aTt	4/16	0.270803659201637	6	FACETS	0.418	0.337	0.51	0.139	0.112	0.17	INDETERMINATE	1	TRUE	3	0.50075620782348	6		382	593	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281778	39281778	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519963	NA	P-0032249-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	74	332	0	ENST00000402219.2:c.697A>T	p.Asn233Tyr	p.N233Y	ENST00000402219	NM_005633.3	233	Aat/Tat	5/23	1	2	FACETS	0.969	0.854	1	0.969	0.854	1	CLONAL	1	TRUE	1	0.420843475992093	2		332	363	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913351	NA	P-0032249-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	237	489	0	ENST00000288602.6:c.1397G>A	p.Gly466Glu	p.G466E	ENST00000288602	NM_004333.4	466	gGa/gAa	11/18	0.420843475992093	3	FACETS	0.997	0.935	1	0.997	0.935	1	CLONAL	2	TRUE	1	0.420843475992093	3		489	684	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092773	27092773	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032249-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	234	556	0	ENST00000324856.7:c.2794C>T	p.Gln932Ter	p.Q932*	ENST00000324856	NM_006015.4	932	Caa/Taa	9/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.420843475992093	2		556	1003	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560046	29560047	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0032249-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	240	314	0	ENST00000356175.3:c.3524_3525del	p.Thr1175LysfsTer19	p.T1175Kfs*19	ENST00000356175	NM_000267.3	1175	ACa/a	27/57	1	2	FACETS	1	0.981	1	1	0.995	1	CLONAL	2	TRUE	1	0.420843475992093	2		314	524	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057831	27057832	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0032249-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1782	491	1096	0	ENST00000324856.7:c.1542_1543del	p.Gln515AlafsTer107	p.Q515Afs*107	ENST00000324856	NM_006015.4	513	tcCTct/tcct	3/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.420843475992093	2		1096	2273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0032340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	627	653	1	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.325355835605603	4	FACETS	1	0.995	1	0.856	0.828	0.885	CLONAL	3	TRUE	0	0.433771986459582	4		654	1210	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359014	81359014	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	156	465	1	ENST00000222390.5:c.947C>A	p.Thr316Asn	p.T316N	ENST00000222390	NM_000601.4	316	aCt/aAt	8/18	0.2036024518753	5	FACETS	0.938	0.862	1	0.625	0.575	0.678	INDETERMINATE	2	TRUE	2	0.433771986459582	5		466	633	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014176	70014176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	96	461	0	ENST00000394351.3:c.1037G>A	p.Gly346Asp	p.G346D	ENST00000394351	NM_000248.3	346	gGc/gAc	9/9	0.342137830300752	3	FACETS	0.754	0.672	0.842	0.377	0.336	0.421	SUBCLONAL	1	TRUE	1	0.433771986459582	3		461	714	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292580	15292580	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867505691	NA	P-0032340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	138	620	0	ENST00000263388.2:c.2599G>A	p.Gly867Ser	p.G867S	ENST00000263388	NM_000435.2	867	Ggc/Agc	17/33	0.296684005266558	3	FACETS	0.876	0.797	0.959			1	CLONAL	1	TRUE	NA	0.433771986459582	3		620	884	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679396	29679396	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	53	350	0	ENST00000356175.3:c.7516G>T	p.Gly2506Trp	p.G2506W	ENST00000356175	NM_000267.3	2506	Ggg/Tgg	50/57	0.35366026639293	3	FACETS	0.658	0.562	0.763	0.219	0.187	0.255	SUBCLONAL	1	TRUE	0	0.433771986459582	3		350	452	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245225	46245225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529386166	NA	P-0032340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	45	406	1	ENST00000334344.6:c.3319G>A	p.Ala1107Thr	p.A1107T	ENST00000334344	NM_152641.2	1107	Gca/Aca	15/21	0.4211211224267	4	FACETS	0.424	0.356	0.501	0.141	0.118	0.167	SUBCLONAL	1	TRUE	1	0.433771986459582	4		407	701	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949104	71949104	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	326	505	2	ENST00000298229.2:c.3571G>T	p.Gly1191Trp	p.G1191W	ENST00000298229	NM_001567.3	1191	Ggg/Tgg	27/28	0.433771986459582	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.433771986459582	3		507	864	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151877	108151877	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs12786957	NA	P-0032340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	128	284	0	ENST00000278616.4:c.3558A>T	p.Glu1186Asp	p.E1186D	ENST00000278616	NM_000051.3	1186	gaA/gaT	24/63	0.433771986459582	3	FACETS	0.911	0.834	0.991	0.911	0.834	0.991	CLONAL	2	TRUE	1	0.433771986459582	3		284	394	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436703	110436703	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	120	737	0	ENST00000375856.3:c.1698C>A	p.Asp566Glu	p.D566E	ENST00000375856	NM_003749.2	566	gaC/gaA	1/2	0.3488372631924	2	FACETS	0.691	0.624	0.762	0.345	0.312	0.381	SUBCLONAL	1	TRUE	0	0.433771986459582	2		737	801	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029555	14029555	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	76	281	0	ENST00000311895.7:c.1767del	p.Gln590SerfsTer14	p.Q590Sfs*14	ENST00000311895	NM_005236.2	589	cGg/cg	8/11	0.318028067515992	3	FACETS	1	0.906	1	0.516	0.455	0.582	CLONAL	1	TRUE	1	0.433771986459582	3		281	413	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268489	198268489	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0032340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	108	333	0	ENST00000335508.6:c.1540-1G>C		p.X514_splice	ENST00000335508	NM_012433.2	514			0.36214733863668	5	FACETS	0.825	0.744	0.91	0.55	0.496	0.607	CLONAL	2	TRUE	2	0.433771986459582	5		333	498	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163932	47163932	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	75	360	0	ENST00000409792.3:c.2194T>G	p.Leu732Val	p.L732V	ENST00000409792	NM_014159.6	732	Ttg/Gtg	3/21	NA	2	FACETS	0.852	0.75	0.96			1	INDETERMINATE	1	TRUE	NA	0.433771986459582	2		360	406	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499326	89499326	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0032340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	54	303	0	ENST00000336596.2:c.2497-1G>T		p.X833_splice	ENST00000336596	NM_005233.5	833			NA	2	FACETS	0.754	0.648	0.87			1	INDETERMINATE	1	TRUE	NA	0.433771986459582	2		303	330	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149243914	149243914	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0032340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	66	341	0	ENST00000360632.3:c.906-2A>T		p.X302_splice	ENST00000360632	NM_015472.4	302			0.29663174318535	4	FACETS	0.786	0.683	0.898			1	SUBCLONAL	1	TRUE	NA	0.433771986459582	4		341	555	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55960974	55960974	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	220	349	0	ENST00000263923.4:c.2966A>T	p.Glu989Val	p.E989V	ENST00000263923	NM_002253.2	989	gAg/gTg	21/30	0.433771986459582	4	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	2	0.433771986459582	4		349	723	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056039	26056039	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs61742488	NA	P-0032340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	57	358	0	ENST00000343677.2:c.618G>C	p.Lys206Asn	p.K206N	ENST00000343677	NM_005319.3	206	aaG/aaC	1/1	0.325355835605603	4	FACETS	0.746	0.641	0.861	0.187	0.16	0.216	SUBCLONAL	1	TRUE	0	0.433771986459582	4		358	505	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771157	161771157	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	266	498	0	ENST00000366898.1:c.1372A>T	p.Met458Leu	p.M458L	ENST00000366898	NM_004562.2	458	Atg/Ttg	12/12	0.299751643523775	5	FACETS	1	0.979	1			1	CLONAL	2	TRUE	NA	0.433771986459582	5		498	927	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161990386	161990386	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0032340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	93	326	0	ENST00000366898.1:c.933+1G>T		p.X311_splice	ENST00000366898	NM_004562.2	311			0.299751643523775	5	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.433771986459582	5		326	495	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975456	13975456	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	386	341	0	ENST00000405192.2:c.431del	p.Pro144GlnfsTer111	p.P144Qfs*111	ENST00000405192	NM_001163147.1	144	cCa/ca	7/12	0.433771986459582	7	FACETS	0.949	0.908	0.99			1	CLONAL	5	TRUE	NA	0.433771986459582	7		341	782	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345971	152345971	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs770454123	NA	P-0032340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	185	463	0	ENST00000359321.1:c.599A>C	p.Gln200Pro	p.Q200P	ENST00000359321	NM_005431.1	200	cAg/cCg	3/3	0.2036024518753	5	FACETS	0.899	0.832	0.969	0.599	0.554	0.646	INDETERMINATE	2	TRUE	2	0.433771986459582	5		463	783	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228340	53228340	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	251	442	1	ENST00000375401.3:c.2062G>T	p.Gly688Cys	p.G688C	ENST00000375401	NM_004187.3	688	Ggt/Tgt	15/26	0.336884448678545	3	FACETS	1	0.989	1	0.794	0.749	0.84	CLONAL	2	TRUE	0	0.433771986459582	3		443	591	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412500	63412500	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	95	610	0	ENST00000330258.3:c.667G>T	p.Ala223Ser	p.A223S	ENST00000330258	NM_152424.3	223	Gcc/Tcc	2/2	0.336884448678545	3	FACETS	0.66	0.588	0.738	0.22	0.196	0.246	SUBCLONAL	1	TRUE	0	0.433771986459582	3		610	807	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0032401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	290	384	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.504228917887504	2	FACETS	0.884	0.839	0.929	0.884	0.839	0.929	CLONAL	2	TRUE	0	0.530936153115322	2		384	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0032401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	255	522	1	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.530936153115322	1	FACETS	0.99	0.931	1	0.99	0.931	1	CLONAL	1	TRUE	0	0.530936153115322	1		523	713	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907432	32907432	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs80358469	NA	P-0032401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	85	230	0	ENST00000380152.3:c.1817C>A	p.Pro606Gln	p.P606Q	ENST00000380152		606	cCg/cAg	10/27	0.138264943639079	0	FACETS	0.43	0.383	0.48			1	INDETERMINATE	1	TRUE	0	0.530936153115322	0		230	349	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437892	110437892	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	38	76	0	ENST00000375856.3:c.509C>A	p.Ala170Asp	p.A170D	ENST00000375856	NM_003749.2	170	gCc/gAc	1/2	0.366792182986373	3	FACETS	1	0.933	1	0.612	0.515	0.717	CLONAL	1	TRUE	1	0.530936153115322	3		76	148	SUCCESS
BLM	641	MSKCC	GRCh37	15	91295124	91295124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	122	322	0	ENST00000355112.3:c.907C>T	p.Pro303Ser	p.P303S	ENST00000355112	NM_000057.2	303	Cct/Tct	4/22	1	2	FACETS	0.93	0.846	1	0.93	0.846	1	CLONAL	1	TRUE	1	0.530936153115322	2		322	494	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439897	56439908	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGCTCACCGGC	CTGCTCACCGGC	-	novel	NA	P-0032401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	171	358	0	ENST00000407977.2:c.684_687+8del		p.X228_splice	ENST00000407977		228		6/10	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.530936153115322	2		358	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577129	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519986	NA	P-0032437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	126	683	1	ENST00000269305.4:c.809T>C	p.Phe270Ser	p.F270S	ENST00000269305	NM_001126112.2	270	tTt/tCt	8/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.25	2		684	754	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	55	618	1	ENST00000322088.6:c.767C>A	p.Ser256Tyr	p.S256Y	ENST00000322088	NM_014225.5	256	tCc/tAc	6/15	1	2	FACETS	0.818	0.7	0.947	0.818	0.7	0.947	CLONAL	1	TRUE	1	0.25	2		619	538	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039668	47039668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	52	814	1	ENST00000377604.3:c.1120G>A	p.Gly374Ser	p.G374S	ENST00000377604	NM_001204468.1	374	Ggc/Agc	11/24	0.3	1	FACETS	0.486	0.413	0.567	0.486	0.413	0.567	SUBCLONAL	1	TRUE	0	0.25	1		815	749	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0032458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	162	879	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.382657831256116	1	FACETS	0.878	0.807	0.952	0.878	0.807	0.952	CLONAL	1	TRUE	0	0.382657831256116	1		879	780	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0032458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	95	488	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.325666125414946	1	FACETS	0.634	0.565	0.708	0.634	0.565	0.708	SUBCLONAL	1	TRUE	0	0.382657831256116	1		488	633	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946798	71946801	+	splice_donor_variant,intron_variant	Splice_Site	DEL	GTGA	GTGA	-	novel	NA	P-0032458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	137	629	0	ENST00000298229.2:c.2738+2_2738+5del		p.X913_splice	ENST00000298229	NM_001567.3	913			0.382657831256116	1	FACETS	0.895	0.816	0.977	0.895	0.816	0.977	CLONAL	1	TRUE	0	0.382657831256116	1		629	647	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246387	53246387	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1556852362	NA	P-0032458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	221	706	1	ENST00000375401.3:c.595C>T	p.Gln199Ter	p.Q199*	ENST00000375401	NM_004187.3	199	Cag/Tag	5/26	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.382657831256116	2		707	1136	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	253	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.925	0.869	0.982	0.925	0.869	0.982	CLONAL	1	TRUE	1	0.699571594017709	2		493	782	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0032462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	101	254	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.364106720269557	1	FACETS	0.432	0.388	0.477	0.432	0.388	0.477	INDETERMINATE	1	TRUE	0	0.699571594017709	1		254	435	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746028	162746028	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	37	269	0	ENST00000367921.3:c.2151A>T	p.Leu717Phe	p.L717F	ENST00000367921	NM_006182.2	717	ttA/ttT	16/18	1	2	FACETS	0.178	0.146	0.214	0.178	0.146	0.214	SUBCLONAL	1	TRUE	1	0.699571594017709	2		269	594	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075301	16075301	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	33	273	0	ENST00000268712.3:c.251A>G	p.Glu84Gly	p.E84G	ENST00000268712	NM_006311.3	84	gAa/gGa	4/46	1	2	FACETS	0.158	0.128	0.192	0.158	0.128	0.192	SUBCLONAL	1	TRUE	1	0.699571594017709	2		273	598	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120115	70120115	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	69	97	2	ENST00000245479.2:c.1121del	p.Pro374ArgfsTer9	p.P374Rfs*9	ENST00000245479	NM_000346.3	373	Ccc/cc	3/3	0.346774405786877	2	FACETS	1	0.98	1	0.736	0.663	0.809	INDETERMINATE	1	TRUE	0	0.699571594017709	2		99	134	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121912580	NA	P-0032462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	202	319	0	ENST00000342988.3:c.1157G>T	p.Gly386Val	p.G386V	ENST00000342988	NM_005359.5	386	gGt/gTt	10/12	0.699571594017709	1	FACETS	0.983	0.926	1	0.983	0.926	1	CLONAL	1	TRUE	0	0.699571594017709	1		319	382	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022394	26022394	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	264	351	2	ENST00000435504.4:c.263C>A	p.Pro88Gln	p.P88Q	ENST00000435504		88	cCg/cAg	5/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.699571594017709	2		353	714	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010449	48010451	+	inframe_deletion	In_Frame_Del	DEL	GGG	GGG	-	novel	NA	P-0032462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	110	344	0	ENST00000234420.5:c.77_79del	p.Arg26_Ala27delinsThr	p.R26_A27delinsT	ENST00000234420	NM_000179.2	26	aGGGcc/acc	1/10	1	2	FACETS	0.534	0.481	0.59	0.534	0.481	0.59	SUBCLONAL	1	TRUE	1	0.699571594017709	2		344	589	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248599	212248599	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1281587425	NA	P-0032462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	43	451	0	ENST00000342788.4:c.3668A>G	p.Lys1223Arg	p.K1223R	ENST00000342788	NM_005235.2	1223	aAg/aGg	28/28	1	2	FACETS	0.155	0.129	0.184	0.155	0.129	0.184	SUBCLONAL	1	TRUE	1	0.699571594017709	2		451	792	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332853	153332853	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751626529	NA	P-0032462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	178	417	0	ENST00000281708.4:c.103C>T	p.Arg35Cys	p.R35C	ENST00000281708	NM_033632.3	35	Cgt/Tgt	2/12	0.364106720269557	1	FACETS	0.453	0.419	0.489	0.453	0.419	0.489	INDETERMINATE	1	TRUE	0	0.699571594017709	1		417	730	SUCCESS
APC	324	MSKCC	GRCh37	5	112175360	112175360	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	127	207	0	ENST00000257430.4:c.4069G>T	p.Gly1357Ter	p.G1357*	ENST00000257430	NM_000038.5	1357	Gga/Tga	16/16	0.364106720269557	1	FACETS	0.766	0.705	0.829	0.766	0.705	0.829	INDETERMINATE	1	TRUE	0	0.699571594017709	1		207	308	SUCCESS
APC	324	MSKCC	GRCh37	5	112178544	112178544	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	71	265	0	ENST00000257430.4:c.7253G>T	p.Arg2418Ile	p.R2418I	ENST00000257430	NM_000038.5	2418	aGa/aTa	16/16	0.364106720269557	1	FACETS	0.362	0.317	0.409	0.362	0.317	0.409	INDETERMINATE	1	TRUE	0	0.699571594017709	1		265	365	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376670	8376670	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	131	376	0	ENST00000356435.5:c.4443A>C	p.Gln1481His	p.Q1481H	ENST00000356435		1481	caA/caC	27/35	1	2	FACETS	0.508	0.461	0.557	0.508	0.461	0.557	SUBCLONAL	1	TRUE	1	0.699571594017709	2		376	737	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564131	139564131	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs117990760	NA	P-0032462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	193	471	2	ENST00000308874.7:c.271G>T	p.Gly91Cys	p.G91C	ENST00000308874		91	Ggc/Tgc	5/10	1	2	FACETS	0.617	0.571	0.665	0.617	0.571	0.665	SUBCLONAL	1	TRUE	1	0.699571594017709	2		473	894	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0032466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	290	384	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.364794016390061	14	FACETS	0.959	0.903	1	0.4	0.376	0.424	CLONAL	5	TRUE	2	0.364794016390061	14		384	1057	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579585	7579585	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	297	588	0	ENST00000269305.4:c.102del	p.Leu35CysfsTer9	p.L35Cfs*9	ENST00000269305	NM_001126112.2	34	ccC/cc	4/11	0.344994603913466	3	FACETS	0.948	0.899	0.997			1	CLONAL	3	TRUE	NA	0.364794016390061	3		588	677	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937670	36937670	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	301	762	0	ENST00000361632.4:c.1068G>C	p.Trp356Cys	p.W356C	ENST00000361632		356	tgG/tgC	8/16	0.315759252904219	3	FACETS	1	0.991	1	0.817	0.773	0.862	CLONAL	2	TRUE	0	0.364794016390061	3		762	796	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726969	46726969	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	107	654	0	ENST00000371975.4:c.803C>T	p.Ser268Phe	p.S268F	ENST00000371975	NM_003579.3	268	tCt/tTt	8/18	0.323778914858935	3	FACETS	1	0.965	1	0.389	0.349	0.43	CLONAL	1	TRUE	0	0.364794016390061	3		654	595	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446079	49446079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	217	983	1	ENST00000301067.7:c.1387G>A	p.Glu463Lys	p.E463K	ENST00000301067	NM_003482.3	463	Gag/Aag	10/54	0.364794016390061	5	FACETS	1	0.99	1	0.349	0.323	0.375	CLONAL	1	TRUE	1	0.364794016390061	5		984	1320	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714152	43714152	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	170	812	0	ENST00000382044.4:c.4001G>A	p.Ser1334Asn	p.S1334N	ENST00000382044	NM_001141980.1	1334	aGc/aAc	19/28	0.311677334605494	4	FACETS	1	0.983	1	0.625	0.574	0.679	CLONAL	1	TRUE	2	0.364794016390061	4		812	1017	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349651	89349651	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	201	900	0	ENST00000301030.4:c.3299C>G	p.Ser1100Cys	p.S1100C	ENST00000301030	NM_001256183.1	1100	tCt/tGt	9/13	0.315759252904219	3	FACETS	0.758	0.704	0.815	0.506	0.469	0.543	SUBCLONAL	2	TRUE	0	0.364794016390061	3		900	859	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164850	47164850	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	33	344	0	ENST00000409792.3:c.1276C>G	p.His426Asp	p.H426D	ENST00000409792	NM_014159.6	426	Cat/Gat	3/21	0.364794016390061	2	FACETS	0.56	0.457	0.676	0.28	0.228	0.338	SUBCLONAL	1	TRUE	0	0.364794016390061	2		344	323	SUCCESS
ATR	545	MSKCC	GRCh37	3	142184017	142184017	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	40	555	0	ENST00000350721.4:c.6963C>G	p.Phe2321Leu	p.F2321L	ENST00000350721	NM_001184.3	2321	ttC/ttG	41/47	0.193152045042695	4	FACETS	0.756	0.629	0.897	0.378	0.314	0.449	INDETERMINATE	1	TRUE	2	0.364794016390061	4		555	396	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433730	149433730	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	288	722	0	ENST00000286301.3:c.2821G>T	p.Glu941Ter	p.E941*	ENST00000286301	NM_005211.3	941	Gag/Tag	22/22	0.364794016390061	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.364794016390061	2		722	711	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397813	116397813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750276956	NA	P-0032466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	88	703	1	ENST00000397752.3:c.2087C>T	p.Thr696Ile	p.T696I	ENST00000397752	NM_000245.2	696	aCa/aTa	8/21	0.329004068820366	3	FACETS	1	0.969	1	0.418	0.372	0.467	CLONAL	1	TRUE	0	0.364794016390061	3		704	455	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611828	100611828	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	126	707	0	ENST00000308731.7:c.1293G>A	p.Met431Ile	p.M431I	ENST00000308731	NM_000061.2	431	atG/atA	14/19	0.364794016390061	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.364794016390061	1		707	511	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0032479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	143	488	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.881	0.803	0.962	1	0.99	1	CLONAL	2	TRUE	1	0.2	2		488	812	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0032479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	56	996	1	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	1	2	FACETS	0.728	0.623	0.844	0.728	0.623	0.844	SUBCLONAL	1	TRUE	1	0.2	2		997	769	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949351	71949351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	62	584	0	ENST00000298229.2:c.3731C>T	p.Pro1244Leu	p.P1244L	ENST00000298229	NM_001567.3	1244	cCg/cTg	28/28	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.2	2		584	577	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290235	15290235	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	51	691	0	ENST00000263388.2:c.3400G>T	p.Gly1134Trp	p.G1134W	ENST00000263388	NM_000435.2	1134	Ggg/Tgg	21/33	1	2	FACETS	0.748	0.634	0.873	0.748	0.634	0.873	SUBCLONAL	1	TRUE	1	0.2	2		691	682	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155052	55155052	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	40	375	0	ENST00000257290.5:c.2761G>T	p.Ala921Ser	p.A921S	ENST00000257290	NM_006206.4	921	Gct/Tct	20/23	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.2	2		375	386	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499127	149499127	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	33	513	0	ENST00000261799.4:c.2701G>T	p.Gly901Cys	p.G901C	ENST00000261799	NM_002609.3	901	Ggc/Tgc	20/23	1	2	FACETS	0.652	0.53	0.79	0.652	0.53	0.79	SUBCLONAL	1	TRUE	1	0.2	2		513	506	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911584	101911584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	35	372	0	ENST00000374994.4:c.1509G>A	p.Met503Ile	p.M503I	ENST00000374994	NM_004612.2	503	atG/atA	9/9	1	2	FACETS	0.635	0.52	0.765	0.635	0.52	0.765	SUBCLONAL	1	TRUE	1	0.2	2		372	551	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356216	70356216	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	73	712	0	ENST00000374080.3:c.5111G>T	p.Trp1704Leu	p.W1704L	ENST00000374080		1704	tGg/tTg	37/45	1	2	FACETS	0.94	0.821	1	0.94	0.821	1	CLONAL	1	TRUE	1	0.2	2		712	777	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038781	47038783	+	stop_gained	Nonsense_Mutation	TNP	GGG	GGG	TGT	novel	NA	P-0032479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	57	685	0	ENST00000377604.3:c.788_790delinsTGT	p.Arg263_Glu264delinsLeuTer	p.R263_E264delinsL*	ENST00000377604	NM_001204468.1	263	cGGGag/cTGTag	9/24	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.2	2		685	561	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0032516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	187	558	0				ENST00000310581	NM_198253.2	-/1132			0.275632824029306	1	FACETS	0.556	0.518	0.595	0.556	0.518	0.595	INDETERMINATE	1	FALSE	0	0.791734665938512	1		558	513	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0032516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	158	234	0	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	FALSE	1	0.791734665938512	2		234	391	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412337	139412339	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0032516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	248	165	0	ENST00000277541.6:c.1306_1308del	p.Phe436del	p.F436del	ENST00000277541	NM_017617.3	436	TTC/-	8/34	0.506678574893486	1	FACETS	0.456	0.427	0.485	0.456	0.427	0.485	SUBCLONAL	1	FALSE	0	0.791734665938512	1		165	830	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791799	42791799	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	240	123	0	ENST00000575354.2:c.685A>C	p.Thr229Pro	p.T229P	ENST00000575354	NM_015125.3	229	Acc/Ccc	5/20	0.791734665938512	1	FACETS	0.977	0.931	1	0.977	0.931	1	CLONAL	1	FALSE	0	0.791734665938512	1		123	375	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229234	123229237	+	frameshift_variant	Frame_Shift_Del	DEL	AACA	AACA	-	novel	NA	P-0032516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	171	21	0	ENST00000218089.9:c.3718_3721del	p.Asn1240AspfsTer7	p.N1240Dfs*7	ENST00000218089	NM_001042749.1	1240	AACAga/ga	34/35	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	0	0.791734665938512	1		21	212	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0032572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	219	732	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.270020012781965	2	FACETS	0.972	0.906	1	0.972	0.906	1	CLONAL	2	TRUE	0	0.27084974887068	2		732	832	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779056	3779056	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756378412	NA	P-0032572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	135	626	0	ENST00000262367.5:c.5992G>A	p.Val1998Met	p.V1998M	ENST00000262367	NM_004380.2	1998	Gtg/Atg	31/31	0.267907016615019	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.27084974887068	2		626	439	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39321509	39321509	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	130	580	0	ENST00000373001.3:c.512T>C	p.Met171Thr	p.M171T	ENST00000373001	NM_022157.3	171	aTg/aCg	3/7	0.270020012781965	2	FACETS	0.984	0.898	1	0.984	0.898	1	CLONAL	2	TRUE	0	0.27084974887068	2		580	488	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347165	347165	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	232	843	1	ENST00000262320.3:c.1846A>G	p.Ser616Gly	p.S616G	ENST00000262320	NM_003502.3	616	Agc/Ggc	7/11	0.267907016615019	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.27084974887068	2		844	830	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141677	202141677	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	81	281	0	ENST00000358485.4:c.965C>A	p.Thr322Lys	p.T322K	ENST00000358485	NM_001080125.1	322	aCa/aAa	7/9	0.267907016615019	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	2	TRUE	0	0.27084974887068	2		281	293	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0032600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	68	879	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.748	0.651	0.854	0.748	0.651	0.854	SUBCLONAL	1	TRUE	1	0.27	2		879	673	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560500	65560500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs387906651	NA	P-0032600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	83	437	0	ENST00000358664.4:c.97C>T	p.Arg33Ter	p.R33*	ENST00000358664	NM_002382.4	33	Cga/Tga	3/5	1	2	FACETS	0.891	0.786	1	0.891	0.786	1	CLONAL	1	TRUE	1	0.27	2		437	690	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0032600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	58	400	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	1	2	FACETS	0.863	0.742	0.994	0.863	0.742	0.994	CLONAL	1	TRUE	1	0.27	2		400	498	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576093	88576093	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	76	764	0	ENST00000360948.2:c.1580A>G	p.Asp527Gly	p.D527G	ENST00000360948	NM_001012338.2	527	gAc/gGc	13/19	1	2	FACETS	0.78	0.683	0.884	0.78	0.683	0.884	SUBCLONAL	1	TRUE	1	0.27	2		764	722	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750362	133750362	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	52	559	0	ENST00000318560.5:c.1193G>T	p.Gly398Val	p.G398V	ENST00000318560	NM_005157.4	398	gGa/gTa	7/11	1	2	FACETS	0.628	0.534	0.732	0.628	0.534	0.732	SUBCLONAL	1	TRUE	1	0.27	2		559	613	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435616	18435616	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	31	307	0	ENST00000266497.5:c.601G>C	p.Val201Leu	p.V201L	ENST00000266497		201	Gtg/Ctg	1/31	1	2	FACETS	0.601	0.486	0.731	0.601	0.486	0.731	SUBCLONAL	1	TRUE	1	0.27	2		307	382	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556307	29556307	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	75	661	0	ENST00000356175.3:c.2674A>C	p.Ser892Arg	p.S892R	ENST00000356175	NM_000267.3	892	Agc/Cgc	21/57	1	2	FACETS	0.687	0.601	0.78	0.687	0.601	0.78	SUBCLONAL	1	TRUE	1	0.27	2		661	809	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899198	78899198	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	66	545	0	ENST00000306801.3:c.2837G>T	p.Gly946Val	p.G946V	ENST00000306801	NM_020761.2	946	gGa/gTa	24/34	NA	2	FACETS	0.871	0.757	0.995			1	INDETERMINATE	1	TRUE	NA	0.27	2		545	561	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899203	78899203	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0032600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	59	563	1	ENST00000306801.3:c.2842A>T	p.Lys948Ter	p.K948*	ENST00000306801	NM_020761.2	948	Aaa/Taa	24/34	NA	2	FACETS	0.767	0.66	0.883			1	INDETERMINATE	1	TRUE	NA	0.27	2		564	570	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778261	27778261	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0032600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	35	427	0	ENST00000369163.2:c.410G>C	p.Ter137SerextTer6	p.*137Sext*6	ENST00000369163	NM_003536.2	137	tGa/tCa	1/1	1	2	FACETS	0.628	0.515	0.755	0.628	0.515	0.755	SUBCLONAL	1	TRUE	1	0.27	2		427	413	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929271	44929271	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	82	786	0	ENST00000377967.4:c.2371A>G	p.Asn791Asp	p.N791D	ENST00000377967	NM_021140.2	791	Aat/Gat	17/29	0.224311091709665	1	FACETS	0.63	0.555	0.711	0.63	0.555	0.711	SUBCLONAL	1	TRUE	0	0.27	1		786	834	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0032626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	104	384	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.37690880824089	1	FACETS	0.45	0.405	0.498	0.45	0.405	0.498	INDETERMINATE	1	TRUE	0	0.651576910421081	1		384	478	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0032626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	15	407	1	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	0.651576910421081	1	FACETS	0.107	0.078	0.143	0.107	0.078	0.143	SUBCLONAL	1	TRUE	0	0.651576910421081	1		408	289	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347957	347957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149849071	NA	P-0032626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	116	772	1	ENST00000262320.3:c.1549G>A	p.Val517Ile	p.V517I	ENST00000262320	NM_003502.3	517	Gta/Ata	6/11	0.651576910421081	3	FACETS	0.525	0.472	0.58	0.262	0.236	0.29	SUBCLONAL	1	TRUE	1	0.651576910421081	3		773	900	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437376	110437376	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776945626	NA	P-0032626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	35	136	0	ENST00000375856.3:c.1025C>T	p.Ser342Leu	p.S342L	ENST00000375856	NM_003749.2	342	tCg/tTg	1/2	1	2	FACETS	0.643	0.534	0.762	0.643	0.534	0.762	SUBCLONAL	1	TRUE	1	0.651576910421081	2		136	167	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341583	89341583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1336341769	NA	P-0032626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	39	364	0	ENST00000301030.4:c.7487C>T	p.Ser2496Phe	p.S2496F	ENST00000301030	NM_001256183.1	2496	tCc/tTc	10/13	0.651576910421081	1	FACETS	0.32	0.267	0.379	0.32	0.267	0.379	SUBCLONAL	1	TRUE	0	0.651576910421081	1		364	252	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217257	7217258	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0032626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	197	502	0	ENST00000380728.2:c.447_448del	p.Arg149SerfsTer56	p.R149Sfs*56	ENST00000380728		149	agAGcc/agcc	6/11	0.651576910421081	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.651576910421081	1		502	391	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379775	17379775	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	59	686	0	ENST00000359435.4:c.160G>A	p.Glu54Lys	p.E54K	ENST00000359435	NM_001033549.1	54	Gag/Aag	2/9	0.394342065862793	1	FACETS	0.198	0.17	0.228	0.198	0.17	0.228	SUBCLONAL	1	TRUE	0	0.651576910421081	1		686	617	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188386	32188386	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	69	453	0	ENST00000375023.3:c.955G>A	p.Glu319Lys	p.E319K	ENST00000375023	NM_004557.3	319	Gag/Aag	6/30	1	2	FACETS	0.48	0.419	0.545	0.48	0.419	0.545	SUBCLONAL	1	TRUE	1	0.651576910421081	2		453	441	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410763	63410763	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	31	544	0	ENST00000330258.3:c.2404G>A	p.Glu802Lys	p.E802K	ENST00000330258	NM_152424.3	802	Gag/Aag	2/2	0.651576910421081	1	FACETS	0.166	0.134	0.202	0.166	0.134	0.202	SUBCLONAL	1	TRUE	0	0.651576910421081	1		544	386	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735431	204735431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	14	310	0	ENST00000302823.3:c.232G>A	p.Asp78Asn	p.D78N	ENST00000302823	NM_005214.4	78	Gac/Aac	2/4	0.394342065862793	1	FACETS	0.106	0.076	0.142	0.106	0.076	0.142	SUBCLONAL	1	TRUE	0	0.651576910421081	1		310	273	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0032632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	14	478	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	1	2	FACETS	0.659	0.476	0.879	0.659	0.476	0.879	SUBCLONAL	1	TRUE	1	0.192370059522297	2		478	221	SUCCESS
APC	324	MSKCC	GRCh37	5	112154907	112154907	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1114167545	NA	P-0032632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	29	665	0	ENST00000257430.4:c.1178C>G	p.Ser393Ter	p.S393*	ENST00000257430	NM_000038.5	393	tCa/tGa	10/16	0.192370059522297	1	FACETS	0.868	0.698	1	0.868	0.698	1	CLONAL	1	TRUE	0	0.192370059522297	1		665	314	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510560	38510560	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	30	487	0	ENST00000254066.5:c.814C>G	p.Arg272Gly	p.R272G	ENST00000254066	NM_000964.3	272	Cgg/Ggg	7/9	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.192370059522297	2		487	292	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451518	70451518	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	29	690	0	ENST00000373644.4:c.6358G>C	p.Val2120Leu	p.V2120L	ENST00000373644	NM_030625.2	2120	Gtg/Ctg	12/12	0.192370059522297	1	FACETS	0.683	0.548	0.837	0.683	0.548	0.837	SUBCLONAL	1	TRUE	0	0.192370059522297	1		690	399	SUCCESS
ATM	472	MSKCC	GRCh37	11	108127045	108127045	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	10	465	0	ENST00000278616.4:c.2228C>A	p.Ser743Ter	p.S743*	ENST00000278616	NM_000051.3	743	tCa/tAa	14/63	1	2	FACETS	0.562	0.381	0.789	0.562	0.381	0.789	SUBCLONAL	1	TRUE	1	0.192370059522297	2		465	185	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373623	118373623	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	13	483	0	ENST00000534358.1:c.7016A>G	p.His2339Arg	p.H2339R	ENST00000534358	NM_005933.3	2339	cAt/cGt	27/36	1	2	FACETS	0.583	0.415	0.786	0.583	0.415	0.786	SUBCLONAL	1	TRUE	1	0.192370059522297	2		483	232	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719492	61719492	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	14	584	0	ENST00000401558.2:c.1691C>G	p.Thr564Ser	p.T564S	ENST00000401558	NM_003400.3	564	aCt/aGt	15/25	1	2	FACETS	0.809	0.586	1	0.809	0.586	1	CLONAL	1	TRUE	1	0.192370059522297	2		584	180	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888739	76888739	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	15	320	0	ENST00000373344.5:c.5090G>C	p.Ser1697Thr	p.S1697T	ENST00000373344	NM_000489.3	1697	aGt/aCt	19/35	1	1	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	0	0.192370059522297	1		320	105	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371409680	NA	P-0032656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	93	861	0	ENST00000269305.4:c.848G>C	p.Arg283Pro	p.R283P	ENST00000269305	NM_001126112.2	283	cGc/cCc	8/11	0.157635490926485	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.157635490926485	2		861	489	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0032659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	141	359	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	0.734386385017357	2	FACETS	0.795	0.747	0.841	0.795	0.747	0.841	SUBCLONAL	2	TRUE	0	0.825031196056776	2		359	215	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0032659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	618	658	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.74820083974873	2	FACETS	0.948	0.926	0.969	0.948	0.926	0.969	CLONAL	2	TRUE	0	0.825031196056776	2		658	790	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98244319	98244319	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs768776930	NA	P-0032659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	41	442	0	ENST00000331920.6:c.658A>G	p.Ile220Val	p.I220V	ENST00000331920	NM_000264.3	220	Ata/Gta	5/24	0.747972602345065	2	FACETS	0.452	0.38	0.53	0.226	0.19	0.265	SUBCLONAL	1	TRUE	0	0.825031196056776	2		442	220	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168953	11168953	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	434	503	0	ENST00000358026.2:c.4543G>T	p.Glu1515Ter	p.E1515*	ENST00000358026	NM_001128849.1	1515	Gag/Tag	32/36	0.742818812888971	2	FACETS	0.918	0.892	0.944	0.918	0.892	0.944	CLONAL	2	TRUE	0	0.825031196056776	2		503	573	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	54	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.984	0.84	1	0.984	0.84	1	CLONAL	1	TRUE	1	0.18	2		539	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0032671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	80	650	1	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	1	2	FACETS	0.994	0.874	1	0.994	0.874	1	CLONAL	1	TRUE	1	0.18	2		651	894	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0032676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	66	256	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.891	0.776	1	0.891	0.776	1	CLONAL	1	TRUE	1	0.372405409966281	2		256	398	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084145	47084146	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0032676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	110	452	0	ENST00000409792.3:c.7143dup	p.Ser2382LeufsTer47	p.S2382Lfs*47	ENST00000409792	NM_014159.6	2381	-/C	17/21	1	2	FACETS	0.85	0.764	0.94	0.85	0.764	0.94	CLONAL	1	TRUE	1	0.372405409966281	2		452	695	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11292537	11292537	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	32	365	0	ENST00000361445.4:c.2470A>G	p.Ile824Val	p.I824V	ENST00000361445	NM_004958.3	824	Atc/Gtc	16/58	1	2	FACETS	0.367	0.297	0.446	0.367	0.297	0.446	SUBCLONAL	1	TRUE	1	0.372405409966281	2		365	468	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162722920	162722920	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	37	626	0	ENST00000367921.3:c.118C>T	p.Gln40Ter	p.Q40*	ENST00000367921	NM_006182.2	40	Cag/Tag	4/18	1	2	FACETS	0.274	0.225	0.329	0.274	0.225	0.329	SUBCLONAL	1	TRUE	1	0.372405409966281	2		626	726	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098922	47098924	+	frameshift_variant	Frame_Shift_Del	DEL	TAG	TAG	AC	novel	NA	P-0032676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	141	670	2	ENST00000409792.3:c.6350_6352delinsGT	p.Ser2117CysfsTer30	p.S2117Cfs*30	ENST00000409792	NM_014159.6	2117	tCTAca/tGTca	15/21	1	2	FACETS	0.87	0.793	0.952	0.87	0.793	0.952	CLONAL	1	TRUE	1	0.372405409966281	2		672	870	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0032678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	249	503	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.477809435220625	2	FACETS	0.857	0.808	0.906	0.857	0.808	0.906	CLONAL	2	TRUE	0	0.497460570138708	2		504	584	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971170	21971170	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	92	199	0	ENST00000304494.5:c.188T>C	p.Leu63Pro	p.L63P	ENST00000304494	NM_000077.4	63	cTg/cCg	2/3	0.497460570138708	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.497460570138708	1		199	223	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271870	15271870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528151296	NA	P-0032678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	184	523	1	ENST00000263388.2:c.6569C>T	p.Ala2190Val	p.A2190V	ENST00000263388	NM_000435.2	2190	gCg/gTg	33/33	0.222442986633977	1	FACETS	0.85	0.788	0.914	0.85	0.788	0.914	INDETERMINATE	1	TRUE	0	0.497460570138708	1		524	654	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570237	95570237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368588781	NA	P-0032678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	43	356	0	ENST00000393063.1:c.3496G>A	p.Val1166Ile	p.V1166I	ENST00000393063	NM_030621.3	1166	Gtt/Att	22/28	NA	2	FACETS	0.341	0.285	0.403			1	INDETERMINATE	1	TRUE	NA	0.497460570138708	2		356	507	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589815	212589815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866956005	NA	P-0032678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	37	328	0	ENST00000342788.4:c.727G>A	p.Asp243Asn	p.D243N	ENST00000342788	NM_005235.2	243	Gac/Aac	6/28	0.497460570138708	3	FACETS	0.346	0.285	0.415	0.173	0.142	0.208	SUBCLONAL	1	TRUE	1	0.497460570138708	3		328	537	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38960022	38960022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	102	246	0	ENST00000357387.3:c.1910C>T	p.Ser637Leu	p.S637L	ENST00000357387	NM_152756.3	637	tCa/tTa	21/38	0.155705559113782	5	FACETS	1	0.936	1			1	INDETERMINATE	2	TRUE	NA	0.497460570138708	5		246	342	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0032694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	98	388	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.124193339188995	3	FACETS	0.947	0.849	1	0.947	0.849	1	INDETERMINATE	2	TRUE	1	0.243224327902916	3		388	477	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0032694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	41	536	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.556	0.462	0.661	0.556	0.462	0.661	SUBCLONAL	1	TRUE	1	0.243224327902916	2		536	606	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115437	115115437	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	178	710	0	ENST00000257566.3:c.889A>C	p.Asn297His	p.N297H	ENST00000257566	NM_016569.3	297	Aac/Cac	5/8	0.214519562319475	2	FACETS	0.846	0.78	0.914	0.846	0.78	0.914	CLONAL	2	TRUE	0	0.243224327902916	2		710	865	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104353406	104353407	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0032694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	82	772	1	ENST00000369902.3:c.611_612delinsTT	p.Cys204Phe	p.C204F	ENST00000369902	NM_016169.3	204	tGC/tTT	5/12	1	2	FACETS	0.868	0.764	0.979	0.868	0.764	0.979	CLONAL	1	TRUE	1	0.243224327902916	2		773	777	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772310	68772316	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CAGAGGT	CAGAGGT	-	novel	NA	P-0032694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	86	634	0	ENST00000261769.5:c.159_163+2del		p.X53_splice	ENST00000261769	NM_004360.3	53		2/16	NA	2	FACETS	0.979	0.866	1			1	INDETERMINATE	1	TRUE	NA	0.243224327902916	2		634	722	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565596	41565596	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs769846473	NA	P-0032694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	68	502	0	ENST00000263253.7:c.4262A>G	p.Tyr1421Cys	p.Y1421C	ENST00000263253	NM_001429.3	1421	tAt/tGt	26/31	0.243224327902916	1	FACETS	0.834	0.726	0.951	0.834	0.726	0.951	CLONAL	1	TRUE	0	0.243224327902916	1		502	589	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106434	27106434	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	190	499	1	ENST00000324856.7:c.6046del	p.Leu2016CysfsTer14	p.L2016Cfs*14	ENST00000324856	NM_006015.4	2015	atC/at	20/20	1	2	FACETS	0.909	0.846	0.973	0.909	0.846	0.973	CLONAL	1	TRUE	1	0.758605850873005	2		500	551	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989018	41989018	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	157	493	0	ENST00000219905.7:c.1810C>T	p.Gln604Ter	p.Q604*	ENST00000219905	NM_001164273.1	604	Cag/Tag	3/24	1	2	FACETS	0.898	0.83	0.968	0.898	0.83	0.968	CLONAL	1	TRUE	1	0.758605850873005	2		493	461	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042395	42042395	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	201	473	0	ENST00000219905.7:c.6590del	p.Ala2197GlufsTer5	p.A2197Efs*5	ENST00000219905	NM_001164273.1	2197	gCa/ga	17/24	1	2	FACETS	0.907	0.847	0.97	0.907	0.847	0.97	CLONAL	1	TRUE	1	0.758605850873005	2		473	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0032704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	353	614	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.895093293723872	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.899650147479144	1		615	430	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156918	89156920	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	rs768142526	NA	P-0032704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	202	541	0	ENST00000336596.2:c.27_29del	p.Leu11del	p.L11del	ENST00000336596	NM_005233.5	7	aTCCtc/atc	1/17	1	2	FACETS	0.847	0.792	0.903	0.847	0.792	0.903	CLONAL	1	TRUE	1	0.899650147479144	2		541	530	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148526846	148526846	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs797044844	NA	P-0032740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	265	343	0	ENST00000320356.2:c.458A>G	p.Tyr153Cys	p.Y153C	ENST00000320356	NM_004456.4	153	tAt/tGt	5/20	1	2	FACETS	0.994	0.941	1	0.994	0.941	1	CLONAL	1	TRUE	1	0.900402464841442	2		343	592	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0032743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	103	455	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.861	0.774	0.952	0.861	0.774	0.952	CLONAL	1	TRUE	1	0.491375757833468	2		455	487	SUCCESS
APC	324	MSKCC	GRCh37	5	112175513	112175513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	154	329	0	ENST00000257430.4:c.4222G>T	p.Glu1408Ter	p.E1408*	ENST00000257430	NM_000038.5	1408	Gaa/Taa	16/16	0.491375757833468	2	FACETS	0.97	0.903	1	0.97	0.903	1	CLONAL	2	TRUE	0	0.491375757833468	2		329	323	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0032743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	115	434	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.491375757833468	2		434	457	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791757	42791757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568504941	NA	P-0032743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	93	519	0	ENST00000575354.2:c.643C>T	p.Arg215Trp	p.R215W	ENST00000575354	NM_015125.3	215	Cgg/Tgg	5/20	1	2	FACETS	0.966	0.865	1	0.966	0.865	1	CLONAL	1	TRUE	1	0.491375757833468	2		519	392	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0032743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	67	402	2	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	0.491375757833468	1	FACETS	0.8	0.704	0.902	0.8	0.704	0.902	CLONAL	1	TRUE	0	0.491375757833468	1		404	257	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877391	40877391	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372713520	NA	P-0032743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	137	550	0	ENST00000373198.4:c.2305G>A	p.Val769Met	p.V769M	ENST00000373198	NM_133170.3	769	Gtg/Atg	15/32	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.491375757833468	2		550	517	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828881	26828881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	33	270	0	ENST00000381527.3:c.103G>A	p.Val35Ile	p.V35I	ENST00000381527	NM_001260.1	35	Gtc/Atc	1/13	1	2	FACETS	0.436	0.356	0.526	0.436	0.356	0.526	SUBCLONAL	1	TRUE	1	0.491375757833468	2		270	308	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724436	43724436	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	172	664	0	ENST00000382044.4:c.3631C>A	p.Pro1211Thr	p.P1211T	ENST00000382044	NM_001141980.1	1211	Cca/Aca	17/28	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.491375757833468	2		664	668	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821615	72821638	+	inframe_deletion	In_Frame_Del	DEL	GCCACCGCCGCCGCCGCCGCCACT	GCCACCGCCGCCGCCGCCGCCACT	-	rs750348888	NA	P-0032743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	23	45	0	ENST00000268489.5:c.10537_10560del	p.Ser3513_Gly3520del	p.S3513_G3520del	ENST00000268489	NM_006885.3	3513	AGTGGCGGCGGCGGCGGCGGTGGC/-	10/10	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.491375757833468	2		45	67	SUCCESS
APC	324	MSKCC	GRCh37	5	112175511	112175511	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	154	332	0	ENST00000257430.4:c.4220G>T	p.Ser1407Ile	p.S1407I	ENST00000257430	NM_000038.5	1407	aGt/aTt	16/16	0.491375757833468	2	FACETS	0.967	0.901	1	0.967	0.901	1	CLONAL	2	TRUE	0	0.491375757833468	2		332	324	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056509	26056509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779648984	NA	P-0032743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	45	211	0	ENST00000343677.2:c.148G>A	p.Ala50Thr	p.A50T	ENST00000343677	NM_005319.3	50	Gcc/Acc	1/1	1	2	FACETS	0.84	0.714	0.977	0.84	0.714	0.977	CLONAL	1	TRUE	1	0.491375757833468	2		211	218	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	310	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.54565027304906	6	FACETS	0.887	0.843	0.931			1	CLONAL	4	TRUE	NA	0.54565027304906	6		539	670	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0032747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	324	653	1	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.537290607930357	2	FACETS	1	0.992	1	0.636	0.602	0.67	CLONAL	1	TRUE	0	0.54565027304906	2		654	934	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934152	48934152	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0032747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	103	348	0	ENST00000267163.4:c.610del		p.X204_splice	ENST00000267163	NM_000321.2	204			0.498146737898113	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	0	0.54565027304906	2		348	185	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893231	32893231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	12	318	0	ENST00000380152.3:c.85C>T	p.Leu29Phe	p.L29F	ENST00000380152		29	Ctt/Ttt	3/27	0.498146737898113	2	FACETS	0.251	0.177	0.343	0.126	0.088	0.172	SUBCLONAL	1	TRUE	0	0.54565027304906	2		318	175	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993723	72993723	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	126	554	0	ENST00000268489.5:c.322C>G	p.Leu108Val	p.L108V	ENST00000268489	NM_006885.3	108	Ctg/Gtg	2/10	0.350586375061227	4	FACETS	0.896	0.811	0.985	0.224	0.202	0.247	CLONAL	1	TRUE	0	0.54565027304906	4		554	797	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120509066	120509066	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032760-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	268	561	0	ENST00000256646.2:c.1500C>A	p.Ser500Arg	p.S500R	ENST00000256646	NM_024408.3	500	agC/agA	9/34	1	2	FACETS	0.884	0.835	0.934	0.884	0.835	0.934	CLONAL	1	TRUE	1	0.898078842853849	2		561	675	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0032810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	94	403	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	1	2	FACETS	0.858	0.771	0.948	0.858	0.771	0.948	CLONAL	1	TRUE	1	0.672376944584726	2		403	326	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273029	55273029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770749711	NA	P-0032810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	198	621	0	ENST00000275493.2:c.3352G>A	p.Ala1118Thr	p.A1118T	ENST00000275493	NM_005228.3	1118	Gcg/Acg	28/28	0.672376944584726	3	FACETS	1	0.938	1	0.506	0.469	0.543	CLONAL	1	TRUE	1	0.672376944584726	3		621	778	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913384	NA	P-0032817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	136	322	0	ENST00000304494.5:c.262G>T	p.Glu88Ter	p.E88*	ENST00000304494	NM_000077.4	88	Gag/Tag	2/3	0.435152204166875	3	FACETS	1	0.986	1	0.817	0.765	0.869	CLONAL	2	TRUE	0	0.654224520080835	3		322	225	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602314	10602314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	203	745	0	ENST00000171111.5:c.1264G>A	p.Asp422Asn	p.D422N	ENST00000171111	NM_203500.1	422	Gat/Aat	3/6	0.288077912174358	4	FACETS	0.965	0.902	1	0.965	0.902	1	INDETERMINATE	2	TRUE	2	0.654224520080835	4		745	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs878854073	NA	P-0032817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	253	443	0	ENST00000269305.4:c.673-1G>A		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.4971775106901	4	FACETS	0.876	0.839	0.912	0.876	0.839	0.912	CLONAL	4	TRUE	0	0.654224520080835	4		443	365	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156840	106156840	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560827535	NA	P-0032817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	64	350	0	ENST00000380013.4:c.1741C>T	p.Arg581Cys	p.R581C	ENST00000380013	NM_001127208.2	581	Cgt/Tgt	3/11	0.453045203908469	3	FACETS	0.908	0.793	1	0.303	0.264	0.344	CLONAL	1	TRUE	0	0.654224520080835	3		350	286	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246078863	246078863	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	212	616	0	ENST00000388985.4:c.782G>T	p.Cys261Phe	p.C261F	ENST00000388985		261	tGt/tTt	8/12	0.444603341769513	4	FACETS	0.776	0.724	0.829	0.776	0.724	0.829	SUBCLONAL	2	TRUE	2	0.654224520080835	4		616	691	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929117	32929117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	130	488	0	ENST00000380152.3:c.7127C>T	p.Ala2376Val	p.A2376V	ENST00000380152		2376	gCa/gTa	14/27	0.478785150433816	2	FACETS	1	0.988	1	0.715	0.661	0.769	CLONAL	1	TRUE	0	0.654224520080835	2		488	278	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278210	15278210	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	138	561	0	ENST00000263388.2:c.5212G>C	p.Gly1738Arg	p.G1738R	ENST00000263388	NM_000435.2	1738	Ggc/Cgc	29/33	0.288077912174358	4	FACETS	0.825	0.758	0.894	0.825	0.758	0.894	INDETERMINATE	2	TRUE	2	0.654224520080835	4		561	423	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979403	2979403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	157	601	0	ENST00000396946.4:c.844G>A	p.Glu282Lys	p.E282K	ENST00000396946	NM_032415.4	282	Gag/Aag	6/25	0.288077912174358	4	FACETS	0.822	0.759	0.887	0.822	0.759	0.887	INDETERMINATE	2	TRUE	2	0.654224520080835	4		601	483	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	145	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.39378360552494	2	FACETS	0.792	0.732	0.852	0.792	0.732	0.852	SUBCLONAL	2	TRUE	0	0.515807101127593	2		539	355	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221243	1221243	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1057520606	NA	P-0032823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	205	612	0	ENST00000326873.7:c.766G>T	p.Glu256Ter	p.E256*	ENST00000326873	NM_000455.4	256	Gaa/Taa	6/10	0.515807101127593	1	FACETS	0.926	0.864	0.99	0.926	0.864	0.99	CLONAL	1	TRUE	0	0.515807101127593	1		612	637	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608310	43608311	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0032823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	171	993	1	ENST00000355710.3:c.1658_1659delinsTT	p.Arg553Ile	p.R553I	ENST00000355710	NM_020975.4	553	aGG/aTT	9/20	1	2	FACETS	0.672	0.617	0.728	0.672	0.617	0.728	SUBCLONAL	1	TRUE	1	0.515807101127593	2		994	987	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741924	17741924	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	65	157	0	ENST00000250003.3:c.595G>C	p.Ala199Pro	p.A199P	ENST00000250003	NM_002478.4	199	Gcg/Ccg	1/3	0.243216630977916	0	FACETS	0.613	0.541	0.689			1	INDETERMINATE	1	TRUE	0	0.515807101127593	0		157	199	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348125	348126	+	missense_variant	Missense_Mutation	DNP	CC	CC	TG	novel	NA	P-0032823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	211	765	1	ENST00000262320.3:c.1380_1381delinsCA	p.Asp461Asn	p.D461N	ENST00000262320	NM_003502.3	460	cgGGat/cgCAat	6/11	0.296741245875396	3	FACETS	1	0.988	1	0.636	0.592	0.682	INDETERMINATE	1	TRUE	1	0.515807101127593	3		766	809	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122347	17122347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1261069493	NA	P-0032823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	67	489	0	ENST00000285071.4:c.1048C>T	p.Arg350Trp	p.R350W	ENST00000285071	NM_144997.5	350	Cgg/Tgg	9/14	1	2	FACETS	0.514	0.448	0.586	0.514	0.448	0.586	SUBCLONAL	1	TRUE	1	0.515807101127593	2		489	505	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610441	10610442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0032823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	255	730	0	ENST00000171111.5:c.268dup	p.Ala90GlyfsTer37	p.A90Gfs*37	ENST00000171111	NM_203500.1	90	gcc/gGcc	2/6	0.515807101127593	1	FACETS	0.958	0.9	1	0.958	0.9	1	CLONAL	1	TRUE	0	0.515807101127593	1		730	766	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661202	227661202	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	170	823	0	ENST00000305123.5:c.2253C>A	p.Tyr751Ter	p.Y751*	ENST00000305123	NM_005544.2	751	taC/taA	1/2	1	2	FACETS	0.736	0.677	0.798	0.736	0.677	0.798	SUBCLONAL	1	TRUE	1	0.515807101127593	2		823	895	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231194	142231194	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	69	608	0	ENST00000350721.4:c.4760A>G	p.His1587Arg	p.H1587R	ENST00000350721	NM_001184.3	1587	cAt/cGt	27/47	0.195479404697301	0	FACETS	0.25	0.217	0.284			1	INDETERMINATE	1	TRUE	0	0.515807101127593	0		608	519	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671646	30671646	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	358	766	0	ENST00000376406.3:c.5314G>T	p.Glu1772Ter	p.E1772*	ENST00000376406	NM_014641.2	1772	Gag/Tag	10/15	0.306092640337043	3	FACETS	0.993	0.945	1	0.662	0.63	0.695	INDETERMINATE	2	TRUE	0	0.515807101127593	3		766	879	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0032852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	62	460	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.71	0.614	0.814	0.71	0.614	0.814	SUBCLONAL	1	TRUE	1	0.325900249266847	2		460	536	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882292	89882292	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1170236785	NA	P-0032852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	23	439	0	ENST00000389301.3:c.182T>G	p.Leu61Trp	p.L61W	ENST00000389301	NM_000135.2	61	tTg/tGg	2/43	1	2	FACETS	0.331	0.257	0.416	0.331	0.257	0.416	SUBCLONAL	1	TRUE	1	0.325900249266847	2		439	427	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1800982	1800982	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	rs747890000	NA	P-0032852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	29	668	0	ENST00000260795.2:c.111A>C	p.Glu37Asp	p.E37D	ENST00000260795		37	gaA/gaC	2/17	1	2	FACETS	0.352	0.282	0.433	0.352	0.282	0.433	SUBCLONAL	1	TRUE	1	0.325900249266847	2		668	505	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161345	55161345	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	31	396	0	ENST00000257290.5:c.3176T>G	p.Phe1059Cys	p.F1059C	ENST00000257290	NM_006206.4	1059	tTc/tGc	23/23	1	2	FACETS	0.404	0.326	0.492	0.404	0.326	0.492	SUBCLONAL	1	TRUE	1	0.325900249266847	2		396	471	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971146	21971200	+	frameshift_variant	Frame_Shift_Del	DEL	TTGGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCTGCCCATCA	TTGGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCTGCCCATCA	-	novel	NA	P-0032852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	38	311	0	ENST00000304494.5:c.158_212del	p.Met53ThrfsTer75	p.M53Tfs*75	ENST00000304494	NM_000077.4	53	aTGATGGGCAGCGCCCGAGTGGCGGAGCTGCTGCTGCTCCACGGCGCGGAGCCCAAc/ac	2/3	1	2	FACETS	0.755	0.626	0.897	0.755	0.626	0.897	SUBCLONAL	1	TRUE	1	0.325900249266847	2		311	309	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482182	87482182	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	42	638	0	ENST00000277120.3:c.1469A>C	p.Asp490Ala	p.D490A	ENST00000277120		490	gAt/gCt	14/19	1	2	FACETS	0.39	0.325	0.463	0.39	0.325	0.463	SUBCLONAL	1	TRUE	1	0.325900249266847	2		638	661	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498313	29498313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768256091	NA	P-0032871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	181	656	0	ENST00000389048.3:c.1867G>A	p.Val623Met	p.V623M	ENST00000389048	NM_004304.4	623	Gtg/Atg	10/29	1	2	FACETS	0.969	0.897	1	0.969	0.897	1	CLONAL	1	TRUE	1	0.581155722847147	2		656	643	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165949	118165950	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0032871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	200	517	1	ENST00000369448.3:c.459_460delinsAG	p.Ser153_Leu154delinsArgVal	p.S153_L154delinsRV	ENST00000369448	NM_017709.3	153	agCCtg/agAGtg	2/2	0.295131073148245	3	FACETS	0.753	0.702	0.805	0.753	0.702	0.805	INDETERMINATE	2	TRUE	1	0.581155722847147	3		518	590	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390445	56390445	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	173	395	0	ENST00000348428.3:c.1184T>C	p.Val395Ala	p.V395A	ENST00000348428	NM_006785.3	395	gTg/gCg	10/17	0.581155722847147	2	FACETS	1	0.971	1	0.546	0.506	0.588	CLONAL	1	TRUE	0	0.581155722847147	2		395	545	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910758	29910774	+	frameshift_variant	Frame_Shift_Del	DEL	GTGGACCTGGGGACCCT	GTGGACCTGGGGACCCT	-	novel	NA	P-0032871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	120	870	0	ENST00000376809.5:c.299_315del	p.Val100AlafsTer71	p.V100Afs*71	ENST00000376809	NM_002116.7	100	GTGGACCTGGGGACCCTg/g	2/8	0.581155722847147	1	FACETS	0.627	0.57	0.687	0.627	0.57	0.687	SUBCLONAL	1	TRUE	0	0.581155722847147	1		870	467	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	134	349	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.70262844691536	2		349	345	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0032988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	510	627	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.70262844691536	2	FACETS	0.934	0.905	0.963	0.934	0.905	0.963	CLONAL	2	TRUE	0	0.70262844691536	2		627	777	SUCCESS
AR	367	MSKCC	GRCh37	X	66765159	66765185	+	inframe_deletion	In_Frame_Del	DEL	GCAGCAGCAGCAGCAGCAGCAGCAGCA	GCAGCAGCAGCAGCAGCAGCAGCAGCA	-	rs3032358	NA	P-0032988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	26	122	0	ENST00000374690.3:c.213_239del	p.Gln72_Gln80del	p.Q72_Q80del	ENST00000374690	NM_000044.3	57	ctGCAGCAGCAGCAGCAGCAGCAGCAGCAg/ctg	1/8	1	1	FACETS	0.421	0.339	0.511	0.421	0.339	0.511	SUBCLONAL	1	TRUE	0	0.70262844691536	1		122	114	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184589	11184589	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	290	630	0	ENST00000361445.4:c.6628G>C	p.Ala2210Pro	p.A2210P	ENST00000361445	NM_004958.3	2210	Gcc/Ccc	47/58	0.67591117845948	2	FACETS	1	0.987	1	0.57	0.539	0.601	CLONAL	1	TRUE	0	0.70262844691536	2		630	724	SUCCESS
FH	2271	MSKCC	GRCh37	1	241672038	241672038	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	661	487	0	ENST00000366560.3:c.603A>G	p.Ile201Met	p.I201M	ENST00000366560	NM_000143.3	201	atA/atG	5/10	0.687716039026539	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	1	0.70262844691536	4		487	1058	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39647358	39647358	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	163	399	0	ENST00000262039.4:c.2530G>A	p.Asp844Asn	p.D844N	ENST00000262039	NM_002647.2	844	Gat/Aat	24/25	1	2	FACETS	0.921	0.851	0.992	0.921	0.851	0.992	CLONAL	1	TRUE	1	0.70262844691536	2		399	504	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582102	52582102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	150	291	0	ENST00000394830.3:c.4726G>A	p.Ala1576Thr	p.A1576T	ENST00000394830	NM_018313.4	1576	Gca/Aca	30/30	1	2	FACETS	0.89	0.819	0.962	0.89	0.819	0.962	CLONAL	1	TRUE	1	0.70262844691536	2		291	480	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945671	38945671	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	144	331	0	ENST00000357387.3:c.4555A>T	p.Asn1519Tyr	p.N1519Y	ENST00000357387	NM_152756.3	1519	Aac/Tac	34/38	1	2	FACETS	0.878	0.807	0.951	0.878	0.807	0.951	CLONAL	1	TRUE	1	0.70262844691536	2		331	467	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0033006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	35	527	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		527	453	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842471	68842471	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1131690808	NA	P-0033006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	37	389	0	ENST00000261769.5:c.531+1G>A		p.X177_splice	ENST00000261769	NM_004360.3	177			1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		389	366	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713591	30713591	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	45	329	0	ENST00000295754.5:c.916C>T	p.Gln306Ter	p.Q306*	ENST00000295754	NM_003242.5	306	Cag/Tag	4/7	0.154473655879875	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		329	420	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15833990	15833990	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	37	518	0	ENST00000307771.7:c.748G>T	p.Val250Leu	p.V250L	ENST00000307771	NM_005089.3	250	Gtg/Ttg	8/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		518	631	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084145	47084146	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0033037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	84	452	0	ENST00000409792.3:c.7143dup	p.Ser2382LeufsTer47	p.S2382Lfs*47	ENST00000409792	NM_014159.6	2381	-/C	17/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.192710271828898	2		452	627	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637540	52637540	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0033037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	58	399	0	ENST00000394830.3:c.2776A>T	p.Arg926Ter	p.R926*	ENST00000394830	NM_018313.4	926	Aga/Tga	18/30	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.192710271828898	2		399	516	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613390	100613390	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	28	241	0	ENST00000308731.7:c.1010G>T	p.Cys337Phe	p.C337F	ENST00000308731	NM_000061.2	337	tGt/tTt	12/19	1	1	FACETS	0.775	0.62	0.951	0.775	0.62	0.951	CLONAL	1	TRUE	0	0.192710271828898	1		241	339	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	42	349	0				ENST00000310581	NM_198253.2	-/1132			0.194824151354975	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.683729781263955	0		349	126	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0033057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	147	256	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	FALSE	1	0.683729781263955	2		256	389	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125010	46125011	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0033057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	116	220	0	ENST00000334344.6:c.198dup	p.Asn67GlufsTer8	p.N67Efs*8	ENST00000334344	NM_152641.2	66	aag/aaGg	3/21	0.117476271681069	4	FACETS	0.754	0.686	0.824	0.754	0.686	0.824	INDETERMINATE	2	FALSE	2	0.683729781263955	4		220	379	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796945	42796945	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	124	626	0	ENST00000575354.2:c.3403C>G	p.Pro1135Ala	p.P1135A	ENST00000575354	NM_015125.3	1135	Ccc/Gcc	14/20	1	2	FACETS	0.864	0.788	0.942	0.864	0.788	0.942	CLONAL	1	FALSE	1	0.683729781263955	2		626	420	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570070	212570070	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745408040	NA	P-0033070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	134	427	0	ENST00000342788.4:c.1171G>A	p.Val391Ile	p.V391I	ENST00000342788	NM_005235.2	391	Gtc/Atc	10/28	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.661493025206023	2		427	393	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591825	48591825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767342	NA	P-0033070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	141	491	0	ENST00000342988.3:c.988G>A	p.Glu330Lys	p.E330K	ENST00000342988	NM_005359.5	330	Gaa/Aaa	9/12	0.632193670482282	1	FACETS	0.994	0.923	1	0.994	0.923	1	CLONAL	1	TRUE	0	0.661493025206023	1		491	287	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251859	212251859	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147514533	NA	P-0033070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	76	229	0	ENST00000342788.4:c.3200G>A	p.Arg1067Gln	p.R1067Q	ENST00000342788	NM_005235.2	1067	cGa/cAa	27/28	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.661493025206023	2		229	228	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	18	349	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.459	0.345	0.594	0.459	0.345	0.594	SUBCLONAL	1	TRUE	1	0.251205319289806	2		349	312	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0033074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	36	256	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.162422947315951	3	FACETS	1	0.839	1	0.509	0.419	0.608	CLONAL	1	TRUE	1	0.251205319289806	3		256	317	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262370	16262371	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	23	263	0	ENST00000375759.3:c.9635_9636delinsTT	p.Ala3212Val	p.A3212V	ENST00000375759	NM_015001.2	3212	gCC/gTT	11/15	1	2	FACETS	0.583	0.455	0.732	0.583	0.455	0.732	SUBCLONAL	1	TRUE	1	0.251205319289806	2		263	314	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720658	89720658	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	16	242	0	ENST00000371953.3:c.809T>A	p.Met270Lys	p.M270K	ENST00000371953	NM_000314.4	270	aTg/aAg	8/9	0.251205319289806	1	FACETS	0.509	0.376	0.666	0.509	0.376	0.666	SUBCLONAL	1	TRUE	0	0.251205319289806	1		242	219	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285080	15285080	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	48	536	0	ENST00000263388.2:c.4535T>G	p.Val1512Gly	p.V1512G	ENST00000263388	NM_000435.2	1512	gTg/gGg	25/33	1	2	FACETS	0.534	0.45	0.626	0.534	0.45	0.626	SUBCLONAL	1	TRUE	1	0.251205319289806	2		536	716	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750437	41750437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	47	394	1	ENST00000226382.2:c.191C>T	p.Ser64Phe	p.S64F	ENST00000226382	NM_003924.3	64	tCc/tTc	1/3	1	2	FACETS	0.633	0.534	0.743	0.633	0.534	0.743	SUBCLONAL	1	TRUE	1	0.251205319289806	2		395	591	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673073	30673073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	58	608	0	ENST00000376406.3:c.3887C>T	p.Ser1296Phe	p.S1296F	ENST00000376406	NM_014641.2	1296	tCc/tTc	10/15	1	2	FACETS	0.555	0.476	0.642	0.555	0.476	0.642	SUBCLONAL	1	TRUE	1	0.251205319289806	2		608	832	SUCCESS
AR	367	MSKCC	GRCh37	X	66937404	66937404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057523747	NA	P-0033074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	53	320	0	ENST00000374690.3:c.2258G>A	p.Arg753Gln	p.R753Q	ENST00000374690	NM_000044.3	753	cGa/cAa	5/8	1	1	FACETS	0.941	0.805	1	0.941	0.805	1	CLONAL	1	TRUE	0	0.251205319289806	1		320	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0033107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	906	699	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.962634958944585	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.962634958944585	2		699	932	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479175	50479175	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs758191233	NA	P-0033107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	209	395	0	ENST00000394963.4:c.23A>G	p.Gln8Arg	p.Q8R	ENST00000394963	NM_003076.4	8	cAg/cGg	1/13	0.962634958944585	3	FACETS	0.969	0.904	1	0.484	0.452	0.518	CLONAL	1	TRUE	1	0.962634958944585	3		395	664	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881428	48881435	+	frameshift_variant	Frame_Shift_Del	DEL	AGAAACAG	AGAAACAG	-	novel	NA	P-0033107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	357	219	0	ENST00000267163.4:c.151_158del	p.Glu51ArgfsTer3	p.E51Rfs*3	ENST00000267163	NM_000321.2	50	gaAGAAACAGaa/gaaa	2/27	0.959352561982992	4	FACETS	0.986	0.973	0.997	0.986	0.973	0.997	CLONAL	4	TRUE	0	0.962634958944585	4		219	369	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6438321	6438321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	302	497	0	ENST00000356142.4:c.254C>T	p.Thr85Ile	p.T85I	ENST00000356142	NM_018890.3	85	aCc/aTc	4/7	0.463791482649653	4	FACETS	1	0.992	1	0.44	0.415	0.465	INDETERMINATE	1	TRUE	1	0.962634958944585	4		497	933	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248998	55248999	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCCAGCG	rs727504263	NA	P-0033110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	19	525	0	ENST00000275493.2:c.2300_2308dup	p.Ala767_Val769dup	p.A767_V769dup	ENST00000275493	NM_005228.3	767	atg/aTGGCCAGCGtg	20/28	0.219230720691916	3	FACETS	0.407	0.308	0.524	0.203	0.154	0.262	SUBCLONAL	1	FALSE	1	0.218638586966392	3		525	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576858	7576858	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	84	733	8	ENST00000269305.4:c.988del	p.Leu330PhefsTer15	p.L330Ffs*15	ENST00000269305	NM_001126112.2	330	Ctt/tt	9/11	0.301807055771676	2	FACETS	0.766	0.69	0.845	0.766	0.69	0.845	INDETERMINATE	2	FALSE	0	0.512115811701969	2		741	214	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696689	47696689	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519972	NA	P-0033135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	197	496	0	ENST00000347630.2:c.259T>A	p.Tyr87Asn	p.Y87N	ENST00000347630	NM_001007230.1	87	Tac/Aac	5/11	1	2	FACETS	0.93	0.862	1	0.93	0.862	1	CLONAL	1	TRUE	1	0.503920681342501	2		496	841	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023750	27023750	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	133	343	0	ENST00000324856.7:c.856A>T	p.Thr286Ser	p.T286S	ENST00000324856	NM_006015.4	286	Act/Tct	1/20	1	2	FACETS	0.998	0.911	1	0.998	0.911	1	CLONAL	1	TRUE	1	0.503920681342501	2		343	529	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121516	108121516	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501574	NA	P-0033135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	165	401	1	ENST00000278616.4:c.1324C>T	p.Leu442Phe	p.L442F	ENST00000278616	NM_000051.3	442	Ctt/Ttt	10/63	1	2	FACETS	0.9	0.828	0.974	0.9	0.828	0.974	CLONAL	1	TRUE	1	0.503920681342501	2		402	728	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163408	32163408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764021089	NA	P-0033135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	255	636	0	ENST00000375023.3:c.5818C>T	p.Arg1940Cys	p.R1940C	ENST00000375023	NM_004557.3	1940	Cgc/Tgc	30/30	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.503920681342501	2		636	931	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0033142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	221	577	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	0.891	0.829	0.954	0.891	0.829	0.954	CLONAL	1	TRUE	1	0.513158131835835	2		577	967	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717769	89717770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	215	334	0	ENST00000371953.3:c.800dup	p.Asp268GlyfsTer30	p.D268Gfs*30	ENST00000371953	NM_000314.4	265	cta/ctAa	7/9	0.513158131835835	2	FACETS	0.83	0.779	0.881	0.83	0.779	0.881	CLONAL	2	TRUE	0	0.513158131835835	2		334	505	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630626	158630626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912678	NA	P-0033142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	70	240	0	ENST00000263640.3:c.617G>A	p.Arg206His	p.R206H	ENST00000263640	NM_001105.4	206	cGc/cAc	6/11	1	2	FACETS	0.782	0.686	0.884	0.782	0.686	0.884	SUBCLONAL	1	TRUE	1	0.513158131835835	2		240	349	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913409	NA	P-0033142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	121	349	0	ENST00000349496.5:c.134C>G	p.Ser45Cys	p.S45C	ENST00000349496	NM_001904.3	45	tCt/tGt	3/15	1	2	FACETS	0.925	0.84	1	0.925	0.84	1	CLONAL	1	TRUE	1	0.513158131835835	2		349	510	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023849	27023862	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCCCCAGGACGG	GGGCCCCAGGACGG	-	novel	NA	P-0033142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	60	189	0	ENST00000324856.7:c.959_972del	p.Pro320ArgfsTer75	p.P320Rfs*75	ENST00000324856	NM_006015.4	319	GGGCCCCAGGACGGg/g	1/20	1	2	FACETS	0.764	0.663	0.872	0.764	0.663	0.872	SUBCLONAL	1	TRUE	1	0.513158131835835	2		189	306	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189357	56189357	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0033142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	202	478	0	ENST00000399503.3:c.4390-1G>C		p.X1464_splice	ENST00000399503	NM_005921.1	1464			1	2	FACETS	0.989	0.919	1	0.989	0.919	1	CLONAL	1	TRUE	1	0.513158131835835	2		478	796	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589593	67589594	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAC	novel	NA	P-0033142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	99	207	0	ENST00000274335.5:c.1358_1360dup	p.Asn453dup	p.N453dup	ENST00000274335		453	-/AAC	10/15	1	2	FACETS	0.902	0.81	0.998	0.902	0.81	0.998	CLONAL	1	TRUE	1	0.513158131835835	2		207	428	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206851	162206851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769230602	NA	P-0033142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	56	397	0	ENST00000366898.1:c.824G>A	p.Arg275Gln	p.R275Q	ENST00000366898	NM_004562.2	275	cGg/cAg	7/12	1	2	FACETS	0.36	0.308	0.417	0.36	0.308	0.417	SUBCLONAL	1	TRUE	1	0.513158131835835	2		397	606	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023212	27023222	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGGGCCCTA	CGCGGGCCCTA	G	novel	NA	P-0033142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	47	139	0	ENST00000324856.7:c.318_328delinsG	p.Asn106LysfsTer5	p.N106Kfs*5	ENST00000324856	NM_006015.4	106	aaCGCGGGCCCTAgg/aaGgg	1/20	1	2	FACETS	0.852	0.727	0.986	0.852	0.727	0.986	CLONAL	1	TRUE	1	0.513158131835835	2		139	215	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0033150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	332	751	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.815935625213694	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.815935625213694	1		751	477	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926888	112926888	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397507546	NA	P-0033150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	436	630	2	ENST00000351677.2:c.1508G>T	p.Gly503Val	p.G503V	ENST00000351677	NM_002834.3	503	gGg/gTg	13/16	0.815935625213694	3	FACETS	0.883	0.848	0.918	0.883	0.848	0.918	CLONAL	2	TRUE	1	0.815935625213694	3		632	852	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417337	139417337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs537766290	NA	P-0033150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	261	677	0	ENST00000277541.6:c.707C>T	p.Thr236Met	p.T236M	ENST00000277541	NM_017617.3	236	aCg/aTg	4/34	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.815935625213694	2		677	604	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249315	110249315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	423	850	0	ENST00000374672.4:c.1258C>T	p.His420Tyr	p.H420Y	ENST00000374672	NM_004235.4	420	Cac/Tac	4/5	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.815935625213694	2		850	1028	SUCCESS
APC	324	MSKCC	GRCh37	5	112164604	112164604	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554082118	NA	P-0033150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	224	445	0	ENST00000257430.4:c.1682del	p.Lys561ArgfsTer9	p.K561Rfs*9	ENST00000257430	NM_000038.5	560	Aaa/aa	14/16	0.815935625213694	1	FACETS	0.913	0.868	0.957	0.913	0.868	0.957	CLONAL	1	TRUE	0	0.815935625213694	1		445	356	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023288	31023288	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs387907077	NA	P-0033150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	290	602	0	ENST00000375687.4:c.2773C>T	p.Gln925Ter	p.Q925*	ENST00000375687	NM_015338.5	925	Cag/Tag	13/13	1	2	FACETS	0.966	0.914	1	0.966	0.914	1	CLONAL	1	TRUE	1	0.815935625213694	2		602	736	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17380502	17380502	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs962717797	NA	P-0033150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	297	576	0	ENST00000375499.3:c.13G>T	p.Val5Phe	p.V5F	ENST00000375499	NM_003000.2	5	Gtc/Ttc	1/8	0.763082324081014	1	FACETS	0.889	0.85	0.927	0.889	0.85	0.927	CLONAL	1	TRUE	0	0.815935625213694	1		576	485	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306620	163306620	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369947700	NA	P-0033150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	285	450	0	ENST00000271452.3:c.417G>A	p.Met139Ile	p.M139I	ENST00000271452	NM_145697.2	139	atG/atA	6/14	1	2	FACETS	0.892	0.842	0.943	0.892	0.842	0.943	CLONAL	1	TRUE	1	0.815935625213694	2		450	783	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940144	71940144	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	305	680	0	ENST00000298229.2:c.529G>T	p.Gly177Trp	p.G177W	ENST00000298229	NM_001567.3	177	Ggg/Tgg	5/28	NA	2	FACETS	0.997	0.945	1			1	INDETERMINATE	1	TRUE	NA	0.815935625213694	2		680	750	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	441001	441001	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	229	422	0	ENST00000399788.2:c.1757T>G	p.Phe586Cys	p.F586C	ENST00000399788	NM_001042603.1	586	tTc/tGc	13/28	1	2	FACETS	0.923	0.866	0.981	0.923	0.866	0.981	CLONAL	1	TRUE	1	0.815935625213694	2		422	608	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005332	29005332	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	368	724	2	ENST00000282397.4:c.929C>A	p.Thr310Asn	p.T310N	ENST00000282397	NM_002019.4	310	aCt/aAt	7/30	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.815935625213694	2		726	902	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528044	103528044	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	206	437	0	ENST00000355739.4:c.3352G>C	p.Ala1118Pro	p.A1118P	ENST00000355739	NM_000123.3	1118	Gct/Cct	15/15	0.815935625213694	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.815935625213694	1		437	289	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610304	10610304	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	404	814	0	ENST00000171111.5:c.406del	p.Leu136SerfsTer21	p.L136Sfs*21	ENST00000171111	NM_203500.1	136	Ctc/tc	2/6	0.815935625213694	1	FACETS	0.987	0.953	1	0.987	0.953	1	CLONAL	1	TRUE	0	0.815935625213694	1		814	594	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225360629	225360632	+	frameshift_variant	Frame_Shift_Del	DEL	GTGT	GTGT	-	novel	NA	P-0033150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	301	528	0	ENST00000264414.4:c.1759_1762del	p.Thr587GlyfsTer12	p.T587Gfs*12	ENST00000264414	NM_003590.4	587	ACACgg/gg	13/16	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.815935625213694	2		528	731	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561088	9561088	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	230	520	0	ENST00000353224.5:c.694T>A	p.Phe232Ile	p.F232I	ENST00000353224	NM_177990.2	232	Ttc/Atc	4/10	1	2	FACETS	0.993	0.933	1	0.993	0.933	1	CLONAL	1	TRUE	1	0.815935625213694	2		520	568	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390109	89390109	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	238	447	0	ENST00000336596.2:c.858G>T	p.Lys286Asn	p.K286N	ENST00000336596	NM_005233.5	286	aaG/aaT	4/17	0.815935625213694	1	FACETS	0.954	0.91	0.997	0.954	0.91	0.997	CLONAL	1	TRUE	0	0.815935625213694	1		447	362	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968529	55968529	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	275	525	0	ENST00000263923.4:c.2134G>T	p.Gly712Cys	p.G712C	ENST00000263923	NM_002253.2	712	Ggc/Tgc	14/30	1	2	FACETS	0.997	0.942	1	0.997	0.942	1	CLONAL	1	TRUE	1	0.815935625213694	2		525	676	SUCCESS
APC	324	MSKCC	GRCh37	5	112174590	112174590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224541	NA	P-0033150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	295	538	0	ENST00000257430.4:c.3299C>T	p.Ser1100Phe	p.S1100F	ENST00000257430	NM_000038.5	1100	tCt/tTt	16/16	0.815935625213694	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.815935625213694	1		538	405	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056715	180056715	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	208	619	0	ENST00000261937.6:c.797G>C	p.Trp266Ser	p.W266S	ENST00000261937	NM_182925.4	266	tGg/tCg	6/30	0.815935625213694	1	FACETS	0.893	0.847	0.938	0.893	0.847	0.938	CLONAL	1	TRUE	0	0.815935625213694	1		619	338	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818288	32818288	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	269	586	1	ENST00000354258.4:c.1237G>A	p.Glu413Lys	p.E413K	ENST00000354258	NM_000593.5	413	Gaa/Aaa	5/11	0.190771888647023	3	FACETS	1	0.991	1	0.626	0.59	0.663	INDETERMINATE	1	TRUE	1	0.815935625213694	3		587	741	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109309858	109309858	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	427	671	0	ENST00000436639.2:c.1457A>T	p.Gln486Leu	p.Q486L	ENST00000436639	NM_014454.2	486	cAg/cTg	9/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.815935625213694	2		671	998	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141549486	141549486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	220	569	0	ENST00000220592.5:c.2102G>A	p.Gly701Glu	p.G701E	ENST00000220592	NM_012154.3	701	gGg/gAg	16/19	0.815935625213694	4	FACETS	1	0.97	1			1	CLONAL	1	TRUE	NA	0.815935625213694	4		569	913	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486065	8486065	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779664035	NA	P-0033150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	301	681	0	ENST00000356435.5:c.2752C>A	p.Pro918Thr	p.P918T	ENST00000356435		918	Cca/Aca	17/35	0.815935625213694	1	FACETS	0.988	0.949	1	0.988	0.949	1	CLONAL	1	TRUE	0	0.815935625213694	1		681	442	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0033168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	42	432	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.895	0.752	1	0.895	0.752	1	CLONAL	1	TRUE	1	0.344960828528764	2		432	272	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092685	27092711	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TCTCTCACTTTCCATCTTCTTCCTTAG	TCTCTCACTTTCCATCTTCTTCCTTAG	-	novel	NA	P-0033168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	52	315	0	ENST00000324856.7:c.2733-27_2733-1del		p.X911_splice	ENST00000324856	NM_006015.4	911			0.295640021608479	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.344960828528764	2		315	130	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692892	89692892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554898129	NA	P-0033168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	53	462	0	ENST00000371953.3:c.376G>A	p.Ala126Thr	p.A126T	ENST00000371953	NM_000314.4	126	Gct/Act	5/9	0.283241028212361	4	FACETS	0.998	0.863	1	0.998	0.863	1	CLONAL	2	TRUE	2	0.344960828528764	4		462	207	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949372	71949372	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	45	601	0	ENST00000298229.2:c.3752T>A	p.Leu1251Gln	p.L1251Q	ENST00000298229	NM_001567.3	1251	cTg/cAg	28/28	1	2	FACETS	0.919	0.777	1	0.919	0.777	1	CLONAL	1	TRUE	1	0.344960828528764	2		601	284	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662402	67662402	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	51	884	0	ENST00000264010.4:c.1649del	p.Phe550SerfsTer34	p.F550Sfs*34	ENST00000264010	NM_006565.3	550	Ttc/tc	9/12	1	2	FACETS	0.68	0.579	0.79	0.68	0.579	0.79	SUBCLONAL	1	TRUE	1	0.344960828528764	2		884	435	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591259	67591261	+	inframe_deletion	In_Frame_Del	DEL	AAA	AAA	-	novel	NA	P-0033168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	25	478	0	ENST00000274335.5:c.1759_1761del	p.Lys587del	p.K587del	ENST00000274335		586	cAAAaa/caa	13/15	1	2	FACETS	0.69	0.547	0.853	0.69	0.547	0.853	SUBCLONAL	1	TRUE	1	0.344960828528764	2		478	210	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008892	152008892	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	82	445	0	ENST00000262189.6:c.730G>T	p.Asp244Tyr	p.D244Y	ENST00000262189	NM_170606.2	244	Gat/Tat	5/59	0.283241028212361	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.344960828528764	4		445	272	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271264	38271264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746602135	NA	P-0033168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	44	848	1	ENST00000425967.3:c.2444G>A	p.Arg815Gln	p.R815Q	ENST00000425967	NM_001174067.1	815	cGg/cAg	19/19	1	2	FACETS	0.719	0.604	0.844	0.719	0.604	0.844	SUBCLONAL	1	TRUE	1	0.344960828528764	2		849	355	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589283	67589292	+	stop_gained	Nonsense_Mutation	DEL	TACTTTATCC	TACTTTATCC	A	novel	NA	P-0033168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	20	287	0	ENST00000274335.5:c.1271_1280delinsA	p.Leu424_Pro427delinsTer	p.L424_P427delins*	ENST00000274335		424	tTACTTTATCCa/tAa	9/15	1	2	FACETS	0.913	0.707	1	0.913	0.707	1	CLONAL	1	TRUE	1	0.344960828528764	2		287	127	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	168	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.242990888560699	3	FACETS	0.942	0.871	1			1	CLONAL	2	TRUE	NA	0.387943391928803	3		493	549	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0033171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	128	776	4	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.387943391928803	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.387943391928803	1		780	520	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794583	42794583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	63	803	1	ENST00000575354.2:c.1663G>A	p.Gly555Arg	p.G555R	ENST00000575354	NM_015125.3	555	Gga/Aga	10/20	0.387943391928803	1	FACETS	0.393	0.339	0.451	0.393	0.339	0.451	SUBCLONAL	1	TRUE	0	0.387943391928803	1		804	666	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971095	21971095	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	42	436	0	ENST00000304494.5:c.263del	p.Glu88GlyfsTer58	p.E88Gfs*58	ENST00000304494	NM_000077.4	88	gAg/gg	2/3	0.387943391928803	1	FACETS	0.626	0.525	0.736	0.626	0.525	0.736	SUBCLONAL	1	TRUE	0	0.387943391928803	1		436	279	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293675	137293675	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	124	751	0	ENST00000481739.1:c.226T>G	p.Ser76Ala	p.S76A	ENST00000481739	NM_002957.4	76	Tcc/Gcc	2/10	0.221728782868986	1	FACETS	0.893	0.811	0.979	0.893	0.811	0.979	INDETERMINATE	1	TRUE	0	0.387943391928803	1		751	577	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225791	26225791	+	stop_lost	Nonstop_Mutation	SNP	T	T	A	novel	NA	P-0033179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	139	286	0	ENST00000360408.1:c.409T>A	p.Ter137ArgextTer?	p.*137Rext*?	ENST00000360408	NM_003532.2	137	Tga/Aga	1/1	0.277792399415962	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.291483335684524	2		286	427	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0033183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	79	400	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.999	0.883	1	0.999	0.883	1	CLONAL	1	TRUE	1	0.380318191842507	2		400	416	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207064	1207065	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1131690917	NA	P-0033183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	125	561	0	ENST00000326873.7:c.157dup	p.Asp53GlyfsTer110	p.D53Gfs*110	ENST00000326873	NM_000455.4	51	atg/atGg	1/10	0.380318191842507	1	FACETS	0.822	0.745	0.902	0.822	0.745	0.902	CLONAL	1	TRUE	0	0.380318191842507	1		561	648	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991697	72991699	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	rs757316139	NA	P-0033183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	11	153	1	ENST00000268489.5:c.2346_2348del	p.Ala784del	p.A784del	ENST00000268489	NM_006885.3	782	gcGGCa/gca	2/10	1	2	FACETS	0.278	0.192	0.385	0.278	0.192	0.385	SUBCLONAL	1	TRUE	1	0.380318191842507	2		154	208	SUCCESS
APC	324	MSKCC	GRCh37	5	112173956	112173957	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0033183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	66	339	0	ENST00000257430.4:c.2666_2667del	p.Lys889SerfsTer22	p.K889Sfs*22	ENST00000257430	NM_000038.5	889	AAa/a	16/16	0.380318191842507	1	FACETS	0.925	0.809	1	0.925	0.809	1	CLONAL	1	TRUE	0	0.380318191842507	1		339	304	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602367	10602367	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	142	705	3	ENST00000171111.5:c.1211C>A	p.Ser404Ter	p.S404*	ENST00000171111	NM_203500.1	404	tCg/tAg	3/6	0.380318191842507	1	FACETS	0.864	0.789	0.942	0.864	0.789	0.942	CLONAL	1	TRUE	0	0.380318191842507	1		708	700	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102080285	102080286	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0033183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	93	483	0	ENST00000282441.5:c.1022_1023del	p.Pro341GlnfsTer9	p.P341Qfs*9	ENST00000282441	NM_001130145.2	341	cCA/c	6/9	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.380318191842507	2		483	457	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912810	32912811	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs397507328	NA	P-0033183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	72	432	0	ENST00000380152.3:c.4319_4320del	p.Lys1440ArgfsTer4	p.K1440Rfs*4	ENST00000380152		1440	AAa/a	11/27	1	2	FACETS	0.966	0.848	1	0.966	0.848	1	CLONAL	1	TRUE	1	0.380318191842507	2		432	392	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620583	52620583	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0033183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	126	540	0	ENST00000394830.3:c.3170C>G	p.Ser1057Ter	p.S1057*	ENST00000394830	NM_018313.4	1057	tCa/tGa	21/30	0.380318191842507	1	FACETS	0.999	0.909	1	0.999	0.909	1	CLONAL	1	TRUE	0	0.380318191842507	1		540	537	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268766	41268766	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	96	353	0	ENST00000349496.5:c.1004A>C	p.Lys335Thr	p.K335T	ENST00000349496	NM_001904.3	335	aAa/aCa	7/15	1	2	FACETS	0.825	0.745	0.908	0.825	0.745	0.908	CLONAL	1	TRUE	1	0.786086914059083	2		353	296	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212252701	212252701	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	30	125	0	ENST00000342788.4:c.3152G>T	p.Ser1051Ile	p.S1051I	ENST00000342788	NM_005235.2	1051	aGc/aTc	26/28	0.786086914059083	3	FACETS	0.718	0.587	0.863	0.359	0.293	0.432	SUBCLONAL	1	TRUE	1	0.786086914059083	3		125	148	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418484	49418484	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	129	439	0	ENST00000301067.7:c.15929G>T	p.Gly5310Val	p.G5310V	ENST00000301067	NM_003482.3	5310	gGg/gTg	50/54	0.734382785529121	5	FACETS	1	0.955	1	0.361	0.328	0.396	CLONAL	1	TRUE	2	0.786086914059083	5		439	660	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119585451	119585451	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	79	226	0	ENST00000316626.5:c.934A>G	p.Thr312Ala	p.T312A	ENST00000316626		312	Acc/Gcc	9/12	0.767318898403348	3	FACETS	0.897	0.797	1	0.299	0.265	0.335	CLONAL	1	TRUE	0	0.786086914059083	3		226	312	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300146	137300146	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0033191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	90	356	0	ENST00000481739.1:c.430+1G>T		p.X144_splice	ENST00000481739	NM_002957.4	144			0.767093861731294	2	FACETS	0.923	0.833	1	0.462	0.416	0.508	CLONAL	1	TRUE	0	0.786086914059083	2		356	248	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246091232	246091234	+	splice_donor_variant,coding_sequence_variant	Splice_Site	TNP	CCT	CCT	ACC	novel	NA	P-0033191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	61	254	0	ENST00000388985.4:c.701_702+1delinsGGT		p.X234_splice	ENST00000388985		234		7/12	0.695288722830998	3	FACETS	0.7	0.608	0.798	0.35	0.304	0.399	SUBCLONAL	1	TRUE	1	0.786086914059083	3		254	309	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578532	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	212	741	0	ENST00000269305.4:c.398T>A	p.Met133Lys	p.M133K	ENST00000269305	NM_001126112.2	133	aTg/aAg	5/11	0.183645105230746	2	FACETS	0.883	0.819	0.948	0.883	0.819	0.948	CLONAL	2	TRUE	0	0.228768162968282	2		741	1050	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509127	66509127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	20	257	0	ENST00000273854.3:c.200G>C	p.Arg67Pro	p.R67P	ENST00000273854	NM_004439.5	67	cGc/cCc	2/18	0.228768162968282	1	FACETS	0.41	0.313	0.524	0.41	0.313	0.524	SUBCLONAL	1	TRUE	0	0.228768162968282	1		257	378	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983148	201983148	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	75	389	0	ENST00000359651.3:c.997A>G	p.Met333Val	p.M333V	ENST00000359651		333	Atg/Gtg	7/8	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.228768162968282	2		389	576	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651113	206651113	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	76	565	0	ENST00000367120.3:c.723G>T	p.Lys241Asn	p.K241N	ENST00000367120	NM_014002.3	241	aaG/aaT	8/22	1	2	FACETS	0.823	0.721	0.934	0.823	0.721	0.934	CLONAL	1	TRUE	1	0.228768162968282	2		565	807	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409092	4409092	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1199884235	NA	P-0033202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	70	271	0	ENST00000261254.3:c.787C>T	p.Gln263Ter	p.Q263*	ENST00000261254	NM_001759.3	263	Cag/Tag	5/5	0.228768162968282	3	FACETS	1	0.959	1	0.623	0.544	0.709	CLONAL	1	TRUE	1	0.228768162968282	3		271	547	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246497	46246497	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	28	230	0	ENST00000334344.6:c.4591C>T	p.Pro1531Ser	p.P1531S	ENST00000334344	NM_152641.2	1531	Cca/Tca	15/21	1	2	FACETS	0.699	0.559	0.859	0.699	0.559	0.859	SUBCLONAL	1	TRUE	1	0.228768162968282	2		230	350	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439712	49439712	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	74	506	0	ENST00000301067.7:c.4732A>G	p.Lys1578Glu	p.K1578E	ENST00000301067	NM_003482.3	1578	Aaa/Gaa	18/54	1	2	FACETS	0.824	0.72	0.936	0.824	0.72	0.936	CLONAL	1	TRUE	1	0.228768162968282	2		506	785	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857825	89857825	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	69	481	0	ENST00000389301.3:c.1345G>A	p.Ala449Thr	p.A449T	ENST00000389301	NM_000135.2	449	Gca/Aca	14/43	1	2	FACETS	0.85	0.739	0.969	0.85	0.739	0.969	CLONAL	1	TRUE	1	0.228768162968282	2		481	710	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86642488	86642488	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0033202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	34	302	0	ENST00000274376.6:c.1050-1G>C		p.X350_splice	ENST00000274376	NM_002890.2	350			0.228768162968282	1	FACETS	0.597	0.487	0.72	0.597	0.487	0.72	SUBCLONAL	1	TRUE	0	0.228768162968282	1		302	441	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965668	93965668	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	47	382	0	ENST00000369303.4:c.2260T>C	p.Tyr754His	p.Y754H	ENST00000369303	NM_004440.3	754	Tat/Cat	13/17	1	2	FACETS	0.652	0.549	0.766	0.652	0.549	0.766	SUBCLONAL	1	TRUE	1	0.228768162968282	2		382	630	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995517	68995517	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	93	574	1	ENST00000288368.4:c.1921G>T	p.Gly641Cys	p.G641C	ENST00000288368	NM_024870.2	641	Ggt/Tgt	18/40	1	2	FACETS	0.774	0.687	0.868	0.774	0.687	0.868	SUBCLONAL	1	TRUE	1	0.228768162968282	2		575	1050	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900243	101900243	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	57	291	0	ENST00000374994.4:c.677G>T	p.Gly226Val	p.G226V	ENST00000374994	NM_004612.2	226	gGa/gTa	4/9	0.228768162968282	1	FACETS	0.834	0.716	0.963	0.834	0.716	0.963	CLONAL	1	TRUE	0	0.228768162968282	1		291	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0033217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	108	527	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		527	625	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023160	150023160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	28	525	0	ENST00000253339.5:c.103C>T	p.Arg35Trp	p.R35W	ENST00000253339		35	Cgg/Tgg	1/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		525	428	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838301	156838302	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0033217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	42	922	2	ENST00000524377.1:c.579_580delinsTT	p.Pro194Ser	p.P194S	ENST00000524377	NM_002529.3	193	gtGCcc/gtTTcc	6/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		924	697	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777721	3777721	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	novel	NA	P-0033217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	60	1081	2	ENST00000262367.5:c.7327T>C	p.Ter2443GlnextTer23	p.*2443Qext*23	ENST00000262367	NM_004380.2	2443	Tag/Cag	31/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1083	803	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663654	29663654	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	32	374	0	ENST00000356175.3:c.6086T>C	p.Val2029Ala	p.V2029A	ENST00000356175	NM_000267.3	2029	gTt/gCt	41/57	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		374	255	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	155	349	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.597471738861681	2		349	494	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0033292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	336	256	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.512099800502722	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	2	0.597471738861681	4		256	893	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532589	63532589	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	341	1140	1	ENST00000307078.5:c.1990G>A	p.Gly664Arg	p.G664R	ENST00000307078	NM_004655.3	664	Ggg/Agg	8/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.597471738861681	2		1141	1111	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799475	72799475	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	359	920	0	ENST00000325599.8:c.1694A>T	p.Asn565Ile	p.N565I	ENST00000325599	NM_018130.2	565	aAt/aTt	11/11	1	2	FACETS	0.954	0.904	1	0.954	0.904	1	CLONAL	1	TRUE	1	0.597471738861681	2		920	1260	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538172	187538172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	263	749	0	ENST00000441802.2:c.9062C>T	p.Pro3021Leu	p.P3021L	ENST00000441802	NM_005245.3	3021	cCa/cTa	11/27	0.597471738861681	3	FACETS	0.976	0.914	1	0.488	0.457	0.52	CLONAL	1	TRUE	1	0.597471738861681	3		749	1172	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492907	8492907	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	129	780	0	ENST00000356435.5:c.2422G>C	p.Asp808His	p.D808H	ENST00000356435		808	Gat/Cat	16/35	0.597471738861681	1	FACETS	0.411	0.373	0.452	0.411	0.373	0.452	SUBCLONAL	1	TRUE	0	0.597471738861681	1		780	736	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0033294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	593	614	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.883612254136918	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.879509419781134	2		615	650	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0033294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	576	356	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.879509419781134	7	FACETS	0.982	0.954	1			1	CLONAL	5	TRUE	NA	0.879509419781134	7		356	853	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717630	89717630	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554825168	NA	P-0033294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	652	464	1	ENST00000371953.3:c.655C>T	p.Gln219Ter	p.Q219*	ENST00000371953	NM_000314.4	219	Cag/Tag	7/9	0.883612254136918	4	FACETS	1	0.998	1	1	0.998	1	CLONAL	4	TRUE	0	0.879509419781134	4		465	673	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156660	2156660	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	246	808	0	ENST00000434045.2:c.262C>A	p.Leu88Met	p.L88M	ENST00000434045	NM_001127598.1	88	Ctg/Atg	3/5	0.883612254136918	3	FACETS	1	0.979	1	0.547	0.513	0.581	CLONAL	1	TRUE	1	0.879509419781134	3		808	736	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272502	11272502	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs752142242	NA	P-0033294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	168	407	0	ENST00000361445.4:c.3428C>A	p.Thr1143Lys	p.T1143K	ENST00000361445	NM_004958.3	1143	aCg/aAg	23/58	0.727258101900191	4	FACETS	1	0.947	1	0.517	0.477	0.559	CLONAL	1	TRUE	2	0.879509419781134	4		407	694	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256972	16256972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	260	740	0	ENST00000375759.3:c.4237G>A	p.Asp1413Asn	p.D1413N	ENST00000375759	NM_015001.2	1413	Gac/Aac	11/15	0.727258101900191	4	FACETS	1	0.98	1	0.551	0.517	0.587	CLONAL	1	TRUE	2	0.879509419781134	4		740	1008	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838008	156838008	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	333	1155	1	ENST00000524377.1:c.541G>A	p.Gly181Arg	p.G181R	ENST00000524377	NM_002529.3	181	Ggg/Agg	5/17	0.727258101900191	4	FACETS	0.948	0.894	1	0.474	0.447	0.502	CLONAL	1	TRUE	2	0.879509419781134	4		1156	1501	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535464	187535464	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	117	437	0	ENST00000441802.2:c.9110T>C	p.Leu3037Pro	p.L3037P	ENST00000441802	NM_005245.3	3037	cTt/cCt	12/27	0.883612254136918	6	FACETS	0.827	0.745	0.913	0.207	0.186	0.229	CLONAL	1	TRUE	2	0.879509419781134	6		437	888	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319956	8319956	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1195271322	NA	P-0033294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6	212	285	0	ENST00000356435.5:c.5545G>C	p.Gly1849Arg	p.G1849R	ENST00000356435		1849	Gga/Cga	34/35	0.883612254136918	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.879509419781134	2		285	218	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0033300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	173	537	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.3	2		537	942	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61710176	61710177	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0033300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	118	398	0	ENST00000401558.2:c.2726_2727dup	p.Ala910LeufsTer22	p.A910Lfs*22	ENST00000401558	NM_003400.3	909	-/CT	22/25	0.124528937896927	3	FACETS	1	0.975	1			1	INDETERMINATE	1	FALSE	NA	0.3	3		398	723	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0033317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	31	256	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.872	0.705	1	0.872	0.705	1	CLONAL	1	TRUE	1	0.18	2		256	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882025	NA	P-0033317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	92	666	1	ENST00000269305.4:c.646G>T	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ttg	6/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.18	2		667	833	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376262	225376262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	77	380	0	ENST00000264414.4:c.692C>T	p.Ser231Leu	p.S231L	ENST00000264414	NM_003590.4	231	tCa/tTa	6/16	0.182326625106669	2	FACETS	0.977	0.861	1	0.977	0.861	1	CLONAL	2	TRUE	0	0.18	2		380	438	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376271	225376271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1284026173	NA	P-0033317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	69	339	0	ENST00000264414.4:c.683A>G	p.Asn228Ser	p.N228S	ENST00000264414	NM_003590.4	228	aAt/aGt	6/16	0.182326625106669	2	FACETS	0.991	0.867	1	0.991	0.867	1	CLONAL	2	TRUE	0	0.18	2		339	387	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159038	143159038	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	26	287	0	ENST00000262992.4:c.815A>G	p.His272Arg	p.H272R	ENST00000262992	NM_001101669.1	272	cAc/cGc	10/24	1	2	FACETS	0.976	0.775	1	0.976	0.775	1	CLONAL	1	TRUE	1	0.18	2		287	296	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0033320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	560	871	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.479576251121585	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.479576251121585	3		871	891	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249002	55249003	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCGTGGA	rs397517109	NA	P-0033320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	1509	447	0	ENST00000275493.2:c.2303_2311dup	p.Ser768_Asp770dup	p.S768_D770dup	ENST00000275493	NM_005228.3	768	gcc/gcCAGCGTGGAc	20/28	0.479576251121585	19	FACETS	0.969	0.952	0.986			1	CLONAL	15	TRUE	NA	0.479576251121585	19		447	2197	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518264	204518271	+	frameshift_variant	Frame_Shift_Del	DEL	CAAGAAAT	CAAGAAAT	-	novel	NA	P-0033320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	485	455	0	ENST00000367182.3:c.927_934del	p.Lys310Ter	p.K310*	ENST00000367182	NM_001278516.1	309	tgCAAGAAATtt/tgtt	11/11	0.479576251121585	8	FACETS	0.937	0.903	0.971	0.937	0.903	0.971	CLONAL	6	TRUE	2	0.479576251121585	8		455	877	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118391571	118391571	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	43	344	1	ENST00000534358.1:c.11484G>T	p.Lys3828Asn	p.K3828N	ENST00000534358	NM_005933.3	3828	aaG/aaT	34/36	0.479576251121585	4	FACETS	0.709	0.595	0.836	0.236	0.198	0.279	SUBCLONAL	1	TRUE	1	0.479576251121585	4		345	374	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144467	11144467	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764152134	NA	P-0033320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	135	679	0	ENST00000358026.2:c.3799G>A	p.Gly1267Ser	p.G1267S	ENST00000358026	NM_001128849.1	1267	Ggc/Agc	27/36	0.479576251121585	3	FACETS	0.982	0.894	1	0.327	0.298	0.358	CLONAL	1	TRUE	0	0.479576251121585	3		679	711	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741019	40741020	+	missense_variant	Missense_Mutation	DNP	CT	CT	AC	novel	NA	P-0033320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	144	824	1	ENST00000392038.2:c.1298_1299delinsGT	p.Glu433Gly	p.E433G	ENST00000392038	NM_001626.4	433	gAG/gGT	13/14	0.479576251121585	4	FACETS	0.904	0.824	0.988	0.226	0.206	0.247	CLONAL	1	TRUE	0	0.479576251121585	4		825	983	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890197	72890197	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	58	380	0	ENST00000325599.8:c.485A>T	p.Gln162Leu	p.Q162L	ENST00000325599	NM_018130.2	162	cAg/cTg	4/11	0.479576251121585	3	FACETS	0.842	0.727	0.966	0.421	0.363	0.483	CLONAL	1	TRUE	1	0.479576251121585	3		380	356	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0033323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	59	527	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.24655603245826	1	FACETS	0.874	0.759	0.997	0.874	0.759	0.997	CLONAL	1	TRUE	0	0.391953348234078	1		527	277	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468289	50468289	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	45	472	0	ENST00000331340.3:c.1524C>A	p.His508Gln	p.H508Q	ENST00000331340	NM_006060.4	508	caC/caA	8/8	1	2	FACETS	0.467	0.392	0.549	0.467	0.392	0.549	SUBCLONAL	1	TRUE	1	0.391953348234078	2		472	492	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	140	641	0	ENST00000227507.2:c.859C>T	p.Pro287Ser	p.P287S	ENST00000227507	NM_053056.2	287	Ccc/Tcc	5/5	1	2	FACETS	0.97	0.882	1	0.97	0.882	1	CLONAL	1	TRUE	1	0.28	2		641	1031	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	70	365	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.28	2		366	481	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	165	796	3	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.984	0.902	1	0.984	0.902	1	CLONAL	1	TRUE	1	0.28	2		799	1198	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	49	556	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.931	0.791	1	0.931	0.791	1	CLONAL	1	TRUE	1	0.28	2		557	376	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	70	412	1	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	1	2	FACETS	0.907	0.792	1	0.907	0.792	1	CLONAL	1	TRUE	1	0.28	2		413	551	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	108	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.28524411039025	2	FACETS	0.815	0.736	0.899	0.815	0.736	0.899	CLONAL	2	TRUE	0	0.28	2		493	473	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692940	89692940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746152219	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	69	538	1	ENST00000371953.3:c.424C>T	p.Arg142Trp	p.R142W	ENST00000371953	NM_000314.4	142	Cgg/Tgg	5/9	1	2	FACETS	0.918	0.8	1	0.918	0.8	1	CLONAL	1	TRUE	1	0.28	2		539	537	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	57	511	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.596	0.511	0.69	0.596	0.511	0.69	SUBCLONAL	1	TRUE	1	0.28	2		511	683	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	91	600	3	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	2	FACETS	0.82	0.727	0.919	0.82	0.727	0.919	CLONAL	1	TRUE	1	0.28	2		603	793	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435317	56435317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200066146	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	139	692	1	ENST00000407977.2:c.1820C>T	p.Ser607Leu	p.S607L	ENST00000407977		607	tCg/tTg	9/10	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.28	2		693	977	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779211	3779211	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783507	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	64	450	2	ENST00000262367.5:c.5837del	p.Pro1946HisfsTer30	p.P1946Hfs*30	ENST00000262367	NM_004380.2	1946	cCa/ca	31/31	1	2	FACETS	0.771	0.668	0.883	0.771	0.668	0.883	SUBCLONAL	1	TRUE	1	0.28	2		452	593	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	90	449	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.911	0.808	1	0.911	0.808	1	CLONAL	1	TRUE	1	0.28	2		449	706	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918921	76918921	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	94	664	4	ENST00000373344.5:c.4070del	p.Lys1357ArgfsTer18	p.K1357Rfs*18	ENST00000373344	NM_000489.3	1357	aAg/ag	12/35	1	2	FACETS	0.699	0.62	0.783	0.699	0.62	0.783	SUBCLONAL	1	TRUE	1	0.28	2		668	961	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641389	18641389	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1229278001	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	36	197	0	ENST00000266497.5:c.2393del	p.Asn798MetfsTer16	p.N798Mfs*16	ENST00000266497		796	ctA/ct	17/31	0.28524411039025	2	FACETS	1	0.89	1	0.552	0.457	0.657	CLONAL	1	TRUE	0	0.28	2		197	233	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	84	438	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.886	0.783	0.997	0.886	0.783	0.997	CLONAL	1	TRUE	1	0.28	2		438	677	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134449	2134449	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768684515	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	152	813	1	ENST00000219476.3:c.4226G>A	p.Arg1409Gln	p.R1409Q	ENST00000219476	NM_000548.3	1409	cGg/cAg	34/42	1	2	FACETS	0.964	0.88	1	0.964	0.88	1	CLONAL	1	TRUE	1	0.28	2		814	1126	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	132	634	0	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.87	0.788	0.956	0.87	0.788	0.956	CLONAL	1	TRUE	1	0.28	2		634	1084	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467434	66467434	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369606981	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	40	278	0	ENST00000273854.3:c.835G>A	p.Glu279Lys	p.E279K	ENST00000273854	NM_004439.5	279	Gaa/Aaa	3/18	1	2	FACETS	0.677	0.563	0.804	0.677	0.563	0.804	SUBCLONAL	1	TRUE	1	0.28	2		278	422	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798364	42798364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	139	673	0	ENST00000575354.2:c.4235G>A	p.Arg1412His	p.R1412H	ENST00000575354	NM_015125.3	1412	cGc/cAc	18/20	1	2	FACETS	0.976	0.888	1	0.976	0.888	1	CLONAL	1	TRUE	1	0.28	2		673	1017	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567719	226567719	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	86	501	1	ENST00000366794.5:c.1447del	p.Ala483GlnfsTer3	p.A483Qfs*3	ENST00000366794	NM_001618.3	483	Gca/ca	10/23	1	2	FACETS	0.865	0.765	0.972	0.865	0.765	0.972	CLONAL	1	TRUE	1	0.28	2		502	710	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101117	27101117	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	121	659	0	ENST00000324856.7:c.4403del	p.Pro1468LeufsTer13	p.P1468Lfs*13	ENST00000324856	NM_006015.4	1467	Ccc/cc	18/20	1	2	FACETS	0.924	0.834	1	0.924	0.834	1	CLONAL	1	TRUE	1	0.28	2		659	935	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845624	63845627	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	38	184	0	ENST00000279873.7:c.1366_1369del	p.Glu456MetfsTer22	p.E456Mfs*22	ENST00000279873	NM_032199.2	455	AAAGaa/aa	9/10	1	2	FACETS	0.991	0.823	1	0.991	0.823	1	CLONAL	1	TRUE	1	0.28	2		184	274	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957465	175957465	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	80	464	2	ENST00000367669.3:c.1931del	p.Asn644ThrfsTer3	p.N644Tfs*3	ENST00000367669	NM_022457.5	644	aAc/ac	17/20	1	2	FACETS	0.973	0.858	1	0.973	0.858	1	CLONAL	1	TRUE	1	0.28	2		466	587	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249361	153249361	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	79	393	2	ENST00000281708.4:c.1417del	p.Arg473GlufsTer25	p.R473Efs*25	ENST00000281708	NM_033632.3	473	Aga/ga	9/12	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.28	2		395	489	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217705	7217707	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs757139280	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	77	495	0	ENST00000380728.2:c.220_222del	p.Glu74del	p.E74del	ENST00000380728		74	GAG/-	4/11	1	2	FACETS	0.733	0.643	0.831	0.733	0.643	0.831	SUBCLONAL	1	TRUE	1	0.28	2		495	750	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572092	64572093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs767319284	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	114	586	0	ENST00000312049.6:c.1546dup	p.Arg516ProfsTer15	p.R516Pfs*15	ENST00000312049	NM_130799.2	516	cgg/cCgg	10/10	1	2	FACETS	0.917	0.825	1	0.917	0.825	1	CLONAL	1	TRUE	1	0.28	2		586	888	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572350	41572350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	67	692	0	ENST00000263253.7:c.4879C>T	p.Arg1627Trp	p.R1627W	ENST00000263253	NM_001429.3	1627	Cgg/Tgg	30/31	1	2	FACETS	0.487	0.422	0.558	0.487	0.422	0.558	SUBCLONAL	1	TRUE	1	0.28	2		692	983	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41267751	41267751	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	59	415	0	ENST00000357654.3:c.126A>G	p.Ile42Met	p.I42M	ENST00000357654	NM_007294.3	42	atA/atG	3/23	1	2	FACETS	0.885	0.763	1	0.885	0.763	1	CLONAL	1	TRUE	1	0.28	2		415	476	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324892	31324892	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs765875917	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	30	155	0	ENST00000412585.2:c.44del	p.Ala15GlyfsTer5	p.A15Gfs*5	ENST00000412585	NM_005514.6	15	gCg/gg	1/8	1	2	FACETS	1	0.816	1	1	0.816	1	CLONAL	1	TRUE	1	0.28	2		155	213	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1978254	1978254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754405808	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	145	767	0	ENST00000382891.5:c.3674C>T	p.Thr1225Met	p.T1225M	ENST00000382891	NM_133335.3	1225	aCg/aTg	21/22	1	2	FACETS	0.944	0.86	1	0.944	0.86	1	CLONAL	1	TRUE	1	0.28	2		767	1097	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448480	49448480	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	101	498	0	ENST00000301067.7:c.231del	p.His77GlnfsTer53	p.H77Qfs*53	ENST00000301067	NM_003482.3	77	caC/ca	3/54	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.28	2		498	713	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36208923	36208925	+	start_lost,inframe_deletion	Translation_Start_Site	DEL	GGC	GGC	-	rs898578503	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	12	16	0	ENST00000222270.7:c.14_16del	p.Ala5?	p.A5?	ENST00000222270	NM_014727.1	1	atGGCg/atg	1/37	1	2	FACETS	0.893	0.663	1	1	0.924	1	CLONAL	3	TRUE	1	0.28	2		16	32	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225540	133225540	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766168647	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	115	513	2	ENST00000320574.5:c.4124C>T	p.Ala1375Val	p.A1375V	ENST00000320574	NM_006231.2	1375	gCg/gTg	32/49	1	2	FACETS	0.935	0.841	1	0.935	0.841	1	CLONAL	1	TRUE	1	0.28	2		515	879	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18958623	18958623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	117	522	0	ENST00000262803.5:c.442C>T	p.Arg148Cys	p.R148C	ENST00000262803	NM_002911.3	148	Cgt/Tgt	3/24	1	2	FACETS	0.955	0.861	1	0.955	0.861	1	CLONAL	1	TRUE	1	0.28	2		522	875	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713421	40713421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199947379	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	79	592	2	ENST00000373198.4:c.4094C>T	p.Thr1365Met	p.T1365M	ENST00000373198	NM_133170.3	1365	aCg/aTg	30/32	1	2	FACETS	0.656	0.576	0.743	0.656	0.576	0.743	SUBCLONAL	1	TRUE	1	0.28	2		594	860	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967091	18967092	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1384543747	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	130	672	0	ENST00000262803.5:c.1814_1815del	p.Glu605AlafsTer17	p.E605Afs*17	ENST00000262803	NM_002911.3	602	gcAGag/gcag	13/24	1	2	FACETS	0.953	0.864	1	0.953	0.864	1	CLONAL	1	TRUE	1	0.28	2		672	974	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984380	201984380	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs756566923	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	102	488	1	ENST00000359651.3:c.1045C>T	p.Arg349Ter	p.R349*	ENST00000359651		349	Cga/Tga	8/8	1	2	FACETS	0.854	0.763	0.951	0.854	0.763	0.951	CLONAL	1	TRUE	1	0.28	2		489	853	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300039	137300040	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755912201	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	119	783	9	ENST00000481739.1:c.331dup	p.Leu111ProfsTer70	p.L111Pfs*70	ENST00000481739	NM_002957.4	108	-/C	3/10	1	2	FACETS	0.732	0.659	0.81	0.732	0.659	0.81	SUBCLONAL	1	TRUE	1	0.28	2		792	1161	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405960	157405960	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	55	457	0	ENST00000346085.5:c.2204del	p.Pro735HisfsTer10	p.P735Hfs*10	ENST00000346085	NM_020732.3	734	ggC/gg	6/20	1	2	FACETS	0.547	0.467	0.635	0.547	0.467	0.635	SUBCLONAL	1	TRUE	1	0.28	2		457	718	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44733169	44733169	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	92	420	0	ENST00000377967.4:c.162-1G>A		p.X54_splice	ENST00000377967	NM_021140.2	54			1	2	FACETS	0.876	0.778	0.981	0.876	0.778	0.981	CLONAL	1	TRUE	1	0.28	2		420	750	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643770	52643770	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	136	581	1	ENST00000394830.3:c.2126T>A	p.Ile709Asn	p.I709N	ENST00000394830	NM_018313.4	709	aTt/aAt	17/30	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.28	2		582	855	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522202	157522202	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	101	502	0	ENST00000346085.5:c.4474G>T	p.Gly1492Cys	p.G1492C	ENST00000346085	NM_020732.3	1492	Ggc/Tgc	18/20	1	2	FACETS	0.97	0.867	1	0.97	0.867	1	CLONAL	1	TRUE	1	0.28	2		502	744	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752444	55752444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1422545682	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	176	848	1	ENST00000284073.2:c.902C>T	p.Ala301Val	p.A301V	ENST00000284073	NM_138962.2	301	gCg/gTg	12/14	1	2	FACETS	0.996	0.916	1	0.996	0.916	1	CLONAL	1	TRUE	1	0.28	2		849	1262	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55991436	55991436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	134	684	0	ENST00000263923.4:c.25G>A	p.Val9Ile	p.V9I	ENST00000263923	NM_002253.2	9	Gtc/Atc	1/30	1	2	FACETS	0.926	0.84	1	0.926	0.84	1	CLONAL	1	TRUE	1	0.28	2		684	1034	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617557	100617557	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	132	595	0	ENST00000308731.7:c.512G>T	p.Arg171Met	p.R171M	ENST00000308731	NM_000061.2	171	aGg/aTg	6/19	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.28	2		595	863	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262447	16262447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	29	266	0	ENST00000375759.3:c.9712G>A	p.Asp3238Asn	p.D3238N	ENST00000375759	NM_015001.2	3238	Gat/Aat	11/15	1	2	FACETS	0.662	0.532	0.809	0.662	0.532	0.809	SUBCLONAL	1	TRUE	1	0.28	2		266	313	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106403	108106403	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	23	177	0	ENST00000278616.4:c.338C>A	p.Pro113His	p.P113H	ENST00000278616	NM_000051.3	113	cCt/cAt	5/63	1	2	FACETS	0.918	0.721	1	0.918	0.721	1	CLONAL	1	TRUE	1	0.28	2		177	179	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230572	46230572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1170640220	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	72	423	0	ENST00000334344.6:c.821G>A	p.Arg274Gln	p.R274Q	ENST00000334344	NM_152641.2	274	cGa/cAa	8/21	1	2	FACETS	0.932	0.815	1	0.932	0.815	1	CLONAL	1	TRUE	1	0.28	2		423	552	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562709	21562709	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	83	329	0	ENST00000382592.4:c.1210A>C	p.Ser404Arg	p.S404R	ENST00000382592	NM_014572.2	404	Agc/Cgc	4/8	1	2	FACETS	0.904	0.798	1	0.904	0.798	1	CLONAL	1	TRUE	1	0.28	2		329	656	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28908266	28908266	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	66	386	1	ENST00000282397.4:c.2489G>A	p.Gly830Asp	p.G830D	ENST00000282397	NM_002019.4	830	gGc/gAc	18/30	1	2	FACETS	0.923	0.802	1	0.923	0.802	1	CLONAL	1	TRUE	1	0.28	2		387	511	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335545	73335546	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	51	298	0	ENST00000377767.4:c.2625dup	p.Glu876Ter	p.E876*	ENST00000377767	NM_014953.3	875	-/T	19/21	1	2	FACETS	0.859	0.732	0.998	0.859	0.732	0.998	CLONAL	1	TRUE	1	0.28	2		298	424	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614560	38614560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	75	526	1	ENST00000299084.4:c.326C>T	p.Ala109Val	p.A109V	ENST00000299084	NM_152594.2	109	gCt/gTt	3/7	1	2	FACETS	0.887	0.778	1	0.887	0.778	1	CLONAL	1	TRUE	1	0.28	2		527	604	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779763	3779764	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	117	732	0	ENST00000262367.5:c.5284_5285del	p.Lys1762GlufsTer203	p.K1762Efs*203	ENST00000262367	NM_004380.2	1762	AAg/g	31/31	1	2	FACETS	0.848	0.763	0.937	0.848	0.763	0.937	CLONAL	1	TRUE	1	0.28	2		732	986	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900744	3900744	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	105	534	0	ENST00000262367.5:c.352A>G	p.Met118Val	p.M118V	ENST00000262367	NM_004380.2	118	Atg/Gtg	2/31	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.28	2		534	739	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346226	89346226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	50	254	0	ENST00000301030.4:c.6724G>A	p.Ala2242Thr	p.A2242T	ENST00000301030	NM_001256183.1	2242	Gcg/Acg	9/13	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.28	2		254	333	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489576	40489576	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	129	614	0	ENST00000264657.5:c.674del	p.Leu225CysfsTer36	p.L225Cfs*36	ENST00000264657	NM_139276.2	225	tTg/tg	8/24	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.28	2		614	919	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926593	59926593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	57	484	0	ENST00000259008.2:c.404C>T	p.Ala135Val	p.A135V	ENST00000259008	NM_032043.2	135	gCt/gTt	5/20	1	2	FACETS	0.872	0.749	1	0.872	0.749	1	CLONAL	1	TRUE	1	0.28	2		484	467	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511559	66511559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369210646	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	54	251	0	ENST00000358598.2:c.19G>A	p.Ala7Thr	p.A7T	ENST00000358598	NM_212471.2	7	Gcc/Acc	2/11	1	2	FACETS	0.893	0.764	1	0.893	0.764	1	CLONAL	1	TRUE	1	0.28	2		251	432	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221162	5221162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	146	702	2	ENST00000357368.4:c.3304C>T	p.Arg1102Cys	p.R1102C	ENST00000357368	NM_002850.3	1102	Cgc/Tgc	20/38	1	2	FACETS	0.919	0.837	1	0.919	0.837	1	CLONAL	1	TRUE	1	0.28	2		704	1135	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257143	19257144	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	52	416	0	ENST00000162023.5:c.819dup	p.Thr274HisfsTer11	p.T274Hfs*11	ENST00000162023		273	-/C	12/13	1	2	FACETS	0.623	0.53	0.725	0.623	0.53	0.725	SUBCLONAL	1	TRUE	1	0.28	2		416	596	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158637068	158637069	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CA	CA	-	rs141073095	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	113	876	3	ENST00000263640.3:c.111_112del	p.Cys37Ter	p.C37*	ENST00000263640	NM_001105.4	37	tgTGaa/tgaa	4/11	1	2	FACETS	0.983	0.884	1	0.983	0.884	1	CLONAL	1	TRUE	1	0.28	2		879	821	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42861508	42861508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	88	470	0	ENST00000398585.3:c.362C>T	p.Ala121Val	p.A121V	ENST00000398585	NM_001135099.1	121	gCa/gTa	4/14	1	2	FACETS	0.879	0.779	0.986	0.879	0.779	0.986	CLONAL	1	TRUE	1	0.28	2		470	715	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572961	41572961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759298489	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	181	677	0	ENST00000263253.7:c.5246G>A	p.Arg1749Gln	p.R1749Q	ENST00000263253	NM_001429.3	1749	cGg/cAg	31/31	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.28	2		677	974	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935638	49935638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	99	465	0	ENST00000296474.3:c.1726C>T	p.Pro576Ser	p.P576S	ENST00000296474	NM_002447.2	576	Ccc/Tcc	5/20	1	2	FACETS	0.984	0.878	1	0.984	0.878	1	CLONAL	1	TRUE	1	0.28	2		465	719	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664760	138664761	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs797044528	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	33	195	0	ENST00000330315.3:c.804dup	p.Gly269ArgfsTer265	p.G269Rfs*265	ENST00000330315	NM_023067.3	268	-/C	1/1	1	2	FACETS	0.576	0.469	0.697	0.576	0.469	0.697	SUBCLONAL	1	TRUE	1	0.28	2		195	409	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146614	55146614	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	37	513	0	ENST00000257290.5:c.2288A>G	p.Asp763Gly	p.D763G	ENST00000257290	NM_006206.4	763	gAt/gGt	16/23	1	2	FACETS	0.396	0.326	0.476	0.396	0.326	0.476	SUBCLONAL	1	TRUE	1	0.28	2		513	667	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218815	66218815	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	26	208	0	ENST00000273854.3:c.2243C>T	p.Pro748Leu	p.P748L	ENST00000273854	NM_004439.5	748	cCa/cTa	13/18	1	2	FACETS	0.767	0.61	0.946	0.767	0.61	0.946	CLONAL	1	TRUE	1	0.28	2		208	242	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168654	56168654	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	69	361	0	ENST00000399503.3:c.1508A>T	p.His503Leu	p.H503L	ENST00000399503	NM_005921.1	503	cAc/cTc	9/20	1	2	FACETS	0.963	0.84	1	0.963	0.84	1	CLONAL	1	TRUE	1	0.28	2		361	512	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112025264	112025264	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	108	470	0	ENST00000368678.4:c.485A>G	p.Gln162Arg	p.Q162R	ENST00000368678		162	cAg/cGg	6/13	1	2	FACETS	0.976	0.876	1	0.976	0.876	1	CLONAL	1	TRUE	1	0.28	2		470	790	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069192	5069193	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	32	305	0	ENST00000381652.3:c.1502dup	p.Pro503AlafsTer4	p.P503Afs*4	ENST00000381652	NM_004972.3	499	-/C	11/25	1	2	FACETS	0.653	0.531	0.791	0.653	0.531	0.791	SUBCLONAL	1	TRUE	1	0.28	2		305	350	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126331	5126331	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	35	244	0	ENST00000381652.3:c.3178-2A>G		p.X1060_splice	ENST00000381652	NM_004972.3	1060			1	2	FACETS	1	0.844	1	1	0.844	1	CLONAL	1	TRUE	1	0.28	2		244	244	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969463	44969463	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	26	356	0	ENST00000377967.4:c.4145A>G	p.Asp1382Gly	p.D1382G	ENST00000377967	NM_021140.2	1382	gAc/gGc	28/29	1	2	FACETS	0.359	0.284	0.446	0.359	0.284	0.446	SUBCLONAL	1	TRUE	1	0.28	2		356	517	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652342	48652342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	146	971	1	ENST00000376670.3:c.1013C>T	p.Ala338Val	p.A338V	ENST00000376670	NM_002049.3	338	gCt/gTt	6/6	1	2	FACETS	0.823	0.749	0.901	0.823	0.749	0.901	CLONAL	1	TRUE	1	0.28	2		972	1267	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0033356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	1194	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.449266523062248	12	FACETS	0.972	0.956	0.986			1	CLONAL	12	TRUE	NA	0.449266523062248	12		539	1480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0033356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	557	823	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.449266523062248	2	FACETS	0.993	0.956	1	0.993	0.956	1	CLONAL	2	TRUE	0	0.449266523062248	2		823	1248	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100425	8100425	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	570	831	2	ENST00000346208.3:c.404del	p.Pro135ArgfsTer60	p.P135Rfs*60	ENST00000346208		133	taC/ta	3/6	0.449266523062248	2	FACETS	0.913	0.878	0.949	0.913	0.878	0.949	CLONAL	2	TRUE	0	0.449266523062248	2		833	1389	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987067	36987067	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	917	867	2	ENST00000354822.5:c.622C>T	p.Arg208Ter	p.R208*	ENST00000354822	NM_001079668.2	208	Cga/Tga	3/3	0.449266523062248	3	FACETS	0.985	0.959	1	0.985	0.959	1	CLONAL	3	TRUE	0	0.449266523062248	3		869	1691	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971209	21971209	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1554654224	NA	P-0033356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	374	311	0	ENST00000304494.5:c.151-2A>G		p.X51_splice	ENST00000304494	NM_000077.4	51			0.449266523062248	6	FACETS	1	0.99	1	1	0.996	1	CLONAL	4	TRUE	3	0.449266523062248	6		311	710	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741739	17741739	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	204	696	2	ENST00000250003.3:c.410C>T	p.Ser137Leu	p.S137L	ENST00000250003	NM_002478.4	137	tCg/tTg	1/3	0.449266523062248	3	FACETS	0.853	0.789	0.919	0.426	0.394	0.46	CLONAL	1	TRUE	1	0.449266523062248	3		698	1304	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303934	30303934	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	187	490	0	ENST00000262643.3:c.170G>T	p.Cys57Phe	p.C57F	ENST00000262643	NM_001238.2	57	tGt/tTt	4/12	0.449266523062248	3	FACETS	0.978	0.903	1	0.489	0.451	0.529	CLONAL	1	TRUE	1	0.449266523062248	3		490	1042	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009147	27009147	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	150	103	1	ENST00000335756.4:c.83G>A	p.Arg28Gln	p.R28Q	ENST00000335756	NM_001809.3	28	cGg/cAg	1/5	0.445739032514265	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	3	TRUE	0	0.449266523062248	3		104	265	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279815	46279847	+	inframe_deletion	In_Frame_Del	DEL	GCAGCAGCAGCAGCAGCAGCAACAGCAGCAGCA	GCAGCAGCAGCAGCAGCAGCAACAGCAGCAGCA	-	rs1299097534	NA	P-0033356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1359	294	614	0	ENST00000371998.3:c.3759_3791del	p.Gln1266_Gln1276del	p.Q1266_Q1276del	ENST00000371998		1247	atGCAGCAGCAGCAGCAGCAGCAACAGCAGCAGCAg/atg	20/23	0.449266523062248	5	FACETS	1	0.991	1	0.442	0.414	0.47	CLONAL	1	TRUE	2	0.449266523062248	5		614	1653	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0033380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	26	539	1	ENST00000311936.3:c.34_35delinsTT	p.Gly12Phe	p.G12F	ENST00000311936	NM_004985.3	12	GGt/TTt	2/5	1	2	FACETS	0.706	0.557	0.877	0.706	0.557	0.877	SUBCLONAL	1	TRUE	1	0.12	2		540	614	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987196	36987199	+	frameshift_variant	Frame_Shift_Del	DEL	TGCC	TGCC	GCA	novel	NA	P-0033380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	54	1173	2	ENST00000354822.5:c.490_493delinsTGC	p.Gly164CysfsTer2	p.G164Cfs*2	ENST00000354822	NM_001079668.2	164	GGCAtg/TGCtg	3/3	1	2	FACETS	0.923	0.786	1	0.923	0.786	1	CLONAL	1	TRUE	1	0.12	2		1175	975	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0033383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	378	503	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.463105055568103	2		504	742	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	305	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.463105055568103	6	FACETS	0.956	0.903	1	0.956	0.903	1	CLONAL	3	TRUE	3	0.463105055568103	6		493	885	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518024	187518024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147405100	NA	P-0033383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	152	776	3	ENST00000441802.2:c.12670G>A	p.Ala4224Thr	p.A4224T	ENST00000441802	NM_005245.3	4224	Gct/Act	25/27	0.463105055568103	3	FACETS	1	0.957	1	0.535	0.49	0.582	CLONAL	1	TRUE	1	0.463105055568103	3		779	756	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030378	49030378	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs267603840	NA	P-0033383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	235	380	0	ENST00000267163.4:c.1853C>A	p.Ser618Ter	p.S618*	ENST00000267163	NM_000321.2	618	tCa/tAa	19/27	0.463105055568103	4	FACETS	0.908	0.861	0.953	0.908	0.861	0.953	CLONAL	4	TRUE	0	0.463105055568103	4		380	409	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827804	72827804	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	519	1023	0	ENST00000268489.5:c.8777C>T	p.Pro2926Leu	p.P2926L	ENST00000268489	NM_006885.3	2926	cCg/cTg	9/10	0.462630018540989	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	TRUE	0	0.463105055568103	3		1023	913	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118993	70119015	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGAGGAGGCCACGGAGCAGAC	GCAGAGGAGGCCACGGAGCAGAC	-	novel	NA	P-0033398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	38	761	0	ENST00000245479.2:c.568_590del	p.Glu190HisfsTer54	p.E190Hfs*54	ENST00000245479	NM_000346.3	189	GCAGAGGAGGCCACGGAGCAGACg/g	2/3	1	2	FACETS	0.635	0.526	0.757	0.635	0.526	0.757	SUBCLONAL	1	TRUE	1	0.329607136969217	2		761	363	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0033401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	63	313	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	0.19	2		313	534	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624260	89624260	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	29	158	0	ENST00000371953.3:c.34A>C	p.Asn12His	p.N12H	ENST00000371953	NM_000314.4	12	Aac/Cac	1/9	1	2	FACETS	0.596	0.477	0.732	0.596	0.477	0.732	SUBCLONAL	1	TRUE	1	0.19	2		158	512	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	14	349	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		349	255	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577150	7577156	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	TTACCAC	TTACCAC	-	novel	NA	P-0033426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	34	485	0	ENST00000269305.4:c.783-1_788del		p.X261_splice	ENST00000269305	NM_001126112.2	261		8/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		485	431	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0033478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	16	364	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	1	2	FACETS	0.057	0.041	0.075	0.057	0.041	0.075	SUBCLONAL	1	TRUE	1	1	2		364	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057520000	NA	P-0033487-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	263	857	0	ENST00000269305.4:c.452C>G	p.Pro151Arg	p.P151R	ENST00000269305	NM_001126112.2	151	cCc/cGc	5/11	0.45617306759835	1	FACETS	0.927	0.87	0.986	0.927	0.87	0.986	CLONAL	1	TRUE	0	0.45617306759835	1		857	960	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872460	35872461	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033487-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	204	563	0	ENST00000216797.5:c.442_443insA	p.Leu148HisfsTer6	p.L148Hfs*6	ENST00000216797	NM_020529.2	148	cta/cAta	3/6	0.45617306759835	1	FACETS	0.947	0.881	1	0.947	0.881	1	CLONAL	1	TRUE	0	0.45617306759835	1		563	729	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095616	178095616	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033487-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	149	519	0	ENST00000397062.3:c.1715A>G	p.Asp572Gly	p.D572G	ENST00000397062	NM_006164.4	572	gAt/gGt	5/5	1	2	FACETS	0.896	0.82	0.975	0.896	0.82	0.975	CLONAL	1	TRUE	1	0.45617306759835	2		519	729	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86676334	86676334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033487-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	65	263	0	ENST00000274376.6:c.2612G>T	p.Arg871Ile	p.R871I	ENST00000274376	NM_002890.2	871	aGa/aTa	20/25	0.45617306759835	1	FACETS	0.853	0.748	0.964	0.853	0.748	0.964	CLONAL	1	TRUE	0	0.45617306759835	1		263	258	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704495	117704495	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033487-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	87	359	0	ENST00000368508.3:c.2481G>C	p.Trp827Cys	p.W827C	ENST00000368508	NM_002944.2	827	tgG/tgC	16/43	0.250687420074239	1	FACETS	0.755	0.673	0.842	0.755	0.673	0.842	INDETERMINATE	1	TRUE	0	0.45617306759835	1		359	390	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940374	13940374	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1373470302	NA	P-0033487-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	115	413	0	ENST00000405192.2:c.1132A>T	p.Ile378Phe	p.I378F	ENST00000405192	NM_001163147.1	378	Att/Ttt	11/12	1	2	FACETS	0.939	0.849	1	0.939	0.849	1	CLONAL	1	TRUE	1	0.45617306759835	2		413	537	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877057	151877061	+	frameshift_variant	Frame_Shift_Del	DEL	GGTCT	GGTCT	-	novel	NA	P-0033487-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	115	460	0	ENST00000262189.6:c.7300_7304del	p.Arg2434ProfsTer9	p.R2434Pfs*9	ENST00000262189	NM_170606.2	2434	AGACCc/c	37/59	1	2	FACETS	0.803	0.725	0.885	0.803	0.725	0.885	CLONAL	1	TRUE	1	0.45617306759835	2		460	628	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371806	55371806	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033487-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	156	240	0	ENST00000297316.4:c.496G>C	p.Ala166Pro	p.A166P	ENST00000297316	NM_022454.3	166	Gcg/Ccg	2/2	0.195703435917594	3	FACETS	0.937	0.866	1	0.937	0.866	1	INDETERMINATE	2	TRUE	1	0.45617306759835	3		240	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912656	NA	P-0033491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	76	678	0	ENST00000269305.4:c.734G>C	p.Gly245Ala	p.G245A	ENST00000269305	NM_001126112.2	245	gGc/gCc	7/11	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.19	2		678	767	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0033491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	83	850	2	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.94	0.828	1	0.94	0.828	1	CLONAL	1	TRUE	1	0.19	2		852	929	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390494	118390494	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	26	473	0	ENST00000534358.1:c.11308G>T	p.Glu3770Ter	p.E3770*	ENST00000534358	NM_005933.3	3770	Gaa/Taa	32/36	1	2	FACETS	0.573	0.452	0.711	0.573	0.452	0.711	SUBCLONAL	1	TRUE	1	0.19	2		473	478	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713444	30713444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	36	623	0	ENST00000295754.5:c.769G>A	p.Glu257Lys	p.E257K	ENST00000295754	NM_003242.5	257	Gag/Aag	4/7	1	2	FACETS	0.648	0.531	0.779	0.648	0.531	0.779	SUBCLONAL	1	TRUE	1	0.19	2		623	585	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0033501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	121	308	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.730686174681082	2		308	326	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763282	59763282	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	160	622	0	ENST00000259008.2:c.2820G>C	p.Lys940Asn	p.K940N	ENST00000259008	NM_032043.2	940	aaG/aaC	19/20	0.730686174681082	3	FACETS	1	0.963	1	0.538	0.496	0.581	CLONAL	1	TRUE	1	0.730686174681082	3		622	556	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299983	15299983	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1390414547	NA	P-0033501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	136	616	0	ENST00000263388.2:c.1195G>A	p.Ala399Thr	p.A399T	ENST00000263388	NM_000435.2	399	Gcc/Acc	8/33	1	2	FACETS	0.88	0.807	0.955	0.88	0.807	0.955	CLONAL	1	TRUE	1	0.730686174681082	2		616	423	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715660	30715660	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	96	388	0	ENST00000295754.5:c.1318G>A	p.Glu440Lys	p.E440K	ENST00000295754	NM_003242.5	440	Gag/Aag	5/7	0.730686174681082	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.730686174681082	1		388	165	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527318	137527318	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	130	625	0	ENST00000367739.4:c.328G>T	p.Glu110Ter	p.E110*	ENST00000367739	NM_000416.2	110	Gaa/Taa	3/7	0.730686174681082	1	FACETS	0.896	0.831	0.961	0.896	0.831	0.961	CLONAL	1	TRUE	0	0.730686174681082	1		625	252	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280314	1280314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561203868	NA	P-0033501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	154	671	0	ENST00000310581.5:c.1909G>A	p.Asp637Asn	p.D637N	ENST00000310581	NM_198253.2	637	Gac/Aac	4/16	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.730686174681082	2		671	414	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56801452	56801452	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367846829	NA	P-0033501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	100	421	1	ENST00000337432.4:c.956G>A	p.Arg319Gln	p.R319Q	ENST00000337432	NM_058216.2	319	cGa/cAa	7/9	0.730686174681082	3	FACETS	0.89	0.8	0.984	0.445	0.4	0.492	CLONAL	1	TRUE	1	0.730686174681082	3		422	420	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030850	69030850	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150128151	NA	P-0033501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	95	415	0	ENST00000288368.4:c.3392C>T	p.Ser1131Leu	p.S1131L	ENST00000288368	NM_024870.2	1131	tCg/tTg	27/40	0.193254507325859	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.730686174681082	0		415	293	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86667950	86667950	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	92	326	0	ENST00000274376.6:c.1714C>G	p.Leu572Val	p.L572V	ENST00000274376	NM_002890.2	572	Ctg/Gtg	13/25	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.730686174681082	2		326	230	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733140	74733140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	128	475	0	ENST00000359995.5:c.103G>A	p.Glu35Lys	p.E35K	ENST00000359995	NM_001195427.1	35	Gag/Aag	1/3	0.730686174681082	3	FACETS	0.988	0.901	1	0.494	0.45	0.54	CLONAL	1	TRUE	1	0.730686174681082	3		475	484	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176132984	176132984	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	121	478	0	ENST00000367669.3:c.609G>C	p.Lys203Asn	p.K203N	ENST00000367669	NM_022457.5	203	aaG/aaC	4/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.730686174681082	2		478	321	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441813	49441813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	120	485	0	ENST00000301067.7:c.4171G>A	p.Glu1391Lys	p.E1391K	ENST00000301067	NM_003482.3	1391	Gag/Aag	14/54	1	2	FACETS	0.897	0.819	0.978	0.897	0.819	0.978	CLONAL	1	TRUE	1	0.730686174681082	2		485	366	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112919974	112919974	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	87	415	0	ENST00000351677.2:c.1189A>T	p.Thr397Ser	p.T397S	ENST00000351677	NM_002834.3	397	Acg/Tcg	10/16	1	2	FACETS	0.866	0.777	0.958	0.866	0.777	0.958	CLONAL	1	TRUE	1	0.730686174681082	2		415	275	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066703	30066703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	101	407	0	ENST00000331968.5:c.2428C>T	p.His810Tyr	p.H810Y	ENST00000331968	NM_002742.2	810	Cat/Tat	16/18	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.730686174681082	2		407	262	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690602	88690602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745856667	NA	P-0033501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	95	427	0	ENST00000360948.2:c.428C>T	p.Ser143Leu	p.S143L	ENST00000360948	NM_001012338.2	143	tCg/tTg	5/19	1	2	FACETS	0.985	0.891	1	0.985	0.891	1	CLONAL	1	TRUE	1	0.730686174681082	2		427	264	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467754	99467754	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1222573938	NA	P-0033501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	75	273	0	ENST00000268035.6:c.2623G>A	p.Asp875Asn	p.D875N	ENST00000268035	NM_000875.3	875	Gat/Aat	13/21	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.730686174681082	2		273	193	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993987	72993987	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	143	641	0	ENST00000268489.5:c.58C>T	p.Gln20Ter	p.Q20*	ENST00000268489	NM_006885.3	20	Cag/Tag	2/10	1	2	FACETS	0.979	0.902	1	0.979	0.902	1	CLONAL	1	TRUE	1	0.730686174681082	2		641	400	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55334154	55334160	+	frameshift_variant	Frame_Shift_Del	DEL	GCACGAC	GCACGAC	-	novel	NA	P-0033501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	104	260	0	ENST00000284073.2:c.51_57del	p.Gln17HisfsTer10	p.Q17Hfs*10	ENST00000284073	NM_138962.2	17	caGCACGAC/ca	1/14	0.730686174681082	3	FACETS	0.771	0.703	0.84	0.771	0.703	0.84	SUBCLONAL	2	TRUE	1	0.730686174681082	3		260	252	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796887	78796887	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	110	503	0	ENST00000306801.3:c.1000C>T	p.Gln334Ter	p.Q334*	ENST00000306801	NM_020761.2	334	Caa/Taa	9/34	0.730686174681082	3	FACETS	0.896	0.809	0.986	0.448	0.404	0.493	CLONAL	1	TRUE	1	0.730686174681082	3		503	459	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561114	9561114	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	111	451	0	ENST00000353224.5:c.668C>G	p.Ser223Trp	p.S223W	ENST00000353224	NM_177990.2	223	tCg/tGg	4/10	1	2	FACETS	0.983	0.896	1	0.983	0.896	1	CLONAL	1	TRUE	1	0.730686174681082	2		451	309	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170016897	170016897	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs145084763	NA	P-0033501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	145	489	1	ENST00000295797.4:c.1702G>A	p.Asp568Asn	p.D568N	ENST00000295797	NM_002740.5	568	Gat/Aat	17/18	0.730686174681082	3	FACETS	1	0.925	1	0.505	0.463	0.548	CLONAL	1	TRUE	1	0.730686174681082	3		490	537	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132841	152132841	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	190	386	0	ENST00000262189.6:c.31C>T	p.Gln11Ter	p.Q11*	ENST00000262189	NM_170606.2	11	Cag/Tag	1/59	0.366145654483018	2	FACETS	0.97	0.924	1	0.97	0.924	1	INDETERMINATE	2	TRUE	0	0.730686174681082	2		386	268	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866415	56866415	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	120	470	0	ENST00000519728.1:c.662G>A	p.Arg221Lys	p.R221K	ENST00000519728	NM_002350.3	221	aGa/aAa	8/13	1	2	FACETS	0.963	0.881	1	0.963	0.881	1	CLONAL	1	TRUE	1	0.730686174681082	2		470	341	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0033512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	540	776	4	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.914947604871836	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.914947604871836	1		780	581	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717609	89717609	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs876661024	NA	P-0033512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	260	435	0	ENST00000371953.3:c.635-1G>A		p.X212_splice	ENST00000371953	NM_000314.4	212			0.914947604871836	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.914947604871836	1		435	297	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212573	36212573	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	435	910	0	ENST00000222270.7:c.2324C>A	p.Ala775Asp	p.A775D	ENST00000222270	NM_014727.1	775	gCc/gAc	3/37	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.914947604871836	2		910	933	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439188	52439188	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	376	774	0	ENST00000460680.1:c.1054C>G	p.Pro352Ala	p.P352A	ENST00000460680	NM_004656.3	352	Ccc/Gcc	11/17	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.914947604871836	2		774	804	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033539-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	110	349	0				ENST00000310581	NM_198253.2	-/1132			0.416987043787734	4	FACETS	0.853	0.78	0.927	1	0.981	1	CLONAL	3	TRUE	2	0.488572892128552	4		349	262	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0033539-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	112	559	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	NA	2	FACETS	0.928	0.839	1			1	INDETERMINATE	1	TRUE	NA	0.488572892128552	2		559	494	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403217	116403217	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033539-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	177	547	0	ENST00000397752.3:c.2479del	p.Leu827PhefsTer22	p.L827Ffs*22	ENST00000397752	NM_000245.2	826	atC/at	11/21	0.488572892128552	4	FACETS	0.817	0.756	0.88	0.817	0.756	0.88	CLONAL	2	TRUE	2	0.488572892128552	4		547	660	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933302	39933303	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0033539-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	338	393	0	ENST00000378444.4:c.1296_1297insTG	p.Thr433Ter	p.T433*	ENST00000378444	NM_001123385.1	432	-/TG	4/15	0.442811903771227	2	FACETS	0.892	0.858	0.926			1	CLONAL	3	TRUE	NA	0.488572892128552	2		393	517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0033548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	299	599	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.296037722621595	3	FACETS	0.952	0.901	1	0.952	0.901	1	CLONAL	3	TRUE	0	0.313960261090819	3		599	772	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6048636	6048636	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	76	432	0	ENST00000265849.7:c.15G>C	p.Glu5Asp	p.E5D	ENST00000265849	NM_000535.5	5	gaG/gaC	1/15	1	2	FACETS	0.814	0.714	0.92	0.814	0.714	0.92	CLONAL	1	TRUE	1	0.313960261090819	2		432	595	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589168	67589168	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	65	301	0	ENST00000274335.5:c.1156C>G	p.Arg386Gly	p.R386G	ENST00000274335		386	Cga/Gga	9/15	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.313960261090819	2		301	400	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39550291	39550300	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CATGTTTCGC	CATGTTTCGC	-	novel	NA	P-0033548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	38	225	0	ENST00000262039.4:c.404_413del	p.Met135LysfsTer6	p.M135Kfs*6	ENST00000262039	NM_002647.2	134	ggCATGTTTCGC/gg	4/25	1	2	FACETS	0.807	0.67	0.959	0.807	0.67	0.959	CLONAL	1	TRUE	1	0.313960261090819	2		225	300	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022913	27022938	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGCCGCCGCCAGCAGCCTGGGCAA	CCCGCCGCCGCCAGCAGCCTGGGCAA	-	rs797045262	NA	P-0033552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	10	14	0	ENST00000324856.7:c.31_56del	p.Ser11AlafsTer91	p.S11Afs*91	ENST00000324856	NM_006015.4	7	CCCGCCGCCGCCAGCAGCCTGGGCAAc/c	1/20	0.584539366334301	3	FACETS	1	0.737	1	0.529	0.37	0.713	CLONAL	1	TRUE	1	0.58089872776679	3		14	42	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864522	57864522	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1420836393	NA	P-0033552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	569	599	0	ENST00000228682.2:c.1999C>A	p.Pro667Thr	p.P667T	ENST00000228682	NM_005269.2	667	Ccc/Acc	12/12	0.58089872776679	7	FACETS	1	0.993	1			1	CLONAL	4	TRUE	NA	0.58089872776679	7		599	1083	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308378	15308378	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	165	597	0	ENST00000263388.2:c.130C>G	p.Leu44Val	p.L44V	ENST00000263388	NM_000435.2	44	Ctg/Gtg	2/33	0.478264238939657	1	FACETS	0.69	0.637	0.745	0.69	0.637	0.745	SUBCLONAL	1	TRUE	0	0.58089872776679	1		597	584	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859420	151859420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148366561	NA	P-0033552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	59	457	0	ENST00000262189.6:c.11242G>A	p.Ala3748Thr	p.A3748T	ENST00000262189	NM_170606.2	3748	Gct/Act	43/59	0.441681413611201	5	FACETS	0.489	0.42	0.565	0.163	0.14	0.189	SUBCLONAL	1	TRUE	2	0.58089872776679	5		457	777	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412046	116412046	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	G	novel	NA	P-0033584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	258	850	0	ENST00000397752.3:c.3028+3A>G		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.331529894797062	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.331529894797062	1		850	1064	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721462	176721462	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1026514188	NA	P-0033584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	125	503	0	ENST00000439151.2:c.7093A>G	p.Ile2365Val	p.I2365V	ENST00000439151	NM_022455.4	2365	Ata/Gta	23/23	1	2	FACETS	0.996	0.902	1	0.996	0.902	1	CLONAL	1	TRUE	1	0.331529894797062	2		503	757	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412031	116412038	+	frameshift_variant	Frame_Shift_Del	DEL	ACTTTTCC	ACTTTTCC	-	novel	NA	P-0033584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	238	856	0	ENST00000397752.3:c.3017_3024del	p.Thr1006ArgfsTer6	p.T1006Rfs*6	ENST00000397752	NM_000245.2	1006	ACTTTTCCa/a	14/21	0.331529894797062	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.331529894797062	1		856	1068	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352389	70352389	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0033584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	95	424	0	ENST00000374080.3:c.4415+1G>T		p.X1472_splice	ENST00000374080		1472			1	2	FACETS	0.821	0.731	0.917	0.821	0.731	0.917	CLONAL	1	TRUE	1	0.331529894797062	2		424	698	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0033612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	84	547	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	0.29	2		547	441	SUCCESS
APC	324	MSKCC	GRCh37	5	112111345	112111345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	23	129	0	ENST00000257430.4:c.442C>T	p.Leu148Phe	p.L148F	ENST00000257430	NM_000038.5	148	Ctt/Ttt	5/16	1	2	FACETS	0.922	0.725	1	0.922	0.725	1	CLONAL	1	TRUE	1	0.29	2		129	172	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843748	151843748	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778512	NA	P-0033613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	120	342	0	ENST00000262189.6:c.13967C>T	p.Ala4656Val	p.A4656V	ENST00000262189	NM_170606.2	4656	gCg/gTg	53/59	0.553913148495159	3	FACETS	1	0.951	1	0.537	0.487	0.589	CLONAL	1	TRUE	1	0.550512142346808	3		342	518	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106759	27106759	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	311	493	0	ENST00000324856.7:c.6370A>G	p.Lys2124Glu	p.K2124E	ENST00000324856	NM_006015.4	2124	Aaa/Gaa	20/20	0.553913148495159	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.550512142346808	3		493	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578471	7578732	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGCGGGGGTGTGGAATCAACCCACAGCTGCACAGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAAGCAACTGGAAGACGGCAGCAAAGAAACAAACATGCGTAAGCACCTCCTGCAACCCACTAGCGAGCTAGAGAGAGTTGGCGTCTACACCTCAGGAGCTTTTCTTTTTTTTTTTTTTTTTTGAG	GGGCGGGGGTGTGGAATCAACCCACAGCTGCACAGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAAGCAACTGGAAGACGGCAGCAAAGAAACAAACATGCGTAAGCACCTCCTGCAACCCACTAGCGAGCTAGAGAGAGTTGGCGTCTACACCTCAGGAGCTTTTCTTTTTTTTTTTTTTTTTTGAG	-	novel	NA	P-0033613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	230	669	0	ENST00000269305.4:c.376-178_459del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	NA	2	FACETS	0.765	0.72	0.811			1	INDETERMINATE	2	TRUE	NA	0.550512142346808	2		669	546	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257889	19257889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1482048547	NA	P-0033613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1252	218	785	1	ENST00000162023.5:c.497G>A	p.Arg166His	p.R166H	ENST00000162023		166	cGc/cAc	9/13	0.477421501290278	4	FACETS	0.835	0.775	0.899	0.418	0.387	0.45	CLONAL	1	TRUE	2	0.550512142346808	4		786	1470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0033634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	665	620	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.658972499839651	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.658972499839651	3		620	830	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625456	69625456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781938977	NA	P-0033634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	151	671	1	ENST00000334134.2:c.337G>A	p.Ala113Thr	p.A113T	ENST00000334134	NM_005247.2	113	Gcc/Acc	3/3	0.658972499839651	3	FACETS	0.973	0.893	1	0.487	0.446	0.529	CLONAL	1	TRUE	1	0.658972499839651	3		672	626	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755663	39755663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	185	699	1	ENST00000288319.7:c.1102G>A	p.Ala368Thr	p.A368T	ENST00000288319	NM_182918.3	368	Gcc/Acc	10/10	0.658972499839651	2	FACETS	0.978	0.909	1	0.489	0.454	0.525	CLONAL	1	TRUE	0	0.658972499839651	2		700	574	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69032434	69032434	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	32	561	0	ENST00000288368.4:c.3508G>C	p.Asp1170His	p.D1170H	ENST00000288368	NM_024870.2	1170	Gat/Cat	29/40	1	2	FACETS	0.2	0.162	0.244	0.2	0.162	0.244	SUBCLONAL	1	TRUE	1	0.658972499839651	2		561	485	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845572	128845572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775852783	NA	P-0033634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	169	601	2	ENST00000249373.3:c.869G>A	p.Arg290His	p.R290H	ENST00000249373	NM_005631.4	290	cGc/cAc	4/12	0.446371287068056	4	FACETS	1	0.941	1	0.513	0.472	0.556	CLONAL	1	TRUE	2	0.658972499839651	4		603	829	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259432	11259432	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	118	539	1	ENST00000361445.4:c.4136G>T	p.Gly1379Val	p.G1379V	ENST00000361445	NM_004958.3	1379	gGc/gTc	28/58	0.308450772149495	2	FACETS	1	0.945	1	0.524	0.478	0.571	INDETERMINATE	1	TRUE	0	0.658972499839651	2		540	342	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795198	42795198	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	121	889	0	ENST00000575354.2:c.2278G>T	p.Val760Phe	p.V760F	ENST00000575354	NM_015125.3	760	Gtc/Ttc	10/20	0.446371287068056	4	FACETS	0.729	0.658	0.803	0.364	0.329	0.402	SUBCLONAL	1	TRUE	2	0.658972499839651	4		889	836	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089136	37089136	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	120	552	0	ENST00000231790.2:c.1858G>C	p.Glu620Gln	p.E620Q	ENST00000231790	NM_000249.3	620	Gag/Cag	16/19	0.658972499839651	4	FACETS	0.935	0.846	1	0.234	0.211	0.258	CLONAL	1	TRUE	0	0.658972499839651	4		552	646	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164781	47164781	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs902395542	NA	P-0033634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	102	418	0	ENST00000409792.3:c.1345C>A	p.Pro449Thr	p.P449T	ENST00000409792	NM_014159.6	449	Cca/Aca	3/21	0.658972499839651	2	FACETS	0.759	0.683	0.838	0.379	0.341	0.419	SUBCLONAL	1	TRUE	0	0.658972499839651	2		418	408	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952384	38952384	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	68	349	0	ENST00000357387.3:c.3041A>T	p.Glu1014Val	p.E1014V	ENST00000357387	NM_152756.3	1014	gAa/gTa	30/38	0.597497794207427	5	FACETS	0.948	0.827	1	0.316	0.275	0.359	CLONAL	1	TRUE	2	0.658972499839651	5		349	433	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057713	180057713	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	177	843	0	ENST00000261937.6:c.242T>A	p.Val81Glu	p.V81E	ENST00000261937	NM_182925.4	81	gTg/gAg	3/30	0.597497794207427	5	FACETS	0.965	0.888	1	0.322	0.296	0.349	CLONAL	1	TRUE	2	0.658972499839651	5		843	1107	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005699	150005699	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	265	383	0	ENST00000253339.5:c.526C>T	p.Gln176Ter	p.Q176*	ENST00000253339		176	Cag/Tag	3/7	0.658972499839651	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.658972499839651	2		383	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578518	7578518	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934875	NA	P-0033660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	519	685	0	ENST00000269305.4:c.412G>C	p.Ala138Pro	p.A138P	ENST00000269305	NM_001126112.2	138	Gcc/Ccc	5/11	0.717253905512087	2	FACETS	0.988	0.96	1	0.988	0.96	1	CLONAL	2	TRUE	0	0.717578267886398	2		685	732	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450367	50450367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs869312885	NA	P-0033660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	123	373	1	ENST00000331340.3:c.551G>A	p.Arg184Gln	p.R184Q	ENST00000331340	NM_006060.4	184	cGg/cAg	5/8	0.625714629620482	3	FACETS	1	0.957	1	0.542	0.493	0.592	CLONAL	1	TRUE	1	0.717578267886398	3		374	430	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056199	26056210	+	inframe_deletion	In_Frame_Del	DEL	TTCTTAGCGCTC	TTCTTAGCGCTC	-	novel	NA	P-0033660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	282	439	0	ENST00000343677.2:c.447_458del	p.Ser150_Lys153del	p.S150_K153del	ENST00000343677	NM_005319.3	149	aaGAGCGCTAAGAAa/aaa	1/1	0.717578267886398	3	FACETS	0.91	0.863	0.956	0.91	0.863	0.956	CLONAL	2	TRUE	1	0.717578267886398	3		439	587	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332734	65332734	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0033660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	140	366	0	ENST00000342505.4:c.805A>T	p.Lys269Ter	p.K269*	ENST00000342505	NM_002227.2	269	Aaa/Taa	7/25	0.671141955314909	4	FACETS	0.947	0.864	1	0.473	0.432	0.517	CLONAL	1	TRUE	2	0.717578267886398	4		366	708	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431694	431694	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	40	508	0	ENST00000399788.2:c.2315A>T	p.Asp772Val	p.D772V	ENST00000399788	NM_001042603.1	772	gAt/gTt	17/28	0.717578267886398	2	FACETS	0.215	0.178	0.256	0.108	0.089	0.128	SUBCLONAL	1	TRUE	0	0.717578267886398	2		508	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519985	NA	P-0033667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	11	533	0	ENST00000269305.4:c.857A>G	p.Glu286Gly	p.E286G	ENST00000269305	NM_001126112.2	286	gAa/gGa	8/11	1	2	FACETS	0.127	0.087	0.178	0.127	0.087	0.178	SUBCLONAL	1	TRUE	1	0.42	2		533	411	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16247477	16247477	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	24	158	0	ENST00000375759.3:c.1748A>G	p.Lys583Arg	p.K583R	ENST00000375759	NM_015001.2	583	aAg/aGg	9/15	1	2	FACETS	0.84	0.667	1	0.84	0.667	1	CLONAL	1	TRUE	1	0.42	2		158	136	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778083	3778084	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0033667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	80	747	0	ENST00000262367.5:c.6964_6965del	p.Ser2322ArgfsTer18	p.S2322Rfs*18	ENST00000262367	NM_004380.2	2322	TCa/a	31/31	0.3	1	FACETS	0.697	0.616	0.782	0.697	0.616	0.782	SUBCLONAL	1	TRUE	0	0.42	1		747	432	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0033681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	122	234	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.996	0.915	1	0.996	0.915	1	CLONAL	1	TRUE	1	0.830112263830669	2		234	295	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560500	65560500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs387906651	NA	P-0033681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	237	437	0	ENST00000358664.4:c.97C>T	p.Arg33Ter	p.R33*	ENST00000358664	NM_002382.4	33	Cga/Tga	3/5	0.830112263830669	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.830112263830669	1		437	328	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0033742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	377	547	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.436380625440803	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.436380625440803	2		547	704	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332337	70332337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761821309	NA	P-0033742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	92	378	1	ENST00000373644.4:c.242G>A	p.Arg81His	p.R81H	ENST00000373644	NM_030625.2	81	cGc/cAc	2/12	1	2	FACETS	0.825	0.736	0.92	0.825	0.736	0.92	CLONAL	1	TRUE	1	0.436380625440803	2		379	511	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488657	212488657	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374970657	NA	P-0033742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	193	317	0	ENST00000342788.4:c.2192C>T	p.Thr731Met	p.T731M	ENST00000342788	NM_005235.2	731	aCg/aTg	18/28	0.255436055813513	2	FACETS	0.779	0.725	0.833	0.779	0.725	0.833	INDETERMINATE	2	TRUE	0	0.436380625440803	2		317	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0033742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	320	599	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.436380625440803	2	FACETS	0.864	0.819	0.909	0.864	0.819	0.909	CLONAL	2	TRUE	0	0.436380625440803	2		599	849	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380346	14380346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	67	204	0	ENST00000256196.4:c.71G>A	p.Gly24Asp	p.G24D	ENST00000256196		24	gGc/gAc	1/6	1	2	FACETS	0.917	0.802	1	0.917	0.802	1	CLONAL	1	TRUE	1	0.436380625440803	2		204	335	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15374334	15374334	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201883209	NA	P-0033742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	35	486	0	ENST00000263377.2:c.1238G>A	p.Arg413His	p.R413H	ENST00000263377	NM_058243.2	413	cGt/cAt	7/20	1	2	FACETS	0.231	0.189	0.28	0.231	0.189	0.28	SUBCLONAL	1	TRUE	1	0.436380625440803	2		486	693	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717644	89717645	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0033742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	165	418	0	ENST00000371953.3:c.674_675dup	p.Ser226IlefsTer31	p.S226Ifs*31	ENST00000371953	NM_000314.4	223	-/AT	7/9	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.436380625440803	2		418	650	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881415	48881415	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0033742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	103	167	0	ENST00000267163.4:c.138-1G>A		p.X46_splice	ENST00000267163	NM_000321.2	46			0.431318644261604	2	FACETS	0.871	0.792	0.952	0.871	0.792	0.952	CLONAL	2	TRUE	0	0.436380625440803	2		167	271	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0033764-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	131	256	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.613143830988658	5	FACETS	1	0.91	1	0.251	0.227	0.275	CLONAL	1	TRUE	1	0.613162024510929	5		256	818	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0033764-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	511	650	1	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.539039709380546	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.613162024510929	2		651	812	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0033764-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	819	562	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.613162024510929	6	FACETS	1	0.994	1	1	0.994	1	CLONAL	5	TRUE	1	0.613162024510929	6		562	1137	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396464	396464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033764-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	273	742	0	ENST00000262320.3:c.562G>A	p.Glu188Lys	p.E188K	ENST00000262320	NM_003502.3	188	Gaa/Aaa	2/11	0.613535873157631	3	FACETS	1	0.978	1	0.543	0.509	0.577	CLONAL	1	TRUE	1	0.613162024510929	3		742	1072	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056244	26056244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781319824	NA	P-0033764-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1340	154	415	0	ENST00000343677.2:c.413C>T	p.Pro138Leu	p.P138L	ENST00000343677	NM_005319.3	138	cCc/cTc	1/1	0.613162024510929	8	FACETS	0.955	0.871	1	0.159	0.145	0.174	CLONAL	1	TRUE	2	0.613162024510929	8		415	1494	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987305	2987305	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033764-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1201	160	459	1	ENST00000396946.4:c.124C>T	p.Leu42Phe	p.L42F	ENST00000396946	NM_032415.4	42	Ctc/Ttc	3/25	0.613535873157631	4	FACETS	0.619	0.565	0.675			1	SUBCLONAL	1	TRUE	NA	0.613162024510929	4		460	1361	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106058	8106058	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	205	404	0	ENST00000346208.3:c.878T>G	p.Met293Arg	p.M293R	ENST00000346208		293	aTg/aGg	4/6	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.760799129856335	2		404	511	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061508	38061508	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs773810596	NA	P-0033793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	68	300	0	ENST00000250448.2:c.481A>G	p.Thr161Ala	p.T161A	ENST00000250448	NM_004496.3	161	Acg/Gcg	2/2	1	2	FACETS	0.627	0.551	0.708	0.627	0.551	0.708	SUBCLONAL	1	FALSE	1	0.760799129856335	2		300	285	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	299	658	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	1	2	FACETS	0.877	0.836	0.919	1	0.996	1	CLONAL	2	TRUE	1	0.600062039965839	2		658	568	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412375	139412375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1341448592	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	175	542	0	ENST00000277541.6:c.1270G>A	p.Glu424Lys	p.E424K	ENST00000277541	NM_017617.3	424	Gag/Aag	8/34	0.600062039965839	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.600062039965839	1		542	346	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36846865	36846865	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	97	400	0	ENST00000358127.4:c.1074G>A	p.Trp358Ter	p.W358*	ENST00000358127	NM_001280556.1	358	tgG/tgA	9/10	0.546273220131921	3	FACETS	0.827	0.74	0.919	0.414	0.37	0.46	CLONAL	1	TRUE	1	0.600062039965839	3		400	508	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629589	187629589	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	149	613	0	ENST00000441802.2:c.1393C>T	p.Gln465Ter	p.Q465*	ENST00000441802	NM_005245.3	465	Cag/Tag	2/27	1	2	FACETS	0.932	0.856	1	0.932	0.856	1	CLONAL	1	TRUE	1	0.600062039965839	2		613	533	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042616	42042616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	240	373	0	ENST00000219905.7:c.6811C>T	p.Gln2271Ter	p.Q2271*	ENST00000219905	NM_001164273.1	2271	Cag/Tag	17/24	0.596805185564946	2	FACETS	0.968	0.92	1	0.968	0.92	1	CLONAL	2	TRUE	0	0.600062039965839	2		373	413	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641487	18641487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	106	320	0	ENST00000266497.5:c.2486C>T	p.Ser829Phe	p.S829F	ENST00000266497		829	tCc/tTc	17/31	1	2	FACETS	0.952	0.862	1	0.952	0.862	1	CLONAL	1	TRUE	1	0.600062039965839	2		320	371	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678406	88678406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	486	779	0	ENST00000360948.2:c.1130C>T	p.Thr377Ile	p.T377I	ENST00000360948	NM_001012338.2	377	aCc/aTc	9/19	0.596805185564946	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.600062039965839	2		779	769	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28980009	28980009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866351272	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	117	515	0	ENST00000282397.4:c.1459G>A	p.Glu487Lys	p.E487K	ENST00000282397	NM_002019.4	487	Gaa/Aaa	11/30	1	2	FACETS	0.907	0.824	0.993	0.907	0.824	0.993	CLONAL	1	TRUE	1	0.600062039965839	2		515	430	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133538	55133538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770343276	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	126	367	0	ENST00000257290.5:c.842C>T	p.Thr281Met	p.T281M	ENST00000257290	NM_006206.4	281	aCg/aTg	6/23	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.600062039965839	2		367	420	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131410	202131411	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	125	416	0	ENST00000358485.4:c.378_379delinsTT	p.Arg127Ter	p.R127*	ENST00000358485	NM_001080125.1	126	ttCCga/ttTTga	2/9	1	2	FACETS	0.997	0.91	1	0.997	0.91	1	CLONAL	1	TRUE	1	0.600062039965839	2		416	418	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444849	49444849	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	187	652	0	ENST00000301067.7:c.2617C>T	p.Gln873Ter	p.Q873*	ENST00000301067	NM_003482.3	873	Caa/Taa	10/54	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.600062039965839	2		652	619	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839984	27839984	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	46	447	0	ENST00000328488.2:c.110A>T	p.Lys37Met	p.K37M	ENST00000328488	NM_003533.2	37	aAg/aTg	1/1	0.316003666110274	3	FACETS	0.361	0.304	0.425	0.181	0.152	0.213	INDETERMINATE	1	TRUE	1	0.600062039965839	3		447	552	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073454	8073455	+	missense_variant	Missense_Mutation	DNP	GG	GG	AC	novel	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	121	478	1	ENST00000377482.5:c.1204_1205delinsGT	p.Pro402Val	p.P402V	ENST00000377482	NM_018948.3	402	CCa/GTa	4/4	1	2	FACETS	0.794	0.721	0.87	0.794	0.721	0.87	SUBCLONAL	1	TRUE	1	0.600062039965839	2		479	508	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258953	16258953	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553179827	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	146	471	0	ENST00000375759.3:c.6218C>T	p.Ser2073Phe	p.S2073F	ENST00000375759	NM_015001.2	2073	tCc/tTc	11/15	1	2	FACETS	0.964	0.885	1	0.964	0.885	1	CLONAL	1	TRUE	1	0.600062039965839	2		471	505	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726935	46726935	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	129	413	0	ENST00000371975.4:c.769G>A	p.Gly257Arg	p.G257R	ENST00000371975	NM_003579.3	257	Gga/Aga	8/18	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.600062039965839	2		413	429	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484246	120484246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	147	457	0	ENST00000256646.2:c.2884G>A	p.Gly962Arg	p.G962R	ENST00000256646	NM_024408.3	962	Ggg/Agg	18/34	1	2	FACETS	0.93	0.854	1	0.93	0.854	1	CLONAL	1	TRUE	1	0.600062039965839	2		457	527	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631107	69631107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782695249	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	142	499	0	ENST00000334134.2:c.305G>A	p.Arg102Lys	p.R102K	ENST00000334134	NM_005247.2	102	aGg/aAg	2/3	1	2	FACETS	0.907	0.831	0.985	0.907	0.831	0.985	CLONAL	1	TRUE	1	0.600062039965839	2		499	522	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424091	49424092	+	missense_variant	Missense_Mutation	DNP	AG	AG	GA	novel	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	191	701	0	ENST00000301067.7:c.13970_13971delinsTC	p.Ser4657Phe	p.S4657F	ENST00000301067	NM_003482.3	4657	tCT/tTC	42/54	1	2	FACETS	0.923	0.856	0.991	0.923	0.856	0.991	CLONAL	1	TRUE	1	0.600062039965839	2		701	690	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562757	21562758	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	140	412	0	ENST00000382592.4:c.1161_1162delinsAA	p.Ala388Thr	p.A388T	ENST00000382592	NM_014572.2	387	gaGGcg/gaAAcg	4/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.600062039965839	2		412	414	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830870	3830870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	121	470	0	ENST00000262367.5:c.1686G>A	p.Met562Ile	p.M562I	ENST00000262367	NM_004380.2	562	atG/atA	8/31	1	2	FACETS	0.845	0.768	0.926	0.845	0.768	0.926	CLONAL	1	TRUE	1	0.600062039965839	2		470	477	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858232	9858232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1187237144	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	133	463	1	ENST00000330684.3:c.3169G>A	p.Ala1057Thr	p.A1057T	ENST00000330684	NM_001134407.1	1057	Gcc/Acc	13/13	1	2	FACETS	0.951	0.87	1	0.951	0.87	1	CLONAL	1	TRUE	1	0.600062039965839	2		464	466	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89809309	89809310	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	128	489	1	ENST00000389301.3:c.3663_3664delinsAA	p.Asn1221_Pro1222delinsLysThr	p.N1221_P1222delinsKT	ENST00000389301	NM_000135.2	1221	aaCCcg/aaAAcg	37/43	1	2	FACETS	0.792	0.721	0.865	0.792	0.721	0.865	SUBCLONAL	1	TRUE	1	0.600062039965839	2		490	539	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244458	5244458	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	212	770	0	ENST00000357368.4:c.1024G>A	p.Glu342Lys	p.E342K	ENST00000357368	NM_002850.3	342	Gag/Aag	11/38	1	2	FACETS	0.96	0.895	1	0.96	0.895	1	CLONAL	1	TRUE	1	0.600062039965839	2		770	736	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170803	11170804	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	137	533	1	ENST00000358026.2:c.4947_4948delinsTT	p.Arg1650Ter	p.R1650*	ENST00000358026	NM_001128849.1	1649	agCCga/agTTga	35/36	1	2	FACETS	0.882	0.806	0.959	0.882	0.806	0.959	CLONAL	1	TRUE	1	0.600062039965839	2		534	518	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725044	47725044	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752056442	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	200	681	0	ENST00000449228.1:c.700C>T	p.Pro234Ser	p.P234S	ENST00000449228	NM_001127240.2	234	Ccg/Tcg	4/4	1	2	FACETS	0.925	0.86	0.991	0.925	0.86	0.991	CLONAL	1	TRUE	1	0.600062039965839	2		681	721	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082362	16082362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	235	715	0	ENST00000281043.3:c.176C>T	p.Pro59Leu	p.P59L	ENST00000281043	NM_005378.4	59	cCc/cTc	2/3	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.600062039965839	2		715	729	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966142	25966142	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	146	586	0	ENST00000435504.4:c.3064A>G	p.Lys1022Glu	p.K1022E	ENST00000435504		1022	Aaa/Gaa	13/13	1	2	FACETS	0.858	0.787	0.932	0.858	0.787	0.932	CLONAL	1	TRUE	1	0.600062039965839	2		586	567	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62323149	62323150	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	97	400	0	ENST00000360203.5:c.2611_2612delinsTT	p.Pro871Leu	p.P871L	ENST00000360203	NM_001283009.1	871	CCg/TTg	28/35	1	2	FACETS	0.816	0.733	0.904	0.816	0.733	0.904	CLONAL	1	TRUE	1	0.600062039965839	2		400	396	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573121	41573122	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	122	678	1	ENST00000263253.7:c.5406_5407delinsAA	p.Val1803Met	p.V1803M	ENST00000263253	NM_001429.3	1802	ccGGtg/ccAAtg	31/31	1	2	FACETS	0.708	0.642	0.777	0.708	0.642	0.777	SUBCLONAL	1	TRUE	1	0.600062039965839	2		679	574	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932929	49932930	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	113	734	0	ENST00000296474.3:c.3014_3015delinsTT	p.Ala1005Val	p.A1005V	ENST00000296474	NM_002447.2	1005	gCC/gTT	13/20	1	2	FACETS	0.658	0.594	0.726	0.658	0.594	0.726	SUBCLONAL	1	TRUE	1	0.600062039965839	2		734	572	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521672	89521672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	156	412	0	ENST00000336596.2:c.2749G>A	p.Gly917Ser	p.G917S	ENST00000336596	NM_005233.5	917	Ggt/Agt	16/17	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.600062039965839	2		412	425	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539093	187539093	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	150	567	0	ENST00000441802.2:c.8647T>C	p.Tyr2883His	p.Y2883H	ENST00000441802	NM_005245.3	2883	Tac/Cac	10/27	1	2	FACETS	0.949	0.872	1	0.949	0.872	1	CLONAL	1	TRUE	1	0.600062039965839	2		567	527	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449510	31449510	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	88	294	0	ENST00000344624.3:c.2699C>T	p.Pro900Leu	p.P900L	ENST00000344624		900	cCa/cTa	19/33	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.600062039965839	2		294	284	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176718972	176718973	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	51	167	1	ENST00000439151.2:c.6276_6277delinsAA	p.Glu2093Lys	p.E2093K	ENST00000439151	NM_022455.4	2092	acGGaa/acAAaa	22/23	1	2	FACETS	0.885	0.764	1	0.885	0.764	1	CLONAL	1	TRUE	1	0.600062039965839	2		168	192	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979317	93979317	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs267601170	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	157	396	0	ENST00000369303.4:c.1511A>T	p.Asn504Ile	p.N504I	ENST00000369303	NM_004440.3	504	aAt/aTt	7/17	0.316003666110274	3	FACETS	0.824	0.763	0.886	0.824	0.763	0.886	INDETERMINATE	2	TRUE	1	0.600062039965839	3		396	413	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679033	117679033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	205	472	1	ENST00000368508.3:c.3788C>T	p.Pro1263Leu	p.P1263L	ENST00000368508	NM_002944.2	1263	cCc/cTc	24/43	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.600062039965839	NA		473	524	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469821	157469822	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	186	592	0	ENST00000346085.5:c.2615_2616delinsTT	p.Pro872Leu	p.P872L	ENST00000346085	NM_020732.3	872	cCC/cTT	9/20	0.316003666110274	3	FACETS	1	0.983	1	0.6	0.556	0.645	INDETERMINATE	1	TRUE	1	0.600062039965839	3		592	672	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146931	38146931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	212	695	0	ENST00000317025.8:c.3211C>T	p.Pro1071Ser	p.P1071S	ENST00000317025	NM_023034.1	1071	Cct/Tct	18/24	1	2	FACETS	0.904	0.842	0.967	0.904	0.842	0.967	CLONAL	1	TRUE	1	0.600062039965839	2		695	782	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741687	145741688	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	201	698	2	ENST00000428558.2:c.815_816delinsTT	p.Pro272Leu	p.P272L	ENST00000428558	NM_004260.3	272	cCC/cTT	5/22	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.600062039965839	2		700	643	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220311	98220311	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060502301	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	85	264	0	ENST00000331920.6:c.3152G>A	p.Trp1051Ter	p.W1051*	ENST00000331920	NM_000264.3	1051	tGg/tAg	18/24	0.600062039965839	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.600062039965839	1		264	184	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760962	133760963	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	159	635	2	ENST00000318560.5:c.3285_3286delinsAA	p.Glu1096Lys	p.E1096K	ENST00000318560	NM_005157.4	1095	cgGGag/cgAAag	11/11	0.600062039965839	1	FACETS	0.994	0.924	1	0.994	0.924	1	CLONAL	1	TRUE	0	0.600062039965839	1		637	373	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626635	100626635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	118	182	0	ENST00000308731.7:c.295C>T	p.Pro99Ser	p.P99S	ENST00000308731	NM_000061.2	99	Cct/Tct	4/19	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.600062039965839	1		182	207	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170804	11170804	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1306144699	NA	P-0033811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	137	533	0	ENST00000358026.2:c.4948C>T	p.Arg1650Ter	p.R1650*	ENST00000358026	NM_001128849.1	1650	Cga/Tga	35/36	1	2	FACETS	0.89	0.814	0.969	0.89	0.814	0.969	CLONAL	1	TRUE	1	0.600062039965839	2		533	513	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0033822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	71	547	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.520561040225416	3	FACETS	0.966	0.848	1	0.483	0.424	0.546	CLONAL	1	TRUE	1	0.520561040225416	3		547	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0033822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	235	623	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	NA	2	FACETS	0.94	0.888	0.993			1	INDETERMINATE	2	TRUE	NA	0.520561040225416	2		623	480	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125496724	125496724	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	67	370	0	ENST00000428830.2:c.62del	p.Gly21GlufsTer7	p.G21Efs*7	ENST00000428830	NM_001114121.2	21	Gga/ga	2/14	0.520561040225416	3	FACETS	0.863	0.754	0.98	0.431	0.377	0.49	CLONAL	1	TRUE	1	0.520561040225416	3		370	376	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62305351	62305351	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	109	785	1	ENST00000360203.5:c.824G>A	p.Gly275Glu	p.G275E	ENST00000360203	NM_001283009.1	275	gGa/gAa	10/35	0.520561040225416	3	FACETS	0.726	0.652	0.804	0.363	0.326	0.402	SUBCLONAL	1	TRUE	1	0.520561040225416	3		786	727	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0033834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	124	328	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	0.962	0.873	1	0.962	0.873	1	CLONAL	1	TRUE	1	0.454752892367748	2		328	567	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115681	108115681	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs876660933	NA	P-0033834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	72	414	0	ENST00000278616.4:c.829G>T	p.Glu277Ter	p.E277*	ENST00000278616	NM_000051.3	277	Gaa/Taa	7/63	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.454752892367748	2		414	306	SUCCESS
APC	324	MSKCC	GRCh37	5	112170746	112170747	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	98	625	0	ENST00000257430.4:c.1847dup	p.Leu616PhefsTer18	p.L616Ffs*18	ENST00000257430	NM_000038.5	614	-/T	15/16	0.454752892367748	1	FACETS	0.795	0.714	0.88	0.795	0.714	0.88	SUBCLONAL	1	TRUE	0	0.454752892367748	1		625	419	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0033845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	2585	562	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.3790776259701	27	FACETS	0.99	0.98	0.999			1	CLONAL	26	TRUE	NA	0.3790776259701	27		562	3042	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372744	81372744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1168082930	NA	P-0033845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	34	324	1	ENST00000222390.5:c.790G>A	p.Asp264Asn	p.D264N	ENST00000222390	NM_000601.4	264	Gat/Aat	7/18	0.330825918436851	4	FACETS	0.511	0.417	0.617	0.17	0.139	0.206	SUBCLONAL	1	TRUE	1	0.3790776259701	4		325	484	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271969	18271969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1418268495	NA	P-0033845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	49	291	0	ENST00000222254.8:c.572C>T	p.Ser191Leu	p.S191L	ENST00000222254	NM_005027.3	191	tCg/tTg	5/16	1	2	FACETS	0.665	0.564	0.774	0.665	0.564	0.774	SUBCLONAL	1	TRUE	1	0.3790776259701	2		291	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876659802	NA	P-0033845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	157	675	2	ENST00000269305.4:c.833C>A	p.Pro278His	p.P278H	ENST00000269305	NM_001126112.2	278	cCt/cAt	8/11	0.204337706632256	2	FACETS	1	0.978	1	0.59	0.542	0.64	INDETERMINATE	1	TRUE	0	0.3790776259701	2		677	702	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81957138	81957138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	131	426	0	ENST00000359376.3:c.2356G>A	p.Asp786Asn	p.D786N	ENST00000359376	NM_002661.3	786	Gat/Aat	22/33	0.348582916104027	2	FACETS	1	0.98	1	0.638	0.581	0.696	CLONAL	1	TRUE	0	0.3790776259701	2		426	542	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445091	89445091	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	50	321	0	ENST00000336596.2:c.1411G>A	p.Glu471Lys	p.E471K	ENST00000336596	NM_005233.5	471	Gag/Aag	6/17	0.3790776259701	3	FACETS	0.699	0.594	0.814	0.349	0.297	0.407	SUBCLONAL	1	TRUE	1	0.3790776259701	3		321	449	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198897	67198897	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	61	425	0	ENST00000312629.5:c.368T>C	p.Leu123Pro	p.L123P	ENST00000312629	NM_003952.2	123	cTa/cCa	5/15	0.3790776259701	3	FACETS	0.52	0.448	0.599	0.26	0.224	0.3	SUBCLONAL	1	TRUE	1	0.3790776259701	3		425	736	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569984	95569984	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	66	517	0	ENST00000393063.1:c.3749C>A	p.Ser1250Tyr	p.S1250Y	ENST00000393063	NM_030621.3	1250	tCt/tAt	22/28	0.303712517721461	5	FACETS	0.637	0.551	0.73	0.212	0.183	0.244	SUBCLONAL	1	TRUE	2	0.3790776259701	5		517	858	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223514	2223514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	87	608	1	ENST00000326181.6:c.1045G>A	p.Glu349Lys	p.E349K	ENST00000326181	NM_032271.2	349	Gag/Aag	11/21	0.269945624124192	5	FACETS	0.679	0.599	0.764	0.226	0.199	0.255	SUBCLONAL	1	TRUE	2	0.3790776259701	5		609	1061	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641289	3641289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	76	549	0	ENST00000294008.3:c.2350C>T	p.His784Tyr	p.H784Y	ENST00000294008	NM_032444.2	784	Cac/Tac	12/15	0.269945624124192	5	FACETS	0.629	0.55	0.714	0.21	0.183	0.238	SUBCLONAL	1	TRUE	2	0.3790776259701	5		549	1000	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367906	15367906	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	113	664	1	ENST00000263377.2:c.1420C>A	p.Pro474Thr	p.P474T	ENST00000263377	NM_058243.2	474	Ccc/Acc	8/20	1	2	FACETS	0.807	0.726	0.892	0.807	0.726	0.892	CLONAL	1	TRUE	1	0.3790776259701	2		665	739	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224552	36224552	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1421	76	800	1	ENST00000222270.7:c.7014T>A	p.Asp2338Glu	p.D2338E	ENST00000222270	NM_014727.1	2338	gaT/gaA	29/37	0.3790776259701	6	FACETS	0.471	0.411	0.536	0.094	0.082	0.108	SUBCLONAL	1	TRUE	1	0.3790776259701	6		801	1497	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664901	138664901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	22	141	0	ENST00000330315.3:c.664G>A	p.Ala222Thr	p.A222T	ENST00000330315	NM_023067.3	222	Gca/Aca	1/1	0.3790776259701	3	FACETS	0.59	0.459	0.742	0.295	0.229	0.371	SUBCLONAL	1	TRUE	1	0.3790776259701	3		141	234	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0033848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	519	740	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.670540603093078	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.670540603093078	1		740	820	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102121	27102121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	347	572	0	ENST00000324856.7:c.5047G>A	p.Glu1683Lys	p.E1683K	ENST00000324856	NM_006015.4	1683	Gag/Aag	19/20	0.670540603093078	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.670540603093078	1		572	557	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725046	89725054	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GAAGCTGTA	GAAGCTGTA	-	novel	NA	P-0033848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	58	205	0	ENST00000371953.3:c.1029_1037del	p.Lys344_Tyr346del	p.K344_Y346del	ENST00000371953	NM_000314.4	343	gtGAAGCTGTAc/gtc	9/9	0.311809385852865	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.670540603093078	0		205	190	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104357006	104357006	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149016373	NA	P-0033848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	162	465	1	ENST00000369902.3:c.866G>A	p.Arg289Gln	p.R289Q	ENST00000369902	NM_016169.3	289	cGg/cAg	7/12	0.311809385852865	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.670540603093078	0		466	418	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566153	95566153	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	198	472	0	ENST00000393063.1:c.4170C>A	p.Asp1390Glu	p.D1390E	ENST00000393063	NM_030621.3	1390	gaC/gaA	23/28	0.650100889419278	2	FACETS	0.962	0.896	1	0.481	0.448	0.515	CLONAL	1	TRUE	0	0.670540603093078	2		472	614	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750390	41750390	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	135	378	0	ENST00000226382.2:c.238G>C	p.Ala80Pro	p.A80P	ENST00000226382	NM_003924.3	80	Gca/Cca	1/3	0.662436879208223	1	FACETS	0.946	0.876	1	0.946	0.876	1	CLONAL	1	TRUE	0	0.670540603093078	1		378	283	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004918	150004918	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	262	541	0	ENST00000253339.5:c.1307C>A	p.Ser436Ter	p.S436*	ENST00000253339		436	tCa/tAa	3/7	0.635602734671822	1	FACETS	0.991	0.94	1	0.991	0.94	1	CLONAL	1	TRUE	0	0.670540603093078	1		541	524	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970951	21970973	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCCCGCAGCCGCGCGCAGGTA	CCCCCCGCAGCCGCGCGCAGGTA	-	novel	NA	P-0033848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	568	589	0	ENST00000304494.5:c.385_407del	p.Tyr129HisfsTer5	p.Y129Hfs*5	ENST00000304494	NM_000077.4	129	TACCTGCGCGCGGCTGCGGGGGGc/c	2/3	0.670540603093078	2	FACETS	0.991	0.962	1	0.991	0.962	1	CLONAL	2	TRUE	0	0.670540603093078	2		589	855	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815613	139815613	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs374009362	NA	P-0033848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	168	609	0	ENST00000247668.2:c.1084G>T	p.Ala362Ser	p.A362S	ENST00000247668	NM_021138.3	362	Gcc/Tcc	9/11	0.660644920842912	2	FACETS	0.695	0.64	0.752	0.347	0.32	0.376	SUBCLONAL	1	TRUE	0	0.670540603093078	2		609	721	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258744	115258744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434596	NA	P-0033849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	146	365	0	ENST00000369535.4:c.38G>A	p.Gly13Asp	p.G13D	ENST00000369535	NM_002524.4	13	gGt/gAt	2/7	0.191714753667966	5	FACETS	0.804	0.737	0.873	0.536	0.491	0.582	INDETERMINATE	2	TRUE	2	0.610201227046384	5		365	570	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790171	40790171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760735173	NA	P-0033849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	134	393	1	ENST00000373198.4:c.2560C>T	p.Arg854Cys	p.R854C	ENST00000373198	NM_133170.3	854	Cgc/Tgc	18/32	0.175631130570366	5	FACETS	0.937	0.858	1	0.624	0.572	0.679	INDETERMINATE	2	TRUE	2	0.610201227046384	5		394	449	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225060	NA	P-0033849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	256	414	0	ENST00000263967.3:c.311C>T	p.Pro104Leu	p.P104L	ENST00000263967	NM_006218.2	104	cCa/cTa	2/21	0.175631130570366	5	FACETS	1	0.986	1	0.764	0.719	0.81	INDETERMINATE	2	TRUE	2	0.610201227046384	5		414	701	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578527	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	391	701	0	ENST00000269305.4:c.403dup	p.Cys135LeufsTer14	p.C135Lfs*14	ENST00000269305	NM_001126112.2	135	tgc/tTgc	5/11	0.610201227046384	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.610201227046384	1		701	740	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717776	89717776	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	rs1060500110	NA	P-0033849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	30	316	0	ENST00000371953.3:c.801+1del		p.K267fs	ENST00000371953	NM_000314.4	267	aaG/aa	7/9	0.610201227046384	1	FACETS	0.246	0.198	0.299	0.246	0.198	0.299	SUBCLONAL	1	TRUE	0	0.610201227046384	1		316	278	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443481	49443481	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781156556	NA	P-0033849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	102	393	1	ENST00000301067.7:c.3890G>A	p.Arg1297His	p.R1297H	ENST00000301067	NM_003482.3	1297	cGt/cAt	11/54	0.381948280438331	1	FACETS	0.738	0.668	0.81	0.738	0.668	0.81	SUBCLONAL	1	TRUE	0	0.610201227046384	1		394	315	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268442	142268442	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	135	374	0	ENST00000350721.4:c.3050T>C	p.Leu1017Ser	p.L1017S	ENST00000350721	NM_001184.3	1017	tTa/tCa	15/47	0.175631130570366	5	FACETS	0.762	0.696	0.831	0.508	0.464	0.554	INDETERMINATE	2	TRUE	2	0.610201227046384	5		374	556	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0033855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	116	400	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	0.581500011628649	2		400	423	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261832	16261832	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	20	434	0	ENST00000375759.3:c.9098del	p.Pro3033HisfsTer58	p.P3033Hfs*58	ENST00000375759	NM_015001.2	3033	Cca/ca	11/15	0.581500011628649	1	FACETS	0.135	0.103	0.173	0.135	0.103	0.173	SUBCLONAL	1	TRUE	0	0.581500011628649	1		434	362	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220707	1220708	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0033855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	278	528	1	ENST00000326873.7:c.725_726delinsTT	p.Gly242Val	p.G242V	ENST00000326873	NM_000455.4	242	gGG/gTT	5/10	0.581500011628649	2	FACETS	0.943	0.898	0.988	0.943	0.898	0.988	CLONAL	2	TRUE	0	0.581500011628649	2		529	507	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597494	10597494	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	368	478	0	ENST00000171111.5:c.1709G>T	p.Gly570Val	p.G570V	ENST00000171111	NM_203500.1	570	gGa/gTa	6/6	0.581500011628649	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.581500011628649	2		478	587	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593488	55593488	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	94	365	0	ENST00000288135.5:c.1645C>A	p.Gln549Lys	p.Q549K	ENST00000288135	NM_000222.2	549	Cag/Aag	10/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.581500011628649	2		365	269	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922321	178922321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	226	358	0	ENST00000263967.3:c.1090G>A	p.Gly364Arg	p.G364R	ENST00000263967	NM_006218.2	364	Gga/Aga	6/21	0.610597108651339	4	FACETS	0.976	0.916	1	0.976	0.916	1	CLONAL	2	FALSE	2	0.662522223749765	4		358	581	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115462	115115462	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0033888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	230	461	0	ENST00000257566.3:c.865-1G>C		p.X289_splice	ENST00000257566	NM_016569.3	289			0.662522223749765	6	FACETS	0.945	0.883	1	0.473	0.441	0.505	CLONAL	2	FALSE	2	0.662522223749765	6		461	854	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579442	7579442	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs534447939	NA	P-0033899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	8	652	0	ENST00000269305.4:c.245C>T	p.Pro82Leu	p.P82L	ENST00000269305	NM_001126112.2	82	cCg/cTg	4/11	0.166362934930622	3	FACETS	0.109	0.069	0.161	0.055	0.034	0.081	INDETERMINATE	1	FALSE	1	0.468083841629398	3		652	387	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27228259	27228259	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	99	549	0	ENST00000380036.4:c.3256G>T	p.Ala1086Ser	p.A1086S	ENST00000380036	NM_000459.3	1086	Gcc/Tcc	22/23	1	2	FACETS	0.75	0.679	0.823	1	0.984	1	SUBCLONAL	2	FALSE	1	0.468083841629398	2		549	282	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0033900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	197	565	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.174299889755847	2	FACETS	0.893	0.829	0.958	1	0.989	1	CLONAL	3	TRUE	0	0.195644702448744	2		565	752	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771330	68771330	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555509636	NA	P-0033900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	70	273	0	ENST00000261769.5:c.12G>A	p.Trp4Ter	p.W4*	ENST00000261769	NM_004360.3	4	tgG/tgA	1/16	0.196647233815144	1	FACETS	1	0.886	1	1	0.982	1	CLONAL	2	TRUE	0	0.195644702448744	1		273	320	SUCCESS
AR	367	MSKCC	GRCh37	X	66766561	66766561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	49	646	0	ENST00000374690.3:c.1573G>A	p.Gly525Ser	p.G525S	ENST00000374690	NM_000044.3	525	Ggc/Agc	1/8	1	2	FACETS	0.56	0.473	0.657	0.56	0.473	0.657	SUBCLONAL	1	TRUE	1	0.195644702448744	2		646	894	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012385	152012386	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	127	344	0	ENST00000262189.6:c.427dup	p.Ser143LysfsTer27	p.S143Kfs*27	ENST00000262189	NM_170606.2	143	agt/aAgt	4/59	0.195644702448744	5	FACETS	1	0.976	1	0.818	0.743	0.898	CLONAL	2	TRUE	2	0.195644702448744	5		344	684	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481806	56481806	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	84	596	0	ENST00000267101.3:c.734C>T	p.Ala245Val	p.A245V	ENST00000267101	NM_001982.3	245	gCc/gTc	7/28	1	2	FACETS	0.837	0.739	0.943	0.837	0.739	0.943	CLONAL	1	TRUE	1	0.26	2		596	772	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875645	35875645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201449880	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	53	398	0	ENST00000303115.3:c.832G>A	p.Asp278Asn	p.D278N	ENST00000303115	NM_002185.3	278	Gat/Aat	7/8	1	2	FACETS	0.772	0.659	0.896	0.772	0.659	0.896	SUBCLONAL	1	TRUE	1	0.26	2		398	528	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230641	46230641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	85	580	0	ENST00000334344.6:c.890C>T	p.Ser297Phe	p.S297F	ENST00000334344	NM_152641.2	297	tCc/tTc	8/21	1	2	FACETS	0.881	0.779	0.991	0.881	0.779	0.991	CLONAL	1	TRUE	1	0.26	2		580	742	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657405	29657405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	77	644	0	ENST00000356175.3:c.5638C>T	p.Pro1880Ser	p.P1880S	ENST00000356175	NM_000267.3	1880	Cct/Tct	38/57	1	2	FACETS	0.691	0.606	0.784	0.691	0.606	0.784	SUBCLONAL	1	TRUE	1	0.26	2		644	857	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750440	41750440	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	67	453	0	ENST00000226382.2:c.188G>A	p.Gly63Glu	p.G63E	ENST00000226382	NM_003924.3	63	gGa/gAa	1/3	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.26	2		453	483	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912815	100912815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1000609240	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	53	455	0	ENST00000325455.5:c.2507G>A	p.Arg836Gln	p.R836Q	ENST00000325455	NM_001202474.3	836	cGa/cAa	7/8	0.151791117870713	2	FACETS	0.701	0.597	0.814	0.35	0.298	0.407	INDETERMINATE	1	TRUE	0	0.26	2		455	582	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358940	81358940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	68	531	0	ENST00000222390.5:c.1021C>T	p.Pro341Ser	p.P341S	ENST00000222390	NM_000601.4	341	Cct/Tct	8/18	1	2	FACETS	0.869	0.756	0.991	0.869	0.756	0.991	CLONAL	1	TRUE	1	0.26	2		531	602	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566827	212566827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202247795	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	173	325	0	ENST00000342788.4:c.1354G>A	p.Glu452Lys	p.E452K	ENST00000342788	NM_005235.2	452	Gaa/Aaa	12/28	0.151791117870713	2	FACETS	1	0.983	1	1	0.983	1	INDETERMINATE	2	TRUE	0	0.26	2		325	553	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926270	112926270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918457	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	85	592	1	ENST00000351677.2:c.1403C>T	p.Thr468Met	p.T468M	ENST00000351677	NM_002834.3	468	aCg/aTg	12/16	1	2	FACETS	0.752	0.663	0.846	0.752	0.663	0.846	SUBCLONAL	1	TRUE	1	0.26	2		593	870	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879903	37879903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	82	685	0	ENST00000269571.5:c.2198C>T	p.Thr733Ile	p.T733I	ENST00000269571		733	aCa/aTa	18/27	1	2	FACETS	0.895	0.789	1	0.895	0.789	1	CLONAL	1	TRUE	1	0.26	2		685	705	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924309	112924309	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1306943402	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	75	588	2	ENST00000351677.2:c.1255C>T	p.His419Tyr	p.H419Y	ENST00000351677	NM_002834.3	419	Cac/Tac	11/16	1	2	FACETS	0.794	0.695	0.9	0.794	0.695	0.9	SUBCLONAL	1	TRUE	1	0.26	2		590	727	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576880	212576880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	54	389	0	ENST00000342788.4:c.1019G>A	p.Gly340Glu	p.G340E	ENST00000342788	NM_005235.2	340	gGa/gAa	9/28	0.151791117870713	2	FACETS	0.691	0.59	0.802	0.346	0.295	0.401	INDETERMINATE	1	TRUE	0	0.26	2		389	601	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805735	43805735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	87	672	0	ENST00000372470.3:c.791C>T	p.Ser264Phe	p.S264F	ENST00000372470	NM_005373.2	264	tCc/tTc	5/12	1	2	FACETS	0.903	0.799	1	0.903	0.799	1	CLONAL	1	TRUE	1	0.26	2		672	741	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68999972	68999972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	66	602	0	ENST00000288368.4:c.2041C>T	p.Pro681Ser	p.P681S	ENST00000288368	NM_024870.2	681	Cca/Tca	19/40	1	2	FACETS	0.609	0.527	0.697	0.609	0.527	0.697	SUBCLONAL	1	TRUE	1	0.26	2		602	834	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152082	11152082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866735560	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	40	497	1	ENST00000358026.2:c.4366C>T	p.Pro1456Ser	p.P1456S	ENST00000358026	NM_001128849.1	1456	Ccg/Tcg	31/36	1	2	FACETS	0.684	0.568	0.812	0.684	0.568	0.812	SUBCLONAL	1	TRUE	1	0.26	2		498	450	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624897	9624897	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	89	540	0	ENST00000353224.5:c.80C>T	p.Pro27Leu	p.P27L	ENST00000353224	NM_177990.2	27	cCa/cTa	3/10	1	2	FACETS	0.967	0.857	1	0.967	0.857	1	CLONAL	1	TRUE	1	0.26	2		540	708	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192078	108192078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200431631	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	108	616	0	ENST00000278616.4:c.6503C>T	p.Ser2168Leu	p.S2168L	ENST00000278616	NM_000051.3	2168	tCg/tTg	45/63	0.151791117870713	2	FACETS	0.863	0.773	0.958	0.431	0.386	0.479	INDETERMINATE	1	TRUE	0	0.26	2		616	963	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351703	89351703	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773132293	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	148	766	0	ENST00000301030.4:c.1247C>T	p.Ala416Val	p.A416V	ENST00000301030	NM_001256183.1	416	gCg/gTg	9/13	0.3	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.26	1		766	947	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582204	189582204	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	45	396	0	ENST00000264731.3:c.763G>A	p.Glu255Lys	p.E255K	ENST00000264731	NM_003722.4	255	Gag/Aag	5/14	1	2	FACETS	0.828	0.697	0.973	0.828	0.697	0.973	CLONAL	1	TRUE	1	0.26	2		396	418	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11276260	11276260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	62	474	0	ENST00000361445.4:c.3062C>T	p.Ser1021Phe	p.S1021F	ENST00000361445	NM_004958.3	1021	tCc/tTc	20/58	1	2	FACETS	0.828	0.715	0.95	0.828	0.715	0.95	CLONAL	1	TRUE	1	0.26	2		474	576	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649578	206649578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553385247	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	83	578	0	ENST00000367120.3:c.413C>T	p.Pro138Leu	p.P138L	ENST00000367120	NM_014002.3	138	cCg/cTg	6/22	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.26	2		578	620	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670428	246670428	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	116	528	0	ENST00000388985.4:c.92T>A	p.Phe31Tyr	p.F31Y	ENST00000388985		31	tTc/tAc	1/12	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.26	2		528	657	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612035	43612035	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	91	815	0	ENST00000355710.3:c.2140G>C	p.Asp714His	p.D714H	ENST00000355710	NM_020975.4	714	Gat/Cat	12/20	1	2	FACETS	0.738	0.654	0.829	0.738	0.654	0.829	SUBCLONAL	1	TRUE	1	0.26	2		815	948	SUCCESS
EED	8726	MSKCC	GRCh37	11	85961417	85961417	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	43	275	0	ENST00000263360.6:c.194G>A	p.Arg65Lys	p.R65K	ENST00000263360	NM_003797.3	65	aGg/aAg	2/12	0.151791117870713	2	FACETS	0.757	0.634	0.893	0.378	0.317	0.447	INDETERMINATE	1	TRUE	0	0.26	2		275	437	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359417	118359417	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	62	432	1	ENST00000534358.1:c.4421G>A	p.Trp1474Ter	p.W1474*	ENST00000534358	NM_005933.3	1474	tGg/tAg	11/36	0.3	1	FACETS	0.7	0.604	0.803	0.7	0.604	0.803	SUBCLONAL	1	TRUE	0	0.26	1		433	593	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445206	49445206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	76	755	0	ENST00000301067.7:c.2260C>T	p.Pro754Ser	p.P754S	ENST00000301067	NM_003482.3	754	Ccc/Tcc	10/54	1	2	FACETS	0.85	0.745	0.962	0.85	0.745	0.962	CLONAL	1	TRUE	1	0.26	2		755	688	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913065	32913065	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	75	477	0	ENST00000380152.3:c.4573C>T	p.His1525Tyr	p.H1525Y	ENST00000380152		1525	Cat/Tat	11/27	1	2	FACETS	0.975	0.855	1	0.975	0.855	1	CLONAL	1	TRUE	1	0.26	2		477	592	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134879	41134880	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	56	473	2	ENST00000379561.5:c.748_749delinsTT	p.Pro250Phe	p.P250F	ENST00000379561	NM_002015.3	250	CCt/TTt	2/3	1	2	FACETS	0.674	0.577	0.781	0.674	0.577	0.781	SUBCLONAL	1	TRUE	1	0.26	2		475	639	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987004	36987004	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	88	503	0	ENST00000354822.5:c.685C>T	p.His229Tyr	p.H229Y	ENST00000354822	NM_001079668.2	229	Cac/Tac	3/3	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.26	2		503	545	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862774	9862774	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555483666	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	72	517	0	ENST00000330684.3:c.2529G>A	p.Trp843Ter	p.W843*	ENST00000330684	NM_001134407.1	843	tgG/tgA	12/13	1	2	FACETS	0.855	0.747	0.971	0.855	0.747	0.971	CLONAL	1	TRUE	1	0.26	2		517	648	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068441	16068441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	33	105	0	ENST00000268712.3:c.470C>T	p.Ser157Phe	p.S157F	ENST00000268712	NM_006311.3	157	tCc/tTc	5/46	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.26	2		105	175	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670123	29670123	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	80	517	0	ENST00000356175.3:c.7097del	p.Asn2366ThrfsTer9	p.N2366Tfs*9	ENST00000356175	NM_000267.3	2366	Aac/ac	47/57	1	2	FACETS	0.792	0.696	0.895	0.792	0.696	0.895	SUBCLONAL	1	TRUE	1	0.26	2		517	777	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791019	42791019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369933486	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	64	509	0	ENST00000575354.2:c.164C>T	p.Pro55Leu	p.P55L	ENST00000575354	NM_015125.3	55	cCg/cTg	2/20	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.26	2		509	469	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095663	178095663	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	150	585	0	ENST00000397062.3:c.1668A>T	p.Gln556His	p.Q556H	ENST00000397062	NM_006164.4	556	caA/caT	5/5	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.26	2		585	816	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439975	220439975	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	173	884	1	ENST00000243786.2:c.828G>A	p.Trp276Ter	p.W276*	ENST00000243786	NM_002191.3	276	tgG/tgA	2/2	0.151791117870713	2	FACETS	1	0.989	1	0.742	0.683	0.803	INDETERMINATE	1	TRUE	0	0.26	2		885	897	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375087	31375087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	88	632	0	ENST00000328111.2:c.484C>T	p.Pro162Ser	p.P162S	ENST00000328111	NM_006892.3	162	Ccc/Tcc	6/23	1	2	FACETS	0.948	0.84	1	0.948	0.84	1	CLONAL	1	TRUE	1	0.26	2		632	714	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090674	71090674	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	43	312	0	ENST00000318789.4:c.674C>T	p.Pro225Leu	p.P225L	ENST00000318789	NM_032682.5	225	cCa/cTa	11/21	1	2	FACETS	0.753	0.631	0.889	0.753	0.631	0.889	SUBCLONAL	1	TRUE	1	0.26	2		312	439	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169985720	169985720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	84	499	0	ENST00000295797.4:c.382G>A	p.Gly128Ser	p.G128S	ENST00000295797	NM_002740.5	128	Ggt/Agt	5/18	1	2	FACETS	0.85	0.75	0.957	0.85	0.75	0.957	CLONAL	1	TRUE	1	0.26	2		499	760	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456526	189456526	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	53	482	0	ENST00000264731.3:c.287T>G	p.Ile96Ser	p.I96S	ENST00000264731	NM_003722.4	96	aTc/aGc	3/14	1	2	FACETS	0.688	0.586	0.799	0.688	0.586	0.799	SUBCLONAL	1	TRUE	1	0.26	2		482	593	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1978387	1978388	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	48	636	1	ENST00000382891.5:c.3807_3808delinsTT	p.Leu1270Phe	p.L1270F	ENST00000382891	NM_133335.3	1269	ggCCtt/ggTTtt	21/22	1	2	FACETS	0.579	0.488	0.679	0.579	0.488	0.679	SUBCLONAL	1	TRUE	1	0.26	2		637	638	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55960987	55960987	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	63	463	0	ENST00000263923.4:c.2953G>A	p.Asp985Asn	p.D985N	ENST00000263923	NM_002253.2	985	Gat/Aat	21/30	1	2	FACETS	0.914	0.792	1	0.914	0.792	1	CLONAL	1	TRUE	1	0.26	2		463	530	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923661	131923661	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	50	301	0	ENST00000265335.6:c.931C>T	p.His311Tyr	p.H311Y	ENST00000265335		311	Cac/Tac	7/25	1	2	FACETS	0.882	0.75	1	0.882	0.75	1	CLONAL	1	TRUE	1	0.26	2		301	436	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459687	149459687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	71	750	0	ENST00000286301.3:c.520G>A	p.Asp174Asn	p.D174N	ENST00000286301	NM_005211.3	174	Gac/Aac	4/22	1	2	FACETS	0.724	0.631	0.825	0.724	0.631	0.825	SUBCLONAL	1	TRUE	1	0.26	2		750	754	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499656	149499656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	80	478	0	ENST00000261799.4:c.2617G>A	p.Glu873Lys	p.E873K	ENST00000261799	NM_002609.3	873	Gag/Aag	19/23	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.26	2		478	573	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523660	176523660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	91	741	0	ENST00000292408.4:c.2071C>T	p.Pro691Ser	p.P691S	ENST00000292408	NM_213647.1	691	Cct/Tct	16/18	1	2	FACETS	0.838	0.743	0.94	0.838	0.743	0.94	CLONAL	1	TRUE	1	0.26	2		741	835	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681786	30681786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139461560	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	74	585	0	ENST00000376406.3:c.311C>T	p.Pro104Leu	p.P104L	ENST00000376406	NM_014641.2	104	cCt/cTt	3/15	1	2	FACETS	0.769	0.673	0.873	0.769	0.673	0.873	SUBCLONAL	1	TRUE	1	0.26	2		585	740	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042188	6042188	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	69	624	0	ENST00000265849.7:c.433C>T	p.Gln145Ter	p.Q145*	ENST00000265849	NM_000535.5	145	Cag/Tag	5/15	1	2	FACETS	0.728	0.633	0.831	0.728	0.633	0.831	SUBCLONAL	1	TRUE	1	0.26	2		624	729	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266472	55266472	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs961150162	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	66	599	0	ENST00000275493.2:c.2764G>A	p.Glu922Lys	p.E922K	ENST00000275493	NM_005228.3	922	Gag/Aag	23/28	1	2	FACETS	0.741	0.643	0.848	0.741	0.643	0.848	SUBCLONAL	1	TRUE	1	0.26	2		599	685	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851969	128851969	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	57	691	0	ENST00000249373.3:c.2041G>A	p.Glu681Lys	p.E681K	ENST00000249373	NM_005631.4	681	Gag/Aag	12/12	0.202101175497855	3	FACETS	0.692	0.593	0.801	0.346	0.296	0.401	SUBCLONAL	1	TRUE	1	0.26	3		691	716	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523566	148523566	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	41	287	0	ENST00000320356.2:c.887T>C	p.Leu296Pro	p.L296P	ENST00000320356	NM_004456.4	296	cTa/cCa	8/20	0.202101175497855	3	FACETS	0.968	0.809	1	0.484	0.404	0.573	CLONAL	1	TRUE	1	0.26	3		287	368	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500842	8500842	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	63	583	0	ENST00000356435.5:c.2040G>A	p.Trp680Ter	p.W680*	ENST00000356435		680	tgG/tgA	13/35	0.3	1	FACETS	0.748	0.647	0.857	0.748	0.647	0.857	SUBCLONAL	1	TRUE	0	0.26	1		583	564	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500871	8500871	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	54	610	0	ENST00000356435.5:c.2011A>T	p.Lys671Ter	p.K671*	ENST00000356435		671	Aaa/Taa	13/35	0.3	1	FACETS	0.628	0.537	0.729	0.628	0.537	0.729	SUBCLONAL	1	TRUE	0	0.26	1		610	575	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128305427	128305427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	91	647	0	ENST00000265960.3:c.869C>T	p.Ser290Phe	p.S290F	ENST00000265960	NM_001006617.1	290	tCc/tTc	7/12	1	2	FACETS	0.814	0.722	0.913	0.814	0.722	0.913	CLONAL	1	TRUE	1	0.26	2		647	860	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938968	76938968	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	101	682	1	ENST00000373344.5:c.1780T>A	p.Ser594Thr	p.S594T	ENST00000373344	NM_000489.3	594	Tcc/Acc	9/35	0.3	1	FACETS	0.828	0.74	0.923	0.828	0.74	0.923	CLONAL	1	TRUE	0	0.26	1		683	816	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538296	9538298	+	missense_variant	Missense_Mutation	TNP	CCC	CCC	TCT	novel	NA	P-0033935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	86	545	0	ENST00000353224.5:c.1700_1702delinsAGA	p.Arg567_Asp568delinsLysAsn	p.R567_D568delinsKN	ENST00000353224	NM_177990.2	567	aGGGac/aAGAac	7/10	1	2	FACETS	0.83	0.734	0.934	0.83	0.734	0.934	CLONAL	1	TRUE	1	0.26	2		545	797	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046761	42046761	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	80	518	0	ENST00000219905.7:c.7135C>T	p.Gln2379Ter	p.Q2379*	ENST00000219905	NM_001164273.1	2379	Cag/Tag	18/24	1	2	FACETS	0.789	0.695	0.89	0.789	0.695	0.89	SUBCLONAL	1	TRUE	1	0.32	2		518	634	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575110	64575111	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1555165565	NA	P-0033996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	321	611	0	ENST00000312049.6:c.696dup	p.Lys233GlnfsTer16	p.K233Qfs*16	ENST00000312049	NM_130799.2	232	-/C	4/10	0.747847547250151	1	FACETS	0.975	0.933	1	0.975	0.933	1	CLONAL	1	TRUE	0	0.747847547250151	1		611	551	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505489	25505489	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs769476651	NA	P-0033996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	371	615	0	ENST00000264709.3:c.269A>G	p.Asn90Ser	p.N90S	ENST00000264709	NM_175629.2	90	aAt/aGt	4/23	0.747847547250151	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.747847547250151	1		615	593	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643789	52643789	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	63	707	2	ENST00000394830.3:c.2107C>A	p.Pro703Thr	p.P703T	ENST00000394830	NM_018313.4	703	Ccc/Acc	17/30	0.747847547250151	1	FACETS	0.161	0.138	0.185	0.161	0.138	0.185	SUBCLONAL	1	TRUE	0	0.747847547250151	1		709	657	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0034032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	24	313	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.351	0.275	0.439	0.351	0.275	0.439	SUBCLONAL	1	TRUE	1	0.37120489012916	2		313	368	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106058	8106058	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	75	345	0	ENST00000346208.3:c.878T>A	p.Met293Lys	p.M293K	ENST00000346208		293	aTg/aAg	4/6	1	2	FACETS	0.935	0.823	1	0.935	0.823	1	CLONAL	1	TRUE	1	0.37120489012916	2		345	432	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168771	56168771	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	110	370	0	ENST00000399503.3:c.1625del	p.Thr542IlefsTer15	p.T542Ifs*15	ENST00000399503	NM_005921.1	542	aCt/at	9/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.37120489012916	2		370	514	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174843	56174862	+	frameshift_variant	Frame_Shift_Del	DEL	CACAGTTTAGCGGAAAGAAT	CACAGTTTAGCGGAAAGAAT	-	novel	NA	P-0034032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	57	332	0	ENST00000399503.3:c.2004_2023del	p.His668GlnfsTer22	p.H668Qfs*22	ENST00000399503	NM_005921.1	668	CACAGTTTAGCGGAAAGAATc/c	11/20	1	2	FACETS	0.676	0.581	0.78	0.676	0.581	0.78	SUBCLONAL	1	TRUE	1	0.37120489012916	2		332	454	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0034035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	18	395	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.503157059143374	2	FACETS	0.174	0.131	0.226	0.087	0.065	0.113	SUBCLONAL	1	TRUE	0	0.532593465779585	2		396	388	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78931513	78931513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750857501	NA	P-0034035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	161	397	1	ENST00000306801.3:c.3460C>T	p.Arg1154Cys	p.R1154C	ENST00000306801	NM_020761.2	1154	Cgt/Tgt	29/34	0.471000519542305	4	FACETS	0.965	0.893	1	0.965	0.893	1	CLONAL	2	TRUE	2	0.532593465779585	4		398	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576908	7576908	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	57	620	0	ENST00000269305.4:c.938del	p.Ser313ThrfsTer32	p.S313Tfs*32	ENST00000269305	NM_001126112.2	313	aGc/ac	9/11	1	2	FACETS	0.808	0.695	0.93	1	0.971	1	CLONAL	2	TRUE	1	0.17	2		620	415	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737116	145737116	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034080-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	73	595	0	ENST00000428558.2:c.3450G>C	p.Arg1150Ser	p.R1150S	ENST00000428558	NM_004260.3	1150	agG/agC	21/22	1	2	FACETS	0.414	0.361	0.471	0.414	0.361	0.471	SUBCLONAL	1	TRUE	1	0.42	2		595	840	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555526097	NA	P-0034086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	144	936	0	ENST00000269305.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000269305	NM_001126112.2	167	Cag/Tag	5/11	0.15794567830581	2	FACETS	1	0.985	1	0.697	0.635	0.762	CLONAL	1	TRUE	0	0.208978862353359	2		936	989	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392803	118392803	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	63	628	0	ENST00000534358.1:c.11835del	p.Tyr3945Ter	p.Y3945*	ENST00000534358	NM_005933.3	3945	taC/ta	36/36	1	2	FACETS	0.847	0.731	0.972	0.847	0.731	0.972	CLONAL	1	TRUE	1	0.208978862353359	2		628	712	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	39	1027	2	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.306734361892619	1	FACETS	0.29	0.239	0.347	0.29	0.239	0.347	SUBCLONAL	1	TRUE	0	0.306734361892619	1		1029	743	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0034091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	209	1013	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.306734361892619	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.306734361892619	1		1013	930	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578215	28578216	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0034091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	144	715	0	ENST00000241453.7:c.2955_2956del	p.Pro986AlafsTer27	p.P986Afs*27	ENST00000241453	NM_004119.2	985	tcTCcg/tccg	24/24	0.306734361892619	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.306734361892619	1		715	722	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946495	71946495	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs747360226	NA	P-0034091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	132	717	0	ENST00000298229.2:c.2659G>A	p.Glu887Lys	p.E887K	ENST00000298229	NM_001567.3	887	Gag/Aag	23/28	0.306734361892619	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.306734361892619	1		717	610	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881446	48881446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	84	320	0	ENST00000267163.4:c.171del	p.Phe57LeufsTer8	p.F57Lfs*8	ENST00000267163	NM_000321.2	56	gaT/ga	2/27	0.306734361892619	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.306734361892619	1		320	414	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37055934	37055934	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	36	370	0	ENST00000231790.2:c.689A>C	p.Glu230Ala	p.E230A	ENST00000231790	NM_000249.3	230	gAa/gCa	9/19	0.306734361892619	1	FACETS	0.557	0.458	0.666	0.557	0.458	0.666	SUBCLONAL	1	TRUE	0	0.306734361892619	1		370	357	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37055941	37055982	+	inframe_deletion	In_Frame_Del	DEL	ATGTGAGGATAAAACCCTAGCCTTCAAAATGAATGGTTACAT	ATGTGAGGATAAAACCCTAGCCTTCAAAATGAATGGTTACAT	-	novel	NA	P-0034091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	34	386	0	ENST00000231790.2:c.698_739del	p.Cys233_Ile246del	p.C233_I246del	ENST00000231790	NM_000249.3	232	ggATGTGAGGATAAAACCCTAGCCTTCAAAATGAATGGTTACATa/gga	9/19	0.306734361892619	1	FACETS	0.499	0.408	0.601	0.499	0.408	0.601	SUBCLONAL	1	TRUE	0	0.306734361892619	1		386	376	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70362068	70362068	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	novel	NA	P-0034091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	52	503	0	ENST00000374080.3:c.6534A>G	p.Ter2178TrpextTer18	p.*2178Wext*18	ENST00000374080		2178	tgA/tgG	45/45	1	1	FACETS	0.538	0.458	0.625	0.538	0.458	0.625	SUBCLONAL	1	TRUE	0	0.306734361892619	1		503	534	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0034092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	193	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.124375622052399	6	FACETS	1	0.963	1			1	INDETERMINATE	2	TRUE	NA	0.537205593564412	6		539	705	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249510	153249510	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1157879635	NA	P-0034092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	273	673	0	ENST00000281708.4:c.1268G>T	p.Gly423Val	p.G423V	ENST00000281708	NM_033632.3	423	gGa/gTa	9/12	0.46664191386187	4	FACETS	0.931	0.877	0.987	0.931	0.877	0.987	CLONAL	2	TRUE	2	0.537205593564412	4		673	839	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0034092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	141	328	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	0.528776578146792	3	FACETS	0.791	0.727	0.856	0.791	0.727	0.856	SUBCLONAL	2	TRUE	1	0.537205593564412	3		328	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863224683	NA	P-0034092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	543	945	0	ENST00000269305.4:c.388C>T	p.Leu130Phe	p.L130F	ENST00000269305	NM_001126112.2	130	Ctc/Ttc	5/11	0.537205593564412	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.537205593564412	2		945	943	SUCCESS
APC	324	MSKCC	GRCh37	5	112164565	112164566	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1554082091	NA	P-0034092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	65	260	0	ENST00000257430.4:c.1643dup	p.Leu548PhefsTer12	p.L548Ffs*12	ENST00000257430	NM_000038.5	547	gtt/gTtt	14/16	0.528776578146792	3	FACETS	0.855	0.746	0.972	0.428	0.373	0.486	CLONAL	1	TRUE	1	0.537205593564412	3		260	359	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370254	40370254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750053820	NA	P-0034092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	194	763	1	ENST00000293328.3:c.1084G>A	p.Val362Met	p.V362M	ENST00000293328	NM_012448.3	362	Gtg/Atg	9/19	0.525267728017407	3	FACETS	0.994	0.92	1	0.497	0.46	0.535	CLONAL	1	TRUE	1	0.537205593564412	3		764	922	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411832	63411832	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0034092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	455	559	0	ENST00000330258.3:c.1335T>G	p.Tyr445Ter	p.Y445*	ENST00000330258	NM_152424.3	445	taT/taG	2/2	0.432733496257841	2	FACETS	0.861	0.834	0.887			1	CLONAL	3	TRUE	NA	0.537205593564412	2		559	656	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0034094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	483	588	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	0.825884855272367	4	FACETS	0.876	0.84	0.913	0.876	0.84	0.913	CLONAL	2	TRUE	2	0.86668368861943	4		588	1187	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004281	29004281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	292	372	0	ENST00000282397.4:c.1012C>T	p.His338Tyr	p.H338Y	ENST00000282397	NM_002019.4	338	Cat/Tat	8/30	0.865052251279462	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.86668368861943	2		372	337	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814209	76814209	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	184	226	0	ENST00000373344.5:c.6435C>G	p.Ile2145Met	p.I2145M	ENST00000373344	NM_000489.3	2145	atC/atG	29/35	0.851375226593836	2	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.86668368861943	2		226	378	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0034097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	67	437	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.28	2		437	473	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654643	67654643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs968244943	NA	P-0034097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	52	755	1	ENST00000264010.4:c.1130G>A	p.Arg377His	p.R377H	ENST00000264010	NM_006565.3	377	cGt/cAt	6/12	1	2	FACETS	0.47	0.399	0.548	0.47	0.399	0.548	SUBCLONAL	1	TRUE	1	0.28	2		756	790	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247367	153247367	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747241612	NA	P-0034097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	31	284	0	ENST00000281708.4:c.1435C>G	p.Arg479Gly	p.R479G	ENST00000281708	NM_033632.3	479	Cga/Gga	10/12	1	2	FACETS	0.748	0.607	0.907	0.748	0.607	0.907	CLONAL	1	TRUE	1	0.28	2		284	296	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023126	27023126	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	14	84	0	ENST00000324856.7:c.232G>T	p.Glu78Ter	p.E78*	ENST00000324856	NM_006015.4	78	Gag/Tag	1/20	1	2	FACETS	0.971	0.71	1	0.971	0.71	1	CLONAL	1	TRUE	1	0.28	2		84	103	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106561	27106561	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	113	897	0	ENST00000324856.7:c.6172G>T	p.Glu2058Ter	p.E2058*	ENST00000324856	NM_006015.4	2058	Gaa/Taa	20/20	1	2	FACETS	0.931	0.837	1	0.931	0.837	1	CLONAL	1	TRUE	1	0.28	2		897	867	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717665	89717665	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	92	760	0	ENST00000371953.3:c.690del	p.Thr232HisfsTer24	p.T232Hfs*24	ENST00000371953	NM_000314.4	230	ggA/gg	7/9	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.28	2		760	656	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202690	108202690	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	39	451	0	ENST00000278616.4:c.7714del	p.Leu2572Ter	p.L2572*	ENST00000278616	NM_000051.3	2572	Ctg/tg	52/63	1	2	FACETS	0.645	0.535	0.768	0.645	0.535	0.768	SUBCLONAL	1	TRUE	1	0.28	2		451	432	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927983	178927988	+	inframe_deletion	In_Frame_Del	DEL	CCATTG	CCATTG	-	novel	NA	P-0034097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	34	458	0	ENST00000263967.3:c.1261_1266del	p.Pro421_Leu422del	p.P421_L422del	ENST00000263967	NM_006218.2	421	CCATTG/-	8/21	1	2	FACETS	0.655	0.535	0.788	0.655	0.535	0.788	SUBCLONAL	1	TRUE	1	0.28	2		458	371	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	226	349	0				ENST00000310581	NM_198253.2	-/1132			0.347871708105594	4	FACETS	0.99	0.927	1	0.99	0.927	1	CLONAL	2	TRUE	2	0.498713433275994	4		349	686	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0034098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	145	590	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.498713433275994	3	FACETS	0.998	0.912	1	0.499	0.456	0.544	CLONAL	1	TRUE	1	0.498713433275994	3		590	728	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023769	27023769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	329	547	3	ENST00000324856.7:c.879del	p.Thr294ProfsTer69	p.T294Pfs*69	ENST00000324856	NM_006015.4	292	aCc/ac	1/20	0.453963805634121	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.498713433275994	4		550	952	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692775	89692775	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554898053	NA	P-0034098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	276	495	0	ENST00000371953.3:c.259C>T	p.Gln87Ter	p.Q87*	ENST00000371953	NM_000314.4	87	Caa/Taa	5/9	0.498713433275994	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.498713433275994	3		495	682	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692895	89692895	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs587781255	NA	P-0034098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	129	506	0	ENST00000371953.3:c.379G>T	p.Gly127Ter	p.G127*	ENST00000371953	NM_000314.4	127	Gga/Tga	5/9	0.498713433275994	3	FACETS	1	0.925	1	0.51	0.463	0.558	CLONAL	1	TRUE	1	0.498713433275994	3		506	634	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374828	149374828	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	720	565	0	ENST00000360632.3:c.266C>G	p.Ser89Trp	p.S89W	ENST00000360632	NM_015472.4	89	tCg/tGg	2/7	0.498713433275994	4	FACETS	0.98	0.954	1	1	0.997	1	CLONAL	4	TRUE	1	0.498713433275994	4		565	1104	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0034099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	191	851	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.418671244114045	1	FACETS	0.403	0.374	0.434	0.403	0.374	0.434	INDETERMINATE	1	TRUE	0	0.784405887794171	1		851	734	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0034099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	188	558	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.908	0.845	0.972	0.908	0.845	0.972	CLONAL	1	TRUE	1	0.784405887794171	2		558	528	SUCCESS
MET	4233	MSKCC	GRCh37	7	116409789	116409789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761243391	NA	P-0034099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	90	339	2	ENST00000397752.3:c.2674G>A	p.Val892Ile	p.V892I	ENST00000397752	NM_000245.2	892	Gtt/Att	12/21	0.766116863686534	3	FACETS	0.617	0.549	0.689	0.308	0.274	0.345	SUBCLONAL	1	TRUE	1	0.784405887794171	3		341	518	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240690	55240690	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs772046081	NA	P-0034099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17323	7711	952	7	ENST00000275493.2:c.1934C>G	p.Ser645Cys	p.S645C	ENST00000275493	NM_005228.3	645	tCc/tGc	17/28	0.784405887794171	32	FACETS	1	0.991	1	0.323	0.319	0.328	CLONAL	10	TRUE	1	0.784405887794171	32		959	25034	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0034100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	48	432	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.13	2		432	718	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0034100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	32	868	1	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	1	2	FACETS	0.552	0.446	0.673	0.552	0.446	0.673	SUBCLONAL	1	TRUE	1	0.13	2		869	892	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0034111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	86	432	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.0445165544926047	3	FACETS	0.99	0.877	1	0.495	0.438	0.555	INDETERMINATE	1	TRUE	1	0.336058250115204	3		432	604	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223059	1223059	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913325	NA	P-0034111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	170	670	0	ENST00000326873.7:c.996G>A	p.Trp332Ter	p.W332*	ENST00000326873	NM_000455.4	332	tgG/tgA	8/10	0.336058250115204	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.336058250115204	1		670	738	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006897	47006897	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	113	763	2	ENST00000377604.3:c.17G>A	p.Arg6His	p.R6H	ENST00000377604	NM_001204468.1	6	cGt/cAt	2/24	1	2	FACETS	0.886	0.798	0.98	0.886	0.798	0.98	CLONAL	1	TRUE	1	0.336058250115204	2		765	759	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508804	29508804	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1060500274	NA	P-0034111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	57	420	0	ENST00000356175.3:c.730+1G>T		p.X244_splice	ENST00000356175	NM_000267.3	244			1	2	FACETS	0.817	0.703	0.941	0.817	0.703	0.941	CLONAL	1	TRUE	1	0.336058250115204	2		420	415	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982309	201982309	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0034111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	287	641	0	ENST00000359651.3:c.689-1G>T		p.X230_splice	ENST00000359651		230			0.247386959779835	2	FACETS	0.95	0.896	1	0.95	0.896	1	CLONAL	2	TRUE	0	0.336058250115204	2		641	899	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100321	8100321	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	147	731	0	ENST00000346208.3:c.296del	p.Gly99AlafsTer96	p.G99Afs*96	ENST00000346208		99	Ggc/gc	3/6	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.336058250115204	2		731	667	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701847	43701847	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	74	285	0	ENST00000382044.4:c.5398C>T	p.Gln1800Ter	p.Q1800*	ENST00000382044	NM_001141980.1	1800	Cag/Tag	25/28	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.336058250115204	2		285	433	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610288	10610301	+	frameshift_variant	Frame_Shift_Del	DEL	TAGGCGAATTCAAT	TAGGCGAATTCAAT	-	novel	NA	P-0034111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	181	839	0	ENST00000171111.5:c.409_422del	p.Ile137HisfsTer32	p.I137Hfs*32	ENST00000171111	NM_203500.1	137	ATTGAATTCGCCTAc/c	2/6	0.336058250115204	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.336058250115204	1		839	797	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121204	11121204	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0034111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	144	565	0	ENST00000358026.2:c.2271C>G	p.Tyr757Ter	p.Y757*	ENST00000358026	NM_001128849.1	757	taC/taG	15/36	0.336058250115204	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.336058250115204	1		565	557	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726610	41726610	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	136	574	0	ENST00000301178.4:c.155G>T	p.Gly52Val	p.G52V	ENST00000301178	NM_021913.4	52	gGc/gTc	2/20	0.0381243010146151	3	FACETS	1	0.982	1	0.653	0.594	0.714	INDETERMINATE	1	TRUE	1	0.336058250115204	3		574	724	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855600	45855600	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs557601608	NA	P-0034111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	95	564	0	ENST00000391945.4:c.2057G>T	p.Arg686Leu	p.R686L	ENST00000391945	NM_000400.3	686	cGt/cTt	22/23	0.0381243010146151	3	FACETS	1	0.954	1	0.565	0.504	0.63	INDETERMINATE	1	TRUE	1	0.336058250115204	3		564	584	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143348	30143348	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1031804606	NA	P-0034111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	89	454	1	ENST00000389048.3:c.178G>T	p.Val60Leu	p.V60L	ENST00000389048	NM_004304.4	60	Gtg/Ttg	1/29	1	2	FACETS	0.941	0.836	1	0.941	0.836	1	CLONAL	1	TRUE	1	0.336058250115204	2		455	563	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184794	32184794	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	108	543	0	ENST00000375023.3:c.1789C>A	p.Pro597Thr	p.P597T	ENST00000375023	NM_004557.3	597	Cca/Aca	11/30	1	2	FACETS	0.997	0.896	1	0.997	0.896	1	CLONAL	1	TRUE	1	0.336058250115204	2		543	645	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2972183	2972183	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	117	682	0	ENST00000396946.4:c.1556C>A	p.Thr519Lys	p.T519K	ENST00000396946	NM_032415.4	519	aCa/aAa	11/25	1	2	FACETS	0.777	0.7	0.859	0.777	0.7	0.859	SUBCLONAL	1	TRUE	1	0.336058250115204	2		682	896	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248120	110248120	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	85	474	0	ENST00000374672.4:c.1352C>A	p.Thr451Lys	p.T451K	ENST00000374672	NM_004235.4	451	aCg/aAg	5/5	1	2	FACETS	0.872	0.772	0.979	0.872	0.772	0.979	CLONAL	1	TRUE	1	0.336058250115204	2		474	580	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409887	63409887	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	60	438	2	ENST00000330258.3:c.3280C>A	p.His1094Asn	p.H1094N	ENST00000330258	NM_152424.3	1094	Cac/Aac	2/2	1	2	FACETS	0.88	0.76	1	0.88	0.76	1	CLONAL	1	TRUE	1	0.336058250115204	2		440	406	SUCCESS
AR	367	MSKCC	GRCh37	X	66766042	66766042	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	141	795	0	ENST00000374690.3:c.1054G>T	p.Ala352Ser	p.A352S	ENST00000374690	NM_000044.3	352	Gca/Tca	1/8	1	2	FACETS	0.999	0.91	1	0.999	0.91	1	CLONAL	1	TRUE	1	0.336058250115204	2		795	840	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184095	123184095	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	82	518	0	ENST00000218089.9:c.953T>C	p.Met318Thr	p.M318T	ENST00000218089	NM_001042749.1	318	aTg/aCg	11/35	1	2	FACETS	0.923	0.815	1	0.923	0.815	1	CLONAL	1	TRUE	1	0.336058250115204	2		518	529	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0034138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	61	384	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.963	0.835	1	0.963	0.835	1	CLONAL	1	TRUE	1	0.338726477735649	2		384	374	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0034138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	139	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.338726477735649	3	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	1	0.338726477735649	3		539	468	SUCCESS
APC	324	MSKCC	GRCh37	5	112175749	112175756	+	frameshift_variant	Frame_Shift_Del	DEL	TACTTTAT	TACTTTAT	-	novel	NA	P-0034138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	71	234	0	ENST00000257430.4:c.4461_4468del	p.Leu1488PhefsTer23	p.L1488Ffs*23	ENST00000257430	NM_000038.5	1486	gaTACTTTATta/gata	16/16	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.338726477735649	2		234	343	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476286	88476286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	30	482	0	ENST00000360948.2:c.1846G>A	p.Val616Ile	p.V616I	ENST00000360948	NM_001012338.2	616	Gtc/Atc	15/19	1	2	FACETS	0.437	0.352	0.534	0.437	0.352	0.534	SUBCLONAL	1	TRUE	1	0.338726477735649	2		482	405	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866987936	NA	P-0034138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	30	187	0	ENST00000281708.4:c.1436G>T	p.Arg479Leu	p.R479L	ENST00000281708	NM_033632.3	479	cGa/cTa	10/12	1	2	FACETS	0.751	0.608	0.91	0.751	0.608	0.91	CLONAL	1	TRUE	1	0.338726477735649	2		187	236	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	26	443	0	ENST00000342988.3:c.1081del	p.Arg361AlafsTer23	p.R361Afs*23	ENST00000342988	NM_005359.5	361	Cgc/gc	9/12	1	2	FACETS	0.376	0.297	0.467	0.376	0.297	0.467	SUBCLONAL	1	TRUE	1	0.338726477735649	2		443	408	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212397	5212397	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	41	609	0	ENST00000357368.4:c.4720G>T	p.Val1574Phe	p.V1574F	ENST00000357368	NM_002850.3	1574	Gtc/Ttc	31/38	0.338726477735649	3	FACETS	0.481	0.4	0.571	0.24	0.2	0.286	SUBCLONAL	1	TRUE	1	0.338726477735649	3		609	589	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223060	5223060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1379163672	NA	P-0034138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	55	447	0	ENST00000357368.4:c.2743G>A	p.Glu915Lys	p.E915K	ENST00000357368	NM_002850.3	915	Gag/Aag	18/38	0.338726477735649	3	FACETS	0.869	0.745	1	0.434	0.372	0.502	CLONAL	1	TRUE	1	0.338726477735649	3		447	437	SUCCESS
APC	324	MSKCC	GRCh37	5	112155004	112155010	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTCAT	AGCTCAT	-	novel	NA	P-0034138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	59	442	0	ENST00000257430.4:c.1275_1281del	p.Ala426AsnfsTer26	p.A426Nfs*26	ENST00000257430	NM_000038.5	425	gaAGCTCAT/ga	10/16	1	2	FACETS	0.72	0.62	0.828	0.72	0.62	0.828	SUBCLONAL	1	TRUE	1	0.338726477735649	2		442	484	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127164	22127164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057519911	NA	P-0034140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	41	389	0	ENST00000215832.6:c.964G>A	p.Glu322Lys	p.E322K	ENST00000215832	NM_002745.4	322	Gag/Aag	7/9	1	2	FACETS	0.524	0.438	0.619	0.524	0.438	0.619	SUBCLONAL	1	TRUE	1	0.491889301431484	2		389	318	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732996	30732996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893809	NA	P-0034140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	73	318	1	ENST00000295754.5:c.1609C>T	p.Arg537Cys	p.R537C	ENST00000295754	NM_003242.5	537	Cgc/Tgc	7/7	0.491356017207285	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.491889301431484	1		319	201	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385324	4385324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	78	248	0	ENST00000261254.3:c.349C>T	p.Pro117Ser	p.P117S	ENST00000261254	NM_001759.3	117	Ccg/Tcg	2/5	NA	2	FACETS	1	0.923	1			1	INDETERMINATE	1	TRUE	NA	0.491889301431484	2		248	302	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424114	49424114	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	29	560	0	ENST00000301067.7:c.13948G>T	p.Glu4650Ter	p.E4650*	ENST00000301067	NM_003482.3	4650	Gag/Tag	42/54	1	2	FACETS	0.245	0.196	0.3	0.245	0.196	0.3	SUBCLONAL	1	TRUE	1	0.491889301431484	2		560	482	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524373	187524373	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs777434907	NA	P-0034140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	123	430	0	ENST00000441802.2:c.11307del	p.Phe3769LeufsTer2	p.F3769Lfs*2	ENST00000441802	NM_005245.3	3769	ttT/tt	19/27	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.491889301431484	2		430	462	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123891	46123891	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0034141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	121	272	0	ENST00000334344.6:c.157A>T	p.Arg53Ter	p.R53*	ENST00000334344	NM_152641.2	53	Aga/Tga	2/21	0.197296839467474	3	FACETS	1	0.956	1	0.72	0.656	0.785	INDETERMINATE	2	TRUE	0	0.332531044627551	3		272	393	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839735	42839735	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	59	422	0	ENST00000398585.3:c.1504T>C	p.Cys502Arg	p.C502R	ENST00000398585	NM_001135099.1	502	Tgt/Cgt	13/14	0.187604989170423	3	FACETS	0.603	0.518	0.696	0.302	0.259	0.348	INDETERMINATE	1	TRUE	1	0.332531044627551	3		422	686	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	52	556	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.803	0.684	0.933	0.803	0.684	0.933	CLONAL	1	TRUE	1	0.270349597855211	2		557	479	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	99	757	5	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.974	0.869	1	0.974	0.869	1	CLONAL	1	TRUE	1	0.270349597855211	2		762	752	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158637068	158637069	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CA	CA	-	rs141073095	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	92	876	3	ENST00000263640.3:c.111_112del	p.Cys37Ter	p.C37*	ENST00000263640	NM_001105.4	37	tgTGaa/tgaa	4/11	1	2	FACETS	0.804	0.713	0.9	0.804	0.713	0.9	CLONAL	1	TRUE	1	0.270349597855211	2		879	847	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9770626	9770626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761349863	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	68	786	1	ENST00000377346.4:c.113G>A	p.Arg38His	p.R38H	ENST00000377346	NM_005026.3	38	cGc/cAc	3/24	0.253656701551886	3	FACETS	0.623	0.54	0.712	0.311	0.27	0.356	SUBCLONAL	1	TRUE	1	0.270349597855211	3		787	917	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577525	7577527	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	157	995	0	ENST00000269305.4:c.754_756del	p.Leu252del	p.L252del	ENST00000269305	NM_001126112.2	252	CTC/-	7/11	0.270349597855211	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.270349597855211	1		995	830	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803183	1803183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764712450	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	60	1085	5	ENST00000260795.2:c.535G>A	p.Ala179Thr	p.A179T	ENST00000260795		179	Gct/Act	4/17	1	2	FACETS	0.43	0.369	0.497	0.43	0.369	0.497	SUBCLONAL	1	TRUE	1	0.270349597855211	2		1090	1032	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533517	63533517	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555577625	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	70	1028	3	ENST00000307078.5:c.1637del	p.Gly546AlafsTer143	p.G546Afs*143	ENST00000307078	NM_004655.3	546	gGc/gc	6/11	1	2	FACETS	0.592	0.515	0.675	0.592	0.515	0.675	SUBCLONAL	1	TRUE	1	0.270349597855211	2		1031	875	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779701	3779701	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	45	1063	1	ENST00000262367.5:c.5347T>C	p.Cys1783Arg	p.C1783R	ENST00000262367	NM_004380.2	1783	Tgc/Cgc	31/31	0.270349597855211	1	FACETS	0.371	0.311	0.439	0.371	0.311	0.439	SUBCLONAL	1	TRUE	0	0.270349597855211	1		1064	775	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821344	72821344	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	56	540	1	ENST00000268489.5:c.10831del	p.His3611ThrfsTer83	p.H3611Tfs*83	ENST00000268489	NM_006885.3	3611	Cac/ac	10/10	0.270349597855211	1	FACETS	0.857	0.736	0.988	0.857	0.736	0.988	CLONAL	1	TRUE	0	0.270349597855211	1		541	418	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655225	45655225	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	47	1007	0	ENST00000407780.3:c.627del	p.Ser210AlafsTer2	p.S210Afs*2	ENST00000407780	NM_001283052.1	209	ccC/cc	4/7	0.135272563438364	3	FACETS	0.427	0.359	0.503	0.214	0.179	0.252	INDETERMINATE	1	TRUE	1	0.270349597855211	3		1007	924	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196093	138196093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1405321250	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	63	566	0	ENST00000237289.4:c.407G>A	p.Arg136His	p.R136H	ENST00000237289	NM_001270507.1	136	cGc/cAc	3/9	1	2	FACETS	0.762	0.658	0.873	0.762	0.658	0.873	SUBCLONAL	1	TRUE	1	0.270349597855211	2		566	612	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549526	5549526	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	103	1114	1	ENST00000397747.3:c.557del	p.Pro186LeufsTer14	p.P186Lfs*14	ENST00000397747	NM_025239.3	185	Ccc/cc	4/7	1	2	FACETS	0.729	0.651	0.813	0.729	0.651	0.813	SUBCLONAL	1	TRUE	1	0.270349597855211	2		1115	1045	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197072	106197072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	25	518	0	ENST00000380013.4:c.5405C>T	p.Pro1802Leu	p.P1802L	ENST00000380013	NM_001127208.2	1802	cCa/cTa	11/11	1	2	FACETS	0.397	0.312	0.495	0.397	0.312	0.495	SUBCLONAL	1	TRUE	1	0.270349597855211	2		518	466	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258827	16258827	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	64	737	0	ENST00000375759.3:c.6092A>T	p.Lys2031Met	p.K2031M	ENST00000375759	NM_015001.2	2031	aAg/aTg	11/15	0.253656701551886	3	FACETS	0.62	0.535	0.712	0.31	0.267	0.356	SUBCLONAL	1	TRUE	1	0.270349597855211	3		737	867	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261319	16261319	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	68	909	0	ENST00000375759.3:c.8584A>T	p.Thr2862Ser	p.T2862S	ENST00000375759	NM_015001.2	2862	Aca/Tca	11/15	0.253656701551886	3	FACETS	0.64	0.556	0.732	0.32	0.278	0.366	SUBCLONAL	1	TRUE	1	0.270349597855211	3		909	892	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17349143	17349143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs74315368	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	79	934	2	ENST00000375499.3:c.725G>A	p.Arg242His	p.R242H	ENST00000375499	NM_003000.2	242	cGc/cAc	7/8	0.253656701551886	3	FACETS	0.708	0.621	0.802	0.354	0.31	0.401	SUBCLONAL	1	TRUE	1	0.270349597855211	3		936	937	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107131	27107134	+	frameshift_variant	Frame_Shift_Del	DEL	CACT	CACT	-	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	43	876	0	ENST00000324856.7:c.6744_6747del	p.His2248GlnfsTer18	p.H2248Qfs*18	ENST00000324856	NM_006015.4	2248	CACTca/ca	20/20	1	2	FACETS	0.412	0.343	0.488	0.412	0.343	0.488	SUBCLONAL	1	TRUE	1	0.270349597855211	2		876	773	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935399	36935399	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	52	1080	0	ENST00000361632.4:c.1328A>G	p.His443Arg	p.H443R	ENST00000361632		443	cAc/cGc	10/16	1	2	FACETS	0.411	0.349	0.48	0.411	0.349	0.48	SUBCLONAL	1	TRUE	1	0.270349597855211	2		1080	936	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944262	206944262	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	36	699	0	ENST00000423557.1:c.368T>C	p.Leu123Pro	p.L123P	ENST00000423557	NM_000572.2	123	cTa/cCa	3/5	1	2	FACETS	0.385	0.315	0.463	0.385	0.315	0.463	SUBCLONAL	1	TRUE	1	0.270349597855211	2		699	692	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572072	64572072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760683615	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	111	1077	0	ENST00000312049.6:c.1567G>A	p.Ala523Thr	p.A523T	ENST00000312049	NM_130799.2	523	Gct/Act	10/10	1	2	FACETS	0.874	0.784	0.969	0.874	0.784	0.969	CLONAL	1	TRUE	1	0.270349597855211	2		1077	940	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200486	67200486	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	103	1084	0	ENST00000312629.5:c.680A>G	p.His227Arg	p.H227R	ENST00000312629	NM_003952.2	227	cAc/cGc	8/15	1	2	FACETS	0.741	0.661	0.825	0.741	0.661	0.825	SUBCLONAL	1	TRUE	1	0.270349597855211	2		1084	1029	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377094	118377094	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555048446	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	69	589	0	ENST00000534358.1:c.10487T>C	p.Met3496Thr	p.M3496T	ENST00000534358	NM_005933.3	3496	aTg/aCg	27/36	1	2	FACETS	0.947	0.826	1	0.947	0.826	1	CLONAL	1	TRUE	1	0.270349597855211	2		589	539	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444696	49444696	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	81	1265	0	ENST00000301067.7:c.2770T>C	p.Ser924Pro	p.S924P	ENST00000301067	NM_003482.3	924	Tcc/Ccc	10/54	1	2	FACETS	0.654	0.575	0.739	0.654	0.575	0.739	SUBCLONAL	1	TRUE	1	0.270349597855211	2		1265	916	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257251	133257251	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	66	813	0	ENST00000320574.5:c.227A>C	p.Lys76Thr	p.K76T	ENST00000320574	NM_006231.2	76	aAg/aCg	3/49	1	2	FACETS	0.623	0.54	0.713	0.623	0.54	0.713	SUBCLONAL	1	TRUE	1	0.270349597855211	2		813	784	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052669	42052669	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	97	944	0	ENST00000219905.7:c.7340A>G	p.Lys2447Arg	p.K2447R	ENST00000219905	NM_001164273.1	2447	aAg/aGg	20/24	1	2	FACETS	0.905	0.806	1	0.905	0.806	1	CLONAL	1	TRUE	1	0.270349597855211	2		944	793	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748450	43748450	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	92	1151	0	ENST00000382044.4:c.2356T>C	p.Cys786Arg	p.C786R	ENST00000382044	NM_001141980.1	786	Tgc/Cgc	12/28	1	2	FACETS	0.688	0.61	0.772	0.688	0.61	0.772	SUBCLONAL	1	TRUE	1	0.270349597855211	2		1151	989	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636677	2636677	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	34	757	0	ENST00000342085.4:c.1126T>C	p.Tyr376His	p.Y376H	ENST00000342085	NM_002613.4	376	Tat/Cat	11/14	0.270349597855211	1	FACETS	0.359	0.292	0.434	0.359	0.292	0.434	SUBCLONAL	1	TRUE	0	0.270349597855211	1		757	606	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661891	29661891	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	41	867	0	ENST00000356175.3:c.5785A>G	p.Thr1929Ala	p.T1929A	ENST00000356175	NM_000267.3	1929	Act/Gct	39/57	1	2	FACETS	0.374	0.31	0.445	0.374	0.31	0.445	SUBCLONAL	1	TRUE	1	0.270349597855211	2		867	811	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870588	40870588	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	85	1039	0	ENST00000428826.2:c.815A>T	p.Gln272Leu	p.Q272L	ENST00000428826		272	cAg/cTg	9/21	1	2	FACETS	0.606	0.534	0.684	0.606	0.534	0.684	SUBCLONAL	1	TRUE	1	0.270349597855211	2		1039	1037	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533911	63533911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	53	710	0	ENST00000307078.5:c.1243G>A	p.Glu415Lys	p.E415K	ENST00000307078	NM_004655.3	415	Gag/Aag	6/11	1	2	FACETS	0.66	0.562	0.767	0.66	0.562	0.767	SUBCLONAL	1	TRUE	1	0.270349597855211	2		710	594	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207094	1207094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	66	1058	0	ENST00000326873.7:c.182G>A	p.Gly61Asp	p.G61D	ENST00000326873	NM_000455.4	61	gGc/gAc	1/10	0.270349597855211	1	FACETS	0.444	0.385	0.51	0.444	0.385	0.51	SUBCLONAL	1	TRUE	0	0.270349597855211	1		1058	950	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191189	2191189	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	68	1024	0	ENST00000398665.3:c.443T>C	p.Ile148Thr	p.I148T	ENST00000398665	NM_032482.2	148	aTt/aCt	5/28	0.270349597855211	1	FACETS	0.509	0.442	0.582	0.509	0.442	0.582	SUBCLONAL	1	TRUE	0	0.270349597855211	1		1024	855	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290173	15290173	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	92	1035	0	ENST00000263388.2:c.3460+2T>A		p.X1154_splice	ENST00000263388	NM_000435.2	1154			0.270349597855211	1	FACETS	0.842	0.748	0.942	0.842	0.748	0.942	CLONAL	1	TRUE	0	0.270349597855211	1		1035	699	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961504	18961504	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	39	671	0	ENST00000262803.5:c.637T>C	p.Cys213Arg	p.C213R	ENST00000262803	NM_002911.3	213	Tgt/Cgt	5/24	0.270349597855211	1	FACETS	0.492	0.407	0.587	0.492	0.407	0.587	SUBCLONAL	1	TRUE	0	0.270349597855211	1		671	507	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858934	45858934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772572683	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	92	918	0	ENST00000391945.4:c.1532G>A	p.Arg511Gln	p.R511Q	ENST00000391945	NM_000400.3	511	cGg/cAg	16/23	0.270349597855211	1	FACETS	0.734	0.652	0.822	0.734	0.652	0.822	SUBCLONAL	1	TRUE	0	0.270349597855211	1		918	802	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026015	48026015	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765237563	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	45	608	0	ENST00000234420.5:c.893G>A	p.Arg298Gln	p.R298Q	ENST00000234420	NM_000179.2	298	cGa/cAa	4/10	0.123430329863502	5	FACETS	0.636	0.533	0.75			1	INDETERMINATE	1	TRUE	NA	0.270349597855211	5		608	736	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440081	220440081	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	57	1193	0	ENST00000243786.2:c.934C>A	p.Pro312Thr	p.P312T	ENST00000243786	NM_002191.3	312	Cct/Act	2/2	1	2	FACETS	0.433	0.37	0.503	0.433	0.37	0.503	SUBCLONAL	1	TRUE	1	0.270349597855211	2		1193	973	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62322302	62322302	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	97	1035	0	ENST00000360203.5:c.2556+2T>C		p.X852_splice	ENST00000360203	NM_001283009.1	852			1	2	FACETS	0.715	0.636	0.8	0.715	0.636	0.8	SUBCLONAL	1	TRUE	1	0.270349597855211	2		1035	1003	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058710	47058710	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	63	799	0	ENST00000409792.3:c.7568A>C	p.Tyr2523Ser	p.Y2523S	ENST00000409792	NM_014159.6	2523	tAc/tCc	21/21	1	2	FACETS	0.578	0.498	0.664	0.578	0.498	0.664	SUBCLONAL	1	TRUE	1	0.270349597855211	2		799	807	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664808	138664808	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	42	353	1	ENST00000330315.3:c.757G>A	p.Ala253Thr	p.A253T	ENST00000330315	NM_023067.3	253	Gcc/Acc	1/1	1	2	FACETS	0.785	0.656	0.927	0.785	0.656	0.927	CLONAL	1	TRUE	1	0.270349597855211	2		354	396	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1977066	1977066	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	57	1176	1	ENST00000382891.5:c.3565del	p.Thr1189ArgfsTer140	p.T1189Rfs*140	ENST00000382891	NM_133335.3	1187	gAa/ga	20/22	1	2	FACETS	0.423	0.362	0.491	0.423	0.362	0.491	SUBCLONAL	1	TRUE	1	0.270349597855211	2		1177	996	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467373	66467373	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	26	419	0	ENST00000273854.3:c.896del	p.Asn299MetfsTer123	p.N299Mfs*123	ENST00000273854	NM_004439.5	299	aAt/at	3/18	1	2	FACETS	0.517	0.409	0.641	0.517	0.409	0.641	SUBCLONAL	1	TRUE	1	0.270349597855211	2		419	372	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31504699	31504699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1032572786	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	117	1005	0	ENST00000344624.3:c.1631G>A	p.Arg544His	p.R544H	ENST00000344624		544	cGc/cAc	8/33	1	2	FACETS	0.887	0.798	0.981	0.887	0.798	0.981	CLONAL	1	TRUE	1	0.270349597855211	2		1005	976	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591318	67591318	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	30	453	0	ENST00000274335.5:c.1814+2T>C		p.X605_splice	ENST00000274335		605			1	2	FACETS	0.516	0.415	0.63	0.516	0.415	0.63	SUBCLONAL	1	TRUE	1	0.270349597855211	2		453	430	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176666829	176666829	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	35	560	0	ENST00000439151.2:c.4265T>A	p.Phe1422Tyr	p.F1422Y	ENST00000439151	NM_022455.4	1422	tTt/tAt	8/23	1	2	FACETS	0.474	0.388	0.571	0.474	0.388	0.571	SUBCLONAL	1	TRUE	1	0.270349597855211	2		560	546	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519598	137519598	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	63	761	0	ENST00000367739.4:c.1040A>G	p.Glu347Gly	p.E347G	ENST00000367739	NM_000416.2	347	gAa/gGa	7/7	1	2	FACETS	0.546	0.471	0.628	0.546	0.471	0.628	SUBCLONAL	1	TRUE	1	0.270349597855211	2		761	854	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502166	157502166	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	45	620	0	ENST00000346085.5:c.3199C>A	p.Pro1067Thr	p.P1067T	ENST00000346085	NM_020732.3	1067	Cca/Aca	12/20	1	2	FACETS	0.513	0.43	0.605	0.513	0.43	0.605	SUBCLONAL	1	TRUE	1	0.270349597855211	2		620	649	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426869	6426869	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	107	944	0	ENST00000356142.4:c.62T>G	p.Ile21Ser	p.I21S	ENST00000356142	NM_018890.3	21	aTc/aGc	2/7	1	2	FACETS	0.825	0.739	0.917	0.825	0.739	0.917	CLONAL	1	TRUE	1	0.270349597855211	2		944	959	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444467	50444467	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1271291854	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	41	548	0	ENST00000331340.3:c.397A>G	p.Met133Val	p.M133V	ENST00000331340	NM_006060.4	133	Atg/Gtg	4/8	1	2	FACETS	0.604	0.503	0.717	0.604	0.503	0.717	SUBCLONAL	1	TRUE	1	0.270349597855211	2		548	502	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501359	140501359	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	37	400	0	ENST00000288602.6:c.713T>C	p.Val238Ala	p.V238A	ENST00000288602	NM_004333.4	238	gTa/gCa	6/18	1	2	FACETS	0.883	0.731	1	0.883	0.731	1	CLONAL	1	TRUE	1	0.270349597855211	2		400	310	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860160	151860160	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	56	837	0	ENST00000262189.6:c.10502T>A	p.Phe3501Tyr	p.F3501Y	ENST00000262189	NM_170606.2	3501	tTc/tAc	43/59	1	2	FACETS	0.535	0.457	0.62	0.535	0.457	0.62	SUBCLONAL	1	TRUE	1	0.270349597855211	2		837	775	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006062	22006062	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	72	896	2	ENST00000276925.6:c.341G>A	p.Arg114His	p.R114H	ENST00000276925	NM_004936.3	114	cGt/cAt	2/2	1	2	FACETS	0.696	0.607	0.792	0.696	0.607	0.792	SUBCLONAL	1	TRUE	1	0.270349597855211	2		898	765	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397655	139397655	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	59	1010	0	ENST00000277541.6:c.5146T>C	p.Tyr1716His	p.Y1716H	ENST00000277541	NM_017617.3	1716	Tac/Cac	27/34	1	2	FACETS	0.45	0.385	0.52	0.45	0.385	0.52	SUBCLONAL	1	TRUE	1	0.270349597855211	2		1010	971	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932017	39932017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758345075	NA	P-0034172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	28	542	2	ENST00000378444.4:c.2582G>A	p.Arg861His	p.R861H	ENST00000378444	NM_001123385.1	861	cGc/cAc	4/15	1	1	FACETS	0.339	0.27	0.417	0.339	0.27	0.417	SUBCLONAL	1	TRUE	0	0.270349597855211	1		544	529	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380254	25380254	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	392	726	1	ENST00000311936.3:c.204G>T	p.Arg68Ser	p.R68S	ENST00000311936	NM_004985.3	68	agG/agT	3/5	0.287529883021352	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.418235080691823	3		727	992	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851558	134851558	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs770155473	NA	P-0034180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	162	562	0	ENST00000398015.3:c.964G>A	p.Val322Ile	p.V322I	ENST00000398015	NM_004441.4	322	Gtc/Atc	5/16	0.418235080691823	3	FACETS	1	0.988	1	0.723	0.665	0.782	CLONAL	1	TRUE	1	0.418235080691823	3		562	648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747342068	NA	P-0034180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	326	1018	0	ENST00000269305.4:c.394A>G	p.Lys132Glu	p.K132E	ENST00000269305	NM_001126112.2	132	Aag/Gag	5/11	0.306326710440555	2	FACETS	0.827	0.783	0.871	0.827	0.783	0.871	CLONAL	2	TRUE	0	0.418235080691823	2		1018	943	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29662034	29662034	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs876660696	NA	P-0034180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	128	513	0	ENST00000356175.3:c.5928G>A	p.Trp1976Ter	p.W1976*	ENST00000356175	NM_000267.3	1976	tgG/tgA	39/57	0.418235080691823	3	FACETS	1	0.985	1	0.482	0.439	0.527	CLONAL	1	TRUE	0	0.418235080691823	3		513	512	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122771	7122771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202160383	NA	P-0034180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	79	657	0	ENST00000302850.5:c.3383G>A	p.Arg1128His	p.R1128H	ENST00000302850	NM_000208.2	1128	cGc/cAc	19/22	0.373926000193098	3	FACETS	0.574	0.504	0.649	0.287	0.252	0.325	SUBCLONAL	1	TRUE	1	0.418235080691823	3		657	796	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864713	37864713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370959592	NA	P-0034180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	94	714	0	ENST00000269571.5:c.365C>T	p.Pro122Leu	p.P122L	ENST00000269571		122	cCg/cTg	3/27	0.418235080691823	3	FACETS	0.526	0.467	0.59	0.175	0.155	0.197	SUBCLONAL	1	TRUE	0	0.418235080691823	3		714	1033	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729316	41729316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	273	662	0	ENST00000242208.4:c.1213G>A	p.Asp405Asn	p.D405N	ENST00000242208	NM_002192.2	405	Gat/Aat	3/3	0.265620025291604	5	FACETS	1	0.981	1	0.733	0.689	0.778	CLONAL	2	TRUE	2	0.418235080691823	5		662	966	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763927	76763927	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	107	767	0	ENST00000373344.5:c.7381C>A	p.Gln2461Lys	p.Q2461K	ENST00000373344	NM_000489.3	2461	Cag/Aag	35/35	0.287529883021352	3	FACETS	0.719	0.645	0.799	0.36	0.322	0.4	SUBCLONAL	1	TRUE	1	0.418235080691823	3		767	860	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800882	18800882	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	77	632	1	ENST00000266497.5:c.4258G>T	p.Val1420Leu	p.V1420L	ENST00000266497		1420	Gtg/Ttg	31/31	0.418235080691823	1	FACETS	0.756	0.668	0.85	0.756	0.668	0.85	SUBCLONAL	1	TRUE	0	0.418235080691823	1		633	385	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281840	49281840	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	116	861	0	ENST00000282018.3:c.887C>A	p.Ala296Asp	p.A296D	ENST00000282018	NM_020377.2	296	gCc/gAc	1/1	0.168082415599116	2	FACETS	0.687	0.619	0.759	0.344	0.309	0.38	INDETERMINATE	1	TRUE	0	0.418235080691823	2		861	807	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519958	66519958	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0034180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	320	577	0	ENST00000358598.2:c.440+1G>A		p.X147_splice	ENST00000358598	NM_212471.2	147			0.418235080691823	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	0	0.418235080691823	3		577	586	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729271	41729271	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	94	579	0	ENST00000242208.4:c.1258G>T	p.Val420Leu	p.V420L	ENST00000242208	NM_002192.2	420	Gtg/Ttg	3/3	0.265620025291604	5	FACETS	0.888	0.789	0.993	0.296	0.263	0.331	CLONAL	1	TRUE	2	0.418235080691823	5		579	824	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652216	48652216	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	74	593	0	ENST00000376670.3:c.887C>G	p.Thr296Ser	p.T296S	ENST00000376670	NM_002049.3	296	aCc/aGc	6/6	0.287529883021352	3	FACETS	0.646	0.566	0.733	0.323	0.283	0.367	SUBCLONAL	1	TRUE	1	0.418235080691823	3		593	662	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652428	48652428	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	305	906	0	ENST00000376670.3:c.1099C>G	p.Leu367Val	p.L367V	ENST00000376670	NM_002049.3	367	Ctg/Gtg	6/6	0.287529883021352	3	FACETS	0.852	0.804	0.901	0.852	0.804	0.901	CLONAL	2	TRUE	1	0.418235080691823	3		906	1035	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611131	100611131	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	122	774	0	ENST00000308731.7:c.1475G>T	p.Arg492Leu	p.R492L	ENST00000308731	NM_000061.2	492	cGc/cTc	15/19	0.287529883021352	3	FACETS	0.712	0.642	0.785	0.356	0.321	0.393	SUBCLONAL	1	TRUE	1	0.418235080691823	3		774	991	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0034215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	48	432	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.946	0.8	1	0.946	0.8	1	CLONAL	1	TRUE	1	0.19	2		432	534	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221998	1221998	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690945	NA	P-0034215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	63	711	0	ENST00000326873.7:c.913C>T	p.Gln305Ter	p.Q305*	ENST00000326873	NM_000455.4	305	Cag/Tag	7/10	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.19	2		711	606	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977959	131977959	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	63	530	0	ENST00000265335.6:c.3842A>T	p.Glu1281Val	p.E1281V	ENST00000265335		1281	gAa/gTa	25/25	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.19	2		530	540	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249806	39249806	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	57	681	0	ENST00000402219.2:c.1763T>A	p.Phe588Tyr	p.F588Y	ENST00000402219	NM_005633.3	588	tTt/tAt	10/23	1	2	FACETS	0.942	0.808	1	0.942	0.808	1	CLONAL	1	TRUE	1	0.19	2		681	637	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981748	70981748	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	89	967	1	ENST00000276594.2:c.348C>G	p.Ser116Arg	p.S116R	ENST00000276594	NM_024504.3	116	agC/agG	2/8	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.19	2		968	864	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557630	95557630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	183	364	0	ENST00000393063.1:c.5437G>A	p.Glu1813Lys	p.E1813K	ENST00000393063	NM_030621.3	1813	Gag/Aag	26/28	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		364	633	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566116	95566116	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0034218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	114	226	0	ENST00000393063.1:c.4206+1del		p.X1402_splice	ENST00000393063	NM_030621.3	1402			1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		226	373	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48922000	48922000	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1566187856	NA	P-0034220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	14	336	0	ENST00000267163.4:c.539+1G>A		p.X180_splice	ENST00000267163	NM_000321.2	180			1	2	FACETS	0.916	0.664	1	0.916	0.664	1	CLONAL	1	TRUE	1	0.16	2		336	191	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481405	140481405	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397507473	NA	P-0034220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	32	367	0	ENST00000288602.6:c.1403T>C	p.Phe468Ser	p.F468S	ENST00000288602	NM_004333.4	468	tTt/tCt	11/18	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.16	2		367	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0034221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	515	608	0	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.868434055388682	1	FACETS	0.984	0.958	1	0.984	0.958	1	CLONAL	1	TRUE	0	0.868434055388682	1		608	682	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625601	1625601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554419240	NA	P-0034221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	596	787	2	ENST00000344749.5:c.473G>A	p.Arg158Gln	p.R158Q	ENST00000344749	NM_001136139.2	158	cGg/cAg	7/19	0.373226840681415	1	FACETS	0.52	0.5	0.54	0.52	0.5	0.54	INDETERMINATE	1	TRUE	0	0.868434055388682	1		789	1494	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	161	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.272644207426361	3	FACETS	0.842	0.773	0.914	0.842	0.773	0.914	CLONAL	2	TRUE	1	0.272644207426361	3		493	797	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0034222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	104	879	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.272644207426361	1	FACETS	0.757	0.677	0.842	0.757	0.677	0.842	SUBCLONAL	1	TRUE	0	0.272644207426361	1		879	870	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202741	133202741	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369549727	NA	P-0034222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	139	559	0	ENST00000320574.5:c.6493C>T	p.Arg2165Cys	p.R2165C	ENST00000320574	NM_006231.2	2165	Cgc/Tgc	46/49	0.219234877877036	2	FACETS	0.836	0.763	0.911	0.836	0.763	0.911	CLONAL	2	TRUE	0	0.272644207426361	2		559	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0034225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	273	730	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.405520594167209	2	FACETS	0.978	0.924	1	0.978	0.924	1	CLONAL	2	TRUE	0	0.404949293031797	2		730	689	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743924	40743924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199514226	NA	P-0034236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	53	709	0	ENST00000373198.4:c.3071C>T	p.Thr1024Met	p.T1024M	ENST00000373198	NM_133170.3	1024	aCg/aTg	23/32	0.259393397666681	5	FACETS	0.487	0.414	0.567	0.162	0.138	0.189	INDETERMINATE	1	TRUE	2	0.546240557135125	5		709	725	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115903	8115904	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0034236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	163	599	0	ENST00000346208.3:c.1251dup	p.Thr418HisfsTer89	p.T418Hfs*89	ENST00000346208		417	acc/aCcc	6/6	0.546240557135125	3	FACETS	1	0.978	1	0.585	0.539	0.633	CLONAL	1	TRUE	1	0.546240557135125	3		599	649	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	97	349	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.941	0.844	1	0.941	0.844	1	CLONAL	1	TRUE	1	0.46	2		349	448	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0034237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	84	256	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.46	2		256	363	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0034237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	208	706	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.46	2		706	901	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73108193	73108193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	10	77	1	ENST00000356692.5:c.293C>T	p.Pro98Leu	p.P98L	ENST00000356692		98	cCt/cTt	4/9	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.46	2		78	31	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	97	349	0				ENST00000310581	NM_198253.2	-/1132			0.274288527418009	6	FACETS	1	0.945	1	0.544	0.487	0.605	CLONAL	2	TRUE	2	0.274288527418009	6		349	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0034238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	237	967	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.274288527418009	2	FACETS	0.93	0.869	0.993	0.93	0.869	0.993	CLONAL	2	TRUE	0	0.274288527418009	2		968	929	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	242	972	0	ENST00000269305.4:c.859G>T	p.Glu287Ter	p.E287*	ENST00000269305	NM_001126112.2	287	Gag/Tag	8/11	0.274288527418009	2	FACETS	0.938	0.877	1	0.938	0.877	1	CLONAL	2	TRUE	0	0.274288527418009	2		972	941	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056518	26056518	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	31	282	0	ENST00000343677.2:c.139G>T	p.Ala47Ser	p.A47S	ENST00000343677	NM_005319.3	47	Gct/Tct	1/1	0.274288527418009	3	FACETS	0.846	0.686	1	0.423	0.343	0.513	CLONAL	1	TRUE	1	0.274288527418009	3		282	304	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281758	49281758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777488065	NA	P-0034238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	237	884	0	ENST00000282018.3:c.805G>A	p.Val269Ile	p.V269I	ENST00000282018	NM_020377.2	269	Gtc/Atc	1/1	0.194236661881308	2	FACETS	0.982	0.918	1	0.982	0.918	1	CLONAL	2	TRUE	0	0.274288527418009	2		884	880	SUCCESS
H3C13	653604	MSKCC	GRCh37	1	149784866	149784866	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	23	275	0	ENST00000331491.1:c.371A>G	p.Asp124Gly	p.D124G	ENST00000331491	NM_001123375.2	124	gAc/gGc	1/1	0.257460890190872	4	FACETS	0.732	0.571	0.917	0.244	0.19	0.306	CLONAL	1	TRUE	1	0.274288527418009	4		275	292	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247605	123247605	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	81	665	0	ENST00000358487.5:c.1886C>G	p.Ala629Gly	p.A629G	ENST00000358487	NM_000141.4	629	gCc/gGc	14/18	0.274288527418009	2	FACETS	0.921	0.812	1	0.461	0.406	0.519	CLONAL	1	TRUE	0	0.274288527418009	2		665	641	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316103	14316103	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	44	356	0	ENST00000256196.4:c.322C>G	p.Gln108Glu	p.Q108E	ENST00000256196		108	Caa/Gaa	4/6	1	2	FACETS	0.969	0.816	1	0.969	0.816	1	CLONAL	1	TRUE	1	0.274288527418009	2		356	331	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105611	30105611	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	231	960	2	ENST00000331968.5:c.1075G>A	p.Asp359Asn	p.D359N	ENST00000331968	NM_002742.2	359	Gat/Aat	7/18	0.274288527418009	5	FACETS	1	0.934	1	0.669	0.623	0.717	CLONAL	2	TRUE	2	0.274288527418009	5		962	1185	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863574	68863574	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	218	679	3	ENST00000261769.5:c.2313del	p.Gln771HisfsTer12	p.Q771Hfs*12	ENST00000261769	NM_004360.3	771	caG/ca	15/16	0.274288527418009	2	FACETS	0.981	0.915	1	0.981	0.915	1	CLONAL	2	TRUE	0	0.274288527418009	2		682	810	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315338	30315338	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0034238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	50	435	0	ENST00000322652.5:c.1024-1G>C		p.X342_splice	ENST00000322652	NM_015355.2	342			0.186397399510923	4	FACETS	0.83	0.704	0.968	0.415	0.352	0.484	CLONAL	1	TRUE	2	0.274288527418009	4		435	560	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227019	2227019	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	201	760	0	ENST00000398665.3:c.4499C>A	p.Ser1500Tyr	p.S1500Y	ENST00000398665	NM_032482.2	1500	tCt/tAt	27/28	0.186397399510923	4	FACETS	0.965	0.894	1	0.965	0.894	1	CLONAL	2	TRUE	2	0.274288527418009	4		760	968	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5239019	5239019	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	102	780	0	ENST00000357368.4:c.1760A>G	p.Asn587Ser	p.N587S	ENST00000357368	NM_002850.3	587	aAc/aGc	13/38	0.186397399510923	4	FACETS	0.967	0.863	1	0.484	0.431	0.539	CLONAL	1	TRUE	2	0.274288527418009	4		780	980	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526199	189526199	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	407	696	0	ENST00000264731.3:c.463A>G	p.Thr155Ala	p.T155A	ENST00000264731	NM_003722.4	155	Acc/Gcc	4/14	0.274288527418009	7	FACETS	0.969	0.922	1	0.969	0.922	1	CLONAL	4	TRUE	3	0.274288527418009	7		696	1291	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197118	26197137	+	frameshift_variant	Frame_Shift_Del	DEL	TGATAGTCACTCGCTTGGCG	TGATAGTCACTCGCTTGGCG	-	novel	NA	P-0034238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	52	609	0	ENST00000356476.2:c.342_361del	p.Lys116GlnfsTer?	p.K116Qfs*?	ENST00000356476		114	caCGCCAAGCGAGTGACTATCAtg/catg	1/1	0.274288527418009	3	FACETS	0.657	0.559	0.766	0.329	0.279	0.383	SUBCLONAL	1	TRUE	1	0.274288527418009	3		609	656	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6442006	6442006	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	80	435	0	ENST00000356142.4:c.565G>C	p.Asp189His	p.D189H	ENST00000356142	NM_018890.3	189	Gac/Cac	7/7	0.274288527418009	5	FACETS	0.775	0.684	0.873	0.517	0.456	0.582	SUBCLONAL	2	TRUE	2	0.274288527418009	5		435	531	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339856	116339856	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	132	632	0	ENST00000397752.3:c.718G>C	p.Glu240Gln	p.E240Q	ENST00000397752	NM_000245.2	240	Gag/Cag	2/21	0.274288527418009	3	FACETS	0.929	0.847	1	0.929	0.847	1	CLONAL	2	TRUE	1	0.274288527418009	3		632	589	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152373128	152373128	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	109	589	0	ENST00000359321.1:c.37G>A	p.Glu13Lys	p.E13K	ENST00000359321	NM_005431.1	13	Gag/Aag	1/3	0.274288527418009	3	FACETS	1	0.978	1	0.665	0.597	0.736	CLONAL	1	TRUE	1	0.274288527418009	3		589	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0034240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	284	460	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.962	0.915	1	1	0.996	1	CLONAL	2	TRUE	1	0.541784475279172	2		460	545	SUCCESS
APC	324	MSKCC	GRCh37	5	112163677	112163677	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0034240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	144	355	0	ENST00000257430.4:c.1600A>T	p.Lys534Ter	p.K534*	ENST00000257430	NM_000038.5	534	Aaa/Taa	13/16	0.495617615695934	4	FACETS	0.868	0.798	0.941	0.868	0.798	0.941	CLONAL	2	TRUE	2	0.541784475279172	4		355	472	SUCCESS
APC	324	MSKCC	GRCh37	5	112175198	112175198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	91	218	0	ENST00000257430.4:c.3907C>T	p.Gln1303Ter	p.Q1303*	ENST00000257430	NM_000038.5	1303	Caa/Taa	16/16	0.495617615695934	4	FACETS	0.938	0.845	1	0.938	0.845	1	CLONAL	2	TRUE	2	0.541784475279172	4		218	276	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220147	5220147	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	195	677	0	ENST00000357368.4:c.3568C>T	p.Arg1190Trp	p.R1190W	ENST00000357368	NM_002850.3	1190	Cgg/Tgg	22/38	0.541784475279172	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.541784475279172	3		677	432	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101923	11101923	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502063	NA	P-0034240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	173	795	1	ENST00000358026.2:c.1343G>A	p.Arg448His	p.R448H	ENST00000358026	NM_001128849.1	448	cGc/cAc	8/36	0.541784475279172	3	FACETS	1	0.961	1	0.533	0.492	0.576	CLONAL	1	TRUE	1	0.541784475279172	3		796	761	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220965	36220965	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	91	506	0	ENST00000222270.7:c.5015G>A	p.Cys1672Tyr	p.C1672Y	ENST00000222270	NM_014727.1	1672	tGc/tAc	23/37	0.541784475279172	3	FACETS	0.966	0.862	1	0.483	0.431	0.538	CLONAL	1	TRUE	1	0.541784475279172	3		506	442	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273152	198273152	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	361	772	0	ENST00000335508.6:c.1058T>A	p.Leu353Gln	p.L353Q	ENST00000335508	NM_012433.2	353	cTg/cAg	8/25	0.495617615695934	4	FACETS	0.971	0.922	1	0.971	0.922	1	CLONAL	2	TRUE	2	0.541784475279172	4		772	1058	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245375	153245375	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	347	677	0	ENST00000281708.4:c.1816T>A	p.Trp606Arg	p.W606R	ENST00000281708	NM_033632.3	606	Tgg/Agg	11/12	0.519768468163371	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.541784475279172	2		677	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0034250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	175	756	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.445079306423981	1	FACETS	0.888	0.821	0.958	0.888	0.821	0.958	CLONAL	1	TRUE	0	0.445711517838828	1		756	687	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	422337	422337	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	70	530	0	ENST00000399788.2:c.2921T>C	p.Leu974Ser	p.L974S	ENST00000399788	NM_001042603.1	974	tTa/tCa	20/28	0.231193210696197	6	FACETS	0.781	0.68	0.89			1	INDETERMINATE	1	TRUE	NA	0.445711517838828	6		530	761	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243950	41243950	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs62625307	NA	P-0034250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	147	771	1	ENST00000357654.3:c.3598C>T	p.Gln1200Ter	p.Q1200*	ENST00000357654	NM_007294.3	1200	Cag/Tag	10/23	0.445079306423981	1	FACETS	0.866	0.794	0.941	0.866	0.794	0.941	CLONAL	1	TRUE	0	0.445711517838828	1		772	592	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29196000	29196022	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGATCTCCACAGGACCCCCCTGC	GGATCTCCACAGGACCCCCCTGC	ACAA	novel	NA	P-0034250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	119	745	5	ENST00000240100.2:c.580-4_598delinsTTGT		p.X194_splice	ENST00000240100	NM_001394.6	194		3/4	1	2	FACETS	0.73	0.66	0.805	0.73	0.66	0.805	SUBCLONAL	1	TRUE	1	0.445711517838828	2		750	731	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164769	36164769	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755073984	NA	P-0034253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	39	859	0	ENST00000300305.3:c.1106C>T	p.Ser369Leu	p.S369L	ENST00000300305		369	tCg/tTg	8/8	1	2	FACETS	0.867	0.718	1	0.867	0.718	1	CLONAL	1	TRUE	1	0.17	2		859	529	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0034255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	223	384	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.257183653297999	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.317849314509468	3		384	658	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0034255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	102	460	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.317849314509468	1	FACETS	0.964	0.865	1	0.964	0.865	1	CLONAL	1	TRUE	0	0.317849314509468	1		460	560	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	149	820	2	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	0.301313931440656	2	FACETS	0.846	0.777	0.918	0.846	0.777	0.918	CLONAL	2	TRUE	0	0.317849314509468	2		822	554	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138642	55138642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143344944	NA	P-0034255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	92	675	1	ENST00000257290.5:c.1319C>T	p.Thr440Met	p.T440M	ENST00000257290	NM_006206.4	440	aCg/aTg	9/23	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.317849314509468	2		676	495	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821601	72821618	+	inframe_deletion	In_Frame_Del	DEL	CCGCCGCCGCCGCCGCCA	CCGCCGCCGCCGCCGCCA	-	rs778016374	NA	P-0034255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	16	96	0	ENST00000268489.5:c.10557_10574del	p.Gly3522_Gly3527del	p.G3522_G3527del	ENST00000268489	NM_006885.3	3519	ggTGGCGGCGGCGGCGGCGGc/ggc	10/10	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.317849314509468	2		96	71	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793521	42793521	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	195	934	1	ENST00000575354.2:c.1323G>A	p.Met441Ile	p.M441I	ENST00000575354	NM_015125.3	441	atG/atA	8/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.317849314509468	2		935	988	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792029	42792029	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	126	742	0	ENST00000575354.2:c.833G>T	p.Ser278Ile	p.S278I	ENST00000575354	NM_015125.3	278	aGc/aTc	6/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.317849314509468	2		742	714	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793120	42793120	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1434474645	NA	P-0034255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	193	890	4	ENST00000575354.2:c.1012G>A	p.Ala338Thr	p.A338T	ENST00000575354	NM_015125.3	338	Gca/Aca	7/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.317849314509468	2		894	1002	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266057	41266360	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGC	AAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGC	-	novel	NA	P-0034255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	24	367	0	ENST00000349496.5:c.56_242-83del		p.X19_splice	ENST00000349496	NM_001904.3	19		3/15	0.317849314509468	1	FACETS	0.49	0.385	0.611	0.49	0.385	0.611	SUBCLONAL	1	TRUE	0	0.317849314509468	1		367	259	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814891	139814891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1564420928	NA	P-0034255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	144	792	0	ENST00000247668.2:c.884G>A	p.Arg295Lys	p.R295K	ENST00000247668	NM_021138.3	295	aGg/aAg	8/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.317849314509468	2		792	660	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858176	152858176	+	synonymous_variant	Silent	SNP	G	G	A	rs782265242	NA	P-0034255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	150	546	0	ENST00000406277.2:c.439C>T	p.Leu147=	p.L147=	ENST00000406277	NM_152274.4	147	Ctg/Ttg	6/7	0.049270453152686	2	FACETS	1	0.955	1			1	INDETERMINATE	2	TRUE	NA	0.317849314509468	2		546	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0034257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	250	537	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.302125976809461	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.302125976809461	2		537	721	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0034257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	54	254	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.302125976809461	3	FACETS	0.816	0.698	0.946	0.408	0.349	0.473	CLONAL	1	TRUE	1	0.302125976809461	3		254	504	SUCCESS
APC	324	MSKCC	GRCh37	5	112175749	112175756	+	frameshift_variant	Frame_Shift_Del	DEL	TACTTTAT	TACTTTAT	-	novel	NA	P-0034257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	107	234	0	ENST00000257430.4:c.4461_4468del	p.Leu1488PhefsTer23	p.L1488Ffs*23	ENST00000257430	NM_000038.5	1486	gaTACTTTATta/gata	16/16	0.302125976809461	3	FACETS	0.848	0.764	0.935	0.848	0.764	0.935	CLONAL	2	TRUE	1	0.302125976809461	3		234	481	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372320	55372320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	164	579	0	ENST00000297316.4:c.1010C>T	p.Pro337Leu	p.P337L	ENST00000297316	NM_022454.3	337	cCg/cTg	2/2	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.302125976809461	2		579	879	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426725	47426725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773318953	NA	P-0034257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	263	323	0	ENST00000377045.4:c.970G>A	p.Val324Met	p.V324M	ENST00000377045	NM_001654.4	324	Gtg/Atg	10/16	0.278765367857813	2	FACETS	0.999	0.945	1			1	CLONAL	3	TRUE	NA	0.302125976809461	2		323	581	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198390	138198390	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	73	282	0	ENST00000237289.4:c.983C>G	p.Ala328Gly	p.A328G	ENST00000237289	NM_001270507.1	328	gCa/gGa	6/9	0.302125976809461	3	FACETS	1	0.899	1	0.515	0.451	0.584	CLONAL	1	TRUE	1	0.302125976809461	3		282	540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0034260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	159	474	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.23830367711815	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.23830367711815	2		474	601	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39613837	39613837	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	58	428	0	ENST00000262039.4:c.1755G>T	p.Leu585Phe	p.L585F	ENST00000262039	NM_002647.2	585	ttG/ttT	16/25	0.224183996070096	3	FACETS	0.987	0.848	1	0.493	0.424	0.569	CLONAL	1	TRUE	1	0.23830367711815	3		428	552	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900767	3900767	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	64	480	0	ENST00000262367.5:c.329C>G	p.Ala110Gly	p.A110G	ENST00000262367	NM_004380.2	110	gCt/gGt	2/31	0.206913209673252	4	FACETS	0.999	0.864	1	0.499	0.432	0.573	CLONAL	1	TRUE	2	0.23830367711815	4		480	666	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070644	67070644	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0034260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	61	160	0	ENST00000412916.2:c.268A>T	p.Arg90Ter	p.R90*	ENST00000412916		90	Aga/Tga	3/6	0.23830367711815	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.23830367711815	2		160	223	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519897	66519897	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	32	371	0	ENST00000358598.2:c.380C>T	p.Ala127Val	p.A127V	ENST00000358598	NM_212471.2	127	gCt/gTt	4/11	0.23830367711815	2	FACETS	0.487	0.394	0.592	0.243	0.197	0.296	SUBCLONAL	1	TRUE	0	0.23830367711815	2		371	552	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547023	9547023	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	34	182	0	ENST00000353224.5:c.999C>A	p.Tyr333Ter	p.Y333*	ENST00000353224	NM_177990.2	333	taC/taA	5/10	NA	2	FACETS	1	0.887	1			1	INDETERMINATE	1	TRUE	NA	0.23830367711815	2		182	257	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938718	76938718	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	93	620	0	ENST00000373344.5:c.2030C>A	p.Ser677Ter	p.S677*	ENST00000373344	NM_000489.3	677	tCa/tAa	9/35	0.206913209673252	4	FACETS	0.921	0.817	1	0.461	0.408	0.517	CLONAL	1	TRUE	2	0.23830367711815	4		620	1049	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0034261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	194	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.610568432154878	2		539	630	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0034261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	248	776	4	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.610568432154878	1	FACETS	0.937	0.884	0.992	0.937	0.884	0.992	CLONAL	1	TRUE	0	0.610568432154878	1		780	602	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604665	48604665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660045	NA	P-0034261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	173	453	0	ENST00000342988.3:c.1487G>A	p.Arg496His	p.R496H	ENST00000342988	NM_005359.5	496	cGt/cAt	12/12	0.610568432154878	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.610568432154878	1		453	340	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0034265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	273	588	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	1	2	FACETS	0.896	0.845	0.948	0.896	0.845	0.948	CLONAL	1	TRUE	1	0.79849520187072	2		588	763	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273039	115273040	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0034265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	190	510	0	ENST00000438362.2:c.1333dup	p.Met445AsnfsTer11	p.M445Nfs*11	ENST00000438362	NM_001242891.1	445	atg/aAtg	12/20	0.79849520187072	1	FACETS	0.969	0.919	1	0.969	0.919	1	CLONAL	1	TRUE	0	0.79849520187072	1		510	295	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041794	42041794	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	137	431	0	ENST00000219905.7:c.5989G>T	p.Glu1997Ter	p.E1997*	ENST00000219905	NM_001164273.1	1997	Gaa/Taa	17/24	0.79849520187072	1	FACETS	0.912	0.854	0.969	0.912	0.854	0.969	CLONAL	1	TRUE	0	0.79849520187072	1		431	226	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350723	89350723	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	375	812	0	ENST00000301030.4:c.2227G>T	p.Glu743Ter	p.E743*	ENST00000301030	NM_001256183.1	743	Gaa/Taa	9/13	1	2	FACETS	0.942	0.897	0.988	0.942	0.897	0.988	CLONAL	1	TRUE	1	0.79849520187072	2		812	997	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247788	10247788	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	302	757	0	ENST00000340748.4:c.4414C>A	p.Leu1472Ile	p.L1472I	ENST00000340748		1472	Ctc/Atc	36/40	1	2	FACETS	0.857	0.81	0.905	0.857	0.81	0.905	CLONAL	1	TRUE	1	0.79849520187072	2		757	883	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044573	128044573	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs538080445	NA	P-0034265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	212	395	0	ENST00000285398.2:c.1048G>A	p.Gly350Ser	p.G350S	ENST00000285398	NM_000122.1	350	Ggt/Agt	8/15	0.794072104171201	2	FACETS	0.973	0.911	1	0.486	0.455	0.518	CLONAL	1	TRUE	0	0.79849520187072	2		395	546	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	20	493	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		493	508	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0034279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	24	313	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	1	0.13	2		313	348	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0034279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	34	366	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.13	2		366	448	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128053	30128053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1246728652	NA	P-0034279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	33	698	0	ENST00000263025.4:c.1076G>A	p.Arg359Gln	p.R359Q	ENST00000263025	NM_002746.2	359	cGg/cAg	8/9	1	2	FACETS	0.791	0.642	0.959	0.791	0.642	0.959	CLONAL	1	TRUE	1	0.13	2		698	642	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416189	29416189	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	26	535	0	ENST00000389048.3:c.4764A>C	p.Gln1588His	p.Q1588H	ENST00000389048	NM_004304.4	1588	caA/caC	29/29	1	2	FACETS	0.851	0.673	1	0.851	0.673	1	CLONAL	1	TRUE	1	0.13	2		535	470	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715744	61715744	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	26	328	0	ENST00000401558.2:c.2185T>G	p.Ser729Ala	p.S729A	ENST00000401558	NM_003400.3	729	Tct/Gct	18/25	1	2	FACETS	0.868	0.686	1	0.868	0.686	1	CLONAL	1	TRUE	1	0.13	2		328	461	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168727	56168727	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	35	395	0	ENST00000399503.3:c.1583del	p.Leu528TrpfsTer29	p.L528Wfs*29	ENST00000399503	NM_005921.1	527	ccT/cc	9/20	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.13	2		395	489	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635121	87635121	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	19	321	0	ENST00000277120.3:c.2173G>C	p.Val725Leu	p.V725L	ENST00000277120		725	Gtc/Ctc	18/19	1	2	FACETS	1	0.778	1	1	0.778	1	CLONAL	1	TRUE	1	0.13	2		321	285	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs17849781	NA	P-0034280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	150	568	0	ENST00000269305.4:c.832C>A	p.Pro278Thr	p.P278T	ENST00000269305	NM_001126112.2	278	Cct/Act	8/11	0.33557250022857	2	FACETS	0.97	0.894	1	0.97	0.894	1	CLONAL	2	TRUE	0	0.346776896782685	2		568	446	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015151	37015151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	106	538	0	ENST00000358127.4:c.253G>A	p.Gly85Arg	p.G85R	ENST00000358127	NM_001280556.1	85	Gga/Aga	3/10	0.346776896782685	0	FACETS	1	0.965	1			1	CLONAL	1	TRUE	0	0.346776896782685	0		538	351	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117383	115117383	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	71	375	0	ENST00000257566.3:c.791del	p.Pro264LeufsTer18	p.P264Lfs*18	ENST00000257566	NM_016569.3	264	cCt/ct	4/8	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.346776896782685	2		375	371	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291560	15291560	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	110	585	0	ENST00000263388.2:c.3074C>T	p.Pro1025Leu	p.P1025L	ENST00000263388	NM_000435.2	1025	cCc/cTc	19/33	0.219571973047912	5	FACETS	0.837	0.759	0.918	0.837	0.759	0.918	CLONAL	3	TRUE	2	0.346776896782685	5		585	384	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872433	35872433	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	123	538	0	ENST00000216797.5:c.470T>A	p.Leu157Gln	p.L157Q	ENST00000216797	NM_020529.2	157	cTg/cAg	3/6	0.275642064307108	4	FACETS	0.777	0.704	0.853	0.777	0.704	0.853	SUBCLONAL	2	TRUE	2	0.346776896782685	4		538	615	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842371	68842374	+	frameshift_variant	Frame_Shift_Del	DEL	CTCC	CTCC	-	novel	NA	P-0034280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	123	499	0	ENST00000261769.5:c.432_435del	p.Ser145LeufsTer69	p.S145Lfs*69	ENST00000261769	NM_004360.3	144	aaCTCC/aa	4/16	0.346776896782685	0	FACETS	0.793	0.729	0.858			1	SUBCLONAL	2	TRUE	0	0.346776896782685	0		499	292	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0034281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	127	256	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.642645930638097	4	FACETS	1	0.984	1	0.692	0.631	0.756	CLONAL	1	TRUE	2	0.642645930638097	4		256	469	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	245	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.98	1	1	0.996	1	CLONAL	4	TRUE	1	0.192611726037644	2		493	586	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0034284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	264	521	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.969	0.917	1	1	0.997	1	CLONAL	5	TRUE	1	0.192611726037644	2		521	566	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510153	149510153	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746042729	NA	P-0034284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	429	683	0	ENST00000261799.4:c.1316G>A	p.Arg439Gln	p.R439Q	ENST00000261799	NM_002609.3	439	cGg/cAg	9/23	0.192611726037644	1	FACETS	1	0.984	1	1	0.998	1	CLONAL	5	TRUE	0	0.192611726037644	1		683	771	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069644	69069644	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	56	461	0	ENST00000288368.4:c.4319A>T	p.Lys1440Met	p.K1440M	ENST00000288368	NM_024870.2	1440	aAg/aTg	35/40	0.192611726037644	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.192611726037644	1		461	431	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0034288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	350	256	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.896425586891077	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.896425586891077	2		256	377	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0034288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	303	558	0				ENST00000310581	NM_198253.2	-/1132			0.838935415856932	3	FACETS	1	0.983	1	0.548	0.517	0.578	CLONAL	1	TRUE	1	0.896425586891077	3		558	894	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653796	89653798	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs1554893765	NA	P-0034288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	195	382	0	ENST00000371953.3:c.97_99del	p.Ile33del	p.I33del	ENST00000371953	NM_000314.4	32	ATT/-	2/9	0.896425586891077	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.896425586891077	1		382	240	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0034288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	176	393	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	1	2	FACETS	0.899	0.837	0.961	0.899	0.837	0.961	CLONAL	1	TRUE	1	0.896425586891077	2		393	437	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858184	9858184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	332	621	0	ENST00000330684.3:c.3217G>A	p.Glu1073Lys	p.E1073K	ENST00000330684	NM_001134407.1	1073	Gaa/Aaa	13/13	0.853003754851805	3	FACETS	0.941	0.89	0.993	0.47	0.445	0.497	CLONAL	1	TRUE	1	0.896425586891077	3		621	1140	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145430	58145430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894340	NA	P-0034288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	478	429	0	ENST00000257904.6:c.71G>A	p.Arg24His	p.R24H	ENST00000257904	NM_000075.3	24	cGt/cAt	2/8	0.896425586891077	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.896425586891077	2		429	524	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434944	110434946	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0034288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	556	993	0	ENST00000375856.3:c.3455_3457del	p.Phe1152del	p.F1152del	ENST00000375856	NM_003749.2	1152	tTCTcc/tcc	1/2	0.896425586891077	1	FACETS	0.985	0.962	1	0.985	0.962	1	CLONAL	1	TRUE	0	0.896425586891077	1		993	695	SUCCESS
ALK	238	MSKCC	GRCh37	2	29420414	29420414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	263	498	0	ENST00000389048.3:c.4067G>A	p.Gly1356Glu	p.G1356E	ENST00000389048	NM_004304.4	1356	gGg/gAg	27/29	1	2	FACETS	0.923	0.871	0.975	0.923	0.871	0.975	CLONAL	1	TRUE	1	0.896425586891077	2		498	636	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94910992	94910992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	741	680	0	ENST00000536441.1:c.1138C>T	p.Arg380Trp	p.R380W	ENST00000536441	NM_144665.3	380	Cgg/Tgg	8/10	0.896425586891077	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.896425586891077	2		680	827	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3651077	3651089	+	frameshift_variant	Frame_Shift_Del	DEL	ACTGCTTCAAGTG	ACTGCTTCAAGTG	-	novel	NA	P-0034288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	385	708	0	ENST00000294008.3:c.1054_1066del	p.His352ValfsTer3	p.H352Vfs*3	ENST00000294008	NM_032444.2	352	CACTTGAAGCAGTgt/gt	5/15	0.853003754851805	3	FACETS	0.879	0.834	0.925	0.44	0.417	0.463	CLONAL	1	TRUE	1	0.896425586891077	3		708	1415	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78820366	78820366	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777839906	NA	P-0034288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	316	577	0	ENST00000306801.3:c.1306G>A	p.Val436Ile	p.V436I	ENST00000306801	NM_020761.2	436	Gtc/Atc	11/34	0.895783761896016	4	FACETS	0.935	0.881	0.991	0.234	0.22	0.248	CLONAL	1	TRUE	0	0.896425586891077	4		577	1430	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217024	2217024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1375	402	823	1	ENST00000398665.3:c.2479C>T	p.Pro827Ser	p.P827S	ENST00000398665	NM_032482.2	827	Cct/Tct	21/28	0.772536547146395	4	FACETS	0.957	0.908	1	0.319	0.302	0.336	CLONAL	1	TRUE	1	0.896425586891077	4		824	1777	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244141	5244141	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	1083	731	0	ENST00000357368.4:c.1341G>A	p.Trp447Ter	p.W447*	ENST00000357368	NM_002850.3	447	tgG/tgA	11/38	0.772536547146395	4	FACETS	0.999	0.979	1	0.999	0.979	1	CLONAL	3	TRUE	1	0.896425586891077	4		731	1529	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224670	36224671	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0034288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	626	881	0	ENST00000222270.7:c.7056_7057delinsTT	p.Gln2353Ter	p.Q2353*	ENST00000222270	NM_014727.1	2352	ctCCag/ctTTag	30/37	0.896425586891077	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.896425586891077	1		881	716	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753512	42753512	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	535	705	1	ENST00000222329.4:c.752C>T	p.Ser251Leu	p.S251L	ENST00000222329	NM_006494.2	251	tCg/tTg	4/4	0.896425586891077	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.896425586891077	1		706	614	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024380	31024380	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	682	662	0	ENST00000375687.4:c.3865C>G	p.Arg1289Gly	p.R1289G	ENST00000375687	NM_015338.5	1289	Cgg/Ggg	13/13	0.766537381491687	4	FACETS	0.959	0.927	0.992	0.959	0.927	0.992	CLONAL	2	TRUE	2	0.896425586891077	4		662	1504	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172090	32172090	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	814	814	0	ENST00000375023.3:c.2942G>A	p.Gly981Glu	p.G981E	ENST00000375023	NM_004557.3	981	gGa/gAa	19/30	0.838935415856932	3	FACETS	0.912	0.887	0.937	0.912	0.887	0.937	CLONAL	2	TRUE	1	0.896425586891077	3		814	1442	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371728	55371728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	341	572	1	ENST00000297316.4:c.418C>T	p.Arg140Trp	p.R140W	ENST00000297316	NM_022454.3	140	Cgg/Tgg	2/2	0.853003754851805	3	FACETS	1	0.974	1	0.522	0.494	0.55	CLONAL	1	TRUE	1	0.896425586891077	3		573	1056	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519966	NA	P-0034289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	264	554	0	ENST00000347630.2:c.397T>A	p.Phe133Ile	p.F133I	ENST00000347630	NM_001007230.1	133	Ttc/Atc	6/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.677618173993576	2		554	768	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305242	39305242	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	270	537	0	ENST00000373001.3:c.1183C>G	p.Pro395Ala	p.P395A	ENST00000373001	NM_022157.3	395	Cca/Gca	7/7	1	2	FACETS	0.996	0.938	1	0.996	0.938	1	CLONAL	1	TRUE	1	0.677618173993576	2		537	800	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692815	89692815	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	40	309	0	ENST00000371953.3:c.299T>G	p.Leu100Arg	p.L100R	ENST00000371953	NM_000314.4	100	cTt/cGt	5/9	1	2	FACETS	0.257	0.213	0.305	0.257	0.213	0.305	SUBCLONAL	1	TRUE	1	0.677618173993576	2		309	460	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041753	42041753	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	22	388	0	ENST00000219905.7:c.5948C>A	p.Ser1983Ter	p.S1983*	ENST00000219905	NM_001164273.1	1983	tCa/tAa	17/24	0.677618173993576	1	FACETS	0.121	0.093	0.153	0.121	0.093	0.153	SUBCLONAL	1	TRUE	0	0.677618173993576	1		388	356	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42057151	42057179	+	frameshift_variant	Frame_Shift_Del	DEL	GCTCACCCTAAAAGGTCCCCTATTCTCAG	GCTCACCCTAAAAGGTCCCCTATTCTCAG	-	novel	NA	P-0034289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	54	652	0	ENST00000219905.7:c.7813_7841del	p.Leu2605ThrfsTer8	p.L2605Tfs*8	ENST00000219905	NM_001164273.1	2604	ttGCTCACCCTAAAAGGTCCCCTATTCTCAGga/ttga	23/24	0.677618173993576	1	FACETS	0.196	0.167	0.227	0.196	0.167	0.227	SUBCLONAL	1	TRUE	0	0.677618173993576	1		652	538	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135800974	135800975	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	TTGAGACA	novel	NA	P-0034289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	100	309	0	ENST00000298552.3:c.355_362dup	p.Lys121AsnfsTer19	p.K121Nfs*19	ENST00000298552	NM_001162426.1	121	aag/aaTGTCTCAAg	5/23	1	2	FACETS	0.708	0.636	0.783	0.708	0.636	0.783	SUBCLONAL	1	TRUE	1	0.677618173993576	2		309	417	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891480	76891480	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	355	375	0	ENST00000373344.5:c.4625A>G	p.Asp1542Gly	p.D1542G	ENST00000373344	NM_000489.3	1542	gAt/gGt	16/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.677618173993576	1		375	483	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059454	42059465	+	frameshift_variant	Frame_Shift_Del	DEL	CTCACCAAGTTC	CTCACCAAGTTC	G	novel	NA	P-0034289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	65	347	0	ENST00000219905.7:c.9174_9185delinsG	p.Ser3059CysfsTer19	p.S3059Cfs*19	ENST00000219905	NM_001164273.1	3058	gcCTCACCAAGTTCt/gcGt	24/24	0.677618173993576	1	FACETS	0.494	0.433	0.558	0.494	0.433	0.558	SUBCLONAL	1	TRUE	0	0.677618173993576	1		347	257	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	146	349	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.806630322264341	2		349	340	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	248	557	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.806630322264341	2		557	612	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222829	36222829	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	381	952	0	ENST00000222270.7:c.5458C>A	p.Pro1820Thr	p.P1820T	ENST00000222270	NM_014727.1	1820	Ccc/Acc	27/37	1	2	FACETS	0.975	0.929	1	0.975	0.929	1	CLONAL	1	TRUE	1	0.806630322264341	2		952	969	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051665	30051673	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTGAGGCC	GGTGAGGCC	-	novel	NA	P-0034291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	114	317	0	ENST00000338641.4:c.599_599+8del		p.X200_splice	ENST00000338641	NM_000268.3	200		6/16	0.806630322264341	1	FACETS	0.907	0.843	0.969	0.907	0.843	0.969	CLONAL	1	TRUE	0	0.806630322264341	1		317	186	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92462582	92462582	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	163	524	0	ENST00000265734.4:c.56T>C	p.Ile19Thr	p.I19T	ENST00000265734	NM_001259.6	19	aTc/aCc	2/8	1	2	FACETS	0.908	0.842	0.976	0.908	0.842	0.976	CLONAL	1	TRUE	1	0.806630322264341	2		524	445	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570427	87570427	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	248	716	0	ENST00000277120.3:c.2167T>G	p.Tyr723Asp	p.Y723D	ENST00000277120		723	Tac/Gac	17/19	1	2	FACETS	0.964	0.907	1	0.964	0.907	1	CLONAL	1	TRUE	1	0.806630322264341	2		716	638	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	101	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.248684579174069	3	FACETS	0.852	0.764	0.945	0.852	0.764	0.945	CLONAL	2	TRUE	1	0.248684579174069	3		493	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0034293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	205	685	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.248684579174069	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.248684579174069	2		685	725	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0034293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	10	198	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.119771998318395	4	FACETS	0.321	0.216	0.453	0.16	0.108	0.227	INDETERMINATE	1	TRUE	2	0.248684579174069	4		198	313	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143164	30143164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779147984	NA	P-0034293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	140	677	0	ENST00000389048.3:c.362G>A	p.Arg121Gln	p.R121Q	ENST00000389048	NM_004304.4	121	cGg/cAg	1/29	0.119771998318395	4	FACETS	1	0.947	1	1	0.947	1	INDETERMINATE	2	TRUE	2	0.248684579174069	4		677	668	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146788	185146788	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	177	576	1	ENST00000265026.3:c.419C>T	p.Pro140Leu	p.P140L	ENST00000265026	NM_004721.4	140	cCt/cTt	2/14	0.119771998318395	4	FACETS	1	0.981	1	1	0.981	1	INDETERMINATE	2	TRUE	2	0.248684579174069	4		577	749	SUCCESS
APC	324	MSKCC	GRCh37	5	112151285	112151286	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0034293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	76	299	0	ENST00000257430.4:c.930dup	p.Lys311GlnfsTer16	p.K311Qfs*16	ENST00000257430	NM_000038.5	310	acc/aCcc	9/16	0.248684579174069	3	FACETS	0.976	0.862	1	0.976	0.862	1	CLONAL	2	TRUE	1	0.248684579174069	3		299	352	SUCCESS
APC	324	MSKCC	GRCh37	5	112173535	112173547	+	frameshift_variant	Frame_Shift_Del	DEL	CTTGCCATCTCTT	CTTGCCATCTCTT	-	novel	NA	P-0034293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	22	318	0	ENST00000257430.4:c.2245_2257del	p.Leu749MetfsTer8	p.L749Mfs*8	ENST00000257430	NM_000038.5	748	agCTTGCCATCTCTT/ag	16/16	0.248684579174069	3	FACETS	0.585	0.453	0.738	0.293	0.226	0.369	SUBCLONAL	1	TRUE	1	0.248684579174069	3		318	340	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709479	176709479	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	47	333	0	ENST00000439151.2:c.5906A>G	p.Asn1969Ser	p.N1969S	ENST00000439151	NM_022455.4	1969	aAt/aGt	19/23	0.248684579174069	3	FACETS	1	0.899	1	0.542	0.458	0.634	CLONAL	1	TRUE	1	0.248684579174069	3		333	392	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140810	37140810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	149	477	0	ENST00000373509.5:c.646C>T	p.His216Tyr	p.H216Y	ENST00000373509	NM_002648.3	216	Cat/Tat	5/6	0.119771998318395	4	FACETS	0.947	0.866	1	0.947	0.866	1	INDETERMINATE	2	TRUE	2	0.248684579174069	4		477	790	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	36	349	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.592	0.489	0.707	0.592	0.489	0.707	SUBCLONAL	1	TRUE	1	0.412109295515942	2		349	295	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119635000	119635000	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs201787969	NA	P-0034294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	14	177	0	ENST00000316626.5:c.499C>T	p.Arg167Ter	p.R167*	ENST00000316626		167	Cga/Tga	5/12	1	2	FACETS	1	0.839	1	1	0.839	1	CLONAL	1	TRUE	1	0.412109295515942	2		177	57	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039501	49039501	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0034294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	45	520	0	ENST00000267163.4:c.2486C>G	p.Ser829Ter	p.S829*	ENST00000267163	NM_000321.2	829	tCa/tGa	23/27	0.412109295515942	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.412109295515942	1		520	131	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577595	7577598	+	frameshift_variant	Frame_Shift_Del	DEL	CAGT	CAGT	-	novel	NA	P-0034294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	105	607	0	ENST00000269305.4:c.683_686del	p.Asp228ValfsTer18	p.D228Vfs*18	ENST00000269305	NM_001126112.2	228	gACTGt/gt	7/11	0.385160866622472	2	FACETS	0.849	0.771	0.929	0.849	0.771	0.929	CLONAL	2	TRUE	0	0.412109295515942	2		607	300	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0034295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	147	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.421043309615872	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.421043309615872	1		539	381	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0034295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	83	254	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.421043309615872	2		254	307	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0034295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	411	967	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	2	TRUE	NA	0.421043309615872	2		968	918	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125509	7125509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147176789	NA	P-0034295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	120	633	1	ENST00000302850.5:c.3043G>A	p.Glu1015Lys	p.E1015K	ENST00000302850	NM_000208.2	1015	Gag/Aag	17/22	1	2	FACETS	0.912	0.826	1	0.912	0.826	1	CLONAL	1	TRUE	1	0.421043309615872	2		634	625	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176715853	176715853	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	91	494	0	ENST00000439151.2:c.6185G>A	p.Cys2062Tyr	p.C2062Y	ENST00000439151	NM_022455.4	2062	tGt/tAt	21/23	1	2	FACETS	0.83	0.739	0.926	0.83	0.739	0.926	CLONAL	1	TRUE	1	0.421043309615872	2		494	521	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426597	49426597	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	208	844	0	ENST00000301067.7:c.11891A>T	p.Gln3964Leu	p.Q3964L	ENST00000301067	NM_003482.3	3964	cAg/cTg	39/54	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.421043309615872	2		844	985	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591805	48591805	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	52	484	0	ENST00000342988.3:c.969del	p.Trp323CysfsTer13	p.W323Cfs*13	ENST00000342988	NM_005359.5	323	tGg/tg	9/12	0.415285903222251	1	FACETS	0.696	0.597	0.803	0.696	0.597	0.803	SUBCLONAL	1	TRUE	0	0.421043309615872	1		484	280	SUCCESS
APC	324	MSKCC	GRCh37	5	112175879	112175879	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	44	241	1	ENST00000257430.4:c.4588G>T	p.Glu1530Ter	p.E1530*	ENST00000257430	NM_000038.5	1530	Gaa/Taa	16/16	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.421043309615872	2		242	170	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196879	106196881	+	frameshift_variant	Frame_Shift_Del	DEL	TCT	TCT	CC	novel	NA	P-0034296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	59	349	0	ENST00000380013.4:c.5212_5214delinsCC	p.Ser1738ProfsTer7	p.S1738Pfs*7	ENST00000380013	NM_001127208.2	1738	TCT/CC	11/11	0.443747640862209	5	FACETS	0.839	0.736	0.946	0.839	0.736	0.946	CLONAL	3	FALSE	2	0.443747640862209	5		349	176	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0034304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	269	710	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	0.360539479649794	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.360539479649794	1		710	924	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983930	2983930	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	154	994	0	ENST00000396946.4:c.600C>A	p.Asp200Glu	p.D200E	ENST00000396946	NM_032415.4	200	gaC/gaA	5/25	0.177867817787339	2	FACETS	0.881	0.805	0.96	0.44	0.402	0.48	INDETERMINATE	1	TRUE	0	0.360539479649794	2		994	970	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177562	56177562	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	51	430	0	ENST00000399503.3:c.2536del	p.Ser846ProfsTer11	p.S846Pfs*11	ENST00000399503	NM_005921.1	845	agT/ag	14/20	1	2	FACETS	0.523	0.444	0.609	0.523	0.444	0.609	SUBCLONAL	1	TRUE	1	0.360539479649794	2		430	541	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561418	9561418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	185	686	0	ENST00000353224.5:c.364G>A	p.Glu122Lys	p.E122K	ENST00000353224	NM_177990.2	122	Gaa/Aaa	4/10	1	2	FACETS	0.501	0.463	0.541	0.501	0.463	0.541	SUBCLONAL	1	TRUE	1	0.910999407221987	2		686	810	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233127	55233127	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	672	657	0	ENST00000275493.2:c.1877A>G	p.Tyr626Cys	p.Y626C	ENST00000275493	NM_005228.3	626	tAc/tGc	15/28	0.383128174812412	6	FACETS	1	0.996	1	0.416	0.401	0.432	INDETERMINATE	2	TRUE	0	0.910999407221987	6		657	1666	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458822	120458822	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	30	827	0	ENST00000256646.2:c.6523A>G	p.Ile2175Val	p.I2175V	ENST00000256646	NM_024408.3	2175	Atc/Gtc	34/34	0.457565953542082	1	FACETS	0.074	0.059	0.091	0.074	0.059	0.091	INDETERMINATE	1	TRUE	0	0.910999407221987	1		827	485	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0034352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	281	256	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	0.794563783362812	2		256	702	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222006	1222006	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0034352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	572	545	0	ENST00000326873.7:c.920+1G>T		p.X307_splice	ENST00000326873	NM_000455.4	307			NA	2	FACETS	0.974	0.95	0.997			1	INDETERMINATE	2	TRUE	NA	0.794563783362812	2		545	739	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114192	115114192	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	247	808	0	ENST00000257566.3:c.1025A>G	p.Glu342Gly	p.E342G	ENST00000257566	NM_016569.3	342	gAa/gGa	6/8	0.434838124177442	1	FACETS	0.369	0.345	0.394	0.369	0.345	0.394	INDETERMINATE	1	TRUE	0	0.794563783362812	1		808	1015	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023096	33023097	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0034352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	117	394	1	ENST00000300177.4:c.205_206delinsAA	p.Pro69Asn	p.P69N	ENST00000300177	NM_001191322.1	69	CCc/AAc	2/2	0.773288388343991	1	FACETS	0.443	0.402	0.484	0.443	0.402	0.484	SUBCLONAL	1	TRUE	0	0.794563783362812	1		395	401	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577017	7577017	+	splice_donor_variant	Splice_Site	DEL	A	A	-	novel	NA	P-0034352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	592	744	2	ENST00000269305.4:c.919+2del		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.794563783362812	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.794563783362812	1		746	831	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251788	212251788	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1347967434	NA	P-0034352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	125	359	0	ENST00000342788.4:c.3271G>T	p.Ala1091Ser	p.A1091S	ENST00000342788	NM_005235.2	1091	Gct/Tct	27/28	0.605861798711532	1	FACETS	0.388	0.353	0.424	0.388	0.353	0.424	SUBCLONAL	1	TRUE	0	0.794563783362812	1		359	489	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445055	89445055	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	137	471	0	ENST00000336596.2:c.1375G>T	p.Glu459Ter	p.E459*	ENST00000336596	NM_005233.5	459	Gaa/Taa	6/17	0.533025276691262	1	FACETS	0.326	0.297	0.356	0.326	0.297	0.356	SUBCLONAL	1	TRUE	0	0.794563783362812	1		471	638	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285801	87285801	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	221	712	0	ENST00000277120.3:c.138C>A	p.Ser46Arg	p.S46R	ENST00000277120		46	agC/agA	2/19	0.627988768423211	1	FACETS	0.349	0.325	0.374	0.349	0.325	0.374	SUBCLONAL	1	TRUE	0	0.794563783362812	1		712	960	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410538	63410538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1162990577	NA	P-0034352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	268	394	1	ENST00000330258.3:c.2629G>A	p.Gly877Ser	p.G877S	ENST00000330258	NM_152424.3	877	Ggc/Agc	2/2	0.794563783362812	0	FACETS		NA	1			1	NA	1	TRUE	NA	0.794563783362812	0		395	412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	147	653	1	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.161551707166402	2	FACETS	1	0.984	1	0.673	0.614	0.734	CLONAL	1	TRUE	0	0.241249912658158	2		654	906	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048662	180048662	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1468150967	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	64	549	0	ENST00000261937.6:c.1900G>A	p.Ala634Thr	p.A634T	ENST00000261937	NM_182925.4	634	Gcc/Acc	13/30	0.241249912658158	1	FACETS	0.653	0.565	0.75	0.653	0.565	0.75	SUBCLONAL	1	TRUE	0	0.241249912658158	1		549	714	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268379	142268380	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1559984993	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	37	362	0	ENST00000350721.4:c.3112dup	p.Ser1038PhefsTer11	p.S1038Ffs*11	ENST00000350721	NM_001184.3	1038	tct/tTct	15/47	0.241249912658158	1	FACETS	0.569	0.469	0.681	0.569	0.469	0.681	SUBCLONAL	1	TRUE	0	0.241249912658158	1		362	474	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971003	21971003	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	52	413	0	ENST00000304494.5:c.355G>T	p.Glu119Ter	p.E119*	ENST00000304494	NM_000077.4	119	Gag/Tag	2/3	0.241249912658158	1	FACETS	0.589	0.5	0.686	0.589	0.5	0.686	SUBCLONAL	1	TRUE	0	0.241249912658158	1		413	644	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624263	89624263	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1554890348	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	29	299	0	ENST00000371953.3:c.37A>T	p.Lys13Ter	p.K13*	ENST00000371953	NM_000314.4	13	Aaa/Taa	1/9	1	2	FACETS	0.615	0.493	0.753	0.615	0.493	0.753	SUBCLONAL	1	TRUE	1	0.241249912658158	2		299	391	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776220	135776220	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs118203706	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	37	333	0	ENST00000298552.3:c.2507C>G	p.Ser836Ter	p.S836*	ENST00000298552	NM_001162426.1	836	tCa/tGa	20/23	0.241249912658158	1	FACETS	0.518	0.426	0.62	0.518	0.426	0.62	SUBCLONAL	1	TRUE	0	0.241249912658158	1		333	521	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967087	25967087	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	56	507	0	ENST00000435504.4:c.2119G>T	p.Gly707Trp	p.G707W	ENST00000435504		707	Ggg/Tgg	13/13	1	2	FACETS	0.7	0.599	0.811	0.7	0.599	0.811	SUBCLONAL	1	TRUE	1	0.241249912658158	2		507	663	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813907	50813907	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	47	456	0	ENST00000398568.2:c.1461G>T	p.Trp487Cys	p.W487C	ENST00000398568	NM_001042412.1	487	tgG/tgT	8/18	0.241249912658158	1	FACETS	0.499	0.42	0.587	0.499	0.42	0.587	SUBCLONAL	1	TRUE	0	0.241249912658158	1		456	686	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492907	8492907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	83	534	2	ENST00000356435.5:c.2422G>A	p.Asp808Asn	p.D808N	ENST00000356435		808	Gat/Aat	16/35	0.241249912658158	1	FACETS	0.747	0.658	0.842	0.747	0.658	0.842	SUBCLONAL	1	TRUE	0	0.241249912658158	1		536	810	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390980	139390980	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	71	706	0	ENST00000277541.6:c.7211A>T	p.Gln2404Leu	p.Q2404L	ENST00000277541	NM_017617.3	2404	cAg/cTg	34/34	0.241249912658158	1	FACETS	0.533	0.463	0.608	0.533	0.463	0.608	SUBCLONAL	1	TRUE	0	0.241249912658158	1		706	972	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197245	106197245	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	55	326	0	ENST00000380013.4:c.5582del	p.Gly1861GlufsTer26	p.G1861Efs*26	ENST00000380013	NM_001127208.2	1860	Ggg/gg	11/11	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.241249912658158	2		326	453	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253850	30253850	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751979681	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	50	456	0	ENST00000307677.4:c.604G>A	p.Glu202Lys	p.E202K	ENST00000307677	NM_138578.1	202	Gag/Aag	3/3	1	2	FACETS	0.553	0.468	0.647	0.553	0.468	0.647	SUBCLONAL	1	TRUE	1	0.241249912658158	2		456	750	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711876	89711876	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs786204863	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	53	399	0	ENST00000371953.3:c.494G>T	p.Gly165Val	p.G165V	ENST00000371953	NM_000314.4	165	gGa/gTa	6/9	1	2	FACETS	0.724	0.617	0.841	0.724	0.617	0.841	SUBCLONAL	1	TRUE	1	0.241249912658158	2		399	607	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70412311	70412311	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	24	265	0	ENST00000373644.4:c.4421A>T	p.Lys1474Ile	p.K1474I	ENST00000373644	NM_030625.2	1474	aAa/aTa	6/12	1	2	FACETS	0.492	0.385	0.616	0.492	0.385	0.616	SUBCLONAL	1	TRUE	1	0.241249912658158	2		265	404	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163297295	163297295	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	71	435	0	ENST00000271452.3:c.141G>C	p.Met47Ile	p.M47I	ENST00000271452	NM_145697.2	47	atG/atC	3/14	0.161551707166402	2	FACETS	0.818	0.713	0.931	0.409	0.356	0.466	CLONAL	1	TRUE	0	0.241249912658158	2		435	720	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717694	89717694	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	49	396	0	ENST00000371953.3:c.719A>G	p.Tyr240Cys	p.Y240C	ENST00000371953	NM_000314.4	240	tAc/tGc	7/9	1	2	FACETS	0.602	0.509	0.705	0.602	0.509	0.705	SUBCLONAL	1	TRUE	1	0.241249912658158	2		396	675	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104375050	104375050	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	34	455	0	ENST00000369902.3:c.1048G>T	p.Asp350Tyr	p.D350Y	ENST00000369902	NM_016169.3	350	Gac/Tac	9/12	1	2	FACETS	0.418	0.34	0.506	0.418	0.34	0.506	SUBCLONAL	1	TRUE	1	0.241249912658158	2		455	674	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248544	8248544	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs201874026	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	36	507	0	ENST00000335790.3:c.343G>C	p.Ala115Pro	p.A115P	ENST00000335790	NM_002315.2	115	Gcc/Ccc	3/4	0.241249912658158	1	FACETS	0.39	0.319	0.469	0.39	0.319	0.469	SUBCLONAL	1	TRUE	0	0.241249912658158	1		507	673	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589554	69589554	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	19	145	0	ENST00000168712.1:c.299C>A	p.Pro100His	p.P100H	ENST00000168712	NM_002007.2	100	cCc/cAc	1/3	1	2	FACETS	0.567	0.43	0.727	0.567	0.43	0.727	SUBCLONAL	1	TRUE	1	0.241249912658158	2		145	278	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77051785	77051785	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	100	405	0	ENST00000356341.3:c.1022G>A	p.Trp341Ter	p.W341*	ENST00000356341	NM_002576.4	341	tGg/tAg	11/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.241249912658158	2		405	691	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206942	102206942	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	26	306	0	ENST00000263464.3:c.1570C>A	p.His524Asn	p.H524N	ENST00000263464	NM_001165.4	524	Cat/Aat	7/9	1	2	FACETS	0.435	0.343	0.54	0.435	0.343	0.54	SUBCLONAL	1	TRUE	1	0.241249912658158	2		306	496	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143554	108143554	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	53	441	0	ENST00000278616.4:c.3259A>T	p.Met1087Leu	p.M1087L	ENST00000278616	NM_000051.3	1087	Atg/Ttg	22/63	1	2	FACETS	0.666	0.567	0.774	0.666	0.567	0.774	SUBCLONAL	1	TRUE	1	0.241249912658158	2		441	660	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202225	108202225	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs769142993	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	38	420	0	ENST00000278616.4:c.7570G>T	p.Ala2524Ser	p.A2524S	ENST00000278616	NM_000051.3	2524	Gct/Tct	51/63	1	2	FACETS	0.446	0.368	0.534	0.446	0.368	0.534	SUBCLONAL	1	TRUE	1	0.241249912658158	2		420	706	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373407	118373407	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	80	442	0	ENST00000534358.1:c.6800C>T	p.Ser2267Leu	p.S2267L	ENST00000534358	NM_005933.3	2267	tCa/tTa	27/36	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.241249912658158	2		442	626	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125499135	125499135	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	68	515	0	ENST00000428830.2:c.298A>T	p.Ile100Leu	p.I100L	ENST00000428830	NM_001114121.2	100	Ata/Tta	4/14	1	2	FACETS	0.849	0.738	0.969	0.849	0.738	0.969	CLONAL	1	TRUE	1	0.241249912658158	2		515	664	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433749	49433749	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	78	718	1	ENST00000301067.7:c.7804G>T	p.Gly2602Trp	p.G2602W	ENST00000301067	NM_003482.3	2602	Ggg/Tgg	31/54	1	2	FACETS	0.675	0.592	0.765	0.675	0.592	0.765	SUBCLONAL	1	TRUE	1	0.241249912658158	2		719	958	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447076	49447076	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	73	508	0	ENST00000301067.7:c.868G>T	p.Val290Phe	p.V290F	ENST00000301067	NM_003482.3	290	Gtt/Ttt	7/54	1	2	FACETS	0.837	0.731	0.951	0.837	0.731	0.951	CLONAL	1	TRUE	1	0.241249912658158	2		508	723	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114169	115114169	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	86	563	0	ENST00000257566.3:c.1048G>T	p.Ala350Ser	p.A350S	ENST00000257566	NM_016569.3	350	Gcc/Tcc	6/8	1	2	FACETS	0.852	0.753	0.958	0.852	0.753	0.958	CLONAL	1	TRUE	1	0.241249912658158	2		563	837	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281513	49281513	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	75	625	0	ENST00000282018.3:c.560G>T	p.Cys187Phe	p.C187F	ENST00000282018	NM_020377.2	187	tGc/tTc	1/1	0.241249912658158	1	FACETS	0.714	0.625	0.81	0.714	0.625	0.81	SUBCLONAL	1	TRUE	0	0.241249912658158	1		625	766	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524625	103524625	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	34	289	0	ENST00000355739.4:c.2756G>C	p.Arg919Pro	p.R919P	ENST00000355739	NM_000123.3	919	cGg/cCg	13/15	0.241249912658158	1	FACETS	0.614	0.501	0.74	0.614	0.501	0.74	SUBCLONAL	1	TRUE	0	0.241249912658158	1		289	404	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435772	110435772	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	23	105	0	ENST00000375856.3:c.2629C>A	p.Pro877Thr	p.P877T	ENST00000375856	NM_003749.2	877	Ccg/Acg	1/2	0.241249912658158	1	FACETS	0.843	0.661	1	0.843	0.661	1	CLONAL	1	TRUE	0	0.241249912658158	1		105	199	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610581	81610581	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	36	331	0	ENST00000298171.2:c.2179G>C	p.Glu727Gln	p.E727Q	ENST00000298171	NM_000369.2	727	Gag/Cag	10/10	1	2	FACETS	0.543	0.445	0.652	0.543	0.445	0.652	SUBCLONAL	1	TRUE	1	0.241249912658158	2		331	550	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059011	42059011	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	40	405	0	ENST00000219905.7:c.8731G>A	p.Glu2911Lys	p.E2911K	ENST00000219905	NM_001164273.1	2911	Gag/Aag	24/24	0.241249912658158	1	FACETS	0.563	0.467	0.67	0.563	0.467	0.67	SUBCLONAL	1	TRUE	0	0.241249912658158	1		405	518	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122875	2122876	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	63	521	0	ENST00000219476.3:c.2246_2247del	p.Arg749ProfsTer12	p.R749Pfs*12	ENST00000219476	NM_000548.3	749	cGG/c	21/42	0.241249912658158	1	FACETS	0.629	0.543	0.723	0.629	0.543	0.723	SUBCLONAL	1	TRUE	0	0.241249912658158	1		521	730	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857708	9857708	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	42	457	0	ENST00000330684.3:c.3693G>T	p.Arg1231Ser	p.R1231S	ENST00000330684	NM_001134407.1	1231	agG/agT	13/13	0.241249912658158	1	FACETS	0.552	0.46	0.654	0.552	0.46	0.654	SUBCLONAL	1	TRUE	0	0.241249912658158	1		457	555	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934560	9934560	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1085307961	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	51	387	0	ENST00000330684.3:c.1595G>T	p.Gly532Val	p.G532V	ENST00000330684	NM_001134407.1	532	gGa/gTa	7/13	0.241249912658158	1	FACETS	0.651	0.553	0.759	0.651	0.553	0.759	SUBCLONAL	1	TRUE	0	0.241249912658158	1		387	571	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041798	14041798	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1176371705	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	45	499	0	ENST00000311895.7:c.2345A>G	p.Asn782Ser	p.N782S	ENST00000311895	NM_005236.2	782	aAt/aGt	11/11	0.241249912658158	1	FACETS	0.464	0.389	0.547	0.464	0.389	0.547	SUBCLONAL	1	TRUE	0	0.241249912658158	1		499	707	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028665	12028665	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	78	412	0	ENST00000353533.5:c.868G>T	p.Val290Phe	p.V290F	ENST00000353533	NM_003010.3	290	Gtc/Ttc	8/11	0.161551707166402	2	FACETS	0.986	0.866	1	0.493	0.433	0.557	CLONAL	1	TRUE	0	0.241249912658158	2		412	656	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562698	29562698	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	119	471	0	ENST00000356175.3:c.3778A>T	p.Met1260Leu	p.M1260L	ENST00000356175	NM_000267.3	1260	Atg/Ttg	28/57	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.241249912658158	2		471	838	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30302714	30302714	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	83	445	0	ENST00000322652.5:c.805G>C	p.Glu269Gln	p.E269Q	ENST00000322652	NM_015355.2	269	Gaa/Caa	7/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.241249912658158	2		445	580	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511673	38511673	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	51	441	0	ENST00000254066.5:c.1171G>T	p.Gly391Trp	p.G391W	ENST00000254066	NM_000964.3	391	Ggg/Tgg	8/9	1	2	FACETS	0.673	0.571	0.785	0.673	0.571	0.785	SUBCLONAL	1	TRUE	1	0.241249912658158	2		441	628	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732917	74732917	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	34	176	0	ENST00000359995.5:c.326G>T	p.Arg109Met	p.R109M	ENST00000359995	NM_001195427.1	109	aGg/aTg	1/3	0.161551707166402	2	FACETS	0.774	0.634	0.932	0.387	0.317	0.466	CLONAL	1	TRUE	0	0.241249912658158	2		176	364	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573553	48573553	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	38	241	0	ENST00000342988.3:c.137A>T	p.Lys46Met	p.K46M	ENST00000342988	NM_005359.5	46	aAg/aTg	2/12	1	2	FACETS	0.816	0.676	0.973	0.816	0.676	0.973	CLONAL	1	TRUE	1	0.241249912658158	2		241	386	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602463	10602463	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	92	561	0	ENST00000171111.5:c.1115G>T	p.Gly372Val	p.G372V	ENST00000171111	NM_203500.1	372	gGg/gTg	3/6	0.241249912658158	1	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	0	0.241249912658158	1		561	669	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955048	17955048	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	93	635	0	ENST00000458235.1:c.179C>A	p.Ala60Asp	p.A60D	ENST00000458235	NM_000215.3	60	gCc/gAc	2/24	0.241249912658158	1	FACETS	0.859	0.764	0.962	0.859	0.764	0.962	CLONAL	1	TRUE	0	0.241249912658158	1		635	789	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792385	33792385	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1248876880	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	38	570	1	ENST00000498907.2:c.936G>T	p.Gln312His	p.Q312H	ENST00000498907	NM_004364.3	312	caG/caT	1/1	0.241249912658158	1	FACETS	0.369	0.304	0.443	0.369	0.304	0.443	SUBCLONAL	1	TRUE	0	0.241249912658158	1		571	750	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082536	16082536	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	55	497	0	ENST00000281043.3:c.350G>T	p.Trp117Leu	p.W117L	ENST00000281043	NM_005378.4	117	tGg/tTg	2/3	1	2	FACETS	0.739	0.632	0.857	0.739	0.632	0.857	SUBCLONAL	1	TRUE	1	0.241249912658158	2		497	617	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469622	25469622	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1239154786	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	52	608	0	ENST00000264709.3:c.1146G>C	p.Lys382Asn	p.K382N	ENST00000264709	NM_175629.2	382	aaG/aaC	10/23	1	2	FACETS	0.559	0.475	0.652	0.559	0.475	0.652	SUBCLONAL	1	TRUE	1	0.241249912658158	2		608	771	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446286	29446286	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	80	638	0	ENST00000389048.3:c.3281C>A	p.Pro1094His	p.P1094H	ENST00000389048	NM_004304.4	1094	cCc/cAc	20/29	1	2	FACETS	0.762	0.67	0.862	0.762	0.67	0.862	SUBCLONAL	1	TRUE	1	0.241249912658158	2		638	870	SUCCESS
ALK	238	MSKCC	GRCh37	2	29473971	29473971	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	36	535	0	ENST00000389048.3:c.2204G>C	p.Ser735Thr	p.S735T	ENST00000389048	NM_004304.4	735	aGc/aCc	12/29	1	2	FACETS	0.471	0.386	0.566	0.471	0.386	0.566	SUBCLONAL	1	TRUE	1	0.241249912658158	2		535	634	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474077	29474077	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	40	578	0	ENST00000389048.3:c.2098C>T	p.Gln700Ter	p.Q700*	ENST00000389048	NM_004304.4	700	Cag/Tag	12/29	1	2	FACETS	0.459	0.38	0.547	0.459	0.38	0.547	SUBCLONAL	1	TRUE	1	0.241249912658158	2		578	723	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143423	30143423	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	51	311	0	ENST00000389048.3:c.103G>T	p.Gly35Trp	p.G35W	ENST00000389048	NM_004304.4	35	Ggg/Tgg	1/29	1	2	FACETS	0.836	0.71	0.973	0.836	0.71	0.973	CLONAL	1	TRUE	1	0.241249912658158	2		311	506	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99181134	99181134	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	55	516	0	ENST00000074304.5:c.2075A>T	p.Lys692Met	p.K692M	ENST00000074304	NM_001134224.1	692	aAg/aTg	20/26	1	2	FACETS	0.653	0.558	0.758	0.653	0.558	0.758	SUBCLONAL	1	TRUE	1	0.241249912658158	2		516	698	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376233	225376233	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	78	446	0	ENST00000264414.4:c.721A>G	p.Ile241Val	p.I241V	ENST00000264414	NM_003590.4	241	Att/Gtt	6/16	1	2	FACETS	0.937	0.823	1	0.937	0.823	1	CLONAL	1	TRUE	1	0.241249912658158	2		446	690	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794431	242794431	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	53	612	0	ENST00000334409.5:c.511G>T	p.Val171Phe	p.V171F	ENST00000334409	NM_005018.2	171	Gtt/Ttt	3/5	1	2	FACETS	0.562	0.478	0.654	0.562	0.478	0.654	SUBCLONAL	1	TRUE	1	0.241249912658158	2		612	782	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017842	31017842	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	66	571	1	ENST00000375687.4:c.704G>T	p.Arg235Leu	p.R235L	ENST00000375687	NM_015338.5	235	cGg/cTg	8/13	1	2	FACETS	0.712	0.617	0.816	0.712	0.617	0.816	SUBCLONAL	1	TRUE	1	0.241249912658158	2		572	768	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384628	31384628	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	72	569	0	ENST00000328111.2:c.1330G>T	p.Val444Leu	p.V444L	ENST00000328111	NM_006892.3	444	Gtg/Ttg	13/23	1	2	FACETS	0.711	0.62	0.81	0.711	0.62	0.81	SUBCLONAL	1	TRUE	1	0.241249912658158	2		569	839	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394054	31394054	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	82	330	0	ENST00000328111.2:c.2341A>G	p.Ile781Val	p.I781V	ENST00000328111	NM_006892.3	781	Atc/Gtc	22/23	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.241249912658158	2		330	530	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961561	54961561	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	30	388	0	ENST00000312783.6:c.71G>T	p.Arg24Leu	p.R24L	ENST00000312783	NM_198436.1	24	cGt/cTt	4/10	1	2	FACETS	0.432	0.347	0.529	0.432	0.347	0.529	SUBCLONAL	1	TRUE	1	0.241249912658158	2		388	576	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478617	57478617	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	55	438	0	ENST00000371085.3:c.289A>T	p.Asn97Tyr	p.N97Y	ENST00000371085	NM_000516.4	97	Aac/Tac	4/13	1	2	FACETS	0.636	0.543	0.738	0.636	0.543	0.738	SUBCLONAL	1	TRUE	1	0.241249912658158	2		438	717	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484255	57484255	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	108	400	0	ENST00000371085.3:c.569A>C	p.Tyr190Ser	p.Y190S	ENST00000371085	NM_000516.4	190	tAt/tCt	7/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.241249912658158	2		400	651	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147497	47147497	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	86	444	0	ENST00000409792.3:c.4829A>G	p.Lys1610Arg	p.K1610R	ENST00000409792	NM_014159.6	1610	aAg/aGg	6/21	0.241249912658158	1	FACETS	0.918	0.812	1	0.918	0.812	1	CLONAL	1	TRUE	0	0.241249912658158	1		444	683	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623272	52623272	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	33	238	0	ENST00000394830.3:c.2780-1G>A		p.X927_splice	ENST00000394830	NM_018313.4	927			0.241249912658158	1	FACETS	0.699	0.57	0.844	0.699	0.57	0.844	SUBCLONAL	1	TRUE	0	0.241249912658158	1		238	344	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52649433	52649433	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	100	600	0	ENST00000394830.3:c.1858G>T	p.Glu620Ter	p.E620*	ENST00000394830	NM_018313.4	620	Gag/Tag	16/30	0.241249912658158	1	FACETS	0.917	0.819	1	0.917	0.819	1	CLONAL	1	TRUE	0	0.241249912658158	1		600	795	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55524249	55524249	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	83	396	0	ENST00000288135.5:c.67+1G>T		p.X23_splice	ENST00000288135	NM_000222.2	23			0.241249912658158	1	FACETS	0.959	0.847	1	0.959	0.847	1	CLONAL	1	TRUE	0	0.241249912658158	1		396	631	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155876	106155876	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	70	435	0	ENST00000380013.4:c.777G>T	p.Glu259Asp	p.E259D	ENST00000380013	NM_001127208.2	259	gaG/gaT	3/11	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.241249912658158	2		435	538	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953183	38953183	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	57	255	1	ENST00000357387.3:c.2801G>T	p.Gly934Val	p.G934V	ENST00000357387	NM_152756.3	934	gGc/gTc	29/38	0.197318564193681	3	FACETS	1	0.953	1	0.633	0.545	0.729	CLONAL	1	TRUE	1	0.241249912658158	3		256	418	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056560	26056560	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	24	225	0	ENST00000343677.2:c.97C>A	p.Arg33Ser	p.R33S	ENST00000343677	NM_005319.3	33	Cgt/Agt	1/1	0.197318564193681	3	FACETS	0.585	0.458	0.732	0.293	0.229	0.366	SUBCLONAL	1	TRUE	1	0.241249912658158	3		225	381	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056576	26056576	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs151213047	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	51	228	0	ENST00000343677.2:c.81G>T	p.Lys27Asn	p.K27N	ENST00000343677	NM_005319.3	27	aaG/aaT	1/1	0.197318564193681	3	FACETS	1	0.951	1	0.646	0.551	0.749	CLONAL	1	TRUE	1	0.241249912658158	3		228	367	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197463	26197463	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	55	248	0	ENST00000356476.2:c.16C>A	p.Gln6Lys	p.Q6K	ENST00000356476		6	Cag/Aag	1/1	0.197318564193681	3	FACETS	1	0.949	1	0.625	0.536	0.721	CLONAL	1	TRUE	1	0.241249912658158	3		248	409	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168659	32168659	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	124	501	0	ENST00000375023.3:c.4264G>T	p.Glu1422Ter	p.E1422*	ENST00000375023	NM_004557.3	1422	Gag/Tag	23/30	0.197318564193681	3	FACETS	0.753	0.681	0.828	0.753	0.681	0.828	SUBCLONAL	2	TRUE	1	0.241249912658158	3		501	765	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178542	32178542	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	91	429	0	ENST00000375023.3:c.2852G>T	p.Gly951Val	p.G951V	ENST00000375023	NM_004557.3	951	gGg/gTg	18/30	0.197318564193681	3	FACETS	1	0.976	1	0.696	0.619	0.779	CLONAL	1	TRUE	1	0.241249912658158	3		429	607	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94128982	94128982	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	36	325	0	ENST00000369303.4:c.78G>T	p.Glu26Asp	p.E26D	ENST00000369303	NM_004440.3	26	gaG/gaT	1/17	0.241249912658158	1	FACETS	0.564	0.464	0.677	0.564	0.464	0.677	SUBCLONAL	1	TRUE	0	0.241249912658158	1		325	465	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38139077	38139077	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	108	506	0	ENST00000317025.8:c.3526G>T	p.Gly1176Cys	p.G1176C	ENST00000317025	NM_023034.1	1176	Ggt/Tgt	20/24	1	2	FACETS	0.939	0.841	1	0.939	0.841	1	CLONAL	1	TRUE	1	0.241249912658158	2		506	954	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68984783	68984783	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	62	367	0	ENST00000288368.4:c.1547T>A	p.Leu516Gln	p.L516Q	ENST00000288368	NM_024870.2	516	cTg/cAg	14/40	1	2	FACETS	0.9	0.778	1	0.9	0.778	1	CLONAL	1	TRUE	1	0.241249912658158	2		367	571	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993699	90993699	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782179	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	30	293	0	ENST00000265433.3:c.224G>T	p.Gly75Val	p.G75V	ENST00000265433	NM_002485.4	75	gGt/gTt	3/16	1	2	FACETS	0.424	0.34	0.519	0.424	0.34	0.519	SUBCLONAL	1	TRUE	1	0.241249912658158	2		293	587	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449734	8449734	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs773381158	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	54	452	0	ENST00000356435.5:c.3979C>G	p.Gln1327Glu	p.Q1327E	ENST00000356435		1327	Caa/Gaa	23/35	0.241249912658158	1	FACETS	0.516	0.44	0.6	0.516	0.44	0.6	SUBCLONAL	1	TRUE	0	0.241249912658158	1		452	763	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485981	8485981	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	72	494	0	ENST00000356435.5:c.2836G>T	p.Glu946Ter	p.E946*	ENST00000356435		946	Gag/Tag	17/35	0.241249912658158	1	FACETS	0.769	0.671	0.874	0.769	0.671	0.874	SUBCLONAL	1	TRUE	0	0.241249912658158	1		494	683	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157971	27157971	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	51	490	0	ENST00000380036.4:c.195G>C	p.Met65Ile	p.M65I	ENST00000380036	NM_000459.3	65	atG/atC	2/23	0.241249912658158	1	FACETS	0.521	0.442	0.609	0.521	0.442	0.609	SUBCLONAL	1	TRUE	0	0.241249912658158	1		490	713	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37006527	37006527	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	46	364	0	ENST00000358127.4:c.418C>G	p.Arg140Gly	p.R140G	ENST00000358127	NM_001280556.1	140	Cgg/Ggg	4/10	0.241249912658158	1	FACETS	0.59	0.497	0.694	0.59	0.497	0.694	SUBCLONAL	1	TRUE	0	0.241249912658158	1		364	568	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250028	110250028	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	56	534	0	ENST00000374672.4:c.647A>T	p.Gln216Leu	p.Q216L	ENST00000374672	NM_004235.4	216	cAg/cTg	3/5	0.241249912658158	1	FACETS	0.663	0.567	0.767	0.663	0.567	0.767	SUBCLONAL	1	TRUE	0	0.241249912658158	1		534	616	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139562798	139562798	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	59	640	0	ENST00000308874.7:c.64C>G	p.His22Asp	p.H22D	ENST00000308874		22	Cac/Gac	3/10	0.241249912658158	1	FACETS	0.591	0.507	0.682	0.591	0.507	0.682	SUBCLONAL	1	TRUE	0	0.241249912658158	1		640	728	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239954	53239954	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	88	272	0	ENST00000375401.3:c.1487G>T	p.Gly496Val	p.G496V	ENST00000375401	NM_004187.3	496	gGc/gTc	11/26	0.0843656296701538	2	FACETS	0.765	0.68	0.854			1	INDETERMINATE	2	TRUE	NA	0.241249912658158	2		272	477	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492758	50492760	+	missense_variant	Missense_Mutation	TNP	AAG	AAG	CAT	novel	NA	P-0034364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	70	500	0	ENST00000394963.4:c.1523_1525delinsCAT	p.Gln508_Ala509delinsProSer	p.Q508_A509delinsPS	ENST00000394963	NM_003076.4	508	cAAGcc/cCATcc	13/13	1	2	FACETS	0.786	0.685	0.896	0.786	0.685	0.896	SUBCLONAL	1	TRUE	1	0.241249912658158	2		500	738	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0034366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	259	530	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.650694020464005	3	FACETS	1	0.97	1	0.529	0.495	0.563	CLONAL	1	TRUE	1	0.650694020464005	3		530	998	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475061	40475063	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0034366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	83	583	0	ENST00000264657.5:c.1847_1849del	p.Glu616del	p.E616del	ENST00000264657	NM_139276.2	616	gAAGga/gga	20/24	0.650694020464005	3	FACETS	0.343	0.302	0.387	0.171	0.151	0.194	SUBCLONAL	1	TRUE	1	0.650694020464005	3		583	986	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17125831	17125831	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879255664	NA	P-0034366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	73	557	0	ENST00000285071.4:c.763C>T	p.His255Tyr	p.H255Y	ENST00000285071	NM_144997.5	255	Cac/Tac	7/14	0.299690315075898	1	FACETS	0.253	0.221	0.287	0.253	0.221	0.287	INDETERMINATE	1	TRUE	0	0.650694020464005	1		557	599	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0034367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	29	384	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.81	1	1	0.81	1	CLONAL	1	TRUE	1	0.12	2		384	478	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0034367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	37	310	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.826	1	1	0.826	1	CLONAL	1	TRUE	1	0.12	2		310	614	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0034367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	23	437	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.734	0.571	0.925	0.734	0.571	0.925	CLONAL	1	TRUE	1	0.12	2		437	522	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228979	36228979	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555734923	NA	P-0034367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	48	438	0	ENST00000222270.7:c.7759C>T	p.Arg2587Ter	p.R2587*	ENST00000222270	NM_014727.1	2587	Cga/Tga	36/37	1	2	FACETS	0.891	0.751	1	0.891	0.751	1	CLONAL	1	TRUE	1	0.12	2		438	898	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133887	41133887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755827604	NA	P-0034367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	31	238	0	ENST00000379561.5:c.1741G>A	p.Val581Met	p.V581M	ENST00000379561	NM_002015.3	581	Gtg/Atg	2/3	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.12	2		238	438	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650665	67650665	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	47	302	0	ENST00000264010.4:c.970T>C	p.Cys324Arg	p.C324R	ENST00000264010	NM_006565.3	324	Tgc/Cgc	5/12	1	2	FACETS	0.943	0.793	1	0.943	0.793	1	CLONAL	1	TRUE	1	0.12	2		302	831	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7141749	7141749	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	54	446	0	ENST00000302850.5:c.2621C>T	p.Pro874Leu	p.P874L	ENST00000302850	NM_000208.2	874	cCg/cTg	13/22	1	2	FACETS	0.917	0.781	1	0.917	0.781	1	CLONAL	1	TRUE	1	0.12	2		446	981	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160239	22160239	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	32	247	0	ENST00000215832.6:c.392A>T	p.Tyr131Phe	p.Y131F	ENST00000215832	NM_002745.4	131	tAc/tTc	3/9	1	2	FACETS	1	0.827	1	1	0.827	1	CLONAL	1	TRUE	1	0.12	2		247	522	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0034375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	648	258	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	0.664969193703294	4	FACETS	0.975	0.953	0.996	0.975	0.953	0.996	CLONAL	4	TRUE	0	0.664969193703294	4		258	832	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555526268	NA	P-0034375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	252	528	0	ENST00000269305.4:c.406C>G	p.Gln136Glu	p.Q136E	ENST00000269305	NM_001126112.2	136	Caa/Gaa	5/11	0.656174334410839	3	FACETS	0.892	0.834	0.952	0.446	0.417	0.476	CLONAL	1	TRUE	1	0.664969193703294	3		528	1132	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578525	7578525	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519976	NA	P-0034375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	530	526	0	ENST00000269305.4:c.405C>G	p.Cys135Trp	p.C135W	ENST00000269305	NM_001126112.2	135	tgC/tgG	5/11	0.656174334410839	3	FACETS	0.94	0.904	0.975	0.94	0.904	0.975	CLONAL	2	TRUE	1	0.664969193703294	3		526	1130	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818230	32818230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147332077	NA	P-0034375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	190	483	0	ENST00000354258.4:c.1295C>T	p.Ser432Leu	p.S432L	ENST00000354258	NM_000593.5	432	tCg/tTg	5/11	0.656174334410839	3	FACETS	0.875	0.81	0.943	0.438	0.405	0.472	CLONAL	1	TRUE	1	0.664969193703294	3		483	870	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261134	16261134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367966477	NA	P-0034375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	178	344	0	ENST00000375759.3:c.8399C>T	p.Ala2800Val	p.A2800V	ENST00000375759	NM_015001.2	2800	gCg/gTg	11/15	0.58632395882484	2	FACETS	1	0.962	1	0.527	0.489	0.565	CLONAL	1	TRUE	0	0.664969193703294	2		344	508	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004224	29004224	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	236	257	0	ENST00000282397.4:c.1069A>G	p.Met357Val	p.M357V	ENST00000282397	NM_002019.4	357	Atg/Gtg	8/30	0.588162398452262	2	FACETS	0.778	0.736	0.82	0.778	0.736	0.82	SUBCLONAL	2	TRUE	0	0.664969193703294	2		257	456	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30047489	30047489	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	131	327	0	ENST00000331968.5:c.2512T>G	p.Trp838Gly	p.W838G	ENST00000331968	NM_002742.2	838	Tgg/Ggg	17/18	1	2	FACETS	0.835	0.763	0.91	0.835	0.763	0.91	CLONAL	1	TRUE	1	0.664969193703294	2		327	472	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288489	15288489	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	383	185	0	ENST00000263388.2:c.4250G>T	p.Cys1417Phe	p.C1417F	ENST00000263388	NM_000435.2	1417	tGc/tTc	24/33	0.646804900522363	4	FACETS	0.991	0.962	1	0.991	0.962	1	CLONAL	4	TRUE	0	0.664969193703294	4		185	484	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248541	212248541	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	302	484	0	ENST00000342788.4:c.3726C>A	p.Tyr1242Ter	p.Y1242*	ENST00000342788	NM_005235.2	1242	taC/taA	28/28	0.441611108641126	3	FACETS	0.756	0.715	0.797	0.756	0.715	0.797	SUBCLONAL	2	TRUE	1	0.664969193703294	3		484	801	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42840432	42840432	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs769565200	NA	P-0034375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	168	413	0	ENST00000398585.3:c.1316T>C	p.Val439Ala	p.V439A	ENST00000398585	NM_001135099.1	439	gTg/gCg	12/14	0.58632395882484	2	FACETS	0.801	0.739	0.865	0.4	0.369	0.433	CLONAL	1	TRUE	0	0.664969193703294	2		413	631	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448540	89448540	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs75391524	NA	P-0034375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	295	309	0	ENST00000336596.2:c.1504G>T	p.Asp502Tyr	p.D502Y	ENST00000336596	NM_005233.5	502	Gac/Tac	7/17	0.58632395882484	2	FACETS	0.855	0.816	0.894	0.855	0.816	0.894	CLONAL	2	TRUE	0	0.664969193703294	2		309	519	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462358	89462358	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	301	378	1	ENST00000336596.2:c.1830T>A	p.His610Gln	p.H610Q	ENST00000336596	NM_005233.5	610	caT/caA	10/17	0.58632395882484	2	FACETS	0.854	0.815	0.892	0.854	0.815	0.892	CLONAL	2	TRUE	0	0.664969193703294	2		379	530	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55130079	55130079	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	156	446	1	ENST00000257290.5:c.613G>T	p.Val205Phe	p.V205F	ENST00000257290	NM_006206.4	205	Gtt/Ttt	4/23	0.463678021899527	3	FACETS	0.838	0.769	0.91			1	CLONAL	1	TRUE	NA	0.664969193703294	3		447	746	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80088550	80088550	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0034375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	80	178	0	ENST00000265081.6:c.2544-2A>T		p.X848_splice	ENST00000265081	NM_002439.4	848			0.45506028811393	3	FACETS	0.954	0.847	1	0.477	0.423	0.534	CLONAL	1	TRUE	1	0.664969193703294	3		178	336	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0034378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	41	395	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.369136215861597	1	FACETS	0.633	0.531	0.743	0.633	0.531	0.743	SUBCLONAL	1	TRUE	0	0.439662571530351	1		396	230	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37665992	37665992	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	73	425	0	ENST00000447079.4:c.2644C>T	p.Arg882Trp	p.R882W	ENST00000447079	NM_015083.1	882	Cgg/Tgg	7/14	0.203534082987764	5	FACETS	0.792	0.697	0.892			1	INDETERMINATE	2	TRUE	NA	0.439662571530351	5		425	348	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571444	95571451	+	frameshift_variant	Frame_Shift_Del	DEL	GCATCGCT	GCATCGCT	-	novel	NA	P-0034378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	84	279	0	ENST00000393063.1:c.3226_3233del	p.Ser1076TrpfsTer12	p.S1076Wfs*12	ENST00000393063	NM_030621.3	1076	AGCGATGCt/t	21/28	0.354802792340082	3	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	1	0.439662571530351	3		279	222	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650818	37650818	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	159	592	0	ENST00000447079.4:c.2292del	p.Glu765ArgfsTer17	p.E765Rfs*17	ENST00000447079	NM_015083.1	764	Aaa/aa	5/14	0.203534082987764	5	FACETS	0.978	0.907	1			1	INDETERMINATE	3	TRUE	NA	0.439662571530351	5		592	409	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602838	10602838	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	56	738	1	ENST00000171111.5:c.740A>T	p.His247Leu	p.H247L	ENST00000171111	NM_203500.1	247	cAc/cTc	3/6	1	2	FACETS	0.551	0.473	0.637	0.551	0.473	0.637	SUBCLONAL	1	TRUE	1	0.439662571530351	2		739	462	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537103	80537103	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	42	572	0	ENST00000286548.4:c.295A>T	p.Ile99Phe	p.I99F	ENST00000286548	NM_002072.3	99	Atc/Ttc	2/7	NA	2	FACETS	0.481	0.402	0.569			1	INDETERMINATE	1	TRUE	NA	0.439662571530351	2		572	397	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0034380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	47	438	1	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.224473014714554	2	FACETS	1	0.943	1	0.61	0.522	0.704	INDETERMINATE	1	FALSE	0	0.418569253369796	2		439	184	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0034380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	41	378	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.207769064636215	1	FACETS	0.688	0.579	0.808	0.688	0.579	0.808	INDETERMINATE	1	FALSE	0	0.418569253369796	1		378	225	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057520005	NA	P-0034380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	104	633	0	ENST00000269305.4:c.820G>C	p.Val274Leu	p.V274L	ENST00000269305	NM_001126112.2	274	Gtt/Ctt	8/11	0.386294367235948	1	FACETS	0.709	0.637	0.785	0.709	0.637	0.785	SUBCLONAL	1	FALSE	0	0.418569253369796	1		633	554	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167577	NA	P-0034380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	30	312	0	ENST00000257430.4:c.4463del	p.Leu1488TyrfsTer19	p.L1488Yfs*19	ENST00000257430	NM_000038.5	1487	acT/ac	16/16	0.207769064636215	1	FACETS	0.527	0.427	0.639	0.527	0.427	0.639	INDETERMINATE	1	FALSE	0	0.418569253369796	1		312	215	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513309	44513309	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568949835	NA	P-0034380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	78	540	3	ENST00000291552.4:c.626G>A	p.Arg209His	p.R209H	ENST00000291552	NM_006758.2	209	cGt/cAt	8/8	1	2	FACETS	0.574	0.505	0.649	0.574	0.505	0.649	SUBCLONAL	1	FALSE	1	0.418569253369796	2		543	649	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003452	42003452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	19	473	0	ENST00000219905.7:c.2989G>A	p.Asp997Asn	p.D997N	ENST00000219905	NM_001164273.1	997	Gac/Aac	8/24	0.418569253369796	1	FACETS	0.297	0.225	0.38	0.297	0.225	0.38	SUBCLONAL	1	FALSE	0	0.418569253369796	1		473	242	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	180	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.116105069919659	0	FACETS	1	0.964	1			1	INDETERMINATE	2	FALSE	0	0.246934928423973	0		493	518	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0034382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	126	155	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	0.246934928423973	5	FACETS	1	0.972	1	0.868	0.793	0.945	CLONAL	3	FALSE	1	0.246934928423973	5		155	403	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962930	2962930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1349831751	NA	P-0034382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	240	190	0	ENST00000396946.4:c.1978C>T	p.Arg660Trp	p.R660W	ENST00000396946	NM_032415.4	660	Cgg/Tgg	16/25	0.246934928423973	4	FACETS	0.911	0.856	0.968			1	CLONAL	4	FALSE	NA	0.246934928423973	4		190	665	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468381	89468381	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754102338	NA	P-0034382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	116	189	0	ENST00000336596.2:c.1915C>T	p.Arg639Cys	p.R639C	ENST00000336596	NM_005233.5	639	Cgc/Tgc	11/17	0.246934928423973	1	FACETS	0.874	0.799	0.951	1	0.991	1	CLONAL	3	FALSE	0	0.246934928423973	1		189	314	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244064	46244064	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	199	312	0	ENST00000334344.6:c.2158C>T	p.Gln720Ter	p.Q720*	ENST00000334344	NM_152641.2	720	Cag/Tag	15/21	0.116105069919659	0	FACETS	1	0.966	1			1	INDETERMINATE	2	FALSE	0	0.246934928423973	0		312	575	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007900	45007900	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs111352556	NA	P-0034382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	152	234	0	ENST00000558401.1:c.346+1G>A		p.X116_splice	ENST00000558401	NM_004048.2	116			0.246934928423973	0	FACETS	0.81	0.757	0.864			1	CLONAL	4	FALSE	0	0.246934928423973	0		234	286	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273821	18273821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	171	234	0	ENST00000222254.8:c.1154G>A	p.Gly385Glu	p.G385E	ENST00000222254	NM_005027.3	385	gGg/gAg	10/16	0.147345278944554	4	FACETS	0.855	0.79	0.923	1	0.985	1	INDETERMINATE	3	FALSE	2	0.246934928423973	4		234	673	SUCCESS
APC	324	MSKCC	GRCh37	5	112175537	112175537	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	258	176	0	ENST00000257430.4:c.4247del	p.Gly1416AlafsTer3	p.G1416Afs*3	ENST00000257430	NM_000038.5	1416	Ggc/gc	16/16	0.246934928423973	5	FACETS	0.955	0.905	1	1	0.994	1	CLONAL	6	FALSE	1	0.246934928423973	5		176	500	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141582942	141582942	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	52	253	0	ENST00000220592.5:c.305C>G	p.Thr102Arg	p.T102R	ENST00000220592	NM_012154.3	102	aCa/aGa	3/19	0.246934928423973	5	FACETS	0.655	0.556	0.765	0.218	0.185	0.255	SUBCLONAL	1	FALSE	2	0.246934928423973	5		253	881	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0034385-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	38	547	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.549532450113852	3	FACETS	0.899	0.767	1	0.899	0.767	1	CLONAL	2	TRUE	1	0.549532450113852	3		547	98	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034385-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	355	912	0	ENST00000269305.4:c.383del	p.Pro128LeufsTer42	p.P128Lfs*42	ENST00000269305	NM_001126112.2	128	cCt/ct	5/11	0.52388616398142	2	FACETS	0.906	0.865	0.947	0.906	0.865	0.947	CLONAL	2	TRUE	0	0.549532450113852	2		912	713	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593455	215593455	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881425	NA	P-0034385-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	67	310	0	ENST00000260947.4:c.2279C>T	p.Ser760Leu	p.S760L	ENST00000260947	NM_000465.2	760	tCg/tTg	11/11	1	2	FACETS	0.9	0.79	1	0.9	0.79	1	CLONAL	1	TRUE	1	0.549532450113852	2		310	271	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0034390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	143	527	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.69	0.631	0.752	0.69	0.631	0.752	SUBCLONAL	1	TRUE	1	0.619381929419716	2		527	669	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0034390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	99	427	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.549	0.491	0.611	0.549	0.491	0.611	SUBCLONAL	1	TRUE	1	0.619381929419716	2		427	582	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654615	67654615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	136	485	0	ENST00000264010.4:c.1102C>T	p.Arg368Cys	p.R368C	ENST00000264010	NM_006565.3	368	Cgt/Tgt	6/12	0.552247029643355	1	FACETS	0.486	0.443	0.531	0.486	0.443	0.531	SUBCLONAL	1	TRUE	0	0.619381929419716	1		485	624	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209525	98209525	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771238114	NA	P-0034391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	67	591	0	ENST00000331920.6:c.4013G>A	p.Arg1338His	p.R1338H	ENST00000331920	NM_000264.3	1338	cGc/cAc	23/24	0.255635311226833	1	FACETS	0.629	0.546	0.72	0.629	0.546	0.72	SUBCLONAL	1	TRUE	0	0.24	1		591	781	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576910	7576981	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTGTTGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAAAGTGAATCTGAGGCATAACTGCACCC	GGTGTTGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAAAGTGAATCTGAGGCATAACTGCACCC	-	novel	NA	P-0034391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	191	620	0	ENST00000269305.4:c.919+38_936del		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	0.3	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.24	1		620	988	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120330	94120330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465849290	NA	P-0034391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	40	389	0	ENST00000369303.4:c.721G>A	p.Glu241Lys	p.E241K	ENST00000369303	NM_004440.3	241	Gaa/Aaa	3/17	1	2	FACETS	0.636	0.528	0.757	0.636	0.528	0.757	SUBCLONAL	1	TRUE	1	0.24	2		389	524	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943749	9943749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	299	673	0	ENST00000330684.3:c.1192G>A	p.Asp398Asn	p.D398N	ENST00000330684	NM_001134407.1	398	Gac/Aac	5/13	0.348916732909387	3	FACETS	1	0.986	1	0.572	0.539	0.606	INDETERMINATE	1	TRUE	1	0.663545956032455	3		673	1049	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196170	108196170	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	294	596	0	ENST00000278616.4:c.6706G>T	p.Glu2236Ter	p.E2236*	ENST00000278616	NM_000051.3	2236	Gaa/Taa	46/63	0.663545956032455	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.663545956032455	1		596	565	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0034394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	172	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.172950673394383	5	FACETS	0.91	0.838	0.984	0.606	0.559	0.656	INDETERMINATE	2	TRUE	2	0.38322784897876	5		539	777	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0034394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	441	460	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.154605538115923	3	FACETS	1	0.988	1			1	INDETERMINATE	3	TRUE	NA	0.38322784897876	3		460	854	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381436	81381436	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	112	332	0	ENST00000222390.5:c.625G>A	p.Val209Ile	p.V209I	ENST00000222390	NM_000601.4	209	Gtt/Att	5/18	0.101491198925383	4	FACETS	0.949	0.86	1	0.949	0.86	1	INDETERMINATE	2	TRUE	2	0.38322784897876	4		332	426	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	80	349	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.835	0.741	0.934	1	0.981	1	CLONAL	2	FALSE	1	0.288528688643749	2		349	332	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0034398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	93	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.288528688643749	2		539	544	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0034398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	52	246	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	FALSE	1	0.288528688643749	2		246	326	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0034398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	68	254	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	1	0.288528688643749	2		254	408	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894916	101894916	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060502040	NA	P-0034398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	102	408	2	ENST00000374994.4:c.469C>T	p.Arg157Ter	p.R157*	ENST00000374994	NM_004612.2	157	Cga/Tga	3/9	0.288528688643749	0	FACETS	1	0.957	1			1	CLONAL	1	FALSE	0	0.288528688643749	0		410	449	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919653	50919653	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	157	610	0	ENST00000440232.2:c.2821G>A	p.Asp941Asn	p.D941N	ENST00000440232	NM_002691.3	941	Gac/Aac	23/27	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.288528688643749	2		610	800	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437842	52437843	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0034399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	120	557	0	ENST00000460680.1:c.1318_1319del	p.Leu440AlafsTer10	p.L440Afs*10	ENST00000460680	NM_004656.3	440	CTg/g	13/17	1	2	FACETS	0.801	0.724	0.882	1	0.986	1	CLONAL	2	TRUE	1	0.204384322860922	2		557	733	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	139	405	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.278423011144438	2		408	670	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	339	506	13	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.846	0.803	0.891	1	0.997	1	CLONAL	3	TRUE	1	0.278423011144438	2		519	959	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	183	614	1	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	0.278423011144438	2		615	1034	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	177	634	0	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.278423011144438	2		634	1000	SUCCESS
APC	324	MSKCC	GRCh37	5	112170746	112170747	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	176	625	0	ENST00000257430.4:c.1847dup	p.Leu616PhefsTer18	p.L616Ffs*18	ENST00000257430	NM_000038.5	614	-/T	15/16	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.278423011144438	2		625	974	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913559	32913559	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359479	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	72	399	2	ENST00000380152.3:c.5073del	p.Lys1691AsnfsTer15	p.K1691Nfs*15	ENST00000380152		1689	gcA/gc	11/27	1	2	FACETS	0.817	0.714	0.928	0.817	0.714	0.928	CLONAL	1	TRUE	1	0.278423011144438	2		401	633	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243923	5243923	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778260386	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	123	450	0	ENST00000357368.4:c.1559C>T	p.Thr520Met	p.T520M	ENST00000357368	NM_002850.3	520	aCg/aTg	11/38	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.278423011144438	2		450	678	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	75	340	3	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.278423011144438	2		343	477	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539996	187539996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376609881	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	39	439	0	ENST00000441802.2:c.7744G>A	p.Val2582Met	p.V2582M	ENST00000441802	NM_005245.3	2582	Gtg/Atg	10/27	1	2	FACETS	0.391	0.323	0.468	0.391	0.323	0.468	SUBCLONAL	1	TRUE	1	0.278423011144438	2		439	716	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	135	492	3	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.278423011144438	2		495	723	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827886	40827886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201911869	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	139	475	1	ENST00000373198.4:c.2542G>A	p.Gly848Arg	p.G848R	ENST00000373198	NM_133170.3	848	Gga/Aga	17/32	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.278423011144438	2		476	816	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020764	37020764	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	151	448	1	ENST00000358127.4:c.81del	p.Phe27LeufsTer2	p.F27Lfs*2	ENST00000358127	NM_001280556.1	27	ttT/tt	2/10	0.278423011144438	3	FACETS	1	0.985	1	0.678	0.62	0.739	CLONAL	1	TRUE	1	0.278423011144438	3		449	911	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157385	106157385	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	78	327	1	ENST00000380013.4:c.2290del	p.Gln764LysfsTer49	p.Q764Kfs*49	ENST00000380013	NM_001127208.2	762	caC/ca	3/11	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.278423011144438	2		328	506	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394367	162394367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144032774	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	134	487	1	ENST00000366898.1:c.701G>A	p.Arg234Gln	p.R234Q	ENST00000366898	NM_004562.2	234	cGg/cAg	6/12	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.278423011144438	2		488	711	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182601	99182601	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	112	400	1	ENST00000074304.5:c.2404G>T	p.Gly802Cys	p.G802C	ENST00000074304	NM_001134224.1	802	Ggc/Tgc	22/26	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.278423011144438	2		401	666	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	205	696	1	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.278423011144438	2		697	1171	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324917	31324917	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	191	470	0	ENST00000412585.2:c.19del	p.Arg7GlufsTer13	p.R7Efs*13	ENST00000412585	NM_005514.6	7	Cga/ga	1/8	1	2	FACETS	0.945	0.876	1	1	0.993	1	CLONAL	2	TRUE	1	0.278423011144438	2		470	726	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089123	37089125	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs63751247	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	130	494	0	ENST00000231790.2:c.1852_1854del	p.Lys618del	p.K618del	ENST00000231790	NM_000249.3	615	ctGAAg/ctg	16/19	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.278423011144438	2		494	826	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26911748	26911748	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	100	352	0	ENST00000381527.3:c.173G>T	p.Gly58Val	p.G58V	ENST00000381527	NM_001260.1	58	gGg/gTg	2/13	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.278423011144438	2		352	631	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681462	30681463	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1185288475	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	129	467	0	ENST00000376406.3:c.549dup	p.Ser184IlefsTer14	p.S184Ifs*14	ENST00000376406	NM_014641.2	183	-/A	4/15	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.278423011144438	2		467	839	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753233	42753233	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377467874	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	228	647	1	ENST00000222329.4:c.1031G>A	p.Arg344His	p.R344H	ENST00000222329	NM_006494.2	344	cGc/cAc	4/4	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.278423011144438	2		648	1111	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443530	49443530	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755192273	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	154	507	0	ENST00000301067.7:c.3841G>A	p.Gly1281Arg	p.G1281R	ENST00000301067	NM_003482.3	1281	Gga/Aga	11/54	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.278423011144438	2		507	916	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923269	26923269	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	118	466	1	ENST00000381527.3:c.265G>A	p.Ala89Thr	p.A89T	ENST00000381527	NM_001260.1	89	Gct/Act	3/13	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.278423011144438	2		467	733	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821341	72821341	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200494604	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	78	310	0	ENST00000268489.5:c.10834G>A	p.Ala3612Thr	p.A3612T	ENST00000268489	NM_006885.3	3612	Gcc/Acc	10/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.278423011144438	2		310	428	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108229	8108229	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879004728	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	146	544	0	ENST00000585124.1:c.995G>A	p.Arg332Gln	p.R332Q	ENST00000585124	NM_004217.3	332	cGg/cAg	9/9	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.278423011144438	2		544	910	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215573	5215573	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	125	620	0	ENST00000357368.4:c.4130A>T	p.Asp1377Val	p.D1377V	ENST00000357368	NM_002850.3	1377	gAc/gTc	27/38	1	2	FACETS	0.856	0.773	0.943	0.856	0.773	0.943	CLONAL	1	TRUE	1	0.278423011144438	2		620	1049	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212162	36212162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	122	384	0	ENST00000222270.7:c.1913C>T	p.Ala638Val	p.A638V	ENST00000222270	NM_014727.1	638	gCc/gTc	3/37	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.278423011144438	2		384	652	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852421	42852421	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	174	460	0	ENST00000398585.3:c.665G>A	p.Cys222Tyr	p.C222Y	ENST00000398585	NM_001135099.1	222	tGc/tAc	6/14	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.278423011144438	2		460	906	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467733	66467733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	127	424	0	ENST00000273854.3:c.536C>T	p.Ala179Val	p.A179V	ENST00000273854	NM_004439.5	179	gCc/gTc	3/18	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.278423011144438	2		424	697	SUCCESS
APC	324	MSKCC	GRCh37	5	112173317	112173318	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	68	234	0	ENST00000257430.4:c.2027_2028del	p.Ile676SerfsTer3	p.I676Sfs*3	ENST00000257430	NM_000038.5	676	ATa/a	16/16	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.278423011144438	2		234	400	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503846	149503846	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770122404	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	162	553	1	ENST00000261799.4:c.1990G>A	p.Val664Met	p.V664M	ENST00000261799	NM_002609.3	664	Gtg/Atg	14/23	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.278423011144438	2		554	851	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100399	157100399	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	12	88	0	ENST00000346085.5:c.1337del	p.Pro446ArgfsTer56	p.P446Rfs*56	ENST00000346085	NM_020732.3	446	Ccg/cg	1/20	1	2	FACETS	0.582	0.411	0.791	0.582	0.411	0.791	SUBCLONAL	1	TRUE	1	0.278423011144438	2		88	148	SUCCESS
MET	4233	MSKCC	GRCh37	7	116381069	116381069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	197	568	0	ENST00000397752.3:c.1691C>T	p.Ala564Val	p.A564V	ENST00000397752	NM_000245.2	564	gCa/gTa	5/21	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.278423011144438	2		568	987	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275466	38275466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	179	605	0	ENST00000425967.3:c.1567G>A	p.Val523Met	p.V523M	ENST00000425967	NM_001174067.1	523	Gtg/Atg	12/19	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.278423011144438	2		605	1057	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041567	47041567	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	155	308	0	ENST00000377604.3:c.1792T>C	p.Tyr598His	p.Y598H	ENST00000377604	NM_001204468.1	598	Tac/Cac	17/24	1	1	FACETS	1	0.955	1	1	0.992	1	CLONAL	2	TRUE	0	0.278423011144438	1		308	457	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246416	53246416	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	40	325	0	ENST00000375401.3:c.566A>G	p.Glu189Gly	p.E189G	ENST00000375401	NM_004187.3	189	gAa/gGa	5/26	1	1	FACETS	0.4	0.331	0.476	0.4	0.331	0.476	SUBCLONAL	1	TRUE	0	0.278423011144438	1		325	619	SUCCESS
AR	367	MSKCC	GRCh37	X	66905902	66905902	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	24	224	0	ENST00000374690.3:c.1819T>A	p.Phe607Ile	p.F607I	ENST00000374690	NM_000044.3	607	Ttc/Atc	3/8	1	1	FACETS	0.391	0.306	0.488	0.391	0.306	0.488	SUBCLONAL	1	TRUE	0	0.278423011144438	1		224	380	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89866042	89866042	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752799441	NA	P-0034401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	140	462	2	ENST00000389301.3:c.797C>T	p.Thr266Met	p.T266M	ENST00000389301	NM_000135.2	266	aCg/aTg	9/43	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.278423011144438	2		464	804	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491645	56491645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	105	503	0	ENST00000267101.3:c.2537G>T	p.Ser846Ile	p.S846I	ENST00000267101	NM_001982.3	846	aGt/aTt	21/28	0.0937345531106142	3	FACETS	1	0.939	1	0.534	0.479	0.593	INDETERMINATE	1	TRUE	1	0.319205641933078	3		503	714	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056560	26056560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766992808	NA	P-0034408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	48	233	0	ENST00000343677.2:c.97C>T	p.Arg33Cys	p.R33C	ENST00000343677	NM_005319.3	33	Cgt/Tgt	1/1	1	2	FACETS	0.85	0.721	0.99	0.85	0.721	0.99	CLONAL	1	TRUE	1	0.319205641933078	2		233	354	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099014	27099015	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0034408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	97	422	0	ENST00000324856.7:c.3432_3433del	p.Gln1145AspfsTer47	p.Q1145Dfs*47	ENST00000324856	NM_006015.4	1144	CCc/c	13/20	0.319205641933078	1	FACETS	0.973	0.87	1	0.973	0.87	1	CLONAL	1	TRUE	0	0.319205641933078	1		422	525	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81557427	81557427	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	75	497	0	ENST00000298171.2:c.407C>A	p.Thr136Asn	p.T136N	ENST00000298171	NM_000369.2	136	aCt/aAt	5/10	1	2	FACETS	0.82	0.719	0.928	0.82	0.719	0.928	CLONAL	1	TRUE	1	0.319205641933078	2		497	573	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs80338963	NA	P-0034408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	102	490	0	ENST00000342988.3:c.1081C>G	p.Arg361Gly	p.R361G	ENST00000342988	NM_005359.5	361	Cgc/Ggc	9/12	0.319205641933078	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.319205641933078	1		490	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0034411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	372	851	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.438074869440188	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.438074869440188	2		851	756	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	373	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.438074869440188	3	FACETS	0.893	0.853	0.933	1	0.995	1	CLONAL	3	TRUE	1	0.438074869440188	3		493	775	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0034411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	134	255	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.220337894832832	3	FACETS	1	0.963	1	0.718	0.661	0.777	INDETERMINATE	2	TRUE	0	0.438074869440188	3		255	346	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094360	27094360	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	42	468	0	ENST00000324856.7:c.3068G>A	p.Trp1023Ter	p.W1023*	ENST00000324856	NM_006015.4	1023	tGg/tAg	11/20	0.142099634246742	3	FACETS	0.296	0.246	0.351	0.148	0.123	0.176	INDETERMINATE	1	TRUE	1	0.438074869440188	3		468	791	SUCCESS
APC	324	MSKCC	GRCh37	5	112175351	112175351	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	50	232	0	ENST00000257430.4:c.4063del	p.Ser1355LeufsTer60	p.S1355Lfs*60	ENST00000257430	NM_000038.5	1354	Ttt/tt	16/16	0.220337894832832	3	FACETS	0.875	0.746	1	0.292	0.248	0.339	INDETERMINATE	1	TRUE	0	0.438074869440188	3		232	318	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460389	149460389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761230419	NA	P-0034411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	112	487	0	ENST00000286301.3:c.248G>A	p.Arg83His	p.R83H	ENST00000286301	NM_005211.3	83	cGc/cAc	3/22	0.220337894832832	3	FACETS	0.787	0.708	0.871	0.262	0.236	0.291	INDETERMINATE	1	TRUE	0	0.438074869440188	3		487	792	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971135	18971135	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1195464113	NA	P-0034411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	63	515	0	ENST00000262803.5:c.2188C>T	p.Arg730Cys	p.R730C	ENST00000262803	NM_002911.3	730	Cgt/Tgt	16/24	0.438074869440188	3	FACETS	0.344	0.296	0.396	0.172	0.148	0.198	SUBCLONAL	1	TRUE	1	0.438074869440188	3		515	1019	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576913	7576914	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0034411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	68	527	0	ENST00000269305.4:c.932dup	p.Asn311LysfsTer26	p.N311Kfs*26	ENST00000269305	NM_001126112.2	311	aac/aaAc	9/11	0.438074869440188	2	FACETS	0.41	0.356	0.468	0.205	0.178	0.234	SUBCLONAL	1	TRUE	0	0.438074869440188	2		527	758	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64288422	64288423	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATCC	novel	NA	P-0034411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	43	319	0	ENST00000370651.3:c.189_192dup	p.Val65ProfsTer4	p.V65Pfs*4	ENST00000370651	NM_003463.4	62	-/ATCC	3/6	0.438074869440188	3	FACETS	0.376	0.314	0.446	0.188	0.157	0.223	SUBCLONAL	1	TRUE	1	0.438074869440188	3		319	636	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0034412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	154	520	1	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.323568996858131	1	FACETS	0.892	0.824	0.962	1	0.991	1	CLONAL	2	TRUE	0	0.323568996858131	1		521	447	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	133	348	0	ENST00000263967.3:c.3132T>G	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaG	21/21	0.323568996858131	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	3	TRUE	0	0.323568996858131	3		348	304	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091782	29091782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373073383	NA	P-0034412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	97	408	2	ENST00000328354.6:c.1175C>T	p.Ala392Val	p.A392V	ENST00000328354	NM_007194.3	392	gCg/gTg	11/15	0.276524953677396	0	FACETS	0.743	0.672	0.816			1	SUBCLONAL	2	TRUE	0	0.323568996858131	0		410	273	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5239043	5239043	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	54	475	0	ENST00000357368.4:c.1736A>C	p.Tyr579Ser	p.Y579S	ENST00000357368	NM_002850.3	579	tAc/tCc	13/38	1	2	FACETS	0.738	0.632	0.855	0.738	0.632	0.855	SUBCLONAL	1	TRUE	1	0.323568996858131	2		475	452	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741974	145741974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	49	521	0	ENST00000428558.2:c.529G>A	p.Ala177Thr	p.A177T	ENST00000428558	NM_004260.3	177	Gca/Aca	5/22	1	2	FACETS	0.773	0.656	0.9	0.773	0.656	0.9	SUBCLONAL	1	TRUE	1	0.323568996858131	2		521	392	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0034413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	90	547	0	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	0.617594732950575	2		547	270	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0034413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	258	395	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.617594732950575	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.617594732950575	2		396	379	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844187	156844187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752761451	NA	P-0034413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	192	618	3	ENST00000524377.1:c.1190C>T	p.Pro397Leu	p.P397L	ENST00000524377	NM_002529.3	397	cCg/cTg	9/17	1	2	FACETS	0.996	0.926	1	0.996	0.926	1	CLONAL	1	TRUE	1	0.617594732950575	2		621	624	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922301	178922301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	84	314	0	ENST00000263967.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000263967	NM_006218.2	357	cGa/cAa	6/21	1	2	FACETS	0.892	0.796	0.992	0.892	0.796	0.992	CLONAL	1	TRUE	1	0.617594732950575	2		314	305	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604754	48604754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	144	363	0	ENST00000342988.3:c.1576G>A	p.Glu526Lys	p.E526K	ENST00000342988	NM_005359.5	526	Gaa/Aaa	12/12	0.617594732950575	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.617594732950575	1		363	317	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643942	52643943	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0034413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	138	427	0	ENST00000394830.3:c.1953dup	p.Ser652IlefsTer13	p.S652Ifs*13	ENST00000394830	NM_018313.4	651	-/A	17/30	0.617594732950575	1	FACETS	0.928	0.857	1	0.928	0.857	1	CLONAL	1	TRUE	0	0.617594732950575	1		427	333	SUCCESS
APC	324	MSKCC	GRCh37	5	112175452	112175452	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0034413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	280	325	0	ENST00000257430.4:c.4161T>A	p.Cys1387Ter	p.C1387*	ENST00000257430	NM_000038.5	1387	tgT/tgA	16/16	0.617594732950575	3	FACETS	0.996	0.957	1	0.996	0.957	1	CLONAL	3	TRUE	0	0.617594732950575	3		325	397	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980307	201980307	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	196	610	0	ENST00000359651.3:c.43T>G	p.Phe15Val	p.F15V	ENST00000359651		15	Ttc/Gtc	1/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.617594732950575	2		610	580	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578379	7578380	+	missense_variant	Missense_Mutation	DNP	TC	TC	CA	novel	NA	P-0034413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	141	504	0	ENST00000269305.4:c.550_551delinsTG	p.Asp184Cys	p.D184C	ENST00000269305	NM_001126112.2	184	GAt/TGt	5/11	0.617594732950575	1	FACETS	0.977	0.904	1	0.977	0.904	1	CLONAL	1	TRUE	0	0.617594732950575	1		504	323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578386	7578401	+	frameshift_variant	Frame_Shift_Del	DEL	AGCGCTCATGGTGGGG	AGCGCTCATGGTGGGG	-	novel	NA	P-0034413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	149	509	1	ENST00000269305.4:c.529_544del	p.Pro177AlafsTer65	p.P177Afs*65	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTgc/gc	5/11	0.617594732950575	1	FACETS	0.987	0.915	1	0.987	0.915	1	CLONAL	1	TRUE	0	0.617594732950575	1		510	338	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579315	7579315	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1555526478	NA	P-0034415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	269	376	1	ENST00000269305.4:c.372C>A	p.Cys124Ter	p.C124*	ENST00000269305	NM_001126112.2	124	tgC/tgA	4/11	0.709792327999881	2	FACETS	0.955	0.915	0.993	0.955	0.915	0.993	CLONAL	2	TRUE	0	0.709792327999881	2		377	397	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342602	70342602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1268612180	NA	P-0034415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	163	500	0	ENST00000374080.3:c.1363C>T	p.Arg455Trp	p.R455W	ENST00000374080		455	Cgg/Tgg	10/45	0.709792327999881	1	FACETS	0.988	0.925	1	0.988	0.925	1	CLONAL	1	TRUE	0	0.709792327999881	1		500	300	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137323779	137323779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368400425	NA	P-0034415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	183	582	2	ENST00000481739.1:c.1072C>T	p.Arg358Trp	p.R358W	ENST00000481739	NM_002957.4	358	Cgg/Tgg	8/10	1	2	FACETS	0.995	0.926	1	0.995	0.926	1	CLONAL	1	TRUE	1	0.709792327999881	2		584	518	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295694	212295694	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	128	408	0	ENST00000342788.4:c.2619A>C	p.Lys873Asn	p.K873N	ENST00000342788	NM_005235.2	873	aaA/aaC	21/28	0.709792327999881	3	FACETS	1	0.958	1	0.542	0.494	0.591	CLONAL	1	TRUE	1	0.709792327999881	3		408	451	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663430	29663432	+	missense_variant	Missense_Mutation	TNP	AGG	AGG	GGT	novel	NA	P-0034415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	111	467	0	ENST00000356175.3:c.6023_6025delinsGGT	p.Glu2008_Val2009delinsGlyLeu	p.E2008_V2009delinsGL	ENST00000356175	NM_000267.3	2008	gAGGtg/gGGTtg	40/57	0.709792327999881	2	FACETS	0.736	0.666	0.809	0.368	0.333	0.405	SUBCLONAL	1	TRUE	0	0.709792327999881	2		467	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0034419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	290	669	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.282839659925888	2	FACETS	0.782	0.736	0.829	0.782	0.736	0.829	SUBCLONAL	2	TRUE	0	0.364732264335043	2		669	1017	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274034	10274034	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	249	667	0	ENST00000330684.3:c.235C>T	p.Pro79Ser	p.P79S	ENST00000330684	NM_001134407.1	79	Ccc/Tcc	2/13	0.169597934710031	4	FACETS	0.813	0.76	0.868	0.813	0.76	0.868	INDETERMINATE	2	TRUE	2	0.364732264335043	4		667	1146	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0034422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	228	652	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.308593155090974	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.308593155090974	2		652	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0034422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	230	658	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.308593155090974	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.308593155090974	2		658	641	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0034422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	113	356	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.308593155090974	5	FACETS	1	0.97	1	0.59	0.534	0.648	CLONAL	2	TRUE	1	0.308593155090974	5		356	454	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100175	27100176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0034422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	148	489	0	ENST00000324856.7:c.3977dup	p.Gln1327AlafsTer11	p.Q1327Afs*11	ENST00000324856	NM_006015.4	1324	tac/taCc	16/20	0.308593155090974	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.308593155090974	2		489	430	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	161	421	0	ENST00000397062.3:c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	NM_006164.4	34	Cga/Gga	2/5	0.190076858872922	4	FACETS	0.852	0.787	0.92	1	0.985	1	CLONAL	3	TRUE	2	0.308593155090974	4		421	534	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494148	140494148	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267601317	NA	P-0034422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	278	875	0	ENST00000288602.6:c.1100C>T	p.Pro367Leu	p.P367L	ENST00000288602	NM_004333.4	367	cCc/cTc	8/18	0.140243243068696	3	FACETS	1	0.987	1	0.775	0.73	0.822	INDETERMINATE	2	TRUE	0	0.308593155090974	3		875	894	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21968242	21968242	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0034422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	138	404	0	ENST00000304494.5:c.458-1G>T		p.X153_splice	ENST00000304494	NM_000077.4	153			0.308593155090974	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.308593155090974	2		404	389	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440489	49440501	+	frameshift_variant	Frame_Shift_Del	DEL	GTGAGGGGTCGGA	GTGAGGGGTCGGA	-	novel	NA	P-0034422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	251	691	0	ENST00000301067.7:c.4309_4321del	p.Ser1437AlafsTer65	p.S1437Afs*65	ENST00000301067	NM_003482.3	1437	TCCGACCCCTCACgc/gc	15/54	0.190076858872922	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.308593155090974	4		691	917	SUCCESS
NF2	4771	MSKCC	GRCh37	22	29999988	29999988	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1319282473	NA	P-0034422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	74	243	0	ENST00000338641.4:c.1A>G	p.Met1?	p.M1?	ENST00000338641	NM_000268.3	1	Atg/Gtg	1/16	0.190076858872922	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	2	0.308593155090974	4		243	272	SUCCESS
APC	324	MSKCC	GRCh37	5	112137003	112137003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	80	413	0	ENST00000257430.4:c.758del	p.Gly253AlafsTer40	p.G253Afs*40	ENST00000257430	NM_000038.5	253	Ggc/gc	8/16	0.308593155090974	2	FACETS	1	0.966	1	0.625	0.553	0.701	CLONAL	1	TRUE	0	0.308593155090974	2		413	415	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714402	117714402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1217639125	NA	P-0034422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	37	534	0	ENST00000368508.3:c.1247C>T	p.Ala416Val	p.A416V	ENST00000368508	NM_002944.2	416	gCt/gTt	11/43	0.272575282994393	3	FACETS	0.633	0.522	0.758	0.317	0.261	0.379	SUBCLONAL	1	TRUE	1	0.308593155090974	3		534	437	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001034	150001034	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	67	482	0	ENST00000253339.5:c.2570A>G	p.His857Arg	p.H857R	ENST00000253339		857	cAc/cGc	4/7	0.272575282994393	3	FACETS	1	0.942	1	0.573	0.5	0.653	CLONAL	1	TRUE	1	0.308593155090974	3		482	437	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450257	50450257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	158	427	0	ENST00000331340.3:c.441C>G	p.Cys147Trp	p.C147W	ENST00000331340	NM_006060.4	147	tgC/tgG	5/8	0.225516581106784	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.308593155090974	4		427	623	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508424	106508424	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	70	275	0	ENST00000359195.3:c.418C>G	p.Arg140Gly	p.R140G	ENST00000359195	NM_002649.2	140	Cgg/Ggg	2/11	NA	2	FACETS	1	0.942	1			1	INDETERMINATE	2	TRUE	NA	0.308593155090974	2		275	206	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339818	116339818	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1226545782	NA	P-0034422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	219	576	0	ENST00000397752.3:c.680T>C	p.Met227Thr	p.M227T	ENST00000397752	NM_000245.2	227	aTg/aCg	2/21	0.308593155090974	5	FACETS	0.969	0.905	1			1	CLONAL	3	TRUE	NA	0.308593155090974	5		576	714	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90976730	90976730	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034435-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	202	277	0	ENST00000265433.3:c.902G>T	p.Gly301Val	p.G301V	ENST00000265433	NM_002485.4	301	gGt/gTt	8/16	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.707050740793712	2		277	557	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0034463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	403	590	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.608079239663659	2	FACETS	0.915	0.879	0.95	0.915	0.879	0.95	CLONAL	2	TRUE	0	0.620518602886127	2		590	710	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0034463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	229	547	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.620518602886127	2		547	736	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0034463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	148	365	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	0.97	0.892	1	0.97	0.892	1	CLONAL	1	TRUE	1	0.620518602886127	2		365	492	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087542	27087543	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0034463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	680	746	0	ENST00000324856.7:c.2118dup	p.Ala707CysfsTer110	p.A707Cfs*110	ENST00000324856	NM_006015.4	706	gtt/gTtt	5/20	0.608079239663659	2	FACETS	0.961	0.933	0.989	0.961	0.933	0.989	CLONAL	2	TRUE	0	0.620518602886127	2		746	1140	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466022	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCA	novel	NA	P-0034463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	392	755	1	ENST00000227507.2:c.862_864dup	p.Thr288dup	p.T288dup	ENST00000227507	NM_053056.2	288	ccc/cCCAcc	5/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.620518602886127	2		756	1199	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219218	94219218	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	42	450	0	ENST00000323929.3:c.186T>A	p.Phe62Leu	p.F62L	ENST00000323929	NM_005591.3	62	ttT/ttA	4/20	1	2	FACETS	0.21	0.175	0.249	0.21	0.175	0.249	SUBCLONAL	1	TRUE	1	0.620518602886127	2		450	645	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802655	139802655	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs549406018	NA	P-0034463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	263	528	1	ENST00000247668.2:c.500G>A	p.Arg167Gln	p.R167Q	ENST00000247668	NM_021138.3	167	cGg/cAg	5/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.620518602886127	2		529	825	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611167	100611167	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	167	598	0	ENST00000308731.7:c.1439G>C	p.Gly480Ala	p.G480A	ENST00000308731	NM_000061.2	480	gGc/gCc	15/19	1	2	FACETS	0.588	0.54	0.638	0.588	0.54	0.638	SUBCLONAL	1	TRUE	1	0.620518602886127	2		598	915	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579401	7579401	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	372	876	0	ENST00000269305.4:c.286del	p.Ser96LeufsTer27	p.S96Lfs*27	ENST00000269305	NM_001126112.2	96	Tct/ct	4/11	NA	2	FACETS	0.938	0.9	0.976			1	INDETERMINATE	2	TRUE	NA	0.614603250230342	2		876	645	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455239	29455239	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	185	742	0	ENST00000389048.3:c.2563A>T	p.Thr855Ser	p.T855S	ENST00000389048	NM_004304.4	855	Acg/Tcg	15/29	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.614603250230342	2		742	577	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345312	70345312	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	65	871	0	ENST00000374080.3:c.2338A>G	p.Lys780Glu	p.K780E	ENST00000374080		780	Aag/Gag	16/45	1	2	FACETS	0.343	0.297	0.393	0.343	0.297	0.393	SUBCLONAL	1	TRUE	1	0.614603250230342	2		871	616	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593603	55593615	+	protein_altering_variant	In_Frame_Del	DEL	TGGAAGGTTGTTG	TGGAAGGTTGTTG	C	novel	NA	P-0034471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	133	544	0	ENST00000288135.5:c.1669_1681delinsC	p.Trp557_Glu561delinsGln	p.W557_E561delinsQ	ENST00000288135	NM_000222.2	557	TGGAAGGTTGTTGag/Cag	11/21	1	2	FACETS	0.863	0.789	0.939	0.863	0.789	0.939	CLONAL	1	TRUE	1	0.655736849027468	2		544	470	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0034472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	271	384	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.991	0.936	1	0.991	0.936	1	CLONAL	1	TRUE	1	0.777835165231841	2		384	703	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0034472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	164	328	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	0.945	0.877	1	0.945	0.877	1	CLONAL	1	TRUE	1	0.777835165231841	2		328	446	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0034472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	475	836	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	0.992	1	CLONAL	1	TRUE	1	0.777835165231841	2		836	1086	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0034472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	222	498	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	0.931	0.872	0.991	0.931	0.872	0.991	CLONAL	1	TRUE	1	0.777835165231841	2		498	613	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061317	38061317	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	452	787	0	ENST00000250448.2:c.672C>A	p.Phe224Leu	p.F224L	ENST00000250448	NM_004496.3	224	ttC/ttA	2/2	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.777835165231841	2		787	1075	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026193	71026193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	230	473	0	ENST00000318789.4:c.1429G>C	p.Ala477Pro	p.A477P	ENST00000318789	NM_032682.5	477	Gcc/Ccc	17/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.777835165231841	2		473	520	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	112	349	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.708432336342171	2		349	285	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0034483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	183	249	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	0.708432336342171	2		249	456	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053267	180053267	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0034483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	254	636	0	ENST00000261937.6:c.1104-2A>T		p.X368_splice	ENST00000261937	NM_182925.4	368			1	2	FACETS	0.862	0.809	0.916	0.862	0.809	0.916	CLONAL	1	TRUE	1	0.708432336342171	2		636	832	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971092	21971092	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	150	243	1	ENST00000304494.5:c.266G>T	p.Gly89Val	p.G89V	ENST00000304494	NM_000077.4	89	gGc/gTc	2/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.708432336342171	2		244	361	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937833	76937836	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0034540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	480	526	0	ENST00000373344.5:c.2912_2915del	p.Lys971ThrfsTer31	p.K971Tfs*31	ENST00000373344	NM_000489.3	971	aAAGAc/ac	9/35	0.927030086104386	2	FACETS	0.885	0.864	0.905	0.885	0.864	0.905	CLONAL	2	TRUE	0	0.927030086104386	2		526	585	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928358	69928358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774545277	NA	P-0034540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	146	326	0	ENST00000352241.4:c.178C>T	p.Arg60Cys	p.R60C	ENST00000352241	NM_198159.2	60	Cgc/Tgc	2/10	0.793285115783604	4	FACETS	1	0.967	1			1	CLONAL	1	TRUE	NA	0.927030086104386	4		326	549	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136840	69136840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746734356	NA	P-0034540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	26	289	0	ENST00000288368.4:c.4754G>A	p.Arg1585Gln	p.R1585Q	ENST00000288368	NM_024870.2	1585	cGg/cAg	39/40	0.867796739706463	3	FACETS	0.174	0.137	0.216	0.087	0.068	0.108	SUBCLONAL	1	TRUE	1	0.927030086104386	3		289	473	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913719	32913720	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0034540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	116	328	0	ENST00000380152.3:c.5227_5228del	p.Ser1743Ter	p.S1743*	ENST00000380152		1743	AGt/t	11/27	0.283343935007227	5	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.927030086104386	5		328	447	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627152	37627152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753119390	NA	P-0034540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	152	337	0	ENST00000447079.4:c.1067G>A	p.Arg356Lys	p.R356K	ENST00000447079	NM_015083.1	356	aGa/aAa	2/14	NA	2	FACETS	0.951	0.883	1			1	INDETERMINATE	1	TRUE	NA	0.927030086104386	2		337	345	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627221	37627221	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	216	379	0	ENST00000447079.4:c.1136G>C	p.Ser379Thr	p.S379T	ENST00000447079	NM_015083.1	379	aGt/aCt	2/14	NA	2	FACETS	1	0.947	1			1	INDETERMINATE	1	TRUE	NA	0.927030086104386	2		379	463	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277076	18277076	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	181	409	0	ENST00000222254.8:c.1523G>T	p.Arg508Leu	p.R508L	ENST00000222254	NM_005027.3	508	cGc/cTc	12/16	0.879948937151474	5	FACETS	0.974	0.899	1			1	CLONAL	1	TRUE	NA	0.927030086104386	5		409	958	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054787	5054787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1293103784	NA	P-0034540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	124	308	0	ENST00000381652.3:c.839C>T	p.Ser280Leu	p.S280L	ENST00000381652	NM_004972.3	280	tCa/tTa	7/25	0.437386508190876	6	FACETS	1	0.98	1	0.431	0.391	0.473	INDETERMINATE	1	TRUE	3	0.927030086104386	6		308	590	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054826	5054826	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	122	316	0	ENST00000381652.3:c.878A>G	p.Asn293Ser	p.N293S	ENST00000381652	NM_004972.3	293	aAc/aGc	7/25	0.437386508190876	6	FACETS	1	0.978	1	0.42	0.381	0.461	INDETERMINATE	1	TRUE	3	0.927030086104386	6		316	596	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0034554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	88	432	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.484938622605741	2		432	265	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0034554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	28	577	1	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	0.453765280016656	1	FACETS	0.12	0.095	0.148	0.12	0.095	0.148	SUBCLONAL	1	TRUE	0	0.484938622605741	1		578	730	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954272	32954273	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359752	NA	P-0034554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	12	350	1	ENST00000380152.3:c.9253dup	p.Thr3085AsnfsTer26	p.T3085Nfs*26	ENST00000380152		3082	-/A	24/27	1	2	FACETS	0.26	0.183	0.355	0.26	0.183	0.355	SUBCLONAL	1	TRUE	1	0.484938622605741	2		351	190	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610409	10610409	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	207	610	0	ENST00000171111.5:c.301G>A	p.Ala101Thr	p.A101T	ENST00000171111	NM_203500.1	101	Gcc/Acc	2/6	0.453765280016656	1	FACETS	0.808	0.752	0.867	0.808	0.752	0.867	CLONAL	1	TRUE	0	0.484938622605741	1		610	800	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245932	16245932	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	43	315	0	ENST00000375759.3:c.1555G>T	p.Val519Leu	p.V519L	ENST00000375759	NM_015001.2	519	Gtg/Ttg	8/15	0.171010884904684	0	FACETS	0.266	0.223	0.313			1	INDETERMINATE	1	TRUE	0	0.484938622605741	0		315	344	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481781	40481781	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs781724933	NA	P-0034554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	90	349	0	ENST00000264657.5:c.1123G>T	p.Val375Phe	p.V375F	ENST00000264657	NM_139276.2	375	Gtt/Ttt	12/24	0.204486729536359	3	FACETS	1	0.951	1	0.557	0.497	0.62	INDETERMINATE	1	TRUE	1	0.484938622605741	3		349	414	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206807	162206807	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	40	265	0	ENST00000366898.1:c.868G>T	p.Val290Leu	p.V290L	ENST00000366898	NM_004562.2	290	Gtg/Ttg	7/12	0.453765280016656	1	FACETS	0.844	0.714	0.983	0.844	0.714	0.983	CLONAL	1	TRUE	0	0.484938622605741	1		265	148	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136173	11136173	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	115	519	0	ENST00000358026.2:c.3157C>T	p.Gln1053Ter	p.Q1053*	ENST00000358026	NM_001128849.1	1053	Cag/Tag	22/36	0.238482590987934	2	FACETS	0.827	0.748	0.909	0.827	0.748	0.909	CLONAL	2	TRUE	0	0.266501267510246	2		519	522	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786767	3786767	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587783495	NA	P-0034559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	44	501	0	ENST00000262367.5:c.4444T>G	p.Tyr1482Asp	p.Y1482D	ENST00000262367	NM_004380.2	1482	Tac/Gac	27/31	0.195523221312638	3	FACETS	0.591	0.495	0.698	0.296	0.247	0.349	SUBCLONAL	1	TRUE	1	0.266501267510246	3		501	633	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397719	49397719	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	71	565	0	ENST00000418115.1:c.505G>T	p.Glu169Ter	p.E169*	ENST00000418115	NM_001664.2	169	Gag/Tag	5/5	0.195523221312638	3	FACETS	0.829	0.723	0.944	0.415	0.361	0.472	CLONAL	1	TRUE	1	0.266501267510246	3		565	728	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691003	NA	P-0034559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	113	544	0	ENST00000269305.4:c.96+1G>T		p.X32_splice	ENST00000269305	NM_001126112.2	32			0.238482590987934	2	FACETS	0.788	0.712	0.868	0.788	0.712	0.868	SUBCLONAL	2	TRUE	0	0.266501267510246	2		544	538	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539267	187539267	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202043464	NA	P-0034559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	38	422	0	ENST00000441802.2:c.8473G>A	p.Gly2825Arg	p.G2825R	ENST00000441802	NM_005245.3	2825	Gga/Aga	10/27	0.223267760002578	2	FACETS	0.634	0.524	0.756	0.317	0.262	0.378	SUBCLONAL	1	TRUE	0	0.266501267510246	2		422	450	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229688	98229688	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs547954117	NA	P-0034559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	20	214	0	ENST00000331920.6:c.2270T>C	p.Phe757Ser	p.F757S	ENST00000331920	NM_000264.3	757	tTt/tCt	15/24	0.238482590987934	2	FACETS	0.685	0.526	0.871	0.343	0.263	0.436	SUBCLONAL	1	TRUE	0	0.266501267510246	2		214	219	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257167	16257167	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	49	475	0	ENST00000375759.3:c.4432A>G	p.Lys1478Glu	p.K1478E	ENST00000375759	NM_015001.2	1478	Aaa/Gaa	11/15	0.195523221312638	3	FACETS	0.706	0.598	0.826	0.353	0.299	0.413	SUBCLONAL	1	TRUE	1	0.266501267510246	3		475	590	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511657	46511657	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	134	550	0	ENST00000262741.5:c.1120G>C	p.Gly374Arg	p.G374R	ENST00000262741	NM_003629.3	374	Ggg/Cgg	9/10	0.195523221312638	3	FACETS	0.807	0.734	0.883	0.807	0.734	0.883	CLONAL	2	TRUE	1	0.266501267510246	3		550	706	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332984	70332984	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	129	654	2	ENST00000373644.4:c.889T>C	p.Tyr297His	p.Y297H	ENST00000373644	NM_030625.2	297	Tac/Cac	2/12	0.195523221312638	3	FACETS	0.757	0.687	0.83	0.757	0.687	0.83	SUBCLONAL	2	TRUE	1	0.266501267510246	3		656	725	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891691	28891691	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	159	596	0	ENST00000282397.4:c.3330C>A	p.Cys1110Ter	p.C1110*	ENST00000282397	NM_002019.4	1110	tgC/tgA	25/30	0.171519943594099	3	FACETS	1	0.979	1	0.791	0.729	0.855	CLONAL	2	TRUE	0	0.266501267510246	3		596	570	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437968	110437968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	17	149	0	ENST00000375856.3:c.433G>A	p.Glu145Lys	p.E145K	ENST00000375856	NM_003749.2	145	Gag/Aag	1/2	0.266501267510246	4	FACETS	0.918	0.689	1	0.23	0.172	0.297	CLONAL	1	TRUE	0	0.266501267510246	4		149	176	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30069011	30069011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1278395721	NA	P-0034559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	35	420	0	ENST00000331968.5:c.1918C>T	p.Pro640Ser	p.P640S	ENST00000331968	NM_002742.2	640	Cct/Tct	14/18	0.266501267510246	3	FACETS	0.669	0.548	0.805	0.334	0.274	0.403	SUBCLONAL	1	TRUE	1	0.266501267510246	3		420	445	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120456	2120456	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs45517192	NA	P-0034559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	61	524	0	ENST00000219476.3:c.1717-1G>T		p.X573_splice	ENST00000219476	NM_000548.3	573			0.195523221312638	3	FACETS	0.838	0.723	0.964	0.419	0.361	0.482	CLONAL	1	TRUE	1	0.266501267510246	3		524	619	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786752	3786752	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	52	542	0	ENST00000262367.5:c.4459C>A	p.His1487Asn	p.H1487N	ENST00000262367	NM_004380.2	1487	Cac/Aac	27/31	0.195523221312638	3	FACETS	0.632	0.537	0.736	0.316	0.268	0.368	SUBCLONAL	1	TRUE	1	0.266501267510246	3		542	700	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984640	72984640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	146	714	1	ENST00000268489.5:c.2944del	p.Asp982ThrfsTer87	p.D982Tfs*87	ENST00000268489	NM_006885.3	982	Gac/ac	3/10	0.266501267510246	6	FACETS	1	0.986	1	0.247	0.225	0.271	CLONAL	1	TRUE	0	0.266501267510246	6		715	1133	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836623	89836623	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	544	652	0	ENST00000389301.3:c.2267G>T	p.Arg756Leu	p.R756L	ENST00000389301	NM_000135.2	756	cGt/cTt	25/43	0.266501267510246	6	FACETS	0.999	0.964	1	0.999	0.964	1	CLONAL	6	TRUE	0	0.266501267510246	6		652	1044	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89871762	89871762	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	299	516	0	ENST00000389301.3:c.635G>C	p.Arg212Thr	p.R212T	ENST00000389301	NM_000135.2	212	aGg/aCg	7/43	0.266501267510246	6	FACETS	1	0.958	1	0.677	0.64	0.715	CLONAL	4	TRUE	0	0.266501267510246	6		516	847	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654551	29654551	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	71	222	0	ENST00000356175.3:c.5240A>T	p.Glu1747Val	p.E1747V	ENST00000356175	NM_000267.3	1747	gAg/gTg	37/57	0.201084919845476	4	FACETS	0.961	0.845	1	0.961	0.845	1	CLONAL	2	TRUE	2	0.266501267510246	4		222	351	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440741	56440741	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	56	503	0	ENST00000407977.2:c.477G>T	p.Trp159Cys	p.W159C	ENST00000407977		159	tgG/tgT	5/10	0.195523221312638	3	FACETS	0.885	0.759	1	0.443	0.379	0.512	CLONAL	1	TRUE	1	0.266501267510246	3		503	538	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383634	15383634	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	34	405	0	ENST00000263377.2:c.277A>T	p.Asn93Tyr	p.N93Y	ENST00000263377	NM_058243.2	93	Aac/Tac	2/20	0.238482590987934	2	FACETS	0.624	0.51	0.752	0.312	0.255	0.376	SUBCLONAL	1	TRUE	0	0.266501267510246	2		405	409	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248393	212248393	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	21	282	0	ENST00000342788.4:c.3874C>A	p.Pro1292Thr	p.P1292T	ENST00000342788	NM_005235.2	1292	Cca/Aca	28/28	0.266501267510246	3	FACETS	0.567	0.436	0.719	0.283	0.218	0.36	SUBCLONAL	1	TRUE	1	0.266501267510246	3		282	315	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967176	134967176	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	31	349	0	ENST00000398015.3:c.2515C>A	p.Gln839Lys	p.Q839K	ENST00000398015	NM_004441.4	839	Cag/Aag	14/16	0.216628712489308	5	FACETS	0.637	0.514	0.777	0.212	0.171	0.259	SUBCLONAL	1	TRUE	2	0.266501267510246	5		349	511	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967333	134967333	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	92	401	0	ENST00000398015.3:c.2672T>C	p.Val891Ala	p.V891A	ENST00000398015	NM_004441.4	891	gTg/gCg	14/16	0.216628712489308	5	FACETS	0.897	0.799	1	0.598	0.532	0.667	CLONAL	2	TRUE	2	0.266501267510246	5		401	539	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510201	187510201	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	34	454	0	ENST00000441802.2:c.13312C>A	p.Pro4438Thr	p.P4438T	ENST00000441802	NM_005245.3	4438	Ccc/Acc	27/27	0.223267760002578	2	FACETS	0.528	0.431	0.638	0.264	0.215	0.319	SUBCLONAL	1	TRUE	0	0.266501267510246	2		454	483	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31493340	31493340	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs745898205	NA	P-0034559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	25	272	0	ENST00000344624.3:c.1816A>G	p.Met606Val	p.M606V	ENST00000344624		606	Atg/Gtg	10/33	0.266501267510246	5	FACETS	0.642	0.505	0.8	0.161	0.126	0.2	SUBCLONAL	1	TRUE	1	0.266501267510246	5		272	409	SUCCESS
APC	324	MSKCC	GRCh37	5	112176294	112176294	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	75	263	0	ENST00000257430.4:c.5003A>T	p.Glu1668Val	p.E1668V	ENST00000257430	NM_000038.5	1668	gAg/gTg	16/16	0.185322852488991	2	FACETS	0.858	0.758	0.964	0.858	0.758	0.964	CLONAL	2	TRUE	0	0.266501267510246	2		263	328	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120249	94120249	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	31	308	0	ENST00000369303.4:c.802G>T	p.Gly268Cys	p.G268C	ENST00000369303	NM_004440.3	268	Ggc/Tgc	3/17	0.266501267510246	3	FACETS	0.666	0.538	0.81	0.333	0.269	0.405	SUBCLONAL	1	TRUE	1	0.266501267510246	3		308	396	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423470	116423470	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	35	320	0	ENST00000397752.3:c.3745T>C	p.Trp1249Arg	p.W1249R	ENST00000397752	NM_000245.2	1249	Tgg/Cgg	19/21	0.185322852488991	2	FACETS	0.72	0.591	0.864	0.36	0.295	0.432	SUBCLONAL	1	TRUE	0	0.266501267510246	2		320	365	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879241	151879241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	92	510	0	ENST00000262189.6:c.5704G>A	p.Val1902Ile	p.V1902I	ENST00000262189	NM_170606.2	1902	Gtt/Att	36/59	0.185322852488991	2	FACETS	0.794	0.709	0.883	0.794	0.709	0.883	SUBCLONAL	2	TRUE	0	0.266501267510246	2		510	435	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796929	78796929	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	83	530	0	ENST00000306801.3:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000306801	NM_020761.2	348	Cga/Tga	9/34	0.756755842869701	3	FACETS	0.389	0.343	0.439	0.195	0.171	0.22	SUBCLONAL	1	TRUE	1	0.756755842869701	3		530	777	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175942	176175942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs964768927	NA	P-0034567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	11	64	0	ENST00000367669.3:c.173C>T	p.Ser58Leu	p.S58L	ENST00000367669	NM_022457.5	58	tCg/tTg	1/20	0.541696144636254	4	FACETS	0.543	0.379	0.742	0.272	0.189	0.371	SUBCLONAL	1	TRUE	2	0.756755842869701	4		64	94	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295220	1295220	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0034567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	73	210	0				ENST00000310581	NM_198253.2	-/1132			0.369595592008077	4	FACETS	1	0.913	1			1	INDETERMINATE	1	TRUE	NA	0.756755842869701	4		210	325	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119022	3119022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	128	600	5	ENST00000078429.4:c.706G>A	p.Asp236Asn	p.D236N	ENST00000078429	NM_002067.2	236	Gac/Aac	5/7	0.674908826156835	1	FACETS	0.645	0.593	0.698	0.645	0.593	0.698	SUBCLONAL	1	TRUE	0	0.756755842869701	1		605	326	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814566	43814566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	230	339	0	ENST00000372470.3:c.1361G>A	p.Arg454Gln	p.R454Q	ENST00000372470	NM_005373.2	454	cGa/cAa	9/12	0.594536716963219	4	FACETS	0.962	0.905	1	0.641	0.603	0.68	CLONAL	2	TRUE	1	0.756755842869701	4		339	555	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199939	108199947	+	inframe_deletion	In_Frame_Del	DEL	TAGGGAACA	TAGGGAACA	-	novel	NA	P-0034567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	115	133	0	ENST00000278616.4:c.7283_7291del	p.Arg2428_His2430del	p.R2428_H2430del	ENST00000278616	NM_000051.3	2427	ctTAGGGAACAt/ctt	49/63	0.538931637445254	4	FACETS	0.989	0.922	1	0.742	0.691	0.79	CLONAL	3	TRUE	0	0.756755842869701	4		133	180	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281488	49281488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	98	595	0	ENST00000282018.3:c.535G>A	p.Glu179Lys	p.E179K	ENST00000282018	NM_020377.2	179	Gag/Aag	1/1	0.756755842869701	3	FACETS	0.528	0.471	0.588	0.264	0.235	0.294	SUBCLONAL	1	TRUE	1	0.756755842869701	3		595	676	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041037	42041037	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	322	540	0	ENST00000219905.7:c.5415del	p.Asn1805LysfsTer33	p.N1805Kfs*33	ENST00000219905	NM_001164273.1	1805	aaT/aa	16/24	0.57791645442729	2	FACETS	0.781	0.747	0.814	0.781	0.747	0.814	SUBCLONAL	2	TRUE	0	0.756755842869701	2		540	545	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857178	9857178	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs763219483	NA	P-0034567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	62	345	0	ENST00000330684.3:c.4223C>A	p.Thr1408Lys	p.T1408K	ENST00000330684	NM_001134407.1	1408	aCg/aAg	13/13	0.143952078590645	3	FACETS	0.547	0.474	0.626			1	INDETERMINATE	1	TRUE	NA	0.756755842869701	3		345	413	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271919	15271919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376494303	NA	P-0034567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	113	527	0	ENST00000263388.2:c.6520C>T	p.Arg2174Trp	p.R2174W	ENST00000263388	NM_000435.2	2174	Cgg/Tgg	33/33	1	2	FACETS	0.743	0.674	0.814	0.743	0.674	0.814	SUBCLONAL	1	TRUE	1	0.756755842869701	2		527	402	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539216	187539216	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	89	419	0	ENST00000441802.2:c.8524G>T	p.Gly2842Cys	p.G2842C	ENST00000441802	NM_005245.3	2842	Ggc/Tgc	10/27	1	2	FACETS	0.766	0.687	0.849	0.766	0.687	0.849	SUBCLONAL	1	TRUE	1	0.756755842869701	2		419	307	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197318	26197318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1347100402	NA	P-0034567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	48	323	0	ENST00000356476.2:c.161G>A	p.Arg54His	p.R54H	ENST00000356476		54	cGc/cAc	1/1	0.578464917129222	5	FACETS	0.593	0.501	0.693	0.198	0.167	0.231	SUBCLONAL	1	TRUE	2	0.756755842869701	5		323	457	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979257	93979257	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	70	307	0	ENST00000369303.4:c.1571G>T	p.Gly524Val	p.G524V	ENST00000369303	NM_004440.3	524	gGa/gTa	7/17	1	2	FACETS	0.661	0.582	0.744	0.661	0.582	0.744	SUBCLONAL	1	TRUE	1	0.756755842869701	2		307	280	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120828	94120828	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	117	519	0	ENST00000369303.4:c.223C>T	p.Gln75Ter	p.Q75*	ENST00000369303	NM_004440.3	75	Caa/Taa	3/17	1	2	FACETS	0.647	0.587	0.71	0.647	0.587	0.71	SUBCLONAL	1	TRUE	1	0.756755842869701	2		519	478	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911407	39911407	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	138	424	0	ENST00000378444.4:c.5223del	p.Glu1742SerfsTer26	p.E1742Sfs*26	ENST00000378444	NM_001123385.1	1741	gtA/gt	15/15	0.244498825968257	5	FACETS	1	0.977	1	0.401	0.366	0.438	INDETERMINATE	1	TRUE	2	0.756755842869701	5		424	647	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937702	76937702	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	163	475	0	ENST00000373344.5:c.3046A>T	p.Thr1016Ser	p.T1016S	ENST00000373344	NM_000489.3	1016	Act/Tct	9/35	NA	2	FACETS	0.83	0.767	0.895			1	INDETERMINATE	1	TRUE	NA	0.756755842869701	2		475	519	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182133	11182133	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1429	88	537	3	ENST00000361445.4:c.6713G>A	p.Gly2238Asp	p.G2238D	ENST00000361445	NM_004958.3	2238	gGc/gAc	48/58	0.277304329600198	4	FACETS	0.443	0.391	0.5	0.148	0.13	0.167	SUBCLONAL	1	TRUE	1	0.354303827464939	4		540	1517	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0034580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	121	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.196560174308611	3	FACETS	1	0.954	1	0.725	0.657	0.796	CLONAL	2	TRUE	0	0.212288053956039	3		539	580	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243777010	243777010	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200428825	NA	P-0034580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	40	373	0	ENST00000263826.5:c.659G>A	p.Arg220His	p.R220H	ENST00000263826	NM_005465.4	220	cGt/cAt	7/13	0.20425809286197	4	FACETS	0.693	0.575	0.826	0.347	0.287	0.413	SUBCLONAL	1	TRUE	2	0.212288053956039	4		373	659	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18964135	18964135	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	44	438	0	ENST00000262803.5:c.1132G>T	p.Gly378Cys	p.G378C	ENST00000262803	NM_002911.3	378	Ggc/Tgc	8/24	1	2	FACETS	0.685	0.574	0.809	0.685	0.574	0.809	SUBCLONAL	1	TRUE	1	0.212288053956039	2		438	605	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24129414	24129414	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	47	347	0	ENST00000263121.7:c.58G>C	p.Glu20Gln	p.E20Q	ENST00000263121	NM_003073.3	20	Gag/Cag	1/9	1	2	FACETS	0.861	0.727	1	0.861	0.727	1	CLONAL	1	TRUE	1	0.212288053956039	2		347	514	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317476	1317476	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	66	643	0	ENST00000400841.2:c.589G>C	p.Asp197His	p.D197H	ENST00000400841		197	Gac/Cac	5/6	1	2	FACETS	0.739	0.64	0.847	0.739	0.64	0.847	SUBCLONAL	1	TRUE	1	0.212288053956039	2		643	841	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0034604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	59	472	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	1	2	FACETS	0.65	0.561	0.747	0.65	0.561	0.747	SUBCLONAL	1	FALSE	1	0.421264243609667	2		472	431	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21272398	21272398	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	138	839	1	ENST00000354336.3:c.176C>T	p.Ser59Phe	p.S59F	ENST00000354336	NM_005207.3	59	tCc/tTc	1/3	0.273545150790486	1	FACETS	0.65	0.591	0.711	0.65	0.591	0.711	SUBCLONAL	1	FALSE	0	0.421264243609667	1		840	796	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199562	16199562	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	109	589	0	ENST00000375759.3:c.335G>T	p.Gly112Val	p.G112V	ENST00000375759	NM_015001.2	112	gGa/gTa	2/15	1	2	FACETS	0.914	0.824	1	0.914	0.824	1	CLONAL	1	FALSE	1	0.421264243609667	2		589	566	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242445	55242445	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	68	474	0	ENST00000275493.2:c.2215A>C	p.Lys739Gln	p.K739Q	ENST00000275493	NM_005228.3	739	Aaa/Caa	19/28	1	2	FACETS	0.713	0.622	0.81	0.713	0.622	0.81	SUBCLONAL	1	FALSE	1	0.421264243609667	2		474	453	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859597	151859597	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	128	649	0	ENST00000262189.6:c.11065T>C	p.Phe3689Leu	p.F3689L	ENST00000262189	NM_170606.2	3689	Ttc/Ctc	43/59	1	2	FACETS	0.938	0.852	1	0.938	0.852	1	CLONAL	1	FALSE	1	0.421264243609667	2		649	648	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0034643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	94	562	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.482849499904912	1	FACETS	0.481	0.429	0.537	0.481	0.429	0.537	SUBCLONAL	1	TRUE	0	0.496886926129114	1		562	591	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589663	67589663	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587777709	NA	P-0034643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	54	188	0	ENST00000274335.5:c.1425+1G>T		p.X475_splice	ENST00000274335		475			1	2	FACETS	0.966	0.835	1	0.966	0.835	1	CLONAL	1	TRUE	1	0.496886926129114	2		188	225	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180645	56180645	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	108	333	0	ENST00000399503.3:c.3974G>C	p.Trp1325Ser	p.W1325S	ENST00000399503	NM_005921.1	1325	tGg/tCg	16/20	1	2	FACETS	0.966	0.872	1	0.966	0.872	1	CLONAL	1	TRUE	1	0.496886926129114	2		333	450	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044973	47044995	+	frameshift_variant	Frame_Shift_Del	DEL	CAGTTCCCCAGCAAAGAGGCGCT	CAGTTCCCCAGCAAAGAGGCGCT	-	novel	NA	P-0034643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	208	396	0	ENST00000377604.3:c.2301_2323del	p.Gln767HisfsTer15	p.Q767Hfs*15	ENST00000377604	NM_001204468.1	767	CAGTTCCCCAGCAAAGAGGCGCTc/c	20/24	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.496886926129114	1		396	452	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0034647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	28	384	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	FALSE	1	0.461033214224722	2		384	109	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247516	123247516	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519795	NA	P-0034647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	54	578	0	ENST00000358487.5:c.1975A>G	p.Lys659Glu	p.K659E	ENST00000358487	NM_000141.4	659	Aag/Gag	14/18	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	FALSE	1	0.461033214224722	2		578	230	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109993	115109993	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	61	765	1	ENST00000257566.3:c.1885del	p.Leu629SerfsTer3	p.L629Sfs*3	ENST00000257566	NM_016569.3	629	Ctc/tc	8/8	1	2	FACETS	0.888	0.772	1	0.888	0.772	1	CLONAL	1	FALSE	1	0.461033214224722	2		766	298	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772253	68772263	+	frameshift_variant	Frame_Shift_Del	DEL	CGAGAGCTACA	CGAGAGCTACA	-	novel	NA	P-0034647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	105	833	0	ENST00000261769.5:c.104_114del	p.Glu35ValfsTer20	p.E35Vfs*20	ENST00000261769	NM_004360.3	34	gcCGAGAGCTACAcg/gccg	2/16	0.461033214224722	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	0	0.461033214224722	1		833	289	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051217	13051217	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	49	329	0	ENST00000316448.5:c.653A>T	p.Asp218Val	p.D218V	ENST00000316448	NM_004343.3	218	gAc/gTc	5/9	1	2	FACETS	0.821	0.701	0.95	0.821	0.701	0.95	CLONAL	1	FALSE	1	0.461033214224722	2		329	259	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181432	38181432	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	52	429	0	ENST00000396334.3:c.445A>C	p.Ser149Arg	p.S149R	ENST00000396334	NM_002468.4	149	Agc/Cgc	2/5	1	2	FACETS	0.878	0.754	1	0.878	0.754	1	CLONAL	1	FALSE	1	0.461033214224722	2		429	257	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508683	106508683	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1490061702	NA	P-0034647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	65	449	0	ENST00000359195.3:c.677G>A	p.Arg226His	p.R226H	ENST00000359195	NM_002649.2	226	cGc/cAc	2/11	0.109751620661982	4	FACETS	1	0.968	1	0.687	0.6	0.779	INDETERMINATE	1	FALSE	2	0.461033214224722	4		449	300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs786201838	NA	P-0034649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	209	578	0	ENST00000269305.4:c.578A>C	p.His193Pro	p.H193P	ENST00000269305	NM_001126112.2	193	cAt/cCt	6/11	0.788188414044132	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.788188414044132	1		578	307	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300837	137300837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	210	688	2	ENST00000481739.1:c.482G>A	p.Arg161Gln	p.R161Q	ENST00000481739	NM_002957.4	161	cGg/cAg	4/10	1	2	FACETS	0.936	0.876	0.998	0.936	0.876	0.998	CLONAL	1	TRUE	1	0.788188414044132	2		690	569	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474614	138474614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	172	504	0	ENST00000289153.2:c.379G>A	p.Gly127Arg	p.G127R	ENST00000289153	NM_006219.2	127	Gga/Aga	2/22	1	2	FACETS	0.896	0.832	0.962	0.896	0.832	0.962	CLONAL	1	TRUE	1	0.788188414044132	2		504	487	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458321	12458321	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	410	654	1	ENST00000287820.6:c.938G>T	p.Cys313Phe	p.C313F	ENST00000287820	NM_015869.4	313	tGc/tTc	6/7	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.704384372471762	2		655	1009	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100095	157100116	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCGGCGGCAGCAGCAGGA	GGCGGCGGCGGCAGCAGCAGGA	-	novel	NA	P-0034680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	11	15	0	ENST00000346085.5:c.1044_1065del	p.Gly351MetfsTer11	p.G351Mfs*11	ENST00000346085	NM_020732.3	344	gcGGCGGCGGCGGCAGCAGCAGGA/gc	1/20	1	2	FACETS	0.651	0.463	0.867	0.651	0.463	0.867	SUBCLONAL	1	TRUE	1	0.704384372471762	2		15	48	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115809	8115812	+	frameshift_variant	Frame_Shift_Del	DEL	CCCC	CCCC	-	novel	NA	P-0034680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	248	561	0	ENST00000346208.3:c.1155_1158del	p.Phe385LeufsTer18	p.F385Lfs*18	ENST00000346208		385	ttCCCC/tt	6/6	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.704384372471762	2		561	684	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49419984	49419986	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0034680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	179	410	0	ENST00000301067.7:c.15763_15765del	p.Phe5255del	p.F5255del	ENST00000301067	NM_003482.3	5255	TTC/-	48/54	0.143013062322591	3	FACETS	1	0.987	1	0.642	0.596	0.689	INDETERMINATE	1	TRUE	1	0.704384372471762	3		410	535	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426691	49426691	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	116	316	0	ENST00000301067.7:c.11797C>T	p.Gln3933Ter	p.Q3933*	ENST00000301067	NM_003482.3	3933	Cag/Tag	39/54	0.143013062322591	3	FACETS	1	0.985	1	0.705	0.644	0.767	INDETERMINATE	1	TRUE	1	0.704384372471762	3		316	316	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708506	43708506	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	94	740	0	ENST00000382044.4:c.4790A>G	p.Gln1597Arg	p.Q1597R	ENST00000382044	NM_001141980.1	1597	cAa/cGa	22/28	1	2	FACETS	0.332	0.294	0.371	0.332	0.294	0.371	SUBCLONAL	1	TRUE	1	0.704384372471762	2		740	805	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680785	88680785	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	31	533	0	ENST00000360948.2:c.472G>C	p.Glu158Gln	p.E158Q	ENST00000360948	NM_001012338.2	158	Gag/Cag	6/19	1	2	FACETS	0.184	0.148	0.224	0.184	0.148	0.224	SUBCLONAL	1	TRUE	1	0.704384372471762	2		533	479	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832476	72832476	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	144	391	0	ENST00000268489.5:c.4105C>T	p.Gln1369Ter	p.Q1369*	ENST00000268489	NM_006885.3	1369	Cag/Tag	9/10	1	2	FACETS	0.895	0.823	0.969	0.895	0.823	0.969	CLONAL	1	TRUE	1	0.704384372471762	2		391	457	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774094	56774094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	89	549	0	ENST00000337432.4:c.445G>A	p.Gly149Arg	p.G149R	ENST00000337432	NM_058216.2	149	Gga/Aga	3/9	1	2	FACETS	0.312	0.276	0.35	0.312	0.276	0.35	SUBCLONAL	1	TRUE	1	0.704384372471762	2		549	811	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216215	36216215	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	186	669	1	ENST00000222270.7:c.3623C>A	p.Ala1208Asp	p.A1208D	ENST00000222270	NM_014727.1	1208	gCc/gAc	11/37	1	2	FACETS	0.971	0.903	1	0.971	0.903	1	CLONAL	1	TRUE	1	0.704384372471762	2		670	544	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540088	187540149	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGTAAATATCTGTCCTCTCTCATTTATGTAAAATCTGTCTTTGGCAAAGTCATTTACAAT	AAAGTAAATATCTGTCCTCTCTCATTTATGTAAAATCTGTCTTTGGCAAAGTCATTTACAAT	-	novel	NA	P-0034680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	216	472	0	ENST00000441802.2:c.7591_7652del	p.Ile2531GlyfsTer4	p.I2531Gfs*4	ENST00000441802	NM_005245.3	2531	ATTGTAAATGACTTTGCCAAAGACAGATTTTACATAAATGAGAGAGGACAGATATTTACTTTg/g	10/27	0.243872290277212	4	FACETS	0.855	0.8	0.912	0.855	0.8	0.912	INDETERMINATE	2	TRUE	2	0.704384372471762	4		472	611	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs967461896	NA	P-0034698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	87	686	0	ENST00000269305.4:c.526T>C	p.Cys176Arg	p.C176R	ENST00000269305	NM_001126112.2	176	Tgc/Cgc	5/11	1	2	FACETS	0.812	0.718	0.913	1	0.981	1	CLONAL	2	TRUE	1	0.13	2		686	824	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615083	43615083	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377767422	NA	P-0034755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	118	755	0	ENST00000355710.3:c.2497C>T	p.Arg833Cys	p.R833C	ENST00000355710	NM_020975.4	833	Cgc/Tgc	14/20	1	2	FACETS	0.339	0.305	0.374	0.339	0.305	0.374	SUBCLONAL	1	TRUE	1	0.78476789424116	2		755	888	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593603	55593603	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913235	NA	P-0034755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	323	489	0	ENST00000288135.5:c.1669T>A	p.Trp557Arg	p.W557R	ENST00000288135	NM_000222.2	557	Tgg/Agg	11/21	0.773435798781471	3	FACETS	0.913	0.87	0.955	0.913	0.87	0.955	CLONAL	2	TRUE	1	0.78476789424116	3		489	628	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276472	115276472	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	87	721	1	ENST00000438362.2:c.856G>T	p.Glu286Ter	p.E286*	ENST00000438362	NM_001242891.1	286	Gaa/Taa	9/20	0.78476789424116	1	FACETS	0.316	0.281	0.353	0.316	0.281	0.353	SUBCLONAL	1	TRUE	0	0.78476789424116	1		722	426	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489202	2489202	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	101	771	1	ENST00000355716.4:c.107C>T	p.Ala36Val	p.A36V	ENST00000355716	NM_003820.2	36	gCc/gTc	2/8	0.78476789424116	1	FACETS	0.26	0.233	0.289	0.26	0.233	0.289	SUBCLONAL	1	TRUE	0	0.78476789424116	1		772	601	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56878424	56878424	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	87	487	0	ENST00000308159.5:c.2363A>T	p.Gln788Leu	p.Q788L	ENST00000308159	NM_014669.4	788	cAa/cTa	22/22	1	2	FACETS	0.346	0.306	0.388	0.346	0.306	0.388	SUBCLONAL	1	TRUE	1	0.78476789424116	2		487	641	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020909	26020913	+	frameshift_variant	Frame_Shift_Del	DEL	TAAAC	TAAAC	-	novel	NA	P-0034755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	97	486	0	ENST00000357647.3:c.194_198del	p.Lys65ThrfsTer14	p.K65Tfs*14	ENST00000357647	NM_003529.2	64	cgTAAACta/cgta	1/1	1	2	FACETS	0.441	0.394	0.491	0.441	0.394	0.491	SUBCLONAL	1	TRUE	1	0.78476789424116	2		486	560	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0034765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	244	599	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	0.986	0.93	1	0.986	0.93	1	CLONAL	1	TRUE	1	0.901917589549812	2		599	549	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0034767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	401	427	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			0.211849351311595	7	FACETS	1	0.987	1	1	0.996	1	CLONAL	8	FALSE	1	0.211849351311595	7		427	685	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90949255	90949255	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0034767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	118	314	0	ENST00000265433.3:c.2233A>T	p.Arg745Ter	p.R745*	ENST00000265433	NM_002485.4	745	Aga/Tga	15/16	0.194777894168485	1	FACETS	0.912	0.838	0.987	1	0.992	1	CLONAL	4	FALSE	0	0.211849351311595	1		314	273	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070642	67070644	+	frameshift_variant	Frame_Shift_Ins	INS	AAA	AAA	TTTCT	novel	NA	P-0034767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	108	239	0	ENST00000412916.2:c.266_268delinsTTTCT	p.Glu89ValfsTer10	p.E89Vfs*10	ENST00000412916		89	gAAAga/gTTTCTga	3/6	0.211849351311595	0	FACETS	0.89	0.846	0.928			1	CLONAL	7	FALSE	0	0.211849351311595	0		239	129	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0034769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	85	996	1	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.580532654699303	1	FACETS	0.961	0.866	1	0.961	0.866	1	CLONAL	1	TRUE	0	0.583085940037385	1		997	215	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468490	89468490	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	54	339	0	ENST00000336596.2:c.2024G>T	p.Gly675Val	p.G675V	ENST00000336596	NM_005233.5	675	gGa/gTa	11/17	NA	2	FACETS	0.878	0.76	1			1	INDETERMINATE	1	TRUE	NA	0.583085940037385	2		339	211	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141502	11141502	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	74	818	0	ENST00000358026.2:c.3479G>T	p.Gly1160Val	p.G1160V	ENST00000358026	NM_001128849.1	1160	gGg/gTg	25/36	0.583085940037385	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.583085940037385	1		818	170	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174485	11174485	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	72	754	0	ENST00000361445.4:c.7190G>T	p.Arg2397Ile	p.R2397I	ENST00000361445	NM_004958.3	2397	aGa/aTa	53/58	0.429065790285784	1	FACETS	0.792	0.703	0.884	0.792	0.703	0.884	SUBCLONAL	1	TRUE	0	0.583085940037385	1		754	221	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32439188	32439188	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	37	638	1	ENST00000332351.3:c.885C>A	p.Tyr295Ter	p.Y295*	ENST00000332351	NM_024426.4	295	taC/taA	4/10	0.579606007085454	1	FACETS	0.478	0.399	0.565	0.478	0.399	0.565	SUBCLONAL	1	TRUE	0	0.583085940037385	1		639	188	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233826	133233826	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777401444	NA	P-0034769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	65	846	1	ENST00000320574.5:c.3478C>T	p.Arg1160Cys	p.R1160C	ENST00000320574	NM_006231.2	1160	Cgt/Tgt	29/49	1	2	FACETS	0.851	0.746	0.962	0.851	0.746	0.962	CLONAL	1	TRUE	1	0.583085940037385	2		847	262	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557822	21557822	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	84	977	1	ENST00000382592.4:c.2023G>T	p.Gly675Trp	p.G675W	ENST00000382592	NM_014572.2	675	Ggg/Tgg	5/8	0.525826063660025	1	FACETS	0.945	0.851	1	0.945	0.851	1	CLONAL	1	TRUE	0	0.583085940037385	1		978	216	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046467	30046467	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs777521591	NA	P-0034769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	69	765	0	ENST00000331968.5:c.2716G>T	p.Gly906Cys	p.G906C	ENST00000331968	NM_002742.2	906	Ggt/Tgt	18/18	0.525525240225198	1	FACETS	0.798	0.707	0.893	0.798	0.707	0.893	SUBCLONAL	1	TRUE	0	0.583085940037385	1		765	210	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606049	81606049	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs911354556	NA	P-0034769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	64	569	0	ENST00000298171.2:c.719C>A	p.Ala240Asp	p.A240D	ENST00000298171	NM_000369.2	240	gCc/gAc	9/10	1	2	FACETS	0.907	0.795	1	0.907	0.795	1	CLONAL	1	TRUE	1	0.583085940037385	2		569	242	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95593048	95593048	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	48	578	0	ENST00000393063.1:c.772G>T	p.Gly258Ter	p.G258*	ENST00000393063	NM_030621.3	258	Gga/Tga	8/28	1	2	FACETS	0.678	0.578	0.785	0.678	0.578	0.785	SUBCLONAL	1	TRUE	1	0.583085940037385	2		578	243	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243056	105243056	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	68	988	0	ENST00000349310.3:c.227G>C	p.Arg76Pro	p.R76P	ENST00000349310	NM_001014432.1	76	cGc/cCc	5/15	NA	2	FACETS	0.956	0.843	1			1	INDETERMINATE	1	TRUE	NA	0.583085940037385	2		988	244	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003170	42003170	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0034769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	46	840	1	ENST00000219905.7:c.2707A>T	p.Arg903Ter	p.R903*	ENST00000219905	NM_001164273.1	903	Aga/Tga	8/24	0.524212228683097	1	FACETS	0.576	0.491	0.667	0.576	0.491	0.667	SUBCLONAL	1	TRUE	0	0.583085940037385	1		841	194	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097200	11097200	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	67	809	0	ENST00000358026.2:c.691G>T	p.Gly231Cys	p.G231C	ENST00000358026	NM_001128849.1	231	Ggc/Tgc	4/36	0.583085940037385	1	FACETS	0.999	0.89	1	0.999	0.89	1	CLONAL	1	TRUE	0	0.583085940037385	1		809	163	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952331	17952331	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	96	949	1	ENST00000458235.1:c.1009G>T	p.Glu337Ter	p.E337*	ENST00000458235	NM_000215.3	337	Gag/Tag	8/24	0.583085940037385	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.583085940037385	1		950	226	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940470	29940470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	31	502	0	ENST00000389048.3:c.761C>T	p.Pro254Leu	p.P254L	ENST00000389048	NM_004304.4	254	cCt/cTt	2/29	0.157146375847901	0	FACETS	0.265	0.217	0.319			1	INDETERMINATE	1	TRUE	0	0.583085940037385	0		502	167	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54948551	54948551	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	165	547	0	ENST00000312783.6:c.767A>T	p.Asp256Val	p.D256V	ENST00000312783	NM_198436.1	256	gAc/gTc	8/10	0.477224060037966	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.583085940037385	4		547	374	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575613	55575613	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	42	520	0	ENST00000288135.5:c.1139C>G	p.Thr380Arg	p.T380R	ENST00000288135	NM_000222.2	380	aCg/aGg	7/21	0.583085940037385	1	FACETS	0.63	0.535	0.732	0.63	0.535	0.732	SUBCLONAL	1	TRUE	0	0.583085940037385	1		520	162	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984875	55984875	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	66	728	0	ENST00000263923.4:c.254G>A	p.Cys85Tyr	p.C85Y	ENST00000263923	NM_002253.2	85	tGt/tAt	3/30	0.583085940037385	1	FACETS	0.943	0.838	1	0.943	0.838	1	CLONAL	1	TRUE	0	0.583085940037385	1		728	170	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218805	66218805	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	39	387	0	ENST00000273854.3:c.2253C>G	p.Ile751Met	p.I751M	ENST00000273854	NM_004439.5	751	atC/atG	13/18	0.525431140881971	1	FACETS	0.645	0.544	0.753	0.645	0.544	0.753	SUBCLONAL	1	TRUE	0	0.583085940037385	1		387	147	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230803	66230803	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs374393697	NA	P-0034769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	30	563	0	ENST00000273854.3:c.2168G>C	p.Gly723Ala	p.G723A	ENST00000273854	NM_004439.5	723	gGt/gCt	12/18	0.525431140881971	1	FACETS	0.464	0.379	0.559	0.464	0.379	0.559	SUBCLONAL	1	TRUE	0	0.583085940037385	1		563	157	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228396	228396	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	48	714	0	ENST00000264932.6:c.718G>T	p.Glu240Ter	p.E240*	ENST00000264932	NM_004168.2	240	Gag/Tag	6/15	0.479683312519958	3	FACETS	0.925	0.79	1	0.462	0.395	0.535	CLONAL	1	TRUE	1	0.583085940037385	3		714	230	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524615	176524615	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	64	1150	0	ENST00000292408.4:c.2347A>T	p.Ser783Cys	p.S783C	ENST00000292408	NM_213647.1	783	Agc/Tgc	18/18	0.583085940037385	1	FACETS	0.972	0.862	1	0.972	0.862	1	CLONAL	1	TRUE	0	0.583085940037385	1		1150	160	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176618991	176618991	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	56	687	2	ENST00000439151.2:c.1034C>A	p.Pro345Gln	p.P345Q	ENST00000439151	NM_022455.4	345	cCg/cAg	3/23	0.583085940037385	1	FACETS	0.728	0.634	0.826	0.728	0.634	0.826	SUBCLONAL	1	TRUE	0	0.583085940037385	1		689	187	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453074	140453074	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0034769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	27	371	1	ENST00000288602.6:c.1860+1G>A		p.X620_splice	ENST00000288602	NM_004333.4	620			0.583085940037385	1	FACETS	0.547	0.443	0.661	0.547	0.443	0.661	SUBCLONAL	1	TRUE	0	0.583085940037385	1		372	120	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981575	70981575	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	61	1247	0	ENST00000276594.2:c.521C>A	p.Pro174His	p.P174H	ENST00000276594	NM_024504.3	174	cCc/cAc	2/8	0.532213058408351	2	FACETS	0.702	0.61	0.8	0.351	0.305	0.4	SUBCLONAL	1	TRUE	0	0.583085940037385	2		1247	298	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974820	21974820	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs947790209	NA	P-0034769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	37	78	0	ENST00000304494.5:c.7C>A	p.Pro3Thr	p.P3T	ENST00000304494	NM_000077.4	3	Ccg/Acg	1/3	0.539073286550985	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.583085940037385	1		78	71	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357446	70357446	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	93	542	1	ENST00000374080.3:c.5787G>T	p.Gln1929His	p.Q1929H	ENST00000374080		1929	caG/caT	40/45	1	1	FACETS	0.753	0.695	0.809	1	0.987	1	SUBCLONAL	2	TRUE	0	0.583085940037385	1		543	150	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579415	7579415	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	530	678	1	ENST00000269305.4:c.272G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tGg/tAg	4/11	0.564392699252795	6	FACETS	0.97	0.945	0.994			1	CLONAL	6	TRUE	NA	0.564392699252795	6		679	687	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074300	8074300	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	23	541	0	ENST00000377482.5:c.359T>G	p.Val120Gly	p.V120G	ENST00000377482	NM_018948.3	120	gTg/gGg	4/4	NA	2	FACETS	0.182	0.141	0.229			1	INDETERMINATE	1	TRUE	NA	0.564392699252795	2		541	448	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650863	37650863	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	187	645	0	ENST00000447079.4:c.2335del	p.Arg779ValfsTer3	p.R779Vfs*3	ENST00000447079	NM_015083.1	779	Cgt/gt	5/14	0.561442623480101	2	FACETS	0.952	0.896	1	0.952	0.896	1	CLONAL	2	TRUE	0	0.564392699252795	2		645	348	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141568671	141568671	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	79	576	0	ENST00000220592.5:c.791G>A	p.Gly264Asp	p.G264D	ENST00000220592	NM_012154.3	264	gGt/gAt	7/19	0.564392699252795	10	FACETS	0.848	0.743	0.96	0.094	0.082	0.107	CLONAL	1	TRUE	1	0.564392699252795	10		576	1076	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0034817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	143	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.258609780033562	3	FACETS	0.804	0.733	0.877	0.804	0.733	0.877	CLONAL	2	TRUE	1	0.258609780033562	3		539	777	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0034817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	76	484	0	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.258609780033562	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.258609780033562	1		484	456	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928100	178928100	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	76	539	0	ENST00000263967.3:c.1378G>A	p.Gly460Ser	p.G460S	ENST00000263967	NM_006218.2	460	Ggt/Agt	8/21	1	2	FACETS	0.854	0.749	0.968	0.854	0.749	0.968	CLONAL	1	TRUE	1	0.258609780033562	2		539	688	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156732	20156732	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	181	389	0	ENST00000379607.5:c.25G>C	p.Gly9Arg	p.G9R	ENST00000379607	NM_001412.3	9	Ggt/Cgt	2/7	1	2	FACETS	0.991	0.919	1	0.991	0.919	1	CLONAL	1	TRUE	1	0.607653873906594	2		389	601	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106248	27106249	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0034858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	180	455	0	ENST00000324856.7:c.5860dup	p.Ile1954AsnfsTer9	p.I1954Nfs*9	ENST00000324856	NM_006015.4	1953	-/A	20/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.607653873906594	2		455	584	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202221	108202221	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs775621333	NA	P-0034858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	108	365	0	ENST00000278616.4:c.7566A>T	p.Gln2522His	p.Q2522H	ENST00000278616	NM_000051.3	2522	caA/caT	51/63	0.607653873906594	1	FACETS	0.92	0.84	1	0.92	0.84	1	CLONAL	1	TRUE	0	0.607653873906594	1		365	269	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0034859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	149	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.181251950957255	5	FACETS	1	0.975	1	0.772	0.708	0.838	INDETERMINATE	2	TRUE	2	0.329318266112354	5		539	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0034859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	304	447	1	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.315862060660307	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.329318266112354	2		448	811	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974715	21974732	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCCCCCGCCTCCA	GCAGCGCCCCCGCCTCCA	-	novel	NA	P-0034859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	89	220	0	ENST00000304494.5:c.95_112del	p.Leu32_Leu37del	p.L32_L37del	ENST00000304494	NM_000077.4	32	cTGGAGGCGGGGGCGCTGCcc/ccc	1/3	0.329318266112354	2	FACETS	0.793	0.709	0.88	0.793	0.709	0.88	SUBCLONAL	2	TRUE	0	0.329318266112354	2		220	341	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870205	44870205	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0034859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	128	196	0	ENST00000377967.4:c.385-1G>T		p.X129_splice	ENST00000377967	NM_021140.2	129			0.307790403488586	2	FACETS	1	0.98	1			1	CLONAL	2	TRUE	NA	0.329318266112354	2		196	319	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914808	32914808	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0121441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	114	320	0	ENST00000380152.3:c.6316C>G	p.Leu2106Val	p.L2106V	ENST00000380152		2106	Ctt/Gtt	11/27	0.655493112390059	3	FACETS	0.889	0.804	0.977	0.444	0.402	0.489	CLONAL	1	NA	1	0.661885316845714	3		320	516	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023169	27023212	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGGCCCGGCGCGGAGCCGGACCTGAAGAACTCGAACGGGAAC	GCGGGCCCGGCGCGGAGCCGGACCTGAAGAACTCGAACGGGAAC	-	novel	NA	P-0034864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	42	71	0	ENST00000324856.7:c.283_326del	p.Gly95Ter	p.G95*	ENST00000324856	NM_006015.4	92	gGCGGGCCCGGCGCGGAGCCGGACCTGAAGAACTCGAACGGGAAC/g	1/20	1	2	FACETS	0.913	0.782	1	0.913	0.782	1	CLONAL	1	TRUE	1	0.78	2		71	118	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023768	27023769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0034864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	149	309	0	ENST00000324856.7:c.878_879dup	p.Thr294ProfsTer70	p.T294Pfs*70	ENST00000324856	NM_006015.4	292	acc/aCCcc	1/20	1	2	FACETS	0.809	0.745	0.875	0.809	0.745	0.875	CLONAL	1	TRUE	1	0.78	2		309	472	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720831	89720831	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	97	167	0	ENST00000371953.3:c.982del	p.Ala328GlnfsTer16	p.A328Qfs*16	ENST00000371953	NM_000314.4	328	Gca/ca	8/9	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.78	2		167	213	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0034864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	129	348	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	1	2	FACETS	0.88	0.806	0.955	0.88	0.806	0.955	CLONAL	1	TRUE	1	0.78	2		348	376	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577295	64577295	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	265	435	0	ENST00000312049.6:c.287A>G	p.Gln96Arg	p.Q96R	ENST00000312049	NM_130799.2	96	cAg/cGg	2/10	1	2	FACETS	0.975	0.919	1	0.975	0.919	1	CLONAL	1	TRUE	1	0.78	2		435	697	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	219	641	0	ENST00000227507.2:c.859C>T	p.Pro287Ser	p.P287S	ENST00000227507	NM_053056.2	287	Ccc/Tcc	5/5	1	2	FACETS	0.95	0.89	1	0.95	0.89	1	CLONAL	1	TRUE	1	0.78	2		641	591	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873760	35873760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	219	384	2	ENST00000216797.5:c.91G>A	p.Asp31Asn	p.D31N	ENST00000216797	NM_020529.2	31	Gac/Aac	1/6	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.78	2		386	558	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061174	38061174	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1208147234	NA	P-0034864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	116	299	0	ENST00000250448.2:c.815C>T	p.Pro272Leu	p.P272L	ENST00000250448	NM_004496.3	272	cCg/cTg	2/2	1	2	FACETS	0.775	0.705	0.847	0.775	0.705	0.847	SUBCLONAL	1	TRUE	1	0.78	2		299	384	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136276	2136276	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	235	444	0	ENST00000219476.3:c.4745T>G	p.Ile1582Ser	p.I1582S	ENST00000219476	NM_000548.3	1582	aTc/aGc	37/42	1	2	FACETS	0.909	0.853	0.966	0.909	0.853	0.966	CLONAL	1	TRUE	1	0.78	2		444	663	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0034864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	136	365	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.935	0.86	1	0.935	0.86	1	CLONAL	1	TRUE	1	0.78	2		366	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0034864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	220	409	0	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.78	2		409	506	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56367802	56367802	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775236927	NA	P-0034864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	154	315	1	ENST00000348428.3:c.628G>A	p.Asp210Asn	p.D210N	ENST00000348428	NM_006785.3	210	Gac/Aac	4/17	1	2	FACETS	0.942	0.872	1	0.942	0.872	1	CLONAL	1	TRUE	1	0.78	2		316	419	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1620991	1620992	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0034864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	222	513	0	ENST00000344749.5:c.1068dup	p.Val357ArgfsTer36	p.V357Rfs*36	ENST00000344749	NM_001136139.2	356	-/C	13/19	1	2	FACETS	0.794	0.742	0.847	0.794	0.742	0.847	SUBCLONAL	1	TRUE	1	0.78	2		513	717	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097625	11097625	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	216	362	3	ENST00000358026.2:c.810del	p.Met272CysfsTer31	p.M272Cfs*31	ENST00000358026	NM_001128849.1	269	Ccc/cc	5/36	1	2	FACETS	0.853	0.798	0.91	0.853	0.798	0.91	CLONAL	1	TRUE	1	0.78	2		365	649	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141498	11141498	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	199	454	0	ENST00000358026.2:c.3480del	p.Leu1161SerfsTer3	p.L1161Sfs*3	ENST00000358026	NM_001128849.1	1159	Ggg/gg	25/36	1	2	FACETS	0.898	0.838	0.96	0.898	0.838	0.96	CLONAL	1	TRUE	1	0.78	2		454	568	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0034864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	265	796	3	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.981	0.925	1	0.981	0.925	1	CLONAL	1	TRUE	1	0.78	2		799	693	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213971	36213971	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	275	572	0	ENST00000222270.7:c.2801del	p.Gly934GlufsTer52	p.G934Efs*52	ENST00000222270	NM_014727.1	933	Ggg/gg	6/37	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.78	2		572	664	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905727	50905727	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761250116	NA	P-0034864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	263	508	0	ENST00000440232.2:c.775G>A	p.Asp259Asn	p.D259N	ENST00000440232	NM_002691.3	259	Gac/Aac	7/27	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.78	2		508	658	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723074	52723074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	166	312	0	ENST00000322088.6:c.1259G>A	p.Arg420Gln	p.R420Q	ENST00000322088	NM_014225.5	420	cGg/cAg	10/15	1	2	FACETS	0.976	0.906	1	0.976	0.906	1	CLONAL	1	TRUE	1	0.78	2		312	436	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164728	36164728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	34	454	0	ENST00000300305.3:c.1147C>T	p.Pro383Ser	p.P383S	ENST00000300305		383	Ccg/Tcg	8/8	1	2	FACETS	0.15	0.122	0.181	0.15	0.122	0.181	SUBCLONAL	1	TRUE	1	0.78	2		454	583	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149243869	149243869	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	214	374	1	ENST00000360632.3:c.949G>T	p.Gly317Trp	p.G317W	ENST00000360632	NM_015472.4	317	Ggg/Tgg	6/7	1	2	FACETS	0.982	0.92	1	0.982	0.92	1	CLONAL	1	TRUE	1	0.78	2		375	559	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0034864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	119	384	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	0.78	2		384	291	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133465	55133465	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	96	259	0	ENST00000257290.5:c.769G>T	p.Gly257Cys	p.G257C	ENST00000257290	NM_006206.4	257	Ggc/Tgc	6/23	1	2	FACETS	0.815	0.735	0.898	0.815	0.735	0.898	CLONAL	1	TRUE	1	0.78	2		259	302	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638614	176638614	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784098	NA	P-0034864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	260	460	1	ENST00000439151.2:c.3214C>T	p.Arg1072Ter	p.R1072*	ENST00000439151	NM_022455.4	1072	Cga/Tga	5/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.78	2		461	625	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554958	106554958	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	170	337	0	ENST00000369096.4:c.2075G>A	p.Cys692Tyr	p.C692Y	ENST00000369096	NM_001198.3	692	tGc/tAc	7/7	1	2	FACETS	0.933	0.866	1	0.933	0.866	1	CLONAL	1	TRUE	1	0.78	2		337	467	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121913370	NA	P-0034864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	63	173	0	ENST00000288602.6:c.1742A>G	p.Asn581Ser	p.N581S	ENST00000288602	NM_004333.4	581	aAt/aGt	15/18	1	2	FACETS	0.892	0.787	1	0.892	0.787	1	CLONAL	1	TRUE	1	0.78	2		173	181	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001305	150001305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568586257	NA	P-0034867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	41	391	0	ENST00000253339.5:c.2299C>T	p.Arg767Cys	p.R767C	ENST00000253339		767	Cgt/Tgt	4/7	0.313152780406825	1	FACETS	0.424	0.353	0.503	0.424	0.353	0.503	SUBCLONAL	1	TRUE	0	0.313152780406825	1		391	521	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941240	71941240	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	38	468	0	ENST00000298229.2:c.1015G>C	p.Glu339Gln	p.E339Q	ENST00000298229	NM_001567.3	339	Gag/Cag	9/28	1	2	FACETS	0.359	0.296	0.43	0.359	0.296	0.43	SUBCLONAL	1	TRUE	1	0.313152780406825	2		468	676	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	463358	463358	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	66	233	0	ENST00000399788.2:c.913G>T	p.Glu305Ter	p.E305*	ENST00000399788	NM_001042603.1	305	Gaa/Taa	8/28	1	2	FACETS	0.891	0.775	1	0.891	0.775	1	CLONAL	1	TRUE	1	0.313152780406825	2		233	473	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250252	133250252	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	71	442	0	ENST00000320574.5:c.1268A>T	p.Asn423Ile	p.N423I	ENST00000320574	NM_006231.2	423	aAt/aTt	13/49	1	2	FACETS	0.837	0.731	0.95	0.837	0.731	0.95	CLONAL	1	TRUE	1	0.313152780406825	2		442	542	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43700140	43700140	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1166678498	NA	P-0034867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	72	269	0	ENST00000382044.4:c.5746+1G>A		p.X1916_splice	ENST00000382044	NM_001141980.1	1916			0.313152780406825	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.313152780406825	1		269	302	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351098	89351098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140370885	NA	P-0034867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	34	506	0	ENST00000301030.4:c.1852G>A	p.Ala618Thr	p.A618T	ENST00000301030	NM_001256183.1	618	Gct/Act	9/13	1	2	FACETS	0.346	0.282	0.419	0.346	0.282	0.419	SUBCLONAL	1	TRUE	1	0.313152780406825	2		506	627	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490265	29490288	+	inframe_deletion	In_Frame_Del	DEL	TCTGCCATTTTCTTCACACCTGTC	TCTGCCATTTTCTTCACACCTGTC	-	novel	NA	P-0034867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	215	308	0	ENST00000356175.3:c.350_373del	p.Ile117_Arg125delinsSer	p.I117_R125delinsS	ENST00000356175	NM_000267.3	117	aTCTGCCATTTTCTTCACACCTGTCgt/agt	4/57	0.239456258685007	3	FACETS	0.848	0.793	0.905	0.848	0.793	0.905	CLONAL	3	TRUE	0	0.313152780406825	3		308	624	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45391478	45391478	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	46	253	0	ENST00000262160.6:c.682G>T	p.Glu228Ter	p.E228*	ENST00000262160	NM_005901.5	228	Gaa/Taa	6/11	0.275787302190961	2	FACETS	0.543	0.457	0.638	0.272	0.228	0.319	SUBCLONAL	1	TRUE	0	0.313152780406825	2		253	541	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39239469	39239469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1558469016	NA	P-0034867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	92	280	0	ENST00000402219.2:c.2188G>T	p.Val730Phe	p.V730F	ENST00000402219	NM_005633.3	730	Gtt/Ttt	14/23	1	2	FACETS	0.933	0.83	1	0.933	0.83	1	CLONAL	1	TRUE	1	0.313152780406825	2		280	630	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911143	40911143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370795038	NA	P-0034867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	46	265	0	ENST00000373198.4:c.2162G>A	p.Arg721His	p.R721H	ENST00000373198	NM_133170.3	721	cGt/cAt	13/32	0.313152780406825	1	FACETS	0.532	0.448	0.624	0.532	0.448	0.624	SUBCLONAL	1	TRUE	0	0.313152780406825	1		265	466	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130419	29130419	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	35	414	0	ENST00000328354.6:c.291G>C	p.Trp97Cys	p.W97C	ENST00000328354	NM_007194.3	97	tgG/tgC	2/15	1	2	FACETS	0.471	0.385	0.567	0.471	0.385	0.567	SUBCLONAL	1	TRUE	1	0.313152780406825	2		414	475	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294283	1294283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	90	526	1	ENST00000310581.5:c.718C>T	p.Arg240Cys	p.R240C	ENST00000310581	NM_198253.2	240	Cgt/Tgt	2/16	0.297326467250894	3	FACETS	0.966	0.858	1	0.483	0.429	0.541	CLONAL	1	TRUE	1	0.313152780406825	3		527	688	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564516	86564517	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0034867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	84	379	0	ENST00000274376.6:c.248_249insT	p.Ala84SerfsTer28	p.A84Sfs*28	ENST00000274376	NM_002890.2	83	gga/ggTa	1/25	0.2512552417847	2	FACETS	1	0.976	1	0.693	0.616	0.775	CLONAL	1	TRUE	0	0.313152780406825	2		379	387	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2949773	2949773	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	80	406	0	ENST00000396946.4:c.3171del	p.Ile1058SerfsTer7	p.I1058Sfs*7	ENST00000396946	NM_032415.4	1057	ggG/gg	24/25	1	2	FACETS	0.791	0.696	0.892	0.791	0.696	0.892	SUBCLONAL	1	TRUE	1	0.313152780406825	2		406	646	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026409	6026409	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1554297061	NA	P-0034867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	35	250	0	ENST00000265849.7:c.1987G>T	p.Glu663Ter	p.E663*	ENST00000265849	NM_000535.5	663	Gaa/Taa	11/15	1	2	FACETS	0.433	0.354	0.522	0.433	0.354	0.522	SUBCLONAL	1	TRUE	1	0.313152780406825	2		250	516	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55225388	55225388	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	48	356	0	ENST00000275493.2:c.1240A>G	p.Arg414Gly	p.R414G	ENST00000275493	NM_005228.3	414	Agg/Ggg	11/28	1	2	FACETS	0.522	0.441	0.612	0.522	0.441	0.612	SUBCLONAL	1	TRUE	1	0.313152780406825	2		356	587	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465651	8465651	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	72	305	0	ENST00000356435.5:c.3529C>A	p.Arg1177Ser	p.R1177S	ENST00000356435		1177	Cgc/Agc	21/35	0.313152780406825	1	FACETS	0.994	0.873	1	0.994	0.873	1	CLONAL	1	TRUE	0	0.313152780406825	1		305	390	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034465	47034465	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	53	535	0	ENST00000377604.3:c.550G>T	p.Ala184Ser	p.A184S	ENST00000377604	NM_001204468.1	184	Gct/Tct	6/24	0.299732339851669	0	FACETS	0.395	0.336	0.459			1	SUBCLONAL	1	TRUE	0	0.313152780406825	0		535	589	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227970	53227970	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	37	441	1	ENST00000375401.3:c.2344G>T	p.Glu782Ter	p.E782*	ENST00000375401	NM_004187.3	782	Gag/Tag	16/26	0.299732339851669	0	FACETS	0.308	0.253	0.369			1	SUBCLONAL	1	TRUE	0	0.313152780406825	0		442	527	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0034904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	78	308	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	0.986	0.883	1	0.986	0.883	1	CLONAL	1	TRUE	1	0.735517812951348	2		308	215	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629582	187629582	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748957825	NA	P-0034904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	118	649	1	ENST00000441802.2:c.1400C>T	p.Ala467Val	p.A467V	ENST00000441802	NM_005245.3	467	gCg/gTg	2/27	0.735517812951348	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.735517812951348	1		650	202	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910371	29910371	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs2230954	NA	P-0034904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	114	728	0	ENST00000376809.5:c.41C>A	p.Ser14Ter	p.S14*	ENST00000376809	NM_002116.7	14	tCg/tAg	1/8	0.735517812951348	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.735517812951348	1		728	188	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434396	121434396	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	21	790	0	ENST00000257555.6:c.1160A>G	p.His387Arg	p.H387R	ENST00000257555		387	cAc/cGc	6/10	1	2	FACETS	0.161	0.123	0.205	0.161	0.123	0.205	SUBCLONAL	1	TRUE	1	0.735517812951348	2		790	355	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29002033	29002033	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	102	389	0	ENST00000282397.4:c.1132G>A	p.Glu378Lys	p.E378K	ENST00000282397	NM_002019.4	378	Gag/Aag	9/30	0.312952085780065	3	FACETS	0.771	0.702	0.841	0.771	0.702	0.841	INDETERMINATE	2	TRUE	1	0.735517812951348	3		389	246	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128036818	128036818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	120	617	0	ENST00000285398.2:c.1661G>A	p.Arg554Lys	p.R554K	ENST00000285398	NM_000122.1	554	aGg/aAg	10/15	1	2	FACETS	0.901	0.823	0.982	0.901	0.823	0.982	CLONAL	1	TRUE	1	0.735517812951348	2		617	362	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634690	158634690	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	71	416	0	ENST00000263640.3:c.496A>G	p.Thr166Ala	p.T166A	ENST00000263640	NM_001105.4	166	Act/Gct	5/11	1	2	FACETS	0.811	0.718	0.909	0.811	0.718	0.909	CLONAL	1	TRUE	1	0.735517812951348	2		416	238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0034905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	10	767	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	0.76965454020821	1	FACETS	0.035	0.023	0.05	0.035	0.023	0.05	SUBCLONAL	1	TRUE	0	0.76965454020821	1		767	460	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692791	89692791	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	90	336	0	ENST00000371953.3:c.275A>T	p.Asp92Val	p.D92V	ENST00000371953	NM_000314.4	92	gAc/gTc	5/9	1	2	FACETS	0.787	0.707	0.871	0.787	0.707	0.871	SUBCLONAL	1	TRUE	1	0.76965454020821	2		336	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578496	7578496	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587782197	NA	P-0034905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	494	1040	1	ENST00000269305.4:c.434T>A	p.Leu145Gln	p.L145Q	ENST00000269305	NM_001126112.2	145	cTg/cAg	5/11	0.76965454020821	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.76965454020821	1		1041	678	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938931	178938931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	99	402	0	ENST00000263967.3:c.2173G>A	p.Asp725Asn	p.D725N	ENST00000263967	NM_006218.2	725	Gat/Aat	14/21	1	2	FACETS	0.843	0.762	0.927	0.843	0.762	0.927	CLONAL	1	TRUE	1	0.76965454020821	2		402	305	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259116	89259117	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0034905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	104	345	0	ENST00000336596.2:c.264dup	p.Arg89GlnfsTer20	p.R89Qfs*20	ENST00000336596	NM_005233.5	87	gtc/gtCc	3/17	0.76965454020821	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.76965454020821	1		345	161	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593258	67593258	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	114	276	0	ENST00000274335.5:c.2004del	p.Lys668AsnfsTer5	p.K668Nfs*5	ENST00000274335		668	aaG/aa	15/15	0.767335558008855	1	FACETS	0.836	0.772	0.9	0.836	0.772	0.9	CLONAL	1	TRUE	0	0.76965454020821	1		276	218	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1977	211	349	0				ENST00000310581	NM_198253.2	-/1132			0.542659235772036	9	FACETS	1	0.947	1	0.129	0.119	0.139	CLONAL	1	TRUE	1	0.542659235772036	9		349	2188	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0034906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	260	765	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.542659235772036	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.542659235772036	1		765	689	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013691	12013691	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0034906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	133	368	0	ENST00000353533.5:c.634-1G>C		p.X212_splice	ENST00000353533	NM_003010.3	212			0.542659235772036	1	FACETS	0.958	0.88	1	0.958	0.88	1	CLONAL	1	TRUE	0	0.542659235772036	1		368	373	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785992	135785992	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0034906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	298	653	0	ENST00000298552.3:c.1229C>G	p.Ser410Ter	p.S410*	ENST00000298552	NM_001162426.1	410	tCa/tGa	12/23	0.542659235772036	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.542659235772036	1		653	711	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983140	201983141	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0034906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	230	465	0	ENST00000359651.3:c.991dup	p.Arg331ProfsTer140	p.R331Pfs*140	ENST00000359651		330	agc/agCc	7/8	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.542659235772036	2		465	826	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226568832	226568832	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	65	733	0	ENST00000366794.5:c.1237G>C	p.Glu413Gln	p.E413Q	ENST00000366794	NM_001618.3	413	Gag/Cag	9/23	1	2	FACETS	0.215	0.186	0.248	0.215	0.186	0.248	SUBCLONAL	1	TRUE	1	0.542659235772036	2		733	1113	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288499	15288499	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393495970	NA	P-0034906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	129	329	0	ENST00000263388.2:c.4240G>A	p.Gly1414Ser	p.G1414S	ENST00000263388	NM_000435.2	1414	Ggc/Agc	24/33	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.542659235772036	2		329	467	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527506	41527506	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	54	514	0	ENST00000263253.7:c.1397G>C	p.Arg466Thr	p.R466T	ENST00000263253	NM_001429.3	466	aGa/aCa	6/31	1	2	FACETS	0.243	0.207	0.283	0.243	0.207	0.283	SUBCLONAL	1	TRUE	1	0.542659235772036	2		514	819	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932666	49932666	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	290	823	0	ENST00000296474.3:c.3205G>C	p.Glu1069Gln	p.E1069Q	ENST00000296474	NM_002447.2	1069	Gag/Cag	14/20	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.542659235772036	2		823	1065	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670478	134670478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	65	588	0	ENST00000398015.3:c.389C>T	p.Ser130Phe	p.S130F	ENST00000398015	NM_004441.4	130	tCt/tTt	3/16	1	2	FACETS	0.253	0.218	0.291	0.253	0.218	0.291	SUBCLONAL	1	TRUE	1	0.542659235772036	2		588	947	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524325	148524325	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs537373788	NA	P-0034906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	31	393	0	ENST00000320356.2:c.659C>T	p.Ser220Phe	p.S220F	ENST00000320356	NM_004456.4	220	tCt/tTt	7/20	1	2	FACETS	0.208	0.168	0.255	0.208	0.168	0.255	SUBCLONAL	1	TRUE	1	0.542659235772036	2		393	548	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995536	68995536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	68	660	0	ENST00000288368.4:c.1940G>A	p.Arg647Lys	p.R647K	ENST00000288368	NM_024870.2	647	aGa/aAa	18/40	0.542659235772036	3	FACETS	0.279	0.241	0.319	0.139	0.12	0.16	SUBCLONAL	1	TRUE	1	0.542659235772036	3		660	1144	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	79	349	0				ENST00000310581	NM_198253.2	-/1132			0.47637225894901	9	FACETS	0.883	0.774	1	0.11	0.096	0.125	CLONAL	1	TRUE	1	0.47637225894901	9		349	1002	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0034906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	118	765	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.471298887275371	1	FACETS	0.854	0.776	0.935	0.854	0.776	0.935	CLONAL	1	TRUE	0	0.47637225894901	1		765	442	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013691	12013691	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0034906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	88	368	0	ENST00000353533.5:c.634-1G>C		p.X212_splice	ENST00000353533	NM_003010.3	212			0.471298887275371	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.47637225894901	1		368	233	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785992	135785992	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0034906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	147	653	0	ENST00000298552.3:c.1229C>G	p.Ser410Ter	p.S410*	ENST00000298552	NM_001162426.1	410	tCa/tGa	12/23	0.47637225894901	1	FACETS	0.975	0.897	1	0.975	0.897	1	CLONAL	1	TRUE	0	0.47637225894901	1		653	482	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983140	201983141	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0034906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	93	465	0	ENST00000359651.3:c.991dup	p.Arg331ProfsTer140	p.R331Pfs*140	ENST00000359651		330	agc/agCc	7/8	1	2	FACETS	0.834	0.745	0.928	0.834	0.745	0.928	CLONAL	1	TRUE	1	0.47637225894901	2		465	468	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288499	15288499	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393495970	NA	P-0034906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	75	329	0	ENST00000263388.2:c.4240G>A	p.Gly1414Ser	p.G1414S	ENST00000263388	NM_000435.2	1414	Ggc/Agc	24/33	1	2	FACETS	0.975	0.862	1	0.975	0.862	1	CLONAL	1	TRUE	1	0.47637225894901	2		329	323	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527344	137527344	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	54	656	0	ENST00000367739.4:c.302G>C	p.Arg101Thr	p.R101T	ENST00000367739	NM_000416.2	101	aGa/aCa	3/7	0.471298887275371	1	FACETS	0.493	0.423	0.57	0.493	0.423	0.57	SUBCLONAL	1	TRUE	0	0.47637225894901	1		656	350	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932323	36932323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	34	820	0	ENST00000361632.4:c.2146G>A	p.Glu716Lys	p.E716K	ENST00000361632		716	Gag/Aag	16/16	1	2	FACETS	0.21	0.171	0.254	0.21	0.171	0.254	SUBCLONAL	1	TRUE	1	0.47637225894901	2		820	680	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256620	133256620	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1565980334	NA	P-0034906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	43	403	0	ENST00000320574.5:c.343G>A	p.Glu115Lys	p.E115K	ENST00000320574	NM_006231.2	115	Gaa/Aaa	5/49	1	2	FACETS	0.496	0.416	0.584	0.496	0.416	0.584	SUBCLONAL	1	TRUE	1	0.47637225894901	2		403	364	SUCCESS
ALK	238	MSKCC	GRCh37	2	29419689	29419689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437829239	NA	P-0034906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	115	390	0	ENST00000389048.3:c.4111G>A	p.Glu1371Lys	p.E1371K	ENST00000389048	NM_004304.4	1371	Gaa/Aaa	28/29	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.47637225894901	2		390	435	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620704	52620704	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	25	252	0	ENST00000394830.3:c.3049G>A	p.Glu1017Lys	p.E1017K	ENST00000394830	NM_018313.4	1017	Gaa/Aaa	21/30	1	2	FACETS	0.479	0.379	0.593	0.479	0.379	0.593	SUBCLONAL	1	TRUE	1	0.47637225894901	2		252	219	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254576	1254576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1432	151	714	0	ENST00000310581.5:c.3202G>A	p.Glu1068Lys	p.E1068K	ENST00000310581	NM_198253.2	1068	Gag/Aag	15/16	0.47637225894901	9	FACETS	1	0.952	1	0.134	0.121	0.147	CLONAL	1	TRUE	1	0.47637225894901	9		714	1583	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877860	151877860	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	24	413	0	ENST00000262189.6:c.7085C>T	p.Ser2362Leu	p.S2362L	ENST00000262189	NM_170606.2	2362	tCa/tTa	36/59	1	2	FACETS	0.272	0.213	0.341	0.272	0.213	0.341	SUBCLONAL	1	TRUE	1	0.47637225894901	2		413	370	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878053	151878053	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	21	402	1	ENST00000262189.6:c.6892C>A	p.Pro2298Thr	p.P2298T	ENST00000262189	NM_170606.2	2298	Ccc/Acc	36/59	1	2	FACETS	0.244	0.187	0.31	0.244	0.187	0.31	SUBCLONAL	1	TRUE	1	0.47637225894901	2		403	362	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934379	39934379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747350059	NA	P-0034907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	216	541	2	ENST00000378444.4:c.220C>T	p.Arg74Cys	p.R74C	ENST00000378444	NM_001123385.1	74	Cgc/Tgc	4/15	0.273698772388021	5	FACETS	0.916	0.854	0.979	0.611	0.569	0.653	INDETERMINATE	2	TRUE	2	0.580324650684564	5		543	760	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579382	7579397	+	frameshift_variant	Frame_Shift_Del	DEL	GTTTTCTGGGAAGGGA	GTTTTCTGGGAAGGGA	-	novel	NA	P-0034907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	577	661	0	ENST00000269305.4:c.290_305del	p.Val97AlafsTer21	p.V97Afs*21	ENST00000269305	NM_001126112.2	97	gTCCCTTCCCAGAAAACc/gc	4/11	0.493881623977366	4	FACETS	1	0.991	1			1	CLONAL	4	TRUE	NA	0.580324650684564	4		661	760	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108206	8108206	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	258	546	0	ENST00000585124.1:c.1018C>A	p.Leu340Ile	p.L340I	ENST00000585124	NM_004217.3	340	Ctt/Att	9/9	0.493881623977366	4	FACETS	0.949	0.893	1			1	CLONAL	2	TRUE	NA	0.580324650684564	4		546	740	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657322	29657322	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	158	502	0	ENST00000356175.3:c.5555C>A	p.Ala1852Asp	p.A1852D	ENST00000356175	NM_000267.3	1852	gCc/gAc	38/57	0.585699669378751	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.580324650684564	2		502	259	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664842	29664842	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	86	301	0	ENST00000356175.3:c.6585C>G	p.Cys2195Trp	p.C2195W	ENST00000356175	NM_000267.3	2195	tgC/tgG	43/57	0.585699669378751	2	FACETS	0.988	0.905	1	0.988	0.905	1	CLONAL	2	TRUE	0	0.580324650684564	2		301	150	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215390	41215390	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs41293461	NA	P-0034907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	265	468	0	ENST00000357654.3:c.5153G>A	p.Trp1718Ter	p.W1718*	ENST00000357654	NM_007294.3	1718	tGg/tAg	18/23	0.585699669378751	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	4	TRUE	0	0.580324650684564	4		468	347	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197351	26197763	+	coding_sequence_variant,5_prime_UTR_variant	Frame_Shift_Del	DEL	CGGTAACGGTGGGGCTTCTTCACGCCGCCGGTGGCTGGAGCGCTCTTTCGAGCAGCCTTGGTGGCCAGCTGCTTGCGTGGCGCTTTCCCACCCGTGGACTTGCGAGCAGTCTGCTTGGTACGAGCCATTGCGAACTTCTAAACCCTGCTAAATGACGAAAAAACGAAAGTCTAGCCTTTCGTACCCGTATATATAAAGACACCCCTGTTCTGATTGGACAAGGCAGCCTTTCCCCTGCAGCTCGATTGGTGGAGACGCCCACTCCCTGACAGAACATCTCCTGCATGTAGACCAAATATTAAAACTTTCCTCCGTCCATCTTTAACTGCTGGTGTTTTCAACCCTTTCCCCTCTGTGCCATGTTTCTAGCTTTTATTTAAAACGTACTTTGGTTTTCCTTGGCAAAATTGTGT	CGGTAACGGTGGGGCTTCTTCACGCCGCCGGTGGCTGGAGCGCTCTTTCGAGCAGCCTTGGTGGCCAGCTGCTTGCGTGGCGCTTTCCCACCCGTGGACTTGCGAGCAGTCTGCTTGGTACGAGCCATTGCGAACTTCTAAACCCTGCTAAATGACGAAAAAACGAAAGTCTAGCCTTTCGTACCCGTATATATAAAGACACCCCTGTTCTGATTGGACAAGGCAGCCTTTCCCCTGCAGCTCGATTGGTGGAGACGCCCACTCCCTGACAGAACATCTCCTGCATGTAGACCAAATATTAAAACTTTCCTCCGTCCATCTTTAACTGCTGGTGTTTTCAACCCTTTCCCCTCTGTGCCATGTTTCTAGCTTTTATTTAAAACGTACTTTGGTTTTCCTTGGCAAAATTGTGT	-	novel	NA	P-0034907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	509	128	0				ENST00000356476		?-43/136		1/1	0.580324650684564	7	FACETS	0.898	0.862	0.934	0.513	0.492	0.534	CLONAL	4	TRUE	0	0.580324650684564	7		128	1197	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150457	157150457	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554256715	NA	P-0034907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	250	505	0	ENST00000346085.5:c.1639G>T	p.Gly547Ter	p.G547*	ENST00000346085	NM_020732.3	547	Gga/Tga	2/20	0.585699669378751	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.580324650684564	2		505	425	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201692	66201692	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753118521	NA	P-0034909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	135	573	0	ENST00000273854.3:c.2810G>A	p.Arg937His	p.R937H	ENST00000273854	NM_004439.5	937	cGt/cAt	16/18	1	2	FACETS	0.633	0.576	0.694	0.633	0.576	0.694	SUBCLONAL	1	TRUE	1	0.514166510221964	2		573	829	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939032	131939032	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	25	322	0	ENST00000265335.6:c.2248T>G	p.Leu750Val	p.L750V	ENST00000265335		750	Tta/Gta	14/25	0.332570842743332	1	FACETS	0.334	0.265	0.414	0.334	0.265	0.414	SUBCLONAL	1	TRUE	0	0.514166510221964	1		322	216	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271211	26271211	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	93	451	0	ENST00000305910.3:c.402G>C	p.Glu134Asp	p.E134D	ENST00000305910	NM_003534.2	134	gaG/gaC	1/1	1	2	FACETS	0.776	0.693	0.864	0.776	0.693	0.864	SUBCLONAL	1	TRUE	1	0.514166510221964	2		451	466	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0034910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	37	590	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		590	325	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	119	349	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.999	0.901	1	0.999	0.901	1	CLONAL	1	TRUE	1	0.28	2		349	851	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0034911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	97	669	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	1	2	FACETS	0.715	0.636	0.799	0.715	0.636	0.799	SUBCLONAL	1	TRUE	1	0.28	2		669	969	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361160	70361160	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs79912241	NA	P-0034911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	113	388	0	ENST00000374080.3:c.6348C>A	p.His2116Gln	p.H2116Q	ENST00000374080		2116	caC/caA	43/45	1	1	FACETS	0.84	0.756	0.93	0.84	0.756	0.93	CLONAL	1	TRUE	0	0.28	1		388	826	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937055	48937055	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	17	269	0	ENST00000267163.4:c.823G>T	p.Glu275Ter	p.E275*	ENST00000267163	NM_000321.2	275	Gaa/Taa	8/27	1	2	FACETS	0.437	0.326	0.569	0.437	0.326	0.569	SUBCLONAL	1	TRUE	1	0.28	2		269	278	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274911	41274911	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	222	446	0	ENST00000349496.5:c.1161T>G	p.Asn387Lys	p.N387K	ENST00000349496	NM_001904.3	387	aaT/aaG	8/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.633863161166537	2		446	671	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344553	118344553	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	181	421	0	ENST00000534358.1:c.2679G>C	p.Arg893Ser	p.R893S	ENST00000534358	NM_005933.3	893	agG/agC	3/36	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.633863161166537	2		421	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578274	7578275	+	protein_altering_variant	In_Frame_Ins	INS	-	-	CAG	novel	NA	P-0034912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	265	577	0	ENST00000269305.4:c.574_575insCTG	p.Gln192delinsProGlu	p.Q192delinsPE	ENST00000269305	NM_001126112.2	192	cag/cCTGag	6/11	1	2	FACETS	0.971	0.913	1	0.971	0.913	1	CLONAL	1	TRUE	1	0.633863161166537	2		577	861	SUCCESS
APC	324	MSKCC	GRCh37	5	112175793	112175793	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	114	271	0	ENST00000257430.4:c.4502C>G	p.Ser1501Cys	p.S1501C	ENST00000257430	NM_000038.5	1501	tCt/tGt	16/16	1	2	FACETS	0.852	0.773	0.935	0.852	0.773	0.935	CLONAL	1	TRUE	1	0.633863161166537	2		271	422	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0034916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	65	303	1	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.39151610835207	1	FACETS	0.542	0.47	0.619	0.542	0.47	0.619	SUBCLONAL	1	TRUE	0	0.39151610835207	1		304	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578523	7578523	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1567554216	NA	P-0034916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	477	836	0	ENST00000269305.4:c.407A>C	p.Gln136Pro	p.Q136P	ENST00000269305	NM_001126112.2	136	cAa/cCa	5/11	0.367925319681855	2	FACETS	0.962	0.92	1	0.962	0.92	1	CLONAL	2	TRUE	0	0.39151610835207	2		836	1267	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106687	27106687	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	162	540	0	ENST00000324856.7:c.6298C>T	p.Gln2100Ter	p.Q2100*	ENST00000324856	NM_006015.4	2100	Cag/Tag	20/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.39151610835207	2		540	754	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338632	70338632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	107	510	1	ENST00000374080.3:c.28G>A	p.Glu10Lys	p.E10K	ENST00000374080		10	Gaa/Aaa	1/45	1	2	FACETS	0.804	0.722	0.891	0.804	0.722	0.891	CLONAL	1	TRUE	1	0.39151610835207	2		511	680	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092947	27092947	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0034916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	85	278	0	ENST00000324856.7:c.2879-1G>A		p.X960_splice	ENST00000324856	NM_006015.4	960			1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.39151610835207	2		278	418	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097749	8097749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1215707952	NA	P-0034916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	155	562	0	ENST00000346208.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000346208		44	cCg/cTg	2/6	0.39151610835207	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.39151610835207	1		562	633	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199700	11199700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	106	450	0	ENST00000361445.4:c.4888G>A	p.Val1630Ile	p.V1630I	ENST00000361445	NM_004958.3	1630	Gta/Ata	35/58	1	2	FACETS	0.858	0.771	0.951	0.858	0.771	0.951	CLONAL	1	TRUE	1	0.39151610835207	2		450	631	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860212	151860212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	116	506	0	ENST00000262189.6:c.10450C>T	p.Gln3484Ter	p.Q3484*	ENST00000262189	NM_170606.2	3484	Cag/Tag	43/59	1	2	FACETS	0.835	0.753	0.921	0.835	0.753	0.921	CLONAL	1	TRUE	1	0.39151610835207	2		506	710	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020359	123020359	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	65	399	0	ENST00000355640.3:c.847C>A	p.Gln283Lys	p.Q283K	ENST00000355640		283	Cag/Aag	2/7	1	2	FACETS	0.693	0.602	0.791	0.693	0.602	0.791	SUBCLONAL	1	TRUE	1	0.39151610835207	2		399	479	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654553	29654553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876657714	NA	P-0034918-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	16	200	0	ENST00000356175.3:c.5242C>T	p.Arg1748Ter	p.R1748*	ENST00000356175	NM_000267.3	1748	Cga/Tga	37/57	1	2	FACETS	0.801	0.593	1	0.801	0.593	1	CLONAL	1	TRUE	1	0.17	2		200	235	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0034918-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	14	558	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.707	0.511	0.944	0.707	0.511	0.944	CLONAL	1	TRUE	1	0.17	2		558	233	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711874	89711874	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0034918-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	32	418	0	ENST00000371953.3:c.493-1G>C		p.X165_splice	ENST00000371953	NM_000314.4	165			1	2	FACETS	1	0.828	1	1	0.828	1	CLONAL	1	TRUE	1	0.17	2		418	369	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431955	49431955	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0034918-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	59	708	2	ENST00000301067.7:c.9184A>T	p.Lys3062Ter	p.K3062*	ENST00000301067	NM_003482.3	3062	Aag/Tag	34/54	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.17	2		710	609	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554855	106554855	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034918-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	23	277	0	ENST00000369096.4:c.1972C>A	p.Pro658Thr	p.P658T	ENST00000369096	NM_001198.3	658	Cca/Aca	7/7	1	2	FACETS	0.838	0.653	1	0.838	0.653	1	CLONAL	1	TRUE	1	0.17	2		277	323	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162107	22162107	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	209	389	0	ENST00000215832.6:c.148C>G	p.Arg50Gly	p.R50G	ENST00000215832	NM_002745.4	50	Cga/Gga	2/9	0.658668650708337	1	FACETS	0.994	0.936	1	0.994	0.936	1	CLONAL	1	TRUE	0	0.658668650708337	1		389	428	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115848	8115849	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CACATGTCCT	novel	NA	P-0034920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	205	511	2	ENST00000346208.3:c.1196_1205dup	p.Leu403HisfsTer107	p.L403Hfs*107	ENST00000346208		398	-/CACATGTCCT	6/6	1	2	FACETS	0.874	0.814	0.936	0.874	0.814	0.936	CLONAL	1	TRUE	1	0.658668650708337	2		513	712	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55229302	55229302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	212	394	0	ENST00000275493.2:c.1609G>T	p.Asp537Tyr	p.D537Y	ENST00000275493	NM_005228.3	537	Gac/Tac	13/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.658668650708337	2		394	601	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804407	46804407	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0034923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	271	325	0	ENST00000290295.7:c.602-2A>C		p.X201_splice	ENST00000290295	NM_006361.5	201			1	2	FACETS	0.847	0.8	0.895	0.847	0.8	0.895	CLONAL	1	TRUE	1	0.932342171908729	2		325	686	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794430	42794431	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0034923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	777	905	0	ENST00000575354.2:c.1513dup	p.His505ProfsTer9	p.H505Pfs*9	ENST00000575354	NM_015125.3	504	acc/aCcc	10/20	0.932342171908729	1	FACETS	0.951	0.933	0.967	0.951	0.933	0.967	CLONAL	1	TRUE	0	0.932342171908729	1		905	936	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5029810	5029810	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	212	434	0	ENST00000381652.3:c.254T>G	p.Phe85Cys	p.F85C	ENST00000381652	NM_004972.3	85	tTt/tGt	4/25	1	2	FACETS	0.906	0.85	0.962	0.906	0.85	0.962	CLONAL	1	TRUE	1	0.932342171908729	2		434	502	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923604	39923604	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	326	682	2	ENST00000378444.4:c.3487C>T	p.Arg1163Ter	p.R1163*	ENST00000378444	NM_001123385.1	1163	Cga/Tga	7/15	0.150375085774072	1	FACETS	0.834	0.793	0.876	1	0.997	1	INDETERMINATE	3	FALSE	0	0.3	1		684	738	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0034925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	13	246	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.34	0.242	0.459	0.34	0.242	0.459	SUBCLONAL	1	FALSE	1	0.315069904177946	2		246	243	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0034925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	137	967	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	FALSE	1	0.315069904177946	2		968	867	SUCCESS
APC	324	MSKCC	GRCh37	5	112174112	112174112	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	46	263	0	ENST00000257430.4:c.2821G>T	p.Glu941Ter	p.E941*	ENST00000257430	NM_000038.5	941	Gaa/Taa	16/16	1	2	FACETS	0.804	0.679	0.941	0.804	0.679	0.941	CLONAL	1	FALSE	1	0.315069904177946	2		263	363	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634810	158634810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	25	230	0	ENST00000263640.3:c.376C>T	p.Leu126Phe	p.L126F	ENST00000263640	NM_001105.4	126	Ctc/Ttc	5/11	1	2	FACETS	0.365	0.287	0.455	0.365	0.287	0.455	SUBCLONAL	1	FALSE	1	0.315069904177946	2		230	435	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739792	41739792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749899848	NA	P-0034925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	270	533	1	ENST00000242208.4:c.181C>T	p.His61Tyr	p.H61Y	ENST00000242208	NM_002192.2	61	Cac/Tac	2/3	0.315069904177946	4	FACETS	1	0.978	1	0.726	0.681	0.772	CLONAL	2	FALSE	1	0.315069904177946	4		534	1035	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0034926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	100	432	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.234576004663511	2	FACETS	1	0.975	1	0.653	0.585	0.725	CLONAL	1	TRUE	0	0.27	2		432	567	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0034926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	58	553	0	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	1	2	FACETS	0.534	0.458	0.618	0.534	0.458	0.618	SUBCLONAL	1	TRUE	1	0.27	2		553	804	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70432801	70432801	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs755912455	NA	P-0034926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	39	298	0	ENST00000373644.4:c.4823A>G	p.His1608Arg	p.H1608R	ENST00000373644	NM_030625.2	1608	cAt/cGt	8/12	1	2	FACETS	0.691	0.573	0.822	0.691	0.573	0.822	SUBCLONAL	1	TRUE	1	0.27	2		298	418	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196711	67196711	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1296312712	NA	P-0034926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	31	269	0	ENST00000312629.5:c.240G>T	p.Lys80Asn	p.K80N	ENST00000312629	NM_003952.2	80	aaG/aaT	3/15	1	2	FACETS	0.402	0.324	0.491	0.402	0.324	0.491	SUBCLONAL	1	TRUE	1	0.27	2		269	571	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231141	46231141	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	73	364	0	ENST00000334344.6:c.1061T>C	p.Leu354Pro	p.L354P	ENST00000334344	NM_152641.2	354	cTg/cCg	9/21	0.234576004663511	2	FACETS	1	0.958	1	0.606	0.532	0.686	CLONAL	1	TRUE	0	0.27	2		364	446	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335928	73335929	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0034926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	69	268	0	ENST00000377767.4:c.2366_2367delinsTT	p.Arg789Leu	p.R789L	ENST00000377767	NM_014953.3	789	cGG/cTT	18/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.27	2		268	435	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600002	10600002	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	88	590	0	ENST00000171111.5:c.1574A>C	p.Tyr525Ser	p.Y525S	ENST00000171111	NM_203500.1	525	tAt/tCt	5/6	1	2	FACETS	0.678	0.6	0.763	0.678	0.6	0.763	SUBCLONAL	1	TRUE	1	0.27	2		590	961	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683483	182683483	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	47	434	0	ENST00000292782.4:c.62C>A	p.Ser21Tyr	p.S21Y	ENST00000292782	NM_020640.2	21	tCt/tAt	2/7	1	2	FACETS	0.547	0.46	0.642	0.547	0.46	0.642	SUBCLONAL	1	TRUE	1	0.27	2		434	637	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729618	41729618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	45	442	0	ENST00000242208.4:c.911C>T	p.Pro304Leu	p.P304L	ENST00000242208	NM_002192.2	304	cCt/cTt	3/3	1	2	FACETS	0.519	0.435	0.612	0.519	0.435	0.612	SUBCLONAL	1	TRUE	1	0.27	2		442	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0034929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	41	623	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	1	2	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	1	0.12	2		623	668	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245919	5245919	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	45	924	0	ENST00000357368.4:c.856A>G	p.Thr286Ala	p.T286A	ENST00000357368	NM_002850.3	286	Acc/Gcc	10/38	1	2	FACETS	0.833	0.698	0.984	0.833	0.698	0.984	CLONAL	1	TRUE	1	0.12	2		924	900	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0034931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	34	522	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.420411148585638	1	FACETS	0.158	0.128	0.192	0.158	0.128	0.192	SUBCLONAL	1	TRUE	0	0.446761236056013	1		522	747	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0034931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	42	378	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.313354121941658	1	FACETS	0.347	0.29	0.41	0.347	0.29	0.41	SUBCLONAL	1	TRUE	0	0.446761236056013	1		378	421	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0034931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	46	213	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	0.313354121941658	1	FACETS	0.72	0.613	0.836	0.72	0.613	0.836	SUBCLONAL	1	TRUE	0	0.446761236056013	1		213	222	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578456	7578457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGGACGCGGGTGC	novel	NA	P-0034931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	159	719	0	ENST00000269305.4:c.461_473dup	p.Ala159HisfsTer26	p.A159Hfs*26	ENST00000269305	NM_001126112.2	158	cgc/cgGCACCCGCGTCCGc	5/11	0.420411148585638	1	FACETS	0.595	0.545	0.647	0.595	0.545	0.647	SUBCLONAL	1	TRUE	0	0.446761236056013	1		719	929	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166782	32166782	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	200	644	1	ENST00000375023.3:c.4456G>T	p.Gly1486Cys	p.G1486C	ENST00000375023	NM_004557.3	1486	Ggt/Tgt	24/30	1	2	FACETS	0.903	0.837	0.972	0.903	0.837	0.972	CLONAL	1	TRUE	1	0.446761236056013	2		645	991	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099587	157099588	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1554247525	NA	P-0034931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	26	68	0	ENST00000346085.5:c.527dup	p.Pro177AlafsTer55	p.P177Afs*55	ENST00000346085	NM_020732.3	175	ggc/ggCc	1/20	1	2	FACETS	0.946	0.762	1	0.946	0.762	1	CLONAL	1	TRUE	1	0.446761236056013	2		68	123	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578473	7578473	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064795860	NA	P-0034931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	22	751	1	ENST00000269305.4:c.457C>T	p.Pro153Ser	p.P153S	ENST00000269305	NM_001126112.2	153	Ccc/Tcc	5/11	0.420411148585638	1	FACETS	0.08	0.062	0.103	0.08	0.062	0.103	SUBCLONAL	1	TRUE	0	0.446761236056013	1		752	951	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	29	493	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	0.13	2		493	382	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0034932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1451	83	728	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	1	2	FACETS	0.832	0.731	0.942	0.832	0.731	0.942	CLONAL	1	TRUE	1	0.13	2		728	1534	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971116	21971116	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs11552823	NA	P-0034932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	77	505	0	ENST00000304494.5:c.242C>G	p.Pro81Arg	p.P81R	ENST00000304494	NM_000077.4	81	cCc/cGc	2/3	1	2	FACETS	0.976	0.854	1	0.976	0.854	1	CLONAL	1	TRUE	1	0.13	2		505	1214	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082216	16082216	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1643	113	877	0	ENST00000281043.3:c.32del	p.Gly11AlafsTer2	p.G11Afs*2	ENST00000281043	NM_005378.4	10	ccG/cc	2/3	1	2	FACETS	0.99	0.887	1	0.99	0.887	1	CLONAL	1	TRUE	1	0.13	2		877	1756	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702367	47702367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs549467183	NA	P-0034934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	38	281	0	ENST00000233146.2:c.1963G>A	p.Val655Ile	p.V655I	ENST00000233146	NM_000251.2	655	Gta/Ata	12/16	1	2	FACETS	0.461	0.381	0.551	0.461	0.381	0.551	SUBCLONAL	1	TRUE	1	0.352135148098955	2		281	468	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794713	120794713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	133	495	0	ENST00000257552.2:c.644G>A	p.Gly215Asp	p.G215D	ENST00000257552	NM_002442.3	215	gGc/gAc	9/15	0.251913038487335	1	FACETS	0.89	0.81	0.975	0.89	0.81	0.975	CLONAL	1	TRUE	0	0.352135148098955	1		495	699	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579557	7579558	+	frameshift_variant	Frame_Shift_Ins	INS	TC	TC	AAA	novel	NA	P-0034934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	228	602	2	ENST00000269305.4:c.129_130delinsTTT	p.Leu43PhefsTer9	p.L43Ffs*9	ENST00000269305	NM_001126112.2	43	ttGAtg/ttTTTtg	4/11	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.352135148098955	2		604	909	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850297	128850297	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	58	644	0	ENST00000249373.3:c.1560del	p.Asn521ThrfsTer12	p.N521Tfs*12	ENST00000249373	NM_005631.4	520	atC/at	9/12	1	2	FACETS	0.344	0.294	0.398	0.344	0.294	0.398	SUBCLONAL	1	TRUE	1	0.352135148098955	2		644	958	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0034939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	307	445	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.713641443774846	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.713641443774846	1		445	521	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0034939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	443	384	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.713641443774846	3	FACETS	0.928	0.89	0.965	0.928	0.89	0.965	CLONAL	2	TRUE	1	0.713641443774846	3		384	908	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0034939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	299	472	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.713641443774846	1	FACETS	0.971	0.926	1	0.971	0.926	1	CLONAL	1	TRUE	0	0.713641443774846	1		472	555	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528741	8528741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1277243866	NA	P-0034939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	134	277	0	ENST00000356435.5:c.391G>A	p.Gly131Ser	p.G131S	ENST00000356435		131	Ggc/Agc	4/35	0.713641443774846	1	FACETS	0.842	0.779	0.905	0.842	0.779	0.905	CLONAL	1	TRUE	0	0.713641443774846	1		277	287	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848528	151848528	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	121	250	0	ENST00000262189.6:c.12665del	p.Lys4222ArgfsTer10	p.K4222Rfs*10	ENST00000262189	NM_170606.2	4222	aAg/ag	50/59	1	2	FACETS	0.841	0.767	0.919	0.841	0.767	0.919	CLONAL	1	TRUE	1	0.713641443774846	2		250	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0034946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	669	744	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.704979780412851	3	FACETS	1	0.995	1			1	CLONAL	3	TRUE	NA	0.704979780412851	3		744	809	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306996	65306997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0034946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	270	524	5	ENST00000342505.4:c.2580dup	p.Pro861ThrfsTer4	p.P861Tfs*4	ENST00000342505	NM_002227.2	860	-/A	19/25	0.704979780412851	3	FACETS	0.898	0.85	0.945	0.898	0.85	0.945	CLONAL	2	TRUE	1	0.704979780412851	3		529	577	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267359	198267359	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs377023736	NA	P-0034946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	177	580	0	ENST00000335508.6:c.1998G>C	p.Lys666Asn	p.K666N	ENST00000335508	NM_012433.2	666	aaG/aaC	14/25	0.704979780412851	3	FACETS	0.928	0.857	1	0.464	0.428	0.501	CLONAL	1	TRUE	1	0.704979780412851	3		580	732	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325801	65325801	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	140	432	0	ENST00000342505.4:c.1321C>G	p.His441Asp	p.H441D	ENST00000342505	NM_002227.2	441	Cat/Gat	9/25	0.704979780412851	3	FACETS	1	0.968	1	0.556	0.51	0.604	CLONAL	1	TRUE	1	0.704979780412851	3		432	483	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061135	38061153	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCCCCCGCTTCCGCTCC	CTGCCCCCGCTTCCGCTCC	-	novel	NA	P-0034946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	117	89	0	ENST00000250448.2:c.836_854del	p.Gly279AlafsTer36	p.G279Afs*36	ENST00000250448	NM_004496.3	279	gGGAGCGGAAGCGGGGGCAGc/gc	2/2	0.691138687986205	4	FACETS	0.916	0.849	0.981	1	0.987	1	CLONAL	3	TRUE	2	0.704979780412851	4		89	206	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827656	72827656	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	250	717	0	ENST00000268489.5:c.8925del	p.Glu2975AspfsTer32	p.E2975Dfs*32	ENST00000268489	NM_006885.3	2975	gaA/ga	9/10	0.704979780412851	3	FACETS	1	0.989	1	0.613	0.575	0.651	CLONAL	1	TRUE	1	0.704979780412851	3		717	783	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061162	38061192	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCCGGCCCCCGGCTGCTTCTCGCACTTGA	CCGCCGGCCCCCGGCTGCTTCTCGCACTTGA	GCGGGGGCGGG	novel	NA	P-0034946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	171	408	3	ENST00000250448.2:c.797_827delinsCCCGCCCCCGC	p.Phe266SerfsTer20	p.F266Sfs*20	ENST00000250448	NM_004496.3	266	tTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGc/tCCCGCCCCCGCc	2/2	0.691138687986205	4	FACETS	1	0.982	1	0.608	0.561	0.657	CLONAL	1	TRUE	2	0.704979780412851	4		411	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0034968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	421	740	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.663745352893166	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	FALSE	0	0.747405074713752	2		740	537	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	226	604	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.747405074713752	7	FACETS	0.817	0.76	0.875	0.327	0.304	0.35	CLONAL	2	FALSE	2	0.747405074713752	7		604	1062	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249457	153249457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	343	604	1	ENST00000281708.4:c.1321C>T	p.Arg441Trp	p.R441W	ENST00000281708	NM_033632.3	441	Cgg/Tgg	9/12	0.549876341355541	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	FALSE	2	0.747405074713752	4		605	721	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37882019	37882019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781070018	NA	P-0034968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	359	723	0	ENST00000269571.5:c.2785C>T	p.Arg929Trp	p.R929W	ENST00000269571		929	Cgg/Tgg	23/27	0.747405074713752	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	FALSE	2	0.747405074713752	4		723	818	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094466	27094468	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0034968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	516	602	0	ENST00000324856.7:c.3175_3177del	p.Lys1059del	p.K1059del	ENST00000324856	NM_006015.4	1058	gtGAAg/gtg	11/20	0.747405074713752	4	FACETS	0.941	0.918	0.963	0.941	0.918	0.963	CLONAL	4	FALSE	0	0.747405074713752	4		602	641	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52729031	52729031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1158328586	NA	P-0034968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	652	586	0	ENST00000322088.6:c.1723G>A	p.Val575Ile	p.V575I	ENST00000322088	NM_014225.5	575	Gtc/Atc	14/15	0.747405074713752	7	FACETS	1	0.995	1	1	0.995	1	CLONAL	5	FALSE	2	0.747405074713752	7		586	912	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533670	41533671	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0034968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	272	560	0	ENST00000263253.7:c.1636_1637insC	p.Glu546AlafsTer71	p.E546Afs*71	ENST00000263253	NM_001429.3	546	gaa/gCaa	8/31	0.747405074713752	4	FACETS	0.942	0.89	0.995	0.942	0.89	0.995	CLONAL	2	FALSE	2	0.747405074713752	4		560	675	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258940	153258957	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTGATAATCTTTACCTCT	TTGATAATCTTTACCTCT	-	novel	NA	P-0034968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	132	263	0	ENST00000281708.4:c.858_861+14del		p.X286_splice	ENST00000281708	NM_033632.3	286		5/12	0.549876341355541	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	FALSE	2	0.747405074713752	4		263	294	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0034969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	69	558	0				ENST00000310581	NM_198253.2	-/1132			0.0442008150834998	3	FACETS	1	0.906	1	1	0.984	1	INDETERMINATE	4	TRUE	1	0.22	3		558	171	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0034969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	71	678	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	1	2	FACETS	1	0.956	1	1	0.987	1	CLONAL	3	TRUE	1	0.22	2		678	187	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0034971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	32	388	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.285365681375978	3	FACETS	0.922	0.761	1	0.922	0.761	1	CLONAL	2	TRUE	1	0.285365681375978	3		388	139	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911579	134911579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs959853730	NA	P-0034971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	20	541	1	ENST00000398015.3:c.2044C>T	p.Arg682Cys	p.R682C	ENST00000398015	NM_004441.4	682	Cgc/Tgc	11/16	1	2	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	TRUE	1	0.285365681375978	2		542	122	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578175	7578175	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0034971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	17	630	1	ENST00000269305.4:c.672+2T>G		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.269526065131154	0	FACETS	0.835	0.632	1			1	CLONAL	1	TRUE	0	0.285365681375978	0		631	102	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0034973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	99	384	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.971	0.871	1	0.971	0.871	1	CLONAL	1	TRUE	1	0.405250106122565	2		384	503	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0034973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	14	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.402696252456082	3	FACETS	0.145	0.104	0.195	0.072	0.052	0.098	SUBCLONAL	1	TRUE	1	0.405250106122565	3		539	575	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	190	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.402696252456082	3	FACETS	0.981	0.912	1	0.981	0.912	1	CLONAL	2	TRUE	1	0.405250106122565	3		493	575	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0034973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	87	575	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.873	0.775	0.976	0.873	0.775	0.976	CLONAL	1	TRUE	1	0.405250106122565	2		575	492	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0034973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	63	254	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.901	0.784	1	0.901	0.784	1	CLONAL	1	TRUE	1	0.405250106122565	2		254	345	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129399	2129399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45517287	NA	P-0034973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	120	611	0	ENST00000219476.3:c.3254C>T	p.Ser1085Leu	p.S1085L	ENST00000219476	NM_000548.3	1085	tCg/tTg	28/42	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.405250106122565	2		611	444	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216476	36216476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	396	935	1	ENST00000222270.7:c.3739C>T	p.Arg1247Cys	p.R1247C	ENST00000222270	NM_014727.1	1247	Cgt/Tgt	12/37	0.405250106122565	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	1	0.405250106122565	4		936	878	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66518973	66518973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	78	425	0	ENST00000358598.2:c.254C>G	p.Pro85Arg	p.P85R	ENST00000358598	NM_212471.2	85	cCt/cGt	3/11	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.405250106122565	2		425	345	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120214	70120215	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	ACTA	novel	NA	P-0034973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	144	626	0	ENST00000245479.2:c.1217_1220dup	p.Tyr407Ter	p.Y407*	ENST00000245479	NM_000346.3	406	cac/cACTAac	3/3	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.405250106122565	2		626	567	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932788	49932788	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	123	833	0	ENST00000296474.3:c.3083G>T	p.Gly1028Val	p.G1028V	ENST00000296474	NM_002447.2	1028	gGt/gTt	14/20	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.405250106122565	2		833	576	SUCCESS
APC	324	MSKCC	GRCh37	5	112175799	112175799	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	67	338	0	ENST00000257430.4:c.4508del	p.Ser1503TyrfsTer4	p.S1503Yfs*4	ENST00000257430	NM_000038.5	1503	tCa/ta	16/16	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.405250106122565	2		338	287	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910657	29910676	+	frameshift_variant	Frame_Shift_Del	DEL	GCCAGAGGATGGAGCCGCGG	GCCAGAGGATGGAGCCGCGG	-	novel	NA	P-0034973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	43	1050	0	ENST00000376809.5:c.199_218del	p.Gln67AlafsTer25	p.Q67Afs*25	ENST00000376809	NM_002116.7	66	aGCCAGAGGATGGAGCCGCGG/a	2/8	1	2	FACETS	0.354	0.296	0.419	0.354	0.296	0.419	SUBCLONAL	1	TRUE	1	0.405250106122565	2		1050	599	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528740	8528740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	69	455	0	ENST00000356435.5:c.392G>A	p.Gly131Asp	p.G131D	ENST00000356435		131	gGc/gAc	4/35	1	2	FACETS	0.889	0.778	1	0.889	0.778	1	CLONAL	1	TRUE	1	0.405250106122565	2		455	383	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576917	7576917	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	448	626	0	ENST00000269305.4:c.929del	p.Asn310ThrfsTer35	p.N310Tfs*35	ENST00000269305	NM_001126112.2	310	aAc/ac	9/11	0.491582362089411	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	3	TRUE	0	0.491582362089411	3		626	756	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0034977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	51	313	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.161549751757918	1	FACETS	0.662	0.564	0.769	0.662	0.564	0.769	INDETERMINATE	1	TRUE	0	0.313782411710442	1		313	414	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0034977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	61	536	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.161549751757918	1	FACETS	0.491	0.423	0.566	0.491	0.423	0.566	INDETERMINATE	1	TRUE	0	0.313782411710442	1		536	667	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845757	68845757	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587780784	NA	P-0034977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	81	331	0	ENST00000261769.5:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000261769	NM_004360.3	335	Cga/Tga	7/16	0.313782411710442	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.313782411710442	1		331	380	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685305	89685305	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	64	182	0	ENST00000371953.3:c.200T>G	p.Ile67Arg	p.I67R	ENST00000371953	NM_000314.4	67	aTa/aGa	3/9	0.313782411710442	1	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	0	0.313782411710442	1		182	341	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682275	37682275	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	112	424	0	ENST00000447079.4:c.3466T>A	p.Ser1156Thr	p.S1156T	ENST00000447079	NM_015083.1	1156	Tcc/Acc	13/14	0.161549751757918	1	FACETS	0.933	0.841	1	0.933	0.841	1	INDETERMINATE	1	TRUE	0	0.313782411710442	1		424	645	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225362541	225362541	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs767240461	NA	P-0034981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	180	621	0	ENST00000264414.4:c.1636C>T	p.Arg546Ter	p.R546*	ENST00000264414	NM_003590.4	546	Cga/Tga	12/16	1	2	FACETS	0.857	0.795	0.92	0.857	0.795	0.92	CLONAL	1	TRUE	1	0.75023172184653	2		621	560	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244235	153244235	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	89	578	0	ENST00000281708.4:c.1922C>T	p.Ser641Leu	p.S641L	ENST00000281708	NM_033632.3	641	tCa/tTa	12/12	0.75023172184653	1	FACETS	0.46	0.412	0.511	0.46	0.412	0.511	SUBCLONAL	1	TRUE	0	0.75023172184653	1		578	322	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947585	48947585	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0034981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	219	632	0	ENST00000267163.4:c.1172C>G	p.Ser391Ter	p.S391*	ENST00000267163	NM_000321.2	391	tCa/tGa	12/27	0.746149337388871	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.75023172184653	1		632	357	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742805	17742805	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1417386162	NA	P-0034981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	41	774	0	ENST00000250003.3:c.713C>T	p.Pro238Leu	p.P238L	ENST00000250003	NM_002478.4	238	cCc/cTc	3/3	0.75023172184653	1	FACETS	0.181	0.15	0.214	0.181	0.15	0.214	SUBCLONAL	1	TRUE	0	0.75023172184653	1		774	378	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218387	69218387	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	130	677	0	ENST00000462284.1:c.479C>T	p.Ser160Phe	p.S160F	ENST00000462284	NM_002392.5	160	tCt/tTt	7/11	1	2	FACETS	0.501	0.455	0.549	0.501	0.455	0.549	SUBCLONAL	1	TRUE	1	0.75023172184653	2		677	692	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349063	11349063	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	48	201	0	ENST00000332029.2:c.273G>C	p.Glu91Asp	p.E91D	ENST00000332029	NM_003745.1	91	gaG/gaC	2/2	0.75023172184653	3	FACETS	0.579	0.492	0.673	0.193	0.164	0.225	SUBCLONAL	1	TRUE	0	0.75023172184653	3		201	304	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667527	29667541	+	inframe_deletion	In_Frame_Del	DEL	CGCCTCTGCACAAAG	CGCCTCTGCACAAAG	-	novel	NA	P-0034981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	215	721	1	ENST00000356175.3:c.6864_6878del	p.Pro2289_Ala2293del	p.P2289_A2293del	ENST00000356175	NM_000267.3	2288	tCGCCTCTGCACAAAGcc/tcc	46/57	1	2	FACETS	0.98	0.917	1	0.98	0.917	1	CLONAL	1	TRUE	1	0.75023172184653	2		722	585	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245910	41245910	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	265	959	1	ENST00000357654.3:c.1638G>T	p.Met546Ile	p.M546I	ENST00000357654	NM_007294.3	546	atG/atT	10/23	1	2	FACETS	0.93	0.875	0.985	0.93	0.875	0.985	CLONAL	1	TRUE	1	0.75023172184653	2		960	760	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224384	36224384	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs868232650	NA	P-0034981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	144	1001	0	ENST00000222270.7:c.6934C>A	p.Gln2312Lys	p.Q2312K	ENST00000222270	NM_014727.1	2312	Cag/Aag	28/37	0.75023172184653	3	FACETS	0.463	0.421	0.507	0.232	0.21	0.254	SUBCLONAL	1	TRUE	1	0.75023172184653	3		1001	1140	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097227	178097227	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	106	547	0	ENST00000397062.3:c.487C>G	p.Gln163Glu	p.Q163E	ENST00000397062	NM_006164.4	163	Cag/Gag	4/5	0.746044096833619	3	FACETS	0.489	0.438	0.544	0.245	0.219	0.272	SUBCLONAL	1	TRUE	1	0.75023172184653	3		547	794	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394394	162394394	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356263061	NA	P-0034981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	160	586	0	ENST00000366898.1:c.674C>T	p.Ala225Val	p.A225V	ENST00000366898	NM_004562.2	225	gCt/gTt	6/12	0.75023172184653	1	FACETS	0.976	0.917	1	0.976	0.917	1	CLONAL	1	TRUE	0	0.75023172184653	1		586	273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0034982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	15	685	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.824	0.605	1	0.824	0.605	1	CLONAL	1	TRUE	1	0.2	2		685	182	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872380	45872380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	39	665	1	ENST00000391945.4:c.131C>T	p.Ser44Leu	p.S44L	ENST00000391945	NM_000400.3	44	tCa/tTa	3/23	0.131434394238011	3	FACETS	0.933	0.779	1	0.933	0.779	1	CLONAL	2	TRUE	1	0.2	3		666	230	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89880961	89880961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	14	464	0	ENST00000389301.3:c.250G>A	p.Glu84Lys	p.E84K	ENST00000389301	NM_000135.2	84	Gag/Aag	3/43	1	2	FACETS	0.693	0.502	0.924	0.693	0.502	0.924	SUBCLONAL	1	TRUE	1	0.2	2		464	202	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37863341	37863341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	22	698	0	ENST00000269571.5:c.172G>A	p.Gly58Arg	p.G58R	ENST00000269571		58	Gga/Aga	2/27	1	2	FACETS	1	0.805	1	1	0.805	1	CLONAL	1	TRUE	1	0.2	2		698	212	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845902	156845902	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	25	745	0	ENST00000524377.1:c.1532T>A	p.Val511Glu	p.V511E	ENST00000524377	NM_002529.3	511	gTg/gAg	13/17	0.3	1	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	0	0.2	1		745	199	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999371	100999371	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	12	809	1	ENST00000325455.5:c.431G>T	p.Gly144Val	p.G144V	ENST00000325455	NM_001202474.3	144	gGc/gTc	1/8	1	2	FACETS	0.603	0.424	0.823	0.603	0.424	0.823	SUBCLONAL	1	TRUE	1	0.2	2		810	199	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955530	48955554	+	frameshift_variant	Frame_Shift_Del	DEL	ATTTAGAACGATGTGAACATCGAAT	ATTTAGAACGATGTGAACATCGAAT	CCA	novel	NA	P-0034982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	19	321	1	ENST00000267163.4:c.1646_1670delinsCCA	p.His549ProfsTer55	p.H549Pfs*55	ENST00000267163	NM_000321.2	549	cATTTAGAACGATGTGAACATCGAATc/cCCAc	17/27	0.272412131104738	3	FACETS	0.741	0.563	0.951	0.371	0.281	0.476	CLONAL	1	TRUE	1	0.2	3		322	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs985033810	NA	P-0034983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	265	666	0	ENST00000269305.4:c.731G>T	p.Gly244Val	p.G244V	ENST00000269305	NM_001126112.2	244	gGc/gTc	7/11	NA	2	FACETS	0.995	0.936	1			1	INDETERMINATE	2	TRUE	NA	0.327496250619857	2		666	813	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576863	7576863	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	91	654	0	ENST00000269305.4:c.983del	p.Phe328SerfsTer17	p.F328Sfs*17	ENST00000269305	NM_001126112.2	328	tTc/tc	9/11	1	2	FACETS	0.985	0.874	1	0.985	0.874	1	CLONAL	1	TRUE	1	0.225511449600208	2		654	819	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0034987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	135	506	0	ENST00000311936.3:c.34_35delinsCT	p.Gly12Leu	p.G12L	ENST00000311936	NM_004985.3	12	GGt/CTt	2/5	0.252502750937251	8	FACETS	0.814	0.738	0.894	0.232	0.21	0.256	CLONAL	2	TRUE	1	0.252502750937251	8		506	1155	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99454589	99454589	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	83	625	0	ENST00000268035.6:c.1508A>T	p.Asn503Ile	p.N503I	ENST00000268035	NM_000875.3	503	aAt/aTt	7/21	0.252502750937251	1	FACETS	0.954	0.843	1	0.954	0.843	1	CLONAL	1	TRUE	0	0.252502750937251	1		625	602	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6414400	6414400	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	24	139	0	ENST00000356142.4:c.34G>C	p.Gly12Arg	p.G12R	ENST00000356142	NM_018890.3	12	Gga/Cga	1/7	0.252502750937251	5	FACETS	1	0.874	1			1	CLONAL	1	TRUE	NA	0.252502750937251	5		139	225	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852158	128852158	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141955434	NA	P-0034989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	288	762	2	ENST00000249373.3:c.2230C>T	p.Pro744Ser	p.P744S	ENST00000249373	NM_005631.4	744	Cct/Tct	12/12	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.558805472305651	2		764	850	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0034989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	122	426	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.558805472305651	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.558805472305651	1		426	299	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578196	7578196	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	235	599	1	ENST00000269305.4:c.653T>A	p.Val218Glu	p.V218E	ENST00000269305	NM_001126112.2	218	gTg/gAg	6/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.558805472305651	2		600	734	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0034989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	59	90	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.558805472305651	2		91	157	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546560	9546560	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771840400	NA	P-0034989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	147	539	0	ENST00000353224.5:c.1462C>T	p.Arg488Ter	p.R488*	ENST00000353224	NM_177990.2	488	Cga/Tga	5/10	1	2	FACETS	0.915	0.839	0.994	0.915	0.839	0.994	CLONAL	1	TRUE	1	0.558805472305651	2		539	575	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435198	49435199	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755159728	NA	P-0034989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	57	458	0	ENST00000301067.7:c.6354dup	p.Ala2119ArgfsTer36	p.A2119Rfs*36	ENST00000301067	NM_003482.3	2118	-/C	31/54	1	2	FACETS	0.459	0.395	0.53	0.459	0.395	0.53	SUBCLONAL	1	TRUE	1	0.558805472305651	2		458	444	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015385	176015385	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	84	404	1	ENST00000367669.3:c.1353C>A	p.Asp451Glu	p.D451E	ENST00000367669	NM_022457.5	451	gaC/gaA	12/20	0.558805472305651	4	FACETS	0.501	0.441	0.565	0.167	0.147	0.189	SUBCLONAL	1	TRUE	1	0.558805472305651	4		405	936	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433029	49433029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766197076	NA	P-0034989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	238	547	0	ENST00000301067.7:c.8342C>T	p.Pro2781Leu	p.P2781L	ENST00000301067	NM_003482.3	2781	cCt/cTt	33/54	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.558805472305651	2		547	686	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295184	15295185	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0034989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	210	798	3	ENST00000263388.2:c.2487_2488delinsAA	p.Ala830Thr	p.A830T	ENST00000263388	NM_000435.2	829	ctGGca/ctAAca	16/33	1	2	FACETS	0.95	0.885	1	0.95	0.885	1	CLONAL	1	TRUE	1	0.558805472305651	2		801	791	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972873	25972873	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	181	505	0	ENST00000435504.4:c.1552C>T	p.Gln518Ter	p.Q518*	ENST00000435504		518	Caa/Taa	12/13	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.558805472305651	2		505	631	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095787	178095787	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	212	458	0	ENST00000397062.3:c.1544G>A	p.Arg515Lys	p.R515K	ENST00000397062	NM_006164.4	515	aGa/aAa	5/5	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.558805472305651	2		458	675	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573031	41573032	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGGAAAACCAATGG	novel	NA	P-0034989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	80	817	0	ENST00000263253.7:c.5320_5333dup	p.Cys1779LysfsTer34	p.C1779Kfs*34	ENST00000263253	NM_001429.3	1772	-/CGGAAAACCAATGG	31/31	1	2	FACETS	0.348	0.306	0.394	0.348	0.306	0.394	SUBCLONAL	1	TRUE	1	0.558805472305651	2		817	822	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528602	89528602	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	30	214	0	ENST00000336596.2:c.2902A>G	p.Ser968Gly	p.S968G	ENST00000336596	NM_005233.5	968	Agc/Ggc	17/17	1	2	FACETS	0.438	0.355	0.532	0.438	0.355	0.532	SUBCLONAL	1	TRUE	1	0.558805472305651	2		214	245	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1976723	1976723	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	216	521	0	ENST00000382891.5:c.3506T>A	p.Ile1169Asn	p.I1169N	ENST00000382891	NM_133335.3	1169	aTt/aAt	19/22	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.558805472305651	2		521	650	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535353	187535354	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0034989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	175	451	0	ENST00000441802.2:c.9220_9221delinsTT	p.Pro3074Leu	p.P3074L	ENST00000441802	NM_005245.3	3074	CCa/TTa	12/27	1	2	FACETS	0.92	0.85	0.992	0.92	0.85	0.992	CLONAL	1	TRUE	1	0.558805472305651	2		451	681	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985579	2985579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	108	399	0	ENST00000396946.4:c.232G>A	p.Asp78Asn	p.D78N	ENST00000396946	NM_032415.4	78	Gac/Aac	4/25	1	2	FACETS	0.918	0.83	1	0.918	0.83	1	CLONAL	1	TRUE	1	0.558805472305651	2		399	421	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240470	98240470	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0034989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	154	309	1	ENST00000331920.6:c.1216-2A>T		p.X406_splice	ENST00000331920	NM_000264.3	406			0.558805472305651	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.558805472305651	1		310	300	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0034992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	116	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.325082508092538	2		539	698	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0034992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	57	249	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.31923382337202	1	FACETS	0.89	0.768	1	0.89	0.768	1	CLONAL	1	TRUE	0	0.325082508092538	1		249	330	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520017	NA	P-0034992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	121	462	0	ENST00000326873.7:c.647C>T	p.Ser216Phe	p.S216F	ENST00000326873	NM_000455.4	216	tCc/tTc	5/10	0.325082508092538	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.325082508092538	1		462	616	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953369	17953369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	134	653	0	ENST00000458235.1:c.617G>A	p.Ser206Asn	p.S206N	ENST00000458235	NM_000215.3	206	aGc/aAc	6/24	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.325082508092538	2		653	813	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250350	110250358	+	frameshift_variant	Frame_Shift_Del	DEL	GAATAAAGT	GAATAAAGT	AAAAAAGG	novel	NA	P-0034992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	131	635	3	ENST00000374672.4:c.317_325delinsCCTTTTTT	p.Asp106AlafsTer8	p.D106Afs*8	ENST00000374672	NM_004235.4	106	gACTTTATTCtc/gCCTTTTTTtc	3/5	1	2	FACETS	0.865	0.784	0.95	0.865	0.784	0.95	CLONAL	1	TRUE	1	0.325082508092538	2		638	932	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0034997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	372	472	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.396730294000512	3	FACETS	0.948	0.906	0.991	0.948	0.906	0.991	CLONAL	3	TRUE	0	0.396730294000512	3		472	790	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600392	10600392	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	402	759	1	ENST00000171111.5:c.1463A>T	p.Glu488Val	p.E488V	ENST00000171111	NM_203500.1	488	gAg/gTg	4/6	0.396730294000512	2	FACETS	0.993	0.948	1	0.993	0.948	1	CLONAL	2	TRUE	0	0.396730294000512	2		760	1020	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087358	27087363	+	frameshift_variant	Frame_Shift_Del	DEL	TTCAAT	TTCAAT	CGTG	novel	NA	P-0034997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	132	457	1	ENST00000324856.7:c.1932_1937delinsCGTG	p.Ser645ValfsTer3	p.S645Vfs*3	ENST00000324856	NM_006015.4	644	ggTTCAATa/ggCGTGa	5/20	0.396730294000512	2	FACETS	0.995	0.905	1	0.497	0.452	0.545	CLONAL	1	TRUE	0	0.396730294000512	2		458	669	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32449546	32449546	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	123	573	0	ENST00000332351.3:c.828C>G	p.Ser276Arg	p.S276R	ENST00000332351	NM_024426.4	276	agC/agG	3/10	0.38991206590684	3	FACETS	0.914	0.827	1	0.305	0.275	0.336	CLONAL	1	TRUE	0	0.396730294000512	3		573	813	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235836	108235836	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	221	428	0	ENST00000278616.4:c.8878T>G	p.Trp2960Gly	p.W2960G	ENST00000278616	NM_000051.3	2960	Tgg/Ggg	62/63	0.396730294000512	2	FACETS	0.887	0.831	0.945	0.887	0.831	0.945	CLONAL	2	TRUE	0	0.396730294000512	2		428	628	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118355592	118355592	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	269	499	0	ENST00000534358.1:c.4234G>A	p.Glu1412Lys	p.E1412K	ENST00000534358	NM_005933.3	1412	Gaa/Aaa	10/36	0.396730294000512	2	FACETS	0.891	0.84	0.943	0.891	0.84	0.943	CLONAL	2	TRUE	0	0.396730294000512	2		499	761	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435415	110435415	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	216	424	0	ENST00000375856.3:c.2986G>T	p.Gly996Cys	p.G996C	ENST00000375856	NM_003749.2	996	Ggc/Tgc	1/2	0.396730294000512	5	FACETS	0.924	0.86	0.99	0.616	0.573	0.66	CLONAL	2	TRUE	2	0.396730294000512	5		424	940	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560224	95560225	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0034997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	71	214	0	ENST00000393063.1:c.5364_5364+1delinsTT		p.X1788_splice	ENST00000393063	NM_030621.3	1788		25/28	1	2	FACETS	0.957	0.84	1	0.957	0.84	1	CLONAL	1	TRUE	1	0.396730294000512	2		214	374	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041861	14041861	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	91	340	0	ENST00000311895.7:c.2408G>T	p.Cys803Phe	p.C803F	ENST00000311895	NM_005236.2	803	tGc/tTc	11/11	1	2	FACETS	0.894	0.797	0.998	0.894	0.797	0.998	CLONAL	1	TRUE	1	0.396730294000512	2		340	513	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527613	29527613	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs1131691118	NA	P-0034997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	92	462	0	ENST00000356175.3:c.1062G>C	p.Lys354Asn	p.K354N	ENST00000356175	NM_000267.3	354	aaG/aaC	9/57	0.378307908977471	3	FACETS	0.775	0.689	0.867	0.388	0.344	0.434	SUBCLONAL	1	TRUE	1	0.396730294000512	3		462	717	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149845	99149845	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	165	312	0	ENST00000074304.5:c.157A>T	p.Ser53Cys	p.S53C	ENST00000074304	NM_001134224.1	53	Agt/Tgt	5/26	0.353305876832913	4	FACETS	0.954	0.88	1	0.954	0.88	1	CLONAL	2	TRUE	2	0.396730294000512	4		312	609	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480437	89480438	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0034997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	175	326	0	ENST00000336596.2:c.2274_2275del	p.Leu758PhefsTer3	p.L758Ffs*3	ENST00000336596	NM_005233.5	758	ttGGtg/tttg	13/17	0.396730294000512	2	FACETS	0.931	0.865	0.997	0.931	0.865	0.997	CLONAL	2	TRUE	0	0.396730294000512	2		326	474	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911563	134911563	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	124	452	0	ENST00000398015.3:c.2028C>A	p.Asp676Glu	p.D676E	ENST00000398015	NM_004441.4	676	gaC/gaA	11/16	0.378307908977471	3	FACETS	1	0.964	1	0.565	0.512	0.621	CLONAL	1	TRUE	1	0.396730294000512	3		452	663	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969937	161969937	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	219	433	0	ENST00000366898.1:c.1032G>C	p.Glu344Asp	p.E344D	ENST00000366898	NM_004562.2	344	gaG/gaC	9/12	0.396730294000512	2	FACETS	0.998	0.936	1	0.998	0.936	1	CLONAL	2	TRUE	0	0.396730294000512	2		433	553	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55229299	55229299	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	219	432	2	ENST00000275493.2:c.1606G>T	p.Val536Leu	p.V536L	ENST00000275493	NM_005228.3	536	Gtg/Ttg	13/28	0.353305876832913	4	FACETS	0.875	0.815	0.937	0.875	0.815	0.937	CLONAL	2	TRUE	2	0.396730294000512	4		434	881	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508823	106508823	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	146	407	0	ENST00000359195.3:c.817C>A	p.Arg273Ser	p.R273S	ENST00000359195	NM_002649.2	273	Cgc/Agc	2/11	0.353305876832913	4	FACETS	0.776	0.711	0.845	0.776	0.711	0.845	SUBCLONAL	2	TRUE	2	0.396730294000512	4		407	662	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411659	116411659	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	364	703	0	ENST00000397752.3:c.2838del	p.Leu946PhefsTer10	p.L946Ffs*10	ENST00000397752	NM_000245.2	946	ttA/tt	13/21	0.353305876832913	4	FACETS	0.995	0.943	1	0.995	0.943	1	CLONAL	2	TRUE	2	0.396730294000512	4		703	1288	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852087	128852087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1262023810	NA	P-0034997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	329	599	0	ENST00000249373.3:c.2159G>A	p.Gly720Glu	p.G720E	ENST00000249373	NM_005631.4	720	gGa/gAa	12/12	0.353305876832913	4	FACETS	0.953	0.901	1	0.953	0.901	1	CLONAL	2	TRUE	2	0.396730294000512	4		599	1215	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949766	151949766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	98	427	0	ENST00000262189.6:c.1334C>T	p.Ser445Phe	p.S445F	ENST00000262189	NM_170606.2	445	tCt/tTt	10/59	0.353305876832913	4	FACETS	0.907	0.809	1	0.453	0.404	0.506	CLONAL	1	TRUE	2	0.396730294000512	4		427	761	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863339	56863339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	147	276	0	ENST00000519728.1:c.486del	p.Gly163GlufsTer45	p.G163Efs*45	ENST00000519728	NM_002350.3	161	ttA/tt	6/13	0.353305876832913	4	FACETS	0.902	0.827	0.979	0.902	0.827	0.979	CLONAL	2	TRUE	2	0.396730294000512	4		276	574	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90992995	90992995	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	236	439	0	ENST00000265433.3:c.447C>G	p.His149Gln	p.H149Q	ENST00000265433	NM_002485.4	149	caC/caG	4/16	0.353305876832913	4	FACETS	0.906	0.847	0.967	0.906	0.847	0.967	CLONAL	2	TRUE	2	0.396730294000512	4		439	917	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864210	117864210	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	229	515	0	ENST00000297338.2:c.1447del	p.Ile483LeufsTer6	p.I483Lfs*6	ENST00000297338	NM_006265.2	483	Att/tt	11/14	0.353305876832913	4	FACETS	0.85	0.793	0.909	0.85	0.793	0.909	CLONAL	2	TRUE	2	0.396730294000512	4		515	948	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738291	133738291	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1368288944	NA	P-0034997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	230	409	0	ENST00000318560.5:c.691A>G	p.Asn231Asp	p.N231D	ENST00000318560	NM_005157.4	231	Aac/Gac	4/11	0.353305876832913	4	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	2	0.396730294000512	4		409	777	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0034999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	237	503	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.461176220506714	2	FACETS	0.872	0.822	0.923	0.872	0.822	0.923	CLONAL	2	TRUE	0	0.501172613175236	2		504	542	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988426	36988426	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1341967476	NA	P-0034999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	140	258	1	ENST00000354822.5:c.227C>T	p.Ala76Val	p.A76V	ENST00000354822	NM_001079668.2	76	gCg/gTg	2/3	0.352229341134946	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.501172613175236	1		259	369	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212474	5212474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753499659	NA	P-0034999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	69	447	1	ENST00000357368.4:c.4643G>A	p.Arg1548His	p.R1548H	ENST00000357368	NM_002850.3	1548	cGc/cAc	31/38	0.501172613175236	1	FACETS	0.47	0.411	0.534	0.47	0.411	0.534	SUBCLONAL	1	TRUE	0	0.501172613175236	1		448	439	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0035000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	304	432	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.569304330500186	3	FACETS	0.96	0.911	1	0.96	0.911	1	CLONAL	2	TRUE	1	0.586549899644383	3		432	698	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220382	1220382	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	171	562	0	ENST00000326873.7:c.475C>T	p.Gln159Ter	p.Q159*	ENST00000326873	NM_000455.4	159	Cag/Tag	4/10	0.586549899644383	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.586549899644383	1		562	388	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107030	11107030	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	102	365	0	ENST00000358026.2:c.1735G>T	p.Glu579Ter	p.E579*	ENST00000358026	NM_001128849.1	579	Gag/Tag	10/36	0.586549899644383	1	FACETS	0.979	0.892	1	0.979	0.892	1	CLONAL	1	TRUE	0	0.586549899644383	1		365	251	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098418	108098418	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs746235533	NA	P-0035000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	136	330	0	ENST00000278616.4:c.67C>T	p.Arg23Ter	p.R23*	ENST00000278616	NM_000051.3	23	Cga/Tga	2/63	1	2	FACETS	0.924	0.845	1	0.924	0.845	1	CLONAL	1	TRUE	1	0.586549899644383	2		330	502	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610501	10610501	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	207	637	1	ENST00000171111.5:c.209T>A	p.Leu70Gln	p.L70Q	ENST00000171111	NM_203500.1	70	cTg/cAg	2/6	0.586549899644383	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.586549899644383	1		638	470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0035003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	170	776	4	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.272766497984802	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.272766497984802	1		780	830	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55143599	55143599	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	91	294	0	ENST00000257290.5:c.1831A>G	p.Thr611Ala	p.T611A	ENST00000257290	NM_006206.4	611	Aca/Gca	13/23	0.272766497984802	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.272766497984802	1		294	482	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221240	5221240	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	137	525	0	ENST00000357368.4:c.3226G>A	p.Asp1076Asn	p.D1076N	ENST00000357368	NM_002850.3	1076	Gat/Aat	20/38	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.272766497984802	2		525	855	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17386615	17386615	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	170	616	0	ENST00000359435.4:c.550G>A	p.Glu184Lys	p.E184K	ENST00000359435	NM_001033549.1	184	Gaa/Aaa	6/9	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.272766497984802	2		616	1031	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5055682	5055682	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	79	257	0	ENST00000381652.3:c.950A>T	p.Tyr317Phe	p.Y317F	ENST00000381652	NM_004972.3	317	tAt/tTt	8/25	0.272766497984802	5	FACETS	1	0.969	1	0.44	0.387	0.496	CLONAL	1	TRUE	2	0.272766497984802	5		257	619	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42842606	42842606	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778628616	NA	P-0035004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	96	545	0	ENST00000398585.3:c.1251G>A	p.Trp417Ter	p.W417*	ENST00000398585	NM_001135099.1	417	tgG/tgA	11/14	0.630536212590182	1	FACETS	0.406	0.363	0.452	0.406	0.363	0.452	SUBCLONAL	1	TRUE	0	0.630536212590182	1		545	513	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249504	153249504	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	87	515	0	ENST00000281708.4:c.1274G>A	p.Trp425Ter	p.W425*	ENST00000281708	NM_033632.3	425	tGg/tAg	9/12	0.630536212590182	1	FACETS	0.306	0.271	0.344	0.306	0.271	0.344	SUBCLONAL	1	TRUE	0	0.630536212590182	1		515	617	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981084	201981084	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0035004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	155	390	0	ENST00000359651.3:c.164-1G>C		p.X55_splice	ENST00000359651		55			NA	2	FACETS	1	0.947	1			1	INDETERMINATE	1	TRUE	NA	0.630536212590182	2		390	476	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022570	12022570	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs924726546	NA	P-0035004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	396	443	1	ENST00000396373.4:c.676G>C	p.Glu226Gln	p.E226Q	ENST00000396373	NM_001987.4	226	Gag/Cag	5/8	0.630536212590182	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.630536212590182	3		444	735	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340037	116340037	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	128	224	0	ENST00000397752.3:c.899T>A	p.Leu300His	p.L300H	ENST00000397752	NM_000245.2	300	cTc/cAc	2/21	0.630536212590182	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.630536212590182	1		224	236	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044889	47044889	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	244	722	0	ENST00000377604.3:c.2215G>C	p.Glu739Gln	p.E739Q	ENST00000377604	NM_001204468.1	739	Gag/Cag	20/24	0.630536212590182	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.630536212590182	1		722	516	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218178	1218434	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGCCCTCGCCGGCCGATGACAGACTAGAGGGCGCTGTGCTCCCACCCCCTACCGCCCTGAGCCTGGACGCGTGGCCCCTGCAGGGCCCTTTCCCACAGCACTGTGAACTCACAGCTTCTCTCTAGGGAAGGGAGGAGGTACGCCACTTCCACAGGGAGATGGGGAGGCCGACTCCAGGGATCCAGGCCATCATCCTGACGTTGGGTCGGCTGATACACCCCTGTCCTCTCTGTCCCAGGGAAATTCAACTACTGAGG	AGCCCTCGCCGGCCGATGACAGACTAGAGGGCGCTGTGCTCCCACCCCCTACCGCCCTGAGCCTGGACGCGTGGCCCCTGCAGGGCCCTTTCCCACAGCACTGTGAACTCACAGCTTCTCTCTAGGGAAGGGAGGAGGTACGCCACTTCCACAGGGAGATGGGGAGGCCGACTCCAGGGATCCAGGCCATCATCCTGACGTTGGGTCGGCTGATACACCCCTGTCCTCTCTGTCCCAGGGAAATTCAACTACTGAGG	-	novel	NA	P-0035004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	110	42	1	ENST00000326873.7:c.291-236_311del		p.X97_splice	ENST00000326873	NM_000455.4	97		2/10	0.630536212590182	1	FACETS	1	0.968	1	1	0.993	1	CLONAL	2	TRUE	0	0.630536212590182	1		43	119	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	269	611	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.435524979082082	2		617	538	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	85	463	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.435524979082082	2		463	367	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	115	506	13	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.945	0.854	1	0.945	0.854	1	CLONAL	1	TRUE	1	0.435524979082082	2		519	559	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	140	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.435524979082082	3	FACETS	0.876	0.804	0.949	0.876	0.804	0.949	CLONAL	2	TRUE	1	0.435524979082082	3		493	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	140	879	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.994	0.908	1	0.994	0.908	1	CLONAL	1	TRUE	1	0.435524979082082	2		879	647	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551082	41551082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750235600	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	138	565	0	ENST00000263253.7:c.3226C>T	p.Arg1076Cys	p.R1076C	ENST00000263253	NM_001429.3	1076	Cgt/Tgt	17/31	1	2	FACETS	0.885	0.807	0.967	0.885	0.807	0.967	CLONAL	1	TRUE	1	0.435524979082082	2		565	716	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	89	283	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.435524979082082	2		283	400	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	78	307	3	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	0.435524979082082	3	FACETS	1	0.943	1	0.556	0.492	0.625	CLONAL	1	TRUE	1	0.435524979082082	3		310	392	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	99	757	5	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.906	0.812	1	0.906	0.812	1	CLONAL	1	TRUE	1	0.435524979082082	2		762	502	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	150	603	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.435524979082082	2		603	593	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982356	25982356	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	66	209	0	ENST00000435504.4:c.934C>T	p.Arg312Ter	p.R312*	ENST00000435504		312	Cga/Tga	9/13	0.435524979082082	2	FACETS	1	0.928	1	0.543	0.476	0.614	CLONAL	1	TRUE	0	0.435524979082082	2		209	279	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671655	67671655	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1400980130	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	111	366	2	ENST00000264010.4:c.2070del	p.Glu691SerfsTer30	p.E691Sfs*30	ENST00000264010	NM_006565.3	688	gtA/gt	12/12	1	2	FACETS	0.994	0.897	1	0.994	0.897	1	CLONAL	1	TRUE	1	0.435524979082082	2		368	513	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927019	131927019	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140333740	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	37	212	0	ENST00000265335.6:c.1556G>A	p.Arg519His	p.R519H	ENST00000265335		519	cGt/cAt	10/25	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.435524979082082	2		212	161	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664989	138664989	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	59	184	0	ENST00000330315.3:c.576del	p.Lys193SerfsTer78	p.K193Sfs*78	ENST00000330315	NM_023067.3	192	ccC/cc	1/1	1	2	FACETS	0.891	0.772	1	0.891	0.772	1	CLONAL	1	TRUE	1	0.435524979082082	2		184	304	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534473	187534473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	75	329	1	ENST00000441802.2:c.9253del	p.Asp3086IlefsTer30	p.D3086Ifs*30	ENST00000441802	NM_005245.3	3085	Ctt/tt	13/27	1	2	FACETS	0.906	0.799	1	0.906	0.799	1	CLONAL	1	TRUE	1	0.435524979082082	2		330	380	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	179	601	3	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	0.435524979082082	3	FACETS	1	0.948	1	0.518	0.477	0.561	CLONAL	1	TRUE	1	0.435524979082082	3		604	966	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391799	139391799	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1455334351	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	107	632	3	ENST00000277541.6:c.6392del	p.Gly2131AlafsTer117	p.G2131Afs*117	ENST00000277541	NM_017617.3	2131	gGc/gc	34/34	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.435524979082082	2		635	479	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199873	128199873	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780263343	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	67	362	0	ENST00000341105.2:c.1432G>A	p.Ala478Thr	p.A478T	ENST00000341105	NM_032638.4	478	Gcc/Acc	6/6	1	2	FACETS	0.913	0.799	1	0.913	0.799	1	CLONAL	1	TRUE	1	0.435524979082082	2		362	337	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791392	42791392	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1349864904	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	148	560	0	ENST00000575354.2:c.452C>T	p.Ala151Val	p.A151V	ENST00000575354	NM_015125.3	151	gCc/gTc	3/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.435524979082082	2		560	562	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098363	11098363	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	143	545	0	ENST00000358026.2:c.885del	p.Thr296ArgfsTer7	p.T296Rfs*7	ENST00000358026	NM_001128849.1	294	gCc/gc	6/36	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.435524979082082	2		545	589	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41489075	41489076	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555902247	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	108	339	0	ENST00000263253.7:c.70_71del	p.Ser24GlyfsTer14	p.S24Gfs*14	ENST00000263253	NM_001429.3	23	CTc/c	1/31	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.435524979082082	2		339	430	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337684	73337684	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771690280	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	117	260	3	ENST00000377767.4:c.2032del	p.Ile678PhefsTer59	p.I678Ffs*59	ENST00000377767	NM_014953.3	678	Att/tt	16/21	0.435524979082082	3	FACETS	0.914	0.833	0.997	0.914	0.833	0.997	CLONAL	2	TRUE	1	0.435524979082082	3		263	358	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347909	347909	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	214	829	1	ENST00000262320.3:c.1597C>T	p.Arg533Ter	p.R533*	ENST00000262320	NM_003502.3	533	Cga/Tga	6/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.435524979082082	2		830	834	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628282	90628282	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765712414	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	202	748	3	ENST00000330062.3:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000330062	NM_002168.2	377	Cgt/Tgt	9/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.435524979082082	2		751	814	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621035	1621035	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747273925	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	195	822	1	ENST00000344749.5:c.1025C>T	p.Pro342Leu	p.P342L	ENST00000344749	NM_001136139.2	342	cCg/cTg	13/19	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.435524979082082	2		823	795	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190745	108190746	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs863225466	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	73	394	0	ENST00000278616.4:c.6415_6416del	p.Glu2139IlefsTer6	p.E2139Ifs*6	ENST00000278616	NM_000051.3	2138	AGa/a	44/63	1	2	FACETS	0.989	0.871	1	0.989	0.871	1	CLONAL	1	TRUE	1	0.435524979082082	2		394	339	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058476	69058476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267601977	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	68	505	1	ENST00000288368.4:c.4120C>T	p.Arg1374Trp	p.R1374W	ENST00000288368	NM_024870.2	1374	Cgg/Tgg	34/40	0.435524979082082	3	FACETS	0.759	0.662	0.864	0.38	0.331	0.432	SUBCLONAL	1	TRUE	1	0.435524979082082	3		506	501	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152038	55152038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370600501	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	119	517	0	ENST00000257290.5:c.2470G>A	p.Val824Ile	p.V824I	ENST00000257290	NM_006206.4	824	Gtc/Atc	18/23	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.435524979082082	2		517	546	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458270	12458270	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	141	472	3	ENST00000287820.6:c.892del	p.Leu298CysfsTer38	p.L298Cfs*38	ENST00000287820	NM_015869.4	296	aCc/ac	6/7	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.435524979082082	2		475	614	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	174	801	1	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.435524979082082	2		802	731	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	359972	359972	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	144	513	0	ENST00000262320.3:c.1116+1G>A		p.X372_splice	ENST00000262320	NM_003502.3	372			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.435524979082082	2		513	557	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211679	36211679	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1486583393	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	90	458	0	ENST00000222270.7:c.1430G>A	p.Ser477Asn	p.S477N	ENST00000222270	NM_014727.1	477	aGc/aAc	3/37	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.435524979082082	2		458	380	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435199	49435199	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	184	452	0	ENST00000301067.7:c.6354del	p.Ala2119LeufsTer25	p.A2119Lfs*25	ENST00000301067	NM_003482.3	2118	ccC/cc	31/54	0.435524979082082	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	1	0.435524979082082	3		452	503	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453399	40453399	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs759027671	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	213	706	11	ENST00000345506.4:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000345506	NM_003152.3	366	Ccc/cc	10/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.435524979082082	2		717	795	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844244	68844244	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	102	394	0	ENST00000261769.5:c.832G>T	p.Gly278Ter	p.G278*	ENST00000261769	NM_004360.3	278	Gga/Tga	6/16	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.435524979082082	2		394	444	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386587	81386587	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1032300573	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	53	496	0	ENST00000222390.5:c.400C>T	p.Arg134Cys	p.R134C	ENST00000222390	NM_000601.4	134	Cgc/Tgc	4/18	1	2	FACETS	0.624	0.534	0.722	0.624	0.534	0.722	SUBCLONAL	1	TRUE	1	0.435524979082082	2		496	390	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371798	116371798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs986139438	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	84	390	2	ENST00000397752.3:c.1277G>A	p.Arg426His	p.R426H	ENST00000397752	NM_000245.2	426	cGc/cAc	3/21	1	2	FACETS	0.752	0.666	0.844	0.752	0.666	0.844	SUBCLONAL	1	TRUE	1	0.435524979082082	2		392	513	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11314018	11314018	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	160	524	1	ENST00000361445.4:c.718G>T	p.Glu240Ter	p.E240*	ENST00000361445	NM_004958.3	240	Gaa/Taa	6/58	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.435524979082082	2		525	585	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245485	16245485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	86	435	0	ENST00000375759.3:c.1460C>T	p.Ala487Val	p.A487V	ENST00000375759	NM_015001.2	487	gCt/gTt	7/15	1	2	FACETS	0.968	0.861	1	0.968	0.861	1	CLONAL	1	TRUE	1	0.435524979082082	2		435	408	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623617	43623617	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	111	478	1	ENST00000355710.3:c.3245G>T	p.Gly1082Val	p.G1082V	ENST00000355710	NM_020975.4	1082	gGc/gTc	20/20	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.435524979082082	2		479	507	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741381	17741381	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773493435	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	191	641	1	ENST00000250003.3:c.52G>A	p.Gly18Ser	p.G18S	ENST00000250003	NM_002478.4	18	Ggc/Agc	1/3	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.435524979082082	2		642	728	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189498	94189498	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761458720	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	98	378	0	ENST00000323929.3:c.1507C>T	p.Arg503Cys	p.R503C	ENST00000323929	NM_005591.3	503	Cgt/Tgt	14/20	1	2	FACETS	0.928	0.831	1	0.928	0.831	1	CLONAL	1	TRUE	1	0.435524979082082	2		378	485	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199897	108199897	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	27	174	0	ENST00000278616.4:c.7239G>T	p.Lys2413Asn	p.K2413N	ENST00000278616	NM_000051.3	2413	aaG/aaT	49/63	1	2	FACETS	0.747	0.6	0.911	0.747	0.6	0.911	CLONAL	1	TRUE	1	0.435524979082082	2		174	166	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446070	49446070	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201512665	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	188	762	0	ENST00000301067.7:c.1396C>T	p.Arg466Cys	p.R466C	ENST00000301067	NM_003482.3	466	Cgc/Tgc	10/54	0.435524979082082	3	FACETS	0.872	0.804	0.942	0.436	0.402	0.471	CLONAL	1	TRUE	1	0.435524979082082	3		762	1206	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046481	30046481	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	101	554	0	ENST00000331968.5:c.2702A>G	p.Glu901Gly	p.E901G	ENST00000331968	NM_002742.2	901	gAa/gGa	18/18	1	2	FACETS	0.857	0.769	0.951	0.857	0.769	0.951	CLONAL	1	TRUE	1	0.435524979082082	2		554	541	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500369	99500369	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	131	610	0	ENST00000268035.6:c.3802G>T	p.Glu1268Ter	p.E1268*	ENST00000268035	NM_000875.3	1268	Gag/Tag	21/21	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.435524979082082	2		610	577	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842705	68842705	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	146	505	0	ENST00000261769.5:c.641T>C	p.Leu214Pro	p.L214P	ENST00000261769	NM_004360.3	214	cTg/cCg	5/16	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.435524979082082	2		505	615	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687295	37687295	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	151	488	0	ENST00000447079.4:c.4199A>G	p.Asp1400Gly	p.D1400G	ENST00000447079	NM_015083.1	1400	gAc/gGc	14/14	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.435524979082082	2		488	623	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212251	5212251	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	128	513	0	ENST00000357368.4:c.4780G>T	p.Gly1594Cys	p.G1594C	ENST00000357368	NM_002850.3	1594	Ggc/Tgc	32/38	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.435524979082082	2		513	510	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657029	47657029	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs151244108	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	165	295	0	ENST00000233146.2:c.1225C>T	p.Gln409Ter	p.Q409*	ENST00000233146	NM_000251.2	409	Cag/Tag	7/16	0.435524979082082	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.435524979082082	2		295	343	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265558	198265558	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	109	541	1	ENST00000335508.6:c.2599del	p.Met867TrpfsTer2	p.M867Wfs*2	ENST00000335508	NM_012433.2	867	Atg/tg	18/25	1	2	FACETS	0.936	0.843	1	0.936	0.843	1	CLONAL	1	TRUE	1	0.435524979082082	2		542	535	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659926	227659926	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	138	565	0	ENST00000305123.5:c.3529C>A	p.Leu1177Ile	p.L1177I	ENST00000305123	NM_005544.2	1177	Ctt/Att	1/2	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.435524979082082	2		565	550	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031223	36031223	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1056084684	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	148	492	3	ENST00000358208.4:c.1342G>A	p.Val448Met	p.V448M	ENST00000358208		448	Gtg/Atg	11/12	0.435524979082082	2	FACETS	1	0.946	1	0.522	0.478	0.568	CLONAL	1	TRUE	0	0.435524979082082	2		495	651	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750783	39750783	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	168	555	1	ENST00000361337.2:c.2183T>C	p.Ile728Thr	p.I728T	ENST00000361337	NM_003286.2	728	aTc/aCc	20/21	0.435524979082082	2	FACETS	1	0.975	1	0.566	0.522	0.612	CLONAL	1	TRUE	0	0.435524979082082	2		556	681	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770558	40770558	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1473163818	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	95	413	0	ENST00000373198.4:c.2824T>C	p.Ser942Pro	p.S942P	ENST00000373198	NM_133170.3	942	Tcc/Ccc	19/32	0.435524979082082	2	FACETS	1	0.946	1	0.544	0.487	0.603	CLONAL	1	TRUE	0	0.435524979082082	2		413	401	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899046	40899046	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	103	457	1	ENST00000373198.4:c.2224C>A	p.Leu742Ile	p.L742I	ENST00000373198	NM_133170.3	742	Ctc/Atc	14/32	0.435524979082082	2	FACETS	1	0.922	1	0.514	0.462	0.568	CLONAL	1	TRUE	0	0.435524979082082	2		458	460	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167563	24167563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	116	483	0	ENST00000263121.7:c.947G>A	p.Arg316Gln	p.R316Q	ENST00000263121	NM_003073.3	316	cGg/cAg	7/9	1	2	FACETS	0.972	0.879	1	0.972	0.879	1	CLONAL	1	TRUE	1	0.435524979082082	2		483	548	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566540	41566540	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	94	283	0	ENST00000263253.7:c.4418del	p.Lys1473ArgfsTer23	p.K1473Rfs*23	ENST00000263253	NM_001429.3	1473	Aag/ag	27/31	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.435524979082082	2		283	401	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52692235	52692236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	90	380	0	ENST00000394830.3:c.624dup	p.Gln209SerfsTer6	p.Q209Sfs*6	ENST00000394830	NM_018313.4	208	-/T	6/30	1	2	FACETS	0.975	0.87	1	0.975	0.87	1	CLONAL	1	TRUE	1	0.435524979082082	2		380	424	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114718	73114718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764238159	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	51	263	0	ENST00000356692.5:c.1099G>A	p.Glu367Lys	p.E367K	ENST00000356692		367	Gaa/Aaa	9/9	1	2	FACETS	0.944	0.81	1	0.944	0.81	1	CLONAL	1	TRUE	1	0.435524979082082	2		263	248	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467802	66467802	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	75	373	0	ENST00000273854.3:c.467T>G	p.Phe156Cys	p.F156C	ENST00000273854	NM_004439.5	156	tTt/tGt	3/18	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.435524979082082	2		373	324	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721750	176721750	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763421218	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	84	391	0	ENST00000439151.2:c.7381C>A	p.Leu2461Ile	p.L2461I	ENST00000439151	NM_022455.4	2461	Cta/Ata	23/23	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.435524979082082	2		391	373	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109323524	109323524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767306041	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	119	565	0	ENST00000436639.2:c.302G>A	p.Arg101Gln	p.R101Q	ENST00000436639	NM_014454.2	101	cGa/cAa	2/10	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.435524979082082	2		565	539	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272102	38272102	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375611478	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	269	600	1	ENST00000425967.3:c.2116C>T	p.Arg706Trp	p.R706W	ENST00000425967	NM_001174067.1	706	Cgg/Tgg	16/19	0.435524979082082	3	FACETS	0.996	0.939	1	0.996	0.939	1	CLONAL	2	TRUE	1	0.435524979082082	3		601	755	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005916	69005916	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	223	554	0	ENST00000288368.4:c.2327C>A	p.Pro776His	p.P776H	ENST00000288368	NM_024870.2	776	cCt/cAt	21/40	0.435524979082082	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.435524979082082	3		554	581	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499825	8499825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780704033	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	74	437	0	ENST00000356435.5:c.2144C>T	p.Pro715Leu	p.P715L	ENST00000356435		715	cCt/cTt	14/35	1	2	FACETS	0.897	0.79	1	0.897	0.79	1	CLONAL	1	TRUE	1	0.435524979082082	2		437	379	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224243	53224243	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	153	329	1	ENST00000375401.3:c.3308G>A	p.Cys1103Tyr	p.C1103Y	ENST00000375401	NM_004187.3	1103	tGc/tAc	22/26	1	1	FACETS	0.851	0.792	0.91	1	0.992	1	CLONAL	2	TRUE	0	0.435524979082082	1		330	323	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411772	63411772	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	155	351	0	ENST00000330258.3:c.1395del	p.Asn466IlefsTer75	p.N466Ifs*75	ENST00000330258	NM_152424.3	465	ccC/cc	2/2	1	1	FACETS	0.841	0.783	0.9	1	0.992	1	CLONAL	2	TRUE	0	0.435524979082082	1		351	331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0035009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	267	379	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	0.480866793415263	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	3	TRUE	0	0.480866793415263	3		379	451	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176145058	176145058	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	156	226	0	ENST00000367669.3:c.553C>T	p.Pro185Ser	p.P185S	ENST00000367669	NM_022457.5	185	Cct/Tct	3/20	0.40543923212581	5	FACETS	1	0.948	1	1	0.948	1	CLONAL	3	TRUE	2	0.480866793415263	5		226	363	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427299	49427341	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTGCATACGTTGCTGCTGCAGCTGCAGCTGCCTTTCCTGTA	AGCTGCATACGTTGCTGCTGCAGCTGCAGCTGCCTTTCCTGTA	-	novel	NA	P-0035009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	150	365	0	ENST00000301067.7:c.11147_11189del	p.Leu3716TrpfsTer19	p.L3716Wfs*19	ENST00000301067	NM_003482.3	3716	tTACAGGAAAGGCAGCTGCAGCTGCAGCAGCAACGTATGCAGCTg/tg	39/54	0.480866793415263	3	FACETS	0.948	0.876	1	0.948	0.876	1	CLONAL	2	TRUE	1	0.480866793415263	3		365	408	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105236690	105236690	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	177	412	0	ENST00000349310.3:c.1431C>A	p.Ser477Arg	p.S477R	ENST00000349310	NM_001014432.1	477	agC/agA	15/15	0.404041445596651	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.480866793415263	4		412	521	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40855772	40855772	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	223	374	0	ENST00000428826.2:c.2084A>C	p.Asn695Thr	p.N695T	ENST00000428826		695	aAc/aCc	19/21	0.480866793415263	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.480866793415263	3		374	526	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275285	142275285	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	195	315	0	ENST00000350721.4:c.2018G>C	p.Ser673Thr	p.S673T	ENST00000350721	NM_001184.3	673	aGt/aCt	9/47	0.480866793415263	6	FACETS	1	0.972	1	0.546	0.507	0.587	CLONAL	2	TRUE	2	0.480866793415263	6		315	728	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971122	21971123	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0035009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	145	302	0	ENST00000304494.5:c.235_236del	p.Thr79ProfsTer40	p.T79Pfs*40	ENST00000304494	NM_000077.4	79	ACc/c	2/3	0.480866793415263	2	FACETS	0.998	0.928	1	0.998	0.928	1	CLONAL	2	TRUE	0	0.480866793415263	2		302	302	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650569	48650569	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	161	212	0	ENST00000376670.3:c.539T>C	p.Leu180Pro	p.L180P	ENST00000376670	NM_002049.3	180	cTc/cCc	3/6	0.31125695104982	2	FACETS	1	0.983	1			1	CLONAL	2	TRUE	NA	0.480866793415263	2		212	291	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0035012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	14	313	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.645	0.464	0.864	0.645	0.464	0.864	SUBCLONAL	1	TRUE	1	0.12	2		313	362	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0035013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	973	432	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.270579244834618	8	FACETS	1	0.994	1	1	0.998	1	CLONAL	9	TRUE	2	0.270579244834618	8		432	1392	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602354	10602354	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	169	713	0	ENST00000171111.5:c.1224del	p.Met409Ter	p.M409*	ENST00000171111	NM_203500.1	408	ccC/cc	3/6	0.239110178408157	2	FACETS	0.764	0.703	0.827	0.764	0.703	0.827	SUBCLONAL	2	TRUE	0	0.270579244834618	2		713	818	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219336	1219336	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	169	683	1	ENST00000326873.7:c.388G>T	p.Glu130Ter	p.E130*	ENST00000326873	NM_000455.4	130	Gag/Tag	3/10	0.239110178408157	2	FACETS	0.8	0.736	0.866	0.8	0.736	0.866	SUBCLONAL	2	TRUE	0	0.270579244834618	2		684	781	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795382	42795382	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	115	529	1	ENST00000575354.2:c.2462G>A	p.Gly821Glu	p.G821E	ENST00000575354	NM_015125.3	821	gGa/gAa	10/20	0.270763155118483	3	FACETS	1	0.983	1	0.726	0.655	0.8	CLONAL	1	TRUE	1	0.270579244834618	3		530	665	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851249	63851249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	66	552	0	ENST00000279873.7:c.2027C>T	p.Pro676Leu	p.P676L	ENST00000279873	NM_032199.2	676	cCc/cTc	10/10	NA	2	FACETS	0.786	0.682	0.898			1	INDETERMINATE	1	TRUE	NA	0.270579244834618	2		552	621	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549097	21549097	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762135360	NA	P-0035013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	59	482	0	ENST00000382592.4:c.3179G>T	p.Gly1060Val	p.G1060V	ENST00000382592	NM_014572.2	1060	gGa/gTa	8/8	1	2	FACETS	0.94	0.81	1	0.94	0.81	1	CLONAL	1	TRUE	1	0.270579244834618	2		482	464	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000020	42000020	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	140	431	0	ENST00000219905.7:c.2287del	p.Trp763GlyfsTer54	p.W763Gfs*54	ENST00000219905	NM_001164273.1	761	ccT/cc	6/24	0.212854060548438	2	FACETS	0.845	0.773	0.921	0.845	0.773	0.921	CLONAL	2	TRUE	0	0.270579244834618	2		431	612	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144106	11144106	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	170	686	0	ENST00000358026.2:c.3687C>G	p.Ile1229Met	p.I1229M	ENST00000358026	NM_001128849.1	1229	atC/atG	26/36	0.239110178408157	2	FACETS	0.852	0.786	0.922	0.852	0.786	0.922	CLONAL	2	TRUE	0	0.270579244834618	2		686	737	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972103	55972103	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	80	375	0	ENST00000263923.4:c.1541T>A	p.Val514Glu	p.V514E	ENST00000263923	NM_002253.2	514	gTa/gAa	12/30	0.240291254923089	3	FACETS	0.765	0.676	0.859	0.765	0.676	0.859	SUBCLONAL	2	TRUE	1	0.270579244834618	3		375	439	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555033	106555033	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	67	459	0	ENST00000369096.4:c.2150G>T	p.Gly717Val	p.G717V	ENST00000369096	NM_001198.3	717	gGg/gTg	7/7	0.270763155118483	3	FACETS	1	0.87	1	0.5	0.435	0.571	CLONAL	1	TRUE	1	0.270579244834618	3		459	562	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104012	69104012	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	80	267	1	ENST00000288368.4:c.4402T>A	p.Tyr1468Asn	p.Y1468N	ENST00000288368	NM_024870.2	1468	Tat/Aat	36/40	0.207951957053871	4	FACETS	0.937	0.829	1	0.937	0.829	1	CLONAL	2	TRUE	2	0.270579244834618	4		268	401	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463296	25463297	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	T	novel	NA	P-0035013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	105	387	0	ENST00000264709.3:c.2196_2197delinsA	p.Phe732LeufsTer47	p.F732Lfs*47	ENST00000264709	NM_175629.2	732	ttTGag/ttAag	19/23	0.264966224945509	3	FACETS	0.866	0.779	0.957	0.866	0.779	0.957	CLONAL	2	TRUE	1	0.270579244834618	3		387	509	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0035014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	48	256	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.811	0.689	0.945	0.811	0.689	0.945	CLONAL	1	TRUE	1	0.349070870741768	2		256	339	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063358	67063359	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	77	177	0	ENST00000412916.2:c.54dup	p.Arg19Ter	p.R19*	ENST00000412916		16	-/T	1/6	0.349070870741768	1	FACETS	0.946	0.835	1	0.946	0.835	1	CLONAL	1	TRUE	0	0.349070870741768	1		177	385	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929412	44929415	+	frameshift_variant	Frame_Shift_Del	DEL	ACAA	ACAA	-	rs786205676	NA	P-0035014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	111	474	0	ENST00000377967.4:c.2515_2518del	p.Asn839ValfsTer27	p.N839Vfs*27	ENST00000377967	NM_021140.2	838	ACAAac/ac	17/29	0.349070870741768	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.349070870741768	1		474	494	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849663	68849663	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587780113	NA	P-0035014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	78	292	0	ENST00000261769.5:c.1565+1G>T		p.X522_splice	ENST00000261769	NM_004360.3	522			0.349070870741768	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.349070870741768	1		292	325	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356332	66356332	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs553493695	NA	P-0035014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	79	357	0	ENST00000273854.3:c.1165G>A	p.Val389Met	p.V389M	ENST00000273854	NM_004439.5	389	Gtg/Atg	5/18	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.349070870741768	2		357	438	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023267	27023286	+	frameshift_variant	Frame_Shift_Del	DEL	GGTGGCGGCAGCAGCGATGG	GGTGGCGGCAGCAGCGATGG	-	novel	NA	P-0035014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	30	136	0	ENST00000324856.7:c.378_397del	p.Ser128AlafsTer265	p.S128Afs*265	ENST00000324856	NM_006015.4	125	GGTGGCGGCAGCAGCGATGGg/g	1/20	0.349070870741768	1	FACETS	0.775	0.631	0.936	0.775	0.631	0.936	CLONAL	1	TRUE	0	0.349070870741768	1		136	183	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0035017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	179	488	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.350982965678383	3	FACETS	0.914	0.846	0.984	0.914	0.846	0.984	CLONAL	2	TRUE	1	0.350982965678383	3		488	656	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0035017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	396	823	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.289267396247235	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	3	TRUE	0	0.350982965678383	3		823	880	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912149	114912149	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	109	381	1	ENST00000543371.1:c.1219C>T	p.Arg407Ter	p.R407*	ENST00000543371	NM_001198531.1	407	Cga/Tga	11/14	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.350982965678383	2		382	536	SUCCESS
APC	324	MSKCC	GRCh37	5	112175758	112175765	+	frameshift_variant	Frame_Shift_Del	DEL	ACATTTTG	ACATTTTG	-	novel	NA	P-0035017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	54	274	0	ENST00000257430.4:c.4467_4474del	p.Leu1489PhefsTer22	p.L1489Ffs*22	ENST00000257430	NM_000038.5	1489	ttACATTTTGcc/ttcc	16/16	0.350744514191047	1	FACETS	0.79	0.679	0.911	0.79	0.679	0.911	CLONAL	1	TRUE	0	0.350982965678383	1		274	321	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0035021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	72	313	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	0.552487202896622	4	FACETS	0.902	0.8	1	0.902	0.8	1	CLONAL	2	TRUE	2	0.550105519545849	4		313	225	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0035024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	107	313	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.452945190204929	3	FACETS	0.751	0.68	0.826	0.751	0.68	0.826	SUBCLONAL	2	TRUE	1	0.465703366310933	3		313	377	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952088	178952088	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553826184	NA	P-0035024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	106	286	0	ENST00000263967.3:c.3143A>G	p.His1048Arg	p.H1048R	ENST00000263967	NM_006218.2	1048	cAt/cGt	21/21	0.452945190204929	3	FACETS	1	0.984	1	0.746	0.675	0.82	CLONAL	1	TRUE	1	0.465703366310933	3		286	376	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522416	176522416	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519792	NA	P-0035024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	343	650	0	ENST00000292408.4:c.1605C>G	p.Asn535Lys	p.N535K	ENST00000292408	NM_213647.1	535	aaC/aaG	12/18	0.465703366310933	5	FACETS	0.966	0.914	1	0.644	0.609	0.68	CLONAL	2	TRUE	2	0.465703366310933	5		650	1295	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576851	7576851	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0035024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	309	676	0	ENST00000269305.4:c.993+2T>C		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.465703366310933	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.465703366310933	2		676	624	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988516	36988516	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	200	794	0	ENST00000354822.5:c.137T>G	p.Ile46Ser	p.I46S	ENST00000354822	NM_001079668.2	46	aTc/aGc	2/3	0.318840043474685	3	FACETS	1	0.988	1	0.651	0.604	0.7	CLONAL	1	TRUE	1	0.465703366310933	3		794	813	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169080	32169080	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	292	811	0	ENST00000375023.3:c.3953T>C	p.Val1318Ala	p.V1318A	ENST00000375023	NM_004557.3	1318	gTg/gCg	22/30	0.465703366310933	4	FACETS	0.871	0.82	0.923	0.871	0.82	0.923	CLONAL	2	TRUE	2	0.465703366310933	4		811	1055	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0035027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	199	313	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.408091444473091	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.408091444473091	4		313	628	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	224	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.392226788725562	3	FACETS	0.914	0.855	0.975	0.914	0.855	0.975	CLONAL	2	TRUE	1	0.408091444473091	3		493	723	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0035027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	85	378	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.392226788725562	3	FACETS	0.88	0.779	0.987	0.44	0.389	0.494	CLONAL	1	TRUE	1	0.408091444473091	3		378	570	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625434	69625434	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs571671602	NA	P-0035027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	186	899	3	ENST00000334134.2:c.359G>A	p.Arg120Gln	p.R120Q	ENST00000334134	NM_005247.2	120	cGg/cAg	3/3	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.408091444473091	2		902	753	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46240655	46240656	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	T	novel	NA	P-0035027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	82	436	0	ENST00000334344.6:c.1515_1516delinsT	p.Ala506ArgfsTer10	p.A506Rfs*10	ENST00000334344	NM_152641.2	505	gtAGcg/gtTcg	12/21	0.392226788725562	3	FACETS	0.804	0.709	0.905	0.402	0.354	0.453	CLONAL	1	TRUE	1	0.408091444473091	3		436	602	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0035028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	141	227	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	0.510981147128076	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	1	0.510981147128076	3		227	332	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0035028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	100	558	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.919	0.84	0.998			1	INDETERMINATE	2	TRUE	NA	0.510981147128076	2		558	213	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	116	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.265682584315224	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	2	0.266587690140279	4		493	474	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971110	21971110	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519881	NA	P-0035029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	48	308	0	ENST00000304494.5:c.248A>G	p.His83Arg	p.H83R	ENST00000304494	NM_000077.4	83	cAc/cGc	2/3	0.266587690140279	2	FACETS	0.75	0.64	0.869	0.75	0.64	0.869	SUBCLONAL	2	TRUE	0	0.266587690140279	2		308	240	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	rs886039483	NA	P-0035029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	227	880	0	ENST00000269305.4:c.376T>A	p.Tyr126Asn	p.Y126N	ENST00000269305	NM_001126112.2	126	Tac/Aac	5/11	0.266587690140279	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.266587690140279	2		880	795	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341328	89341328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	105	494	0	ENST00000301030.4:c.7607G>A	p.Arg2536Gln	p.R2536Q	ENST00000301030	NM_001256183.1	2536	cGg/cAg	11/13	0.265682584315224	4	FACETS	0.971	0.873	1	0.971	0.873	1	CLONAL	2	TRUE	2	0.266587690140279	4		494	514	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	44	349	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.448486376514189	2		349	174	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0035034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	80	256	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.929	0.823	1	0.929	0.823	1	CLONAL	1	TRUE	1	0.448486376514189	2		256	384	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034446	47034447	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	197	484	0	ENST00000377604.3:c.534dup	p.Ser179Ter	p.S179*	ENST00000377604	NM_001204468.1	177	-/T	6/24	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.448486376514189	1		484	466	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0035063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	166	540	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.714874343825955	2		540	440	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399155	139399155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749490844	NA	P-0035063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	43	421	0	ENST00000277541.6:c.4988G>A	p.Arg1663Gln	p.R1663Q	ENST00000277541	NM_017617.3	1663	cGg/cAg	26/34	1	2	FACETS	0.94	0.805	1	0.94	0.805	1	CLONAL	1	TRUE	1	0.714874343825955	2		421	128	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115444	115115445	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0035063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	64	546	0	ENST00000257566.3:c.881_882insGT	p.Ile294MetfsTer2	p.I294Mfs*2	ENST00000257566	NM_016569.3	294	ata/atGTa	5/8	0.149815542570908	4	FACETS	1	0.955	1	0.604	0.529	0.684	INDETERMINATE	1	TRUE	2	0.714874343825955	4		546	254	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916920	178916928	+	inframe_deletion	In_Frame_Del	DEL	GAACCAGTA	GAACCAGTA	-	novel	NA	P-0035063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	68	420	0	ENST00000263967.3:c.308_316del	p.Glu103_Val105del	p.E103_V105del	ENST00000263967	NM_006218.2	103	GAACCAGTA/-	2/21	0.235145988201519	3	FACETS	0.751	0.668	0.835	0.751	0.668	0.835	INDETERMINATE	2	TRUE	1	0.714874343825955	3		420	172	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	18	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.506	0.379	0.657	0.506	0.379	0.657	SUBCLONAL	1	TRUE	1	0.1	2		493	712	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847399	68847399	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0035067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	29	454	0	ENST00000261769.5:c.1320+1G>T		p.X440_splice	ENST00000261769	NM_004360.3	440			1	2	FACETS	0.885	0.708	1	0.885	0.708	1	CLONAL	1	TRUE	1	0.1	2		454	655	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	29	349	0				ENST00000310581	NM_198253.2	-/1132			0.491515284687597	1	FACETS	0.627	0.51	0.755	0.627	0.51	0.755	SUBCLONAL	1	TRUE	0	0.491515284687597	1		349	142	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519938	NA	P-0035076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	74	500	0	ENST00000263967.3:c.1034A>C	p.Asn345Thr	p.N345T	ENST00000263967	NM_006218.2	345	aAt/aCt	5/21	0.191676399739412	5	FACETS	0.937	0.83	1	0.625	0.553	0.701	INDETERMINATE	2	TRUE	2	0.491515284687597	5		500	279	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265605	10265605	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0035076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	137	545	0	ENST00000340748.4:c.1572T>A	p.Tyr524Ter	p.Y524*	ENST00000340748		524	taT/taA	19/40	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.491515284687597	2		545	436	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010467	48010467	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	26	333	0	ENST00000234420.5:c.95G>C	p.Gly32Ala	p.G32A	ENST00000234420	NM_000179.2	32	gGc/gCc	1/10	1	2	FACETS	0.434	0.345	0.535	0.434	0.345	0.535	SUBCLONAL	1	TRUE	1	0.491515284687597	2		333	244	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442078	52442078	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	173	413	0	ENST00000460680.1:c.271del	p.Cys91ValfsTer7	p.C91Vfs*7	ENST00000460680	NM_004656.3	91	Tgt/gt	5/17	0.427154864370726	2	FACETS	0.924	0.862	0.986	0.924	0.862	0.986	CLONAL	2	TRUE	0	0.491515284687597	2		413	381	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524339	176524339	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	78	752	0	ENST00000292408.4:c.2200C>A	p.Pro734Thr	p.P734T	ENST00000292408	NM_213647.1	734	Cct/Act	17/18	0.491515284687597	1	FACETS	0.649	0.574	0.728	0.649	0.574	0.728	SUBCLONAL	1	TRUE	0	0.491515284687597	1		752	369	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816578	32816578	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	70	739	1	ENST00000354258.4:c.1597G>T	p.Gly533Cys	p.G533C	ENST00000354258	NM_000593.5	533	Ggc/Tgc	7/11	1	2	FACETS	0.423	0.368	0.482	0.423	0.368	0.482	SUBCLONAL	1	TRUE	1	0.491515284687597	2		740	674	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976789	2976789	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs79513324	NA	P-0035076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	188	871	1	ENST00000396946.4:c.1223G>T	p.Arg408Leu	p.R408L	ENST00000396946	NM_032415.4	408	cGc/cTc	9/25	0.198664288454683	2	FACETS	1	0.987	1	0.634	0.589	0.681	INDETERMINATE	1	TRUE	0	0.491515284687597	2		872	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0035077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	322	588	0	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	0.496913689609659	2	FACETS	1	0.994	1	0.718	0.682	0.755	CLONAL	1	TRUE	0	0.567318135387403	2		588	790	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101195	27101195	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	448	783	0	ENST00000324856.7:c.4477C>T	p.Gln1493Ter	p.Q1493*	ENST00000324856	NM_006015.4	1493	Cag/Tag	18/20	0.548935982526155	2	FACETS	0.949	0.913	0.985	0.949	0.913	0.985	CLONAL	2	TRUE	0	0.567318135387403	2		783	832	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414221	32414221	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0035077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	71	405	0	ENST00000332351.3:c.1330A>T	p.Arg444Ter	p.R444*	ENST00000332351	NM_024426.4	444	Aga/Tga	8/10	0.5674467693184	3	FACETS	0.408	0.356	0.465			1	SUBCLONAL	1	TRUE	NA	0.567318135387403	3		405	787	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94179021	94179021	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs770184763	NA	P-0035077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	79	417	0	ENST00000323929.3:c.1822T>G	p.Ser608Ala	p.S608A	ENST00000323929	NM_005591.3	608	Tca/Gca	16/20	0.316534857552941	3	FACETS	0.608	0.535	0.686	0.304	0.267	0.343	INDETERMINATE	1	TRUE	1	0.567318135387403	3		417	588	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707812	43707812	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	118	750	0	ENST00000382044.4:c.5069A>C	p.Lys1690Thr	p.K1690T	ENST00000382044	NM_001141980.1	1690	aAg/aCg	23/28	1	2	FACETS	0.49	0.442	0.541	0.49	0.442	0.541	SUBCLONAL	1	TRUE	1	0.567318135387403	2		750	849	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250899	99250899	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	108	420	0	ENST00000268035.6:c.203A>G	p.Glu68Gly	p.E68G	ENST00000268035	NM_000875.3	68	gAg/gGg	2/21	1	2	FACETS	0.551	0.495	0.61	0.551	0.495	0.61	SUBCLONAL	1	TRUE	1	0.567318135387403	2		420	691	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858295	9858295	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	160	425	0	ENST00000330684.3:c.3106G>A	p.Glu1036Lys	p.E1036K	ENST00000330684	NM_001134407.1	1036	Gag/Aag	13/13	0.5674467693184	3	FACETS	0.89	0.816	0.966	0.445	0.408	0.483	CLONAL	1	TRUE	1	0.567318135387403	3		425	814	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241963	39241963	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	61	337	0	ENST00000402219.2:c.1883T>C	p.Leu628Pro	p.L628P	ENST00000402219	NM_005633.3	628	cTt/cCt	11/23	0.511818440773492	2	FACETS	0.618	0.536	0.706	0.309	0.268	0.353	SUBCLONAL	1	TRUE	0	0.567318135387403	2		337	348	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872813	136872813	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	74	347	0	ENST00000241393.3:c.685T>G	p.Ser229Ala	p.S229A	ENST00000241393	NM_003467.2	229	Tcc/Gcc	2/2	0.19214926668284	3	FACETS	0.569	0.498	0.644	0.19	0.166	0.215	INDETERMINATE	1	TRUE	0	0.567318135387403	3		347	589	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395695	31395695	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	65	431	0	ENST00000328111.2:c.2548T>G	p.Phe850Val	p.F850V	ENST00000328111	NM_006892.3	850	Ttt/Gtt	23/23	0.435181605558406	5	FACETS	0.435	0.375	0.499	0.145	0.125	0.167	SUBCLONAL	1	TRUE	2	0.567318135387403	5		431	976	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287187	33287187	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1282	90	526	0	ENST00000374542.5:c.1910A>C	p.Lys637Thr	p.K637T	ENST00000374542	NM_001141970.1	637	aAg/aCg	6/8	0.418183708489929	6	FACETS	0.494	0.436	0.556	0.165	0.145	0.186	SUBCLONAL	1	TRUE	3	0.567318135387403	6		526	1372	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979547	2979547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	99	476	0	ENST00000396946.4:c.700C>T	p.His234Tyr	p.H234Y	ENST00000396946	NM_032415.4	234	Cac/Tac	6/25	0.273830721829737	2	FACETS	0.534	0.477	0.594	0.267	0.238	0.297	INDETERMINATE	1	TRUE	0	0.567318135387403	2		476	654	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739653	41739653	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1001765662	NA	P-0035077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1257	139	617	0	ENST00000242208.4:c.320T>C	p.Ile107Thr	p.I107T	ENST00000242208	NM_002192.2	107	aTt/aCt	2/3	0.284857384652603	4	FACETS	0.55	0.499	0.604	0.275	0.249	0.302	INDETERMINATE	1	TRUE	2	0.567318135387403	4		617	1396	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468276	50468276	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	102	485	0	ENST00000331340.3:c.1511A>G	p.Glu504Gly	p.E504G	ENST00000331340	NM_006060.4	504	gAg/gGg	8/8	0.284857384652603	4	FACETS	0.636	0.568	0.709	0.318	0.284	0.355	INDETERMINATE	1	TRUE	2	0.567318135387403	4		485	886	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106519995	106519995	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	29	197	0	ENST00000359195.3:c.2423A>C	p.Lys808Thr	p.K808T	ENST00000359195	NM_002649.2	808	aAa/aCa	6/11	0.273665731266642	5	FACETS	0.612	0.492	0.748			1	INDETERMINATE	1	TRUE	NA	0.567318135387403	5		197	309	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226010	53226010	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	163	368	0	ENST00000375401.3:c.2839T>G	p.Leu947Val	p.L947V	ENST00000375401	NM_004187.3	947	Ttg/Gtg	19/26	1	1	FACETS	0.655	0.604	0.709	0.655	0.604	0.709	SUBCLONAL	1	TRUE	0	0.567318135387403	1		368	628	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435798	110435798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1240854451	NA	P-0035081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	36	113	0	ENST00000375856.3:c.2603C>T	p.Ser868Leu	p.S868L	ENST00000375856	NM_003749.2	868	tCg/tTg	1/2	NA	2	FACETS	0.934	0.786	1			1	INDETERMINATE	1	TRUE	NA	0.664850898375057	2		113	116	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77085381	77085381	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	106	291	0	ENST00000356341.3:c.469A>G	p.Asn157Asp	p.N157D	ENST00000356341	NM_002576.4	157	Aat/Gat	5/15	0.659164681756802	3	FACETS	0.865	0.779	0.956	0.288	0.259	0.319	CLONAL	1	TRUE	0	0.664850898375057	3		291	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577510	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0035081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	369	663	0	ENST00000269305.4:c.771_772delinsTT	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	257	ctGGaa/ctTTaa	7/11	0.657118743294056	2	FACETS	0.993	0.957	1	0.993	0.957	1	CLONAL	2	TRUE	0	0.664850898375057	2		663	559	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52621395	52621395	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	181	496	0	ENST00000394830.3:c.3022G>C	p.Gly1008Arg	p.G1008R	ENST00000394830	NM_018313.4	1008	Ggc/Cgc	20/30	1	2	FACETS	0.974	0.904	1	0.974	0.904	1	CLONAL	1	TRUE	1	0.664850898375057	2		496	559	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068117	94068117	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	59	194	0	ENST00000369303.4:c.845G>T	p.Gly282Val	p.G282V	ENST00000369303	NM_004440.3	282	gGg/gTg	4/17	0.664850898375057	2	FACETS	1	0.889	1	0.507	0.445	0.572	CLONAL	1	TRUE	0	0.664850898375057	2		194	175	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204992	128204992	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	55	628	0	ENST00000341105.2:c.449G>A	p.Gly150Glu	p.G150E	ENST00000341105	NM_032638.4	150	gGa/gAa	3/6	0.171010130128857	4	FACETS	0.822	0.701	0.955	0.274	0.233	0.319	CLONAL	1	TRUE	1	0.171010130128857	4		628	916	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31493381	31493381	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs768481311	NA	P-0035082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	26	308	0	ENST00000344624.3:c.1775T>C	p.Ile592Thr	p.I592T	ENST00000344624		592	aTa/aCa	10/33	0.171010130128857	4	FACETS	0.751	0.594	0.932	0.25	0.198	0.311	CLONAL	1	TRUE	1	0.171010130128857	4		308	474	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	294	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.264856720118886	5	FACETS	1	0.988	1	0.682	0.646	0.718	CLONAL	3	TRUE	0	0.393450710049094	5		493	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	93	774	0	ENST00000269305.4:c.380C>A	p.Ser127Tyr	p.S127Y	ENST00000269305	NM_001126112.2	127	tCc/tAc	5/11	0.344021380824996	4	FACETS	0.75	0.666	0.84	0.375	0.333	0.42	SUBCLONAL	1	TRUE	2	0.393450710049094	4		774	878	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725043	89725043	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1057517809	NA	P-0035084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	116	177	0	ENST00000371953.3:c.1027-1G>A		p.X343_splice	ENST00000371953	NM_000314.4	343			0.393450710049094	3	FACETS	1	0.974	1	0.781	0.715	0.85	CLONAL	2	TRUE	0	0.393450710049094	3		177	301	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934141	39934141	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	114	671	1	ENST00000378444.4:c.458C>A	p.Pro153His	p.P153H	ENST00000378444	NM_001123385.1	153	cCt/cAt	4/15	0.312841585757308	4	FACETS	1	0.935	1	0.525	0.473	0.58	CLONAL	1	TRUE	2	0.393450710049094	4		672	769	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056233	27056233	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	133	520	0	ENST00000324856.7:c.1229G>T	p.Gly410Val	p.G410V	ENST00000324856	NM_006015.4	410	gGa/gTa	2/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.393450710049094	2		520	546	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458168	120458168	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	170	538	1	ENST00000256646.2:c.7177G>T	p.Ala2393Ser	p.A2393S	ENST00000256646	NM_024408.3	2393	Gct/Tct	34/34	0.276617950651052	5	FACETS	0.896	0.825	0.969	0.597	0.55	0.646	CLONAL	2	TRUE	2	0.393450710049094	5		539	767	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612692	228612692	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	82	904	0	ENST00000366696.1:c.335T>A	p.Val112Asp	p.V112D	ENST00000366696	NM_003493.2	112	gTc/gAc	1/1	0.282845926507721	1	FACETS	0.434	0.382	0.489	0.434	0.382	0.489	SUBCLONAL	1	TRUE	0	0.393450710049094	1		904	772	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885620	111885620	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	105	758	0	ENST00000341259.2:c.1397C>G	p.Ser466Cys	p.S466C	ENST00000341259	NM_005475.2	466	tCc/tGc	7/8	0.248578898906096	3	FACETS	0.779	0.697	0.866			1	SUBCLONAL	1	TRUE	NA	0.393450710049094	3		758	820	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991321	41991321	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	56	440	0	ENST00000219905.7:c.2152C>G	p.Arg718Gly	p.R718G	ENST00000219905	NM_001164273.1	718	Cgg/Ggg	5/24	1	2	FACETS	0.539	0.462	0.623	0.539	0.462	0.623	SUBCLONAL	1	TRUE	1	0.393450710049094	2		440	528	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631599	90631599	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	66	545	0	ENST00000330062.3:c.670del	p.Thr224ProfsTer25	p.T224Pfs*25	ENST00000330062	NM_002168.2	224	Acc/cc	5/11	1	2	FACETS	0.683	0.594	0.779	0.683	0.594	0.779	SUBCLONAL	1	TRUE	1	0.393450710049094	2		545	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576862	7576862	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	85	672	0	ENST00000269305.4:c.984C>G	p.Phe328Leu	p.F328L	ENST00000269305	NM_001126112.2	328	ttC/ttG	9/11	0.344021380824996	4	FACETS	0.796	0.703	0.896	0.398	0.351	0.448	SUBCLONAL	1	TRUE	2	0.393450710049094	4		672	756	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445020	89445020	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	61	362	1	ENST00000336596.2:c.1340G>T	p.Arg447Leu	p.R447L	ENST00000336596	NM_005233.5	447	cGg/cTg	6/17	0.393450710049094	3	FACETS	0.651	0.562	0.748	0.326	0.281	0.374	SUBCLONAL	1	TRUE	1	0.393450710049094	3		363	570	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939738	131939738	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	83	283	0	ENST00000265335.6:c.2524G>A	p.Val842Ile	p.V842I	ENST00000265335		842	Gtt/Att	15/25	0.393450710049094	3	FACETS	0.812	0.724	0.904	0.812	0.724	0.904	CLONAL	2	TRUE	1	0.393450710049094	3		283	311	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032160	26032161	+	missense_variant	Missense_Mutation	DNP	GC	GC	AT	novel	NA	P-0035084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	118	349	2	ENST00000244661.2:c.128_129delinsAT	p.Arg43His	p.R43H	ENST00000244661	NM_003537.3	43	cGC/cAT	1/1	0.393450710049094	4	FACETS	0.793	0.719	0.871	0.529	0.479	0.581	SUBCLONAL	2	TRUE	1	0.393450710049094	4		351	527	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979216	93979216	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	161	286	0	ENST00000369303.4:c.1612G>A	p.Ala538Thr	p.A538T	ENST00000369303	NM_004440.3	538	Gct/Act	7/17	0.264856720118886	5	FACETS	0.927	0.858	0.998	0.556	0.514	0.599	CLONAL	3	TRUE	0	0.393450710049094	5		286	468	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563515	87563515	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	149	642	1	ENST00000277120.3:c.1903T>A	p.Tyr635Asn	p.Y635N	ENST00000277120		635	Tac/Aac	16/19	0.271841783545893	3	FACETS	1	0.988	1	0.749	0.687	0.813	CLONAL	1	TRUE	1	0.393450710049094	3		643	605	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	153	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.250076698141224	2	FACETS	0.97	0.892	1	0.485	0.446	0.526	INDETERMINATE	1	TRUE	0	0.543951812067126	2		493	580	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0035086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	19	127	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.254	0.193	0.326	0.254	0.193	0.326	SUBCLONAL	1	TRUE	1	0.543951812067126	2		127	275	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952088	178952088	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553826184	NA	P-0035086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	35	286	0	ENST00000263967.3:c.3143A>G	p.His1048Arg	p.H1048R	ENST00000263967	NM_006218.2	1048	cAt/cGt	21/21	1	2	FACETS	0.368	0.302	0.441	0.368	0.302	0.441	SUBCLONAL	1	TRUE	1	0.543951812067126	2		286	350	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469672	NA	P-0035086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	16	521	0	ENST00000374080.3:c.131G>A	p.Gly44Asp	p.G44D	ENST00000374080		44	gGt/gAt	2/45	1	2	FACETS	0.078	0.057	0.103	0.078	0.057	0.103	SUBCLONAL	1	TRUE	1	0.543951812067126	2		521	758	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685270	89685271	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	32	49	0	ENST00000371953.3:c.170dup	p.Leu57PhefsTer6	p.L57Ffs*6	ENST00000371953	NM_000314.4	55	-/T	3/9	1	2	FACETS	0.516	0.421	0.621	0.516	0.421	0.621	SUBCLONAL	1	TRUE	1	0.543951812067126	2		49	228	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280139	66280139	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	41	286	0	ENST00000273854.3:c.1550T>C	p.Ile517Thr	p.I517T	ENST00000273854	NM_004439.5	517	aTt/aCt	7/18	1	2	FACETS	0.409	0.341	0.483	0.409	0.341	0.483	SUBCLONAL	1	TRUE	1	0.543951812067126	2		286	369	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637416	176637417	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0035086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	37	388	0	ENST00000439151.2:c.2019_2020del	p.Asn674HisfsTer8	p.N674Hfs*8	ENST00000439151	NM_022455.4	672	acAGag/acag	5/23	1	2	FACETS	0.273	0.225	0.327	0.273	0.225	0.327	SUBCLONAL	1	TRUE	1	0.543951812067126	2		388	498	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176719059	176719059	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs587784192	NA	P-0035086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	36	260	0	ENST00000439151.2:c.6366del	p.Phe2122LeufsTer28	p.F2122Lfs*28	ENST00000439151	NM_022455.4	2121	tgT/tg	22/23	1	2	FACETS	0.32	0.263	0.384	0.32	0.263	0.384	SUBCLONAL	1	TRUE	1	0.543951812067126	2		260	414	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997757	149997757	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1156492707	NA	P-0035086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	52	421	2	ENST00000253339.5:c.2710C>T	p.Arg904Ter	p.R904*	ENST00000253339		904	Cga/Tga	5/7	1	2	FACETS	0.341	0.29	0.397	0.341	0.29	0.397	SUBCLONAL	1	TRUE	1	0.543951812067126	2		423	560	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	381	432	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.49095003365192	4	FACETS	0.997	0.955	1	0.997	0.955	1	CLONAL	3	TRUE	1	0.535893258754958	4		432	730	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	304	611	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.520804028061521	3	FACETS	0.906	0.858	0.955	0.906	0.858	0.955	CLONAL	2	TRUE	1	0.535893258754958	3		617	794	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	133	412	1	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	0.535893258754958	4	FACETS	1	0.974	1	0.594	0.54	0.649	CLONAL	1	TRUE	2	0.535893258754958	4		413	642	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	279	506	13	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.520804028061521	3	FACETS	0.908	0.858	0.959	0.908	0.858	0.959	CLONAL	2	TRUE	1	0.535893258754958	3		519	727	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190747	11190747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759603938	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	206	830	2	ENST00000361445.4:c.5452C>T	p.Arg1818Cys	p.R1818C	ENST00000361445	NM_004958.3	1818	Cgt/Tgt	39/58	0.520804028061521	3	FACETS	1	0.952	1	0.516	0.479	0.555	CLONAL	1	TRUE	1	0.535893258754958	3		832	944	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100941	27100941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	324	538	1	ENST00000324856.7:c.4225del	p.Gln1409SerfsTer72	p.Q1409Sfs*72	ENST00000324856	NM_006015.4	1408	gCc/gc	18/20	0.520804028061521	3	FACETS	0.998	0.948	1	0.998	0.948	1	CLONAL	2	TRUE	1	0.535893258754958	3		539	768	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275431	115275431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	193	438	0	ENST00000438362.2:c.982C>T	p.Pro328Ser	p.P328S	ENST00000438362	NM_001242891.1	328	Cca/Tca	10/20	0.520804028061521	3	FACETS	0.957	0.895	1	0.957	0.895	1	CLONAL	2	TRUE	1	0.535893258754958	3		438	477	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163309259	163309260	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	209	406	0	ENST00000271452.3:c.604dup	p.Thr202AsnfsTer24	p.T202Nfs*24	ENST00000271452	NM_145697.2	200	caa/cAaa	8/14	0.535893258754958	6	FACETS	1	0.948	1	0.682	0.634	0.731	CLONAL	2	TRUE	3	0.535893258754958	6		406	790	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193205413	193205413	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	104	537	1	ENST00000367435.3:c.1344G>T	p.Gln448His	p.Q448H	ENST00000367435	NM_024529.4	448	caG/caT	15/17	0.535893258754958	6	FACETS	0.732	0.653	0.815	0.244	0.217	0.272	SUBCLONAL	1	TRUE	3	0.535893258754958	6		538	1099	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651525	206651525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	247	504	0	ENST00000367120.3:c.835C>T	p.Pro279Ser	p.P279S	ENST00000367120	NM_014002.3	279	Ccc/Tcc	9/22	0.535893258754958	6	FACETS	1	0.947	1	0.675	0.632	0.72	CLONAL	2	TRUE	3	0.535893258754958	6		504	943	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652308	206652308	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1288	160	688	0	ENST00000367120.3:c.1015del	p.Val339CysfsTer41	p.V339Cfs*41	ENST00000367120	NM_014002.3	339	Gtg/tg	10/22	0.535893258754958	6	FACETS	0.854	0.781	0.932	0.285	0.26	0.311	CLONAL	1	TRUE	3	0.535893258754958	6		688	1448	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741892	17741894	+	inframe_deletion	In_Frame_Del	DEL	GCG	GCG	-	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	76	125	0	ENST00000250003.3:c.569_571del	p.Gly190del	p.G190del	ENST00000250003	NM_002478.4	188	cGCGgc/cgc	1/3	0.482508734598816	4	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	2	0.535893258754958	4		125	198	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94201026	94201026	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757492041	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	85	423	1	ENST00000323929.3:c.1051C>T	p.Arg351Cys	p.R351C	ENST00000323929	NM_005591.3	351	Cgt/Tgt	10/20	0.482508734598816	4	FACETS	0.831	0.736	0.933	0.416	0.368	0.467	CLONAL	1	TRUE	2	0.535893258754958	4		424	586	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102033204	102033204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	121	499	0	ENST00000282441.5:c.590C>T	p.Thr197Ile	p.T197I	ENST00000282441	NM_001130145.2	197	aCa/aTa	3/9	0.482508734598816	4	FACETS	0.866	0.782	0.954	0.433	0.391	0.477	CLONAL	1	TRUE	2	0.535893258754958	4		499	801	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165765	108165765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555101921	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	168	375	0	ENST00000278616.4:c.4888G>A	p.Asp1630Asn	p.D1630N	ENST00000278616	NM_000051.3	1630	Gac/Aac	32/63	0.482508734598816	4	FACETS	0.874	0.808	0.941	0.874	0.808	0.941	CLONAL	2	TRUE	2	0.535893258754958	4		375	551	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919613	28919613	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	125	613	1	ENST00000282397.4:c.2324T>C	p.Leu775Pro	p.L775P	ENST00000282397	NM_002019.4	775	cTa/cCa	16/30	0.454568248480361	3	FACETS	0.894	0.81	0.981	0.447	0.405	0.491	CLONAL	1	TRUE	1	0.535893258754958	3		614	662	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972768	32972768	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	208	441	0	ENST00000380152.3:c.10118C>G	p.Pro3373Arg	p.P3373R	ENST00000380152		3373	cCc/cGc	27/27	0.454568248480361	3	FACETS	0.887	0.83	0.945	0.887	0.83	0.945	CLONAL	2	TRUE	1	0.535893258754958	3		441	555	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574277	95574277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	86	352	0	ENST00000393063.1:c.2590G>A	p.Ala864Thr	p.A864T	ENST00000393063	NM_030621.3	864	Gca/Aca	17/28	0.482508734598816	4	FACETS	0.85	0.753	0.953	0.425	0.376	0.477	CLONAL	1	TRUE	2	0.535893258754958	4		352	580	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632500	3632500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	230	922	0	ENST00000294008.3:c.5348C>T	p.Ala1783Val	p.A1783V	ENST00000294008	NM_032444.2	1783	gCa/gTa	15/15	0.520804028061521	3	FACETS	0.994	0.926	1	0.497	0.463	0.532	CLONAL	1	TRUE	1	0.535893258754958	3		922	1095	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	103	468	1	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	0.520804028061521	3	FACETS	0.903	0.81	1	0.451	0.405	0.5	CLONAL	1	TRUE	1	0.535893258754958	3		469	540	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50820799	50820799	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	76	394	0	ENST00000398568.2:c.1974A>T	p.Lys658Asn	p.K658N	ENST00000398568	NM_001042412.1	658	aaA/aaT	12/18	0.520804028061521	3	FACETS	0.725	0.638	0.819	0.363	0.319	0.41	SUBCLONAL	1	TRUE	1	0.535893258754958	3		394	496	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821890	72821890	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	155	416	0	ENST00000268489.5:c.10285del	p.Arg3429ValfsTer56	p.R3429Vfs*56	ENST00000268489	NM_006885.3	3429	Cgt/gt	10/10	0.520804028061521	3	FACETS	1	0.989	1	0.748	0.69	0.808	CLONAL	1	TRUE	1	0.535893258754958	3		416	490	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347188	89347188	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	281	450	0	ENST00000301030.4:c.5762C>T	p.Ala1921Val	p.A1921V	ENST00000301030	NM_001256183.1	1921	gCc/gTc	9/13	0.520804028061521	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.535893258754958	3		450	646	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572991	7572991	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	252	472	2	ENST00000269305.4:c.1118del	p.Lys373ArgfsTer49	p.K373Rfs*49	ENST00000269305	NM_001126112.2	373	aAg/ag	11/11	0.520804028061521	3	FACETS	0.835	0.785	0.886	0.835	0.785	0.886	CLONAL	2	TRUE	1	0.535893258754958	3		474	714	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	168	776	3	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	0.520804028061521	3	FACETS	0.813	0.747	0.882	0.406	0.373	0.441	CLONAL	1	TRUE	1	0.535893258754958	3		779	978	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78921133	78921133	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	110	475	0	ENST00000306801.3:c.3247C>T	p.Leu1083Phe	p.L1083F	ENST00000306801	NM_020761.2	1083	Ctt/Ttt	27/34	0.535893258754958	3	FACETS	0.757	0.68	0.837	0.378	0.34	0.419	SUBCLONAL	1	TRUE	1	0.535893258754958	3		475	688	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581268	48581268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752575871	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	151	535	0	ENST00000342988.3:c.572C>T	p.Ser191Leu	p.S191L	ENST00000342988	NM_005359.5	191	tCg/tTg	5/12	0.520804028061521	3	FACETS	1	0.939	1	0.515	0.472	0.56	CLONAL	1	TRUE	1	0.535893258754958	3		535	694	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56412969	56412969	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	183	400	1	ENST00000348428.3:c.1983G>T	p.Lys661Asn	p.K661N	ENST00000348428	NM_006785.3	661	aaG/aaT	16/17	0.520804028061521	3	FACETS	0.885	0.825	0.947	0.885	0.825	0.947	CLONAL	2	TRUE	1	0.535893258754958	3		401	489	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602340	10602340	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	597	852	0	ENST00000171111.5:c.1238G>T	p.Arg413Leu	p.R413L	ENST00000171111	NM_203500.1	413	cGt/cTt	3/6	0.507549005382082	3	FACETS	0.931	0.901	0.96	0.931	0.901	0.96	CLONAL	3	TRUE	0	0.535893258754958	3		852	1012	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610102	10610102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	542	710	1	ENST00000171111.5:c.608C>T	p.Ala203Val	p.A203V	ENST00000171111	NM_203500.1	203	gCc/gTc	2/6	0.507549005382082	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	TRUE	0	0.535893258754958	3		711	852	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097084	11097084	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	588	771	0	ENST00000358026.2:c.579del	p.Gln194SerfsTer109	p.Q194Sfs*109	ENST00000358026	NM_001128849.1	192	aGg/ag	4/36	0.507549005382082	3	FACETS	0.909	0.88	0.938	0.909	0.88	0.938	CLONAL	3	TRUE	0	0.535893258754958	3		771	1020	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212443	36212443	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1194	215	791	0	ENST00000222270.7:c.2194C>T	p.Gln732Ter	p.Q732*	ENST00000222270	NM_014727.1	732	Cag/Tag	3/37	0.535893258754958	5	FACETS	1	0.948	1	0.342	0.317	0.369	CLONAL	1	TRUE	2	0.535893258754958	5		791	1409	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797955	42797955	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1353	203	834	0	ENST00000575354.2:c.4007C>A	p.Pro1336Gln	p.P1336Q	ENST00000575354	NM_015125.3	1336	cCg/cAg	16/20	0.535893258754958	5	FACETS	0.878	0.812	0.948	0.293	0.27	0.316	CLONAL	1	TRUE	2	0.535893258754958	5		834	1556	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725019	47725019	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs762488821	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	354	848	0	ENST00000449228.1:c.725del	p.Gly242AlafsTer48	p.G242Afs*48	ENST00000449228	NM_001127240.2	242	gGc/gc	4/4	0.535893258754958	5	FACETS	0.794	0.75	0.838	0.529	0.5	0.559	SUBCLONAL	2	TRUE	2	0.535893258754958	5		848	1501	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656939	47656939	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	214	381	1	ENST00000233146.2:c.1135G>A	p.Asp379Asn	p.D379N	ENST00000233146	NM_000251.2	379	Gat/Aat	7/16	0.516282554148744	5	FACETS	0.981	0.915	1	0.491	0.457	0.525	CLONAL	2	TRUE	1	0.535893258754958	5		382	734	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030692	48030692	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs267608092	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	96	466	0	ENST00000234420.5:c.3312del	p.Phe1104LeufsTer11	p.F1104Lfs*11	ENST00000234420	NM_000179.2	1102	acT/ac	5/10	0.516282554148744	5	FACETS	0.761	0.677	0.851	0.19	0.169	0.213	SUBCLONAL	1	TRUE	1	0.535893258754958	5		466	849	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589845	212589845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	111	483	0	ENST00000342788.4:c.697G>A	p.Glu233Lys	p.E233K	ENST00000342788	NM_005235.2	233	Gaa/Aaa	6/28	0.520804028061521	3	FACETS	0.864	0.778	0.954	0.432	0.389	0.477	CLONAL	1	TRUE	1	0.535893258754958	3		483	608	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794794	242794794	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764852072	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	99	460	0	ENST00000334409.5:c.415C>T	p.Arg139Trp	p.R139W	ENST00000334409	NM_005018.2	139	Cgg/Tgg	2/5	0.520804028061521	3	FACETS	0.816	0.73	0.907	0.408	0.365	0.454	CLONAL	1	TRUE	1	0.535893258754958	3		460	574	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741453	39741453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	137	316	0	ENST00000361337.2:c.1340C>T	p.Ala447Val	p.A447V	ENST00000361337	NM_003286.2	447	gCt/gTt	14/21	0.535893258754958	4	FACETS	1	0.985	1	0.691	0.631	0.754	CLONAL	1	TRUE	2	0.535893258754958	4		316	568	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067448	37067448	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs267607821	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	414	460	1	ENST00000231790.2:c.1362del	p.Thr455LeufsTer36	p.T455Lfs*36	ENST00000231790	NM_000249.3	453	aaG/aa	12/19	0.496695375097441	4	FACETS	1	0.994	1	0.864	0.831	0.895	CLONAL	3	TRUE	0	0.535893258754958	4		461	687	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275121	41275121	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	431	383	0	ENST00000349496.5:c.1287C>G	p.Cys429Trp	p.C429W	ENST00000349496	NM_001904.3	429	tgC/tgG	9/15	0.496695375097441	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	4	TRUE	0	0.535893258754958	4		383	608	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437614	52437614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755719248	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	402	718	0	ENST00000460680.1:c.1547C>T	p.Pro516Leu	p.P516L	ENST00000460680	NM_004656.3	516	cCg/cTg	13/17	0.496695375097441	4	FACETS	1	0.985	1	0.536	0.511	0.562	CLONAL	2	TRUE	0	0.535893258754958	4		718	1074	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437912	52437912	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	770	820	1	ENST00000460680.1:c.1251-2A>G		p.X417_splice	ENST00000460680	NM_004656.3	417			0.496695375097441	4	FACETS	0.977	0.953	1	0.977	0.953	1	CLONAL	4	TRUE	0	0.535893258754958	4		821	1129	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528621	89528621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780470195	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	41	206	0	ENST00000336596.2:c.2921C>T	p.Thr974Met	p.T974M	ENST00000336596	NM_005233.5	974	aCg/aTg	17/17	0.496695375097441	4	FACETS	0.723	0.604	0.854	0.181	0.151	0.214	SUBCLONAL	1	TRUE	0	0.535893258754958	4		206	325	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134872999	134872999	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	252	504	0	ENST00000398015.3:c.1303T>G	p.Ser435Ala	p.S435A	ENST00000398015	NM_004441.4	435	Tcc/Gcc	6/16	0.496695375097441	4	FACETS	0.993	0.934	1	0.497	0.467	0.527	CLONAL	2	TRUE	0	0.535893258754958	4		504	727	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136808	55136808	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	153	381	0	ENST00000257290.5:c.1130G>T	p.Ser377Ile	p.S377I	ENST00000257290	NM_006206.4	377	aGc/aTc	8/23	0.520804028061521	3	FACETS	0.86	0.795	0.926	0.86	0.795	0.926	CLONAL	2	TRUE	1	0.535893258754958	3		381	421	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509084	66509085	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	64	332	0	ENST00000273854.3:c.242dup	p.Asn81LysfsTer8	p.N81Kfs*8	ENST00000273854	NM_004439.5	81	aat/aaAt	2/18	0.520804028061521	3	FACETS	0.856	0.745	0.974	0.428	0.372	0.487	CLONAL	1	TRUE	1	0.535893258754958	3		332	354	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	141	367	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.520804028061521	3	FACETS	1	0.925	1	0.507	0.463	0.553	CLONAL	1	TRUE	1	0.535893258754958	3		367	658	SUCCESS
APC	324	MSKCC	GRCh37	5	112174484	112174484	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	87	269	0	ENST00000257430.4:c.3193C>T	p.Gln1065Ter	p.Q1065*	ENST00000257430	NM_000038.5	1065	Caa/Taa	16/16	0.520804028061521	3	FACETS	1	0.938	1	0.539	0.48	0.601	CLONAL	1	TRUE	1	0.535893258754958	3		269	382	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637121	176637122	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1299932363	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	127	629	0	ENST00000439151.2:c.1727dup	p.Asn576LysfsTer8	p.N576Kfs*8	ENST00000439151	NM_022455.4	574	gga/ggAa	5/23	0.520804028061521	3	FACETS	0.774	0.702	0.851	0.387	0.351	0.426	SUBCLONAL	1	TRUE	1	0.535893258754958	3		629	776	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047187	180047187	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	178	687	0	ENST00000261937.6:c.2528A>T	p.Glu843Val	p.E843V	ENST00000261937	NM_182925.4	843	gAg/gTg	17/30	0.520804028061521	3	FACETS	1	0.951	1	0.52	0.48	0.562	CLONAL	1	TRUE	1	0.535893258754958	3		687	810	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397219	397219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143144957	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	65	299	0	ENST00000380956.4:c.604G>A	p.Gly202Ser	p.G202S	ENST00000380956	NM_001195286.1	202	Ggc/Agc	5/9	0.520804028061521	3	FACETS	0.736	0.64	0.839	0.368	0.32	0.42	SUBCLONAL	1	TRUE	1	0.535893258754958	3		299	418	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323362	31323363	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748204482	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	176	463	0	ENST00000412585.2:c.626dup	p.Thr211AspfsTer10	p.T211Dfs*10	ENST00000412585	NM_005514.6	209	cca/ccCa	4/8	0.520804028061521	3	FACETS	0.871	0.81	0.934	0.871	0.81	0.934	CLONAL	2	TRUE	1	0.535893258754958	3		463	478	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638347	117638347	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	134	511	0	ENST00000368508.3:c.6094G>T	p.Gly2032Ter	p.G2032*	ENST00000368508	NM_002944.2	2032	Gga/Tga	38/43	0.197836369151621	3	FACETS	1	0.954	1			1	INDETERMINATE	1	TRUE	NA	0.535893258754958	3		511	591	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137528151	137528151	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	73	298	0	ENST00000367739.4:c.149A>G	p.Tyr50Cys	p.Y50C	ENST00000367739	NM_000416.2	50	tAc/tGc	2/7	0.520804028061521	3	FACETS	0.868	0.763	0.98	0.434	0.381	0.49	CLONAL	1	TRUE	1	0.535893258754958	3		298	398	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859696	151859696	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	198	440	1	ENST00000262189.6:c.10966G>A	p.Ala3656Thr	p.A3656T	ENST00000262189	NM_170606.2	3656	Gcc/Acc	43/59	0.498477678790668	5	FACETS	0.915	0.851	0.982	0.61	0.567	0.655	CLONAL	2	TRUE	2	0.535893258754958	5		441	728	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68984785	68984785	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	207	457	0	ENST00000288368.4:c.1549A>G	p.Ile517Val	p.I517V	ENST00000288368	NM_024870.2	517	Ata/Gta	14/40	0.535893258754958	3	FACETS	0.951	0.891	1	0.951	0.891	1	CLONAL	2	TRUE	1	0.535893258754958	3		457	515	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737619	145737621	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs772583454	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	186	797	0	ENST00000428558.2:c.3142_3144del	p.Lys1048del	p.K1048del	ENST00000428558	NM_004260.3	1048	AAG/-	19/22	0.535893258754958	3	FACETS	0.927	0.857	1	0.464	0.428	0.501	CLONAL	1	TRUE	1	0.535893258754958	3		797	949	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341719	8341719	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	124	702	0	ENST00000356435.5:c.4921G>T	p.Val1641Phe	p.V1641F	ENST00000356435		1641	Gtc/Ttc	29/35	0.454568248480361	3	FACETS	0.756	0.684	0.832	0.378	0.342	0.416	SUBCLONAL	1	TRUE	1	0.535893258754958	3		702	776	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015094	37015094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	311	696	0	ENST00000358127.4:c.310C>T	p.Arg104Cys	p.R104C	ENST00000358127	NM_001280556.1	104	Cgc/Tgc	3/10	0.454568248480361	3	FACETS	0.9	0.852	0.948	0.9	0.852	0.948	CLONAL	2	TRUE	1	0.535893258754958	3		696	818	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128321972	128321972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	252	613	1	ENST00000265960.3:c.788C>T	p.Ala263Val	p.A263V	ENST00000265960	NM_001006617.1	263	gCc/gTc	6/12	0.454568248480361	3	FACETS	0.858	0.807	0.91	0.858	0.807	0.91	CLONAL	2	TRUE	1	0.535893258754958	3		614	695	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400261	139400261	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	165	752	0	ENST00000277541.6:c.4087T>C	p.Cys1363Arg	p.C1363R	ENST00000277541	NM_017617.3	1363	Tgc/Cgc	25/34	0.454568248480361	3	FACETS	0.901	0.827	0.977	0.45	0.413	0.489	CLONAL	1	TRUE	1	0.535893258754958	3		752	867	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430388	47430388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	273	629	0	ENST00000377045.4:c.1663G>A	p.Glu555Lys	p.E555K	ENST00000377045	NM_001654.4	555	Gag/Aag	15/16	0.270674694666899	5	FACETS	1	0.968	1	0.695	0.653	0.737	INDETERMINATE	2	TRUE	2	0.535893258754958	5		629	882	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652527	48652527	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	145	589	1	ENST00000376670.3:c.1203del	p.Thr402ProfsTer30	p.T402Pfs*30	ENST00000376670	NM_002049.3	400	Ccc/cc	6/6	0.270674694666899	5	FACETS	1	0.968	1	0.377	0.343	0.411	INDETERMINATE	1	TRUE	2	0.535893258754958	5		590	864	SUCCESS
AR	367	MSKCC	GRCh37	X	66765623	66765623	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	214	963	0	ENST00000374690.3:c.635G>T	p.Arg212Met	p.R212M	ENST00000374690	NM_000044.3	212	aGg/aTg	1/8	0.270674694666899	5	FACETS	1	0.98	1	0.384	0.356	0.414	INDETERMINATE	1	TRUE	2	0.535893258754958	5		963	1249	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344928	70344928	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	165	679	0	ENST00000374080.3:c.2158G>T	p.Gly720Trp	p.G720W	ENST00000374080		720	Ggg/Tgg	15/45	0.270674694666899	5	FACETS	1	0.98	1	0.402	0.369	0.437	INDETERMINATE	1	TRUE	2	0.535893258754958	5		679	921	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123041021	123041021	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	12	185	0	ENST00000355640.3:c.1484T>C	p.Phe495Ser	p.F495S	ENST00000355640		495	tTt/tCt	7/7	0.270674694666899	5	FACETS	0.434	0.305	0.592	0.145	0.101	0.198	INDETERMINATE	1	TRUE	2	0.535893258754958	5		185	186	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196755	123196755	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	127	320	0	ENST00000218089.9:c.1642C>A	p.Leu548Ile	p.L548I	ENST00000218089	NM_001042749.1	548	Ctt/Att	18/35	0.270674694666899	5	FACETS	1	0.955	1	0.712	0.651	0.775	INDETERMINATE	2	TRUE	2	0.535893258754958	5		320	400	SUCCESS
AR	367	MSKCC	GRCh37	X	66766424	66766424	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	18	201	0	ENST00000374690.3:c.1440del	p.Tyr481ThrfsTer29	p.Y481Tfs*29	ENST00000374690	NM_000044.3	479	gCc/gc	1/8	0.270674694666899	5	FACETS	0.349	0.262	0.452	0.116	0.087	0.151	INDETERMINATE	1	TRUE	2	0.535893258754958	5		201	347	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0035095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	254	575	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.386949818309948	3	FACETS	0.91	0.861	0.959			1	CLONAL	3	TRUE	NA	0.430670726178971	3		575	525	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263890	133263890	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	163	358	0	ENST00000320574.5:c.12G>T	p.Arg4Ser	p.R4S	ENST00000320574	NM_006231.2	4	agG/agT	1/49	0.370377954361389	3	FACETS	0.989	0.916	1	0.989	0.916	1	CLONAL	2	TRUE	1	0.430670726178971	3		358	465	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803005	32803005	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	354	662	0	ENST00000374899.4:c.871C>T	p.Arg291Ter	p.R291*	ENST00000374899	NM_018833.2	291	Cga/Tga	5/12	0.410392697963753	3	FACETS	0.921	0.88	0.963	0.921	0.88	0.963	CLONAL	3	TRUE	0	0.430670726178971	3		662	723	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389243	8389243	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	299	684	1	ENST00000356435.5:c.4375G>A	p.Glu1459Lys	p.E1459K	ENST00000356435		1459	Gaa/Aaa	26/35	0.38619619718171	3	FACETS	0.859	0.815	0.902	0.859	0.815	0.902	CLONAL	3	TRUE	0	0.430670726178971	3		685	655	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352972	70352972	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0035095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	241	335	0	ENST00000374080.3:c.4528-1G>A		p.X1510_splice	ENST00000374080		1510			0.376009418546666	2	FACETS	0.897	0.852	0.941			1	CLONAL	3	TRUE	NA	0.430670726178971	2		335	416	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200076	123200076	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	218	320	0	ENST00000218089.9:c.2148G>C	p.Leu716Phe	p.L716F	ENST00000218089	NM_001042749.1	716	ttG/ttC	22/35	0.376009418546666	2	FACETS	0.89	0.843	0.937			1	CLONAL	3	TRUE	NA	0.430670726178971	2		320	379	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	111	463	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.655	0.587	0.726	0.655	0.587	0.726	SUBCLONAL	1	TRUE	1	0.35	2		463	969	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	108	405	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.35	2		408	419	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	112	283	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.150453203060051	3	FACETS	1	0.982	1	0.705	0.637	0.777	INDETERMINATE	1	TRUE	1	0.35	3		283	533	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	97	438	1	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.869	0.776	0.968	0.869	0.776	0.968	CLONAL	1	TRUE	1	0.35	2		439	638	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	70	260	1	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.35	2		261	347	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004217	150004217	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1431439182	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	69	371	0	ENST00000253339.5:c.2008C>T	p.Arg670Trp	p.R670W	ENST00000253339		670	Cgg/Tgg	3/7	1	2	FACETS	0.785	0.685	0.893	0.785	0.685	0.893	SUBCLONAL	1	TRUE	1	0.35	2		371	502	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	127	484	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	1	2	FACETS	0.764	0.691	0.841	0.764	0.691	0.841	SUBCLONAL	1	TRUE	1	0.35	2		484	950	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	59	307	3	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	0.671976960377247	3	FACETS	0.657	0.565	0.757	0.328	0.282	0.379	SUBCLONAL	1	TRUE	1	0.35	3		310	603	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	21	275	1	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	0.150453203060051	3	FACETS	0.365	0.281	0.464	0.183	0.14	0.232	INDETERMINATE	1	TRUE	1	0.35	3		276	386	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39644793	39644793	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	63	267	0	ENST00000262039.4:c.2522A>G	p.Lys841Arg	p.K841R	ENST00000262039	NM_002647.2	841	aAg/aGg	23/25	1	2	FACETS	0.973	0.846	1	0.973	0.846	1	CLONAL	1	TRUE	1	0.35	2		267	370	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	106	506	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	0.798	0.715	0.886	0.798	0.715	0.886	SUBCLONAL	1	TRUE	1	0.35	2		506	759	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	82	263	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.35	2		263	378	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971292	13971292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772105404	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	56	429	0	ENST00000405192.2:c.637C>T	p.Arg213Cys	p.R213C	ENST00000405192	NM_001163147.1	213	Cgc/Tgc	8/12	1	2	FACETS	0.519	0.444	0.6	0.519	0.444	0.6	SUBCLONAL	1	TRUE	1	0.35	2		429	617	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119781	70119781	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1274036689	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	108	544	0	ENST00000245479.2:c.788del	p.Gly263AlafsTer16	p.G263Afs*16	ENST00000245479	NM_000346.3	261	gaG/ga	3/3	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.35	2		544	613	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117594	70117594	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	88	539	1	ENST00000245479.2:c.66del	p.Ser23AlafsTer38	p.S23Afs*38	ENST00000245479	NM_000346.3	21	gCc/gc	1/3	1	2	FACETS	0.938	0.833	1	0.938	0.833	1	CLONAL	1	TRUE	1	0.35	2		540	536	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121266	29121266	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730881701	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	49	746	0	ENST00000328354.6:c.409C>T	p.Arg137Ter	p.R137*	ENST00000328354	NM_007194.3	137	Cga/Tga	3/15	1	2	FACETS	0.375	0.317	0.44	0.375	0.317	0.44	SUBCLONAL	1	TRUE	1	0.35	2		746	746	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743896	41743896	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	87	791	1	ENST00000301178.4:c.836del	p.Pro279GlnfsTer18	p.P279Qfs*18	ENST00000301178	NM_021913.4	277	gaC/ga	7/20	1	2	FACETS	0.618	0.546	0.694	0.618	0.546	0.694	SUBCLONAL	1	TRUE	1	0.35	2		792	805	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411678	63411678	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	122	406	0	ENST00000330258.3:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000330258	NM_152424.3	497	Cga/Tga	2/2	1	1	FACETS	1	0.943	1	1	0.991	1	CLONAL	2	TRUE	0	0.35	1		406	279	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612344	1612344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1320707074	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	134	801	1	ENST00000344749.5:c.1675G>A	p.Val559Met	p.V559M	ENST00000344749	NM_001136139.2	559	Gtg/Atg	18/19	0.3	2	FACETS	0.875	0.795	0.96			1	CLONAL	1	TRUE	NA	0.35	2		802	875	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912349	97912349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs182879858	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	45	349	0	ENST00000289081.3:c.542C>T	p.Ala181Val	p.A181V	ENST00000289081	NM_000136.2	181	gCg/gTg	7/15	1	2	FACETS	0.644	0.543	0.757	0.644	0.543	0.757	SUBCLONAL	1	TRUE	1	0.35	2		349	399	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430936	181430936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	50	731	0	ENST00000325404.1:c.788C>T	p.Ala263Val	p.A263V	ENST00000325404	NM_003106.3	263	gCg/gTg	1/1	0.150453203060051	4	FACETS	0.706	0.599	0.824	0.353	0.299	0.412	INDETERMINATE	1	TRUE	2	0.35	4		731	546	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	33	302	2				ENST00000310581	NM_198253.2	-/1132			0.150453203060051	0	FACETS	0.466	0.381	0.561			1	INDETERMINATE	1	TRUE	0	0.35	0		304	263	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878530	151878530	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1396109953	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	45	608	0	ENST00000262189.6:c.6415C>T	p.Arg2139Ter	p.R2139*	ENST00000262189	NM_170606.2	2139	Cga/Tga	36/59	1	2	FACETS	0.363	0.304	0.429	0.363	0.304	0.429	SUBCLONAL	1	TRUE	1	0.35	2		608	708	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210893	36210893	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	43	702	3	ENST00000222270.7:c.649del	p.Arg217GlyfsTer22	p.R217Gfs*22	ENST00000222270	NM_014727.1	215	aCc/ac	3/37	1	2	FACETS	0.391	0.326	0.462	0.391	0.326	0.462	SUBCLONAL	1	TRUE	1	0.35	2		705	629	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309141	137309141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767968089	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	74	796	1	ENST00000481739.1:c.748G>A	p.Val250Met	p.V250M	ENST00000481739	NM_002957.4	250	Gtg/Atg	5/10	1	2	FACETS	0.672	0.589	0.762	0.672	0.589	0.762	SUBCLONAL	1	TRUE	1	0.35	2		797	629	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933561	36933561	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs373888342	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	46	647	4	ENST00000361632.4:c.1726G>A	p.Ala576Thr	p.A576T	ENST00000361632		576	Gcc/Acc	13/16	1	2	FACETS	0.538	0.453	0.631	0.538	0.453	0.631	SUBCLONAL	1	TRUE	1	0.35	2		651	489	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65312344	65312344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	46	430	0	ENST00000342505.4:c.1975C>T	p.Arg659Cys	p.R659C	ENST00000342505	NM_002227.2	659	Cgc/Tgc	14/25	1	2	FACETS	0.509	0.429	0.599	0.509	0.429	0.599	SUBCLONAL	1	TRUE	1	0.35	2		430	516	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210431	36210431	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs748888652	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	91	621	0	ENST00000222270.7:c.424C>T	p.Arg142Ter	p.R142*	ENST00000222270	NM_014727.1	142	Cga/Tga	2/37	1	2	FACETS	0.872	0.776	0.975	0.872	0.776	0.975	CLONAL	1	TRUE	1	0.35	2		621	596	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480611	120480611	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	69	397	0	ENST00000256646.2:c.3206G>T	p.Arg1069Leu	p.R1069L	ENST00000256646	NM_024408.3	1069	cGg/cTg	20/34	1	2	FACETS	0.74	0.645	0.842	0.74	0.645	0.842	SUBCLONAL	1	TRUE	1	0.35	2		397	533	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099332	193099332	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	99	352	0	ENST00000367435.3:c.266C>A	p.Pro89His	p.P89H	ENST00000367435	NM_024529.4	89	cCt/cAt	3/17	1	2	FACETS	0.887	0.793	0.986	0.887	0.793	0.986	CLONAL	1	TRUE	1	0.35	2		352	638	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514056	69514056	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138132534	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	93	584	0	ENST00000294312.3:c.625G>A	p.Val209Met	p.V209M	ENST00000294312	NM_005117.2	209	Gtg/Atg	3/3	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.35	2		584	510	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426625	49426633	+	inframe_deletion	In_Frame_Del	DEL	GCTGCTGTT	GCTGCTGTT	-	rs765742357	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	41	582	1	ENST00000301067.7:c.11855_11863del	p.Gln3952_Gln3954del	p.Q3952_Q3954del	ENST00000301067	NM_003482.3	3952	cAACAGCAGCta/cta	39/54	0.34550996545425	4	FACETS	0.449	0.373	0.534	0.224	0.186	0.267	SUBCLONAL	1	TRUE	2	0.35	4		583	705	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434351	49434351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375115132	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	83	716	1	ENST00000301067.7:c.7202G>A	p.Arg2401His	p.R2401H	ENST00000301067	NM_003482.3	2401	cGc/cAc	31/54	0.34550996545425	4	FACETS	0.794	0.7	0.896	0.397	0.35	0.448	SUBCLONAL	1	TRUE	2	0.35	4		717	806	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554443	63554443	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	175	593	0	ENST00000307078.5:c.296T>C	p.Leu99Pro	p.L99P	ENST00000307078	NM_004655.3	99	cTg/cCg	2/11	1	2	FACETS	0.754	0.697	0.813	1	0.99	1	SUBCLONAL	2	TRUE	1	0.35	2		593	663	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2206761	2206761	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs201645007	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	91	567	0	ENST00000398665.3:c.821C>A	p.Pro274His	p.P274H	ENST00000398665	NM_032482.2	274	cCt/cAt	10/28	0.3	2	FACETS	0.64	0.568	0.718			1	SUBCLONAL	1	TRUE	NA	0.35	2		567	812	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716287	52716287	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1468288521	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	21	631	0	ENST00000322088.6:c.731T>C	p.Val244Ala	p.V244A	ENST00000322088	NM_014225.5	244	gTg/gCg	6/15	1	2	FACETS	0.299	0.23	0.381	0.299	0.23	0.381	SUBCLONAL	1	TRUE	1	0.35	2		631	401	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031619	36031619	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753395244	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	81	632	0	ENST00000358208.4:c.1448G>A	p.Arg483Gln	p.R483Q	ENST00000358208		483	cGg/cAg	12/12	1	2	FACETS	0.894	0.789	1	0.894	0.789	1	CLONAL	1	TRUE	1	0.35	2		632	518	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37622733	37622733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	50	681	1	ENST00000249071.6:c.559C>T	p.Arg187Cys	p.R187C	ENST00000249071	NM_002872.4	187	Cgc/Tgc	6/7	1	2	FACETS	0.362	0.306	0.424	0.362	0.306	0.424	SUBCLONAL	1	TRUE	1	0.35	2		682	789	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801196	1801196	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	89	799	0	ENST00000260795.2:c.325T>G	p.Cys109Gly	p.C109G	ENST00000260795		109	Tgc/Ggc	2/17	0.150453203060051	0	FACETS	0.56	0.497	0.627			1	INDETERMINATE	1	TRUE	0	0.35	0		799	590	SUCCESS
APC	324	MSKCC	GRCh37	5	112163630	112163630	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371453363	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	18	233	0	ENST00000257430.4:c.1553C>T	p.Thr518Met	p.T518M	ENST00000257430	NM_000038.5	518	aCg/aTg	13/16	1	2	FACETS	0.315	0.236	0.407	0.315	0.236	0.407	SUBCLONAL	1	TRUE	1	0.35	2		233	327	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497191	149497192	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	42	502	0	ENST00000261799.4:c.3126dup	p.Ser1043GlnfsTer9	p.S1043Qfs*9	ENST00000261799	NM_002609.3	1042	-/C	22/23	1	2	FACETS	0.442	0.368	0.524	0.442	0.368	0.524	SUBCLONAL	1	TRUE	1	0.35	2		502	543	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197242	26197242	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs557343198	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	190	431	0	ENST00000356476.2:c.237C>A	p.Phe79Leu	p.F79L	ENST00000356476		79	ttC/ttA	1/1	0.3	8	FACETS	1	0.982	1			1	CLONAL	2	TRUE	NA	0.35	8		431	935	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162158	38162158	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1341789304	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	55	471	0	ENST00000317025.8:c.2558G>A	p.Arg853Gln	p.R853Q	ENST00000317025	NM_023034.1	853	cGg/cAg	14/24	0.522994568715846	3	FACETS	0.418	0.356	0.486	0.209	0.178	0.243	SUBCLONAL	1	TRUE	1	0.35	3		471	884	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966698	36966698	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	40	373	0	ENST00000358127.4:c.628A>G	p.Asn210Asp	p.N210D	ENST00000358127	NM_001280556.1	210	Aac/Gac	6/10	1	2	FACETS	0.819	0.684	0.968	0.819	0.684	0.968	CLONAL	1	TRUE	1	0.35	2		373	279	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658385	18658385	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	113	355	1	ENST00000266497.5:c.3190G>T	p.Gly1064Trp	p.G1064W	ENST00000266497		1064	Ggg/Tgg	22/31	0.226510169037537	3	FACETS	0.849	0.767	0.935	0.283	0.255	0.312	INDETERMINATE	1	TRUE	0	0.644466475970224	3		356	546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0035101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	338	721	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	0.644466475970224	1	FACETS	0.983	0.937	1	0.983	0.937	1	CLONAL	1	TRUE	0	0.644466475970224	1		721	723	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0035101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	437	554	1	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	NA	2	FACETS	0.962	0.928	0.995			1	INDETERMINATE	2	TRUE	NA	0.644466475970224	2		555	705	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41267743	41267764	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TTGCAAAATATGTGGTCACACT	TTGCAAAATATGTGGTCACACT	-	novel	NA	P-0035101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	183	458	0	ENST00000357654.3:c.113_134del	p.Lys38AsnfsTer5	p.K38Nfs*5	ENST00000357654	NM_007294.3	38	aAGTGTGACCACATATTTTGCAAa/aa	3/23	0.644466475970224	2	FACETS	1	0.99	1	0.693	0.647	0.738	CLONAL	1	TRUE	0	0.644466475970224	2		458	410	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713430	40713430	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	256	586	0	ENST00000373198.4:c.4085A>C	p.Tyr1362Ser	p.Y1362S	ENST00000373198	NM_133170.3	1362	tAc/tCc	30/32	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.644466475970224	2		586	734	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259125	89259125	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1211863735	NA	P-0035101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	132	353	0	ENST00000336596.2:c.269A>T	p.Asn90Ile	p.N90I	ENST00000336596	NM_005233.5	90	aAc/aTc	3/17	NA	2	FACETS	0.955	0.874	1			1	INDETERMINATE	1	TRUE	NA	0.644466475970224	2		353	429	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150022935	150022935	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	209	490	0	ENST00000253339.5:c.328C>T	p.Gln110Ter	p.Q110*	ENST00000253339		110	Caa/Taa	1/7	0.644466475970224	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.644466475970224	1		490	425	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0035102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	251	384	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.215642867420398	3	FACETS	0.838	0.784	0.893	1	0.989	1	CLONAL	3	TRUE	1	0.215642867420398	3		384	1026	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793008	33793010	+	inframe_deletion	In_Frame_Del	DEL	CGC	CGC	-	rs780345232	NA	P-0035102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	11	100	1	ENST00000498907.2:c.311_313del	p.Gly104del	p.G104del	ENST00000498907	NM_004364.3	104	gGCGac/gac	1/1	1	2	FACETS	0.911	0.634	1	0.911	0.634	1	CLONAL	1	TRUE	1	0.215642867420398	2		101	112	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733218	74733218	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	79	601	0	ENST00000359995.5:c.25G>A	p.Asp9Asn	p.D9N	ENST00000359995	NM_001195427.1	9	Gat/Aat	1/3	0.215642867420398	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.215642867420398	1		601	528	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933311	39933311	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	117	773	0	ENST00000378444.4:c.1288C>T	p.Gln430Ter	p.Q430*	ENST00000378444	NM_001123385.1	430	Cag/Tag	4/15	NA	2	FACETS	1	0.943	1			1	INDETERMINATE	1	TRUE	NA	0.215642867420398	2		773	1015	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465542	8465542	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	103	657	0	ENST00000356435.5:c.3638G>A	p.Gly1213Glu	p.G1213E	ENST00000356435		1213	gGa/gAa	21/35	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.215642867420398	2		657	850	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733140	74733140	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	63	592	0	ENST00000359995.5:c.103G>C	p.Glu35Gln	p.E35Q	ENST00000359995	NM_001195427.1	35	Gag/Cag	1/3	0.215642867420398	1	FACETS	0.873	0.755	1	0.873	0.755	1	CLONAL	1	TRUE	0	0.215642867420398	1		592	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579503	7579503	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567556752	NA	P-0035102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	92	735	0	ENST00000269305.4:c.184G>T	p.Glu62Ter	p.E62*	ENST00000269305	NM_001126112.2	62	Gaa/Taa	4/11	0.215642867420398	1	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	0	0.215642867420398	1		735	747	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851627	134851627	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	59	530	0	ENST00000398015.3:c.1033C>G	p.Pro345Ala	p.P345A	ENST00000398015	NM_004441.4	345	Cca/Gca	5/16	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.215642867420398	2		530	525	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260068	16260068	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	71	519	0	ENST00000375759.3:c.7333C>T	p.Gln2445Ter	p.Q2445*	ENST00000375759	NM_015001.2	2445	Caa/Taa	11/15	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.215642867420398	2		519	582	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8105964	8105964	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	54	422	0	ENST00000346208.3:c.784G>C	p.Glu262Gln	p.E262Q	ENST00000346208		262	Gag/Cag	4/6	1	2	FACETS	0.868	0.741	1	0.868	0.741	1	CLONAL	1	TRUE	1	0.215642867420398	2		422	577	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112760301	112760301	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	48	254	0	ENST00000369452.4:c.970G>C	p.Glu324Gln	p.E324Q	ENST00000369452	NM_007373.3	324	Gag/Cag	4/9	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.215642867420398	2		254	430	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122706	108122706	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	78	454	0	ENST00000278616.4:c.1750C>A	p.Gln584Lys	p.Q584K	ENST00000278616	NM_000051.3	584	Cag/Aag	11/63	0.210061217706384	4	FACETS	1	0.904	1			1	CLONAL	1	TRUE	NA	0.215642867420398	4		454	849	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842666	68842667	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	126	587	0	ENST00000261769.5:c.603dup	p.Val202CysfsTer7	p.V202Cfs*7	ENST00000261769	NM_004360.3	201	cct/ccTt	5/16	0.215642867420398	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.215642867420398	1		587	808	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46608737	46608737	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	79	628	0	ENST00000263734.3:c.2048C>A	p.Ser683Tyr	p.S683Y	ENST00000263734	NM_001430.4	683	tCt/tAt	13/16	1	2	FACETS	0.954	0.838	1	0.954	0.838	1	CLONAL	1	TRUE	1	0.215642867420398	2		628	768	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035134	37035134	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1553637356	NA	P-0035102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	44	334	0	ENST00000231790.2:c.96C>G	p.Ile32Met	p.I32M	ENST00000231790	NM_000249.3	32	atC/atG	1/19	1	2	FACETS	0.878	0.736	1	0.878	0.736	1	CLONAL	1	TRUE	1	0.215642867420398	2		334	465	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890252	72890252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	87	457	1	ENST00000325599.8:c.430C>T	p.Pro144Ser	p.P144S	ENST00000325599	NM_018130.2	144	Ccg/Tcg	4/11	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.215642867420398	2		458	802	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149498385	149498385	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	82	560	0	ENST00000261799.4:c.2829G>C	p.Glu943Asp	p.E943D	ENST00000261799	NM_002609.3	943	gaG/gaC	21/23	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.215642867420398	2		560	662	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858546	27858546	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	34	363	0	ENST00000359303.2:c.25C>G	p.Arg9Gly	p.R9G	ENST00000359303	NM_003535.2	9	Cgc/Ggc	1/1	1	2	FACETS	0.744	0.608	0.897	0.744	0.608	0.897	SUBCLONAL	1	TRUE	1	0.215642867420398	2		363	424	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555174	106555174	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	59	468	0	ENST00000369096.4:c.2291G>C	p.Arg764Thr	p.R764T	ENST00000369096	NM_001198.3	764	aGa/aCa	7/7	1	2	FACETS	0.871	0.749	1	0.871	0.749	1	CLONAL	1	TRUE	1	0.215642867420398	2		468	628	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859228	151859228	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	88	443	1	ENST00000262189.6:c.11434G>T	p.Glu3812Ter	p.E3812*	ENST00000262189	NM_170606.2	3812	Gag/Tag	43/59	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.215642867420398	2		444	731	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732894	44732894	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	52	441	0	ENST00000377967.4:c.97G>A	p.Glu33Lys	p.E33K	ENST00000377967	NM_021140.2	33	Gag/Aag	1/29	NA	2	FACETS	1	0.874	1			1	INDETERMINATE	1	TRUE	NA	0.215642867420398	2		441	469	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743943	40743943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs763964405	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	254	469	0	ENST00000373198.4:c.3052C>T	p.Arg1018Ter	p.R1018*	ENST00000373198	NM_133170.3	1018	Cga/Tga	23/32	0.294968381306107	4	FACETS	0.964	0.902	1	0.642	0.601	0.685	CLONAL	2	TRUE	1	0.334297154811356	4		469	1052	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	189	373	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.922	0.857	0.989	1	0.993	1	CLONAL	2	TRUE	1	0.334297154811356	2		373	613	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929041	32929041	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358930	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	265	559	0	ENST00000380152.3:c.7051G>A	p.Ala2351Thr	p.A2351T	ENST00000380152		2351	Gca/Aca	14/27	1	2	FACETS	0.92	0.864	0.976	1	0.995	1	CLONAL	2	TRUE	1	0.334297154811356	2		559	862	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911534	101911534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111426349	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	62	406	0	ENST00000374994.4:c.1459C>T	p.Arg487Trp	p.R487W	ENST00000374994	NM_004612.2	487	Cgg/Tgg	9/9	1	2	FACETS	0.584	0.504	0.671	0.584	0.504	0.671	SUBCLONAL	1	TRUE	1	0.334297154811356	2		406	635	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259477	89259477	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200567888	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	255	569	0	ENST00000336596.2:c.621G>T	p.Lys207Asn	p.K207N	ENST00000336596	NM_005233.5	207	aaG/aaT	3/17	1	2	FACETS	0.877	0.823	0.932	1	0.994	1	CLONAL	2	TRUE	1	0.334297154811356	2		569	870	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426123	138426123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217537873	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	247	420	0	ENST00000289153.2:c.1408G>A	p.Glu470Lys	p.E470K	ENST00000289153	NM_006219.2	470	Gaa/Aaa	9/22	1	2	FACETS	0.994	0.934	1	1	0.995	1	CLONAL	2	TRUE	1	0.334297154811356	2		420	743	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453486	138453486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451809865	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	236	445	0	ENST00000289153.2:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000289153	NM_006219.2	321	cGa/cAa	5/22	1	2	FACETS	0.964	0.904	1	1	0.994	1	CLONAL	2	TRUE	1	0.334297154811356	2		445	732	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242774	66242774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151302542	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	67	222	0	ENST00000273854.3:c.1798G>A	p.Glu600Lys	p.E600K	ENST00000273854	NM_004439.5	600	Gaa/Aaa	9/18	0.334297154811356	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.334297154811356	1		222	309	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509796	187509796	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777463346	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	54	278	1	ENST00000441802.2:c.13717G>A	p.Glu4573Lys	p.E4573K	ENST00000441802	NM_005245.3	4573	Gaa/Aaa	27/27	0.334297154811356	1	FACETS	0.743	0.637	0.858	0.743	0.637	0.858	SUBCLONAL	1	TRUE	0	0.334297154811356	1		279	362	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591278	67591278	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	75	374	0	ENST00000274335.5:c.1776G>T	p.Lys592Asn	p.K592N	ENST00000274335		592	aaG/aaT	13/15	1	2	FACETS	0.616	0.54	0.699	0.616	0.54	0.699	SUBCLONAL	1	TRUE	1	0.334297154811356	2		374	728	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971393	15971393	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759642635	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	316	604	0	ENST00000268712.3:c.4556C>T	p.Ser1519Leu	p.S1519L	ENST00000268712	NM_006311.3	1519	tCg/tTg	32/46	1	2	FACETS	0.942	0.89	0.994	1	0.996	1	CLONAL	2	TRUE	1	0.334297154811356	2		604	1004	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115600	108115600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772821016	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	81	615	0	ENST00000278616.4:c.748C>T	p.Arg250Ter	p.R250*	ENST00000278616	NM_000051.3	250	Cga/Tga	7/63	1	2	FACETS	0.519	0.456	0.587	0.519	0.456	0.587	SUBCLONAL	1	TRUE	1	0.334297154811356	2		615	933	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	154	340	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	0.974	0.899	1	1	0.992	1	CLONAL	2	TRUE	1	0.334297154811356	2		340	473	SUCCESS
APC	324	MSKCC	GRCh37	5	112177203	112177203	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs754691867	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	174	343	0	ENST00000257430.4:c.5912C>A	p.Ser1971Tyr	p.S1971Y	ENST00000257430	NM_000038.5	1971	tCt/tAt	16/16	1	2	FACETS	0.99	0.918	1	1	0.993	1	CLONAL	2	TRUE	1	0.334297154811356	2		343	526	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740264	162740264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756149068	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	140	340	0	ENST00000367921.3:c.1466G>A	p.Arg489Gln	p.R489Q	ENST00000367921	NM_006182.2	489	cGa/cAa	12/18	0.334297154811356	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.334297154811356	1		340	508	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598084	55598084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746503007	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	77	451	0	ENST00000288135.5:c.2281G>A	p.Glu761Lys	p.E761K	ENST00000288135	NM_000222.2	761	Gag/Aag	16/21	0.334297154811356	1	FACETS	0.523	0.459	0.593	0.523	0.459	0.593	SUBCLONAL	1	TRUE	0	0.334297154811356	1		451	733	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126757	5126757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775495966	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	165	414	0	ENST00000381652.3:c.3365G>A	p.Arg1122Gln	p.R1122Q	ENST00000381652	NM_004972.3	1122	cGa/cAa	25/25	1	2	FACETS	0.794	0.732	0.857	1	0.99	1	SUBCLONAL	2	TRUE	1	0.334297154811356	2		414	622	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938406	76938406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	154	429	0	ENST00000373344.5:c.2342G>A	p.Arg781Gln	p.R781Q	ENST00000373344	NM_000489.3	781	cGa/cAa	9/35	0.334297154811356	3	FACETS	0.983	0.898	1			1	CLONAL	1	TRUE	NA	0.334297154811356	3		429	1094	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718123	117718123	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	341	633	0	ENST00000368508.3:c.734G>T	p.Arg245Ile	p.R245I	ENST00000368508	NM_002944.2	245	aGa/aTa	7/43	1	2	FACETS	0.956	0.906	1	1	0.996	1	CLONAL	2	TRUE	1	0.334297154811356	2		633	1067	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710666	114710666	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	166	330	0	ENST00000543371.1:c.151G>T	p.Glu51Ter	p.E51*	ENST00000543371	NM_001198531.1	51	Gaa/Taa	1/14	1	2	FACETS	0.817	0.754	0.882	1	0.991	1	CLONAL	2	TRUE	1	0.334297154811356	2		330	608	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095626	178095626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750553272	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	103	545	0	ENST00000397062.3:c.1705C>T	p.Arg569Cys	p.R569C	ENST00000397062	NM_006164.4	569	Cgt/Tgt	5/5	1	2	FACETS	0.65	0.581	0.724	0.65	0.581	0.724	SUBCLONAL	1	TRUE	1	0.334297154811356	2		545	948	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841000	15841000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754101239	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	93	271	0	ENST00000307771.7:c.1084G>A	p.Glu362Lys	p.E362K	ENST00000307771	NM_005089.3	362	Gaa/Aaa	11/11	0.334297154811356	3	FACETS	0.834	0.741	0.933			1	CLONAL	1	TRUE	NA	0.334297154811356	3		271	779	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589618	67589618	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519838	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	106	223	1	ENST00000274335.5:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000274335		461	Cga/Tga	10/15	1	2	FACETS	0.807	0.729	0.888	1	0.985	1	CLONAL	2	TRUE	1	0.334297154811356	2		224	393	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624245	89624245	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554890335	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	139	216	0	ENST00000371953.3:c.19G>T	p.Glu7Ter	p.E7*	ENST00000371953	NM_000314.4	7	Gag/Tag	1/9	1	2	FACETS	1	0.966	1	1	0.992	1	CLONAL	2	TRUE	1	0.334297154811356	2		216	381	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059183	27059183	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	233	416	0	ENST00000324856.7:c.1820C>A	p.Ser607Ter	p.S607*	ENST00000324856	NM_006015.4	607	tCa/tAa	4/20	0.334297154811356	1	FACETS	0.903	0.847	0.959	1	0.994	1	CLONAL	2	TRUE	0	0.334297154811356	1		416	643	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004349	150004349	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	317	550	0	ENST00000253339.5:c.1876C>T	p.Arg626Ter	p.R626*	ENST00000253339		626	Cga/Tga	3/7	1	2	FACETS	0.986	0.932	1	1	0.996	1	CLONAL	2	TRUE	1	0.334297154811356	2		550	962	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934864	9934864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766162952	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	283	610	0	ENST00000330684.3:c.1426G>A	p.Asp476Asn	p.D476N	ENST00000330684	NM_001134407.1	476	Gac/Aac	6/13	1	2	FACETS	0.877	0.826	0.93	1	0.995	1	CLONAL	2	TRUE	1	0.334297154811356	2		610	965	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455151	50455151	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446212014	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	116	282	0	ENST00000331340.3:c.698C>T	p.Pro233Leu	p.P233L	ENST00000331340	NM_006060.4	233	cCg/cTg	6/8	1	2	FACETS	0.901	0.82	0.986	1	0.988	1	CLONAL	2	TRUE	1	0.334297154811356	2		282	385	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435088	18435088	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs777959749	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	301	355	0	ENST00000266497.5:c.73C>A	p.Leu25Ile	p.L25I	ENST00000266497		25	Ctc/Atc	1/31	0.334297154811356	3	FACETS	1	0.979	1	1	0.995	1	CLONAL	3	TRUE	1	0.334297154811356	3		355	663	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661672	227661672	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772676919	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	50	601	1	ENST00000305123.5:c.1783C>T	p.Arg595Trp	p.R595W	ENST00000305123	NM_005544.2	595	Cgg/Tgg	1/2	1	2	FACETS	0.394	0.333	0.461	0.394	0.333	0.461	SUBCLONAL	1	TRUE	1	0.334297154811356	2		602	759	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426835	70426835	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	163	394	0	ENST00000373644.4:c.4495C>A	p.Leu1499Ile	p.L1499I	ENST00000373644	NM_030625.2	1499	Ctt/Att	7/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.334297154811356	2		394	789	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609349	39609349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201418439	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	71	368	0	ENST00000262039.4:c.1651C>T	p.Arg551Trp	p.R551W	ENST00000262039	NM_002647.2	551	Cgg/Tgg	15/25	0.334297154811356	1	FACETS	0.572	0.5	0.651	0.572	0.5	0.651	SUBCLONAL	1	TRUE	0	0.334297154811356	1		368	618	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249857	133249857	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1565972665	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	307	357	0	ENST00000320574.5:c.1366G>C	p.Ala456Pro	p.A456P	ENST00000320574	NM_006231.2	456	Gcc/Ccc	14/49	0.334297154811356	3	FACETS	1	0.983	1	1	0.995	1	CLONAL	3	TRUE	1	0.334297154811356	3		357	665	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650879	37650879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs191899574	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	123	647	1	ENST00000447079.4:c.2351G>A	p.Arg784Gln	p.R784Q	ENST00000447079	NM_015083.1	784	cGa/cAa	5/14	1	2	FACETS	0.686	0.619	0.757	0.686	0.619	0.757	SUBCLONAL	1	TRUE	1	0.334297154811356	2		648	1073	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167750	185167750	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	85	496	0	ENST00000265026.3:c.1073C>A	p.Ser358Tyr	p.S358Y	ENST00000265026	NM_004721.4	358	tCt/tAt	6/14	1	2	FACETS	0.549	0.484	0.619	0.549	0.484	0.619	SUBCLONAL	1	TRUE	1	0.334297154811356	2		496	926	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404837	404837	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	116	530	0	ENST00000399788.2:c.4357G>A	p.Asp1453Asn	p.D1453N	ENST00000399788	NM_001042603.1	1453	Gat/Aat	26/28	0.334297154811356	3	FACETS	0.673	0.605	0.746	0.337	0.302	0.373	SUBCLONAL	1	TRUE	1	0.334297154811356	3		530	1203	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582935	95582935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs965350808	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	58	471	0	ENST00000393063.1:c.1607G>A	p.Arg536His	p.R536H	ENST00000393063	NM_030621.3	536	cGt/cAt	11/28	1	2	FACETS	0.46	0.394	0.531	0.46	0.394	0.531	SUBCLONAL	1	TRUE	1	0.334297154811356	2		471	755	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521884	157521884	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760245781	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	247	435	0	ENST00000346085.5:c.4156C>T	p.Arg1386Cys	p.R1386C	ENST00000346085	NM_020732.3	1386	Cgc/Tgc	18/20	1	2	FACETS	1	0.974	1	1	0.995	1	CLONAL	2	TRUE	1	0.334297154811356	2		435	694	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255845	16255845	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	50	359	0	ENST00000375759.3:c.3110G>A	p.Arg1037Lys	p.R1037K	ENST00000375759	NM_015001.2	1037	aGa/aAa	11/15	0.334297154811356	1	FACETS	0.445	0.377	0.519	0.445	0.377	0.519	SUBCLONAL	1	TRUE	0	0.334297154811356	1		359	560	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66520200	66520200	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	287	588	0	ENST00000358598.2:c.484G>A	p.Glu162Lys	p.E162K	ENST00000358598	NM_212471.2	162	Gag/Aag	5/11	1	2	FACETS	0.937	0.883	0.992	1	0.995	1	CLONAL	2	TRUE	1	0.334297154811356	2		588	916	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961459	41961459	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	304	552	0	ENST00000219905.7:c.367C>A	p.Leu123Ile	p.L123I	ENST00000219905	NM_001164273.1	123	Ctt/Att	2/24	1	2	FACETS	0.942	0.89	0.996	1	0.995	1	CLONAL	2	TRUE	1	0.334297154811356	2		552	965	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165729	108165729	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs762083530	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	66	399	0	ENST00000278616.4:c.4852C>T	p.Arg1618Ter	p.R1618*	ENST00000278616	NM_000051.3	1618	Cga/Tga	32/63	1	2	FACETS	0.55	0.477	0.63	0.55	0.477	0.63	SUBCLONAL	1	TRUE	1	0.334297154811356	2		399	718	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631341	117631341	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	72	435	0	ENST00000368508.3:c.6337G>T	p.Asp2113Tyr	p.D2113Y	ENST00000368508	NM_002944.2	2113	Gat/Tat	40/43	1	2	FACETS	0.641	0.56	0.729	0.641	0.56	0.729	SUBCLONAL	1	TRUE	1	0.334297154811356	2		435	672	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952013	178952013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	68	475	1	ENST00000263967.3:c.3068G>A	p.Arg1023Gln	p.R1023Q	ENST00000263967	NM_006218.2	1023	cGa/cAa	21/21	1	2	FACETS	0.54	0.469	0.617	0.54	0.469	0.617	SUBCLONAL	1	TRUE	1	0.334297154811356	2		476	754	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980735	70980735	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	43	580	0	ENST00000276594.2:c.733G>T	p.Asp245Tyr	p.D245Y	ENST00000276594	NM_024504.3	245	Gac/Tac	3/8	0.334297154811356	1	FACETS	0.273	0.227	0.323	0.273	0.227	0.323	SUBCLONAL	1	TRUE	0	0.334297154811356	1		580	786	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031691	69031691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748595305	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	82	566	0	ENST00000288368.4:c.3446G>A	p.Arg1149His	p.R1149H	ENST00000288368	NM_024870.2	1149	cGc/cAc	28/40	0.334297154811356	1	FACETS	0.495	0.436	0.559	0.495	0.436	0.559	SUBCLONAL	1	TRUE	0	0.334297154811356	1		566	825	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911655	134911655	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	67	381	0	ENST00000398015.3:c.2120C>A	p.Ser707Tyr	p.S707Y	ENST00000398015	NM_004441.4	707	tCt/tAt	11/16	1	2	FACETS	0.702	0.61	0.801	0.702	0.61	0.801	SUBCLONAL	1	TRUE	1	0.334297154811356	2		381	571	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67132676	67132676	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536749790	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	285	521	0	ENST00000412916.2:c.559C>T	p.Arg187Cys	p.R187C	ENST00000412916		187	Cgt/Tgt	6/6	1	2	FACETS	0.969	0.913	1	1	0.995	1	CLONAL	2	TRUE	1	0.334297154811356	2		521	880	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027747	152027747	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	455	771	0	ENST00000262189.6:c.328C>T	p.Arg110Ter	p.R110*	ENST00000262189	NM_170606.2	110	Cga/Tga	3/59	1	2	FACETS	0.992	0.947	1	1	0.997	1	CLONAL	2	TRUE	1	0.334297154811356	2		771	1372	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922251	100922251	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	60	378	2	ENST00000325455.5:c.2261C>A	p.Ser754Tyr	p.S754Y	ENST00000325455	NM_001202474.3	754	tCt/tAt	5/8	1	2	FACETS	0.529	0.455	0.609	0.529	0.455	0.609	SUBCLONAL	1	TRUE	1	0.334297154811356	2		380	679	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350734	89350734	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146294483	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1637	99	995	0	ENST00000301030.4:c.2216C>T	p.Ser739Leu	p.S739L	ENST00000301030	NM_001256183.1	739	tCg/tTg	9/13	1	2	FACETS	0.341	0.303	0.382	0.341	0.303	0.382	SUBCLONAL	1	TRUE	1	0.334297154811356	2		995	1736	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827388	72827388	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	126	861	0	ENST00000268489.5:c.9193G>T	p.Glu3065Ter	p.E3065*	ENST00000268489	NM_006885.3	3065	Gaa/Taa	9/10	1	2	FACETS	0.584	0.527	0.644	0.584	0.527	0.644	SUBCLONAL	1	TRUE	1	0.334297154811356	2		861	1291	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103322	119103322	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	243	510	1	ENST00000264033.4:c.360G>T	p.Glu120Asp	p.E120D	ENST00000264033	NM_005188.3	120	gaG/gaT	2/16	1	2	FACETS	0.857	0.803	0.913	1	0.994	1	CLONAL	2	TRUE	1	0.334297154811356	2		511	848	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749297	43749297	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs748115671	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	425	721	0	ENST00000382044.4:c.1509G>T	p.Lys503Asn	p.K503N	ENST00000382044	NM_001141980.1	503	aaG/aaT	12/28	1	2	FACETS	0.996	0.95	1	1	0.997	1	CLONAL	2	TRUE	1	0.334297154811356	2		721	1276	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465526	99465526	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	89	528	0	ENST00000268035.6:c.2351A>G	p.Asn784Ser	p.N784S	ENST00000268035	NM_000875.3	784	aAc/aGc	11/21	1	2	FACETS	0.602	0.533	0.677	0.602	0.533	0.677	SUBCLONAL	1	TRUE	1	0.334297154811356	2		528	884	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450609	70450609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759851979	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	213	377	0	ENST00000373644.4:c.5449G>A	p.Glu1817Lys	p.E1817K	ENST00000373644	NM_030625.2	1817	Gaa/Aaa	12/12	1	2	FACETS	0.9	0.84	0.962	1	0.993	1	CLONAL	2	TRUE	1	0.334297154811356	2		377	708	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907822	76907822	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	56	154	0	ENST00000373344.5:c.4339G>A	p.Glu1447Lys	p.E1447K	ENST00000373344	NM_000489.3	1447	Gag/Aag	15/35	0.334297154811356	3	FACETS	0.992	0.853	1			1	CLONAL	1	TRUE	NA	0.334297154811356	3		154	394	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956198	55956198	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	86	556	0	ENST00000263923.4:c.3117G>T	p.Lys1039Asn	p.K1039N	ENST00000263923	NM_002253.2	1039	aaG/aaT	23/30	0.334297154811356	1	FACETS	0.523	0.462	0.588	0.523	0.462	0.588	SUBCLONAL	1	TRUE	0	0.334297154811356	1		556	820	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112566	115112566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1298	142	807	0	ENST00000257566.3:c.1174G>A	p.Ala392Thr	p.A392T	ENST00000257566	NM_016569.3	392	Gcg/Acg	7/8	0.334297154811356	3	FACETS	0.689	0.625	0.755	0.344	0.312	0.378	SUBCLONAL	1	TRUE	1	0.334297154811356	3		807	1440	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812165	212812165	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	45	363	0	ENST00000342788.4:c.411G>T	p.Lys137Asn	p.K137N	ENST00000342788	NM_005235.2	137	aaG/aaT	3/28	1	2	FACETS	0.469	0.394	0.553	0.469	0.394	0.553	SUBCLONAL	1	TRUE	1	0.334297154811356	2		363	574	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647553	117647553	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	108	644	0	ENST00000368508.3:c.5391G>T	p.Gln1797His	p.Q1797H	ENST00000368508	NM_002944.2	1797	caG/caT	33/43	1	2	FACETS	0.618	0.553	0.687	0.618	0.553	0.687	SUBCLONAL	1	TRUE	1	0.334297154811356	2		644	1046	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961360	1961360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1047838051	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	74	586	0	ENST00000382891.5:c.3148G>A	p.Glu1050Lys	p.E1050K	ENST00000382891	NM_133335.3	1050	Gag/Aag	17/22	0.334297154811356	1	FACETS	0.397	0.347	0.452	0.397	0.347	0.452	SUBCLONAL	1	TRUE	0	0.334297154811356	1		586	928	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255367	16255367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763982034	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	138	459	0	ENST00000375759.3:c.2632G>A	p.Val878Met	p.V878M	ENST00000375759	NM_015001.2	878	Gtg/Atg	11/15	0.334297154811356	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.334297154811356	1		459	641	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39321554	39321554	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs756733917	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	156	446	0	ENST00000373001.3:c.467G>T	p.Arg156Ile	p.R156I	ENST00000373001	NM_022157.3	156	aGa/aTa	3/7	0.334297154811356	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.334297154811356	1		446	711	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749975	162749975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147604927	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	89	519	0	ENST00000367921.3:c.2507C>T	p.Thr836Met	p.T836M	ENST00000367921	NM_006182.2	836	aCg/aTg	18/18	0.334297154811356	1	FACETS	0.553	0.49	0.621	0.553	0.49	0.621	SUBCLONAL	1	TRUE	0	0.334297154811356	1		519	802	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104684	193104684	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	130	388	0	ENST00000367435.3:c.388G>T	p.Glu130Ter	p.E130*	ENST00000367435	NM_024529.4	130	Gaa/Taa	5/17	0.334297154811356	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.334297154811356	1		388	587	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736239	243736239	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	49	336	0	ENST00000263826.5:c.808C>T	p.Arg270Cys	p.R270C	ENST00000263826	NM_005465.4	270	Cgt/Tgt	8/13	0.334297154811356	1	FACETS	0.551	0.467	0.643	0.551	0.467	0.643	SUBCLONAL	1	TRUE	0	0.334297154811356	1		336	443	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711913	89711913	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs878853012	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	165	652	0	ENST00000371953.3:c.531T>G	p.Tyr177Ter	p.Y177*	ENST00000371953	NM_000314.4	177	taT/taG	6/9	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.334297154811356	2		652	922	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112769098	112769098	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	84	452	0	ENST00000369452.4:c.1377A>C	p.Lys459Asn	p.K459N	ENST00000369452	NM_007373.3	459	aaA/aaC	7/9	1	2	FACETS	0.635	0.56	0.715	0.635	0.56	0.715	SUBCLONAL	1	TRUE	1	0.334297154811356	2		452	792	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414232	32414232	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	230	441	0	ENST00000332351.3:c.1319G>T	p.Arg440Ile	p.R440I	ENST00000332351	NM_024426.4	440	aGa/aTa	8/10	1	2	FACETS	0.883	0.826	0.942	1	0.994	1	CLONAL	2	TRUE	1	0.334297154811356	2		441	779	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205313	61205313	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1300112394	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	305	562	0	ENST00000301761.2:c.253C>A	p.Leu85Ile	p.L85I	ENST00000301761	NM_017841.2	85	Ctt/Att	2/4	1	2	FACETS	1	0.948	1	1	0.996	1	CLONAL	2	TRUE	1	0.334297154811356	2		562	909	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988119	85988119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	266	510	0	ENST00000263360.6:c.1064G>A	p.Arg355Gln	p.R355Q	ENST00000263360	NM_003797.3	355	cGa/cAa	10/12	1	2	FACETS	0.93	0.874	0.986	1	0.995	1	CLONAL	2	TRUE	1	0.334297154811356	2		510	856	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118361991	118361991	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1472952558	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	98	395	0	ENST00000534358.1:c.4777C>T	p.Arg1593Cys	p.R1593C	ENST00000534358	NM_005933.3	1593	Cgc/Tgc	14/36	1	2	FACETS	0.737	0.657	0.823	0.737	0.657	0.823	SUBCLONAL	1	TRUE	1	0.334297154811356	2		395	795	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431455	121431455	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	106	542	0	ENST00000257555.6:c.659G>A	p.Arg220Lys	p.R220K	ENST00000257555		220	aGg/aAg	3/10	0.334297154811356	3	FACETS	0.666	0.595	0.741	0.333	0.297	0.371	SUBCLONAL	1	TRUE	1	0.334297154811356	3		542	1112	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012447	29012447	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	60	522	0	ENST00000282397.4:c.424A>C	p.Ile142Leu	p.I142L	ENST00000282397	NM_002019.4	142	Atc/Ctc	4/30	1	2	FACETS	0.403	0.346	0.465	0.403	0.346	0.465	SUBCLONAL	1	TRUE	1	0.334297154811356	2		522	891	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337737	73337737	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	137	214	0	ENST00000377767.4:c.1979A>G	p.Asn660Ser	p.N660S	ENST00000377767	NM_014953.3	660	aAt/aGt	16/21	1	2	FACETS	0.942	0.864	1	1	0.991	1	CLONAL	2	TRUE	1	0.334297154811356	2		214	435	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068968	30068968	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	316	637	0	ENST00000331968.5:c.1961G>T	p.Arg654Ile	p.R654I	ENST00000331968	NM_002742.2	654	aGa/aTa	14/18	1	2	FACETS	0.927	0.876	0.979	1	0.996	1	CLONAL	2	TRUE	1	0.334297154811356	2		637	1020	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105236736	105236736	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	236	679	0	ENST00000349310.3:c.1385A>G	p.Asp462Gly	p.D462G	ENST00000349310	NM_001014432.1	462	gAc/gGc	15/15	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.334297154811356	2		679	1110	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988603	41988603	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	169	488	0	ENST00000219905.7:c.1395G>T	p.Lys465Asn	p.K465N	ENST00000219905	NM_001164273.1	465	aaG/aaT	3/24	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.334297154811356	2		488	824	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701157	43701157	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	280	563	0	ENST00000382044.4:c.5538G>T	p.Gln1846His	p.Q1846H	ENST00000382044	NM_001141980.1	1846	caG/caT	26/28	1	2	FACETS	0.983	0.926	1	1	0.995	1	CLONAL	2	TRUE	1	0.334297154811356	2		563	852	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708548	43708548	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	409	754	0	ENST00000382044.4:c.4748G>T	p.Arg1583Ile	p.R1583I	ENST00000382044	NM_001141980.1	1583	aGa/aTa	22/28	1	2	FACETS	0.953	0.907	1	1	0.997	1	CLONAL	2	TRUE	1	0.334297154811356	2		754	1284	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748582	43748582	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	502	1071	0	ENST00000382044.4:c.2224G>T	p.Glu742Ter	p.E742*	ENST00000382044	NM_001141980.1	742	Gaa/Taa	12/28	1	2	FACETS	0.939	0.898	0.981	1	0.997	1	CLONAL	2	TRUE	1	0.334297154811356	2		1071	1599	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483943	88483943	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	105	680	0	ENST00000360948.2:c.1627G>T	p.Glu543Ter	p.E543*	ENST00000360948	NM_001012338.2	543	Gaa/Taa	14/19	1	2	FACETS	0.62	0.554	0.69	0.62	0.554	0.69	SUBCLONAL	1	TRUE	1	0.334297154811356	2		680	1013	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465378	99465378	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	52	297	0	ENST00000268035.6:c.2203C>T	p.Pro735Ser	p.P735S	ENST00000268035	NM_000875.3	735	Cct/Tct	11/21	1	2	FACETS	0.611	0.52	0.711	0.611	0.52	0.711	SUBCLONAL	1	TRUE	1	0.334297154811356	2		297	509	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925121	81925121	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs918438427	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	76	539	1	ENST00000359376.3:c.912G>T	p.Glu304Asp	p.E304D	ENST00000359376	NM_002661.3	304	gaG/gaT	11/33	1	2	FACETS	0.483	0.423	0.549	0.483	0.423	0.549	SUBCLONAL	1	TRUE	1	0.334297154811356	2		540	941	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350669	89350669	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1764	217	1090	0	ENST00000301030.4:c.2281T>G	p.Tyr761Asp	p.Y761D	ENST00000301030	NM_001256183.1	761	Tac/Gac	9/13	1	2	FACETS	0.655	0.607	0.706	0.655	0.607	0.706	SUBCLONAL	1	TRUE	1	0.334297154811356	2		1090	1981	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990631	7990631	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	300	570	0	ENST00000319144.4:c.130G>T	p.Asp44Tyr	p.D44Y	ENST00000319144	NM_001139.2	44	Gac/Tac	1/15	1	2	FACETS	0.873	0.823	0.924	1	0.995	1	CLONAL	2	TRUE	1	0.334297154811356	2		570	1028	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15967469	15967469	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	59	547	0	ENST00000268712.3:c.5134G>A	p.Ala1712Thr	p.A1712T	ENST00000268712	NM_006311.3	1712	Gct/Act	35/46	1	2	FACETS	0.392	0.336	0.453	0.392	0.336	0.453	SUBCLONAL	1	TRUE	1	0.334297154811356	2		547	900	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586089	29586089	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	189	550	0	ENST00000356175.3:c.4309G>T	p.Glu1437Ter	p.E1437*	ENST00000356175	NM_000267.3	1437	Gaa/Taa	32/57	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.334297154811356	2		550	928	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243927	41243927	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	357	729	0	ENST00000357654.3:c.3621G>T	p.Lys1207Asn	p.K1207N	ENST00000357654	NM_007294.3	1207	aaG/aaT	10/23	1	2	FACETS	0.976	0.926	1	1	0.996	1	CLONAL	2	TRUE	1	0.334297154811356	2		729	1094	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244942	41244942	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1192	142	786	0	ENST00000357654.3:c.2606T>G	p.Phe869Cys	p.F869C	ENST00000357654	NM_007294.3	869	tTt/tGt	10/23	1	2	FACETS	0.637	0.578	0.698	0.637	0.578	0.698	SUBCLONAL	1	TRUE	1	0.334297154811356	2		786	1334	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374971	45374971	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	99	563	0	ENST00000262160.6:c.872A>G	p.His291Arg	p.H291R	ENST00000262160	NM_005901.5	291	cAt/cGt	8/11	0.334297154811356	1	FACETS	0.582	0.519	0.65	0.582	0.519	0.65	SUBCLONAL	1	TRUE	0	0.334297154811356	1		563	847	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584519	48584519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	68	403	0	ENST00000342988.3:c.692G>A	p.Gly231Asp	p.G231D	ENST00000342988	NM_005359.5	231	gGc/gAc	6/12	0.334297154811356	1	FACETS	0.575	0.501	0.656	0.575	0.501	0.656	SUBCLONAL	1	TRUE	0	0.334297154811356	1		403	589	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917840	29917840	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	193	700	0	ENST00000389048.3:c.828T>G	p.Tyr276Ter	p.Y276*	ENST00000389048	NM_004304.4	276	taT/taG	3/29	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.334297154811356	2		700	1010	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39347481	39347481	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	72	416	0	ENST00000402219.2:c.83A>C	p.Lys28Thr	p.K28T	ENST00000402219	NM_005633.3	28	aAa/aCa	1/23	1	2	FACETS	0.647	0.565	0.735	0.647	0.565	0.735	SUBCLONAL	1	TRUE	1	0.334297154811356	2		416	666	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095884	178095884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	91	591	1	ENST00000397062.3:c.1447G>A	p.Glu483Lys	p.E483K	ENST00000397062	NM_006164.4	483	Gaa/Aaa	5/5	1	2	FACETS	0.587	0.52	0.659	0.587	0.52	0.659	SUBCLONAL	1	TRUE	1	0.334297154811356	2		592	927	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267451	198267451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	87	441	0	ENST00000335508.6:c.1906G>A	p.Ala636Thr	p.A636T	ENST00000335508	NM_012433.2	636	Gcc/Acc	14/25	1	2	FACETS	0.676	0.598	0.76	0.676	0.598	0.76	SUBCLONAL	1	TRUE	1	0.334297154811356	2		441	770	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202122998	202122998	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	73	466	0	ENST00000358485.4:c.44G>T	p.Arg15Ile	p.R15I	ENST00000358485	NM_001080125.1	15	aGa/aTa	1/9	1	2	FACETS	0.582	0.509	0.662	0.582	0.509	0.662	SUBCLONAL	1	TRUE	1	0.334297154811356	2		466	750	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209108234	209108234	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	93	579	0	ENST00000345146.2:c.615G>A	p.Trp205Ter	p.W205*	ENST00000345146	NM_005896.2	205	tgG/tgA	6/10	1	2	FACETS	0.538	0.477	0.603	0.538	0.477	0.603	SUBCLONAL	1	TRUE	1	0.334297154811356	2		579	1035	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523334	9523334	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	250	492	0	ENST00000353224.5:c.1903G>T	p.Glu635Ter	p.E635*	ENST00000353224	NM_177990.2	635	Gaa/Taa	9/10	0.294968381306107	4	FACETS	0.928	0.868	0.99	0.619	0.579	0.66	CLONAL	2	TRUE	1	0.334297154811356	4		492	1075	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743866	40743866	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	328	587	0	ENST00000373198.4:c.3129C>A	p.Tyr1043Ter	p.Y1043*	ENST00000373198	NM_133170.3	1043	taC/taA	23/32	0.294968381306107	4	FACETS	1	0.971	1	0.695	0.657	0.735	CLONAL	2	TRUE	1	0.334297154811356	4		587	1255	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944557	40944557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	57	484	0	ENST00000373198.4:c.1945C>T	p.Pro649Ser	p.P649S	ENST00000373198	NM_133170.3	649	Ccc/Tcc	12/32	0.294968381306107	4	FACETS	0.533	0.456	0.617	0.178	0.152	0.206	SUBCLONAL	1	TRUE	1	0.334297154811356	4		484	854	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39772513	39772513	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	74	537	0	ENST00000288319.7:c.728G>T	p.Arg243Ile	p.R243I	ENST00000288319	NM_182918.3	243	aGa/aTa	6/10	1	2	FACETS	0.501	0.438	0.57	0.501	0.438	0.57	SUBCLONAL	1	TRUE	1	0.334297154811356	2		537	883	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275276	41275276	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	220	436	0	ENST00000349496.5:c.1442C>T	p.Ala481Val	p.A481V	ENST00000349496	NM_001904.3	481	gCc/gTc	9/15	1	2	FACETS	1	0.942	1	1	0.994	1	CLONAL	2	TRUE	1	0.334297154811356	2		436	653	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162677	47162677	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	88	522	0	ENST00000409792.3:c.3449G>T	p.Arg1150Ile	p.R1150I	ENST00000409792	NM_014159.6	1150	aGa/aTa	3/21	1	2	FACETS	0.614	0.543	0.69	0.614	0.543	0.69	SUBCLONAL	1	TRUE	1	0.334297154811356	2		522	858	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49929245	49929245	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	361	764	1	ENST00000296474.3:c.3298G>T	p.Glu1100Ter	p.E1100*	ENST00000296474	NM_002447.2	1100	Gaa/Taa	15/20	1	2	FACETS	0.968	0.918	1	1	0.996	1	CLONAL	2	TRUE	1	0.334297154811356	2		765	1116	SUCCESS
ATR	545	MSKCC	GRCh37	3	142257331	142257331	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	236	440	0	ENST00000350721.4:c.3718G>T	p.Glu1240Ter	p.E1240*	ENST00000350721	NM_001184.3	1240	Gaa/Taa	19/47	1	2	FACETS	0.96	0.9	1	1	0.994	1	CLONAL	2	TRUE	1	0.334297154811356	2		440	735	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279115	142279115	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	72	399	0	ENST00000350721.4:c.1531A>C	p.Asn511His	p.N511H	ENST00000350721	NM_001184.3	511	Aac/Cac	6/47	1	2	FACETS	0.617	0.539	0.702	0.617	0.539	0.702	SUBCLONAL	1	TRUE	1	0.334297154811356	2		399	698	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919111	178919111	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	29	310	0	ENST00000263967.3:c.596C>A	p.Ser199Tyr	p.S199Y	ENST00000263967	NM_006218.2	199	tCt/tAt	4/21	1	2	FACETS	0.314	0.251	0.386	0.314	0.251	0.386	SUBCLONAL	1	TRUE	1	0.334297154811356	2		310	553	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191451	185191451	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	144	717	1	ENST00000265026.3:c.2332G>T	p.Glu778Ter	p.E778*	ENST00000265026	NM_004721.4	778	Gaa/Taa	11/14	1	2	FACETS	0.734	0.668	0.804	0.734	0.668	0.804	SUBCLONAL	1	TRUE	1	0.334297154811356	2		718	1173	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981172	55981172	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	98	561	0	ENST00000263923.4:c.527G>T	p.Arg176Ile	p.R176I	ENST00000263923	NM_002253.2	176	aGa/aTa	5/30	0.334297154811356	1	FACETS	0.613	0.547	0.684	0.613	0.547	0.684	SUBCLONAL	1	TRUE	0	0.334297154811356	1		561	796	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539736	187539736	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1400631217	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	172	510	1	ENST00000441802.2:c.8004C>A	p.Phe2668Leu	p.F2668L	ENST00000441802	NM_005245.3	2668	ttC/ttA	10/27	0.334297154811356	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.334297154811356	1		511	674	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950571	38950571	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs577991926	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	120	622	0	ENST00000357387.3:c.3379A>G	p.Ser1127Gly	p.S1127G	ENST00000357387	NM_152756.3	1127	Agc/Ggc	31/38	1	2	FACETS	0.724	0.653	0.8	0.724	0.653	0.8	SUBCLONAL	1	TRUE	1	0.334297154811356	2		622	991	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176993	56176993	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	95	457	0	ENST00000399503.3:c.2263C>A	p.Leu755Ile	p.L755I	ENST00000399503	NM_005921.1	755	Ctt/Att	13/20	1	2	FACETS	0.689	0.613	0.77	0.689	0.613	0.77	SUBCLONAL	1	TRUE	1	0.334297154811356	2		457	825	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753027	57753027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1192733931	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	202	427	0	ENST00000274289.3:c.989G>A	p.Arg330Gln	p.R330Q	ENST00000274289	NM_006622.3	330	cGa/cAa	7/14	1	2	FACETS	0.931	0.867	0.996	1	0.993	1	CLONAL	2	TRUE	1	0.334297154811356	2		427	649	SUCCESS
APC	324	MSKCC	GRCh37	5	112090654	112090654	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	90	291	0	ENST00000257430.4:c.67C>A	p.Leu23Ile	p.L23I	ENST00000257430	NM_000038.5	23	Ctt/Att	2/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.334297154811356	2		291	445	SUCCESS
APC	324	MSKCC	GRCh37	5	112116529	112116529	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	165	286	1	ENST00000257430.4:c.574G>T	p.Glu192Ter	p.E192*	ENST00000257430	NM_000038.5	192	Gaa/Taa	6/16	1	2	FACETS	0.919	0.85	0.991	1	0.992	1	CLONAL	2	TRUE	1	0.334297154811356	2		287	537	SUCCESS
APC	324	MSKCC	GRCh37	5	112177403	112177403	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	53	338	0	ENST00000257430.4:c.6112C>A	p.Leu2038Met	p.L2038M	ENST00000257430	NM_000038.5	2038	Ctg/Atg	16/16	1	2	FACETS	0.623	0.531	0.723	0.623	0.531	0.723	SUBCLONAL	1	TRUE	1	0.334297154811356	2		338	509	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401593	401593	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	71	493	0	ENST00000380956.4:c.915G>T	p.Glu305Asp	p.E305D	ENST00000380956	NM_001195286.1	305	gaG/gaT	7/9	1	2	FACETS	0.627	0.547	0.714	0.627	0.547	0.714	SUBCLONAL	1	TRUE	1	0.334297154811356	2		493	677	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405061	405061	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	236	466	0	ENST00000380956.4:c.1143C>A	p.Phe381Leu	p.F381L	ENST00000380956	NM_001195286.1	381	ttC/ttA	8/9	1	2	FACETS	0.946	0.887	1	1	0.994	1	CLONAL	2	TRUE	1	0.334297154811356	2		466	746	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964441	93964441	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1348945329	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	97	647	0	ENST00000369303.4:c.2456T>C	p.Val819Ala	p.V819A	ENST00000369303	NM_004440.3	819	gTa/gCa	14/17	1	2	FACETS	0.597	0.531	0.668	0.597	0.531	0.668	SUBCLONAL	1	TRUE	1	0.334297154811356	2		647	972	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683872	117683872	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	205	639	0	ENST00000368508.3:c.3275G>T	p.Ser1092Ile	p.S1092I	ENST00000368508	NM_002944.2	1092	aGt/aTt	21/43	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.334297154811356	2		639	1000	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708103	117708103	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	227	505	0	ENST00000368508.3:c.2074A>C	p.Asn692His	p.N692H	ENST00000368508	NM_002944.2	692	Aat/Cat	14/43	1	2	FACETS	0.872	0.815	0.93	1	0.994	1	CLONAL	2	TRUE	1	0.334297154811356	2		505	779	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997741	149997741	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	255	427	0	ENST00000253339.5:c.2726C>A	p.Ser909Tyr	p.S909Y	ENST00000253339		909	tCt/tAt	5/7	1	2	FACETS	1	0.945	1	1	0.995	1	CLONAL	2	TRUE	1	0.334297154811356	2		427	759	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001560	150001560	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	258	515	0	ENST00000253339.5:c.2044A>G	p.Arg682Gly	p.R682G	ENST00000253339		682	Aga/Gga	4/7	1	2	FACETS	0.885	0.831	0.941	1	0.994	1	CLONAL	2	TRUE	1	0.334297154811356	2		515	872	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151174437	151174437	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	66	381	0	ENST00000262187.5:c.257C>A	p.Ser86Tyr	p.S86Y	ENST00000262187	NM_005614.3	86	tCt/tAt	4/8	1	2	FACETS	0.508	0.44	0.582	0.508	0.44	0.582	SUBCLONAL	1	TRUE	1	0.334297154811356	2		381	777	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38178654	38178654	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	121	574	0	ENST00000317025.8:c.1745G>T	p.Arg582Ile	p.R582I	ENST00000317025	NM_023034.1	582	aGa/aTa	8/24	0.334297154811356	1	FACETS	0.647	0.584	0.714	0.647	0.584	0.714	SUBCLONAL	1	TRUE	0	0.334297154811356	1		574	932	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995501	68995501	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1326956245	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	115	608	0	ENST00000288368.4:c.1905G>T	p.Lys635Asn	p.K635N	ENST00000288368	NM_024870.2	635	aaG/aaT	18/40	0.334297154811356	1	FACETS	0.644	0.579	0.712	0.644	0.579	0.712	SUBCLONAL	1	TRUE	0	0.334297154811356	1		608	890	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202911	27202911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	321	650	0	ENST00000380036.4:c.2003C>T	p.Ser668Phe	p.S668F	ENST00000380036	NM_000459.3	668	tCt/tTt	13/23	1	2	FACETS	0.97	0.918	1	1	0.996	1	CLONAL	2	TRUE	1	0.334297154811356	2		650	990	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206730	27206730	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	88	578	1	ENST00000380036.4:c.2515C>A	p.Leu839Ile	p.L839I	ENST00000380036	NM_000459.3	839	Ctt/Att	15/23	1	2	FACETS	0.634	0.56	0.712	0.634	0.56	0.712	SUBCLONAL	1	TRUE	1	0.334297154811356	2		579	831	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209460	98209460	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	260	603	0	ENST00000331920.6:c.4078T>A	p.Ser1360Thr	p.S1360T	ENST00000331920	NM_000264.3	1360	Tcc/Acc	23/24	1	2	FACETS	0.922	0.866	0.979	1	0.995	1	CLONAL	2	TRUE	1	0.334297154811356	2		603	844	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939692	76939692	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	121	365	0	ENST00000373344.5:c.1056G>T	p.Met352Ile	p.M352I	ENST00000373344	NM_000489.3	352	atG/atT	9/35	0.334297154811356	3	FACETS	0.768	0.692	0.848			1	SUBCLONAL	1	TRUE	NA	0.334297154811356	3		365	1100	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123041020	123041020	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	37	67	0	ENST00000355640.3:c.1483T>G	p.Phe495Val	p.F495V	ENST00000355640		495	Ttt/Gtt	7/7	0.334297154811356	3	FACETS	0.99	0.847	1			1	CLONAL	3	TRUE	NA	0.334297154811356	3		67	87	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0035104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	56	384	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.734	0.627	0.851	0.734	0.627	0.851	SUBCLONAL	1	TRUE	1	0.17	2		384	898	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0035104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	39	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.0787431696945987	3	FACETS	0.749	0.619	0.894	0.374	0.309	0.447	INDETERMINATE	1	TRUE	1	0.17	3		539	665	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0035104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	66	463	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.982	0.851	1	0.982	0.851	1	CLONAL	1	TRUE	1	0.17	2		463	791	SUCCESS
APC	324	MSKCC	GRCh37	5	112175755	112175755	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	23	248	0	ENST00000257430.4:c.4464del	p.Leu1488PhefsTer19	p.L1488Ffs*19	ENST00000257430	NM_000038.5	1488	ttA/tt	16/16	0.138932280559682	3	FACETS	0.663	0.516	0.834	0.331	0.258	0.417	SUBCLONAL	1	TRUE	1	0.17	3		248	443	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0035104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	29	303	1	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.555	0.444	0.682	0.555	0.444	0.682	SUBCLONAL	1	TRUE	1	0.17	2		304	615	SUCCESS
APC	324	MSKCC	GRCh37	5	112173730	112173730	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	27	294	1	ENST00000257430.4:c.2442del	p.Phe814LeufsTer6	p.F814Lfs*6	ENST00000257430	NM_000038.5	813	aaT/aa	16/16	0.138932280559682	3	FACETS	0.753	0.598	0.93	0.376	0.299	0.465	CLONAL	1	TRUE	1	0.17	3		295	458	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481620	56481620	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	78	565	0	ENST00000267101.3:c.655T>C	p.Phe219Leu	p.F219L	ENST00000267101	NM_001982.3	219	Ttt/Ctt	6/28	0.0787431696945987	3	FACETS	1	0.957	1	0.603	0.529	0.683	INDETERMINATE	1	TRUE	1	0.17	3		565	826	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223325	2223325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	51	538	2	ENST00000326181.6:c.937G>A	p.Ala313Thr	p.A313T	ENST00000326181	NM_032271.2	313	Gcc/Acc	10/21	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.17	2		540	591	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982987	201982987	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	93	552	0	ENST00000359651.3:c.836T>C	p.Ile279Thr	p.I279T	ENST00000359651		279	aTc/aCc	7/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.17	2		552	817	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579732	7579873	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGAGCAGAAAGTCAGTCCCATGGAATTTTCGCTTCCCACAGGTCTCTGCTAGGGGGCTGGGGTTGGGGTGGGGGTGGTGGGCCTGCCCTTCCAATGGATCCACTCACAGTTTCCATAGGTCTGAAAATGTTTCCTGACTCAG	AGAGCAGAAAGTCAGTCCCATGGAATTTTCGCTTCCCACAGGTCTCTGCTAGGGGGCTGGGGTTGGGGTGGGGGTGGTGGGCCTGCCCTTCCAATGGATCCACTCACAGTTTCCATAGGTCTGAAAATGTTTCCTGACTCAG	-	novel	NA	P-0035104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	34	450	0	ENST00000269305.4:c.40_75-11del		p.X14_splice	ENST00000269305	NM_001126112.2	14		2/11	1	2	FACETS	0.673	0.549	0.814	0.673	0.549	0.814	SUBCLONAL	1	TRUE	1	0.17	2		450	594	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117677	70117677	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	142	507	2	ENST00000245479.2:c.145C>T	p.Gln49Ter	p.Q49*	ENST00000245479	NM_000346.3	49	Cag/Tag	1/3	1	2	FACETS	0.853	0.779	0.929	1	0.992	1	CLONAL	3	TRUE	1	0.17	2		509	653	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530132	212530132	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	40	335	0	ENST00000342788.4:c.1787G>T	p.Gly596Val	p.G596V	ENST00000342788	NM_005235.2	596	gGc/gTc	15/28	1	2	FACETS	0.763	0.633	0.908	0.763	0.633	0.908	CLONAL	1	TRUE	1	0.17	2		335	617	SUCCESS
APC	324	MSKCC	GRCh37	5	112173388	112173388	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1060503282	NA	P-0035104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	20	228	0	ENST00000257430.4:c.2097G>A	p.Trp699Ter	p.W699*	ENST00000257430	NM_000038.5	699	tgG/tgA	16/16	0.138932280559682	3	FACETS	0.698	0.533	0.891	0.349	0.266	0.446	SUBCLONAL	1	TRUE	1	0.17	3		228	366	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944382	131944385	+	frameshift_variant	Frame_Shift_Del	DEL	AAAA	AAAA	-	novel	NA	P-0035104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	19	189	0	ENST00000265335.6:c.2798_2801del	p.Lys933IlefsTer6	p.K933Ifs*6	ENST00000265335		932	AAAAaa/aa	17/25	0.138932280559682	3	FACETS	0.668	0.506	0.859	0.334	0.253	0.43	SUBCLONAL	1	TRUE	1	0.17	3		189	363	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910659	29910659	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	78	729	0	ENST00000376809.5:c.199C>T	p.Gln67Ter	p.Q67*	ENST00000376809	NM_002116.7	67	Cag/Tag	2/8	0.0787431696945987	3	FACETS	0.925	0.811	1	0.463	0.405	0.525	INDETERMINATE	1	TRUE	1	0.17	3		729	1076	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15378248	15378248	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	44	598	0	ENST00000263377.2:c.538G>T	p.Gly180Ter	p.G180*	ENST00000263377	NM_058243.2	180	Gga/Tga	4/20	1	2	FACETS	0.724	0.606	0.856	0.724	0.606	0.856	SUBCLONAL	1	TRUE	1	0.17	2		598	715	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12043910	12043910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772935596	NA	P-0035122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	135	371	0	ENST00000396373.4:c.1289G>A	p.Arg430Gln	p.R430Q	ENST00000396373	NM_001987.4	430	cGa/cAa	8/8	0.836678296040939	8	FACETS	1	0.956	1	0.429	0.392	0.468	CLONAL	2	FALSE	3	0.836678296040939	8		371	528	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513371	106513371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765080806	NA	P-0035122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	64	282	0	ENST00000359195.3:c.2275G>A	p.Val759Ile	p.V759I	ENST00000359195	NM_002649.2	759	Gtc/Atc	4/11	0.836678296040939	3	FACETS	0.893	0.783	1	0.446	0.391	0.505	CLONAL	1	FALSE	1	0.836678296040939	3		282	243	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873744	35873745	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0035122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	560	514	0	ENST00000216797.5:c.106_107del	p.Ser36HisfsTer49	p.S36Hfs*49	ENST00000216797	NM_020529.2	36	TCc/c	1/6	0.781184717377351	4	FACETS	0.91	0.875	0.945	0.91	0.875	0.945	CLONAL	2	FALSE	2	0.836678296040939	4		514	1351	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50830381	50830381	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	134	434	0	ENST00000398568.2:c.2824T>C	p.Cys942Arg	p.C942R	ENST00000398568	NM_001042412.1	942	Tgc/Cgc	18/18	0.824943186948148	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	FALSE	0	0.836678296040939	2		434	155	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876593	59876593	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202780	NA	P-0035122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	165	500	0	ENST00000259008.2:c.1208G>A	p.Arg403Gln	p.R403Q	ENST00000259008	NM_032043.2	403	cGg/cAg	9/20	0.836678296040939	4	FACETS	0.879	0.817	0.942	0.879	0.817	0.942	CLONAL	2	FALSE	2	0.836678296040939	4		500	412	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38975651	38975651	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	95	624	0	ENST00000357387.3:c.877C>T	p.Arg293Ter	p.R293*	ENST00000357387	NM_152756.3	293	Cga/Tga	10/38	0.243272682290435	3	FACETS	0.866	0.777	0.959	0.289	0.259	0.32	INDETERMINATE	1	FALSE	0	0.836678296040939	3		624	372	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519990	NA	P-0035124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	93	545	0	ENST00000269305.4:c.796G>C	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Cga	8/11	0.207316329872497	1	FACETS	0.845	0.75	0.946	0.845	0.75	0.946	CLONAL	1	FALSE	0	0.22394959351391	1		545	873	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215970	41215970	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	rs80358066	NA	P-0035124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	34	342	0	ENST00000357654.3:c.5075-2A>C		p.X1692_splice	ENST00000357654	NM_007294.3	1692			0.207316329872497	1	FACETS	0.667	0.545	0.804	0.667	0.545	0.804	SUBCLONAL	1	FALSE	0	0.22394959351391	1		342	404	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221959	1221959	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	56	727	0	ENST00000326873.7:c.874T>G	p.Tyr292Asp	p.Y292D	ENST00000326873	NM_000455.4	292	Tac/Gac	7/10	1	2	FACETS	0.47	0.401	0.545	0.47	0.401	0.545	SUBCLONAL	1	FALSE	1	0.22394959351391	2		727	1065	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	158	349	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.584553436434234	2		349	454	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0035126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	284	384	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.965	0.908	1	0.965	0.908	1	CLONAL	1	TRUE	1	0.584553436434234	2		384	1007	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0035126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	476	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.584553436434234	2	FACETS	0.941	0.907	0.976	0.941	0.907	0.976	CLONAL	2	TRUE	0	0.584553436434234	2		539	865	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682781	190682781	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	155	334	0	ENST00000441310.2:c.457C>T	p.Pro153Ser	p.P153S	ENST00000441310	NM_000534.4	153	Cct/Tct	5/13	1	2	FACETS	0.937	0.862	1	0.937	0.862	1	CLONAL	1	TRUE	1	0.584553436434234	2		334	566	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819725	170819725	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	97	182	0	ENST00000296930.5:c.364G>C	p.Asp122His	p.D122H	ENST00000296930	NM_002520.6	122	Gat/Cat	5/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.584553436434234	2		182	300	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916143	9916143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762659685	NA	P-0035131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	155	497	0	ENST00000330684.3:c.2146G>A	p.Ala716Thr	p.A716T	ENST00000330684	NM_001134407.1	716	Gcc/Acc	10/13	1	2	FACETS	0.945	0.876	1	0.945	0.876	1	CLONAL	1	FALSE	1	0.870346233919682	2		497	377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578474	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	333	752	0	ENST00000269305.4:c.456del	p.Gly154AlafsTer16	p.G154Afs*16	ENST00000269305	NM_001126112.2	152	ccG/cc	5/11	0.870346233919682	1	FACETS	0.924	0.891	0.955	0.924	0.891	0.955	CLONAL	1	FALSE	0	0.870346233919682	1		752	468	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28885786	28885786	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	118	441	0	ENST00000282397.4:c.3576C>A	p.Asp1192Glu	p.D1192E	ENST00000282397	NM_002019.4	1192	gaC/gaA	27/30	0.870346233919682	1	FACETS	0.906	0.85	0.959	0.906	0.85	0.959	CLONAL	1	FALSE	0	0.870346233919682	1		441	169	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	15	349	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.839	0.63	1	0.839	0.63	1	CLONAL	1	TRUE	1	0.56765247914856	2		349	63	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0035134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	90	713	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.878	0.786	0.976	0.878	0.786	0.976	CLONAL	1	TRUE	1	0.56765247914856	2		713	361	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578211	226578211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147537486	NA	P-0035134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	58	597	0	ENST00000366794.5:c.517C>T	p.Arg173Trp	p.R173W	ENST00000366794	NM_001618.3	173	Cgg/Tgg	4/23	0.425070878663326	3	FACETS	0.917	0.795	1	0.459	0.397	0.525	CLONAL	1	TRUE	1	0.56765247914856	3		597	286	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230661	46230661	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	112	563	0	ENST00000334344.6:c.910A>G	p.Lys304Glu	p.K304E	ENST00000334344	NM_152641.2	304	Aag/Gag	8/21	0.143661656636498	3	FACETS	1	0.981	1	0.667	0.605	0.73	INDETERMINATE	1	TRUE	1	0.56765247914856	3		563	380	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233144	46233144	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs994352749	NA	P-0035134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	62	362	0	ENST00000334344.6:c.1363C>T	p.Gln455Ter	p.Q455*	ENST00000334344	NM_152641.2	455	Cag/Tag	11/21	0.143661656636498	3	FACETS	1	0.918	1	0.535	0.467	0.608	INDETERMINATE	1	TRUE	1	0.56765247914856	3		362	262	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245192	46245192	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	73	491	0	ENST00000334344.6:c.3286C>T	p.Gln1096Ter	p.Q1096*	ENST00000334344	NM_152641.2	1096	Cag/Tag	15/21	0.143661656636498	3	FACETS	0.771	0.686	0.86	0.771	0.686	0.86	INDETERMINATE	2	TRUE	1	0.56765247914856	3		491	214	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582908	95582908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1344891057	NA	P-0035134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	100	486	0	ENST00000393063.1:c.1634C>T	p.Ser545Phe	p.S545F	ENST00000393063	NM_030621.3	545	tCc/tTc	11/28	1	2	FACETS	0.96	0.865	1	0.96	0.865	1	CLONAL	1	TRUE	1	0.56765247914856	2		486	367	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005440	42005440	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	65	669	0	ENST00000219905.7:c.3176C>T	p.Ser1059Phe	p.S1059F	ENST00000219905	NM_001164273.1	1059	tCc/tTc	9/24	0.550880856549754	3	FACETS	0.726	0.632	0.827	0.363	0.316	0.414	SUBCLONAL	1	TRUE	1	0.56765247914856	3		669	405	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0035134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	123	638	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	0.56765247914856	3	FACETS	0.94	0.864	1	0.94	0.864	1	CLONAL	2	TRUE	1	0.56765247914856	3		638	296	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526122	189526122	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193287780	NA	P-0035134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	57	566	0	ENST00000264731.3:c.386C>T	p.Ser129Leu	p.S129L	ENST00000264731	NM_003722.4	129	tCg/tTg	4/14	1	2	FACETS	0.837	0.726	0.955	0.837	0.726	0.955	CLONAL	1	TRUE	1	0.56765247914856	2		566	240	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980367	55980367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778428	NA	P-0035134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	74	514	0	ENST00000263923.4:c.724C>T	p.Leu242Phe	p.L242F	ENST00000263923	NM_002253.2	242	Ctt/Ttt	6/30	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.56765247914856	2		514	242	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526835	31526835	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780968053	NA	P-0035134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	71	769	0	ENST00000344624.3:c.205C>T	p.Pro69Ser	p.P69S	ENST00000344624		69	Ccc/Tcc	2/33	1	2	FACETS	0.951	0.84	1	0.951	0.84	1	CLONAL	1	TRUE	1	0.56765247914856	2		769	263	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562448	176562448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770893683	NA	P-0035134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	92	776	0	ENST00000439151.2:c.344C>T	p.Ser115Phe	p.S115F	ENST00000439151	NM_022455.4	115	tCc/tTc	2/23	1	2	FACETS	0.951	0.853	1	0.951	0.853	1	CLONAL	1	TRUE	1	0.56765247914856	2		776	341	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562849	176562849	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	68	551	1	ENST00000439151.2:c.745G>A	p.Glu249Lys	p.E249K	ENST00000439151	NM_022455.4	249	Gaa/Aaa	2/23	1	2	FACETS	0.761	0.667	0.86	0.761	0.667	0.86	SUBCLONAL	1	TRUE	1	0.56765247914856	2		552	315	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964323	70964323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	34	412	0	ENST00000276594.2:c.1705G>A	p.Glu569Lys	p.E569K	ENST00000276594	NM_024504.3	569	Gaa/Aaa	8/8	0.216972869683778	1	FACETS	0.584	0.484	0.691	0.584	0.484	0.691	INDETERMINATE	1	TRUE	0	0.56765247914856	1		412	147	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93607806	93607806	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	59	421	0	ENST00000375746.1:c.508C>T	p.His170Tyr	p.H170Y	ENST00000375746	NM_001174167.1	170	Cat/Tat	3/14	0.16962550793845	0	FACETS	0.494	0.433	0.558			1	INDETERMINATE	1	TRUE	0	0.56765247914856	0		421	182	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0035135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	282	562	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.284868037635287	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.390779871697079	4		562	980	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0035135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	170	537	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.390779871697079	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.390779871697079	1		537	635	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	57	349	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.45352356610526	2		349	248	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0035136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	92	256	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	0.45352356610526	2		256	388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934874	NA	P-0035136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	27	705	1	ENST00000269305.4:c.451C>A	p.Pro151Thr	p.P151T	ENST00000269305	NM_001126112.2	151	Ccc/Acc	5/11	1	2	FACETS	0.167	0.132	0.207	0.167	0.132	0.207	SUBCLONAL	1	TRUE	1	0.45352356610526	2		706	714	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632331	1632334	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CCGG	CCGG	-	novel	NA	P-0035136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	87	719	0	ENST00000344749.5:c.216_219del	p.Ser72ArgfsTer48	p.S72Rfs*48	ENST00000344749	NM_001136139.2	72	agCCGG/ag	4/19	1	2	FACETS	0.522	0.462	0.586	0.522	0.462	0.586	SUBCLONAL	1	TRUE	1	0.45352356610526	2		719	735	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098811	47098811	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	51	715	0	ENST00000409792.3:c.6463C>T	p.Leu2155Phe	p.L2155F	ENST00000409792	NM_014159.6	2155	Ctt/Ttt	15/21	1	2	FACETS	0.306	0.26	0.358	0.306	0.26	0.358	SUBCLONAL	1	TRUE	1	0.45352356610526	2		715	734	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926888	112926888	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397507546	NA	P-0035139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	83	630	2	ENST00000351677.2:c.1508G>T	p.Gly503Val	p.G503V	ENST00000351677	NM_002834.3	503	gGg/gTg	13/16	1	2	FACETS	0.827	0.729	0.931	0.827	0.729	0.931	CLONAL	1	TRUE	1	0.282400710707232	2		632	711	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710625	114710625	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	72	425	0	ENST00000543371.1:c.110C>G	p.Ala37Gly	p.A37G	ENST00000543371	NM_001198531.1	37	gCa/gGa	1/14	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.282400710707232	2		425	482	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606123	81606123	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	68	546	0	ENST00000298171.2:c.793C>T	p.Leu265Phe	p.L265F	ENST00000298171	NM_000369.2	265	Ctt/Ttt	9/10	1	2	FACETS	0.779	0.678	0.889	0.779	0.678	0.889	SUBCLONAL	1	TRUE	1	0.282400710707232	2		546	618	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95556978	95556978	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	100	542	1	ENST00000393063.1:c.5626G>T	p.Gly1876Trp	p.G1876W	ENST00000393063	NM_030621.3	1876	Ggg/Tgg	28/28	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.282400710707232	2		543	676	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858407	89858407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757760966	NA	P-0035139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	116	695	0	ENST00000389301.3:c.1153C>T	p.His385Tyr	p.H385Y	ENST00000389301	NM_000135.2	385	Cac/Tac	13/43	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.282400710707232	2		695	771	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161673	47161673	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	82	233	0	ENST00000409792.3:c.4453del	p.Arg1485GlufsTer30	p.R1485Efs*30	ENST00000409792	NM_014159.6	1485	Aga/ga	3/21	0.282400710707232	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	2	TRUE	0	0.282400710707232	2		233	288	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911406	39911406	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs867019053	NA	P-0035139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	126	548	0	ENST00000378444.4:c.5224G>T	p.Glu1742Ter	p.E1742*	ENST00000378444	NM_001123385.1	1742	Gag/Tag	15/15	0.282400710707232	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.282400710707232	1		548	623	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039903	47039903	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	99	782	0	ENST00000377604.3:c.1246C>T	p.Gln416Ter	p.Q416*	ENST00000377604	NM_001204468.1	416	Cag/Tag	12/24	0.282400710707232	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.282400710707232	1		782	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577557	7577557	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519982	NA	P-0035142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	38	613	2	ENST00000269305.4:c.724T>A	p.Cys242Ser	p.C242S	ENST00000269305	NM_001126112.2	242	Tgc/Agc	7/11	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.208721225341566	2		615	332	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17129606	17129606	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	43	734	0	ENST00000285071.4:c.280G>T	p.Gly94Ter	p.G94*	ENST00000285071	NM_144997.5	94	Gga/Tga	5/14	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.208721225341566	2		734	341	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231103	46231103	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0035142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	32	422	0	ENST00000334344.6:c.1024-1G>T		p.X342_splice	ENST00000334344	NM_152641.2	342			1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.208721225341566	2		422	260	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665451	176665451	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	15	482	0	ENST00000439151.2:c.4135C>G	p.Pro1379Ala	p.P1379A	ENST00000439151	NM_022455.4	1379	Ccg/Gcg	7/23	1	2	FACETS	0.489	0.357	0.648	0.489	0.357	0.648	SUBCLONAL	1	TRUE	1	0.208721225341566	2		482	294	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470594	25470594	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs755769867	NA	P-0035142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	21	651	0	ENST00000264709.3:c.880G>T	p.Glu294Ter	p.E294*	ENST00000264709	NM_175629.2	294	Gag/Tag	8/23	1	2	FACETS	0.737	0.568	0.933	0.737	0.568	0.933	CLONAL	1	TRUE	1	0.208721225341566	2		651	273	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099344	27099344	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	17	605	0	ENST00000324856.7:c.3581G>C	p.Gly1194Ala	p.G1194A	ENST00000324856	NM_006015.4	1194	gGa/gCa	14/20	1	2	FACETS	0.558	0.416	0.726	0.558	0.416	0.726	SUBCLONAL	1	TRUE	1	0.208721225341566	2		605	292	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251899	8251899	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	29	663	0	ENST00000335790.3:c.178G>T	p.Glu60Ter	p.E60*	ENST00000335790	NM_002315.2	60	Gag/Tag	2/4	1	2	FACETS	1	0.816	1	1	0.816	1	CLONAL	1	TRUE	1	0.208721225341566	2		663	274	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69207402	69207402	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	14	348	0	ENST00000462284.1:c.168G>C	p.Met56Ile	p.M56I	ENST00000462284	NM_002392.5	56	atG/atC	3/11	1	2	FACETS	0.486	0.351	0.65	0.486	0.351	0.65	SUBCLONAL	1	TRUE	1	0.208721225341566	2		348	276	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112482	115112482	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	23	634	0	ENST00000257566.3:c.1258G>T	p.Glu420Ter	p.E420*	ENST00000257566	NM_016569.3	420	Gag/Tag	7/8	1	2	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	TRUE	1	0.208721225341566	2		634	200	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831714	72831714	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	32	671	0	ENST00000268489.5:c.4867A>G	p.Lys1623Glu	p.K1623E	ENST00000268489	NM_006885.3	1623	Aag/Gag	9/10	1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	1	0.208721225341566	2		671	295	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968852	15968852	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	22	581	0	ENST00000268712.3:c.4898G>C	p.Arg1633Thr	p.R1633T	ENST00000268712	NM_006311.3	1633	aGa/aCa	33/46	1	2	FACETS	0.565	0.437	0.714	0.565	0.437	0.714	SUBCLONAL	1	TRUE	1	0.208721225341566	2		581	373	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441516	40441516	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	39	738	1	ENST00000345506.4:c.87G>T	p.Glu29Asp	p.E29D	ENST00000345506	NM_003152.3	29	gaG/gaT	3/20	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.208721225341566	2		739	267	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419981	41419981	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	20	522	0	ENST00000373198.4:c.340A>T	p.Arg114Trp	p.R114W	ENST00000373198	NM_133170.3	114	Agg/Tgg	3/32	1	2	FACETS	0.687	0.526	0.875	0.687	0.526	0.875	SUBCLONAL	1	TRUE	1	0.208721225341566	2		522	279	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713335	30713335	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	29	442	0	ENST00000295754.5:c.661del	p.Glu221LysfsTer43	p.E221Kfs*43	ENST00000295754	NM_003242.5	220	ctG/ct	4/7	1	2	FACETS	1	0.811	1	1	0.811	1	CLONAL	1	TRUE	1	0.208721225341566	2		442	276	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903760	41903760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142862109	NA	P-0035142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	18	620	0	ENST00000372991.4:c.797C>T	p.Ala266Val	p.A266V	ENST00000372991	NM_001760.3	266	gCg/gTg	5/5	1	2	FACETS	0.713	0.537	0.919	0.713	0.537	0.919	CLONAL	1	TRUE	1	0.208721225341566	2		620	242	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340184	116340184	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	36	329	1	ENST00000397752.3:c.1046G>T	p.Ser349Ile	p.S349I	ENST00000397752	NM_000245.2	349	aGc/aTc	2/21	0.179803371293257	3	FACETS	1	0.95	1	0.741	0.613	0.883	CLONAL	1	TRUE	1	0.208721225341566	3		330	257	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978544	70978544	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	21	570	0	ENST00000276594.2:c.1109A>T	p.Tyr370Phe	p.Y370F	ENST00000276594	NM_024504.3	370	tAt/tTt	5/8	0.208721225341566	1	FACETS	0.699	0.539	0.884	0.699	0.539	0.884	SUBCLONAL	1	TRUE	0	0.208721225341566	1		570	258	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391352	139391352	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	13	706	0	ENST00000277541.6:c.6839C>G	p.Ser2280Cys	p.S2280C	ENST00000277541	NM_017617.3	2280	tCt/tGt	34/34	1	2	FACETS	0.496	0.354	0.671	0.496	0.354	0.671	SUBCLONAL	1	TRUE	1	0.208721225341566	2		706	251	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413096	63413096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	25	378	0	ENST00000330258.3:c.71C>T	p.Thr24Ile	p.T24I	ENST00000330258	NM_152424.3	24	aCa/aTa	2/2	1	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.208721225341566	1		378	156	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	74	746	0	ENST00000397752.3:c.3028G>C	p.Asp1010His	p.D1010H	ENST00000397752	NM_000245.2	1010	Gat/Cat	14/21	1	2	FACETS	0.958	0.836	1	0.958	0.836	1	CLONAL	1	TRUE	1	0.14	2		746	1104	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93973590	93973590	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	36	410	2	ENST00000369303.4:c.1786C>A	p.Leu596Ile	p.L596I	ENST00000369303	NM_004440.3	596	Ctt/Att	9/17	1	2	FACETS	0.993	0.815	1	0.993	0.815	1	CLONAL	1	TRUE	1	0.14	2		412	518	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	109	589	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.883	0.792	0.979	0.883	0.792	0.979	CLONAL	1	TRUE	1	0.28	2		589	882	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	87	554	1	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	0.152359903317228	1	FACETS	0.816	0.723	0.915	0.816	0.723	0.915	INDETERMINATE	1	TRUE	0	0.28	1		555	655	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453486	138453486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451809865	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	36	445	0	ENST00000289153.2:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000289153	NM_006219.2	321	cGa/cAa	5/22	1	2	FACETS	0.784	0.646	0.937	0.784	0.646	0.937	CLONAL	1	TRUE	1	0.28	2		445	328	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	39	340	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	0.967	0.806	1	0.967	0.806	1	CLONAL	1	TRUE	1	0.28	2		340	288	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775722	9775722	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	110	731	0	ENST00000377346.4:c.265C>A	p.Leu89Met	p.L89M	ENST00000377346	NM_005026.3	89	Ctg/Atg	4/24	1	2	FACETS	0.783	0.702	0.869	0.783	0.702	0.869	SUBCLONAL	1	TRUE	1	0.28	2		731	1004	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217325	11217325	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	104	691	0	ENST00000361445.4:c.4353G>T	p.Glu1451Asp	p.E1451D	ENST00000361445	NM_004958.3	1451	gaG/gaT	30/58	1	2	FACETS	0.825	0.738	0.918	0.825	0.738	0.918	CLONAL	1	TRUE	1	0.28	2		691	900	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307755	11307755	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	92	581	0	ENST00000361445.4:c.1152G>T	p.Lys384Asn	p.K384N	ENST00000361445	NM_004958.3	384	aaG/aaT	8/58	1	2	FACETS	0.809	0.718	0.906	0.809	0.718	0.906	CLONAL	1	TRUE	1	0.28	2		581	812	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255862	16255862	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	65	399	0	ENST00000375759.3:c.3127G>T	p.Glu1043Ter	p.E1043*	ENST00000375759	NM_015001.2	1043	Gaa/Taa	11/15	1	2	FACETS	0.819	0.71	0.936	0.819	0.71	0.936	CLONAL	1	TRUE	1	0.28	2		399	567	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106364	27106364	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	87	601	0	ENST00000324856.7:c.5975C>A	p.Ser1992Ter	p.S1992*	ENST00000324856	NM_006015.4	1992	tCa/tAa	20/20	1	2	FACETS	0.741	0.655	0.833	0.741	0.655	0.833	SUBCLONAL	1	TRUE	1	0.28	2		601	839	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366955	40366955	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	54	543	1	ENST00000397332.2:c.242C>A	p.Ala81Glu	p.A81E	ENST00000397332	NM_001033082.2	81	gCa/gAa	2/3	1	2	FACETS	0.706	0.603	0.819	0.706	0.603	0.819	SUBCLONAL	1	TRUE	1	0.28	2		544	546	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058628	72058628	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	76	550	0	ENST00000357731.5:c.812T>G	p.Ile271Ser	p.I271S	ENST00000357731	NM_173808.2	271	aTt/aGt	6/7	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.28	2		550	520	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261278	115261278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	74	540	0	ENST00000438362.2:c.2443C>T	p.Arg815Cys	p.R815C	ENST00000438362	NM_001242891.1	815	Cgc/Tgc	19/20	1	2	FACETS	0.694	0.606	0.788	0.694	0.606	0.788	SUBCLONAL	1	TRUE	1	0.28	2		540	762	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273024	115273024	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	96	618	0	ENST00000438362.2:c.1349G>T	p.Arg450Ile	p.R450I	ENST00000438362	NM_001242891.1	450	aGa/aTa	12/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.28	2		618	551	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156836706	156836706	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	101	717	0	ENST00000524377.1:c.364C>A	p.Leu122Ile	p.L122I	ENST00000524377	NM_002529.3	122	Ctc/Atc	4/17	1	2	FACETS	0.692	0.617	0.772	0.692	0.617	0.772	SUBCLONAL	1	TRUE	1	0.28	2		717	1043	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851255	156851255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1480681042	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	74	556	0	ENST00000524377.1:c.2212G>A	p.Asp738Asn	p.D738N	ENST00000524377	NM_002529.3	738	Gac/Aac	17/17	1	2	FACETS	0.747	0.653	0.847	0.747	0.653	0.847	SUBCLONAL	1	TRUE	1	0.28	2		556	708	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741993	162741993	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	77	467	0	ENST00000367921.3:c.1684C>A	p.Leu562Ile	p.L562I	ENST00000367921	NM_006182.2	562	Ctc/Atc	13/18	1	2	FACETS	0.835	0.733	0.944	0.835	0.733	0.944	CLONAL	1	TRUE	1	0.28	2		467	659	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850642	63850642	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	27	300	0	ENST00000279873.7:c.1420G>T	p.Glu474Ter	p.E474*	ENST00000279873	NM_032199.2	474	Gaa/Taa	10/10	1	2	FACETS	0.554	0.441	0.683	0.554	0.441	0.683	SUBCLONAL	1	TRUE	1	0.28	2		300	348	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852632	63852632	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	100	605	0	ENST00000279873.7:c.3410C>A	p.Ser1137Tyr	p.S1137Y	ENST00000279873	NM_032199.2	1137	tCt/tAt	10/10	1	2	FACETS	0.876	0.782	0.977	0.876	0.782	0.977	CLONAL	1	TRUE	1	0.28	2		605	815	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852688	63852688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779001361	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	105	644	0	ENST00000279873.7:c.3466G>A	p.Asp1156Asn	p.D1156N	ENST00000279873	NM_032199.2	1156	Gac/Aac	10/10	1	2	FACETS	0.867	0.776	0.964	0.867	0.776	0.964	CLONAL	1	TRUE	1	0.28	2		644	865	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624244	89624244	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	35	216	0	ENST00000371953.3:c.18A>C	p.Lys6Asn	p.K6N	ENST00000371953	NM_000314.4	6	aaA/aaC	1/9	1	2	FACETS	0.926	0.763	1	0.926	0.763	1	CLONAL	1	TRUE	1	0.28	2		216	270	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	59	310	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.28	2		310	401	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720870	89720870	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1554825652	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	56	247	0	ENST00000371953.3:c.1021T>G	p.Phe341Val	p.F341V	ENST00000371953	NM_000314.4	341	Ttt/Gtt	8/9	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.28	2		247	281	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161456	2161456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs970922682	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	115	597	0	ENST00000434045.2:c.71G>A	p.Arg24His	p.R24H	ENST00000434045	NM_001127598.1	24	cGc/cAc	2/5	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.28	2		597	802	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456400	32456400	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	68	577	0	ENST00000332351.3:c.492T>G	p.Phe164Leu	p.F164L	ENST00000332351	NM_024426.4	164	ttT/ttG	1/10	1	2	FACETS	0.736	0.64	0.84	0.736	0.64	0.84	SUBCLONAL	1	TRUE	1	0.28	2		577	660	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588217	69588217	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	71	576	0	ENST00000168712.1:c.481C>A	p.Leu161Ile	p.L161I	ENST00000168712	NM_002007.2	161	Ctc/Atc	3/3	1	2	FACETS	0.71	0.619	0.809	0.71	0.619	0.809	SUBCLONAL	1	TRUE	1	0.28	2		576	714	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94923009	94923009	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	70	600	0	ENST00000536441.1:c.459A>C	p.Lys153Asn	p.K153N	ENST00000536441	NM_144665.3	153	aaA/aaC	4/10	1	2	FACETS	0.96	0.838	1	0.96	0.838	1	CLONAL	1	TRUE	1	0.28	2		600	521	SUCCESS
ATM	472	MSKCC	GRCh37	11	108154992	108154992	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786203618	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	54	518	0	ENST00000278616.4:c.3785G>T	p.Arg1262Ile	p.R1262I	ENST00000278616	NM_000051.3	1262	aGa/aTa	26/63	1	2	FACETS	0.95	0.814	1	0.95	0.814	1	CLONAL	1	TRUE	1	0.28	2		518	406	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203492	108203492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs138941496	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	85	273	0	ENST00000278616.4:c.7792C>T	p.Arg2598Ter	p.R2598*	ENST00000278616	NM_000051.3	2598	Cga/Tga	53/63	1	2	FACETS	0.876	0.788	0.967	1	0.988	1	CLONAL	3	TRUE	1	0.28	2		273	231	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342513	118342513	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	11	236	0	ENST00000534358.1:c.639A>C	p.Lys213Asn	p.K213N	ENST00000534358	NM_005933.3	213	aaA/aaC	3/36	1	2	FACETS	0.393	0.271	0.544	0.393	0.271	0.544	SUBCLONAL	1	TRUE	1	0.28	2		236	200	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170426	119170426	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1435757249	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	78	453	1	ENST00000264033.4:c.2656G>A	p.Glu886Lys	p.E886K	ENST00000264033	NM_005188.3	886	Gag/Aag	16/16	1	2	FACETS	0.806	0.708	0.912	0.806	0.708	0.912	CLONAL	1	TRUE	1	0.28	2		454	691	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552648	18552648	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	78	622	0	ENST00000266497.5:c.2059G>T	p.Glu687Ter	p.E687*	ENST00000266497		687	Gaa/Taa	14/31	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.28	2		622	519	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793408	18793408	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	41	518	2	ENST00000266497.5:c.4105C>T	p.Leu1369Phe	p.L1369F	ENST00000266497		1369	Ctt/Ttt	30/31	1	2	FACETS	0.669	0.557	0.792	0.669	0.557	0.792	SUBCLONAL	1	TRUE	1	0.28	2		520	438	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445674	49445674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778514296	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	168	977	0	ENST00000301067.7:c.1792C>T	p.Arg598Cys	p.R598C	ENST00000301067	NM_003482.3	598	Cgt/Tgt	10/54	1	2	FACETS	0.901	0.826	0.98	0.901	0.826	0.98	CLONAL	1	TRUE	1	0.28	2		977	1332	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109794	115109794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772126133	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	68	566	0	ENST00000257566.3:c.2084G>A	p.Arg695His	p.R695H	ENST00000257566	NM_016569.3	695	cGc/cAc	8/8	1	2	FACETS	0.657	0.571	0.751	0.657	0.571	0.751	SUBCLONAL	1	TRUE	1	0.28	2		566	739	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	82	548	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	0.714	0.629	0.806	0.714	0.629	0.806	SUBCLONAL	1	TRUE	1	0.28	2		548	820	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878170	48878170	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	14	99	0	ENST00000267163.4:c.122A>G	p.Asp41Gly	p.D41G	ENST00000267163	NM_000321.2	41	gAc/gGc	1/27	1	2	FACETS	0.769	0.56	1	0.769	0.56	1	CLONAL	1	TRUE	1	0.28	2		99	130	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103513972	103513972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61749896	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	36	405	0	ENST00000355739.4:c.788G>A	p.Arg263Gln	p.R263Q	ENST00000355739	NM_000123.3	263	cGa/cAa	7/15	1	2	FACETS	0.656	0.54	0.786	0.656	0.54	0.786	SUBCLONAL	1	TRUE	1	0.28	2		405	392	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515211	103515211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759628522	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	46	392	0	ENST00000355739.4:c.1712C>T	p.Pro571Leu	p.P571L	ENST00000355739	NM_000123.3	571	cCg/cTg	8/15	1	2	FACETS	0.733	0.618	0.86	0.733	0.618	0.86	SUBCLONAL	1	TRUE	1	0.28	2		392	448	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396458	30396458	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	29	283	0	ENST00000331968.5:c.261G>T	p.Gln87His	p.Q87H	ENST00000331968	NM_002742.2	87	caG/caT	1/18	1	2	FACETS	0.658	0.529	0.804	0.658	0.529	0.804	SUBCLONAL	1	TRUE	1	0.28	2		283	315	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353744	68353744	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs371376587	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	40	337	0	ENST00000487270.1:c.579A>C	p.Glu193Asp	p.E193D	ENST00000487270	NM_133509.3	193	gaA/gaC	7/11	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.28	2		337	257	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023106	33023106	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	52	429	0	ENST00000300177.4:c.215A>C	p.Glu72Ala	p.E72A	ENST00000300177	NM_001191322.1	72	gAg/gCg	2/2	1	2	FACETS	0.827	0.705	0.96	0.827	0.705	0.96	CLONAL	1	TRUE	1	0.28	2		429	449	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3799632	3799632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267606752	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	58	505	0	ENST00000262367.5:c.3832G>A	p.Glu1278Lys	p.E1278K	ENST00000262367	NM_004380.2	1278	Gaa/Aaa	21/31	1	2	FACETS	0.88	0.757	1	0.88	0.757	1	CLONAL	1	TRUE	1	0.28	2		505	471	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3824685	3824685	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	90	449	0	ENST00000262367.5:c.2168C>A	p.Ser723Ter	p.S723*	ENST00000262367	NM_004380.2	723	tCa/tAa	12/31	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.28	2		449	625	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647640	23647640	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	51	417	0	ENST00000261584.4:c.227T>C	p.Ile76Thr	p.I76T	ENST00000261584	NM_024675.3	76	aTa/aCa	4/13	1	2	FACETS	0.813	0.692	0.945	0.813	0.692	0.945	CLONAL	1	TRUE	1	0.28	2		417	448	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67132649	67132649	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	67	606	0	ENST00000412916.2:c.532T>G	p.Leu178Val	p.L178V	ENST00000412916		178	Tta/Gta	6/6	1	2	FACETS	0.835	0.726	0.953	0.835	0.726	0.953	CLONAL	1	TRUE	1	0.28	2		606	573	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844181	68844181	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	97	675	0	ENST00000261769.5:c.769G>T	p.Asp257Tyr	p.D257Y	ENST00000261769	NM_004360.3	257	Gac/Tac	6/16	1	2	FACETS	0.811	0.722	0.906	0.811	0.722	0.906	CLONAL	1	TRUE	1	0.28	2		675	854	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011200	12011200	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	45	397	0	ENST00000353533.5:c.607G>T	p.Glu203Ter	p.E203*	ENST00000353533	NM_003010.3	203	Gaa/Taa	5/11	0.230562071670125	3	FACETS	1	0.846	1	0.502	0.423	0.589	CLONAL	1	TRUE	1	0.28	3		397	365	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661910	29661910	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	84	607	0	ENST00000356175.3:c.5804T>G	p.Leu1935Arg	p.L1935R	ENST00000356175	NM_000267.3	1935	cTa/cGa	39/57	0.152359903317228	1	FACETS	1	0.886	1	1	0.886	1	INDETERMINATE	1	TRUE	0	0.28	1		607	516	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40490816	40490816	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	82	485	0	ENST00000264657.5:c.483A>C	p.Lys161Asn	p.K161N	ENST00000264657	NM_139276.2	161	aaA/aaC	6/24	0.152359903317228	1	FACETS	0.949	0.838	1	0.949	0.838	1	INDETERMINATE	1	TRUE	0	0.28	1		485	531	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761387	59761387	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs886053214	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	36	607	0	ENST00000259008.2:c.3020C>A	p.Ser1007Tyr	p.S1007Y	ENST00000259008	NM_032043.2	1007	tCt/tAt	20/20	0.152359903317228	1	FACETS	0.393	0.322	0.472	0.393	0.322	0.472	INDETERMINATE	1	TRUE	0	0.28	1		607	563	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763515	59763515	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876660452	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	49	554	0	ENST00000259008.2:c.2587T>C	p.Trp863Arg	p.W863R	ENST00000259008	NM_032043.2	863	Tgg/Cgg	19/20	0.152359903317228	1	FACETS	0.798	0.678	0.93	0.798	0.678	0.93	INDETERMINATE	1	TRUE	0	0.28	1		554	377	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853881	59853881	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	55	472	1	ENST00000259008.2:c.1978C>A	p.Leu660Ile	p.L660I	ENST00000259008	NM_032043.2	660	Ctc/Atc	14/20	0.152359903317228	1	FACETS	0.828	0.71	0.956	0.828	0.71	0.956	INDETERMINATE	1	TRUE	0	0.28	1		473	408	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609382	39609382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1463795009	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	64	361	0	ENST00000262039.4:c.1684G>A	p.Glu562Lys	p.E562K	ENST00000262039	NM_002647.2	562	Gaa/Aaa	15/25	1	2	FACETS	0.72	0.623	0.825	0.72	0.623	0.825	SUBCLONAL	1	TRUE	1	0.28	2		361	635	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284964	15284964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	104	619	0	ENST00000263388.2:c.4651G>A	p.Gly1551Ser	p.G1551S	ENST00000263388	NM_000435.2	1551	Ggc/Agc	25/33	1	2	FACETS	0.802	0.717	0.893	0.802	0.717	0.893	CLONAL	1	TRUE	1	0.28	2		619	926	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375267	15375267	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs368786412	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	100	640	0	ENST00000263377.2:c.1160T>C	p.Leu387Pro	p.L387P	ENST00000263377	NM_058243.2	387	cTa/cCa	6/20	1	2	FACETS	0.794	0.708	0.885	0.794	0.708	0.885	SUBCLONAL	1	TRUE	1	0.28	2		640	900	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965460	25965460	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	106	773	0	ENST00000435504.4:c.3746T>A	p.Leu1249Gln	p.L1249Q	ENST00000435504		1249	cTg/cAg	13/13	1	2	FACETS	0.722	0.646	0.804	0.722	0.646	0.804	SUBCLONAL	1	TRUE	1	0.28	2		773	1048	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99203950	99203950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755469992	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	55	373	0	ENST00000074304.5:c.2813G>A	p.Arg938Gln	p.R938Q	ENST00000074304	NM_001134224.1	938	cGa/cAa	26/26	1	2	FACETS	0.907	0.778	1	0.907	0.778	1	CLONAL	1	TRUE	1	0.28	2		373	433	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096261	178096261	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	102	608	1	ENST00000397062.3:c.1070C>T	p.Pro357Leu	p.P357L	ENST00000397062	NM_006164.4	357	cCa/cTa	5/5	1	2	FACETS	0.927	0.829	1	0.927	0.829	1	CLONAL	1	TRUE	1	0.28	2		609	786	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682825	190682825	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	75	489	0	ENST00000441310.2:c.501T>A	p.Asp167Glu	p.D167E	ENST00000441310	NM_000534.4	167	gaT/gaA	5/13	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.28	2		489	441	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131315	202131315	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	64	504	0	ENST00000358485.4:c.283G>T	p.Glu95Ter	p.E95*	ENST00000358485	NM_001080125.1	95	Gaa/Taa	2/9	1	2	FACETS	0.742	0.642	0.85	0.742	0.642	0.85	SUBCLONAL	1	TRUE	1	0.28	2		504	616	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419841	41419841	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	76	401	1	ENST00000373198.4:c.480C>A	p.Phe160Leu	p.F160L	ENST00000373198	NM_133170.3	160	ttC/ttA	3/32	1	2	FACETS	0.949	0.833	1	0.949	0.833	1	CLONAL	1	TRUE	1	0.28	2		402	572	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46275971	46275971	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	91	544	0	ENST00000371998.3:c.3407A>C	p.Asn1136Thr	p.N1136T	ENST00000371998		1136	aAc/aCc	18/23	1	2	FACETS	0.876	0.778	0.981	0.876	0.778	0.981	CLONAL	1	TRUE	1	0.28	2		544	742	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12393128	12393128	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	40	572	0	ENST00000287820.6:c.37G>T	p.Glu13Ter	p.E13*	ENST00000287820	NM_015869.4	13	Gaa/Taa	1/7	1	2	FACETS	0.438	0.363	0.522	0.438	0.363	0.522	SUBCLONAL	1	TRUE	1	0.28	2		572	652	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162904	47162904	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs757432733	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	62	502	0	ENST00000409792.3:c.3222G>T	p.Lys1074Asn	p.K1074N	ENST00000409792	NM_014159.6	1074	aaG/aaT	3/21	1	2	FACETS	0.834	0.721	0.956	0.834	0.721	0.956	CLONAL	1	TRUE	1	0.28	2		502	531	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165319	47165319	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	62	526	0	ENST00000409792.3:c.807A>C	p.Gln269His	p.Q269H	ENST00000409792	NM_014159.6	269	caA/caC	3/21	1	2	FACETS	0.9	0.779	1	0.9	0.779	1	CLONAL	1	TRUE	1	0.28	2		526	492	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405962	49405962	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	97	456	0	ENST00000418115.1:c.176A>G	p.Asp59Gly	p.D59G	ENST00000418115	NM_001664.2	59	gAc/gGc	3/5	1	2	FACETS	0.893	0.796	0.996	0.893	0.796	0.996	CLONAL	1	TRUE	1	0.28	2		456	776	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682438	52682438	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	84	494	0	ENST00000394830.3:c.735T>G	p.Ile245Met	p.I245M	ENST00000394830	NM_018313.4	245	atT/atG	8/30	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.28	2		494	485	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72866502	72866502	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757958098	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	54	369	0	ENST00000325599.8:c.761G>A	p.Arg254Gln	p.R254Q	ENST00000325599	NM_018130.2	254	cGa/cAa	7/11	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.28	2		369	379	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73113266	73113266	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	22	189	0	ENST00000356692.5:c.607A>C	p.Asn203His	p.N203H	ENST00000356692		203	Aat/Cat	7/9	1	2	FACETS	0.741	0.577	0.93	0.741	0.577	0.93	CLONAL	1	TRUE	1	0.28	2		189	212	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468507	89468507	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	38	338	1	ENST00000336596.2:c.2041A>T	p.Asn681Tyr	p.N681Y	ENST00000336596	NM_005233.5	681	Aat/Tat	11/17	1	2	FACETS	0.83	0.688	0.987	0.83	0.688	0.987	CLONAL	1	TRUE	1	0.28	2		339	327	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374245	138374245	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	73	585	0	ENST00000289153.2:c.3199G>T	p.Asp1067Tyr	p.D1067Y	ENST00000289153	NM_006219.2	1067	Gac/Tac	22/22	1	2	FACETS	0.692	0.604	0.786	0.692	0.604	0.786	SUBCLONAL	1	TRUE	1	0.28	2		585	754	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260177	149260177	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	105	611	0	ENST00000360632.3:c.716G>T	p.Arg239Ile	p.R239I	ENST00000360632	NM_015472.4	239	aGa/aTa	4/7	1	2	FACETS	0.89	0.796	0.989	0.89	0.796	0.989	CLONAL	1	TRUE	1	0.28	2		611	843	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127355	55127355	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	68	637	0	ENST00000257290.5:c.143G>T	p.Arg48Ile	p.R48I	ENST00000257290	NM_006206.4	48	aGa/aTa	3/23	1	2	FACETS	0.62	0.539	0.709	0.62	0.539	0.709	SUBCLONAL	1	TRUE	1	0.28	2		637	783	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946206	55946206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	96	498	0	ENST00000263923.4:c.3973G>A	p.Glu1325Lys	p.E1325K	ENST00000263923	NM_002253.2	1325	Gaa/Aaa	30/30	1	2	FACETS	0.874	0.778	0.976	0.874	0.778	0.976	CLONAL	1	TRUE	1	0.28	2		498	785	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189918	66189918	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	69	370	0	ENST00000273854.3:c.3028G>A	p.Val1010Met	p.V1010M	ENST00000273854	NM_004439.5	1010	Gtg/Atg	18/18	1	2	FACETS	0.914	0.797	1	0.914	0.797	1	CLONAL	1	TRUE	1	0.28	2		370	539	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467768	66467768	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	42	506	0	ENST00000273854.3:c.501G>T	p.Lys167Asn	p.K167N	ENST00000273854	NM_004439.5	167	aaG/aaT	3/18	1	2	FACETS	0.641	0.535	0.758	0.641	0.535	0.758	SUBCLONAL	1	TRUE	1	0.28	2		506	468	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142950056	142950056	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568595082	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	37	462	2	ENST00000262992.4:c.2654G>A	p.Arg885His	p.R885H	ENST00000262992	NM_001101669.1	885	cGc/cAc	24/24	1	2	FACETS	0.701	0.579	0.837	0.701	0.579	0.837	SUBCLONAL	1	TRUE	1	0.28	2		464	377	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539951	187539951	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs777631605	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	76	445	0	ENST00000441802.2:c.7789C>T	p.Arg2597Ter	p.R2597*	ENST00000441802	NM_005245.3	2597	Cga/Tga	10/27	1	2	FACETS	0.919	0.806	1	0.919	0.806	1	CLONAL	1	TRUE	1	0.28	2		445	591	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591007	67591007	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	21	240	0	ENST00000274335.5:c.1600C>T	p.Arg534Ter	p.R534*	ENST00000274335		534	Cga/Tga	12/15	1	2	FACETS	0.732	0.566	0.923	0.732	0.566	0.923	CLONAL	1	TRUE	1	0.28	2		240	205	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628323	86628323	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	32	401	0	ENST00000274376.6:c.693-1G>A		p.X231_splice	ENST00000274376	NM_002890.2	231			1	2	FACETS	0.853	0.695	1	0.853	0.695	1	CLONAL	1	TRUE	1	0.28	2		401	268	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649005	86649005	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	38	393	0	ENST00000274376.6:c.1285G>T	p.Glu429Ter	p.E429*	ENST00000274376	NM_002890.2	429	Gaa/Taa	9/25	1	2	FACETS	0.818	0.678	0.973	0.818	0.678	0.973	CLONAL	1	TRUE	1	0.28	2		393	332	SUCCESS
APC	324	MSKCC	GRCh37	5	112175127	112175127	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	37	281	0	ENST00000257430.4:c.3836C>A	p.Ser1279Tyr	p.S1279Y	ENST00000257430	NM_000038.5	1279	tCt/tAt	16/16	1	2	FACETS	0.853	0.705	1	0.853	0.705	1	CLONAL	1	TRUE	1	0.28	2		281	310	SUCCESS
APC	324	MSKCC	GRCh37	5	112175486	112175486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424719678	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	52	373	1	ENST00000257430.4:c.4195C>T	p.Arg1399Cys	p.R1399C	ENST00000257430	NM_000038.5	1399	Cgt/Tgt	16/16	1	2	FACETS	0.639	0.544	0.744	0.639	0.544	0.744	SUBCLONAL	1	TRUE	1	0.28	2		374	581	SUCCESS
APC	324	MSKCC	GRCh37	5	112177793	112177793	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	43	327	0	ENST00000257430.4:c.6502C>A	p.Leu2168Ile	p.L2168I	ENST00000257430	NM_000038.5	2168	Cta/Ata	16/16	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.28	2		327	270	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939098	131939098	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	28	497	3	ENST00000265335.6:c.2314G>T	p.Glu772Ter	p.E772*	ENST00000265335		772	Gaa/Taa	14/25	1	2	FACETS	0.472	0.376	0.58	0.472	0.376	0.58	SUBCLONAL	1	TRUE	1	0.28	2		500	424	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048729	180048729	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	121	784	0	ENST00000261937.6:c.1833G>T	p.Lys611Asn	p.K611N	ENST00000261937	NM_182925.4	611	aaG/aaT	13/30	1	2	FACETS	0.873	0.787	0.964	0.873	0.787	0.964	CLONAL	1	TRUE	1	0.28	2		784	990	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120378	94120378	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	53	384	0	ENST00000369303.4:c.673T>C	p.Ser225Pro	p.S225P	ENST00000369303	NM_004440.3	225	Tcc/Ccc	3/17	1	2	FACETS	0.816	0.697	0.946	0.816	0.697	0.946	CLONAL	1	TRUE	1	0.28	2		384	464	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663588	117663588	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	90	713	0	ENST00000368508.3:c.4644G>T	p.Glu1548Asp	p.E1548D	ENST00000368508	NM_002944.2	1548	gaG/gaT	28/43	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.28	2		713	629	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001395	150001395	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	81	682	1	ENST00000253339.5:c.2209C>T	p.Arg737Ter	p.R737*	ENST00000253339		737	Cga/Tga	4/7	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.28	2		683	554	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240795	55240795	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	98	741	1	ENST00000275493.2:c.2039G>T	p.Arg680Leu	p.R680L	ENST00000275493	NM_005228.3	680	cGg/cTg	17/28	1	2	FACETS	0.719	0.64	0.804	0.719	0.64	0.804	SUBCLONAL	1	TRUE	1	0.28	2		742	973	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242511	55242511	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs121913418	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	38	288	0	ENST00000275493.2:c.2281G>A	p.Asp761Asn	p.D761N	ENST00000275493	NM_005228.3	761	Gat/Aat	19/28	1	2	FACETS	0.57	0.471	0.681	0.57	0.471	0.681	SUBCLONAL	1	TRUE	1	0.28	2		288	476	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268059	55268059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	105	749	0	ENST00000275493.2:c.2899G>A	p.Glu967Lys	p.E967K	ENST00000275493	NM_005228.3	967	Gaa/Aaa	24/28	1	2	FACETS	0.732	0.654	0.814	0.732	0.654	0.814	SUBCLONAL	1	TRUE	1	0.28	2		749	1025	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381567	81381567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370760302	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	41	288	0	ENST00000222390.5:c.494C>T	p.Ser165Leu	p.S165L	ENST00000222390	NM_000601.4	165	tCg/tTg	5/18	1	2	FACETS	0.74	0.617	0.875	0.74	0.617	0.875	SUBCLONAL	1	TRUE	1	0.28	2		288	396	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392061	81392061	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	52	473	0	ENST00000222390.5:c.216T>G	p.Asn72Lys	p.N72K	ENST00000222390	NM_000601.4	72	aaT/aaG	2/18	1	2	FACETS	0.876	0.747	1	0.876	0.747	1	CLONAL	1	TRUE	1	0.28	2		473	424	SUCCESS
MET	4233	MSKCC	GRCh37	7	116413981	116413981	+	intron_variant	Intron	SNP	G	G	T	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	134	1026	0	ENST00000397752.3:c.3029-954G>T		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.28	2		1026	831	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856013	151856013	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	115	594	0	ENST00000262189.6:c.11605A>G	p.Lys3869Glu	p.K3869E	ENST00000262189	NM_170606.2	3869	Aaa/Gaa	44/59	1	2	FACETS	0.85	0.765	0.941	0.85	0.765	0.941	CLONAL	1	TRUE	1	0.28	2		594	966	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132745	152132745	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1327515855	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	42	339	0	ENST00000262189.6:c.127G>T	p.Asp43Tyr	p.D43Y	ENST00000262189	NM_170606.2	43	Gat/Tat	1/59	1	2	FACETS	0.624	0.521	0.738	0.624	0.521	0.738	SUBCLONAL	1	TRUE	1	0.28	2		339	481	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38137162	38137162	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	97	701	0	ENST00000317025.8:c.3656C>A	p.Ser1219Tyr	p.S1219Y	ENST00000317025	NM_023034.1	1219	tCt/tAt	21/24	1	2	FACETS	0.899	0.801	1	0.899	0.801	1	CLONAL	1	TRUE	1	0.28	2		701	771	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90960060	90960060	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	58	397	0	ENST00000265433.3:c.1906G>T	p.Glu636Ter	p.E636*	ENST00000265433	NM_002485.4	636	Gaa/Taa	12/16	1	2	FACETS	0.907	0.781	1	0.907	0.781	1	CLONAL	1	TRUE	1	0.28	2		397	457	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869571	117869571	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	61	565	0	ENST00000297338.2:c.623A>G	p.His208Arg	p.H208R	ENST00000297338	NM_006265.2	208	cAt/cGt	6/14	1	2	FACETS	0.968	0.837	1	0.968	0.837	1	CLONAL	1	TRUE	1	0.28	2		565	450	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157883	27157883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	97	564	0	ENST00000380036.4:c.107C>T	p.Ser36Phe	p.S36F	ENST00000380036	NM_000459.3	36	tCt/tTt	2/23	1	2	FACETS	0.901	0.803	1	0.901	0.803	1	CLONAL	1	TRUE	1	0.28	2		564	769	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197472	27197472	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	109	639	0	ENST00000380036.4:c.1784G>T	p.Gly595Val	p.G595V	ENST00000380036	NM_000459.3	595	gGc/gTc	12/23	1	2	FACETS	0.834	0.747	0.925	0.834	0.747	0.925	CLONAL	1	TRUE	1	0.28	2		639	934	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410342	63410342	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368031008	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	102	781	0	ENST00000330258.3:c.2825G>A	p.Arg942Gln	p.R942Q	ENST00000330258	NM_152424.3	942	cGa/cAa	2/2	1	2	FACETS	0.7	0.624	0.78	0.7	0.624	0.78	SUBCLONAL	1	TRUE	1	0.28	2		781	1041	SUCCESS
AR	367	MSKCC	GRCh37	X	66931429	66931429	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs978916227	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	113	604	1	ENST00000374690.3:c.2071G>A	p.Asp691Asn	p.D691N	ENST00000374690	NM_000044.3	691	Gac/Aac	4/8	1	2	FACETS	0.857	0.77	0.949	0.857	0.77	0.949	CLONAL	1	TRUE	1	0.28	2		605	942	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937577	76937577	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	62	513	0	ENST00000373344.5:c.3171G>T	p.Lys1057Asn	p.K1057N	ENST00000373344	NM_000489.3	1057	aaG/aaT	9/35	1	2	FACETS	0.925	0.8	1	0.925	0.8	1	CLONAL	1	TRUE	1	0.28	2		513	479	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937580	76937580	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	71	510	0	ENST00000373344.5:c.3168G>T	p.Lys1056Asn	p.K1056N	ENST00000373344	NM_000489.3	1056	aaG/aaT	9/35	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.28	2		510	477	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0035155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	141	547	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	0.544712074286207	2		547	427	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	257	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.544712074286207	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.544712074286207	3		493	581	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0035155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	88	468	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.67	0.596	0.749	0.67	0.596	0.749	SUBCLONAL	1	TRUE	1	0.544712074286207	2		468	482	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0035155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	125	254	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.544712074286207	3	FACETS	1	0.91	1	0.501	0.455	0.549	CLONAL	1	TRUE	1	0.544712074286207	3		254	583	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928067	178928067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	58	580	0	ENST00000263967.3:c.1345C>T	p.Pro449Ser	p.P449S	ENST00000263967	NM_006218.2	449	Cct/Tct	8/21	1	2	FACETS	0.354	0.304	0.409	0.354	0.304	0.409	SUBCLONAL	1	TRUE	1	0.544712074286207	2		580	602	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47709954	47709954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	196	328	1	ENST00000233146.2:c.2671G>A	p.Val891Met	p.V891M	ENST00000233146	NM_000251.2	891	Gtg/Atg	16/16	0.544712074286207	3	FACETS	0.931	0.87	0.992	0.931	0.87	0.992	CLONAL	2	TRUE	1	0.544712074286207	3		329	492	SUCCESS
APC	324	MSKCC	GRCh37	5	112175641	112175641	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	234	305	0	ENST00000257430.4:c.4350del	p.Glu1451LysfsTer22	p.E1451Kfs*22	ENST00000257430	NM_000038.5	1450	cgA/cg	16/16	0.544712074286207	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	1	0.544712074286207	3		305	543	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020566	69020566	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs764136224	NA	P-0035155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	47	433	0	ENST00000288368.4:c.2938G>A	p.Gly980Arg	p.G980R	ENST00000288368	NM_024870.2	980	Ggg/Agg	24/40	0.544712074286207	3	FACETS	0.325	0.274	0.382	0.163	0.137	0.191	SUBCLONAL	1	TRUE	1	0.544712074286207	3		433	675	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742835	145742835	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	24	294	0	ENST00000428558.2:c.176T>C	p.Leu59Pro	p.L59P	ENST00000428558	NM_004260.3	59	cTc/cCc	3/22	0.544712074286207	3	FACETS	0.24	0.187	0.3	0.12	0.093	0.15	SUBCLONAL	1	TRUE	1	0.544712074286207	3		294	468	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0035157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	63	388	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.891	0.771	1	0.891	0.771	1	CLONAL	1	TRUE	1	0.26	2		388	544	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	101	648	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.282926138791934	1	FACETS	0.917	0.82	1	0.917	0.82	1	CLONAL	1	TRUE	0	0.26	1		648	737	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36014525	36014525	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	91	498	0	ENST00000358208.4:c.298G>A	p.Glu100Lys	p.E100K	ENST00000358208		100	Gag/Aag	3/12	1	2	FACETS	0.937	0.832	1	0.937	0.832	1	CLONAL	1	TRUE	1	0.26	2		498	747	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935630	15935630	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	54	375	0	ENST00000268712.3:c.7303del	p.Leu2435CysfsTer56	p.L2435Cfs*56	ENST00000268712	NM_006311.3	2435	Ctg/tg	46/46	0.282926138791934	1	FACETS	0.759	0.649	0.879	0.759	0.649	0.879	SUBCLONAL	1	TRUE	0	0.26	1		375	476	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61717905	61717912	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	TATGAACC	TATGAACC	-	novel	NA	P-0035157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	87	400	0	ENST00000401558.2:c.1888-1_1894del		p.X630_splice	ENST00000401558	NM_003400.3	630		17/25	1	2	FACETS	0.922	0.816	1	0.922	0.816	1	CLONAL	1	TRUE	1	0.26	2		400	726	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92247444	92247444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	52	282	0	ENST00000265734.4:c.776C>T	p.Ala259Val	p.A259V	ENST00000265734	NM_001259.6	259	gCc/gTc	7/8	1	2	FACETS	0.864	0.737	1	0.864	0.737	1	CLONAL	1	TRUE	1	0.26	2		282	463	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	76	349	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.857223816279406	2		349	171	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952100	178952100	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	148	328	0	ENST00000263967.3:c.3155C>A	p.Thr1052Lys	p.T1052K	ENST00000263967	NM_006218.2	1052	aCa/aAa	21/21	1	2	FACETS	0.89	0.822	0.959	0.89	0.822	0.959	CLONAL	1	TRUE	1	0.857223816279406	2		328	388	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725042	89725042	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	rs1085308041	NA	P-0035158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	37	218	0	ENST00000371953.3:c.1027-2A>C		p.X343_splice	ENST00000371953	NM_000314.4	343			0.857223816279406	1	FACETS	0.31	0.259	0.365	0.31	0.259	0.365	SUBCLONAL	1	TRUE	0	0.857223816279406	1		218	159	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577557	7577557	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519982	NA	P-0035158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	617	613	2	ENST00000269305.4:c.724T>A	p.Cys242Ser	p.C242S	ENST00000269305	NM_001126112.2	242	Tgc/Agc	7/11	0.855891088899137	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.857223816279406	2		615	693	SUCCESS
MET	4233	MSKCC	GRCh37	7	116409829	116409829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753091019	NA	P-0035158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	244	326	0	ENST00000397752.3:c.2714G>A	p.Ser905Asn	p.S905N	ENST00000397752	NM_000245.2	905	aGc/aAc	12/21	0.857223816279406	6	FACETS	0.875	0.819	0.932	0.35	0.327	0.373	CLONAL	2	TRUE	1	0.857223816279406	6		326	883	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641162	93641162	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	519	547	0	ENST00000375746.1:c.1509del	p.Thr504ProfsTer58	p.T504Pfs*58	ENST00000375746	NM_001174167.1	503	gTt/gt	11/14	0.857223816279406	3	FACETS	0.944	0.912	0.977	0.944	0.912	0.977	CLONAL	2	TRUE	1	0.857223816279406	3		547	916	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0035159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	24	547	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.455965813763445	3	FACETS	0.225	0.175	0.282	0.112	0.087	0.141	SUBCLONAL	1	TRUE	1	0.455965813763445	3		547	575	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	53	349	0				ENST00000310581	NM_198253.2	-/1132			0.161603430988608	6	FACETS	0.922	0.809	1	1	0.957	1	INDETERMINATE	4	TRUE	3	0.401758076332811	6		349	129	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413900	139413900	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	226	481	0	ENST00000277541.6:c.860G>A	p.Trp287Ter	p.W287*	ENST00000277541	NM_017617.3	287	tGg/tAg	5/34	0.401758076332811	5	FACETS	0.886	0.834	0.938	1	0.987	1	CLONAL	4	TRUE	2	0.401758076332811	5		481	509	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847282	68847282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	129	464	0	ENST00000261769.5:c.1204G>A	p.Asp402Asn	p.D402N	ENST00000261769	NM_004360.3	402	Gat/Aat	9/16	0.161603430988608	6	FACETS	0.963	0.881	1	0.963	0.881	1	INDETERMINATE	3	TRUE	3	0.401758076332811	6		464	401	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390197	89390197	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	93	432	0	ENST00000336596.2:c.946G>A	p.Asp316Asn	p.D316N	ENST00000336596	NM_005233.5	316	Gac/Aac	4/17	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.401758076332811	2		432	322	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518560	204518560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	58	341	0	ENST00000367182.3:c.1223C>T	p.Ser408Leu	p.S408L	ENST00000367182	NM_001278516.1	408	tCa/tTa	11/11	0.161603430988608	6	FACETS	0.886	0.773	1	0.886	0.773	1	INDETERMINATE	3	TRUE	3	0.401758076332811	6		341	196	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796963	78796963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	224	535	0	ENST00000306801.3:c.1076C>T	p.Ser359Leu	p.S359L	ENST00000306801	NM_020761.2	359	tCg/tTg	9/34	0.161603430988608	6	FACETS	1	0.981	1	1	0.981	1	INDETERMINATE	3	TRUE	3	0.401758076332811	6		535	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578549	7578550	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	121	604	0	ENST00000269305.4:c.380_381delinsTT	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCC/tTT	5/11	0.401758076332811	2	FACETS	0.95	0.871	1	0.95	0.871	1	CLONAL	2	TRUE	0	0.401758076332811	2		604	317	SUCCESS
APC	324	MSKCC	GRCh37	5	112178988	112178988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	79	322	0	ENST00000257430.4:c.7697G>A	p.Arg2566Lys	p.R2566K	ENST00000257430	NM_000038.5	2566	aGa/aAa	16/16	0.401758076332811	2	FACETS	0.973	0.874	1	0.973	0.874	1	CLONAL	2	TRUE	0	0.401758076332811	2		322	202	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860517	151860517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772864510	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	129	656	3	ENST00000262189.6:c.10145G>A	p.Arg3382Gln	p.R3382Q	ENST00000262189	NM_170606.2	3382	cGg/cAg	43/59	0.226002294588738	5	FACETS	1	0.954	1	0.713	0.651	0.778	INDETERMINATE	2	TRUE	2	0.401758076332811	5		659	481	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939076	36939083	+	frameshift_variant	Frame_Shift_Del	DEL	GGTCCCCA	GGTCCCCA	-	novel	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	78	548	1	ENST00000361632.4:c.626_633del	p.Leu209GlnfsTer9	p.L209Qfs*9	ENST00000361632		209	cTGGGGACC/c	5/16	0.401758076332811	5	FACETS	1	0.937	1	0.275	0.242	0.311	CLONAL	1	TRUE	1	0.401758076332811	5		549	565	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617428	43617428	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377767432	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	133	531	1	ENST00000355710.3:c.2765C>T	p.Ser922Phe	p.S922F	ENST00000355710	NM_020975.4	922	tCc/tTc	16/20	0.401758076332811	2	FACETS	0.949	0.873	1	0.949	0.873	1	CLONAL	2	TRUE	0	0.401758076332811	2		532	349	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202715	108202715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761790685	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	96	400	0	ENST00000278616.4:c.7739G>A	p.Arg2580Lys	p.R2580K	ENST00000278616	NM_000051.3	2580	aGa/aAa	52/63	0.280860760869582	3	FACETS	1	0.96	1	0.741	0.671	0.813	CLONAL	2	TRUE	0	0.401758076332811	3		400	258	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864720	57864720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	131	535	0	ENST00000228682.2:c.2197G>A	p.Gly733Arg	p.G733R	ENST00000228682	NM_005269.2	733	Ggg/Agg	12/12	0.401758076332811	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.401758076332811	3		535	340	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945176	32945177	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	62	408	2	ENST00000380152.3:c.8571_8572delinsTT	p.Gln2858Ter	p.Q2858*	ENST00000380152		2857	gcCCaa/gcTTaa	20/27	0.283045655855855	3	FACETS	0.842	0.738	0.952	0.562	0.492	0.635	CLONAL	2	TRUE	0	0.401758076332811	3		410	220	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639374	3639374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	105	588	1	ENST00000294008.3:c.4265C>T	p.Pro1422Leu	p.P1422L	ENST00000294008	NM_032444.2	1422	cCa/cTa	12/15	0.362016520029706	3	FACETS	0.865	0.782	0.95	0.865	0.782	0.95	CLONAL	2	TRUE	1	0.401758076332811	3		589	363	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032302	10032302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	68	562	0	ENST00000330684.3:c.521C>T	p.Thr174Ile	p.T174I	ENST00000330684	NM_001134407.1	174	aCc/aTc	3/13	0.362016520029706	3	FACETS	1	0.926	1	0.542	0.474	0.615	CLONAL	1	TRUE	1	0.401758076332811	3		562	375	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650699	67650699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	158	568	0	ENST00000264010.4:c.1004G>A	p.Gly335Glu	p.G335E	ENST00000264010	NM_006565.3	335	gGa/gAa	5/12	0.161603430988608	6	FACETS	1	0.979	1	0.789	0.727	0.854	INDETERMINATE	2	TRUE	3	0.401758076332811	6		568	599	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827805	72827805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	142	529	0	ENST00000268489.5:c.8776C>T	p.Pro2926Ser	p.P2926S	ENST00000268489	NM_006885.3	2926	Ccg/Tcg	9/10	0.161603430988608	6	FACETS	0.843	0.773	0.915	0.843	0.773	0.915	INDETERMINATE	3	TRUE	3	0.401758076332811	6		529	504	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991569	72991569	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	81	697	0	ENST00000268489.5:c.2476G>C	p.Glu826Gln	p.E826Q	ENST00000268489	NM_006885.3	826	Gag/Cag	2/10	0.161603430988608	6	FACETS	1	0.958	1	0.398	0.351	0.449	INDETERMINATE	1	TRUE	3	0.401758076332811	6		697	609	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226519	41226519	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357383	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	99	466	1	ENST00000357654.3:c.4504C>T	p.Pro1502Ser	p.P1502S	ENST00000357654	NM_007294.3	1502	Cca/Tca	14/23	0.161603430988608	6	FACETS	0.912	0.823	1	0.912	0.823	1	INDETERMINATE	3	TRUE	3	0.401758076332811	6		467	325	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434897	56434897	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	182	517	0	ENST00000407977.2:c.2240G>A	p.Trp747Ter	p.W747*	ENST00000407977		747	tGg/tAg	9/10	0.161603430988608	6	FACETS	1	0.974	1	1	0.974	1	INDETERMINATE	3	TRUE	3	0.401758076332811	6		517	498	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726651	41726651	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1413460761	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	44	466	1	ENST00000301178.4:c.196G>A	p.Glu66Lys	p.E66K	ENST00000301178	NM_021913.4	66	Gag/Aag	2/20	0.362016520029706	3	FACETS	0.601	0.504	0.707	0.3	0.252	0.354	SUBCLONAL	1	TRUE	1	0.401758076332811	3		467	438	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39284007	39284007	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	65	332	0	ENST00000402219.2:c.346G>A	p.Glu116Lys	p.E116K	ENST00000402219	NM_005633.3	116	Gag/Aag	4/23	0.401758076332811	3	FACETS	0.899	0.792	1	0.899	0.792	1	CLONAL	2	TRUE	1	0.401758076332811	3		332	216	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225360586	225360586	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	52	362	0	ENST00000264414.4:c.1805del	p.Leu602Ter	p.L602*	ENST00000264414	NM_003590.4	602	tTa/ta	13/16	0.401758076332811	3	FACETS	1	0.956	1	0.653	0.562	0.751	CLONAL	1	TRUE	1	0.401758076332811	3		362	238	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000014	30000014	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	77	260	0	ENST00000338641.4:c.27G>A	p.Met9Ile	p.M9I	ENST00000338641	NM_000268.3	9	atG/atA	1/16	0.13424961276234	3	FACETS	1	0.917	1	0.688	0.614	0.764	INDETERMINATE	2	TRUE	0	0.401758076332811	3		260	223	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114601	73114601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	60	312	0	ENST00000356692.5:c.982G>A	p.Glu328Lys	p.E328K	ENST00000356692		328	Gaa/Aaa	9/9	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.401758076332811	2		312	218	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99806213	99806213	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	45	486	0	ENST00000280892.6:c.460-1G>C		p.X154_splice	ENST00000280892	NM_001130678.1	154			0.362016520029706	3	FACETS	0.897	0.758	1	0.448	0.379	0.525	CLONAL	1	TRUE	1	0.401758076332811	3		486	300	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410862	31410863	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	175	615	0	ENST00000344624.3:c.3657_3658delinsTT	p.Leu1220Phe	p.L1220F	ENST00000344624		1219	gaCCtt/gaTTtt	28/33	0.161603430988608	6	FACETS	1	0.974	1	0.748	0.691	0.807	INDETERMINATE	2	TRUE	3	0.401758076332811	6		615	700	SUCCESS
APC	324	MSKCC	GRCh37	5	112179651	112179651	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1561622555	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	85	363	0	ENST00000257430.4:c.8360A>G	p.Asn2787Ser	p.N2787S	ENST00000257430	NM_000038.5	2787	aAc/aGc	16/16	0.401758076332811	2	FACETS	0.874	0.785	0.966	0.874	0.785	0.966	CLONAL	2	TRUE	0	0.401758076332811	2		363	242	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673256	30673256	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1463662106	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	121	450	0	ENST00000376406.3:c.3704C>A	p.Ser1235Tyr	p.S1235Y	ENST00000376406	NM_014641.2	1235	tCc/tAc	10/15	0.401758076332811	3	FACETS	0.904	0.824	0.987	0.904	0.824	0.987	CLONAL	2	TRUE	1	0.401758076332811	3		450	400	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92244475	92244476	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	94	401	2	ENST00000265734.4:c.959_960delinsTT	p.Thr320Ile	p.T320I	ENST00000265734	NM_001259.6	320	aCC/aTT	8/8	0.236348302994536	6	FACETS	0.938	0.839	1	0.625	0.559	0.695	INDETERMINATE	2	TRUE	3	0.401758076332811	6		403	450	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862985	117862985	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	123	484	0	ENST00000297338.2:c.1492G>A	p.Glu498Lys	p.E498K	ENST00000297338	NM_006265.2	498	Gaa/Aaa	12/14	0.236348302994536	6	FACETS	0.893	0.815	0.975	0.893	0.815	0.975	INDETERMINATE	3	TRUE	3	0.401758076332811	6		484	412	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554367	141554368	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	174	624	0	ENST00000220592.5:c.1783_1784delinsAA	p.Gly595Lys	p.G595K	ENST00000220592	NM_012154.3	595	GGa/AAa	14/19	0.312466643530557	5	FACETS	1	0.967	1	0.722	0.667	0.778	CLONAL	2	TRUE	2	0.401758076332811	5		624	641	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209417	98209417	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	119	419	0	ENST00000331920.6:c.4121C>T	p.Ser1374Phe	p.S1374F	ENST00000331920	NM_000264.3	1374	tCt/tTt	23/24	0.401758076332811	5	FACETS	1	0.93	1	0.685	0.622	0.75	CLONAL	2	TRUE	2	0.401758076332811	5		419	462	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400983	139400983	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	86	382	0	ENST00000277541.6:c.4010del	p.Pro1337LeufsTer108	p.P1337Lfs*108	ENST00000277541	NM_017617.3	1337	cCt/ct	24/34	0.401758076332811	5	FACETS	0.871	0.775	0.972	0.58	0.517	0.648	CLONAL	2	TRUE	2	0.401758076332811	5		382	394	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357160	70357160	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	150	249	0	ENST00000374080.3:c.5675C>G	p.Ser1892Cys	p.S1892C	ENST00000374080		1892	tCt/tGt	39/45	0.375025703344442	2	FACETS	0.902	0.843	0.961			1	CLONAL	3	TRUE	NA	0.401758076332811	2		249	276	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	518	527	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.178756595732706	5	FACETS	1	0.992	1			1	INDETERMINATE	3	TRUE	NA	0.877433758700843	5		527	843	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673806	37673806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201661022	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	285	566	0	ENST00000447079.4:c.2960C>T	p.Ser987Phe	p.S987F	ENST00000447079	NM_015083.1	987	tCt/tTt	10/14	1	2	FACETS	0.935	0.884	0.986	0.935	0.884	0.986	CLONAL	1	TRUE	1	0.877433758700843	2		566	695	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144588	119144588	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	157	350	0	ENST00000264033.4:c.601C>T	p.Pro201Ser	p.P201S	ENST00000264033	NM_005188.3	201	Cct/Tct	4/16	0.165251691391078	3	FACETS	1	0.989	1	0.703	0.653	0.754	INDETERMINATE	1	TRUE	1	0.877433758700843	3		350	366	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944913	31944913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	144	332	1	ENST00000340398.3:c.188G>A	p.Arg63Gln	p.R63Q	ENST00000340398	NM_001013699.2	63	cGg/cAg	1/1	1	2	FACETS	0.977	0.904	1	0.977	0.904	1	CLONAL	1	TRUE	1	0.877433758700843	2		333	336	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518111	8518111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	228	551	0	ENST00000356435.5:c.1280G>A	p.Arg427Gln	p.R427Q	ENST00000356435		427	cGa/cAa	10/35	0.126414894523596	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.877433758700843	0		551	495	SUCCESS
AR	367	MSKCC	GRCh37	X	66941766	66941766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	249	283	0	ENST00000374690.3:c.2410G>A	p.Glu804Lys	p.E804K	ENST00000374690	NM_000044.3	804	Gaa/Aaa	6/8	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.877433758700843	1		283	301	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430402	78430402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372081866	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	244	545	1	ENST00000370768.2:c.766C>T	p.Arg256Cys	p.R256C	ENST00000370768	NM_003902.3	256	Cgt/Tgt	10/20	1	2	FACETS	0.91	0.857	0.964	0.91	0.857	0.964	CLONAL	1	TRUE	1	0.877433758700843	2		546	611	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626775	28626775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	295	513	0	ENST00000241453.7:c.521G>A	p.Arg174Lys	p.R174K	ENST00000241453	NM_004119.2	174	aGa/aAa	5/24	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.877433758700843	2		513	649	SUCCESS
APC	324	MSKCC	GRCh37	5	112173396	112173396	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658289	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	178	340	0	ENST00000257430.4:c.2105G>A	p.Gly702Glu	p.G702E	ENST00000257430	NM_000038.5	702	gGg/gAg	16/16	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.877433758700843	2		340	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577540	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	rs1555525498	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	299	673	2	ENST00000269305.4:c.741_742delinsTT	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	247	aaCCgg/aaTTgg	7/11	0.851273305757266	1	FACETS	0.976	0.942	1	0.976	0.942	1	CLONAL	1	TRUE	0	0.877433758700843	1		675	392	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996161	73996161	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1223303121	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	490	838	1	ENST00000318443.5:c.895G>A	p.Glu299Lys	p.E299K	ENST00000318443	NM_001024736.1	299	Gaa/Aaa	5/10	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.877433758700843	2		839	1033	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17371289	17371289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	305	581	0	ENST00000375499.3:c.167C>T	p.Pro56Leu	p.P56L	ENST00000375499	NM_003000.2	56	cCt/cTt	2/8	1	2	FACETS	0.936	0.887	0.985	0.936	0.887	0.985	CLONAL	1	TRUE	1	0.877433758700843	2		581	743	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117712774	117712785	+	inframe_deletion	In_Frame_Del	DEL	TAATGATGATGC	TAATGATGATGC	-	novel	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	158	413	0	ENST00000369458.3:c.41_52del	p.Ser14_Ile17del	p.S14_I17del	ENST00000369458	NM_024626.3	14	aGCATCATCATTAtt/att	2/6	1	2	FACETS	0.838	0.775	0.901	0.838	0.775	0.901	CLONAL	1	TRUE	1	0.877433758700843	2		413	430	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88678958	88678959	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	126	272	1	ENST00000372037.3:c.898_899delinsAA	p.Gly300Asn	p.G300N	ENST00000372037	NM_004329.2	300	GGt/AAt	10/13	0.877433758700843	1	FACETS	0.901	0.847	0.951	0.901	0.847	0.951	CLONAL	1	TRUE	0	0.877433758700843	1		273	179	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989553	85989553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	245	454	0	ENST00000263360.6:c.1312G>A	p.Asp438Asn	p.D438N	ENST00000263360	NM_003797.3	438	Gat/Aat	12/12	1	2	FACETS	0.934	0.88	0.989	0.934	0.88	0.989	CLONAL	1	TRUE	1	0.877433758700843	2		454	598	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158438	108158438	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	209	444	0	ENST00000278616.4:c.4105T>G	p.Ser1369Ala	p.S1369A	ENST00000278616	NM_000051.3	1369	Tca/Gca	27/63	0.165251691391078	3	FACETS	1	0.99	1	0.647	0.605	0.688	INDETERMINATE	1	TRUE	1	0.877433758700843	3		444	530	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025530	1025531	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	276	759	1	ENST00000358495.3:c.844_845delinsTT	p.Pro282Leu	p.P282L	ENST00000358495	NM_134424.2	282	CCg/TTg	9/12	1	2	FACETS	0.895	0.845	0.945	0.895	0.845	0.945	CLONAL	1	TRUE	1	0.877433758700843	2		760	703	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425183	49425184	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	366	864	1	ENST00000301067.7:c.13304_13305delinsTT	p.Ala4435Val	p.A4435V	ENST00000301067	NM_003482.3	4435	gCC/gTT	39/54	1	2	FACETS	0.932	0.888	0.977	0.932	0.888	0.977	CLONAL	1	TRUE	1	0.877433758700843	2		865	895	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120535064	120535064	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	299	556	0	ENST00000229340.5:c.591del	p.Lys198AsnfsTer95	p.K198Nfs*95	ENST00000229340	NM_006861.6	197	aaG/aa	6/6	1	2	FACETS	0.981	0.93	1	0.981	0.93	1	CLONAL	1	TRUE	1	0.877433758700843	2		556	695	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220143	133220143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	265	512	0	ENST00000320574.5:c.4294C>T	p.Pro1432Ser	p.P1432S	ENST00000320574	NM_006231.2	1432	Ccg/Tcg	34/49	1	2	FACETS	0.973	0.919	1	0.973	0.919	1	CLONAL	1	TRUE	1	0.877433758700843	2		512	621	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549329	21549330	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	293	706	0	ENST00000382592.4:c.2946_2947delinsTT	p.Arg983Trp	p.R983W	ENST00000382592	NM_014572.2	982	atCCgg/atTTgg	8/8	1	2	FACETS	0.975	0.924	1	0.975	0.924	1	CLONAL	1	TRUE	1	0.877433758700843	2		706	685	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870073	40870073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	219	444	0	ENST00000428826.2:c.944C>T	p.Thr315Ile	p.T315I	ENST00000428826		315	aCc/aTc	10/21	1	2	FACETS	0.909	0.853	0.966	0.909	0.853	0.966	CLONAL	1	TRUE	1	0.877433758700843	2		444	549	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39537537	39537537	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	139	307	0	ENST00000262039.4:c.71G>A	p.Gly24Glu	p.G24E	ENST00000262039	NM_002647.2	24	gGa/gAa	2/25	1	2	FACETS	0.9	0.83	0.971	0.9	0.83	0.971	CLONAL	1	TRUE	1	0.877433758700843	2		307	352	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10244926	10244926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	324	619	0	ENST00000340748.4:c.4783T>C	p.Cys1595Arg	p.C1595R	ENST00000340748		1595	Tgt/Cgt	39/40	1	2	FACETS	0.95	0.903	0.999	0.95	0.903	0.999	CLONAL	1	TRUE	1	0.877433758700843	2		619	777	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610496	10610496	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	388	771	1	ENST00000171111.5:c.214C>T	p.Leu72Phe	p.L72F	ENST00000171111	NM_203500.1	72	Ctc/Ttc	2/6	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.877433758700843	2		772	871	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276252	15276253	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	328	646	2	ENST00000263388.2:c.5741_5742delinsTT	p.Ala1914Val	p.A1914V	ENST00000263388	NM_000435.2	1914	gCC/gTT	31/33	1	2	FACETS	0.99	0.942	1	0.99	0.942	1	CLONAL	1	TRUE	1	0.877433758700843	2		648	755	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791795	42791796	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	294	659	2	ENST00000575354.2:c.681_682delinsTT	p.Arg228Trp	p.R228W	ENST00000575354	NM_015125.3	227	aaCCgg/aaTTgg	5/20	1	2	FACETS	0.921	0.872	0.97	0.921	0.872	0.97	CLONAL	1	TRUE	1	0.877433758700843	2		661	728	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47735799	47735799	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	343	634	0	ENST00000449228.1:c.61del	p.Thr21ArgfsTer208	p.T21Rfs*208	ENST00000449228	NM_001127240.2	21	Acg/cg	1/4	1	2	FACETS	0.98	0.932	1	0.98	0.932	1	CLONAL	1	TRUE	1	0.877433758700843	2		634	798	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426649	212426649	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	253	557	0	ENST00000342788.4:c.2466C>A	p.Asn822Lys	p.N822K	ENST00000342788	NM_005235.2	822	aaC/aaA	20/28	0.877433758700843	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.877433758700843	1		557	322	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178206	142178206	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	325	310	0	ENST00000350721.4:c.7212A>T	p.Lys2404Asn	p.K2404N	ENST00000350721	NM_001184.3	2404	aaA/aaT	43/47	0.877433758700843	3	FACETS	0.98	0.938	1	0.98	0.938	1	CLONAL	2	TRUE	1	0.877433758700843	3		310	544	SUCCESS
ATR	545	MSKCC	GRCh37	3	142184064	142184064	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	183	363	0	ENST00000350721.4:c.6916C>T	p.Leu2306Phe	p.L2306F	ENST00000350721	NM_001184.3	2306	Ctt/Ttt	41/47	0.877433758700843	3	FACETS	0.928	0.86	0.997	0.464	0.43	0.499	CLONAL	1	TRUE	1	0.877433758700843	3		363	647	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198280	185198280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	275	554	0	ENST00000265026.3:c.2762C>T	p.Ser921Phe	p.S921F	ENST00000265026	NM_004721.4	921	tCt/tTt	13/14	0.877433758700843	3	FACETS	0.951	0.895	1	0.476	0.447	0.505	CLONAL	1	TRUE	1	0.877433758700843	3		554	948	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514365	149514366	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	242	604	1	ENST00000261799.4:c.578_579delinsTT	p.Thr193Ile	p.T193I	ENST00000261799	NM_002609.3	193	aCC/aTT	4/23	0.126414894523596	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.877433758700843	0		605	638	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637108	176637108	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	273	599	0	ENST00000439151.2:c.1708T>G	p.Phe570Val	p.F570V	ENST00000439151	NM_022455.4	570	Ttt/Gtt	5/23	1	2	FACETS	0.965	0.912	1	0.965	0.912	1	CLONAL	1	TRUE	1	0.877433758700843	2		599	645	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214314	55214315	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	243	579	2	ENST00000275493.2:c.440_441delinsTT	p.Ala147Val	p.A147V	ENST00000275493	NM_005228.3	147	gCC/gTT	4/28	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.877433758700843	2		581	544	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221796	55221797	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	267	663	2	ENST00000275493.2:c.840_841delinsTT	p.Pro281Ser	p.P281S	ENST00000275493	NM_005228.3	280	aaCCcc/aaTTcc	7/28	1	2	FACETS	0.944	0.891	0.996	0.944	0.891	0.996	CLONAL	1	TRUE	1	0.877433758700843	2		665	645	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836780	151836780	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	267	491	1	ENST00000262189.6:c.14440G>A	p.Glu4814Lys	p.E4814K	ENST00000262189	NM_170606.2	4814	Gag/Aag	56/59	1	2	FACETS	0.972	0.919	1	0.972	0.919	1	CLONAL	1	TRUE	1	0.877433758700843	2		492	626	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209505	98209506	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	464	589	2	ENST00000331920.6:c.4032_4033delinsTT	p.Arg1345Cys	p.R1345C	ENST00000331920	NM_000264.3	1344	gcCCgt/gcTTgt	23/24	0.877433758700843	3	FACETS	0.922	0.888	0.956	0.922	0.888	0.956	CLONAL	2	TRUE	1	0.877433758700843	3		591	825	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907013	101907013	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	160	339	0	ENST00000374994.4:c.974-1G>A		p.X325_splice	ENST00000374994	NM_004612.2	325			0.877433758700843	3	FACETS	0.959	0.885	1	0.48	0.442	0.518	CLONAL	1	TRUE	1	0.877433758700843	3		339	547	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401386	139401388	+	frameshift_variant	Frame_Shift_Del	DEL	GGG	GGG	AT	novel	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	691	699	1	ENST00000277541.6:c.3681_3683delinsAT	p.Pro1228SerfsTer217	p.P1228Sfs*217	ENST00000277541	NM_017617.3	1227	ccCCCc/ccATc	23/34	0.869346638706384	2	FACETS	0.982	0.965	0.998	0.982	0.965	0.998	CLONAL	2	TRUE	0	0.877433758700843	2		700	802	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044737	47044737	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	356	398	0	ENST00000377604.3:c.2137C>T	p.Leu713Phe	p.L713F	ENST00000377604	NM_001204468.1	713	Ctc/Ttc	19/24	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.877433758700843	1		398	406	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0035166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	270	879	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.655600483745399	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.655600483745399	2		879	395	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202727	108202727	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	126	425	0	ENST00000278616.4:c.7751C>T	p.Thr2584Ile	p.T2584I	ENST00000278616	NM_000051.3	2584	aCt/aTt	52/63	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.655600483745399	2		425	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0035167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	442	879	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.632965918564707	2	FACETS	0.972	0.938	1	0.972	0.938	1	CLONAL	2	TRUE	0	0.638430352460411	2		879	712	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0035167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	560	679	0	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	0.6384290631525	3	FACETS	0.964	0.937	0.991	0.964	0.937	0.991	CLONAL	3	TRUE	0	0.638430352460411	3		679	800	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961002	55961002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	321	665	2	ENST00000263923.4:c.2938G>A	p.Glu980Lys	p.E980K	ENST00000263923	NM_002253.2	980	Gag/Aag	21/30	0.619591335497984	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.638430352460411	2		667	470	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80343568	80343568	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	157	474	0	ENST00000286548.4:c.751A>T	p.Ser251Cys	p.S251C	ENST00000286548	NM_002072.3	251	Agc/Tgc	6/7	0.638430352460411	3	FACETS	0.938	0.861	1	0.469	0.43	0.509	CLONAL	1	TRUE	1	0.638430352460411	3		474	692	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912356	97912356	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs769039987	NA	P-0035167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	236	423	0	ENST00000289081.3:c.535C>T	p.Arg179Ter	p.R179*	ENST00000289081	NM_000136.2	179	Cga/Tga	7/15	0.638430352460411	3	FACETS	0.96	0.906	1	0.96	0.906	1	CLONAL	2	TRUE	1	0.638430352460411	3		423	508	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046038	180046038	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0121587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	54	117	0	ENST00000261937.6:c.2833G>A	p.Ala945Thr	p.A945T	ENST00000261937	NM_182925.4	945	Gcc/Acc	20/30	0.631672710917893	1	FACETS	0.646	0.569	0.723	0.646	0.569	0.723	SUBCLONAL	1	NA	0	0.821510729088636	1		117	120	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262682	16262682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0121587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	126	351	0	ENST00000375759.3:c.9947C>T	p.Pro3316Leu	p.P3316L	ENST00000375759	NM_015001.2	3316	cCc/cTc	11/15	0.357654398322972	0	FACETS		NA	1			1	INDETERMINATE	1	NA	0	0.821510729088636	0		351	189	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699543	117699543	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0121587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	117	268	0	ENST00000369458.3:c.98G>A	p.Gly33Glu	p.G33E	ENST00000369458	NM_024626.3	33	gGg/gAg	3/6	0.619221315814603	3	FACETS	1	0.928	1			1	CLONAL	1	NA	NA	0.821510729088636	3		268	393	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456269	32456269	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0121587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	176	608	0	ENST00000332351.3:c.623G>C	p.Ser208Thr	p.S208T	ENST00000332351	NM_024426.4	208	aGc/aCc	1/10	1	2	FACETS	0.923	0.859	0.989	0.923	0.859	0.989	CLONAL	1	NA	1	0.821510729088636	2		608	464	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944836	31944836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148314204	NA	P-0035174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	131	738	0	ENST00000340398.3:c.265G>A	p.Val89Ile	p.V89I	ENST00000340398	NM_001013699.2	89	Gtc/Atc	1/1	1	2	FACETS	0.785	0.712	0.862	0.785	0.712	0.862	SUBCLONAL	1	TRUE	1	0.380355678696966	2		738	877	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222212	2222212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375286771	NA	P-0035174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	145	643	0	ENST00000326181.6:c.496G>A	p.Val166Ile	p.V166I	ENST00000326181	NM_032271.2	166	Gtc/Atc	8/21	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.380355678696966	2		643	720	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139794948	139794948	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	266	573	0	ENST00000247668.2:c.342G>A	p.Trp114Ter	p.W114*	ENST00000247668	NM_021138.3	114	tgG/tgA	4/11	0.380355678696966	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.380355678696966	2		573	619	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115931	8115947	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGCCTGTCCTTTGGA	CCAGCCTGTCCTTTGGA	-	novel	NA	P-0035176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	121	412	0	ENST00000346208.3:c.1280_1296del	p.Ser427ThrfsTer74	p.S427Tfs*74	ENST00000346208		426	tCCAGCCTGTCCTTTGGA/t	6/6	1	2	FACETS	0.942	0.855	1	0.942	0.855	1	CLONAL	1	TRUE	1	0.461969463558252	2		412	556	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996167	73996167	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149869002	NA	P-0035176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	187	771	0	ENST00000318443.5:c.901C>T	p.Arg301Trp	p.R301W	ENST00000318443	NM_001024736.1	301	Cgg/Tgg	5/10	1	2	FACETS	0.757	0.698	0.817	0.757	0.698	0.817	SUBCLONAL	1	TRUE	1	0.461969463558252	2		771	1070	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0035177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	199	384	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	0.725870351905114	2		384	522	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0035177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	316	566	0	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.725870351905114	2		566	828	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222319	53222319	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	309	742	0	ENST00000375401.3:c.4513G>T	p.Glu1505Ter	p.E1505*	ENST00000375401	NM_004187.3	1505	Gag/Tag	26/26	0.550281562689739	3	FACETS	0.999	0.942	1	0.5	0.471	0.529	CLONAL	1	TRUE	1	0.725870351905114	3		742	1161	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244136	153244136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	272	522	1	ENST00000281708.4:c.2021G>A	p.Arg674Gln	p.R674Q	ENST00000281708	NM_033632.3	674	cGg/cAg	12/12	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.725870351905114	2		523	672	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56376768	56376768	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	143	380	0	ENST00000348428.3:c.808G>A	p.Glu270Lys	p.E270K	ENST00000348428	NM_006785.3	270	Gag/Aag	5/17	1	2	FACETS	0.811	0.744	0.879	0.811	0.744	0.879	CLONAL	1	TRUE	1	0.725870351905114	2		380	486	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155721	56155722	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0035177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	320	317	0	ENST00000399503.3:c.816_817del	p.Arg273SerfsTer27	p.R273Sfs*27	ENST00000399503	NM_005921.1	271	agAAaa/agaa	3/20	0.725870351905114	3	FACETS	0.922	0.878	0.965	0.922	0.878	0.965	CLONAL	2	TRUE	1	0.725870351905114	3		317	652	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827589	72827589	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343025200	NA	P-0035177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	598	634	3	ENST00000268489.5:c.8992C>T	p.Arg2998Trp	p.R2998W	ENST00000268489	NM_006885.3	2998	Cgg/Tgg	9/10	0.725870351905114	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.725870351905114	2		637	824	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831117	72831118	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	520	540	0	ENST00000268489.5:c.5463dup	p.Leu1822ThrfsTer107	p.L1822Tfs*107	ENST00000268489	NM_006885.3	1821	-/A	9/10	0.725870351905114	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.725870351905114	2		540	715	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15960927	15960927	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0035177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	213	395	0	ENST00000268712.3:c.6293C>G	p.Ser2098Ter	p.S2098*	ENST00000268712	NM_006311.3	2098	tCa/tGa	40/46	1	2	FACETS	0.947	0.885	1	0.947	0.885	1	CLONAL	1	TRUE	1	0.725870351905114	2		395	620	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33433424	33433424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780491769	NA	P-0035177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	249	635	1	ENST00000345365.6:c.557G>A	p.Arg186Gln	p.R186Q	ENST00000345365	NM_002878.3	186	cGa/cAa	6/10	1	2	FACETS	0.937	0.881	0.995	0.937	0.881	0.995	CLONAL	1	TRUE	1	0.725870351905114	2		636	732	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095912	29095912	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	257	488	0	ENST00000328354.6:c.922G>C	p.Glu308Gln	p.E308Q	ENST00000328354	NM_007194.3	308	Gag/Cag	9/15	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.725870351905114	2		488	706	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924945	49924945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	298	596	0	ENST00000296474.3:c.3998C>T	p.Thr1333Ile	p.T1333I	ENST00000296474	NM_002447.2	1333	aCc/aTc	20/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.725870351905114	2		596	770	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447721	187447721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746850741	NA	P-0035177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	280	513	0	ENST00000232014.4:c.472C>T	p.Arg158Trp	p.R158W	ENST00000232014	NM_001130845.1	158	Cgg/Tgg	5/10	1	2	FACETS	0.999	0.943	1	0.999	0.943	1	CLONAL	1	TRUE	1	0.725870351905114	2		513	772	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944592	38944592	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	151	404	0	ENST00000357387.3:c.4869G>C	p.Leu1623Phe	p.L1623F	ENST00000357387	NM_152756.3	1623	ttG/ttC	36/38	0.725870351905114	3	FACETS	0.782	0.716	0.851	0.391	0.358	0.426	SUBCLONAL	1	TRUE	1	0.725870351905114	3		404	725	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944618	38944618	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	156	429	0	ENST00000357387.3:c.4843G>C	p.Glu1615Gln	p.E1615Q	ENST00000357387	NM_152756.3	1615	Gaa/Caa	36/38	0.725870351905114	3	FACETS	0.826	0.758	0.897	0.413	0.379	0.449	CLONAL	1	TRUE	1	0.725870351905114	3		429	709	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176969	56176969	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	242	413	1	ENST00000399503.3:c.2239G>T	p.Glu747Ter	p.E747*	ENST00000399503	NM_005921.1	747	Gaa/Taa	13/20	0.725870351905114	3	FACETS	1	0.948	1	0.508	0.475	0.541	CLONAL	1	TRUE	1	0.725870351905114	3		414	895	SUCCESS
APC	324	MSKCC	GRCh37	5	112175021	112175021	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs79122263	NA	P-0035177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	128	238	0	ENST00000257430.4:c.3730C>G	p.Gln1244Glu	p.Q1244E	ENST00000257430	NM_000038.5	1244	Caa/Gaa	16/16	0.725870351905114	3	FACETS	1	0.954	1	0.534	0.487	0.582	CLONAL	1	TRUE	1	0.725870351905114	3		238	450	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64288863	64288863	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	316	620	0	ENST00000370651.3:c.259C>G	p.Leu87Val	p.L87V	ENST00000370651	NM_003463.4	87	Ctt/Gtt	4/6	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.725870351905114	2		620	831	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004481	150004481	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	359	675	0	ENST00000253339.5:c.1744G>C	p.Glu582Gln	p.E582Q	ENST00000253339		582	Gag/Cag	3/7	0.725870351905114	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.725870351905114	1		675	585	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0035178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	64	432	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	0.23	2		432	495	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690802	89690802	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1114167621	NA	P-0035178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	37	290	0	ENST00000371953.3:c.210-1G>A		p.X70_splice	ENST00000371953	NM_000314.4	70			1	2	FACETS	0.919	0.76	1	0.919	0.76	1	CLONAL	1	TRUE	1	0.23	2		290	350	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023177	27023178	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0035178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	12	54	0	ENST00000324856.7:c.287_288dup	p.Glu97ArgfsTer5	p.E97Rfs*5	ENST00000324856	NM_006015.4	95	ggc/gGCgc	1/20	0.283417195932268	2	FACETS	1	0.822	1	1	0.822	1	CLONAL	2	TRUE	0	0.23	2		54	44	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216639	36216639	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	59	569	0	ENST00000222270.7:c.3805G>T	p.Glu1269Ter	p.E1269*	ENST00000222270	NM_014727.1	1269	Gag/Tag	13/37	0.158965099995912	0	FACETS	1	0.893	1			1	CLONAL	1	TRUE	0	0.23	0		569	380	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0035179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	162	567	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.841	0.779	0.903	0.841	0.779	0.903	CLONAL	1	TRUE	1	0.894269876869515	2		567	431	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	240	594	0	ENST00000335508.6:c.2704G>A	p.Glu902Lys	p.E902K	ENST00000335508	NM_012433.2	902	Gaa/Aaa	18/25	1	2	FACETS	0.96	0.905	1	0.96	0.905	1	CLONAL	1	TRUE	1	0.894269876869515	2		594	559	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171455	123171455	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	76	249	0	ENST00000218089.9:c.367C>T	p.Gln123Ter	p.Q123*	ENST00000218089	NM_001042749.1	123	Cag/Tag	6/35	1	1	FACETS	0.359	0.318	0.401	0.359	0.318	0.401	SUBCLONAL	1	TRUE	0	0.894269876869515	1		249	262	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838145	89838145	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	286	643	0	ENST00000389301.3:c.2092G>A	p.Glu698Lys	p.E698K	ENST00000389301	NM_000135.2	698	Gag/Aag	23/43	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.894269876869515	2		643	611	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438647	49438647	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	308	721	0	ENST00000301067.7:c.4843C>T	p.Arg1615Ter	p.R1615*	ENST00000301067	NM_003482.3	1615	Cga/Tga	19/54	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.894269876869515	2		721	668	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944608	40944608	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs752116362	NA	P-0035179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	156	313	1	ENST00000373198.4:c.1894C>T	p.Arg632Ter	p.R632*	ENST00000373198	NM_133170.3	632	Cga/Tga	12/32	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.894269876869515	2		314	342	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483332	120483332	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	56	355	0	ENST00000256646.2:c.3029C>G	p.Ser1010Cys	p.S1010C	ENST00000256646	NM_024408.3	1010	tCt/tGt	19/34	1	2	FACETS	0.305	0.262	0.352	0.305	0.262	0.352	SUBCLONAL	1	TRUE	1	0.894269876869515	2		355	411	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150022942	150022943	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTGTGGATTAACTTCTGTGGATTTGTGGATTAACTTC	novel	NA	P-0035179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	128	565	0	ENST00000253339.5:c.320_321insGAAGTTAATCCACAAATCCACAGAAGTTAATCCACAA	p.Asp108LysfsTer20	p.D108Kfs*20	ENST00000253339		107	caa/caGAAGTTAATCCACAAATCCACAGAAGTTAATCCACAAa	1/7	1	2	FACETS	0.539	0.491	0.589	0.539	0.491	0.589	SUBCLONAL	1	TRUE	1	0.894269876869515	2		565	531	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874525	151874526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACAA	novel	NA	P-0035179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	238	442	0	ENST00000262189.6:c.8012_8013insTTGT	p.Ser2672CysfsTer3	p.S2672Cfs*3	ENST00000262189	NM_170606.2	2671	acg/acTTGTg	38/59	0.317998486892102	3	FACETS	0.763	0.72	0.806	0.763	0.72	0.806	INDETERMINATE	2	TRUE	1	0.894269876869515	3		442	505	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	43	349	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.324762476742994	2		349	259	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0035210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	101	547	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.77	0.693	0.85	1	0.983	1	SUBCLONAL	2	TRUE	1	0.324762476742994	2		547	404	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0035210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	148	405	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.324762476742994	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.324762476742994	2		408	406	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	44	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.919	0.774	1	0.919	0.774	1	CLONAL	1	TRUE	1	0.324762476742994	2		493	295	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188188	32188188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370312303	NA	P-0035210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	75	532	0	ENST00000375023.3:c.1153C>T	p.Arg385Cys	p.R385C	ENST00000375023	NM_004557.3	385	Cgc/Tgc	6/30	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.324762476742994	2		532	441	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911579	134911579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs959853730	NA	P-0035210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	98	541	1	ENST00000398015.3:c.2044C>T	p.Arg682Cys	p.R682C	ENST00000398015	NM_004441.4	682	Cgc/Tgc	11/16	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.324762476742994	2		542	601	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591846	48591846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	68	560	0	ENST00000342988.3:c.1009G>A	p.Glu337Lys	p.E337K	ENST00000342988	NM_005359.5	337	Gag/Aag	9/12	0.324762476742994	1	FACETS	0.864	0.755	0.981	0.864	0.755	0.981	CLONAL	1	TRUE	0	0.324762476742994	1		560	406	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119031	70119032	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCAT	novel	NA	P-0035210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	75	622	1	ENST00000245479.2:c.604_608dup	p.Ile203MetfsTer18	p.I203Mfs*18	ENST00000245479	NM_000346.3	201	-/GCCAT	2/3	1	2	FACETS	0.871	0.765	0.986	0.871	0.765	0.986	CLONAL	1	TRUE	1	0.324762476742994	2		623	530	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593505	48593505	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	55	347	0	ENST00000342988.3:c.1256G>C	p.Gly419Ala	p.G419A	ENST00000342988	NM_005359.5	419	gGg/gCg	10/12	0.324762476742994	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.324762476742994	1		347	251	SUCCESS
APC	324	MSKCC	GRCh37	5	112174108	112174112	+	frameshift_variant	Frame_Shift_Del	DEL	GTCGG	GTCGG	-	novel	NA	P-0035210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	28	328	0	ENST00000257430.4:c.2817_2821del	p.Ser940LysfsTer4	p.S940Kfs*4	ENST00000257430	NM_000038.5	939	aaGTCGGaa/aaaa	16/16	1	2	FACETS	1	0.814	1	1	0.814	1	CLONAL	1	TRUE	1	0.324762476742994	2		328	171	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44515577	44515577	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	189	565	0	ENST00000291552.4:c.319G>C	p.Asp107His	p.D107H	ENST00000291552	NM_006758.2	107	Gac/Cac	5/8	0.348315930138981	2	FACETS	0.645	0.597	0.696	0.323	0.298	0.348	INDETERMINATE	1	TRUE	0	0.632498949432667	2		565	926	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014076	70014076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759306986	NA	P-0035211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	125	403	2	ENST00000394351.3:c.937C>T	p.Arg313Trp	p.R313W	ENST00000394351	NM_000248.3	313	Cgg/Tgg	9/9	0.638710729898992	2	FACETS	0.697	0.633	0.764	0.349	0.316	0.382	SUBCLONAL	1	TRUE	0	0.632498949432667	2		405	567	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0035211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	1281	669	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.555660160651166	4	FACETS	1	0.998	1			1	CLONAL	4	TRUE	NA	0.632498949432667	4		669	1513	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088700	27088700	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	367	547	0	ENST00000324856.7:c.2309C>A	p.Ala770Asp	p.A770D	ENST00000324856	NM_006015.4	770	gCc/gAc	7/20	0.300371492677129	3	FACETS	1	0.995	1			1	INDETERMINATE	1	TRUE	NA	0.632498949432667	3		547	1021	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8246263	8246263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	90	330	0	ENST00000335790.3:c.371G>A	p.Cys124Tyr	p.C124Y	ENST00000335790	NM_002315.2	124	tGt/tAt	4/4	0.638710729898992	1	FACETS	0.614	0.55	0.68	0.614	0.55	0.68	SUBCLONAL	1	TRUE	0	0.632498949432667	1		330	317	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497567	125497567	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	77	270	0	ENST00000428830.2:c.131G>C	p.Arg44Pro	p.R44P	ENST00000428830	NM_001114121.2	44	cGt/cCt	3/14	NA	2	FACETS	0.678	0.599	0.762			1	INDETERMINATE	1	TRUE	NA	0.632498949432667	2		270	359	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298829	46298829	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	99	186	0	ENST00000334344.6:c.5476G>T	p.Glu1826Ter	p.E1826*	ENST00000334344	NM_152641.2	1826	Gaa/Taa	21/21	NA	2	FACETS	0.877	0.79	0.967			1	INDETERMINATE	1	TRUE	NA	0.632498949432667	2		186	357	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428235	49428235	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	208	601	0	ENST00000301067.7:c.10465C>T	p.Gln3489Ter	p.Q3489*	ENST00000301067	NM_003482.3	3489	Cag/Tag	37/54	NA	2	FACETS	0.752	0.698	0.807			1	INDETERMINATE	1	TRUE	NA	0.632498949432667	2		601	875	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440152	49440152	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	342	438	0	ENST00000301067.7:c.4474C>T	p.Gln1492Ter	p.Q1492*	ENST00000301067	NM_003482.3	1492	Cag/Tag	16/54	NA	2	FACETS	0.762	0.726	0.797			1	INDETERMINATE	2	TRUE	NA	0.632498949432667	2		438	710	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37871774	37871774	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2804	198	517	0	ENST00000269571.5:c.1298G>C	p.Gly433Ala	p.G433A	ENST00000269571		433	gGa/gCa	11/27	0.632498949432667	10	FACETS	0.736	0.678	0.798			1	SUBCLONAL	1	TRUE	NA	0.632498949432667	10		517	3002	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447531	12447531	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	330	431	0	ENST00000287820.6:c.770C>G	p.Thr257Ser	p.T257S	ENST00000287820	NM_015869.4	257	aCc/aGc	5/7	0.638710729898992	3	FACETS	0.823	0.782	0.866	0.549	0.521	0.577	CLONAL	2	TRUE	0	0.632498949432667	3		431	834	SUCCESS
BTK	695	MSKCC	GRCh37	X	100625025	100625025	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	148	236	0	ENST00000308731.7:c.352G>C	p.Glu118Gln	p.E118Q	ENST00000308731	NM_000061.2	118	Gaa/Caa	5/19	0.609082842449073	0	FACETS	0.764	0.72	0.807			1	SUBCLONAL	1	TRUE	NA	0.632498949432667	0		236	225	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922049	39922049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1395	197	690	0	ENST00000378444.4:c.4123C>T	p.Arg1375Trp	p.R1375W	ENST00000378444	NM_001123385.1	1375	Cgg/Tgg	9/15	0.562084426236142	6	FACETS	0.935	0.863	1			1	CLONAL	1	TRUE	NA	0.562084426236142	6		690	1592	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2224022	2224024	+	inframe_deletion	In_Frame_Del	DEL	CAG	CAG	-	novel	NA	P-0035213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	83	707	0	ENST00000326181.6:c.1236_1238del	p.Ser413del	p.S413del	ENST00000326181	NM_032271.2	412	ttCAGt/ttt	13/21	0.562084426236142	3	FACETS	0.393	0.346	0.444	0.197	0.173	0.222	SUBCLONAL	1	TRUE	1	0.562084426236142	3		707	962	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257731	198257731	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs769195785	NA	P-0035213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	137	334	0	ENST00000335508.6:c.3721A>G	p.Ile1241Val	p.I1241V	ENST00000335508	NM_012433.2	1241	Att/Gtt	24/25	0.562084426236142	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.562084426236142	2		334	223	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939369	76939369	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0035213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	245	708	0	ENST00000373344.5:c.1379C>G	p.Ser460Ter	p.S460*	ENST00000373344	NM_000489.3	460	tCa/tGa	9/35	0.33227332792218	5	FACETS	1	0.987	1	0.791	0.744	0.84	INDETERMINATE	2	TRUE	2	0.562084426236142	5		708	677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519991	NA	P-0035219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	41	489	0	ENST00000269305.4:c.536A>C	p.His179Pro	p.H179P	ENST00000269305	NM_001126112.2	179	cAt/cCt	5/11	0.3	1	FACETS	0.718	0.599	0.849	0.718	0.599	0.849	SUBCLONAL	1	TRUE	0	0.27	1		489	366	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026123	71026124	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAAA	novel	NA	P-0035219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	116	329	0	ENST00000318789.4:c.1495_1498dup	p.Ala500ValfsTer18	p.A500Vfs*18	ENST00000318789	NM_032682.5	500	gct/gTTTGct	17/21	0.3	3	FACETS	0.882	0.798	0.97			1	CLONAL	2	TRUE	NA	0.27	3		329	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578460	+	inframe_deletion	In_Frame_Del	DEL	CGCGGA	CGCGGA	-	novel	NA	P-0035222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	212	546	0	ENST00000269305.4:c.470_475del	p.Val157_Arg158del	p.V157_R158del	ENST00000269305	NM_001126112.2	157	gTCCGCGcc/gcc	5/11	0.491495368477255	1	FACETS	0.99	0.925	1	0.99	0.925	1	CLONAL	1	TRUE	0	0.491495368477255	1		546	657	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446967	187446967	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763470720	NA	P-0035222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	110	500	0	ENST00000232014.4:c.1226C>T	p.Thr409Met	p.T409M	ENST00000232014	NM_001130845.1	409	aCg/aTg	5/10	0.332956547122755	1	FACETS	0.5	0.45	0.553	0.5	0.45	0.553	SUBCLONAL	1	TRUE	0	0.491495368477255	1		500	675	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007388	143007399	+	inframe_deletion	In_Frame_Del	DEL	TGTTCCTGAAAA	TGTTCCTGAAAA	-	novel	NA	P-0035222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	76	233	0	ENST00000262992.4:c.2385_2396del	p.His795_Glu798del	p.H795_E798del	ENST00000262992	NM_001101669.1	795	caTTTTCAGGAACAa/caa	22/24	0.491495368477255	1	FACETS	0.62	0.547	0.698	0.62	0.547	0.698	SUBCLONAL	1	TRUE	0	0.491495368477255	1		233	376	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0035225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	261	384	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.562903240658807	4	FACETS	0.959	0.903	1	0.639	0.602	0.677	CLONAL	2	TRUE	1	0.590636968928153	4		384	733	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443701	49443701	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	192	534	0	ENST00000301067.7:c.3670G>C	p.Glu1224Gln	p.E1224Q	ENST00000301067	NM_003482.3	1224	Gag/Cag	11/54	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.590636968928153	2		534	642	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3799654	3799654	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	109	360	0	ENST00000262367.5:c.3810G>C	p.Lys1270Asn	p.K1270N	ENST00000262367	NM_004380.2	1270	aaG/aaC	21/31	0.590636968928153	3	FACETS	0.843	0.759	0.931	0.281	0.253	0.311	CLONAL	1	TRUE	0	0.590636968928153	3		360	567	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40490790	40490790	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	282	358	0	ENST00000264657.5:c.509A>T	p.Asp170Val	p.D170V	ENST00000264657	NM_139276.2	170	gAt/gTt	6/24	0.590636968928153	3	FACETS	0.965	0.914	1	0.965	0.914	1	CLONAL	2	TRUE	1	0.590636968928153	3		358	641	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216592	2216592	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	237	638	0	ENST00000398665.3:c.2236G>A	p.Glu746Lys	p.E746K	ENST00000398665	NM_032482.2	746	Gag/Aag	20/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.590636968928153	2		638	744	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513694	41513694	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	151	413	0	ENST00000263253.7:c.598C>T	p.Arg200Ter	p.R200*	ENST00000263253	NM_001429.3	200	Cga/Tga	2/31	1	2	FACETS	0.987	0.908	1	0.987	0.908	1	CLONAL	1	TRUE	1	0.590636968928153	2		413	518	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271447	26271447	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1453083205	NA	P-0035225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	124	365	0	ENST00000305910.3:c.166C>T	p.Gln56Ter	p.Q56*	ENST00000305910	NM_003534.2	56	Cag/Tag	1/1	0.590636968928153	2	FACETS	0.871	0.793	0.953	0.436	0.396	0.477	CLONAL	1	TRUE	0	0.590636968928153	2		365	482	SUCCESS
APC	324	MSKCC	GRCh37	5	112175153	112175153	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	27	194	0	ENST00000257430.4:c.3862G>T	p.Gly1288Ter	p.G1288*	ENST00000257430	NM_000038.5	1288	Gga/Tga	16/16	0.684547875759172	1	FACETS	0.752	0.622	0.888	0.752	0.622	0.888	SUBCLONAL	1	TRUE	0	0.684547875759172	1		194	69	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-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	63	450	0	ENST00000371085.3:c.718+1_719-1del		p.X240_splice	ENST00000371085	NM_000516.4	240		9/13	0.347593227100263	3	FACETS	0.304	0.262	0.35			1	INDETERMINATE	1	TRUE	NA	0.684547875759172	3		450	813	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484858	57485003	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTTTGTGGAGTGACCGCCCACCCCCTGCGCTTGCCCAGGAGGCCCTGGTCTGCACTGTTTATAGAGAAGAACCCCGTGCAAGCATTCCAGACCCCTGGCCGAAAGCGCGCTTCTCCCAAGCATTCACACGGCCTCCCTTCTTGT	AGGTTTGTGGAGTGACCGCCCACCCCCTGCGCTTGCCCAGGAGGCCCTGGTCTGCACTGTTTATAGAGAAGAACCCCGTGCAAGCATTCCAGACCCCTGGCCGAAAGCGCGCTTCTCCCAAGCATTCACACGGCCTCCCTTCTTGT	-	novel	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	79	371	0	ENST00000371085.3:c.839+1_840-1del		p.X280_splice	ENST00000371085	NM_000516.4	280		10/13	0.347593227100263	3	FACETS	0.475	0.418	0.537			1	INDETERMINATE	1	TRUE	NA	0.684547875759172	3		371	652	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-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	48	250	0	ENST00000371085.3:c.970+1_971-1del		p.X324_splice	ENST00000371085	NM_000516.4	324		11/13	0.347593227100263	3	FACETS	0.458	0.388	0.535			1	INDETERMINATE	1	TRUE	NA	0.684547875759172	3		250	411	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474041	29474041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs78723472	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	127	591	0	ENST00000389048.3:c.2134G>A	p.Val712Met	p.V712M	ENST00000389048	NM_004304.4	712	Gtg/Atg	12/29	1	2	FACETS	0.499	0.453	0.549	0.499	0.453	0.549	SUBCLONAL	1	TRUE	1	0.684547875759172	2		591	743	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761381	59761381	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	214	426	1	ENST00000259008.2:c.3026del	p.Gly1009AspfsTer50	p.G1009Dfs*50	ENST00000259008	NM_032043.2	1009	gGa/ga	20/20	0.684547875759172	3	FACETS	0.862	0.809	0.914	0.862	0.809	0.914	CLONAL	2	TRUE	1	0.684547875759172	3		427	487	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965707	93965707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752253692	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	94	282	0	ENST00000369303.4:c.2221G>A	p.Gly741Arg	p.G741R	ENST00000369303	NM_004440.3	741	Gga/Aga	13/17	0.684547875759172	1	FACETS	0.936	0.854	1	0.936	0.854	1	CLONAL	1	TRUE	0	0.684547875759172	1		282	193	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-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	65	250	0	ENST00000371085.3:c.1038+1_1039-1del		p.X346_splice	ENST00000371085	NM_000516.4	346		12/13	0.347593227100263	3	FACETS	0.491	0.426	0.561			1	INDETERMINATE	1	TRUE	NA	0.684547875759172	3		250	519	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95593014	95593014	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	87	377	0	ENST00000393063.1:c.806G>T	p.Arg269Ile	p.R269I	ENST00000393063	NM_030621.3	269	aGa/aTa	8/28	0.270663004544483	3	FACETS	0.992	0.886	1	0.496	0.443	0.552	INDETERMINATE	1	TRUE	1	0.684547875759172	3		377	344	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121536	2121536	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	311	632	0	ENST00000219476.3:c.1865G>T	p.Arg622Leu	p.R622L	ENST00000219476	NM_000548.3	622	cGg/cTg	18/42	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.684547875759172	2		632	901	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457216	89457216	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	84	329	0	ENST00000336596.2:c.1698-1G>T		p.X566_splice	ENST00000336596	NM_005233.5	566			1	2	FACETS	0.93	0.832	1	0.93	0.832	1	CLONAL	1	TRUE	1	0.684547875759172	2		329	264	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106495	27106495	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	238	438	2	ENST00000324856.7:c.6106G>T	p.Glu2036Ter	p.E2036*	ENST00000324856	NM_006015.4	2036	Gaa/Taa	20/20	1	2	FACETS	0.96	0.901	1	0.96	0.901	1	CLONAL	1	TRUE	1	0.684547875759172	2		440	724	SUCCESS
FH	2271	MSKCC	GRCh37	1	241669312	241669312	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	54	309	0	ENST00000366560.3:c.895G>T	p.Ala299Ser	p.A299S	ENST00000366560	NM_000143.3	299	Gca/Tca	6/10	0.433542260160639	1	FACETS	0.354	0.304	0.408	0.354	0.304	0.408	SUBCLONAL	1	TRUE	0	0.684547875759172	1		309	293	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104269045	104269045	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	202	410	0	ENST00000369902.3:c.302del	p.Asp101AlafsTer20	p.D101Afs*20	ENST00000369902	NM_016169.3	101	gAc/gc	2/12	0.378878938072675	3	FACETS	1	0.966	1	0.355	0.33	0.381	INDETERMINATE	1	TRUE	0	0.684547875759172	3		410	744	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572252	64572252	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	288	296	0	ENST00000312049.6:c.1387G>T	p.Glu463Ter	p.E463*	ENST00000312049	NM_130799.2	463	Gag/Tag	10/10	0.220106928595687	3	FACETS	1	0.979	1	0.701	0.667	0.735	INDETERMINATE	2	TRUE	0	0.684547875759172	3		296	537	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998274	100998275	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	58	60	0	ENST00000325455.5:c.1527dup	p.Ala510ArgfsTer64	p.A510Rfs*64	ENST00000325455	NM_001202474.3	509	-/C	1/8	0.645339508565968	2	FACETS	1	0.967	1	0.647	0.572	0.722	CLONAL	1	TRUE	0	0.684547875759172	2		60	131	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360559	118360559	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	152	325	0	ENST00000534358.1:c.4532G>T	p.Gly1511Val	p.G1511V	ENST00000534358	NM_005933.3	1511	gGa/gTa	12/36	0.645339508565968	2	FACETS	0.851	0.797	0.903	0.851	0.797	0.903	CLONAL	2	TRUE	0	0.684547875759172	2		325	261	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858625	57858625	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs150011919	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	354	436	0	ENST00000228682.2:c.363C>A	p.Tyr121Ter	p.Y121*	ENST00000228682	NM_005269.2	121	taC/taA	4/12	0.638386994350469	2	FACETS	0.909	0.873	0.944	0.909	0.873	0.944	CLONAL	2	TRUE	0	0.684547875759172	2		436	569	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112418	115112418	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	503	419	0	ENST00000257566.3:c.1322C>A	p.Thr441Asn	p.T441N	ENST00000257566	NM_016569.3	441	aCc/aAc	7/8	0.684547875759172	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.684547875759172	2		419	665	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423637	88423637	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	85	294	0	ENST00000360948.2:c.2198C>G	p.Pro733Arg	p.P733R	ENST00000360948	NM_001012338.2	733	cCc/cGc	18/19	0.165420106264339	2	FACETS	0.624	0.555	0.697	0.312	0.277	0.349	INDETERMINATE	1	TRUE	0	0.684547875759172	2		294	398	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476354	88476354	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	305	482	1	ENST00000360948.2:c.1778C>A	p.Thr593Asn	p.T593N	ENST00000360948	NM_001012338.2	593	aCc/aAc	15/19	0.165420106264339	2	FACETS	1	0.993	1	0.656	0.623	0.69	INDETERMINATE	1	TRUE	0	0.684547875759172	2		483	679	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2093595	2093595	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	302	547	0	ENST00000219066.1:c.682G>T	p.Val228Leu	p.V228L	ENST00000219066	NM_002528.5	228	Gtg/Ttg	4/6	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.684547875759172	2		547	838	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576849	7576874	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTACCTGAAGGGTGAAATATTCTCCA	GTACCTGAAGGGTGAAATATTCTCCA	TCCT	novel	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	150	518	1	ENST00000269305.4:c.972_993+4delinsAGGA		p.X324_splice	ENST00000269305	NM_001126112.2	324		9/11	0.684547875759172	1	FACETS	0.927	0.862	0.991	0.927	0.862	0.991	CLONAL	1	TRUE	0	0.684547875759172	1		519	311	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371855	45372032	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTATGATTAAAAAAGGTAAAAGAAATTGTCAAAAGAGTATCATTATTAAAAAGTAATTTTAAAAGGGTTACAAGTTTTAGAATATGAGCATGCAATCATCTACTGATTCCTAAAATTAGCAACAAGAAAAACTAAGCAAGTTGACATGATAGGTTTATGTACATTATTGAATCCATA	CCTATGATTAAAAAAGGTAAAAGAAATTGTCAAAAGAGTATCATTATTAAAAAGTAATTTTAAAAGGGTTACAAGTTTTAGAATATGAGCATGCAATCATCTACTGATTCCTAAAATTAGCAACAAGAAAAACTAAGCAAGTTGACATGATAGGTTTATGTACATTATTGAATCCATA	-	novel	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	17	243	0	ENST00000262160.6:c.1135+2_1136del		p.X379_splice	ENST00000262160	NM_005901.5	379		10/11	0.346138962988588	4	FACETS	0.294	0.219	0.382			1	INDETERMINATE	1	TRUE	NA	0.684547875759172	4		243	285	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519840	29519840	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	204	422	0	ENST00000389048.3:c.1731A>T	p.Gln577His	p.Q577H	ENST00000389048	NM_004304.4	577	caA/caT	9/29	1	2	FACETS	0.98	0.915	1	0.98	0.915	1	CLONAL	1	TRUE	1	0.684547875759172	2		422	608	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940457	29940457	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	64	239	0	ENST00000389048.3:c.774T>A	p.His258Gln	p.H258Q	ENST00000389048	NM_004304.4	258	caT/caA	2/29	1	2	FACETS	0.984	0.868	1	0.984	0.868	1	CLONAL	1	TRUE	1	0.684547875759172	2		239	190	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403171	213403171	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	135	244	0	ENST00000342788.4:c.82+2T>A		p.X28_splice	ENST00000342788	NM_005235.2	28			1	2	FACETS	0.984	0.903	1	0.984	0.903	1	CLONAL	1	TRUE	1	0.684547875759172	2		244	401	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484479	57484575	+	splice_acceptor_variant,splice_donor_variant,intron_variant	Splice_Site	DEL	GTAAGCCAACTGTTACCTTTTTATATAACAGAGATCATGGTTTCTTGACATTCACCCCAGTCCCTCTGGAATAACCAGCTGTCCTCCTCCCCACCAG	GTAAGCCAACTGTTACCTTTTTATATAACAGAGATCATGGTTTCTTGACATTCACCCCAGTCCCTCTGGAATAACCAGCTGTCCTCCTCCCCACCAG	-	novel	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	27	367	0	ENST00000371085.3:c.659+1_660-1del		p.X220_splice	ENST00000371085	NM_000516.4	220			0.347593227100263	3	FACETS	0.202	0.16	0.25			1	INDETERMINATE	1	TRUE	NA	0.684547875759172	3		367	525	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513510	41513510	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	173	413	0	ENST00000263253.7:c.416del	p.Gly139AlafsTer15	p.G139Afs*15	ENST00000263253	NM_001429.3	138	atG/at	2/31	0.684547875759172	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.684547875759172	1		413	314	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199923	128199923	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	180	407	0	ENST00000341105.2:c.1382C>A	p.Pro461His	p.P461H	ENST00000341105	NM_032638.4	461	cCc/cAc	6/6	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.684547875759172	2		407	483	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202797	128202797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	248	501	0	ENST00000341105.2:c.923G>A	p.Arg308Gln	p.R308Q	ENST00000341105	NM_032638.4	308	cGg/cAg	4/6	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.684547875759172	2		501	721	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196877	106196877	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1371075754	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	78	238	0	ENST00000380013.4:c.5210C>T	p.Thr1737Ile	p.T1737I	ENST00000380013	NM_001127208.2	1737	aCc/aTc	11/11	0.684547875759172	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.684547875759172	1		238	130	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31483684	31483684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	27	136	0	ENST00000344624.3:c.2048C>T	p.Pro683Leu	p.P683L	ENST00000344624		683	cCa/cTa	13/33	0.451708184966499	1	FACETS	0.295	0.236	0.36	0.295	0.236	0.36	SUBCLONAL	1	TRUE	0	0.684547875759172	1		136	176	SUCCESS
APC	324	MSKCC	GRCh37	5	112177725	112177725	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1554087422	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	37	244	0	ENST00000257430.4:c.6434G>C	p.Gly2145Ala	p.G2145A	ENST00000257430	NM_000038.5	2145	gGa/gCa	16/16	0.684547875759172	1	FACETS	0.603	0.508	0.702	0.603	0.508	0.702	SUBCLONAL	1	TRUE	0	0.684547875759172	1		244	118	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20483034	20483034	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	105	267	0	ENST00000346618.3:c.767G>A	p.Cys256Tyr	p.C256Y	ENST00000346618	NM_001949.4	256	tGt/tAt	4/7	0.323352893968832	6	FACETS	0.828	0.746	0.913			1	INDETERMINATE	2	TRUE	NA	0.684547875759172	6		267	439	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197445	26197445	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1258094123	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	92	249	0	ENST00000356476.2:c.34A>T	p.Thr12Ser	p.T12S	ENST00000356476		12	Acg/Tcg	1/1	0.323352893968832	6	FACETS	0.812	0.727	0.902			1	INDETERMINATE	2	TRUE	NA	0.684547875759172	6		249	392	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148529772	148529772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	81	269	0	ENST00000320356.2:c.317C>T	p.Ser106Leu	p.S106L	ENST00000320356	NM_004456.4	106	tCa/tTa	4/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.684547875759172	2		269	223	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860713	151860713	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	184	426	0	ENST00000262189.6:c.9949A>T	p.Thr3317Ser	p.T3317S	ENST00000262189	NM_170606.2	3317	Aca/Tca	43/59	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.684547875759172	2		426	532	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046368	69046368	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	103	420	0	ENST00000288368.4:c.3841C>G	p.Gln1281Glu	p.Q1281E	ENST00000288368	NM_024870.2	1281	Cag/Gag	32/40	0.356099980688015	1	FACETS	0.438	0.394	0.484	0.438	0.394	0.484	INDETERMINATE	1	TRUE	0	0.684547875759172	1		420	452	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080579	5080579	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	26	291	0	ENST00000381652.3:c.2330G>A	p.Trp777Ter	p.W777*	ENST00000381652	NM_004972.3	777	tGg/tAg	18/25	0.684547875759172	1	FACETS	0.52	0.422	0.627	0.52	0.422	0.627	SUBCLONAL	1	TRUE	0	0.684547875759172	1		291	96	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247149	53247149	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	112	267	0	ENST00000375401.3:c.352-1G>T		p.X118_splice	ENST00000375401	NM_004187.3	118			0.684547875759172	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.684547875759172	1		267	193	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351955	70351955	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	227	479	1	ENST00000374080.3:c.4152G>T	p.Lys1384Asn	p.K1384N	ENST00000374080		1384	aaG/aaT	30/45	0.684547875759172	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.684547875759172	1		480	403	SUCCESS
BTK	695	MSKCC	GRCh37	X	100612517	100612517	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	145	434	0	ENST00000308731.7:c.1157C>A	p.Ser386Tyr	p.S386Y	ENST00000308731	NM_000061.2	386	tCc/tAc	13/19	0.684547875759172	1	FACETS	0.945	0.878	1	0.945	0.878	1	CLONAL	1	TRUE	0	0.684547875759172	1		434	295	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	39	349	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.775	0.647	0.915	0.775	0.647	0.915	CLONAL	1	TRUE	1	0.421268057667473	2		349	239	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506210	148506210	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	43	437	0	ENST00000320356.2:c.2148del	p.Phe716LeufsTer24	p.F716Lfs*24	ENST00000320356	NM_004456.4	716	ttT/tt	19/20	1	2	FACETS	0.4	0.334	0.472	0.4	0.334	0.472	SUBCLONAL	1	TRUE	1	0.421268057667473	2		437	511	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212460	36212484	+	frameshift_variant	Frame_Shift_Del	DEL	ACTGCAGCCCCTGCAGGCCTTGCAA	ACTGCAGCCCCTGCAGGCCTTGCAA	-	novel	NA	P-0035228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	78	611	0	ENST00000222270.7:c.2213_2237del	p.Leu738ProfsTer43	p.L738Pfs*43	ENST00000222270	NM_014727.1	737	ctACTGCAGCCCCTGCAGGCCTTGCAA/ct	3/37	1	2	FACETS	0.485	0.426	0.549	0.485	0.426	0.549	SUBCLONAL	1	TRUE	1	0.421268057667473	2		611	763	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	52	365	0	ENST00000263967.3:c.333G>T	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaT	2/21	1	2	FACETS	0.932	0.794	1	0.932	0.794	1	CLONAL	1	TRUE	1	0.24	2		365	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0035240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	70	652	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.275685802309575	1	FACETS	0.96	0.838	1	0.96	0.838	1	CLONAL	1	TRUE	0	0.24	1		652	535	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0035240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	44	331	1	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	0.275685802309575	1	FACETS	0.801	0.673	0.942	0.801	0.673	0.942	CLONAL	1	TRUE	0	0.24	1		332	403	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93953233	93953233	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	58	459	0	ENST00000369303.4:c.2908C>A	p.Leu970Met	p.L970M	ENST00000369303	NM_004440.3	970	Ctg/Atg	17/17	0.275685802309575	1	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	0	0.24	1		459	408	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102066	27102066	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0035240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	49	465	0	ENST00000324856.7:c.4994-2A>T		p.X1665_splice	ENST00000324856	NM_006015.4	1665			1	2	FACETS	0.89	0.754	1	0.89	0.754	1	CLONAL	1	TRUE	1	0.24	2		465	459	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363564	40363564	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	65	550	0	ENST00000397332.2:c.665G>T	p.Arg222Leu	p.R222L	ENST00000397332	NM_001033082.2	222	cGa/cTa	3/3	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.24	2		550	477	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400971	72400971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	32	264	0	ENST00000357731.5:c.200C>T	p.Ser67Leu	p.S67L	ENST00000357731	NM_173808.2	67	tCa/tTa	2/7	1	2	FACETS	0.749	0.609	0.907	0.749	0.609	0.907	CLONAL	1	TRUE	1	0.24	2		264	356	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910588	32910588	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	42	347	0	ENST00000380152.3:c.2096A>T	p.Gln699Leu	p.Q699L	ENST00000380152		699	cAg/cTg	11/27	1	2	FACETS	0.847	0.708	1	0.847	0.708	1	CLONAL	1	TRUE	1	0.24	2		347	413	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937089	48937089	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	29	189	0	ENST00000267163.4:c.857A>T	p.Asp286Val	p.D286V	ENST00000267163	NM_000321.2	286	gAt/gTt	8/27	1	2	FACETS	0.885	0.713	1	0.885	0.713	1	CLONAL	1	TRUE	1	0.24	2		189	273	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95578585	95578585	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0035240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	37	248	0	ENST00000393063.1:c.2041-1G>T		p.X681_splice	ENST00000393063	NM_030621.3	681			1	2	FACETS	1	0.839	1	1	0.839	1	CLONAL	1	TRUE	1	0.24	2		248	304	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727421	66727421	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	29	354	0	ENST00000307102.5:c.137A>G	p.Gln46Arg	p.Q46R	ENST00000307102	NM_002755.3	46	cAg/cGg	2/11	1	2	FACETS	0.753	0.605	0.92	0.753	0.605	0.92	CLONAL	1	TRUE	1	0.24	2		354	321	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593533	48593533	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	32	207	1	ENST00000342988.3:c.1284G>T	p.Lys428Asn	p.K428N	ENST00000342988	NM_005359.5	428	aaG/aaT	10/12	1	2	FACETS	1	0.832	1	1	0.832	1	CLONAL	1	TRUE	1	0.24	2		208	261	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273159	198273159	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	83	582	0	ENST00000335508.6:c.1051C>T	p.Pro351Ser	p.P351S	ENST00000335508	NM_012433.2	351	Cca/Tca	8/25	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.24	2		582	670	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39704928	39704928	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	12	132	0	ENST00000361337.2:c.273G>C	p.Glu91Asp	p.E91D	ENST00000361337	NM_003286.2	91	gaG/gaC	4/21	0.3	1	FACETS	0.55	0.388	0.748	0.55	0.388	0.748	SUBCLONAL	1	TRUE	0	0.24	1		132	160	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729941	30729941	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0035240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	40	267	0	ENST00000295754.5:c.1462A>T	p.Lys488Ter	p.K488*	ENST00000295754	NM_003242.5	488	Aag/Tag	6/7	0.275685802309575	1	FACETS	0.801	0.667	0.95	0.801	0.667	0.95	CLONAL	1	TRUE	0	0.24	1		267	366	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468376	89468376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	22	178	0	ENST00000336596.2:c.1910G>A	p.Ser637Asn	p.S637N	ENST00000336596	NM_005233.5	637	aGt/aAt	11/17	0.275685802309575	1	FACETS	0.708	0.55	0.889	0.708	0.55	0.889	SUBCLONAL	1	TRUE	0	0.24	1		178	228	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526130	189526130	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	46	538	0	ENST00000264731.3:c.394A>C	p.Ser132Arg	p.S132R	ENST00000264731	NM_003722.4	132	Agt/Cgt	4/14	1	2	FACETS	0.839	0.707	0.984	0.839	0.707	0.984	CLONAL	1	TRUE	1	0.24	2		538	457	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522464	187522464	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	69	619	0	ENST00000441802.2:c.11599G>T	p.Val3867Phe	p.V3867F	ENST00000441802	NM_005245.3	3867	Gtt/Ttt	21/27	1	2	FACETS	0.9	0.784	1	0.9	0.784	1	CLONAL	1	TRUE	1	0.24	2		619	639	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524165	187524165	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	32	364	0	ENST00000441802.2:c.11374C>A	p.His3792Asn	p.H3792N	ENST00000441802	NM_005245.3	3792	Cat/Aat	20/27	1	2	FACETS	0.826	0.672	0.999	0.826	0.672	0.999	CLONAL	1	TRUE	1	0.24	2		364	323	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155713	56155713	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	34	273	0	ENST00000399503.3:c.805G>T	p.Val269Leu	p.V269L	ENST00000399503	NM_005921.1	269	Gta/Tta	3/20	1	2	FACETS	0.848	0.695	1	0.848	0.695	1	CLONAL	1	TRUE	1	0.24	2		273	334	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637957	176637957	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	57	538	0	ENST00000439151.2:c.2557G>C	p.Glu853Gln	p.E853Q	ENST00000439151	NM_022455.4	853	Gaa/Caa	5/23	0.275685802309575	1	FACETS	0.844	0.725	0.974	0.844	0.725	0.974	CLONAL	1	TRUE	0	0.24	1		538	495	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158628	26158629	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0035240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	21	210	0	ENST00000289316.2:c.231_232delinsTT	p.Glu77_Ala78delinsAspSer	p.E77_A78delinsDS	ENST00000289316	NM_138720.2	77	gaGGct/gaTTct	1/2	0.275685802309575	1	FACETS	0.933	0.724	1	0.933	0.724	1	CLONAL	1	TRUE	0	0.24	1		210	165	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395465	116395465	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	114	479	0	ENST00000397752.3:c.1758G>C	p.Trp586Cys	p.W586C	ENST00000397752	NM_000245.2	586	tgG/tgC	6/21	0.3	3	FACETS	0.971	0.877	1	0.971	0.877	1	CLONAL	2	TRUE	1	0.24	3		479	548	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989678	68989678	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	60	588	0	ENST00000288368.4:c.1616T>A	p.Leu539His	p.L539H	ENST00000288368	NM_024870.2	539	cTc/cAc	15/40	0.275685802309575	1	FACETS	0.903	0.78	1	0.903	0.78	1	CLONAL	1	TRUE	0	0.24	1		588	487	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504102	123504102	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	63	223	0	ENST00000371139.4:c.278G>T	p.Gly93Val	p.G93V	ENST00000371139	NM_001114937.2	93	gGc/gTc	3/4	1	1	FACETS	0.899	0.786	1	1	0.979	1	CLONAL	2	TRUE	0	0.24	1		223	257	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438164	110438164	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	39	287	0	ENST00000375856.3:c.237G>T	p.Glu79Asp	p.E79D	ENST00000375856	NM_003749.2	79	gaG/gaT	1/2	1	2	FACETS	0.886	0.736	1	0.886	0.736	1	CLONAL	1	TRUE	1	0.24	2		287	367	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438159	110438159	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	37	322	0	ENST00000375856.3:c.242del	p.Lys81SerfsTer12	p.K81Sfs*12	ENST00000375856	NM_003749.2	81	aAg/ag	1/2	1	2	FACETS	0.775	0.639	0.926	0.775	0.639	0.926	CLONAL	1	TRUE	1	0.24	2		322	398	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32802930	32802932	+	splice_donor_variant,coding_sequence_variant	Splice_Site	TNP	CCT	CCT	ACA	novel	NA	P-0035240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	32	319	0	ENST00000374899.4:c.944_945+1delinsTGT		p.X315_splice	ENST00000374899	NM_018833.2	315		5/12	0.275685802309575	1	FACETS	0.994	0.812	1	0.994	0.812	1	CLONAL	1	TRUE	0	0.24	1		319	236	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266135	41266146	+	inframe_deletion	In_Frame_Del	DEL	TTCTCTGAGTGG	TTCTCTGAGTGG	-	novel	NA	P-0035245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	69	255	0	ENST00000349496.5:c.133_144del	p.Ser45_Gly48del	p.S45_G48del	ENST00000349496	NM_001904.3	44	ccTTCTCTGAGTGGt/cct	3/15	1	2	FACETS	0.833	0.733	0.939	1	0.979	1	CLONAL	2	TRUE	1	0.3	2		255	276	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	12	349	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.153	0.107	0.208	0.153	0.107	0.208	SUBCLONAL	1	TRUE	1	0.85	2		349	185	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0035247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	54	650	1	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	1	2	FACETS	0.154	0.13	0.179	0.154	0.13	0.179	SUBCLONAL	1	TRUE	1	0.85	2		651	827	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438673	49438673	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0035247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	54	490	0	ENST00000301067.7:c.4817C>G	p.Ser1606Ter	p.S1606*	ENST00000301067	NM_003482.3	1606	tCa/tGa	19/54	1	2	FACETS	0.175	0.149	0.203	0.175	0.149	0.203	SUBCLONAL	1	TRUE	1	0.85	2		490	727	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440042	49440042	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0035247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	32	399	1	ENST00000301067.7:c.4583+1G>A		p.X1528_splice	ENST00000301067	NM_003482.3	1528			1	2	FACETS	0.12	0.097	0.147	0.12	0.097	0.147	SUBCLONAL	1	TRUE	1	0.85	2		400	625	SUCCESS
ATR	545	MSKCC	GRCh37	3	142180842	142180842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	31	368	0	ENST00000350721.4:c.7132G>A	p.Glu2378Lys	p.E2378K	ENST00000350721	NM_001184.3	2378	Gaa/Aaa	42/47	1	2	FACETS	0.128	0.103	0.156	0.128	0.103	0.156	SUBCLONAL	1	TRUE	1	0.85	2		368	570	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0035268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	47	388	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.125040563193124	4	FACETS	0.951	0.822	1	0.951	0.822	1	INDETERMINATE	2	TRUE	2	0.598651737729397	4		388	132	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	14	378	0	ENST00000263967.3:c.3012G>A	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atA	21/21	0.125040563193124	4	FACETS	0.282	0.203	0.377	0.141	0.101	0.189	INDETERMINATE	1	TRUE	2	0.598651737729397	4		378	265	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577069	7577069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55819519	NA	P-0035268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	9	618	1	ENST00000269305.4:c.869G>A	p.Arg290His	p.R290H	ENST00000269305	NM_001126112.2	290	cGc/cAc	8/11	1	2	FACETS	0.068	0.044	0.099	0.068	0.044	0.099	SUBCLONAL	1	TRUE	1	0.598651737729397	2		619	441	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061288	38061288	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	62	472	2	ENST00000250448.2:c.701C>T	p.Ser234Phe	p.S234F	ENST00000250448	NM_004496.3	234	tCc/tTc	2/2	0.186277104571075	4	FACETS	0.673	0.582	0.771	0.337	0.291	0.386	INDETERMINATE	1	TRUE	2	0.598651737729397	4		474	492	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177896	56177896	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	42	335	0	ENST00000399503.3:c.2869C>T	p.Gln957Ter	p.Q957*	ENST00000399503	NM_005921.1	957	Caa/Taa	14/20	0.125040563193124	4	FACETS	0.963	0.811	1	0.481	0.405	0.564	INDETERMINATE	1	TRUE	2	0.598651737729397	4		335	233	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578188	7578188	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201592	NA	P-0035270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	382	567	0	ENST00000269305.4:c.661G>T	p.Glu221Ter	p.E221*	ENST00000269305	NM_001126112.2	221	Gag/Tag	6/11	0.863664241364551	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.863664241364551	1		567	493	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593605	55593610	+	inframe_deletion	In_Frame_Del	DEL	GAAGGT	GAAGGT	-	novel	NA	P-0035271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	88	306	0	ENST00000288135.5:c.1671_1676del	p.Trp557_Val559delinsCys	p.W557_V559delinsC	ENST00000288135	NM_000222.2	557	tgGAAGGTt/tgt	11/21	1	2	FACETS	0.914	0.815	1	0.914	0.815	1	CLONAL	1	TRUE	1	0.469594348537297	2		306	410	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0035272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	151	527	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	0.701163301508768	2		527	353	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402595	20402603	+	inframe_deletion	In_Frame_Del	DEL	CGCCGCCGC	CGCCGCCGC	-	rs559169760	NA	P-0035272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	298	186	0	ENST00000346618.3:c.141_149del	p.Ala51_Ala53del	p.A51_A53del	ENST00000346618	NM_001949.4	44	ttCGCCGCCGCc/ttc	1/7	0.49726565561492	4	FACETS	0.972	0.929	1	0.729	0.697	0.76	CLONAL	3	TRUE	0	0.701163301508768	4		186	496	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163309193	163309193	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	150	432	0	ENST00000271452.3:c.532G>C	p.Glu178Gln	p.E178Q	ENST00000271452	NM_145697.2	178	Gaa/Caa	8/14	0.701163301508768	4	FACETS	0.816	0.746	0.89			1	CLONAL	1	TRUE	NA	0.701163301508768	4		432	892	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218946	193218946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	113	268	0	ENST00000367435.3:c.1504C>T	p.His502Tyr	p.H502Y	ENST00000367435	NM_024529.4	502	Cac/Tac	16/17	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.701163301508768	2		268	303	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578459	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAC	novel	NA	P-0035272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	210	660	0	ENST00000269305.4:c.469_471dup	p.Val157dup	p.V157dup	ENST00000269305	NM_001126112.2	157	-/GTC	5/11	0.701163301508768	1	FACETS	0.931	0.877	0.984	0.931	0.877	0.984	CLONAL	1	TRUE	0	0.701163301508768	1		660	418	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046488	69046488	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	188	470	0	ENST00000288368.4:c.3961C>G	p.Gln1321Glu	p.Q1321E	ENST00000288368	NM_024870.2	1321	Cag/Gag	32/40	1	2	FACETS	0.925	0.86	0.991	0.925	0.86	0.991	CLONAL	1	TRUE	1	0.701163301508768	2		470	580	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133710900	133710900	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	118	260	0	ENST00000318560.5:c.67T>A	p.Cys23Ser	p.C23S	ENST00000318560	NM_005157.4	23	Tgt/Agt	1/11	0.701163301508768	1	FACETS	0.976	0.902	1	0.976	0.902	1	CLONAL	1	TRUE	0	0.701163301508768	1		260	224	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0035275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	162	879	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.228550784839747	3	FACETS	1	0.939	1	1	0.99	1	CLONAL	3	TRUE	1	0.228550784839747	3		879	517	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0035275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	121	488	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.228550784839747	5	FACETS	0.992	0.901	1	0.992	0.901	1	CLONAL	3	TRUE	2	0.228550784839747	5		488	478	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0035275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	405	314	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	0.228550784839747	20	FACETS	1	0.971	1			1	CLONAL	16	TRUE	NA	0.228550784839747	20		314	670	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662637	227662637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755496379	NA	P-0035275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	80	368	0	ENST00000305123.5:c.818C>T	p.Ser273Leu	p.S273L	ENST00000305123	NM_005544.2	273	tCg/tTg	1/2	0.228550784839747	3	FACETS	0.886	0.784	0.996	0.886	0.784	0.996	CLONAL	2	TRUE	1	0.228550784839747	3		368	440	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405231	139405231	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762050048	NA	P-0035275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	52	438	0	ENST00000277541.6:c.2614G>A	p.Glu872Lys	p.E872K	ENST00000277541	NM_017617.3	872	Gag/Aag	17/34	0.228550784839747	3	FACETS	0.944	0.804	1	0.472	0.402	0.549	CLONAL	1	TRUE	1	0.228550784839747	3		438	537	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419065	419065	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	52	345	0	ENST00000399788.2:c.3282del	p.Glu1095AsnfsTer2	p.E1095Nfs*2	ENST00000399788	NM_001042603.1	1094	aaA/aa	22/28	0.173314097720676	3	FACETS	1	0.955	1	0.662	0.565	0.767	CLONAL	1	TRUE	1	0.228550784839747	3		345	383	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576870	7576870	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs876659384	NA	P-0035276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	300	566	2	ENST00000269305.4:c.976G>T	p.Glu326Ter	p.E326*	ENST00000269305	NM_001126112.2	326	Gaa/Taa	9/11	0.582186623011198	2	FACETS	0.881	0.841	0.92	0.881	0.841	0.92	CLONAL	2	TRUE	0	0.652240802058633	2		568	522	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115272990	115272990	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	165	640	0	ENST00000438362.2:c.1383G>C	p.Lys461Asn	p.K461N	ENST00000438362	NM_001242891.1	461	aaG/aaC	12/20	0.652240802058633	4	FACETS	0.88	0.808	0.955	0.44	0.404	0.478	CLONAL	1	TRUE	2	0.652240802058633	4		640	950	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992453	72992453	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	185	714	0	ENST00000268489.5:c.1592C>T	p.Ser531Phe	p.S531F	ENST00000268489	NM_006885.3	531	tCt/tTt	2/10	0.6166155295411	3	FACETS	0.834	0.77	0.9	0.417	0.385	0.45	CLONAL	1	TRUE	1	0.652240802058633	3		714	902	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120092	70120092	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1201663893	NA	P-0035276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	36	36	0	ENST00000245479.2:c.1094C>T	p.Ala365Val	p.A365V	ENST00000245479	NM_000346.3	365	gCg/gTg	3/3	0.652240802058633	6	FACETS	0.883	0.761	1	0.883	0.761	1	CLONAL	4	TRUE	2	0.652240802058633	6		36	72	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56367670	56367676	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGATTC	CAGATTC	-	novel	NA	P-0035276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	20	221	0	ENST00000348428.3:c.499-1_504del		p.X167_splice	ENST00000348428	NM_006785.3	167		4/17	0.596590641609722	4	FACETS	0.299	0.228	0.382	0.149	0.114	0.191	SUBCLONAL	1	TRUE	2	0.652240802058633	4		221	339	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617480	158617480	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1282994566	NA	P-0035276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	60	340	0	ENST00000263640.3:c.1176G>C	p.Gln392His	p.Q392H	ENST00000263640	NM_001105.4	392	caG/caC	9/11	0.652240802058633	6	FACETS	0.629	0.541	0.725	0.157	0.135	0.182	SUBCLONAL	1	TRUE	2	0.652240802058633	6		340	674	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317138	87317138	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	93	379	0	ENST00000277120.3:c.277C>G	p.Leu93Val	p.L93V	ENST00000277120		93	Ctg/Gtg	3/19	0.330026357749063	5	FACETS	1	0.931	1			1	INDETERMINATE	1	TRUE	NA	0.652240802058633	5		379	533	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0035278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	149	384	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	0.972	1	CLONAL	1	TRUE	1	0.314871536577617	2		384	824	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0035278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	133	432	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.302243283856803	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.314871536577617	1		432	663	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	183	722	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.314871536577617	1	FACETS	0.977	0.902	1	0.977	0.902	1	CLONAL	1	TRUE	0	0.314871536577617	1		722	1002	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180459	94180459	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	164	692	0	ENST00000323929.3:c.1709G>A	p.Arg570Lys	p.R570K	ENST00000323929	NM_005591.3	570	aGa/aAa	15/20	1	2	FACETS	0.933	0.856	1	0.933	0.856	1	CLONAL	1	TRUE	1	0.314871536577617	2		692	1116	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687583	29687583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	93	627	0	ENST00000356175.3:c.8176G>A	p.Asp2726Asn	p.D2726N	ENST00000356175	NM_000267.3	2726	Gat/Aat	56/57	1	2	FACETS	0.494	0.438	0.555	0.494	0.438	0.555	SUBCLONAL	1	TRUE	1	0.314871536577617	2		627	1195	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546725	9546725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210292896	NA	P-0035278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	72	345	1	ENST00000353224.5:c.1297C>T	p.Arg433Trp	p.R433W	ENST00000353224	NM_177990.2	433	Cgg/Tgg	5/10	1	2	FACETS	0.953	0.835	1	0.953	0.835	1	CLONAL	1	TRUE	1	0.314871536577617	2		346	480	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37622769	37622769	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	205	813	0	ENST00000249071.6:c.523G>T	p.Ala175Ser	p.A175S	ENST00000249071	NM_002872.4	175	Gcc/Tcc	6/7	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.314871536577617	2		813	1278	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781645	9781645	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	68	680	0	ENST00000377346.4:c.1955G>T	p.Arg652Leu	p.R652L	ENST00000377346	NM_005026.3	652	cGc/cTc	15/24	1	2	FACETS	0.483	0.419	0.553	0.483	0.419	0.553	SUBCLONAL	1	TRUE	1	0.314871536577617	2		680	894	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937868	36937868	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	173	973	0	ENST00000361632.4:c.968C>T	p.Pro323Leu	p.P323L	ENST00000361632		323	cCc/cTc	7/16	1	2	FACETS	0.978	0.898	1	0.978	0.898	1	CLONAL	1	TRUE	1	0.314871536577617	2		973	1124	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100792	8100792	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758290866	NA	P-0035278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	59	611	0	ENST00000346208.3:c.766C>T	p.Arg256Trp	p.R256W	ENST00000346208		256	Cgg/Tgg	3/6	1	2	FACETS	0.5	0.43	0.578	0.5	0.43	0.578	SUBCLONAL	1	TRUE	1	0.314871536577617	2		611	749	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32449596	32449596	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	93	692	0	ENST00000332351.3:c.778C>T	p.Gln260Ter	p.Q260*	ENST00000332351	NM_024426.4	260	Cag/Tag	3/10	1	2	FACETS	0.791	0.703	0.885	0.791	0.703	0.885	SUBCLONAL	1	TRUE	1	0.314871536577617	2		692	747	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	359999	359999	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	198	766	1	ENST00000262320.3:c.1090G>T	p.Gly364Trp	p.G364W	ENST00000262320	NM_003502.3	364	Ggg/Tgg	4/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.314871536577617	2		767	1141	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223335	2223335	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	136	736	0	ENST00000326181.6:c.947G>T	p.Arg316Leu	p.R316L	ENST00000326181	NM_032271.2	316	cGc/cTc	10/21	1	2	FACETS	0.844	0.767	0.926	0.844	0.767	0.926	CLONAL	1	TRUE	1	0.314871536577617	2		736	1023	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845809	72845809	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	57	592	0	ENST00000268489.5:c.3658G>C	p.Glu1220Gln	p.E1220Q	ENST00000268489	NM_006885.3	1220	Gag/Cag	6/10	1	2	FACETS	0.413	0.353	0.479	0.413	0.353	0.479	SUBCLONAL	1	TRUE	1	0.314871536577617	2		592	876	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214701	36214701	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	56	698	0	ENST00000222270.7:c.3127C>G	p.Pro1043Ala	p.P1043A	ENST00000222270	NM_014727.1	1043	Cca/Gca	8/37	1	2	FACETS	0.475	0.406	0.551	0.475	0.406	0.551	SUBCLONAL	1	TRUE	1	0.314871536577617	2		698	749	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505431	25505431	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	112	650	1	ENST00000264709.3:c.327del	p.Gln110ArgfsTer52	p.Q110Rfs*52	ENST00000264709	NM_175629.2	109	ggG/gg	4/23	1	2	FACETS	0.923	0.83	1	0.923	0.83	1	CLONAL	1	TRUE	1	0.314871536577617	2		651	771	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648460	30648460	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	52	439	0	ENST00000295754.5:c.85C>G	p.Gln29Glu	p.Q29E	ENST00000295754	NM_003242.5	29	Cag/Gag	1/7	0.314871536577617	1	FACETS	0.569	0.485	0.661	0.569	0.485	0.661	SUBCLONAL	1	TRUE	0	0.314871536577617	1		439	489	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957850	1957850	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	163	674	0	ENST00000382891.5:c.2816A>T	p.Tyr939Phe	p.Y939F	ENST00000382891	NM_133335.3	939	tAc/tTc	15/22	0.314871536577617	1	FACETS	0.949	0.871	1	0.949	0.871	1	CLONAL	1	TRUE	0	0.314871536577617	1		674	919	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896469	151896469	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	42	430	0	ENST00000262189.6:c.4168G>C	p.Gly1390Arg	p.G1390R	ENST00000262189	NM_170606.2	1390	Gga/Cga	27/59	1	2	FACETS	0.441	0.367	0.523	0.441	0.367	0.523	SUBCLONAL	1	TRUE	1	0.314871536577617	2		430	605	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346399	152346399	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	86	615	0	ENST00000359321.1:c.171G>T	p.Met57Ile	p.M57I	ENST00000359321	NM_005431.1	57	atG/atT	3/3	1	2	FACETS	0.579	0.511	0.652	0.579	0.511	0.652	SUBCLONAL	1	TRUE	1	0.314871536577617	2		615	943	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207488	29207488	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1188486918	NA	P-0035278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	70	337	0	ENST00000240100.2:c.308C>T	p.Ser103Leu	p.S103L	ENST00000240100	NM_001394.6	103	tCg/tTg	1/4	0.247180754567315	1	FACETS	0.996	0.874	1	0.996	0.874	1	CLONAL	1	TRUE	0	0.314871536577617	1		337	376	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574237	95574242	+	frameshift_variant	Frame_Shift_Del	DEL	CAGTAT	CAGTAT	A	novel	NA	P-0035278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	63	333	0	ENST00000393063.1:c.2625_2630delinsT	p.Tyr876CysfsTer5	p.Y876Cfs*5	ENST00000393063	NM_030621.3	875	gcATACTGt/gcTt	17/28	1	2	FACETS	0.825	0.715	0.944	0.825	0.715	0.944	CLONAL	1	TRUE	1	0.314871536577617	2		333	485	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575470	64575470	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	213	608	0	ENST00000312049.6:c.547T>A	p.Trp183Arg	p.W183R	ENST00000312049	NM_130799.2	183	Tgg/Agg	3/10	0.425776975608516	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.425776975608516	1		608	762	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164937	47164937	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	76	297	0	ENST00000409792.3:c.1189G>T	p.Glu397Ter	p.E397*	ENST00000409792	NM_014159.6	397	Gaa/Taa	3/21	0.425776975608516	1	FACETS	0.699	0.616	0.787	0.699	0.616	0.787	SUBCLONAL	1	TRUE	0	0.425776975608516	1		297	402	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288369	33288369	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0035279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	141	361	0	ENST00000374542.5:c.1040-1G>A		p.X347_splice	ENST00000374542	NM_001141970.1	347			0.425776975608516	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.425776975608516	1		361	462	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	213	746	0	ENST00000397752.3:c.3028G>C	p.Asp1010His	p.D1010H	ENST00000397752	NM_000245.2	1010	Gat/Cat	14/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.277108470139968	2		746	1251	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225360568	225360568	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	43	162	0	ENST00000264414.4:c.1823G>C	p.Arg608Thr	p.R608T	ENST00000264414	NM_003590.4	608	aGa/aCa	13/16	1	2	FACETS	0.874	0.734	1	0.874	0.734	1	CLONAL	1	TRUE	1	0.277108470139968	2		162	355	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456342	32456342	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	108	1031	2	ENST00000332351.3:c.550C>A	p.Pro184Thr	p.P184T	ENST00000332351	NM_024426.4	184	Ccg/Acg	1/10	1	2	FACETS	0.7	0.626	0.778	0.7	0.626	0.778	SUBCLONAL	1	TRUE	1	0.277108470139968	2		1033	1114	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004226	150004226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	57	257	1	ENST00000253339.5:c.1999G>A	p.Glu667Lys	p.E667K	ENST00000253339		667	Gaa/Aaa	3/7	1	2	FACETS	0.821	0.705	0.947	0.821	0.705	0.947	CLONAL	1	TRUE	1	0.277108470139968	2		258	501	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411682	116411682	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	200	752	0	ENST00000397752.3:c.2861G>A	p.Trp954Ter	p.W954*	ENST00000397752	NM_000245.2	954	tGg/tAg	13/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.277108470139968	2		752	1334	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	114	365	0	ENST00000263967.3:c.333G>T	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaT	2/21	1	2	FACETS	0.79	0.711	0.873	0.79	0.711	0.873	SUBCLONAL	1	TRUE	1	0.35	2		365	825	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784473	9784473	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	115	439	0	ENST00000377346.4:c.2858T>G	p.Phe953Cys	p.F953C	ENST00000377346	NM_005026.3	953	tTt/tGt	22/24	1	2	FACETS	0.879	0.792	0.97	0.879	0.792	0.97	CLONAL	1	TRUE	1	0.35	2		439	748	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263838	16263838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs183490080	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	197	648	0	ENST00000375759.3:c.10207C>T	p.Arg3403Cys	p.R3403C	ENST00000375759	NM_015001.2	3403	Cgc/Tgc	12/15	1	2	FACETS	0.985	0.911	1	0.985	0.911	1	CLONAL	1	TRUE	1	0.35	2		648	1143	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	412	589	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.965	0.919	1	1	0.997	1	CLONAL	2	TRUE	1	0.35	2		589	1220	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322629	39322629	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	185	565	0	ENST00000373001.3:c.363G>T	p.Met121Ile	p.M121I	ENST00000373001	NM_022157.3	121	atG/atT	2/7	1	2	FACETS	0.889	0.819	0.962	0.889	0.819	0.962	CLONAL	1	TRUE	1	0.35	2		565	1189	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675433	241675433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	81	306	0	ENST00000366560.3:c.389G>A	p.Gly130Asp	p.G130D	ENST00000366560	NM_000143.3	130	gGt/gAt	4/10	1	2	FACETS	0.88	0.777	0.99	0.88	0.777	0.99	CLONAL	1	TRUE	1	0.35	2		306	526	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852511	63852511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752105540	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	95	489	0	ENST00000279873.7:c.3289G>A	p.Ala1097Thr	p.A1097T	ENST00000279873	NM_032199.2	1097	Gct/Act	10/10	1	2	FACETS	0.564	0.501	0.631	0.564	0.501	0.631	SUBCLONAL	1	TRUE	1	0.35	2		489	963	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685280	89685280	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060500118	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	62	270	0	ENST00000371953.3:c.175T>C	p.Ser59Pro	p.S59P	ENST00000371953	NM_000314.4	59	Tca/Cca	3/9	1	2	FACETS	0.824	0.714	0.943	0.824	0.714	0.943	CLONAL	1	TRUE	1	0.35	2		270	430	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692940	89692940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746152219	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	181	538	1	ENST00000371953.3:c.424C>T	p.Arg142Trp	p.R142W	ENST00000371953	NM_000314.4	142	Cgg/Tgg	5/9	1	2	FACETS	0.968	0.892	1	0.968	0.892	1	CLONAL	1	TRUE	1	0.35	2		539	1068	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711887	89711887	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	171	513	0	ENST00000371953.3:c.505C>T	p.Pro169Ser	p.P169S	ENST00000371953	NM_000314.4	169	Ccc/Tcc	6/9	1	2	FACETS	0.94	0.863	1	0.94	0.863	1	CLONAL	1	TRUE	1	0.35	2		513	1040	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720857	89720857	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	140	308	0	ENST00000371953.3:c.1008C>A	p.Tyr336Ter	p.Y336*	ENST00000371953	NM_000314.4	336	taC/taA	8/9	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.35	2		308	704	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112764538	112764538	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	107	316	0	ENST00000369452.4:c.1147A>G	p.Lys383Glu	p.K383E	ENST00000369452	NM_007373.3	383	Aag/Gag	5/9	1	2	FACETS	0.9	0.809	0.998	0.9	0.809	0.998	CLONAL	1	TRUE	1	0.35	2		316	679	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251992	8251992	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769743200	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1214	261	806	0	ENST00000335790.3:c.85C>T	p.Arg29Cys	p.R29C	ENST00000335790	NM_002315.2	29	Cgc/Tgc	2/4	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.35	2		806	1475	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141989	108141989	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	144	422	0	ENST00000278616.4:c.2933C>A	p.Ser978Tyr	p.S978Y	ENST00000278616	NM_000051.3	978	tCt/tAt	20/63	1	2	FACETS	0.922	0.841	1	0.922	0.841	1	CLONAL	1	TRUE	1	0.35	2		422	892	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175528	108175528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs376603775	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	163	435	1	ENST00000278616.4:c.5623C>T	p.Arg1875Ter	p.R1875*	ENST00000278616	NM_000051.3	1875	Cga/Tga	37/63	1	2	FACETS	0.925	0.848	1	0.925	0.848	1	CLONAL	1	TRUE	1	0.35	2		436	1007	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	493277	493277	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	164	444	0	ENST00000399788.2:c.286A>C	p.Lys96Gln	p.K96Q	ENST00000399788	NM_001042603.1	96	Aaa/Caa	3/28	1	2	FACETS	0.92	0.843	0.999	0.92	0.843	0.999	CLONAL	1	TRUE	1	0.35	2		444	1019	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	249	619	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.35	2		619	1327	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230627	46230627	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	205	521	0	ENST00000334344.6:c.876T>G	p.Ile292Met	p.I292M	ENST00000334344	NM_152641.2	292	atT/atG	8/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.35	2		521	1089	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431915	49431915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1337	239	816	0	ENST00000301067.7:c.9224C>T	p.Ser3075Leu	p.S3075L	ENST00000301067	NM_003482.3	3075	tCg/tTg	34/54	1	2	FACETS	0.867	0.806	0.929	0.867	0.806	0.929	CLONAL	1	TRUE	1	0.35	2		816	1576	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112919983	112919983	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1392	80	599	1	ENST00000351677.2:c.1198G>T	p.Glu400Ter	p.E400*	ENST00000351677	NM_002834.3	400	Gaa/Taa	10/16	1	2	FACETS	0.311	0.272	0.352	0.311	0.272	0.352	SUBCLONAL	1	TRUE	1	0.35	2		600	1472	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536921	120536921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1252	126	691	0	ENST00000229340.5:c.265G>A	p.Asp89Asn	p.D89N	ENST00000229340	NM_006861.6	89	Gac/Aac	4/6	1	2	FACETS	0.522	0.471	0.577	0.522	0.471	0.577	SUBCLONAL	1	TRUE	1	0.35	2		691	1378	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	143	477	0	ENST00000320574.5:c.1231G>C	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ctg	13/49	1	2	FACETS	0.956	0.871	1	0.956	0.871	1	CLONAL	1	TRUE	1	0.35	2		477	855	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911088	32911088	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs864622476	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	115	353	0	ENST00000380152.3:c.2596G>T	p.Glu866Ter	p.E866*	ENST00000380152		866	Gaa/Taa	11/27	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.35	2		353	585	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912942	32912942	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	129	389	0	ENST00000380152.3:c.4450G>T	p.Asp1484Tyr	p.D1484Y	ENST00000380152		1484	Gac/Tac	11/27	1	2	FACETS	0.978	0.887	1	0.978	0.887	1	CLONAL	1	TRUE	1	0.35	2		389	754	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953748	48953748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759079385	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	37	228	0	ENST00000267163.4:c.1351C>T	p.Arg451Cys	p.R451C	ENST00000267163	NM_000321.2	451	Cgc/Tgc	14/27	1	2	FACETS	0.355	0.292	0.426	0.355	0.292	0.426	SUBCLONAL	1	TRUE	1	0.35	2		228	596	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281275	49281275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200289548	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1448	287	844	1	ENST00000282018.3:c.322G>A	p.Asp108Asn	p.D108N	ENST00000282018	NM_020377.2	108	Gac/Aac	1/1	1	2	FACETS	0.945	0.886	1	0.945	0.886	1	CLONAL	1	TRUE	1	0.35	2		845	1735	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281356	49281356	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1804	324	955	0	ENST00000282018.3:c.403G>C	p.Val135Leu	p.V135L	ENST00000282018	NM_020377.2	135	Gtg/Ctg	1/1	1	2	FACETS	0.87	0.818	0.924	0.87	0.818	0.924	CLONAL	1	TRUE	1	0.35	2		955	2128	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527667	103527667	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	56	209	0	ENST00000355739.4:c.2975G>T	p.Arg992Leu	p.R992L	ENST00000355739	NM_000123.3	992	cGa/cTa	15/15	1	2	FACETS	0.842	0.724	0.97	0.842	0.724	0.97	CLONAL	1	TRUE	1	0.35	2		209	380	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557638	95557638	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	197	562	0	ENST00000393063.1:c.5429A>G	p.Asp1810Gly	p.D1810G	ENST00000393063	NM_030621.3	1810	gAt/gGt	26/28	1	2	FACETS	0.922	0.852	0.995	0.922	0.852	0.995	CLONAL	1	TRUE	1	0.35	2		562	1221	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590698	95590698	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	121	404	0	ENST00000393063.1:c.1211G>T	p.Arg404Ile	p.R404I	ENST00000393063	NM_030621.3	404	aGa/aTa	9/28	1	2	FACETS	0.802	0.724	0.884	0.802	0.724	0.884	CLONAL	1	TRUE	1	0.35	2		404	862	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590864	95590864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	149	413	0	ENST00000393063.1:c.1045G>A	p.Asp349Asn	p.D349N	ENST00000393063	NM_030621.3	349	Gac/Aac	9/28	1	2	FACETS	0.95	0.868	1	0.95	0.868	1	CLONAL	1	TRUE	1	0.35	2		413	896	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590989	95590989	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149718671	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	74	266	0	ENST00000393063.1:c.920G>A	p.Arg307His	p.R307H	ENST00000393063	NM_030621.3	307	cGt/cAt	9/28	1	2	FACETS	0.837	0.735	0.947	0.837	0.735	0.947	CLONAL	1	TRUE	1	0.35	2		266	505	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023435	33023435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1202	258	712	1	ENST00000300177.4:c.544G>A	p.Asp182Asn	p.D182N	ENST00000300177	NM_001191322.1	182	Gat/Aat	2/2	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.35	2		713	1460	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021428	42021428	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	198	543	0	ENST00000219905.7:c.3724C>T	p.Arg1242Ter	p.R1242*	ENST00000219905	NM_001164273.1	1242	Cga/Tga	11/24	1	2	FACETS	0.965	0.892	1	0.965	0.892	1	CLONAL	1	TRUE	1	0.35	2		543	1173	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42057230	42057230	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	195	558	2	ENST00000219905.7:c.7891C>T	p.Gln2631Ter	p.Q2631*	ENST00000219905	NM_001164273.1	2631	Caa/Taa	23/24	1	2	FACETS	0.879	0.812	0.95	0.879	0.812	0.95	CLONAL	1	TRUE	1	0.35	2		560	1267	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724405	43724405	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747342463	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1344	267	753	0	ENST00000382044.4:c.3662C>T	p.Ser1221Leu	p.S1221L	ENST00000382044	NM_001141980.1	1221	tCg/tTg	17/28	1	2	FACETS	0.947	0.885	1	0.947	0.885	1	CLONAL	1	TRUE	1	0.35	2		753	1611	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457295	67457295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886038803	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	222	666	3	ENST00000327367.4:c.269G>A	p.Arg90His	p.R90H	ENST00000327367	NM_005902.3	90	cGc/cAc	2/9	1	2	FACETS	0.98	0.911	1	0.98	0.911	1	CLONAL	1	TRUE	1	0.35	2		669	1294	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828297	72828297	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	189	639	0	ENST00000268489.5:c.8284G>T	p.Gly2762Ter	p.G2762*	ENST00000268489	NM_006885.3	2762	Gga/Tga	9/10	1	2	FACETS	0.854	0.788	0.924	0.854	0.788	0.924	CLONAL	1	TRUE	1	0.35	2		639	1264	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828558	72828558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1610	109	746	0	ENST00000268489.5:c.8023G>A	p.Ala2675Thr	p.A2675T	ENST00000268489	NM_006885.3	2675	Gca/Aca	9/10	1	2	FACETS	0.362	0.324	0.404	0.362	0.324	0.404	SUBCLONAL	1	TRUE	1	0.35	2		746	1719	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830958	72830958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393698686	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	182	540	0	ENST00000268489.5:c.5623G>A	p.Glu1875Lys	p.E1875K	ENST00000268489	NM_006885.3	1875	Gaa/Aaa	9/10	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.35	2		540	1006	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831513	72831513	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs776994080	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	216	766	0	ENST00000268489.5:c.5068A>G	p.Met1690Val	p.M1690V	ENST00000268489	NM_006885.3	1690	Atg/Gtg	9/10	1	2	FACETS	0.922	0.856	0.992	0.922	0.856	0.992	CLONAL	1	TRUE	1	0.35	2		766	1338	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831996	72831996	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1204	228	678	0	ENST00000268489.5:c.4585A>G	p.Lys1529Glu	p.K1529E	ENST00000268489	NM_006885.3	1529	Aaa/Gaa	9/10	1	2	FACETS	0.91	0.846	0.977	0.91	0.846	0.977	CLONAL	1	TRUE	1	0.35	2		678	1432	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89383370	89383370	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1403247303	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1278	215	722	0	ENST00000301030.4:c.58G>A	p.Asp20Asn	p.D20N	ENST00000301030	NM_001256183.1	20	Gac/Aac	3/13	1	2	FACETS	0.823	0.763	0.886	0.823	0.763	0.886	CLONAL	1	TRUE	1	0.35	2		722	1493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1442	84	778	3	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.315	0.276	0.356	0.315	0.276	0.356	SUBCLONAL	1	TRUE	1	0.35	2		781	1526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578245	7578245	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780072	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	233	576	0	ENST00000269305.4:c.604C>T	p.Arg202Cys	p.R202C	ENST00000269305	NM_001126112.2	202	Cgt/Tgt	6/11	1	2	FACETS	0.968	0.901	1	0.968	0.901	1	CLONAL	1	TRUE	1	0.35	2		576	1375	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586128	29586128	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	200	493	0	ENST00000356175.3:c.4348A>G	p.Asn1450Asp	p.N1450D	ENST00000356175	NM_000267.3	1450	Aac/Gac	32/57	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.35	2		493	1016	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	41	418	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.357	0.296	0.424	0.357	0.296	0.424	SUBCLONAL	1	TRUE	1	0.35	2		418	657	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492733	56492733	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	253	691	0	ENST00000407977.2:c.206T>G	p.Phe69Cys	p.F69C	ENST00000407977		69	tTt/tGt	2/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.35	2		691	1333	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780563	56780563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782332	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1152	129	687	0	ENST00000337432.4:c.578G>A	p.Arg193Gln	p.R193Q	ENST00000337432	NM_058216.2	193	cGa/cAa	4/9	1	2	FACETS	0.575	0.52	0.634	0.575	0.52	0.634	SUBCLONAL	1	TRUE	1	0.35	2		687	1281	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780619	56780619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137947462	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1226	222	713	0	ENST00000337432.4:c.634C>T	p.Arg212Cys	p.R212C	ENST00000337432	NM_058216.2	212	Cgc/Tgc	4/9	1	2	FACETS	0.876	0.813	0.942	0.876	0.813	0.942	CLONAL	1	TRUE	1	0.35	2		713	1448	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39575856	39575856	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs140660681	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	108	265	0	ENST00000262039.4:c.789G>T	p.Glu263Asp	p.E263D	ENST00000262039	NM_002647.2	263	gaG/gaT	8/25	1	2	FACETS	0.963	0.866	1	0.963	0.866	1	CLONAL	1	TRUE	1	0.35	2		265	641	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619401	1619401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200307903	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	52	492	1	ENST00000344749.5:c.1240G>A	p.Asp414Asn	p.D414N	ENST00000344749	NM_001136139.2	414	Gac/Aac	15/19	1	2	FACETS	0.304	0.258	0.356	0.304	0.258	0.356	SUBCLONAL	1	TRUE	1	0.35	2		493	976	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267638	7267638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs896894246	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1258	293	697	0	ENST00000302850.5:c.370G>A	p.Glu124Lys	p.E124K	ENST00000302850	NM_000208.2	124	Gag/Aag	2/22	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.35	2		697	1551	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250363	10250363	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767041788	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	32	263	0	ENST00000340748.4:c.3889G>A	p.Gly1297Ser	p.G1297S	ENST00000340748		1297	Ggc/Agc	33/40	1	2	FACETS	0.356	0.288	0.432	0.356	0.288	0.432	SUBCLONAL	1	TRUE	1	0.35	2		263	514	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098443	11098443	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1344296942	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	112	264	2	ENST00000358026.2:c.961G>A	p.Ala321Thr	p.A321T	ENST00000358026	NM_001128849.1	321	Gcc/Acc	6/36	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.35	2		266	553	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314680	30314680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141578348	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	131	472	0	ENST00000262643.3:c.1229C>T	p.Ala410Val	p.A410V	ENST00000262643	NM_001238.2	410	gCg/gTg	12/12	1	2	FACETS	0.828	0.751	0.909	0.828	0.751	0.909	CLONAL	1	TRUE	1	0.35	2		472	904	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210808	36210808	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1216	237	797	0	ENST00000222270.7:c.559G>T	p.Glu187Ter	p.E187*	ENST00000222270	NM_014727.1	187	Gaa/Taa	3/37	1	2	FACETS	0.932	0.868	0.999	0.932	0.868	0.999	CLONAL	1	TRUE	1	0.35	2		797	1453	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223761	36223761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747697534	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1508	182	942	0	ENST00000222270.7:c.6311G>A	p.Arg2104Gln	p.R2104Q	ENST00000222270	NM_014727.1	2104	cGg/cAg	28/37	1	2	FACETS	0.615	0.565	0.668	0.615	0.565	0.668	SUBCLONAL	1	TRUE	1	0.35	2		942	1690	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741906	40741906	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568518786	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1420	166	781	2	ENST00000392038.2:c.1066G>A	p.Glu356Lys	p.E356K	ENST00000392038	NM_001626.4	356	Gag/Aag	11/14	1	2	FACETS	0.598	0.547	0.652	0.598	0.547	0.652	SUBCLONAL	1	TRUE	1	0.35	2		783	1586	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762374	41762374	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	139	485	0	ENST00000301178.4:c.2054C>T	p.Ser685Phe	p.S685F	ENST00000301178	NM_021913.4	685	tCc/tTc	18/20	1	2	FACETS	0.913	0.831	0.999	0.913	0.831	0.999	CLONAL	1	TRUE	1	0.35	2		485	870	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464450	25464450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369713081	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	52	455	0	ENST00000264709.3:c.2063G>A	p.Arg688His	p.R688H	ENST00000264709	NM_175629.2	688	cGc/cAc	17/23	1	2	FACETS	0.347	0.294	0.405	0.347	0.294	0.405	SUBCLONAL	1	TRUE	1	0.35	2		455	856	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917803	29917803	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	219	644	0	ENST00000389048.3:c.865T>C	p.Ser289Pro	p.S289P	ENST00000389048	NM_004304.4	289	Tcc/Ccc	3/29	1	2	FACETS	0.92	0.854	0.989	0.92	0.854	0.989	CLONAL	1	TRUE	1	0.35	2		644	1360	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940456	29940456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771593278	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	100	346	0	ENST00000389048.3:c.775C>T	p.Arg259Cys	p.R259C	ENST00000389048	NM_004304.4	259	Cgc/Tgc	2/29	1	2	FACETS	0.956	0.855	1	0.956	0.855	1	CLONAL	1	TRUE	1	0.35	2		346	598	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	21	487	0	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	1	2	FACETS	0.121	0.092	0.154	0.121	0.092	0.154	SUBCLONAL	1	TRUE	1	0.35	2		487	994	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038122	128038122	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	184	498	0	ENST00000285398.2:c.1428A>C	p.Lys476Asn	p.K476N	ENST00000285398	NM_000122.1	476	aaA/aaC	9/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.35	2		498	970	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098787	178098787	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1543	120	695	0	ENST00000397062.3:c.258T>G	p.Ile86Met	p.I86M	ENST00000397062	NM_006164.4	86	atT/atG	2/5	1	2	FACETS	0.412	0.371	0.457	0.412	0.371	0.457	SUBCLONAL	1	TRUE	1	0.35	2		695	1663	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190670397	190670397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576285843	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	59	465	0	ENST00000441310.2:c.335C>T	p.Thr112Met	p.T112M	ENST00000441310	NM_000534.4	112	aCg/aTg	4/13	1	2	FACETS	0.472	0.405	0.544	0.472	0.405	0.544	SUBCLONAL	1	TRUE	1	0.35	2		465	715	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719120	190719120	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	70	370	0	ENST00000441310.2:c.1122A>C	p.Glu374Asp	p.E374D	ENST00000441310	NM_000534.4	374	gaA/gaC	9/13	1	2	FACETS	0.707	0.617	0.804	0.707	0.617	0.804	SUBCLONAL	1	TRUE	1	0.35	2		370	566	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131412	202131412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339962485	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	78	465	0	ENST00000358485.4:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000358485	NM_001080125.1	127	cGa/cAa	2/9	1	2	FACETS	0.447	0.391	0.507	0.447	0.391	0.507	SUBCLONAL	1	TRUE	1	0.35	2		465	998	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593483	215593483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139785364	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	110	327	0	ENST00000260947.4:c.2251C>T	p.Arg751Trp	p.R751W	ENST00000260947	NM_000465.2	751	Cgg/Tgg	11/11	1	2	FACETS	0.951	0.856	1	0.951	0.856	1	CLONAL	1	TRUE	1	0.35	2		327	661	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728847	39728847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	41	311	1	ENST00000361337.2:c.1127G>A	p.Arg376Gln	p.R376Q	ENST00000361337	NM_003286.2	376	cGa/cAa	12/21	1	2	FACETS	0.36	0.299	0.429	0.36	0.299	0.429	SUBCLONAL	1	TRUE	1	0.35	2		312	650	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46276102	46276102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	155	487	0	ENST00000371998.3:c.3538G>A	p.Gly1180Ser	p.G1180S	ENST00000371998		1180	Ggc/Agc	18/23	1	2	FACETS	0.848	0.775	0.924	0.848	0.775	0.924	CLONAL	1	TRUE	1	0.35	2		487	1045	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485442	57485442	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	144	365	0	ENST00000371085.3:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000371085	NM_000516.4	342	Cga/Tga	12/13	1	2	FACETS	0.965	0.88	1	0.965	0.88	1	CLONAL	1	TRUE	1	0.35	2		365	853	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171607	36171607	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1569008655	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	102	314	0	ENST00000300305.3:c.958C>T	p.Arg320Ter	p.R320*	ENST00000300305		320	Cga/Tga	7/8	1	2	FACETS	0.875	0.784	0.972	0.875	0.784	0.972	CLONAL	1	TRUE	1	0.35	2		314	666	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064380	30064380	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	74	419	0	ENST00000338641.4:c.944C>A	p.Ser315Tyr	p.S315Y	ENST00000338641	NM_000268.3	315	tCt/tAt	10/16	1	2	FACETS	0.505	0.441	0.574	0.505	0.441	0.574	SUBCLONAL	1	TRUE	1	0.35	2		419	838	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551082	41551082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750235600	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1271	139	565	0	ENST00000263253.7:c.3226C>T	p.Arg1076Cys	p.R1076C	ENST00000263253	NM_001429.3	1076	Cgt/Tgt	17/31	1	2	FACETS	0.563	0.511	0.619	0.563	0.511	0.619	SUBCLONAL	1	TRUE	1	0.35	2		565	1410	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37083778	37083778	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876660124	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	183	534	0	ENST00000231790.2:c.1687A>C	p.Ile563Leu	p.I563L	ENST00000231790	NM_000249.3	563	Ata/Cta	15/19	1	2	FACETS	0.945	0.871	1	0.945	0.871	1	CLONAL	1	TRUE	1	0.35	2		534	1106	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165023	47165023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1385695873	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	145	390	0	ENST00000409792.3:c.1103G>A	p.Arg368Gln	p.R368Q	ENST00000409792	NM_014159.6	368	cGa/cAa	3/21	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.35	2		390	802	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613108	52613108	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	144	485	0	ENST00000394830.3:c.3420C>A	p.Phe1140Leu	p.F1140L	ENST00000394830	NM_018313.4	1140	ttC/ttA	22/30	1	2	FACETS	0.823	0.75	0.9	0.823	0.75	0.9	CLONAL	1	TRUE	1	0.35	2		485	1000	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259601	89259601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773846066	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	148	399	0	ENST00000336596.2:c.745G>A	p.Glu249Lys	p.E249K	ENST00000336596	NM_005233.5	249	Gaa/Aaa	3/17	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.35	2		399	772	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374347	138374347	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	164	498	0	ENST00000289153.2:c.3097A>G	p.Ser1033Gly	p.S1033G	ENST00000289153	NM_006219.2	1033	Agt/Ggt	22/22	1	2	FACETS	0.923	0.847	1	0.923	0.847	1	CLONAL	1	TRUE	1	0.35	2		498	1015	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	198	511	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.885	0.818	0.955	0.885	0.818	0.955	CLONAL	1	TRUE	1	0.35	2		511	1278	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807361	1807361	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	131	447	0	ENST00000260795.2:c.1610A>G	p.Asn537Ser	p.N537S	ENST00000260795		537	aAc/aGc	11/17	1	2	FACETS	0.874	0.793	0.96	0.874	0.793	0.96	CLONAL	1	TRUE	1	0.35	2		447	856	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920265	1920265	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	213	641	0	ENST00000382891.5:c.1325A>C	p.Lys442Thr	p.K442T	ENST00000382891	NM_133335.3	442	aAg/aCg	5/22	1	2	FACETS	0.958	0.888	1	0.958	0.888	1	CLONAL	1	TRUE	1	0.35	2		641	1271	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980345	55980345	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	185	528	0	ENST00000263923.4:c.746G>T	p.Arg249Ile	p.R249I	ENST00000263923	NM_002253.2	249	aGa/aTa	6/30	1	2	FACETS	0.982	0.905	1	0.982	0.905	1	CLONAL	1	TRUE	1	0.35	2		528	1077	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286173	66286173	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	103	364	0	ENST00000273854.3:c.1513A>C	p.Lys505Gln	p.K505Q	ENST00000273854	NM_004439.5	505	Aag/Cag	6/18	1	2	FACETS	0.937	0.84	1	0.937	0.84	1	CLONAL	1	TRUE	1	0.35	2		364	628	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	82	266	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.889	0.786	0.999	0.889	0.786	0.999	CLONAL	1	TRUE	1	0.35	2		266	527	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332915	153332915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200698994	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	153	455	0	ENST00000281708.4:c.41G>A	p.Arg14Gln	p.R14Q	ENST00000281708	NM_033632.3	14	cGa/cAa	2/12	1	2	FACETS	0.946	0.865	1	0.946	0.865	1	CLONAL	1	TRUE	1	0.35	2		455	924	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522574	187522574	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	160	414	0	ENST00000441802.2:c.11489C>A	p.Ser3830Ter	p.S3830*	ENST00000441802	NM_005245.3	3830	tCa/tAa	21/27	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.35	2		414	825	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535369	187535369	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	175	554	0	ENST00000441802.2:c.9205A>C	p.Lys3069Gln	p.K3069Q	ENST00000441802	NM_005245.3	3069	Aaa/Caa	12/27	1	2	FACETS	0.893	0.821	0.968	0.893	0.821	0.968	CLONAL	1	TRUE	1	0.35	2		554	1120	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554954	187554954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560351512	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	129	402	0	ENST00000441802.2:c.4207G>A	p.Asp1403Asn	p.D1403N	ENST00000441802	NM_005245.3	1403	Gat/Aat	7/27	1	2	FACETS	0.908	0.823	0.997	0.908	0.823	0.997	CLONAL	1	TRUE	1	0.35	2		402	812	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950099	38950099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757900166	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	64	512	0	ENST00000357387.3:c.3851C>T	p.Ser1284Leu	p.S1284L	ENST00000357387	NM_152756.3	1284	tCg/tTg	31/38	1	2	FACETS	0.316	0.273	0.364	0.316	0.273	0.364	SUBCLONAL	1	TRUE	1	0.35	2		512	1156	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958874	38958874	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	90	298	0	ENST00000357387.3:c.2238C>A	p.Phe746Leu	p.F746L	ENST00000357387	NM_152756.3	746	ttC/ttA	23/38	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.35	2		298	513	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982000	38982000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1259225174	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	166	482	0	ENST00000357387.3:c.722G>A	p.Arg241Gln	p.R241Q	ENST00000357387	NM_152756.3	241	cGa/cAa	8/38	1	2	FACETS	0.979	0.899	1	0.979	0.899	1	CLONAL	1	TRUE	1	0.35	2		482	969	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189455	56189455	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	84	595	0	ENST00000399503.3:c.4487G>A	p.Arg1496Lys	p.R1496K	ENST00000399503	NM_005921.1	1496	aGa/aAa	20/20	1	2	FACETS	0.399	0.351	0.45	0.399	0.351	0.45	SUBCLONAL	1	TRUE	1	0.35	2		595	1204	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629109	86629109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374823017	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	78	334	0	ENST00000274376.6:c.854G>A	p.Arg285Gln	p.R285Q	ENST00000274376	NM_002890.2	285	cGa/cAa	4/25	1	2	FACETS	0.902	0.795	1	0.902	0.795	1	CLONAL	1	TRUE	1	0.35	2		334	494	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672759	86672759	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	109	371	0	ENST00000274376.6:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000274376	NM_002890.2	749	cGa/cAa	17/25	1	2	FACETS	0.952	0.857	1	0.952	0.857	1	CLONAL	1	TRUE	1	0.35	2		371	654	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86686620	86686620	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373643445	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	70	227	0	ENST00000274376.6:c.3064G>A	p.Val1022Ile	p.V1022I	ENST00000274376	NM_002890.2	1022	Gta/Ata	25/25	1	2	FACETS	0.889	0.778	1	0.889	0.778	1	CLONAL	1	TRUE	1	0.35	2		227	450	SUCCESS
APC	324	MSKCC	GRCh37	5	112175640	112175640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782678	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	111	315	0	ENST00000257430.4:c.4349G>A	p.Arg1450Gln	p.R1450Q	ENST00000257430	NM_000038.5	1450	cGa/cAa	16/16	1	2	FACETS	0.988	0.89	1	0.988	0.89	1	CLONAL	1	TRUE	1	0.35	2		315	642	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696697	176696697	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	131	373	0	ENST00000439151.2:c.5398G>T	p.Gly1800Ter	p.G1800*	ENST00000439151	NM_022455.4	1800	Gga/Tga	16/23	1	2	FACETS	0.939	0.853	1	0.939	0.853	1	CLONAL	1	TRUE	1	0.35	2		373	797	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720928	176720928	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784209	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	80	506	0	ENST00000439151.2:c.6559C>T	p.Arg2187Ter	p.R2187*	ENST00000439151	NM_022455.4	2187	Cga/Tga	23/23	1	2	FACETS	0.428	0.375	0.485	0.428	0.375	0.485	SUBCLONAL	1	TRUE	1	0.35	2		506	1068	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20483077	20483077	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	103	307	0	ENST00000346618.3:c.810G>T	p.Glu270Asp	p.E270D	ENST00000346618	NM_001949.4	270	gaG/gaT	4/7	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.35	2		307	573	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803059	32803059	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs61736923	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	208	670	1	ENST00000374899.4:c.817C>G	p.Arg273Gly	p.R273G	ENST00000374899	NM_018833.2	273	Cga/Gga	5/12	1	2	FACETS	0.981	0.91	1	0.981	0.91	1	CLONAL	1	TRUE	1	0.35	2		671	1211	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287809	33287809	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150463674	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1882	363	1008	0	ENST00000374542.5:c.1444G>A	p.Glu482Lys	p.E482K	ENST00000374542	NM_001141970.1	482	Gaa/Aaa	5/8	1	2	FACETS	0.924	0.872	0.978	0.924	0.872	0.978	CLONAL	1	TRUE	1	0.35	2		1008	2245	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287941	33287941	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756719415	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	64	614	0	ENST00000374542.5:c.1312G>A	p.Glu438Lys	p.E438K	ENST00000374542	NM_001141970.1	438	Gaa/Aaa	5/8	1	2	FACETS	0.312	0.269	0.36	0.312	0.269	0.36	SUBCLONAL	1	TRUE	1	0.35	2		614	1171	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662700	117662700	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	166	464	0	ENST00000368508.3:c.4765G>T	p.Glu1589Ter	p.E1589*	ENST00000368508	NM_002944.2	1589	Gaa/Taa	29/43	1	2	FACETS	0.958	0.88	1	0.958	0.88	1	CLONAL	1	TRUE	1	0.35	2		464	990	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686826	117686826	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	109	300	0	ENST00000368508.3:c.2891G>T	p.Ser964Ile	p.S964I	ENST00000368508	NM_002944.2	964	aGt/aTt	19/43	1	2	FACETS	0.966	0.869	1	0.966	0.869	1	CLONAL	1	TRUE	1	0.35	2		300	645	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715350	117715350	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1466068877	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	61	281	0	ENST00000368508.3:c.1139G>T	p.Arg380Ile	p.R380I	ENST00000368508	NM_002944.2	380	aGa/aTa	10/43	1	2	FACETS	0.655	0.566	0.752	0.655	0.566	0.752	SUBCLONAL	1	TRUE	1	0.35	2		281	532	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001305	150001305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568586257	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	219	391	0	ENST00000253339.5:c.2299C>T	p.Arg767Cys	p.R767C	ENST00000253339		767	Cgt/Tgt	4/7	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.35	2		391	1200	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023019	150023019	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1267	245	731	0	ENST00000253339.5:c.244C>T	p.Arg82Ter	p.R82*	ENST00000253339		82	Cga/Tga	1/7	1	2	FACETS	0.926	0.863	0.991	0.926	0.863	0.991	CLONAL	1	TRUE	1	0.35	2		731	1512	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954975	2954975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368119340	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	228	694	0	ENST00000396946.4:c.2735G>A	p.Arg912Gln	p.R912Q	ENST00000396946	NM_032415.4	912	cGg/cAg	21/25	1	2	FACETS	0.983	0.914	1	0.983	0.914	1	CLONAL	1	TRUE	1	0.35	2		694	1325	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6038780	6038780	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1552	103	681	0	ENST00000265849.7:c.664A>T	p.Ser222Cys	p.S222C	ENST00000265849	NM_000535.5	222	Agc/Tgc	6/15	1	2	FACETS	0.356	0.317	0.397	0.356	0.317	0.397	SUBCLONAL	1	TRUE	1	0.35	2		681	1655	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509660	106509660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757849968	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	137	504	0	ENST00000359195.3:c.1654C>T	p.Arg552Cys	p.R552C	ENST00000359195	NM_002649.2	552	Cgc/Tgc	2/11	1	2	FACETS	0.887	0.806	0.971	0.887	0.806	0.971	CLONAL	1	TRUE	1	0.35	2		504	883	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520103	106520103	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	66	254	0	ENST00000359195.3:c.2531T>G	p.Ile844Ser	p.I844S	ENST00000359195	NM_002649.2	844	aTt/aGt	6/11	1	2	FACETS	0.898	0.782	1	0.898	0.782	1	CLONAL	1	TRUE	1	0.35	2		254	420	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285606	38285606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1033377277	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	102	421	0	ENST00000425967.3:c.547G>A	p.Ala183Thr	p.A183T	ENST00000425967	NM_001174067.1	183	Gct/Act	6/19	1	2	FACETS	0.77	0.689	0.856	0.77	0.689	0.856	SUBCLONAL	1	TRUE	1	0.35	2		421	757	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864630	56864630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210415750	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	218	621	0	ENST00000519728.1:c.593G>A	p.Arg198Gln	p.R198Q	ENST00000519728	NM_002350.3	198	cGa/cAa	7/13	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.35	2		621	1211	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129915	69129915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752310428	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	91	341	0	ENST00000288368.4:c.4669C>T	p.Arg1557Cys	p.R1557C	ENST00000288368	NM_024870.2	1557	Cgt/Tgt	38/40	1	2	FACETS	0.82	0.729	0.917	0.82	0.729	0.917	CLONAL	1	TRUE	1	0.35	2		341	634	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430559	80430559	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	174	513	0	ENST00000286548.4:c.449A>C	p.Glu150Ala	p.E150A	ENST00000286548	NM_002072.3	150	gAa/gCa	3/7	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.35	2		513	956	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430633	80430633	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	95	295	0	ENST00000286548.4:c.375G>T	p.Glu125Asp	p.E125D	ENST00000286548	NM_002072.3	125	gaG/gaT	3/7	1	2	FACETS	0.966	0.862	1	0.966	0.862	1	CLONAL	1	TRUE	1	0.35	2		295	562	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537246	80537246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	227	641	0	ENST00000286548.4:c.152G>A	p.Gly51Asp	p.G51D	ENST00000286548	NM_002072.3	51	gGc/gAc	2/7	1	2	FACETS	0.881	0.819	0.946	0.881	0.819	0.946	CLONAL	1	TRUE	1	0.35	2		641	1472	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798780	135798780	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	102	281	0	ENST00000298552.3:c.463T>G	p.Phe155Val	p.F155V	ENST00000298552	NM_001162426.1	155	Ttt/Gtt	6/23	1	2	FACETS	0.939	0.841	1	0.939	0.841	1	CLONAL	1	TRUE	1	0.35	2		281	621	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413142	139413142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779061035	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1492	323	976	0	ENST00000277541.6:c.1000G>A	p.Glu334Lys	p.E334K	ENST00000277541	NM_017617.3	334	Gag/Aag	6/34	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.35	2		976	1815	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15833986	15833986	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1319	267	621	2	ENST00000307771.7:c.744G>T	p.Lys248Asn	p.K248N	ENST00000307771	NM_005089.3	248	aaG/aaT	8/11	1	2	FACETS	0.962	0.899	1	0.962	0.899	1	CLONAL	1	TRUE	1	0.35	2		623	1586	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030658	47030658	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs782679832	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	65	661	0	ENST00000377604.3:c.432+1G>A		p.X144_splice	ENST00000377604	NM_001204468.1	144			1	2	FACETS	0.343	0.296	0.394	0.343	0.296	0.394	SUBCLONAL	1	TRUE	1	0.35	2		661	1084	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412109	63412109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1157288902	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1815	106	1027	1	ENST00000330258.3:c.1058G>A	p.Arg353Gln	p.R353Q	ENST00000330258	NM_152424.3	353	cGa/cAa	2/2	1	2	FACETS	0.315	0.281	0.352	0.315	0.281	0.352	SUBCLONAL	1	TRUE	1	0.35	2		1028	1921	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888725	76888725	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	171	609	0	ENST00000373344.5:c.5104G>T	p.Glu1702Ter	p.E1702*	ENST00000373344	NM_000489.3	1702	Gaa/Taa	19/35	1	2	FACETS	0.856	0.786	0.93	0.856	0.786	0.93	CLONAL	1	TRUE	1	0.35	2		609	1141	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907620	76907620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	184	563	0	ENST00000373344.5:c.4541G>A	p.Arg1514Gln	p.R1514Q	ENST00000373344	NM_000489.3	1514	cGa/cAa	15/35	1	2	FACETS	0.819	0.754	0.887	0.819	0.754	0.887	CLONAL	1	TRUE	1	0.35	2		563	1284	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937351	76937351	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	107	629	0	ENST00000373344.5:c.3397G>T	p.Glu1133Ter	p.E1133*	ENST00000373344	NM_000489.3	1133	Gaa/Taa	9/35	1	2	FACETS	0.619	0.555	0.689	0.619	0.555	0.689	SUBCLONAL	1	TRUE	1	0.35	2		629	987	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937377	76937377	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	162	623	0	ENST00000373344.5:c.3371C>A	p.Ser1124Tyr	p.S1124Y	ENST00000373344	NM_000489.3	1124	tCt/tAt	9/35	1	2	FACETS	0.939	0.861	1	0.939	0.861	1	CLONAL	1	TRUE	1	0.35	2		623	986	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020002	123020002	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1169	198	705	2	ENST00000355640.3:c.490G>A	p.Glu164Lys	p.E164K	ENST00000355640		164	Gaa/Aaa	2/7	1	2	FACETS	0.828	0.765	0.894	0.828	0.765	0.894	CLONAL	1	TRUE	1	0.35	2		707	1367	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123159747	123159747	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	78	345	0	ENST00000218089.9:c.102C>A	p.Asn34Lys	p.N34K	ENST00000218089	NM_001042749.1	34	aaC/aaA	4/35	1	2	FACETS	0.816	0.719	0.921	0.816	0.719	0.921	CLONAL	1	TRUE	1	0.35	2		345	546	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710637	114710637	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0035282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	43	519	0	ENST00000543371.1:c.122T>G	p.Leu41Ter	p.L41*	ENST00000543371	NM_001198531.1	41	tTa/tGa	1/14	1	2	FACETS	0.727	0.608	0.859	0.727	0.608	0.859	SUBCLONAL	1	TRUE	1	0.227963271709834	2		519	519	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0035283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	361	614	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.461080610172589	1	FACETS	0.985	0.938	1	0.985	0.938	1	CLONAL	1	TRUE	0	0.604618274858774	1		615	846	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998222	100998222	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	158	282	0	ENST00000325455.5:c.1580C>A	p.Ala527Asp	p.A527D	ENST00000325455	NM_001202474.3	527	gCc/gAc	1/8	0.599996411655599	3	FACETS	1	0.971	1	0.557	0.512	0.603	CLONAL	1	TRUE	1	0.604618274858774	3		282	611	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0035285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	108	313	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.654260436938652	3	FACETS	0.858	0.774	0.947	0.429	0.387	0.474	CLONAL	1	TRUE	1	0.665347713654429	3		313	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0035285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	564	879	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.648003597279966	2	FACETS	0.937	0.907	0.965	0.937	0.907	0.965	CLONAL	2	TRUE	0	0.665347713654429	2		879	905	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0035285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	326	445	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.648003597279966	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.665347713654429	2		445	421	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0035285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	63	127	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.684	0.597	0.776	0.684	0.597	0.776	SUBCLONAL	1	TRUE	1	0.665347713654429	2		127	277	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653814	89653814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780004	NA	P-0035285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	191	369	0	ENST00000371953.3:c.112C>T	p.Pro38Ser	p.P38S	ENST00000371953	NM_000314.4	38	Cct/Tct	2/9	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.665347713654429	2		369	507	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281778	39281778	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519963	NA	P-0035285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	131	332	0	ENST00000402219.2:c.697A>T	p.Asn233Tyr	p.N233Y	ENST00000402219	NM_005633.3	233	Aat/Tat	5/23	1	2	FACETS	0.992	0.909	1	0.992	0.909	1	CLONAL	1	TRUE	1	0.665347713654429	2		332	397	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247280	153247280	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	159	316	0	ENST00000281708.4:c.1522C>T	p.Gln508Ter	p.Q508*	ENST00000281708	NM_033632.3	508	Caa/Taa	10/12	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.665347713654429	2		316	452	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607817	46607817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778733586	NA	P-0035285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	353	747	0	ENST00000263734.3:c.2006C>T	p.Pro669Leu	p.P669L	ENST00000263734	NM_001430.4	669	cCc/cTc	12/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.665347713654429	2		747	984	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0035286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	559	460	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.863744414530091	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.863744414530091	3		460	593	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933278	100933280	+	inframe_deletion	In_Frame_Del	DEL	GTC	GTC	-	novel	NA	P-0035286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	92	734	0	ENST00000325455.5:c.2110_2112del	p.Asp704del	p.D704del	ENST00000325455	NM_001202474.3	704	GAC/-	4/8	0.863744414530091	3	FACETS	0.357	0.317	0.4	0.119	0.105	0.134	SUBCLONAL	1	TRUE	0	0.863744414530091	3		734	854	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772094	135772094	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1263094349	NA	P-0035286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	415	593	0	ENST00000298552.3:c.3023A>G	p.Asn1008Ser	p.N1008S	ENST00000298552	NM_001162426.1	1008	aAt/aGt	23/23	0.761764305424877	6	FACETS	0.995	0.953	1	0.995	0.953	1	CLONAL	3	TRUE	3	0.863744414530091	6		593	878	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434768	49434768	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	37	574	0	ENST00000301067.7:c.6785G>T	p.Gly2262Val	p.G2262V	ENST00000301067	NM_003482.3	2262	gGg/gTg	31/54	1	2	FACETS	0.451	0.371	0.541	0.451	0.371	0.541	SUBCLONAL	1	TRUE	1	0.261344240833332	2		574	628	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411865	116411901	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CCGTCTTTAACAAGCTCTTTCTTTCTCTCTGTTTTAA	CCGTCTTTAACAAGCTCTTTCTTTCTCTCTGTTTTAA	-	novel	NA	P-0035293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	71	816	0	ENST00000397752.3:c.2888-38_2888-2del		p.X963_splice	ENST00000397752	NM_000245.2	963			1	2	FACETS	0.473	0.411	0.54	0.473	0.411	0.54	SUBCLONAL	1	TRUE	1	0.261344240833332	2		816	1149	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412046	116412046	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	C	novel	NA	P-0035293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	27	630	1	ENST00000397752.3:c.3028+3A>C		p.X1010_splice	ENST00000397752	NM_000245.2	1010			1	2	FACETS	0.22	0.174	0.273	0.22	0.174	0.273	SUBCLONAL	1	TRUE	1	0.261344240833332	2		631	941	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	43	349	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.553969799512325	2		349	139	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720876	89720876	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs786201041	NA	P-0035294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	38	247	0	ENST00000371953.3:c.1026+1G>A		p.X342_splice	ENST00000371953	NM_000314.4	342			0.275893902944247	1	FACETS	0.8	0.676	0.931	0.8	0.676	0.931	INDETERMINATE	1	TRUE	0	0.553969799512325	1		247	124	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47079255	47079255	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	103	379	0	ENST00000409792.3:c.7251G>A	p.Trp2417Ter	p.W2417*	ENST00000409792	NM_014159.6	2417	tgG/tgA	18/21	0.553969799512325	1	FACETS	0.985	0.895	1	0.985	0.895	1	CLONAL	1	TRUE	0	0.553969799512325	1		379	273	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041687	42041687	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	110	491	0	ENST00000219905.7:c.5882A>G	p.Gln1961Arg	p.Q1961R	ENST00000219905	NM_001164273.1	1961	cAg/cGg	17/24	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.553969799512325	2		491	397	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342961	225342961	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	116	541	0	ENST00000264414.4:c.2131del	p.Met711Ter	p.M711*	ENST00000264414	NM_003590.4	711	Atg/tg	15/16	1	2	FACETS	0.878	0.796	0.964	0.878	0.796	0.964	CLONAL	1	TRUE	1	0.553969799512325	2		541	477	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183791	10183792	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	174	652	0	ENST00000256474.2:c.261dup	p.Trp88MetfsTer44	p.W88Mfs*44	ENST00000256474	NM_000551.3	87	gta/gtAa	1/3	0.553969799512325	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.553969799512325	1		652	430	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651289	52651289	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	99	467	0	ENST00000394830.3:c.1807G>T	p.Glu603Ter	p.E603*	ENST00000394830	NM_018313.4	603	Gag/Tag	15/30	0.553969799512325	1	FACETS	0.923	0.836	1	0.923	0.836	1	CLONAL	1	TRUE	0	0.553969799512325	1		467	280	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931291	131931293	+	frameshift_variant	Frame_Shift_Del	DEL	TAC	TAC	AA	novel	NA	P-0035294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	70	378	0	ENST00000265335.6:c.1996_1998delinsAA	p.Tyr666AsnfsTer8	p.Y666Nfs*8	ENST00000265335		666	TAC/AA	13/25	1	2	FACETS	0.75	0.658	0.847	0.75	0.658	0.847	SUBCLONAL	1	TRUE	1	0.553969799512325	2		378	337	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163717	32163717	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200319129	NA	P-0035294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	110	335	0	ENST00000375023.3:c.5509G>A	p.Ala1837Thr	p.A1837T	ENST00000375023	NM_004557.3	1837	Gct/Act	30/30	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.553969799512325	2		335	351	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0035299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	525	526	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.832096591452319	6	FACETS	1	0.993	1	1	0.993	1	CLONAL	4	TRUE	2	0.832096591452319	6		527	780	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0035299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	277	520	1	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.786687949677376	3	FACETS	0.976	0.949	1	0.976	0.949	1	CLONAL	3	TRUE	0	0.832096591452319	3		521	322	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874261	155874261	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs483352822	NA	P-0035299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	197	397	0	ENST00000368323.3:c.270G>C	p.Met90Ile	p.M90I	ENST00000368323	NM_006912.5	90	atG/atC	5/6	0.791976059933402	3	FACETS	0.926	0.873	0.979	0.926	0.873	0.979	CLONAL	2	TRUE	1	0.832096591452319	3		397	362	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260674	1260674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759490631	NA	P-0035299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	84	477	1	ENST00000310581.5:c.2885G>A	p.Arg962His	p.R962H	ENST00000310581	NM_198253.2	962	cGc/cAc	12/16	0.832323990179249	5	FACETS	0.587	0.518	0.661	0.196	0.172	0.221	SUBCLONAL	1	TRUE	2	0.832096591452319	5		478	773	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464947	120464947	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	195	398	0	ENST00000256646.2:c.5125C>G	p.Leu1709Val	p.L1709V	ENST00000256646	NM_024408.3	1709	Ctc/Gtc	28/34	0.791976059933402	3	FACETS	0.883	0.83	0.935	0.883	0.83	0.935	CLONAL	2	TRUE	1	0.832096591452319	3		398	376	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32449599	32449599	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	200	507	0	ENST00000332351.3:c.775C>A	p.Gln259Lys	p.Q259K	ENST00000332351	NM_024426.4	259	Cag/Aag	3/10	0.274233121478012	6	FACETS	0.93	0.872	0.989	0.93	0.872	0.989	INDETERMINATE	3	TRUE	3	0.832096591452319	6		507	459	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18747471	18747471	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	208	307	0	ENST00000266497.5:c.3934del	p.Thr1312GlnfsTer10	p.T1312Qfs*10	ENST00000266497		1311	cAa/ca	28/31	0.814539949363381	4	FACETS	0.872	0.817	0.929	0.872	0.817	0.929	CLONAL	2	TRUE	2	0.832096591452319	4		307	525	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005607	42005607	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	173	356	0	ENST00000219905.7:c.3343G>T	p.Gly1115Ter	p.G1115*	ENST00000219905	NM_001164273.1	1115	Gga/Tga	9/24	NA	2	FACETS	0.995	0.956	1			1	INDETERMINATE	2	TRUE	NA	0.832096591452319	2		356	209	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476343	88476343	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	232	492	0	ENST00000360948.2:c.1789C>G	p.His597Asp	p.H597D	ENST00000360948	NM_001012338.2	597	Cat/Gat	15/19	0.80779382454674	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.832096591452319	2		492	278	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753089	42753089	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	230	572	0	ENST00000222329.4:c.1175G>T	p.Gly392Val	p.G392V	ENST00000222329	NM_006494.2	392	gGg/gTg	4/4	0.535067196200457	4	FACETS	0.961	0.905	1	0.961	0.905	1	CLONAL	2	TRUE	2	0.832096591452319	4		572	527	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719221	61719221	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	179	342	0	ENST00000401558.2:c.1836T>A	p.Asp612Glu	p.D612E	ENST00000401558	NM_003400.3	612	gaT/gaA	16/25	0.832323990179249	3	FACETS	0.989	0.932	1	0.989	0.932	1	CLONAL	2	TRUE	1	0.832096591452319	3		342	308	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155021	55155021	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	147	377	0	ENST00000257290.5:c.2730G>T	p.Lys910Asn	p.K910N	ENST00000257290	NM_006206.4	910	aaG/aaT	20/23	0.832323990179249	3	FACETS	0.937	0.875	0.998	0.937	0.875	0.998	CLONAL	2	TRUE	1	0.832096591452319	3		377	267	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595501	55595501	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	65	326	0	ENST00000288135.5:c.1991G>T	p.Gly664Val	p.G664V	ENST00000288135	NM_000222.2	664	gGg/gTg	14/21	0.832323990179249	3	FACETS	0.674	0.589	0.766	0.337	0.294	0.383	SUBCLONAL	1	TRUE	1	0.832096591452319	3		326	328	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876106	35876106	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	256	377	0	ENST00000303115.3:c.898C>A	p.Pro300Thr	p.P300T	ENST00000303115	NM_002185.3	300	Cct/Act	8/8	0.832323990179249	5	FACETS	0.967	0.918	1	0.967	0.918	1	CLONAL	3	TRUE	2	0.832096591452319	5		377	477	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80071569	80071569	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	141	294	0	ENST00000265081.6:c.2310G>T	p.Lys770Asn	p.K770N	ENST00000265081	NM_002439.4	770	aaG/aaT	16/24	NA	2	FACETS	0.936	0.89	0.979			1	INDETERMINATE	2	TRUE	NA	0.832096591452319	2		294	181	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376678	8376678	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	513	373	0	ENST00000356435.5:c.4435C>A	p.Leu1479Ile	p.L1479I	ENST00000356435		1479	Ctc/Atc	27/35	0.832096591452319	6	FACETS	0.971	0.938	1	0.971	0.938	1	CLONAL	4	TRUE	2	0.832096591452319	6		373	846	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465658	8465659	+	stop_gained	Nonsense_Mutation	DNP	AG	AG	TT	novel	NA	P-0035299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	365	378	0	ENST00000356435.5:c.3521_3522delinsAA	p.Ser1174Ter	p.S1174*	ENST00000356435		1174	tCT/tAA	21/35	0.832096591452319	6	FACETS	0.938	0.9	0.975	0.938	0.9	0.975	CLONAL	4	TRUE	2	0.832096591452319	6		378	623	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8733793	8733794	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0035299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	77	386	0	ENST00000356435.5:c.50_51delinsTT	p.Arg17Leu	p.R17L	ENST00000356435		17	cGC/cTT	1/35	0.832096591452319	6	FACETS	0.831	0.731	0.94	0.208	0.182	0.235	CLONAL	1	TRUE	2	0.832096591452319	6		386	593	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27203076	27203076	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	260	419	0	ENST00000380036.4:c.2168C>A	p.Pro723Gln	p.P723Q	ENST00000380036	NM_000459.3	723	cCa/cAa	13/23	0.832096591452319	6	FACETS	1	0.941	1	0.501	0.47	0.532	CLONAL	2	TRUE	2	0.832096591452319	6		419	831	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314936	1314936	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	238	431	0	ENST00000400841.2:c.725T>A	p.Leu242Gln	p.L242Q	ENST00000400841		242	cTg/cAg	6/6	0.596701559263897	6	FACETS	1	0.965	1	1	0.965	1	CLONAL	4	TRUE	2	0.832096591452319	6		431	375	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652345	48652345	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	310	811	0	ENST00000376670.3:c.1016G>T	p.Gly339Val	p.G339V	ENST00000376670	NM_002049.3	339	gGg/gTg	6/6	0.739134166143746	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	2	0.832096591452319	4		811	679	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	36	349	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.862	0.714	1	0.862	0.714	1	CLONAL	1	TRUE	1	0.36	2		349	232	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0035300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	105	537	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.298837761618424	1	FACETS	0.797	0.716	0.883	0.797	0.716	0.883	SUBCLONAL	1	TRUE	0	0.36	1		537	600	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792284	33792284	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	134	692	0	ENST00000498907.2:c.1037C>T	p.Pro346Leu	p.P346L	ENST00000498907	NM_004364.3	346	cCa/cTa	1/1	NA	2	FACETS	0.826	0.75	0.906			1	INDETERMINATE	1	TRUE	NA	0.36	2		692	901	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437782	52437782	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0035314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	38	560	0	ENST00000460680.1:c.1379C>G	p.Ser460Ter	p.S460*	ENST00000460680	NM_004656.3	460	tCa/tGa	13/17	0.38609505237407	1	FACETS	0.299	0.247	0.358	0.299	0.247	0.358	SUBCLONAL	1	TRUE	0	0.38609505237407	1		560	531	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183835	10183836	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	G	novel	NA	P-0035314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	123	498	0	ENST00000256474.2:c.304_305delinsG	p.Pro102GlyfsTer57	p.P102Gfs*57	ENST00000256474	NM_000551.3	102	CCg/Gg	1/3	0.38609505237407	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.38609505237407	1		498	448	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0035317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	34	546	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.8	0.652	0.968	0.8	0.652	0.968	CLONAL	1	TRUE	1	0.12	2		546	708	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0035317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	29	566	0	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	1	2	FACETS	0.712	0.569	0.875	0.712	0.569	0.875	SUBCLONAL	1	TRUE	1	0.12	2		566	679	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100967	27100967	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	39	594	1	ENST00000324856.7:c.4249C>T	p.Gln1417Ter	p.Q1417*	ENST00000324856	NM_006015.4	1417	Caa/Taa	18/20	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.12	2		595	631	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0035323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	53	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.835	0.71	0.972	0.835	0.71	0.972	CLONAL	1	FALSE	1	0.165803553249165	2		539	766	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0035323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	47	526	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.62	0.521	0.729	0.62	0.521	0.729	SUBCLONAL	1	FALSE	1	0.165803553249165	2		527	915	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584513	48584514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs377767334	NA	P-0035323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	44	433	0	ENST00000342988.3:c.692dup	p.Ser232GlnfsTer3	p.S232Qfs*3	ENST00000342988	NM_005359.5	229	ctg/ctGg	6/12	1	2	FACETS	0.789	0.66	0.932	0.789	0.66	0.932	CLONAL	1	FALSE	1	0.165803553249165	2		433	673	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244652	46244652	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	62	535	0	ENST00000334344.6:c.2746C>T	p.Gln916Ter	p.Q916*	ENST00000334344	NM_152641.2	916	Caa/Taa	15/21	1	2	FACETS	0.942	0.812	1	0.942	0.812	1	CLONAL	1	FALSE	1	0.165803553249165	2		535	794	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0035324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	1152	593	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.207496095839579	20	FACETS	0.982	0.961	1			1	CLONAL	18	TRUE	NA	0.207496095839579	20		593	1802	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0035324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	161	627	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.131945787969069	3	FACETS	0.997	0.915	1	0.665	0.61	0.722	CLONAL	2	TRUE	0	0.207496095839579	3		627	859	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259439	55259439	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs397517126	NA	P-0035324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	908	454	0	ENST00000275493.2:c.2497T>G	p.Leu833Val	p.L833V	ENST00000275493	NM_005228.3	833	Ttg/Gtg	21/28	0.207496095839579	20	FACETS	1	0.989	1			1	CLONAL	18	TRUE	NA	0.207496095839579	20		454	1365	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022824	31022824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	58	532	0	ENST00000375687.4:c.2309C>T	p.Ser770Leu	p.S770L	ENST00000375687	NM_015338.5	770	tCa/tTa	13/13	0.166975280147603	3	FACETS	0.976	0.838	1	0.488	0.419	0.564	CLONAL	1	TRUE	1	0.207496095839579	3		532	632	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612157	189612157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	64	602	0	ENST00000264731.3:c.1909C>T	p.Arg637Cys	p.R637C	ENST00000264731	NM_003722.4	637	Cgt/Tgt	14/14	0.201463747941016	4	FACETS	1	0.918	1	0.362	0.313	0.415	CLONAL	1	TRUE	1	0.207496095839579	4		602	686	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40497608	40497608	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1344978308	NA	P-0035324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	79	638	0	ENST00000264657.5:c.341G>A	p.Arg114His	p.R114H	ENST00000264657	NM_139276.2	114	cGc/cAc	4/24	0.207496095839579	3	FACETS	0.819	0.718	0.928	0.41	0.359	0.464	CLONAL	1	TRUE	1	0.207496095839579	3		638	1026	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99440002	99440002	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	52	348	0	ENST00000268035.6:c.970T>A	p.Cys324Ser	p.C324S	ENST00000268035	NM_000875.3	324	Tgt/Agt	4/21	0.102123097734554	3	FACETS	1	0.91	1	0.549	0.467	0.638	INDETERMINATE	1	TRUE	1	0.207496095839579	3		348	504	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969782	81969782	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	44	461	0	ENST00000359376.3:c.2851G>T	p.Asp951Tyr	p.D951Y	ENST00000359376	NM_002661.3	951	Gac/Tac	27/33	1	2	FACETS	0.857	0.719	1	0.857	0.719	1	CLONAL	1	TRUE	1	0.207496095839579	2		461	495	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793352	42793352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776199073	NA	P-0035324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	91	695	0	ENST00000575354.2:c.1154C>T	p.Ser385Leu	p.S385L	ENST00000575354	NM_015125.3	385	tCg/tTg	8/20	0.162286032978645	4	FACETS	1	0.969	1	0.425	0.377	0.477	CLONAL	1	TRUE	1	0.207496095839579	4		695	830	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0035326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	298	879	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.507350694180677	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.507350694180677	1		879	861	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0035326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	246	438	1	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.507350694180677	2		439	816	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	231	328	0	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	0.507350694180677	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.507350694180677	1		328	571	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001374	150001376	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs753305883	NA	P-0035326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	240	666	0	ENST00000253339.5:c.2228_2230del	p.Leu743del	p.L743del	ENST00000253339		743	cTTCga/cga	4/7	1	2	FACETS	0.946	0.884	1	0.946	0.884	1	CLONAL	1	TRUE	1	0.507350694180677	2		666	1000	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479833	67479833	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	340	499	1	ENST00000327367.4:c.1140G>A	p.Trp380Ter	p.W380*	ENST00000327367	NM_005902.3	380	tgG/tgA	8/9	0.507350694180677	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.507350694180677	1		500	759	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371711	45371711	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	160	479	0	ENST00000262160.6:c.1280G>A	p.Arg427Gln	p.R427Q	ENST00000262160	NM_005901.5	427	cGa/cAa	10/11	0.507350694180677	1	FACETS	0.865	0.798	0.934	0.865	0.798	0.934	CLONAL	1	TRUE	0	0.507350694180677	1		479	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0035333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	330	503	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.342844338628971	3	FACETS	1	0.993	1	0.832	0.792	0.873	CLONAL	2	TRUE	0	0.440038176251574	3		504	733	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0035333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	202	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.289784894113361	4	FACETS	0.843	0.783	0.905	0.843	0.783	0.905	CLONAL	2	TRUE	2	0.440038176251574	4		539	784	SUCCESS
APC	324	MSKCC	GRCh37	5	112174096	112174096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs137854575	NA	P-0035333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	53	382	0	ENST00000257430.4:c.2805C>A	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	taC/taA	16/16	1	2	FACETS	0.726	0.622	0.838	0.726	0.622	0.838	SUBCLONAL	1	TRUE	1	0.440038176251574	2		382	332	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916947	178916947	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	62	399	0	ENST00000263967.3:c.334A>T	p.Ile112Phe	p.I112F	ENST00000263967	NM_006218.2	112	Atc/Ttc	2/21	0.440038176251574	3	FACETS	0.631	0.545	0.724	0.21	0.181	0.242	SUBCLONAL	1	TRUE	0	0.440038176251574	3		399	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138729528	NA	P-0035333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	361	678	1	ENST00000269305.4:c.523C>T	p.Arg175Cys	p.R175C	ENST00000269305	NM_001126112.2	175	Cgc/Tgc	5/11	0.342844338628971	3	FACETS	0.859	0.819	0.898	0.859	0.819	0.898	CLONAL	3	TRUE	0	0.440038176251574	3		679	777	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215674186	215674186	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	98	526	0	ENST00000260947.4:c.108C>G	p.His36Gln	p.H36Q	ENST00000260947	NM_000465.2	36	caC/caG	1/11	0.209600991484789	4	FACETS	0.841	0.75	0.937	0.42	0.375	0.469	INDETERMINATE	1	TRUE	2	0.440038176251574	4		526	763	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0035337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	168	384	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.405732737570966	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.40512312766863	3		384	401	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142584	119142584	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	37	318	0	ENST00000264033.4:c.583G>T	p.Gly195Trp	p.G195W	ENST00000264033	NM_005188.3	195	Ggg/Tgg	3/16	0.288693198263165	3	FACETS	0.672	0.555	0.801	0.336	0.277	0.401	SUBCLONAL	1	TRUE	1	0.40512312766863	3		318	327	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0035337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	283	432	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.33714315797041	4	FACETS	1	0.99	1	0.869	0.825	0.912	CLONAL	3	TRUE	0	0.40512312766863	4		432	565	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29002038	29002038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757020625	NA	P-0035337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	53	411	0	ENST00000282397.4:c.1127C>T	p.Ala376Val	p.A376V	ENST00000282397	NM_002019.4	376	gCg/gTg	9/30	0.405732737570966	4	FACETS	0.659	0.562	0.765	0.22	0.187	0.255	SUBCLONAL	1	TRUE	1	0.40512312766863	4		411	558	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724782	43724783	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	90	650	0	ENST00000382044.4:c.3284dup	p.Met1095IlefsTer5	p.M1095Ifs*5	ENST00000382044	NM_001141980.1	1095	atg/atTg	17/28	0.288693198263165	3	FACETS	0.858	0.762	0.96	0.429	0.381	0.48	CLONAL	1	TRUE	1	0.40512312766863	3		650	623	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217667	7217667	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	174	499	2	ENST00000380728.2:c.260T>C	p.Phe87Ser	p.F87S	ENST00000380728		87	tTc/tCc	4/11	0.357045722538663	2	FACETS	0.79	0.732	0.849	0.79	0.732	0.849	SUBCLONAL	2	TRUE	0	0.40512312766863	2		501	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578263	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	185	587	3	ENST00000269305.4:c.586_587insT	p.Arg196LeufsTer13	p.R196Lfs*13	ENST00000269305	NM_001126112.2	196	cga/cTga	6/11	0.357045722538663	2	FACETS	0.846	0.786	0.906	0.846	0.786	0.906	CLONAL	2	TRUE	0	0.40512312766863	2		590	540	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526546	66526546	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs387906692	NA	P-0035337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	61	381	1	ENST00000358598.2:c.1102C>T	p.Arg368Ter	p.R368*	ENST00000358598	NM_212471.2	368	Cga/Tga	11/11	0.357045722538663	2	FACETS	0.683	0.591	0.783	0.341	0.295	0.392	SUBCLONAL	1	TRUE	0	0.40512312766863	2		382	441	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794982	242794982	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749156039	NA	P-0035337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	196	844	10	ENST00000334409.5:c.227C>T	p.Thr76Met	p.T76M	ENST00000334409	NM_005018.2	76	aCg/aTg	2/5	0.384535020482698	3	FACETS	0.794	0.737	0.852	0.794	0.737	0.852	SUBCLONAL	2	TRUE	1	0.40512312766863	3		854	733	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775482	39775482	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs568944041	NA	P-0035337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	77	607	1	ENST00000288319.7:c.538A>G	p.Thr180Ala	p.T180A	ENST00000288319	NM_182918.3	180	Acc/Gcc	4/10	0.288693198263165	3	FACETS	0.792	0.696	0.895	0.396	0.348	0.448	SUBCLONAL	1	TRUE	1	0.40512312766863	3		608	577	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131146	55131146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752886996	NA	P-0035337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	140	566	1	ENST00000257290.5:c.689C>T	p.Thr230Met	p.T230M	ENST00000257290	NM_006206.4	230	aCg/aTg	5/23	0.365832136871441	2	FACETS	0.819	0.753	0.887	0.819	0.753	0.887	CLONAL	2	TRUE	0	0.40512312766863	2		567	422	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0035337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	68	246	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	NA	2	FACETS	0.792	0.7	0.887			1	INDETERMINATE	2	TRUE	NA	0.40512312766863	2		246	212	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158619	26158682	+	frameshift_variant	Frame_Shift_Del	DEL	CGCAGGCGAGGCTTCCCGCCTGGCGCATTACAACAAGCGCTCGACCATCACCTCCAGGGAGATC	CGCAGGCGAGGCTTCCCGCCTGGCGCATTACAACAAGCGCTCGACCATCACCTCCAGGGAGATC	-	novel	NA	P-0035337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	58	212	0	ENST00000289316.2:c.223_286del	p.Ala75ArgfsTer39	p.A75Rfs*39	ENST00000289316	NM_138720.2	74	atCGCAGGCGAGGCTTCCCGCCTGGCGCATTACAACAAGCGCTCGACCATCACCTCCAGGGAGATC/at	1/2	0.40512312766863	7	FACETS	1	0.952	1			1	CLONAL	1	TRUE	NA	0.40512312766863	7		212	461	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162475192	162475192	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	50	352	0	ENST00000366898.1:c.549G>A	p.Trp183Ter	p.W183*	ENST00000366898	NM_004562.2	183	tgG/tgA	5/12	0.288693198263165	3	FACETS	0.779	0.663	0.906	0.39	0.331	0.453	CLONAL	1	TRUE	1	0.40512312766863	3		352	381	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953088	2953088	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	102	660	0	ENST00000396946.4:c.2852A>C	p.Glu951Ala	p.E951A	ENST00000396946	NM_032415.4	951	gAg/gCg	22/25	0.33714315797041	4	FACETS	0.792	0.708	0.883	0.198	0.177	0.221	SUBCLONAL	1	TRUE	0	0.40512312766863	4		660	893	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372279	55372280	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0035337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	58	360	0	ENST00000297316.4:c.969_970delinsAA	p.His323_Gln324delinsGlnLys	p.H323_Q324delinsQK	ENST00000297316	NM_022454.3	323	caCCag/caAAag	2/2	1	2	FACETS	0.677	0.583	0.778	0.677	0.583	0.778	SUBCLONAL	1	TRUE	1	0.40512312766863	2		360	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0035339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	249	460	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.286530558008345	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	TRUE	0	0.286530558008345	3		460	636	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63537592	63537592	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	65	539	0	ENST00000307078.5:c.1040T>C	p.Val347Ala	p.V347A	ENST00000307078	NM_004655.3	347	gTg/gCg	4/11	0.245205252048422	3	FACETS	0.833	0.722	0.953	0.278	0.24	0.318	CLONAL	1	TRUE	0	0.286530558008345	3		539	623	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0035366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	193	540	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.483391728253393	NA		540	827	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344781	65344781	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0035366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	60	247	0	ENST00000342505.4:c.256A>T	p.Lys86Ter	p.K86*	ENST00000342505	NM_002227.2	86	Aag/Tag	4/25	0.269933517950282	1	FACETS	0.322	0.277	0.371	0.322	0.277	0.371	INDETERMINATE	1	TRUE	0	0.483391728253393	1		247	584	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024632	14024632	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	226	332	0	ENST00000311895.7:c.858G>C	p.Gln286His	p.Q286H	ENST00000311895	NM_005236.2	286	caG/caC	5/11	0.419724690338346	3	FACETS	1	0.989	1			1	CLONAL	1	TRUE	NA	0.483391728253393	3		332	901	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0035367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	240	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.210884670188102	5	FACETS	0.961	0.901	1			1	INDETERMINATE	2	TRUE	NA	0.698849853364291	5		539	732	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0035367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	456	776	4	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.621144468770178	2	FACETS	0.948	0.917	0.979	0.948	0.917	0.979	CLONAL	2	TRUE	0	0.698849853364291	2		780	688	SUCCESS
APC	324	MSKCC	GRCh37	5	112174091	112174094	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1131691143	NA	P-0035367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	92	351	0	ENST00000257430.4:c.2802_2805del	p.Tyr935IlefsTer19	p.Y935Ifs*19	ENST00000257430	NM_000038.5	934	ACTTac/ac	16/16	0.314546087952311	3	FACETS	1	0.946	1	0.697	0.638	0.755	INDETERMINATE	2	TRUE	0	0.698849853364291	3		351	170	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380572	31380572	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	53	385	0	ENST00000328111.2:c.1062A>T	p.Gln354His	p.Q354H	ENST00000328111	NM_006892.3	354	caA/caT	9/23	0.698849853364291	6	FACETS	0.359	0.304	0.418	0.12	0.101	0.14	SUBCLONAL	1	TRUE	3	0.698849853364291	6		385	1014	SUCCESS
APC	324	MSKCC	GRCh37	5	112175522	112175577	+	frameshift_variant	Frame_Shift_Del	DEL	AGTGGAATGGTAAGTGGCATTATAAGCCCCAGTGATCTTCCAGATAGCCCTGGACA	AGTGGAATGGTAAGTGGCATTATAAGCCCCAGTGATCTTCCAGATAGCCCTGGACA	-	novel	NA	P-0035367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	58	419	0	ENST00000257430.4:c.4232_4287del	p.Ser1411AsnfsTer8	p.S1411Nfs*8	ENST00000257430	NM_000038.5	1411	AGTGGAATGGTAAGTGGCATTATAAGCCCCAGTGATCTTCCAGATAGCCCTGGACAa/a	16/16	0.314546087952311	3	FACETS	0.469	0.403	0.54	0.156	0.134	0.18	INDETERMINATE	1	TRUE	0	0.698849853364291	3		419	478	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176666812	176666812	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	17	279	0	ENST00000439151.2:c.4248T>A	p.Asn1416Lys	p.N1416K	ENST00000439151	NM_022455.4	1416	aaT/aaA	8/23	0.314546087952311	3	FACETS	0.501	0.377	0.645	0.167	0.125	0.215	INDETERMINATE	1	TRUE	0	0.698849853364291	3		279	131	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0035368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	285	432	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.406866676901465	4	FACETS	0.864	0.817	0.913	0.864	0.817	0.913	CLONAL	3	TRUE	1	0.406866676901465	4		432	760	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	72	367	1	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.406866676901465	2		368	344	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986988	36986988	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	174	482	1	ENST00000354822.5:c.701A>T	p.Gln234Leu	p.Q234L	ENST00000354822	NM_001079668.2	234	cAg/cTg	3/3	0.406866676901465	2	FACETS	0.946	0.88	1	0.946	0.88	1	CLONAL	2	TRUE	0	0.406866676901465	2		483	452	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683183	88683183	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	58	359	0	ENST00000372037.3:c.1393C>G	p.Pro465Ala	p.P465A	ENST00000372037	NM_004329.2	465	Ccg/Gcg	12/13	1	2	FACETS	0.902	0.78	1	0.902	0.78	1	CLONAL	1	TRUE	1	0.406866676901465	2		359	316	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348741	118348741	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	67	409	1	ENST00000534358.1:c.3394A>G	p.Ile1132Val	p.I1132V	ENST00000534358	NM_005933.3	1132	Att/Gtt	5/36	1	2	FACETS	0.992	0.868	1	0.992	0.868	1	CLONAL	1	TRUE	1	0.406866676901465	2		410	332	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0035370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	447	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.535849317500293	2	FACETS	0.901	0.866	0.935	0.901	0.866	0.935	CLONAL	2	TRUE	0	0.585343192745505	2		539	848	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0035370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	335	710	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	0.53822461622437	1	FACETS	0.94	0.893	0.988	0.94	0.893	0.988	CLONAL	1	TRUE	0	0.585343192745505	1		710	861	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575671	48575671	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	159	256	0	ENST00000342988.3:c.431C>A	p.Ser144Ter	p.S144*	ENST00000342988	NM_005359.5	144	tCa/tAa	4/12	0.53822461622437	1	FACETS	0.935	0.867	1	0.935	0.867	1	CLONAL	1	TRUE	0	0.585343192745505	1		256	411	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149516579	149516579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465066628	NA	P-0035370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	374	676	1	ENST00000261799.4:c.32C>T	p.Ala11Val	p.A11V	ENST00000261799	NM_002609.3	11	gCc/gTc	2/23	1	2	FACETS	0.998	0.946	1	0.998	0.946	1	CLONAL	1	TRUE	1	0.585343192745505	2		677	1281	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0035372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	150	778	3	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.3	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.31	1		781	757	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0035372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	75	400	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.0800695349384393	3	FACETS	0.705	0.617	0.8	0.352	0.308	0.4	INDETERMINATE	1	TRUE	1	0.31	3		400	793	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635191	87635191	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367769334	NA	P-0035372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	49	640	2	ENST00000277120.3:c.2243C>T	p.Thr748Met	p.T748M	ENST00000277120		748	aCg/aTg	18/19	1	2	FACETS	0.558	0.472	0.652	0.558	0.472	0.652	SUBCLONAL	1	TRUE	1	0.31	2		642	567	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566818	212566818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762866612	NA	P-0035372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	76	443	0	ENST00000342788.4:c.1363G>A	p.Ala455Thr	p.A455T	ENST00000342788	NM_005235.2	455	Gca/Aca	12/28	1	2	FACETS	0.883	0.776	0.999	0.883	0.776	0.999	CLONAL	1	TRUE	1	0.31	2		443	555	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456623	32456623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	23	92	1	ENST00000332351.3:c.269G>A	p.Gly90Asp	p.G90D	ENST00000332351	NM_024426.4	90	gGc/gAc	1/10	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.31	2		93	134	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223255	41223255	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	75	506	1	ENST00000357654.3:c.4676A>G	p.Glu1559Gly	p.E1559G	ENST00000357654	NM_007294.3	1559	gAg/gGg	15/23	0.3	1	FACETS	0.863	0.758	0.974	0.863	0.758	0.974	CLONAL	1	TRUE	0	0.31	1		507	474	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014064	70014064	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	38	612	0	ENST00000394351.3:c.925G>T	p.Asp309Tyr	p.D309Y	ENST00000394351	NM_000248.3	309	Gat/Tat	9/9	1	2	FACETS	0.392	0.323	0.469	0.392	0.323	0.469	SUBCLONAL	1	TRUE	1	0.31	2		612	626	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591315	67591318	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	GAGT	GAGT	-	novel	NA	P-0035372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	56	353	0	ENST00000274335.5:c.1813_1814+2del		p.X605_splice	ENST00000274335		605		13/15	1	2	FACETS	0.852	0.732	0.983	0.852	0.732	0.983	CLONAL	1	TRUE	1	0.31	2		353	424	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336660	81336660	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	32	364	0	ENST00000222390.5:c.1562G>T	p.Gly521Val	p.G521V	ENST00000222390	NM_000601.4	521	gGa/gTa	14/18	0.0800695349384393	3	FACETS	0.521	0.422	0.632	0.26	0.211	0.316	INDETERMINATE	1	TRUE	1	0.31	3		364	458	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030570	47030571	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAGGAGGAGGAGGAT	novel	NA	P-0035372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	21	394	0	ENST00000377604.3:c.360_374dup	p.Asp120_Glu124dup	p.D120_E124dup	ENST00000377604	NM_001204468.1	120	-/GAGGAGGAGGAGGAT	4/24	0.0432354185397066	2	FACETS	0.491	0.378	0.622			1	INDETERMINATE	1	TRUE	NA	0.31	2		394	276	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	225	349	0				ENST00000310581	NM_198253.2	-/1132			0.449391396616544	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.465620518903074	3		349	522	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29115386	29115386	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	104	638	2	ENST00000328354.6:c.680G>A	p.Gly227Glu	p.G227E	ENST00000328354	NM_007194.3	227	gGa/gAa	5/15	0.277590330152615	0	FACETS	0.536	0.483	0.592			1	INDETERMINATE	1	TRUE	0	0.465620518903074	0		640	445	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925611	114925611	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	314	754	3	ENST00000543371.1:c.1689G>T	p.Leu563Phe	p.L563F	ENST00000543371	NM_001198531.1	563	ttG/ttT	14/14	0.465620518903074	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.465620518903074	1		757	1032	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557699	21557699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	224	835	1	ENST00000382592.4:c.2146G>A	p.Glu716Lys	p.E716K	ENST00000382592	NM_014572.2	716	Gag/Aag	5/8	1	2	FACETS	0.733	0.681	0.787	0.733	0.681	0.787	SUBCLONAL	1	TRUE	1	0.465620518903074	2		836	1313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0035374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	142	711	0	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	0.422518339899128	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.422518339899128	1		711	485	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778230	27778230	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	141	614	0	ENST00000369163.2:c.379C>G	p.Leu127Val	p.L127V	ENST00000369163	NM_003536.2	127	Ctc/Gtc	1/1	0.345873038383118	3	FACETS	1	0.967	1	0.374	0.341	0.408	CLONAL	1	TRUE	0	0.422518339899128	3		614	721	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581201	48581201	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	124	625	1	ENST00000342988.3:c.505C>T	p.Gln169Ter	p.Q169*	ENST00000342988	NM_005359.5	169	Cag/Tag	5/12	0.422518339899128	1	FACETS	0.991	0.903	1	0.991	0.903	1	CLONAL	1	TRUE	0	0.422518339899128	1		626	467	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402602	20402613	+	inframe_deletion	In_Frame_Del	DEL	GCCGCCGCCGCT	GCCGCCGCCGCT	-	rs759216279	NA	P-0035374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	80	176	0	ENST00000346618.3:c.148_159del	p.Ala50_Ala53del	p.A50_A53del	ENST00000346618	NM_001949.4	47	GCCGCCGCCGCT/-	1/7	0.345873038383118	3	FACETS	1	0.978	1	0.493	0.438	0.551	CLONAL	1	TRUE	0	0.422518339899128	3		176	310	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031991	26031991	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	144	468	0	ENST00000244661.2:c.298T>C	p.Tyr100His	p.Y100H	ENST00000244661	NM_003537.3	100	Tac/Cac	1/1	0.345873038383118	3	FACETS	1	0.987	1	0.487	0.446	0.53	CLONAL	1	TRUE	0	0.422518339899128	3		468	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0035375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	379	650	1	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	1	2	FACETS	0.993	0.944	1	0.993	0.944	1	CLONAL	1	TRUE	1	0.678868022074379	2		651	1125	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	396	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.158491128388649	6	FACETS	0.999	0.954	1			1	INDETERMINATE	3	TRUE	NA	0.678868022074379	6		493	918	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0035375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	272	565	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.678868022074379	2		565	765	SUCCESS
APC	324	MSKCC	GRCh37	5	112163677	112163677	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0035375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	164	355	0	ENST00000257430.4:c.1600A>T	p.Lys534Ter	p.K534*	ENST00000257430	NM_000038.5	534	Aaa/Taa	13/16	0.667677479730989	3	FACETS	0.964	0.888	1	0.482	0.444	0.522	CLONAL	1	TRUE	1	0.678868022074379	3		355	671	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0035375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	433	464	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	0.667677479730989	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.678868022074379	3		464	823	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11015696	11015696	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	283	707	0	ENST00000327064.4:c.290C>T	p.Ser97Phe	p.S97F	ENST00000327064	NM_199141.1	97	tCc/tTc	2/16	0.667677479730989	3	FACETS	0.94	0.883	0.999	0.47	0.441	0.5	CLONAL	1	TRUE	1	0.678868022074379	3		707	1188	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482809	67482809	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	283	651	0	ENST00000327367.4:c.1213C>T	p.Gln405Ter	p.Q405*	ENST00000327367	NM_005902.3	405	Cag/Tag	9/9	1	2	FACETS	0.997	0.941	1	0.997	0.941	1	CLONAL	1	TRUE	1	0.678868022074379	2		651	836	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120291	70120292	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	423	911	0	ENST00000245479.2:c.1294dup	p.Tyr432LeufsTer146	p.Y432Lfs*146	ENST00000245479	NM_000346.3	431	-/T	3/3	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.678868022074379	2		911	1207	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56378178	56378196	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CACTGAAGGTAGTGTAAGT	CACTGAAGGTAGTGTAAGT	-	novel	NA	P-0035375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	124	543	0	ENST00000348428.3:c.952_958+12del		p.X318_splice	ENST00000348428	NM_006785.3	318		7/17	0.678868022074379	1	FACETS	0.688	0.629	0.747	0.688	0.629	0.747	SUBCLONAL	1	TRUE	0	0.678868022074379	1		543	351	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962663	38962663	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	196	443	0	ENST00000357387.3:c.1592A>C	p.Asn531Thr	p.N531T	ENST00000357387	NM_152756.3	531	aAc/aCc	18/38	0.667677479730989	3	FACETS	1	0.934	1	0.504	0.467	0.541	CLONAL	1	TRUE	1	0.678868022074379	3		443	768	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845590	128845590	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772693769	NA	P-0035375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	255	668	0	ENST00000249373.3:c.887G>A	p.Arg296His	p.R296H	ENST00000249373	NM_005631.4	296	cGt/cAt	4/12	NA	2	FACETS	1	0.962	1			1	INDETERMINATE	1	TRUE	NA	0.678868022074379	2		668	730	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371005	55371005	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	28	506	0	ENST00000297316.4:c.307G>T	p.Gly103Cys	p.G103C	ENST00000297316	NM_022454.3	103	Ggc/Tgc	1/2	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		506	478	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0035385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	86	547	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.787	0.704	0.875	0.787	0.704	0.875	SUBCLONAL	1	TRUE	1	0.700092798108464	2		547	312	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427899	49427899	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	348	826	0	ENST00000301067.7:c.10691del	p.Leu3564ProfsTer94	p.L3564Pfs*94	ENST00000301067	NM_003482.3	3564	cTc/cc	38/54	NA	2	FACETS	0.971	0.921	1			1	INDETERMINATE	1	TRUE	NA	0.700092798108464	2		826	1024	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060867	38060868	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	442	668	0	ENST00000250448.2:c.1121dup	p.His374GlnfsTer41	p.H374Qfs*41	ENST00000250448	NM_004496.3	374	cac/caAc	2/2	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.700092798108464	2		668	1150	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849475	68849476	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0035385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	381	743	0	ENST00000261769.5:c.1379_1380dup	p.Pro461TyrfsTer21	p.P461Yfs*21	ENST00000261769	NM_004360.3	460	gta/gTAta	10/16	0.700092798108464	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.700092798108464	1		743	655	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178501	56178501	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	84	326	0	ENST00000399503.3:c.3474del	p.Glu1159LysfsTer13	p.E1159Kfs*13	ENST00000399503	NM_005921.1	1158	ccT/cc	14/20	NA	2	FACETS	0.777	0.693	0.864			1	INDETERMINATE	1	TRUE	NA	0.700092798108464	2		326	309	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0035386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	151	590	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.944	1	1	0.992	1	CLONAL	2	TRUE	1	0.22	2		590	661	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0035386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	63	537	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.716	0.618	0.823	0.716	0.618	0.823	SUBCLONAL	1	TRUE	1	0.22	2		537	800	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528572	89528572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762601076	NA	P-0035386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	35	237	0	ENST00000336596.2:c.2872G>A	p.Val958Met	p.V958M	ENST00000336596	NM_005233.5	958	Gtg/Atg	17/17	1	2	FACETS	0.71	0.582	0.854	0.71	0.582	0.854	SUBCLONAL	1	TRUE	1	0.22	2		237	448	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098396	11098396	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138097741	NA	P-0035386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	43	471	0	ENST00000358026.2:c.914C>T	p.Pro305Leu	p.P305L	ENST00000358026	NM_001128849.1	305	cCg/cTg	6/36	1	2	FACETS	0.484	0.404	0.574	0.484	0.404	0.574	SUBCLONAL	1	TRUE	1	0.22	2		471	807	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0035386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	49	682	4	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.51	0.43	0.598	0.51	0.43	0.598	SUBCLONAL	1	TRUE	1	0.22	2		686	874	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0035388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	74	547	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.338569831298673	2		547	432	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0035388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	107	582	1	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	1	2	FACETS	0.824	0.739	0.914	0.824	0.739	0.914	CLONAL	1	TRUE	1	0.338569831298673	2		583	767	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435306	49435306	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	114	569	1	ENST00000301067.7:c.6247C>T	p.Gln2083Ter	p.Q2083*	ENST00000301067	NM_003482.3	2083	Cag/Tag	31/54	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.338569831298673	2		570	659	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070600	67070601	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0035388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	78	297	0	ENST00000412916.2:c.226_227del	p.Glu76ThrfsTer6	p.E76Tfs*6	ENST00000412916		75	gGA/g	3/6	0.338569831298673	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.338569831298673	1		297	357	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857526	68857526	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1567513504	NA	P-0035388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	101	450	0	ENST00000261769.5:c.2161C>G	p.Leu721Val	p.L721V	ENST00000261769	NM_004360.3	721	Cta/Gta	13/16	0.338569831298673	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.338569831298673	1		450	441	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0035431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	157	432	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	0.992	1	CLONAL	2	TRUE	1	0.25	2		432	604	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0035431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	20	284	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.532	0.406	0.678	0.532	0.406	0.678	SUBCLONAL	1	TRUE	1	0.25	2		284	301	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0035431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	36	765	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.142910377913592	1	FACETS	0.419	0.343	0.504	0.419	0.343	0.504	INDETERMINATE	1	TRUE	0	0.25	1		765	602	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573628	48573628	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	27	386	1	ENST00000342988.3:c.212G>T	p.Cys71Phe	p.C71F	ENST00000342988	NM_005359.5	71	tGt/tTt	2/12	1	2	FACETS	0.684	0.545	0.842	0.684	0.545	0.842	SUBCLONAL	1	TRUE	1	0.25	2		387	316	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518781	204518781	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	16	319	0	ENST00000367182.3:c.1444C>G	p.Gln482Glu	p.Q482E	ENST00000367182	NM_001278516.1	482	Cag/Gag	11/11	1	2	FACETS	0.446	0.329	0.586	0.446	0.329	0.586	SUBCLONAL	1	TRUE	1	0.25	2		319	287	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617449	43617449	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	49	549	0	ENST00000355710.3:c.2786C>T	p.Thr929Ile	p.T929I	ENST00000355710	NM_020975.4	929	aCc/aTc	16/20	1	2	FACETS	0.677	0.573	0.792	0.677	0.573	0.792	SUBCLONAL	1	TRUE	1	0.25	2		549	579	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589793	28589793	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	39	505	0	ENST00000241453.7:c.2587G>T	p.Gly863Cys	p.G863C	ENST00000241453	NM_004119.2	863	Ggc/Tgc	21/24	1	2	FACETS	0.671	0.556	0.799	0.671	0.556	0.799	SUBCLONAL	1	TRUE	1	0.25	2		505	465	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348112	348112	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	48	825	1	ENST00000262320.3:c.1394A>C	p.Glu465Ala	p.E465A	ENST00000262320	NM_003502.3	465	gAg/gCg	6/11	1	2	FACETS	0.487	0.41	0.571	0.487	0.41	0.571	SUBCLONAL	1	TRUE	1	0.25	2		826	789	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945741	17945741	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	61	761	0	ENST00000458235.1:c.2119G>T	p.Asp707Tyr	p.D707Y	ENST00000458235	NM_000215.3	707	Gac/Tac	16/24	1	2	FACETS	0.64	0.551	0.738	0.64	0.551	0.738	SUBCLONAL	1	TRUE	1	0.25	2		761	762	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278041	18278041	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	57	694	0	ENST00000222254.8:c.1661G>C	p.Arg554Thr	p.R554T	ENST00000222254	NM_005027.3	554	aGa/aCa	13/16	1	2	FACETS	0.607	0.52	0.703	0.607	0.52	0.703	SUBCLONAL	1	TRUE	1	0.25	2		694	751	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308353	30308353	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	47	571	0	ENST00000262643.3:c.367A>G	p.Lys123Glu	p.K123E	ENST00000262643	NM_001238.2	123	Aag/Gag	6/12	1	2	FACETS	0.59	0.497	0.693	0.59	0.497	0.693	SUBCLONAL	1	TRUE	1	0.25	2		571	637	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268891	55268891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779583988	NA	P-0035431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	53	772	0	ENST00000275493.2:c.2957G>A	p.Arg986Lys	p.R986K	ENST00000275493	NM_005228.3	986	aGa/aAa	25/28	1	2	FACETS	0.552	0.47	0.643	0.552	0.47	0.643	SUBCLONAL	1	TRUE	1	0.25	2		772	768	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227682	53227682	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	42	599	0	ENST00000375401.3:c.2506C>T	p.Gln836Ter	p.Q836*	ENST00000375401	NM_004187.3	836	Cag/Tag	17/26	0.142910377913592	1	FACETS	0.52	0.434	0.617	0.52	0.434	0.617	INDETERMINATE	1	TRUE	0	0.25	1		599	565	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960039	134960039	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs533462328	NA	P-0035436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	139	555	0	ENST00000398015.3:c.2396G>A	p.Arg799His	p.R799H	ENST00000398015	NM_004441.4	799	cGc/cAc	13/16	0.468784998907291	1	FACETS	0.59	0.537	0.644	0.59	0.537	0.644	SUBCLONAL	1	TRUE	0	0.476405559780466	1		555	754	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039451	49039457	+	frameshift_variant	Frame_Shift_Del	DEL	ATATAAA	ATATAAA	-	novel	NA	P-0035436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	121	457	0	ENST00000267163.4:c.2438_2444del	p.Tyr813PhefsTer11	p.Y813Ffs*11	ENST00000267163	NM_000321.2	812	ccATATAAA/cc	23/27	0.476405559780466	1	FACETS	0.872	0.793	0.953	0.872	0.793	0.953	CLONAL	1	TRUE	0	0.476405559780466	1		457	444	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051431	13051431	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	30	391	0	ENST00000316448.5:c.779A>T	p.Glu260Val	p.E260V	ENST00000316448	NM_004343.3	260	gAg/gTg	6/9	0.476405559780466	1	FACETS	0.313	0.252	0.381	0.313	0.252	0.381	SUBCLONAL	1	TRUE	0	0.476405559780466	1		391	307	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589587	67589588	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAATATAACACTCAGTTTCAAGAAAAAAGTCGAGAATATGATAGATTATATGAA	novel	NA	P-0035436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	38	190	0	ENST00000274335.5:c.1358_1411dup	p.Asn453_Tyr470dup	p.N453_Y470dup	ENST00000274335		453	-/GAATATAACACTCAGTTTCAAGAAAAAAGTCGAGAATATGATAGATTATATGAA	10/15	0.476405559780466	2	FACETS	0.604	0.502	0.717	0.302	0.251	0.359	SUBCLONAL	1	TRUE	0	0.476405559780466	2		190	264	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0035438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	65	590	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.632	0.55	0.72	0.632	0.55	0.72	SUBCLONAL	1	TRUE	1	0.502839421560923	2		590	409	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0035438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	102	537	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.617	0.552	0.685	0.617	0.552	0.685	SUBCLONAL	1	TRUE	1	0.502839421560923	2		537	658	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0035438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	45	268	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.443	0.373	0.52	0.443	0.373	0.52	SUBCLONAL	1	TRUE	1	0.502839421560923	2		268	404	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0035438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	24	227	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	1	2	FACETS	0.562	0.444	0.695	0.562	0.444	0.695	SUBCLONAL	1	TRUE	1	0.502839421560923	2		227	170	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098975	178098975	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1328994103	NA	P-0035438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	35	221	0	ENST00000397062.3:c.70T>C	p.Trp24Arg	p.W24R	ENST00000397062	NM_006164.4	24	Tgg/Cgg	2/5	1	2	FACETS	0.48	0.395	0.575	0.48	0.395	0.575	SUBCLONAL	1	TRUE	1	0.502839421560923	2		221	290	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097608	27097608	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0035438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	67	364	0	ENST00000324856.7:c.3199-2A>T		p.X1067_splice	ENST00000324856	NM_006015.4	1067			1	2	FACETS	0.545	0.474	0.621	0.545	0.474	0.621	SUBCLONAL	1	TRUE	1	0.502839421560923	2		364	489	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696405	47696405	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	88	442	0	ENST00000347630.2:c.418G>T	p.Asp140Tyr	p.D140Y	ENST00000347630	NM_001007230.1	140	Gat/Tat	6/11	1	2	FACETS	0.507	0.449	0.568	0.507	0.449	0.568	SUBCLONAL	1	TRUE	1	0.502839421560923	2		442	691	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16174567	16174567	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1470842405	NA	P-0035438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	41	232	0	ENST00000375759.3:c.5T>C	p.Val2Ala	p.V2A	ENST00000375759	NM_015001.2	2	gTc/gCc	1/15	1	2	FACETS	0.375	0.312	0.444	0.375	0.312	0.444	SUBCLONAL	1	TRUE	1	0.502839421560923	2		232	435	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685273	89685278	+	inframe_deletion	In_Frame_Del	DEL	TTTGGA	TTTGGA	-	novel	NA	P-0035438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	23	208	0	ENST00000371953.3:c.170_175del	p.Leu57_Asp58del	p.L57_D58del	ENST00000371953	NM_000314.4	56	ttTTTGGAt/ttt	3/9	1	2	FACETS	0.403	0.315	0.504	0.403	0.315	0.504	SUBCLONAL	1	TRUE	1	0.502839421560923	2		208	227	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463250	25463250	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	91	397	0	ENST00000264709.3:c.2243A>G	p.Asp748Gly	p.D748G	ENST00000264709	NM_175629.2	748	gAt/gGt	19/23	1	2	FACETS	0.571	0.507	0.639	0.571	0.507	0.639	SUBCLONAL	1	TRUE	1	0.502839421560923	2		397	634	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0035439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	80	590	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.150334211238661	3	FACETS	0.877	0.773	0.989	0.877	0.773	0.989	CLONAL	2	TRUE	1	0.17	3		590	582	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374293	138374293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	87	590	0	ENST00000289153.2:c.3151G>A	p.Glu1051Lys	p.E1051K	ENST00000289153	NM_006219.2	1051	Gaa/Aaa	22/22	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.17	2		590	896	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0035439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	46	713	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.652	0.547	0.768	0.652	0.547	0.768	SUBCLONAL	1	TRUE	1	0.17	2		713	830	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37092047	37092047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs566928243	NA	P-0035439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	35	511	2	ENST00000231790.2:c.2174G>A	p.Arg725His	p.R725H	ENST00000231790	NM_000249.3	725	cGc/cAc	19/19	1	2	FACETS	0.65	0.532	0.785	0.65	0.532	0.785	SUBCLONAL	1	TRUE	1	0.17	2		513	633	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932096	39932096	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1302902354	NA	P-0035439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	55	750	1	ENST00000378444.4:c.2503G>A	p.Ala835Thr	p.A835T	ENST00000378444	NM_001123385.1	835	Gct/Act	4/15	1	2	FACETS	0.694	0.592	0.807	0.694	0.592	0.807	SUBCLONAL	1	TRUE	1	0.17	2		751	932	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105656	27105660	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCT	CAGCT	-	novel	NA	P-0035439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	41	435	0	ENST00000324856.7:c.5268_5272del	p.Ala1757HisfsTer14	p.A1757Hfs*14	ENST00000324856	NM_006015.4	1756	cCAGCT/c	20/20	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.17	2		435	445	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720705	89720706	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0035439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	14	161	0	ENST00000371953.3:c.858dup	p.Ser287LeufsTer11	p.S287Lfs*11	ENST00000371953	NM_000314.4	286	acc/aCcc	8/9	0.150334211238661	3	FACETS	0.777	0.562	1	0.388	0.281	0.519	CLONAL	1	TRUE	1	0.17	3		161	230	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593252	67593253	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0035439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	19	228	0	ENST00000274335.5:c.1999_2000dup	p.Lys668Ter	p.K668*	ENST00000274335		666	-/GT	15/15	1	2	FACETS	0.712	0.54	0.914	0.712	0.54	0.914	CLONAL	1	TRUE	1	0.17	2		228	314	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0035444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	85	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.92	0.815	1	0.92	0.815	1	CLONAL	1	TRUE	1	0.329318042718129	2		539	561	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876449	35876449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2229232	NA	P-0035444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	83	687	1	ENST00000303115.3:c.1241C>T	p.Thr414Met	p.T414M	ENST00000303115	NM_002185.3	414	aCg/aTg	8/8	1	2	FACETS	0.81	0.716	0.912	0.81	0.716	0.912	CLONAL	1	TRUE	1	0.329318042718129	2		688	622	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241093	39241093	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	86	587	0	ENST00000402219.2:c.1978C>T	p.Arg660Cys	p.R660C	ENST00000402219	NM_005633.3	660	Cgc/Tgc	12/23	1	2	FACETS	0.969	0.859	1	0.969	0.859	1	CLONAL	1	TRUE	1	0.329318042718129	2		587	539	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577149	7577149	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	462	520	0	ENST00000269305.4:c.789del	p.Leu264TyrfsTer81	p.L264Yfs*81	ENST00000269305	NM_001126112.2	263	aaT/aa	8/11	0.362389000032464	4	FACETS	0.955	0.918	0.991	0.955	0.918	0.991	CLONAL	4	TRUE	0	0.390953768182669	4		520	861	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098944	178098944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	135	338	0	ENST00000397062.3:c.101G>A	p.Arg34Gln	p.R34Q	ENST00000397062	NM_006164.4	34	cGa/cAa	2/5	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.390953768182669	2		338	563	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371732	55371732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	114	421	0	ENST00000297316.4:c.422G>A	p.Arg141Gln	p.R141Q	ENST00000297316	NM_022454.3	141	cGg/cAg	2/2	0.390953768182669	3	FACETS	1	0.957	1	0.554	0.5	0.611	CLONAL	1	TRUE	1	0.390953768182669	3		421	629	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971177	21971178	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0035446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	185	307	0	ENST00000304494.5:c.180_181delinsTT	p.Glu61Ter	p.E61*	ENST00000304494	NM_000077.4	60	gcGGag/gcTTag	2/3	0.377459839856725	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.390953768182669	2		307	420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0035448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1198	116	851	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.431	0.387	0.477	0.431	0.387	0.477	SUBCLONAL	1	TRUE	1	0.41	2		851	1314	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0035449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	784	590	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.365066149633606	5	FACETS	1	0.995	1	1	0.998	1	CLONAL	6	TRUE	0	0.365066149633606	5		590	1039	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0035449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	107	547	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.348298643629249	3	FACETS	1	0.908	1	0.506	0.454	0.561	CLONAL	1	TRUE	1	0.365066149633606	3		547	685	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0035449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	358	683	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.334721440279029	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	1	0.365066149633606	4		683	782	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	173	701	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.365066149633606	2		701	638	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371810	55371831	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGCCCCGAGGGCGGCCGCGT	TGGGCCCCGAGGGCGGCCGCGT	-	novel	NA	P-0035449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	43	102	0	ENST00000297316.4:c.500_521del	p.Leu167ArgfsTer213	p.L167Rfs*213	ENST00000297316	NM_022454.3	167	cTGGGCCCCGAGGGCGGCCGCGTg/cg	2/2	0.365066149633606	3	FACETS	0.852	0.735	0.973	1	0.953	1	CLONAL	3	TRUE	1	0.365066149633606	3		102	109	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729163	66729163	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs397516792	NA	P-0035449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	53	881	2	ENST00000307102.5:c.371C>A	p.Pro124Gln	p.P124Q	ENST00000307102	NM_002755.3	124	cCg/cAg	3/11	1	2	FACETS	0.391	0.332	0.455	0.391	0.332	0.455	SUBCLONAL	1	TRUE	1	0.365066149633606	2		883	743	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099914	27099914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs953652494	NA	P-0035449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	52	726	2	ENST00000324856.7:c.3793G>A	p.Gly1265Ser	p.G1265S	ENST00000324856	NM_006015.4	1265	Ggc/Agc	15/20	1	2	FACETS	0.495	0.421	0.577	0.495	0.421	0.577	SUBCLONAL	1	TRUE	1	0.365066149633606	2		728	575	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099124	27099125	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0035449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	99	515	0	ENST00000324856.7:c.3539+2dup		p.X1180_splice	ENST00000324856	NM_006015.4	1180			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.365066149633606	2		515	380	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56477595	56477595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759044259	NA	P-0035449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	373	825	0	ENST00000267101.3:c.143C>T	p.Thr48Ile	p.T48I	ENST00000267101	NM_001982.3	48	aCa/aTa	2/28	0.350054725780702	4	FACETS	0.898	0.858	0.937	1	0.993	1	CLONAL	4	TRUE	1	0.365066149633606	4		825	777	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779794	3779794	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	60	1060	0	ENST00000262367.5:c.5254G>T	p.Glu1752Ter	p.E1752*	ENST00000262367	NM_004380.2	1752	Gag/Tag	31/31	0.365066149633606	3	FACETS	0.457	0.393	0.528	0.229	0.196	0.264	SUBCLONAL	1	TRUE	1	0.365066149633606	3		1060	850	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458453	120458454	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0121496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	107	519	0	ENST00000256646.2:c.6891dup	p.Arg2298SerfsTer15	p.R2298Sfs*15	ENST00000256646	NM_024408.3	2297	-/T	34/34	0.253075247944642	2	FACETS	0.652	0.587	0.72	0.326	0.293	0.36	INDETERMINATE	1	NA	0	0.631659505907677	2		519	520	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356429	66356429	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0121496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	25	319	1	ENST00000273854.3:c.1068A>T	p.Arg356Ser	p.R356S	ENST00000273854	NM_004439.5	356	agA/agT	5/18	1	2	FACETS	0.2	0.157	0.249	0.2	0.157	0.249	SUBCLONAL	1	NA	1	0.631659505907677	2		320	396	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400176	139400176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238653760	NA	P-0121496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	262	784	1	ENST00000277541.6:c.4172G>A	p.Cys1391Tyr	p.C1391Y	ENST00000277541	NM_017617.3	1391	tGc/tAc	25/34	0.631066578103189	2	FACETS	1	0.964	1	0.517	0.486	0.549	CLONAL	1	NA	0	0.631659505907677	2		785	802	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440372	52440372	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	33	527	0	ENST00000460680.1:c.680G>C	p.Arg227Pro	p.R227P	ENST00000460680	NM_004656.3	227	cGc/cCc	9/17	1	2	FACETS	0.673	0.547	0.815	0.673	0.547	0.815	SUBCLONAL	1	TRUE	1	0.18	2		527	545	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981097	201981097	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	52	545	0	ENST00000359651.3:c.176G>A	p.Trp59Ter	p.W59*	ENST00000359651		59	tGg/tAg	2/8	1	2	FACETS	0.926	0.788	1	0.926	0.788	1	CLONAL	1	TRUE	1	0.18	2		545	624	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421040	49421561	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CACATCCAGATTGGAGACATTGTAGGTATAGCTGTGCTGAGTGGGTGGCTCTGGGGCGGGGCTCTCCTGTAGGAGGGTGCCCTGTATCATTAGTGCCAGCTCCTCATCTAACTAGCTCCCTCCTTCCCCTCACCCATATGCCACCCTCCCAAAAGGCCTCCACATTCTTTGCCCTAGACAGCCTCTTTTTTCTTTTCTTTTCTTTTTTTTTTGAGACACAGTCTTGCTCTGTTGCCCAGGCTGGATCCAGTGGCACAATCTTGGCTCACTGCAACCTCTGCCTCCTGGGTTCAAGGGATTCTCATGCCTCAGCCTTTCGAGTAGCTGGGATTACAGGCACGCACCATCACGCCTGGCTACTGTTTTGTTTTTGTTTTTAGTAGAGACGGGGTTTCGCCATGTTGGCCAGGCTGGTCTCAAACTCCTGGCCTAAAGTGATTCACTCGCCTTGCCTCCCAAAGCACTGGGATTACAGATGTGAGCCACCGCGCCTGGCCGGCAGCCCCTTTTTTCTAACACCCA	CACATCCAGATTGGAGACATTGTAGGTATAGCTGTGCTGAGTGGGTGGCTCTGGGGCGGGGCTCTCCTGTAGGAGGGTGCCCTGTATCATTAGTGCCAGCTCCTCATCTAACTAGCTCCCTCCTTCCCCTCACCCATATGCCACCCTCCCAAAAGGCCTCCACATTCTTTGCCCTAGACAGCCTCTTTTTTCTTTTCTTTTCTTTTTTTTTTGAGACACAGTCTTGCTCTGTTGCCCAGGCTGGATCCAGTGGCACAATCTTGGCTCACTGCAACCTCTGCCTCCTGGGTTCAAGGGATTCTCATGCCTCAGCCTTTCGAGTAGCTGGGATTACAGGCACGCACCATCACGCCTGGCTACTGTTTTGTTTTTGTTTTTAGTAGAGACGGGGTTTCGCCATGTTGGCCAGGCTGGTCTCAAACTCCTGGCCTAAAGTGATTCACTCGCCTTGCCTCCCAAAGCACTGGGATTACAGATGTGAGCCACCGCGCCTGGCCGGCAGCCCCTTTTTTCTAACACCCA	-	novel	NA	P-0035451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	37	523	0	ENST00000301067.7:c.14643+25_14709del		p.X4881_splice	ENST00000301067	NM_003482.3	4881		48/54	0.240647961217111	3	FACETS	0.729	0.599	0.874	0.364	0.299	0.437	SUBCLONAL	1	TRUE	1	0.18	3		523	615	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059062	42059063	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTGTTATT	novel	NA	P-0035451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	27	392	0	ENST00000219905.7:c.8783_8790dup	p.Asp2931LeufsTer7	p.D2931Lfs*7	ENST00000219905	NM_001164273.1	2928	att/aTTGTTATTtt	24/24	1	2	FACETS	0.634	0.504	0.784	0.634	0.504	0.784	SUBCLONAL	1	TRUE	1	0.18	2		392	473	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351594	89351595	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	69	978	2	ENST00000301030.4:c.1355dup	p.Asn452LysfsTer2	p.N452Kfs*2	ENST00000301030	NM_001256183.1	452	aat/aaAt	9/13	1	2	FACETS	0.732	0.636	0.837	0.732	0.636	0.837	SUBCLONAL	1	TRUE	1	0.18	2		980	1047	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621882	1621882	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561310316	NA	P-0035451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	64	739	1	ENST00000344749.5:c.910G>A	p.Val304Ile	p.V304I	ENST00000344749	NM_001136139.2	304	Gtc/Atc	11/19	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.18	2		740	599	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953957	17953957	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1342240526	NA	P-0035451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	72	681	4	ENST00000458235.1:c.445C>T	p.Arg149Cys	p.R149C	ENST00000458235	NM_000215.3	149	Cgc/Tgc	5/24	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.18	2		685	752	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266531	198266531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	50	486	0	ENST00000335508.6:c.2305G>A	p.Val769Met	p.V769M	ENST00000335508	NM_012433.2	769	Gtg/Atg	16/25	1	2	FACETS	0.712	0.603	0.833	0.712	0.603	0.833	SUBCLONAL	1	TRUE	1	0.18	2		486	780	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437901	52437901	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	64	817	0	ENST00000460680.1:c.1260del	p.Lys421ArgfsTer9	p.K421Rfs*9	ENST00000460680	NM_004656.3	420	ggG/gg	13/17	1	2	FACETS	0.757	0.654	0.87	0.757	0.654	0.87	SUBCLONAL	1	TRUE	1	0.18	2		817	939	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860287	151860288	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	34	546	0	ENST00000262189.6:c.10374dup	p.Pro3459ThrfsTer3	p.P3459Tfs*3	ENST00000262189	NM_170606.2	3458	-/A	43/59	1	2	FACETS	0.662	0.539	0.8	0.662	0.539	0.8	SUBCLONAL	1	TRUE	1	0.18	2		546	571	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	231	467	6	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	0.39246130320106	2		473	800	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	231	535	1	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.811	0.759	0.864	1	0.993	1	CLONAL	2	TRUE	1	0.39246130320106	2		536	726	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	109	313	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.844	0.767	0.924	1	0.987	1	CLONAL	2	TRUE	1	0.39246130320106	2		313	329	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	133	556	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.797	0.73	0.866	1	0.988	1	SUBCLONAL	2	TRUE	1	0.39246130320106	2		557	425	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	476	611	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.976	1	1	0.998	1	CLONAL	3	TRUE	1	0.39246130320106	2		617	797	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs967461896	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	153	686	0	ENST00000269305.4:c.526T>C	p.Cys176Arg	p.C176R	ENST00000269305	NM_001126112.2	176	Tgc/Cgc	5/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.39246130320106	2		686	563	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	45	226	1	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.39246130320106	2		227	229	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	321	463	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.39246130320106	1	FACETS	1	0.991	1	1	0.997	1	CLONAL	2	TRUE	0	0.39246130320106	1		463	577	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099402	157099403	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAG	rs587779743	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	20	171	0	ENST00000346085.5:c.360_362dup	p.Gln131dup	p.Q131dup	ENST00000346085	NM_020732.3	131	-/CAG	1/20	1	2	FACETS	0.413	0.316	0.525	0.413	0.316	0.525	SUBCLONAL	1	TRUE	1	0.39246130320106	2		171	247	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796883	42796883	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	352	866	2	ENST00000575354.2:c.3347del	p.Pro1116GlnfsTer45	p.P1116Qfs*45	ENST00000575354	NM_015125.3	1114	gCc/gc	14/20	1	2	FACETS	0.857	0.814	0.902	1	0.996	1	CLONAL	2	TRUE	1	0.39246130320106	2		868	1046	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	31	412	1	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	1	2	FACETS	0.284	0.229	0.347	0.284	0.229	0.347	SUBCLONAL	1	TRUE	1	0.39246130320106	2		413	556	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	87	297	2	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	1	2	FACETS	0.901	0.801	1	0.901	0.801	1	CLONAL	1	TRUE	1	0.39246130320106	2		299	492	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675571	86675571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1561325048	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	33	162	1	ENST00000274376.6:c.2513del	p.Asn838MetfsTer4	p.N838Mfs*4	ENST00000274376	NM_002890.2	836	gAa/ga	19/25	1	2	FACETS	0.574	0.469	0.691	0.574	0.469	0.691	SUBCLONAL	1	TRUE	1	0.39246130320106	2		163	293	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	320	702	2	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.789	0.745	0.833	1	0.995	1	SUBCLONAL	2	TRUE	1	0.39246130320106	2		704	1034	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069060	5069060	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	100	240	0	ENST00000381652.3:c.1370del	p.Asn457MetfsTer22	p.N457Mfs*22	ENST00000381652	NM_004972.3	455	acA/ac	11/25	0.39246130320106	0	FACETS	0.707	0.645	0.769			1	SUBCLONAL	2	TRUE	0	0.39246130320106	0		240	219	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287469	46287469	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	165	389	0	ENST00000334344.6:c.5333del	p.Asn1778IlefsTer13	p.N1778Ifs*13	ENST00000334344	NM_152641.2	1776	ttA/tt	20/21	1	2	FACETS	0.79	0.73	0.852	1	0.99	1	SUBCLONAL	2	TRUE	1	0.39246130320106	2		389	532	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	262	655	3	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.39246130320106	2		658	984	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204842	128204842	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs768767517	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	191	785	3	ENST00000341105.2:c.599del	p.Gly200ValfsTer18	p.G200Vfs*18	ENST00000341105	NM_032638.4	200	gGt/gt	3/6	1	2	FACETS	0.901	0.833	0.973	0.901	0.833	0.973	CLONAL	1	TRUE	1	0.39246130320106	2		788	1080	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	303	616	2	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	1	2	FACETS	0.79	0.746	0.836	1	0.995	1	SUBCLONAL	2	TRUE	1	0.39246130320106	2		618	977	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172331	7172331	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758151117	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	203	400	1	ENST00000302850.5:c.1238G>A	p.Arg413His	p.R413H	ENST00000302850	NM_000208.2	413	cGt/cAt	5/22	1	2	FACETS	0.822	0.767	0.879	1	0.993	1	CLONAL	2	TRUE	1	0.39246130320106	2		401	629	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	159	405	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.39246130320106	2		408	571	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	232	323	0	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	1	1	FACETS	0.852	0.81	0.892	1	0.996	1	CLONAL	3	TRUE	0	0.39246130320106	1		323	372	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	233	453	14	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	0.114544143693791	3	FACETS	1	0.988	1	0.796	0.748	0.844	INDETERMINATE	2	TRUE	0	0.39246130320106	3		467	595	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131719	2131719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746588726	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	103	751	0	ENST00000219476.3:c.3734G>A	p.Arg1245Gln	p.R1245Q	ENST00000219476	NM_000548.3	1245	cGg/cAg	31/42	1	2	FACETS	0.485	0.432	0.54	0.485	0.432	0.54	SUBCLONAL	1	TRUE	1	0.39246130320106	2		751	1083	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740467	58740467	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs773389405	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	234	565	0	ENST00000305921.3:c.1372C>T	p.Arg458Ter	p.R458*	ENST00000305921	NM_003620.3	458	Cga/Tga	6/6	1	2	FACETS	0.806	0.755	0.858	1	0.993	1	CLONAL	2	TRUE	1	0.39246130320106	2		565	740	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774681	73774682	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	32	101	0	ENST00000254810.4:c.405_406del	p.Arg135SerfsTer12	p.R135Sfs*12	ENST00000254810	NM_005324.3	135	agAGct/agct	4/4	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.39246130320106	2		101	139	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	59	378	1	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	0.39176569025204	3	FACETS	0.617	0.531	0.711	0.308	0.265	0.356	SUBCLONAL	1	TRUE	1	0.39246130320106	3		379	583	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269009	142269009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369913351	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	202	387	4	ENST00000350721.4:c.2941G>A	p.Val981Ile	p.V981I	ENST00000350721	NM_001184.3	981	Gtt/Att	14/47	1	2	FACETS	0.782	0.728	0.837	1	0.992	1	SUBCLONAL	2	TRUE	1	0.39246130320106	2		391	658	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370927	55370927	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	318	533	2	ENST00000297316.4:c.229G>A	p.Val77Met	p.V77M	ENST00000297316	NM_022454.3	77	Gtg/Atg	1/2	1	2	FACETS	0.879	0.832	0.927	1	0.995	1	CLONAL	2	TRUE	1	0.39246130320106	2		535	922	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264985	46264985	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	215	432	0	ENST00000371998.3:c.1860del	p.Lys620AsnfsTer18	p.K620Nfs*18	ENST00000371998		619	Aaa/aa	12/23	1	2	FACETS	0.951	0.891	1	1	0.994	1	CLONAL	2	TRUE	1	0.39246130320106	2		432	576	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346157	89346158	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs878855327	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	53	184	0	ENST00000301030.4:c.6792dup	p.Ala2265ArgfsTer8	p.A2265Rfs*8	ENST00000301030	NM_001256183.1	2264	-/C	9/13	0.39176569025204	3	FACETS	1	0.957	1	0.654	0.563	0.751	CLONAL	1	TRUE	1	0.39246130320106	3		184	247	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37882874	37882874	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758973569	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	272	758	0	ENST00000269571.5:c.2932C>T	p.Arg978Cys	p.R978C	ENST00000269571		978	Cgc/Tgc	24/27	1	2	FACETS	0.766	0.72	0.813	1	0.994	1	SUBCLONAL	2	TRUE	1	0.39246130320106	2		758	905	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119910	70119910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1297203260	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	108	429	1	ENST00000245479.2:c.916del	p.Val306CysfsTer77	p.V306Cfs*77	ENST00000245479	NM_000346.3	304	ccG/cc	3/3	1	2	FACETS	0.853	0.767	0.944	0.853	0.767	0.944	CLONAL	1	TRUE	1	0.39246130320106	2		430	645	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3114952	3114952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	283	619	0	ENST00000078429.4:c.487G>A	p.Asp163Asn	p.D163N	ENST00000078429	NM_002067.2	163	Gac/Aac	4/7	1	2	FACETS	0.902	0.852	0.954	1	0.995	1	CLONAL	2	TRUE	1	0.39246130320106	2		619	799	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946319	2946319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373819371	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	384	817	0	ENST00000396946.4:c.3418G>A	p.Gly1140Ser	p.G1140S	ENST00000396946	NM_032415.4	1140	Ggc/Agc	25/25	1	2	FACETS	0.842	0.8	0.884	1	0.996	1	CLONAL	2	TRUE	1	0.39246130320106	2		817	1162	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296203	15296204	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CA	CA	-	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	257	699	3	ENST00000263388.2:c.2160_2161del	p.Cys720Ter	p.C720*	ENST00000263388	NM_000435.2	720	tgTGag/tgag	14/33	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.39246130320106	2		702	928	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	433	506	13	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.995	0.958	1	1	0.998	1	CLONAL	3	TRUE	1	0.39246130320106	2		519	739	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	166	753	0	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	1	2	FACETS	0.691	0.633	0.751	0.691	0.633	0.751	SUBCLONAL	1	TRUE	1	0.39246130320106	2		753	1225	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209593	98209593	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	29	451	1	ENST00000331920.6:c.3945del	p.Tyr1316ThrfsTer56	p.Y1316Tfs*56	ENST00000331920	NM_000264.3	1315	ccC/cc	23/24	1	2	FACETS	0.27	0.216	0.332	0.27	0.216	0.332	SUBCLONAL	1	TRUE	1	0.39246130320106	2		452	547	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647657	3647657	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs774532876	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	378	825	2	ENST00000294008.3:c.1406del	p.Pro469HisfsTer4	p.P469Hfs*4	ENST00000294008	NM_032444.2	469	cCa/ca	7/15	1	2	FACETS	0.854	0.812	0.897	1	0.996	1	CLONAL	2	TRUE	1	0.39246130320106	2		827	1128	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250676	26250676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	194	571	0	ENST00000446824.2:c.158G>A	p.Arg53His	p.R53H	ENST00000446824	NM_021018.2	53	cGc/cAc	1/1	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.39246130320106	2		571	737	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200877	67200877	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	247	526	0	ENST00000312629.5:c.870del	p.Tyr291ThrfsTer14	p.Y291Tfs*14	ENST00000312629	NM_003952.2	289	Ccc/cc	10/15	1	2	FACETS	0.845	0.793	0.898	1	0.994	1	CLONAL	2	TRUE	1	0.39246130320106	2		526	745	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467736	50467736	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	119	448	0	ENST00000331340.3:c.971C>G	p.Ala324Gly	p.A324G	ENST00000331340	NM_006060.4	324	gCc/gGc	8/8	1	2	FACETS	0.986	0.892	1	0.986	0.892	1	CLONAL	1	TRUE	1	0.39246130320106	2		448	615	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165657	118165657	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs565811357	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	185	342	0	ENST00000369448.3:c.167G>A	p.Arg56His	p.R56H	ENST00000369448	NM_017709.3	56	cGc/cAc	2/2	1	2	FACETS	0.952	0.887	1	1	0.993	1	CLONAL	2	TRUE	1	0.39246130320106	2		342	495	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242899	142242899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750252420	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	230	474	0	ENST00000350721.4:c.4088C>T	p.Ala1363Val	p.A1363V	ENST00000350721	NM_001184.3	1363	gCg/gTg	22/47	1	2	FACETS	0.753	0.704	0.803	1	0.992	1	SUBCLONAL	2	TRUE	1	0.39246130320106	2		474	778	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324463	31324463	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	103	560	0	ENST00000412585.2:c.343+2T>C		p.X115_splice	ENST00000412585	NM_005514.6	115			1	2	FACETS	0.711	0.637	0.791	0.711	0.637	0.791	SUBCLONAL	1	TRUE	1	0.39246130320106	2		560	738	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910259	50910259	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1043752384	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	272	614	0	ENST00000440232.2:c.1514G>A	p.Arg505His	p.R505H	ENST00000440232	NM_002691.3	505	cGc/cAc	13/27	1	2	FACETS	0.817	0.769	0.866	1	0.994	1	CLONAL	2	TRUE	1	0.39246130320106	2		614	848	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803500	32803500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550712305	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	339	638	1	ENST00000374899.4:c.659G>A	p.Arg220Gln	p.R220Q	ENST00000374899	NM_018833.2	220	cGa/cAa	4/12	1	2	FACETS	0.828	0.785	0.873	1	0.995	1	CLONAL	2	TRUE	1	0.39246130320106	2		639	1043	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444933	49444933	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767415197	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	139	480	4	ENST00000301067.7:c.2533del	p.Arg845GlyfsTer85	p.R845Gfs*85	ENST00000301067	NM_003482.3	845	Cgg/gg	10/54	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.39246130320106	2		484	631	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849873	151849873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141718495	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	163	325	1	ENST00000262189.6:c.12443C>T	p.Pro4148Leu	p.P4148L	ENST00000262189	NM_170606.2	4148	cCg/cTg	49/59	1	2	FACETS	0.822	0.76	0.886	1	0.991	1	CLONAL	2	TRUE	1	0.39246130320106	2		326	505	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244233	5244233	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	75	643	0	ENST00000357368.4:c.1249G>A	p.Val417Met	p.V417M	ENST00000357368	NM_002850.3	417	Gtg/Atg	11/38	1	2	FACETS	0.462	0.404	0.525	0.462	0.404	0.525	SUBCLONAL	1	TRUE	1	0.39246130320106	2		643	827	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31464435	31464435	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1471632102	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	81	726	0	ENST00000344624.3:c.2482del	p.Ile828TyrfsTer7	p.I828Yfs*7	ENST00000344624		828	Ata/ta	17/33	1	2	FACETS	0.351	0.308	0.398	0.351	0.308	0.398	SUBCLONAL	1	TRUE	1	0.39246130320106	2		726	1176	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405373	70405373	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	110	528	0	ENST00000373644.4:c.2887A>G	p.Ser963Gly	p.S963G	ENST00000373644	NM_030625.2	963	Agt/Ggt	4/12	1	2	FACETS	0.817	0.735	0.904	0.817	0.735	0.904	CLONAL	1	TRUE	1	0.39246130320106	2		528	686	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741574	17741574	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1371486239	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	48	192	0	ENST00000250003.3:c.245G>A	p.Arg82His	p.R82H	ENST00000250003	NM_002478.4	82	cGc/cAc	1/3	1	2	FACETS	0.792	0.673	0.921	0.792	0.673	0.921	CLONAL	1	TRUE	1	0.39246130320106	2		192	309	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212014	94212014	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876660609	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	148	348	0	ENST00000323929.3:c.431T>C	p.Leu144Ser	p.L144S	ENST00000323929	NM_005591.3	144	tTa/tCa	6/20	1	2	FACETS	0.871	0.803	0.941	1	0.991	1	CLONAL	2	TRUE	1	0.39246130320106	2		348	433	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216524	108216525	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	74	367	0	ENST00000278616.4:c.8477dup	p.Asn2826LysfsTer22	p.N2826Kfs*22	ENST00000278616	NM_000051.3	2825	caa/cAaa	58/63	1	2	FACETS	0.814	0.715	0.921	0.814	0.715	0.921	CLONAL	1	TRUE	1	0.39246130320106	2		367	463	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245921	46245921	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	101	305	0	ENST00000334344.6:c.4015C>T	p.Gln1339Ter	p.Q1339*	ENST00000334344	NM_152641.2	1339	Cag/Tag	15/21	1	2	FACETS	0.814	0.737	0.895	1	0.985	1	CLONAL	2	TRUE	1	0.39246130320106	2		305	316	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431576	49431576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762206028	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	194	570	1	ENST00000301067.7:c.9563C>T	p.Thr3188Met	p.T3188M	ENST00000301067	NM_003482.3	3188	aCg/aTg	34/54	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.39246130320106	2		571	665	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492534	50492534	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1200935521	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	296	630	1	ENST00000394963.4:c.1430G>A	p.Arg477His	p.R477H	ENST00000394963	NM_003076.4	477	cGc/cAc	12/13	1	2	FACETS	0.863	0.815	0.912	1	0.995	1	CLONAL	2	TRUE	1	0.39246130320106	2		631	874	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112229	115112229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	136	235	1	ENST00000257566.3:c.1511C>T	p.Ala504Val	p.A504V	ENST00000257566	NM_016569.3	504	gCc/gTc	7/8	1	2	FACETS	1	0.933	1	1	0.991	1	CLONAL	2	TRUE	1	0.39246130320106	2		236	342	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800903	120800903	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748469666	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	209	691	1	ENST00000257552.2:c.345del	p.Leu116CysfsTer3	p.L116Cfs*3	ENST00000257552	NM_002442.3	115	ggG/gg	6/15	1	2	FACETS	0.991	0.919	1	0.991	0.919	1	CLONAL	1	TRUE	1	0.39246130320106	2		692	1075	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355756	73355756	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	106	363	0	ENST00000377767.4:c.215T>A	p.Val72Glu	p.V72E	ENST00000377767	NM_014953.3	72	gTg/gAg	1/21	1	2	FACETS	0.928	0.834	1	0.928	0.834	1	CLONAL	1	TRUE	1	0.39246130320106	2		363	582	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606144	81606144	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	247	456	0	ENST00000298171.2:c.814C>A	p.Leu272Ile	p.L272I	ENST00000298171	NM_000369.2	272	Ctc/Atc	9/10	1	2	FACETS	0.777	0.729	0.827	1	0.993	1	SUBCLONAL	2	TRUE	1	0.39246130320106	2		456	810	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572081	95572081	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	220	573	0	ENST00000393063.1:c.3027del	p.Ala1011ArgfsTer4	p.A1011Rfs*4	ENST00000393063	NM_030621.3	1009	ggG/gg	20/28	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.39246130320106	2		573	818	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42053989	42053989	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	16	278	0	ENST00000219905.7:c.7451A>T	p.Gln2484Leu	p.Q2484L	ENST00000219905	NM_001164273.1	2484	cAg/cTg	21/24	0.39246130320106	1	FACETS	0.225	0.166	0.296	0.225	0.166	0.296	SUBCLONAL	1	TRUE	0	0.39246130320106	1		278	291	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43771722	43771722	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	377	517	1	ENST00000382044.4:c.661A>T	p.Ile221Phe	p.I221F	ENST00000382044	NM_001141980.1	221	Att/Ttt	7/28	0.39246130320106	1	FACETS	1	0.994	1	1	0.997	1	CLONAL	2	TRUE	0	0.39246130320106	1		518	642	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041606	14041606	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	226	462	0	ENST00000311895.7:c.2153T>A	p.Leu718His	p.L718H	ENST00000311895	NM_005236.2	718	cTc/cAc	11/11	1	2	FACETS	0.885	0.829	0.942	1	0.994	1	CLONAL	2	TRUE	1	0.39246130320106	2		462	651	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641061	23641061	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	126	742	0	ENST00000261584.4:c.2414T>C	p.Val805Ala	p.V805A	ENST00000261584	NM_024675.3	805	gTc/gCc	5/13	1	2	FACETS	0.562	0.507	0.619	0.562	0.507	0.619	SUBCLONAL	1	TRUE	1	0.39246130320106	2		742	1143	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822112	72822112	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	37	500	0	ENST00000268489.5:c.10063C>A	p.Leu3355Met	p.L3355M	ENST00000268489	NM_006885.3	3355	Ctg/Atg	10/10	0.39176569025204	3	FACETS	0.335	0.275	0.402	0.167	0.137	0.201	SUBCLONAL	1	TRUE	1	0.39246130320106	3		500	674	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828399	72828399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	256	578	0	ENST00000268489.5:c.8182G>A	p.Ala2728Thr	p.A2728T	ENST00000268489	NM_006885.3	2728	Gct/Act	9/10	0.39176569025204	3	FACETS	0.876	0.822	0.931	0.876	0.822	0.931	CLONAL	2	TRUE	1	0.39246130320106	3		578	891	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830402	72830402	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	25	340	0	ENST00000268489.5:c.6179C>A	p.Ser2060Tyr	p.S2060Y	ENST00000268489	NM_006885.3	2060	tCc/tAc	9/10	0.39176569025204	3	FACETS	0.354	0.278	0.441	0.177	0.139	0.221	SUBCLONAL	1	TRUE	1	0.39246130320106	3		340	431	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350806	89350806	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1179	241	955	0	ENST00000301030.4:c.2144A>G	p.Glu715Gly	p.E715G	ENST00000301030	NM_001256183.1	715	gAa/gGa	9/13	0.39176569025204	3	FACETS	1	0.956	1	0.517	0.482	0.554	CLONAL	1	TRUE	1	0.39246130320106	3		955	1420	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16062155	16062157	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	286	517	0	ENST00000268712.3:c.649_651del	p.Pro217del	p.P217del	ENST00000268712	NM_006311.3	217	CCT/-	6/46	1	2	FACETS	0.768	0.723	0.814	1	0.994	1	SUBCLONAL	2	TRUE	1	0.39246130320106	2		517	949	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215948	41215948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55770810	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	143	355	0	ENST00000357654.3:c.5095C>T	p.Arg1699Trp	p.R1699W	ENST00000357654	NM_007294.3	1699	Cgg/Tgg	17/23	1	2	FACETS	0.78	0.717	0.846	1	0.989	1	SUBCLONAL	2	TRUE	1	0.39246130320106	2		355	467	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437588	56437588	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	172	450	0	ENST00000407977.2:c.874C>A	p.His292Asn	p.H292N	ENST00000407977		292	Cat/Aat	8/10	1	2	FACETS	0.791	0.732	0.851	1	0.991	1	SUBCLONAL	2	TRUE	1	0.39246130320106	2		450	554	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66525011	66525011	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	97	249	0	ENST00000358598.2:c.770A>T	p.Glu257Val	p.E257V	ENST00000358598	NM_212471.2	257	gAg/gTg	9/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.39246130320106	2		249	384	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753479	42753479	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555750721	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	48	700	0	ENST00000222329.4:c.785del	p.Pro262LeufsTer9	p.P262Lfs*9	ENST00000222329	NM_006494.2	262	cCt/ct	4/4	1	2	FACETS	0.266	0.223	0.312	0.266	0.223	0.312	SUBCLONAL	1	TRUE	1	0.39246130320106	2		700	921	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796772	42796772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	320	768	0	ENST00000575354.2:c.3230G>A	p.Ser1077Asn	p.S1077N	ENST00000575354	NM_015125.3	1077	aGt/aAt	14/20	1	2	FACETS	0.774	0.731	0.817	1	0.995	1	SUBCLONAL	2	TRUE	1	0.39246130320106	2		768	1054	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39214661	39214661	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	134	564	0	ENST00000402219.2:c.3463C>T	p.Pro1155Ser	p.P1155S	ENST00000402219	NM_005633.3	1155	Cca/Tca	22/23	1	2	FACETS	0.737	0.669	0.808	0.737	0.669	0.808	SUBCLONAL	1	TRUE	1	0.39246130320106	2		564	927	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46611734	46611734	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779305044	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	289	661	1	ENST00000263734.3:c.2548G>A	p.Val850Met	p.V850M	ENST00000263734	NM_001430.4	850	Gtg/Atg	16/16	1	2	FACETS	0.836	0.788	0.884	1	0.995	1	CLONAL	2	TRUE	1	0.39246130320106	2		662	881	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149611	202149611	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	256	455	0	ENST00000358485.4:c.1052T>A	p.Ile351Asn	p.I351N	ENST00000358485	NM_001080125.1	351	aTc/aAc	8/9	1	2	FACETS	0.897	0.844	0.951	1	0.995	1	CLONAL	2	TRUE	1	0.39246130320106	2		455	727	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587118	212587118	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs74898139	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	136	325	0	ENST00000342788.4:c.883C>T	p.His295Tyr	p.H295Y	ENST00000342788	NM_005235.2	295	Cat/Tat	7/28	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.39246130320106	2		325	485	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538286	9538286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	233	515	1	ENST00000353224.5:c.1712G>A	p.Ser571Asn	p.S571N	ENST00000353224	NM_177990.2	571	aGt/aAt	7/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.39246130320106	2		516	852	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790011	40790011	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	228	493	0	ENST00000373198.4:c.2720G>T	p.Gly907Val	p.G907V	ENST00000373198	NM_133170.3	907	gGg/gTg	18/32	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.39246130320106	2		493	801	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268568	46268568	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	112	268	0	ENST00000371998.3:c.2953+2T>C		p.X985_splice	ENST00000371998		985			1	2	FACETS	0.903	0.823	0.985	1	0.988	1	CLONAL	2	TRUE	1	0.39246130320106	2		268	316	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292834	62292834	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1218949514	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	135	264	0	ENST00000360203.5:c.286G>A	p.Ala96Thr	p.A96T	ENST00000360203	NM_001283009.1	96	Gct/Act	3/35	1	2	FACETS	0.958	0.882	1	1	0.991	1	CLONAL	2	TRUE	1	0.39246130320106	2		264	359	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648436	30648436	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	122	455	1	ENST00000295754.5:c.61G>A	p.Ala21Thr	p.A21T	ENST00000295754	NM_003242.5	21	Gcc/Acc	1/7	1	2	FACETS	0.92	0.833	1	0.92	0.833	1	CLONAL	1	TRUE	1	0.39246130320106	2		456	676	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478152	138478152	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	173	395	0	ENST00000289153.2:c.34G>A	p.Ala12Thr	p.A12T	ENST00000289153	NM_006219.2	12	Gca/Aca	1/22	1	2	FACETS	0.818	0.758	0.879	1	0.991	1	CLONAL	2	TRUE	1	0.39246130320106	2		395	539	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947131	178947131	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	177	315	0	ENST00000263967.3:c.2567C>A	p.Thr856Asn	p.T856N	ENST00000263967	NM_006218.2	856	aCt/aAt	18/21	1	2	FACETS	0.784	0.727	0.843	1	0.991	1	SUBCLONAL	2	TRUE	1	0.39246130320106	2		315	575	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1955081	1955081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	340	739	0	ENST00000382891.5:c.2168G>A	p.Ser723Asn	p.S723N	ENST00000382891	NM_133335.3	723	aGc/aAc	12/22	1	2	FACETS	0.761	0.72	0.802	1	0.995	1	SUBCLONAL	2	TRUE	1	0.39246130320106	2		739	1139	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244200	153244200	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	43	456	1	ENST00000281708.4:c.1957del	p.Thr653ArgfsTer8	p.T653Rfs*8	ENST00000281708	NM_033632.3	653	Acg/cg	12/12	1	2	FACETS	0.35	0.292	0.414	0.35	0.292	0.414	SUBCLONAL	1	TRUE	1	0.39246130320106	2		457	626	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264594	1264594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387907251	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	284	654	1	ENST00000310581.5:c.2768C>T	p.Pro923Leu	p.P923L	ENST00000310581	NM_198253.2	923	cCg/cTg	11/16	1	2	FACETS	0.813	0.766	0.861	1	0.994	1	CLONAL	2	TRUE	1	0.39246130320106	2		655	890	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31421419	31421419	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	60	487	0	ENST00000344624.3:c.3485T>C	p.Leu1162Ser	p.L1162S	ENST00000344624		1162	tTa/tCa	27/33	1	2	FACETS	0.514	0.442	0.592	0.514	0.442	0.592	SUBCLONAL	1	TRUE	1	0.39246130320106	2		487	595	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871174	35871174	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	61	301	0	ENST00000303115.3:c.399del	p.Phe133LeufsTer3	p.F133Lfs*3	ENST00000303115	NM_002185.3	132	ccT/cc	4/8	1	2	FACETS	0.653	0.564	0.749	0.653	0.564	0.749	SUBCLONAL	1	TRUE	1	0.39246130320106	2		301	476	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395919	395919	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1561712197	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	169	395	0	ENST00000380956.4:c.476C>A	p.Pro159His	p.P159H	ENST00000380956	NM_001195286.1	159	cCt/cAt	4/9	1	2	FACETS	0.966	0.897	1	1	0.993	1	CLONAL	2	TRUE	1	0.39246130320106	2		395	446	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816536	32816536	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1392845171	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	389	684	1	ENST00000354258.4:c.1639C>T	p.Arg547Cys	p.R547C	ENST00000354258	NM_000593.5	547	Cgc/Tgc	7/11	1	2	FACETS	0.881	0.838	0.924	1	0.996	1	CLONAL	2	TRUE	1	0.39246130320106	2		685	1125	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983866	2983866	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1037289774	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	318	616	0	ENST00000396946.4:c.664A>G	p.Ser222Gly	p.S222G	ENST00000396946	NM_032415.4	222	Agc/Ggc	5/25	1	2	FACETS	0.835	0.79	0.881	1	0.995	1	CLONAL	2	TRUE	1	0.39246130320106	2		616	970	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836296	151836296	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771641625	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	240	447	0	ENST00000262189.6:c.14509G>A	p.Ala4837Thr	p.A4837T	ENST00000262189	NM_170606.2	4837	Gcg/Acg	57/59	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.39246130320106	2		447	912	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38315000	38315000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200766494	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	365	674	0	ENST00000425967.3:c.64G>A	p.Gly22Arg	p.G22R	ENST00000425967	NM_001174067.1	22	Gga/Aga	3/19	1	2	FACETS	0.872	0.829	0.917	1	0.996	1	CLONAL	2	TRUE	1	0.39246130320106	2		674	1066	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104574	69104574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs771377093	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	346	670	0	ENST00000288368.4:c.4418T>C	p.Met1473Thr	p.M1473T	ENST00000288368	NM_024870.2	1473	aTg/aCg	37/40	1	2	FACETS	0.858	0.813	0.903	1	0.996	1	CLONAL	2	TRUE	1	0.39246130320106	2		670	1028	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27204926	27204926	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	30	378	0	ENST00000380036.4:c.2232del	p.Lys745ArgfsTer5	p.K745Rfs*5	ENST00000380036	NM_000459.3	743	Ggg/gg	14/23	0.39246130320106	0	FACETS	0.201	0.161	0.246			1	SUBCLONAL	1	TRUE	0	0.39246130320106	0		378	462	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864065	97864065	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	54	608	0	ENST00000289081.3:c.1601A>C	p.Asn534Thr	p.N534T	ENST00000289081	NM_000136.2	534	aAt/aCt	15/15	1	2	FACETS	0.299	0.255	0.349	0.299	0.255	0.349	SUBCLONAL	1	TRUE	1	0.39246130320106	2		608	919	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209366	98209366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773676486	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	185	502	0	ENST00000331920.6:c.4172G>A	p.Arg1391Gln	p.R1391Q	ENST00000331920	NM_000264.3	1391	cGg/cAg	23/24	1	2	FACETS	0.81	0.752	0.869	1	0.992	1	CLONAL	2	TRUE	1	0.39246130320106	2		502	582	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900369	101900371	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	79	219	0	ENST00000374994.4:c.803_805del	p.Lys268_Asp269delinsAsn	p.K268_D269delinsN	ENST00000374994	NM_004612.2	268	aAAGac/aac	4/9	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.39246130320106	2		219	314	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395216	139395216	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	167	788	1	ENST00000277541.6:c.5722G>A	p.Ala1908Thr	p.A1908T	ENST00000277541	NM_017617.3	1908	Gcc/Acc	31/34	1	2	FACETS	0.835	0.767	0.907	0.835	0.767	0.907	CLONAL	1	TRUE	1	0.39246130320106	2		789	1019	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428988	47428988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	147	308	0	ENST00000377045.4:c.1351G>A	p.Ala451Thr	p.A451T	ENST00000377045	NM_001654.4	451	Gcc/Acc	13/16	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.39246130320106	1		308	475	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246353	53246353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	35	271	0	ENST00000375401.3:c.629G>A	p.Gly210Asp	p.G210D	ENST00000375401	NM_004187.3	210	gGc/gAc	5/26	1	1	FACETS	0.291	0.238	0.35	0.291	0.238	0.35	SUBCLONAL	1	TRUE	0	0.39246130320106	1		271	493	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411979	63411979	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	257	370	0	ENST00000330258.3:c.1188G>T	p.Glu396Asp	p.E396D	ENST00000330258	NM_152424.3	396	gaG/gaT	2/2	1	1	FACETS	0.882	0.842	0.92	1	0.996	1	CLONAL	3	TRUE	0	0.39246130320106	1		370	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0035466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	57	851	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.955	0.819	1	0.955	0.819	1	CLONAL	1	TRUE	1	0.18	2		851	663	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0035466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	29	313	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	0.294113047511246	3	FACETS	0.631	0.505	0.774	0.315	0.252	0.387	SUBCLONAL	1	TRUE	1	0.18	3		313	557	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641180	3641180	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	167	1217	1	ENST00000294008.3:c.2459G>C	p.Arg820Thr	p.R820T	ENST00000294008	NM_032444.2	820	aGg/aCg	12/15	0.219485460458077	3	FACETS	0.823	0.754	0.895	0.823	0.754	0.895	CLONAL	2	TRUE	1	0.18	3		1218	1229	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36022653	36022653	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	50	502	0	ENST00000358208.4:c.526C>G	p.Leu176Val	p.L176V	ENST00000358208		176	Ctc/Gtc	5/12	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.18	2		502	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0035468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	444	751	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.543548667650565	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.543548667650565	2		751	794	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321372	1321372	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1319865856	NA	P-0035468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	121	499	0	ENST00000400841.2:c.383C>T	p.Ser128Leu	p.S128L	ENST00000400841		128	tCg/tTg	4/6	1	1	FACETS	0.565	0.512	0.62	0.565	0.512	0.62	SUBCLONAL	1	TRUE	0	0.543548667650565	1		499	574	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841231	15841236	+	inframe_deletion	In_Frame_Del	DEL	AGCCGG	AGCCGG	-	rs752736259	NA	P-0035468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	40	139	0	ENST00000307771.7:c.1338_1343del	p.Ser447_Arg448del	p.S447_R448del	ENST00000307771	NM_005089.3	439	AGCCGG/-	11/11	1	1	FACETS	0.766	0.649	0.89	0.766	0.649	0.89	SUBCLONAL	1	TRUE	0	0.543548667650565	1		139	140	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928935	44928935	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	275	253	0	ENST00000377967.4:c.2035C>T	p.Gln679Ter	p.Q679*	ENST00000377967	NM_021140.2	679	Cag/Tag	17/29	0.543548667650565	3	FACETS	0.957	0.905	1			1	CLONAL	2	TRUE	NA	0.543548667650565	3		253	672	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600470	10600470	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	405	681	0	ENST00000171111.5:c.1385G>T	p.Gly462Val	p.G462V	ENST00000171111	NM_203500.1	462	gGg/gTg	4/6	0.444794530769433	3	FACETS	0.886	0.851	0.92			1	CLONAL	3	TRUE	NA	0.543548667650565	3		681	713	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097658	27097658	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	254	609	0	ENST00000324856.7:c.3247G>C	p.Gly1083Arg	p.G1083R	ENST00000324856	NM_006015.4	1083	Ggc/Cgc	12/20	0.543548667650565	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.543548667650565	1		609	592	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432468	49432471	+	frameshift_variant	Frame_Shift_Del	DEL	CAGG	CAGG	GGT	novel	NA	P-0035468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	352	786	1	ENST00000301067.7:c.8668_8671delinsACC	p.Pro2890ThrfsTer20	p.P2890Tfs*20	ENST00000301067	NM_003482.3	2890	CCTGgg/ACCgg	34/54	0.543548667650565	2	FACETS	0.95	0.908	0.991	0.95	0.908	0.991	CLONAL	2	TRUE	0	0.543548667650565	2		787	682	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73340152	73340152	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	108	247	0	ENST00000377767.4:c.1928G>T	p.Ser643Ile	p.S643I	ENST00000377767	NM_014953.3	643	aGt/aTt	15/21	0.543548667650565	1	FACETS	0.94	0.855	1	0.94	0.855	1	CLONAL	1	TRUE	0	0.543548667650565	1		247	308	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527956	103527956	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	91	394	0	ENST00000355739.4:c.3264G>T	p.Leu1088Phe	p.L1088F	ENST00000355739	NM_000123.3	1088	ttG/ttT	15/15	0.543548667650565	1	FACETS	0.726	0.65	0.804	0.726	0.65	0.804	SUBCLONAL	1	TRUE	0	0.543548667650565	1		394	336	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42002891	42002891	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	120	337	0	ENST00000219905.7:c.2428G>C	p.Gly810Arg	p.G810R	ENST00000219905	NM_001164273.1	810	Gga/Cga	8/24	0.442246448697713	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.543548667650565	1		337	320	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862710	9862710	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	143	349	0	ENST00000330684.3:c.2593A>G	p.Arg865Gly	p.R865G	ENST00000330684	NM_001134407.1	865	Agg/Ggg	12/13	0.543548667650565	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.543548667650565	1		349	300	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89846359	89846359	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	249	621	0	ENST00000389301.3:c.1633A>T	p.Ser545Cys	p.S545C	ENST00000389301	NM_000135.2	545	Agc/Tgc	18/43	0.444794530769433	3	FACETS	0.776	0.728	0.824			1	SUBCLONAL	2	TRUE	NA	0.543548667650565	3		621	751	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716292	52716292	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	349	690	0	ENST00000322088.6:c.736C>G	p.Pro246Ala	p.P246A	ENST00000322088	NM_014225.5	246	Ccc/Gcc	6/15	0.543548667650565	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.543548667650565	2		690	639	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576886	212576886	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	79	336	0	ENST00000342788.4:c.1013G>T	p.Gly338Val	p.G338V	ENST00000342788	NM_005235.2	338	gGc/gTc	9/28	0.188575801383373	1	FACETS	0.519	0.459	0.583	0.519	0.459	0.583	INDETERMINATE	1	TRUE	0	0.543548667650565	1		336	408	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793331	242793331	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	169	921	2	ENST00000334409.5:c.746C>A	p.Ala249Asp	p.A249D	ENST00000334409	NM_005018.2	249	gCc/gAc	5/5	0.188575801383373	1	FACETS	0.645	0.595	0.697	0.645	0.595	0.697	INDETERMINATE	1	TRUE	0	0.543548667650565	1		923	702	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670565	134670565	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	446	891	0	ENST00000398015.3:c.476A>G	p.Asn159Ser	p.N159S	ENST00000398015	NM_004441.4	159	aAc/aGc	3/16	0.482577339354353	3	FACETS	0.987	0.945	1	0.987	0.945	1	CLONAL	2	TRUE	1	0.543548667650565	3		891	1057	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604620	55604620	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	254	593	0	ENST00000288135.5:c.2828G>T	p.Ser943Ile	p.S943I	ENST00000288135	NM_000222.2	943	aGc/aTc	21/21	0.543548667650565	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.543548667650565	1		593	543	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628829	187628829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	158	655	0	ENST00000441802.2:c.2153G>A	p.Ser718Asn	p.S718N	ENST00000441802	NM_005245.3	718	aGc/aAc	2/27	0.518632723817826	2	FACETS	0.776	0.712	0.843	0.388	0.356	0.422	SUBCLONAL	1	TRUE	0	0.543548667650565	2		655	749	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526398	31526399	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	839	1293	0	ENST00000344624.3:c.641dup	p.Ala215GlyfsTer4	p.A215Gfs*4	ENST00000344624		214	aag/aaAg	2/33	0.543548667650565	4	FACETS	0.949	0.922	0.977	0.949	0.922	0.977	CLONAL	3	TRUE	1	0.543548667650565	4		1293	1673	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704527	117704527	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	116	465	0	ENST00000368508.3:c.2449del	p.Glu817LysfsTer17	p.E817Kfs*17	ENST00000368508	NM_002944.2	817	Gaa/aa	16/43	0.188575801383373	1	FACETS	0.533	0.482	0.587	0.533	0.482	0.587	INDETERMINATE	1	TRUE	0	0.543548667650565	1		465	583	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332862	152332862	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	159	587	0	ENST00000206249.3:c.1168G>T	p.Gly390Cys	p.G390C	ENST00000206249	NM_000125.3	390	Ggt/Tgt	5/8	0.188575801383373	1	FACETS	0.783	0.722	0.846	0.783	0.722	0.846	INDETERMINATE	1	TRUE	0	0.543548667650565	1		587	544	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515231	106515231	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	340	389	0	ENST00000359195.3:c.2374A>C	p.Lys792Gln	p.K792Q	ENST00000359195	NM_002649.2	792	Aaa/Caa	5/11	0.543548667650565	5	FACETS	1	0.992	1	0.829	0.787	0.872	CLONAL	2	TRUE	2	0.543548667650565	5		389	913	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151871274	151871274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	378	593	0	ENST00000262189.6:c.9316G>A	p.Gly3106Ser	p.G3106S	ENST00000262189	NM_170606.2	3106	Ggt/Agt	39/59	0.167327817026396	4	FACETS	0.896	0.856	0.936	0.672	0.642	0.702	INDETERMINATE	3	TRUE	0	0.543548667650565	4		593	799	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570403	87570403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	334	743	0	ENST00000277120.3:c.2143C>T	p.Arg715Trp	p.R715W	ENST00000277120		715	Cgg/Tgg	17/19	0.543548667650565	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.543548667650565	1		743	653	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107003	11107003	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	TGCGGT	novel	NA	P-0035468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	457	662	0	ENST00000358026.2:c.1708delinsTGCGGT	p.Gln570CysfsTer45	p.Q570Cfs*45	ENST00000358026	NM_001128849.1	570	Cag/TGCGGTag	10/36	0.444794530769433	3	FACETS	0.908	0.875	0.941			1	CLONAL	3	TRUE	NA	0.543548667650565	3		662	785	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696438	47696438	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	199	567	0	ENST00000347630.2:c.385A>G	p.Lys129Glu	p.K129E	ENST00000347630	NM_001007230.1	129	Aaa/Gaa	6/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.646898720740195	2		567	575	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385152	41385152	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751630191	NA	P-0035472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	190	632	1	ENST00000373198.4:c.809G>A	p.Arg270His	p.R270H	ENST00000373198	NM_133170.3	270	cGc/cAc	6/32	1	2	FACETS	0.858	0.796	0.921	0.858	0.796	0.921	CLONAL	1	TRUE	1	0.646898720740195	2		633	685	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579477	7579477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	254	715	0	ENST00000269305.4:c.210del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	70	gcT/gc	4/11	0.646898720740195	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.646898720740195	1		715	526	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827820	72827821	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	209	708	0	ENST00000268489.5:c.8760dup	p.Ala2921CysfsTer19	p.A2921Cfs*19	ENST00000268489	NM_006885.3	2920	-/T	9/10	1	2	FACETS	0.906	0.845	0.97	0.906	0.845	0.97	CLONAL	1	TRUE	1	0.646898720740195	2		708	713	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249350	110249350	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	365	1114	0	ENST00000374672.4:c.1223C>T	p.Thr408Ile	p.T408I	ENST00000374672	NM_004235.4	408	aCa/aTa	4/5	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.646898720740195	2		1114	1089	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0003614-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	111	270	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.964	0.878	1	0.964	0.878	1	CLONAL	1	TRUE	1	0.735882142918421	2		270	313	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0003614-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	131	331	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.97	0.891	1			1	INDETERMINATE	1	TRUE	NA	0.735882142918421	2		331	367	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589583	67589584	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACATGAATATAACACTCA	novel	NA	P-0003614-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	33	144	0	ENST00000274335.5:c.1347_1364dup	p.His450_Gln455dup	p.H450_Q455dup	ENST00000274335		450	tta/ttACATGAATATAACACTCAa	10/15	1	2	FACETS	0.627	0.519	0.745	0.627	0.519	0.745	SUBCLONAL	1	TRUE	1	0.735882142918421	2		144	143	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346918	70346918	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	58	610	0	ENST00000374080.3:c.2785G>T	p.Val929Phe	p.V929F	ENST00000374080		929	Gtc/Ttc	20/45	1	2	FACETS	0.743	0.638	0.858	0.743	0.638	0.858	SUBCLONAL	1	TRUE	1	0.246904382081668	2		610	632	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411881	116411893	+	intron_variant	Intron	DEL	CTTTCTTTCTCTC	CTTTCTTTCTCTC	T	novel	NA	P-0003879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	151	957	0	ENST00000397752.3:c.2888-22_2888-10delinsT		p.*963*	ENST00000397752	NM_000245.2	-/1390			0.246904382081668	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.246904382081668	1		957	958	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003879-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	391	840	0	ENST00000397752.3:c.3028G>C	p.Asp1010His	p.D1010H	ENST00000397752	NM_000245.2	1010	Gat/Cat	14/21	0.53546468361142	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	1	0.53546468361142	4		840	721	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411709	116411709	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003879-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	143	952	0	ENST00000397752.3:c.2887+1G>A		p.X963_splice	ENST00000397752	NM_000245.2	963			0.53546468361142	4	FACETS	0.823	0.749	0.9	0.274	0.249	0.3	CLONAL	1	TRUE	1	0.53546468361142	4		952	997	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955109	17955109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140784576	NA	P-0003879-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	155	650	1	ENST00000458235.1:c.118C>T	p.Arg40Cys	p.R40C	ENST00000458235	NM_000215.3	40	Cgc/Tgc	2/24	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.53546468361142	2		651	550	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231106	53231106	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556842168	NA	P-0003879-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	168	570	0	ENST00000375401.3:c.1796G>A	p.Arg599His	p.R599H	ENST00000375401	NM_004187.3	599	cGt/cAt	13/26	0.53546468361142	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.53546468361142	1		570	405	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155312	106155316	+	frameshift_variant	Frame_Shift_Del	DEL	TAGTC	TAGTC	-	novel	NA	P-0003879-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	167	375	0	ENST00000380013.4:c.213_217del	p.Asn71LysfsTer5	p.N71Kfs*5	ENST00000380013	NM_001127208.2	71	aaTAGTCgt/aagt	3/11	0.383790137193361	6	FACETS	1	0.952	1	0.773	0.718	0.828	CLONAL	3	TRUE	2	0.53546468361142	6		375	418	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423407	116423407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913671	NA	P-0003879-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	120	355	0	ENST00000397752.3:c.3682G>A	p.Asp1228Asn	p.D1228N	ENST00000397752	NM_000245.2	1228	Gac/Aac	19/21	0.53546468361142	4	FACETS	0.953	0.87	1	0.635	0.58	0.693	CLONAL	2	TRUE	1	0.53546468361142	4		355	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579310	7579310	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1555526469	NA	P-0003879-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	347	446	0	ENST00000269305.4:c.375+2T>C		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.53546468361142	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	0	0.53546468361142	3		446	533	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054217	30054217	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003879-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	98	507	0	ENST00000338641.4:c.639C>A	p.Asp213Glu	p.D213E	ENST00000338641	NM_000268.3	213	gaC/gaA	7/16	1	2	FACETS	0.917	0.824	1	0.917	0.824	1	CLONAL	1	TRUE	1	0.53546468361142	2		507	399	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812204	43812204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs751975712	NA	P-0004263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	380	348	0	ENST00000372470.3:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000372470	NM_005373.2	357	Cga/Tga	7/12	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.704509369374926	2		348	506	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880497	155880497	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	37	340	0	ENST00000368323.3:c.56C>A	p.Ser19Ter	p.S19*	ENST00000368323	NM_006912.5	19	tCa/tAa	2/6	0.684111048098713	2	FACETS	0.18	0.148	0.217	0.09	0.074	0.109	SUBCLONAL	1	TRUE	0	0.704509369374926	2		340	582	SUCCESS
ATR	545	MSKCC	GRCh37	3	142286983	142286983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1353411105	NA	P-0004263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	218	254	0	ENST00000350721.4:c.73G>A	p.Glu25Lys	p.E25K	ENST00000350721	NM_001184.3	25	Gaa/Aaa	2/47	0.414029644211203	3	FACETS	1	0.983	1	0.578	0.539	0.617	INDETERMINATE	1	TRUE	1	0.704509369374926	3		254	724	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972041	55972041	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	138	275	0	ENST00000263923.4:c.1603A>G	p.Lys535Glu	p.K535E	ENST00000263923	NM_002253.2	535	Aaa/Gaa	12/30	0.649550730626559	1	FACETS	0.671	0.618	0.726	0.671	0.618	0.726	SUBCLONAL	1	TRUE	0	0.704509369374926	1		275	378	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294125	1294127	+	missense_variant	Missense_Mutation	TNP	CGT	CGT	AGG	novel	NA	P-0004263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	77	230	0	ENST00000310581.5:c.874_876delinsCCT	p.Thr292Pro	p.T292P	ENST00000310581	NM_198253.2	292	ACG/CCT	2/16	0.361912599825679	4	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.704509369374926	4		230	286	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645162	86645162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	316	191	0	ENST00000274376.6:c.1234G>A	p.Gly412Arg	p.G412R	ENST00000274376	NM_002890.2	412	Gga/Aga	8/25	0.684497777682431	2	FACETS	0.931	0.894	0.967	0.931	0.894	0.967	CLONAL	2	TRUE	0	0.704509369374926	2		191	482	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419910	152419910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778116774	NA	P-0004263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	205	201	0	ENST00000206249.3:c.1597G>A	p.Val533Met	p.V533M	ENST00000206249	NM_000125.3	533	Gtg/Atg	8/8	0.32025287629603	3	FACETS	1	0.978	1	0.715	0.675	0.754	INDETERMINATE	2	TRUE	0	0.704509369374926	3		201	367	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150455	157150455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	253	275	0	ENST00000346085.5:c.1637C>T	p.Pro546Leu	p.P546L	ENST00000346085	NM_020732.3	546	cCa/cTa	2/20	0.32025287629603	3	FACETS	1	0.985	1	0.726	0.69	0.762	INDETERMINATE	2	TRUE	0	0.704509369374926	3		275	446	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444491	50444492	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	TT	novel	NA	P-0004263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	107	45	0	ENST00000331340.3:c.421_421+1delinsTT		p.X141_splice	ENST00000331340	NM_006060.4	141		4/8	0.704509369374926	6	FACETS	1	0.925	1	0.759	0.695	0.824	CLONAL	3	TRUE	2	0.704509369374926	6		45	241	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50490686	50490686	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	376	322	0	ENST00000394963.4:c.1323G>T	p.Met441Ile	p.M441I	ENST00000394963	NM_003076.4	441	atG/atT	11/13	0.451624384715404	3	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.704509369374926	3		322	604	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109773	115109773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199572544	NA	P-0004263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	171	277	0	ENST00000257566.3:c.2105G>A	p.Ser702Asn	p.S702N	ENST00000257566	NM_016569.3	702	aGc/aAc	8/8	0.456303087712234	3	FACETS	1	0.943	1	0.671	0.629	0.713	CLONAL	2	TRUE	0	0.704509369374926	3		277	326	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28963995	28963995	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	236	318	0	ENST00000282397.4:c.1907G>T	p.Cys636Phe	p.C636F	ENST00000282397	NM_002019.4	636	tGc/tTc	13/30	0.704509369374926	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.704509369374926	1		318	386	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99454619	99454619	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	355	262	0	ENST00000268035.6:c.1538G>T	p.Arg513Leu	p.R513L	ENST00000268035	NM_000875.3	513	cGg/cTg	7/21	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.704509369374926	2		262	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0004263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	246	196	0	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.704509369374926	2		196	321	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246014	41246014	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41286294	NA	P-0004263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	295	278	0	ENST00000357654.3:c.1534C>T	p.Leu512Phe	p.L512F	ENST00000357654	NM_007294.3	512	Ctt/Ttt	10/23	NA	2	FACETS	0.972	0.933	1			1	INDETERMINATE	2	TRUE	NA	0.704509369374926	2		278	431	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740677	58740677	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0004263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	231	580	0	ENST00000305921.3:c.1582A>T	p.Arg528Ter	p.R528*	ENST00000305921	NM_003620.3	528	Aga/Tga	6/6	0.704509369374926	3	FACETS	1	0.96	1	0.519	0.484	0.554	CLONAL	1	TRUE	1	0.704509369374926	3		580	855	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220443	1220443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202466	NA	P-0004263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	255	384	0	ENST00000326873.7:c.536C>T	p.Pro179Leu	p.P179L	ENST00000326873	NM_000455.4	179	cCg/cTg	4/10	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	2	TRUE	NA	0.704509369374926	2		384	354	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543551	9543551	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	310	327	0	ENST00000353224.5:c.1603G>C	p.Val535Leu	p.V535L	ENST00000353224	NM_177990.2	535	Gtg/Ctg	6/10	0.361912599825679	4	FACETS	0.916	0.875	0.956			1	INDETERMINATE	3	TRUE	NA	0.704509369374926	4		327	546	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543586	9543586	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	365	387	1	ENST00000353224.5:c.1568T>A	p.Met523Lys	p.M523K	ENST00000353224	NM_177990.2	523	aTg/aAg	6/10	0.361912599825679	4	FACETS	0.921	0.883	0.959			1	INDETERMINATE	3	TRUE	NA	0.704509369374926	4		388	639	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256753	46256753	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	772	446	0	ENST00000371998.3:c.809G>C	p.Arg270Thr	p.R270T	ENST00000371998		270	aGa/aCa	8/23	NA	2	FACETS	1	0.997	1			1	INDETERMINATE	2	TRUE	NA	0.704509369374926	2		446	982	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129670	11129671	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	195	293	0	ENST00000358026.2:c.2481dup	p.Ser828LeufsTer117	p.S828Lfs*117	ENST00000358026	NM_001128849.1	826	gcc/gCcc	17/36	0.704509369374926	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.704509369374926	1		293	319	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0004985-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	11	440	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.254012433983916	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		440	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0004985-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	15	621	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.188591752178452	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		621	322	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346222	89346222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004985-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	10	362	0	ENST00000301030.4:c.6728C>T	p.Pro2243Leu	p.P2243L	ENST00000301030	NM_001256183.1	2243	cCc/cTc	9/13	0.254012433983916	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		362	127	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0005213-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	216	808	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.225575126314087	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	FALSE	1	0.221777834880224	3		808	1017	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696688	47696688	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519971	NA	P-0005213-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	69	535	0	ENST00000347630.2:c.260A>G	p.Tyr87Cys	p.Y87C	ENST00000347630	NM_001007230.1	87	tAc/tGc	5/11	0.214235483662262	3	FACETS	0.755	0.656	0.863	0.378	0.328	0.432	SUBCLONAL	1	FALSE	1	0.221777834880224	3		535	915	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609314	39609314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766344105	NA	P-0005213-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	81	268	1	ENST00000262039.4:c.1616G>A	p.Arg539His	p.R539H	ENST00000262039	NM_002647.2	539	cGt/cAt	15/25	0.214235483662262	3	FACETS	0.76	0.671	0.855	0.76	0.671	0.855	SUBCLONAL	2	FALSE	1	0.221777834880224	3		269	534	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864390	162864390	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs750884521	NA	P-0005817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	43	364	0	ENST00000366898.1:c.123G>C	p.Leu41Phe	p.L41F	ENST00000366898	NM_004562.2	41	ttG/ttC	2/12	1	2	FACETS	0.189	0.158	0.224	0.189	0.158	0.224	SUBCLONAL	1	TRUE	1	0.874021917594187	2		364	520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0006372-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	47	691	2	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	1	2	FACETS	0.671	0.565	0.79	0.671	0.565	0.79	SUBCLONAL	1	TRUE	1	0.16	2		693	875	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0006372-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	26	624	2	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	0.664	0.526	0.824	0.664	0.526	0.824	SUBCLONAL	1	TRUE	1	0.19	2		626	412	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006372-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	19	341	0	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	1	2	FACETS	0.437	0.33	0.563	0.437	0.33	0.563	SUBCLONAL	1	TRUE	1	0.19	2		341	458	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006372-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	130	948	0	ENST00000397752.3:c.3028G>A	p.Asp1010Asn	p.D1010N	ENST00000397752	NM_000245.2	1010	Gat/Aat	14/21	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.19	2		948	1234	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934630	9934630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006372-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	47	450	0	ENST00000330684.3:c.1525G>A	p.Val509Ile	p.V509I	ENST00000330684	NM_001134407.1	509	Gtt/Att	7/13	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.19	2		450	431	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033823	49033823	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0006372-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	27	354	0	ENST00000267163.4:c.1961-1G>T		p.X654_splice	ENST00000267163	NM_000321.2	654			1	2	FACETS	0.607	0.482	0.751	0.607	0.482	0.751	SUBCLONAL	1	TRUE	1	0.19	2		354	468	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673224	30673224	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006372-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	57	832	0	ENST00000376406.3:c.3736A>T	p.Thr1246Ser	p.T1246S	ENST00000376406	NM_014641.2	1246	Aca/Tca	10/15	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.19	2		832	578	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360504	70360504	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006372-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	59	1269	0	ENST00000374080.3:c.6064C>T	p.Gln2022Ter	p.Q2022*	ENST00000374080		2022	Cag/Tag	42/45	1	2	FACETS	0.662	0.568	0.765	0.662	0.568	0.765	SUBCLONAL	1	TRUE	1	0.19	2		1269	938	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006601-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	152	494	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.522221111714732	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.522221111714732	1		494	388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0006601-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	178	646	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.522221111714732	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.522221111714732	1		646	461	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220116	5220116	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781371580	NA	P-0006601-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	145	666	0	ENST00000357368.4:c.3599G>A	p.Arg1200His	p.R1200H	ENST00000357368	NM_002850.3	1200	cGt/cAt	22/38	0.522221111714732	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.522221111714732	1		666	390	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115457	115115458	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006601-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	131	525	0	ENST00000257566.3:c.868dup	p.Thr290AsnfsTer37	p.T290Nfs*37	ENST00000257566	NM_016569.3	290	acc/aAcc	5/8	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.522221111714732	2		525	474	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720701	89720701	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006601-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	44	188	0	ENST00000371953.3:c.853del	p.Glu285LysfsTer6	p.E285Kfs*6	ENST00000371953	NM_000314.4	284	gaG/ga	8/9	0.522221111714732	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.522221111714732	1		188	105	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943810	71943810	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0006601-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	135	648	0	ENST00000298229.2:c.1851+2T>G		p.X617_splice	ENST00000298229	NM_001567.3	617			0.522221111714732	1	FACETS	0.96	0.881	1	0.96	0.881	1	CLONAL	1	TRUE	0	0.522221111714732	1		648	398	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	88	697	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	0.23	2		697	733	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252394	133252394	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	80	265	0	ENST00000320574.5:c.1033C>T	p.Gln345Ter	p.Q345*	ENST00000320574	NM_006231.2	345	Caa/Taa	11/49	1	2	FACETS	0.85	0.748	0.961	0.85	0.748	0.961	CLONAL	1	TRUE	1	0.23	2		265	818	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0008854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	288	454	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.985	1	1	0.996	1	CLONAL	2	TRUE	1	0.232921048661829	2		454	1093	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577555	7577555	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs375874539	NA	P-0008854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	139	356	0	ENST00000269305.4:c.726C>G	p.Cys242Trp	p.C242W	ENST00000269305	NM_001126112.2	242	tgC/tgG	7/11	0.232921048661829	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.232921048661829	1		356	945	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576214	88576214	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	53	287	0	ENST00000360948.2:c.1459G>C	p.Gly487Arg	p.G487R	ENST00000360948	NM_001012338.2	487	Ggc/Cgc	13/19	1	2	FACETS	0.655	0.557	0.762	0.655	0.557	0.762	SUBCLONAL	1	TRUE	1	0.232921048661829	2		287	695	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259640	16259640	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	85	392	0	ENST00000375759.3:c.6905G>T	p.Arg2302Ile	p.R2302I	ENST00000375759	NM_015001.2	2302	aGa/aTa	11/15	0.232921048661829	1	FACETS	0.663	0.585	0.748	0.663	0.585	0.748	SUBCLONAL	1	TRUE	0	0.232921048661829	1		392	972	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086081	16086081	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	130	385	1	ENST00000281043.3:c.1257G>T	p.Lys419Asn	p.K419N	ENST00000281043	NM_005378.4	419	aaG/aaT	3/3	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.232921048661829	2		386	1042	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871236	35871236	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	205	478	0	ENST00000303115.3:c.458C>A	p.Ser153Ter	p.S153*	ENST00000303115	NM_002185.3	153	tCa/tAa	4/8	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.232921048661829	2		478	1340	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177899	56177899	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	138	425	0	ENST00000399503.3:c.2872A>T	p.Thr958Ser	p.T958S	ENST00000399503	NM_005921.1	958	Aca/Tca	14/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.232921048661829	2		425	1006	SUCCESS
APC	324	MSKCC	GRCh37	5	112175538	112175538	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782112	NA	P-0008854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	42	343	1	ENST00000257430.4:c.4247G>A	p.Gly1416Asp	p.G1416D	ENST00000257430	NM_000038.5	1416	gGc/gAc	16/16	1	2	FACETS	0.537	0.448	0.638	0.537	0.448	0.638	SUBCLONAL	1	TRUE	1	0.232921048661829	2		344	671	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748582	43748582	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1335	136	563	0	ENST00000523873.1:c.536C>G	p.Pro179Arg	p.P179R	ENST00000523873		179	cCt/cGt	6/8	0.232921048661829	1	FACETS	0.701	0.635	0.771	0.701	0.635	0.771	SUBCLONAL	1	TRUE	0	0.232921048661829	1		563	1471	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729267	41729267	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1867	123	621	0	ENST00000242208.4:c.1262A>T	p.Glu421Val	p.E421V	ENST00000242208	NM_002192.2	421	gAg/gTg	3/3	0.232921048661829	5	FACETS	0.716	0.644	0.793	0.239	0.214	0.265	SUBCLONAL	1	TRUE	2	0.232921048661829	5		621	1990	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372500	55372500	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	118	447	0	ENST00000297316.4:c.1190C>A	p.Ser397Ter	p.S397*	ENST00000297316	NM_022454.3	397	tCg/tAg	2/2	1	2	FACETS	0.826	0.743	0.915	0.826	0.743	0.915	CLONAL	1	TRUE	1	0.232921048661829	2		447	1226	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104353818	104353818	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	77	344	0	ENST00000369902.3:c.752T>G	p.Leu251Arg	p.L251R	ENST00000369902	NM_016169.3	251	cTg/cGg	6/12	0.232921048661829	1	FACETS	0.737	0.646	0.835	0.737	0.646	0.835	SUBCLONAL	1	TRUE	0	0.232921048661829	1		344	793	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828905	26828905	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	54	333	0	ENST00000381527.3:c.127G>T	p.Gly43Trp	p.G43W	ENST00000381527	NM_001260.1	43	Ggg/Tgg	1/13	1	2	FACETS	0.598	0.509	0.695	0.598	0.509	0.695	SUBCLONAL	1	TRUE	1	0.232921048661829	2		333	776	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906828	32906828	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	72	519	0	ENST00000380152.3:c.1213G>T	p.Gly405Ter	p.G405*	ENST00000380152		405	Gga/Tga	10/27	1	2	FACETS	0.607	0.529	0.692	0.607	0.529	0.692	SUBCLONAL	1	TRUE	1	0.232921048661829	2		519	1018	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3795339	3795339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1355176917	NA	P-0008854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	91	411	0	ENST00000262367.5:c.3853G>A	p.Glu1285Lys	p.E1285K	ENST00000262367	NM_004380.2	1285	Gag/Aag	22/31	1	2	FACETS	0.795	0.704	0.892	0.795	0.704	0.892	SUBCLONAL	1	TRUE	1	0.232921048661829	2		411	983	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864541	56864541	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs992173424	NA	P-0008854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1344	142	643	0	ENST00000308159.5:c.1029C>G	p.His343Gln	p.H343Q	ENST00000308159	NM_014669.4	343	caC/caG	10/22	1	2	FACETS	0.821	0.745	0.9	0.821	0.745	0.9	CLONAL	1	TRUE	1	0.232921048661829	2		643	1486	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644891	67644891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	106	433	3	ENST00000264010.4:c.156G>T	p.Gln52His	p.Q52H	ENST00000264010	NM_006565.3	52	caG/caT	3/12	1	2	FACETS	0.922	0.825	1	0.922	0.825	1	CLONAL	1	TRUE	1	0.232921048661829	2		436	987	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993572	72993572	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	123	563	0	ENST00000268489.5:c.473G>T	p.Gly158Val	p.G158V	ENST00000268489	NM_006885.3	158	gGg/gTg	2/10	1	2	FACETS	0.844	0.761	0.932	0.844	0.761	0.932	CLONAL	1	TRUE	1	0.232921048661829	2		563	1251	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245841	5245841	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	95	433	1	ENST00000357368.4:c.934G>T	p.Val312Leu	p.V312L	ENST00000357368	NM_002850.3	312	Gtg/Ttg	10/38	0.232921048661829	1	FACETS	0.658	0.584	0.737	0.658	0.584	0.737	SUBCLONAL	1	TRUE	0	0.232921048661829	1		434	1096	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413151	63413151	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	63	269	0	ENST00000330258.3:c.16G>C	p.Asp6His	p.D6H	ENST00000330258	NM_152424.3	6	Gat/Cat	2/2	0.188510197574355	0	FACETS	0.596	0.515	0.685			1	SUBCLONAL	1	TRUE	0	0.232921048661829	0		269	696	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231723	66231723	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	88	493	0	ENST00000273854.3:c.1977del	p.Asn660IlefsTer11	p.N660Ifs*11	ENST00000273854	NM_004439.5	659	ccC/cc	11/18	1	2	FACETS	0.781	0.69	0.878	0.781	0.69	0.878	SUBCLONAL	1	TRUE	1	0.232921048661829	2		493	968	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133812	55133816	+	missense_variant	Missense_Mutation	ONP	ACCCA	ACCCA	GCCCT	novel	NA	P-0008854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	76	467	0	ENST00000257290.5:c.1025_1029delinsGCCCT	p.Tyr342Cys	p.Y342C	ENST00000257290	NM_006206.4	342	tACCCA/tGCCCT	7/23	1	2	FACETS	0.688	0.602	0.781	0.688	0.602	0.781	SUBCLONAL	1	TRUE	1	0.232921048661829	2		467	949	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0008913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	66	647	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.3	1	FACETS	0.71	0.617	0.81	0.71	0.617	0.81	SUBCLONAL	1	TRUE	0	0.3	1		647	527	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0008913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	60	333	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.20129036760859	2	FACETS	0.758	0.659	0.862	0.758	0.659	0.862	SUBCLONAL	2	TRUE	0	0.3	2		333	264	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048812	180048812	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	86	787	0	ENST00000261937.6:c.1750A>G	p.Lys584Glu	p.K584E	ENST00000261937	NM_182925.4	584	Aag/Gag	13/30	0.20129036760859	2	FACETS	0.867	0.768	0.974	0.434	0.384	0.487	CLONAL	1	TRUE	0	0.3	2		787	661	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200338	138200338	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753284576	NA	P-0008913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	27	380	0	ENST00000237289.4:c.1756G>A	p.Ala586Thr	p.A586T	ENST00000237289	NM_001270507.1	586	Gcc/Acc	7/9	0.251218402102325	2	FACETS	0.432	0.343	0.533	0.216	0.171	0.267	SUBCLONAL	1	TRUE	0	0.3	2		380	417	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359433	118359433	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	21	365	0	ENST00000534358.1:c.4437C>A	p.Cys1479Ter	p.C1479*	ENST00000534358	NM_005933.3	1479	tgC/tgA	11/36	0.251218402102325	2	FACETS	0.353	0.271	0.448	0.176	0.135	0.224	SUBCLONAL	1	TRUE	0	0.3	2		365	397	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877357	40877357	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	32	401	0	ENST00000373198.4:c.2339T>C	p.Leu780Pro	p.L780P	ENST00000373198	NM_133170.3	780	cTc/cCc	15/32	0.187443287953409	3	FACETS	0.523	0.424	0.635	0.262	0.212	0.318	SUBCLONAL	1	TRUE	1	0.3	3		401	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	10	808	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.911814542572312	1	FACETS	0.03	0.02	0.043	0.03	0.02	0.043	SUBCLONAL	1	TRUE	0	0.911814542572312	1		808	396	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101402	27101402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	107	501	3	ENST00000324856.7:c.4689del	p.Met1564Ter	p.M1564*	ENST00000324856	NM_006015.4	1562	Ccc/cc	18/20	1	2	FACETS	0.472	0.425	0.521	0.472	0.425	0.521	SUBCLONAL	1	TRUE	1	0.911814542572312	2		504	497	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268766	41268766	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	258	590	0	ENST00000349496.5:c.1004A>T	p.Lys335Ile	p.K335I	ENST00000349496	NM_001904.3	335	aAa/aTa	7/15	NA	2	FACETS	0.979	0.925	1			1	INDETERMINATE	1	TRUE	NA	0.911814542572312	2		590	578	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11273503	11273503	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751901845	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	190	586	2	ENST00000361445.4:c.3238C>T	p.Arg1080Cys	p.R1080C	ENST00000361445	NM_004958.3	1080	Cgt/Tgt	21/58	1	2	FACETS	0.662	0.614	0.71	0.662	0.614	0.71	SUBCLONAL	1	TRUE	1	0.911814542572312	2		588	630	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439637	51439637	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs781400938	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	271	438	0	ENST00000262662.1:c.202C>T	p.Arg68Ter	p.R68*	ENST00000262662		68	Cga/Tga	4/4	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.911814542572312	2		438	570	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	275	560	1	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	0.86	0.813	0.909	0.86	0.813	0.909	CLONAL	1	TRUE	1	0.911814542572312	2		561	701	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687472	37687472	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	49	326	2	ENST00000447079.4:c.4382del	p.Gly1461AlafsTer38	p.G1461Afs*38	ENST00000447079	NM_015083.1	1459	tGg/tg	14/14	1	2	FACETS	0.297	0.252	0.346	0.297	0.252	0.346	SUBCLONAL	1	TRUE	1	0.911814542572312	2		328	362	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870921	12870922	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	169	327	0	ENST00000228872.4:c.151_152del	p.Asp51HisfsTer73	p.D51Hfs*73	ENST00000228872	NM_004064.3	50	AGa/a	1/3	0.552831977508713	3	FACETS	1	0.973	1	0.552	0.511	0.593	CLONAL	1	TRUE	1	0.911814542572312	3		327	489	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781375	3781375	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	203	681	0	ENST00000262367.5:c.4990C>T	p.Arg1664Cys	p.R1664C	ENST00000262367	NM_004380.2	1664	Cgc/Tgc	30/31	1	2	FACETS	0.649	0.604	0.695	0.649	0.604	0.695	SUBCLONAL	1	TRUE	1	0.911814542572312	2		681	686	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511667	38511667	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773956341	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	68	557	1	ENST00000254066.5:c.1165G>A	p.Ala389Thr	p.A389T	ENST00000254066	NM_000964.3	389	Gcc/Acc	8/9	0.385228656681808	1	FACETS	0.174	0.152	0.198	0.174	0.152	0.198	INDETERMINATE	1	TRUE	0	0.911814542572312	1		558	466	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	291	710	1	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	0.385228656681808	1	FACETS	0.545	0.517	0.573	0.545	0.517	0.573	INDETERMINATE	1	TRUE	0	0.911814542572312	1		711	637	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939260	71939260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	270	697	3	ENST00000298229.2:c.209G>A	p.Arg70His	p.R70H	ENST00000298229	NM_001567.3	70	cGc/cAc	2/28	1	2	FACETS	0.915	0.865	0.966	0.915	0.865	0.966	CLONAL	1	TRUE	1	0.911814542572312	2		700	647	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	300	819	3	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	0.552831977508713	3	FACETS	1	0.963	1	0.513	0.484	0.542	CLONAL	1	TRUE	1	0.911814542572312	3		822	934	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670340	134670340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415689583	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	26	457	0	ENST00000398015.3:c.251G>A	p.Arg84His	p.R84H	ENST00000398015	NM_004441.4	84	cGc/cAc	3/16	1	2	FACETS	0.142	0.112	0.176	0.142	0.112	0.176	SUBCLONAL	1	TRUE	1	0.911814542572312	2		457	403	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258614	16258614	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867058967	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	238	476	2	ENST00000375759.3:c.5879C>T	p.Ala1960Val	p.A1960V	ENST00000375759	NM_015001.2	1960	gCc/gTc	11/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.911814542572312	2		478	492	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263881	16263881	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	320	781	0	ENST00000375759.3:c.10250C>A	p.Thr3417Asn	p.T3417N	ENST00000375759	NM_015001.2	3417	aCc/aAc	12/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.911814542572312	2		781	683	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578195	226578195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202057244	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	71	524	0	ENST00000366794.5:c.533C>T	p.Ala178Val	p.A178V	ENST00000366794	NM_001618.3	178	gCg/gTg	4/23	1	2	FACETS	0.277	0.241	0.315	0.277	0.241	0.315	SUBCLONAL	1	TRUE	1	0.911814542572312	2		524	563	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600579	43600579	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	255	559	0	ENST00000355710.3:c.805G>A	p.Ala269Thr	p.A269T	ENST00000355710	NM_020975.4	269	Gcg/Acg	4/20	0.911814542572312	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.911814542572312	1		559	276	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343148	118343148	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	216	440	0	ENST00000534358.1:c.1274C>A	p.Pro425His	p.P425H	ENST00000534358	NM_005933.3	425	cCt/cAt	3/36	1	2	FACETS	0.929	0.872	0.986	0.929	0.872	0.986	CLONAL	1	TRUE	1	0.911814542572312	2		440	510	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344076	118344076	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	204	404	0	ENST00000534358.1:c.2206del	p.Arg736GlyfsTer20	p.R736Gfs*20	ENST00000534358	NM_005933.3	734	agA/ag	3/36	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.911814542572312	2		404	410	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372411	118372411	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	282	617	0	ENST00000534358.1:c.6344A>G	p.Asn2115Ser	p.N2115S	ENST00000534358	NM_005933.3	2115	aAc/aGc	26/36	1	2	FACETS	0.934	0.884	0.985	0.934	0.884	0.985	CLONAL	1	TRUE	1	0.911814542572312	2		617	662	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	463300	463300	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	430	650	0	ENST00000399788.2:c.971T>G	p.Ile324Ser	p.I324S	ENST00000399788	NM_001042603.1	324	aTt/aGt	8/28	0.552831977508713	3	FACETS	0.899	0.864	0.933	0.899	0.864	0.933	CLONAL	2	TRUE	1	0.911814542572312	3		650	764	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937093	48937093	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	131	253	0	ENST00000267163.4:c.861G>T	p.Glu287Asp	p.E287D	ENST00000267163	NM_000321.2	287	gaG/gaT	8/27	0.911814542572312	1	FACETS	0.989	0.945	1	0.989	0.945	1	CLONAL	1	TRUE	0	0.911814542572312	1		253	158	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434638	110434638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	43	756	0	ENST00000375856.3:c.3763G>A	p.Ala1255Thr	p.A1255T	ENST00000375856	NM_003749.2	1255	Gcc/Acc	1/2	1	2	FACETS	0.13	0.108	0.154	0.13	0.108	0.154	SUBCLONAL	1	TRUE	1	0.911814542572312	2		756	726	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720287	43720287	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151132652	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	378	659	3	ENST00000382044.4:c.3755G>A	p.Arg1252His	p.R1252H	ENST00000382044	NM_001141980.1	1252	cGc/cAc	18/28	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.911814542572312	2		662	717	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656606	3656606	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	369	830	1	ENST00000294008.3:c.629T>A	p.Leu210Gln	p.L210Q	ENST00000294008	NM_032444.2	210	cTa/cAa	3/15	1	2	FACETS	0.982	0.937	1	0.982	0.937	1	CLONAL	1	TRUE	1	0.911814542572312	2		831	824	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843467	3843467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	287	563	0	ENST00000262367.5:c.1136C>T	p.Ala379Val	p.A379V	ENST00000262367	NM_004380.2	379	gCc/gTc	4/31	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.911814542572312	2		563	613	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830370	72830370	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1266748072	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	111	358	0	ENST00000268489.5:c.6211A>C	p.Ile2071Leu	p.I2071L	ENST00000268489	NM_006885.3	2071	Atc/Ctc	9/10	1	2	FACETS	0.876	0.8	0.953	0.876	0.8	0.953	CLONAL	1	TRUE	1	0.911814542572312	2		358	278	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347528	89347528	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	264	610	0	ENST00000301030.4:c.5422A>C	p.Lys1808Gln	p.K1808Q	ENST00000301030	NM_001256183.1	1808	Aag/Cag	9/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.911814542572312	2		610	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578226	7578226	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1464727668	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	351	735	0	ENST00000269305.4:c.623A>G	p.Asp208Gly	p.D208G	ENST00000269305	NM_001126112.2	208	gAc/gGc	6/11	0.911814542572312	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.911814542572312	1		735	389	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122397	17122398	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	rs1555608515	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	277	675	1	ENST00000285071.4:c.997_998del	p.Ser333ArgfsTer56	p.S333Rfs*56	ENST00000285071	NM_144997.5	333	TCa/a	9/14	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.911814542572312	2		676	592	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302406	15302406	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	335	779	1	ENST00000263388.2:c.865G>T	p.Gly289Cys	p.G289C	ENST00000263388	NM_000435.2	289	Ggt/Tgt	6/33	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.911814542572312	2		780	709	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607774	46607774	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	346	757	0	ENST00000263734.3:c.1966del	p.Asp656IlefsTer40	p.D656Ifs*40	ENST00000263734	NM_001430.4	655	Ggg/gg	12/16	1	2	FACETS	0.996	0.949	1	0.996	0.949	1	CLONAL	1	TRUE	1	0.911814542572312	2		757	762	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025882	48025882	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	206	397	0	ENST00000234420.5:c.760T>G	p.Ser254Ala	p.S254A	ENST00000234420	NM_000179.2	254	Tct/Gct	4/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.911814542572312	2		397	426	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437218	220437218	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	396	846	0	ENST00000243786.2:c.122T>C	p.Leu41Ser	p.L41S	ENST00000243786	NM_002191.3	41	tTg/tCg	1/2	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.911814542572312	2		846	837	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388073	31388073	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	352	413	0	ENST00000328111.2:c.1874T>C	p.Val625Ala	p.V625A	ENST00000328111	NM_006892.3	625	gTg/gCg	17/23	0.911814542572312	3	FACETS	0.935	0.897	0.973	0.935	0.897	0.973	CLONAL	2	TRUE	1	0.911814542572312	3		413	601	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72864526	72864526	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	272	504	0	ENST00000325599.8:c.911T>C	p.Leu304Pro	p.L304P	ENST00000325599	NM_018130.2	304	cTg/cCg	8/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.911814542572312	2		504	544	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188343	142188343	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	256	594	0	ENST00000350721.4:c.6388A>G	p.Thr2130Ala	p.T2130A	ENST00000350721	NM_001184.3	2130	Aca/Gca	38/47	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.911814542572312	2		594	561	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679218	30679218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761034847	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	97	637	0	ENST00000376406.3:c.2192G>A	p.Gly731Asp	p.G731D	ENST00000376406	NM_014641.2	731	gGc/gAc	7/15	1	2	FACETS	0.303	0.27	0.338	0.303	0.27	0.338	SUBCLONAL	1	TRUE	1	0.911814542572312	2		637	703	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752942	128752942	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	168	396	0	ENST00000377970.2:c.1103A>T	p.Asn368Ile	p.N368I	ENST00000377970	NM_002467.4	368	aAt/aTt	3/3	1	2	FACETS	0.94	0.875	1	0.94	0.875	1	CLONAL	1	TRUE	1	0.911814542572312	2		396	392	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760600	133760600	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs934451374	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	49	860	0	ENST00000318560.5:c.2923C>A	p.Pro975Thr	p.P975T	ENST00000318560	NM_005157.4	975	Ccc/Acc	11/11	1	2	FACETS	0.142	0.119	0.167	0.142	0.119	0.167	SUBCLONAL	1	TRUE	1	0.911814542572312	2		860	758	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247486	53247486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782276964	NA	P-0009006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	43	360	0	ENST00000375401.3:c.323G>A	p.Arg108Gln	p.R108Q	ENST00000375401	NM_004187.3	108	cGg/cAg	3/26	1	1	FACETS	0.162	0.136	0.191	0.162	0.136	0.191	SUBCLONAL	1	TRUE	0	0.911814542572312	1		360	316	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0009333-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	427	454	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.639048133529611	4	FACETS	0.962	0.925	0.999	0.962	0.925	0.999	CLONAL	3	TRUE	1	0.639048133529611	4		454	759	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009333-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	325	494	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.639048133529611	3	FACETS	1	0.977	1			1	CLONAL	2	TRUE	NA	0.639048133529611	3		494	646	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69998291	69998291	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009333-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	107	477	0	ENST00000394351.3:c.531C>A	p.Asn177Lys	p.N177K	ENST00000394351	NM_000248.3	177	aaC/aaA	5/9	0.211667610825524	3	FACETS	1	0.969	1	0.584	0.529	0.642	INDETERMINATE	1	TRUE	1	0.639048133529611	3		477	378	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222572	69222572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009333-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2094	236	464	0	ENST00000462284.1:c.545C>T	p.Ser182Phe	p.S182F	ENST00000462284	NM_002392.5	182	tCt/tTt	8/11	0.639048133529611	14	FACETS	0.766	0.711	0.824			1	SUBCLONAL	2	TRUE	NA	0.639048133529611	14		464	2330	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222704	69222704	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009333-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2439	234	507	0	ENST00000462284.1:c.677C>G	p.Ser226Trp	p.S226W	ENST00000462284	NM_002392.5	226	tCg/tGg	8/11	0.639048133529611	14	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.639048133529611	14		507	2673	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404570	8404570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009333-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	73	323	0	ENST00000356435.5:c.4177G>A	p.Asp1393Asn	p.D1393N	ENST00000356435		1393	Gat/Aat	25/35	0.199120415083624	1	FACETS	0.614	0.544	0.688	0.614	0.544	0.688	INDETERMINATE	1	TRUE	0	0.639048133529611	1		323	253	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010654-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	78	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.826081817077441	2		248	187	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380254	25380254	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010654-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	346	642	0	ENST00000311936.3:c.204G>C	p.Arg68Ser	p.R68S	ENST00000311936	NM_004985.3	68	agG/agC	3/5	1	2	FACETS	0.95	0.903	0.997	0.95	0.903	0.997	CLONAL	1	TRUE	1	0.826081817077441	2		642	882	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309887	65309887	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1304838920	NA	P-0010654-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	209	432	0	ENST00000342505.4:c.2263C>T	p.Arg755Ter	p.R755*	ENST00000342505	NM_002227.2	755	Cga/Tga	17/25	0.826081817077441	1	FACETS	0.955	0.909	0.999	0.955	0.909	0.999	CLONAL	1	TRUE	0	0.826081817077441	1		432	311	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931847	39931848	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTAA	novel	NA	P-0010654-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	290	302	0	ENST00000378444.4:c.2751_2752insTTAC	p.Gln918LeufsTer29	p.Q918Lfs*29	ENST00000378444	NM_001123385.1	917	-/TTAC	4/15	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.826081817077441	1		302	364	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524645	103524645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010654-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	171	359	0	ENST00000355739.4:c.2776G>T	p.Gly926Cys	p.G926C	ENST00000355739	NM_000123.3	926	Ggc/Tgc	13/15	1	2	FACETS	0.729	0.674	0.785	0.729	0.674	0.785	SUBCLONAL	1	TRUE	1	0.826081817077441	2		359	568	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027517	48027517	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	183	347	0	ENST00000234420.5:c.2395A>T	p.Met799Leu	p.M799L	ENST00000234420	NM_000179.2	799	Atg/Ttg	4/10	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.79250334349642	2		347	448	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863033	56863033	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1184	250	482	1	ENST00000519728.1:c.300G>T	p.Trp100Cys	p.W100C	ENST00000519728	NM_002350.3	100	tgG/tgT	5/13	0.79250334349642	5	FACETS	0.963	0.898	1	0.241	0.224	0.258	CLONAL	1	TRUE	1	0.79250334349642	5		483	1434	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561764	55561764	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913505	NA	P-0011037-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	241	613	0	ENST00000288135.5:c.154G>A	p.Asp52Asn	p.D52N	ENST00000288135	NM_000222.2	52	Gac/Aac	2/21	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.594716866754339	2		613	636	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638326	117638326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752085591	NA	P-0011037-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	119	723	1	ENST00000368508.3:c.6115C>T	p.Arg2039Cys	p.R2039C	ENST00000368508	NM_002944.2	2039	Cgt/Tgt	38/43	NA	2	FACETS	0.67	0.607	0.737			1	INDETERMINATE	1	TRUE	NA	0.594716866754339	2		724	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579374	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0011037-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	23	1035	2	ENST00000269305.4:c.313_314delinsTT	p.Gly105Phe	p.G105F	ENST00000269305	NM_001126112.2	105	GGc/TTc	4/11	1	2	FACETS	0.075	0.058	0.096	0.075	0.058	0.096	SUBCLONAL	1	TRUE	1	0.594716866754339	2		1037	1027	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107008	27107008	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	47	342	0	ENST00000324856.7:c.6619C>T	p.Gln2207Ter	p.Q2207*	ENST00000324856	NM_006015.4	2207	Cag/Tag	20/20	0.512155804713418	3	FACETS	0.844	0.718	0.982	0.422	0.359	0.491	CLONAL	1	TRUE	1	0.512155804713418	3		342	273	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856469	111856469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	16	98	1	ENST00000341259.2:c.520G>A	p.Ala174Thr	p.A174T	ENST00000341259	NM_005475.2	174	Gcc/Acc	2/8	0.442954700986764	5	FACETS	0.898	0.671	1			1	CLONAL	1	TRUE	NA	0.512155804713418	5		99	123	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256885	41256885	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	123	371	0	ENST00000357654.3:c.301T>A	p.Tyr101Asn	p.Y101N	ENST00000357654	NM_007294.3	101	Tat/Aat	5/23	0.294716579339569	6	FACETS	1	0.976	1	0.603	0.55	0.658	INDETERMINATE	2	TRUE	2	0.512155804713418	6		371	403	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180504	56180505	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0011042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	81	199	0	ENST00000399503.3:c.3836dup	p.Asn1279LysfsTer5	p.N1279Kfs*5	ENST00000399503	NM_005921.1	1278	aga/agAa	16/20	0.512155804713418	6	FACETS	0.988	0.887	1	0.741	0.665	0.819	CLONAL	3	TRUE	2	0.512155804713418	6		199	216	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168691	56168692	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0011042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	124	268	1	ENST00000399503.3:c.1546dup	p.Arg516LysfsTer25	p.R516Kfs*25	ENST00000399503	NM_005921.1	515	-/A	9/20	0.512155804713418	6	FACETS	1	0.972	1	0.581	0.53	0.634	CLONAL	2	TRUE	2	0.512155804713418	6		269	422	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419921	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0011042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	119	411	1	ENST00000206249.3:c.1607_1608delinsAT	p.Leu536His	p.L536H	ENST00000206249	NM_000125.3	536	cTC/cAT	8/8	0.367282185292955	2	FACETS	0.926	0.853	0.999	0.926	0.853	0.999	CLONAL	2	TRUE	0	0.512155804713418	2		412	251	SUCCESS
APC	324	MSKCC	GRCh37	5	112175621	112175621	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011100-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	170	283	0	ENST00000257430.4:c.4330C>T	p.Gln1444Ter	p.Q1444*	ENST00000257430	NM_000038.5	1444	Caa/Taa	16/16	0.787931111439938	1	FACETS	0.987	0.932	1	0.987	0.932	1	CLONAL	1	TRUE	0	0.787931111439938	1		283	265	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562746	29562746	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs199474742	NA	P-0011100-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	255	405	1	ENST00000356175.3:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000356175	NM_000267.3	1276	Cga/Tga	28/57	0.760586436094921	1	FACETS	0.976	0.931	1	0.976	0.931	1	CLONAL	1	TRUE	0	0.787931111439938	1		406	402	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242481	+	inframe_deletion	In_Frame_Del	DEL	AATTAAGAGAAGCAA	AATTAAGAGAAGCAA	-	rs121913425	NA	P-0011100-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	155	365	0	ENST00000275493.2:c.2237_2251del	p.Glu746_Thr751delinsAla	p.E746_T751delinsA	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAAca/gca	19/28	1	2	FACETS	0.846	0.781	0.913	0.846	0.781	0.913	CLONAL	1	TRUE	1	0.787931111439938	2		365	465	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070839	30070840	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0011100-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	227	339	0	ENST00000338641.4:c.1355_1356del	p.Asp452AlafsTer42	p.D452Afs*42	ENST00000338641	NM_000268.3	452	gAT/g	13/16	0.764544645173985	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.787931111439938	1		339	328	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0011125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	412	454	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.637588754693888	2	FACETS	0.962	0.927	0.997	0.962	0.927	0.997	CLONAL	2	TRUE	0	0.648775296764199	2		454	660	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190742131	190742131	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	366	198	0	ENST00000441310.2:c.2768A>G	p.His923Arg	p.H923R	ENST00000441310	NM_000534.4	923	cAt/cGt	13/13	0.637588754693888	2	FACETS	0.932	0.896	0.969	0.932	0.896	0.969	CLONAL	2	TRUE	0	0.648775296764199	2		198	605	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215617274	215617274	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	345	202	0	ENST00000260947.4:c.1574T>G	p.Ile525Arg	p.I525R	ENST00000260947	NM_000465.2	525	aTa/aGa	7/11	0.637588754693888	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.648775296764199	2		202	510	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662124	227662124	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	475	325	0	ENST00000305123.5:c.1331G>T	p.Ser444Ile	p.S444I	ENST00000305123	NM_005544.2	444	aGt/aTt	1/2	0.637588754693888	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.648775296764199	2		325	728	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176683978	176683978	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	1317	527	0	ENST00000439151.2:c.4792C>T	p.Gln1598Ter	p.Q1598*	ENST00000439151	NM_022455.4	1598	Cag/Tag	13/23	0.632392103404839	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.648775296764199	3		527	1785	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508049	106508049	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	211	176	0	ENST00000359195.3:c.43G>T	p.Asp15Tyr	p.D15Y	ENST00000359195	NM_002649.2	15	Gac/Tac	2/11	0.624151944754327	3	FACETS	0.947	0.89	1	0.947	0.89	1	CLONAL	2	TRUE	1	0.648775296764199	3		176	455	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864360	57864360	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	1039	627	0	ENST00000228682.2:c.1837G>T	p.Gly613Cys	p.G613C	ENST00000228682	NM_005269.2	613	Ggt/Tgt	12/12	0.632392103404839	3	FACETS	0.955	0.935	0.974	0.955	0.935	0.974	CLONAL	3	TRUE	0	0.648775296764199	3		627	1481	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726665	88726665	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	228	324	1	ENST00000360948.2:c.379C>A	p.Pro127Thr	p.P127T	ENST00000360948	NM_001012338.2	127	Ccc/Acc	4/19	1	2	FACETS	0.978	0.915	1	0.978	0.915	1	CLONAL	1	TRUE	1	0.648775296764199	2		325	719	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692990	89692990	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0011125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	391	180	0	ENST00000371953.3:c.475del	p.Arg159GlyfsTer8	p.R159Gfs*8	ENST00000371953	NM_000314.4	158	gtA/gt	5/9	0.638078443286989	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.648775296764199	2		180	560	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021480	42021480	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	553	610	0	ENST00000219905.7:c.3779del	p.Pro1260HisfsTer31	p.P1260Hfs*31	ENST00000219905	NM_001164273.1	1259	tCc/tc	11/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.648775296764199	2		610	1616	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371708	225371708	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	303	644	0	ENST00000264414.4:c.896T>G	p.Met299Arg	p.M299R	ENST00000264414	NM_003590.4	299	aTg/aGg	7/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.650468686091568	2		644	866	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0012286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	187	351	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.650468686091568	2		351	537	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059189	27059189	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	128	485	1	ENST00000324856.7:c.1826G>A	p.Gly609Glu	p.G609E	ENST00000324856	NM_006015.4	609	gGg/gAg	4/20	1	2	FACETS	0.605	0.549	0.663	0.605	0.549	0.663	SUBCLONAL	1	TRUE	1	0.650468686091568	2		486	651	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939391	71939391	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0012286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	313	682	0	ENST00000298229.2:c.247-1G>A		p.X83_splice	ENST00000298229	NM_001567.3	83			1	2	FACETS	0.923	0.871	0.975	0.923	0.871	0.975	CLONAL	1	TRUE	1	0.650468686091568	2		682	1043	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060637	38060637	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	438	884	1	ENST00000250448.2:c.1352A>G	p.Glu451Gly	p.E451G	ENST00000250448	NM_004496.3	451	gAg/gGg	2/2	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.650468686091568	2		885	1284	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0012555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	99	653	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.3	2	FACETS	0.763	0.681	0.849			1	SUBCLONAL	2	TRUE	NA	0.19	2		653	683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0013445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	270	446	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.899479495589535	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.908286145996388	1		446	314	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463592	25463592	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	251	580	1	ENST00000264709.3:c.2090A>T	p.Glu697Val	p.E697V	ENST00000264709	NM_175629.2	697	gAg/gTg	18/23	1	2	FACETS	0.862	0.812	0.913	0.862	0.812	0.913	CLONAL	1	TRUE	1	0.908286145996388	2		581	641	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100451	8100451	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	109	680	0	ENST00000346208.3:c.425C>A	p.Ser142Ter	p.S142*	ENST00000346208		142	tCg/tAg	3/6	0.101890710777146	4	FACETS	0.463	0.414	0.514	0.231	0.207	0.257	INDETERMINATE	1	TRUE	2	0.908286145996388	4		680	990	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173634	108173634	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555106405	NA	P-0013445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	38	295	0	ENST00000278616.4:c.5374A>G	p.Ile1792Val	p.I1792V	ENST00000278616	NM_000051.3	1792	Ata/Gta	36/63	0.796401142565994	3	FACETS	0.247	0.204	0.295	0.123	0.102	0.148	SUBCLONAL	1	TRUE	1	0.908286145996388	3		295	493	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659982	227659984	+	inframe_deletion	In_Frame_Del	DEL	CCC	CCC	-	novel	NA	P-0013445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	262	620	0	ENST00000305123.5:c.3471_3473del	p.Gly1158del	p.G1158del	ENST00000305123	NM_005544.2	1157	ggGGGa/gga	1/2	0.150978856371117	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.908286145996388	0		620	624	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938683	76938683	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	255	679	0	ENST00000373344.5:c.2065del	p.Gln689LysfsTer7	p.Q689Kfs*7	ENST00000373344	NM_000489.3	689	Caa/aa	9/35	0.182468683386856	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.908286145996388	0		679	632	SUCCESS
AR	367	MSKCC	GRCh37	X	66765080	66765081	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0013445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	354	712	0	ENST00000374690.3:c.92_93delinsTT	p.Arg31Leu	p.R31L	ENST00000374690	NM_000044.3	31	cGC/cTT	1/8	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.908286145996388	2		712	747	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	45	440	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.11	2		440	802	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176338	24176338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	43	843	1	ENST00000263121.7:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000263121	NM_003073.3	377	Cgt/Tgt	9/9	1	2	FACETS	0.761	0.634	0.903	0.761	0.634	0.903	CLONAL	1	TRUE	1	0.11	2		844	1027	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998898	11998898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	11	323	1	ENST00000353533.5:c.400C>T	p.Arg134Trp	p.R134W	ENST00000353533	NM_003010.3	134	Cgg/Tgg	4/11	1	2	FACETS	0.414	0.284	0.577	0.414	0.284	0.577	SUBCLONAL	1	TRUE	1	0.11	2		324	483	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442854	187442854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867576130	NA	P-0013721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	19	478	0	ENST00000232014.4:c.1852C>T	p.Arg618Cys	p.R618C	ENST00000232014	NM_001130845.1	618	Cgt/Tgt	9/10	1	2	FACETS	0.563	0.425	0.726	0.563	0.425	0.726	SUBCLONAL	1	TRUE	1	0.11	2		478	614	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575127	48575127	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	61	486	0	ENST00000342988.3:c.321del	p.Asn107LysfsTer3	p.N107Kfs*3	ENST00000342988	NM_005359.5	107	aaT/aa	3/12	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.11	2		486	820	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020748	112020748	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	33	456	0	ENST00000368678.4:c.823G>A	p.Gly275Ser	p.G275S	ENST00000368678		275	Ggt/Agt	8/13	1	2	FACETS	0.915	0.743	1	0.915	0.743	1	CLONAL	1	TRUE	1	0.11	2		456	656	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18762498	18762498	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013756-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	253	572	0	ENST00000266497.5:c.3994G>T	p.Val1332Leu	p.V1332L	ENST00000266497		1332	Gtg/Ttg	29/31	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.622239904548567	2		572	804	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155821	106155821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771996203	NA	P-0013756-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	217	482	2	ENST00000380013.4:c.722C>T	p.Ala241Val	p.A241V	ENST00000380013	NM_001127208.2	241	gCg/gTg	3/11	1	2	FACETS	0.955	0.892	1	0.955	0.892	1	CLONAL	1	TRUE	1	0.622239904548567	2		484	730	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123246880	123246880	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013756-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	219	646	0	ENST00000358487.5:c.2045A>T	p.His682Leu	p.H682L	ENST00000358487	NM_000141.4	682	cAt/cTt	15/18	1	2	FACETS	0.738	0.687	0.791	0.738	0.687	0.791	SUBCLONAL	1	TRUE	1	0.622239904548567	2		646	954	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274102	10274102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	399	622	0	ENST00000330684.3:c.167G>A	p.Gly56Asp	p.G56D	ENST00000330684	NM_001134407.1	56	gGc/gAc	2/13	0.412374189853771	5	FACETS	0.953	0.908	0.999	0.953	0.908	0.999	CLONAL	3	TRUE	2	0.412374189853771	5		622	1095	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173754	108173754	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	112	312	0	ENST00000278616.4:c.5494G>T	p.Glu1832Ter	p.E1832*	ENST00000278616	NM_000051.3	1832	Gaa/Taa	36/63	0.412374189853771	2	FACETS	0.927	0.846	1	0.927	0.846	1	CLONAL	2	TRUE	0	0.412374189853771	2		312	293	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518267	187518267	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	170	348	0	ENST00000441802.2:c.12427G>T	p.Glu4143Ter	p.E4143*	ENST00000441802	NM_005245.3	4143	Gag/Tag	25/27	0.406329670455517	4	FACETS	0.962	0.889	1	0.962	0.889	1	CLONAL	2	TRUE	2	0.412374189853771	4		348	605	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584593	52584593	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1361004473	NA	P-0014304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	145	636	0	ENST00000394830.3:c.4420G>A	p.Ala1474Thr	p.A1474T	ENST00000394830	NM_018313.4	1474	Gct/Act	29/30	0.406329670455517	4	FACETS	1	0.918	1	0.504	0.459	0.551	CLONAL	1	TRUE	2	0.412374189853771	4		636	986	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476265	88476265	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014872-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	119	341	1	ENST00000360948.2:c.1867G>A	p.Gly623Arg	p.G623R	ENST00000360948	NM_001012338.2	623	Gga/Aga	15/19	0.362149433348217	3	FACETS	0.76	0.685	0.84	0.38	0.342	0.42	SUBCLONAL	1	TRUE	1	0.362149433348217	3		342	1021	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0015097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	482	482	1	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.78246057916062	3	FACETS	0.982	0.959	1	0.982	0.959	1	CLONAL	3	TRUE	0	0.78246057916062	3		483	582	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0015097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	312	264	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.78246057916062	3	FACETS	0.973	0.944	1	0.973	0.944	1	CLONAL	3	TRUE	0	0.78246057916062	3		264	380	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	198	487	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.78246057916062	5	FACETS	0.989	0.915	1	0.33	0.305	0.356	CLONAL	1	TRUE	2	0.78246057916062	5		487	1112	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748596	40748596	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754546663	NA	P-0015097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	110	379	0	ENST00000373198.4:c.2920C>T	p.Arg974Trp	p.R974W	ENST00000373198	NM_133170.3	974	Cgg/Tgg	21/32	0.770293664538778	3	FACETS	0.887	0.802	0.976	0.443	0.401	0.488	CLONAL	1	TRUE	1	0.78246057916062	3		379	441	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167801	56167802	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	207	433	0	ENST00000399503.3:c.1368dup	p.Thr457TyrfsTer4	p.T457Yfs*4	ENST00000399503	NM_005921.1	456	ctt/cTtt	7/20	0.770293664538778	3	FACETS	0.975	0.908	1	0.487	0.453	0.522	CLONAL	1	TRUE	1	0.78246057916062	3		433	755	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645920	67645920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567609067	NA	P-0015097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	312	497	0	ENST00000264010.4:c.848G>A	p.Arg283His	p.R283H	ENST00000264010	NM_006565.3	283	cGt/cAt	4/12	0.761833347806227	2	FACETS	0.915	0.881	0.947	0.915	0.881	0.947	CLONAL	2	TRUE	0	0.78246057916062	2		497	436	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939859	49939859	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766244325	NA	P-0015097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	729	756	1	ENST00000296474.3:c.1184G>A	p.Arg395Gln	p.R395Q	ENST00000296474	NM_002447.2	395	cGg/cAg	1/20	0.78246057916062	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.78246057916062	3		757	841	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168654	56168655	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0015097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	280	368	0	ENST00000399503.3:c.1509dup	p.Glu504ArgfsTer37	p.E504Rfs*37	ENST00000399503	NM_005921.1	503	cac/caCc	9/20	0.770293664538778	3	FACETS	0.915	0.87	0.96	0.915	0.87	0.96	CLONAL	2	TRUE	1	0.78246057916062	3		368	544	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484206	8484206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768568228	NA	P-0015097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	46	563	1	ENST00000356435.5:c.3326G>A	p.Arg1109His	p.R1109H	ENST00000356435		1109	cGt/cAt	19/35	0.595435075084399	4	FACETS	0.29	0.243	0.342	0.145	0.121	0.171	SUBCLONAL	1	TRUE	2	0.78246057916062	4		564	723	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858353	59858353	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	151	378	0	ENST00000259008.2:c.1642T>C	p.Tyr548His	p.Y548H	ENST00000259008	NM_032043.2	548	Tat/Cat	12/20	0.78246057916062	3	FACETS	1	0.972	1	0.559	0.515	0.605	CLONAL	1	TRUE	1	0.78246057916062	3		378	480	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281260	15281260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1379085406	NA	P-0015097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	190	661	0	ENST00000263388.2:c.4996C>T	p.Arg1666Trp	p.R1666W	ENST00000263388	NM_000435.2	1666	Cgg/Tgg	27/33	0.770293664538778	3	FACETS	0.994	0.922	1	0.497	0.461	0.534	CLONAL	1	TRUE	1	0.78246057916062	3		661	680	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853290	151853290	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	293	426	0	ENST00000262189.6:c.11812G>A	p.Val3938Ile	p.V3938I	ENST00000262189	NM_170606.2	3938	Gtt/Att	45/59	0.78246057916062	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.78246057916062	3		426	470	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209358	98209358	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1297685477	NA	P-0015097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	114	506	0	ENST00000331920.6:c.4180C>T	p.Arg1394Ter	p.R1394*	ENST00000331920	NM_000264.3	1394	Cga/Tga	23/24	0.595435075084399	4	FACETS	0.911	0.823	1	0.456	0.411	0.502	CLONAL	1	TRUE	2	0.78246057916062	4		506	570	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0015745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	151	442	1	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	0.555355562509441	2	FACETS	0.985	0.91	1	0.492	0.455	0.531	CLONAL	1	TRUE	0	0.740636603650809	2		443	414	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412303	139412303	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs869025494	NA	P-0015745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	208	636	1	ENST00000277541.6:c.1342C>T	p.Arg448Ter	p.R448*	ENST00000277541	NM_017617.3	448	Cga/Tga	8/34	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.740636603650809	2		637	543	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519665	137519665	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	151	309	0	ENST00000367739.4:c.973C>G	p.Pro325Ala	p.P325A	ENST00000367739	NM_000416.2	325	Ccg/Gcg	7/7	0.740636603650809	3	FACETS	0.968	0.89	1	0.484	0.445	0.525	CLONAL	1	TRUE	1	0.740636603650809	3		309	577	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0016008-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	125	296	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.109763440468961	4	FACETS	0.794	0.726	0.865	0.794	0.726	0.865	INDETERMINATE	2	TRUE	2	0.685146100497798	4		296	387	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092811	27092811	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016008-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	221	495	0	ENST00000324856.7:c.2832G>T	p.Gln944His	p.Q944H	ENST00000324856	NM_006015.4	944	caG/caT	9/20	0.685146100497798	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.685146100497798	1		495	406	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330628	65330628	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0016008-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	192	407	0	ENST00000342505.4:c.1018A>T	p.Lys340Ter	p.K340*	ENST00000342505	NM_002227.2	340	Aaa/Taa	8/25	0.610738603241672	1	FACETS	0.869	0.814	0.924	0.869	0.814	0.924	CLONAL	1	TRUE	0	0.685146100497798	1		407	424	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042322	16042322	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016008-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	57	342	0	ENST00000268712.3:c.1352A>C	p.Lys451Thr	p.K451T	ENST00000268712	NM_006311.3	451	aAg/aCg	12/46	1	2	FACETS	0.378	0.325	0.436	0.378	0.325	0.436	SUBCLONAL	1	TRUE	1	0.685146100497798	2		342	440	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29120968	29120968	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016008-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	230	472	0	ENST00000328354.6:c.589A>G	p.Lys197Glu	p.K197E	ENST00000328354	NM_007194.3	197	Aaa/Gaa	4/15	0.685146100497798	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.685146100497798	1		472	429	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940079	49940079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778931500	NA	P-0016008-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	430	1043	0	ENST00000296474.3:c.964C>T	p.Arg322Trp	p.R322W	ENST00000296474	NM_002447.2	322	Cgg/Tgg	1/20	0.627361181411377	2	FACETS	0.935	0.903	0.967	0.935	0.903	0.967	CLONAL	2	TRUE	0	0.685146100497798	2		1043	671	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188973	142188973	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016008-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	46	425	0	ENST00000350721.4:c.6274A>C	p.Thr2092Pro	p.T2092P	ENST00000350721	NM_001184.3	2092	Act/Cct	37/47	0.109763440468961	4	FACETS	0.326	0.274	0.384	0.163	0.137	0.192	INDETERMINATE	1	TRUE	2	0.685146100497798	4		425	694	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748245	41748245	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016008-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	72	1229	0	ENST00000226382.2:c.524A>G	p.Lys175Arg	p.K175R	ENST00000226382	NM_003924.3	175	aAg/aGg	3/3	0.685146100497798	1	FACETS	0.174	0.151	0.198	0.174	0.151	0.198	SUBCLONAL	1	TRUE	0	0.685146100497798	1		1229	794	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295382	1295382	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0016008-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	127	357	0				ENST00000310581	NM_198253.2	-/1132			0.109763440468961	4	FACETS	1	0.939	1	1	0.939	1	INDETERMINATE	2	TRUE	2	0.685146100497798	4		357	305	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662622	117662622	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1456345928	NA	P-0016008-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	151	431	0	ENST00000368508.3:c.4843A>G	p.Asn1615Asp	p.N1615D	ENST00000368508	NM_002944.2	1615	Aat/Gat	29/43	1	2	FACETS	0.903	0.832	0.977	0.903	0.832	0.977	CLONAL	1	TRUE	1	0.685146100497798	2		431	488	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626629	100626630	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0016008-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	27	203	0	ENST00000308731.7:c.299_300dup	p.Pro101IlefsTer21	p.P101Ifs*21	ENST00000308731	NM_000061.2	100	-/AT	4/19	1	1	FACETS	0.189	0.151	0.233	0.189	0.151	0.233	SUBCLONAL	1	TRUE	0	0.685146100497798	1		203	274	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0016244-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	199	466	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.426774878038511	2	FACETS	0.914	0.855	0.975	0.914	0.855	0.975	CLONAL	2	TRUE	0	0.433552757851796	2		466	502	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509249	106509249	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016244-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	230	459	0	ENST00000359195.3:c.1243G>C	p.Glu415Gln	p.E415Q	ENST00000359195	NM_002649.2	415	Gag/Cag	2/11	0.363291462576393	2	FACETS	0.995	0.937	1	0.995	0.937	1	CLONAL	2	TRUE	0	0.433552757851796	2		459	533	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131787	2131787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1020561347	NA	P-0016244-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	231	514	0	ENST00000219476.3:c.3802C>T	p.Arg1268Cys	p.R1268C	ENST00000219476	NM_000548.3	1268	Cgc/Tgc	31/42	0.260240636682026	5	FACETS	0.907	0.851	0.965	0.907	0.851	0.965	CLONAL	3	TRUE	2	0.433552757851796	5		514	646	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256832	16256832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs887977680	NA	P-0016244-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	211	571	1	ENST00000375759.3:c.4097G>A	p.Arg1366Gln	p.R1366Q	ENST00000375759	NM_015001.2	1366	cGa/cAa	11/15	0.371004130417333	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.433552757851796	1		572	594	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1650196	1650196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199639167	NA	P-0016244-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	283	652	0	ENST00000344749.5:c.52G>A	p.Asp18Asn	p.D18N	ENST00000344749	NM_001136139.2	18	Gac/Aac	2/19	0.387110655521243	2	FACETS	0.929	0.878	0.98	0.929	0.878	0.98	CLONAL	2	TRUE	0	0.433552757851796	2		652	703	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294132	1294132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147056740	NA	P-0016244-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	163	748	0	ENST00000310581.5:c.869C>T	p.Ser290Phe	p.S290F	ENST00000310581	NM_198253.2	290	tCt/tTt	2/16	0.433552757851796	4	FACETS	0.951	0.872	1	0.317	0.29	0.345	CLONAL	1	TRUE	1	0.433552757851796	4		748	1133	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992734	68992734	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016244-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	303	524	0	ENST00000288368.4:c.1699G>A	p.Glu567Lys	p.E567K	ENST00000288368	NM_024870.2	567	Gag/Aag	16/40	0.433552757851796	7	FACETS	1	0.988	1	0.472	0.444	0.501	CLONAL	2	TRUE	2	0.433552757851796	7		524	1234	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026494	48026494	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016244-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	41	459	0	ENST00000234420.5:c.1372C>G	p.His458Asp	p.H458D	ENST00000234420	NM_000179.2	458	Cat/Gat	4/10	0.196456350697112	3	FACETS	0.462	0.385	0.548	0.231	0.192	0.274	INDETERMINATE	1	TRUE	1	0.433552757851796	3		459	498	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0016870-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	240	454	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.576747747034907	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	3	TRUE	0	0.576747747034907	3		454	355	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0016870-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	509	480	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.389478995369877	4	FACETS	1	0.988	1			1	CLONAL	4	TRUE	NA	0.576747747034907	4		480	677	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240752	53240752	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016870-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	361	627	0	ENST00000375401.3:c.1328A>T	p.Asp443Val	p.D443V	ENST00000375401	NM_004187.3	443	gAc/gTc	10/26	0.576747747034907	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.576747747034907	3		627	745	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235838	108235838	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016870-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	271	477	0	ENST00000278616.4:c.8880G>T	p.Trp2960Cys	p.W2960C	ENST00000278616	NM_000051.3	2960	tgG/tgT	62/63	0.576747747034907	3	FACETS	0.919	0.878	0.96	0.919	0.878	0.96	CLONAL	3	TRUE	0	0.576747747034907	3		477	439	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870853	12870853	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016870-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	130	144	1	ENST00000228872.4:c.80C>A	p.Ser27Ter	p.S27*	ENST00000228872	NM_004064.3	27	tCg/tAg	1/3	0.576747747034907	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	0	0.576747747034907	3		145	178	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019443	42019443	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016870-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	240	593	0	ENST00000219905.7:c.3496G>T	p.Glu1166Ter	p.E1166*	ENST00000219905	NM_001164273.1	1166	Gaa/Taa	10/24	0.576747747034907	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.576747747034907	2		593	399	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670886	134670886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1432628958	NA	P-0016870-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	139	250	1	ENST00000398015.3:c.797C>T	p.Ala266Val	p.A266V	ENST00000398015	NM_004441.4	266	gCa/gTa	3/16	0.271595891742457	5	FACETS	0.928	0.858	0.999	0.928	0.858	0.999	INDETERMINATE	3	TRUE	2	0.576747747034907	5		251	323	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005429	29005429	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016870-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	20	360	0	ENST00000282397.4:c.832G>T	p.Val278Leu	p.V278L	ENST00000282397	NM_002019.4	278	Gta/Tta	7/30	0.565703738099772	2	FACETS	0.244	0.187	0.312	0.122	0.093	0.156	SUBCLONAL	1	TRUE	0	0.576747747034907	2		360	284	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300039	137300039	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016870-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	345	683	0	ENST00000481739.1:c.324G>C	p.Lys108Asn	p.K108N	ENST00000481739	NM_002957.4	108	aaG/aaC	3/10	0.57289936931532	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.576747747034907	4		683	924	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912050	76912050	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016870-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	76	396	0	ENST00000373344.5:c.4214G>T	p.Arg1405Met	p.R1405M	ENST00000373344	NM_000489.3	1405	aGg/aTg	13/35	0.576747747034907	3	FACETS	0.905	0.799	1	0.453	0.399	0.509	CLONAL	1	TRUE	1	0.576747747034907	3		396	375	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0017535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	26	427	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.119	0.093	0.148	0.119	0.093	0.148	SUBCLONAL	1	TRUE	1	0.510328775552378	2		427	859	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0017535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1592	63	735	2	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.149	0.128	0.172	0.149	0.128	0.172	SUBCLONAL	1	TRUE	1	0.510328775552378	2		737	1655	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0017535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	53	486	1	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	1	2	FACETS	0.223	0.189	0.26	0.223	0.189	0.26	SUBCLONAL	1	TRUE	1	0.510328775552378	2		487	932	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266116	41266142	+	inframe_deletion	In_Frame_Del	DEL	GTGCCACTACCACAGCTCCTTCTCTGA	GTGCCACTACCACAGCTCCTTCTCTGA	-	novel	NA	P-0017535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	78	443	0	ENST00000349496.5:c.116_142del	p.Ala39_Ser47del	p.A39_S47del	ENST00000349496	NM_001904.3	38	gGTGCCACTACCACAGCTCCTTCTCTGAgt/ggt	3/15	1	2	FACETS	0.342	0.299	0.387	0.342	0.299	0.387	SUBCLONAL	1	TRUE	1	0.510328775552378	2		443	895	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015348	176015348	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	126	397	0	ENST00000367669.3:c.1390G>C	p.Glu464Gln	p.E464Q	ENST00000367669	NM_022457.5	464	Gag/Cag	12/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.510328775552378	2		397	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579529	7579529	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658483	NA	P-0017541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	449	403	0	ENST00000269305.4:c.158G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tGg/tAg	4/11	0.762859840975889	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.762859840975889	1		403	698	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241932	72241932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1362	798	985	1	ENST00000357731.5:c.458G>A	p.Gly153Glu	p.G153E	ENST00000357731	NM_173808.2	153	gGa/gAa	3/7	1	2	FACETS	0.969	0.936	1	0.969	0.936	1	CLONAL	1	TRUE	1	0.762859840975889	2		986	2160	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166113	118166113	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	483	460	0	ENST00000369448.3:c.623C>T	p.Pro208Leu	p.P208L	ENST00000369448	NM_017709.3	208	cCc/cTc	2/2	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.762859840975889	2		460	1251	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138073	64138073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	380	458	0	ENST00000334205.4:c.1996G>A	p.Glu666Lys	p.E666K	ENST00000334205	NM_003942.2	666	Gag/Aag	16/17	0.279263820815867	1	FACETS	0.588	0.559	0.617	0.588	0.559	0.617	INDETERMINATE	1	TRUE	0	0.762859840975889	1		458	1048	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627688	37627688	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771063488	NA	P-0017541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	757	705	0	ENST00000447079.4:c.1603C>T	p.Pro535Ser	p.P535S	ENST00000447079	NM_015083.1	535	Ccc/Tcc	2/14	0.762859840975889	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.762859840975889	1		705	1178	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39575945	39575945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	237	287	0	ENST00000262039.4:c.878G>A	p.Arg293Lys	p.R293K	ENST00000262039	NM_002647.2	293	aGa/aAa	8/25	1	2	FACETS	0.881	0.827	0.937	0.881	0.827	0.937	CLONAL	1	TRUE	1	0.762859840975889	2		287	705	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15374260	15374260	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	583	529	2	ENST00000263377.2:c.1312G>A	p.Glu438Lys	p.E438K	ENST00000263377	NM_058243.2	438	Gag/Aag	7/20	1	2	FACETS	0.993	0.954	1	0.993	0.954	1	CLONAL	1	TRUE	1	0.762859840975889	2		531	1540	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248403	212248403	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1440705268	NA	P-0017541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	411	382	0	ENST00000342788.4:c.3864C>G	p.Phe1288Leu	p.F1288L	ENST00000342788	NM_005235.2	1288	ttC/ttG	28/28	0.762859840975889	1	FACETS	0.993	0.957	1	0.993	0.957	1	CLONAL	1	TRUE	0	0.762859840975889	1		382	671	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953900	55953901	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0017541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	307	312	0	ENST00000263923.4:c.3535_3536delinsTT	p.Pro1179Leu	p.P1179L	ENST00000263923	NM_002253.2	1179	CCg/TTg	27/30	0.762859840975889	1	FACETS	0.932	0.891	0.973	0.932	0.891	0.973	CLONAL	1	TRUE	0	0.762859840975889	1		312	534	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411137	63411137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	700	311	0	ENST00000330258.3:c.2030C>T	p.Ser677Phe	p.S677F	ENST00000330258	NM_152424.3	677	tCc/tTc	2/2	1	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.762859840975889	1		311	919	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220524	123220524	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017630-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	51	314	0	ENST00000218089.9:c.3181A>C	p.Ser1061Arg	p.S1061R	ENST00000218089	NM_001042749.1	1061	Agt/Cgt	30/35	1	1	FACETS	0.2	0.17	0.234	0.2	0.17	0.234	SUBCLONAL	1	TRUE	0	0.696822853702164	1		314	476	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0017976-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	488	454	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.415187636651065	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	1	0.411822383725434	3		454	1152	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17354353	17354353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017976-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	141	468	0	ENST00000375499.3:c.431G>A	p.Ser144Asn	p.S144N	ENST00000375499	NM_003000.2	144	aGc/aAc	5/8	1	2	FACETS	0.96	0.877	1	0.96	0.877	1	CLONAL	1	TRUE	1	0.411822383725434	2		468	713	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636350	87636350	+	stop_lost	Nonstop_Mutation	SNP	T	T	C	novel	NA	P-0017976-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	120	549	0	ENST00000277120.3:c.2515T>C	p.Ter839GlnextTer17	p.*839Qext*17	ENST00000277120		839	Tag/Cag	19/19	0.411822383725434	2	FACETS	0.741	0.67	0.817	0.371	0.335	0.409	SUBCLONAL	1	TRUE	0	0.411822383725434	2		549	786	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827589	72827589	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343025200	NA	P-0018064-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	147	667	1	ENST00000268489.5:c.8992C>T	p.Arg2998Trp	p.R2998W	ENST00000268489	NM_006885.3	2998	Cgg/Tgg	9/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.58226483358286	2		668	436	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0018064-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	243	747	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.58226483358286	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.58226483358286	3		747	336	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855966	68855966	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35187787	NA	P-0018064-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	66	498	0	ENST00000261769.5:c.1774G>A	p.Ala592Thr	p.A592T	ENST00000261769	NM_004360.3	592	Gcc/Acc	12/16	1	2	FACETS	0.798	0.699	0.903	0.798	0.699	0.903	CLONAL	1	TRUE	1	0.58226483358286	2		498	284	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584684	187584684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149295542	NA	P-0018064-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	82	444	0	ENST00000441802.2:c.3349G>A	p.Val1117Met	p.V1117M	ENST00000441802	NM_005245.3	1117	Gtg/Atg	3/27	0.58226483358286	3	FACETS	1	0.892	1	0.502	0.446	0.562	CLONAL	1	TRUE	1	0.58226483358286	3		444	362	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225362541	225362541	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs767240461	NA	P-0018064-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	141	446	0	ENST00000264414.4:c.1636C>T	p.Arg546Ter	p.R546*	ENST00000264414	NM_003590.4	546	Cga/Tga	12/16	0.469275231929725	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	2	0.58226483358286	4		446	339	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344126	70344126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519381	NA	P-0018064-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	106	683	0	ENST00000374080.3:c.1862G>A	p.Arg621Gln	p.R621Q	ENST00000374080		621	cGa/cAa	13/45	0.58226483358286	3	FACETS	0.933	0.84	1	0.466	0.42	0.515	CLONAL	1	TRUE	1	0.58226483358286	3		683	504	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624970	9624970	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018064-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	28	213	1	ENST00000353224.5:c.7G>T	p.Gly3Trp	p.G3W	ENST00000353224	NM_177990.2	3	Ggg/Tgg	3/10	0.58226483358286	5	FACETS	0.665	0.533	0.814	0.222	0.177	0.272	SUBCLONAL	1	TRUE	2	0.58226483358286	5		214	271	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197800	123197800	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018064-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	63	474	0	ENST00000218089.9:c.1924G>A	p.Glu642Lys	p.E642K	ENST00000218089	NM_001042749.1	642	Gaa/Aaa	20/35	0.58226483358286	3	FACETS	0.91	0.793	1	0.455	0.396	0.518	CLONAL	1	TRUE	1	0.58226483358286	3		474	307	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40384023	40384023	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018064-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	70	415	0	ENST00000293328.3:c.123A>T	p.Gln41His	p.Q41H	ENST00000293328	NM_012448.3	41	caA/caT	2/19	0.548074726235477	3	FACETS	0.902	0.792	1	0.451	0.396	0.51	CLONAL	1	TRUE	1	0.58226483358286	3		415	344	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753750	42753750	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763588724	NA	P-0018064-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	108	723	0	ENST00000222329.4:c.514C>T	p.Leu172Phe	p.L172F	ENST00000222329	NM_006494.2	172	Ctc/Ttc	4/4	1	2	FACETS	0.885	0.8	0.974	0.885	0.8	0.974	CLONAL	1	TRUE	1	0.58226483358286	2		723	419	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376078	8376078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018064-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	43	293	0	ENST00000356435.5:c.4519G>A	p.Glu1507Lys	p.E1507K	ENST00000356435		1507	Gag/Aag	28/35	0.548074726235477	3	FACETS	1	0.864	1	0.51	0.432	0.594	CLONAL	1	TRUE	1	0.58226483358286	3		293	187	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139438549	139438549	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018064-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	107	540	1	ENST00000277541.6:c.67C>T	p.Arg23Ter	p.R23*	ENST00000277541	NM_017617.3	23	Cga/Tga	2/34	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.58226483358286	NA		541	457	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4094474	4094474	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs945585174	NA	P-0018178-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	39	713	3	ENST00000262948.5:c.1069C>T	p.Arg357Trp	p.R357W	ENST00000262948	NM_030662.3	357	Cgg/Tgg	10/11	1	2	FACETS	0.285	0.235	0.341	0.285	0.235	0.341	SUBCLONAL	1	FALSE	1	0.386540104572766	2		716	708	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692819	89692823	+	frameshift_variant	Frame_Shift_Del	DEL	CAAAC	CAAAC	-	novel	NA	P-0018178-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	55	213	0	ENST00000371953.3:c.304_308del	p.Lys102LeufsTer3	p.K102Lfs*3	ENST00000371953	NM_000314.4	101	atCAAACcc/atcc	5/9	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	1	0.386540104572766	2		213	244	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0018182-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	218	587	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.151715174494869	3	FACETS	1	0.973	1	0.727	0.676	0.779	CLONAL	2	FALSE	0	0.234449109647838	3		587	953	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954325	48954327	+	missense_variant	Missense_Mutation	TNP	TCA	TCA	AAT	novel	NA	P-0018182-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	66	451	1	ENST00000267163.4:c.1446_1448delinsAAT	p.Phe482_His483delinsLeuIle	p.F482_H483delinsLI	ENST00000267163	NM_000321.2	482	ttTCAt/ttAATt	16/27	0.234449109647838	1	FACETS	0.633	0.549	0.725	0.633	0.549	0.725	SUBCLONAL	1	FALSE	0	0.234449109647838	1		452	785	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967268	25967268	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018182-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	80	464	0	ENST00000435504.4:c.1938del	p.Thr647LeufsTer152	p.T647Lfs*152	ENST00000435504		646	atC/at	13/13	1	2	FACETS	0.828	0.728	0.936	0.828	0.728	0.936	CLONAL	1	FALSE	1	0.234449109647838	2		464	824	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428478	72428478	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018182-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	134	589	0	ENST00000477973.2:c.526C>T	p.Gln176Ter	p.Q176*	ENST00000477973	NM_012234.5	176	Cag/Tag	2/4	1	2	FACETS	0.899	0.814	0.988	0.899	0.814	0.988	CLONAL	1	FALSE	1	0.234449109647838	2		589	1272	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854976	76854976	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018182-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	127	773	1	ENST00000373344.5:c.5860G>C	p.Val1954Leu	p.V1954L	ENST00000373344	NM_000489.3	1954	Gtg/Ctg	25/35	1	2	FACETS	0.848	0.766	0.935	0.848	0.766	0.935	CLONAL	1	FALSE	1	0.234449109647838	2		774	1278	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106648	27106648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553153748	NA	P-0018394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	94	638	1	ENST00000324856.7:c.6259G>A	p.Gly2087Arg	p.G2087R	ENST00000324856	NM_006015.4	2087	Gga/Aga	20/20	0.699062966504046	1	FACETS	0.925	0.85	0.999	0.925	0.85	0.999	CLONAL	1	TRUE	0	0.756775915745002	1		639	167	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0018394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	76	264	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.756775915745002	3	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	1	0.756775915745002	3		264	134	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842745	68842751	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	ATACACT	ATACACT	-	novel	NA	P-0018394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	57	430	0	ENST00000261769.5:c.681_687del	p.Tyr228SerfsTer20	p.Y228Sfs*20	ENST00000261769	NM_004360.3	227	acATACACT/ac	5/16	0.756775915745002	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.756775915745002	1		430	79	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634811	158634812	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0018394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	23	287	0	ENST00000263640.3:c.374_375delinsTT	p.Gly125Val	p.G125V	ENST00000263640	NM_001105.4	125	gGC/gTT	5/11	1	2	FACETS	0.741	0.593	0.902	0.741	0.593	0.902	CLONAL	1	TRUE	1	0.756775915745002	2		287	82	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520008	NA	P-0018607-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	88	570	0	ENST00000269305.4:c.613T>C	p.Tyr205His	p.Y205H	ENST00000269305	NM_001126112.2	205	Tat/Cat	6/11	0.686268071325426	1	FACETS	0.385	0.343	0.43	0.385	0.343	0.43	SUBCLONAL	1	TRUE	0	0.690948434867778	1		570	433	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0018607-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	59	406	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	1	2	FACETS	0.311	0.267	0.359	0.311	0.267	0.359	SUBCLONAL	1	TRUE	1	0.690948434867778	2		406	549	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931463	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622007	NA	P-0018607-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	33	269	0	ENST00000374690.3:c.2105T>A	p.Leu702His	p.L702H	ENST00000374690	NM_000044.3	702	cTc/cAc	4/8	0.52405864377607	2	FACETS	0.187	0.152	0.227			1	SUBCLONAL	1	TRUE	NA	0.690948434867778	2		269	511	SUCCESS
AR	367	MSKCC	GRCh37	X	66765159	66765200	+	inframe_deletion	In_Frame_Del	DEL	GCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA	GCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA	-	rs3032358	NA	P-0018607-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	125	93	0	ENST00000374690.3:c.198_239del	p.Gln67_Gln80del	p.Q67_Q80del	ENST00000374690	NM_000044.3	57	ctGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAg/ctg	1/8	0.52405864377607	2	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.690948434867778	2		93	303	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573983	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0018607-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	31	617	1	ENST00000269305.4:c.1044_1045delinsTT	p.Leu348_Glu349delinsPheTer	p.L348_E349delinsF*	ENST00000269305	NM_001126112.2	348	ttGGaa/ttTTaa	10/11	0.686268071325426	1	FACETS	0.12	0.096	0.146	0.12	0.096	0.146	SUBCLONAL	1	TRUE	0	0.690948434867778	1		618	491	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42026794	42026794	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0018607-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	162	310	0	ENST00000219905.7:c.3916+2T>A		p.X1306_splice	ENST00000219905	NM_001164273.1	1306			1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.690948434867778	2		310	467	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615695	1615695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018607-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	283	672	0	ENST00000344749.5:c.1576G>A	p.Ala526Thr	p.A526T	ENST00000344749	NM_001136139.2	526	Gcc/Acc	17/19	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.690948434867778	2		672	752	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577560	7577560	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520002	NA	P-0018718-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	296	505	0	ENST00000269305.4:c.721T>C	p.Ser241Pro	p.S241P	ENST00000269305	NM_001126112.2	241	Tcc/Ccc	7/11	NA	2	FACETS	0.983	0.934	1			1	INDETERMINATE	2	TRUE	NA	0.490337773993244	2		505	614	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355374	15355374	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781044333	NA	P-0018770-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	148	726	1	ENST00000263377.2:c.2249C>T	p.Pro750Leu	p.P750L	ENST00000263377	NM_058243.2	750	cCg/cTg	13/20	0.476167912059275	4	FACETS	0.6	0.547	0.656	0.3	0.273	0.328	INDETERMINATE	1	TRUE	2	0.842537234015718	4		727	1079	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840564	36840564	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771002648	NA	P-0018770-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	224	1261	0	ENST00000358127.4:c.1169G>A	p.Arg390His	p.R390H	ENST00000358127	NM_001280556.1	390	cGt/cAt	10/10	1	2	FACETS	0.454	0.422	0.487	0.454	0.422	0.487	SUBCLONAL	1	TRUE	1	0.842537234015718	2		1261	1171	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55569942	55569942	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018770-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	35	368	0	ENST00000288135.5:c.809A>G	p.Glu270Gly	p.E270G	ENST00000288135	NM_000222.2	270	gAa/gGa	5/21	1	2	FACETS	0.201	0.164	0.242	0.201	0.164	0.242	SUBCLONAL	1	TRUE	1	0.842537234015718	2		368	414	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019025-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	97	504	1	ENST00000346208.3:c.1220_1221insA	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcAg	6/6	0.192026515864124	3	FACETS	0.801	0.716	0.892	0.801	0.716	0.892	CLONAL	2	TRUE	1	0.225197070518266	3		505	598	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937602	76937603	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019025-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	35	554	0	ENST00000373344.5:c.3145dup	p.Ile1049AsnfsTer4	p.I1049Nfs*4	ENST00000373344	NM_000489.3	1049	ata/aAta	9/35	0.192026515864124	3	FACETS	0.725	0.594	0.873	0.363	0.297	0.437	SUBCLONAL	1	TRUE	1	0.225197070518266	3		554	477	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552831	226552838	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCTTCA	CGCCTTCA	-	novel	NA	P-0019025-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	66	547	0	ENST00000366794.5:c.2523_2530del	p.Glu842MetfsTer8	p.E842Mfs*8	ENST00000366794	NM_001618.3	841	cgTGAAGGCGaa/cgaa	19/23	0.225197070518266	5	FACETS	0.817	0.711	0.931	0.545	0.474	0.621	CLONAL	2	TRUE	2	0.225197070518266	5		547	480	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795109	42795109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752503838	NA	P-0019025-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	70	654	0	ENST00000575354.2:c.2189C>T	p.Ser730Leu	p.S730L	ENST00000575354	NM_015125.3	730	tCg/tTg	10/20	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.225197070518266	2		654	583	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939232	71939232	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0019025-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	31	551	0	ENST00000298229.2:c.183-2A>T		p.X61_splice	ENST00000298229	NM_001567.3	61			0.169555866641772	2	FACETS	0.586	0.473	0.714	0.293	0.236	0.357	SUBCLONAL	1	TRUE	0	0.225197070518266	2		551	470	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940603	71940603	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs756452267	NA	P-0019025-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	49	623	1	ENST00000298229.2:c.753+1G>A		p.X251_splice	ENST00000298229	NM_001567.3	251			0.169555866641772	2	FACETS	0.901	0.764	1	0.45	0.382	0.526	CLONAL	1	TRUE	0	0.225197070518266	2		624	483	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208040	5208040	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019402-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	201	424	0	ENST00000357368.4:c.5671A>G	p.Ile1891Val	p.I1891V	ENST00000357368	NM_002850.3	1891	Atc/Gtc	37/38	1	2	FACETS	0.925	0.865	0.986	0.925	0.865	0.986	CLONAL	1	TRUE	1	0.845665126779923	2		424	514	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61717779	61717779	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019402-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	213	402	0	ENST00000401558.2:c.2020A>G	p.Lys674Glu	p.K674E	ENST00000401558	NM_003400.3	674	Aaa/Gaa	17/25	1	2	FACETS	0.921	0.863	0.98	0.921	0.863	0.98	CLONAL	1	TRUE	1	0.845665126779923	2		402	547	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0019772-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	241	597	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.283583493190488	7	FACETS	1	0.941	1	0.802	0.753	0.853	CLONAL	4	TRUE	2	0.283583493190488	7		597	724	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0019772-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	104	606	0	ENST00000269305.4:c.673-2A>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.283583493190488	3	FACETS	1	0.949	1	0.719	0.649	0.792	CLONAL	2	TRUE	0	0.283583493190488	3		606	388	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243969	46243969	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019772-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	43	590	0	ENST00000334344.6:c.2063C>G	p.Pro688Arg	p.P688R	ENST00000334344	NM_152641.2	688	cCt/cGt	15/21	1	2	FACETS	0.637	0.533	0.752	0.637	0.533	0.752	SUBCLONAL	1	TRUE	1	0.283583493190488	2		590	476	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46252756	46252756	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019772-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	36	419	0	ENST00000371998.3:c.185T>C	p.Phe62Ser	p.F62S	ENST00000371998		62	tTc/tCc	4/23	0.273642626923259	3	FACETS	0.767	0.631	0.919	0.256	0.21	0.307	CLONAL	1	TRUE	0	0.283583493190488	3		419	378	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14015924	14015924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019772-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	36	315	0	ENST00000311895.7:c.244G>A	p.Glu82Lys	p.E82K	ENST00000311895	NM_005236.2	82	Gaa/Aaa	2/11	0.283583493190488	3	FACETS	0.819	0.674	0.98	0.409	0.337	0.49	CLONAL	1	TRUE	1	0.283583493190488	3		315	354	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967952	93967952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019772-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	59	623	0	ENST00000369303.4:c.1975G>A	p.Asp659Asn	p.D659N	ENST00000369303	NM_004440.3	659	Gat/Aat	11/17	0.283583493190488	3	FACETS	0.745	0.64	0.859	0.372	0.32	0.43	SUBCLONAL	1	TRUE	1	0.283583493190488	3		623	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs786202525	NA	P-0019856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	313	710	1	ENST00000269305.4:c.532del	p.His178ThrfsTer69	p.H178Tfs*69	ENST00000269305	NM_001126112.2	178	Cac/ac	5/11	0.464250815209518	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.475125909794094	2		711	630	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249007	+	missense_variant	Missense_Mutation	TNP	GCG	GCG	TCT	novel	NA	P-0019856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	632	569	1	ENST00000275493.2:c.2303_2305delinsTCT	p.Ser768_Val769delinsIleLeu	p.S768_V769delinsIL	ENST00000275493	NM_005228.3	768	aGCGtg/aTCTtg	20/28	0.475125909794094	9	FACETS	1	0.983	1	1	0.983	1	CLONAL	7	TRUE	2	0.475125909794094	9		570	994	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976733	55976733	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	198	606	0	ENST00000263923.4:c.1092G>C	p.Trp364Cys	p.W364C	ENST00000263923	NM_002253.2	364	tgG/tgC	9/30	0.475125909794094	4	FACETS	0.979	0.911	1	0.979	0.911	1	CLONAL	2	TRUE	2	0.475125909794094	4		606	628	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246858	41246858	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	83	476	0	ENST00000357654.3:c.690G>C	p.Glu230Asp	p.E230D	ENST00000357654	NM_007294.3	230	gaG/gaC	10/23	0.475125909794094	4	FACETS	0.865	0.764	0.972	0.432	0.382	0.486	CLONAL	1	TRUE	2	0.475125909794094	4		476	596	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794794	42794794	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1336743202	NA	P-0019856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	72	625	0	ENST00000575354.2:c.1874G>A	p.Gly625Glu	p.G625E	ENST00000575354	NM_015125.3	625	gGa/gAa	10/20	0.424390727843566	5	FACETS	0.699	0.61	0.795	0.233	0.203	0.265	SUBCLONAL	1	TRUE	2	0.475125909794094	5		625	743	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215595173	215595173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	107	576	1	ENST00000260947.4:c.1963G>A	p.Glu655Lys	p.E655K	ENST00000260947	NM_000465.2	655	Gaa/Aaa	10/11	0.475125909794094	3	FACETS	0.867	0.779	0.96	0.433	0.389	0.48	CLONAL	1	TRUE	1	0.475125909794094	3		577	643	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675392	30675392	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	100	641	0	ENST00000376406.3:c.2964C>A	p.Ser988Arg	p.S988R	ENST00000376406	NM_014641.2	988	agC/agA	8/15	0.409224821388674	4	FACETS	0.904	0.808	1	0.452	0.404	0.503	CLONAL	1	TRUE	2	0.475125909794094	4		641	687	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0020825-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	122	459	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.262506684768026	2		459	901	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0020825-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	67	462	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.745	0.647	0.852	0.745	0.647	0.852	SUBCLONAL	1	TRUE	1	0.262506684768026	2		462	685	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249092	55249092	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020825-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	62	636	0	ENST00000275493.2:c.2390G>C	p.Cys797Ser	p.C797S	ENST00000275493	NM_005228.3	797	tGc/tCc	20/28	1	2	FACETS	0.531	0.457	0.611	0.531	0.457	0.611	SUBCLONAL	1	TRUE	1	0.262506684768026	2		636	890	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404576	8404576	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146844299	NA	P-0020825-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	55	368	0	ENST00000356435.5:c.4171G>A	p.Ala1391Thr	p.A1391T	ENST00000356435		1391	Gca/Aca	25/35	1	2	FACETS	0.998	0.856	1	0.998	0.856	1	CLONAL	1	TRUE	1	0.262506684768026	2		368	420	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653780	89653781	+	splice_acceptor_variant	Splice_Site	DEL	AG	AG	-	rs1554893747	NA	P-0020825-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	53	320	0	ENST00000371953.3:c.80-1_80del		p.X27_splice	ENST00000371953	NM_000314.4	27			0.262506684768026	1	FACETS	0.997	0.854	1	0.997	0.854	1	CLONAL	1	TRUE	0	0.262506684768026	1		320	352	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679790	88679790	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020825-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	106	545	0	ENST00000360948.2:c.673G>T	p.Asp225Tyr	p.D225Y	ENST00000360948	NM_001012338.2	225	Gac/Tac	7/19	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.262506684768026	2		545	652	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919556	78919556	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368881284	NA	P-0020825-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	40	476	0	ENST00000306801.3:c.3115G>A	p.Ala1039Thr	p.A1039T	ENST00000306801	NM_020761.2	1039	Gcc/Acc	26/34	0.262506684768026	3	FACETS	0.552	0.457	0.657	0.276	0.228	0.329	SUBCLONAL	1	TRUE	1	0.262506684768026	3		476	625	SUCCESS
APC	324	MSKCC	GRCh37	5	112154965	112154968	+	frameshift_variant	Frame_Shift_Del	DEL	GATA	GATA	-	novel	NA	P-0020825-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	82	607	0	ENST00000257430.4:c.1236_1239del	p.Gln412HisfsTer41	p.Q412Hfs*41	ENST00000257430	NM_000038.5	412	caGATA/ca	10/16	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.262506684768026	2		607	593	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053133	180053133	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020943-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	222	594	0	ENST00000261937.6:c.1236C>G	p.Ile412Met	p.I412M	ENST00000261937	NM_182925.4	412	atC/atG	9/30	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		594	564	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021067-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	166	264	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.611901439042708	3	FACETS	0.892	0.832	0.954	0.892	0.832	0.954	CLONAL	2	TRUE	1	0.666715115449643	3		264	372	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740546	58740546	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs766524048	NA	P-0021067-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	176	415	0	ENST00000305921.3:c.1451T>G	p.Leu484Ter	p.L484*	ENST00000305921	NM_003620.3	484	tTa/tGa	6/6	1	2	FACETS	0.989	0.917	1	0.989	0.917	1	CLONAL	1	TRUE	1	0.666715115449643	2		415	534	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891456	76891456	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021067-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	182	252	0	ENST00000373344.5:c.4649T>A	p.Val1550Glu	p.V1550E	ENST00000373344	NM_000489.3	1550	gTg/gAg	16/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.666715115449643	1		252	249	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858069	40858069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021067-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	151	592	0	ENST00000428826.2:c.1795G>A	p.Val599Met	p.V599M	ENST00000428826		599	Gtg/Atg	16/21	1	2	FACETS	0.96	0.884	1	0.96	0.884	1	CLONAL	1	TRUE	1	0.666715115449643	2		592	472	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485295	8485295	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1341469793	NA	P-0021067-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	91	347	0	ENST00000356435.5:c.3085G>A	p.Val1029Ile	p.V1029I	ENST00000356435		1029	Gta/Ata	18/35	1	2	FACETS	0.864	0.775	0.956	0.864	0.775	0.956	CLONAL	1	TRUE	1	0.666715115449643	2		347	316	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0021295-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	598	357	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.738712232596585	8	FACETS	1	0.978	1			1	CLONAL	5	TRUE	NA	0.738712232596585	8		357	1029	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0021295-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	1138	459	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.738712232596585	8	FACETS	1	0.994	1			1	CLONAL	4	TRUE	NA	0.738712232596585	8		459	2331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576853	7576853	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs11575996	NA	P-0021295-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	630	827	0	ENST00000269305.4:c.993G>T	p.Gln331His	p.Q331H	ENST00000269305	NM_001126112.2	331	caG/caT	9/11	0.707795900425291	2	FACETS	0.959	0.934	0.984	0.959	0.934	0.984	CLONAL	2	TRUE	0	0.738712232596585	2		827	889	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120460296	120460296	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021295-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	79	588	0	ENST00000256646.2:c.6019G>A	p.Asp2007Asn	p.D2007N	ENST00000256646	NM_024408.3	2007	Gac/Aac	33/34	0.360304299212849	2	FACETS	0.462	0.408	0.52	0.231	0.204	0.26	INDETERMINATE	1	TRUE	0	0.738712232596585	2		588	463	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104375118	104375118	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021295-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	46	732	0	ENST00000369902.3:c.1116A>T	p.Lys372Asn	p.K372N	ENST00000369902	NM_016169.3	372	aaA/aaT	9/12	0.677046781446368	2	FACETS	0.164	0.138	0.194	0.082	0.069	0.097	SUBCLONAL	1	TRUE	0	0.738712232596585	2		732	758	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543330	65543330	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021295-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1252	182	739	0	ENST00000358664.4:c.347C>T	p.Pro116Leu	p.P116L	ENST00000358664	NM_002382.4	116	cCc/cTc	5/5	0.324957131909084	3	FACETS	0.471	0.433	0.51	0.235	0.216	0.255	INDETERMINATE	1	TRUE	1	0.738712232596585	3		739	1434	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151882692	151882692	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021295-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	61	534	0	ENST00000262189.6:c.5033T>C	p.Ile1678Thr	p.I1678T	ENST00000262189	NM_170606.2	1678	aTt/aCt	34/59	0.401343165579313	5	FACETS	0.633	0.546	0.727	0.211	0.182	0.243	INDETERMINATE	1	TRUE	2	0.738712232596585	5		534	550	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578234	7578234	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs786202222	NA	P-0021647-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	145	663	13	ENST00000269305.4:c.615T>A	p.Tyr205Ter	p.Y205*	ENST00000269305	NM_001126112.2	205	taT/taA	6/11	0.794775257879143	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.794775257879143	1		676	193	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939436	36939436	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021647-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	191	753	8	ENST00000361632.4:c.414C>A	p.Ser138Arg	p.S138R	ENST00000361632		138	agC/agA	4/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.794775257879143	2		761	453	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	340	487	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	0.891	0.847	0.937	0.891	0.847	0.937	CLONAL	1	TRUE	1	0.86984077194507	2		487	877	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748129	41748129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776131193	NA	P-0021664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	127	143	1	ENST00000226382.2:c.640G>A	p.Gly214Ser	p.G214S	ENST00000226382	NM_003924.3	214	Ggc/Agc	3/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.86984077194507	2		144	249	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0021905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	335	563	0	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	0.660653431752482	1	FACETS	0.941	0.896	0.986	0.941	0.896	0.986	CLONAL	1	TRUE	0	0.660653431752482	1		563	722	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339328	70339328	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0021905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	187	344	0	ENST00000374080.3:c.204+1G>A		p.X68_splice	ENST00000374080		68			0.62026690468337	1	FACETS	0.874	0.817	0.931	0.874	0.817	0.931	CLONAL	1	TRUE	0	0.660653431752482	1		344	434	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679177	88679177	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	260	419	0	ENST00000360948.2:c.860A>G	p.Glu287Gly	p.E287G	ENST00000360948	NM_001012338.2	287	gAg/gGg	8/19	0.660653431752482	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.660653431752482	1		419	519	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191359	185191359	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	113	449	0	ENST00000265026.3:c.2240C>G	p.Ser747Cys	p.S747C	ENST00000265026	NM_004721.4	747	tCt/tGt	11/14	0.660653431752482	3	FACETS	0.494	0.443	0.547	0.247	0.221	0.274	SUBCLONAL	1	TRUE	1	0.660653431752482	3		449	922	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	52	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.809	0.69	0.939	1	0.968	1	CLONAL	2	TRUE	1	0.149757389316334	2		248	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0022450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	156	639	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.149757389316334	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.149757389316334	3		640	943	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453136	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	rs397516897	NA	P-0022450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	101	365	0	ENST00000288602.6:c.1799_1801del	p.Val600_Lys601delinsGlu	p.V600_K601delinsE	ENST00000288602	NM_004333.4	600	gTGAaa/gaa	15/18	0.149757389316334	4	FACETS	1	0.919	1	1	0.919	1	CLONAL	3	TRUE	1	0.149757389316334	4		365	503	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239529	123239529	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs201752803	NA	P-0022450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	62	883	0	ENST00000358487.5:c.2308T>G	p.Leu770Val	p.L770V	ENST00000358487	NM_000141.4	770	Ttg/Gtg	18/18	1	2	FACETS	0.758	0.653	0.874	0.758	0.653	0.874	SUBCLONAL	1	TRUE	1	0.149757389316334	2		883	1092	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341561	89341561	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	47	446	0	ENST00000301030.4:c.7509del	p.Glu2503AspfsTer24	p.E2503Dfs*24	ENST00000301030	NM_001256183.1	2503	gaG/ga	10/13	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.149757389316334	2		446	616	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348533	89348533	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1244497015	NA	P-0022450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	108	909	0	ENST00000301030.4:c.4417A>G	p.Lys1473Glu	p.K1473E	ENST00000301030	NM_001256183.1	1473	Aag/Gag	9/13	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.149757389316334	2		909	1134	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972969	25972969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1246090124	NA	P-0022450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	58	441	0	ENST00000435504.4:c.1456G>A	p.Glu486Lys	p.E486K	ENST00000435504		486	Gag/Aag	12/13	0.149757389316334	4	FACETS	1	0.966	1	0.729	0.626	0.841	CLONAL	1	TRUE	2	0.149757389316334	4		441	611	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981790	70981790	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	107	821	0	ENST00000276594.2:c.306C>A	p.Tyr102Ter	p.Y102*	ENST00000276594	NM_024504.3	102	taC/taA	2/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.149757389316334	2		821	998	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960139	151960139	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022474-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	70	649	0	ENST00000262189.6:c.1261G>T	p.Val421Phe	p.V421F	ENST00000262189	NM_170606.2	421	Gtt/Ttt	9/59	0.529280360136542	4	FACETS	0.684	0.597	0.778	0.228	0.199	0.26	SUBCLONAL	1	TRUE	1	0.528467988533768	4		649	592	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44948987	44948987	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs796568156	NA	P-0022474-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	74	364	0	ENST00000377967.4:c.3549-1G>A		p.X1183_splice	ENST00000377967	NM_021140.2	1183			0.529280360136542	1	FACETS	0.808	0.717	0.904	0.808	0.717	0.904	CLONAL	1	TRUE	0	0.528467988533768	1		364	255	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164919	123164919	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022474-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	88	408	0	ENST00000218089.9:c.232G>C	p.Gly78Arg	p.G78R	ENST00000218089	NM_001042749.1	78	Gga/Cga	5/35	0.529280360136542	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.528467988533768	1		408	227	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579361	7579374	+	frameshift_variant	Frame_Shift_Del	DEL	AAACCGTAGCTGCC	AAACCGTAGCTGCC	-	novel	NA	P-0022474-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	114	684	0	ENST00000269305.4:c.313_326del	p.Gly105ProfsTer39	p.G105Pfs*39	ENST00000269305	NM_001126112.2	105	GGCAGCTACGGTTTc/c	4/11	0.501329147254284	1	FACETS	0.808	0.734	0.885	0.808	0.734	0.885	CLONAL	1	TRUE	0	0.528467988533768	1		684	393	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250883	153250883	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022588-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	194	386	1	ENST00000281708.4:c.1177C>T	p.Arg393Ter	p.R393*	ENST00000281708	NM_033632.3	393	Cga/Tga	8/12	0.601326842956855	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	0	0.626275998775116	1		387	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574026	7574026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022588-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	338	502	0	ENST00000269305.4:c.1001G>T	p.Gly334Val	p.G334V	ENST00000269305	NM_001126112.2	334	gGg/gTg	10/11	0.601326842956855	1	FACETS	0.894	0.85	0.939	0.894	0.85	0.939	CLONAL	1	FALSE	0	0.626275998775116	1		502	829	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028875	47028875	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022588-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	240	439	0	ENST00000377604.3:c.179C>A	p.Ser60Ter	p.S60*	ENST00000377604	NM_001204468.1	60	tCa/tAa	3/24	1	2	FACETS	0.826	0.772	0.881	0.826	0.772	0.881	CLONAL	1	FALSE	1	0.626275998775116	2		439	928	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245441	133245441	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022588-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	332	489	2	ENST00000320574.5:c.1879G>T	p.Val627Leu	p.V627L	ENST00000320574	NM_006231.2	627	Gtg/Ttg	17/49	1	2	FACETS	0.974	0.921	1	0.974	0.921	1	CLONAL	1	FALSE	1	0.626275998775116	2		491	1089	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794409	42794409	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022588-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	339	659	0	ENST00000575354.2:c.1489C>T	p.Pro497Ser	p.P497S	ENST00000575354	NM_015125.3	497	Cct/Tct	10/20	1	2	FACETS	0.739	0.698	0.781	0.739	0.698	0.781	SUBCLONAL	1	FALSE	1	0.626275998775116	2		659	1465	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933194	39933194	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022588-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	474	692	0	ENST00000378444.4:c.1405A>T	p.Ser469Cys	p.S469C	ENST00000378444	NM_001123385.1	469	Agc/Tgc	4/15	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.626275998775116	2		692	1381	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653844	89653844	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022588-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	250	495	0	ENST00000371953.3:c.142A>T	p.Asn48Tyr	p.N48Y	ENST00000371953	NM_000314.4	48	Aac/Tac	2/9	0.440167904447255	0	FACETS	0.559	0.528	0.59			1	SUBCLONAL	1	FALSE	0	0.626275998775116	0		495	534	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678565	88678565	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022588-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	157	323	0	ENST00000360948.2:c.971T>C	p.Val324Ala	p.V324A	ENST00000360948	NM_001012338.2	324	gTg/gCg	9/19	1	2	FACETS	0.854	0.786	0.924	0.854	0.786	0.924	CLONAL	1	FALSE	1	0.626275998775116	2		323	587	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892312	9892312	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022588-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	145	273	0	ENST00000330684.3:c.2178C>A	p.Asp726Glu	p.D726E	ENST00000330684	NM_001134407.1	726	gaC/gaA	11/13	1	2	FACETS	0.82	0.751	0.89	0.82	0.751	0.89	CLONAL	1	FALSE	1	0.626275998775116	2		273	565	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675619	86675619	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022588-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	183	361	0	ENST00000274376.6:c.2555T>G	p.Leu852Arg	p.L852R	ENST00000274376	NM_002890.2	852	cTt/cGt	19/25	0.626275998775116	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	0	0.626275998775116	1		361	376	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665337	176665337	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022588-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	245	292	0	ENST00000439151.2:c.4021G>T	p.Glu1341Ter	p.E1341*	ENST00000439151	NM_022455.4	1341	Gag/Tag	7/23	0.626275998775116	1	FACETS	0.963	0.909	1	0.963	0.909	1	CLONAL	1	FALSE	0	0.626275998775116	1		292	558	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631839	90631839	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519906	NA	P-0023374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	63	613	1	ENST00000330062.3:c.514A>T	p.Arg172Trp	p.R172W	ENST00000330062	NM_002168.2	172	Agg/Tgg	4/11	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.15359321662392	2		614	727	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441220	52441220	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	38	373	0	ENST00000460680.1:c.550G>C	p.Asp184His	p.D184H	ENST00000460680	NM_004656.3	184	Gat/Cat	7/17	0.15359321662392	1	FACETS	0.993	0.821	1	0.993	0.821	1	CLONAL	1	TRUE	0	0.15359321662392	1		373	460	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863464	57863464	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1372547639	NA	P-0023440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	89	422	0	ENST00000228682.2:c.1559C>T	p.Pro520Leu	p.P520L	ENST00000228682	NM_005269.2	520	cCc/cTc	11/12	0.457311031553379	2	FACETS	0.931	0.83	1	0.466	0.415	0.519	CLONAL	1	TRUE	0	0.457311031553379	2		422	418	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857552	57857553	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	T	novel	NA	P-0023440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	113	611	2	ENST00000228682.2:c.78_79delinsT	p.Ala27ProfsTer51	p.A27Pfs*51	ENST00000228682	NM_005269.2	26	ggGGcc/ggTcc	2/12	0.457311031553379	2	FACETS	0.92	0.831	1	0.46	0.415	0.507	CLONAL	1	TRUE	0	0.457311031553379	2		613	537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0023479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	71	808	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.78	0.68	0.888	0.78	0.68	0.888	SUBCLONAL	1	TRUE	1	0.25	2		808	728	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0023479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	137	816	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.25	2		817	735	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0023479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	60	860	3	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.689	0.592	0.794	0.689	0.592	0.794	SUBCLONAL	1	TRUE	1	0.25	2		863	697	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0023479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	168	851	2	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.922	0.849	0.997	1	0.992	1	CLONAL	2	TRUE	1	0.25	2		853	729	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	102	532	1	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	0.3	1	FACETS	0.992	0.895	1	1	0.988	1	CLONAL	2	TRUE	0	0.25	1		533	360	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919466	78919466	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0023479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	93	740	0	ENST00000306801.3:c.3026-1G>T		p.X1009_splice	ENST00000306801	NM_020761.2	1009			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.25	2		740	590	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982440	25982440	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	45	548	1	ENST00000435504.4:c.850C>T	p.Arg284Ter	p.R284*	ENST00000435504		284	Cga/Tga	9/13	NA	2	FACETS	0.608	0.51	0.717			1	INDETERMINATE	1	TRUE	NA	0.25	2		549	592	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270529	98270530	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs751977093	NA	P-0023479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	45	474	1	ENST00000331920.6:c.114dup	p.Leu39AlafsTer51	p.L39Afs*51	ENST00000331920	NM_000264.3	38	-/G	1/24	0.3	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.25	1		475	260	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339494	339494	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144411078	NA	P-0023479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	145	840	3	ENST00000262320.3:c.2408G>A	p.Arg803His	p.R803H	ENST00000262320	NM_003502.3	803	cGc/cAc	10/11	1	2	FACETS	0.772	0.706	0.842	1	0.988	1	SUBCLONAL	2	TRUE	1	0.25	2		843	751	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129462	30129462	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768111899	NA	P-0023479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	58	805	0	ENST00000263025.4:c.566G>A	p.Arg189Gln	p.R189Q	ENST00000263025	NM_002746.2	189	cGg/cAg	4/9	1	2	FACETS	0.767	0.659	0.885	0.767	0.659	0.885	SUBCLONAL	1	TRUE	1	0.25	2		805	605	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356133	66356133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1349813115	NA	P-0023479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	69	610	0	ENST00000273854.3:c.1364G>A	p.Arg455Gln	p.R455Q	ENST00000273854	NM_004439.5	455	cGg/cAg	5/18	1	2	FACETS	0.982	0.856	1	0.982	0.856	1	CLONAL	1	TRUE	1	0.25	2		610	562	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15967388	15967388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776176516	NA	P-0023479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	64	530	1	ENST00000268712.3:c.5215C>T	p.Arg1739Trp	p.R1739W	ENST00000268712	NM_006311.3	1739	Cgg/Tgg	35/46	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.25	2		531	464	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21553919	21553919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368473445	NA	P-0023479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	105	503	0	ENST00000382592.4:c.2683G>A	p.Asp895Asn	p.D895N	ENST00000382592	NM_014572.2	895	Gac/Aac	7/8	0.3	1	FACETS	0.764	0.688	0.844	1	0.983	1	SUBCLONAL	2	TRUE	0	0.25	1		503	481	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118992	3118992	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	43	888	0	ENST00000078429.4:c.676A>G	p.Ile226Val	p.I226V	ENST00000078429	NM_002067.2	226	Atc/Gtc	5/7	1	2	FACETS	0.561	0.469	0.664	0.561	0.469	0.664	SUBCLONAL	1	TRUE	1	0.25	2		888	613	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752724	42752724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764618715	NA	P-0023479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	99	873	0	ENST00000222329.4:c.1540C>T	p.Arg514Cys	p.R514C	ENST00000222329	NM_006494.2	514	Cgt/Tgt	4/4	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.25	2		873	562	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919936	50919936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763747258	NA	P-0023479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	82	774	0	ENST00000440232.2:c.3023G>A	p.Arg1008His	p.R1008H	ENST00000440232	NM_002691.3	1008	cGc/cAc	24/27	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.25	2		774	511	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285232	198285232	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	56	699	0	ENST00000335508.6:c.335T>C	p.Ile112Thr	p.I112T	ENST00000335508	NM_012433.2	112	aTt/aCt	4/25	1	2	FACETS	0.702	0.601	0.813	0.702	0.601	0.813	SUBCLONAL	1	TRUE	1	0.25	2		699	638	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309877	30309878	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1308464449	NA	P-0023479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	51	653	0	ENST00000307677.4:c.144dup	p.Ser49GlnfsTer50	p.S49Qfs*50	ENST00000307677	NM_138578.1	48	-/C	2/3	1	2	FACETS	0.735	0.625	0.857	0.735	0.625	0.857	SUBCLONAL	1	TRUE	1	0.25	2		653	555	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39726973	39726973	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	42	361	0	ENST00000361337.2:c.971A>G	p.Lys324Arg	p.K324R	ENST00000361337	NM_003286.2	324	aAa/aGa	11/21	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.25	2		361	317	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458533	12458533	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	145	813	0	ENST00000287820.6:c.1150C>A	p.Leu384Met	p.L384M	ENST00000287820	NM_015869.4	384	Ctg/Atg	6/7	0.227572135974685	2	FACETS	0.895	0.819	0.974	0.895	0.819	0.974	CLONAL	2	TRUE	0	0.25	2		813	648	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31429602	31429602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370990538	NA	P-0023479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	40	710	0	ENST00000344624.3:c.3196C>T	p.Arg1066Cys	p.R1066C	ENST00000344624		1066	Cgc/Tgc	24/33	0.278848627688283	3	FACETS	0.583	0.484	0.695	0.292	0.242	0.348	SUBCLONAL	1	TRUE	1	0.25	3		710	617	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947420	38947421	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0023479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	50	397	0	ENST00000357387.3:c.4259dup	p.Ser1421PhefsTer3	p.S1421Ffs*3	ENST00000357387	NM_152756.3	1420	ggt/ggGt	32/38	0.278848627688283	3	FACETS	1	0.902	1	0.541	0.46	0.63	CLONAL	1	TRUE	1	0.25	3		397	416	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036037	180036037	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	91	896	0	ENST00000261937.6:c.3824G>A	p.Ser1275Asn	p.S1275N	ENST00000261937	NM_182925.4	1275	aGt/aAt	29/30	0.278848627688283	3	FACETS	1	0.974	1	0.669	0.595	0.748	CLONAL	1	TRUE	1	0.25	3		896	612	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673386	30673386	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	37	751	0	ENST00000376406.3:c.3574del	p.Ser1192ValfsTer169	p.S1192Vfs*169	ENST00000376406	NM_014641.2	1192	Agt/gt	10/15	0.3	1	FACETS	0.407	0.334	0.488	0.407	0.334	0.488	SUBCLONAL	1	TRUE	0	0.25	1		751	637	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553389	106553389	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	65	444	0	ENST00000369096.4:c.1354G>A	p.Gly452Ser	p.G452S	ENST00000369096	NM_001198.3	452	Ggt/Agt	5/7	0.3	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.25	1		444	311	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997732	149997732	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	107	566	0	ENST00000253339.5:c.2735G>T	p.Gly912Val	p.G912V	ENST00000253339		912	gGg/gTg	5/7	0.3	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.25	1		566	510	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845193	151845193	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	28	622	0	ENST00000262189.6:c.13819G>T	p.Gly4607Trp	p.G4607W	ENST00000262189	NM_170606.2	4607	Ggg/Tgg	52/59	0.3	1	FACETS	0.407	0.324	0.501	0.407	0.324	0.501	SUBCLONAL	1	TRUE	0	0.25	1		622	482	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345760	152345760	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	51	441	0	ENST00000359321.1:c.810del	p.Phe270LeufsTer27	p.F270Lfs*27	ENST00000359321	NM_005431.1	270	ttT/tt	3/3	0.3	1	FACETS	0.771	0.656	0.897	0.771	0.656	0.897	SUBCLONAL	1	TRUE	0	0.25	1		441	463	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739584	145739584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772515188	NA	P-0023479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	90	883	2	ENST00000428558.2:c.1867C>T	p.Arg623Cys	p.R623C	ENST00000428558	NM_004260.3	623	Cgc/Tgc	11/22	0.3	7	FACETS	1	0.933	1			1	CLONAL	1	TRUE	NA	0.25	7		885	1085	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549490	5549490	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	78	942	0	ENST00000397747.3:c.517C>A	p.Leu173Ile	p.L173I	ENST00000397747	NM_025239.3	173	Ctc/Atc	4/7	0.3	1	FACETS	0.707	0.621	0.8	0.707	0.621	0.8	SUBCLONAL	1	TRUE	0	0.25	1		942	772	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918328	44918328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	46	381	0	ENST00000377967.4:c.953C>T	p.Ala318Val	p.A318V	ENST00000377967	NM_021140.2	318	gCa/gTa	11/29	0.278190733277439	2	FACETS	0.927	0.782	1			1	CLONAL	1	TRUE	NA	0.25	2		381	397	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937770	76937770	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	130	407	1	ENST00000373344.5:c.2978del	p.Lys993ArgfsTer10	p.K993Rfs*10	ENST00000373344	NM_000489.3	993	aAg/ag	9/35	1	1	FACETS	0.896	0.817	0.977	1	0.989	1	CLONAL	2	TRUE	0	0.25	1		408	508	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0023568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	1260	791	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.385840964004605	5	FACETS	0.908	0.889	0.926			1	INDETERMINATE	4	TRUE	NA	0.736405475543424	5		791	1984	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934874	NA	P-0023568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	437	1031	0	ENST00000269305.4:c.451C>A	p.Pro151Thr	p.P151T	ENST00000269305	NM_001126112.2	151	Ccc/Acc	5/11	0.736405475543424	1	FACETS	0.989	0.952	1	0.989	0.952	1	CLONAL	1	TRUE	0	0.736405475543424	1		1031	758	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716352	52716352	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0023568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	188	758	1	ENST00000322088.6:c.796A>T	p.Lys266Ter	p.K266*	ENST00000322088	NM_014225.5	266	Aag/Tag	6/15	0.374872963270203	1	FACETS	0.4	0.37	0.431	0.4	0.37	0.431	INDETERMINATE	1	TRUE	0	0.736405475543424	1		759	807	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436560	110436560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567423781	NA	P-0023568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	368	981	2	ENST00000375856.3:c.1841C>T	p.Pro614Leu	p.P614L	ENST00000375856	NM_003749.2	614	cCg/cTg	1/2	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.736405475543424	2		983	968	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874011	123874013	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs780061449	NA	P-0023568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	10	78	0	ENST00000330479.4:c.62_64del	p.Ala21del	p.A21del	ENST00000330479	NM_020382.3	14	gaGGCg/gag	2/9	0.374872963270203	1	FACETS	0.145	0.099	0.203	0.145	0.099	0.203	INDETERMINATE	1	TRUE	0	0.736405475543424	1		78	118	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812317	212812317	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs143662416	NA	P-0023568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	165	481	0	ENST00000342788.4:c.259G>T	p.Val87Leu	p.V87L	ENST00000342788	NM_005235.2	87	Gtg/Ttg	3/28	0.537644775807094	1	FACETS	0.761	0.709	0.814	0.761	0.709	0.814	SUBCLONAL	1	TRUE	0	0.736405475543424	1		481	372	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105657	11105657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	356	794	0	ENST00000358026.2:c.1573G>T	p.Glu525Ter	p.E525*	ENST00000358026	NM_001128849.1	525	Gag/Tag	9/36	0.736405475543424	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.736405475543424	1		794	589	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272419	11272419	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	143	700	1	ENST00000361445.4:c.3511T>A	p.Ser1171Thr	p.S1171T	ENST00000361445	NM_004958.3	1171	Tcc/Acc	23/58	0.374872963270203	1	FACETS	0.338	0.309	0.369	0.338	0.309	0.369	INDETERMINATE	1	TRUE	0	0.736405475543424	1		701	725	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444643	78444643	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	263	640	0	ENST00000370768.2:c.46G>A	p.Gly16Ser	p.G16S	ENST00000370768	NM_003902.3	16	Ggt/Agt	1/20	0.467769961277029	1	FACETS	0.836	0.792	0.88	0.836	0.792	0.88	CLONAL	1	TRUE	0	0.736405475543424	1		640	540	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600466	43600466	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	282	742	0	ENST00000355710.3:c.692G>T	p.Arg231Leu	p.R231L	ENST00000355710	NM_020975.4	231	cGc/cTc	4/20	0.237738682228375	1	FACETS	0.692	0.654	0.73	0.692	0.654	0.73	INDETERMINATE	1	TRUE	0	0.736405475543424	1		742	699	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406112	70406112	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	165	831	0	ENST00000373644.4:c.3626T>A	p.Val1209Glu	p.V1209E	ENST00000373644	NM_030625.2	1209	gTa/gAa	4/12	0.237738682228375	1	FACETS	0.324	0.297	0.352	0.324	0.297	0.352	INDETERMINATE	1	TRUE	0	0.736405475543424	1		831	874	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450871	70450871	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	228	681	0	ENST00000373644.4:c.5711T>G	p.Leu1904Arg	p.L1904R	ENST00000373644	NM_030625.2	1904	cTt/cGt	12/12	0.237738682228375	1	FACETS	0.626	0.587	0.666	0.626	0.587	0.666	INDETERMINATE	1	TRUE	0	0.736405475543424	1		681	625	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715635	18715635	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0023568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	134	359	0	ENST00000266497.5:c.3468-2A>T		p.X1156_splice	ENST00000266497		1156			0.542263570424692	1	FACETS	0.69	0.636	0.746	0.69	0.636	0.746	SUBCLONAL	1	TRUE	0	0.736405475543424	1		359	333	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438295	49438295	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1412790128	NA	P-0023568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	148	701	0	ENST00000301067.7:c.4974G>T	p.Glu1658Asp	p.E1658D	ENST00000301067	NM_003482.3	1658	gaG/gaT	20/54	0.374872963270203	1	FACETS	0.425	0.389	0.461	0.425	0.389	0.461	INDETERMINATE	1	TRUE	0	0.736405475543424	1		701	598	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445377	49445377	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755350858	NA	P-0023568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	255	1290	0	ENST00000301067.7:c.2089C>T	p.Pro697Ser	p.P697S	ENST00000301067	NM_003482.3	697	Ccc/Tcc	10/54	0.374872963270203	1	FACETS	0.387	0.362	0.413	0.387	0.362	0.413	INDETERMINATE	1	TRUE	0	0.736405475543424	1		1290	1131	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093449	30093449	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	105	653	0	ENST00000331968.5:c.1814C>A	p.Thr605Lys	p.T605K	ENST00000331968	NM_002742.2	605	aCa/aAa	13/18	0.542263570424692	1	FACETS	0.376	0.338	0.416	0.376	0.338	0.416	SUBCLONAL	1	TRUE	0	0.736405475543424	1		653	479	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591953	48591953	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	82	525	0	ENST00000342988.3:c.1116G>C	p.Arg372Ser	p.R372S	ENST00000342988	NM_005359.5	372	agG/agC	9/12	0.237738682228375	1	FACETS	0.291	0.257	0.327	0.291	0.257	0.327	INDETERMINATE	1	TRUE	0	0.736405475543424	1		525	483	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221316	1221317	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	358	891	1	ENST00000326873.7:c.839_840insT	p.Leu282AlafsTer3	p.L282Afs*3	ENST00000326873	NM_000455.4	280	ccc/ccTc	6/10	0.736405475543424	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.736405475543424	1		892	593	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661668	227661668	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1367671533	NA	P-0023568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	102	645	1	ENST00000305123.5:c.1787G>T	p.Gly596Val	p.G596V	ENST00000305123	NM_005544.2	596	gGg/gTg	1/2	0.537644775807094	1	FACETS	0.4	0.359	0.442	0.4	0.359	0.442	SUBCLONAL	1	TRUE	0	0.736405475543424	1		646	438	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264519	1264519	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	101	481	0	ENST00000310581.5:c.2843G>T	p.Ser948Ile	p.S948I	ENST00000310581	NM_198253.2	948	aGc/aTc	11/16	1	2	FACETS	0.564	0.507	0.625	0.564	0.507	0.625	SUBCLONAL	1	TRUE	1	0.736405475543424	2		481	486	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755536	57755536	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	167	868	1	ENST00000274289.3:c.251G>T	p.Arg84Leu	p.R84L	ENST00000274289	NM_006622.3	84	cGg/cTg	1/14	1	2	FACETS	0.467	0.428	0.507	0.467	0.428	0.507	SUBCLONAL	1	TRUE	1	0.736405475543424	2		869	972	SUCCESS
APC	324	MSKCC	GRCh37	5	112173499	112173499	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	110	495	0	ENST00000257430.4:c.2208G>T	p.Lys736Asn	p.K736N	ENST00000257430	NM_000038.5	736	aaG/aaT	16/16	1	2	FACETS	0.582	0.525	0.642	0.582	0.525	0.642	SUBCLONAL	1	TRUE	1	0.736405475543424	2		495	513	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149450100	149450100	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	183	952	0	ENST00000286301.3:c.1117C>A	p.Pro373Thr	p.P373T	ENST00000286301	NM_005211.3	373	Ccc/Acc	8/22	0.417352385738536	1	FACETS	0.359	0.332	0.388	0.359	0.332	0.388	INDETERMINATE	1	TRUE	0	0.736405475543424	1		952	874	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180605	32180605	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	101	609	1	ENST00000375023.3:c.2522G>T	p.Cys841Phe	p.C841F	ENST00000375023	NM_004557.3	841	tGc/tTc	16/30	0.417352385738536	1	FACETS	0.372	0.334	0.412	0.372	0.334	0.412	INDETERMINATE	1	TRUE	0	0.736405475543424	1		610	466	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468102	50468102	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	90	527	0	ENST00000331340.3:c.1337A>T	p.Gln446Leu	p.Q446L	ENST00000331340	NM_006060.4	446	cAg/cTg	8/8	1	2	FACETS	0.478	0.426	0.534	0.478	0.426	0.534	SUBCLONAL	1	TRUE	1	0.736405475543424	2		527	511	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70971078	70971078	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0023568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	353	973	0	ENST00000276594.2:c.1184-1G>T		p.X395_splice	ENST00000276594	NM_024504.3	395			0.237738682228375	1	FACETS	0.639	0.607	0.671	0.639	0.607	0.671	INDETERMINATE	1	TRUE	0	0.736405475543424	1		973	948	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521444	8521444	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	200	845	1	ENST00000356435.5:c.794C>A	p.Pro265His	p.P265H	ENST00000356435		265	cCt/cAt	9/35	0.736405475543424	1	FACETS	0.501	0.466	0.537	0.501	0.466	0.537	SUBCLONAL	1	TRUE	0	0.736405475543424	1		846	685	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772828	135772828	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	186	904	0	ENST00000298552.3:c.2795A>T	p.Asp932Val	p.D932V	ENST00000298552	NM_001162426.1	932	gAt/gTt	21/23	0.736405475543424	1	FACETS	0.476	0.441	0.512	0.476	0.441	0.512	SUBCLONAL	1	TRUE	0	0.736405475543424	1		904	671	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	219	697	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.409173226436054	5	FACETS	0.919	0.855	0.984	0.613	0.57	0.656	CLONAL	2	TRUE	2	0.409173226436054	5		697	940	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0023571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	222	454	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.277415496510185	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.409173226436054	4		454	625	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0023571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	215	557	0	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.409173226436054	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.409173226436054	2		557	511	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52692244	52692244	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1359676390	NA	P-0023571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	181	448	0	ENST00000394830.3:c.616G>A	p.Glu206Lys	p.E206K	ENST00000394830	NM_018313.4	206	Gaa/Aaa	6/30	0.277415496510185	4	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	2	0.409173226436054	4		448	607	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970893	21970905	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTCCTCACCTGAG	GTCCTCACCTGAG	-	novel	NA	P-0023571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	262	719	0	ENST00000304494.5:c.453_457+8del		p.X151_splice	ENST00000304494	NM_000077.4	151		2/3	0.409173226436054	2	FACETS	0.973	0.918	1	0.973	0.918	1	CLONAL	2	TRUE	0	0.409173226436054	2		719	658	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	58	697	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	0.17	2		697	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0023646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	39	863	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	1	2	FACETS	0.719	0.595	0.859	0.719	0.595	0.859	SUBCLONAL	1	TRUE	1	0.17	2		863	638	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40872305	40872305	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773742282	NA	P-0023646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	39	969	0	ENST00000428826.2:c.650G>A	p.Arg217Gln	p.R217Q	ENST00000428826		217	cGa/cAa	7/21	1	2	FACETS	0.657	0.543	0.785	0.657	0.543	0.785	SUBCLONAL	1	TRUE	1	0.17	2		969	698	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061191	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs879499034	NA	P-0023770-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	226	645	1	ENST00000250448.2:c.798C>A	p.Phe266Leu	p.F266L	ENST00000250448	NM_004496.3	266	ttC/ttA	2/2	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.75179211409762	2		646	584	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060782	38060784	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0023770-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	458	1649	0	ENST00000250448.2:c.1205_1207del	p.Ile402del	p.I402del	ENST00000250448	NM_004496.3	402	aTCAac/aac	2/2	1	2	FACETS	0.879	0.839	0.919	0.879	0.839	0.919	CLONAL	1	TRUE	1	0.75179211409762	2		1649	1386	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650654	67650654	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023770-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	30	516	0	ENST00000264010.4:c.959G>A	p.Arg320His	p.R320H	ENST00000264010	NM_006565.3	320	cGt/cAt	5/12	0.75179211409762	1	FACETS	0.153	0.123	0.186	0.153	0.123	0.186	SUBCLONAL	1	TRUE	0	0.75179211409762	1		516	326	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971153	21971153	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913383	NA	P-0023994-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	101	266	0	ENST00000304494.5:c.205G>T	p.Glu69Ter	p.E69*	ENST00000304494	NM_000077.4	69	Gag/Tag	2/3	0.422997994143336	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.422997994143336	1		266	310	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0023994-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	88	264	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	0.422997994143336	2		264	364	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115928	8115929	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023994-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	86	426	0	ENST00000346208.3:c.1275dup	p.Ser426IlefsTer81	p.S426Ifs*81	ENST00000346208		425	cca/ccAa	6/6	NA	2	FACETS	0.715	0.633	0.801			1	INDETERMINATE	1	TRUE	NA	0.422997994143336	2		426	569	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405968	49405968	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023994-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	94	359	0	ENST00000418115.1:c.170T>C	p.Leu57Ser	p.L57S	ENST00000418115	NM_001664.2	57	tTg/tCg	3/5	1	2	FACETS	0.831	0.741	0.925	0.831	0.741	0.925	CLONAL	1	TRUE	1	0.422997994143336	2		359	535	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873687	151873688	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATGA	novel	NA	P-0023994-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	213	445	0	ENST00000262189.6:c.8847_8850dup	p.Val2951SerfsTer18	p.V2951Sfs*18	ENST00000262189	NM_170606.2	2950	-/TCAT	38/59	0.422997994143336	3	FACETS	0.827	0.771	0.884	0.827	0.771	0.884	CLONAL	2	TRUE	1	0.422997994143336	3		445	738	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878867	151878868	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0023994-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	150	480	0	ENST00000262189.6:c.6077dup	p.Tyr2026Ter	p.Y2026*	ENST00000262189	NM_170606.2	2026	tat/taAt	36/59	0.422997994143336	3	FACETS	1	0.942	1	0.519	0.474	0.565	CLONAL	1	TRUE	1	0.422997994143336	3		480	828	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111462	8111463	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGT	novel	NA	P-0023994-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	128	417	0	ENST00000346208.3:c.949_951dup	p.Cys317dup	p.C317dup	ENST00000346208		317	-/TGT	5/6	NA	2	FACETS	0.845	0.767	0.927			1	INDETERMINATE	1	TRUE	NA	0.422997994143336	2		417	716	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	393	454	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.295096859475726	6	FACETS	0.914	0.877	0.951	0.914	0.877	0.951	INDETERMINATE	4	TRUE	2	0.743291067236536	6		454	719	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717615	89717615	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909227	NA	P-0024123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	18	311	0	ENST00000371953.3:c.640C>T	p.Gln214Ter	p.Q214*	ENST00000371953	NM_000314.4	214	Cag/Tag	7/9	0.719776843857208	1	FACETS	0.098	0.074	0.128	0.098	0.074	0.128	SUBCLONAL	1	TRUE	0	0.743291067236536	1		311	309	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934874	NA	P-0024123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	409	660	0	ENST00000269305.4:c.451C>G	p.Pro151Ala	p.P151A	ENST00000269305	NM_001126112.2	151	Ccc/Gcc	5/11	0.731491471609276	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.743291067236536	1		660	669	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934194	48934194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	177	358	0	ENST00000267163.4:c.649C>T	p.Gln217Ter	p.Q217*	ENST00000267163	NM_000321.2	217	Cag/Tag	7/27	0.731491471609276	1	FACETS	0.907	0.852	0.962	0.907	0.852	0.962	CLONAL	1	TRUE	0	0.743291067236536	1		358	330	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060904	38060904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	267	377	0	ENST00000250448.2:c.1085C>T	p.Ser362Phe	p.S362F	ENST00000250448	NM_004496.3	362	tCc/tTc	2/2	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.743291067236536	2		377	694	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016673	12016674	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0024123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	147	286	0	ENST00000353533.5:c.809_810insA	p.Met270IlefsTer4	p.M270Ifs*4	ENST00000353533	NM_003010.3	270	atg/atAg	7/11	0.731491471609276	1	FACETS	0.975	0.912	1	0.975	0.912	1	CLONAL	1	TRUE	0	0.743291067236536	1		286	255	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221626	36221626	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	402	660	1	ENST00000222270.7:c.5295G>A	p.Trp1765Ter	p.W1765*	ENST00000222270	NM_014727.1	1765	tgG/tgA	26/37	0.15938723154975	3	FACETS	1	0.996	1	0.734	0.7	0.768	INDETERMINATE	1	TRUE	1	0.743291067236536	3		661	1011	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518509	204518509	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1496	137	251	0	ENST00000367182.3:c.1172C>T	p.Ser391Leu	p.S391L	ENST00000367182	NM_001278516.1	391	tCa/tTa	11/11	0.743291067236536	10	FACETS	0.897	0.813	0.986			1	CLONAL	1	TRUE	NA	0.743291067236536	10		251	1633	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999347	100999347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	96	673	0	ENST00000325455.5:c.455C>T	p.Pro152Leu	p.P152L	ENST00000325455	NM_001202474.3	152	cCg/cTg	1/8	0.743291067236536	1	FACETS	0.308	0.275	0.343	0.308	0.275	0.343	SUBCLONAL	1	TRUE	0	0.743291067236536	1		673	527	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116146	67116149	+	frameshift_variant	Frame_Shift_Ins	INS	GAAG	GAAG	AAAAA	novel	NA	P-0024123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	41	342	1	ENST00000412916.2:c.430_433delinsAAAAA	p.Glu144LysfsTer11	p.E144Kfs*11	ENST00000412916		144	GAAGag/AAAAAag	5/6	0.545923949360982	3	FACETS	0.314	0.261	0.373			1	SUBCLONAL	1	TRUE	NA	0.743291067236536	3		343	482	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447444	187447444	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	116	545	0	ENST00000232014.4:c.749C>A	p.Ser250Tyr	p.S250Y	ENST00000232014	NM_001130845.1	250	tCc/tAc	5/10	0.295096859475726	6	FACETS	0.682	0.613	0.755	0.171	0.153	0.189	INDETERMINATE	1	TRUE	2	0.743291067236536	6		545	1138	SUCCESS
APC	324	MSKCC	GRCh37	5	112174460	112174460	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	96	233	0	ENST00000257430.4:c.3169G>C	p.Glu1057Gln	p.E1057Q	ENST00000257430	NM_000038.5	1057	Gaa/Caa	16/16	1	2	FACETS	0.885	0.799	0.974	0.885	0.799	0.974	CLONAL	1	TRUE	1	0.743291067236536	2		233	292	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508916	106508916	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	31	307	0	ENST00000359195.3:c.910C>T	p.His304Tyr	p.H304Y	ENST00000359195	NM_002649.2	304	Cac/Tac	2/11	1	2	FACETS	0.194	0.156	0.236	0.194	0.156	0.236	SUBCLONAL	1	TRUE	1	0.743291067236536	2		307	431	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	205	667	2	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.752410146512345	2		669	534	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	150	539	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.929	0.858	1	0.929	0.858	1	CLONAL	1	TRUE	1	0.752410146512345	2		539	429	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	157	556	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.938	0.867	1	0.938	0.867	1	CLONAL	1	TRUE	1	0.752410146512345	2		556	445	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	245	797	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.752410146512345	2		797	631	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	212	597	1	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	0.752410146512345	2		598	515	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717777	89717777	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	224	458	0	ENST00000371953.3:c.801+1G>T		p.X267_splice	ENST00000371953	NM_000314.4	267			1	2	FACETS	1	0.965	1	1	0.996	1	CLONAL	2	TRUE	1	0.752410146512345	2		458	296	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	268	878	0	ENST00000397062.3:c.246A>T	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaT	2/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.752410146512345	2		878	662	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941696	48941696	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	135	625	0	ENST00000267163.4:c.1010del	p.Leu337TrpfsTer12	p.L337Wfs*12	ENST00000267163	NM_000321.2	336	Ttt/tt	10/27	1	2	FACETS	0.949	0.873	1	0.949	0.873	1	CLONAL	1	TRUE	1	0.752410146512345	2		625	378	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	252	733	1	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	0.752410146512345	2		734	583	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	427	818	13	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	0.572661012570462	3	FACETS	0.967	0.928	1	0.967	0.928	1	CLONAL	2	TRUE	1	0.752410146512345	3		831	808	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	311	621	20	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	0.572661012570462	3	FACETS	0.862	0.82	0.904	0.862	0.82	0.904	CLONAL	2	TRUE	1	0.752410146512345	3		641	660	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	142	684	0	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	0.852	0.783	0.923	0.852	0.783	0.923	CLONAL	1	TRUE	1	0.752410146512345	2		684	443	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	142	556	8	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.864	0.794	0.935	0.864	0.794	0.935	CLONAL	1	TRUE	1	0.752410146512345	2		564	437	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938230	76938230	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	45	872	11	ENST00000373344.5:c.2518del	p.Arg840GlufsTer29	p.R840Efs*29	ENST00000373344	NM_000489.3	840	Aga/ga	9/35	1	2	FACETS	0.2	0.167	0.236	0.2	0.167	0.236	SUBCLONAL	1	TRUE	1	0.752410146512345	2		883	599	SUCCESS
APC	324	MSKCC	GRCh37	5	112175101	112175101	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs587783033	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	111	345	0	ENST00000257430.4:c.3814del	p.Ser1272GlnfsTer16	p.S1272Qfs*16	ENST00000257430	NM_000038.5	1270	tgT/tg	16/16	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.752410146512345	2		345	284	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931468	131931468	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369560280	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	156	581	1	ENST00000265335.6:c.2173C>T	p.Arg725Trp	p.R725W	ENST00000265335		725	Cgg/Tgg	13/25	1	2	FACETS	0.969	0.896	1	0.969	0.896	1	CLONAL	1	TRUE	1	0.752410146512345	2		582	428	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435777	56435777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1055597951	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	176	638	1	ENST00000407977.2:c.1360C>T	p.Arg454Cys	p.R454C	ENST00000407977		454	Cgc/Tgc	9/10	1	2	FACETS	0.995	0.926	1	0.995	0.926	1	CLONAL	1	TRUE	1	0.752410146512345	2		639	470	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395664	45395664	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	189	732	3	ENST00000262160.6:c.470del	p.Lys157ArgfsTer6	p.K157Rfs*6	ENST00000262160	NM_005901.5	157	aAg/ag	4/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.752410146512345	2		735	486	SUCCESS
APC	324	MSKCC	GRCh37	5	112177265	112177265	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1554087123	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	118	507	2	ENST00000257430.4:c.5978del	p.Pro1993LeufsTer51	p.P1993Lfs*51	ENST00000257430	NM_000038.5	1992	Ccc/cc	16/16	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.752410146512345	2		509	307	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681327	88681327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780107	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	108	383	2	ENST00000372037.3:c.1217G>A	p.Arg406His	p.R406H	ENST00000372037	NM_004329.2	406	cGc/cAc	11/13	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.752410146512345	2		385	284	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	223	809	10	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	1	2	FACETS	0.97	0.909	1	0.97	0.909	1	CLONAL	1	TRUE	1	0.752410146512345	2		819	611	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041262	29041262	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	151	573	0	ENST00000282397.4:c.166del	p.Glu56LysfsTer12	p.E56Kfs*12	ENST00000282397	NM_002019.4	56	Gaa/aa	3/30	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.752410146512345	2		573	395	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927430	178927430	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748197872	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	171	723	0	ENST00000263967.3:c.1193G>A	p.Arg398His	p.R398H	ENST00000263967	NM_006218.2	398	cGt/cAt	7/21	0.752410146512345	3	FACETS	1	0.969	1	0.544	0.503	0.586	CLONAL	1	TRUE	1	0.752410146512345	3		723	575	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	118	1008	0	ENST00000293328.3:c.1101_1102dup	p.Gln368ProfsTer3	p.Q368Pfs*3	ENST00000293328	NM_012448.3	368	cag/cCCag	9/19	1	2	FACETS	0.39	0.352	0.431	0.39	0.352	0.431	SUBCLONAL	1	TRUE	1	0.752410146512345	2		1008	804	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180486	94180486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	150	729	0	ENST00000323929.3:c.1682G>A	p.Ser561Asn	p.S561N	ENST00000323929	NM_005591.3	561	aGc/aAc	15/20	0.752410146512345	2	FACETS	0.814	0.749	0.88	0.407	0.374	0.44	CLONAL	1	TRUE	0	0.752410146512345	2		729	490	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424495	49424496	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	438	793	0	ENST00000301067.7:c.13727_13728del	p.Phe4576CysfsTer29	p.F4576Cfs*29	ENST00000301067	NM_003482.3	4576	tTT/t	41/54	0.572661012570462	3	FACETS	0.968	0.93	1	0.968	0.93	1	CLONAL	2	TRUE	1	0.752410146512345	3		793	828	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626686	28626686	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	177	668	2	ENST00000241453.7:c.610del	p.Glu204LysfsTer26	p.E204Kfs*26	ENST00000241453	NM_004119.2	204	Gaa/aa	5/24	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.752410146512345	2		670	463	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423552	88423552	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	246	953	0	ENST00000360948.2:c.2283G>T	p.Trp761Cys	p.W761C	ENST00000360948	NM_001012338.2	761	tgG/tgT	18/19	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.752410146512345	2		953	645	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628102	90628102	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	292	898	0	ENST00000330062.3:c.1217T>C	p.Val406Ala	p.V406A	ENST00000330062	NM_002168.2	406	gTg/gCg	10/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.752410146512345	2		898	736	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781402	3781402	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	239	859	0	ENST00000262367.5:c.4963del	p.Leu1655CysfsTer89	p.L1655Cfs*89	ENST00000262367	NM_004380.2	1655	Ctg/tg	30/31	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.752410146512345	2		859	628	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347798	89347800	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-	novel	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	216	764	0	ENST00000301030.4:c.5150_5152del	p.Glu1717del	p.E1717del	ENST00000301030	NM_001256183.1	1717	gAGGtg/gtg	9/13	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.752410146512345	2		764	571	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40379600	40379600	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	250	1027	2	ENST00000293328.3:c.232del	p.Glu78LysfsTer6	p.E78Kfs*6	ENST00000293328	NM_012448.3	78	Gaa/aa	3/19	1	2	FACETS	0.885	0.831	0.94	0.885	0.831	0.94	CLONAL	1	TRUE	1	0.752410146512345	2		1029	751	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394825	45394825	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	116	419	0	ENST00000262160.6:c.524del	p.Leu175CysfsTer5	p.L175Cfs*5	ENST00000262160	NM_005901.5	175	tTg/tg	5/11	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.752410146512345	2		419	308	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095961	11095961	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs767638396	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	263	836	0	ENST00000358026.2:c.235A>G	p.Met79Val	p.M79V	ENST00000358026	NM_001128849.1	79	Atg/Gtg	3/36	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.752410146512345	2		836	661	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953334	17953334	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs553739688	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	286	854	1	ENST00000458235.1:c.652C>T	p.Arg218Cys	p.R218C	ENST00000458235	NM_000215.3	218	Cgc/Tgc	6/24	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.752410146512345	2		855	665	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797254	42797254	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	256	784	0	ENST00000575354.2:c.3616C>A	p.Gln1206Lys	p.Q1206K	ENST00000575354	NM_015125.3	1206	Cag/Aag	15/20	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.752410146512345	2		784	679	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99180099	99180099	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs746971958	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	170	590	0	ENST00000074304.5:c.2042C>T	p.Thr681Met	p.T681M	ENST00000074304	NM_001134224.1	681	aCg/aTg	19/26	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.752410146512345	2		590	433	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682809	190682810	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587778609	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	134	607	0	ENST00000441310.2:c.492dup	p.Cys165MetfsTer2	p.C165Mfs*2	ENST00000441310	NM_000534.4	162	gca/gcAa	5/13	1	2	FACETS	0.797	0.73	0.866	0.797	0.73	0.866	SUBCLONAL	1	TRUE	1	0.752410146512345	2		607	447	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719328	190719328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	121	542	0	ENST00000441310.2:c.1330G>A	p.Val444Ile	p.V444I	ENST00000441310	NM_000534.4	444	Gta/Ata	9/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.752410146512345	2		542	302	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143009	47143010	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	214	794	0	ENST00000409792.3:c.4952_4953dup	p.Thr1652LeufsTer12	p.T1652Lfs*12	ENST00000409792	NM_014159.6	1651	-/TT	8/21	0.752410146512345	3	FACETS	0.961	0.895	1	0.48	0.447	0.514	CLONAL	1	TRUE	1	0.752410146512345	3		794	815	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805423	1805423	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778617562	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	201	667	1	ENST00000260795.2:c.935C>T	p.Ala312Val	p.A312V	ENST00000260795		312	gCg/gTg	7/17	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.752410146512345	2		668	501	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591130	67591134	+	frameshift_variant	Frame_Shift_Del	DEL	AAGAC	AAGAC	-	novel	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	100	476	0	ENST00000274335.5:c.1723_1727del	p.Lys575GlufsTer25	p.K575Efs*25	ENST00000274335		575	AAGACg/g	12/15	1	2	FACETS	0.91	0.824	0.999	0.91	0.824	0.999	CLONAL	1	TRUE	1	0.752410146512345	2		476	292	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205604	38205604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	310	1032	4	ENST00000317025.8:c.86G>A	p.Arg29His	p.R29H	ENST00000317025	NM_023034.1	29	cGt/cAt	2/24	0.752410146512345	3	FACETS	1	0.977	1	0.532	0.502	0.563	CLONAL	1	TRUE	1	0.752410146512345	3		1036	1066	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559231	141559231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	259	715	0	ENST00000220592.5:c.1570G>A	p.Gly524Ser	p.G524S	ENST00000220592	NM_012154.3	524	Ggc/Agc	12/19	0.752410146512345	3	FACETS	1	0.984	1	0.567	0.532	0.602	CLONAL	1	TRUE	1	0.752410146512345	3		715	836	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595398	141595398	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1008896578	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	199	763	0	ENST00000220592.5:c.35C>A	p.Pro12His	p.P12H	ENST00000220592	NM_012154.3	12	cCt/cAt	2/19	0.752410146512345	3	FACETS	0.954	0.886	1	0.477	0.443	0.512	CLONAL	1	TRUE	1	0.752410146512345	3		763	763	SUCCESS
AR	367	MSKCC	GRCh37	X	66905959	66905959	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	162	753	0	ENST00000374690.3:c.1876A>G	p.Thr626Ala	p.T626A	ENST00000374690	NM_000044.3	626	Act/Gct	3/8	1	2	FACETS	0.979	0.907	1	0.979	0.907	1	CLONAL	1	TRUE	1	0.752410146512345	2		753	440	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046541	30046541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1181118001	NA	P-0024484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	205	627	0	ENST00000331968.5:c.2642C>T	p.Pro881Leu	p.P881L	ENST00000331968	NM_002742.2	881	cCc/cTc	18/18	0.349526455385501	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.349526455385501	1		627	879	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442601	52442601	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	122	354	0	ENST00000460680.1:c.144C>A	p.Phe48Leu	p.F48L	ENST00000460680	NM_004656.3	48	ttC/ttA	4/17	0.349526455385501	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.349526455385501	1		354	556	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628239	187628239	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	209	664	0	ENST00000441802.2:c.2743G>C	p.Val915Leu	p.V915L	ENST00000441802	NM_005245.3	915	Gta/Cta	2/27	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.349526455385501	2		664	1181	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156749	2156749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781634507	NA	P-0024487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	176	732	0	ENST00000434045.2:c.173G>A	p.Gly58Glu	p.G58E	ENST00000434045	NM_001127598.1	58	gGa/gAa	3/5	1	2	FACETS	0.957	0.883	1	0.957	0.883	1	CLONAL	1	TRUE	1	0.498619937707202	2		732	738	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993469	72993476	+	frameshift_variant	Frame_Shift_Del	DEL	CGGGTACA	CGGGTACA	-	novel	NA	P-0024487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	215	737	0	ENST00000268489.5:c.569_576del	p.Val190AlafsTer17	p.V190Afs*17	ENST00000268489	NM_006885.3	190	gTGTACCCG/g	2/10	1	2	FACETS	0.893	0.83	0.957	0.893	0.83	0.957	CLONAL	1	TRUE	1	0.498619937707202	2		737	966	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574002	7574003	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0024487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	242	835	0	ENST00000269305.4:c.1024dup	p.Arg342ProfsTer5	p.R342Pfs*5	ENST00000269305	NM_001126112.2	342	cga/cCga	10/11	0.477319221243134	1	FACETS	0.993	0.931	1	0.993	0.931	1	CLONAL	1	TRUE	0	0.498619937707202	1		835	734	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224177	39224177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	182	487	0	ENST00000402219.2:c.2967G>C	p.Arg989Ser	p.R989S	ENST00000402219	NM_005633.3	989	agG/agC	19/23	0.198669878063095	1	FACETS	0.894	0.829	0.961	0.894	0.829	0.961	INDETERMINATE	1	TRUE	0	0.498619937707202	1		487	613	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294984	1294984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	35	73	0	ENST00000310581.5:c.121C>T	p.Arg41Cys	p.R41C	ENST00000310581	NM_198253.2	41	Cgc/Tgc	1/16	0.498619937707202	11	FACETS	0.816	0.672	0.976			1	CLONAL	2	TRUE	NA	0.498619937707202	11		73	279	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228310	53228310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057517955	NA	P-0024487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	237	378	2	ENST00000375401.3:c.2092G>A	p.Glu698Lys	p.E698K	ENST00000375401	NM_004187.3	698	Gag/Aag	15/26	1	1	FACETS	0.779	0.737	0.821	1	0.994	1	SUBCLONAL	2	TRUE	0	0.498619937707202	1		380	458	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	74	440	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	0.839	0.735	0.951			1	INDETERMINATE	1	TRUE	NA	0.31	2		440	569	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003747	45003747	+	start_lost	Translation_Start_Site	SNP	G	G	T	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	92	558	2	ENST00000558401.1:c.3G>T	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	atG/atT	1/4	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.31	2		560	572	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	15	152	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	1	2	FACETS	0.806	0.595	1	0.806	0.595	1	CLONAL	1	TRUE	1	0.31	2		152	120	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	19	238	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.619	0.472	0.791	0.619	0.472	0.791	SUBCLONAL	1	TRUE	1	0.31	2		238	198	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	73	559	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	1	2	FACETS	0.913	0.8	1	0.913	0.8	1	CLONAL	1	TRUE	1	0.31	2		559	516	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	79	860	3	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.625	0.548	0.707	0.625	0.548	0.707	SUBCLONAL	1	TRUE	1	0.31	2		863	816	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825518	50825519	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1219062549	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	42	579	0	ENST00000398568.2:c.2156dup	p.Asn719LysfsTer2	p.N719Kfs*2	ENST00000398568	NM_001042412.1	717	gaa/gAaa	14/18	1	2	FACETS	0.541	0.451	0.64	0.541	0.451	0.64	SUBCLONAL	1	TRUE	1	0.31	2		579	501	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101268	27101268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	104	638	1	ENST00000324856.7:c.4555del	p.Gln1519ArgfsTer8	p.Q1519Rfs*8	ENST00000324856	NM_006015.4	1517	gCc/gc	18/20	1	2	FACETS	0.971	0.87	1	0.971	0.87	1	CLONAL	1	TRUE	1	0.31	2		639	691	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317189	11317189	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	62	669	0	ENST00000361445.4:c.305C>T	p.Thr102Ile	p.T102I	ENST00000361445	NM_004958.3	102	aCc/aTc	4/58	1	2	FACETS	0.577	0.498	0.664	0.577	0.498	0.664	SUBCLONAL	1	TRUE	1	0.31	2		669	693	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319406	11319406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149221273	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	130	735	1	ENST00000361445.4:c.61G>A	p.Val21Ile	p.V21I	ENST00000361445	NM_004958.3	21	Gtc/Atc	2/58	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.31	2		736	789	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256126	16256126	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	65	663	0	ENST00000375759.3:c.3395del	p.Asn1132ThrfsTer22	p.N1132Tfs*22	ENST00000375759	NM_015001.2	1131	Aaa/aa	11/15	1	2	FACETS	0.582	0.504	0.667	0.582	0.504	0.667	SUBCLONAL	1	TRUE	1	0.31	2		663	720	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263869	16263869	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	90	724	0	ENST00000375759.3:c.10238C>A	p.Pro3413His	p.P3413H	ENST00000375759	NM_015001.2	3413	cCt/cAt	12/15	1	2	FACETS	0.796	0.707	0.893	0.796	0.707	0.893	SUBCLONAL	1	TRUE	1	0.31	2		724	729	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023390	27023390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	75	436	0	ENST00000324856.7:c.496G>A	p.Ala166Thr	p.A166T	ENST00000324856	NM_006015.4	166	Gcc/Acc	1/20	1	2	FACETS	0.987	0.868	1	0.987	0.868	1	CLONAL	1	TRUE	1	0.31	2		436	490	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088687	27088687	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	70	825	1	ENST00000324856.7:c.2296C>T	p.Gln766Ter	p.Q766*	ENST00000324856	NM_006015.4	766	Cag/Tag	7/20	1	2	FACETS	0.447	0.388	0.511	0.447	0.388	0.511	SUBCLONAL	1	TRUE	1	0.31	2		826	1010	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	82	696	0	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.769	0.678	0.867	0.769	0.678	0.867	SUBCLONAL	1	TRUE	1	0.31	2		696	688	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439667	51439667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	87	538	2	ENST00000262662.1:c.232G>A	p.Ala78Thr	p.A78T	ENST00000262662		78	Gcc/Acc	4/4	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.31	2		540	510	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439824	51439825	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	56	465	0	ENST00000262662.1:c.393dup	p.His132AlafsTer5	p.H132Afs*5	ENST00000262662		130	gtg/gtGg	4/4	1	2	FACETS	0.737	0.632	0.852	0.737	0.632	0.852	SUBCLONAL	1	TRUE	1	0.31	2		465	490	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551951	150551952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs750805885	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	47	589	2	ENST00000369026.2:c.55dup	p.Ala19GlyfsTer91	p.A19Gfs*91	ENST00000369026	NM_021960.4	19	gcc/gGcc	1/3	1	2	FACETS	0.488	0.411	0.573	0.488	0.411	0.573	SUBCLONAL	1	TRUE	1	0.31	2		591	621	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834548	156834548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763164402	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	162	878	1	ENST00000524377.1:c.316G>A	p.Val106Met	p.V106M	ENST00000524377	NM_002529.3	106	Gtg/Atg	3/17	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.31	2		879	952	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156848930	156848930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	83	701	1	ENST00000524377.1:c.1822G>A	p.Ala608Thr	p.A608T	ENST00000524377	NM_002529.3	608	Gcc/Acc	15/17	1	2	FACETS	0.708	0.625	0.798	0.708	0.625	0.798	SUBCLONAL	1	TRUE	1	0.31	2		702	756	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317605	163317605	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	48	468	0	ENST00000271452.3:c.1001T>C	p.Leu334Ser	p.L334S	ENST00000271452	NM_145697.2	334	tTg/tCg	12/14	1	2	FACETS	0.786	0.666	0.917	0.786	0.666	0.917	CLONAL	1	TRUE	1	0.31	2		468	394	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015429	176015430	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	56	600	0	ENST00000367669.3:c.1308dup	p.Ala437CysfsTer10	p.A437Cfs*10	ENST00000367669	NM_022457.5	436	-/T	12/20	1	2	FACETS	0.748	0.642	0.864	0.748	0.642	0.864	SUBCLONAL	1	TRUE	1	0.31	2		600	483	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226564969	226564969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776941221	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	93	687	0	ENST00000366794.5:c.1781C>T	p.Thr594Met	p.T594M	ENST00000366794	NM_001618.3	594	aCg/aTg	13/23	1	2	FACETS	0.752	0.668	0.842	0.752	0.668	0.842	SUBCLONAL	1	TRUE	1	0.31	2		687	798	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100425	8100425	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	59	822	5	ENST00000346208.3:c.404del	p.Pro135ArgfsTer60	p.P135Rfs*60	ENST00000346208		133	taC/ta	3/6	1	2	FACETS	0.489	0.42	0.565	0.489	0.42	0.565	SUBCLONAL	1	TRUE	1	0.31	2		827	778	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63661975	63661975	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs202030299	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	41	554	0	ENST00000279873.7:c.79T>A	p.Phe27Ile	p.F27I	ENST00000279873	NM_032199.2	27	Ttc/Atc	2/10	1	2	FACETS	0.461	0.383	0.547	0.461	0.383	0.547	SUBCLONAL	1	TRUE	1	0.31	2		554	574	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450739	70450739	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	72	598	1	ENST00000373644.4:c.5579C>A	p.Ala1860Asp	p.A1860D	ENST00000373644	NM_030625.2	1860	gCt/gAt	12/12	1	2	FACETS	0.703	0.614	0.799	0.703	0.614	0.799	SUBCLONAL	1	TRUE	1	0.31	2		599	661	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692941	89692941	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	67	624	0	ENST00000371953.3:c.428del	p.Gly143AlafsTer4	p.G143Afs*4	ENST00000371953	NM_000314.4	142	cGg/cg	5/9	1	2	FACETS	0.98	0.855	1	0.98	0.855	1	CLONAL	1	TRUE	1	0.31	2		624	441	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112745490	112745490	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	31	631	0	ENST00000369452.4:c.808C>A	p.His270Asn	p.H270N	ENST00000369452	NM_007373.3	270	Cac/Aac	3/9	1	2	FACETS	0.431	0.348	0.525	0.431	0.348	0.525	SUBCLONAL	1	TRUE	1	0.31	2		631	464	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633687	69633687	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	19	111	0	ENST00000334134.2:c.15G>A	p.Trp5Ter	p.W5*	ENST00000334134	NM_005247.2	5	tgG/tgA	1/3	1	2	FACETS	0.973	0.747	1	0.973	0.747	1	CLONAL	1	TRUE	1	0.31	2		111	126	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	140	877	1	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.31	2		878	879	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363830	118363830	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	91	615	1	ENST00000534358.1:c.5067del	p.Glu1690LysfsTer20	p.E1690Kfs*20	ENST00000534358	NM_005933.3	1688	tCc/tc	16/36	1	2	FACETS	0.916	0.814	1	0.916	0.814	1	CLONAL	1	TRUE	1	0.31	2		616	641	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499653	18499653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	77	730	0	ENST00000266497.5:c.1508C>T	p.Ala503Val	p.A503V	ENST00000266497		503	gCa/gTa	10/31	NA	2	FACETS	0.764	0.671	0.865			1	INDETERMINATE	1	TRUE	NA	0.31	2		730	650	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244418	46244418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	65	606	2	ENST00000334344.6:c.2512G>A	p.Ala838Thr	p.A838T	ENST00000334344	NM_152641.2	838	Gct/Act	15/21	0.0148227650351136	3	FACETS	0.829	0.719	0.949	0.415	0.359	0.475	INDETERMINATE	1	TRUE	1	0.31	3		608	584	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418672	49418672	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	114	676	0	ENST00000301067.7:c.15842T>C	p.Leu5281Pro	p.L5281P	ENST00000301067	NM_003482.3	5281	cTg/cCg	49/54	0.0148227650351136	3	FACETS	0.973	0.875	1	0.487	0.437	0.539	INDETERMINATE	1	TRUE	1	0.31	3		676	873	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434082	49434082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745796849	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	73	634	0	ENST00000301067.7:c.7471G>A	p.Ala2491Thr	p.A2491T	ENST00000301067	NM_003482.3	2491	Gct/Act	31/54	0.0148227650351136	3	FACETS	1	0.894	1	0.511	0.448	0.58	INDETERMINATE	1	TRUE	1	0.31	3		634	532	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440207	49440207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	68	489	0	ENST00000301067.7:c.4419G>A	p.Trp1473Ter	p.W1473*	ENST00000301067	NM_003482.3	1473	tgG/tgA	16/54	0.0148227650351136	3	FACETS	0.945	0.824	1	0.473	0.412	0.539	INDETERMINATE	1	TRUE	1	0.31	3		489	536	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864957	57864957	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771559868	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	82	698	0	ENST00000228682.2:c.2434G>A	p.Val812Met	p.V812M	ENST00000228682	NM_005269.2	812	Gtg/Atg	12/12	0.0148227650351136	3	FACETS	0.79	0.696	0.892	0.395	0.348	0.446	INDETERMINATE	1	TRUE	1	0.31	3		698	773	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856284	111856284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	15	75	1	ENST00000341259.2:c.335C>T	p.Ala112Val	p.A112V	ENST00000341259	NM_005475.2	112	gCc/gTc	2/8	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.31	2		76	69	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112379	115112379	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758811184	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	52	525	0	ENST00000257566.3:c.1361G>A	p.Arg454His	p.R454H	ENST00000257566	NM_016569.3	454	cGc/cAc	7/8	1	2	FACETS	0.679	0.579	0.789	0.679	0.579	0.789	SUBCLONAL	1	TRUE	1	0.31	2		525	494	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563430	21563430	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	75	868	0	ENST00000382592.4:c.489G>A	p.Met163Ile	p.M163I	ENST00000382592	NM_014572.2	163	atG/atA	4/8	1	2	FACETS	0.519	0.454	0.59	0.519	0.454	0.59	SUBCLONAL	1	TRUE	1	0.31	2		868	932	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975607	26975607	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	45	359	0	ENST00000381527.3:c.1115A>G	p.Asn372Ser	p.N372S	ENST00000381527	NM_001260.1	372	aAc/aGc	12/13	1	2	FACETS	0.928	0.783	1	0.928	0.783	1	CLONAL	1	TRUE	1	0.31	2		359	313	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964011	28964011	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	47	493	0	ENST00000282397.4:c.1891T>C	p.Ser631Pro	p.S631P	ENST00000282397	NM_002019.4	631	Tca/Cca	13/30	1	2	FACETS	0.804	0.681	0.94	0.804	0.681	0.94	CLONAL	1	TRUE	1	0.31	2		493	377	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912222	32912222	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786202091	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	66	718	0	ENST00000380152.3:c.3730A>G	p.Ile1244Val	p.I1244V	ENST00000380152		1244	Att/Gtt	11/27	1	2	FACETS	0.738	0.641	0.843	0.738	0.641	0.843	SUBCLONAL	1	TRUE	1	0.31	2		718	577	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574680	95574680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749834289	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	39	477	0	ENST00000393063.1:c.2417C>T	p.Thr806Met	p.T806M	ENST00000393063	NM_030621.3	806	aCg/aTg	16/28	1	2	FACETS	0.612	0.508	0.728	0.612	0.508	0.728	SUBCLONAL	1	TRUE	1	0.31	2		477	411	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000375	42000375	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	47	502	0	ENST00000219905.7:c.2394A>T	p.Lys798Asn	p.K798N	ENST00000219905	NM_001164273.1	798	aaA/aaT	7/24	1	2	FACETS	0.636	0.537	0.745	0.636	0.537	0.745	SUBCLONAL	1	TRUE	1	0.31	2		502	477	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054012	42054012	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1411818407	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	57	438	0	ENST00000219905.7:c.7474C>T	p.Arg2492Trp	p.R2492W	ENST00000219905	NM_001164273.1	2492	Cgg/Tgg	21/24	1	2	FACETS	0.906	0.78	1	0.906	0.78	1	CLONAL	1	TRUE	1	0.31	2		438	406	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636891	2636891	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	43	729	1	ENST00000342085.4:c.1340C>A	p.Pro447His	p.P447H	ENST00000342085	NM_002613.4	447	cCt/cAt	11/14	1	2	FACETS	0.344	0.287	0.408	0.344	0.287	0.408	SUBCLONAL	1	TRUE	1	0.31	2		730	806	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647657	3647657	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs774532876	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	106	879	2	ENST00000294008.3:c.1406del	p.Pro469HisfsTer4	p.P469Hfs*4	ENST00000294008	NM_032444.2	469	cCa/ca	7/15	1	2	FACETS	0.673	0.602	0.749	0.673	0.602	0.749	SUBCLONAL	1	TRUE	1	0.31	2		881	1016	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779565	3779565	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	117	1060	0	ENST00000262367.5:c.5483A>G	p.Tyr1828Cys	p.Y1828C	ENST00000262367	NM_004380.2	1828	tAc/tGc	31/31	1	2	FACETS	0.671	0.603	0.743	0.671	0.603	0.743	SUBCLONAL	1	TRUE	1	0.31	2		1060	1125	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274173	10274173	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	70	468	1	ENST00000330684.3:c.96del	p.Ala33ArgfsTer2	p.A33Rfs*2	ENST00000330684	NM_001134407.1	32	ccC/cc	2/13	1	2	FACETS	0.997	0.872	1	0.997	0.872	1	CLONAL	1	TRUE	1	0.31	2		469	453	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274189	10274189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367543129	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	41	431	0	ENST00000330684.3:c.80C>T	p.Ala27Val	p.A27V	ENST00000330684	NM_001134407.1	27	gCg/gTg	2/13	1	2	FACETS	0.615	0.513	0.729	0.615	0.513	0.729	SUBCLONAL	1	TRUE	1	0.31	2		431	430	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134473	30134473	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	61	478	0	ENST00000263025.4:c.58del	p.Val20SerfsTer12	p.V20Sfs*12	ENST00000263025	NM_002746.2	20	Gtc/tc	1/9	1	2	FACETS	0.85	0.735	0.975	0.85	0.735	0.975	CLONAL	1	TRUE	1	0.31	2		478	463	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862157	68862157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776975632	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	136	658	1	ENST00000261769.5:c.2245C>T	p.Arg749Trp	p.R749W	ENST00000261769	NM_004360.3	749	Cgg/Tgg	14/16	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.31	2		659	875	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829371	72829371	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	104	649	0	ENST00000268489.5:c.7210T>C	p.Ser2404Pro	p.S2404P	ENST00000268489	NM_006885.3	2404	Tcc/Ccc	9/10	1	2	FACETS	0.993	0.89	1	0.993	0.89	1	CLONAL	1	TRUE	1	0.31	2		649	676	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832362	72832362	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	75	633	0	ENST00000268489.5:c.4219A>G	p.Ser1407Gly	p.S1407G	ENST00000268489	NM_006885.3	1407	Agc/Ggc	9/10	1	2	FACETS	0.793	0.695	0.898	0.793	0.695	0.898	SUBCLONAL	1	TRUE	1	0.31	2		633	610	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993366	72993366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140855443	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	110	759	2	ENST00000268489.5:c.679G>A	p.Val227Ile	p.V227I	ENST00000268489	NM_006885.3	227	Gtc/Atc	2/10	1	2	FACETS	0.858	0.771	0.951	0.858	0.771	0.951	CLONAL	1	TRUE	1	0.31	2		761	827	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993731	72993731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	41	509	1	ENST00000268489.5:c.314del	p.Pro105ArgfsTer4	p.P105Rfs*4	ENST00000268489	NM_006885.3	105	cCg/cg	2/10	1	2	FACETS	0.548	0.456	0.65	0.548	0.456	0.65	SUBCLONAL	1	TRUE	1	0.31	2		510	483	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216944	7216944	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	70	572	1	ENST00000380728.2:c.577C>T	p.Pro193Ser	p.P193S	ENST00000380728		193	Ccc/Tcc	7/11	1	2	FACETS	0.743	0.648	0.845	0.743	0.648	0.845	SUBCLONAL	1	TRUE	1	0.31	2		573	608	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217705	7217707	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs757139280	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	68	573	0	ENST00000380728.2:c.220_222del	p.Glu74del	p.E74del	ENST00000380728		74	GAG/-	4/11	1	2	FACETS	0.829	0.722	0.945	0.829	0.722	0.945	CLONAL	1	TRUE	1	0.31	2		573	529	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979987	7979987	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746723399	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	108	697	0	ENST00000319144.4:c.1350del	p.Leu451SerfsTer16	p.L451Sfs*16	ENST00000319144	NM_001139.2	450	ggG/gg	10/15	1	2	FACETS	0.905	0.812	1	0.905	0.812	1	CLONAL	1	TRUE	1	0.31	2		697	770	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961893	15961893	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs529539748	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	37	434	0	ENST00000268712.3:c.5902A>G	p.Thr1968Ala	p.T1968A	ENST00000268712	NM_006311.3	1968	Aca/Gca	38/46	1	2	FACETS	0.491	0.404	0.588	0.491	0.404	0.588	SUBCLONAL	1	TRUE	1	0.31	2		434	486	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971226	15971227	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	43	500	0	ENST00000268712.3:c.4722dup	p.His1575SerfsTer42	p.H1575Sfs*42	ENST00000268712	NM_006311.3	1574	-/T	32/46	1	2	FACETS	0.462	0.386	0.547	0.462	0.386	0.547	SUBCLONAL	1	TRUE	1	0.31	2		500	600	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	109	621	0	ENST00000356175.3:c.2032_2033dup	p.Ile679ArgfsTer10	p.I679Rfs*10	ENST00000356175	NM_000267.3	676	acc/aCCcc	18/57	1	2	FACETS	0.928	0.833	1	0.928	0.833	1	CLONAL	1	TRUE	1	0.31	2		621	758	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618945	37618946	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	76	671	0	ENST00000447079.4:c.625dup	p.Ser209LysfsTer21	p.S209Kfs*21	ENST00000447079	NM_015083.1	207	-/A	1/14	1	2	FACETS	0.634	0.556	0.719	0.634	0.556	0.719	SUBCLONAL	1	TRUE	1	0.31	2		671	773	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646967	37646967	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	45	702	0	ENST00000447079.4:c.2089C>A	p.Pro697Thr	p.P697T	ENST00000447079	NM_015083.1	697	Cca/Aca	3/14	1	2	FACETS	0.375	0.314	0.442	0.375	0.314	0.442	SUBCLONAL	1	TRUE	1	0.31	2		702	775	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226422	41226422	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	58	829	0	ENST00000357654.3:c.4601T>C	p.Val1534Ala	p.V1534A	ENST00000357654	NM_007294.3	1534	gTg/gCg	14/23	1	2	FACETS	0.415	0.356	0.481	0.415	0.356	0.481	SUBCLONAL	1	TRUE	1	0.31	2		829	901	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740749	58740749	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs779070661	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	78	642	0	ENST00000305921.3:c.1654C>T	p.Arg552Ter	p.R552*	ENST00000305921	NM_003620.3	552	Cga/Tga	6/6	1	2	FACETS	0.794	0.698	0.897	0.794	0.698	0.897	SUBCLONAL	1	TRUE	1	0.31	2		642	634	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736949	736949	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	43	574	0	ENST00000314574.4:c.1150A>G	p.Met384Val	p.M384V	ENST00000314574	NM_005433.3	384	Atg/Gtg	10/12	1	2	FACETS	0.577	0.483	0.681	0.577	0.483	0.681	SUBCLONAL	1	TRUE	1	0.31	2		574	481	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3114952	3114952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	96	775	0	ENST00000078429.4:c.487G>A	p.Asp163Asn	p.D163N	ENST00000078429	NM_002067.2	163	Gac/Aac	4/7	1	2	FACETS	0.821	0.732	0.917	0.821	0.732	0.917	CLONAL	1	TRUE	1	0.31	2		775	754	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115052	3115052	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	134	1012	1	ENST00000078429.4:c.587T>C	p.Leu196Pro	p.L196P	ENST00000078429	NM_002067.2	196	cTg/cCg	4/7	1	2	FACETS	0.807	0.732	0.887	0.807	0.732	0.887	CLONAL	1	TRUE	1	0.31	2		1013	1071	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211661	5211661	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	95	772	0	ENST00000357368.4:c.5174A>G	p.Gln1725Arg	p.Q1725R	ENST00000357368	NM_002850.3	1725	cAa/cGa	33/38	1	2	FACETS	0.809	0.72	0.903	0.809	0.72	0.903	CLONAL	1	TRUE	1	0.31	2		772	758	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5225813	5225813	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs756860719	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	99	789	1	ENST00000357368.4:c.2419A>G	p.Ile807Val	p.I807V	ENST00000357368	NM_002850.3	807	Atc/Gtc	17/38	1	2	FACETS	0.763	0.681	0.851	0.763	0.681	0.851	SUBCLONAL	1	TRUE	1	0.31	2		790	837	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602619	10602619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	127	729	1	ENST00000171111.5:c.959G>A	p.Arg320Gln	p.R320Q	ENST00000171111	NM_203500.1	320	cGg/cAg	3/6	1	2	FACETS	0.984	0.891	1	0.984	0.891	1	CLONAL	1	TRUE	1	0.31	2		730	833	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610283	10610283	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	137	831	2	ENST00000171111.5:c.427G>A	p.Ala143Thr	p.A143T	ENST00000171111	NM_203500.1	143	Gcc/Acc	2/6	1	2	FACETS	0.978	0.889	1	0.978	0.889	1	CLONAL	1	TRUE	1	0.31	2		833	904	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296359	15296359	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	104	784	1	ENST00000263388.2:c.2083C>A	p.Pro695Thr	p.P695T	ENST00000263388	NM_000435.2	695	Ccg/Acg	13/33	1	2	FACETS	0.904	0.81	1	0.904	0.81	1	CLONAL	1	TRUE	1	0.31	2		785	742	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943625	17943625	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	100	851	0	ENST00000458235.1:c.2464C>A	p.Leu822Ile	p.L822I	ENST00000458235	NM_000215.3	822	Ctc/Atc	18/24	1	2	FACETS	0.671	0.598	0.748	0.671	0.598	0.748	SUBCLONAL	1	TRUE	1	0.31	2		851	962	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953903	17953903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs973863737	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	102	710	0	ENST00000458235.1:c.499G>A	p.Val167Met	p.V167M	ENST00000458235	NM_000215.3	167	Gtg/Atg	5/24	1	2	FACETS	0.868	0.776	0.966	0.868	0.776	0.966	CLONAL	1	TRUE	1	0.31	2		710	758	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271352	18271352	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	77	757	0	ENST00000222254.8:c.394G>T	p.Val132Leu	p.V132L	ENST00000222254	NM_005027.3	132	Gtg/Ttg	3/16	1	2	FACETS	0.604	0.529	0.684	0.604	0.529	0.684	SUBCLONAL	1	TRUE	1	0.31	2		757	823	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793218	33793218	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1383328991	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	18	169	0	ENST00000498907.2:c.103del	p.Arg35GlyfsTer125	p.R35Gfs*125	ENST00000498907	NM_004364.3	35	Cgg/gg	1/1	1	2	FACETS	0.735	0.557	0.942	0.735	0.557	0.942	CLONAL	1	TRUE	1	0.31	2		169	158	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214893	36214894	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	93	797	2	ENST00000222270.7:c.3325dup	p.Arg1109ProfsTer4	p.R1109Pfs*4	ENST00000222270	NM_014727.1	1107	acc/aCcc	8/37	1	2	FACETS	0.696	0.618	0.78	0.696	0.618	0.78	SUBCLONAL	1	TRUE	1	0.31	2		799	862	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791268	42791268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	98	705	0	ENST00000575354.2:c.332del	p.Pro111HisfsTer94	p.P111Hfs*94	ENST00000575354	NM_015125.3	110	Ccc/cc	3/20	1	2	FACETS	0.945	0.844	1	0.945	0.844	1	CLONAL	1	TRUE	1	0.31	2		705	669	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796763	42796763	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	80	783	2	ENST00000575354.2:c.3221C>A	p.Pro1074His	p.P1074H	ENST00000575354	NM_015125.3	1074	cCt/cAt	14/20	1	2	FACETS	0.648	0.57	0.733	0.648	0.57	0.733	SUBCLONAL	1	TRUE	1	0.31	2		785	796	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868194	45868194	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1032384332	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	136	781	1	ENST00000391945.4:c.496C>T	p.Arg166Cys	p.R166C	ENST00000391945	NM_000400.3	166	Cgt/Tgt	7/23	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.31	2		782	759	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905324	50905324	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	114	823	2	ENST00000440232.2:c.537del	p.Arg180GlyfsTer3	p.R180Gfs*3	ENST00000440232	NM_002691.3	178	Ggg/gg	5/27	1	2	FACETS	0.832	0.748	0.921	0.832	0.748	0.921	CLONAL	1	TRUE	1	0.31	2		825	884	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082596	16082596	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	44	278	4	ENST00000281043.3:c.410G>A	p.Gly137Asp	p.G137D	ENST00000281043	NM_005378.4	137	gGc/gAc	2/3	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.31	2		282	275	SUCCESS
ALK	238	MSKCC	GRCh37	2	29448327	29448327	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	120	930	1	ENST00000389048.3:c.3172G>A	p.Val1058Met	p.V1058M	ENST00000389048	NM_004304.4	1058	Gtg/Atg	19/29	1	2	FACETS	0.854	0.77	0.942	0.854	0.77	0.942	CLONAL	1	TRUE	1	0.31	2		931	907	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474107	29474107	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	33	583	0	ENST00000389048.3:c.2068del	p.Ala690ProfsTer21	p.A690Pfs*21	ENST00000389048	NM_004304.4	690	Gcc/cc	12/29	1	2	FACETS	0.363	0.294	0.44	0.363	0.294	0.44	SUBCLONAL	1	TRUE	1	0.31	2		583	587	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143380	30143380	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	111	650	0	ENST00000389048.3:c.146T>C	p.Leu49Pro	p.L49P	ENST00000389048	NM_004304.4	49	cTg/cCg	1/29	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.31	2		650	640	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	85	633	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.681	0.601	0.767	0.681	0.601	0.767	SUBCLONAL	1	TRUE	1	0.31	2		635	805	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660639	190660639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772181508	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	39	489	1	ENST00000441310.2:c.277C>T	p.Arg93Cys	p.R93C	ENST00000441310	NM_000534.4	93	Cgt/Tgt	3/13	1	2	FACETS	0.584	0.484	0.695	0.584	0.484	0.695	SUBCLONAL	1	TRUE	1	0.31	2		490	431	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150022	202150022	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	110	670	0	ENST00000358485.4:c.1463T>C	p.Leu488Pro	p.L488P	ENST00000358485	NM_001080125.1	488	cTg/cCg	8/9	1	2	FACETS	0.85	0.763	0.942	0.85	0.763	0.942	CLONAL	1	TRUE	1	0.31	2		670	835	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662610	227662610	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	81	561	0	ENST00000305123.5:c.845T>C	p.Val282Ala	p.V282A	ENST00000305123	NM_005544.2	282	gTc/gCc	1/2	1	2	FACETS	0.933	0.824	1	0.933	0.824	1	CLONAL	1	TRUE	1	0.31	2		561	560	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663421	227663421	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	18	411	0	ENST00000305123.5:c.34G>A	p.Asp12Asn	p.D12N	ENST00000305123	NM_005544.2	12	Gac/Aac	1/2	1	2	FACETS	0.334	0.251	0.432	0.334	0.251	0.432	SUBCLONAL	1	TRUE	1	0.31	2		411	348	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017772	31017772	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	61	667	0	ENST00000375687.4:c.634C>A	p.Leu212Met	p.L212M	ENST00000375687	NM_015338.5	212	Ctg/Atg	8/13	1	2	FACETS	0.661	0.57	0.76	0.661	0.57	0.76	SUBCLONAL	1	TRUE	1	0.31	2		667	595	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019280	31019280	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	75	570	0	ENST00000375687.4:c.875A>T	p.Asp292Val	p.D292V	ENST00000375687	NM_015338.5	292	gAc/gTc	9/13	1	2	FACETS	0.77	0.675	0.873	0.77	0.675	0.873	SUBCLONAL	1	TRUE	1	0.31	2		570	628	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39751924	39751924	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1466190769	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	61	528	0	ENST00000361337.2:c.2285A>T	p.Asp762Val	p.D762V	ENST00000361337	NM_003286.2	762	gAc/gTc	21/21	1	2	FACETS	0.719	0.621	0.826	0.719	0.621	0.826	SUBCLONAL	1	TRUE	1	0.31	2		528	547	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484429	57484429	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	102	512	0	ENST00000371085.3:c.610A>G	p.Thr204Ala	p.T204A	ENST00000371085	NM_000516.4	204	Act/Gct	8/13	1	2	FACETS	0.994	0.89	1	0.994	0.89	1	CLONAL	1	TRUE	1	0.31	2		512	662	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62297392	62297392	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	70	544	0	ENST00000360203.5:c.574C>A	p.Leu192Met	p.L192M	ENST00000360203	NM_001283009.1	192	Ctg/Atg	7/35	1	2	FACETS	0.696	0.606	0.792	0.696	0.606	0.792	SUBCLONAL	1	TRUE	1	0.31	2		544	649	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326204	62326204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780364760	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	87	680	0	ENST00000360203.5:c.3220G>A	p.Ala1074Thr	p.A1074T	ENST00000360203	NM_001283009.1	1074	Gcg/Acg	32/35	1	2	FACETS	0.89	0.788	0.998	0.89	0.788	0.998	CLONAL	1	TRUE	1	0.31	2		680	631	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573017	41573017	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	118	819	0	ENST00000263253.7:c.5302A>G	p.Thr1768Ala	p.T1768A	ENST00000263253	NM_001429.3	1768	Acc/Gcc	31/31	1	2	FACETS	0.87	0.784	0.961	0.87	0.784	0.961	CLONAL	1	TRUE	1	0.31	2		819	875	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627233	12627233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs941573221	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	81	643	2	ENST00000251849.4:c.1483C>T	p.Arg495Cys	p.R495C	ENST00000251849	NM_002880.3	495	Cgc/Tgc	14/17	0.295587846532658	2	FACETS	0.76	0.669	0.857	0.38	0.334	0.429	SUBCLONAL	1	TRUE	0	0.31	2		645	688	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035155	37035155	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs267607709	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	133	352	1	ENST00000231790.2:c.116+1G>A		p.X39_splice	ENST00000231790	NM_000249.3	39			0.295587846532658	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	2	TRUE	0	0.31	2		353	427	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067498	37067498	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	74	631	0	ENST00000231790.2:c.1409G>T	p.Arg470Ile	p.R470I	ENST00000231790	NM_000249.3	470	aGa/aTa	12/19	0.295587846532658	2	FACETS	0.792	0.693	0.897	0.396	0.346	0.449	SUBCLONAL	1	TRUE	0	0.31	2		631	603	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927494	49927494	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	75	570	1	ENST00000296474.3:c.3811-1G>T		p.X1271_splice	ENST00000296474	NM_002447.2	1271			1	2	FACETS	0.766	0.671	0.867	0.766	0.671	0.867	SUBCLONAL	1	TRUE	1	0.31	2		571	632	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643654	52643654	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	55	590	0	ENST00000394830.3:c.2242G>A	p.Asp748Asn	p.D748N	ENST00000394830	NM_018313.4	748	Gat/Aat	17/30	1	2	FACETS	0.612	0.523	0.709	0.612	0.523	0.709	SUBCLONAL	1	TRUE	1	0.31	2		590	580	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682400	52682400	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	73	594	0	ENST00000394830.3:c.773del	p.Asn258MetfsTer25	p.N258Mfs*25	ENST00000394830	NM_018313.4	258	aAt/at	8/30	1	2	FACETS	0.823	0.721	0.934	0.823	0.721	0.934	CLONAL	1	TRUE	1	0.31	2		594	572	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70005612	70005614	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs1553704814	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	51	552	0	ENST00000394351.3:c.649_651del	p.Arg217del	p.R217del	ENST00000394351	NM_000248.3	214	cGAAga/cga	7/9	1	2	FACETS	0.835	0.712	0.97	0.835	0.712	0.97	CLONAL	1	TRUE	1	0.31	2		552	394	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014000	70014000	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	rs137904015	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	24	380	0	ENST00000394351.3:c.861A>T	p.Glu287Asp	p.E287D	ENST00000394351	NM_000248.3	287	gaA/gaT	9/9	1	2	FACETS	0.363	0.284	0.454	0.363	0.284	0.454	SUBCLONAL	1	TRUE	1	0.31	2		380	427	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204842	128204842	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs768767517	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	111	851	4	ENST00000341105.2:c.599del	p.Gly200ValfsTer18	p.G200Vfs*18	ENST00000341105	NM_032638.4	200	gGt/gt	3/6	1	2	FACETS	0.813	0.73	0.901	0.813	0.73	0.901	CLONAL	1	TRUE	1	0.31	2		855	881	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205777	128205777	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	107	689	0	ENST00000341105.2:c.98A>G	p.Tyr33Cys	p.Y33C	ENST00000341105	NM_032638.4	33	tAc/tGc	2/6	1	2	FACETS	0.968	0.869	1	0.968	0.869	1	CLONAL	1	TRUE	1	0.31	2		689	713	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185169118	185169118	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	43	624	0	ENST00000265026.3:c.1213A>G	p.Met405Val	p.M405V	ENST00000265026	NM_004721.4	405	Atg/Gtg	7/14	1	2	FACETS	0.371	0.309	0.44	0.371	0.309	0.44	SUBCLONAL	1	TRUE	1	0.31	2		624	748	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586486	189586486	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	38	514	0	ENST00000264731.3:c.1110C>G	p.Asn370Lys	p.N370K	ENST00000264731	NM_003722.4	370	aaC/aaG	8/14	1	2	FACETS	0.427	0.352	0.511	0.427	0.352	0.511	SUBCLONAL	1	TRUE	1	0.31	2		514	574	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808898	1808898	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1416045205	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	81	810	0	ENST00000260795.2:c.2334del	p.Ser779AlafsTer41	p.S779Afs*41	ENST00000260795		777	aCc/ac	17/17	1	2	FACETS	0.65	0.572	0.734	0.65	0.572	0.734	SUBCLONAL	1	TRUE	1	0.31	2		810	804	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808979	1808979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751115449	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	59	471	0	ENST00000260795.2:c.2411C>T	p.Ser804Leu	p.S804L	ENST00000260795		804	tCg/tTg	17/17	1	2	FACETS	0.81	0.698	0.931	0.81	0.698	0.931	CLONAL	1	TRUE	1	0.31	2		471	470	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747855	41747855	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	92	555	0	ENST00000226382.2:c.914A>G	p.Lys305Arg	p.K305R	ENST00000226382	NM_003924.3	305	aAa/aGa	3/3	1	2	FACETS	0.922	0.82	1	0.922	0.82	1	CLONAL	1	TRUE	1	0.31	2		555	644	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141077	55141077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	34	560	0	ENST00000257290.5:c.1723G>A	p.Val575Met	p.V575M	ENST00000257290	NM_006206.4	575	Gtg/Atg	12/23	1	2	FACETS	0.449	0.367	0.543	0.449	0.367	0.543	SUBCLONAL	1	TRUE	1	0.31	2		560	488	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156649	55156649	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	77	629	0	ENST00000257290.5:c.3050G>A	p.Gly1017Asp	p.G1017D	ENST00000257290	NM_006206.4	1017	gGc/gAc	22/23	1	2	FACETS	0.765	0.672	0.866	0.765	0.672	0.866	SUBCLONAL	1	TRUE	1	0.31	2		629	649	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955920	55955920	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	69	689	0	ENST00000263923.4:c.3242T>C	p.Val1081Ala	p.V1081A	ENST00000263923	NM_002253.2	1081	gTg/gCg	24/30	1	2	FACETS	0.795	0.693	0.905	0.795	0.693	0.905	CLONAL	1	TRUE	1	0.31	2		689	560	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467389	66467389	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	48	253	0	ENST00000273854.3:c.880G>A	p.Gly294Arg	p.G294R	ENST00000273854	NM_004439.5	294	Gga/Aga	3/18	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.31	2		253	306	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535352	66535352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368790458	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	124	616	3	ENST00000273854.3:c.109C>T	p.Arg37Trp	p.R37W	ENST00000273854	NM_004439.5	37	Cgg/Tgg	1/18	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.31	2		619	701	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391545	84391545	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	60	542	1	ENST00000321945.7:c.287T>C	p.Val96Ala	p.V96A	ENST00000321945	NM_139076.2	96	gTg/gCg	5/9	1	2	FACETS	0.858	0.741	0.985	0.858	0.741	0.985	CLONAL	1	TRUE	1	0.31	2		543	451	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197246	106197246	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	36	358	1	ENST00000380013.4:c.5579G>A	p.Gly1860Glu	p.G1860E	ENST00000380013	NM_001127208.2	1860	gGg/gAg	11/11	1	2	FACETS	0.596	0.49	0.714	0.596	0.49	0.714	SUBCLONAL	1	TRUE	1	0.31	2		359	390	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	85	648	1	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	0.725	0.641	0.816	0.725	0.641	0.816	SUBCLONAL	1	TRUE	1	0.31	2		649	756	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867541	35867541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	20	408	2	ENST00000303115.3:c.361del	p.Ile121Ter	p.I121*	ENST00000303115	NM_002185.3	119	Aaa/aa	3/8	1	2	FACETS	0.327	0.249	0.418	0.327	0.249	0.418	SUBCLONAL	1	TRUE	1	0.31	2		410	395	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672705	86672705	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	18	319	1	ENST00000274376.6:c.2192T>C	p.Leu731Pro	p.L731P	ENST00000274376	NM_002890.2	731	cTg/cCg	17/25	1	2	FACETS	0.55	0.415	0.709	0.55	0.415	0.709	SUBCLONAL	1	TRUE	1	0.31	2		320	211	SUCCESS
APC	324	MSKCC	GRCh37	5	112179480	112179480	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	56	450	0	ENST00000257430.4:c.8192del	p.Pro2731LeufsTer8	p.P2731Lfs*8	ENST00000257430	NM_000038.5	2730	gCc/gc	16/16	1	2	FACETS	0.854	0.734	0.985	0.854	0.734	0.985	CLONAL	1	TRUE	1	0.31	2		450	423	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	163	463	0	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.902	0.832	0.974	1	0.992	1	CLONAL	2	TRUE	1	0.31	2		463	583	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490629	20490629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	78	601	0	ENST00000346618.3:c.1366C>T	p.Leu456Phe	p.L456F	ENST00000346618	NM_001949.4	456	Ctc/Ttc	7/7	1	2	FACETS	0.639	0.56	0.723	0.639	0.56	0.723	SUBCLONAL	1	TRUE	1	0.31	2		601	788	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225657	26225657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202067024	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	72	609	0	ENST00000360408.1:c.275C>T	p.Ala92Val	p.A92V	ENST00000360408	NM_003532.2	92	gCg/gTg	1/1	1	2	FACETS	0.67	0.585	0.762	0.67	0.585	0.762	SUBCLONAL	1	TRUE	1	0.31	2		609	693	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908322	41908322	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	44	525	0	ENST00000372991.4:c.200T>C	p.Val67Ala	p.V67A	ENST00000372991	NM_001760.3	67	gTa/gCa	2/5	1	2	FACETS	0.475	0.397	0.561	0.475	0.397	0.561	SUBCLONAL	1	TRUE	1	0.31	2		525	598	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956636	93956636	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	68	506	0	ENST00000369303.4:c.2600A>G	p.Gln867Arg	p.Q867R	ENST00000369303	NM_004440.3	867	cAg/cGg	15/17	1	2	FACETS	0.745	0.648	0.849	0.745	0.648	0.849	SUBCLONAL	1	TRUE	1	0.31	2		506	589	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109319826	109319826	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	65	670	0	ENST00000436639.2:c.862G>T	p.Gly288Cys	p.G288C	ENST00000436639	NM_014454.2	288	Ggt/Tgt	5/10	1	2	FACETS	0.702	0.609	0.804	0.702	0.609	0.804	SUBCLONAL	1	TRUE	1	0.31	2		670	597	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983042	111983042	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	75	735	2	ENST00000368678.4:c.1505del	p.Lys502ArgfsTer53	p.K502Rfs*53	ENST00000368678		502	aAg/ag	13/13	1	2	FACETS	0.616	0.539	0.7	0.616	0.539	0.7	SUBCLONAL	1	TRUE	1	0.31	2		737	785	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020801	112020801	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	97	559	0	ENST00000368678.4:c.770C>T	p.Ala257Val	p.A257V	ENST00000368678		257	gCt/gTt	8/13	1	2	FACETS	0.873	0.778	0.973	0.873	0.778	0.973	CLONAL	1	TRUE	1	0.31	2		559	717	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662735	117662735	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	22	467	0	ENST00000368508.3:c.4730C>A	p.Ser1577Tyr	p.S1577Y	ENST00000368508	NM_002944.2	1577	tCt/tAt	29/43	1	2	FACETS	0.393	0.304	0.497	0.393	0.304	0.497	SUBCLONAL	1	TRUE	1	0.31	2		467	361	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681102	117681102	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	58	694	0	ENST00000368508.3:c.3518A>G	p.Gln1173Arg	p.Q1173R	ENST00000368508	NM_002944.2	1173	cAa/cGa	23/43	1	2	FACETS	0.616	0.529	0.712	0.616	0.529	0.712	SUBCLONAL	1	TRUE	1	0.31	2		694	607	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527886	157527886	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	73	526	0	ENST00000346085.5:c.5614del	p.Ser1872AlafsTer3	p.S1872Afs*3	ENST00000346085	NM_020732.3	1871	Aaa/aa	20/20	1	2	FACETS	0.737	0.645	0.837	0.737	0.645	0.837	SUBCLONAL	1	TRUE	1	0.31	2		526	639	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978455	2978455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747972220	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	102	712	0	ENST00000396946.4:c.875G>A	p.Arg292His	p.R292H	ENST00000396946	NM_032415.4	292	cGc/cAc	7/25	1	2	FACETS	0.803	0.718	0.894	0.803	0.718	0.894	CLONAL	1	TRUE	1	0.31	2		712	819	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984030	2984030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778144020	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	80	653	1	ENST00000396946.4:c.500C>T	p.Thr167Met	p.T167M	ENST00000396946	NM_032415.4	167	aCg/aTg	5/25	1	2	FACETS	0.736	0.648	0.831	0.736	0.648	0.831	SUBCLONAL	1	TRUE	1	0.31	2		654	701	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92247469	92247469	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	64	437	0	ENST00000265734.4:c.751A>G	p.Arg251Gly	p.R251G	ENST00000265734	NM_001259.6	251	Agg/Ggg	7/8	1	2	FACETS	0.806	0.699	0.922	0.806	0.699	0.922	CLONAL	1	TRUE	1	0.31	2		437	512	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148507423	148507423	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	54	584	0	ENST00000320356.2:c.2029+2T>C		p.X677_splice	ENST00000320356	NM_004456.4	677			1	2	FACETS	0.539	0.46	0.626	0.539	0.46	0.626	SUBCLONAL	1	TRUE	1	0.31	2		584	646	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845559	151845559	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	93	753	0	ENST00000262189.6:c.13453T>C	p.Phe4485Leu	p.F4485L	ENST00000262189	NM_170606.2	4485	Ttc/Ctc	52/59	1	2	FACETS	0.766	0.681	0.857	0.766	0.681	0.857	SUBCLONAL	1	TRUE	1	0.31	2		753	783	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874029	151874030	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	79	651	0	ENST00000262189.6:c.8508dup	p.Cys2837MetfsTer2	p.C2837Mfs*2	ENST00000262189	NM_170606.2	2836	-/A	38/59	1	2	FACETS	0.823	0.725	0.929	0.823	0.725	0.929	CLONAL	1	TRUE	1	0.31	2		651	619	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012386	152012386	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	44	457	1	ENST00000262189.6:c.427del	p.Ser143ValfsTer3	p.S143Vfs*3	ENST00000262189	NM_170606.2	143	Agt/gt	4/59	1	2	FACETS	0.8	0.673	0.939	0.8	0.673	0.939	CLONAL	1	TRUE	1	0.31	2		458	355	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752846	128752846	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	71	362	0	ENST00000377970.2:c.1007C>T	p.Ala336Val	p.A336V	ENST00000377970	NM_002467.4	336	gCt/gTt	3/3	1	2	FACETS	0.935	0.818	1	0.935	0.818	1	CLONAL	1	TRUE	1	0.31	2		362	490	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050803	5050803	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs935518281	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	44	635	0	ENST00000381652.3:c.586A>G	p.Thr196Ala	p.T196A	ENST00000381652	NM_004972.3	196	Acc/Gcc	6/25	1	2	FACETS	0.507	0.425	0.598	0.507	0.425	0.598	SUBCLONAL	1	TRUE	1	0.31	2		635	560	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485313	8485313	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	44	519	0	ENST00000356435.5:c.3067A>G	p.Asn1023Asp	p.N1023D	ENST00000356435		1023	Aat/Gat	18/35	1	2	FACETS	0.662	0.555	0.779	0.662	0.555	0.779	SUBCLONAL	1	TRUE	1	0.31	2		519	429	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528722	8528722	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	39	516	0	ENST00000356435.5:c.410T>A	p.Val137Asp	p.V137D	ENST00000356435		137	gTt/gAt	4/35	1	2	FACETS	0.455	0.376	0.543	0.455	0.376	0.543	SUBCLONAL	1	TRUE	1	0.31	2		516	553	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27173219	27173219	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	70	555	0	ENST00000380036.4:c.761-1G>A		p.X254_splice	ENST00000380036	NM_000459.3	254			1	2	FACETS	0.698	0.608	0.795	0.698	0.608	0.795	SUBCLONAL	1	TRUE	1	0.31	2		555	647	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570231	87570231	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	40	422	1	ENST00000277120.3:c.1971G>T	p.Glu657Asp	p.E657D	ENST00000277120		657	gaG/gaT	17/19	1	2	FACETS	0.642	0.534	0.762	0.642	0.534	0.762	SUBCLONAL	1	TRUE	1	0.31	2		423	402	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	57	532	1	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.761	0.654	0.878	0.761	0.654	0.878	SUBCLONAL	1	TRUE	1	0.31	2		533	483	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98222067	98222067	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	64	425	0	ENST00000331920.6:c.2704-2A>G		p.X902_splice	ENST00000331920	NM_000264.3	902			1	2	FACETS	0.884	0.767	1	0.884	0.767	1	CLONAL	1	TRUE	1	0.31	2		425	467	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250305	110250305	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751611404	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	41	793	2	ENST00000374672.4:c.370G>A	p.Val124Met	p.V124M	ENST00000374672	NM_004235.4	124	Gtg/Atg	3/5	1	2	FACETS	0.326	0.271	0.388	0.326	0.271	0.388	SUBCLONAL	1	TRUE	1	0.31	2		795	811	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760451	133760451	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	67	661	0	ENST00000318560.5:c.2774A>T	p.Glu925Val	p.E925V	ENST00000318560	NM_005157.4	925	gAg/gTg	11/11	1	2	FACETS	0.749	0.651	0.855	0.749	0.651	0.855	SUBCLONAL	1	TRUE	1	0.31	2		661	577	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135777004	135777004	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	70	659	0	ENST00000298552.3:c.2474A>G	p.Glu825Gly	p.E825G	ENST00000298552	NM_001162426.1	825	gAg/gGg	19/23	1	2	FACETS	0.687	0.599	0.783	0.687	0.599	0.783	SUBCLONAL	1	TRUE	1	0.31	2		659	657	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404251	139404251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781201059	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	109	704	0	ENST00000277541.6:c.2903C>T	p.Thr968Met	p.T968M	ENST00000277541	NM_017617.3	968	aCg/aTg	18/34	1	2	FACETS	0.881	0.791	0.977	0.881	0.791	0.977	CLONAL	1	TRUE	1	0.31	2		704	798	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405660	139405660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	154	859	0	ENST00000277541.6:c.2531G>A	p.Cys844Tyr	p.C844Y	ENST00000277541	NM_017617.3	844	tGc/tAc	16/34	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.31	2		859	936	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921435	39921435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	89	551	0	ENST00000378444.4:c.4385C>T	p.Ala1462Val	p.A1462V	ENST00000378444	NM_001123385.1	1462	gCt/gTt	10/15	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.31	2		551	572	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937723	44937723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	34	625	0	ENST00000377967.4:c.2911C>T	p.Arg971Cys	p.R971C	ENST00000377967	NM_021140.2	971	Cgt/Tgt	19/29	1	2	FACETS	0.393	0.32	0.475	0.393	0.32	0.475	SUBCLONAL	1	TRUE	1	0.31	2		625	558	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224537	53224537	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	144	787	3	ENST00000375401.3:c.3176G>A	p.Arg1059Gln	p.R1059Q	ENST00000375401	NM_004187.3	1059	cGg/cAg	21/26	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.31	2		790	849	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411929	63411929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750083174	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	110	873	2	ENST00000330258.3:c.1238C>T	p.Ala413Val	p.A413V	ENST00000330258	NM_152424.3	413	gCc/gTc	2/2	1	2	FACETS	0.835	0.75	0.925	0.835	0.75	0.925	CLONAL	1	TRUE	1	0.31	2		875	850	SUCCESS
AR	367	MSKCC	GRCh37	X	66765666	66765667	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	53	858	0	ENST00000374690.3:c.683dup	p.Thr229HisfsTer6	p.T229Hfs*6	ENST00000374690	NM_000044.3	226	-/G	1/8	1	2	FACETS	0.387	0.329	0.451	0.387	0.329	0.451	SUBCLONAL	1	TRUE	1	0.31	2		858	883	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340820	70340820	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	52	541	1	ENST00000374080.3:c.554-1G>A		p.X185_splice	ENST00000374080		185			1	2	FACETS	0.628	0.535	0.731	0.628	0.535	0.731	SUBCLONAL	1	TRUE	1	0.31	2		542	534	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346287	70346287	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	46	921	0	ENST00000374080.3:c.2638A>G	p.Met880Val	p.M880V	ENST00000374080		880	Atg/Gtg	19/45	1	2	FACETS	0.346	0.29	0.408	0.346	0.29	0.408	SUBCLONAL	1	TRUE	1	0.31	2		921	858	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875957	76875958	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	52	689	0	ENST00000373344.5:c.5177dup	p.Asn1726LysfsTer2	p.N1726Kfs*2	ENST00000373344	NM_000489.3	1726	aat/aaAt	20/35	1	2	FACETS	0.596	0.507	0.693	0.596	0.507	0.693	SUBCLONAL	1	TRUE	1	0.31	2		689	563	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937744	76937745	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	57	733	0	ENST00000373344.5:c.3003dup	p.Val1002SerfsTer3	p.V1002Sfs*3	ENST00000373344	NM_000489.3	1001	-/A	9/35	1	2	FACETS	0.62	0.532	0.717	0.62	0.532	0.717	SUBCLONAL	1	TRUE	1	0.31	2		733	593	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938215	76938215	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	68	762	0	ENST00000373344.5:c.2533A>G	p.Lys845Glu	p.K845E	ENST00000373344	NM_000489.3	845	Aaa/Gaa	9/35	1	2	FACETS	0.652	0.567	0.744	0.652	0.567	0.744	SUBCLONAL	1	TRUE	1	0.31	2		762	673	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245524	153245524	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	187	464	0	ENST00000281708.4:c.1667G>A	p.Ser556Asn	p.S556N	ENST00000281708	NM_033632.3	556	aGt/aAt	11/12	0.439965734577351	2	FACETS	0.771	0.719	0.823	0.771	0.719	0.823	SUBCLONAL	2	TRUE	0	0.525304988320459	2		464	462	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054362	42054363	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0024792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	223	446	0	ENST00000219905.7:c.7549_7550del	p.Ile2517LeufsTer20	p.I2517Lfs*20	ENST00000219905	NM_001164273.1	2516	TAt/t	22/24	0.439965734577351	2	FACETS	0.839	0.789	0.889	0.839	0.789	0.889	CLONAL	2	TRUE	0	0.525304988320459	2		446	506	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176715900	176715900	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	189	663	2	ENST00000439151.2:c.6232A>T	p.Ser2078Cys	p.S2078C	ENST00000439151	NM_022455.4	2078	Agt/Tgt	21/23	0.413517564948634	3	FACETS	0.866	0.8	0.935	0.433	0.4	0.468	CLONAL	1	TRUE	1	0.525304988320459	3		665	1049	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30668270	30668270	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	96	488	0	ENST00000376406.3:c.6242T>C	p.Leu2081Pro	p.L2081P	ENST00000376406	NM_014641.2	2081	cTc/cCc	15/15	0.413517564948634	3	FACETS	0.742	0.662	0.827	0.371	0.331	0.414	SUBCLONAL	1	TRUE	1	0.525304988320459	3		488	622	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190826	11190826	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	151	381	0	ENST00000361445.4:c.5373T>A	p.His1791Gln	p.H1791Q	ENST00000361445	NM_004958.3	1791	caT/caA	39/58	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.710878084348095	2		381	413	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115269680	115269682	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	novel	NA	P-0024893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	88	546	0	ENST00000438362.2:c.1524_1526del	p.Asp509del	p.D509del	ENST00000438362	NM_001242891.1	508	gaTGAc/gac	13/20	1	2	FACETS	0.675	0.602	0.751	0.675	0.602	0.751	SUBCLONAL	1	TRUE	1	0.710878084348095	2		546	367	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	22	248	0				ENST00000310581	NM_198253.2	-/1132			0.276456158223949	1	FACETS	0.491	0.384	0.612	0.491	0.384	0.612	INDETERMINATE	1	TRUE	0	0.472004222184192	1		248	145	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971000	21971000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	104	359	0	ENST00000304494.5:c.358G>T	p.Glu120Ter	p.E120*	ENST00000304494	NM_000077.4	120	Gag/Tag	2/3	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.472004222184192	2		359	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578433	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555526101	NA	P-0025115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	158	530	0	ENST00000269305.4:c.497C>G	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	166	tCa/tGa	5/11	0.342374721234184	2	FACETS	1	0.99	1	0.749	0.693	0.806	CLONAL	1	TRUE	0	0.472004222184192	2		530	447	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023717	31023717	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764651405	NA	P-0025115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	94	420	0	ENST00000375687.4:c.3202C>T	p.Arg1068Ter	p.R1068*	ENST00000375687	NM_015338.5	1068	Cga/Tga	13/13	0.221901241887197	1	FACETS	0.684	0.612	0.76	0.684	0.612	0.76	INDETERMINATE	1	TRUE	0	0.472004222184192	1		420	445	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216782	7216782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324992597	NA	P-0025115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	78	292	0	ENST00000380728.2:c.641C>T	p.Ser214Leu	p.S214L	ENST00000380728		214	tCg/tTg	8/11	0.342374721234184	2	FACETS	0.999	0.885	1	0.499	0.442	0.559	CLONAL	1	TRUE	0	0.472004222184192	2		292	331	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235879	108235879	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139379666	NA	P-0025115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	95	384	0	ENST00000278616.4:c.8921C>T	p.Pro2974Leu	p.P2974L	ENST00000278616	NM_000051.3	2974	cCg/cTg	62/63	1	2	FACETS	0.873	0.781	0.97	0.873	0.781	0.97	CLONAL	1	TRUE	1	0.472004222184192	2		384	461	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434587	49434587	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	55	442	0	ENST00000301067.7:c.6966G>C	p.Lys2322Asn	p.K2322N	ENST00000301067	NM_003482.3	2322	aaG/aaC	31/54	1	2	FACETS	0.711	0.611	0.818	0.711	0.611	0.818	SUBCLONAL	1	TRUE	1	0.472004222184192	2		442	328	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446249	187446249	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	79	465	0	ENST00000232014.4:c.1439C>G	p.Ser480Cys	p.S480C	ENST00000232014	NM_001130845.1	480	tCt/tGt	6/10	1	2	FACETS	0.809	0.715	0.908	0.809	0.715	0.908	CLONAL	1	TRUE	1	0.472004222184192	2		465	414	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540690	187540690	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs373205385	NA	P-0025115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	113	292	0	ENST00000441802.2:c.7050C>G	p.Tyr2350Ter	p.Y2350*	ENST00000441802	NM_005245.3	2350	taC/taG	10/27	0.342374721234184	2	FACETS	0.812	0.741	0.883	0.812	0.741	0.883	CLONAL	2	TRUE	0	0.472004222184192	2		292	295	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056346	26056346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1467030162	NA	P-0025115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	114	281	0	ENST00000343677.2:c.311C>T	p.Ser104Phe	p.S104F	ENST00000343677	NM_005319.3	104	tCc/tTc	1/1	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.472004222184192	2		281	360	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056380	26056380	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs751365843	NA	P-0025115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	40	269	0	ENST00000343677.2:c.277C>G	p.Leu93Val	p.L93V	ENST00000343677	NM_005319.3	93	Ctg/Gtg	1/1	1	2	FACETS	0.525	0.437	0.621	0.525	0.437	0.621	SUBCLONAL	1	TRUE	1	0.472004222184192	2		269	323	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32191650	32191650	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0025115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	41	543	0	ENST00000375023.3:c.56C>G	p.Ser19Ter	p.S19*	ENST00000375023	NM_004557.3	19	tCa/tGa	1/30	0.221901241887197	1	FACETS	0.329	0.274	0.39	0.329	0.274	0.39	INDETERMINATE	1	TRUE	0	0.472004222184192	1		543	403	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527706	157527706	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs749183221	NA	P-0025115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	90	398	0	ENST00000346085.5:c.5431G>C	p.Glu1811Gln	p.E1811Q	ENST00000346085	NM_020732.3	1811	Gag/Cag	20/20	1	2	FACETS	0.74	0.659	0.827	0.74	0.659	0.827	SUBCLONAL	1	TRUE	1	0.472004222184192	2		398	515	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760703	133760703	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1462634813	NA	P-0025115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	86	673	0	ENST00000318560.5:c.3026G>A	p.Arg1009Gln	p.R1009Q	ENST00000318560	NM_005157.4	1009	cGa/cAa	11/11	0.221901241887197	1	FACETS	0.619	0.55	0.692	0.619	0.55	0.692	INDETERMINATE	1	TRUE	0	0.472004222184192	1		673	450	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611800	100611800	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	100	251	0	ENST00000308731.7:c.1321G>C	p.Glu441Gln	p.E441Q	ENST00000308731	NM_000061.2	441	Gaa/Caa	14/19	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.472004222184192	1		251	242	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209303	133209303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749132017	NA	P-0121525-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	282	580	0	ENST00000320574.5:c.6083G>A	p.Arg2028Lys	p.R2028K	ENST00000320574	NM_006231.2	2028	aGg/aAg	44/49	1	2	FACETS	0.856	0.81	0.902	1	0.995	1	CLONAL	2	NA	1	0.493119078862734	2		580	668	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433894	49433894	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	294	616	0	ENST00000301067.7:c.7659G>C	p.Gln2553His	p.Q2553H	ENST00000301067	NM_003482.3	2553	caG/caC	31/54	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.760978332391247	2		616	685	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0026573-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	173	264	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.399258345697413	3	FACETS	0.971	0.901	1	0.971	0.901	1	CLONAL	2	TRUE	1	0.419215332255438	3		264	514	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0026573-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	102	434	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	0.92	0.826	1	0.92	0.826	1	CLONAL	1	TRUE	1	0.419215332255438	2		434	529	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061240	38061240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026573-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	172	661	0	ENST00000250448.2:c.749C>T	p.Ser250Phe	p.S250F	ENST00000250448	NM_004496.3	250	tCc/tTc	2/2	1	2	FACETS	0.996	0.917	1	0.996	0.917	1	CLONAL	1	TRUE	1	0.419215332255438	2		661	824	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842468	68842468	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1555515232	NA	P-0026573-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	164	625	0	ENST00000261769.5:c.529C>T	p.Gln177Ter	p.Q177*	ENST00000261769	NM_004360.3	177	Cag/Tag	4/16	0.419215332255438	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.419215332255438	1		625	611	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588993	67588993	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026573-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	88	356	0	ENST00000274335.5:c.1084del	p.Thr362LeufsTer11	p.T362Lfs*11	ENST00000274335		362	Act/ct	8/15	1	2	FACETS	0.907	0.807	1	0.907	0.807	1	CLONAL	1	TRUE	1	0.419215332255438	2		356	463	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692893	89692893	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026573-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	84	479	0	ENST00000371953.3:c.377C>G	p.Ala126Gly	p.A126G	ENST00000371953	NM_000314.4	126	gCt/gGt	5/9	1	2	FACETS	0.784	0.695	0.88	0.784	0.695	0.88	SUBCLONAL	1	TRUE	1	0.419215332255438	2		479	511	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5462874	5462874	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026573-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	69	301	0	ENST00000381577.3:c.435T>A	p.Asp145Glu	p.D145E	ENST00000381577	NM_014143.3	145	gaT/gaA	4/7	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.419215332255438	2		301	326	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026876-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	292	494	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.931	0.878	0.985	0.931	0.878	0.985	CLONAL	1	TRUE	1	0.670402853469371	2		494	936	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204511930	204511930	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026876-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1664	121	293	0	ENST00000367182.3:c.530A>T	p.Asn177Ile	p.N177I	ENST00000367182	NM_001278516.1	177	aAt/aTt	8/11	0.670402853469371	9	FACETS	0.677	0.609	0.749			1	SUBCLONAL	1	TRUE	NA	0.670402853469371	9		293	1785	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115869	8115873	+	frameshift_variant	Frame_Shift_Del	DEL	CATCT	CATCT	-	novel	NA	P-0026876-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	313	545	0	ENST00000346208.3:c.1216_1220del	p.Ile406AlafsTer99	p.I406Afs*99	ENST00000346208		405	caCATCTcg/cacg	6/6	1	2	FACETS	0.935	0.883	0.987	0.935	0.883	0.987	CLONAL	1	TRUE	1	0.670402853469371	2		545	999	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492748	50492765	+	inframe_deletion	In_Frame_Del	DEL	GAATTAGAGCAAGCCCTG	GAATTAGAGCAAGCCCTG	-	novel	NA	P-0026876-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	229	524	2	ENST00000394963.4:c.1514_1531del	p.Glu505_Leu510del	p.E505_L510del	ENST00000394963	NM_003076.4	505	GAATTAGAGCAAGCCCTG/-	13/13	1	2	FACETS	0.87	0.814	0.928	0.87	0.814	0.928	CLONAL	1	TRUE	1	0.670402853469371	2		526	785	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094310	27094311	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0026876-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	133	410	1	ENST00000324856.7:c.3019_3020dup	p.Ile1008ArgfsTer32	p.I1008Rfs*32	ENST00000324856	NM_006015.4	1006	-/AA	11/20	1	2	FACETS	0.501	0.455	0.549	0.501	0.455	0.549	SUBCLONAL	1	TRUE	1	0.670402853469371	2		411	792	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112272	115112272	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs544562535	NA	P-0027208-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	74	290	0	ENST00000257566.3:c.1468G>T	p.Ala490Ser	p.A490S	ENST00000257566	NM_016569.3	490	Gcc/Tcc	7/8	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.418766219826542	2		290	336	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120776	115120776	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027208-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	189	820	0	ENST00000257566.3:c.230del	p.Pro77ArgfsTer11	p.P77Rfs*11	ENST00000257566	NM_016569.3	77	cCg/cg	1/8	1	2	FACETS	0.939	0.868	1	0.939	0.868	1	CLONAL	1	TRUE	1	0.418766219826542	2		820	961	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842595	68842595	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs771085839	NA	P-0027208-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	124	583	1	ENST00000261769.5:c.532-1G>C		p.X178_splice	ENST00000261769	NM_004360.3	178			0.418766219826542	1	FACETS	0.942	0.857	1	0.942	0.857	1	CLONAL	1	TRUE	0	0.418766219826542	1		584	497	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738340	190738340	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027208-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	21	297	0	ENST00000441310.2:c.2592A>C	p.Glu864Asp	p.E864D	ENST00000441310	NM_000534.4	864	gaA/gaC	12/13	1	2	FACETS	0.254	0.195	0.323	0.254	0.195	0.323	SUBCLONAL	1	TRUE	1	0.418766219826542	2		297	395	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0027470-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	164	442	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.776361817685104	4	FACETS	1	0.928	1	0.504	0.464	0.546	CLONAL	1	TRUE	2	0.893728627685156	4		442	689	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412905	49412905	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519951	NA	P-0027470-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	292	729	0	ENST00000418115.1:c.118G>C	p.Glu40Gln	p.E40Q	ENST00000418115	NM_001664.2	40	Gag/Cag	2/5	0.572166899386412	6	FACETS	1	0.992	1	0.444	0.417	0.472	CLONAL	1	TRUE	3	0.893728627685156	6		729	1367	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793008	33793010	+	inframe_deletion	In_Frame_Del	DEL	CGC	CGC	-	rs780345232	NA	P-0027470-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	10	88	0	ENST00000498907.2:c.311_313del	p.Gly104del	p.G104del	ENST00000498907	NM_004364.3	104	gGCGac/gac	1/1	0.692896227855883	4	FACETS	0.273	0.185	0.383			1	SUBCLONAL	1	TRUE	NA	0.893728627685156	4		88	155	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946225	81946225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1325870340	NA	P-0027470-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	56	524	0	ENST00000359376.3:c.1958G>A	p.Arg653His	p.R653H	ENST00000359376	NM_002661.3	653	cGc/cAc	19/33	0.893728627685156	3	FACETS	0.291	0.249	0.337	0.097	0.083	0.113	SUBCLONAL	1	TRUE	0	0.893728627685156	3		524	623	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351980	89351980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027470-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	1006	812	0	ENST00000301030.4:c.970G>A	p.Glu324Lys	p.E324K	ENST00000301030	NM_001256183.1	324	Gaa/Aaa	9/13	0.893728627685156	3	FACETS	0.998	0.987	1	0.998	0.987	1	CLONAL	3	TRUE	0	0.893728627685156	3		812	1088	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497530	125497530	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027470-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	158	326	0	ENST00000428830.2:c.94G>A	p.Glu32Lys	p.E32K	ENST00000428830	NM_001114121.2	32	Gaa/Aaa	3/14	0.893728627685156	4	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.893728627685156	4		326	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578512	7578532	+	inframe_deletion	In_Frame_Del	DEL	TCTTGGCCAGTTGGCAAAACA	TCTTGGCCAGTTGGCAAAACA	-	novel	NA	P-0027470-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	975	716	0	ENST00000269305.4:c.398_418del	p.Met133_Lys139del	p.M133_K139del	ENST00000269305	NM_001126112.2	133	aTGTTTTGCCAACTGGCCAAGAcc/acc	5/11	0.893728627685156	4	FACETS	0.962	0.95	0.973	0.962	0.95	0.973	CLONAL	4	TRUE	0	0.893728627685156	4		716	1074	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488681	212488681	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027470-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	216	507	0	ENST00000342788.4:c.2168T>C	p.Val723Ala	p.V723A	ENST00000342788	NM_005235.2	723	gTc/gCc	18/28	1	2	FACETS	0.944	0.886	1	0.944	0.886	1	CLONAL	1	TRUE	1	0.893728627685156	2		507	512	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530118	212530118	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027470-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	213	473	0	ENST00000342788.4:c.1801A>C	p.Asn601His	p.N601H	ENST00000342788	NM_005235.2	601	Aac/Cac	15/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.893728627685156	2		473	443	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805086	89805086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027470-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	220	537	0	ENST00000389301.3:c.4291G>A	p.Glu1431Lys	p.E1431K	ENST00000389301	NM_000135.2	1431	Gag/Aag	43/43	0.893728627685156	3	FACETS	1	0.98	1	0.372	0.347	0.396	CLONAL	1	TRUE	0	0.893728627685156	3		537	639	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728520	190728520	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027470-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	155	432	0	ENST00000441310.2:c.1908G>C	p.Lys636Asn	p.K636N	ENST00000441310	NM_000534.4	636	aaG/aaC	10/13	NA	2	FACETS	0.785	0.725	0.846			1	INDETERMINATE	1	TRUE	NA	0.893728627685156	2		432	442	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0027600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	409	357	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.368698816399604	3	FACETS	1	0.995	1	0.688	0.655	0.721	INDETERMINATE	1	TRUE	1	0.657638974050366	3		357	1201	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0027600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	527	572	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.640037330189254	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.657638974050366	1		572	1030	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406211	70406211	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	395	695	0	ENST00000373644.4:c.3725T>A	p.Ile1242Lys	p.I1242K	ENST00000373644	NM_030625.2	1242	aTa/aAa	4/12	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.657638974050366	2		695	1075	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991914	72991914	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	289	535	0	ENST00000268489.5:c.2131C>G	p.Pro711Ala	p.P711A	ENST00000268489	NM_006885.3	711	Ccc/Gcc	2/10	0.318777945605586	1	FACETS	0.701	0.662	0.742	0.701	0.662	0.742	INDETERMINATE	1	TRUE	0	0.657638974050366	1		535	841	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	321	248	0				ENST00000310581	NM_198253.2	-/1132			0.417464225171094	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.417608015457941	3		248	877	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913237	NA	P-0027605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	148	512	0	ENST00000369535.4:c.35G>T	p.Gly12Val	p.G12V	ENST00000369535	NM_002524.4	12	gGt/gTt	2/7	1	2	FACETS	0.845	0.772	0.921	0.845	0.772	0.921	CLONAL	1	TRUE	1	0.417608015457941	2		512	839	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366668	40366668	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	195	654	1	ENST00000397332.2:c.529C>A	p.Pro177Thr	p.P177T	ENST00000397332	NM_001033082.2	177	Ccg/Acg	2/3	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.417608015457941	2		655	861	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843594	3843594	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	197	618	0	ENST00000262367.5:c.1009A>G	p.Thr337Ala	p.T337A	ENST00000262367	NM_004380.2	337	Aca/Gca	4/31	1	2	FACETS	0.925	0.856	0.996	0.925	0.856	0.996	CLONAL	1	TRUE	1	0.417608015457941	2		618	1020	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969969	81969969	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	125	504	0	ENST00000359376.3:c.3038A>T	p.Asn1013Ile	p.N1013I	ENST00000359376	NM_002661.3	1013	aAt/aTt	27/33	1	2	FACETS	0.865	0.784	0.95	0.865	0.784	0.95	CLONAL	1	TRUE	1	0.417608015457941	2		504	692	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027721-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	57	697	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.266475013524032	3	FACETS	1	0.958	1	0.652	0.562	0.75	CLONAL	1	TRUE	1	0.27621814745908	3		697	360	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0027750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	95	454	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.889	0.797	0.986	0.889	0.797	0.986	CLONAL	1	TRUE	1	0.519935712303455	2		454	411	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208246	5208246	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0027750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	192	597	0	ENST00000357368.4:c.5642+2T>G		p.X1881_splice	ENST00000357368	NM_002850.3	1881			1	2	FACETS	0.807	0.747	0.87	0.807	0.747	0.87	CLONAL	1	TRUE	1	0.519935712303455	2		597	915	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161733	56161734	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	84	596	0	ENST00000399503.3:c.1233dup	p.Val412CysfsTer14	p.V412Cfs*14	ENST00000399503	NM_005921.1	410	-/T	6/20	1	2	FACETS	0.814	0.723	0.91	0.814	0.723	0.91	CLONAL	1	TRUE	1	0.519935712303455	2		596	397	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0028711-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	52	357	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.15733218536852	2	FACETS	0.942	0.803	1	0.471	0.401	0.548	CLONAL	1	FALSE	0	0.217715449220779	2		357	507	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0028711-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	25	459	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.15733218536852	2	FACETS	0.294	0.23	0.368	0.147	0.115	0.184	SUBCLONAL	1	FALSE	0	0.217715449220779	2		459	781	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577049	7577049	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028711-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	109	588	0	ENST00000269305.4:c.889del	p.His297ThrfsTer48	p.H297Tfs*48	ENST00000269305	NM_001126112.2	297	Cac/ac	8/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.217715449220779	2		588	832	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477858	140477858	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028711-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	67	455	0	ENST00000288602.6:c.1450A>G	p.Met484Val	p.M484V	ENST00000288602	NM_004333.4	484	Atg/Gtg	12/18	0.160359040004075	3	FACETS	0.943	0.818	1	0.471	0.409	0.539	CLONAL	1	FALSE	1	0.217715449220779	3		455	724	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0028838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	543	639	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.664445087274006	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.664445087274006	2		640	781	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0028838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	144	459	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	1	2	FACETS	0.667	0.61	0.726	0.667	0.61	0.726	SUBCLONAL	1	TRUE	1	0.664445087274006	2		459	650	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0028838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	127	537	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.664445087274006	2		537	382	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648243	206648243	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	100	756	0	ENST00000367120.3:c.264C>A	p.Tyr88Ter	p.Y88*	ENST00000367120	NM_014002.3	88	taC/taA	5/22	0.261626225143797	5	FACETS	0.744	0.664	0.829			1	INDETERMINATE	1	TRUE	NA	0.664445087274006	5		756	808	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103541	77103541	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1438267597	NA	P-0028838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	67	496	1	ENST00000356341.3:c.25C>T	p.Gln9Ter	p.Q9*	ENST00000356341	NM_002576.4	9	Caa/Taa	2/15	1	2	FACETS	0.465	0.405	0.529	0.465	0.405	0.529	SUBCLONAL	1	TRUE	1	0.664445087274006	2		497	434	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032237	10032237	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	103	894	0	ENST00000330684.3:c.586G>C	p.Val196Leu	p.V196L	ENST00000330684	NM_001134407.1	196	Gtg/Ctg	3/13	0.428004335640963	3	FACETS	0.565	0.506	0.628	0.188	0.168	0.21	SUBCLONAL	1	TRUE	0	0.664445087274006	3		894	731	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016164	31016164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1285138418	NA	P-0028838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	72	670	0	ENST00000375687.4:c.410C>T	p.Ser137Phe	p.S137F	ENST00000375687	NM_015338.5	137	tCt/tTt	6/13	0.664445087274006	3	FACETS	0.418	0.365	0.475	0.209	0.182	0.238	SUBCLONAL	1	TRUE	1	0.664445087274006	3		670	691	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177075	56177075	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	42	465	0	ENST00000399503.3:c.2345C>T	p.Ser782Leu	p.S782L	ENST00000399503	NM_005921.1	782	tCa/tTa	13/20	0.13181890634955	4	FACETS	0.832	0.699	0.976	0.416	0.349	0.488	INDETERMINATE	1	TRUE	2	0.664445087274006	4		465	253	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682399	52682400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	77	433	0	ENST00000394830.3:c.773dup	p.Asn258LysfsTer6	p.N258Kfs*6	ENST00000394830	NM_018313.4	258	aat/aaAt	8/30	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.26	2		433	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0028913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	93	808	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.26	2		808	639	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087503	27087503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	80	665	1	ENST00000324856.7:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000324856	NM_006015.4	693	Cga/Tga	5/20	1	2	FACETS	0.802	0.706	0.906	0.802	0.706	0.906	CLONAL	1	TRUE	1	0.26	2		666	767	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459032	120459032	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372538600	NA	P-0028913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	52	621	0	ENST00000256646.2:c.6313C>T	p.Arg2105Trp	p.R2105W	ENST00000256646	NM_024408.3	2105	Cgg/Tgg	34/34	1	2	FACETS	0.787	0.671	0.915	0.787	0.671	0.915	CLONAL	1	TRUE	1	0.26	2		621	508	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	35	427	1	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	0.146918464818299	3	FACETS	0.905	0.744	1	0.453	0.372	0.543	INDETERMINATE	1	TRUE	1	0.26	3		428	336	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0028913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	60	385	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.876	0.755	1	0.876	0.755	1	CLONAL	1	TRUE	1	0.26	2		385	527	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683192	88683192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199907158	NA	P-0028913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	43	386	0	ENST00000372037.3:c.1402G>A	p.Glu468Lys	p.E468K	ENST00000372037	NM_004329.2	468	Gaa/Aaa	12/13	1	2	FACETS	0.927	0.778	1	0.927	0.778	1	CLONAL	1	TRUE	1	0.26	2		386	357	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912664	NA	P-0028913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	78	594	0	ENST00000269305.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000269305	NM_001126112.2	337	cGc/cAc	10/11	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.26	2		594	577	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510153	187510153	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367799188	NA	P-0028913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	67	483	0	ENST00000441802.2:c.13360G>A	p.Glu4454Lys	p.E4454K	ENST00000441802	NM_005245.3	4454	Gaa/Aaa	27/27	0.0540000657333499	3	FACETS	1	0.971	1	0.724	0.632	0.823	INDETERMINATE	1	TRUE	1	0.26	3		483	402	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099103	27099103	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	43	427	0	ENST00000324856.7:c.3524del	p.Pro1175HisfsTer5	p.P1175Hfs*5	ENST00000324856	NM_006015.4	1173	atC/at	13/20	1	2	FACETS	0.759	0.635	0.895	0.759	0.635	0.895	SUBCLONAL	1	TRUE	1	0.26	2		427	436	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264985	46264985	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	47	396	0	ENST00000371998.3:c.1860del	p.Lys620AsnfsTer18	p.K620Nfs*18	ENST00000371998		619	Aaa/aa	12/23	1	2	FACETS	0.827	0.699	0.968	0.827	0.699	0.968	CLONAL	1	TRUE	1	0.26	2		396	437	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426644	47426644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755638812	NA	P-0028913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	60	287	0	ENST00000377045.4:c.889C>T	p.Arg297Trp	p.R297W	ENST00000377045	NM_001654.4	297	Cgg/Tgg	10/16	0.0717361362811921	2	FACETS	1	0.896	1			1	INDETERMINATE	2	TRUE	NA	0.26	2		287	224	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513451	149513451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754451292	NA	P-0028913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	53	513	0	ENST00000261799.4:c.752G>A	p.Arg251His	p.R251H	ENST00000261799	NM_002609.3	251	cGc/cAc	5/23	1	2	FACETS	0.89	0.76	1	0.89	0.76	1	CLONAL	1	TRUE	1	0.26	2		513	458	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0028913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	39	732	1	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	0.0990037708473006	4	FACETS	0.689	0.57	0.821	0.344	0.285	0.411	INDETERMINATE	1	TRUE	2	0.26	4		733	549	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291084	10291084	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	82	717	2	ENST00000340748.4:c.387del	p.Lys130AsnfsTer129	p.K130Nfs*129	ENST00000340748		129	ccC/cc	4/40	1	2	FACETS	0.946	0.834	1	0.946	0.834	1	CLONAL	1	TRUE	1	0.26	2		719	667	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46715684	46715684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369982284	NA	P-0028913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	67	480	1	ENST00000371975.4:c.103C>T	p.Arg35Trp	p.R35W	ENST00000371975	NM_003579.3	35	Cgg/Tgg	3/18	1	2	FACETS	0.978	0.851	1	0.978	0.851	1	CLONAL	1	TRUE	1	0.26	2		481	527	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458578	120458578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148759277	NA	P-0028913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	62	504	2	ENST00000256646.2:c.6767G>A	p.Arg2256His	p.R2256H	ENST00000256646	NM_024408.3	2256	cGc/cAc	34/34	1	2	FACETS	0.973	0.842	1	0.973	0.842	1	CLONAL	1	TRUE	1	0.26	2		506	490	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830809	156830809	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	26	206	0	ENST00000524377.1:c.83T>C	p.Leu28Pro	p.L28P	ENST00000524377	NM_002529.3	28	cTg/cCg	1/17	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.26	2		206	174	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417859	32417859	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121907904	NA	P-0028913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	48	495	0	ENST00000332351.3:c.1193G>A	p.Cys398Tyr	p.C398Y	ENST00000332351	NM_024426.4	398	tGc/tAc	7/10	1	2	FACETS	0.803	0.679	0.938	0.803	0.679	0.938	CLONAL	1	TRUE	1	0.26	2		495	460	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628408	21628408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780808359	NA	P-0028913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	83	501	0	ENST00000421138.2:c.1210C>T	p.Arg404Cys	p.R404C	ENST00000421138		404	Cgt/Tgt	11/16	0.0990037708473006	4	FACETS	1	0.963	1	0.616	0.544	0.693	INDETERMINATE	1	TRUE	2	0.26	4		501	653	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418616	49418616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	83	561	0	ENST00000301067.7:c.15898G>A	p.Ala5300Thr	p.A5300T	ENST00000301067	NM_003482.3	5300	Gcc/Acc	49/54	0.0990037708473006	4	FACETS	0.75	0.664	0.843	0.75	0.664	0.843	INDETERMINATE	2	TRUE	2	0.26	4		561	536	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117398	115117398	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	35	381	0	ENST00000257566.3:c.776A>T	p.Asp259Val	p.D259V	ENST00000257566	NM_016569.3	259	gAc/gTc	4/8	0.3	1	FACETS	0.699	0.574	0.839	0.699	0.574	0.839	SUBCLONAL	1	TRUE	0	0.26	1		381	335	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061796	38061796	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	84	602	0	ENST00000250448.2:c.193A>G	p.Asn65Asp	p.N65D	ENST00000250448	NM_004496.3	65	Aac/Gac	2/2	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.26	2		602	629	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99486218	99486218	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	59	580	0	ENST00000268035.6:c.3524C>T	p.Pro1175Leu	p.P1175L	ENST00000268035	NM_000875.3	1175	cCc/cTc	19/21	1	2	FACETS	0.855	0.736	0.984	0.855	0.736	0.984	CLONAL	1	TRUE	1	0.26	2		580	531	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124240	2124240	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1366556255	NA	P-0028913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	92	800	0	ENST00000219476.3:c.2395C>T	p.Arg799Cys	p.R799C	ENST00000219476	NM_000548.3	799	Cgc/Tgc	22/42	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.26	2		800	581	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821802	72821802	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	74	424	0	ENST00000268489.5:c.10373T>C	p.Val3458Ala	p.V3458A	ENST00000268489	NM_006885.3	3458	gTt/gCt	10/10	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.26	2		424	467	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831344	89831345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0028913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	58	525	0	ENST00000389301.3:c.2730_2731dup	p.Trp911SerfsTer11	p.W911Sfs*11	ENST00000389301	NM_000135.2	911	tgg/tCTgg	28/43	1	2	FACETS	0.775	0.665	0.894	0.775	0.665	0.894	SUBCLONAL	1	TRUE	1	0.26	2		525	576	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221752	36221752	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	83	791	0	ENST00000222270.7:c.5424del	p.Ala1809ProfsTer86	p.A1809Pfs*86	ENST00000222270	NM_014727.1	1807	agC/ag	26/37	1	2	FACETS	0.939	0.829	1	0.939	0.829	1	CLONAL	1	TRUE	1	0.26	2		791	680	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630408	47630408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	82	546	0	ENST00000233146.2:c.78G>A	p.Met26Ile	p.M26I	ENST00000233146	NM_000251.2	26	atG/atA	1/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.26	2		546	536	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872617	136872617	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	45	458	0	ENST00000241393.3:c.881A>G	p.His294Arg	p.H294R	ENST00000241393	NM_003467.2	294	cAc/cGc	2/2	0.146918464818299	3	FACETS	0.727	0.611	0.856	0.364	0.305	0.428	INDETERMINATE	1	TRUE	1	0.26	3		458	538	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794899	242794899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	60	718	1	ENST00000334409.5:c.310C>T	p.Arg104Cys	p.R104C	ENST00000334409	NM_005018.2	104	Cgt/Tgt	2/5	0.3	1	FACETS	0.739	0.637	0.85	0.739	0.637	0.85	SUBCLONAL	1	TRUE	0	0.26	1		719	543	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31464401	31464401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	114	823	2	ENST00000344624.3:c.2516C>T	p.Thr839Met	p.T839M	ENST00000344624		839	aCg/aTg	17/33	0.207601956474776	0	FACETS	0.671	0.603	0.743			1	SUBCLONAL	1	TRUE	0	0.26	0		825	967	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064742	80064742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200612739	NA	P-0028913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	58	430	0	ENST00000265081.6:c.2173G>A	p.Glu725Lys	p.E725K	ENST00000265081	NM_002439.4	725	Gag/Aag	15/24	0.146918464818299	3	FACETS	0.883	0.759	1	0.441	0.379	0.509	INDETERMINATE	1	TRUE	1	0.26	3		430	571	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468224	50468224	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	49	540	1	ENST00000331340.3:c.1459C>T	p.Arg487Cys	p.R487C	ENST00000331340	NM_006060.4	487	Cgt/Tgt	8/8	0.3	1	FACETS	0.561	0.474	0.656	0.561	0.474	0.656	SUBCLONAL	1	TRUE	0	0.26	1		541	585	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259449	55259449	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146121458	NA	P-0028913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	64	353	0	ENST00000275493.2:c.2507G>A	p.Arg836His	p.R836H	ENST00000275493	NM_005228.3	836	cGc/cAc	21/28	0.3	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.26	1		353	304	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24133941	24133941	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0028950-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	210	227	0	ENST00000263121.7:c.94-2A>T		p.X32_splice	ENST00000263121	NM_003073.3	32			0.549800773561353	2	FACETS	0.972	0.917	1	0.972	0.917	1	CLONAL	2	TRUE	0	0.549800773561353	2		227	393	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885620	23885620	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028950-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	41	372	0	ENST00000374561.5:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000374561	NM_002167.4	100	Cag/Tag	1/3	1	2	FACETS	0.275	0.228	0.326	0.275	0.228	0.326	SUBCLONAL	1	TRUE	1	0.549800773561353	2		372	543	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953246	17953255	+	frameshift_variant	Frame_Shift_Del	DEL	GGATCCAGCC	GGATCCAGCC	-	novel	NA	P-0029222-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	50	789	1	ENST00000458235.1:c.731_740del	p.Arg244GlnfsTer53	p.R244Qfs*53	ENST00000458235	NM_000215.3	244	cGGCTGGATCCa/ca	6/24	1	2	FACETS	0.371	0.314	0.435	0.371	0.314	0.435	SUBCLONAL	1	TRUE	1	0.27	2		790	997	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022914	27022942	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCCGCCGCCAGCAGCCTGGGCAACCCG	CCGCCGCCGCCAGCAGCCTGGGCAACCCG	-	novel	NA	P-0029576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	14	39	0	ENST00000324856.7:c.31_59del	p.Ser11AlafsTer90	p.S11Afs*90	ENST00000324856	NM_006015.4	7	cCCGCCGCCGCCAGCAGCCTGGGCAACCCG/c	1/20	0.470751774976024	1	FACETS	0.7	0.518	0.907	0.7	0.518	0.907	SUBCLONAL	1	TRUE	0	0.470751774976024	1		39	65	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155654	56155654	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	123	381	0	ENST00000399503.3:c.746del	p.Arg249ProfsTer14	p.R249Pfs*14	ENST00000399503	NM_005921.1	249	cGc/cc	3/20	1	2	FACETS	0.787	0.713	0.865	0.787	0.713	0.865	SUBCLONAL	1	TRUE	1	0.470751774976024	2		381	664	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0029617-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	102	639	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.213370638184155	1	FACETS	0.821	0.733	0.916	0.821	0.733	0.916	CLONAL	1	TRUE	0	0.213370638184155	1		640	1040	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323150	31323150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029617-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	111	612	0	ENST00000412585.2:c.839G>A	p.Arg280Lys	p.R280K	ENST00000412585	NM_005514.6	280	aGa/aAa	4/8	0.213370638184155	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.213370638184155	1		612	803	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0029833-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	8	454	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.502	0.323	0.736	0.502	0.323	0.736	SUBCLONAL	1	TRUE	1	0.13	2		454	245	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011150	12011150	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029833-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	18	440	0	ENST00000353533.5:c.557A>G	p.Asp186Gly	p.D186G	ENST00000353533	NM_003010.3	186	gAt/gGt	5/11	1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	1	0.13	2		440	247	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40368072	40368072	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555548678	NA	P-0029833-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	30	708	1	ENST00000293328.3:c.1433C>T	p.Ala478Val	p.A478V	ENST00000293328	NM_012448.3	478	gCg/gTg	12/19	1	2	FACETS	0.893	0.718	1	0.893	0.718	1	CLONAL	1	TRUE	1	0.13	2		709	517	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293050	91293050	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	103	672	0	ENST00000355112.3:c.552G>C	p.Gln184His	p.Q184H	ENST00000355112	NM_000057.2	184	caG/caC	3/22	1	2	FACETS	0.752	0.671	0.839	0.752	0.671	0.839	SUBCLONAL	1	TRUE	1	0.245579617684957	2		672	1115	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506669	103506669	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs188898060	NA	P-0030928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	39	410	0	ENST00000355739.4:c.412C>T	p.Arg138Ter	p.R138*	ENST00000355739	NM_000123.3	138	Cga/Tga	4/15	0.245579617684957	3	FACETS	0.515	0.426	0.616	0.258	0.213	0.308	SUBCLONAL	1	TRUE	1	0.245579617684957	3		410	692	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196791	108196791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039471	NA	P-0030928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	45	405	0	ENST00000278616.4:c.6814G>A	p.Glu2272Lys	p.E2272K	ENST00000278616	NM_000051.3	2272	Gaa/Aaa	47/63	1	2	FACETS	0.542	0.455	0.639	0.542	0.455	0.639	SUBCLONAL	1	TRUE	1	0.245579617684957	2		405	676	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983026	201983028	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	novel	NA	P-0030928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	339	855	0	ENST00000359651.3:c.876_878del	p.Met293del	p.M293del	ENST00000359651		292	cTCAtg/ctg	7/8	0.230236781575731	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.245579617684957	2		855	1366	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559777	29559777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs902739109	NA	P-0030928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	39	412	0	ENST00000356175.3:c.3374C>T	p.Ala1125Val	p.A1125V	ENST00000356175	NM_000267.3	1125	gCg/gTg	26/57	0.245579617684957	3	FACETS	0.47	0.388	0.562	0.235	0.194	0.281	SUBCLONAL	1	TRUE	1	0.245579617684957	3		412	759	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762863	40762863	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2008	525	605	0	ENST00000392038.2:c.145C>A	p.Leu49Ile	p.L49I	ENST00000392038	NM_001626.4	49	Cta/Ata	3/14	0.245579617684957	17	FACETS	0.959	0.915	1	0.32	0.305	0.335	CLONAL	5	TRUE	2	0.245579617684957	17		605	2533	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222482	39222482	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0030928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	58	791	0	ENST00000402219.2:c.3128C>G	p.Ser1043Ter	p.S1043*	ENST00000402219	NM_005633.3	1043	tCa/tGa	20/23	1	2	FACETS	0.41	0.351	0.476	0.41	0.351	0.476	SUBCLONAL	1	TRUE	1	0.245579617684957	2		791	1151	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918588	44918589	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTAGGCACTCTCTATGAAT	novel	NA	P-0030928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	94	347	0	ENST00000377967.4:c.1073_1091dup	p.Cys365ArgfsTer5	p.C365Rfs*5	ENST00000377967	NM_021140.2	357	-/CTAGGCACTCTCTATGAAT	12/29	0.245579617684957	2	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.245579617684957	2		347	571	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374741	118374741	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	267	380	0	ENST00000534358.1:c.8134T>C	p.Cys2712Arg	p.C2712R	ENST00000534358	NM_005933.3	2712	Tgt/Cgt	27/36	0.463515640277281	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.463515640277281	2		380	535	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555632	21555636	+	frameshift_variant	Frame_Shift_Del	DEL	TGTAG	TGTAG	-	novel	NA	P-0030953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	216	518	0	ENST00000382592.4:c.2634_2638del	p.Tyr879ArgfsTer15	p.Y879Rfs*15	ENST00000382592	NM_014572.2	878	aaCTACAtc/aatc	6/8	0.463515640277281	2	FACETS	0.869	0.815	0.924	0.869	0.815	0.924	CLONAL	2	TRUE	0	0.463515640277281	2		518	536	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572415	95572415	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	123	445	0	ENST00000393063.1:c.2950A>C	p.Asn984His	p.N984H	ENST00000393063	NM_030621.3	984	Aac/Cac	19/28	0.443501408685275	3	FACETS	0.937	0.848	1	0.312	0.282	0.344	CLONAL	1	TRUE	0	0.463515640277281	3		445	698	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89866048	89866048	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0030953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	137	433	0	ENST00000389301.3:c.793-2A>T		p.X265_splice	ENST00000389301	NM_000135.2	265			0.463515640277281	2	FACETS	0.922	0.841	1	0.461	0.42	0.504	CLONAL	1	TRUE	0	0.463515640277281	2		433	641	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573806	41573806	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs199650847	NA	P-0030953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	645	737	0	ENST00000263253.7:c.6091C>G	p.Pro2031Ala	p.P2031A	ENST00000263253	NM_001429.3	2031	Cca/Gca	31/31	0.463515640277281	3	FACETS	0.99	0.959	1	0.99	0.959	1	CLONAL	3	TRUE	0	0.463515640277281	3		737	1154	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0031020-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	66	308	1	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.16	2		309	773	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248525	59248525	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031020-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	42	259	0	ENST00000371222.2:c.218C>T	p.Ser73Leu	p.S73L	ENST00000371222	NM_002228.3	73	tCg/tTg	1/1	1	2	FACETS	0.856	0.714	1	0.856	0.714	1	CLONAL	1	TRUE	1	0.16	2		259	613	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626752	28626752	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031020-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	38	306	0	ENST00000241453.7:c.544C>G	p.Leu182Val	p.L182V	ENST00000241453	NM_004119.2	182	Ctg/Gtg	5/24	1	2	FACETS	0.7	0.577	0.837	0.7	0.577	0.837	SUBCLONAL	1	TRUE	1	0.16	2		306	679	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374844	149374844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031020-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	21	132	0	ENST00000360632.3:c.250C>T	p.His84Tyr	p.H84Y	ENST00000360632	NM_015472.4	84	Cat/Tat	2/7	1	2	FACETS	0.68	0.523	0.864	0.68	0.523	0.864	SUBCLONAL	1	TRUE	1	0.16	2		132	386	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884476	151884476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031020-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	42	219	1	ENST00000262189.6:c.4879G>A	p.Asp1627Asn	p.D1627N	ENST00000262189	NM_170606.2	1627	Gac/Aac	33/59	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.16	2		220	490	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0031039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	65	440	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.202317938080828	3	FACETS	1	0.901	1			1	CLONAL	1	TRUE	NA	0.24	3		440	580	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244857	46244858	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0031039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	90	535	0	ENST00000334344.6:c.2954dup	p.Thr986TyrfsTer71	p.T986Yfs*71	ENST00000334344	NM_152641.2	984	gtc/gtCc	15/21	1	2	FACETS	0.945	0.837	1	0.945	0.837	1	CLONAL	1	TRUE	1	0.24	2		535	794	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0031184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	251	745	0	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	0.411188144031737	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.411188144031737	1		745	915	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023169	27023212	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGGCCCGGCGCGGAGCCGGACCTGAAGAACTCGAACGGGAAC	GCGGGCCCGGCGCGGAGCCGGACCTGAAGAACTCGAACGGGAAC	-	novel	NA	P-0031184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	37	102	0	ENST00000324856.7:c.283_326del	p.Gly95Ter	p.G95*	ENST00000324856	NM_006015.4	92	gGCGGGCCCGGCGCGGAGCCGGACCTGAAGAACTCGAACGGGAAC/g	1/20	0.411188144031737	1	FACETS	1	0.839	1	1	0.839	1	CLONAL	1	TRUE	0	0.411188144031737	1		102	143	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099319	193099319	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	135	406	0	ENST00000367435.3:c.253G>T	p.Val85Leu	p.V85L	ENST00000367435	NM_024529.4	85	Gtg/Ttg	3/17	1	2	FACETS	0.806	0.732	0.883	0.806	0.732	0.883	CLONAL	1	TRUE	1	0.411188144031737	2		406	815	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046590	30046590	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	194	624	0	ENST00000331968.5:c.2593G>A	p.Asp865Asn	p.D865N	ENST00000331968	NM_002742.2	865	Gat/Aat	18/18	0.328788547404858	1	FACETS	0.87	0.806	0.936	0.87	0.806	0.936	CLONAL	1	TRUE	0	0.411188144031737	1		624	862	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59870961	59870961	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567824994	NA	P-0031184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	147	478	1	ENST00000259008.2:c.1470G>T	p.Leu490Phe	p.L490F	ENST00000259008	NM_032043.2	490	ttG/ttT	10/20	1	2	FACETS	0.882	0.805	0.961	0.882	0.805	0.961	CLONAL	1	TRUE	1	0.411188144031737	2		479	811	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4090687	4090687	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730880514	NA	P-0031184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	259	797	0	ENST00000262948.5:c.1112G>T	p.Arg371Leu	p.R371L	ENST00000262948	NM_030662.3	371	cGg/cTg	11/11	0.411188144031737	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.411188144031737	1		797	918	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602859	10602859	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	257	804	0	ENST00000171111.5:c.719del	p.Arg240ProfsTer37	p.R240Pfs*37	ENST00000171111	NM_203500.1	240	cGc/cc	3/6	0.411188144031737	1	FACETS	0.944	0.884	1	0.944	0.884	1	CLONAL	1	TRUE	0	0.411188144031737	1		804	1052	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736113	204736113	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	109	415	1	ENST00000302823.3:c.470G>T	p.Cys157Phe	p.C157F	ENST00000302823	NM_005214.4	157	tGc/tTc	3/4	0.328788547404858	1	FACETS	0.787	0.71	0.869	0.787	0.71	0.869	SUBCLONAL	1	TRUE	0	0.411188144031737	1		416	535	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440018	220440018	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	96	931	1	ENST00000243786.2:c.871T>C	p.Cys291Arg	p.C291R	ENST00000243786	NM_002191.3	291	Tgt/Cgt	2/2	0.328788547404858	1	FACETS	0.338	0.3	0.379	0.338	0.3	0.379	SUBCLONAL	1	TRUE	0	0.411188144031737	1		932	1097	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31390233	31390233	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1240056301	NA	P-0031184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	105	601	0	ENST00000328111.2:c.2188C>T	p.His730Tyr	p.H730Y	ENST00000328111	NM_006892.3	730	Cac/Tac	20/23	0.411188144031737	1	FACETS	0.428	0.382	0.476	0.428	0.382	0.476	SUBCLONAL	1	TRUE	0	0.411188144031737	1		601	949	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217223	66217223	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	172	553	0	ENST00000273854.3:c.2392C>A	p.His798Asn	p.H798N	ENST00000273854	NM_004439.5	798	Cat/Aat	14/18	0.411188144031737	1	FACETS	0.932	0.86	1	0.932	0.86	1	CLONAL	1	TRUE	0	0.411188144031737	1		553	713	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271278	26271278	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1268814858	NA	P-0031184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	163	574	0	ENST00000305910.3:c.335C>T	p.Ala112Val	p.A112V	ENST00000305910	NM_003534.2	112	gCc/gTc	1/1	1	2	FACETS	0.961	0.883	1	0.961	0.883	1	CLONAL	1	TRUE	1	0.411188144031737	2		574	825	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410019	63410019	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	127	621	1	ENST00000330258.3:c.3148G>T	p.Asp1050Tyr	p.D1050Y	ENST00000330258	NM_152424.3	1050	Gat/Tat	2/2	0.328788547404858	1	FACETS	0.678	0.615	0.744	0.678	0.615	0.744	SUBCLONAL	1	TRUE	0	0.411188144031737	1		622	724	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410697	63410697	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	178	756	0	ENST00000330258.3:c.2470G>A	p.Glu824Lys	p.E824K	ENST00000330258	NM_152424.3	824	Gag/Aag	2/2	0.328788547404858	1	FACETS	0.759	0.7	0.821	0.759	0.7	0.821	SUBCLONAL	1	TRUE	0	0.411188144031737	1		756	906	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433004	49433017	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CCGGCTGTTCACAT	CCGGCTGTTCACAT	-	novel	NA	P-0031315-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	97	453	0	ENST00000301067.7:c.8354_8366+1del		p.X2785_splice	ENST00000301067	NM_003482.3	2785		33/54	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		453	307	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944516	71944516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293622519	NA	P-0031523-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	155	746	0	ENST00000298229.2:c.2072G>A	p.Arg691Gln	p.R691Q	ENST00000298229	NM_001567.3	691	cGg/cAg	18/28	0.620374891099215	1	FACETS	0.438	0.401	0.476	0.438	0.401	0.476	SUBCLONAL	1	TRUE	0	0.620374891099215	1		746	787	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945018	31945018	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031523-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	474	985	0	ENST00000340398.3:c.83A>T	p.Lys28Ile	p.K28I	ENST00000340398	NM_001013699.2	28	aAa/aTa	1/1	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.620374891099215	2		985	1525	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	124	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.988	0.909	1	0.988	0.909	1	CLONAL	1	TRUE	1	0.862709023467838	2		248	291	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0031753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	286	464	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.862709023467838	1	FACETS	0.972	0.936	1	0.972	0.936	1	CLONAL	1	TRUE	0	0.862709023467838	1		465	388	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69011988	69011988	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	102	675	0	ENST00000288368.4:c.2625A>C	p.Glu875Asp	p.E875D	ENST00000288368	NM_024870.2	875	gaA/gaC	23/40	0.159284968529828	2	FACETS	1	0.978	1	0.687	0.615	0.762	CLONAL	1	TRUE	0	0.23917935160466	2		675	621	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589887	212589887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757597004	NA	P-0031955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	35	563	0	ENST00000342788.4:c.655G>A	p.Gly219Ser	p.G219S	ENST00000342788	NM_005235.2	219	Ggc/Agc	6/28	1	2	FACETS	0.468	0.383	0.565	0.468	0.383	0.565	SUBCLONAL	1	TRUE	1	0.23917935160466	2		563	625	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42057086	42057086	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	29	477	0	ENST00000219905.7:c.7747A>C	p.Asn2583His	p.N2583H	ENST00000219905	NM_001164273.1	2583	Aat/Cat	23/24	1	2	FACETS	0.59	0.473	0.723	0.59	0.473	0.723	SUBCLONAL	1	TRUE	1	0.23917935160466	2		477	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577115	7577116	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0031955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	90	718	0	ENST00000269305.4:c.822_823del	p.Ala276LeufsTer29	p.A276Lfs*29	ENST00000269305	NM_001126112.2	274	gtTTgt/gtgt	8/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.23917935160466	2		718	640	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866361	42866361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	62	754	1	ENST00000398585.3:c.271C>T	p.Pro91Ser	p.P91S	ENST00000398585	NM_001135099.1	91	Ccg/Tcg	3/14	0.23917935160466	1	FACETS	0.986	0.854	1	0.986	0.854	1	CLONAL	1	TRUE	0	0.23917935160466	1		755	463	SUCCESS
APC	324	MSKCC	GRCh37	5	112137010	112137011	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGATG	novel	NA	P-0031955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	26	446	0	ENST00000257430.4:c.765_769dup	p.Ala257ValfsTer38	p.A257Vfs*38	ENST00000257430	NM_000038.5	255	cat/caTGATGt	8/16	1	2	FACETS	0.571	0.452	0.707	0.571	0.452	0.707	SUBCLONAL	1	TRUE	1	0.23917935160466	2		446	381	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672376	30672376	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1182289271	NA	P-0031955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	38	770	0	ENST00000376406.3:c.4584A>C	p.Glu1528Asp	p.E1528D	ENST00000376406	NM_014641.2	1528	gaA/gaC	10/15	0.23917935160466	4	FACETS	0.622	0.513	0.744	0.311	0.256	0.372	SUBCLONAL	1	TRUE	2	0.23917935160466	4		770	633	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126418	5126418	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0031955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	38	375	0	ENST00000381652.3:c.3263T>G	p.Leu1088Ter	p.L1088*	ENST00000381652	NM_004972.3	1088	tTa/tGa	24/25	0.23917935160466	1	FACETS	0.784	0.649	0.933	0.784	0.649	0.933	CLONAL	1	TRUE	0	0.23917935160466	1		375	357	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112593	115112593	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032331-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	87	784	0	ENST00000257566.3:c.1147G>A	p.Glu383Lys	p.E383K	ENST00000257566	NM_016569.3	383	Gag/Aag	7/8	1	2	FACETS	0.385	0.34	0.434	0.385	0.34	0.434	SUBCLONAL	1	TRUE	1	0.399149586337992	2		784	1132	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772264	68772265	+	stop_gained,inframe_insertion	Nonsense_Mutation	INS	-	-	GTA	novel	NA	P-0032331-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	211	823	0	ENST00000261769.5:c.115_116insAGT	p.Thr38_Phe39insTer	p.T38_F39ins*	ENST00000261769	NM_004360.3	38	acg/acGTAg	2/16	0.399149586337992	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.399149586337992	1		823	780	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916923	178916929	+	protein_altering_variant	In_Frame_Del	DEL	CCAGTAG	CCAGTAG	GTGT	novel	NA	P-0032331-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	106	564	1	ENST00000263967.3:c.310_316delinsGTGT	p.Pro104_Gly106delinsValCys	p.P104_G106delinsVC	ENST00000263967	NM_006218.2	104	CCAGTAGgc/GTGTgc	2/21	1	2	FACETS	0.713	0.639	0.791	0.713	0.639	0.791	SUBCLONAL	1	TRUE	1	0.399149586337992	2		565	745	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0032473-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	34	264	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.754	0.62	0.904	0.754	0.62	0.904	CLONAL	1	TRUE	1	0.357826227214376	2		264	252	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0032473-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	55	375	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.888	0.764	1	0.888	0.764	1	CLONAL	1	TRUE	1	0.357826227214376	2		375	346	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111494	8111495	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTGGAGG	novel	NA	P-0032553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	119	376	1	ENST00000346208.3:c.981_987dup	p.Arg330LeufsTer24	p.R330Lfs*24	ENST00000346208		327	ctc/ctCTGGAGGc	5/6	0.611784433313672	3	FACETS	0.691	0.625	0.76	0.345	0.312	0.38	SUBCLONAL	1	TRUE	1	0.747630541467234	3		377	633	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057945	27057958	+	frameshift_variant	Frame_Shift_Del	DEL	CTCACAGCCACAGG	CTCACAGCCACAGG	-	novel	NA	P-0032553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	125	498	0	ENST00000324856.7:c.1657_1670del	p.Gln553ValfsTer65	p.Q553Vfs*65	ENST00000324856	NM_006015.4	551	taCTCACAGCCACAGGct/tact	3/20	0.551081153152394	3	FACETS	1	0.96	1			1	CLONAL	1	TRUE	NA	0.747630541467234	3		498	421	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032567	12032567	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	78	304	0	ENST00000353533.5:c.1003G>T	p.Glu335Ter	p.E335*	ENST00000353533	NM_003010.3	335	Gaa/Taa	9/11	0.747630541467234	3	FACETS	0.913	0.81	1	0.456	0.405	0.511	CLONAL	1	TRUE	1	0.747630541467234	3		304	314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576888	7576888	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0032646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	109	820	0	ENST00000269305.4:c.958A>T	p.Lys320Ter	p.K320*	ENST00000269305	NM_001126112.2	320	Aag/Tag	9/11	0.375786210969268	0	FACETS	0.791	0.726	0.856			1	SUBCLONAL	2	TRUE	0	0.375786210969268	0		820	229	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034782	42034782	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	79	533	0	ENST00000219905.7:c.4624G>A	p.Val1542Met	p.V1542M	ENST00000219905	NM_001164273.1	1542	Gtg/Atg	15/24	1	2	FACETS	0.914	0.807	1	0.914	0.807	1	CLONAL	1	TRUE	1	0.375786210969268	2		533	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0032649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	313	750	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.668203439300006	1	FACETS	0.99	0.945	1	0.99	0.945	1	CLONAL	1	TRUE	0	0.692993655934272	1		752	596	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	247	505	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	1	2	FACETS	0.932	0.875	0.99	0.932	0.875	0.99	CLONAL	1	TRUE	1	0.692993655934272	2		505	765	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945533	151945534	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0032649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	196	509	0	ENST00000262189.6:c.1985_1986del	p.Val662AlafsTer12	p.V662Afs*12	ENST00000262189	NM_170606.2	662	gTG/g	14/59	NA	2	FACETS	0.999	0.932	1			1	INDETERMINATE	1	TRUE	NA	0.692993655934272	2		509	566	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	104	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.58765385195057	2		248	276	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	352	434	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.58765385195057	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.58765385195057	3		434	727	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038659	14038659	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs2020955	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	100	292	0	ENST00000311895.7:c.1984T>C	p.Ser662Pro	p.S662P	ENST00000311895	NM_005236.2	662	Tct/Cct	10/11	1	2	FACETS	0.948	0.855	1	0.948	0.855	1	CLONAL	1	TRUE	1	0.58765385195057	2		292	359	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188836	32188836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1046104152	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	479	685	1	ENST00000375023.3:c.718C>T	p.Pro240Ser	p.P240S	ENST00000375023	NM_004557.3	240	Cct/Tct	4/30	0.58765385195057	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.58765385195057	3		686	994	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306677	41306677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs724159835	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	252	735	1	ENST00000373198.4:c.982C>T	p.Arg328Cys	p.R328C	ENST00000373198	NM_133170.3	328	Cgc/Tgc	7/32	1	2	FACETS	0.996	0.934	1	0.996	0.934	1	CLONAL	1	TRUE	1	0.58765385195057	2		736	861	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857656	9857656	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754286517	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	160	429	0	ENST00000330684.3:c.3745G>A	p.Asp1249Asn	p.D1249N	ENST00000330684	NM_001134407.1	1249	Gat/Aat	13/13	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.58765385195057	2		429	544	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265323	152265323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866869178	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	108	344	0	ENST00000206249.3:c.776G>A	p.Arg259Gln	p.R259Q	ENST00000206249	NM_000125.3	259	cGa/cAa	4/8	0.58765385195057	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.58765385195057	1		344	259	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560970	9560970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781706438	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	157	519	0	ENST00000353224.5:c.812C>T	p.Ser271Leu	p.S271L	ENST00000353224	NM_177990.2	271	tCg/tTg	4/10	1	2	FACETS	0.87	0.8	0.943	0.87	0.8	0.943	CLONAL	1	TRUE	1	0.58765385195057	2		519	614	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537975	212537975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267599192	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	123	351	1	ENST00000342788.4:c.1630C>T	p.Arg544Trp	p.R544W	ENST00000342788	NM_005235.2	544	Cgg/Tgg	14/28	1	2	FACETS	0.992	0.904	1	0.992	0.904	1	CLONAL	1	TRUE	1	0.58765385195057	2		352	422	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804343	46804343	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	117	579	0	ENST00000290295.7:c.664C>T	p.Pro222Ser	p.P222S	ENST00000290295	NM_006361.5	222	Ccg/Tcg	2/2	0.231514463386455	1	FACETS	0.481	0.435	0.529	0.481	0.435	0.529	INDETERMINATE	1	TRUE	0	0.58765385195057	1		579	585	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32439124	32439124	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	222	596	0	ENST00000332351.3:c.949G>A	p.Gly317Arg	p.G317R	ENST00000332351	NM_024426.4	317	Gga/Aga	4/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.58765385195057	2		596	706	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087521	27087521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	317	761	0	ENST00000324856.7:c.2095C>T	p.Pro699Ser	p.P699S	ENST00000324856	NM_006015.4	699	Cct/Tct	5/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.58765385195057	2		761	1014	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675103	40675103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	299	820	0	ENST00000249776.8:c.67G>A	p.Asp23Asn	p.D23N	ENST00000249776	NM_033286.3	23	Gat/Aat	1/9	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.58765385195057	2		820	962	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961097	55961097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	240	679	1	ENST00000263923.4:c.2843G>A	p.Gly948Glu	p.G948E	ENST00000263923	NM_002253.2	948	gGg/gAg	21/30	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.58765385195057	2		680	805	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544088	18544088	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	61	352	0	ENST00000266497.5:c.1905G>A	p.Met635Ile	p.M635I	ENST00000266497		635	atG/atA	13/31	0.291479931434	0	FACETS	0.284	0.247	0.324			1	INDETERMINATE	1	TRUE	0	0.58765385195057	0		352	301	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467841	50467841	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752909152	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	134	378	0	ENST00000331340.3:c.1076C>T	p.Pro359Leu	p.P359L	ENST00000331340	NM_006060.4	359	cCg/cTg	8/8	1	2	FACETS	0.998	0.914	1	0.998	0.914	1	CLONAL	1	TRUE	1	0.58765385195057	2		378	457	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670153	29670153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1135402900	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	145	404	0	ENST00000356175.3:c.7126G>A	p.Gly2376Arg	p.G2376R	ENST00000356175	NM_000267.3	2376	Ggg/Agg	47/57	0.231514463386455	1	FACETS	0.741	0.682	0.803	0.741	0.682	0.803	INDETERMINATE	1	TRUE	0	0.58765385195057	1		404	470	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843731	156843731	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	399	969	0	ENST00000524377.1:c.1157A>G	p.Asn386Ser	p.N386S	ENST00000524377	NM_002529.3	386	aAc/aGc	8/17	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.58765385195057	2		969	1116	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16001803	16001803	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771889820	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	123	545	0	ENST00000268712.3:c.2698C>T	p.Pro900Ser	p.P900S	ENST00000268712	NM_006311.3	900	Cct/Tct	21/46	0.231514463386455	1	FACETS	0.53	0.481	0.581	0.53	0.481	0.581	INDETERMINATE	1	TRUE	0	0.58765385195057	1		545	558	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28586380	28586380	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	136	373	0	ENST00000253063.3:c.22T>A	p.Cys8Ser	p.C8S	ENST00000253063	NM_031459.4	8	Tgc/Agc	1/10	1	2	FACETS	0.972	0.89	1	0.972	0.89	1	CLONAL	1	TRUE	1	0.58765385195057	2		373	476	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805786	43805786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	220	655	0	ENST00000372470.3:c.842C>T	p.Pro281Leu	p.P281L	ENST00000372470	NM_005373.2	281	cCt/cTt	5/12	1	2	FACETS	0.928	0.865	0.992	0.928	0.865	0.992	CLONAL	1	TRUE	1	0.58765385195057	2		655	807	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733388	85733388	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	197	482	0	ENST00000370580.1:c.624G>T	p.Gln208His	p.Q208H	ENST00000370580	NM_003921.4	208	caG/caT	3/3	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.58765385195057	2		482	631	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615018	43615018	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	201	663	0	ENST00000355710.3:c.2432C>T	p.Ser811Phe	p.S811F	ENST00000355710	NM_020975.4	811	tCc/tTc	14/20	0.58765385195057	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.58765385195057	1		663	477	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248559	8248559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	252	727	0	ENST00000335790.3:c.328C>T	p.His110Tyr	p.H110Y	ENST00000335790	NM_002315.2	110	Cac/Tac	3/4	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.58765385195057	2		727	831	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343064	118343064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781933899	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	104	303	0	ENST00000534358.1:c.1190G>A	p.Arg397Lys	p.R397K	ENST00000534358	NM_005933.3	397	aGa/aAa	3/36	0.58765385195057	1	FACETS	0.976	0.89	1	0.976	0.89	1	CLONAL	1	TRUE	0	0.58765385195057	1		303	256	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134438	41134438	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751653854	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	229	567	0	ENST00000379561.5:c.1190C>T	p.Thr397Ile	p.T397I	ENST00000379561	NM_002015.3	397	aCc/aTc	2/3	0.178740630357872	3	FACETS	1	0.985	1	0.592	0.553	0.633	INDETERMINATE	1	TRUE	1	0.58765385195057	3		567	851	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134966	41134966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	171	308	0	ENST00000379561.5:c.662G>A	p.Ser221Asn	p.S221N	ENST00000379561	NM_002015.3	221	aGc/aAc	2/3	0.178740630357872	3	FACETS	0.844	0.785	0.905	0.844	0.785	0.905	INDETERMINATE	2	TRUE	1	0.58765385195057	3		308	446	SUCCESS
B2M	567	MSKCC	GRCh37	15	45008523	45008532	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATAGATCGAG	ATAGATCGAG	-	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	108	346	0	ENST00000558401.1:c.347-3_353del		p.X116_splice	ENST00000558401	NM_004048.2	116		3/4	1	2	FACETS	0.863	0.78	0.95	0.863	0.78	0.95	CLONAL	1	TRUE	1	0.58765385195057	2		346	426	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310253	91310254	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	73	287	0	ENST00000355112.3:c.2307_2307+1delinsAA		p.X769_splice	ENST00000355112	NM_000057.2	769		10/22	1	2	FACETS	0.784	0.691	0.882	0.784	0.691	0.882	SUBCLONAL	1	TRUE	1	0.58765385195057	2		287	317	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467879	99467879	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	104	337	0	ENST00000268035.6:c.2748G>A	p.Trp916Ter	p.W916*	ENST00000268035	NM_000875.3	916	tgG/tgA	13/21	1	2	FACETS	0.819	0.738	0.904	0.819	0.738	0.904	CLONAL	1	TRUE	1	0.58765385195057	2		337	432	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632540	3632541	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	285	873	1	ENST00000294008.3:c.5307_5308delinsAA	p.Val1770Met	p.V1770M	ENST00000294008	NM_032444.2	1769	aaGGtg/aaAAtg	15/15	1	2	FACETS	0.988	0.93	1	0.988	0.93	1	CLONAL	1	TRUE	1	0.58765385195057	2		874	982	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965230	81965230	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	183	549	0	ENST00000359376.3:c.2710C>T	p.Arg904Ter	p.R904*	ENST00000359376	NM_002661.3	904	Cga/Tga	25/33	0.58765385195057	1	FACETS	0.92	0.857	0.984	0.92	0.857	0.984	CLONAL	1	TRUE	0	0.58765385195057	1		549	478	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971331	15971331	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	135	572	0	ENST00000268712.3:c.4618C>T	p.Pro1540Ser	p.P1540S	ENST00000268712	NM_006311.3	1540	Cct/Tct	32/46	0.231514463386455	1	FACETS	0.508	0.463	0.555	0.508	0.463	0.555	INDETERMINATE	1	TRUE	0	0.58765385195057	1		572	639	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16056710	16056710	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	137	337	0	ENST00000268712.3:c.733-1G>A		p.X245_splice	ENST00000268712	NM_006311.3	245			0.231514463386455	1	FACETS	0.687	0.629	0.747	0.687	0.629	0.747	INDETERMINATE	1	TRUE	0	0.58765385195057	1		337	479	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585505	29585506	+	missense_variant	Missense_Mutation	DNP	GA	GA	AC	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	37	237	1	ENST00000356175.3:c.4254_4255delinsAC	p.Lys1419Gln	p.K1419Q	ENST00000356175	NM_000267.3	1418	ttGAag/ttACag	31/57	0.231514463386455	1	FACETS	0.35	0.29	0.416	0.35	0.29	0.416	INDETERMINATE	1	TRUE	0	0.58765385195057	1		238	254	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30293206	30293206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	183	477	0	ENST00000322652.5:c.496C>T	p.His166Tyr	p.H166Y	ENST00000322652	NM_015355.2	166	Cac/Tac	5/16	0.231514463386455	1	FACETS	0.781	0.726	0.838	0.781	0.726	0.838	INDETERMINATE	1	TRUE	0	0.58765385195057	1		477	563	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276263	15276263	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	209	657	0	ENST00000263388.2:c.5731A>C	p.Ile1911Leu	p.I1911L	ENST00000263388	NM_000435.2	1911	Atc/Ctc	31/33	1	2	FACETS	0.887	0.825	0.95	0.887	0.825	0.95	CLONAL	1	TRUE	1	0.58765385195057	2		657	802	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945692	17945692	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	251	744	0	ENST00000458235.1:c.2168C>T	p.Thr723Ile	p.T723I	ENST00000458235	NM_000215.3	723	aCc/aTc	16/24	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.58765385195057	2		744	778	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241910	39241910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	144	311	0	ENST00000402219.2:c.1936G>A	p.Glu646Lys	p.E646K	ENST00000402219	NM_005633.3	646	Gaa/Aaa	11/23	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.58765385195057	2		311	486	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251826	212251826	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	119	352	0	ENST00000342788.4:c.3233C>A	p.Ser1078Tyr	p.S1078Y	ENST00000342788	NM_005235.2	1078	tCt/tAt	27/28	1	2	FACETS	0.918	0.835	1	0.918	0.835	1	CLONAL	1	TRUE	1	0.58765385195057	2		352	441	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980722	40980723	+	splice_donor_variant	Splice_Site	DNP	AC	AC	GT	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	95	361	1	ENST00000373198.4:c.1762+1_1762+2inv		p.X588_splice	ENST00000373198	NM_133170.3	588			1	2	FACETS	0.808	0.725	0.896	0.808	0.725	0.896	CLONAL	1	TRUE	1	0.58765385195057	2		362	400	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755737	39755737	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	114	561	0	ENST00000288319.7:c.1028A>G	p.Asp343Gly	p.D343G	ENST00000288319	NM_182918.3	343	gAt/gGt	10/10	0.231514463386455	1	FACETS	0.45	0.406	0.496	0.45	0.406	0.496	INDETERMINATE	1	TRUE	0	0.58765385195057	1		561	609	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475594	12475594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	208	435	0	ENST00000287820.6:c.1468G>A	p.Asp490Asn	p.D490N	ENST00000287820	NM_015869.4	490	Gac/Aac	7/7	0.178740630357872	3	FACETS	0.751	0.701	0.801	0.751	0.701	0.801	INDETERMINATE	2	TRUE	1	0.58765385195057	3		435	610	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935009	49935009	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1427192436	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	304	721	0	ENST00000296474.3:c.1990C>T	p.Pro664Ser	p.P664S	ENST00000296474	NM_002447.2	664	Ccg/Tcg	6/20	0.178740630357872	3	FACETS	1	0.994	1	0.719	0.679	0.76	INDETERMINATE	1	TRUE	1	0.58765385195057	3		721	931	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037196	71037196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868431423	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	172	481	0	ENST00000318789.4:c.1095G>A	p.Met365Ile	p.M365I	ENST00000318789	NM_032682.5	365	atG/atA	14/21	0.178740630357872	3	FACETS	1	0.984	1	0.618	0.571	0.666	INDETERMINATE	1	TRUE	1	0.58765385195057	3		481	613	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428522	72428522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878889009	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	246	510	0	ENST00000477973.2:c.482C>T	p.Thr161Ile	p.T161I	ENST00000477973	NM_012234.5	161	aCc/aTc	2/4	0.178740630357872	3	FACETS	0.776	0.729	0.824	0.776	0.729	0.824	INDETERMINATE	2	TRUE	1	0.58765385195057	3		510	698	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259321	89259321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	193	506	0	ENST00000336596.2:c.465G>A	p.Met155Ile	p.M155I	ENST00000336596	NM_005233.5	155	atG/atA	3/17	0.178740630357872	3	FACETS	1	0.989	1	0.676	0.628	0.724	INDETERMINATE	1	TRUE	1	0.58765385195057	3		506	629	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169993023	169993023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	157	347	1	ENST00000295797.4:c.653C>T	p.Pro218Leu	p.P218L	ENST00000295797	NM_002740.5	218	cCa/cTa	8/18	0.178740630357872	3	FACETS	1	0.983	1	0.624	0.575	0.675	INDETERMINATE	1	TRUE	1	0.58765385195057	3		348	554	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155695	106155696	+	missense_variant	Missense_Mutation	DNP	TA	TA	AT	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	120	381	0	ENST00000380013.4:c.596_597delinsAT	p.Leu199Tyr	p.L199Y	ENST00000380013	NM_001127208.2	199	tTA/tAT	3/11	1	2	FACETS	0.896	0.814	0.98	0.896	0.814	0.98	CLONAL	1	TRUE	1	0.58765385195057	2		381	456	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628389	86628389	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	164	367	0	ENST00000274376.6:c.758T>G	p.Ile253Arg	p.I253R	ENST00000274376	NM_002890.2	253	aTa/aGa	3/25	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.58765385195057	2		367	526	SUCCESS
APC	324	MSKCC	GRCh37	5	112179638	112179638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	111	284	0	ENST00000257430.4:c.8347C>T	p.Pro2783Ser	p.P2783S	ENST00000257430	NM_000038.5	2783	Cct/Tct	16/16	1	2	FACETS	0.964	0.874	1	0.964	0.874	1	CLONAL	1	TRUE	1	0.58765385195057	2		284	392	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925489	131925489	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501946	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	158	308	0	ENST00000265335.6:c.1412C>T	p.Ser471Leu	p.S471L	ENST00000265335		471	tCa/tTa	9/25	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.58765385195057	2		308	465	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968285	2968286	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	297	812	1	ENST00000396946.4:c.1700_1701delinsTT	p.Pro567Leu	p.P567L	ENST00000396946	NM_032415.4	567	cCC/cTT	13/25	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.58765385195057	2		813	947	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268908	55268908	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	253	803	0	ENST00000275493.2:c.2974C>T	p.Pro992Ser	p.P992S	ENST00000275493	NM_005228.3	992	Cct/Tct	25/28	1	2	FACETS	0.969	0.908	1	0.969	0.908	1	CLONAL	1	TRUE	1	0.58765385195057	2		803	889	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56860194	56860194	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	184	559	0	ENST00000519728.1:c.196G>C	p.Asp66His	p.D66H	ENST00000519728	NM_002350.3	66	Gac/Cac	4/13	1	2	FACETS	0.825	0.763	0.889	0.825	0.763	0.889	CLONAL	1	TRUE	1	0.58765385195057	2		559	759	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981343	68981343	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	139	391	0	ENST00000288368.4:c.1415G>A	p.Arg472Lys	p.R472K	ENST00000288368	NM_024870.2	472	aGa/aAa	12/40	1	2	FACETS	0.933	0.855	1	0.933	0.855	1	CLONAL	1	TRUE	1	0.58765385195057	2		391	507	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995538	68995538	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	227	698	0	ENST00000288368.4:c.1942C>T	p.Pro648Ser	p.P648S	ENST00000288368	NM_024870.2	648	Cct/Tct	18/40	1	2	FACETS	0.904	0.843	0.965	0.904	0.843	0.965	CLONAL	1	TRUE	1	0.58765385195057	2		698	855	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933497	39933497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	264	343	0	ENST00000378444.4:c.1102C>T	p.Pro368Ser	p.P368S	ENST00000378444	NM_001123385.1	368	Cct/Tct	4/15	1	1	FACETS	0.778	0.743	0.811	1	0.995	1	SUBCLONAL	2	TRUE	0	0.58765385195057	1		343	408	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611080	100611080	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	256	408	0	ENST00000308731.7:c.1526T>G	p.Met509Arg	p.M509R	ENST00000308731	NM_000061.2	509	aTg/aGg	15/19	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.58765385195057	1		408	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0032654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	229	466	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.307638739952879	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.351351825516483	2		466	598	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846279	156846279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368806213	NA	P-0032654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	498	672	0	ENST00000524377.1:c.1720C>T	p.Arg574Cys	p.R574C	ENST00000524377	NM_002529.3	574	Cgc/Tgc	14/17	0.302011187790798	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.351351825516483	3		672	1009	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577062	7577062	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	632	253	0	ENST00000269305.4:c.876del	p.Glu294SerfsTer51	p.E294Sfs*51	ENST00000269305	NM_001126112.2	292	aaA/aa	8/11	0.762969760802735	3	FACETS	0.912	0.892	0.932			1	CLONAL	3	TRUE	NA	0.801676819760004	3		253	807	SUCCESS
ALK	238	MSKCC	GRCh37	2	29430035	29430035	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0032657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	208	208	0	ENST00000389048.3:c.3938+2T>A		p.X1313_splice	ENST00000389048	NM_004304.4	1313			0.693288616254947	4	FACETS	1	0.984	1	0.595	0.554	0.638	CLONAL	1	TRUE	2	0.801676819760004	4		208	785	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0032681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	53	653	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	1	2	FACETS	0.695	0.592	0.808	0.695	0.592	0.808	SUBCLONAL	1	TRUE	1	0.240659891875448	2		653	634	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254684	16254684	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs777527531	NA	P-0032681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	79	487	0	ENST00000375759.3:c.1949A>G	p.Tyr650Cys	p.Y650C	ENST00000375759	NM_015001.2	650	tAt/tGt	11/15	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.240659891875448	2		487	628	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674234	86674234	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	31	310	0	ENST00000274376.6:c.2366G>C	p.Arg789Pro	p.R789P	ENST00000274376	NM_002890.2	789	cGa/cCa	18/25	1	2	FACETS	0.694	0.562	0.844	0.694	0.562	0.844	SUBCLONAL	1	TRUE	1	0.240659891875448	2		310	371	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969194	93969194	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	82	377	0	ENST00000369303.4:c.1802A>C	p.Lys601Thr	p.K601T	ENST00000369303	NM_004440.3	601	aAa/aCa	10/17	0.447477651449987	1	FACETS	0.971	0.866	1	0.971	0.866	1	CLONAL	1	TRUE	0	0.447477651449987	1		377	293	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637711	52637711	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	127	552	1	ENST00000394830.3:c.2605C>T	p.Gln869Ter	p.Q869*	ENST00000394830	NM_018313.4	869	Cag/Tag	18/30	0.447477651449987	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.447477651449987	1		553	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579360	7579361	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	140	611	1	ENST00000269305.4:c.326dup	p.Arg110ProfsTer39	p.R110Pfs*39	ENST00000269305	NM_001126112.2	109	ttc/ttTc	4/11	0.447477651449987	1	FACETS	0.964	0.883	1	0.964	0.883	1	CLONAL	1	TRUE	0	0.447477651449987	1		612	504	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111129	193111129	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	71	280	0	ENST00000367435.3:c.662C>A	p.Thr221Asn	p.T221N	ENST00000367435	NM_024529.4	221	aCc/aAc	7/17	1	2	FACETS	0.922	0.811	1	0.922	0.811	1	CLONAL	1	TRUE	1	0.447477651449987	2		280	344	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636818	8636818	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	95	450	0	ENST00000356435.5:c.91G>T	p.Val31Phe	p.V31F	ENST00000356435		31	Gtt/Ttt	2/35	0.447477651449987	1	FACETS	0.931	0.837	1	0.931	0.837	1	CLONAL	1	TRUE	0	0.447477651449987	1		450	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0032700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	116	905	1	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.2661435631421	2		906	757	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924914	49924914	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	57	845	0	ENST00000296474.3:c.4029G>C	p.Gln1343His	p.Q1343H	ENST00000296474	NM_002447.2	1343	caG/caC	20/20	1	2	FACETS	0.63	0.54	0.729	0.63	0.54	0.729	SUBCLONAL	1	TRUE	1	0.2661435631421	2		845	680	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928097	178928097	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	212	695	0	ENST00000263967.3:c.1375A>G	p.Ile459Val	p.I459V	ENST00000263967	NM_006218.2	459	Att/Gtt	8/21	0.164541001897626	3	FACETS	1	0.984	1	0.792	0.738	0.847	CLONAL	2	TRUE	0	0.2661435631421	3		695	760	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0032717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	853	653	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.860404894702819	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.860404894702819	1		653	999	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0032717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	86	306	1	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.434701570010308	1	FACETS	0.365	0.326	0.406	0.365	0.326	0.406	INDETERMINATE	1	TRUE	0	0.860404894702819	1		307	312	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426771	49426772	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs944680171	NA	P-0032717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	249	372	2	ENST00000301067.7:c.11714_11716dup	p.Gln3905dup	p.Q3905dup	ENST00000301067	NM_003482.3	3905	ctg/cAGCtg	39/54	0.373286908811255	3	FACETS	1	0.99	1	0.628	0.591	0.666	INDETERMINATE	1	TRUE	1	0.860404894702819	3		374	659	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	36	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.72	0.593	0.862	0.72	0.593	0.862	SUBCLONAL	1	FALSE	1	0.262442123199402	2		248	381	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0032729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	64	328	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.922	0.799	1	0.922	0.799	1	CLONAL	1	FALSE	1	0.262442123199402	2		328	529	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0032729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	99	296	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.213277028809468	3	FACETS	0.796	0.713	0.884	0.796	0.713	0.884	SUBCLONAL	2	FALSE	1	0.262442123199402	3		296	536	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436102	51436103	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0032729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	64	283	0	ENST00000262662.1:c.62_63del	p.Leu21HisfsTer2	p.L21Hfs*2	ENST00000262662		21	cTT/c	3/4	1	2	FACETS	0.999	0.867	1	0.999	0.867	1	CLONAL	1	FALSE	1	0.262442123199402	2		283	488	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102098221	102098221	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	95	429	0	ENST00000282441.5:c.1185T>G	p.Asp395Glu	p.D395E	ENST00000282441	NM_001130145.2	395	gaT/gaG	8/9	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	1	0.262442123199402	2		429	693	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746017	162746017	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	35	407	0	ENST00000367921.3:c.2140C>T	p.Arg714Ter	p.R714*	ENST00000367921	NM_006182.2	714	Cga/Tga	16/18	1	2	FACETS	0.442	0.362	0.533	0.442	0.362	0.533	SUBCLONAL	1	FALSE	1	0.262442123199402	2		407	603	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	88	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.39	2		248	446	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0032729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	113	328	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	0.39	2		328	453	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0032729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	16	296	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.22	0.162	0.29	0.22	0.162	0.29	SUBCLONAL	1	TRUE	1	0.39	2		296	373	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436102	51436103	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0032729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	92	283	0	ENST00000262662.1:c.62_63del	p.Leu21HisfsTer2	p.L21Hfs*2	ENST00000262662		21	cTT/c	3/4	1	2	FACETS	0.751	0.668	0.84	0.751	0.668	0.84	SUBCLONAL	1	TRUE	1	0.39	2		283	628	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102098221	102098221	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	94	429	0	ENST00000282441.5:c.1185T>G	p.Asp395Glu	p.D395E	ENST00000282441	NM_001130145.2	395	gaT/gaG	8/9	1	2	FACETS	0.69	0.614	0.771	0.69	0.614	0.771	SUBCLONAL	1	TRUE	1	0.39	2		429	699	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0032729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	20	316	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	1	2	FACETS	0.244	0.186	0.313	0.244	0.186	0.313	SUBCLONAL	1	TRUE	1	0.39	2		316	420	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032729-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	104	248	0				ENST00000310581	NM_198253.2	-/1132			0.211697628913751	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.29	3		248	349	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0032729-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	17	296	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.211697628913751	3	FACETS	0.75	0.562	0.971	0.375	0.281	0.486	CLONAL	1	TRUE	1	0.29	3		296	179	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436102	51436103	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0032729-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	52	283	0	ENST00000262662.1:c.62_63del	p.Leu21HisfsTer2	p.L21Hfs*2	ENST00000262662		21	cTT/c	3/4	1	2	FACETS	0.961	0.822	1	0.961	0.822	1	CLONAL	1	TRUE	1	0.29	2		283	373	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102098221	102098221	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032729-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	36	429	0	ENST00000282441.5:c.1185T>G	p.Asp395Glu	p.D395E	ENST00000282441	NM_001130145.2	395	gaT/gaG	8/9	1	2	FACETS	0.637	0.524	0.763	0.637	0.524	0.763	SUBCLONAL	1	TRUE	1	0.29	2		429	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0032731-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	425	863	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.734874635546372	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.734874635546372	1		863	612	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143324090	143324090	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0032731-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	160	318	0	ENST00000262992.4:c.372+1del		p.X124_splice	ENST00000262992	NM_001101669.1	124			NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.734874635546372	2		318	329	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0032739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	17	328	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.597	0.447	0.773	0.597	0.447	0.773	SUBCLONAL	1	TRUE	1	0.314737708900475	2		328	181	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0032739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	39	331	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.314737708900475	2		331	238	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396235	396235	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	93	509	0	ENST00000262320.3:c.791C>T	p.Pro264Leu	p.P264L	ENST00000262320	NM_003502.3	264	cCc/cTc	2/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.314737708900475	2		509	495	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878185	48878186	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0032739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	21	80	0	ENST00000267163.4:c.137_137+1delinsAA		p.X46_splice	ENST00000267163	NM_000321.2	46		1/27	0.314737708900475	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.314737708900475	1		80	78	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650875	37650875	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	62	407	0	ENST00000447079.4:c.2347C>T	p.His783Tyr	p.H783Y	ENST00000447079	NM_015083.1	783	Cac/Tac	5/14	0.314737708900475	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.314737708900475	1		407	290	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246668	41246668	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1567801705	NA	P-0032739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	69	471	0	ENST00000357654.3:c.880A>G	p.Lys294Glu	p.K294E	ENST00000357654	NM_007294.3	294	Aaa/Gaa	10/23	0.314737708900475	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.314737708900475	1		471	322	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965359	25965359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377609636	NA	P-0032739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	116	463	0	ENST00000435504.4:c.3847C>T	p.Arg1283Cys	p.R1283C	ENST00000435504		1283	Cgt/Tgt	13/13	0.314737708900475	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.314737708900475	1		463	540	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710607	40710607	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	102	467	0	ENST00000373198.4:c.4244A>T	p.Glu1415Val	p.E1415V	ENST00000373198	NM_133170.3	1415	gAg/gTg	31/32	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.314737708900475	2		467	552	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980724	40980724	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	56	271	0	ENST00000373198.4:c.1762G>A	p.Ala588Thr	p.A588T	ENST00000373198	NM_133170.3	588	Gct/Act	10/32	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.314737708900475	2		271	301	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177950	56177950	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	72	413	1	ENST00000399503.3:c.2923C>T	p.His975Tyr	p.H975Y	ENST00000399503	NM_005921.1	975	Cat/Tat	14/20	0.314737708900475	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.314737708900475	1		414	291	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526717	106526717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	26	347	0	ENST00000359195.3:c.3010C>T	p.Pro1004Ser	p.P1004S	ENST00000359195	NM_002649.2	1004	Cca/Tca	10/11	1	2	FACETS	0.802	0.639	0.986	0.802	0.639	0.986	CLONAL	1	TRUE	1	0.314737708900475	2		347	206	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224197	98224198	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0032739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	56	343	1	ENST00000331920.6:c.2643_2644delinsTT	p.Leu882Phe	p.L882F	ENST00000331920	NM_000264.3	881	gtCCtt/gtTTtt	16/24	1	2	FACETS	0.841	0.723	0.97	0.841	0.723	0.97	CLONAL	1	TRUE	1	0.314737708900475	2		344	423	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191540	10191540	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs5030822	NA	P-0032741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	587	458	0	ENST00000256474.2:c.533T>C	p.Leu178Pro	p.L178P	ENST00000256474	NM_000551.3	178	cTg/cCg	3/3	0.825032827206066	3	FACETS	0.971	0.952	0.989	0.971	0.952	0.989	CLONAL	3	TRUE	0	0.825032827206066	3		458	690	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274018	10274018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1354238435	NA	P-0032741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	539	650	1	ENST00000330684.3:c.251C>T	p.Thr84Met	p.T84M	ENST00000330684	NM_001134407.1	84	aCg/aTg	2/13	0.692020616722375	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	2	0.825032827206066	4		651	1119	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509421	149509421	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	244	567	0	ENST00000261799.4:c.1478G>T	p.Ser493Ile	p.S493I	ENST00000261799	NM_002609.3	493	aGc/aTc	10/23	0.81170134493159	3	FACETS	0.943	0.883	1	0.471	0.441	0.503	CLONAL	1	TRUE	1	0.825032827206066	3		567	886	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350201	15350201	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0032741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	211	582	1	ENST00000263377.2:c.3576+2T>C		p.X1192_splice	ENST00000263377	NM_058243.2	1192			0.81170134493159	3	FACETS	0.952	0.887	1	0.476	0.443	0.51	CLONAL	1	TRUE	1	0.825032827206066	3		583	759	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191540	10191540	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs5030822	NA	P-0032741-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	377	458	0	ENST00000256474.2:c.533T>C	p.Leu178Pro	p.L178P	ENST00000256474	NM_000551.3	178	cTg/cCg	3/3	0.60426452371625	3	FACETS	0.999	0.965	1	0.999	0.965	1	CLONAL	3	TRUE	0	0.60426452371625	3		458	542	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274018	10274018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1354238435	NA	P-0032741-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	270	650	1	ENST00000330684.3:c.251C>T	p.Thr84Met	p.T84M	ENST00000330684	NM_001134407.1	84	aCg/aTg	2/13	0.471688918892336	4	FACETS	0.936	0.882	0.991	0.936	0.882	0.991	CLONAL	2	TRUE	2	0.60426452371625	4		651	766	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509421	149509421	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032741-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	152	567	0	ENST00000261799.4:c.1478G>T	p.Ser493Ile	p.S493I	ENST00000261799	NM_002609.3	493	aGc/aTc	10/23	0.60426452371625	3	FACETS	0.931	0.853	1	0.465	0.426	0.506	CLONAL	1	TRUE	1	0.60426452371625	3		567	704	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350201	15350201	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0032741-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	162	582	1	ENST00000263377.2:c.3576+2T>C		p.X1192_splice	ENST00000263377	NM_058243.2	1192			0.540343108195048	3	FACETS	1	0.948	1	0.519	0.478	0.563	CLONAL	1	TRUE	1	0.60426452371625	3		583	672	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	187	697	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.838	0.776	0.902	1	0.992	1	CLONAL	2	TRUE	1	0.294311197480521	2		697	758	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs1202793339	NA	P-0032744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	75	463	0	ENST00000269305.4:c.560-1G>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.294311197480521	1	FACETS	0.857	0.753	0.969	0.857	0.753	0.969	CLONAL	1	TRUE	0	0.294311197480521	1		463	507	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	220	248	0				ENST00000310581	NM_198253.2	-/1132			0.677372479558187	4	FACETS	0.907	0.859	0.955	0.907	0.859	0.955	CLONAL	3	TRUE	1	0.708260524570157	4		248	390	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714670	52714670	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112759633	NA	P-0032746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	220	523	0	ENST00000322088.6:c.428C>T	p.Ser143Phe	p.S143F	ENST00000322088	NM_014225.5	143	tCc/tTc	4/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.708260524570157	2		523	582	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0032746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	129	347	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	1	2	FACETS	0.934	0.856	1	0.934	0.856	1	CLONAL	1	TRUE	1	0.708260524570157	2		347	390	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0032746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	206	339	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.708260524570157	3	FACETS	0.897	0.843	0.951	0.897	0.843	0.951	CLONAL	2	TRUE	1	0.708260524570157	3		339	439	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248766	212248766	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs549128376	NA	P-0032746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	104	298	0	ENST00000342788.4:c.3501G>T	p.Glu1167Asp	p.E1167D	ENST00000342788	NM_005235.2	1167	gaG/gaT	28/28	1	2	FACETS	0.985	0.895	1	0.985	0.895	1	CLONAL	1	TRUE	1	0.708260524570157	2		298	298	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259079	89259079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267599943	NA	P-0032746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	114	267	0	ENST00000336596.2:c.223G>A	p.Asp75Asn	p.D75N	ENST00000336596	NM_005233.5	75	Gac/Aac	3/17	1	2	FACETS	0.978	0.892	1	0.978	0.892	1	CLONAL	1	TRUE	1	0.708260524570157	2		267	329	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410618	32410618	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866837692	NA	P-0032746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	187	422	0	ENST00000332351.3:c.1540C>T	p.Gln514Ter	p.Q514*	ENST00000332351	NM_024426.4	514	Cag/Tag	10/10	1	2	FACETS	0.965	0.898	1	0.965	0.898	1	CLONAL	1	TRUE	1	0.708260524570157	2		422	547	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256192	123256192	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1564875577	NA	P-0032746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	156	379	0	ENST00000358487.5:c.1717C>T	p.Arg573Ter	p.R573*	ENST00000358487	NM_000141.4	573	Cga/Tga	13/18	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.708260524570157	2		379	434	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410327	63410327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	394	662	1	ENST00000330258.3:c.2840C>T	p.Ser947Phe	p.S947F	ENST00000330258	NM_152424.3	947	tCc/tTc	2/2	0.511497733698974	3	FACETS	0.925	0.886	0.965	0.925	0.886	0.965	CLONAL	2	TRUE	1	0.708260524570157	3		663	814	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253990	133253990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	170	494	1	ENST00000320574.5:c.760C>T	p.Pro254Ser	p.P254S	ENST00000320574	NM_006231.2	254	Ccg/Tcg	8/49	1	2	FACETS	0.876	0.811	0.943	0.876	0.811	0.943	CLONAL	1	TRUE	1	0.708260524570157	2		495	548	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281708	49281708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1168461332	NA	P-0032746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	343	681	0	ENST00000282018.3:c.755C>T	p.Thr252Ile	p.T252I	ENST00000282018	NM_020377.2	252	aCc/aTc	1/1	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.708260524570157	2		681	875	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068385	16068385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	13	47	0	ENST00000268712.3:c.526C>T	p.Leu176Phe	p.L176F	ENST00000268712	NM_006311.3	176	Ctc/Ttc	5/46	1	2	FACETS	0.765	0.565	0.99	0.765	0.565	0.99	CLONAL	1	TRUE	1	0.708260524570157	2		47	48	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272228	15272228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	102	459	0	ENST00000263388.2:c.6211G>A	p.Gly2071Arg	p.G2071R	ENST00000263388	NM_000435.2	2071	Ggg/Agg	33/33	1	2	FACETS	0.917	0.83	1	0.917	0.83	1	CLONAL	1	TRUE	1	0.708260524570157	2		459	314	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170032	32170032	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	224	612	0	ENST00000375023.3:c.3576T>G	p.Ser1192Arg	p.S1192R	ENST00000375023	NM_004557.3	1192	agT/agG	21/30	0.708260524570157	3	FACETS	1	0.955	1	0.515	0.48	0.55	CLONAL	1	TRUE	1	0.708260524570157	3		612	832	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117639403	117639403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	223	387	0	ENST00000368508.3:c.5953G>A	p.Gly1985Ser	p.G1985S	ENST00000368508	NM_002944.2	1985	Ggt/Agt	37/43	0.708260524570157	3	FACETS	0.907	0.855	0.96	0.907	0.855	0.96	CLONAL	2	TRUE	1	0.708260524570157	3		387	470	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622234	162622234	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	369	393	0	ENST00000366898.1:c.463C>T	p.Gln155Ter	p.Q155*	ENST00000366898	NM_004562.2	155	Caa/Taa	4/12	0.708260524570157	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.708260524570157	3		393	662	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141582990	141582990	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	234	531	0	ENST00000220592.5:c.257T>G	p.Ile86Ser	p.I86S	ENST00000220592	NM_012154.3	86	aTc/aGc	3/19	1	2	FACETS	0.933	0.875	0.993	0.933	0.875	0.993	CLONAL	1	TRUE	1	0.708260524570157	2		531	708	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779195	135779195	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	140	377	0	ENST00000298552.3:c.2051C>T	p.Pro684Leu	p.P684L	ENST00000298552	NM_001162426.1	684	cCt/cTt	17/23	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.708260524570157	2		377	395	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888835	76888835	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	139	561	1	ENST00000373344.5:c.4994G>A	p.Arg1665Lys	p.R1665K	ENST00000373344	NM_000489.3	1665	aGa/aAa	19/35	0.511497733698974	3	FACETS	0.844	0.77	0.92	0.422	0.385	0.46	CLONAL	1	TRUE	1	0.708260524570157	3		562	630	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673712	176673717	+	stop_gained	Nonsense_Mutation	ONP	GAAAAC	GAAAAC	AAAATT	novel	NA	P-0032746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	96	274	1	ENST00000439151.2:c.4412_4417delinsAAAATT	p.Arg1471_Arg1473delinsGlnAsnTer	p.R1471_R1473delinsQN*	ENST00000439151	NM_022455.4	1471	cGAAAACga/cAAAATTga	10/23	0.708260524570157	1	FACETS	0.761	0.692	0.832	0.761	0.692	0.832	SUBCLONAL	1	TRUE	0	0.708260524570157	1		275	230	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562747	29562747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137854556	NA	P-0032779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	112	435	0	ENST00000356175.3:c.3827G>A	p.Arg1276Gln	p.R1276Q	ENST00000356175	NM_000267.3	1276	cGa/cAa	28/57	0.675419943954831	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.690481339880157	1		435	211	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941629	48941629	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1131690860	NA	P-0032779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	48	196	0	ENST00000267163.4:c.940-1G>A		p.X314_splice	ENST00000267163	NM_000321.2	314			0.675419943954831	1	FACETS	0.728	0.633	0.827	0.728	0.633	0.827	SUBCLONAL	1	TRUE	0	0.690481339880157	1		196	125	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857402	68857403	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACCTTAGAGGTCAGCGTGTGTGACTGGG	novel	NA	P-0032779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	116	438	0	ENST00000261769.5:c.2063_2064insGGACCTTAGAGGTCAGCGTGTGTGACTG	p.Cys688TrpfsTer9	p.C688Wfs*9	ENST00000261769	NM_004360.3	679	-/ACCTTAGAGGTCAGCGTGTGTGACTGGG	13/16	0.690481339880157	1	FACETS	0.629	0.573	0.686	0.629	0.573	0.686	SUBCLONAL	1	TRUE	0	0.690481339880157	1		438	350	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252853	36252854	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0032779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	176	249	0	ENST00000300305.3:c.507_508dup	p.Gly170GlufsTer7	p.G170Efs*7	ENST00000300305		170	ggg/gAGgg		1	2	FACETS	0.894	0.829	0.962	0.894	0.829	0.962	CLONAL	1	TRUE	1	0.690481339880157	2		249	570	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759580	133759580	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771154274	NA	P-0032779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	100	538	0	ENST00000318560.5:c.1903G>A	p.Glu635Lys	p.E635K	ENST00000318560	NM_005157.4	635	Gag/Aag	11/11	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.690481339880157	2		538	285	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0032800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	149	631	1	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.305088635418922	3	FACETS	1	0.981	1	0.631	0.576	0.688	CLONAL	1	TRUE	1	0.317694272894268	3		632	862	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0032800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	51	331	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.317694272894268	2		331	304	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs864622237	NA	P-0032800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	180	573	0	ENST00000269305.4:c.700T>C	p.Tyr234His	p.Y234H	ENST00000269305	NM_001126112.2	234	Tac/Cac	7/11	0.260310592984664	2	FACETS	0.82	0.759	0.883	0.82	0.759	0.883	CLONAL	2	TRUE	0	0.317694272894268	2		573	691	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612073	189612073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142762485	NA	P-0032800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	197	467	1	ENST00000264731.3:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000264731	NM_003722.4	609	Gaa/Aaa	14/14	0.252053728033621	4	FACETS	0.917	0.85	0.987	0.917	0.85	0.987	CLONAL	2	TRUE	2	0.317694272894268	4		468	891	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149242	119149242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779039234	NA	P-0032800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	220	489	0	ENST00000264033.4:c.1250C>T	p.Pro417Leu	p.P417L	ENST00000264033	NM_005188.3	417	cCt/cTt	9/16	0.303122905729378	2	FACETS	0.986	0.922	1	0.986	0.922	1	CLONAL	2	TRUE	0	0.317694272894268	2		489	702	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981315	68981315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866864487	NA	P-0032800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	101	272	0	ENST00000288368.4:c.1387C>T	p.Arg463Cys	p.R463C	ENST00000288368	NM_024870.2	463	Cgc/Tgc	12/40	0.252053728033621	4	FACETS	0.983	0.885	1	0.983	0.885	1	CLONAL	2	TRUE	2	0.317694272894268	4		272	426	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995569	68995569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775560862	NA	P-0032800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	184	583	0	ENST00000288368.4:c.1973C>T	p.Ser658Leu	p.S658L	ENST00000288368	NM_024870.2	658	tCg/tTg	18/40	0.252053728033621	4	FACETS	0.942	0.871	1	0.942	0.871	1	CLONAL	2	TRUE	2	0.317694272894268	4		583	810	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180931	32180931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771147216	NA	P-0032800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	71	457	0	ENST00000375023.3:c.2419C>T	p.Arg807Cys	p.R807C	ENST00000375023	NM_004557.3	807	Cgc/Tgc	15/30	0.305088635418922	3	FACETS	0.838	0.732	0.953	0.419	0.366	0.477	CLONAL	1	TRUE	1	0.317694272894268	3		457	618	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183713	10183713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746582207	NA	P-0032800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	163	496	0	ENST00000256474.2:c.182C>T	p.Pro61Leu	p.P61L	ENST00000256474	NM_000551.3	61	cCc/cTc	1/3	0.303122905729378	2	FACETS	0.959	0.886	1	0.959	0.886	1	CLONAL	2	TRUE	0	0.317694272894268	2		496	535	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223166	41223166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357002	NA	P-0032800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	50	453	0	ENST00000357654.3:c.4765C>T	p.Arg1589Cys	p.R1589C	ENST00000357654	NM_007294.3	1589	Cgt/Tgt	15/23	0.260310592984664	2	FACETS	0.529	0.448	0.618	0.265	0.224	0.309	SUBCLONAL	1	TRUE	0	0.317694272894268	2		453	595	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117684026	117684026	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1185167609	NA	P-0032800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	89	324	0	ENST00000368508.3:c.3121C>T	p.Pro1041Ser	p.P1041S	ENST00000368508	NM_002944.2	1041	Cca/Tca	21/43	0.305088635418922	3	FACETS	0.873	0.78	0.97	0.873	0.78	0.97	CLONAL	2	TRUE	1	0.317694272894268	3		324	372	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981275	201981276	+	missense_variant	Missense_Mutation	DNP	GG	GG	CA	novel	NA	P-0032800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	186	645	1	ENST00000359651.3:c.354_355delinsCA	p.Asp119Asn	p.D119N	ENST00000359651		118	ggGGac/ggCAac	2/8	0.260310592984664	2	FACETS	0.829	0.768	0.892	0.829	0.768	0.892	CLONAL	2	TRUE	0	0.317694272894268	2		646	706	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683399	88683399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	107	425	0	ENST00000372037.3:c.1522C>T	p.Pro508Ser	p.P508S	ENST00000372037	NM_004329.2	508	Cca/Tca	13/13	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.317694272894268	2		425	581	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118365100	118365100	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	135	412	0	ENST00000534358.1:c.5276C>T	p.Ser1759Phe	p.S1759F	ENST00000534358	NM_005933.3	1759	tCc/tTc	17/36	0.303122905729378	2	FACETS	0.885	0.81	0.963	0.885	0.81	0.963	CLONAL	2	TRUE	0	0.317694272894268	2		412	480	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006654	62006654	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	244	564	0	ENST00000392795.3:c.625G>A	p.Glu209Lys	p.E209K	ENST00000392795	NM_001039933.1	209	Gag/Aag	6/6	0.296296708062198	4	FACETS	1	0.959	1	0.517	0.483	0.552	CLONAL	2	TRUE	0	0.317694272894268	4		564	979	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533688	63533688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	167	430	1	ENST00000307078.5:c.1466C>T	p.Pro489Leu	p.P489L	ENST00000307078	NM_004655.3	489	cCc/cTc	6/11	0.296296708062198	4	FACETS	1	0.961	1	0.533	0.491	0.576	CLONAL	2	TRUE	0	0.317694272894268	4		431	650	SUCCESS
REL	5966	MSKCC	GRCh37	2	61148975	61148975	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	120	315	0	ENST00000295025.8:c.1165C>T	p.Pro389Ser	p.P389S	ENST00000295025	NM_002908.2	389	Ccc/Tcc	11/11	0.153336777000259	3	FACETS	0.956	0.869	1	0.637	0.579	0.698	INDETERMINATE	2	TRUE	0	0.317694272894268	3		315	458	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543557	9543557	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	144	403	1	ENST00000353224.5:c.1597G>A	p.Asp533Asn	p.D533N	ENST00000353224	NM_177990.2	533	Gac/Aac	6/10	0.305088635418922	3	FACETS	0.846	0.774	0.92	0.846	0.774	0.92	CLONAL	2	TRUE	1	0.317694272894268	3		404	621	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024291	31024291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201338763	NA	P-0032800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	179	426	0	ENST00000375687.4:c.3776C>T	p.Pro1259Leu	p.P1259L	ENST00000375687	NM_015338.5	1259	cCa/cTa	13/13	0.305088635418922	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.317694272894268	3		426	583	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651281	52651282	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0032800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	152	397	0	ENST00000394830.3:c.1814_1815delinsTT	p.Ser605Phe	p.S605F	ENST00000394830	NM_018313.4	605	tCC/tTT	15/30	0.303122905729378	2	FACETS	0.891	0.82	0.965	0.891	0.82	0.965	CLONAL	2	TRUE	0	0.317694272894268	2		397	537	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402728	20402728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759274608	NA	P-0032800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	55	292	0	ENST00000346618.3:c.265C>T	p.Pro89Ser	p.P89S	ENST00000346618	NM_001949.4	89	Ccc/Tcc	1/7	0.305088635418922	3	FACETS	0.882	0.756	1	0.441	0.378	0.51	CLONAL	1	TRUE	1	0.317694272894268	3		292	455	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196942	138196942	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	97	271	0	ENST00000237289.4:c.604A>G	p.Ile202Val	p.I202V	ENST00000237289	NM_001270507.1	202	Atc/Gtc	4/9	0.305088635418922	3	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	1	0.317694272894268	3		271	343	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963948	2963948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	190	560	0	ENST00000396946.4:c.1859C>T	p.Ser620Phe	p.S620F	ENST00000396946	NM_032415.4	620	tCc/tTc	15/25	0.252053728033621	4	FACETS	0.847	0.784	0.914	0.847	0.784	0.914	CLONAL	2	TRUE	2	0.317694272894268	4		560	930	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56912099	56912099	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	71	588	0	ENST00000519728.1:c.1327C>T	p.Pro443Ser	p.P443S	ENST00000519728	NM_002350.3	443	Ccc/Tcc	12/13	0.252053728033621	4	FACETS	0.81	0.706	0.922	0.405	0.353	0.461	CLONAL	1	TRUE	2	0.317694272894268	4		588	727	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249438	110249438	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	387	802	0	ENST00000374672.4:c.1135C>T	p.Pro379Ser	p.P379S	ENST00000374672	NM_004235.4	379	Ccc/Tcc	4/5	0.305088635418922	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.317694272894268	3		802	1229	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0032801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	80	226	1	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.790273633181417	1	FACETS	0.98	0.9	1	0.98	0.9	1	CLONAL	1	TRUE	0	0.790273633181417	1		227	125	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0032801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	181	634	1	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.78892688272693	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.790273633181417	1		635	266	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814548	43814548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1445777626	NA	P-0032801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	102	346	0	ENST00000372470.3:c.1343C>T	p.Thr448Ile	p.T448I	ENST00000372470	NM_005373.2	448	aCc/aTc	9/12	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.790273633181417	2		346	231	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0032802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	86	454	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	NA	2	FACETS	0.511	0.452	0.575			1	INDETERMINATE	1	TRUE	NA	0.476367593692424	2		454	706	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253911	NA	P-0032802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	178	428	0	ENST00000269305.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000269305	NM_001126112.2	180	Gag/Aag	5/11	0.476367593692424	1	FACETS	0.957	0.887	1	0.957	0.887	1	CLONAL	1	TRUE	0	0.476367593692424	1		428	595	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111494	8111495	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTGG	novel	NA	P-0032802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	151	423	0	ENST00000346208.3:c.981_984dup	p.Arg329LeufsTer24	p.R329Lfs*24	ENST00000346208		327	ctc/ctCTGGc	5/6	1	2	FACETS	0.765	0.699	0.833	0.765	0.699	0.833	SUBCLONAL	1	TRUE	1	0.476367593692424	2		423	829	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717615	89717616	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	122	276	0	ENST00000371953.3:c.641dup	p.Phe215ValfsTer28	p.F215Vfs*28	ENST00000371953	NM_000314.4	214	cag/cAag	7/9	0.476367593692424	1	FACETS	0.877	0.798	0.958	0.877	0.798	0.958	CLONAL	1	TRUE	0	0.476367593692424	1		276	445	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244604	46244604	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	170	367	0	ENST00000334344.6:c.2698C>G	p.Pro900Ala	p.P900A	ENST00000334344	NM_152641.2	900	Cct/Gct	15/21	1	2	FACETS	0.987	0.91	1	0.987	0.91	1	CLONAL	1	TRUE	1	0.476367593692424	2		367	723	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687120	37687120	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1158026447	NA	P-0032802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	130	356	0	ENST00000447079.4:c.4024G>C	p.Asp1342His	p.D1342H	ENST00000447079	NM_015083.1	1342	Gat/Cat	14/14	1	2	FACETS	0.916	0.834	1	0.916	0.834	1	CLONAL	1	TRUE	1	0.476367593692424	2		356	596	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs760043106	NA	P-0032809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	30	567	0	ENST00000269305.4:c.584T>A	p.Ile195Asn	p.I195N	ENST00000269305	NM_001126112.2	195	aTc/aAc	6/11	0.3	2	FACETS	0.679	0.546	0.831			1	SUBCLONAL	1	TRUE	NA	0.16	2		567	552	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0032811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	86	264	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	0.3889382055075	2		264	426	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636204	87636204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs532184896	NA	P-0032811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	83	333	0	ENST00000277120.3:c.2369G>A	p.Arg790Gln	p.R790Q	ENST00000277120		790	cGa/cAa	19/19	1	2	FACETS	0.934	0.828	1	0.934	0.828	1	CLONAL	1	TRUE	1	0.3889382055075	2		333	457	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842683	68842684	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	167	519	0	ENST00000261769.5:c.621dup	p.Glu208Ter	p.E208*	ENST00000261769	NM_004360.3	207	att/aTtt	5/16	0.3889382055075	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.3889382055075	1		519	654	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057706	27057706	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	68	649	0	ENST00000324856.7:c.1414A>G	p.Asn472Asp	p.N472D	ENST00000324856	NM_006015.4	472	Aac/Gac	3/20	1	2	FACETS	0.959	0.835	1	0.959	0.835	1	CLONAL	1	FALSE	1	0.250509919413281	2		649	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0032822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	492	637	2	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.367361976941938	4	FACETS	0.987	0.95	1	0.987	0.95	1	CLONAL	4	TRUE	0	0.367361976941938	4		639	928	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0032822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	2472	462	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.367361976941938	30	FACETS	1	0.997	1			1	CLONAL	30	TRUE	NA	0.367361976941938	30		462	2729	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0032822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	56	343	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.346272992143791	4	FACETS	0.986	0.847	1	0.493	0.423	0.568	CLONAL	1	TRUE	2	0.367361976941938	4		343	423	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044898	47044898	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	409	398	0	ENST00000377604.3:c.2224C>T	p.Gln742Ter	p.Q742*	ENST00000377604	NM_001204468.1	742	Cag/Tag	20/24	0.367361976941938	3	FACETS	1	0.989	1			1	CLONAL	4	TRUE	NA	0.367361976941938	3		398	622	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748421	162748421	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	75	436	0	ENST00000367921.3:c.2335G>T	p.Glu779Ter	p.E779*	ENST00000367921	NM_006182.2	779	Gag/Tag	17/18	0.367689828202943	5	FACETS	1	0.884	1	0.336	0.294	0.381	CLONAL	1	TRUE	2	0.367361976941938	5		436	628	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271269	153271269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	26	209	0	ENST00000281708.4:c.509G>A	p.Arg170Lys	p.R170K	ENST00000281708	NM_033632.3	170	aGa/aAa	3/12	0.330380937816379	3	FACETS	0.926	0.739	1	0.463	0.369	0.568	CLONAL	1	TRUE	1	0.367361976941938	3		209	181	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	268	440	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.963	0.91	1	0.963	0.91	1	CLONAL	1	TRUE	1	0.89222625909207	2		440	624	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0032825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	358	637	2	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.887302632845852	1	FACETS	0.992	0.963	1	0.992	0.963	1	CLONAL	1	TRUE	0	0.89222625909207	1		639	448	SUCCESS
APC	324	MSKCC	GRCh37	5	112154942	112154942	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779780	NA	P-0032825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	345	612	1	ENST00000257430.4:c.1213C>T	p.Arg405Ter	p.R405*	ENST00000257430	NM_000038.5	405	Cga/Tga	10/16	0.887302632845852	1	FACETS	0.982	0.953	1	0.982	0.953	1	CLONAL	1	TRUE	0	0.89222625909207	1		613	436	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69207357	69207357	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	252	460	0	ENST00000462284.1:c.123G>T	p.Leu41Phe	p.L41F	ENST00000462284	NM_002392.5	41	ttG/ttT	3/11	1	2	FACETS	0.938	0.885	0.992	0.938	0.885	0.992	CLONAL	1	TRUE	1	0.89222625909207	2		460	602	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774157	56774158	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	369	526	2	ENST00000337432.4:c.509dup	p.Asp171ArgfsTer32	p.D171Rfs*32	ENST00000337432	NM_058216.2	170	gta/gTta	3/9	0.89222625909207	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.89222625909207	1		528	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0032826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	192	808	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.623960229710192	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.623960229710192	1		808	383	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955538	48955538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913303	NA	P-0032826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	101	337	0	ENST00000267163.4:c.1654C>T	p.Arg552Ter	p.R552*	ENST00000267163	NM_000321.2	552	Cga/Tga	17/27	0.623960229710192	1	FACETS	0.981	0.896	1	0.981	0.896	1	CLONAL	1	TRUE	0	0.623960229710192	1		337	227	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0032826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	33	96	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	1	2	FACETS	0.998	0.833	1	0.998	0.833	1	CLONAL	1	TRUE	1	0.623960229710192	2		96	106	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926872	112926872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507541	NA	P-0032826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	147	736	3	ENST00000351677.2:c.1492C>T	p.Arg498Trp	p.R498W	ENST00000351677	NM_002834.3	498	Cgg/Tgg	13/16	1	2	FACETS	0.877	0.806	0.952	0.877	0.806	0.952	CLONAL	1	TRUE	1	0.623960229710192	2		739	537	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0032827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	307	357	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.820625868479781	4	FACETS	1	0.992	1	0.802	0.766	0.839	CLONAL	2	TRUE	1	0.864889544827435	4		357	550	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0032827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	1106	863	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.80751167668955	4	FACETS	0.971	0.959	0.982	0.971	0.959	0.982	CLONAL	4	TRUE	0	0.864889544827435	4		863	1228	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954327	48954328	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0032827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	796	448	0	ENST00000267163.4:c.1450_1451del	p.Met484ValfsTer8	p.M484Vfs*8	ENST00000267163	NM_000321.2	483	cAT/c	16/27	0.798635652790306	5	FACETS	0.96	0.947	0.972	0.96	0.947	0.972	CLONAL	5	TRUE	0	0.864889544827435	5		448	881	SUCCESS
APC	324	MSKCC	GRCh37	5	112178355	112178355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	333	474	0	ENST00000257430.4:c.7064C>T	p.Ser2355Leu	p.S2355L	ENST00000257430	NM_000038.5	2355	tCa/tTa	16/16	0.811862747705938	2	FACETS	0.897	0.869	0.925	0.897	0.869	0.925	CLONAL	2	TRUE	0	0.864889544827435	2		474	429	SUCCESS
APC	324	MSKCC	GRCh37	5	112173600	112173600	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1060503310	NA	P-0032827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	264	364	0	ENST00000257430.4:c.2309C>G	p.Ser770Ter	p.S770*	ENST00000257430	NM_000038.5	770	tCa/tGa	16/16	0.811862747705938	2	FACETS	0.882	0.85	0.913	0.882	0.85	0.913	CLONAL	2	TRUE	0	0.864889544827435	2		364	346	SUCCESS
APC	324	MSKCC	GRCh37	5	112177323	112177323	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554087155	NA	P-0032827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	243	406	1	ENST00000257430.4:c.6032C>T	p.Ser2011Leu	p.S2011L	ENST00000257430	NM_000038.5	2011	tCa/tTa	16/16	0.811862747705938	2	FACETS	0.881	0.847	0.913	0.881	0.847	0.913	CLONAL	2	TRUE	0	0.864889544827435	2		407	319	SUCCESS
APC	324	MSKCC	GRCh37	5	112173275	112173275	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	139	244	1	ENST00000257430.4:c.1984C>G	p.Leu662Val	p.L662V	ENST00000257430	NM_000038.5	662	Cta/Gta	16/16	0.811862747705938	2	FACETS	0.924	0.88	0.964	0.924	0.88	0.964	CLONAL	2	TRUE	0	0.864889544827435	2		245	174	SUCCESS
APC	324	MSKCC	GRCh37	5	112173642	112173642	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs778287168	NA	P-0032827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	267	428	0	ENST00000257430.4:c.2351C>G	p.Ser784Cys	p.S784C	ENST00000257430	NM_000038.5	784	tCt/tGt	16/16	0.811862747705938	2	FACETS	0.895	0.863	0.925	0.895	0.863	0.925	CLONAL	2	TRUE	0	0.864889544827435	2		428	345	SUCCESS
APC	324	MSKCC	GRCh37	5	112173992	112173992	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	269	378	0	ENST00000257430.4:c.2701C>G	p.Gln901Glu	p.Q901E	ENST00000257430	NM_000038.5	901	Cag/Gag	16/16	0.811862747705938	2	FACETS	0.948	0.918	0.977	0.948	0.918	0.977	CLONAL	2	TRUE	0	0.864889544827435	2		378	328	SUCCESS
APC	324	MSKCC	GRCh37	5	112174979	112174979	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	187	279	0	ENST00000257430.4:c.3688C>G	p.Gln1230Glu	p.Q1230E	ENST00000257430	NM_000038.5	1230	Cag/Gag	16/16	0.811862747705938	2	FACETS	0.924	0.887	0.959	0.924	0.887	0.959	CLONAL	2	TRUE	0	0.864889544827435	2		279	234	SUCCESS
APC	324	MSKCC	GRCh37	5	112175502	112175502	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	267	424	0	ENST00000257430.4:c.4211C>G	p.Ser1404Cys	p.S1404C	ENST00000257430	NM_000038.5	1404	tCc/tGc	16/16	0.811862747705938	2	FACETS	0.897	0.865	0.928	0.897	0.865	0.928	CLONAL	2	TRUE	0	0.864889544827435	2		424	344	SUCCESS
APC	324	MSKCC	GRCh37	5	112176234	112176234	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	320	463	0	ENST00000257430.4:c.4943C>G	p.Pro1648Arg	p.P1648R	ENST00000257430	NM_000038.5	1648	cCt/cGt	16/16	0.811862747705938	2	FACETS	0.93	0.901	0.956	0.93	0.901	0.956	CLONAL	2	TRUE	0	0.864889544827435	2		463	398	SUCCESS
APC	324	MSKCC	GRCh37	5	112176269	112176269	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs767271480	NA	P-0032827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	273	446	0	ENST00000257430.4:c.4978C>G	p.Leu1660Val	p.L1660V	ENST00000257430	NM_000038.5	1660	Cta/Gta	16/16	0.811862747705938	2	FACETS	0.931	0.9	0.96	0.931	0.9	0.96	CLONAL	2	TRUE	0	0.864889544827435	2		446	339	SUCCESS
APC	324	MSKCC	GRCh37	5	112176285	112176287	+	frameshift_variant	Frame_Shift_Del	DEL	CTC	CTC	TT	novel	NA	P-0032827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	235	439	1	ENST00000257430.4:c.4994_4996delinsTT	p.Pro1665LeufsTer5	p.P1665Lfs*5	ENST00000257430	NM_000038.5	1665	cCTCca/cTTca	16/16	0.811862747705938	2	FACETS	0.882	0.848	0.915	0.882	0.848	0.915	CLONAL	2	TRUE	0	0.864889544827435	2		440	308	SUCCESS
APC	324	MSKCC	GRCh37	5	112176774	112176774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs971100064	NA	P-0032827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	280	414	1	ENST00000257430.4:c.5483C>T	p.Pro1828Leu	p.P1828L	ENST00000257430	NM_000038.5	1828	cCa/cTa	16/16	0.811862747705938	2	FACETS	0.928	0.897	0.956	0.928	0.897	0.956	CLONAL	2	TRUE	0	0.864889544827435	2		415	349	SUCCESS
APC	324	MSKCC	GRCh37	5	112178385	112178385	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0032827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	321	480	0	ENST00000257430.4:c.7094C>G	p.Ser2365Ter	p.S2365*	ENST00000257430	NM_000038.5	2365	tCa/tGa	16/16	0.811862747705938	2	FACETS	0.903	0.874	0.931	0.903	0.874	0.931	CLONAL	2	TRUE	0	0.864889544827435	2		480	411	SUCCESS
APC	324	MSKCC	GRCh37	5	112178562	112178562	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	257	419	0	ENST00000257430.4:c.7271C>T	p.Ser2424Leu	p.S2424L	ENST00000257430	NM_000038.5	2424	tCa/tTa	16/16	0.811862747705938	2	FACETS	0.884	0.852	0.915	0.884	0.852	0.915	CLONAL	2	TRUE	0	0.864889544827435	2		419	336	SUCCESS
APC	324	MSKCC	GRCh37	5	112178633	112178633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561614782	NA	P-0032827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	263	445	1	ENST00000257430.4:c.7342C>T	p.Pro2448Ser	p.P2448S	ENST00000257430	NM_000038.5	2448	Cca/Tca	16/16	0.811862747705938	2	FACETS	0.91	0.879	0.94	0.91	0.879	0.94	CLONAL	2	TRUE	0	0.864889544827435	2		446	334	SUCCESS
APC	324	MSKCC	GRCh37	5	112178753	112178753	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	400	544	0	ENST00000257430.4:c.7462C>G	p.Leu2488Val	p.L2488V	ENST00000257430	NM_000038.5	2488	Ctt/Gtt	16/16	0.811862747705938	2	FACETS	0.919	0.894	0.944	0.919	0.894	0.944	CLONAL	2	TRUE	0	0.864889544827435	2		544	503	SUCCESS
APC	324	MSKCC	GRCh37	5	112179591	112179591	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0032827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	300	412	0	ENST00000257430.4:c.8300C>G	p.Ser2767Ter	p.S2767*	ENST00000257430	NM_000038.5	2767	tCa/tGa	16/16	0.811862747705938	2	FACETS	0.943	0.914	0.97	0.943	0.914	0.97	CLONAL	2	TRUE	0	0.864889544827435	2		412	368	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907702	76907702	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	481	664	0	ENST00000373344.5:c.4459G>A	p.Asp1487Asn	p.D1487N	ENST00000373344	NM_000489.3	1487	Gat/Aat	15/35	0.60774482954407	3	FACETS	0.907	0.874	0.94	0.907	0.874	0.94	CLONAL	2	TRUE	1	0.864889544827435	3		664	878	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0032830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	108	331	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.494484733231206	2		331	358	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0032830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1532	7777	470	0	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.494484733231206	59	FACETS	1	0.994	1	0.864	0.859	0.87	CLONAL	51	TRUE	0	0.494484733231206	59		470	9309	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	381	248	0				ENST00000310581	NM_198253.2	-/1132			0.758183936203427	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	1	0.758183936203427	4		248	539	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023151	27023179	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	-	novel	NA	P-0032840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	110	19	0	ENST00000324856.7:c.267_295del	p.Ser90ProfsTer11	p.S90Pfs*11	ENST00000324856	NM_006015.4	86	gGCGGAGCCGGCAGCGGCGGCGGGCCCGGC/g	1/20	0.386215833576258	3	FACETS	0.933	0.88	0.981	1	0.99	1	INDETERMINATE	3	TRUE	1	0.758183936203427	3		19	143	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436611	49436612	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0032840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	494	589	0	ENST00000301067.7:c.5693_5694dup	p.Leu1899PhefsTer17	p.L1899Ffs*17	ENST00000301067	NM_003482.3	1898	-/TT	26/54	0.386215833576258	3	FACETS	0.879	0.845	0.913	0.879	0.845	0.913	INDETERMINATE	2	TRUE	1	0.758183936203427	3		589	1022	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578548	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0032840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	909	648	0	ENST00000269305.4:c.382_383del	p.Pro128CysfsTer20	p.P128Cfs*20	ENST00000269305	NM_001126112.2	128	CCt/t	5/11	0.735420987001406	3	FACETS	0.96	0.942	0.977	0.96	0.942	0.977	CLONAL	3	TRUE	0	0.758183936203427	3		648	1148	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238418	98238435	+	inframe_deletion	In_Frame_Del	DEL	CTTCAGGCACTCCCCGGT	CTTCAGGCACTCCCCGGT	-	novel	NA	P-0032840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	247	337	0	ENST00000331920.6:c.1609_1626del	p.Thr537_Lys542del	p.T537_K542del	ENST00000331920	NM_000264.3	537	ACCGGGGAGTGCCTGAAG/-	12/24	0.716397655332605	2	FACETS	0.942	0.903	0.979	0.942	0.903	0.979	CLONAL	2	TRUE	0	0.758183936203427	2		337	346	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397633	139397633	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0032840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	424	593	0	ENST00000277541.6:c.5167+1G>A		p.X1723_splice	ENST00000277541	NM_017617.3	1723			0.716397655332605	2	FACETS	0.912	0.882	0.941	0.912	0.882	0.941	CLONAL	2	TRUE	0	0.758183936203427	2		593	613	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0032855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	210	454	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.390942166891963	2	FACETS	0.912	0.853	0.972	0.912	0.853	0.972	CLONAL	2	TRUE	0	0.390942166891963	2		454	589	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0032855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	40	331	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.961	0.806	1			1	INDETERMINATE	1	TRUE	NA	0.390942166891963	2		331	213	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423565	88423565	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	97	646	0	ENST00000360948.2:c.2270G>T	p.Gly757Val	p.G757V	ENST00000360948	NM_001012338.2	757	gGg/gTg	18/19	1	2	FACETS	0.938	0.839	1	0.938	0.839	1	CLONAL	1	TRUE	1	0.390942166891963	2		646	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577526	7577526	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121912653	NA	P-0032855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	116	676	0	ENST00000269305.4:c.755T>C	p.Leu252Pro	p.L252P	ENST00000269305	NM_001126112.2	252	cTc/cCc	7/11	0.359813504751586	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	0	0.390942166891963	1		676	477	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220612	1220612	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201213	NA	P-0032855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	104	601	0	ENST00000326873.7:c.630C>A	p.Cys210Ter	p.C210*	ENST00000326873	NM_000455.4	210	tgC/tgA	5/10	0.390942166891963	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.390942166891963	1		601	386	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137522134	137522134	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	59	188	0	ENST00000367739.4:c.745A>C	p.Ile249Leu	p.I249L	ENST00000367739	NM_000416.2	249	Att/Ctt	6/7	0.359813504751586	1	FACETS	0.93	0.809	1	0.93	0.809	1	CLONAL	1	TRUE	0	0.390942166891963	1		188	261	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	216	248	0				ENST00000310581	NM_198253.2	-/1132			0.457226736700066	7	FACETS	0.991	0.93	1	0.792	0.744	0.841	CLONAL	4	TRUE	2	0.457226736700066	7		248	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0032858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	234	660	2	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.206262932394351	4	FACETS	0.886	0.828	0.945	0.886	0.828	0.945	INDETERMINATE	2	TRUE	2	0.457226736700066	4		662	842	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220640	1220640	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690940	NA	P-0032858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	301	785	1	ENST00000326873.7:c.658C>T	p.Gln220Ter	p.Q220*	ENST00000326873	NM_000455.4	220	Cag/Tag	5/10	0.451770867044069	2	FACETS	0.997	0.947	1	0.997	0.947	1	CLONAL	2	TRUE	0	0.457226736700066	2		786	660	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422137	81422137	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	88	497	0	ENST00000298171.2:c.113G>C	p.Arg38Thr	p.R38T	ENST00000298171	NM_000369.2	38	aGa/aCa	1/10	0.457226736700066	2	FACETS	0.816	0.725	0.911	0.408	0.362	0.456	CLONAL	1	TRUE	0	0.457226736700066	2		497	472	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281778	39281778	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519963	NA	P-0032858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	95	417	0	ENST00000402219.2:c.697A>T	p.Asn233Tyr	p.N233Y	ENST00000402219	NM_005633.3	233	Aat/Tat	5/23	1	2	FACETS	0.917	0.821	1	0.917	0.821	1	CLONAL	1	TRUE	1	0.457226736700066	2		417	453	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141824	108141824	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	220	510	0	ENST00000278616.4:c.2872G>T	p.Glu958Ter	p.E958*	ENST00000278616	NM_000051.3	958	Gag/Tag	19/63	0.457226736700066	2	FACETS	0.846	0.793	0.899	0.846	0.793	0.899	CLONAL	2	TRUE	0	0.457226736700066	2		510	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578453	7578504	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGCGGACGCGGGTGCCGGGCGGGGGTGTGGAATCAACCCACAGCTGCACA	GGCGCGGACGCGGGTGCCGGGCGGGGGTGTGGAATCAACCCACAGCTGCACA	-	novel	NA	P-0032858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	214	719	1	ENST00000269305.4:c.426_477del	p.Val143TrpfsTer10	p.V143Wfs*10	ENST00000269305	NM_001126112.2	142	ccTGTGCAGCTGTGGGTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGCGCC/cc	5/11	0.206262932394351	4	FACETS	0.779	0.725	0.835	0.779	0.725	0.835	INDETERMINATE	2	TRUE	2	0.457226736700066	4		720	875	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619344	1619344	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	251	701	1	ENST00000344749.5:c.1297A>T	p.Met433Leu	p.M433L	ENST00000344749	NM_001136139.2	433	Atg/Ttg	15/19	0.451770867044069	2	FACETS	0.956	0.903	1	0.956	0.903	1	CLONAL	2	TRUE	0	0.457226736700066	2		702	574	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505424	25505425	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0032858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	84	536	2	ENST00000264709.3:c.333_334delinsTT	p.Lys111_Gly112delinsAsnCys	p.K111_G112delinsNC	ENST00000264709	NM_175629.2	111	aaGGgc/aaTTgc	4/23	1	2	FACETS	0.795	0.705	0.891	0.795	0.705	0.891	SUBCLONAL	1	TRUE	1	0.457226736700066	2		538	462	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607705	46607705	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	162	736	0	ENST00000263734.3:c.1894G>T	p.Gly632Trp	p.G632W	ENST00000263734	NM_001430.4	632	Ggg/Tgg	12/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.457226736700066	2		736	621	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657030	215657030	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	60	412	0	ENST00000260947.4:c.355G>C	p.Glu119Gln	p.E119Q	ENST00000260947	NM_000465.2	119	Gag/Cag	3/11	1	2	FACETS	0.509	0.438	0.585	0.509	0.438	0.585	SUBCLONAL	1	TRUE	1	0.457226736700066	2		412	516	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026793	71026793	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0032858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	155	276	0	ENST00000318789.4:c.1428+1G>T		p.X476_splice	ENST00000318789	NM_032682.5	476			0.216686853722077	2	FACETS	0.781	0.722	0.841	0.781	0.722	0.841	INDETERMINATE	2	TRUE	0	0.457226736700066	2		276	434	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005183	150005183	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	102	556	0	ENST00000253339.5:c.1042C>T	p.Gln348Ter	p.Q348*	ENST00000253339		348	Cag/Tag	3/7	1	2	FACETS	0.839	0.753	0.929	0.839	0.753	0.929	CLONAL	1	TRUE	1	0.457226736700066	2		556	532	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521431	8521431	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	169	689	0	ENST00000356435.5:c.807G>T	p.Trp269Cys	p.W269C	ENST00000356435		269	tgG/tgT	9/35	0.457482131144014	3	FACETS	0.835	0.766	0.906	0.417	0.383	0.453	CLONAL	1	TRUE	1	0.457226736700066	3		689	1088	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434736	128434737	+	missense_variant	Missense_Mutation	DNP	TC	TC	CA	novel	NA	P-0032858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	142	672	0	ENST00000265960.3:c.117_118delinsTG	p.Glu39_Lys40delinsAspGlu	p.E39_K40delinsDE	ENST00000265960	NM_001006617.1	39	gaGAag/gaTGag	2/12	1	2	FACETS	0.899	0.821	0.98	0.899	0.821	0.98	CLONAL	1	TRUE	1	0.457226736700066	2		672	691	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255121	16255121	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs749597868	NA	P-0032859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	81	281	0	ENST00000375759.3:c.2386A>T	p.Thr796Ser	p.T796S	ENST00000375759	NM_015001.2	796	Act/Tct	11/15	0.419451447122155	4	FACETS	1	0.963	1	0.605	0.537	0.677	CLONAL	1	TRUE	2	0.571983035619423	4		281	368	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424464	49424465	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	195	523	0	ENST00000301067.7:c.13758dup	p.Gly4587TrpfsTer19	p.G4587Wfs*19	ENST00000301067	NM_003482.3	4586	-/T	41/54	0.449456667083644	3	FACETS	1	0.988	1	0.796	0.75	0.843	CLONAL	2	TRUE	0	0.571983035619423	3		523	367	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443688	49443688	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	226	538	0	ENST00000301067.7:c.3683G>T	p.Gly1228Val	p.G1228V	ENST00000301067	NM_003482.3	1228	gGc/gTc	11/54	0.449456667083644	3	FACETS	0.871	0.826	0.915	0.871	0.826	0.915	CLONAL	3	TRUE	0	0.571983035619423	3		538	389	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951140	48951140	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	161	342	0	ENST00000267163.4:c.1304del	p.Gly435AspfsTer22	p.G435Dfs*22	ENST00000267163	NM_000321.2	434	gtG/gt	13/27	0.437131592046961	3	FACETS	1	0.938	1	0.672	0.626	0.719	CLONAL	2	TRUE	0	0.571983035619423	3		342	359	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675097	40675097	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	235	604	0	ENST00000249776.8:c.61G>A	p.Glu21Lys	p.E21K	ENST00000249776	NM_033286.3	21	Gag/Aag	1/9	0.483989634152324	4	FACETS	0.997	0.936	1	0.997	0.936	1	CLONAL	2	TRUE	2	0.571983035619423	4		604	648	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857803	9857803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	177	491	0	ENST00000330684.3:c.3598C>T	p.His1200Tyr	p.H1200Y	ENST00000330684	NM_001134407.1	1200	Cac/Tac	13/13	0.483989634152324	4	FACETS	0.965	0.897	1	0.965	0.897	1	CLONAL	2	TRUE	2	0.571983035619423	4		491	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519989	NA	P-0032859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	194	575	0	ENST00000269305.4:c.730G>C	p.Gly244Arg	p.G244R	ENST00000269305	NM_001126112.2	244	Ggc/Cgc	7/11	0.511665682802575	2	FACETS	0.929	0.875	0.983	0.929	0.875	0.983	CLONAL	2	TRUE	0	0.571983035619423	2		575	365	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632040	1632040	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	174	625	0	ENST00000344749.5:c.295G>T	p.Gly99Ter	p.G99*	ENST00000344749	NM_001136139.2	99	Gga/Tga	5/19	0.483989634152324	4	FACETS	0.889	0.824	0.955	0.889	0.824	0.955	CLONAL	2	TRUE	2	0.571983035619423	4		625	538	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584661	187584662	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	189	409	0	ENST00000441802.2:c.3371dup	p.Ile1125AspfsTer6	p.I1125Dfs*6	ENST00000441802	NM_005245.3	1124	gag/gaAg	3/27	0.507403101456202	2	FACETS	0.9	0.846	0.954	0.9	0.846	0.954	CLONAL	2	TRUE	0	0.571983035619423	2		409	367	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100441	8100442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0032861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	128	642	0	ENST00000346208.3:c.417dup	p.Ser140LeufsTer163	p.S140Lfs*163	ENST00000346208		139	tcc/tCcc	3/6	1	2	FACETS	0.62	0.563	0.681	0.62	0.563	0.681	SUBCLONAL	1	TRUE	1	0.57097722334309	2		642	723	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	20	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.956	0.733	1	0.956	0.733	1	CLONAL	1	TRUE	1	0.17	2		248	246	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188240	10188240	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	16	694	0	ENST00000256474.2:c.383T>A	p.Leu128His	p.L128H	ENST00000256474	NM_000551.3	128	cTt/cAt	2/3	1	2	FACETS	0.7	0.517	0.918	0.7	0.517	0.918	SUBCLONAL	1	TRUE	1	0.17	2		694	269	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406306	70406307	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0032863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	23	642	1	ENST00000373644.4:c.3820_3821delinsAT	p.Gly1274Met	p.G1274M	ENST00000373644	NM_030625.2	1274	GGg/ATg	4/12	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.17	2		643	227	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783814	50783814	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	12	578	0	ENST00000398568.2:c.205C>T	p.Gln69Ter	p.Q69*	ENST00000398568	NM_001042412.1	69	Cag/Tag	3/18	1	2	FACETS	0.888	0.626	1	0.888	0.626	1	CLONAL	1	TRUE	1	0.17	2		578	159	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598250	52598250	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0032863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	12	345	0	ENST00000394830.3:c.3617-1G>A		p.X1206_splice	ENST00000394830	NM_018313.4	1206			1	2	FACETS	0.967	0.683	1	0.967	0.683	1	CLONAL	1	TRUE	1	0.17	2		345	146	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535354	66535354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	27	521	0	ENST00000273854.3:c.107G>A	p.Arg36Gln	p.R36Q	ENST00000273854	NM_004439.5	36	cGa/cAa	1/18	1	2	FACETS	1	0.82	1	1	0.82	1	CLONAL	1	TRUE	1	0.17	2		521	308	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786025	135786037	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGCTGGAGGAG	GGGGCTGGAGGAG	-	novel	NA	P-0032863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	22	692	0	ENST00000298552.3:c.1184_1196del	p.Pro395HisfsTer41	p.P395Hfs*41	ENST00000298552	NM_001162426.1	395	cCTCCTCCAGCCCCa/ca	12/23	1	2	FACETS	0.7	0.542	0.883	0.7	0.542	0.883	SUBCLONAL	1	TRUE	1	0.17	2		692	370	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0032868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	344	207	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	0.922912032843615	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.922912032843615	3		207	540	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061317	38061317	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	336	426	0	ENST00000250448.2:c.672C>A	p.Phe224Leu	p.F224L	ENST00000250448	NM_004496.3	224	ttC/ttA	2/2	1	2	FACETS	0.981	0.934	1	0.981	0.934	1	CLONAL	1	TRUE	1	0.922912032843615	2		426	742	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805149	43805149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	75	466	0	ENST00000372470.3:c.599C>T	p.Pro200Leu	p.P200L	ENST00000372470	NM_005373.2	200	cCt/cTt	4/12	0.880328543177322	1	FACETS	0.218	0.191	0.246	0.218	0.191	0.246	SUBCLONAL	1	TRUE	0	0.880328543177322	1		466	438	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567721	226567721	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	52	517	0	ENST00000366794.5:c.1445G>A	p.Gly482Glu	p.G482E	ENST00000366794	NM_001618.3	482	gGg/gAg	10/23	0.880328543177322	1	FACETS	0.151	0.128	0.175	0.151	0.128	0.175	SUBCLONAL	1	TRUE	0	0.880328543177322	1		517	439	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608331	43608331	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	61	774	0	ENST00000355710.3:c.1679C>T	p.Pro560Leu	p.P560L	ENST00000355710	NM_020975.4	560	cCc/cTc	9/20	1	2	FACETS	0.127	0.109	0.147	0.127	0.109	0.147	SUBCLONAL	1	TRUE	1	0.880328543177322	2		774	1093	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63810754	63810754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	270	352	0	ENST00000279873.7:c.841G>A	p.Ala281Thr	p.A281T	ENST00000279873	NM_032199.2	281	Gcc/Acc	5/10	0.880328543177322	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.880328543177322	1		352	331	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406146	70406146	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	36	518	0	ENST00000373644.4:c.3660G>A	p.Trp1220Ter	p.W1220*	ENST00000373644	NM_030625.2	1220	tgG/tgA	4/12	0.880328543177322	1	FACETS	0.096	0.079	0.116	0.096	0.079	0.116	SUBCLONAL	1	TRUE	0	0.880328543177322	1		518	476	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129442	64129442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	55	584	0	ENST00000334205.4:c.874G>A	p.Ala292Thr	p.A292T	ENST00000334205	NM_003942.2	292	Gca/Aca	8/17	0.880328543177322	1	FACETS	0.145	0.124	0.168	0.145	0.124	0.168	SUBCLONAL	1	TRUE	0	0.880328543177322	1		584	483	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574687	64574687	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1114167502	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	296	489	0	ENST00000312049.6:c.788T>C	p.Leu263Pro	p.L263P	ENST00000312049	NM_130799.2	263	cTg/cCg	5/10	0.880328543177322	1	FACETS	0.927	0.893	0.96	0.927	0.893	0.96	CLONAL	1	TRUE	0	0.880328543177322	1		489	406	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482351	56482351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	54	500	1	ENST00000267101.3:c.899C>T	p.Ser300Phe	p.S300F	ENST00000267101	NM_001982.3	300	tCc/tTc	8/28	1	2	FACETS	0.144	0.122	0.168	0.144	0.122	0.168	SUBCLONAL	1	TRUE	1	0.880328543177322	2		501	852	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490384	56490384	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	49	333	0	ENST00000267101.3:c.2153G>A	p.Gly718Asp	p.G718D	ENST00000267101	NM_001982.3	718	gGt/gAt	18/28	1	2	FACETS	0.177	0.149	0.207	0.177	0.149	0.207	SUBCLONAL	1	TRUE	1	0.880328543177322	2		333	630	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495508	56495508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	47	496	0	ENST00000267101.3:c.3698C>T	p.Ala1233Val	p.A1233V	ENST00000267101	NM_001982.3	1233	gCc/gTc	28/28	1	2	FACETS	0.124	0.104	0.147	0.124	0.104	0.147	SUBCLONAL	1	TRUE	1	0.880328543177322	2		496	858	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202244	133202244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	50	573	0	ENST00000320574.5:c.6644C>T	p.Thr2215Ile	p.T2215I	ENST00000320574	NM_006231.2	2215	aCc/aTc	47/49	1	2	FACETS	0.138	0.116	0.162	0.138	0.116	0.162	SUBCLONAL	1	TRUE	1	0.880328543177322	2		573	825	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220027	133220027	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	59	547	0	ENST00000320574.5:c.4410G>A	p.Met1470Ile	p.M1470I	ENST00000320574	NM_006231.2	1470	atG/atA	34/49	1	2	FACETS	0.161	0.138	0.187	0.161	0.138	0.187	SUBCLONAL	1	TRUE	1	0.880328543177322	2		547	831	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256601	133256602	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	83	364	0	ENST00000320574.5:c.361_362del	p.Ser121GlnfsTer82	p.S121Qfs*82	ENST00000320574	NM_006231.2	121	TCc/c	5/49	1	2	FACETS	0.309	0.272	0.347	0.309	0.272	0.347	SUBCLONAL	1	TRUE	1	0.880328543177322	2		364	611	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563153	21563153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	371	633	0	ENST00000382592.4:c.766C>T	p.Pro256Ser	p.P256S	ENST00000382592	NM_014572.2	256	Ccg/Tcg	4/8	1	2	FACETS	0.961	0.916	1	0.961	0.916	1	CLONAL	1	TRUE	1	0.880328543177322	2		633	877	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436879	110436879	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370070067	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	67	537	0	ENST00000375856.3:c.1522G>A	p.Gly508Ser	p.G508S	ENST00000375856	NM_003749.2	508	Ggc/Agc	1/2	1	2	FACETS	0.215	0.187	0.246	0.215	0.187	0.246	SUBCLONAL	1	TRUE	1	0.880328543177322	2		537	707	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988952	41988952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	29	425	0	ENST00000219905.7:c.1744G>A	p.Asp582Asn	p.D582N	ENST00000219905	NM_001164273.1	582	Gac/Aac	3/24	0.880328543177322	1	FACETS	0.104	0.083	0.128	0.104	0.083	0.128	SUBCLONAL	1	TRUE	0	0.880328543177322	1		425	355	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130373	2130373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	58	553	0	ENST00000219476.3:c.3605C>T	p.Pro1202Leu	p.P1202L	ENST00000219476	NM_000548.3	1202	cCc/cTc	30/42	0.880328543177322	1	FACETS	0.17	0.146	0.196	0.17	0.146	0.196	SUBCLONAL	1	TRUE	0	0.880328543177322	1		553	434	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827969	72827969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761344241	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	72	736	0	ENST00000268489.5:c.8612C>T	p.Pro2871Leu	p.P2871L	ENST00000268489	NM_006885.3	2871	cCc/cTc	9/10	0.880328543177322	1	FACETS	0.144	0.125	0.164	0.144	0.125	0.164	SUBCLONAL	1	TRUE	0	0.880328543177322	1		736	638	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832355	72832355	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	57	491	0	ENST00000268489.5:c.4226C>T	p.Ala1409Val	p.A1409V	ENST00000268489	NM_006885.3	1409	gCc/gTc	9/10	0.880328543177322	1	FACETS	0.175	0.15	0.202	0.175	0.15	0.202	SUBCLONAL	1	TRUE	0	0.880328543177322	1		491	415	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993300	72993300	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745631900	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	47	746	0	ENST00000268489.5:c.745G>A	p.Gly249Ser	p.G249S	ENST00000268489	NM_006885.3	249	Ggt/Agt	2/10	0.880328543177322	1	FACETS	0.095	0.079	0.112	0.095	0.079	0.112	SUBCLONAL	1	TRUE	0	0.880328543177322	1		746	631	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108239	8108239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	53	546	1	ENST00000585124.1:c.985G>A	p.Ala329Thr	p.A329T	ENST00000585124	NM_004217.3	329	Gcc/Acc	9/9	1	2	FACETS	0.134	0.113	0.156	0.134	0.113	0.156	SUBCLONAL	1	TRUE	1	0.880328543177322	2		547	899	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619277	37619277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	33	385	1	ENST00000447079.4:c.953C>T	p.Ser318Phe	p.S318F	ENST00000447079	NM_015083.1	318	tCt/tTt	1/14	1	2	FACETS	0.124	0.1	0.15	0.124	0.1	0.15	SUBCLONAL	1	TRUE	1	0.880328543177322	2		386	607	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873598	37873598	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	64	631	0	ENST00000269571.5:c.1763C>T	p.Ala588Val	p.A588V	ENST00000269571		588	gCc/gTc	15/27	1	2	FACETS	0.144	0.124	0.166	0.144	0.124	0.166	SUBCLONAL	1	TRUE	1	0.880328543177322	2		631	1010	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487508	38487508	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761512575	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	38	437	0	ENST00000254066.5:c.38G>A	p.Gly13Asp	p.G13D	ENST00000254066	NM_000964.3	13	gGc/gAc	2/9	1	2	FACETS	0.126	0.103	0.151	0.126	0.103	0.151	SUBCLONAL	1	TRUE	1	0.880328543177322	2		437	686	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216629	2216629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776898259	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	54	690	0	ENST00000398665.3:c.2273C>T	p.Pro758Leu	p.P758L	ENST00000398665	NM_032482.2	758	cCg/cTg	20/28	1	2	FACETS	0.125	0.106	0.146	0.125	0.106	0.146	SUBCLONAL	1	TRUE	1	0.880328543177322	2		690	983	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125503	7125503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	55	529	0	ENST00000302850.5:c.3049G>A	p.Glu1017Lys	p.E1017K	ENST00000302850	NM_000208.2	1017	Gag/Aag	17/22	1	2	FACETS	0.151	0.129	0.176	0.151	0.129	0.176	SUBCLONAL	1	TRUE	1	0.880328543177322	2		529	826	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249152	10249152	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	59	592	1	ENST00000340748.4:c.4030G>A	p.Val1344Met	p.V1344M	ENST00000340748		1344	Gtg/Atg	34/40	1	2	FACETS	0.146	0.125	0.169	0.146	0.125	0.169	SUBCLONAL	1	TRUE	1	0.880328543177322	2		593	919	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946809	17946809	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257320432	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	53	656	1	ENST00000458235.1:c.1838G>A	p.Arg613Gln	p.R613Q	ENST00000458235	NM_000215.3	613	cGa/cAa	14/24	1	2	FACETS	0.131	0.111	0.153	0.131	0.111	0.153	SUBCLONAL	1	TRUE	1	0.880328543177322	2		657	921	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974278	18974278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	62	492	0	ENST00000262803.5:c.2632G>A	p.Ala878Thr	p.A878T	ENST00000262803	NM_002911.3	878	Gca/Aca	19/24	1	2	FACETS	0.18	0.155	0.207	0.18	0.155	0.207	SUBCLONAL	1	TRUE	1	0.880328543177322	2		492	783	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974411	18974411	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	34	387	0	ENST00000262803.5:c.2765C>T	p.Thr922Ile	p.T922I	ENST00000262803	NM_002911.3	922	aCt/aTt	19/24	1	2	FACETS	0.136	0.111	0.165	0.136	0.111	0.165	SUBCLONAL	1	TRUE	1	0.880328543177322	2		387	566	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796745	42796745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	56	645	0	ENST00000575354.2:c.3203G>A	p.Gly1068Asp	p.G1068D	ENST00000575354	NM_015125.3	1068	gGt/gAt	14/20	1	2	FACETS	0.134	0.114	0.156	0.134	0.114	0.156	SUBCLONAL	1	TRUE	1	0.880328543177322	2		645	950	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523052	25523052	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	54	590	1	ENST00000264709.3:c.133G>A	p.Ala45Thr	p.A45T	ENST00000264709	NM_175629.2	45	Gca/Aca	3/23	0.880328543177322	1	FACETS	0.129	0.11	0.15	0.129	0.11	0.15	SUBCLONAL	1	TRUE	0	0.880328543177322	1		591	531	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033729	48033729	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1416452389	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	33	297	0	ENST00000234420.5:c.3940C>T	p.Gln1314Ter	p.Q1314*	ENST00000234420	NM_000179.2	1314	Caa/Taa	9/10	0.880328543177322	1	FACETS	0.128	0.104	0.155	0.128	0.104	0.155	SUBCLONAL	1	TRUE	0	0.880328543177322	1		297	327	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248612	212248612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	38	552	0	ENST00000342788.4:c.3655G>A	p.Ala1219Thr	p.A1219T	ENST00000342788	NM_005235.2	1219	Gct/Act	28/28	0.880328543177322	1	FACETS	0.1	0.082	0.12	0.1	0.082	0.12	SUBCLONAL	1	TRUE	0	0.880328543177322	1		552	484	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267219	41267219	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	39	409	0	ENST00000349496.5:c.803G>A	p.Gly268Glu	p.G268E	ENST00000349496	NM_001904.3	268	gGa/gAa	6/15	1	2	FACETS	0.124	0.102	0.149	0.124	0.102	0.149	SUBCLONAL	1	TRUE	1	0.880328543177322	2		409	712	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275654	41275654	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	44	480	0	ENST00000349496.5:c.1549C>T	p.Leu517Phe	p.L517F	ENST00000349496	NM_001904.3	517	Ctt/Ttt	10/15	1	2	FACETS	0.138	0.115	0.163	0.138	0.115	0.163	SUBCLONAL	1	TRUE	1	0.880328543177322	2		480	726	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498438	89498438	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	40	357	0	ENST00000336596.2:c.2410G>A	p.Ala804Thr	p.A804T	ENST00000336596	NM_005233.5	804	Gcc/Acc	14/17	1	2	FACETS	0.143	0.118	0.17	0.143	0.118	0.17	SUBCLONAL	1	TRUE	1	0.880328543177322	2		357	637	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960089	134960089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1224986515	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	50	585	1	ENST00000398015.3:c.2446G>A	p.Glu816Lys	p.E816K	ENST00000398015	NM_004441.4	816	Gaa/Aaa	13/16	0.880328543177322	1	FACETS	0.123	0.104	0.144	0.123	0.104	0.144	SUBCLONAL	1	TRUE	0	0.880328543177322	1		586	515	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281495	142281495	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	54	589	0	ENST00000350721.4:c.749G>A	p.Ser250Asn	p.S250N	ENST00000350721	NM_001184.3	250	aGc/aAc	4/47	0.880328543177322	1	FACETS	0.132	0.112	0.153	0.132	0.112	0.153	SUBCLONAL	1	TRUE	0	0.880328543177322	1		589	521	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178942603	178942603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	35	251	1	ENST00000263967.3:c.2410G>A	p.Gly804Arg	p.G804R	ENST00000263967	NM_006218.2	804	Ggg/Agg	16/21	0.880328543177322	1	FACETS	0.181	0.149	0.216	0.181	0.149	0.216	SUBCLONAL	1	TRUE	0	0.880328543177322	1		252	246	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980628	1980628	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs548852837	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	27	333	0	ENST00000382891.5:c.4090G>A	p.Gly1364Ser	p.G1364S	ENST00000382891	NM_133335.3	1364	Ggc/Agc	22/22	1	2	FACETS	0.144	0.114	0.178	0.144	0.114	0.178	SUBCLONAL	1	TRUE	1	0.880328543177322	2		333	426	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594057	55594057	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	49	452	2	ENST00000288135.5:c.1843G>A	p.Asp615Asn	p.D615N	ENST00000288135	NM_000222.2	615	Gat/Aat	12/21	1	2	FACETS	0.183	0.155	0.215	0.183	0.155	0.215	SUBCLONAL	1	TRUE	1	0.880328543177322	2		454	607	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244197	153244197	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	46	436	1	ENST00000281708.4:c.1960G>A	p.Gly654Ser	p.G654S	ENST00000281708	NM_033632.3	654	Ggt/Agt	12/12	1	2	FACETS	0.131	0.11	0.155	0.131	0.11	0.155	SUBCLONAL	1	TRUE	1	0.880328543177322	2		437	797	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294598	1294598	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200843534	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	36	307	0	ENST00000310581.5:c.403G>A	p.Gly135Arg	p.G135R	ENST00000310581	NM_198253.2	135	Ggg/Agg	2/16	NA	2	FACETS	0.162	0.133	0.195			1	INDETERMINATE	1	TRUE	NA	0.880328543177322	2		307	505	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520306	176520306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	56	559	1	ENST00000292408.4:c.1225C>T	p.Leu409Phe	p.L409F	ENST00000292408	NM_213647.1	409	Ctc/Ttc	9/18	NA	2	FACETS	0.151	0.128	0.175			1	INDETERMINATE	1	TRUE	NA	0.880328543177322	2		560	844	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401646	401646	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	38	407	0	ENST00000380956.4:c.968G>A	p.Gly323Glu	p.G323E	ENST00000380956	NM_001195286.1	323	gGg/gAg	7/9	0.880328543177322	1	FACETS	0.151	0.124	0.179	0.151	0.124	0.179	SUBCLONAL	1	TRUE	0	0.880328543177322	1		407	321	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956610	93956610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748985745	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	26	420	0	ENST00000369303.4:c.2626G>A	p.Glu876Lys	p.E876K	ENST00000369303	NM_004440.3	876	Gag/Aag	15/17	0.880328543177322	1	FACETS	0.086	0.068	0.107	0.086	0.068	0.107	SUBCLONAL	1	TRUE	0	0.880328543177322	1		420	383	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041059	112041059	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1229456829	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	25	441	1	ENST00000368678.4:c.196G>A	p.Gly66Ser	p.G66S	ENST00000368678		66	Ggt/Agt	3/13	0.880328543177322	1	FACETS	0.077	0.06	0.097	0.077	0.06	0.097	SUBCLONAL	1	TRUE	0	0.880328543177322	1		442	411	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210074	55210074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	66	561	0	ENST00000275493.2:c.184C>T	p.Leu62Phe	p.L62F	ENST00000275493	NM_005228.3	62	Ctt/Ttt	2/28	1	2	FACETS	0.167	0.144	0.192	0.167	0.144	0.192	SUBCLONAL	1	TRUE	1	0.880328543177322	2		561	899	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435966	116435966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	53	548	1	ENST00000397752.3:c.3961C>T	p.His1321Tyr	p.H1321Y	ENST00000397752	NM_000245.2	1321	Cac/Tac	21/21	1	2	FACETS	0.132	0.112	0.154	0.132	0.112	0.154	SUBCLONAL	1	TRUE	1	0.880328543177322	2		549	914	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151164230	151164230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767187355	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	17	195	0	ENST00000262187.5:c.530G>A	p.Gly177Asp	p.G177D	ENST00000262187	NM_005614.3	177	gGc/gAc	8/8	1	2	FACETS	0.137	0.102	0.179	0.137	0.102	0.179	SUBCLONAL	1	TRUE	1	0.880328543177322	2		195	281	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956748	68956748	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	63	561	0	ENST00000288368.4:c.866C>T	p.Thr289Ile	p.T289I	ENST00000288368	NM_024870.2	289	aCa/aTa	8/40	0.880328543177322	2	FACETS	0.127	0.109	0.147	0.064	0.054	0.074	SUBCLONAL	1	TRUE	0	0.880328543177322	2		561	1126	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635254	87635254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	48	401	0	ENST00000277120.3:c.2306C>T	p.Pro769Leu	p.P769L	ENST00000277120		769	cCc/cTc	18/19	1	2	FACETS	0.155	0.13	0.182	0.155	0.13	0.182	SUBCLONAL	1	TRUE	1	0.880328543177322	2		401	703	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250196	110250196	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867637928	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	63	546	0	ENST00000374672.4:c.479C>T	p.Pro160Leu	p.P160L	ENST00000374672	NM_004235.4	160	cCg/cTg	3/5	1	2	FACETS	0.187	0.161	0.215	0.187	0.161	0.215	SUBCLONAL	1	TRUE	1	0.880328543177322	2		546	766	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395300	139395300	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	52	518	0	ENST00000277541.6:c.5639-1G>A		p.X1880_splice	ENST00000277541	NM_017617.3	1880			NA	2	FACETS	0.177	0.15	0.206			1	INDETERMINATE	1	TRUE	NA	0.880328543177322	2		518	668	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422398	47422398	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	34	193	0	ENST00000377045.4:c.32G>A	p.Gly11Glu	p.G11E	ENST00000377045	NM_001654.4	11	gGg/gAg	2/16	1	1	FACETS	0.142	0.116	0.171	0.142	0.116	0.171	SUBCLONAL	1	TRUE	0	0.880328543177322	1		193	304	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240692	53240692	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	40	274	0	ENST00000375401.3:c.1388C>T	p.Thr463Ile	p.T463I	ENST00000375401	NM_004187.3	463	aCc/aTc	10/26	1	1	FACETS	0.112	0.092	0.133	0.112	0.092	0.133	SUBCLONAL	1	TRUE	0	0.880328543177322	1		274	455	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197837	123197837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	49	235	0	ENST00000218089.9:c.1961G>A	p.Arg654Lys	p.R654K	ENST00000218089	NM_001042749.1	654	aGa/aAa	20/35	1	1	FACETS	0.154	0.131	0.18	0.154	0.131	0.18	SUBCLONAL	1	TRUE	0	0.880328543177322	1		235	404	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112919912	112919912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	16	125	0	ENST00000351677.2:c.1127C>T	p.Ala376Val	p.A376V	ENST00000351677	NM_002834.3	376	gCt/gTt	10/16	1	2	FACETS	0.156	0.115	0.205	0.156	0.115	0.205	SUBCLONAL	1	TRUE	1	0.880328543177322	2		125	233	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219388	1219388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780717	NA	P-0032870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	73	423	0	ENST00000326873.7:c.440G>A	p.Arg147His	p.R147H	ENST00000326873	NM_000455.4	147	cGt/cAt	3/10	0.309077384915428	3	FACETS	0.761	0.665	0.864	0.38	0.332	0.432	SUBCLONAL	1	TRUE	1	0.309077384915428	3		423	717	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141874	108141874	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587781558	NA	P-0032870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	23	301	0	ENST00000278616.4:c.2921+1G>A		p.X974_splice	ENST00000278616	NM_000051.3	974			1	2	FACETS	0.633	0.495	0.792	0.633	0.495	0.792	SUBCLONAL	1	TRUE	1	0.309077384915428	2		301	235	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0032870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	49	386	0	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.309077384915428	3	FACETS	0.731	0.619	0.853	0.365	0.309	0.427	SUBCLONAL	1	TRUE	1	0.309077384915428	3		386	501	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032377	10032377	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1348316426	NA	P-0032870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	18	242	0	ENST00000330684.3:c.446C>T	p.Ala149Val	p.A149V	ENST00000330684	NM_001134407.1	149	gCg/gTg	3/13	0.262598472372068	1	FACETS	0.44	0.332	0.567	0.44	0.332	0.567	SUBCLONAL	1	TRUE	0	0.309077384915428	1		242	224	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736916	736916	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1465077979	NA	P-0032870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	104	542	1	ENST00000314574.4:c.1183C>T	p.Arg395Ter	p.R395*	ENST00000314574	NM_005433.3	395	Cga/Tga	10/12	0.169277704589758	2	FACETS	1	0.978	1	0.664	0.597	0.734	INDETERMINATE	1	TRUE	0	0.309077384915428	2		543	507	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921550	178921551	+	inframe_insertion	In_Frame_Ins	INS	-	-	AATGTA	novel	NA	P-0032870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	33	244	0	ENST00000263967.3:c.1036_1041dup	p.Val346_Asn347dup	p.V346_N347dup	ENST00000263967	NM_006218.2	346	-/AATGTA	5/21	0.309077384915428	3	FACETS	0.923	0.756	1	0.462	0.378	0.556	CLONAL	1	TRUE	1	0.309077384915428	3		244	267	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503985	186503985	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	30	218	0	ENST00000323963.5:c.550G>T	p.Glu184Ter	p.E184*	ENST00000323963		184	Gaa/Taa	6/11	0.309077384915428	3	FACETS	0.556	0.448	0.679	0.278	0.224	0.34	SUBCLONAL	1	TRUE	1	0.309077384915428	3		218	403	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903703	41903703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	154	487	0	ENST00000372991.4:c.854C>T	p.Thr285Ile	p.T285I	ENST00000372991	NM_001760.3	285	aCa/aTa	5/5	0.309077384915428	3	FACETS	0.999	0.919	1	0.999	0.919	1	CLONAL	2	TRUE	1	0.309077384915428	3		487	576	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020718	112020718	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	63	186	0	ENST00000368678.4:c.853G>C	p.Gly285Arg	p.G285R	ENST00000368678		285	Ggt/Cgt	8/13	0.309077384915428	6	FACETS	1	0.964	1			1	CLONAL	1	TRUE	NA	0.309077384915428	6		186	485	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900032	151900032	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	17	324	0	ENST00000262189.6:c.4079C>T	p.Pro1360Leu	p.P1360L	ENST00000262189	NM_170606.2	1360	cCt/cTt	26/59	1	2	FACETS	0.4	0.298	0.521	0.4	0.298	0.521	SUBCLONAL	1	TRUE	1	0.309077384915428	2		324	275	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90996759	90996759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764914981	NA	P-0032870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	41	325	1	ENST00000265433.3:c.31G>A	p.Ala11Thr	p.A11T	ENST00000265433	NM_002485.4	11	Gca/Aca	1/16	0.219953931596335	4	FACETS	0.868	0.724	1	0.289	0.241	0.343	CLONAL	1	TRUE	1	0.309077384915428	4		326	400	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772713	135772713	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	30	413	0	ENST00000298552.3:c.2833G>C	p.Glu945Gln	p.E945Q	ENST00000298552	NM_001162426.1	945	Gag/Cag	22/23	1	2	FACETS	0.434	0.349	0.531	0.434	0.349	0.531	SUBCLONAL	1	TRUE	1	0.309077384915428	2		413	447	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0032873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	39	333	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	1	2	FACETS	0.955	0.793	1	0.955	0.793	1	CLONAL	1	TRUE	1	0.212169175416623	2		333	385	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0032873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	69	641	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	0.212169175416623	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.212169175416623	1		641	470	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267436	198267436	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1373012215	NA	P-0032873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	49	400	0	ENST00000335508.6:c.1921A>G	p.Ile641Val	p.I641V	ENST00000335508	NM_012433.2	641	Att/Gtt	14/25	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.212169175416623	2		400	408	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0032874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	89	466	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	1	2	FACETS	0.811	0.718	0.909	0.811	0.718	0.909	CLONAL	1	FALSE	1	0.3	2		466	732	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249002	55249003	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCGTGGA	rs397517109	NA	P-0032874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	188	421	0	ENST00000275493.2:c.2303_2311dup	p.Ser768_Asp770dup	p.S768_D770dup	ENST00000275493	NM_005228.3	768	gcc/gcCAGCGTGGAc	20/28	0.3	4	FACETS	0.93	0.86	1	0.62	0.573	0.669	CLONAL	2	FALSE	1	0.3	4		421	876	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984143	2984143	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	74	327	0	ENST00000396946.4:c.387C>G	p.His129Gln	p.H129Q	ENST00000396946	NM_032415.4	129	caC/caG	5/25	0.193442988804821		FACETS		0.859	1				CLONAL	1	FALSE	1	0.3	3		327	579	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0032875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	99	653	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.2	2		653	848	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0032875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	30	321	1	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	0.613	0.493	0.75	0.613	0.493	0.75	SUBCLONAL	1	TRUE	1	0.2	2		322	489	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888273	112888273	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397507516	NA	P-0032875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	42	378	0	ENST00000351677.2:c.289G>C	p.Glu97Gln	p.E97Q	ENST00000351677	NM_002834.3	97	Gag/Cag	3/16	1	2	FACETS	0.797	0.665	0.944	0.797	0.665	0.944	CLONAL	1	TRUE	1	0.2	2		378	527	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484197	8484198	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0032875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	72	497	0	ENST00000356435.5:c.3334_3335del	p.Pro1112CysfsTer18	p.P1112Cfs*18	ENST00000356435		1112	CCt/t	19/35	1	2	FACETS	0.927	0.809	1	0.927	0.809	1	CLONAL	1	TRUE	1	0.2	2		497	777	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	245	248	0				ENST00000310581	NM_198253.2	-/1132			0.883384906807512	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.883384906807512	3		248	392	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0032888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	198	328	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.956	0.895	1	0.956	0.895	1	CLONAL	1	TRUE	1	0.883384906807512	2		328	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0032894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	311	570	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.555566651741329	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.555566651741329	1		570	711	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560085	29560085	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	124	251	0	ENST00000356175.3:c.3562C>T	p.Gln1188Ter	p.Q1188*	ENST00000356175	NM_000267.3	1188	Caa/Taa	27/57	0.269888199513921	3	FACETS	1	0.972	1	0.587	0.534	0.642	INDETERMINATE	1	TRUE	1	0.555566651741329	3		251	486	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15952272	15952272	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	52	450	0	ENST00000268712.3:c.6423C>G	p.His2141Gln	p.H2141Q	ENST00000268712	NM_006311.3	2141	caC/caG	41/46	0.555566651741329	1	FACETS	0.205	0.174	0.239	0.205	0.174	0.239	SUBCLONAL	1	TRUE	0	0.555566651741329	1		450	661	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790400	3790400	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs121434626	NA	P-0032894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	372	262	0	ENST00000262367.5:c.4133G>C	p.Arg1378Pro	p.R1378P	ENST00000262367	NM_004380.2	1378	cGg/cCg	24/31	0.555566651741329	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	0	0.555566651741329	3		262	543	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046509	69046509	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs557338072	NA	P-0032894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	191	410	0	ENST00000288368.4:c.3982T>G	p.Leu1328Val	p.L1328V	ENST00000288368	NM_024870.2	1328	Ttg/Gtg	32/40	0.149873515109478	3	FACETS	1	0.987	1	0.645	0.599	0.693	INDETERMINATE	1	TRUE	1	0.555566651741329	3		410	681	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427730	49427732	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0032894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	282	541	0	ENST00000301067.7:c.10756_10758del	p.Lys3586del	p.K3586del	ENST00000301067	NM_003482.3	3586	AAG/-	39/54	0.318724047578593	1	FACETS	0.848	0.799	0.897	0.848	0.799	0.897	INDETERMINATE	1	TRUE	0	0.555566651741329	1		541	865	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107906	30107906	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	189	329	0	ENST00000331968.5:c.901T>C	p.Cys301Arg	p.C301R	ENST00000331968	NM_002742.2	301	Tgc/Cgc	5/18	0.555566651741329	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.555566651741329	1		329	418	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422504	225422504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745998120	NA	P-0032894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	55	455	0	ENST00000264414.4:c.136C>T	p.Arg46Cys	p.R46C	ENST00000264414	NM_003590.4	46	Cgt/Tgt	2/16	0.555566651741329	1	FACETS	0.276	0.236	0.32	0.276	0.236	0.32	SUBCLONAL	1	TRUE	0	0.555566651741329	1		455	518	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665549	138665549	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1160694577	NA	P-0032894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	136	188	0	ENST00000330315.3:c.16C>A	p.Pro6Thr	p.P6T	ENST00000330315	NM_023067.3	6	Ccc/Acc	1/1	0.555566651741329	4	FACETS	1	0.978	1	0.411	0.374	0.449	CLONAL	1	TRUE	1	0.555566651741329	4		188	618	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444666	187444666	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	178	309	0	ENST00000232014.4:c.1561A>C	p.Asn521His	p.N521H	ENST00000232014	NM_001130845.1	521	Aat/Cat	7/10	0.555566651741329	6	FACETS	1	0.939	1	0.205	0.188	0.223	CLONAL	1	TRUE	1	0.555566651741329	6		309	1319	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139829	55139829	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	51	306	0	ENST00000257290.5:c.1490T>C	p.Ile497Thr	p.I497T	ENST00000257290	NM_006206.4	497	aTc/aCc	10/23	0.412947800064629	1	FACETS	0.288	0.244	0.335	0.288	0.244	0.335	SUBCLONAL	1	TRUE	0	0.555566651741329	1		306	461	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0032896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	105	248	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.781357890090661	3	FACETS	1	0.969	1	0.582	0.528	0.638	CLONAL	1	FALSE	1	0.781357890090661	3		248	321	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0032896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	261	331	0				ENST00000310581	NM_198253.2	-/1132			0.781357890090661	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	FALSE	0	0.781357890090661	2		331	293	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0032896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	577	496	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.781357890090661	3	FACETS	0.987	0.966	1	0.987	0.966	1	CLONAL	3	FALSE	0	0.781357890090661	3		496	694	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	184	385	0	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	0.781357890090661	3	FACETS	0.923	0.854	0.993	0.461	0.427	0.497	CLONAL	1	FALSE	1	0.781357890090661	3		385	710	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862944	9862944	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	324	335	0	ENST00000330684.3:c.2359G>A	p.Glu787Lys	p.E787K	ENST00000330684	NM_001134407.1	787	Gag/Aag	12/13	0.781357890090661	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	FALSE	1	0.781357890090661	3		335	553	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157993	27157993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	409	395	0	ENST00000380036.4:c.217G>A	p.Glu73Lys	p.E73K	ENST00000380036	NM_000459.3	73	Gaa/Aaa	2/23	0.781357890090661	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	FALSE	0	0.781357890090661	2		395	481	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267306	41267306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759085197	NA	P-0032896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	109	267	1	ENST00000349496.5:c.890C>T	p.Thr297Met	p.T297M	ENST00000349496	NM_001904.3	297	aCg/aTg	6/15	0.781357890090661	4	FACETS	0.943	0.85	1	0.314	0.283	0.347	CLONAL	1	FALSE	1	0.781357890090661	4		268	527	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449728	8449728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	365	361	0	ENST00000356435.5:c.3985C>T	p.Pro1329Ser	p.P1329S	ENST00000356435		1329	Ccg/Tcg	23/35	0.781357890090661	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	FALSE	0	0.781357890090661	2		361	459	SUCCESS
AR	367	MSKCC	GRCh37	X	66942672	66942672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	260	134	0	ENST00000374690.3:c.2453C>T	p.Pro818Leu	p.P818L	ENST00000374690	NM_000044.3	818	cCa/cTa	7/8	0.723922588778448	2	FACETS	1	0.995	1			1	CLONAL	2	FALSE	NA	0.781357890090661	2		134	292	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0032900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	85	306	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.611180753109036	3	FACETS	0.922	0.821	1	0.461	0.41	0.515	CLONAL	1	TRUE	1	0.633679639978604	3		306	383	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0032900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	497	513	1	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	0.610107517213165	3	FACETS	0.97	0.941	0.998	0.97	0.941	0.998	CLONAL	3	TRUE	0	0.633679639978604	3		514	710	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0032900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	168	274	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.561257765046979	4	FACETS	0.906	0.84	0.974	0.906	0.84	0.974	CLONAL	2	TRUE	2	0.633679639978604	4		274	478	SUCCESS
APC	324	MSKCC	GRCh37	5	112175147	112175147	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	111	250	1	ENST00000257430.4:c.3856G>T	p.Glu1286Ter	p.E1286*	ENST00000257430	NM_000038.5	1286	Gaa/Taa	16/16	0.611180753109036	3	FACETS	0.857	0.784	0.932	0.857	0.784	0.932	CLONAL	2	TRUE	1	0.633679639978604	3		251	269	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003202	143003202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766146483	NA	P-0032900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	162	406	0	ENST00000262992.4:c.2624C>T	p.Ala875Val	p.A875V	ENST00000262992	NM_001101669.1	875	gCg/gTg	23/24	0.611180753109036	3	FACETS	0.813	0.755	0.873	0.813	0.755	0.873	CLONAL	2	TRUE	1	0.633679639978604	3		406	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573998	7573999	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0032900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	473	557	4	ENST00000269305.4:c.1028_1029del	p.Glu343AlafsTer3	p.E343Afs*3	ENST00000269305	NM_001126112.2	343	gAG/g	10/11	0.610107517213165	3	FACETS	0.972	0.943	1	0.972	0.943	1	CLONAL	3	TRUE	0	0.633679639978604	3		561	674	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862737	9862737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201072838	NA	P-0032900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	85	368	0	ENST00000330684.3:c.2566C>T	p.Arg856Trp	p.R856W	ENST00000330684	NM_001134407.1	856	Cgg/Tgg	12/13	0.611180753109036	3	FACETS	0.818	0.726	0.915	0.409	0.363	0.458	CLONAL	1	TRUE	1	0.633679639978604	3		368	432	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260775	16260775	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	265	430	1	ENST00000375759.3:c.8040A>T	p.Lys2680Asn	p.K2680N	ENST00000375759	NM_015001.2	2680	aaA/aaT	11/15	0.335823948818001	3	FACETS	0.872	0.833	0.911	0.872	0.833	0.911	INDETERMINATE	3	TRUE	0	0.633679639978604	3		431	421	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023213	27023222	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGGCCCTA	GCGGGCCCTA	-	novel	NA	P-0032900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	57	61	0	ENST00000324856.7:c.320_329del	p.Ala107GlyfsTer4	p.A107Gfs*4	ENST00000324856	NM_006015.4	107	GCGGGCCCTAgg/gg	1/20	0.335823948818001	3	FACETS	1	0.959	1	0.774	0.693	0.854	INDETERMINATE	2	TRUE	0	0.633679639978604	3		61	102	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119751	70119752	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0032900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	375	449	2	ENST00000245479.2:c.754_755dup	p.Lys253Ter	p.K253*	ENST00000245479	NM_000346.3	251	-/CT	3/3	0.610107517213165	3	FACETS	0.955	0.922	0.987	0.955	0.922	0.987	CLONAL	3	TRUE	0	0.633679639978604	3		451	544	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591946	48591946	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	237	352	0	ENST00000342988.3:c.1109T>G	p.Val370Gly	p.V370G	ENST00000342988	NM_005359.5	370	gTc/gGc	9/12	0.633679639978604	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.633679639978604	2		352	360	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	16	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.513	0.38	0.67	0.513	0.38	0.67	SUBCLONAL	1	TRUE	1	0.32	2		248	195	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0032931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	112	343	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.32	2		343	515	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266713	198266713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776846119	NA	P-0032936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	89	541	1	ENST00000335508.6:c.2219G>A	p.Gly740Glu	p.G740E	ENST00000335508	NM_012433.2	740	gGa/gAa	15/25	1	2	FACETS	0.976	0.866	1	0.976	0.866	1	CLONAL	1	TRUE	1	0.290899598320926	2		542	627	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984022	2984022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753614569	NA	P-0032936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	79	597	1	ENST00000396946.4:c.508C>T	p.Arg170Cys	p.R170C	ENST00000396946	NM_032415.4	170	Cgc/Tgc	5/25	1	2	FACETS	0.849	0.747	0.958	0.849	0.747	0.958	CLONAL	1	TRUE	1	0.290899598320926	2		598	640	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057789	27057790	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0032950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	266	1010	0	ENST00000324856.7:c.1498_1499insTT	p.Tyr500PhefsTer120	p.Y500Ffs*120	ENST00000324856	NM_006015.4	499	-/TT	3/20	1	2	FACETS	0.823	0.784	0.862	1	0.995	1	CLONAL	2	TRUE	1	0.705837060306768	2		1010	458	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060610	38060611	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	195	994	0	ENST00000250448.2:c.1378dup	p.Tyr460LeufsTer98	p.Y460Lfs*98	ENST00000250448	NM_004496.3	460	tac/tTac	2/2	1	2	FACETS	0.817	0.757	0.879	0.817	0.757	0.879	CLONAL	1	TRUE	1	0.550121467529415	2		994	868	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857530	68857530	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0032957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	111	391	0	ENST00000261769.5:c.2164+1G>A		p.X722_splice	ENST00000261769	NM_004360.3	722			0.446512810526572	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.446512810526572	1		391	331	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447791	49447791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	99	441	0	ENST00000301067.7:c.643C>T	p.Pro215Ser	p.P215S	ENST00000301067	NM_003482.3	215	Cca/Tca	5/54	1	2	FACETS	0.899	0.806	0.998	0.899	0.806	0.998	CLONAL	1	TRUE	1	0.446512810526572	2		441	493	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341506	89341506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	104	474	0	ENST00000301030.4:c.7564G>A	p.Glu2522Lys	p.E2522K	ENST00000301030	NM_001256183.1	2522	Gag/Aag	10/13	0.446512810526572	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.446512810526572	1		474	354	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252856	36252856	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	86	278	0	ENST00000300305.3:c.506G>T	p.Arg169Ile	p.R169I	ENST00000300305		169	aGa/aTa	4/8	1	2	FACETS	0.97	0.864	1	0.97	0.864	1	CLONAL	1	TRUE	1	0.446512810526572	2		278	397	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	45	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.26	2		248	234	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266717	18266717	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	48	441	0	ENST00000222254.8:c.28C>G	p.Arg10Gly	p.R10G	ENST00000222254	NM_005027.3	10	Cgc/Ggc	2/16	0.297791578003555	7	FACETS	0.865	0.73	1			1	CLONAL	1	TRUE	NA	0.26	7		441	704	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170510	11170510	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	119	600	0	ENST00000358026.2:c.4813G>T	p.Glu1605Ter	p.E1605*	ENST00000358026	NM_001128849.1	1605	Gag/Tag	34/36	1	2	FACETS	0.957	0.867	1	0.957	0.867	1	CLONAL	1	TRUE	1	0.436964756301372	2		600	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs879253911	NA	P-0032965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	381	543	0	ENST00000269305.4:c.538G>T	p.Glu180Ter	p.E180*	ENST00000269305	NM_001126112.2	180	Gag/Tag	5/11	0.760773752242657	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.815937882250678	1		543	512	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417935	32417935	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	292	358	0	ENST00000332351.3:c.1117G>T	p.Gly373Ter	p.G373*	ENST00000332351	NM_024426.4	373	Gga/Tga	7/10	0.815937882250678	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.815937882250678	1		358	389	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267710	198267710	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	145	330	0	ENST00000335508.6:c.1769G>T	p.Arg590Ile	p.R590I	ENST00000335508	NM_012433.2	590	aGa/aTa	13/25	1	2	FACETS	0.923	0.852	0.996	0.923	0.852	0.996	CLONAL	1	TRUE	1	0.815937882250678	2		330	385	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786784	3786784	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	320	427	0	ENST00000262367.5:c.4427C>G	p.Pro1476Arg	p.P1476R	ENST00000262367	NM_004380.2	1476	cCa/cGa	27/31	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.815937882250678	2		427	755	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371577	225371577	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	107	390	0	ENST00000264414.4:c.1027C>T	p.Gln343Ter	p.Q343*	ENST00000264414	NM_003590.4	343	Cag/Tag	7/16	0.575027274601247	1	FACETS	0.664	0.608	0.72	0.664	0.608	0.72	SUBCLONAL	1	TRUE	0	0.815937882250678	1		390	234	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975648	26975649	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0032965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	136	299	1	ENST00000381527.3:c.1156_1157delinsAA	p.Gly386Asn	p.G386N	ENST00000381527	NM_001260.1	386	GGc/AAc	12/13	1	2	FACETS	0.702	0.643	0.763	0.702	0.643	0.763	SUBCLONAL	1	TRUE	1	0.815937882250678	2		300	475	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683757	162683757	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	289	434	0	ENST00000366898.1:c.212A>T	p.Gln71Leu	p.Q71L	ENST00000366898	NM_004562.2	71	cAg/cTg	3/12	NA	2	FACETS	0.977	0.924	1			1	INDETERMINATE	1	TRUE	NA	0.815937882250678	2		434	725	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981440	70981440	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	510	677	0	ENST00000276594.2:c.656T>C	p.Leu219Pro	p.L219P	ENST00000276594	NM_024504.3	219	cTg/cCg	2/8	0.49500422449922	1	FACETS	0.771	0.743	0.799	0.771	0.743	0.799	SUBCLONAL	1	TRUE	0	0.815937882250678	1		677	960	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0032979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	132	546	1	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	0.208494463559923	3	FACETS	1	0.983	1	0.681	0.619	0.745	CLONAL	1	TRUE	1	0.330260878164325	3		547	684	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0032979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	121	516	0	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	0.330260878164325	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.330260878164325	1		516	529	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524541	176524541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759861753	NA	P-0032979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	58	720	0	ENST00000292408.4:c.2273G>A	p.Arg758His	p.R758H	ENST00000292408	NM_213647.1	758	cGc/cAc	18/18	0.163440158604016	4	FACETS	0.605	0.519	0.7	0.303	0.259	0.35	INDETERMINATE	1	TRUE	2	0.330260878164325	4		720	772	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912654	NA	P-0032979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	140	691	0	ENST00000269305.4:c.469G>A	p.Val157Ile	p.V157I	ENST00000269305	NM_001126112.2	157	Gtc/Atc	5/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.330260878164325	2		691	686	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328332	137328332	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	121	533	1	ENST00000481739.1:c.1261C>T	p.Arg421Cys	p.R421C	ENST00000481739	NM_002957.4	421	Cgc/Tgc	10/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.330260878164325	2		534	635	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859878	117859878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780692465	NA	P-0032979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	29	237	0	ENST00000297338.2:c.1757G>A	p.Arg586Gln	p.R586Q	ENST00000297338	NM_006265.2	586	cGa/cAa	14/14	1	2	FACETS	0.625	0.503	0.763	0.625	0.503	0.763	SUBCLONAL	1	TRUE	1	0.330260878164325	2		237	281	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112990	2112990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	50	522	0	ENST00000219476.3:c.1379C>T	p.Ala460Val	p.A460V	ENST00000219476	NM_000548.3	460	gCc/gTc	14/42	0.330260878164325	1	FACETS	0.537	0.456	0.626	0.537	0.456	0.626	SUBCLONAL	1	TRUE	0	0.330260878164325	1		522	471	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944567	71944567	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0032979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	124	511	0	ENST00000298229.2:c.2122+1G>A		p.X708_splice	ENST00000298229	NM_001567.3	708			0.330260878164325	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.330260878164325	1		511	497	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402031	402031	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	78	463	0	ENST00000399788.2:c.4760del	p.Lys1587ArgfsTer37	p.K1587Rfs*37	ENST00000399788	NM_001042603.1	1587	aAg/ag	27/28	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.330260878164325	2		463	466	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563060	21563060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1367601934	NA	P-0032979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	55	674	1	ENST00000382592.4:c.859G>A	p.Ala287Thr	p.A287T	ENST00000382592	NM_014572.2	287	Gcc/Acc	4/8	1	2	FACETS	0.465	0.396	0.539	0.465	0.396	0.539	SUBCLONAL	1	TRUE	1	0.330260878164325	2		675	717	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893590	28893590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752645756	NA	P-0032979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	60	363	1	ENST00000282397.4:c.3256G>A	p.Gly1086Arg	p.G1086R	ENST00000282397	NM_002019.4	1086	Gga/Aga	24/30	1	2	FACETS	0.927	0.802	1	0.927	0.802	1	CLONAL	1	TRUE	1	0.330260878164325	2		364	392	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988389	36988390	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	72	244	0	ENST00000354822.5:c.263dup	p.His90AlafsTer349	p.H90Afs*349	ENST00000354822	NM_001079668.2	88	gtg/gtTg	2/3	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.330260878164325	2		244	294	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712797	43712797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746329471	NA	P-0032979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	152	683	0	ENST00000382044.4:c.4387C>T	p.Arg1463Cys	p.R1463C	ENST00000382044	NM_001141980.1	1463	Cgt/Tgt	21/28	0.330260878164325	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.330260878164325	1		683	576	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106685	2106685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	143	648	3	ENST00000219476.3:c.689G>A	p.Cys230Tyr	p.C230Y	ENST00000219476	NM_000548.3	230	tGc/tAc	8/42	0.330260878164325	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.330260878164325	1		651	601	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134712	2134712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45517344	NA	P-0032979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	41	548	0	ENST00000219476.3:c.4489C>T	p.Pro1497Ser	p.P1497S	ENST00000219476	NM_000548.3	1497	Ccc/Tcc	34/42	0.330260878164325	1	FACETS	0.416	0.346	0.494	0.416	0.346	0.494	SUBCLONAL	1	TRUE	0	0.330260878164325	1		548	498	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649018	37649018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1367487092	NA	P-0032979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	21	285	0	ENST00000447079.4:c.2123G>A	p.Arg708His	p.R708H	ENST00000447079	NM_015083.1	708	cGt/cAt	4/14	1	2	FACETS	0.451	0.347	0.571	0.451	0.347	0.571	SUBCLONAL	1	TRUE	1	0.330260878164325	2		285	282	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222826	36222826	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	84	726	0	ENST00000222270.7:c.5455G>A	p.Asp1819Asn	p.D1819N	ENST00000222270	NM_014727.1	1819	Gac/Aac	27/37	1	2	FACETS	0.74	0.654	0.833	0.74	0.654	0.833	SUBCLONAL	1	TRUE	1	0.330260878164325	2		726	687	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139022	50139022	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1428526675	NA	P-0032979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	96	718	2	ENST00000246792.3:c.541G>A	p.Glu181Lys	p.E181K	ENST00000246792	NM_006270.3	181	Gag/Aag	5/6	1	2	FACETS	0.825	0.735	0.92	0.825	0.735	0.92	CLONAL	1	TRUE	1	0.330260878164325	2		720	705	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703574	47703574	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750232	NA	P-0032979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	138	592	0	ENST00000233146.2:c.2074G>A	p.Gly692Arg	p.G692R	ENST00000233146	NM_000251.2	692	Ggg/Agg	13/16	0.330260878164325	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.330260878164325	1		592	492	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55962446	55962446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	33	486	0	ENST00000263923.4:c.2678G>A	p.Gly893Asp	p.G893D	ENST00000263923	NM_002253.2	893	gGt/gAt	19/30	1	2	FACETS	0.405	0.329	0.49	0.405	0.329	0.49	SUBCLONAL	1	TRUE	1	0.330260878164325	2		486	494	SUCCESS
APC	324	MSKCC	GRCh37	5	112173527	112173527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	23	289	0	ENST00000257430.4:c.2236G>A	p.Gly746Ser	p.G746S	ENST00000257430	NM_000038.5	746	Ggc/Agc	16/16	0.163440158604016	4	FACETS	0.584	0.456	0.733	0.292	0.228	0.367	INDETERMINATE	1	TRUE	2	0.330260878164325	4		289	317	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032023	26032023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	64	248	0	ENST00000244661.2:c.266C>T	p.Ala89Val	p.A89V	ENST00000244661	NM_003537.3	89	gCg/gTg	1/1	0.250934015330758	2	FACETS	0.754	0.66	0.853	0.754	0.66	0.853	SUBCLONAL	2	TRUE	0	0.330260878164325	2		248	257	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911261	29911261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3129017	NA	P-0032979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	14	211	0	ENST00000376809.5:c.560C>T	p.Thr187Met	p.T187M	ENST00000376809	NM_002116.7	187	aCg/aTg	3/8	0.250934015330758	2	FACETS	0.461	0.334	0.614	0.23	0.167	0.307	SUBCLONAL	1	TRUE	0	0.330260878164325	2		211	184	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288833	33288833	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	78	356	0	ENST00000374542.5:c.719G>A	p.Cys240Tyr	p.C240Y	ENST00000374542	NM_001141970.1	240	tGt/tAt	3/8	0.250934015330758	2	FACETS	1	0.968	1	0.638	0.564	0.717	CLONAL	1	TRUE	0	0.330260878164325	2		356	370	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759937	133759937	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	35	601	0	ENST00000318560.5:c.2260G>A	p.Gly754Arg	p.G754R	ENST00000318560	NM_005157.4	754	Ggg/Agg	11/11	1	2	FACETS	0.339	0.277	0.409	0.339	0.277	0.409	SUBCLONAL	1	TRUE	1	0.330260878164325	2		601	625	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223602	53223602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	18	244	0	ENST00000375401.3:c.3757C>T	p.Pro1253Ser	p.P1253S	ENST00000375401	NM_004187.3	1253	Ccg/Tcg	23/26	0.193664455090635	2	FACETS	0.353	0.265	0.456			1	INDETERMINATE	1	TRUE	NA	0.330260878164325	2		244	309	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	209	440	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.51895899235535	3	FACETS	0.959	0.898	1	0.959	0.898	1	CLONAL	2	TRUE	1	0.51895899235535	3		440	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0032981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	161	572	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.51895899235535	1	FACETS	0.963	0.891	1	0.963	0.891	1	CLONAL	1	TRUE	0	0.51895899235535	1		572	477	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459418	40459418	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0032981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	286	392	0	ENST00000345506.4:c.1681-2A>C		p.X561_splice	ENST00000345506	NM_003152.3	561			0.51895899235535	3	FACETS	0.942	0.899	0.985	0.942	0.899	0.985	CLONAL	3	TRUE	0	0.51895899235535	3		392	491	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634294	23634294	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	127	530	0	ENST00000261584.4:c.2992G>C	p.Gly998Arg	p.G998R	ENST00000261584	NM_024675.3	998	Gga/Cga	9/13	NA	2	FACETS	0.911	0.83	0.997			1	INDETERMINATE	1	TRUE	NA	0.51895899235535	2		530	537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0032983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	237	587	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.754482966870524	2		587	609	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	171	440	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.754482966870524	3	FACETS	0.96	0.9	1	0.96	0.9	1	CLONAL	2	TRUE	1	0.754482966870524	3		440	325	SUCCESS
APC	324	MSKCC	GRCh37	5	112175876	112175876	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085992	NA	P-0032983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	41	207	0	ENST00000257430.4:c.4585C>T	p.Gln1529Ter	p.Q1529*	ENST00000257430	NM_000038.5	1529	Cag/Tag	16/16	0.754482966870524	1	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	0	0.754482966870524	1		207	65	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489571	56489571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	279	395	0	ENST00000267101.3:c.2036G>A	p.Arg679Gln	p.R679Q	ENST00000267101	NM_001982.3	679	cGa/cAa	17/28	0.754482966870524	2	FACETS	0.948	0.911	0.984	0.948	0.911	0.984	CLONAL	2	TRUE	0	0.754482966870524	2		395	390	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471048	8471048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	86	385	0	ENST00000356435.5:c.3451C>T	p.Arg1151Cys	p.R1151C	ENST00000356435		1151	Cgc/Tgc	20/35	1	2	FACETS	0.894	0.803	0.988	0.894	0.803	0.988	CLONAL	1	TRUE	1	0.754482966870524	2		385	255	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403604	138403604	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	105	551	0	ENST00000289153.2:c.2178C>G	p.Ile726Met	p.I726M	ENST00000289153	NM_006219.2	726	atC/atG	15/22	1	2	FACETS	0.881	0.799	0.965	0.881	0.799	0.965	CLONAL	1	TRUE	1	0.754482966870524	2		551	316	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112352	115112352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1247378046	NA	P-0032983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	325	240	0	ENST00000257566.3:c.1388C>T	p.Ala463Val	p.A463V	ENST00000257566	NM_016569.3	463	gCg/gTg	7/8	0.363634026260767	3	FACETS	1	0.994	1	0.793	0.761	0.823	INDETERMINATE	2	TRUE	0	0.754482966870524	3		240	499	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996078	73996078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760558160	NA	P-0032983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	245	728	0	ENST00000318443.5:c.812C>T	p.Ser271Phe	p.S271F	ENST00000318443	NM_001024736.1	271	tCc/tTc	5/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.754482966870524	2		728	563	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347459	89347459	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	168	494	0	ENST00000301030.4:c.5491G>C	p.Asp1831His	p.D1831H	ENST00000301030	NM_001256183.1	1831	Gac/Cac	9/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.754482966870524	2		494	381	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10283780	10283780	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	189	671	1	ENST00000340748.4:c.706G>A	p.Glu236Lys	p.E236K	ENST00000340748		236	Gaa/Aaa	8/40	0.168522241477746	3	FACETS	1	0.989	1	0.676	0.63	0.723	INDETERMINATE	1	TRUE	1	0.754482966870524	3		672	510	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10283819	10283819	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	183	600	0	ENST00000340748.4:c.667G>A	p.Glu223Lys	p.E223K	ENST00000340748		223	Gaa/Aaa	8/40	0.168522241477746	3	FACETS	1	0.985	1	0.608	0.565	0.653	INDETERMINATE	1	TRUE	1	0.754482966870524	3		600	549	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403515	138403515	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	140	551	0	ENST00000289153.2:c.2267C>T	p.Ser756Phe	p.S756F	ENST00000289153	NM_006219.2	756	tCt/tTt	15/22	1	2	FACETS	0.834	0.766	0.904	0.834	0.766	0.904	CLONAL	1	TRUE	1	0.754482966870524	2		551	445	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831378	72831378	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	140	364	0	ENST00000268489.5:c.5203C>T	p.Gln1735Ter	p.Q1735*	ENST00000268489	NM_006885.3	1735	Caa/Taa	9/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.634760696835084	2		364	353	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	61	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.804	0.699	0.916	1	0.974	1	CLONAL	2	TRUE	1	0.257985659587107	2		248	294	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607367	46607367	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs377001303	NA	P-0032992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	40	696	2	ENST00000263734.3:c.1556C>T	p.Thr519Met	p.T519M	ENST00000263734	NM_001430.4	519	aCg/aTg	12/16	1	2	FACETS	0.548	0.454	0.652	0.548	0.454	0.652	SUBCLONAL	1	TRUE	1	0.257985659587107	2		698	566	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557703	21557703	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	70	889	1	ENST00000382592.4:c.2142G>C	p.Lys714Asn	p.K714N	ENST00000382592	NM_014572.2	714	aaG/aaC	5/8	1	2	FACETS	0.189	0.164	0.216	0.189	0.164	0.216	SUBCLONAL	1	TRUE	1	0.872613109407157	2		890	850	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157924	27157924	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	228	657	3	ENST00000380036.4:c.148C>G	p.Arg50Gly	p.R50G	ENST00000380036	NM_000459.3	50	Cgc/Ggc	2/23	1	2	FACETS	0.868	0.815	0.922	0.868	0.815	0.922	CLONAL	1	TRUE	1	0.872613109407157	2		660	602	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	42	667	2	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.265	0.221	0.314	0.265	0.221	0.314	SUBCLONAL	1	TRUE	1	0.54	2		669	587	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	250	430	0	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	1	2	FACETS	0.908	0.859	0.957	1	0.995	1	CLONAL	2	TRUE	1	0.54	2		430	510	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717712	89717712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782350	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	147	440	1	ENST00000371953.3:c.737C>T	p.Pro246Leu	p.P246L	ENST00000371953	NM_000314.4	246	cCg/cTg	7/9	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.54	2		441	519	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	274	735	2	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.953	0.895	1	0.953	0.895	1	CLONAL	1	TRUE	1	0.54	2		737	1065	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214871	36214871	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	238	723	5	ENST00000222270.7:c.3302del	p.Pro1101LeufsTer81	p.P1101Lfs*81	ENST00000222270	NM_014727.1	1099	ggC/gg	8/37	1	2	FACETS	0.881	0.822	0.941	0.881	0.822	0.941	CLONAL	1	TRUE	1	0.54	2		728	1001	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	108	556	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.837	0.755	0.923	0.837	0.755	0.923	CLONAL	1	TRUE	1	0.54	2		556	478	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	360	661	14	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.906	0.865	0.946	1	0.996	1	CLONAL	2	TRUE	1	0.54	2		675	736	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	207	714	7	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.949	0.882	1	0.949	0.882	1	CLONAL	1	TRUE	1	0.54	2		721	808	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106733	27106734	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	160	582	0	ENST00000324856.7:c.6347_6348del	p.Arg2116ThrfsTer33	p.R2116Tfs*33	ENST00000324856	NM_006015.4	2115	cAG/c	20/20	1	2	FACETS	0.835	0.767	0.905	0.835	0.767	0.905	CLONAL	1	TRUE	1	0.54	2		582	710	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303646	65303647	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	40	608	0	ENST00000342505.4:c.3108dup	p.Val1037ArgfsTer4	p.V1037Rfs*4	ENST00000342505	NM_002227.2	1036	-/C	22/25	1	2	FACETS	0.194	0.16	0.232	0.194	0.16	0.232	SUBCLONAL	1	TRUE	1	0.54	2		608	763	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622119	43622119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	156	475	0	ENST00000355710.3:c.3136G>A	p.Ala1046Thr	p.A1046T	ENST00000355710	NM_020975.4	1046	Gcc/Acc	19/20	1	2	FACETS	0.861	0.791	0.934	0.861	0.791	0.934	CLONAL	1	TRUE	1	0.54	2		475	671	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623593	43623593	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	142	454	0	ENST00000355710.3:c.3221C>A	p.Pro1074His	p.P1074H	ENST00000355710	NM_020975.4	1074	cCt/cAt	20/20	1	2	FACETS	0.946	0.866	1	0.946	0.866	1	CLONAL	1	TRUE	1	0.54	2		454	556	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649922	88649922	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786201038	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	141	531	1	ENST00000372037.3:c.176del	p.Leu59Ter	p.L59*	ENST00000372037	NM_004329.2	57	ccT/cc	4/13	1	2	FACETS	0.941	0.861	1	0.941	0.861	1	CLONAL	1	TRUE	1	0.54	2		532	555	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720733	89720734	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	rs1564568350	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	20	148	0	ENST00000371953.3:c.885_886del	p.Cys296Ter	p.C296*	ENST00000371953	NM_000314.4	295	cTA/c	8/9	1	2	FACETS	0.602	0.466	0.757	0.602	0.466	0.757	SUBCLONAL	1	TRUE	1	0.54	2		148	123	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725043	89725043	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	50	240	1	ENST00000371953.3:c.1027-1G>T		p.X343_splice	ENST00000371953	NM_000314.4	343			1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.54	2		241	168	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316389	14316389	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	145	540	0	ENST00000256196.4:c.216A>T	p.Gln72His	p.Q72H	ENST00000256196		72	caA/caT	3/6	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.54	2		540	497	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71947024	71947024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	64	766	0	ENST00000298229.2:c.2877del	p.Arg960GlyfsTer2	p.R960Gfs*2	ENST00000298229	NM_001567.3	958	aCc/ac	25/28	1	2	FACETS	0.244	0.21	0.28	0.244	0.21	0.28	SUBCLONAL	1	TRUE	1	0.54	2		766	973	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	246	663	5	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.944	0.883	1	0.944	0.883	1	CLONAL	1	TRUE	1	0.54	2		668	965	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448188	49448188	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1438744754	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	82	516	0	ENST00000301067.7:c.412G>A	p.Ala138Thr	p.A138T	ENST00000301067	NM_003482.3	138	Gct/Act	4/54	1	2	FACETS	0.499	0.44	0.562	0.499	0.44	0.562	SUBCLONAL	1	TRUE	1	0.54	2		516	609	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	508	851	2	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.907	0.873	0.942	1	0.997	1	CLONAL	2	TRUE	1	0.54	2		853	1037	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112154	115112154	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	84	635	0	ENST00000257566.3:c.1586del	p.Gly529AlafsTer103	p.G529Afs*103	ENST00000257566	NM_016569.3	529	gGc/gc	7/8	1	2	FACETS	0.44	0.388	0.495	0.44	0.388	0.495	SUBCLONAL	1	TRUE	1	0.54	2		635	707	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626685	28626686	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	33	434	0	ENST00000241453.7:c.610dup	p.Glu204GlyfsTer4	p.E204Gfs*4	ENST00000241453	NM_004119.2	204	gaa/gGaa	5/24	1	2	FACETS	0.192	0.155	0.233	0.192	0.155	0.233	SUBCLONAL	1	TRUE	1	0.54	2		434	637	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913837	32913837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359507	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	39	470	2	ENST00000380152.3:c.5351del	p.Asn1784ThrfsTer7	p.N1784Tfs*7	ENST00000380152		1782	cAa/ca	11/27	1	2	FACETS	0.431	0.358	0.512	0.431	0.358	0.512	SUBCLONAL	1	TRUE	1	0.54	2		472	335	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240184	41240184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	28	28	0	ENST00000379561.5:c.166G>A	p.Ala56Thr	p.A56T	ENST00000379561	NM_002015.3	56	Gcg/Acg	1/3	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.54	2		28	88	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303500	91303500	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776516663	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	99	387	0	ENST00000355112.3:c.1211G>A	p.Arg404Gln	p.R404Q	ENST00000355112	NM_000057.2	404	cGg/cAg	6/22	1	2	FACETS	0.894	0.804	0.989	0.894	0.804	0.989	CLONAL	1	TRUE	1	0.54	2		387	410	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778349	3778349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	170	613	0	ENST00000262367.5:c.6699G>T	p.Gln2233His	p.Q2233H	ENST00000262367	NM_004380.2	2233	caG/caT	31/31	1	2	FACETS	0.967	0.893	1	0.967	0.893	1	CLONAL	1	TRUE	1	0.54	2		613	651	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	128	469	4	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	0.833	0.758	0.912	0.833	0.758	0.912	CLONAL	1	TRUE	1	0.54	2		473	569	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663406	67663406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775874494	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	109	309	0	ENST00000264010.4:c.1807C>T	p.Arg603Cys	p.R603C	ENST00000264010	NM_006565.3	603	Cgc/Tgc	10/12	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.54	2		309	382	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821890	72821890	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	143	386	4	ENST00000268489.5:c.10285del	p.Arg3429ValfsTer56	p.R3429Vfs*56	ENST00000268489	NM_006885.3	3429	Cgt/gt	10/10	1	2	FACETS	0.974	0.892	1	0.974	0.892	1	CLONAL	1	TRUE	1	0.54	2		390	544	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827753	72827753	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772200448	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	184	569	0	ENST00000268489.5:c.8828G>A	p.Arg2943Gln	p.R2943Q	ENST00000268489	NM_006885.3	2943	cGg/cAg	9/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.54	2		569	659	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350876	89350876	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149939914	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	305	920	3	ENST00000301030.4:c.2074G>A	p.Asp692Asn	p.D692N	ENST00000301030	NM_001256183.1	692	Gac/Aac	9/13	1	2	FACETS	0.999	0.941	1	0.999	0.941	1	CLONAL	1	TRUE	1	0.54	2		923	1131	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553478	29553478	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781807	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	188	591	4	ENST00000356175.3:c.2033del	p.Pro678ArgfsTer10	p.P678Rfs*10	ENST00000356175	NM_000267.3	676	aCc/ac	18/57	1	2	FACETS	0.784	0.725	0.845	0.784	0.725	0.845	SUBCLONAL	1	TRUE	1	0.54	2		595	888	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661945	29661945	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854552	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	123	592	0	ENST00000356175.3:c.5839C>T	p.Arg1947Ter	p.R1947*	ENST00000356175	NM_000267.3	1947	Cga/Tga	39/57	1	2	FACETS	0.982	0.894	1	0.982	0.894	1	CLONAL	1	TRUE	1	0.54	2		592	464	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733094	74733094	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	63	522	0	ENST00000359995.5:c.149A>G	p.Tyr50Cys	p.Y50C	ENST00000359995	NM_001195427.1	50	tAc/tGc	1/3	1	2	FACETS	0.394	0.341	0.452	0.394	0.341	0.452	SUBCLONAL	1	TRUE	1	0.54	2		522	592	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262425	10262425	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	182	522	0	ENST00000340748.4:c.2069+1G>A		p.X690_splice	ENST00000340748		690			1	2	FACETS	0.875	0.809	0.944	0.875	0.809	0.944	CLONAL	1	TRUE	1	0.54	2		522	770	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121203	11121203	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	197	526	0	ENST00000358026.2:c.2270A>G	p.Tyr757Cys	p.Y757C	ENST00000358026	NM_001128849.1	757	tAc/tGc	15/36	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.54	2		526	662	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276861	15276861	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	225	680	0	ENST00000263388.2:c.5404del	p.Ala1802LeufsTer23	p.A1802Lfs*23	ENST00000263388	NM_000435.2	1802	Gct/ct	30/33	1	2	FACETS	0.955	0.89	1	0.955	0.89	1	CLONAL	1	TRUE	1	0.54	2		680	873	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353843	15353843	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1325249458	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	206	504	0	ENST00000263377.2:c.3037C>T	p.Pro1013Ser	p.P1013S	ENST00000263377	NM_058243.2	1013	Cca/Tca	14/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.54	2		504	659	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279905	18279905	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	212	557	0	ENST00000222254.8:c.1988G>A	p.Gly663Asp	p.G663D	ENST00000222254	NM_005027.3	663	gGc/gAc	16/16	1	2	FACETS	0.995	0.927	1	0.995	0.927	1	CLONAL	1	TRUE	1	0.54	2		557	789	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	262	821	3	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.54	2		824	958	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905174	50905175	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	120	741	0	ENST00000440232.2:c.461dup	p.Gly155TrpfsTer9	p.G155Wfs*9	ENST00000440232	NM_002691.3	152	-/C	4/27	1	2	FACETS	0.427	0.385	0.472	0.427	0.385	0.472	SUBCLONAL	1	TRUE	1	0.54	2		741	1040	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96930905	96930905	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	190	614	0	ENST00000258439.3:c.215T>C	p.Leu72Ser	p.L72S	ENST00000258439	NM_001193304.2	72	tTg/tCg	2/4	1	2	FACETS	0.795	0.736	0.857	0.795	0.736	0.857	SUBCLONAL	1	TRUE	1	0.54	2		614	885	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178129268	178129268	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	91	317	0	ENST00000397062.3:c.37T>C	p.Ser13Pro	p.S13P	ENST00000397062	NM_006164.4	13	Tcc/Ccc	1/5	1	2	FACETS	0.851	0.761	0.946	0.851	0.761	0.946	CLONAL	1	TRUE	1	0.54	2		317	396	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212615424	212615424	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752051535	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	44	415	0	ENST00000342788.4:c.562C>T	p.Arg188Cys	p.R188C	ENST00000342788	NM_005235.2	188	Cgt/Tgt	5/28	1	2	FACETS	0.257	0.215	0.304	0.257	0.215	0.304	SUBCLONAL	1	TRUE	1	0.54	2		415	634	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370686	225370686	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1232071537	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	97	387	3	ENST00000264414.4:c.1193del	p.Lys398ArgfsTer6	p.K398Rfs*6	ENST00000264414	NM_003590.4	398	aAg/ag	8/16	1	2	FACETS	0.971	0.873	1	0.971	0.873	1	CLONAL	1	TRUE	1	0.54	2		390	370	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750659	39750661	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	116	341	0	ENST00000361337.2:c.2065_2067del	p.Lys689del	p.K689del	ENST00000361337	NM_003286.2	687	AAG/-	20/21	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.54	2		341	383	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764347	39764347	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	198	498	0	ENST00000288319.7:c.765del	p.Arg256GlyfsTer35	p.R256Gfs*35	ENST00000288319	NM_182918.3	255	ccC/cc	7/10	1	2	FACETS	0.969	0.9	1	0.969	0.9	1	CLONAL	1	TRUE	1	0.54	2		498	757	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633229	12633229	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	173	531	1	ENST00000251849.4:c.1171A>G	p.Arg391Gly	p.R391G	ENST00000251849	NM_002880.3	391	Agg/Ggg	11/17	0.5431281439368	2	FACETS	0.833	0.768	0.901	0.417	0.384	0.451	CLONAL	1	TRUE	0	0.54	2		532	769	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643905	52643905	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1315914230	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	140	594	4	ENST00000394830.3:c.1991A>G	p.Glu664Gly	p.E664G	ENST00000394830	NM_018313.4	664	gAg/gGg	17/30	1	2	FACETS	0.879	0.804	0.957	0.879	0.804	0.957	CLONAL	1	TRUE	1	0.54	2		598	590	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987136	69987136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141679911	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	84	439	0	ENST00000394351.3:c.197C>T	p.Pro66Leu	p.P66L	ENST00000394351	NM_000248.3	66	cCg/cTg	2/9	1	2	FACETS	0.495	0.438	0.557	0.495	0.438	0.557	SUBCLONAL	1	TRUE	1	0.54	2		439	628	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281525	142281525	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1354835562	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	152	623	0	ENST00000350721.4:c.719G>A	p.Gly240Asp	p.G240D	ENST00000350721	NM_001184.3	240	gGt/gAt	4/47	1	2	FACETS	0.964	0.886	1	0.964	0.886	1	CLONAL	1	TRUE	1	0.54	2		623	584	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114337	143114337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747045725	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	30	422	0	ENST00000262992.4:c.1084G>A	p.Asp362Asn	p.D362N	ENST00000262992	NM_001101669.1	362	Gat/Aat	13/24	1	2	FACETS	0.228	0.183	0.279	0.228	0.183	0.279	SUBCLONAL	1	TRUE	1	0.54	2		422	487	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	209	526	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.54	2		526	769	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187560905	187560905	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1302189943	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	133	426	0	ENST00000441802.2:c.3613C>T	p.Arg1205Ter	p.R1205*	ENST00000441802	NM_005245.3	1205	Cga/Tga	4/27	1	2	FACETS	0.991	0.906	1	0.991	0.906	1	CLONAL	1	TRUE	1	0.54	2		426	497	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950138	38950138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573790456	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	148	555	0	ENST00000357387.3:c.3812C>T	p.Thr1271Met	p.T1271M	ENST00000357387	NM_152756.3	1271	aCg/aTg	31/38	1	2	FACETS	0.873	0.8	0.949	0.873	0.8	0.949	CLONAL	1	TRUE	1	0.54	2		555	628	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589576	67589576	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1289537429	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	23	220	0	ENST00000274335.5:c.1344del	p.Lys448AsnfsTer32	p.K448Nfs*32	ENST00000274335		447	Aaa/aa	10/15	1	2	FACETS	0.536	0.421	0.665	0.536	0.421	0.665	SUBCLONAL	1	TRUE	1	0.54	2		220	159	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589619	67589620	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	37	243	0	ENST00000274335.5:c.1384_1385del	p.Glu462IlefsTer2	p.E462Ifs*2	ENST00000274335		461	cGA/c	10/15	1	2	FACETS	0.659	0.548	0.78	0.659	0.548	0.78	SUBCLONAL	1	TRUE	1	0.54	2		243	208	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645099	86645099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1305400293	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	74	352	1	ENST00000274376.6:c.1171C>T	p.Arg391Trp	p.R391W	ENST00000274376	NM_002890.2	391	Cgg/Tgg	8/25	1	2	FACETS	0.859	0.759	0.966	0.859	0.759	0.966	CLONAL	1	TRUE	1	0.54	2		353	319	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672329	86672329	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	103	367	0	ENST00000274376.6:c.2131C>G	p.Arg711Gly	p.R711G	ENST00000274376	NM_002890.2	711	Cga/Gga	16/25	1	2	FACETS	0.833	0.749	0.921	0.833	0.749	0.921	CLONAL	1	TRUE	1	0.54	2		367	458	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402539	20402539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs185222077	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	27	399	2	ENST00000346618.3:c.76G>A	p.Ala26Thr	p.A26T	ENST00000346618	NM_001949.4	26	Gcc/Acc	1/7	1	2	FACETS	0.211	0.167	0.261	0.211	0.167	0.261	SUBCLONAL	1	TRUE	1	0.54	2		401	474	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911051	29911051	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs199474473	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	69	663	0	ENST00000376809.5:c.350A>G	p.His117Arg	p.H117R	ENST00000376809	NM_002116.7	117	cAc/cGc	3/8	1	2	FACETS	0.324	0.282	0.371	0.324	0.282	0.371	SUBCLONAL	1	TRUE	1	0.54	2		663	788	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166784	32166784	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	104	707	1	ENST00000375023.3:c.4454del	p.Pro1485LeufsTer20	p.P1485Lfs*20	ENST00000375023	NM_004557.3	1485	cCt/ct	24/30	1	2	FACETS	0.432	0.386	0.481	0.432	0.386	0.481	SUBCLONAL	1	TRUE	1	0.54	2		708	892	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552792	106552792	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	173	545	0	ENST00000369096.4:c.757A>C	p.Ile253Leu	p.I253L	ENST00000369096	NM_001198.3	253	Atc/Ctc	5/7	1	2	FACETS	0.909	0.839	0.981	0.909	0.839	0.981	CLONAL	1	TRUE	1	0.54	2		545	705	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149982872	149982872	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	93	418	0	ENST00000253339.5:c.3386A>G	p.Tyr1129Cys	p.Y1129C	ENST00000253339		1129	tAt/tGt	7/7	1	2	FACETS	0.89	0.797	0.987	0.89	0.797	0.987	CLONAL	1	TRUE	1	0.54	2		418	387	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345769	152345769	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs759063323	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	23	339	0	ENST00000359321.1:c.801del	p.Lys267AsnfsTer30	p.K267Nfs*30	ENST00000359321	NM_005431.1	267	aaA/aa	3/3	1	2	FACETS	0.211	0.164	0.266	0.211	0.164	0.266	SUBCLONAL	1	TRUE	1	0.54	2		339	403	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006078	22006078	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	204	553	0	ENST00000276925.6:c.325C>T	p.Arg109Cys	p.R109C	ENST00000276925	NM_004936.3	109	Cgc/Tgc	2/2	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.54	2		553	707	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636210	87636210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs957713208	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	39	487	0	ENST00000277120.3:c.2375G>A	p.Arg792His	p.R792H	ENST00000277120		792	cGc/cAc	19/19	1	2	FACETS	0.262	0.216	0.312	0.262	0.216	0.312	SUBCLONAL	1	TRUE	1	0.54	2		487	552	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222246	53222246	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556832161	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	129	786	4	ENST00000375401.3:c.4586C>T	p.Ala1529Val	p.A1529V	ENST00000375401	NM_004187.3	1529	gCg/gTg	26/26	1	2	FACETS	0.508	0.46	0.559	0.508	0.46	0.559	SUBCLONAL	1	TRUE	1	0.54	2		790	940	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246362	53246362	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs782070676	NA	P-0032994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	127	720	0	ENST00000375401.3:c.620A>G	p.Asn207Ser	p.N207S	ENST00000375401	NM_004187.3	207	aAc/aGc	5/26	1	2	FACETS	0.455	0.411	0.501	0.455	0.411	0.501	SUBCLONAL	1	TRUE	1	0.54	2		720	1034	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0033002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	442	409	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.617125977166285	4	FACETS	0.995	0.967	1	0.995	0.967	1	CLONAL	4	TRUE	0	0.633280399943902	4		409	573	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	226	423	0	ENST00000263967.3:c.323G>T	p.Arg108Leu	p.R108L	ENST00000263967	NM_006218.2	108	cGt/cTt	2/21	0.383589638975589	3	FACETS	1	0.987	1	0.758	0.718	0.799	CLONAL	2	TRUE	0	0.633280399943902	3		423	413	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615625	100615625	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	76	587	0	ENST00000308731.7:c.707G>C	p.Arg236Pro	p.R236P	ENST00000308731	NM_000061.2	236	cGg/cCg	8/19	0.633280399943902	1	FACETS	0.409	0.36	0.461	0.409	0.36	0.461	SUBCLONAL	1	TRUE	0	0.633280399943902	1		587	401	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0033004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	250	699	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.894362891109809	2		699	547	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754512	41754512	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	81	584	0	ENST00000301178.4:c.1631A>G	p.Glu544Gly	p.E544G	ENST00000301178	NM_021913.4	544	gAg/gGg	13/20	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.728429740614811	NA		584	304	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267638	7267638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs896894246	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	63	590	1	ENST00000302850.5:c.370G>A	p.Glu124Lys	p.E124K	ENST00000302850	NM_000208.2	124	Gag/Aag	2/22	1	2	FACETS	0.983	0.849	1	0.983	0.849	1	CLONAL	1	TRUE	1	0.18	2		591	712	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316389	14316389	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	44	528	0	ENST00000256196.4:c.216A>C	p.Gln72His	p.Q72H	ENST00000256196		72	caA/caC	3/6	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.18	2		528	415	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242646	16242646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	28	418	0	ENST00000375759.3:c.1267C>T	p.Arg423Cys	p.R423C	ENST00000375759	NM_015001.2	423	Cgc/Tgc	6/15	1	2	FACETS	0.774	0.618	0.952	0.774	0.618	0.952	CLONAL	1	TRUE	1	0.18	2		418	402	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22413036	22413036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	14	265	0	ENST00000344548.3:c.283G>A	p.Glu95Lys	p.E95K	ENST00000344548	NM_001039802.1	95	Gaa/Aaa	5/7	1	2	FACETS	0.645	0.466	0.862	0.645	0.466	0.862	SUBCLONAL	1	TRUE	1	0.18	2		265	241	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932232	36932232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1382959301	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	38	563	1	ENST00000361632.4:c.2237C>T	p.Thr746Ile	p.T746I	ENST00000361632		746	aCc/aTc	16/16	1	2	FACETS	0.862	0.712	1	0.862	0.712	1	CLONAL	1	TRUE	1	0.18	2		564	490	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743846	46743846	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	69	610	0	ENST00000371975.4:c.2136G>T	p.Lys712Asn	p.K712N	ENST00000371975	NM_003579.3	712	aaG/aaT	18/18	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.18	2		610	584	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120457933	120457933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769520444	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	30	405	0	ENST00000256646.2:c.7412C>T	p.Ala2471Val	p.A2471V	ENST00000256646	NM_024408.3	2471	gCg/gTg	34/34	1	2	FACETS	0.686	0.552	0.838	0.686	0.552	0.838	SUBCLONAL	1	TRUE	1	0.18	2		405	486	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845627	63845627	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	12	205	0	ENST00000279873.7:c.1366G>T	p.Glu456Ter	p.E456*	ENST00000279873	NM_032199.2	456	Gaa/Taa	9/10	1	2	FACETS	0.737	0.519	1	0.737	0.519	1	CLONAL	1	TRUE	1	0.18	2		205	181	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692940	89692940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746152219	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	48	570	0	ENST00000371953.3:c.424C>T	p.Arg142Trp	p.R142W	ENST00000371953	NM_000314.4	142	Cgg/Tgg	5/9	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.18	2		570	473	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692978	89692978	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	45	485	0	ENST00000371953.3:c.462C>A	p.Phe154Leu	p.F154L	ENST00000371953	NM_000314.4	154	ttC/ttA	5/9	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.18	2		485	383	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161456	2161456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs970922682	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	30	515	0	ENST00000434045.2:c.71G>A	p.Arg24His	p.R24H	ENST00000434045	NM_001127598.1	24	cGc/cAc	2/5	1	2	FACETS	0.58	0.466	0.71	0.58	0.466	0.71	SUBCLONAL	1	TRUE	1	0.18	2		515	575	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216596	108216596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778080	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	20	370	0	ENST00000278616.4:c.8545C>T	p.Arg2849Ter	p.R2849*	ENST00000278616	NM_000051.3	2849	Cga/Tga	58/63	1	2	FACETS	0.606	0.462	0.774	0.606	0.462	0.774	SUBCLONAL	1	TRUE	1	0.18	2		370	367	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022684	12022684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745867456	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	29	448	0	ENST00000396373.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000396373	NM_001987.4	264	Cgc/Tgc	5/8	0.3	2	FACETS	0.76	0.609	0.931			1	CLONAL	1	TRUE	NA	0.18	2		448	424	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435295	18435295	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752140066	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	20	344	1	ENST00000266497.5:c.280C>T	p.Arg94Cys	p.R94C	ENST00000266497		94	Cgt/Tgt	1/31	1	2	FACETS	0.671	0.513	0.857	0.671	0.513	0.857	SUBCLONAL	1	TRUE	1	0.18	2		345	331	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444297	49444297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746163543	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	53	755	0	ENST00000301067.7:c.3074C>T	p.Ser1025Leu	p.S1025L	ENST00000301067	NM_003482.3	1025	tCg/tTg	11/54	1	2	FACETS	0.899	0.766	1	0.899	0.766	1	CLONAL	1	TRUE	1	0.18	2		755	655	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	46	544	0	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	1	2	FACETS	0.975	0.821	1	0.975	0.821	1	CLONAL	1	TRUE	1	0.18	2		544	524	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493621	56493621	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs1343971705	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	13	290	0	ENST00000267101.3:c.2938-1G>T		p.X980_splice	ENST00000267101	NM_001982.3	980			1	2	FACETS	0.56	0.399	0.757	0.56	0.399	0.757	SUBCLONAL	1	TRUE	1	0.18	2		290	258	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495034	56495034	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150312718	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	35	526	0	ENST00000267101.3:c.3391G>A	p.Ala1131Thr	p.A1131T	ENST00000267101	NM_001982.3	1131	Gcc/Acc	27/28	1	2	FACETS	0.633	0.518	0.764	0.633	0.518	0.764	SUBCLONAL	1	TRUE	1	0.18	2		526	614	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495468	56495468	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	31	616	0	ENST00000267101.3:c.3658C>A	p.Leu1220Met	p.L1220M	ENST00000267101	NM_001982.3	1220	Ctg/Atg	28/28	1	2	FACETS	0.571	0.461	0.697	0.571	0.461	0.697	SUBCLONAL	1	TRUE	1	0.18	2		616	603	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858468	57858468	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	31	461	0	ENST00000228682.2:c.206C>A	p.Ser69Tyr	p.S69Y	ENST00000228682	NM_005269.2	69	tCt/tAt	4/12	1	2	FACETS	0.685	0.553	0.835	0.685	0.553	0.835	SUBCLONAL	1	TRUE	1	0.18	2		461	503	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864956	57864956	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	29	623	0	ENST00000228682.2:c.2433A>C	p.Gln811His	p.Q811H	ENST00000228682	NM_005269.2	811	caA/caC	12/12	1	2	FACETS	0.631	0.505	0.774	0.631	0.505	0.774	SUBCLONAL	1	TRUE	1	0.18	2		623	511	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118710	115118710	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	31	580	0	ENST00000257566.3:c.631A>G	p.Asn211Asp	p.N211D	ENST00000257566	NM_016569.3	211	Aac/Gac	2/8	1	2	FACETS	0.567	0.458	0.692	0.567	0.458	0.692	SUBCLONAL	1	TRUE	1	0.18	2		580	607	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253151	133253151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	38	396	0	ENST00000320574.5:c.890C>T	p.Ser297Phe	p.S297F	ENST00000320574	NM_006231.2	297	tCc/tTc	9/49	1	2	FACETS	0.869	0.718	1	0.869	0.718	1	CLONAL	1	TRUE	1	0.18	2		396	486	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589759	28589759	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	27	479	0	ENST00000241453.7:c.2621A>T	p.Tyr874Phe	p.Y874F	ENST00000241453	NM_004119.2	874	tAt/tTt	21/24	1	2	FACETS	0.719	0.572	0.888	0.719	0.572	0.888	SUBCLONAL	1	TRUE	1	0.18	2		479	417	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28611388	28611388	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	43	561	0	ENST00000241453.7:c.1243G>T	p.Glu415Ter	p.E415*	ENST00000241453	NM_004119.2	415	Gaa/Taa	10/24	1	2	FACETS	0.983	0.823	1	0.983	0.823	1	CLONAL	1	TRUE	1	0.18	2		561	486	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893318	32893318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507603	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	28	337	0	ENST00000380152.3:c.172G>A	p.Glu58Lys	p.E58K	ENST00000380152		58	Gaa/Aaa	3/27	1	2	FACETS	0.886	0.709	1	0.886	0.709	1	CLONAL	1	TRUE	1	0.18	2		337	351	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911921	32911921	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	28	510	0	ENST00000380152.3:c.3429A>C	p.Glu1143Asp	p.E1143D	ENST00000380152		1143	gaA/gaC	11/27	1	2	FACETS	0.645	0.515	0.795	0.645	0.515	0.795	SUBCLONAL	1	TRUE	1	0.18	2		510	482	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941654	48941654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776534331	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	15	268	0	ENST00000267163.4:c.964G>A	p.Glu322Lys	p.E322K	ENST00000267163	NM_000321.2	322	Gaa/Aaa	10/27	1	2	FACETS	0.718	0.526	0.949	0.718	0.526	0.949	CLONAL	1	TRUE	1	0.18	2		268	232	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103525652	103525652	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	21	409	1	ENST00000355739.4:c.2923G>T	p.Glu975Ter	p.E975*	ENST00000355739	NM_000123.3	975	Gaa/Taa	14/15	1	2	FACETS	0.579	0.445	0.736	0.579	0.445	0.736	SUBCLONAL	1	TRUE	1	0.18	2		410	403	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528224	103528224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768302699	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	16	228	0	ENST00000355739.4:c.3532C>T	p.Arg1178Cys	p.R1178C	ENST00000355739	NM_000123.3	1178	Cgt/Tgt	15/15	1	2	FACETS	0.668	0.494	0.877	0.668	0.494	0.877	SUBCLONAL	1	TRUE	1	0.18	2		228	266	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643719	38643719	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	52	698	0	ENST00000299084.4:c.1189G>A	p.Asp397Asn	p.D397N	ENST00000299084	NM_152594.2	397	Gac/Aac	7/7	1	2	FACETS	0.671	0.57	0.783	0.671	0.57	0.783	SUBCLONAL	1	TRUE	1	0.18	2		698	861	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434776	99434776	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	38	493	0	ENST00000268035.6:c.863C>T	p.Ala288Val	p.A288V	ENST00000268035	NM_000875.3	288	gCc/gTc	3/21	1	2	FACETS	0.699	0.577	0.836	0.699	0.577	0.836	SUBCLONAL	1	TRUE	1	0.18	2		493	604	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992964	72992964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561634666	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	42	790	1	ENST00000268489.5:c.1081G>A	p.Gly361Arg	p.G361R	ENST00000268489	NM_006885.3	361	Gga/Aga	2/10	1	2	FACETS	0.573	0.477	0.681	0.573	0.477	0.681	SUBCLONAL	1	TRUE	1	0.18	2		791	814	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969848	81969848	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568724894	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	27	457	1	ENST00000359376.3:c.2917G>A	p.Asp973Asn	p.D973N	ENST00000359376	NM_002661.3	973	Gac/Aac	27/33	1	2	FACETS	0.662	0.526	0.818	0.662	0.526	0.818	SUBCLONAL	1	TRUE	1	0.18	2		458	453	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	29	350	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.18	2		350	295	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627887	37627887	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	55	596	1	ENST00000447079.4:c.1802C>A	p.Ser601Tyr	p.S601Y	ENST00000447079	NM_015083.1	601	tCt/tAt	2/14	1	2	FACETS	0.926	0.791	1	0.926	0.791	1	CLONAL	1	TRUE	1	0.18	2		597	660	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38504686	38504686	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	33	596	1	ENST00000254066.5:c.297C>A	p.His99Gln	p.H99Q	ENST00000254066	NM_000964.3	99	caC/caA	3/9	1	2	FACETS	0.607	0.493	0.736	0.607	0.493	0.736	SUBCLONAL	1	TRUE	1	0.18	2		597	604	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2199895	2199895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1304185199	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	30	591	0	ENST00000398665.3:c.664G>A	p.Asp222Asn	p.D222N	ENST00000398665	NM_032482.2	222	Gat/Aat	8/28	1	2	FACETS	0.57	0.458	0.698	0.57	0.458	0.698	SUBCLONAL	1	TRUE	1	0.18	2		591	585	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279331	18279331	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	27	399	0	ENST00000222254.8:c.1783C>A	p.Leu595Met	p.L595M	ENST00000222254	NM_005027.3	595	Ctg/Atg	14/16	1	2	FACETS	0.642	0.51	0.794	0.642	0.51	0.794	SUBCLONAL	1	TRUE	1	0.18	2		399	467	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229409	36229409	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	24	425	0	ENST00000222270.7:c.8099A>G	p.Lys2700Arg	p.K2700R	ENST00000222270	NM_014727.1	2700	aAg/aGg	37/37	1	2	FACETS	0.627	0.491	0.785	0.627	0.491	0.785	SUBCLONAL	1	TRUE	1	0.18	2		425	425	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727103	41727103	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	38	678	1	ENST00000301178.4:c.361C>A	p.Leu121Met	p.L121M	ENST00000301178	NM_021913.4	121	Ctg/Atg	3/20	1	2	FACETS	0.606	0.499	0.725	0.606	0.499	0.725	SUBCLONAL	1	TRUE	1	0.18	2		679	697	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716272	52716272	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	33	577	0	ENST00000322088.6:c.716A>T	p.Asp239Val	p.D239V	ENST00000322088	NM_014225.5	239	gAt/gTt	6/15	1	2	FACETS	0.678	0.551	0.821	0.678	0.551	0.821	SUBCLONAL	1	TRUE	1	0.18	2		577	541	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690230	47690230	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63749947	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	52	415	0	ENST00000233146.2:c.1447G>T	p.Glu483Ter	p.E483*	ENST00000233146	NM_000251.2	483	Gaa/Taa	9/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.18	2		415	437	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139656	202139656	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs146816437	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	32	279	0	ENST00000358485.4:c.817G>T	p.Glu273Ter	p.E273*	ENST00000358485	NM_001080125.1	273	Gaa/Taa	6/9	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.18	2		279	312	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812259	212812259	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs991337964	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	20	341	0	ENST00000342788.4:c.317G>A	p.Arg106His	p.R106H	ENST00000342788	NM_005235.2	106	cGt/cAt	3/28	1	2	FACETS	0.777	0.595	0.99	0.777	0.595	0.99	CLONAL	1	TRUE	1	0.18	2		341	286	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790089	40790089	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759416965	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	39	545	1	ENST00000373198.4:c.2642G>A	p.Arg881Gln	p.R881Q	ENST00000373198	NM_133170.3	881	cGg/cAg	18/32	1	2	FACETS	0.756	0.626	0.902	0.756	0.626	0.902	CLONAL	1	TRUE	1	0.18	2		546	573	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62323133	62323133	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	23	404	0	ENST00000360203.5:c.2595G>T	p.Lys865Asn	p.K865N	ENST00000360203	NM_001283009.1	865	aaG/aaT	28/35	1	2	FACETS	0.592	0.46	0.744	0.592	0.46	0.744	SUBCLONAL	1	TRUE	1	0.18	2		404	432	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162904	47162904	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs757432733	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	40	449	0	ENST00000409792.3:c.3222G>T	p.Lys1074Asn	p.K1074N	ENST00000409792	NM_014159.6	1074	aaG/aaT	3/21	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.18	2		449	386	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799481	72799481	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144498351	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	44	646	0	ENST00000325599.8:c.1688G>A	p.Arg563His	p.R563H	ENST00000325599	NM_018130.2	563	cGc/cAc	11/11	1	2	FACETS	0.693	0.58	0.82	0.693	0.58	0.82	SUBCLONAL	1	TRUE	1	0.18	2		646	705	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272768	142272768	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	52	525	0	ENST00000350721.4:c.2431A>C	p.Asn811His	p.N811H	ENST00000350721	NM_001184.3	811	Aat/Cat	11/47	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.18	2		525	566	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	32	381	0	ENST00000263967.3:c.333G>T	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaT	2/21	1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	1	0.18	2		381	350	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	9	393	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	1	2	FACETS	0.281	0.185	0.404	0.281	0.185	0.404	SUBCLONAL	1	TRUE	1	0.18	2		393	356	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198253	185198253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370479462	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	45	466	2	ENST00000265026.3:c.2735C>T	p.Ala912Val	p.A912V	ENST00000265026	NM_004721.4	912	gCc/gTc	13/14	1	2	FACETS	0.871	0.731	1	0.871	0.731	1	CLONAL	1	TRUE	1	0.18	2		468	574	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156716	106156716	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	27	289	0	ENST00000380013.4:c.1617G>T	p.Glu539Asp	p.E539D	ENST00000380013	NM_001127208.2	539	gaG/gaT	3/11	1	2	FACETS	0.94	0.749	1	0.94	0.749	1	CLONAL	1	TRUE	1	0.18	2		289	319	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540061	187540061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530048131	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	26	364	0	ENST00000441802.2:c.7679C>T	p.Ala2560Val	p.A2560V	ENST00000441802	NM_005245.3	2560	gCg/gTg	10/27	1	2	FACETS	0.641	0.506	0.795	0.641	0.506	0.795	SUBCLONAL	1	TRUE	1	0.18	2		364	451	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	33	265	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.18	2		265	252	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86682712	86682712	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	12	259	0	ENST00000274376.6:c.2917G>T	p.Glu973Ter	p.E973*	ENST00000274376	NM_002890.2	973	Gaa/Taa	23/25	1	2	FACETS	0.565	0.397	0.772	0.565	0.397	0.772	SUBCLONAL	1	TRUE	1	0.18	2		259	236	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818713	170818713	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	23	359	0	ENST00000296930.5:c.262T>A	p.Ser88Thr	p.S88T	ENST00000296930	NM_002520.6	88	Tcc/Acc	4/11	1	2	FACETS	0.628	0.489	0.789	0.628	0.489	0.789	SUBCLONAL	1	TRUE	1	0.18	2		359	407	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481448	20481448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1225039532	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	20	249	0	ENST00000346618.3:c.517C>T	p.Pro173Ser	p.P173S	ENST00000346618	NM_001949.4	173	Ccc/Tcc	3/7	1	2	FACETS	0.772	0.59	0.983	0.772	0.59	0.983	CLONAL	1	TRUE	1	0.18	2		249	288	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956553	93956553	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1035177735	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	47	435	1	ENST00000369303.4:c.2683C>T	p.Arg895Ter	p.R895*	ENST00000369303	NM_004440.3	895	Cga/Tga	15/17	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.18	2		436	440	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686836	117686836	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	17	320	0	ENST00000368508.3:c.2881A>C	p.Asn961His	p.N961H	ENST00000368508	NM_002944.2	961	Aat/Cat	19/43	1	2	FACETS	0.598	0.446	0.779	0.598	0.446	0.779	SUBCLONAL	1	TRUE	1	0.18	2		320	316	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521848	157521848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747088591	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	22	381	0	ENST00000346085.5:c.4120C>T	p.Arg1374Cys	p.R1374C	ENST00000346085	NM_020732.3	1374	Cgc/Tgc	18/20	1	2	FACETS	0.672	0.52	0.848	0.672	0.52	0.848	SUBCLONAL	1	TRUE	1	0.18	2		381	364	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983863	2983863	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	29	597	1	ENST00000396946.4:c.667C>T	p.Arg223Ter	p.R223*	ENST00000396946	NM_032415.4	223	Cga/Tga	5/25	1	2	FACETS	0.566	0.453	0.696	0.566	0.453	0.696	SUBCLONAL	1	TRUE	1	0.18	2		598	569	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392080	81392080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	36	430	0	ENST00000222390.5:c.197C>T	p.Thr66Ile	p.T66I	ENST00000222390	NM_000601.4	66	aCt/aTt	2/18	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.18	2		430	379	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508514	106508514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1406220505	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	11	215	0	ENST00000359195.3:c.508G>A	p.Asp170Asn	p.D170N	ENST00000359195	NM_002649.2	170	Gac/Aac	2/11	1	2	FACETS	0.664	0.459	0.918	0.664	0.459	0.918	SUBCLONAL	1	TRUE	1	0.18	2		215	184	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90949278	90949278	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	19	253	0	ENST00000265433.3:c.2210A>C	p.Glu737Ala	p.E737A	ENST00000265433	NM_002485.4	737	gAg/gCg	15/16	1	2	FACETS	0.723	0.549	0.928	0.723	0.549	0.928	CLONAL	1	TRUE	1	0.18	2		253	292	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982713	90982713	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	32	358	0	ENST00000265433.3:c.775G>T	p.Glu259Ter	p.E259*	ENST00000265433	NM_002485.4	259	Gaa/Taa	7/16	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.18	2		358	338	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566283	141566283	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	26	459	0	ENST00000220592.5:c.1129G>T	p.Glu377Ter	p.E377*	ENST00000220592	NM_012154.3	377	Gaa/Taa	9/19	1	2	FACETS	0.621	0.491	0.771	0.621	0.491	0.771	SUBCLONAL	1	TRUE	1	0.18	2		459	465	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331724	8331724	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs763525789	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	30	345	0	ENST00000356435.5:c.5392C>G	p.Arg1798Gly	p.R1798G	ENST00000356435		1798	Cga/Gga	33/35	1	2	FACETS	0.79	0.636	0.964	0.79	0.636	0.964	CLONAL	1	TRUE	1	0.18	2		345	422	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908873	101908873	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200595614	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	38	563	1	ENST00000374994.4:c.1237C>T	p.Arg413Ter	p.R413*	ENST00000374994	NM_004612.2	413	Cga/Tga	7/9	1	2	FACETS	0.823	0.68	0.983	0.823	0.68	0.983	CLONAL	1	TRUE	1	0.18	2		564	513	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127920662	127920662	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	15	331	0	ENST00000373547.4:c.238-1G>T		p.X80_splice	ENST00000373547	NM_002721.4	80			1	2	FACETS	0.575	0.42	0.761	0.575	0.42	0.761	SUBCLONAL	1	TRUE	1	0.18	2		331	290	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793317	139793317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755436517	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	41	568	1	ENST00000247668.2:c.125G>A	p.Arg42His	p.R42H	ENST00000247668	NM_021138.3	42	cGc/cAc	2/11	1	2	FACETS	0.856	0.713	1	0.856	0.713	1	CLONAL	1	TRUE	1	0.18	2		569	532	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732929	44732929	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	14	342	0	ENST00000377967.4:c.132G>T	p.Glu44Asp	p.E44D	ENST00000377967	NM_021140.2	44	gaG/gaT	1/29	1	2	FACETS	0.56	0.404	0.748	0.56	0.404	0.748	SUBCLONAL	1	TRUE	1	0.18	2		342	278	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412899	63412899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781369600	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	49	751	0	ENST00000330258.3:c.268C>T	p.Leu90Phe	p.L90F	ENST00000330258	NM_152424.3	90	Ctc/Ttc	2/2	1	2	FACETS	0.687	0.581	0.806	0.687	0.581	0.806	SUBCLONAL	1	TRUE	1	0.18	2		751	792	SUCCESS
AR	367	MSKCC	GRCh37	X	66765049	66765049	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	35	658	0	ENST00000374690.3:c.61G>T	p.Gly21Ter	p.G21*	ENST00000374690	NM_000044.3	21	Gga/Tga	1/8	1	2	FACETS	0.581	0.475	0.701	0.581	0.475	0.701	SUBCLONAL	1	TRUE	1	0.18	2		658	669	SUCCESS
BTK	695	MSKCC	GRCh37	X	100609658	100609658	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782740486	NA	P-0033016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	33	371	0	ENST00000308731.7:c.1591G>A	p.Asp531Asn	p.D531N	ENST00000308731	NM_000061.2	531	Gat/Aat	16/19	1	2	FACETS	0.782	0.636	0.946	0.782	0.636	0.946	CLONAL	1	TRUE	1	0.18	2		371	469	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183692	10183693	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs869025615	NA	P-0033020-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	195	476	0	ENST00000256474.2:c.163dup	p.Glu55GlyfsTer77	p.E55Gfs*77	ENST00000256474	NM_000551.3	54	atg/atGg	1/3	0.579309096025797	1	FACETS	0.889	0.83	0.95	0.889	0.83	0.95	CLONAL	1	TRUE	0	0.579899260996805	1		476	537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578191	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs530941076	NA	P-0033020-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	22	506	0	ENST00000269305.4:c.658T>C	p.Tyr220His	p.Y220H	ENST00000269305	NM_001126112.2	220	Tat/Cat	6/11	1	2	FACETS	0.09	0.069	0.114	0.09	0.069	0.114	SUBCLONAL	1	TRUE	1	0.579899260996805	2		506	845	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651361	52651361	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0033020-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	261	537	0	ENST00000394830.3:c.1735A>T	p.Lys579Ter	p.K579*	ENST00000394830	NM_018313.4	579	Aaa/Taa	15/30	0.579309096025797	1	FACETS	0.98	0.925	1	0.98	0.925	1	CLONAL	1	TRUE	0	0.579899260996805	1		537	652	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594195	55594195	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033020-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	152	306	0	ENST00000288135.5:c.1898A>G	p.Glu633Gly	p.E633G	ENST00000288135	NM_000222.2	633	gAa/gGa	13/21	1	2	FACETS	0.859	0.789	0.932	0.859	0.789	0.932	CLONAL	1	TRUE	1	0.579899260996805	2		306	610	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223773	53223789	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCCAGCACCTGCCCA	CAGCCAGCACCTGCCCA	-	novel	NA	P-0033020-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	284	401	0	ENST00000375401.3:c.3570_3586del	p.Cys1190TrpfsTer8	p.C1190Wfs*8	ENST00000375401	NM_004187.3	1190	tgTGGGCAGGTGCTGGCTGgg/tggg	23/26	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.579899260996805	1		401	546	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228307	53228307	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033020-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	294	261	0	ENST00000375401.3:c.2095C>G	p.Leu699Val	p.L699V	ENST00000375401	NM_004187.3	699	Ctg/Gtg	15/26	1	1	FACETS	0.756	0.723	0.789	1	0.995	1	SUBCLONAL	2	TRUE	0	0.579899260996805	1		261	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0033030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	77	587	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.229743109252847	1	FACETS	0.991	0.871	1	0.991	0.871	1	CLONAL	1	TRUE	0	0.238096968586895	1		587	575	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	75	697	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	0.238096968586895	2		697	572	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250243	133250244	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0033030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	63	482	0	ENST00000320574.5:c.1276dup	p.Ala426GlyfsTer10	p.A426Gfs*10	ENST00000320574	NM_006231.2	426	gcg/gGcg	13/49	1	2	FACETS	0.892	0.772	1	0.892	0.772	1	CLONAL	1	TRUE	1	0.238096968586895	2		482	593	SUCCESS
APC	324	MSKCC	GRCh37	5	112175738	112175738	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	90	269	0	ENST00000257430.4:c.4448del	p.Pro1483GlnfsTer24	p.P1483Qfs*24	ENST00000257430	NM_000038.5	1483	Cca/ca	16/16	0.238096968586895	2	FACETS	0.849	0.757	0.947	0.849	0.757	0.947	CLONAL	2	TRUE	0	0.238096968586895	2		269	445	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	129	697	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.287545612317556	4	FACETS	0.85	0.777	0.925	1	0.981	1	CLONAL	3	TRUE	2	0.309746353959751	4		697	428	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0033039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	58	442	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.309746353959751	3	FACETS	1	0.966	1	0.471	0.407	0.539	CLONAL	1	TRUE	0	0.309746353959751	3		442	306	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0033039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	114	373	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.287545612317556	4	FACETS	0.986	0.892	1	0.986	0.892	1	CLONAL	2	TRUE	2	0.309746353959751	4		373	489	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39620648	39620648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	46	507	0	ENST00000262039.4:c.2046G>A	p.Met682Ile	p.M682I	ENST00000262039	NM_002647.2	682	atG/atA	19/25	1	2	FACETS	0.94	0.795	1	0.94	0.795	1	CLONAL	1	TRUE	1	0.309746353959751	2		507	316	SUCCESS
APC	324	MSKCC	GRCh37	5	112175328	112175328	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0033039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	53	227	0	ENST00000257430.4:c.4037C>G	p.Ser1346Ter	p.S1346*	ENST00000257430	NM_000038.5	1346	tCa/tGa	16/16	0.287545612317556	4	FACETS	1	0.957	1	0.667	0.572	0.77	CLONAL	1	TRUE	2	0.309746353959751	4		227	336	SUCCESS
APC	324	MSKCC	GRCh37	5	112178561	112178607	+	frameshift_variant	Frame_Shift_Del	DEL	TCAAGTGGAAGTGAATCTGATAGATCAGAAAGACCTGTATTAGTACG	TCAAGTGGAAGTGAATCTGATAGATCAGAAAGACCTGTATTAGTACG	-	novel	NA	P-0033039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	29	320	0	ENST00000257430.4:c.7270_7316del	p.Ser2424ProfsTer24	p.S2424Pfs*24	ENST00000257430	NM_000038.5	2424	TCAAGTGGAAGTGAATCTGATAGATCAGAAAGACCTGTATTAGTACGc/c	16/16	0.287545612317556	4	FACETS	0.776	0.624	0.948	0.388	0.312	0.474	CLONAL	1	TRUE	2	0.309746353959751	4		320	316	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001529	150001529	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	97	619	0	ENST00000253339.5:c.2075A>G	p.Tyr692Cys	p.Y692C	ENST00000253339		692	tAc/tGc	4/7	0.309746353959751	3	FACETS	1	0.98	1	0.715	0.64	0.794	CLONAL	1	TRUE	1	0.309746353959751	3		619	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0033056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	85	863	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	1	2	FACETS	0.698	0.616	0.786	0.698	0.616	0.786	SUBCLONAL	1	TRUE	1	0.27	2		863	902	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246091235	246091235	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	rs769217941	NA	P-0033056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	28	419	0	ENST00000388985.4:c.700G>T	p.Glu234Ter	p.E234*	ENST00000388985		234	Gag/Tag	7/12	1	2	FACETS	0.394	0.314	0.486	0.394	0.314	0.486	SUBCLONAL	1	TRUE	1	0.27	2		419	526	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231588	5231588	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	37	256	1	ENST00000357368.4:c.1888G>T	p.Val630Leu	p.V630L	ENST00000357368	NM_002850.3	630	Gtg/Ttg	14/38	1	2	FACETS	0.873	0.722	1	0.873	0.722	1	CLONAL	1	TRUE	1	0.27	2		257	314	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107018	11107018	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	54	537	0	ENST00000358026.2:c.1723C>T	p.Gln575Ter	p.Q575*	ENST00000358026	NM_001128849.1	575	Cag/Tag	10/36	1	2	FACETS	0.777	0.664	0.9	0.777	0.664	0.9	SUBCLONAL	1	TRUE	1	0.27	2		537	515	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444571	187444571	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	66	678	0	ENST00000232014.4:c.1656G>T	p.Gln552His	p.Q552H	ENST00000232014	NM_001130845.1	552	caG/caT	7/10	0.114209182807305	3	FACETS	0.651	0.564	0.746	0.326	0.282	0.373	INDETERMINATE	1	TRUE	1	0.27	3		678	852	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662564	117662564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	44	499	2	ENST00000368508.3:c.4901A>T	p.Lys1634Met	p.K1634M	ENST00000368508	NM_002944.2	1634	aAg/aTg	29/43	1	2	FACETS	0.686	0.576	0.809	0.686	0.576	0.809	SUBCLONAL	1	TRUE	1	0.27	2		501	475	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853062	151853062	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	53	514	0	ENST00000262189.6:c.11893G>T	p.Gly3965Cys	p.G3965C	ENST00000262189	NM_170606.2	3965	Ggc/Tgc	46/59	1	2	FACETS	0.594	0.506	0.691	0.594	0.506	0.691	SUBCLONAL	1	TRUE	1	0.27	2		514	661	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914739	32914739	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	45	582	0	ENST00000380152.3:c.6247T>C	p.Phe2083Leu	p.F2083L	ENST00000380152		2083	Ttt/Ctt	11/27	0.455964029143889	1	FACETS	0.282	0.236	0.332	0.282	0.236	0.332	SUBCLONAL	1	TRUE	0	0.44815422695598	1		582	553	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129143	2129143	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	85	857	0	ENST00000219476.3:c.3077G>T	p.Cys1026Phe	p.C1026F	ENST00000219476	NM_000548.3	1026	tGt/tTt	27/42	0.455964029143889	4	FACETS	0.458	0.403	0.517	0.114	0.1	0.13	SUBCLONAL	1	TRUE	0	0.44815422695598	4		857	1200	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588812	52588812	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	34	596	0	ENST00000394830.3:c.4216C>G	p.Leu1406Val	p.L1406V	ENST00000394830	NM_018313.4	1406	Ctt/Gtt	27/30	0.455964029143889	2	FACETS	0.369	0.301	0.445	0.185	0.15	0.223	SUBCLONAL	1	TRUE	0	0.44815422695598	2		596	411	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396745	139396745	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	35	747	0	ENST00000277541.6:c.5363G>T	p.Gly1788Val	p.G1788V	ENST00000277541	NM_017617.3	1788	gGc/gTc	28/34	0.455964029143889	2	FACETS	0.326	0.267	0.393	0.163	0.133	0.197	SUBCLONAL	1	TRUE	0	0.44815422695598	2		747	479	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0033068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	51	328	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.223278900425308	2		328	364	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47061249	47061249	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0033068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	69	535	0	ENST00000409792.3:c.7431+1G>T		p.X2477_splice	ENST00000409792	NM_014159.6	2477			1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.223278900425308	2		535	513	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170632	7170632	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	51	702	0	ENST00000302850.5:c.1399del	p.His467ThrfsTer20	p.H467Tfs*20	ENST00000302850	NM_000208.2	467	Cac/ac	6/22	1	2	FACETS	0.632	0.536	0.738	0.632	0.536	0.738	SUBCLONAL	1	TRUE	1	0.223278900425308	2		702	723	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129917	55129917	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1449637193	NA	P-0033068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	87	589	0	ENST00000257290.5:c.451C>T	p.Arg151Cys	p.R151C	ENST00000257290	NM_006206.4	151	Cgc/Tgc	4/23	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.223278900425308	2		589	618	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505513	25505513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	52	673	1	ENST00000264709.3:c.245C>T	p.Ser82Leu	p.S82L	ENST00000264709	NM_175629.2	82	tCa/tTa	4/23	1	2	FACETS	0.585	0.497	0.681	0.585	0.497	0.681	SUBCLONAL	1	TRUE	1	0.28	2		674	635	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411927	116411976	+	frameshift_variant	Frame_Shift_Del	DEL	ACGATGCAAGAGTACACACTCCTCATTTGGATAGGCTTGTAAGTGCCCGA	ACGATGCAAGAGTACACACTCCTCATTTGGATAGGCTTGTAAGTGCCCGA	-	novel	NA	P-0033072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	160	847	0	ENST00000397752.3:c.2913_2962del	p.Tyr971Ter	p.Y971*	ENST00000397752	NM_000245.2	971	tACGATGCAAGAGTACACACTCCTCATTTGGATAGGCTTGTAAGTGCCCGA/t	14/21	0.177086865948704	2	FACETS	1	0.982	1	0.626	0.574	0.68	CLONAL	1	TRUE	0	0.28	2		847	913	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0033075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	25	462	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.319650149954305	9	FACETS	1	0.868	1	0.552	0.445	0.67	CLONAL	3	TRUE	3	0.319650149954305	9		462	100	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28908205	28908205	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	17	589	0	ENST00000282397.4:c.2550G>C	p.Lys850Asn	p.K850N	ENST00000282397	NM_002019.4	850	aaG/aaC	18/30	0.319650149954305	2	FACETS	0.794	0.609	1	0.794	0.609	1	CLONAL	2	TRUE	0	0.319650149954305	2		589	67	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103421	2103421	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	19	614	0	ENST00000219476.3:c.304C>A	p.Leu102Met	p.L102M	ENST00000219476	NM_000548.3	102	Ctg/Atg	4/42	0.319650149954305	4	FACETS	1	0.89	1	0.83	0.651	1	CLONAL	2	TRUE	1	0.319650149954305	4		614	63	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738456	145738456	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	14	612	0	ENST00000428558.2:c.2529G>C	p.Lys843Asn	p.K843N	ENST00000428558	NM_004260.3	843	aaG/aaC	16/22	0.319650149954305	3	FACETS	1	0.881	1	0.715	0.528	0.931	CLONAL	1	TRUE	1	0.319650149954305	3		612	71	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0033078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	370	517	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.647040394213897	5	FACETS	1	0.97	1	0.763	0.73	0.797	CLONAL	3	TRUE	1	0.679637465532203	5		517	720	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691039	NA	P-0033078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	283	822	0	ENST00000269305.4:c.919+1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.611427869165283	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.679637465532203	1		822	548	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950697	79950705	+	inframe_deletion	In_Frame_Del	DEL	GCTGCAGCG	GCTGCAGCG	-	rs758595508	NA	P-0033078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	27	218	1	ENST00000265081.6:c.162_170del	p.Ala60_Ala62del	p.A60_A62del	ENST00000265081	NM_002439.4	51	GCTGCAGCG/-	1/24	0.352575725898076	2	FACETS	0.353	0.282	0.433	0.177	0.141	0.217	INDETERMINATE	1	TRUE	0	0.679637465532203	2		219	225	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024607	14024607	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	164	622	0	ENST00000311895.7:c.833G>C	p.Gly278Ala	p.G278A	ENST00000311895	NM_005236.2	278	gGa/gCa	5/11	0.479922472012858	5	FACETS	0.943	0.865	1			1	CLONAL	1	TRUE	NA	0.679637465532203	5		622	1033	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847366	68847366	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	253	684	1	ENST00000261769.5:c.1288G>T	p.Val430Leu	p.V430L	ENST00000261769	NM_004360.3	430	Gtg/Ttg	9/16	0.679637465532203	3	FACETS	1	0.962	1			1	CLONAL	1	TRUE	NA	0.679637465532203	3		685	962	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89842153	89842153	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	227	611	0	ENST00000389301.3:c.1897G>T	p.Glu633Ter	p.E633*	ENST00000389301	NM_000135.2	633	Gaa/Taa	21/43	0.679637465532203	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.679637465532203	1		611	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0033079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	364	816	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.778904614323966	1	FACETS	0.987	0.949	1	0.987	0.949	1	CLONAL	1	TRUE	0	0.778904614323966	1		817	578	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	306	519	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	0.924	0.875	0.975	0.924	0.875	0.975	CLONAL	1	TRUE	1	0.778904614323966	2		519	850	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797934	45797934	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	351	603	0	ENST00000450313.1:c.837C>G	p.Asn279Lys	p.N279K	ENST00000450313	NM_012222.2	279	aaC/aaG	10/16	NA	2	FACETS	0.993	0.944	1			1	INDETERMINATE	1	TRUE	NA	0.778904614323966	2		603	908	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519998	NA	P-0033082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	118	671	0	ENST00000269305.4:c.581T>C	p.Leu194Pro	p.L194P	ENST00000269305	NM_001126112.2	194	cTt/cCt	6/11	0.162261165845447	2	FACETS	0.887	0.8	0.979	0.887	0.8	0.979	CLONAL	2	TRUE	0	0.163566958178492	2		671	813	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805762	43805762	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	66	720	0	ENST00000372470.3:c.818C>G	p.Ser273Cys	p.S273C	ENST00000372470	NM_005373.2	273	tCc/tGc	5/12	0.163566958178492	3	FACETS	0.952	0.824	1	0.476	0.412	0.546	CLONAL	1	TRUE	1	0.163566958178492	3		720	917	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464953	120464953	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	103	592	0	ENST00000256646.2:c.5119G>T	p.Gly1707Cys	p.G1707C	ENST00000256646	NM_024408.3	1707	Ggc/Tgc	28/34	0.163566958178492	2	FACETS	0.859	0.769	0.955	0.859	0.769	0.955	CLONAL	2	TRUE	0	0.163566958178492	2		592	733	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915901	127915901	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	139	683	0	ENST00000373547.4:c.580C>A	p.Leu194Met	p.L194M	ENST00000373547	NM_002721.4	194	Ctg/Atg	6/7	0.163566958178492	2	FACETS	0.955	0.869	1	0.955	0.869	1	CLONAL	2	TRUE	0	0.163566958178492	2		683	890	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0033082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	50	476	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	0.146232813992197	4	FACETS	1	0.871	1	0.515	0.436	0.603	CLONAL	1	TRUE	2	0.163566958178492	4		476	690	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433730	149433730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1484584245	NA	P-0033082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	64	808	0	ENST00000286301.3:c.2821G>A	p.Glu941Lys	p.E941K	ENST00000286301	NM_005211.3	941	Gag/Aag	22/22	0.110523315357772	4	FACETS	0.724	0.625	0.833	0.362	0.312	0.417	SUBCLONAL	1	TRUE	2	0.163566958178492	4		808	1257	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176493	123176493	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	25	181	0	ENST00000218089.9:c.460G>A	p.Glu154Lys	p.E154K	ENST00000218089	NM_001042749.1	154	Gag/Aag	7/35	0.154629059272613	2	FACETS	1	0.809	1			1	CLONAL	1	TRUE	NA	0.163566958178492	2		181	298	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242484	+	inframe_deletion	In_Frame_Del	DEL	AATTAAGAGAAGCAACAT	AATTAAGAGAAGCAACAT	-	rs121913422	NA	P-0033082-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	55	366	0	ENST00000275493.2:c.2237_2254del	p.Glu746_Ser752delinsAla	p.E746_S752delinsA	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATct/gct	19/28	1	2	FACETS	0.728	0.625	0.841	0.728	0.625	0.841	SUBCLONAL	1	TRUE	1	0.355368409909517	2		366	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519998	NA	P-0033082-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	126	671	0	ENST00000269305.4:c.581T>C	p.Leu194Pro	p.L194P	ENST00000269305	NM_001126112.2	194	cTt/cCt	6/11	0.355368409909517	1	FACETS	0.926	0.84	1	0.926	0.84	1	CLONAL	1	TRUE	0	0.355368409909517	1		671	630	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868972	117868972	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033082-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	40	386	0	ENST00000297338.2:c.727G>C	p.Asp243His	p.D243H	ENST00000297338	NM_006265.2	243	Gat/Cat	7/14	0.264454636844394	3	FACETS	0.389	0.322	0.464	0.195	0.161	0.232	SUBCLONAL	1	TRUE	1	0.355368409909517	3		386	681	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805762	43805762	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033082-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	67	720	0	ENST00000372470.3:c.818C>G	p.Ser273Cys	p.S273C	ENST00000372470	NM_005373.2	273	tCc/tGc	5/12	0.268136104770669	1	FACETS	0.427	0.37	0.489	0.427	0.37	0.489	SUBCLONAL	1	TRUE	0	0.355368409909517	1		720	726	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464953	120464953	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033082-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	111	592	0	ENST00000256646.2:c.5119G>T	p.Gly1707Cys	p.G1707C	ENST00000256646	NM_024408.3	1707	Ggc/Tgc	28/34	0.355368409909517	1	FACETS	0.973	0.878	1	0.973	0.878	1	CLONAL	1	TRUE	0	0.355368409909517	1		592	528	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915901	127915901	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033082-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	120	683	0	ENST00000373547.4:c.580C>A	p.Leu194Met	p.L194M	ENST00000373547	NM_002721.4	194	Ctg/Atg	6/7	0.355368409909517	1	FACETS	0.889	0.804	0.977	0.889	0.804	0.977	CLONAL	1	TRUE	0	0.355368409909517	1		683	625	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114917802	114917802	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033082-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	27	352	0	ENST00000543371.1:c.1292G>C	p.Arg431Thr	p.R431T	ENST00000543371	NM_001198531.1	431	aGg/aCg	12/14	0.225838272951872	0	FACETS	0.266	0.211	0.329			1	SUBCLONAL	1	TRUE	0	0.355368409909517	0		352	368	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060928	38060928	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033082-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	38	404	0	ENST00000250448.2:c.1061C>A	p.Ser354Tyr	p.S354Y	ENST00000250448	NM_004496.3	354	tCc/tAc	2/2	1	2	FACETS	0.47	0.388	0.561	0.47	0.388	0.561	SUBCLONAL	1	TRUE	1	0.355368409909517	2		404	455	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14015911	14015911	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033082-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	21	209	0	ENST00000311895.7:c.231G>C	p.Lys77Asn	p.K77N	ENST00000311895	NM_005236.2	77	aaG/aaC	2/11	1	2	FACETS	0.309	0.237	0.392	0.309	0.237	0.392	SUBCLONAL	1	TRUE	1	0.355368409909517	2		209	383	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134512	30134512	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033082-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	20	209	0	ENST00000263025.4:c.19C>T	p.Gln7Ter	p.Q7*	ENST00000263025	NM_002746.2	7	Cag/Tag	1/9	1	2	FACETS	0.492	0.377	0.625	0.492	0.377	0.625	SUBCLONAL	1	TRUE	1	0.355368409909517	2		209	229	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250933	10250934	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0033082-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	67	604	0	ENST00000340748.4:c.3546dup	p.Gly1183ArgfsTer128	p.G1183Rfs*128	ENST00000340748		1182	-/C	32/40	0.268136104770669	1	FACETS	0.424	0.368	0.485	0.424	0.368	0.485	SUBCLONAL	1	TRUE	0	0.355368409909517	1		604	731	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579386	7579386	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0033084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	636	659	0	ENST00000269305.4:c.301A>T	p.Lys101Ter	p.K101*	ENST00000269305	NM_001126112.2	101	Aaa/Taa	4/11	0.615612522496675	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.615612522496675	2		659	968	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131926976	131926976	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs193921012	NA	P-0033084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	144	258	0	ENST00000265335.6:c.1513A>G	p.Ile505Val	p.I505V	ENST00000265335		505	Ata/Gta	10/25	0.210486088816889	2	FACETS	1	0.983	1	0.62	0.573	0.669	INDETERMINATE	1	TRUE	0	0.615612522496675	2		258	377	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038879	12038879	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	179	308	0	ENST00000396373.4:c.1172A>G	p.Tyr391Cys	p.Y391C	ENST00000396373	NM_001987.4	391	tAt/tGt	7/8	0.20143226487879	2	FACETS	1	0.982	1	0.584	0.543	0.626	INDETERMINATE	1	TRUE	0	0.615612522496675	2		308	498	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40491411	40491411	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1195908534	NA	P-0033084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	377	582	0	ENST00000264657.5:c.389A>G	p.Asn130Ser	p.N130S	ENST00000264657	NM_139276.2	130	aAc/aGc	5/24	0.615612522496675	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.615612522496675	1		582	696	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170750	99170751	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0033084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	114	438	0	ENST00000074304.5:c.1381dup	p.Val461GlyfsTer20	p.V461Gfs*20	ENST00000074304	NM_001134224.1	460	acg/acGg	16/26	0.588972700980163	2	FACETS	0.59	0.532	0.651	0.295	0.266	0.326	SUBCLONAL	1	TRUE	0	0.615612522496675	2		438	628	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0033089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	167	328	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.247019924988892	4	FACETS	0.924	0.854	0.996	0.924	0.854	0.996	CLONAL	3	TRUE	1	0.270951950063437	4		328	565	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031891	10031891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	46	584	0	ENST00000330684.3:c.932C>T	p.Ser311Phe	p.S311F	ENST00000330684	NM_001134407.1	311	tCc/tTc	3/13	1	2	FACETS	0.486	0.408	0.572	0.486	0.408	0.572	SUBCLONAL	1	TRUE	1	0.270951950063437	2		584	699	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967203	134967203	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	61	418	0	ENST00000398015.3:c.2542G>A	p.Asp848Asn	p.D848N	ENST00000398015	NM_004441.4	848	Gac/Aac	14/16	1	2	FACETS	0.899	0.776	1	0.899	0.776	1	CLONAL	1	TRUE	1	0.270951950063437	2		418	501	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591137	67591137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	33	317	0	ENST00000274335.5:c.1730G>A	p.Arg577Lys	p.R577K	ENST00000274335		577	aGa/aAa	12/15	1	2	FACETS	0.6	0.489	0.725	0.6	0.489	0.725	SUBCLONAL	1	TRUE	1	0.270951950063437	2		317	406	SUCCESS
APC	324	MSKCC	GRCh37	5	112178711	112178712	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	75	495	0	ENST00000257430.4:c.7420_7421delinsTT	p.Pro2474Phe	p.P2474F	ENST00000257430	NM_000038.5	2474	CCc/TTc	16/16	1	2	FACETS	0.873	0.765	0.989	0.873	0.765	0.989	CLONAL	1	TRUE	1	0.270951950063437	2		495	634	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942754	68942754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569463208	NA	P-0033089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	79	424	0	ENST00000288368.4:c.566G>A	p.Arg189Gln	p.R189Q	ENST00000288368	NM_024870.2	189	cGg/cAg	6/40	0.270951950063437	4	FACETS	1	0.889	1	0.337	0.296	0.382	CLONAL	1	TRUE	1	0.270951950063437	4		424	732	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0033093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	544	357	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.393820989326422	13	FACETS	1	0.986	1	0.937	0.908	0.965	CLONAL	10	TRUE	2	0.393820989326422	13		357	849	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0033093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	114	756	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.302323181695932	2	FACETS	1	0.985	1	0.75	0.681	0.821	CLONAL	1	TRUE	0	0.393820989326422	2		756	386	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575209	48575209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767326	NA	P-0033093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	47	480	0	ENST00000342988.3:c.403C>T	p.Arg135Ter	p.R135*	ENST00000342988	NM_005359.5	135	Cga/Tga	3/12	0.393820989326422	3	FACETS	1	0.868	1	1	0.868	1	CLONAL	2	TRUE	1	0.393820989326422	3		480	142	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39595510	39595510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	18	370	0	ENST00000262039.4:c.1396C>T	p.Pro466Ser	p.P466S	ENST00000262039	NM_002647.2	466	Cca/Tca	12/25	0.393820989326422	3	FACETS	0.495	0.374	0.638	0.248	0.186	0.319	SUBCLONAL	1	TRUE	1	0.393820989326422	3		370	221	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942662	48942662	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0033093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	41	355	2	ENST00000267163.4:c.1050-1G>T		p.X350_splice	ENST00000267163	NM_000321.2	350			0.393820989326422	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	2	TRUE	0	0.393820989326422	2		357	100	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236684	236684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	44	362	0	ENST00000264932.6:c.1402G>A	p.Ala468Thr	p.A468T	ENST00000264932	NM_004168.2	468	Gcc/Acc	10/15	0.393820989326422	8	FACETS	1	0.868	1			1	CLONAL	1	TRUE	NA	0.393820989326422	8		362	469	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0033095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	72	239	1	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.438216564597606	3	FACETS	1	0.944	1	0.564	0.496	0.636	CLONAL	1	TRUE	1	0.477962378362439	3		240	331	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249002	55249003	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCGTGGA	rs397517109	NA	P-0033095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	119	421	0	ENST00000275493.2:c.2303_2311dup	p.Ser768_Asp770dup	p.S768_D770dup	ENST00000275493	NM_005228.3	768	gcc/gcCAGCGTGGAc	20/28	0.434829892131054	4	FACETS	1	0.985	1	0.736	0.668	0.807	CLONAL	1	TRUE	2	0.477962378362439	4		421	500	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066683	94066683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759223701	NA	P-0033095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	94	512	1	ENST00000369303.4:c.1076G>A	p.Gly359Glu	p.G359E	ENST00000369303	NM_004440.3	359	gGa/gAa	5/17	0.477962378362439	3	FACETS	0.78	0.695	0.87	0.39	0.347	0.435	SUBCLONAL	1	TRUE	1	0.477962378362439	3		513	625	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317088	11317088	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	216	496	0	ENST00000361445.4:c.406del	p.Ala136GlnfsTer14	p.A136Qfs*14	ENST00000361445	NM_004958.3	136	Gca/ca	4/58	0.434829892131054	4	FACETS	0.938	0.876	1	0.938	0.876	1	CLONAL	2	TRUE	2	0.477962378362439	4		496	712	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578170	7578198	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACCAGACCTCAGGCGGCTCATAGGGCACC	ACCAGACCTCAGGCGGCTCATAGGGCACC	-	novel	NA	P-0033095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	162	514	0	ENST00000269305.4:c.651_672+7del		p.X217_splice	ENST00000269305	NM_001126112.2	217		6/11	0.477962378362439	2	FACETS	0.772	0.715	0.83	0.772	0.715	0.83	SUBCLONAL	2	TRUE	0	0.477962378362439	2		514	439	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974697	21974743	+	frameshift_variant	Frame_Shift_Del	DEL	AACTATTCGGTGCGTTGGGCAGCGCCCCCGCCTCCAGCAGCGCCCGC	AACTATTCGGTGCGTTGGGCAGCGCCCCCGCCTCCAGCAGCGCCCGC	-	novel	NA	P-0033095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	90	303	0	ENST00000304494.5:c.84_130del	p.Ala30SerfsTer74	p.A30Sfs*74	ENST00000304494	NM_000077.4	28	gtGCGGGCGCTGCTGGAGGCGGGGGCGCTGCCCAACGCACCGAATAGTTac/gtac	1/3	0.438216564597606	3	FACETS	0.799	0.718	0.883	0.799	0.718	0.883	SUBCLONAL	2	TRUE	1	0.477962378362439	3		303	292	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	100	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.66898027324462	2		248	248	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0033097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	254	328	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.530148929523439	3	FACETS	0.881	0.832	0.93	0.881	0.832	0.93	CLONAL	2	TRUE	1	0.66898027324462	3		328	575	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310859	123310859	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759750319	NA	P-0033097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	87	569	0	ENST00000358487.5:c.569G>A	p.Arg190Gln	p.R190Q	ENST00000358487	NM_000141.4	190	cGg/cAg	5/18	0.66898027324462	1	FACETS	0.28	0.248	0.314	0.28	0.248	0.314	SUBCLONAL	1	TRUE	0	0.66898027324462	1		569	618	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758775	41758775	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374737642	NA	P-0033097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	243	679	0	ENST00000301178.4:c.1829G>A	p.Arg610Gln	p.R610Q	ENST00000301178	NM_021913.4	610	cGa/cAa	16/20	1	2	FACETS	0.86	0.805	0.916	0.86	0.805	0.916	CLONAL	1	TRUE	1	0.66898027324462	2		679	845	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443870	52443870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	213	472	0	ENST00000460680.1:c.25G>A	p.Glu9Lys	p.E9K	ENST00000460680	NM_004656.3	9	Gag/Aag	1/17	1	2	FACETS	0.977	0.912	1	0.977	0.912	1	CLONAL	1	TRUE	1	0.66898027324462	2		472	652	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248600	8248600	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	279	553	0	ENST00000335790.3:c.287C>T	p.Pro96Leu	p.P96L	ENST00000335790	NM_002315.2	96	cCa/cTa	3/4	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.66898027324462	2		553	831	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650682	18650682	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	75	325	0	ENST00000266497.5:c.2893G>A	p.Gly965Arg	p.G965R	ENST00000266497		965	Gga/Aga	20/31	1	2	FACETS	0.776	0.687	0.869	0.776	0.687	0.869	SUBCLONAL	1	TRUE	1	0.66898027324462	2		325	289	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445496	49445496	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779943229	NA	P-0033097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	265	614	2	ENST00000301067.7:c.1970C>T	p.Pro657Leu	p.P657L	ENST00000301067	NM_003482.3	657	cCt/cTt	10/54	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.66898027324462	2		616	770	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909745	50909745	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	317	612	1	ENST00000440232.2:c.1465G>C	p.Val489Leu	p.V489L	ENST00000440232	NM_002691.3	489	Gtg/Ctg	12/27	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.66898027324462	2		613	900	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730840	40730840	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	135	591	1	ENST00000373198.4:c.3695C>T	p.Pro1232Leu	p.P1232L	ENST00000373198	NM_133170.3	1232	cCt/cTt	27/32	1	2	FACETS	0.474	0.431	0.52	0.474	0.431	0.52	SUBCLONAL	1	TRUE	1	0.66898027324462	2		592	851	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604206	189604206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	113	553	1	ENST00000264731.3:c.1373C>T	p.Ser458Leu	p.S458L	ENST00000264731	NM_003722.4	458	tCa/tTa	11/14	0.386563281849592	1	FACETS	0.387	0.349	0.427	0.387	0.349	0.427	INDETERMINATE	1	TRUE	0	0.66898027324462	1		554	581	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201678	66201678	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	205	466	0	ENST00000273854.3:c.2824C>A	p.Leu942Met	p.L942M	ENST00000273854	NM_004439.5	942	Ctg/Atg	16/18	0.386563281849592	1	FACETS	0.697	0.651	0.744	0.697	0.651	0.744	INDETERMINATE	1	TRUE	0	0.66898027324462	1		466	585	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31464404	31464404	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	340	758	3	ENST00000344624.3:c.2513T>A	p.Val838Glu	p.V838E	ENST00000344624		838	gTa/gAa	17/33	1	2	FACETS	0.861	0.814	0.908	0.861	0.814	0.908	CLONAL	1	TRUE	1	0.66898027324462	2		761	1181	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696739	176696740	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	213	434	0	ENST00000439151.2:c.5440_5441delinsTT	p.Pro1814Phe	p.P1814F	ENST00000439151	NM_022455.4	1814	CCt/TTt	16/23	1	2	FACETS	0.992	0.927	1	0.992	0.927	1	CLONAL	1	TRUE	1	0.66898027324462	2		434	642	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170095	32170095	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1262	296	645	0	ENST00000375023.3:c.3513G>T	p.Gln1171His	p.Q1171H	ENST00000375023	NM_004557.3	1171	caG/caT	21/30	0.66898027324462	4	FACETS	0.948	0.89	1	0.316	0.296	0.336	CLONAL	1	TRUE	1	0.66898027324462	4		645	1558	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977642	2977642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	445	643	0	ENST00000396946.4:c.1042G>A	p.Glu348Lys	p.E348K	ENST00000396946	NM_032415.4	348	Gag/Aag	8/25	0.530148929523439	3	FACETS	0.844	0.808	0.88	0.844	0.808	0.88	CLONAL	2	TRUE	1	0.66898027324462	3		643	1052	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778087	135778087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	231	653	1	ENST00000298552.3:c.2296G>A	p.Glu766Lys	p.E766K	ENST00000298552	NM_001162426.1	766	Gag/Aag	18/23	1	2	FACETS	0.814	0.761	0.869	0.814	0.761	0.869	CLONAL	1	TRUE	1	0.66898027324462	2		654	848	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441430	52441430	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	143	541	0	ENST00000460680.1:c.422A>G	p.His141Arg	p.H141R	ENST00000460680	NM_004656.3	141	cAt/cGt	6/17	0.493440781172796	1	FACETS	0.857	0.786	0.929	0.857	0.786	0.929	CLONAL	1	FALSE	0	0.500621048360064	1		541	500	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279634	123279645	+	inframe_deletion	In_Frame_Del	DEL	GGCATTTGCCGG	GGCATTTGCCGG	-	novel	NA	P-0033098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	180	504	0	ENST00000358487.5:c.787_798del	p.Pro263_Ala266del	p.P263_A266del	ENST00000358487	NM_000141.4	263	CCGGCAAATGCC/-	7/18	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.500621048360064	2		504	615	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233984	133233984	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	145	595	0	ENST00000320574.5:c.3410T>A	p.Leu1137Gln	p.L1137Q	ENST00000320574	NM_006231.2	1137	cTg/cAg	28/49	0.323653923712177	3	FACETS	0.878	0.801	0.958	0.439	0.4	0.479	CLONAL	1	FALSE	1	0.500621048360064	3		595	825	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646120	215646120	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	238	557	0	ENST00000260947.4:c.478A>G	p.Lys160Glu	p.K160E	ENST00000260947	NM_000465.2	160	Aaa/Gaa	4/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.500621048360064	2		557	880	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613136	52613137	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0033098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	161	508	0	ENST00000394830.3:c.3391_3392del	p.Met1131ValfsTer24	p.M1131Vfs*24	ENST00000394830	NM_018313.4	1131	ATg/g	22/30	0.493440781172796	1	FACETS	0.842	0.776	0.909	0.842	0.776	0.909	CLONAL	1	FALSE	0	0.500621048360064	1		508	573	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	47	697	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.909	0.766	1	0.909	0.766	1	CLONAL	1	TRUE	1	0.16	2		697	646	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0033102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	57	750	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.16	2		752	677	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101268	27101268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	32	638	1	ENST00000324856.7:c.4555del	p.Gln1519ArgfsTer8	p.Q1519Rfs*8	ENST00000324856	NM_006015.4	1517	gCc/gc	18/20	1	2	FACETS	0.794	0.643	0.964	0.794	0.643	0.964	CLONAL	1	TRUE	1	0.16	2		639	504	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770576	40770576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	45	591	2	ENST00000373198.4:c.2806C>T	p.Arg936Ter	p.R936*	ENST00000373198	NM_133170.3	936	Cga/Tga	19/32	1	2	FACETS	0.882	0.74	1	0.882	0.74	1	CLONAL	1	TRUE	1	0.16	2		593	638	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	61	248	0				ENST00000310581	NM_198253.2	-/1132			0.313662630693236	3	FACETS	0.835	0.728	0.949	0.835	0.728	0.949	CLONAL	2	TRUE	1	0.323949917635717	3		248	262	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0033113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	200	742	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.323949917635717	2	FACETS	0.98	0.913	1	0.98	0.913	1	CLONAL	2	TRUE	0	0.323949917635717	2		743	630	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160227	22160227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	82	490	0	ENST00000215832.6:c.404G>A	p.Arg135Lys	p.R135K	ENST00000215832	NM_002745.4	135	aGa/aAa	3/9	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.323949917635717	2		490	474	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862791	9862791	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1555483677	NA	P-0033113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	56	665	0	ENST00000330684.3:c.2512G>T	p.Glu838Ter	p.E838*	ENST00000330684	NM_001134407.1	838	Gag/Tag	12/13	0.323949917635717	1	FACETS	0.557	0.477	0.644	0.557	0.477	0.644	SUBCLONAL	1	TRUE	0	0.323949917635717	1		665	520	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934342	39934342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	58	657	0	ENST00000378444.4:c.257G>A	p.Gly86Glu	p.G86E	ENST00000378444	NM_001123385.1	86	gGa/gAa	4/15	0.323949917635717	1	FACETS	0.511	0.439	0.59	0.511	0.439	0.59	SUBCLONAL	1	TRUE	0	0.323949917635717	1		657	587	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978935	25978935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	45	434	0	ENST00000435504.4:c.988G>A	p.Glu330Lys	p.E330K	ENST00000435504		330	Gaa/Aaa	10/13	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		434	571	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577157	7577157	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0033126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	205	422	0	ENST00000269305.4:c.783-2A>C		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	0.909	0.848	0.971	1	0.993	1	CLONAL	2	FALSE	1	0.377204811737301	2		422	598	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042193	42042193	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	85	482	1	ENST00000219905.7:c.6390del	p.Pro2131GlnfsTer48	p.P2131Qfs*48	ENST00000219905	NM_001164273.1	2130	Ttt/tt	17/24	1	2	FACETS	0.7	0.619	0.786	0.7	0.619	0.786	SUBCLONAL	1	FALSE	1	0.377204811737301	2		483	644	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0033127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	61	264	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.136568086043088	2	FACETS	0.947	0.821	1	0.947	0.821	1	CLONAL	2	TRUE	0	0.187860600276658	2		264	343	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs17849781	NA	P-0033127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	66	736	0	ENST00000269305.4:c.832C>G	p.Pro278Ala	p.P278A	ENST00000269305	NM_001126112.2	278	Cct/Gct	8/11	1	2	FACETS	0.795	0.688	0.911	0.795	0.688	0.911	CLONAL	1	TRUE	1	0.187860600276658	2		736	884	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246390	53246390	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	88	757	0	ENST00000375401.3:c.592C>T	p.Arg198Ter	p.R198*	ENST00000375401	NM_004187.3	198	Cga/Tga	5/26	1	2	FACETS	0.829	0.732	0.933	0.829	0.732	0.933	CLONAL	1	TRUE	1	0.187860600276658	2		757	1130	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439925	56439925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755478993	NA	P-0033127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	80	512	1	ENST00000407977.2:c.667C>T	p.Arg223Cys	p.R223C	ENST00000407977		223	Cgc/Tgc	6/10	1	2	FACETS	0.957	0.841	1	0.957	0.841	1	CLONAL	1	TRUE	1	0.187860600276658	2		513	890	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254641	46254641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	51	543	0	ENST00000334344.6:c.4831C>T	p.Gln1611Ter	p.Q1611*	ENST00000334344	NM_152641.2	1611	Cag/Tag	16/21	1	2	FACETS	0.848	0.72	0.99	0.848	0.72	0.99	CLONAL	1	TRUE	1	0.187860600276658	2		543	640	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622362	1622362	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770464889	NA	P-0033127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	47	653	2	ENST00000344749.5:c.602C>T	p.Pro201Leu	p.P201L	ENST00000344749	NM_001136139.2	201	cCg/cTg	9/19	1	2	FACETS	0.619	0.52	0.727	0.619	0.52	0.727	SUBCLONAL	1	TRUE	1	0.187860600276658	2		655	809	SUCCESS
APC	324	MSKCC	GRCh37	5	112175483	112175483	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	32	442	1	ENST00000257430.4:c.4192del	p.Ser1398ValfsTer17	p.S1398Vfs*17	ENST00000257430	NM_000038.5	1398	Agt/gt	16/16	1	2	FACETS	0.596	0.482	0.724	0.596	0.482	0.724	SUBCLONAL	1	TRUE	1	0.187860600276658	2		443	572	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	130	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.894	0.821	0.969	0.894	0.821	0.969	CLONAL	1	TRUE	1	0.81	2		248	359	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0033130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	161	454	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.984	0.913	1	0.984	0.913	1	CLONAL	1	TRUE	1	0.81	2		454	404	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0033130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	438	503	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.882	0.855	0.909	1	0.997	1	CLONAL	2	TRUE	1	0.81	2		503	613	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584560	48584560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	239	401	0	ENST00000342988.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000342988	NM_005359.5	245	Cag/Tag	6/12	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.81	2		401	583	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188865	32188865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138205668	NA	P-0033130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	254	485	1	ENST00000375023.3:c.689G>A	p.Arg230His	p.R230H	ENST00000375023	NM_004557.3	230	cGt/cAt	4/30	1	2	FACETS	0.867	0.816	0.92	0.867	0.816	0.92	CLONAL	1	TRUE	1	0.81	2		486	723	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143521	30143521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1459946897	NA	P-0033130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	137	218	0	ENST00000389048.3:c.5G>A	p.Gly2Glu	p.G2E	ENST00000389048	NM_004304.4	2	gGa/gAa	1/29	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.81	2		218	288	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244283	46244283	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	227	309	0	ENST00000334344.6:c.2377C>T	p.Gln793Ter	p.Q793*	ENST00000334344	NM_152641.2	793	Caa/Taa	15/21	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.81	2		309	553	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196243	106196243	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs777761555	NA	P-0033130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	179	237	0	ENST00000380013.4:c.4576C>T	p.Gln1526Ter	p.Q1526*	ENST00000380013	NM_001127208.2	1526	Cag/Tag	11/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.81	2		237	427	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557362	187557362	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1223493108	NA	P-0033130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	262	437	0	ENST00000441802.2:c.4000C>T	p.Gln1334Ter	p.Q1334*	ENST00000441802	NM_005245.3	1334	Caa/Taa	6/27	1	2	FACETS	0.9	0.848	0.953	0.9	0.848	0.953	CLONAL	1	TRUE	1	0.81	2		437	719	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929235	44929235	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	316	523	0	ENST00000377967.4:c.2335C>T	p.Gln779Ter	p.Q779*	ENST00000377967	NM_021140.2	779	Cag/Tag	17/29	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.81	2		523	753	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457254	25457254	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	266	427	0	ENST00000264709.3:c.2633C>T	p.Ser878Phe	p.S878F	ENST00000264709	NM_175629.2	878	tCc/tTc	23/23	1	2	FACETS	0.976	0.921	1	0.976	0.921	1	CLONAL	1	TRUE	1	0.81	2		427	673	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945647	206945647	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550164520	NA	P-0033130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	241	477	0	ENST00000423557.1:c.134G>A	p.Arg45Gln	p.R45Q	ENST00000423557	NM_000572.2	45	cGa/cAa	1/5	1	2	FACETS	0.911	0.856	0.967	0.911	0.856	0.967	CLONAL	1	TRUE	1	0.81	2		477	653	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265489	198265489	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1332070905	NA	P-0033130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	232	547	0	ENST00000335508.6:c.2668G>A	p.Glu890Lys	p.E890K	ENST00000335508	NM_012433.2	890	Gaa/Aaa	18/25	1	2	FACETS	0.884	0.829	0.94	0.884	0.829	0.94	CLONAL	1	TRUE	1	0.81	2		547	648	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242715	16242715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	267	514	0	ENST00000375759.3:c.1336G>A	p.Glu446Lys	p.E446K	ENST00000375759	NM_015001.2	446	Gaa/Aaa	6/15	1	2	FACETS	0.954	0.9	1	0.954	0.9	1	CLONAL	1	TRUE	1	0.81	2		514	691	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023153	27023153	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	24	31	0	ENST00000324856.7:c.259G>T	p.Gly87Ter	p.G87*	ENST00000324856	NM_006015.4	87	Gga/Tga	1/20	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.81	2		31	56	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28605630	28605630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	234	429	0	ENST00000253063.3:c.1234G>A	p.Glu412Lys	p.E412K	ENST00000253063	NM_031459.4	412	Gag/Aag	9/10	1	2	FACETS	0.935	0.878	0.993	0.935	0.878	0.993	CLONAL	1	TRUE	1	0.81	2		429	618	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115801	8115801	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	247	469	0	ENST00000346208.3:c.1147G>A	p.Glu383Lys	p.E383K	ENST00000346208		383	Gag/Aag	6/6	1	2	FACETS	0.88	0.827	0.934	0.88	0.827	0.934	CLONAL	1	TRUE	1	0.81	2		469	693	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859634	57859634	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	225	457	0	ENST00000228682.2:c.688G>A	p.Glu230Lys	p.E230K	ENST00000228682	NM_005269.2	230	Gaa/Aaa	7/12	1	2	FACETS	0.882	0.826	0.938	0.882	0.826	0.938	CLONAL	1	TRUE	1	0.81	2		457	630	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396767	396767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	264	498	0	ENST00000262320.3:c.259G>A	p.Glu87Lys	p.E87K	ENST00000262320	NM_003502.3	87	Gag/Aag	2/11	1	2	FACETS	0.859	0.809	0.91	0.859	0.809	0.91	CLONAL	1	TRUE	1	0.81	2		498	759	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098728	2098728	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs137854355	NA	P-0033130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	297	485	1	ENST00000219476.3:c.114del	p.Phe38LeufsTer8	p.F38Lfs*8	ENST00000219476	NM_000548.3	38	Ttt/tt	2/42	1	2	FACETS	0.956	0.905	1	0.956	0.905	1	CLONAL	1	TRUE	1	0.81	2		486	767	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640791	3640791	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	323	598	0	ENST00000294008.3:c.2848G>C	p.Glu950Gln	p.E950Q	ENST00000294008	NM_032444.2	950	Gag/Cag	12/15	1	2	FACETS	0.919	0.871	0.967	0.919	0.871	0.967	CLONAL	1	TRUE	1	0.81	2		598	868	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897339	78897339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	297	543	0	ENST00000306801.3:c.2674G>A	p.Val892Met	p.V892M	ENST00000306801	NM_020761.2	892	Gtg/Atg	23/34	1	2	FACETS	0.945	0.894	0.997	0.945	0.894	0.997	CLONAL	1	TRUE	1	0.81	2		543	776	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855817	45855817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	310	596	0	ENST00000391945.4:c.1993G>A	p.Gly665Ser	p.G665S	ENST00000391945	NM_000400.3	665	Ggt/Agt	21/23	1	2	FACETS	0.912	0.864	0.962	0.912	0.864	0.962	CLONAL	1	TRUE	1	0.81	2		596	839	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422504	225422504	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	54	471	0	ENST00000264414.4:c.136C>A	p.Arg46Ser	p.R46S	ENST00000264414	NM_003590.4	46	Cgt/Agt	2/16	1	2	FACETS	0.237	0.202	0.275	0.237	0.202	0.275	SUBCLONAL	1	TRUE	1	0.81	2		471	563	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663226	227663226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	285	474	0	ENST00000305123.5:c.229G>A	p.Asp77Asn	p.D77N	ENST00000305123	NM_005544.2	77	Gac/Aac	1/2	1	2	FACETS	0.972	0.919	1	0.972	0.919	1	CLONAL	1	TRUE	1	0.81	2		474	724	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866475	42866475	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866966575	NA	P-0033130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	395	693	1	ENST00000398585.3:c.157G>A	p.Glu53Lys	p.E53K	ENST00000398585	NM_001135099.1	53	Gaa/Aaa	3/14	1	2	FACETS	0.936	0.892	0.98	0.936	0.892	0.98	CLONAL	1	TRUE	1	0.81	2		694	1042	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440379	52440379	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	131	424	0	ENST00000460680.1:c.673G>C	p.Asp225His	p.D225H	ENST00000460680	NM_004656.3	225	Gac/Cac	9/17	1	2	FACETS	0.582	0.53	0.636	0.582	0.53	0.636	SUBCLONAL	1	TRUE	1	0.81	2		424	556	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751429	57751429	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	198	361	0	ENST00000274289.3:c.1562C>T	p.Ser521Leu	p.S521L	ENST00000274289	NM_006622.3	521	tCa/tTa	11/14	1	2	FACETS	0.886	0.826	0.946	0.886	0.826	0.946	CLONAL	1	TRUE	1	0.81	2		361	552	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672477	30672477	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	355	628	0	ENST00000376406.3:c.4483G>C	p.Glu1495Gln	p.E1495Q	ENST00000376406	NM_014641.2	1495	Gag/Cag	10/15	1	2	FACETS	0.962	0.915	1	0.962	0.915	1	CLONAL	1	TRUE	1	0.81	2		628	911	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652126	36652145	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGAGGCCGGGATGAGTTG	GGCGAGGCCGGGATGAGTTG	-	novel	NA	P-0033130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	296	523	0	ENST00000244741.5:c.250_269del	p.Gly85ArgfsTer37	p.G85Rfs*37	ENST00000244741	NM_000389.4	83	cGGCGAGGCCGGGATGAGTTG/c	2/3	1	2	FACETS	0.958	0.906	1	0.958	0.906	1	CLONAL	1	TRUE	1	0.81	2		523	763	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793907	89793907	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	112	239	0	ENST00000336032.3:c.976C>T	p.Gln326Ter	p.Q326*	ENST00000336032	NM_006813.2	326	Caa/Taa	2/2	1	2	FACETS	0.743	0.675	0.814	0.743	0.675	0.814	SUBCLONAL	1	TRUE	1	0.81	2		239	372	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494990	56494990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	218	423	0	ENST00000267101.3:c.3347G>A	p.Arg1116Lys	p.R1116K	ENST00000267101	NM_001982.3	1116	aGg/aAg	27/28	1	2	FACETS	0.837	0.783	0.892	0.837	0.783	0.892	CLONAL	1	TRUE	1	0.81	2		423	643	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30323856	30323856	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	128	357	0	ENST00000322652.5:c.1834G>T	p.Glu612Ter	p.E612*	ENST00000322652	NM_015355.2	612	Gaa/Taa	15/16	1	2	FACETS	0.876	0.797	0.96	0.876	0.797	0.96	CLONAL	1	TRUE	1	0.478946393973847	2		357	610	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467462	66467462	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	82	309	0	ENST00000273854.3:c.807T>A	p.Asp269Glu	p.D269E	ENST00000273854	NM_004439.5	269	gaT/gaA	3/18	0.172487891197525	0	FACETS	0.514	0.457	0.575			1	INDETERMINATE	1	TRUE	0	0.478946393973847	0		309	347	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664864	138664893	+	inframe_deletion	In_Frame_Del	DEL	GCGGCTGCAGCCGCAGCTGCTGCAGCCGCT	GCGGCTGCAGCCGCAGCTGCTGCAGCCGCT	-	rs387906321	NA	P-0033136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	67	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	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.478946393973847	2		92	207	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0033139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	150	479	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.722046914333463	3	FACETS	0.972	0.906	1	0.972	0.906	1	CLONAL	2	TRUE	1	0.722046914333463	3		479	291	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0033139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	110	226	1	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.690790662672011	2	FACETS	0.901	0.84	0.96	0.901	0.84	0.96	CLONAL	2	TRUE	0	0.722046914333463	2		227	169	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250870	153250870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	64	367	0	ENST00000281708.4:c.1190G>A	p.Gly397Asp	p.G397D	ENST00000281708	NM_033632.3	397	gGt/gAt	8/12	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.722046914333463	2		367	171	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589625	67589627	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	novel	NA	P-0033139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	93	216	0	ENST00000274335.5:c.1390_1392del	p.Asp464del	p.D464del	ENST00000274335		463	tATGat/tat	10/15	0.690790662672011	2	FACETS	0.913	0.847	0.977	0.913	0.847	0.977	CLONAL	2	TRUE	0	0.722046914333463	2		216	141	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420802	49420802	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0033139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	223	522	0	ENST00000301067.7:c.14947A>T	p.Lys4983Ter	p.K4983*	ENST00000301067	NM_003482.3	4983	Aaa/Taa	48/54	0.722046914333463	3	FACETS	1	0.962	1	0.522	0.487	0.558	CLONAL	1	TRUE	1	0.722046914333463	3		522	805	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412351	63412351	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	533	706	0	ENST00000330258.3:c.816del	p.Lys273SerfsTer9	p.K273Sfs*9	ENST00000330258	NM_152424.3	272	ccC/cc	2/2	0.722046914333463	3	FACETS	0.977	0.942	1	0.977	0.942	1	CLONAL	2	TRUE	1	0.722046914333463	3		706	1028	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791715	42791715	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1157030312	NA	P-0033140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	40	536	0	ENST00000575354.2:c.601C>T	p.Arg201Trp	p.R201W	ENST00000575354	NM_015125.3	201	Cgg/Tgg	5/20	0.893219434994792	1	FACETS	0.181	0.151	0.214	0.181	0.151	0.214	SUBCLONAL	1	TRUE	0	0.893219434994792	1		536	274	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0033140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	162	270	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.967	0.9	1	0.967	0.9	1	CLONAL	1	TRUE	1	0.893219434994792	2		270	375	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0033140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	116	331	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.931	1			1	INDETERMINATE	1	TRUE	NA	0.893219434994792	2		331	256	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791757	42791757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568504941	NA	P-0033140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	25	556	0	ENST00000575354.2:c.643C>T	p.Arg215Trp	p.R215W	ENST00000575354	NM_015125.3	215	Cgg/Tgg	5/20	0.893219434994792	1	FACETS	0.102	0.08	0.127	0.102	0.08	0.127	SUBCLONAL	1	TRUE	0	0.893219434994792	1		556	305	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791950	42791979	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCTCCTGCCAGGTGAAGGAGGCCCACTTC	CTCTCCTGCCAGGTGAAGGAGGCCCACTTC	TTGACA	novel	NA	P-0033140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	22	609	3	ENST00000575354.2:c.766-12_783delinsTTGACA		p.X256_splice	ENST00000575354	NM_015125.3	256		6/20	0.893219434994792	1	FACETS	0.082	0.063	0.104	0.082	0.063	0.104	SUBCLONAL	1	TRUE	0	0.893219434994792	1		612	333	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797987	42797990	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	AAGT	AAGT	-	novel	NA	P-0033140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	73	646	0	ENST00000575354.2:c.4039_4040+2del		p.X1347_splice	ENST00000575354	NM_015125.3	1347		16/20	0.893219434994792	1	FACETS	0.294	0.259	0.33	0.294	0.259	0.33	SUBCLONAL	1	TRUE	0	0.893219434994792	1		646	308	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0033141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	34	465	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	0.875	0.713	1	0.875	0.713	1	CLONAL	1	TRUE	1	0.13	2		465	598	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691039	NA	P-0033141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	57	628	1	ENST00000269305.4:c.919+1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			1	2	FACETS	0.983	0.841	1	0.983	0.841	1	CLONAL	1	TRUE	1	0.13	2		629	892	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803817	43803817	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs148434485	NA	P-0033141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	45	639	1	ENST00000372470.3:c.127C>T	p.Arg43Ter	p.R43*	ENST00000372470	NM_005373.2	43	Cga/Tga	2/12	1	2	FACETS	0.842	0.706	0.994	0.842	0.706	0.994	CLONAL	1	TRUE	1	0.13	2		640	822	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114116	115114116	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0033141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	36	431	0	ENST00000257566.3:c.1099+2T>G		p.X367_splice	ENST00000257566	NM_016569.3	367			1	2	FACETS	0.939	0.77	1	0.939	0.77	1	CLONAL	1	TRUE	1	0.13	2		431	590	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477161	67477161	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758586312	NA	P-0033141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	38	490	0	ENST00000327367.4:c.968G>A	p.Arg323His	p.R323H	ENST00000327367	NM_005902.3	323	cGc/cAc	7/9	1	2	FACETS	0.798	0.657	0.955	0.798	0.657	0.955	CLONAL	1	TRUE	1	0.13	2		490	733	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391121	89391121	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	42	451	0	ENST00000336596.2:c.1187T>C	p.Val396Ala	p.V396A	ENST00000336596	NM_005233.5	396	gTg/gCg	5/17	1	2	FACETS	0.826	0.688	0.981	0.826	0.688	0.981	CLONAL	1	TRUE	1	0.13	2		451	782	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674219	86674219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	28	256	0	ENST00000274376.6:c.2351C>T	p.Ala784Val	p.A784V	ENST00000274376	NM_002890.2	784	gCc/gTc	18/25	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.13	2		256	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0033156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	99	795	1	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	0.216242510635532	1	FACETS	0.966	0.862	1	0.966	0.862	1	CLONAL	1	FALSE	0	0.216242510635532	1		796	845	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248998	55248999	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCCAGTG	novel	NA	P-0033156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	111	552	0	ENST00000275493.2:c.2303_2304insTGTGGCCAG	p.Ala767_Val769dup	p.A767_V769dup	ENST00000275493	NM_005228.3	767	atg/aTGGCCAGTGtg	20/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.216242510635532	2		552	720	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0033173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	130	309	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.202446143479962	8	FACETS	1	0.946	1	0.745	0.682	0.809	CLONAL	5	FALSE	1	0.202446143479962	8		309	396	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711885	89711885	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	393	442	0	ENST00000371953.3:c.504del	p.Ser170ValfsTer13	p.S170Vfs*13	ENST00000371953	NM_000314.4	168	aTt/at	6/9	0.202446143479962	8	FACETS	1	0.976	1	1	0.996	1	CLONAL	10	FALSE	1	0.202446143479962	8		442	614	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022913	27022938	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGCCGCCGCCAGCAGCCTGGGCAA	CCCGCCGCCGCCAGCAGCCTGGGCAA	-	rs797045262	NA	P-0033173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	16	30	0	ENST00000324856.7:c.31_56del	p.Ser11AlafsTer91	p.S11Afs*91	ENST00000324856	NM_006015.4	7	CCCGCCGCCGCCAGCAGCCTGGGCAAc/c	1/20	0.178827946002893	3	FACETS	0.967	0.748	1	1	0.931	1	CLONAL	4	FALSE	1	0.202446143479962	3		30	45	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931589	NA	P-0033173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	142	257	0	ENST00000349496.5:c.101G>A	p.Gly34Glu	p.G34E	ENST00000349496	NM_001904.3	34	gGa/gAa	3/15	1	2	FACETS	1	0.926	1	1	0.994	1	CLONAL	4	FALSE	1	0.202446143479962	2		257	350	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210688	36210688	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	223	569	0	ENST00000222270.7:c.439C>T	p.Arg147Ter	p.R147*	ENST00000222270	NM_014727.1	147	Cga/Tga	3/37	1	2	FACETS	1	0.975	1	1	0.996	1	CLONAL	4	FALSE	1	0.202446143479962	2		569	515	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624305	89624305	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	279	611	0	ENST00000371953.3:c.79T>G	p.Tyr27Asp	p.Y27D	ENST00000371953	NM_000314.4	27	Tat/Gat	1/9	0.202446143479962	8	FACETS	0.992	0.934	1	0.709	0.667	0.751	CLONAL	5	FALSE	1	0.202446143479962	8		611	893	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563174	21563174	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	189	802	1	ENST00000382592.4:c.745C>A	p.Gln249Lys	p.Q249K	ENST00000382592	NM_014572.2	249	Cag/Aag	4/8	NA	2	FACETS	1	0.955	1			1	INDETERMINATE	4	FALSE	NA	0.202446143479962	2		803	454	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40469199	40469199	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0033173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	117	271	0	ENST00000264657.5:c.2144+1G>A		p.X715_splice	ENST00000264657	NM_139276.2	715			1	2	FACETS	1	0.958	1	1	0.993	1	CLONAL	4	FALSE	1	0.202446143479962	2		271	270	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475589	40475589	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0033173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	163	440	0	ENST00000264657.5:c.1653+2T>C		p.X551_splice	ENST00000264657	NM_139276.2	551			1	2	FACETS	1	0.939	1	1	0.994	1	CLONAL	4	FALSE	1	0.202446143479962	2		440	398	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3114961	3114961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	187	601	1	ENST00000078429.4:c.496C>T	p.Arg166Cys	p.R166C	ENST00000078429	NM_002067.2	166	Cgc/Tgc	4/7	1	2	FACETS	1	0.973	1	1	0.995	1	CLONAL	4	FALSE	1	0.202446143479962	2		602	429	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589575	67589576	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAAAAATTACATGAATATAACACT	novel	NA	P-0033173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	96	183	0	ENST00000274335.5:c.1339_1362dup	p.Lys447_Thr454dup	p.K447_T454dup	ENST00000274335		447	-/AAAAAATTACATGAATATAACACT	10/15	0.202446143479962	8	FACETS	0.962	0.867	1	0.687	0.619	0.758	CLONAL	5	FALSE	1	0.202446143479962	8		183	317	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151927359	151927360	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0033173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	26	56	0	ENST00000262189.6:c.2816_2817del	p.Ser939TyrfsTer10	p.S939Yfs*10	ENST00000262189	NM_170606.2	939	tCT/t	17/59	0.202446143479962	7	FACETS	0.979	0.8	1	0.816	0.667	0.975	CLONAL	5	FALSE	1	0.202446143479962	7		56	79	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252155	226252155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	16	114	0	ENST00000366813.1:c.103G>T	p.Gly35Trp	p.G35W	ENST00000366813		35	Ggg/Tgg	1/3	0.429374185155533	1	FACETS	0.244	0.181	0.316	0.244	0.181	0.316	SUBCLONAL	1	TRUE	0	0.7	1		114	122	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120399	70120420	+	frameshift_variant	Frame_Shift_Del	DEL	CTACATGAACCCCGCTCAGCGC	CTACATGAACCCCGCTCAGCGC	GG	novel	NA	P-0033177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	109	841	3	ENST00000245479.2:c.1401_1422delinsGG	p.Tyr468AlafsTer103	p.Y468Afs*103	ENST00000245479	NM_000346.3	467	acCTACATGAACCCCGCTCAGCGC/acGG	3/3	1	2	FACETS	0.265	0.237	0.295	0.265	0.237	0.295	SUBCLONAL	1	TRUE	1	0.7	2		844	1175	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216526	2216526	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	74	611	0	ENST00000398665.3:c.2170G>T	p.Gly724Cys	p.G724C	ENST00000398665	NM_032482.2	724	Ggt/Tgt	20/28	1	2	FACETS	0.343	0.3	0.389	0.343	0.3	0.389	SUBCLONAL	1	TRUE	1	0.7	2		611	616	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638658	176638658	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	86	471	0	ENST00000439151.2:c.3258T>G	p.Ser1086Arg	p.S1086R	ENST00000439151	NM_022455.4	1086	agT/agG	5/23	1	2	FACETS	0.336	0.297	0.378	0.336	0.297	0.378	SUBCLONAL	1	TRUE	1	0.7	2		471	732	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0033178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	167	233	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	1	FACETS	0.912	0.854	0.97	0.912	0.854	0.97	CLONAL	1	TRUE	0	0.725133404784424	1		233	322	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039347	47039347	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	196	369	0	ENST00000377604.3:c.970G>C	p.Ala324Pro	p.A324P	ENST00000377604	NM_001204468.1	324	Gcg/Ccg	10/24	1	1	FACETS	0.789	0.739	0.838	0.789	0.739	0.838	SUBCLONAL	1	TRUE	0	0.725133404784424	1		369	437	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244361	46244361	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	39	387	0	ENST00000334344.6:c.2455C>T	p.Gln819Ter	p.Q819*	ENST00000334344	NM_152641.2	819	Caa/Taa	15/21	1	2	FACETS	0.193	0.159	0.23	0.193	0.159	0.23	SUBCLONAL	1	TRUE	1	0.725133404784424	2		387	558	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114719	108114719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	65	435	0	ENST00000278616.4:c.536C>T	p.Ser179Leu	p.S179L	ENST00000278616	NM_000051.3	179	tCa/tTa	6/63	1	2	FACETS	0.318	0.275	0.364	0.318	0.275	0.364	SUBCLONAL	1	TRUE	1	0.725133404784424	2		435	564	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78425869	78425869	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	96	326	0	ENST00000370768.2:c.1576G>T	p.Ala526Ser	p.A526S	ENST00000370768	NM_003902.3	526	Gct/Tct	16/20	1	2	FACETS	0.588	0.527	0.653	0.588	0.527	0.653	SUBCLONAL	1	TRUE	1	0.725133404784424	2		326	450	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405889	70405889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	54	534	0	ENST00000373644.4:c.3403C>T	p.His1135Tyr	p.H1135Y	ENST00000373644	NM_030625.2	1135	Cat/Tat	4/12	1	2	FACETS	0.234	0.199	0.272	0.234	0.199	0.272	SUBCLONAL	1	TRUE	1	0.725133404784424	2		534	637	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219321	1219334	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	ACGTATATGGTGAT	ACGTATATGGTGAT	-	novel	NA	P-0033178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	125	450	0	ENST00000326873.7:c.375-2_386del		p.X125_splice	ENST00000326873	NM_000455.4	125		3/10	0.594522008143126	1	FACETS	0.512	0.467	0.559	0.512	0.467	0.559	SUBCLONAL	1	TRUE	0	0.725133404784424	1		450	429	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600527	10600527	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	150	468	0	ENST00000171111.5:c.1328A>G	p.Tyr443Cys	p.Y443C	ENST00000171111	NM_203500.1	443	tAt/tGt	4/6	0.526288529015075	1	FACETS	0.605	0.558	0.653	0.605	0.558	0.653	SUBCLONAL	1	TRUE	0	0.725133404784424	1		468	436	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170550	11170550	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs773055372	NA	P-0033178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	138	562	0	ENST00000358026.2:c.4853C>G	p.Ser1618Cys	p.S1618C	ENST00000358026	NM_001128849.1	1618	tCc/tGc	34/36	0.526288529015075	1	FACETS	0.494	0.452	0.537	0.494	0.452	0.537	SUBCLONAL	1	TRUE	0	0.725133404784424	1		562	491	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1268709	1268709	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	176	713	0	ENST00000310581.5:c.2508C>G	p.Ile836Met	p.I836M	ENST00000310581	NM_198253.2	836	atC/atG	9/16	1	2	FACETS	0.615	0.568	0.665	0.615	0.568	0.665	SUBCLONAL	1	TRUE	1	0.725133404784424	2		713	789	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0033180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	94	240	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.330605948264157	3	FACETS	0.895	0.805	0.989	0.895	0.805	0.989	CLONAL	2	TRUE	1	0.378397566286545	3		240	330	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075128	16075128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	46	292	0	ENST00000268712.3:c.424G>A	p.Asp142Asn	p.D142N	ENST00000268712	NM_006311.3	142	Gat/Aat	4/46	1	2	FACETS	0.911	0.772	1	0.911	0.772	1	CLONAL	1	TRUE	1	0.378397566286545	2		292	267	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029178	26029194	+	protein_altering_variant	In_Frame_Del	DEL	CATTCAGGCATGCAAGA	CATTCAGGCATGCAAGA	TT	novel	NA	P-0033180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	48	394	2	ENST00000435504.4:c.156_172delinsAA	p.Leu53_Ala58delinsThr	p.L53_A58delinsT	ENST00000435504		52	ccTCTTGCATGCCTGAATGca/ccAAca	4/13	1	2	FACETS	0.63	0.533	0.735	0.63	0.533	0.735	SUBCLONAL	1	TRUE	1	0.378397566286545	2		396	403	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020724	26020724	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1426138687	NA	P-0033180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	38	261	0	ENST00000357647.3:c.7C>T	p.Arg3Cys	p.R3C	ENST00000357647	NM_003529.2	3	Cgc/Tgc	1/1	1	2	FACETS	0.816	0.68	0.967	0.816	0.68	0.967	CLONAL	1	TRUE	1	0.378397566286545	2		261	246	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396462	139396462	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	126	695	0	ENST00000277541.6:c.5463G>C	p.Lys1821Asn	p.K1821N	ENST00000277541	NM_017617.3	1821	aaG/aaC	29/34	1	2	FACETS	0.965	0.875	1	0.965	0.875	1	CLONAL	1	TRUE	1	0.378397566286545	2		695	690	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0033181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	124	750	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.216874464539626	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.216874464539626	2		752	497	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430338	181430338	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	30	239	0	ENST00000325404.1:c.190C>A	p.Pro64Thr	p.P64T	ENST00000325404	NM_003106.3	64	Ccc/Acc	1/1	0.216874464539626	5	FACETS	1	0.936	1	0.476	0.385	0.578	CLONAL	1	TRUE	2	0.216874464539626	5		239	257	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870848	12870848	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	81	134	1	ENST00000228872.4:c.75del	p.Lys25AsnfsTer17	p.K25Nfs*17	ENST00000228872	NM_004064.3	25	aaG/aa	1/3	0.583947380340345	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	0	0.623701986026825	2		135	128	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741528	39741528	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	202	278	0	ENST00000361337.2:c.1415T>G	p.Val472Gly	p.V472G	ENST00000361337	NM_003286.2	472	gTc/gGc	14/21	0.623701986026825	3	FACETS	0.993	0.933	1	0.993	0.933	1	CLONAL	2	TRUE	1	0.623701986026825	3		278	428	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226568869	226568869	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	49	561	0	ENST00000366794.5:c.1200G>T	p.Lys400Asn	p.K400N	ENST00000366794	NM_001618.3	400	aaG/aaT	9/23	1	2	FACETS	0.42	0.354	0.492	0.42	0.354	0.492	SUBCLONAL	1	TRUE	1	0.31	2		561	753	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851287	63851287	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	144	581	0	ENST00000279873.7:c.2065C>G	p.Pro689Ala	p.P689A	ENST00000279873	NM_032199.2	689	Cca/Gca	10/10	0.224838015399025	1	FACETS	0.975	0.89	1	0.975	0.89	1	CLONAL	1	TRUE	0	0.31	1		581	805	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741493	17741493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	183	438	1	ENST00000250003.3:c.164C>A	p.Ala55Glu	p.A55E	ENST00000250003	NM_002478.4	55	gCg/gAg	1/3	0.162925725089048	1	FACETS	0.865	0.797	0.936	0.865	0.797	0.936	INDETERMINATE	1	TRUE	0	0.31	1		439	1153	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102033252	102033252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	108	518	2	ENST00000282441.5:c.638C>T	p.Thr213Ile	p.T213I	ENST00000282441	NM_001130145.2	213	aCa/aTa	3/9	0.162925725089048	1	FACETS	0.613	0.549	0.681	0.613	0.549	0.681	INDETERMINATE	1	TRUE	0	0.31	1		520	961	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446856	49446856	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0033186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	88	394	0	ENST00000301067.7:c.955-1G>T		p.X319_splice	ENST00000301067	NM_003482.3	319			0.301655355191632	3	FACETS	0.879	0.778	0.987	0.44	0.389	0.494	CLONAL	1	TRUE	1	0.31	3		394	746	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831472	89831472	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	65	426	0	ENST00000389301.3:c.2604T>G	p.Phe868Leu	p.F868L	ENST00000389301	NM_000135.2	868	ttT/ttG	28/43	1	2	FACETS	0.784	0.68	0.896	0.784	0.68	0.896	SUBCLONAL	1	TRUE	1	0.31	2		426	535	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560179	29560179	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs878853885	NA	P-0033186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	28	335	0	ENST00000356175.3:c.3656G>T	p.Gly1219Val	p.G1219V	ENST00000356175	NM_000267.3	1219	gGa/gTa	27/57	0.301655355191632	1	FACETS	0.664	0.533	0.811	0.664	0.533	0.811	SUBCLONAL	1	TRUE	0	0.31	1		335	230	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222179	2222179	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs766661005	NA	P-0033186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1237	223	751	0	ENST00000398665.3:c.3011A>G	p.His1004Arg	p.H1004R	ENST00000398665	NM_032482.2	1004	cAc/cGc	24/28	1	2	FACETS	0.985	0.915	1	0.985	0.915	1	CLONAL	1	TRUE	1	0.31	2		751	1460	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578352	212578352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	19	365	0	ENST00000342788.4:c.905G>A	p.Ser302Asn	p.S302N	ENST00000342788	NM_005235.2	302	aGt/aAt	8/28	0.162925725089048	1	FACETS	0.635	0.486	0.809	0.635	0.486	0.809	INDETERMINATE	1	TRUE	0	0.31	1		365	163	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932222	39932222	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	123	514	0	ENST00000378444.4:c.2377C>T	p.Gln793Ter	p.Q793*	ENST00000378444	NM_001123385.1	793	Caa/Taa	4/15	1	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.31	1		514	657	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309841	104309841	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	42	313	0	ENST00000369902.3:c.432G>C	p.Leu144Phe	p.L144F	ENST00000369902	NM_016169.3	144	ttG/ttC	3/12	1	2	FACETS	0.745	0.621	0.883	0.745	0.621	0.883	SUBCLONAL	1	TRUE	1	0.203854448689143	2		313	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0033193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	428	651	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.773173509144085	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.779779331903235	2		651	538	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531809	46531809	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	95	405	0	ENST00000262741.5:c.538A>C	p.Lys180Gln	p.K180Q	ENST00000262741	NM_003629.3	180	Aaa/Caa	5/10	0.779779331903235	6	FACETS	0.793	0.712	0.879	0.397	0.356	0.44	SUBCLONAL	2	TRUE	2	0.779779331903235	6		405	393	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193181204	193181204	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	44	285	0	ENST00000367435.3:c.1040C>G	p.Ala347Gly	p.A347G	ENST00000367435	NM_024529.4	347	gCa/gGa	12/17	0.779779331903235	3	FACETS	0.71	0.601	0.827	0.355	0.3	0.414	SUBCLONAL	1	TRUE	1	0.779779331903235	3		285	221	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444983	49444983	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	122	477	0	ENST00000301067.7:c.2483C>T	p.Pro828Leu	p.P828L	ENST00000301067	NM_003482.3	828	cCt/cTt	10/54	0.572496931836648	6	FACETS	1	0.956	1	0.365	0.33	0.402	CLONAL	1	TRUE	3	0.779779331903235	6		477	731	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245391	41245391	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	296	627	0	ENST00000357654.3:c.2157del	p.Glu720AsnfsTer16	p.E720Nfs*16	ENST00000357654	NM_007294.3	719	aaA/aa	10/23	0.773173509144085	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.779779331903235	2		627	349	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982076	70982076	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	127	456	0	ENST00000276594.2:c.20G>C	p.Ser7Thr	p.S7T	ENST00000276594	NM_024504.3	7	aGt/aCt	2/8	0.624014896384175	3	FACETS	1	0.964	1	0.552	0.504	0.601	CLONAL	1	TRUE	1	0.779779331903235	3		456	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0033194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	253	380	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.658556340379745	1	FACETS	0.985	0.933	1	0.985	0.933	1	CLONAL	1	TRUE	0	0.658556340379745	1		380	523	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211491	98211491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747181820	NA	P-0033194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	371	342	1	ENST00000331920.6:c.3664G>A	p.Asp1222Asn	p.D1222N	ENST00000331920	NM_000264.3	1222	Gac/Aac	22/24	0.658556340379745	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.658556340379745	3		343	694	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	108	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.800127622540467	2		248	237	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0033195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	160	270	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	0.800127622540467	2		270	391	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367350	50367350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369417059	NA	P-0033195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	133	346	1	ENST00000331340.3:c.157G>A	p.Val53Met	p.V53M	ENST00000331340	NM_006060.4	53	Gtg/Atg	3/8	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.800127622540467	2		347	321	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799051	42799051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	49	779	3	ENST00000575354.2:c.4535G>A	p.Arg1512His	p.R1512H	ENST00000575354	NM_015125.3	1512	cGt/cAt	20/20	0.800127622540467	1	FACETS	0.133	0.112	0.156	0.133	0.112	0.156	SUBCLONAL	1	TRUE	0	0.800127622540467	1		782	551	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428460	78428464	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTT	TCTTT	-	novel	NA	P-0033195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	246	426	0	ENST00000370768.2:c.1335_1339del	p.Glu445AspfsTer44	p.E445Dfs*44	ENST00000370768	NM_003902.3	445	gaAAAGAtt/gatt	14/20	0.800127622540467	1	FACETS	0.953	0.909	0.996	0.953	0.909	0.996	CLONAL	1	TRUE	0	0.800127622540467	1		426	387	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492560	50492560	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	206	637	0	ENST00000394963.4:c.1456T>C	p.Trp486Arg	p.W486R	ENST00000394963	NM_003076.4	486	Tgg/Cgg	12/13	1	2	FACETS	0.699	0.65	0.748	0.699	0.65	0.748	SUBCLONAL	1	TRUE	1	0.800127622540467	2		637	737	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791796	42791796	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	26	553	0	ENST00000575354.2:c.682C>T	p.Arg228Trp	p.R228W	ENST00000575354	NM_015125.3	228	Cgg/Tgg	5/20	0.800127622540467	1	FACETS	0.098	0.077	0.122	0.098	0.077	0.122	SUBCLONAL	1	TRUE	0	0.800127622540467	1		553	396	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794384	42794394	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GGGCTTTGGTC	GGGCTTTGGTC	-	novel	NA	P-0033195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	33	736	0	ENST00000575354.2:c.1466_1476del		p.X489_splice	ENST00000575354	NM_015125.3	489		10/20	0.800127622540467	1	FACETS	0.097	0.078	0.118	0.097	0.078	0.118	SUBCLONAL	1	TRUE	0	0.800127622540467	1		736	510	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799062	42799062	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	133	752	0	ENST00000575354.2:c.4546C>G	p.Gln1516Glu	p.Q1516E	ENST00000575354	NM_015125.3	1516	Cag/Gag	20/20	0.800127622540467	1	FACETS	0.369	0.337	0.403	0.369	0.337	0.403	SUBCLONAL	1	TRUE	0	0.800127622540467	1		752	540	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930105	68930105	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	71	367	0	ENST00000288368.4:c.166T>C	p.Cys56Arg	p.C56R	ENST00000288368	NM_024870.2	56	Tgt/Cgt	2/40	1	2	FACETS	0.302	0.263	0.343	0.302	0.263	0.343	SUBCLONAL	1	TRUE	1	0.800127622540467	2		367	588	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870204	44870204	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0033195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	32	288	0	ENST00000377967.4:c.385-2A>C		p.X129_splice	ENST00000377967	NM_021140.2	129			1	1	FACETS	0.126	0.102	0.153	0.126	0.102	0.153	SUBCLONAL	1	TRUE	0	0.800127622540467	1		288	381	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	20	697	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.436231785836609	3	FACETS	0.206	0.157	0.264	0.103	0.078	0.132	SUBCLONAL	1	TRUE	1	0.439868673753368	3		697	538	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0033196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	197	387	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.436231785836609	3	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	1	0.439868673753368	3		387	541	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0033196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	124	454	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.439868673753368	2		454	560	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0033196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	90	207	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.439868673753368	2		207	291	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0033196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	57	255	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.841	0.727	0.965	0.841	0.727	0.965	CLONAL	1	TRUE	1	0.439868673753368	2		255	308	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0033196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	37	215	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	0.475	0.392	0.567	0.475	0.392	0.567	SUBCLONAL	1	TRUE	1	0.439868673753368	2		215	354	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100385	8100385	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750735308	NA	P-0033196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	129	558	0	ENST00000346208.3:c.359C>T	p.Thr120Met	p.T120M	ENST00000346208		120	aCg/aTg	3/6	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.439868673753368	2		558	554	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123629	108123629	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148191382	NA	P-0033196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	67	300	1	ENST00000278616.4:c.1888G>A	p.Val630Met	p.V630M	ENST00000278616	NM_000051.3	630	Gtg/Atg	12/63	1	2	FACETS	0.849	0.742	0.963	0.849	0.742	0.963	CLONAL	1	TRUE	1	0.439868673753368	2		301	359	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602396	28602396	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	120	365	0	ENST00000241453.7:c.1972C>A	p.Leu658Ile	p.L658I	ENST00000241453	NM_004119.2	658	Ctc/Atc	16/24	1	2	FACETS	0.957	0.867	1	0.957	0.867	1	CLONAL	1	TRUE	1	0.439868673753368	2		365	570	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554543	63554543	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	25	415	0	ENST00000307078.5:c.196G>C	p.Glu66Gln	p.E66Q	ENST00000307078	NM_004655.3	66	Gag/Cag	2/11	1	2	FACETS	0.364	0.287	0.453	0.364	0.287	0.453	SUBCLONAL	1	TRUE	1	0.439868673753368	2		415	312	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251789	212251789	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	34	258	0	ENST00000342788.4:c.3270A>C	p.Glu1090Asp	p.E1090D	ENST00000342788	NM_005235.2	1090	gaA/gaC	27/28	1	2	FACETS	0.482	0.394	0.579	0.482	0.394	0.579	SUBCLONAL	1	TRUE	1	0.439868673753368	2		258	321	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523747	41523747	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	116	452	0	ENST00000263253.7:c.1163G>T	p.Cys388Phe	p.C388F	ENST00000263253	NM_001429.3	388	tGc/tTc	4/31	1	2	FACETS	0.77	0.695	0.849	0.77	0.695	0.849	SUBCLONAL	1	TRUE	1	0.439868673753368	2		452	685	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143033768	143033768	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775041987	NA	P-0033196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	105	391	0	ENST00000262992.4:c.2203G>A	p.Glu735Lys	p.E735K	ENST00000262992	NM_001101669.1	735	Gaa/Aaa	20/24	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.439868673753368	2		391	476	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181937	32181937	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	133	557	0	ENST00000375023.3:c.2117G>A	p.Cys706Tyr	p.C706Y	ENST00000375023	NM_004557.3	706	tGc/tAc	13/30	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.439868673753368	2		557	591	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340420	8340420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	54	394	0	ENST00000356435.5:c.5176G>A	p.Glu1726Lys	p.E1726K	ENST00000356435		1726	Gaa/Aaa	31/35	0.439868673753368	3	FACETS	0.439	0.374	0.51	0.219	0.187	0.255	SUBCLONAL	1	TRUE	1	0.439868673753368	3		394	683	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966769	44966769	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	287	510	0	ENST00000377967.4:c.3993T>G	p.Cys1331Trp	p.C1331W	ENST00000377967	NM_021140.2	1331	tgT/tgG	27/29	0.439868673753368	3	FACETS	0.974	0.92	1	0.974	0.92	1	CLONAL	2	TRUE	1	0.439868673753368	3		510	817	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24133953	24134002	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTCCGTATGTTCCGAGGTTCTCTGTACAAGAGATACCCCTCACTCTGG	ACCTCCGTATGTTCCGAGGTTCTCTGTACAAGAGATACCCCTCACTCTGG	-	novel	NA	P-0033198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	43	148	0	ENST00000263121.7:c.105_154del	p.Tyr35Ter	p.Y35*	ENST00000263121	NM_003073.3	35	tACCTCCGTATGTTCCGAGGTTCTCTGTACAAGAGATACCCCTCACTCTGG/t	2/9	1	2	FACETS	0.951	0.804	1	1	0.97	1	CLONAL	2	TRUE	1	0.2	2		148	226	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405847	70405847	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368453444	NA	P-0033205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	47	439	1	ENST00000373644.4:c.3361G>A	p.Gly1121Ser	p.G1121S	ENST00000373644	NM_030625.2	1121	Ggc/Agc	4/12	0.41206730242832	3	FACETS	0.75	0.634	0.876	0.375	0.317	0.438	SUBCLONAL	1	FALSE	1	0.41206730242832	3		440	367	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591612	38591612	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	68	373	0	ENST00000299084.4:c.71G>T	p.Arg24Leu	p.R24L	ENST00000299084	NM_152594.2	24	cGa/cTa	2/7	0.106863882137991	5	FACETS	1	0.967	1			1	INDETERMINATE	1	FALSE	NA	0.41206730242832	5		373	396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs879253911	NA	P-0033205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	127	543	0	ENST00000269305.4:c.538G>T	p.Glu180Ter	p.E180*	ENST00000269305	NM_001126112.2	180	Gag/Tag	5/11	0.41206730242832	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	FALSE	0	0.41206730242832	2		543	248	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221302	1221302	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	89	427	2	ENST00000326873.7:c.827del	p.Gly276AlafsTer11	p.G276Afs*11	ENST00000326873	NM_000455.4	275	ccG/cc	6/10	0.41206730242832	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	0	0.41206730242832	1		429	245	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295780	15295781	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0033205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	58	697	2	ENST00000263388.2:c.2346_2347delinsCT	p.Gly783Trp	p.G783W	ENST00000263388	NM_000435.2	782	caTGgg/caCTgg	15/33	0.41206730242832	1	FACETS	0.883	0.767	1	0.883	0.767	1	CLONAL	1	FALSE	0	0.41206730242832	1		699	253	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561320	9561320	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	57	429	0	ENST00000353224.5:c.462T>A	p.Asp154Glu	p.D154E	ENST00000353224	NM_177990.2	154	gaT/gaA	4/10	0.41206730242832	5	FACETS	1	0.903	1	0.354	0.305	0.408	CLONAL	1	FALSE	2	0.41206730242832	5		429	421	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380450	31380450	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	76	341	0	ENST00000328111.2:c.940G>T	p.Gly314Cys	p.G314C	ENST00000328111	NM_006892.3	314	Ggc/Tgc	9/23	0.41206730242832	5	FACETS	1	0.946	1	0.742	0.659	0.83	CLONAL	2	FALSE	2	0.41206730242832	5		341	268	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430642	181430642	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	60	327	0	ENST00000325404.1:c.494G>C	p.Gly165Ala	p.G165A	ENST00000325404	NM_003106.3	165	gGc/gCc	1/1	0.302193721987956	3	FACETS	1	0.952	1	0.406	0.353	0.464	CLONAL	1	FALSE	0	0.41206730242832	3		327	288	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541039	187541039	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	34	256	0	ENST00000441802.2:c.6701G>A	p.Gly2234Glu	p.G2234E	ENST00000441802	NM_005245.3	2234	gGa/gAa	10/27	0.41206730242832	7	FACETS	0.875	0.715	1	0.219	0.178	0.264	CLONAL	1	FALSE	3	0.41206730242832	7		256	383	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045717	26045717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	49	202	0	ENST00000540144.1:c.79C>T	p.Arg27Cys	p.R27C	ENST00000540144	NM_003531.2	27	Cgt/Tgt	1/1	0.41206730242832	5	FACETS	1	0.861	1	1	0.861	1	CLONAL	2	FALSE	3	0.41206730242832	5		202	192	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945120	151945120	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1332973759	NA	P-0033205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	67	483	0	ENST00000262189.6:c.2399A>T	p.Tyr800Phe	p.Y800F	ENST00000262189	NM_170606.2	800	tAc/tTc	14/59	0.41206730242832	5	FACETS	1	0.948	1			1	CLONAL	1	FALSE	NA	0.41206730242832	5		483	448	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226961	53226961	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	72	474	0	ENST00000375401.3:c.2614G>T	p.Asp872Tyr	p.D872Y	ENST00000375401	NM_004187.3	872	Gat/Tat	18/26	0.348722299304913	3	FACETS	1	0.962	1	0.622	0.547	0.701	CLONAL	1	FALSE	1	0.41206730242832	3		474	339	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342984	70342984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	72	460	0	ENST00000374080.3:c.1525G>A	p.Glu509Lys	p.E509K	ENST00000374080		509	Gaa/Aaa	11/45	0.41206730242832	5	FACETS	1	0.889	1			1	CLONAL	1	FALSE	NA	0.41206730242832	5		460	556	SUCCESS
BTK	695	MSKCC	GRCh37	X	100625035	100625035	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	63	430	0	ENST00000308731.7:c.342C>A	p.Phe114Leu	p.F114L	ENST00000308731	NM_000061.2	114	ttC/ttA	5/19	0.41206730242832	6	FACETS	0.89	0.769	1			1	CLONAL	1	FALSE	NA	0.41206730242832	6		430	627	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196968	123196968	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	54	364	0	ENST00000218089.9:c.1734C>A	p.Tyr578Ter	p.Y578*	ENST00000218089	NM_001042749.1	578	taC/taA	19/35	0.41206730242832	6	FACETS	0.861	0.736	0.999			1	CLONAL	1	FALSE	NA	0.41206730242832	6		364	555	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057799	27057799	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	103	787	0	ENST00000324856.7:c.1507C>T	p.Gln503Ter	p.Q503*	ENST00000324856	NM_006015.4	503	Cag/Tag	3/20	0.560201394220624	1	FACETS	0.378	0.338	0.42	0.378	0.338	0.42	SUBCLONAL	1	TRUE	0	0.560201394220624	1		787	701	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0033210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	260	627	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.566288390011749	2		627	848	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549364	187549364	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs111886222	NA	P-0033210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	211	557	0	ENST00000441802.2:c.4754C>T	p.Thr1585Met	p.T1585M	ENST00000441802	NM_005245.3	1585	aCg/aTg	9/27	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.566288390011749	2		557	721	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252878	36252878	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	150	382	0	ENST00000300305.3:c.484A>T	p.Arg162Trp	p.R162W	ENST00000300305		162	Agg/Tgg	4/8	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.566288390011749	2		382	504	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115722	8115727	+	inframe_deletion	In_Frame_Del	DEL	GAAGAA	GAAGAA	-	novel	NA	P-0033210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	105	275	0	ENST00000346208.3:c.1069_1074del	p.Lys357_Lys358del	p.K357_K358del	ENST00000346208		356	atGAAGAAg/atg	6/6	1	2	FACETS	0.932	0.841	1	0.932	0.841	1	CLONAL	1	TRUE	1	0.566288390011749	2		275	398	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645934	67645934	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	187	524	0	ENST00000264010.4:c.862C>G	p.His288Asp	p.H288D	ENST00000264010	NM_006565.3	288	Cac/Gac	4/12	0.566288390011749	1	FACETS	0.953	0.888	1	0.953	0.888	1	CLONAL	1	TRUE	0	0.566288390011749	1		524	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519998	NA	P-0033223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	301	557	0	ENST00000269305.4:c.581T>A	p.Leu194His	p.L194H	ENST00000269305	NM_001126112.2	194	cTt/cAt	6/11	0.351464596354343	3	FACETS	0.894	0.849	0.94	0.894	0.849	0.94	CLONAL	3	TRUE	0	0.403133296332788	3		557	669	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837949	156837949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150271893	NA	P-0033223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	105	719	0	ENST00000524377.1:c.482G>A	p.Arg161His	p.R161H	ENST00000524377	NM_002529.3	161	cGc/cAc	5/17	0.404697631250312	3	FACETS	0.577	0.515	0.642	0.288	0.257	0.321	SUBCLONAL	1	TRUE	1	0.403133296332788	3		719	1085	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435744	56435744	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	73	489	0	ENST00000407977.2:c.1393G>T	p.Asp465Tyr	p.D465Y	ENST00000407977		465	Gac/Tac	9/10	0.338387438950409	2	FACETS	0.726	0.636	0.822	0.363	0.318	0.411	SUBCLONAL	1	TRUE	0	0.403133296332788	2		489	499	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728704	190728704	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	56	325	0	ENST00000441310.2:c.2092C>A	p.Gln698Lys	p.Q698K	ENST00000441310	NM_000534.4	698	Cag/Aag	10/13	NA	2	FACETS	1	0.93	1			1	INDETERMINATE	1	TRUE	NA	0.403133296332788	2		325	248	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306996	65306997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	52	352	5	ENST00000342505.4:c.2580dup	p.Pro861ThrfsTer4	p.P861Tfs*4	ENST00000342505	NM_002227.2	860	-/A	19/25	0.501948552938481	4	FACETS	0.77	0.665	0.882	0.77	0.665	0.882	SUBCLONAL	2	TRUE	2	0.501948552938481	4		357	202	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349562	15349562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	48	847	0	ENST00000263377.2:c.4012C>T	p.Arg1338Trp	p.R1338W	ENST00000263377	NM_058243.2	1338	Cgg/Tgg	19/20	0.216255085644095	5	FACETS	0.78	0.66	0.911	0.26	0.22	0.304	INDETERMINATE	1	TRUE	2	0.501948552938481	5		847	430	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288341	21288341	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	102	647	0	ENST00000354336.3:c.586A>G	p.Asn196Asp	p.N196D	ENST00000354336	NM_005207.3	196	Aac/Gac	2/3	0.239089786686255	4	FACETS	1	0.975	1	0.807	0.735	0.881	INDETERMINATE	2	TRUE	1	0.501948552938481	4		647	252	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0033227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	66	440	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.45995140039416	1	FACETS	0.925	0.813	1	0.925	0.813	1	CLONAL	1	TRUE	0	0.45995140039416	1		440	239	SUCCESS
APC	324	MSKCC	GRCh37	5	112175651	112175651	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	44	253	0	ENST00000257430.4:c.4364del	p.Asn1455IlefsTer18	p.N1455Ifs*18	ENST00000257430	NM_000038.5	1454	Aaa/aa	16/16	0.390534837258361	1	FACETS	0.632	0.535	0.738	0.632	0.535	0.738	SUBCLONAL	1	TRUE	0	0.45995140039416	1		253	233	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604787	48604787	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	86	330	0	ENST00000342988.3:c.1609G>C	p.Asp537His	p.D537H	ENST00000342988	NM_005359.5	537	Gac/Cac	12/12	0.45995140039416	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.45995140039416	1		330	275	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577128	7577128	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	155	607	0	ENST00000269305.4:c.810T>A	p.Phe270Leu	p.F270L	ENST00000269305	NM_001126112.2	270	ttT/ttA	8/11	0.45995140039416	1	FACETS	0.933	0.859	1	0.933	0.859	1	CLONAL	1	TRUE	0	0.45995140039416	1		607	556	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31401640	31401640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561462275	NA	P-0033227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	39	473	0	ENST00000344624.3:c.4024C>T	p.Arg1342Trp	p.R1342W	ENST00000344624		1342	Cgg/Tgg	33/33	0.390534837258361	1	FACETS	0.331	0.275	0.394	0.331	0.275	0.394	SUBCLONAL	1	TRUE	0	0.45995140039416	1		473	394	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67197011	67197011	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	73	288	0	ENST00000312629.5:c.254G>T	p.Arg85Leu	p.R85L	ENST00000312629	NM_003952.2	85	cGa/cTa	4/15	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.45995140039416	2		288	291	SUCCESS
APC	324	MSKCC	GRCh37	5	112173894	112173894	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	23	296	0	ENST00000257430.4:c.2606del	p.Asn869IlefsTer47	p.N869Ifs*47	ENST00000257430	NM_000038.5	868	gAa/ga	16/16	0.390534837258361	1	FACETS	0.312	0.243	0.39	0.312	0.243	0.39	SUBCLONAL	1	TRUE	0	0.45995140039416	1		296	247	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	76	697	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.368437801953305	3	FACETS	0.981	0.873	1	0.981	0.873	1	CLONAL	2	TRUE	1	0.368437801953305	3		697	249	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0033239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	178	380	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.36696621213289	2	FACETS	0.972	0.904	1	0.972	0.904	1	CLONAL	2	TRUE	0	0.368437801953305	2		380	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0033240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	177	587	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.408059738221292	3	FACETS	1	0.983	1			1	CLONAL	2	TRUE	NA	0.408059738221292	3		587	444	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275842	38275842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367715495	NA	P-0033240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	37	319	0	ENST00000425967.3:c.1427G>A	p.Arg476Gln	p.R476Q	ENST00000425967	NM_001174067.1	476	cGg/cAg	11/19	0.331943607131406	3	FACETS	0.613	0.507	0.732	0.307	0.253	0.366	SUBCLONAL	1	TRUE	1	0.408059738221292	3		319	356	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612642	228612642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	40	346	2	ENST00000366696.1:c.385C>T	p.Arg129Cys	p.R129C	ENST00000366696	NM_003493.2	129	Cgc/Tgc	1/1	0.408059738221292	4	FACETS	0.554	0.46	0.659	0.185	0.153	0.22	SUBCLONAL	1	TRUE	1	0.408059738221292	4		348	498	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856571	111856571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	13	71	0	ENST00000341259.2:c.622G>A	p.Glu208Lys	p.E208K	ENST00000341259	NM_005475.2	208	Gag/Aag	2/8	0.229169329881281	3	FACETS	0.799	0.577	1	0.266	0.192	0.354	INDETERMINATE	1	TRUE	0	0.408059738221292	3		71	96	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033206	69033206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1344491711	NA	P-0033240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	37	259	0	ENST00000288368.4:c.3646C>T	p.Leu1216Phe	p.L1216F	ENST00000288368	NM_024870.2	1216	Ctt/Ttt	30/40	0.224716813499579	4	FACETS	0.667	0.55	0.797			1	INDETERMINATE	1	TRUE	NA	0.408059738221292	4		259	383	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931589	NA	P-0033245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	67	257	0	ENST00000349496.5:c.101G>A	p.Gly34Glu	p.G34E	ENST00000349496	NM_001904.3	34	gGa/gAa	3/15	1	2	FACETS	0.997	0.873	1	0.997	0.873	1	CLONAL	1	TRUE	1	0.401114686882691	2		257	335	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0033245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	154	393	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.401114686882691	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.401114686882691	2		393	375	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0033245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	100	556	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.401114686882691	2		556	419	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174440	11174440	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	264	512	0	ENST00000361445.4:c.7235A>T	p.Asp2412Val	p.D2412V	ENST00000361445	NM_004958.3	2412	gAc/gTc	53/58	0.399764003875394	2	FACETS	0.869	0.819	0.921	0.869	0.819	0.921	CLONAL	2	TRUE	0	0.401114686882691	2		512	757	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106849	27106850	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCCTCAGTGACCGAAAGAA	novel	NA	P-0033245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	133	428	0	ENST00000324856.7:c.6461_6479dup	p.Val2162GlnfsTer2	p.V2162Qfs*2	ENST00000324856	NM_006015.4	2154	ttc/tTCCTCAGTGACCGAAAGAAtc	20/20	0.401114686882691	2	FACETS	1	0.982	1	0.648	0.591	0.706	CLONAL	1	TRUE	0	0.401114686882691	2		428	512	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211002	36211003	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0033245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	155	700	0	ENST00000222270.7:c.758dup	p.Pro254ThrfsTer80	p.P254Tfs*80	ENST00000222270	NM_014727.1	251	-/C	3/37	1	2	FACETS	0.904	0.828	0.983	0.904	0.828	0.983	CLONAL	1	TRUE	1	0.401114686882691	2		700	855	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617469	158617469	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	77	355	0	ENST00000263640.3:c.1187T>G	p.Phe396Cys	p.F396C	ENST00000263640	NM_001105.4	396	tTc/tGc	9/11	1	2	FACETS	0.72	0.634	0.813	0.72	0.634	0.813	SUBCLONAL	1	TRUE	1	0.401114686882691	2		355	533	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591268	67591268	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	88	303	0	ENST00000274335.5:c.1767del	p.Arg590GlyfsTer5	p.R590Gfs*5	ENST00000274335		589	gTt/gt	13/15	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.401114686882691	2		303	393	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652416	206652416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	44	426	0	ENST00000367120.3:c.1123G>A	p.Ala375Thr	p.A375T	ENST00000367120	NM_014002.3	375	Gca/Aca	10/22	0.167325438373679	3	FACETS	1	0.933	1	0.614	0.515	0.724	CLONAL	1	FALSE	1	0.167257121730982	3		426	464	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098966	178098966	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	379	193	0	ENST00000397062.3:c.79G>T	p.Asp27Tyr	p.D27Y	ENST00000397062	NM_006164.4	27	Gat/Tat	2/5	0.929192072393552	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.929192072393552	2		193	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0033249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	1425	532	4	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.929192072393552	2	FACETS	1	0.999	1	1	0.999	1	CLONAL	2	TRUE	0	0.929192072393552	2		536	1444	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58701094	58701094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	60	374	0	ENST00000305921.3:c.685G>A	p.Glu229Lys	p.E229K	ENST00000305921	NM_003620.3	229	Gaa/Aaa	2/6	0.929192072393552	3	FACETS	0.248	0.213	0.286	0.124	0.106	0.143	SUBCLONAL	1	TRUE	1	0.929192072393552	3		374	763	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878114	48878115	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0033249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	33	47	0	ENST00000267163.4:c.68dup	p.Pro24AlafsTer7	p.P24Afs*7	ENST00000267163	NM_000321.2	22	-/C	1/27	0.929192072393552	1	FACETS	0.809	0.714	0.895	0.809	0.714	0.895	CLONAL	1	TRUE	0	0.929192072393552	1		47	47	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739669	41739669	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	814	501	0	ENST00000242208.4:c.304G>C	p.Glu102Gln	p.E102Q	ENST00000242208	NM_002192.2	102	Gag/Cag	2/3	0.929192072393552	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.929192072393552	2		501	840	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263973	104263974	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776579	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	52	193	1	ENST00000369902.3:c.71dup	p.Ala25GlyfsTer23	p.A25Gfs*23	ENST00000369902	NM_016169.3	22	gcc/gCcc	1/12	0.644333926299633	2	FACETS	0.811	0.7	0.929	0.406	0.35	0.465	CLONAL	1	TRUE	0	0.644333926299633	2		194	199	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	19	559	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	1	2	FACETS	0.155	0.117	0.2	0.155	0.117	0.2	SUBCLONAL	1	TRUE	1	0.644333926299633	2		559	380	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720833	89720836	+	frameshift_variant	Frame_Shift_Del	DEL	AAAT	AAAT	-	rs587782304	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	208	276	0	ENST00000371953.3:c.987_990del	p.Asn329LysfsTer14	p.N329Kfs*14	ENST00000371953	NM_000314.4	328	gcAAAT/gc	8/9	0.644333926299633	2	FACETS	0.955	0.906	1	0.955	0.906	1	CLONAL	2	TRUE	0	0.644333926299633	2		276	338	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	104	661	14	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.752	0.678	0.83	0.752	0.678	0.83	SUBCLONAL	1	TRUE	1	0.644333926299633	2		675	429	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749415085	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	16	250	0	ENST00000263967.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000263967	NM_006218.2	38	Cgt/Tgt	2/21	1	2	FACETS	0.15	0.111	0.198	0.15	0.111	0.198	SUBCLONAL	1	TRUE	1	0.644333926299633	2		250	330	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654642	67654642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	174	364	0	ENST00000264010.4:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000264010	NM_006565.3	377	Cgt/Tgt	6/12	1	2	FACETS	0.977	0.905	1	0.977	0.905	1	CLONAL	1	TRUE	1	0.644333926299633	2		364	553	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660469	67660469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	148	310	0	ENST00000264010.4:c.1369C>T	p.Arg457Ter	p.R457*	ENST00000264010	NM_006565.3	457	Cga/Tga	8/12	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.644333926299633	2		310	405	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528640	157528640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	65	516	4	ENST00000346085.5:c.6365G>A	p.Arg2122His	p.R2122H	ENST00000346085	NM_020732.3	2122	cGc/cAc	20/20	1	2	FACETS	0.351	0.305	0.402	0.351	0.305	0.402	SUBCLONAL	1	TRUE	1	0.644333926299633	2		520	574	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	125	294	4	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.644333926299633	2		298	343	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142885	30142885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766999851	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	143	465	0	ENST00000389048.3:c.641G>A	p.Arg214His	p.R214H	ENST00000389048	NM_004304.4	214	cGc/cAc	1/29	1	2	FACETS	0.923	0.847	1	0.923	0.847	1	CLONAL	1	TRUE	1	0.644333926299633	2		465	481	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434503	110434503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	133	419	1	ENST00000375856.3:c.3898G>A	p.Gly1300Ser	p.G1300S	ENST00000375856	NM_003749.2	1300	Ggc/Agc	1/2	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.644333926299633	2		420	412	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058093	27058093	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	109	244	0	ENST00000324856.7:c.1801C>T	p.Gln601Ter	p.Q601*	ENST00000324856	NM_006015.4	601	Cag/Tag	3/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.644333926299633	2		244	293	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661663	227661664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761880048	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	82	356	8	ENST00000305123.5:c.1791dup	p.His598AlafsTer13	p.H598Afs*13	ENST00000305123	NM_005544.2	597	-/G	1/2	1	2	FACETS	0.805	0.717	0.898	0.805	0.717	0.898	CLONAL	1	TRUE	1	0.644333926299633	2		364	316	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372109	55372109	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	16	345	1	ENST00000297316.4:c.799G>A	p.Ala267Thr	p.A267T	ENST00000297316	NM_022454.3	267	Gcc/Acc	2/2	1	2	FACETS	0.157	0.116	0.207	0.157	0.116	0.207	SUBCLONAL	1	TRUE	1	0.644333926299633	2		346	316	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518900	187518900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745695748	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	164	355	0	ENST00000441802.2:c.12304G>A	p.Gly4102Arg	p.G4102R	ENST00000441802	NM_005245.3	4102	Gga/Aga	24/27	1	2	FACETS	0.975	0.902	1	0.975	0.902	1	CLONAL	1	TRUE	1	0.644333926299633	2		355	522	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099468	157099470	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	rs1429292576	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	29	187	0	ENST00000346085.5:c.413_415del	p.Asn138del	p.N138del	ENST00000346085	NM_020732.3	135	tcCAAc/tcc	1/20	1	2	FACETS	0.592	0.481	0.715	0.592	0.481	0.715	SUBCLONAL	1	TRUE	1	0.644333926299633	2		187	152	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	260	714	7	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.957	1	1	0.996	1	CLONAL	2	TRUE	1	0.644333926299633	2		721	403	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224440	39224440	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs727505016	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	260	571	0	ENST00000402219.2:c.2918A>T	p.Gln973Leu	p.Q973L	ENST00000402219	NM_005633.3	973	cAg/cTg	18/23	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.644333926299633	2		571	728	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076785	72076785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576347795	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	147	364	0	ENST00000357731.5:c.712G>A	p.Gly238Arg	p.G238R	ENST00000357731	NM_173808.2	238	Gga/Aga	5/7	1	2	FACETS	0.914	0.841	0.991	0.914	0.841	0.991	CLONAL	1	TRUE	1	0.644333926299633	2		364	499	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	167	860	3	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.936	0.865	1	0.936	0.865	1	CLONAL	1	TRUE	1	0.644333926299633	2		863	554	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466000	69466000	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	166	518	0	ENST00000227507.2:c.838G>T	p.Glu280Ter	p.E280*	ENST00000227507	NM_053056.2	280	Gag/Tag	5/5	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.644333926299633	2		518	492	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520088	106520088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1484305297	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	78	219	0	ENST00000359195.3:c.2516G>A	p.Arg839His	p.R839H	ENST00000359195	NM_002649.2	839	cGc/cAc	6/11	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.644333926299633	2		219	230	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189847	11189847	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	115	343	0	ENST00000361445.4:c.5662T>C	p.Phe1888Leu	p.F1888L	ENST00000361445	NM_004958.3	1888	Ttc/Ctc	40/58	1	2	FACETS	0.707	0.64	0.777	0.707	0.64	0.777	SUBCLONAL	1	TRUE	1	0.644333926299633	2		343	505	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266128	198266128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	140	265	3	ENST00000335508.6:c.2492G>A	p.Arg831Gln	p.R831Q	ENST00000335508	NM_012433.2	831	cGa/cAa	17/25	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.644333926299633	2		268	401	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825518	50825519	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1219062549	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	119	579	0	ENST00000398568.2:c.2156dup	p.Asn719LysfsTer2	p.N719Kfs*2	ENST00000398568	NM_001042412.1	717	gaa/gAaa	14/18	1	2	FACETS	0.791	0.718	0.867	0.791	0.718	0.867	SUBCLONAL	1	TRUE	1	0.644333926299633	2		579	467	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056211	27056211	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs878853088	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	101	388	0	ENST00000324856.7:c.1207C>T	p.Gln403Ter	p.Q403*	ENST00000324856	NM_006015.4	403	Cag/Tag	2/20	1	2	FACETS	0.871	0.786	0.96	0.871	0.786	0.96	CLONAL	1	TRUE	1	0.644333926299633	2		388	360	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087420	27087420	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	192	551	0	ENST00000324856.7:c.1994G>T	p.Gly665Val	p.G665V	ENST00000324856	NM_006015.4	665	gGg/gTg	5/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.644333926299633	2		551	578	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464919	120464919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774915799	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	149	394	0	ENST00000256646.2:c.5153G>A	p.Arg1718His	p.R1718H	ENST00000256646	NM_024408.3	1718	cGc/cAc	28/34	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.644333926299633	2		394	449	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650070	206650070	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782265530	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	35	449	0	ENST00000367120.3:c.590C>T	p.Ala197Val	p.A197V	ENST00000367120	NM_014002.3	197	gCg/gTg	7/22	0.625012780464781	3	FACETS	0.218	0.178	0.264	0.109	0.089	0.132	SUBCLONAL	1	TRUE	1	0.644333926299633	3		449	658	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724459	724459	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	243	555	0	ENST00000314574.4:c.1597A>T	p.Thr533Ser	p.T533S	ENST00000314574	NM_005433.3	533	Aca/Tca	12/12	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.644333926299633	2		555	733	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223018	5223018	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	130	489	0	ENST00000357368.4:c.2785del	p.Arg929ValfsTer72	p.R929Vfs*72	ENST00000357368	NM_002850.3	929	Cgt/gt	18/38	1	2	FACETS	0.911	0.833	0.992	0.911	0.833	0.992	CLONAL	1	TRUE	1	0.644333926299633	2		489	443	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42788873	42788873	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	102	299	0	ENST00000575354.2:c.17G>T	p.Arg6Met	p.R6M	ENST00000575354	NM_015125.3	6	aGg/aTg	1/20	1	2	FACETS	0.858	0.774	0.945	0.858	0.774	0.945	CLONAL	1	TRUE	1	0.644333926299633	2		299	369	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531859	41531859	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1452596865	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	61	492	0	ENST00000263253.7:c.1571C>T	p.Thr524Met	p.T524M	ENST00000263253	NM_001429.3	524	aCg/aTg	7/31	1	2	FACETS	0.305	0.263	0.351	0.305	0.263	0.351	SUBCLONAL	1	TRUE	1	0.644333926299633	2		492	621	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928313	69928313	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	41	309	0	ENST00000352241.4:c.133A>G	p.Lys45Glu	p.K45E	ENST00000352241	NM_198159.2	45	Aag/Gag	2/10	1	2	FACETS	0.355	0.297	0.421	0.355	0.297	0.421	SUBCLONAL	1	TRUE	1	0.644333926299633	2		309	358	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670513	134670513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	157	490	2	ENST00000398015.3:c.424G>A	p.Ala142Thr	p.A142T	ENST00000398015	NM_004441.4	142	Gca/Aca	3/16	1	2	FACETS	0.883	0.813	0.955	0.883	0.813	0.955	CLONAL	1	TRUE	1	0.644333926299633	2		492	552	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880926	134880926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371083718	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	125	398	2	ENST00000398015.3:c.1489C>T	p.Arg497Trp	p.R497W	ENST00000398015	NM_004441.4	497	Cgg/Tgg	7/16	1	2	FACETS	0.965	0.882	1	0.965	0.882	1	CLONAL	1	TRUE	1	0.644333926299633	2		400	402	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549454	187549454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201060026	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	144	320	0	ENST00000441802.2:c.4664C>T	p.Thr1555Met	p.T1555M	ENST00000441802	NM_005245.3	1555	aCg/aTg	9/27	1	2	FACETS	0.907	0.833	0.983	0.907	0.833	0.983	CLONAL	1	TRUE	1	0.644333926299633	2		320	493	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589573	67589573	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	27	176	0	ENST00000274335.5:c.1336G>T	p.Gly446Trp	p.G446W	ENST00000274335		446	Ggg/Tgg	10/15	1	2	FACETS	0.31	0.247	0.382	0.31	0.247	0.382	SUBCLONAL	1	TRUE	1	0.644333926299633	2		176	270	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27205056	27205056	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	128	415	0	ENST00000380036.4:c.2360del	p.Asn787ThrfsTer2	p.N787Tfs*2	ENST00000380036	NM_000459.3	786	cAa/ca	14/23	1	2	FACETS	0.842	0.768	0.918	0.842	0.768	0.918	CLONAL	1	TRUE	1	0.644333926299633	2		415	472	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933955	39933955	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1333086341	NA	P-0033253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	169	502	0	ENST00000378444.4:c.644T>C	p.Leu215Pro	p.L215P	ENST00000378444	NM_001123385.1	215	cTg/cCg	4/15	0.644333926299633	1	FACETS	0.958	0.894	1	0.958	0.894	1	CLONAL	1	TRUE	0	0.644333926299633	1		502	371	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0033254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	99	454	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	0.34580507188926	2		454	495	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0033254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	45	503	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.824	0.695	0.964	0.824	0.695	0.964	CLONAL	1	TRUE	1	0.34580507188926	2		503	316	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934194	48934194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	29	358	0	ENST00000267163.4:c.649C>T	p.Gln217Ter	p.Q217*	ENST00000267163	NM_000321.2	217	Cag/Tag	7/27	1	2	FACETS	0.363	0.291	0.445	0.363	0.291	0.445	SUBCLONAL	1	TRUE	1	0.34580507188926	2		358	462	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405958	70405958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370887665	NA	P-0033254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	27	405	0	ENST00000373644.4:c.3472C>T	p.Arg1158Trp	p.R1158W	ENST00000373644	NM_030625.2	1158	Cgg/Tgg	4/12	1	2	FACETS	0.329	0.261	0.407	0.329	0.261	0.407	SUBCLONAL	1	TRUE	1	0.34580507188926	2		405	475	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173724	108173724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	53	309	0	ENST00000278616.4:c.5464G>A	p.Glu1822Lys	p.E1822K	ENST00000278616	NM_000051.3	1822	Gaa/Aaa	36/63	0.34580507188926	1	FACETS	0.932	0.801	1	0.932	0.801	1	CLONAL	1	TRUE	0	0.34580507188926	1		309	272	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349514	73349514	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0033254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	45	270	0	ENST00000377767.4:c.823-1G>C		p.X275_splice	ENST00000377767	NM_014953.3	275			1	2	FACETS	0.808	0.682	0.946	0.808	0.682	0.946	CLONAL	1	TRUE	1	0.34580507188926	2		270	322	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396572	30396572	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	22	192	0	ENST00000331968.5:c.147C>G	p.Ile49Met	p.I49M	ENST00000331968	NM_002742.2	49	atC/atG	1/18	1	2	FACETS	0.573	0.446	0.72	0.573	0.446	0.72	SUBCLONAL	1	TRUE	1	0.34580507188926	2		192	222	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138578	2138578	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs571792728	NA	P-0033254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	68	465	0	ENST00000219476.3:c.5391C>G	p.Ile1797Met	p.I1797M	ENST00000219476	NM_000548.3	1797	atC/atG	42/42	1	2	FACETS	0.853	0.744	0.97	0.853	0.744	0.97	CLONAL	1	TRUE	1	0.34580507188926	2		465	461	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990667	7990667	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	52	456	0	ENST00000319144.4:c.94G>C	p.Glu32Gln	p.E32Q	ENST00000319144	NM_001139.2	32	Gag/Cag	1/15	1	2	FACETS	0.466	0.396	0.542	0.466	0.396	0.542	SUBCLONAL	1	TRUE	1	0.34580507188926	2		456	646	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40498622	40498622	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	70	371	0	ENST00000264657.5:c.238C>T	p.Gln80Ter	p.Q80*	ENST00000264657	NM_139276.2	80	Cag/Tag	3/24	1	2	FACETS	0.854	0.747	0.97	0.854	0.747	0.97	CLONAL	1	TRUE	1	0.34580507188926	2		371	474	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244249	41244249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	96	583	0	ENST00000357654.3:c.3299G>A	p.Gly1100Glu	p.G1100E	ENST00000357654	NM_007294.3	1100	gGa/gAa	10/23	1	2	FACETS	0.901	0.804	1	0.901	0.804	1	CLONAL	1	TRUE	1	0.34580507188926	2		583	616	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244327	41244327	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	106	619	2	ENST00000357654.3:c.3221G>A	p.Arg1074Lys	p.R1074K	ENST00000357654	NM_007294.3	1074	aGa/aAa	10/23	1	2	FACETS	0.965	0.867	1	0.965	0.867	1	CLONAL	1	TRUE	1	0.34580507188926	2		621	635	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355303	15355303	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	33	277	0	ENST00000263377.2:c.2320del	p.Gln774SerfsTer20	p.Q774Sfs*20	ENST00000263377	NM_058243.2	774	Cag/ag	13/20	1	2	FACETS	0.86	0.705	1	0.86	0.705	1	CLONAL	1	TRUE	1	0.34580507188926	2		277	222	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726642	41726642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	80	463	0	ENST00000301178.4:c.187G>A	p.Glu63Lys	p.E63K	ENST00000301178	NM_021913.4	63	Gag/Aag	2/20	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.34580507188926	2		463	424	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754431	41754431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	63	404	0	ENST00000301178.4:c.1550G>A	p.Gly517Asp	p.G517D	ENST00000301178	NM_021913.4	517	gGc/gAc	13/20	1	2	FACETS	0.841	0.73	0.962	0.841	0.73	0.962	CLONAL	1	TRUE	1	0.34580507188926	2		404	433	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467080	25467080	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	32	407	0	ENST00000264709.3:c.1795G>C	p.Glu599Gln	p.E599Q	ENST00000264709	NM_175629.2	599	Gag/Cag	15/23	1	2	FACETS	0.429	0.348	0.521	0.429	0.348	0.521	SUBCLONAL	1	TRUE	1	0.34580507188926	2		407	431	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376218	225376218	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	80	472	0	ENST00000264414.4:c.736G>C	p.Glu246Gln	p.E246Q	ENST00000264414	NM_003590.4	246	Gaa/Caa	6/16	1	2	FACETS	0.995	0.879	1	0.995	0.879	1	CLONAL	1	TRUE	1	0.34580507188926	2		472	465	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545883	41545883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	102	471	0	ENST00000263253.7:c.2498C>T	p.Ser833Leu	p.S833L	ENST00000263253	NM_001429.3	833	tCg/tTg	14/31	1	2	FACETS	0.912	0.817	1	0.912	0.817	1	CLONAL	1	TRUE	1	0.34580507188926	2		471	647	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268805	41268805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	90	364	0	ENST00000349496.5:c.1043C>T	p.Ser348Phe	p.S348F	ENST00000349496	NM_001904.3	348	tCt/tTt	7/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.34580507188926	2		364	434	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186856	142186856	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	47	341	0	ENST00000350721.4:c.6607C>G	p.His2203Asp	p.H2203D	ENST00000350721	NM_001184.3	2203	Cat/Gat	39/47	1	2	FACETS	0.772	0.654	0.902	0.772	0.654	0.902	CLONAL	1	TRUE	1	0.34580507188926	2		341	352	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271277	153271277	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0033254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	31	165	0	ENST00000281708.4:c.502-1G>C		p.X168_splice	ENST00000281708	NM_033632.3	168			1	2	FACETS	0.883	0.72	1	0.883	0.72	1	CLONAL	1	TRUE	1	0.34580507188926	2		165	203	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323370	31323370	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0033254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	111	311	0	ENST00000412585.2:c.620-1G>C		p.X207_splice	ENST00000412585	NM_005514.6	207			0.338093509329588	2	FACETS	0.985	0.896	1	0.985	0.896	1	CLONAL	2	TRUE	0	0.34580507188926	2		311	326	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739743	145739743	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373178405	NA	P-0033254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	37	399	0	ENST00000428558.2:c.1708C>T	p.Arg570Trp	p.R570W	ENST00000428558	NM_004260.3	570	Cgg/Tgg	11/22	0.315363317413049	3	FACETS	0.635	0.524	0.759	0.318	0.262	0.38	SUBCLONAL	1	TRUE	1	0.34580507188926	3		399	395	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0033296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	298	747	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.299384239590899	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.29	2		747	909	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41197781	41197781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80356942	NA	P-0033296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	61	927	0	ENST00000357654.3:c.5506G>A	p.Glu1836Lys	p.E1836K	ENST00000357654	NM_007294.3	1836	Gag/Aag	23/23	0.299384239590899	2	FACETS	0.362	0.311	0.418	0.181	0.155	0.209	SUBCLONAL	1	TRUE	0	0.29	2		927	1162	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36421175	36421175	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	53	355	0	ENST00000300305.3:c.22G>C	p.Glu8Gln	p.E8Q	ENST00000300305		8	Gag/Cag	1/8	0.160884262784535	3	FACETS	0.758	0.646	0.881	0.253	0.215	0.294	INDETERMINATE	1	TRUE	0	0.29	3		355	552	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420127	49420127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756218008	NA	P-0033296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	75	743	0	ENST00000301067.7:c.15622G>A	p.Val5208Met	p.V5208M	ENST00000301067	NM_003482.3	5208	Gtg/Atg	48/54	1	2	FACETS	0.538	0.47	0.611	0.538	0.47	0.611	SUBCLONAL	1	TRUE	1	0.29	2		743	962	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355084	73355084	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	70	610	0	ENST00000377767.4:c.286C>T	p.Gln96Ter	p.Q96*	ENST00000377767	NM_014953.3	96	Caa/Taa	2/21	0.264962762844353	3	FACETS	0.542	0.471	0.62	0.181	0.157	0.207	SUBCLONAL	1	TRUE	0	0.29	3		610	1019	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435321	110435321	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	37	489	0	ENST00000375856.3:c.3080C>A	p.Ser1027Ter	p.S1027*	ENST00000375856	NM_003749.2	1027	tCg/tAg	1/2	0.264962762844353	3	FACETS	0.429	0.353	0.515	0.143	0.117	0.172	SUBCLONAL	1	TRUE	0	0.29	3		489	681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577044	7577045	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	488	1102	0	ENST00000269305.4:c.893dup	p.Leu299AlafsTer7	p.L299Afs*7	ENST00000269305	NM_001126112.2	298	gag/gaAg	8/11	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.29	2		1102	1508	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40874924	40874924	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	73	747	0	ENST00000428826.2:c.376G>A	p.Glu126Lys	p.E126K	ENST00000428826		126	Gag/Aag	6/21	0.299384239590899	2	FACETS	0.484	0.422	0.552	0.242	0.211	0.276	SUBCLONAL	1	TRUE	0	0.29	2		747	1040	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696408	47696408	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0033296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	277	673	0	ENST00000347630.2:c.415A>T	p.Arg139Ter	p.R139*	ENST00000347630	NM_001007230.1	139	Aga/Tga	6/11	0.299384239590899	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.29	2		673	907	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129372	152129372	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	143	718	0	ENST00000206249.3:c.325A>C	p.Met109Leu	p.M109L	ENST00000206249	NM_000125.3	109	Atg/Ctg	1/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.29	2		718	849	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099130	157099130	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	37	354	0	ENST00000346085.5:c.67G>C	p.Ala23Pro	p.A23P	ENST00000346085	NM_020732.3	23	Gcg/Ccg	1/20	1	2	FACETS	0.549	0.452	0.657	0.549	0.452	0.657	SUBCLONAL	1	TRUE	1	0.29	2		354	465	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864693	68864693	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	59	619	0	ENST00000288368.4:c.64C>T	p.Arg22Cys	p.R22C	ENST00000288368	NM_024870.2	22	Cgc/Tgc	1/40	0.105201512734034	3	FACETS	0.526	0.451	0.608	0.175	0.15	0.203	INDETERMINATE	1	TRUE	0	0.29	3		619	886	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0033315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	1415	517	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.567806647863836	28	FACETS	1	0.993	1	0.86	0.846	0.873	CLONAL	22	TRUE	2	0.567806647863836	28		517	1869	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748576	40748576	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	95	295	0	ENST00000373198.4:c.2940A>C	p.Gln980His	p.Q980H	ENST00000373198	NM_133170.3	980	caA/caC	21/32	0.293480212208785	4	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.567806647863836	4		295	439	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941068	36941068	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779487638	NA	P-0033315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	176	701	0	ENST00000361632.4:c.271C>T	p.His91Tyr	p.H91Y	ENST00000361632		91	Cac/Tac	3/16	0.567806647863836	3	FACETS	0.85	0.783	0.92	0.425	0.391	0.46	CLONAL	1	TRUE	1	0.567806647863836	3		701	936	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925123	81925123	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	290	437	0	ENST00000359376.3:c.914A>C	p.Lys305Thr	p.K305T	ENST00000359376	NM_002661.3	305	aAg/aCg	11/33	0.567806647863836	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.567806647863836	3		437	596	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578246	7578247	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	359	615	0	ENST00000269305.4:c.602dup	p.Leu201PhefsTer8	p.L201Ffs*8	ENST00000269305	NM_001126112.2	201	ttg/ttTg	6/11	0.567806647863836	2	FACETS	0.982	0.941	1	0.982	0.941	1	CLONAL	2	TRUE	0	0.567806647863836	2		615	644	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978973	25978973	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	190	351	0	ENST00000435504.4:c.950A>G	p.Asp317Gly	p.D317G	ENST00000435504		317	gAt/gGt	10/13	0.496378021544823	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	2	0.567806647863836	4		351	504	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971147	21971225	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCTGCCCATCATCATGACCTGCCAGAGAGAACAGAA	TGGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCTGCCCATCATCATGACCTGCCAGAGAGAACAGAA	-	novel	NA	P-0033315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	115	352	0	ENST00000304494.5:c.151-18_211del		p.X51_splice	ENST00000304494	NM_000077.4	51		2/3	0.567806647863836	2	FACETS	1	0.959	1	0.547	0.498	0.599	CLONAL	1	TRUE	0	0.567806647863836	2		352	370	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923045	44923048	+	frameshift_variant	Frame_Shift_Del	DEL	CTAT	CTAT	-	rs398122969	NA	P-0033316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	72	252	0	ENST00000377967.4:c.1909_1912del	p.Ser637ThrfsTer53	p.S637Tfs*53	ENST00000377967	NM_021140.2	636	CTATct/ct	16/29	1	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	0	0.37	1		252	307	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0033318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	340	816	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.359251361832893	2	FACETS	0.815	0.773	0.857	0.815	0.773	0.857	CLONAL	2	TRUE	0	0.451468087354101	2		817	924	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42790946	42790946	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	209	863	0	ENST00000575354.2:c.91T>A	p.Ser31Thr	p.S31T	ENST00000575354	NM_015125.3	31	Tct/Act	2/20	0.21439872669429	2	FACETS	1	0.934	1	0.503	0.467	0.54	INDETERMINATE	1	TRUE	0	0.451468087354101	2		863	921	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0033321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	47	442	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.410380974432064	3	FACETS	0.37	0.312	0.434	0.185	0.156	0.217	INDETERMINATE	1	TRUE	1	0.734550333828986	3		442	473	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0033321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	83	454	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.410380974432064	3	FACETS	0.563	0.498	0.632	0.281	0.249	0.316	INDETERMINATE	1	TRUE	1	0.734550333828986	3		454	549	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0033321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	23	371	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.410380974432064	3	FACETS	0.19	0.148	0.24	0.095	0.074	0.12	INDETERMINATE	1	TRUE	1	0.734550333828986	3		371	450	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0033321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	154	547	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.251989709322838	4	FACETS	1	0.979	1	0.599	0.55	0.65	INDETERMINATE	1	TRUE	2	0.734550333828986	4		547	607	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692902	89692902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909218	NA	P-0033321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	18	359	0	ENST00000371953.3:c.386G>A	p.Gly129Glu	p.G129E	ENST00000371953	NM_000314.4	129	gGa/gAa	5/9	0.410380974432064	3	FACETS	0.193	0.144	0.25	0.096	0.072	0.125	INDETERMINATE	1	TRUE	1	0.734550333828986	3		359	348	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509249	106509249	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	49	459	0	ENST00000359195.3:c.1243G>C	p.Glu415Gln	p.E415Q	ENST00000359195	NM_002649.2	415	Gag/Cag	2/11	0.251989709322838	4	FACETS	0.596	0.506	0.695	0.298	0.253	0.348	INDETERMINATE	1	TRUE	2	0.734550333828986	4		459	388	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405978	49405978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	92	442	0	ENST00000418115.1:c.160G>A	p.Glu54Lys	p.E54K	ENST00000418115	NM_001664.2	54	Gag/Aag	3/5	0.13191286606943	4	FACETS	0.768	0.691	0.847	0.768	0.691	0.847	INDETERMINATE	2	TRUE	2	0.734550333828986	4		442	283	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347299	89347299	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0033321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	45	499	0	ENST00000301030.4:c.5651C>G	p.Ser1884Ter	p.S1884*	ENST00000301030	NM_001256183.1	1884	tCa/tGa	9/13	0.734550333828986	1	FACETS	0.417	0.355	0.483	0.417	0.355	0.483	SUBCLONAL	1	TRUE	0	0.734550333828986	1		499	186	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858351	27858351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	35	541	0	ENST00000359303.2:c.220G>A	p.Glu74Lys	p.E74K	ENST00000359303	NM_003535.2	74	Gaa/Aaa	1/1	0.734550333828986	4	FACETS	0.256	0.209	0.309			1	SUBCLONAL	1	TRUE	NA	0.734550333828986	4		541	646	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306627	163306627	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	35	246	0	ENST00000271452.3:c.424C>G	p.Leu142Val	p.L142V	ENST00000271452	NM_145697.2	142	Ctt/Gtt	6/14	0.734550333828986	4	FACETS	0.323	0.264	0.389	0.108	0.088	0.13	SUBCLONAL	1	TRUE	1	0.734550333828986	4		246	512	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281040	49281040	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	22	561	0	ENST00000282018.3:c.87G>T	p.Arg29Ser	p.R29S	ENST00000282018	NM_020377.2	29	agG/agT	1/1	0.30589256729373	4	FACETS	0.293	0.226	0.37	0.146	0.113	0.185	INDETERMINATE	1	TRUE	2	0.734550333828986	4		561	355	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348277	89348277	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	99	958	0	ENST00000301030.4:c.4673C>G	p.Ser1558Cys	p.S1558C	ENST00000301030	NM_001256183.1	1558	tCc/tGc	9/13	0.734550333828986	1	FACETS	0.559	0.505	0.615	0.559	0.505	0.615	SUBCLONAL	1	TRUE	0	0.734550333828986	1		958	305	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213896	36213896	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0033321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	54	584	0	ENST00000222270.7:c.2723-1G>A		p.X908_splice	ENST00000222270	NM_014727.1	908			1	2	FACETS	0.49	0.421	0.564	0.49	0.421	0.564	SUBCLONAL	1	TRUE	1	0.734550333828986	2		584	300	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513233	149513233	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771094828	NA	P-0033321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	66	627	0	ENST00000261799.4:c.850G>A	p.Glu284Lys	p.E284K	ENST00000261799	NM_002609.3	284	Gaa/Aaa	6/23	1	2	FACETS	0.467	0.407	0.531	0.467	0.407	0.531	SUBCLONAL	1	TRUE	1	0.734550333828986	2		627	385	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858480	27858480	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	21	372	0	ENST00000359303.2:c.91C>G	p.Pro31Ala	p.P31A	ENST00000359303	NM_003535.2	31	Cca/Gca	1/1	0.734550333828986	4	FACETS	0.254	0.195	0.323			1	SUBCLONAL	1	TRUE	NA	0.734550333828986	4		372	390	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860875	151860875	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	31	354	0	ENST00000262189.6:c.9787G>A	p.Glu3263Lys	p.E3263K	ENST00000262189	NM_170606.2	3263	Gaa/Aaa	43/59	0.251989709322838	4	FACETS	0.353	0.285	0.43	0.176	0.142	0.215	INDETERMINATE	1	TRUE	2	0.734550333828986	4		354	415	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028871	47028871	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	31	520	0	ENST00000377604.3:c.175G>A	p.Asp59Asn	p.D59N	ENST00000377604	NM_001204468.1	59	Gac/Aac	3/24	0.45878898515296	1	FACETS	0.232	0.189	0.281	0.232	0.189	0.281	SUBCLONAL	1	TRUE	0	0.734550333828986	1		520	230	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222759	53222759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	109	887	1	ENST00000375401.3:c.4177G>A	p.Glu1393Lys	p.E1393K	ENST00000375401	NM_004187.3	1393	Gag/Aag	25/26	0.45878898515296	1	FACETS	0.492	0.445	0.54	0.492	0.445	0.54	SUBCLONAL	1	TRUE	0	0.734550333828986	1		888	382	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610405	10610405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	157	689	0	ENST00000171111.5:c.305C>T	p.Ser102Leu	p.S102L	ENST00000171111	NM_203500.1	102	tCa/tTa	2/6	0.370502899099135	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.370502899099135	1		689	626	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221260	1221260	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0033325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	259	646	0	ENST00000326873.7:c.783C>G	p.Tyr261Ter	p.Y261*	ENST00000326873	NM_000455.4	261	taC/taG	6/10	0.309403487873898	2	FACETS	0.902	0.848	0.957	0.902	0.848	0.957	CLONAL	2	TRUE	0	0.370502899099135	2		646	775	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742468	17742468	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	79	472	0	ENST00000250003.3:c.650C>A	p.Pro217Gln	p.P217Q	ENST00000250003	NM_002478.4	217	cCg/cAg	2/3	1	2	FACETS	0.835	0.736	0.94	0.835	0.736	0.94	CLONAL	1	TRUE	1	0.370502899099135	2		472	511	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244426	41244426	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397509035	NA	P-0033325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	117	637	0	ENST00000357654.3:c.3122C>T	p.Ser1041Leu	p.S1041L	ENST00000357654	NM_007294.3	1041	tCa/tTa	10/23	1	2	FACETS	0.883	0.797	0.974	0.883	0.797	0.974	CLONAL	1	TRUE	1	0.370502899099135	2		637	715	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71008510	71008510	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	78	321	0	ENST00000318789.4:c.1922A>T	p.Asp641Val	p.D641V	ENST00000318789	NM_032682.5	641	gAt/gTt	21/21	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.370502899099135	2		321	399	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439614	140439614	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1554389828	NA	P-0033325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	120	566	0	ENST00000288602.6:c.2125C>A	p.Gln709Lys	p.Q709K	ENST00000288602	NM_004333.4	709	Caa/Aaa	17/18	1	2	FACETS	0.895	0.809	0.985	0.895	0.809	0.985	CLONAL	1	TRUE	1	0.370502899099135	2		566	724	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517995	8517995	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	29	393	0	ENST00000356435.5:c.1396T>A	p.Trp466Arg	p.W466R	ENST00000356435		466	Tgg/Agg	10/35	1	2	FACETS	0.275	0.22	0.338	0.275	0.22	0.338	SUBCLONAL	1	TRUE	1	0.370502899099135	2		393	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0033328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	175	742	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.207839992368498	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.228184146369559	2		743	736	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027168	49027168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913305	NA	P-0033328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	123	416	0	ENST00000267163.4:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	579	Cga/Tga	18/27	0.204134771607281	2	FACETS	0.991	0.9	1	0.991	0.9	1	CLONAL	2	TRUE	0	0.228184146369559	2		416	544	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2193747	2193747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767206745	NA	P-0033328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	127	656	0	ENST00000398665.3:c.553G>A	p.Val185Ile	p.V185I	ENST00000398665	NM_032482.2	185	Gtc/Atc	6/28	0.207839992368498	2	FACETS	0.811	0.736	0.89	0.811	0.736	0.89	CLONAL	2	TRUE	0	0.228184146369559	2		656	686	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295338	1295338	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0033328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	59	345	0				ENST00000310581	NM_198253.2	-/1132			0.207839992368498	2	FACETS	0.823	0.713	0.942	0.823	0.713	0.942	CLONAL	2	TRUE	0	0.228184146369559	2		345	314	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920370	134920370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542190087	NA	P-0033328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	125	497	2	ENST00000398015.3:c.2185G>A	p.Ala729Thr	p.A729T	ENST00000398015	NM_004441.4	729	Gct/Act	12/16	0.207839992368498	2	FACETS	0.941	0.855	1	0.941	0.855	1	CLONAL	2	TRUE	0	0.228184146369559	2		499	582	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156050	99156050	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866440781	NA	P-0033328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	118	613	0	ENST00000074304.5:c.730C>T	p.Arg244Trp	p.R244W	ENST00000074304	NM_001134224.1	244	Cgg/Tgg	10/26	0.207839992368498	2	FACETS	0.762	0.688	0.839	0.762	0.688	0.839	SUBCLONAL	2	TRUE	0	0.228184146369559	2		613	679	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220637	2220637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750885564	NA	P-0033328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	170	662	0	ENST00000326181.6:c.254G>A	p.Arg85His	p.R85H	ENST00000326181	NM_032271.2	85	cGc/cAc	5/21	0.207839992368498	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.228184146369559	2		662	692	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10244971	10244971	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	95	485	0	ENST00000340748.4:c.4738G>A	p.Val1580Met	p.V1580M	ENST00000340748		1580	Gtg/Atg	39/40	0.207839992368498	2	FACETS	0.804	0.718	0.894	0.804	0.718	0.894	CLONAL	2	TRUE	0	0.228184146369559	2		485	518	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031609	36031609	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479989919	NA	P-0033328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	152	702	2	ENST00000358208.4:c.1438C>T	p.Arg480Trp	p.R480W	ENST00000358208		480	Cgg/Tgg	12/12	0.211392132220122	2	FACETS	0.925	0.848	1	0.925	0.848	1	CLONAL	2	TRUE	0	0.228184146369559	2		704	720	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927456	49927456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764873666	NA	P-0033328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	127	664	1	ENST00000296474.3:c.3848G>A	p.Arg1283Gln	p.R1283Q	ENST00000296474	NM_002447.2	1283	cGg/cAg	19/20	0.207839992368498	2	FACETS	0.82	0.744	0.899	0.82	0.744	0.899	CLONAL	2	TRUE	0	0.228184146369559	2		665	679	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631130	176631130	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1217840079	NA	P-0033328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	100	396	0	ENST00000439151.2:c.1073G>A	p.Arg358Gln	p.R358Q	ENST00000439151	NM_022455.4	358	cGg/cAg	4/23	0.207839992368498	2	FACETS	0.828	0.743	0.919	0.828	0.743	0.919	CLONAL	2	TRUE	0	0.228184146369559	2		396	529	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32819912	32819912	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779607865	NA	P-0033328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	171	668	1	ENST00000354258.4:c.998C>T	p.Thr333Met	p.T333M	ENST00000354258	NM_000593.5	333	aCg/aTg	3/11	0.207839992368498	2	FACETS	0.855	0.787	0.926	0.855	0.787	0.926	CLONAL	2	TRUE	0	0.228184146369559	2		669	876	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864653	56864653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759824481	NA	P-0033328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	119	534	0	ENST00000519728.1:c.616G>A	p.Asp206Asn	p.D206N	ENST00000519728	NM_002350.3	206	Gac/Aac	7/13	0.207839992368498	2	FACETS	0.907	0.821	0.997	0.907	0.821	0.997	CLONAL	2	TRUE	0	0.228184146369559	2		534	575	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0033329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	124	440	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	0.405438442069895	2		440	595	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0033329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	151	442	0	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	0.405438442069895	2		442	633	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0033329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	223	668	2	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.405438442069895	1	FACETS	0.984	0.918	1	0.984	0.918	1	CLONAL	1	TRUE	0	0.405438442069895	1		670	891	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726655	88726655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772754430	NA	P-0033329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	118	417	0	ENST00000360948.2:c.389G>A	p.Arg130His	p.R130H	ENST00000360948	NM_001012338.2	130	cGt/cAt	4/19	1	2	FACETS	0.901	0.815	0.992	0.901	0.815	0.992	CLONAL	1	TRUE	1	0.405438442069895	2		417	646	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591821	48591821	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	122	452	0	ENST00000342988.3:c.984C>A	p.Tyr328Ter	p.Y328*	ENST00000342988	NM_005359.5	328	taC/taA	9/12	0.405438442069895	1	FACETS	0.9	0.817	0.987	0.9	0.817	0.987	CLONAL	1	TRUE	0	0.405438442069895	1		452	533	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204511944	204511945	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	93	322	0	ENST00000367182.3:c.547dup	p.Thr183AsnfsTer3	p.T183Nfs*3	ENST00000367182	NM_001278516.1	182	gaa/gAaa	8/11	0.405438442069895	3	FACETS	0.914	0.814	1	0.457	0.407	0.51	CLONAL	1	TRUE	1	0.405438442069895	3		322	604	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0033343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	28	351	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	1	2	FACETS	0.655	0.521	0.808	0.655	0.521	0.808	SUBCLONAL	1	TRUE	1	0.13	2		351	658	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0033343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	24	278	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.835	0.654	1	0.835	0.654	1	CLONAL	1	TRUE	1	0.13	2		278	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876659675	NA	P-0033345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	750	542	0	ENST00000269305.4:c.764T>A	p.Ile255Asn	p.I255N	ENST00000269305	NM_001126112.2	255	aTc/aAc	7/11	0.785418803896883	4	FACETS	0.969	0.953	0.985	0.969	0.953	0.985	CLONAL	4	TRUE	0	0.800688525246327	4		542	870	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0033353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	149	742	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.22	2		743	1089	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	33	739	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	1	2	FACETS	0.359	0.291	0.437	0.359	0.291	0.437	SUBCLONAL	1	TRUE	1	0.22	2		739	835	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085680	16085680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776847158	NA	P-0033353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	95	652	1	ENST00000281043.3:c.856C>T	p.Arg286Cys	p.R286C	ENST00000281043	NM_005378.4	286	Cgt/Tgt	3/3	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.22	2		653	863	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0033354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	93	328	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.194816551278933	3	FACETS	0.906	0.812	1	0.906	0.812	1	CLONAL	3	TRUE	0	0.205569727198477	3		328	367	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683747	162683747	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	80	744	0	ENST00000366898.1:c.222G>T	p.Trp74Cys	p.W74C	ENST00000366898	NM_004562.2	74	tgG/tgT	3/12	0.112518362134867	4	FACETS	1	0.954	1	0.588	0.517	0.665	INDETERMINATE	1	TRUE	2	0.205569727198477	4		744	798	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505312	25505312	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs767055283	NA	P-0033354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	38	753	0	ENST00000264709.3:c.446C>T	p.Ala149Val	p.A149V	ENST00000264709	NM_175629.2	149	gCg/gTg	4/23	0.205569727198477	3	FACETS	0.544	0.448	0.652	0.272	0.224	0.326	SUBCLONAL	1	TRUE	1	0.205569727198477	3		753	749	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952117	178952117	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	118	301	0	ENST00000263967.3:c.3172A>C	p.Ile1058Leu	p.I1058L	ENST00000263967	NM_006218.2	1058	Atc/Ctc	21/21	1	2	FACETS	0.935	0.849	1	0.935	0.849	1	CLONAL	1	TRUE	1	0.516954002026274	2		301	488	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368229	45368229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	44	442	0	ENST00000262160.6:c.1373C>T	p.Ser458Phe	p.S458F	ENST00000262160	NM_005901.5	458	tCc/tTc	11/11	1	2	FACETS	0.225	0.188	0.267	0.225	0.188	0.267	SUBCLONAL	1	TRUE	1	0.516954002026274	2		442	756	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920506	50920506	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	192	673	0	ENST00000440232.2:c.3198C>G	p.His1066Gln	p.H1066Q	ENST00000440232	NM_002691.3	1066	caC/caG	26/27	1	2	FACETS	0.952	0.883	1	0.952	0.883	1	CLONAL	1	TRUE	1	0.516954002026274	2		673	780	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024384	31024384	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	217	766	0	ENST00000375687.4:c.3869C>G	p.Ala1290Gly	p.A1290G	ENST00000375687	NM_015338.5	1290	gCc/gGc	13/13	1	2	FACETS	0.846	0.787	0.908	0.846	0.787	0.908	CLONAL	1	TRUE	1	0.516954002026274	2		766	992	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73096508	73096508	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0033357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	106	232	0	ENST00000356692.5:c.287+1G>T		p.X96_splice	ENST00000356692		96			0.516954002026274	1	FACETS	0.831	0.752	0.913	0.831	0.752	0.913	CLONAL	1	TRUE	0	0.516954002026274	1		232	366	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	44	248	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.509	0.429	0.598			1	INDETERMINATE	1	TRUE	NA	0.528371592609026	2		248	327	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0033358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	8723	508	0	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.528371592609026	42	FACETS	1	0.999	1			1	CLONAL	40	TRUE	NA	0.528371592609026	42		508	9485	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968633	55968633	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200338299	NA	P-0033358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	127	681	0	ENST00000263923.4:c.2030C>T	p.Thr677Met	p.T677M	ENST00000263923	NM_002253.2	677	aCg/aTg	14/30	1	2	FACETS	0.736	0.668	0.807	0.736	0.668	0.807	SUBCLONAL	1	TRUE	1	0.528371592609026	2		681	653	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735609	204735609	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553657429	NA	P-0033358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	80	394	0	ENST00000302823.3:c.410C>T	p.Pro137Leu	p.P137L	ENST00000302823	NM_005214.4	137	cCg/cTg	2/4	1	2	FACETS	0.808	0.715	0.905	0.808	0.715	0.905	CLONAL	1	TRUE	1	0.528371592609026	2		394	375	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880501	155880501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	121	592	0	ENST00000368323.3:c.52C>T	p.Leu18Phe	p.L18F	ENST00000368323	NM_006912.5	18	Ctc/Ttc	2/6	1	2	FACETS	0.792	0.718	0.87	0.792	0.718	0.87	SUBCLONAL	1	TRUE	1	0.528371592609026	2		592	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0033359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	100	1003	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.263299536911694	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	FALSE	0	0.263299536911694	1		1003	630	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624242	89624243	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs121913290	NA	P-0033359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	18	245	0	ENST00000371953.3:c.17_18del	p.Lys6ArgfsTer4	p.K6Rfs*4	ENST00000371953	NM_000314.4	6	AAa/a	1/9	1	2	FACETS	0.79	0.598	1	0.79	0.598	1	CLONAL	1	FALSE	1	0.263299536911694	2		245	173	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772216	68772222	+	frameshift_variant	Frame_Shift_Del	DEL	GCCAGGA	GCCAGGA	-	novel	NA	P-0033359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	104	1157	0	ENST00000261769.5:c.68_74del	p.Gln23ArgfsTer31	p.Q23Rfs*31	ENST00000261769	NM_004360.3	22	tGCCAGGAg/tg	2/16	0.263299536911694	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	0	0.263299536911694	1		1157	513	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451405	187451405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	118	423	0	ENST00000232014.4:c.77G>A	p.Arg26Gln	p.R26Q	ENST00000232014	NM_001130845.1	26	cGg/cAg	3/10	1	2	FACETS	0.613	0.554	0.674	0.613	0.554	0.674	SUBCLONAL	1	TRUE	1	0.606717688661325	2		423	635	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101099	27101099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	185	869	1	ENST00000324856.7:c.4381C>T	p.Arg1461Ter	p.R1461*	ENST00000324856	NM_006015.4	1461	Cga/Tga	18/20	1	2	FACETS	0.577	0.532	0.624	0.577	0.532	0.624	SUBCLONAL	1	TRUE	1	0.606717688661325	2		870	1057	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155725	56155726	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0033361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	68	319	0	ENST00000399503.3:c.819_820del	p.Arg273SerfsTer27	p.R273Sfs*27	ENST00000399503	NM_005921.1	273	AGa/a	3/20	1	2	FACETS	0.5	0.436	0.569	0.5	0.436	0.569	SUBCLONAL	1	TRUE	1	0.606717688661325	2		319	448	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690847	89690847	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776667	NA	P-0033361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	218	367	0	ENST00000371953.3:c.253+1G>A		p.X85_splice	ENST00000371953	NM_000314.4	85			0.316019345489433	3	FACETS	0.858	0.805	0.912	0.572	0.536	0.608	INDETERMINATE	2	TRUE	0	0.606717688661325	3		367	546	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074242	8074246	+	frameshift_variant	Frame_Shift_Del	DEL	AAGGG	AAGGG	-	novel	NA	P-0033361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	95	398	0	ENST00000377482.5:c.413_417del	p.Ser138PhefsTer8	p.S138Ffs*8	ENST00000377482	NM_018948.3	138	tCCCTT/t	4/4	1	2	FACETS	0.541	0.482	0.603	0.541	0.482	0.603	SUBCLONAL	1	TRUE	1	0.606717688661325	2		398	579	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31381401	31381401	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs201681031	NA	P-0033361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	87	424	0	ENST00000328111.2:c.1126G>A	p.Glu376Lys	p.E376K	ENST00000328111	NM_006892.3	376	Gag/Aag	10/23	1	2	FACETS	0.484	0.429	0.543	0.484	0.429	0.543	SUBCLONAL	1	TRUE	1	0.606717688661325	2		424	592	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202555	67202555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201231114	NA	P-0033361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	121	1075	0	ENST00000312629.5:c.1364C>T	p.Pro455Leu	p.P455L	ENST00000312629	NM_003952.2	455	cCg/cTg	15/15	1	2	FACETS	0.369	0.332	0.407	0.369	0.332	0.407	SUBCLONAL	1	TRUE	1	0.606717688661325	2		1075	1082	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059165	42059165	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	77	401	0	ENST00000219905.7:c.8885C>T	p.Ser2962Phe	p.S2962F	ENST00000219905	NM_001164273.1	2962	tCc/tTc	24/24	1	2	FACETS	0.567	0.499	0.638	0.567	0.499	0.638	SUBCLONAL	1	TRUE	1	0.606717688661325	2		401	448	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808955	3808955	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	137	564	0	ENST00000262367.5:c.3269del	p.Leu1090TyrfsTer9	p.L1090Yfs*9	ENST00000262367	NM_004380.2	1090	tTa/ta	17/31	1	2	FACETS	0.543	0.494	0.595	0.543	0.494	0.595	SUBCLONAL	1	TRUE	1	0.606717688661325	2		564	831	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928078	178928113	+	inframe_deletion	In_Frame_Del	DEL	AGAAGATTTGCTGAACCCTATTGGTGTTACTGGATC	AGAAGATTTGCTGAACCCTATTGGTGTTACTGGATC	-	novel	NA	P-0033361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	70	638	0	ENST00000263967.3:c.1357_1392del	p.Glu453_Ser464del	p.E453_S464del	ENST00000263967	NM_006218.2	452	ttAGAAGATTTGCTGAACCCTATTGGTGTTACTGGATCa/tta	8/21	1	2	FACETS	0.297	0.258	0.339	0.297	0.258	0.339	SUBCLONAL	1	TRUE	1	0.606717688661325	2		638	777	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0033362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	80	331	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.181480084157064	2		331	595	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347546	89347546	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	57	774	0	ENST00000301030.4:c.5404G>A	p.Glu1802Lys	p.E1802K	ENST00000301030	NM_001256183.1	1802	Gaa/Aaa	9/13	0.181480084157064	3	FACETS	0.706	0.603	0.818	0.353	0.301	0.409	SUBCLONAL	1	TRUE	1	0.181480084157064	3		774	971	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579317	7579317	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs730881997	NA	P-0033362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	79	655	0	ENST00000269305.4:c.370T>G	p.Cys124Gly	p.C124G	ENST00000269305	NM_001126112.2	124	Tgc/Ggc	4/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.181480084157064	2		655	740	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348354	89348354	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1673	104	1416	0	ENST00000301030.4:c.4596G>T	p.Glu1532Asp	p.E1532D	ENST00000301030	NM_001256183.1	1532	gaG/gaT	9/13	0.181480084157064	3	FACETS	0.704	0.627	0.786	0.352	0.313	0.393	SUBCLONAL	1	TRUE	1	0.181480084157064	3		1416	1777	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347750	89347750	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	48	820	1	ENST00000301030.4:c.5200G>A	p.Asp1734Asn	p.D1734N	ENST00000301030	NM_001256183.1	1734	Gac/Aac	9/13	0.181480084157064	3	FACETS	0.609	0.513	0.716	0.305	0.256	0.358	SUBCLONAL	1	TRUE	1	0.181480084157064	3		821	947	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794506	242794506	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0033362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	71	923	0	ENST00000334409.5:c.437-1G>A		p.X146_splice	ENST00000334409	NM_005018.2	146			1	2	FACETS	0.71	0.618	0.811	0.71	0.618	0.811	SUBCLONAL	1	TRUE	1	0.181480084157064	2		923	1102	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575551	64575551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1085307471	NA	P-0033362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	105	557	0	ENST00000312049.6:c.466G>A	p.Gly156Ser	p.G156S	ENST00000312049	NM_130799.2	156	Ggt/Agt	3/10	1	2	FACETS	0.805	0.721	0.893	1	0.984	1	CLONAL	2	TRUE	1	0.181480084157064	2		557	719	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794935	242794935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1384	93	1274	0	ENST00000334409.5:c.274G>A	p.Asp92Asn	p.D92N	ENST00000334409	NM_005018.2	92	Gac/Aac	2/5	1	2	FACETS	0.694	0.614	0.779	0.694	0.614	0.779	SUBCLONAL	1	TRUE	1	0.181480084157064	2		1274	1477	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981528	201981529	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1253	369	1314	0	ENST00000359651.3:c.443dup	p.Met148IlefsTer13	p.M148Ifs*13	ENST00000359651		148	atg/aTtg	3/8	0.181480084157064	2	FACETS	0.836	0.791	0.882	1	0.992	1	CLONAL	3	TRUE	0	0.181480084157064	2		1314	1622	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437499	110437499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1418	105	1059	1	ENST00000375856.3:c.902G>A	p.Arg301Gln	p.R301Q	ENST00000375856	NM_003749.2	301	cGg/cAg	1/2	0.181480084157064	3	FACETS	0.829	0.739	0.924	0.414	0.369	0.462	CLONAL	1	TRUE	1	0.181480084157064	3		1060	1523	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786045	3786048	+	frameshift_variant	Frame_Shift_Del	DEL	TTTC	TTTC	AA	novel	NA	P-0033362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	95	981	2	ENST00000262367.5:c.4717_4720delinsTT	p.Glu1573PhefsTer3	p.E1573Ffs*3	ENST00000262367	NM_004380.2	1573	GAAAcc/TTcc	28/31	1	2	FACETS	0.811	0.72	0.909	0.811	0.72	0.909	CLONAL	1	TRUE	1	0.181480084157064	2		983	1291	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346796	89346796	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	32	422	0	ENST00000301030.4:c.6154G>C	p.Glu2052Gln	p.E2052Q	ENST00000301030	NM_001256183.1	2052	Gag/Cag	9/13	0.181480084157064	3	FACETS	0.698	0.565	0.849	0.349	0.282	0.425	SUBCLONAL	1	TRUE	1	0.181480084157064	3		422	551	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347533	89347533	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	59	753	0	ENST00000301030.4:c.5417G>C	p.Gly1806Ala	p.G1806A	ENST00000301030	NM_001256183.1	1806	gGa/gCa	9/13	0.181480084157064	3	FACETS	0.737	0.632	0.852	0.369	0.316	0.426	SUBCLONAL	1	TRUE	1	0.181480084157064	3		753	962	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347859	89347859	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	57	873	1	ENST00000301030.4:c.5091G>T	p.Gln1697His	p.Q1697H	ENST00000301030	NM_001256183.1	1697	caG/caT	9/13	0.181480084157064	3	FACETS	0.685	0.586	0.794	0.343	0.293	0.397	SUBCLONAL	1	TRUE	1	0.181480084157064	3		874	1000	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349586	89349586	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1547	91	1190	0	ENST00000301030.4:c.3364G>A	p.Glu1122Lys	p.E1122K	ENST00000301030	NM_001256183.1	1122	Gag/Aag	9/13	0.181480084157064	3	FACETS	0.668	0.59	0.751	0.334	0.295	0.376	SUBCLONAL	1	TRUE	1	0.181480084157064	3		1190	1638	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349589	89349589	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1536	92	1187	0	ENST00000301030.4:c.3361G>A	p.Asp1121Asn	p.D1121N	ENST00000301030	NM_001256183.1	1121	Gat/Aat	9/13	0.181480084157064	3	FACETS	0.679	0.601	0.764	0.34	0.3	0.382	SUBCLONAL	1	TRUE	1	0.181480084157064	3		1187	1628	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349649	89349649	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1568	108	1152	0	ENST00000301030.4:c.3301G>C	p.Glu1101Gln	p.E1101Q	ENST00000301030	NM_001256183.1	1101	Gaa/Caa	9/13	0.181480084157064	3	FACETS	0.775	0.692	0.863	0.387	0.346	0.432	SUBCLONAL	1	TRUE	1	0.181480084157064	3		1152	1676	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350229	89350229	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371498492	NA	P-0033362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1722	113	1384	0	ENST00000301030.4:c.2721G>C	p.Lys907Asn	p.K907N	ENST00000301030	NM_001256183.1	907	aaG/aaC	9/13	0.181480084157064	3	FACETS	0.74	0.663	0.823	0.37	0.331	0.412	SUBCLONAL	1	TRUE	1	0.181480084157064	3		1384	1835	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0033363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	26	328	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.129474310652261	3	FACETS	1	0.926	1	0.717	0.569	0.886	CLONAL	1	TRUE	1	0.13	3		328	297	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	27	514	0	ENST00000304494.5:c.143C>T	p.Pro48Leu	p.P48L	ENST00000304494	NM_000077.4	48	cCg/cTg	1/3	0.0886247897163476	0	FACETS	0.688	0.546	0.851			1	SUBCLONAL	1	TRUE	0	0.13	0		514	525	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686965	37686965	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	48	588	0	ENST00000447079.4:c.3869C>T	p.Pro1290Leu	p.P1290L	ENST00000447079	NM_015083.1	1290	cCc/cTc	14/14	0.0886247897163476	0	FACETS	0.932	0.787	1			1	CLONAL	1	TRUE	0	0.13	0		588	689	SUCCESS
ATR	545	MSKCC	GRCh37	3	142257364	142257364	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	200	539	0	ENST00000350721.4:c.3685G>T	p.Glu1229Ter	p.E1229*	ENST00000350721	NM_001184.3	1229	Gaa/Taa	19/47	1	2	FACETS	0.984	0.917	1	0.984	0.917	1	CLONAL	1	TRUE	1	0.626142702004423	2		539	649	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0033365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	119	503	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.519457581759646	1	FACETS	0.664	0.605	0.726	0.664	0.605	0.726	SUBCLONAL	1	TRUE	0	0.626142702004423	1		503	393	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0033365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	248	797	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	0.953	0.894	1	0.953	0.894	1	CLONAL	1	TRUE	1	0.626142702004423	2		797	831	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412228	139412228	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	317	1158	0	ENST00000277541.6:c.1417G>T	p.Glu473Ter	p.E473*	ENST00000277541	NM_017617.3	473	Gag/Tag	8/34	0.626142702004423	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.626142702004423	1		1158	653	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268887	55268887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	243	951	0	ENST00000275493.2:c.2953G>A	p.Glu985Lys	p.E985K	ENST00000275493	NM_005228.3	985	Gaa/Aaa	25/28	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.626142702004423	2		951	752	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332444	70332444	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	202	665	0	ENST00000373644.4:c.349C>T	p.Gln117Ter	p.Q117*	ENST00000373644	NM_030625.2	117	Caa/Taa	2/12	1	2	FACETS	0.984	0.916	1	0.984	0.916	1	CLONAL	1	TRUE	1	0.626142702004423	2		665	656	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114724337	114724337	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	59	622	1	ENST00000543371.1:c.404C>T	p.Thr135Ile	p.T135I	ENST00000543371	NM_001198531.1	135	aCa/aTa	4/14	1	2	FACETS	0.23	0.197	0.266	0.23	0.197	0.266	SUBCLONAL	1	TRUE	1	0.626142702004423	2		623	818	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981837	101981837	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	199	1283	0	ENST00000282441.5:c.258G>C	p.Met86Ile	p.M86I	ENST00000282441	NM_001130145.2	86	atG/atC	1/9	0.519457581759646	1	FACETS	0.475	0.44	0.511	0.475	0.44	0.511	SUBCLONAL	1	TRUE	0	0.626142702004423	1		1283	919	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415628	49415628	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	119	455	0	ENST00000301067.7:c.16549G>C	p.Glu5517Gln	p.E5517Q	ENST00000301067	NM_003482.3	5517	Gag/Cag	54/54	1	2	FACETS	0.882	0.802	0.965	0.882	0.802	0.965	CLONAL	1	TRUE	1	0.626142702004423	2		455	431	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426270	49426270	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	324	1434	0	ENST00000301067.7:c.12218C>A	p.Ser4073Ter	p.S4073*	ENST00000301067	NM_003482.3	4073	tCa/tAa	39/54	1	2	FACETS	0.988	0.934	1	0.988	0.934	1	CLONAL	1	TRUE	1	0.626142702004423	2		1434	1048	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604710	48604710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773367516	NA	P-0033365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	128	423	1	ENST00000342988.3:c.1532C>T	p.Pro511Leu	p.P511L	ENST00000342988	NM_005359.5	511	cCg/cTg	12/12	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.626142702004423	2		424	403	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288454	15288454	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	136	615	1	ENST00000263388.2:c.4285G>T	p.Glu1429Ter	p.E1429*	ENST00000263388	NM_000435.2	1429	Gag/Tag	24/33	0.574076605977945	1	FACETS	0.938	0.867	1	0.938	0.867	1	CLONAL	1	TRUE	0	0.626142702004423	1		616	318	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939144	131939144	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060501947	NA	P-0033365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	104	662	0	ENST00000265335.6:c.2360T>C	p.Val787Ala	p.V787A	ENST00000265335		787	gTa/gCa	14/25	1	2	FACETS	0.596	0.535	0.661	0.596	0.535	0.661	SUBCLONAL	1	TRUE	1	0.626142702004423	2		662	557	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433759	149433759	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	336	1256	0	ENST00000286301.3:c.2792G>C	p.Arg931Thr	p.R931T	ENST00000286301	NM_005211.3	931	aGa/aCa	22/22	0.574076605977945	1	FACETS	0.867	0.824	0.911	0.867	0.824	0.911	CLONAL	1	TRUE	0	0.626142702004423	1		1256	850	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852139	128852139	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	324	1504	0	ENST00000249373.3:c.2211C>G	p.Phe737Leu	p.F737L	ENST00000249373	NM_005631.4	737	ttC/ttG	12/12	1	2	FACETS	0.971	0.918	1	0.971	0.918	1	CLONAL	1	TRUE	1	0.626142702004423	2		1504	1066	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146945	38146945	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	303	1005	0	ENST00000317025.8:c.3197A>G	p.Asn1066Ser	p.N1066S	ENST00000317025	NM_023034.1	1066	aAc/aGc	18/24	0.626142702004423	1	FACETS	0.632	0.596	0.669	0.632	0.596	0.669	SUBCLONAL	1	TRUE	0	0.626142702004423	1		1005	1052	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76953073	76953073	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	127	538	0	ENST00000373344.5:c.240G>C	p.Lys80Asn	p.K80N	ENST00000373344	NM_000489.3	80	aaG/aaC	4/35	0.574076605977945	1	FACETS	0.449	0.407	0.492	0.449	0.407	0.492	SUBCLONAL	1	TRUE	0	0.626142702004423	1		538	621	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	105	697	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.823	0.739	0.912	0.823	0.739	0.912	CLONAL	1	TRUE	1	0.418156563477738	2		697	610	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0033379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	119	676	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	1	2	FACETS	0.818	0.739	0.901	0.818	0.739	0.901	CLONAL	1	TRUE	1	0.418156563477738	2		676	696	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579355	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519997	NA	P-0033379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	150	814	0	ENST00000269305.4:c.332T>G	p.Leu111Arg	p.L111R	ENST00000269305	NM_001126112.2	111	cTg/cGg	4/11	0.418156563477738	1	FACETS	0.803	0.735	0.873	0.803	0.735	0.873	CLONAL	1	TRUE	0	0.418156563477738	1		814	707	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971132	21971133	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0033379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	139	691	0	ENST00000304494.5:c.225dup	p.Ala76ArgfsTer44	p.A76Rfs*44	ENST00000304494	NM_000077.4	75	-/C	2/3	0.418156563477738	0	FACETS	0.602	0.549	0.656			1	SUBCLONAL	1	TRUE	0	0.418156563477738	0		691	643	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	133	487	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.673344408351612	1	FACETS	0.464	0.423	0.507	0.464	0.423	0.507	SUBCLONAL	1	TRUE	0	0.673344408351612	1		487	565	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249348	110249348	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	591	1881	0	ENST00000374672.4:c.1225A>C	p.Lys409Gln	p.K409Q	ENST00000374672	NM_004235.4	409	Aag/Cag	4/5	0.335527166739458	1	FACETS	0.776	0.747	0.806	0.776	0.747	0.806	INDETERMINATE	1	TRUE	0	0.673344408351612	1		1881	1500	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417152	417152	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	57	369	1	ENST00000399788.2:c.3398G>A	p.Arg1133Gln	p.R1133Q	ENST00000399788	NM_001042603.1	1133	cGg/cAg	23/28	NA	2	FACETS	0.519	0.448	0.596			1	INDETERMINATE	1	TRUE	NA	0.673344408351612	2		370	326	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684303	29684303	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	222	597	0	ENST00000356175.3:c.7823del	p.Tyr2608LeufsTer15	p.Y2608Lfs*15	ENST00000356175	NM_000267.3	2608	tAt/tt	53/57	0.673344408351612	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.673344408351612	1		597	410	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40468861	40468861	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	95	532	0	ENST00000264657.5:c.2203A>G	p.Met735Val	p.M735V	ENST00000264657	NM_139276.2	735	Atg/Gtg	23/24	0.673344408351612	1	FACETS	0.48	0.43	0.532	0.48	0.43	0.532	SUBCLONAL	1	TRUE	0	0.673344408351612	1		532	390	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032867	30032867	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0033396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	76	341	0	ENST00000338641.4:c.240+2T>C		p.X80_splice	ENST00000338641	NM_000268.3	80			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		341	235	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115928	8115929	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	119	426	0	ENST00000346208.3:c.1275dup	p.Ser426IlefsTer81	p.S426Ifs*81	ENST00000346208		425	cca/ccAa	6/6	0.305929076611192	4	FACETS	1	0.967	1	0.572	0.519	0.627	INDETERMINATE	1	TRUE	2	0.720435299644448	4		426	497	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699358	47699358	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1248	238	503	0	ENST00000347630.2:c.150A>C	p.Glu50Asp	p.E50D	ENST00000347630	NM_001007230.1	50	gaA/gaC	4/11	0.720435299644448	7	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.720435299644448	7		503	1486	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119038	3119038	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	82	714	0	ENST00000078429.4:c.722A>T	p.Glu241Val	p.E241V	ENST00000078429	NM_002067.2	241	gAg/gTg	5/7	0.322875859663246	3	FACETS	0.593	0.524	0.667	0.297	0.262	0.334	INDETERMINATE	1	TRUE	1	0.720435299644448	3		714	522	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434563	140434563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727502904	NA	P-0033399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	14	200	0	ENST00000288602.6:c.2135C>T	p.Ala712Val	p.A712V	ENST00000288602	NM_004333.4	712	gCc/gTc	18/18	0.277420758995911	5	FACETS	0.33	0.238	0.441	0.11	0.079	0.147	INDETERMINATE	1	TRUE	2	0.720435299644448	5		200	245	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0033405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	375	808	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.565522094944655	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.565522094944655	2		808	629	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0033405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	1304	521	1	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.565522094944655	10	FACETS	1	0.994	1	1	0.994	1	CLONAL	8	TRUE	2	0.565522094944655	10		522	1828	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950082	44950082	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0033405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	110	264	1	ENST00000377967.4:c.3851C>G	p.Ser1284Ter	p.S1284*	ENST00000377967	NM_021140.2	1284	tCa/tGa	26/29	1	1	FACETS	0.826	0.769	0.88	1	0.99	1	CLONAL	2	TRUE	0	0.565522094944655	1		265	169	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393677	139393677	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	207	759	0	ENST00000277541.6:c.5969C>A	p.Ala1990Asp	p.A1990D	ENST00000277541	NM_017617.3	1990	gCc/gAc	32/34	0.565522094944655	3	FACETS	1	0.959	1	0.523	0.486	0.562	CLONAL	1	TRUE	1	0.565522094944655	3		759	897	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0033406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	58	440	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.39	0.335	0.45	0.39	0.335	0.45	SUBCLONAL	1	TRUE	1	0.578272193847484	2		440	514	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25368492	25368492	+	intron_variant	Intron	SNP	T	T	A	novel	NA	P-0033406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	66	289	0	ENST00000311936.3:c.451-5647A>T		p.*151*	ENST00000311936	NM_004985.3	151/189			1	2	FACETS	0.564	0.491	0.641	0.564	0.491	0.641	SUBCLONAL	1	TRUE	1	0.578272193847484	2		289	405	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986615	36986616	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	43	224	0	ENST00000354822.5:c.1073_1074insA	p.Asp359GlyfsTer80	p.D359Gfs*80	ENST00000354822	NM_001079668.2	358	ccg/ccAg	3/3	0.398258277497982	1	FACETS	0.529	0.447	0.616	0.529	0.447	0.616	SUBCLONAL	1	TRUE	0	0.578272193847484	1		224	200	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460544	8460544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159860	NA	P-0033406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	43	314	0	ENST00000356435.5:c.3742G>A	p.Asp1248Asn	p.D1248N	ENST00000356435		1248	Gac/Aac	22/35	0.501666600751305	1	FACETS	0.187	0.156	0.222	0.187	0.156	0.222	SUBCLONAL	1	TRUE	0	0.578272193847484	1		314	565	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0033408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	68	440	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.0220548938936136	3	FACETS	0.93	0.813	1			1	INDETERMINATE	2	TRUE	NA	0.202866662950287	3		440	397	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579529	7579529	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658483	NA	P-0033408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	80	403	0	ENST00000269305.4:c.158G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tGg/tAg	4/11	0.202866662950287	4	FACETS	1	0.96	1	0.797	0.705	0.893	CLONAL	2	TRUE	1	0.202866662950287	4		403	397	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0033408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	32	530	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.173122006450326	3	FACETS	0.971	0.789	1	0.485	0.394	0.588	CLONAL	1	TRUE	1	0.202866662950287	3		530	358	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0033408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	17	261	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.0627037850434937	4	FACETS	1	0.893	1	0.71	0.534	0.915	INDETERMINATE	1	TRUE	2	0.202866662950287	4		261	142	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597850	43597850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138265837	NA	P-0033408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	48	804	3	ENST00000355710.3:c.398G>A	p.Arg133His	p.R133H	ENST00000355710	NM_020975.4	133	cGt/cAt	3/20	0.202866662950287	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.202866662950287	1		807	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0033412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	199	825	0	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	0.276105826029361	2	FACETS	0.76	0.707	0.815	0.76	0.707	0.815	SUBCLONAL	2	TRUE	0	0.38	2		825	689	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175481	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0033412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	41	304	0	ENST00000257430.4:c.4192_4193del	p.Arg1399PhefsTer9	p.R1399Ffs*9	ENST00000257430	NM_000038.5	1397	GAg/g	16/16	0.267116653460703	3	FACETS	0.783	0.654	0.925	0.391	0.327	0.463	CLONAL	1	TRUE	1	0.38	3		304	328	SUCCESS
APC	324	MSKCC	GRCh37	5	112170777	112170780	+	frameshift_variant	Frame_Shift_Del	DEL	CAGA	CAGA	-	rs878853420	NA	P-0033412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	121	644	0	ENST00000257430.4:c.1875_1878del	p.Asn627LeufsTer2	p.N627Lfs*2	ENST00000257430	NM_000038.5	625	CAGAca/ca	15/16	0.267116653460703	3	FACETS	1	0.98	1	0.656	0.594	0.72	CLONAL	1	TRUE	1	0.38	3		644	578	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610299	81610299	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28937584	NA	P-0033412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	31	413	0	ENST00000298171.2:c.1897G>A	p.Asp633Asn	p.D633N	ENST00000298171	NM_000369.2	633	Gac/Aac	10/10	1	2	FACETS	0.511	0.414	0.621	0.511	0.414	0.621	SUBCLONAL	1	TRUE	1	0.38	2		413	319	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784959	9784959	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	58	541	0	ENST00000377346.4:c.2962G>A	p.Glu988Lys	p.E988K	ENST00000377346	NM_005026.3	988	Gag/Aag	23/24	0.267116653460703	3	FACETS	0.76	0.654	0.875	0.38	0.327	0.438	SUBCLONAL	1	TRUE	1	0.38	3		541	478	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80168956	80168956	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	73	749	0	ENST00000265081.6:c.3152A>G	p.Asp1051Gly	p.D1051G	ENST00000265081	NM_002439.4	1051	gAt/gGt	23/24	0.267116653460703	3	FACETS	0.723	0.633	0.821	0.362	0.316	0.411	SUBCLONAL	1	TRUE	1	0.38	3		749	632	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0033417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	10	462	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.656	0.451	0.904	0.656	0.451	0.904	SUBCLONAL	1	TRUE	1	0.423413338336886	2		462	72	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483984	88483984	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	11	410	0	ENST00000360948.2:c.1586A>C	p.Tyr529Ser	p.Y529S	ENST00000360948	NM_001012338.2	529	tAt/tCt	14/19	0.423413338336886	8	FACETS	0.655	0.453	0.906			1	SUBCLONAL	1	TRUE	NA	0.423413338336886	8		410	180	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224766	36224767	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAG	novel	NA	P-0033417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	21	829	0	ENST00000222270.7:c.7152_7153insCAG	p.His2384_Tyr2385insGln	p.H2384_Y2385insQ	ENST00000222270	NM_014727.1	2384	-/CAG	30/37	1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	1	0.423413338336886	2		829	91	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	162	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.840438263970861	2		248	359	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0033427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	442	503	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.981	0.957	1	1	0.998	1	CLONAL	2	TRUE	1	0.840438263970861	2		503	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0033427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	319	589	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.840438263970861	2		589	751	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098957	178098957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	380	345	0	ENST00000397062.3:c.88C>T	p.Leu30Phe	p.L30F	ENST00000397062	NM_006164.4	30	Ctt/Ttt	2/5	0.840438263970861	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.840438263970861	2		345	436	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622197	162622197	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1801474	NA	P-0033427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	262	403	0	ENST00000366898.1:c.500G>A	p.Ser167Asn	p.S167N	ENST00000366898	NM_004562.2	167	aGc/aAc	4/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.840438263970861	2		403	574	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542109	187542110	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1560943587	NA	P-0033427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	211	393	0	ENST00000441802.2:c.5630dup	p.Val1878CysfsTer8	p.V1878Cfs*8	ENST00000441802	NM_005245.3	1877	cct/ccCt	10/27	1	2	FACETS	0.876	0.82	0.934	0.876	0.82	0.934	CLONAL	1	TRUE	1	0.840438263970861	2		393	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578281	7578281	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	312	611	0	ENST00000269305.4:c.568C>G	p.Pro190Ala	p.P190A	ENST00000269305	NM_001126112.2	190	Cct/Gct	6/11	1	2	FACETS	0.999	0.948	1	0.999	0.948	1	CLONAL	1	TRUE	1	0.840438263970861	2		611	743	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450663	70450663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	213	430	2	ENST00000373644.4:c.5503C>T	p.Pro1835Ser	p.P1835S	ENST00000373644	NM_030625.2	1835	Cca/Tca	12/12	1	2	FACETS	0.92	0.862	0.979	0.92	0.862	0.979	CLONAL	1	TRUE	1	0.840438263970861	2		432	551	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115272928	115272928	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	381	722	0	ENST00000438362.2:c.1445C>G	p.Ala482Gly	p.A482G	ENST00000438362	NM_001242891.1	482	gCc/gGc	12/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.840438263970861	2		722	825	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252950	36252950	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	236	386	0	ENST00000300305.3:c.412G>T	p.Glu138Ter	p.E138*	ENST00000300305		138	Gaa/Taa	4/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.840438263970861	2		386	530	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803170	1803170	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	668	756	0	ENST00000260795.2:c.522C>G	p.Phe174Leu	p.F174L	ENST00000260795		174	ttC/ttG	4/17	1	2	FACETS	0.995	0.975	1	1	0.998	1	CLONAL	2	TRUE	1	0.840438263970861	2		756	799	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950638	79950638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	216	355	1	ENST00000265081.6:c.92C>T	p.Thr31Met	p.T31M	ENST00000265081	NM_002439.4	31	aCg/aTg	1/24	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.840438263970861	2		356	461	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519218	137519218	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1166342418	NA	P-0033427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	172	328	1	ENST00000367739.4:c.1420G>T	p.Glu474Ter	p.E474*	ENST00000367739	NM_000416.2	474	Gag/Tag	7/7	1	2	FACETS	0.95	0.884	1	0.95	0.884	1	CLONAL	1	TRUE	1	0.840438263970861	2		329	431	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224263	98224263	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	340	314	0	ENST00000331920.6:c.2578G>C	p.Asp860His	p.D860H	ENST00000331920	NM_000264.3	860	Gac/Cac	16/24	0.840438263970861	2	FACETS	0.989	0.962	1	0.989	0.962	1	CLONAL	2	TRUE	0	0.840438263970861	2		314	409	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399402	139399402	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	355	773	0	ENST00000277541.6:c.4741C>G	p.Pro1581Ala	p.P1581A	ENST00000277541	NM_017617.3	1581	Ccg/Gcg	26/34	0.840438263970861	2	FACETS	1	0.967	1	0.51	0.485	0.534	CLONAL	1	TRUE	0	0.840438263970861	2		773	829	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969444	44969444	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	271	475	2	ENST00000377967.4:c.4126G>T	p.Glu1376Ter	p.E1376*	ENST00000377967	NM_021140.2	1376	Gaa/Taa	28/29	0.792002881010573	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.840438263970861	1		477	360	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210260	123210264	+	frameshift_variant	Frame_Shift_Del	DEL	TAATT	TAATT	-	novel	NA	P-0033427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	257	554	0	ENST00000218089.9:c.2612_2616del	p.Leu871ArgfsTer22	p.L871Rfs*22	ENST00000218089	NM_001042749.1	871	cTAATT/c	26/35	1	2	FACETS	0.907	0.855	0.961	0.907	0.855	0.961	CLONAL	1	TRUE	1	0.840438263970861	2		554	674	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659675	NA	P-0033429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	118	691	0	ENST00000269305.4:c.764T>C	p.Ile255Thr	p.I255T	ENST00000269305	NM_001126112.2	255	aTc/aCc	7/11	0.503742662653092	1	FACETS	0.855	0.778	0.935	0.855	0.778	0.935	CLONAL	1	TRUE	0	0.503742662653092	1		691	410	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259397	11259397	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	134	656	0	ENST00000361445.4:c.4171C>G	p.Arg1391Gly	p.R1391G	ENST00000361445	NM_004958.3	1391	Cga/Gga	28/58	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.503742662653092	2		656	458	SUCCESS
APC	324	MSKCC	GRCh37	5	112175096	112175097	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs786203760	NA	P-0033429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	43	264	0	ENST00000257430.4:c.3807_3808del	p.Ile1269MetfsTer6	p.I1269Mfs*6	ENST00000257430	NM_000038.5	1269	ATa/a	16/16	1	2	FACETS	0.88	0.746	1	0.88	0.746	1	CLONAL	1	TRUE	1	0.503742662653092	2		264	194	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621866	1621866	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376627351	NA	P-0033429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	22	621	0	ENST00000344749.5:c.926C>T	p.Pro309Leu	p.P309L	ENST00000344749	NM_001136139.2	309	cCg/cTg	11/19	0.438471564953392	1	FACETS	0.189	0.146	0.239	0.189	0.146	0.239	SUBCLONAL	1	TRUE	0	0.503742662653092	1		621	346	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7152906	7152906	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761229082	NA	P-0033429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	34	600	0	ENST00000302850.5:c.2062C>T	p.Pro688Ser	p.P688S	ENST00000302850	NM_000208.2	688	Cca/Tca	10/22	0.438471564953392	1	FACETS	0.26	0.212	0.314	0.26	0.212	0.314	SUBCLONAL	1	TRUE	0	0.503742662653092	1		600	388	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	62	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.700765104031124	2		248	172	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117799	108117799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202160435	NA	P-0033442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	186	384	0	ENST00000278616.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000278616	NM_000051.3	337	cGt/cAt	8/63	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.700765104031124	2		384	522	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577523	7577524	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	267	628	0	ENST00000269305.4:c.757dup	p.Thr253AsnfsTer11	p.T253Nfs*11	ENST00000269305	NM_001126112.2	253	acc/aAcc	7/11	0.700765104031124	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.700765104031124	1		628	455	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943779	9943779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1211198789	NA	P-0033442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	213	419	0	ENST00000330684.3:c.1162G>A	p.Ala388Thr	p.A388T	ENST00000330684	NM_001134407.1	388	Gcc/Acc	5/13	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.700765104031124	2		419	568	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	63	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.794	0.689	0.907	0.794	0.689	0.907	CLONAL	1	TRUE	1	0.39	2		248	407	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0033445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	107	503	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.82	0.737	0.909	0.82	0.737	0.909	CLONAL	1	TRUE	1	0.39	2		503	669	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645294	67645294	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	101	464	0	ENST00000264010.4:c.559G>T	p.Glu187Ter	p.E187*	ENST00000264010	NM_006565.3	187	Gaa/Taa	3/12	1	2	FACETS	0.835	0.748	0.928	0.835	0.748	0.928	CLONAL	1	TRUE	1	0.39	2		464	620	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266018	41266622	+	splice_donor_variant,splice_acceptor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	TGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGAT	TGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGAT	-	novel	NA	P-0033445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	58	226	0	ENST00000349496.5:c.16_420del		p.X6_splice	ENST00000349496	NM_001904.3	6	gcTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATt/gct	3-4/15	1	2	FACETS	0.899	0.777	1	0.899	0.777	1	CLONAL	1	TRUE	1	0.39	2		226	331	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186501400	186501400	+	start_lost	Translation_Start_Site	SNP	A	A	C	novel	NA	P-0033445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	79	365	0	ENST00000323963.5:c.1A>C	p.Met1?	p.M1?	ENST00000323963		1	Atg/Ctg	1/11	1	2	FACETS	0.775	0.683	0.873	0.775	0.683	0.873	SUBCLONAL	1	TRUE	1	0.39	2		365	523	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422858	12422858	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	114	498	0	ENST00000287820.6:c.349del	p.Ser117LeufsTer53	p.S117Lfs*53	ENST00000287820	NM_015869.4	116	taT/ta	3/7	1	2	FACETS	0.812	0.732	0.897	0.812	0.732	0.897	CLONAL	1	TRUE	1	0.39	2		498	720	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675882	30675882	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	162	855	2	ENST00000376406.3:c.2474G>T	p.Gly825Val	p.G825V	ENST00000376406	NM_014641.2	825	gGc/gTc	8/15	0.3	3	FACETS	0.751	0.687	0.818	0.375	0.343	0.409	SUBCLONAL	1	TRUE	1	0.39	3		857	1322	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774928	73774928	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	39	493	0	ENST00000254810.4:c.245del	p.Asp82AlafsTer2	p.D82Afs*2	ENST00000254810	NM_005324.3	82	gAc/gc	3/4	1	2	FACETS	0.992	0.822	1	0.992	0.822	1	CLONAL	1	TRUE	1	0.15	2		493	524	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0033465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	495	454	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.132252026544346	5	FACETS	0.905	0.87	0.94			1	INDETERMINATE	3	TRUE	NA	0.795938569828408	5		454	1005	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0033465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	366	390	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.393819695148834	3	FACETS	0.87	0.831	0.908	0.87	0.831	0.908	INDETERMINATE	2	TRUE	1	0.795938569828408	3		390	739	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0033465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	91	238	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.795938569828408	1	FACETS	0.678	0.616	0.741	0.678	0.616	0.741	SUBCLONAL	1	TRUE	0	0.795938569828408	1		238	203	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999551	100999551	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	598	969	0	ENST00000325455.5:c.251A>G	p.Glu84Gly	p.E84G	ENST00000325455	NM_001202474.3	84	gAg/gGg	1/8	0.795938569828408	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.795938569828408	1		969	905	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134112	41134112	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	367	544	0	ENST00000379561.5:c.1516A>G	p.Thr506Ala	p.T506A	ENST00000379561	NM_002015.3	506	Acc/Gcc	2/3	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.795938569828408	2		544	874	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039401	49039401	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	465	721	0	ENST00000267163.4:c.2386C>T	p.Pro796Ser	p.P796S	ENST00000267163	NM_000321.2	796	Ccc/Tcc	23/27	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.795938569828408	2		721	1129	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982376	25982376	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	217	348	0	ENST00000435504.4:c.914del	p.Leu305TyrfsTer6	p.L305Yfs*6	ENST00000435504		305	tTa/ta	9/13	1	2	FACETS	0.937	0.878	0.997	0.937	0.878	0.997	CLONAL	1	TRUE	1	0.795938569828408	2		348	582	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7218344	7218344	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	103	574	1	ENST00000380728.2:c.28C>A	p.Leu10Ile	p.L10I	ENST00000380728		10	Ctt/Att	2/11	1	2	FACETS	0.881	0.788	0.98	0.881	0.788	0.98	CLONAL	1	TRUE	1	0.278972657008056	2		575	838	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	134	819	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.226548526146334	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.226548526146334	1		819	1032	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949665	151949665	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	114	675	1	ENST00000262189.6:c.1435C>T	p.Gln479Ter	p.Q479*	ENST00000262189	NM_170606.2	479	Cag/Tag	10/59	NA	2	FACETS	0.922	0.829	1			1	INDETERMINATE	1	TRUE	NA	0.226548526146334	2		676	1091	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955559	48955559	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1131690869	NA	P-0033479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	118	525	0	ENST00000267163.4:c.1675G>T	p.Glu559Ter	p.E559*	ENST00000267163	NM_000321.2	559	Gaa/Taa	17/27	0.175771988545733	2	FACETS	1	0.981	1	0.684	0.618	0.755	CLONAL	1	TRUE	0	0.226548526146334	2		525	761	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	38	487	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.256320065516444	1	FACETS	0.623	0.515	0.743	0.623	0.515	0.743	SUBCLONAL	1	TRUE	0	0.256320065516444	1		487	415	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347299	89347299	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0033482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	41	499	0	ENST00000301030.4:c.5651C>G	p.Ser1884Ter	p.S1884*	ENST00000301030	NM_001256183.1	1884	tCa/tGa	9/13	0.256320065516444	0	FACETS	1	0.86	1			1	CLONAL	1	TRUE	0	0.256320065516444	0		499	232	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916929	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519931	NA	P-0033482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	96	406	0	ENST00000263967.3:c.316G>C	p.Gly106Arg	p.G106R	ENST00000263967	NM_006218.2	106	Ggc/Cgc	2/21	1	2	FACETS	1	0.915	1	1	0.987	1	CLONAL	2	TRUE	1	0.256320065516444	2		406	367	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061463	38061463	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	56	364	0	ENST00000250448.2:c.526A>G	p.Ile176Val	p.I176V	ENST00000250448	NM_004496.3	176	Atc/Gtc	2/2	0.256320065516444	3	FACETS	1	0.968	1	0.749	0.645	0.861	CLONAL	1	TRUE	1	0.256320065516444	3		364	329	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023630	27023630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	10	203	0	ENST00000324856.7:c.736G>A	p.Ala246Thr	p.A246T	ENST00000324856	NM_006015.4	246	Gct/Act	1/20	0.256320065516444	1	FACETS	0.38	0.257	0.534	0.38	0.257	0.534	SUBCLONAL	1	TRUE	0	0.256320065516444	1		203	179	SUCCESS
EED	8726	MSKCC	GRCh37	11	85968615	85968615	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	44	350	0	ENST00000263360.6:c.611A>T	p.Asn204Ile	p.N204I	ENST00000263360	NM_003797.3	204	aAt/aTt	6/12	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.256320065516444	2		350	329	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216083	7216083	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	56	322	0	ENST00000380728.2:c.976del	p.His326ThrfsTer19	p.H326Tfs*19	ENST00000380728		326	Cac/ac	11/11	0.256320065516444	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.256320065516444	1		322	343	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664823	138664823	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	40	89	0	ENST00000330315.3:c.742C>A	p.Leu248Met	p.L248M	ENST00000330315	NM_023067.3	248	Ctg/Atg	1/1	1	2	FACETS	1	0.906	1	1	0.972	1	CLONAL	2	TRUE	1	0.256320065516444	2		89	142	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541528	187541528	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	33	422	0	ENST00000441802.2:c.6212T>C	p.Val2071Ala	p.V2071A	ENST00000441802	NM_005245.3	2071	gTa/gCa	10/27	1	2	FACETS	0.687	0.56	0.829	0.687	0.56	0.829	SUBCLONAL	1	TRUE	1	0.256320065516444	2		422	375	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210196	123210196	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765291092	NA	P-0033482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	61	455	0	ENST00000218089.9:c.2548G>A	p.Asp850Asn	p.D850N	ENST00000218089	NM_001042749.1	850	Gat/Aat	26/35	0.169361972985896	1	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	0	0.256320065516444	1		455	411	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300565	11300565	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	19	908	0	ENST00000361445.4:c.1581G>T	p.Gln527His	p.Q527H	ENST00000361445	NM_004958.3	527	caG/caT	11/58	0.297237646271284	2	FACETS	0.77	0.598	0.963	0.77	0.598	0.963	CLONAL	2	TRUE	0	0.297237646271284	2		908	83	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115722	8115723	+	stop_gained	Nonsense_Mutation	DNP	GA	GA	AT	novel	NA	P-0033483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	27	465	1	ENST00000346208.3:c.1068_1069delinsAT	p.Met356_Lys357delinsIleTer	p.M356_K357delinsI*	ENST00000346208		356	atGAag/atATag	6/6	0.297237646271284	3	FACETS	0.828	0.67	1	0.828	0.67	1	CLONAL	2	TRUE	1	0.297237646271284	3		466	126	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166842	32166842	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	16	799	3	ENST00000375023.3:c.4396C>A	p.Leu1466Ile	p.L1466I	ENST00000375023	NM_004557.3	1466	Ctc/Atc	24/30	0.202758355432875	4	FACETS	1	0.881	1	0.452	0.338	0.583	CLONAL	1	TRUE	1	0.297237646271284	4		802	103	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032271	26032271	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1278314228	NA	P-0033484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	32	292	0	ENST00000244661.2:c.18G>C	p.Gln6His	p.Q6H	ENST00000244661	NM_003537.3	6	caG/caC	1/1	1	2	FACETS	0.825	0.673	0.995	0.825	0.673	0.995	CLONAL	1	FALSE	1	0.312750575036966	2		292	248	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916421	39916421	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	100	675	0	ENST00000378444.4:c.4582del	p.Gln1528ArgfsTer40	p.Q1528Rfs*40	ENST00000378444	NM_001123385.1	1528	Cag/ag	11/15	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	FALSE	1	0.312750575036966	2		675	599	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044964	47044964	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	117	886	0	ENST00000377604.3:c.2290T>G	p.Cys764Gly	p.C764G	ENST00000377604	NM_001204468.1	764	Tgc/Ggc	20/24	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	FALSE	1	0.312750575036966	2		886	696	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0033485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	97	680	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	1	2	FACETS	0.879	0.786	0.977	1	0.985	1	CLONAL	2	TRUE	1	0.2	2		680	552	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs869320707	NA	P-0033485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	152	940	0	ENST00000397752.3:c.3028+1G>T		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.24169606916037	3	FACETS	0.839	0.767	0.915	0.839	0.767	0.915	CLONAL	2	TRUE	1	0.2	3		940	996	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106138	27106138	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	39	559	0	ENST00000324856.7:c.5749A>G	p.Thr1917Ala	p.T1917A	ENST00000324856	NM_006015.4	1917	Act/Gct	20/20	0.151269137510427	4	FACETS	0.836	0.692	0.997	0.418	0.346	0.499	CLONAL	1	TRUE	2	0.2	4		559	560	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1650231	1650231	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	37	699	0	ENST00000344749.5:c.17G>C	p.Arg6Thr	p.R6T	ENST00000344749	NM_001136139.2	6	aGg/aCg	2/19	1	2	FACETS	0.604	0.496	0.724	0.604	0.496	0.724	SUBCLONAL	1	TRUE	1	0.2	2		699	613	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371809	116371809	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	45	587	0	ENST00000397752.3:c.1289del	p.Phe430SerfsTer10	p.F430Sfs*10	ENST00000397752	NM_000245.2	430	Ttc/tc	3/21	0.24169606916037	3	FACETS	0.798	0.67	0.941	0.399	0.335	0.471	CLONAL	1	TRUE	1	0.2	3		587	620	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033485-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	33	697	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.779	0.633	0.944	0.779	0.633	0.944	CLONAL	1	TRUE	1	0.15	2		697	565	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039906	47039906	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0033485-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	72	345	0	ENST00000377604.3:c.1248+1G>T		p.X416_splice	ENST00000377604	NM_001204468.1	416			0.0828209613825077	2	FACETS	1	0.907	1			1	INDETERMINATE	2	TRUE	NA	0.15	2		345	461	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226589952	226589952	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033485-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	65	515	0	ENST00000366794.5:c.249G>T	p.Gln83His	p.Q83H	ENST00000366794	NM_001618.3	83	caG/caT	2/23	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.15	2		515	708	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69230471	69230471	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033485-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	38	358	0	ENST00000462284.1:c.860A>G	p.Tyr287Cys	p.Y287C	ENST00000462284	NM_002392.5	287	tAt/tGt	10/11	1	2	FACETS	0.887	0.732	1	0.887	0.732	1	CLONAL	1	TRUE	1	0.15	2		358	571	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993828	72993828	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033485-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	67	474	2	ENST00000268489.5:c.217G>T	p.Glu73Ter	p.E73*	ENST00000268489	NM_006885.3	73	Gag/Tag	2/10	1	2	FACETS	0.893	0.778	1	1	0.978	1	CLONAL	2	TRUE	1	0.15	2		476	500	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685543	29685543	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033485-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	36	411	0	ENST00000356175.3:c.7953C>G	p.Cys2651Trp	p.C2651W	ENST00000356175	NM_000267.3	2651	tgC/tgG	54/57	1	2	FACETS	0.897	0.737	1	0.897	0.737	1	CLONAL	1	TRUE	1	0.15	2		411	535	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0033487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	355	503	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.923	0.899	0.946	1	0.997	1	CLONAL	4	TRUE	1	0.45235690238112	2		503	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0033487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	356	691	2	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	1	2	FACETS	0.986	0.94	1	1	0.996	1	CLONAL	2	TRUE	1	0.45235690238112	2		693	798	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266611	198266611	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs755415626	NA	P-0033487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	188	452	0	ENST00000335508.6:c.2225G>A	p.Gly742Asp	p.G742D	ENST00000335508	NM_012433.2	742	gGt/gAt	16/25	1	2	FACETS	0.924	0.863	0.985	1	0.993	1	CLONAL	2	TRUE	1	0.45235690238112	2		452	450	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936083	178936083	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519927	NA	P-0033487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	8	494	1	ENST00000263967.3:c.1625A>T	p.Glu542Val	p.E542V	ENST00000263967	NM_006218.2	542	gAa/gTa	10/21	1	2	FACETS	0.112	0.071	0.164	0.112	0.071	0.164	SUBCLONAL	1	TRUE	1	0.45235690238112	2		495	317	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098795	47098795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745996964	NA	P-0033487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	378	753	0	ENST00000409792.3:c.6479C>T	p.Pro2160Leu	p.P2160L	ENST00000409792	NM_014159.6	2160	cCg/cTg	15/21	1	2	FACETS	0.953	0.909	0.997	1	0.997	1	CLONAL	2	TRUE	1	0.45235690238112	2		753	877	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111167	193111168	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAA	novel	NA	P-0033487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	27	452	0	ENST00000367435.3:c.701_703dup	p.Arg234dup	p.R234dup	ENST00000367435	NM_024529.4	234	cga/cGAAga	7/17	1	2	FACETS	0.372	0.296	0.458	0.372	0.296	0.458	SUBCLONAL	1	TRUE	1	0.45235690238112	2		452	321	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778744	3778744	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0033487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	67	780	1	ENST00000262367.5:c.6304A>T	p.Lys2102Ter	p.K2102*	ENST00000262367	NM_004380.2	2102	Aaa/Taa	31/31	0.447514940238647	0	FACETS	0.361	0.315	0.411			1	SUBCLONAL	1	TRUE	0	0.45235690238112	0		781	449	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789695	3789699	+	frameshift_variant	Frame_Shift_Del	DEL	AGATT	AGATT	-	novel	NA	P-0033487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	25	458	0	ENST00000262367.5:c.4160_4164del	p.Glu1387ValfsTer12	p.E1387Vfs*12	ENST00000262367	NM_004380.2	1387	gAATCT/g	25/31	0.447514940238647	0	FACETS	0.201	0.158	0.25			1	SUBCLONAL	1	TRUE	0	0.45235690238112	0		458	301	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800163	32800163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	255	485	0	ENST00000374899.4:c.1219G>A	p.Gly407Ser	p.G407S	ENST00000374899	NM_018833.2	407	Ggc/Agc	7/12	1	2	FACETS	1	0.958	1	1	0.995	1	CLONAL	2	TRUE	1	0.45235690238112	2		485	555	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929263	44929270	+	frameshift_variant	Frame_Shift_Del	DEL	CCAATAAC	CCAATAAC	-	novel	NA	P-0033487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	335	381	0	ENST00000377967.4:c.2363_2370del	p.Ala788GlufsTer8	p.A788Efs*8	ENST00000377967	NM_021140.2	788	gCCAATAAC/g	17/29	1	1	FACETS	0.998	0.973	1	1	0.997	1	CLONAL	3	TRUE	0	0.45235690238112	1		381	383	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195660	123195661	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0033487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	184	223	0	ENST00000218089.9:c.1575dup	p.Leu526AlafsTer5	p.L526Afs*5	ENST00000218089	NM_001042749.1	525	atg/atGg	17/35	1	1	FACETS	1	0.971	1	1	0.996	1	CLONAL	3	TRUE	0	0.45235690238112	1		223	209	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717735	89717739	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGT	AAAGT	-	rs606231169	NA	P-0033488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	136	573	0	ENST00000371953.3:c.761_765del	p.Lys254ArgfsTer42	p.K254Rfs*42	ENST00000371953	NM_000314.4	254	AAAGTa/a	7/9	0.399761213560621	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.399761213560621	1		573	470	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0033489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	99	328	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	0.18	2		328	744	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098815	178098815	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1162	110	680	0	ENST00000397062.3:c.230A>T	p.Asp77Val	p.D77V	ENST00000397062	NM_006164.4	77	gAt/gTt	2/5	1	2	FACETS	0.961	0.861	1	0.961	0.861	1	CLONAL	1	TRUE	1	0.18	2		680	1272	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8246143	8246172	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	TGGAGGCCAGGCGCCGGGCGTTACTGAACT	TGGAGGCCAGGCGCCGGGCGTTACTGAACT	-	novel	NA	P-0033489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	55	452	0	ENST00000335790.3:c.462_*20del		p.*154*	ENST00000335790	NM_002315.2	154		4/4	1	2	FACETS	0.967	0.826	1	0.967	0.826	1	CLONAL	1	TRUE	1	0.18	2		452	632	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610331	10610331	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	91	917	0	ENST00000171111.5:c.379G>T	p.Gly127Cys	p.G127C	ENST00000171111	NM_203500.1	127	Ggt/Tgt	2/6	0.173851326460769	1	FACETS	0.848	0.751	0.952	0.848	0.751	0.952	CLONAL	1	TRUE	0	0.18	1		917	1085	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134270	11134270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs797045981	NA	P-0033489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	65	605	1	ENST00000358026.2:c.2936G>A	p.Arg979Gln	p.R979Q	ENST00000358026	NM_001128849.1	979	cGa/cAa	20/36	0.173851326460769	1	FACETS	0.879	0.761	1	0.879	0.761	1	CLONAL	1	TRUE	0	0.18	1		606	748	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390911	89390911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	34	381	0	ENST00000336596.2:c.977C>T	p.Pro326Leu	p.P326L	ENST00000336596	NM_005233.5	326	cCa/cTa	5/17	0.173851326460769	1	FACETS	0.611	0.498	0.738	0.611	0.498	0.738	SUBCLONAL	1	TRUE	0	0.18	1		381	563	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459840	149459840	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	91	773	0	ENST00000286301.3:c.367G>T	p.Ala123Ser	p.A123S	ENST00000286301	NM_005211.3	123	Gca/Tca	4/22	1	2	FACETS	0.947	0.838	1	0.947	0.838	1	CLONAL	1	TRUE	1	0.18	2		773	1068	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609881	117609881	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	110	640	0	ENST00000368508.3:c.6818A>T	p.Asn2273Ile	p.N2273I	ENST00000368508	NM_002944.2	2273	aAc/aTc	43/43	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.18	2		640	1136	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0033492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	63	264	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.964	0.835	1	0.964	0.835	1	CLONAL	1	TRUE	1	0.253867774554672	2		264	515	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782082	NA	P-0033492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	77	617	0	ENST00000269305.4:c.745A>T	p.Arg249Trp	p.R249W	ENST00000269305	NM_001126112.2	249	Agg/Tgg	7/11	1	2	FACETS	0.749	0.656	0.849	0.749	0.656	0.849	SUBCLONAL	1	TRUE	1	0.253867774554672	2		617	810	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060743	38060743	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	54	841	1	ENST00000250448.2:c.1246G>T	p.Asp416Tyr	p.D416Y	ENST00000250448	NM_004496.3	416	Gac/Tac	2/2	0.154663647032912	2	FACETS	0.402	0.342	0.468	0.201	0.171	0.234	SUBCLONAL	1	TRUE	0	0.253867774554672	2		842	1058	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574649	41574649	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	46	715	0	ENST00000263253.7:c.6934C>G	p.Pro2312Ala	p.P2312A	ENST00000263253	NM_001429.3	2312	Cct/Gct	31/31	0.154663647032912	2	FACETS	0.401	0.337	0.473	0.201	0.168	0.237	SUBCLONAL	1	TRUE	0	0.253867774554672	2		715	903	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520735	176520735	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750637669	NA	P-0033492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	65	550	0	ENST00000292408.4:c.1478G>A	p.Arg493Gln	p.R493Q	ENST00000292408	NM_213647.1	493	cGg/cAg	11/18	0.253867774554672	1	FACETS	0.732	0.634	0.837	0.732	0.634	0.837	SUBCLONAL	1	TRUE	0	0.253867774554672	1		550	611	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034816	42034818	+	missense_variant	Missense_Mutation	TNP	TAC	TAC	AAG	novel	NA	P-0033492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	57	571	0	ENST00000219905.7:c.4658_4660delinsAAG	p.Ile1553_Pro1554delinsLysAla	p.I1553_P1554delinsKA	ENST00000219905	NM_001164273.1	1553	aTACct/aAAGct	15/24	1	2	FACETS	0.608	0.52	0.703	0.608	0.52	0.703	SUBCLONAL	1	TRUE	1	0.253867774554672	2		571	739	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789597	3789597	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	116	368	0	ENST00000262367.5:c.4262G>T	p.Cys1421Phe	p.C1421F	ENST00000262367	NM_004380.2	1421	tGc/tTc	25/31	0.112896429924659	5	FACETS	0.972	0.882	1	0.648	0.588	0.711	INDETERMINATE	2	TRUE	2	0.435731309284301	5		368	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0033496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	179	563	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.435731309284301	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.435731309284301	1		563	525	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439769	220439769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111982983	NA	P-0033496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	213	698	0	ENST00000243786.2:c.622C>T	p.Arg208Trp	p.R208W	ENST00000243786	NM_002191.3	208	Cgg/Tgg	2/2	0.435731309284301	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.435731309284301	1		698	537	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945702	17945702	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs905946477	NA	P-0033496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	65	695	0	ENST00000458235.1:c.2158A>T	p.Ser720Cys	p.S720C	ENST00000458235	NM_000215.3	720	Agt/Tgt	16/24	0.289268493036448	1	FACETS	0.407	0.352	0.465	0.407	0.352	0.465	SUBCLONAL	1	TRUE	0	0.435731309284301	1		695	574	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467418	25467418	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs773613277	NA	P-0033496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	55	508	0	ENST00000264709.3:c.1658A>G	p.Asn553Ser	p.N553S	ENST00000264709	NM_175629.2	553	aAc/aGc	14/23	0.170238010862984	2	FACETS	0.504	0.431	0.583	0.252	0.215	0.292	INDETERMINATE	1	TRUE	0	0.435731309284301	2		508	501	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0033498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	151	747	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.220342962281181	2	FACETS	1	0.987	1	0.696	0.64	0.754	INDETERMINATE	1	TRUE	0	0.409406744293293	2		747	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0033498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	14	756	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.409406744293293	1	FACETS	0.101	0.072	0.136	0.101	0.072	0.136	SUBCLONAL	1	TRUE	0	0.409406744293293	1		756	539	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0033498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	38	816	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.409406744293293	1	FACETS	0.254	0.209	0.304	0.254	0.209	0.304	SUBCLONAL	1	TRUE	0	0.409406744293293	1		817	581	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0033498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	27	622	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.409406744293293	1	FACETS	0.186	0.147	0.231	0.186	0.147	0.231	SUBCLONAL	1	TRUE	0	0.409406744293293	1		622	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0033498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	15	563	0	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	0.409406744293293	1	FACETS	0.121	0.087	0.161	0.121	0.087	0.161	SUBCLONAL	1	TRUE	0	0.409406744293293	1		563	483	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52725373	52725374	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGGA	novel	NA	P-0033498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	77	523	0	ENST00000322088.6:c.1541_1544dup	p.Asp515GlufsTer46	p.D515Efs*46	ENST00000322088	NM_014225.5	514	cag/cAGGAag	13/15	1	2	FACETS	0.674	0.593	0.761	0.674	0.593	0.761	SUBCLONAL	1	TRUE	1	0.409406744293293	2		523	558	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	45	504	1	ENST00000346208.3:c.1220_1221insA	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcAg	6/6	1	2	FACETS	0.592	0.498	0.695	0.592	0.498	0.695	SUBCLONAL	1	TRUE	1	0.373667319207719	2		505	407	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246445	105246445	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	113	611	0	ENST00000349310.3:c.155T>G	p.Leu52Arg	p.L52R	ENST00000349310	NM_001014432.1	52	cTc/cGc	4/15	0.233736449567371	2	FACETS	1	0.982	1	0.689	0.624	0.756	CLONAL	1	TRUE	0	0.373667319207719	2		611	439	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257158	16257158	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	153	568	0	ENST00000375759.3:c.4423C>T	p.Arg1475Ter	p.R1475*	ENST00000375759	NM_015001.2	1475	Cga/Tga	11/15	0.305255318059554	2	FACETS	0.9	0.831	0.971	0.9	0.831	0.971	CLONAL	2	TRUE	0	0.373667319207719	2		568	455	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639941	3639941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	43	681	0	ENST00000294008.3:c.3698G>A	p.Gly1233Glu	p.G1233E	ENST00000294008	NM_032444.2	1233	gGg/gAg	12/15	0.373667319207719	3	FACETS	0.507	0.424	0.599	0.253	0.212	0.3	SUBCLONAL	1	TRUE	1	0.373667319207719	3		681	539	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584526	52584526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs563717316	NA	P-0033499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	63	593	1	ENST00000394830.3:c.4487G>A	p.Arg1496Gln	p.R1496Q	ENST00000394830	NM_018313.4	1496	cGg/cAg	29/30	1	2	FACETS	0.664	0.575	0.76	0.664	0.575	0.76	SUBCLONAL	1	TRUE	1	0.373667319207719	2		594	508	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160711	56160711	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	62	412	0	ENST00000399503.3:c.985A>T	p.Ile329Phe	p.I329F	ENST00000399503	NM_005921.1	329	Att/Ttt	4/20	1	2	FACETS	0.847	0.734	0.967	0.847	0.734	0.967	CLONAL	1	TRUE	1	0.373667319207719	2		412	392	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0033500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	109	432	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.3169891202051	2		432	506	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032515	12032515	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	83	401	0	ENST00000353533.5:c.952del	p.Thr318HisfsTer4	p.T318Hfs*4	ENST00000353533	NM_003010.3	317	ctA/ct	9/11	0.3169891202051	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.3169891202051	1		401	372	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485837	8485837	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	21	420	0	ENST00000356435.5:c.2980G>C	p.Val994Leu	p.V994L	ENST00000356435		994	Gta/Cta	17/35	1	2	FACETS	0.319	0.244	0.405	0.319	0.244	0.405	SUBCLONAL	1	TRUE	1	0.3169891202051	2		420	416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577533	7577541	+	frameshift_variant	Frame_Shift_Del	DEL	GCCTCCGGT	GCCTCCGGT	C	novel	NA	P-0033500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	115	615	0	ENST00000269305.4:c.740_748delinsG	p.Asn247SerfsTer14	p.N247Sfs*14	ENST00000269305	NM_001126112.2	247	aACCGGAGGCcc/aGcc	7/11	0.3169891202051	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.3169891202051	1		615	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0033502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	390	617	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.314161287066184	3	FACETS	0.965	0.922	1	0.965	0.922	1	CLONAL	3	TRUE	0	0.375052761173007	3		617	853	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000087	30000087	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	235	486	0	ENST00000338641.4:c.100G>T	p.Glu34Ter	p.E34*	ENST00000338641	NM_000268.3	34	Gag/Tag	1/16	0.375052761173007	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	0	0.375052761173007	2		486	625	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	176	387	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.312597531751273	3	FACETS	1	0.989	1	0.707	0.654	0.762	CLONAL	1	TRUE	1	0.462863161407364	3		387	662	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	36	544	0	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	0.257	0.211	0.309	0.257	0.211	0.309	SUBCLONAL	1	TRUE	1	0.462863161407364	2		544	605	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	130	207	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.462863161407364	2		207	443	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11293469	11293469	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	102	746	0	ENST00000361445.4:c.2407G>T	p.Gly803Ter	p.G803*	ENST00000361445	NM_004958.3	803	Gga/Tga	15/58	1	2	FACETS	0.596	0.533	0.663	0.596	0.533	0.663	SUBCLONAL	1	TRUE	1	0.462863161407364	2		746	739	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258927	16258928	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	93	692	1	ENST00000375759.3:c.6198dup	p.Pro2067ThrfsTer4	p.P2067Tfs*4	ENST00000375759	NM_015001.2	2064	-/A	11/15	1	2	FACETS	0.453	0.402	0.507	0.453	0.402	0.507	SUBCLONAL	1	TRUE	1	0.462863161407364	2		693	888	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087886	27087886	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	131	641	0	ENST00000324856.7:c.2174del	p.Pro725HisfsTer17	p.P725Hfs*17	ENST00000324856	NM_006015.4	725	Cca/ca	6/20	1	2	FACETS	0.688	0.624	0.755	0.688	0.624	0.755	SUBCLONAL	1	TRUE	1	0.462863161407364	2		641	823	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597990	43597990	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs76449634	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	128	750	3	ENST00000355710.3:c.538C>T	p.Arg180Ter	p.R180*	ENST00000355710	NM_020975.4	180	Cga/Tga	3/20	1	2	FACETS	0.628	0.569	0.69	0.628	0.569	0.69	SUBCLONAL	1	TRUE	1	0.462863161407364	2		753	881	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263973	104263974	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776579	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	29	193	1	ENST00000369902.3:c.71dup	p.Ala25GlyfsTer23	p.A25Gfs*23	ENST00000369902	NM_016169.3	22	gcc/gCcc	1/12	1	2	FACETS	0.608	0.492	0.739	0.608	0.492	0.739	SUBCLONAL	1	TRUE	1	0.462863161407364	2		194	206	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94910926	94910926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145434950	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	122	656	1	ENST00000536441.1:c.1204C>T	p.Arg402Cys	p.R402C	ENST00000536441	NM_144665.3	402	Cgc/Tgc	8/10	1	2	FACETS	0.798	0.722	0.877	0.798	0.722	0.877	SUBCLONAL	1	TRUE	1	0.462863161407364	2		657	661	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998796	100998796	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	46	548	0	ENST00000325455.5:c.1006G>A	p.Ala336Thr	p.A336T	ENST00000325455	NM_001202474.3	336	Gcc/Acc	1/8	1	2	FACETS	0.348	0.293	0.409	0.348	0.293	0.409	SUBCLONAL	1	TRUE	1	0.462863161407364	2		548	571	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195839	102195839	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	79	527	1	ENST00000263464.3:c.599G>T	p.Gly200Val	p.G200V	ENST00000263464	NM_001165.4	200	gGa/gTa	2/9	1	2	FACETS	0.636	0.56	0.717	0.636	0.56	0.717	SUBCLONAL	1	TRUE	1	0.462863161407364	2		528	537	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1036330	1036330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1352571686	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	308	610	0	ENST00000358495.3:c.448G>A	p.Gly150Arg	p.G150R	ENST00000358495	NM_134424.2	150	Ggg/Agg	6/12	0.10476255909246	3	FACETS	0.774	0.73	0.818			1	INDETERMINATE	2	TRUE	NA	0.462863161407364	3		610	1059	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	163	735	2	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	0.312597531751273	3	FACETS	0.664	0.607	0.723	0.332	0.303	0.362	SUBCLONAL	1	TRUE	1	0.462863161407364	3		737	1307	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486569	56486569	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	289	602	0	ENST00000267101.3:c.1148A>G	p.Lys383Arg	p.K383R	ENST00000267101	NM_001982.3	383	aAg/aGg	10/28	0.312597531751273	3	FACETS	0.796	0.75	0.843	0.796	0.75	0.843	SUBCLONAL	2	TRUE	1	0.462863161407364	3		602	966	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989087	41989087	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	86	561	1	ENST00000219905.7:c.1879C>T	p.Arg627Ter	p.R627*	ENST00000219905	NM_001164273.1	627	Cga/Tga	3/24	1	2	FACETS	0.659	0.584	0.739	0.659	0.584	0.739	SUBCLONAL	1	TRUE	1	0.462863161407364	2		562	564	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000305	42000305	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1272090898	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	60	474	0	ENST00000219905.7:c.2324C>T	p.Ala775Val	p.A775V	ENST00000219905	NM_001164273.1	775	gCg/gTg	7/24	1	2	FACETS	0.656	0.568	0.752	0.656	0.568	0.752	SUBCLONAL	1	TRUE	1	0.462863161407364	2		474	395	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2097756	2097756	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	33	541	0	ENST00000219066.1:c.93del	p.Cys32ValfsTer24	p.C32Vfs*24	ENST00000219066	NM_002528.5	31	ggG/gg	1/6	1	2	FACETS	0.258	0.209	0.313	0.258	0.209	0.313	SUBCLONAL	1	TRUE	1	0.462863161407364	2		541	553	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660508	67660508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	88	589	0	ENST00000264010.4:c.1408C>T	p.Arg470Cys	p.R470C	ENST00000264010	NM_006565.3	470	Cgt/Tgt	8/12	1	2	FACETS	0.463	0.409	0.52	0.463	0.409	0.52	SUBCLONAL	1	TRUE	1	0.462863161407364	2		589	822	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347765	89347765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368667754	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	101	565	0	ENST00000301030.4:c.5185G>A	p.Ala1729Thr	p.A1729T	ENST00000301030	NM_001256183.1	1729	Gcc/Acc	9/13	1	2	FACETS	0.701	0.627	0.778	0.701	0.627	0.778	SUBCLONAL	1	TRUE	1	0.462863161407364	2		565	623	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964935	15964935	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	112	686	0	ENST00000268712.3:c.5661del	p.Pro1888GlnfsTer11	p.P1888Qfs*11	ENST00000268712	NM_006311.3	1887	ttT/tt	37/46	1	2	FACETS	0.685	0.616	0.757	0.685	0.616	0.757	SUBCLONAL	1	TRUE	1	0.462863161407364	2		686	707	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	127	734	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.698	0.633	0.767	0.698	0.633	0.767	SUBCLONAL	1	TRUE	1	0.462863161407364	2		734	786	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	88	595	4	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	0.64	0.568	0.717	0.64	0.568	0.717	SUBCLONAL	1	TRUE	1	0.462863161407364	2		599	594	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857255	78857255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765037698	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	108	608	2	ENST00000306801.3:c.1621G>A	p.Val541Met	p.V541M	ENST00000306801	NM_020761.2	541	Gtg/Atg	15/34	1	2	FACETS	0.609	0.547	0.676	0.609	0.547	0.676	SUBCLONAL	1	TRUE	1	0.462863161407364	2		610	766	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214871	36214871	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	329	723	5	ENST00000222270.7:c.3302del	p.Pro1101LeufsTer81	p.P1101Lfs*81	ENST00000222270	NM_014727.1	1099	ggC/gg	8/37	0.323146652930953	3	FACETS	0.83	0.785	0.875	0.83	0.785	0.875	CLONAL	2	TRUE	1	0.462863161407364	3		728	1055	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	157	408	0	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	0.323146652930953	3	FACETS	0.851	0.785	0.918	0.851	0.785	0.918	CLONAL	2	TRUE	1	0.462863161407364	3		408	491	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467200	25467200	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	30	479	1	ENST00000264709.3:c.1675del	p.Cys559AlafsTer92	p.C559Afs*92	ENST00000264709	NM_175629.2	559	Tgc/gc	15/23	1	2	FACETS	0.249	0.2	0.305	0.249	0.2	0.305	SUBCLONAL	1	TRUE	1	0.462863161407364	2		480	521	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128030517	128030517	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	120	543	2	ENST00000285398.2:c.1751C>T	p.Thr584Met	p.T584M	ENST00000285398	NM_000122.1	584	aCg/aTg	11/15	1	2	FACETS	0.779	0.704	0.857	0.779	0.704	0.857	SUBCLONAL	1	TRUE	1	0.462863161407364	2		545	666	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610562	215610562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146946984	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	34	573	0	ENST00000260947.4:c.1694G>A	p.Arg565His	p.R565H	ENST00000260947	NM_000465.2	565	cGt/cAt	8/11	1	2	FACETS	0.234	0.19	0.283	0.234	0.19	0.283	SUBCLONAL	1	TRUE	1	0.462863161407364	2		573	629	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662544	227662544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756485509	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	43	522	0	ENST00000305123.5:c.911G>A	p.Arg304His	p.R304H	ENST00000305123	NM_005544.2	304	cGc/cAc	1/2	1	2	FACETS	0.311	0.26	0.368	0.311	0.26	0.368	SUBCLONAL	1	TRUE	1	0.462863161407364	2		522	597	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715612	30715612	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1559467821	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	24	346	0	ENST00000295754.5:c.1270T>C	p.Tyr424His	p.Y424H	ENST00000295754	NM_003242.5	424	Tac/Cac	5/7	1	2	FACETS	0.26	0.203	0.325	0.26	0.203	0.325	SUBCLONAL	1	TRUE	1	0.462863161407364	2		346	399	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37038119	37038119	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63750867	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	48	244	0	ENST00000231790.2:c.129del	p.Lys43AsnfsTer7	p.K43Nfs*7	ENST00000231790	NM_000249.3	42	gcA/gc	2/19	1	2	FACETS	0.795	0.677	0.922	0.795	0.677	0.922	CLONAL	1	TRUE	1	0.462863161407364	2		244	261	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37091981	37091981	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	92	516	0	ENST00000231790.2:c.2109del	p.Val704CysfsTer79	p.V704Cfs*79	ENST00000231790	NM_000249.3	703	gAa/ga	19/19	1	2	FACETS	0.67	0.597	0.749	0.67	0.597	0.749	SUBCLONAL	1	TRUE	1	0.462863161407364	2		516	593	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723037	49723037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767971831	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	72	300	0	ENST00000449682.2:c.1379G>A	p.Arg460Gln	p.R460Q	ENST00000449682	NM_020998.3	460	cGa/cAa	11/18	1	2	FACETS	0.741	0.65	0.838	0.741	0.65	0.838	SUBCLONAL	1	TRUE	1	0.462863161407364	2		300	420	SUCCESS
APC	324	MSKCC	GRCh37	5	112170823	112170823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1273594465	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	85	606	1	ENST00000257430.4:c.1919G>A	p.Arg640Gln	p.R640Q	ENST00000257430	NM_000038.5	640	cGg/cAg	15/16	1	2	FACETS	0.671	0.595	0.753	0.671	0.595	0.753	SUBCLONAL	1	TRUE	1	0.462863161407364	2		607	547	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910371	29910372	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	37	471	0	ENST00000376809.5:c.46dup	p.Ala16GlyfsTer83	p.A16Gfs*83	ENST00000376809	NM_002116.7	14	tcg/tcGg	1/8	1	2	FACETS	0.33	0.272	0.396	0.33	0.272	0.396	SUBCLONAL	1	TRUE	1	0.462863161407364	2		471	484	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31939801	31939801	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	127	659	0	ENST00000375333.2:c.28G>A	p.Asp10Asn	p.D10N	ENST00000375333	NM_032454.1	10	Gat/Aat	1/8	1	2	FACETS	0.653	0.592	0.718	0.653	0.592	0.718	SUBCLONAL	1	TRUE	1	0.462863161407364	2		659	840	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287213	33287213	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	39	617	0	ENST00000374542.5:c.1884del	p.Cys629AlafsTer16	p.C629Afs*16	ENST00000374542	NM_001141970.1	628	ccC/cc	6/8	1	2	FACETS	0.238	0.197	0.285	0.238	0.197	0.285	SUBCLONAL	1	TRUE	1	0.462863161407364	2		617	707	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935615	13935615	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	45	564	0	ENST00000405192.2:c.1241A>T	p.Asp414Val	p.D414V	ENST00000405192	NM_001163147.1	414	gAc/gTc	12/12	0.323146652930953	3	FACETS	0.302	0.252	0.356	0.151	0.126	0.178	SUBCLONAL	1	TRUE	1	0.462863161407364	3		564	794	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508395	106508395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747797529	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	99	282	0	ENST00000359195.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000359195	NM_002649.2	130	cGg/cAg	2/11	0.323146652930953	3	FACETS	1	0.98	1	0.691	0.622	0.764	CLONAL	1	TRUE	1	0.462863161407364	3		282	381	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508725	106508725	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	102	574	2	ENST00000359195.3:c.723del	p.Gly242AlafsTer17	p.G242Afs*17	ENST00000359195	NM_002649.2	240	aCc/ac	2/11	0.323146652930953	3	FACETS	0.622	0.555	0.692	0.311	0.277	0.346	SUBCLONAL	1	TRUE	1	0.462863161407364	3		576	873	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	96	712	0	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	0.323146652930953	3	FACETS	0.615	0.548	0.688	0.308	0.274	0.344	SUBCLONAL	1	TRUE	1	0.462863161407364	3		712	830	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494163	140494163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	291	862	0	ENST00000288602.6:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000288602	NM_004333.4	362	cGa/cAa	8/18	0.323146652930953	3	FACETS	1	0.993	1	0.714	0.671	0.757	CLONAL	1	TRUE	1	0.462863161407364	3		862	1085	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786922	135786922	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375956049	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	89	473	0	ENST00000298552.3:c.947G>A	p.Arg316Gln	p.R316Q	ENST00000298552	NM_001162426.1	316	cGg/cAg	10/23	1	2	FACETS	0.612	0.543	0.686	0.612	0.543	0.686	SUBCLONAL	1	TRUE	1	0.462863161407364	2		473	628	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938475	44938475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	29	268	0	ENST00000377967.4:c.3023C>T	p.Ala1008Val	p.A1008V	ENST00000377967	NM_021140.2	1008	gCa/gTa	20/29	0.159485717465811	3	FACETS	0.43	0.345	0.526			1	INDETERMINATE	1	TRUE	NA	0.462863161407364	3		268	359	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411366	63411366	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	224	353	0	ENST00000330258.3:c.1801C>T	p.Arg601Ter	p.R601*	ENST00000330258	NM_152424.3	601	Cga/Tga	2/2	0.159485717465811	3	FACETS	0.849	0.8	0.898			1	INDETERMINATE	3	TRUE	NA	0.462863161407364	3		353	468	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411777	63411777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767567473	NA	P-0033503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	235	402	1	ENST00000330258.3:c.1390G>A	p.Ala464Thr	p.A464T	ENST00000330258	NM_152424.3	464	Gcc/Acc	2/2	0.159485717465811	3	FACETS	1	0.987	1			1	INDETERMINATE	2	TRUE	NA	0.462863161407364	3		403	533	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593431	55593431	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs72550822	NA	P-0033505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	79	627	0	ENST00000288135.5:c.1588G>A	p.Val530Ile	p.V530I	ENST00000288135	NM_000222.2	530	Gta/Ata	10/21	1	2	FACETS	0.463	0.408	0.521	0.463	0.408	0.521	SUBCLONAL	1	TRUE	1	0.667169899876436	2		627	512	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170742	7170742	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	220	785	0	ENST00000302850.5:c.1289T>C	p.Leu430Ser	p.L430S	ENST00000302850	NM_000208.2	430	tTg/tCg	6/22	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.667169899876436	2		785	585	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604685	55604685	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	143	548	0	ENST00000288135.5:c.2893T>C	p.Ser965Pro	p.S965P	ENST00000288135	NM_000222.2	965	Tcc/Ccc	21/21	0.608839003096943	3	FACETS	0.992	0.908	1	0.496	0.454	0.54	CLONAL	1	TRUE	1	0.642617660880543	3		548	593	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250525	26250525	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	115	583	0	ENST00000446824.2:c.309del	p.Leu104SerfsTer15	p.L104Sfs*15	ENST00000446824	NM_021018.2	103	ggG/gg	1/1	0.642617660880543	3	FACETS	0.908	0.821	0.998	0.454	0.41	0.499	CLONAL	1	TRUE	1	0.642617660880543	3		583	521	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855291	76855291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0033507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	184	191	0	ENST00000373344.5:c.5698-2A>C		p.X1900_splice	ENST00000373344	NM_000489.3	1900			0.596220668795935	2	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.642617660880543	2		191	230	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0033508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	110	462	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.172437819929541	3	FACETS	0.773	0.695	0.856	0.258	0.231	0.286	INDETERMINATE	1	TRUE	0	0.484188999357354	3		462	730	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0033508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	17	308	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.394817088874438	1	FACETS	0.142	0.105	0.186	0.142	0.105	0.186	SUBCLONAL	1	TRUE	0	0.484188999357354	1		308	375	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514077	125514077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	167	563	0	ENST00000428830.2:c.1015G>A	p.Val339Ile	p.V339I	ENST00000428830	NM_001114121.2	339	Gta/Ata	10/14	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.484188999357354	2		563	532	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	27	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.288791260222458	2		248	163	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100995	41100995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	81	620	0	ENST00000373198.4:c.1361C>T	p.Pro454Leu	p.P454L	ENST00000373198	NM_133170.3	454	cCc/cTc	8/32	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.288791260222458	2		620	526	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039471	49039471	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	82	551	0	ENST00000267163.4:c.2456del	p.Leu819ArgfsTer7	p.L819Rfs*7	ENST00000267163	NM_000321.2	819	cTg/cg	23/27	0.187457547948006	2	FACETS	1	0.927	1	0.534	0.472	0.6	CLONAL	1	TRUE	0	0.288791260222458	2		551	532	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943671	9943671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	53	652	0	ENST00000330684.3:c.1270C>T	p.Pro424Ser	p.P424S	ENST00000330684	NM_001134407.1	424	Ccc/Tcc	5/13	1	2	FACETS	0.899	0.765	1	0.899	0.765	1	CLONAL	1	FALSE	1	0.160810792193266	2		652	733	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0033516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	33	261	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.263765975685588	3	FACETS	0.856	0.698	1	0.428	0.349	0.516	CLONAL	1	TRUE	1	0.263765975685588	3		261	331	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0033516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	127	484	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.263765975685588	3	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	1	0.263765975685588	3		484	527	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	227	774	0	ENST00000269305.4:c.880del	p.Glu294SerfsTer51	p.E294Sfs*51	ENST00000269305	NM_001126112.2	294	Gag/ag	8/11	0.261100649602214	2	FACETS	0.997	0.931	1	0.997	0.931	1	CLONAL	2	TRUE	0	0.263765975685588	2		774	863	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920381	114920381	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	134	538	0	ENST00000543371.1:c.1322C>A	p.Ala441Glu	p.A441E	ENST00000543371	NM_001198531.1	441	gCa/gAa	13/14	0.21171079463315	4	FACETS	0.888	0.808	0.972	0.888	0.808	0.972	CLONAL	2	TRUE	2	0.263765975685588	4		538	723	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961256	41961256	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	91	624	0	ENST00000219905.7:c.164C>A	p.Ser55Ter	p.S55*	ENST00000219905	NM_001164273.1	55	tCa/tAa	2/24	0.21171079463315	4	FACETS	0.983	0.872	1	0.492	0.436	0.552	CLONAL	1	TRUE	2	0.263765975685588	4		624	887	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098751	2098752	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GA	GA	-	rs137854117	NA	P-0033516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	143	568	0	ENST00000219476.3:c.138_138+1del		p.LR45fs	ENST00000219476	NM_000548.3	45	ctGAga/ctga	2/42	0.261100649602214	2	FACETS	0.855	0.782	0.931	0.855	0.782	0.931	CLONAL	2	TRUE	0	0.263765975685588	2		568	634	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247344	153247344	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	163	356	1	ENST00000281708.4:c.1458G>T	p.Trp486Cys	p.W486C	ENST00000281708	NM_033632.3	486	tgG/tgT	10/12	0.263765975685588	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	3	TRUE	0	0.263765975685588	3		357	453	SUCCESS
APC	324	MSKCC	GRCh37	5	112174511	112174511	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs962456431	NA	P-0033516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	86	376	0	ENST00000257430.4:c.3220A>G	p.Thr1074Ala	p.T1074A	ENST00000257430	NM_000038.5	1074	Act/Gct	16/16	0.263765975685588	3	FACETS	0.77	0.684	0.862	0.77	0.684	0.862	SUBCLONAL	2	TRUE	1	0.263765975685588	3		376	479	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	37	248	0				ENST00000310581	NM_198253.2	-/1132			0.387137839844022	1	FACETS	0.701	0.583	0.831	0.701	0.583	0.831	SUBCLONAL	1	TRUE	0	0.388498367003906	1		248	219	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0033517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	110	464	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.388498367003906	1	FACETS	0.996	0.9	1	0.996	0.9	1	CLONAL	1	TRUE	0	0.388498367003906	1		465	458	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164218	47164218	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	102	521	0	ENST00000409792.3:c.1908del	p.Phe636LeufsTer6	p.F636Lfs*6	ENST00000409792	NM_014159.6	636	ttT/tt	3/21	1	2	FACETS	0.991	0.889	1	0.991	0.889	1	CLONAL	1	TRUE	1	0.388498367003906	2		521	530	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820300	139820300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1019096282	NA	P-0033517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	52	736	0	ENST00000247668.2:c.1453G>A	p.Val485Met	p.V485M	ENST00000247668	NM_021138.3	485	Gtg/Atg	11/11	1	2	FACETS	0.436	0.371	0.508	0.436	0.371	0.508	SUBCLONAL	1	TRUE	1	0.388498367003906	2		736	614	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0033523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	501	750	2	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	0.539942508193578	2		752	834	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251033	99251037	+	frameshift_variant	Frame_Shift_Del	DEL	TACAA	TACAA	-	novel	NA	P-0033523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	109	427	0	ENST00000268035.6:c.337_341del	p.Tyr113LeufsTer30	p.Y113Lfs*30	ENST00000268035	NM_000875.3	113	TACAAc/c	2/21	0.467139962234018	4	FACETS	0.835	0.75	0.924			1	CLONAL	1	TRUE	NA	0.539942508193578	4		427	745	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37665979	37665979	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	279	403	0	ENST00000447079.4:c.2631T>G	p.Asp877Glu	p.D877E	ENST00000447079	NM_015083.1	877	gaT/gaG	7/14	0.538692769595601	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.539942508193578	2		403	493	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066656	94066656	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0033523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	95	462	0	ENST00000369303.4:c.1103T>A	p.Leu368Ter	p.L368*	ENST00000369303	NM_004440.3	368	tTg/tAg	5/17	0.539942508193578	3	FACETS	0.631	0.562	0.705	0.316	0.281	0.353	SUBCLONAL	1	TRUE	1	0.539942508193578	3		462	708	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778096	135778096	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203671	NA	P-0033525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	196	630	0	ENST00000298552.3:c.2287C>T	p.Gln763Ter	p.Q763*	ENST00000298552	NM_001162426.1	763	Cag/Tag	18/23	0.230400979197499	2	FACETS	0.803	0.744	0.865	0.803	0.744	0.865	CLONAL	2	TRUE	0	0.260637493585234	2		630	936	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807460	36807460	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775387498	NA	P-0033525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	123	703	0	ENST00000373129.3:c.1204C>T	p.Arg402Trp	p.R402W	ENST00000373129	NM_032017.1	402	Cgg/Tgg	12/12	0.237010365295514	3	FACETS	0.904	0.815	0.998	0.301	0.271	0.333	CLONAL	1	TRUE	0	0.260637493585234	3		703	1180	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562837	95562837	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	159	381	0	ENST00000393063.1:c.4420A>T	p.Thr1474Ser	p.T1474S	ENST00000393063	NM_030621.3	1474	Acc/Tcc	24/28	0.260637493585234	4	FACETS	1	0.956	1	0.53	0.487	0.575	CLONAL	2	TRUE	0	0.260637493585234	4		381	725	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892267	9892267	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	76	457	0	ENST00000330684.3:c.2223G>C	p.Arg741Ser	p.R741S	ENST00000330684	NM_001134407.1	741	agG/agC	11/13	0.230400979197499	2	FACETS	0.815	0.714	0.923	0.407	0.357	0.462	CLONAL	1	TRUE	0	0.260637493585234	2		457	716	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273988	10273988	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1179489169	NA	P-0033525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	144	766	0	ENST00000330684.3:c.281G>T	p.Arg94Leu	p.R94L	ENST00000330684	NM_001134407.1	94	cGc/cTc	2/13	0.230400979197499	2	FACETS	1	0.94	1	0.52	0.474	0.569	CLONAL	1	TRUE	0	0.260637493585234	2		766	1062	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992326	72992326	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	102	810	0	ENST00000268489.5:c.1719C>G	p.Asn573Lys	p.N573K	ENST00000268489	NM_006885.3	573	aaC/aaG	2/10	0.260637493585234	3	FACETS	0.734	0.655	0.819	0.367	0.327	0.41	SUBCLONAL	1	TRUE	1	0.260637493585234	3		810	1205	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578209	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0033525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	216	650	0	ENST00000269305.4:c.640_641del	p.His214Ter	p.H214*	ENST00000269305	NM_001126112.2	214	CAt/t	6/11	0.230400979197499	2	FACETS	0.88	0.818	0.943	0.88	0.818	0.943	CLONAL	2	TRUE	0	0.260637493585234	2		650	942	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143485	30143485	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	34	241	0	ENST00000389048.3:c.41T>C	p.Leu14Pro	p.L14P	ENST00000389048	NM_004304.4	14	cTt/cCt	1/29	0.216044058915862	3	FACETS	0.7	0.572	0.845	0.35	0.286	0.423	SUBCLONAL	1	TRUE	1	0.260637493585234	3		241	421	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31407021	31407021	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1174002360	NA	P-0033525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	80	495	0	ENST00000344624.3:c.3886C>T	p.Arg1296Ter	p.R1296*	ENST00000344624		1296	Cga/Tga	31/33	0.225827704816487	5	FACETS	0.803	0.704	0.909	0.201	0.176	0.228	CLONAL	1	TRUE	1	0.260637493585234	5		495	1064	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627301	86627301	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	48	346	0	ENST00000274376.6:c.676G>C	p.Val226Leu	p.V226L	ENST00000274376	NM_002890.2	226	Gtt/Ctt	2/25	1	2	FACETS	0.696	0.588	0.815	0.696	0.588	0.815	SUBCLONAL	1	TRUE	1	0.260637493585234	2		346	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0033529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	42	742	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.712	0.593	0.846	0.712	0.593	0.846	SUBCLONAL	1	TRUE	1	0.13	2		743	907	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512196	120512196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	81	524	1	ENST00000256646.2:c.1046C>T	p.Pro349Leu	p.P349L	ENST00000256646	NM_024408.3	349	cCa/cTa	6/34	1	2	FACETS	0.798	0.702	0.901	1	0.979	1	CLONAL	2	TRUE	1	0.13	2		525	781	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21968242	21968242	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0033529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	26	441	0	ENST00000304494.5:c.458-1G>T		p.X153_splice	ENST00000304494	NM_000077.4	153			0.110541157655236	0	FACETS	0.806	0.637	0.999			1	CLONAL	1	TRUE	0	0.13	0		441	432	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0033553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	165	270	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.233795743999249	2	FACETS	1	0.988	1	0.645	0.603	0.687	INDETERMINATE	1	TRUE	0	0.784380734103826	2		270	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579349	7579349	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1567555667	NA	P-0033553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	316	536	0	ENST00000269305.4:c.338T>G	p.Phe113Cys	p.F113C	ENST00000269305	NM_001126112.2	113	tTc/tGc	4/11	0.239769300737578	4	FACETS	0.922	0.874	0.969	0.922	0.874	0.969	INDETERMINATE	2	TRUE	2	0.784380734103826	4		536	780	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0033553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	308	460	0	ENST00000269305.4:c.559+1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.239769300737578	4	FACETS	0.926	0.878	0.974	0.926	0.878	0.974	INDETERMINATE	2	TRUE	2	0.784380734103826	4		460	757	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572011	64572011	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	174	568	0	ENST00000312049.6:c.1628C>T	p.Ser543Leu	p.S543L	ENST00000312049	NM_130799.2	543	tCa/tTa	10/10	0.239769300737578	4	FACETS	0.712	0.654	0.772	0.356	0.327	0.386	INDETERMINATE	1	TRUE	2	0.784380734103826	4		568	1112	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938827	76938827	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	308	576	0	ENST00000373344.5:c.1921G>T	p.Glu641Ter	p.E641*	ENST00000373344	NM_000489.3	641	Gaa/Taa	9/35	0.110690931745195	5	FACETS	1	0.951	1	0.67	0.634	0.707	INDETERMINATE	2	TRUE	2	0.784380734103826	5		576	850	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034454	123034454	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	128	362	0	ENST00000355640.3:c.1211A>G	p.Tyr404Cys	p.Y404C	ENST00000355640		404	tAt/tGt	6/7	0.110690931745195	5	FACETS	1	0.98	1	0.426	0.387	0.466	INDETERMINATE	1	TRUE	2	0.784380734103826	5		362	556	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	92	697	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.125493685349653	3	FACETS	0.969	0.863	1	0.484	0.431	0.541	INDETERMINATE	1	FALSE	1	0.397400487925434	3		697	573	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511270	157511270	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	61	360	1	ENST00000346085.5:c.3788G>T	p.Gly1263Val	p.G1263V	ENST00000346085	NM_020732.3	1263	gGc/gTc	15/20	1	2	FACETS	0.66	0.571	0.757	0.66	0.571	0.757	SUBCLONAL	1	FALSE	1	0.397400487925434	2		361	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0033558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	22	770	0	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	0.198534803130906	4	FACETS	0.405	0.312	0.513	0.202	0.156	0.257	SUBCLONAL	1	TRUE	2	0.22	4		770	603	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117656	70117656	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	36	632	0	ENST00000245479.2:c.124G>T	p.Asp42Tyr	p.D42Y	ENST00000245479	NM_000346.3	42	Gac/Tac	1/3	0.198534803130906	4	FACETS	1	0.909	1	0.585	0.482	0.7	CLONAL	1	TRUE	2	0.22	4		632	341	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117664	70117664	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	40	624	0	ENST00000245479.2:c.132G>C	p.Glu44Asp	p.E44D	ENST00000245479	NM_000346.3	44	gaG/gaC	1/3	0.198534803130906	4	FACETS	1	0.929	1	0.616	0.513	0.73	CLONAL	1	TRUE	2	0.22	4		624	360	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523342	176523342	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1199129089	NA	P-0033567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	378	642	1	ENST00000292408.4:c.1999A>G	p.Thr667Ala	p.T667A	ENST00000292408	NM_213647.1	667	Aca/Gca	15/18	0.605008641302344	1	FACETS	0.987	0.941	1	0.987	0.941	1	CLONAL	1	TRUE	0	0.605217906433755	1		643	883	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134277	11134277	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	230	400	0	ENST00000358026.2:c.2943G>T	p.Lys981Asn	p.K981N	ENST00000358026	NM_001128849.1	981	aaG/aaT	20/36	0.605217906433755	1	FACETS	0.962	0.905	1	0.962	0.905	1	CLONAL	1	TRUE	0	0.605217906433755	1		400	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0033567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	295	463	0	ENST00000269305.4:c.560-2A>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.605008641302344	1	FACETS	0.987	0.935	1	0.987	0.935	1	CLONAL	1	TRUE	0	0.605217906433755	1		463	689	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990615	7990615	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs143526675	NA	P-0033567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	208	381	0	ENST00000319144.4:c.146C>T	p.Ala49Val	p.A49V	ENST00000319144	NM_001139.2	49	gCg/gTg	1/15	0.605008641302344	1	FACETS	0.901	0.844	0.959	0.901	0.844	0.959	CLONAL	1	TRUE	0	0.605217906433755	1		381	532	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780069	9780069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762320758	NA	P-0033567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	329	530	2	ENST00000377346.4:c.1333G>A	p.Val445Ile	p.V445I	ENST00000377346	NM_005026.3	445	Gtc/Atc	10/24	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.605217906433755	2		532	1051	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466485	120466485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	289	567	1	ENST00000256646.2:c.4634G>A	p.Gly1545Asp	p.G1545D	ENST00000256646	NM_024408.3	1545	gGt/gAt	26/34	1	2	FACETS	0.948	0.893	1	0.948	0.893	1	CLONAL	1	TRUE	1	0.605217906433755	2		568	1007	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942647	71942647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	120	447	0	ENST00000298229.2:c.1603G>A	p.Ala535Thr	p.A535T	ENST00000298229	NM_001567.3	535	Gcc/Acc	13/28	0.588428426306579	1	FACETS	0.401	0.362	0.441	0.401	0.362	0.441	SUBCLONAL	1	TRUE	0	0.605217906433755	1		447	690	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552728	18552728	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	227	480	2	ENST00000266497.5:c.2139G>T	p.Leu713Phe	p.L713F	ENST00000266497		713	ttG/ttT	14/31	1	2	FACETS	0.932	0.87	0.995	0.932	0.87	0.995	CLONAL	1	TRUE	1	0.605217906433755	2		482	805	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589386	28589386	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	167	309	0	ENST00000241453.7:c.2661T>A	p.Asn887Lys	p.N887K	ENST00000241453	NM_004119.2	887	aaT/aaA	22/24	0.605008641302344	1	FACETS	0.948	0.882	1	0.948	0.882	1	CLONAL	1	TRUE	0	0.605217906433755	1		309	406	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680709	88680709	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	307	591	0	ENST00000360948.2:c.548A>G	p.Asn183Ser	p.N183S	ENST00000360948	NM_001012338.2	183	aAc/aGc	6/19	0.605008641302344	1	FACETS	0.938	0.89	0.988	0.938	0.89	0.988	CLONAL	1	TRUE	0	0.605217906433755	1		591	754	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437588	56437588	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	167	328	0	ENST00000407977.2:c.874C>T	p.His292Tyr	p.H292Y	ENST00000407977		292	Cat/Tat	8/10	1	2	FACETS	0.759	0.699	0.821	0.759	0.699	0.821	SUBCLONAL	1	TRUE	1	0.605217906433755	2		328	727	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513217	106513217	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	161	278	0	ENST00000359195.3:c.2121A>T	p.Arg707Ser	p.R707S	ENST00000359195	NM_002649.2	707	agA/agT	4/11	0.605008641302344	1	FACETS	0.916	0.85	0.983	0.916	0.85	0.983	CLONAL	1	TRUE	0	0.605217906433755	1		278	405	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	84	697	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.119056635434618	3	FACETS	0.803	0.71	0.902	0.803	0.71	0.902	INDETERMINATE	2	TRUE	1	0.201294200141032	3		697	572	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0033568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	43	528	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.8	0.669	0.946	0.8	0.669	0.946	CLONAL	1	TRUE	1	0.201294200141032	2		528	534	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0033568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	54	589	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	1	2	FACETS	0.864	0.737	1	0.864	0.737	1	CLONAL	1	TRUE	1	0.201294200141032	2		589	621	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0033568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	26	207	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.119056635434618	3	FACETS	0.758	0.6	0.939	0.379	0.3	0.47	INDETERMINATE	1	TRUE	1	0.201294200141032	3		207	375	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0033568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	34	539	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	1	2	FACETS	0.627	0.511	0.757	0.627	0.511	0.757	SUBCLONAL	1	TRUE	1	0.201294200141032	2		539	539	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604750	48604750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	74	308	0	ENST00000342988.3:c.1572G>T	p.Trp524Cys	p.W524C	ENST00000342988	NM_005359.5	524	tgG/tgT	12/12	0.188218995650016	2	FACETS	0.857	0.753	0.968	0.857	0.753	0.968	CLONAL	2	TRUE	0	0.201294200141032	2		308	429	SUCCESS
AR	367	MSKCC	GRCh37	X	66943658	66943658	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	43	386	0	ENST00000374690.3:c.2738A>G	p.Lys913Arg	p.K913R	ENST00000374690	NM_000044.3	913	aAg/aGg	8/8	1	2	FACETS	0.737	0.616	0.871	0.737	0.616	0.871	SUBCLONAL	1	TRUE	1	0.201294200141032	2		386	580	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119790	70119791	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGC	novel	NA	P-0033568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	108	567	0	ENST00000245479.2:c.794_797dup	p.Pro267AlafsTer30	p.P267Afs*30	ENST00000245479	NM_000346.3	264	-/CAGC	3/3	0.201294200141032	1	FACETS	0.95	0.856	1	1	0.988	1	CLONAL	2	TRUE	0	0.201294200141032	1		567	508	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934753	49934753	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375003602	NA	P-0033568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	71	641	0	ENST00000296474.3:c.2143C>T	p.Arg715Trp	p.R715W	ENST00000296474	NM_002447.2	715	Cgg/Tgg	7/20	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.201294200141032	2		641	656	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177981	56177981	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	41	363	0	ENST00000399503.3:c.2957del	p.Pro986LeufsTer96	p.P986Lfs*96	ENST00000399503	NM_005921.1	985	aCc/ac	14/20	0.119056635434618	3	FACETS	0.764	0.635	0.907	0.382	0.317	0.454	INDETERMINATE	1	TRUE	1	0.201294200141032	3		363	587	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760529	133760529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371656033	NA	P-0033568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	57	744	0	ENST00000318560.5:c.2852C>T	p.Pro951Leu	p.P951L	ENST00000318560	NM_005157.4	951	cCg/cTg	11/11	0.201294200141032	2	FACETS	0.882	0.756	1	0.441	0.378	0.51	CLONAL	1	TRUE	0	0.201294200141032	2		744	642	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216396	7216397	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0033574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	28	633	0	ENST00000380728.2:c.851dup	p.Leu285ThrfsTer?	p.L285Tfs*?	ENST00000380728		284	gga/ggGa	10/11	0.63340609246221	1	FACETS	0.114	0.09	0.141	0.114	0.09	0.141	SUBCLONAL	1	TRUE	0	0.63340609246221	1		633	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs786203436	NA	P-0033577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	42	760	0	ENST00000269305.4:c.487T>A	p.Tyr163Asn	p.Y163N	ENST00000269305	NM_001126112.2	163	Tac/Aac	5/11	0.416829191569302	1	FACETS	0.269	0.224	0.319	0.269	0.224	0.319	SUBCLONAL	1	TRUE	0	0.416829191569302	1		760	593	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902592	1902592	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	250	699	0	ENST00000382891.5:c.211C>G	p.Leu71Val	p.L71V	ENST00000382891	NM_133335.3	71	Ctg/Gtg	2/22	1	2	FACETS	0.964	0.903	1	0.964	0.903	1	CLONAL	1	TRUE	1	0.542543538019082	2		699	956	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407567	407567	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	85	382	1	ENST00000380956.4:c.1325G>A	p.Arg442Lys	p.R442K	ENST00000380956	NM_001195286.1	442	aGa/aAa	9/9	0.440450034632401	4	FACETS	0.395	0.348	0.446			1	SUBCLONAL	1	TRUE	NA	0.542543538019082	4		383	1224	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0033579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	221	597	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	0.542543538019082	2		597	771	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0033581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	167	454	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.314137387333195	3	FACETS	0.87	0.802	0.941	0.87	0.802	0.941	CLONAL	2	TRUE	1	0.32132012972338	3		454	693	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0033581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	45	373	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	1	2	FACETS	0.629	0.529	0.74	0.629	0.529	0.74	SUBCLONAL	1	TRUE	1	0.32132012972338	2		373	445	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951994	178951994	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	70	521	0	ENST00000263967.3:c.3049G>C	p.Asp1017His	p.D1017H	ENST00000263967	NM_006218.2	1017	Gat/Cat	21/21	1	2	FACETS	0.692	0.603	0.787	0.692	0.603	0.787	SUBCLONAL	1	TRUE	1	0.32132012972338	2		521	630	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990375	81990375	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	68	548	0	ENST00000359376.3:c.3646C>G	p.Leu1216Val	p.L1216V	ENST00000359376	NM_002661.3	1216	Ctg/Gtg	32/33	1	2	FACETS	0.647	0.563	0.739	0.647	0.563	0.739	SUBCLONAL	1	TRUE	1	0.32132012972338	2		548	654	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223667	36223667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	78	854	1	ENST00000222270.7:c.6217G>A	p.Glu2073Lys	p.E2073K	ENST00000222270	NM_014727.1	2073	Gag/Aag	28/37	1	2	FACETS	0.496	0.434	0.562	0.496	0.434	0.562	SUBCLONAL	1	TRUE	1	0.32132012972338	2		855	979	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845313	76845313	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	160	461	0	ENST00000373344.5:c.6208A>C	p.Ile2070Leu	p.I2070L	ENST00000373344	NM_000489.3	2070	Att/Ctt	27/35	0.311486028430241	3	FACETS	0.904	0.832	0.979	0.904	0.832	0.979	CLONAL	2	TRUE	1	0.32132012972338	3		461	639	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889054	76889054	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	120	388	0	ENST00000373344.5:c.4956G>T	p.Glu1652Asp	p.E1652D	ENST00000373344	NM_000489.3	1652	gaG/gaT	18/35	0.311486028430241	3	FACETS	0.89	0.808	0.975	0.89	0.808	0.975	CLONAL	2	TRUE	1	0.32132012972338	3		388	487	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	38	697	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.26572120096681	1	FACETS	0.472	0.39	0.565	0.472	0.39	0.565	SUBCLONAL	1	FALSE	0	0.26572120096681	1		697	525	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971110	21971110	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519881	NA	P-0033600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	46	349	0	ENST00000304494.5:c.248A>G	p.His83Arg	p.H83R	ENST00000304494	NM_000077.4	83	cAc/cGc	2/3	1	2	FACETS	0.626	0.527	0.736	0.626	0.527	0.736	SUBCLONAL	1	FALSE	1	0.26572120096681	2		349	553	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220489	1220489	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202134	NA	P-0033600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	80	565	0	ENST00000326873.7:c.582C>A	p.Asp194Glu	p.D194E	ENST00000326873	NM_000455.4	194	gaC/gaA	4/10	1	2	FACETS	0.675	0.593	0.764	0.675	0.593	0.764	SUBCLONAL	1	FALSE	1	0.26572120096681	2		565	892	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039620	47039620	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	64	584	0	ENST00000377604.3:c.1072C>T	p.Gln358Ter	p.Q358*	ENST00000377604	NM_001204468.1	358	Cag/Tag	11/24	1	2	FACETS	0.658	0.569	0.755	0.658	0.569	0.755	SUBCLONAL	1	FALSE	1	0.26572120096681	2		584	732	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713685	30713685	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	66	371	0	ENST00000295754.5:c.1010T>C	p.Leu337Pro	p.L337P	ENST00000295754	NM_003242.5	337	cTg/cCg	4/7	1	2	FACETS	0.992	0.862	1	0.992	0.862	1	CLONAL	1	FALSE	1	0.26572120096681	2		371	501	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144170	55144170	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	50	338	0	ENST00000257290.5:c.1999T>A	p.Ser667Thr	p.S667T	ENST00000257290	NM_006206.4	667	Tca/Aca	14/23	1	2	FACETS	0.617	0.523	0.721	0.617	0.523	0.721	SUBCLONAL	1	FALSE	1	0.26572120096681	2		338	610	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057657	180057657	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	110	864	0	ENST00000261937.6:c.298G>T	p.Glu100Ter	p.E100*	ENST00000261937	NM_182925.4	100	Gag/Tag	3/30	1	2	FACETS	0.678	0.607	0.754	0.678	0.607	0.754	SUBCLONAL	1	FALSE	1	0.26572120096681	2		864	1221	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508538	106508538	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	21	241	0	ENST00000359195.3:c.532C>A	p.Arg178Ser	p.R178S	ENST00000359195	NM_002649.2	178	Cgt/Agt	2/11	1	2	FACETS	0.48	0.37	0.61	0.48	0.37	0.61	SUBCLONAL	1	FALSE	1	0.26572120096681	2		241	329	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460540	8460540	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	50	363	0	ENST00000356435.5:c.3746C>A	p.Pro1249His	p.P1249H	ENST00000356435		1249	cCc/cAc	22/35	1	2	FACETS	0.613	0.519	0.716	0.613	0.519	0.716	SUBCLONAL	1	FALSE	1	0.26572120096681	2		363	614	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870998	12870998	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs139727620	NA	P-0033601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	270	311	0	ENST00000228872.4:c.225G>C	p.Glu75Asp	p.E75D	ENST00000228872	NM_004064.3	75	gaG/gaC	1/3	1	2	FACETS	0.948	0.898	0.999	0.948	0.898	0.999	CLONAL	1	TRUE	1	0.969883163216051	2		311	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577555	7577556	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0033601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	650	597	0	ENST00000269305.4:c.725_726delinsTT	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGC/tTT	7/11	0.969883163216051	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.969883163216051	1		597	679	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422612	49422612	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	596	474	0	ENST00000301067.7:c.14381del	p.Lys4794ArgfsTer3	p.K4794Rfs*3	ENST00000301067	NM_003482.3	4794	aAg/ag	45/54	1	2	FACETS	0.987	0.952	1	0.987	0.952	1	CLONAL	1	TRUE	1	0.969883163216051	2		474	1245	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434595	49434595	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	780	685	0	ENST00000301067.7:c.6958G>T	p.Glu2320Ter	p.E2320*	ENST00000301067	NM_003482.3	2320	Gag/Tag	31/54	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.969883163216051	2		685	1585	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444938	49444939	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	513	513	1	ENST00000301067.7:c.2527dup	p.Ser843PhefsTer5	p.S843Ffs*5	ENST00000301067	NM_003482.3	843	tcc/tTcc	10/54	1	2	FACETS	0.931	0.895	0.968	0.931	0.895	0.968	CLONAL	1	TRUE	1	0.969883163216051	2		514	1136	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379835	17379835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	1194	898	3	ENST00000359435.4:c.220C>T	p.Gln74Ter	p.Q74*	ENST00000359435	NM_001033549.1	74	Cag/Tag	2/9	0.969883163216051	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.969883163216051	1		901	1238	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607666	46607666	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745687417	NA	P-0033601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	734	745	2	ENST00000263734.3:c.1855C>T	p.Pro619Ser	p.P619S	ENST00000263734	NM_001430.4	619	Ccg/Tcg	12/16	0.49250196160546	1	FACETS	0.666	0.647	0.684	0.666	0.647	0.684	INDETERMINATE	1	TRUE	0	0.969883163216051	1		747	1171	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602799	10602799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1182	199	915	0	ENST00000171111.5:c.779G>T	p.Arg260Leu	p.R260L	ENST00000171111	NM_203500.1	260	cGa/cTa	3/6	0.250699495381064	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.250699495381064	1		915	1381	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937900	36937900	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	181	944	0	ENST00000361632.4:c.936G>T	p.Trp312Cys	p.W312C	ENST00000361632		312	tgG/tgT	7/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.250699495381064	2		944	1260	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858133	9858133	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	120	737	0	ENST00000330684.3:c.3268G>C	p.Val1090Leu	p.V1090L	ENST00000330684	NM_001134407.1	1090	Gtg/Ctg	13/13	1	2	FACETS	0.968	0.873	1	0.968	0.873	1	CLONAL	1	TRUE	1	0.250699495381064	2		737	989	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858149	9858149	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	121	715	0	ENST00000330684.3:c.3252C>A	p.Asp1084Glu	p.D1084E	ENST00000330684	NM_001134407.1	1084	gaC/gaA	13/13	1	2	FACETS	0.992	0.895	1	0.992	0.895	1	CLONAL	1	TRUE	1	0.250699495381064	2		715	973	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821601	72821642	+	inframe_deletion	In_Frame_Del	DEL	CCGCCGCCGCCGCCGCCACCGCCGCCGCCGCCGCCACTGCCA	CCGCCGCCGCCGCCGCCACCGCCGCCGCCGCCGCCACTGCCA	-	rs749325118	NA	P-0033603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	42	85	0	ENST00000268489.5:c.10533_10574del	p.Ser3513_Gly3526del	p.S3513_G3526del	ENST00000268489	NM_006885.3	3511	ggTGGCAGTGGCGGCGGCGGCGGCGGTGGCGGCGGCGGCGGCGGc/ggc	10/10	1	2	FACETS	0.991	0.84	1	1	0.971	1	CLONAL	2	TRUE	1	0.250699495381064	2		85	169	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220588	1220595	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGTTCG	CCCGTTCG	-	novel	NA	P-0033603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	143	660	0	ENST00000326873.7:c.607_614del	p.Pro203GlyfsTer60	p.P203Gfs*60	ENST00000326873	NM_000455.4	202	caCCCGTTCGcg/cacg	5/10	0.250699495381064	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.250699495381064	1		660	910	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155459	47155459	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	54	454	0	ENST00000409792.3:c.4622A>T	p.Asn1541Ile	p.N1541I	ENST00000409792	NM_014159.6	1541	aAt/aTt	5/21	1	2	FACETS	0.718	0.613	0.833	0.718	0.613	0.833	SUBCLONAL	1	TRUE	1	0.250699495381064	2		454	600	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165654	47165654	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	57	561	0	ENST00000409792.3:c.472G>T	p.Ala158Ser	p.A158S	ENST00000409792	NM_014159.6	158	Gct/Tct	3/21	1	2	FACETS	0.651	0.558	0.754	0.651	0.558	0.754	SUBCLONAL	1	TRUE	1	0.250699495381064	2		561	698	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128420028	128420028	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	131	774	0	ENST00000265960.3:c.400C>A	p.Pro134Thr	p.P134T	ENST00000265960	NM_001006617.1	134	Cca/Aca	4/12	0.250699495381064	1	FACETS	0.947	0.859	1	0.947	0.859	1	CLONAL	1	TRUE	0	0.250699495381064	1		774	965	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137325955	137325955	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	143	622	0	ENST00000481739.1:c.1143G>C	p.Lys381Asn	p.K381N	ENST00000481739	NM_002957.4	381	aaG/aaC	9/10	0.250699495381064	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.250699495381064	1		622	839	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129621	11129637	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTGTTCCATCAGAACGC	TTGTTCCATCAGAACGC	G	novel	NA	P-0033603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	97	550	0	ENST00000358026.2:c.2439-12_2443delinsG		p.X813_splice	ENST00000358026	NM_001128849.1	813		17/36	0.250699495381064	1	FACETS	0.866	0.771	0.966	0.866	0.771	0.966	CLONAL	1	TRUE	0	0.250699495381064	1		550	782	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0033607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	179	445	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.955	0.882	1	0.955	0.882	1	CLONAL	1	TRUE	1	0.468168513417745	2		445	801	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293955	1293955	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs904848231	NA	P-0033607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1324	83	936	0	ENST00000310581.5:c.1046C>G	p.Ser349Cys	p.S349C	ENST00000310581	NM_198253.2	349	tCt/tGt	2/16	0.361550953609154	1	FACETS	0.193	0.169	0.219	0.193	0.169	0.219	SUBCLONAL	1	TRUE	0	0.468168513417745	1		936	1407	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223978	2223978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	321	868	1	ENST00000326181.6:c.1192C>T	p.Pro398Ser	p.P398S	ENST00000326181	NM_032271.2	398	Cct/Tct	13/21	0.236952660244626	1	FACETS	0.855	0.806	0.904	0.855	0.806	0.904	INDETERMINATE	1	TRUE	0	0.468168513417745	1		869	1229	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069333	30069333	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	234	509	1	ENST00000338641.4:c.1198C>T	p.Gln400Ter	p.Q400*	ENST00000338641	NM_000268.3	400	Cag/Tag	12/16	0.468168513417745	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.468168513417745	1		510	731	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294237	1294237	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	77	604	0	ENST00000310581.5:c.764C>G	p.Ser255Cys	p.S255C	ENST00000310581	NM_198253.2	255	tCc/tGc	2/16	0.361550953609154	1	FACETS	0.282	0.247	0.32	0.282	0.247	0.32	SUBCLONAL	1	TRUE	0	0.468168513417745	1		604	893	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687016	176687016	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	203	484	0	ENST00000439151.2:c.4993C>T	p.Pro1665Ser	p.P1665S	ENST00000439151	NM_022455.4	1665	Cct/Tct	14/23	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.468168513417745	2		484	790	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972941	68972941	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs761058511	NA	P-0033607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	171	413	0	ENST00000288368.4:c.1266T>G	p.Ile422Met	p.I422M	ENST00000288368	NM_024870.2	422	atT/atG	11/40	0.468168513417745	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.468168513417745	1		413	555	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223877	53223877	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	357	890	0	ENST00000375401.3:c.3482T>A	p.Ile1161Asn	p.I1161N	ENST00000375401	NM_004187.3	1161	aTc/aAc	23/26	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.468168513417745	2		890	1457	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342129	70342129	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	186	554	0	ENST00000374080.3:c.1181T>G	p.Leu394Arg	p.L394R	ENST00000374080		394	cTt/cGt	8/45	1	2	FACETS	0.856	0.791	0.924	0.856	0.791	0.924	CLONAL	1	TRUE	1	0.468168513417745	2		554	928	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0033611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	49	791	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.304853327523803	2	FACETS	0.872	0.751	1	0.872	0.751	1	CLONAL	2	TRUE	0	0.324968927204201	2		791	173	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584787	48584787	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	13	550	0	ENST00000342988.3:c.865C>T	p.Gln289Ter	p.Q289*	ENST00000342988	NM_005359.5	289	Cag/Tag	7/12	0.211044904055462	2	FACETS	0.343	0.245	0.464	0.172	0.122	0.232	SUBCLONAL	1	TRUE	0	0.324968927204201	2		550	233	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577544	7577544	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587780074	NA	P-0033611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	32	853	0	ENST00000269305.4:c.737T>A	p.Met246Lys	p.M246K	ENST00000269305	NM_001126112.2	246	aTg/aAg	7/11	0.211044904055462	2	FACETS	1	0.935	1	0.665	0.548	0.794	CLONAL	1	TRUE	0	0.324968927204201	2		853	148	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984364	201984365	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0033611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	36	703	0	ENST00000359651.3:c.1030dup	p.Arg344ProfsTer127	p.R344Pfs*127	ENST00000359651		343	-/C	8/8	0.22389111133519	4	FACETS	0.858	0.715	1	0.858	0.715	1	CLONAL	2	TRUE	2	0.324968927204201	4		703	171	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43773136	43773136	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	22	769	0	ENST00000382044.4:c.456A>T	p.Glu152Asp	p.E152D	ENST00000382044	NM_001141980.1	152	gaA/gaT	5/28	0.205113706615241	0	FACETS	0.635	0.497	0.791			1	SUBCLONAL	1	TRUE	0	0.324968927204201	0		769	144	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664465	29664465	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	14	717	0	ENST00000356175.3:c.6444A>T	p.Lys2148Asn	p.K2148N	ENST00000356175	NM_000267.3	2148	aaA/aaT	42/57	1	2	FACETS	0.598	0.435	0.794	0.598	0.435	0.794	SUBCLONAL	1	TRUE	1	0.324968927204201	2		717	144	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291058	10291058	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	16	716	0	ENST00000340748.4:c.413C>G	p.Pro138Arg	p.P138R	ENST00000340748		138	cCc/cGc	4/40	0.324968927204201	1	FACETS	0.63	0.469	0.817	0.63	0.469	0.817	SUBCLONAL	1	TRUE	0	0.324968927204201	1		716	131	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505414	25505414	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	16	729	0	ENST00000264709.3:c.344C>T	p.Pro115Leu	p.P115L	ENST00000264709	NM_175629.2	115	cCa/cTa	4/23	1	2	FACETS	0.708	0.528	0.921	0.708	0.528	0.921	CLONAL	1	TRUE	1	0.324968927204201	2		729	139	SUCCESS
ALK	238	MSKCC	GRCh37	2	29473997	29473998	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0033611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	15	1005	0	ENST00000389048.3:c.2177_2178delinsAT	p.Trp726Tyr	p.W726Y	ENST00000389048	NM_004304.4	726	tGG/tAT	12/29	1	2	FACETS	0.54	0.396	0.711	0.54	0.396	0.711	SUBCLONAL	1	TRUE	1	0.324968927204201	2		1005	171	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138400821	138400822	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0033611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	12	384	3	ENST00000289153.2:c.2491_2492delinsTT	p.Gly831Phe	p.G831F	ENST00000289153	NM_006219.2	831	GGt/TTt	17/22	1	2	FACETS	0.659	0.467	0.891	0.659	0.467	0.891	SUBCLONAL	1	TRUE	1	0.324968927204201	2		387	112	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980379	55980379	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	20	502	0	ENST00000263923.4:c.712G>T	p.Val238Phe	p.V238F	ENST00000263923	NM_002253.2	238	Gtt/Ttt	6/30	0.324968927204201	3	FACETS	0.9	0.694	1	0.45	0.347	0.569	CLONAL	1	TRUE	1	0.324968927204201	3		502	159	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99809063	99809063	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	23	199	0	ENST00000280892.6:c.322G>T	p.Gly108Cys	p.G108C	ENST00000280892	NM_001130678.1	108	Ggc/Tgc	4/7	0.324968927204201	3	FACETS	1	0.924	1	0.722	0.572	0.889	CLONAL	1	TRUE	1	0.324968927204201	3		199	114	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045815	143045815	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	26	690	1	ENST00000262992.4:c.1819C>T	p.Leu607Phe	p.L607F	ENST00000262992	NM_001101669.1	607	Ctt/Ttt	17/24	0.324968927204201	3	FACETS	0.75	0.604	0.912	0.75	0.604	0.912	CLONAL	2	TRUE	1	0.324968927204201	3		691	124	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449799	8449799	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	24	704	0	ENST00000356435.5:c.3914C>G	p.Pro1305Arg	p.P1305R	ENST00000356435		1305	cCg/cGg	23/35	0.178545681870123	5	FACETS	1	0.884	1	0.398	0.314	0.493	INDETERMINATE	1	TRUE	2	0.324968927204201	5		704	184	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27190572	27190572	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	29	902	1	ENST00000380036.4:c.1373A>T	p.His458Leu	p.H458L	ENST00000380036	NM_000459.3	458	cAt/cTt	10/23	0.178545681870123	5	FACETS	0.785	0.637	0.95	0.524	0.425	0.634	INDETERMINATE	2	TRUE	2	0.324968927204201	5		903	169	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	35	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.756	0.626	0.898	0.756	0.626	0.898	SUBCLONAL	1	TRUE	1	0.49	2		248	189	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0033614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	144	699	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.985	0.902	1	0.985	0.902	1	CLONAL	1	TRUE	1	0.49	2		699	597	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831919	72831920	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	178	770	0	ENST00000268489.5:c.4661dup	p.Thr1555HisfsTer18	p.T1555Hfs*18	ENST00000268489	NM_006885.3	1554	ttc/ttTc	9/10	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.49	2		770	706	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260875	16260875	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	331	364	0	ENST00000375759.3:c.8140A>T	p.Thr2714Ser	p.T2714S	ENST00000375759	NM_015001.2	2714	Acg/Tcg	11/15	0.692996765055647	3	FACETS	0.906	0.873	0.939	1	0.996	1	CLONAL	3	TRUE	1	0.692996765055647	3		364	473	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175996735	175996735	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	695	372	0	ENST00000367669.3:c.1702A>G	p.Arg568Gly	p.R568G	ENST00000367669	NM_022457.5	568	Aga/Gga	15/20	0.692996765055647	5	FACETS	0.944	0.924	0.963	0.944	0.924	0.963	CLONAL	5	TRUE	0	0.692996765055647	5		372	867	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375575	118375575	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	199	207	0	ENST00000534358.1:c.8968G>T	p.Gly2990Cys	p.G2990C	ENST00000534358	NM_005933.3	2990	Ggc/Tgc	27/36	0.614158281344319	3	FACETS	0.904	0.862	0.946	0.904	0.862	0.946	CLONAL	3	TRUE	0	0.692996765055647	3		207	285	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428422	49428422	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs915492855	NA	P-0033615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	369	538	0	ENST00000301067.7:c.10383G>T	p.Arg3461Ser	p.R3461S	ENST00000301067	NM_003482.3	3461	agG/agT	36/54	0.601159397324045	3	FACETS	0.863	0.823	0.903	0.863	0.823	0.903	CLONAL	2	TRUE	1	0.692996765055647	3		538	831	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	356	582	0	ENST00000267101.3:c.273G>C	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atC	3/28	0.601159397324045	3	FACETS	0.873	0.833	0.914	0.873	0.833	0.914	CLONAL	2	TRUE	1	0.692996765055647	3		582	792	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	145	392	0	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	0.601159397324045	3	FACETS	0.851	0.779	0.927	0.426	0.389	0.464	CLONAL	1	TRUE	1	0.692996765055647	3		392	662	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226451	133226451	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	97	358	0	ENST00000320574.5:c.3607G>C	p.Asp1203His	p.D1203H	ENST00000320574	NM_006231.2	1203	Gac/Cac	30/49	0.601159397324045	3	FACETS	0.812	0.728	0.901	0.406	0.364	0.451	CLONAL	1	TRUE	1	0.692996765055647	3		358	464	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951140	48951141	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AT	novel	NA	P-0033615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	192	314	0	ENST00000267163.4:c.1302_1303delinsAT	p.Gly435Ter	p.G435*	ENST00000267163	NM_000321.2	434	gtGGga/gtATga	13/27	0.569683833952641	2	FACETS	1	0.991	1	0.681	0.638	0.723	CLONAL	1	TRUE	0	0.692996765055647	2		314	407	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986947	36986947	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	263	442	0	ENST00000354822.5:c.742C>T	p.Arg248Cys	p.R248C	ENST00000354822	NM_001079668.2	248	Cgc/Tgc	3/3	0.542066517345042	5	FACETS	0.865	0.812	0.919	0.577	0.541	0.613	CLONAL	2	TRUE	2	0.692996765055647	5		442	895	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242099	105242099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768800433	NA	P-0033615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	515	581	1	ENST00000349310.3:c.325G>A	p.Gly109Ser	p.G109S	ENST00000349310	NM_001014432.1	109	Ggc/Agc	6/15	0.542066517345042	5	FACETS	0.939	0.903	0.975	0.939	0.903	0.975	CLONAL	3	TRUE	2	0.692996765055647	5		582	1076	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472469	88472469	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	149	457	0	ENST00000360948.2:c.2086G>C	p.Gly696Arg	p.G696R	ENST00000360948	NM_001012338.2	696	Ggg/Cgg	16/19	1	2	FACETS	0.872	0.803	0.944	0.872	0.803	0.944	CLONAL	1	TRUE	1	0.692996765055647	2		457	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0033615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	329	523	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.561545138715267	2	FACETS	0.911	0.875	0.947	0.911	0.875	0.947	CLONAL	2	TRUE	0	0.692996765055647	2		523	521	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876531	59876531	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	305	415	0	ENST00000259008.2:c.1270A>T	p.Ser424Cys	p.S424C	ENST00000259008	NM_032043.2	424	Agt/Tgt	9/20	0.543360443868086	4	FACETS	0.915	0.866	0.965	0.915	0.866	0.965	CLONAL	2	TRUE	2	0.692996765055647	4		415	814	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216495	2216495	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	306	593	0	ENST00000398665.3:c.2139G>C	p.Met713Ile	p.M713I	ENST00000398665	NM_032482.2	713	atG/atC	20/28	0.550159084622729	3	FACETS	0.862	0.818	0.906			1	CLONAL	2	TRUE	NA	0.692996765055647	3		593	690	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097641	11097641	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	381	654	0	ENST00000358026.2:c.821G>T	p.Gly274Val	p.G274V	ENST00000358026	NM_001128849.1	274	gGc/gTc	5/36	0.569683833952641	2	FACETS	0.869	0.835	0.902	0.869	0.835	0.902	CLONAL	2	TRUE	0	0.692996765055647	2		654	633	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17382451	17382451	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	355	503	0	ENST00000359435.4:c.331G>T	p.Glu111Ter	p.E111*	ENST00000359435	NM_001033549.1	111	Gag/Tag	3/9	0.569683833952641	2	FACETS	0.822	0.788	0.856	0.822	0.788	0.856	CLONAL	2	TRUE	0	0.692996765055647	2		503	623	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735395	204735395	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	73	294	0	ENST00000302823.3:c.196del	p.Ala66ProfsTer6	p.A66Pfs*6	ENST00000302823	NM_005214.4	66	Gcc/cc	2/4	0.601159397324045	3	FACETS	0.829	0.731	0.934	0.415	0.365	0.467	CLONAL	1	TRUE	1	0.692996765055647	3		294	342	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660381	227660381	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	46	342	0	ENST00000305123.5:c.3074G>C	p.Ser1025Thr	p.S1025T	ENST00000305123	NM_005544.2	1025	aGc/aCc	1/2	0.601159397324045	3	FACETS	0.449	0.379	0.526	0.225	0.189	0.263	SUBCLONAL	1	TRUE	1	0.692996765055647	3		342	398	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793290	242793290	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143359677	NA	P-0033615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	162	589	0	ENST00000334409.5:c.787G>A	p.Ala263Thr	p.A263T	ENST00000334409	NM_005018.2	263	Gcc/Acc	5/5	0.601159397324045	3	FACETS	0.912	0.839	0.988	0.456	0.419	0.494	CLONAL	1	TRUE	1	0.692996765055647	3		589	690	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267198	41267198	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	269	362	0	ENST00000349496.5:c.782A>G	p.Asn261Ser	p.N261S	ENST00000349496	NM_001904.3	261	aAc/aGc	6/15	0.561545138715267	2	FACETS	0.84	0.801	0.879	0.84	0.801	0.879	CLONAL	2	TRUE	0	0.692996765055647	2		362	462	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164198	47164198	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs776293901	NA	P-0033615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	195	342	0	ENST00000409792.3:c.1928A>G	p.His643Arg	p.H643R	ENST00000409792	NM_014159.6	643	cAt/cGt	3/21	0.561545138715267	2	FACETS	1	0.992	1	0.729	0.685	0.773	CLONAL	1	TRUE	0	0.692996765055647	2		342	386	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021817	71021817	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	154	193	0	ENST00000318789.4:c.1541G>T	p.Arg514Leu	p.R514L	ENST00000318789	NM_032682.5	514	cGt/cTt	18/21	0.561545138715267	2	FACETS	0.882	0.829	0.934	0.882	0.829	0.934	CLONAL	2	TRUE	0	0.692996765055647	2		193	252	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665360	138665360	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	88	577	0	ENST00000330315.3:c.205G>C	p.Glu69Gln	p.E69Q	ENST00000330315	NM_023067.3	69	Gag/Cag	1/1	0.692996765055647	4	FACETS	0.406	0.358	0.457	0.135	0.119	0.153	SUBCLONAL	1	TRUE	1	0.692996765055647	4		577	1060	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170015099	170015099	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	176	480	0	ENST00000295797.4:c.1505A>T	p.Lys502Met	p.K502M	ENST00000295797	NM_002740.5	502	aAg/aTg	16/18	0.692996765055647	4	FACETS	0.76	0.699	0.823	0.253	0.233	0.275	SUBCLONAL	1	TRUE	1	0.692996765055647	4		480	1132	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948138	55948138	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0033615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	128	367	0	ENST00000263923.4:c.3833T>A	p.Leu1278Ter	p.L1278*	ENST00000263923	NM_002253.2	1278	tTa/tAa	29/30	0.601159397324045	3	FACETS	0.768	0.697	0.841	0.384	0.348	0.421	SUBCLONAL	1	TRUE	1	0.692996765055647	3		367	648	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356150	66356150	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1228970137	NA	P-0033615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	274	432	0	ENST00000273854.3:c.1347C>A	p.Asp449Glu	p.D449E	ENST00000273854	NM_004439.5	449	gaC/gaA	5/18	0.601159397324045	3	FACETS	0.808	0.764	0.852	0.808	0.764	0.852	CLONAL	2	TRUE	1	0.692996765055647	3		432	659	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542826	187542826	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	215	376	0	ENST00000441802.2:c.4914A>T	p.Lys1638Asn	p.K1638N	ENST00000441802	NM_005245.3	1638	aaA/aaT	10/27	0.601159397324045	3	FACETS	0.794	0.745	0.844	0.794	0.745	0.844	SUBCLONAL	2	TRUE	1	0.692996765055647	3		376	526	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683656	162683656	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	142	376	0	ENST00000366898.1:c.313G>C	p.Val105Leu	p.V105L	ENST00000366898	NM_004562.2	105	Gtg/Ctg	3/12	0.627620943739501	4	FACETS	0.964	0.88	1	0.321	0.293	0.351	CLONAL	1	TRUE	1	0.692996765055647	4		376	720	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289853	15289854	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	T	novel	NA	P-0033615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	165	593	0	ENST00000263388.2:c.3700_3701delinsA	p.Cys1234IlefsTer38	p.C1234Ifs*38	ENST00000263388	NM_000435.2	1234	TGt/At	22/33	0.569683833952641	2	FACETS	0.745	0.687	0.806	0.373	0.343	0.403	SUBCLONAL	1	TRUE	0	0.692996765055647	2		593	639	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511550	38511550	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1271139288	NA	P-0033616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	27	490	0	ENST00000254066.5:c.1048A>G	p.Met350Val	p.M350V	ENST00000254066	NM_000964.3	350	Atg/Gtg	8/9	1	2	FACETS	0.267	0.213	0.33	0.267	0.213	0.33	SUBCLONAL	1	TRUE	1	0.554714893005398	2		490	364	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685307	89685307	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123317	NA	P-0033623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	33	401	0	ENST00000371953.3:c.202T>C	p.Tyr68His	p.Y68H	ENST00000371953	NM_000314.4	68	Tac/Cac	3/9	0.880005973486206	1	FACETS	0.142	0.116	0.172	0.142	0.116	0.172	SUBCLONAL	1	TRUE	0	0.880005973486206	1		401	295	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217276	123217276	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	185	264	1	ENST00000218089.9:c.2930G>A	p.Gly977Asp	p.G977D	ENST00000218089	NM_001042749.1	977	gGc/gAc	29/35	1	1	FACETS	0.663	0.623	0.703	0.663	0.623	0.703	SUBCLONAL	1	TRUE	0	0.880005973486206	1		265	355	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965808	25965808	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768613233	NA	P-0033623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	111	731	0	ENST00000435504.4:c.3398G>A	p.Arg1133Gln	p.R1133Q	ENST00000435504		1133	cGg/cAg	13/13	1	2	FACETS	0.253	0.226	0.28	0.253	0.226	0.28	SUBCLONAL	1	TRUE	1	0.880005973486206	2		731	999	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0033629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	59	464	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	NA	2	FACETS	0.688	0.593	0.792			1	INDETERMINATE	1	TRUE	NA	0.341427926046476	2		465	502	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0033629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	49	232	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	0.154460797823507	2	FACETS	0.963	0.821	1	0.482	0.41	0.559	INDETERMINATE	1	TRUE	0	0.341427926046476	2		232	298	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220640	1220640	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690940	NA	P-0033629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	96	785	1	ENST00000326873.7:c.658C>T	p.Gln220Ter	p.Q220*	ENST00000326873	NM_000455.4	220	Cag/Tag	5/10	0.323547190640635	0	FACETS	0.641	0.572	0.714			1	SUBCLONAL	1	TRUE	0	0.341427926046476	0		786	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0033629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	50	500	0	ENST00000269305.4:c.673-1G>C		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.308435110700672	1	FACETS	0.678	0.578	0.788	0.678	0.578	0.788	SUBCLONAL	1	TRUE	0	0.341427926046476	1		500	358	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576105	29576105	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555617368	NA	P-0033629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	73	498	1	ENST00000356175.3:c.4078C>T	p.Gln1360Ter	p.Q1360*	ENST00000356175	NM_000267.3	1360	Caa/Taa	30/57	0.308435110700672	1	FACETS	0.725	0.636	0.821	0.725	0.636	0.821	SUBCLONAL	1	TRUE	0	0.341427926046476	1		499	489	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220576	123220576	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	81	214	0	ENST00000218089.9:c.3233C>G	p.Ser1078Cys	p.S1078C	ENST00000218089	NM_001042749.1	1078	tCt/tGt	30/35	0.341427926046476	2	FACETS	0.76	0.676	0.848			1	SUBCLONAL	2	TRUE	NA	0.341427926046476	2		214	312	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	24	697	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.526	0.412	0.659	0.526	0.412	0.659	SUBCLONAL	1	TRUE	1	0.19	2		697	480	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588210	69588210	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	57	688	0	ENST00000168712.1:c.488C>A	p.Pro163His	p.P163H	ENST00000168712	NM_002007.2	163	cCc/cAc	3/3	1	2	FACETS	0.943	0.809	1	0.943	0.809	1	CLONAL	1	TRUE	1	0.19	2		688	636	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986552	36986553	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	69	741	0	ENST00000354822.5:c.1136dup	p.His379GlnfsTer60	p.H379Qfs*60	ENST00000354822	NM_001079668.2	379	cac/caAc	3/3	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.19	2		741	634	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0033644-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	257	454	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.407972876768277	3	FACETS	0.976	0.919	1	0.976	0.919	1	CLONAL	2	TRUE	1	0.466794608551595	3		454	696	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0033644-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	299	747	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.466794608551595	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.466794608551595	2		747	583	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780071	NA	P-0033644-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	166	534	0	ENST00000269305.4:c.580C>T	p.Leu194Phe	p.L194F	ENST00000269305	NM_001126112.2	194	Ctt/Ttt	6/11	0.459379144887165	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.466794608551595	1		534	537	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947596	48947596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1566196458	NA	P-0033644-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	175	354	0	ENST00000267163.4:c.1183C>T	p.Gln395Ter	p.Q395*	ENST00000267163	NM_000321.2	395	Caa/Taa	12/27	0.44859307316603	2	FACETS	0.846	0.788	0.906	0.846	0.788	0.906	CLONAL	2	TRUE	0	0.466794608551595	2		354	443	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0033644-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	221	648	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.466794608551595	2		648	864	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070577	67070578	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033644-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	77	262	0	ENST00000412916.2:c.207dup	p.Pro70SerfsTer13	p.P70Sfs*13	ENST00000412916		67	-/T	3/6	0.410085329628266	1	FACETS	0.933	0.829	1	0.933	0.829	1	CLONAL	1	TRUE	0	0.466794608551595	1		262	271	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710622	114710622	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1282664682	NA	P-0033644-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	97	295	0	ENST00000543371.1:c.107C>T	p.Ser36Leu	p.S36L	ENST00000543371	NM_001198531.1	36	tCg/tTg	1/14	1	2	FACETS	0.9	0.806	0.998	0.9	0.806	0.998	CLONAL	1	TRUE	1	0.466794608551595	2		295	462	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210837	133210837	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033644-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	198	639	0	ENST00000320574.5:c.5939G>A	p.Trp1980Ter	p.W1980*	ENST00000320574	NM_006231.2	1980	tGg/tAg	43/49	1	2	FACETS	0.999	0.927	1	0.999	0.927	1	CLONAL	1	TRUE	1	0.466794608551595	2		639	849	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842378	68842378	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033644-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	146	541	0	ENST00000261769.5:c.440del	p.Pro147LeufsTer68	p.P147Lfs*68	ENST00000261769	NM_004360.3	147	Cct/ct	4/16	0.410085329628266	1	FACETS	0.907	0.832	0.983	0.907	0.832	0.983	CLONAL	1	TRUE	0	0.466794608551595	1		541	529	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437166	121437166	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033644-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	221	734	0	ENST00000257555.6:c.1597C>G	p.Leu533Val	p.L533V	ENST00000257555		533	Ctg/Gtg	8/10	1	2	FACETS	0.883	0.822	0.947	0.883	0.822	0.947	CLONAL	1	TRUE	1	0.466794608551595	2		734	1072	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104608	209104608	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033644-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	157	451	0	ENST00000345146.2:c.970G>T	p.Glu324Ter	p.E324*	ENST00000345146	NM_005896.2	324	Gag/Tag	8/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.466794608551595	2		451	600	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504027	186504027	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033644-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	80	271	0	ENST00000323963.5:c.592T>A	p.Tyr198Asn	p.Y198N	ENST00000323963		198	Tat/Aat	6/11	0.407972876768277	3	FACETS	0.931	0.823	1	0.466	0.411	0.523	CLONAL	1	TRUE	1	0.466794608551595	3		271	454	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511284	157511284	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773135175	NA	P-0033644-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	108	355	0	ENST00000346085.5:c.3802G>A	p.Asp1268Asn	p.D1268N	ENST00000346085	NM_020732.3	1268	Gat/Aat	15/20	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.466794608551595	2		355	460	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841846	151841846	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033644-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	125	315	0	ENST00000262189.6:c.14295G>A	p.Met4765Ile	p.M4765I	ENST00000262189	NM_170606.2	4765	atG/atA	55/59	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.466794608551595	2		315	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0033651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	195	835	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.538829817174438	1	FACETS	0.819	0.762	0.877	0.819	0.762	0.877	CLONAL	1	TRUE	0	0.555531586039117	1		835	619	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654770	29654772	+	frameshift_variant	Frame_Shift_Del	DEL	AAC	AAC	T	novel	NA	P-0033651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	92	405	0	ENST00000356175.3:c.5459_5461delinsT	p.Gln1820LeufsTer20	p.Q1820Lfs*20	ENST00000356175	NM_000267.3	1820	cAACac/cTac	37/57	0.555531586039117	1	FACETS	0.752	0.676	0.832	0.752	0.676	0.832	SUBCLONAL	1	TRUE	0	0.555531586039117	1		405	318	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579476	7579476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567556576	NA	P-0033664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	31	674	0	ENST00000269305.4:c.211C>T	p.Pro71Ser	p.P71S	ENST00000269305	NM_001126112.2	71	Ccc/Tcc	4/11	0.894881295145223	1	FACETS	0.083	0.066	0.101	0.083	0.066	0.101	SUBCLONAL	1	TRUE	0	0.894881295145223	1		674	464	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579476	7579477	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	404	653	0	ENST00000269305.4:c.210dup	p.Pro71SerfsTer78	p.P71Sfs*78	ENST00000269305	NM_001126112.2	70	-/T	4/11	0.894881295145223	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.894881295145223	1		653	461	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256572	115256572	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	90	499	0	ENST00000369535.4:c.139G>C	p.Asp47His	p.D47H	ENST00000369535	NM_002524.4	47	Gat/Cat	3/7	1	2	FACETS	0.372	0.331	0.416	0.372	0.331	0.416	SUBCLONAL	1	TRUE	1	0.894881295145223	2		499	540	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878186	48878186	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1131690855	NA	P-0033664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2	57	44	0	ENST00000267163.4:c.137+1G>T		p.X46_splice	ENST00000267163	NM_000321.2	46			0.894881295145223	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.894881295145223	1		44	59	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610291	81610291	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	144	401	0	ENST00000298171.2:c.1889T>C	p.Ile630Thr	p.I630T	ENST00000298171	NM_000369.2	630	aTc/aCc	10/10	0.48584351485538	1	FACETS	0.415	0.382	0.45	0.415	0.382	0.45	INDETERMINATE	1	TRUE	0	0.894881295145223	1		401	428	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57567452	57567452	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	301	181	0	ENST00000316660.6:c.43G>T	p.Ala15Ser	p.A15S	ENST00000316660	NM_021127.2	15	Gcg/Tcg	1/2	0.581044142277011	3	FACETS	0.951	0.909	0.993	0.951	0.909	0.993	CLONAL	2	TRUE	1	0.894881295145223	3		181	512	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60795976	60795976	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	215	353	0	ENST00000333681.4:c.602T>G	p.Leu201Arg	p.L201R	ENST00000333681		201	cTg/cGg	3/3	0.581044142277011	3	FACETS	1	0.982	1	0.567	0.53	0.605	CLONAL	1	TRUE	1	0.894881295145223	3		353	613	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216448	2216448	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	143	623	0	ENST00000398665.3:c.2092A>C	p.Lys698Gln	p.K698Q	ENST00000398665	NM_032482.2	698	Aag/Cag	20/28	1	2	FACETS	0.516	0.472	0.562	0.516	0.472	0.562	SUBCLONAL	1	TRUE	1	0.894881295145223	2		623	619	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966219	25966219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372572337	NA	P-0033664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	287	593	0	ENST00000435504.4:c.2987C>T	p.Thr996Ile	p.T996I	ENST00000435504		996	aCc/aTc	13/13	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.894881295145223	2		593	631	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524185	187524185	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	85	326	0	ENST00000441802.2:c.11354del	p.Gly3785GlufsTer48	p.G3785Efs*48	ENST00000441802	NM_005245.3	3785	gGa/ga	20/27	0.32116798429579	2	FACETS	0.655	0.586	0.727	0.328	0.293	0.364	INDETERMINATE	1	TRUE	0	0.894881295145223	2		326	290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0033669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	283	647	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.535416337761042	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.575399804249396	1		647	585	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068121	94068121	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	87	205	0	ENST00000369303.4:c.841C>G	p.Arg281Gly	p.R281G	ENST00000369303	NM_004440.3	281	Cgt/Ggt	4/17	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.575399804249396	2		205	294	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372044	55372044	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	57	246	0	ENST00000297316.4:c.734G>C	p.Cys245Ser	p.C245S	ENST00000297316	NM_022454.3	245	tGc/tCc	2/2	1	2	FACETS	0.953	0.829	1	0.953	0.829	1	CLONAL	1	TRUE	1	0.575399804249396	2		246	208	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293628	137293628	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs560113107	NA	P-0033669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	247	1024	1	ENST00000481739.1:c.179G>T	p.Gly60Val	p.G60V	ENST00000481739	NM_002957.4	60	gGc/gTc	2/10	0.575399804249396	1	FACETS	0.971	0.914	1	0.971	0.914	1	CLONAL	1	TRUE	0	0.575399804249396	1		1025	630	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0033670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	14	240	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.3	3	FACETS	0.425	0.306	0.569	0.212	0.153	0.285	SUBCLONAL	1	TRUE	1	0.19	3		240	380	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0033670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	60	660	2	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.19	2		662	612	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0033670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	88	421	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.19	2		421	643	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576183	88576183	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	29	496	0	ENST00000360948.2:c.1490G>T	p.Gly497Val	p.G497V	ENST00000360948	NM_001012338.2	497	gGg/gTg	13/19	1	2	FACETS	0.541	0.433	0.665	0.541	0.433	0.665	SUBCLONAL	1	TRUE	1	0.19	2		496	564	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11291440	11291440	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	56	412	0	ENST00000361445.4:c.2566G>T	p.Glu856Ter	p.E856*	ENST00000361445	NM_004958.3	856	Gag/Tag	17/58	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.19	2		412	583	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162735810	162735810	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	36	482	0	ENST00000367921.3:c.1119C>A	p.Asn373Lys	p.N373K	ENST00000367921	NM_006182.2	373	aaC/aaA	10/18	0.177209867248292	3	FACETS	0.613	0.502	0.738	0.306	0.251	0.369	SUBCLONAL	1	TRUE	1	0.19	3		482	677	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404720	70404720	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	32	360	1	ENST00000373644.4:c.2234del	p.Arg745GlnfsTer12	p.R745Qfs*12	ENST00000373644	NM_030625.2	745	cGa/ca	4/12	1	2	FACETS	0.592	0.479	0.72	0.592	0.479	0.72	SUBCLONAL	1	TRUE	1	0.19	2		361	569	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702349	47702349	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	33	338	0	ENST00000233146.2:c.1945G>T	p.Ala649Ser	p.A649S	ENST00000233146	NM_000251.2	649	Gca/Tca	12/16	1	2	FACETS	0.634	0.515	0.768	0.634	0.515	0.768	SUBCLONAL	1	TRUE	1	0.19	2		338	548	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500450	149500450	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0033670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	26	395	0	ENST00000261799.4:c.2586+1G>T		p.X862_splice	ENST00000261799	NM_002609.3	862			0.249573608838407	1	FACETS	0.552	0.436	0.684	0.552	0.436	0.684	SUBCLONAL	1	TRUE	0	0.19	1		395	449	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331636	8331636	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	37	446	0	ENST00000356435.5:c.5480T>A	p.Val1827Asp	p.V1827D	ENST00000356435		1827	gTc/gAc	33/35	1	2	FACETS	0.702	0.578	0.841	0.702	0.578	0.841	SUBCLONAL	1	TRUE	1	0.19	2		446	555	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132516	11132516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867713307	NA	P-0033671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	89	581	0	ENST00000358026.2:c.2732G>A	p.Gly911Asp	p.G911D	ENST00000358026	NM_001128849.1	911	gGc/gAc	19/36	1	2	FACETS	0.971	0.861	1	0.971	0.861	1	CLONAL	1	TRUE	1	0.27	2		581	679	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0033676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	153	756	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.642023320037192	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.642023320037192	1		756	276	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0033676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	365	343	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.642023320037192	7	FACETS	1	0.987	1			1	CLONAL	6	TRUE	NA	0.642023320037192	7		343	477	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883981	37883981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1357550606	NA	P-0033676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	318	540	0	ENST00000269571.5:c.3452C>T	p.Ser1151Leu	p.S1151L	ENST00000269571		1151	tCg/tTg	27/27	0.138516753722587	4	FACETS	0.941	0.899	0.983	1	0.995	1	INDETERMINATE	3	TRUE	2	0.642023320037192	4		540	576	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	485	134	0	ENST00000256196.4:c.68G>A	p.Gly23Asp	p.G23D	ENST00000256196		23	gGc/gAc	1/6	0.24380745442298	3	FACETS	1	0.993	1	1	0.998	1	INDETERMINATE	3	TRUE	1	0.642023320037192	3		134	624	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201903	102201903	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	43	257	0	ENST00000263464.3:c.1255G>T	p.Asp419Tyr	p.D419Y	ENST00000263464	NM_001165.4	419	Gac/Tac	6/9	0.24380745442298	3	FACETS	1	0.954	1	0.665	0.569	0.766	INDETERMINATE	1	TRUE	1	0.642023320037192	3		257	133	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947540	48947540	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0033678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	120	399	0	ENST00000267163.4:c.1128-1G>A		p.X376_splice	ENST00000267163	NM_000321.2	376			1	2	FACETS	0.866	0.791	0.944	0.866	0.791	0.944	CLONAL	1	TRUE	1	0.78257174775036	2		399	354	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717712	89717712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782350	NA	P-0033678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	57	440	1	ENST00000371953.3:c.737C>T	p.Pro246Leu	p.P246L	ENST00000371953	NM_000314.4	246	cCg/cTg	7/9	1	2	FACETS	0.451	0.389	0.518	0.451	0.389	0.518	SUBCLONAL	1	TRUE	1	0.78257174775036	2		441	323	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	47	697	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.0895773027764817	4	FACETS	1	0.93	1	0.593	0.501	0.695	INDETERMINATE	1	TRUE	2	0.203282126267922	4		697	469	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0033680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	62	445	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.203282126267922	2		445	462	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023253	27023269	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCCGGCGGCGGCGGT	CGCCCGGCGGCGGCGGT	-	novel	NA	P-0033680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	39	73	0	ENST00000324856.7:c.359_375del	p.Pro120ArgfsTer274	p.P120Rfs*274	ENST00000324856	NM_006015.4	120	cCGCCCGGCGGCGGCGGT/c	1/20	1	2	FACETS	1	0.911	1	1	0.972	1	CLONAL	2	TRUE	1	0.203282126267922	2		73	170	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0033683-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	17	357	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.135277343349964	4	FACETS	0.463	0.344	0.604	0.231	0.172	0.302	INDETERMINATE	1	TRUE	2	0.23	4		357	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0033683-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	47	577	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	1	2	FACETS	0.71	0.598	0.833	0.71	0.598	0.833	SUBCLONAL	1	TRUE	1	0.23	2		577	576	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510620	38510620	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033683-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	25	544	0	ENST00000254066.5:c.874C>G	p.Leu292Val	p.L292V	ENST00000254066	NM_000964.3	292	Ctg/Gtg	7/9	1	2	FACETS	0.436	0.342	0.543	0.436	0.342	0.543	SUBCLONAL	1	TRUE	1	0.23	2		544	499	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399350	139399350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755124691	NA	P-0033683-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	17	578	1	ENST00000277541.6:c.4793G>A	p.Arg1598His	p.R1598H	ENST00000277541	NM_017617.3	1598	cGc/cAc	26/34	1	2	FACETS	0.283	0.21	0.37	0.283	0.21	0.37	SUBCLONAL	1	TRUE	1	0.23	2		579	523	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952088	178952088	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553826184	NA	P-0033687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	36	317	0	ENST00000263967.3:c.3143A>G	p.His1048Arg	p.H1048R	ENST00000263967	NM_006218.2	1048	cAt/cGt	21/21	1	2	FACETS	0.345	0.284	0.413	0.345	0.284	0.413	SUBCLONAL	1	TRUE	1	0.580102304868204	2		317	360	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944588	38944588	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	169	378	0	ENST00000357387.3:c.4873del	p.Ser1625ValfsTer13	p.S1625Vfs*13	ENST00000357387	NM_152756.3	1625	Agt/gt	36/38	1	2	FACETS	0.996	0.921	1	0.996	0.921	1	CLONAL	1	TRUE	1	0.580102304868204	2		378	585	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035078	30035078	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0033688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	50	286	0	ENST00000338641.4:c.241-1G>A		p.X81_splice	ENST00000338641	NM_000268.3	81			0.425511814473054	1	FACETS	0.774	0.663	0.893	0.774	0.663	0.893	SUBCLONAL	1	TRUE	0	0.425511814473054	1		286	239	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667355	241667355	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	187	333	0	ENST00000366560.3:c.1095C>A	p.Ser365Arg	p.S365R	ENST00000366560	NM_000143.3	365	agC/agA	7/10	0.342032872973209	3	FACETS	1	0.983	1	0.772	0.721	0.824	CLONAL	2	TRUE	0	0.425511814473054	3		333	460	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123626	46123626	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	30	105	0	ENST00000334344.6:c.7A>G	p.Asn3Asp	p.N3D	ENST00000334344	NM_152641.2	3	Aac/Gac	1/21	1	2	FACETS	0.953	0.778	1	0.953	0.778	1	CLONAL	1	TRUE	1	0.425511814473054	2		105	148	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435279	121435279	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	81	394	0	ENST00000257555.6:c.1312C>G	p.Leu438Val	p.L438V	ENST00000257555		438	Ctg/Gtg	7/10	1	2	FACETS	0.959	0.85	1	0.959	0.85	1	CLONAL	1	TRUE	1	0.425511814473054	2		394	397	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928888	44928898	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGGCCTTCC	CTGGGCCTTCC	-	novel	NA	P-0033688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	64	393	0	ENST00000377967.4:c.1989_1999del	p.Gly664AlafsTer20	p.G664Afs*20	ENST00000377967	NM_021140.2	663	aCTGGGCCTTCC/a	17/29	0.425511814473054	1	FACETS	0.663	0.578	0.755	0.663	0.578	0.755	SUBCLONAL	1	TRUE	0	0.425511814473054	1		393	357	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519920	NA	P-0033691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	155	304	0	ENST00000397062.3:c.85G>A	p.Asp29Asn	p.D29N	ENST00000397062	NM_006164.4	29	Gat/Aat	2/5	0.483294516026241	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.4929559931771	3		304	363	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841849	151841849	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	124	364	0	ENST00000262189.6:c.14292G>C	p.Lys4764Asn	p.K4764N	ENST00000262189	NM_170606.2	4764	aaG/aaC	55/59	0.483294516026241	3	FACETS	0.936	0.858	1	0.936	0.858	1	CLONAL	2	TRUE	1	0.4929559931771	3		364	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0033691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	180	456	0	ENST00000269305.4:c.375+1G>C		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.456384619630481	3	FACETS	0.942	0.887	0.997	0.942	0.887	0.997	CLONAL	3	TRUE	0	0.4929559931771	3		456	322	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625374	69625374	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782226740	NA	P-0033691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	83	630	1	ENST00000334134.2:c.419C>T	p.Thr140Met	p.T140M	ENST00000334134	NM_005247.2	140	aCg/aTg	3/3	0.4929559931771	8	FACETS	0.941	0.829	1	0.157	0.138	0.177	CLONAL	1	TRUE	2	0.4929559931771	8		631	887	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101711	27102066	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTAAGGAGATCTTCCTCATTCGGTTGCCTAATCTGCCCCTTTCCATCTTGTCCATTGTTCCCTCCACCTTACTATTCTGGATGAGGTTGAATCTGGTCCAGTGTTGACTAAAATAGAACCAAAGAACTTTGGAAAAGGAAGAAATAAGCTAACTAAAGGTTCTCCTTCATTGCCATGCAATGAAGTCCTAGACAGACAGCTTAGAAGCCATGAGGGGCTGGTGTGTTTCATCTCCCAGACAGAAACTGCCTTCCACCTTGTGTTATCTTCAGAGTAGCTTCACTGATGGGGCAGCCCTAGGGGTGCCTCCAGCCAACCTGGGCTTGGTGGATAGACGACATGGAGGTTTATTTCA	GGTAAGGAGATCTTCCTCATTCGGTTGCCTAATCTGCCCCTTTCCATCTTGTCCATTGTTCCCTCCACCTTACTATTCTGGATGAGGTTGAATCTGGTCCAGTGTTGACTAAAATAGAACCAAAGAACTTTGGAAAAGGAAGAAATAAGCTAACTAAAGGTTCTCCTTCATTGCCATGCAATGAAGTCCTAGACAGACAGCTTAGAAGCCATGAGGGGCTGGTGTGTTTCATCTCCCAGACAGAAACTGCCTTCCACCTTGTGTTATCTTCAGAGTAGCTTCACTGATGGGGCAGCCCTAGGGGTGCCTCCAGCCAACCTGGGCTTGGTGGATAGACGACATGGAGGTTTATTTCA	-	novel	NA	P-0033691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	97	666	0	ENST00000324856.7:c.4993+2_4994del		p.X1665_splice	ENST00000324856	NM_006015.4	1665		18/20	0.4929559931771	3	FACETS	0.647	0.577	0.722	0.324	0.288	0.361	SUBCLONAL	1	TRUE	1	0.4929559931771	3		666	758	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488324	56488324	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	76	402	0	ENST00000267101.3:c.1843G>C	p.Glu615Gln	p.E615Q	ENST00000267101	NM_001982.3	615	Gag/Cag	15/28	0.4929559931771	3	FACETS	1	0.91	1	0.518	0.457	0.583	CLONAL	1	TRUE	1	0.4929559931771	3		402	371	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030707	48030707	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	141	362	0	ENST00000234420.5:c.3321T>A	p.Asp1107Glu	p.D1107E	ENST00000234420	NM_000179.2	1107	gaT/gaA	5/10	0.4929559931771	3	FACETS	0.914	0.842	0.988	0.914	0.842	0.988	CLONAL	2	TRUE	1	0.4929559931771	3		362	390	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500883	149500883	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1359322474	NA	P-0033691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	70	480	0	ENST00000261799.4:c.2347C>A	p.Pro783Thr	p.P783T	ENST00000261799	NM_002609.3	783	Cct/Act	17/23	0.4929559931771	1	FACETS	0.631	0.554	0.713	0.631	0.554	0.713	SUBCLONAL	1	TRUE	0	0.4929559931771	1		480	339	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181501	32181501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	76	609	0	ENST00000375023.3:c.2284C>T	p.Pro762Ser	p.P762S	ENST00000375023	NM_004557.3	762	Ccc/Tcc	14/30	0.4929559931771	3	FACETS	0.834	0.734	0.94	0.417	0.367	0.47	CLONAL	1	TRUE	1	0.4929559931771	3		609	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0033692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	234	451	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.729707074874853	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.738612541795987	1		451	390	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879854	37879854	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	268	576	0	ENST00000269571.5:c.2149G>A	p.Glu717Lys	p.E717K	ENST00000269571		717	Gag/Aag	18/27	0.729707074874853	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.738612541795987	1		576	457	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845334	76845334	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	155	362	0	ENST00000373344.5:c.6187G>T	p.Glu2063Ter	p.E2063*	ENST00000373344	NM_000489.3	2063	Gaa/Taa	27/35	1	2	FACETS	0.807	0.744	0.873	0.807	0.744	0.873	CLONAL	1	TRUE	1	0.738612541795987	2		362	520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578214	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs864309495	NA	P-0033693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	200	679	4	ENST00000269305.4:c.635_636del	p.Phe212SerfsTer3	p.F212Sfs*3	ENST00000269305	NM_001126112.2	212	tTT/t	6/11	0.236714059961406	3	FACETS	0.815	0.758	0.874	0.543	0.505	0.583	INDETERMINATE	2	TRUE	0	0.415632700725042	3		683	713	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227000	53227000	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	56	727	0	ENST00000375401.3:c.2575C>T	p.Gln859Ter	p.Q859*	ENST00000375401	NM_004187.3	859	Cag/Tag	18/26	0.41624651005575	1	FACETS	0.54	0.464	0.623	0.54	0.464	0.623	SUBCLONAL	1	TRUE	0	0.415632700725042	1		727	395	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0033694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	106	270	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.888	0.81	0.968	0.888	0.81	0.968	CLONAL	1	TRUE	1	0.893900314141854	2		270	267	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413070	139413072	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0033694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	86	491	0	ENST00000277541.6:c.1070_1072del	p.Phe357del	p.F357del	ENST00000277541	NM_017617.3	357	tTCTac/tac	6/34	1	2	FACETS	0.436	0.388	0.488	0.436	0.388	0.488	SUBCLONAL	1	TRUE	1	0.893900314141854	2		491	441	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412663	139412663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	49	652	0	ENST00000277541.6:c.1181G>A	p.Gly394Asp	p.G394D	ENST00000277541	NM_017617.3	394	gGc/gAc	7/34	1	2	FACETS	0.169	0.142	0.198	0.169	0.142	0.198	SUBCLONAL	1	TRUE	1	0.893900314141854	2		652	650	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0033694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	89	331	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.893900314141854	2		331	187	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919719	96919719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	23	440	0	ENST00000258439.3:c.544G>A	p.Gly182Arg	p.G182R	ENST00000258439	NM_001193304.2	182	Gga/Aga	4/4	1	2	FACETS	0.126	0.098	0.159	0.126	0.098	0.159	SUBCLONAL	1	TRUE	1	0.893900314141854	2		440	407	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429300	78429304	+	frameshift_variant	Frame_Shift_Del	DEL	AAATT	AAATT	-	novel	NA	P-0033694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	254	413	0	ENST00000370768.2:c.1138_1142del	p.Asn380TyrfsTer16	p.N380Yfs*16	ENST00000370768	NM_003902.3	380	AATTTt/t	13/20	0.893900314141854	1	FACETS	0.967	0.932	1	0.967	0.932	1	CLONAL	1	TRUE	0	0.893900314141854	1		413	325	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610453	81610453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	173	366	0	ENST00000298171.2:c.2051C>T	p.Ala684Val	p.A684V	ENST00000298171	NM_000369.2	684	gCc/gTc	10/10	0.862008140480903	1	FACETS	0.996	0.954	1	0.996	0.954	1	CLONAL	1	TRUE	0	0.893900314141854	1		366	215	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435287	56435287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	231	562	0	ENST00000407977.2:c.1850G>A	p.Arg617Lys	p.R617K	ENST00000407977		617	aGg/aAg	9/10	1	2	FACETS	0.981	0.924	1	0.981	0.924	1	CLONAL	1	TRUE	1	0.893900314141854	2		562	527	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729892	47729892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	13	214	1	ENST00000449228.1:c.497C>T	p.Thr166Ile	p.T166I	ENST00000449228	NM_001127240.2	166	aCa/aTa	3/4	0.893900314141854	1	FACETS	0.129	0.092	0.173	0.129	0.092	0.173	SUBCLONAL	1	TRUE	0	0.893900314141854	1		215	125	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099246	157099247	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0033694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	127	342	0	ENST00000346085.5:c.185_186del	p.Gly62AlafsTer169	p.G62Afs*169	ENST00000346085	NM_020732.3	61	acGGgg/acgg	1/20	1	2	FACETS	0.74	0.677	0.805	0.74	0.677	0.805	SUBCLONAL	1	TRUE	1	0.893900314141854	2		342	384	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395205	139395205	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	30	646	0	ENST00000277541.6:c.5733del	p.Asp1912ThrfsTer69	p.D1912Tfs*69	ENST00000277541	NM_017617.3	1911	tcC/tc	31/34	1	2	FACETS	0.113	0.09	0.138	0.113	0.09	0.138	SUBCLONAL	1	TRUE	1	0.893900314141854	2		646	596	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849300	76849302	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs782391479	NA	P-0033694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	38	372	0	ENST00000373344.5:c.5974_5976del	p.Ser1992del	p.S1992del	ENST00000373344	NM_000489.3	1992	TCT/-	26/35	1	2	FACETS	0.172	0.141	0.206	0.172	0.141	0.206	SUBCLONAL	1	TRUE	1	0.893900314141854	2		372	495	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799044	42799045	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0033694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	44	646	0	ENST00000575354.2:c.4528_4529del	p.Lys1510AspfsTer3	p.K1510Dfs*3	ENST00000575354	NM_015125.3	1510	AAg/g	20/20	0.893900314141854	1	FACETS	0.159	0.134	0.187	0.159	0.134	0.187	SUBCLONAL	1	TRUE	0	0.893900314141854	1		646	342	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0033740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	288	791	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.526762236405616	3	FACETS	0.959	0.908	1	0.959	0.908	1	CLONAL	2	TRUE	1	0.526762236405616	3		791	720	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069158	5069158	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0033740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	194	269	0	ENST00000381652.3:c.1463C>G	p.Ser488Ter	p.S488*	ENST00000381652	NM_004972.3	488	tCa/tGa	11/25	0.526762236405616	2	FACETS	0.93	0.873	0.987	0.93	0.873	0.987	CLONAL	2	TRUE	0	0.526762236405616	2		269	396	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999210	100999210	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	328	470	0	ENST00000325455.5:c.592C>A	p.Pro198Thr	p.P198T	ENST00000325455	NM_001202474.3	198	Ccg/Acg	1/8	0.526762236405616	3	FACETS	0.969	0.92	1	0.969	0.92	1	CLONAL	2	TRUE	1	0.526762236405616	3		470	812	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602745	10602745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1040740503	NA	P-0033740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	505	602	0	ENST00000171111.5:c.833C>T	p.Pro278Leu	p.P278L	ENST00000171111	NM_203500.1	278	cCg/cTg	3/6	0.526762236405616	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.526762236405616	2		602	886	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135067	11135067	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	477	592	0	ENST00000358026.2:c.3034C>T	p.Gln1012Ter	p.Q1012*	ENST00000358026	NM_001128849.1	1012	Cag/Tag	21/36	0.526762236405616	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.526762236405616	2		592	866	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073755	8073756	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0033740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	328	331	0	ENST00000377482.5:c.903dup	p.Ser302ValfsTer10	p.S302Vfs*10	ENST00000377482	NM_018948.3	301	-/G	4/4	0.258725479778962	3	FACETS	0.917	0.877	0.956			1	INDETERMINATE	3	TRUE	NA	0.526762236405616	3		331	572	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633568	69633568	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	57	130	0	ENST00000334134.2:c.134G>C	p.Arg45Pro	p.R45P	ENST00000334134	NM_005247.2	45	cGc/cCc	1/3	0.526762236405616	3	FACETS	0.824	0.711	0.945	0.412	0.355	0.473	CLONAL	1	TRUE	1	0.526762236405616	3		130	332	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2105515	2105515	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	186	429	2	ENST00000219476.3:c.594G>T	p.Met198Ile	p.M198I	ENST00000219476	NM_000548.3	198	atG/atT	6/42	0.332315347215215	3	FACETS	1	0.985	1	0.619	0.573	0.666	CLONAL	1	TRUE	1	0.526762236405616	3		431	721	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284978	15284978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	459	558	3	ENST00000263388.2:c.4637G>A	p.Arg1546His	p.R1546H	ENST00000263388	NM_000435.2	1546	cGc/cAc	25/33	0.526762236405616	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.526762236405616	2		561	784	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910623	50910623	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	578	598	0	ENST00000440232.2:c.1726G>C	p.Glu576Gln	p.E576Q	ENST00000440232	NM_002691.3	576	Gag/Cag	14/27	0.517726870923558	3	FACETS	0.969	0.938	0.999	0.969	0.938	0.999	CLONAL	3	TRUE	0	0.526762236405616	3		598	954	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274791	142274791	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	260	402	0	ENST00000350721.4:c.2269C>T	p.Gln757Ter	p.Q757*	ENST00000350721	NM_001184.3	757	Caa/Taa	10/47	0.280358274119598	5	FACETS	1	0.987	1	0.774	0.728	0.821	INDETERMINATE	2	TRUE	2	0.526762236405616	5		402	761	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749554	41749554	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0033740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	123	331	0	ENST00000226382.2:c.242-1G>T		p.X81_splice	ENST00000226382	NM_003924.3	81			1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.526762236405616	2		331	457	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971022	55971023	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0033740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	149	484	0	ENST00000263923.4:c.1774_1775delinsAA	p.Pro592Lys	p.P592K	ENST00000263923	NM_002253.2	592	CCa/AAa	13/30	1	2	FACETS	0.848	0.777	0.922	0.848	0.777	0.922	CLONAL	1	TRUE	1	0.526762236405616	2		484	667	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515306	149515306	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	176	462	0	ENST00000261799.4:c.176C>A	p.Pro59Gln	p.P59Q	ENST00000261799	NM_002609.3	59	cCg/cAg	3/23	0.332315347215215	3	FACETS	1	0.966	1	0.54	0.499	0.584	CLONAL	1	TRUE	1	0.526762236405616	3		462	781	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951891	2951891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	320	564	0	ENST00000396946.4:c.3059C>A	p.Thr1020Lys	p.T1020K	ENST00000396946	NM_032415.4	1020	aCg/aAg	23/25	0.239497665996617	5	FACETS	0.989	0.934	1	0.659	0.622	0.696	INDETERMINATE	2	TRUE	2	0.526762236405616	5		564	1100	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963866	2963866	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0033740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	259	410	0	ENST00000396946.4:c.1940+1G>T		p.X647_splice	ENST00000396946	NM_032415.4	647			0.239497665996617	5	FACETS	0.978	0.918	1	0.652	0.612	0.693	INDETERMINATE	2	TRUE	2	0.526762236405616	5		410	900	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332459	70332459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751344073	NA	P-0033743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	49	473	0	ENST00000373644.4:c.364G>A	p.Val122Ile	p.V122I	ENST00000373644	NM_030625.2	122	Gta/Ata	2/12	NA	2	FACETS	0.413	0.348	0.484			1	INDETERMINATE	1	TRUE	NA	0.316708359444673	2		473	750	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405948	49405948	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	81	474	0	ENST00000418115.1:c.190G>A	p.Glu64Lys	p.E64K	ENST00000418115	NM_001664.2	64	Gaa/Aaa	3/5	0.144120250181842	0	FACETS	0.496	0.436	0.559			1	INDETERMINATE	1	TRUE	0	0.316708359444673	0		474	705	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046324	69046324	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	268	437	0	ENST00000288368.4:c.3797T>G	p.Val1266Gly	p.V1266G	ENST00000288368	NM_024870.2	1266	gTt/gGt	32/40	0.281885469824544	3	FACETS	0.901	0.85	0.954	0.901	0.85	0.954	CLONAL	3	TRUE	0	0.316708359444673	3		437	725	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478037	138478037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	42	309	0	ENST00000289153.2:c.149C>T	p.Ala50Val	p.A50V	ENST00000289153	NM_006219.2	50	gCt/gTt	1/22	0.297373971862544	3	FACETS	0.5	0.416	0.592	0.167	0.138	0.198	SUBCLONAL	1	TRUE	0	0.316708359444673	3		309	615	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748089	41748089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779913205	NA	P-0033743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	16	26	0	ENST00000226382.2:c.680C>T	p.Ala227Val	p.A227V	ENST00000226382	NM_003924.3	227	gCg/gTg	3/3	0.316708359444673	1	FACETS	0.802	0.615	1	1	0.915	1	CLONAL	2	TRUE	0	0.316708359444673	1		26	53	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265352	152265352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142712646	NA	P-0033744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	234	300	0	ENST00000206249.3:c.805C>T	p.Arg269Cys	p.R269C	ENST00000206249	NM_000125.3	269	Cgc/Tgc	4/8	1	2	FACETS	0.858	0.807	0.91	0.858	0.807	0.91	CLONAL	1	TRUE	1	0.948156000998525	2		300	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0033744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	345	624	2	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.948156000998525	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.948156000998525	1		626	369	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176662833	176662833	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	224	302	1	ENST00000439151.2:c.3808G>T	p.Glu1270Ter	p.E1270*	ENST00000439151	NM_022455.4	1270	Gag/Tag	6/23	1	2	FACETS	0.951	0.895	1	0.951	0.895	1	CLONAL	1	TRUE	1	0.948156000998525	2		303	497	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514440	103514440	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	184	217	0	ENST00000355739.4:c.941T>G	p.Met314Arg	p.M314R	ENST00000355739	NM_000123.3	314	aTg/aGg	8/15	0.948156000998525	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.948156000998525	1		217	196	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040843	42040843	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	262	364	1	ENST00000219905.7:c.5221G>T	p.Ala1741Ser	p.A1741S	ENST00000219905	NM_001164273.1	1741	Gct/Tct	16/24	0.948156000998525	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.948156000998525	1		365	285	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362443	40362443	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	368	479	0	ENST00000293328.3:c.1753C>G	p.Leu585Val	p.L585V	ENST00000293328	NM_012448.3	585	Ctc/Gtc	14/19	1	2	FACETS	0.955	0.911	0.999	0.955	0.911	0.999	CLONAL	1	TRUE	1	0.948156000998525	2		479	813	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521217	187521217	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	413	550	0	ENST00000441802.2:c.11938A>G	p.Ile3980Val	p.I3980V	ENST00000441802	NM_005245.3	3980	Att/Gtt	22/27	0.948156000998525	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.948156000998525	1		550	444	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683756	162683756	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	364	415	0	ENST00000366898.1:c.213G>T	p.Gln71His	p.Q71H	ENST00000366898	NM_004562.2	71	caG/caT	3/12	1	2	FACETS	0.976	0.931	1	0.976	0.931	1	CLONAL	1	TRUE	1	0.948156000998525	2		415	787	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968143	68968143	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	320	412	0	ENST00000288368.4:c.1172G>C	p.Arg391Thr	p.R391T	ENST00000288368	NM_024870.2	391	aGa/aCa	10/40	0.948156000998525	3	FACETS	1	0.959	1	0.508	0.48	0.536	CLONAL	1	TRUE	1	0.948156000998525	3		412	979	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417618	139417618	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	512	565	0	ENST00000277541.6:c.426C>A	p.Asp142Glu	p.D142E	ENST00000277541	NM_017617.3	142	gaC/gaA	4/34	0.306866232387627	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.948156000998525	0		565	1096	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	192	697	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.343781889922757	2	FACETS	1	0.991	1	0.728	0.677	0.78	CLONAL	1	TRUE	0	0.436494473619345	2		697	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0033747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	231	808	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.362820213292268	2	FACETS	1	0.992	1	0.745	0.698	0.794	CLONAL	1	TRUE	0	0.436494473619345	2		808	710	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0033747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	231	371	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.436494473619345	3	FACETS	0.883	0.833	0.933	0.883	0.833	0.933	CLONAL	3	TRUE	0	0.436494473619345	3		371	487	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030426	49030426	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0033747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	146	284	0	ENST00000267163.4:c.1901C>G	p.Ser634Ter	p.S634*	ENST00000267163	NM_000321.2	634	tCa/tGa	19/27	0.343781889922757	2	FACETS	1	0.987	1	0.7	0.643	0.758	CLONAL	1	TRUE	0	0.436494473619345	2		284	478	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019536	42019542	+	frameshift_variant	Frame_Shift_Del	DEL	ACTGTGA	ACTGTGA	-	novel	NA	P-0033747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	162	431	0	ENST00000219905.7:c.3590_3596del	p.Thr1197ArgfsTer21	p.T1197Rfs*21	ENST00000219905	NM_001164273.1	1197	ACTGTGAag/ag	10/24	0.265660118771925	2	FACETS	1	0.973	1	0.564	0.519	0.611	CLONAL	1	TRUE	0	0.436494473619345	2		431	658	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0033749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	562	808	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	NA	2	FACETS	1	0.969	1			1	INDETERMINATE	2	TRUE	NA	0.522373438678762	2		808	1072	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0033749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	90	357	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.23964048984062	3	FACETS	0.739	0.657	0.827	0.37	0.328	0.414	INDETERMINATE	1	TRUE	1	0.522373438678762	3		357	588	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033758-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	228	697	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.536709115703935	2	FACETS	0.95	0.899	1	0.95	0.899	1	CLONAL	2	TRUE	0	0.561910287094372	2		697	427	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692911	89692911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909241	NA	P-0033758-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	227	436	0	ENST00000371953.3:c.395G>A	p.Gly132Asp	p.G132D	ENST00000371953	NM_000314.4	132	gGt/gAt	5/9	0.531024989708379	2	FACETS	0.929	0.878	0.979	0.929	0.878	0.979	CLONAL	2	TRUE	0	0.561910287094372	2		436	435	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939263	71939264	+	missense_variant	Missense_Mutation	DNP	TT	TT	AC	novel	NA	P-0033758-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	212	595	1	ENST00000298229.2:c.212_213delinsAC	p.Ile71Asn	p.I71N	ENST00000298229	NM_001567.3	71	aTT/aAC	2/28	0.561910287094372	1	FACETS	0.86	0.803	0.918	0.86	0.803	0.918	CLONAL	1	TRUE	0	0.561910287094372	1		596	631	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348771	11348771	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033758-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	70	335	0	ENST00000332029.2:c.565G>T	p.Glu189Ter	p.E189*	ENST00000332029	NM_003745.1	189	Gag/Tag	2/2	1	2	FACETS	0.562	0.492	0.638	0.562	0.492	0.638	SUBCLONAL	1	TRUE	1	0.561910287094372	2		335	443	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916143	9916143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762659685	NA	P-0033763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	35	415	0	ENST00000330684.3:c.2146G>A	p.Ala716Thr	p.A716T	ENST00000330684	NM_001134407.1	716	Gcc/Acc	10/13	1	2	FACETS	0.224	0.183	0.271	0.224	0.183	0.271	SUBCLONAL	1	TRUE	1	0.562363071951831	2		415	555	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589223	67589225	+	inframe_deletion	In_Frame_Del	DEL	TAA	TAA	-	novel	NA	P-0033763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	78	249	0	ENST00000274335.5:c.1214_1216del	p.Ile405del	p.I405del	ENST00000274335		404	tTAAta/tta	9/15	1	2	FACETS	0.907	0.804	1	0.907	0.804	1	CLONAL	1	TRUE	1	0.562363071951831	2		249	306	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061357	38061358	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGTTCTGCC	novel	NA	P-0033763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	148	473	0	ENST00000250448.2:c.623_631dup	p.Arg208_Asn210dup	p.R208_N210dup	ENST00000250448	NM_004496.3	208	cag/cGGCAGAACCag	2/2	1	2	FACETS	0.707	0.646	0.77	0.707	0.646	0.77	SUBCLONAL	1	TRUE	1	0.562363071951831	2		473	745	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0033765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	168	643	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.214991393285625	2	FACETS	0.979	0.901	1	0.979	0.901	1	CLONAL	2	TRUE	0	0.221804398498351	2		643	774	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163375	108163375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201594549	NA	P-0033765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	39	539	0	ENST00000278616.4:c.4466G>A	p.Arg1489His	p.R1489H	ENST00000278616	NM_000051.3	1489	cGt/cAt	30/63	1	2	FACETS	0.497	0.411	0.594	0.497	0.411	0.594	SUBCLONAL	1	TRUE	1	0.221804398498351	2		539	707	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445035	89445035	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	115	405	0	ENST00000336596.2:c.1355G>T	p.Ser452Ile	p.S452I	ENST00000336596	NM_005233.5	452	aGc/aTc	6/17	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.322747848294418	2		405	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	542	668	2	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.322747848294418	7	FACETS	0.95	0.918	0.981	0.95	0.918	0.981	CLONAL	7	TRUE	0	0.322747848294418	7		670	913	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	15	152	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	0.281299587324035	3	FACETS	1	0.797	1	1	0.797	1	CLONAL	2	TRUE	1	0.322747848294418	3		152	51	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510914	157510914	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	54	372	0	ENST00000346085.5:c.3689G>T	p.Arg1230Ile	p.R1230I	ENST00000346085	NM_020732.3	1230	aGa/aTa	14/20	1	2	FACETS	0.849	0.728	0.981	0.849	0.728	0.981	CLONAL	1	TRUE	1	0.322747848294418	2		372	394	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920518	50920518	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	46	463	0	ENST00000440232.2:c.3210C>G	p.Ile1070Met	p.I1070M	ENST00000440232	NM_002691.3	1070	atC/atG	26/27	0.299239971024403	3	FACETS	0.724	0.61	0.85	0.241	0.203	0.284	SUBCLONAL	1	TRUE	0	0.322747848294418	3		463	457	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372049	55372049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1254366651	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	51	281	0	ENST00000297316.4:c.739G>A	p.Ala247Thr	p.A247T	ENST00000297316	NM_022454.3	247	Gcg/Acg	2/2	0.29740828844672	4	FACETS	1	0.913	1	0.368	0.313	0.427	CLONAL	1	TRUE	1	0.322747848294418	4		281	379	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62009619	62009619	+	start_lost	Translation_Start_Site	SNP	C	C	A	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	140	486	0	ENST00000392795.3:c.3G>T	p.Met1?	p.M1?	ENST00000392795	NM_001039933.1	1	atG/atT	1/6	0.239330397581042	4	FACETS	0.948	0.867	1	0.948	0.867	1	CLONAL	2	TRUE	2	0.322747848294418	4		486	605	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612870	228612870	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	123	454	0	ENST00000366696.1:c.157C>T	p.Arg53Cys	p.R53C	ENST00000366696	NM_003493.2	53	Cgc/Tgc	1/1	0.281299587324035	3	FACETS	0.786	0.714	0.862	0.786	0.714	0.862	SUBCLONAL	2	TRUE	1	0.322747848294418	3		454	563	SUCCESS
AR	367	MSKCC	GRCh37	X	66863241	66863241	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs750677165	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	100	456	0	ENST00000374690.3:c.1760C>A	p.Ala587Asp	p.A587D	ENST00000374690	NM_000044.3	587	gCc/gAc	2/8	0.17222744054255	2	FACETS	1	0.963	1	0.582	0.522	0.646	INDETERMINATE	1	TRUE	0	0.322747848294418	2		456	532	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687607	29687607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	177	539	0	ENST00000356175.3:c.8200C>T	p.Leu2734Phe	p.L2734F	ENST00000356175	NM_000267.3	2734	Ctc/Ttc	56/57	0.183785177521111	5	FACETS	1	0.975	1	0.749	0.692	0.809	INDETERMINATE	2	TRUE	2	0.322747848294418	5		539	724	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789643	3789643	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	82	384	1	ENST00000262367.5:c.4216G>T	p.Asp1406Tyr	p.D1406Y	ENST00000262367	NM_004380.2	1406	Gat/Tat	25/31	1	2	FACETS	0.906	0.8	1	0.906	0.8	1	CLONAL	1	TRUE	1	0.322747848294418	2		385	561	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412500	63412500	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	68	518	0	ENST00000330258.3:c.667G>T	p.Ala223Ser	p.A223S	ENST00000330258	NM_152424.3	223	Gcc/Tcc	2/2	0.17222744054255	2	FACETS	0.711	0.618	0.81	0.355	0.309	0.405	INDETERMINATE	1	TRUE	0	0.322747848294418	2		518	593	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78426050	78426050	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	150	463	0	ENST00000370768.2:c.1475G>T	p.Gly492Val	p.G492V	ENST00000370768	NM_003902.3	492	gGa/gTa	15/20	0.239330397581042	4	FACETS	0.979	0.898	1	0.979	0.898	1	CLONAL	2	TRUE	2	0.322747848294418	4		463	628	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273043	115273043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	79	440	0	ENST00000438362.2:c.1330G>T	p.Asp444Tyr	p.D444Y	ENST00000438362	NM_001242891.1	444	Gat/Tat	12/20	0.281299587324035	3	FACETS	1	0.948	1	0.569	0.501	0.64	CLONAL	1	TRUE	1	0.322747848294418	3		440	500	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163297320	163297320	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs142683655	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	114	439	1	ENST00000271452.3:c.166G>T	p.Val56Leu	p.V56L	ENST00000271452	NM_145697.2	56	Gta/Tta	3/14	0.183785177521111	5	FACETS	0.953	0.861	1	0.635	0.574	0.7	INDETERMINATE	2	TRUE	2	0.322747848294418	5		440	550	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981145	201981145	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	171	589	1	ENST00000359651.3:c.224G>T	p.Trp75Leu	p.W75L	ENST00000359651		75	tGg/tTg	2/8	0.183785177521111	5	FACETS	1	0.968	1	0.73	0.673	0.789	INDETERMINATE	2	TRUE	2	0.322747848294418	5		590	718	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578289	226578289	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	137	463	0	ENST00000366794.5:c.439G>T	p.Glu147Ter	p.E147*	ENST00000366794	NM_001618.3	147	Gag/Tag	4/23	0.281299587324035	3	FACETS	0.879	0.803	0.958	0.879	0.803	0.958	CLONAL	2	TRUE	1	0.322747848294418	3		463	561	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115582	108115582	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	67	430	0	ENST00000278616.4:c.730G>A	p.Ala244Thr	p.A244T	ENST00000278616	NM_000051.3	244	Gct/Act	7/63	0.281299587324035	3	FACETS	0.901	0.784	1	0.451	0.392	0.514	CLONAL	1	TRUE	1	0.322747848294418	3		430	535	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245271	46245271	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	123	377	0	ENST00000334344.6:c.3366del	p.Gln1124SerfsTer32	p.Q1124Sfs*32	ENST00000334344	NM_152641.2	1122	gTt/gt	15/21	0.300581880616608	2	FACETS	0.821	0.748	0.898	0.821	0.748	0.898	CLONAL	2	TRUE	0	0.322747848294418	2		377	464	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541629	120541629	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1416625402	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	35	393	1	ENST00000229340.5:c.227+1G>A		p.X76_splice	ENST00000229340	NM_006861.6	76			0.322747848294418	4	FACETS	0.545	0.446	0.657	0.136	0.111	0.165	SUBCLONAL	1	TRUE	0	0.322747848294418	4		394	526	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434437	110434437	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	65	459	0	ENST00000375856.3:c.3964A>T	p.Ser1322Cys	p.S1322C	ENST00000375856	NM_003749.2	1322	Agc/Tgc	1/2	0.322747848294418	1	FACETS	0.795	0.691	0.906	0.795	0.691	0.906	CLONAL	1	TRUE	0	0.322747848294418	1		459	425	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434482	110434482	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	50	399	0	ENST00000375856.3:c.3919G>T	p.Gly1307Trp	p.G1307W	ENST00000375856	NM_003749.2	1307	Ggg/Tgg	1/2	0.322747848294418	1	FACETS	0.771	0.657	0.895	0.771	0.657	0.895	SUBCLONAL	1	TRUE	0	0.322747848294418	1		399	337	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105602	30105602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	96	732	0	ENST00000331968.5:c.1084G>A	p.Glu362Lys	p.E362K	ENST00000331968	NM_002742.2	362	Gaa/Aaa	7/18	0.279484964725148	3	FACETS	0.893	0.795	0.997	0.446	0.397	0.499	CLONAL	1	TRUE	1	0.322747848294418	3		732	774	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003788	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	123	496	0	ENST00000558401.1:c.45_46del	p.Ser16TrpfsTer40	p.S16Wfs*40	ENST00000558401	NM_004048.2	15	cTT/c	1/4	0.300581880616608	2	FACETS	0.786	0.715	0.86	0.786	0.715	0.86	SUBCLONAL	2	TRUE	0	0.322747848294418	2		496	485	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844199	68844199	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1555515453	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	151	521	0	ENST00000261769.5:c.787A>T	p.Thr263Ser	p.T263S	ENST00000261769	NM_004360.3	263	Acc/Tcc	6/16	0.183785177521111	5	FACETS	1	0.956	1	0.709	0.65	0.77	INDETERMINATE	2	TRUE	2	0.322747848294418	5		521	653	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923730	72923730	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	64	533	0	ENST00000268489.5:c.3348G>T	p.Glu1116Asp	p.E1116D	ENST00000268489	NM_006885.3	1116	gaG/gaT	4/10	0.183785177521111	5	FACETS	1	0.92	1	0.362	0.313	0.415	INDETERMINATE	1	TRUE	2	0.322747848294418	5		533	542	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428357	33428357	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1567725026	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	171	537	0	ENST00000345365.6:c.766G>C	p.Asp256His	p.D256H	ENST00000345365	NM_002878.3	256	Gac/Cac	9/10	0.183785177521111	5	FACETS	0.964	0.888	1	0.642	0.592	0.695	INDETERMINATE	2	TRUE	2	0.322747848294418	5		537	816	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41209073	41209073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	159	514	1	ENST00000357654.3:c.5273G>A	p.Arg1758Lys	p.R1758K	ENST00000357654	NM_007294.3	1758	aGa/aAa	19/23	0.281299587324035	3	FACETS	0.853	0.784	0.924	0.853	0.784	0.924	CLONAL	2	TRUE	1	0.322747848294418	3		515	671	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435252	56435252	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	192	549	0	ENST00000407977.2:c.1885G>T	p.Ala629Ser	p.A629S	ENST00000407977		629	Gcc/Tcc	9/10	0.239330397581042	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.322747848294418	4		549	676	SUCCESS
YES1	7525	MSKCC	GRCh37	18	742925	742925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388595429	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	30	342	0	ENST00000314574.4:c.1053G>A	p.Met351Ile	p.M351I	ENST00000314574	NM_005433.3	351	atG/atA	8/12	0.281299587324035	3	FACETS	0.668	0.539	0.814	0.334	0.269	0.407	SUBCLONAL	1	TRUE	1	0.322747848294418	3		342	323	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56415048	56415048	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	111	357	0	ENST00000348428.3:c.2449G>C	p.Asp817His	p.D817H	ENST00000348428	NM_006785.3	817	Gac/Cac	17/17	0.281299587324035	3	FACETS	0.925	0.837	1	0.925	0.837	1	CLONAL	2	TRUE	1	0.322747848294418	3		357	432	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214706	5214706	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1457749790	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	270	522	1	ENST00000357368.4:c.4360G>T	p.Gly1454Cys	p.G1454C	ENST00000357368	NM_002850.3	1454	Ggc/Tgc	29/38	0.299239971024403	3	FACETS	0.939	0.886	0.992	0.939	0.886	0.992	CLONAL	3	TRUE	0	0.322747848294418	3		523	690	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215604	5215604	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	193	480	0	ENST00000357368.4:c.4099A>G	p.Met1367Val	p.M1367V	ENST00000357368	NM_002850.3	1367	Atg/Gtg	27/38	0.299239971024403	3	FACETS	0.932	0.87	0.994	0.932	0.87	0.994	CLONAL	3	TRUE	0	0.322747848294418	3		480	497	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982542	10982542	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	66	105	0	ENST00000327064.4:c.164C>T	p.Ala55Val	p.A55V	ENST00000327064	NM_199141.1	55	gCg/gTg	1/16	0.299239971024403	3	FACETS	0.928	0.834	1	1	0.97	1	CLONAL	4	TRUE	0	0.322747848294418	3		105	128	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144471	11144471	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	270	504	0	ENST00000358026.2:c.3803G>C	p.Ser1268Thr	p.S1268T	ENST00000358026	NM_001128849.1	1268	aGt/aCt	27/36	0.299239971024403	3	FACETS	0.943	0.89	0.996	0.943	0.89	0.996	CLONAL	3	TRUE	0	0.322747848294418	3		504	687	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366933	15366933	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	288	661	0	ENST00000263377.2:c.1693G>T	p.Ala565Ser	p.A565S	ENST00000263377	NM_058243.2	565	Gcc/Tcc	9/20	0.299239971024403	3	FACETS	0.901	0.851	0.951	0.901	0.851	0.951	CLONAL	3	TRUE	0	0.322747848294418	3		661	767	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222928	36222928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	305	726	1	ENST00000222270.7:c.5557C>T	p.Pro1853Ser	p.P1853S	ENST00000222270	NM_014727.1	1853	Cct/Tct	27/37	0.299239971024403	3	FACETS	0.917	0.868	0.966	0.917	0.868	0.966	CLONAL	3	TRUE	0	0.322747848294418	3		727	798	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47601021	47601021	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	84	508	0	ENST00000263735.4:c.259G>T	p.Ala87Ser	p.A87S	ENST00000263735	NM_002354.2	87	Gcc/Tcc	3/9	0.19669617673781	4	FACETS	0.844	0.744	0.951			1	CLONAL	1	TRUE	NA	0.322747848294418	4		508	816	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659821	227659821	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	130	332	0	ENST00000305123.5:c.3634G>A	p.Gly1212Ser	p.G1212S	ENST00000305123	NM_005544.2	1212	Ggc/Agc	1/2	0.299239971024403	3	FACETS	1	0.932	1	1	0.932	1	CLONAL	3	TRUE	0	0.322747848294418	3		332	308	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560966	9560966	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	124	504	1	ENST00000353224.5:c.816C>A	p.Tyr272Ter	p.Y272*	ENST00000353224	NM_177990.2	272	taC/taA	4/10	1	2	FACETS	0.771	0.702	0.844	1	0.986	1	SUBCLONAL	2	TRUE	1	0.322747848294418	2		505	498	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309898	30309898	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	63	526	0	ENST00000307677.4:c.124G>C	p.Glu42Gln	p.E42Q	ENST00000307677	NM_138578.1	42	Gaa/Caa	2/3	1	2	FACETS	0.647	0.56	0.743	0.647	0.56	0.743	SUBCLONAL	1	TRUE	1	0.322747848294418	2		526	603	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050305	37050305	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs748417604	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	34	251	0	ENST00000231790.2:c.454G>T	p.Val152Leu	p.V152L	ENST00000231790	NM_000249.3	152	Gtg/Ttg	6/19	1	2	FACETS	0.804	0.66	0.964	0.804	0.66	0.964	CLONAL	1	TRUE	1	0.322747848294418	2		251	262	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71064709	71064709	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	71	334	0	ENST00000318789.4:c.965C>A	p.Ser322Ter	p.S322*	ENST00000318789	NM_032682.5	322	tCa/tAa	12/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.322747848294418	2		334	335	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825440	134825440	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	51	424	2	ENST00000398015.3:c.956G>T	p.Cys319Phe	p.C319F	ENST00000398015	NM_004441.4	319	tGc/tTc	4/16	0.279484964725148	3	FACETS	0.763	0.649	0.888	0.382	0.324	0.444	SUBCLONAL	1	TRUE	1	0.322747848294418	3		426	481	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226945	142226945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	106	325	0	ENST00000350721.4:c.4859C>T	p.Thr1620Ile	p.T1620I	ENST00000350721	NM_001184.3	1620	aCt/aTt	28/47	0.279484964725148	3	FACETS	0.897	0.81	0.989	0.897	0.81	0.989	CLONAL	2	TRUE	1	0.322747848294418	3		325	425	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55962504	55962504	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	125	422	0	ENST00000263923.4:c.2620G>T	p.Ala874Ser	p.A874S	ENST00000263923	NM_002253.2	874	Gca/Tca	19/30	0.281299587324035	3	FACETS	0.971	0.885	1	0.971	0.885	1	CLONAL	2	TRUE	1	0.322747848294418	3		422	463	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143326395	143326395	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	50	415	0	ENST00000262992.4:c.219G>T	p.Gln73His	p.Q73H	ENST00000262992	NM_001101669.1	73	caG/caT	4/24	0.322747848294418	3	FACETS	0.64	0.543	0.747	0.32	0.271	0.374	SUBCLONAL	1	TRUE	1	0.322747848294418	3		415	562	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264591	1264592	+	missense_variant	Missense_Mutation	DNP	GC	GC	AG	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	70	530	1	ENST00000310581.5:c.2770_2771delinsCT	p.Ala924Leu	p.A924L	ENST00000310581	NM_198253.2	924	GCc/CTc	11/16	0.322747848294418	3	FACETS	0.967	0.845	1	0.483	0.422	0.55	CLONAL	1	TRUE	1	0.322747848294418	3		531	521	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31435899	31435899	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	139	362	0	ENST00000344624.3:c.3015G>C	p.Gln1005His	p.Q1005H	ENST00000344624		1005	caG/caC	22/33	0.322747848294418	3	FACETS	0.988	0.905	1	0.988	0.905	1	CLONAL	2	TRUE	1	0.322747848294418	3		362	506	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861056	35861056	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	147	363	0	ENST00000303115.3:c.185C>A	p.Pro62Gln	p.P62Q	ENST00000303115	NM_002185.3	62	cCa/cAa	2/8	0.322747848294418	3	FACETS	0.998	0.917	1	0.998	0.917	1	CLONAL	2	TRUE	1	0.322747848294418	3		363	530	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871289	35871289	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	91	270	0	ENST00000303115.3:c.511C>A	p.Gln171Lys	p.Q171K	ENST00000303115	NM_002185.3	171	Cag/Aag	4/8	0.322747848294418	3	FACETS	0.857	0.767	0.952	0.857	0.767	0.952	CLONAL	2	TRUE	1	0.322747848294418	3		270	382	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754357	57754357	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	137	308	0	ENST00000274289.3:c.496-2A>T		p.X166_splice	ENST00000274289	NM_006622.3	166			0.322747848294418	4	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	2	0.322747848294418	4		308	534	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046043	180046043	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	32	106	1	ENST00000261937.6:c.2828G>T	p.Arg943Leu	p.R943L	ENST00000261937	NM_182925.4	943	cGg/cTg	20/30	0.281299587324035	3	FACETS	1	0.947	1	0.743	0.611	0.887	CLONAL	1	TRUE	1	0.322747848294418	3		107	155	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673738	30673738	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1339693761	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	95	441	0	ENST00000376406.3:c.3222C>G	p.Ile1074Met	p.I1074M	ENST00000376406	NM_014641.2	1074	atC/atG	10/15	0.279484964725148	3	FACETS	1	0.964	1	0.595	0.53	0.663	CLONAL	1	TRUE	1	0.322747848294418	3		441	575	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168999	32168999	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	101	656	2	ENST00000375023.3:c.4034C>A	p.Ala1345Asp	p.A1345D	ENST00000375023	NM_004557.3	1345	gCc/gAc	22/30	0.281299587324035	3	FACETS	0.993	0.888	1	0.496	0.444	0.553	CLONAL	1	TRUE	1	0.322747848294418	3		658	732	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287964	33287964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	59	432	0	ENST00000374542.5:c.1289C>T	p.Ala430Val	p.A430V	ENST00000374542	NM_001141970.1	430	gCc/gTc	5/8	0.281299587324035	3	FACETS	0.788	0.678	0.907	0.394	0.339	0.454	CLONAL	1	TRUE	1	0.322747848294418	3		432	539	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336627	81336627	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	101	245	0	ENST00000222390.5:c.1595C>A	p.Ala532Glu	p.A532E	ENST00000222390	NM_000601.4	532	gCa/gAa	14/18	0.239330397581042	4	FACETS	1	0.902	1	1	0.902	1	CLONAL	2	TRUE	2	0.322747848294418	4		245	413	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372738	81372739	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	116	344	2	ENST00000222390.5:c.795_796delinsTT	p.Gln266Ter	p.Q266*	ENST00000222390	NM_000601.4	265	ggCCag/ggTTag	7/18	0.239330397581042	4	FACETS	0.941	0.853	1	0.941	0.853	1	CLONAL	2	TRUE	2	0.322747848294418	4		346	505	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508430	106508430	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	65	229	0	ENST00000359195.3:c.424C>G	p.Pro142Ala	p.P142A	ENST00000359195	NM_002649.2	142	Ccg/Gcg	2/11	0.239330397581042	4	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	2	0.322747848294418	4		229	248	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931877	68931877	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	60	463	0	ENST00000288368.4:c.307C>G	p.Gln103Glu	p.Q103E	ENST00000288368	NM_024870.2	103	Caa/Gaa	3/40	0.29740828844672	4	FACETS	0.691	0.594	0.796	0.23	0.198	0.266	SUBCLONAL	1	TRUE	1	0.322747848294418	4		463	712	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864194	117864194	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	59	429	0	ENST00000297338.2:c.1463T>G	p.Val488Gly	p.V488G	ENST00000297338	NM_006265.2	488	gTg/gGg	11/14	0.29740828844672	4	FACETS	0.716	0.616	0.826	0.239	0.205	0.276	SUBCLONAL	1	TRUE	1	0.322747848294418	4		429	675	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486044	8486044	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	134	537	0	ENST00000356435.5:c.2773C>A	p.Leu925Ile	p.L925I	ENST00000356435		925	Ctt/Att	17/35	0.300581880616608	2	FACETS	0.772	0.705	0.842	0.772	0.705	0.842	SUBCLONAL	2	TRUE	0	0.322747848294418	2		537	538	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518175	8518179	+	frameshift_variant	Frame_Shift_Del	DEL	CGCTG	CGCTG	TGCT	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	104	433	1	ENST00000356435.5:c.1212_1216delinsAGCA	p.Ser405AlafsTer5	p.S405Afs*5	ENST00000356435		404	ccCAGCGaa/ccAGCAaa	10/35	0.300581880616608	2	FACETS	0.753	0.679	0.831	0.753	0.679	0.831	SUBCLONAL	2	TRUE	0	0.322747848294418	2		434	428	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974769	21974769	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	55	147	0	ENST00000304494.5:c.58G>A	p.Ala20Thr	p.A20T	ENST00000304494	NM_000077.4	20	Gcg/Acg	1/3	0.300581880616608	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	2	TRUE	0	0.322747848294418	2		147	158	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339241	87339241	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	63	488	0	ENST00000277120.3:c.823G>T	p.Asp275Tyr	p.D275Y	ENST00000277120		275	Gat/Tat	8/19	0.322747848294418	3	FACETS	0.694	0.6	0.797	0.347	0.3	0.399	SUBCLONAL	1	TRUE	1	0.322747848294418	3		488	653	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781208	135781208	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	59	539	0	ENST00000298552.3:c.1757G>C	p.Cys586Ser	p.C586S	ENST00000298552	NM_001162426.1	586	tGt/tCt	15/23	0.322747848294418	3	FACETS	0.645	0.555	0.744	0.323	0.277	0.372	SUBCLONAL	1	TRUE	1	0.322747848294418	3		539	658	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356169	70356169	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	152	671	0	ENST00000374080.3:c.5064G>T	p.Trp1688Cys	p.W1688C	ENST00000374080		1688	tgG/tgT	37/45	0.17222744054255	2	FACETS	1	0.977	1	0.596	0.546	0.649	INDETERMINATE	1	TRUE	0	0.322747848294418	2		671	790	SUCCESS
BTK	695	MSKCC	GRCh37	X	100604929	100604929	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	26	393	0	ENST00000308731.7:c.1924C>A	p.Pro642Thr	p.P642T	ENST00000308731	NM_000061.2	642	Ccc/Acc	19/19	0.168537285439553	0	FACETS	0.317	0.251	0.393			1	INDETERMINATE	1	TRUE	0	0.322747848294418	0		393	344	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019892	123019892	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	94	601	0	ENST00000355640.3:c.380T>A	p.Phe127Tyr	p.F127Y	ENST00000355640		127	tTt/tAt	2/7	0.168537285439553	0	FACETS	0.799	0.713	0.889			1	INDETERMINATE	1	TRUE	0	0.322747848294418	0		601	494	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0033772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	26	454	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.137	0.107	0.17	0.137	0.107	0.17	SUBCLONAL	1	TRUE	1	0.604939475480221	2		454	629	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0033772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	19	647	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.08	0.06	0.104	0.08	0.06	0.104	SUBCLONAL	1	TRUE	1	0.604939475480221	2		647	786	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0033772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	108	454	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.195496743705286	4	FACETS	1	0.906	1	0.504	0.453	0.557	INDETERMINATE	1	TRUE	2	0.604939475480221	4		454	569	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189585728	189585728	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	80	345	0	ENST00000264731.3:c.989G>C	p.Arg330Thr	p.R330T	ENST00000264731	NM_003722.4	330	aGa/aCa	7/14	0.195496743705286	4	FACETS	0.697	0.614	0.786	0.349	0.307	0.393	INDETERMINATE	1	TRUE	2	0.604939475480221	4		345	609	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972633	25972633	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	176	345	0	ENST00000435504.4:c.1792C>T	p.Gln598Ter	p.Q598*	ENST00000435504		598	Cag/Tag	12/13	0.223618581636557	2	FACETS	0.945	0.874	1	0.472	0.437	0.509	INDETERMINATE	1	TRUE	0	0.604939475480221	2		345	616	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534789	18534789	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	116	374	0	ENST00000266497.5:c.1847G>T	p.Ser616Ile	p.S616I	ENST00000266497		616	aGt/aTt	12/31	1	2	FACETS	0.667	0.603	0.734	0.667	0.603	0.734	SUBCLONAL	1	TRUE	1	0.604939475480221	2		374	575	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879773	123879773	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	40	166	1	ENST00000330479.4:c.469C>G	p.Leu157Val	p.L157V	ENST00000330479	NM_020382.3	157	Ctg/Gtg	4/9	1	2	FACETS	0.442	0.369	0.523	0.442	0.369	0.523	SUBCLONAL	1	TRUE	1	0.604939475480221	2		167	299	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435928	110435928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	42	445	0	ENST00000375856.3:c.2473C>T	p.Leu825Phe	p.L825F	ENST00000375856	NM_003749.2	825	Ctc/Ttc	1/2	0.604939475480221	2	FACETS	0.221	0.184	0.263	0.111	0.092	0.132	SUBCLONAL	1	TRUE	0	0.604939475480221	2		445	628	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149989	202149989	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	309	468	0	ENST00000358485.4:c.1430G>A	p.Gly477Glu	p.G477E	ENST00000358485	NM_001080125.1	477	gGa/gAa	8/9	0.604939475480221	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.604939475480221	1		468	605	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551085	41551085	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	89	442	0	ENST00000263253.7:c.3229C>T	p.Gln1077Ter	p.Q1077*	ENST00000263253	NM_001429.3	1077	Caa/Taa	17/31	1	2	FACETS	0.35	0.31	0.393	0.35	0.31	0.393	SUBCLONAL	1	TRUE	1	0.604939475480221	2		442	841	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628560	187628560	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	278	544	0	ENST00000441802.2:c.2422del	p.Leu808TyrfsTer24	p.L808Yfs*24	ENST00000441802	NM_005245.3	808	Cta/ta	2/27	0.285420973865383	2	FACETS	0.922	0.867	0.978	0.461	0.433	0.489	INDETERMINATE	1	TRUE	0	0.604939475480221	2		544	997	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696742	176696742	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	138	320	0	ENST00000439151.2:c.5443T>A	p.Tyr1815Asn	p.Y1815N	ENST00000439151	NM_022455.4	1815	Tac/Aac	16/23	0.604939475480221	1	FACETS	0.917	0.846	0.99	0.917	0.846	0.99	CLONAL	1	TRUE	0	0.604939475480221	1		320	347	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323296	31323297	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0033772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	107	86	0	ENST00000412585.2:c.692_693insC	p.Tyr233LeufsTer21	p.Y233Lfs*21	ENST00000412585	NM_005514.6	231	ggt/ggCt	4/8	1	2	FACETS	1	0.949	1	1	0.991	1	CLONAL	2	TRUE	1	0.604939475480221	2		86	172	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	97	264	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.907	0.813	1	0.907	0.813	1	CLONAL	1	TRUE	1	0.458985996135993	2		264	466	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	187	640	1	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.975	0.902	1	0.975	0.902	1	CLONAL	1	TRUE	1	0.458985996135993	2		641	836	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	112	539	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	0.458985996135993	1	FACETS	0.843	0.763	0.926	0.843	0.763	0.926	CLONAL	1	TRUE	0	0.458985996135993	1		539	446	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436009	110436009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767024195	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	152	538	1	ENST00000375856.3:c.2392G>A	p.Val798Ile	p.V798I	ENST00000375856	NM_003749.2	798	Gtt/Att	1/2	1	2	FACETS	0.86	0.788	0.936	0.86	0.788	0.936	CLONAL	1	TRUE	1	0.458985996135993	2		539	770	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601863	43601863	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	145	488	1	ENST00000355710.3:c.907G>A	p.Val303Met	p.V303M	ENST00000355710	NM_020975.4	303	Gtg/Atg	5/20	1	2	FACETS	0.863	0.789	0.941	0.863	0.789	0.941	CLONAL	1	TRUE	1	0.458985996135993	2		489	732	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246482	105246482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	111	472	1	ENST00000349310.3:c.118G>A	p.Glu40Lys	p.E40K	ENST00000349310	NM_001014432.1	40	Gag/Aag	4/15	NA	2	FACETS	0.603	0.542	0.668			1	INDETERMINATE	1	TRUE	NA	0.458985996135993	2		473	802	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	126	334	1	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.458985996135993	2		335	524	SUCCESS
AR	367	MSKCC	GRCh37	X	66943543	66943543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852581	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	142	169	0	ENST00000374690.3:c.2623C>T	p.His875Tyr	p.H875Y	ENST00000374690	NM_000044.3	875	Cat/Tat	8/8	0.379278446372515	2	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.458985996135993	2		169	416	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216477	108216477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587782558	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	73	224	1	ENST00000278616.4:c.8432del	p.Lys2811SerfsTer46	p.K2811Sfs*46	ENST00000278616	NM_000051.3	2809	cAa/ca	58/63	0.458985996135993	3	FACETS	0.895	0.786	1	0.447	0.393	0.506	CLONAL	1	TRUE	1	0.458985996135993	3		225	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	146	470	1	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	1	2	FACETS	0.967	0.885	1	0.967	0.885	1	CLONAL	1	TRUE	1	0.458985996135993	2		471	658	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056427	26056427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs182693914	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	101	307	0	ENST00000343677.2:c.230A>G	p.Asn77Ser	p.N77S	ENST00000343677	NM_005319.3	77	aAc/aGc	1/1	1	2	FACETS	0.965	0.867	1	0.965	0.867	1	CLONAL	1	TRUE	1	0.458985996135993	2		307	456	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	197	564	1	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.458985996135993	2		565	830	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294078	1294078	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	175	709	0	ENST00000310581.5:c.923del	p.Pro308HisfsTer43	p.P308Hfs*43	ENST00000310581	NM_198253.2	308	cCa/ca	2/16	1	2	FACETS	0.906	0.835	0.979	0.906	0.835	0.979	CLONAL	1	TRUE	1	0.458985996135993	2		709	842	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255883	16255883	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	96	309	1	ENST00000375759.3:c.3154del	p.Ile1052SerfsTer40	p.I1052Sfs*40	ENST00000375759	NM_015001.2	1050	Aaa/aa	11/15	0.448436374515564	1	FACETS	0.924	0.831	1	0.924	0.831	1	CLONAL	1	TRUE	0	0.458985996135993	1		310	349	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453398	40453399	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs759027671	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	96	626	2	ENST00000345506.4:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000345506	NM_003152.3	365	-/C	10/20	1	2	FACETS	0.557	0.496	0.622	0.557	0.496	0.622	SUBCLONAL	1	TRUE	1	0.458985996135993	2		628	751	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11264661	11264661	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	45	501	0	ENST00000361445.4:c.3901C>T	p.Arg1301Cys	p.R1301C	ENST00000361445	NM_004958.3	1301	Cgc/Tgc	26/58	1	2	FACETS	0.267	0.223	0.315	0.267	0.223	0.315	SUBCLONAL	1	TRUE	1	0.458985996135993	2		501	735	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	160	544	0	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	0.458985996135993	3	FACETS	1	0.942	1	0.516	0.474	0.561	CLONAL	1	TRUE	1	0.458985996135993	3		544	830	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984813	55984813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200544155	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	151	403	0	ENST00000263923.4:c.316C>T	p.Arg106Trp	p.R106W	ENST00000263923	NM_002253.2	106	Cgg/Tgg	3/30	1	2	FACETS	0.923	0.845	1	0.923	0.845	1	CLONAL	1	TRUE	1	0.458985996135993	2		403	713	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606273	93606273	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	167	505	2	ENST00000375746.1:c.98del	p.Gly33AlafsTer2	p.G33Afs*2	ENST00000375746	NM_001174167.1	31	caG/ca	2/14	1	2	FACETS	0.959	0.883	1	0.959	0.883	1	CLONAL	1	TRUE	1	0.458985996135993	2		507	759	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224583	108224583	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881329	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	81	268	0	ENST00000278616.4:c.8762C>T	p.Thr2921Met	p.T2921M	ENST00000278616	NM_000051.3	2921	aCg/aTg	60/63	0.458985996135993	3	FACETS	0.805	0.711	0.906	0.403	0.355	0.453	CLONAL	1	TRUE	1	0.458985996135993	3		268	539	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125296	7125296	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs777937157	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	276	424	0	ENST00000302850.5:c.3256G>A	p.Val1086Met	p.V1086M	ENST00000302850	NM_000208.2	1086	Gtg/Atg	17/22	0.455559343922295	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.458985996135993	2		424	594	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971080	21971080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	115	269	0	ENST00000304494.5:c.278C>T	p.Thr93Met	p.T93M	ENST00000304494	NM_000077.4	93	aCg/aTg	2/3	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.458985996135993	2		269	408	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	242	476	1	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	0.458985996135993	2		477	740	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532556	63532556	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555577121	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	183	568	1	ENST00000307078.5:c.2023del	p.Arg675ValfsTer14	p.R675Vfs*14	ENST00000307078	NM_004655.3	675	Cgt/gt	8/11	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.458985996135993	2		569	792	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216189	36216189	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	193	538	2	ENST00000222270.7:c.3602del	p.Pro1201ArgfsTer154	p.P1201Rfs*154	ENST00000222270	NM_014727.1	1199	ggC/gg	11/37	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.458985996135993	2		540	832	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424970	49424970	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783691	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	170	541	0	ENST00000301067.7:c.13518del	p.Ser4507AlafsTer12	p.S4507Afs*12	ENST00000301067	NM_003482.3	4506	ccC/cc	39/54	1	2	FACETS	0.936	0.863	1	0.936	0.863	1	CLONAL	1	TRUE	1	0.458985996135993	2		541	791	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518197	187518197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376106855	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	28	307	0	ENST00000441802.2:c.12497C>T	p.Ala4166Val	p.A4166V	ENST00000441802	NM_005245.3	4166	gCg/gTg	25/27	1	2	FACETS	0.265	0.211	0.327	0.265	0.211	0.327	SUBCLONAL	1	TRUE	1	0.458985996135993	2		307	460	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707977	43707977	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	190	592	0	ENST00000382044.4:c.4904G>A	p.Arg1635His	p.R1635H	ENST00000382044	NM_001141980.1	1635	cGc/cAc	23/28	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.458985996135993	2		592	827	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646980	23646981	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	163	571	1	ENST00000261584.4:c.886dup	p.Met296AsnfsTer7	p.M296Nfs*7	ENST00000261584	NM_024675.3	296	atg/aAtg	4/13	1	2	FACETS	0.804	0.738	0.873	0.804	0.738	0.873	CLONAL	1	TRUE	1	0.458985996135993	2		572	883	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440712	56440712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	163	429	0	ENST00000407977.2:c.506C>T	p.Ala169Val	p.A169V	ENST00000407977		169	gCt/gTt	5/10	1	2	FACETS	0.988	0.909	1	0.988	0.909	1	CLONAL	1	TRUE	1	0.458985996135993	2		429	719	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99181169	99181169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778648043	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	161	430	0	ENST00000074304.5:c.2110C>T	p.Arg704Cys	p.R704C	ENST00000074304	NM_001134224.1	704	Cgc/Tgc	20/26	1	2	FACETS	0.994	0.914	1	0.994	0.914	1	CLONAL	1	TRUE	1	0.458985996135993	2		430	706	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617690	39617690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141329274	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	132	343	1	ENST00000262039.4:c.1874C>T	p.Thr625Met	p.T625M	ENST00000262039	NM_002647.2	625	aCg/aTg	17/25	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.458985996135993	2		344	554	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905959	50905959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201010746	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	197	550	1	ENST00000440232.2:c.931C>T	p.Arg311Cys	p.R311C	ENST00000440232	NM_002691.3	311	Cgc/Tgc	8/27	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.458985996135993	2		551	806	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970951	21970951	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	40	424	0	ENST00000304494.5:c.407del	p.Gly136AlafsTer10	p.G136Afs*10	ENST00000304494	NM_000077.4	136	gGc/gc	2/3	1	2	FACETS	0.244	0.202	0.292	0.244	0.202	0.292	SUBCLONAL	1	TRUE	1	0.458985996135993	2		424	713	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543659	9543659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755638779	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	42	360	0	ENST00000353224.5:c.1495C>T	p.Arg499Trp	p.R499W	ENST00000353224	NM_177990.2	499	Cgg/Tgg	6/10	1	2	FACETS	0.317	0.264	0.376	0.317	0.264	0.376	SUBCLONAL	1	TRUE	1	0.458985996135993	2		360	577	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140454004	140454004	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	75	216	0	ENST00000288602.6:c.1724G>A	p.Arg575Lys	p.R575K	ENST00000288602	NM_004333.4	575	aGa/aAa	14/18	1	2	FACETS	0.961	0.849	1	0.961	0.849	1	CLONAL	1	TRUE	1	0.458985996135993	2		216	340	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012710	36012710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1228673150	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	27	50	0	ENST00000358208.4:c.154G>A	p.Ala52Thr	p.A52T	ENST00000358208		52	Gcg/Acg	2/12	1	2	FACETS	1	0.847	1	1	0.962	1	CLONAL	2	TRUE	1	0.458985996135993	2		50	58	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257220	16257221	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	154	376	0	ENST00000375759.3:c.4490dup	p.Lys1498GlufsTer4	p.K1498Efs*4	ENST00000375759	NM_015001.2	1495	-/A	11/15	0.448436374515564	1	FACETS	0.998	0.92	1	0.998	0.92	1	CLONAL	1	TRUE	0	0.458985996135993	1		376	518	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984444	201984444	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768235554	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	118	314	1	ENST00000359651.3:c.1109G>A	p.Arg370Gln	p.R370Q	ENST00000359651		370	cGg/cAg	8/8	1	2	FACETS	0.991	0.898	1	0.991	0.898	1	CLONAL	1	TRUE	1	0.458985996135993	2		315	519	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552824	226552824	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	147	456	0	ENST00000366794.5:c.2537A>G	p.Gln846Arg	p.Q846R	ENST00000366794	NM_001618.3	846	cAg/cGg	19/23	1	2	FACETS	0.999	0.915	1	0.999	0.915	1	CLONAL	1	TRUE	1	0.458985996135993	2		456	641	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981838	101981838	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	141	460	0	ENST00000282441.5:c.259A>G	p.Arg87Gly	p.R87G	ENST00000282441	NM_001130145.2	87	Agg/Ggg	1/9	0.458985996135993	3	FACETS	0.938	0.855	1	0.469	0.427	0.513	CLONAL	1	TRUE	1	0.458985996135993	3		460	805	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200974	108200974	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	108	337	0	ENST00000278616.4:c.7341G>T	p.Leu2447Phe	p.L2447F	ENST00000278616	NM_000051.3	2447	ttG/ttT	50/63	0.458985996135993	3	FACETS	0.879	0.79	0.973	0.44	0.395	0.487	CLONAL	1	TRUE	1	0.458985996135993	3		337	658	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426652	49426652	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	100	296	0	ENST00000301067.7:c.11836C>T	p.Gln3946Ter	p.Q3946*	ENST00000301067	NM_003482.3	3946	Caa/Taa	39/54	1	2	FACETS	0.995	0.894	1	0.995	0.894	1	CLONAL	1	TRUE	1	0.458985996135993	2		296	438	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26970451	26970451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	29	111	0	ENST00000381527.3:c.820C>T	p.Pro274Ser	p.P274S	ENST00000381527	NM_001260.1	274	Cct/Tct	8/13	1	2	FACETS	0.599	0.484	0.728	0.599	0.484	0.728	SUBCLONAL	1	TRUE	1	0.458985996135993	2		111	211	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923102	48923102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	93	289	0	ENST00000267163.4:c.550G>A	p.Glu184Lys	p.E184K	ENST00000267163	NM_000321.2	184	Gaa/Aaa	6/27	1	2	FACETS	0.958	0.857	1	0.958	0.857	1	CLONAL	1	TRUE	1	0.458985996135993	2		289	423	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436575	110436575	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768562587	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	197	531	0	ENST00000375856.3:c.1826C>T	p.Ala609Val	p.A609V	ENST00000375856	NM_003749.2	609	gCg/gTg	1/2	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.458985996135993	2		531	821	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817763	3817763	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	188	596	0	ENST00000262367.5:c.3208A>T	p.Thr1070Ser	p.T1070S	ENST00000262367	NM_004380.2	1070	Aca/Tca	16/31	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.458985996135993	2		596	794	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632708	23632708	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1040452708	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	134	406	0	ENST00000261584.4:c.3088A>G	p.Thr1030Ala	p.T1030A	ENST00000261584	NM_024675.3	1030	Act/Gct	10/13	1	2	FACETS	0.928	0.846	1	0.928	0.846	1	CLONAL	1	TRUE	1	0.458985996135993	2		406	629	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371689	89371691	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-	novel	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	204	523	0	ENST00000301030.4:c.149_151del	p.Glu50del	p.E50del	ENST00000301030	NM_001256183.1	50	gAGGtg/gtg	4/13	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.458985996135993	2		523	863	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15967427	15967427	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1468999160	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	129	434	0	ENST00000268712.3:c.5176C>T	p.Arg1726Trp	p.R1726W	ENST00000268712	NM_006311.3	1726	Cgg/Tgg	35/46	1	2	FACETS	0.789	0.717	0.866	0.789	0.717	0.866	SUBCLONAL	1	TRUE	1	0.458985996135993	2		434	712	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37865601	37865601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745921471	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	192	595	0	ENST00000269571.5:c.470G>A	p.Arg157Gln	p.R157Q	ENST00000269571		157	cGg/cAg	4/27	1	2	FACETS	0.961	0.889	1	0.961	0.889	1	CLONAL	1	TRUE	1	0.458985996135993	2		595	871	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369264	40369264	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	130	462	1	ENST00000293328.3:c.1294del	p.Ala432GlnfsTer4	p.A432Qfs*4	ENST00000293328	NM_012448.3	432	Gca/ca	11/19	1	2	FACETS	0.866	0.787	0.949	0.866	0.787	0.949	CLONAL	1	TRUE	1	0.458985996135993	2		463	654	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40500428	40500428	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	124	375	0	ENST00000264657.5:c.107C>A	p.Pro36His	p.P36H	ENST00000264657	NM_139276.2	36	cCt/cAt	2/24	1	2	FACETS	0.982	0.893	1	0.982	0.893	1	CLONAL	1	TRUE	1	0.458985996135993	2		375	550	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761412	59761415	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	rs786203717	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	161	385	0	ENST00000259008.2:c.2992_2995del	p.Lys998GlufsTer60	p.K998Efs*60	ENST00000259008	NM_032043.2	998	AAGAga/ga	20/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.458985996135993	2		385	617	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022455	31022455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745371501	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	72	220	0	ENST00000375687.4:c.1940C>T	p.Pro647Leu	p.P647L	ENST00000375687	NM_015338.5	647	cCg/cTg	13/13	1	2	FACETS	0.939	0.827	1	0.939	0.827	1	CLONAL	1	TRUE	1	0.458985996135993	2		220	334	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032757	30032757	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	102	334	0	ENST00000338641.4:c.132G>T	p.Lys44Asn	p.K44N	ENST00000338641	NM_000268.3	44	aaG/aaT	2/16	1	2	FACETS	0.856	0.769	0.949	0.856	0.769	0.949	CLONAL	1	TRUE	1	0.458985996135993	2		334	519	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139458	47139458	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	141	441	0	ENST00000409792.3:c.5129G>A	p.Arg1710His	p.R1710H	ENST00000409792	NM_014159.6	1710	cGt/cAt	9/21	1	2	FACETS	0.932	0.852	1	0.932	0.852	1	CLONAL	1	TRUE	1	0.458985996135993	2		441	659	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582123	189582123	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	101	375	0	ENST00000264731.3:c.682A>G	p.Met228Val	p.M228V	ENST00000264731	NM_003722.4	228	Atg/Gtg	5/14	1	2	FACETS	0.797	0.715	0.884	0.797	0.715	0.884	SUBCLONAL	1	TRUE	1	0.458985996135993	2		375	552	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1955186	1955186	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	149	485	0	ENST00000382891.5:c.2273G>A	p.Arg758His	p.R758H	ENST00000382891	NM_133335.3	758	cGc/cAc	12/22	1	2	FACETS	0.875	0.801	0.953	0.875	0.801	0.953	CLONAL	1	TRUE	1	0.458985996135993	2		485	742	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133529	55133529	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	107	387	0	ENST00000257290.5:c.833C>A	p.Pro278His	p.P278H	ENST00000257290	NM_006206.4	278	cCc/cAc	6/23	1	2	FACETS	0.72	0.646	0.797	0.72	0.646	0.797	SUBCLONAL	1	TRUE	1	0.458985996135993	2		387	648	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31401568	31401569	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	rs1561100337	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	171	531	0	ENST00000344624.3:c.4094_4095dup	p.Pro1366SerfsTer24	p.P1366Sfs*24	ENST00000344624		1365	-/AG	33/33	1	2	FACETS	0.847	0.779	0.917	0.847	0.779	0.917	CLONAL	1	TRUE	1	0.458985996135993	2		531	880	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629124	86629124	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	82	234	0	ENST00000274376.6:c.869A>G	p.Tyr290Cys	p.Y290C	ENST00000274376	NM_002890.2	290	tAc/tGc	4/25	1	2	FACETS	0.857	0.759	0.96	0.857	0.759	0.96	CLONAL	1	TRUE	1	0.458985996135993	2		234	417	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509478	149509478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	189	568	1	ENST00000261799.4:c.1421G>A	p.Ser474Asn	p.S474N	ENST00000261799	NM_002609.3	474	aGc/aAc	10/23	1	2	FACETS	0.979	0.906	1	0.979	0.906	1	CLONAL	1	TRUE	1	0.458985996135993	2		569	841	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6027062	6027062	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554297872	NA	P-0033773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	98	342	0	ENST00000265849.7:c.1334G>A	p.Ser445Asn	p.S445N	ENST00000265849	NM_000535.5	445	aGc/aAc	11/15	1	2	FACETS	0.947	0.849	1	0.947	0.849	1	CLONAL	1	TRUE	1	0.458985996135993	2		342	451	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211882	36211882	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519279	NA	P-0121567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	27	728	1	ENST00000222270.7:c.1633C>T	p.Arg545Ter	p.R545*	ENST00000222270	NM_014727.1	545	Cga/Tga	3/37	0.176497697419554	0	FACETS	0.756	0.603	0.93			1	CLONAL	1	NA	0	0.195532404603731	0		729	294	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586388	189586388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1404019220	NA	P-0121567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	15	371	1	ENST00000264731.3:c.1012C>T	p.Arg338Cys	p.R338C	ENST00000264731	NM_003722.4	338	Cgc/Tgc	8/14	1	2	FACETS	0.606	0.443	0.802	0.606	0.443	0.802	SUBCLONAL	1	NA	1	0.195532404603731	2		372	253	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971137	21971137	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	105	340	0	ENST00000304494.5:c.221A>G	p.Asp74Gly	p.D74G	ENST00000304494	NM_000077.4	74	gAc/gGc	2/3	0.3	1	FACETS	0.889	0.8	0.981	1	0.986	1	CLONAL	2	TRUE	0	0.22	1		340	478	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542109	187542110	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0033780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	98	515	0	ENST00000441802.2:c.5630_5631del	p.Pro1877ArgfsTer8	p.P1877Rfs*8	ENST00000441802	NM_005245.3	1877	cCT/c	10/27	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.22	2		515	623	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849798	151849798	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	47	313	0	ENST00000262189.6:c.12518C>A	p.Thr4173Lys	p.T4173K	ENST00000262189	NM_170606.2	4173	aCa/aAa	49/59	0.139746871958052	3	FACETS	0.95	0.802	1	0.475	0.401	0.557	CLONAL	1	TRUE	1	0.22	3		313	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577600	7577602	+	frameshift_variant	Frame_Shift_Del	DEL	AGA	AGA	C	novel	NA	P-0033780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	104	545	0	ENST00000269305.4:c.679_681delinsG	p.Ser227GlyfsTer12	p.S227Gfs*12	ENST00000269305	NM_001126112.2	227	TCT/G	7/11	0.276981309061111	1	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	0	0.22	1		545	833	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0033782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	237	257	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.893424016067828	2		258	504	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11269433	11269433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747210595	NA	P-0033782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	441	673	0	ENST00000361445.4:c.3737C>T	p.Ala1246Val	p.A1246V	ENST00000361445	NM_004958.3	1246	gCt/gTt	25/58	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.893424016067828	2		673	958	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8105964	8105964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	327	559	0	ENST00000346208.3:c.784G>A	p.Glu262Lys	p.E262K	ENST00000346208		262	Gag/Aag	4/6	1	2	FACETS	0.927	0.88	0.973	0.927	0.88	0.973	CLONAL	1	TRUE	1	0.893424016067828	2		559	790	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342667	118342667	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	137	207	1	ENST00000534358.1:c.793C>T	p.Gln265Ter	p.Q265*	ENST00000534358	NM_005933.3	265	Cag/Tag	3/36	0.893424016067828	1	FACETS	0.998	0.951	1	0.998	0.951	1	CLONAL	1	TRUE	0	0.893424016067828	1		208	170	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432719	49432719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1410236197	NA	P-0033782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	503	823	0	ENST00000301067.7:c.8420C>T	p.Ser2807Phe	p.S2807F	ENST00000301067	NM_003482.3	2807	tCc/tTc	34/54	1	2	FACETS	0.915	0.878	0.953	0.915	0.878	0.953	CLONAL	1	TRUE	1	0.893424016067828	2		823	1230	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112910842	112910842	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	218	456	0	ENST00000351677.2:c.851C>T	p.Pro284Leu	p.P284L	ENST00000351677	NM_002834.3	284	cCc/cTc	7/16	0.865125964017442	3	FACETS	0.78	0.726	0.836	0.39	0.363	0.418	SUBCLONAL	1	TRUE	1	0.893424016067828	3		456	905	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120642	115120642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	490	779	0	ENST00000257566.3:c.364G>A	p.Glu122Lys	p.E122K	ENST00000257566	NM_016569.3	122	Gag/Aag	1/8	0.865125964017442	3	FACETS	0.928	0.886	0.971	0.464	0.443	0.486	CLONAL	1	TRUE	1	0.893424016067828	3		779	1710	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678491	88678491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	433	679	1	ENST00000360948.2:c.1045C>T	p.His349Tyr	p.H349Y	ENST00000360948	NM_001012338.2	349	Cat/Tat	9/19	1	2	FACETS	0.965	0.924	1	0.965	0.924	1	CLONAL	1	TRUE	1	0.893424016067828	2		680	1004	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533791	63533791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779863826	NA	P-0033782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	428	541	0	ENST00000307078.5:c.1363C>T	p.Pro455Ser	p.P455S	ENST00000307078	NM_004655.3	455	Cca/Tca	6/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.893424016067828	2		541	954	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961038	18961038	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	400	560	0	ENST00000262803.5:c.616G>T	p.Val206Leu	p.V206L	ENST00000262803	NM_002911.3	206	Gtg/Ttg	4/24	1	2	FACETS	0.971	0.928	1	0.971	0.928	1	CLONAL	1	TRUE	1	0.893424016067828	2		560	922	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561090	9561090	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	306	488	0	ENST00000353224.5:c.692C>T	p.Ser231Leu	p.S231L	ENST00000353224	NM_177990.2	231	tCa/tTa	4/10	1	2	FACETS	0.979	0.929	1	0.979	0.929	1	CLONAL	1	TRUE	1	0.893424016067828	2		488	700	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651262	45651262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1214509737	NA	P-0033782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	511	746	0	ENST00000407780.3:c.763G>A	p.Ala255Thr	p.A255T	ENST00000407780	NM_001283052.1	255	Gcc/Acc	5/7	1	2	FACETS	0.992	0.953	1	0.992	0.953	1	CLONAL	1	TRUE	1	0.893424016067828	2		746	1153	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572330	41572330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	609	767	1	ENST00000263253.7:c.4859C>T	p.Pro1620Leu	p.P1620L	ENST00000263253	NM_001429.3	1620	cCc/cTc	30/31	1	2	FACETS	0.981	0.945	1	0.981	0.945	1	CLONAL	1	TRUE	1	0.893424016067828	2		768	1390	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721812	49721812	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs142690032	NA	P-0033782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	21	2	0	ENST00000449682.2:c.1951C>T	p.Arg651Ter	p.R651*	ENST00000449682	NM_020998.3	651	Cga/Tga	17/18	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.893424016067828	2		2	35	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499484	89499484	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	209	538	0	ENST00000336596.2:c.2654C>T	p.Pro885Leu	p.P885L	ENST00000336596	NM_005233.5	885	cCc/cTc	15/17	NA	2	FACETS	0.91	0.853	0.968			1	INDETERMINATE	1	TRUE	NA	0.893424016067828	2		538	514	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955063	55955063	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	338	502	2	ENST00000263923.4:c.3482G>A	p.Gly1161Glu	p.G1161E	ENST00000263923	NM_002253.2	1161	gGa/gAa	26/30	NA	2	FACETS	1	0.96	1			1	INDETERMINATE	1	TRUE	NA	0.893424016067828	2		504	750	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158154	106158154	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	205	407	0	ENST00000380013.4:c.3055G>T	p.Val1019Leu	p.V1019L	ENST00000380013	NM_001127208.2	1019	Gtg/Ttg	3/11	1	2	FACETS	0.964	0.904	1	0.964	0.904	1	CLONAL	1	TRUE	1	0.893424016067828	2		407	476	SUCCESS
APC	324	MSKCC	GRCh37	5	112175396	112175396	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	176	312	0	ENST00000257430.4:c.4105C>T	p.Pro1369Ser	p.P1369S	ENST00000257430	NM_000038.5	1369	Ccc/Tcc	16/16	1	2	FACETS	0.947	0.883	1	0.947	0.883	1	CLONAL	1	TRUE	1	0.893424016067828	2		312	416	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176666777	176666777	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	172	273	0	ENST00000439151.2:c.4213C>T	p.Gln1405Ter	p.Q1405*	ENST00000439151	NM_022455.4	1405	Caa/Taa	8/23	1	2	FACETS	0.93	0.866	0.995	0.93	0.866	0.995	CLONAL	1	TRUE	1	0.893424016067828	2		273	414	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797211	32797211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196693711	NA	P-0033782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1223	604	750	0	ENST00000374899.4:c.1898C>T	p.Ala633Val	p.A633V	ENST00000374899	NM_018833.2	633	gCt/gTt	11/12	0.865125964017442	3	FACETS	1	0.988	1	0.535	0.514	0.557	CLONAL	1	TRUE	1	0.893424016067828	3		750	1827	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32814973	32814973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	377	519	1	ENST00000354258.4:c.2092G>A	p.Glu698Lys	p.E698K	ENST00000354258	NM_000593.5	698	Gag/Aag	10/11	0.865125964017442	3	FACETS	0.961	0.912	1	0.481	0.456	0.506	CLONAL	1	TRUE	1	0.893424016067828	3		520	1270	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967864	93967864	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	320	636	1	ENST00000369303.4:c.2063A>T	p.Gln688Leu	p.Q688L	ENST00000369303	NM_004440.3	688	cAg/cTg	11/17	0.162902316419566	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.893424016067828	0		637	732	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979219	93979219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1009626356	NA	P-0033782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	139	354	0	ENST00000369303.4:c.1609G>A	p.Glu537Lys	p.E537K	ENST00000369303	NM_004440.3	537	Gaa/Aaa	7/17	0.162902316419566	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.893424016067828	0		354	331	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681040	117681040	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753216129	NA	P-0033782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	328	570	0	ENST00000368508.3:c.3580G>A	p.Glu1194Lys	p.E1194K	ENST00000368508	NM_002944.2	1194	Gag/Aag	23/43	0.162902316419566	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.893424016067828	0		570	750	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005438	150005438	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1437806382	NA	P-0033782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	418	601	1	ENST00000253339.5:c.787C>T	p.Pro263Ser	p.P263S	ENST00000253339		263	Cca/Tca	3/7	1	2	FACETS	0.995	0.952	1	0.995	0.952	1	CLONAL	1	TRUE	1	0.893424016067828	2		602	940	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730008	41730008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537531066	NA	P-0033782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	461	654	1	ENST00000242208.4:c.521G>A	p.Arg174His	p.R174H	ENST00000242208	NM_002192.2	174	cGc/cAc	3/3	1	2	FACETS	0.94	0.9	0.98	0.94	0.9	0.98	CLONAL	1	TRUE	1	0.893424016067828	2		655	1098	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444401	50444401	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	318	434	1	ENST00000331340.3:c.331C>T	p.Arg111Ter	p.R111*	ENST00000331340	NM_006060.4	111	Cga/Tga	4/8	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.893424016067828	2		435	710	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106512998	106512998	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	213	358	0	ENST00000359195.3:c.2012C>T	p.Pro671Leu	p.P671L	ENST00000359195	NM_002649.2	671	cCa/cTa	3/11	0.220455239961119	5	FACETS	0.81	0.756	0.865	0.324	0.302	0.346	INDETERMINATE	2	TRUE	0	0.893424016067828	5		358	689	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434507	140434507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1562931107	NA	P-0033782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2462	286	418	0	ENST00000288602.6:c.2191C>T	p.Pro731Ser	p.P731S	ENST00000288602	NM_004333.4	731	Ccc/Tcc	18/18	0.893424016067828	8	FACETS	0.857	0.802	0.916	0.122	0.114	0.131	CLONAL	1	TRUE	1	0.893424016067828	8		418	2748	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0033782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	2196	434	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.893424016067828	8	FACETS	1	0.997	1	1	0.997	1	CLONAL	7	TRUE	1	0.893424016067828	8		434	2528	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38176411	38176411	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0033782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	295	451	0	ENST00000317025.8:c.1855+2T>G		p.X619_splice	ENST00000317025	NM_023034.1	619			1	2	FACETS	0.96	0.91	1	0.96	0.91	1	CLONAL	1	TRUE	1	0.893424016067828	2		451	688	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104681	69104681	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	417	684	1	ENST00000288368.4:c.4525G>A	p.Gly1509Arg	p.G1509R	ENST00000288368	NM_024870.2	1509	Gga/Aga	37/40	1	2	FACETS	0.956	0.914	0.999	0.956	0.914	0.999	CLONAL	1	TRUE	1	0.893424016067828	2		685	976	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0033784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	175	756	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.393367101212017	3	FACETS	0.871	0.807	0.937	0.871	0.807	0.937	CLONAL	2	TRUE	1	0.433233089451266	3		756	564	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0033784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	28	309	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.285019233855945	4	FACETS	0.477	0.381	0.587	0.239	0.19	0.294	SUBCLONAL	1	TRUE	2	0.433233089451266	4		309	388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519999	NA	P-0033784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	106	651	0	ENST00000269305.4:c.716A>G	p.Asn239Ser	p.N239S	ENST00000269305	NM_001126112.2	239	aAc/aGc	7/11	0.393367101212017	3	FACETS	0.932	0.837	1	0.466	0.418	0.516	CLONAL	1	TRUE	1	0.433233089451266	3		651	639	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025509	1025509	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs777120221	NA	P-0033784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	36	584	1	ENST00000358495.3:c.865+1G>A		p.X289_splice	ENST00000358495	NM_134424.2	289			0.433233089451266	5	FACETS	0.436	0.357	0.524	0.109	0.089	0.131	SUBCLONAL	1	TRUE	1	0.433233089451266	5		585	629	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38960627	38960627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376491170	NA	P-0033784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	20	202	0	ENST00000357387.3:c.1724G>A	p.Arg575Gln	p.R575Q	ENST00000357387	NM_152756.3	575	cGa/cAa	20/38	0.329200515034505	3	FACETS	0.562	0.431	0.713	0.187	0.143	0.238	SUBCLONAL	1	TRUE	0	0.433233089451266	3		202	200	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884353	151884353	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	92	288	0	ENST00000262189.6:c.5002T>G	p.Phe1668Val	p.F1668V	ENST00000262189	NM_170606.2	1668	Ttc/Gtc	33/59	0.234753695584837	5	FACETS	1	0.955	1	0.744	0.668	0.823	INDETERMINATE	2	TRUE	2	0.433233089451266	5		288	314	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0033785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	24	296	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.531652315828751	1	FACETS	0.558	0.447	0.68	0.558	0.447	0.68	SUBCLONAL	1	TRUE	0	0.623104501914602	1		296	95	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539564	187539564	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	15	534	1	ENST00000441802.2:c.8176C>T	p.Arg2726Ter	p.R2726*	ENST00000441802	NM_005245.3	2726	Cga/Tga	10/27	1	2	FACETS	0.802	0.604	1	0.802	0.604	1	CLONAL	1	TRUE	1	0.623104501914602	2		535	60	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188977	32188977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760997487	NA	P-0033785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	58	832	1	ENST00000375023.3:c.577C>T	p.Arg193Cys	p.R193C	ENST00000375023	NM_004557.3	193	Cgt/Tgt	4/30	0.251563935463556	4	FACETS	1	0.907	1	1	0.907	1	INDETERMINATE	2	TRUE	2	0.623104501914602	4		833	146	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610525	10610525	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	66	948	0	ENST00000171111.5:c.185A>C	p.Gln62Pro	p.Q62P	ENST00000171111	NM_203500.1	62	cAg/cCg	2/6	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.623104501914602	2		948	190	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0033786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	48	629	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	1	2	FACETS	0.76	0.641	0.891	0.76	0.641	0.891	SUBCLONAL	1	TRUE	1	0.19	2		629	665	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0033786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	63	660	2	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	0.849	0.733	0.976	0.849	0.733	0.976	CLONAL	1	TRUE	1	0.19	2		662	781	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242511	55242511	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913418	NA	P-0033786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	23	285	0	ENST00000275493.2:c.2281G>T	p.Asp761Tyr	p.D761Y	ENST00000275493	NM_005228.3	761	Gat/Tat	19/28	1	2	FACETS	0.674	0.525	0.847	0.674	0.525	0.847	SUBCLONAL	1	TRUE	1	0.19	2		285	359	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39321381	39321381	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	68	471	0	ENST00000373001.3:c.640del	p.Ser214AlafsTer4	p.S214Afs*4	ENST00000373001	NM_022157.3	214	Agc/gc	3/7	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.19	2		471	713	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523315	9523315	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	56	577	0	ENST00000353224.5:c.1922C>A	p.Pro641His	p.P641H	ENST00000353224	NM_177990.2	641	cCc/cAc	9/10	1	2	FACETS	0.914	0.782	1	0.914	0.782	1	CLONAL	1	TRUE	1	0.19	2		577	645	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852430	42852430	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	62	637	0	ENST00000398585.3:c.656G>C	p.Arg219Pro	p.R219P	ENST00000398585	NM_001135099.1	219	cGg/cCg	6/14	1	2	FACETS	0.947	0.817	1	0.947	0.817	1	CLONAL	1	TRUE	1	0.19	2		637	689	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091779	29091779	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881690	NA	P-0033786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	64	514	0	ENST00000328354.6:c.1178C>T	p.Pro393Leu	p.P393L	ENST00000328354	NM_007194.3	393	cCt/cTt	11/15	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.19	2		514	615	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127951915	127951925	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGCTCACCTT	GGGCTCACCTT	-	novel	NA	P-0033786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	88	553	0	ENST00000373547.4:c.73_75+8del		p.X25_splice	ENST00000373547	NM_002721.4	25		1/7	1	2	FACETS	0.836	0.742	0.936	1	0.982	1	CLONAL	2	TRUE	1	0.19	2		553	554	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0033787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	186	742	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.314127569722314	2	FACETS	0.997	0.926	1	0.997	0.926	1	CLONAL	2	TRUE	0	0.314127569722314	2		743	594	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910318	50910318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201804732	NA	P-0033787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	94	695	2	ENST00000440232.2:c.1573C>T	p.Arg525Trp	p.R525W	ENST00000440232	NM_002691.3	525	Cgg/Tgg	13/27	0.290561553147599	3	FACETS	0.834	0.742	0.933	0.417	0.371	0.467	CLONAL	1	TRUE	1	0.314127569722314	3		697	830	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691784	30691784	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	128	454	0	ENST00000295754.5:c.286A>T	p.Thr96Ser	p.T96S	ENST00000295754	NM_003242.5	96	Aca/Tca	3/7	0.314127569722314	5	FACETS	0.891	0.809	0.977	0.594	0.539	0.651	CLONAL	2	TRUE	2	0.314127569722314	5		454	673	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0033788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	55	454	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.26707750334506	5	FACETS	0.998	0.87	1	0.998	0.87	1	CLONAL	3	TRUE	2	0.319745211763107	5		454	170	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699360	47699360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	21	415	0	ENST00000347630.2:c.148G>A	p.Glu50Lys	p.E50K	ENST00000347630	NM_001007230.1	50	Gaa/Aaa	4/11	0.319745211763107	3	FACETS	0.861	0.667	1	0.43	0.333	0.542	CLONAL	1	TRUE	1	0.319745211763107	3		415	177	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134230	2134230	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs148527903	NA	P-0033788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	137	502	0	ENST00000219476.3:c.4007C>T	p.Ser1336Leu	p.S1336L	ENST00000219476	NM_000548.3	1336	tCg/tTg	34/42	0.278731261741706	3	FACETS	1	0.958	1			1	CLONAL	1	TRUE	NA	0.319745211763107	3		502	909	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686293	30686294	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0033788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	17	429	0	ENST00000295754.5:c.152_153del	p.Cys51Ter	p.C51*	ENST00000295754	NM_003242.5	50	cTG/c	2/7	0.144014192417982	2	FACETS	0.837	0.631	1	0.419	0.315	0.539	INDETERMINATE	1	TRUE	0	0.319745211763107	2		429	127	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843499	3843499	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	77	548	0	ENST00000262367.5:c.1104G>T	p.Gln368His	p.Q368H	ENST00000262367	NM_004380.2	368	caG/caT	4/31	0.319745211763107	4	FACETS	0.793	0.699	0.892			1	SUBCLONAL	2	TRUE	NA	0.319745211763107	4		548	401	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40457711	40457711	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	263	513	0	ENST00000345506.4:c.1464T>G	p.Phe488Leu	p.F488L	ENST00000345506	NM_003152.3	488	ttT/ttG	13/20	0.164882318453213	1	FACETS	0.866	0.815	0.918	1	0.994	1	INDETERMINATE	2	TRUE	0	0.319745211763107	1		513	798	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419941	41419941	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	51	482	0	ENST00000373198.4:c.380A>T	p.Asn127Ile	p.N127I	ENST00000373198	NM_133170.3	127	aAt/aTt	3/32	0.249490789265517	4	FACETS	0.765	0.656	0.884	0.765	0.656	0.884	SUBCLONAL	2	TRUE	2	0.319745211763107	4		482	275	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478171	138478171	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1163476279	NA	P-0033788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	17	398	0	ENST00000289153.2:c.15C>G	p.Phe5Leu	p.F5L	ENST00000289153	NM_006219.2	5	ttC/ttG	1/22	0.26707750334506	5	FACETS	0.756	0.566	0.981	0.252	0.188	0.327	CLONAL	1	TRUE	2	0.319745211763107	5		398	208	SUCCESS
ATR	545	MSKCC	GRCh37	3	142257415	142257415	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	17	376	0	ENST00000350721.4:c.3634C>G	p.Leu1212Val	p.L1212V	ENST00000350721	NM_001184.3	1212	Ctc/Gtc	19/47	0.26707750334506	5	FACETS	0.942	0.707	1	0.314	0.235	0.406	CLONAL	1	TRUE	2	0.319745211763107	5		376	167	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238377	98238377	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	31	487	0	ENST00000331920.6:c.1667T>A	p.Val556Asp	p.V556D	ENST00000331920	NM_000264.3	556	gTc/gAc	12/24	0.319745211763107	5	FACETS	0.628	0.507	0.765	0.126	0.101	0.153	SUBCLONAL	1	TRUE	0	0.319745211763107	5		487	457	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412557	139412591	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CACCTGGCCGCACCCCCTGTGCTGGCACCTACCCA	CACCTGGCCGCACCCCCTGTGCTGGCACCTACCCA	-	novel	NA	P-0033788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	1171	418	0	ENST00000277541.6:c.1253_1255+32del		p.X418_splice	ENST00000277541	NM_017617.3	418		7/34	0.319745211763107	6	FACETS	1	0.996	1	1	0.998	1	CLONAL	7	TRUE	0	0.319745211763107	6		418	1620	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0033789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	442	637	0	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.867330478864578	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.867330478864578	2		637	496	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916804	48916804	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	545	426	0	ENST00000267163.4:c.334G>T	p.Glu112Ter	p.E112*	ENST00000267163	NM_000321.2	112	Gag/Tag	3/27	0.867330478864578	3	FACETS	0.981	0.964	0.998	0.981	0.964	0.998	CLONAL	3	TRUE	0	0.867330478864578	3		426	612	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467807	99467815	+	inframe_deletion	In_Frame_Del	DEL	GCTAAACCG	GCTAAACCG	-	novel	NA	P-0033789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	49	347	0	ENST00000268035.6:c.2684_2692del	p.Arg895_Asn897del	p.R895_N897del	ENST00000268035	NM_000875.3	892	aaGCTAAACCGg/aag	13/21	0.867330478864578	5	FACETS	0.312	0.264	0.367	0.062	0.052	0.074	SUBCLONAL	1	TRUE	0	0.867330478864578	5		347	832	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435821	56435822	+	missense_variant	Missense_Mutation	DNP	CT	CT	GG	novel	NA	P-0033789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	115	498	0	ENST00000407977.2:c.1315_1316delinsCC	p.Arg439Pro	p.R439P	ENST00000407977		439	AGg/CCg	9/10	0.772362379760643	5	FACETS	0.847	0.764	0.936	0.282	0.254	0.312	CLONAL	1	TRUE	2	0.867330478864578	5		498	720	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17389756	17389756	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	228	793	0	ENST00000359435.4:c.891del	p.Lys297AsnfsTer72	p.K297Nfs*72	ENST00000359435	NM_001033549.1	297	Aaa/aa	9/9	0.86645049253947	3	FACETS	1	0.962	1	0.52	0.486	0.554	CLONAL	1	TRUE	1	0.867330478864578	3		793	725	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998096	169998096	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1945	287	622	0	ENST00000295797.4:c.787G>C	p.Gly263Arg	p.G263R	ENST00000295797	NM_002740.5	263	Gga/Cga	9/18	0.867330478864578	8	FACETS	1	0.972	1	0.178	0.166	0.19	CLONAL	1	TRUE	2	0.867330478864578	8		622	2232	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589619	67589624	+	inframe_deletion	In_Frame_Del	DEL	GAGAAT	GAGAAT	-	novel	NA	P-0033789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	141	219	0	ENST00000274335.5:c.1382_1387del	p.Arg461_Tyr463delinsHis	p.R461_Y463delinsH	ENST00000274335		461	cGAGAATat/cat	10/15	0.450171947079524	4	FACETS	1	0.943	1	0.679	0.63	0.729	INDETERMINATE	2	TRUE	1	0.867330478864578	4		219	298	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591010	67591038	+	frameshift_variant	Frame_Shift_Del	DEL	ATCAGTGAAATTATTGACAGTAGAAGAAG	ATCAGTGAAATTATTGACAGTAGAAGAAG	-	novel	NA	P-0033789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	73	205	0	ENST00000274335.5:c.1605_1633del	p.Ser536GlyfsTer10	p.S536Gfs*10	ENST00000274335		535	ATCAGTGAAATTATTGACAGTAGAAGAAGa/a	12/15	0.450171947079524	4	FACETS	1	0.906	1	0.344	0.303	0.386	INDETERMINATE	1	TRUE	1	0.867330478864578	4		205	305	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207501	29207501	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	41	393	0	ENST00000240100.2:c.295T>A	p.Ser99Thr	p.S99T	ENST00000240100	NM_001394.6	99	Tcc/Acc	1/4	0.867330478864578	2	FACETS	0.377	0.316	0.443	0.188	0.158	0.222	SUBCLONAL	1	TRUE	0	0.867330478864578	2		393	251	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0033792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	71	459	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.344278904925555	7	FACETS	1	0.933	1	0.648	0.573	0.725	CLONAL	3	TRUE	2	0.344278904925555	7		459	237	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0033792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	101	462	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.344278904925555	7	FACETS	0.91	0.829	0.992	0.91	0.829	0.992	CLONAL	5	TRUE	2	0.344278904925555	7		462	240	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249092	55249092	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	51	636	0	ENST00000275493.2:c.2390G>C	p.Cys797Ser	p.C797S	ENST00000275493	NM_005228.3	797	tGc/tCc	20/28	0.344278904925555	7	FACETS	1	0.929	1	0.456	0.391	0.525	CLONAL	2	TRUE	2	0.344278904925555	7		636	242	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	364595	364595	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	29	723	0	ENST00000262320.3:c.967C>T	p.Gln323Ter	p.Q323*	ENST00000262320	NM_003502.3	323	Cag/Tag	3/11	0.344278904925555	7	FACETS	0.97	0.78	1	0.194	0.156	0.238	CLONAL	1	TRUE	2	0.344278904925555	7		723	323	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222867	5222867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1193352037	NA	P-0033792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	11	369	0	ENST00000357368.4:c.2936G>A	p.Arg979Gln	p.R979Q	ENST00000357368	NM_002850.3	979	cGa/cAa	18/38	0.247123920705021	4	FACETS	1	0.707	1	0.505	0.353	0.689	CLONAL	1	TRUE	2	0.344278904925555	4		369	85	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54956508	54956508	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	21	369	0	ENST00000312783.6:c.686A>T	p.Asp229Val	p.D229V	ENST00000312783	NM_198436.1	229	gAt/gTt	7/10	0.232558160712198	5	FACETS	1	0.872	1	0.398	0.309	0.5	CLONAL	1	TRUE	2	0.344278904925555	5		369	155	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432289	432289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376128815	NA	P-0033794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	119	481	0	ENST00000399788.2:c.2234G>A	p.Arg745His	p.R745H	ENST00000399788	NM_001042603.1	745	cGt/cAt	16/28	0.544422311853086	3	FACETS	0.845	0.767	0.928			1	CLONAL	1	TRUE	NA	0.740298628028539	3		481	521	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	360011	360011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759808424	NA	P-0033794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	155	663	1	ENST00000262320.3:c.1078G>A	p.Val360Met	p.V360M	ENST00000262320	NM_003502.3	360	Gtg/Atg	4/11	0.595320936853595	4	FACETS	1	0.945	1	0.519	0.476	0.564	CLONAL	1	TRUE	2	0.740298628028539	4		664	702	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741245	40741245	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	122	580	0	ENST00000392038.2:c.1188del	p.Ser398AlafsTer177	p.S398Afs*177	ENST00000392038	NM_001626.4	396	ggG/gg	12/14	0.514028605834968	4	FACETS	0.885	0.802	0.973	0.443	0.401	0.487	CLONAL	1	TRUE	2	0.740298628028539	4		580	648	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255818	16255818	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	153	284	0	ENST00000375759.3:c.3084del	p.Leu1029CysfsTer2	p.L1029Cfs*2	ENST00000375759	NM_015001.2	1028	aTt/at	11/15	0.595320936853595	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.740298628028539	4		284	341	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741252	40741252	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	126	567	1	ENST00000392038.2:c.1181G>T	p.Gly394Val	p.G394V	ENST00000392038	NM_001626.4	394	gGt/gTt	12/14	0.514028605834968	4	FACETS	0.918	0.834	1	0.459	0.417	0.504	CLONAL	1	TRUE	2	0.740298628028539	4		568	645	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156741	20156787	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CTGATGGTTTAAAAAAAAGAAAAGGAGGTAAATGACATTAATTATCT	CTGATGGTTTAAAAAAAAGAAAAGGAGGTAAATGACATTAATTATCT	-	novel	NA	P-0033794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	70	463	0	ENST00000379607.5:c.17-47_17-1del		p.X6_splice	ENST00000379607	NM_001412.3	6			0.740298628028539	2	FACETS	1	0.97	1	0.626	0.562	0.691	CLONAL	1	TRUE	0	0.740298628028539	2		463	151	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0033797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	49	264	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	0.22	2		264	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0033797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	18	572	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	1	2	FACETS	0.253	0.189	0.328	0.253	0.189	0.328	SUBCLONAL	1	TRUE	1	0.22	2		572	648	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52693429	52693429	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0033797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	38	558	1	ENST00000322088.6:c.78+2T>A		p.X26_splice	ENST00000322088	NM_014225.5	26			1	2	FACETS	0.597	0.492	0.714	0.597	0.492	0.714	SUBCLONAL	1	TRUE	1	0.22	2		559	579	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363243	40363243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	117	636	0	ENST00000397332.2:c.986C>T	p.Ser329Leu	p.S329L	ENST00000397332	NM_001033082.2	329	tCg/tTg	3/3	0.457037595611234	3	FACETS	1	0.969	1	0.585	0.529	0.643	CLONAL	1	TRUE	1	0.457037595611234	3		636	538	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397742	49397742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552757	NA	P-0033799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	216	645	0	ENST00000418115.1:c.482C>T	p.Ala161Val	p.A161V	ENST00000418115	NM_001664.2	161	gCa/gTa	5/5	0.338870323839006	4	FACETS	0.978	0.913	1	0.978	0.913	1	CLONAL	2	TRUE	2	0.457037595611234	4		645	704	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521253	187521253	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	193	692	0	ENST00000441802.2:c.11902C>T	p.Gln3968Ter	p.Q3968*	ENST00000441802	NM_005245.3	3968	Caa/Taa	22/27	0.305987011226713	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.457037595611234	2		692	408	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216899	7216899	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	159	523	0	ENST00000380728.2:c.622C>T	p.Gln208Ter	p.Q208*	ENST00000380728		208	Cag/Tag	7/11	0.338870323839006	4	FACETS	0.927	0.854	1	0.927	0.854	1	CLONAL	2	TRUE	2	0.457037595611234	4		523	547	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056181	27056181	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	179	493	0	ENST00000324856.7:c.1177C>T	p.Gln393Ter	p.Q393*	ENST00000324856	NM_006015.4	393	Cag/Tag	2/20	0.457037595611234	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.457037595611234	3		493	419	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797891	45797891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199840380	NA	P-0033799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	98	782	1	ENST00000450313.1:c.880C>T	p.Arg294Cys	p.R294C	ENST00000450313	NM_012222.2	294	Cgc/Tgc	10/16	0.457037595611234	3	FACETS	0.967	0.865	1	0.483	0.432	0.537	CLONAL	1	TRUE	1	0.457037595611234	3		783	545	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118354897	118354897	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0033799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	157	429	0	ENST00000534358.1:c.4087-1G>A		p.X1363_splice	ENST00000534358	NM_005933.3	1363			0.177751638624323	5	FACETS	0.858	0.793	0.924	0.858	0.793	0.924	INDETERMINATE	3	TRUE	2	0.457037595611234	5		429	450	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807967	3807967	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	106	655	1	ENST00000262367.5:c.3452G>A	p.Trp1151Ter	p.W1151*	ENST00000262367	NM_004380.2	1151	tGg/tAg	18/31	0.392125105354229	3	FACETS	0.933	0.838	1	0.466	0.419	0.517	CLONAL	1	TRUE	1	0.457037595611234	3		656	611	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56401603	56401603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	74	475	0	ENST00000348428.3:c.1465G>A	p.Gly489Arg	p.G489R	ENST00000348428	NM_006785.3	489	Gga/Aga	12/17	0.457037595611234	3	FACETS	0.886	0.778	1	0.443	0.389	0.501	CLONAL	1	TRUE	1	0.457037595611234	3		475	449	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56402522	56402522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	18	254	0	ENST00000348428.3:c.1564G>A	p.Asp522Asn	p.D522N	ENST00000348428	NM_006785.3	522	Gat/Aat	13/17	0.457037595611234	3	FACETS	0.491	0.371	0.632	0.246	0.185	0.316	SUBCLONAL	1	TRUE	1	0.457037595611234	3		254	197	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513814	41513814	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	167	551	0	ENST00000263253.7:c.718C>T	p.Gln240Ter	p.Q240*	ENST00000263253	NM_001429.3	240	Cag/Tag	2/31	0.338870323839006	4	FACETS	0.918	0.848	0.99	0.918	0.848	0.99	CLONAL	2	TRUE	2	0.457037595611234	4		551	580	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659164	86659164	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0033799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	35	165	0	ENST00000274376.6:c.1454-1G>A		p.X485_splice	ENST00000274376	NM_002890.2	485			0.457037595611234	3	FACETS	1	0.95	1	0.713	0.595	0.839	CLONAL	1	TRUE	1	0.457037595611234	3		165	132	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138913	37138913	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	131	570	0	ENST00000373509.5:c.253C>T	p.Arg85Ter	p.R85*	ENST00000373509	NM_002648.3	85	Cga/Tga	4/6	0.417278624125365	4	FACETS	0.892	0.815	0.972	0.892	0.815	0.972	CLONAL	2	TRUE	2	0.457037595611234	4		570	468	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918645	44918646	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AATGC	novel	NA	P-0033799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	183	262	0	ENST00000377967.4:c.1131_1135dup	p.Thr379MetfsTer62	p.T379Mfs*62	ENST00000377967	NM_021140.2	376	-/AATGC	12/29	0.362990588594461	2	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.457037595611234	2		262	333	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842658	68842659	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	310	618	1	ENST00000261769.5:c.595dup	p.Thr199AsnfsTer10	p.T199Nfs*10	ENST00000261769	NM_004360.3	198	-/A	5/16	0.437827941108388	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.437827941108388	2		619	701	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0033806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	59	454	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.23006029027189	4	FACETS	0.926	0.805	1	0.926	0.805	1	CLONAL	2	FALSE	2	0.338426519957838	4		454	252	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0033806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	114	454	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.338426519957838	3	FACETS	0.878	0.802	0.956	1	0.982	1	CLONAL	3	FALSE	1	0.338426519957838	3		454	299	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864663	68864663	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773560075	NA	P-0033806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	92	197	0	ENST00000288368.4:c.34G>A	p.Glu12Lys	p.E12K	ENST00000288368	NM_024870.2	12	Gag/Aag	1/40	0.23006029027189	4	FACETS	1	0.91	1	1	0.983	1	CLONAL	3	FALSE	2	0.338426519957838	4		197	241	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207627	2207627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	210	532	1	ENST00000398665.3:c.911C>T	p.Ser304Leu	p.S304L	ENST00000398665	NM_032482.2	304	tCg/tTg	11/28	0.23006029027189	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	FALSE	2	0.338426519957838	4		533	791	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247554	123247554	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	186	619	0	ENST00000358487.5:c.1937G>T	p.Gly646Val	p.G646V	ENST00000358487	NM_000141.4	646	gGa/gTa	14/18	0.23006029027189	4	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	FALSE	2	0.338426519957838	4		619	693	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900956	3900956	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs536856848	NA	P-0033806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	182	550	0	ENST00000262367.5:c.140A>G	p.Asn47Ser	p.N47S	ENST00000262367	NM_004380.2	47	aAt/aGt	2/31	0.338426519957838	6	FACETS	1	0.973	1	0.556	0.514	0.6	CLONAL	2	FALSE	2	0.338426519957838	6		550	811	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532484	63532484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567754013	NA	P-0033806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	101	643	0	ENST00000307078.5:c.2095G>A	p.Glu699Lys	p.E699K	ENST00000307078	NM_004655.3	699	Gag/Aag	8/11	0.338426519957838	3	FACETS	1	0.926	1	0.522	0.466	0.58	CLONAL	1	FALSE	1	0.338426519957838	3		643	669	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144848	11144848	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	177	411	0	ENST00000358026.2:c.3923G>T	p.Arg1308Leu	p.R1308L	ENST00000358026	NM_001128849.1	1308	cGg/cTg	28/36	0.23006029027189	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	FALSE	2	0.338426519957838	4		411	616	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511132	148511133	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0033806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	79	391	0	ENST00000320356.2:c.1769dup	p.Cys590TrpfsTer8	p.C590Wfs*8	ENST00000320356	NM_004456.4	590	tgt/tgGt	15/20	0.338426519957838	3	FACETS	1	0.921	1	0.529	0.466	0.596	CLONAL	1	FALSE	1	0.338426519957838	3		391	516	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212732	27212732	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	287	624	2	ENST00000380036.4:c.2714C>A	p.Ala905Glu	p.A905E	ENST00000380036	NM_000459.3	905	gCg/gAg	17/23	0.23006029027189	4	FACETS	0.85	0.802	0.9	1	0.991	1	CLONAL	3	FALSE	2	0.338426519957838	4		626	890	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412155	63412155	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	440	857	0	ENST00000330258.3:c.1012del	p.Asp338ThrfsTer3	p.D338Tfs*3	ENST00000330258	NM_152424.3	338	Gac/ac	2/2	0.227074558383786	4	FACETS	0.884	0.847	0.922	0.884	0.847	0.922	CLONAL	4	FALSE	0	0.338426519957838	4		857	984	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0033807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	110	699	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.788	0.709	0.871	0.788	0.709	0.871	SUBCLONAL	1	TRUE	1	0.425599608855191	2		699	656	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0033807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	187	905	1	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.425599608855191	1	FACETS	0.909	0.842	0.979	0.909	0.842	0.979	CLONAL	1	TRUE	0	0.425599608855191	1		906	761	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0033807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	59	296	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.9	0.78	1	0.9	0.78	1	CLONAL	1	TRUE	1	0.425599608855191	2		296	308	SUCCESS
APC	324	MSKCC	GRCh37	5	112175789	112175789	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	69	266	0	ENST00000257430.4:c.4501del	p.Ser1501LeufsTer6	p.S1501Lfs*6	ENST00000257430	NM_000038.5	1500	Ttt/tt	16/16	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.425599608855191	2		266	311	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593496	48593496	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	113	256	1	ENST00000342988.3:c.1247G>A	p.Arg416Lys	p.R416K	ENST00000342988	NM_005359.5	416	aGa/aAa	10/12	0.425599608855191	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.425599608855191	1		257	352	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588751	29588751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760703505	NA	P-0033810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	54	276	0	ENST00000356175.3:c.4537C>T	p.Arg1513Ter	p.R1513*	ENST00000356175	NM_000267.3	1513	Cga/Tga	34/57	0.138751779392097	6	FACETS	1	0.964	1	0.479	0.411	0.552	INDETERMINATE	1	TRUE	3	0.423637450431261	6		276	328	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950304	38950304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs895560221	NA	P-0033810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	118	528	0	ENST00000357387.3:c.3646C>T	p.Arg1216Cys	p.R1216C	ENST00000357387	NM_152756.3	1216	Cgt/Tgt	31/38	0.38040535150993	4	FACETS	1	0.981	1	0.45	0.407	0.495	CLONAL	1	TRUE	1	0.423637450431261	4		528	588	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142981	30142981	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	131	662	0	ENST00000389048.3:c.545A>C	p.Glu182Ala	p.E182A	ENST00000389048	NM_004304.4	182	gAa/gCa	1/29	0.284995258861498	3	FACETS	1	0.986	1	0.733	0.669	0.8	CLONAL	1	TRUE	1	0.423637450431261	3		662	511	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047393	128047393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139690693	NA	P-0033810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	19	333	1	ENST00000285398.2:c.529G>A	p.Val177Ile	p.V177I	ENST00000285398	NM_000122.1	177	Gtt/Att	5/15	0.240988569117639	4	FACETS	0.408	0.309	0.524	0.204	0.154	0.262	INDETERMINATE	1	TRUE	2	0.423637450431261	4		334	313	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542615	141542615	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	41	545	0	ENST00000220592.5:c.2371G>T	p.Val791Leu	p.V791L	ENST00000220592	NM_012154.3	791	Gtg/Ttg	18/19	0.187221928494847	5	FACETS	0.617	0.514	0.732	0.206	0.171	0.244	INDETERMINATE	1	TRUE	2	0.423637450431261	5		545	513	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564144	139564144	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	38	770	0	ENST00000308874.7:c.284C>A	p.Thr95Asn	p.T95N	ENST00000308874		95	aCc/aAc	5/10	0.275497486327452	3	FACETS	0.375	0.309	0.449	0.125	0.103	0.15	SUBCLONAL	1	TRUE	0	0.423637450431261	3		770	580	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0033815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	148	462	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.711067386582458	6	FACETS	0.92	0.859	0.981	1	0.986	1	CLONAL	4	FALSE	3	0.711067386582458	6		462	274	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0033815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	59	745	0	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	0.447919386282982	2	FACETS	1	0.879	1	0.5	0.439	0.563	CLONAL	1	FALSE	0	0.711067386582458	2		745	166	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984856	72984856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	101	310	0	ENST00000268489.5:c.2728G>A	p.Glu910Lys	p.E910K	ENST00000268489	NM_006885.3	910	Gag/Aag	3/10	0.718439562230091	4	FACETS	0.957	0.87	1	0.638	0.58	0.697	CLONAL	2	FALSE	1	0.711067386582458	4		310	254	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1040454	1040454	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs769802409	NA	P-0033815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	93	651	0	ENST00000358495.3:c.118C>G	p.Gln40Glu	p.Q40E	ENST00000358495	NM_134424.2	40	Cag/Gag	3/12	0.711067386582458	6	FACETS	0.835	0.754	0.917			1	CLONAL	3	FALSE	NA	0.711067386582458	6		651	253	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	184	697	0	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	0.994	1	CLONAL	2	TRUE	1	0.218993909276117	2		697	676	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0033823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	123	808	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.814	0.737	0.895	1	0.987	1	CLONAL	2	TRUE	1	0.218993909276117	2		808	690	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584513	48584514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs377767334	NA	P-0033823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	37	328	0	ENST00000342988.3:c.692dup	p.Ser232GlnfsTer3	p.S232Qfs*3	ENST00000342988	NM_005359.5	229	ctg/ctGg	6/12	0.218993909276117	1	FACETS	0.875	0.723	1	0.875	0.723	1	CLONAL	1	TRUE	0	0.218993909276117	1		328	344	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229215	36229215	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0121482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	41	551	0	ENST00000222270.7:c.7905C>G	p.Asp2635Glu	p.D2635E	ENST00000222270	NM_014727.1	2635	gaC/gaG	37/37	1	2	FACETS	0.429	0.358	0.508	0.429	0.358	0.508	SUBCLONAL	1	NA	1	0.499945815185111	2		551	382	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136900	55136900	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0121482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	21	355	1	ENST00000257290.5:c.1222G>T	p.Glu408Ter	p.E408*	ENST00000257290	NM_006206.4	408	Gaa/Taa	8/23	0.195320722658253	3	FACETS	0.259	0.198	0.329	0.129	0.099	0.165	INDETERMINATE	1	NA	1	0.499945815185111	3		356	406	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872196	76872196	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	32	276	0	ENST00000373344.5:c.5451G>T	p.Arg1817Ser	p.R1817S	ENST00000373344	NM_000489.3	1817	agG/agT	22/35	1	2	FACETS	0.375	0.305	0.455	0.375	0.305	0.455	SUBCLONAL	1	NA	1	0.499945815185111	2		276	341	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0033825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	92	454	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.25394297564783	3	FACETS	1	0.971	1	0.643	0.572	0.718	CLONAL	1	TRUE	1	0.260472070274963	3		454	621	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65349050	65349050	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	135	459	0	ENST00000342505.4:c.115A>G	p.Ile39Val	p.I39V	ENST00000342505	NM_002227.2	39	Atc/Gtc	3/25	0.189896723827683	4	FACETS	0.902	0.821	0.987			1	CLONAL	2	TRUE	NA	0.260472070274963	4		459	724	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111510	8111511	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AATGGGGACCCTGTCTGCAATGCCTGTGGGCTCTACTACA	novel	NA	P-0033825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	91	467	0	ENST00000346208.3:c.998_1037dup	p.Leu347TrpfsTer18	p.L347Wfs*18	ENST00000346208		332	-/AATGGGGACCCTGTCTGCAATGCCTGTGGGCTCTACTACA	5/6	0.192962601979393	4	FACETS	1	0.951	1	0.566	0.502	0.634	CLONAL	1	TRUE	2	0.260472070274963	4		467	778	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936995	48936995	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778842	NA	P-0033832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	79	409	0	ENST00000267163.4:c.763C>T	p.Arg255Ter	p.R255*	ENST00000267163	NM_000321.2	255	Cga/Tga	8/27	0.455348011388695	3	FACETS	0.85	0.768	0.933	0.85	0.768	0.933	CLONAL	3	TRUE	0	0.455348011388695	3		409	167	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	484	770	0	ENST00000269305.4:c.745del	p.Arg249GlyfsTer96	p.R249Gfs*96	ENST00000269305	NM_001126112.2	249	Agg/gg	7/11	0.421628885357693	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.455348011388695	2		770	949	SUCCESS
APC	324	MSKCC	GRCh37	5	112175256	112175256	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	61	267	0	ENST00000257430.4:c.3966del	p.Val1323PhefsTer92	p.V1323Ffs*92	ENST00000257430	NM_000038.5	1322	gAa/ga	16/16	0.169996119539692	1	FACETS	1	0.974	1	1	0.974	1	INDETERMINATE	1	TRUE	0	0.455348011388695	1		267	145	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594221	55594221	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913512	NA	P-0033833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	683	514	0	ENST00000288135.5:c.1924A>G	p.Lys642Glu	p.K642E	ENST00000288135	NM_000222.2	642	Aaa/Gaa	13/21	0.733863357627944	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.733863357627944	3		514	798	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0033833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	583	570	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.697110689092764	2	FACETS	0.986	0.96	1	0.986	0.96	1	CLONAL	2	TRUE	0	0.733863357627944	2		570	806	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624270	89624270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123324	NA	P-0033833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	359	408	0	ENST00000371953.3:c.44G>A	p.Arg15Lys	p.R15K	ENST00000371953	NM_000314.4	15	aGa/aAa	1/9	0.733863357627944	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.733863357627944	2		408	477	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146661	185146661	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	122	545	0	ENST00000265026.3:c.292T>A	p.Ser98Thr	p.S98T	ENST00000265026	NM_004721.4	98	Tct/Act	2/14	0.294867576914338	2	FACETS	0.545	0.494	0.599	0.273	0.247	0.3	INDETERMINATE	1	TRUE	0	0.733863357627944	2		545	610	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0033837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	75	454	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	0.21	2		454	540	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061240	38061240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	77	661	0	ENST00000250448.2:c.749C>T	p.Ser250Phe	p.S250F	ENST00000250448	NM_004496.3	250	tCc/tTc	2/2	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.21	2		661	533	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106058	8106058	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	59	410	0	ENST00000346208.3:c.878T>A	p.Met293Lys	p.M293K	ENST00000346208		293	aTg/aAg	4/6	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.21	2		410	460	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031973	26031973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	33	342	0	ENST00000244661.2:c.316G>C	p.Glu106Gln	p.E106Q	ENST00000244661	NM_003537.3	106	Gag/Cag	1/1	0.260409268913499	4	FACETS	0.814	0.663	0.986	0.407	0.331	0.493	CLONAL	1	TRUE	2	0.21	4		342	467	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0033837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	83	406	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.21	2		406	600	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440078	220440078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759385742	NA	P-0033837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	47	860	0	ENST00000243786.2:c.931C>T	p.Pro311Ser	p.P311S	ENST00000243786	NM_002191.3	311	Ccc/Tcc	2/2	1	2	FACETS	0.795	0.67	0.933	0.795	0.67	0.933	CLONAL	1	TRUE	1	0.21	2		860	563	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160206	22160206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	38	337	0	ENST00000215832.6:c.425C>T	p.Ser142Leu	p.S142L	ENST00000215832	NM_002745.4	142	tCa/tTa	3/9	1	2	FACETS	0.83	0.686	0.99	0.83	0.686	0.99	CLONAL	1	TRUE	1	0.21	2		337	436	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061226	38061226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	45	465	1	ENST00000250448.2:c.763G>A	p.Glu255Lys	p.E255K	ENST00000250448	NM_004496.3	255	Gag/Aag	2/2	1	2	FACETS	0.876	0.737	1	0.876	0.737	1	CLONAL	1	TRUE	1	0.21	2		466	489	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638363	176638363	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	92	642	0	ENST00000439151.2:c.2963C>G	p.Ser988Cys	p.S988C	ENST00000439151	NM_022455.4	988	tCt/tGt	5/23	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.21	2		642	602	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200485	67200485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	65	599	0	ENST00000312629.5:c.679C>T	p.His227Tyr	p.H227Y	ENST00000312629	NM_003952.2	227	Cac/Tac	8/15	0.3	3	FACETS	1	0.92	1			1	CLONAL	1	TRUE	NA	0.21	3		599	629	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344472	118344472	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	20	254	0	ENST00000534358.1:c.2598G>C	p.Lys866Asn	p.K866N	ENST00000534358	NM_005933.3	866	aaG/aaC	3/36	1	2	FACETS	0.666	0.51	0.849	0.666	0.51	0.849	SUBCLONAL	1	TRUE	1	0.21	2		254	286	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344704	118344704	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	30	383	0	ENST00000534358.1:c.2830G>C	p.Asp944His	p.D944H	ENST00000534358	NM_005933.3	944	Gat/Cat	3/36	1	2	FACETS	0.682	0.549	0.833	0.682	0.549	0.833	SUBCLONAL	1	TRUE	1	0.21	2		383	419	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431671	431671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	47	613	0	ENST00000399788.2:c.2338C>T	p.Leu780Phe	p.L780F	ENST00000399788	NM_001042603.1	780	Ctc/Ttc	17/28	0.3	2	FACETS	0.685	0.577	0.805			1	SUBCLONAL	1	TRUE	NA	0.21	2		613	653	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144853	11144853	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398457701	NA	P-0033837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	26	503	1	ENST00000358026.2:c.3928G>A	p.Glu1310Lys	p.E1310K	ENST00000358026	NM_001128849.1	1310	Gag/Aag	28/36	1	2	FACETS	0.592	0.469	0.735	0.592	0.469	0.735	SUBCLONAL	1	TRUE	1	0.21	2		504	418	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719187	61719187	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	64	365	0	ENST00000401558.2:c.1870G>C	p.Asp624His	p.D624H	ENST00000401558	NM_003400.3	624	Gat/Cat	16/25	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.21	2		365	425	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288623	198288623	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	89	594	0	ENST00000335508.6:c.104C>G	p.Ser35Cys	p.S35C	ENST00000335508	NM_012433.2	35	tCt/tGt	2/25	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.21	2		594	739	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166754	32166754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	84	745	1	ENST00000375023.3:c.4484C>T	p.Ser1495Leu	p.S1495L	ENST00000375023	NM_004557.3	1495	tCa/tTa	24/30	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.21	2		746	640	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117632274	117632274	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	50	398	0	ENST00000368508.3:c.6142G>T	p.Gly2048Cys	p.G2048C	ENST00000368508	NM_002944.2	2048	Ggt/Tgt	39/43	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.21	2		398	410	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949801	151949801	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0033837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	61	296	0	ENST00000262189.6:c.1300-1G>C		p.X434_splice	ENST00000262189	NM_170606.2	434			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.21	2		296	413	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5456116	5456116	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs111401207	NA	P-0033837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	58	349	1	ENST00000381577.3:c.3G>A	p.Met1?	p.M1?	ENST00000381577	NM_014143.3	1	atG/atA	2/7	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.21	2		350	425	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15821840	15821840	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	43	260	0	ENST00000307771.7:c.233G>C	p.Arg78Thr	p.R78T	ENST00000307771	NM_005089.3	78	aGa/aCa	4/11	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.21	2		260	333	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0033841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	134	454	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.355170937648239	2		454	709	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206943239	206943239	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	162	302	0	ENST00000423557.1:c.379C>G	p.His127Asp	p.H127D	ENST00000423557	NM_000572.2	127	Cat/Gat	4/5	0.192321807586109	3	FACETS	1	0.976	1	0.755	0.699	0.813	INDETERMINATE	2	TRUE	0	0.355170937648239	3		302	474	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450669	70450669	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs146039331	NA	P-0033841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	43	394	0	ENST00000373644.4:c.5509G>T	p.Ala1837Ser	p.A1837S	ENST00000373644	NM_030625.2	1837	Gct/Tct	12/12	1	2	FACETS	0.493	0.412	0.583	0.493	0.412	0.583	SUBCLONAL	1	TRUE	1	0.355170937648239	2		394	491	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858233	9858233	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	57	468	0	ENST00000330684.3:c.3168G>A	p.Met1056Ile	p.M1056I	ENST00000330684	NM_001134407.1	1056	atG/atA	13/13	0.337901840054448	4	FACETS	0.549	0.469	0.635	0.183	0.156	0.212	SUBCLONAL	1	TRUE	1	0.355170937648239	4		468	793	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965470	15965470	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs373678242	NA	P-0033841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	104	387	0	ENST00000268712.3:c.5336A>G	p.Asn1779Ser	p.N1779S	ENST00000268712	NM_006311.3	1779	aAt/aGt	36/46	1	2	FACETS	0.998	0.896	1	0.998	0.896	1	CLONAL	1	TRUE	1	0.355170937648239	2		387	587	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533299	29533299	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1555611570	NA	P-0033841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	55	314	0	ENST00000356175.3:c.1302T>A	p.Cys434Ter	p.C434*	ENST00000356175	NM_000267.3	434	tgT/tgA	12/57	1	2	FACETS	0.547	0.468	0.634	0.547	0.468	0.634	SUBCLONAL	1	TRUE	1	0.355170937648239	2		314	566	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807309	1807309	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	145	551	0	ENST00000260795.2:c.1558T>A	p.Ser520Thr	p.S520T	ENST00000260795		520	Tcg/Acg	11/17	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.355170937648239	2		551	594	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520214	176520214	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	137	664	0	ENST00000292408.4:c.1133T>A	p.Leu378Gln	p.L378Q	ENST00000292408	NM_213647.1	378	cTg/cAg	9/18	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.355170937648239	2		664	731	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411612	63411612	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	137	680	0	ENST00000330258.3:c.1555C>A	p.Pro519Thr	p.P519T	ENST00000330258	NM_152424.3	519	Cca/Aca	2/2	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.355170937648239	2		680	764	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610154	10610154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	95	612	1	ENST00000171111.5:c.556G>A	p.Gly186Ser	p.G186S	ENST00000171111	NM_203500.1	186	Ggc/Agc	2/6	0.503095900441428	2	FACETS	0.355	0.315	0.396	0.177	0.157	0.198	SUBCLONAL	1	TRUE	0	0.728012326101237	2		613	736	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242474	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGA	GAATTAAGA	-	rs121913436	NA	P-0033851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	212	573	0	ENST00000275493.2:c.2239_2247del	p.Leu747_Glu749del	p.L747_E749del	ENST00000275493	NM_005228.3	746	GAATTAAGA/-	19/28	0.365161204571366	6	FACETS	1	0.969	1	0.708	0.661	0.757	INDETERMINATE	2	TRUE	3	0.728012326101237	6		573	673	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041719	14041719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201501958	NA	P-0033851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	53	438	0	ENST00000311895.7:c.2266G>A	p.Val756Met	p.V756M	ENST00000311895	NM_005236.2	756	Gtg/Atg	11/11	0.489708773026084	2	FACETS	0.247	0.21	0.287	0.123	0.105	0.144	SUBCLONAL	1	TRUE	0	0.728012326101237	2		438	590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577143	+	inframe_deletion	In_Frame_Del	DEL	AAGCTGTTCCGTCCC	AAGCTGTTCCGTCCC	-	novel	NA	P-0033851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	431	570	0	ENST00000269305.4:c.795_809del	p.Gly266_Phe270del	p.G266_F270del	ENST00000269305	NM_001126112.2	265	ctGGGACGGAACAGCTTt/ctt	8/11	0.685368157063329	2	FACETS	0.878	0.848	0.909	0.878	0.848	0.909	CLONAL	2	TRUE	0	0.728012326101237	2		570	674	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335684	81335684	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	58	428	0	ENST00000222390.5:c.1676A>C	p.Glu559Ala	p.E559A	ENST00000222390	NM_000601.4	559	gAg/gCg	15/18	0.365161204571366	6	FACETS	0.371	0.317	0.43	0.124	0.105	0.144	INDETERMINATE	1	TRUE	3	0.728012326101237	6		428	1055	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0033854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	479	454	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.555977270588644	4	FACETS	0.932	0.897	0.966	0.932	0.897	0.966	CLONAL	3	TRUE	1	0.640534153559859	4		454	878	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0033854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	275	651	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.263493347540999	1	FACETS	0.615	0.578	0.653	0.615	0.578	0.653	INDETERMINATE	1	TRUE	0	0.640534153559859	1		651	949	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579716	7579716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1192416464	NA	P-0033854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	101	558	0	ENST00000269305.4:c.80del	p.Pro27LeufsTer17	p.P27Lfs*17	ENST00000269305	NM_001126112.2	27	cCt/ct	3/11	0.263493347540999	1	FACETS	0.268	0.239	0.298	0.268	0.239	0.298	INDETERMINATE	1	TRUE	0	0.640534153559859	1		558	801	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105679	27105679	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	157	381	0	ENST00000324856.7:c.5290G>T	p.Glu1764Ter	p.E1764*	ENST00000324856	NM_006015.4	1764	Gaa/Taa	20/20	1	2	FACETS	0.888	0.818	0.96	0.888	0.818	0.96	CLONAL	1	TRUE	1	0.640534153559859	2		381	552	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212615399	212615399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369165560	NA	P-0033854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	171	383	0	ENST00000342788.4:c.587G>A	p.Arg196His	p.R196H	ENST00000342788	NM_005235.2	196	cGt/cAt	5/28	1	2	FACETS	0.813	0.75	0.877	0.813	0.75	0.877	CLONAL	1	TRUE	1	0.640534153559859	2		383	657	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971138	21971138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760640852	NA	P-0033854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	128	376	0	ENST00000304494.5:c.220G>A	p.Asp74Asn	p.D74N	ENST00000304494	NM_000077.4	74	Gac/Aac	2/3	0.263493347540999	1	FACETS	0.417	0.379	0.458	0.417	0.379	0.458	INDETERMINATE	1	TRUE	0	0.640534153559859	1		376	651	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371684	55371684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	240	523	0	ENST00000297316.4:c.374G>A	p.Arg125His	p.R125H	ENST00000297316	NM_022454.3	125	cGc/cAc	2/2	0.525936311435355	3	FACETS	0.863	0.805	0.923	0.432	0.402	0.462	CLONAL	1	TRUE	1	0.640534153559859	3		523	1146	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721547	49721547	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	87	460	0	ENST00000449682.2:c.2092G>A	p.Val698Ile	p.V698I	ENST00000449682	NM_020998.3	698	Gta/Ata	18/18	0.263493347540999	1	FACETS	0.241	0.213	0.271	0.241	0.213	0.271	INDETERMINATE	1	TRUE	0	0.640534153559859	1		460	766	SUCCESS
AR	367	MSKCC	GRCh37	X	66765694	66765694	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1305696138	NA	P-0033854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	474	797	0	ENST00000374690.3:c.706G>A	p.Ala236Thr	p.A236T	ENST00000374690	NM_000044.3	236	Gcc/Acc	1/8	0.284354474802977	3	FACETS	1	0.995	1	0.644	0.615	0.674	INDETERMINATE	1	TRUE	1	0.640534153559859	3		797	1516	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0033857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	46	482	1	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.201398481579824	5	FACETS	0.521	0.437	0.613	0.174	0.145	0.205	SUBCLONAL	1	TRUE	2	0.326186181921651	5		483	807	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578525	7578525	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	344	786	0	ENST00000269305.4:c.405C>A	p.Cys135Ter	p.C135*	ENST00000269305	NM_001126112.2	135	tgC/tgA	5/11	0.326186181921651	2	FACETS	0.883	0.841	0.926	1	0.994	1	CLONAL	3	TRUE	0	0.326186181921651	2		786	796	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128013	30128013	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	91	606	0	ENST00000263025.4:c.1116G>C	p.Gln372His	p.Q372H	ENST00000263025	NM_002746.2	372	caG/caC	8/9	0.301933861675132	3	FACETS	0.899	0.798	1	0.449	0.399	0.503	CLONAL	1	TRUE	1	0.326186181921651	3		606	722	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549134	87549134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1281250433	NA	P-0033857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	87	513	0	ENST00000277120.3:c.1691C>T	p.Ala564Val	p.A564V	ENST00000277120		564	gCc/gTc	15/19	0.326186181921651	3	FACETS	1	0.949	1	0.562	0.498	0.63	CLONAL	1	TRUE	1	0.326186181921651	3		513	552	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435987	56435987	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	20	384	1	ENST00000407977.2:c.1150G>A	p.Gly384Ser	p.G384S	ENST00000407977		384	Ggc/Agc	9/10	0.326186181921651	2	FACETS	0.324	0.247	0.415	0.162	0.123	0.208	SUBCLONAL	1	TRUE	0	0.326186181921651	2		385	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0033884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	153	572	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.305440088381194	1	FACETS	0.364	0.333	0.396	0.364	0.333	0.396	INDETERMINATE	1	TRUE	0	0.701885943534418	1		572	777	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578188	7578188	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201592	NA	P-0033884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	349	566	0	ENST00000269305.4:c.661G>T	p.Glu221Ter	p.E221*	ENST00000269305	NM_001126112.2	221	Gag/Tag	6/11	0.305440088381194	1	FACETS	0.849	0.81	0.889	0.849	0.81	0.889	INDETERMINATE	1	TRUE	0	0.701885943534418	1		566	760	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205211	46205211	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0033884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	445	343	0	ENST00000334344.6:c.295A>T	p.Lys99Ter	p.K99*	ENST00000334344	NM_152641.2	99	Aag/Tag	4/21	0.701885943534418	3	FACETS	0.958	0.93	0.985	0.958	0.93	0.985	CLONAL	3	TRUE	0	0.701885943534418	3		343	596	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602284	10602302	+	frameshift_variant	Frame_Shift_Del	DEL	GGGAGCCGCCGACGGCATA	GGGAGCCGCCGACGGCATA	-	novel	NA	P-0033884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	339	614	0	ENST00000171111.5:c.1276_1294del	p.Tyr426ThrfsTer26	p.Y426Tfs*26	ENST00000171111	NM_203500.1	426	TATGCCGTCGGCGGCTCCCac/ac	3/6	0.701885943534418	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.701885943534418	1		614	580	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40744858	40744865	+	frameshift_variant	Frame_Shift_Del	DEL	GTCTGGAA	GTCTGGAA	CTCT	novel	NA	P-0033884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	296	530	2	ENST00000392038.2:c.655_662delinsAGAG	p.Phe219ArgfsTer9	p.F219Rfs*9	ENST00000392038	NM_001626.4	219	TTCCAGACc/AGAGc	8/14	0.701885943534418	1	FACETS	0.999	0.952	1	0.999	0.952	1	CLONAL	1	TRUE	0	0.701885943534418	1		532	548	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868196	45868196	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	347	663	0	ENST00000391945.4:c.494G>T	p.Gly165Val	p.G165V	ENST00000391945	NM_000400.3	165	gGg/gTg	7/23	0.701885943534418	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.701885943534418	1		663	604	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456429	89456429	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1257548456	NA	P-0033884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	221	325	0	ENST00000336596.2:c.1605C>G	p.Ile535Met	p.I535M	ENST00000336596	NM_005233.5	535	atC/atG	8/17	0.638062543427242	2	FACETS	0.963	0.918	1	0.963	0.918	1	CLONAL	2	TRUE	0	0.701885943534418	2		325	327	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424216	47424216	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	192	472	0	ENST00000377045.4:c.221G>T	p.Trp74Leu	p.W74L	ENST00000377045	NM_001654.4	74	tGg/tTg	4/16	1	2	FACETS	0.762	0.707	0.819	0.762	0.707	0.819	SUBCLONAL	1	TRUE	1	0.701885943534418	2		472	718	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179176	123179176	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	102	517	0	ENST00000218089.9:c.625G>T	p.Asp209Tyr	p.D209Y	ENST00000218089	NM_001042749.1	209	Gac/Tac	8/35	0.387611992778119	1	FACETS	0.455	0.409	0.502	0.455	0.409	0.502	INDETERMINATE	1	TRUE	0	0.701885943534418	1		517	415	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0033886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	36	454	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.985	0.817	1	1	0.965	1	CLONAL	2	TRUE	1	0.17	2		454	215	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0033886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	28	587	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.661	0.528	0.815	0.661	0.528	0.815	SUBCLONAL	1	TRUE	1	0.17	2		587	498	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748278	41748278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	27	669	2	ENST00000226382.2:c.491C>T	p.Ala164Val	p.A164V	ENST00000226382	NM_003924.3	164	gCg/gTg	3/3	1	2	FACETS	0.729	0.579	0.9	0.729	0.579	0.9	SUBCLONAL	1	TRUE	1	0.17	2		671	436	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52705255	52705255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	26	422	0	ENST00000322088.6:c.137G>A	p.Arg46Lys	p.R46K	ENST00000322088	NM_014225.5	46	aGg/aAg	2/15	1	2	FACETS	0.818	0.648	1	0.818	0.648	1	CLONAL	1	TRUE	1	0.17	2		422	374	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951127	17951127	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	38	572	0	ENST00000458235.1:c.1166T>A	p.Leu389His	p.L389H	ENST00000458235	NM_000215.3	389	cTc/cAc	9/24	1	2	FACETS	0.871	0.72	1	0.871	0.72	1	CLONAL	1	TRUE	1	0.17	2		572	513	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396452	396452	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	56	797	2	ENST00000262320.3:c.574A>G	p.Thr192Ala	p.T192A	ENST00000262320	NM_003502.3	192	Act/Gct	2/11	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.17	2		799	556	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846342	156846342	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	37	650	1	ENST00000524377.1:c.1783G>T	p.Gly595Trp	p.G595W	ENST00000524377	NM_002529.3	595	Ggg/Tgg	14/17	NA	2	FACETS	0.899	0.741	1			1	INDETERMINATE	1	TRUE	NA	0.17	2		651	484	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28624257	28624257	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	32	623	1	ENST00000241453.7:c.717G>T	p.Arg239Ser	p.R239S	ENST00000241453	NM_004119.2	239	agG/agT	6/24	1	2	FACETS	0.975	0.792	1	0.975	0.792	1	CLONAL	1	TRUE	1	0.17	2		624	386	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396364	396364	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1448250803	NA	P-0033886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	43	729	0	ENST00000262320.3:c.662G>A	p.Cys221Tyr	p.C221Y	ENST00000262320	NM_003502.3	221	tGt/tAt	2/11	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.17	2		729	454	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38504699	38504699	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	30	586	0	ENST00000254066.5:c.310G>T	p.Ala104Ser	p.A104S	ENST00000254066	NM_000964.3	104	Gcc/Tcc	3/9	1	2	FACETS	0.72	0.579	0.881	0.72	0.579	0.881	SUBCLONAL	1	TRUE	1	0.17	2		586	490	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245921	41245921	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	23	787	0	ENST00000357654.3:c.1627G>T	p.Gly543Cys	p.G543C	ENST00000357654	NM_007294.3	543	Ggt/Tgt	10/23	1	2	FACETS	0.936	0.731	1	0.936	0.731	1	CLONAL	1	TRUE	1	0.17	2		787	289	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78935211	78935211	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs757285630	NA	P-0033886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	33	552	0	ENST00000306801.3:c.3623G>T	p.Arg1208Leu	p.R1208L	ENST00000306801	NM_020761.2	1208	cGg/cTg	31/34	1	2	FACETS	0.863	0.702	1	0.863	0.702	1	CLONAL	1	TRUE	1	0.17	2		552	450	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50916762	50916762	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	30	453	0	ENST00000440232.2:c.2234A>G	p.Tyr745Cys	p.Y745C	ENST00000440232	NM_002691.3	745	tAc/tGc	18/27	1	2	FACETS	0.894	0.72	1	0.894	0.72	1	CLONAL	1	TRUE	1	0.17	2		453	395	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455208	29455208	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	23	579	0	ENST00000389048.3:c.2594C>A	p.Ser865Tyr	p.S865Y	ENST00000389048	NM_004304.4	865	tCc/tAc	15/29	1	2	FACETS	0.631	0.491	0.793	0.631	0.491	0.793	SUBCLONAL	1	TRUE	1	0.17	2		579	429	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99812455	99812455	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	15	428	0	ENST00000280892.6:c.214A>G	p.Lys72Glu	p.K72E	ENST00000280892	NM_001130678.1	72	Aaa/Gaa	3/7	1	2	FACETS	0.929	0.681	1	0.929	0.681	1	CLONAL	1	TRUE	1	0.17	2		428	190	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687362	117687362	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1410939393	NA	P-0033886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	20	443	0	ENST00000368508.3:c.2689T>C	p.Trp897Arg	p.W897R	ENST00000368508	NM_002944.2	897	Tgg/Cgg	18/43	1	2	FACETS	0.862	0.66	1	0.862	0.66	1	CLONAL	1	TRUE	1	0.17	2		443	273	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683631	162683631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1404458540	NA	P-0033886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	26	469	0	ENST00000366898.1:c.338C>T	p.Pro113Leu	p.P113L	ENST00000366898	NM_004562.2	113	cCa/cTa	3/12	0.099064554421648	4	FACETS	0.92	0.728	1	0.46	0.364	0.57	INDETERMINATE	1	TRUE	2	0.17	4		469	389	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	68	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.384383722035177	2		248	295	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346592	81346592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764869064	NA	P-0033887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	74	309	0	ENST00000222390.5:c.1361C>T	p.Thr454Met	p.T454M	ENST00000222390	NM_000601.4	454	aCg/aTg	11/18	1	2	FACETS	0.773	0.678	0.875	0.773	0.678	0.875	SUBCLONAL	1	FALSE	1	0.384383722035177	2		309	498	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183692	10183693	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs869025615	NA	P-0033887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	77	476	0	ENST00000256474.2:c.163dup	p.Glu55GlyfsTer77	p.E55Gfs*77	ENST00000256474	NM_000551.3	54	atg/atGg	1/3	0.384383722035177	1	FACETS	0.809	0.714	0.91	0.809	0.714	0.91	CLONAL	1	FALSE	0	0.384383722035177	1		476	400	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942114	71942114	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	107	627	0	ENST00000298229.2:c.1378G>A	p.Val460Met	p.V460M	ENST00000298229	NM_001567.3	460	Gtg/Atg	12/28	1	2	FACETS	0.871	0.783	0.965	0.871	0.783	0.965	CLONAL	1	FALSE	1	0.384383722035177	2		627	639	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44515623	44515625	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0033887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	149	624	0	ENST00000291552.4:c.271_273del	p.Glu91del	p.E91del	ENST00000291552	NM_006758.2	91	GAG/-	5/8	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	FALSE	1	0.384383722035177	2		624	770	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0033889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	20	207	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	1	2	FACETS	0.687	0.524	0.88	0.687	0.524	0.88	SUBCLONAL	1	TRUE	1	0.11	2		207	529	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097859	8097859	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	17	292	0	ENST00000346208.3:c.241G>T	p.Gly81Trp	p.G81W	ENST00000346208		81	Ggg/Tgg	2/6	1	2	FACETS	0.928	0.692	1	0.928	0.692	1	CLONAL	1	TRUE	1	0.11	2		292	333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0033892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	339	639	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.452719374828116	2	FACETS	0.99	0.943	1	0.99	0.943	1	CLONAL	2	TRUE	0	0.468984877597134	2		640	730	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430953	181430953	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	417	652	1	ENST00000325404.1:c.805G>T	p.Asp269Tyr	p.D269Y	ENST00000325404	NM_003106.3	269	Gac/Tac	1/1	0.468984877597134	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	0	0.468984877597134	3		653	711	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554613	29554613	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	42	247	0	ENST00000356175.3:c.2398G>T	p.Glu800Ter	p.E800*	ENST00000356175	NM_000267.3	800	Gaa/Taa	20/57	0.468984877597134	3	FACETS	0.801	0.673	0.942	0.401	0.336	0.471	CLONAL	1	TRUE	1	0.468984877597134	3		247	276	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974816	15974816	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	49	473	0	ENST00000268712.3:c.4059G>C	p.Glu1353Asp	p.E1353D	ENST00000268712	NM_006311.3	1353	gaG/gaC	30/46	0.452719374828116	2	FACETS	0.434	0.368	0.507	0.217	0.184	0.254	SUBCLONAL	1	TRUE	0	0.468984877597134	2		473	481	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684328	29684328	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	226	573	0	ENST00000356175.3:c.7849del	p.Ile2617PhefsTer6	p.I2617Ffs*6	ENST00000356175	NM_000267.3	2616	cgA/cg	53/57	0.468984877597134	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.468984877597134	3		573	562	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299114	15299114	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	292	662	0	ENST00000263388.2:c.1424G>C	p.Ser475Thr	p.S475T	ENST00000263388	NM_000435.2	475	aGt/aCt	9/33	0.468984877597134	2	FACETS	0.996	0.946	1	0.996	0.946	1	CLONAL	2	TRUE	0	0.468984877597134	2		662	625	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873183	136873183	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	67	376	0	ENST00000241393.3:c.315del	p.Asn106ThrfsTer62	p.N106Tfs*62	ENST00000241393	NM_003467.2	105	ggG/gg	2/2	0.466245712827607	4	FACETS	0.81	0.705	0.924	0.27	0.235	0.308	CLONAL	1	TRUE	1	0.468984877597134	4		376	518	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728665	190728665	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	59	394	0	ENST00000441310.2:c.2053C>G	p.Gln685Glu	p.Q685E	ENST00000441310	NM_000534.4	685	Caa/Gaa	10/13	0.466245712827607	4	FACETS	0.919	0.794	1	0.306	0.264	0.352	CLONAL	1	TRUE	1	0.468984877597134	4		394	402	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22153387	22153387	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	34	412	0	ENST00000215832.6:c.523G>T	p.Asp175Tyr	p.D175Y	ENST00000215832	NM_002745.4	175	Gat/Tat	4/9	0.468984877597134	3	FACETS	0.306	0.25	0.371	0.102	0.083	0.124	SUBCLONAL	1	TRUE	0	0.468984877597134	3		412	584	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524316	176524316	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	1413	691	0	ENST00000292408.4:c.2177G>T	p.Trp726Leu	p.W726L	ENST00000292408	NM_213647.1	726	tGg/tTg	17/18	0.468984877597134	9	FACETS	1	0.995	1	1	0.995	1	CLONAL	8	TRUE	1	0.468984877597134	9		691	1927	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958189	2958189	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1211022340	NA	P-0033892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	104	531	0	ENST00000396946.4:c.2543G>A	p.Arg848His	p.R848H	ENST00000396946	NM_032415.4	848	cGc/cAc	19/25	0.468984877597134	4	FACETS	0.834	0.747	0.927	0.278	0.249	0.309	CLONAL	1	TRUE	1	0.468984877597134	4		531	781	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410941	63410941	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	132	628	0	ENST00000330258.3:c.2226G>T	p.Arg742Ser	p.R742S	ENST00000330258	NM_152424.3	742	agG/agT	2/2	0.468984877597134	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.468984877597134	1		628	408	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0033894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	602	454	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.504792304877319	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	4	TRUE	0	0.504792304877319	4		454	842	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0033894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	399	693	1	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.472852007294425	3	FACETS	0.902	0.859	0.945	0.902	0.859	0.945	CLONAL	2	TRUE	1	0.504792304877319	3		694	1098	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977852	134977852	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0033894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	278	298	0	ENST00000398015.3:c.2847-2A>G		p.X949_splice	ENST00000398015	NM_004441.4	949			0.504792304877319	5	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	2	0.504792304877319	5		298	611	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578262	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs483352697	NA	P-0033894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	180	488	0	ENST00000269305.4:c.587G>T	p.Arg196Leu	p.R196L	ENST00000269305	NM_001126112.2	196	cGa/cTa	6/11	0.472852007294425	3	FACETS	0.988	0.911	1	0.494	0.455	0.534	CLONAL	1	TRUE	1	0.504792304877319	3		488	904	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576898	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0033894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	194	603	0	ENST00000269305.4:c.948_949del	p.Gln317AlafsTer19	p.Q317Afs*19	ENST00000269305	NM_001126112.2	316	ccCCag/ccag	9/11	0.472852007294425	3	FACETS	0.969	0.897	1	0.485	0.448	0.523	CLONAL	1	TRUE	1	0.504792304877319	3		603	993	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115252323	115252323	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	213	369	0	ENST00000369535.4:c.317C>A	p.Ser106Ter	p.S106*	ENST00000369535	NM_002524.4	106	tCg/tAg	4/7	0.472852007294425	3	FACETS	0.919	0.86	0.979	0.919	0.86	0.979	CLONAL	2	TRUE	1	0.504792304877319	3		369	575	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263308	115263309	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0033894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	157	544	1	ENST00000438362.2:c.2041_2042delinsTT	p.Gly681Phe	p.G681F	ENST00000438362	NM_001242891.1	681	GGc/TTc	17/20	0.472852007294425	3	FACETS	0.84	0.77	0.914	0.42	0.385	0.457	CLONAL	1	TRUE	1	0.504792304877319	3		545	927	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280667	115280667	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	155	521	0	ENST00000438362.2:c.364G>T	p.Asp122Tyr	p.D122Y	ENST00000438362	NM_001242891.1	122	Gac/Tac	4/20	0.472852007294425	3	FACETS	0.979	0.897	1	0.489	0.448	0.532	CLONAL	1	TRUE	1	0.504792304877319	3		521	786	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741944	17741944	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	49	193	0	ENST00000250003.3:c.615C>A	p.Asn205Lys	p.N205K	ENST00000250003	NM_002478.4	205	aaC/aaA	1/3	0.504792304877319	3	FACETS	0.805	0.686	0.935	0.403	0.343	0.468	CLONAL	1	TRUE	1	0.504792304877319	3		193	302	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061261	38061262	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	275	532	1	ENST00000250448.2:c.727dup	p.Tyr243LeufsTer50	p.Y243Lfs*50	ENST00000250448	NM_004496.3	243	tac/tTac	2/2	0.504792304877319	3	FACETS	0.863	0.813	0.913	0.863	0.813	0.913	CLONAL	2	TRUE	1	0.504792304877319	3		533	791	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379820	17379820	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199925580	NA	P-0033894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	228	671	1	ENST00000359435.4:c.205G>T	p.Gly69Cys	p.G69C	ENST00000359435	NM_001033549.1	69	Ggc/Tgc	2/9	1	2	FACETS	0.941	0.877	1	0.941	0.877	1	CLONAL	1	TRUE	1	0.504792304877319	2		672	960	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368136	31368136	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	134	484	1	ENST00000328111.2:c.7G>T	p.Gly3Ter	p.G3*	ENST00000328111	NM_006892.3	3	Gga/Tga	2/23	0.472852007294425	3	FACETS	0.998	0.909	1	0.499	0.454	0.546	CLONAL	1	TRUE	1	0.504792304877319	3		485	666	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332593	153332593	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	266	437	0	ENST00000281708.4:c.363G>C	p.Glu121Asp	p.E121D	ENST00000281708	NM_033632.3	121	gaG/gaC	2/12	0.248191474613035	4	FACETS	1	0.987	1	0.767	0.724	0.811	INDETERMINATE	2	TRUE	1	0.504792304877319	4		437	689	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410892	31410892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774665139	NA	P-0033894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	159	601	0	ENST00000344624.3:c.3628G>A	p.Val1210Met	p.V1210M	ENST00000344624		1210	Gtg/Atg	28/33	0.504792304877319	3	FACETS	0.895	0.82	0.972	0.447	0.41	0.486	CLONAL	1	TRUE	1	0.504792304877319	3		601	882	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180035992	180035992	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1262	163	625	0	ENST00000261937.6:c.3869G>T	p.Arg1290Met	p.R1290M	ENST00000261937	NM_182925.4	1290	aGg/aTg	29/30	0.504792304877319	5	FACETS	0.796	0.728	0.868	0.199	0.182	0.217	SUBCLONAL	1	TRUE	1	0.504792304877319	5		625	1425	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047629	180047629	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	496	465	0	ENST00000261937.6:c.2386A>T	p.Ile796Phe	p.I796F	ENST00000261937	NM_182925.4	796	Atc/Ttc	16/30	0.504792304877319	5	FACETS	0.956	0.922	0.99	0.956	0.922	0.99	CLONAL	4	TRUE	1	0.504792304877319	5		465	903	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455118	50455118	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200163039	NA	P-0033894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	131	296	0	ENST00000331340.3:c.665G>T	p.Arg222Leu	p.R222L	ENST00000331340	NM_006060.4	222	cGc/cTc	6/8	0.38606282741846	4	FACETS	0.862	0.788	0.939	0.862	0.788	0.939	CLONAL	2	TRUE	2	0.504792304877319	4		296	453	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902259	151902259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	153	290	0	ENST00000262189.6:c.3893C>T	p.Thr1298Ile	p.T1298I	ENST00000262189	NM_170606.2	1298	aCc/aTc	25/59	0.38606282741846	4	FACETS	0.996	0.919	1	0.996	0.919	1	CLONAL	2	TRUE	2	0.504792304877319	4		290	458	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372253	55372253	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	136	440	3	ENST00000297316.4:c.943C>T	p.Pro315Ser	p.P315S	ENST00000297316	NM_022454.3	315	Ccg/Tcg	2/2	0.504792304877319	5	FACETS	0.926	0.841	1			1	CLONAL	1	TRUE	NA	0.504792304877319	5		443	1022	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228342	53228342	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0033894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	143	444	0	ENST00000375401.3:c.2062-2A>G		p.X688_splice	ENST00000375401	NM_004187.3	688			0.504792304877319	1	FACETS	0.948	0.871	1	0.948	0.871	1	CLONAL	1	TRUE	0	0.504792304877319	1		444	447	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76764011	76764011	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	623	701	0	ENST00000373344.5:c.7297C>G	p.Leu2433Val	p.L2433V	ENST00000373344	NM_000489.3	2433	Ctg/Gtg	35/35	0.472178908478462	3	FACETS	0.973	0.943	1	0.973	0.943	1	CLONAL	3	TRUE	0	0.504792304877319	3		701	1059	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0033896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	154	538	0	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	0.326504799602931	2	FACETS	1	0.988	1	0.745	0.684	0.808	CLONAL	1	TRUE	0	0.326504799602931	2		538	633	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981516	70981516	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	125	897	1	ENST00000276594.2:c.580C>T	p.Arg194Trp	p.R194W	ENST00000276594	NM_024504.3	194	Cgg/Tgg	2/8	0.326504799602931	5	FACETS	0.895	0.807	0.987	0.298	0.269	0.329	CLONAL	1	TRUE	2	0.326504799602931	5		898	1275	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411619	116411622	+	frameshift_variant	Frame_Shift_Del	DEL	GATT	GATT	-	novel	NA	P-0033896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	90	520	0	ENST00000397752.3:c.2803_2806del	p.Ile935LeufsTer20	p.I935Lfs*20	ENST00000397752	NM_000245.2	933	gGATTg/gg	13/21	0.326504799602931	3	FACETS	1	0.956	1	0.576	0.512	0.644	CLONAL	1	TRUE	1	0.326504799602931	3		520	557	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411872	116411891	+	intron_variant	Intron	DEL	TAACAAGCTCTTTCTTTCTC	TAACAAGCTCTTTCTTTCTC	-	novel	NA	P-0033896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	270	965	0	ENST00000397752.3:c.2888-30_2888-11del		p.*963*	ENST00000397752	NM_000245.2	-/1390			0.326504799602931	3	FACETS	0.922	0.866	0.98	0.922	0.866	0.98	CLONAL	2	TRUE	1	0.326504799602931	3		965	1043	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	19	518	0	ENST00000206249.3:c.1610A>G	p.Tyr537Cys	p.Y537C	ENST00000206249	NM_000125.3	537	tAt/tGt	8/8	1	2	FACETS	0.06	0.045	0.077	0.06	0.045	0.077	SUBCLONAL	1	TRUE	1	1.01	2		518	630	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186807	11186807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	29	451	0	ENST00000361445.4:c.6398G>A	p.Cys2133Tyr	p.C2133Y	ENST00000361445	NM_004958.3	2133	tGc/tAc	46/58	1	2	FACETS	0.11	0.087	0.135	0.11	0.087	0.135	SUBCLONAL	1	TRUE	1	1.01	2		451	524	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859565	151859565	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0033902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	35	498	0	ENST00000262189.6:c.11097T>G	p.Tyr3699Ter	p.Y3699*	ENST00000262189	NM_170606.2	3699	taT/taG	43/59	1	2	FACETS	0.102	0.083	0.124	0.102	0.083	0.124	SUBCLONAL	1	TRUE	1	1.01	2		498	678	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	330	248	0				ENST00000310581	NM_198253.2	-/1132			0.476421180962276	6	FACETS	1	0.962	1	1	0.962	1	CLONAL	5	TRUE	1	0.476421180962276	6		248	539	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0033925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	543	625	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.439663601669189	5	FACETS	1	0.993	1	0.873	0.845	0.901	CLONAL	4	TRUE	0	0.476421180962276	5		625	895	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242758	16242758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1366443836	NA	P-0033925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	122	613	0	ENST00000375759.3:c.1379G>A	p.Arg460His	p.R460H	ENST00000375759	NM_015001.2	460	cGc/cAc	6/15	0.234205747022065	5	FACETS	1	0.971	1	0.397	0.359	0.437	INDETERMINATE	1	TRUE	2	0.476421180962276	5		613	738	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78829313	78829313	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	372	605	1	ENST00000306801.3:c.1364G>T	p.Arg455Ile	p.R455I	ENST00000306801	NM_020761.2	455	aGa/aTa	12/34	0.469214358592461	5	FACETS	0.859	0.817	0.902	0.515	0.49	0.541	CLONAL	3	TRUE	0	0.476421180962276	5		606	1039	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134234	11134234	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	222	563	0	ENST00000358026.2:c.2900G>T	p.Arg967Leu	p.R967L	ENST00000358026	NM_001128849.1	967	cGt/cTt	20/36	0.357233539007005	3	FACETS	0.932	0.873	0.992	0.932	0.873	0.992	CLONAL	2	TRUE	1	0.476421180962276	3		563	619	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259347	36259347	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	153	432	0	ENST00000300305.3:c.144C>A	p.Ser48Arg	p.S48R	ENST00000300305		48	agC/agA	3/8	0.442937795971643	3	FACETS	1	0.986	1	0.681	0.626	0.738	CLONAL	1	TRUE	1	0.476421180962276	3		432	584	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170837540	170837540	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	29	128	0	ENST00000296930.5:c.856G>T	p.Asp286Tyr	p.D286Y	ENST00000296930	NM_002520.6	286	Gat/Tat	11/11	0.467747592569129	3	FACETS	1	0.823	1	0.337	0.274	0.407	CLONAL	1	TRUE	0	0.476421180962276	3		128	149	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652007	36652008	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0033925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	385	625	0	ENST00000244741.5:c.131_132dup	p.Ala45ArgfsTer104	p.A45Rfs*104	ENST00000244741	NM_000389.4	43	-/GA	2/3	0.476421180962276	5	FACETS	0.837	0.796	0.878	0.837	0.796	0.878	CLONAL	3	TRUE	2	0.476421180962276	5		625	1104	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953011	2953011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1172378918	NA	P-0033925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	114	669	3	ENST00000396946.4:c.2929G>A	p.Val977Met	p.V977M	ENST00000396946	NM_032415.4	977	Gtg/Atg	22/25	0.219655130718314	3	FACETS	0.818	0.737	0.904	0.273	0.245	0.302	INDETERMINATE	1	TRUE	0	0.476421180962276	3		672	724	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0033926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	57	440	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.812	0.695	0.94	0.812	0.695	0.94	CLONAL	1	TRUE	1	0.19	2		440	739	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0033926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	32	240	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.714	0.579	0.866	0.714	0.579	0.866	SUBCLONAL	1	TRUE	1	0.19	2		240	472	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925432	114925432	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	67	587	0	ENST00000543371.1:c.1510C>T	p.Pro504Ser	p.P504S	ENST00000543371	NM_001198531.1	504	Ccc/Tcc	14/14	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.19	2		587	687	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944926	31944926	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs768639345	NA	P-0033926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	21	298	0	ENST00000340398.3:c.175G>T	p.Glu59Ter	p.E59*	ENST00000340398	NM_001013699.2	59	Gag/Tag	1/1	1	2	FACETS	0.658	0.506	0.835	0.658	0.506	0.835	SUBCLONAL	1	TRUE	1	0.19	2		298	336	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724720	43724720	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	63	760	0	ENST00000382044.4:c.3347G>T	p.Gly1116Val	p.G1116V	ENST00000382044	NM_001141980.1	1116	gGg/gTg	17/28	1	2	FACETS	0.902	0.779	1	0.902	0.779	1	CLONAL	1	TRUE	1	0.19	2		760	735	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72873703	72873703	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0033926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	45	325	0	ENST00000325599.8:c.600-1G>T		p.X200_splice	ENST00000325599	NM_018130.2	200			1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.19	2		325	461	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907069	101907069	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	41	413	0	ENST00000374994.4:c.1029G>T	p.Lys343Asn	p.K343N	ENST00000374994	NM_004612.2	343	aaG/aaT	6/9	1	2	FACETS	0.845	0.703	1	0.845	0.703	1	CLONAL	1	TRUE	1	0.19	2		413	511	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035979	47035979	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	55	638	0	ENST00000377604.3:c.657C>A	p.Cys219Ter	p.C219*	ENST00000377604	NM_001204468.1	219	tgC/tgA	7/24	1	2	FACETS	0.8	0.683	0.928	0.8	0.683	0.928	CLONAL	1	TRUE	1	0.19	2		638	724	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410427	63410427	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	57	646	0	ENST00000330258.3:c.2740G>T	p.Gly914Cys	p.G914C	ENST00000330258	NM_152424.3	914	Ggc/Tgc	2/2	1	2	FACETS	0.96	0.823	1	0.96	0.823	1	CLONAL	1	TRUE	1	0.19	2		646	625	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938909	76938909	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	64	706	1	ENST00000373344.5:c.1839T>A	p.Asp613Glu	p.D613E	ENST00000373344	NM_000489.3	613	gaT/gaA	9/35	0.3	2	FACETS	0.805	0.695	0.924			1	CLONAL	1	TRUE	NA	0.19	2		707	837	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0033928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	51	328	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.939	0.808	1	1	0.982	1	CLONAL	4	FALSE	1	0.125163046985998	2		328	217	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0033928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	95	257	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.937	1	1	0.991	1	CLONAL	5	FALSE	1	0.125163046985998	2		258	289	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546122	29546122	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs894292181	NA	P-0033928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	81	419	0	ENST00000356175.3:c.1627C>T	p.Gln543Ter	p.Q543*	ENST00000356175	NM_000267.3	543	Cag/Tag	14/57	0.121626843251749	0	FACETS	0.925	0.823	1			1	CLONAL	4	FALSE	0	0.125163046985998	0		419	306	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814673	43814673	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs923814653	NA	P-0033928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	12	311	1	ENST00000372470.3:c.1468G>A	p.Ala490Thr	p.A490T	ENST00000372470	NM_005373.2	490	Gcc/Acc	9/12	1	2	FACETS	0.88	0.618	1	0.88	0.618	1	CLONAL	1	FALSE	1	0.125163046985998	2		312	218	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0033931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	108	599	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.26560249832137	2		599	557	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357768	70357768	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	111	726	0	ENST00000374080.3:c.6019G>T	p.Gly2007Ter	p.G2007*	ENST00000374080		2007	Gga/Tga	41/45	1	2	FACETS	0.838	0.756	0.922	1	0.986	1	CLONAL	2	TRUE	1	0.26560249832137	2		726	499	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415846	49415846	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886041398	NA	P-0033932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	81	517	0	ENST00000301067.7:c.16501C>T	p.Arg5501Ter	p.R5501*	ENST00000301067	NM_003482.3	5501	Cga/Tga	53/54	0.778889860686993	1	FACETS	0.266	0.235	0.299	0.266	0.235	0.299	SUBCLONAL	1	TRUE	0	0.778889860686993	1		517	477	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438735	49438739	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGT	AAAGT	-	novel	NA	P-0033932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	30	631	0	ENST00000301067.7:c.4751_4755del	p.Tyr1584SerfsTer17	p.Y1584Sfs*17	ENST00000301067	NM_003482.3	1584	tACTTT/t	19/54	0.778889860686993	1	FACETS	0.081	0.064	0.099	0.081	0.064	0.099	SUBCLONAL	1	TRUE	0	0.778889860686993	1		631	584	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484288	50484288	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	426	679	1	ENST00000394963.4:c.1048C>T	p.Gln350Ter	p.Q350*	ENST00000394963	NM_003076.4	350	Caa/Taa	9/13	0.778889860686993	1	FACETS	0.941	0.906	0.975	0.941	0.906	0.975	CLONAL	1	TRUE	0	0.778889860686993	1		680	710	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0033939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	170	454	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.975	0.9	1	0.975	0.9	1	CLONAL	1	TRUE	1	0.524564912224127	2		454	665	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796754	135796754	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203434	NA	P-0033939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	102	412	1	ENST00000298552.3:c.733C>T	p.Arg245Ter	p.R245*	ENST00000298552	NM_001162426.1	245	Cga/Tga	8/23	1	2	FACETS	0.909	0.818	1	0.909	0.818	1	CLONAL	1	TRUE	1	0.524564912224127	2		413	428	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128044	64128044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	38	779	0	ENST00000334205.4:c.442G>A	p.Ala148Thr	p.A148T	ENST00000334205	NM_003942.2	148	Gcc/Acc	4/17	1	2	FACETS	0.201	0.165	0.241	0.201	0.165	0.241	SUBCLONAL	1	TRUE	1	0.524564912224127	2		779	721	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438266	49438266	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	166	656	1	ENST00000301067.7:c.5003G>T	p.Gly1668Val	p.G1668V	ENST00000301067	NM_003482.3	1668	gGc/gTc	20/54	1	2	FACETS	0.984	0.908	1	0.984	0.908	1	CLONAL	1	TRUE	1	0.524564912224127	2		657	643	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291070	10291070	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	125	676	0	ENST00000340748.4:c.401A>T	p.Lys134Ile	p.K134I	ENST00000340748		134	aAa/aTa	4/40	0.524564912224127	1	FACETS	0.671	0.61	0.734	0.671	0.61	0.734	SUBCLONAL	1	TRUE	0	0.524564912224127	1		676	524	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462377	89462377	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	140	613	0	ENST00000336596.2:c.1849G>C	p.Asp617His	p.D617H	ENST00000336596	NM_005233.5	617	Gat/Cat	10/17	1	2	FACETS	0.662	0.603	0.724	0.662	0.603	0.724	SUBCLONAL	1	TRUE	1	0.524564912224127	2		613	806	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515439	149515439	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs148853962	NA	P-0033939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	40	455	0	ENST00000261799.4:c.43G>A	p.Glu15Lys	p.E15K	ENST00000261799	NM_002609.3	15	Gag/Aag	3/23	1	2	FACETS	0.329	0.273	0.392	0.329	0.273	0.392	SUBCLONAL	1	TRUE	1	0.524564912224127	2		455	463	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847282	68847282	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	58	466	0	ENST00000261769.5:c.1204G>T	p.Asp402Tyr	p.D402Y	ENST00000261769	NM_004360.3	402	Gat/Tat	9/16	1	2	FACETS	0.844	0.727	0.972	0.844	0.727	0.972	CLONAL	1	TRUE	1	0.288065776065709	2		466	477	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0033940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	77	635	0	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.18353400046819	2	FACETS	1	0.892	1	0.507	0.446	0.573	CLONAL	1	TRUE	0	0.288065776065709	2		635	527	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120508085	120508085	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	23	321	0	ENST00000256646.2:c.1672T>C	p.Cys558Arg	p.C558R	ENST00000256646	NM_024408.3	558	Tgt/Cgt	10/34	0.170646018756011	2	FACETS	0.46	0.358	0.578	0.23	0.179	0.289	INDETERMINATE	1	TRUE	0	0.288065776065709	2		321	347	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022792	12022792	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	35	428	0	ENST00000396373.4:c.898G>C	p.Glu300Gln	p.E300Q	ENST00000396373	NM_001987.4	300	Gaa/Caa	5/8	0.218167538391473	4	FACETS	0.805	0.66	0.967	0.402	0.33	0.484	CLONAL	1	TRUE	2	0.288065776065709	4		428	389	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81902896	81902896	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	32	383	0	ENST00000359376.3:c.557A>C	p.Lys186Thr	p.K186T	ENST00000359376	NM_002661.3	186	aAg/aCg	6/33	1	2	FACETS	0.474	0.384	0.575	0.474	0.384	0.575	SUBCLONAL	1	TRUE	1	0.288065776065709	2		383	469	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537227	41537227	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0033940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	59	345	0	ENST00000263253.7:c.2053+1G>A		p.X685_splice	ENST00000263253	NM_001429.3	685			0.288065776065709	1	FACETS	0.713	0.614	0.82	0.713	0.614	0.82	SUBCLONAL	1	TRUE	0	0.288065776065709	1		345	492	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519589	137519589	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	68	428	0	ENST00000367739.4:c.1049C>G	p.Ser350Cys	p.S350C	ENST00000367739	NM_000416.2	350	tCt/tGt	7/7	0.136506979861393	3	FACETS	0.963	0.838	1	0.321	0.279	0.366	INDETERMINATE	1	TRUE	0	0.288065776065709	3		428	561	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396217	139396217	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	24	665	0	ENST00000277541.6:c.5621T>G	p.Val1874Gly	p.V1874G	ENST00000277541	NM_017617.3	1874	gTc/gGc	30/34	0.18353400046819	2	FACETS	0.378	0.295	0.473	0.189	0.147	0.237	SUBCLONAL	1	TRUE	0	0.288065776065709	2		665	441	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650462	48650462	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	40	378	0	ENST00000376670.3:c.432C>A	p.Asp144Glu	p.D144E	ENST00000376670	NM_002049.3	144	gaC/gaA	3/6	0.102442335984894	2	FACETS	0.741	0.617	0.878			1	INDETERMINATE	1	TRUE	NA	0.288065776065709	2		378	375	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0033948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	63	539	1	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.19	2		540	625	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0033948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	59	474	1	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.19	2		475	614	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0033948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	37	375	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.668	0.55	0.801	0.668	0.55	0.801	SUBCLONAL	1	TRUE	1	0.19	2		375	583	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37081727	37081727	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63751277	NA	P-0033948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	51	515	0	ENST00000231790.2:c.1609C>T	p.Gln537Ter	p.Q537*	ENST00000231790	NM_000249.3	537	Cag/Tag	14/19	1	2	FACETS	0.869	0.738	1	0.869	0.738	1	CLONAL	1	TRUE	1	0.19	2		515	618	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572092	64572093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs767319284	NA	P-0033948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	69	550	0	ENST00000312049.6:c.1546dup	p.Arg516ProfsTer15	p.R516Pfs*15	ENST00000312049	NM_130799.2	516	cgg/cCgg	10/10	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.19	2		550	679	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164163	108164164	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs864622164	NA	P-0033948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	27	281	0	ENST00000278616.4:c.4741dup	p.Ile1581AsnfsTer5	p.I1581Nfs*5	ENST00000278616	NM_000051.3	1579	caa/cAaa	31/63	1	2	FACETS	0.627	0.498	0.775	0.627	0.498	0.775	SUBCLONAL	1	TRUE	1	0.19	2		281	453	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788609	3788609	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs945398646	NA	P-0033948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	29	344	1	ENST00000262367.5:c.4345G>A	p.Val1449Ile	p.V1449I	ENST00000262367	NM_004380.2	1449	Gtt/Att	26/31	1	2	FACETS	0.683	0.547	0.837	0.683	0.547	0.837	SUBCLONAL	1	TRUE	1	0.19	2		345	447	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057641	27057641	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0033951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	33	505	0	ENST00000324856.7:c.1351-2A>G		p.X451_splice	ENST00000324856	NM_006015.4	451			1	2	FACETS	0.601	0.488	0.729	0.601	0.488	0.729	SUBCLONAL	1	TRUE	1	0.18	2		505	610	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087503	27087503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	66	665	1	ENST00000324856.7:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000324856	NM_006015.4	693	Cga/Tga	5/20	1	2	FACETS	0.788	0.682	0.903	0.788	0.682	0.903	CLONAL	1	TRUE	1	0.18	2		666	931	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692793	89692793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	42	375	0	ENST00000371953.3:c.277C>T	p.His93Tyr	p.H93Y	ENST00000371953	NM_000314.4	93	Cat/Tat	5/9	1	2	FACETS	0.974	0.814	1	0.974	0.814	1	CLONAL	1	TRUE	1	0.18	2		375	479	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	31	583	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.478	0.385	0.584	0.478	0.385	0.584	SUBCLONAL	1	TRUE	1	0.18	2		583	721	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576848	7576852	+	splice_donor_variant,intron_variant	Splice_Site	DEL	AGTAC	AGTAC	-	novel	NA	P-0033951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	73	647	0	ENST00000269305.4:c.993+1_993+5del		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.3	2	FACETS	0.945	0.825	1			1	CLONAL	1	TRUE	NA	0.18	2		647	858	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10286227	10286227	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	81	632	0	ENST00000340748.4:c.589G>C	p.Asp197His	p.D197H	ENST00000340748		197	Gac/Cac	6/40	1	2	FACETS	0.984	0.865	1	0.984	0.865	1	CLONAL	1	TRUE	1	0.18	2		632	915	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0033951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	19	528	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.283	0.214	0.366	0.283	0.214	0.366	SUBCLONAL	1	TRUE	1	0.18	2		528	745	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589599	67589603	+	protein_altering_variant	In_Frame_Del	DEL	TCAGT	TCAGT	AC	novel	NA	P-0033951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	13	198	0	ENST00000274335.5:c.1362_1366delinsAC	p.Gln455_Phe456delinsLeu	p.Q455_F456delinsL	ENST00000274335		454	acTCAGTtt/acACtt	10/15	1	2	FACETS	0.602	0.429	0.813	0.602	0.429	0.813	SUBCLONAL	1	TRUE	1	0.18	2		198	240	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370985	55370985	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	83	575	0	ENST00000297316.4:c.287C>G	p.Ala96Gly	p.A96G	ENST00000297316	NM_022454.3	96	gCc/gGc	1/2	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.18	2		575	781	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	126	248	0				ENST00000310581	NM_198253.2	-/1132			0.308384086374649	5	FACETS	0.907	0.828	0.99	0.907	0.828	0.99	CLONAL	3	TRUE	2	0.308384086374649	5		248	439	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226568865	226568865	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	243	520	0	ENST00000366794.5:c.1204T>G	p.Ser402Ala	p.S402A	ENST00000366794	NM_001618.3	402	Tcc/Gcc	9/23	0.308384086374649	6	FACETS	1	0.975	1	0.546	0.509	0.584	CLONAL	2	TRUE	2	0.308384086374649	6		520	1167	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492896	56492896	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	54	306	0	ENST00000407977.2:c.43T>A	p.Trp15Arg	p.W15R	ENST00000407977		15	Tgg/Agg	2/10	0.308384086374649	3	FACETS	0.842	0.72	0.975	0.421	0.36	0.488	CLONAL	1	TRUE	1	0.308384086374649	3		306	480	SUCCESS
REL	5966	MSKCC	GRCh37	2	61148900	61148900	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	24	302	0	ENST00000295025.8:c.1090C>T	p.Pro364Ser	p.P364S	ENST00000295025	NM_002908.2	364	Cca/Tca	11/11	0.308384086374649	3	FACETS	0.447	0.35	0.559	0.223	0.175	0.28	SUBCLONAL	1	TRUE	1	0.308384086374649	3		302	402	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447712	187447712	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	123	538	0	ENST00000232014.4:c.481G>C	p.Glu161Gln	p.E161Q	ENST00000232014	NM_001130845.1	161	Gag/Cag	5/10	0.308384086374649	3	FACETS	1	0.972	1	0.6	0.543	0.661	CLONAL	1	TRUE	1	0.308384086374649	3		538	767	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630329	187630329	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	210	614	0	ENST00000441802.2:c.653A>G	p.Tyr218Cys	p.Y218C	ENST00000441802	NM_005245.3	218	tAt/tGt	2/27	0.308384086374649	3	FACETS	0.904	0.841	0.97	0.904	0.841	0.97	CLONAL	2	TRUE	1	0.308384086374649	3		614	869	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0033958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	97	254	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	1	2	FACETS	0.871	0.781	0.965	0.871	0.781	0.965	CLONAL	1	TRUE	1	0.523993526856327	2		254	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0033958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	247	637	2	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.523993526856327	1	FACETS	0.968	0.909	1	0.968	0.909	1	CLONAL	1	TRUE	0	0.523993526856327	1		639	719	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913255	NA	P-0033958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	241	546	0	ENST00000369535.4:c.183A>T	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caT	3/7	1	2	FACETS	0.908	0.848	0.97	0.908	0.848	0.97	CLONAL	1	TRUE	1	0.523993526856327	2		546	1013	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675170	30675172	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs1472156046	NA	P-0033958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	229	484	0	ENST00000376406.3:c.3073_3075del	p.Lys1025del	p.K1025del	ENST00000376406	NM_014641.2	1025	AAG/-	9/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.523993526856327	2		484	833	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100645	8100645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1218595084	NA	P-0033958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	116	589	0	ENST00000346208.3:c.619G>A	p.Ala207Thr	p.A207T	ENST00000346208		207	Gcc/Acc	3/6	0.265011383626834	1	FACETS	0.355	0.319	0.393	0.355	0.319	0.393	INDETERMINATE	1	TRUE	0	0.523993526856327	1		589	921	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884785	111884785	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751330475	NA	P-0033958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	211	434	1	ENST00000341259.2:c.874G>A	p.Glu292Lys	p.E292K	ENST00000341259	NM_005475.2	292	Gag/Aag	4/8	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.523993526856327	2		435	771	SUCCESS
APC	324	MSKCC	GRCh37	5	112173601	112173601	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	137	315	0	ENST00000257430.4:c.2310del	p.Glu771LysfsTer6	p.E771Kfs*6	ENST00000257430	NM_000038.5	770	tcA/tc	16/16	1	2	FACETS	0.951	0.869	1	0.951	0.869	1	CLONAL	1	TRUE	1	0.523993526856327	2		315	550	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0033961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	408	651	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	NA	2	FACETS	0.892	0.856	0.929			1	INDETERMINATE	2	TRUE	NA	0.580368797600238	2		651	788	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696689	47696689	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519972	NA	P-0033961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	330	578	0	ENST00000347630.2:c.259T>A	p.Tyr87Asn	p.Y87N	ENST00000347630	NM_001007230.1	87	Tac/Aac	5/11	0.318332789689226	3	FACETS	0.768	0.728	0.809	0.768	0.728	0.809	INDETERMINATE	2	TRUE	1	0.580368797600238	3		578	955	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891078	112891078	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs267606989	NA	P-0033961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	158	525	0	ENST00000351677.2:c.412C>T	p.Arg138Ter	p.R138*	ENST00000351677	NM_002834.3	138	Cga/Tga	4/16	0.318332789689226	3	FACETS	0.752	0.689	0.818	0.376	0.344	0.409	INDETERMINATE	1	TRUE	1	0.580368797600238	3		525	934	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38942407	38942407	+	stop_lost	Nonstop_Mutation	SNP	C	C	A	novel	NA	P-0033963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	66	388	0	ENST00000357387.3:c.5126G>T	p.Ter1709LeuextTer29	p.*1709Lext*29	ENST00000357387	NM_152756.3	1709	tGa/tTa	38/38	0.648438635340491	10	FACETS	0.698	0.604	0.801			1	SUBCLONAL	1	TRUE	NA	0.648438635340491	10		388	1048	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492634	56492634	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	160	438	0	ENST00000267101.3:c.2784G>C	p.Glu928Asp	p.E928D	ENST00000267101	NM_001982.3	928	gaG/gaC	23/28	0.648438635340491	3	FACETS	1	0.966	1	0.544	0.501	0.588	CLONAL	1	TRUE	1	0.648438635340491	3		438	601	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541850	187541850	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	166	474	0	ENST00000441802.2:c.5890T>G	p.Ser1964Ala	p.S1964A	ENST00000441802	NM_005245.3	1964	Tct/Gct	10/27	0.630421420771131	4	FACETS	1	0.949	1	0.521	0.479	0.565	CLONAL	1	TRUE	2	0.648438635340491	4		474	810	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540131	23540141	+	frameshift_variant	Frame_Shift_Del	DEL	GCCAGCGTCTC	GCCAGCGTCTC	-	novel	NA	P-0033964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	21	59	0	ENST00000380871.4:c.262_272del	p.Glu88ArgfsTer16	p.E88Rfs*16	ENST00000380871	NM_006167.3	88	GAGACGCTGGCa/a	1/2	0.0868208338489582	3	FACETS	0.899	0.712	1	1	0.913	1	INDETERMINATE	3	FALSE	1	0.231797597556684	3		59	75	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0033967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	300	639	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.300570346660337	3	FACETS	0.845	0.8	0.891	0.845	0.8	0.891	CLONAL	3	TRUE	0	0.360495076607896	3		640	775	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115654	108115654	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs557012154	NA	P-0033967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	105	512	0	ENST00000278616.4:c.802C>T	p.Gln268Ter	p.Q268*	ENST00000278616	NM_000051.3	268	Caa/Taa	7/63	0.309687891700431	2	FACETS	0.759	0.685	0.835	0.759	0.685	0.835	SUBCLONAL	2	TRUE	0	0.360495076607896	2		512	384	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974725	21974742	+	inframe_deletion	In_Frame_Del	DEL	CGCCTCCAGCAGCGCCCG	CGCCTCCAGCAGCGCCCG	-	novel	NA	P-0033967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	31	231	0	ENST00000304494.5:c.85_102del	p.Arg29_Ala34del	p.R29_A34del	ENST00000304494	NM_000077.4	29	CGGGCGCTGCTGGAGGCG/-	1/3	0.360495076607896	1	FACETS	0.681	0.555	0.821	0.681	0.555	0.821	SUBCLONAL	1	TRUE	0	0.360495076607896	1		231	207	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0033968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	72	264	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	0.406691978349547	2		264	325	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0033968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	165	750	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.406691978349547	3	FACETS	1	0.97	1	0.559	0.513	0.606	CLONAL	1	TRUE	1	0.406691978349547	3		752	874	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28931588	NA	P-0033968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	64	307	0	ENST00000349496.5:c.94G>C	p.Asp32His	p.D32H	ENST00000349496	NM_001904.3	32	Gac/Cac	3/15	1	2	FACETS	0.91	0.792	1	0.91	0.792	1	CLONAL	1	TRUE	1	0.406691978349547	2		307	346	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922321	178922321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	42	367	0	ENST00000263967.3:c.1090G>A	p.Gly364Arg	p.G364R	ENST00000263967	NM_006218.2	364	Gga/Aga	6/21	1	2	FACETS	0.509	0.425	0.601	0.509	0.425	0.601	SUBCLONAL	1	TRUE	1	0.406691978349547	2		367	406	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246498694	246498694	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	72	557	0	ENST00000388985.4:c.311T>A	p.Leu104His	p.L104H	ENST00000388985		104	cTt/cAt	3/12	NA	2	FACETS	0.41	0.357	0.467			1	INDETERMINATE	1	TRUE	NA	0.406691978349547	2		557	863	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085741	16085741	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	88	457	0	ENST00000281043.3:c.917C>A	p.Ala306Glu	p.A306E	ENST00000281043	NM_005378.4	306	gCa/gAa	3/3	1	2	FACETS	0.852	0.757	0.952	0.852	0.757	0.952	CLONAL	1	TRUE	1	0.406691978349547	2		457	508	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091165	29091167	+	inframe_deletion	In_Frame_Del	DEL	CTG	CTG	-	novel	NA	P-0033968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	105	392	0	ENST00000328354.6:c.1323_1325del	p.Ser442del	p.S442del	ENST00000328354	NM_007194.3	441	acCAGt/act	12/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.406691978349547	2		392	415	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922336	178922336	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	44	375	0	ENST00000263967.3:c.1105G>C	p.Asp369His	p.D369H	ENST00000263967	NM_006218.2	369	Gac/Cac	6/21	1	2	FACETS	0.533	0.448	0.627	0.533	0.448	0.627	SUBCLONAL	1	TRUE	1	0.406691978349547	2		375	406	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724429	117724429	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	102	416	0	ENST00000368508.3:c.450A>C	p.Arg150Ser	p.R150S	ENST00000368508	NM_002944.2	150	agA/agC	6/43	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.406691978349547	2		416	476	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509297	106509297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371891504	NA	P-0033968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	70	448	0	ENST00000359195.3:c.1291C>T	p.Leu431Phe	p.L431F	ENST00000359195	NM_002649.2	431	Ctc/Ttc	2/11	1	2	FACETS	0.729	0.638	0.828	0.729	0.638	0.828	SUBCLONAL	1	TRUE	1	0.406691978349547	2		448	472	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0033972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	425	440	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.27351207624243	4	FACETS	1	0.976	1	1	0.997	1	CLONAL	4	TRUE	2	0.329409266128468	4		440	838	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520008	NA	P-0033972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	157	472	0	ENST00000269305.4:c.613T>G	p.Tyr205Asp	p.Y205D	ENST00000269305	NM_001126112.2	205	Tat/Gat	6/11	0.329409266128468	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.329409266128468	2		472	448	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436182	56436182	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	97	330	1	ENST00000407977.2:c.955G>T	p.Gly319Ter	p.G319*	ENST00000407977		319	Gga/Tga	9/10	NA	2	FACETS	0.998	0.902	1			1	INDETERMINATE	2	TRUE	NA	0.329409266128468	2		331	295	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971098	21971098	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	AG	novel	NA	P-0033972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	37	131	0	ENST00000304494.5:c.260delinsCT	p.Arg87ProfsTer33	p.R87Pfs*33	ENST00000304494	NM_000077.4	87	cGg/cCTg	2/3	0.327278826814514	2	FACETS	0.838	0.705	0.981	0.838	0.705	0.981	CLONAL	2	TRUE	0	0.329409266128468	2		131	134	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183871	10183871	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs869025636	NA	P-0033972-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	19	222	0	ENST00000256474.2:c.340G>C	p.Gly114Arg	p.G114R	ENST00000256474	NM_000551.3	114	Ggt/Cgt	1/3	0.231022006370181	1	FACETS	0.841	0.642	1	0.841	0.642	1	CLONAL	1	TRUE	0	0.231022006370181	1		222	173	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341868	8341868	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033972-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	31	447	0	ENST00000356435.5:c.4772A>C	p.Gln1591Pro	p.Q1591P	ENST00000356435		1591	cAg/cCg	29/35	1	2	FACETS	0.528	0.426	0.644	0.528	0.426	0.644	SUBCLONAL	1	TRUE	1	0.231022006370181	2		447	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0033975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	347	587	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.464065512565996	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.464065512565996	3		587	568	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348239	348239	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770548875	NA	P-0033975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	261	509	0	ENST00000262320.3:c.1267G>A	p.Glu423Lys	p.E423K	ENST00000262320	NM_003502.3	423	Gag/Aag	6/11	0.435795266247614	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.464065512565996	3		509	639	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023471	27023471	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	229	210	0	ENST00000324856.7:c.577G>T	p.Glu193Ter	p.E193*	ENST00000324856	NM_006015.4	193	Gag/Tag	1/20	0.464065512565996	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	0	0.464065512565996	3		210	381	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141551	11141551	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	72	411	0	ENST00000358026.2:c.3528C>A	p.Ser1176Arg	p.S1176R	ENST00000358026	NM_001128849.1	1176	agC/agA	25/36	0.464065512565996	2	FACETS	0.839	0.737	0.947	0.419	0.368	0.474	CLONAL	1	TRUE	0	0.464065512565996	2		411	370	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307684	11307684	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	217	313	0	ENST00000361445.4:c.1223C>G	p.Thr408Arg	p.T408R	ENST00000361445	NM_004958.3	408	aCa/aGa	8/58	0.125044042536726	4	FACETS	1	0.983	1			1	INDETERMINATE	3	TRUE	NA	0.464065512565996	4		313	412	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163744	72163744	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	212	504	0	ENST00000357731.5:c.614C>A	p.Ala205Glu	p.A205E	ENST00000357731	NM_173808.2	205	gCg/gAg	4/7	0.464065512565996	3	FACETS	0.936	0.883	0.988	0.936	0.883	0.988	CLONAL	3	TRUE	0	0.464065512565996	3		504	401	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112511	115112511	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	207	448	0	ENST00000257566.3:c.1229C>T	p.Pro410Leu	p.P410L	ENST00000257566	NM_016569.3	410	cCc/cTc	7/8	0.44830606930473	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.464065512565996	2		448	441	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955434	48955434	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	156	296	0	ENST00000267163.4:c.1551del	p.Leu518Ter	p.L518*	ENST00000267163	NM_000321.2	517	aTt/at	17/27	0.450837803833479	3	FACETS	0.914	0.854	0.975	0.914	0.854	0.975	CLONAL	3	TRUE	0	0.464065512565996	3		296	302	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226893	2226893	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	57	92	0	ENST00000398665.3:c.4373C>A	p.Ala1458Asp	p.A1458D	ENST00000398665	NM_032482.2	1458	gCc/gAc	27/28	0.464065512565996	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.464065512565996	2		92	108	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602473	10602473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	179	315	0	ENST00000171111.5:c.1105G>A	p.Val369Met	p.V369M	ENST00000171111	NM_203500.1	369	Gtg/Atg	3/6	0.464065512565996	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.464065512565996	2		315	349	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881699	111881699	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	101	376	0	ENST00000393256.3:c.377A>T	p.His126Leu	p.H126L	ENST00000393256	NM_006538.4	126	cAc/cTc	2/4	0.365188930889307	3	FACETS	0.923	0.827	1	0.462	0.413	0.513	CLONAL	1	TRUE	1	0.464065512565996	3		376	581	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434135	12434135	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	33	257	0	ENST00000287820.6:c.503G>A	p.Arg168Lys	p.R168K	ENST00000287820	NM_015869.4	168	aGa/aAa	4/7	0.451793811957636	2	FACETS	0.533	0.436	0.641	0.266	0.218	0.321	SUBCLONAL	1	TRUE	0	0.464065512565996	2		257	267	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197229	26197229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	137	258	0	ENST00000356476.2:c.250C>T	p.Arg84Cys	p.R84C	ENST00000356476		84	Cgt/Tgt	1/1	0.375394588534	5	FACETS	0.939	0.859	1	0.47	0.429	0.512	CLONAL	2	TRUE	1	0.464065512565996	5		258	533	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839876	27839876	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	96	295	0	ENST00000328488.2:c.218G>T	p.Arg73Leu	p.R73L	ENST00000328488	NM_003533.2	73	cGg/cTg	1/1	0.375394588534	5	FACETS	1	0.967	1	0.304	0.271	0.338	CLONAL	1	TRUE	1	0.464065512565996	5		295	578	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	60	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.993	0.88	1	1	0.985	1	CLONAL	3	TRUE	1	0.292020632669032	2		248	138	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0033977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	316	519	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	1	2	FACETS	1	0.951	1	1	0.997	1	CLONAL	3	TRUE	1	0.292020632669032	2		519	721	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757274881	NA	P-0033977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	335	606	2	ENST00000269305.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	144	Cag/Tag	5/11	1	2	FACETS	0.983	0.935	1	1	0.997	1	CLONAL	3	TRUE	1	0.292020632669032	2		608	778	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233730	233730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1483236652	NA	P-0033977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	322	512	0	ENST00000264932.6:c.1034G>A	p.Arg345Gln	p.R345Q	ENST00000264932	NM_004168.2	345	cGg/cAg	8/15	1	2	FACETS	0.941	0.894	0.989	1	0.997	1	CLONAL	3	TRUE	1	0.292020632669032	2		512	781	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484803	57484803	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	188	376	0	ENST00000371085.3:c.783C>G	p.Asn261Lys	p.N261K	ENST00000371085	NM_000516.4	261	aaC/aaG	10/13	1	2	FACETS	0.909	0.849	0.971	1	0.995	1	CLONAL	3	TRUE	1	0.292020632669032	2		376	472	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866648	117866648	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	59	423	0	ENST00000297338.2:c.997G>C	p.Asp333His	p.D333H	ENST00000297338	NM_006265.2	333	Gat/Cat	9/14	1	2	FACETS	0.591	0.508	0.682	0.591	0.508	0.682	SUBCLONAL	1	TRUE	1	0.292020632669032	2		423	684	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148724	20148728	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGCTA	AGCTA	-	novel	NA	P-0033977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	125	158	0	ENST00000379607.5:c.338-3_339del		p.X113_splice	ENST00000379607	NM_001412.3	113		6/7	1	1	FACETS	1	0.983	1	1	0.994	1	CLONAL	4	TRUE	0	0.292020632669032	1		158	165	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0033978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	23	454	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.942	0.734	1	0.942	0.734	1	CLONAL	1	TRUE	1	0.147586205087786	2		454	331	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047527	49047527	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587778850	NA	P-0033978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	13	188	0	ENST00000267163.4:c.2520+1G>T		p.X840_splice	ENST00000267163	NM_000321.2	840			0.147586205087786	1	FACETS	0.77	0.549	1	0.77	0.549	1	CLONAL	1	TRUE	0	0.147586205087786	1		188	212	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089672	5089672	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0033978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	15	130	0	ENST00000381652.3:c.2572-2A>T		p.X858_splice	ENST00000381652	NM_004972.3	858			1	2	FACETS	1	0.802	1	1	0.802	1	CLONAL	1	TRUE	1	0.147586205087786	2		130	182	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945969	17945969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758959409	NA	P-0033981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	12	550	0	ENST00000458235.1:c.1970G>A	p.Arg657Gln	p.R657Q	ENST00000458235	NM_000215.3	657	cGg/cAg	15/24	0.499638646408132	7	FACETS	0.191	0.133	0.263	0.032	0.022	0.044	SUBCLONAL	1	TRUE	1	0.499638646408132	7		550	566	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023501	27023502	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	133	212	0	ENST00000324856.7:c.608dup	p.His203GlnfsTer197	p.H203Qfs*197	ENST00000324856	NM_006015.4	203	cac/cAac	1/20	0.276812839853787	3	FACETS	0.787	0.721	0.854	0.787	0.721	0.854	INDETERMINATE	2	TRUE	1	0.499638646408132	3		212	423	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463509	25463509	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	10	311	0	ENST00000264709.3:c.2173G>A	p.Glu725Lys	p.E725K	ENST00000264709	NM_175629.2	725	Gag/Aag	18/23	0.193755606174126	2	FACETS	0.29	0.197	0.406	0.145	0.098	0.203	INDETERMINATE	1	TRUE	0	0.499638646408132	2		311	138	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514631	103514631	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	21	229	0	ENST00000355739.4:c.1132G>C	p.Val378Leu	p.V378L	ENST00000355739	NM_000123.3	378	Gta/Cta	8/15	0.350947102164139	1	FACETS	0.671	0.527	0.831	0.671	0.527	0.831	SUBCLONAL	1	TRUE	0	0.499638646408132	1		229	94	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368299	45368299	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	25	284	0	ENST00000262160.6:c.1303C>G	p.Pro435Ala	p.P435A	ENST00000262160	NM_005901.5	435	Cct/Gct	11/11	0.154888729600007	3	FACETS	0.802	0.652	0.963	0.802	0.652	0.963	INDETERMINATE	2	TRUE	1	0.499638646408132	3		284	78	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919027	50919027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775310798	NA	P-0033981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	10	422	0	ENST00000440232.2:c.2764G>A	p.Val922Ile	p.V922I	ENST00000440232	NM_002691.3	922	Gtc/Atc	22/27	0.499638646408132	1	FACETS	0.158	0.107	0.222	0.158	0.107	0.222	SUBCLONAL	1	TRUE	0	0.499638646408132	1		422	190	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109321818	109321818	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs374094607	NA	P-0033984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	151	725	0	ENST00000436639.2:c.605A>T	p.His202Leu	p.H202L	ENST00000436639	NM_014454.2	202	cAt/cTt	4/10	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.338199726763364	2		725	874	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0033987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	64	442	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.123815954912498	4	FACETS	1	0.944	1	0.59	0.51	0.676	CLONAL	1	TRUE	2	0.198519395330033	4		442	655	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111491	8111492	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	113	748	0	ENST00000346208.3:c.978dup	p.Leu327ThrfsTer25	p.L327Tfs*25	ENST00000346208		326	aca/acAa	5/6	1	2	FACETS	0.819	0.738	0.905	1	0.986	1	CLONAL	2	TRUE	1	0.198519395330033	2		748	695	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696644	47696644	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519964	NA	P-0033989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	110	707	0	ENST00000347630.2:c.304T>G	p.Phe102Val	p.F102V	ENST00000347630	NM_001007230.1	102	Ttc/Gtc	5/11	1	2	FACETS	0.961	0.866	1	0.961	0.866	1	CLONAL	1	FALSE	1	0.414051733697641	2		707	553	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630794	187630794	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	161	842	0	ENST00000441802.2:c.188T>G	p.Ile63Ser	p.I63S	ENST00000441802	NM_005245.3	63	aTt/aGt	2/27	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.414051733697641	2		842	709	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	230	697	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.905	0.845	0.966	0.905	0.845	0.966	CLONAL	1	TRUE	1	0.579216082002904	2		697	878	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0033991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	178	373	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.946	0.875	1	0.946	0.875	1	CLONAL	1	TRUE	1	0.579216082002904	2		373	650	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710518	114710518	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0033991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	157	279	0	ENST00000543371.1:c.3G>A	p.Met1?	p.M1?	ENST00000543371	NM_001198531.1	1	atG/atA	1/14	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.579216082002904	2		279	533	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088669	27088669	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	300	797	0	ENST00000324856.7:c.2281del	p.Gln761SerfsTer72	p.Q761Sfs*72	ENST00000324856	NM_006015.4	760	Ccc/cc	7/20	0.579216082002904	1	FACETS	0.913	0.864	0.963	0.913	0.864	0.963	CLONAL	1	TRUE	0	0.579216082002904	1		797	806	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849997	151849997	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768535474	NA	P-0033991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	119	368	0	ENST00000262189.6:c.12319G>A	p.Val4107Ile	p.V4107I	ENST00000262189	NM_170606.2	4107	Gtc/Atc	49/59	1	2	FACETS	0.921	0.837	1	0.921	0.837	1	CLONAL	1	TRUE	1	0.579216082002904	2		368	446	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0033994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	67	467	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	0.255824630641804	3	FACETS	0.897	0.779	1	0.448	0.389	0.512	CLONAL	1	TRUE	1	0.255824630641804	3		467	659	SUCCESS
APC	324	MSKCC	GRCh37	5	112175524	112175524	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	104	385	0	ENST00000257430.4:c.4233del	p.Ser1411ArgfsTer4	p.S1411Rfs*4	ENST00000257430	NM_000038.5	1411	agT/ag	16/16	0.255824630641804	3	FACETS	0.831	0.746	0.92	0.831	0.746	0.92	CLONAL	2	TRUE	1	0.255824630641804	3		385	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579346	7579346	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	237	708	0	ENST00000269305.4:c.341del	p.Leu114CysfsTer9	p.L114Cfs*9	ENST00000269305	NM_001126112.2	114	tTg/tg	4/11	0.23986666087987	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.255824630641804	2		708	793	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16021243	16021243	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	172	436	0	ENST00000268712.3:c.2014C>T	p.Arg672Ter	p.R672*	ENST00000268712	NM_006311.3	672	Cga/Tga	18/46	0.23986666087987	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.255824630641804	2		436	629	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483242	120483242	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	116	489	0	ENST00000256646.2:c.3119G>T	p.Cys1040Phe	p.C1040F	ENST00000256646	NM_024408.3	1040	tGt/tTt	19/34	0.255824630641804	3	FACETS	0.807	0.729	0.889	0.807	0.729	0.889	CLONAL	2	TRUE	1	0.255824630641804	3		489	634	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687589	29687589	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	110	718	0	ENST00000356175.3:c.8182G>T	p.Glu2728Ter	p.E2728*	ENST00000356175	NM_000267.3	2728	Gaa/Taa	56/57	0.255824630641804	4	FACETS	0.918	0.823	1	0.459	0.411	0.51	CLONAL	1	TRUE	2	0.255824630641804	4		718	1176	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576431	67576431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	142	549	1	ENST00000274335.5:c.710G>A	p.Trp237Ter	p.W237*	ENST00000274335		237	tGg/tAg	5/15	0.255824630641804	3	FACETS	0.806	0.735	0.88	0.806	0.735	0.88	CLONAL	2	TRUE	1	0.255824630641804	3		550	777	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534492	140534492	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	94	551	0	ENST00000288602.6:c.421C>G	p.Pro141Ala	p.P141A	ENST00000288602	NM_004333.4	141	Ccc/Gcc	3/18	0.255824630641804	4	FACETS	0.983	0.873	1	0.328	0.291	0.367	CLONAL	1	TRUE	1	0.255824630641804	4		551	939	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	59	709	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	1	2	FACETS	0.746	0.642	0.86	0.746	0.642	0.86	SUBCLONAL	1	TRUE	1	0.284853599181687	2		709	555	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	53	270	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.959	0.821	1	0.959	0.821	1	CLONAL	1	TRUE	1	0.284853599181687	2		270	388	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519902	29519902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200364883	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	99	549	1	ENST00000389048.3:c.1669C>T	p.Arg557Cys	p.R557C	ENST00000389048	NM_004304.4	557	Cgt/Tgt	9/29	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.284853599181687	2		550	656	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469898	157469898	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs794727977	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	114	718	1	ENST00000346085.5:c.2692C>T	p.Arg898Ter	p.R898*	ENST00000346085	NM_020732.3	898	Cga/Tga	9/20	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.284853599181687	2		719	781	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111958593	111958593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555186772	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	167	747	2	ENST00000375549.3:c.65G>A	p.Arg22Gln	p.R22Q	ENST00000375549	NM_003002.3	22	cGa/cAa	2/4	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.284853599181687	2		749	800	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509539	106509539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	132	621	0	ENST00000359195.3:c.1533G>T	p.Glu511Asp	p.E511D	ENST00000359195	NM_002649.2	511	gaG/gaT	2/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.284853599181687	2		621	765	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720870	89720870	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1554825652	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	46	358	0	ENST00000371953.3:c.1021T>G	p.Phe341Val	p.F341V	ENST00000371953	NM_000314.4	341	Ttt/Gtt	8/9	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.284853599181687	2		358	320	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	116	673	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	0.959	0.864	1	0.959	0.864	1	CLONAL	1	TRUE	1	0.284853599181687	2		673	849	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743864	41743864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753706427	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	133	853	0	ENST00000301178.4:c.799G>A	p.Asp267Asn	p.D267N	ENST00000301178	NM_021913.4	267	Gat/Aat	7/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.284853599181687	2		853	848	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089730	27089730	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	91	677	0	ENST00000324856.7:c.2686G>T	p.Glu896Ter	p.E896*	ENST00000324856	NM_006015.4	896	Gaa/Taa	8/20	1	2	FACETS	0.834	0.74	0.934	0.834	0.74	0.934	CLONAL	1	TRUE	1	0.284853599181687	2		677	766	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845086	128845086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761395599	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	150	836	0	ENST00000249373.3:c.580G>A	p.Glu194Lys	p.E194K	ENST00000249373	NM_005631.4	194	Gaa/Aaa	3/12	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.284853599181687	2		836	1011	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224793	123224793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	90	710	0	ENST00000218089.9:c.3557G>A	p.Arg1186Gln	p.R1186Q	ENST00000218089	NM_001042749.1	1186	cGa/cAa	32/35	1	2	FACETS	0.833	0.738	0.933	0.833	0.738	0.933	CLONAL	1	TRUE	1	0.284853599181687	2		710	759	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	96	808	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.93	0.828	1	0.93	0.828	1	CLONAL	1	TRUE	1	0.284853599181687	2		808	725	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47710037	47710037	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1553370893	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	30	308	0	ENST00000233146.2:c.2754G>T	p.Lys918Asn	p.K918N	ENST00000233146	NM_000251.2	918	aaG/aaT	16/16	1	2	FACETS	0.807	0.653	0.98	0.807	0.653	0.98	CLONAL	1	TRUE	1	0.284853599181687	2		308	261	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	44	657	1	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	1	2	FACETS	0.421	0.352	0.498	0.421	0.352	0.498	SUBCLONAL	1	TRUE	1	0.284853599181687	2		658	733	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107258	193107258	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	33	418	0	ENST00000367435.3:c.467G>A	p.Arg156His	p.R156H	ENST00000367435	NM_024529.4	156	cGt/cAt	6/17	1	2	FACETS	0.535	0.436	0.647	0.535	0.436	0.647	SUBCLONAL	1	TRUE	1	0.284853599181687	2		418	433	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430668	80430668	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	67	572	0	ENST00000286548.4:c.340C>T	p.Arg114Ter	p.R114*	ENST00000286548	NM_002072.3	114	Cga/Tga	3/7	1	2	FACETS	0.884	0.769	1	0.884	0.769	1	CLONAL	1	TRUE	1	0.284853599181687	2		572	532	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332915	153332915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200698994	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	98	585	0	ENST00000281708.4:c.41G>A	p.Arg14Gln	p.R14Q	ENST00000281708	NM_033632.3	14	cGa/cAa	2/12	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.284853599181687	2		585	676	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915943	127915943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781486938	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	105	686	0	ENST00000373547.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000373547	NM_002721.4	180	Gaa/Aaa	6/7	1	2	FACETS	0.939	0.841	1	0.939	0.841	1	CLONAL	1	TRUE	1	0.284853599181687	2		686	785	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566734	139566734	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144969763	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	63	759	0	ENST00000308874.7:c.818C>T	p.Ser273Leu	p.S273L	ENST00000308874		273	tCg/tTg	10/10	1	2	FACETS	0.522	0.45	0.6	0.522	0.45	0.6	SUBCLONAL	1	TRUE	1	0.284853599181687	2		759	848	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752839	57752839	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	74	610	0	ENST00000274289.3:c.1089C>A	p.Phe363Leu	p.F363L	ENST00000274289	NM_006622.3	363	ttC/ttA	8/14	1	2	FACETS	0.904	0.792	1	0.904	0.792	1	CLONAL	1	TRUE	1	0.284853599181687	2		610	575	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858276	9858276	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	48	610	0	ENST00000330684.3:c.3125G>T	p.Arg1042Met	p.R1042M	ENST00000330684	NM_001134407.1	1042	aGg/aTg	13/13	1	2	FACETS	0.523	0.441	0.613	0.523	0.441	0.613	SUBCLONAL	1	TRUE	1	0.284853599181687	2		610	645	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92252390	92252390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373488172	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	21	316	0	ENST00000265734.4:c.658C>T	p.Arg220Cys	p.R220C	ENST00000265734	NM_001259.6	220	Cgt/Tgt	6/8	1	2	FACETS	0.397	0.305	0.505	0.397	0.305	0.505	SUBCLONAL	1	TRUE	1	0.284853599181687	2		316	371	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115600	108115600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772821016	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	60	707	1	ENST00000278616.4:c.748C>T	p.Arg250Ter	p.R250*	ENST00000278616	NM_000051.3	250	Cga/Tga	7/63	1	2	FACETS	0.664	0.572	0.765	0.664	0.572	0.765	SUBCLONAL	1	TRUE	1	0.284853599181687	2		708	634	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589298	28589298	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	87	474	0	ENST00000241453.7:c.2749G>T	p.Glu917Ter	p.E917*	ENST00000241453	NM_004119.2	917	Gaa/Taa	22/24	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.284853599181687	2		474	480	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858600	57858600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756282060	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	77	870	0	ENST00000228682.2:c.338G>A	p.Arg113Gln	p.R113Q	ENST00000228682	NM_005269.2	113	cGa/cAa	4/12	1	2	FACETS	0.574	0.503	0.651	0.574	0.503	0.651	SUBCLONAL	1	TRUE	1	0.284853599181687	2		870	942	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404693	70404693	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756914683	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	40	622	0	ENST00000373644.4:c.2207C>T	p.Ser736Leu	p.S736L	ENST00000373644	NM_030625.2	736	tCg/tTg	4/12	1	2	FACETS	0.469	0.389	0.558	0.469	0.389	0.558	SUBCLONAL	1	TRUE	1	0.284853599181687	2		622	599	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291527	15291527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756527298	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	69	739	1	ENST00000263388.2:c.3107G>A	p.Arg1036Gln	p.R1036Q	ENST00000263388	NM_000435.2	1036	cGa/cAa	19/33	1	2	FACETS	0.646	0.562	0.737	0.646	0.562	0.737	SUBCLONAL	1	TRUE	1	0.284853599181687	2		740	750	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66468014	66468014	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	20	352	0	ENST00000273854.3:c.255G>T	p.Glu85Asp	p.E85D	ENST00000273854	NM_004439.5	85	gaG/gaT	3/18	1	2	FACETS	0.388	0.296	0.496	0.388	0.296	0.496	SUBCLONAL	1	TRUE	1	0.284853599181687	2		352	362	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142954	47142954	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	65	514	0	ENST00000409792.3:c.5009G>T	p.Arg1670Ile	p.R1670I	ENST00000409792	NM_014159.6	1670	aGa/aTa	8/21	1	2	FACETS	0.866	0.752	0.989	0.866	0.752	0.989	CLONAL	1	TRUE	1	0.284853599181687	2		514	527	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046289	128046289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746827111	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	114	573	0	ENST00000285398.2:c.974G>A	p.Arg325Gln	p.R325Q	ENST00000285398	NM_000122.1	325	cGa/cAa	7/15	1	2	FACETS	0.944	0.849	1	0.944	0.849	1	CLONAL	1	TRUE	1	0.284853599181687	2		573	848	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11269467	11269467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	81	657	1	ENST00000361445.4:c.3703C>T	p.Arg1235Trp	p.R1235W	ENST00000361445	NM_004958.3	1235	Cgg/Tgg	25/58	1	2	FACETS	0.729	0.642	0.823	0.729	0.642	0.823	SUBCLONAL	1	TRUE	1	0.284853599181687	2		658	780	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375016	45375016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226662382	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	113	503	0	ENST00000262160.6:c.827C>T	p.Ser276Leu	p.S276L	ENST00000262160	NM_005901.5	276	tCg/tTg	8/11	1	2	FACETS	0.828	0.749	0.911	1	0.986	1	CLONAL	2	TRUE	1	0.284853599181687	2		503	479	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829797	72829797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs953863150	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	132	921	4	ENST00000268489.5:c.6784G>A	p.Asp2262Asn	p.D2262N	ENST00000268489	NM_006885.3	2262	Gat/Aat	9/10	1	2	FACETS	0.907	0.822	0.996	0.907	0.822	0.996	CLONAL	1	TRUE	1	0.284853599181687	2		925	1022	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821940	59821940	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	25	480	0	ENST00000259008.2:c.2110T>G	p.Leu704Val	p.L704V	ENST00000259008	NM_032043.2	704	Tta/Gta	15/20	1	2	FACETS	0.424	0.334	0.528	0.424	0.334	0.528	SUBCLONAL	1	TRUE	1	0.284853599181687	2		480	414	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012441	29012441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55974987	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	73	689	0	ENST00000282397.4:c.430G>A	p.Glu144Lys	p.E144K	ENST00000282397	NM_002019.4	144	Gaa/Aaa	4/30	1	2	FACETS	0.701	0.613	0.797	0.701	0.613	0.797	SUBCLONAL	1	TRUE	1	0.284853599181687	2		689	731	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944562	40944562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868189942	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	91	559	0	ENST00000373198.4:c.1940C>T	p.Ser647Leu	p.S647L	ENST00000373198	NM_133170.3	647	tCg/tTg	12/32	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.284853599181687	2		559	599	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417934	32417934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	57	563	0	ENST00000332351.3:c.1118G>A	p.Gly373Glu	p.G373E	ENST00000332351	NM_024426.4	373	gGa/gAa	7/10	1	2	FACETS	0.551	0.472	0.638	0.551	0.472	0.638	SUBCLONAL	1	TRUE	1	0.284853599181687	2		563	726	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436128	56436128	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	113	746	1	ENST00000407977.2:c.1009C>T	p.Arg337Ter	p.R337*	ENST00000407977		337	Cga/Tga	9/10	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.284853599181687	2		747	763	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812205	43812205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866559375	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	127	673	0	ENST00000372470.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000372470	NM_005373.2	357	cGa/cAa	7/12	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.284853599181687	2		673	814	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561190	9561190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762286985	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	85	594	0	ENST00000353224.5:c.592G>A	p.Asp198Asn	p.D198N	ENST00000353224	NM_177990.2	198	Gat/Aat	4/10	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.284853599181687	2		594	572	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649005	86649005	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	43	362	0	ENST00000274376.6:c.1285G>T	p.Glu429Ter	p.E429*	ENST00000274376	NM_002890.2	429	Gaa/Taa	9/25	1	2	FACETS	0.724	0.607	0.854	0.724	0.607	0.854	SUBCLONAL	1	TRUE	1	0.284853599181687	2		362	417	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961103	55961103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140041720	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	102	762	0	ENST00000263923.4:c.2837G>A	p.Arg946His	p.R946H	ENST00000263923	NM_002253.2	946	cGt/cAt	21/30	1	2	FACETS	0.932	0.834	1	0.932	0.834	1	CLONAL	1	TRUE	1	0.284853599181687	2		762	768	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273266	198273266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	46	660	0	ENST00000335508.6:c.944G>A	p.Arg315Gln	p.R315Q	ENST00000335508	NM_012433.2	315	cGa/cAa	8/25	1	2	FACETS	0.426	0.357	0.501	0.426	0.357	0.501	SUBCLONAL	1	TRUE	1	0.284853599181687	2		660	759	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281544	198281544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	86	793	1	ENST00000335508.6:c.587G>A	p.Arg196Gln	p.R196Q	ENST00000335508	NM_012433.2	196	cGa/cAa	6/25	1	2	FACETS	0.576	0.508	0.649	0.576	0.508	0.649	SUBCLONAL	1	TRUE	1	0.284853599181687	2		794	1049	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196499	106196499	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs527895107	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	85	610	0	ENST00000380013.4:c.4832C>A	p.Ser1611Tyr	p.S1611Y	ENST00000380013	NM_001127208.2	1611	tCt/tAt	11/11	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.284853599181687	2		610	580	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953874	131953874	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121912628	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	49	456	0	ENST00000265335.6:c.3277C>T	p.Arg1093Ter	p.R1093*	ENST00000265335		1093	Cga/Tga	21/25	1	2	FACETS	0.737	0.624	0.86	0.737	0.624	0.86	SUBCLONAL	1	TRUE	1	0.284853599181687	2		456	467	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405915	70405915	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1430579993	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	110	676	0	ENST00000373644.4:c.3429G>T	p.Lys1143Asn	p.K1143N	ENST00000373644	NM_030625.2	1143	aaG/aaT	4/12	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.284853599181687	2		676	726	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138509	11138509	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	52	710	1	ENST00000358026.2:c.3265C>A	p.Leu1089Ile	p.L1089I	ENST00000358026	NM_001128849.1	1089	Ctt/Att	24/36	1	2	FACETS	0.479	0.406	0.558	0.479	0.406	0.558	SUBCLONAL	1	TRUE	1	0.284853599181687	2		711	763	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939266	76939266	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	81	1010	1	ENST00000373344.5:c.1482G>T	p.Lys494Asn	p.K494N	ENST00000373344	NM_000489.3	494	aaG/aaT	9/35	1	2	FACETS	0.673	0.592	0.76	0.673	0.592	0.76	SUBCLONAL	1	TRUE	1	0.284853599181687	2		1011	845	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267638	7267638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs896894246	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	155	590	1	ENST00000302850.5:c.370G>A	p.Glu124Lys	p.E124K	ENST00000302850	NM_000208.2	124	Gag/Aag	2/22	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.284853599181687	2		591	1024	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137487	202137487	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	146	540	0	ENST00000358485.4:c.715G>T	p.Glu239Ter	p.E239*	ENST00000358485	NM_001080125.1	239	Gaa/Taa	4/9	1	2	FACETS	0.856	0.784	0.93	1	0.99	1	CLONAL	2	TRUE	1	0.284853599181687	2		540	599	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007580	62007580	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778771873	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	61	859	0	ENST00000392795.3:c.287G>A	p.Arg96His	p.R96H	ENST00000392795	NM_001039933.1	96	cGc/cAc	3/6	1	2	FACETS	0.436	0.374	0.503	0.436	0.374	0.503	SUBCLONAL	1	TRUE	1	0.284853599181687	2		859	983	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143015	7143015	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145643501	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	130	712	0	ENST00000302850.5:c.2354C>T	p.Ser785Leu	p.S785L	ENST00000302850	NM_000208.2	785	tCg/tTg	12/22	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.284853599181687	2		712	814	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484291	50484291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253128772	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	136	875	3	ENST00000394963.4:c.1051C>T	p.Arg351Cys	p.R351C	ENST00000394963	NM_003076.4	351	Cgt/Tgt	9/13	1	2	FACETS	0.923	0.838	1	0.923	0.838	1	CLONAL	1	TRUE	1	0.284853599181687	2		878	1035	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736480	85736480	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	76	641	0	ENST00000370580.1:c.167C>A	p.Ser56Tyr	p.S56Y	ENST00000370580	NM_003921.4	56	tCt/tAt	2/3	1	2	FACETS	0.881	0.773	0.996	0.881	0.773	0.996	CLONAL	1	TRUE	1	0.284853599181687	2		641	606	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026290	48026290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147737737	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	83	528	1	ENST00000234420.5:c.1168G>A	p.Asp390Asn	p.D390N	ENST00000234420	NM_000179.2	390	Gat/Aat	4/10	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.284853599181687	2		529	544	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961036	15961036	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	69	458	0	ENST00000268712.3:c.6184G>T	p.Asp2062Tyr	p.D2062Y	ENST00000268712	NM_006311.3	2062	Gat/Tat	40/46	1	2	FACETS	0.904	0.788	1	0.904	0.788	1	CLONAL	1	TRUE	1	0.284853599181687	2		458	536	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754575	57754575	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	58	630	0	ENST00000274289.3:c.472C>A	p.Leu158Ile	p.L158I	ENST00000274289	NM_006622.3	158	Ctc/Atc	3/14	1	2	FACETS	0.753	0.647	0.868	0.753	0.647	0.868	SUBCLONAL	1	TRUE	1	0.284853599181687	2		630	541	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937236	76937236	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	80	883	0	ENST00000373344.5:c.3512G>T	p.Arg1171Ile	p.R1171I	ENST00000373344	NM_000489.3	1171	aGa/aTa	9/35	1	2	FACETS	0.861	0.759	0.972	0.861	0.759	0.972	CLONAL	1	TRUE	1	0.284853599181687	2		883	652	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754304	57754304	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	84	676	0	ENST00000274289.3:c.547C>T	p.Arg183Ter	p.R183*	ENST00000274289	NM_006622.3	183	Cga/Tga	4/14	1	2	FACETS	0.854	0.754	0.96	0.854	0.754	0.96	CLONAL	1	TRUE	1	0.284853599181687	2		676	691	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410883	31410883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	196	812	0	ENST00000344624.3:c.3637C>T	p.Arg1213Cys	p.R1213C	ENST00000344624		1213	Cgc/Tgc	28/33	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.284853599181687	2		812	1082	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739669	41739669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	68	873	0	ENST00000242208.4:c.304G>A	p.Glu102Lys	p.E102K	ENST00000242208	NM_002192.2	102	Gag/Aag	2/3	1	2	FACETS	0.511	0.443	0.584	0.511	0.443	0.584	SUBCLONAL	1	TRUE	1	0.284853599181687	2		873	935	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993335	72993335	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773329700	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	177	914	0	ENST00000268489.5:c.710G>A	p.Arg237Gln	p.R237Q	ENST00000268489	NM_006885.3	237	cGa/cAa	2/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.284853599181687	2		914	1051	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624296	89624296	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786201995	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	101	645	0	ENST00000371953.3:c.70G>T	p.Asp24Tyr	p.D24Y	ENST00000371953	NM_000314.4	24	Gac/Tac	1/9	1	2	FACETS	0.886	0.792	0.987	0.886	0.792	0.987	CLONAL	1	TRUE	1	0.284853599181687	2		645	800	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741780	17741780	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	112	469	0	ENST00000250003.3:c.451C>T	p.Arg151Cys	p.R151C	ENST00000250003	NM_002478.4	151	Cgc/Tgc	1/3	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.284853599181687	2		469	532	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965644	93965644	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	33	570	0	ENST00000369303.4:c.2284C>T	p.Arg762Cys	p.R762C	ENST00000369303	NM_004440.3	762	Cgc/Tgc	13/17	1	2	FACETS	0.387	0.314	0.469	0.387	0.314	0.469	SUBCLONAL	1	TRUE	1	0.284853599181687	2		570	599	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420030	41420030	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	118	520	0	ENST00000373198.4:c.291G>T	p.Glu97Asp	p.E97D	ENST00000373198	NM_133170.3	97	gaG/gaT	3/32	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.284853599181687	2		520	595	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119720	108119720	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1555069657	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	50	299	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	0.284853599181687	2		299	311	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906888	32906889	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	55	645	0	ENST00000380152.3:c.1278dup	p.Asp427ArgfsTer25	p.D427Rfs*25	ENST00000380152		425	gaa/gAaa	10/27	1	2	FACETS	0.782	0.669	0.904	0.782	0.669	0.904	CLONAL	1	TRUE	1	0.284853599181687	2		645	494	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118354911	118354911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550235275	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	75	567	2	ENST00000534358.1:c.4100C>T	p.Pro1367Leu	p.P1367L	ENST00000534358	NM_005933.3	1367	cCg/cTg	9/36	1	2	FACETS	0.87	0.763	0.986	0.87	0.763	0.986	CLONAL	1	TRUE	1	0.284853599181687	2		569	605	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515335	103515335	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	34	391	0	ENST00000355739.4:c.1836G>T	p.Glu612Asp	p.E612D	ENST00000355739	NM_000123.3	612	gaG/gaT	8/15	1	2	FACETS	0.559	0.457	0.674	0.559	0.457	0.674	SUBCLONAL	1	TRUE	1	0.284853599181687	2		391	427	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260151	149260151	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1307297959	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	97	656	1	ENST00000360632.3:c.742C>T	p.Arg248Ter	p.R248*	ENST00000360632	NM_015472.4	248	Cga/Tga	4/7	1	2	FACETS	0.961	0.857	1	0.961	0.857	1	CLONAL	1	TRUE	1	0.284853599181687	2		657	709	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582249	52582249	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	39	276	0	ENST00000394830.3:c.4579C>T	p.Arg1527Ter	p.R1527*	ENST00000394830	NM_018313.4	1527	Cga/Tga	30/30	1	2	FACETS	0.697	0.578	0.829	0.697	0.578	0.829	SUBCLONAL	1	TRUE	1	0.284853599181687	2		276	393	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795032	45795032	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs768671057	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	147	670	0	ENST00000450313.1:c.1596C>A	p.Phe532Leu	p.F532L	ENST00000450313	NM_012222.2	532	ttC/ttA	16/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.284853599181687	2		670	916	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729740	162729740	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	138	703	0	ENST00000367921.3:c.826G>T	p.Asp276Tyr	p.D276Y	ENST00000367921	NM_006182.2	276	Gac/Tac	8/18	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.284853599181687	2		703	797	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451152	70451152	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	66	835	0	ENST00000373644.4:c.5992G>T	p.Glu1998Ter	p.E1998*	ENST00000373644	NM_030625.2	1998	Gag/Tag	12/12	1	2	FACETS	0.508	0.44	0.583	0.508	0.44	0.583	SUBCLONAL	1	TRUE	1	0.284853599181687	2		835	912	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168656	56168656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764525244	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	94	500	0	ENST00000399503.3:c.1510G>A	p.Glu504Lys	p.E504K	ENST00000399503	NM_005921.1	504	Gag/Aag	9/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.284853599181687	2		500	616	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57474003	57474003	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	99	409	0	ENST00000371085.3:c.220G>A	p.Glu74Lys	p.E74K	ENST00000371085	NM_000516.4	74	Gaa/Aaa	3/13	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.284853599181687	2		409	594	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172161	99172161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs571358585	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	105	702	0	ENST00000074304.5:c.1727C>T	p.Pro576Leu	p.P576L	ENST00000074304	NM_001134224.1	576	cCg/cTg	17/26	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.284853599181687	2		702	703	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969194	93969194	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	36	377	0	ENST00000369303.4:c.1802A>C	p.Lys601Thr	p.K601T	ENST00000369303	NM_004440.3	601	aAa/aCa	10/17	1	2	FACETS	0.578	0.475	0.694	0.578	0.475	0.694	SUBCLONAL	1	TRUE	1	0.284853599181687	2		377	437	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39317318	39317318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	72	610	1	ENST00000373001.3:c.868G>A	p.Asp290Asn	p.D290N	ENST00000373001	NM_022157.3	290	Gat/Aat	5/7	1	2	FACETS	0.86	0.752	0.976	0.86	0.752	0.976	CLONAL	1	TRUE	1	0.284853599181687	2		611	588	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526547	66526547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	46	460	1	ENST00000358598.2:c.1103G>A	p.Arg368Gln	p.R368Q	ENST00000358598	NM_212471.2	368	cGa/cAa	11/11	1	2	FACETS	0.494	0.415	0.581	0.494	0.415	0.581	SUBCLONAL	1	TRUE	1	0.284853599181687	2		461	654	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872646	37872646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	60	889	1	ENST00000269571.5:c.1606C>T	p.Arg536Trp	p.R536W	ENST00000269571		536	Cgg/Tgg	13/27	1	2	FACETS	0.43	0.369	0.497	0.43	0.369	0.497	SUBCLONAL	1	TRUE	1	0.284853599181687	2		890	980	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295291	1295291	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	45	438	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.604	0.507	0.711	0.604	0.507	0.711	SUBCLONAL	1	TRUE	1	0.284853599181687	2		439	523	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256943	16256943	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1308286819	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	53	769	1	ENST00000375759.3:c.4208G>A	p.Arg1403Gln	p.R1403Q	ENST00000375759	NM_015001.2	1403	cGa/cAa	11/15	1	2	FACETS	0.433	0.368	0.505	0.433	0.368	0.505	SUBCLONAL	1	TRUE	1	0.284853599181687	2		770	859	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047230	180047230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	135	905	1	ENST00000261937.6:c.2485G>A	p.Glu829Lys	p.E829K	ENST00000261937	NM_182925.4	829	Gaa/Aaa	17/30	1	2	FACETS	0.99	0.899	1	0.99	0.899	1	CLONAL	1	TRUE	1	0.284853599181687	2		906	957	SUCCESS
APC	324	MSKCC	GRCh37	5	112128170	112128170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768233232	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	30	484	0	ENST00000257430.4:c.673G>A	p.Glu225Lys	p.E225K	ENST00000257430	NM_000038.5	225	Gaa/Aaa	7/16	1	2	FACETS	0.377	0.303	0.462	0.377	0.303	0.462	SUBCLONAL	1	TRUE	1	0.284853599181687	2		484	558	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920495	134920495	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	58	764	0	ENST00000398015.3:c.2310G>T	p.Gln770His	p.Q770H	ENST00000398015	NM_004441.4	770	caG/caT	12/16	1	2	FACETS	0.488	0.418	0.565	0.488	0.418	0.565	SUBCLONAL	1	TRUE	1	0.284853599181687	2		764	834	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739852	41739852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs984438766	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	86	542	0	ENST00000242208.4:c.121G>A	p.Ala41Thr	p.A41T	ENST00000242208	NM_002192.2	41	Gcc/Acc	2/3	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.284853599181687	2		542	549	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055755	152055755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1403418496	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	87	601	0	ENST00000262189.6:c.167G>A	p.Arg56Gln	p.R56Q	ENST00000262189	NM_170606.2	56	cGa/cAa	2/59	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.284853599181687	2		601	595	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499420	89499420	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	42	610	0	ENST00000336596.2:c.2590G>T	p.Asp864Tyr	p.D864Y	ENST00000336596	NM_005233.5	864	Gac/Tac	15/17	1	2	FACETS	0.437	0.364	0.518	0.437	0.364	0.518	SUBCLONAL	1	TRUE	1	0.284853599181687	2		610	675	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014163	70014163	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868519483	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	50	690	2	ENST00000394351.3:c.1024G>A	p.Asp342Asn	p.D342N	ENST00000394351	NM_000248.3	342	Gat/Aat	9/9	1	2	FACETS	0.414	0.35	0.485	0.414	0.35	0.485	SUBCLONAL	1	TRUE	1	0.284853599181687	2		692	847	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971327	13971327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751178726	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	44	586	1	ENST00000405192.2:c.602C>T	p.Pro201Leu	p.P201L	ENST00000405192	NM_001163147.1	201	cCg/cTg	8/12	0.284853599181687	2	FACETS	0.484	0.405	0.572	0.242	0.202	0.286	SUBCLONAL	1	TRUE	0	0.284853599181687	2		587	638	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623637	28623637	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	85	774	1	ENST00000241453.7:c.920G>T	p.Arg307Ile	p.R307I	ENST00000241453	NM_004119.2	307	aGa/aTa	8/24	1	2	FACETS	0.847	0.748	0.952	0.847	0.748	0.952	CLONAL	1	TRUE	1	0.284853599181687	2		775	705	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784496	43784496	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	114	752	0	ENST00000382044.4:c.178G>T	p.Glu60Ter	p.E60*	ENST00000382044	NM_001141980.1	60	Gaa/Taa	2/28	1	2	FACETS	0.964	0.868	1	0.964	0.868	1	CLONAL	1	TRUE	1	0.284853599181687	2		752	830	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938995	76938995	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs886044898	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	88	868	0	ENST00000373344.5:c.1753G>T	p.Glu585Ter	p.E585*	ENST00000373344	NM_000489.3	585	Gaa/Taa	9/35	1	2	FACETS	0.775	0.686	0.871	0.775	0.686	0.871	SUBCLONAL	1	TRUE	1	0.284853599181687	2		868	797	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741256	145741256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766026341	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	79	833	3	ENST00000428558.2:c.1150C>T	p.Arg384Trp	p.R384W	ENST00000428558	NM_004260.3	384	Cgg/Tgg	6/22	1	2	FACETS	0.541	0.474	0.613	0.541	0.474	0.613	SUBCLONAL	1	TRUE	1	0.284853599181687	2		836	1026	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710875	117710875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140178288	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	47	621	0	ENST00000368508.3:c.1397G>A	p.Arg466Gln	p.R466Q	ENST00000368508	NM_002944.2	466	cGa/cAa	12/43	1	2	FACETS	0.473	0.398	0.557	0.473	0.398	0.557	SUBCLONAL	1	TRUE	1	0.284853599181687	2		621	697	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519596	137519596	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	105	510	0	ENST00000367739.4:c.1042G>T	p.Glu348Ter	p.E348*	ENST00000367739	NM_000416.2	348	Gaa/Taa	7/7	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.284853599181687	2		510	648	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519308	137519308	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	36	566	0	ENST00000367739.4:c.1330G>T	p.Glu444Ter	p.E444*	ENST00000367739	NM_000416.2	444	Gag/Tag	7/7	1	2	FACETS	0.487	0.4	0.585	0.487	0.4	0.585	SUBCLONAL	1	TRUE	1	0.284853599181687	2		566	519	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340213	116340213	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs753762177	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	44	397	1	ENST00000397752.3:c.1075C>T	p.Arg359Ter	p.R359*	ENST00000397752	NM_000245.2	359	Cga/Tga	2/21	1	2	FACETS	0.623	0.522	0.734	0.623	0.522	0.734	SUBCLONAL	1	TRUE	1	0.284853599181687	2		398	496	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316389	14316389	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	99	528	0	ENST00000256196.4:c.216A>C	p.Gln72His	p.Q72H	ENST00000256196		72	caA/caC	3/6	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.284853599181687	2		528	667	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508803	106508803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	36	573	0	ENST00000359195.3:c.797G>A	p.Ser266Asn	p.S266N	ENST00000359195	NM_002649.2	266	aGc/aAc	2/11	1	2	FACETS	0.374	0.307	0.451	0.374	0.307	0.451	SUBCLONAL	1	TRUE	1	0.284853599181687	2		573	675	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285851	87285851	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	98	675	0	ENST00000277120.3:c.188T>C	p.Val63Ala	p.V63A	ENST00000277120		63	gTa/gCa	2/19	1	2	FACETS	0.909	0.811	1	0.909	0.811	1	CLONAL	1	TRUE	1	0.284853599181687	2		675	757	SUCCESS
ATR	545	MSKCC	GRCh37	3	142257364	142257364	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	65	539	0	ENST00000350721.4:c.3685G>T	p.Glu1229Ter	p.E1229*	ENST00000350721	NM_001184.3	1229	Gaa/Taa	19/47	1	2	FACETS	0.671	0.581	0.769	0.671	0.581	0.769	SUBCLONAL	1	TRUE	1	0.284853599181687	2		539	680	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784945	9784945	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs975282953	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	149	788	3	ENST00000377346.4:c.2948C>T	p.Ala983Val	p.A983V	ENST00000377346	NM_005026.3	983	gCg/gTg	23/24	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.284853599181687	2		791	867	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11273618	11273618	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	24	458	0	ENST00000361445.4:c.3123C>A	p.Phe1041Leu	p.F1041L	ENST00000361445	NM_004958.3	1041	ttC/ttA	21/58	1	2	FACETS	0.402	0.315	0.503	0.402	0.315	0.503	SUBCLONAL	1	TRUE	1	0.284853599181687	2		458	419	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303184	11303184	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	42	639	0	ENST00000361445.4:c.1399G>T	p.Asp467Tyr	p.D467Y	ENST00000361445	NM_004958.3	467	Gac/Tac	9/58	1	2	FACETS	0.421	0.35	0.499	0.421	0.35	0.499	SUBCLONAL	1	TRUE	1	0.284853599181687	2		639	701	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16247442	16247442	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	23	350	0	ENST00000375759.3:c.1713G>T	p.Glu571Asp	p.E571D	ENST00000375759	NM_015001.2	571	gaG/gaT	9/15	1	2	FACETS	0.357	0.278	0.45	0.357	0.278	0.45	SUBCLONAL	1	TRUE	1	0.284853599181687	2		350	452	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255902	16255902	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	38	488	0	ENST00000375759.3:c.3167G>T	p.Arg1056Ile	p.R1056I	ENST00000375759	NM_015001.2	1056	aGa/aTa	11/15	1	2	FACETS	0.471	0.388	0.563	0.471	0.388	0.563	SUBCLONAL	1	TRUE	1	0.284853599181687	2		488	567	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257530	16257530	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	49	546	0	ENST00000375759.3:c.4795G>T	p.Glu1599Ter	p.E1599*	ENST00000375759	NM_015001.2	1599	Gaa/Taa	11/15	1	2	FACETS	0.657	0.556	0.767	0.657	0.556	0.767	SUBCLONAL	1	TRUE	1	0.284853599181687	2		546	524	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511612	46511612	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	49	644	0	ENST00000262741.5:c.1165G>T	p.Gly389Ter	p.G389*	ENST00000262741	NM_003629.3	389	Gga/Tga	9/10	1	2	FACETS	0.519	0.439	0.608	0.519	0.439	0.608	SUBCLONAL	1	TRUE	1	0.284853599181687	2		644	663	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531836	46531836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	21	424	0	ENST00000262741.5:c.511G>A	p.Glu171Lys	p.E171K	ENST00000262741	NM_003629.3	171	Gaa/Aaa	5/10	1	2	FACETS	0.38	0.292	0.483	0.38	0.292	0.483	SUBCLONAL	1	TRUE	1	0.284853599181687	2		424	388	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46715681	46715681	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	47	693	0	ENST00000371975.4:c.100A>C	p.Lys34Gln	p.K34Q	ENST00000371975	NM_003579.3	34	Aaa/Caa	3/18	1	2	FACETS	0.485	0.408	0.569	0.485	0.408	0.569	SUBCLONAL	1	TRUE	1	0.284853599181687	2		693	681	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739344	46739344	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	131	638	0	ENST00000371975.4:c.1535G>T	p.Ser512Ile	p.S512I	ENST00000371975	NM_003579.3	512	aGc/aTc	14/18	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.284853599181687	2		638	834	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301869	65301869	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	56	301	0	ENST00000342505.4:c.3170A>C	p.Lys1057Thr	p.K1057T	ENST00000342505	NM_002227.2	1057	aAa/aCa	23/25	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.284853599181687	2		301	391	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733537	85733537	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	38	658	0	ENST00000370580.1:c.475G>T	p.Glu159Ter	p.E159*	ENST00000370580	NM_003921.4	159	Gaa/Taa	3/3	1	2	FACETS	0.375	0.309	0.45	0.375	0.309	0.45	SUBCLONAL	1	TRUE	1	0.284853599181687	2		658	711	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256601	115256601	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	82	490	0	ENST00000369535.4:c.112-2A>G		p.X38_splice	ENST00000369535	NM_002524.4	38			1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.284853599181687	2		490	517	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276421	115276421	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	49	799	1	ENST00000438362.2:c.907G>T	p.Asp303Tyr	p.D303Y	ENST00000438362	NM_001242891.1	303	Gat/Tat	9/20	1	2	FACETS	0.456	0.385	0.535	0.456	0.385	0.535	SUBCLONAL	1	TRUE	1	0.284853599181687	2		800	754	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165800	118165800	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	70	570	1	ENST00000369448.3:c.310G>T	p.Glu104Ter	p.E104*	ENST00000369448	NM_017709.3	104	Gaa/Taa	2/2	1	2	FACETS	0.812	0.708	0.924	0.812	0.708	0.924	CLONAL	1	TRUE	1	0.284853599181687	2		571	605	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551332	150551332	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	157	884	0	ENST00000369026.2:c.675G>T	p.Glu225Asp	p.E225D	ENST00000369026	NM_021960.4	225	gaG/gaT	1/3	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.284853599181687	2		884	1087	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724974	162724974	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	91	610	2	ENST00000367921.3:c.446A>T	p.Asp149Val	p.D149V	ENST00000367921	NM_006182.2	149	gAc/gTc	6/18	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.284853599181687	2		612	609	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218892	193218892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1225502334	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	34	389	0	ENST00000367435.3:c.1450C>T	p.Arg484Cys	p.R484C	ENST00000367435	NM_024529.4	484	Cgt/Tgt	16/17	1	2	FACETS	0.713	0.583	0.857	0.713	0.583	0.857	SUBCLONAL	1	TRUE	1	0.284853599181687	2		389	335	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218998	193218998	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	17	364	0	ENST00000367435.3:c.1556A>G	p.Asp519Gly	p.D519G	ENST00000367435	NM_024529.4	519	gAc/gGc	16/17	1	2	FACETS	0.361	0.268	0.47	0.361	0.268	0.47	SUBCLONAL	1	TRUE	1	0.284853599181687	2		364	331	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800957	243800957	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	59	665	0	ENST00000263826.5:c.517T>G	p.Tyr173Asp	p.Y173D	ENST00000263826	NM_005465.4	173	Tac/Gac	5/13	1	2	FACETS	0.696	0.599	0.802	0.696	0.599	0.802	SUBCLONAL	1	TRUE	1	0.284853599181687	2		665	595	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828172	243828172	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	84	634	0	ENST00000263826.5:c.186G>T	p.Met62Ile	p.M62I	ENST00000263826	NM_005465.4	62	atG/atT	3/13	1	2	FACETS	0.926	0.818	1	0.926	0.818	1	CLONAL	1	TRUE	1	0.284853599181687	2		634	637	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106073	8106073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	92	505	1	ENST00000346208.3:c.893G>A	p.Arg298Gln	p.R298Q	ENST00000346208		298	cGg/cAg	4/6	1	2	FACETS	0.971	0.864	1	0.971	0.864	1	CLONAL	1	TRUE	1	0.284853599181687	2		506	665	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692973	89692973	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	82	569	0	ENST00000371953.3:c.457G>T	p.Asp153Tyr	p.D153Y	ENST00000371953	NM_000314.4	153	Gat/Tat	5/9	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.284853599181687	2		569	545	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456696	32456696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	39	488	1	ENST00000332351.3:c.196C>T	p.Pro66Ser	p.P66S	ENST00000332351	NM_024426.4	66	Ccg/Tcg	1/10	1	2	FACETS	0.541	0.448	0.645	0.541	0.448	0.645	SUBCLONAL	1	TRUE	1	0.284853599181687	2		489	506	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941880	71941880	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	69	764	0	ENST00000298229.2:c.1238A>C	p.Asn413Thr	p.N413T	ENST00000298229	NM_001567.3	413	aAc/aCc	11/28	1	2	FACETS	0.564	0.49	0.644	0.564	0.49	0.644	SUBCLONAL	1	TRUE	1	0.284853599181687	2		764	859	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998823	100998823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	53	743	1	ENST00000325455.5:c.979G>A	p.Glu327Lys	p.E327K	ENST00000325455	NM_001202474.3	327	Gaa/Aaa	1/8	1	2	FACETS	0.487	0.414	0.567	0.487	0.414	0.567	SUBCLONAL	1	TRUE	1	0.284853599181687	2		744	764	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402036	402036	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	47	726	0	ENST00000399788.2:c.4755G>T	p.Glu1585Asp	p.E1585D	ENST00000399788	NM_001042603.1	1585	gaG/gaT	27/28	1	2	FACETS	0.435	0.366	0.511	0.435	0.366	0.511	SUBCLONAL	1	TRUE	1	0.284853599181687	2		726	759	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230728	46230728	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	37	525	0	ENST00000334344.6:c.977C>A	p.Ser326Tyr	p.S326Y	ENST00000334344	NM_152641.2	326	tCt/tAt	8/21	1	2	FACETS	0.457	0.376	0.548	0.457	0.376	0.548	SUBCLONAL	1	TRUE	1	0.284853599181687	2		525	568	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243904	46243904	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	82	511	0	ENST00000334344.6:c.1998A>C	p.Gln666His	p.Q666H	ENST00000334344	NM_152641.2	666	caA/caC	15/21	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.284853599181687	2		511	528	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435898	49435898	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	67	898	0	ENST00000301067.7:c.6083T>G	p.Phe2028Cys	p.F2028C	ENST00000301067	NM_003482.3	2028	tTt/tGt	28/54	1	2	FACETS	0.498	0.432	0.571	0.498	0.432	0.571	SUBCLONAL	1	TRUE	1	0.284853599181687	2		898	944	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480323	56480323	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	85	482	0	ENST00000267101.3:c.430T>C	p.Ser144Pro	p.S144P	ENST00000267101	NM_001982.3	144	Tca/Cca	4/28	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.284853599181687	2		482	587	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865090	57865090	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	75	966	0	ENST00000228682.2:c.2567C>A	p.Pro856His	p.P856H	ENST00000228682	NM_005269.2	856	cCt/cAt	12/12	1	2	FACETS	0.506	0.442	0.576	0.506	0.442	0.576	SUBCLONAL	1	TRUE	1	0.284853599181687	2		966	1040	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811747	102811747	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	65	836	0	ENST00000307046.8:c.437C>A	p.Ser146Tyr	p.S146Y	ENST00000307046	NM_001111285.1	146	tCt/tAt	4/4	1	2	FACETS	0.516	0.446	0.592	0.516	0.446	0.592	SUBCLONAL	1	TRUE	1	0.284853599181687	2		836	885	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885886	111885886	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs781623667	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	80	822	1	ENST00000341259.2:c.1508C>A	p.Ser503Tyr	p.S503Y	ENST00000341259	NM_005475.2	503	tCt/tAt	8/8	1	2	FACETS	0.587	0.515	0.664	0.587	0.515	0.664	SUBCLONAL	1	TRUE	1	0.284853599181687	2		823	957	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926839	112926839	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	75	1023	0	ENST00000351677.2:c.1459G>A	p.Asp487Asn	p.D487N	ENST00000351677	NM_002834.3	487	Gat/Aat	13/16	1	2	FACETS	0.48	0.419	0.547	0.48	0.419	0.547	SUBCLONAL	1	TRUE	1	0.284853599181687	2		1023	1096	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120785275	120785275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778099314	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	83	730	3	ENST00000257552.2:c.833C>T	p.Ala278Val	p.A278V	ENST00000257552	NM_002442.3	278	gCg/gTg	12/15	1	2	FACETS	0.677	0.596	0.764	0.677	0.596	0.764	SUBCLONAL	1	TRUE	1	0.284853599181687	2		733	861	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26928012	26928012	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	33	643	0	ENST00000381527.3:c.451G>T	p.Asp151Tyr	p.D151Y	ENST00000381527	NM_001260.1	151	Gat/Tat	4/13	1	2	FACETS	0.385	0.312	0.467	0.385	0.312	0.467	SUBCLONAL	1	TRUE	1	0.284853599181687	2		643	602	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967572	26967572	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	29	692	0	ENST00000381527.3:c.715G>T	p.Glu239Ter	p.E239*	ENST00000381527	NM_001260.1	239	Gag/Tag	7/13	1	2	FACETS	0.366	0.293	0.45	0.366	0.293	0.45	SUBCLONAL	1	TRUE	1	0.284853599181687	2		692	556	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608117	28608117	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	40	704	0	ENST00000241453.7:c.1849G>T	p.Gly617Ter	p.G617*	ENST00000241453	NM_004119.2	617	Gga/Tga	15/24	1	2	FACETS	0.369	0.305	0.44	0.369	0.305	0.44	SUBCLONAL	1	TRUE	1	0.284853599181687	2		704	762	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28903812	28903812	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	43	765	0	ENST00000282397.4:c.2647A>G	p.Thr883Ala	p.T883A	ENST00000282397	NM_002019.4	883	Acc/Gcc	19/30	1	2	FACETS	0.371	0.31	0.44	0.371	0.31	0.44	SUBCLONAL	1	TRUE	1	0.284853599181687	2		765	813	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911446	32911446	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	47	502	0	ENST00000380152.3:c.2954A>C	p.Lys985Thr	p.K985T	ENST00000380152		985	aAa/aCa	11/27	1	2	FACETS	0.862	0.729	1	0.862	0.729	1	CLONAL	1	TRUE	1	0.284853599181687	2		502	383	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913603	32913603	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	39	446	0	ENST00000380152.3:c.5111G>T	p.Arg1704Ile	p.R1704I	ENST00000380152		1704	aGa/aTa	11/27	1	2	FACETS	0.789	0.656	0.937	0.789	0.656	0.937	CLONAL	1	TRUE	1	0.284853599181687	2		446	347	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913878	32913878	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1064793715	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	59	593	0	ENST00000380152.3:c.5386G>T	p.Asp1796Tyr	p.D1796Y	ENST00000380152		1796	Gat/Tat	11/27	1	2	FACETS	0.859	0.741	0.988	0.859	0.741	0.988	CLONAL	1	TRUE	1	0.284853599181687	2		593	482	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133772	41133772	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs745385825	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	83	519	0	ENST00000379561.5:c.1856G>T	p.Arg619Leu	p.R619L	ENST00000379561	NM_002015.3	619	cGg/cTg	2/3	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.284853599181687	2		519	525	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939073	48939073	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1208736713	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	26	417	0	ENST00000267163.4:c.905C>A	p.Ser302Tyr	p.S302Y	ENST00000267163	NM_000321.2	302	tCt/tAt	9/27	1	2	FACETS	0.433	0.342	0.537	0.433	0.342	0.537	SUBCLONAL	1	TRUE	1	0.284853599181687	2		417	422	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514532	103514532	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	53	339	0	ENST00000355739.4:c.1033T>G	p.Leu345Val	p.L345V	ENST00000355739	NM_000123.3	345	Tta/Gta	8/15	1	2	FACETS	0.979	0.838	1	0.979	0.838	1	CLONAL	1	TRUE	1	0.284853599181687	2		339	380	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434945	110434945	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	82	861	0	ENST00000375856.3:c.3456C>A	p.Phe1152Leu	p.F1152L	ENST00000375856	NM_003749.2	1152	ttC/ttA	1/2	1	2	FACETS	0.573	0.504	0.648	0.573	0.504	0.648	SUBCLONAL	1	TRUE	1	0.284853599181687	2		861	1004	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435579	110435579	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	52	449	1	ENST00000375856.3:c.2822C>T	p.Ser941Leu	p.S941L	ENST00000375856	NM_003749.2	941	tCg/tTg	1/2	1	2	FACETS	0.738	0.628	0.857	0.738	0.628	0.857	SUBCLONAL	1	TRUE	1	0.284853599181687	2		450	495	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243091	105243091	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	152	835	0	ENST00000349310.3:c.192G>T	p.Lys64Asn	p.K64N	ENST00000349310	NM_001014432.1	64	aaG/aaT	5/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.284853599181687	2		835	872	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058802	42058802	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	34	423	0	ENST00000219905.7:c.8522C>A	p.Ser2841Tyr	p.S2841Y	ENST00000219905	NM_001164273.1	2841	tCt/tAt	24/24	1	2	FACETS	0.485	0.396	0.586	0.485	0.396	0.586	SUBCLONAL	1	TRUE	1	0.284853599181687	2		423	492	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396722	396722	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	101	694	0	ENST00000262320.3:c.304T>C	p.Phe102Leu	p.F102L	ENST00000262320	NM_003502.3	102	Ttc/Ctc	2/11	1	2	FACETS	0.939	0.84	1	0.939	0.84	1	CLONAL	1	TRUE	1	0.284853599181687	2		694	755	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14022037	14022037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370864937	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	29	675	0	ENST00000311895.7:c.737C>T	p.Ser246Leu	p.S246L	ENST00000311895	NM_005236.2	246	tCg/tTg	4/11	1	2	FACETS	0.353	0.283	0.434	0.353	0.283	0.434	SUBCLONAL	1	TRUE	1	0.284853599181687	2		675	576	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785686	50785686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763792744	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	45	769	0	ENST00000398568.2:c.676G>A	p.Glu226Lys	p.E226K	ENST00000398568	NM_001042412.1	226	Gaa/Aaa	4/18	1	2	FACETS	0.388	0.325	0.458	0.388	0.325	0.458	SUBCLONAL	1	TRUE	1	0.284853599181687	2		769	815	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56862898	56862898	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	80	462	0	ENST00000308159.5:c.804T>G	p.Asn268Lys	p.N268K	ENST00000308159	NM_014669.4	268	aaT/aaG	9/22	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.284853599181687	2		462	516	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822454	72822454	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	71	973	0	ENST00000268489.5:c.9721A>C	p.Lys3241Gln	p.K3241Q	ENST00000268489	NM_006885.3	3241	Aag/Cag	10/10	1	2	FACETS	0.483	0.42	0.551	0.483	0.42	0.551	SUBCLONAL	1	TRUE	1	0.284853599181687	2		973	1033	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828301	72828301	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	107	742	0	ENST00000268489.5:c.8280G>T	p.Met2760Ile	p.M2760I	ENST00000268489	NM_006885.3	2760	atG/atT	9/10	1	2	FACETS	0.946	0.849	1	0.946	0.849	1	CLONAL	1	TRUE	1	0.284853599181687	2		742	794	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81914532	81914532	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	123	604	0	ENST00000359376.3:c.666A>C	p.Lys222Asn	p.K222N	ENST00000359376	NM_002661.3	222	aaA/aaC	8/33	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.284853599181687	2		604	788	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347658	89347658	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	133	701	0	ENST00000301030.4:c.5292C>A	p.Phe1764Leu	p.F1764L	ENST00000301030	NM_001256183.1	1764	ttC/ttA	9/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.284853599181687	2		701	687	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350521	89350521	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	62	832	0	ENST00000301030.4:c.2429A>G	p.Glu810Gly	p.E810G	ENST00000301030	NM_001256183.1	810	gAa/gGa	9/13	1	2	FACETS	0.474	0.408	0.546	0.474	0.408	0.546	SUBCLONAL	1	TRUE	1	0.284853599181687	2		832	919	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371746	89371746	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	98	573	0	ENST00000301030.4:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000301030	NM_001256183.1	32	Gat/Tat	4/13	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.284853599181687	2		573	680	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217829	7217829	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	159	893	2	ENST00000380728.2:c.182C>A	p.Ser61Ter	p.S61*	ENST00000380728		61	tCa/tAa	3/11	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.284853599181687	2		895	1102	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110145	8110145	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	47	659	0	ENST00000585124.1:c.460C>A	p.Leu154Ile	p.L154I	ENST00000585124	NM_004217.3	154	Cta/Ata	6/9	1	2	FACETS	0.421	0.354	0.496	0.421	0.354	0.496	SUBCLONAL	1	TRUE	1	0.284853599181687	2		659	783	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983798	15983798	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	75	711	0	ENST00000268712.3:c.3324A>C	p.Glu1108Asp	p.E1108D	ENST00000268712	NM_006311.3	1108	gaA/gaC	25/46	1	2	FACETS	0.576	0.503	0.654	0.576	0.503	0.654	SUBCLONAL	1	TRUE	1	0.284853599181687	2		711	915	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004954	16004954	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	64	896	0	ENST00000268712.3:c.2300T>G	p.Leu767Ter	p.L767*	ENST00000268712	NM_006311.3	767	tTa/tGa	20/46	1	2	FACETS	0.417	0.36	0.48	0.417	0.36	0.48	SUBCLONAL	1	TRUE	1	0.284853599181687	2		896	1077	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16056688	16056688	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	30	438	0	ENST00000268712.3:c.754A>C	p.Lys252Gln	p.K252Q	ENST00000268712	NM_006311.3	252	Aaa/Caa	7/46	1	2	FACETS	0.407	0.327	0.498	0.407	0.327	0.498	SUBCLONAL	1	TRUE	1	0.284853599181687	2		438	517	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486058	29486058	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	55	488	0	ENST00000356175.3:c.235T>G	p.Leu79Val	p.L79V	ENST00000356175	NM_000267.3	79	Tta/Gta	3/57	1	2	FACETS	0.906	0.777	1	0.906	0.777	1	CLONAL	1	TRUE	1	0.284853599181687	2		488	426	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556356	29556356	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	103	656	0	ENST00000356175.3:c.2723A>C	p.Lys908Thr	p.K908T	ENST00000356175	NM_000267.3	908	aAa/aCa	21/57	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.284853599181687	2		656	655	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576065	29576065	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	50	677	0	ENST00000356175.3:c.4038C>A	p.Phe1346Leu	p.F1346L	ENST00000356175	NM_000267.3	1346	ttC/ttA	30/57	1	2	FACETS	0.416	0.352	0.488	0.416	0.352	0.488	SUBCLONAL	1	TRUE	1	0.284853599181687	2		677	843	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627290	37627290	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	49	670	0	ENST00000447079.4:c.1205A>C	p.Lys402Thr	p.K402T	ENST00000447079	NM_015083.1	402	aAa/aCa	2/14	1	2	FACETS	0.481	0.406	0.564	0.481	0.406	0.564	SUBCLONAL	1	TRUE	1	0.284853599181687	2		670	715	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40855818	40855818	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	92	653	1	ENST00000428826.2:c.2038C>T	p.Arg680Trp	p.R680W	ENST00000428826		680	Cgg/Tgg	19/21	1	2	FACETS	0.833	0.74	0.933	0.833	0.74	0.933	CLONAL	1	TRUE	1	0.284853599181687	2		654	775	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245080	41245080	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876659731	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	70	1082	0	ENST00000357654.3:c.2468G>T	p.Arg823Ile	p.R823I	ENST00000357654	NM_007294.3	823	aGa/aTa	10/23	1	2	FACETS	0.543	0.472	0.62	0.543	0.472	0.62	SUBCLONAL	1	TRUE	1	0.284853599181687	2		1082	905	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696405	47696405	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	97	651	0	ENST00000347630.2:c.418G>T	p.Asp140Tyr	p.D140Y	ENST00000347630	NM_001007230.1	140	Gat/Tat	6/11	1	2	FACETS	0.883	0.787	0.986	0.883	0.787	0.986	CLONAL	1	TRUE	1	0.284853599181687	2		651	771	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740814	58740814	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	61	592	0	ENST00000305921.3:c.1719G>T	p.Lys573Asn	p.K573N	ENST00000305921	NM_003620.3	573	aaG/aaT	6/6	1	2	FACETS	0.551	0.474	0.635	0.551	0.474	0.635	SUBCLONAL	1	TRUE	1	0.284853599181687	2		592	777	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796998	78796998	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	82	659	1	ENST00000306801.3:c.1111C>T	p.Pro371Ser	p.P371S	ENST00000306801	NM_020761.2	371	Ccg/Tcg	9/34	1	2	FACETS	0.677	0.595	0.764	0.677	0.595	0.764	SUBCLONAL	1	TRUE	1	0.284853599181687	2		660	851	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39570490	39570490	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	51	380	0	ENST00000262039.4:c.686A>C	p.Lys229Thr	p.K229T	ENST00000262039	NM_002647.2	229	aAg/aCg	6/25	1	2	FACETS	0.859	0.731	0.998	0.859	0.731	0.998	CLONAL	1	TRUE	1	0.284853599181687	2		380	417	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218488	1218488	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	35	617	0	ENST00000326873.7:c.363G>T	p.Glu121Asp	p.E121D	ENST00000326873	NM_000455.4	121	gaG/gaT	2/10	1	2	FACETS	0.385	0.314	0.464	0.385	0.314	0.464	SUBCLONAL	1	TRUE	1	0.284853599181687	2		617	639	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101111	4101111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	32	449	1	ENST00000262948.5:c.611C>A	p.Ser204Tyr	p.S204Y	ENST00000262948	NM_030662.3	204	tCt/tAt	6/11	1	2	FACETS	0.404	0.327	0.491	0.404	0.327	0.491	SUBCLONAL	1	TRUE	1	0.284853599181687	2		450	556	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245787	5245787	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	43	741	0	ENST00000357368.4:c.988T>G	p.Ser330Ala	p.S330A	ENST00000357368	NM_002850.3	330	Tct/Gct	10/38	1	2	FACETS	0.361	0.301	0.428	0.361	0.301	0.428	SUBCLONAL	1	TRUE	1	0.284853599181687	2		741	836	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7128930	7128930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765227638	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	61	544	0	ENST00000302850.5:c.2878G>A	p.Gly960Ser	p.G960S	ENST00000302850	NM_000208.2	960	Ggc/Agc	15/22	1	2	FACETS	0.751	0.648	0.863	0.751	0.648	0.863	SUBCLONAL	1	TRUE	1	0.284853599181687	2		544	570	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7132172	7132172	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	139	650	0	ENST00000302850.5:c.2839T>G	p.Tyr947Asp	p.Y947D	ENST00000302850	NM_000208.2	947	Tat/Gat	14/22	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.284853599181687	2		650	737	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7163078	7163078	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	60	806	0	ENST00000302850.5:c.1994A>G	p.Asp665Gly	p.D665G	ENST00000302850	NM_000208.2	665	gAc/gGc	9/22	1	2	FACETS	0.438	0.376	0.506	0.438	0.376	0.506	SUBCLONAL	1	TRUE	1	0.284853599181687	2		806	962	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170713	7170713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1375755714	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	144	944	0	ENST00000302850.5:c.1318G>A	p.Asp440Asn	p.D440N	ENST00000302850	NM_000208.2	440	Gac/Aac	6/22	1	2	FACETS	0.913	0.831	1	0.913	0.831	1	CLONAL	1	TRUE	1	0.284853599181687	2		944	1107	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10271064	10271064	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	44	710	0	ENST00000340748.4:c.991G>T	p.Glu331Ter	p.E331*	ENST00000340748		331	Gaa/Taa	13/40	1	2	FACETS	0.366	0.306	0.433	0.366	0.306	0.433	SUBCLONAL	1	TRUE	1	0.284853599181687	2		710	844	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10273385	10273385	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	72	775	0	ENST00000340748.4:c.918A>C	p.Lys306Asn	p.K306N	ENST00000340748		306	aaA/aaC	12/40	1	2	FACETS	0.508	0.442	0.579	0.508	0.442	0.579	SUBCLONAL	1	TRUE	1	0.284853599181687	2		775	995	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024608	11024608	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	65	704	0	ENST00000327064.4:c.725T>G	p.Val242Gly	p.V242G	ENST00000327064	NM_199141.1	242	gTg/gGg	6/16	1	2	FACETS	0.619	0.536	0.71	0.619	0.536	0.71	SUBCLONAL	1	TRUE	1	0.284853599181687	2		704	737	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299878	15299878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	152	902	1	ENST00000263388.2:c.1300G>A	p.Glu434Lys	p.E434K	ENST00000263388	NM_000435.2	434	Gag/Aag	8/33	1	2	FACETS	0.979	0.894	1	0.979	0.894	1	CLONAL	1	TRUE	1	0.284853599181687	2		903	1090	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719291	52719291	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	62	754	1	ENST00000322088.6:c.957G>T	p.Glu319Asp	p.E319D	ENST00000322088	NM_014225.5	319	gaG/gaT	8/15	1	2	FACETS	0.524	0.452	0.604	0.524	0.452	0.604	SUBCLONAL	1	TRUE	1	0.284853599181687	2		755	830	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972963	25972963	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	52	565	0	ENST00000435504.4:c.1462C>A	p.Leu488Ile	p.L488I	ENST00000435504		488	Ctc/Atc	12/13	1	2	FACETS	0.578	0.491	0.673	0.578	0.491	0.673	SUBCLONAL	1	TRUE	1	0.284853599181687	2		565	632	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015055	27015055	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	40	568	0	ENST00000335756.4:c.157A>C	p.Lys53Gln	p.K53Q	ENST00000335756	NM_001809.3	53	Aag/Cag	2/5	1	2	FACETS	0.431	0.357	0.514	0.431	0.357	0.514	SUBCLONAL	1	TRUE	1	0.284853599181687	2		568	651	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224174	39224174	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	37	459	0	ENST00000402219.2:c.2970C>A	p.Phe990Leu	p.F990L	ENST00000402219	NM_005633.3	990	ttC/ttA	19/23	1	2	FACETS	0.629	0.519	0.752	0.629	0.519	0.752	SUBCLONAL	1	TRUE	1	0.284853599181687	2		459	413	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39239301	39239301	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	69	785	0	ENST00000402219.2:c.2356C>T	p.Arg786Ter	p.R786*	ENST00000402219	NM_005633.3	786	Cga/Tga	14/23	1	2	FACETS	0.665	0.578	0.758	0.665	0.578	0.758	SUBCLONAL	1	TRUE	1	0.284853599181687	2		785	729	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46525071	46525071	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	121	626	0	ENST00000263734.3:c.21G>T	p.Lys7Asn	p.K7N	ENST00000263734	NM_001430.4	7	aaG/aaT	1/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.284853599181687	2		626	740	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018191	48018191	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	50	787	0	ENST00000234420.5:c.386T>C	p.Val129Ala	p.V129A	ENST00000234420	NM_000179.2	129	gTt/gCt	2/10	1	2	FACETS	0.371	0.313	0.434	0.371	0.313	0.434	SUBCLONAL	1	TRUE	1	0.284853599181687	2		787	947	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026386	48026386	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	49	737	0	ENST00000234420.5:c.1264G>T	p.Asp422Tyr	p.D422Y	ENST00000234420	NM_000179.2	422	Gat/Tat	4/10	1	2	FACETS	0.495	0.418	0.58	0.495	0.418	0.58	SUBCLONAL	1	TRUE	1	0.284853599181687	2		737	695	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027453	48027453	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs876660037	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	76	617	1	ENST00000234420.5:c.2331G>A	p.Trp777Ter	p.W777*	ENST00000234420	NM_000179.2	777	tgG/tgA	4/10	1	2	FACETS	0.857	0.752	0.969	0.857	0.752	0.969	CLONAL	1	TRUE	1	0.284853599181687	2		618	623	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715729	61715729	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	36	489	0	ENST00000401558.2:c.2200G>T	p.Ala734Ser	p.A734S	ENST00000401558	NM_003400.3	734	Gct/Tct	18/25	1	2	FACETS	0.51	0.418	0.612	0.51	0.418	0.612	SUBCLONAL	1	TRUE	1	0.284853599181687	2		489	496	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721129	61721129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	46	627	0	ENST00000401558.2:c.1145G>A	p.Arg382Lys	p.R382K	ENST00000401558	NM_003400.3	382	aGa/aAa	12/25	1	2	FACETS	0.44	0.369	0.518	0.44	0.369	0.518	SUBCLONAL	1	TRUE	1	0.284853599181687	2		627	734	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61722621	61722621	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	33	456	0	ENST00000401558.2:c.1016A>C	p.Lys339Thr	p.K339T	ENST00000401558	NM_003400.3	339	aAa/aCa	11/25	1	2	FACETS	0.435	0.353	0.527	0.435	0.353	0.527	SUBCLONAL	1	TRUE	1	0.284853599181687	2		456	533	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198283259	198283259	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs868198796	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	43	840	0	ENST00000335508.6:c.469C>T	p.Arg157Ter	p.R157*	ENST00000335508	NM_012433.2	157	Cga/Tga	5/25	1	2	FACETS	0.434	0.362	0.515	0.434	0.362	0.515	SUBCLONAL	1	TRUE	1	0.284853599181687	2		840	695	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543901	212543901	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	84	411	0	ENST00000342788.4:c.1498G>T	p.Gly500Ter	p.G500*	ENST00000342788	NM_005235.2	500	Gga/Tga	13/28	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.284853599181687	2		411	506	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793215	242793215	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	125	767	0	ENST00000334409.5:c.862C>A	p.Leu288Ile	p.L288I	ENST00000334409	NM_005018.2	288	Ctc/Atc	5/5	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.284853599181687	2		767	773	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525099	9525099	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	37	465	0	ENST00000353224.5:c.1786G>T	p.Glu596Ter	p.E596*	ENST00000353224	NM_177990.2	596	Gag/Tag	8/10	1	2	FACETS	0.424	0.348	0.508	0.424	0.348	0.508	SUBCLONAL	1	TRUE	1	0.284853599181687	2		465	613	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31379493	31379493	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	54	568	0	ENST00000328111.2:c.900A>C	p.Lys300Asn	p.K300N	ENST00000328111	NM_006892.3	300	aaA/aaC	8/23	1	2	FACETS	0.562	0.479	0.653	0.562	0.479	0.653	SUBCLONAL	1	TRUE	1	0.284853599181687	2		568	675	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389195	31389195	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	42	680	0	ENST00000328111.2:c.2108A>C	p.Lys703Thr	p.K703T	ENST00000328111	NM_006892.3	703	aAg/aCg	19/23	1	2	FACETS	0.361	0.3	0.429	0.361	0.3	0.429	SUBCLONAL	1	TRUE	1	0.284853599181687	2		680	817	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62322185	62322185	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	133	896	0	ENST00000360203.5:c.2441G>A	p.Ser814Asn	p.S814N	ENST00000360203	NM_001283009.1	814	aGt/aAt	27/35	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.284853599181687	2		896	852	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092891	29092891	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	76	593	0	ENST00000328354.6:c.1093A>C	p.Lys365Gln	p.K365Q	ENST00000328354	NM_007194.3	365	Aag/Cag	10/15	1	2	FACETS	0.834	0.731	0.944	0.834	0.731	0.944	CLONAL	1	TRUE	1	0.284853599181687	2		593	640	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057247	30057247	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	59	645	0	ENST00000338641.4:c.729T>G	p.Ile243Met	p.I243M	ENST00000338641	NM_000268.3	243	atT/atG	8/16	1	2	FACETS	0.52	0.446	0.6	0.52	0.446	0.6	SUBCLONAL	1	TRUE	1	0.284853599181687	2		645	797	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537151	41537151	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	97	693	0	ENST00000263253.7:c.1978A>C	p.Asn660His	p.N660H	ENST00000263253	NM_001429.3	660	Aat/Cat	10/31	1	2	FACETS	0.868	0.773	0.968	0.868	0.773	0.968	CLONAL	1	TRUE	1	0.284853599181687	2		693	785	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545919	41545919	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs202070031	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	169	896	0	ENST00000263253.7:c.2534C>A	p.Thr845Asn	p.T845N	ENST00000263253	NM_001429.3	845	aCt/aAt	14/31	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.284853599181687	2		896	1028	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572362	41572362	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	76	831	0	ENST00000263253.7:c.4891C>A	p.Leu1631Ile	p.L1631I	ENST00000263253	NM_001429.3	1631	Ctc/Atc	30/31	1	2	FACETS	0.572	0.5	0.649	0.572	0.5	0.649	SUBCLONAL	1	TRUE	1	0.284853599181687	2		831	933	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434240	12434241	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	39	518	0	ENST00000287820.6:c.609_610del	p.Met203IlefsTer3	p.M203Ifs*3	ENST00000287820	NM_015869.4	203	aTG/a	4/7	1	2	FACETS	0.456	0.377	0.544	0.456	0.377	0.544	SUBCLONAL	1	TRUE	1	0.284853599181687	2		518	601	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267288	41267288	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	36	614	0	ENST00000349496.5:c.872T>C	p.Val291Ala	p.V291A	ENST00000349496	NM_001904.3	291	gTt/gCt	6/15	1	2	FACETS	0.373	0.306	0.449	0.373	0.306	0.449	SUBCLONAL	1	TRUE	1	0.284853599181687	2		614	677	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267291	41267291	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	100	593	0	ENST00000349496.5:c.875A>C	p.Lys292Thr	p.K292T	ENST00000349496	NM_001904.3	292	aAa/aCa	6/15	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.284853599181687	2		593	664	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125437	47125437	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	88	631	0	ENST00000409792.3:c.5833G>T	p.Glu1945Ter	p.E1945*	ENST00000409792	NM_014159.6	1945	Gaa/Taa	12/21	1	2	FACETS	0.843	0.747	0.946	0.843	0.747	0.946	CLONAL	1	TRUE	1	0.284853599181687	2		631	733	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637713	52637713	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	43	676	0	ENST00000394830.3:c.2603T>G	p.Leu868Arg	p.L868R	ENST00000394830	NM_018313.4	868	cTt/cGt	18/30	1	2	FACETS	0.428	0.357	0.507	0.428	0.357	0.507	SUBCLONAL	1	TRUE	1	0.284853599181687	2		676	706	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702632	52702632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	37	584	0	ENST00000394830.3:c.266C>T	p.Ser89Phe	p.S89F	ENST00000394830	NM_018313.4	89	tCt/tTt	4/30	1	2	FACETS	0.525	0.432	0.629	0.525	0.432	0.629	SUBCLONAL	1	TRUE	1	0.284853599181687	2		584	495	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428561	72428561	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	34	479	0	ENST00000477973.2:c.443C>A	p.Ser148Tyr	p.S148Y	ENST00000477973	NM_012234.5	148	tCt/tAt	2/4	1	2	FACETS	0.422	0.344	0.51	0.422	0.344	0.51	SUBCLONAL	1	TRUE	1	0.284853599181687	2		479	566	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461560	138461560	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	117	663	0	ENST00000289153.2:c.461A>C	p.Lys154Thr	p.K154T	ENST00000289153	NM_006219.2	154	aAa/aCa	3/22	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.284853599181687	2		663	697	SUCCESS
ATR	545	MSKCC	GRCh37	3	142259853	142259853	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	79	599	0	ENST00000350721.4:c.3474G>T	p.Leu1158Phe	p.L1158F	ENST00000350721	NM_001184.3	1158	ttG/ttT	18/47	1	2	FACETS	0.817	0.718	0.923	0.817	0.718	0.923	CLONAL	1	TRUE	1	0.284853599181687	2		599	679	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272779	142272779	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	44	662	0	ENST00000350721.4:c.2420G>A	p.Gly807Glu	p.G807E	ENST00000350721	NM_001184.3	807	gGa/gAa	11/47	1	2	FACETS	0.481	0.403	0.569	0.481	0.403	0.569	SUBCLONAL	1	TRUE	1	0.284853599181687	2		662	642	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937006	178937006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	38	672	0	ENST00000263967.3:c.1687G>A	p.Glu563Lys	p.E563K	ENST00000263967	NM_006218.2	563	Gaa/Aaa	11/21	1	2	FACETS	0.434	0.358	0.519	0.434	0.358	0.519	SUBCLONAL	1	TRUE	1	0.284853599181687	2		672	615	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951962	178951962	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	75	670	0	ENST00000263967.3:c.3017T>G	p.Leu1006Arg	p.L1006R	ENST00000263967	NM_006218.2	1006	cTt/cGt	21/21	1	2	FACETS	0.84	0.736	0.951	0.84	0.736	0.951	CLONAL	1	TRUE	1	0.284853599181687	2		670	627	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182681824	182681824	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	49	639	0	ENST00000292782.4:c.234G>T	p.Glu78Asp	p.E78D	ENST00000292782	NM_020640.2	78	gaG/gaT	3/7	1	2	FACETS	0.469	0.396	0.549	0.469	0.396	0.549	SUBCLONAL	1	TRUE	1	0.284853599181687	2		639	734	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683542	182683542	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	68	531	0	ENST00000292782.4:c.4-1G>T		p.X2_splice	ENST00000292782	NM_020640.2	2			1	2	FACETS	0.913	0.795	1	0.913	0.795	1	CLONAL	1	TRUE	1	0.284853599181687	2		531	523	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165607	185165607	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	83	478	0	ENST00000265026.3:c.882A>C	p.Lys294Asn	p.K294N	ENST00000265026	NM_004721.4	294	aaA/aaC	5/14	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.284853599181687	2		478	552	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146565	55146565	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	70	542	0	ENST00000257290.5:c.2239G>T	p.Glu747Ter	p.E747*	ENST00000257290	NM_006206.4	747	Gaa/Taa	16/23	1	2	FACETS	0.926	0.808	1	0.926	0.808	1	CLONAL	1	TRUE	1	0.284853599181687	2		542	531	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593383	55593383	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	34	485	0	ENST00000288135.5:c.1541-1G>T		p.X514_splice	ENST00000288135	NM_000222.2	514			1	2	FACETS	0.465	0.38	0.562	0.465	0.38	0.562	SUBCLONAL	1	TRUE	1	0.284853599181687	2		485	513	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598096	55598096	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs760112920	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	56	589	0	ENST00000288135.5:c.2293G>T	p.Asp765Tyr	p.D765Y	ENST00000288135	NM_000222.2	765	Gac/Tac	16/21	1	2	FACETS	0.477	0.408	0.554	0.477	0.408	0.554	SUBCLONAL	1	TRUE	1	0.284853599181687	2		589	824	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55603365	55603365	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	69	446	0	ENST00000288135.5:c.2721G>A	p.Trp907Ter	p.W907*	ENST00000288135	NM_000222.2	907	tgG/tgA	20/21	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.284853599181687	2		446	430	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956125	55956125	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs139868970	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	95	563	0	ENST00000263923.4:c.3190G>A	p.Asp1064Asn	p.D1064N	ENST00000263923	NM_002253.2	1064	Gat/Aat	23/30	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.284853599181687	2		563	646	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217171	66217171	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	89	641	0	ENST00000273854.3:c.2444A>C	p.Lys815Thr	p.K815T	ENST00000273854	NM_004439.5	815	aAa/aCa	14/18	1	2	FACETS	0.824	0.731	0.925	0.824	0.731	0.925	CLONAL	1	TRUE	1	0.284853599181687	2		641	758	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003187	143003187	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	84	519	0	ENST00000262992.4:c.2639G>T	p.Arg880Ile	p.R880I	ENST00000262992	NM_001101669.1	880	aGa/aTa	23/24	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.284853599181687	2		519	568	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045761	143045761	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	40	537	0	ENST00000262992.4:c.1873G>T	p.Asp625Tyr	p.D625Y	ENST00000262992	NM_001101669.1	625	Gac/Tac	17/24	1	2	FACETS	0.379	0.314	0.452	0.379	0.314	0.452	SUBCLONAL	1	TRUE	1	0.284853599181687	2		537	741	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629679	187629679	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	134	879	0	ENST00000441802.2:c.1303G>T	p.Glu435Ter	p.E435*	ENST00000441802	NM_005245.3	435	Gaa/Taa	2/27	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.284853599181687	2		879	933	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515591	31515591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	56	443	0	ENST00000344624.3:c.1028C>T	p.Ser343Phe	p.S343F	ENST00000344624		343	tCt/tTt	4/33	1	2	FACETS	0.809	0.694	0.934	0.809	0.694	0.934	CLONAL	1	TRUE	1	0.284853599181687	2		443	486	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161261	56161261	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	43	582	0	ENST00000399503.3:c.1130G>T	p.Arg377Ile	p.R377I	ENST00000399503	NM_005921.1	377	aGa/aTa	5/20	1	2	FACETS	0.665	0.557	0.785	0.665	0.557	0.785	SUBCLONAL	1	TRUE	1	0.284853599181687	2		582	454	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183258	56183258	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	106	718	0	ENST00000399503.3:c.4168G>T	p.Gly1390Ter	p.G1390*	ENST00000399503	NM_005921.1	1390	Gga/Tga	18/20	1	2	FACETS	0.902	0.808	1	0.902	0.808	1	CLONAL	1	TRUE	1	0.284853599181687	2		718	825	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754855	57754855	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	78	507	0	ENST00000274289.3:c.335T>G	p.Ile112Ser	p.I112S	ENST00000274289	NM_006622.3	112	aTt/aGt	2/14	1	2	FACETS	0.875	0.769	0.988	0.875	0.769	0.988	CLONAL	1	TRUE	1	0.284853599181687	2		507	626	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589147	67589147	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	32	368	0	ENST00000274335.5:c.1135A>C	p.Lys379Gln	p.K379Q	ENST00000274335		379	Aaa/Caa	9/15	1	2	FACETS	0.829	0.676	1	0.829	0.676	1	CLONAL	1	TRUE	1	0.284853599181687	2		368	271	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590455	67590455	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	29	274	0	ENST00000274335.5:c.1517A>G	p.Lys506Arg	p.K506R	ENST00000274335		506	aAa/aGa	11/15	1	2	FACETS	0.653	0.525	0.797	0.653	0.525	0.797	SUBCLONAL	1	TRUE	1	0.284853599181687	2		274	312	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629098	86629098	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	23	375	0	ENST00000274376.6:c.843A>C	p.Arg281Ser	p.R281S	ENST00000274376	NM_002890.2	281	agA/agC	4/25	1	2	FACETS	0.45	0.35	0.565	0.45	0.35	0.565	SUBCLONAL	1	TRUE	1	0.284853599181687	2		375	359	SUCCESS
APC	324	MSKCC	GRCh37	5	112174995	112174995	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1554085244	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	50	283	0	ENST00000257430.4:c.3704C>A	p.Ser1235Tyr	p.S1235Y	ENST00000257430	NM_000038.5	1235	tCt/tAt	16/16	1	2	FACETS	0.893	0.76	1	0.893	0.76	1	CLONAL	1	TRUE	1	0.284853599181687	2		283	393	SUCCESS
APC	324	MSKCC	GRCh37	5	112175104	112175104	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	58	304	0	ENST00000257430.4:c.3813T>G	p.Phe1271Leu	p.F1271L	ENST00000257430	NM_000038.5	1271	ttT/ttG	16/16	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.284853599181687	2		304	393	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170827158	170827158	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	16	274	3	ENST00000296930.5:c.526G>T	p.Asp176Tyr	p.D176Y	ENST00000296930	NM_002520.6	176	Gat/Tat	7/11	1	2	FACETS	0.415	0.306	0.544	0.415	0.306	0.544	SUBCLONAL	1	TRUE	1	0.284853599181687	2		277	271	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520480	176520480	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1465632616	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	174	898	1	ENST00000292408.4:c.1325G>T	p.Gly442Val	p.G442V	ENST00000292408	NM_213647.1	442	gGc/gTc	10/18	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.284853599181687	2		899	1006	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639082	176639082	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1161564727	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	41	646	0	ENST00000439151.2:c.3682G>T	p.Asp1228Tyr	p.D1228Y	ENST00000439151	NM_022455.4	1228	Gat/Tat	5/23	1	2	FACETS	0.351	0.292	0.419	0.351	0.292	0.419	SUBCLONAL	1	TRUE	1	0.284853599181687	2		646	819	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045816	180045816	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	60	663	1	ENST00000261937.6:c.2955C>A	p.Phe985Leu	p.F985L	ENST00000261937	NM_182925.4	985	ttC/ttA	21/30	1	2	FACETS	0.559	0.481	0.645	0.559	0.481	0.645	SUBCLONAL	1	TRUE	1	0.284853599181687	2		664	753	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778091	27778091	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	31	599	1	ENST00000369163.2:c.240G>T	p.Lys80Asn	p.K80N	ENST00000369163	NM_003536.2	80	aaG/aaT	1/1	1	2	FACETS	0.366	0.295	0.447	0.366	0.295	0.447	SUBCLONAL	1	TRUE	1	0.284853599181687	2		600	594	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821159	32821159	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	57	875	0	ENST00000354258.4:c.435A>C	p.Glu145Asp	p.E145D	ENST00000354258	NM_000593.5	145	gaA/gaC	1/11	1	2	FACETS	0.538	0.46	0.623	0.538	0.46	0.623	SUBCLONAL	1	TRUE	1	0.284853599181687	2		875	744	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140814	37140814	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1244024334	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	59	686	0	ENST00000373509.5:c.650G>A	p.Arg217His	p.R217H	ENST00000373509	NM_002648.3	217	cGc/cAc	5/6	1	2	FACETS	0.55	0.472	0.635	0.55	0.472	0.635	SUBCLONAL	1	TRUE	1	0.284853599181687	2		686	753	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109315798	109315798	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	50	649	0	ENST00000436639.2:c.987C>A	p.Phe329Leu	p.F329L	ENST00000436639	NM_014454.2	329	ttC/ttA	6/10	1	2	FACETS	0.531	0.45	0.621	0.531	0.45	0.621	SUBCLONAL	1	TRUE	1	0.284853599181687	2		649	661	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622214	117622214	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	65	629	0	ENST00000368508.3:c.6656G>T	p.Arg2219Ile	p.R2219I	ENST00000368508	NM_002944.2	2219	aGa/aTa	42/43	1	2	FACETS	0.869	0.755	0.993	0.869	0.755	0.993	CLONAL	1	TRUE	1	0.284853599181687	2		629	525	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647553	117647553	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	33	746	0	ENST00000368508.3:c.5391G>T	p.Gln1797His	p.Q1797H	ENST00000368508	NM_002944.2	1797	caG/caT	33/43	1	2	FACETS	0.377	0.306	0.458	0.377	0.306	0.458	SUBCLONAL	1	TRUE	1	0.284853599181687	2		746	614	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001559	150001559	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	43	659	0	ENST00000253339.5:c.2045G>T	p.Arg682Ile	p.R682I	ENST00000253339		682	aGa/aTa	4/7	1	2	FACETS	0.533	0.446	0.631	0.533	0.446	0.631	SUBCLONAL	1	TRUE	1	0.284853599181687	2		659	566	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005678	150005678	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	106	553	0	ENST00000253339.5:c.547G>T	p.Glu183Ter	p.E183*	ENST00000253339		183	Gaa/Taa	3/7	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.284853599181687	2		553	594	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729708	41729708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs569482596	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	78	710	0	ENST00000242208.4:c.821G>A	p.Gly274Glu	p.G274E	ENST00000242208	NM_002192.2	274	gGa/gAa	3/3	1	2	FACETS	0.799	0.702	0.904	0.799	0.702	0.904	CLONAL	1	TRUE	1	0.284853599181687	2		710	685	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55219051	55219051	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	41	516	0	ENST00000275493.2:c.624G>T	p.Gln208His	p.Q208H	ENST00000275493	NM_005228.3	208	caG/caT	5/28	1	2	FACETS	0.441	0.366	0.524	0.441	0.366	0.524	SUBCLONAL	1	TRUE	1	0.284853599181687	2		516	653	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335667	81335667	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	84	738	0	ENST00000222390.5:c.1693C>A	p.Leu565Ile	p.L565I	ENST00000222390	NM_000601.4	565	Ctc/Atc	15/18	1	2	FACETS	0.89	0.786	1	0.89	0.786	1	CLONAL	1	TRUE	1	0.284853599181687	2		738	663	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515187	106515187	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	40	542	0	ENST00000359195.3:c.2330C>A	p.Ser777Tyr	p.S777Y	ENST00000359195	NM_002649.2	777	tCt/tAt	5/11	1	2	FACETS	0.438	0.363	0.522	0.438	0.363	0.522	SUBCLONAL	1	TRUE	1	0.284853599181687	2		542	641	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515002	148515002	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	119	702	0	ENST00000320356.2:c.1207G>T	p.Glu403Ter	p.E403*	ENST00000320356	NM_004456.4	403	Gaa/Taa	10/20	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.284853599181687	2		702	806	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151167700	151167700	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	55	450	0	ENST00000262187.5:c.419C>A	p.Ser140Tyr	p.S140Y	ENST00000262187	NM_005614.3	140	tCt/tAt	7/8	1	2	FACETS	0.839	0.719	0.97	0.839	0.719	0.97	CLONAL	1	TRUE	1	0.284853599181687	2		450	460	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874638	151874638	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	49	563	0	ENST00000262189.6:c.7900G>T	p.Glu2634Ter	p.E2634*	ENST00000262189	NM_170606.2	2634	Gag/Tag	38/59	1	2	FACETS	0.483	0.408	0.565	0.483	0.408	0.565	SUBCLONAL	1	TRUE	1	0.284853599181687	2		563	713	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945586	151945586	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	22	344	0	ENST00000262189.6:c.1933G>T	p.Asp645Tyr	p.D645Y	ENST00000262189	NM_170606.2	645	Gat/Tat	14/59	1	2	FACETS	0.579	0.449	0.728	0.579	0.449	0.728	SUBCLONAL	1	TRUE	1	0.284853599181687	2		344	267	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346188	152346188	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	108	778	0	ENST00000359321.1:c.382C>A	p.Leu128Ile	p.L128I	ENST00000359321	NM_005431.1	128	Ctt/Att	3/3	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.284853599181687	2		778	731	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38178660	38178660	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	42	592	0	ENST00000317025.8:c.1739C>A	p.Ser580Ter	p.S580*	ENST00000317025	NM_023034.1	580	tCa/tAa	8/24	1	2	FACETS	0.404	0.336	0.48	0.404	0.336	0.48	SUBCLONAL	1	TRUE	1	0.284853599181687	2		592	730	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27190529	27190529	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	109	670	0	ENST00000380036.4:c.1330C>A	p.Leu444Ile	p.L444I	ENST00000380036	NM_000459.3	444	Ctt/Att	10/23	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.284853599181687	2		670	758	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537093	80537093	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	49	817	0	ENST00000286548.4:c.305A>C	p.Lys102Thr	p.K102T	ENST00000286548	NM_002072.3	102	aAg/aCg	2/7	1	2	FACETS	0.415	0.35	0.487	0.415	0.35	0.487	SUBCLONAL	1	TRUE	1	0.284853599181687	2		817	829	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127933372	127933372	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	87	656	0	ENST00000373547.4:c.163C>G	p.His55Asp	p.H55D	ENST00000373547	NM_002721.4	55	Cat/Gat	2/7	1	2	FACETS	0.832	0.736	0.935	0.832	0.736	0.935	CLONAL	1	TRUE	1	0.284853599181687	2		656	734	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786877	135786877	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	65	551	0	ENST00000298552.3:c.992G>T	p.Ser331Ile	p.S331I	ENST00000298552	NM_001162426.1	331	aGt/aTt	10/23	1	2	FACETS	0.576	0.499	0.661	0.576	0.499	0.661	SUBCLONAL	1	TRUE	1	0.284853599181687	2		551	792	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933983	39933983	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	133	811	0	ENST00000378444.4:c.616T>C	p.Phe206Leu	p.F206L	ENST00000378444	NM_001123385.1	206	Ttc/Ctc	4/15	1	2	FACETS	0.959	0.87	1	0.959	0.87	1	CLONAL	1	TRUE	1	0.284853599181687	2		811	974	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938417	44938417	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	39	593	0	ENST00000377967.4:c.2965T>G	p.Leu989Val	p.L989V	ENST00000377967	NM_021140.2	989	Ttg/Gtg	20/29	1	2	FACETS	0.44	0.364	0.526	0.44	0.364	0.526	SUBCLONAL	1	TRUE	1	0.284853599181687	2		593	622	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041212	47041212	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	92	946	0	ENST00000377604.3:c.1640C>A	p.Ser547Tyr	p.S547Y	ENST00000377604	NM_001204468.1	547	tCt/tAt	15/24	1	2	FACETS	0.588	0.521	0.66	0.588	0.521	0.66	SUBCLONAL	1	TRUE	1	0.284853599181687	2		946	1099	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424231	47424231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	86	784	0	ENST00000377045.4:c.236C>T	p.Ala79Val	p.A79V	ENST00000377045	NM_001654.4	79	gCt/gTt	4/16	1	2	FACETS	0.708	0.625	0.797	0.708	0.625	0.797	SUBCLONAL	1	TRUE	1	0.284853599181687	2		784	853	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410418	63410418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	67	891	0	ENST00000330258.3:c.2749G>A	p.Glu917Lys	p.E917K	ENST00000330258	NM_152424.3	917	Gag/Aag	2/2	1	2	FACETS	0.563	0.488	0.644	0.563	0.488	0.644	SUBCLONAL	1	TRUE	1	0.284853599181687	2		891	836	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411410	63411410	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1179031603	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	41	821	1	ENST00000330258.3:c.1757G>A	p.Arg586Gln	p.R586Q	ENST00000330258	NM_152424.3	586	cGa/cAa	2/2	1	2	FACETS	0.358	0.297	0.426	0.358	0.297	0.426	SUBCLONAL	1	TRUE	1	0.284853599181687	2		822	804	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344691	70344691	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	98	750	1	ENST00000374080.3:c.2052C>A	p.Phe684Leu	p.F684L	ENST00000374080		684	ttC/ttA	14/45	1	2	FACETS	0.875	0.781	0.976	0.875	0.781	0.976	CLONAL	1	TRUE	1	0.284853599181687	2		751	786	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357228	70357228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1291836233	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	65	611	0	ENST00000374080.3:c.5743C>T	p.Leu1915Phe	p.L1915F	ENST00000374080		1915	Ctc/Ttc	39/45	1	2	FACETS	0.702	0.608	0.804	0.702	0.608	0.804	SUBCLONAL	1	TRUE	1	0.284853599181687	2		611	650	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888868	76888868	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	40	666	0	ENST00000373344.5:c.4961C>A	p.Ser1654Tyr	p.S1654Y	ENST00000373344	NM_000489.3	1654	tCt/tAt	19/35	1	2	FACETS	0.446	0.369	0.531	0.446	0.369	0.531	SUBCLONAL	1	TRUE	1	0.284853599181687	2		666	630	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937759	76937759	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	92	749	0	ENST00000373344.5:c.2989G>T	p.Asp997Tyr	p.D997Y	ENST00000373344	NM_000489.3	997	Gac/Tac	9/35	1	2	FACETS	0.875	0.778	0.98	0.875	0.778	0.98	CLONAL	1	TRUE	1	0.284853599181687	2		749	738	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938284	76938284	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs782687417	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	42	732	0	ENST00000373344.5:c.2464G>T	p.Glu822Ter	p.E822*	ENST00000373344	NM_000489.3	822	Gaa/Taa	9/35	1	2	FACETS	0.417	0.347	0.495	0.417	0.347	0.495	SUBCLONAL	1	TRUE	1	0.284853599181687	2		732	707	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938681	76938681	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	80	923	0	ENST00000373344.5:c.2067A>C	p.Gln689His	p.Q689H	ENST00000373344	NM_000489.3	689	caA/caC	9/35	1	2	FACETS	0.693	0.609	0.783	0.693	0.609	0.783	SUBCLONAL	1	TRUE	1	0.284853599181687	2		923	811	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939948	76939948	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	112	827	0	ENST00000373344.5:c.800T>G	p.Ile267Ser	p.I267S	ENST00000373344	NM_000489.3	267	aTt/aGt	9/35	1	2	FACETS	0.941	0.846	1	0.941	0.846	1	CLONAL	1	TRUE	1	0.284853599181687	2		827	836	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944359	76944359	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	50	688	0	ENST00000373344.5:c.546A>C	p.Gln182His	p.Q182H	ENST00000373344	NM_000489.3	182	caA/caC	7/35	1	2	FACETS	0.566	0.48	0.662	0.566	0.48	0.662	SUBCLONAL	1	TRUE	1	0.284853599181687	2		688	620	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617612	100617612	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs782559289	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	105	922	2	ENST00000308731.7:c.457C>A	p.Leu153Ile	p.L153I	ENST00000308731	NM_000061.2	153	Ctc/Atc	6/19	1	2	FACETS	0.775	0.693	0.862	0.775	0.693	0.862	SUBCLONAL	1	TRUE	1	0.284853599181687	2		924	951	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626688	100626688	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	64	530	0	ENST00000308731.7:c.242G>A	p.Arg81Lys	p.R81K	ENST00000308731	NM_000061.2	81	aGa/aAa	4/19	1	2	FACETS	0.89	0.772	1	0.89	0.772	1	CLONAL	1	TRUE	1	0.284853599181687	2		530	505	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229233	123229233	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	66	470	0	ENST00000218089.9:c.3717G>T	p.Lys1239Asn	p.K1239N	ENST00000218089	NM_001042749.1	1239	aaG/aaT	34/35	1	2	FACETS	0.879	0.764	1	0.879	0.764	1	CLONAL	1	TRUE	1	0.284853599181687	2		470	527	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437605	56437605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329721997	NA	P-0033997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	202	419	0	ENST00000407977.2:c.857G>A	p.Arg286Gln	p.R286Q	ENST00000407977		286	cGg/cAg	8/10	0.125991676395816	4	FACETS	0.828	0.771	0.887	0.828	0.771	0.887	INDETERMINATE	2	TRUE	2	0.55945250289352	4		419	680	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098966	178098966	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	154	193	0	ENST00000397062.3:c.79G>T	p.Asp27Tyr	p.D27Y	ENST00000397062	NM_006164.4	27	Gat/Tat	2/5	0.245612545468362	3	FACETS	1	0.984	1	0.644	0.593	0.697	INDETERMINATE	1	TRUE	1	0.55945250289352	3		193	547	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051469	13051469	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0033997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	213	429	0	ENST00000316448.5:c.816+1G>A		p.X272_splice	ENST00000316448	NM_004343.3	272			0.125991676395816	4	FACETS	0.832	0.776	0.889	0.832	0.776	0.889	INDETERMINATE	2	TRUE	2	0.55945250289352	4		429	714	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609504	81609504	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	253	471	0	ENST00000298171.2:c.1102C>A	p.Gln368Lys	p.Q368K	ENST00000298171	NM_000369.2	368	Cag/Aag	10/10	0.125991676395816	4	FACETS	0.873	0.819	0.927	0.873	0.819	0.927	INDETERMINATE	2	TRUE	2	0.55945250289352	4		471	808	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005392	42005393	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0033997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	282	542	0	ENST00000219905.7:c.3128_3129delinsTT	p.Arg1043Leu	p.R1043L	ENST00000219905	NM_001164273.1	1043	cGA/cTT	9/24	0.55945250289352	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.55945250289352	1		542	617	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578397	7578398	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	389	690	0	ENST00000269305.4:c.532_533insT	p.His178LeufsTer3	p.H178Lfs*3	ENST00000269305	NM_001126112.2	178	cac/cTac	5/11	0.450247022131105	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.55945250289352	1		690	776	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470614	25470614	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	538	612	0	ENST00000264709.3:c.860G>T	p.Gly287Val	p.G287V	ENST00000264709	NM_175629.2	287	gGc/gTc	8/23	0.55945250289352	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.55945250289352	3		612	1156	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528937	157528937	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	305	592	1	ENST00000346085.5:c.6662G>T	p.Arg2221Leu	p.R2221L	ENST00000346085	NM_020732.3	2221	cGg/cTg	20/20	0.204040360837479	2	FACETS	1	0.993	1	0.655	0.62	0.691	INDETERMINATE	1	TRUE	0	0.55945250289352	2		593	832	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	36	248	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	0.474794624514496	2		248	344	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240285	41240285	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	27	295	0	ENST00000379561.5:c.65C>G	p.Ser22Trp	p.S22W	ENST00000379561	NM_002015.3	22	tCg/tGg	1/3	1	2	FACETS	0.227	0.18	0.281	0.227	0.18	0.281	SUBCLONAL	1	TRUE	1	0.474794624514496	2		295	501	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0034021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	23	427	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.247	0.192	0.311	0.247	0.192	0.311	SUBCLONAL	1	TRUE	1	0.474794624514496	2		427	392	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610589	52610589	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	37	455	0	ENST00000394830.3:c.3584T>A	p.Leu1195Gln	p.L1195Q	ENST00000394830	NM_018313.4	1195	cTg/cAg	23/30	1	2	FACETS	0.221	0.181	0.265	0.221	0.181	0.265	SUBCLONAL	1	TRUE	1	0.474794624514496	2		455	706	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045706	26045706	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769895262	NA	P-0034021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	21	245	0	ENST00000540144.1:c.68C>T	p.Thr23Ile	p.T23I	ENST00000540144	NM_003531.2	23	aCt/aTt	1/1	1	2	FACETS	0.246	0.189	0.312	0.246	0.189	0.312	SUBCLONAL	1	TRUE	1	0.474794624514496	2		245	360	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	66	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.869	0.763	0.981	0.869	0.763	0.981	CLONAL	1	TRUE	1	0.577605321467575	2		248	263	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	155	697	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	0.577605321467575	2		697	528	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817754	3817754	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	224	612	0	ENST00000262367.5:c.3217C>T	p.Gln1073Ter	p.Q1073*	ENST00000262367	NM_004380.2	1073	Cag/Tag	16/31	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.577605321467575	2		612	715	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245843	46245843	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	85	310	0	ENST00000334344.6:c.3937C>T	p.Gln1313Ter	p.Q1313*	ENST00000334344	NM_152641.2	1313	Caa/Taa	15/21	1	2	FACETS	0.868	0.774	0.967	0.868	0.774	0.967	CLONAL	1	TRUE	1	0.577605321467575	2		310	339	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937684	44937684	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	202	255	0	ENST00000377967.4:c.2872C>T	p.Gln958Ter	p.Q958*	ENST00000377967	NM_021140.2	958	Caa/Taa	19/29	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.577605321467575	1		255	333	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023633	27023634	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCGGCTC	novel	NA	P-0034023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	58	234	0	ENST00000324856.7:c.741_747dup	p.Lys250ArgfsTer152	p.K250Rfs*152	ENST00000324856	NM_006015.4	247	gcc/gCCGGCTCcc	1/20	1	2	FACETS	0.725	0.628	0.828	0.725	0.628	0.828	SUBCLONAL	1	TRUE	1	0.577605321467575	2		234	277	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870966	12870966	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	92	284	0	ENST00000228872.4:c.193C>T	p.Gln65Ter	p.Q65*	ENST00000228872	NM_004064.3	65	Cag/Tag	1/3	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.577605321467575	2		284	307	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911757	32911757	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs80358573	NA	P-0034023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	194	540	1	ENST00000380152.3:c.3265C>T	p.Gln1089Ter	p.Q1089*	ENST00000380152		1089	Cag/Tag	11/27	1	2	FACETS	0.968	0.899	1	0.968	0.899	1	CLONAL	1	TRUE	1	0.577605321467575	2		541	694	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107014	27107014	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	127	436	0	ENST00000324856.7:c.6625C>T	p.Gln2209Ter	p.Q2209*	ENST00000324856	NM_006015.4	2209	Cag/Tag	20/20	1	2	FACETS	0.909	0.828	0.992	0.909	0.828	0.992	CLONAL	1	TRUE	1	0.577605321467575	2		436	484	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043376	6043376	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	21	81	0	ENST00000265849.7:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000265849	NM_000535.5	100	Cag/Tag	4/15	1	2	FACETS	0.782	0.615	0.968	0.782	0.615	0.968	CLONAL	1	TRUE	1	0.577605321467575	2		81	93	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488224	56488224	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	196	505	0	ENST00000267101.3:c.1743T>A	p.Asp581Glu	p.D581E	ENST00000267101	NM_001982.3	581	gaT/gaA	15/28	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.577605321467575	2		505	622	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281791	46281791	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	196	605	0	ENST00000371998.3:c.4238C>T	p.Ser1413Phe	p.S1413F	ENST00000371998		1413	tCt/tTt	22/23	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.577605321467575	2		605	666	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629973	187629973	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs747050641	NA	P-0034023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	204	636	0	ENST00000441802.2:c.1009C>T	p.Gln337Ter	p.Q337*	ENST00000441802	NM_005245.3	337	Cag/Tag	2/27	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.577605321467575	2		636	657	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850280	128850280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	214	727	0	ENST00000249373.3:c.1543C>T	p.Leu515Phe	p.L515F	ENST00000249373	NM_005631.4	515	Ctt/Ttt	9/12	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.577605321467575	2		727	731	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137320961	137320961	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	217	721	0	ENST00000481739.1:c.918T>G	p.Asn306Lys	p.N306K	ENST00000481739	NM_002957.4	306	aaT/aaG	7/10	1	2	FACETS	0.985	0.919	1	0.985	0.919	1	CLONAL	1	TRUE	1	0.577605321467575	2		721	763	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0034024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	240	587	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.342173006092204	3	FACETS	0.938	0.889	0.986	1	0.992	1	CLONAL	4	TRUE	0	0.342173006092204	3		587	438	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	169	697	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.342173006092204	2	FACETS	0.96	0.898	1	1	0.991	1	CLONAL	3	TRUE	0	0.342173006092204	2		697	343	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987039	36987039	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1447379564	NA	P-0034024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	18	529	0	ENST00000354822.5:c.650C>T	p.Ser217Leu	p.S217L	ENST00000354822	NM_001079668.2	217	tCg/tTg	3/3	0.342173006092204	3	FACETS	0.367	0.276	0.475	0.183	0.138	0.238	SUBCLONAL	1	TRUE	1	0.342173006092204	3		529	336	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141549428	141549428	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	40	237	0	ENST00000220592.5:c.2160G>C	p.Lys720Asn	p.K720N	ENST00000220592	NM_012154.3	720	aaG/aaC	16/19	0.342173006092204	7	FACETS	1	0.936	1	0.212	0.176	0.251	CLONAL	1	TRUE	1	0.342173006092204	7		237	341	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	103	697	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.208694244717349	3	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	1	0.301228189251732	3		697	380	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710540	114710540	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	59	278	0	ENST00000543371.1:c.28del	p.Asp10MetfsTer3	p.D10Mfs*3	ENST00000543371	NM_001198531.1	9	Ggg/gg	1/14	0.28423374973525	3	FACETS	1	0.956	1	0.637	0.55	0.729	CLONAL	1	TRUE	1	0.301228189251732	3		278	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577529	7577529	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs730882027	NA	P-0034026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	195	613	0	ENST00000269305.4:c.752T>C	p.Ile251Thr	p.I251T	ENST00000269305	NM_001126112.2	251	aTc/aCc	7/11	0.235439097598328	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.301228189251732	2		613	562	SUCCESS
APC	324	MSKCC	GRCh37	5	112174389	112174389	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	34	212	0	ENST00000257430.4:c.3098del	p.Asp1033ValfsTer4	p.D1033Vfs*4	ENST00000257430	NM_000038.5	1033	gAt/gt	16/16	0.208694244717349	3	FACETS	0.822	0.681	0.976	0.822	0.681	0.976	CLONAL	2	TRUE	1	0.301228189251732	3		212	158	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407582	407582	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	26	351	0	ENST00000380956.4:c.1340C>G	p.Ser447Cys	p.S447C	ENST00000380956	NM_001195286.1	447	tCc/tGc	9/9	0.28423374973525	3	FACETS	0.543	0.43	0.672	0.271	0.215	0.336	SUBCLONAL	1	TRUE	1	0.301228189251732	3		351	366	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	154	248	0				ENST00000310581	NM_198253.2	-/1132			0.418221174066902	1	FACETS	0.551	0.511	0.591	0.551	0.511	0.591	INDETERMINATE	1	TRUE	0	0.873157449454505	1		248	361	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912874	32912874	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	318	434	0	ENST00000380152.3:c.4382C>T	p.Ser1461Phe	p.S1461F	ENST00000380152		1461	tCc/tTc	11/27	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.873157449454505	2		434	691	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	460	631	1	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	0.969	0.929	1	0.969	0.929	1	CLONAL	1	TRUE	1	0.873157449454505	2		632	1087	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295824	212295824	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	259	487	0	ENST00000342788.4:c.2489G>A	p.Gly830Glu	p.G830E	ENST00000342788	NM_005235.2	830	gGa/gAa	21/28	1	2	FACETS	0.87	0.82	0.921	0.87	0.82	0.921	CLONAL	1	TRUE	1	0.873157449454505	2		487	682	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691241	18691241	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	185	382	0	ENST00000266497.5:c.3352G>A	p.Glu1118Lys	p.E1118K	ENST00000266497		1118	Gaa/Aaa	23/31	1	2	FACETS	0.937	0.875	1	0.937	0.875	1	CLONAL	1	TRUE	1	0.873157449454505	2		382	452	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602625	10602625	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	340	728	1	ENST00000171111.5:c.953C>T	p.Pro318Leu	p.P318L	ENST00000171111	NM_203500.1	318	cCc/cTc	3/6	1	2	FACETS	0.965	0.918	1	0.965	0.918	1	CLONAL	1	TRUE	1	0.873157449454505	2		729	807	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638350	117638350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	266	609	1	ENST00000368508.3:c.6091G>A	p.Gly2031Arg	p.G2031R	ENST00000368508	NM_002944.2	2031	Gga/Aga	38/43	0.873157449454505	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.873157449454505	1		610	343	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862866	9862866	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	330	704	0	ENST00000330684.3:c.2437G>A	p.Asp813Asn	p.D813N	ENST00000330684	NM_001134407.1	813	Gac/Aac	12/13	0.873157449454505	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.873157449454505	1		704	420	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028504	42028504	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751169367	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	340	534	2	ENST00000219905.7:c.4042C>T	p.Arg1348Trp	p.R1348W	ENST00000219905	NM_001164273.1	1348	Cgg/Tgg	13/24	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.873157449454505	2		536	738	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658353	18658353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868506094	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	331	548	0	ENST00000266497.5:c.3158G>A	p.Gly1053Glu	p.G1053E	ENST00000266497		1053	gGa/gAa	22/31	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.873157449454505	2		548	732	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670154	29670154	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1555535455	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	266	443	0	ENST00000356175.3:c.7126+1G>A		p.X2376_splice	ENST00000356175	NM_000267.3	2376			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.873157449454505	2		443	606	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212236	36212236	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301144035	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	372	740	0	ENST00000222270.7:c.1987G>A	p.Glu663Lys	p.E663K	ENST00000222270	NM_014727.1	663	Gaa/Aaa	3/37	1	2	FACETS	0.991	0.945	1	0.991	0.945	1	CLONAL	1	TRUE	1	0.873157449454505	2		740	860	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494644	2494644	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	286	655	0	ENST00000355716.4:c.784C>T	p.Pro262Ser	p.P262S	ENST00000355716	NM_003820.2	262	Ccg/Tcg	8/8	1	2	FACETS	0.956	0.905	1	0.956	0.905	1	CLONAL	1	TRUE	1	0.873157449454505	2		655	685	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186825	11186825	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	256	465	0	ENST00000361445.4:c.6380C>T	p.Ser2127Phe	p.S2127F	ENST00000361445	NM_004958.3	2127	tCc/tTc	46/58	1	2	FACETS	0.994	0.939	1	0.994	0.939	1	CLONAL	1	TRUE	1	0.873157449454505	2		465	590	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161293411	161293411	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	354	595	0	ENST00000367975.2:c.28G>A	p.Gly10Ser	p.G10S	ENST00000367975	NM_003001.3	10	Ggt/Agt	2/6	1	2	FACETS	0.864	0.822	0.908	0.864	0.822	0.908	CLONAL	1	TRUE	1	0.873157449454505	2		595	938	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102199635	102199635	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1481844237	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	282	350	0	ENST00000263464.3:c.1040C>T	p.Ser347Phe	p.S347F	ENST00000263464	NM_001165.4	347	tCc/tTc	5/9	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.873157449454505	2		350	605	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350186	89350186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	528	932	0	ENST00000301030.4:c.2764G>A	p.Glu922Lys	p.E922K	ENST00000301030	NM_001256183.1	922	Gag/Aag	9/13	0.873157449454505	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.873157449454505	1		932	665	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761145	59761145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878855154	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	411	737	1	ENST00000259008.2:c.3262C>T	p.His1088Tyr	p.H1088Y	ENST00000259008	NM_032043.2	1088	Cat/Tat	20/20	1	2	FACETS	0.998	0.954	1	0.998	0.954	1	CLONAL	1	TRUE	1	0.873157449454505	2		738	943	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144827	11144828	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	262	614	1	ENST00000358026.2:c.3902_3903delinsTT	p.Thr1301Ile	p.T1301I	ENST00000358026	NM_001128849.1	1301	aCC/aTT	28/36	1	2	FACETS	0.904	0.853	0.956	0.904	0.853	0.956	CLONAL	1	TRUE	1	0.873157449454505	2		615	664	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291630	15291630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	361	828	0	ENST00000263388.2:c.3004G>A	p.Asp1002Asn	p.D1002N	ENST00000263388	NM_000435.2	1002	Gat/Aat	19/33	1	2	FACETS	0.984	0.938	1	0.984	0.938	1	CLONAL	1	TRUE	1	0.873157449454505	2		828	840	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606651	29606651	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760717114	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	318	545	0	ENST00000389048.3:c.1229G>A	p.Gly410Glu	p.G410E	ENST00000389048	NM_004304.4	410	gGa/gAa	5/29	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.873157449454505	2		545	726	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881596	111881597	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	388	730	0	ENST00000393256.3:c.274_275delinsAT	p.Ser92Ile	p.S92I	ENST00000393256	NM_006538.4	92	TCc/ATc	2/4	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.873157449454505	2		730	876	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274557	198274557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	359	669	1	ENST00000335508.6:c.841C>T	p.His281Tyr	p.H281Y	ENST00000335508	NM_012433.2	281	Cat/Tat	7/25	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.873157449454505	2		670	821	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645916	215645916	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	342	759	0	ENST00000260947.4:c.682G>A	p.Glu228Lys	p.E228K	ENST00000260947	NM_000465.2	228	Gaa/Aaa	4/11	1	2	FACETS	0.862	0.818	0.906	0.862	0.818	0.906	CLONAL	1	TRUE	1	0.873157449454505	2		759	909	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021322	31021322	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	254	535	0	ENST00000375687.4:c.1321T>A	p.Ser441Thr	p.S441T	ENST00000375687	NM_015338.5	441	Tct/Act	12/13	1	2	FACETS	0.952	0.898	1	0.952	0.898	1	CLONAL	1	TRUE	1	0.873157449454505	2		535	611	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021340	31021340	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	245	513	0	ENST00000375687.4:c.1339C>T	p.Pro447Ser	p.P447S	ENST00000375687	NM_015338.5	447	Ccc/Tcc	12/13	1	2	FACETS	0.961	0.906	1	0.961	0.906	1	CLONAL	1	TRUE	1	0.873157449454505	2		513	584	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031230	36031231	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	280	641	1	ENST00000358208.4:c.1349_1350delinsTT	p.Ser450Phe	p.S450F	ENST00000358208		450	tCC/tTT	11/12	0.873157449454505	1	FACETS	0.977	0.941	1	0.977	0.941	1	CLONAL	1	TRUE	0	0.873157449454505	1		642	370	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650401	12650401	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1559433480	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	244	419	1	ENST00000251849.4:c.445C>T	p.Leu149Phe	p.L149F	ENST00000251849	NM_002880.3	149	Ctt/Ttt	5/17	1	2	FACETS	0.89	0.837	0.943	0.89	0.837	0.943	CLONAL	1	TRUE	1	0.873157449454505	2		420	628	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	218534	218534	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	29	88	0	ENST00000264932.6:c.63+1G>C		p.X21_splice	ENST00000264932	NM_004168.2	21			0.418221174066902	1	FACETS	0.506	0.421	0.594	0.506	0.421	0.594	INDETERMINATE	1	TRUE	0	0.873157449454505	1		88	74	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322304	31322304	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	234	472	0	ENST00000412585.2:c.1046-1G>T		p.X349_splice	ENST00000412585	NM_005514.6	349			0.121595614139207	3	FACETS	1	0.991	1	0.654	0.614	0.693	INDETERMINATE	1	TRUE	1	0.873157449454505	3		472	589	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609849	117609849	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	410	700	0	ENST00000368508.3:c.6850G>A	p.Gly2284Ser	p.G2284S	ENST00000368508	NM_002944.2	2284	Ggt/Agt	43/43	0.873157449454505	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.873157449454505	1		700	513	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505561	157505561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	132	177	0	ENST00000346085.5:c.3542C>T	p.Pro1181Leu	p.P1181L	ENST00000346085	NM_020732.3	1181	cCa/cTa	13/20	0.873157449454505	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.873157449454505	1		177	170	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853389	151853389	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	296	515	0	ENST00000262189.6:c.11713C>T	p.Pro3905Ser	p.P3905S	ENST00000262189	NM_170606.2	3905	Cct/Tct	45/59	1	2	FACETS	0.943	0.893	0.993	0.943	0.893	0.993	CLONAL	1	TRUE	1	0.873157449454505	2		515	719	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128322042	128322042	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	281	550	0	ENST00000265960.3:c.718G>A	p.Glu240Lys	p.E240K	ENST00000265960	NM_001006617.1	240	Gag/Aag	6/12	0.873157449454505	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.873157449454505	1		550	356	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615599	100615599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	365	337	0	ENST00000308731.7:c.733G>A	p.Glu245Lys	p.E245K	ENST00000308731	NM_000061.2	245	Gag/Aag	8/19	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.873157449454505	1		337	420	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236570	236570	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	17	30	0	ENST00000264932.6:c.1288C>T	p.Gln430Ter	p.Q430*	ENST00000264932	NM_004168.2	430	Cag/Tag	10/15	0.418221174066902	1	FACETS	0.563	0.444	0.685	0.563	0.444	0.685	INDETERMINATE	1	TRUE	0	0.873157449454505	1		30	39	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	115	697	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.811	0.733	0.891	1	0.986	1	CLONAL	2	TRUE	1	0.273371333148928	2		697	519	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0034059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	105	647	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.270895876698521	1	FACETS	0.968	0.868	1	0.968	0.868	1	CLONAL	1	TRUE	0	0.273371333148928	1		647	685	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106648	27106648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553153748	NA	P-0034059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	110	638	1	ENST00000324856.7:c.6259G>A	p.Gly2087Arg	p.G2087R	ENST00000324856	NM_006015.4	2087	Gga/Aga	20/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.273371333148928	2		639	698	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443536	49443536	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	90	437	0	ENST00000301067.7:c.3835del	p.Ile1279SerfsTer51	p.I1279Sfs*51	ENST00000301067	NM_003482.3	1279	Atc/tc	11/54	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.273371333148928	2		437	658	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562387	95562387	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	77	317	0	ENST00000393063.1:c.4870G>T	p.Ala1624Ser	p.A1624S	ENST00000393063	NM_030621.3	1624	Gct/Tct	24/28	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.273371333148928	2		317	522	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573556	48573556	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	28	192	0	ENST00000342988.3:c.140T>C	p.Leu47Pro	p.L47P	ENST00000342988	NM_005359.5	47	cTg/cCg	2/12	0.270895876698521	1	FACETS	0.88	0.708	1	0.88	0.708	1	CLONAL	1	TRUE	0	0.273371333148928	1		192	201	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	63	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.879	0.771	0.993	0.879	0.771	0.993	CLONAL	1	TRUE	1	0.633969151092716	2		248	226	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685287	89685287	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs398123316	NA	P-0034065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	24	240	0	ENST00000371953.3:c.182A>T	p.His61Leu	p.H61L	ENST00000371953	NM_000314.4	61	cAt/cTt	3/9	0.633969151092716	1	FACETS	0.205	0.161	0.256	0.205	0.161	0.256	SUBCLONAL	1	TRUE	0	0.633969151092716	1		240	252	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720703	89720703	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	14	125	0	ENST00000371953.3:c.856del	p.Thr286ProfsTer5	p.T286Pfs*5	ENST00000371953	NM_000314.4	285	gAa/ga	8/9	0.633969151092716	1	FACETS	0.214	0.155	0.284	0.214	0.155	0.284	SUBCLONAL	1	TRUE	0	0.633969151092716	1		125	141	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588880	69588880	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1240828791	NA	P-0034065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	82	450	0	ENST00000168712.1:c.356C>G	p.Ser119Trp	p.S119W	ENST00000168712	NM_002007.2	119	tCg/tGg	2/3	1	2	FACETS	0.806	0.717	0.899	0.806	0.717	0.899	CLONAL	1	TRUE	1	0.633969151092716	2		450	321	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955383	48955383	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	114	225	0	ENST00000267163.4:c.1499G>T	p.Arg500Ile	p.R500I	ENST00000267163	NM_000321.2	500	aGa/aTa	17/27	0.633969151092716	1	FACETS	0.938	0.86	1	0.938	0.86	1	CLONAL	1	TRUE	0	0.633969151092716	1		225	262	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664851	29664852	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATTCCAACGTGCAAGTGGCTGGACCAGTGGACAGAACTAGCTCAAA	novel	NA	P-0034065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	66	333	0	ENST00000356175.3:c.6595_6640dup	p.Arg2214AsnfsTer22	p.R2214Nfs*22	ENST00000356175	NM_000267.3	2198	-/ATTCCAACGTGCAAGTGGCTGGACCAGTGGACAGAACTAGCTCAAA	43/57	1	2	FACETS	0.379	0.329	0.433	0.379	0.329	0.433	SUBCLONAL	1	TRUE	1	0.633969151092716	2		333	549	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520090	106520090	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	76	235	0	ENST00000359195.3:c.2518C>T	p.Gln840Ter	p.Q840*	ENST00000359195	NM_002649.2	840	Caa/Taa	6/11	0.633969151092716	3	FACETS	0.741	0.653	0.835	0.371	0.326	0.418	SUBCLONAL	1	TRUE	1	0.633969151092716	3		235	426	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0034066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	43	479	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.14	2		479	475	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0034066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	10	215	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	0.501	0.338	0.707	0.501	0.338	0.707	SUBCLONAL	1	TRUE	1	0.14	2		215	285	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0034067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	203	629	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.230926096002482	3	FACETS	0.964	0.894	1	0.964	0.894	1	CLONAL	2	TRUE	1	0.230926096002482	3		629	1017	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0034067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	126	553	0	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	0.221226025138924	1	FACETS	0.832	0.752	0.917	0.832	0.752	0.917	CLONAL	1	TRUE	0	0.230926096002482	1		553	1160	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241678	55241678	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517085	NA	P-0034067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	256	536	0	ENST00000275493.2:c.2126A>C	p.Glu709Ala	p.E709A	ENST00000275493	NM_005228.3	709	gAa/gCa	18/28	0.230926096002482	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.230926096002482	3		536	1179	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193121527	193121527	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	36	241	0	ENST00000367435.3:c.925A>G	p.Ile309Val	p.I309V	ENST00000367435	NM_024529.4	309	Att/Gtt	10/17	0.179470151480024	3	FACETS	1	0.924	1	0.617	0.509	0.736	CLONAL	1	TRUE	1	0.230926096002482	3		241	282	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063684	67063684	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	52	253	0	ENST00000412916.2:c.133C>T	p.Gln45Ter	p.Q45*	ENST00000412916		45	Cag/Tag	2/6	0.415141009859808	1	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	0	0.415141009859808	1		253	191	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0034068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	70	432	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.415141009859808	2		432	326	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	382	442	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.310850386886192	5	FACETS	1	0.992	1			1	INDETERMINATE	3	TRUE	NA	0.634113549799246	5		442	693	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	54	422	1	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	1	2	FACETS	0.332	0.283	0.385	0.332	0.283	0.385	SUBCLONAL	1	TRUE	1	0.634113549799246	2		423	513	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	104	667	2	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.954	0.863	1	0.954	0.863	1	CLONAL	1	TRUE	1	0.634113549799246	2		669	344	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339111	65339111	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	91	308	2	ENST00000342505.4:c.425del	p.Lys142ArgfsTer26	p.K142Rfs*26	ENST00000342505	NM_002227.2	142	aAg/ag	5/25	1	2	FACETS	0.621	0.554	0.692	0.621	0.554	0.692	SUBCLONAL	1	TRUE	1	0.634113549799246	2		310	462	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696432	47696432	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519968	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	145	368	0	ENST00000347630.2:c.391T>G	p.Trp131Gly	p.W131G	ENST00000347630	NM_001007230.1	131	Tgg/Ggg	6/11	1	2	FACETS	0.951	0.874	1	0.951	0.874	1	CLONAL	1	TRUE	1	0.634113549799246	2		368	481	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	24	430	0	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	1	2	FACETS	0.227	0.178	0.284	0.227	0.178	0.284	SUBCLONAL	1	TRUE	1	0.634113549799246	2		430	333	SUCCESS
AR	367	MSKCC	GRCh37	X	66931247	66931247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868669253	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	93	115	0	ENST00000374690.3:c.1889G>A	p.Arg630Gln	p.R630Q	ENST00000374690	NM_000044.3	630	cGg/cAg	4/8	1	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.634113549799246	1		115	149	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	15	104	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	0.382	0.281	0.5	0.382	0.281	0.5	SUBCLONAL	1	TRUE	1	0.634113549799246	2		104	124	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262117	10262119	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	novel	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	167	508	0	ENST00000340748.4:c.2172_2174del	p.Lys725del	p.K725del	ENST00000340748		724	aaGAAa/aaa	23/40	1	2	FACETS	0.837	0.773	0.904	0.837	0.773	0.904	CLONAL	1	TRUE	1	0.634113549799246	2		508	629	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	125	349	7	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	0.61733997248132	1	FACETS	0.895	0.823	0.968	0.895	0.823	0.968	CLONAL	1	TRUE	0	0.634113549799246	1		356	301	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508182	38508184	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs751811710	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	18	236	0	ENST00000254066.5:c.499_501del	p.Lys167del	p.K167del	ENST00000254066	NM_000964.3	164	AAG/-	5/9	1	2	FACETS	0.204	0.153	0.264	0.204	0.153	0.264	SUBCLONAL	1	TRUE	1	0.634113549799246	2		236	278	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654643	67654643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs968244943	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	123	348	0	ENST00000264010.4:c.1130G>A	p.Arg377His	p.R377H	ENST00000264010	NM_006565.3	377	cGt/cAt	6/12	1	2	FACETS	0.919	0.838	1	0.919	0.838	1	CLONAL	1	TRUE	1	0.634113549799246	2		348	422	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40497584	40497584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774724351	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	37	399	1	ENST00000264657.5:c.365C>T	p.Ala122Val	p.A122V	ENST00000264657	NM_139276.2	122	gCg/gTg	4/24	1	2	FACETS	0.211	0.173	0.253	0.211	0.173	0.253	SUBCLONAL	1	TRUE	1	0.634113549799246	2		400	554	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120178	70120178	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057518216	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	108	306	0	ENST00000245479.2:c.1180C>T	p.Arg394Ter	p.R394*	ENST00000245479	NM_000346.3	394	Cga/Tga	3/3	1	2	FACETS	0.979	0.888	1	0.979	0.888	1	CLONAL	1	TRUE	1	0.634113549799246	2		306	348	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247836	10247836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	206	509	0	ENST00000340748.4:c.4366C>T	p.Arg1456Trp	p.R1456W	ENST00000340748		1456	Cgg/Tgg	36/40	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.634113549799246	2		509	638	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567647	226567647	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	116	382	2	ENST00000366794.5:c.1519del	p.Ser507AlafsTer17	p.S507Afs*17	ENST00000366794	NM_001618.3	507	Agc/gc	10/23	1	2	FACETS	0.845	0.767	0.926	0.845	0.767	0.926	CLONAL	1	TRUE	1	0.634113549799246	2		384	433	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612346	1612346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769011342	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	193	577	0	ENST00000344749.5:c.1673G>A	p.Arg558His	p.R558H	ENST00000344749	NM_001136139.2	558	cGc/cAc	18/19	1	2	FACETS	0.969	0.901	1	0.969	0.901	1	CLONAL	1	TRUE	1	0.634113549799246	2		577	628	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574679	41574679	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	170	610	4	ENST00000263253.7:c.6970del	p.His2324ThrfsTer29	p.H2324Tfs*29	ENST00000263253	NM_001429.3	2322	Ccc/cc	31/31	1	2	FACETS	0.85	0.785	0.917	0.85	0.785	0.917	CLONAL	1	TRUE	1	0.634113549799246	2		614	631	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171732	36171732	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759227406	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	85	235	0	ENST00000300305.3:c.833C>T	p.Pro278Leu	p.P278L	ENST00000300305		278	cCg/cTg	7/8	1	2	FACETS	0.882	0.788	0.98	0.882	0.788	0.98	CLONAL	1	TRUE	1	0.634113549799246	2		235	304	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313315	65313315	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	25	355	0	ENST00000342505.4:c.1799G>A	p.Gly600Glu	p.G600E	ENST00000342505	NM_002227.2	600	gGg/gAg	13/25	1	2	FACETS	0.164	0.128	0.204	0.164	0.128	0.204	SUBCLONAL	1	TRUE	1	0.634113549799246	2		355	482	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023290	27023290	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	37	85	0	ENST00000324856.7:c.400del	p.Ala134ArgfsTer98	p.A134Rfs*98	ENST00000324856	NM_006015.4	132	gtG/gt	1/20	1	2	FACETS	0.964	0.813	1	0.964	0.813	1	CLONAL	1	TRUE	1	0.634113549799246	2		85	121	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	38	640	1	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.188	0.155	0.225	0.188	0.155	0.225	SUBCLONAL	1	TRUE	1	0.634113549799246	2		641	638	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853077	151853077	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	125	259	1	ENST00000262189.6:c.11878C>T	p.Arg3960Ter	p.R3960*	ENST00000262189	NM_170606.2	3960	Cga/Tga	46/59	0.634113549799246	3	FACETS	1	0.949	1	0.531	0.483	0.581	CLONAL	1	TRUE	1	0.634113549799246	3		260	489	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625345	69625345	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200088042	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	103	445	0	ENST00000334134.2:c.448G>A	p.Glu150Lys	p.E150K	ENST00000334134	NM_005247.2	150	Gag/Aag	3/3	1	2	FACETS	0.725	0.653	0.801	0.725	0.653	0.801	SUBCLONAL	1	TRUE	1	0.634113549799246	2		445	448	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426774	49426774	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1334139538	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	70	246	2	ENST00000301067.7:c.11714A>T	p.Gln3905Leu	p.Q3905L	ENST00000301067	NM_003482.3	3905	cAg/cTg	39/54	1	2	FACETS	0.791	0.697	0.891	0.791	0.697	0.891	SUBCLONAL	1	TRUE	1	0.634113549799246	2		248	279	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39726940	39726940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757344214	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	59	121	0	ENST00000361337.2:c.938C>T	p.Thr313Met	p.T313M	ENST00000361337	NM_003286.2	313	aCg/aTg	11/21	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.634113549799246	2		121	185	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037144	71037144	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	64	258	0	ENST00000318789.4:c.1146+1G>A		p.X382_splice	ENST00000318789	NM_032682.5	382			1	2	FACETS	0.734	0.642	0.832	0.734	0.642	0.832	SUBCLONAL	1	TRUE	1	0.634113549799246	2		258	275	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732617	190732617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375020232	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	117	319	0	ENST00000441310.2:c.2435G>A	p.Arg812His	p.R812H	ENST00000441310	NM_000534.4	812	cGt/cAt	11/13	1	2	FACETS	0.822	0.746	0.901	0.822	0.746	0.901	CLONAL	1	TRUE	1	0.634113549799246	2		319	449	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661917	29661917	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	118	382	0	ENST00000356175.3:c.5815del	p.Cys1939AlafsTer19	p.C1939Afs*19	ENST00000356175	NM_000267.3	1937	cgT/cg	39/57	1	2	FACETS	0.668	0.605	0.734	0.668	0.605	0.734	SUBCLONAL	1	TRUE	1	0.634113549799246	2		382	557	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326690	62326690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375593361	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	170	536	0	ENST00000360203.5:c.3509G>A	p.Arg1170Gln	p.R1170Q	ENST00000360203	NM_001283009.1	1170	cGg/cAg	34/35	1	2	FACETS	0.987	0.914	1	0.987	0.914	1	CLONAL	1	TRUE	1	0.634113549799246	2		536	543	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099211	4099211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770521279	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	124	362	0	ENST00000262948.5:c.907C>T	p.Arg303Cys	p.R303C	ENST00000262948	NM_030662.3	303	Cgc/Tgc	7/11	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.634113549799246	2		362	387	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300216	15300216	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	144	468	0	ENST00000263388.2:c.1060G>A	p.Ala354Thr	p.A354T	ENST00000263388	NM_000435.2	354	Gcc/Acc	7/33	1	2	FACETS	0.935	0.858	1	0.935	0.858	1	CLONAL	1	TRUE	1	0.634113549799246	2		468	486	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693856	47693856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755818010	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	109	223	0	ENST00000233146.2:c.1570C>T	p.Arg524Cys	p.R524C	ENST00000233146	NM_000251.2	524	Cgt/Tgt	10/16	0.61733997248132	1	FACETS	0.974	0.893	1	0.974	0.893	1	CLONAL	1	TRUE	0	0.634113549799246	1		223	241	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934994	49934994	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771121262	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	121	480	1	ENST00000296474.3:c.2005C>T	p.Arg669Trp	p.R669W	ENST00000296474	NM_002447.2	669	Cgg/Tgg	6/20	1	2	FACETS	0.771	0.7	0.845	0.771	0.7	0.845	SUBCLONAL	1	TRUE	1	0.634113549799246	2		481	495	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289862	15289862	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778176344	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	138	549	0	ENST00000263388.2:c.3692G>A	p.Arg1231His	p.R1231H	ENST00000263388	NM_000435.2	1231	cGt/cAt	22/33	1	2	FACETS	0.7	0.639	0.763	0.7	0.639	0.763	SUBCLONAL	1	TRUE	1	0.634113549799246	2		549	622	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263982	104263982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	76	205	0	ENST00000369902.3:c.73G>A	p.Ala25Thr	p.A25T	ENST00000369902	NM_016169.3	25	Gcc/Acc	1/12	1	2	FACETS	0.915	0.813	1	0.915	0.813	1	CLONAL	1	TRUE	1	0.634113549799246	2		205	262	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628438	21628438	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	178	417	0	ENST00000421138.2:c.1180T>A	p.Ser394Thr	p.S394T	ENST00000421138		394	Tcc/Acc	11/16	1	2	FACETS	0.898	0.832	0.967	0.898	0.832	0.967	CLONAL	1	TRUE	1	0.634113549799246	2		417	625	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427428	49427428	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	170	494	1	ENST00000301067.7:c.11060G>A	p.Gly3687Asp	p.G3687D	ENST00000301067	NM_003482.3	3687	gGt/gAt	39/54	1	2	FACETS	0.946	0.875	1	0.946	0.875	1	CLONAL	1	TRUE	1	0.634113549799246	2		495	567	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578254	28578254	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs191501493	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	70	246	0	ENST00000241453.7:c.2917C>T	p.Arg973Ter	p.R973*	ENST00000241453	NM_004119.2	973	Cga/Tga	24/24	1	2	FACETS	0.563	0.493	0.638	0.563	0.493	0.638	SUBCLONAL	1	TRUE	1	0.634113549799246	2		246	392	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023064	33023064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1278786063	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	27	252	0	ENST00000300177.4:c.173G>A	p.Arg58Gln	p.R58Q	ENST00000300177	NM_001191322.1	58	cGg/cAg	2/2	1	2	FACETS	0.269	0.214	0.332	0.269	0.214	0.332	SUBCLONAL	1	TRUE	1	0.634113549799246	2		252	316	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782084	66782084	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	98	244	0	ENST00000307102.5:c.1051G>C	p.Asp351His	p.D351H	ENST00000307102	NM_002755.3	351	Gat/Cat	10/11	1	2	FACETS	0.914	0.824	1	0.914	0.824	1	CLONAL	1	TRUE	1	0.634113549799246	2		244	338	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827157	72827157	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	24	274	0	ENST00000268489.5:c.9424A>G	p.Thr3142Ala	p.T3142A	ENST00000268489	NM_006885.3	3142	Aca/Gca	9/10	1	2	FACETS	0.216	0.169	0.27	0.216	0.169	0.27	SUBCLONAL	1	TRUE	1	0.634113549799246	2		274	351	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191212	2191212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	129	447	0	ENST00000398665.3:c.466G>A	p.Asp156Asn	p.D156N	ENST00000398665	NM_032482.2	156	Gac/Aac	5/28	1	2	FACETS	0.824	0.751	0.899	0.824	0.751	0.899	CLONAL	1	TRUE	1	0.634113549799246	2		447	494	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214613	5214613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765806159	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	157	515	1	ENST00000357368.4:c.4453G>A	p.Ala1485Thr	p.A1485T	ENST00000357368	NM_002850.3	1485	Gcg/Acg	29/38	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.634113549799246	2		516	489	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252730	10252730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747265409	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	137	416	1	ENST00000340748.4:c.3235G>A	p.Gly1079Ser	p.G1079S	ENST00000340748		1079	Ggc/Agc	29/40	1	2	FACETS	0.939	0.861	1	0.939	0.861	1	CLONAL	1	TRUE	1	0.634113549799246	2		417	460	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17389781	17389781	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1281173724	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	212	533	0	ENST00000359435.4:c.914G>A	p.Arg305Gln	p.R305Q	ENST00000359435	NM_001033549.1	305	cGg/cAg	9/9	1	2	FACETS	0.994	0.927	1	0.994	0.927	1	CLONAL	1	TRUE	1	0.634113549799246	2		533	673	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223502	36223502	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1250580167	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	164	542	2	ENST00000222270.7:c.6052G>A	p.Gly2018Arg	p.G2018R	ENST00000222270	NM_014727.1	2018	Ggg/Agg	28/37	1	2	FACETS	0.925	0.854	0.998	0.925	0.854	0.998	CLONAL	1	TRUE	1	0.634113549799246	2		544	559	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469969	25469969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1191462913	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	144	436	1	ENST00000264709.3:c.1073C>T	p.Thr358Met	p.T358M	ENST00000264709	NM_175629.2	358	aCg/aTg	9/23	1	2	FACETS	0.914	0.839	0.991	0.914	0.839	0.991	CLONAL	1	TRUE	1	0.634113549799246	2		437	497	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095765	178095767	+	inframe_deletion	In_Frame_Del	DEL	TAT	TAT	-	novel	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	127	331	0	ENST00000397062.3:c.1564_1566del	p.Ile522del	p.I522del	ENST00000397062	NM_006164.4	522	ATA/-	5/5	1	2	FACETS	0.9	0.822	0.981	0.9	0.822	0.981	CLONAL	1	TRUE	1	0.634113549799246	2		331	445	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657077	215657077	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	34	296	0	ENST00000260947.4:c.308G>T	p.Ser103Ile	p.S103I	ENST00000260947	NM_000465.2	103	aGc/aTc	3/11	1	2	FACETS	0.212	0.173	0.256	0.212	0.173	0.256	SUBCLONAL	1	TRUE	1	0.634113549799246	2		296	506	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22161960	22161960	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	125	320	1	ENST00000215832.6:c.295A>G	p.Lys99Glu	p.K99E	ENST00000215832	NM_002745.4	99	Aaa/Gaa	2/9	1	2	FACETS	0.853	0.778	0.932	0.853	0.778	0.932	CLONAL	1	TRUE	1	0.634113549799246	2		321	462	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162429	47162429	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	27	278	0	ENST00000409792.3:c.3697del	p.Thr1233GlnfsTer3	p.T1233Qfs*3	ENST00000409792	NM_014159.6	1233	Aca/ca	3/21	1	2	FACETS	0.218	0.173	0.27	0.218	0.173	0.27	SUBCLONAL	1	TRUE	1	0.634113549799246	2		278	390	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114287	73114287	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	43	130	0	ENST00000356692.5:c.923A>C	p.Glu308Ala	p.E308A	ENST00000356692		308	gAa/gCa	8/9	1	2	FACETS	0.869	0.74	1	0.869	0.74	1	CLONAL	1	TRUE	1	0.634113549799246	2		130	156	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332665	153332667	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	rs781017774	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	30	337	0	ENST00000281708.4:c.289_291del	p.Glu97del	p.E97del	ENST00000281708	NM_033632.3	97	GAA/-	2/12	1	2	FACETS	0.183	0.147	0.224	0.183	0.147	0.224	SUBCLONAL	1	TRUE	1	0.634113549799246	2		337	518	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627782	187627782	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	26	344	0	ENST00000441802.2:c.3200G>T	p.Gly1067Val	p.G1067V	ENST00000441802	NM_005245.3	1067	gGg/gTg	2/27	1	2	FACETS	0.187	0.148	0.233	0.187	0.148	0.233	SUBCLONAL	1	TRUE	1	0.634113549799246	2		344	438	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170827870	170827870	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	101	239	0	ENST00000296930.5:c.610G>A	p.Ala204Thr	p.A204T	ENST00000296930	NM_002520.6	204	Gca/Aca	8/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.634113549799246	2		239	295	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729442	41729442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	121	399	0	ENST00000242208.4:c.1087G>A	p.Gly363Arg	p.G363R	ENST00000242208	NM_002192.2	363	Ggg/Agg	3/3	0.634113549799246	3	FACETS	0.896	0.813	0.983	0.448	0.406	0.492	CLONAL	1	TRUE	1	0.634113549799246	3		399	561	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223603	55223603	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1343888047	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	75	310	0	ENST00000275493.2:c.970C>T	p.Arg324Cys	p.R324C	ENST00000275493	NM_005228.3	324	Cgc/Tgc	8/28	0.634113549799246	3	FACETS	0.728	0.641	0.821	0.364	0.32	0.411	SUBCLONAL	1	TRUE	1	0.634113549799246	3		310	428	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900086	151900086	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	154	304	0	ENST00000262189.6:c.4025A>G	p.Glu1342Gly	p.E1342G	ENST00000262189	NM_170606.2	1342	gAa/gGa	26/59	0.634113549799246	3	FACETS	1	0.968	1	0.551	0.506	0.597	CLONAL	1	TRUE	1	0.634113549799246	3		304	581	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132815	152132815	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	45	406	0	ENST00000262189.6:c.57del	p.Glu20ArgfsTer85	p.E20Rfs*85	ENST00000262189	NM_170606.2	19	ccC/cc	1/59	0.634113549799246	3	FACETS	0.277	0.232	0.327	0.138	0.116	0.164	SUBCLONAL	1	TRUE	1	0.634113549799246	3		406	675	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738476	145738476	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs766090166	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	142	457	0	ENST00000428558.2:c.2509A>G	p.Thr837Ala	p.T837A	ENST00000428558	NM_004260.3	837	Acg/Gcg	16/22	0.634113549799246	3	FACETS	0.782	0.714	0.854	0.391	0.357	0.427	SUBCLONAL	1	TRUE	1	0.634113549799246	3		457	754	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499681	8499681	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs781164830	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	176	331	1	ENST00000356435.5:c.2288C>A	p.Pro763His	p.P763H	ENST00000356435		763	cCc/cAc	14/35	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.634113549799246	2		332	502	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759676	133759676	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	25	441	1	ENST00000318560.5:c.2002del	p.Val668SerfsTer26	p.V668Sfs*26	ENST00000318560	NM_005157.4	667	Ggg/gg	11/11	1	2	FACETS	0.197	0.155	0.246	0.197	0.155	0.246	SUBCLONAL	1	TRUE	1	0.634113549799246	2		442	400	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139563037	139563037	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757508218	NA	P-0034070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	163	535	1	ENST00000308874.7:c.109G>A	p.Gly37Arg	p.G37R	ENST00000308874		37	Ggg/Agg	4/10	1	2	FACETS	0.877	0.809	0.948	0.877	0.809	0.948	CLONAL	1	TRUE	1	0.634113549799246	2		536	586	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0034071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	76	264	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.32875945334846	3	FACETS	0.854	0.756	0.956	0.854	0.756	0.956	CLONAL	2	TRUE	1	0.356901992193562	3		264	294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0034071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	103	653	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.356901992193562	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.356901992193562	1		653	463	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044449	12044466	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCAATTTTCTTGCAGAAA	TCAATTTTCTTGCAGAAA	-	novel	NA	P-0034071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	39	200	0	ENST00000353533.5:c.1087-15_1089del		p.X363_splice	ENST00000353533	NM_003010.3	363		11/11	0.356901992193562	1	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	0	0.356901992193562	1		200	169	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0034072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	32	808	0	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	1	2	FACETS	0.545	0.441	0.664	0.545	0.441	0.664	SUBCLONAL	1	TRUE	1	0.16	2		808	734	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524996	8524996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	28	353	0	ENST00000356435.5:c.608G>A	p.Gly203Glu	p.G203E	ENST00000356435		203	gGa/gAa	7/35	1	2	FACETS	0.956	0.765	1	0.956	0.765	1	CLONAL	1	TRUE	1	0.16	2		353	366	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874287	155874287	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs869025194	NA	P-0034072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	35	381	0	ENST00000368323.3:c.244T>G	p.Phe82Val	p.F82V	ENST00000368323	NM_006912.5	82	Ttt/Gtt	5/6	1	2	FACETS	0.917	0.751	1	0.917	0.751	1	CLONAL	1	TRUE	1	0.16	2		381	477	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46543186	46543187	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0034072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	24	327	1	ENST00000262741.5:c.314_314+1delinsAA		p.X105_splice	ENST00000262741	NM_003629.3	105		3/10	1	2	FACETS	0.792	0.62	0.99	0.792	0.62	0.99	CLONAL	1	TRUE	1	0.16	2		328	379	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112100	115112100	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	29	553	0	ENST00000257566.3:c.1640C>T	p.Ser547Phe	p.S547F	ENST00000257566	NM_016569.3	547	tCt/tTt	7/8	1	2	FACETS	0.66	0.529	0.811	0.66	0.529	0.811	SUBCLONAL	1	TRUE	1	0.16	2		553	549	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008283	29008283	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	27	347	0	ENST00000282397.4:c.588T>G	p.Asn196Lys	p.N196K	ENST00000282397	NM_002019.4	196	aaT/aaG	5/30	1	2	FACETS	0.778	0.618	0.96	0.778	0.618	0.96	CLONAL	1	TRUE	1	0.16	2		347	434	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858486	9858486	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	51	500	0	ENST00000330684.3:c.2915A>C	p.Lys972Thr	p.K972T	ENST00000330684	NM_001134407.1	972	aAg/aCg	13/13	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.16	2		500	536	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50916715	50916715	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	24	415	0	ENST00000440232.2:c.2187G>T	p.Glu729Asp	p.E729D	ENST00000440232	NM_002691.3	729	gaG/gaT	18/27	1	2	FACETS	0.767	0.601	0.959	0.767	0.601	0.959	CLONAL	1	TRUE	1	0.16	2		415	391	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0034163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	148	440	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.99	0.906	1	0.99	0.906	1	CLONAL	1	TRUE	1	0.408467799194179	2		440	732	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134512	30134512	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	54	316	0	ENST00000263025.4:c.19C>A	p.Gln7Lys	p.Q7K	ENST00000263025	NM_002746.2	7	Cag/Aag	1/9	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.408467799194179	2		316	249	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221320	1221320	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587776656	NA	P-0034163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	196	723	0	ENST00000326873.7:c.843del	p.Leu282SerfsTer5	p.L282Sfs*5	ENST00000326873	NM_000455.4	281	ccG/cc	6/10	0.408467799194179	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.408467799194179	1		723	657	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610358	10610358	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	232	952	2	ENST00000171111.5:c.352C>T	p.Gln118Ter	p.Q118*	ENST00000171111	NM_203500.1	118	Cag/Tag	2/6	0.408467799194179	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.408467799194179	1		954	788	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390995	89390995	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	116	671	0	ENST00000336596.2:c.1061G>T	p.Arg354Leu	p.R354L	ENST00000336596	NM_005233.5	354	cGg/cTg	5/17	1	2	FACETS	0.89	0.804	0.981	0.89	0.804	0.981	CLONAL	1	TRUE	1	0.408467799194179	2		671	638	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696431	47696431	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519969	NA	P-0034177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	60	671	0	ENST00000347630.2:c.392G>C	p.Trp131Ser	p.W131S	ENST00000347630	NM_001007230.1	131	tGg/tCg	6/11	1	2	FACETS	0.778	0.668	0.898	0.778	0.668	0.898	SUBCLONAL	1	TRUE	1	0.16	2		671	964	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0034185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	125	248	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.352961047581386	4	FACETS	0.832	0.757	0.911	0.832	0.757	0.911	CLONAL	2	TRUE	2	0.401771436834912	4		248	524	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0034185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	222	442	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.401771436834912	5	FACETS	1	0.979	1	0.746	0.697	0.798	CLONAL	2	TRUE	2	0.401771436834912	5		442	791	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682399	52682400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0034185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	360	433	0	ENST00000394830.3:c.773dup	p.Asn258LysfsTer6	p.N258Kfs*6	ENST00000394830	NM_018313.4	258	aat/aaAt	8/30	0.371574782464982	3	FACETS	0.907	0.865	0.949	0.907	0.865	0.949	CLONAL	3	TRUE	0	0.401771436834912	3		433	791	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827589	72827589	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343025200	NA	P-0034185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	285	667	1	ENST00000268489.5:c.8992C>T	p.Arg2998Trp	p.R2998W	ENST00000268489	NM_006885.3	2998	Cgg/Tgg	9/10	0.343941153667282	4	FACETS	0.889	0.836	0.944	0.889	0.836	0.944	CLONAL	2	TRUE	2	0.401771436834912	4		668	1118	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087894	27087907	+	frameshift_variant	Frame_Shift_Del	DEL	GCCACCCAGTGGCC	GCCACCCAGTGGCC	-	novel	NA	P-0034185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	294	588	1	ENST00000324856.7:c.2181_2194del	p.Pro728ValfsTer84	p.P728Vfs*84	ENST00000324856	NM_006015.4	727	cgGCCACCCAGTGGCCag/cgag	6/20	0.380734114989191	2	FACETS	0.968	0.916	1	0.968	0.916	1	CLONAL	2	TRUE	0	0.401771436834912	2		589	756	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0034191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	134	328	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.153224788090907	3	FACETS	1	0.986	1	0.714	0.655	0.775	INDETERMINATE	1	TRUE	1	0.591881723415534	3		328	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0034191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	507	654	5	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.591881723415534	2	FACETS	0.989	0.955	1	0.989	0.955	1	CLONAL	2	TRUE	0	0.591881723415534	2		659	866	SUCCESS
APC	324	MSKCC	GRCh37	5	112174490	112174493	+	frameshift_variant	Frame_Shift_Del	DEL	CAAT	CAAT	-	rs587779353	NA	P-0034191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	104	357	0	ENST00000257430.4:c.3202_3205del	p.Ser1068GlyfsTer57	p.S1068Gfs*57	ENST00000257430	NM_000038.5	1067	CAATca/ca	16/16	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.591881723415534	2		357	321	SUCCESS
APC	324	MSKCC	GRCh37	5	112175650	112175651	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0034191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	157	340	0	ENST00000257430.4:c.4364dup	p.Asn1455LysfsTer2	p.N1455Kfs*2	ENST00000257430	NM_000038.5	1453	-/A	16/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.591881723415534	2		340	441	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112283	115112283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1018135320	NA	P-0034191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	102	247	0	ENST00000257566.3:c.1457C>T	p.Thr486Met	p.T486M	ENST00000257566	NM_016569.3	486	aCg/aTg	7/8	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.591881723415534	2		247	297	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039183	49039183	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	87	464	0	ENST00000267163.4:c.2261T>C	p.Val754Ala	p.V754A	ENST00000267163	NM_000321.2	754	gTa/gCa	22/27	0.462172484672449	3	FACETS	0.627	0.555	0.703	0.313	0.277	0.352	SUBCLONAL	1	TRUE	1	0.591881723415534	3		464	608	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222371	2222371	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1419349453	NA	P-0034191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	167	619	0	ENST00000326181.6:c.655C>T	p.Arg219Trp	p.R219W	ENST00000326181	NM_032271.2	219	Cgg/Tgg	8/21	0.21350347278106	3	FACETS	0.884	0.813	0.958	0.442	0.406	0.479	INDETERMINATE	1	TRUE	1	0.591881723415534	3		619	827	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734200	58734200	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	150	476	0	ENST00000305921.3:c.1258A>C	p.Lys420Gln	p.K420Q	ENST00000305921	NM_003620.3	420	Aag/Cag	5/6	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.591881723415534	2		476	497	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732923	30732924	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTGTGTGAGACGTTGACTGAGTGCTGGGACCAC	novel	NA	P-0034191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	52	287	0	ENST00000295754.5:c.1538_1570dup	p.Val513_His523dup	p.V513_H523dup	ENST00000295754	NM_003242.5	513	-/GTGTGTGAGACGTTGACTGAGTGCTGGGACCAC	7/7	0.591881723415534	1	FACETS	0.417	0.357	0.481	0.417	0.357	0.481	SUBCLONAL	1	TRUE	0	0.591881723415534	1		287	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057519990	NA	P-0034192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	344	573	0	ENST00000269305.4:c.796G>T	p.Gly266Ter	p.G266*	ENST00000269305	NM_001126112.2	266	Gga/Tga	8/11	0.549280818495546	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.549280818495546	1		573	755	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0034192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	172	467	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	0.549280818495546	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.549280818495546	1		467	412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0001575-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	176	1011	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.189361043250995	2	FACETS	0.771	0.711	0.835	0.771	0.711	0.835	SUBCLONAL	2	TRUE	0	0.247704664740226	2		1012	921	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908128	41908128	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001575-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	93	611	0	ENST00000372991.4:c.394G>T	p.Val132Phe	p.V132F	ENST00000372991	NM_001760.3	132	Gtc/Ttc	2/5	0.189128320579311	3	FACETS	0.823	0.73	0.922	0.274	0.243	0.308	CLONAL	1	TRUE	0	0.247704664740226	3		611	1026	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860106	152860243	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTCCAGGGGCTCACCGCTTGGGTTAAAGTACCTGCGCAGAGAAATGGCAATGCTTCAGCAGCCAGGGCAGTCTCCTGAGCACTGGATGGCTCAAATTGCTTAAGTCACACAATGTCCAGATGCAAACTACATCGTCC	ATTCCAGGGGCTCACCGCTTGGGTTAAAGTACCTGCGCAGAGAAATGGCAATGCTTCAGCAGCCAGGGCAGTCTCCTGAGCACTGGATGGCTCAAATTGCTTAAGTCACACAATGTCCAGATGCAAACTACATCGTCC	-	novel	NA	P-0001575-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	60	677	0	ENST00000406277.2:c.291-106_322del		p.X97_splice	ENST00000406277	NM_152274.4	97		5/7	0.166389116908168		FACETS		0.368	0.495				SUBCLONAL	1	TRUE	0	0.247704664740226	1		677	990	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	121	258	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.937	0.861	1	0.937	0.861	1	CLONAL	1	TRUE	1	0.9	2		258	287	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0002986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	186	319	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.996	0.932	1	0.996	0.932	1	CLONAL	1	TRUE	1	0.9	2		319	415	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911490	39911490	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	303	332	1	ENST00000378444.4:c.5140del	p.Glu1714LysfsTer11	p.E1714Kfs*11	ENST00000378444	NM_001123385.1	1714	Gaa/aa	15/15	1	1	FACETS	0.99	0.96	1	0.99	0.96	1	CLONAL	1	TRUE	0	0.9	1		333	374	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503217	125503217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	29	370	0	ENST00000428830.2:c.584G>A	p.Gly195Glu	p.G195E	ENST00000428830	NM_001114121.2	195	gGa/gAa	6/14	1	2	FACETS	0.146	0.117	0.18	0.146	0.117	0.18	SUBCLONAL	1	TRUE	1	0.9	2		370	440	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986930	36986931	+	missense_variant	Missense_Mutation	DNP	CT	CT	AA	novel	NA	P-0002986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	209	603	1	ENST00000354822.5:c.758_759delinsTT	p.Lys253Ile	p.K253I	ENST00000354822	NM_001079668.2	253	aAG/aTT	3/3	1	2	FACETS	0.873	0.818	0.929	0.873	0.818	0.929	CLONAL	1	TRUE	1	0.9	2		604	532	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55087048	55087048	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	101	302	0	ENST00000275493.2:c.79del	p.Glu27LysfsTer53	p.E27Kfs*53	ENST00000275493	NM_005228.3	26	gaG/ga	1/28	1	2	FACETS	0.837	0.761	0.916	0.837	0.761	0.916	CLONAL	1	TRUE	1	0.9	2		302	268	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593599	55593655	+	inframe_deletion	In_Frame_Del	DEL	ACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCCAAC	ACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCCAAC	-	novel	NA	P-0003384-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	188	347	0	ENST00000288135.5:c.1668_1724del	p.Trp557_Gln575del	p.W557_Q575del	ENST00000288135	NM_000222.2	555	gtACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCCAACa/gta	11/21	1	2	FACETS	0.908	0.846	0.971	0.908	0.846	0.971	CLONAL	1	TRUE	1	0.797873422331262	2		347	519	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599333	55599333	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003384-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	19	415	0	ENST00000288135.5:c.2459A>C	p.Asp820Ala	p.D820A	ENST00000288135	NM_000222.2	820	gAt/gCt	17/21	1	2	FACETS	0.069	0.052	0.09	0.069	0.052	0.09	SUBCLONAL	1	TRUE	1	0.797873422331262	2		415	688	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0004530-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	48	460	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.856	0.722	1	0.856	0.722	1	CLONAL	1	TRUE	1	0.17	2		460	660	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199365	11199365	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004530-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	53	494	0	ENST00000361445.4:c.5126G>T	p.Arg1709Leu	p.R1709L	ENST00000361445	NM_004958.3	1709	cGc/cTc	36/58	1	2	FACETS	0.872	0.742	1	0.872	0.742	1	CLONAL	1	TRUE	1	0.17	2		494	715	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987076	36987076	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs137852693	NA	P-0004530-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	79	557	0	ENST00000354822.5:c.613G>T	p.Glu205Ter	p.E205*	ENST00000354822	NM_001079668.2	205	Gag/Tag	3/3	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.17	2		557	923	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988386	36988386	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004530-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	16	202	0	ENST00000354822.5:c.267del	p.His90ThrfsTer11	p.H90Tfs*11	ENST00000354822	NM_001079668.2	89	ggG/gg	2/3	1	2	FACETS	0.596	0.44	0.783	0.596	0.44	0.783	SUBCLONAL	1	TRUE	1	0.17	2		202	316	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44919278	44919310	+	inframe_deletion	In_Frame_Del	DEL	TAACCTTCCACAAGGTAGTCTACAGAATAAAAC	TAACCTTCCACAAGGTAGTCTACAGAATAAAAC	-	novel	NA	P-0004530-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	30	218	0	ENST00000377967.4:c.1209_1241del	p.Asn403_Thr413del	p.N403_T413del	ENST00000377967	NM_021140.2	402	tgTAACCTTCCACAAGGTAGTCTACAGAATAAAACt/tgt	13/29	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.17	2		218	297	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0004892-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	238	604	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	0.145310019466474	5	FACETS	1	0.939	1	0.752	0.704	0.801	INDETERMINATE	3	TRUE	1	0.289703671266798	5		604	784	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463208	25463208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004892-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	50	605	0	ENST00000264709.3:c.2285G>A	p.Gly762Asp	p.G762D	ENST00000264709	NM_175629.2	762	gGc/gAc	19/23	0.228783141412973	3	FACETS	0.754	0.64	0.88			1	SUBCLONAL	1	TRUE	NA	0.289703671266798	3		605	524	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747918	41747918	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004892-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	38	364	0	ENST00000226382.2:c.851C>A	p.Pro284Gln	p.P284Q	ENST00000226382	NM_003924.3	284	cCg/cAg	3/3	NA	2	FACETS	0.698	0.578	0.831			1	INDETERMINATE	1	TRUE	NA	0.289703671266798	2		364	376	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798735	135798735	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004892-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	32	255	0	ENST00000298552.3:c.508G>T	p.Gly170Cys	p.G170C	ENST00000298552	NM_001162426.1	170	Ggc/Tgc	6/23	0.208129259977757	3	FACETS	0.803	0.653	0.971	0.401	0.326	0.486	CLONAL	1	TRUE	1	0.289703671266798	3		255	315	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247836	10247836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004892-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	134	590	0	ENST00000340748.4:c.4366C>T	p.Arg1456Trp	p.R1456W	ENST00000340748		1456	Cgg/Tgg	36/40	0.183891559959272	4	FACETS	0.808	0.735	0.885	0.808	0.735	0.885	CLONAL	2	TRUE	2	0.289703671266798	4		590	738	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272230	15272230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763603215	NA	P-0004892-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	115	472	0	ENST00000263388.2:c.6209C>T	p.Ala2070Val	p.A2070V	ENST00000263388	NM_000435.2	2070	gCg/gTg	33/33	0.183891559959272	4	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	2	0.289703671266798	4		472	490	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506374	120506378	+	frameshift_variant	Frame_Shift_Del	DEL	GGCAA	GGCAA	-	novel	NA	P-0004892-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	129	473	0	ENST00000256646.2:c.1734_1738del	p.Cys579ProfsTer9	p.C579Pfs*9	ENST00000256646	NM_024408.3	578	ccTTGCCac/ccac	11/34	0.246233278584744	4	FACETS	0.884	0.803	0.968	0.884	0.803	0.968	CLONAL	2	TRUE	2	0.289703671266798	4		473	650	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021821	69021821	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004892-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	65	534	0	ENST00000288368.4:c.3109C>G	p.Leu1037Val	p.L1037V	ENST00000288368	NM_024870.2	1037	Ctg/Gtg	25/40	0.246233278584744	4	FACETS	0.821	0.711	0.94	0.41	0.355	0.47	CLONAL	1	TRUE	2	0.289703671266798	4		534	705	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878994	151878995	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004892-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	149	463	0	ENST00000262189.6:c.5950dup	p.Leu1984ProfsTer22	p.L1984Pfs*22	ENST00000262189	NM_170606.2	1984	cta/cCta	36/59	0.200240243004531	5	FACETS	1	0.921	1	0.671	0.614	0.731	CLONAL	2	TRUE	2	0.289703671266798	5		463	733	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879016	151879016	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004892-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	151	464	0	ENST00000262189.6:c.5929C>A	p.Gln1977Lys	p.Q1977K	ENST00000262189	NM_170606.2	1977	Caa/Aaa	36/59	0.200240243004531	5	FACETS	1	0.934	1	0.682	0.624	0.742	CLONAL	2	TRUE	2	0.289703671266798	5		464	731	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372103	55372103	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004892-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	32	308	1	ENST00000297316.4:c.793C>T	p.Pro265Ser	p.P265S	ENST00000297316	NM_022454.3	265	Cct/Tct	2/2	0.246233278584744	4	FACETS	0.661	0.536	0.802	0.331	0.268	0.401	SUBCLONAL	1	TRUE	2	0.289703671266798	4		309	431	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005631-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	318	378	0	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	0.682523935213901	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.682523935213901	2		378	460	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0005631-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	217	415	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.682523935213901	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.682523935213901	1		415	416	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430906	181430906	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005631-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	356	829	0	ENST00000325404.1:c.758C>T	p.Pro253Leu	p.P253L	ENST00000325404	NM_003106.3	253	cCt/cTt	1/1	0.682523935213901	2	FACETS	0.941	0.892	0.99	0.47	0.446	0.495	CLONAL	1	TRUE	0	0.682523935213901	2		829	1109	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923712	131923712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005631-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	99	259	0	ENST00000265335.6:c.982G>A	p.Glu328Lys	p.E328K	ENST00000265335		328	Gaa/Aaa	7/25	0.349753261484824	3	FACETS	0.869	0.78	0.962	0.434	0.39	0.481	INDETERMINATE	1	TRUE	1	0.682523935213901	3		259	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577586	7577586	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587781589	NA	P-0005631-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	412	612	0	ENST00000269305.4:c.695T>G	p.Ile232Ser	p.I232S	ENST00000269305	NM_001126112.2	232	aTc/aGc	7/11	0.645169537069769	2	FACETS	0.902	0.869	0.935	0.902	0.869	0.935	CLONAL	2	TRUE	0	0.682523935213901	2		612	669	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142570	119142570	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005631-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	83	358	0	ENST00000264033.4:c.569G>A	p.Trp190Ter	p.W190*	ENST00000264033	NM_005188.3	190	tGg/tAg	3/16	0.382519620484448	3	FACETS	0.514	0.453	0.578	0.257	0.226	0.289	INDETERMINATE	1	TRUE	1	0.682523935213901	3		358	635	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0006671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	143	427	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.922	0.85	0.996	0.922	0.85	0.996	CLONAL	1	TRUE	1	0.78157181998134	2		427	397	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0006671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	330	378	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.78157181998134	2		378	838	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0006671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	204	297	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	0.767922346829061	3	FACETS	0.942	0.876	1	0.471	0.438	0.505	CLONAL	1	TRUE	1	0.78157181998134	3		297	771	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0006671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	208	427	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.853	0.795	0.912	0.853	0.795	0.912	CLONAL	1	TRUE	1	0.726984655102815	2		427	671	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0006671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	139	378	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.726984655102815	2		378	333	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0006671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	94	297	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	0.700852631534266	3	FACETS	0.715	0.639	0.796	0.358	0.319	0.398	SUBCLONAL	1	TRUE	1	0.726984655102815	3		297	493	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0006671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	128	558	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.700852631534266	3	FACETS	0.936	0.853	1	0.468	0.426	0.511	CLONAL	1	TRUE	1	0.726984655102815	3		558	513	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0007901-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	126	778	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	FALSE	NA	0.16474311935204	2		779	1162	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0007901-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	88	716	1	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	FALSE	1	0.16474311935204	2		717	1067	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68290313	68290313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768576952	NA	P-0007901-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	54	541	0	ENST00000487270.1:c.53G>A	p.Arg18His	p.R18H	ENST00000487270	NM_133509.3	18	cGt/cAt	2/11	1	2	FACETS	0.833	0.71	0.968	0.833	0.71	0.968	CLONAL	1	FALSE	1	0.16474311935204	2		541	787	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115904	8115904	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1271005545	NA	P-0007901-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	48	600	0	ENST00000346208.3:c.1250C>A	p.Thr417Asn	p.T417N	ENST00000346208		417	aCc/aAc	6/6	1	2	FACETS	0.703	0.592	0.825	0.703	0.592	0.825	SUBCLONAL	1	FALSE	1	0.16474311935204	2		600	829	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17116982	17116982	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007901-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	330	610	0	ENST00000285071.4:c.1727A>G	p.Glu576Gly	p.E576G	ENST00000285071	NM_144997.5	576	gAg/gGg	14/14	0.16474311935204	5	FACETS	0.912	0.862	0.962			1	CLONAL	5	FALSE	NA	0.16474311935204	5		610	1096	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008359-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	40	612	0	ENST00000269305.4:c.313G>T	p.Gly105Cys	p.G105C	ENST00000269305	NM_001126112.2	105	Ggc/Tgc	4/11	0.164793681881462	2	FACETS	0.971	0.806	1	0.485	0.403	0.577	CLONAL	1	TRUE	0	0.164793681881462	2		612	500	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645983	215645984	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1559425604	NA	P-0008359-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	61	473	0	ENST00000260947.4:c.614dup	p.Gln206AlafsTer8	p.Q206Afs*8	ENST00000260947	NM_000465.2	205	aag/aaAg	4/11	0.164793681881462	3	FACETS	0.989	0.857	1	0.989	0.857	1	CLONAL	2	TRUE	1	0.164793681881462	3		473	405	SUCCESS
REL	5966	MSKCC	GRCh37	2	61121613	61121613	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008359-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	110	333	0	ENST00000295025.8:c.235T>G	p.Leu79Val	p.L79V	ENST00000295025	NM_002908.2	79	Tta/Gta	3/11	0.164793681881462	5	FACETS	1	0.927	1	1	0.927	1	CLONAL	4	TRUE	1	0.164793681881462	5		333	405	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141140	55141140	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008359-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	50	301	0	ENST00000257290.5:c.1786G>C	p.Gly596Arg	p.G596R	ENST00000257290	NM_006206.4	596	Ggt/Cgt	12/23	0.164793681881462	6	FACETS	0.965	0.821	1	0.483	0.41	0.562	CLONAL	2	TRUE	2	0.164793681881462	6		301	418	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146588	55146588	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0008359-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	110	466	1	ENST00000257290.5:c.2262T>A	p.Tyr754Ter	p.Y754*	ENST00000257290	NM_006206.4	754	taT/taA	16/23	0.164793681881462	6	FACETS	0.996	0.897	1	0.747	0.673	0.825	CLONAL	3	TRUE	2	0.164793681881462	6		467	594	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294330	1294330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388678536	NA	P-0008359-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	24	395	1	ENST00000310581.5:c.671G>A	p.Arg224His	p.R224H	ENST00000310581	NM_198253.2	224	cGc/cAc	2/16	0.164793681881462	3	FACETS	0.881	0.69	1	0.44	0.345	0.55	CLONAL	1	TRUE	1	0.164793681881462	3		396	358	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495610	56495610	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008359-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	63	434	0	ENST00000267101.3:c.3800G>T	p.Arg1267Leu	p.R1267L	ENST00000267101	NM_001982.3	1267	cGa/cTa	28/28	0.164793681881462	3	FACETS	0.995	0.863	1	0.995	0.863	1	CLONAL	2	TRUE	1	0.164793681881462	3		434	416	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478132	99478132	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008359-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	46	428	0	ENST00000268035.6:c.3036G>A	p.Met1012Ile	p.M1012I	ENST00000268035	NM_000875.3	1012	atG/atA	16/21	0.164793681881462	3	FACETS	0.757	0.639	0.887	0.757	0.639	0.887	SUBCLONAL	2	TRUE	1	0.164793681881462	3		428	399	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73334738	73334740	+	inframe_deletion	In_Frame_Del	DEL	TAA	TAA	-	novel	NA	P-0008359-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	54	326	0	ENST00000377767.4:c.2720_2722del	p.Val907_Lys908delinsGlu	p.V907_K908delinsE	ENST00000377767	NM_014953.3	907	gTTAaa/gaa	20/21	0.158465083947823	2	FACETS	0.91	0.781	1	0.91	0.781	1	CLONAL	2	TRUE	0	0.164793681881462	2		326	360	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509620	29509621	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008359-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	87	517	0	ENST00000356175.3:c.827dup	p.Leu276PhefsTer15	p.L276Ffs*15	ENST00000356175	NM_000267.3	275	-/T	8/57	0.164793681881462	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.164793681881462	2		517	474	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946948	71946948	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008359-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	38	672	1	ENST00000298229.2:c.2797G>T	p.Glu933Ter	p.E933*	ENST00000298229	NM_001567.3	933	Gaa/Taa	25/28	0.164793681881462	4	FACETS	0.785	0.648	0.94	0.393	0.324	0.47	CLONAL	1	TRUE	2	0.164793681881462	4		673	684	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59886112	59886113	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0008359-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	40	339	1	ENST00000259008.2:c.633dup	p.Gly212TrpfsTer5	p.G212Wfs*5	ENST00000259008	NM_032043.2	211	-/T	7/20	0.164793681881462	5	FACETS	0.814	0.678	0.965	0.543	0.452	0.643	CLONAL	2	TRUE	2	0.164793681881462	5		340	372	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69000024	69000024	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008359-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	100	533	0	ENST00000288368.4:c.2093T>C	p.Val698Ala	p.V698A	ENST00000288368	NM_024870.2	698	gTt/gCt	19/40	NA	2	FACETS	0.855	0.768	0.947			1	INDETERMINATE	3	TRUE	NA	0.164793681881462	2		533	473	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845757	68845757	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587780784	NA	P-0008398-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	218	348	1	ENST00000261769.5:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000261769	NM_004360.3	335	Cga/Tga	7/16	0.718548429657276	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.718548429657276	1		349	379	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259368	89259368	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008398-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	335	590	0	ENST00000336596.2:c.512T>C	p.Val171Ala	p.V171A	ENST00000336596	NM_005233.5	171	gTa/gCa	3/17	1	2	FACETS	0.994	0.943	1	0.994	0.943	1	CLONAL	1	TRUE	1	0.718548429657276	2		590	938	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873518	151873518	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008398-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	348	610	0	ENST00000262189.6:c.9020del	p.Gly3007GlufsTer25	p.G3007Efs*25	ENST00000262189	NM_170606.2	3007	gGa/ga	38/59	1	2	FACETS	0.896	0.849	0.944	0.896	0.849	0.944	CLONAL	1	TRUE	1	0.718548429657276	2		610	1081	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780677	56780677	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060502588	NA	P-0008398-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	323	554	0	ENST00000337432.4:c.692C>T	p.Ser231Leu	p.S231L	ENST00000337432	NM_058216.2	231	tCa/tTa	4/9	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.718548429657276	2		554	835	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878356	151878356	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008398-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	365	559	1	ENST00000262189.6:c.6589C>T	p.Gln2197Ter	p.Q2197*	ENST00000262189	NM_170606.2	2197	Cag/Tag	36/59	1	2	FACETS	0.941	0.893	0.989	0.941	0.893	0.989	CLONAL	1	TRUE	1	0.718548429657276	2		560	1080	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878785	151878785	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008398-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	251	457	0	ENST00000262189.6:c.6160C>G	p.Gln2054Glu	p.Q2054E	ENST00000262189	NM_170606.2	2054	Cag/Gag	36/59	1	2	FACETS	0.908	0.853	0.965	0.908	0.853	0.965	CLONAL	1	TRUE	1	0.718548429657276	2		457	769	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891702	28891702	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008398-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	344	640	0	ENST00000282397.4:c.3319G>A	p.Glu1107Lys	p.E1107K	ENST00000282397	NM_002019.4	1107	Gag/Aag	25/30	0.718548429657276	1	FACETS	0.988	0.945	1	0.988	0.945	1	CLONAL	1	TRUE	0	0.718548429657276	1		640	621	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76949427	76949427	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0008398-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	144	453	0	ENST00000373344.5:c.371-1G>A		p.X124_splice	ENST00000373344	NM_000489.3	124			1	2	FACETS	0.816	0.75	0.885	0.816	0.75	0.885	CLONAL	1	TRUE	1	0.718548429657276	2		453	491	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92354977	92354977	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	71	288	0	ENST00000265734.4:c.500C>T	p.Ala167Val	p.A167V	ENST00000265734	NM_001259.6	167	gCc/gTc	4/8	NA	2	FACETS	0.195	0.169	0.223			1	INDETERMINATE	1	TRUE	NA	0.888137758036614	2		288	820	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660508	227660508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	31	189	1	ENST00000305123.5:c.2947C>T	p.Pro983Ser	p.P983S	ENST00000305123	NM_005544.2	983	Ccc/Tcc	1/2	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.11	2		190	438	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200001	128200001	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	68	428	0	ENST00000341105.2:c.1304G>T	p.Gly435Val	p.G435V	ENST00000341105	NM_032638.4	435	gGa/gTa	6/6	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.11	2		428	1061	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542642	187542642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	76	566	0	ENST00000441802.2:c.5098G>A	p.Glu1700Lys	p.E1700K	ENST00000441802	NM_005245.3	1700	Gaa/Aaa	10/27	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.11	2		566	1269	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679544	86679544	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	35	293	0	ENST00000274376.6:c.2705T>C	p.Leu902Pro	p.L902P	ENST00000274376	NM_002890.2	902	cTt/cCt	21/25	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.11	2		293	603	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020734	26020734	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1781	119	817	0	ENST00000357647.3:c.17A>T	p.Gln6Leu	p.Q6L	ENST00000357647	NM_003529.2	6	cAa/cTa	1/1	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.11	2		817	1900	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485234	8485234	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	60	458	0	ENST00000356435.5:c.3146C>A	p.Pro1049His	p.P1049H	ENST00000356435		1049	cCt/cAt	18/35	1	2	FACETS	0.963	0.827	1	0.963	0.827	1	CLONAL	1	TRUE	1	0.11	2		458	1133	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443490	49443490	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	55	301	1	ENST00000301067.7:c.3881C>A	p.Ser1294Tyr	p.S1294Y	ENST00000301067	NM_003482.3	1294	tCc/tAc	11/54	0.149373251680099	2	FACETS	1	0.944	1	0.613	0.523	0.712	CLONAL	1	TRUE	0	0.11	2		302	816	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514499	103514499	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	40	259	0	ENST00000355739.4:c.1000G>T	p.Glu334Ter	p.E334*	ENST00000355739	NM_000123.3	334	Gag/Tag	8/15	1	2	FACETS	0.913	0.756	1	0.913	0.756	1	CLONAL	1	TRUE	1	0.11	2		259	797	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103520541	103520541	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs772219063	NA	P-0009110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	68	508	1	ENST00000355739.4:c.2612G>T	p.Cys871Phe	p.C871F	ENST00000355739	NM_000123.3	871	tGt/tTt	12/15	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.11	2		509	1224	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225398	2225398	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	57	390	0	ENST00000326181.6:c.1483G>T	p.Gly495Cys	p.G495C	ENST00000326181	NM_032271.2	495	Ggc/Tgc	16/21	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.11	2		390	853	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576853	7576853	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs11575996	NA	P-0009110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	126	370	0	ENST00000269305.4:c.993G>T	p.Gln331His	p.Q331H	ENST00000269305	NM_001126112.2	331	caG/caT	9/11	1	2	FACETS	1	0.93	1	1	0.99	1	CLONAL	2	TRUE	1	0.11	2		370	1106	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602340	10602340	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	90	483	0	ENST00000171111.5:c.1238G>A	p.Arg413His	p.R413H	ENST00000171111	NM_203500.1	413	cGt/cAt	3/6	1	2	FACETS	0.81	0.717	0.91	1	0.981	1	CLONAL	2	TRUE	1	0.11	2		483	1010	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121151	11121151	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	86	525	0	ENST00000358026.2:c.2218G>T	p.Glu740Ter	p.E740*	ENST00000358026	NM_001128849.1	740	Gag/Tag	15/36	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.11	2		525	1239	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909559	50909559	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1513	104	608	0	ENST00000440232.2:c.1363G>T	p.Val455Leu	p.V455L	ENST00000440232	NM_002691.3	455	Gtg/Ttg	11/27	0.149373251680099	2	FACETS	1	0.961	1	0.585	0.521	0.653	CLONAL	1	TRUE	0	0.11	2		608	1617	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739036	40739036	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	48	333	0	ENST00000373198.4:c.3248G>C	p.Gly1083Ala	p.G1083A	ENST00000373198	NM_133170.3	1083	gGc/gCc	24/32	1	2	FACETS	0.94	0.792	1	0.94	0.792	1	CLONAL	1	TRUE	1	0.11	2		333	928	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295810	212295810	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	79	392	0	ENST00000342788.4:c.2503del	p.Glu835LysfsTer16	p.E835Kfs*16	ENST00000342788	NM_005235.2	835	Gaa/aa	21/28	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.11	2		392	1083	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223028	41223029	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0009110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1503	151	611	0	ENST00000357654.3:c.4902_4903delinsTT	p.Arg1634_Glu1635delinsSerTer	p.R1634_E1635delinsS*	ENST00000357654	NM_007294.3	1634	agGGag/agTTag	15/23	1	2	FACETS	0.83	0.756	0.908	1	0.989	1	CLONAL	2	TRUE	1	0.11	2		611	1654	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911579	134911579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs959853730	NA	P-0009654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1228	148	550	0	ENST00000398015.3:c.2044C>T	p.Arg682Cys	p.R682C	ENST00000398015	NM_004441.4	682	Cgc/Tgc	11/16	0.504391479584584	9	FACETS	1	0.974	1	0.197	0.179	0.216	CLONAL	1	TRUE	3	0.504391479584584	9		550	1376	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054366	13054366	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs748221094	NA	P-0009654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	256	495	0	ENST00000316448.5:c.976A>G	p.Ile326Val	p.I326V	ENST00000316448	NM_004343.3	326	Atc/Gtc	8/9	0.4943591192757	4	FACETS	0.958	0.9	1	0.958	0.9	1	CLONAL	2	TRUE	2	0.504391479584584	4		495	797	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910455	32910455	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555282375	NA	P-0009654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	124	375	0	ENST00000380152.3:c.1964del	p.Pro655GlnfsTer5	p.P655Qfs*5	ENST00000380152		655	Cca/ca	11/27	0.504391479584584	2	FACETS	0.866	0.797	0.935	0.866	0.797	0.935	CLONAL	2	TRUE	0	0.504391479584584	2		375	284	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46603721	46603721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	294	654	1	ENST00000263734.3:c.1078G>A	p.Glu360Lys	p.E360K	ENST00000263734	NM_001430.4	360	Gaa/Aaa	9/16	0.504391479584584	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.504391479584584	3		655	698	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910456	32910477	+	protein_altering_variant	In_Frame_Del	DEL	CAACTTTGTCCTTAACTAGCTC	CAACTTTGTCCTTAACTAGCTC	AACTTTGTTG	novel	NA	P-0009654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	44	385	1	ENST00000380152.3:c.1964_1985delinsAACTTTGTTG	p.Pro655_Ser662delinsGlnLeuCysCys	p.P655_S662delinsQLCC	ENST00000380152		655	cCAACTTTGTCCTTAACTAGCTCt/cAACTTTGTTGt	11/27	0.504391479584584	2	FACETS	0.602	0.507	0.705	0.301	0.253	0.353	SUBCLONAL	1	TRUE	0	0.504391479584584	2		386	290	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50818322	50818322	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	109	364	0	ENST00000398568.2:c.1900C>G	p.Gln634Glu	p.Q634E	ENST00000398568	NM_001042412.1	634	Caa/Gaa	11/18	0.4943591192757	4	FACETS	0.847	0.767	0.929	0.847	0.767	0.929	CLONAL	2	TRUE	2	0.504391479584584	4		364	384	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40461480	40461480	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	158	815	0	ENST00000345506.4:c.2200C>G	p.Pro734Ala	p.P734A	ENST00000345506	NM_003152.3	734	Ccc/Gcc	19/20	0.504391479584584	3	FACETS	0.916	0.84	0.996	0.458	0.42	0.498	CLONAL	1	TRUE	1	0.504391479584584	3		815	856	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589573	67589602	+	inframe_deletion	In_Frame_Del	DEL	GGGAAAAAATTACATGAATATAACACTCAG	GGGAAAAAATTACATGAATATAACACTCAG	-	novel	NA	P-0009654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	27	163	0	ENST00000274335.5:c.1336_1365del	p.Gly446_Gln455del	p.G446_Q455del	ENST00000274335		446	GGGAAAAAATTACATGAATATAACACTCAG/-	10/15	0.434500775049241	4	FACETS	0.797	0.639	0.976	0.399	0.319	0.488	CLONAL	1	TRUE	2	0.504391479584584	4		163	202	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800159	32800159	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	73	408	0	ENST00000374899.4:c.1223G>C	p.Ser408Thr	p.S408T	ENST00000374899	NM_018833.2	408	aGc/aCc	7/12	0.4943591192757	4	FACETS	0.769	0.674	0.872	0.385	0.337	0.436	SUBCLONAL	1	TRUE	2	0.504391479584584	4		408	566	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933350	39933350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	227	429	0	ENST00000378444.4:c.1249G>A	p.Asp417Asn	p.D417N	ENST00000378444	NM_001123385.1	417	Gac/Aac	4/15	0.474673566438989	2	FACETS	1	0.992	1			1	CLONAL	1	TRUE	NA	0.504391479584584	2		429	640	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010331-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	159	609	4	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.847	0.776	0.921	0.847	0.776	0.921	CLONAL	1	TRUE	1	0.39041749863994	2		613	962	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010331-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	129	495	0	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	0.39041749863994	1	FACETS	0.897	0.816	0.981	0.897	0.816	0.981	CLONAL	1	TRUE	0	0.39041749863994	1		495	593	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719125	52719125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771769470	NA	P-0010331-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	157	641	1	ENST00000322088.6:c.901G>A	p.Ala301Thr	p.A301T	ENST00000322088	NM_014225.5	301	Gca/Aca	7/15	1	2	FACETS	0.766	0.701	0.834	0.766	0.701	0.834	SUBCLONAL	1	TRUE	1	0.39041749863994	2		642	1050	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0010331-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1226	219	734	1	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.776	0.72	0.835	0.776	0.72	0.835	SUBCLONAL	1	TRUE	1	0.39041749863994	2		735	1445	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204842	128204842	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs768767517	NA	P-0010331-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1300	242	960	7	ENST00000341105.2:c.599del	p.Gly200ValfsTer18	p.G200Vfs*18	ENST00000341105	NM_032638.4	200	gGt/gt	3/6	1	2	FACETS	0.804	0.749	0.861	0.804	0.749	0.861	CLONAL	1	TRUE	1	0.39041749863994	2		967	1542	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794422	242794422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758959367	NA	P-0010331-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	224	867	0	ENST00000334409.5:c.520G>A	p.Val174Met	p.V174M	ENST00000334409	NM_005018.2	174	Gtg/Atg	3/5	1	2	FACETS	0.86	0.799	0.924	0.86	0.799	0.924	CLONAL	1	TRUE	1	0.39041749863994	2		867	1334	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491390	18491390	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1377942847	NA	P-0010331-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	52	200	1	ENST00000266497.5:c.1309del	p.Ile437TyrfsTer5	p.I437Yfs*5	ENST00000266497		435	Aaa/aa	8/31	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.39041749863994	2		201	242	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118924	70118926	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0010331-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	222	773	0	ENST00000245479.2:c.499_501del	p.Lys167del	p.K167del	ENST00000245479	NM_000346.3	166	AAG/-	2/3	1	2	FACETS	0.877	0.814	0.942	0.877	0.814	0.942	CLONAL	1	TRUE	1	0.39041749863994	2		773	1297	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306930	65306930	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010331-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	124	406	0	ENST00000342505.4:c.2647G>T	p.Glu883Ter	p.E883*	ENST00000342505	NM_002227.2	883	Gag/Tag	19/25	0.39041749863994	1	FACETS	0.926	0.841	1	0.926	0.841	1	CLONAL	1	TRUE	0	0.39041749863994	1		406	552	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098755	47098755	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010331-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	217	680	0	ENST00000409792.3:c.6519G>A	p.Met2173Ile	p.M2173I	ENST00000409792	NM_014159.6	2173	atG/atA	15/21	0.39041749863994	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.39041749863994	1		680	888	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630275	187630275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010331-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	227	680	0	ENST00000441802.2:c.707G>A	p.Gly236Asp	p.G236D	ENST00000441802	NM_005245.3	236	gGc/gAc	2/27	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.39041749863994	2		680	1096	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760526	133760526	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010331-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1198	233	798	0	ENST00000318560.5:c.2849A>G	p.Gln950Arg	p.Q950R	ENST00000318560	NM_005157.4	950	cAg/cGg	11/11	1	2	FACETS	0.834	0.776	0.895	0.834	0.776	0.895	CLONAL	1	TRUE	1	0.39041749863994	2		798	1431	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829617	72829617	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010331-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	211	668	0	ENST00000268489.5:c.6964C>T	p.Arg2322Ter	p.R2322*	ENST00000268489	NM_006885.3	2322	Cga/Tga	9/10	1	2	FACETS	0.886	0.821	0.953	0.886	0.821	0.953	CLONAL	1	TRUE	1	0.39041749863994	2		668	1220	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579344	7579344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010331-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	172	694	0	ENST00000269305.4:c.343C>T	p.His115Tyr	p.H115Y	ENST00000269305	NM_001126112.2	115	Cat/Tat	4/11	1	2	FACETS	0.775	0.712	0.841	0.775	0.712	0.841	SUBCLONAL	1	TRUE	1	0.39041749863994	2		694	1137	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121082	11121082	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010331-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	212	733	0	ENST00000358026.2:c.2149G>T	p.Glu717Ter	p.E717*	ENST00000358026	NM_001128849.1	717	Gaa/Taa	15/36	1	2	FACETS	0.877	0.813	0.943	0.877	0.813	0.943	CLONAL	1	TRUE	1	0.39041749863994	2		733	1239	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366384	15366384	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010331-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	130	465	0	ENST00000263377.2:c.1771A>G	p.Met591Val	p.M591V	ENST00000263377	NM_058243.2	591	Atg/Gtg	10/20	1	2	FACETS	0.884	0.803	0.97	0.884	0.803	0.97	CLONAL	1	TRUE	1	0.39041749863994	2		465	753	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52621443	52621445	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0010331-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	86	477	0	ENST00000394830.3:c.2972_2974del	p.Glu991del	p.E991del	ENST00000394830	NM_018313.4	991	gAAGtt/gtt	20/30	0.39041749863994	1	FACETS	0.844	0.751	0.943	0.844	0.751	0.943	CLONAL	1	TRUE	0	0.39041749863994	1		477	420	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213600	36213600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755335733	NA	P-0010331-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1330	258	1022	0	ENST00000222270.7:c.2702G>A	p.Arg901Gln	p.R901Q	ENST00000222270	NM_014727.1	901	cGg/cAg	5/37	1	2	FACETS	0.832	0.777	0.89	0.832	0.777	0.89	CLONAL	1	TRUE	1	0.39041749863994	2		1022	1588	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0010331-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1475	267	819	0	ENST00000220592.5:c.1805_1806dup	p.Ala603ProfsTer93	p.A603Pfs*93	ENST00000220592	NM_012154.3	602	-/CC	14/19	0.331373311292389	3	FACETS	0.938	0.877	1	0.469	0.438	0.501	CLONAL	1	TRUE	1	0.39041749863994	3		819	1742	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073615	8073616	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0010331-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	92	427	0	ENST00000377482.5:c.1043dup	p.Thr349AspfsTer7	p.T349Dfs*7	ENST00000377482	NM_018948.3	348	ccg/ccCg	4/4	0.39041749863994	1	FACETS	0.561	0.499	0.628	0.561	0.499	0.628	SUBCLONAL	1	TRUE	0	0.39041749863994	1		427	676	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562999	21562999	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010331-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	197	788	1	ENST00000382592.4:c.920del	p.Pro307LeufsTer126	p.P307Lfs*126	ENST00000382592	NM_014572.2	307	cCt/ct	4/8	0.39041749863994	1	FACETS	0.681	0.629	0.735	0.681	0.629	0.735	SUBCLONAL	1	TRUE	0	0.39041749863994	1		789	1193	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134897	41134897	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010331-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	154	493	0	ENST00000379561.5:c.731G>A	p.Gly244Asp	p.G244D	ENST00000379561	NM_002015.3	244	gGc/gAc	2/3	0.39041749863994	1	FACETS	0.948	0.87	1	0.948	0.87	1	CLONAL	1	TRUE	0	0.39041749863994	1		493	670	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274088	10274088	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750050760	NA	P-0010331-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	207	711	0	ENST00000330684.3:c.181G>A	p.Ala61Thr	p.A61T	ENST00000330684	NM_001134407.1	61	Gcg/Acg	2/13	1	2	FACETS	0.866	0.803	0.933	0.866	0.803	0.933	CLONAL	1	TRUE	1	0.39041749863994	2		711	1224	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984213	7984213	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1280726065	NA	P-0010331-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	126	574	0	ENST00000319144.4:c.516del	p.Asn173ThrfsTer24	p.N173Tfs*24	ENST00000319144	NM_001139.2	172	ccC/cc	4/15	1	2	FACETS	0.6	0.542	0.661	0.6	0.542	0.661	SUBCLONAL	1	TRUE	1	0.39041749863994	2		574	1076	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55339537	55339537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010331-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	131	569	0	ENST00000284073.2:c.296G>A	p.Arg99His	p.R99H	ENST00000284073	NM_138962.2	99	cGt/cAt	5/14	1	2	FACETS	0.881	0.8	0.966	0.881	0.8	0.966	CLONAL	1	TRUE	1	0.39041749863994	2		569	762	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207626	2207626	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010331-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	230	683	0	ENST00000398665.3:c.910T>C	p.Ser304Pro	p.S304P	ENST00000398665	NM_032482.2	304	Tcg/Ccg	11/28	1	2	FACETS	0.891	0.828	0.955	0.891	0.828	0.955	CLONAL	1	TRUE	1	0.39041749863994	2		683	1323	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228593	36228594	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010331-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1267	254	824	0	ENST00000222270.7:c.7607_7608insT	p.Glu2536AspfsTer6	p.E2536Dfs*6	ENST00000222270	NM_014727.1	2536	gag/gaTg	34/37	1	2	FACETS	0.855	0.798	0.915	0.855	0.798	0.915	CLONAL	1	TRUE	1	0.39041749863994	2		824	1521	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334983	81334983	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010331-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	51	402	0	ENST00000222390.5:c.1844A>G	p.Tyr615Cys	p.Y615C	ENST00000222390	NM_000601.4	615	tAt/tGt	16/18	1	2	FACETS	0.636	0.541	0.739	0.636	0.541	0.739	SUBCLONAL	1	TRUE	1	0.39041749863994	2		402	411	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864717	68864717	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010331-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	173	564	1	ENST00000288368.4:c.88G>A	p.Glu30Lys	p.E30K	ENST00000288368	NM_024870.2	30	Gag/Aag	1/40	0.39041749863994	1	FACETS	0.884	0.815	0.956	0.884	0.815	0.956	CLONAL	1	TRUE	0	0.39041749863994	1		565	807	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293522	137293522	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010331-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1536	247	1057	0	ENST00000481739.1:c.73C>T	p.Arg25Ter	p.R25*	ENST00000481739	NM_002957.4	25	Cga/Tga	2/10	1	2	FACETS	0.71	0.661	0.76	0.71	0.661	0.76	SUBCLONAL	1	TRUE	1	0.39041749863994	2		1057	1783	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59924505	59924505	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs4988347	NA	P-0010827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	80	426	0	ENST00000259008.2:c.584T>C	p.Leu195Pro	p.L195P	ENST00000259008	NM_032043.2	195	cTc/cCc	6/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.965457918309013	2		426	151	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0010827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	1383	720	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	NA	2	FACETS	1	0.999	1			1	INDETERMINATE	2	TRUE	NA	0.965457918309013	2		720	1401	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729601	41729601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	400	504	1	ENST00000242208.4:c.928C>T	p.Arg310Trp	p.R310W	ENST00000242208	NM_002192.2	310	Cgg/Tgg	3/3	0.965457918309013	2	FACETS	1	0.981	1	0.521	0.499	0.543	CLONAL	1	TRUE	0	0.965457918309013	2		505	795	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260837	16260837	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	396	466	1	ENST00000375759.3:c.8102C>T	p.Thr2701Met	p.T2701M	ENST00000375759	NM_015001.2	2701	aCg/aTg	11/15	0.965457918309013	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.965457918309013	1		467	411	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276958	123276958	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	121	242	0	ENST00000358487.5:c.959C>T	p.Thr320Met	p.T320M	ENST00000358487	NM_000141.4	320	aCg/aTg	8/18	NA	2	FACETS	0.932	0.858	1			1	INDETERMINATE	1	TRUE	NA	0.965457918309013	2		242	269	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057651	27057651	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	297	460	0	ENST00000324856.7:c.1360del	p.Tyr454MetfsTer165	p.Y454Mfs*165	ENST00000324856	NM_006015.4	453	ccT/cc	3/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.965457918309013	2		460	590	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604680	43604680	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0010827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	391	437	0	ENST00000355710.3:c.1263+2T>G		p.X421_splice	ENST00000355710	NM_020975.4	421			0.965457918309013	3	FACETS	0.833	0.799	0.867	0.555	0.532	0.578	CLONAL	2	TRUE	0	0.965457918309013	3		437	721	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375246	118375246	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	164	345	0	ENST00000534358.1:c.8639T>G	p.Leu2880Arg	p.L2880R	ENST00000534358	NM_005933.3	2880	cTt/cGt	27/36	0.668661922357169	5	FACETS	0.773	0.714	0.834	0.386	0.357	0.417	SUBCLONAL	2	TRUE	1	0.965457918309013	5		345	538	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155995	119155995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1273	1049	631	0	ENST00000264033.4:c.1660G>A	p.Val554Ile	p.V554I	ENST00000264033	NM_005188.3	554	Gtt/Att	11/16	0.668661922357169	5	FACETS	1	0.996	1	0.573	0.557	0.589	CLONAL	2	TRUE	1	0.965457918309013	5		631	2322	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562723	21562723	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1536	429	507	2	ENST00000382592.4:c.1196A>G	p.Asp399Gly	p.D399G	ENST00000382592	NM_014572.2	399	gAc/gGc	4/8	0.811808606193177	4	FACETS	0.889	0.844	0.935	0.444	0.422	0.468	CLONAL	1	TRUE	2	0.965457918309013	4		509	1965	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943620	9943620	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	354	513	0	ENST00000330684.3:c.1321A>G	p.Lys441Glu	p.K441E	ENST00000330684	NM_001134407.1	441	Aaa/Gaa	5/13	0.890049347831343	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.965457918309013	1		513	371	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100935	41100935	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	378	562	0	ENST00000373198.4:c.1421A>T	p.Glu474Val	p.E474V	ENST00000373198	NM_133170.3	474	gAg/gTg	8/32	0.965457918309013	2	FACETS	0.835	0.795	0.875	0.417	0.397	0.438	CLONAL	1	TRUE	0	0.965457918309013	2		562	938	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441391	149441391	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs781108577	NA	P-0010827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	438	626	0	ENST00000286301.3:c.1648T>A	p.Trp550Arg	p.W550R	ENST00000286301	NM_005211.3	550	Tgg/Agg	12/22	0.958984282323123	2	FACETS	0.938	0.899	0.978	0.469	0.449	0.489	CLONAL	1	TRUE	0	0.965457918309013	2		626	967	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26046049	26046049	+	stop_lost	Nonstop_Mutation	SNP	A	A	C	novel	NA	P-0010827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	89	226	0	ENST00000540144.1:c.411A>C	p.Ter137TyrextTer8	p.*137Yext*8	ENST00000540144	NM_003531.2	137	taA/taC	1/1	1	2	FACETS	0.926	0.841	1	0.926	0.841	1	CLONAL	1	TRUE	1	0.965457918309013	2		226	199	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553624	106553624	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	204	331	1	ENST00000369096.4:c.1589A>T	p.Gln530Leu	p.Q530L	ENST00000369096	NM_001198.3	530	cAg/cTg	5/7	1	2	FACETS	0.974	0.915	1	0.974	0.915	1	CLONAL	1	TRUE	1	0.965457918309013	2		332	434	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873795	151873795	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	220	528	0	ENST00000262189.6:c.8743A>C	p.Thr2915Pro	p.T2915P	ENST00000262189	NM_170606.2	2915	Act/Cct	38/59	0.965457918309013	2	FACETS	1	0.944	1	0.501	0.472	0.53	CLONAL	1	TRUE	0	0.965457918309013	2		528	455	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869688	117869688	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	70	364	0	ENST00000297338.2:c.506A>C	p.Glu169Ala	p.E169A	ENST00000297338	NM_006265.2	169	gAg/gCg	6/14	0.953821828084788	4	FACETS	0.826	0.725	0.934	0.275	0.241	0.312	CLONAL	1	TRUE	1	0.965457918309013	4		364	345	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010930-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	88	554	0	ENST00000346208.3:c.1220_1221insA	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcAg	6/6	0.173446546371865	2	FACETS	0.963	0.851	1	0.481	0.425	0.541	CLONAL	1	TRUE	0	0.195568641744614	2		554	935	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957540	175957540	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010930-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	47	408	0	ENST00000367669.3:c.1856A>G	p.Asp619Gly	p.D619G	ENST00000367669	NM_022457.5	619	gAc/gGc	17/20	0.195568641744614	6	FACETS	0.802	0.674	0.943	0.16	0.134	0.189	CLONAL	1	TRUE	1	0.195568641744614	6		408	834	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281298	142281298	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012818-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	179	515	0	ENST00000350721.4:c.946G>C	p.Val316Leu	p.V316L	ENST00000350721	NM_001184.3	316	Gtc/Ctc	4/47	0.763210683636613	4	FACETS	0.757	0.703	0.813	0.757	0.703	0.813	SUBCLONAL	2	FALSE	2	0.763210683636613	4		515	546	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038234	30038236	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	AGG	AGG	TGCAGTAGAGCAC	novel	NA	P-0012818-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	85	745	0	ENST00000338641.4:c.407_409delinsTGCAGTAGAGCAC	p.Glu136ValfsTer3	p.E136Vfs*3	ENST00000338641	NM_000268.3	136	gAGGct/gTGCAGTAGAGCACct	4/16	0.457446618824998	3	FACETS	0.789	0.702	0.881	0.263	0.234	0.294	INDETERMINATE	1	FALSE	0	0.763210683636613	3		745	390	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0013016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	302	814	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.557853468881711	4	FACETS	1	0.989	1	0.397	0.374	0.421	CLONAL	1	FALSE	1	0.711203000616024	4		814	1220	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255409	16255409	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	70	663	0	ENST00000375759.3:c.2674G>C	p.Asp892His	p.D892H	ENST00000375759	NM_015001.2	892	Gac/Cac	11/15	0.133626148908207	4	FACETS	0.373	0.324	0.426	0.187	0.162	0.213	INDETERMINATE	1	FALSE	2	0.711203000616024	4		663	903	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705331	43705331	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750512252	NA	P-0013016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	1030	723	1	ENST00000382044.4:c.5291G>A	p.Ser1764Asn	p.S1764N	ENST00000382044	NM_001141980.1	1764	aGt/aAt	24/28	0.715584777194584	4	FACETS	1	0.997	1	1	0.997	1	CLONAL	4	FALSE	0	0.711203000616024	4		724	1182	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577595	7577598	+	frameshift_variant	Frame_Shift_Del	DEL	CAGT	CAGT	-	novel	NA	P-0013016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	1020	623	0	ENST00000269305.4:c.683_686del	p.Asp228ValfsTer18	p.D228Vfs*18	ENST00000269305	NM_001126112.2	228	gACTGt/gt	7/11	0.715584777194584	4	FACETS	1	0.997	1	1	0.997	1	CLONAL	4	FALSE	0	0.711203000616024	4		623	1166	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965425	15965425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1286197692	NA	P-0013016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	49	429	0	ENST00000268712.3:c.5381G>A	p.Arg1794Gln	p.R1794Q	ENST00000268712	NM_006311.3	1794	cGa/cAa	36/46	0.715584777194584	5	FACETS	0.342	0.288	0.401	0.085	0.072	0.101	SUBCLONAL	1	FALSE	1	0.711203000616024	5		429	833	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679417	29679417	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs779737221	NA	P-0013016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	232	535	0	ENST00000356175.3:c.7537A>G	p.Thr2513Ala	p.T2513A	ENST00000356175	NM_000267.3	2513	Act/Gct	50/57	0.715584777194584	5	FACETS	1	0.992	1	0.375	0.35	0.401	CLONAL	1	FALSE	1	0.711203000616024	5		535	899	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109315791	109315791	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	204	596	0	ENST00000436639.2:c.994G>T	p.Val332Phe	p.V332F	ENST00000436639	NM_014454.2	332	Gtt/Ttt	6/10	0.412265831340639	4	FACETS	1	0.968	1	0.269	0.249	0.289	INDETERMINATE	1	FALSE	0	0.711203000616024	4		596	913	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997764	149997764	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	651	548	0	ENST00000253339.5:c.2703G>T	p.Gln901His	p.Q901H	ENST00000253339		901	caG/caT	5/7	0.412265831340639	4	FACETS	1	0.997	1	0.872	0.85	0.893	INDETERMINATE	3	FALSE	0	0.711203000616024	4		548	898	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38148019	38148019	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	69	645	0	ENST00000317025.8:c.3092C>G	p.Thr1031Ser	p.T1031S	ENST00000317025	NM_023034.1	1031	aCt/aGt	17/24	0.715584777194584	3	FACETS	0.27	0.234	0.309	0.09	0.078	0.103	SUBCLONAL	1	FALSE	0	0.711203000616024	3		645	974	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981798	70981798	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1460	105	723	1	ENST00000276594.2:c.298C>T	p.Pro100Ser	p.P100S	ENST00000276594	NM_024504.3	100	Ccg/Tcg	2/8	0.715584777194584	5	FACETS	0.39	0.348	0.435	0.097	0.087	0.109	SUBCLONAL	1	FALSE	1	0.711203000616024	5		724	1565	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760961	133760961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1003322722	NA	P-0013036-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	197	817	1	ENST00000318560.5:c.3284G>A	p.Arg1095Gln	p.R1095Q	ENST00000318560	NM_005157.4	1095	cGg/cAg	11/11	0.326769405166208	4	FACETS	0.827	0.767	0.889	0.827	0.767	0.889	CLONAL	2	TRUE	2	0.403441599055111	4		818	829	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717733	89717733	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1554825235	NA	P-0013036-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	70	531	0	ENST00000371953.3:c.758T>A	p.Ile253Asn	p.I253N	ENST00000371953	NM_000314.4	253	aTc/aAc	7/9	0.303127524864615	2	FACETS	0.761	0.673	0.852	0.761	0.673	0.852	SUBCLONAL	2	TRUE	0	0.403441599055111	2		531	228	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551426	150551426	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013036-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	376	925	0	ENST00000369026.2:c.581A>C	p.Lys194Thr	p.K194T	ENST00000369026	NM_021960.4	194	aAg/aCg	1/3	0.283627782341874	5	FACETS	0.838	0.796	0.881	0.838	0.796	0.881	CLONAL	3	TRUE	2	0.403441599055111	5		925	1190	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436593	8436593	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013036-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	63	545	0	ENST00000356435.5:c.4085A>T	p.Glu1362Val	p.E1362V	ENST00000356435		1362	gAg/gTg	24/35	0.326769405166208	4	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	2	0.403441599055111	4		545	204	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871044	12871044	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013036-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	89	276	0	ENST00000228872.4:c.275del	p.Pro92ArgfsTer27	p.P92Rfs*27	ENST00000228872	NM_004064.3	91	Ccc/cc	1/3	0.354190818178652	2	FACETS	1	0.98	1	0.723	0.648	0.801	CLONAL	1	TRUE	0	0.403441599055111	2		276	305	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194100	94194100	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0013036-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	67	538	0	ENST00000323929.3:c.1326+2T>C		p.X442_splice	ENST00000323929	NM_005591.3	442			0.403441599055111	3	FACETS	0.783	0.688	0.882	0.783	0.688	0.882	SUBCLONAL	2	TRUE	1	0.403441599055111	3		538	255	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0013091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	291	391	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.307501330921163	7	FACETS	0.956	0.906	1	0.956	0.906	1	CLONAL	5	TRUE	2	0.307501330921163	7		391	700	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052632	42052632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779811318	NA	P-0013091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	171	505	1	ENST00000219905.7:c.7303C>T	p.Arg2435Trp	p.R2435W	ENST00000219905	NM_001164273.1	2435	Cgg/Tgg	20/24	0.307501330921163	2	FACETS	0.947	0.876	1	0.947	0.876	1	CLONAL	2	TRUE	0	0.307501330921163	2		506	587	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309731	30309731	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	185	616	0	ENST00000307677.4:c.291T>G	p.Phe97Leu	p.F97L	ENST00000307677	NM_138578.1	97	ttT/ttG	2/3	0.307501330921163	5	FACETS	0.915	0.845	0.988	0.61	0.563	0.659	CLONAL	2	TRUE	2	0.307501330921163	5		616	961	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907719	76907719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	200	635	1	ENST00000373344.5:c.4442G>A	p.Arg1481Gln	p.R1481Q	ENST00000373344	NM_000489.3	1481	cGg/cAg	15/35	0.286930076877445	4	FACETS	0.89	0.825	0.958	0.89	0.825	0.958	CLONAL	2	TRUE	2	0.307501330921163	4		636	955	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624224	89624228	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	GACAT	GACAT	-	novel	NA	P-0013091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	35	113	0	ENST00000371953.3:c.2_6del	p.Met1_?2	p.M1_?2	ENST00000371953	NM_000314.4	1		1/9	0.24490847746849	3	FACETS	0.853	0.709	1	0.853	0.709	1	CLONAL	2	TRUE	1	0.307501330921163	3		113	154	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0013091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	389	718	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.304353082263822	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	3	TRUE	0	0.307501330921163	3		718	967	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225565	225565	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	14	88	0	ENST00000264932.6:c.344A>T	p.Glu115Val	p.E115V	ENST00000264932	NM_004168.2	115	gAg/gTg	4/15	0.307501330921163	4	FACETS	0.984	0.717	1	0.328	0.239	0.434	CLONAL	1	TRUE	1	0.307501330921163	4		88	121	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117799	108117799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202160435	NA	P-0013143-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	28	378	0	ENST00000278616.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000278616	NM_000051.3	337	cGt/cAt	8/63	0.268292130384731	4	FACETS	0.862	0.69	1	0.431	0.345	0.528	CLONAL	1	TRUE	2	0.275416096998391	4		378	301	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242448	55242449	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTCCCGTCGCTATCAAGG	novel	NA	P-0013143-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	135	426	0	ENST00000275493.2:c.2219_2236dup	p.Lys745_Glu746insValProValAlaIleLys	p.K745_E746insVPVAIK	ENST00000275493	NM_005228.3	740	att/aTTCCCGTCGCTATCAAGGtt	19/28	0.275416096998391	5	FACETS	0.919	0.836	1	0.612	0.557	0.67	CLONAL	2	TRUE	2	0.275416096998391	5		426	754	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955100	55955100	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013143-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	99	396	1	ENST00000263923.4:c.3445C>T	p.Gln1149Ter	p.Q1149*	ENST00000263923	NM_002253.2	1149	Cag/Tag	26/30	0.275416096998391	3	FACETS	1	0.954	1	0.375	0.335	0.418	CLONAL	1	TRUE	0	0.275416096998391	3		397	727	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411007	63411007	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013143-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	80	685	0	ENST00000330258.3:c.2160G>T	p.Gln720His	p.Q720H	ENST00000330258	NM_152424.3	720	caG/caT	2/2	0.263539736733043	4	FACETS	0.618	0.542	0.701	0.309	0.271	0.351	SUBCLONAL	1	TRUE	2	0.275416096998391	4		685	1198	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0013145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	331	712	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.645636063537947	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.645636063537947	1		712	619	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856122	68856122	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781696	NA	P-0013145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	251	558	0	ENST00000261769.5:c.1930G>A	p.Asp644Asn	p.D644N	ENST00000261769	NM_004360.3	644	Gac/Aac	12/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.645636063537947	2		558	739	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591051	67591072	+	protein_altering_variant	In_Frame_Del	DEL	CTTGAAGAAGCAGGCAGCTGAG	CTTGAAGAAGCAGGCAGCTGAG	T	novel	NA	P-0013145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	109	297	0	ENST00000274335.5:c.1644_1665delinsT	p.Leu549_Glu555del	p.L549_E555del	ENST00000274335		548	gaCTTGAAGAAGCAGGCAGCTGAG/gaT	12/15	0.645636063537947	1	FACETS	0.775	0.706	0.846	0.775	0.706	0.846	SUBCLONAL	1	TRUE	0	0.645636063537947	1		297	295	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	249	258	0				ENST00000310581	NM_198253.2	-/1132			0.536257699139866	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.536257699139866	3		258	366	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0013341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	63	314	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.507669538653676	3	FACETS	0.842	0.732	0.959	0.421	0.366	0.48	CLONAL	1	TRUE	1	0.536257699139866	3		314	354	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0013341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	446	319	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.442700990609955	5	FACETS	0.989	0.947	1	0.989	0.947	1	CLONAL	3	TRUE	2	0.536257699139866	5		319	1012	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873660	35873660	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs201559094	NA	P-0013341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	135	478	0	ENST00000303115.3:c.616C>T	p.Arg206Ter	p.R206*	ENST00000303115	NM_002185.3	206	Cga/Tga	5/8	0.186803890660065	6	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.536257699139866	6		478	896	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524329	148524329	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	385	420	0	ENST00000320356.2:c.655C>T	p.Pro219Ser	p.P219S	ENST00000320356	NM_004456.4	219	Cct/Tct	7/20	0.442700990609955	5	FACETS	0.99	0.946	1	0.99	0.946	1	CLONAL	3	TRUE	2	0.536257699139866	5		420	872	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733635	85733635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1320962678	NA	P-0013341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	199	636	0	ENST00000370580.1:c.377C>T	p.Pro126Leu	p.P126L	ENST00000370580	NM_003921.4	126	cCa/cTa	3/3	0.524678707891116	2	FACETS	0.88	0.817	0.946	0.44	0.408	0.473	CLONAL	1	TRUE	0	0.536257699139866	2		636	843	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849897	156849897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	312	603	0	ENST00000524377.1:c.2153G>A	p.Trp718Ter	p.W718*	ENST00000524377	NM_002529.3	718	tGg/tAg	16/17	0.198187567071716	6	FACETS	1	0.99	1	0.803	0.759	0.848	INDETERMINATE	2	TRUE	3	0.536257699139866	6		603	1001	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445417	29445417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769855519	NA	P-0013341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	217	611	1	ENST00000389048.3:c.3416C>T	p.Pro1139Leu	p.P1139L	ENST00000389048	NM_004304.4	1139	cCc/cTc	21/29	0.536257699139866	3	FACETS	1	0.978	1	0.374	0.348	0.401	CLONAL	1	TRUE	0	0.536257699139866	3		612	914	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267156	41267156	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	109	349	2	ENST00000349496.5:c.740C>T	p.Pro247Leu	p.P247L	ENST00000349496	NM_001904.3	247	cCa/cTa	6/15	0.507669538653676	3	FACETS	0.934	0.841	1	0.467	0.42	0.516	CLONAL	1	TRUE	1	0.536257699139866	3		351	552	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89478294	89478294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	220	486	0	ENST00000336596.2:c.2113G>A	p.Gly705Ser	p.G705S	ENST00000336596	NM_005233.5	705	Ggt/Agt	12/17	0.507669538653676	3	FACETS	0.804	0.752	0.857	0.804	0.752	0.857	CLONAL	2	TRUE	1	0.536257699139866	3		486	647	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748095	41748095	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	32	45	0	ENST00000226382.2:c.674G>A	p.Gly225Glu	p.G225E	ENST00000226382	NM_003924.3	225	gGg/gAg	3/3	0.507669538653676	3	FACETS	1	0.912	1	1	0.912	1	CLONAL	2	TRUE	1	0.536257699139866	3		45	68	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961023	55961023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868853292	NA	P-0013341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	191	513	0	ENST00000263923.4:c.2917G>A	p.Ala973Thr	p.A973T	ENST00000263923	NM_002253.2	973	Gcc/Acc	21/30	0.507669538653676	3	FACETS	1	0.98	1	0.58	0.537	0.624	CLONAL	1	TRUE	1	0.536257699139866	3		513	779	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722272	176722272	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	221	567	0	ENST00000439151.2:c.7903G>A	p.Gly2635Arg	p.G2635R	ENST00000439151	NM_022455.4	2635	Ggg/Agg	23/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.536257699139866	2		567	729	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052998	180052998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867280522	NA	P-0013341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	155	524	0	ENST00000261937.6:c.1292C>T	p.Ser431Phe	p.S431F	ENST00000261937	NM_182925.4	431	tCc/tTc	10/30	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.536257699139866	2		524	409	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977657	2977657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	326	491	0	ENST00000396946.4:c.1027G>A	p.Glu343Lys	p.E343K	ENST00000396946	NM_032415.4	343	Gag/Aag	8/25	0.442700990609955	5	FACETS	1	0.965	1	0.685	0.647	0.723	CLONAL	2	TRUE	2	0.536257699139866	5		491	1068	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530108	63530108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	228	623	0	ENST00000307078.5:c.2327C>T	p.Pro776Leu	p.P776L	ENST00000307078	NM_004655.3	776	cCa/cTa	10/11	0.507669538653676	3	FACETS	1	0.97	1	0.535	0.498	0.573	CLONAL	1	TRUE	1	0.536257699139866	3		623	1008	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106952	11106952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	214	636	0	ENST00000358026.2:c.1657C>T	p.Leu553Phe	p.L553F	ENST00000358026	NM_001128849.1	553	Ctc/Ttc	10/36	0.400424607176374	4	FACETS	1	0.962	1	0.528	0.49	0.568	CLONAL	1	TRUE	2	0.536257699139866	4		636	1161	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246443	53246443	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	257	390	1	ENST00000375401.3:c.539C>T	p.Pro180Leu	p.P180L	ENST00000375401	NM_004187.3	180	cCa/cTa	5/26	0.422811319154553	2	FACETS	1	0.993	1			1	CLONAL	1	TRUE	NA	0.536257699139866	2		391	666	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133242010	133242011	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0013341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	291	399	0	ENST00000320574.5:c.2345_2346delinsAT	p.Ala782Asp	p.A782D	ENST00000320574	NM_006231.2	782	gCC/gAT	21/49	0.507669538653676	3	FACETS	0.976	0.924	1	0.976	0.924	1	CLONAL	2	TRUE	1	0.536257699139866	3		399	705	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0013484-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	415	372	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.615356673375448	5	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.788954344338036	5		372	931	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0013484-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	317	489	2	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.668038233205682	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.788954344338036	1		491	418	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849822	156849822	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013484-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	382	512	3	ENST00000524377.1:c.2078G>A	p.Trp693Ter	p.W693*	ENST00000524377	NM_002529.3	693	tGg/tAg	16/17	0.788954344338036	4	FACETS	1	0.993	1	0.421	0.399	0.443	CLONAL	1	TRUE	1	0.788954344338036	4		515	1372	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037877	49037877	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013484-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	348	445	0	ENST00000267163.4:c.2117G>A	p.Cys706Tyr	p.C706Y	ENST00000267163	NM_000321.2	706	tGt/tAt	21/27	0.788954344338036	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.788954344338036	3		445	405	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061655	38061656	+	missense_variant	Missense_Mutation	DNP	CG	CG	AA	novel	NA	P-0013484-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	59	176	0	ENST00000250448.2:c.333_334delinsTT	p.Gly112Cys	p.G112C	ENST00000250448	NM_004496.3	111	agCGgc/agTTgc	2/2	0.788954344338036	7	FACETS	0.661	0.568	0.762	0.165	0.142	0.191	SUBCLONAL	1	TRUE	3	0.788954344338036	7		176	673	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644916	67644916	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013484-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	381	502	0	ENST00000264010.4:c.181G>T	p.Val61Leu	p.V61L	ENST00000264010	NM_006565.3	61	Gtg/Ttg	3/12	0.788954344338036	3	FACETS	0.983	0.943	1	0.983	0.943	1	CLONAL	2	TRUE	1	0.788954344338036	3		502	685	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577560	7577565	+	inframe_deletion	In_Frame_Del	DEL	AACTGT	AACTGT	-	novel	NA	P-0013484-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	464	628	1	ENST00000269305.4:c.716_721del	p.Asn239_Ser241delinsThr	p.N239_S241delinsT	ENST00000269305	NM_001126112.2	239	aACAGTTcc/acc	7/11	0.771682617884237	2	FACETS	0.987	0.96	1	0.987	0.96	1	CLONAL	2	TRUE	0	0.788954344338036	2		629	596	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383070	42383070	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013484-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	87	359	0	ENST00000221972.3:c.90C>A	p.Cys30Ter	p.C30*	ENST00000221972	NM_021601.3	30	tgC/tgA	2/5	1	2	FACETS	0.52	0.463	0.581	0.52	0.463	0.581	SUBCLONAL	1	TRUE	1	0.788954344338036	2		359	424	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755745	39755745	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013484-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	665	486	2	ENST00000288319.7:c.1020G>T	p.Lys340Asn	p.K340N	ENST00000288319	NM_182918.3	340	aaG/aaT	10/10	0.788954344338036	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.788954344338036	3		488	768	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169970	32169970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013484-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1498	158	694	1	ENST00000375023.3:c.3638G>A	p.Gly1213Asp	p.G1213D	ENST00000375023	NM_004557.3	1213	gGc/gAc	21/30	0.788954344338036	6	FACETS	0.624	0.569	0.681	0.156	0.142	0.171	SUBCLONAL	1	TRUE	2	0.788954344338036	6		695	1656	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519538	137519538	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs148158267	NA	P-0013484-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	241	476	0	ENST00000367739.4:c.1100C>G	p.Pro367Arg	p.P367R	ENST00000367739	NM_000416.2	367	cCg/cGg	7/7	0.788954344338036	4	FACETS	1	0.988	1	0.411	0.384	0.438	CLONAL	1	TRUE	1	0.788954344338036	4		476	887	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332789	152332790	+	splice_acceptor_variant	Splice_Site	DNP	AG	AG	GT	novel	NA	P-0013484-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	119	599	0	ENST00000206249.3:c.1097-2_1097-1delinsGT		p.X366_splice	ENST00000206249	NM_000125.3	366			0.788954344338036	4	FACETS	0.436	0.392	0.482	0.145	0.13	0.161	SUBCLONAL	1	TRUE	1	0.788954344338036	4		599	1239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0013486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	268	508	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.485087807503999	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.485087807503999	2		509	539	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683892	117683892	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	133	507	1	ENST00000368508.3:c.3255C>G	p.Phe1085Leu	p.F1085L	ENST00000368508	NM_002944.2	1085	ttC/ttG	21/43	0.485087807503999	3	FACETS	1	0.952	1	0.535	0.487	0.585	CLONAL	1	TRUE	1	0.485087807503999	3		508	637	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102098222	102098222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	91	387	1	ENST00000282441.5:c.1186G>A	p.Glu396Lys	p.E396K	ENST00000282441	NM_001130145.2	396	Gag/Aag	8/9	0.485087807503999	3	FACETS	0.89	0.792	0.993	0.445	0.396	0.497	CLONAL	1	TRUE	1	0.485087807503999	3		388	524	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720741	89720741	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs371387815	NA	P-0013486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	65	148	0	ENST00000371953.3:c.892C>T	p.Gln298Ter	p.Q298*	ENST00000371953	NM_000314.4	298	Caa/Taa	8/9	0.445854882554125	4	FACETS	0.884	0.788	0.983			1	CLONAL	3	TRUE	NA	0.485087807503999	4		148	150	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659982	227659982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1166934768	NA	P-0013486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	116	505	2	ENST00000305123.5:c.3473G>A	p.Gly1158Glu	p.G1158E	ENST00000305123	NM_005544.2	1158	gGa/gAa	1/2	0.485087807503999	3	FACETS	1	0.955	1	0.547	0.495	0.602	CLONAL	1	TRUE	1	0.485087807503999	3		507	543	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591127	67591129	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0013486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	52	222	0	ENST00000274335.5:c.1721_1723del	p.Arg574del	p.R574del	ENST00000274335		574	AGA/-	12/15	1	2	FACETS	0.812	0.697	0.936	0.812	0.697	0.936	CLONAL	1	TRUE	1	0.485087807503999	2		222	264	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781912	9781912	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	183	510	4	ENST00000377346.4:c.2049G>T	p.Met683Ile	p.M683I	ENST00000377346	NM_005026.3	683	atG/atT	16/24	0.485087807503999	4	FACETS	0.923	0.856	0.992	0.615	0.571	0.661	CLONAL	2	TRUE	1	0.485087807503999	4		514	607	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262204	16262204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757464458	NA	P-0013486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	50	186	0	ENST00000375759.3:c.9469G>A	p.Glu3157Lys	p.E3157K	ENST00000375759	NM_015001.2	3157	Gag/Aag	11/15	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.485087807503999	2		186	187	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458068	120458068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	229	464	5	ENST00000256646.2:c.7277C>T	p.Ser2426Leu	p.S2426L	ENST00000256646	NM_024408.3	2426	tCa/tTa	34/34	0.407792347533768	3	FACETS	1	0.954	1			1	CLONAL	2	TRUE	NA	0.485087807503999	3		469	576	SUCCESS
ALK	238	MSKCC	GRCh37	2	29436872	29436872	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	62	415	0	ENST00000389048.3:c.3721G>C	p.Glu1241Gln	p.E1241Q	ENST00000389048	NM_004304.4	1241	Gag/Cag	24/29	0.485087807503999	3	FACETS	0.742	0.643	0.849	0.371	0.321	0.425	SUBCLONAL	1	TRUE	1	0.485087807503999	3		415	428	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47612334	47612334	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	176	291	0	ENST00000263735.4:c.888G>C	p.Lys296Asn	p.K296N	ENST00000263735	NM_002354.2	296	aaG/aaC	8/9	0.485087807503999	3	FACETS	0.995	0.926	1	0.995	0.926	1	CLONAL	2	TRUE	1	0.485087807503999	3		291	453	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147730	61147730	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	60	239	0	ENST00000295025.8:c.1040G>C	p.Arg347Thr	p.R347T	ENST00000295025	NM_002908.2	347	aGa/aCa	10/11	0.485087807503999	3	FACETS	0.894	0.774	1	0.447	0.387	0.511	CLONAL	1	TRUE	1	0.485087807503999	3		239	344	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660458	227660458	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs747866903	NA	P-0013486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	93	420	5	ENST00000305123.5:c.2997G>C	p.Gln999His	p.Q999H	ENST00000305123	NM_005544.2	999	caG/caC	1/2	0.485087807503999	3	FACETS	0.976	0.872	1	0.488	0.436	0.544	CLONAL	1	TRUE	1	0.485087807503999	3		425	488	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356281	66356281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	87	468	1	ENST00000273854.3:c.1216G>A	p.Glu406Lys	p.E406K	ENST00000273854	NM_004439.5	406	Gag/Aag	5/18	1	2	FACETS	0.991	0.884	1	0.991	0.884	1	CLONAL	1	TRUE	1	0.485087807503999	2		469	362	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539282	187539282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	81	387	0	ENST00000441802.2:c.8458G>A	p.Glu2820Lys	p.E2820K	ENST00000441802	NM_005245.3	2820	Gaa/Aaa	10/27	1	2	FACETS	0.938	0.833	1	0.938	0.833	1	CLONAL	1	TRUE	1	0.485087807503999	2		387	356	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628788	187628788	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	114	544	1	ENST00000441802.2:c.2194G>A	p.Val732Met	p.V732M	ENST00000441802	NM_005245.3	732	Gtg/Atg	2/27	1	2	FACETS	0.934	0.845	1	0.934	0.845	1	CLONAL	1	TRUE	1	0.485087807503999	2		545	503	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527839	157527839	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs771295398	NA	P-0013486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	71	334	0	ENST00000346085.5:c.5564G>C	p.Arg1855Thr	p.R1855T	ENST00000346085	NM_020732.3	1855	aGa/aCa	20/20	0.485087807503999	3	FACETS	0.991	0.87	1	0.496	0.435	0.56	CLONAL	1	TRUE	1	0.485087807503999	3		334	367	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404456	70404456	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	66	192	0	ENST00000373644.4:c.1970C>A	p.Ala657Glu	p.A657E	ENST00000373644	NM_030625.2	657	gCa/gAa	4/12	0.485087807503999	3	FACETS	1	0.924	1			1	CLONAL	1	TRUE	NA	0.485087807503999	3		192	313	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242668	46242668	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	83	308	0	ENST00000334344.6:c.1630G>T	p.Glu544Ter	p.E544*	ENST00000334344	NM_152641.2	544	Gaa/Taa	13/21	0.485087807503999	3	FACETS	0.877	0.776	0.984			1	CLONAL	1	TRUE	NA	0.485087807503999	3		308	485	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572101	95572101	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1060503605	NA	P-0013486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	107	419	3	ENST00000393063.1:c.3007C>T	p.Arg1003Ter	p.R1003*	ENST00000393063	NM_030621.3	1003	Cga/Tga	20/28	0.485087807503999	3	FACETS	0.965	0.868	1	0.483	0.434	0.534	CLONAL	1	TRUE	1	0.485087807503999	3		422	568	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763940	76763940	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	111	540	3	ENST00000373344.5:c.7368G>A	p.Met2456Ile	p.M2456I	ENST00000373344	NM_000489.3	2456	atG/atA	35/35	1	2	FACETS	0.819	0.738	0.903	0.819	0.738	0.903	CLONAL	1	TRUE	1	0.485087807503999	2		543	559	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178236	56178236	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	54	221	0	ENST00000399503.3:c.3209del	p.Thr1070LysfsTer12	p.T1070Kfs*12	ENST00000399503	NM_005921.1	1070	aCa/aa	14/20	1	2	FACETS	0.866	0.747	0.994	0.866	0.747	0.994	CLONAL	1	TRUE	1	0.485087807503999	2		221	257	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632620	3632620	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144057906	NA	P-0013486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	158	646	1	ENST00000294008.3:c.5228C>T	p.Ser1743Leu	p.S1743L	ENST00000294008	NM_032444.2	1743	tCg/tTg	15/15	0.320058874363012	5	FACETS	1	0.984	1	0.436	0.4	0.474	CLONAL	1	TRUE	2	0.485087807503999	5		647	860	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658904	3658904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	100	446	0	ENST00000294008.3:c.62C>T	p.Ser21Phe	p.S21F	ENST00000294008	NM_032444.2	21	tCt/tTt	2/15	0.320058874363012	5	FACETS	1	0.961	1	0.385	0.344	0.428	CLONAL	1	TRUE	2	0.485087807503999	5		446	617	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217238	66217238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	68	379	2	ENST00000273854.3:c.2377G>A	p.Asp793Asn	p.D793N	ENST00000273854	NM_004439.5	793	Gac/Aac	14/18	1	2	FACETS	0.963	0.846	1	0.963	0.846	1	CLONAL	1	TRUE	1	0.485087807503999	2		381	291	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21968242	21968242	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0013486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	66	302	2	ENST00000304494.5:c.458-1G>C		p.X153_splice	ENST00000304494	NM_000077.4	153			NA	2	FACETS	1	0.962	1			1	INDETERMINATE	1	TRUE	NA	0.485087807503999	2		304	219	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383937	15383969	+	splice_acceptor_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	CAGGCACTCTACAAAGGAAGAGAAGAGCCCCCG	CAGGCACTCTACAAAGGAAGAGAAGAGCCCCCG	-	novel	NA	P-0013486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	39	260	0	ENST00000263377.2:c.-34-25_-27del		p.X12_splice	ENST00000263377	NM_058243.2	12		2/20	0.485087807503999	4	FACETS	0.706	0.587	0.839			1	SUBCLONAL	1	TRUE	NA	0.485087807503999	4		260	338	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	41	354	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.724	0.601	0.861	0.724	0.601	0.861	SUBCLONAL	1	TRUE	1	0.15	2		354	755	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333696	70333696	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	64	714	0	ENST00000373644.4:c.1601C>T	p.Ser534Phe	p.S534F	ENST00000373644	NM_030625.2	534	tCt/tTt	2/12	1	2	FACETS	0.95	0.821	1	0.95	0.821	1	CLONAL	1	TRUE	1	0.15	2		714	898	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087494	27087502	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGGCATC	CCTGGCATC	G	novel	NA	P-0013839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	74	737	0	ENST00000324856.7:c.2068_2076delinsG	p.Pro690AlafsTer124	p.P690Afs*124	ENST00000324856	NM_006015.4	690	CCTGGCATC/G	5/20	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.15	2		737	978	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0014409-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	581	686	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.485481589124993	5	FACETS	0.951	0.923	0.978	0.951	0.923	0.978	CLONAL	5	TRUE	0	0.485481589124993	5		686	870	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782609	9782609	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014409-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	198	834	0	ENST00000377346.4:c.2371C>G	p.Leu791Val	p.L791V	ENST00000377346	NM_005026.3	791	Ctg/Gtg	19/24	0.411578252810496	4	FACETS	0.867	0.806	0.929	0.867	0.806	0.929	CLONAL	2	TRUE	2	0.485481589124993	4		834	699	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640853	3640853	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs117707719	NA	P-0014409-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	224	782	0	ENST00000294008.3:c.2786C>T	p.Pro929Leu	p.P929L	ENST00000294008	NM_032444.2	929	cCg/cTg	12/15	0.485481589124993	6	FACETS	0.967	0.902	1	0.484	0.451	0.518	CLONAL	2	TRUE	2	0.485481589124993	6		782	940	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953818	131953818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014409-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	186	624	1	ENST00000265335.6:c.3221C>T	p.Ala1074Val	p.A1074V	ENST00000265335		1074	gCa/gTa	21/25	0.358510133123274	5	FACETS	0.991	0.919	1	0.661	0.613	0.71	CLONAL	2	TRUE	2	0.485481589124993	5		625	668	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566057	141566057	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1379212767	NA	P-0014409-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	108	815	0	ENST00000220592.5:c.1207G>C	p.Asp403His	p.D403H	ENST00000220592	NM_012154.3	403	Gat/Cat	10/19	0.485481589124993	6	FACETS	0.926	0.83	1	0.309	0.276	0.343	CLONAL	1	TRUE	3	0.485481589124993	6		815	947	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882981	89882981	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1567660116	NA	P-0014409-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	26	189	0	ENST00000389301.3:c.43C>G	p.Pro15Ala	p.P15A	ENST00000389301	NM_000135.2	15	Cca/Gca	1/43	0.485481589124993	3	FACETS	0.918	0.736	1	0.459	0.368	0.561	CLONAL	1	TRUE	1	0.485481589124993	3		189	145	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014409-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	149	902	0	ENST00000269305.4:c.610G>C	p.Glu204Gln	p.E204Q	ENST00000269305	NM_001126112.2	204	Gag/Cag	6/11	0.485481589124993	5	FACETS	1	0.956	1	0.215	0.196	0.235	CLONAL	1	TRUE	0	0.485481589124993	5		902	988	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487250	56487250	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	407	638	0	ENST00000267101.3:c.1396C>A	p.His466Asn	p.H466N	ENST00000267101	NM_001982.3	466	Cac/Aac	12/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.638997000311284	2		638	1217	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061066	38061066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	160	240	0	ENST00000250448.2:c.923C>T	p.Pro308Leu	p.P308L	ENST00000250448	NM_004496.3	308	cCc/cTc	2/2	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.638997000311284	2		240	436	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657518	37657520	+	inframe_deletion	In_Frame_Del	DEL	TAT	TAT	-	novel	NA	P-0014467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	488	454	0	ENST00000447079.4:c.2436_2438del	p.Phe813del	p.F813del	ENST00000447079	NM_015083.1	812	gTATtt/gtt	6/14	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.638997000311284	2		454	725	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241737	55241737	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0014467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	74	415	0	ENST00000275493.2:c.2184+1G>C		p.X728_splice	ENST00000275493	NM_005228.3	728			0.164760597032666	3	FACETS	0.375	0.327	0.426	0.187	0.163	0.213	INDETERMINATE	1	TRUE	1	0.638997000311284	3		415	815	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037972	49037972	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0014903-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	247	399	0	ENST00000267163.4:c.2211+1G>A		p.X737_splice	ENST00000267163	NM_000321.2	737			0.808835199468557	2	FACETS	0.916	0.88	0.951	0.916	0.88	0.951	CLONAL	2	TRUE	0	0.811892041016934	2		399	332	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577017	7577017	+	splice_donor_variant	Splice_Site	SNP	A	A	C	rs1131691016	NA	P-0014903-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	446	596	0	ENST00000269305.4:c.919+2T>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.811892041016934	2	FACETS	0.979	0.953	1	0.979	0.953	1	CLONAL	2	TRUE	0	0.811892041016934	2		596	561	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249378	110249379	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CA	CA	-	novel	NA	P-0014903-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	514	834	0	ENST00000374672.4:c.1194_1195del	p.Cys398Ter	p.C398*	ENST00000374672	NM_004235.4	398	tgTGat/tgat	4/5	0.808835199468557	2	FACETS	0.975	0.951	0.999	0.975	0.951	0.999	CLONAL	2	TRUE	0	0.811892041016934	2		834	649	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0015092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	262	732	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.977	0.921	1	0.977	0.921	1	CLONAL	1	TRUE	1	0.790132162128757	2		732	679	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771163	161771163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755627153	NA	P-0015092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	106	666	0	ENST00000366898.1:c.1366G>A	p.Val456Ile	p.V456I	ENST00000366898	NM_004562.2	456	Gtc/Atc	12/12	1	2	FACETS	0.475	0.427	0.526	0.475	0.427	0.526	SUBCLONAL	1	TRUE	1	0.790132162128757	2		666	565	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617177	100617177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555978785	NA	P-0015092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	230	743	0	ENST00000308731.7:c.572C>T	p.Thr191Met	p.T191M	ENST00000308731	NM_000061.2	191	aCg/aTg	7/19	0.529771576032847	3	FACETS	1	0.984	1	0.574	0.537	0.611	CLONAL	1	TRUE	1	0.790132162128757	3		743	708	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682995	241682995	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201507555	NA	P-0015092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	86	587	0	ENST00000366560.3:c.28C>T	p.Arg10Cys	p.R10C	ENST00000366560	NM_000143.3	10	Cgc/Tgc	1/10	0.619534943942047	3	FACETS	0.418	0.37	0.47	0.209	0.185	0.235	SUBCLONAL	1	TRUE	1	0.790132162128757	3		587	726	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993705	90993705	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	39	499	0	ENST00000265433.3:c.218A>T	p.Lys73Met	p.K73M	ENST00000265433	NM_002485.4	73	aAg/aTg	3/16	0.475796360280904	1	FACETS	0.114	0.094	0.137	0.114	0.094	0.137	SUBCLONAL	1	TRUE	0	0.790132162128757	1		499	523	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404543	8404544	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	65	369	0	ENST00000356435.5:c.4203dup	p.Ile1402TyrfsTer8	p.I1402Yfs*8	ENST00000356435		1401	-/T	25/35	0.478111176028635	3	FACETS	0.475	0.413	0.543	0.158	0.137	0.181	SUBCLONAL	1	TRUE	0	0.790132162128757	3		369	483	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0016375-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	201	814	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.248614741004679	4	FACETS	0.958	0.889	1	0.958	0.889	1	CLONAL	2	TRUE	2	0.322178731612962	4		814	861	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727455	66727455	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs869025608	NA	P-0016375-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	23	396	0	ENST00000307102.5:c.171G>T	p.Lys57Asn	p.K57N	ENST00000307102	NM_002755.3	57	aaG/aaT	2/11	0.322178731612962	3	FACETS	0.274	0.212	0.345	0.137	0.106	0.173	SUBCLONAL	1	TRUE	1	0.322178731612962	3		396	606	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039658	47039659	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016375-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	310	829	0	ENST00000377604.3:c.1111dup	p.Thr371AsnfsTer10	p.T371Nfs*10	ENST00000377604	NM_001204468.1	370	-/A	11/24	0.300986870287076	5	FACETS	1	0.955	1	0.678	0.638	0.719	CLONAL	2	TRUE	2	0.322178731612962	5		829	1403	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246021826	246021826	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016375-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	80	625	0	ENST00000388985.4:c.1048T>C	p.Tyr350His	p.Y350H	ENST00000388985		350	Tat/Cat	10/12	0.322178731612962	4	FACETS	0.552	0.484	0.626			1	SUBCLONAL	1	TRUE	NA	0.322178731612962	4		625	1189	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376469	118376469	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016375-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	132	314	0	ENST00000534358.1:c.9862A>G	p.Ile3288Val	p.I3288V	ENST00000534358	NM_005933.3	3288	Atc/Gtc	27/36	0.322178731612962	3	FACETS	0.863	0.787	0.943			1	CLONAL	2	TRUE	NA	0.322178731612962	3		314	551	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197399	26197399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016375-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	24	200	0	ENST00000356476.2:c.80G>A	p.Arg27Gln	p.R27Q	ENST00000356476		27	cGa/cAa	1/1	0.161254822383374	5	FACETS	0.596	0.467	0.745	0.199	0.155	0.249	INDETERMINATE	1	TRUE	2	0.322178731612962	5		200	371	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476264	88476264	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016507-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	345	509	0	ENST00000360948.2:c.1868G>A	p.Gly623Glu	p.G623E	ENST00000360948	NM_001012338.2	623	gGa/gAa	15/19	0.161170860758085	5	FACETS	1	0.985	1			1	INDETERMINATE	2	TRUE	NA	0.515177059207092	5		509	1076	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751095	57751141	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAAGCCACAGTACTTACATCCATGAGGTTCTCCTCCATGTAATGAGA	AAAGCCACAGTACTTACATCCATGAGGTTCTCCTCCATGTAATGAGA	-	novel	NA	P-0016507-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	47	256	0	ENST00000274289.3:c.1726_1755+17del		p.X576_splice	ENST00000274289	NM_006622.3	576		12/14	1	2	FACETS	0.707	0.601	0.822	0.707	0.601	0.822	SUBCLONAL	1	TRUE	1	0.515177059207092	2		256	258	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971155	21971164	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCCGTGGA	GCGCCGTGGA	-	novel	NA	P-0016507-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	261	353	0	ENST00000304494.5:c.194_203del	p.Leu65ArgfsTer78	p.L65Rfs*78	ENST00000304494	NM_000077.4	65	cTCCACGGCGCg/cg	2/3	0.480937885875188	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.515177059207092	2		353	474	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0016654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	60	634	1	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	0.12	2		635	961	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0016654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	24	317	0	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	1	2	FACETS	0.648	0.506	0.813	0.648	0.506	0.813	SUBCLONAL	1	TRUE	1	0.12	2		317	617	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236087	108236087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781894	NA	P-0016654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	71	448	0	ENST00000278616.4:c.9023G>A	p.Arg3008His	p.R3008H	ENST00000278616	NM_000051.3	3008	cGt/cAt	63/63	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.12	2		448	925	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101621	27101622	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0016654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1823	116	677	0	ENST00000324856.7:c.4905dup	p.Arg1636SerfsTer12	p.R1636Sfs*12	ENST00000324856	NM_006015.4	1635	att/aTtt	18/20	1	2	FACETS	0.997	0.894	1	0.997	0.894	1	CLONAL	1	TRUE	1	0.12	2		677	1939	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248072	59248072	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	36	188	0	ENST00000371222.2:c.671C>T	p.Ala224Val	p.A224V	ENST00000371222	NM_002228.3	224	gCc/gTc	1/1	1	2	FACETS	0.982	0.806	1	0.982	0.806	1	CLONAL	1	TRUE	1	0.12	2		188	611	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs397517201	NA	P-0016654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1238	61	566	1	ENST00000263967.3:c.1637A>T	p.Gln546Leu	p.Q546L	ENST00000263967	NM_006218.2	546	cAg/cTg	10/21	1	2	FACETS	0.783	0.672	0.904	0.783	0.672	0.904	CLONAL	1	TRUE	1	0.12	2		567	1299	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412095	63412095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852217	NA	P-0016662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	19	446	1	ENST00000330258.3:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000330258	NM_152424.3	358	Cga/Tga	2/2	1	1	FACETS	0.547	0.415	0.703	0.547	0.415	0.703	SUBCLONAL	1	TRUE	0	0.19	1		447	331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577575	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587782289	NA	P-0016662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	29	458	0	ENST00000269305.4:c.706T>A	p.Tyr236Asn	p.Y236N	ENST00000269305	NM_001126112.2	236	Tac/Aac	7/11	1	2	FACETS	0.565	0.453	0.694	0.565	0.453	0.694	SUBCLONAL	1	TRUE	1	0.19	2		458	540	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0016666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	112	427	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	0.15	2		427	1236	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0016666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	62	485	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.785	0.676	0.905	0.785	0.676	0.905	CLONAL	1	TRUE	1	0.15	2		485	1053	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712017	89712017	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0016666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	15	145	0	ENST00000371953.3:c.634+1G>A		p.X212_splice	ENST00000371953	NM_000314.4	212			1	2	FACETS	0.702	0.513	0.929	0.702	0.513	0.929	CLONAL	1	TRUE	1	0.15	2		145	285	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298581	11298581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	66	463	0	ENST00000361445.4:c.1880C>T	p.Ser627Phe	p.S627F	ENST00000361445	NM_004958.3	627	tCc/tTc	12/58	1	2	FACETS	0.888	0.769	1	0.888	0.769	1	CLONAL	1	TRUE	1	0.15	2		463	991	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717646	89717647	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	77	438	0	ENST00000371953.3:c.672dup	p.Tyr225IlefsTer18	p.Y225Ifs*18	ENST00000371953	NM_000314.4	224	ata/atAa	7/9	1	2	FACETS	0.962	0.842	1	0.962	0.842	1	CLONAL	1	TRUE	1	0.15	2		438	1067	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316397	14316397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782457908	NA	P-0016666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	65	510	0	ENST00000256196.4:c.208G>A	p.Ala70Thr	p.A70T	ENST00000256196		70	Gca/Aca	3/6	1	2	FACETS	0.856	0.74	0.983	0.856	0.74	0.983	CLONAL	1	TRUE	1	0.15	2		510	1012	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407576	407576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756602021	NA	P-0016666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	83	426	1	ENST00000380956.4:c.1334G>A	p.Arg445His	p.R445H	ENST00000380956	NM_001195286.1	445	cGc/cAc	9/9	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.15	2		427	1017	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339251	70339251	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs199469668	NA	P-0016666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1584	80	682	0	ENST00000374080.3:c.128A>C	p.Gln43Pro	p.Q43P	ENST00000374080		43	cAa/cCa	2/45	1	2	FACETS	0.641	0.562	0.727	0.641	0.562	0.727	SUBCLONAL	1	TRUE	1	0.15	2		682	1664	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	109	354	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.216443556593777	3	FACETS	1	0.982	1	0.722	0.649	0.798	CLONAL	1	TRUE	1	0.28639223847284	3		354	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0017779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	24	496	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.239455399706249	1	FACETS	0.487	0.382	0.607	0.487	0.382	0.607	SUBCLONAL	1	TRUE	0	0.28639223847284	1		496	295	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0017779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	38	349	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.239455399706249	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.28639223847284	1		349	182	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0017779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	45	361	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	0.28639223847284	3	FACETS	0.87	0.732	1	0.435	0.366	0.511	CLONAL	1	TRUE	1	0.28639223847284	3		361	413	SUCCESS
APC	324	MSKCC	GRCh37	5	112174475	112174475	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554084818	NA	P-0017907-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	74	284	0	ENST00000257430.4:c.3184C>T	p.Gln1062Ter	p.Q1062*	ENST00000257430	NM_000038.5	1062	Caa/Taa	16/16	0.602606790062008	1	FACETS	0.594	0.525	0.666	0.594	0.525	0.666	SUBCLONAL	1	FALSE	0	0.602606790062008	1		284	289	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259183	36259183	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	80	543	0	ENST00000300305.3:c.308C>T	p.Pro103Leu	p.P103L	ENST00000300305		103	cCt/cTt	3/8	0.438422804508682	2	FACETS	0.582	0.513	0.655	0.291	0.256	0.328	SUBCLONAL	1	TRUE	0	0.51212786054941	2		543	537	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0018298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	616	513	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.51212786054941	9	FACETS	1	0.983	1	0.877	0.849	0.905	CLONAL	6	TRUE	2	0.51212786054941	9		513	1094	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74002009	74002009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	236	650	0	ENST00000318443.5:c.1525G>A	p.Glu509Lys	p.E509K	ENST00000318443	NM_001024736.1	509	Gag/Aag	8/10	0.4690541440808	4	FACETS	1	0.981	1			1	CLONAL	2	TRUE	NA	0.51212786054941	4		650	628	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120572	2120572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934872	NA	P-0018298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	337	678	1	ENST00000219476.3:c.1832G>A	p.Arg611Gln	p.R611Q	ENST00000219476	NM_000548.3	611	cGg/cAg	17/42	0.498150375551036	3	FACETS	0.861	0.822	0.899	0.861	0.822	0.899	CLONAL	3	TRUE	0	0.51212786054941	3		679	640	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993495	72993495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	97	655	1	ENST00000268489.5:c.550C>T	p.Pro184Ser	p.P184S	ENST00000268489	NM_006885.3	184	Cct/Tct	2/10	0.51212786054941	4	FACETS	0.802	0.715	0.895	0.267	0.238	0.299	CLONAL	1	TRUE	1	0.51212786054941	4		656	714	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217181	66217181	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	169	560	1	ENST00000273854.3:c.2434C>T	p.Leu812Phe	p.L812F	ENST00000273854	NM_004439.5	812	Ctt/Ttt	14/18	0.302299300378101	5	FACETS	0.841	0.775	0.909	0.561	0.517	0.606	INDETERMINATE	2	TRUE	2	0.51212786054941	5		561	694	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002844	69002844	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	62	324	0	ENST00000288368.4:c.2144C>G	p.Pro715Arg	p.P715R	ENST00000288368	NM_024870.2	715	cCt/cGt	20/40	0.51212786054941	6	FACETS	0.67	0.578	0.771			1	SUBCLONAL	1	TRUE	NA	0.51212786054941	6		324	731	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579409	7579409	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1567556114	NA	P-0018534-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	334	637	0	ENST00000269305.4:c.278del	p.Leu93ArgfsTer30	p.L93Rfs*30	ENST00000269305	NM_001126112.2	93	cTg/cg	4/11	0.408654180476223	2	FACETS	0.956	0.91	1	0.956	0.91	1	CLONAL	2	TRUE	0	0.472354002490504	2		637	740	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123246934	123246934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554907364	NA	P-0018534-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	72	351	0	ENST00000358487.5:c.1991G>A	p.Arg664Gln	p.R664Q	ENST00000358487	NM_000141.4	664	cGg/cAg	15/18	0.395991739505527	3	FACETS	0.843	0.739	0.954	0.422	0.369	0.477	CLONAL	1	TRUE	1	0.472354002490504	3		351	447	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242679	98242679	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1564055259	NA	P-0018534-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	40	440	0	ENST00000331920.6:c.938C>G	p.Ser313Ter	p.S313*	ENST00000331920	NM_000264.3	313	tCa/tGa	6/24	1	2	FACETS	0.344	0.286	0.409	0.344	0.286	0.409	SUBCLONAL	1	TRUE	1	0.472354002490504	2		440	492	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	46	354	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.172	0.144	0.203	0.172	0.144	0.203	SUBCLONAL	1	TRUE	1	0.51	2		354	1048	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0018585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	32	425	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.139	0.112	0.17	0.139	0.112	0.17	SUBCLONAL	1	TRUE	1	0.51	2		425	900	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0018585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	41	289	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.203	0.168	0.242	0.203	0.168	0.242	SUBCLONAL	1	TRUE	1	0.51	2		289	792	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577564	7577564	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057522275	NA	P-0018585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	38	492	0	ENST00000269305.4:c.717C>G	p.Asn239Lys	p.N239K	ENST00000269305	NM_001126112.2	239	aaC/aaG	7/11	1	2	FACETS	0.197	0.162	0.237	0.197	0.162	0.237	SUBCLONAL	1	TRUE	1	0.51	2		492	755	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411936	63411936	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	55	799	1	ENST00000330258.3:c.1231G>T	p.Glu411Ter	p.E411*	ENST00000330258	NM_152424.3	411	Gaa/Taa	2/2	1	2	FACETS	0.201	0.171	0.234	0.201	0.171	0.234	SUBCLONAL	1	TRUE	1	0.51	2		800	1073	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0018760-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	251	603	1	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.132423018051524	3	FACETS	1	0.992	1	0.688	0.647	0.731	INDETERMINATE	1	TRUE	1	0.660785086635209	3		604	734	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0018760-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	121	237	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.660785086635209	3	FACETS	0.937	0.863	1	0.937	0.863	1	CLONAL	2	TRUE	1	0.660785086635209	3		237	260	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577579	7577579	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0018760-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	255	492	0	ENST00000269305.4:c.702C>G	p.Tyr234Ter	p.Y234*	ENST00000269305	NM_001126112.2	234	taC/taG	7/11	0.132423018051524	3	FACETS	0.779	0.734	0.825	0.779	0.734	0.825	INDETERMINATE	2	TRUE	1	0.660785086635209	3		492	659	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223237	5223237	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018760-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	413	519	1	ENST00000357368.4:c.2566G>T	p.Ala856Ser	p.A856S	ENST00000357368	NM_002850.3	856	Gct/Tct	18/38	0.382594965481968	4	FACETS	0.977	0.933	1	0.977	0.933	1	INDETERMINATE	2	TRUE	2	0.660785086635209	4		520	1062	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161479	2161479	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018760-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	229	435	0	ENST00000434045.2:c.48A>C	p.Glu16Asp	p.E16D	ENST00000434045	NM_001127598.1	16	gaA/gaC	2/5	0.30949933086746	5	FACETS	1	0.988	1	0.42	0.391	0.45	INDETERMINATE	1	TRUE	2	0.660785086635209	5		435	1096	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32918718	32918718	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018760-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	25	146	0	ENST00000380152.3:c.6865T>G	p.Leu2289Val	p.L2289V	ENST00000380152		2289	Tta/Gta	12/27	0.660785086635209	6	FACETS	0.729	0.577	0.903	0.182	0.144	0.226	CLONAL	1	TRUE	2	0.660785086635209	6		146	241	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1800982	1800982	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	rs747890000	NA	P-0018760-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	61	564	0	ENST00000260795.2:c.111A>C	p.Glu37Asp	p.E37D	ENST00000260795		37	gaA/gaC	2/17	0.660785086635209	3	FACETS	0.264	0.227	0.305	0.132	0.113	0.153	SUBCLONAL	1	TRUE	1	0.660785086635209	3		564	930	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738635	145738635	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018760-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	204	409	0	ENST00000428558.2:c.2429A>G	p.Gln810Arg	p.Q810R	ENST00000428558	NM_004260.3	810	cAg/cGg	15/22	0.547713739328189	4	FACETS	1	0.984	1	0.599	0.556	0.643	CLONAL	1	TRUE	2	0.660785086635209	4		409	856	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396463	139396463	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018760-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1579	147	511	0	ENST00000277541.6:c.5462A>C	p.Lys1821Thr	p.K1821T	ENST00000277541	NM_017617.3	1821	aAg/aCg	29/34	0.660785086635209	5	FACETS	0.513	0.466	0.563	0.171	0.155	0.188	SUBCLONAL	1	TRUE	2	0.660785086635209	5		511	1726	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0018986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	274	620	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.833565954128809	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.837620184712793	1		621	364	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405953	157405954	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1554294674	NA	P-0018986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	218	406	1	ENST00000346085.5:c.2201dup	p.Ser736IlefsTer27	p.S736Ifs*27	ENST00000346085	NM_020732.3	732	ccg/ccGg	6/20	1	2	FACETS	0.926	0.868	0.985	0.926	0.868	0.985	CLONAL	1	TRUE	1	0.837620184712793	2		407	562	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489571	56489571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	229	424	0	ENST00000267101.3:c.2036G>A	p.Arg679Gln	p.R679Q	ENST00000267101	NM_001982.3	679	cGa/cAa	17/28	1	2	FACETS	0.992	0.933	1	0.992	0.933	1	CLONAL	1	TRUE	1	0.837620184712793	2		424	551	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088681	27088682	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0018986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	300	570	0	ENST00000324856.7:c.2296dup	p.Gln766ProfsTer51	p.Q766Pfs*51	ENST00000324856	NM_006015.4	764	tcc/tCcc	7/20	1	2	FACETS	0.984	0.932	1	0.984	0.932	1	CLONAL	1	TRUE	1	0.837620184712793	2		570	728	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917782	29917782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56077855	NA	P-0018986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	283	499	3	ENST00000389048.3:c.886G>A	p.Glu296Lys	p.E296K	ENST00000389048	NM_004304.4	296	Gag/Aag	3/29	1	2	FACETS	0.974	0.921	1	0.974	0.921	1	CLONAL	1	TRUE	1	0.837620184712793	2		502	694	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057712	27057712	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	305	606	0	ENST00000324856.7:c.1420C>T	p.Gln474Ter	p.Q474*	ENST00000324856	NM_006015.4	474	Caa/Taa	3/20	1	2	FACETS	0.979	0.928	1	0.979	0.928	1	CLONAL	1	TRUE	1	0.837620184712793	2		606	744	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359423	118359425	+	inframe_deletion	In_Frame_Del	DEL	GTC	GTC	-	novel	NA	P-0018986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	163	367	0	ENST00000534358.1:c.4432_4434del	p.Arg1478del	p.R1478del	ENST00000534358	NM_005933.3	1476	tGTCgt/tgt	11/36	0.214641307043221	1	FACETS	0.491	0.454	0.528	0.491	0.454	0.528	INDETERMINATE	1	TRUE	0	0.837620184712793	1		367	461	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813823	50813823	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	294	569	1	ENST00000398568.2:c.1377G>A	p.Met459Ile	p.M459I	ENST00000398568	NM_001042412.1	459	atG/atA	8/18	0.215326308096867	1	FACETS	0.59	0.559	0.621	0.59	0.559	0.621	INDETERMINATE	1	TRUE	0	0.837620184712793	1		570	692	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627844	14627844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766997470	NA	P-0018986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	319	535	0	ENST00000254322.2:c.226G>A	p.Gly76Ser	p.G76S	ENST00000254322	NM_006145.1	76	Ggc/Agc	2/3	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.837620184712793	2		535	762	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591109	67591114	+	inframe_deletion	In_Frame_Del	DEL	CCAGAC	CCAGAC	-	novel	NA	P-0018986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	214	364	0	ENST00000274335.5:c.1703_1708del	p.Pro568_Asp569del	p.P568_D569del	ENST00000274335		568	CCAGAC/-	12/15	0.837620184712793	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.837620184712793	1		364	297	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459891	149459891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143025739	NA	P-0018986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	309	515	0	ENST00000286301.3:c.316C>T	p.Arg106Trp	p.R106W	ENST00000286301	NM_005211.3	106	Cgg/Tgg	4/22	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.837620184712793	2		515	695	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021826	69021826	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	310	565	0	ENST00000288368.4:c.3114A>C	p.Lys1038Asn	p.K1038N	ENST00000288368	NM_024870.2	1038	aaA/aaC	25/40	1	2	FACETS	0.995	0.944	1	0.995	0.944	1	CLONAL	1	TRUE	1	0.837620184712793	2		565	744	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0019001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	126	363	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.522646581464124	2		363	343	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0019001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	285	686	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.522646581464124	2	FACETS	0.898	0.862	0.932	1	0.995	1	CLONAL	3	TRUE	0	0.522646581464124	2		686	405	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998867	100998867	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1415882766	NA	P-0019001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	34	1050	0	ENST00000325455.5:c.935A>G	p.Asn312Ser	p.N312S	ENST00000325455	NM_001202474.3	312	aAt/aGt	1/8	1	2	FACETS	0.685	0.565	0.816	0.685	0.565	0.816	SUBCLONAL	1	TRUE	1	0.522646581464124	2		1050	190	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281225	46281225	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	26	731	0	ENST00000371998.3:c.4022G>C	p.Gly1341Ala	p.G1341A	ENST00000371998		1341	gGt/gCt	21/23	1	2	FACETS	0.216	0.171	0.269	0.216	0.171	0.269	SUBCLONAL	1	TRUE	1	0.522646581464124	2		731	460	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866456	42866456	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	93	1188	1	ENST00000398585.3:c.176C>A	p.Pro59Gln	p.P59Q	ENST00000398585	NM_001135099.1	59	cCg/cAg	3/14	0.269070367861542	0	FACETS	0.568	0.511	0.627			1	INDETERMINATE	1	TRUE	0	0.522646581464124	0		1189	299	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937720	76937721	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0019001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	133	860	0	ENST00000373344.5:c.3026_3027dup	p.Glu1010MetfsTer24	p.E1010Mfs*24	ENST00000373344	NM_000489.3	1009	-/AT	9/35	0.522646581464124	1	FACETS	0.774	0.72	0.827	1	0.99	1	SUBCLONAL	2	TRUE	0	0.522646581464124	1		860	243	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411902	116411902	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0019023-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	162	796	0	ENST00000397752.3:c.2888-1G>A		p.X963_splice	ENST00000397752	NM_000245.2	963			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		796	1003	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019341-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	52	258	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.339222117461886	2		258	264	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562738	29562739	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555615472	NA	P-0019341-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	164	659	0	ENST00000356175.3:c.3822_3823del	p.Phe1275ProfsTer8	p.F1275Pfs*8	ENST00000356175	NM_000267.3	1273	aCT/a	28/57	0.29992916538638	2	FACETS	0.859	0.793	0.927	0.859	0.793	0.927	CLONAL	2	TRUE	0	0.339222117461886	2		659	563	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692884	89692884	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121909222	NA	P-0019341-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	61	407	0	ENST00000371953.3:c.368A>G	p.His123Arg	p.H123R	ENST00000371953	NM_000314.4	123	cAc/cGc	5/9	0.339222117461886	1	FACETS	0.9	0.781	1	0.9	0.781	1	CLONAL	1	TRUE	0	0.339222117461886	1		407	332	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549304	21549304	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019341-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	120	971	1	ENST00000382592.4:c.2972C>A	p.Pro991His	p.P991H	ENST00000382592	NM_014572.2	991	cCc/cAc	8/8	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.339222117461886	2		972	655	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916646	178916646	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019341-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	62	402	0	ENST00000263967.3:c.33G>A	p.Trp11Ter	p.W11*	ENST00000263967	NM_006218.2	11	tgG/tgA	2/21	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.339222117461886	2		402	315	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240702	53240702	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372082304	NA	P-0019341-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	92	759	1	ENST00000375401.3:c.1378C>T	p.Arg460Trp	p.R460W	ENST00000375401	NM_004187.3	460	Cgg/Tgg	10/26	1	2	FACETS	0.827	0.735	0.924	0.827	0.735	0.924	CLONAL	1	TRUE	1	0.339222117461886	2		760	656	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0020236-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	283	814	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.282632387067301	5	FACETS	1	0.987	1	0.784	0.736	0.833	CLONAL	2	TRUE	2	0.282632387067301	5		814	1212	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001231	150001231	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020236-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	228	543	0	ENST00000253339.5:c.2373G>C	p.Met791Ile	p.M791I	ENST00000253339		791	atG/atC	4/7	0.195078734100047	3	FACETS	1	0.974	1	0.722	0.674	0.771	CLONAL	2	TRUE	0	0.282632387067301	3		543	850	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0020360-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	515	718	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.587007267354118	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.587007267354118	3		718	729	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160760	56160761	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020360-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	218	268	0	ENST00000399503.3:c.1035+1dup		p.Q345fs	ENST00000399503	NM_005921.1	345	cag/caGg	4/20	0.587007267354118	3	FACETS	0.95	0.904	0.995	0.95	0.904	0.995	CLONAL	3	TRUE	0	0.587007267354118	3		268	337	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0020383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	216	460	1	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.869	0.813	0.926	0.869	0.813	0.926	CLONAL	1	TRUE	1	0.809827904500813	2		461	614	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562482	21562483	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGGCG	rs550642106	NA	P-0020383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	11	86	0	ENST00000382592.4:c.1431_1436dup	p.Pro479_Ala480dup	p.P479_A480dup	ENST00000382592	NM_014572.2	479	ccg/ccCGCCCCg	4/8	0.809827904500813	3	FACETS	0.289	0.2	0.398	0.145	0.1	0.199	SUBCLONAL	1	TRUE	1	0.809827904500813	3		86	132	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519938	NA	P-0020383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	186	425	0	ENST00000263967.3:c.1034A>T	p.Asn345Ile	p.N345I	ENST00000263967	NM_006218.2	345	aAt/aTt	5/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.809827904500813	2		425	422	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913250	NA	P-0020383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	216	389	0	ENST00000369535.4:c.34G>T	p.Gly12Cys	p.G12C	ENST00000369535	NM_002524.4	12	Ggt/Tgt	2/7	0.809827904500813	1	FACETS	0.998	0.952	1	0.998	0.952	1	CLONAL	1	TRUE	0	0.809827904500813	1		389	318	SUCCESS
APC	324	MSKCC	GRCh37	5	112173835	112173838	+	frameshift_variant	Frame_Shift_Del	DEL	AGAT	AGAT	-	rs398123118	NA	P-0020383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	179	418	0	ENST00000257430.4:c.2547_2550del	p.Asp849GlufsTer11	p.D849Efs*11	ENST00000257430	NM_000038.5	848	aaAGAT/aa	16/16	0.809827904500813	1	FACETS	0.996	0.945	1	0.996	0.945	1	CLONAL	1	TRUE	0	0.809827904500813	1		418	264	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711272	114711273	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	173	289	0	ENST00000543371.1:c.291dup	p.Pro98AlafsTer47	p.P98Afs*47	ENST00000543371	NM_001198531.1	96	aag/aaGg	3/14	1	2	FACETS	0.917	0.852	0.983	0.917	0.852	0.983	CLONAL	1	TRUE	1	0.809827904500813	2		289	466	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0021285-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	295	434	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.3	9	FACETS	0.972	0.921	1			1	CLONAL	8	TRUE	NA	0.17	9		434	712	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0021285-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	83	778	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	0.17	2		779	765	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974697	21974701	+	frameshift_variant	Frame_Shift_Del	DEL	AACTA	AACTA	-	novel	NA	P-0021285-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	27	400	0	ENST00000304494.5:c.126_130del	p.Asn42LysfsTer76	p.N42Kfs*76	ENST00000304494	NM_000077.4	42	aaTAGTTac/aaac	1/3	1	2	FACETS	0.923	0.735	1	0.923	0.735	1	CLONAL	1	TRUE	1	0.17	2		400	344	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112989	2112989	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137854154	NA	P-0023567-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	305	557	0	ENST00000219476.3:c.1378G>A	p.Ala460Thr	p.A460T	ENST00000219476	NM_000548.3	460	Gcc/Acc	14/42	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.842489051812302	2		557	641	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691025	NA	P-0023567-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	535	536	5	ENST00000269305.4:c.785G>T	p.Gly262Val	p.G262V	ENST00000269305	NM_001126112.2	262	gGt/gTt	8/11	0.842489051812302	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.842489051812302	2		541	622	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244226	46244226	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023567-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	172	388	0	ENST00000334344.6:c.2320C>G	p.Pro774Ala	p.P774A	ENST00000334344	NM_152641.2	774	Cca/Gca	15/21	0.842489051812302	2	FACETS	0.936	0.871	1	0.468	0.435	0.502	CLONAL	1	TRUE	0	0.842489051812302	2		388	436	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602379	10602379	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023567-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	392	877	2	ENST00000171111.5:c.1199C>G	p.Thr400Ser	p.T400S	ENST00000171111	NM_203500.1	400	aCc/aGc	3/6	0.842489051812302	2	FACETS	1	0.961	1	0.504	0.48	0.527	CLONAL	1	TRUE	0	0.842489051812302	2		879	924	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778143	27778143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023567-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	284	640	0	ENST00000369163.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000369163	NM_003536.2	98	Gag/Aag	1/1	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.842489051812302	2		640	635	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137522066	137522066	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023567-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	153	327	0	ENST00000367739.4:c.813G>C	p.Lys271Asn	p.K271N	ENST00000367739	NM_000416.2	271	aaG/aaC	6/7	0.842489051812302	3	FACETS	1	0.928	1	0.504	0.464	0.545	CLONAL	1	TRUE	1	0.842489051812302	3		327	512	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145588	11145588	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs1308562238	NA	P-0024127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	276	366	8	ENST00000358026.2:c.3952-2A>T		p.X1318_splice	ENST00000358026	NM_001128849.1	1318			0.681119973385648	2	FACETS	0.961	0.921	1	0.961	0.921	1	CLONAL	2	TRUE	0	0.703740687495085	2		374	408	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172106	32172106	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	290	691	0	ENST00000375023.3:c.2926C>A	p.Pro976Thr	p.P976T	ENST00000375023	NM_004557.3	976	Ccc/Acc	19/30	1	2	FACETS	0.942	0.889	0.996	0.942	0.889	0.996	CLONAL	1	TRUE	1	0.703740687495085	2		691	875	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	457	258	0				ENST00000310581	NM_198253.2	-/1132			0.659036807619971	7	FACETS	1	0.984	1	1	0.984	1	CLONAL	5	TRUE	2	0.659036807619971	7		258	712	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0024797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	544	614	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.659036807619971	3	FACETS	0.987	0.961	1	0.987	0.961	1	CLONAL	3	TRUE	0	0.659036807619971	3		616	741	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438587	49438587	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	181	582	0	ENST00000301067.7:c.4903del	p.Gly1636AlafsTer86	p.G1636Afs*86	ENST00000301067	NM_003482.3	1635	Ctt/tt	19/54	0.659036807619971	3	FACETS	0.994	0.919	1	0.497	0.459	0.536	CLONAL	1	TRUE	1	0.659036807619971	3		582	735	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934194	48934194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	110	488	0	ENST00000267163.4:c.649C>T	p.Gln217Ter	p.Q217*	ENST00000267163	NM_000321.2	217	Cag/Tag	7/27	0.623742373561878	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.659036807619971	1		488	222	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095002	11095002	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1315494799	NA	P-0024797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	613	604	0	ENST00000358026.2:c.175C>T	p.Gln59Ter	p.Q59*	ENST00000358026	NM_001128849.1	59	Cag/Tag	2/36	0.659036807619971	3	FACETS	0.965	0.94	0.99	0.965	0.94	0.99	CLONAL	3	TRUE	0	0.659036807619971	3		604	854	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207631	29207632	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0024797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	169	549	0	ENST00000240100.2:c.164dup	p.His56AlafsTer15	p.H56Afs*15	ENST00000240100	NM_001394.6	55	gcg/gcCg	1/4	1	2	FACETS	0.932	0.863	1	0.932	0.863	1	CLONAL	1	TRUE	1	0.659036807619971	2		549	550	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0025017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	173	686	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.238729363338543	2	FACETS	1	0.99	1	0.74	0.684	0.799	CLONAL	1	TRUE	0	0.356789777789926	2		686	655	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0025017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	58	460	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.211489878516109	0	FACETS	0.382	0.328	0.441			1	INDETERMINATE	1	TRUE	0	0.356789777789926	0		460	547	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0025017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	44	369	1	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.661	0.556	0.777	0.661	0.556	0.777	SUBCLONAL	1	TRUE	1	0.356789777789926	2		370	373	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114917779	114917779	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0025017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	50	309	0	ENST00000543371.1:c.1270-1G>A		p.X424_splice	ENST00000543371	NM_001198531.1	424			1	2	FACETS	0.801	0.682	0.93	0.801	0.682	0.93	CLONAL	1	TRUE	1	0.356789777789926	2		309	350	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180040015	180040015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564369853	NA	P-0025017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	75	703	0	ENST00000261937.6:c.3427G>A	p.Ala1143Thr	p.A1143T	ENST00000261937	NM_182925.4	1143	Gcc/Acc	25/30	1	2	FACETS	0.58	0.508	0.658	0.58	0.508	0.658	SUBCLONAL	1	TRUE	1	0.356789777789926	2		703	725	SUCCESS
APC	324	MSKCC	GRCh37	5	112175344	112175345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTTGAATTTTCTTCAG	novel	NA	P-0025017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	24	288	0	ENST00000257430.4:c.4055_4070dup	p.Ala1358Ter	p.A1358*	ENST00000257430	NM_000038.5	1351	-/GTTGAATTTTCTTCAG	16/16	1	2	FACETS	0.456	0.358	0.569	0.456	0.358	0.569	SUBCLONAL	1	TRUE	1	0.356789777789926	2		288	295	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039839	47039887	+	frameshift_variant	Frame_Shift_Del	DEL	CAGTCGCATCAGTGCTGCCTCTGTGGCCAGCACTGCCATTGCTGCGGCC	CAGTCGCATCAGTGCTGCCTCTGTGGCCAGCACTGCCATTGCTGCGGCC	-	novel	NA	P-0025017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	35	461	0	ENST00000377604.3:c.1186_1234del	p.Arg396GlyfsTer73	p.R396Gfs*73	ENST00000377604	NM_001204468.1	394	ggCAGTCGCATCAGTGCTGCCTCTGTGGCCAGCACTGCCATTGCTGCGGCC/gg	12/24	0.227194454780091	2	FACETS	0.322	0.263	0.389			1	SUBCLONAL	1	TRUE	NA	0.356789777789926	2		461	609	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128028995	128028995	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025924-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	28	525	1	ENST00000285398.2:c.1862A>T	p.Asn621Ile	p.N621I	ENST00000285398	NM_000122.1	621	aAt/aTt	12/15	1	2	FACETS	0.592	0.472	0.729	0.592	0.472	0.729	SUBCLONAL	1	TRUE	1	0.2	2		526	473	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513263	106513263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025924-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	39	411	1	ENST00000359195.3:c.2167G>A	p.Gly723Ser	p.G723S	ENST00000359195	NM_002649.2	723	Ggc/Agc	4/11	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.2	2		412	332	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877140	151877140	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025924-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	36	555	0	ENST00000262189.6:c.7221del	p.Ser2408HisfsTer44	p.S2408Hfs*44	ENST00000262189	NM_170606.2	2407	ggG/gg	37/59	1	2	FACETS	0.828	0.68	0.992	0.828	0.68	0.992	CLONAL	1	TRUE	1	0.2	2		555	435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0026114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	296	620	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.654489373493634	2	FACETS	0.975	0.934	1	0.975	0.934	1	CLONAL	2	TRUE	0	0.654489373493634	2		621	464	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370813	225370813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1206525768	NA	P-0026114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	122	433	1	ENST00000264414.4:c.1066C>T	p.Leu356Phe	p.L356F	ENST00000264414	NM_003590.4	356	Ctc/Ttc	8/16	0.654489373493634	3	FACETS	0.844	0.766	0.927	0.422	0.383	0.464	CLONAL	1	TRUE	1	0.654489373493634	3		434	586	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259401	89259401	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	124	553	1	ENST00000336596.2:c.545C>T	p.Ala182Val	p.A182V	ENST00000336596	NM_005233.5	182	gCa/gTa	3/17	1	2	FACETS	0.775	0.705	0.848	0.775	0.705	0.848	SUBCLONAL	1	TRUE	1	0.654489373493634	2		554	489	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778831	9778831	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375873391	NA	P-0026114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	153	584	3	ENST00000377346.4:c.1100C>T	p.Ser367Leu	p.S367L	ENST00000377346	NM_005026.3	367	tCg/tTg	9/24	1	2	FACETS	0.958	0.883	1	0.958	0.883	1	CLONAL	1	TRUE	1	0.654489373493634	2		587	488	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435317	56435317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200066146	NA	P-0026670-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1969	136	593	0	ENST00000407977.2:c.1820C>T	p.Ser607Leu	p.S607L	ENST00000407977		607	tCg/tTg	9/10	0.456062611037288	13	FACETS	0.994	0.899	1	0.099	0.089	0.11	CLONAL	1	FALSE	3	0.456062611037288	13		593	2105	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026670-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	143	636	0	ENST00000206249.3:c.1610A>G	p.Tyr537Cys	p.Y537C	ENST00000206249	NM_000125.3	537	tAt/tGt	8/8	0.428049901901609	2	FACETS	0.994	0.909	1	0.497	0.454	0.541	CLONAL	1	FALSE	0	0.456062611037288	2		636	631	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115889	8115926	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGCCACATGCTGACCACGCCCACGCCGATGCACCCG	CCAGCCACATGCTGACCACGCCCACGCCGATGCACCCG	-	novel	NA	P-0026670-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	217	553	1	ENST00000346208.3:c.1238_1275del	p.Ser413IlefsTer81	p.S413Ifs*81	ENST00000346208		412	tCCAGCCACATGCTGACCACGCCCACGCCGATGCACCCG/t	6/6	0.456062611037288	3	FACETS	1	0.991	1	0.715	0.666	0.765	CLONAL	1	FALSE	1	0.456062611037288	3		554	817	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201476	67201476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201850616	NA	P-0026670-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	168	685	1	ENST00000312629.5:c.917G>A	p.Arg306Gln	p.R306Q	ENST00000312629	NM_003952.2	306	cGg/cAg	11/15	0.456062611037288	3	FACETS	1	0.958	1	0.355	0.326	0.385	CLONAL	1	FALSE	0	0.456062611037288	3		686	850	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119984	70119984	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886053351	NA	P-0026670-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	54	248	1	ENST00000245479.2:c.986C>T	p.Ala329Val	p.A329V	ENST00000245479	NM_000346.3	329	gCg/gTg	3/3	0.456062611037288	13	FACETS	0.882	0.751	1	0.088	0.075	0.103	CLONAL	1	FALSE	3	0.456062611037288	13		249	942	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191635	10191635	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774380450	NA	P-0026670-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	131	595	1	ENST00000256474.2:c.628C>T	p.Arg210Trp	p.R210W	ENST00000256474	NM_000551.3	210	Cgg/Tgg	3/3	0.456062611037288	4	FACETS	0.879	0.796	0.965	0.293	0.265	0.322	CLONAL	1	FALSE	1	0.456062611037288	4		596	952	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0026688-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	189	447	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.365447817194357	4	FACETS	0.844	0.784	0.906	0.844	0.784	0.906	CLONAL	2	FALSE	2	0.543057025147944	4		447	636	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602763	10602763	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs774469695	NA	P-0026688-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	275	989	0	ENST00000171111.5:c.815G>T	p.Arg272Leu	p.R272L	ENST00000171111	NM_203500.1	272	cGc/cTc	3/6	0.431114876366307	2	FACETS	0.758	0.717	0.8	0.758	0.717	0.8	SUBCLONAL	2	FALSE	0	0.543057025147944	2		989	668	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22417972	22417972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026688-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	23	112	0	ENST00000344548.3:c.538C>T	p.Pro180Ser	p.P180S	ENST00000344548	NM_001039802.1	180	Cca/Tca	7/7	0.44514623819579	3	FACETS	0.89	0.704	1	0.445	0.352	0.549	CLONAL	1	FALSE	1	0.543057025147944	3		112	121	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945357	71945357	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026688-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	295	901	1	ENST00000298229.2:c.2245G>T	p.Glu749Ter	p.E749*	ENST00000298229	NM_001567.3	749	Gag/Tag	20/28	0.44514623819579	3	FACETS	0.887	0.839	0.935	0.887	0.839	0.935	CLONAL	2	FALSE	1	0.543057025147944	3		902	779	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226469	133226469	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026688-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	91	460	0	ENST00000320574.5:c.3589A>G	p.Met1197Val	p.M1197V	ENST00000320574	NM_006231.2	1197	Atg/Gtg	30/49	0.365447817194357	4	FACETS	1	0.976	1	0.67	0.599	0.744	CLONAL	1	FALSE	2	0.543057025147944	4		460	386	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919688	28919689	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0026688-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	103	369	2	ENST00000282397.4:c.2249-1_2249delinsTT		p.X750_splice	ENST00000282397	NM_002019.4	750		16/30	0.431114876366307	2	FACETS	1	0.983	1	0.708	0.644	0.773	CLONAL	1	FALSE	0	0.543057025147944	2		371	268	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778802	3778802	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026688-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	191	984	0	ENST00000262367.5:c.6246G>T	p.Gln2082His	p.Q2082H	ENST00000262367	NM_004380.2	2082	caG/caT	31/31	0.29417039020005	5	FACETS	0.804	0.745	0.865	0.536	0.496	0.577	INDETERMINATE	2	FALSE	2	0.543057025147944	5		984	794	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39870295	39870295	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026688-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	52	261	0	ENST00000288319.7:c.10A>G	p.Thr4Ala	p.T4A	ENST00000288319	NM_182918.3	4	Act/Gct	1/10	0.44514623819579	3	FACETS	0.698	0.597	0.808	0.349	0.298	0.404	SUBCLONAL	1	FALSE	1	0.543057025147944	3		261	349	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928394	69928394	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026688-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	153	435	1	ENST00000352241.4:c.214G>T	p.Glu72Ter	p.E72*	ENST00000352241	NM_198159.2	72	Gag/Tag	2/10	0.543057025147944	3	FACETS	0.857	0.792	0.923	0.857	0.792	0.923	CLONAL	2	FALSE	1	0.543057025147944	3		436	418	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888750	76888750	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026688-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	217	643	0	ENST00000373344.5:c.5079G>T	p.Arg1693Ser	p.R1693S	ENST00000373344	NM_000489.3	1693	agG/agT	19/35	0.29417039020005	5	FACETS	0.864	0.805	0.925	0.576	0.537	0.617	INDETERMINATE	2	FALSE	2	0.543057025147944	5		643	839	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938103	76938106	+	frameshift_variant	Frame_Shift_Del	DEL	TTTC	TTTC	-	novel	NA	P-0026688-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	199	781	0	ENST00000373344.5:c.2642_2645del	p.Arg881AsnfsTer23	p.R881Nfs*23	ENST00000373344	NM_000489.3	881	aGAAAa/aa	9/35	0.29417039020005	5	FACETS	1	0.989	1	0.462	0.428	0.498	INDETERMINATE	1	FALSE	2	0.543057025147944	5		781	959	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165782	108165783	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	A	novel	NA	P-0026688-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	132	343	0	ENST00000278616.4:c.4905_4906delinsA	p.Gln1636ArgfsTer10	p.Q1636Rfs*10	ENST00000278616	NM_000051.3	1635	tcTCag/tcAag	32/63	0.329462457173812	3	FACETS	1	0.929	1	0.671	0.619	0.724	CLONAL	2	FALSE	0	0.543057025147944	3		343	307	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533630	63533631	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	A	novel	NA	P-0026688-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	231	821	0	ENST00000307078.5:c.1523_1524delinsT	p.Lys508IlefsTer181	p.K508Ifs*181	ENST00000307078	NM_004655.3	508	aAG/aT	6/11	0.29417039020005	5	FACETS	1	0.941	1	0.671	0.628	0.715	INDETERMINATE	2	FALSE	2	0.543057025147944	5		821	767	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0026821-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	329	814	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.499599245695637	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.499599245695637	1		814	838	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976742	2976742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1225008718	NA	P-0026821-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	63	796	1	ENST00000396946.4:c.1270C>T	p.Arg424Trp	p.R424W	ENST00000396946	NM_032415.4	424	Cgg/Tgg	9/25	1	2	FACETS	0.225	0.193	0.259	0.225	0.193	0.259	SUBCLONAL	1	TRUE	1	0.499599245695637	2		797	1122	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0027010-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	112	447	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.849	0.768	0.934	1	0.987	1	CLONAL	2	FALSE	1	0.271375030307783	2		447	486	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027183-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	144	258	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.757923913878047	2		258	370	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098426	11098426	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1170997392	NA	P-0027183-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	229	438	0	ENST00000358026.2:c.944C>T	p.Pro315Leu	p.P315L	ENST00000358026	NM_001128849.1	315	cCc/cTc	6/36	0.715001258878491	3	FACETS	1	0.979	1	0.556	0.519	0.592	CLONAL	1	TRUE	1	0.757923913878047	3		438	750	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224324	55224324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027183-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	184	585	0	ENST00000275493.2:c.1105C>T	p.Leu369Phe	p.L369F	ENST00000275493	NM_005228.3	369	Ctc/Ttc	9/28	0.756056283273163	3	FACETS	0.595	0.548	0.643	0.297	0.274	0.322	SUBCLONAL	1	TRUE	1	0.757923913878047	3		585	1126	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	144	620	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.958	0.878	1	0.958	0.878	1	CLONAL	1	TRUE	1	0.569609506254483	2		621	528	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959120	28959120	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753133916	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	150	485	3	ENST00000282397.4:c.2018C>T	p.Ala673Val	p.A673V	ENST00000282397	NM_002019.4	673	gCc/gTc	14/30	0.569609506254483	1	FACETS	0.939	0.868	1	0.939	0.868	1	CLONAL	1	TRUE	0	0.569609506254483	1		488	401	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	113	325	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.64	0.577	0.706	0.64	0.577	0.706	SUBCLONAL	1	TRUE	1	0.569609506254483	2		325	620	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931463	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622007	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	170	353	0	ENST00000374690.3:c.2105T>A	p.Leu702His	p.L702H	ENST00000374690	NM_000044.3	702	cTc/cAc	4/8	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.569609506254483	1		353	357	SUCCESS
AR	367	MSKCC	GRCh37	X	66943543	66943543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852581	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	190	299	2	ENST00000374690.3:c.2623C>T	p.His875Tyr	p.H875Y	ENST00000374690	NM_000044.3	875	Cat/Tat	8/8	1	1	FACETS	0.864	0.822	0.905	1	0.994	1	CLONAL	2	TRUE	0	0.569609506254483	1		301	276	SUCCESS
AR	367	MSKCC	GRCh37	X	66931247	66931247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868669253	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	77	212	0	ENST00000374690.3:c.1889G>A	p.Arg630Gln	p.R630Q	ENST00000374690	NM_000044.3	630	cGg/cAg	4/8	1	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.569609506254483	1		212	142	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371708	225371708	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	166	584	0	ENST00000264414.4:c.896T>G	p.Met299Arg	p.M299R	ENST00000264414	NM_003590.4	299	aTg/aGg	7/16	1	2	FACETS	0.846	0.779	0.915	0.846	0.779	0.915	CLONAL	1	TRUE	1	0.569609506254483	2		584	689	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11554273	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	173	547	0	ENST00000371085.3:c.601C>A	p.Arg201Ser	p.R201S	ENST00000371085	NM_000516.4	201	Cgt/Agt	8/13	1	2	FACETS	0.837	0.772	0.904	0.837	0.772	0.904	CLONAL	1	TRUE	1	0.569609506254483	2		547	726	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138729528	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	111	694	0	ENST00000269305.4:c.523C>T	p.Arg175Cys	p.R175C	ENST00000269305	NM_001126112.2	175	Cgc/Tgc	5/11	1	2	FACETS	0.731	0.66	0.806	0.731	0.66	0.806	SUBCLONAL	1	TRUE	1	0.569609506254483	2		694	533	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	124	241	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.569609506254483	2		241	386	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857933	89857933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780135578	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	35	551	0	ENST00000389301.3:c.1237C>T	p.Arg413Cys	p.R413C	ENST00000389301	NM_000135.2	413	Cgt/Tgt	14/43	1	2	FACETS	0.213	0.174	0.257	0.213	0.174	0.257	SUBCLONAL	1	TRUE	1	0.569609506254483	2		551	578	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795269	42795269	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs34000070	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	96	676	2	ENST00000575354.2:c.2353del	p.Ala785ProfsTer139	p.A785Pfs*139	ENST00000575354	NM_015125.3	783	caG/ca	10/20	1	2	FACETS	0.856	0.768	0.947	0.856	0.768	0.947	CLONAL	1	TRUE	1	0.569609506254483	2		678	394	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3841994	3841994	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	121	245	2	ENST00000262367.5:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000262367	NM_004380.2	440	Cga/Tga	5/31	1	2	FACETS	0.626	0.566	0.688	0.626	0.566	0.688	SUBCLONAL	1	TRUE	1	0.569609506254483	2		247	679	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713414	40713414	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	178	418	0	ENST00000373198.4:c.4101del	p.Ser1368ProfsTer31	p.S1368Pfs*31	ENST00000373198	NM_133170.3	1367	ccC/cc	30/32	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.569609506254483	2		418	589	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574679	41574679	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	47	814	0	ENST00000263253.7:c.6970del	p.His2324ThrfsTer29	p.H2324Tfs*29	ENST00000263253	NM_001429.3	2322	Ccc/cc	31/31	1	2	FACETS	0.234	0.196	0.275	0.234	0.196	0.275	SUBCLONAL	1	TRUE	1	0.569609506254483	2		814	706	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156729	106156729	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1440692352	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	146	489	1	ENST00000380013.4:c.1630C>T	p.Arg544Ter	p.R544*	ENST00000380013	NM_001127208.2	544	Cga/Tga	3/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.569609506254483	2		490	438	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830135	72830135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	215	669	0	ENST00000268489.5:c.6446G>A	p.Arg2149His	p.R2149H	ENST00000268489	NM_006885.3	2149	cGc/cAc	9/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.569609506254483	2		669	735	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246488	46246488	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761166036	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	82	343	0	ENST00000334344.6:c.4582G>A	p.Ala1528Thr	p.A1528T	ENST00000334344	NM_152641.2	1528	Gca/Aca	15/21	0.175178280838584	3	FACETS	1	0.976	1	0.685	0.612	0.761	INDETERMINATE	1	TRUE	1	0.569609506254483	3		343	270	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209593	98209593	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	82	537	0	ENST00000331920.6:c.3945del	p.Tyr1316ThrfsTer56	p.Y1316Tfs*56	ENST00000331920	NM_000264.3	1315	ccC/cc	23/24	1	2	FACETS	0.742	0.658	0.831	0.742	0.658	0.831	SUBCLONAL	1	TRUE	1	0.569609506254483	2		537	388	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998888	100998888	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	91	694	0	ENST00000325455.5:c.914A>G	p.His305Arg	p.H305R	ENST00000325455	NM_001202474.3	305	cAc/cGc	1/8	1	2	FACETS	0.692	0.617	0.771	0.692	0.617	0.771	SUBCLONAL	1	TRUE	1	0.569609506254483	2		694	462	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118391565	118391565	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	44	440	0	ENST00000534358.1:c.11483del	p.Lys3828ArgfsTer31	p.K3828Rfs*31	ENST00000534358	NM_005933.3	3826	ttA/tt	34/36	1	2	FACETS	0.277	0.232	0.327	0.277	0.232	0.327	SUBCLONAL	1	TRUE	1	0.569609506254483	2		440	558	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992720	68992721	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs764112302	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	170	697	12	ENST00000288368.4:c.1693dup	p.Ser565PhefsTer3	p.S565Ffs*3	ENST00000288368	NM_024870.2	562	cgt/cgTt	16/40	1	2	FACETS	0.732	0.674	0.793	0.732	0.674	0.793	SUBCLONAL	1	TRUE	1	0.569609506254483	2		709	815	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511574	66511574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	149	383	0	ENST00000358598.2:c.34G>A	p.Ala12Thr	p.A12T	ENST00000358598	NM_212471.2	12	Gca/Aca	2/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.569609506254483	2		383	460	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959366	26959366	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1418353379	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	99	510	0	ENST00000381527.3:c.533G>A	p.Arg178Gln	p.R178Q	ENST00000381527	NM_001260.1	178	cGa/cAa	6/13	0.569609506254483	1	FACETS	0.733	0.661	0.808	0.733	0.661	0.808	SUBCLONAL	1	TRUE	0	0.569609506254483	1		510	339	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831345	89831346	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs878853663	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	131	656	4	ENST00000389301.3:c.2730_2731del	p.Trp911AspfsTer31	p.W911Dfs*31	ENST00000389301	NM_000135.2	910	ctCTgg/ctgg	28/43	1	2	FACETS	0.762	0.693	0.833	0.762	0.693	0.833	SUBCLONAL	1	TRUE	1	0.569609506254483	2		660	604	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622410	1622410	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	145	651	0	ENST00000344749.5:c.554A>G	p.Tyr185Cys	p.Y185C	ENST00000344749	NM_001136139.2	185	tAc/tGc	9/19	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.569609506254483	2		651	491	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599938	28599938	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148305939	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	33	613	2	ENST00000253063.3:c.820C>T	p.Arg274Trp	p.R274W	ENST00000253063	NM_031459.4	274	Cgg/Tgg	6/10	1	2	FACETS	0.208	0.169	0.253	0.208	0.169	0.253	SUBCLONAL	1	TRUE	1	0.569609506254483	2		615	556	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321263	65321263	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	148	693	1	ENST00000342505.4:c.1577T>C	p.Leu526Pro	p.L526P	ENST00000342505	NM_002227.2	526	cTc/cCc	11/25	1	2	FACETS	0.77	0.705	0.838	0.77	0.705	0.838	SUBCLONAL	1	TRUE	1	0.569609506254483	2		694	675	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440528	49440528	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	74	828	0	ENST00000301067.7:c.4282A>G	p.Ile1428Val	p.I1428V	ENST00000301067	NM_003482.3	1428	Att/Gtt	15/54	0.569609506254483	3	FACETS	0.299	0.26	0.341	0.149	0.13	0.171	SUBCLONAL	1	TRUE	1	0.569609506254483	3		828	1117	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608530	28608530	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1320131173	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	180	621	0	ENST00000241453.7:c.1612A>G	p.Ile538Val	p.I538V	ENST00000241453	NM_004119.2	538	Atc/Gtc	13/24	0.569609506254483	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.569609506254483	1		621	445	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606082	81606082	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	173	604	1	ENST00000298171.2:c.752A>T	p.Glu251Val	p.E251V	ENST00000298171	NM_000369.2	251	gAa/gTa	9/10	1	2	FACETS	0.946	0.874	1	0.946	0.874	1	CLONAL	1	TRUE	1	0.569609506254483	2		605	642	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99482481	99482481	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774388898	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	191	641	0	ENST00000268035.6:c.3349G>A	p.Gly1117Arg	p.G1117R	ENST00000268035	NM_000875.3	1117	Gga/Aga	18/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.569609506254483	2		641	625	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129088	2129088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397514985	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	154	610	0	ENST00000219476.3:c.3022G>A	p.Val1008Met	p.V1008M	ENST00000219476	NM_000548.3	1008	Gtg/Atg	27/42	1	2	FACETS	0.967	0.89	1	0.967	0.89	1	CLONAL	1	TRUE	1	0.569609506254483	2		610	559	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647685	3647685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1160715108	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	231	842	0	ENST00000294008.3:c.1378C>T	p.Arg460Cys	p.R460C	ENST00000294008	NM_032444.2	460	Cgc/Tgc	7/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.569609506254483	2		842	772	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56381339	56381339	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	120	369	0	ENST00000348428.3:c.983C>A	p.Pro328His	p.P328H	ENST00000348428	NM_006785.3	328	cCt/cAt	8/17	1	2	FACETS	0.843	0.765	0.924	0.843	0.765	0.924	CLONAL	1	TRUE	1	0.569609506254483	2		369	500	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223057	1223057	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	152	782	0	ENST00000326873.7:c.994T>C	p.Trp332Arg	p.W332R	ENST00000326873	NM_000455.4	332	Tgg/Cgg	8/10	1	2	FACETS	0.555	0.507	0.605	0.555	0.507	0.605	SUBCLONAL	1	TRUE	1	0.569609506254483	2		782	962	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353755	15353755	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	141	668	0	ENST00000263377.2:c.3125A>G	p.His1042Arg	p.H1042R	ENST00000263377	NM_058243.2	1042	cAc/cGc	14/20	1	2	FACETS	0.643	0.586	0.702	0.643	0.586	0.702	SUBCLONAL	1	TRUE	1	0.569609506254483	2		668	770	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957865	1957865	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756624618	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	171	629	1	ENST00000382891.5:c.2831G>A	p.Arg944Gln	p.R944Q	ENST00000382891	NM_133335.3	944	cGg/cAg	15/22	NA	2	FACETS	0.854	0.788	0.923			1	INDETERMINATE	1	TRUE	NA	0.569609506254483	2		630	703	SUCCESS
APC	324	MSKCC	GRCh37	5	112173251	112173251	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	57	238	0	ENST00000257430.4:c.1960C>T	p.Gln654Ter	p.Q654*	ENST00000257430	NM_000038.5	654	Caa/Taa	16/16	1	2	FACETS	0.958	0.833	1	0.958	0.833	1	CLONAL	1	TRUE	1	0.569609506254483	2		238	209	SUCCESS
APC	324	MSKCC	GRCh37	5	112179089	112179089	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	73	410	0	ENST00000257430.4:c.7798C>T	p.Gln2600Ter	p.Q2600*	ENST00000257430	NM_000038.5	2600	Caa/Taa	16/16	1	2	FACETS	0.832	0.734	0.936	0.832	0.734	0.936	CLONAL	1	TRUE	1	0.569609506254483	2		410	308	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170208	32170208	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	152	806	0	ENST00000375023.3:c.3400T>C	p.Cys1134Arg	p.C1134R	ENST00000375023	NM_004557.3	1134	Tgt/Cgt	21/30	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.569609506254483	2		806	490	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001258	150001258	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	165	718	0	ENST00000253339.5:c.2346G>A	p.Met782Ile	p.M782I	ENST00000253339		782	atG/atA	4/7	1	2	FACETS	0.925	0.853	1	0.925	0.853	1	CLONAL	1	TRUE	1	0.569609506254483	2		718	626	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945685	151945685	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	218	853	0	ENST00000262189.6:c.1834A>G	p.Asn612Asp	p.N612D	ENST00000262189	NM_170606.2	612	Aat/Gat	14/59	0.307286127973657	3	FACETS	0.959	0.891	1	0.479	0.445	0.514	INDETERMINATE	1	TRUE	1	0.569609506254483	3		853	1026	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145736926	145736926	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs779070043	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	154	728	0	ENST00000428558.2:c.3515A>G	p.Tyr1172Cys	p.Y1172C	ENST00000428558	NM_004260.3	1172	tAc/tGc	22/22	1	2	FACETS	0.878	0.807	0.952	0.878	0.807	0.952	CLONAL	1	TRUE	1	0.569609506254483	2		728	616	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352259	70352259	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	18	374	0	ENST00000374080.3:c.4286C>T	p.Ala1429Val	p.A1429V	ENST00000374080		1429	gCc/gTc	31/45	1	1	FACETS	0.137	0.102	0.177	0.137	0.102	0.177	SUBCLONAL	1	TRUE	0	0.569609506254483	1		374	331	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0028265-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	298	314	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.423768846279958	1	FACETS	0.757	0.722	0.793	0.757	0.722	0.793	INDETERMINATE	1	TRUE	0	0.833247976889013	1		314	551	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028265-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	384	495	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	0.974	0.929	1	0.974	0.929	1	CLONAL	1	TRUE	1	0.833247976889013	2		495	946	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121744	108121744	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028265-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	326	517	0	ENST00000278616.4:c.1552G>A	p.Glu518Lys	p.E518K	ENST00000278616	NM_000051.3	518	Gag/Aag	10/63	0.833247976889013	1	FACETS	0.963	0.927	0.998	0.963	0.927	0.998	CLONAL	1	TRUE	0	0.833247976889013	1		517	474	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183733	10183764	+	frameshift_variant	Frame_Shift_Del	DEL	TCGCGCGAGCCCTCCCAGGTCATCTTCTGCAA	TCGCGCGAGCCCTCCCAGGTCATCTTCTGCAA	-	novel	NA	P-0028313-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	84	660	0	ENST00000256474.2:c.206_237del	p.Arg69GlnfsTer52	p.R69Qfs*52	ENST00000256474	NM_000551.3	68	TCGCGCGAGCCCTCCCAGGTCATCTTCTGCAAt/t	1/3	0.391420419145457	1	FACETS	0.846	0.752	0.946	0.846	0.752	0.946	CLONAL	1	TRUE	0	0.391420419145457	1		660	408	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144871	47144871	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028313-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	175	703	0	ENST00000409792.3:c.4882A>G	p.Asn1628Asp	p.N1628D	ENST00000409792	NM_014159.6	1628	Aat/Gat	7/21	0.391420419145457	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.391420419145457	1		703	687	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597511	52597511	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0028313-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	77	334	0	ENST00000394830.3:c.3801-2A>C		p.X1267_splice	ENST00000394830	NM_018313.4	1267			0.391420419145457	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.391420419145457	1		334	303	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508373	106508373	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028313-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	34	302	0	ENST00000359195.3:c.367C>A	p.Arg123Ser	p.R123S	ENST00000359195	NM_002649.2	123	Cgc/Agc	2/11	1	2	FACETS	0.668	0.549	0.801	0.668	0.549	0.801	SUBCLONAL	1	TRUE	1	0.391420419145457	2		302	260	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436296	110436297	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGG	rs34412495	NA	P-0121528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	27	108	1	ENST00000375856.3:c.2102_2104dup	p.Ala701dup	p.A701dup	ENST00000375856	NM_003749.2	701	gtg/gCCGtg	1/2	0.659009480230097	4	FACETS	0.859	0.692	1	0.429	0.346	0.523	CLONAL	1	NA	2	0.729961136881846	4		109	149	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	149	258	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.986	0.911	1	0.986	0.911	1	CLONAL	1	TRUE	1	0.727963731615234	2		258	415	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264568	1264568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761308654	NA	P-0028868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	206	514	0	ENST00000310581.5:c.2794G>A	p.Gly932Ser	p.G932S	ENST00000310581	NM_198253.2	932	Ggc/Agc	11/16	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.727963731615234	2		514	554	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061534	38061534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1325602525	NA	P-0028868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	142	351	0	ENST00000250448.2:c.455G>A	p.Arg152His	p.R152H	ENST00000250448	NM_004496.3	152	cGc/cAc	2/2	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.727963731615234	2		351	366	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211861	36211861	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	367	941	0	ENST00000222270.7:c.1612C>A	p.Arg538Ser	p.R538S	ENST00000222270	NM_014727.1	538	Cgt/Agt	3/37	0.727963731615234	3	FACETS	0.982	0.93	1	0.491	0.465	0.518	CLONAL	1	TRUE	1	0.727963731615234	3		941	1401	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348484	89348497	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTGATGCCGCAG	CTGTGATGCCGCAG	-	novel	NA	P-0028868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	62	778	0	ENST00000301030.4:c.4453_4466del	p.Leu1485GlyfsTer64	p.L1485Gfs*64	ENST00000301030	NM_001256183.1	1485	CTGCGGCATCACAGg/g	9/13	1	2	FACETS	0.166	0.143	0.192	0.166	0.143	0.192	SUBCLONAL	1	TRUE	1	0.727963731615234	2		778	1025	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	135	325	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.864	0.786	0.945	0.864	0.786	0.945	CLONAL	1	TRUE	1	0.435302438171811	2		325	718	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	199	632	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.992	0.919	1	0.992	0.919	1	CLONAL	1	TRUE	1	0.435302438171811	2		636	922	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	147	315	6	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	TRUE	1	0.435302438171811	2		321	670	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	129	253	6	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.435302438171811	2		259	518	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	231	540	7	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.435302438171811	2		547	1020	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552144	29552144	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	83	158	0	ENST00000356175.3:c.1882del	p.Tyr628ThrfsTer3	p.Y628Tfs*3	ENST00000356175	NM_000267.3	626	cTt/ct	17/57	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.435302438171811	2		158	318	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022940	27022942	+	inframe_deletion	In_Frame_Del	DEL	CCG	CCG	-	rs748085214	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	15	24	0	ENST00000324856.7:c.60_62del	p.Pro21del	p.P21del	ENST00000324856	NM_006015.4	16	CCG/-	1/20	0.435302438171811	3	FACETS	0.976	0.747	1	0.976	0.747	1	CLONAL	2	TRUE	1	0.435302438171811	3		24	43	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	111	417	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	NA	2	FACETS	0.832	0.75	0.919			1	INDETERMINATE	1	TRUE	NA	0.435302438171811	2		417	613	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	132	282	2	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.435302438171811	2		284	530	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175786	176175786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1227	360	648	0	ENST00000367669.3:c.329G>A	p.Ser110Asn	p.S110N	ENST00000367669	NM_022457.5	110	aGc/aAc	1/20	0.435302438171811	3	FACETS	1	0.992	1	0.635	0.6	0.67	CLONAL	1	TRUE	1	0.435302438171811	3		648	1587	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578215	28578216	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	231	496	0	ENST00000241453.7:c.2955_2956del	p.Pro986AlafsTer27	p.P986Afs*27	ENST00000241453	NM_004119.2	985	tcTCcg/tccg	24/24	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.435302438171811	2		496	1011	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056427	26056427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs182693914	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	121	277	0	ENST00000343677.2:c.230A>G	p.Asn77Ser	p.N77S	ENST00000343677	NM_005319.3	77	aAc/aGc	1/1	NA	2	FACETS	1	0.932	1			1	INDETERMINATE	1	TRUE	NA	0.435302438171811	2		277	538	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556463	29556463	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1567849208	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	158	365	0	ENST00000356175.3:c.2835del	p.Phe945LeufsTer9	p.F945Lfs*9	ENST00000356175	NM_000267.3	944	Ttt/tt	21/57	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.435302438171811	2		365	717	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129671	11129671	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	302	557	0	ENST00000358026.2:c.2481del	p.Ser828ProfsTer3	p.S828Pfs*3	ENST00000358026	NM_001128849.1	826	gCc/gc	17/36	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.435302438171811	2		557	1218	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs397518442	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	324	723	0	ENST00000326873.7:c.650del	p.Pro217ArgfsTer70	p.P217Rfs*70	ENST00000326873	NM_000455.4	216	tCc/tc	5/10	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.435302438171811	2		723	1462	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270530	98270530	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs751977093	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	142	296	1	ENST00000331920.6:c.114del	p.Leu39CysfsTer41	p.L39Cfs*41	ENST00000331920	NM_000264.3	38	ggG/gg	1/24	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.435302438171811	2		297	647	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268793	98268793	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1554708751	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	201	383	2	ENST00000331920.6:c.290del	p.Asn97ThrfsTer20	p.N97Tfs*20	ENST00000331920	NM_000264.3	97	aAc/ac	2/24	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.435302438171811	2		385	857	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161939	47161939	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	134	319	2	ENST00000409792.3:c.4187del	p.Asn1396MetfsTer16	p.N1396Mfs*16	ENST00000409792	NM_014159.6	1396	aAt/at	3/21	1	2	FACETS	0.895	0.815	0.979	0.895	0.815	0.979	CLONAL	1	TRUE	1	0.435302438171811	2		321	688	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306550	41306550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760520624	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	174	460	0	ENST00000373198.4:c.1109C>T	p.Thr370Met	p.T370M	ENST00000373198	NM_133170.3	370	aCg/aTg	7/32	1	2	FACETS	0.962	0.887	1	0.962	0.887	1	CLONAL	1	TRUE	1	0.435302438171811	2		460	831	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101170	41101170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41279256	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	218	541	0	ENST00000373198.4:c.1186G>A	p.Val396Ile	p.V396I	ENST00000373198	NM_133170.3	396	Gta/Ata	8/32	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.435302438171811	2		541	939	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540654	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	258	580	2	ENST00000269305.4:c.329G>A	p.Arg110His	p.R110H	ENST00000269305	NM_001126112.2	110	cGt/cAt	4/11	1	2	FACETS	0.97	0.907	1	0.97	0.907	1	CLONAL	1	TRUE	1	0.435302438171811	2		582	1222	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822586	72822586	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	189	437	5	ENST00000268489.5:c.9589del	p.Gln3197SerfsTer44	p.Q3197Sfs*44	ENST00000268489	NM_006885.3	3197	Cag/ag	10/10	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.435302438171811	2		442	846	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852245	63852245	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1376484834	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	99	397	0	ENST00000279873.7:c.3023C>T	p.Ala1008Val	p.A1008V	ENST00000279873	NM_032199.2	1008	gCg/gTg	10/10	1	2	FACETS	0.631	0.563	0.703	0.631	0.563	0.703	SUBCLONAL	1	TRUE	1	0.435302438171811	2		397	721	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435873	110435873	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	246	511	1	ENST00000375856.3:c.2528C>T	p.Ala843Val	p.A843V	ENST00000375856	NM_003749.2	843	gCc/gTc	1/2	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.435302438171811	2		512	1048	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	327	704	4	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.435302438171811	2		708	1422	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924240	11924240	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1462414385	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	12	18	0	ENST00000353533.5:c.41del	p.Gly14AlafsTer11	p.G14Afs*11	ENST00000353533	NM_003010.3	13	Ggg/gg	1/11	1	2	FACETS	1	0.806	1	1	0.806	1	CLONAL	1	TRUE	1	0.435302438171811	2		18	48	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427369	49427369	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1565779294	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	282	549	1	ENST00000301067.7:c.11119C>T	p.Arg3707Ter	p.R3707*	ENST00000301067	NM_003482.3	3707	Cga/Tga	39/54	0.148557604459668	4	FACETS	0.826	0.776	0.877	0.826	0.776	0.877	INDETERMINATE	2	TRUE	2	0.435302438171811	4		550	1126	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578284	7578284	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	231	466	0	ENST00000269305.4:c.565G>C	p.Ala189Pro	p.A189P	ENST00000269305	NM_001126112.2	189	Gcc/Ccc	6/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.435302438171811	2		466	970	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457276	25457276	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	185	404	1	ENST00000264709.3:c.2611C>T	p.Pro871Ser	p.P871S	ENST00000264709	NM_175629.2	871	Cca/Tca	23/23	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.435302438171811	2		405	841	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435868	110435868	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754439736	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	249	491	0	ENST00000375856.3:c.2533C>T	p.Pro845Ser	p.P845S	ENST00000375856	NM_003749.2	845	Cca/Tca	1/2	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.435302438171811	2		491	1035	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662195	227662195	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	232	544	1	ENST00000305123.5:c.1260del	p.Ser421AlafsTer42	p.S421Afs*42	ENST00000305123	NM_005544.2	420	ccC/cc	1/2	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.435302438171811	2		545	968	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426093	47426094	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1431646407	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	360	768	0	ENST00000377045.4:c.619dup	p.Leu207ProfsTer36	p.L207Pfs*36	ENST00000377045	NM_001654.4	205	gcc/gCcc	7/16	0.435302438171811	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.435302438171811	1		768	1180	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678547	88678547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	132	370	0	ENST00000360948.2:c.989del	p.Pro330HisfsTer84	p.P330Hfs*84	ENST00000360948	NM_001012338.2	330	cCa/ca	9/19	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.435302438171811	2		370	576	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527742	157527742	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	187	365	2	ENST00000346085.5:c.5471del	p.Gly1824ValfsTer27	p.G1824Vfs*27	ENST00000346085	NM_020732.3	1823	Ggg/gg	20/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.435302438171811	2		367	843	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220612	1220612	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201213	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	366	635	0	ENST00000326873.7:c.630C>A	p.Cys210Ter	p.C210*	ENST00000326873	NM_000455.4	210	tgC/tgA	5/10	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.435302438171811	2		635	1307	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214714	36214714	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	162	367	2	ENST00000222270.7:c.3145del	p.Ala1049ArgfsTer133	p.A1049Rfs*133	ENST00000222270	NM_014727.1	1047	cGg/cg	8/37	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.435302438171811	2		369	708	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161298227	161298227	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772450693	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	165	352	0	ENST00000367975.2:c.119G>A	p.Arg40Gln	p.R40Q	ENST00000367975	NM_003001.3	40	cGg/cAg	3/6	0.426970745093303	4	FACETS	1	0.971	1	0.375	0.344	0.407	CLONAL	1	TRUE	1	0.435302438171811	4		352	968	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784059	9784059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1332	296	593	1	ENST00000377346.4:c.2627C>T	p.Thr876Ile	p.T876I	ENST00000377346	NM_005026.3	876	aCc/aTc	21/24	0.435302438171811	3	FACETS	1	0.952	1	0.509	0.477	0.541	CLONAL	1	TRUE	1	0.435302438171811	3		594	1628	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120612014	120612014	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782113557	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	10	63	0	ENST00000256646.2:c.7G>A	p.Ala3Thr	p.A3T	ENST00000256646	NM_024408.3	3	Gcc/Acc	1/34	1	2	FACETS	0.319	0.217	0.447	0.319	0.217	0.447	SUBCLONAL	1	TRUE	1	0.435302438171811	2		63	144	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615183	43615183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	316	636	0	ENST00000355710.3:c.2597C>T	p.Ala866Val	p.A866V	ENST00000355710	NM_020975.4	866	gCc/gTc	14/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.435302438171811	2		636	1311	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333933	70333933	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	126	244	0	ENST00000373644.4:c.1838A>G	p.Lys613Arg	p.K613R	ENST00000373644	NM_030625.2	613	aAg/aGg	2/12	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.435302438171811	2		244	524	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741619	17741619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1305048709	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	189	241	0	ENST00000250003.3:c.290C>T	p.Ala97Val	p.A97V	ENST00000250003	NM_002478.4	97	gCc/gTc	1/3	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.435302438171811	2		241	667	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344947	118344947	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	100	190	0	ENST00000534358.1:c.3073A>G	p.Ser1025Gly	p.S1025G	ENST00000534358	NM_005933.3	1025	Agc/Ggc	3/36	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.435302438171811	2		190	372	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406318	406318	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	196	435	2	ENST00000399788.2:c.4123del	p.Cys1375ValfsTer13	p.C1375Vfs*13	ENST00000399788	NM_001042603.1	1375	Tgt/gt	25/28	NA	2	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.435302438171811	2		437	834	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425847	49425847	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	266	607	0	ENST00000301067.7:c.12641T>G	p.Leu4214Ter	p.L4214*	ENST00000301067	NM_003482.3	4214	tTa/tGa	39/54	0.148557604459668	4	FACETS	0.808	0.757	0.859	0.808	0.757	0.859	INDETERMINATE	2	TRUE	2	0.435302438171811	4		607	1086	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878061	48878061	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs898303682	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	86	165	0	ENST00000267163.4:c.13A>C	p.Thr5Pro	p.T5P	ENST00000267163	NM_000321.2	5	Acc/Ccc	1/27	1	2	FACETS	0.993	0.884	1	0.993	0.884	1	CLONAL	1	TRUE	1	0.435302438171811	2		165	398	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986604	36986604	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	129	340	0	ENST00000354822.5:c.1085A>G	p.His362Arg	p.H362R	ENST00000354822	NM_001079668.2	362	cAc/cGc	3/3	1	2	FACETS	0.991	0.902	1	0.991	0.902	1	CLONAL	1	TRUE	1	0.435302438171811	2		340	598	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56870607	56870607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	151	389	0	ENST00000308159.5:c.1877C>T	p.Ala626Val	p.A626V	ENST00000308159	NM_014669.4	626	gCa/gTa	17/22	1	2	FACETS	0.906	0.829	0.986	0.906	0.829	0.986	CLONAL	1	TRUE	1	0.435302438171811	2		389	766	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117876	70117876	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567910274	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	188	372	0	ENST00000245479.2:c.344G>A	p.Trp115Ter	p.W115*	ENST00000245479	NM_000346.3	115	tGg/tAg	1/3	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.435302438171811	2		372	713	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144047	11144047	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	294	566	0	ENST00000358026.2:c.3628G>C	p.Val1210Leu	p.V1210L	ENST00000358026	NM_001128849.1	1210	Gtg/Ctg	26/36	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.435302438171811	2		566	1240	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303101	15303101	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555729554	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	370	742	0	ENST00000263388.2:c.349T>C	p.Cys117Arg	p.C117R	ENST00000263388	NM_000435.2	117	Tgc/Cgc	4/33	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.435302438171811	2		742	1462	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727134	41727134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866511270	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	95	595	4	ENST00000301178.4:c.392G>A	p.Gly131Asp	p.G131D	ENST00000301178	NM_021913.4	131	gGc/gAc	3/20	1	2	FACETS	0.355	0.315	0.398	0.355	0.315	0.398	SUBCLONAL	1	TRUE	1	0.435302438171811	2		599	1230	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660409	227660409	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771924555	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	196	444	0	ENST00000305123.5:c.3046C>T	p.Arg1016Ter	p.R1016*	ENST00000305123	NM_005544.2	1016	Cga/Tga	1/2	1	2	FACETS	0.967	0.896	1	0.967	0.896	1	CLONAL	1	TRUE	1	0.435302438171811	2		444	931	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561508	9561510	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	195	479	0	ENST00000353224.5:c.272_274del	p.Asn91del	p.N91del	ENST00000353224	NM_177990.2	91	aACAtc/atc	4/10	1	2	FACETS	0.992	0.919	1	0.992	0.919	1	CLONAL	1	TRUE	1	0.435302438171811	2		479	903	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266670	41266670	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	149	378	0	ENST00000349496.5:c.467T>C	p.Leu156Pro	p.L156P	ENST00000349496	NM_001904.3	156	cTg/cCg	4/15	1	2	FACETS	0.854	0.78	0.93	0.854	0.78	0.93	CLONAL	1	TRUE	1	0.435302438171811	2		378	802	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412892	49412892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	315	649	0	ENST00000418115.1:c.131C>T	p.Ala44Val	p.A44V	ENST00000418115	NM_001664.2	44	gCa/gTa	2/5	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.435302438171811	2		649	1356	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940018	49940018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775113261	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1181	147	554	0	ENST00000296474.3:c.1025G>A	p.Gly342Asp	p.G342D	ENST00000296474	NM_002447.2	342	gGc/gAc	1/20	1	2	FACETS	0.509	0.463	0.557	0.509	0.463	0.557	SUBCLONAL	1	TRUE	1	0.435302438171811	2		554	1328	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383922	84383922	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	167	506	0	ENST00000321945.7:c.930C>A	p.Ser310Arg	p.S310R	ENST00000321945	NM_139076.2	310	agC/agA	9/9	1	2	FACETS	0.877	0.806	0.951	0.877	0.806	0.951	CLONAL	1	TRUE	1	0.435302438171811	2		506	875	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628988	187628988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	89	542	0	ENST00000441802.2:c.1994C>T	p.Ala665Val	p.A665V	ENST00000441802	NM_005245.3	665	gCc/gTc	2/27	1	2	FACETS	0.401	0.355	0.451	0.401	0.355	0.451	SUBCLONAL	1	TRUE	1	0.435302438171811	2		542	1019	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959376	38959376	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	118	394	0	ENST00000357387.3:c.2099T>C	p.Leu700Pro	p.L700P	ENST00000357387	NM_152756.3	700	cTt/cCt	22/38	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.435302438171811	2		394	538	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564396	86564396	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	88	444	0	ENST00000274376.6:c.128C>A	p.Pro43His	p.P43H	ENST00000274376	NM_002890.2	43	cCt/cAt	1/25	1	2	FACETS	0.446	0.394	0.502	0.446	0.394	0.502	SUBCLONAL	1	TRUE	1	0.435302438171811	2		444	906	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86681208	86681208	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	107	255	0	ENST00000274376.6:c.2847+2T>C		p.X949_splice	ENST00000274376	NM_002890.2	949			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.435302438171811	2		255	398	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677942	117677942	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	195	472	0	ENST00000368508.3:c.3991G>A	p.Val1331Met	p.V1331M	ENST00000368508	NM_002944.2	1331	Gtg/Atg	25/43	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.435302438171811	2		472	827	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977569	2977569	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	330	590	0	ENST00000396946.4:c.1115T>C	p.Leu372Pro	p.L372P	ENST00000396946	NM_032415.4	372	cTg/cCg	8/25	0.435302438171811	2	FACETS	1	0.983	1	0.552	0.521	0.584	CLONAL	1	TRUE	0	0.435302438171811	2		590	1373	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38186910	38186910	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	198	472	0	ENST00000317025.8:c.1567G>T	p.Val523Phe	p.V523F	ENST00000317025	NM_023034.1	523	Gtt/Ttt	6/24	0.435302438171811	3	FACETS	1	0.967	1	0.54	0.5	0.582	CLONAL	1	TRUE	1	0.435302438171811	3		472	1026	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741598	145741598	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1242395636	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1583	395	796	0	ENST00000428558.2:c.905C>A	p.Pro302His	p.P302H	ENST00000428558	NM_004260.3	302	cCt/cAt	5/22	0.435302438171811	3	FACETS	1	0.987	1	0.559	0.529	0.589	CLONAL	1	TRUE	1	0.435302438171811	3		796	1978	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328378	137328380	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs763369916	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	318	820	0	ENST00000481739.1:c.1315_1317del	p.Phe439del	p.F439del	ENST00000481739	NM_002957.4	436	cTCTtc/ctc	10/10	1	2	FACETS	0.973	0.917	1	0.973	0.917	1	CLONAL	1	TRUE	1	0.435302438171811	2		820	1501	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411936	63411936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1434752067	NA	P-0028932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	359	742	0	ENST00000330258.3:c.1231G>A	p.Glu411Lys	p.E411K	ENST00000330258	NM_152424.3	411	Gaa/Aaa	2/2	0.435302438171811	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.435302438171811	1		742	1114	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0029133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	119	415	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.298551484632851	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.324496435780999	2		415	338	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0029133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	47	348	0	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	0.602	0.508	0.706	0.602	0.508	0.706	SUBCLONAL	1	TRUE	1	0.324496435780999	2		348	481	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023202	27023202	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	22	137	0	ENST00000324856.7:c.308C>A	p.Ser103Ter	p.S103*	ENST00000324856	NM_006015.4	103	tCg/tAg	1/20	1	2	FACETS	0.646	0.503	0.81	0.646	0.503	0.81	SUBCLONAL	1	TRUE	1	0.324496435780999	2		137	210	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675571	86675571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1561325048	NA	P-0029133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	12	99	0	ENST00000274376.6:c.2513del	p.Asn838MetfsTer4	p.N838Mfs*4	ENST00000274376	NM_002890.2	836	gAa/ga	19/25	1	2	FACETS	0.569	0.402	0.771	0.569	0.402	0.771	SUBCLONAL	1	TRUE	1	0.324496435780999	2		99	130	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183833	10183833	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1553619456	NA	P-0029133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	64	630	0	ENST00000256474.2:c.302T>C	p.Leu101Pro	p.L101P	ENST00000256474	NM_000551.3	101	cTg/cCg	1/3	1	2	FACETS	0.52	0.45	0.597	0.52	0.45	0.597	SUBCLONAL	1	TRUE	1	0.324496435780999	2		630	758	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133236047	133236047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs948001596	NA	P-0029133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	73	426	0	ENST00000320574.5:c.3109C>T	p.Arg1037Cys	p.R1037C	ENST00000320574	NM_006231.2	1037	Cgt/Tgt	26/49	0.324496435780999	1	FACETS	0.553	0.484	0.629	0.553	0.484	0.629	SUBCLONAL	1	TRUE	0	0.324496435780999	1		426	681	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434991	110434991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	49	650	3	ENST00000375856.3:c.3410G>A	p.Arg1137His	p.R1137H	ENST00000375856	NM_003749.2	1137	cGc/cAc	1/2	1	2	FACETS	0.405	0.342	0.475	0.405	0.342	0.475	SUBCLONAL	1	TRUE	1	0.324496435780999	2		653	745	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276860	15276861	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs753725730	NA	P-0029133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	45	570	0	ENST00000263388.2:c.5404dup	p.Ala1802GlyfsTer8	p.A1802Gfs*8	ENST00000263388	NM_000435.2	1802	gct/gGct	30/33	1	2	FACETS	0.372	0.311	0.439	0.372	0.311	0.439	SUBCLONAL	1	TRUE	1	0.324496435780999	2		570	746	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211899	36211899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	133	733	6	ENST00000222270.7:c.1656del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	550	gaC/ga	3/37	1	2	FACETS	0.798	0.724	0.877	0.798	0.724	0.877	SUBCLONAL	1	TRUE	1	0.324496435780999	2		739	1027	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347444	89347444	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529180532	NA	P-0029133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	93	775	0	ENST00000301030.4:c.5506C>T	p.Pro1836Ser	p.P1836S	ENST00000301030	NM_001256183.1	1836	Ccc/Tcc	9/13	1	2	FACETS	0.784	0.697	0.877	0.784	0.697	0.877	SUBCLONAL	1	TRUE	1	0.324496435780999	2		775	731	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210244	123210244	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	40	210	0	ENST00000218089.9:c.2596G>T	p.Ala866Ser	p.A866S	ENST00000218089	NM_001042749.1	866	Gca/Tca	26/35	0.324496435780999	1	FACETS	0.561	0.467	0.665	0.561	0.467	0.665	SUBCLONAL	1	TRUE	0	0.324496435780999	1		210	368	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466327	120466327	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	33	351	0	ENST00000256646.2:c.4792G>A	p.Ala1598Thr	p.A1598T	ENST00000256646	NM_024408.3	1598	Gct/Act	26/34	1	2	FACETS	0.309	0.251	0.375	0.309	0.251	0.375	SUBCLONAL	1	TRUE	1	0.324496435780999	2		351	658	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946981	71946981	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	70	864	0	ENST00000298229.2:c.2834del	p.Pro945GlnfsTer13	p.P945Qfs*13	ENST00000298229	NM_001567.3	944	Ccc/cc	25/28	1	2	FACETS	0.543	0.472	0.619	0.543	0.472	0.619	SUBCLONAL	1	TRUE	1	0.324496435780999	2		864	795	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347640	118347640	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	66	308	0	ENST00000534358.1:c.3277C>A	p.Leu1093Met	p.L1093M	ENST00000534358	NM_005933.3	1093	Ctg/Atg	4/36	1	2	FACETS	0.514	0.445	0.588	0.514	0.445	0.588	SUBCLONAL	1	TRUE	1	0.324496435780999	2		308	792	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972784	25972784	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	51	258	0	ENST00000435504.4:c.1641G>T	p.Gln547His	p.Q547H	ENST00000435504		547	caG/caT	12/13	1	2	FACETS	0.585	0.497	0.682	0.585	0.497	0.682	SUBCLONAL	1	TRUE	1	0.324496435780999	2		258	537	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375099	31375099	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	63	790	0	ENST00000328111.2:c.496C>A	p.Leu166Ile	p.L166I	ENST00000328111	NM_006892.3	166	Ctt/Att	6/23	1	2	FACETS	0.505	0.436	0.58	0.505	0.436	0.58	SUBCLONAL	1	TRUE	1	0.324496435780999	2		790	769	SUCCESS
APC	324	MSKCC	GRCh37	5	112154669	112154669	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1554079946	NA	P-0029133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	22	188	0	ENST00000257430.4:c.940A>G	p.Met314Val	p.M314V	ENST00000257430	NM_000038.5	314	Atg/Gtg	10/16	1	2	FACETS	0.413	0.32	0.522	0.413	0.32	0.522	SUBCLONAL	1	TRUE	1	0.324496435780999	2		188	328	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814235	76814235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557060350	NA	P-0029133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	34	187	0	ENST00000373344.5:c.6409G>A	p.Ala2137Thr	p.A2137T	ENST00000373344	NM_000489.3	2137	Gct/Act	29/35	0.324496435780999	1	FACETS	0.643	0.528	0.772	0.643	0.528	0.772	SUBCLONAL	1	TRUE	0	0.324496435780999	1		187	273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0029607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	89	720	4	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.993	0.886	1	1	0.986	1	CLONAL	2	TRUE	1	0.226892201075817	2		724	395	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913277	NA	P-0029607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	32	377	1	ENST00000263967.3:c.3145G>A	p.Gly1049Ser	p.G1049S	ENST00000263967	NM_006218.2	1049	Ggt/Agt	21/21	1	2	FACETS	0.916	0.754	1	1	0.959	1	CLONAL	2	TRUE	1	0.226892201075817	2		378	154	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578199	7578208	+	frameshift_variant	Frame_Shift_Del	DEL	ACCACACTAT	ACCACACTAT	-	novel	NA	P-0029640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	161	824	0	ENST00000269305.4:c.641_650del	p.His214ArgfsTer30	p.H214Rfs*30	ENST00000269305	NM_001126112.2	214	cATAGTGTGGTg/cg	6/11	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	FALSE	NA	0.245446022892506	2		824	1035	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441521	40441521	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	54	961	0	ENST00000345506.4:c.92G>C	p.Arg31Pro	p.R31P	ENST00000345506	NM_003152.3	31	cGg/cCg	3/20	1	2	FACETS	0.423	0.359	0.492	0.423	0.359	0.492	SUBCLONAL	1	FALSE	1	0.245446022892506	2		961	1041	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0029709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	170	354	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.419924463361023	3	FACETS	0.886	0.821	0.954	0.886	0.821	0.954	CLONAL	2	TRUE	1	0.44491681021755	3		354	527	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249229	133249229	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	236	463	0	ENST00000320574.5:c.1670C>G	p.Pro557Arg	p.P557R	ENST00000320574	NM_006231.2	557	cCt/cGt	15/49	0.44491681021755	2	FACETS	0.91	0.856	0.964	0.91	0.856	0.964	CLONAL	2	TRUE	0	0.44491681021755	2		463	583	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851694	134851694	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749032472	NA	P-0029709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	283	462	0	ENST00000398015.3:c.1100G>A	p.Arg367His	p.R367H	ENST00000398015	NM_004441.4	367	cGc/cAc	5/16	0.382655982575688	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.44491681021755	4		462	857	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177763	56177763	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	97	347	0	ENST00000399503.3:c.2739del	p.Gly914AspfsTer7	p.G914Dfs*7	ENST00000399503	NM_005921.1	912	ggA/gg	14/20	1	2	FACETS	0.852	0.763	0.946	0.852	0.763	0.946	CLONAL	1	TRUE	1	0.468421869179633	2		347	486	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061210	38061210	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0029923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	112	437	2	ENST00000250448.2:c.779T>A	p.Leu260Ter	p.L260*	ENST00000250448	NM_004496.3	260	tTg/tAg	2/2	1	2	FACETS	0.866	0.782	0.955	0.866	0.782	0.955	CLONAL	1	TRUE	1	0.468421869179633	2		439	552	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177459	56177460	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0029923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	134	363	0	ENST00000399503.3:c.2434dup	p.Val812GlyfsTer51	p.V812Gfs*51	ENST00000399503	NM_005921.1	811	atg/atGg	14/20	1	2	FACETS	0.963	0.878	1	0.963	0.878	1	CLONAL	1	TRUE	1	0.468421869179633	2		363	594	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382230	152382230	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	140	458	0	ENST00000206249.3:c.1340G>A	p.Cys447Tyr	p.C447Y	ENST00000206249	NM_000125.3	447	tGc/tAc	6/8	1	2	FACETS	0.931	0.85	1	0.931	0.85	1	CLONAL	1	TRUE	1	0.468421869179633	2		458	642	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878955	117878955	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	113	301	0	ENST00000297338.2:c.14A>G	p.His5Arg	p.H5R	ENST00000297338	NM_006265.2	5	cAt/cGt	2/14	0.437353472714621	5	FACETS	1	0.912	1	0.254	0.228	0.281	CLONAL	1	TRUE	1	0.468421869179633	5		301	810	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0029936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	56	354	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.622	0.533	0.72	0.622	0.533	0.72	SUBCLONAL	1	TRUE	1	0.305216649299472	2		354	590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	41	626	0	ENST00000269305.4:c.503A>T	p.His168Leu	p.H168L	ENST00000269305	NM_001126112.2	168	cAc/cTc	5/11	1	2	FACETS	0.318	0.264	0.379	0.318	0.264	0.379	SUBCLONAL	1	TRUE	1	0.305216649299472	2		626	844	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057685	27057685	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	45	622	0	ENST00000324856.7:c.1393C>T	p.Gln465Ter	p.Q465*	ENST00000324856	NM_006015.4	465	Cag/Tag	3/20	1	2	FACETS	0.337	0.282	0.398	0.337	0.282	0.398	SUBCLONAL	1	TRUE	1	0.305216649299472	2		622	876	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795612	42795612	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775832698	NA	P-0029936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	65	807	0	ENST00000575354.2:c.2692C>T	p.Pro898Ser	p.P898S	ENST00000575354	NM_015125.3	898	Ccc/Tcc	10/20	1	2	FACETS	0.418	0.361	0.48	0.418	0.361	0.48	SUBCLONAL	1	TRUE	1	0.305216649299472	2		807	1019	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356160	66356160	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	71	468	0	ENST00000273854.3:c.1337G>T	p.Gly446Val	p.G446V	ENST00000273854	NM_004439.5	446	gGa/gTa	5/18	1	2	FACETS	0.717	0.625	0.816	0.717	0.625	0.816	SUBCLONAL	1	TRUE	1	0.305216649299472	2		468	649	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239954	53239954	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	64	638	0	ENST00000375401.3:c.1487G>C	p.Gly496Ala	p.G496A	ENST00000375401	NM_004187.3	496	gGc/gCc	11/26	0.263475572554485	1	FACETS	0.407	0.351	0.468	0.407	0.351	0.468	SUBCLONAL	1	TRUE	0	0.305216649299472	1		638	873	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	172	358	0	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	0.879	0.814	0.946	0.879	0.814	0.946	CLONAL	1	TRUE	1	0.697656799446467	2		358	561	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	185	325	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.957	0.89	1	0.957	0.89	1	CLONAL	1	TRUE	1	0.697656799446467	2		325	554	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256528	16256528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	300	659	1	ENST00000375759.3:c.3793C>T	p.Arg1265Ter	p.R1265*	ENST00000375759	NM_015001.2	1265	Cga/Tga	11/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.697656799446467	2		660	804	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	256	382	1	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	0.697656799446467	2		383	722	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111487	8111487	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	253	655	0	ENST00000346208.3:c.973A>G	p.Thr325Ala	p.T325A	ENST00000346208		325	Acc/Gcc	5/6	1	2	FACETS	0.912	0.857	0.969	0.912	0.857	0.969	CLONAL	1	TRUE	1	0.697656799446467	2		655	795	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	73	179	2	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	1	2	FACETS	0.45	0.395	0.509	0.45	0.395	0.509	SUBCLONAL	1	TRUE	1	0.697656799446467	2		181	465	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333089	70333089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	131	716	0	ENST00000373644.4:c.994G>A	p.Ala332Thr	p.A332T	ENST00000373644	NM_030625.2	332	Gca/Aca	2/12	1	2	FACETS	0.384	0.348	0.422	0.384	0.348	0.422	SUBCLONAL	1	TRUE	1	0.697656799446467	2		716	978	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70441223	70441223	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	251	558	0	ENST00000373644.4:c.4892C>A	p.Ala1631Asp	p.A1631D	ENST00000373644	NM_030625.2	1631	gCt/gAt	9/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.697656799446467	2		558	662	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	105	489	2	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.587	0.528	0.649	0.587	0.528	0.649	SUBCLONAL	1	TRUE	1	0.697656799446467	2		491	513	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989562	85989562	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs767548896	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	151	371	0	ENST00000263360.6:c.1321C>T	p.Arg441Ter	p.R441*	ENST00000263360	NM_003797.3	441	Cga/Tga	12/12	1	2	FACETS	0.933	0.86	1	0.933	0.86	1	CLONAL	1	TRUE	1	0.697656799446467	2		371	464	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933297	100933297	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	114	582	0	ENST00000325455.5:c.2093T>C	p.Val698Ala	p.V698A	ENST00000325455	NM_001202474.3	698	gTg/gCg	4/8	1	2	FACETS	0.482	0.434	0.532	0.482	0.434	0.532	SUBCLONAL	1	TRUE	1	0.697656799446467	2		582	678	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153507	108153507	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1565444784	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	210	434	0	ENST00000278616.4:c.3647A>G	p.Tyr1216Cys	p.Y1216C	ENST00000278616	NM_000051.3	1216	tAt/tGt	25/63	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.697656799446467	2		434	590	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	292	677	3	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.923	0.871	0.976	0.923	0.871	0.976	CLONAL	1	TRUE	1	0.697656799446467	2		680	907	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	396	430	7	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	0.957	0.924	0.99	1	0.997	1	CLONAL	2	TRUE	1	0.697656799446467	2		437	593	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416537	49416537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761987042	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	250	543	0	ENST00000301067.7:c.16174C>T	p.Arg5392Cys	p.R5392C	ENST00000301067	NM_003482.3	5392	Cgc/Tgc	51/54	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.697656799446467	2		543	677	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444933	49444933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746841307	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	277	618	0	ENST00000301067.7:c.2533C>T	p.Arg845Trp	p.R845W	ENST00000301067	NM_003482.3	845	Cgg/Tgg	10/54	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.697656799446467	2		618	716	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885970	111885970	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371681526	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	215	585	0	ENST00000341259.2:c.1592C>T	p.Ser531Leu	p.S531L	ENST00000341259	NM_005475.2	531	tCg/tTg	8/8	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.697656799446467	2		585	615	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249308	133249308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748489355	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	339	783	0	ENST00000320574.5:c.1591G>A	p.Gly531Arg	p.G531R	ENST00000320574	NM_006231.2	531	Gga/Aga	15/49	1	2	FACETS	0.9	0.852	0.948	0.9	0.852	0.948	CLONAL	1	TRUE	1	0.697656799446467	2		783	1080	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008200	29008200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1014160326	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	178	309	0	ENST00000282397.4:c.671G>A	p.Arg224Gln	p.R224Q	ENST00000282397	NM_002019.4	224	cGa/cAa	5/30	0.285513144621681	3	FACETS	0.765	0.712	0.818	0.765	0.712	0.818	INDETERMINATE	2	TRUE	1	0.697656799446467	3		309	450	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569817	95569817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	55	233	0	ENST00000393063.1:c.3916G>A	p.Ala1306Thr	p.A1306T	ENST00000393063	NM_030621.3	1306	Gct/Act	22/28	1	2	FACETS	0.365	0.313	0.422	0.365	0.313	0.422	SUBCLONAL	1	TRUE	1	0.697656799446467	2		233	432	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005513	42005517	+	frameshift_variant	Frame_Shift_Del	DEL	GAAAA	GAAAA	-	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	298	654	0	ENST00000219905.7:c.3255_3259del	p.Arg1085SerfsTer5	p.R1085Sfs*5	ENST00000219905	NM_001164273.1	1083	ttGAAAAga/ttga	9/24	1	2	FACETS	0.905	0.854	0.957	0.905	0.854	0.957	CLONAL	1	TRUE	1	0.697656799446467	2		654	944	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005668	42005668	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1042566083	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	23	283	2	ENST00000219905.7:c.3404A>G	p.Lys1135Arg	p.K1135R	ENST00000219905	NM_001164273.1	1135	aAa/aGa	9/24	1	2	FACETS	0.208	0.162	0.261	0.208	0.162	0.261	SUBCLONAL	1	TRUE	1	0.697656799446467	2		285	317	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996708	73996708	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	22	110	0	ENST00000318443.5:c.1264G>A	p.Val422Met	p.V422M	ENST00000318443	NM_001024736.1	422	Gtg/Atg	6/10	1	2	FACETS	0.693	0.549	0.852	0.693	0.549	0.852	SUBCLONAL	1	TRUE	1	0.697656799446467	2		110	91	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104304	2104304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764529584	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	235	553	0	ENST00000219476.3:c.344G>A	p.Arg115His	p.R115H	ENST00000219476	NM_000548.3	115	cGt/cAt	5/42	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.697656799446467	2		553	653	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108765	2108765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755631210	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	287	670	2	ENST00000219476.3:c.866C>T	p.Ala289Val	p.A289V	ENST00000219476	NM_000548.3	289	gCg/gTg	10/42	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.697656799446467	2		672	809	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857974	9857974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61758996	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	241	603	1	ENST00000330684.3:c.3427G>A	p.Glu1143Lys	p.E1143K	ENST00000330684	NM_001134407.1	1143	Gag/Aag	13/13	1	2	FACETS	0.957	0.898	1	0.957	0.898	1	CLONAL	1	TRUE	1	0.697656799446467	2		604	722	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346158	89346158	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs878855327	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	91	235	1	ENST00000301030.4:c.6792del	p.Ala2265ProfsTer72	p.A2265Pfs*72	ENST00000301030	NM_001256183.1	2264	ccC/cc	9/13	0.697656799446467	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.697656799446467	1		236	161	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89825027	89825027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773070418	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	284	573	4	ENST00000389301.3:c.2939C>T	p.Ala980Val	p.A980V	ENST00000389301	NM_000135.2	980	gCg/gTg	30/43	0.697656799446467	1	FACETS	0.98	0.932	1	0.98	0.932	1	CLONAL	1	TRUE	0	0.697656799446467	1		577	541	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	313	574	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.957	0.905	1	0.957	0.905	1	CLONAL	1	TRUE	1	0.697656799446467	2		574	938	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942868	15942868	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1290753263	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	120	542	0	ENST00000268712.3:c.6834A>T	p.Lys2278Asn	p.K2278N	ENST00000268712	NM_006311.3	2278	aaA/aaT	44/46	1	2	FACETS	0.52	0.471	0.573	0.52	0.471	0.573	SUBCLONAL	1	TRUE	1	0.697656799446467	2		542	661	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	164	321	8	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	1	2	FACETS	0.838	0.774	0.904	0.838	0.774	0.904	CLONAL	1	TRUE	1	0.697656799446467	2		329	561	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17129522	17129522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	65	641	1	ENST00000285071.4:c.364C>T	p.Arg122Cys	p.R122C	ENST00000285071	NM_144997.5	122	Cgc/Tgc	5/14	1	2	FACETS	0.224	0.194	0.258	0.224	0.194	0.258	SUBCLONAL	1	TRUE	1	0.697656799446467	2		642	831	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687507	37687508	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	140	408	0	ENST00000447079.4:c.4413_4414del	p.Tyr1472SerfsTer40	p.Y1472Sfs*40	ENST00000447079	NM_015083.1	1471	CTc/c	14/14	1	2	FACETS	0.863	0.792	0.936	0.863	0.792	0.936	CLONAL	1	TRUE	1	0.697656799446467	2		408	465	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38506128	38506128	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	305	627	0	ENST00000254066.5:c.420C>A	p.Cys140Ter	p.C140*	ENST00000254066	NM_000964.3	140	tgC/tgA	4/9	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.697656799446467	2		627	836	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40371821	40371821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326533398	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	286	704	0	ENST00000293328.3:c.590G>A	p.Arg197His	p.R197H	ENST00000293328	NM_012448.3	197	cGt/cAt	6/19	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.697656799446467	2		704	757	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245587	41245587	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357522	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	132	771	4	ENST00000357654.3:c.1961del	p.Lys654SerfsTer47	p.K654Sfs*47	ENST00000357654	NM_007294.3	654	aAg/ag	10/23	1	2	FACETS	0.439	0.398	0.482	0.439	0.398	0.482	SUBCLONAL	1	TRUE	1	0.697656799446467	2		775	862	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	232	654	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.697656799446467	1	FACETS	0.962	0.91	1	0.962	0.91	1	CLONAL	1	TRUE	0	0.697656799446467	1		657	450	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63537616	63537616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	105	592	2	ENST00000307078.5:c.1016G>A	p.Arg339His	p.R339H	ENST00000307078	NM_004655.3	339	cGc/cAc	4/11	1	2	FACETS	0.388	0.347	0.431	0.388	0.347	0.431	SUBCLONAL	1	TRUE	1	0.697656799446467	2		594	776	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732279	74732279	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	72	305	0	ENST00000359995.5:c.630del	p.Lys211SerfsTer21	p.K211Sfs*21	ENST00000359995	NM_001195427.1	210	ccC/cc	2/3	1	2	FACETS	0.54	0.474	0.61	0.54	0.474	0.61	SUBCLONAL	1	TRUE	1	0.697656799446467	2		305	382	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220680	1220680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	317	781	1	ENST00000326873.7:c.698G>A	p.Gly233Asp	p.G233D	ENST00000326873	NM_000455.4	233	gGc/gAc	5/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.697656799446467	2		782	903	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262170	10262172	+	inframe_deletion	In_Frame_Del	DEL	ATC	ATC	-	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	300	723	0	ENST00000340748.4:c.2119_2121del	p.Asp707del	p.D707del	ENST00000340748		707	GAT/-	23/40	1	2	FACETS	0.958	0.905	1	0.958	0.905	1	CLONAL	1	TRUE	1	0.697656799446467	2		723	898	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118628	11118630	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	273	684	3	ENST00000358026.2:c.2056_2058del	p.Glu686del	p.E686del	ENST00000358026	NM_001128849.1	684	gtGGAg/gtg	14/36	1	2	FACETS	0.932	0.877	0.987	0.932	0.877	0.987	CLONAL	1	TRUE	1	0.697656799446467	2		687	840	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054389	13054390	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	107	548	0	ENST00000316448.5:c.1001dup	p.Asn334LysfsTer3	p.N334Kfs*3	ENST00000316448	NM_004343.3	333	-/A	8/9	1	2	FACETS	0.414	0.371	0.459	0.414	0.371	0.459	SUBCLONAL	1	TRUE	1	0.697656799446467	2		548	741	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272266	15272266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1363323415	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	265	764	0	ENST00000263388.2:c.6173C>T	p.Ser2058Leu	p.S2058L	ENST00000263388	NM_000435.2	2058	tCg/tTg	33/33	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.697656799446467	2		764	724	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279920	18279920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	151	727	2	ENST00000222254.8:c.2003G>A	p.Cys668Tyr	p.C668Y	ENST00000222254	NM_005027.3	668	tGc/tAc	16/16	1	2	FACETS	0.491	0.449	0.536	0.491	0.449	0.536	SUBCLONAL	1	TRUE	1	0.697656799446467	2		729	881	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968144	18968144	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	195	603	1	ENST00000262803.5:c.1984G>A	p.Asp662Asn	p.D662N	ENST00000262803	NM_002911.3	662	Gac/Aac	15/24	1	2	FACETS	0.883	0.822	0.946	0.883	0.822	0.946	CLONAL	1	TRUE	1	0.697656799446467	2		604	633	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727800	41727800	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	287	824	0	ENST00000301178.4:c.425T>C	p.Leu142Pro	p.L142P	ENST00000301178	NM_021913.4	142	cTg/cCg	4/20	1	2	FACETS	0.925	0.873	0.979	0.925	0.873	0.979	CLONAL	1	TRUE	1	0.697656799446467	2		824	889	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754520	42754520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	296	810	0	ENST00000222329.4:c.220C>T	p.Pro74Ser	p.P74S	ENST00000222329	NM_006494.2	74	Ccc/Tcc	2/4	1	2	FACETS	0.906	0.854	0.958	0.906	0.854	0.958	CLONAL	1	TRUE	1	0.697656799446467	2		810	937	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918709	50918709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501818	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	92	511	3	ENST00000440232.2:c.2579C>T	p.Ala860Val	p.A860V	ENST00000440232	NM_002691.3	860	gCg/gTg	21/27	1	2	FACETS	0.454	0.404	0.507	0.454	0.404	0.507	SUBCLONAL	1	TRUE	1	0.697656799446467	2		514	581	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921750	111921750	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs185078669	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	184	434	0	ENST00000393256.3:c.539G>A	p.Arg180Gln	p.R180Q	ENST00000393256	NM_006538.4	180	cGa/cAa	4/4	1	2	FACETS	0.947	0.88	1	0.947	0.88	1	CLONAL	1	TRUE	1	0.697656799446467	2		434	557	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	69	244	2	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.776	0.684	0.872	0.776	0.684	0.872	SUBCLONAL	1	TRUE	1	0.697656799446467	2		246	255	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31381401	31381401	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs201681031	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	199	427	0	ENST00000328111.2:c.1126G>A	p.Glu376Lys	p.E376K	ENST00000328111	NM_006892.3	376	Gag/Aag	10/23	1	2	FACETS	0.977	0.911	1	0.977	0.911	1	CLONAL	1	TRUE	1	0.697656799446467	2		427	584	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264407	46264407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529456958	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	197	465	1	ENST00000371998.3:c.1454G>A	p.Arg485His	p.R485H	ENST00000371998		485	cGt/cAt	11/23	1	2	FACETS	0.989	0.922	1	0.989	0.922	1	CLONAL	1	TRUE	1	0.697656799446467	2		466	571	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268333	46268333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747268479	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	157	404	0	ENST00000371998.3:c.2720G>A	p.Arg907Gln	p.R907Q	ENST00000371998		907	cGa/cAa	15/23	1	2	FACETS	0.958	0.885	1	0.958	0.885	1	CLONAL	1	TRUE	1	0.697656799446467	2		404	470	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958198	54958198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756121188	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	220	522	1	ENST00000312783.6:c.409C>T	p.Arg137Cys	p.R137C	ENST00000312783	NM_198436.1	137	Cgc/Tgc	6/10	1	2	FACETS	0.876	0.818	0.935	0.876	0.818	0.935	CLONAL	1	TRUE	1	0.697656799446467	2		523	720	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755611	39755611	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	255	571	0	ENST00000288319.7:c.1154G>A	p.Arg385His	p.R385H	ENST00000288319	NM_182918.3	385	cGc/cAc	10/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.697656799446467	2		571	652	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37055932	37055932	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	281	359	0	ENST00000231790.2:c.687A>G	p.Ile229Met	p.I229M	ENST00000231790	NM_000249.3	229	atA/atG	9/19	0.697656799446467	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.697656799446467	3		359	540	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	167	325	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.697656799446467	3	FACETS	0.983	0.906	1	0.491	0.453	0.531	CLONAL	1	TRUE	1	0.697656799446467	3		325	657	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156926	89156928	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs1257815746	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	384	510	0	ENST00000336596.2:c.30_32del	p.Leu11del	p.L11del	ENST00000336596	NM_005233.5	10	CTT/-	1/17	0.697656799446467	2	FACETS	0.946	0.912	0.979	0.946	0.912	0.979	CLONAL	2	TRUE	0	0.697656799446467	2		510	582	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582341	119582342	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	100	349	0	ENST00000316626.5:c.1059dup	p.Asp354Ter	p.D354*	ENST00000316626		353	-/T	10/12	0.653211552358603	3	FACETS	0.5	0.446	0.557	0.25	0.223	0.279	SUBCLONAL	1	TRUE	1	0.697656799446467	3		349	774	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803351	1803351	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	269	718	0	ENST00000260795.2:c.620G>A	p.Arg207Gln	p.R207Q	ENST00000260795		207	cGg/cAg	5/17	1	2	FACETS	0.99	0.932	1	0.99	0.932	1	CLONAL	1	TRUE	1	0.697656799446467	2		718	779	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957897	1957897	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs934745655	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	262	533	0	ENST00000382891.5:c.2863G>A	p.Gly955Arg	p.G955R	ENST00000382891	NM_133335.3	955	Gga/Aga	15/22	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.697656799446467	2		533	747	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980614	1980614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1560827075	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	174	493	1	ENST00000382891.5:c.4076G>A	p.Arg1359Gln	p.R1359Q	ENST00000382891	NM_133335.3	1359	cGg/cAg	22/22	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.697656799446467	2		494	488	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35857110	35857111	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	135	246	0	ENST00000303115.3:c.37dup	p.Ser13PhefsTer25	p.S13Ffs*25	ENST00000303115	NM_002185.3	11	gtt/gTtt	1/8	1	2	FACETS	0.928	0.851	1	0.928	0.851	1	CLONAL	1	TRUE	1	0.697656799446467	2		246	417	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	326	632	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.994	0.942	1	0.994	0.942	1	CLONAL	1	TRUE	1	0.697656799446467	2		636	940	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441113	149441113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200788902	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	328	849	2	ENST00000286301.3:c.1799C>T	p.Thr600Met	p.T600M	ENST00000286301	NM_005211.3	600	aCg/aTg	13/22	1	2	FACETS	0.966	0.915	1	0.966	0.915	1	CLONAL	1	TRUE	1	0.697656799446467	2		851	973	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503812	149503812	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	206	506	0	ENST00000261799.4:c.2023+1G>A		p.X675_splice	ENST00000261799	NM_002609.3	675			1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.697656799446467	2		506	567	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562195	176562195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	297	685	0	ENST00000439151.2:c.91C>T	p.Pro31Ser	p.P31S	ENST00000439151	NM_022455.4	31	Cct/Tct	2/23	1	2	FACETS	0.992	0.938	1	0.992	0.938	1	CLONAL	1	TRUE	1	0.697656799446467	2		685	858	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721771	176721771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767815479	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	195	446	2	ENST00000439151.2:c.7402C>T	p.Arg2468Trp	p.R2468W	ENST00000439151	NM_022455.4	2468	Cgg/Tgg	23/23	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.697656799446467	2		448	552	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481463	20481463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	154	338	0	ENST00000346618.3:c.532C>T	p.Arg178Trp	p.R178W	ENST00000346618	NM_001949.4	178	Cgg/Tgg	3/7	1	2	FACETS	0.937	0.865	1	0.937	0.865	1	CLONAL	1	TRUE	1	0.697656799446467	2		338	471	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969087	93969087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1270476760	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	127	269	0	ENST00000369303.4:c.1909C>T	p.Arg637Cys	p.R637C	ENST00000369303	NM_004440.3	637	Cgt/Tgt	10/17	1	2	FACETS	0.895	0.818	0.974	0.895	0.818	0.974	CLONAL	1	TRUE	1	0.697656799446467	2		269	407	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681120	117681120	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs748436511	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	183	516	0	ENST00000368508.3:c.3500del	p.Leu1167Ter	p.L1167*	ENST00000368508	NM_002944.2	1167	tTa/ta	23/43	1	2	FACETS	0.838	0.777	0.901	0.838	0.777	0.901	CLONAL	1	TRUE	1	0.697656799446467	2		516	626	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517316	157517316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	94	425	0	ENST00000346085.5:c.3880C>T	p.Pro1294Ser	p.P1294S	ENST00000346085	NM_020732.3	1294	Ccc/Tcc	16/20	1	2	FACETS	0.489	0.436	0.545	0.489	0.436	0.545	SUBCLONAL	1	TRUE	1	0.697656799446467	2		425	551	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513001	106513001	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs770625280	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	28	263	0	ENST00000359195.3:c.2015A>G	p.Tyr672Cys	p.Y672C	ENST00000359195	NM_002649.2	672	tAc/tGc	3/11	0.697656799446467	3	FACETS	0.249	0.199	0.307	0.125	0.099	0.154	SUBCLONAL	1	TRUE	1	0.697656799446467	3		263	434	SUCCESS
MET	4233	MSKCC	GRCh37	7	116381017	116381017	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	343	641	0	ENST00000397752.3:c.1639C>T	p.Arg547Ter	p.R547*	ENST00000397752	NM_000245.2	547	Cga/Tga	5/21	0.697656799446467	3	FACETS	1	0.948	1	0.501	0.474	0.529	CLONAL	1	TRUE	1	0.697656799446467	3		641	1323	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	404	508	21	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	0.697656799446467	3	FACETS	0.943	0.903	0.983	0.943	0.903	0.983	CLONAL	2	TRUE	1	0.697656799446467	3		529	828	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012386	152012386	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	119	333	2	ENST00000262189.6:c.427del	p.Ser143ValfsTer3	p.S143Vfs*3	ENST00000262189	NM_170606.2	143	Agt/gt	4/59	0.697656799446467	3	FACETS	0.897	0.814	0.984	0.448	0.407	0.492	CLONAL	1	TRUE	1	0.697656799446467	3		335	513	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187222	38187222	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1412	118	818	1	ENST00000317025.8:c.1255del	p.Thr419ProfsTer8	p.T419Pfs*8	ENST00000317025	NM_023034.1	419	Acc/cc	6/24	0.653211552358603	3	FACETS	0.298	0.268	0.331	0.149	0.134	0.166	SUBCLONAL	1	TRUE	1	0.697656799446467	3		819	1530	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272320	38272320	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751038400	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	117	659	0	ENST00000425967.3:c.2047G>A	p.Asp683Asn	p.D683N	ENST00000425967	NM_001174067.1	683	Gac/Aac	15/19	0.653211552358603	3	FACETS	0.44	0.396	0.487	0.22	0.198	0.244	SUBCLONAL	1	TRUE	1	0.697656799446467	3		659	1028	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275747	38275747	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	217	575	0	ENST00000425967.3:c.1522A>G	p.Arg508Gly	p.R508G	ENST00000425967	NM_001174067.1	508	Aga/Gga	11/19	0.653211552358603	3	FACETS	0.917	0.854	0.983	0.459	0.427	0.492	CLONAL	1	TRUE	1	0.697656799446467	3		575	915	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372007	55372007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	418	499	1	ENST00000297316.4:c.697G>A	p.Asp233Asn	p.D233N	ENST00000297316	NM_022454.3	233	Gac/Aac	2/2	0.653211552358603	3	FACETS	0.966	0.926	1	0.966	0.926	1	CLONAL	2	TRUE	1	0.697656799446467	3		500	837	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950475	68950475	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371711855	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	543	459	0	ENST00000288368.4:c.787C>T	p.Arg263Trp	p.R263W	ENST00000288368	NM_024870.2	263	Cgg/Tgg	7/40	0.653211552358603	3	FACETS	0.954	0.928	0.978	1	0.997	1	CLONAL	3	TRUE	1	0.697656799446467	3		459	734	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741256	145741256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766026341	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	699	823	4	ENST00000428558.2:c.1150C>T	p.Arg384Trp	p.R384W	ENST00000428558	NM_004260.3	384	Cgg/Tgg	6/22	0.653211552358603	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.697656799446467	3		827	1334	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390963	139390963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1379904495	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	332	894	1	ENST00000277541.6:c.7228C>T	p.Pro2410Ser	p.P2410S	ENST00000277541	NM_017617.3	2410	Ccg/Tcg	34/34	0.697656799446467	3	FACETS	0.884	0.834	0.935	0.442	0.417	0.468	CLONAL	1	TRUE	1	0.697656799446467	3		895	1452	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410144	139410144	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	513	614	0	ENST00000277541.6:c.1694T>C	p.Val565Ala	p.V565A	ENST00000277541	NM_017617.3	565	gTg/gCg	11/34	0.697656799446467	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.697656799446467	3		614	912	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566450	139566450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370929489	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	148	750	1	ENST00000308874.7:c.709G>A	p.Gly237Ser	p.G237S	ENST00000308874		237	Ggc/Agc	9/10	0.697656799446467	3	FACETS	0.506	0.461	0.554	0.253	0.23	0.277	SUBCLONAL	1	TRUE	1	0.697656799446467	3		751	1130	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937164	39937164	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	132	366	0	ENST00000378444.4:c.19del	p.Leu7CysfsTer9	p.L7Cfs*9	ENST00000378444	NM_001123385.1	7	Ctg/tg	2/15	1	1	FACETS	0.535	0.489	0.582	0.535	0.489	0.582	SUBCLONAL	1	TRUE	0	0.697656799446467	1		366	461	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922980	44922983	+	frameshift_variant	Frame_Shift_Del	DEL	CACT	CACT	-	novel	NA	P-0030013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	271	327	0	ENST00000377967.4:c.1846_1849del	p.Thr616TyrfsTer8	p.T616Yfs*8	ENST00000377967	NM_021140.2	614	gCACTc/gc	16/29	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.697656799446467	1		327	420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579584	7579585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0030054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	114	475	0	ENST00000269305.4:c.102dup	p.Pro36AlafsTer7	p.P36Afs*7	ENST00000269305	NM_001126112.2	34	-/C	4/11	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.435835545274881	2		475	508	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188078	11188078	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	194	507	0	ENST00000361445.4:c.6016G>T	p.Val2006Phe	p.V2006F	ENST00000361445	NM_004958.3	2006	Gtc/Ttc	43/58	0.391629377778965	3	FACETS	0.919	0.856	0.984	0.919	0.856	0.984	CLONAL	2	TRUE	1	0.435835545274881	3		507	590	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136988	64136988	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	138	645	0	ENST00000334205.4:c.1499A>G	p.His500Arg	p.H500R	ENST00000334205	NM_003942.2	500	cAc/cGc	13/17	1	2	FACETS	0.947	0.863	1	0.947	0.863	1	CLONAL	1	TRUE	1	0.435835545274881	2		645	669	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244889	41244889	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	64	684	0	ENST00000357654.3:c.2659G>C	p.Ala887Pro	p.A887P	ENST00000357654	NM_007294.3	887	Gcc/Ccc	10/23	1	2	FACETS	0.674	0.585	0.769	0.674	0.585	0.769	SUBCLONAL	1	TRUE	1	0.435835545274881	2		684	436	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182511	99182511	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	109	657	0	ENST00000074304.5:c.2314G>T	p.Val772Phe	p.V772F	ENST00000074304	NM_001134224.1	772	Gtc/Ttc	22/26	1	2	FACETS	0.808	0.727	0.893	0.808	0.727	0.893	CLONAL	1	TRUE	1	0.435835545274881	2		657	619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0030169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	188	620	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.776090075013819	1	FACETS	0.932	0.88	0.984	0.932	0.88	0.984	CLONAL	1	TRUE	0	0.776090075013819	1		621	318	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0030169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	94	460	1	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.571	0.511	0.635	0.571	0.511	0.635	SUBCLONAL	1	TRUE	1	0.776090075013819	2		461	424	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952086	178952086	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	16	503	0	ENST00000263967.3:c.3141T>A	p.His1047Gln	p.H1047Q	ENST00000263967	NM_006218.2	1047	caT/caA	21/21	1	2	FACETS	0.162	0.119	0.212	0.162	0.119	0.212	SUBCLONAL	1	TRUE	1	0.776090075013819	2		503	255	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200493	67200493	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	185	729	0	ENST00000312629.5:c.687C>G	p.Phe229Leu	p.F229L	ENST00000312629	NM_003952.2	229	ttC/ttG	8/15	0.407951146909351	4	FACETS	0.902	0.833	0.974	0.225	0.208	0.244	INDETERMINATE	1	TRUE	0	0.776090075013819	4		729	939	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120836	115120865	+	inframe_deletion	In_Frame_Del	DEL	GGCAGCGAGAGCGCCGCCGCGCCGTTGGGA	GGCAGCGAGAGCGCCGCCGCGCCGTTGGGA	-	novel	NA	P-0030169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	43	454	0	ENST00000257566.3:c.141_170del	p.Pro48_Pro57del	p.P48_P57del	ENST00000257566	NM_016569.3	47	ccTCCCAACGGCGCGGCGGCGCTCTCGCTGCCg/ccg	1/8	1	2	FACETS	0.393	0.33	0.461	0.393	0.33	0.461	SUBCLONAL	1	TRUE	1	0.776090075013819	2		454	282	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48586274	48586274	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	27	488	0	ENST00000342988.3:c.943T>C	p.Ser315Pro	p.S315P	ENST00000342988	NM_005359.5	315	Tcc/Ccc	8/12	1	2	FACETS	0.152	0.121	0.189	0.152	0.121	0.189	SUBCLONAL	1	TRUE	1	0.776090075013819	2		488	457	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739066	40739066	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	174	564	1	ENST00000373198.4:c.3218G>T	p.Gly1073Val	p.G1073V	ENST00000373198	NM_133170.3	1073	gGc/gTc	24/32	0.170230474386949	3	FACETS	0.647	0.595	0.701	0.216	0.198	0.234	INDETERMINATE	1	TRUE	0	0.776090075013819	3		565	962	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278285	142278285	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0030169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	145	515	0	ENST00000350721.4:c.1542-2A>C		p.X514_splice	ENST00000350721	NM_001184.3	514			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.776090075013819	2		515	343	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0030249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	14	447	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.355850907334273	4	FACETS	1	0.762	1	0.523	0.382	0.688	CLONAL	1	TRUE	2	0.36075957396068	4		447	101	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs878854073	NA	P-0030311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	193	327	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		327	466	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0030336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	153	447	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	0.513631065456428	2		447	594	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0030336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	171	518	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.513631065456428	1	FACETS	0.959	0.889	1	0.959	0.889	1	CLONAL	1	TRUE	0	0.513631065456428	1		518	516	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925328	114925328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	179	463	0	ENST00000543371.1:c.1406G>A	p.Cys469Tyr	p.C469Y	ENST00000543371	NM_001198531.1	469	tGc/tAc	14/14	0.254420234663916	1	FACETS	0.817	0.757	0.879	0.817	0.757	0.879	INDETERMINATE	1	TRUE	0	0.513631065456428	1		463	634	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457942	69457942	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	145	385	0	ENST00000227507.2:c.342G>C	p.Lys114Asn	p.K114N	ENST00000227507	NM_053056.2	114	aaG/aaC	2/5	0.213960273269929	1	FACETS	0.853	0.783	0.924	0.853	0.783	0.924	INDETERMINATE	1	TRUE	0	0.513631065456428	1		385	492	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435688	18435688	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	53	176	0	ENST00000266497.5:c.673A>G	p.Ile225Val	p.I225V	ENST00000266497		225	Ata/Gta	1/31	1	2	FACETS	0.909	0.784	1	0.909	0.784	1	CLONAL	1	TRUE	1	0.513631065456428	2		176	227	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21643285	21643285	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	195	492	0	ENST00000421138.2:c.242A>G	p.Asp81Gly	p.D81G	ENST00000421138		81	gAt/gGt	5/16	1	2	FACETS	0.98	0.909	1	0.98	0.909	1	CLONAL	1	TRUE	1	0.513631065456428	2		492	775	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118949	115118949	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	83	216	0	ENST00000257566.3:c.392G>T	p.Arg131Leu	p.R131L	ENST00000257566	NM_016569.3	131	cGa/cTa	2/8	1	2	FACETS	0.885	0.787	0.989	0.885	0.787	0.989	CLONAL	1	TRUE	1	0.513631065456428	2		216	365	SUCCESS
ALK	238	MSKCC	GRCh37	2	29436908	29436908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776228721	NA	P-0030336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	157	526	0	ENST00000389048.3:c.3685G>A	p.Val1229Met	p.V1229M	ENST00000389048	NM_004304.4	1229	Gtg/Atg	24/29	1	2	FACETS	0.918	0.843	0.995	0.918	0.843	0.995	CLONAL	1	TRUE	1	0.513631065456428	2		526	666	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390945	89390945	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	113	374	0	ENST00000336596.2:c.1011C>G	p.Asn337Lys	p.N337K	ENST00000336596	NM_005233.5	337	aaC/aaG	5/17	1	2	FACETS	0.829	0.749	0.912	0.829	0.749	0.912	CLONAL	1	TRUE	1	0.513631065456428	2		374	531	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945418	71945422	+	frameshift_variant	Frame_Shift_Del	DEL	TCTAC	TCTAC	-	novel	NA	P-0030370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	159	569	0	ENST00000298229.2:c.2311_2315del	p.Ser771LeufsTer10	p.S771Lfs*10	ENST00000298229	NM_001567.3	769	tTCTAC/t	20/28	0.485307021376912	1	FACETS	0.857	0.79	0.927	0.857	0.79	0.927	CLONAL	1	TRUE	0	0.485307021376912	1		569	579	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867255	68867256	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	173	486	0	ENST00000261769.5:c.2503dup	p.Tyr835LeufsTer2	p.Y835Lfs*2	ENST00000261769	NM_004360.3	834	-/T	16/16	0.485307021376912	1	FACETS	0.989	0.916	1	0.989	0.916	1	CLONAL	1	TRUE	0	0.485307021376912	1		486	546	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0030396-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	98	340	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.512643356314558	2		340	375	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954172	32954172	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs200924727	NA	P-0030396-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	134	359	0	ENST00000380152.3:c.9146A>G	p.Tyr3049Cys	p.Y3049C	ENST00000380152		3049	tAc/tGc	24/27	1	2	FACETS	0.84	0.766	0.918	0.84	0.766	0.918	CLONAL	1	TRUE	1	0.512643356314558	2		359	622	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89383342	89383342	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	41	504	2	ENST00000301030.4:c.86del	p.Lys29ArgfsTer8	p.K29Rfs*8	ENST00000301030	NM_001256183.1	29	aAg/ag	3/13	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.12	2		506	654	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989699	15989699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs557813338	NA	P-0030465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	23	326	0	ENST00000268712.3:c.3074C>T	p.Pro1025Leu	p.P1025L	ENST00000268712	NM_006311.3	1025	cCg/cTg	23/46	1	2	FACETS	0.875	0.681	1	0.875	0.681	1	CLONAL	1	TRUE	1	0.12	2		326	438	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47709917	47709917	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs267608020	NA	P-0030465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	22	424	0	ENST00000233146.2:c.2635-1G>A		p.X879_splice	ENST00000233146	NM_000251.2	879			0.120231591370408	0	FACETS	1	0.821	1			1	CLONAL	1	TRUE	0	0.12	0		424	302	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155680	106155680	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	26	437	0	ENST00000380013.4:c.581A>T	p.Asp194Val	p.D194V	ENST00000380013	NM_001127208.2	194	gAc/gTc	3/11	1	2	FACETS	0.932	0.737	1	0.932	0.737	1	CLONAL	1	TRUE	1	0.12	2		437	465	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522740	67522741	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	19	255	0	ENST00000274335.5:c.244dup	p.Ile82AsnfsTer24	p.I82Nfs*24	ENST00000274335		79	-/A	1/15	1	2	FACETS	0.875	0.663	1	0.875	0.663	1	CLONAL	1	TRUE	1	0.12	2		255	362	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486247	8486247	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139171396	NA	P-0030465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	28	351	0	ENST00000356435.5:c.2570G>A	p.Arg857His	p.R857H	ENST00000356435		857	cGt/cAt	17/35	1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	1	0.12	2		351	450	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	192	466	0	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	0.198979070629005	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.198979070629005	3		466	990	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248550	59248550	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	120	606	0	ENST00000371222.2:c.193G>T	p.Asp65Tyr	p.D65Y	ENST00000371222	NM_002228.3	65	Gac/Tac	1/1	0.198979070629005	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.198979070629005	1		606	975	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557353	187557353	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	69	481	0	ENST00000441802.2:c.4009T>G	p.Ser1337Ala	p.S1337A	ENST00000441802	NM_005245.3	1337	Tca/Gca	6/27	1	2	FACETS	0.722	0.627	0.826	0.722	0.627	0.826	SUBCLONAL	1	TRUE	1	0.198979070629005	2		481	960	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0030481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	80	571	2	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		573	1139	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495732	72495732	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	159	454	0	ENST00000477973.2:c.340T>G	p.Trp114Gly	p.W114G	ENST00000477973	NM_012234.5	114	Tgg/Ggg	1/4	1	2	FACETS	0.896	0.829	0.964	0.896	0.829	0.964	CLONAL	1	TRUE	1	0.801429915286565	2		454	443	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070543	67070543	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	96	221	0	ENST00000412916.2:c.167C>A	p.Ala56Asp	p.A56D	ENST00000412916		56	gCt/gAt	3/6	1	2	FACETS	0.871	0.788	0.957	0.871	0.788	0.957	CLONAL	1	TRUE	1	0.801429915286565	2		221	275	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827572	72827574	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs751017331	NA	P-0030521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	213	659	0	ENST00000268489.5:c.9007_9009del	p.Lys3003del	p.K3003del	ENST00000268489	NM_006885.3	3003	AAG/-	9/10	1	2	FACETS	0.898	0.84	0.957	0.898	0.84	0.957	CLONAL	1	TRUE	1	0.801429915286565	2		659	592	SUCCESS
APC	324	MSKCC	GRCh37	5	112175851	112175851	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	98	274	0	ENST00000257430.4:c.4561del	p.Glu1521AsnfsTer2	p.E1521Nfs*2	ENST00000257430	NM_000038.5	1520	gtG/gt	16/16	0.63303247689275	1	FACETS	0.814	0.748	0.88	0.814	0.748	0.88	CLONAL	1	TRUE	0	0.801429915286565	1		274	180	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056988	180056988	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	201	884	0	ENST00000261937.6:c.631G>C	p.Gly211Arg	p.G211R	ENST00000261937	NM_182925.4	211	Gga/Cga	5/30	1	2	FACETS	0.862	0.804	0.921	0.862	0.804	0.921	CLONAL	1	TRUE	1	0.801429915286565	2		884	582	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0030565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	121	334	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.998	0.905	1	0.998	0.905	1	CLONAL	1	TRUE	1	0.449077320414469	2		334	540	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602340	10602340	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	400	664	0	ENST00000171111.5:c.1238G>T	p.Arg413Leu	p.R413L	ENST00000171111	NM_203500.1	413	cGt/cTt	3/6	0.449077320414469	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.449077320414469	2		664	890	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712520	52712520	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	137	334	0	ENST00000394830.3:c.232C>T	p.Arg78Ter	p.R78*	ENST00000394830	NM_018313.4	78	Cga/Tga	3/30	0.449077320414469	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.449077320414469	1		334	428	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714601	52714601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755649324	NA	P-0030565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	300	494	0	ENST00000322088.6:c.359C>T	p.Ser120Leu	p.S120L	ENST00000322088	NM_014225.5	120	tCg/tTg	4/15	0.449077320414469	2	FACETS	0.978	0.928	1	0.978	0.928	1	CLONAL	2	TRUE	0	0.449077320414469	2		494	683	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466569	120466569	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	108	428	0	ENST00000256646.2:c.4550A>T	p.His1517Leu	p.H1517L	ENST00000256646	NM_024408.3	1517	cAc/cTc	26/34	0.449077320414469	1	FACETS	0.91	0.823	1	0.91	0.823	1	CLONAL	1	TRUE	0	0.449077320414469	1		428	410	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422940	49422940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1191846376	NA	P-0030565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	157	526	0	ENST00000301067.7:c.14155G>A	p.Ala4719Thr	p.A4719T	ENST00000301067	NM_003482.3	4719	Gcc/Acc	44/54	1	2	FACETS	0.925	0.849	1	0.925	0.849	1	CLONAL	1	TRUE	1	0.449077320414469	2		526	756	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220494	1220506	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	GCGTGGCCGAGGT	GCGTGGCCGAGGT	ATA	novel	NA	P-0030565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	313	515	3	ENST00000326873.7:c.587_597+2delinsATA		p.X196_splice	ENST00000326873	NM_000455.4	196		4/10	0.449077320414469	2	FACETS	0.989	0.939	1	0.989	0.939	1	CLONAL	2	TRUE	0	0.449077320414469	2		518	705	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222458	2222458	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	293	439	2	ENST00000398665.3:c.3290C>T	p.Pro1097Leu	p.P1097L	ENST00000398665	NM_032482.2	1097	cCc/cTc	24/28	0.449077320414469	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.449077320414469	2		441	634	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272297	15272297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	335	563	0	ENST00000263388.2:c.6142G>A	p.Ala2048Thr	p.A2048T	ENST00000263388	NM_000435.2	2048	Gcc/Acc	33/33	0.449077320414469	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.449077320414469	2		563	735	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753081	57753081	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1234436072	NA	P-0030565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	123	357	0	ENST00000274289.3:c.935C>G	p.Ala312Gly	p.A312G	ENST00000274289	NM_006622.3	312	gCt/gGt	7/14	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.449077320414469	2		357	528	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937001	48937005	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAA	CAGAA	-	rs1566192530	NA	P-0030573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	149	450	1	ENST00000267163.4:c.772_776del	p.Asn258GlufsTer11	p.N258Efs*11	ENST00000267163	NM_000321.2	257	CAGAAc/c	8/27	0.864402307381226	2	FACETS	0.963	0.923	0.998	0.963	0.923	0.998	CLONAL	2	TRUE	0	0.869685806006985	2		451	178	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551727	150551744	+	inframe_deletion	In_Frame_Del	DEL	CGGGGGTCGCGGTGACGT	CGGGGGTCGCGGTGACGT	-	novel	NA	P-0030573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	117	235	0	ENST00000369026.2:c.263_280del	p.Asp88_Pro93del	p.D88_P93del	ENST00000369026	NM_021960.4	88	gACGTCACCGCGACCCCCGcg/gcg	1/3	0.747927307594262	6	FACETS	0.887	0.814	0.961			1	CLONAL	3	TRUE	NA	0.869685806006985	6		235	277	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750406	41750406	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	84	437	0	ENST00000226382.2:c.222G>C	p.Gln74His	p.Q74H	ENST00000226382	NM_003924.3	74	caG/caC	1/3	0.818654233119163	4	FACETS	1	0.952	1			1	CLONAL	1	TRUE	NA	0.869685806006985	4		437	322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578338	7578383	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGCCCTGTCGTCTCTCCAGCCCCAGCTGCTCACCATCGCTATCTGA	AGCCCTGTCGTCTCTCCAGCCCCAGCTGCTCACCATCGCTATCTGA	T	novel	NA	P-0030573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	492	465	0	ENST00000269305.4:c.547_559+33delinsA		p.X183_splice	ENST00000269305	NM_001126112.2	183		5/11	0.869685806006985	4	FACETS	0.987	0.97	1			1	CLONAL	4	TRUE	NA	0.869685806006985	4		465	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1555525429	NA	P-0030642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	154	549	0	ENST00000269305.4:c.782+1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.627951806932747	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	4	FALSE	0	0.712834329971405	4		549	179	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841422	156841422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	20	398	0	ENST00000524377.1:c.725G>A	p.Gly242Glu	p.G242E	ENST00000524377	NM_002529.3	242	gGg/gAg	7/17	0.520713483341435	3	FACETS	0.827	0.645	1	0.414	0.322	0.516	CLONAL	1	FALSE	1	0.712834329971405	3		398	92	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17125855	17125855	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	94	584	2	ENST00000285071.4:c.739G>A	p.Asp247Asn	p.D247N	ENST00000285071	NM_144997.5	247	Gat/Aat	7/14	0.627951806932747	4	FACETS	1	0.958	1	0.546	0.496	0.595	CLONAL	2	FALSE	0	0.712834329971405	4		586	207	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0030653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	85	596	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.42	2		596	334	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243048	105243048	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519804	NA	P-0030653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	142	707	0	ENST00000349310.3:c.235C>A	p.Gln79Lys	p.Q79K	ENST00000349310	NM_001014432.1	79	Cag/Aag	5/15	1	2	FACETS	0.944	0.862	1	0.944	0.862	1	CLONAL	1	TRUE	1	0.42	2		707	716	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782082	NA	P-0030653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	122	542	0	ENST00000269305.4:c.745A>T	p.Arg249Trp	p.R249W	ENST00000269305	NM_001126112.2	249	Agg/Tgg	7/11	1	2	FACETS	0.993	0.901	1	0.993	0.901	1	CLONAL	1	TRUE	1	0.42	2		542	585	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43699737	43699739	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	rs754334940	NA	P-0030653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	40	424	0	ENST00000382044.4:c.5776_5778del	p.Val1926del	p.V1926del	ENST00000382044	NM_001141980.1	1926	GTG/-	28/28	1	2	FACETS	0.345	0.286	0.411	0.345	0.286	0.411	SUBCLONAL	1	TRUE	1	0.42	2		424	552	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0030659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	143	447	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.89	0.813	0.971	0.89	0.813	0.971	CLONAL	1	TRUE	1	0.442631820474302	2		447	726	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0030659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	120	391	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.809	0.732	0.891	0.809	0.732	0.891	CLONAL	1	TRUE	1	0.442631820474302	2		391	670	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0030659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	180	528	0	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.442631820474302	2		528	792	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842595	68842595	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0030659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	186	500	0	ENST00000261769.5:c.532-1G>A		p.X178_splice	ENST00000261769	NM_004360.3	178			0.442631820474302	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.442631820474302	1		500	632	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061277	38061277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866443101	NA	P-0030659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	185	475	0	ENST00000250448.2:c.712C>T	p.Pro238Ser	p.P238S	ENST00000250448	NM_004496.3	238	Ccg/Tcg	2/2	1	2	FACETS	0.986	0.911	1	0.986	0.911	1	CLONAL	1	TRUE	1	0.442631820474302	2		475	848	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340949	70340949	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	152	569	0	ENST00000374080.3:c.682G>A	p.Val228Met	p.V228M	ENST00000374080		228	Gtg/Atg	5/45	1	2	FACETS	0.792	0.725	0.863	0.792	0.725	0.863	SUBCLONAL	1	TRUE	1	0.442631820474302	2		569	867	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855281	76855281	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	101	388	0	ENST00000373344.5:c.5706del	p.Phe1902LeufsTer10	p.F1902Lfs*10	ENST00000373344	NM_000489.3	1902	ttT/tt	24/35	1	2	FACETS	0.879	0.789	0.975	0.879	0.789	0.975	CLONAL	1	TRUE	1	0.442631820474302	2		388	519	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0030669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	317	358	0	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	0.93096511409444	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.93096511409444	2		358	333	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0030669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	199	367	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.93096511409444	3	FACETS	0.967	0.916	1	0.967	0.916	1	CLONAL	2	TRUE	1	0.93096511409444	3		367	324	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0030669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	624	496	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.93096511409444	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.93096511409444	2		496	652	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478633	57478633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1131691999	NA	P-0030669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	292	479	1	ENST00000371085.3:c.305C>T	p.Ala102Val	p.A102V	ENST00000371085	NM_000516.4	102	gCg/gTg	4/13	0.913093832008858	3	FACETS	0.936	0.882	0.991	0.468	0.441	0.496	CLONAL	1	TRUE	1	0.93096511409444	3		480	982	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923155	48923156	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	53	312	0	ENST00000267163.4:c.606dup	p.Gly203ArgfsTer9	p.G203Rfs*9	ENST00000267163	NM_000321.2	201	-/A	6/27	0.93096511409444	1	FACETS	0.966	0.898	1	0.966	0.898	1	CLONAL	1	TRUE	0	0.93096511409444	1		312	63	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371646	89371646	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	257	519	0	ENST00000301030.4:c.194G>T	p.Gly65Val	p.G65V	ENST00000301030	NM_001256183.1	65	gGc/gTc	4/13	0.93096511409444	1	FACETS	0.922	0.891	0.952	0.922	0.891	0.952	CLONAL	1	TRUE	0	0.93096511409444	1		519	320	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0030701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	194	354	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.168080146918173	2	FACETS	0.838	0.781	0.896	0.838	0.781	0.896	INDETERMINATE	2	TRUE	0	0.41429413319628	2		354	559	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807537	1807537	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146672976	NA	P-0030701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	182	549	0	ENST00000260795.2:c.1706C>T	p.Ala569Val	p.A569V	ENST00000260795		569	gCg/gTg	12/17	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.41429413319628	2		549	721	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0030701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	58	270	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.208550179387456	3	FACETS	0.667	0.573	0.768	0.222	0.191	0.256	INDETERMINATE	1	TRUE	0	0.41429413319628	3		270	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520008	NA	P-0030701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	350	713	0	ENST00000269305.4:c.613T>C	p.Tyr205His	p.Y205H	ENST00000269305	NM_001126112.2	205	Tat/Cat	6/11	0.41429413319628	2	FACETS	0.992	0.943	1	0.992	0.943	1	CLONAL	2	TRUE	0	0.41429413319628	2		713	852	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176329	24176329	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1568963596	NA	P-0030701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	193	645	0	ENST00000263121.7:c.1120C>T	p.Arg374Trp	p.R374W	ENST00000263121	NM_003073.3	374	Cgg/Tgg	9/9	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.41429413319628	2		645	732	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50827561	50827561	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	271	534	0	ENST00000398568.2:c.2446A>G	p.Thr816Ala	p.T816A	ENST00000398568	NM_001042412.1	816	Acc/Gcc	16/18	0.307847033052786	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.41429413319628	3		534	757	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347347	89347347	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1257832454	NA	P-0030701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	78	773	0	ENST00000301030.4:c.5603C>A	p.Pro1868Gln	p.P1868Q	ENST00000301030	NM_001256183.1	1868	cCa/cAa	9/13	0.307847033052786	3	FACETS	0.458	0.401	0.52	0.229	0.2	0.26	SUBCLONAL	1	TRUE	1	0.41429413319628	3		773	992	SUCCESS
APC	324	MSKCC	GRCh37	5	112173817	112173820	+	frameshift_variant	Frame_Shift_Del	DEL	TAGT	TAGT	-	rs879254091	NA	P-0030701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	255	515	0	ENST00000257430.4:c.2527_2530del	p.Ser843LeufsTer17	p.S843Lfs*17	ENST00000257430	NM_000038.5	842	gaTAGT/ga	16/16	0.208550179387456	3	FACETS	1	0.986	1	0.763	0.719	0.808	INDETERMINATE	2	TRUE	0	0.41429413319628	3		515	649	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179114	123179114	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	261	310	0	ENST00000218089.9:c.563A>G	p.Tyr188Cys	p.Y188C	ENST00000218089	NM_001042749.1	188	tAt/tGt	8/35	0.377145468794904	2	FACETS	0.998	0.952	1			1	CLONAL	3	TRUE	NA	0.41429413319628	2		310	421	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0030705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	76	493	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	1	2	FACETS	0.864	0.759	0.976	0.864	0.759	0.976	CLONAL	1	TRUE	1	0.32	2		493	550	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0030799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	99	447	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.42	0.375	0.469	0.42	0.375	0.469	SUBCLONAL	1	FALSE	1	0.590532444773646	2		447	798	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0030799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	32	471	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	1	2	FACETS	0.203	0.164	0.247	0.203	0.164	0.247	SUBCLONAL	1	FALSE	1	0.590532444773646	2		471	533	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759553	133759553	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767173632	NA	P-0030799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	557	658	2	ENST00000318560.5:c.1876G>A	p.Gly626Ser	p.G626S	ENST00000318560	NM_005157.4	626	Ggc/Agc	11/11	1	2	FACETS	0.837	0.807	0.867	1	0.997	1	CLONAL	2	FALSE	1	0.590532444773646	2		660	1127	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996640	100996866	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTTATAAGAAACAAGGAATAATTGAAATCTATACAATATTAGATGGTCTCCATTTACAATTAAACCAATAATAAAGGATCAGGGGAAAGGAGCCTACCTTCCATTGCCCTCTTAAAGAAGACCTTACAGCTCCCACAGGTAAGGACACCATAATGACAGCCTGATGCTTCATCCCCACAGATTAAACAAATCTTCTGAGGTAATGACTCGAAGCTGTATTGTGGGC	TCTTATAAGAAACAAGGAATAATTGAAATCTATACAATATTAGATGGTCTCCATTTACAATTAAACCAATAATAAAGGATCAGGGGAAAGGAGCCTACCTTCCATTGCCCTCTTAAAGAAGACCTTACAGCTCCCACAGGTAAGGACACCATAATGACAGCCTGATGCTTCATCCCCACAGATTAAACAAATCTTCTGAGGTAATGACTCGAAGCTGTATTGTGGGC	-	novel	NA	P-0030799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	24	110	0	ENST00000325455.5:c.1661_1789+98del		p.X554_splice	ENST00000325455	NM_001202474.3	554		2/8	1	2	FACETS	0.528	0.418	0.652	0.528	0.418	0.652	SUBCLONAL	1	FALSE	1	0.590532444773646	2		110	154	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919042	50919042	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs768642194	NA	P-0030799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	482	649	1	ENST00000440232.2:c.2779A>C	p.Ile927Leu	p.I927L	ENST00000440232	NM_002691.3	927	Atc/Ctc	22/27	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	FALSE	1	0.590532444773646	2		650	1099	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0030799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	382	447	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.840456077343388	3	FACETS	1	0.995	1	0.684	0.652	0.716	CLONAL	1	FALSE	1	0.840456077343388	3		447	944	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0030799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	131	471	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	1	2	FACETS	0.637	0.582	0.695	0.637	0.582	0.695	SUBCLONAL	1	FALSE	1	0.840456077343388	2		471	489	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759553	133759553	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767173632	NA	P-0030799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	545	658	2	ENST00000318560.5:c.1876G>A	p.Gly626Ser	p.G626S	ENST00000318560	NM_005157.4	626	Ggc/Agc	11/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.840456077343388	2		660	1296	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996640	100996866	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTTATAAGAAACAAGGAATAATTGAAATCTATACAATATTAGATGGTCTCCATTTACAATTAAACCAATAATAAAGGATCAGGGGAAAGGAGCCTACCTTCCATTGCCCTCTTAAAGAAGACCTTACAGCTCCCACAGGTAAGGACACCATAATGACAGCCTGATGCTTCATCCCCACAGATTAAACAAATCTTCTGAGGTAATGACTCGAAGCTGTATTGTGGGC	TCTTATAAGAAACAAGGAATAATTGAAATCTATACAATATTAGATGGTCTCCATTTACAATTAAACCAATAATAAAGGATCAGGGGAAAGGAGCCTACCTTCCATTGCCCTCTTAAAGAAGACCTTACAGCTCCCACAGGTAAGGACACCATAATGACAGCCTGATGCTTCATCCCCACAGATTAAACAAATCTTCTGAGGTAATGACTCGAAGCTGTATTGTGGGC	-	novel	NA	P-0030799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	47	110	0	ENST00000325455.5:c.1661_1789+98del		p.X554_splice	ENST00000325455	NM_001202474.3	554		2/8	1	2	FACETS	0.777	0.67	0.889	0.777	0.67	0.889	SUBCLONAL	1	FALSE	1	0.840456077343388	2		110	144	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919042	50919042	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs768642194	NA	P-0030799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	473	649	1	ENST00000440232.2:c.2779A>C	p.Ile927Leu	p.I927L	ENST00000440232	NM_002691.3	927	Atc/Ctc	22/27	1	2	FACETS	0.975	0.934	1	0.975	0.934	1	CLONAL	1	FALSE	1	0.840456077343388	2		650	1155	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589168	67589168	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	44	264	0	ENST00000274335.5:c.1156C>G	p.Arg386Gly	p.R386G	ENST00000274335		386	Cga/Gga	9/15	1	2	FACETS	0.274	0.23	0.323	0.274	0.23	0.323	SUBCLONAL	1	FALSE	1	0.840456077343388	2		264	382	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436167	51436167	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	29	296	0	ENST00000262662.1:c.127C>A	p.Gln43Lys	p.Q43K	ENST00000262662		43	Cag/Aag	3/4	0.321056865761654	1	FACETS	0.545	0.445	0.653	0.545	0.445	0.653	INDETERMINATE	1	TRUE	0	0.618218024111497	1		296	119	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0030870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	251	327	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.782651906131724	3	FACETS	0.947	0.899	0.996	0.632	0.599	0.664	CLONAL	2	TRUE	0	0.782651906131724	3		327	471	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913396	NA	P-0030870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	174	229	0	ENST00000349496.5:c.95A>G	p.Asp32Gly	p.D32G	ENST00000349496	NM_001904.3	32	gAc/gGc	3/15	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.782651906131724	2		229	433	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187857	11187857	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519780	NA	P-0030870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	199	370	0	ENST00000361445.4:c.6040G>A	p.Glu2014Lys	p.E2014K	ENST00000361445	NM_004958.3	2014	Gag/Aag	44/58	0.740962490767998	2	FACETS	0.958	0.895	1	0.479	0.447	0.511	CLONAL	1	TRUE	0	0.782651906131724	2		370	531	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465638	8465638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781067774	NA	P-0030870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	120	297	0	ENST00000356435.5:c.3542G>A	p.Arg1181His	p.R1181H	ENST00000356435		1181	cGt/cAt	21/35	1	2	FACETS	0.732	0.666	0.8	0.732	0.666	0.8	SUBCLONAL	1	TRUE	1	0.782651906131724	2		297	419	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692815	89692815	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	250	194	0	ENST00000371953.3:c.300del	p.Ile101SerfsTer12	p.I101Sfs*12	ENST00000371953	NM_000314.4	100	cTt/ct	5/9	0.782651906131724	3	FACETS	0.95	0.917	0.981	0.95	0.917	0.981	CLONAL	3	TRUE	0	0.782651906131724	3		194	312	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645450	67645450	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	169	300	0	ENST00000264010.4:c.715G>T	p.Glu239Ter	p.E239*	ENST00000264010	NM_006565.3	239	Gag/Tag	3/12	1	2	FACETS	0.903	0.838	0.97	0.903	0.838	0.97	CLONAL	1	TRUE	1	0.782651906131724	2		300	478	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106100	27106100	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	391	375	0	ENST00000324856.7:c.5715del	p.Lys1905AsnfsTer18	p.K1905Nfs*18	ENST00000324856	NM_006015.4	1904	gAa/ga	20/20	0.740962490767998	2	FACETS	0.999	0.97	1	0.999	0.97	1	CLONAL	2	TRUE	0	0.782651906131724	2		375	500	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830697	72830697	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	235	451	0	ENST00000268489.5:c.5884G>T	p.Glu1962Ter	p.E1962*	ENST00000268489	NM_006885.3	1962	Gag/Tag	9/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.782651906131724	2		451	587	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993153	72993154	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	291	496	0	ENST00000268489.5:c.891dup	p.Val298CysfsTer7	p.V298Cfs*7	ENST00000268489	NM_006885.3	297	-/T	2/10	1	2	FACETS	0.905	0.854	0.956	0.905	0.854	0.956	CLONAL	1	TRUE	1	0.782651906131724	2		496	822	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589220	67589228	+	inframe_deletion	In_Frame_Del	DEL	AATTAATAA	AATTAATAA	-	novel	NA	P-0030870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	145	255	0	ENST00000274335.5:c.1209_1217del	p.Glu403_Asn406delinsAsp	p.E403_N406delinsD	ENST00000274335		403	gAATTAATAAac/gac	9/15	1	2	FACETS	0.922	0.85	0.995	0.922	0.85	0.995	CLONAL	1	TRUE	1	0.782651906131724	2		255	402	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593351	67593352	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0030870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	171	252	0	ENST00000274335.5:c.2101_2102del	p.Thr701LeufsTer39	p.T701Lfs*39	ENST00000274335		699	caACac/caac	15/15	1	2	FACETS	0.926	0.859	0.994	0.926	0.859	0.994	CLONAL	1	TRUE	1	0.782651906131724	2		252	472	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370951	55370952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0030870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	225	332	0	ENST00000297316.4:c.255dup	p.Leu86AlafsTer76	p.L86Afs*76	ENST00000297316	NM_022454.3	85	cgg/cGgg	1/2	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.782651906131724	2		332	563	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912188	114912188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	73	466	0	ENST00000543371.1:c.1258C>T	p.Arg420Trp	p.R420W	ENST00000543371	NM_001198531.1	420	Cgg/Tgg	11/14	1	2	FACETS	0.712	0.622	0.809	0.712	0.622	0.809	SUBCLONAL	1	TRUE	1	0.29	2		466	707	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239445	123239445	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	84	563	0	ENST00000358487.5:c.2392T>C	p.Phe798Leu	p.F798L	ENST00000358487	NM_000141.4	798	Ttt/Ctt	18/18	1	2	FACETS	0.684	0.603	0.771	0.684	0.603	0.771	SUBCLONAL	1	TRUE	1	0.29	2		563	847	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646730	23646730	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	95	575	0	ENST00000261584.4:c.1137G>T	p.Lys379Asn	p.K379N	ENST00000261584	NM_024675.3	379	aaG/aaT	4/13	1	2	FACETS	0.77	0.685	0.861	0.77	0.685	0.861	SUBCLONAL	1	TRUE	1	0.29	2		575	851	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578445	7578445	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	80	557	0	ENST00000269305.4:c.485del	p.Ile162ThrfsTer8	p.I162Tfs*8	ENST00000269305	NM_001126112.2	162	aTc/ac	5/11	1	2	FACETS	0.715	0.628	0.807	0.715	0.628	0.807	SUBCLONAL	1	TRUE	1	0.29	2		557	772	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713304	30713305	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0030875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	112	380	0	ENST00000295754.5:c.631dup	p.Glu211GlyfsTer13	p.E211Gfs*13	ENST00000295754	NM_003242.5	210	atg/atGg	4/7	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.29	2		380	575	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066490	94066490	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	31	358	0	ENST00000369303.4:c.1269C>G	p.Asp423Glu	p.D423E	ENST00000369303	NM_004440.3	423	gaC/gaG	5/17	1	2	FACETS	0.428	0.345	0.521	0.428	0.345	0.521	SUBCLONAL	1	TRUE	1	0.29	2		358	500	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035234	6035234	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	46	402	0	ENST00000265849.7:c.834T>G	p.His278Gln	p.H278Q	ENST00000265849	NM_000535.5	278	caT/caG	8/15	1	2	FACETS	0.395	0.331	0.465	0.395	0.331	0.465	SUBCLONAL	1	TRUE	1	0.29	2		402	804	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120457996	120457996	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs756211019	NA	P-0030893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	68	448	1	ENST00000256646.2:c.7349G>T	p.Gly2450Val	p.G2450V	ENST00000256646	NM_024408.3	2450	gGa/gTa	34/34	0.0965171957791917	4	FACETS	1	0.957	1	0.618	0.538	0.704	INDETERMINATE	1	TRUE	2	0.270992950294523	4		449	516	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741883	17741883	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	18	37	0	ENST00000250003.3:c.554C>A	p.Pro185His	p.P185H	ENST00000250003	NM_002478.4	185	cCc/cAc	1/3	0.270992950294523	3	FACETS	0.992	0.795	1	1	0.943	1	CLONAL	4	TRUE	1	0.270992950294523	3		37	38	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94169065	94169065	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs876658165	NA	P-0030893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	29	321	0	ENST00000323929.3:c.1927G>T	p.Val643Leu	p.V643L	ENST00000323929	NM_005591.3	643	Gtg/Ttg	18/20	0.270992950294523	3	FACETS	0.767	0.616	0.937	0.383	0.308	0.469	CLONAL	1	TRUE	1	0.270992950294523	3		321	317	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28931779	28931779	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	100	371	1	ENST00000282397.4:c.2160A>T	p.Arg720Ser	p.R720S	ENST00000282397	NM_002019.4	720	agA/agT	15/30	0.270992950294523	3	FACETS	0.823	0.738	0.913	0.823	0.738	0.913	CLONAL	2	TRUE	1	0.270992950294523	3		372	509	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663299	67663300	+	splice_acceptor_variant	Splice_Site	DNP	AG	AG	TT	novel	NA	P-0030893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	67	379	0	ENST00000264010.4:c.1702-2_1702-1delinsTT		p.X568_splice	ENST00000264010	NM_006565.3	568			0.117584847974503	5	FACETS	0.809	0.705	0.92	0.539	0.47	0.613	INDETERMINATE	2	TRUE	2	0.270992950294523	5		379	430	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0030893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	191	591	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.267265008338287	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.270992950294523	2		591	630	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556993	29556993	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1135402836	NA	P-0030893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	22	149	0	ENST00000356175.3:c.2990+1G>A		p.X997_splice	ENST00000356175	NM_000267.3	997			0.270992950294523	5	FACETS	0.865	0.679	1	0.577	0.452	0.717	CLONAL	2	TRUE	2	0.270992950294523	5		149	132	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663772	29663773	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	224	523	0	ENST00000356175.3:c.6206dup	p.Asn2070GlnfsTer5	p.N2070Qfs*5	ENST00000356175	NM_000267.3	2068	-/T	41/57	0.270992950294523	5	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	2	0.270992950294523	5		523	704	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602289	10602289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1308006383	NA	P-0030893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	156	504	0	ENST00000171111.5:c.1289G>A	p.Gly430Asp	p.G430D	ENST00000171111	NM_203500.1	430	gGc/gAc	3/6	0.267265008338287	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.270992950294523	2		504	548	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161988	47161988	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	52	369	0	ENST00000409792.3:c.4138A>T	p.Thr1380Ser	p.T1380S	ENST00000409792	NM_014159.6	1380	Act/Tct	3/21	0.206395081794294	3	FACETS	0.968	0.826	1	0.484	0.413	0.562	CLONAL	1	TRUE	1	0.270992950294523	3		369	450	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468192	50468192	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	52	496	0	ENST00000331340.3:c.1427T>A	p.Met476Lys	p.M476K	ENST00000331340	NM_006060.4	476	aTg/aAg	8/8	0.270992950294523	6	FACETS	0.863	0.733	1	0.288	0.244	0.335	CLONAL	1	TRUE	3	0.270992950294523	6		496	686	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964831	15964831	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030948-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	98	866	0	ENST00000268712.3:c.5765G>C	p.Arg1922Thr	p.R1922T	ENST00000268712	NM_006311.3	1922	aGa/aCa	37/46	1	2	FACETS	0.776	0.692	0.866	0.776	0.692	0.866	SUBCLONAL	1	TRUE	1	0.31135155814994	2		866	811	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920137	76920137	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030948-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	57	322	0	ENST00000373344.5:c.3940G>T	p.Glu1314Ter	p.E1314*	ENST00000373344	NM_000489.3	1314	Gag/Tag	11/35	0.299569600462254	2	FACETS	0.687	0.59	0.793			1	SUBCLONAL	1	TRUE	NA	0.31135155814994	2		322	533	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913315	NA	P-0031030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	10	722	2	ENST00000326873.7:c.580G>A	p.Asp194Asn	p.D194N	ENST00000326873	NM_000455.4	194	Gac/Aac	4/10	0.874727773814933	1	FACETS	0.027	0.018	0.039	0.027	0.018	0.039	SUBCLONAL	1	TRUE	0	0.874727773814933	1		724	472	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248245	59248245	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	50	47	0	ENST00000371222.2:c.498G>C	p.Glu166Asp	p.E166D	ENST00000371222	NM_002228.3	166	gaG/gaC	1/1	0.195554268343227	1	FACETS	0.473	0.411	0.537	0.473	0.411	0.537	INDETERMINATE	1	TRUE	0	0.874727773814933	1		47	136	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577064	7577065	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0031030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	445	737	1	ENST00000269305.4:c.873_874del	p.Lys292ArgfsTer13	p.K292Rfs*13	ENST00000269305	NM_001126112.2	291	aaGAaa/aaaa	8/11	0.874727773814933	1	FACETS	0.99	0.963	1	0.99	0.963	1	CLONAL	1	TRUE	0	0.874727773814933	1		738	578	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939769	76939769	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	101	586	0	ENST00000373344.5:c.979G>T	p.Glu327Ter	p.E327*	ENST00000373344	NM_000489.3	327	Gaa/Taa	9/35	0.20333311632772	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.874727773814933	0		586	303	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0031112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	94	535	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.161230533248601	1	FACETS	0.77	0.685	0.86	1	0.981	1	SUBCLONAL	2	TRUE	0	0.161230533248601	1		535	696	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098944	178098944	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	19	398	0	ENST00000397062.3:c.101G>C	p.Arg34Pro	p.R34P	ENST00000397062	NM_006164.4	34	cGa/cCa	2/5	0.161230533248601	1	FACETS	0.511	0.387	0.658	0.511	0.387	0.658	SUBCLONAL	1	TRUE	0	0.161230533248601	1		398	424	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571924	64571924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	110	945	0	ENST00000312049.6:c.1715C>T	p.Ser572Leu	p.S572L	ENST00000312049	NM_130799.2	572	tCg/tTg	10/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.161230533248601	2		945	999	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992142	11992142	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	42	392	0	ENST00000396373.4:c.232T>A	p.Ser78Thr	p.S78T	ENST00000396373	NM_001987.4	78	Tct/Act	3/8	1	2	FACETS	0.959	0.8	1	0.959	0.8	1	CLONAL	1	TRUE	1	0.161230533248601	2		392	543	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440141	49440141	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs574622908	NA	P-0031112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	77	580	0	ENST00000301067.7:c.4485C>A	p.Tyr1495Ter	p.Y1495*	ENST00000301067	NM_003482.3	1495	taC/taA	16/54	1	2	FACETS	0.775	0.681	0.877	1	0.977	1	SUBCLONAL	2	TRUE	1	0.161230533248601	2		580	616	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293884	1293884	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	103	891	0	ENST00000310581.5:c.1117C>G	p.Pro373Ala	p.P373A	ENST00000310581	NM_198253.2	373	Cca/Gca	2/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.161230533248601	2		891	967	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39002738	39002738	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	35	376	0	ENST00000357387.3:c.291del	p.Glu98LysfsTer24	p.E98Kfs*24	ENST00000357387	NM_152756.3	97	aaA/aa	5/38	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.161230533248601	2		376	362	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372273	55372273	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	87	600	0	ENST00000297316.4:c.963C>A	p.His321Gln	p.H321Q	ENST00000297316	NM_022454.3	321	caC/caA	2/2	0.161230533248601	1	FACETS	0.887	0.787	0.994	1	0.983	1	CLONAL	2	TRUE	0	0.161230533248601	1		600	559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540652	NA	P-0031185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	50	729	0	ENST00000269305.4:c.743G>C	p.Arg248Pro	p.R248P	ENST00000269305	NM_001126112.2	248	cGg/cCg	7/11	0.696235335205619	1	FACETS	0.875	0.769	0.982	0.875	0.769	0.982	CLONAL	1	TRUE	0	0.696235335205619	1		729	107	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0031185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	55	490	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.244026011688529	1	FACETS	0.763	0.671	0.858	0.763	0.671	0.858	INDETERMINATE	1	TRUE	0	0.696235335205619	1		490	135	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0031185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	28	337	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	0.244026011688529	1	FACETS	0.655	0.541	0.776	0.655	0.541	0.776	INDETERMINATE	1	TRUE	0	0.696235335205619	1		337	80	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361206	70361206	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	70	738	0	ENST00000374080.3:c.6394C>T	p.Gln2132Ter	p.Q2132*	ENST00000374080		2132	Cag/Tag	43/45	0.269805786349616	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.696235335205619	0		738	227	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540652	NA	P-0031185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	405	729	0	ENST00000269305.4:c.743G>C	p.Arg248Pro	p.R248P	ENST00000269305	NM_001126112.2	248	cGg/cCg	7/11	0.307679459612256	1	FACETS	0.924	0.885	0.962	1	0.997	1	CLONAL	3	TRUE	0	0.307679459612256	1		729	804	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0031185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	232	490	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.187874155093791	2	FACETS	1	0.971	1	1	0.994	1	CLONAL	3	TRUE	0	0.307679459612256	2		490	481	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0031185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	206	337	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	0.307679459612256	1	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	0	0.307679459612256	1		337	470	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361206	70361206	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	392	738	0	ENST00000374080.3:c.6394C>T	p.Gln2132Ter	p.Q2132*	ENST00000374080		2132	Cag/Tag	43/45	0.162570139953426	3	FACETS	0.999	0.953	1	1	0.996	1	INDETERMINATE	3	TRUE	1	0.307679459612256	3		738	981	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0031185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	74	314	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.187874155093791	2	FACETS	0.776	0.685	0.871	0.776	0.685	0.871	SUBCLONAL	2	TRUE	0	0.307679459612256	2		314	310	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225365087	225365087	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	80	420	0	ENST00000264414.4:c.1603T>C	p.Phe535Leu	p.F535L	ENST00000264414	NM_003590.4	535	Ttc/Ctc	11/16	0.307679459612256	1	FACETS	0.768	0.677	0.865	0.768	0.677	0.865	SUBCLONAL	1	TRUE	0	0.307679459612256	1		420	573	SUCCESS
AR	367	MSKCC	GRCh37	X	66765159	66765185	+	inframe_deletion	In_Frame_Del	DEL	GCAGCAGCAGCAGCAGCAGCAGCAGCA	GCAGCAGCAGCAGCAGCAGCAGCAGCA	-	rs3032358	NA	P-0031185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	31	286	0	ENST00000374690.3:c.213_239del	p.Gln72_Gln80del	p.Q72_Q80del	ENST00000374690	NM_000044.3	57	ctGCAGCAGCAGCAGCAGCAGCAGCAGCAg/ctg	1/8	0.162570139953426	3	FACETS	0.767	0.622	0.931	0.384	0.311	0.466	INDETERMINATE	1	TRUE	1	0.307679459612256	3		286	303	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	138	354	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.58757876009803	3	FACETS	0.81	0.746	0.876	0.81	0.746	0.876	CLONAL	2	TRUE	1	0.58757876009803	3		354	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0031219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	557	751	3	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	0.529197779910715	3	FACETS	0.882	0.847	0.916	0.882	0.847	0.916	CLONAL	2	TRUE	1	0.58757876009803	3		754	1391	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220439	1220439	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0031219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	622	912	1	ENST00000326873.7:c.532A>T	p.Lys178Ter	p.K178*	ENST00000326873	NM_000455.4	178	Aag/Tag	4/10	0.58757876009803	3	FACETS	0.9	0.873	0.927	0.9	0.873	0.927	CLONAL	3	TRUE	0	0.58757876009803	3		913	1014	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938773	76938773	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	139	729	1	ENST00000373344.5:c.1975G>A	p.Val659Ile	p.V659I	ENST00000373344	NM_000489.3	659	Gta/Ata	9/35	0.393515440025634	4	FACETS	1	0.985	1	0.684	0.626	0.745	CLONAL	1	TRUE	2	0.58757876009803	4		730	549	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461055	120461055	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	131	484	0	ENST00000256646.2:c.5903C>G	p.Ala1968Gly	p.A1968G	ENST00000256646	NM_024408.3	1968	gCg/gGg	32/34	0.491229831263291	2	FACETS	0.841	0.767	0.918	0.421	0.383	0.459	CLONAL	1	TRUE	0	0.58757876009803	2		484	530	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602757	10602757	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	931	976	1	ENST00000171111.5:c.821A>C	p.His274Pro	p.H274P	ENST00000171111	NM_203500.1	274	cAc/cCc	3/6	0.58757876009803	3	FACETS	0.909	0.886	0.931	0.909	0.886	0.931	CLONAL	3	TRUE	0	0.58757876009803	3		977	1504	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300893	137300893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1275	246	893	1	ENST00000481739.1:c.538G>A	p.Asp180Asn	p.D180N	ENST00000481739	NM_002957.4	180	Gac/Aac	4/10	0.58757876009803	4	FACETS	0.874	0.815	0.936	0.437	0.407	0.468	CLONAL	1	TRUE	2	0.58757876009803	4		894	1521	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207162	1207162	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs137853076	NA	P-0031233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	243	802	0	ENST00000326873.7:c.250A>T	p.Lys84Ter	p.K84*	ENST00000326873	NM_000455.4	84	Aag/Tag	1/10	0.378407715583253	1	FACETS	0.848	0.791	0.907	0.848	0.791	0.907	CLONAL	1	TRUE	0	0.378407715583253	1		802	1228	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472621	88472621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1429499898	NA	P-0031233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	64	408	0	ENST00000360948.2:c.1934G>A	p.Arg645His	p.R645H	ENST00000360948	NM_001012338.2	645	cGc/cAc	16/19	1	2	FACETS	0.539	0.467	0.618	0.539	0.467	0.618	SUBCLONAL	1	TRUE	1	0.378407715583253	2		408	627	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78921012	78921032	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTTCTTCCCTTAAGCTTTTG	TCTTCTTCCCTTAAGCTTTTG	-	novel	NA	P-0031233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	72	458	0	ENST00000306801.3:c.3141-15_3146del		p.X1047_splice	ENST00000306801	NM_020761.2	1047		27/34	1	2	FACETS	0.604	0.528	0.686	0.604	0.528	0.686	SUBCLONAL	1	TRUE	1	0.378407715583253	2		458	630	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0031239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	125	501	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	FALSE	1	0.280855468137595	2		501	866	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0031239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	195	612	2	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	0.139017416327477	4	FACETS	0.764	0.706	0.824	0.764	0.706	0.824	INDETERMINATE	2	FALSE	2	0.280855468137595	4		614	1164	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922363	178922363	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	213	504	0	ENST00000263967.3:c.1132T>C	p.Cys378Arg	p.C378R	ENST00000263967	NM_006218.2	378	Tgt/Cgt	6/21	0.280855468137595	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	FALSE	1	0.280855468137595	3		504	806	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578441	7578441	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1567553246	NA	P-0031239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	191	662	0	ENST00000269305.4:c.489C>G	p.Tyr163Ter	p.Y163*	ENST00000269305	NM_001126112.2	163	taC/taG	5/11	0.139017416327477	4	FACETS	1	0.99	1	0.74	0.683	0.799	INDETERMINATE	1	FALSE	2	0.280855468137595	4		662	1177	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309736	30309736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	79	389	0	ENST00000307677.4:c.286G>A	p.Glu96Lys	p.E96K	ENST00000307677	NM_138578.1	96	Gag/Aag	2/3	0.192616167397322	3	FACETS	0.801	0.703	0.906	0.4	0.351	0.453	CLONAL	1	FALSE	1	0.280855468137595	3		389	801	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750740	39750744	+	frameshift_variant	Frame_Shift_Del	DEL	ATTGC	ATTGC	-	novel	NA	P-0031239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	106	426	0	ENST00000361337.2:c.2140_2144del	p.Ile714ProfsTer12	p.I714Pfs*12	ENST00000361337	NM_003286.2	714	ATTGCc/c	20/21	0.192616167397322	3	FACETS	1	0.977	1	0.664	0.596	0.736	CLONAL	1	FALSE	1	0.280855468137595	3		426	648	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469672	NA	P-0031290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	150	514	0	ENST00000374080.3:c.131G>A	p.Gly44Asp	p.G44D	ENST00000374080		44	gGt/gAt	2/45	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.507070155057991	2		514	546	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186637	108186637	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	77	269	0	ENST00000278616.4:c.6094A>G	p.Arg2032Gly	p.R2032G	ENST00000278616	NM_000051.3	2032	Aga/Gga	41/63	0.471953294725754	1	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	0	0.507070155057991	1		269	224	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483254	120483254	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	53	593	0	ENST00000256646.2:c.3107A>G	p.Asn1036Ser	p.N1036S	ENST00000256646	NM_024408.3	1036	aAt/aGt	19/34	0.1844960209687	1	FACETS	0.59	0.502	0.686	0.59	0.502	0.686	SUBCLONAL	1	TRUE	0	0.242932182543771	1		593	650	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111118	193111118	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	62	583	0	ENST00000367435.3:c.651G>T	p.Glu217Asp	p.E217D	ENST00000367435	NM_024529.4	217	gaG/gaT	7/17	0.242932182543771	4	FACETS	0.72	0.62	0.829	0.24	0.206	0.277	SUBCLONAL	1	TRUE	1	0.242932182543771	4		583	881	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609104	43609104	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	145	818	0	ENST00000355710.3:c.1860C>A	p.Cys620Ter	p.C620*	ENST00000355710	NM_020975.4	620	tgC/tgA	10/20	0.119519950184243	3	FACETS	1	0.985	1	0.703	0.641	0.768	INDETERMINATE	1	TRUE	1	0.242932182543771	3		818	952	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347657	118347657	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	114	621	1	ENST00000534358.1:c.3294G>A	p.Trp1098Ter	p.W1098*	ENST00000534358	NM_005933.3	1098	tgG/tgA	4/36	0.242932182543771	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.242932182543771	1		622	696	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0031300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	268	460	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.242932182543771	4	FACETS	0.932	0.875	0.99	0.932	0.875	0.99	CLONAL	3	TRUE	1	0.242932182543771	4		460	981	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149438	61149438	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	47	532	0	ENST00000295025.8:c.1628G>T	p.Ser543Ile	p.S543I	ENST00000295025	NM_002908.2	543	aGt/aTt	11/11	0.119519950184243	3	FACETS	0.582	0.49	0.685	0.291	0.245	0.343	INDETERMINATE	1	TRUE	1	0.242932182543771	3		532	745	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851595	134851595	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	61	647	0	ENST00000398015.3:c.1001A>T	p.Asn334Ile	p.N334I	ENST00000398015	NM_004441.4	334	aAt/aTt	5/16	1	2	FACETS	0.654	0.563	0.753	0.654	0.563	0.753	SUBCLONAL	1	TRUE	1	0.242932182543771	2		647	768	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279177	142279177	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	63	730	0	ENST00000350721.4:c.1469T>C	p.Leu490Ser	p.L490S	ENST00000350721	NM_001184.3	490	tTa/tCa	6/47	0.119519950184243	3	FACETS	0.642	0.554	0.738	0.321	0.277	0.369	INDETERMINATE	1	TRUE	1	0.242932182543771	3		730	906	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526390	31526390	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	170	974	1	ENST00000344624.3:c.650G>T	p.Ser217Ile	p.S217I	ENST00000344624		217	aGt/aTt	2/33	0.196921590796975	3	FACETS	1	0.981	1	0.613	0.562	0.666	CLONAL	1	TRUE	1	0.242932182543771	3		975	1280	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946195	13946195	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	231	635	0	ENST00000405192.2:c.901C>G	p.Arg301Gly	p.R301G	ENST00000405192	NM_001163147.1	301	Cgg/Ggg	10/12	0.242932182543771	5	FACETS	0.859	0.801	0.919	0.859	0.801	0.919	CLONAL	3	TRUE	2	0.242932182543771	5		635	1007	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90971011	90971011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777259845	NA	P-0031300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	47	545	0	ENST00000265433.3:c.1066G>A	p.Ala356Thr	p.A356T	ENST00000265433	NM_002485.4	356	Gcc/Acc	9/16	0.230552410792786	4	FACETS	0.577	0.485	0.678	0.192	0.161	0.226	SUBCLONAL	1	TRUE	1	0.242932182543771	4		545	834	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410915	63410915	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	59	758	0	ENST00000330258.3:c.2252C>A	p.Pro751His	p.P751H	ENST00000330258	NM_152424.3	751	cCt/cAt	2/2	0.242932182543771	1	FACETS	0.522	0.448	0.603	0.522	0.448	0.603	SUBCLONAL	1	TRUE	0	0.242932182543771	1		758	817	SUCCESS
BTK	695	MSKCC	GRCh37	X	100625028	100625028	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs782820524	NA	P-0031300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	119	738	2	ENST00000308731.7:c.349A>T	p.Thr117Ser	p.T117S	ENST00000308731	NM_000061.2	117	Act/Tct	5/19	0.242932182543771	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.242932182543771	1		740	775	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0031319-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	101	322	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.409812305408698	2		322	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0031319-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	221	651	0	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	0.409812305408698	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.409812305408698	2		651	507	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857047	9857047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568622613	NA	P-0031319-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	108	315	0	ENST00000330684.3:c.4354C>T	p.Arg1452Cys	p.R1452C	ENST00000330684	NM_001134407.1	1452	Cgc/Tgc	13/13	0.394303544395661	3	FACETS	0.887	0.804	0.973	0.887	0.804	0.973	CLONAL	2	TRUE	1	0.409812305408698	3		315	358	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242474	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGA	GAATTAAGA	-	rs121913436	NA	P-0031319-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	424	523	0	ENST00000275493.2:c.2239_2247del	p.Leu747_Glu749del	p.L747_E749del	ENST00000275493	NM_005228.3	746	GAATTAAGA/-	19/28	0.409812305408698	8	FACETS	0.944	0.903	0.986	0.787	0.753	0.821	CLONAL	5	TRUE	2	0.409812305408698	8		523	977	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937230	76937230	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031319-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	115	610	0	ENST00000373344.5:c.3518C>A	p.Ser1173Ter	p.S1173*	ENST00000373344	NM_000489.3	1173	tCa/tAa	9/35	0.409812305408698	2	FACETS	1	0.935	1	0.522	0.472	0.574	CLONAL	1	TRUE	0	0.409812305408698	2		610	538	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41219669	41219669	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031319-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	103	490	0	ENST00000357654.3:c.5030C>G	p.Thr1677Ser	p.T1677S	ENST00000357654	NM_007294.3	1677	aCt/aGt	16/23	0.195807936353088	5	FACETS	1	0.946	1	0.363	0.325	0.404	INDETERMINATE	1	TRUE	2	0.409812305408698	5		490	745	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519044	66519044	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031319-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	177	449	0	ENST00000358598.2:c.325G>T	p.Asp109Tyr	p.D109Y	ENST00000358598	NM_212471.2	109	Gat/Tat	3/11	0.195807936353088	5	FACETS	1	0.983	1	0.8	0.742	0.861	INDETERMINATE	2	TRUE	2	0.409812305408698	5		449	581	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222925	36222925	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031319-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	250	835	0	ENST00000222270.7:c.5554G>T	p.Ala1852Ser	p.A1852S	ENST00000222270	NM_014727.1	1852	Gcc/Tcc	27/37	0.409812305408698	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.409812305408698	2		835	580	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61708324	61708324	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031319-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	178	367	0	ENST00000401558.2:c.3065T>A	p.Ile1022Lys	p.I1022K	ENST00000401558	NM_003400.3	1022	aTa/aAa	24/25	0.409812305408698	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.409812305408698	3		367	504	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546878	9546878	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031319-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	185	421	1	ENST00000353224.5:c.1144T>A	p.Leu382Met	p.L382M	ENST00000353224	NM_177990.2	382	Ttg/Atg	5/10	0.409812305408698	4	FACETS	0.895	0.835	0.957	0.895	0.835	0.957	CLONAL	3	TRUE	1	0.409812305408698	4		422	474	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730835	40730835	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031319-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	342	694	0	ENST00000373198.4:c.3700G>C	p.Asp1234His	p.D1234H	ENST00000373198	NM_133170.3	1234	Gac/Cac	27/32	NA	2	FACETS	0.883	0.845	0.921			1	INDETERMINATE	3	TRUE	NA	0.409812305408698	2		694	630	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035145	37035145	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs267607707	NA	P-0031319-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	66	347	0	ENST00000231790.2:c.107T>C	p.Ile36Thr	p.I36T	ENST00000231790	NM_000249.3	36	aTt/aCt	1/19	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.409812305408698	2		347	313	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048144	180048144	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031319-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	90	658	0	ENST00000261937.6:c.2129T>G	p.Val710Gly	p.V710G	ENST00000261937	NM_182925.4	710	gTg/gGg	14/30	0.409812305408698	3	FACETS	1	0.932	1	0.532	0.474	0.594	CLONAL	1	TRUE	1	0.409812305408698	3		658	497	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413027	63413027	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031319-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	146	828	0	ENST00000330258.3:c.140C>A	p.Ser47Tyr	p.S47Y	ENST00000330258	NM_152424.3	47	tCc/tAc	2/2	0.127392520843643	4	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.409812305408698	4		828	731	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937137	76937137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031319-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	96	545	0	ENST00000373344.5:c.3611C>T	p.Ser1204Phe	p.S1204F	ENST00000373344	NM_000489.3	1204	tCt/tTt	9/35	0.409812305408698	2	FACETS	0.993	0.889	1	0.496	0.444	0.551	CLONAL	1	TRUE	0	0.409812305408698	2		545	472	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031409-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	341	354	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.640181945197136	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	0	0.68596778812048	3		354	440	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0031409-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	72	289	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.99	0.88	1	0.99	0.88	1	CLONAL	1	TRUE	1	0.68596778812048	2		289	212	SUCCESS
APC	324	MSKCC	GRCh37	5	112174112	112174112	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031409-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	69	330	0	ENST00000257430.4:c.2821G>T	p.Glu941Ter	p.E941*	ENST00000257430	NM_000038.5	941	Gaa/Taa	16/16	1	2	FACETS	0.931	0.824	1	0.931	0.824	1	CLONAL	1	TRUE	1	0.68596778812048	2		330	216	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0031425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	265	391	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.642829249086883	3	FACETS	0.947	0.897	0.998	0.947	0.897	0.998	CLONAL	2	TRUE	1	0.642829249086883	3		391	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0031425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	439	1011	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.642829249086883	2	FACETS	0.998	0.964	1	0.998	0.964	1	CLONAL	2	TRUE	0	0.642829249086883	2		1012	684	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484318	50484318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141728974	NA	P-0031425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	195	716	1	ENST00000394963.4:c.1078C>T	p.Arg360Trp	p.R360W	ENST00000394963	NM_003076.4	360	Cgg/Tgg	9/13	0.528023682849642	3	FACETS	1	0.966	1			1	CLONAL	1	TRUE	NA	0.642829249086883	3		717	751	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658559	3658559	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1849	171	973	0	ENST00000294008.3:c.407C>G	p.Ser136Cys	p.S136C	ENST00000294008	NM_032444.2	136	tCt/tGt	2/15	0.642829249086883	7	FACETS	0.687	0.629	0.748	0.137	0.125	0.15	SUBCLONAL	1	TRUE	2	0.642829249086883	7		973	2020	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879609	37879609	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1483724551	NA	P-0031425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	250	949	0	ENST00000269571.5:c.1984C>G	p.Leu662Val	p.L662V	ENST00000269571		662	Ctg/Gtg	17/27	0.642829249086883	3	FACETS	1	0.967	1	0.525	0.491	0.56	CLONAL	1	TRUE	1	0.642829249086883	3		949	979	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945385	17945385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377654680	NA	P-0031425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	189	787	0	ENST00000458235.1:c.2345C>T	p.Ser782Phe	p.S782F	ENST00000458235	NM_000215.3	782	tCt/tTt	17/24	1	2	FACETS	0.944	0.877	1	0.944	0.877	1	CLONAL	1	TRUE	1	0.642829249086883	2		787	623	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755559	39755559	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	150	571	0	ENST00000288319.7:c.1206C>G	p.His402Gln	p.H402Q	ENST00000288319	NM_182918.3	402	caC/caG	10/10	1	2	FACETS	0.97	0.894	1	0.97	0.894	1	CLONAL	1	TRUE	1	0.642829249086883	2		571	481	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805325	32805325	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	164	645	0	ENST00000374899.4:c.597C>G	p.Phe199Leu	p.F199L	ENST00000374899	NM_018833.2	199	ttC/ttG	3/12	0.642829249086883	3	FACETS	0.977	0.9	1	0.489	0.45	0.529	CLONAL	1	TRUE	1	0.642829249086883	3		645	690	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873671	151873699	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGGCAAACTTGACACATGATTGGATGG	GGAGGCAAACTTGACACATGATTGGATGG	-	novel	NA	P-0031425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	168	753	0	ENST00000262189.6:c.8839_8867del	p.Pro2947PhefsTer11	p.P2947Ffs*11	ENST00000262189	NM_170606.2	2947	CCATCCAATCATGTGTCAAGTTTGCCTCCt/t	38/59	1	2	FACETS	0.923	0.854	0.995	0.923	0.854	0.995	CLONAL	1	TRUE	1	0.642829249086883	2		753	566	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44921952	44921952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	189	745	1	ENST00000377967.4:c.1486G>A	p.Glu496Lys	p.E496K	ENST00000377967	NM_021140.2	496	Gaa/Aaa	15/29	0.339953909595216	6	FACETS	0.761	0.704	0.82	0.507	0.469	0.547	INDETERMINATE	2	TRUE	3	0.642829249086883	6		746	883	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0031512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	451	530	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.770689408389475	2	FACETS	0.959	0.931	0.985	0.959	0.931	0.985	CLONAL	2	TRUE	0	0.780178121928598	2		530	603	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487621	56487621	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs572923795	NA	P-0031512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	182	512	0	ENST00000267101.3:c.1554G>C	p.Leu518Phe	p.L518F	ENST00000267101	NM_001982.3	518	ttG/ttC	13/28	1	2	FACETS	0.712	0.66	0.766	0.712	0.66	0.766	SUBCLONAL	1	TRUE	1	0.780178121928598	2		512	655	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934198	48934198	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0031512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	162	412	0	ENST00000267163.4:c.653T>A	p.Leu218Ter	p.L218*	ENST00000267163	NM_000321.2	218	tTa/tAa	7/27	0.780178121928598	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.780178121928598	1		412	250	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729096	66729096	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	82	551	0	ENST00000307102.5:c.304G>T	p.Glu102Ter	p.E102*	ENST00000307102	NM_002755.3	102	Gag/Tag	3/11	0.571291084333413	1	FACETS	0.25	0.221	0.281	0.25	0.221	0.281	SUBCLONAL	1	TRUE	0	0.780178121928598	1		551	513	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781373	3781384	+	inframe_deletion	In_Frame_Del	DEL	GCGCCCATCCAT	GCGCCCATCCAT	-	novel	NA	P-0031512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	54	715	0	ENST00000262367.5:c.4981_4992del	p.Met1661_Arg1664del	p.M1661_R1664del	ENST00000262367	NM_004380.2	1661	ATGGATGGGCGC/-	30/31	0.481521964135037	1	FACETS	0.146	0.124	0.17	0.146	0.124	0.17	SUBCLONAL	1	TRUE	0	0.780178121928598	1		715	578	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349228	15349228	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	233	490	0	ENST00000263377.2:c.4049A>T	p.Gln1350Leu	p.Q1350L	ENST00000263377	NM_058243.2	1350	cAg/cTg	20/20	1	2	FACETS	0.981	0.921	1	0.981	0.921	1	CLONAL	1	TRUE	1	0.780178121928598	2		490	609	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707900	47707900	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	201	466	0	ENST00000233146.2:c.2524G>T	p.Glu842Ter	p.E842*	ENST00000233146	NM_000251.2	842	Gag/Tag	15/16	1	2	FACETS	0.969	0.905	1	0.969	0.905	1	CLONAL	1	TRUE	1	0.780178121928598	2		466	532	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979269	40979269	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	207	444	0	ENST00000373198.4:c.1864A>T	p.Ser622Cys	p.S622C	ENST00000373198	NM_133170.3	622	Agt/Tgt	11/32	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.780178121928598	2		444	514	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499337	89499337	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	169	342	0	ENST00000336596.2:c.2507C>G	p.Ala836Gly	p.A836G	ENST00000336596	NM_005233.5	836	gCt/gGt	15/17	0.780178121928598	1	FACETS	0.95	0.896	1	0.95	0.896	1	CLONAL	1	TRUE	0	0.780178121928598	1		342	278	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803447	32803447	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	317	717	0	ENST00000374899.4:c.712C>A	p.Leu238Ile	p.L238I	ENST00000374899	NM_018833.2	238	Ctc/Atc	4/12	0.76931961212511	3	FACETS	0.949	0.896	1	0.475	0.448	0.502	CLONAL	1	TRUE	1	0.780178121928598	3		717	1190	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	143	258	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.90037251563258	2		258	291	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691022	NA	P-0031513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	327	527	0	ENST00000269305.4:c.1024del	p.Arg342GlufsTer3	p.R342Efs*3	ENST00000269305	NM_001126112.2	342	Cga/ga	10/11	0.817068113426137	1	FACETS	0.989	0.959	1	0.989	0.959	1	CLONAL	1	TRUE	0	0.90037251563258	1		527	404	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832031	72832031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144091993	NA	P-0031513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	274	497	0	ENST00000268489.5:c.4550C>T	p.Ser1517Leu	p.S1517L	ENST00000268489	NM_006885.3	1517	tCg/tTg	9/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.90037251563258	2		497	568	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717730	89717730	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121909239	NA	P-0031513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	246	367	0	ENST00000371953.3:c.755A>G	p.Asp252Gly	p.D252G	ENST00000371953	NM_000314.4	252	gAt/gGt	7/9	0.884074808624391	1	FACETS	0.954	0.919	0.987	0.954	0.919	0.987	CLONAL	1	TRUE	0	0.90037251563258	1		367	315	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971035	21971035	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	192	350	0	ENST00000304494.5:c.323A>G	p.Asp108Gly	p.D108G	ENST00000304494	NM_000077.4	108	gAt/gGt	2/3	0.90037251563258	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.90037251563258	1		350	232	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114275	73114275	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	16	223	0	ENST00000356692.5:c.911A>G	p.Asp304Gly	p.D304G	ENST00000356692		304	gAt/gGt	8/9	0.10134896628644	3	FACETS	1	0.861	1	0.633	0.471	0.823	INDETERMINATE	1	TRUE	1	0.2	3		223	139	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858207	9858207	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0031543-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	28	635	0	ENST00000330684.3:c.3194C>G	p.Ser1065Ter	p.S1065*	ENST00000330684	NM_001134407.1	1065	tCa/tGa	13/13	1	2	FACETS	0.265	0.211	0.327	0.265	0.211	0.327	SUBCLONAL	1	TRUE	1	0.383595257566208	2		635	550	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	29	354	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.156	0.125	0.191	0.156	0.125	0.191	SUBCLONAL	1	TRUE	1	0.918804665025756	2		354	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579584	7579585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0031595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	29	475	0	ENST00000269305.4:c.102dup	p.Pro36AlafsTer7	p.P36Afs*7	ENST00000269305	NM_001126112.2	34	-/C	4/11	1	2	FACETS	0.121	0.097	0.149	0.121	0.097	0.149	SUBCLONAL	1	TRUE	1	0.918804665025756	2		475	521	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0031595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	79	349	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	0.361	0.318	0.407	0.361	0.318	0.407	SUBCLONAL	1	TRUE	1	0.918804665025756	2		349	476	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880997	37880998	+	protein_altering_variant	In_Frame_Ins	INS	-	-	TCT	rs397516979	NA	P-0031598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	67	483	0	ENST00000269571.5:c.2326_2327insTCT	p.Gly776delinsValCys	p.G776delinsVC	ENST00000269571		776	ggt/gTCTgt	20/27	0.128020669758279	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		483	1019	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0031602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	50	447	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.184840292868766	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.14	1		447	529	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318848	163318848	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	31	479	0	ENST00000271452.3:c.1238A>C	p.Glu413Ala	p.E413A	ENST00000271452	NM_145697.2	413	gAa/gCa	13/14	1	2	FACETS	0.857	0.692	1	0.857	0.692	1	CLONAL	1	TRUE	1	0.14	2		479	517	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95597917	95597917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	37	400	0	ENST00000393063.1:c.367G>A	p.Glu123Lys	p.E123K	ENST00000393063	NM_030621.3	123	Gaa/Aaa	5/28	1	2	FACETS	0.944	0.777	1	0.944	0.777	1	CLONAL	1	TRUE	1	0.14	2		400	560	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293990	1293990	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	57	853	0	ENST00000310581.5:c.1011C>A	p.Asp337Glu	p.D337E	ENST00000310581	NM_198253.2	337	gaC/gaA	2/16	1	2	FACETS	0.917	0.785	1	0.917	0.785	1	CLONAL	1	TRUE	1	0.14	2		853	888	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0031605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	19	314	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.829	1	1	0.829	1	CLONAL	1	TRUE	1	0.08	2		314	423	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0031605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	16	415	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.823	0.606	1	0.823	0.606	1	CLONAL	1	TRUE	1	0.08	2		415	486	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692884	89692884	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	11	304	0	ENST00000371953.3:c.368A>T	p.His123Leu	p.H123L	ENST00000371953	NM_000314.4	123	cAc/cTc	5/9	1	2	FACETS	0.766	0.527	1	0.766	0.527	1	CLONAL	1	TRUE	1	0.08	2		304	359	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115809	8115809	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	213	504	0	ENST00000346208.3:c.1158del	p.Lys387ArgfsTer17	p.K387Rfs*17	ENST00000346208		385	ttC/tt	6/6	1	2	FACETS	0.912	0.852	0.973	0.912	0.852	0.973	CLONAL	1	TRUE	1	0.746448538686171	2		504	626	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158637053	158637053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112489929	NA	P-0031606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	125	508	0	ENST00000263640.3:c.127G>A	p.Gly43Ser	p.G43S	ENST00000263640	NM_001105.4	43	Ggt/Agt	4/11	0.452791413684115	1	FACETS	0.431	0.392	0.471	0.431	0.392	0.471	SUBCLONAL	1	TRUE	0	0.746448538686171	1		508	487	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056334	27056334	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	71	298	0	ENST00000324856.7:c.1331del	p.Gly444AlafsTer175	p.G444Afs*175	ENST00000324856	NM_006015.4	444	Ggc/gc	2/20	0.452791413684115	1	FACETS	0.395	0.347	0.445	0.395	0.347	0.445	SUBCLONAL	1	TRUE	0	0.746448538686171	1		298	302	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106640	27106651	+	inframe_deletion	In_Frame_Del	DEL	TCCTGGACGGAC	TCCTGGACGGAC	-	novel	NA	P-0031606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	207	512	0	ENST00000324856.7:c.6255_6266del	p.Asp2086_Leu2089del	p.D2086_L2089del	ENST00000324856	NM_006015.4	2084	gTCCTGGACGGACtc/gtc	20/20	0.452791413684115	1	FACETS	0.697	0.653	0.741	0.697	0.653	0.741	SUBCLONAL	1	TRUE	0	0.746448538686171	1		512	499	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111517	8111518	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACCCTGTCTGCAATGCCTGTGGGCTCTACTACAAGCTTCACAATGT	novel	NA	P-0031606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	128	475	0	ENST00000346208.3:c.1005_1047+3dup		p.D335fs	ENST00000346208		335	gac/gACCCTGTCTGCAATGCCTGTGGGCTCTACTACAAGCTTCACAATGTac	5/6	1	2	FACETS	0.441	0.4	0.485	0.441	0.4	0.485	SUBCLONAL	1	TRUE	1	0.746448538686171	2		475	777	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020958	26020958	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs746056479	NA	P-0031606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	91	384	0	ENST00000357647.3:c.241A>G	p.Thr81Ala	p.T81A	ENST00000357647	NM_003529.2	81	Aca/Gca	1/1	0.546613788147612	1	FACETS	0.452	0.405	0.501	0.452	0.405	0.501	SUBCLONAL	1	TRUE	0	0.746448538686171	1		384	338	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527288	137527288	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	142	532	0	ENST00000367739.4:c.358G>T	p.Ala120Ser	p.A120S	ENST00000367739	NM_000416.2	120	Gct/Tct	3/7	1	2	FACETS	0.576	0.527	0.628	0.576	0.527	0.628	SUBCLONAL	1	TRUE	1	0.746448538686171	2		532	660	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0031628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	136	391	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.329796446703064	3	FACETS	0.818	0.747	0.893	0.818	0.747	0.893	CLONAL	2	TRUE	1	0.329796446703064	3		391	587	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0031629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	74	162	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.509103621646354	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.509103621646354	1		162	201	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814238	76814238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	19	253	1	ENST00000373344.5:c.6406G>A	p.Asp2136Asn	p.D2136N	ENST00000373344	NM_000489.3	2136	Gac/Aac	29/35	0.509103621646354	3	FACETS	0.246	0.186	0.317	0.123	0.093	0.159	SUBCLONAL	1	TRUE	1	0.509103621646354	3		254	380	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822615	72822615	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754898697	NA	P-0031629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	110	436	0	ENST00000268489.5:c.9560C>T	p.Thr3187Met	p.T3187M	ENST00000268489	NM_006885.3	3187	aCg/aTg	10/10	1	2	FACETS	0.644	0.579	0.712	0.644	0.579	0.712	SUBCLONAL	1	TRUE	1	0.509103621646354	2		436	671	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336289	80336289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257829666	NA	P-0031629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	163	307	1	ENST00000286548.4:c.1030G>A	p.Val344Ile	p.V344I	ENST00000286548	NM_002072.3	344	Gtc/Atc	7/7	0.509103621646354	3	FACETS	1	0.976	1	0.575	0.529	0.623	CLONAL	1	TRUE	1	0.509103621646354	3		308	698	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0031630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	329	447	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.756155942613321	3	FACETS	0.927	0.884	0.969	0.927	0.884	0.969	CLONAL	2	TRUE	1	0.756155942613321	3		447	647	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268766	41268766	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	113	481	0	ENST00000349496.5:c.1004A>T	p.Lys335Ile	p.K335I	ENST00000349496	NM_001904.3	335	aAa/aTa	7/15	1	2	FACETS	0.528	0.477	0.582	0.528	0.477	0.582	SUBCLONAL	1	TRUE	1	0.756155942613321	2		481	566	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038804	47038804	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	32	584	0	ENST00000377604.3:c.811C>G	p.Pro271Ala	p.P271A	ENST00000377604	NM_001204468.1	271	Ccc/Gcc	9/24	1	2	FACETS	0.134	0.108	0.163	0.134	0.108	0.163	SUBCLONAL	1	TRUE	1	0.756155942613321	2		584	633	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0031634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	140	594	0	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	0.243827255337557	2	FACETS	0.937	0.856	1	0.937	0.856	1	CLONAL	2	TRUE	0	0.243827255337557	2		594	613	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524453	44524453	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1354293371	NA	P-0031634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	45	293	0	ENST00000291552.4:c.104G>A	p.Arg35Gln	p.R35Q	ENST00000291552	NM_006758.2	35	cGg/cAg	2/8	1	2	FACETS	0.969	0.816	1	0.969	0.816	1	CLONAL	1	TRUE	1	0.243827255337557	2		293	381	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991574	72991574	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	54	650	0	ENST00000268489.5:c.2471C>A	p.Thr824Asn	p.T824N	ENST00000268489	NM_006885.3	824	aCc/aAc	2/10	1	2	FACETS	0.239	0.203	0.278	0.239	0.203	0.278	SUBCLONAL	1	TRUE	1	0.5	2		650	905	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139552	47139553	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0031636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	172	310	0	ENST00000409792.3:c.5033_5034dup	p.Phe1679ValfsTer27	p.F1679Vfs*27	ENST00000409792	NM_014159.6	1678	-/GT	9/21	1	2	FACETS	0.821	0.764	0.878	1	0.992	1	CLONAL	2	TRUE	1	0.5	2		310	419	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346338	73346338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	37	402	1	ENST00000377767.4:c.1462G>A	p.Asp488Asn	p.D488N	ENST00000377767	NM_014953.3	488	Gat/Aat	10/21	1	2	FACETS	0.679	0.562	0.808	0.679	0.562	0.808	SUBCLONAL	1	TRUE	1	0.372094479438817	2		403	293	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0031638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	187	501	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.778934189480287	3	FACETS	0.944	0.875	1	0.472	0.437	0.508	CLONAL	1	TRUE	1	0.778934189480287	3		501	707	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178449	56178449	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	118	315	0	ENST00000399503.3:c.3422C>T	p.Pro1141Leu	p.P1141L	ENST00000399503	NM_005921.1	1141	cCt/cTt	14/20	1	2	FACETS	0.974	0.892	1	0.974	0.892	1	CLONAL	1	TRUE	1	0.778934189480287	2		315	311	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0031638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	518	455	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	0.778934189480287	5	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	TRUE	2	0.778934189480287	5		455	958	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0031638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	457	555	0	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.778934189480287	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.778934189480287	2		555	571	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227998	36227998	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	254	729	1	ENST00000222270.7:c.7384G>T	p.Ala2462Ser	p.A2462S	ENST00000222270	NM_014727.1	2462	Gcg/Tcg	33/37	0.778934189480287	4	FACETS	0.964	0.901	1	0.321	0.3	0.343	CLONAL	1	TRUE	1	0.778934189480287	4		730	1204	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1555525585	NA	P-0031683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	233	473	0	ENST00000269305.4:c.673-2A>G		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.748350870999276	1	FACETS	0.992	0.942	1	0.992	0.942	1	CLONAL	1	TRUE	0	0.748350870999276	1		473	393	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998784	100998784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	207	590	1	ENST00000325455.5:c.1018G>A	p.Ala340Thr	p.A340T	ENST00000325455	NM_001202474.3	340	Gcc/Acc	1/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.748350870999276	2		591	519	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182041	38182041	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	236	437	0	ENST00000396334.3:c.665G>A	p.Ser222Asn	p.S222N	ENST00000396334	NM_002468.4	222	aGt/aAt	3/5	0.748350870999276	1	FACETS	0.94	0.891	0.988	0.94	0.891	0.988	CLONAL	1	TRUE	0	0.748350870999276	1		437	420	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875090	151875090	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	39	95	0	ENST00000262189.6:c.7448del	p.Gly2483AspfsTer32	p.G2483Dfs*32	ENST00000262189	NM_170606.2	2483	gGa/ga	38/59	1	2	FACETS	0.778	0.658	0.905	0.778	0.658	0.905	CLONAL	1	TRUE	1	0.748350870999276	2		95	134	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	121	354	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		354	699	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0031686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	64	447	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	0.234762292454416	2		447	527	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141499	11141499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	81	546	0	ENST00000358026.2:c.3476G>A	p.Gly1159Glu	p.G1159E	ENST00000358026	NM_001128849.1	1159	gGg/gAg	25/36	0.234762292454416	1	FACETS	0.97	0.855	1	0.97	0.855	1	CLONAL	1	TRUE	0	0.234762292454416	1		546	628	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600480	10600480	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs755536041	NA	P-0031686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	81	600	1	ENST00000171111.5:c.1375C>T	p.Arg459Ter	p.R459*	ENST00000171111	NM_203500.1	459	Cga/Tga	4/6	0.234762292454416	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	0	0.234762292454416	1		601	591	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161298244	161298248	+	missense_variant	Missense_Mutation	ONP	ATAGG	ATAGG	TTAGT	novel	NA	P-0031686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	51	426	1	ENST00000367975.2:c.136_140delinsTTAGT	p.Ile46_Gly47delinsLeuVal	p.I46_G47delinsLV	ENST00000367975	NM_003001.3	46	ATAGGt/TTAGTt	3/6	0.218609450742617	4	FACETS	0.726	0.616	0.848	0.363	0.308	0.424	SUBCLONAL	1	TRUE	2	0.234762292454416	4		427	739	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111965528	111965528	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0031686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	38	264	0	ENST00000375549.3:c.315-1G>T		p.X105_splice	ENST00000375549	NM_003002.3	105			1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.234762292454416	2		264	299	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426716	212426716	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	78	533	0	ENST00000342788.4:c.2399C>A	p.Pro800His	p.P800H	ENST00000342788	NM_005235.2	800	cCc/cAc	20/28	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.234762292454416	2		533	568	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948199	55948199	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	56	462	0	ENST00000263923.4:c.3772A>G	p.Thr1258Ala	p.T1258A	ENST00000263923	NM_002253.2	1258	Acg/Gcg	29/30	1	2	FACETS	0.966	0.828	1	0.966	0.828	1	CLONAL	1	TRUE	1	0.234762292454416	2		462	494	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130152	143130152	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	54	481	0	ENST00000262992.4:c.864G>C	p.Glu288Asp	p.E288D	ENST00000262992	NM_001101669.1	288	gaG/gaC	11/24	1	2	FACETS	0.885	0.756	1	0.885	0.756	1	CLONAL	1	TRUE	1	0.234762292454416	2		481	520	SUCCESS
APC	324	MSKCC	GRCh37	5	112174970	112174972	+	missense_variant	Missense_Mutation	TNP	AGG	AGG	TGT	novel	NA	P-0031686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	48	310	0	ENST00000257430.4:c.3679_3681delinsTGT	p.Arg1227Cys	p.R1227C	ENST00000257430	NM_000038.5	1227	AGG/TGT	16/16	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.234762292454416	2		310	356	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131930679	131930745	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTGAAAGTGATTTAGACAGGCTTAAAGAGGAAATTGAAAAATCATCAAAACAGCGAGGTAAGTTGT	TTTGAAAGTGATTTAGACAGGCTTAAAGAGGAAATTGAAAAATCATCAAAACAGCGAGGTAAGTTGT	GA	novel	NA	P-0031686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	33	507	2	ENST00000265335.6:c.1912_1969+9delinsGA		p.X638_splice	ENST00000265335		638		12/25	1	2	FACETS	0.481	0.391	0.584	0.481	0.391	0.584	SUBCLONAL	1	TRUE	1	0.234762292454416	2		509	584	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30676075	30676075	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	44	453	0	ENST00000376406.3:c.2281G>T	p.Glu761Ter	p.E761*	ENST00000376406	NM_014641.2	761	Gag/Tag	8/15	1	2	FACETS	0.702	0.588	0.828	0.702	0.588	0.828	SUBCLONAL	1	TRUE	1	0.234762292454416	2		453	534	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2966387	2966387	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	117	533	0	ENST00000396946.4:c.1793C>A	p.Ala598Asp	p.A598D	ENST00000396946	NM_032415.4	598	gCc/gAc	14/25	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.234762292454416	2		533	696	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974776	21974794	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCAGCCAGTCAGCCGAA	GGCCAGCCAGTCAGCCGAA	-	novel	NA	P-0031686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	26	177	0	ENST00000304494.5:c.33_51del	p.Ser12ArgfsTer8	p.S12Rfs*8	ENST00000304494	NM_000077.4	11	ccTTCGGCTGACTGGCTGGCC/cc	1/3	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.234762292454416	2		177	201	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570347	87570347	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	71	588	0	ENST00000277120.3:c.2087G>T	p.Arg696Met	p.R696M	ENST00000277120		696	aGg/aTg	17/19	1	2	FACETS	0.947	0.826	1	0.947	0.826	1	CLONAL	1	TRUE	1	0.234762292454416	2		588	639	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131930678	131930742	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTGAAAGTGATTTAGACAGGCTTAAAGAGGAAATTGAAAAATCATCAAAACAGCGAGGTAAGT	TTTTGAAAGTGATTTAGACAGGCTTAAAGAGGAAATTGAAAAATCATCAAAACAGCGAGGTAAGT	-	novel	NA	P-0031686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	32	498	0	ENST00000265335.6:c.1912_1969+7del		p.X638_splice	ENST00000265335		638		12/25	1	2	FACETS	0.468	0.379	0.57	0.468	0.379	0.57	SUBCLONAL	1	TRUE	1	0.234762292454416	2		498	582	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0031687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	333	496	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.658583592501626	2	FACETS	0.875	0.839	0.91	0.875	0.839	0.91	CLONAL	2	TRUE	0	0.698637760061253	2		496	545	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398032	4398032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	158	424	0	ENST00000261254.3:c.596C>T	p.Pro199Leu	p.P199L	ENST00000261254	NM_001759.3	199	cCg/cTg	4/5	0.233438749398891	3	FACETS	1	0.959	1	0.533	0.49	0.576	INDETERMINATE	1	TRUE	1	0.698637760061253	3		424	573	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155146	106155146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	55	369	0	ENST00000380013.4:c.47C>T	p.Pro16Leu	p.P16L	ENST00000380013	NM_001127208.2	16	cCa/cTa	3/11	0.36417709783319	4	FACETS	0.411	0.351	0.477	0.205	0.175	0.239	INDETERMINATE	1	TRUE	2	0.698637760061253	4		369	651	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528033	157528033	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554237641	NA	P-0031687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	692	472	0	ENST00000346085.5:c.5758G>T	p.Glu1920Ter	p.E1920*	ENST00000346085	NM_020732.3	1920	Gag/Tag	20/20	0.698637760061253	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.698637760061253	2		472	871	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0031688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	35	641	4	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	1	2	FACETS	0.166	0.135	0.201	0.166	0.135	0.201	SUBCLONAL	1	TRUE	1	0.621848026903554	2		645	678	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971153	21971154	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0031688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	37	384	1	ENST00000304494.5:c.204_205delinsTT	p.Glu69Ter	p.E69*	ENST00000304494	NM_000077.4	68	gcGGag/gcTTag	2/3	1	2	FACETS	0.243	0.2	0.292	0.243	0.2	0.292	SUBCLONAL	1	TRUE	1	0.621848026903554	2		385	489	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098684	178098808	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTTTCCTTAAACCTGCCATAACTTTCCCAAGAACTGAGTACTCTGTACCTGGGAGTAGTTGGCAGATCCACTGGTTTCTGACTGGATGTGCTGGGCTGGCTGAATTGGGAGAAATTCACCTGTC	TGTTTCCTTAAACCTGCCATAACTTTCCCAAGAACTGAGTACTCTGTACCTGGGAGTAGTTGGCAGATCCACTGGTTTCTGACTGGATGTGCTGGGCTGGCTGAATTGGGAGAAATTCACCTGTC	-	novel	NA	P-0031688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	25	207	0	ENST00000397062.3:c.237_312+49del		p.X79_splice	ENST00000397062	NM_006164.4	79		2/5	1	2	FACETS	0.242	0.191	0.301	0.242	0.191	0.301	SUBCLONAL	1	TRUE	1	0.621848026903554	2		207	332	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578512	7578512	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	962	708	0	ENST00000269305.4:c.418del	p.Thr140ProfsTer30	p.T140Pfs*30	ENST00000269305	NM_001126112.2	140	Acc/cc	5/11	0.668816542423158	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.668816542423158	3		708	1206	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541525	29541525	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	14	413	0	ENST00000356175.3:c.1449C>A	p.Asp483Glu	p.D483E	ENST00000356175	NM_000267.3	483	gaC/gaA	13/57	0.0855806582913114	1	FACETS	0.896	0.647	1	0.896	0.647	1	CLONAL	1	FALSE	0	0.116386250942196	1		413	253	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224610	224610	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1412534704	NA	P-0031690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	31	350	0	ENST00000264932.6:c.286A>G	p.Thr96Ala	p.T96A	ENST00000264932	NM_004168.2	96	Acc/Gcc	3/15	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	FALSE	1	0.116386250942196	2		350	370	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007089	152007090	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0031690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	30	437	0	ENST00000262189.6:c.810dup	p.Val271SerfsTer19	p.V271Sfs*19	ENST00000262189	NM_170606.2	270	-/A	6/59	0.112252681917201	3	FACETS	1	0.918	1	0.645	0.519	0.787	CLONAL	1	FALSE	1	0.116386250942196	3		437	423	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166467	32166467	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	246	762	0	ENST00000375023.3:c.4576G>T	p.Val1526Leu	p.V1526L	ENST00000375023	NM_004557.3	1526	Gtg/Ttg	25/30	1	2	FACETS	0.792	0.742	0.843	0.792	0.742	0.843	SUBCLONAL	1	TRUE	1	0.738236158063234	2		762	842	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0031693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	3089	427	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.533679774400169	24	FACETS	0.998	0.991	1			1	CLONAL	23	TRUE	NA	0.533679774400169	24		427	3464	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0031693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	481	545	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.533679774400169	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.533679774400169	2		545	840	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199963	108199963	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1160508407	NA	P-0031693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	55	232	0	ENST00000278616.4:c.7305C>A	p.Asn2435Lys	p.N2435K	ENST00000278616	NM_000051.3	2435	aaC/aaA	49/63	1	2	FACETS	0.708	0.61	0.814	0.708	0.61	0.814	SUBCLONAL	1	TRUE	1	0.533679774400169	2		232	291	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134883	41134883	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	131	350	0	ENST00000379561.5:c.745T>C	p.Ser249Pro	p.S249P	ENST00000379561	NM_002015.3	249	Tct/Cct	2/3	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.533679774400169	2		350	434	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543659	9543659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755638779	NA	P-0031693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	475	493	0	ENST00000353224.5:c.1495C>T	p.Arg499Trp	p.R499W	ENST00000353224	NM_177990.2	499	Cgg/Tgg	6/10	0.26639318235089	5	FACETS	0.869	0.832	0.907	0.869	0.832	0.907	INDETERMINATE	3	TRUE	2	0.533679774400169	5		493	1229	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0031694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	147	534	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.370450647967309	3	FACETS	1	0.981	1	0.628	0.574	0.684	CLONAL	1	TRUE	1	0.372821072213296	3		534	745	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0031694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	175	700	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	0.372821072213296	1	FACETS	0.972	0.896	1	0.972	0.896	1	CLONAL	1	TRUE	0	0.372821072213296	1		700	786	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406103	70406104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0031694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	134	645	0	ENST00000373644.4:c.3618_3619insGT	p.Pro1207ValfsTer37	p.P1207Vfs*37	ENST00000373644	NM_030625.2	1206	ttt/ttTGt	4/12	0.372821072213296	1	FACETS	0.962	0.877	1	0.962	0.877	1	CLONAL	1	TRUE	0	0.372821072213296	1		645	608	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857260	9857260	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	67	593	0	ENST00000330684.3:c.4141A>G	p.Arg1381Gly	p.R1381G	ENST00000330684	NM_001134407.1	1381	Aga/Gga	13/13	0.251256281011052	4	FACETS	0.509	0.441	0.583	0.17	0.147	0.195	SUBCLONAL	1	TRUE	1	0.372821072213296	4		593	970	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0031695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	221	314	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.809318882055615	2		314	543	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057835	27057835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	64	670	0	ENST00000324856.7:c.1543C>T	p.Gln515Ter	p.Q515*	ENST00000324856	NM_006015.4	515	Cag/Tag	3/20	1	2	FACETS	0.192	0.166	0.221	0.192	0.166	0.221	SUBCLONAL	1	TRUE	1	0.809318882055615	2		670	822	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0031695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	25	409	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	1	2	FACETS	0.115	0.09	0.144	0.115	0.09	0.144	SUBCLONAL	1	TRUE	1	0.809318882055615	2		409	535	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988856	41988856	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	41	559	0	ENST00000219905.7:c.1648C>T	p.Gln550Ter	p.Q550*	ENST00000219905	NM_001164273.1	550	Cag/Tag	3/24	1	2	FACETS	0.134	0.111	0.16	0.134	0.111	0.16	SUBCLONAL	1	TRUE	1	0.809318882055615	2		559	757	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298695	15298695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	366	570	1	ENST00000263388.2:c.1603G>A	p.Glu535Lys	p.E535K	ENST00000263388	NM_000435.2	535	Gag/Aag	10/33	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.809318882055615	2		571	898	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117443	115117443	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	162	367	0	ENST00000257566.3:c.731C>T	p.Ser244Phe	p.S244F	ENST00000257566	NM_016569.3	244	tCc/tTc	4/8	0.303838431610865	3	FACETS	1	0.981	1	0.596	0.551	0.641	INDETERMINATE	1	TRUE	1	0.809318882055615	3		367	472	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107156	27107156	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	245	507	0	ENST00000324856.7:c.6767C>A	p.Ser2256Ter	p.S2256*	ENST00000324856	NM_006015.4	2256	tCa/tAa	20/20	1	2	FACETS	0.981	0.924	1	0.981	0.924	1	CLONAL	1	TRUE	1	0.809318882055615	2		507	617	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112197	115112204	+	frameshift_variant	Frame_Shift_Del	DEL	CGTTGAAG	CGTTGAAG	-	novel	NA	P-0031695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	249	432	0	ENST00000257566.3:c.1536_1543del	p.Phe512LeufsTer177	p.F512Lfs*177	ENST00000257566	NM_016569.3	512	ttCTTCAACGgg/ttgg	7/8	0.303838431610865	3	FACETS	0.808	0.763	0.852	0.808	0.763	0.852	INDETERMINATE	2	TRUE	1	0.809318882055615	3		432	535	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856029	68856030	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACATCATTGATGCAGACCTTCCTCCCAAT	novel	NA	P-0031695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	182	569	0	ENST00000261769.5:c.1843_1871dup	p.Pro625LeufsTer16	p.P625Lfs*16	ENST00000261769	NM_004360.3	613	aac/aACATCATTGATGCAGACCTTCCTCCCAATac	12/16	0.809318882055615	1	FACETS	0.522	0.485	0.559	0.522	0.485	0.559	SUBCLONAL	1	TRUE	0	0.809318882055615	1		569	513	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160300	22160300	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	144	327	0	ENST00000215832.6:c.331G>C	p.Asp111His	p.D111H	ENST00000215832	NM_002745.4	111	Gat/Cat	3/9	1	2	FACETS	0.917	0.846	0.99	0.917	0.846	0.99	CLONAL	1	TRUE	1	0.809318882055615	2		327	388	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973955	55973955	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	37	535	0	ENST00000263923.4:c.1361A>T	p.His454Leu	p.H454L	ENST00000263923	NM_002253.2	454	cAt/cTt	10/30	1	2	FACETS	0.126	0.103	0.152	0.126	0.103	0.152	SUBCLONAL	1	TRUE	1	0.809318882055615	2		535	725	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0031697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	173	508	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.204431912932222	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.204431912932222	2		509	685	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0031699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	49	314	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.782	0.671	0.9	0.782	0.671	0.9	SUBCLONAL	1	TRUE	1	0.636406794732963	2		314	197	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0031699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	163	334	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.389565120702747	4	FACETS	0.854	0.798	0.911	0.641	0.599	0.683	CLONAL	3	TRUE	0	0.636406794732963	4		334	327	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0031699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	43	344	1	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.521270340882018	1	FACETS	0.552	0.469	0.64	0.552	0.469	0.64	SUBCLONAL	1	TRUE	0	0.636406794732963	1		345	167	SUCCESS
APC	324	MSKCC	GRCh37	5	112175573	112175573	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	195	256	0	ENST00000257430.4:c.4283del	p.Gly1428AspfsTer45	p.G1428Dfs*45	ENST00000257430	NM_000038.5	1428	Gga/ga	16/16	0.636406794732963	3	FACETS	0.898	0.852	0.942	0.898	0.852	0.942	CLONAL	3	TRUE	0	0.636406794732963	3		256	300	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912131	114912131	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	31	389	0	ENST00000543371.1:c.1201G>A	p.Glu401Lys	p.E401K	ENST00000543371	NM_001198531.1	401	Gag/Aag	11/14	1	2	FACETS	0.215	0.173	0.262	0.215	0.173	0.262	SUBCLONAL	1	TRUE	1	0.636406794732963	2		389	453	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100496	8100496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	102	504	1	ENST00000346208.3:c.470C>T	p.Pro157Leu	p.P157L	ENST00000346208		157	cCg/cTg	3/6	1	2	FACETS	0.89	0.804	0.98	0.89	0.804	0.98	CLONAL	1	TRUE	1	0.636406794732963	2		505	360	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532438	63532438	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs762872515	NA	P-0031699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	140	461	0	ENST00000307078.5:c.2141G>A	p.Arg714Gln	p.R714Q	ENST00000307078	NM_004655.3	714	cGg/cAg	8/11	1	2	FACETS	0.824	0.754	0.896	0.824	0.754	0.896	CLONAL	1	TRUE	1	0.636406794732963	2		461	534	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337717	73337717	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	117	233	0	ENST00000377767.4:c.1999A>T	p.Met667Leu	p.M667L	ENST00000377767	NM_014953.3	667	Atg/Ttg	16/21	0.59674224548297	1	FACETS	0.962	0.882	1	0.962	0.882	1	CLONAL	1	TRUE	0	0.59674224548297	1		233	286	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453179	140453179	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913340	NA	P-0031704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	176	352	0	ENST00000288602.6:c.1756G>A	p.Glu586Lys	p.E586K	ENST00000288602	NM_004333.4	586	Gaa/Aaa	15/18	1	2	FACETS	0.959	0.888	1	0.959	0.888	1	CLONAL	1	TRUE	1	0.59674224548297	2		352	615	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222425	2222425	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772319590	NA	P-0031704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	248	557	0	ENST00000398665.3:c.3257G>A	p.Arg1086His	p.R1086H	ENST00000398665	NM_032482.2	1086	cGc/cAc	24/28	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.59674224548297	2		557	790	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541528	29541528	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	188	410	0	ENST00000356175.3:c.1453del	p.Glu485ArgfsTer13	p.E485Rfs*13	ENST00000356175	NM_000267.3	484	ctG/ct	13/57	1	2	FACETS	0.874	0.81	0.94	0.874	0.81	0.94	CLONAL	1	TRUE	1	0.59674224548297	2		410	721	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554253	29554253	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1270674587	NA	P-0031704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	181	408	0	ENST00000356175.3:c.2269A>T	p.Lys757Ter	p.K757*	ENST00000356175	NM_000267.3	757	Aaa/Taa	19/57	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.59674224548297	2		408	560	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532843	187532843	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	245	571	0	ENST00000441802.2:c.9550G>C	p.Glu3184Gln	p.E3184Q	ENST00000441802	NM_005245.3	3184	Gaa/Caa	14/27	1	2	FACETS	0.975	0.914	1	0.975	0.914	1	CLONAL	1	TRUE	1	0.59674224548297	2		571	842	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056417	180056417	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	123	446	0	ENST00000261937.6:c.827del	p.Gly276ValfsTer20	p.G276Vfs*20	ENST00000261937	NM_182925.4	276	gGt/gt	7/30	0.59674224548297	1	FACETS	0.649	0.591	0.709	0.649	0.591	0.709	SUBCLONAL	1	TRUE	0	0.59674224548297	1		446	446	SUCCESS
AR	367	MSKCC	GRCh37	X	66765101	66765101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750105188	NA	P-0031704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	251	565	0	ENST00000374690.3:c.113G>A	p.Gly38Asp	p.G38D	ENST00000374690	NM_000044.3	38	gGc/gAc	1/8	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.59674224548297	2		565	815	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717771	89717771	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1554825260	NA	P-0031707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	43	419	0	ENST00000371953.3:c.796A>T	p.Lys266Ter	p.K266*	ENST00000371953	NM_000314.4	266	Aaa/Taa	7/9	0.21514820337153	1	FACETS	0.807	0.676	0.952	0.807	0.676	0.952	CLONAL	1	TRUE	0	0.21514820337153	1		419	442	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154404	2154404	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	48	750	0	ENST00000434045.2:c.524G>T	p.Trp175Leu	p.W175L	ENST00000434045	NM_001127598.1	175	tGg/tTg	5/5	1	2	FACETS	0.813	0.687	0.952	0.813	0.687	0.952	CLONAL	1	TRUE	1	0.21514820337153	2		750	549	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120836	115120837	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0031707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	30	540	0	ENST00000257566.3:c.169_170delinsAT	p.Pro57Met	p.P57M	ENST00000257566	NM_016569.3	57	CCg/ATg	1/8	0.21514820337153	1	FACETS	0.684	0.551	0.834	0.684	0.551	0.834	SUBCLONAL	1	TRUE	0	0.21514820337153	1		540	364	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577508	7577508	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1060501201	NA	P-0031707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	34	645	0	ENST00000269305.4:c.773A>C	p.Glu258Ala	p.E258A	ENST00000269305	NM_001126112.2	258	gAa/gCa	7/11	1	2	FACETS	0.59	0.481	0.712	0.59	0.481	0.712	SUBCLONAL	1	TRUE	1	0.21514820337153	2		645	536	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265328	46265328	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	40	409	0	ENST00000371998.3:c.2198A>T	p.Glu733Val	p.E733V	ENST00000371998		733	gAg/gTg	12/23	1	2	FACETS	0.67	0.556	0.797	0.67	0.556	0.797	SUBCLONAL	1	TRUE	1	0.21514820337153	2		409	555	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940391	49940391	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs767387553	NA	P-0031707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	50	779	0	ENST00000296474.3:c.652A>G	p.Ile218Val	p.I218V	ENST00000296474	NM_002447.2	218	Atc/Gtc	1/20	1	2	FACETS	0.678	0.574	0.792	0.678	0.574	0.792	SUBCLONAL	1	TRUE	1	0.21514820337153	2		779	686	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391052	89391052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	53	651	0	ENST00000336596.2:c.1118G>A	p.Cys373Tyr	p.C373Y	ENST00000336596	NM_005233.5	373	tGt/tAt	5/17	1	2	FACETS	0.652	0.554	0.759	0.652	0.554	0.759	SUBCLONAL	1	TRUE	1	0.21514820337153	2		651	756	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189585692	189585692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908840	NA	P-0031707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	57	546	0	ENST00000264731.3:c.953G>A	p.Arg318His	p.R318H	ENST00000264731	NM_003722.4	318	cGc/cAc	7/14	1	2	FACETS	0.706	0.604	0.817	0.706	0.604	0.817	SUBCLONAL	1	TRUE	1	0.21514820337153	2		546	751	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1952847	1952847	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	58	688	2	ENST00000382891.5:c.1930G>T	p.Ala644Ser	p.A644S	ENST00000382891	NM_133335.3	644	Gca/Tca	10/22	1	2	FACETS	0.732	0.627	0.846	0.732	0.627	0.846	SUBCLONAL	1	TRUE	1	0.21514820337153	2		690	737	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249022	55249022	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	103	607	0	ENST00000275493.2:c.2320G>T	p.Val774Leu	p.V774L	ENST00000275493	NM_005228.3	774	Gtg/Ttg	20/28	1	2	FACETS	0.784	0.703	0.869	1	0.983	1	SUBCLONAL	2	TRUE	1	0.21514820337153	2		607	611	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359042	81359042	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	45	510	0	ENST00000222390.5:c.919C>T	p.Gln307Ter	p.Q307*	ENST00000222390	NM_000601.4	307	Caa/Taa	8/18	1	2	FACETS	0.603	0.505	0.711	0.603	0.505	0.711	SUBCLONAL	1	TRUE	1	0.21514820337153	2		510	694	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339605	116339605	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	36	461	0	ENST00000397752.3:c.467C>G	p.Ser156Trp	p.S156W	ENST00000397752	NM_000245.2	156	tCg/tGg	2/21	1	2	FACETS	0.699	0.574	0.839	0.699	0.574	0.839	SUBCLONAL	1	TRUE	1	0.21514820337153	2		461	479	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345912	152345912	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	49	610	0	ENST00000359321.1:c.658del	p.Asp220ThrfsTer2	p.D220Tfs*2	ENST00000359321	NM_005431.1	220	Gac/ac	3/3	1	2	FACETS	0.656	0.555	0.769	0.656	0.555	0.769	SUBCLONAL	1	TRUE	1	0.21514820337153	2		610	694	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636241	87636241	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	34	593	0	ENST00000277120.3:c.2406G>T	p.Met802Ile	p.M802I	ENST00000277120		802	atG/atT	19/19	0.21514820337153	1	FACETS	0.609	0.497	0.735	0.609	0.497	0.735	SUBCLONAL	1	TRUE	0	0.21514820337153	1		593	463	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348490	70348490	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	30	286	1	ENST00000374080.3:c.3397G>T	p.Ala1133Ser	p.A1133S	ENST00000374080		1133	Gcc/Tcc	24/45	1	1	FACETS	0.876	0.708	1	0.876	0.708	1	CLONAL	1	TRUE	0	0.21514820337153	1		287	284	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	177	584	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.503499908727626	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.516899949716343	1		584	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352697	NA	P-0031708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	10	568	0	ENST00000269305.4:c.587G>A	p.Arg196Gln	p.R196Q	ENST00000269305	NM_001126112.2	196	cGa/cAa	6/11	0.503499908727626	1	FACETS	0.067	0.045	0.095	0.067	0.045	0.095	SUBCLONAL	1	TRUE	0	0.516899949716343	1		568	427	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111511	8111512	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0031708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	204	499	0	ENST00000346208.3:c.997_998insC	p.Asn333ThrfsTer19	p.N333Tfs*19	ENST00000346208		333	aat/aCat	5/6	1	2	FACETS	0.99	0.921	1	0.99	0.921	1	CLONAL	1	TRUE	1	0.516899949716343	2		499	797	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0031710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	93	574	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.563949859413498	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.568584750195137	1		574	220	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059246	27059246	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs927444249	NA	P-0031710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	86	576	0	ENST00000324856.7:c.1883T>C	p.Met628Thr	p.M628T	ENST00000324856	NM_006015.4	628	aTg/aCg	4/20	0.421375964833128	2	FACETS	1	0.968	1	0.6	0.539	0.664	CLONAL	1	TRUE	0	0.568584750195137	2		576	252	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059259	27059265	+	frameshift_variant	Frame_Shift_Del	DEL	TCAGTCA	TCAGTCA	-	novel	NA	P-0031710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	74	553	0	ENST00000324856.7:c.1896_1902del	p.Gln633AspfsTer12	p.Q633Dfs*12	ENST00000324856	NM_006015.4	632	ctTCAGTCA/ct	4/20	0.421375964833128	2	FACETS	1	0.917	1	0.521	0.462	0.582	CLONAL	1	TRUE	0	0.568584750195137	2		553	250	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259204	89259204	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	17	502	0	ENST00000336596.2:c.348C>A	p.Cys116Ter	p.C116*	ENST00000336596	NM_005233.5	116	tgC/tgA	3/17	1	2	FACETS	0.316	0.237	0.41	0.316	0.237	0.41	SUBCLONAL	1	TRUE	1	0.568584750195137	2		502	189	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624268	89624268	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	160	370	0	ENST00000371953.3:c.42G>C	p.Arg14Ser	p.R14S	ENST00000371953	NM_000314.4	14	agG/agC	1/9	NA	2	FACETS	0.933	0.865	1			1	INDETERMINATE	1	TRUE	NA	0.799103672062023	2		370	429	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279895	18279895	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0031712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	243	507	0	ENST00000222254.8:c.1980-2A>G		p.X660_splice	ENST00000222254	NM_005027.3	660			1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.799103672062023	2		507	585	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442618	52442618	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs772586945	NA	P-0031712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	138	365	0	ENST00000460680.1:c.127G>C	p.Val43Leu	p.V43L	ENST00000460680	NM_004656.3	43	Gta/Cta	4/17	0.799103672062023	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.799103672062023	1		365	193	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339267	70339267	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	309	339	1	ENST00000374080.3:c.144G>T	p.Gln48His	p.Q48H	ENST00000374080		48	caG/caT	2/45	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.799103672062023	1		340	369	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	40	354	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.160227573705009	3	FACETS	0.835	0.692	0.994	0.417	0.346	0.497	CLONAL	1	TRUE	1	0.160227573705009	3		354	646	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0031713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	49	363	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.160227573705009	2	FACETS	1	0.96	1	0.721	0.612	0.841	CLONAL	1	TRUE	0	0.160227573705009	2		363	424	SUCCESS
APC	324	MSKCC	GRCh37	5	112176863	112176863	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1270783041	NA	P-0031713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	71	451	0	ENST00000257430.4:c.5572C>T	p.Arg1858Ter	p.R1858*	ENST00000257430	NM_000038.5	1858	Cga/Tga	16/16	0.160227573705009	2	FACETS	0.897	0.785	1	0.897	0.785	1	CLONAL	2	TRUE	0	0.160227573705009	2		451	494	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414225	32414225	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs772822466	NA	P-0031713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	27	451	0	ENST00000332351.3:c.1326A>C	p.Gln442His	p.Q442H	ENST00000332351	NM_024426.4	442	caA/caC	8/10	0.160227573705009	2	FACETS	0.656	0.521	0.811	0.328	0.26	0.406	SUBCLONAL	1	TRUE	0	0.160227573705009	2		451	514	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898779	134898779	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	66	470	0	ENST00000398015.3:c.1837G>C	p.Glu613Gln	p.E613Q	ENST00000398015	NM_004441.4	613	Gag/Cag	10/16	0.160227573705009	3	FACETS	0.805	0.699	0.919	0.805	0.699	0.919	CLONAL	2	TRUE	1	0.160227573705009	3		470	553	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5534956	5534956	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	54	548	0	ENST00000397747.3:c.267A>G	p.Ile89Met	p.I89M	ENST00000397747	NM_025239.3	89	atA/atG	3/7	0.160227573705009	3	FACETS	1	0.923	1	0.565	0.482	0.656	CLONAL	1	TRUE	1	0.160227573705009	3		548	644	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715802	18715804	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0031713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	34	425	0	ENST00000266497.5:c.3633_3635del	p.Gly1212del	p.G1212del	ENST00000266497		1211	ttAGGg/ttg	25/31	0.160227573705009	3	FACETS	0.988	0.807	1	0.494	0.403	0.596	CLONAL	1	TRUE	1	0.160227573705009	3		425	464	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0031714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	270	573	0	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.375376720656523	2	FACETS	0.965	0.91	1	0.965	0.91	1	CLONAL	2	TRUE	0	0.375376720656523	2		573	745	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201368	133201368	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	268	592	0	ENST00000320574.5:c.6776G>C	p.Arg2259Pro	p.R2259P	ENST00000320574	NM_006231.2	2259	cGg/cCg	49/49	0.375376720656523	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.375376720656523	2		592	662	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751709	57751878	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGAACTCAAGATTATTTTCCAATTCCTGTAATCTTACTACTTCTATGTTAAATTAAGCTACAAAGTAAATTGACTTAAATTATTATGTATTTAGCACTGGCATTTCGAGTTTCATTATTTAAAATACGATTGACAACCACTTACATTCACTGCTGCTGCTACAGCTGCCA	AGAACTCAAGATTATTTTCCAATTCCTGTAATCTTACTACTTCTATGTTAAATTAAGCTACAAAGTAAATTGACTTAAATTATTATGTATTTAGCACTGGCATTTCGAGTTTCATTATTTAAAATACGATTGACAACCACTTACATTCACTGCTGCTGCTACAGCTGCCA	-	novel	NA	P-0031714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	68	140	0	ENST00000274289.3:c.1359_1385-103del		p.X453_splice	ENST00000274289	NM_006622.3	453		10/14	0.375376720656523	2	FACETS	0.871	0.771	0.975	0.871	0.771	0.975	CLONAL	2	TRUE	0	0.375376720656523	2		140	208	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157488183	157488183	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	99	517	0	ENST00000346085.5:c.2889T>G	p.Ser963Arg	p.S963R	ENST00000346085	NM_020732.3	963	agT/agG	10/20	0.300631847316338	5	FACETS	0.897	0.8	1	0.299	0.266	0.334	CLONAL	1	TRUE	2	0.375376720656523	5		517	919	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332108	70332108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140156594	NA	P-0031716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	19	265	0	ENST00000373644.4:c.13C>T	p.Arg5Cys	p.R5C	ENST00000373644	NM_030625.2	5	Cgc/Tgc	2/12	1	2	FACETS	0.722	0.548	0.926	0.722	0.548	0.926	CLONAL	1	TRUE	1	0.190084620488571	2		265	277	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94163112	94163112	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	40	503	0	ENST00000323929.3:c.2035C>G	p.Gln679Glu	p.Q679E	ENST00000323929	NM_005591.3	679	Caa/Gaa	19/20	0.190084620488571	2	FACETS	0.576	0.477	0.686	0.288	0.238	0.343	SUBCLONAL	1	TRUE	0	0.190084620488571	2		503	731	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443475	49443475	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1266718915	NA	P-0031716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	71	486	0	ENST00000301067.7:c.3896G>A	p.Arg1299His	p.R1299H	ENST00000301067	NM_003482.3	1299	cGc/cAc	11/54	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.190084620488571	2		486	547	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100590	67100590	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0031716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	30	439	0	ENST00000412916.2:c.288T>A	p.Tyr96Ter	p.Y96*	ENST00000412916		96	taT/taA	4/6	1	2	FACETS	0.537	0.431	0.657	0.537	0.431	0.657	SUBCLONAL	1	TRUE	1	0.190084620488571	2		439	588	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796856	42796856	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	43	693	1	ENST00000575354.2:c.3314C>A	p.Ser1105Ter	p.S1105*	ENST00000575354	NM_015125.3	1105	tCa/tAa	14/20	1	2	FACETS	0.569	0.475	0.674	0.569	0.475	0.674	SUBCLONAL	1	TRUE	1	0.190084620488571	2		694	795	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969391	44969391	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	113	334	0	ENST00000377967.4:c.4073G>C	p.Cys1358Ser	p.C1358S	ENST00000377967	NM_021140.2	1358	tGc/tCc	28/29	0.163331089129	2	FACETS	1	0.975	1			1	CLONAL	2	TRUE	NA	0.190084620488571	2		334	483	SUCCESS
AR	367	MSKCC	GRCh37	X	66863243	66863243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1034866440	NA	P-0031716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	30	261	0	ENST00000374690.3:c.1762G>A	p.Ala588Thr	p.A588T	ENST00000374690	NM_000044.3	588	Gct/Act	2/8	0.163331089129	2	FACETS	0.855	0.69	1			1	CLONAL	1	TRUE	NA	0.190084620488571	2		261	369	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176917	56176918	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0031718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	82	196	0	ENST00000399503.3:c.2189dup	p.Ile731TyrfsTer5	p.I731Yfs*5	ENST00000399503	NM_005921.1	729	-/G	13/20	1	2	FACETS	0.766	0.675	0.862	0.766	0.675	0.862	SUBCLONAL	1	TRUE	1	0.336310989033228	2		196	637	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928060	178928086	+	inframe_deletion	In_Frame_Del	DEL	GCCAGTACCTCATGGATTAGAAGATTT	GCCAGTACCTCATGGATTAGAAGATTT	-	novel	NA	P-0031718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	74	351	0	ENST00000263967.3:c.1340_1366del	p.Pro447_Leu455del	p.P447_L455del	ENST00000263967	NM_006218.2	446	tgGCCAGTACCTCATGGATTAGAAGATTTg/tgg	8/21	1	2	FACETS	0.443	0.387	0.504	0.443	0.387	0.504	SUBCLONAL	1	TRUE	1	0.336310989033228	2		351	993	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177727	56177739	+	frameshift_variant	Frame_Shift_Del	DEL	TTCCCCTGAGTGC	TTCCCCTGAGTGC	-	novel	NA	P-0031718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	107	486	0	ENST00000399503.3:c.2700_2712del	p.Ser900ArgfsTer5	p.S900Rfs*5	ENST00000399503	NM_005921.1	900	agTTCCCCTGAGTGC/ag	14/20	1	2	FACETS	0.91	0.817	1	0.91	0.817	1	CLONAL	1	TRUE	1	0.336310989033228	2		486	699	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574030	7574030	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	41	625	1	ENST00000269305.4:c.997del	p.Arg333ValfsTer12	p.R333Vfs*12	ENST00000269305	NM_001126112.2	333	Cgt/gt	10/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		626	748	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0031720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	90	660	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.332896314755273	2		660	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578318	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGGATAAGATGCTGAGGAGGGGCCAGACCTAAGAGCAATCAGTGAGGAATCAGAGGC	CGGATAAGATGCTGAGGAGGGGCCAGACCTAAGAGCAATCAGTGAGGAATCAGAGGC	-	novel	NA	P-0031720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	140	854	0	ENST00000269305.4:c.560-29_587del		p.X187_splice	ENST00000269305	NM_001126112.2	187		6/11	0.327164655262097	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.332896314755273	1		854	657	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441430	52441430	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	202	729	0	ENST00000460680.1:c.422A>C	p.His141Pro	p.H141P	ENST00000460680	NM_004656.3	141	cAt/cCt	6/17	0.293150472754197	2	FACETS	0.914	0.851	0.978	0.914	0.851	0.978	CLONAL	2	TRUE	0	0.332896314755273	2		729	664	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281475	142281476	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0031720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	93	903	0	ENST00000350721.4:c.768dup	p.Gln257SerfsTer11	p.Q257Sfs*11	ENST00000350721	NM_001184.3	256	-/T	4/47	0.307694328829675	4	FACETS	0.827	0.734	0.926	0.413	0.367	0.463	CLONAL	1	TRUE	2	0.332896314755273	4		903	901	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0031721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	89	747	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	1	2	FACETS	0.539	0.477	0.605	0.539	0.477	0.605	SUBCLONAL	1	TRUE	1	0.38498811323167	2		747	858	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0031721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	90	636	0	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	1	2	FACETS	0.542	0.48	0.608	0.542	0.48	0.608	SUBCLONAL	1	TRUE	1	0.38498811323167	2		636	863	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102199	27102199	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0031721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	102	369	0	ENST00000324856.7:c.5124+1G>C		p.X1708_splice	ENST00000324856	NM_006015.4	1708			0.192000573571959	2	FACETS	1	0.975	1	0.637	0.573	0.703	INDETERMINATE	1	TRUE	0	0.38498811323167	2		369	416	SUCCESS
AR	367	MSKCC	GRCh37	X	66943642	66943642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	136	310	0	ENST00000374690.3:c.2722C>T	p.Leu908Phe	p.L908F	ENST00000374690	NM_000044.3	908	Ctt/Ttt	8/8	0.147625761029389	2	FACETS	0.82	0.752	0.89			1	INDETERMINATE	2	TRUE	NA	0.38498811323167	2		310	431	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953258	81953258	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	77	318	0	ENST00000359376.3:c.2224C>A	p.Arg742Ser	p.R742S	ENST00000359376	NM_002661.3	742	Cgc/Agc	20/33	1	2	FACETS	0.891	0.785	1	0.891	0.785	1	CLONAL	1	TRUE	1	0.38498811323167	2		318	449	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710984	117710984	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	37	249	0	ENST00000368508.3:c.1288G>T	p.Gly430Cys	p.G430C	ENST00000368508	NM_002944.2	430	Ggc/Tgc	12/43	0.384783687746215	1	FACETS	0.732	0.609	0.867	0.732	0.609	0.867	SUBCLONAL	1	TRUE	0	0.38498811323167	1		249	212	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	154	364	0	ENST00000304494.5:c.341C>G	p.Pro114Arg	p.P114R	ENST00000304494	NM_000077.4	114	cCc/cGc	2/3	0.276661177162695	2	FACETS	1	0.986	1	0.687	0.632	0.745	CLONAL	1	TRUE	0	0.38498811323167	2		364	582	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100495	8100495	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	195	760	1	ENST00000346208.3:c.469C>A	p.Pro157Thr	p.P157T	ENST00000346208		157	Ccg/Acg	3/6	1	2	FACETS	0.939	0.868	1	0.939	0.868	1	CLONAL	1	TRUE	1	0.38498811323167	2		761	1079	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633488	69633488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1419524448	NA	P-0031721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	57	236	0	ENST00000334134.2:c.214G>A	p.Ala72Thr	p.A72T	ENST00000334134	NM_005247.2	72	Gcc/Acc	1/3	1	2	FACETS	0.792	0.682	0.91	0.792	0.682	0.91	CLONAL	1	TRUE	1	0.38498811323167	2		236	374	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205253	46205253	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	74	484	0	ENST00000334344.6:c.337G>T	p.Val113Leu	p.V113L	ENST00000334344	NM_152641.2	113	Gta/Tta	4/21	1	2	FACETS	0.721	0.632	0.817	0.721	0.632	0.817	SUBCLONAL	1	TRUE	1	0.38498811323167	2		484	533	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292847	91292847	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	88	546	0	ENST00000355112.3:c.349G>T	p.Glu117Ter	p.E117*	ENST00000355112	NM_000057.2	117	Gaa/Taa	3/22	1	2	FACETS	0.776	0.689	0.869	0.776	0.689	0.869	SUBCLONAL	1	TRUE	1	0.38498811323167	2		546	589	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992205	72992205	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	177	830	0	ENST00000268489.5:c.1840G>T	p.Gly614Trp	p.G614W	ENST00000268489	NM_006885.3	614	Ggg/Tgg	2/10	1	2	FACETS	0.797	0.733	0.864	0.797	0.733	0.864	SUBCLONAL	1	TRUE	1	0.38498811323167	2		830	1154	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357162	89357162	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0031721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	193	820	3	ENST00000301030.4:c.472A>T	p.Lys158Ter	p.K158*	ENST00000301030	NM_001256183.1	158	Aaa/Taa	6/13	1	2	FACETS	0.901	0.832	0.972	0.901	0.832	0.972	CLONAL	1	TRUE	1	0.38498811323167	2		823	1113	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995262	15995263	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0031721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	74	603	2	ENST00000268712.3:c.2930_2931delinsTT	p.Arg977Leu	p.R977L	ENST00000268712	NM_006311.3	977	cGG/cTT	22/46	1	2	FACETS	0.599	0.524	0.679	0.599	0.524	0.679	SUBCLONAL	1	TRUE	1	0.38498811323167	2		605	642	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554251	29554251	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	106	403	0	ENST00000356175.3:c.2267A>C	p.Gln756Pro	p.Q756P	ENST00000356175	NM_000267.3	756	cAg/cCg	19/57	1	2	FACETS	0.963	0.866	1	0.963	0.866	1	CLONAL	1	TRUE	1	0.38498811323167	2		403	572	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296394	15296394	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	211	1009	0	ENST00000263388.2:c.2048G>T	p.Cys683Phe	p.C683F	ENST00000263388	NM_000435.2	683	tGc/tTc	13/33	1	2	FACETS	0.797	0.738	0.858	0.797	0.738	0.858	SUBCLONAL	1	TRUE	1	0.38498811323167	2		1009	1375	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657020	215657020	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0031721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	51	394	0	ENST00000260947.4:c.364+1G>A		p.X122_splice	ENST00000260947	NM_000465.2	122			0.259770221156753	1	FACETS	0.711	0.608	0.822	0.711	0.608	0.822	SUBCLONAL	1	TRUE	0	0.38498811323167	1		394	301	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944485	40944485	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	164	607	0	ENST00000373198.4:c.2017C>A	p.Leu673Met	p.L673M	ENST00000373198	NM_133170.3	673	Ctg/Atg	12/32	1	2	FACETS	0.982	0.902	1	0.982	0.902	1	CLONAL	1	TRUE	1	0.38498811323167	2		607	868	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71064723	71064723	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	75	452	0	ENST00000318789.4:c.951C>G	p.Cys317Trp	p.C317W	ENST00000318789	NM_032682.5	317	tgC/tgG	12/21	0.384783687746215	1	FACETS	0.701	0.616	0.791	0.701	0.616	0.791	SUBCLONAL	1	TRUE	0	0.38498811323167	1		452	449	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138407760	138407760	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	110	448	0	ENST00000289153.2:c.2093A>T	p.Tyr698Phe	p.Y698F	ENST00000289153	NM_006219.2	698	tAc/tTc	14/22	0.363702915139326	3	FACETS	1	0.973	1	0.615	0.554	0.679	CLONAL	1	TRUE	1	0.38498811323167	3		448	554	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665334	176665334	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	95	359	0	ENST00000439151.2:c.4018G>T	p.Glu1340Ter	p.E1340*	ENST00000439151	NM_022455.4	1340	Gaa/Taa	7/23	0.332440343423953	1	FACETS	0.863	0.772	0.958	0.863	0.772	0.958	CLONAL	1	TRUE	0	0.38498811323167	1		359	462	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028025	69028025	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs200550325	NA	P-0031721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	30	423	0	ENST00000288368.4:c.3184C>G	p.Arg1062Gly	p.R1062G	ENST00000288368	NM_024870.2	1062	Cgt/Ggt	26/40	0.259770221156753	1	FACETS	0.427	0.344	0.519	0.427	0.344	0.519	SUBCLONAL	1	TRUE	0	0.38498811323167	1		423	295	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518418	8518418	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	66	246	0	ENST00000356435.5:c.973C>A	p.Pro325Thr	p.P325T	ENST00000356435		325	Cct/Act	10/35	0.276661177162695	2	FACETS	1	0.937	1	0.558	0.488	0.633	CLONAL	1	TRUE	0	0.38498811323167	2		246	307	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409880	63409880	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	96	204	0	ENST00000330258.3:c.3287A>T	p.Gln1096Leu	p.Q1096L	ENST00000330258	NM_152424.3	1096	cAg/cTg	2/2	0.147625761029389	2	FACETS	0.763	0.687	0.842			1	INDETERMINATE	2	TRUE	NA	0.38498811323167	2		204	327	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326729	62326729	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1216	151	969	1	ENST00000360203.5:c.3548C>G	p.Ser1183Cys	p.S1183C	ENST00000360203	NM_001283009.1	1183	tCc/tGc	34/35	1	2	FACETS	0.574	0.523	0.628	0.574	0.523	0.628	SUBCLONAL	1	TRUE	1	0.38498811323167	2		970	1367	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719930	18719930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	192	655	0	ENST00000266497.5:c.3827G>A	p.Arg1276Lys	p.R1276K	ENST00000266497		1276	aGa/aAa	27/31	0.258462140453481	2	FACETS	0.858	0.795	0.924	0.429	0.397	0.462	INDETERMINATE	1	TRUE	0	0.561963305370871	2		655	796	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219447	5219447	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	84	734	0	ENST00000357368.4:c.3797T>G	p.Phe1266Cys	p.F1266C	ENST00000357368	NM_002850.3	1266	tTc/tGc	23/38	0.204472434064122	1	FACETS	0.456	0.404	0.512	0.456	0.404	0.512	INDETERMINATE	1	TRUE	0	0.561963305370871	1		734	471	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0031724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	388	789	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	0.514919250443061	4	FACETS	0.933	0.887	0.979	0.933	0.887	0.979	CLONAL	2	TRUE	2	0.564606373271905	4		789	1153	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279390	38279390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs981703846	NA	P-0031724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	223	837	2	ENST00000425967.3:c.1099G>A	p.Ala367Thr	p.A367T	ENST00000425967	NM_001174067.1	367	Gca/Aca	9/19	0.564606373271905	2	FACETS	0.932	0.869	0.996	0.466	0.434	0.498	CLONAL	1	TRUE	0	0.564606373271905	2		839	848	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099982	157099993	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGCGGC	GGCGGCGGCGGC	-	rs587779747	NA	P-0031724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	66	100	0	ENST00000346085.5:c.933_944del	p.Gly316_Gly319del	p.G316_G319del	ENST00000346085	NM_020732.3	307	GGCGGCGGCGGC/-	1/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.564606373271905	2		100	168	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0031725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	29	447	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.218774666133134	2	FACETS	1	0.936	1	0.648	0.541	0.759	INDETERMINATE	1	TRUE	0	0.630159572543488	2		447	71	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106078	27106078	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	144	548	0	ENST00000324856.7:c.5693del	p.Pro1898HisfsTer25	p.P1898Hfs*25	ENST00000324856	NM_006015.4	1897	Ccc/cc	20/20	0.630159572543488	3	FACETS	0.966	0.897	1	0.966	0.897	1	CLONAL	2	TRUE	1	0.630159572543488	3		548	311	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222006	1222006	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0031725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	202	444	0	ENST00000326873.7:c.920+1G>T		p.X307_splice	ENST00000326873	NM_000455.4	307			0.626302095968507	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.630159572543488	2		444	282	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186589	108186589	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	21	363	1	ENST00000278616.4:c.6046G>T	p.Asp2016Tyr	p.D2016Y	ENST00000278616	NM_000051.3	2016	Gat/Tat	41/63	0.50077412019423	4	FACETS	1	0.824	1	1	0.824	1	CLONAL	2	TRUE	2	0.630159572543488	4		364	53	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206659	108206659	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0031725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	35	437	1	ENST00000278616.4:c.8239A>T	p.Lys2747Ter	p.K2747*	ENST00000278616	NM_000051.3	2747	Aag/Tag	56/63	0.50077412019423	4	FACETS	0.755	0.632	0.885	0.755	0.632	0.885	SUBCLONAL	2	TRUE	2	0.630159572543488	4		438	120	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730919	40730919	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	67	512	0	ENST00000373198.4:c.3616C>T	p.Pro1206Ser	p.P1206S	ENST00000373198	NM_133170.3	1206	Ccc/Tcc	27/32	0.50077412019423	4	FACETS	0.777	0.677	0.884	0.389	0.338	0.442	SUBCLONAL	1	TRUE	2	0.630159572543488	4		512	446	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156516	55156516	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	81	549	0	ENST00000257290.5:c.2917G>T	p.Asp973Tyr	p.D973Y	ENST00000257290	NM_006206.4	973	Gac/Tac	22/23	0.626302095968507	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	0	0.630159572543488	2		549	126	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0031726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	213	814	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.358274091436067	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.2	3		814	961	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882019	NA	P-0031726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	62	982	0	ENST00000269305.4:c.455dup	p.Pro153AlafsTer28	p.P153Afs*28	ENST00000269305	NM_001126112.2	152	ccg/ccCg	5/11	0.0828240021441206	0	FACETS	0.641	0.552	0.737			1	INDETERMINATE	1	TRUE	0	0.2	0		982	774	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466950	18466950	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	32	468	0	ENST00000266497.5:c.1089G>C	p.Gln363His	p.Q363H	ENST00000266497		363	caG/caC	5/31	1	2	FACETS	0.501	0.405	0.609	0.501	0.405	0.609	SUBCLONAL	1	TRUE	1	0.2	2		468	639	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792835	33792835	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	13	226	0	ENST00000498907.2:c.486G>T	p.Gln162His	p.Q162H	ENST00000498907	NM_004364.3	162	caG/caT	1/1	1	2	FACETS	0.699	0.5	0.941	0.699	0.5	0.941	SUBCLONAL	1	TRUE	1	0.2	2		226	186	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855583	45855583	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0031726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	55	797	0	ENST00000391945.4:c.2074A>T	p.Lys692Ter	p.K692*	ENST00000391945	NM_000400.3	692	Aag/Tag	22/23	1	2	FACETS	0.761	0.65	0.883	0.761	0.65	0.883	SUBCLONAL	1	TRUE	1	0.2	2		797	723	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55524225	55524225	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	70	659	0	ENST00000288135.5:c.44T>A	p.Leu15His	p.L15H	ENST00000288135	NM_000222.2	15	cTc/cAc	1/21	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.2	2		659	634	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55225394	55225394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	217	707	0	ENST00000275493.2:c.1246G>A	p.Asp416Asn	p.D416N	ENST00000275493	NM_005228.3	416	Gac/Aac	11/28	0.358274091436067	3	FACETS	0.963	0.898	1	1	0.991	1	CLONAL	3	TRUE	1	0.2	3		707	826	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0031727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	57	596	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.25	2		596	448	SUCCESS
MET	4233	MSKCC	GRCh37	7	116417463	116417463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913244	NA	P-0031727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	11	494	0	ENST00000397752.3:c.3280C>T	p.His1094Tyr	p.H1094Y	ENST00000397752	NM_000245.2	1094	Cat/Tat	16/21	1	2	FACETS	0.547	0.378	0.754	0.547	0.378	0.754	SUBCLONAL	1	TRUE	1	0.25	2		494	161	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4388020	4388020	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	89	567	0	ENST00000261254.3:c.506A>T	p.Gln169Leu	p.Q169L	ENST00000261254	NM_001759.3	169	cAg/cTg	3/5	0.3	3	FACETS	1	0.934	1			1	CLONAL	1	TRUE	NA	0.25	3		567	744	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897399	78897399	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	85	733	1	ENST00000306801.3:c.2734G>T	p.Ala912Ser	p.A912S	ENST00000306801	NM_020761.2	912	Gct/Tct	23/34	1	2	FACETS	0.704	0.621	0.793	0.704	0.621	0.793	SUBCLONAL	1	TRUE	1	0.25	2		734	966	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0031735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	107	460	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.844	0.76	0.933	0.844	0.76	0.933	CLONAL	1	TRUE	1	0.476533091961925	2		460	532	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221227	1221227	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131690948	NA	P-0031735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	364	855	0	ENST00000326873.7:c.752del	p.Gly251ValfsTer36	p.G251Vfs*36	ENST00000326873	NM_000455.4	250	acG/ac	6/10	0.476533091961925	2	FACETS	0.992	0.947	1	0.992	0.947	1	CLONAL	2	TRUE	0	0.476533091961925	2		855	770	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336123	73336125	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	novel	NA	P-0031735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	25	386	0	ENST00000377767.4:c.2278_2280del	p.Asn760del	p.N760del	ENST00000377767	NM_014953.3	760	AAT/-	17/21	1	2	FACETS	0.25	0.197	0.312	0.25	0.197	0.312	SUBCLONAL	1	TRUE	1	0.476533091961925	2		386	419	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163638	32163638	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	75	511	0	ENST00000375023.3:c.5588C>A	p.Thr1863Lys	p.T1863K	ENST00000375023	NM_004557.3	1863	aCg/aAg	30/30	1	2	FACETS	0.91	0.803	1	0.91	0.803	1	CLONAL	1	TRUE	1	0.476533091961925	2		511	346	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53244006	53244006	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	152	384	0	ENST00000375401.3:c.987del	p.Met329IlefsTer101	p.M329Ifs*101	ENST00000375401	NM_004187.3	329	atG/at	8/26	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.476533091961925	1		384	343	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	83	258	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.851	0.756	0.951	0.851	0.756	0.951	CLONAL	1	TRUE	1	0.514960791913151	2		258	379	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0031736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	79	363	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.707	0.624	0.795	0.707	0.624	0.795	SUBCLONAL	1	TRUE	1	0.514960791913151	2		363	434	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791735	42791735	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	141	622	0	ENST00000575354.2:c.621C>A	p.Phe207Leu	p.F207L	ENST00000575354	NM_015125.3	207	ttC/ttA	5/20	0.503824825955296	1	FACETS	0.746	0.683	0.811	0.746	0.683	0.811	SUBCLONAL	1	TRUE	0	0.514960791913151	1		622	545	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544682	65544682	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	147	816	0	ENST00000358664.4:c.244C>T	p.Gln82Ter	p.Q82*	ENST00000358664	NM_002382.4	82	Cag/Tag	4/5	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.3	2		816	844	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412046	116412046	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	T	novel	NA	P-0031737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	122	693	0	ENST00000397752.3:c.3028+3A>T		p.X1010_splice	ENST00000397752	NM_000245.2	1010			1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.3	2		693	756	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30069007	30069007	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	105	583	0	ENST00000331968.5:c.1922G>C	p.Gly641Ala	p.G641A	ENST00000331968	NM_002742.2	641	gGt/gCt	14/18	NA	2	FACETS	1	0.912	1			1	INDETERMINATE	1	TRUE	NA	0.3	2		583	687	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184662	185184670	+	inframe_deletion	In_Frame_Del	DEL	CCCTGTTCG	CCCTGTTCG	-	novel	NA	P-0031737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	96	615	0	ENST00000265026.3:c.1554_1562del	p.Val520_Pro522del	p.V520_P522del	ENST00000265026	NM_004721.4	518	caCCCTGTTCGt/cat	10/14	1	2	FACETS	0.804	0.716	0.898	0.804	0.716	0.898	CLONAL	1	TRUE	1	0.3	2		615	796	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64288362	64288363	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0031737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	64	321	0	ENST00000370651.3:c.127dup	p.Thr43AsnfsTer8	p.T43Nfs*8	ENST00000370651	NM_003463.4	42	-/A	3/6	1	2	FACETS	0.845	0.733	0.966	0.845	0.733	0.966	CLONAL	1	TRUE	1	0.3	2		321	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0031738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	182	641	4	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.322117684792367	2	FACETS	0.771	0.713	0.83	0.771	0.713	0.83	SUBCLONAL	2	TRUE	0	0.34182573208293	2		645	691	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241679	55241681	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	rs397517086	NA	P-0031738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	484	703	0	ENST00000275493.2:c.2127_2129del	p.Glu709_Thr710delinsAsp	p.E709_T710delinsD	ENST00000275493	NM_005228.3	709	gaAACt/gat	18/28	0.34182573208293	5	FACETS	1	0.993	1	0.875	0.838	0.912	CLONAL	3	TRUE	1	0.34182573208293	5		703	1224	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0031739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	143	460	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.988	0.905	1	1	0.991	1	CLONAL	2	FALSE	1	0.255253360487155	2		460	567	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678508	88678508	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs183806623	NA	P-0031739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	39	563	1	ENST00000360948.2:c.1028G>T	p.Arg343Leu	p.R343L	ENST00000360948	NM_001012338.2	343	cGg/cTg	9/19	0.104131735468503	0	FACETS	0.587	0.487	0.697			1	INDETERMINATE	1	FALSE	0	0.255253360487155	0		564	388	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94201031	94201031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs864622683	NA	P-0031739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	41	477	0	ENST00000323929.3:c.1046G>A	p.Arg349Gln	p.R349Q	ENST00000323929	NM_005591.3	349	cGg/cAg	10/20	1	2	FACETS	0.728	0.607	0.863	0.728	0.607	0.863	SUBCLONAL	1	FALSE	1	0.255253360487155	2		477	441	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206638	108206638	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs866402530	NA	P-0031739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	70	571	0	ENST00000278616.4:c.8218C>T	p.Gln2740Ter	p.Q2740*	ENST00000278616	NM_000051.3	2740	Cag/Tag	56/63	1	2	FACETS	0.969	0.846	1	0.969	0.846	1	CLONAL	1	FALSE	1	0.255253360487155	2		571	566	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206604	108206605	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	TT	novel	NA	P-0031739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	73	585	0	ENST00000278616.4:c.8184_8185delinsTT	p.Met2728_Gln2729delinsIleTer	p.M2728_Q2729delinsI*	ENST00000278616	NM_000051.3	2728	atGCaa/atTTaa	56/63	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	1	0.255253360487155	2		585	501	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022450	12022450	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs372716250	NA	P-0031739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	68	864	0	ENST00000396373.4:c.556A>G	p.Ile186Val	p.I186V	ENST00000396373	NM_001987.4	186	Atc/Gtc	5/8	0.104131735468503	0	FACETS	0.573	0.498	0.654			1	INDETERMINATE	1	FALSE	0	0.255253360487155	0		864	693	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623657	28623657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	72	615	0	ENST00000241453.7:c.900G>A	p.Met300Ile	p.M300I	ENST00000241453	NM_004119.2	300	atG/atA	8/24	0.104131735468503	0	FACETS	0.691	0.604	0.785			1	INDETERMINATE	1	FALSE	0	0.255253360487155	0		615	608	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981917	70981917	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	99	776	0	ENST00000276594.2:c.179C>A	p.Ala60Glu	p.A60E	ENST00000276594	NM_024504.3	60	gCg/gAg	2/8	0.15680286943625	4	FACETS	1	0.974	1	0.65	0.58	0.724	CLONAL	1	FALSE	2	0.255253360487155	4		776	749	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8523525	8523525	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0031739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	25	425	0	ENST00000356435.5:c.680-1G>T		p.X227_splice	ENST00000356435		227			0.255253360487155	1	FACETS	0.515	0.406	0.64	0.515	0.406	0.64	SUBCLONAL	1	FALSE	0	0.255253360487155	1		425	332	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0031740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	511	814	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.32640449272586	6	FACETS	0.936	0.897	0.976	0.936	0.897	0.976	CLONAL	4	TRUE	2	0.32640449272586	6		814	1382	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504401	8504401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757922864	NA	P-0031740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	44	591	0	ENST00000356435.5:c.1682G>A	p.Arg561Gln	p.R561Q	ENST00000356435		561	cGa/cAa	12/35	0.32640449272586	1	FACETS	0.382	0.32	0.452	0.382	0.32	0.452	SUBCLONAL	1	TRUE	0	0.32640449272586	1		591	590	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0031744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	85	329	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.15210245895762	6	FACETS	1	0.944	1	0.728	0.649	0.81	INDETERMINATE	2	TRUE	3	0.44930440940161	6		329	329	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121909229	NA	P-0031744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	238	618	0	ENST00000371953.3:c.389G>C	p.Arg130Pro	p.R130P	ENST00000371953	NM_000314.4	130	cGa/cCa	5/9	0.15210245895762	6	FACETS	0.883	0.828	0.94	0.883	0.828	0.94	INDETERMINATE	3	TRUE	3	0.44930440940161	6		618	759	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466022	69466022	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	121	759	0	ENST00000227507.2:c.860C>A	p.Pro287His	p.P287H	ENST00000227507	NM_053056.2	287	cCc/cAc	5/5	1	2	FACETS	0.938	0.851	1	0.938	0.851	1	CLONAL	1	TRUE	1	0.44930440940161	2		759	574	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059253	27059253	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	263	705	0	ENST00000324856.7:c.1890del	p.Ser631AlafsTer16	p.S631Afs*16	ENST00000324856	NM_006015.4	630	ctG/ct	4/20	0.431901273576543	2	FACETS	0.913	0.862	0.965	0.913	0.862	0.965	CLONAL	2	TRUE	0	0.44930440940161	2		705	641	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699362	47699362	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	240	628	0	ENST00000347630.2:c.146G>T	p.Gly49Val	p.G49V	ENST00000347630	NM_001007230.1	49	gGt/gTt	4/11	0.44833000837791	2	FACETS	0.899	0.846	0.953	0.899	0.846	0.953	CLONAL	2	TRUE	0	0.44930440940161	2		628	594	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589627	67589628	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATAGATTAT	novel	NA	P-0031744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	78	502	0	ENST00000274335.5:c.1393_1401dup	p.Arg465_Tyr467dup	p.R465_Y467dup	ENST00000274335		465	gat/gATAGATTATat	10/15	1	2	FACETS	0.804	0.709	0.904	0.804	0.709	0.904	CLONAL	1	TRUE	1	0.44930440940161	2		502	432	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0031745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	271	319	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	0.996	1	CLONAL	2	TRUE	1	0.33177637857961	2		319	690	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0031746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	302	620	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.372958200460419	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.372958200460419	2		621	787	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0031746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	157	562	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.372958200460419	2		562	828	SUCCESS
APC	324	MSKCC	GRCh37	5	112175235	112175235	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0031746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	82	403	0	ENST00000257430.4:c.3944C>G	p.Ser1315Ter	p.S1315*	ENST00000257430	NM_000038.5	1315	tCa/tGa	16/16	1	2	FACETS	0.907	0.802	1	0.907	0.802	1	CLONAL	1	TRUE	1	0.372958200460419	2		403	485	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306775	41306775	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1339099628	NA	P-0031746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	167	504	0	ENST00000373198.4:c.884C>A	p.Pro295Gln	p.P295Q	ENST00000373198	NM_133170.3	295	cCa/cAa	7/32	0.372958200460419	3	FACETS	0.843	0.778	0.911	0.843	0.778	0.911	CLONAL	2	TRUE	1	0.372958200460419	3		504	630	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	209	599	1	ENST00000269305.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	336	Gag/Tag	10/11	0.3	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.3	1		600	941	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342967	225342967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	146	607	0	ENST00000264414.4:c.2125C>T	p.Arg709Trp	p.R709W	ENST00000264414	NM_003590.4	709	Cgg/Tgg	15/16	0.3	1	FACETS	0.921	0.841	1	0.921	0.841	1	CLONAL	1	TRUE	0	0.3	1		607	898	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970900	21970900	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0031748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	154	609	0	ENST00000304494.5:c.457+1G>T		p.X153_splice	ENST00000304494	NM_000077.4	153			0.3	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.3	1		609	867	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610127	10610127	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	176	682	0	ENST00000171111.5:c.583G>T	p.Gly195Cys	p.G195C	ENST00000171111	NM_203500.1	195	Ggc/Tgc	2/6	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.3	2		682	1109	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	462	853	1	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.537617995658643	2	FACETS	0.961	0.924	0.998	0.961	0.924	0.998	CLONAL	2	TRUE	0	0.537617995658643	2		854	894	SUCCESS
APC	324	MSKCC	GRCh37	5	112128186	112128186	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780545	NA	P-0031749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	105	563	1	ENST00000257430.4:c.689G>A	p.Arg230His	p.R230H	ENST00000257430	NM_000038.5	230	cGt/cAt	7/16	0.537617995658643	4	FACETS	0.507	0.453	0.565			1	SUBCLONAL	1	TRUE	NA	0.537617995658643	4		564	1185	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631285	176631285	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	112	442	0	ENST00000439151.2:c.1228A>T	p.Arg410Trp	p.R410W	ENST00000439151	NM_022455.4	410	Agg/Tgg	4/23	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.537617995658643	2		442	416	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	431	557	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.669589350607755	4	FACETS	0.845	0.811	0.879	0.845	0.811	0.879	CLONAL	3	TRUE	1	0.669589350607755	4		557	848	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	191	632	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.669589350607755	3	FACETS	0.958	0.887	1	0.479	0.443	0.516	CLONAL	1	TRUE	1	0.669589350607755	3		636	795	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	186	600	3	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	0.669589350607755	3	FACETS	0.882	0.815	0.951			1	CLONAL	1	TRUE	NA	0.669589350607755	3		603	841	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	171	427	2	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	0.556551895982938	4	FACETS	1	0.936	1	0.509	0.469	0.552	CLONAL	1	TRUE	2	0.669589350607755	4		429	837	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497245	149497245	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	222	609	2	ENST00000261799.4:c.3073del	p.Leu1025CysfsTer20	p.L1025Cfs*20	ENST00000261799	NM_002609.3	1025	Ctg/tg	22/23	0.556551895982938	4	FACETS	0.979	0.91	1	0.489	0.455	0.525	CLONAL	1	TRUE	2	0.669589350607755	4		611	1131	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578464	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	265	712	0	ENST00000269305.4:c.466C>G	p.Arg156Gly	p.R156G	ENST00000269305	NM_001126112.2	156	Cgc/Ggc	5/11	0.669589350607755	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.669589350607755	1		712	495	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878062	48878062	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	79	147	0	ENST00000267163.4:c.19del	p.Arg7GlufsTer58	p.R7Efs*58	ENST00000267163	NM_000321.2	5	aCc/ac	1/27	0.669589350607755	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.669589350607755	1		147	145	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693003	89693003	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs786204900	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	97	373	1	ENST00000371953.3:c.491del	p.Lys164ArgfsTer3	p.K164Rfs*3	ENST00000371953	NM_000314.4	163	Aaa/aa	5/9	0.669589350607755	1	FACETS	0.959	0.876	1	0.959	0.876	1	CLONAL	1	TRUE	0	0.669589350607755	1		374	201	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	140	436	6	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	0.669589350607755	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.669589350607755	1		442	276	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628571	187628571	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs549553973	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	331	745	5	ENST00000441802.2:c.2411C>T	p.Ala804Val	p.A804V	ENST00000441802	NM_005245.3	804	gCg/gTg	2/27	0.669589350607755	3	FACETS	1	0.987	1	0.569	0.538	0.601	CLONAL	1	TRUE	1	0.669589350607755	3		750	1159	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163217	32163217	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	219	596	0	ENST00000375023.3:c.6009del	p.Lys2003AsnfsTer13	p.K2003Nfs*13	ENST00000375023	NM_004557.3	2003	aaA/aa	30/30	0.669589350607755	3	FACETS	0.945	0.88	1	0.472	0.44	0.506	CLONAL	1	TRUE	1	0.669589350607755	3		596	924	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206739	27206739	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147231791	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	227	587	0	ENST00000380036.4:c.2524C>T	p.Arg842Cys	p.R842C	ENST00000380036	NM_000459.3	842	Cgc/Tgc	15/23	0.347435255593191	3	FACETS	1	0.978	1	0.369	0.344	0.394	INDETERMINATE	1	TRUE	0	0.669589350607755	3		587	818	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550876	150550876	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	185	478	0	ENST00000369026.2:c.780C>A	p.Asn260Lys	p.N260K	ENST00000369026	NM_021960.4	260	aaC/aaA	2/3	0.669589350607755	3	FACETS	0.862	0.796	0.929	0.431	0.398	0.465	CLONAL	1	TRUE	1	0.669589350607755	3		478	856	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163298650	163298650	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	199	536	0	ENST00000271452.3:c.290C>A	p.Pro97His	p.P97H	ENST00000271452	NM_145697.2	97	cCt/cAt	5/14	0.669589350607755	3	FACETS	1	0.952	1	0.516	0.479	0.554	CLONAL	1	TRUE	1	0.669589350607755	3		536	769	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243668608	243668608	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs771193056	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	220	459	1	ENST00000263826.5:c.1383C>G	p.Asp461Glu	p.D461E	ENST00000263826	NM_005465.4	461	gaC/gaG	13/13	0.669589350607755	3	FACETS	1	0.976	1	0.55	0.513	0.588	CLONAL	1	TRUE	1	0.669589350607755	3		460	797	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425275	49425275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555187575	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	218	706	0	ENST00000301067.7:c.13213C>T	p.Gln4405Ter	p.Q4405*	ENST00000301067	NM_003482.3	4405	Cag/Tag	39/54	0.579439476992088	3	FACETS	1	0.99	1	0.447	0.418	0.477	CLONAL	1	TRUE	0	0.669589350607755	3		706	648	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871981	35871981	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	554	486	2	ENST00000216797.5:c.632C>A	p.Ala211Asp	p.A211D	ENST00000216797	NM_020529.2	211	gCt/gAt	4/6	0.669589350607755	5	FACETS	0.982	0.946	1	0.982	0.946	1	CLONAL	3	TRUE	2	0.669589350607755	5		488	1126	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40442026	40442026	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758471182	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	193	672	1	ENST00000345506.4:c.271G>A	p.Ala91Thr	p.A91T	ENST00000345506	NM_003152.3	91	Gcc/Acc	4/20	0.669589350607755	3	FACETS	0.877	0.812	0.945	0.439	0.406	0.473	CLONAL	1	TRUE	1	0.669589350607755	3		673	877	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213547	2213547	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766450500	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	380	543	2	ENST00000398665.3:c.1567G>A	p.Ala523Thr	p.A523T	ENST00000398665	NM_032482.2	523	Gcc/Acc	17/28	0.669589350607755	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.669589350607755	1		545	570	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52693377	52693377	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1298006628	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	166	583	0	ENST00000322088.6:c.28C>G	p.Leu10Val	p.L10V	ENST00000322088	NM_014225.5	10	Ctg/Gtg	1/15	0.669589350607755	4	FACETS	0.916	0.841	0.993	0.458	0.42	0.497	CLONAL	1	TRUE	2	0.669589350607755	4		583	904	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716301	52716301	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	195	640	3	ENST00000322088.6:c.745C>A	p.Arg249Ser	p.R249S	ENST00000322088	NM_014225.5	249	Cgc/Agc	6/15	0.669589350607755	4	FACETS	1	0.941	1	0.51	0.472	0.549	CLONAL	1	TRUE	2	0.669589350607755	4		643	954	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948123	55948123	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	147	446	0	ENST00000263923.4:c.3848G>T	p.Gly1283Val	p.G1283V	ENST00000263923	NM_002253.2	1283	gGt/gTt	29/30	0.669589350607755	3	FACETS	1	0.923	1	0.504	0.462	0.547	CLONAL	1	TRUE	1	0.669589350607755	3		446	582	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535328	66535328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	194	540	1	ENST00000273854.3:c.133C>T	p.Leu45Phe	p.L45F	ENST00000273854	NM_004439.5	45	Ctc/Ttc	1/18	0.669589350607755	3	FACETS	0.978	0.907	1	0.489	0.453	0.526	CLONAL	1	TRUE	1	0.669589350607755	3		541	791	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84388650	84388650	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1376301070	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	92	506	0	ENST00000321945.7:c.638A>G	p.His213Arg	p.H213R	ENST00000321945	NM_139076.2	213	cAt/cGt	7/9	0.669589350607755	3	FACETS	0.867	0.775	0.964	0.434	0.387	0.482	CLONAL	1	TRUE	1	0.669589350607755	3		506	423	SUCCESS
APC	324	MSKCC	GRCh37	5	112173252	112173252	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	60	220	0	ENST00000257430.4:c.1961A>G	p.Gln654Arg	p.Q654R	ENST00000257430	NM_000038.5	654	cAa/cGa	16/16	0.556551895982938	4	FACETS	1	0.941	1	0.573	0.499	0.652	CLONAL	1	TRUE	2	0.669589350607755	4		220	261	SUCCESS
APC	324	MSKCC	GRCh37	5	112178153	112178153	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	125	411	1	ENST00000257430.4:c.6862C>T	p.Gln2288Ter	p.Q2288*	ENST00000257430	NM_000038.5	2288	Cag/Tag	16/16	0.556551895982938	4	FACETS	0.917	0.831	1	0.458	0.415	0.504	CLONAL	1	TRUE	2	0.669589350607755	4		412	680	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056778	180056778	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	469	648	1	ENST00000261937.6:c.734G>T	p.Gly245Val	p.G245V	ENST00000261937	NM_182925.4	245	gGg/gTg	6/30	0.556551895982938	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	2	0.669589350607755	4		649	1136	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672486	30672487	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	198	573	0	ENST00000376406.3:c.4473dup	p.Thr1492HisfsTer4	p.T1492Hfs*4	ENST00000376406	NM_014641.2	1491	-/C	10/15	0.669589350607755	3	FACETS	0.904	0.838	0.972	0.452	0.419	0.486	CLONAL	1	TRUE	1	0.669589350607755	3		573	873	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163800	32163800	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs777430318	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	133	465	1	ENST00000375023.3:c.5426A>G	p.Gln1809Arg	p.Q1809R	ENST00000375023	NM_004557.3	1809	cAa/cGa	30/30	0.669589350607755	3	FACETS	0.888	0.81	0.97	0.444	0.405	0.485	CLONAL	1	TRUE	1	0.669589350607755	3		466	597	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658466	117658466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	93	590	0	ENST00000368508.3:c.5117G>A	p.Cys1706Tyr	p.C1706Y	ENST00000368508	NM_002944.2	1706	tGc/tAc	31/43	0.669589350607755	3	FACETS	0.709	0.632	0.79	0.354	0.316	0.395	SUBCLONAL	1	TRUE	1	0.669589350607755	3		590	523	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551294	141551294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	267	681	1	ENST00000220592.5:c.2003G>A	p.Arg668His	p.R668H	ENST00000220592	NM_012154.3	668	cGc/cAc	15/19	0.669589350607755	3	FACETS	0.992	0.931	1	0.496	0.465	0.528	CLONAL	1	TRUE	1	0.669589350607755	3		682	1073	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5073742	5073742	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	109	420	1	ENST00000381652.3:c.1821G>T	p.Lys607Asn	p.K607N	ENST00000381652	NM_004972.3	607	aaG/aaT	14/25	0.347435255593191	3	FACETS	0.787	0.709	0.869	0.262	0.236	0.29	INDETERMINATE	1	TRUE	0	0.669589350607755	3		421	552	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317430	1317430	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	190	534	0	ENST00000400841.2:c.635G>T	p.Gly212Val	p.G212V	ENST00000400841		212	gGc/gTc	5/6	0.669589350607755	3	FACETS	0.952	0.881	1	0.476	0.44	0.512	CLONAL	1	TRUE	1	0.669589350607755	3		534	796	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430774	47430774	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	282	645	0	ENST00000377045.4:c.1739G>C	p.Ser580Thr	p.S580T	ENST00000377045	NM_001654.4	580	aGt/aCt	16/16	0.669589350607755	3	FACETS	1	0.987	1	0.58	0.546	0.615	CLONAL	1	TRUE	1	0.669589350607755	3		645	969	SUCCESS
AR	367	MSKCC	GRCh37	X	66931496	66931496	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	226	656	2	ENST00000374690.3:c.2138T>C	p.Leu713Pro	p.L713P	ENST00000374690	NM_000044.3	713	cTt/cCt	4/8	0.669589350607755	3	FACETS	0.995	0.928	1	0.497	0.464	0.532	CLONAL	1	TRUE	1	0.669589350607755	3		658	906	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938724	76938724	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	205	624	0	ENST00000373344.5:c.2024C>G	p.Ser675Cys	p.S675C	ENST00000373344	NM_000489.3	675	tCt/tGt	9/35	0.669589350607755	3	FACETS	0.903	0.838	0.97	0.452	0.419	0.485	CLONAL	1	TRUE	1	0.669589350607755	3		624	905	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123505236	123505236	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775191468	NA	P-0031750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	94	463	0	ENST00000371139.4:c.382C>T	p.Pro128Ser	p.P128S	ENST00000371139	NM_001114937.2	128	Cca/Tca	4/4	0.669589350607755	3	FACETS	0.89	0.797	0.988	0.445	0.398	0.494	CLONAL	1	TRUE	1	0.669589350607755	3		463	421	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	72	258	0				ENST00000310581	NM_198253.2	-/1132			0.768597346481321	3	FACETS	1	0.924	1	0.528	0.467	0.591	CLONAL	1	TRUE	1	0.789305090046325	3		258	241	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0031752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	176	363	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.670733984602206	4	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	2	0.789305090046325	4		363	397	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432695	78432751	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GATCATGTTTTCAAAACTTTAAAAATCAAGTTACTTACTGAATCCAACCATTCCATC	GATCATGTTTTCAAAACTTTAAAAATCAAGTTACTTACTGAATCCAACCATTCCATC	-	novel	NA	P-0031752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	179	369	0	ENST00000370768.2:c.325_343+38del		p.X109_splice	ENST00000370768	NM_003902.3	109		5/20	0.789305090046325	2	FACETS	0.904	0.859	0.946	0.904	0.859	0.946	CLONAL	2	TRUE	0	0.789305090046325	2		369	251	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797837	42797846	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGCTCCAG	CCAGCTCCAG	-	novel	NA	P-0031752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	405	757	0	ENST00000575354.2:c.3890_3899del	p.Pro1297LeufsTer2	p.P1297Lfs*2	ENST00000575354	NM_015125.3	1297	CCAGCTCCAGct/ct	16/20	0.789305090046325	3	FACETS	0.964	0.939	0.988	0.964	0.939	0.988	CLONAL	3	TRUE	0	0.789305090046325	3		757	495	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942686	48942686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767011440	NA	P-0031756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	33	517	0	ENST00000267163.4:c.1073G>A	p.Arg358Gln	p.R358Q	ENST00000267163	NM_000321.2	358	cGa/cAa	11/27	1	2	FACETS	0.139	0.113	0.169	0.139	0.113	0.169	SUBCLONAL	1	TRUE	1	0.739371862697074	2		517	642	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752873	42752873	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	445	903	0	ENST00000222329.4:c.1391del	p.Pro464LeufsTer67	p.P464Lfs*67	ENST00000222329	NM_006494.2	464	cCt/ct	4/4	1	2	FACETS	0.966	0.923	1	0.966	0.923	1	CLONAL	1	TRUE	1	0.739371862697074	2		903	1246	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575126	64575126	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs778921501	NA	P-0031756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	414	707	0	ENST00000312049.6:c.681C>A	p.Tyr227Ter	p.Y227*	ENST00000312049	NM_130799.2	227	taC/taA	4/10	0.709577547242788	1	FACETS	0.989	0.951	1	0.989	0.951	1	CLONAL	1	TRUE	0	0.739371862697074	1		707	714	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817730	3817730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748049805	NA	P-0031756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	122	613	0	ENST00000262367.5:c.3241C>T	p.Arg1081Cys	p.R1081C	ENST00000262367	NM_004380.2	1081	Cgc/Tgc	16/31	1	2	FACETS	0.342	0.308	0.377	0.342	0.308	0.377	SUBCLONAL	1	TRUE	1	0.739371862697074	2		613	966	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0031757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	418	836	1	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	0.58277836457268	2	FACETS	0.991	0.953	1	0.991	0.953	1	CLONAL	2	TRUE	0	0.58277836457268	2		837	724	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881002	37881003	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCTCCCCC	novel	NA	P-0031757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	2297	799	0	ENST00000269571.5:c.2339_2340insCGGCTCCCC	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	-/GGCTCCCCC	20/27	0.58277836457268	15	FACETS	0.965	0.952	0.978			1	CLONAL	12	TRUE	NA	0.58277836457268	15		799	3259	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631283	176631283	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	71	433	0	ENST00000439151.2:c.1226A>C	p.Tyr409Ser	p.Y409S	ENST00000439151	NM_022455.4	409	tAt/tCt	4/23	0.58277836457268	7	FACETS	0.566	0.492	0.646			1	SUBCLONAL	1	TRUE	NA	0.58277836457268	7		433	1058	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885830	23885831	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0031758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	71	383	0	ENST00000374561.5:c.87dup	p.Lys30GlufsTer6	p.K30Efs*6	ENST00000374561	NM_002167.4	29	-/G	1/3	NA	2	FACETS	1	0.904	1			1	INDETERMINATE	1	TRUE	NA	0.228228538170678	2		383	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0031759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	336	574	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	NA	2	FACETS	0.944	0.906	0.981			1	INDETERMINATE	2	TRUE	NA	0.666415097703786	2		574	534	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0031759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	252	555	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.462693489353191	3	FACETS	0.905	0.855	0.955	0.905	0.855	0.955	CLONAL	2	TRUE	1	0.666415097703786	3		555	557	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204666	128204666	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768133841	NA	P-0031759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	83	731	0	ENST00000341105.2:c.775G>A	p.Asp259Asn	p.D259N	ENST00000341105	NM_032638.4	259	Gac/Aac	3/6	0.196175279834785	5	FACETS	0.624	0.55	0.704	0.208	0.183	0.235	INDETERMINATE	1	TRUE	2	0.666415097703786	5		731	798	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	73	354	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		354	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0031777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	136	620	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		621	654	SUCCESS
APC	324	MSKCC	GRCh37	5	112173345	112173345	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	36	225	0	ENST00000257430.4:c.2054G>A	p.Trp685Ter	p.W685*	ENST00000257430	NM_000038.5	685	tGg/tAg	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		225	253	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0031777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	49	268	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		268	358	SUCCESS
APC	324	MSKCC	GRCh37	5	112175760	112175761	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs398123122	NA	P-0031777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	49	186	0	ENST00000257430.4:c.4473dup	p.Ala1492CysfsTer22	p.A1492Cfs*22	ENST00000257430	NM_000038.5	1490	cat/caTt	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		186	347	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20486948	20486948	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs773975473	NA	P-0031777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	58	288	0	ENST00000346618.3:c.913C>T	p.Arg305Ter	p.R305*	ENST00000346618	NM_001949.4	305	Cga/Tga	5/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		288	397	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212236	36212236	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301144035	NA	P-0031777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	84	578	1	ENST00000222270.7:c.1987G>A	p.Glu663Lys	p.E663K	ENST00000222270	NM_014727.1	663	Gaa/Aaa	3/37	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		579	1038	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341422	70341422	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	166	412	0	ENST00000374080.3:c.857A>C	p.Glu286Ala	p.E286A	ENST00000374080		286	gAa/gCa	7/45	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		412	928	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0031789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	119	526	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.824	0.747	0.905	0.824	0.747	0.905	CLONAL	1	TRUE	1	0.550998125011414	2		526	524	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120527	70120527	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0031789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	276	721	3	ENST00000245479.2:c.1529G>C	p.Ter510SerextTer49	p.*510Sext*49	ENST00000245479	NM_000346.3	510	tGa/tCa	3/3	0.550998125011414	1	FACETS	0.964	0.909	1	0.964	0.909	1	CLONAL	1	TRUE	0	0.550998125011414	1		724	753	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520006	NA	P-0031789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	270	556	3	ENST00000269305.4:c.821T>C	p.Val274Ala	p.V274A	ENST00000269305	NM_001126112.2	274	gTt/gCt	8/11	0.550998125011414	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.550998125011414	1		559	649	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572033	64572033	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	238	522	2	ENST00000312049.6:c.1606C>T	p.Gln536Ter	p.Q536*	ENST00000312049	NM_130799.2	536	Cag/Tag	10/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.550998125011414	2		524	800	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508735	29508735	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1131691126	NA	P-0031789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	114	450	0	ENST00000356175.3:c.662G>A	p.Trp221Ter	p.W221*	ENST00000356175	NM_000267.3	221	tGg/tAg	7/57	0.550998125011414	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.550998125011414	1		450	267	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176176047	176176047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752538197	NA	P-0031789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	206	542	3	ENST00000367669.3:c.68C>T	p.Ser23Leu	p.S23L	ENST00000367669	NM_022457.5	23	tCg/tTg	1/20	0.550998125011414	3	FACETS	0.958	0.888	1	0.479	0.444	0.515	CLONAL	1	TRUE	1	0.550998125011414	3		545	996	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866514	56866514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1780	392	695	4	ENST00000519728.1:c.761G>A	p.Gly254Asp	p.G254D	ENST00000519728	NM_002350.3	254	gGc/gAc	8/13	0.550998125011414	5	FACETS	1	0.991	1	0.299	0.283	0.316	CLONAL	1	TRUE	1	0.550998125011414	5		699	2172	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0031794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	204	319	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.227260331581289	5	FACETS	0.949	0.882	1	0.632	0.588	0.679	INDETERMINATE	2	FALSE	2	0.44666402052888	5		319	804	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0031794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	202	471	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.44666402052888	2		471	673	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385271	41385271	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	148	350	0	ENST00000373198.4:c.690G>A	p.Trp230Ter	p.W230*	ENST00000373198	NM_133170.3	230	tgG/tgA	6/32	0.245219065449658	3	FACETS	1	0.97	1	0.565	0.516	0.615	INDETERMINATE	1	FALSE	1	0.44666402052888	3		350	718	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419992	41419992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	209	374	1	ENST00000373198.4:c.329C>T	p.Ser110Phe	p.S110F	ENST00000373198	NM_133170.3	110	tCc/tTc	3/32	0.245219065449658	3	FACETS	0.769	0.717	0.824	0.769	0.717	0.824	INDETERMINATE	2	FALSE	1	0.44666402052888	3		375	744	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115871	8115872	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0031798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	142	405	0	ENST00000346208.3:c.1219_1220del	p.Ser407AlafsTer99	p.S407Afs*99	ENST00000346208		406	aTC/a	6/6	0.254330917913614	1	FACETS	0.675	0.617	0.736	0.675	0.617	0.736	INDETERMINATE	1	TRUE	0	0.495738194573457	1		405	638	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434801	49434801	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs189199944	NA	P-0031798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	270	649	1	ENST00000301067.7:c.6752C>T	p.Ser2251Leu	p.S2251L	ENST00000301067	NM_003482.3	2251	tCg/tTg	31/54	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.495738194573457	2		650	1083	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243801045	243801045	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0031798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	209	274	1	ENST00000263826.5:c.430-1G>T		p.X144_splice	ENST00000263826	NM_005465.4	144			0.495738194573457	4	FACETS	1	0.949	1	1	0.949	1	CLONAL	3	TRUE	1	0.495738194573457	4		275	417	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92300822	92300822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1311537790	NA	P-0031798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	137	310	0	ENST00000265734.4:c.565G>A	p.Glu189Lys	p.E189K	ENST00000265734	NM_001259.6	189	Gaa/Aaa	5/8	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.495738194573457	2		310	519	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0031800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	211	508	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.481748755993481	1	FACETS	0.95	0.888	1	0.95	0.888	1	CLONAL	1	TRUE	0	0.522491499591108	1		509	628	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584540	48584541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0031800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	118	378	0	ENST00000342988.3:c.714dup	p.Gln239AlafsTer25	p.Q239Afs*25	ENST00000342988	NM_005359.5	238	ttg/ttGg	6/12	0.522491499591108	1	FACETS	0.849	0.773	0.928	0.849	0.773	0.928	CLONAL	1	TRUE	0	0.522491499591108	1		378	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0031801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	130	1011	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.421525000511987	1	FACETS	0.786	0.715	0.861	0.786	0.715	0.861	SUBCLONAL	1	TRUE	0	0.421525000511987	1		1012	619	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0031801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	75	358	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.855	0.753	0.965	0.855	0.753	0.965	CLONAL	1	TRUE	1	0.421525000511987	2		359	416	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306793	41306793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	49	197	1	ENST00000373198.4:c.866C>T	p.Pro289Leu	p.P289L	ENST00000373198	NM_133170.3	289	cCc/cTc	7/32	NA	2	FACETS	0.915	0.782	1			1	INDETERMINATE	1	TRUE	NA	0.421525000511987	2		198	254	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217255	66217255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	69	245	1	ENST00000273854.3:c.2360G>T	p.Gly787Val	p.G787V	ENST00000273854	NM_004439.5	787	gGa/gTa	14/18	1	2	FACETS	0.907	0.795	1	0.907	0.795	1	CLONAL	1	TRUE	1	0.421525000511987	2		246	361	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589585	67589586	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATG	novel	NA	P-0031801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	51	269	0	ENST00000274335.5:c.1350_1352dup	p.His450_Glu451insAsp	p.H450_E451insD	ENST00000274335		450	cat/cATGat	10/15	1	2	FACETS	0.846	0.724	0.978	0.846	0.724	0.978	CLONAL	1	TRUE	1	0.421525000511987	2		269	286	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687358	117687358	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	44	258	0	ENST00000368508.3:c.2693T>C	p.Ile898Thr	p.I898T	ENST00000368508	NM_002944.2	898	aTc/aCc	18/43	1	2	FACETS	0.665	0.56	0.78	0.665	0.56	0.78	SUBCLONAL	1	TRUE	1	0.421525000511987	2		258	314	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0031825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	71	460	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		460	593	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0031826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	60	369	1	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	0.788	0.69	0.891	0.788	0.69	0.891	SUBCLONAL	1	TRUE	1	0.765012314676208	2		370	199	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654543	29654543	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	91	215	0	ENST00000356175.3:c.5233del	p.Ser1745GlnfsTer8	p.S1745Qfs*8	ENST00000356175	NM_000267.3	1744	acT/ac	37/57	0.765012314676208	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.765012314676208	1		215	146	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138402610	138402610	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	64	398	0	ENST00000289153.2:c.2335A>C	p.Met779Leu	p.M779L	ENST00000289153	NM_006219.2	779	Atg/Ctg	16/22	0.336055088437907	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.765012314676208	0		398	326	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164811	123164811	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	25	173	0	ENST00000218089.9:c.124A>G	p.Thr42Ala	p.T42A	ENST00000218089	NM_001042749.1	42	Act/Gct	5/35	0.296874221900809	1	FACETS	0.336	0.269	0.411	0.336	0.269	0.411	INDETERMINATE	1	TRUE	0	0.765012314676208	1		173	120	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578189	7578189	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0031827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	21	579	0	ENST00000269305.4:c.660T>G	p.Tyr220Ter	p.Y220*	ENST00000269305	NM_001126112.2	220	taT/taG	6/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		579	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578189	7578189	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0031827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	378	579	0	ENST00000269305.4:c.660T>G	p.Tyr220Ter	p.Y220*	ENST00000269305	NM_001126112.2	220	taT/taG	6/11	0.361045643666288	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.361045643666288	2		579	946	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759697	133759697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776289598	NA	P-0031827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	262	479	1	ENST00000318560.5:c.2020C>T	p.Arg674Trp	p.R674W	ENST00000318560	NM_005157.4	674	Cgg/Tgg	11/11	0.361045643666288	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.361045643666288	2		480	645	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098898	47098898	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	216	805	0	ENST00000409792.3:c.6376G>T	p.Glu2126Ter	p.E2126*	ENST00000409792	NM_014159.6	2126	Gag/Tag	15/21	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.361045643666288	2		805	1171	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163374	47163387	+	frameshift_variant	Frame_Shift_Del	DEL	AACTTTTTTTACTC	AACTTTTTTTACTC	-	novel	NA	P-0031827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	107	413	0	ENST00000409792.3:c.2739_2752del	p.Lys913AsnfsTer17	p.K913Nfs*17	ENST00000409792	NM_014159.6	913	aaGAGTAAAAAAAGTTca/aaca	3/21	1	2	FACETS	0.938	0.843	1	0.938	0.843	1	CLONAL	1	TRUE	1	0.361045643666288	2		413	632	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1023835002	NA	P-0031828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	199	382	0	ENST00000558401.1:c.1A>G	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Gtg	1/4	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.581717124108293	2		382	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0031828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	447	610	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.581717124108293	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.581717124108293	2		610	759	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68982086	68982086	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	397	706	0	ENST00000288368.4:c.1460G>T	p.Cys487Phe	p.C487F	ENST00000288368	NM_024870.2	487	tGt/tTt	13/40	0.564968795603054	4	FACETS	0.875	0.832	0.918	0.875	0.832	0.918	CLONAL	2	TRUE	2	0.581717124108293	4		706	1234	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484362	8484362	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	277	349	0	ENST00000356435.5:c.3170G>T	p.Gly1057Val	p.G1057V	ENST00000356435		1057	gGg/gTg	19/35	0.564968795603054	4	FACETS	0.981	0.925	1	0.981	0.925	1	CLONAL	2	TRUE	2	0.581717124108293	4		349	768	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937093	48937093	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs1555284956	NA	P-0031828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	146	157	0	ENST00000267163.4:c.861G>C	p.Glu287Asp	p.E287D	ENST00000267163	NM_000321.2	287	gaG/gaC	8/27	0.581717124108293	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.581717124108293	2		157	242	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101030	41101030	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	384	554	0	ENST00000373198.4:c.1326G>C	p.Gln442His	p.Q442H	ENST00000373198	NM_133170.3	442	caG/caC	8/32	0.581717124108293	3	FACETS	0.999	0.954	1	0.999	0.954	1	CLONAL	2	TRUE	1	0.581717124108293	3		554	853	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395912	395913	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0031828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	240	387	0	ENST00000380956.4:c.469_470delinsAA	p.Pro157Asn	p.P157N	ENST00000380956	NM_001195286.1	157	CCt/AAt	4/9	0.486907362920538	4	FACETS	0.896	0.841	0.953	0.896	0.841	0.953	CLONAL	2	TRUE	2	0.581717124108293	4		387	728	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402531	139402533	+	missense_variant	Missense_Mutation	TNP	TGC	TGC	GAA	novel	NA	P-0031828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	367	721	1	ENST00000277541.6:c.3384_3386delinsTTC	p.His1129Ser	p.H1129S	ENST00000277541	NM_017617.3	1128	acGCAc/acTTCc	21/34	0.431637463554492	4	FACETS	0.803	0.761	0.845			1	CLONAL	2	TRUE	NA	0.581717124108293	4		722	1243	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0031830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	322	508	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.668885510871601	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.668885510871601	1		509	601	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434142	49434142	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057518571	NA	P-0031830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	172	748	0	ENST00000301067.7:c.7411C>T	p.Arg2471Ter	p.R2471*	ENST00000301067	NM_003482.3	2471	Cga/Tga	31/54	0.373016980496753	1	FACETS	0.46	0.424	0.497	0.46	0.424	0.497	INDETERMINATE	1	TRUE	0	0.668885510871601	1		748	744	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491406	18491406	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1298111483	NA	P-0031830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	138	331	0	ENST00000266497.5:c.1319T>C	p.Val440Ala	p.V440A	ENST00000266497		440	gTt/gCt	8/31	NA	2	FACETS	0.897	0.823	0.974			1	INDETERMINATE	1	TRUE	NA	0.668885510871601	2		331	460	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434069	49434075	+	frameshift_variant	Frame_Shift_Del	DEL	GGGAACC	GGGAACC	-	novel	NA	P-0031830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	219	612	0	ENST00000301067.7:c.7478_7484del	p.Gly2493GlufsTer48	p.G2493Efs*48	ENST00000301067	NM_003482.3	2493	gGGTTCCCa/ga	31/54	0.373016980496753	1	FACETS	0.804	0.755	0.854	0.804	0.755	0.854	INDETERMINATE	1	TRUE	0	0.668885510871601	1		612	542	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026112	71026112	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs797045585	NA	P-0031830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	137	413	0	ENST00000318789.4:c.1510C>G	p.Arg504Gly	p.R504G	ENST00000318789	NM_032682.5	504	Cgc/Ggc	17/21	0.668885510871601	1	FACETS	0.614	0.563	0.667	0.614	0.563	0.667	SUBCLONAL	1	TRUE	0	0.668885510871601	1		413	444	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069562	69069562	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	63	347	0	ENST00000288368.4:c.4237G>C	p.Glu1413Gln	p.E1413Q	ENST00000288368	NM_024870.2	1413	Gag/Cag	35/40	1	2	FACETS	0.39	0.338	0.447	0.39	0.338	0.447	SUBCLONAL	1	TRUE	1	0.668885510871601	2		347	483	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507375	8507375	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	58	390	0	ENST00000356435.5:c.1603T>A	p.Ser535Thr	p.S535T	ENST00000356435		535	Tct/Act	11/35	0.668885510871601	1	FACETS	0.357	0.309	0.41	0.357	0.309	0.41	SUBCLONAL	1	TRUE	0	0.668885510871601	1		390	323	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0031831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	49	596	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		596	611	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0031831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	41	574	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		574	772	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0031834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	87	410	0				ENST00000310581	NM_198253.2	-/1132			0.366819685419154	1	FACETS	0.389	0.346	0.435	0.389	0.346	0.435	INDETERMINATE	1	TRUE	0	0.653873887755818	1		410	460	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184122	123184122	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1569512722	NA	P-0031834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	198	467	1	ENST00000218089.9:c.980G>A	p.Ser327Asn	p.S327N	ENST00000218089	NM_001042749.1	327	aGt/aAt	11/35	1	2	FACETS	0.834	0.775	0.895	0.834	0.775	0.895	CLONAL	1	TRUE	1	0.653873887755818	2		468	726	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0031834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	548	773	0	ENST00000269305.4:c.376-1G>C		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.462714794565936	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.653873887755818	1		773	923	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509449	149509449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765124485	NA	P-0031834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	336	782	0	ENST00000261799.4:c.1450G>A	p.Glu484Lys	p.E484K	ENST00000261799	NM_002609.3	484	Gag/Aag	10/23	0.366819685419154	1	FACETS	0.781	0.741	0.821	0.781	0.741	0.821	INDETERMINATE	1	TRUE	0	0.653873887755818	1		782	886	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974696	21974697	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0031835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	85	360	0	ENST00000304494.5:c.130dup	p.Tyr44LeufsTer76	p.Y44Lfs*76	ENST00000304494	NM_000077.4	44	tac/tTac	1/3	0.52711761103024	1	FACETS	0.845	0.756	0.938	0.845	0.756	0.938	CLONAL	1	TRUE	0	0.52711761103024	1		360	281	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602538	10602538	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773835974	NA	P-0031835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	94	695	1	ENST00000171111.5:c.1040C>T	p.Pro347Leu	p.P347L	ENST00000171111	NM_203500.1	347	cCc/cTc	3/6	0.52711761103024	1	FACETS	0.46	0.41	0.513	0.46	0.41	0.513	SUBCLONAL	1	TRUE	0	0.52711761103024	1		696	571	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	143	700	0	ENST00000269305.4:c.818del	p.Arg273LeufsTer72	p.R273Lfs*72	ENST00000269305	NM_001126112.2	273	cGt/ct	8/11	0.467259110062051	1	FACETS	0.871	0.8	0.943	0.871	0.8	0.943	CLONAL	1	TRUE	0	0.52711761103024	1		700	459	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981252	201981253	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0031835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	139	743	0	ENST00000359651.3:c.332dup	p.Leu112SerfsTer23	p.L112Sfs*23	ENST00000359651		111	cgt/cGgt	2/8	1	2	FACETS	0.744	0.678	0.812	0.744	0.678	0.812	SUBCLONAL	1	TRUE	1	0.52711761103024	2		743	709	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710566	40710566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760820896	NA	P-0031835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	94	715	1	ENST00000373198.4:c.4285G>A	p.Val1429Met	p.V1429M	ENST00000373198	NM_133170.3	1429	Gtg/Atg	31/32	0.235737721330814	3	FACETS	0.664	0.591	0.741	0.332	0.295	0.371	INDETERMINATE	1	TRUE	1	0.52711761103024	3		716	679	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427746	72427755	+	frameshift_variant	Frame_Shift_Del	DEL	CAACTGCTGT	CAACTGCTGT	-	novel	NA	P-0031835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	94	364	0	ENST00000477973.2:c.733_742del	p.Gln247Ter	p.Q247*	ENST00000477973	NM_012234.5	245	gcACAGCAGTTG/gc	4/4	0.52711761103024	1	FACETS	0.867	0.781	0.956	0.867	0.781	0.956	CLONAL	1	TRUE	0	0.52711761103024	1		364	303	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630315	187630315	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	142	622	0	ENST00000441802.2:c.667del	p.Leu223SerfsTer7	p.L223Sfs*7	ENST00000441802	NM_005245.3	223	Ctc/tc	2/27	0.52711761103024	1	FACETS	0.965	0.889	1	0.965	0.889	1	CLONAL	1	TRUE	0	0.52711761103024	1		622	411	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0031839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	156	427	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.345798578449445	4	FACETS	1	0.942	1	1	0.942	1	CLONAL	3	TRUE	1	0.345798578449445	4		427	397	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	107	575	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.328697526121312	2	FACETS	1	0.902	1	0.502	0.451	0.555	CLONAL	1	TRUE	0	0.345798578449445	2		575	617	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363231	40363231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768216635	NA	P-0031839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	95	497	0	ENST00000397332.2:c.998C>T	p.Ala333Val	p.A333V	ENST00000397332	NM_001033082.2	333	gCg/gTg	3/3	0.345798578449445	2	FACETS	1	0.959	1	0.574	0.513	0.638	CLONAL	1	TRUE	0	0.345798578449445	2		497	479	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245465	41245465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28897681	NA	P-0031839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	224	746	0	ENST00000357654.3:c.2083G>A	p.Asp695Asn	p.D695N	ENST00000357654	NM_007294.3	695	Gat/Aat	10/23	0.325016518086235	4	FACETS	0.987	0.921	1	0.987	0.921	1	CLONAL	2	TRUE	2	0.345798578449445	4		746	883	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	213	493	0	ENST00000263967.3:c.3012G>T	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atT	21/21	0.345798578449445	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	3	TRUE	1	0.345798578449445	4		493	533	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061261	38061261	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	332	582	1	ENST00000250448.2:c.728A>G	p.Tyr243Cys	p.Y243C	ENST00000250448	NM_004496.3	243	tAc/tGc	2/2	0.345798578449445	3	FACETS	0.865	0.821	0.91	1	0.993	1	CLONAL	3	TRUE	1	0.345798578449445	3		583	868	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479316	50479316	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	106	436	0	ENST00000394963.4:c.164G>C	p.Gly55Ala	p.G55A	ENST00000394963	NM_003076.4	55	gGa/gCa	1/13	0.345798578449445	6	FACETS	1	0.973	1	0.317	0.283	0.352	CLONAL	1	TRUE	2	0.345798578449445	6		436	819	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109742	115109745	+	frameshift_variant	Frame_Shift_Del	DEL	CGCG	CGCG	-	novel	NA	P-0031839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	277	731	0	ENST00000257566.3:c.2133_2136del	p.Cys711TrpfsTer177	p.C711Wfs*177	ENST00000257566	NM_016569.3	711	tgCGCG/tg	8/8	0.345798578449445	6	FACETS	1	0.968	1	0.525	0.492	0.559	CLONAL	2	TRUE	2	0.345798578449445	6		731	1291	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636021	28636021	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	58	594	0	ENST00000241453.7:c.351T>G	p.His117Gln	p.H117Q	ENST00000241453	NM_004119.2	117	caT/caG	3/24	0.345798578449445	3	FACETS	0.594	0.51	0.687	0.297	0.255	0.344	SUBCLONAL	1	TRUE	1	0.345798578449445	3		594	662	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953901	32953901	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	34	391	0	ENST00000380152.3:c.8968T>C	p.Trp2990Arg	p.W2990R	ENST00000380152		2990	Tgg/Cgg	23/27	0.345798578449445	3	FACETS	0.809	0.664	0.971	0.405	0.332	0.486	CLONAL	1	TRUE	1	0.345798578449445	3		391	285	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252942	36252942	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0031839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	148	397	0	ENST00000300305.3:c.420C>G	p.Tyr140Ter	p.Y140*	ENST00000300305		140	taC/taG	4/8	0.325016518086235	4	FACETS	0.986	0.905	1	0.986	0.905	1	CLONAL	2	TRUE	2	0.345798578449445	4		397	584	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859502	151859503	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0031839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	84	448	0	ENST00000262189.6:c.11159_11160del	p.Leu3720ArgfsTer4	p.L3720Rfs*4	ENST00000262189	NM_170606.2	3720	cTG/c	43/59	NA	2	FACETS	0.913	0.809	1			1	INDETERMINATE	1	TRUE	NA	0.345798578449445	2		448	532	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98002975	98002975	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	27	507	0	ENST00000289081.3:c.301G>C	p.Glu101Gln	p.E101Q	ENST00000289081	NM_000136.2	101	Gaa/Caa	4/15	0.345798578449445	3	FACETS	0.595	0.474	0.732	0.297	0.237	0.366	SUBCLONAL	1	TRUE	1	0.345798578449445	3		507	308	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	127	258	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.411072606701069	2		258	470	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	138	431	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.411072606701069	2		431	560	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610345	10610346	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCTCCATGCCCTGCTCCCGCAGCCCG	novel	NA	P-0031840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	127	833	0	ENST00000171111.5:c.339_364dup	p.Val122AlafsTer44	p.V122Afs*44	ENST00000171111	NM_203500.1	122	gtg/gCGGGCTGCGGGAGCAGGGCATGGAGGtg	2/6	0.411072606701069	1	FACETS	0.629	0.57	0.691	0.629	0.57	0.691	SUBCLONAL	1	TRUE	0	0.411072606701069	1		833	781	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143181670	143181670	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1239467286	NA	P-0031840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	160	541	0	ENST00000262992.4:c.663A>C	p.Lys221Asn	p.K221N	ENST00000262992	NM_001101669.1	221	aaA/aaC	9/24	1	2	FACETS	0.969	0.89	1	0.969	0.89	1	CLONAL	1	TRUE	1	0.411072606701069	2		541	803	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0031841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	176	391	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.258944665864743	4	FACETS	0.881	0.82	0.942	0.881	0.82	0.942	INDETERMINATE	2	TRUE	2	0.828857472863023	4		391	441	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41219645	41219645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357043	NA	P-0031841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	31	479	0	ENST00000357654.3:c.5054C>T	p.Thr1685Ile	p.T1685I	ENST00000357654	NM_007294.3	1685	aCt/aTt	16/23	NA	2	FACETS	0.139	0.111	0.169			1	INDETERMINATE	1	TRUE	NA	0.828857472863023	2		479	540	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0031842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	316	734	1	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	0.689512478882807	2	FACETS	0.927	0.876	0.979	0.464	0.438	0.49	CLONAL	1	TRUE	0	0.692082975867897	2		735	985	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0031842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	639	574	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.657732998268547	3	FACETS	0.911	0.888	0.935	0.911	0.888	0.935	CLONAL	3	TRUE	0	0.692082975867897	3		574	909	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0031842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	425	461	1	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.619914426328689	3	FACETS	0.962	0.933	0.99			1	CLONAL	3	TRUE	NA	0.692082975867897	3		462	573	SUCCESS
AR	367	MSKCC	GRCh37	X	66765159	66765197	+	inframe_deletion	In_Frame_Del	DEL	GCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA	GCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA	-	rs3032358	NA	P-0031842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	78	231	0	ENST00000374690.3:c.201_239del	p.Gln68_Gln80del	p.Q68_Q80del	ENST00000374690	NM_000044.3	57	ctGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAg/ctg	1/8	1	1	FACETS	0.627	0.56	0.697	0.627	0.56	0.697	SUBCLONAL	1	TRUE	0	0.692082975867897	1		231	235	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188853	32188853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs192478549	NA	P-0031842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	273	700	1	ENST00000375023.3:c.701G>A	p.Arg234Gln	p.R234Q	ENST00000375023	NM_004557.3	234	cGg/cAg	4/30	1	2	FACETS	0.959	0.903	1	0.959	0.903	1	CLONAL	1	TRUE	1	0.692082975867897	2		701	823	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746114	162746114	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	129	311	0	ENST00000367921.3:c.2237G>T	p.Arg746Leu	p.R746L	ENST00000367921	NM_006182.2	746	cGg/cTg	16/18	0.65540211323648	3	FACETS	0.956	0.871	1	0.478	0.435	0.522	CLONAL	1	TRUE	1	0.692082975867897	3		311	525	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156933	89156933	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	180	519	1	ENST00000336596.2:c.35G>T	p.Ser12Ile	p.S12I	ENST00000336596	NM_005233.5	12	aGc/aTc	1/17	0.65540211323648	3	FACETS	0.88	0.812	0.949	0.44	0.406	0.475	CLONAL	1	TRUE	1	0.692082975867897	3		520	796	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499078	149499078	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	294	694	0	ENST00000261799.4:c.2750T>G	p.Ile917Ser	p.I917S	ENST00000261799	NM_002609.3	917	aTc/aGc	20/23	0.683413028872975	2	FACETS	0.993	0.937	1	0.496	0.468	0.525	CLONAL	1	TRUE	0	0.692082975867897	2		694	856	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393310	393310	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs781441118	NA	P-0031842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	233	512	0	ENST00000380956.4:c.158C>A	p.Pro53His	p.P53H	ENST00000380956	NM_001195286.1	53	cCc/cAc	2/9	NA	2	FACETS	0.879	0.823	0.937			1	INDETERMINATE	1	TRUE	NA	0.692082975867897	2		512	766	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873699	37873699	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	158	700	1	ENST00000269571.5:c.1864G>T	p.Ala622Ser	p.A622S	ENST00000269571		622	Gca/Tca	15/27	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.3	2		701	775	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0031845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	454	772	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.578119042334591	2	FACETS	0.844	0.813	0.875	0.844	0.813	0.875	CLONAL	2	TRUE	0	0.673358851096155	2		772	799	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330610	65330610	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	98	487	0	ENST00000342505.4:c.1036C>A	p.Leu346Met	p.L346M	ENST00000342505	NM_002227.2	346	Ctg/Atg	8/25	0.357790963999012	3	FACETS	0.654	0.584	0.728	0.327	0.292	0.364	INDETERMINATE	1	TRUE	1	0.673358851096155	3		487	595	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984580	72984580	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1512	171	747	1	ENST00000268489.5:c.3004C>T	p.His1002Tyr	p.H1002Y	ENST00000268489	NM_006885.3	1002	Cac/Tac	3/10	0.673358851096155	6	FACETS	0.708	0.649	0.771			1	SUBCLONAL	1	TRUE	NA	0.673358851096155	6		748	1683	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0121479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	413	571	1	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	NA	1	0.745870483595404	2		572	973	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431654	49431654	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	302	588	0	ENST00000301067.7:c.9485G>T	p.Gly3162Val	p.G3162V	ENST00000301067	NM_003482.3	3162	gGc/gTc	34/54	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	NA	1	0.745870483595404	2		588	773	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416620	29416620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0121479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	197	387	0	ENST00000389048.3:c.4333C>T	p.Pro1445Ser	p.P1445S	ENST00000389048	NM_004304.4	1445	Cct/Tct	29/29	0.745870483595404	3	FACETS	0.976	0.907	1	0.488	0.453	0.524	CLONAL	1	NA	1	0.745870483595404	3		387	743	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391922	139391922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1215473021	NA	P-0121479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	371	744	1	ENST00000277541.6:c.6269C>T	p.Thr2090Met	p.T2090M	ENST00000277541	NM_017617.3	2090	aCg/aTg	34/34	1	2	FACETS	0.934	0.888	0.981	0.934	0.888	0.981	CLONAL	1	NA	1	0.745870483595404	2		745	1065	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	22	354	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.11	0.085	0.14	0.11	0.085	0.14	SUBCLONAL	1	TRUE	1	0.747869311544108	2		354	534	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435300	110435302	+	inframe_deletion	In_Frame_Del	DEL	GGT	GGT	-	rs765493638	NA	P-0031848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	16	242	2	ENST00000375856.3:c.3099_3101del	p.Pro1036del	p.P1036del	ENST00000375856	NM_003749.2	1033	ccACCg/ccg	1/2	0.404790195906608	2	FACETS	0.195	0.144	0.257	0.098	0.072	0.129	SUBCLONAL	1	TRUE	0	0.534427063170833	2		244	307	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0031850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	355	427	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.534633680392047	4	FACETS	0.988	0.954	1	0.988	0.954	1	CLONAL	4	TRUE	0	0.579090544352752	4		427	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0031850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	346	614	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.567369789903208	2	FACETS	0.918	0.877	0.958	0.918	0.877	0.958	CLONAL	2	TRUE	0	0.579090544352752	2		616	651	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692926	89692926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	146	605	0	ENST00000371953.3:c.410C>T	p.Ala137Val	p.A137V	ENST00000371953	NM_000314.4	137	gCa/gTa	5/9	0.569224768341285	3	FACETS	0.847	0.782	0.913	0.847	0.782	0.913	CLONAL	2	TRUE	1	0.579090544352752	3		605	384	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822563	72822564	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCTGC	rs376311468	NA	P-0031850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	104	553	0	ENST00000268489.5:c.9606_9611dup	p.Gln3203_Gln3204dup	p.Q3203_Q3204dup	ENST00000268489	NM_006885.3	3203	caa/caGCAGCAa	10/10	0.560962897488216	2	FACETS	0.998	0.902	1	0.499	0.451	0.549	CLONAL	1	TRUE	0	0.579090544352752	2		553	360	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0031851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	312	677	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.651005742576719	3	FACETS	0.931	0.895	0.966	1	0.996	1	CLONAL	3	TRUE	1	0.651005742576719	3		677	455	SUCCESS
ATR	545	MSKCC	GRCh37	3	142168296	142168296	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	155	460	0	ENST00000350721.4:c.7910A>G	p.Tyr2637Cys	p.Y2637C	ENST00000350721	NM_001184.3	2637	tAt/tGt	47/47	0.603269025109021	5	FACETS	0.932	0.859	1			1	CLONAL	2	TRUE	NA	0.651005742576719	5		460	505	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696620	176696620	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	127	284	0	ENST00000439151.2:c.5321T>A	p.Ile1774Asn	p.I1774N	ENST00000439151	NM_022455.4	1774	aTc/aAc	16/23	0.637655650724763	2	FACETS	0.899	0.838	0.959	0.899	0.838	0.959	CLONAL	2	TRUE	0	0.651005742576719	2		284	217	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971193	21971194	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0031851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	208	340	0	ENST00000304494.5:c.163_164dup	p.Ser56AlafsTer91	p.S56Afs*91	ENST00000304494	NM_000077.4	55	ggc/ggGGc	2/3	0.616685267939969	2	FACETS	0.937	0.888	0.985	0.937	0.888	0.985	CLONAL	2	TRUE	0	0.651005742576719	2		340	341	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032069	26032069	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	13	413	0	ENST00000244661.2:c.220G>C	p.Glu74Gln	p.E74Q	ENST00000244661	NM_003537.3	74	Gaa/Caa	1/1	0.327288311910431	4	FACETS	0.131	0.092	0.178	0.065	0.046	0.089	SUBCLONAL	1	TRUE	2	0.450921806717765	4		413	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	465	623	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.450921806717765	3	FACETS	0.985	0.948	1	0.985	0.948	1	CLONAL	3	TRUE	0	0.450921806717765	3		623	855	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696757	176696757	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs752685166	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	188	376	1	ENST00000439151.2:c.5458G>T	p.Val1820Leu	p.V1820L	ENST00000439151	NM_022455.4	1820	Gtg/Ttg	16/23	0.450921806717765	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	0	0.450921806717765	2		377	412	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141453	11141453	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	327	595	0	ENST00000358026.2:c.3430G>T	p.Glu1144Ter	p.E1144*	ENST00000358026	NM_001128849.1	1144	Gag/Tag	25/36	0.450921806717765	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.450921806717765	2		595	692	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937183	76937183	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	73	740	0	ENST00000373344.5:c.3565C>A	p.Leu1189Ile	p.L1189I	ENST00000373344	NM_000489.3	1189	Cta/Ata	9/35	0.26161841274801	1	FACETS	0.63	0.554	0.712	0.63	0.554	0.712	INDETERMINATE	1	TRUE	0	0.450921806717765	1		740	398	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778899	3778899	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	151	549	0	ENST00000262367.5:c.6149G>T	p.Gly2050Val	p.G2050V	ENST00000262367	NM_004380.2	2050	gGg/gTg	31/31	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.450921806717765	2		549	547	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388023	81388023	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	45	514	0	ENST00000222390.5:c.352C>A	p.Leu118Ile	p.L118I	ENST00000222390	NM_000601.4	118	Ctc/Atc	3/18	0.450921806717765	3	FACETS	0.674	0.568	0.79	0.337	0.284	0.395	SUBCLONAL	1	TRUE	1	0.450921806717765	3		514	363	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294312	1294312	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs957794083	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	297	560	1	ENST00000310581.5:c.689G>A	p.Arg230Gln	p.R230Q	ENST00000310581	NM_198253.2	230	cGa/cAa	2/16	0.327288311910431	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.450921806717765	4		561	856	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257634	16257635	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	103	426	0	ENST00000375759.3:c.4901dup	p.Pro1635ThrfsTer26	p.P1635Tfs*26	ENST00000375759	NM_015001.2	1633	-/C	11/15	0.428982510931781	4	FACETS	0.854	0.764	0.95	0.427	0.382	0.475	CLONAL	1	TRUE	2	0.450921806717765	4		426	776	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161453	2161453	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	178	559	0	ENST00000434045.2:c.74C>A	p.Thr25Asn	p.T25N	ENST00000434045	NM_001127598.1	25	aCt/aAt	2/5	0.450921806717765	3	FACETS	1	0.969	1	0.548	0.505	0.592	CLONAL	1	TRUE	1	0.450921806717765	3		559	883	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431673	49431673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	199	614	1	ENST00000301067.7:c.9466C>T	p.Pro3156Ser	p.P3156S	ENST00000301067	NM_003482.3	3156	Cca/Tca	34/54	0.224997148251873	5	FACETS	0.975	0.905	1	0.65	0.603	0.698	INDETERMINATE	2	TRUE	2	0.450921806717765	5		615	759	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112527	115112527	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs370551433	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	381	672	0	ENST00000257566.3:c.1213C>G	p.Arg405Gly	p.R405G	ENST00000257566	NM_016569.3	405	Cgt/Ggt	7/8	0.428982510931781	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	2	0.450921806717765	4		672	1079	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134238	41134238	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	80	402	1	ENST00000379561.5:c.1390G>T	p.Glu464Ter	p.E464*	ENST00000379561	NM_002015.3	464	Gag/Tag	2/3	1	2	FACETS	0.859	0.76	0.964	0.859	0.76	0.964	CLONAL	1	TRUE	1	0.450921806717765	2		403	413	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220661	2220661	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	190	639	0	ENST00000326181.6:c.278G>T	p.Arg93Leu	p.R93L	ENST00000326181	NM_032271.2	93	cGc/cTc	5/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.450921806717765	2		639	743	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923333	9923333	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397518471	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	72	503	0	ENST00000330684.3:c.1954T>G	p.Phe652Val	p.F652V	ENST00000330684	NM_001134407.1	652	Ttc/Gtc	9/13	1	2	FACETS	0.565	0.494	0.642	0.565	0.494	0.642	SUBCLONAL	1	TRUE	1	0.450921806717765	2		503	565	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989643	15989643	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	237	369	0	ENST00000268712.3:c.3130G>T	p.Val1044Leu	p.V1044L	ENST00000268712	NM_006311.3	1044	Gtg/Ttg	23/46	0.450921806717765	3	FACETS	1	0.967	1	0.695	0.653	0.737	CLONAL	2	TRUE	0	0.450921806717765	3		369	618	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17125841	17125841	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	706	571	0	ENST00000285071.4:c.753G>T	p.Trp251Cys	p.W251C	ENST00000285071	NM_144997.5	251	tgG/tgT	7/14	0.450921806717765	3	FACETS	0.894	0.87	0.918	1	0.997	1	CLONAL	4	TRUE	0	0.450921806717765	3		571	1073	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40857134	40857134	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	68	446	1	ENST00000428826.2:c.1907A>T	p.Asn636Ile	p.N636I	ENST00000428826		636	aAc/aTc	17/21	0.450921806717765	3	FACETS	0.712	0.62	0.811	0.356	0.31	0.406	SUBCLONAL	1	TRUE	1	0.450921806717765	3		447	519	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295776	15295776	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	366	779	0	ENST00000263388.2:c.2351del	p.Gly784AlafsTer76	p.G784Afs*76	ENST00000263388	NM_000435.2	784	gGc/gc	15/33	0.450921806717765	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.450921806717765	2		779	773	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657080	47657080	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	41	228	0	ENST00000233146.2:c.1276G>T	p.Gly426Ter	p.G426*	ENST00000233146	NM_000251.2	426	Gga/Tga	7/16	1	2	FACETS	0.834	0.701	0.979	0.834	0.701	0.979	CLONAL	1	TRUE	1	0.450921806717765	2		228	218	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286802	212286802	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	63	394	0	ENST00000342788.4:c.2894C>G	p.Pro965Arg	p.P965R	ENST00000342788	NM_005235.2	965	cCt/cGt	24/28	1	2	FACETS	0.898	0.783	1	0.898	0.783	1	CLONAL	1	TRUE	1	0.450921806717765	2		394	311	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342976	225342976	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	122	603	0	ENST00000264414.4:c.2116G>C	p.Ala706Pro	p.A706P	ENST00000264414	NM_003590.4	706	Gct/Cct	15/16	1	2	FACETS	0.925	0.839	1	0.925	0.839	1	CLONAL	1	TRUE	1	0.450921806717765	2		603	585	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031610	36031610	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	113	602	0	ENST00000358208.4:c.1439G>T	p.Arg480Leu	p.R480L	ENST00000358208		480	cGg/cTg	12/12	1	2	FACETS	0.677	0.61	0.749	0.677	0.61	0.749	SUBCLONAL	1	TRUE	1	0.450921806717765	2		602	740	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790111	40790111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343257768	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	165	521	0	ENST00000373198.4:c.2620C>T	p.Pro874Ser	p.P874S	ENST00000373198	NM_133170.3	874	Cct/Tct	18/32	1	2	FACETS	0.935	0.86	1	0.935	0.86	1	CLONAL	1	TRUE	1	0.450921806717765	2		521	783	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1940256	1940256	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	197	279	0	ENST00000382891.5:c.1753G>T	p.Ala585Ser	p.A585S	ENST00000382891	NM_133335.3	585	Gca/Tca	8/22	0.450921806717765	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.450921806717765	2		279	371	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955141	55955141	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	134	324	0	ENST00000263923.4:c.3405-1G>A		p.X1135_splice	ENST00000263923	NM_002253.2	1135			0.450921806717765	2	FACETS	0.984	0.909	1	0.984	0.909	1	CLONAL	2	TRUE	0	0.450921806717765	2		324	302	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201800	66201800	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	274	516	0	ENST00000273854.3:c.2702T>A	p.Met901Lys	p.M901K	ENST00000273854	NM_004439.5	901	aTg/aAg	16/18	0.450921806717765	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.450921806717765	2		516	525	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155504	106155504	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	68	341	0	ENST00000380013.4:c.405A>T	p.Glu135Asp	p.E135D	ENST00000380013	NM_001127208.2	135	gaA/gaT	3/11	0.450921806717765	2	FACETS	0.89	0.779	1	0.445	0.389	0.504	CLONAL	1	TRUE	0	0.450921806717765	2		341	339	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541136	187541136	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	170	357	0	ENST00000441802.2:c.6604G>T	p.Val2202Phe	p.V2202F	ENST00000441802	NM_005245.3	2202	Gtc/Ttc	10/27	0.450921806717765	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.450921806717765	2		357	370	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629353	187629353	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	164	696	1	ENST00000441802.2:c.1629G>T	p.Trp543Cys	p.W543C	ENST00000441802	NM_005245.3	543	tgG/tgT	2/27	0.450921806717765	2	FACETS	0.912	0.838	0.988	0.456	0.419	0.494	CLONAL	1	TRUE	0	0.450921806717765	2		697	798	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495409	149495409	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	422	779	0	ENST00000261799.4:c.3238G>T	p.Val1080Leu	p.V1080L	ENST00000261799	NM_002609.3	1080	Gtg/Ttg	23/23	0.450921806717765	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.450921806717765	2		779	806	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020820	26020820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1197825644	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	159	314	0	ENST00000357647.3:c.103G>A	p.Gly35Ser	p.G35S	ENST00000357647	NM_003529.2	35	Ggc/Agc	1/1	0.327288311910431	4	FACETS	0.873	0.804	0.944	0.873	0.804	0.944	CLONAL	2	TRUE	2	0.450921806717765	4		314	586	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672759	30672759	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	367	786	0	ENST00000376406.3:c.4201G>T	p.Gly1401Cys	p.G1401C	ENST00000376406	NM_014641.2	1401	Ggc/Tgc	10/15	0.327288311910431	4	FACETS	0.984	0.934	1	0.984	0.934	1	CLONAL	2	TRUE	2	0.450921806717765	4		786	1200	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955032	93955032	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	42	275	0	ENST00000369303.4:c.2866G>T	p.Ala956Ser	p.A956S	ENST00000369303	NM_004440.3	956	Gcc/Tcc	16/17	0.450921806717765	3	FACETS	1	0.911	1	0.56	0.472	0.654	CLONAL	1	TRUE	1	0.450921806717765	3		275	204	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528764	8528764	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	183	332	0	ENST00000356435.5:c.368G>T	p.Arg123Met	p.R123M	ENST00000356435		123	aGg/aTg	4/35	0.450921806717765	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.450921806717765	2		332	370	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397783	139397783	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	105	476	0	ENST00000277541.6:c.5019-1G>T		p.X1673_splice	ENST00000277541	NM_017617.3	1673			0.450921806717765	2	FACETS	0.96	0.865	1	0.48	0.432	0.531	CLONAL	1	TRUE	0	0.450921806717765	2		476	485	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76777841	76777841	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	91	562	1	ENST00000373344.5:c.6875C>A	p.Pro2292Gln	p.P2292Q	ENST00000373344	NM_000489.3	2292	cCa/cAa	32/35	0.26161841274801	1	FACETS	0.739	0.66	0.822	0.739	0.66	0.822	INDETERMINATE	1	TRUE	0	0.450921806717765	1		563	423	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020186	123020186	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	138	748	0	ENST00000355640.3:c.674C>A	p.Pro225His	p.P225H	ENST00000355640		225	cCt/cAt	2/7	0.26161841274801	1	FACETS	0.666	0.607	0.728	0.666	0.607	0.728	INDETERMINATE	1	TRUE	0	0.450921806717765	1		748	712	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0031853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	88	319	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.136568419371096	5	FACETS	0.951	0.847	1	0.634	0.565	0.708	INDETERMINATE	2	TRUE	2	0.311253430077947	5		319	436	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0031853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	63	767	1	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	0.254552025488584	2	FACETS	0.67	0.58	0.769	0.335	0.29	0.385	SUBCLONAL	1	TRUE	0	0.311253430077947	2		768	604	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924382	131924382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757836195	NA	P-0031853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	26	330	0	ENST00000265335.6:c.1055G>A	p.Arg352His	p.R352H	ENST00000265335		352	cGt/cAt	8/25	1	2	FACETS	0.557	0.442	0.688	0.557	0.442	0.688	SUBCLONAL	1	TRUE	1	0.311253430077947	2		330	300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577514	7577515	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGA	novel	NA	P-0031853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	166	816	0	ENST00000269305.4:c.764_766dup	p.Ile255dup	p.I255dup	ENST00000269305	NM_001126112.2	255	aca/aTCAca	7/11	0.254552025488584	2	FACETS	1	0.986	1	0.671	0.617	0.727	CLONAL	1	TRUE	0	0.311253430077947	2		816	795	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004254	29004254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143093353	NA	P-0031853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	56	442	0	ENST00000282397.4:c.1039G>A	p.Val347Ile	p.V347I	ENST00000282397	NM_002019.4	347	Gta/Ata	8/30	0.250940755546341	3	FACETS	0.815	0.699	0.942	0.408	0.349	0.471	CLONAL	1	TRUE	1	0.311253430077947	3		442	510	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491480	18491480	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	41	395	0	ENST00000266497.5:c.1393G>T	p.Glu465Ter	p.E465*	ENST00000266497		465	Gag/Tag	8/31	0.311253430077947	1	FACETS	0.876	0.735	1	0.876	0.735	1	CLONAL	1	TRUE	0	0.311253430077947	1		395	254	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823850	3823850	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746728741	NA	P-0031853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	93	798	0	ENST00000262367.5:c.2365G>A	p.Ala789Thr	p.A789T	ENST00000262367	NM_004380.2	789	Gct/Act	13/31	0.254552025488584	2	FACETS	0.928	0.826	1	0.464	0.413	0.518	CLONAL	1	TRUE	0	0.311253430077947	2		798	644	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965623	25965623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	125	930	0	ENST00000435504.4:c.3583G>A	p.Val1195Met	p.V1195M	ENST00000435504		1195	Gtg/Atg	13/13	0.255489829326451	2	FACETS	1	0.917	1	0.507	0.459	0.558	CLONAL	1	TRUE	0	0.311253430077947	2		930	792	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924480	131924480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139372231	NA	P-0031853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	61	466	0	ENST00000265335.6:c.1153C>T	p.Arg385Cys	p.R385C	ENST00000265335		385	Cgt/Tgt	8/25	1	2	FACETS	0.818	0.707	0.939	0.818	0.707	0.939	CLONAL	1	TRUE	1	0.311253430077947	2		466	479	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468296	50468296	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	90	563	0	ENST00000331340.3:c.1531C>T	p.Arg511Ter	p.R511*	ENST00000331340	NM_006060.4	511	Cga/Tga	8/8	0.250940755546341	3	FACETS	1	0.95	1	0.563	0.5	0.629	CLONAL	1	TRUE	1	0.311253430077947	3		563	594	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922307	39922307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771933828	NA	P-0031853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	59	351	0	ENST00000378444.4:c.3865G>A	p.Gly1289Ser	p.G1289S	ENST00000378444	NM_001123385.1	1289	Ggc/Agc	9/15	0.117380868973707	4	FACETS	1	0.968	1	0.725	0.627	0.83	INDETERMINATE	1	TRUE	2	0.311253430077947	4		351	343	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5465595	5465595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148141792	NA	P-0031854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	112	337	0	ENST00000381577.3:c.779G>A	p.Arg260His	p.R260H	ENST00000381577	NM_014143.3	260	cGt/cAt	5/7	0.486992273210076	3	FACETS	0.876	0.798	0.957	0.876	0.798	0.957	CLONAL	2	TRUE	1	0.487784544469802	3		337	326	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37059000	37059000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63751448	NA	P-0031854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	80	373	0	ENST00000231790.2:c.794G>A	p.Arg265His	p.R265H	ENST00000231790	NM_000249.3	265	cGt/cAt	10/19	0.450726814200682	3	FACETS	0.847	0.748	0.952	0.423	0.374	0.476	CLONAL	1	TRUE	1	0.487784544469802	3		373	482	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640698	3640698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs546628836	NA	P-0031854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	169	742	1	ENST00000294008.3:c.2941G>A	p.Gly981Arg	p.G981R	ENST00000294008	NM_032444.2	981	Ggg/Agg	12/15	0.450726814200682	3	FACETS	0.714	0.654	0.775	0.357	0.327	0.388	SUBCLONAL	1	TRUE	1	0.487784544469802	3		743	1208	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	28	244	2	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.903	0.734	1	1	0.964	1	CLONAL	3	FALSE	1	0.164072779545507	2		246	126	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	152	586	2	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	0.164072779545507	7	FACETS	0.923	0.851	0.997			1	CLONAL	6	FALSE	NA	0.164072779545507	7		588	472	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178198	142178198	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778835776	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	92	340	0	ENST00000350721.4:c.7220G>A	p.Arg2407His	p.R2407H	ENST00000350721	NM_001184.3	2407	cGc/cAc	43/47	0.164072779545507	8	FACETS	0.99	0.907	1	1	0.984	1	CLONAL	10	FALSE	1	0.164072779545507	8		340	169	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	157	476	4	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	0.149434533075905	3	FACETS	1	0.96	1	1	0.992	1	CLONAL	4	FALSE	1	0.164072779545507	3		480	488	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180040015	180040015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564369853	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	192	703	0	ENST00000261937.6:c.3427G>A	p.Ala1143Thr	p.A1143T	ENST00000261937	NM_182925.4	1143	Gcc/Acc	25/30	1	2	FACETS	0.953	0.89	1	1	0.995	1	CLONAL	5	FALSE	1	0.164072779545507	2		703	491	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073432	8073432	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	161	548	0	ENST00000377482.5:c.1227del	p.Lys409AsnfsTer43	p.K409Nfs*43	ENST00000377482	NM_018948.3	409	aaA/aa	4/4	0.149434533075905	3	FACETS	0.965	0.894	1	1	0.993	1	CLONAL	5	FALSE	1	0.164072779545507	3		548	440	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11168275	11168275	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	214	567	0	ENST00000361445.4:c.7597A>G	p.Thr2533Ala	p.T2533A	ENST00000361445	NM_004958.3	2533	Aca/Gca	57/58	0.149434533075905	3	FACETS	1	0.974	1	1	0.995	1	CLONAL	5	FALSE	1	0.164072779545507	3		567	527	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598843	28598843	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146400597	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	291	728	2	ENST00000253063.3:c.403G>A	p.Glu135Lys	p.E135K	ENST00000253063	NM_031459.4	135	Gag/Aag	4/10	0.149434533075905	3	FACETS	1	0.964	1	1	0.996	1	CLONAL	5	FALSE	1	0.164072779545507	3		730	749	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321203	65321203	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	140	394	1	ENST00000342505.4:c.1637C>T	p.Pro546Leu	p.P546L	ENST00000342505	NM_002227.2	546	cCc/cTc	11/25	0.149434533075905	3	FACETS	1	0.946	1	1	0.993	1	CLONAL	5	FALSE	1	0.164072779545507	3		395	358	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	42	382	0	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	0.149434533075905	3	FACETS	1	0.882	1	1	0.963	1	CLONAL	3	FALSE	1	0.164072779545507	3		382	176	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339153	65339153	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1456317552	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	141	495	0	ENST00000342505.4:c.383G>A	p.Arg128His	p.R128H	ENST00000342505	NM_002227.2	128	cGt/cAt	5/25	0.149434533075905	3	FACETS	0.984	0.907	1	1	0.993	1	CLONAL	5	FALSE	1	0.164072779545507	3		495	378	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851292	156851292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758359269	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	189	624	0	ENST00000524377.1:c.2249G>A	p.Arg750His	p.R750H	ENST00000524377	NM_002529.3	750	cGt/cAt	17/17	0.149434533075905	3	FACETS	1	0.936	1	1	0.994	1	CLONAL	5	FALSE	1	0.164072779545507	3		624	497	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749983	162749983	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	136	453	0	ENST00000367921.3:c.2515C>T	p.Arg839Cys	p.R839C	ENST00000367921	NM_006182.2	839	Cgt/Tgt	18/18	0.149434533075905	3	FACETS	1	0.952	1	1	0.991	1	CLONAL	4	FALSE	1	0.164072779545507	3		453	426	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	90	461	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.983	0.884	1	1	0.99	1	CLONAL	4	FALSE	1	0.164072779545507	2		461	279	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	43	249	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	1	0.918	1	1	0.981	1	CLONAL	4	FALSE	1	0.164072779545507	2		249	119	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711026	114711028	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	106	179	0	ENST00000543371.1:c.254_256del	p.Glu85del	p.E85del	ENST00000543371	NM_001198531.1	84	GAA/-	2/14	1	2	FACETS	1	0.916	1	1	0.992	1	CLONAL	4	FALSE	1	0.164072779545507	2		179	320	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981827	101981827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	50	622	0	ENST00000282441.5:c.248C>T	p.Thr83Ile	p.T83I	ENST00000282441	NM_001130145.2	83	aCc/aTc	1/9	1	2	FACETS	0.67	0.566	0.784	0.67	0.566	0.784	SUBCLONAL	1	FALSE	1	0.164072779545507	2		622	910	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343132	118343132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	88	375	0	ENST00000534358.1:c.1258C>T	p.Arg420Trp	p.R420W	ENST00000534358	NM_005933.3	420	Cgg/Tgg	3/36	1	2	FACETS	0.925	0.829	1	1	0.99	1	CLONAL	4	FALSE	1	0.164072779545507	2		375	290	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432352	432352	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	53	199	0	ENST00000399788.2:c.2171A>T	p.Asp724Val	p.D724V	ENST00000399788	NM_001042603.1	724	gAc/gTc	16/28	0.164072779545507	5	FACETS	0.935	0.822	1	1	0.98	1	CLONAL	7	FALSE	2	0.164072779545507	5		199	123	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420784	49420784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369790149	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	217	571	0	ENST00000301067.7:c.14965C>T	p.Arg4989Trp	p.R4989W	ENST00000301067	NM_003482.3	4989	Cgg/Tgg	48/54	0.164072779545507	5	FACETS	0.986	0.925	1	1	0.994	1	CLONAL	6	FALSE	2	0.164072779545507	5		571	557	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438046	49438046	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1372083024	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	247	655	0	ENST00000301067.7:c.5125C>T	p.Arg1709Cys	p.R1709C	ENST00000301067	NM_003482.3	1709	Cgc/Tgc	21/54	0.164072779545507	5	FACETS	0.962	0.905	1	1	0.995	1	CLONAL	6	FALSE	2	0.164072779545507	5		655	650	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440536	49440536	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	257	641	0	ENST00000301067.7:c.4274T>C	p.Val1425Ala	p.V1425A	ENST00000301067	NM_003482.3	1425	gTg/gCg	15/54	0.164072779545507	5	FACETS	1	0.979	1	1	0.995	1	CLONAL	5	FALSE	2	0.164072779545507	5		641	718	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434452	121434452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	187	765	0	ENST00000257555.6:c.1216G>A	p.Ala406Thr	p.A406T	ENST00000257555		406	Gcc/Acc	6/10	0.164072779545507	5	FACETS	1	0.961	1	1	0.993	1	CLONAL	5	FALSE	2	0.164072779545507	5		765	542	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219552	133219552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373468985	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	138	569	0	ENST00000320574.5:c.4582G>A	p.Ala1528Thr	p.A1528T	ENST00000320574	NM_006231.2	1528	Gcc/Acc	36/49	0.164072779545507	5	FACETS	1	0.96	1	1	0.99	1	CLONAL	5	FALSE	2	0.164072779545507	5		569	392	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249827	133249827	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs761765763	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	121	398	0	ENST00000320574.5:c.1396A>G	p.Thr466Ala	p.T466A	ENST00000320574	NM_006231.2	466	Act/Gct	14/49	0.164072779545507	5	FACETS	1	0.953	1	1	0.989	1	CLONAL	5	FALSE	2	0.164072779545507	5		398	346	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28903854	28903854	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	150	496	0	ENST00000282397.4:c.2605G>A	p.Ala869Thr	p.A869T	ENST00000282397	NM_002019.4	869	Gcc/Acc	19/30	0.164072779545507	1	FACETS	1	0.94	1	1	0.994	1	CLONAL	4	FALSE	0	0.164072779545507	1		496	411	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576090	88576090	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs199642370	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	104	642	0	ENST00000360948.2:c.1583C>T	p.Thr528Met	p.T528M	ENST00000360948	NM_001012338.2	528	aCg/aTg	13/19	1	2	FACETS	0.901	0.811	0.995	1	0.99	1	CLONAL	3	FALSE	1	0.164072779545507	2		642	469	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633171	3633171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1218491919	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	269	806	1	ENST00000294008.3:c.5080G>A	p.Ala1694Thr	p.A1694T	ENST00000294008	NM_032444.2	1694	Gcc/Acc	14/15	1	2	FACETS	1	0.975	1	1	0.996	1	CLONAL	4	FALSE	1	0.164072779545507	2		807	772	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662330	67662330	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	184	442	0	ENST00000264010.4:c.1576A>G	p.Ser526Gly	p.S526G	ENST00000264010	NM_006565.3	526	Agc/Ggc	9/12	0.164072779545507	7	FACETS	1	0.957	1			1	CLONAL	6	FALSE	NA	0.164072779545507	7		442	508	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829701	72829701	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	190	720	0	ENST00000268489.5:c.6880C>T	p.Arg2294Ter	p.R2294*	ENST00000268489	NM_006885.3	2294	Cga/Tga	9/10	0.164072779545507	7	FACETS	1	0.959	1			1	CLONAL	6	FALSE	NA	0.164072779545507	7		720	523	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	147	475	1	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	0.164072779545507	7	FACETS	1	0.96	1			1	CLONAL	6	FALSE	NA	0.164072779545507	7		476	397	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341523	89341524	+	missense_variant	Missense_Mutation	DNP	CG	CG	AA	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	187	537	1	ENST00000301030.4:c.7546_7547delinsTT	p.Arg2516Phe	p.R2516F	ENST00000301030	NM_001256183.1	2516	CGt/TTt	10/13	0.109227635698439	0	FACETS	0.98	0.914	1			1	CLONAL	4	FALSE	0	0.164072779545507	0		538	486	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349356	89349356	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	264	945	2	ENST00000301030.4:c.3594del	p.Glu1199ArgfsTer119	p.E1199Rfs*119	ENST00000301030	NM_001256183.1	1198	aaA/aa	9/13	0.109227635698439	0	FACETS	0.904	0.851	0.957			1	CLONAL	4	FALSE	0	0.164072779545507	0		947	744	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349717	89349717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753662123	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	142	854	1	ENST00000301030.4:c.3233C>T	p.Ala1078Val	p.A1078V	ENST00000301030	NM_001256183.1	1078	gCg/gTg	9/13	0.109227635698439	0	FACETS	0.828	0.761	0.896			1	CLONAL	4	FALSE	0	0.164072779545507	0		855	437	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357122	89357122	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200994100	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	224	703	1	ENST00000301030.4:c.512G>A	p.Arg171His	p.R171H	ENST00000301030	NM_001256183.1	171	cGc/cAc	6/13	0.109227635698439	0	FACETS	0.854	0.8	0.91			1	CLONAL	4	FALSE	0	0.164072779545507	0		704	668	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579419	7579420	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs587783062	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	209	625	0	ENST00000269305.4:c.267dup	p.Ser90LeufsTer59	p.S90Lfs*59	ENST00000269305	NM_001126112.2	89	-/C	4/11	1	2	FACETS	1	0.968	1	1	0.996	1	CLONAL	4	FALSE	1	0.164072779545507	2		625	602	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	92	462	0	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	1	2	FACETS	1	0.951	1	1	0.991	1	CLONAL	4	FALSE	1	0.164072779545507	2		462	258	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17124920	17124920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762370059	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	177	451	0	ENST00000285071.4:c.802C>T	p.Arg268Trp	p.R268W	ENST00000285071	NM_144997.5	268	Cgg/Tgg	8/14	1	2	FACETS	1	0.955	1	1	0.995	1	CLONAL	4	FALSE	1	0.164072779545507	2		451	519	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486046	29486046	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	25	362	0	ENST00000356175.3:c.223G>A	p.Ala75Thr	p.A75T	ENST00000356175	NM_000267.3	75	Gct/Act	3/57	1	2	FACETS	1	0.846	1	1	0.967	1	CLONAL	4	FALSE	1	0.164072779545507	2		362	73	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685596	29685596	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	85	503	1	ENST00000356175.3:c.8006A>G	p.Tyr2669Cys	p.Y2669C	ENST00000356175	NM_000267.3	2669	tAc/tGc	54/57	1	2	FACETS	0.964	0.869	1	1	0.99	1	CLONAL	5	FALSE	1	0.164072779545507	2		504	215	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38504637	38504637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751370458	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	239	660	0	ENST00000254066.5:c.248G>A	p.Arg83His	p.R83H	ENST00000254066	NM_000964.3	83	cGc/cAc	3/9	1	2	FACETS	1	0.961	1	1	0.996	1	CLONAL	4	FALSE	1	0.164072779545507	2		660	706	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40874920	40874920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756635466	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	91	573	0	ENST00000428826.2:c.380C>T	p.Thr127Met	p.T127M	ENST00000428826		127	aCg/aTg	6/21	1	2	FACETS	1	0.96	1	1	0.991	1	CLONAL	4	FALSE	1	0.164072779545507	2		573	247	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858199	59858199	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	97	400	0	ENST00000259008.2:c.1794+2T>C		p.X598_splice	ENST00000259008	NM_032043.2	598			1	2	FACETS	1	0.939	1	1	0.991	1	CLONAL	5	FALSE	1	0.164072779545507	2		400	227	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612209	1612209	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs915880927	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	134	422	0	ENST00000344749.5:c.1810C>T	p.Arg604Ter	p.R604*	ENST00000344749	NM_001136139.2	604	Cga/Tga	18/19	0.113413732973168	4	FACETS	1	0.967	1	1	0.993	1	CLONAL	6	FALSE	2	0.164072779545507	4		422	293	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145614	11145614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1482864360	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	171	464	0	ENST00000358026.2:c.3976G>A	p.Glu1326Lys	p.E1326K	ENST00000358026	NM_001128849.1	1326	Gag/Aag	29/36	0.113413732973168	4	FACETS	1	0.968	1	1	0.994	1	CLONAL	5	FALSE	2	0.164072779545507	4		464	453	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375544	15375544	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1405614933	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	261	813	1	ENST00000263377.2:c.883A>C	p.Thr295Pro	p.T295P	ENST00000263377	NM_058243.2	295	Acc/Ccc	6/20	0.113413732973168	4	FACETS	0.98	0.922	1	1	0.996	1	CLONAL	5	FALSE	2	0.164072779545507	4		814	756	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278070	18278070	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs886041602	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	248	604	0	ENST00000222254.8:c.1690A>G	p.Lys564Glu	p.K564E	ENST00000222254	NM_005027.3	564	Aag/Gag	13/16	0.113413732973168	4	FACETS	1	0.97	1	1	0.996	1	CLONAL	5	FALSE	2	0.164072779545507	4		604	671	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974420	18974420	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs189120195	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	121	345	0	ENST00000262803.5:c.2774C>T	p.Pro925Leu	p.P925L	ENST00000262803	NM_002911.3	925	cCg/cTg	19/24	0.113413732973168	4	FACETS	0.992	0.908	1	1	0.991	1	CLONAL	5	FALSE	2	0.164072779545507	4		345	346	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257144	19257144	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	122	484	2	ENST00000162023.5:c.819del	p.Thr274ProfsTer?	p.T274Pfs*?	ENST00000162023		273	ccC/cc	12/13	0.113413732973168	4	FACETS	1	0.967	1	1	0.991	1	CLONAL	4	FALSE	2	0.164072779545507	4		486	386	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383692	42383692	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202097187	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	197	560	1	ENST00000221972.3:c.467C>T	p.Ala156Val	p.A156V	ENST00000221972	NM_021601.3	156	gCg/gTg	3/5	0.113413732973168	4	FACETS	0.94	0.875	1	1	0.994	1	CLONAL	5	FALSE	2	0.164072779545507	4		561	595	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	627	838	1	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	0.113413732973168	4	FACETS	1	0.985	1			1	CLONAL	10	FALSE	2	0.164072779545507	4		839	875	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139958	50139958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369508242	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	325	696	1	ENST00000246792.3:c.371C>T	p.Thr124Met	p.T124M	ENST00000246792	NM_006270.3	124	aCg/aTg	4/6	0.113413732973168	4	FACETS	0.935	0.887	0.983	1	0.997	1	CLONAL	6	FALSE	2	0.164072779545507	4		697	822	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456453	29456453	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1558630501	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	204	590	2	ENST00000389048.3:c.2465del	p.Gly822ValfsTer9	p.G822Vfs*9	ENST00000389048	NM_004304.4	822	gGt/gt	14/29	1	2	FACETS	0.903	0.844	0.963	1	0.996	1	CLONAL	5	FALSE	1	0.164072779545507	2		592	551	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61713075	61713075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	45	321	0	ENST00000401558.2:c.2336del	p.Pro779LeufsTer28	p.P779Lfs*28	ENST00000401558	NM_003400.3	779	cCt/ct	20/25	1	2	FACETS	1	0.884	1	1	0.981	1	CLONAL	4	FALSE	1	0.164072779545507	2		321	133	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046944	128046946	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs761456808	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	143	525	9	ENST00000285398.2:c.789_791del	p.Glu264del	p.E264del	ENST00000285398	NM_000122.1	263	gaAGAg/gag	6/15	1	2	FACETS	1	0.952	1	1	0.994	1	CLONAL	4	FALSE	1	0.164072779545507	2		534	416	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622622	158622622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	94	449	1	ENST00000263640.3:c.877G>A	p.Asp293Asn	p.D293N	ENST00000263640	NM_001105.4	293	Gac/Aac	8/11	1	2	FACETS	1	0.932	1	1	0.991	1	CLONAL	4	FALSE	1	0.164072779545507	2		450	275	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150030	202150030	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs931648756	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	189	531	1	ENST00000358485.4:c.1471C>T	p.Arg491Ter	p.R491*	ENST00000358485	NM_001080125.1	491	Cga/Tga	8/9	1	2	FACETS	1	0.978	1	1	0.995	1	CLONAL	4	FALSE	1	0.164072779545507	2		532	517	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495230	212495230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746560611	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	32	477	0	ENST00000342788.4:c.2036G>A	p.Ser679Asn	p.S679N	ENST00000342788	NM_005235.2	679	aGc/aAc	17/28	1	2	FACETS	1	0.861	1	1	0.963	1	CLONAL	2	FALSE	1	0.164072779545507	2		477	184	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587117	212587117	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	45	342	0	ENST00000342788.4:c.883+1G>A		p.X295_splice	ENST00000342788	NM_005235.2	295			1	2	FACETS	1	0.88	1	1	0.982	1	CLONAL	5	FALSE	1	0.164072779545507	2		342	108	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386391	31386391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1051749732	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	179	529	0	ENST00000328111.2:c.1616G>A	p.Arg539Gln	p.R539Q	ENST00000328111	NM_006892.3	539	cGg/cAg	15/23	1	2	FACETS	0.928	0.864	0.994	1	0.995	1	CLONAL	5	FALSE	1	0.164072779545507	2		529	470	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733321	40733321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	94	454	1	ENST00000373198.4:c.3485C>T	p.Ala1162Val	p.A1162V	ENST00000373198	NM_133170.3	1162	gCg/gTg	26/32	1	2	FACETS	0.958	0.863	1	1	0.99	1	CLONAL	4	FALSE	1	0.164072779545507	2		455	299	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130441	29130441	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	157	545	0	ENST00000328354.6:c.269del	p.Pro90LeufsTer20	p.P90Lfs*20	ENST00000328354	NM_007194.3	90	cCt/ct	2/15	1	2	FACETS	0.965	0.89	1	1	0.994	1	CLONAL	4	FALSE	1	0.164072779545507	2		545	496	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161819	47161819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	134	378	0	ENST00000409792.3:c.4307C>T	p.Thr1436Ile	p.T1436I	ENST00000409792	NM_014159.6	1436	aCa/aTa	3/21	0.164072779545507	8	FACETS	1	0.924	1	0.722	0.661	0.786	CLONAL	5	FALSE	1	0.164072779545507	8		378	482	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936552	49936552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771332656	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	225	625	0	ENST00000296474.3:c.1375G>A	p.Val459Ile	p.V459I	ENST00000296474	NM_002447.2	459	Gtc/Atc	2/20	0.164072779545507	8	FACETS	0.983	0.917	1	0.702	0.655	0.75	CLONAL	5	FALSE	1	0.164072779545507	8		625	833	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440297	52440297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759024400	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	218	536	0	ENST00000460680.1:c.755G>A	p.Arg252His	p.R252H	ENST00000460680	NM_004656.3	252	cGt/cAt	9/17	0.164072779545507	8	FACETS	0.935	0.871	1	0.668	0.622	0.715	CLONAL	5	FALSE	1	0.164072779545507	8		536	848	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564507	55564507	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766253584	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	128	408	0	ENST00000288135.5:c.395C>T	p.Thr132Met	p.T132M	ENST00000288135	NM_000222.2	132	aCg/aTg	3/21	1	2	FACETS	0.94	0.864	1	1	0.993	1	CLONAL	5	FALSE	1	0.164072779545507	2		408	332	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968579	55968579	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	156	580	0	ENST00000263923.4:c.2084del	p.Pro695LeufsTer14	p.P695Lfs*14	ENST00000263923	NM_002253.2	695	cCt/ct	14/30	1	2	FACETS	1	0.937	1	1	0.994	1	CLONAL	4	FALSE	1	0.164072779545507	2		580	468	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217127	66217127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767617774	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	65	434	0	ENST00000273854.3:c.2488G>A	p.Glu830Lys	p.E830K	ENST00000273854	NM_004439.5	830	Gag/Aag	14/18	1	2	FACETS	0.913	0.804	1	1	0.986	1	CLONAL	4	FALSE	1	0.164072779545507	2		434	217	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977992	131977992	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	100	476	1	ENST00000265335.6:c.3875A>G	p.Asn1292Ser	p.N1292S	ENST00000265335		1292	aAc/aGc	25/25	1	2	FACETS	0.956	0.869	1	1	0.991	1	CLONAL	5	FALSE	1	0.164072779545507	2		477	255	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709530	176709530	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749277550	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	75	367	1	ENST00000439151.2:c.5957G>A	p.Arg1986His	p.R1986H	ENST00000439151	NM_022455.4	1986	cGc/cAc	19/23	1	2	FACETS	0.91	0.813	1	1	0.989	1	CLONAL	5	FALSE	1	0.164072779545507	2		368	201	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94067986	94067986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150543233	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	81	245	0	ENST00000369303.4:c.976G>A	p.Val326Ile	p.V326I	ENST00000369303	NM_004440.3	326	Gtt/Att	4/17	1	2	FACETS	1	0.949	1	1	0.989	1	CLONAL	4	FALSE	1	0.164072779545507	2		245	225	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109319849	109319849	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	172	455	0	ENST00000436639.2:c.839T>G	p.Ile280Ser	p.I280S	ENST00000436639	NM_014454.2	280	aTc/aGc	5/10	1	2	FACETS	1	0.961	1	1	0.995	1	CLONAL	5	FALSE	1	0.164072779545507	2		455	401	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946143	13946143	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	328	473	0	ENST00000405192.2:c.953del	p.Leu318TrpfsTer2	p.L318Wfs*2	ENST00000405192	NM_001163147.1	318	tTg/tg	10/12	0.164072779545507	7	FACETS	0.974	0.931	1	1	0.996	1	CLONAL	10	FALSE	1	0.164072779545507	7		473	579	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367244	50367244	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	69	248	0	ENST00000331340.3:c.56del	p.Pro19LeufsTer2	p.P19Lfs*2	ENST00000331340	NM_006060.4	17	agC/ag	3/8	0.164072779545507	7	FACETS	0.901	0.791	1	0.601	0.527	0.679	CLONAL	4	FALSE	1	0.164072779545507	7		248	329	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81340804	81340804	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	30	281	0	ENST00000222390.5:c.1437T>A	p.Asn479Lys	p.N479K	ENST00000222390	NM_000601.4	479	aaT/aaA	12/18	0.164072779545507	7	FACETS	0.982	0.81	1	0.819	0.675	0.973	CLONAL	5	FALSE	1	0.164072779545507	7		281	105	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508133	106508133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1346474355	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	47	189	0	ENST00000359195.3:c.127G>A	p.Val43Met	p.V43M	ENST00000359195	NM_002649.2	43	Gtg/Atg	2/11	0.164072779545507	7	FACETS	1	0.859	1	0.67	0.572	0.774	CLONAL	4	FALSE	1	0.164072779545507	7		189	201	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508932	106508932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	188	338	0	ENST00000359195.3:c.926C>T	p.Thr309Met	p.T309M	ENST00000359195	NM_002649.2	309	aCg/aTg	2/11	0.164072779545507	7	FACETS	0.995	0.932	1	1	0.99	1	CLONAL	8	FALSE	1	0.164072779545507	7		338	406	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879229	151879229	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs763438739	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	225	527	1	ENST00000262189.6:c.5716C>T	p.Arg1906Ter	p.R1906*	ENST00000262189	NM_170606.2	1906	Cga/Tga	36/59	0.164072779545507	7	FACETS	0.999	0.945	1	1	0.994	1	CLONAL	9	FALSE	1	0.164072779545507	7		528	430	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	60	340	2	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	1	2	FACETS	1	0.922	1	1	0.987	1	CLONAL	5	FALSE	1	0.164072779545507	2		342	139	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006054	22006054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	223	532	1	ENST00000276925.6:c.349G>A	p.Val117Met	p.V117M	ENST00000276925	NM_004936.3	117	Gtg/Atg	2/2	0.164072779545507	1	FACETS	0.914	0.858	0.97	1	0.996	1	CLONAL	5	FALSE	0	0.164072779545507	1		533	546	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249884	110249884	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1434085608	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	159	549	2	ENST00000374672.4:c.791C>T	p.Ala264Val	p.A264V	ENST00000374672	NM_004235.4	264	gCg/gTg	3/5	0.164072779545507	1	FACETS	1	0.974	1	1	0.994	1	CLONAL	4	FALSE	0	0.164072779545507	1		551	402	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405177	139405177	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1248255443	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	207	699	0	ENST00000277541.6:c.2668G>A	p.Gly890Ser	p.G890S	ENST00000277541	NM_017617.3	890	Ggc/Agc	17/34	0.164072779545507	1	FACETS	0.992	0.927	1	1	0.995	1	CLONAL	4	FALSE	0	0.164072779545507	1		699	584	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418336	139418336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768517628	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	237	769	1	ENST00000277541.6:c.236G>A	p.Arg79His	p.R79H	ENST00000277541	NM_017617.3	79	cGc/cAc	3/34	0.164072779545507	1	FACETS	0.965	0.905	1	1	0.996	1	CLONAL	4	FALSE	0	0.164072779545507	1		770	687	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923043	44923046	+	frameshift_variant	Frame_Shift_Del	DEL	AACT	AACT	-	novel	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	215	239	0	ENST00000377967.4:c.1905_1908del	p.Gln635HisfsTer55	p.Q635Hfs*55	ENST00000377967	NM_021140.2	635	cAACTa/ca	16/29	0.164072779545507	2	FACETS	1	0.984	1			1	CLONAL	9	FALSE	NA	0.164072779545507	2		239	277	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80149980	80149980	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs758546167	NA	P-0031855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	38	402	0	ENST00000265081.6:c.2845C>T	p.Gln949Ter	p.Q949*	ENST00000265081	NM_002439.4	949	Cag/Tag	21/24	1	2	FACETS	0.936	0.798	1	1	0.978	1	CLONAL	5	FALSE	1	0.164072779545507	2		402	99	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0031856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	65	289	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	0.404634975418054	2		289	289	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0031856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	175	447	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	0.404634975418054	2		447	587	SUCCESS
AR	367	MSKCC	GRCh37	X	66943552	66943552	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137852578	NA	P-0031856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	277	219	0	ENST00000374690.3:c.2632A>G	p.Thr878Ala	p.T878A	ENST00000374690	NM_000044.3	878	Act/Gct	8/8	0.404634975418054	6	FACETS	1	0.978	1			1	CLONAL	4	TRUE	NA	0.404634975418054	6		219	586	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457764	149457764	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	273	472	1	ENST00000286301.3:c.640C>T	p.Arg214Trp	p.R214W	ENST00000286301	NM_005211.3	214	Cgg/Tgg	5/22	0.342970798707958	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.404634975418054	3		473	704	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696688	47696688	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519971	NA	P-0031856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	97	482	0	ENST00000347630.2:c.260A>G	p.Tyr87Cys	p.Y87C	ENST00000347630	NM_001007230.1	87	tAc/tGc	5/11	1	2	FACETS	0.852	0.761	0.947	0.852	0.761	0.947	CLONAL	1	TRUE	1	0.404634975418054	2		482	563	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955016	93955016	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	10	238	0	ENST00000369303.4:c.2882A>C	p.Glu961Ala	p.E961A	ENST00000369303	NM_004440.3	961	gAg/gCg	16/17	0.404634975418054	1	FACETS	0.258	0.175	0.361	0.258	0.175	0.361	SUBCLONAL	1	TRUE	0	0.404634975418054	1		238	153	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771320	68771320	+	start_lost	Translation_Start_Site	SNP	T	T	C	rs1555509623	NA	P-0031857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	41	224	0	ENST00000261769.5:c.2T>C	p.Met1?	p.M1?	ENST00000261769	NM_004360.3	1	aTg/aCg	1/16	0.463223301431801	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	0	0.463223301431801	1		224	111	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395624	31395624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756972254	NA	P-0031857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	24	574	0	ENST00000328111.2:c.2477G>A	p.Arg826His	p.R826H	ENST00000328111	NM_006892.3	826	cGc/cAc	23/23	1	2	FACETS	0.289	0.226	0.361	0.289	0.226	0.361	SUBCLONAL	1	FALSE	1	0.463223301431801	2		574	359	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599997	28599997	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	18	576	0	ENST00000253063.3:c.879G>C	p.Glu293Asp	p.E293D	ENST00000253063	NM_031459.4	293	gaG/gaC	6/10	1	2	FACETS	0.275	0.206	0.355	0.275	0.206	0.355	SUBCLONAL	1	FALSE	1	0.463223301431801	2		576	283	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798977	45798977	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	35	663	1	ENST00000450313.1:c.368T>C	p.Leu123Pro	p.L123P	ENST00000450313	NM_012222.2	123	cTg/cCg	4/16	1	2	FACETS	0.607	0.5	0.725	0.607	0.5	0.725	SUBCLONAL	1	FALSE	1	0.463223301431801	2		664	249	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522600	176522600	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	43	579	2	ENST00000292408.4:c.1697G>A	p.Arg566His	p.R566H	ENST00000292408	NM_213647.1	566	cGc/cAc	13/18	1	2	FACETS	0.582	0.489	0.684	0.582	0.489	0.684	SUBCLONAL	1	FALSE	1	0.463223301431801	2		581	319	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636865	176636865	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	19	442	0	ENST00000439151.2:c.1465G>C	p.Glu489Gln	p.E489Q	ENST00000439151	NM_022455.4	489	Gag/Cag	5/23	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	FALSE	1	0.463223301431801	2		442	65	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056199	26056210	+	inframe_deletion	In_Frame_Del	DEL	TTCTTAGCGCTC	TTCTTAGCGCTC	-	novel	NA	P-0031857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	54	558	0	ENST00000343677.2:c.447_458del	p.Ser150_Lys153del	p.S150_K153del	ENST00000343677	NM_005319.3	149	aaGAGCGCTAAGAAa/aaa	1/1	0.174651217754718	4	FACETS	1	0.938	1	0.584	0.502	0.672	INDETERMINATE	1	FALSE	2	0.463223301431801	4		558	292	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	130	258	0				ENST00000310581	NM_198253.2	-/1132			0.259786755898543	1	FACETS	0.545	0.5	0.592	0.545	0.5	0.592	INDETERMINATE	1	TRUE	0	0.776279605601623	1		258	376	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	79	427	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.619551970813035	3	FACETS	0.323	0.283	0.365	0.161	0.141	0.183	SUBCLONAL	1	TRUE	1	0.776279605601623	3		427	876	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	28	519	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.078	0.061	0.096	0.078	0.061	0.096	SUBCLONAL	1	TRUE	1	0.776279605601623	2		519	930	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	87	585	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	NA	2	FACETS	0.431	0.382	0.483			1	INDETERMINATE	1	TRUE	NA	0.776279605601623	2		585	520	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805369	32805369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	230	468	0	ENST00000374899.4:c.553G>A	p.Asp185Asn	p.D185N	ENST00000374899	NM_018833.2	185	Gac/Aac	3/12	1	2	FACETS	0.976	0.917	1	0.976	0.917	1	CLONAL	1	TRUE	1	0.776279605601623	2		468	607	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	24	515	0	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	1	2	FACETS	0.084	0.065	0.106	0.084	0.065	0.106	SUBCLONAL	1	TRUE	1	0.776279605601623	2		515	737	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989592	212989592	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	167	329	0	ENST00000342788.4:c.119C>T	p.Ser40Phe	p.S40F	ENST00000342788	NM_005235.2	40	tCt/tTt	2/28	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.776279605601623	2		329	369	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480341	56480341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	228	457	0	ENST00000267101.3:c.448G>A	p.Glu150Lys	p.E150K	ENST00000267101	NM_001982.3	150	Gag/Aag	4/28	1	2	FACETS	0.874	0.819	0.931	0.874	0.819	0.931	CLONAL	1	TRUE	1	0.776279605601623	2		457	672	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707939	47707939	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1553370404	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	240	410	0	ENST00000233146.2:c.2563C>T	p.Gln855Ter	p.Q855*	ENST00000233146	NM_000251.2	855	Cag/Tag	15/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.776279605601623	2		410	608	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032045	26032045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	202	418	1	ENST00000244661.2:c.244G>A	p.Asp82Asn	p.D82N	ENST00000244661	NM_003537.3	82	Gat/Aat	1/1	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.776279605601623	2		419	497	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060925	38060925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1388855660	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	145	429	0	ENST00000250448.2:c.1064C>T	p.Ser355Leu	p.S355L	ENST00000250448	NM_004496.3	355	tCa/tTa	2/2	0.205033699377857	2	FACETS	0.775	0.712	0.84	0.388	0.356	0.42	INDETERMINATE	1	TRUE	0	0.776279605601623	2		429	482	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733038	74733038	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	245	446	0	ENST00000359995.5:c.205G>A	p.Glu69Lys	p.E69K	ENST00000359995	NM_001195427.1	69	Gag/Aag	1/3	0.230567792896459	3	FACETS	1	0.991	1	0.653	0.614	0.693	INDETERMINATE	1	TRUE	1	0.776279605601623	3		446	671	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247243	153247243	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	465	389	0	ENST00000281708.4:c.1559A>T	p.Asp520Val	p.D520V	ENST00000281708	NM_033632.3	520	gAt/gTt	10/12	0.776279605601623	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.776279605601623	2		389	582	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44910953	44910953	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	151	112	0	ENST00000377967.4:c.655-1G>A		p.X219_splice	ENST00000377967	NM_021140.2	219			1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.776279605601623	1		112	182	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504620	103504620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	145	277	0	ENST00000355739.4:c.241C>T	p.Pro81Ser	p.P81S	ENST00000355739	NM_000123.3	81	Cca/Tca	2/15	0.20756715765797	2	FACETS	0.759	0.697	0.823	0.38	0.348	0.412	INDETERMINATE	1	TRUE	0	0.776279605601623	2		277	492	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162747	47162747	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	407	413	0	ENST00000409792.3:c.3379C>G	p.Gln1127Glu	p.Q1127E	ENST00000409792	NM_014159.6	1127	Caa/Gaa	3/21	0.619551970813035	3	FACETS	0.963	0.924	1	0.963	0.924	1	CLONAL	2	TRUE	1	0.776279605601623	3		413	756	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183766	10183766	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200885420	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	580	605	0	ENST00000256474.2:c.235C>T	p.Arg79Cys	p.R79C	ENST00000256474	NM_000551.3	79	Cgc/Tgc	1/3	0.776279605601623	3	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.776279605601623	3		605	976	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832721	3832721	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	253	502	0	ENST00000262367.5:c.1537C>T	p.Gln513Ter	p.Q513*	ENST00000262367	NM_004380.2	513	Caa/Taa	6/31	0.368818867280694	1	FACETS	0.7	0.661	0.739	0.7	0.661	0.739	INDETERMINATE	1	TRUE	0	0.776279605601623	1		502	570	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430778	181430778	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	276	669	0	ENST00000325404.1:c.630G>A	p.Met210Ile	p.M210I	ENST00000325404	NM_003106.3	210	atG/atA	1/1	0.619551970813035	3	FACETS	1	0.951	1	0.506	0.476	0.537	CLONAL	1	TRUE	1	0.776279605601623	3		669	975	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456514	29456514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	342	648	0	ENST00000389048.3:c.2404G>A	p.Glu802Lys	p.E802K	ENST00000389048	NM_004304.4	802	Gaa/Aaa	14/29	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.776279605601623	2		648	856	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71050137	71050137	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	262	335	0	ENST00000318789.4:c.1048C>T	p.Gln350Ter	p.Q350*	ENST00000318789	NM_032682.5	350	Cag/Tag	13/21	0.619551970813035	3	FACETS	0.797	0.753	0.841	0.797	0.753	0.841	SUBCLONAL	2	TRUE	1	0.776279605601623	3		335	588	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082599	16082599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	107	234	0	ENST00000281043.3:c.413G>A	p.Arg138His	p.R138H	ENST00000281043	NM_005378.4	138	cGc/cAc	2/3	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.776279605601623	2		234	232	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180841	106180841	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1315871913	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	333	365	0	ENST00000380013.4:c.3869C>T	p.Ser1290Leu	p.S1290L	ENST00000380013	NM_001127208.2	1290	tCa/tTa	7/11	0.776279605601623	2	FACETS	0.973	0.94	1	0.973	0.94	1	CLONAL	2	TRUE	0	0.776279605601623	2		365	441	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258691	115258691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	299	344	0	ENST00000369535.4:c.91G>A	p.Glu31Lys	p.E31K	ENST00000369535	NM_002524.4	31	Gaa/Aaa	2/7	0.182108268461857	5	FACETS	1	0.991	1	0.803	0.762	0.845	INDETERMINATE	2	TRUE	2	0.776279605601623	5		344	692	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349471	73349471	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777245855	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	188	471	0	ENST00000377767.4:c.865G>A	p.Glu289Lys	p.E289K	ENST00000377767	NM_014953.3	289	Gaa/Aaa	6/21	NA	2	FACETS	0.902	0.84	0.966			1	INDETERMINATE	1	TRUE	NA	0.776279605601623	2		471	537	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273887	10273887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	267	694	1	ENST00000330684.3:c.382C>T	p.His128Tyr	p.H128Y	ENST00000330684	NM_001134407.1	128	Cat/Tat	2/13	0.368818867280694	1	FACETS	0.562	0.529	0.595	0.562	0.529	0.595	INDETERMINATE	1	TRUE	0	0.776279605601623	1		695	749	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074358	8074358	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	249	312	0	ENST00000377482.5:c.301G>A	p.Glu101Lys	p.E101K	ENST00000377482	NM_018948.3	101	Gaa/Aaa	4/4	0.182108268461857	5	FACETS	1	0.987	1	0.769	0.725	0.813	INDETERMINATE	2	TRUE	2	0.776279605601623	5		312	602	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17359607	17359607	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	37	405	0	ENST00000375499.3:c.234G>C	p.Lys78Asn	p.K78N	ENST00000375499	NM_003000.2	78	aaG/aaC	3/8	0.182108268461857	5	FACETS	0.3	0.247	0.361	0.1	0.082	0.121	INDETERMINATE	1	TRUE	2	0.776279605601623	5		405	687	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803571	43803571	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	320	562	0	ENST00000372470.3:c.52C>T	p.Gln18Ter	p.Q18*	ENST00000372470	NM_005373.2	18	Caa/Taa	1/12	0.182108268461857	5	FACETS	1	0.991	1	0.796	0.756	0.837	INDETERMINATE	2	TRUE	2	0.776279605601623	5		562	747	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736346	85736346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	340	374	0	ENST00000370580.1:c.301G>A	p.Asp101Asn	p.D101N	ENST00000370580	NM_003921.4	101	Gat/Aat	2/3	0.182108268461857	5	FACETS	1	0.993	1	0.826	0.786	0.866	INDETERMINATE	2	TRUE	2	0.776279605601623	5		374	765	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944377	206944377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	36	452	0	ENST00000423557.1:c.253G>A	p.Glu85Lys	p.E85K	ENST00000423557	NM_000572.2	85	Gag/Aag	3/5	0.182108268461857	5	FACETS	0.293	0.24	0.353	0.098	0.08	0.118	INDETERMINATE	1	TRUE	2	0.776279605601623	5		452	685	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69458740	69458740	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	213	409	0	ENST00000227507.2:c.555C>A	p.Phe185Leu	p.F185L	ENST00000227507	NM_053056.2	185	ttC/ttA	3/5	0.259786755898543	1	FACETS	0.751	0.707	0.796	0.751	0.707	0.796	INDETERMINATE	1	TRUE	0	0.776279605601623	1		409	447	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989556	85989556	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	163	368	0	ENST00000263360.6:c.1315C>T	p.Arg439Ter	p.R439*	ENST00000263360	NM_003797.3	439	Cga/Tga	12/12	0.259786755898543	1	FACETS	0.494	0.456	0.533	0.494	0.456	0.533	INDETERMINATE	1	TRUE	0	0.776279605601623	1		368	520	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115532	108115532	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs762998620	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	253	445	0	ENST00000278616.4:c.680C>G	p.Ser227Ter	p.S227*	ENST00000278616	NM_000051.3	227	tCa/tGa	7/63	0.259786755898543	1	FACETS	0.768	0.727	0.81	0.768	0.727	0.81	INDETERMINATE	1	TRUE	0	0.776279605601623	1		445	519	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125513729	125513729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	274	497	0	ENST00000428830.2:c.857C>T	p.Ser286Phe	p.S286F	ENST00000428830	NM_001114121.2	286	tCt/tTt	9/14	0.259786755898543	1	FACETS	0.726	0.688	0.764	0.726	0.688	0.764	INDETERMINATE	1	TRUE	0	0.776279605601623	1		497	595	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233105	69233105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	190	323	0	ENST00000462284.1:c.970C>T	p.His324Tyr	p.H324Y	ENST00000462284	NM_002392.5	324	Cat/Tat	11/11	1	2	FACETS	0.943	0.879	1	0.943	0.879	1	CLONAL	1	TRUE	1	0.776279605601623	2		323	519	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120791158	120791158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	304	544	0	ENST00000257552.2:c.677C>T	p.Thr226Ile	p.T226I	ENST00000257552	NM_002442.3	226	aCc/aTc	10/15	1	2	FACETS	0.993	0.94	1	0.993	0.94	1	CLONAL	1	TRUE	1	0.776279605601623	2		544	789	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254001	133254001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	271	482	0	ENST00000320574.5:c.749G>A	p.Gly250Glu	p.G250E	ENST00000320574	NM_006231.2	250	gGa/gAa	8/49	1	2	FACETS	0.941	0.887	0.996	0.941	0.887	0.996	CLONAL	1	TRUE	1	0.776279605601623	2		482	742	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26927979	26927979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	338	434	0	ENST00000381527.3:c.418C>T	p.His140Tyr	p.H140Y	ENST00000381527	NM_001260.1	140	Cac/Tac	4/13	0.205033699377857	2	FACETS	1	0.994	1	0.645	0.615	0.675	INDETERMINATE	1	TRUE	0	0.776279605601623	2		434	675	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32905152	32905152	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	184	345	0	ENST00000380152.3:c.778G>T	p.Glu260Ter	p.E260*	ENST00000380152		260	Gaa/Taa	9/27	0.205033699377857	2	FACETS	0.805	0.747	0.864	0.402	0.373	0.432	INDETERMINATE	1	TRUE	0	0.776279605601623	2		345	589	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937011	48937029	+	frameshift_variant	Frame_Shift_Del	DEL	GTGCACGGATAGCAAAACA	GTGCACGGATAGCAAAACA	CC	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	161	324	1	ENST00000267163.4:c.779_797delinsCC	p.Ser260ThrfsTer5	p.S260Tfs*5	ENST00000267163	NM_000321.2	260	aGTGCACGGATAGCAAAACAa/aCCa	8/27	0.205033699377857	2	FACETS	0.974	0.903	1	0.487	0.451	0.523	INDETERMINATE	1	TRUE	0	0.776279605601623	2		325	426	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033964	49033964	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778859	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	158	357	0	ENST00000267163.4:c.2101G>A	p.Asp701Asn	p.D701N	ENST00000267163	NM_000321.2	701	Gac/Aac	20/27	0.205033699377857	2	FACETS	0.698	0.643	0.755	0.349	0.321	0.378	INDETERMINATE	1	TRUE	0	0.776279605601623	2		357	583	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606118	81606118	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	319	495	0	ENST00000298171.2:c.788T>C	p.Leu263Pro	p.L263P	ENST00000298171	NM_000369.2	263	cTt/cCt	9/10	0.205033699377857	2	FACETS	1	0.993	1	0.639	0.609	0.669	INDETERMINATE	1	TRUE	0	0.776279605601623	2		495	643	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675112	40675112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	326	701	0	ENST00000249776.8:c.76C>T	p.Pro26Ser	p.P26S	ENST00000249776	NM_033286.3	26	Cca/Tca	1/9	0.253819485825096	1	FACETS	0.601	0.57	0.633	0.601	0.57	0.633	INDETERMINATE	1	TRUE	0	0.776279605601623	1		701	855	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42026732	42026732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	223	354	0	ENST00000219905.7:c.3856G>A	p.Glu1286Lys	p.E1286K	ENST00000219905	NM_001164273.1	1286	Gaa/Aaa	12/24	0.253819485825096	1	FACETS	0.592	0.555	0.629	0.592	0.555	0.629	INDETERMINATE	1	TRUE	0	0.776279605601623	1		354	594	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772254	68772254	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	329	676	0	ENST00000261769.5:c.103G>C	p.Glu35Gln	p.E35Q	ENST00000261769	NM_004360.3	35	Gag/Cag	2/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.776279605601623	2		676	793	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89828369	89828369	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	243	455	0	ENST00000389301.3:c.2840C>T	p.Ser947Leu	p.S947L	ENST00000389301	NM_000135.2	947	tCa/tTa	29/43	1	2	FACETS	0.852	0.799	0.905	0.852	0.799	0.905	CLONAL	1	TRUE	1	0.776279605601623	2		455	735	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866395	37866395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	410	649	0	ENST00000269571.5:c.700G>A	p.Asp234Asn	p.D234N	ENST00000269571		234	Gac/Aac	6/27	0.230567792896459	3	FACETS	0.824	0.788	0.86	0.824	0.788	0.86	INDETERMINATE	2	TRUE	1	0.776279605601623	3		649	890	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866626	37866626	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	422	545	0	ENST00000269571.5:c.793G>A	p.Glu265Lys	p.E265K	ENST00000269571		265	Gag/Aag	7/27	0.230567792896459	3	FACETS	0.831	0.796	0.866	0.831	0.796	0.866	INDETERMINATE	2	TRUE	1	0.776279605601623	3		545	908	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435305	56435305	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	78	616	0	ENST00000407977.2:c.1832C>G	p.Ser611Cys	p.S611C	ENST00000407977		611	tCt/tGt	9/10	0.230567792896459	3	FACETS	0.385	0.338	0.436	0.193	0.169	0.218	INDETERMINATE	1	TRUE	1	0.776279605601623	3		616	724	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435329	56435329	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	83	656	0	ENST00000407977.2:c.1808C>G	p.Ser603Ter	p.S603*	ENST00000407977		603	tCa/tGa	9/10	0.230567792896459	3	FACETS	0.354	0.312	0.4	0.177	0.156	0.2	INDETERMINATE	1	TRUE	1	0.776279605601623	3		656	838	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379664	17379664	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	203	434	0	ENST00000359435.4:c.49G>A	p.Glu17Lys	p.E17K	ENST00000359435	NM_001033549.1	17	Gag/Aag	2/9	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.776279605601623	2		434	477	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952291	17952291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1376805771	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	272	660	2	ENST00000458235.1:c.1049G>A	p.Arg350Gln	p.R350Q	ENST00000458235	NM_000215.3	350	cGg/cAg	8/24	1	2	FACETS	0.932	0.879	0.986	0.932	0.879	0.986	CLONAL	1	TRUE	1	0.776279605601623	2		662	752	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953388	17953388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	312	688	0	ENST00000458235.1:c.598G>A	p.Asp200Asn	p.D200N	ENST00000458235	NM_000215.3	200	Gac/Aac	6/24	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.776279605601623	2		688	758	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221699	36221699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	390	796	0	ENST00000222270.7:c.5368G>A	p.Glu1790Lys	p.E1790K	ENST00000222270	NM_014727.1	1790	Gaa/Aaa	26/37	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.776279605601623	2		796	883	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753537	42753537	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	281	699	0	ENST00000222329.4:c.727G>T	p.Glu243Ter	p.E243*	ENST00000222329	NM_006494.2	243	Gaa/Taa	4/4	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.776279605601623	2		699	708	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793213	42793213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	371	675	0	ENST00000575354.2:c.1105G>A	p.Asp369Asn	p.D369N	ENST00000575354	NM_015125.3	369	Gac/Aac	7/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.776279605601623	2		675	869	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867689	45867689	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	315	681	2	ENST00000391945.4:c.711C>A	p.His237Gln	p.H237Q	ENST00000391945	NM_000400.3	237	caC/caA	8/23	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.776279605601623	2		683	744	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945393	54945393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	512	539	0	ENST00000312783.6:c.1033G>A	p.Glu345Lys	p.E345K	ENST00000312783	NM_198436.1	345	Gaa/Aaa	10/10	0.619551970813035	3	FACETS	0.955	0.92	0.989	0.955	0.92	0.989	CLONAL	2	TRUE	1	0.776279605601623	3		539	959	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162014	22162014	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	336	615	0	ENST00000215832.6:c.241G>A	p.Glu81Lys	p.E81K	ENST00000215832	NM_002745.4	81	Gag/Aag	2/9	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.776279605601623	2		615	833	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163317	47163317	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	410	436	0	ENST00000409792.3:c.2809C>A	p.Pro937Thr	p.P937T	ENST00000409792	NM_014159.6	937	Cct/Act	3/21	0.619551970813035	3	FACETS	0.94	0.902	0.978	0.94	0.902	0.978	CLONAL	2	TRUE	1	0.776279605601623	3		436	780	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917522	178917522	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	300	319	1	ENST00000263967.3:c.397G>T	p.Asp133Tyr	p.D133Y	ENST00000263967	NM_006218.2	133	Gat/Tat	3/21	0.619551970813035	3	FACETS	0.871	0.828	0.914	0.871	0.828	0.914	CLONAL	2	TRUE	1	0.776279605601623	3		320	616	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446976	187446976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369842677	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	332	748	0	ENST00000232014.4:c.1217G>A	p.Arg406Gln	p.R406Q	ENST00000232014	NM_001130845.1	406	cGa/cAa	5/10	0.619551970813035	3	FACETS	1	0.968	1	0.517	0.488	0.546	CLONAL	1	TRUE	1	0.776279605601623	3		748	1149	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630446	187630446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	731	706	2	ENST00000441802.2:c.536G>A	p.Gly179Glu	p.G179E	ENST00000441802	NM_005245.3	179	gGa/gAa	2/27	0.776279605601623	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.776279605601623	2		708	898	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876511	35876511	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	211	455	0	ENST00000303115.3:c.1303C>T	p.Gln435Ter	p.Q435*	ENST00000303115	NM_002185.3	435	Cag/Tag	8/8	1	2	FACETS	0.972	0.91	1	0.972	0.91	1	CLONAL	1	TRUE	1	0.776279605601623	2		455	559	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950754	38950754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	161	262	0	ENST00000357387.3:c.3196G>A	p.Glu1066Lys	p.E1066K	ENST00000357387	NM_152756.3	1066	Gaa/Aaa	31/38	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.776279605601623	2		262	409	SUCCESS
APC	324	MSKCC	GRCh37	5	112102053	112102053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	123	261	0	ENST00000257430.4:c.166G>A	p.Glu56Lys	p.E56K	ENST00000257430	NM_000038.5	56	Gaa/Aaa	3/16	1	2	FACETS	0.838	0.766	0.913	0.838	0.766	0.913	CLONAL	1	TRUE	1	0.776279605601623	2		261	378	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89791067	89791067	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	44	59	0	ENST00000336032.3:c.454G>A	p.Ala152Thr	p.A152T	ENST00000336032	NM_006813.2	152	Gca/Aca	1/2	0.259786755898543	1	FACETS	0.991	0.881	1	0.991	0.881	1	INDETERMINATE	1	TRUE	0	0.776279605601623	1		59	70	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117861262	117861262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs978197750	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	70	426	0	ENST00000297338.2:c.1627G>A	p.Asp543Asn	p.D543N	ENST00000297338	NM_006265.2	543	Gat/Aat	13/14	1	2	FACETS	0.245	0.213	0.28	0.245	0.213	0.28	SUBCLONAL	1	TRUE	1	0.776279605601623	2		426	736	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80646123	80646123	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	21	43	0	ENST00000286548.4:c.29G>A	p.Cys10Tyr	p.C10Y	ENST00000286548	NM_002072.3	10	tGc/tAc	1/7	1	2	FACETS	0.887	0.709	1	0.887	0.709	1	CLONAL	1	TRUE	1	0.776279605601623	2		43	61	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0031861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	103	530	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.323367820690155	2		530	461	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059176	27059176	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	42	439	0	ENST00000324856.7:c.1813C>T	p.Gln605Ter	p.Q605*	ENST00000324856	NM_006015.4	605	Caa/Taa	4/20	1	2	FACETS	0.799	0.67	0.942	0.799	0.67	0.942	CLONAL	1	TRUE	1	0.323367820690155	2		439	325	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519873	29519873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	23	578	0	ENST00000389048.3:c.1698G>T	p.Leu566Phe	p.L566F	ENST00000389048	NM_004304.4	566	ttG/ttT	9/29	0.323367820690155	1	FACETS	0.344	0.268	0.432	0.344	0.268	0.432	SUBCLONAL	1	TRUE	0	0.323367820690155	1		578	347	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245376	46245376	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0031861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	110	520	0	ENST00000334344.6:c.3470C>G	p.Ser1157Ter	p.S1157*	ENST00000334344	NM_152641.2	1157	tCa/tGa	15/21	0.323367820690155	3	FACETS	1	0.951	1			1	CLONAL	2	TRUE	NA	0.323367820690155	3		520	368	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932281	36932281	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	47	897	0	ENST00000361632.4:c.2188C>T	p.Gln730Ter	p.Q730*	ENST00000361632		730	Cag/Tag	16/16	1	2	FACETS	0.545	0.46	0.64	0.545	0.46	0.64	SUBCLONAL	1	TRUE	1	0.323367820690155	2		897	533	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221270	1221270	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	74	712	0	ENST00000326873.7:c.793G>C	p.Glu265Gln	p.E265Q	ENST00000326873	NM_000455.4	265	Gag/Cag	6/10	0.323367820690155	1	FACETS	0.892	0.784	1	0.892	0.784	1	CLONAL	1	TRUE	0	0.323367820690155	1		712	430	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600334	10600347	+	frameshift_variant	Frame_Shift_Del	DEL	TCGGATGGTGTTCA	TCGGATGGTGTTCA	-	novel	NA	P-0031861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	75	779	0	ENST00000171111.5:c.1508_1521del	p.Met503LysfsTer19	p.M503Kfs*19	ENST00000171111	NM_203500.1	503	aTGAACACCATCCGA/a	4/6	0.323367820690155	1	FACETS	0.898	0.79	1	0.898	0.79	1	CLONAL	1	TRUE	0	0.323367820690155	1		779	433	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264823	46264823	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	48	471	0	ENST00000371998.3:c.1693C>T	p.Gln565Ter	p.Q565*	ENST00000371998		565	Cag/Tag	12/23	1	2	FACETS	0.881	0.748	1	0.881	0.748	1	CLONAL	1	TRUE	1	0.323367820690155	2		471	337	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55225382	55225382	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	91	542	0	ENST00000275493.2:c.1234G>A	p.Glu412Lys	p.E412K	ENST00000275493	NM_005228.3	412	Gaa/Aaa	11/28	0.251713285326128	2	FACETS	1	0.918	1	0.518	0.461	0.579	CLONAL	1	TRUE	0	0.323367820690155	2		542	543	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738163	133738163	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	41	461	0	ENST00000318560.5:c.563C>G	p.Ser188Cys	p.S188C	ENST00000318560	NM_005157.4	188	tCc/tGc	4/11	0.323367820690155	1	FACETS	0.765	0.641	0.901	0.765	0.641	0.901	CLONAL	1	TRUE	0	0.323367820690155	1		461	278	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0031862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	87	427	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.339712446098812	3	FACETS	1	0.895	1	0.502	0.447	0.561	CLONAL	1	TRUE	1	0.547234549409058	3		427	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0031862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	211	597	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.525784246262372	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.547234549409058	1		597	518	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771344	68771344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555509646	NA	P-0031862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	87	306	0	ENST00000261769.5:c.26C>T	p.Ser9Leu	p.S9L	ENST00000261769	NM_004360.3	9	tCg/tTg	1/16	0.546771080882748	2	FACETS	1	0.954	1	0.558	0.5	0.618	CLONAL	1	TRUE	0	0.547234549409058	2		306	285	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941189	36941189	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	149	601	0	ENST00000361632.4:c.150G>C	p.Gln50His	p.Q50H	ENST00000361632		50	caG/caC	3/16	0.547234549409058	3	FACETS	0.935	0.855	1	0.467	0.427	0.509	CLONAL	1	TRUE	1	0.547234549409058	3		601	742	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152009018	152009018	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	88	356	0	ENST00000262189.6:c.604C>T	p.Gln202Ter	p.Q202*	ENST00000262189	NM_170606.2	202	Cag/Tag	5/59	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.547234549409058	2		356	302	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162233	38162233	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2179	120	354	0	ENST00000317025.8:c.2483C>G	p.Ser828Cys	p.S828C	ENST00000317025	NM_023034.1	828	tCt/tGt	14/24	0.547234549409058	21	FACETS	1	0.967	1			1	CLONAL	1	TRUE	NA	0.547234549409058	21		354	2299	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17359597	17359597	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	227	491	0	ENST00000375499.3:c.244G>T	p.Glu82Ter	p.E82*	ENST00000375499	NM_003000.2	82	Gaa/Taa	3/8	0.547234549409058	3	FACETS	0.952	0.895	1	0.952	0.895	1	CLONAL	2	TRUE	1	0.547234549409058	3		491	555	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175996780	175996780	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	116	442	0	ENST00000367669.3:c.1657G>A	p.Glu553Lys	p.E553K	ENST00000367669	NM_022457.5	553	Gag/Aag	15/20	0.535559401298097	3	FACETS	0.998	0.903	1	0.333	0.301	0.366	CLONAL	1	TRUE	0	0.547234549409058	3		442	541	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43767884	43767884	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	105	297	0	ENST00000382044.4:c.964G>C	p.Asp322His	p.D322H	ENST00000382044	NM_001141980.1	322	Gat/Cat	9/28	0.547234549409058	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.547234549409058	1		297	233	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699410	47699410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	89	322	0	ENST00000347630.2:c.98C>T	p.Ser33Phe	p.S33F	ENST00000347630	NM_001007230.1	33	tCc/tTc	4/11	0.547234549409058	3	FACETS	1	0.909	1	0.51	0.455	0.568	CLONAL	1	TRUE	1	0.547234549409058	3		322	406	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25990467	25990467	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	91	418	0	ENST00000435504.4:c.760G>C	p.Glu254Gln	p.E254Q	ENST00000435504		254	Gag/Cag	8/13	1	2	FACETS	0.821	0.734	0.913	0.821	0.734	0.913	CLONAL	1	TRUE	1	0.547234549409058	2		418	405	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413661	138413661	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	105	370	0	ENST00000289153.2:c.1859G>C	p.Arg620Pro	p.R620P	ENST00000289153	NM_006219.2	620	cGa/cCa	12/22	0.547234549409058	3	FACETS	0.956	0.861	1	0.478	0.43	0.529	CLONAL	1	TRUE	1	0.547234549409058	3		370	511	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938311	76938311	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	158	613	0	ENST00000373344.5:c.2437G>C	p.Glu813Gln	p.E813Q	ENST00000373344	NM_000489.3	813	Gag/Cag	9/35	0.547234549409058	3	FACETS	1	0.924	1	0.503	0.462	0.546	CLONAL	1	TRUE	1	0.547234549409058	3		613	731	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0031864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	173	447	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.849	0.785	0.916	0.849	0.785	0.916	CLONAL	1	TRUE	1	0.635464742332077	2		447	641	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0031864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	172	535	0	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	0.635464742332077	1	FACETS	0.937	0.874	1	0.937	0.874	1	CLONAL	1	TRUE	0	0.635464742332077	1		535	394	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0031866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	117	655	1	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.178415173767959	3	FACETS	1	0.978	1	0.662	0.596	0.732	CLONAL	1	TRUE	1	0.209583192433694	3		656	932	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101273	27101273	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	38	488	0	ENST00000324856.7:c.4555C>T	p.Gln1519Ter	p.Q1519*	ENST00000324856	NM_006015.4	1519	Cag/Tag	18/20	1	2	FACETS	0.493	0.406	0.591	0.493	0.406	0.591	SUBCLONAL	1	TRUE	1	0.209583192433694	2		488	735	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939553	68939553	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	24	229	0	ENST00000288368.4:c.538T>G	p.Leu180Val	p.L180V	ENST00000288368	NM_024870.2	180	Ttg/Gtg	5/40	1	2	FACETS	0.727	0.57	0.907	0.727	0.57	0.907	CLONAL	1	TRUE	1	0.209583192433694	2		229	315	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs202179869	NA	P-0031866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	32	366	0	ENST00000342505.4:c.2580A>C	p.Lys860Asn	p.K860N	ENST00000342505	NM_002227.2	860	aaA/aaC	19/25	1	2	FACETS	0.557	0.451	0.677	0.557	0.451	0.677	SUBCLONAL	1	TRUE	1	0.209583192433694	2		366	548	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971733	18971733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	108	585	2	ENST00000262803.5:c.2399G>A	p.Arg800His	p.R800H	ENST00000262803	NM_002911.3	800	cGc/cAc	17/24	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.209583192433694	2		587	824	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877338	89877338	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	73	417	0	ENST00000389301.3:c.425G>A	p.Arg142Lys	p.R142K	ENST00000389301	NM_000135.2	142	aGa/aAa	4/43	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.209583192433694	2		417	648	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965168	15965196	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGGCCTTGGCTTATTGAAGGGCCCCCA	GCAGGCCTTGGCTTATTGAAGGGCCCCCA	-	novel	NA	P-0031866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	57	304	0	ENST00000268712.3:c.5400_5428del	p.Gly1801SerfsTer33	p.G1801Sfs*33	ENST00000268712	NM_006311.3	1800	gcTGGGGGCCCTTCAATAAGCCAAGGCCTGCca/gcca	37/46	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.209583192433694	2		304	427	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265174	46265176	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0031866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	34	303	0	ENST00000371998.3:c.2045_2047del	p.His682del	p.H682del	ENST00000371998		682	CAC/-	12/23	1	2	FACETS	0.771	0.63	0.929	0.771	0.63	0.929	CLONAL	1	TRUE	1	0.209583192433694	2		303	421	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180546	56180546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754608335	NA	P-0031866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	46	272	0	ENST00000399503.3:c.3875G>A	p.Arg1292Lys	p.R1292K	ENST00000399503	NM_005921.1	1292	aGa/aAa	16/20	0.209583192433694	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.209583192433694	1		272	331	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484299	8484299	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	62	464	0	ENST00000356435.5:c.3233A>G	p.Glu1078Gly	p.E1078G	ENST00000356435		1078	gAg/gGg	19/35	0.209583192433694	1	FACETS	0.947	0.819	1	0.947	0.819	1	CLONAL	1	TRUE	0	0.209583192433694	1		464	559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579390	7579400	+	frameshift_variant	Frame_Shift_Del	DEL	GGAAGGGACAG	GGAAGGGACAG	T	novel	NA	P-0031866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	179	572	0	ENST00000269305.4:c.287_297delinsA	p.Ser96TyrfsTer24	p.S96Yfs*24	ENST00000269305	NM_001126112.2	96	tCTGTCCCTTCC/tA	4/11	1	2	FACETS	0.923	0.851	0.998	1	0.992	1	CLONAL	2	TRUE	1	0.209583192433694	2		572	925	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0031867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	109	412	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	0.304273680303899	1	FACETS	0.845	0.76	0.934	0.845	0.76	0.934	CLONAL	1	FALSE	0	0.340059765826059	1		412	630	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434779	99434779	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6773	431	472	0	ENST00000268035.6:c.866A>G	p.Glu289Gly	p.E289G	ENST00000268035	NM_000875.3	289	gAg/gGg	3/21	0.340059765826059	46	FACETS	0.995	0.94	1			1	CLONAL	3	FALSE	NA	0.340059765826059	46		472	7204	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	21	354	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.77	1	1	0.77	1	CLONAL	1	TRUE	1	0.13	2		354	323	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0031868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	18	369	1	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.126579261623336	1	FACETS	0.825	0.62	1	0.825	0.62	1	CLONAL	1	TRUE	0	0.13	1		370	314	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245712	46245712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752984515	NA	P-0031868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	28	322	0	ENST00000334344.6:c.3806C>T	p.Pro1269Leu	p.P1269L	ENST00000334344	NM_152641.2	1269	cCg/cTg	15/21	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.13	2		322	393	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129625	47129625	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	26	412	0	ENST00000409792.3:c.5255T>G	p.Leu1752Arg	p.L1752R	ENST00000409792	NM_014159.6	1752	cTt/cGt	10/21	1	2	FACETS	0.905	0.716	1	0.905	0.716	1	CLONAL	1	TRUE	1	0.13	2		412	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579536	7579536	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567556930	NA	P-0031869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	123	764	0	ENST00000269305.4:c.151G>T	p.Glu51Ter	p.E51*	ENST00000269305	NM_001126112.2	51	Gaa/Taa	4/11	0.151394039704848	2	FACETS	0.957	0.867	1	0.957	0.867	1	CLONAL	2	FALSE	0	0.176497523117735	2		764	728	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652129	36652129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34916193	NA	P-0031869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	55	610	0	ENST00000244741.5:c.251G>A	p.Arg84Gln	p.R84Q	ENST00000244741	NM_000389.4	84	cGa/cAa	2/3	0.149868149938571	3	FACETS	1	0.951	1	0.637	0.545	0.738	CLONAL	1	FALSE	1	0.176497523117735	3		610	532	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922258	100922258	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	14	329	2	ENST00000325455.5:c.2254C>T	p.Gln752Ter	p.Q752*	ENST00000325455	NM_001202474.3	752	Cag/Tag	5/8	0.151394039704848	2	FACETS	0.818	0.592	1	0.409	0.296	0.545	CLONAL	1	FALSE	0	0.176497523117735	2		331	194	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205550	61205550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	63	448	0	ENST00000301761.2:c.335C>T	p.Pro112Leu	p.P112L	ENST00000301761	NM_017841.2	112	cCt/cTt	3/4	0.15450028618868	3	FACETS	0.801	0.694	0.917	0.534	0.462	0.611	CLONAL	2	FALSE	0	0.176497523117735	3		448	485	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619384	1619385	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGCA	novel	NA	P-0031869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	57	782	0	ENST00000344749.5:c.1253_1256dup	p.Pro420AlafsTer56	p.P420Afs*56	ENST00000344749	NM_001136139.2	419	ctg/ctTGCTg	15/19	0.149868149938571	3	FACETS	0.97	0.83	1	0.485	0.415	0.561	CLONAL	1	FALSE	1	0.176497523117735	3		782	725	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231364	98231364	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	100	602	0	ENST00000331920.6:c.1919del	p.Ser640ThrfsTer53	p.S640Tfs*53	ENST00000331920	NM_000264.3	640	aGc/ac	14/24	0.15450028618868	3	FACETS	0.977	0.874	1	0.651	0.583	0.724	CLONAL	2	FALSE	0	0.176497523117735	3		602	631	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849818	156849818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761967383	NA	P-0031870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	68	454	0	ENST00000524377.1:c.2074C>T	p.Arg692Cys	p.R692C	ENST00000524377	NM_002529.3	692	Cgc/Tgc	16/17	1	2	FACETS	0.969	0.843	1	0.969	0.843	1	CLONAL	1	TRUE	1	0.24	2		454	585	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487277	56487277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035001455	NA	P-0031870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	58	444	0	ENST00000267101.3:c.1423C>T	p.Arg475Trp	p.R475W	ENST00000267101	NM_001982.3	475	Cgg/Tgg	12/28	1	2	FACETS	0.802	0.688	0.925	0.802	0.688	0.925	CLONAL	1	TRUE	1	0.24	2		444	603	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591925	48591925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660556	NA	P-0031870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	61	403	0	ENST00000342988.3:c.1088G>A	p.Cys363Tyr	p.C363Y	ENST00000342988	NM_005359.5	363	tGt/tAt	9/12	0.199554914540009	1	FACETS	0.907	0.784	1	0.907	0.784	1	CLONAL	1	TRUE	0	0.24	1		403	493	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102085	27102085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769528458	NA	P-0031870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	92	504	0	ENST00000324856.7:c.5011C>T	p.Arg1671Trp	p.R1671W	ENST00000324856	NM_006015.4	1671	Cgg/Tgg	19/20	0.199554914540009	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.24	1		504	639	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230535	46230535	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	47	327	0	ENST00000334344.6:c.784G>A	p.Gly262Arg	p.G262R	ENST00000334344	NM_152641.2	262	Gga/Aga	8/21	1	2	FACETS	0.863	0.729	1	0.863	0.729	1	CLONAL	1	TRUE	1	0.24	2		327	454	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042188	42042188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765160157	NA	P-0031870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	53	411	0	ENST00000219905.7:c.6383G>A	p.Ser2128Asn	p.S2128N	ENST00000219905	NM_001164273.1	2128	aGt/aAt	17/24	1	2	FACETS	0.909	0.776	1	0.909	0.776	1	CLONAL	1	TRUE	1	0.24	2		411	486	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432678	29432678	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	46	414	0	ENST00000389048.3:c.3810C>A	p.Asp1270Glu	p.D1270E	ENST00000389048	NM_004304.4	1270	gaC/gaA	25/29	0.199554914540009	1	FACETS	0.588	0.494	0.691	0.588	0.494	0.691	SUBCLONAL	1	TRUE	0	0.24	1		414	574	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579362	7579362	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057523496	NA	P-0031871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	203	575	0	ENST00000269305.4:c.325T>G	p.Phe109Val	p.F109V	ENST00000269305	NM_001126112.2	109	Ttc/Gtc	4/11	0.394477455821763	2	FACETS	0.795	0.743	0.846	0.795	0.743	0.846	SUBCLONAL	2	TRUE	0	0.498043287126258	2		575	513	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122649	108122649	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	71	363	0	ENST00000278616.4:c.1693G>A	p.Glu565Lys	p.E565K	ENST00000278616	NM_000051.3	565	Gaa/Aaa	11/63	0.44974372631828	3	FACETS	0.908	0.797	1	0.454	0.398	0.514	CLONAL	1	TRUE	1	0.498043287126258	3		363	392	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634330	23634330	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	86	552	0	ENST00000261584.4:c.2956G>C	p.Asp986His	p.D986H	ENST00000261584	NM_024675.3	986	Gat/Cat	9/13	0.182331599725564	2	FACETS	0.511	0.452	0.574	0.255	0.226	0.287	INDETERMINATE	1	TRUE	0	0.498043287126258	2		552	676	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41242998	41242998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357071	NA	P-0031871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	50	436	0	ENST00000357654.3:c.4148C>T	p.Ser1383Leu	p.S1383L	ENST00000357654	NM_007294.3	1383	tCa/tTa	11/23	0.394477455821763	2	FACETS	0.575	0.49	0.668	0.288	0.245	0.334	SUBCLONAL	1	TRUE	0	0.498043287126258	2		436	349	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243023	41243213	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CACTCTCACACCCAGATGCTGCTTCACCTTAAATAACAAAAACAGAGGTTCAGATGTAAAAGCAGACTATAAACGCTGCAACTTGCTGTGTCTTTTTCTTCTCATTGGCAGGACTGGATTTACTTTCATGTCACACAAAATGATTAAATTCCTTGCTTTGGGACACCTGGATTTGCTTTTATAAAATGAAA	CACTCTCACACCCAGATGCTGCTTCACCTTAAATAACAAAAACAGAGGTTCAGATGTAAAAGCAGACTATAAACGCTGCAACTTGCTGTGTCTTTTTCTTCTCATTGGCAGGACTGGATTTACTTTCATGTCACACAAAATGATTAAATTCCTTGCTTTGGGACACCTGGATTTGCTTTTATAAAATGAAA	-	novel	NA	P-0031871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	46	437	0	ENST00000357654.3:c.4097-164_4123del		p.X1366_splice	ENST00000357654	NM_007294.3	1366		11/23	0.394477455821763	2	FACETS	0.56	0.473	0.654	0.28	0.236	0.327	SUBCLONAL	1	TRUE	0	0.498043287126258	2		437	330	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451761	29451761	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	86	506	0	ENST00000389048.3:c.2804G>T	p.Gly935Val	p.G935V	ENST00000389048	NM_004304.4	935	gGa/gTa	16/29	0.44974372631828	3	FACETS	0.897	0.796	1	0.448	0.398	0.502	CLONAL	1	TRUE	1	0.498043287126258	3		506	481	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99136516	99136516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	94	500	1	ENST00000074304.5:c.5C>T	p.Thr2Ile	p.T2I	ENST00000074304	NM_001134224.1	2	aCa/aTa	3/26	0.44974372631828	3	FACETS	0.945	0.844	1	0.472	0.422	0.526	CLONAL	1	TRUE	1	0.498043287126258	3		501	499	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37038154	37038154	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	29	189	0	ENST00000231790.2:c.161G>C	p.Gly54Ala	p.G54A	ENST00000231790	NM_000249.3	54	gGa/gCa	2/19	0.498043287126258	5	FACETS	0.676	0.544	0.826	0.225	0.181	0.276	SUBCLONAL	1	TRUE	2	0.498043287126258	5		189	301	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	55	258	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.313385736521888	2		258	285	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0031872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	227	597	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.313385736521888	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.313385736521888	2		597	592	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709505	176709505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	50	369	0	ENST00000439151.2:c.5932G>A	p.Glu1978Lys	p.E1978K	ENST00000439151	NM_022455.4	1978	Gaa/Aaa	19/23	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.313385736521888	2		369	299	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11552761	NA	P-0031872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	110	579	0	ENST00000418115.1:c.50G>C	p.Gly17Ala	p.G17A	ENST00000418115	NM_001664.2	17	gGa/gCa	2/5	0.313385736521888	2	FACETS	1	0.978	1	0.654	0.589	0.721	CLONAL	1	TRUE	0	0.313385736521888	2		579	537	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573436	55573436	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	34	247	0	ENST00000288135.5:c.1098G>T	p.Glu366Asp	p.E366D	ENST00000288135	NM_000222.2	366	gaG/gaT	6/21	0.313385736521888	5	FACETS	1	0.896	1	0.38	0.311	0.456	CLONAL	1	TRUE	2	0.313385736521888	5		247	280	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846300	156846300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150579345	NA	P-0031872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	111	613	1	ENST00000524377.1:c.1741G>A	p.Glu581Lys	p.E581K	ENST00000524377	NM_002529.3	581	Gag/Aag	14/17	0.103670442915508	4	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.313385736521888	4		614	714	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032071	26032071	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	96	302	0	ENST00000244661.2:c.218G>C	p.Arg73Pro	p.R73P	ENST00000244661	NM_003537.3	73	cGa/cCa	1/1	0.313385736521888	3	FACETS	0.979	0.88	1	0.979	0.88	1	CLONAL	2	TRUE	1	0.313385736521888	3		302	362	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118355576	118355576	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0031872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	68	392	0	ENST00000534358.1:c.4219-1G>A		p.X1407_splice	ENST00000534358	NM_005933.3	1407			0.313385736521888	3	FACETS	1	0.959	1	0.621	0.543	0.705	CLONAL	1	TRUE	1	0.313385736521888	3		392	404	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420619	49420619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	183	513	0	ENST00000301067.7:c.15130G>A	p.Asp5044Asn	p.D5044N	ENST00000301067	NM_003482.3	5044	Gat/Aat	48/54	0.297178156005374	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.313385736521888	4		513	623	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175422	108175422	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	105	270	0	ENST00000278616.4:c.5517G>C	p.Gln1839His	p.Q1839H	ENST00000278616	NM_000051.3	1839	caG/caC	37/63	0.313385736521888	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.313385736521888	3		270	337	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352680	118352689	+	frameshift_variant	Frame_Shift_Del	DEL	CAAGCAGGTC	CAAGCAGGTC	-	novel	NA	P-0031872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	155	387	0	ENST00000534358.1:c.3885_3894del	p.Lys1296ProfsTer57	p.K1296Pfs*57	ENST00000534358	NM_005933.3	1295	agCAAGCAGGTC/ag	7/36	0.313385736521888	3	FACETS	0.84	0.776	0.906	1	0.984	1	CLONAL	3	TRUE	1	0.313385736521888	3		387	454	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118355688	118355688	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	61	420	0	ENST00000534358.1:c.4330G>C	p.Glu1444Gln	p.E1444Q	ENST00000534358	NM_005933.3	1444	Gag/Cag	10/36	0.313385736521888	3	FACETS	1	0.92	1	0.545	0.472	0.624	CLONAL	1	TRUE	1	0.313385736521888	3		420	413	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008333	29008333	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	49	245	0	ENST00000282397.4:c.538G>C	p.Asp180His	p.D180H	ENST00000282397	NM_002019.4	180	Gat/Cat	5/30	0.313385736521888	3	FACETS	1	0.933	1	0.587	0.5	0.682	CLONAL	1	TRUE	1	0.313385736521888	3		245	308	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65569021	65569021	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0031872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	132	367	0	ENST00000358664.4:c.36+1G>T		p.X12_splice	ENST00000358664	NM_002382.4	12			0.313385736521888	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.313385736521888	2		367	352	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95595950	95595950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1024665554	NA	P-0031872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	89	326	0	ENST00000393063.1:c.593C>T	p.Ser198Leu	p.S198L	ENST00000393063	NM_030621.3	198	tCa/tTa	7/28	0.313385736521888	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	0	0.313385736521888	2		326	269	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789643	3789643	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	145	387	0	ENST00000262367.5:c.4216G>T	p.Asp1406Tyr	p.D1406Y	ENST00000262367	NM_004380.2	1406	Gat/Tat	25/31	0.313385736521888	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.313385736521888	3		387	499	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942049	81942049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	137	375	0	ENST00000359376.3:c.1586G>A	p.Gly529Glu	p.G529E	ENST00000359376	NM_002661.3	529	gGg/gAg	17/33	0.313385736521888	3	FACETS	0.878	0.807	0.95	1	0.985	1	CLONAL	3	TRUE	1	0.313385736521888	3		375	384	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489460	40489460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763564047	NA	P-0031872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	72	425	0	ENST00000264657.5:c.790G>A	p.Glu264Lys	p.E264K	ENST00000264657	NM_139276.2	264	Gaa/Aaa	8/24	0.297178156005374	4	FACETS	1	0.922	1	0.537	0.469	0.61	CLONAL	1	TRUE	2	0.313385736521888	4		425	562	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953259	17953259	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	254	658	0	ENST00000458235.1:c.727G>C	p.Glu243Gln	p.E243Q	ENST00000458235	NM_000215.3	243	Gag/Cag	6/24	0.313385736521888	5	FACETS	0.997	0.936	1	0.997	0.936	1	CLONAL	3	TRUE	2	0.313385736521888	5		658	797	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308132	30308132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	298	453	0	ENST00000262643.3:c.269C>T	p.Ser90Leu	p.S90L	ENST00000262643	NM_001238.2	90	tCa/tTa	5/12	0.313385736521888	6	FACETS	1	0.954	1	1	0.954	1	CLONAL	4	TRUE	2	0.313385736521888	6		453	767	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223391	36223391	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	504	799	1	ENST00000222270.7:c.5941G>T	p.Glu1981Ter	p.E1981*	ENST00000222270	NM_014727.1	1981	Gag/Tag	28/37	0.313385736521888	6	FACETS	0.956	0.918	0.993	1	0.994	1	CLONAL	5	TRUE	2	0.313385736521888	6		800	1095	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37038135	37038135	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587778913	NA	P-0031872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	54	150	0	ENST00000231790.2:c.142C>G	p.Gln48Glu	p.Q48E	ENST00000231790	NM_000249.3	48	Caa/Gaa	2/19	0.297178156005374	4	FACETS	1	0.896	1	1	0.896	1	CLONAL	2	TRUE	2	0.313385736521888	4		150	217	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928992	44928993	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0031872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	162	209	0	ENST00000377967.4:c.2093_2094del	p.His698ProfsTer31	p.H698Pfs*31	ENST00000377967	NM_021140.2	698	CAc/c	17/29	0.313385736521888	2	FACETS	1	0.977	1			1	CLONAL	3	TRUE	NA	0.313385736521888	2		209	313	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0031873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	16	596	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.925	0.687	1	0.925	0.687	1	CLONAL	1	TRUE	1	0.19	2		596	182	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0031873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	11	177	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	1	2	FACETS	1	0.762	1	1	0.762	1	CLONAL	1	TRUE	1	0.19	2		177	104	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560476	95560476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	11	369	0	ENST00000393063.1:c.5113G>A	p.Glu1705Lys	p.E1705K	ENST00000393063	NM_030621.3	1705	Gaa/Aaa	25/28	1	2	FACETS	0.582	0.402	0.805	0.582	0.402	0.805	SUBCLONAL	1	TRUE	1	0.19	2		369	199	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0031874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	145	447	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.195317242776657	4	FACETS	1	0.957	1	0.797	0.732	0.864	CLONAL	3	FALSE	0	0.2314121711124	4		447	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0031874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	86	574	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.161964187854397	2	FACETS	1	0.974	1	0.679	0.602	0.762	CLONAL	1	FALSE	0	0.2314121711124	2		574	547	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715619	30715619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730880224	NA	P-0031874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	41	233	0	ENST00000295754.5:c.1277C>T	p.Ala426Val	p.A426V	ENST00000295754	NM_003242.5	426	gCt/gTt	5/7	0.161964187854397	2	FACETS	1	0.931	1	0.613	0.513	0.723	CLONAL	1	FALSE	0	0.2314121711124	2		233	289	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138879	64138879	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771314909	NA	P-0031874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	38	475	1	ENST00000334205.4:c.2246C>T	p.Ala749Val	p.A749V	ENST00000334205	NM_003942.2	749	gCc/gTc	17/17	0.176170575678308	3	FACETS	0.9	0.745	1	0.45	0.372	0.537	CLONAL	1	FALSE	1	0.2314121711124	3		476	407	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863262	57863262	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	63	414	0	ENST00000228682.2:c.1357T>G	p.Ser453Ala	p.S453A	ENST00000228682	NM_005269.2	453	Tcc/Gcc	11/12	0.161964187854397	2	FACETS	1	0.965	1	0.679	0.589	0.775	CLONAL	1	FALSE	0	0.2314121711124	2		414	401	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142950056	142950056	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568595082	NA	P-0031874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	23	350	0	ENST00000262992.4:c.2654G>A	p.Arg885His	p.R885H	ENST00000262992	NM_001101669.1	885	cGc/cAc	24/24	0.176170575678308	3	FACETS	0.616	0.48	0.774	0.308	0.24	0.387	SUBCLONAL	1	FALSE	1	0.2314121711124	3		350	360	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562910	176562910	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	39	418	0	ENST00000439151.2:c.806A>T	p.Glu269Val	p.E269V	ENST00000439151	NM_022455.4	269	gAg/gTg	2/23	0.176170575678308	3	FACETS	0.843	0.699	1	0.422	0.349	0.502	CLONAL	1	FALSE	1	0.2314121711124	3		418	446	SUCCESS
CBL	867	MSKCC	GRCh37	11	119077183	119077183	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	206	485	0	ENST00000264033.4:c.56G>T	p.Gly19Val	p.G19V	ENST00000264033	NM_005188.3	19	gGc/gTc	1/16	0.7593542630061	2	FACETS	1	0.981	1	0.556	0.522	0.591	CLONAL	1	TRUE	0	0.789941670428875	2		485	469	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940487	31940487	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	103	636	0	ENST00000375333.2:c.520C>G	p.Gln174Glu	p.Q174E	ENST00000375333	NM_032454.1	174	Cag/Gag	3/8	0.763417045210637	3	FACETS	0.326	0.29	0.363	0.163	0.145	0.182	SUBCLONAL	1	TRUE	1	0.789941670428875	3		636	1117	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805331	32805331	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	132	349	0	ENST00000374899.4:c.591C>A	p.Cys197Ter	p.C197*	ENST00000374899	NM_018833.2	197	tgC/tgA	3/12	0.763417045210637	3	FACETS	0.973	0.889	1	0.487	0.444	0.53	CLONAL	1	TRUE	1	0.789941670428875	3		349	479	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538970	23538970	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	207	634	0	ENST00000380871.4:c.469C>A	p.Leu157Met	p.L157M	ENST00000380871	NM_006167.3	157	Ctg/Atg	2/2	0.7593542630061	2	FACETS	0.517	0.48	0.556	0.259	0.24	0.278	SUBCLONAL	1	TRUE	0	0.789941670428875	2		634	1013	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0031881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	92	619	1	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.263169493979741	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.263169493979741	1		620	483	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0031881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	446	680	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.263169493979741	8	FACETS	1	0.965	1			1	CLONAL	6	TRUE	NA	0.263169493979741	8		680	1003	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0031881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	192	1158	2	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	0.213074771702095	2	FACETS	0.758	0.701	0.818	0.758	0.701	0.818	SUBCLONAL	2	TRUE	0	0.263169493979741	2		1160	962	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945775	38945775	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217157165	NA	P-0031881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	44	386	0	ENST00000357387.3:c.4451G>A	p.Arg1484Gln	p.R1484Q	ENST00000357387	NM_152756.3	1484	cGa/cAa	34/38	1	2	FACETS	0.921	0.775	1	0.921	0.775	1	CLONAL	1	TRUE	1	0.263169493979741	2		386	363	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412122	63412122	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	133	617	1	ENST00000330258.3:c.1045C>T	p.Gln349Ter	p.Q349*	ENST00000330258	NM_152424.3	349	Cag/Tag	2/2	1	1	FACETS	0.869	0.794	0.947	1	0.989	1	CLONAL	2	TRUE	0	0.263169493979741	1		618	505	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0031882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	136	391	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.254336584471341	4	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	2	0.254336584471341	4		391	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0031882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	216	620	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	2	TRUE	NA	0.254336584471341	2		621	808	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176917	56176918	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0031882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	38	196	0	ENST00000399503.3:c.2189dup	p.Ile731TyrfsTer5	p.I731Yfs*5	ENST00000399503	NM_005921.1	729	-/G	13/20	1	2	FACETS	0.724	0.599	0.863	0.724	0.599	0.863	SUBCLONAL	1	TRUE	1	0.254336584471341	2		196	413	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263871	16263871	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	113	950	0	ENST00000375759.3:c.10240G>C	p.Glu3414Gln	p.E3414Q	ENST00000375759	NM_015001.2	3414	Gag/Cag	12/15	0.254336584471341	3	FACETS	1	0.919	1	0.513	0.461	0.569	CLONAL	1	TRUE	1	0.254336584471341	3		950	976	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263891	16263891	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1438006067	NA	P-0031882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	120	1005	0	ENST00000375759.3:c.10260G>C	p.Gln3420His	p.Q3420H	ENST00000375759	NM_015001.2	3420	caG/caC	12/15	0.254336584471341	3	FACETS	1	0.915	1	0.508	0.458	0.562	CLONAL	1	TRUE	1	0.254336584471341	3		1005	1046	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720663	89720664	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0031882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	94	340	0	ENST00000371953.3:c.815_816del	p.His272LeufsTer25	p.H272Lfs*25	ENST00000371953	NM_000314.4	272	CAc/c	8/9	0.165115061645769	2	FACETS	0.919	0.83	1	1	0.98	1	CLONAL	3	TRUE	0	0.254336584471341	2		340	268	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575081	48575081	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	58	445	0	ENST00000342988.3:c.275A>T	p.His92Leu	p.H92L	ENST00000342988	NM_005359.5	92	cAt/cTt	3/12	0.254336584471341	1	FACETS	0.911	0.785	1	0.911	0.785	1	CLONAL	1	TRUE	0	0.254336584471341	1		445	437	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878863	151878864	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0031882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	56	689	0	ENST00000262189.6:c.6081_6082del	p.Arg2028ThrfsTer9	p.R2028Tfs*9	ENST00000262189	NM_170606.2	2027	gcACga/gcga	36/59	0.254336584471341	3	FACETS	0.708	0.606	0.82	0.354	0.303	0.41	SUBCLONAL	1	TRUE	1	0.254336584471341	3		689	701	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127916216	127916216	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	67	651	0	ENST00000373547.4:c.428C>T	p.Thr143Ile	p.T143I	ENST00000373547	NM_002721.4	143	aCc/aTc	5/7	0.254336584471341	4	FACETS	0.785	0.681	0.898			1	SUBCLONAL	1	TRUE	NA	0.254336584471341	4		651	842	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0031883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	538	905	2	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.561415940852399	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.561415940852399	2		907	806	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528192	103528192	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	269	520	3	ENST00000355739.4:c.3500C>T	p.Ser1167Phe	p.S1167F	ENST00000355739	NM_000123.3	1167	tCt/tTt	15/15	0.561415940852399	3	FACETS	1	0.989	1	0.614	0.577	0.653	CLONAL	1	TRUE	1	0.561415940852399	3		523	999	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47613711	47613711	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1373578863	NA	P-0031883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	369	547	2	ENST00000263735.4:c.904A>G	p.Ile302Val	p.I302V	ENST00000263735	NM_002354.2	302	Ata/Gta	9/9	0.561415940852399	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.561415940852399	3		549	713	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0031884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	44	447	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.733	0.613	0.867	0.733	0.613	0.867	SUBCLONAL	1	TRUE	1	0.16	2		447	750	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0031884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	49	620	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.727	0.613	0.852	0.727	0.613	0.852	SUBCLONAL	1	TRUE	1	0.16	2		621	843	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0031884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	57	653	0	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.16	2		653	660	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492906	56492919	+	frameshift_variant	Frame_Shift_Del	DEL	GGCAGCCAGCTGCA	GGCAGCCAGCTGCA	-	novel	NA	P-0031884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	18	353	0	ENST00000407977.2:c.20_33del	p.Leu7ProfsTer28	p.L7Pfs*28	ENST00000407977		7	cTGCAGCTGGCTGCC/c	2/10	1	2	FACETS	0.66	0.496	0.854	0.66	0.496	0.854	SUBCLONAL	1	TRUE	1	0.16	2		353	341	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145589	11145589	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0031886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	377	553	0	ENST00000358026.2:c.3952-1G>T		p.X1318_splice	ENST00000358026	NM_001128849.1	1318			0.815623582340091	2	FACETS	0.958	0.93	0.985	0.958	0.93	0.985	CLONAL	2	TRUE	0	0.823223143597963	2		553	478	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245288	46245288	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	404	479	0	ENST00000334344.6:c.3382C>T	p.Gln1128Ter	p.Q1128*	ENST00000334344	NM_152641.2	1128	Cag/Tag	15/21	0.415367855889003	5	FACETS	0.961	0.922	1	0.961	0.922	1	INDETERMINATE	3	TRUE	2	0.823223143597963	5		479	761	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221339	1221339	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	434	536	0	ENST00000326873.7:c.862G>T	p.Gly288Trp	p.G288W	ENST00000326873	NM_000455.4	288	Ggg/Tgg	6/10	0.815623582340091	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.823223143597963	2		536	522	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439329	149439329	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	528	648	1	ENST00000286301.3:c.2066C>A	p.Pro689His	p.P689H	ENST00000286301	NM_005211.3	689	cCc/cAc	15/22	0.815623582340091	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.823223143597963	2		649	631	SUCCESS
ATM	472	MSKCC	GRCh37	11	108099978	108099978	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	544	426	1	ENST00000278616.4:c.259C>T	p.Gln87Ter	p.Q87*	ENST00000278616	NM_000051.3	87	Caa/Taa	4/63	0.766261212949493	4	FACETS	1	0.973	1			1	CLONAL	3	TRUE	NA	0.823223143597963	4		427	801	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041485	42041485	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	245	577	0	ENST00000219905.7:c.5680G>T	p.Val1894Leu	p.V1894L	ENST00000219905	NM_001164273.1	1894	Gtg/Ttg	17/24	0.768026012857872	3	FACETS	1	0.938	1	0.501	0.469	0.533	CLONAL	1	TRUE	1	0.823223143597963	3		577	839	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014111	14014111	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	278	578	0	ENST00000311895.7:c.89A>G	p.Asp30Gly	p.D30G	ENST00000311895	NM_005236.2	30	gAc/gGc	1/11	0.823223143597963	3	FACETS	0.987	0.928	1	0.493	0.464	0.524	CLONAL	1	TRUE	1	0.823223143597963	3		578	966	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828303	50828303	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	171	439	0	ENST00000398568.2:c.2641G>T	p.Ala881Ser	p.A881S	ENST00000398568	NM_001042412.1	881	Gcc/Tcc	17/18	1	2	FACETS	0.911	0.846	0.977	0.911	0.846	0.977	CLONAL	1	TRUE	1	0.823223143597963	2		439	456	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993768	72993768	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	184	526	0	ENST00000268489.5:c.277A>T	p.Thr93Ser	p.T93S	ENST00000268489	NM_006885.3	93	Acc/Tcc	2/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.823223143597963	2		526	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579312	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CG	CG	GA	novel	NA	P-0031886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	641	537	0	ENST00000269305.4:c.374_375delinsTC	p.Thr125Ile	p.T125I	ENST00000269305	NM_001126112.2	125	aCG/aTC	4/11	0.633500456833794	4	FACETS	0.97	0.953	0.986			1	CLONAL	4	TRUE	NA	0.823223143597963	4		537	732	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657372	29657372	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	270	590	1	ENST00000356175.3:c.5605G>T	p.Gly1869Cys	p.G1869C	ENST00000356175	NM_000267.3	1869	Ggc/Tgc	38/57	0.805405867221023	3	FACETS	0.98	0.921	1	0.49	0.46	0.52	CLONAL	1	TRUE	1	0.823223143597963	3		591	945	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619289	37619289	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	170	455	1	ENST00000447079.4:c.965G>T	p.Arg322Leu	p.R322L	ENST00000447079	NM_015083.1	322	cGa/cTa	1/14	0.805405867221023	3	FACETS	0.945	0.873	1	0.472	0.436	0.51	CLONAL	1	TRUE	1	0.823223143597963	3		456	617	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740612	58740612	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	553	600	1	ENST00000305921.3:c.1517C>G	p.Thr506Ser	p.T506S	ENST00000305921	NM_003620.3	506	aCt/aGt	6/6	0.823223143597963	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.823223143597963	3		601	922	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853812	59853812	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs773347072	NA	P-0031886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	211	591	0	ENST00000259008.2:c.2047G>C	p.Val683Leu	p.V683L	ENST00000259008	NM_032043.2	683	Gtg/Ctg	14/20	0.823223143597963	3	FACETS	0.853	0.794	0.915	0.427	0.397	0.458	CLONAL	1	TRUE	1	0.823223143597963	3		591	848	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120256	70120256	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	316	768	1	ENST00000245479.2:c.1258T>A	p.Tyr420Asn	p.Y420N	ENST00000245479	NM_000346.3	420	Tac/Aac	3/3	0.823223143597963	3	FACETS	0.922	0.869	0.975	0.461	0.434	0.488	CLONAL	1	TRUE	1	0.823223143597963	3		769	1176	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597372	10597372	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	539	775	0	ENST00000171111.5:c.1831G>T	p.Glu611Ter	p.E611*	ENST00000171111	NM_203500.1	611	Gag/Tag	6/6	0.815623582340091	2	FACETS	0.964	0.941	0.986	0.964	0.941	0.986	CLONAL	2	TRUE	0	0.823223143597963	2		775	679	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662006	227662006	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	178	663	0	ENST00000305123.5:c.1449C>A	p.Tyr483Ter	p.Y483*	ENST00000305123	NM_005544.2	483	taC/taA	1/2	0.823223143597963	3	FACETS	0.809	0.747	0.873	0.404	0.373	0.437	CLONAL	1	TRUE	1	0.823223143597963	3		663	755	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944595	40944595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs997415297	NA	P-0031886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	163	422	0	ENST00000373198.4:c.1907C>T	p.Ser636Leu	p.S636L	ENST00000373198	NM_133170.3	636	tCa/tTa	12/32	0.823223143597963	5	FACETS	0.845	0.775	0.919	0.211	0.193	0.23	CLONAL	1	TRUE	1	0.823223143597963	5		422	1047	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155203	55155203	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	199	569	0	ENST00000257290.5:c.2802C>A	p.Asn934Lys	p.N934K	ENST00000257290	NM_006206.4	934	aaC/aaA	21/23	1	2	FACETS	0.89	0.831	0.951	0.89	0.831	0.951	CLONAL	1	TRUE	1	0.823223143597963	2		569	543	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197724	66197724	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs773062561	NA	P-0031886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	281	559	0	ENST00000273854.3:c.2975G>T	p.Ser992Ile	p.S992I	ENST00000273854	NM_004439.5	992	aGt/aTt	17/18	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.823223143597963	2		559	600	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187560928	187560928	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	167	417	1	ENST00000441802.2:c.3590C>G	p.Thr1197Arg	p.T1197R	ENST00000441802	NM_005245.3	1197	aCa/aGa	4/27	1	2	FACETS	0.902	0.837	0.968	0.902	0.837	0.968	CLONAL	1	TRUE	1	0.823223143597963	2		418	450	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117650514	117650514	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	575	699	0	ENST00000368508.3:c.5344A>T	p.Thr1782Ser	p.T1782S	ENST00000368508	NM_002944.2	1782	Aca/Tca	32/43	0.819622799195185	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.823223143597963	2		699	692	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527760	157527760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	202	485	0	ENST00000346085.5:c.5485C>T	p.His1829Tyr	p.H1829Y	ENST00000346085	NM_020732.3	1829	Cac/Tac	20/20	0.819622799195185	2	FACETS	0.861	0.804	0.919	0.43	0.402	0.46	CLONAL	1	TRUE	0	0.823223143597963	2		485	570	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14027793	14027793	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	145	308	0	ENST00000405192.2:c.51G>C	p.Gln17His	p.Q17H	ENST00000405192	NM_001163147.1	17	caG/caC	3/12	0.663393526202981	5	FACETS	0.907	0.828	0.99	0.302	0.275	0.33	CLONAL	1	TRUE	2	0.823223143597963	5		308	868	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974702	21974702	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	184	407	0	ENST00000304494.5:c.125A>C	p.Asn42Thr	p.N42T	ENST00000304494	NM_000077.4	42	aAt/aCt	1/3	0.816234454418352	1	FACETS	0.967	0.918	1	0.967	0.918	1	CLONAL	1	TRUE	0	0.823223143597963	1		407	272	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626670	100626670	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	334	263	0	ENST00000308731.7:c.260G>T	p.Ser87Ile	p.S87I	ENST00000308731	NM_000061.2	87	aGt/aTt	4/19	0.766261212949493	2	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.823223143597963	2		263	385	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	92	258	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.783	0.696	0.875	0.783	0.696	0.875	SUBCLONAL	1	TRUE	1	0.360512865265974	2		258	652	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0031887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	477	720	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.360512865265974	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.360512865265974	2		720	1233	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100948	41100948	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	185	584	0	ENST00000373198.4:c.1408C>T	p.Arg470Ter	p.R470*	ENST00000373198	NM_133170.3	470	Cga/Tga	8/32	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.360512865265974	2		584	923	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956220	55956220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190050670	NA	P-0031887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	160	641	0	ENST00000263923.4:c.3095G>A	p.Arg1032Gln	p.R1032Q	ENST00000263923	NM_002253.2	1032	cGa/cAa	23/30	1	2	FACETS	0.866	0.793	0.942	0.866	0.793	0.942	CLONAL	1	TRUE	1	0.360512865265974	2		641	1025	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158215	106158215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111678678	NA	P-0031887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	110	455	0	ENST00000380013.4:c.3116C>T	p.Ser1039Leu	p.S1039L	ENST00000380013	NM_001127208.2	1039	tCg/tTg	3/11	1	2	FACETS	0.786	0.706	0.871	0.786	0.706	0.871	SUBCLONAL	1	TRUE	1	0.360512865265974	2		455	776	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120666	94120666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	126	541	0	ENST00000369303.4:c.385G>A	p.Glu129Lys	p.E129K	ENST00000369303	NM_004440.3	129	Gaa/Aaa	3/17	0.360512865265974	1	FACETS	0.955	0.868	1	0.955	0.868	1	CLONAL	1	TRUE	0	0.360512865265974	1		541	600	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944562	40944562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868189942	NA	P-0031887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	153	564	0	ENST00000373198.4:c.1940C>T	p.Ser647Leu	p.S647L	ENST00000373198	NM_133170.3	647	tCg/tTg	12/32	1	2	FACETS	0.905	0.827	0.986	0.905	0.827	0.986	CLONAL	1	TRUE	1	0.360512865265974	2		564	938	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156493	106156493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	142	539	1	ENST00000380013.4:c.1394C>T	p.Pro465Leu	p.P465L	ENST00000380013	NM_001127208.2	465	cCa/cTa	3/11	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.360512865265974	2		540	765	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434732	49434732	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767236217	NA	P-0031887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	298	973	5	ENST00000301067.7:c.6821C>T	p.Ser2274Leu	p.S2274L	ENST00000301067	NM_003482.3	2274	tCg/tTg	31/54	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.360512865265974	2		978	1397	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374309	118374309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	189	558	0	ENST00000534358.1:c.7702C>T	p.Pro2568Ser	p.P2568S	ENST00000534358	NM_005933.3	2568	Cca/Tca	27/36	0.360512865265974	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.360512865265974	1		558	754	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562773	95562773	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	125	552	0	ENST00000393063.1:c.4484C>A	p.Ser1495Ter	p.S1495*	ENST00000393063	NM_030621.3	1495	tCa/tAa	24/28	1	2	FACETS	0.899	0.814	0.989	0.899	0.814	0.989	CLONAL	1	TRUE	1	0.360512865265974	2		552	771	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748729	43748729	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1182	243	1048	0	ENST00000382044.4:c.2077C>T	p.Pro693Ser	p.P693S	ENST00000382044	NM_001141980.1	693	Ccg/Tcg	12/28	1	2	FACETS	0.946	0.882	1	0.946	0.882	1	CLONAL	1	TRUE	1	0.360512865265974	2		1048	1425	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214377	36214377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	264	807	1	ENST00000222270.7:c.3031C>T	p.Arg1011Trp	p.R1011W	ENST00000222270	NM_014727.1	1011	Cgg/Tgg	7/37	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.360512865265974	2		808	1450	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213342	39213342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1271	275	949	0	ENST00000402219.2:c.3625G>A	p.Glu1209Lys	p.E1209K	ENST00000402219	NM_005633.3	1209	Gaa/Aaa	23/23	1	2	FACETS	0.987	0.924	1	0.987	0.924	1	CLONAL	1	TRUE	1	0.360512865265974	2		949	1546	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220421	123220421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	88	615	0	ENST00000218089.9:c.3078G>A	p.Met1026Ile	p.M1026I	ENST00000218089	NM_001042749.1	1026	atG/atA	30/35	0.349145571538407	1	FACETS	0.453	0.401	0.51	0.453	0.401	0.51	SUBCLONAL	1	TRUE	0	0.360512865265974	1		615	883	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	136	258	0				ENST00000310581	NM_198253.2	-/1132			0.208773368642104	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.865553886639445	0		258	294	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888075	81888075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780140339	NA	P-0031888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	85	557	1	ENST00000359376.3:c.220C>T	p.Arg74Cys	p.R74C	ENST00000359376	NM_002661.3	74	Cgc/Tgc	3/33	0.439540889571048	1	FACETS	0.317	0.283	0.354	0.317	0.283	0.354	INDETERMINATE	1	TRUE	0	0.865553886639445	1		558	351	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825394	134825394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757739384	NA	P-0031888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	122	597	0	ENST00000398015.3:c.910C>T	p.Arg304Trp	p.R304W	ENST00000398015	NM_004441.4	304	Cgg/Tgg	4/16	0.440578981807243	1	FACETS	0.349	0.317	0.382	0.349	0.317	0.382	INDETERMINATE	1	TRUE	0	0.865553886639445	1		597	458	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566005	141566005	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	104	521	0	ENST00000220592.5:c.1259A>G	p.Tyr420Cys	p.Y420C	ENST00000220592	NM_012154.3	420	tAc/tGc	10/19	1	2	FACETS	0.556	0.501	0.614	0.556	0.501	0.614	SUBCLONAL	1	TRUE	1	0.865553886639445	2		521	432	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285699	87285699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777390281	NA	P-0031888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	151	711	0	ENST00000277120.3:c.36G>A	p.Met12Ile	p.M12I	ENST00000277120		12	atG/atA	2/19	0.659231486552908	1	FACETS	0.531	0.491	0.571	0.531	0.491	0.571	SUBCLONAL	1	TRUE	0	0.865553886639445	1		711	373	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	134	354	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.172777361276694	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.172777361276694	3		354	707	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0031889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	47	316	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.172777361276694	2		316	457	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5462968	5462968	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	48	493	0	ENST00000381577.3:c.529G>A	p.Gly177Ser	p.G177S	ENST00000381577	NM_014143.3	177	Ggt/Agt	4/7	0.172777361276694	2	FACETS	0.898	0.758	1	0.449	0.379	0.526	CLONAL	1	TRUE	0	0.172777361276694	2		493	619	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222448	53222481	+	frameshift_variant	Frame_Shift_Del	DEL	TCCGCCGCCGCCGCCTCTCCAGGGCCCGGCCCCG	TCCGCCGCCGCCGCCTCTCCAGGGCCCGGCCCCG	-	novel	NA	P-0031889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	29	460	0	ENST00000375401.3:c.4351_4384del	p.Gly1452TrpfsTer15	p.G1452Wfs*15	ENST00000375401	NM_004187.3	1451	CGGGGCCGGGCCCTGGAGAGGCGGCGGCGGCGGAag/ag	26/26	1	1	FACETS	0.601	0.482	0.738	0.601	0.482	0.738	SUBCLONAL	1	TRUE	0	0.172777361276694	1		460	510	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578440	7578440	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs879254249	NA	P-0031891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	212	792	0	ENST00000269305.4:c.490A>G	p.Lys164Glu	p.K164E	ENST00000269305	NM_001126112.2	164	Aag/Gag	5/11	0.340914788628744	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.340914788628744	1		792	1006	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658356	117658356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	197	1044	0	ENST00000368508.3:c.5227C>T	p.Pro1743Ser	p.P1743S	ENST00000368508	NM_002944.2	1743	Cca/Tca	31/43	1	2	FACETS	0.934	0.863	1	0.934	0.863	1	CLONAL	1	TRUE	1	0.340914788628744	2		1044	1237	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941629	48941629	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs1131690860	NA	P-0031891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	87	305	0	ENST00000267163.4:c.940-1G>T		p.X314_splice	ENST00000267163	NM_000321.2	314			0.340914788628744	1	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	0	0.340914788628744	1		305	421	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783188	9783188	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	138	530	0	ENST00000377346.4:c.2436del	p.Tyr813MetfsTer47	p.Y813Mfs*47	ENST00000377346	NM_005026.3	811	aCc/ac	20/24	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.340914788628744	2		530	666	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298648	11298648	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	94	745	0	ENST00000361445.4:c.1813del	p.His605ThrfsTer7	p.H605Tfs*7	ENST00000361445	NM_004958.3	605	Cac/ac	12/58	1	2	FACETS	0.556	0.494	0.623	0.556	0.494	0.623	SUBCLONAL	1	TRUE	1	0.340914788628744	2		745	991	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257102	16257102	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	240	825	1	ENST00000375759.3:c.4367C>A	p.Ser1456Ter	p.S1456*	ENST00000375759	NM_015001.2	1456	tCa/tAa	11/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.340914788628744	2		826	1187	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120913	115120913	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	112	660	0	ENST00000257566.3:c.93C>G	p.Ser31Arg	p.S31R	ENST00000257566	NM_016569.3	31	agC/agG	1/8	1	2	FACETS	0.951	0.856	1	0.951	0.856	1	CLONAL	1	TRUE	1	0.340914788628744	2		660	691	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202352	133202352	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	158	646	0	ENST00000320574.5:c.6536G>T	p.Gly2179Val	p.G2179V	ENST00000320574	NM_006231.2	2179	gGg/gTg	47/49	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.340914788628744	2		646	819	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562368	95562368	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368343829	NA	P-0031891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	171	481	0	ENST00000393063.1:c.4889G>A	p.Arg1630His	p.R1630H	ENST00000393063	NM_030621.3	1630	cGc/cAc	24/28	0.308110718146082	2	FACETS	0.758	0.699	0.818	0.758	0.699	0.818	SUBCLONAL	2	TRUE	0	0.340914788628744	2		481	662	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968212	134968212	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	165	734	0	ENST00000398015.3:c.2725G>C	p.Asp909His	p.D909H	ENST00000398015	NM_004441.4	909	Gac/Cac	15/16	0.204868451498269	4	FACETS	1	0.983	1	0.639	0.586	0.694	CLONAL	1	TRUE	2	0.340914788628744	4		734	1016	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332504	153332504	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	107	536	0	ENST00000281708.4:c.452A>G	p.Asp151Gly	p.D151G	ENST00000281708	NM_033632.3	151	gAc/gGc	2/12	1	2	FACETS	0.875	0.786	0.971	0.875	0.786	0.971	CLONAL	1	TRUE	1	0.340914788628744	2		536	717	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570383	87570383	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	219	890	0	ENST00000277120.3:c.2123T>A	p.Ile708Asn	p.I708N	ENST00000277120		708	aTc/aAc	17/19	0.112966995831173	3	FACETS	1	0.979	1	0.57	0.529	0.612	INDETERMINATE	1	TRUE	1	0.340914788628744	3		890	1320	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321399	1321399	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	196	826	1	ENST00000400841.2:c.356C>A	p.Pro119His	p.P119H	ENST00000400841		119	cCc/cAc	4/6	1	1	FACETS	0.816	0.754	0.88	0.816	0.754	0.88	CLONAL	1	TRUE	0	0.340914788628744	1		827	1169	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933254	39933254	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	273	494	0	ENST00000378444.4:c.1345G>T	p.Asp449Tyr	p.D449Y	ENST00000378444	NM_001123385.1	449	Gat/Tat	4/15	1	1	FACETS	0.805	0.758	0.853	1	0.994	1	CLONAL	2	TRUE	0	0.340914788628744	1		494	825	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134982	2134984	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs137854239	NA	P-0031892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	26	929	0	ENST00000219476.3:c.4527_4529del	p.Phe1510del	p.F1510del	ENST00000219476	NM_000548.3	1508	ccCTTc/ccc	35/42	0.217738432159986	1	FACETS	0.528	0.418	0.655	0.528	0.418	0.655	SUBCLONAL	1	TRUE	0	0.217738432159986	1		929	403	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914592	32914592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1799954	NA	P-0031892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	43	896	1	ENST00000380152.3:c.6100C>T	p.Arg2034Cys	p.R2034C	ENST00000380152		2034	Cgt/Tgt	11/27	1	2	FACETS	0.463	0.386	0.549	0.463	0.386	0.549	SUBCLONAL	1	TRUE	1	0.217738432159986	2		897	853	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882959	89882959	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs761341952	NA	P-0031892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	20	221	1	ENST00000389301.3:c.65G>A	p.Trp22Ter	p.W22*	ENST00000389301	NM_000135.2	22	tGg/tAg	1/43	0.217738432159986	1	FACETS	0.632	0.484	0.805	0.632	0.484	0.805	SUBCLONAL	1	TRUE	0	0.217738432159986	1		222	259	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602427	10602427	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1365381442	NA	P-0031892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	49	907	0	ENST00000171111.5:c.1151C>T	p.Pro384Leu	p.P384L	ENST00000171111	NM_203500.1	384	cCc/cTc	3/6	0.217738432159986	1	FACETS	0.711	0.602	0.831	0.711	0.602	0.831	SUBCLONAL	1	TRUE	0	0.217738432159986	1		907	564	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290926	15290926	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1331591484	NA	P-0031892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	28	1025	0	ENST00000263388.2:c.3284A>G	p.His1095Arg	p.H1095R	ENST00000263388	NM_000435.2	1095	cAt/cGt	20/33	0.217738432159986	1	FACETS	0.51	0.407	0.628	0.51	0.407	0.628	SUBCLONAL	1	TRUE	0	0.217738432159986	1		1025	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579364	7579364	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	294	634	0	ENST00000269305.4:c.323del	p.Gly108ValfsTer15	p.G108Vfs*15	ENST00000269305	NM_001126112.2	108	gGt/gt	4/11	0.387168059766683	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.405212750800941	2		634	725	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725057	89725074	+	stop_gained,protein_altering_variant	Nonsense_Mutation	DEL	TCACAAAAACAGTAGAGG	TCACAAAAACAGTAGAGG	GCT	novel	NA	P-0031907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	27	141	0	ENST00000371953.3:c.1040_1057delinsGCT	p.Phe347_Glu353delinsCysTer	p.F347_E353delinsC*	ENST00000371953	NM_000314.4	347	tTCACAAAAACAGTAGAGGag/tGCTag	9/9	0.315433302438993	3	FACETS	1	0.928	1	0.453	0.367	0.547	CLONAL	1	TRUE	0	0.405212750800941	3		141	118	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007704	45008034	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CATCCATCCGACATTGAAGTTGACTTACTGAAGAATGGAGAGAGAATTGAAAAAGTGGAGCATTCAGACTTGTCTTTCAGCAAGGACTGGTCTTTCTATCTCTTGTACTACACTGAATTCACCCCCACTGAAAAAGATGAGTATGCCTGCCGTGTGAACCATGTGACTTTGTCACAGCCCAAGATAGTTAAGTGGGGTAAGTCTTACATTCTTTTGTAAGCTGCTGAAAGTTGTGTATGAGTAGTCATATCATAAAGCTGCTTTGATATAAAAAAGGTCTATGGCCATACTACCCTGAATGAGTCCCATCCCATCTGATATAAACAATCTG	CATCCATCCGACATTGAAGTTGACTTACTGAAGAATGGAGAGAGAATTGAAAAAGTGGAGCATTCAGACTTGTCTTTCAGCAAGGACTGGTCTTTCTATCTCTTGTACTACACTGAATTCACCCCCACTGAAAAAGATGAGTATGCCTGCCGTGTGAACCATGTGACTTTGTCACAGCCCAAGATAGTTAAGTGGGGTAAGTCTTACATTCTTTTGTAAGCTGCTGAAAGTTGTGTATGAGTAGTCATATCATAAAGCTGCTTTGATATAAAAAAGGTCTATGGCCATACTACCCTGAATGAGTCCCATCCCATCTGATATAAACAATCTG	-	novel	NA	P-0031907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	89	332	0	ENST00000558401.1:c.154_346+138del		p.X52_splice	ENST00000558401	NM_004048.2	52		2/4	0.294042409494478	3	FACETS	1	0.927	1	0.351	0.312	0.393	CLONAL	1	TRUE	0	0.405212750800941	3		332	501	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99185081	99185090	+	frameshift_variant	Frame_Shift_Del	DEL	TGCGGTTAAA	TGCGGTTAAA	AGT	novel	NA	P-0031907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	65	381	1	ENST00000074304.5:c.2483_2492delinsAGT	p.Val828GlufsTer77	p.V828Efs*77	ENST00000074304	NM_001134224.1	828	gTGCGGTTAAAt/gAGTt	23/26	0.376143618124395	2	FACETS	0.899	0.784	1	0.449	0.392	0.511	CLONAL	1	TRUE	0	0.405212750800941	2		382	357	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874558	35874558	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057520828	NA	P-0031907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	125	459	0	ENST00000303115.3:c.714G>A	p.Met238Ile	p.M238I	ENST00000303115	NM_002185.3	238	atG/atA	6/8	0.294042409494478	3	FACETS	0.793	0.722	0.866	0.528	0.481	0.577	SUBCLONAL	2	TRUE	0	0.405212750800941	3		459	468	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552901	106552901	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	256	596	0	ENST00000369096.4:c.866C>A	p.Pro289His	p.P289H	ENST00000369096	NM_001198.3	289	cCc/cAc	5/7	0.405212750800941	8	FACETS	0.902	0.845	0.961			1	CLONAL	3	TRUE	NA	0.405212750800941	8		596	1034	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228339	53228339	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1556840298	NA	P-0031907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	194	462	0	ENST00000375401.3:c.2063G>A	p.Gly688Asp	p.G688D	ENST00000375401	NM_004187.3	688	gGt/gAt	15/26	0.376143618124395	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.405212750800941	2		462	470	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500491	149500491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770930584	NA	P-0031908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	63	548	0	ENST00000261799.4:c.2546G>A	p.Arg849Gln	p.R849Q	ENST00000261799	NM_002609.3	849	cGa/cAa	18/23	0.466184049251897	3	FACETS	0.272	0.234	0.314	0.136	0.117	0.157	SUBCLONAL	1	TRUE	1	0.477454842669314	3		548	1201	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188249	10188249	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	282	672	0	ENST00000256474.2:c.392A>T	p.Asn131Ile	p.N131I	ENST00000256474	NM_000551.3	131	aAc/aTc	2/3	0.477454842669314	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.477454842669314	1		672	786	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682447	52682447	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0031908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	86	397	0	ENST00000394830.3:c.726C>G	p.Tyr242Ter	p.Y242*	ENST00000394830	NM_018313.4	242	taC/taG	8/30	0.477454842669314	1	FACETS	0.946	0.847	1	0.946	0.847	1	CLONAL	1	TRUE	0	0.477454842669314	1		397	290	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001296	150001296	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	19	416	0	ENST00000253339.5:c.2308T>A	p.Tyr770Asn	p.Y770N	ENST00000253339		770	Tat/Aat	4/7	0.415608590528355	3	FACETS	0.319	0.241	0.41	0.159	0.12	0.205	SUBCLONAL	1	TRUE	1	0.440899812329991	3		416	330	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	160	495	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.760296408818262	1	FACETS	0.506	0.467	0.546	0.506	0.467	0.546	SUBCLONAL	1	TRUE	0	0.760296408818262	1		495	516	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371725	55371725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	84	501	0	ENST00000297316.4:c.415C>T	p.Pro139Ser	p.P139S	ENST00000297316	NM_022454.3	139	Ccg/Tcg	2/2	0.716822272950338	4	FACETS	0.325	0.286	0.368	0.108	0.095	0.123	SUBCLONAL	1	TRUE	1	0.760296408818262	4		501	1195	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146602	55146602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	443	490	2	ENST00000257290.5:c.2276G>A	p.Arg759Lys	p.R759K	ENST00000257290	NM_006206.4	759	aGa/aAa	16/23	0.574693935662934	3	FACETS	0.968	0.93	1	0.968	0.93	1	CLONAL	2	TRUE	1	0.760296408818262	3		492	831	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944378	131944378	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	49	141	0	ENST00000265335.6:c.2790C>G	p.Ile930Met	p.I930M	ENST00000265335		930	atC/atG	17/25	0.575475306213516	3	FACETS	0.729	0.623	0.843	0.365	0.311	0.422	SUBCLONAL	1	TRUE	1	0.760296408818262	3		141	244	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0031911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	200	372	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.265086315661237	7	FACETS	0.921	0.857	0.987			1	CLONAL	4	TRUE	NA	0.265086315661237	7		372	681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0031911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	67	694	0	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	1	2	FACETS	0.63	0.547	0.721	0.63	0.547	0.721	SUBCLONAL	1	TRUE	1	0.265086315661237	2		694	802	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0031914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	215	574	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.3	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.33	1		574	975	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533939	63533942	+	frameshift_variant	Frame_Shift_Del	DEL	CTCT	CTCT	-	rs771001164	NA	P-0031914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	118	387	0	ENST00000307078.5:c.1212_1215del	p.Glu405AlafsTer52	p.E405Afs*52	ENST00000307078	NM_004655.3	404	agAGAG/ag	6/11	0.3	1	FACETS	0.949	0.858	1	0.949	0.858	1	CLONAL	1	TRUE	0	0.33	1		387	629	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146647	185146647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	119	440	0	ENST00000265026.3:c.278C>T	p.Ser93Leu	p.S93L	ENST00000265026	NM_004721.4	93	tCa/tTa	2/14	0.3	1	FACETS	0.848	0.766	0.934	0.848	0.766	0.934	CLONAL	1	TRUE	0	0.33	1		440	710	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591925	48591925	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876660556	NA	P-0031914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	85	433	0	ENST00000342988.3:c.1088G>C	p.Cys363Ser	p.C363S	ENST00000342988	NM_005359.5	363	tGt/tCt	9/12	0.3	1	FACETS	0.631	0.557	0.709	0.631	0.557	0.709	SUBCLONAL	1	TRUE	0	0.33	1		433	682	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839699	27839699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	112	340	0	ENST00000328488.2:c.395G>A	p.Arg132Gln	p.R132Q	ENST00000328488	NM_003533.2	132	cGa/cAa	1/1	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.33	2		340	624	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615160	43615160	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1154	110	779	0	ENST00000355710.3:c.2574C>G	p.Ile858Met	p.I858M	ENST00000355710	NM_020975.4	858	atC/atG	14/20	1	2	FACETS	0.527	0.472	0.586	0.527	0.472	0.586	SUBCLONAL	1	TRUE	1	0.33	2		779	1264	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134468	2134468	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	240	750	0	ENST00000219476.3:c.4245G>C	p.Lys1415Asn	p.K1415N	ENST00000219476	NM_000548.3	1415	aaG/aaC	34/42	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.33	2		750	1306	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398255	25398255	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913236	NA	P-0031920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	201	644	0	ENST00000311936.3:c.64C>A	p.Gln22Lys	p.Q22K	ENST00000311936	NM_004985.3	22	Cag/Aag	2/5	1	2	FACETS	0.942	0.873	1	0.942	0.873	1	CLONAL	1	TRUE	1	0.464024525128272	2		644	920	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248189	59248189	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774994834	NA	P-0031920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	22	50	0	ENST00000371222.2:c.554G>A	p.Gly185Asp	p.G185D	ENST00000371222	NM_002228.3	185	gGc/gAc	1/1	0.464024525128272	3	FACETS	1	0.887	1	0.602	0.476	0.742	CLONAL	1	TRUE	1	0.464024525128272	3		50	97	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028668	12028674	+	frameshift_variant	Frame_Shift_Del	DEL	TGGAGTT	TGGAGTT	-	novel	NA	P-0031920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	175	561	0	ENST00000353533.5:c.874_880del	p.Ser292GlyfsTer24	p.S292Gfs*24	ENST00000353533	NM_003010.3	291	TGGAGTTtg/tg	8/11	0.464024525128272	1	FACETS	0.937	0.867	1	0.937	0.867	1	CLONAL	1	TRUE	0	0.464024525128272	1		561	618	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292463	15292463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	90	843	3	ENST00000263388.2:c.2716G>A	p.Ala906Thr	p.A906T	ENST00000263388	NM_000435.2	906	Gcc/Acc	17/33	1	2	FACETS	0.334	0.295	0.375	0.334	0.295	0.375	SUBCLONAL	1	TRUE	1	0.464024525128272	2		846	1163	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972723	25972723	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	161	458	0	ENST00000435504.4:c.1702A>G	p.Arg568Gly	p.R568G	ENST00000435504		568	Agg/Ggg	12/13	1	2	FACETS	0.977	0.899	1	0.977	0.899	1	CLONAL	1	TRUE	1	0.464024525128272	2		458	710	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32931993	32931993	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	28	326	0	ENST00000380152.3:c.7732G>T	p.Gly2578Ter	p.G2578*	ENST00000380152		2578	Gga/Tga	16/27	0.168909808397776	1	FACETS	0.292	0.233	0.359	0.292	0.233	0.359	INDETERMINATE	1	TRUE	0	0.36133431945483	1		326	435	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0031922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	103	314	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.991	0.889	1	0.991	0.889	1	CLONAL	1	TRUE	1	0.330348765309212	2		314	629	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0031922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	109	414	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	0.985	0.886	1	0.985	0.886	1	CLONAL	1	TRUE	1	0.330348765309212	2		414	670	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155721	56155722	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0031922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	64	281	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	0.702	0.924	0.809	0.702	0.924	CLONAL	1	TRUE	1	0.330348765309212	2		281	479	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183204	56183204	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0031922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	78	284	0	ENST00000399503.3:c.4115-1G>C		p.X1372_splice	ENST00000399503	NM_005921.1	1372			1	2	FACETS	0.83	0.73	0.937	0.83	0.73	0.937	CLONAL	1	TRUE	1	0.330348765309212	2		284	569	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068094	94068094	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1313085656	NA	P-0031922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	35	243	0	ENST00000369303.4:c.868G>A	p.Asp290Asn	p.D290N	ENST00000369303	NM_004440.3	290	Gat/Aat	4/17	1	2	FACETS	0.556	0.456	0.668	0.556	0.456	0.668	SUBCLONAL	1	TRUE	1	0.330348765309212	2		243	381	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0031923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	170	363	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	0.852932082034081	2		363	392	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0031923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	199	410	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.852932082034081	2		410	464	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795593	42795594	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0031923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	84	727	1	ENST00000575354.2:c.2674_2675del	p.Val892ThrfsTer38	p.V892Tfs*38	ENST00000575354	NM_015125.3	891	tcTGta/tcta	10/20	0.852932082034081	1	FACETS	0.228	0.202	0.256	0.228	0.202	0.256	SUBCLONAL	1	TRUE	0	0.852932082034081	1		728	495	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799065	42799065	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	209	851	0	ENST00000575354.2:c.4549A>G	p.Lys1517Glu	p.K1517E	ENST00000575354	NM_015125.3	1517	Aag/Gag	20/20	0.852932082034081	1	FACETS	0.513	0.48	0.547	0.513	0.48	0.547	SUBCLONAL	1	TRUE	0	0.852932082034081	1		851	548	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0031925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	321	636	0	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	0.338299024077388	2	FACETS	0.939	0.89	0.99	0.939	0.89	0.99	CLONAL	2	TRUE	0	0.374239704857031	2		636	913	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105955	27105955	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	220	422	0	ENST00000324856.7:c.5566C>T	p.Gln1856Ter	p.Q1856*	ENST00000324856	NM_006015.4	1856	Cag/Tag	20/20	NA	2	FACETS	1	0.951	1			1	INDETERMINATE	2	TRUE	NA	0.374239704857031	2		422	578	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906916	32906919	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	rs80359277	NA	P-0031925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	167	341	0	ENST00000380152.3:c.1310_1313del	p.Lys437IlefsTer22	p.K437Ifs*22	ENST00000380152		434	aAAAGa/aa	10/27	0.374239704857031	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	0	0.374239704857031	2		341	439	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562791	29562791	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1131691075	NA	P-0031925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	203	416	0	ENST00000356175.3:c.3870+1G>A		p.X1290_splice	ENST00000356175	NM_000267.3	1290			0.338299024077388	2	FACETS	0.976	0.911	1	0.976	0.911	1	CLONAL	2	TRUE	0	0.374239704857031	2		416	556	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89837023	89837023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777032467	NA	P-0031925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	145	668	0	ENST00000389301.3:c.2171C>T	p.Thr724Met	p.T724M	ENST00000389301	NM_000135.2	724	aCg/aTg	24/43	0.306764041451436	4	FACETS	0.871	0.792	0.953	0.435	0.396	0.477	CLONAL	1	TRUE	2	0.374239704857031	4		668	1223	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143165	30143165	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746089013	NA	P-0031925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	408	531	1	ENST00000389048.3:c.361C>T	p.Arg121Trp	p.R121W	ENST00000389048	NM_004304.4	121	Cgg/Tgg	1/29	0.365065793528485	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.374239704857031	3		532	784	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660809	227660809	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	35	452	0	ENST00000305123.5:c.2646G>C	p.Gln882His	p.Q882H	ENST00000305123	NM_005544.2	882	caG/caC	1/2	0.27803665196534	3	FACETS	0.319	0.26	0.385	0.159	0.13	0.193	SUBCLONAL	1	TRUE	1	0.374239704857031	3		452	697	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397774	49397792	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGTTTGCCATATCTCTG	CCTGTTTGCCATATCTCTG	-	novel	NA	P-0031925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	206	672	0	ENST00000418115.1:c.432_450del	p.Arg145LeufsTer17	p.R145Lfs*17	ENST00000418115	NM_001664.2	144	ggCAGAGATATGGCAAACAGG/gg	5/5	0.338299024077388	2	FACETS	1	0.988	1	0.658	0.612	0.707	CLONAL	1	TRUE	0	0.374239704857031	2		672	836	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343015	70343015	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1323878836	NA	P-0031925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	117	711	1	ENST00000374080.3:c.1556G>A	p.Arg519Gln	p.R519Q	ENST00000374080		519	cGg/cAg	11/45	0.374239704857031	3	FACETS	0.595	0.535	0.659	0.298	0.267	0.33	SUBCLONAL	1	TRUE	1	0.374239704857031	3		712	1247	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0031928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	149	358	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.790498334145741	2		359	363	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs104886003	NA	P-0031928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	198	662	0	ENST00000263967.3:c.1633G>C	p.Glu545Gln	p.E545Q	ENST00000263967	NM_006218.2	545	Gag/Cag	10/21	0.790498334145741	3	FACETS	1	0.954	1	0.516	0.48	0.554	CLONAL	1	TRUE	1	0.790498334145741	3		662	677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519999	NA	P-0031928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	342	737	0	ENST00000269305.4:c.716A>G	p.Asn239Ser	p.N239S	ENST00000269305	NM_001126112.2	239	aAc/aGc	7/11	0.790498334145741	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.790498334145741	1		737	475	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730876	40730876	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372862828	NA	P-0031928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	319	653	0	ENST00000373198.4:c.3659G>A	p.Arg1220Gln	p.R1220Q	ENST00000373198	NM_133170.3	1220	cGg/cAg	27/32	1	2	FACETS	0.977	0.926	1	0.977	0.926	1	CLONAL	1	TRUE	1	0.790498334145741	2		653	826	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696461	47696461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	279	436	0	ENST00000347630.2:c.362G>A	p.Arg121Gln	p.R121Q	ENST00000347630	NM_001007230.1	121	cGg/cAg	6/11	0.790498334145741	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.790498334145741	2		436	335	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641388	23641388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780820	NA	P-0031928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	59	932	0	ENST00000261584.4:c.2087C>T	p.Thr696Met	p.T696M	ENST00000261584	NM_024675.3	696	aCg/aTg	5/13	1	2	FACETS	0.199	0.17	0.23	0.199	0.17	0.23	SUBCLONAL	1	TRUE	1	0.790498334145741	2		932	751	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129868	69129868	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776942401	NA	P-0031928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	174	314	1	ENST00000288368.4:c.4622C>T	p.Thr1541Met	p.T1541M	ENST00000288368	NM_024870.2	1541	aCg/aTg	38/40	1	2	FACETS	0.867	0.804	0.93	0.867	0.804	0.93	CLONAL	1	TRUE	1	0.790498334145741	2		315	508	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468388	89468388	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	61	293	0	ENST00000336596.2:c.1922A>T	p.Lys641Ile	p.K641I	ENST00000336596	NM_005233.5	641	aAa/aTa	11/17	0.786891896683927	1	FACETS	0.924	0.835	1	0.924	0.835	1	CLONAL	1	TRUE	0	0.790498334145741	1		293	101	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508614	106508614	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377001952	NA	P-0031929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	112	464	0	ENST00000359195.3:c.608C>T	p.Thr203Met	p.T203M	ENST00000359195	NM_002649.2	203	aCg/aTg	2/11	0.551432899249116	3	FACETS	1	0.935	1	0.522	0.472	0.575	CLONAL	1	TRUE	1	0.551432899249116	3		464	496	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612963	228612963	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375264894	NA	P-0031929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	76	381	1	ENST00000366696.1:c.64G>A	p.Ala22Thr	p.A22T	ENST00000366696	NM_003493.2	22	Gcc/Acc	1/1	0.523144962116624	4	FACETS	0.716	0.629	0.81	0.239	0.209	0.27	SUBCLONAL	1	TRUE	1	0.551432899249116	4		382	597	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058598	42058598	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	60	233	0	ENST00000219905.7:c.8318C>G	p.Ser2773Cys	p.S2773C	ENST00000219905	NM_001164273.1	2773	tCt/tGt	24/24	1	2	FACETS	0.803	0.698	0.915	0.803	0.698	0.915	CLONAL	1	TRUE	1	0.551432899249116	2		233	271	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646331	3646331	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	202	853	0	ENST00000294008.3:c.1747A>T	p.Arg583Trp	p.R583W	ENST00000294008	NM_032444.2	583	Agg/Tgg	8/15	0.523144962116624	4	FACETS	0.918	0.849	0.99	0.306	0.283	0.33	CLONAL	1	TRUE	1	0.551432899249116	4		853	1238	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266822	18266822	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753372060	NA	P-0031929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	180	493	0	ENST00000222254.8:c.133G>A	p.Glu45Lys	p.E45K	ENST00000222254	NM_005027.3	45	Gag/Aag	2/16	0.551432899249116	3	FACETS	1	0.985	1	0.629	0.582	0.677	CLONAL	1	TRUE	1	0.551432899249116	3		493	662	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467891	66467891	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	99	400	0	ENST00000273854.3:c.378C>G	p.Ile126Met	p.I126M	ENST00000273854	NM_004439.5	126	atC/atG	3/18	0.551432899249116	3	FACETS	0.958	0.859	1	0.479	0.429	0.531	CLONAL	1	TRUE	1	0.551432899249116	3		400	478	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539147	187539147	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	160	551	0	ENST00000441802.2:c.8593G>T	p.Glu2865Ter	p.E2865*	ENST00000441802	NM_005245.3	2865	Gaa/Taa	10/27	0.551432899249116	3	FACETS	1	0.972	1	0.563	0.517	0.609	CLONAL	1	TRUE	1	0.551432899249116	3		551	658	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79952279	79952279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373436584	NA	P-0031929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	104	342	1	ENST00000265081.6:c.287C>T	p.Pro96Leu	p.P96L	ENST00000265081	NM_002439.4	96	cCt/cTt	2/24	0.551432899249116	4	FACETS	0.93	0.835	1	0.31	0.278	0.344	CLONAL	1	TRUE	1	0.551432899249116	4		343	629	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0031930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	506	752	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.685093302419508	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.689139467562402	2		752	697	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972913	55972913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	357	721	0	ENST00000263923.4:c.1477G>A	p.Gly493Arg	p.G493R	ENST00000263923	NM_002253.2	493	Gga/Aga	11/30	0.689139467562402	4	FACETS	0.974	0.927	1	0.974	0.927	1	CLONAL	2	TRUE	2	0.689139467562402	4		721	898	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145662	11145662	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	343	572	0	ENST00000358026.2:c.4024G>T	p.Glu1342Ter	p.E1342*	ENST00000358026	NM_001128849.1	1342	Gag/Tag	29/36	0.532656416352403	4	FACETS	0.976	0.928	1	0.976	0.928	1	CLONAL	2	TRUE	2	0.689139467562402	4		572	861	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0031930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	190	335	0	ENST00000267163.4:c.1215+1G>C		p.X405_splice	ENST00000267163	NM_000321.2	405			0.685093302419508	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.689139467562402	2		335	264	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726508	46726508	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0031930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	301	484	1	ENST00000371975.4:c.587T>A	p.Leu196Ter	p.L196*	ENST00000371975	NM_003579.3	196	tTg/tAg	7/18	0.663604366208034	3	FACETS	0.972	0.925	1	0.972	0.925	1	CLONAL	2	TRUE	1	0.689139467562402	3		485	604	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248159	59248159	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	22	70	0	ENST00000371222.2:c.584T>A	p.Leu195Gln	p.L195Q	ENST00000371222	NM_002228.3	195	cTg/cAg	1/1	0.663604366208034	3	FACETS	0.825	0.671	0.985	0.825	0.671	0.985	CLONAL	2	TRUE	1	0.689139467562402	3		70	52	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861983	57861983	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	228	419	0	ENST00000228682.2:c.1284del	p.Arg428SerfsTer2	p.R428Sfs*2	ENST00000228682	NM_005269.2	428	agA/ag	10/12	0.641404304236439	4	FACETS	0.955	0.897	1	0.955	0.897	1	CLONAL	2	TRUE	2	0.689139467562402	4		419	585	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259316	89259316	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	278	493	0	ENST00000336596.2:c.460C>A	p.Gln154Lys	p.Q154K	ENST00000336596	NM_005233.5	154	Caa/Aaa	3/17	0.689139467562402	2	FACETS	0.938	0.898	0.978	0.938	0.898	0.978	CLONAL	2	TRUE	0	0.689139467562402	2		493	430	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205097	128205097	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	198	758	0	ENST00000341105.2:c.344C>G	p.Pro115Arg	p.P115R	ENST00000341105	NM_032638.4	115	cCc/cGc	3/6	0.641404304236439	4	FACETS	1	0.966	1	0.536	0.497	0.577	CLONAL	1	TRUE	2	0.689139467562402	4		758	905	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31946741	31946741	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs756581634	NA	P-0031930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	244	691	0	ENST00000375333.2:c.629A>G	p.His210Arg	p.H210R	ENST00000375333	NM_032454.1	210	cAt/cGt	4/8	0.610046699495358	3	FACETS	1	0.976	1	0.543	0.509	0.579	CLONAL	1	TRUE	1	0.689139467562402	3		691	876	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798189	32798189	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	173	576	0	ENST00000374899.4:c.1490A>T	p.Glu497Val	p.E497V	ENST00000374899	NM_018833.2	497	gAg/gTg	9/12	0.610046699495358	3	FACETS	0.973	0.898	1	0.486	0.449	0.525	CLONAL	1	TRUE	1	0.689139467562402	3		576	694	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265556	152265556	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	352	588	1	ENST00000206249.3:c.1009T>G	p.Phe337Val	p.F337V	ENST00000206249	NM_000125.3	337	Ttc/Gtc	4/8	0.689139467562402	3	FACETS	0.965	0.921	1	0.965	0.921	1	CLONAL	2	TRUE	1	0.689139467562402	3		589	712	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978799	13978799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	469	672	2	ENST00000405192.2:c.308G>T	p.Cys103Phe	p.C103F	ENST00000405192	NM_001163147.1	103	tGc/tTc	6/12	0.641404304236439	4	FACETS	0.978	0.937	1	0.978	0.937	1	CLONAL	2	TRUE	2	0.689139467562402	4		674	1175	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913187	39913187	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	274	200	0	ENST00000378444.4:c.4928A>G	p.Glu1643Gly	p.E1643G	ENST00000378444	NM_001123385.1	1643	gAg/gGg	14/15	0.687916024794019	2	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.689139467562402	2		200	345	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620104	21620104	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	150	610	0	ENST00000382592.4:c.62A>G	p.Glu21Gly	p.E21G	ENST00000382592	NM_014572.2	21	gAg/gGg	2/8	0.320650125667896	3	FACETS	0.912	0.832	0.996			1	CLONAL	1	TRUE	NA	0.378280643703292	3		610	1034	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578217	7578218	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0031932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	291	655	0	ENST00000269305.4:c.631_632del	p.Thr211PhefsTer4	p.T211Ffs*4	ENST00000269305	NM_001126112.2	211	ACt/t	6/11	0.378280643703292	2	FACETS	0.954	0.902	1	0.954	0.902	1	CLONAL	2	TRUE	0	0.378280643703292	2		655	806	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586487	189586492	+	inframe_deletion	In_Frame_Del	DEL	GGTGAT	GGTGAT	-	novel	NA	P-0031932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	80	401	0	ENST00000264731.3:c.1114_1119del	p.Asp372_Gly373del	p.D372_G373del	ENST00000264731	NM_003722.4	371	GGTGAT/-	8/14	0.378280643703292	5	FACETS	0.753	0.662	0.852	0.188	0.165	0.213	SUBCLONAL	1	TRUE	1	0.378280643703292	5		401	880	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753915	133753915	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	240	529	0	ENST00000318560.5:c.1384G>C	p.Glu462Gln	p.E462Q	ENST00000318560	NM_005157.4	462	Gaa/Caa	8/11	0.191723400245116	5	FACETS	1	0.979	1	0.74	0.692	0.789	INDETERMINATE	2	TRUE	2	0.378280643703292	5		529	896	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226553707	226553707	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	52	597	1	ENST00000366794.5:c.2453T>C	p.Val818Ala	p.V818A	ENST00000366794	NM_001618.3	818	gTt/gCt	18/23	0.404919870743887	3	FACETS	0.316	0.268	0.369	0.158	0.134	0.185	SUBCLONAL	1	TRUE	1	0.404919870743887	3		598	977	SUCCESS
FH	2271	MSKCC	GRCh37	1	241671917	241671917	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	82	575	0	ENST00000366560.3:c.724C>G	p.Leu242Val	p.L242V	ENST00000366560	NM_000143.3	242	Ctt/Gtt	5/10	0.404919870743887	3	FACETS	0.608	0.535	0.686	0.304	0.267	0.343	SUBCLONAL	1	TRUE	1	0.404919870743887	3		575	801	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982122	93982122	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1562059593	NA	P-0031933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	150	537	0	ENST00000369303.4:c.1343G>A	p.Gly448Glu	p.G448E	ENST00000369303	NM_004440.3	448	gGa/gAa	6/17	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.404919870743887	2		537	646	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521869	157521869	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1423681879	NA	P-0031933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	79	471	1	ENST00000346085.5:c.4141G>A	p.Gly1381Arg	p.G1381R	ENST00000346085	NM_020732.3	1381	Ggg/Agg	18/20	1	2	FACETS	0.709	0.625	0.8	0.709	0.625	0.8	SUBCLONAL	1	TRUE	1	0.404919870743887	2		472	550	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593595	55593600	+	inframe_deletion	In_Frame_Del	DEL	AAGTAC	AAGTAC	-	novel	NA	P-0031934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	193	422	0	ENST00000288135.5:c.1662_1667del	p.Val555_Gln556del	p.V555_Q556del	ENST00000288135	NM_000222.2	554	gAAGTACag/gag	11/21	1	2	FACETS	0.82	0.762	0.881	0.82	0.762	0.881	CLONAL	1	TRUE	1	0.680091735227699	2		422	692	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188078	11188078	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	451	507	0	ENST00000361445.4:c.6016G>T	p.Val2006Phe	p.V2006F	ENST00000361445	NM_004958.3	2006	Gtc/Ttc	43/58	0.894579984880459	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.920195569769898	1		507	528	SUCCESS
EED	8726	MSKCC	GRCh37	11	85956293	85956293	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	150	210	0	ENST00000263360.6:c.22A>C	p.Thr8Pro	p.T8P	ENST00000263360	NM_003797.3	8	Act/Cct	1/12	1	2	FACETS	0.891	0.825	0.957	0.891	0.825	0.957	CLONAL	1	TRUE	1	0.920195569769898	2		210	366	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953742	48953742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1131690851	NA	P-0031935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	267	338	1	ENST00000267163.4:c.1345G>A	p.Gly449Arg	p.G449R	ENST00000267163	NM_000321.2	449	Gga/Aga	14/27	0.920195569769898	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.920195569769898	1		339	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0031935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	467	527	3	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.90566787889332	1	FACETS	0.987	0.965	1	0.987	0.965	1	CLONAL	1	TRUE	0	0.920195569769898	1		530	555	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670024	29670035	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAGAGTCCAGAG	TAGAGTCCAGAG	ATA	novel	NA	P-0031935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	313	388	2	ENST00000356175.3:c.7000-3_7008delinsATA		p.X2334_splice	ENST00000356175	NM_000267.3	2334		47/57	0.90566787889332	1	FACETS	0.995	0.968	1	0.995	0.968	1	CLONAL	1	TRUE	0	0.920195569769898	1		390	369	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534463	63534463	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0031935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	478	538	1	ENST00000307078.5:c.1060-2A>G		p.X354_splice	ENST00000307078	NM_004655.3	354			0.90566787889332	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.920195569769898	1		539	540	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584593	48584593	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	342	464	1	ENST00000342988.3:c.766C>T	p.Gln256Ter	p.Q256*	ENST00000342988	NM_005359.5	256	Cag/Tag	6/12	0.920195569769898	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.920195569769898	1		465	391	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231558	5231558	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	364	432	0	ENST00000357368.4:c.1918C>G	p.Arg640Gly	p.R640G	ENST00000357368	NM_002850.3	640	Cgc/Ggc	14/38	1	2	FACETS	0.977	0.932	1	0.977	0.932	1	CLONAL	1	TRUE	1	0.920195569769898	2		432	810	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291160	10291160	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	641	722	2	ENST00000340748.4:c.311A>G	p.Asn104Ser	p.N104S	ENST00000340748		104	aAt/aGt	4/40	1	2	FACETS	0.994	0.959	1	0.994	0.959	1	CLONAL	1	TRUE	1	0.920195569769898	2		724	1402	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412900	49412900	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	624	720	2	ENST00000418115.1:c.123C>G	p.Asn41Lys	p.N41K	ENST00000418115	NM_001664.2	41	aaC/aaG	2/5	1	2	FACETS	0.943	0.909	0.977	0.943	0.909	0.977	CLONAL	1	TRUE	1	0.920195569769898	2		722	1438	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587119	189587119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765502786	NA	P-0031935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	1155	432	3	ENST00000264731.3:c.1136G>A	p.Arg379His	p.R379H	ENST00000264731	NM_003722.4	379	cGt/cAt	9/14	0.570130384377715	6	FACETS	0.975	0.959	0.991			1	CLONAL	5	TRUE	NA	0.920195569769898	6		435	1463	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628399	86628399	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0031935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	235	449	1	ENST00000274376.6:c.768C>G	p.Tyr256Ter	p.Y256*	ENST00000274376	NM_002890.2	256	taC/taG	3/25	0.920195569769898	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.920195569769898	1		450	262	SUCCESS
APC	324	MSKCC	GRCh37	5	112170777	112170780	+	frameshift_variant	Frame_Shift_Del	DEL	CAGA	CAGA	-	rs878853420	NA	P-0031935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	428	709	0	ENST00000257430.4:c.1875_1878del	p.Asn627LeufsTer2	p.N627Lfs*2	ENST00000257430	NM_000038.5	625	CAGAca/ca	15/16	0.920195569769898	1	FACETS	0.93	0.905	0.954	0.93	0.905	0.954	CLONAL	1	TRUE	0	0.920195569769898	1		709	540	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521499	8521499	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	540	694	0	ENST00000356435.5:c.739A>T	p.Ile247Phe	p.I247F	ENST00000356435		247	Atc/Ttc	9/35	0.920195569769898	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.920195569769898	1		694	628	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223602	53223602	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	363	474	1	ENST00000375401.3:c.3757C>G	p.Pro1253Ala	p.P1253A	ENST00000375401	NM_004187.3	1253	Ccg/Gcg	23/26	1	2	FACETS	0.91	0.867	0.954	0.91	0.867	0.954	CLONAL	1	TRUE	1	0.920195569769898	2		475	867	SUCCESS
APC	324	MSKCC	GRCh37	5	112175375	112175409	+	frameshift_variant	Frame_Shift_Del	DEL	TCCAAAAGTGGTGCTCAGACACCCAAAAGTCCACC	TCCAAAAGTGGTGCTCAGACACCCAAAAGTCCACC	A	novel	NA	P-0031935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	14	240	0	ENST00000257430.4:c.4084_4118delinsA	p.Ser1362MetfsTer42	p.S1362Mfs*42	ENST00000257430	NM_000038.5	1362	TCCAAAAGTGGTGCTCAGACACCCAAAAGTCCACCt/At	16/16	0.920195569769898	1	FACETS	0.06	0.043	0.081	0.06	0.043	0.081	SUBCLONAL	1	TRUE	0	0.920195569769898	1		240	273	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	121	258	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.734	0.666	0.805	0.734	0.666	0.805	SUBCLONAL	1	TRUE	1	0.630468593086094	2		258	523	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0031937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	179	391	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.748	0.691	0.807	0.748	0.691	0.807	SUBCLONAL	1	TRUE	1	0.630468593086094	2		391	759	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0031937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	194	319	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.809	0.75	0.869	0.809	0.75	0.869	CLONAL	1	TRUE	1	0.630468593086094	2		319	761	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122721	108122721	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	233	588	1	ENST00000278616.4:c.1766del	p.Leu589Ter	p.L589*	ENST00000278616	NM_000051.3	589	Tta/ta	11/63	1	2	FACETS	0.723	0.674	0.774	0.723	0.674	0.774	SUBCLONAL	1	TRUE	1	0.630468593086094	2		589	1022	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217798	2217798	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	280	742	1	ENST00000398665.3:c.2572A>T	p.Ser858Cys	p.S858C	ENST00000398665	NM_032482.2	858	Agc/Tgc	22/28	1	2	FACETS	0.748	0.702	0.795	0.748	0.702	0.795	SUBCLONAL	1	TRUE	1	0.630468593086094	2		743	1188	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853010	151853010	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	131	384	0	ENST00000262189.6:c.11945A>G	p.Asn3982Ser	p.N3982S	ENST00000262189	NM_170606.2	3982	aAt/aGt	46/59	1	2	FACETS	0.679	0.618	0.743	0.679	0.618	0.743	SUBCLONAL	1	TRUE	1	0.630468593086094	2		384	612	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097751	27097751	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	72	581	2	ENST00000324856.7:c.3344del	p.Pro1115GlnfsTer46	p.P1115Qfs*46	ENST00000324856	NM_006015.4	1114	Ccc/cc	12/20	1	2	FACETS	0.638	0.557	0.725	0.638	0.557	0.725	SUBCLONAL	1	TRUE	1	0.331513670866433	2		583	681	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467993	50467993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	69	419	0	ENST00000331340.3:c.1228G>A	p.Gly410Ser	p.G410S	ENST00000331340	NM_006060.4	410	Ggt/Agt	8/8	1	2	FACETS	0.578	0.503	0.66	0.578	0.503	0.66	SUBCLONAL	1	TRUE	1	0.331513670866433	2		419	720	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981830	201981848	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGGCAGCTGTGGCGCAG	CCCGGCAGCTGTGGCGCAG	-	novel	NA	P-0031939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	234	745	0	ENST00000359651.3:c.541_559del	p.Pro181GlufsTer67	p.P181Efs*67	ENST00000359651		181	CCCGGCAGCTGTGGCGCAGga/ga	4/8	0.209062628149004	3	FACETS	0.76	0.709	0.814	0.76	0.709	0.814	SUBCLONAL	2	TRUE	1	0.331513670866433	3		745	1082	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436583	49436583	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	92	809	0	ENST00000301067.7:c.5723del	p.Gly1908ValfsTer7	p.G1908Vfs*7	ENST00000301067	NM_003482.3	1908	gGt/gt	26/54	1	2	FACETS	0.519	0.46	0.583	0.519	0.46	0.583	SUBCLONAL	1	TRUE	1	0.331513670866433	2		809	1069	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835777	68835777	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	45	615	0	ENST00000261769.5:c.368A>C	p.His123Pro	p.H123P	ENST00000261769	NM_004360.3	123	cAc/cCc	3/16	1	2	FACETS	0.335	0.28	0.395	0.335	0.28	0.395	SUBCLONAL	1	TRUE	1	0.331513670866433	2		615	811	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863659	68863659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782162	NA	P-0031939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	74	592	0	ENST00000261769.5:c.2398C>T	p.Arg800Cys	p.R800C	ENST00000261769	NM_004360.3	800	Cgc/Tgc	15/16	1	2	FACETS	0.578	0.505	0.657	0.578	0.505	0.657	SUBCLONAL	1	TRUE	1	0.331513670866433	2		592	772	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540551	187540555	+	frameshift_variant	Frame_Shift_Del	DEL	CTTCA	CTTCA	-	novel	NA	P-0031939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	64	516	0	ENST00000441802.2:c.7185_7189del	p.Glu2396GlnfsTer3	p.E2396Qfs*3	ENST00000441802	NM_005245.3	2395	taTGAAGcc/tacc	10/27	1	2	FACETS	0.576	0.498	0.661	0.576	0.498	0.661	SUBCLONAL	1	TRUE	1	0.331513670866433	2		516	670	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848660	151848663	+	frameshift_variant	Frame_Shift_Del	DEL	GAAA	GAAA	TAT	novel	NA	P-0031939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	48	292	1	ENST00000262189.6:c.12530_12533delinsATA	p.Leu4177HisfsTer41	p.L4177Hfs*41	ENST00000262189	NM_170606.2	4177	cTTTCt/cATAt	50/59	1	2	FACETS	0.76	0.644	0.887	0.76	0.644	0.887	SUBCLONAL	1	TRUE	1	0.331513670866433	2		293	381	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772116	135772116	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	67	474	0	ENST00000298552.3:c.3001T>G	p.Ser1001Ala	p.S1001A	ENST00000298552	NM_001162426.1	1001	Tca/Gca	23/23	1	2	FACETS	0.479	0.416	0.549	0.479	0.416	0.549	SUBCLONAL	1	TRUE	1	0.331513670866433	2		474	843	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0031941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1216	73	769	0	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	1	2	FACETS	0.391	0.34	0.446	0.391	0.34	0.446	SUBCLONAL	1	TRUE	1	0.29	2		769	1289	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0031941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	45	373	0	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	1	2	FACETS	0.568	0.477	0.669	0.568	0.477	0.669	SUBCLONAL	1	TRUE	1	0.29	2		373	546	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962849	2962849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs562372731	NA	P-0031941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	67	695	0	ENST00000396946.4:c.2059G>A	p.Ala687Thr	p.A687T	ENST00000396946	NM_032415.4	687	Gcg/Acg	16/25	1	2	FACETS	0.408	0.353	0.468	0.408	0.353	0.468	SUBCLONAL	1	TRUE	1	0.29	2		695	1132	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934575	NA	P-0031941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1222	70	683	0	ENST00000269305.4:c.733G>C	p.Gly245Arg	p.G245R	ENST00000269305	NM_001126112.2	245	Ggc/Cgc	7/11	1	2	FACETS	0.374	0.324	0.428	0.374	0.324	0.428	SUBCLONAL	1	TRUE	1	0.29	2		683	1292	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0031941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	53	519	0	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	1	2	FACETS	0.415	0.353	0.484	0.415	0.353	0.484	SUBCLONAL	1	TRUE	1	0.29	2		519	880	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0031950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	198	410	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.867095911196328	2		410	432	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340201	116340201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561295443	NA	P-0031950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	183	352	0	ENST00000397752.3:c.1063G>A	p.Glu355Lys	p.E355K	ENST00000397752	NM_000245.2	355	Gaa/Aaa	2/21	0.855409217852778	3	FACETS	0.914	0.847	0.983	0.457	0.423	0.492	CLONAL	1	TRUE	1	0.867095911196328	3		352	662	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249017	55249018	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCA	rs1554350381	NA	P-0031950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	267	478	0	ENST00000275493.2:c.2317_2319dup	p.His773dup	p.H773dup	ENST00000275493	NM_005228.3	773	ccc/ccCCAc	20/28	0.855409217852778	3	FACETS	0.936	0.879	0.995	0.468	0.439	0.498	CLONAL	1	TRUE	1	0.867095911196328	3		478	943	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624296	89624296	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs786201995	NA	P-0031950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	688	591	0	ENST00000371953.3:c.70G>C	p.Asp24His	p.D24H	ENST00000371953	NM_000314.4	24	Gac/Cac	1/9	0.867095911196328	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.867095911196328	2		591	789	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165928	47165929	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	TCCAAATTAACTTTTGTTTTGGTGCCTTTGGGCAAAA	novel	NA	P-0031950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	170	546	0	ENST00000409792.3:c.161_197dup	p.Glu66AspfsTer11	p.E66Dfs*11	ENST00000409792	NM_014159.6	66	gaa/gaTTTTGCCCAAAGGCACCAAAACAAAAGTTAATTTGGAa	3/21	1	2	FACETS	0.411	0.377	0.445	0.411	0.377	0.445	SUBCLONAL	1	TRUE	1	0.867095911196328	2		546	955	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156715	55156715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756081317	NA	P-0031950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	200	308	0	ENST00000257290.5:c.3116G>A	p.Arg1039Lys	p.R1039K	ENST00000257290	NM_006206.4	1039	aGa/aAa	22/23	1	2	FACETS	0.971	0.91	1	0.971	0.91	1	CLONAL	1	TRUE	1	0.867095911196328	2		308	475	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410517	63410517	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	358	653	1	ENST00000330258.3:c.2650C>A	p.Pro884Thr	p.P884T	ENST00000330258	NM_152424.3	884	Cct/Act	2/2	1	2	FACETS	0.988	0.941	1	0.988	0.941	1	CLONAL	1	TRUE	1	0.867095911196328	2		654	836	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575152	48575152	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	37	484	1	ENST00000342988.3:c.346C>T	p.Gln116Ter	p.Q116*	ENST00000342988	NM_005359.5	116	Cag/Tag	3/12	1	2	FACETS	0.703	0.578	0.844	0.703	0.578	0.844	SUBCLONAL	1	TRUE	1	0.164385614961423	2		485	640	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164103	47164103	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	48	429	0	ENST00000409792.3:c.2023G>T	p.Gly675Ter	p.G675*	ENST00000409792	NM_014159.6	675	Gga/Tga	3/21	1	2	FACETS	0.897	0.757	1	0.897	0.757	1	CLONAL	1	TRUE	1	0.164385614961423	2		429	651	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680490	241680490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139642944	NA	P-0031952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	71	598	0	ENST00000366560.3:c.259C>T	p.Arg87Cys	p.R87C	ENST00000366560	NM_000143.3	87	Cgc/Tgc	2/10	1	2	FACETS	0.909	0.792	1	0.909	0.792	1	CLONAL	1	TRUE	1	0.164385614961423	2		598	950	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22408246	22408246	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	79	658	1	ENST00000344548.3:c.137T>C	p.Ile46Thr	p.I46T	ENST00000344548	NM_001039802.1	46	aTt/aCt	4/7	1	2	FACETS	0.945	0.829	1	0.945	0.829	1	CLONAL	1	TRUE	1	0.164385614961423	2		659	1017	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	TG	novel	NA	P-0031952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	121	577	1	ENST00000311936.3:c.34_35delinsCA	p.Gly12His	p.G12H	ENST00000311936	NM_004985.3	12	GGt/CAt	2/5	0.164385614961423	3	FACETS	0.956	0.864	1	0.956	0.864	1	CLONAL	2	TRUE	1	0.164385614961423	3		578	833	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574030	7574031	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GATCT	novel	NA	P-0031952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	75	611	0	ENST00000269305.4:c.994-2_996dup	p.Gly334SerfsTer13	p.G334Sfs*13	ENST00000269305	NM_001126112.2	332	-/AGATC	10/11	0.151272109968899	1	FACETS	0.898	0.785	1	0.898	0.785	1	CLONAL	1	TRUE	0	0.164385614961423	1		611	933	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097070	11097070	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	61	757	1	ENST00000358026.2:c.561C>A	p.Tyr187Ter	p.Y187*	ENST00000358026	NM_001128849.1	187	taC/taA	4/36	0.151272109968899	1	FACETS	0.63	0.542	0.727	0.63	0.542	0.727	SUBCLONAL	1	TRUE	0	0.164385614961423	1		758	1081	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0031954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	151	508	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.786	0.719	0.856	1	0.988	1	SUBCLONAL	2	TRUE	1	0.227955098882685	2		509	843	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0031954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	17	455	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.209282536223217	3	FACETS	0.453	0.337	0.591	0.226	0.168	0.296	SUBCLONAL	1	TRUE	1	0.227955098882685	3		455	367	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372320	55372320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	65	608	1	ENST00000297316.4:c.1010C>T	p.Pro337Leu	p.P337L	ENST00000297316	NM_022454.3	337	cCg/cTg	2/2	0.227955098882685	3	FACETS	0.86	0.744	0.985	0.43	0.372	0.493	CLONAL	1	TRUE	1	0.227955098882685	3		609	739	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056237	26056245	+	inframe_deletion	In_Frame_Del	DEL	CTTCTTGGG	CTTCTTGGG	-	rs749190253	NA	P-0031954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	68	668	0	ENST00000343677.2:c.412_420del	p.Pro138_Lys140del	p.P138_K140del	ENST00000343677	NM_005319.3	138	CCCAAGAAG/-	1/1	0.227955098882685	4	FACETS	0.878	0.763	1			1	CLONAL	1	TRUE	NA	0.227955098882685	4		668	834	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873104	134873104	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202048188	NA	P-0031954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	34	641	2	ENST00000398015.3:c.1408C>T	p.Arg470Trp	p.R470W	ENST00000398015	NM_004441.4	470	Cgg/Tgg	6/16	0.227955098882685	1	FACETS	0.45	0.367	0.544	0.45	0.367	0.544	SUBCLONAL	1	TRUE	0	0.227955098882685	1		643	587	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	155	571	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.356198307194388	2		571	796	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	156	490	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.356198307194388	2		490	718	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070349	37070349	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs63750855	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	132	401	5	ENST00000231790.2:c.1489del	p.Arg497GlyfsTer11	p.R497Gfs*11	ENST00000231790	NM_000249.3	495	aCc/ac	13/19	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.356198307194388	2		406	723	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497245	149497245	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	200	609	2	ENST00000261799.4:c.3073del	p.Leu1025CysfsTer20	p.L1025Cfs*20	ENST00000261799	NM_002609.3	1025	Ctg/tg	22/23	1	2	FACETS	0.996	0.922	1	0.996	0.922	1	CLONAL	1	TRUE	1	0.356198307194388	2		611	1127	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	105	385	5	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.356198307194388	2		390	577	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	231	781	3	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.356198307194388	2		784	1279	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794440	42794441	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	289	920	1	ENST00000575354.2:c.1526dup	p.Leu510ThrfsTer4	p.L510Tfs*4	ENST00000575354	NM_015125.3	507	cgc/cgCc	10/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.356198307194388	2		921	1361	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	137	568	3	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.356198307194388	2		571	751	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	118	456	0	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	0.949	0.857	1	0.949	0.857	1	CLONAL	1	TRUE	1	0.356198307194388	2		456	698	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967270	134967270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374549505	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	194	597	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	0.356198307194388	2		597	931	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120115	70120115	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	25	115	0	ENST00000245479.2:c.1121del	p.Pro374ArgfsTer9	p.P374Rfs*9	ENST00000245479	NM_000346.3	373	Ccc/cc	3/3	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.356198307194388	2		115	108	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099080	157099080	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	30	131	0	ENST00000346085.5:c.17G>C	p.Gly6Ala	p.G6A	ENST00000346085	NM_020732.3	6	gGc/gCc	1/20	1	2	FACETS	0.769	0.624	0.932	0.769	0.624	0.932	CLONAL	1	TRUE	1	0.356198307194388	2		131	219	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639588	47639588	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63749897	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	80	323	0	ENST00000233146.2:c.687del	p.Ala230LeufsTer16	p.A230Lfs*16	ENST00000233146	NM_000251.2	227	agA/ag	4/16	1	2	FACETS	0.996	0.88	1	0.996	0.88	1	CLONAL	1	TRUE	1	0.356198307194388	2		323	451	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928373	69928373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770693882	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	117	359	0	ENST00000352241.4:c.193C>T	p.Arg65Cys	p.R65C	ENST00000352241	NM_198159.2	65	Cgt/Tgt	2/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.356198307194388	2		359	572	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181405	185181405	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201739097	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	139	420	1	ENST00000265026.3:c.1346G>A	p.Arg449Gln	p.R449Q	ENST00000265026	NM_004721.4	449	cGg/cAg	8/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.356198307194388	2		421	626	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811605	102811605	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1565968684	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	182	727	0	ENST00000307046.8:c.579del	p.Gly194GlufsTer8	p.G194Efs*8	ENST00000307046	NM_001111285.1	193	aaA/aa	4/4	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.356198307194388	2		727	884	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866581	117866581	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057524012	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	129	714	0	ENST00000297338.2:c.1064C>T	p.Pro355Leu	p.P355L	ENST00000297338	NM_006265.2	355	cCg/cTg	9/14	0.342377893257272	3	FACETS	0.922	0.835	1	0.461	0.417	0.507	CLONAL	1	TRUE	1	0.356198307194388	3		714	926	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246532	41246532	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357569	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	204	793	1	ENST00000357654.3:c.1016del	p.Lys339ArgfsTer2	p.K339Rfs*2	ENST00000357654	NM_007294.3	339	aAg/ag	10/23	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.356198307194388	2		794	1137	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775583	39775583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369318352	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	155	512	1	ENST00000288319.7:c.437C>T	p.Ala146Val	p.A146V	ENST00000288319	NM_182918.3	146	gCg/gTg	4/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.356198307194388	2		513	807	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	135	694	7	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.874	0.794	0.958	0.874	0.794	0.958	CLONAL	1	TRUE	1	0.356198307194388	2		701	867	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214398	36214398	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs868041281	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	212	576	0	ENST00000222270.7:c.3057del	p.Gly1020AlafsTer4	p.G1020Afs*4	ENST00000222270	NM_014727.1	1018	Aaa/aa	7/37	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.356198307194388	2		576	974	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867058	45867058	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	178	527	1	ENST00000391945.4:c.1061C>T	p.Pro354Leu	p.P354L	ENST00000391945	NM_000400.3	354	cCg/cTg	11/23	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.356198307194388	2		528	954	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350108	89350108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768925695	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	239	774	0	ENST00000301030.4:c.2842G>A	p.Gly948Arg	p.G948R	ENST00000301030	NM_001256183.1	948	Ggg/Agg	9/13	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.356198307194388	2		774	1302	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433394	49433394	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783727	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	158	649	0	ENST00000301067.7:c.8053C>T	p.Arg2685Ter	p.R2685*	ENST00000301067	NM_003482.3	2685	Cga/Tga	32/54	1	2	FACETS	0.891	0.815	0.97	0.891	0.815	0.97	CLONAL	1	TRUE	1	0.356198307194388	2		649	996	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859576	151859576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	149	607	0	ENST00000262189.6:c.11086C>T	p.Gln3696Ter	p.Q3696*	ENST00000262189	NM_170606.2	3696	Caa/Taa	43/59	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.356198307194388	2		607	835	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439668	220439668	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs192760521	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	223	789	0	ENST00000243786.2:c.521C>A	p.Pro174His	p.P174H	ENST00000243786	NM_002191.3	174	cCt/cAt	2/2	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.356198307194388	2		789	1116	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572597	141572597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376660302	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	178	557	0	ENST00000220592.5:c.473C>T	p.Thr158Met	p.T158M	ENST00000220592	NM_012154.3	158	aCg/aTg	4/19	0.342377893257272	3	FACETS	1	0.946	1	0.518	0.476	0.561	CLONAL	1	TRUE	1	0.356198307194388	3		557	1137	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798842	45798842	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs759765956	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	173	583	0	ENST00000450313.1:c.389T>C	p.Val130Ala	p.V130A	ENST00000450313	NM_012222.2	130	gTg/gCg	5/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.356198307194388	2		583	894	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162742013	162742013	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	35	492	2	ENST00000367921.3:c.1704G>T	p.Lys568Asn	p.K568N	ENST00000367921	NM_006182.2	568	aaG/aaT	13/18	1	2	FACETS	0.29	0.237	0.35	0.29	0.237	0.35	SUBCLONAL	1	TRUE	1	0.356198307194388	2		494	678	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154881	2154881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	222	692	1	ENST00000434045.2:c.340C>T	p.Arg114Cys	p.R114C	ENST00000434045	NM_001127598.1	114	Cgt/Tgt	4/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.356198307194388	2		693	1102	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375138	118375138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555047259	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	119	379	0	ENST00000534358.1:c.8531G>A	p.Cys2844Tyr	p.C2844Y	ENST00000534358	NM_005933.3	2844	tGt/tAt	27/36	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.356198307194388	2		379	579	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427455	49427455	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	228	775	1	ENST00000301067.7:c.11033C>T	p.Ala3678Val	p.A3678V	ENST00000301067	NM_003482.3	3678	gCc/gTc	39/54	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.356198307194388	2		776	1067	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435913	49435913	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	268	812	0	ENST00000301067.7:c.6068A>G	p.Tyr2023Cys	p.Y2023C	ENST00000301067	NM_003482.3	2023	tAt/tGt	28/54	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.356198307194388	2		812	1295	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444205	49444205	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	93	904	0	ENST00000301067.7:c.3166A>C	p.Ser1056Arg	p.S1056R	ENST00000301067	NM_003482.3	1056	Agt/Cgt	11/54	1	2	FACETS	0.423	0.374	0.475	0.423	0.374	0.475	SUBCLONAL	1	TRUE	1	0.356198307194388	2		904	1235	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492579	50492579	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	217	647	1	ENST00000394963.4:c.1475G>A	p.Cys492Tyr	p.C492Y	ENST00000394963	NM_003076.4	492	tGc/tAc	12/13	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.356198307194388	2		648	1141	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495740	56495740	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	139	479	0	ENST00000267101.3:c.3934del	p.Thr1312LeufsTer5	p.T1312Lfs*5	ENST00000267101	NM_001982.3	1310	ctA/ct	28/28	1	2	FACETS	0.995	0.907	1	0.995	0.907	1	CLONAL	1	TRUE	1	0.356198307194388	2		479	784	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884573	111884573	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	163	410	0	ENST00000341259.2:c.749T>C	p.Leu250Pro	p.L250P	ENST00000341259	NM_005475.2	250	cTa/cCa	3/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.356198307194388	2		410	776	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536740	120536740	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	212	600	0	ENST00000229340.5:c.353-1G>A		p.X118_splice	ENST00000229340	NM_006861.6	118			1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.356198307194388	2		600	1007	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220452	133220452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	216	694	2	ENST00000320574.5:c.4261C>T	p.Pro1421Ser	p.P1421S	ENST00000320574	NM_006231.2	1421	Cca/Tca	33/49	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.356198307194388	2		696	1171	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32931885	32931885	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	74	396	0	ENST00000380152.3:c.7624A>G	p.Thr2542Ala	p.T2542A	ENST00000380152		2542	Acg/Gcg	16/27	1	2	FACETS	0.903	0.793	1	0.903	0.793	1	CLONAL	1	TRUE	1	0.356198307194388	2		396	460	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68290312	68290312	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747008915	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	97	499	0	ENST00000487270.1:c.52C>T	p.Arg18Cys	p.R18C	ENST00000487270	NM_133509.3	18	Cgt/Tgt	2/11	1	2	FACETS	0.888	0.793	0.989	0.888	0.793	0.989	CLONAL	1	TRUE	1	0.356198307194388	2		499	613	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560271	95560271	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	46	466	0	ENST00000393063.1:c.5318T>C	p.Val1773Ala	p.V1773A	ENST00000393063	NM_030621.3	1773	gTg/gCg	25/28	1	2	FACETS	0.374	0.314	0.44	0.374	0.314	0.44	SUBCLONAL	1	TRUE	1	0.356198307194388	2		466	691	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239602	105239602	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	173	565	0	ENST00000349310.3:c.943T>C	p.Tyr315His	p.Y315H	ENST00000349310	NM_001014432.1	315	Tac/Cac	11/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.356198307194388	2		565	894	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007729	45007729	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	154	479	0	ENST00000558401.1:c.176T>G	p.Leu59Ter	p.L59*	ENST00000558401	NM_004048.2	59	tTa/tGa	2/4	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.356198307194388	2		479	716	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777864	3777864	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs759047530	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	310	928	0	ENST00000262367.5:c.7184T>C	p.Ile2395Thr	p.I2395T	ENST00000262367	NM_004380.2	2395	aTa/aCa	31/31	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.356198307194388	2		928	1431	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129758	30129758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	235	780	0	ENST00000263025.4:c.455G>A	p.Arg152Gln	p.R152Q	ENST00000263025	NM_002746.2	152	cGg/cAg	3/9	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.356198307194388	2		780	1093	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264362	30264362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	84	189	0	ENST00000322652.5:c.97G>A	p.Ala33Thr	p.A33T	ENST00000322652	NM_015355.2	33	Gcg/Acg	1/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.356198307194388	2		189	348	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256971	41256971	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	116	540	0	ENST00000357654.3:c.215G>A	p.Ser72Asn	p.S72N	ENST00000357654	NM_007294.3	72	aGc/aAc	5/23	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.356198307194388	2		540	642	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210644	2210644	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	157	495	0	ENST00000398665.3:c.1141G>A	p.Ala381Thr	p.A381T	ENST00000398665	NM_032482.2	381	Gcg/Acg	14/28	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.356198307194388	2		495	805	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118687	11118687	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1248744047	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	225	712	3	ENST00000358026.2:c.2111G>A	p.Arg704Gln	p.R704Q	ENST00000358026	NM_001128849.1	704	cGg/cAg	14/36	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.356198307194388	2		715	1224	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954296	17954296	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	162	476	0	ENST00000458235.1:c.313del	p.Tyr105ThrfsTer42	p.Y105Tfs*42	ENST00000458235	NM_000215.3	105	Tac/ac	4/24	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.356198307194388	2		476	802	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795247	42795247	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	185	621	0	ENST00000575354.2:c.2327C>A	p.Pro776His	p.P776H	ENST00000575354	NM_015125.3	776	cCt/cAt	10/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.356198307194388	2		621	909	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919653	50919653	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	239	623	1	ENST00000440232.2:c.2821G>T	p.Asp941Tyr	p.D941Y	ENST00000440232	NM_002691.3	941	Gac/Tac	23/27	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.356198307194388	2		624	1169	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978930	25978930	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	108	507	0	ENST00000435504.4:c.993C>A	p.Phe331Leu	p.F331L	ENST00000435504		331	ttC/ttA	10/13	1	2	FACETS	0.846	0.759	0.937	0.846	0.759	0.937	CLONAL	1	TRUE	1	0.356198307194388	2		507	717	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99160395	99160395	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1262643000	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	166	527	0	ENST00000074304.5:c.874C>T	p.Arg292Cys	p.R292C	ENST00000074304	NM_001134224.1	292	Cgc/Tgc	11/26	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.356198307194388	2		527	862	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047293	128047293	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs776433788	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	167	530	0	ENST00000285398.2:c.629T>C	p.Ile210Thr	p.I210T	ENST00000285398	NM_000122.1	210	aTc/aCc	5/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.356198307194388	2		530	832	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932983	49932983	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	198	660	0	ENST00000296474.3:c.2963-2A>C		p.X988_splice	ENST00000296474	NM_002447.2	988			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.356198307194388	2		660	973	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442620	52442620	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	73	286	0	ENST00000460680.1:c.125C>A	p.Pro42His	p.P42H	ENST00000460680	NM_004656.3	42	cCt/cAt	4/17	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.356198307194388	2		286	392	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251564	251564	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1554001966	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	154	623	0	ENST00000264932.6:c.1775A>G	p.His592Arg	p.H592R	ENST00000264932	NM_004168.2	592	cAt/cGt	13/15	1	2	FACETS	0.994	0.91	1	0.994	0.91	1	CLONAL	1	TRUE	1	0.356198307194388	2		623	870	SUCCESS
APC	324	MSKCC	GRCh37	5	112175408	112175408	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	71	369	0	ENST00000257430.4:c.4117C>T	p.Pro1373Ser	p.P1373S	ENST00000257430	NM_000038.5	1373	Cct/Tct	16/16	1	2	FACETS	0.857	0.75	0.972	0.857	0.75	0.972	CLONAL	1	TRUE	1	0.356198307194388	2		369	465	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639157	176639157	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	135	528	1	ENST00000439151.2:c.3757A>G	p.Ile1253Val	p.I1253V	ENST00000439151	NM_022455.4	1253	Att/Gtt	5/23	1	2	FACETS	0.99	0.9	1	0.99	0.9	1	CLONAL	1	TRUE	1	0.356198307194388	2		529	766	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250430	26250431	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs778901635	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	151	473	0	ENST00000446824.2:c.403_404del	p.Arg135GlyfsTer?	p.R135Gfs*?	ENST00000446824	NM_021018.2	135	AGg/g	1/1	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.356198307194388	2		473	723	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940100	31940100	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	232	707	0	ENST00000375333.2:c.242T>C	p.Val81Ala	p.V81A	ENST00000375333	NM_032454.1	81	gTa/gCa	2/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.356198307194388	2		707	1125	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908305	41908305	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	166	545	0	ENST00000372991.4:c.217T>G	p.Cys73Gly	p.C73G	ENST00000372991	NM_001760.3	73	Tgt/Ggt	2/5	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.356198307194388	2		545	908	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505557	157505557	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	72	214	0	ENST00000346085.5:c.3538C>T	p.Pro1180Ser	p.P1180S	ENST00000346085	NM_020732.3	1180	Ccg/Tcg	13/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.356198307194388	2		214	289	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56879441	56879441	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1216734638	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	212	568	0	ENST00000519728.1:c.958G>A	p.Glu320Lys	p.E320K	ENST00000519728	NM_002350.3	320	Gag/Aag	9/13	0.342377893257272	3	FACETS	1	0.979	1	0.571	0.53	0.615	CLONAL	1	TRUE	1	0.356198307194388	3		568	1227	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752909	128752909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1012972478	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	114	328	0	ENST00000377970.2:c.1070G>A	p.Cys357Tyr	p.C357Y	ENST00000377970	NM_002467.4	357	tGc/tAc	3/3	0.342377893257272	3	FACETS	1	0.964	1	0.572	0.516	0.632	CLONAL	1	TRUE	1	0.356198307194388	3		328	659	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542572	141542572	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	147	578	1	ENST00000220592.5:c.2414A>G	p.Tyr805Cys	p.Y805C	ENST00000220592	NM_012154.3	805	tAc/tGc	18/19	0.342377893257272	3	FACETS	0.866	0.789	0.947	0.433	0.394	0.474	CLONAL	1	TRUE	1	0.356198307194388	3		579	1123	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492898	8492898	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377557345	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	179	665	0	ENST00000356435.5:c.2431C>T	p.Arg811Cys	p.R811C	ENST00000356435		811	Cgc/Tgc	16/35	1	2	FACETS	0.968	0.892	1	0.968	0.892	1	CLONAL	1	TRUE	1	0.356198307194388	2		665	1038	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915978	127915978	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	136	493	0	ENST00000373547.4:c.503C>A	p.Pro168His	p.P168H	ENST00000373547	NM_002721.4	168	cCt/cAt	6/7	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.356198307194388	2		493	725	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730186	133730186	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	118	515	0	ENST00000318560.5:c.254-2A>G		p.X85_splice	ENST00000318560	NM_005157.4	85			1	2	FACETS	0.956	0.864	1	0.956	0.864	1	CLONAL	1	TRUE	1	0.356198307194388	2		515	693	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44921908	44921908	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	91	475	0	ENST00000377967.4:c.1442G>T	p.Arg481Leu	p.R481L	ENST00000377967	NM_021140.2	481	cGc/cTc	15/29	1	2	FACETS	0.941	0.838	1	0.941	0.838	1	CLONAL	1	TRUE	1	0.356198307194388	2		475	543	SUCCESS
AR	367	MSKCC	GRCh37	X	66931495	66931495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852595	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	102	629	0	ENST00000374690.3:c.2137C>T	p.Leu713Phe	p.L713F	ENST00000374690	NM_000044.3	713	Ctt/Ttt	4/8	1	2	FACETS	0.641	0.573	0.714	0.641	0.573	0.714	SUBCLONAL	1	TRUE	1	0.356198307194388	2		629	893	SUCCESS
AR	367	MSKCC	GRCh37	X	66937425	66937425	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	109	699	0	ENST00000374690.3:c.2279C>A	p.Ser760Tyr	p.S760Y	ENST00000374690	NM_000044.3	760	tCc/tAc	5/8	1	2	FACETS	0.571	0.511	0.634	0.571	0.511	0.634	SUBCLONAL	1	TRUE	1	0.356198307194388	2		699	1072	SUCCESS
AR	367	MSKCC	GRCh37	X	66941753	66941753	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	188	584	0	ENST00000374690.3:c.2397A>C	p.Gln799His	p.Q799H	ENST00000374690	NM_000044.3	799	caA/caC	6/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.356198307194388	2		584	950	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0031962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	48	778	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.582	0.49	0.683	0.582	0.49	0.683	SUBCLONAL	1	FALSE	1	0.219468199791011	2		779	752	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0031962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	54	385	1	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	FALSE	1	0.219468199791011	2		386	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781504	NA	P-0031962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	99	713	0	ENST00000269305.4:c.314G>T	p.Gly105Val	p.G105V	ENST00000269305	NM_001126112.2	105	gGc/gTc	4/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.219468199791011	2		713	808	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910883	114910883	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1477809102	NA	P-0031962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	84	449	0	ENST00000543371.1:c.1001+1G>A		p.X334_splice	ENST00000543371	NM_001198531.1	334			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.219468199791011	2		449	540	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121648	108121648	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	92	485	0	ENST00000278616.4:c.1456A>G	p.Lys486Glu	p.K486E	ENST00000278616	NM_000051.3	486	Aaa/Gaa	10/63	0.0786366262785383	3	FACETS	1	0.975	1	0.68	0.604	0.761	INDETERMINATE	1	FALSE	1	0.219468199791011	3		485	684	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29099520	29099520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	52	293	5	ENST00000328354.6:c.881C>T	p.Ala294Val	p.A294V	ENST00000328354	NM_007194.3	294	gCa/gTa	8/15	0.219468199791011	1	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	FALSE	0	0.219468199791011	1		298	396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0031968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	292	720	4	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.33718748384436	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.33718748384436	2		724	827	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552922	106552922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1214061937	NA	P-0031968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	85	689	0	ENST00000369096.4:c.887G>A	p.Arg296Gln	p.R296Q	ENST00000369096	NM_001198.3	296	cGg/cAg	5/7	0.336426732770007	3	FACETS	0.881	0.779	0.99	0.44	0.389	0.495	CLONAL	1	TRUE	1	0.33718748384436	3		689	669	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944759	206944759	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	59	413	0	ENST00000423557.1:c.167A>G	p.Gln56Arg	p.Q56R	ENST00000423557	NM_000572.2	56	cAa/cGa	2/5	0.336426732770007	3	FACETS	0.736	0.633	0.847	0.368	0.316	0.424	SUBCLONAL	1	TRUE	1	0.33718748384436	3		413	556	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549247	21549247	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	112	789	0	ENST00000382592.4:c.3029del	p.Pro1010LeufsTer62	p.P1010Lfs*62	ENST00000382592	NM_014572.2	1010	cCt/ct	8/8	0.33718748384436	5	FACETS	0.914	0.82	1	0.305	0.273	0.338	CLONAL	1	TRUE	2	0.33718748384436	5		789	1094	SUCCESS
APC	324	MSKCC	GRCh37	5	112174236	112174236	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	183	311	0	ENST00000257430.4:c.2945C>A	p.Ser982Ter	p.S982*	ENST00000257430	NM_000038.5	982	tCg/tAg	16/16	0.335222564926542	3	FACETS	0.983	0.918	1	0.983	0.918	1	CLONAL	3	TRUE	0	0.33718748384436	3		311	430	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185190	123185190	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	69	548	0	ENST00000218089.9:c.1142A>G	p.Asp381Gly	p.D381G	ENST00000218089	NM_001042749.1	381	gAc/gGc	13/35	1	2	FACETS	0.895	0.78	1	0.895	0.78	1	CLONAL	1	TRUE	1	0.27	2		548	571	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99452077	99452077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1441621301	NA	P-0031970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	22	318	0	ENST00000268035.6:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000268035	NM_000875.3	471	Cgc/Tgc	6/21	1	2	FACETS	0.446	0.346	0.564	0.446	0.346	0.564	SUBCLONAL	1	TRUE	1	0.27	2		318	365	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122613	108122613	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1064796556	NA	P-0031970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	97	475	0	ENST00000278616.4:c.1658del	p.Gly553GlufsTer3	p.G553Efs*3	ENST00000278616	NM_000051.3	553	Gga/ga	11/63	0.242598631382742	2	FACETS	0.857	0.769	0.95	0.857	0.769	0.95	CLONAL	2	TRUE	0	0.27	2		475	419	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226475	2226475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778212913	NA	P-0031970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	138	914	0	ENST00000398665.3:c.3955G>A	p.Gly1319Ser	p.G1319S	ENST00000398665	NM_032482.2	1319	Ggc/Agc	27/28	0.3	1	FACETS	0.963	0.876	1	0.963	0.876	1	CLONAL	1	TRUE	0	0.27	1		914	918	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219012	36219012	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757019411	NA	P-0031970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	119	689	0	ENST00000222270.7:c.4511C>T	p.Ala1504Val	p.A1504V	ENST00000222270	NM_014727.1	1504	gCg/gTg	19/37	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.27	2		689	858	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	135	354	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	0.459461569677103	2		354	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0031988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	220	651	1	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.459461569677103	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.459461569677103	1		652	605	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867343	45867343	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1054768577	NA	P-0031988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	151	546	1	ENST00000391945.4:c.850G>A	p.Glu284Lys	p.E284K	ENST00000391945	NM_000400.3	284	Gag/Aag	10/23	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.459461569677103	2		547	657	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	34	354	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.119332483179067	0	FACETS	1	0.932	1			1	CLONAL	1	TRUE	0	0.119332483179067	0		354	377	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716085	52716085	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1257	82	583	0	ENST00000322088.6:c.650A>G	p.Gln217Arg	p.Q217R	ENST00000322088	NM_014225.5	217	cAg/cGg	5/15	NA	4	FACETS	1	0.948	1	0.574	0.504	0.65	INDETERMINATE	1	TRUE	2	0.119332483179067	4		583	1339	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061313	38061313	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	100	750	0	ENST00000250448.2:c.676G>T	p.Asp226Tyr	p.D226Y	ENST00000250448	NM_004496.3	226	Gac/Tac	2/2	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.2	2		750	987	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260845	16260845	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	62	573	0	ENST00000375759.3:c.8110G>T	p.Val2704Leu	p.V2704L	ENST00000375759	NM_015001.2	2704	Gtg/Ttg	11/15	1	2	FACETS	0.93	0.802	1	0.93	0.802	1	CLONAL	1	TRUE	1	0.2	2		573	667	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241910	133241912	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0031990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	88	582	0	ENST00000320574.5:c.2444_2446del	p.Phe815del	p.F815del	ENST00000320574	NM_006231.2	815	tTCTat/tat	21/49	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.2	2		582	872	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119969	70119969	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	25	257	0	ENST00000245479.2:c.971C>T	p.Thr324Ile	p.T324I	ENST00000245479	NM_000346.3	324	aCc/aTc	3/3	1	2	FACETS	0.72	0.568	0.896	0.72	0.568	0.896	SUBCLONAL	1	TRUE	1	0.2	2		257	347	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649122	37649122	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	194	338	0	ENST00000447079.4:c.2229del	p.Ala744ProfsTer9	p.A744Pfs*9	ENST00000447079	NM_015083.1	743	Aaa/aa	4/14	1	2	FACETS	0.904	0.842	0.968	0.904	0.842	0.968	CLONAL	1	TRUE	1	0.720022193463988	2		338	596	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0031992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	246	597	2	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	TRUE	1	NA	2		599	720	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678970	117678970	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	132	337	0	ENST00000368508.3:c.3851del	p.Leu1284Ter	p.L1284*	ENST00000368508	NM_002944.2	1284	tTa/ta	24/43	0.3	8	FACETS		NA	1			1	NA	NA	TRUE	NA	NA	8		337	874	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0031993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	461	520	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.991	0.949	1	0.991	0.949	1	CLONAL	1	TRUE	1	0.837513658399205	2		520	1111	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44935940	44935940	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0031993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	67	242	0	ENST00000377967.4:c.2703-2A>G		p.X901_splice	ENST00000377967	NM_021140.2	901			1	2	FACETS	0.93	0.827	1	0.93	0.827	1	CLONAL	1	TRUE	1	0.837513658399205	2		242	172	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255882	16255883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0031993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	243	332	0	ENST00000375759.3:c.3154dup	p.Ile1052AsnfsTer7	p.I1052Nfs*7	ENST00000375759	NM_015001.2	1049	-/A	11/15	1	2	FACETS	0.982	0.925	1	0.982	0.925	1	CLONAL	1	TRUE	1	0.837513658399205	2		332	591	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949978	44949978	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0031993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	84	319	0	ENST00000377967.4:c.3747T>A	p.Tyr1249Ter	p.Y1249*	ENST00000377967	NM_021140.2	1249	taT/taA	26/29	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.837513658399205	2		319	190	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0031994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	155	490	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.91	0.837	0.987	0.91	0.837	0.987	CLONAL	1	TRUE	1	0.551113213472838	2		490	618	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0031994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	224	518	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.547877596508585	2	FACETS	0.93	0.879	0.982	0.93	0.879	0.982	CLONAL	2	TRUE	0	0.551113213472838	2		518	437	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	152	534	0	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	0.551113213472838	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.551113213472838	1		534	387	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0031994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	114	349	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.551113213472838	2		349	382	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063717	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0031994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	32	224	0	ENST00000412916.2:c.165+1G>C		p.X55_splice	ENST00000412916		55			0.551113213472838	1	FACETS	0.794	0.66	0.936	0.794	0.66	0.936	CLONAL	1	TRUE	0	0.551113213472838	1		224	106	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273991	10273991	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	168	644	0	ENST00000330684.3:c.278C>G	p.Ala93Gly	p.A93G	ENST00000330684	NM_001134407.1	93	gCa/gGa	2/13	0.511546956577665	3	FACETS	0.941	0.866	1	0.471	0.433	0.51	CLONAL	1	TRUE	1	0.551113213472838	3		644	826	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589151	67589153	+	inframe_deletion	In_Frame_Del	DEL	TAA	TAA	-	novel	NA	P-0031994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	149	248	0	ENST00000274335.5:c.1140_1142del	p.Leu380_Ile381delinsPhe	p.L380_I381delinsF	ENST00000274335		380	tTAAtc/ttc	9/15	0.551113213472838	3	FACETS	0.988	0.916	1	0.988	0.916	1	CLONAL	2	TRUE	1	0.551113213472838	3		248	349	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536112	106536112	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	121	321	0	ENST00000369096.4:c.79C>A	p.Gln27Lys	p.Q27K	ENST00000369096	NM_001198.3	27	Cag/Aag	2/7	0.551113213472838	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.551113213472838	1		321	296	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508899	106508899	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	104	361	0	ENST00000359195.3:c.893A>G	p.Lys298Arg	p.K298R	ENST00000359195	NM_002649.2	298	aAg/aGg	2/11	1	2	FACETS	0.985	0.89	1	0.985	0.89	1	CLONAL	1	TRUE	1	0.551113213472838	2		361	383	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038550	47038550	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	137	553	0	ENST00000377604.3:c.712G>A	p.Val238Met	p.V238M	ENST00000377604	NM_001204468.1	238	Gtg/Atg	8/24	0.390034566638165	3	FACETS	1	0.981	1	0.628	0.574	0.683	CLONAL	1	TRUE	1	0.551113213472838	3		553	505	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871222	35871222	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	34	395	0	ENST00000216797.5:c.951A>T	p.Leu317Phe	p.L317F	ENST00000216797	NM_020529.2	317	ttA/ttT	6/6	1	2	FACETS	0.15	0.121	0.181	0.15	0.121	0.181	SUBCLONAL	1	TRUE	1	0.703934350939571	2		395	646	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210026	55210026	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	304	346	0	ENST00000275493.2:c.136G>A	p.Asp46Asn	p.D46N	ENST00000275493	NM_005228.3	46	Gat/Aat	2/28	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.703934350939571	2		346	864	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459239	120459239	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	179	548	0	ENST00000256646.2:c.6106C>T	p.Arg2036Ter	p.R2036*	ENST00000256646	NM_024408.3	2036	Cga/Tga	34/34	0.85014834752429	2	FACETS	0.986	0.92	1	0.493	0.46	0.527	CLONAL	1	TRUE	0	0.85014834752429	2		548	427	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444401	50444401	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	132	352	0	ENST00000331340.3:c.331C>T	p.Arg111Ter	p.R111*	ENST00000331340	NM_006060.4	111	Cga/Tga	4/8	0.770266459539102	4	FACETS	0.921	0.838	1	0.46	0.419	0.504	CLONAL	1	TRUE	2	0.85014834752429	4		352	624	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144882	47144882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768604404	NA	P-0031998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	130	506	0	ENST00000409792.3:c.4871C>T	p.Ser1624Phe	p.S1624F	ENST00000409792	NM_014159.6	1624	tCt/tTt	7/21	0.85014834752429	2	FACETS	0.879	0.807	0.952	0.439	0.403	0.476	CLONAL	1	TRUE	0	0.85014834752429	2		506	348	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0032000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	122	634	1	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	0.248654420038802	2		635	716	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0032000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	37	470	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.86	0.711	1	0.86	0.711	1	CLONAL	1	TRUE	1	0.248654420038802	2		471	346	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535352	66535352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368790458	NA	P-0032000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	99	712	3	ENST00000273854.3:c.109C>T	p.Arg37Trp	p.R37W	ENST00000273854	NM_004439.5	37	Cgg/Tgg	1/18	1	2	FACETS	0.873	0.778	0.974	0.873	0.778	0.974	CLONAL	1	TRUE	1	0.248654420038802	2		715	912	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557630	95557630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	88	585	0	ENST00000393063.1:c.5437G>A	p.Glu1813Lys	p.E1813K	ENST00000393063	NM_030621.3	1813	Gag/Aag	26/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.248654420038802	2		585	551	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589581	67589583	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	novel	NA	P-0032000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	28	234	0	ENST00000274335.5:c.1345_1347del	p.Leu449del	p.L449del	ENST00000274335		448	aaATTa/aaa	10/15	1	2	FACETS	0.834	0.677	1	1	0.949	1	CLONAL	2	TRUE	1	0.248654420038802	2		234	135	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0032000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	50	434	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	0.248654420038802	2		434	320	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685307	89685307	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123317	NA	P-0032000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	41	392	0	ENST00000371953.3:c.202T>C	p.Tyr68His	p.Y68H	ENST00000371953	NM_000314.4	68	Tac/Cac	3/9	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.248654420038802	2		392	233	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398280	25398281	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0032000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	45	557	0	ENST00000311936.3:c.38_39delinsTT	p.Gly13Val	p.G13V	ENST00000311936	NM_004985.3	13	gGC/gTT	2/5	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.248654420038802	2		557	297	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380338	14380339	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCCCACGCC	novel	NA	P-0032000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	71	265	0	ENST00000256196.4:c.70_78dup	p.Gly24_Gly26dup	p.G24_G26dup	ENST00000256196		24	-/GGCGTGGGC	1/6	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.248654420038802	2		265	465	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574406	95574406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	26	251	0	ENST00000393063.1:c.2461C>T	p.Arg821Cys	p.R821C	ENST00000393063	NM_030621.3	821	Cgc/Tgc	17/28	1	2	FACETS	0.934	0.754	1	1	0.952	1	CLONAL	2	TRUE	1	0.248654420038802	2		251	112	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385120	41385120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	141	716	0	ENST00000373198.4:c.841G>A	p.Ala281Thr	p.A281T	ENST00000373198	NM_133170.3	281	Gcg/Acg	6/32	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.248654420038802	2		716	883	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023985	27024000	+	frameshift_variant	Frame_Shift_Del	DEL	CCGGGAGCAGCGGCGG	CCGGGAGCAGCGGCGG	-	novel	NA	P-0032000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	22	61	0	ENST00000324856.7:c.1092_1107del	p.Ser366GlyfsTer20	p.S366Gfs*20	ENST00000324856	NM_006015.4	364	cCCGGGAGCAGCGGCGGc/cc	1/20	0.248654420038802	3	FACETS	1	0.866	1	0.754	0.598	0.925	CLONAL	2	TRUE	0	0.248654420038802	3		61	88	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624271	89624271	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1064794096	NA	P-0032000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	80	439	0	ENST00000371953.3:c.45A>T	p.Arg15Ser	p.R15S	ENST00000371953	NM_000314.4	15	agA/agT	1/9	1	2	FACETS	0.808	0.716	0.907	1	0.98	1	CLONAL	2	TRUE	1	0.248654420038802	2		439	398	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624274	89624287	+	frameshift_variant	Frame_Shift_Del	DEL	TCAAGAGGATGGAT	TCAAGAGGATGGAT	-	novel	NA	P-0032000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	73	467	0	ENST00000371953.3:c.50_63del	p.Gln17ArgfsTer22	p.Q17Rfs*22	ENST00000371953	NM_000314.4	16	taTCAAGAGGATGGATtc/tatc	1/9	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.248654420038802	2		467	426	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999302	100999302	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	157	953	0	ENST00000325455.5:c.500G>T	p.Arg167Leu	p.R167L	ENST00000325455	NM_001202474.3	167	cGg/cTg	1/8	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.248654420038802	2		953	873	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649570	48649570	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	165	997	0	ENST00000376670.3:c.54T>A	p.Phe18Leu	p.F18L	ENST00000376670	NM_002049.3	18	ttT/ttA	2/6	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.248654420038802	2		997	985	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0032001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	16	391	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		391	298	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711875	89711875	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587782603	NA	P-0032001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	30	572	0	ENST00000371953.3:c.493G>A	p.Gly165Arg	p.G165R	ENST00000371953	NM_000314.4	165	Gga/Aga	6/9	0.153461441367827	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		572	548	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0032003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	185	636	0	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	0.245214694165024	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.245214694165024	1		636	1000	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138667	55138667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	50	446	0	ENST00000257290.5:c.1344G>A	p.Met448Ile	p.M448I	ENST00000257290	NM_006206.4	448	atG/atA	9/23	0.245214694165024	4	FACETS	0.544	0.46	0.637	0.181	0.153	0.213	SUBCLONAL	1	TRUE	1	0.245214694165024	4		446	933	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0032004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	360	427	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.448699562458261	3	FACETS	0.949	0.907	0.991	0.949	0.907	0.991	CLONAL	2	TRUE	1	0.729173780893087	3		427	710	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0032004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	464	620	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.729173780893087	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.729173780893087	1		621	690	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	370	842	1	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.729173780893087	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.729173780893087	1		843	618	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510849	120510849	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	48	434	0	ENST00000256646.2:c.1115T>G	p.Leu372Arg	p.L372R	ENST00000256646	NM_024408.3	372	cTg/cGg	7/34	0.608671880762238	1	FACETS	0.247	0.209	0.288	0.247	0.209	0.288	SUBCLONAL	1	TRUE	0	0.729173780893087	1		434	339	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0032005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	285	427	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.59399211194427	3	FACETS	1	0.965	1	0.518	0.487	0.551	CLONAL	1	TRUE	1	0.650519869577475	3		427	1120	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0032005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	185	337	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	0.650519869577475	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.650519869577475	1		337	367	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442054	52442054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	204	490	0	ENST00000460680.1:c.295G>A	p.Val99Met	p.V99M	ENST00000460680	NM_004656.3	99	Gtg/Atg	5/17	0.650519869577475	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.650519869577475	1		490	396	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790830	89790830	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	316	739	0	ENST00000336032.3:c.217C>G	p.Arg73Gly	p.R73G	ENST00000336032	NM_006813.2	73	Cgc/Ggc	1/2	0.650519869577475	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.650519869577475	1		739	635	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790439	3790439	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0032005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	191	522	0	ENST00000262367.5:c.4094C>G	p.Ser1365Ter	p.S1365*	ENST00000262367	NM_004380.2	1365	tCa/tGa	24/31	1	2	FACETS	0.899	0.835	0.965	0.899	0.835	0.965	CLONAL	1	TRUE	1	0.650519869577475	2		522	653	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467844	66467844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1397271178	NA	P-0032005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	157	420	0	ENST00000273854.3:c.425G>A	p.Gly142Glu	p.G142E	ENST00000273854	NM_004439.5	142	gGa/gAa	3/18	1	2	FACETS	0.897	0.827	0.97	0.897	0.827	0.97	CLONAL	1	TRUE	1	0.650519869577475	2		420	538	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0032011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	62	1222	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.13	2		1222	899	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602314	10602314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	106	875	0	ENST00000171111.5:c.1264G>A	p.Asp422Asn	p.D422N	ENST00000171111	NM_203500.1	422	Gat/Aat	3/6	0.201118587190302	3	FACETS	1	0.975	1	0.661	0.59	0.736	CLONAL	1	TRUE	1	0.13	3		875	1314	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220382	1220382	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	58	691	2	ENST00000326873.7:c.475C>T	p.Gln159Ter	p.Q159*	ENST00000326873	NM_000455.4	159	Cag/Tag	4/10	0.201118587190302	3	FACETS	1	0.894	1	0.526	0.451	0.609	CLONAL	1	TRUE	1	0.13	3		693	903	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983790	15983790	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	37	578	0	ENST00000268712.3:c.3332C>G	p.Ser1111Cys	p.S1111C	ENST00000268712	NM_006311.3	1111	tCt/tGt	25/46	1	2	FACETS	0.942	0.775	1	0.942	0.775	1	CLONAL	1	TRUE	1	0.13	2		578	604	SUCCESS
APC	324	MSKCC	GRCh37	5	112175000	112175000	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	76	216	0	ENST00000257430.4:c.3709C>T	p.Gln1237Ter	p.Q1237*	ENST00000257430	NM_000038.5	1237	Cag/Tag	16/16	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.461333449935465	2		216	287	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242444	55242445	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAAATTCCCGTCGCTATC	rs397517090	NA	P-0032014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	161	440	0	ENST00000275493.2:c.2217_2234dup	p.Ile740_Lys745dup	p.I740_K745dup	ENST00000275493	NM_005228.3	740	-/AAAATTCCCGTCGCTATC	19/28	0.461333449935465	3	FACETS	1	0.97	1	0.557	0.512	0.604	CLONAL	1	TRUE	1	0.461333449935465	3		440	771	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0032014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	152	467	1	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.461333449935465	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.461333449935465	1		468	497	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324496	31324496	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs2308559	NA	P-0032014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	15	70	0	ENST00000412585.2:c.312C>A	p.Asn104Lys	p.N104K	ENST00000412585	NM_005514.6	104	aaC/aaA	2/8	1	2	FACETS	0.57	0.421	0.745	0.57	0.421	0.745	SUBCLONAL	1	TRUE	1	0.461333449935465	2		70	114	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627453	14627453	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	227	682	0	ENST00000254322.2:c.617T>A	p.Ile206Asn	p.I206N	ENST00000254322	NM_006145.1	206	aTc/aAc	2/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.461333449935465	2		682	912	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139818337	139818337	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	75	641	0	ENST00000247668.2:c.1172G>A	p.Cys391Tyr	p.C391Y	ENST00000247668	NM_021138.3	391	tGt/tAt	10/11	0.326914002707859	2	FACETS	0.339	0.296	0.385	0.169	0.148	0.193	SUBCLONAL	1	TRUE	0	0.461333449935465	2		641	960	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs786202525	NA	P-0032017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	94	684	0	ENST00000269305.4:c.532del	p.His178ThrfsTer69	p.H178Tfs*69	ENST00000269305	NM_001126112.2	178	Cac/ac	5/11	0.21830844295598	1	FACETS	0.865	0.768	0.968	0.865	0.768	0.968	CLONAL	1	TRUE	0	0.21830844295598	1		684	887	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906933	32906933	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	53	483	0	ENST00000380152.3:c.1318C>T	p.Leu440Phe	p.L440F	ENST00000380152		440	Ctt/Ttt	10/27	1	2	FACETS	0.804	0.685	0.934	0.804	0.685	0.934	CLONAL	1	TRUE	1	0.21830844295598	2		483	604	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420315	88420315	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773244598	NA	P-0032017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	47	453	1	ENST00000360948.2:c.2371C>T	p.Arg791Trp	p.R791W	ENST00000360948	NM_001012338.2	791	Cgg/Tgg	19/19	1	2	FACETS	0.725	0.611	0.851	0.725	0.611	0.851	SUBCLONAL	1	TRUE	1	0.21830844295598	2		454	594	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467873	50467873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779769920	NA	P-0032017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	44	413	0	ENST00000331340.3:c.1108G>A	p.Val370Met	p.V370M	ENST00000331340	NM_006060.4	370	Gtg/Atg	8/8	1	2	FACETS	0.842	0.706	0.992	0.842	0.706	0.992	CLONAL	1	TRUE	1	0.21830844295598	2		413	479	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859595	57859595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	73	545	1	ENST00000228682.2:c.649G>A	p.Gly217Arg	p.G217R	ENST00000228682	NM_005269.2	217	Ggg/Agg	7/12	1	2	FACETS	0.816	0.712	0.928	0.816	0.712	0.928	CLONAL	1	TRUE	1	0.21830844295598	2		546	820	SUCCESS
APC	324	MSKCC	GRCh37	5	112174936	112174936	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	39	241	0	ENST00000257430.4:c.3645del	p.Ser1215ArgfsTer50	p.S1215Rfs*50	ENST00000257430	NM_000038.5	1215	agT/ag	16/16	0.21830844295598	1	FACETS	1	0.845	1	1	0.845	1	CLONAL	1	TRUE	0	0.21830844295598	1		241	313	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123041	5123042	+	missense_variant	Missense_Mutation	DNP	GT	GT	AG	novel	NA	P-0032017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	53	512	0	ENST00000381652.3:c.3097_3098delinsAG	p.Val1033Arg	p.V1033R	ENST00000381652	NM_004972.3	1033	GTg/AGg	23/25	1	2	FACETS	0.675	0.575	0.786	0.675	0.575	0.786	SUBCLONAL	1	TRUE	1	0.21830844295598	2		512	719	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0032018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	82	496	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	1	2	FACETS	0.951	0.838	1	0.951	0.838	1	CLONAL	1	TRUE	1	0.225468806360494	2		496	765	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0032018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	89	391	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.191870198286539	3	FACETS	0.978	0.872	1	0.978	0.872	1	CLONAL	2	TRUE	1	0.225468806360494	3		391	449	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0032018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	187	535	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.985	1	1	0.994	1	CLONAL	2	TRUE	1	0.225468806360494	2		535	667	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877149	89877149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375648811	NA	P-0032018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	55	479	0	ENST00000389301.3:c.488G>A	p.Arg163His	p.R163H	ENST00000389301	NM_000135.2	163	cGt/cAt	5/43	1	2	FACETS	0.768	0.657	0.891	0.768	0.657	0.891	SUBCLONAL	1	TRUE	1	0.225468806360494	2		479	635	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36022675	36022675	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	159	460	1	ENST00000358208.4:c.548C>A	p.Thr183Lys	p.T183K	ENST00000358208		183	aCg/aAg	5/12	0.191870198286539	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.225468806360494	3		461	705	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266047	41266630	+	splice_donor_variant,splice_acceptor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	AACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATC	AACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATC	-	novel	NA	P-0032018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	50	309	0	ENST00000349496.5:c.46_429del		p.X16_splice	ENST00000349496	NM_001904.3	16	gAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCaa/gaa	3-4/15	0.225468806360494	1	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	0	0.225468806360494	1		309	384	SUCCESS
APC	324	MSKCC	GRCh37	5	112154885	112154885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1312380836	NA	P-0032018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	93	594	1	ENST00000257430.4:c.1156G>A	p.Ala386Thr	p.A386T	ENST00000257430	NM_000038.5	386	Gca/Aca	10/16	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.225468806360494	2		595	761	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0032022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	100	319	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.933	0.84	1	0.933	0.84	1	CLONAL	1	TRUE	1	0.542667193719828	2		319	395	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482342	56482342	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519892	NA	P-0032022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	224	596	2	ENST00000267101.3:c.890A>T	p.Asp297Val	p.D297V	ENST00000267101	NM_001982.3	297	gAt/gTt	8/28	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.542667193719828	2		598	813	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0032024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	177	391	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	0.647260685080255	2		391	460	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0032024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	317	410	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.647260685080255	2		410	839	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	134	258	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.957	0.874	1	0.957	0.874	1	CLONAL	1	TRUE	1	0.55354237583323	2		258	506	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32438081	32438081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	201	520	1	ENST00000332351.3:c.956C>T	p.Ala319Val	p.A319V	ENST00000332351	NM_024426.4	319	gCt/gTt	5/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.55354237583323	2		521	676	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795439	42795439	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	166	490	0	ENST00000575354.2:c.2519C>G	p.Pro840Arg	p.P840R	ENST00000575354	NM_015125.3	840	cCt/cGt	10/20	0.0993483118694115	5	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.55354237583323	5		490	769	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579383	7579383	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	528	760	0	ENST00000269305.4:c.304del	p.Thr102ProfsTer21	p.T102Pfs*21	ENST00000269305	NM_001126112.2	102	Acc/cc	4/11	0.670333164729588	2	FACETS	0.933	0.903	0.963	0.933	0.903	0.963	CLONAL	2	TRUE	0	0.670333164729588	2		760	844	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936558	49936558	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	84	759	0	ENST00000296474.3:c.1369G>T	p.Asp457Tyr	p.D457Y	ENST00000296474	NM_002447.2	457	Gac/Tac	2/20	0.670145121639503	2	FACETS	0.298	0.262	0.336	0.149	0.131	0.168	SUBCLONAL	1	TRUE	0	0.670333164729588	2		759	842	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100906	41100906	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs560503250	NA	P-0032027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	26	527	0	ENST00000373198.4:c.1450G>A	p.Val484Ile	p.V484I	ENST00000373198	NM_133170.3	484	Gtt/Att	8/32	0.685920886636252	1	FACETS	0.096	0.076	0.12	0.096	0.076	0.12	SUBCLONAL	1	TRUE	0	0.685920886636252	1		527	517	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412046	116412046	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	G	novel	NA	P-0032029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	166	942	0	ENST00000397752.3:c.3028+3A>G		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.164636219058581	2	FACETS	1	0.987	1	0.703	0.645	0.763	CLONAL	1	TRUE	0	0.253192417664494	2		942	933	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022307	26022307	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	72	779	0	ENST00000435504.4:c.350G>T	p.Ser117Ile	p.S117I	ENST00000435504		117	aGc/aTc	5/13	1	2	FACETS	0.693	0.604	0.789	0.693	0.604	0.789	SUBCLONAL	1	TRUE	1	0.253192417664494	2		779	821	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864639	68864639	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	11	205	0	ENST00000288368.4:c.10G>A	p.Asp4Asn	p.D4N	ENST00000288368	NM_024870.2	4	Gac/Aac	1/40	1	2	FACETS	0.543	0.376	0.749	0.543	0.376	0.749	SUBCLONAL	1	TRUE	1	0.253192417664494	2		205	160	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0032030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	62	367	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.716	0.62	0.82	0.716	0.62	0.82	SUBCLONAL	1	TRUE	1	0.39086688405946	2		367	443	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847286	68847286	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	155	551	0	ENST00000261769.5:c.1212del	p.Asn405IlefsTer12	p.N405Ifs*12	ENST00000261769	NM_004360.3	403	gCc/gc	9/16	0.39086688405946	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.39086688405946	1		551	571	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945066	151945066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138111015	NA	P-0032030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	56	707	4	ENST00000262189.6:c.2453C>T	p.Ser818Leu	p.S818L	ENST00000262189	NM_170606.2	818	tCa/tTa	14/59	1	2	FACETS	0.325	0.278	0.378	0.325	0.278	0.378	SUBCLONAL	1	TRUE	1	0.39086688405946	2		711	881	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41023350	41023350	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1263727210	NA	P-0032030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	145	573	0	ENST00000267868.3:c.994G>C	p.Asp332His	p.D332H	ENST00000267868	NM_002875.4	332	Gat/Cat	10/10	1	2	FACETS	0.926	0.846	1	0.926	0.846	1	CLONAL	1	TRUE	1	0.39086688405946	2		573	801	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347584	118347584	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	139	467	0	ENST00000534358.1:c.3221G>C	p.Arg1074Thr	p.R1074T	ENST00000534358	NM_005933.3	1074	aGa/aCa	4/36	0.39086688405946	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.39086688405946	1		467	558	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936814	32936814	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	72	389	0	ENST00000380152.3:c.7960C>G	p.Leu2654Val	p.L2654V	ENST00000380152		2654	Ctt/Gtt	17/27	1	2	FACETS	0.881	0.773	0.997	0.881	0.773	0.997	CLONAL	1	TRUE	1	0.39086688405946	2		389	418	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937320	32937320	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1228328393	NA	P-0032030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	76	332	0	ENST00000380152.3:c.7981G>A	p.Asp2661Asn	p.D2661N	ENST00000380152		2661	Gat/Aat	18/27	1	2	FACETS	0.972	0.857	1	0.972	0.857	1	CLONAL	1	TRUE	1	0.39086688405946	2		332	400	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47108581	47108581	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	119	501	0	ENST00000409792.3:c.6088C>T	p.Gln2030Ter	p.Q2030*	ENST00000409792	NM_014159.6	2030	Caa/Taa	13/21	1	2	FACETS	0.903	0.817	0.995	0.903	0.817	0.995	CLONAL	1	TRUE	1	0.39086688405946	2		501	674	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217556	142217556	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	139	554	0	ENST00000350721.4:c.5441G>C	p.Arg1814Thr	p.R1814T	ENST00000350721	NM_001184.3	1814	aGa/aCa	32/47	1	2	FACETS	0.976	0.89	1	0.976	0.89	1	CLONAL	1	TRUE	1	0.39086688405946	2		554	729	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383773	84383773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	134	750	0	ENST00000321945.7:c.1079C>T	p.Ser360Phe	p.S360F	ENST00000321945	NM_139076.2	360	tCt/tTt	9/9	1	2	FACETS	0.752	0.683	0.825	0.752	0.683	0.825	SUBCLONAL	1	TRUE	1	0.39086688405946	2		750	912	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271202	26271202	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	rs767426202	NA	P-0032030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	71	378	0	ENST00000305910.3:c.411G>C	p.Ter137TyrextTer?	p.*137Yext*?	ENST00000305910	NM_003534.2	137	taG/taC	1/1	1	2	FACETS	0.775	0.678	0.878	0.775	0.678	0.878	SUBCLONAL	1	TRUE	1	0.39086688405946	2		378	469	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0032032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	157	427	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.556630230132506	3	FACETS	0.897	0.824	0.974	0.449	0.412	0.487	CLONAL	1	TRUE	1	0.667621558756	3		427	699	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0032032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	467	840	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.667621558756	2	FACETS	0.991	0.959	1	0.991	0.959	1	CLONAL	2	TRUE	0	0.667621558756	2		840	706	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0032032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	97	428	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.823	0.741	0.909	0.823	0.741	0.909	CLONAL	1	TRUE	1	0.667621558756	2		428	353	SUCCESS
APC	324	MSKCC	GRCh37	5	112170865	112170865	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	G	rs879254032	NA	P-0032032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	142	512	0	ENST00000257430.4:c.1958+3A>G		p.X653_splice	ENST00000257430	NM_000038.5	653			1	2	FACETS	0.98	0.901	1	0.98	0.901	1	CLONAL	1	TRUE	1	0.667621558756	2		512	434	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246498726	246498726	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	254	769	0	ENST00000388985.4:c.279C>A	p.Cys93Ter	p.C93*	ENST00000388985		93	tgC/tgA	3/12	0.667621558756	3	FACETS	1	0.952	1	0.509	0.477	0.543	CLONAL	1	TRUE	1	0.667621558756	3		769	996	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573425	55573425	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	84	472	0	ENST00000288135.5:c.1087C>T	p.Pro363Ser	p.P363S	ENST00000288135	NM_000222.2	363	Ccc/Tcc	6/21	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.667621558756	NA		472	472	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573451	55573451	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	56	369	0	ENST00000288135.5:c.1113C>G	p.Ile371Met	p.I371M	ENST00000288135	NM_000222.2	371	atC/atG	6/21	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.667621558756	NA		369	350	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874604	35874604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137868226	NA	P-0032033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	184	660	2	ENST00000303115.3:c.760G>A	p.Ala254Thr	p.A254T	ENST00000303115	NM_002185.3	254	Gct/Act	6/8	1	2	FACETS	0.89	0.824	0.959	0.89	0.824	0.959	CLONAL	1	TRUE	1	0.557147440223519	2		662	742	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347913	73347913	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	120	381	0	ENST00000377767.4:c.1148T>A	p.Ile383Asn	p.I383N	ENST00000377767	NM_014953.3	383	aTt/aAt	8/21	0.228584819109844	1	FACETS	0.861	0.786	0.938	0.861	0.786	0.938	INDETERMINATE	1	TRUE	0	0.557147440223519	1		381	361	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26021068	26021078	+	frameshift_variant	Frame_Shift_Del	DEL	CGTCACTATCA	CGTCACTATCA	-	novel	NA	P-0032033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	81	491	0	ENST00000357647.3:c.351_361del	p.Val118AlafsTer?	p.V118Afs*?	ENST00000357647	NM_003529.2	117	cgCGTCACTATCAtg/cgtg	1/1	0.36280470609987	5	FACETS	0.792	0.698	0.893			1	SUBCLONAL	1	TRUE	NA	0.557147440223519	5		491	674	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955576	90955576	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1038132485	NA	P-0032033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	144	569	0	ENST00000265433.3:c.2089G>A	p.Gly697Arg	p.G697R	ENST00000265433	NM_002485.4	697	Gga/Aga	14/16	0.557147440223519	3	FACETS	1	0.96	1	0.542	0.496	0.59	CLONAL	1	TRUE	1	0.557147440223519	3		569	610	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0032034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	23	391	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.769	0.598	0.966	0.769	0.598	0.966	CLONAL	1	TRUE	1	0.15	2		391	399	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243048	105243048	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519804	NA	P-0032034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	89	707	0	ENST00000349310.3:c.235C>A	p.Gln79Lys	p.Q79K	ENST00000349310	NM_001014432.1	79	Cag/Aag	5/15	0.213975221052774	2	FACETS	1	0.967	1	0.628	0.555	0.706	CLONAL	1	TRUE	0	0.15	2		707	945	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874261	151874261	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0032034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	47	526	0	ENST00000262189.6:c.8277T>G	p.Tyr2759Ter	p.Y2759*	ENST00000262189	NM_170606.2	2759	taT/taG	38/59	1	2	FACETS	0.996	0.84	1	0.996	0.84	1	CLONAL	1	TRUE	1	0.15	2		526	629	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	298	354	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.751602346390716	4	FACETS	0.885	0.837	0.933	0.885	0.837	0.933	CLONAL	2	TRUE	2	0.760102146007447	4		354	780	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023696	27023696	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	199	427	0	ENST00000324856.7:c.802C>T	p.Gln268Ter	p.Q268*	ENST00000324856	NM_006015.4	268	Cag/Tag	1/20	0.749023136844211	3	FACETS	1	0.956	1	0.519	0.483	0.557	CLONAL	1	TRUE	1	0.760102146007447	3		427	696	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057520007	NA	P-0032035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	760	679	0	ENST00000269305.4:c.614A>T	p.Tyr205Phe	p.Y205F	ENST00000269305	NM_001126112.2	205	tAt/tTt	6/11	0.735376975100577	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.760102146007447	3		679	901	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602337	10602337	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	900	907	0	ENST00000171111.5:c.1241A>T	p.Asn414Ile	p.N414I	ENST00000171111	NM_203500.1	414	aAc/aTc	3/6	0.760102146007447	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.760102146007447	3		907	1075	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104608	209104608	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	361	539	1	ENST00000345146.2:c.970G>A	p.Glu324Lys	p.E324K	ENST00000345146	NM_005896.2	324	Gag/Aag	8/10	0.749023136844211	3	FACETS	0.967	0.925	1	0.967	0.925	1	CLONAL	2	TRUE	1	0.760102146007447	3		540	678	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972978	68972978	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	140	505	0	ENST00000288368.4:c.1303G>T	p.Gly435Ter	p.G435*	ENST00000288368	NM_024870.2	435	Gga/Tga	11/40	0.760102146007447	3	FACETS	0.866	0.792	0.943	0.433	0.396	0.472	CLONAL	1	TRUE	1	0.760102146007447	3		505	587	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606170	47606170	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	557	607	0	ENST00000263735.4:c.634G>A	p.Val212Met	p.V212M	ENST00000263735	NM_002354.2	212	Gtg/Atg	6/9	0.760102146007447	4	FACETS	0.966	0.936	0.996	0.966	0.936	0.996	CLONAL	3	TRUE	1	0.760102146007447	4		607	890	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73343051	73343051	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0032035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	269	278	0	ENST00000377767.4:c.1756-1G>T		p.X586_splice	ENST00000377767	NM_014953.3	586			0.760102146007447	3	FACETS	0.969	0.937	1	0.969	0.937	1	CLONAL	3	TRUE	0	0.760102146007447	3		278	336	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1627416	1627416	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	731	743	0	ENST00000344749.5:c.308G>T	p.Gly103Val	p.G103V	ENST00000344749	NM_001136139.2	103	gGt/gTt	6/19	0.760102146007447	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	0	0.760102146007447	3		743	883	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104629	209104629	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	395	575	0	ENST00000345146.2:c.949C>A	p.Arg317Ser	p.R317S	ENST00000345146	NM_005896.2	317	Cgc/Agc	8/10	0.749023136844211	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.760102146007447	3		575	716	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161720	47161720	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	265	423	0	ENST00000409792.3:c.4406T>A	p.Met1469Lys	p.M1469K	ENST00000409792	NM_014159.6	1469	aTg/aAg	3/21	0.751602346390716	4	FACETS	0.996	0.942	1	0.996	0.942	1	CLONAL	2	TRUE	2	0.760102146007447	4		423	616	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542313	187542313	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0032035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	830	400	0	ENST00000441802.2:c.5427T>A	p.Tyr1809Ter	p.Y1809*	ENST00000441802	NM_005245.3	1809	taT/taA	10/27	0.760102146007447	7	FACETS	1	0.995	1	1	0.995	1	CLONAL	6	TRUE	1	0.760102146007447	7		400	1017	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225569	225570	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0032035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	71	137	0	ENST00000264932.6:c.348_349delinsTT	p.Glu116_Asp117delinsAspTyr	p.E116_D117delinsDY	ENST00000264932	NM_004168.2	116	gaGGac/gaTTac	4/15	0.760102146007447	7	FACETS	0.912	0.804	1	0.365	0.321	0.411	CLONAL	2	TRUE	2	0.760102146007447	7		137	297	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671880	30671880	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	835	920	0	ENST00000376406.3:c.5080G>T	p.Val1694Phe	p.V1694F	ENST00000376406	NM_014641.2	1694	Gtt/Ttt	10/15	0.760102146007447	4	FACETS	0.941	0.916	0.965	0.941	0.916	0.965	CLONAL	3	TRUE	1	0.760102146007447	4		920	1370	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526591	106526591	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	461	496	0	ENST00000359195.3:c.2884C>A	p.His962Asn	p.H962N	ENST00000359195	NM_002649.2	962	Cat/Aat	10/11	0.625171818010969	6	FACETS	0.924	0.89	0.958	0.924	0.89	0.958	CLONAL	4	TRUE	2	0.760102146007447	6		496	827	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829156	128829156	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	42	140	0	ENST00000249373.3:c.164C>G	p.Thr55Ser	p.T55S	ENST00000249373	NM_005631.4	55	aCt/aGt	1/12	0.625171818010969	6	FACETS	1	0.89	1	0.269	0.226	0.316	CLONAL	1	TRUE	2	0.760102146007447	6		140	259	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27213539	27213539	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0032035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	206	658	1	ENST00000380036.4:c.2935A>T	p.Lys979Ter	p.K979*	ENST00000380036	NM_000459.3	979	Aaa/Taa	18/23	0.749023136844211	3	FACETS	0.995	0.926	1	0.497	0.463	0.533	CLONAL	1	TRUE	1	0.760102146007447	3		659	752	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139438477	139438477	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	271	866	1	ENST00000277541.6:c.139G>T	p.Val47Phe	p.V47F	ENST00000277541	NM_017617.3	47	Gtc/Ttc	2/34	0.749023136844211	3	FACETS	0.902	0.846	0.959	0.451	0.423	0.48	CLONAL	1	TRUE	1	0.760102146007447	3		867	1091	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0032040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	74	410	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.646211439322295	2		410	201	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934874	NA	P-0032040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	360	890	2	ENST00000269305.4:c.451C>A	p.Pro151Thr	p.P151T	ENST00000269305	NM_001126112.2	151	Ccc/Acc	5/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.646211439322295	2		892	1032	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776011	9776011	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	158	594	0	ENST00000377346.4:c.475T>A	p.Trp159Arg	p.W159R	ENST00000377346	NM_005026.3	159	Tgg/Agg	5/24	1	2	FACETS	0.961	0.887	1	0.961	0.887	1	CLONAL	1	TRUE	1	0.646211439322295	2		594	509	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376260	15376260	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	149	550	0	ENST00000263377.2:c.754C>A	p.Pro252Thr	p.P252T	ENST00000263377	NM_058243.2	252	Cca/Aca	5/20	1	2	FACETS	0.849	0.78	0.921	0.849	0.78	0.921	CLONAL	1	TRUE	1	0.646211439322295	2		550	543	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920518	50920519	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0032040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	121	472	0	ENST00000440232.2:c.3211_3212dup	p.Thr1072AlafsTer53	p.T1072Afs*53	ENST00000440232	NM_002691.3	1070	-/TG	26/27	0.40851657949555	0	FACETS	0.364	0.332	0.397			1	SUBCLONAL	1	TRUE	0	0.646211439322295	0		472	364	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022273	26022274	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	484	753	0	ENST00000435504.4:c.383dup	p.Ser129GlufsTer25	p.S129Efs*25	ENST00000435504		128	aag/aaAg	5/13	0.646211439322295	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.646211439322295	1		753	778	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389119	31389119	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	323	553	0	ENST00000328111.2:c.2032C>A	p.Leu678Met	p.L678M	ENST00000328111	NM_006892.3	678	Ctg/Atg	19/23	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.646211439322295	2		553	869	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004904	150004904	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	196	580	0	ENST00000253339.5:c.1321G>T	p.Ala441Ser	p.A441S	ENST00000253339		441	Gcc/Tcc	3/7	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.646211439322295	2		580	552	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945036	151945036	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	36	381	1	ENST00000262189.6:c.2483C>A	p.Pro828Gln	p.P828Q	ENST00000262189	NM_170606.2	828	cCa/cAa	14/59	0.590669659624258	1	FACETS	0.206	0.169	0.246	0.206	0.169	0.246	SUBCLONAL	1	TRUE	0	0.646211439322295	1		382	367	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0032044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	31	455	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	1	2	FACETS	0.909	0.741	1	0.909	0.741	1	CLONAL	1	TRUE	1	0.334475708091581	2		455	204	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372254	55372254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1358462345	NA	P-0032044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	22	165	0	ENST00000297316.4:c.944C>T	p.Pro315Leu	p.P315L	ENST00000297316	NM_022454.3	315	cCg/cTg	2/2	0.0553751525425306	3	FACETS	0.692	0.538	0.869	0.346	0.269	0.435	INDETERMINATE	1	TRUE	1	0.334475708091581	3		165	222	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579485	7579485	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs869312782	NA	P-0032044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	161	748	0	ENST00000269305.4:c.202G>T	p.Glu68Ter	p.E68*	ENST00000269305	NM_001126112.2	68	Gag/Tag	4/11	0.260484101944304	2	FACETS	0.864	0.797	0.933	0.864	0.797	0.933	CLONAL	2	TRUE	0	0.334475708091581	2		748	557	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368230	31368230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766920119	NA	P-0032044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	187	535	1	ENST00000328111.2:c.101C>T	p.Ser34Leu	p.S34L	ENST00000328111	NM_006892.3	34	tCg/tTg	2/23	0.334475708091581	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.334475708091581	3		536	555	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0032045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	216	363	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.337782710361214	3	FACETS	0.974	0.923	1	0.974	0.923	1	INDETERMINATE	2	FALSE	1	0.839432718675095	3		363	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0032045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	671	574	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.839432718675095	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	FALSE	0	0.839432718675095	2		574	740	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233037	55233037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1477025000	NA	P-0032045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	201	391	0	ENST00000275493.2:c.1787C>T	p.Pro596Leu	p.P596L	ENST00000275493	NM_005228.3	596	cCg/cTg	15/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.839432718675095	2		391	453	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57567468	57567469	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0032045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	115	209	0	ENST00000316660.6:c.58+2dup		p.X20_splice	ENST00000316660	NM_021127.2	20			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.839432718675095	2		209	237	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808315	99808315	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	183	324	0	ENST00000280892.6:c.374A>G	p.Glu125Gly	p.E125G	ENST00000280892	NM_001130678.1	125	gAg/gGg	5/7	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	1	0.839432718675095	2		324	419	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940455	76940455	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0032045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	298	279	0	ENST00000373344.5:c.638C>G	p.Ser213Ter	p.S213*	ENST00000373344	NM_000489.3	213	tCa/tGa	8/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	FALSE	0	0.839432718675095	1		279	337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0032051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	370	703	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	0.735467786382242	2	FACETS	0.919	0.891	0.946	0.919	0.891	0.946	CLONAL	2	TRUE	0	0.838384283383411	2		703	480	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253844	30253844	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	106	576	1	ENST00000307677.4:c.610C>T	p.Arg204Ter	p.R204*	ENST00000307677	NM_138578.1	204	Cga/Tga	3/3	0.718411112153642	5	FACETS	0.725	0.65	0.805	0.242	0.216	0.269	SUBCLONAL	1	TRUE	2	0.838384283383411	5		577	787	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944761	31944761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	16	306	0	ENST00000340398.3:c.340G>A	p.Ala114Thr	p.A114T	ENST00000340398	NM_001013699.2	114	Gct/Act	1/1	0.3	4	FACETS	0.683	0.506	0.893	0.342	0.253	0.447	SUBCLONAL	1	FALSE	2	0.3	4		306	203	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039354	49039354	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	37	720	0	ENST00000267163.4:c.2339C>A	p.Ser780Ter	p.S780*	ENST00000267163	NM_000321.2	780	tCa/tAa	23/27	0.176489653260538	3	FACETS	0.731	0.603	0.874	0.366	0.301	0.437	INDETERMINATE	1	FALSE	1	0.3	3		720	388	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506156	103506156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs544189029	NA	P-0032052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	27	281	1	ENST00000355739.4:c.314C>T	p.Thr105Met	p.T105M	ENST00000355739	NM_000123.3	105	aCg/aTg	3/15	0.3	5	FACETS	0.967	0.772	1	0.322	0.257	0.396	CLONAL	1	FALSE	2	0.3	5		282	270	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56367745	56367745	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1266114717	NA	P-0032052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	27	459	0	ENST00000348428.3:c.571C>T	p.Arg191Ter	p.R191*	ENST00000348428	NM_006785.3	191	Cga/Tga	4/17	0.169529313827176	1	FACETS	0.582	0.464	0.715	0.582	0.464	0.715	INDETERMINATE	1	FALSE	0	0.3	1		459	263	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030470	47030470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1353260604	NA	P-0032052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	66	420	2	ENST00000377604.3:c.245G>A	p.Arg82Gln	p.R82Q	ENST00000377604	NM_001204468.1	82	cGg/cAg	4/24	0.3	2	FACETS	1	0.919	1			1	CLONAL	2	FALSE	NA	0.3	2		422	209	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339138	65339138	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	57	326	0	ENST00000342505.4:c.398del	p.Lys133SerfsTer35	p.K133Sfs*35	ENST00000342505	NM_002227.2	133	aAg/ag	5/25	0.311693721066257	3	FACETS	0.646	0.554	0.747	0.323	0.277	0.374	SUBCLONAL	1	TRUE	1	0.361684161753945	3		326	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519980	NA	P-0032058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	201	415	0	ENST00000269305.4:c.528C>G	p.Cys176Trp	p.C176W	ENST00000269305	NM_001126112.2	176	tgC/tgG	5/11	0.271626635193844	2	FACETS	1	0.991	1	0.738	0.686	0.792	CLONAL	1	TRUE	0	0.361684161753945	2		415	753	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761304	59761304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45437094	NA	P-0032058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	197	437	0	ENST00000259008.2:c.3103C>T	p.Arg1035Cys	p.R1035C	ENST00000259008	NM_032043.2	1035	Cgt/Tgt	20/20	0.271626635193844	2	FACETS	0.805	0.748	0.863	0.805	0.748	0.863	CLONAL	2	TRUE	0	0.361684161753945	2		437	677	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076897	41076897	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	97	337	0	ENST00000373198.4:c.1523C>G	p.Pro508Arg	p.P508R	ENST00000373198	NM_133170.3	508	cCt/cGt	9/32	0.294996246058236	1	FACETS	0.724	0.646	0.806	0.724	0.646	0.806	SUBCLONAL	1	TRUE	0	0.361684161753945	1		337	607	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673166	30673166	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	376	417	0	ENST00000376406.3:c.3794C>G	p.Thr1265Arg	p.T1265R	ENST00000376406	NM_014641.2	1265	aCa/aGa	10/15	0.29865707918775	4	FACETS	1	0.985	1			1	CLONAL	3	TRUE	NA	0.361684161753945	4		417	876	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287213	33287213	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	175	380	0	ENST00000374542.5:c.1884del	p.Cys629AlafsTer16	p.C629Afs*16	ENST00000374542	NM_001141970.1	628	ccC/cc	6/8	0.280788893755437	2	FACETS	1	0.985	1	0.633	0.584	0.684	CLONAL	1	TRUE	0	0.361684161753945	2		380	764	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236087	108236087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781894	NA	P-0032059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	91	448	0	ENST00000278616.4:c.9023G>A	p.Arg3008His	p.R3008H	ENST00000278616	NM_000051.3	3008	cGt/cAt	63/63	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.23	2		448	556	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	394	620	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	0.775408801740343	2		621	878	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	186	319	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.963	0.898	1	0.963	0.898	1	CLONAL	1	TRUE	1	0.775408801740343	2		319	498	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11554273	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	187	547	0	ENST00000371085.3:c.601C>A	p.Arg201Ser	p.R201S	ENST00000371085	NM_000516.4	201	Cgt/Agt	8/13	1	2	FACETS	0.773	0.718	0.83	0.773	0.718	0.83	SUBCLONAL	1	TRUE	1	0.775408801740343	2		547	624	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3841994	3841994	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	179	245	2	ENST00000262367.5:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000262367	NM_004380.2	440	Cga/Tga	5/31	1	2	FACETS	0.779	0.722	0.837	0.779	0.722	0.837	SUBCLONAL	1	TRUE	1	0.775408801740343	2		247	593	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713414	40713414	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	261	418	0	ENST00000373198.4:c.4101del	p.Ser1368ProfsTer31	p.S1368Pfs*31	ENST00000373198	NM_133170.3	1367	ccC/cc	30/32	1	2	FACETS	0.869	0.817	0.921	0.869	0.817	0.921	CLONAL	1	TRUE	1	0.775408801740343	2		418	775	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	111	179	2	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	1	2	FACETS	0.967	0.882	1	0.967	0.882	1	CLONAL	1	TRUE	1	0.775408801740343	2		181	296	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569817	95569817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	107	233	0	ENST00000393063.1:c.3916G>A	p.Ala1306Thr	p.A1306T	ENST00000393063	NM_030621.3	1306	Gct/Act	22/28	1	2	FACETS	0.979	0.892	1	0.979	0.892	1	CLONAL	1	TRUE	1	0.775408801740343	2		233	282	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	214	321	8	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	1	2	FACETS	0.917	0.858	0.977	0.917	0.858	0.977	CLONAL	1	TRUE	1	0.775408801740343	2		329	602	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	548	654	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.967	0.942	0.991	1	0.998	1	CLONAL	2	TRUE	1	0.775408801740343	2		657	731	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	62	244	2	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.74	0.649	0.837	0.74	0.649	0.837	SUBCLONAL	1	TRUE	1	0.775408801740343	2		246	216	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	296	632	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.775408801740343	2		636	756	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11269392	11269392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	265	428	0	ENST00000361445.4:c.3778G>A	p.Val1260Ile	p.V1260I	ENST00000361445	NM_004958.3	1260	Gtc/Atc	25/58	1	2	FACETS	0.773	0.726	0.821	0.773	0.726	0.821	SUBCLONAL	1	TRUE	1	0.775408801740343	2		428	884	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254839	16254839	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	160	323	0	ENST00000375759.3:c.2104C>T	p.Arg702Ter	p.R702*	ENST00000375759	NM_015001.2	702	Cga/Tga	11/15	1	2	FACETS	0.725	0.668	0.784	0.725	0.668	0.784	SUBCLONAL	1	TRUE	1	0.775408801740343	2		323	569	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804359	43804359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749391587	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	295	312	1	ENST00000372470.3:c.359G>A	p.Arg120Gln	p.R120Q	ENST00000372470	NM_005373.2	120	cGg/cAg	3/12	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.775408801740343	2		313	713	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461980	120461980	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	236	400	0	ENST00000256646.2:c.5736T>A	p.Cys1912Ter	p.C1912*	ENST00000256646	NM_024408.3	1912	tgT/tgA	31/34	1	2	FACETS	0.925	0.868	0.983	0.925	0.868	0.983	CLONAL	1	TRUE	1	0.775408801740343	2		400	658	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518503	204518503	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	125	263	0	ENST00000367182.3:c.1166G>A	p.Cys389Tyr	p.C389Y	ENST00000367182	NM_001278516.1	389	tGc/tAc	11/11	1	2	FACETS	0.916	0.839	0.995	0.916	0.839	0.995	CLONAL	1	TRUE	1	0.775408801740343	2		263	352	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100420	8100420	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs991194737	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	278	499	1	ENST00000346208.3:c.394G>A	p.Val132Ile	p.V132I	ENST00000346208		132	Gtc/Atc	3/6	1	2	FACETS	0.906	0.855	0.959	0.906	0.855	0.959	CLONAL	1	TRUE	1	0.775408801740343	2		500	791	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845561	63845565	+	frameshift_variant	Frame_Shift_Del	DEL	AACAA	AACAA	-	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	90	139	0	ENST00000279873.7:c.1307_1311del	p.Thr436SerfsTer10	p.T436Sfs*10	ENST00000279873	NM_032199.2	434	AACAAa/a	9/10	1	2	FACETS	0.853	0.768	0.942	0.853	0.768	0.942	CLONAL	1	TRUE	1	0.775408801740343	2		139	272	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850705	63850705	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs201178069	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	134	231	0	ENST00000279873.7:c.1489del	p.Ile497Ter	p.I497*	ENST00000279873	NM_032199.2	495	Aaa/aa	10/10	1	2	FACETS	0.99	0.912	1	0.99	0.912	1	CLONAL	1	TRUE	1	0.775408801740343	2		231	349	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852118	63852118	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	180	393	1	ENST00000279873.7:c.2901del	p.Lys967AsnfsTer15	p.K967Nfs*15	ENST00000279873	NM_032199.2	966	Aaa/aa	10/10	1	2	FACETS	0.923	0.858	0.989	0.923	0.858	0.989	CLONAL	1	TRUE	1	0.775408801740343	2		394	503	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690828	89690828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202004587	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	19	199	0	ENST00000371953.3:c.235G>A	p.Ala79Thr	p.A79T	ENST00000371953	NM_000314.4	79	Gcc/Acc	4/9	1	2	FACETS	0.134	0.101	0.173	0.134	0.101	0.173	SUBCLONAL	1	TRUE	1	0.775408801740343	2		199	365	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920402	114920402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs927089403	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	297	333	0	ENST00000543371.1:c.1343G>A	p.Arg448Gln	p.R448Q	ENST00000543371	NM_001198531.1	448	cGg/cAg	13/14	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.775408801740343	2		333	741	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	532700	532700	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142218590	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	396	549	0	ENST00000451590.1:c.506G>A	p.Arg169Gln	p.R169Q	ENST00000451590	NM_001130442.1	169	cGg/cAg	5/5	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.775408801740343	2		549	980	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741936	17741936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	126	140	0	ENST00000250003.3:c.607C>T	p.Arg203Cys	p.R203C	ENST00000250003	NM_002478.4	203	Cgc/Tgc	1/3	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.775408801740343	2		140	286	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205157	61205157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144867876	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	200	480	0	ENST00000301761.2:c.97C>T	p.Arg33Cys	p.R33C	ENST00000301761	NM_017841.2	33	Cgc/Tgc	2/4	1	2	FACETS	0.638	0.592	0.685	0.638	0.592	0.685	SUBCLONAL	1	TRUE	1	0.775408801740343	2		480	809	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69458660	69458660	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781118003	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	208	260	0	ENST00000227507.2:c.475G>A	p.Asp159Asn	p.D159N	ENST00000227507	NM_053056.2	159	Gat/Aat	3/5	1	2	FACETS	0.927	0.866	0.988	0.927	0.866	0.988	CLONAL	1	TRUE	1	0.775408801740343	2		260	579	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424970	49424970	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783691	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	387	495	0	ENST00000301067.7:c.13518del	p.Ser4507AlafsTer12	p.S4507Afs*12	ENST00000301067	NM_003482.3	4506	ccC/cc	39/54	0.19506928025012	4	FACETS	0.906	0.864	0.949	0.906	0.864	0.949	INDETERMINATE	2	TRUE	2	0.775408801740343	4		495	978	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112388	115112388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs565848855	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	206	335	0	ENST00000257566.3:c.1352C>T	p.Ala451Val	p.A451V	ENST00000257566	NM_016569.3	451	gCg/gTg	7/8	0.775408801740343	3	FACETS	0.806	0.748	0.865	0.403	0.374	0.433	CLONAL	1	TRUE	1	0.775408801740343	3		335	915	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941657	48941657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1060503077	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	98	140	0	ENST00000267163.4:c.967G>T	p.Glu323Ter	p.E323*	ENST00000267163	NM_000321.2	323	Gaa/Taa	10/27	0.677417860993833	1	FACETS	0.955	0.883	1	0.955	0.883	1	CLONAL	1	TRUE	0	0.775408801740343	1		140	162	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560464	65560465	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	279	311	0	ENST00000358664.4:c.132_133del	p.His44GlnfsTer42	p.H44Qfs*42	ENST00000358664	NM_002382.4	44	caCAgt/cagt	3/5	1	2	FACETS	0.709	0.666	0.753	0.709	0.666	0.753	SUBCLONAL	1	TRUE	1	0.775408801740343	2		311	1015	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562799	95562799	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	181	347	0	ENST00000393063.1:c.4458del	p.Lys1486AsnfsTer4	p.K1486Nfs*4	ENST00000393063	NM_030621.3	1486	aaA/aa	24/28	1	2	FACETS	0.934	0.869	1	0.934	0.869	1	CLONAL	1	TRUE	1	0.775408801740343	2		347	500	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482869	67482869	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	216	292	0	ENST00000327367.4:c.1273T>C	p.Ser425Pro	p.S425P	ENST00000327367	NM_005902.3	425	Tct/Cct	9/9	0.233797377242823	1	FACETS	0.606	0.568	0.645	0.606	0.568	0.645	INDETERMINATE	1	TRUE	0	0.775408801740343	1		292	563	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	172	315	6	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	0.233797377242823	1	FACETS	0.496	0.459	0.534	0.496	0.459	0.534	INDETERMINATE	1	TRUE	0	0.775408801740343	1		321	548	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641103	3641103	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	543	767	0	ENST00000294008.3:c.2536G>T	p.Val846Leu	p.V846L	ENST00000294008	NM_032444.2	846	Gtg/Ttg	12/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.775408801740343	2		767	1397	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	203	343	1	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.808	0.753	0.865	0.808	0.753	0.865	CLONAL	1	TRUE	1	0.775408801740343	2		344	648	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	168	361	0	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	0.799	0.74	0.861	0.799	0.74	0.861	SUBCLONAL	1	TRUE	1	0.775408801740343	2		361	542	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	240	586	2	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	0.853	0.8	0.907	0.853	0.8	0.907	CLONAL	1	TRUE	1	0.775408801740343	2		588	726	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831357	72831358	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTG	rs34918837	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	150	350	1	ENST00000268489.5:c.5221_5223dup	p.Gln1741dup	p.Q1741dup	ENST00000268489	NM_006885.3	1741	-/CAA	9/10	1	2	FACETS	0.928	0.857	1	0.928	0.857	1	CLONAL	1	TRUE	1	0.775408801740343	2		351	417	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883642	37883642	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	373	517	0	ENST00000269571.5:c.3254T>C	p.Val1085Ala	p.V1085A	ENST00000269571		1085	gTa/gCa	26/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.775408801740343	2		517	915	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40865346	40865346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774145217	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	320	388	1	ENST00000428826.2:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000428826		362	cGg/cAg	11/21	1	2	FACETS	0.979	0.928	1	0.979	0.928	1	CLONAL	1	TRUE	1	0.775408801740343	2		389	843	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437606	56437606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886926322	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	200	262	0	ENST00000407977.2:c.856C>T	p.Arg286Trp	p.R286W	ENST00000407977		286	Cgg/Tgg	8/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.775408801740343	2		262	459	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440643	56440643	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	338	403	0	ENST00000407977.2:c.575del	p.Pro192ArgfsTer11	p.P192Rfs*11	ENST00000407977		192	cCg/cg	5/10	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.775408801740343	2		403	863	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	258	388	1	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	0.928	0.874	0.983	0.928	0.874	0.983	CLONAL	1	TRUE	1	0.775408801740343	2		389	717	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120031	70120031	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	30	36	0	ENST00000245479.2:c.1037del	p.Pro346ArgfsTer37	p.P346Rfs*37	ENST00000245479	NM_000346.3	345	Ccc/cc	3/3	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.775408801740343	2		36	65	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896542	78896542	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	374	515	0	ENST00000306801.3:c.2539C>T	p.Pro847Ser	p.P847S	ENST00000306801	NM_020761.2	847	Ccg/Tcg	22/34	1	2	FACETS	0.943	0.897	0.989	0.943	0.897	0.989	CLONAL	1	TRUE	1	0.775408801740343	2		515	1023	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621908	1621910	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs550914200	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	329	548	1	ENST00000344749.5:c.882_884del	p.Ser295del	p.S295del	ENST00000344749	NM_001136139.2	294	tcCTCa/tca	11/19	1	2	FACETS	0.917	0.869	0.966	0.917	0.869	0.966	CLONAL	1	TRUE	1	0.775408801740343	2		549	925	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	322	594	1	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	1	2	FACETS	0.831	0.786	0.876	0.831	0.786	0.876	CLONAL	1	TRUE	1	0.775408801740343	2		595	1000	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224532	36224532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759167832	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	101	646	0	ENST00000222270.7:c.6994C>T	p.Arg2332Cys	p.R2332C	ENST00000222270	NM_014727.1	2332	Cgt/Tgt	29/37	1	2	FACETS	0.217	0.193	0.242	0.217	0.193	0.242	SUBCLONAL	1	TRUE	1	0.775408801740343	2		646	1202	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753728	42753728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369984329	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	337	562	1	ENST00000222329.4:c.536G>A	p.Arg179His	p.R179H	ENST00000222329	NM_006494.2	179	cGc/cAc	4/4	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.775408801740343	2		563	867	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791282	42791282	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	314	464	0	ENST00000575354.2:c.346del	p.Val116TrpfsTer89	p.V116Wfs*89	ENST00000575354	NM_015125.3	114	ttG/tt	3/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.775408801740343	2		464	778	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919865	50919866	+	splice_acceptor_variant	Splice_Site	INS	-	-	G	rs756872503	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	261	468	1	ENST00000440232.2:c.2959dup		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	0.935	0.881	0.99	0.935	0.881	0.99	CLONAL	1	TRUE	1	0.775408801740343	2		469	720	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714552	52714552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	221	405	0	ENST00000322088.6:c.310G>A	p.Val104Met	p.V104M	ENST00000322088	NM_014225.5	104	Gtg/Atg	4/15	1	2	FACETS	0.855	0.799	0.911	0.855	0.799	0.911	CLONAL	1	TRUE	1	0.775408801740343	2		405	667	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967180	25967180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374101562	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	210	320	0	ENST00000435504.4:c.2026G>A	p.Ala676Thr	p.A676T	ENST00000435504		676	Gct/Act	13/13	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.775408801740343	2		320	471	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61720105	61720105	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	225	271	0	ENST00000401558.2:c.1329A>T	p.Glu443Asp	p.E443D	ENST00000401558	NM_003400.3	443	gaA/gaT	13/25	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.775408801740343	2		271	515	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149734	202149734	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	298	432	0	ENST00000358485.4:c.1175T>A	p.Ile392Asn	p.I392N	ENST00000358485	NM_001080125.1	392	aTc/aAc	8/9	1	2	FACETS	0.973	0.92	1	0.973	0.92	1	CLONAL	1	TRUE	1	0.775408801740343	2		432	790	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793362	242793362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137861407	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	376	529	0	ENST00000334409.5:c.715G>A	p.Val239Met	p.V239M	ENST00000334409	NM_005018.2	239	Gtg/Atg	5/5	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.775408801740343	2		529	960	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775477	39775477	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1569069402	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	311	397	0	ENST00000288319.7:c.543del	p.Ser182AlafsTer22	p.S182Afs*22	ENST00000288319	NM_182918.3	181	ccC/cc	4/10	0.235949336251045	3	FACETS	1	0.994	1	0.685	0.648	0.721	INDETERMINATE	1	TRUE	1	0.775408801740343	3		397	813	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655272	45655272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764295138	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	399	519	0	ENST00000407780.3:c.580C>T	p.Arg194Trp	p.R194W	ENST00000407780	NM_001283052.1	194	Cgg/Tgg	4/7	0.235949336251045	3	FACETS	1	0.994	1	0.652	0.621	0.683	INDETERMINATE	1	TRUE	1	0.775408801740343	3		519	1095	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691872	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs79375991	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	332	230	8	ENST00000295754.5:c.383del	p.Lys128SerfsTer35	p.K128Sfs*35	ENST00000295754	NM_003242.5	125	gAa/ga	3/7	1	2	FACETS	0.838	0.805	0.87	1	0.996	1	CLONAL	2	TRUE	1	0.775408801740343	2		238	511	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053348	37053348	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63751653	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	36	309	0	ENST00000231790.2:c.588del	p.Lys196AsnfsTer6	p.K196Nfs*6	ENST00000231790	NM_000249.3	195	Aaa/aa	7/19	1	2	FACETS	0.132	0.108	0.159	0.132	0.108	0.159	SUBCLONAL	1	TRUE	1	0.775408801740343	2		309	703	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143009	47143010	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	214	215	0	ENST00000409792.3:c.4953dup	p.Thr1652TyrfsTer14	p.T1652Yfs*14	ENST00000409792	NM_014159.6	1651	-/T	8/21	1	2	FACETS	0.795	0.742	0.85	0.795	0.742	0.85	SUBCLONAL	1	TRUE	1	0.775408801740343	2		215	694	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165636	47165636	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1436035298	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	280	415	0	ENST00000409792.3:c.490G>A	p.Ala164Thr	p.A164T	ENST00000409792	NM_014159.6	164	Gca/Aca	3/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.775408801740343	2		415	705	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582302	119582302	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	191	244	1	ENST00000316626.5:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000316626		367	Cga/Tga	10/12	1	2	FACETS	0.796	0.74	0.853	0.796	0.74	0.853	SUBCLONAL	1	TRUE	1	0.775408801740343	2		245	619	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134885834	134885834	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	184	286	0	ENST00000398015.3:c.1745A>G	p.Tyr582Cys	p.Y582C	ENST00000398015	NM_004441.4	582	tAc/tGc	9/16	1	2	FACETS	0.949	0.884	1	0.949	0.884	1	CLONAL	1	TRUE	1	0.775408801740343	2		286	500	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474610	138474610	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	38	301	0	ENST00000289153.2:c.383T>G	p.Val128Gly	p.V128G	ENST00000289153	NM_006219.2	128	gTc/gGc	2/22	1	2	FACETS	0.181	0.149	0.217	0.181	0.149	0.217	SUBCLONAL	1	TRUE	1	0.775408801740343	2		301	541	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182662919	182662919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451035070	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	236	350	0	ENST00000292782.4:c.743G>A	p.Arg248His	p.R248H	ENST00000292782	NM_020640.2	248	cGc/cAc	7/7	1	2	FACETS	0.872	0.818	0.927	0.872	0.818	0.927	CLONAL	1	TRUE	1	0.775408801740343	2		350	698	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747967	41747967	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs758728895	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	82	87	0	ENST00000226382.2:c.802G>T	p.Gly268Cys	p.G268C	ENST00000226382	NM_003924.3	268	Ggc/Tgc	3/3	0.775408801740343	1	FACETS	0.544	0.487	0.603	0.544	0.487	0.603	SUBCLONAL	1	TRUE	0	0.775408801740343	1		87	238	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244151	153244151	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	301	342	0	ENST00000281708.4:c.2006G>T	p.Gly669Val	p.G669V	ENST00000281708	NM_033632.3	669	gGg/gTg	12/12	0.235949336251045	3	FACETS	1	0.994	1	0.717	0.679	0.756	INDETERMINATE	1	TRUE	1	0.775408801740343	3		342	751	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268144	153268144	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs920052554	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	239	253	0	ENST00000281708.4:c.664C>T	p.Arg222Ter	p.R222*	ENST00000281708	NM_033632.3	222	Cga/Tga	4/12	0.235949336251045	3	FACETS	1	0.992	1	0.691	0.65	0.733	INDETERMINATE	1	TRUE	1	0.775408801740343	3		253	619	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541928	187541928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	301	370	0	ENST00000441802.2:c.5812G>A	p.Val1938Ile	p.V1938I	ENST00000441802	NM_005245.3	1938	Gtc/Atc	10/27	0.775408801740343	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.775408801740343	1		370	461	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224527	224527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	196	213	0	ENST00000264932.6:c.203G>A	p.Gly68Asp	p.G68D	ENST00000264932	NM_004168.2	68	gGc/gAc	3/15	1	2	FACETS	0.934	0.872	0.998	0.934	0.872	0.998	CLONAL	1	TRUE	1	0.775408801740343	2		213	541	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294577	1294577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	231	238	0	ENST00000310581.5:c.424C>T	p.Arg142Cys	p.R142C	ENST00000310581	NM_198253.2	142	Cgc/Tgc	2/16	1	2	FACETS	0.788	0.737	0.84	0.788	0.737	0.84	SUBCLONAL	1	TRUE	1	0.775408801740343	2		238	756	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958801	38958801	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	78	206	0	ENST00000357387.3:c.2311C>A	p.Leu771Ile	p.L771I	ENST00000357387	NM_152756.3	771	Ctt/Att	23/38	1	2	FACETS	0.635	0.563	0.71	0.635	0.563	0.71	SUBCLONAL	1	TRUE	1	0.775408801740343	2		206	317	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	304	253	6	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.875	0.841	0.909	1	0.996	1	CLONAL	2	TRUE	1	0.775408801740343	2		259	448	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576819	67576819	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs367669362	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	138	254	0	ENST00000274335.5:c.901C>T	p.Arg301Ter	p.R301*	ENST00000274335		301	Cga/Tga	6/15	1	2	FACETS	0.91	0.837	0.985	0.91	0.837	0.985	CLONAL	1	TRUE	1	0.775408801740343	2		254	391	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047927	180047927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	303	590	0	ENST00000261937.6:c.2248G>A	p.Val750Met	p.V750M	ENST00000261937	NM_182925.4	750	Gtg/Atg	15/30	1	2	FACETS	0.823	0.777	0.87	0.823	0.777	0.87	CLONAL	1	TRUE	1	0.775408801740343	2		590	950	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048560	180048560	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	309	509	0	ENST00000261937.6:c.2002A>T	p.Lys668Ter	p.K668*	ENST00000261937	NM_182925.4	668	Aag/Tag	13/30	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.775408801740343	2		509	739	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402540	20402540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	209	232	0	ENST00000346618.3:c.77C>T	p.Ala26Val	p.A26V	ENST00000346618	NM_001949.4	26	gCc/gTc	1/7	1	2	FACETS	0.921	0.861	0.983	0.921	0.861	0.983	CLONAL	1	TRUE	1	0.775408801740343	2		232	585	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166743	32166743	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs961810048	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	364	561	2	ENST00000375023.3:c.4495C>T	p.Arg1499Ter	p.R1499*	ENST00000375023	NM_004557.3	1499	Cga/Tga	24/30	1	2	FACETS	0.899	0.854	0.945	0.899	0.854	0.945	CLONAL	1	TRUE	1	0.775408801740343	2		563	1044	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521957	157521957	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	158	291	0	ENST00000346085.5:c.4229C>T	p.Ser1410Phe	p.S1410F	ENST00000346085	NM_020732.3	1410	tCc/tTc	18/20	1	2	FACETS	0.973	0.901	1	0.973	0.901	1	CLONAL	1	TRUE	1	0.775408801740343	2		291	419	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956939	2956939	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	258	303	1	ENST00000396946.4:c.2688del	p.Phe896LeufsTer18	p.F896Lfs*18	ENST00000396946	NM_032415.4	896	ttT/tt	20/25	1	2	FACETS	0.999	0.942	1	0.999	0.942	1	CLONAL	1	TRUE	1	0.775408801740343	2		304	666	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392132	81392132	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	140	211	0	ENST00000222390.5:c.145A>G	p.Thr49Ala	p.T49A	ENST00000222390	NM_000601.4	49	Acc/Gcc	2/18	1	2	FACETS	0.894	0.822	0.967	0.894	0.822	0.967	CLONAL	1	TRUE	1	0.775408801740343	2		211	404	SUCCESS
MET	4233	MSKCC	GRCh37	7	116422053	116422053	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	175	232	0	ENST00000397752.3:c.3537del	p.Asp1180IlefsTer9	p.D1180Ifs*9	ENST00000397752	NM_000245.2	1178	gtA/gt	18/21	1	2	FACETS	0.94	0.874	1	0.94	0.874	1	CLONAL	1	TRUE	1	0.775408801740343	2		232	480	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187195	38187195	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	430	608	0	ENST00000317025.8:c.1282A>G	p.Thr428Ala	p.T428A	ENST00000317025	NM_023034.1	428	Act/Gct	6/24	0.171417048198404	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.775408801740343	0		608	1170	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	252	525	2	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	0.171417048198404	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.775408801740343	0		527	691	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359975	87359975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752393508	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	109	154	0	ENST00000277120.3:c.1283G>A	p.Arg428Gln	p.R428Q	ENST00000277120		428	cGg/cAg	11/19	0.171417048198404	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.775408801740343	0		154	310	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232166	98232166	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	150	234	0	ENST00000331920.6:c.1776del	p.Pro593LeufsTer30	p.P593Lfs*30	ENST00000331920	NM_000264.3	592	ttT/tt	13/24	0.171417048198404	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.775408801740343	0		234	524	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137321073	137321073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768721235	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	201	361	1	ENST00000481739.1:c.1030G>A	p.Ala344Thr	p.A344T	ENST00000481739	NM_002957.4	344	Gcc/Acc	7/10	0.171417048198404	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.775408801740343	0		362	572	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615679	100615679	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1569292813	NA	P-0032060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	364	445	4	ENST00000308731.7:c.653del	p.Lys218ArgfsTer11	p.K218Rfs*11	ENST00000308731	NM_000061.2	218	aAg/ag	8/19	0.775408801740343	1	FACETS	0.927	0.89	0.964	0.927	0.89	0.964	CLONAL	1	TRUE	0	0.775408801740343	1		449	620	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	42	258	0				ENST00000310581	NM_198253.2	-/1132			0.2768352508743	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	0	0.2768352508743	1		258	202	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913499	NA	P-0032062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	63	242	0	ENST00000345146.2:c.394C>A	p.Arg132Ser	p.R132S	ENST00000345146	NM_005896.2	132	Cgt/Agt	4/10	1	2	FACETS	0.933	0.816	1	1	0.979	1	CLONAL	2	FALSE	1	0.2768352508743	2		242	244	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578530	7578530	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs267605077	NA	P-0032062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	29	685	0	ENST00000269305.4:c.400T>C	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	Ttt/Ctt	5/11	0.2768352508743	1	FACETS	0.317	0.254	0.39	0.317	0.254	0.39	SUBCLONAL	1	FALSE	0	0.2768352508743	1		685	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0032065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	245	614	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.352157502106832	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.696213278001773	0		616	472	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553590	29553591	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTGAGGAAGCAGA	novel	NA	P-0032065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	65	233	0	ENST00000356175.3:c.2141_2154dup	p.Ile719ValfsTer34	p.I719Vfs*34	ENST00000356175	NM_000267.3	713	-/TGTGAGGAAGCAGA	18/57	0.352157502106832	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.696213278001773	0		233	192	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622018	1622143	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCGCCCACCCCCTGCCCCCTGCCCTGGGTCCTACCATACGCTCGTGCTGGTGCAGGCCACCAAACGTGCTGCTGCTTCCACTGCTGCCCACCGGGCCGCTACCGGGCGGGAGGGGCAGCGGGGAT	TCCGCCCACCCCCTGCCCCCTGCCCTGGGTCCTACCATACGCTCGTGCTGGTGCAGGCCACCAAACGTGCTGCTGCTTCCACTGCTGCCCACCGGGCCGCTACCGGGCGGGAGGGGCAGCGGGGAT	-	novel	NA	P-0032065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	166	536	2	ENST00000344749.5:c.732_822+35del		p.X244_splice	ENST00000344749	NM_001136139.2	244		10/19	NA	2	FACETS	0.8	0.739	0.864			1	INDETERMINATE	1	TRUE	NA	0.696213278001773	2		538	596	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660637	227660637	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	197	476	1	ENST00000305123.5:c.2818G>A	p.Glu940Lys	p.E940K	ENST00000305123	NM_005544.2	940	Gag/Aag	1/2	1	2	FACETS	0.917	0.854	0.982	0.917	0.854	0.982	CLONAL	1	TRUE	1	0.696213278001773	2		477	617	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527327	157527330	+	protein_altering_variant	In_Frame_Del	DEL	CGAG	CGAG	T	novel	NA	P-0032065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	144	333	1	ENST00000346085.5:c.5052_5055delinsT	p.Glu1685del	p.E1685del	ENST00000346085	NM_020732.3	1684	gtCGAG/gtT	20/20	1	2	FACETS	0.769	0.705	0.835	0.769	0.705	0.835	SUBCLONAL	1	TRUE	1	0.696213278001773	2		334	538	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0032066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	292	620	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.624881084745427	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	FALSE	0	0.658644442219051	2		621	434	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106094	8106094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	92	317	0	ENST00000346208.3:c.914G>A	p.Arg305Gln	p.R305Q	ENST00000346208		305	cGa/cAa	4/6	0.610166314342392	4	FACETS	1	0.93	1	0.527	0.47	0.586	CLONAL	1	FALSE	2	0.658644442219051	4		317	440	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910549	29910549	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45585732	NA	P-0032066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	13	234	1	ENST00000376809.5:c.89G>A	p.Arg30Lys	p.R30K	ENST00000376809	NM_002116.7	30	aGg/aAg	2/8	0.658644442219051	3	FACETS	0.218	0.155	0.294	0.109	0.077	0.147	SUBCLONAL	1	FALSE	1	0.658644442219051	3		235	241	SUCCESS
APC	324	MSKCC	GRCh37	5	112175225	112175225	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	52	157	0	ENST00000257430.4:c.3934G>T	p.Gly1312Ter	p.G1312*	ENST00000257430	NM_000038.5	1312	Gga/Tga	16/16	0.160959034534015	6	FACETS	1	0.936	1	0.758	0.658	0.862	INDETERMINATE	2	FALSE	3	0.658644442219051	6		157	161	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648405	30648405	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	115	359	0	ENST00000295754.5:c.30G>A	p.Trp10Ter	p.W10*	ENST00000295754	NM_003242.5	10	tgG/tgA	1/7	1	2	FACETS	0.995	0.906	1	0.995	0.906	1	CLONAL	1	FALSE	1	0.658644442219051	2		359	351	SUCCESS
APC	324	MSKCC	GRCh37	5	112136974	112136975	+	splice_acceptor_variant	Splice_Site	DEL	AG	AG	-	rs387906228	NA	P-0032066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	82	209	0	ENST00000257430.4:c.730_731del		p.X244_splice	ENST00000257430	NM_000038.5	244			0.160959034534015	6	FACETS	1	0.97	1	0.822	0.737	0.91	INDETERMINATE	2	FALSE	3	0.658644442219051	6		209	234	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3795193	3795288	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AATGAATGAGATGCAGTAGCCACTGCAACTGCCCCGCCACTGGCTCTGTGCAGAACTGCCCTCCAGGCCAGGGGAAACAACTCACCCTGAAGGCCA	AATGAATGAGATGCAGTAGCCACTGCAACTGCCCCGCCACTGGCTCTGTGCAGAACTGCCCTCCAGGCCAGGGGAAACAACTCACCCTGAAGGCCA	-	novel	NA	P-0032066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	44	132	0	ENST00000262367.5:c.3904_3914+85del		p.X1302_splice	ENST00000262367	NM_004380.2	1302		22/31	0.555815342295338	4	FACETS	0.815	0.699	0.937	0.815	0.699	0.937	CLONAL	2	FALSE	2	0.658644442219051	4		132	136	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385029	31385029	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1169	130	560	0	ENST00000328111.2:c.1414G>A	p.Asp472Asn	p.D472N	ENST00000328111	NM_006892.3	472	Gat/Aat	14/23	0.658644442219051	6	FACETS	0.704	0.637	0.776	0.176	0.159	0.194	SUBCLONAL	1	FALSE	2	0.658644442219051	6		560	1299	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190344	32190344	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	247	500	0	ENST00000375023.3:c.395G>T	p.Arg132Leu	p.R132L	ENST00000375023	NM_004557.3	132	cGc/cTc	3/30	0.658644442219051	3	FACETS	0.993	0.94	1	0.993	0.94	1	CLONAL	2	FALSE	1	0.658644442219051	3		500	502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0032067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	160	651	0	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	0.347703036953514	1	FACETS	0.941	0.864	1	0.941	0.864	1	CLONAL	1	TRUE	0	0.347703036953514	1		651	808	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913558	32913559	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359479	NA	P-0032067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	92	360	1	ENST00000380152.3:c.5073dup	p.Trp1692MetfsTer3	p.W1692Mfs*3	ENST00000380152		1689	gca/gcAa	11/27	0.347703036953514	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.347703036953514	1		361	427	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007818	45007818	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	49	477	0	ENST00000558401.1:c.265G>T	p.Glu89Ter	p.E89*	ENST00000558401	NM_004048.2	89	Gaa/Taa	2/4	0.347703036953514	1	FACETS	0.398	0.337	0.466	0.398	0.337	0.466	SUBCLONAL	1	TRUE	0	0.347703036953514	1		477	585	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784944	9784960	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGCAGGCCTGCCTGA	GCGGCAGGCCTGCCTGA	-	novel	NA	P-0032067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	130	585	0	ENST00000377346.4:c.2949_2965del	p.Ala984GlnfsTer31	p.A984Qfs*31	ENST00000377346	NM_005026.3	983	GCGGCAGGCCTGCCTGAg/g	23/24	0.347703036953514	2	FACETS	0.899	0.815	0.987	0.449	0.407	0.494	CLONAL	1	TRUE	0	0.347703036953514	2		585	832	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939081	36939081	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	76	610	1	ENST00000361632.4:c.628G>T	p.Gly210Trp	p.G210W	ENST00000361632		210	Ggg/Tgg	5/16	0.232346150022829	3	FACETS	0.47	0.411	0.534			1	SUBCLONAL	1	TRUE	NA	0.347703036953514	3		611	1092	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14015946	14015946	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	42	229	0	ENST00000311895.7:c.266C>A	p.Thr89Lys	p.T89K	ENST00000311895	NM_005236.2	89	aCa/aAa	2/11	NA	2	FACETS	0.563	0.47	0.666			1	INDETERMINATE	1	TRUE	NA	0.347703036953514	2		229	429	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281355	15281355	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	51	470	0	ENST00000263388.2:c.4901T>C	p.Leu1634Pro	p.L1634P	ENST00000263388	NM_000435.2	1634	cTg/cCg	27/33	1	2	FACETS	0.401	0.34	0.468	0.401	0.34	0.468	SUBCLONAL	1	TRUE	1	0.347703036953514	2		470	732	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29099525	29099525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772683219	NA	P-0032067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	74	251	0	ENST00000328354.6:c.876del	p.Phe292LeufsTer12	p.F292Lfs*12	ENST00000328354	NM_007194.3	292	ttT/tt	8/15	0.30013227702459	2	FACETS	0.985	0.866	1	0.493	0.433	0.557	CLONAL	1	TRUE	0	0.347703036953514	2		251	432	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513561	41513561	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	93	426	0	ENST00000263253.7:c.465C>G	p.Asn155Lys	p.N155K	ENST00000263253	NM_001429.3	155	aaC/aaG	2/31	0.30013227702459	2	FACETS	0.871	0.776	0.973	0.436	0.388	0.487	CLONAL	1	TRUE	0	0.347703036953514	2		426	614	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748122	41748133	+	inframe_deletion	In_Frame_Del	DEL	CCGCCGCCGCCT	CCGCCGCCGCCT	-	novel	NA	P-0032067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	77	148	0	ENST00000226382.2:c.636_647del	p.Gly214_Gly217del	p.G214_G217del	ENST00000226382	NM_003924.3	212	ggAGGCGGCGGCGGc/ggc	3/3	0.23284622612128	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.347703036953514	1		148	270	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249407	110249407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1279508322	NA	P-0032067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	247	816	0	ENST00000374672.4:c.1166C>T	p.Pro389Leu	p.P389L	ENST00000374672	NM_004235.4	389	cCc/cTc	4/5	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.347703036953514	2		816	1317	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864184	57864189	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTCA	CTGTCA	T	novel	NA	P-0032067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	108	460	0	ENST00000228682.2:c.1661_1666delinsT	p.Thr554MetfsTer86	p.T554Mfs*86	ENST00000228682	NM_005269.2	554	aCTGTCAgc/aTgc	12/12	1	2	FACETS	0.889	0.798	0.984	0.889	0.798	0.984	CLONAL	1	TRUE	1	0.347703036953514	2		460	699	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279450	1279450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs973201915	NA	P-0032069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	100	647	2	ENST00000310581.5:c.2086C>T	p.Arg696Cys	p.R696C	ENST00000310581	NM_198253.2	696	Cgt/Tgt	5/16	1	2	FACETS	0.95	0.848	1	0.95	0.848	1	CLONAL	1	TRUE	1	0.245930009882572	2		649	856	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0032070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	128	574	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.30945256438535	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.30945256438535	1		574	691	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0032070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	97	270	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.283055107409674	2	FACETS	0.992	0.895	1	0.992	0.895	1	CLONAL	2	TRUE	0	0.30945256438535	2		270	316	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0032070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	42	535	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.454	0.378	0.538	0.454	0.378	0.538	SUBCLONAL	1	TRUE	1	0.30945256438535	2		535	598	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699293	18699293	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	49	337	1	ENST00000266497.5:c.3394C>A	p.Gln1132Lys	p.Q1132K	ENST00000266497		1132	Caa/Aaa	24/31	0.279404191569916	0	FACETS	0.602	0.512	0.701			1	SUBCLONAL	1	TRUE	0	0.30945256438535	0		338	363	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218339	69218339	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	47	403	0	ENST00000462284.1:c.431T>A	p.Leu144His	p.L144H	ENST00000462284	NM_002392.5	144	cTt/cAt	7/11	0.30945256438535	1	FACETS	0.486	0.41	0.57	0.486	0.41	0.57	SUBCLONAL	1	TRUE	0	0.30945256438535	1		403	528	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026150	48026150	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	63	332	0	ENST00000234420.5:c.1028C>A	p.Pro343His	p.P343H	ENST00000234420	NM_000179.2	343	cCt/cAt	4/10	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.30945256438535	2		332	377	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183755	10183757	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs5030648	NA	P-0032072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	32	576	0	ENST00000256474.2:c.227_229del	p.Phe76del	p.F76del	ENST00000256474	NM_000551.3	75	aTCTtc/atc	1/3	1	2	FACETS	0.873	0.709	1	0.873	0.709	1	CLONAL	1	TRUE	1	0.17	2		576	431	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068256	30068256	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424422172	NA	P-0032072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	30	373	1	ENST00000331968.5:c.2143G>A	p.Ala715Thr	p.A715T	ENST00000331968	NM_002742.2	715	Gcc/Acc	15/18	1	2	FACETS	0.712	0.572	0.87	0.712	0.572	0.87	SUBCLONAL	1	TRUE	1	0.17	2		374	496	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	58	447	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.221254743489273	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.221254743489273	1		447	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579433	7579433	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1064793279	NA	P-0032074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1363	260	624	1	ENST00000269305.4:c.254del	p.Pro85LeufsTer38	p.P85Lfs*38	ENST00000269305	NM_001126112.2	85	cCt/ct	4/11	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.221254743489273	2		625	1623	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148727	20148727	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0032074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	92	204	0	ENST00000379607.5:c.338-2A>T		p.X113_splice	ENST00000379607	NM_001412.3	113			1	1	FACETS	1	0.936	1	1	0.99	1	CLONAL	3	TRUE	0	0.221254743489273	1		204	236	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0032074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	150	410	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.221254743489273	2		410	1028	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0032075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	178	391	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.20242336419931	2	FACETS	0.785	0.737	0.832	0.785	0.737	0.832	INDETERMINATE	2	TRUE	0	0.675197232401757	2		391	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578175	7578175	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0032075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	237	524	0	ENST00000269305.4:c.672+2T>G		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.675197232401757	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.675197232401757	1		524	416	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116116	67116116	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	111	263	0	ENST00000412916.2:c.400C>T	p.Gln134Ter	p.Q134*	ENST00000412916		134	Cag/Tag	5/6	0.675197232401757	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.675197232401757	1		263	190	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853304	68853305	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0032075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	217	451	0	ENST00000261769.5:c.1690dup	p.Leu564ProfsTer24	p.L564Pfs*24	ENST00000261769	NM_004360.3	563	gcc/gCcc	11/16	0.675197232401757	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.675197232401757	1		451	347	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	54	447	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.709	0.606	0.822	0.709	0.606	0.822	SUBCLONAL	1	TRUE	1	0.291740791376962	2		447	522	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443675	29443675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1034835558	NA	P-0032076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	33	459	2	ENST00000389048.3:c.3542G>A	p.Arg1181His	p.R1181H	ENST00000389048	NM_004304.4	1181	cGc/cAc	23/29	1	2	FACETS	0.346	0.281	0.42	0.346	0.281	0.42	SUBCLONAL	1	TRUE	1	0.291740791376962	2		461	654	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375401	118375401	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	42	284	0	ENST00000534358.1:c.8794T>C	p.Ser2932Pro	p.S2932P	ENST00000534358	NM_005933.3	2932	Tct/Cct	27/36	1	2	FACETS	0.793	0.664	0.936	0.793	0.664	0.936	CLONAL	1	TRUE	1	0.291740791376962	2		284	363	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712510	43712511	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0032076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	85	494	0	ENST00000382044.4:c.4673_4674del	p.Phe1558Ter	p.F1558*	ENST00000382044	NM_001141980.1	1558	tTC/t	21/28	1	2	FACETS	0.762	0.673	0.857	0.762	0.673	0.857	SUBCLONAL	1	TRUE	1	0.291740791376962	2		494	765	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549890	187549890	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	55	419	0	ENST00000441802.2:c.4351G>T	p.Asp1451Tyr	p.D1451Y	ENST00000441802	NM_005245.3	1451	Gac/Tac	8/27	1	2	FACETS	0.66	0.565	0.765	0.66	0.565	0.765	SUBCLONAL	1	TRUE	1	0.291740791376962	2		419	571	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402561	20402561	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	31	322	0	ENST00000346618.3:c.98T>C	p.Met33Thr	p.M33T	ENST00000346618	NM_001949.4	33	aTg/aCg	1/7	1	2	FACETS	0.679	0.55	0.824	0.679	0.55	0.824	SUBCLONAL	1	TRUE	1	0.291740791376962	2		322	313	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045002	47045003	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0032076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	87	342	1	ENST00000377604.3:c.2328_2329delinsTT	p.His777Tyr	p.H777Y	ENST00000377604	NM_001204468.1	776	cgGCac/cgTTac	20/24	1	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.291740791376962	1		343	363	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0032076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	71	460	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.244	0.212	0.277	0.244	0.212	0.277	SUBCLONAL	1	TRUE	1	0.96	2		460	607	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221992	1221992	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	120	537	0	ENST00000326873.7:c.907A>T	p.Ile303Phe	p.I303F	ENST00000326873	NM_000455.4	303	Atc/Ttc	7/10	NA	2	FACETS	0.439	0.397	0.482			1	INDETERMINATE	1	TRUE	NA	0.96	2		537	570	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661790	227661790	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	70	765	0	ENST00000305123.5:c.1665G>T	p.Met555Ile	p.M555I	ENST00000305123	NM_005544.2	555	atG/atT	1/2	1	2	FACETS	0.195	0.169	0.223	0.195	0.169	0.223	SUBCLONAL	1	TRUE	1	0.96	2		765	748	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	41	258	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.682	0.569	0.809	0.682	0.569	0.809	SUBCLONAL	1	TRUE	1	0.27	2		258	445	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0032079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	62	319	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.232740066244117	2	FACETS	1	0.966	1	0.685	0.596	0.782	CLONAL	1	TRUE	0	0.27	2		319	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577085	+	missense_variant	Missense_Mutation	ONP	CCTC	CCTC	TCTT	novel	NA	P-0032079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	156	642	0	ENST00000269305.4:c.853_856delinsAAGA	p.Glu285_Glu286delinsLysLys	p.E285_E286delinsKK	ENST00000269305	NM_001126112.2	285	GAGGaa/AAGAaa	8/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.27	2		642	993	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546761	9546761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768724288	NA	P-0032079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	39	254	0	ENST00000353224.5:c.1261G>A	p.Asp421Asn	p.D421N	ENST00000353224	NM_177990.2	421	Gac/Aac	5/10	0.0835742995688709	3	FACETS	0.918	0.763	1	0.459	0.381	0.546	INDETERMINATE	1	TRUE	1	0.27	3		254	357	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612176	189612176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	73	446	0	ENST00000264731.3:c.1928G>A	p.Arg643Gln	p.R643Q	ENST00000264731	NM_003722.4	643	cGa/cAa	14/14	1	2	FACETS	0.712	0.622	0.81	0.712	0.622	0.81	SUBCLONAL	1	TRUE	1	0.27	2		446	759	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066711	94066711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	85	431	0	ENST00000369303.4:c.1048G>A	p.Glu350Lys	p.E350K	ENST00000369303	NM_004440.3	350	Gaa/Aaa	5/17	1	2	FACETS	0.922	0.815	1	0.922	0.815	1	CLONAL	1	TRUE	1	0.27	2		431	683	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258117	123258117	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	61	369	0	ENST00000358487.5:c.1564G>A	p.Asp522Asn	p.D522N	ENST00000358487	NM_000141.4	522	Gat/Aat	12/18	0.304317956283833	1	FACETS	0.963	0.834	1	0.963	0.834	1	CLONAL	1	TRUE	0	0.27	1		369	406	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264485	16264485	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	88	434	0	ENST00000375759.3:c.10688T>C	p.Val3563Ala	p.V3563A	ENST00000375759	NM_015001.2	3563	gTt/gCt	13/15	0.0835742995688709	3	FACETS	1	0.934	1	0.539	0.478	0.605	INDETERMINATE	1	TRUE	1	0.27	3		434	686	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864639	57864639	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1255413507	NA	P-0032079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	131	635	0	ENST00000228682.2:c.2116G>A	p.Glu706Lys	p.E706K	ENST00000228682	NM_005269.2	706	Gag/Aag	12/12	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.27	2		635	893	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034806	42034806	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	73	424	0	ENST00000219905.7:c.4648C>T	p.Gln1550Ter	p.Q1550*	ENST00000219905	NM_001164273.1	1550	Cag/Tag	15/24	1	2	FACETS	0.7	0.611	0.795	0.7	0.611	0.795	SUBCLONAL	1	TRUE	1	0.27	2		424	773	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973155	25973155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	55	376	0	ENST00000435504.4:c.1270C>A	p.Pro424Thr	p.P424T	ENST00000435504		424	Cca/Aca	12/13	1	2	FACETS	0.709	0.606	0.821	0.709	0.606	0.821	SUBCLONAL	1	TRUE	1	0.27	2		376	575	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447431	12447431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	88	437	1	ENST00000287820.6:c.670G>A	p.Glu224Lys	p.E224K	ENST00000287820	NM_015869.4	224	Gag/Aag	5/7	1	2	FACETS	0.838	0.742	0.941	0.838	0.742	0.941	CLONAL	1	TRUE	1	0.27	2		438	778	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119642255	119642255	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1450227743	NA	P-0032079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	79	461	0	ENST00000316626.5:c.442C>T	p.Arg148Ter	p.R148*	ENST00000316626		148	Cga/Tga	4/12	1	2	FACETS	0.852	0.749	0.962	0.852	0.749	0.962	CLONAL	1	TRUE	1	0.27	2		461	687	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417876	138417876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	69	440	1	ENST00000289153.2:c.1643C>T	p.Ser548Phe	p.S548F	ENST00000289153	NM_006219.2	548	tCt/tTt	11/22	1	2	FACETS	0.913	0.796	1	0.913	0.796	1	CLONAL	1	TRUE	1	0.27	2		441	560	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456486	189456486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	83	402	0	ENST00000264731.3:c.247G>A	p.Asp83Asn	p.D83N	ENST00000264731	NM_003722.4	83	Gat/Aat	3/14	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.27	2		402	586	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965749	93965749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	26	227	0	ENST00000369303.4:c.2179G>A	p.Asp727Asn	p.D727N	ENST00000369303	NM_004440.3	727	Gat/Aat	13/17	1	2	FACETS	0.917	0.731	1	0.917	0.731	1	CLONAL	1	TRUE	1	0.27	2		227	210	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528451	157528451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	77	452	1	ENST00000346085.5:c.6176C>T	p.Pro2059Leu	p.P2059L	ENST00000346085	NM_020732.3	2059	cCg/cTg	20/20	1	2	FACETS	0.8	0.702	0.906	0.8	0.702	0.906	CLONAL	1	TRUE	1	0.27	2		453	713	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528692	8528692	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	62	328	0	ENST00000356435.5:c.440G>T	p.Cys147Phe	p.C147F	ENST00000356435		147	tGt/tTt	4/35	0.304317956283833	1	FACETS	0.847	0.733	0.97	0.847	0.733	0.97	CLONAL	1	TRUE	0	0.27	1		328	469	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21968233	21968234	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0032079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	57	262	0	ENST00000304494.5:c.464_465dup	p.Asp156ProfsTer38	p.D156Pfs*38	ENST00000304494	NM_000077.4	155	-/CC	3/3	0.304317956283833	1	FACETS	0.84	0.722	0.967	0.84	0.722	0.967	CLONAL	1	TRUE	0	0.27	1		262	435	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349571	70349571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	114	216	0	ENST00000374080.3:c.3733G>A	p.Gly1245Arg	p.G1245R	ENST00000374080		1245	Gga/Aga	27/45	0.0084929177856865	2	FACETS	1	0.942	1			1	INDETERMINATE	2	TRUE	NA	0.27	2		216	402	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	211	447	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.301939699756326	0	FACETS	0.346	0.323	0.37			1	INDETERMINATE	1	TRUE	0	0.649113464506312	0		447	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0032106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	408	1011	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.6112233336343	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.649113464506312	1		1012	809	SUCCESS
APC	324	MSKCC	GRCh37	5	112163701	112163701	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	250	303	0	ENST00000257430.4:c.1624C>T	p.Gln542Ter	p.Q542*	ENST00000257430	NM_000038.5	542	Cag/Tag	13/16	0.629966139371328	2	FACETS	0.951	0.906	0.995	0.951	0.906	0.995	CLONAL	2	TRUE	0	0.649113464506312	2		303	405	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248655	59248656	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	374	795	1	ENST00000371222.2:c.87dup	p.Asn30Ter	p.N30*	ENST00000371222	NM_002228.3	29	-/T	1/1	1	2	FACETS	0.947	0.899	0.996	0.947	0.899	0.996	CLONAL	1	TRUE	1	0.649113464506312	2		796	1217	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457246	67457246	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	47	631	0	ENST00000327367.4:c.220C>G	p.Arg74Gly	p.R74G	ENST00000327367	NM_005902.3	74	Cgg/Ggg	2/9	0.543391586484959	1	FACETS	0.142	0.119	0.167	0.142	0.119	0.167	SUBCLONAL	1	TRUE	0	0.649113464506312	1		631	690	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130117	143130117	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	190	652	0	ENST00000262992.4:c.899T>G	p.Val300Gly	p.V300G	ENST00000262992	NM_001101669.1	300	gTc/gGc	11/24	1	2	FACETS	0.818	0.758	0.879	0.818	0.758	0.879	CLONAL	1	TRUE	1	0.649113464506312	2		652	716	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814908	139814908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779553149	NA	P-0032106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	380	630	1	ENST00000247668.2:c.901G>A	p.Glu301Lys	p.E301K	ENST00000247668	NM_021138.3	301	Gag/Aag	8/11	0.622416311079061	2	FACETS	1	0.987	1	0.553	0.526	0.58	CLONAL	1	TRUE	0	0.649113464506312	2		631	1059	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0032109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	181	519	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.471316605036424	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.471316605036424	1		519	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579718	7579718	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	184	687	0	ENST00000269305.4:c.78del	p.Pro27LeufsTer17	p.P27Lfs*17	ENST00000269305	NM_001126112.2	26	ctT/ct	3/11	0.471316605036424	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.471316605036424	1		687	553	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716025	52716025	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	174	666	0	ENST00000322088.6:c.590A>T	p.Glu197Val	p.E197V	ENST00000322088	NM_014225.5	197	gAg/gTg	5/15	1	2	FACETS	0.958	0.883	1	0.958	0.883	1	CLONAL	1	TRUE	1	0.471316605036424	2		666	771	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713522	30713522	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	145	562	0	ENST00000295754.5:c.847G>T	p.Glu283Ter	p.E283*	ENST00000295754	NM_003242.5	283	Gag/Tag	4/7	0.471316605036424	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.471316605036424	1		562	461	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625438	69625438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5349	305	683	0	ENST00000334134.2:c.355G>A	p.Glu119Lys	p.E119K	ENST00000334134	NM_005247.2	119	Gag/Aag	3/3	0.489980629543314	21	FACETS	1	0.989	1			1	CLONAL	1	TRUE	NA	0.489980629543314	21		683	5654	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934576	NA	P-0032111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	401	668	0	ENST00000269305.4:c.818G>C	p.Arg273Pro	p.R273P	ENST00000269305	NM_001126112.2	273	cGt/cCt	8/11	0.490084291777306	2	FACETS	0.974	0.932	1	0.974	0.932	1	CLONAL	2	TRUE	0	0.489980629543314	2		668	840	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89846317	89846317	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	175	634	0	ENST00000389301.3:c.1675G>C	p.Glu559Gln	p.E559Q	ENST00000389301	NM_000135.2	559	Gag/Cag	18/43	0.433677806954194	3	FACETS	0.922	0.848	0.998	0.461	0.424	0.499	CLONAL	1	TRUE	1	0.489980629543314	3		634	965	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416500	49416500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	442	646	0	ENST00000301067.7:c.16211C>T	p.Ser5404Phe	p.S5404F	ENST00000301067	NM_003482.3	5404	tCc/tTc	51/54	0.490084291777306	4	FACETS	1	0.98	1			1	CLONAL	2	TRUE	NA	0.489980629543314	4		646	1284	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440058	49440058	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	365	656	0	ENST00000301067.7:c.4568G>A	p.Cys1523Tyr	p.C1523Y	ENST00000301067	NM_003482.3	1523	tGc/tAc	16/54	0.490084291777306	4	FACETS	0.965	0.916	1			1	CLONAL	2	TRUE	NA	0.489980629543314	4		656	1150	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857892	9857892	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	369	667	0	ENST00000330684.3:c.3509A>T	p.Asn1170Ile	p.N1170I	ENST00000330684	NM_001134407.1	1170	aAc/aTc	13/13	0.153343930270811	6	FACETS	1	0.992	1	0.815	0.773	0.857	INDETERMINATE	2	TRUE	3	0.489980629543314	6		667	1220	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965767	18965767	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1489	85	670	1	ENST00000262803.5:c.1345G>A	p.Glu449Lys	p.E449K	ENST00000262803	NM_002911.3	449	Gag/Aag	10/24	0.40886068807327	5	FACETS	0.382	0.336	0.432			1	SUBCLONAL	1	TRUE	NA	0.489980629543314	5		671	1574	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096569	178096569	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	102	404	0	ENST00000397062.3:c.762C>A	p.Phe254Leu	p.F254L	ENST00000397062	NM_006164.4	254	ttC/ttA	5/5	0.490084291777306	3	FACETS	0.858	0.769	0.952	0.429	0.384	0.476	CLONAL	1	TRUE	1	0.489980629543314	3		404	604	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129466	152129466	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	233	321	0	ENST00000206249.3:c.419C>G	p.Thr140Arg	p.T140R	ENST00000206249	NM_000125.3	140	aCg/aGg	1/8	0.490084291777306	3	FACETS	0.834	0.788	0.881	1	0.991	1	CLONAL	3	TRUE	1	0.489980629543314	3		321	473	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808936	3808939	+	frameshift_variant	Frame_Shift_Ins	INS	TGGC	TGGC	ATCATGCCA	novel	NA	P-0032111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	311	608	0	ENST00000262367.5:c.3285_3288delinsTGGCATGAT	p.Met1095IlefsTer6	p.M1095Ifs*6	ENST00000262367	NM_004380.2	1095	atGCCA/atTGGCATGAT	17/31	0.153343930270811	6	FACETS	1	0.986	1	0.755	0.712	0.799	INDETERMINATE	2	TRUE	3	0.489980629543314	6		608	1110	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494665	2494665	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	63	543	0	ENST00000355716.4:c.805G>C	p.Val269Leu	p.V269L	ENST00000355716	NM_003820.2	269	Gtg/Ctg	8/8	1	2	FACETS	0.901	0.781	1	0.901	0.781	1	CLONAL	1	TRUE	1	0.316465655361098	2		543	442	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115252204	115252204	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	79	360	0	ENST00000369535.4:c.436G>T	p.Ala146Ser	p.A146S	ENST00000369535	NM_002524.4	146	Gcc/Tcc	4/7	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.316465655361098	2		360	423	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261293	115261293	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	41	500	0	ENST00000438362.2:c.2428G>T	p.Asp810Tyr	p.D810Y	ENST00000438362	NM_001242891.1	810	Gat/Tat	19/20	1	2	FACETS	0.561	0.467	0.665	0.561	0.467	0.665	SUBCLONAL	1	TRUE	1	0.316465655361098	2		500	462	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246518396	246518396	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	129	399	0	ENST00000388985.4:c.165del	p.Lys56ArgfsTer4	p.K56Rfs*4	ENST00000388985		55	ggG/gg	2/12	0.316465655361098	3	FACETS	0.873	0.795	0.954	0.873	0.795	0.954	CLONAL	2	TRUE	1	0.316465655361098	3		399	541	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607639	43607639	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	83	745	0	ENST00000355710.3:c.1615G>C	p.Gly539Arg	p.G539R	ENST00000355710	NM_020975.4	539	Ggc/Cgc	8/20	1	2	FACETS	0.942	0.833	1	0.942	0.833	1	CLONAL	1	TRUE	1	0.316465655361098	2		745	557	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263928	104263928	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	17	176	0	ENST00000369902.3:c.19A>G	p.Ser7Gly	p.S7G	ENST00000369902	NM_016169.3	7	Agc/Ggc	1/12	1	2	FACETS	0.751	0.565	0.969	0.751	0.565	0.969	CLONAL	1	TRUE	1	0.316465655361098	2		176	143	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154769	2154769	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	64	589	0	ENST00000434045.2:c.452C>A	p.Ser151Ter	p.S151*	ENST00000434045	NM_001127598.1	151	tCg/tAg	4/5	0.316465655361098	1	FACETS	0.724	0.629	0.828	0.724	0.629	0.828	SUBCLONAL	1	TRUE	0	0.316465655361098	1		589	470	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235809	108235809	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1555151205	NA	P-0032112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	32	323	0	ENST00000278616.4:c.8851G>A	p.Val2951Ile	p.V2951I	ENST00000278616	NM_000051.3	2951	Gtc/Atc	62/63	0.316465655361098	1	FACETS	0.681	0.555	0.821	0.681	0.555	0.821	SUBCLONAL	1	TRUE	0	0.316465655361098	1		323	250	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446861	18446861	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	56	202	0	ENST00000266497.5:c.946del	p.Ala316GlnfsTer19	p.A316Qfs*19	ENST00000266497		316	Gca/ca	4/31	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.316465655361098	2		202	325	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491415	18491415	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	34	162	0	ENST00000266497.5:c.1328G>T	p.Cys443Phe	p.C443F	ENST00000266497		443	tGt/tTt	8/31	1	2	FACETS	0.625	0.511	0.752	0.625	0.511	0.752	SUBCLONAL	1	TRUE	1	0.316465655361098	2		162	344	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678503	88678503	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	28	456	0	ENST00000360948.2:c.1033T>G	p.Ser345Ala	p.S345A	ENST00000360948	NM_001012338.2	345	Tcc/Gcc	9/19	0.316465655361098	1	FACETS	0.508	0.407	0.623	0.508	0.407	0.623	SUBCLONAL	1	TRUE	0	0.316465655361098	1		456	293	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592246	29592246	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0032112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	36	99	0	ENST00000356175.3:c.4662-1G>T		p.X1554_splice	ENST00000356175	NM_000267.3	1554			0.316465655361098	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	2	TRUE	0	0.316465655361098	2		99	113	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59861709	59861709	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786202169	NA	P-0032112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	118	212	0	ENST00000259008.2:c.1550C>T	p.Pro517Leu	p.P517L	ENST00000259008	NM_032043.2	517	cCt/cTt	11/20	0.316465655361098	2	FACETS	0.898	0.817	0.983	0.898	0.817	0.983	CLONAL	2	TRUE	0	0.316465655361098	2		212	415	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10283839	10283839	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758190156	NA	P-0032112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	49	469	0	ENST00000340748.4:c.647C>T	p.Pro216Leu	p.P216L	ENST00000340748		216	cCg/cTg	8/40	1	2	FACETS	0.633	0.537	0.74	0.633	0.537	0.74	SUBCLONAL	1	TRUE	1	0.316465655361098	2		469	489	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46611660	46611660	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	92	695	0	ENST00000263734.3:c.2474G>T	p.Arg825Leu	p.R825L	ENST00000263734	NM_001430.4	825	cGg/cTg	16/16	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.316465655361098	2		695	554	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155430	99155430	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	32	369	0	ENST00000074304.5:c.656C>G	p.Thr219Ser	p.T219S	ENST00000074304	NM_001134224.1	219	aCt/aGt	9/26	1	2	FACETS	0.496	0.402	0.601	0.496	0.402	0.601	SUBCLONAL	1	TRUE	1	0.316465655361098	2		369	408	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047336	128047337	+	missense_variant	Missense_Mutation	DNP	CT	CT	TC	novel	NA	P-0032112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	87	487	1	ENST00000285398.2:c.585_586delinsGA	p.Glu196Lys	p.E196K	ENST00000285398	NM_000122.1	195	cgAGaa/cgGAaa	5/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.316465655361098	2		488	453	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523308	9523308	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	55	499	1	ENST00000353224.5:c.1929C>A	p.Tyr643Ter	p.Y643*	ENST00000353224	NM_177990.2	643	taC/taA	9/10	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.316465655361098	2		500	310	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527599	41527600	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0032112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	27	415	0	ENST00000263253.7:c.1490_1491delinsTT	p.Gly497Val	p.G497V	ENST00000263253	NM_001429.3	497	gGG/gTT	6/31	1	2	FACETS	0.509	0.405	0.628	0.509	0.405	0.628	SUBCLONAL	1	TRUE	1	0.316465655361098	2		415	335	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645698	12645700	+	inframe_deletion	In_Frame_Del	DEL	CGA	CGA	-	novel	NA	P-0032112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	33	304	0	ENST00000251849.4:c.769_771del	p.Ser257del	p.S257del	ENST00000251849	NM_002880.3	257	TCG/-	7/17	1	2	FACETS	0.758	0.62	0.913	0.758	0.62	0.913	CLONAL	1	TRUE	1	0.316465655361098	2		304	275	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281380	142281380	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	66	485	0	ENST00000350721.4:c.864G>T	p.Leu288Phe	p.L288F	ENST00000350721	NM_001184.3	288	ttG/ttT	4/47	1	2	FACETS	0.899	0.782	1	0.899	0.782	1	CLONAL	1	TRUE	1	0.316465655361098	2		485	464	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430971	181430971	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	72	556	0	ENST00000325404.1:c.823A>C	p.Ser275Arg	p.S275R	ENST00000325404	NM_003106.3	275	Agc/Cgc	1/1	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.316465655361098	2		556	409	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99823030	99823030	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	25	365	0	ENST00000280892.6:c.182A>T	p.Asn61Ile	p.N61I	ENST00000280892	NM_001130678.1	61	aAc/aTc	2/7	1	2	FACETS	0.424	0.333	0.527	0.424	0.333	0.527	SUBCLONAL	1	TRUE	1	0.316465655361098	2		365	373	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034492	47034492	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0032112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	74	276	0	ENST00000377604.3:c.576+1G>T		p.X192_splice	ENST00000377604	NM_001204468.1	192			0.0177448687506412	2	FACETS	0.876	0.776	0.981			1	INDETERMINATE	2	TRUE	NA	0.316465655361098	2		276	267	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195080	123195080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	62	195	0	ENST00000218089.9:c.1423G>A	p.Glu475Lys	p.E475K	ENST00000218089	NM_001042749.1	475	Gag/Aag	16/35	0.0177448687506412	2	FACETS	1	0.941	1			1	INDETERMINATE	2	TRUE	NA	0.316465655361098	2		195	176	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	170	258	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.58454051342186	2		258	536	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0032115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	382	460	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.58454051342186	3	FACETS	0.864	0.823	0.906	0.864	0.823	0.906	CLONAL	2	TRUE	1	0.58454051342186	3		460	977	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0032115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	164	415	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.58454051342186	3	FACETS	0.866	0.796	0.94	0.433	0.398	0.47	CLONAL	1	TRUE	1	0.58454051342186	3		415	837	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132522	11132522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778175819	NA	P-0032115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	315	597	2	ENST00000358026.2:c.2738C>T	p.Pro913Leu	p.P913L	ENST00000358026	NM_001128849.1	913	cCg/cTg	19/36	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.58454051342186	2		599	1007	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0032115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	249	534	0	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	1	2	FACETS	0.951	0.891	1	0.951	0.891	1	CLONAL	1	TRUE	1	0.58454051342186	2		534	896	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685281	89685281	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	69	274	0	ENST00000371953.3:c.176C>A	p.Ser59Ter	p.S59*	ENST00000371953	NM_000314.4	59	tCa/tAa	3/9	0.58454051342186	3	FACETS	1	0.968	1	0.649	0.573	0.729	CLONAL	1	TRUE	1	0.58454051342186	3		274	235	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712823	43712823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28903077	NA	P-0032115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	297	682	0	ENST00000382044.4:c.4361G>A	p.Arg1454Gln	p.R1454Q	ENST00000382044	NM_001141980.1	1454	cGa/cAa	21/28	1	2	FACETS	0.819	0.77	0.869	0.819	0.77	0.869	CLONAL	1	TRUE	1	0.58454051342186	2		682	1241	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709524	176709524	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587784169	NA	P-0032115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	147	435	2	ENST00000439151.2:c.5951G>A	p.Arg1984Gln	p.R1984Q	ENST00000439151	NM_022455.4	1984	cGa/cAa	19/23	1	2	FACETS	0.805	0.737	0.875	0.805	0.737	0.875	CLONAL	1	TRUE	1	0.58454051342186	2		437	625	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673749	176673750	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	203	432	0	ENST00000439151.2:c.4455dup	p.Val1486SerfsTer4	p.V1486Sfs*4	ENST00000439151	NM_022455.4	1483	-/A	10/23	1	2	FACETS	0.967	0.9	1	0.967	0.9	1	CLONAL	1	TRUE	1	0.58454051342186	2		432	718	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0032121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	62	410	0				ENST00000310581	NM_198253.2	-/1132			0.176298049507126	4	FACETS	0.87	0.751	0.999	0.435	0.375	0.5	CLONAL	1	TRUE	2	0.28268433508672	4		410	647	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540391	187540391	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0032121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	159	555	0	ENST00000441802.2:c.7349C>G	p.Ser2450Ter	p.S2450*	ENST00000441802	NM_005245.3	2450	tCa/tGa	10/27	0.238023330997346	2	FACETS	0.828	0.761	0.898	0.828	0.761	0.898	CLONAL	2	TRUE	0	0.28268433508672	2		555	679	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462227	120462227	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	158	518	0	ENST00000256646.2:c.5489C>G	p.Thr1830Ser	p.T1830S	ENST00000256646	NM_024408.3	1830	aCc/aGc	31/34	0.212026817334468	4	FACETS	1	0.974	1	0.759	0.698	0.822	CLONAL	2	TRUE	1	0.28268433508672	4		518	630	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943741	9943741	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	98	703	0	ENST00000330684.3:c.1200G>T	p.Glu400Asp	p.E400D	ENST00000330684	NM_001134407.1	400	gaG/gaT	5/13	0.255003575170422	3	FACETS	0.771	0.686	0.861	0.385	0.343	0.431	SUBCLONAL	1	TRUE	1	0.28268433508672	3		703	1027	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577019	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	249	789	0	ENST00000269305.4:c.919_919+1insT	p.Ala307ValfsTer30	p.A307Vfs*30	ENST00000269305	NM_001126112.2	307	gca/gTca		0.238023330997346	2	FACETS	0.849	0.794	0.906	0.849	0.794	0.906	CLONAL	2	TRUE	0	0.28268433508672	2		789	1037	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	325	258	0				ENST00000310581	NM_198253.2	-/1132			0.942253882864022	3	FACETS	0.867	0.829	0.905	0.867	0.829	0.905	CLONAL	2	TRUE	1	0.952689275094183	3		258	581	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033962	49033962	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	258	342	0	ENST00000267163.4:c.2099T>G	p.Leu700Trp	p.L700W	ENST00000267163	NM_000321.2	700	tTg/tGg	20/27	0.8906137678248	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.952689275094183	1		342	272	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577136	7577137	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCGTCC	novel	NA	P-0032125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	722	596	0	ENST00000269305.4:c.801_802insGGACGA	p.Gly266_Arg267dup	p.G266_R267dup	ENST00000269305	NM_001126112.2	266	-/GGACGA	8/11	0.952689275094183	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.952689275094183	2		596	743	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143988	11143988	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	355	576	0	ENST00000358026.2:c.3569C>G	p.Ala1190Gly	p.A1190G	ENST00000358026	NM_001128849.1	1190	gCc/gGc	26/36	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.952689275094183	2		576	713	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100568	157100594	+	inframe_deletion	In_Frame_Del	DEL	GCCCCGGCACCCCCGGACCGACCATGG	GCCCCGGCACCCCCGGACCGACCATGG	-	novel	NA	P-0032125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	48	455	0	ENST00000346085.5:c.1507_1533del	p.Pro503_Gly511del	p.P503_G511del	ENST00000346085	NM_020732.3	502	aGCCCCGGCACCCCCGGACCGACCATGGgc/agc	1/20	0.480129618948829	1	FACETS	0.199	0.169	0.231	0.199	0.169	0.231	INDETERMINATE	1	TRUE	0	0.952689275094183	1		455	265	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0032127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	100	460	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.177887551441287	4	FACETS	0.776	0.694	0.862	0.776	0.694	0.862	SUBCLONAL	2	TRUE	2	0.264694872394368	4		460	616	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0032127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	131	624	0	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	0.204322989090737	2	FACETS	0.778	0.708	0.852	0.778	0.708	0.852	SUBCLONAL	2	TRUE	0	0.264694872394368	2		624	636	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138400860	138400860	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	113	558	0	ENST00000289153.2:c.2453A>T	p.Gln818Leu	p.Q818L	ENST00000289153	NM_006219.2	818	cAa/cTa	17/22	0.204322989090737	2	FACETS	1	0.982	1	0.713	0.643	0.786	CLONAL	1	TRUE	0	0.264694872394368	2		558	599	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415654	152415654	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	111	581	1	ENST00000206249.3:c.1504C>T	p.Gln502Ter	p.Q502*	ENST00000206249	NM_000125.3	502	Cag/Tag	7/8	0.208374489782552	2	FACETS	0.775	0.699	0.855	0.775	0.699	0.855	SUBCLONAL	2	TRUE	0	0.264694872394368	2		582	541	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691238	18691238	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs772546546	NA	P-0032127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	48	365	0	ENST00000266497.5:c.3349C>A	p.Leu1117Met	p.L1117M	ENST00000266497		1117	Ctg/Atg	23/31	0.177887551441287	4	FACETS	1	0.888	1	0.53	0.448	0.619	CLONAL	1	TRUE	2	0.264694872394368	4		365	433	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59820495	59820495	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	85	372	0	ENST00000259008.2:c.2258A>T	p.Asp753Val	p.D753V	ENST00000259008	NM_032043.2	753	gAt/gTt	16/20	0.187970960450919	3	FACETS	0.792	0.703	0.887	0.792	0.703	0.887	SUBCLONAL	2	TRUE	1	0.264694872394368	3		372	459	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207114	1207129	+	frameshift_variant	Frame_Shift_Del	DEL	GACTCGGAGACGCTGT	GACTCGGAGACGCTGT	-	novel	NA	P-0032127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	113	773	0	ENST00000326873.7:c.203_218del	p.Asp68AlafsTer23	p.D68Afs*23	ENST00000326873	NM_000455.4	68	GACTCGGAGACGCTGTgc/gc	1/10	0.208374489782552	2	FACETS	1	0.955	1	0.553	0.498	0.612	CLONAL	1	TRUE	0	0.264694872394368	2		773	772	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37628031	37628031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs578052035	NA	P-0032127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	117	645	0	ENST00000249071.6:c.229G>A	p.Val77Ile	p.V77I	ENST00000249071	NM_002872.4	77	Gtc/Atc	4/7	0.204322989090737	2	FACETS	0.758	0.686	0.834	0.758	0.686	0.834	SUBCLONAL	2	TRUE	0	0.264694872394368	2		645	583	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015731	112015731	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	90	562	0	ENST00000368678.4:c.1111G>A	p.Val371Met	p.V371M	ENST00000368678		371	Gtg/Atg	11/13	0.208374489782552	2	FACETS	1	0.974	1	0.664	0.591	0.742	CLONAL	1	TRUE	0	0.264694872394368	2		562	512	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372343	55372343	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	196	577	0	ENST00000297316.4:c.1034del	p.Gly345AlafsTer42	p.G345Afs*42	ENST00000297316	NM_022454.3	345	Ggc/gc	2/2	0.206939823374567	4	FACETS	0.87	0.808	0.933			1	CLONAL	3	TRUE	NA	0.264694872394368	4		577	718	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376682	8376682	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	49	553	1	ENST00000356435.5:c.4431C>A	p.His1477Gln	p.H1477Q	ENST00000356435		1477	caC/caA	27/35	1	2	FACETS	0.56	0.473	0.656	0.56	0.473	0.656	SUBCLONAL	1	TRUE	1	0.264694872394368	2		554	661	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412722	63412722	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	54	663	0	ENST00000330258.3:c.445G>T	p.Gly149Ter	p.G149*	ENST00000330258	NM_152424.3	149	Gga/Tga	2/2	0.264694872394368	1	FACETS	0.588	0.502	0.683	0.588	0.502	0.683	SUBCLONAL	1	TRUE	0	0.264694872394368	1		663	602	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602829	10602831	+	stop_gained	Nonsense_Mutation	TNP	ATG	ATG	TTT	novel	NA	P-0032127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	184	819	0	ENST00000171111.5:c.747_749delinsAAA	p.Cys249_Ile250delinsTer	p.C249_I250delins*	ENST00000171111	NM_203500.1	249	tgCATc/tgAAAc	3/6	0.208374489782552	2	FACETS	0.773	0.714	0.835	0.773	0.714	0.835	SUBCLONAL	2	TRUE	0	0.264694872394368	2		819	899	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0032129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	56	778	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.223	0.19	0.259	0.223	0.19	0.259	SUBCLONAL	1	TRUE	1	0.493452127635006	2		779	1020	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0032129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	149	535	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.199158969640024	3	FACETS	0.754	0.694	0.817	0.754	0.694	0.817	INDETERMINATE	2	TRUE	1	0.493452127635006	3		535	499	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	167	419	3	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	1	2	FACETS	0.785	0.722	0.851	0.785	0.722	0.851	SUBCLONAL	1	TRUE	1	0.493452127635006	2		422	862	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0032129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	152	361	1	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.493452127635006	2	FACETS	0.883	0.819	0.947	0.883	0.819	0.947	CLONAL	2	TRUE	0	0.493452127635006	2		362	349	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	72	484	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	0.954	0.841	1	0.954	0.841	1	CLONAL	1	TRUE	1	0.493452127635006	2		484	306	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600446	10600446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	22	888	2	ENST00000171111.5:c.1409G>A	p.Arg470His	p.R470H	ENST00000171111	NM_203500.1	470	cGt/cAt	4/6	1	2	FACETS	0.089	0.068	0.113	0.089	0.068	0.113	SUBCLONAL	1	TRUE	1	0.493452127635006	2		890	1004	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092756	27092757	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	199	667	0	ENST00000324856.7:c.2777_2778insA	p.Gly927TrpfsTer9	p.G927Wfs*9	ENST00000324856	NM_006015.4	926	act/acAt	9/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.493452127635006	2		667	760	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659558	88659558	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757608699	NA	P-0032129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	47	642	0	ENST00000372037.3:c.341C>T	p.Pro114Leu	p.P114L	ENST00000372037	NM_004329.2	114	cCa/cTa	6/13	1	2	FACETS	0.29	0.244	0.34	0.29	0.244	0.34	SUBCLONAL	1	TRUE	1	0.493452127635006	2		642	658	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56477631	56477631	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	209	859	0	ENST00000267101.3:c.179T>G	p.Met60Arg	p.M60R	ENST00000267101	NM_001982.3	60	aTg/aGg	2/28	0.199158969640024	3	FACETS	0.977	0.906	1	0.488	0.453	0.525	INDETERMINATE	1	TRUE	1	0.493452127635006	3		859	1081	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315474	30315474	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	174	638	0	ENST00000322652.5:c.1159C>T	p.Gln387Ter	p.Q387*	ENST00000322652	NM_015355.2	387	Cag/Tag	10/16	1	2	FACETS	0.934	0.862	1	0.934	0.862	1	CLONAL	1	TRUE	1	0.493452127635006	2		638	755	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119043	70119044	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0032129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	181	657	0	ENST00000245479.2:c.618_619dup	p.Leu207ArgfsTer13	p.L207Rfs*13	ENST00000245479	NM_000346.3	205	-/GC	2/3	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.493452127635006	2		657	673	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129634	11129634	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	228	811	0	ENST00000358026.2:c.2440A>G	p.Thr814Ala	p.T814A	ENST00000358026	NM_001128849.1	814	Acg/Gcg	17/36	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.493452127635006	2		811	910	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0032131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	384	415	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.625428865146953	2	FACETS	0.932	0.911	0.952	1	0.997	1	CLONAL	3	TRUE	0	0.625428865146953	2		415	439	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0032131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	132	470	1	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	0.625428865146953	2		471	356	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	279	534	0	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	0.298762584935329	2	FACETS	0.876	0.834	0.918	0.876	0.834	0.918	INDETERMINATE	2	TRUE	0	0.625428865146953	2		534	509	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138176	64138176	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	76	610	2	ENST00000334205.4:c.2099C>T	p.Ser700Leu	p.S700L	ENST00000334205	NM_003942.2	700	tCg/tTg	16/17	1	2	FACETS	0.464	0.407	0.524	0.464	0.407	0.524	SUBCLONAL	1	TRUE	1	0.625428865146953	2		612	524	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961250	1961253	+	frameshift_variant	Frame_Shift_Del	DEL	TCCC	TCCC	-	novel	NA	P-0032131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	174	514	0	ENST00000382891.5:c.3039_3042del	p.Pro1014SerfsTer19	p.P1014Sfs*19	ENST00000382891	NM_133335.3	1013	aTCCCt/at	17/22	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.625428865146953	2		514	427	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591127	67591269	+	splice_donor_variant,splice_acceptor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	AGAAAGACGAGAGACCAATACTTGATGTAAGTATTTGAAATGGAATCCTATACATGAATAATTGGTGATTGCTACAATTCAGGATGAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGGTTGACTCAAAAAGGTGTT	AGAAAGACGAGAGACCAATACTTGATGTAAGTATTTGAAATGGAATCCTATACATGAATAATTGGTGATTGCTACAATTCAGGATGAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGGTTGACTCAAAAAGGTGTT	-	novel	NA	P-0032131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	123	246	0	ENST00000274335.5:c.1720_1767del		p.X574_splice	ENST00000274335		574	AGAAAGACGAGAGACCAATACTTGATGTAAGTATTTGAAATGGAATCCTATACATGAATAATTGGTGATTGCTACAATTCAGGATGAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGGTTGACTCAAAAAGGTGTT/-	12-13/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.625428865146953	2		246	314	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97934390	97934390	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	170	270	0	ENST00000289081.3:c.385A>G	p.Lys129Glu	p.K129E	ENST00000289081	NM_000136.2	129	Aaa/Gaa	5/15	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.625428865146953	2		270	390	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	124	258	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.82	2		258	247	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0032134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	52	427	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.186	0.157	0.217	0.186	0.157	0.217	SUBCLONAL	1	TRUE	1	0.82	2		427	683	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0032134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	193	490	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.505	0.467	0.544	0.505	0.467	0.544	SUBCLONAL	1	TRUE	1	0.82	2		490	932	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0032134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	58	447	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.249	0.213	0.287	0.249	0.213	0.287	SUBCLONAL	1	TRUE	1	0.82	2		447	569	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0032134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	84	212	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	1	2	FACETS	0.487	0.432	0.545	0.487	0.432	0.545	SUBCLONAL	1	TRUE	1	0.82	2		212	421	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519925	NA	P-0032134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	39	568	0	ENST00000263967.3:c.1357G>C	p.Glu453Gln	p.E453Q	ENST00000263967	NM_006218.2	453	Gaa/Caa	8/21	1	2	FACETS	0.111	0.091	0.133	0.111	0.091	0.133	SUBCLONAL	1	TRUE	1	0.82	2		568	859	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807889	1807889	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs78311289	NA	P-0032134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	439	695	0	ENST00000260795.2:c.1948A>G	p.Lys650Glu	p.K650E	ENST00000260795		650	Aag/Gag	13/17	1	2	FACETS	0.769	0.742	0.796	1	0.997	1	SUBCLONAL	2	TRUE	1	0.82	2		695	696	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724541	162724541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759709680	NA	P-0032134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	224	518	1	ENST00000367921.3:c.313C>T	p.Arg105Cys	p.R105C	ENST00000367921	NM_006182.2	105	Cgc/Tgc	5/18	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.82	2		519	546	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	274	623	0	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	1	2	FACETS	0.96	0.907	1	0.96	0.907	1	CLONAL	1	TRUE	1	0.82	2		623	696	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175942	176175942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs964768927	NA	P-0032134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	33	57	0	ENST00000367669.3:c.173C>T	p.Ser58Leu	p.S58L	ENST00000367669	NM_022457.5	58	tCg/tTg	1/20	1	2	FACETS	0.994	0.84	1	0.994	0.84	1	CLONAL	1	TRUE	1	0.82	2		57	81	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247516	123247516	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519795	NA	P-0032134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	23	556	0	ENST00000358487.5:c.1975A>G	p.Lys659Glu	p.K659E	ENST00000358487	NM_000141.4	659	Aag/Gag	14/18	1	2	FACETS	0.066	0.051	0.084	0.066	0.051	0.084	SUBCLONAL	1	TRUE	1	0.82	2		556	849	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101089	26101089	+	start_lost	Translation_Start_Site	SNP	C	C	T	rs1559535727	NA	P-0032134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	28	388	0	ENST00000435504.4:c.3G>A	p.Met1?	p.M1?	ENST00000435504		1	atG/atA	1/13	1	2	FACETS	0.134	0.107	0.166	0.134	0.107	0.166	SUBCLONAL	1	TRUE	1	0.82	2		388	509	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495496	56495496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217262342	NA	P-0032134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	164	581	0	ENST00000267101.3:c.3686C>T	p.Ser1229Leu	p.S1229L	ENST00000267101	NM_001982.3	1229	tCa/tTa	28/28	1	2	FACETS	0.579	0.533	0.627	0.579	0.533	0.627	SUBCLONAL	1	TRUE	1	0.82	2		581	691	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393285	393285	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	128	412	0	ENST00000380956.4:c.133G>A	p.Glu45Lys	p.E45K	ENST00000380956	NM_001195286.1	45	Gag/Aag	2/9	1	2	FACETS	0.577	0.525	0.631	0.577	0.525	0.631	SUBCLONAL	1	TRUE	1	0.82	2		412	541	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259183	36259183	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	250	543	0	ENST00000300305.3:c.308C>T	p.Pro103Leu	p.P103L	ENST00000300305		103	cCt/cTt	3/8	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.82	2		543	599	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9787063	9787063	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	118	435	0	ENST00000377346.4:c.3094A>T	p.Asn1032Tyr	p.N1032Y	ENST00000377346	NM_005026.3	1032	Aac/Tac	24/24	1	2	FACETS	0.548	0.497	0.602	0.548	0.497	0.602	SUBCLONAL	1	TRUE	1	0.82	2		435	525	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983074	201983074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	67	633	0	ENST00000359651.3:c.923C>T	p.Ser308Phe	p.S308F	ENST00000359651		308	tCc/tTc	7/8	1	2	FACETS	0.22	0.191	0.252	0.22	0.191	0.252	SUBCLONAL	1	TRUE	1	0.82	2		633	743	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446429	70446429	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	264	358	0	ENST00000373644.4:c.5369C>A	p.Thr1790Lys	p.T1790K	ENST00000373644	NM_030625.2	1790	aCa/aAa	11/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.82	2		358	594	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041587	14041587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	44	514	0	ENST00000311895.7:c.2134G>A	p.Glu712Lys	p.E712K	ENST00000311895	NM_005236.2	712	Gag/Aag	11/11	1	2	FACETS	0.145	0.121	0.172	0.145	0.121	0.172	SUBCLONAL	1	TRUE	1	0.82	2		514	739	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855937	68855937	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	249	444	0	ENST00000261769.5:c.1745del	p.Leu582ArgfsTer2	p.L582Rfs*2	ENST00000261769	NM_004360.3	582	cTg/cg	12/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.82	2		444	586	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657438	29657438	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	363	637	0	ENST00000356175.3:c.5671A>G	p.Ser1891Gly	p.S1891G	ENST00000356175	NM_000267.3	1891	Agt/Ggt	38/57	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.82	2		637	823	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118996	70118996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	134	568	0	ENST00000245479.2:c.568G>A	p.Glu190Lys	p.E190K	ENST00000245479	NM_000346.3	190	Gag/Aag	2/3	1	2	FACETS	0.554	0.505	0.605	0.554	0.505	0.605	SUBCLONAL	1	TRUE	1	0.82	2		568	590	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982457	25982457	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	63	392	0	ENST00000435504.4:c.833T>A	p.Leu278Gln	p.L278Q	ENST00000435504		278	cTg/cAg	9/13	1	2	FACETS	0.231	0.2	0.266	0.231	0.2	0.266	SUBCLONAL	1	TRUE	1	0.82	2		392	664	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180353	38180353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200093616	NA	P-0032134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	47	660	0	ENST00000396334.3:c.201G>A	p.Met67Ile	p.M67I	ENST00000396334	NM_002468.4	67	atG/atA	1/5	1	2	FACETS	0.148	0.125	0.175	0.148	0.125	0.175	SUBCLONAL	1	TRUE	1	0.82	2		660	772	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155793	106155793	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs748785984	NA	P-0032134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	70	454	0	ENST00000380013.4:c.694C>T	p.Gln232Ter	p.Q232*	ENST00000380013	NM_001127208.2	232	Caa/Taa	3/11	1	2	FACETS	0.282	0.246	0.321	0.282	0.246	0.321	SUBCLONAL	1	TRUE	1	0.82	2		454	605	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541048	187541052	+	frameshift_variant	Frame_Shift_Del	DEL	AAGTT	AAGTT	-	novel	NA	P-0032134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	214	444	0	ENST00000441802.2:c.6688_6692del	p.Asn2230GlnfsTer14	p.N2230Qfs*14	ENST00000441802	NM_005245.3	2230	AACTTc/c	10/27	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.82	2		444	472	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152510	56152510	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs387906788	NA	P-0032134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	51	288	0	ENST00000399503.3:c.566T>G	p.Leu189Arg	p.L189R	ENST00000399503	NM_005921.1	189	cTg/cGg	2/20	1	2	FACETS	0.286	0.243	0.333	0.286	0.243	0.333	SUBCLONAL	1	TRUE	1	0.82	2		288	435	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652019	36652040	+	frameshift_variant	Frame_Shift_Del	DEL	GCGATGGAACTTCGACTTTGTC	GCGATGGAACTTCGACTTTGTC	-	novel	NA	P-0032134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	41	677	0	ENST00000244741.5:c.141_162del	p.Arg48ProfsTer93	p.R48Pfs*93	ENST00000244741	NM_000389.4	47	gaGCGATGGAACTTCGACTTTGTC/ga	2/3	1	2	FACETS	0.13	0.108	0.156	0.13	0.108	0.156	SUBCLONAL	1	TRUE	1	0.82	2		677	767	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748474	43748474	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0032134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	135	236	0	ENST00000523873.1:c.428C>G	p.Ser143Ter	p.S143*	ENST00000523873		143	tCa/tGa	6/8	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.82	2		236	288	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519709	137519709	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0032134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	52	377	0	ENST00000367739.4:c.929C>G	p.Ser310Ter	p.S310*	ENST00000367739	NM_000416.2	310	tCa/tGa	7/7	1	2	FACETS	0.216	0.184	0.252	0.216	0.184	0.252	SUBCLONAL	1	TRUE	1	0.82	2		377	586	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346181	152346181	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	333	516	0	ENST00000359321.1:c.389T>C	p.Leu130Pro	p.L130P	ENST00000359321	NM_005431.1	130	cTt/cCt	3/3	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.82	2		516	792	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205119	38205119	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	179	727	0	ENST00000317025.8:c.571G>A	p.Glu191Lys	p.E191K	ENST00000317025	NM_023034.1	191	Gaa/Aaa	2/24	1	2	FACETS	0.416	0.383	0.45	0.416	0.383	0.45	SUBCLONAL	1	TRUE	1	0.82	2		727	1050	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211350	98211350	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0032134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	40	528	0	ENST00000331920.6:c.3804+1G>A		p.X1268_splice	ENST00000331920	NM_000264.3	1268			1	2	FACETS	0.152	0.126	0.181	0.152	0.126	0.181	SUBCLONAL	1	TRUE	1	0.82	2		528	642	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922952	44922952	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	291	241	0	ENST00000377967.4:c.1813G>T	p.Gly605Ter	p.G605*	ENST00000377967	NM_021140.2	605	Gga/Tga	16/29	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.82	1		241	344	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808889	1808900	+	frameshift_variant	Frame_Shift_Del	DEL	GCCAGGACACCC	GCCAGGACACCC	T	novel	NA	P-0032134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	264	654	0	ENST00000260795.2:c.2321_2332delinsT	p.Gly774ValfsTer39	p.G774Vfs*39	ENST00000260795		774	gGCCAGGACACCCcc/gTcc	17/17	1	2	FACETS	0.922	0.87	0.976	0.922	0.87	0.976	CLONAL	1	TRUE	1	0.82	2		654	698	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	226	447	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.324570971051505	3	FACETS	0.949	0.886	1	0.949	0.886	1	CLONAL	2	TRUE	1	0.357177139450847	3		447	786	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0032137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	296	568	1	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	0.357177139450847	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.357177139450847	2		569	733	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	321	324	0	ENST00000257430.4:c.4199C>A	p.Ser1400Ter	p.S1400*	ENST00000257430	NM_000038.5	1400	tCg/tAg	16/16	0.357177139450847	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.357177139450847	3		324	607	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538323	9538323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1243986113	NA	P-0032137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	72	549	0	ENST00000353224.5:c.1675C>T	p.Leu559Phe	p.L559F	ENST00000353224	NM_177990.2	559	Ctt/Ttt	7/10	0.357177139450847	5	FACETS	0.517	0.45	0.59	0.172	0.15	0.197	SUBCLONAL	1	TRUE	2	0.357177139450847	5		549	1198	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	184	258	0				ENST00000310581	NM_198253.2	-/1132			0.281906661990613	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.360898742387684	4		258	661	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653042	29653047	+	inframe_deletion	In_Frame_Del	DEL	TAACTG	TAACTG	-	novel	NA	P-0032138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	97	512	0	ENST00000356175.3:c.4982_4987del	p.Cys1661_Asn1662del	p.C1661_N1662del	ENST00000356175	NM_000267.3	1659	taTAACTGt/tat	36/57	0.167421642173309	4	FACETS	0.901	0.803	1	0.3	0.267	0.336	INDETERMINATE	1	TRUE	1	0.360898742387684	4		512	812	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440940	56440940	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	363	598	0	ENST00000407977.2:c.397G>T	p.Gly133Ter	p.G133*	ENST00000407977		133	Gga/Tga	4/10	0.167421642173309	4	FACETS	0.921	0.875	0.967	0.921	0.875	0.967	INDETERMINATE	3	TRUE	1	0.360898742387684	4		598	991	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919036	50919036	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	74	727	2	ENST00000440232.2:c.2773G>T	p.Val925Leu	p.V925L	ENST00000440232	NM_002691.3	925	Gtg/Ttg	22/27	0.196724794642262	5	FACETS	0.598	0.522	0.681	0.199	0.174	0.227	INDETERMINATE	1	TRUE	2	0.360898742387684	5		729	1057	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259207	89259207	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	75	476	0	ENST00000336596.2:c.351G>T	p.Lys117Asn	p.K117N	ENST00000336596	NM_005233.5	117	aaG/aaT	3/17	0.261816104422522	3	FACETS	0.96	0.843	1	0.48	0.421	0.543	CLONAL	1	TRUE	1	0.360898742387684	3		476	511	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	48	447	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.666	0.562	0.781	0.666	0.562	0.781	SUBCLONAL	1	TRUE	1	0.22	2		447	655	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0032140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	76	436	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.91	0.798	1	0.91	0.798	1	CLONAL	1	TRUE	1	0.22	2		436	759	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0032151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	92	447	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	TRUE	1	0.241707630915437	2		447	578	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509433	106509433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747427177	NA	P-0032151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	72	454	0	ENST00000359195.3:c.1427G>A	p.Arg476His	p.R476H	ENST00000359195	NM_002649.2	476	cGc/cAc	2/11	1	2	FACETS	0.946	0.826	1	0.946	0.826	1	CLONAL	1	TRUE	1	0.241707630915437	2		454	630	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921774	111921774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150291943	NA	P-0032153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	81	390	0	ENST00000393256.3:c.563G>A	p.Arg188His	p.R188H	ENST00000393256	NM_006538.4	188	cGt/cAt	4/4	0.471521484419707	3	FACETS	1	0.931	1	0.535	0.474	0.6	CLONAL	1	TRUE	1	0.479645116775643	3		390	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0032153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	217	582	1	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.479645116775643	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.479645116775643	2		583	443	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195365	102195365	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	179	442	0	ENST00000263464.3:c.125G>T	p.Gly42Val	p.G42V	ENST00000263464	NM_001165.4	42	gGg/gTg	2/9	0.31926701495501	3	FACETS	1	0.986	1	0.805	0.753	0.858	CLONAL	2	TRUE	0	0.479645116775643	3		442	383	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89880984	89880984	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs777209858	NA	P-0032153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	158	467	0	ENST00000389301.3:c.227A>G	p.Lys76Arg	p.K76R	ENST00000389301	NM_000135.2	76	aAa/aGa	3/43	0.479645116775643	3	FACETS	0.994	0.921	1	0.994	0.921	1	CLONAL	2	TRUE	1	0.479645116775643	3		467	411	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	134	575	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.268207533515869	3	FACETS	1	0.95	1			1	CLONAL	1	TRUE	NA	0.367766345947907	3		575	808	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0032156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	127	545	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.367766345947907	1	FACETS	0.879	0.799	0.964	0.879	0.799	0.964	CLONAL	1	TRUE	0	0.367766345947907	1		545	641	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0032158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	15	358	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.525	0.382	0.698	0.525	0.382	0.698	SUBCLONAL	1	TRUE	1	0.12	2		359	476	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0032158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	44	596	1	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.0752511407652585	3	FACETS	0.935	0.782	1	0.468	0.391	0.553	CLONAL	1	TRUE	1	0.12	3		597	831	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988388	36988397	+	frameshift_variant	Frame_Shift_Del	DEL	CCACGGCGTG	CCACGGCGTG	-	novel	NA	P-0032158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	13	162	0	ENST00000354822.5:c.256_265del	p.His86GlyfsTer12	p.H86Gfs*12	ENST00000354822	NM_001079668.2	86	CACGCCGTGGgg/gg	2/3	1	2	FACETS	0.934	0.666	1	0.934	0.666	1	CLONAL	1	TRUE	1	0.12	2		162	232	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0032159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	303	367	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.914	0.867	0.962	0.914	0.867	0.962	CLONAL	1	TRUE	1	0.927258604031679	2		367	715	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161732	47161732	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	42	282	0	ENST00000409792.3:c.4394del	p.Lys1465SerfsTer18	p.K1465Sfs*18	ENST00000409792	NM_014159.6	1465	aAg/ag	3/21	1	2	FACETS	0.195	0.163	0.231	0.195	0.163	0.231	SUBCLONAL	1	TRUE	1	0.927258604031679	2		282	464	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	186	354	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.869	0.808	0.932	0.869	0.808	0.932	CLONAL	1	TRUE	1	0.732875335620991	2		354	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876658468	NA	P-0032168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	282	581	0	ENST00000269305.4:c.577C>G	p.His193Asp	p.H193D	ENST00000269305	NM_001126112.2	193	Cat/Gat	6/11	0.732875335620991	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.732875335620991	1		581	485	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	335	447	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.343965664166222	2	FACETS	0.899	0.858	0.941	0.899	0.858	0.941	CLONAL	2	TRUE	0	0.542143663111101	2		447	687	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs967461896	NA	P-0032169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	125	710	0	ENST00000269305.4:c.526T>C	p.Cys176Arg	p.C176R	ENST00000269305	NM_001126112.2	176	Tgc/Cgc	5/11	0.515133192962586	1	FACETS	0.986	0.904	1	0.986	0.904	1	CLONAL	1	TRUE	0	0.542143663111101	1		710	341	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023860	27023861	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0032169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	50	112	0	ENST00000324856.7:c.971dup	p.Ala325ArgfsTer75	p.A325Rfs*75	ENST00000324856	NM_006015.4	322	-/G	1/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.542143663111101	2		112	158	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604652	48604652	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	70	278	0	ENST00000342988.3:c.1474G>T	p.Val492Phe	p.V492F	ENST00000342988	NM_005359.5	492	Gtt/Ttt	12/12	0.542143663111101	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	0	0.542143663111101	1		278	184	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974787	21974799	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCCGAAGGCTC	CAGCCGAAGGCTC	-	novel	NA	P-0032169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	11	92	0	ENST00000304494.5:c.28_40del	p.Glu10ThrfsTer12	p.E10Tfs*12	ENST00000304494	NM_000077.4	10	GAGCCTTCGGCTGac/ac	1/3	0.542143663111101	1	FACETS	0.528	0.374	0.709	0.528	0.374	0.709	SUBCLONAL	1	TRUE	0	0.542143663111101	1		92	56	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0032170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	13	358	0	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	0.400217297085936	1	FACETS	0.18	0.128	0.244	0.18	0.128	0.244	SUBCLONAL	1	TRUE	0	0.400217297085936	1		358	289	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36824350	36824350	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	89	521	0	ENST00000373129.3:c.186del	p.Tyr63IlefsTer3	p.Y63Ifs*3	ENST00000373129	NM_032017.1	62	ttC/tt	4/12	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.400217297085936	2		521	431	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855210	76855211	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0032170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	35	261	0	ENST00000373344.5:c.5776dup	p.Asp1926GlyfsTer16	p.D1926Gfs*16	ENST00000373344	NM_000489.3	1926	gat/gGat	24/35	0.236765968932625	2	FACETS	1	0.895	1			1	INDETERMINATE	1	TRUE	NA	0.400217297085936	2		261	158	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0032174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	189	596	0	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.310425421018279	NA		596	668	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0032175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	93	814	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.15956882131882	3	FACETS	1	0.967	1	0.617	0.549	0.69	CLONAL	1	TRUE	1	0.254172350993418	3		814	668	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0032175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	178	620	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.189239309025701	2	FACETS	0.875	0.808	0.945	0.875	0.808	0.945	CLONAL	2	TRUE	0	0.254172350993418	2		621	800	SUCCESS
APC	324	MSKCC	GRCh37	5	112111358	112111358	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554071521	NA	P-0032175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	13	206	0	ENST00000257430.4:c.458del	p.Lys153ArgfsTer17	p.K153Rfs*17	ENST00000257430	NM_000038.5	152	gAa/ga	5/16	0.218288125601182	1	FACETS	0.525	0.376	0.706	0.525	0.376	0.706	SUBCLONAL	1	TRUE	0	0.254172350993418	1		206	170	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	55	354	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	0.2	2		354	441	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	63	419	3	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	1	2	FACETS	0.998	0.863	1	0.998	0.863	1	CLONAL	1	TRUE	1	0.2	2		422	631	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0032176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	62	436	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.2	2		436	615	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473723	67473723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223740	NA	P-0032176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	61	494	0	ENST00000327367.4:c.803G>A	p.Arg268His	p.R268H	ENST00000327367	NM_005902.3	268	cGc/cAc	6/9	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.2	2		494	559	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522274	157522274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567836947	NA	P-0032176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	39	624	0	ENST00000346085.5:c.4546G>A	p.Val1516Ile	p.V1516I	ENST00000346085	NM_020732.3	1516	Gtc/Atc	18/20	1	2	FACETS	0.586	0.484	0.699	0.586	0.484	0.699	SUBCLONAL	1	TRUE	1	0.2	2		624	666	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368213	45368213	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	75	292	0	ENST00000262160.6:c.1389C>A	p.Cys463Ter	p.C463*	ENST00000262160	NM_005901.5	463	tgC/tgA	11/11	0.195812852817332	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	0	0.2	2		292	332	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746113	162746113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1364325806	NA	P-0032176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	39	281	1	ENST00000367921.3:c.2236C>T	p.Arg746Trp	p.R746W	ENST00000367921	NM_006182.2	746	Cgg/Tgg	16/18	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.2	2		282	379	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175868	24175868	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886039520	NA	P-0032176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	27	372	0	ENST00000263121.7:c.1096C>T	p.Arg366Cys	p.R366C	ENST00000263121	NM_003073.3	366	Cgc/Tgc	8/9	1	2	FACETS	0.698	0.555	0.861	0.698	0.555	0.861	SUBCLONAL	1	TRUE	1	0.2	2		372	387	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046363	180046363	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	70	473	0	ENST00000261937.6:c.2651G>A	p.Gly884Asp	p.G884D	ENST00000261937	NM_182925.4	884	gGc/gAc	19/30	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.2	2		473	554	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119008	70119008	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	54	572	0	ENST00000245479.2:c.580G>T	p.Glu194Ter	p.E194*	ENST00000245479	NM_000346.3	194	Gag/Tag	2/3	1	2	FACETS	0.827	0.705	0.96	0.827	0.705	0.96	CLONAL	1	TRUE	1	0.2	2		572	653	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564641	55564641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	31	480	0	ENST00000288135.5:c.529C>T	p.Arg177Cys	p.R177C	ENST00000288135	NM_000222.2	177	Cgc/Tgc	3/21	1	2	FACETS	0.521	0.42	0.636	0.521	0.42	0.636	SUBCLONAL	1	TRUE	1	0.2	2		480	595	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128201270	128201270	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	66	534	0	ENST00000265960.3:c.1465C>T	p.Arg489Ter	p.R489*	ENST00000265960	NM_001006617.1	489	Cga/Tga	12/12	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.2	2		534	641	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348478	70348478	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	38	520	1	ENST00000374080.3:c.3385G>A	p.Ala1129Thr	p.A1129T	ENST00000374080		1129	Gct/Act	24/45	1	2	FACETS	0.622	0.513	0.744	0.622	0.513	0.744	SUBCLONAL	1	TRUE	1	0.2	2		521	611	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123159694	123159694	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	25	310	0	ENST00000218089.9:c.49T>C	p.Ser17Pro	p.S17P	ENST00000218089	NM_001042749.1	17	Tca/Cca	4/35	1	2	FACETS	0.66	0.52	0.821	0.66	0.52	0.821	SUBCLONAL	1	TRUE	1	0.2	2		310	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0032178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	146	560	1	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	0.475013725184391	1	FACETS	0.907	0.836	0.98	0.907	0.836	0.98	CLONAL	1	TRUE	0	0.550390360358288	1		561	424	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774081	56774081	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555594589	NA	P-0032178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	72	561	0	ENST00000337432.4:c.432A>G	p.Ile144Met	p.I144M	ENST00000337432	NM_058216.2	144	atA/atG	3/9	0.550390360358288	3	FACETS	0.442	0.386	0.504	0.221	0.193	0.252	SUBCLONAL	1	TRUE	1	0.550390360358288	3		561	754	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435834	116435834	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	142	582	0	ENST00000397752.3:c.3924C>G	p.Cys1308Trp	p.C1308W	ENST00000397752	NM_000245.2	1308	tgC/tgG	20/21	0.181408350280603	5	FACETS	1	0.977	1	0.403	0.367	0.44	INDETERMINATE	1	TRUE	2	0.550390360358288	5		582	780	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	188	354	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.216496407560237	3	FACETS	0.938	0.87	1	1	0.989	1	CLONAL	3	TRUE	1	0.216496407560237	3		354	684	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0032179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	22	322	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.216496407560237	3	FACETS	0.771	0.598	0.972	0.386	0.299	0.486	CLONAL	1	TRUE	1	0.216496407560237	3		322	292	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0032179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	52	619	1	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.216496407560237	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.216496407560237	1		620	291	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0032179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	177	703	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	0.210688194254427	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	2	TRUE	0	0.216496407560237	2		703	817	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102083	27102083	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	119	546	0	ENST00000324856.7:c.5009G>T	p.Trp1670Leu	p.W1670L	ENST00000324856	NM_006015.4	1670	tGg/tTg	19/20	0.216496407560237	3	FACETS	0.847	0.765	0.933	0.847	0.765	0.933	CLONAL	2	TRUE	1	0.216496407560237	3		546	719	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858994	243858995	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0032179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	38	408	0	ENST00000263826.5:c.70_71delinsAG	p.Pro24Arg	p.P24R	ENST00000263826	NM_005465.4	24	CCa/AGa	2/13	0.216496407560237	5	FACETS	0.807	0.666	0.965	0.269	0.222	0.322	CLONAL	1	TRUE	2	0.216496407560237	5		408	576	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226463	133226463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1012418859	NA	P-0032179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	32	406	0	ENST00000320574.5:c.3595G>A	p.Glu1199Lys	p.E1199K	ENST00000320574	NM_006231.2	1199	Gag/Aag	30/49	0.216496407560237	3	FACETS	0.671	0.544	0.815	0.336	0.272	0.408	SUBCLONAL	1	TRUE	1	0.216496407560237	3		406	488	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40684218	40684218	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	99	438	0	ENST00000249776.8:c.816G>T	p.Glu272Asp	p.E272D	ENST00000249776	NM_033286.3	272	gaG/gaT	8/9	0.133205789269112	3	FACETS	0.921	0.825	1	0.921	0.825	1	CLONAL	2	TRUE	1	0.216496407560237	3		438	550	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41999981	41999982	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0032179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	123	716	2	ENST00000219905.7:c.2244_2245delinsTT	p.Leu748_Gly749delinsPheTer	p.L748_G749delinsF*	ENST00000219905	NM_001164273.1	748	ttGGga/ttTTga	6/24	0.133205789269112	3	FACETS	1	0.981	1	0.678	0.613	0.748	CLONAL	1	TRUE	1	0.216496407560237	3		718	928	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89865620	89865620	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	123	506	0	ENST00000389301.3:c.847G>T	p.Ala283Ser	p.A283S	ENST00000389301	NM_000135.2	283	Gct/Tct	10/43	0.216496407560237	3	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	1	0.216496407560237	3		506	605	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678059	58678059	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	66	197	0	ENST00000305921.3:c.284G>C	p.Arg95Pro	p.R95P	ENST00000305921	NM_003620.3	95	cGt/cCt	1/6	0.216496407560237	5	FACETS	1	0.955	1	0.806	0.704	0.915	CLONAL	2	TRUE	2	0.216496407560237	5		197	334	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211848	36211848	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	304	911	0	ENST00000222270.7:c.1599T>G	p.Ser533Arg	p.S533R	ENST00000222270	NM_014727.1	533	agT/agG	3/37	0.216496407560237	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.216496407560237	3		911	1357	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242879	142242879	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	41	495	0	ENST00000350721.4:c.4108G>C	p.Asp1370His	p.D1370H	ENST00000350721	NM_001184.3	1370	Gat/Cat	22/47	0.153914228376551	5	FACETS	0.636	0.528	0.757	0.212	0.176	0.253	SUBCLONAL	1	TRUE	2	0.216496407560237	5		495	789	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608667	189608667	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	63	470	0	ENST00000264731.3:c.1742T>C	p.Met581Thr	p.M581T	ENST00000264731	NM_003722.4	581	aTg/aCg	13/14	0.153914228376551	5	FACETS	1	0.948	1	0.401	0.346	0.46	CLONAL	1	TRUE	2	0.216496407560237	5		470	641	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524595	187524595	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	287	673	1	ENST00000441802.2:c.11085A>T	p.Leu3695Phe	p.L3695F	ENST00000441802	NM_005245.3	3695	ttA/ttT	19/27	0.216496407560237	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	0	0.216496407560237	3		674	939	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538353	187538353	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	124	340	0	ENST00000441802.2:c.8881G>T	p.Gly2961Trp	p.G2961W	ENST00000441802	NM_005245.3	2961	Ggg/Tgg	11/27	0.216496407560237	3	FACETS	0.973	0.887	1	0.973	0.887	1	CLONAL	3	TRUE	0	0.216496407560237	3		340	435	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370829	55370829	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	76	242	0	ENST00000297316.4:c.131T>A	p.Val44Glu	p.V44E	ENST00000297316	NM_022454.3	44	gTg/gAg	1/2	0.216496407560237	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	1	0.216496407560237	3		242	343	SUCCESS
AR	367	MSKCC	GRCh37	X	66765919	66765919	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	91	820	0	ENST00000374690.3:c.931C>G	p.Pro311Ala	p.P311A	ENST00000374690	NM_000044.3	311	Cct/Gct	1/8	1	2	FACETS	0.866	0.767	0.972	0.866	0.767	0.972	CLONAL	1	TRUE	1	0.216496407560237	2		820	971	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371409680	NA	P-0032183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	248	542	0	ENST00000269305.4:c.848G>C	p.Arg283Pro	p.R283P	ENST00000269305	NM_001126112.2	283	cGc/cCc	8/11	NA	2	FACETS	1	0.961	1			1	INDETERMINATE	2	TRUE	NA	0.40588746420626	2		542	596	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386450	31386450	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0032183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	76	425	0	ENST00000328111.2:c.1674+1G>C		p.X558_splice	ENST00000328111	NM_006892.3	558			0.40588746420626	4	FACETS	0.767	0.673	0.869	0.256	0.224	0.29	SUBCLONAL	1	TRUE	1	0.40588746420626	4		425	686	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100403	8100403	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	88	544	0	ENST00000346208.3:c.377C>A	p.Ser126Tyr	p.S126Y	ENST00000346208		126	tCc/tAc	3/6	0.40588746420626	3	FACETS	0.893	0.793	1	0.447	0.396	0.5	CLONAL	1	TRUE	1	0.40588746420626	3		544	584	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670880	134670880	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	59	292	1	ENST00000398015.3:c.791G>T	p.Ser264Ile	p.S264I	ENST00000398015	NM_004441.4	264	aGc/aTc	3/16	0.40588746420626	3	FACETS	0.904	0.781	1	0.452	0.39	0.519	CLONAL	1	TRUE	1	0.40588746420626	3		293	387	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507321	8507321	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750349056	NA	P-0032183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	117	329	0	ENST00000356435.5:c.1657G>A	p.Asp553Asn	p.D553N	ENST00000356435		553	Gat/Aat	11/35	0.40588746420626	2	FACETS	0.848	0.774	0.924	0.848	0.774	0.924	CLONAL	2	TRUE	0	0.40588746420626	2		329	340	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187817	11187817	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	87	414	1	ENST00000361445.4:c.6080G>T	p.Trp2027Leu	p.W2027L	ENST00000361445	NM_004958.3	2027	tGg/tTg	44/58	1	2	FACETS	0.864	0.768	0.967	0.864	0.768	0.967	CLONAL	1	TRUE	1	0.40588746420626	2		415	496	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316145	11316145	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	93	436	0	ENST00000361445.4:c.609G>C	p.Gln203His	p.Q203H	ENST00000361445	NM_004958.3	203	caG/caC	5/58	1	2	FACETS	0.871	0.777	0.971	0.871	0.777	0.971	CLONAL	1	TRUE	1	0.40588746420626	2		436	526	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175996765	175996765	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	74	399	1	ENST00000367669.3:c.1672G>T	p.Val558Leu	p.V558L	ENST00000367669	NM_022457.5	558	Gtg/Ttg	15/20	0.40588746420626	3	FACETS	0.835	0.733	0.946	0.418	0.366	0.473	CLONAL	1	TRUE	1	0.40588746420626	3		400	525	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192687	94192710	+	inframe_deletion	In_Frame_Del	DEL	CCACAAATTCTTGTACTGCTTCAC	CCACAAATTCTTGTACTGCTTCAC	-	novel	NA	P-0032183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	187	470	0	ENST00000323929.3:c.1364_1387del	p.Gly455_Val462del	p.G455_V462del	ENST00000323929	NM_005591.3	455	gGTGAAGCAGTACAAGAATTTGTGGac/gac	13/20	0.287079942006617	5	FACETS	1	0.98	1	0.77	0.714	0.827	CLONAL	2	TRUE	2	0.40588746420626	5		470	642	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204761	94204761	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	80	377	0	ENST00000323929.3:c.824C>A	p.Ser275Tyr	p.S275Y	ENST00000323929	NM_005591.3	275	tCc/tAc	8/20	0.287079942006617	5	FACETS	1	0.953	1	0.387	0.341	0.436	CLONAL	1	TRUE	2	0.40588746420626	5		377	546	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497576	125497576	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	126	265	0	ENST00000428830.2:c.140A>G	p.Asp47Gly	p.D47G	ENST00000428830	NM_001114121.2	47	gAc/gGc	3/14	0.287079942006617	5	FACETS	1	0.97	1	0.764	0.697	0.833	CLONAL	2	TRUE	2	0.40588746420626	5		265	436	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337660	73337660	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1175752033	NA	P-0032183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	45	266	0	ENST00000377767.4:c.2056G>C	p.Ala686Pro	p.A686P	ENST00000377767	NM_014953.3	686	Gct/Cct	16/21	1	2	FACETS	0.739	0.624	0.864	0.739	0.624	0.864	SUBCLONAL	1	TRUE	1	0.40588746420626	2		266	300	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544683	65544684	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0032183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	210	553	0	ENST00000358664.4:c.242_243del	p.His81ProfsTer5	p.H81Pfs*5	ENST00000358664	NM_002382.4	81	cAC/c	4/5	0.40588746420626	2	FACETS	0.887	0.83	0.946	0.887	0.83	0.946	CLONAL	2	TRUE	0	0.40588746420626	2		553	583	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43772156	43772156	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	118	529	0	ENST00000382044.4:c.559G>C	p.Glu187Gln	p.E187Q	ENST00000382044	NM_001141980.1	187	Gag/Cag	6/28	0.40588746420626	2	FACETS	0.969	0.877	1	0.485	0.438	0.533	CLONAL	1	TRUE	0	0.40588746420626	2		529	600	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614983	23614983	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs876658773	NA	P-0032183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	148	285	0	ENST00000261584.4:c.3358G>T	p.Glu1120Ter	p.E1120*	ENST00000261584	NM_024675.3	1120	Gaa/Taa	13/13	0.40588746420626	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.40588746420626	2		285	346	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56867141	56867141	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	233	453	0	ENST00000308159.5:c.1360A>T	p.Thr454Ser	p.T454S	ENST00000308159	NM_014669.4	454	Acg/Tcg	13/22	0.40588746420626	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.40588746420626	2		453	526	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435602	56435602	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	113	534	0	ENST00000407977.2:c.1535G>T	p.Ser512Ile	p.S512I	ENST00000407977		512	aGc/aTc	9/10	0.40588746420626	3	FACETS	1	0.947	1	0.538	0.485	0.594	CLONAL	1	TRUE	1	0.40588746420626	3		534	622	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226361	2226361	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	254	588	1	ENST00000398665.3:c.3841G>T	p.Glu1281Ter	p.E1281*	ENST00000398665	NM_032482.2	1281	Gag/Tag	27/28	0.40588746420626	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.40588746420626	2		589	611	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18964065	18964065	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	186	367	0	ENST00000262803.5:c.1062G>T	p.Met354Ile	p.M354I	ENST00000262803	NM_002911.3	354	atG/atT	8/24	0.40588746420626	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.40588746420626	2		367	429	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794361	242794361	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200312345	NA	P-0032183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	107	511	0	ENST00000334409.5:c.581G>A	p.Arg194Gln	p.R194Q	ENST00000334409	NM_005018.2	194	cGg/cAg	3/5	0.252750612268758	4	FACETS	1	0.972	1			1	CLONAL	1	TRUE	NA	0.40588746420626	4		511	602	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52649469	52649469	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	81	384	0	ENST00000394830.3:c.1822T>G	p.Tyr608Asp	p.Y608D	ENST00000394830	NM_018313.4	608	Tat/Gat	16/30	1	2	FACETS	0.971	0.86	1	0.971	0.86	1	CLONAL	1	TRUE	1	0.40588746420626	2		384	411	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137522018	137522018	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	74	174	0	ENST00000367739.4:c.861G>C	p.Leu287Phe	p.L287F	ENST00000367739	NM_000416.2	287	ttG/ttC	6/7	0.40588746420626	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	2	TRUE	0	0.40588746420626	2		174	173	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69103970	69103970	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	103	473	0	ENST00000288368.4:c.4360G>T	p.Asp1454Tyr	p.D1454Y	ENST00000288368	NM_024870.2	1454	Gac/Tac	36/40	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.40588746420626	2		473	467	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974719	21974721	+	frameshift_variant	Frame_Shift_Del	DEL	CGC	CGC	GG	novel	NA	P-0032183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	126	284	0	ENST00000304494.5:c.106_108delinsCC	p.Ala36ProfsTer17	p.A36Pfs*17	ENST00000304494	NM_000077.4	36	GCG/CC	1/3	0.40588746420626	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.40588746420626	2		284	294	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133748425	133748425	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0032183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	143	284	0	ENST00000318560.5:c.1085+1G>T		p.X362_splice	ENST00000318560	NM_005157.4	362			0.40588746420626	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.40588746420626	2		284	326	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617573	100617574	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0032183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	96	282	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	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.40588746420626	1		282	291	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976710	2976710	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	75	493	0	ENST00000396946.4:c.1302G>T	p.Lys434Asn	p.K434N	ENST00000396946	NM_032415.4	434	aaG/aaT	9/25	1	2	FACETS	0.499	0.437	0.566	0.499	0.437	0.566	SUBCLONAL	1	TRUE	1	0.42733162861991	2		493	703	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141557700	141557700	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	139	477	0	ENST00000220592.5:c.1615G>T	p.Val539Leu	p.V539L	ENST00000220592	NM_012154.3	539	Gtg/Ttg	13/19	1	2	FACETS	0.825	0.751	0.902	0.825	0.751	0.902	CLONAL	1	TRUE	1	0.42733162861991	2		477	789	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0032194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	168	620	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.529523795532758	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.529523795532758	1		621	451	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725264	49725264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142358513	NA	P-0032194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	78	137	3	ENST00000449682.2:c.161C>T	p.Ala54Val	p.A54V	ENST00000449682	NM_020998.3	54	gCg/gTg	2/18	0.529523795532758	3	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	1	0.529523795532758	3		140	179	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902229	151902229	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0032194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	203	377	5	ENST00000262189.6:c.3923C>G	p.Ser1308Ter	p.S1308*	ENST00000262189	NM_170606.2	1308	tCa/tGa	25/59	0.529523795532758	4	FACETS	0.931	0.868	0.995	0.931	0.868	0.995	CLONAL	2	TRUE	2	0.529523795532758	4		382	630	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998745	100998745	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	281	493	3	ENST00000325455.5:c.1057G>T	p.Val353Phe	p.V353F	ENST00000325455	NM_001202474.3	353	Gtc/Ttc	1/8	0.529523795532758	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	2	0.529523795532758	4		496	801	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670279	134670279	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	95	340	0	ENST00000398015.3:c.190T>A	p.Phe64Ile	p.F64I	ENST00000398015	NM_004441.4	64	Ttc/Atc	3/16	0.529523795532758	3	FACETS	1	0.895	1	0.5	0.447	0.555	CLONAL	1	TRUE	1	0.529523795532758	3		340	454	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417861	138417861	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	248	428	3	ENST00000289153.2:c.1658A>T	p.Asn553Ile	p.N553I	ENST00000289153	NM_006219.2	553	aAt/aTt	11/22	0.529523795532758	3	FACETS	0.965	0.909	1	0.965	0.909	1	CLONAL	2	TRUE	1	0.529523795532758	3		431	614	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	188	258	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.645831100875035	2		258	434	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152009018	152009018	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	218	356	0	ENST00000262189.6:c.604C>T	p.Gln202Ter	p.Q202*	ENST00000262189	NM_170606.2	202	Cag/Tag	5/59	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.645831100875035	2		356	527	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0032210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	224	580	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	0.959	0.897	1	0.959	0.897	1	CLONAL	1	TRUE	1	0.645831100875035	2		580	723	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0032210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	240	585	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.645831100875035	2		585	737	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434348	49434348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	336	674	1	ENST00000301067.7:c.7205C>A	p.Ser2402Ter	p.S2402*	ENST00000301067	NM_003482.3	2402	tCa/tAa	31/54	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.645831100875035	2		675	973	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444499	49444500	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	306	623	0	ENST00000301067.7:c.2871dup	p.Glu958ArgfsTer11	p.E958Rfs*11	ENST00000301067	NM_003482.3	957	-/A	11/54	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.645831100875035	2		623	841	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164987	47164987	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1193056929	NA	P-0032210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	195	383	0	ENST00000409792.3:c.1139A>G	p.Tyr380Cys	p.Y380C	ENST00000409792	NM_014159.6	380	tAt/tGt	3/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.645831100875035	2		383	544	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114592	73114592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	122	261	0	ENST00000356692.5:c.973C>T	p.Gln325Ter	p.Q325*	ENST00000356692		325	Caa/Taa	9/9	1	2	FACETS	0.981	0.896	1	0.981	0.896	1	CLONAL	1	TRUE	1	0.645831100875035	2		261	385	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696432	47696432	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519968	NA	P-0032212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	87	534	0	ENST00000347630.2:c.391T>G	p.Trp131Gly	p.W131G	ENST00000347630	NM_001007230.1	131	Tgg/Ggg	6/11	0.136851903562737	3	FACETS	1	0.91	1	0.517	0.457	0.58	INDETERMINATE	1	TRUE	1	0.26236575518523	3		534	726	SUCCESS
AR	367	MSKCC	GRCh37	X	66943553	66943553	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs137852580	NA	P-0032212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	39	220	0	ENST00000374690.3:c.2633C>G	p.Thr878Ser	p.T878S	ENST00000374690	NM_000044.3	878	aCt/aGt	8/8	1	1	FACETS	0.906	0.755	1	0.906	0.755	1	CLONAL	1	TRUE	0	0.26236575518523	1		220	285	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606505	93606505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1303320502	NA	P-0032212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	104	710	0	ENST00000375746.1:c.325C>T	p.Arg109Trp	p.R109W	ENST00000375746	NM_001174167.1	109	Cgg/Tgg	2/14	1	2	FACETS	0.961	0.86	1	0.961	0.86	1	CLONAL	1	TRUE	1	0.26236575518523	2		710	825	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	233	354	0	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	FALSE	1	0.553805488168583	2		354	724	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0032215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	471	712	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.553805488168583	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	FALSE	0	0.553805488168583	2		712	819	SUCCESS
APC	324	MSKCC	GRCh37	5	112175852	112175852	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	103	245	0	ENST00000257430.4:c.4561G>T	p.Glu1521Ter	p.E1521*	ENST00000257430	NM_000038.5	1521	Gaa/Taa	16/16	1	2	FACETS	0.896	0.808	0.989	0.896	0.808	0.989	CLONAL	1	FALSE	1	0.553805488168583	2		245	415	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971142	21971142	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	87	330	0	ENST00000304494.5:c.216C>A	p.Cys72Ter	p.C72*	ENST00000304494	NM_000077.4	72	tgC/tgA	2/3	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	FALSE	1	0.553805488168583	2		330	313	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0032218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	47	680	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.162304156895354	3	FACETS	0.733	0.617	0.86	0.366	0.308	0.43	SUBCLONAL	1	TRUE	1	0.240384570861998	3		680	598	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0032218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	53	752	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.191512042865387	1	FACETS	0.508	0.432	0.591	0.508	0.432	0.591	SUBCLONAL	1	TRUE	0	0.240384570861998	1		752	764	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0032225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	124	620	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.274682518764775	1	FACETS	0.993	0.9	1	0.993	0.9	1	CLONAL	1	TRUE	0	0.322427408909784	1		621	650	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178550	56178550	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	53	216	0	ENST00000399503.3:c.3523C>G	p.Gln1175Glu	p.Q1175E	ENST00000399503	NM_005921.1	1175	Caa/Gaa	14/20	0.307811711820274	3	FACETS	0.886	0.757	1	0.443	0.378	0.513	CLONAL	1	TRUE	1	0.322427408909784	3		216	431	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900040	151900040	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	88	515	0	ENST00000262189.6:c.4071A>C	p.Glu1357Asp	p.E1357D	ENST00000262189	NM_170606.2	1357	gaA/gaC	26/59	0.100065335392274	3	FACETS	0.755	0.668	0.848	0.252	0.222	0.283	INDETERMINATE	1	TRUE	0	0.322427408909784	3		515	840	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649861	88649861	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	24	278	2	ENST00000372037.3:c.110C>T	p.Ser37Leu	p.S37L	ENST00000372037	NM_004329.2	37	tCa/tTa	4/13	1	2	FACETS	0.366	0.286	0.458	0.366	0.286	0.458	SUBCLONAL	1	TRUE	1	0.322427408909784	2		280	407	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177950	56177950	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	95	459	0	ENST00000399503.3:c.2923C>G	p.His975Asp	p.H975D	ENST00000399503	NM_005921.1	975	Cat/Gat	14/20	0.307811711820274	3	FACETS	0.854	0.76	0.955	0.427	0.38	0.478	CLONAL	1	TRUE	1	0.322427408909784	3		459	801	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0032226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	125	391	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.491801258834855	2		391	406	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115940	8115940	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	126	353	0	ENST00000346208.3:c.1287del	p.Phe430LeufsTer45	p.F430Lfs*45	ENST00000346208		429	tCc/tc	6/6	1	2	FACETS	0.972	0.885	1	0.972	0.885	1	CLONAL	1	TRUE	1	0.491801258834855	2		353	527	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859492	151859492	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	287	544	0	ENST00000262189.6:c.11170G>T	p.Glu3724Ter	p.E3724*	ENST00000262189	NM_170606.2	3724	Gag/Tag	43/59	0.370397487412298	2	FACETS	0.908	0.86	0.955	0.908	0.86	0.955	CLONAL	2	TRUE	0	0.491801258834855	2		544	643	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	66	354	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	0.29	2		354	452	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0032229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	29	322	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.647	0.52	0.791	0.647	0.52	0.791	SUBCLONAL	1	TRUE	1	0.29	2		322	309	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562246	21562246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745371213	NA	P-0032229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	140	754	3	ENST00000382592.4:c.1673G>A	p.Arg558His	p.R558H	ENST00000382592	NM_014572.2	558	cGc/cAc	4/8	1	2	FACETS	0.884	0.804	0.969	0.884	0.804	0.969	CLONAL	1	TRUE	1	0.29	2		757	1092	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0032229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	80	471	1	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	1	2	FACETS	0.879	0.774	0.991	0.879	0.774	0.991	CLONAL	1	TRUE	1	0.29	2		472	628	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492875	56492875	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	106	341	1	ENST00000407977.2:c.64C>T	p.Gln22Ter	p.Q22*	ENST00000407977		22	Cag/Tag	2/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.29	2		342	665	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0032231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	882	814	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.33393606182545	14	FACETS	1	0.992	1			1	CLONAL	12	FALSE	NA	0.33393606182545	14		814	1278	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0032231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	147	508	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.289845809383642	2	FACETS	0.785	0.72	0.852	0.785	0.72	0.852	SUBCLONAL	2	FALSE	0	0.33393606182545	2		509	561	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891641	28891642	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0032231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	30	445	1	ENST00000282397.4:c.3379_3380delinsAA	p.Pro1127Asn	p.P1127N	ENST00000282397	NM_002019.4	1127	CCt/AAt	25/30	1	2	FACETS	0.415	0.334	0.507	0.415	0.334	0.507	SUBCLONAL	1	FALSE	1	0.33393606182545	2		446	433	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514757	103514757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374911899	NA	P-0032231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	42	246	1	ENST00000355739.4:c.1258C>T	p.Arg420Cys	p.R420C	ENST00000355739	NM_000123.3	420	Cgt/Tgt	8/15	1	2	FACETS	0.856	0.718	1	0.856	0.718	1	CLONAL	1	FALSE	1	0.33393606182545	2		247	294	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116203	67116203	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	53	346	1	ENST00000412916.2:c.487G>T	p.Glu163Ter	p.E163*	ENST00000412916		163	Gaa/Taa	5/6	0.297288009017689	4	FACETS	0.69	0.587	0.802	0.23	0.195	0.268	SUBCLONAL	1	FALSE	1	0.33393606182545	4		347	614	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0032232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	20	680	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.99	0.759	1	0.99	0.759	1	CLONAL	1	TRUE	1	0.176507294894237	2		680	229	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231335	5231335	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769069932	NA	P-0032232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	36	428	0	ENST00000357368.4:c.2141G>A	p.Arg714His	p.R714H	ENST00000357368	NM_002850.3	714	cGc/cAc	14/38	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.176507294894237	2		428	352	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907117	101907117	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	12	313	0	ENST00000374994.4:c.1078del	p.Ser360GlnfsTer29	p.S360Qfs*29	ENST00000374994	NM_004612.2	359	gaT/ga	6/9	0.176507294894237	1	FACETS	0.821	0.579	1	0.821	0.579	1	CLONAL	1	TRUE	0	0.176507294894237	1		313	151	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0032237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	54	718	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	1	2	FACETS	0.773	0.659	0.899	0.773	0.659	0.899	SUBCLONAL	1	TRUE	1	0.18	2		718	776	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808889	3808889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	62	600	0	ENST00000262367.5:c.3335G>A	p.Arg1112Gln	p.R1112Q	ENST00000262367	NM_004380.2	1112	cGg/cAg	17/31	1	2	FACETS	0.998	0.862	1	0.998	0.862	1	CLONAL	1	TRUE	1	0.18	2		600	690	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0032238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	239	596	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.302134523028781	1	FACETS	0.979	0.922	1	0.979	0.922	1	INDETERMINATE	1	TRUE	0	0.604299622899775	1		596	564	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0032238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	269	358	0	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	0.604299622899775	1	FACETS	0.908	0.857	0.96	0.908	0.857	0.96	CLONAL	1	TRUE	0	0.604299622899775	1		358	684	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0032238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	284	654	0	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	0.604299622899775	1	FACETS	0.985	0.933	1	0.985	0.933	1	CLONAL	1	TRUE	0	0.604299622899775	1		654	666	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122346	17122346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs190786280	NA	P-0032238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	181	426	0	ENST00000285071.4:c.1049G>A	p.Arg350Gln	p.R350Q	ENST00000285071	NM_144997.5	350	cGg/cAg	9/14	0.604299622899775	1	FACETS	0.974	0.91	1	0.974	0.91	1	CLONAL	1	TRUE	0	0.604299622899775	1		426	429	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17117118	17117118	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	90	582	0	ENST00000285071.4:c.1591G>A	p.Asp531Asn	p.D531N	ENST00000285071	NM_144997.5	531	Gac/Aac	14/14	0.604299622899775	1	FACETS	0.335	0.297	0.375	0.335	0.297	0.375	SUBCLONAL	1	TRUE	0	0.604299622899775	1		582	621	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0032278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	233	603	1	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		604	826	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377337	118377337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782625001	NA	P-0032278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	40	255	0	ENST00000534358.1:c.10730C>T	p.Thr3577Met	p.T3577M	ENST00000534358	NM_005933.3	3577	aCg/aTg	27/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		255	434	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266246	198266246	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	24	353	0	ENST00000335508.6:c.2374G>T	p.Val792Leu	p.V792L	ENST00000335508	NM_012433.2	792	Gta/Tta	17/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		353	337	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0032310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	32	329	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.522195827626084	1	FACETS	0.801	0.665	0.948	0.801	0.665	0.948	CLONAL	1	TRUE	0	0.522195827626084	1		329	113	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138651	55138651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4616	1699	497	0	ENST00000257290.5:c.1328C>T	p.Pro443Leu	p.P443L	ENST00000257290	NM_006206.4	443	cCt/cTt	9/23	0.522195827626084	33	FACETS	1	0.992	1			1	CLONAL	9	TRUE	NA	0.522195827626084	33		497	6315	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295192	1295193	+	upstream_gene_variant	5'Flank	INS	-	-	GCGGAAAGGAAGGGGAGGGGCT	novel	NA	P-0032310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	49	243	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.52	0.442	0.605	0.52	0.442	0.605	SUBCLONAL	1	TRUE	1	0.522195827626084	2		243	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0032311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	312	620	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.6613655328759	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.6613655328759	1		621	558	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0032311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	192	535	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.249832585588637	3	FACETS	0.75	0.7	0.802	0.75	0.7	0.802	INDETERMINATE	2	TRUE	1	0.6613655328759	3		535	515	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0032311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	170	273	1	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	0.644112749336741	2	FACETS	0.989	0.935	1	0.989	0.935	1	CLONAL	2	TRUE	0	0.6613655328759	2		274	260	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969968	161969968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746215864	NA	P-0032311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	269	577	2	ENST00000366898.1:c.1001G>A	p.Arg334His	p.R334H	ENST00000366898	NM_004562.2	334	cGc/cAc	9/12	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.6613655328759	2		579	658	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251635	212251635	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1211840752	NA	P-0032311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	172	554	0	ENST00000342788.4:c.3424C>T	p.Arg1142Ter	p.R1142*	ENST00000342788	NM_005235.2	1142	Cga/Tga	27/28	1	2	FACETS	0.926	0.857	0.996	0.926	0.857	0.996	CLONAL	1	TRUE	1	0.6613655328759	2		554	562	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134881022	134881022	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	178	527	2	ENST00000398015.3:c.1585G>A	p.Asp529Asn	p.D529N	ENST00000398015	NM_004441.4	529	Gat/Aat	7/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.6613655328759	2		529	461	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050017	13050017	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	201	512	0	ENST00000316448.5:c.161G>T	p.Gly54Val	p.G54V	ENST00000316448	NM_004343.3	54	gGc/gTc	2/9	0.6613655328759	2	FACETS	1	0.932	1	0.5	0.466	0.535	CLONAL	1	TRUE	0	0.6613655328759	2		512	608	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0032312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	13	680	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.864	0.617	1	0.864	0.617	1	CLONAL	1	TRUE	1	0.14	2		680	215	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0032312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	8	461	1	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.519	0.334	0.761	0.519	0.334	0.761	SUBCLONAL	1	TRUE	1	0.14	2		462	220	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0032312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	25	787	2	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	1	2	FACETS	0.84	0.661	1	0.84	0.661	1	CLONAL	1	TRUE	1	0.14	2		789	425	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	216	258	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		258	519	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439869	51439869	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	143	325	0	ENST00000262662.1:c.434G>T	p.Arg145Met	p.R145M	ENST00000262662		145	aGg/aTg	4/4	0.479611832216195	3	FACETS	0.919	0.848	0.993	0.919	0.848	0.993	CLONAL	2	TRUE	1	0.493337733214908	3		325	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0032315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	190	618	0	ENST00000269305.4:c.559+1del		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.493337733214908	2	FACETS	0.944	0.885	1	0.944	0.885	1	CLONAL	2	TRUE	0	0.493337733214908	2		618	408	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074200	30074200	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	218	505	0	ENST00000338641.4:c.1463del	p.Pro488GlnfsTer27	p.P488Qfs*27	ENST00000338641	NM_000268.3	488	Cca/ca	14/16	0.493337733214908	2	FACETS	0.98	0.923	1	0.98	0.923	1	CLONAL	2	TRUE	0	0.493337733214908	2		505	451	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391907	139391907	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756874994	NA	P-0032315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	213	939	2	ENST00000277541.6:c.6284G>A	p.Arg2095His	p.R2095H	ENST00000277541	NM_017617.3	2095	cGc/cAc	34/34	0.493337733214908	3	FACETS	1	0.986	1	0.616	0.573	0.66	CLONAL	1	TRUE	1	0.493337733214908	3		941	874	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	140	354	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.148472819165735	4	FACETS	1	0.944	1	1	0.944	1	INDETERMINATE	2	TRUE	2	0.314276922136438	4		354	562	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711978	89711980	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	rs1564837980	NA	P-0032334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	132	390	0	ENST00000371953.3:c.597_599del	p.Met199_Phe200delinsIle	p.M199_F200delinsI	ENST00000371953	NM_000314.4	199	aTGTtt/att	6/9	0.262019256490595	2	FACETS	0.975	0.892	1	0.975	0.892	1	CLONAL	2	TRUE	0	0.314276922136438	2		390	431	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807301	3807301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769985879	NA	P-0032334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	93	332	0	ENST00000262367.5:c.3686G>A	p.Ser1229Asn	p.S1229N	ENST00000262367	NM_004380.2	1229	aGc/aAc	19/31	0.314276922136438	3	FACETS	1	0.979	1	0.724	0.646	0.806	CLONAL	1	TRUE	1	0.314276922136438	3		332	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0032334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	179	620	2	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.262019256490595	2	FACETS	0.925	0.857	0.995	0.925	0.857	0.995	CLONAL	2	TRUE	0	0.314276922136438	2		622	616	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325846	30325846	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763509688	NA	P-0032334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	48	315	0	ENST00000322652.5:c.2044C>T	p.Arg682Cys	p.R682C	ENST00000322652	NM_015355.2	682	Cgt/Tgt	16/16	0.262019256490595	2	FACETS	1	0.867	1	0.511	0.434	0.594	CLONAL	1	TRUE	0	0.314276922136438	2		315	299	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006635	62006635	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1169314441	NA	P-0032334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	73	668	0	ENST00000392795.3:c.644G>A	p.Arg215Gln	p.R215Q	ENST00000392795	NM_001039933.1	215	cGg/cAg	6/6	0.262019256490595	2	FACETS	0.703	0.614	0.798	0.351	0.307	0.399	SUBCLONAL	1	TRUE	0	0.314276922136438	2		668	661	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031599	36031599	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs950614364	NA	P-0032334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	70	531	0	ENST00000358208.4:c.1428C>A	p.Asp476Glu	p.D476E	ENST00000358208		476	gaC/gaA	12/12	0.148472819165735	4	FACETS	0.775	0.675	0.884	0.388	0.337	0.442	INDETERMINATE	1	TRUE	2	0.314276922136438	4		531	755	SUCCESS
APC	324	MSKCC	GRCh37	5	112175198	112175198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	27	226	0	ENST00000257430.4:c.3907C>T	p.Gln1303Ter	p.Q1303*	ENST00000257430	NM_000038.5	1303	Caa/Taa	16/16	1	2	FACETS	0.704	0.563	0.864	0.704	0.563	0.864	SUBCLONAL	1	TRUE	1	0.314276922136438	2		226	244	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175520	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAGTGAACCATG	CAGAGTGAACCATG	-	novel	NA	P-0032334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	59	329	0	ENST00000257430.4:c.4219_4232del	p.Ser1407TrpfsTer11	p.S1407Wfs*11	ENST00000257430	NM_000038.5	1406	CAGAGTGAACCATGc/c	16/16	1	2	FACETS	0.983	0.849	1	0.983	0.849	1	CLONAL	1	TRUE	1	0.314276922136438	2		329	382	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930124	68930132	+	frameshift_variant	Frame_Shift_Del	DEL	ACAAAAATG	ACAAAAATG	CCAAAATA	novel	NA	P-0032334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	46	323	0	ENST00000288368.4:c.185_193delinsCCAAAATA	p.Asp62AlafsTer4	p.D62Afs*4	ENST00000288368	NM_024870.2	62	gACAAAAATGtg/gCCAAAATAtg	2/40	0.314276922136438	3	FACETS	0.679	0.572	0.797	0.339	0.286	0.399	SUBCLONAL	1	TRUE	1	0.314276922136438	3		323	499	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0032375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	81	501	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.806	0.713	0.905	0.806	0.713	0.905	CLONAL	1	TRUE	1	0.440988814419544	2		501	456	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0032375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	54	221	0	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS	0.865	0.745	0.995	0.865	0.745	0.995	CLONAL	1	TRUE	1	0.440988814419544	2		221	283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs878854073	NA	P-0032375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	89	374	0	ENST00000269305.4:c.673-1G>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.440988814419544	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	0	0.440988814419544	1		374	310	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526195	63526195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	121	360	0	ENST00000307078.5:c.2431G>A	p.Glu811Lys	p.E811K	ENST00000307078	NM_004655.3	811	Gag/Aag	11/11	1	2	FACETS	0.951	0.862	1	0.951	0.862	1	CLONAL	1	TRUE	1	0.440988814419544	2		360	577	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379758	17379758	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	157	643	0	ENST00000359435.4:c.143G>T	p.Arg48Leu	p.R48L	ENST00000359435	NM_001033549.1	48	cGc/cTc	2/9	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.440988814419544	2		643	711	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	69	258	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.431705000567729	2		258	301	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0032377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	160	425	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.144240167032	2	FACETS	1	0.981	1	0.606	0.558	0.655	INDETERMINATE	1	TRUE	0	0.431705000567729	2		425	612	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0032377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	261	778	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.431705000567729	2	FACETS	0.893	0.842	0.945	0.893	0.842	0.945	CLONAL	2	TRUE	0	0.431705000567729	2		779	677	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476307	88476307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772244244	NA	P-0032377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	79	523	0	ENST00000360948.2:c.1825G>A	p.Asp609Asn	p.D609N	ENST00000360948	NM_001012338.2	609	Gat/Aat	15/19	1	2	FACETS	0.647	0.569	0.729	0.647	0.569	0.729	SUBCLONAL	1	TRUE	1	0.431705000567729	2		523	566	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548886	29548886	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs953440640	NA	P-0032377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	246	539	0	ENST00000356175.3:c.1660C>T	p.Gln554Ter	p.Q554*	ENST00000356175	NM_000267.3	554	Cag/Tag	15/57	0.431705000567729	2	FACETS	0.867	0.816	0.92	0.867	0.816	0.92	CLONAL	2	TRUE	0	0.431705000567729	2		539	657	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6045628	6045628	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573374779	NA	P-0032377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	73	160	0	ENST00000265849.7:c.58C>T	p.Arg20Trp	p.R20W	ENST00000265849	NM_000535.5	20	Cgg/Tgg	2/15	0.12184074200207	5	FACETS	0.957	0.846	1	0.638	0.564	0.717	INDETERMINATE	2	TRUE	2	0.431705000567729	5		160	291	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40709551	40709551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568484928	NA	P-0032377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	130	372	0	ENST00000373198.4:c.4351G>A	p.Glu1451Lys	p.E1451K	ENST00000373198	NM_133170.3	1451	Gag/Aag	32/32	0.173194907012923	2	FACETS	1	0.97	1	0.575	0.524	0.628	INDETERMINATE	1	TRUE	0	0.431705000567729	2		372	524	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914707	32914707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80358862	NA	P-0032377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	56	391	0	ENST00000380152.3:c.6215C>T	p.Ser2072Phe	p.S2072F	ENST00000380152		2072	tCc/tTc	11/27	1	2	FACETS	0.564	0.484	0.651	0.564	0.484	0.651	SUBCLONAL	1	TRUE	1	0.431705000567729	2		391	460	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641698	23641698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	60	339	0	ENST00000261584.4:c.1777C>T	p.His593Tyr	p.H593Y	ENST00000261584	NM_024675.3	593	Cat/Tat	5/13	0.173194907012923	2	FACETS	0.519	0.447	0.596	0.259	0.223	0.298	INDETERMINATE	1	TRUE	0	0.431705000567729	2		339	536	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340201	116340201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561295443	NA	P-0032377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	77	352	0	ENST00000397752.3:c.1063G>A	p.Glu355Lys	p.E355K	ENST00000397752	NM_000245.2	355	Gaa/Aaa	2/21	0.12184074200207	5	FACETS	0.847	0.749	0.95	0.565	0.499	0.634	INDETERMINATE	2	TRUE	2	0.431705000567729	5		352	347	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965117	81965117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11548655	NA	P-0032377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	120	355	0	ENST00000359376.3:c.2597G>A	p.Gly866Glu	p.G866E	ENST00000359376	NM_002661.3	866	gGa/gAa	25/33	0.334776164512949	2	FACETS	1	0.982	1	0.671	0.611	0.734	CLONAL	1	TRUE	0	0.431705000567729	2		355	414	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612211	189612211	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	120	425	0	ENST00000264731.3:c.1963C>T	p.Arg655Ter	p.R655*	ENST00000264731	NM_003722.4	655	Cga/Tga	14/14	0.144240167032	2	FACETS	1	0.962	1	0.557	0.506	0.611	INDETERMINATE	1	TRUE	0	0.431705000567729	2		425	499	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458597	120458597	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	62	455	0	ENST00000256646.2:c.6748C>T	p.Pro2250Ser	p.P2250S	ENST00000256646	NM_024408.3	2250	Cca/Tca	34/34	0.144240167032	2	FACETS	0.531	0.459	0.609	0.265	0.229	0.305	INDETERMINATE	1	TRUE	0	0.431705000567729	2		455	541	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631089	69631089	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs143593259	NA	P-0032377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	74	384	0	ENST00000334134.2:c.323C>T	p.Ser108Leu	p.S108L	ENST00000334134	NM_005247.2	108	tCg/tTg	2/3	1	2	FACETS	0.742	0.652	0.839	0.742	0.652	0.839	SUBCLONAL	1	TRUE	1	0.431705000567729	2		384	462	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940705	71940705	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0032377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	98	502	0	ENST00000298229.2:c.754-2A>T		p.X252_splice	ENST00000298229	NM_001567.3	252			1	2	FACETS	0.792	0.709	0.881	0.792	0.709	0.881	SUBCLONAL	1	TRUE	1	0.431705000567729	2		502	573	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433727	49433728	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0032377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	102	699	3	ENST00000301067.7:c.7825_7826delinsTT	p.Pro2609Leu	p.P2609L	ENST00000301067	NM_003482.3	2609	CCa/TTa	31/54	0.144240167032	2	FACETS	0.592	0.529	0.659	0.296	0.264	0.33	INDETERMINATE	1	TRUE	0	0.431705000567729	2		702	798	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416675	121416675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	172	598	0	ENST00000257555.6:c.104C>T	p.Pro35Leu	p.P35L	ENST00000257555		35	cCc/cTc	1/10	0.144240167032	2	FACETS	1	0.983	1	0.614	0.567	0.662	INDETERMINATE	1	TRUE	0	0.431705000567729	2		598	649	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345052	73345052	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	45	305	0	ENST00000377767.4:c.1745T>A	p.Ile582Asn	p.I582N	ENST00000377767	NM_014953.3	582	aTt/aAt	13/21	1	2	FACETS	0.472	0.397	0.554	0.472	0.397	0.554	SUBCLONAL	1	TRUE	1	0.431705000567729	2		305	442	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992790	72992790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	168	438	0	ENST00000268489.5:c.1255C>T	p.Pro419Ser	p.P419S	ENST00000268489	NM_006885.3	419	Ccc/Tcc	2/10	0.334776164512949	2	FACETS	0.789	0.731	0.849	0.789	0.731	0.849	SUBCLONAL	2	TRUE	0	0.431705000567729	2		438	493	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649102	37649102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	178	286	0	ENST00000447079.4:c.2207G>A	p.Gly736Glu	p.G736E	ENST00000447079	NM_015083.1	736	gGa/gAa	4/14	0.431705000567729	2	FACETS	0.868	0.808	0.93	0.868	0.808	0.93	CLONAL	2	TRUE	0	0.431705000567729	2		286	475	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919608	96919608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	144	441	1	ENST00000258439.3:c.655C>T	p.Pro219Ser	p.P219S	ENST00000258439	NM_001193304.2	219	Ccc/Tcc	4/4	0.191331579927696	3	FACETS	1	0.983	1	0.65	0.595	0.707	INDETERMINATE	1	TRUE	1	0.431705000567729	3		442	624	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62293942	62293942	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	226	676	0	ENST00000360203.5:c.439C>T	p.His147Tyr	p.H147Y	ENST00000360203	NM_001283009.1	147	Cat/Tat	5/35	0.173194907012923	2	FACETS	1	0.987	1	0.619	0.577	0.661	INDETERMINATE	1	TRUE	0	0.431705000567729	2		676	846	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247462	71247462	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	171	538	0	ENST00000318789.4:c.71A>G	p.Asn24Ser	p.N24S	ENST00000318789	NM_032682.5	24	aAc/aGc	6/21	0.144240167032	2	FACETS	1	0.98	1	0.59	0.545	0.637	INDETERMINATE	1	TRUE	0	0.431705000567729	2		538	671	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582440	119582440	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	28	174	0	ENST00000316626.5:c.961C>G	p.Arg321Gly	p.R321G	ENST00000316626		321	Cga/Gga	10/12	0.144240167032	2	FACETS	0.545	0.438	0.666	0.273	0.219	0.333	INDETERMINATE	1	TRUE	0	0.431705000567729	2		174	238	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190474	32190474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	235	654	0	ENST00000375023.3:c.265G>A	p.Gly89Arg	p.G89R	ENST00000375023	NM_004557.3	89	Ggg/Agg	3/30	0.432305552744735	3	FACETS	0.801	0.749	0.854	0.801	0.749	0.854	CLONAL	2	TRUE	1	0.431705000567729	3		654	826	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444414	50444414	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	112	278	0	ENST00000331340.3:c.344G>A	p.Gly115Glu	p.G115E	ENST00000331340	NM_006060.4	115	gGa/gAa	4/8	0.12184074200207	5	FACETS	0.939	0.85	1	0.626	0.567	0.689	INDETERMINATE	2	TRUE	2	0.431705000567729	5		278	455	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974679	21974680	+	stop_gained,splice_region_variant	Nonsense_Mutation	DNP	GG	GG	AT	novel	NA	P-0032377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	180	323	0	ENST00000304494.5:c.147_148delinsAT	p.Gln50Ter	p.Q50*	ENST00000304494	NM_000077.4	49	atCCag/atATag	1/3	0.431705000567729	2	FACETS	0.974	0.909	1	0.974	0.909	1	CLONAL	2	TRUE	0	0.431705000567729	2		323	428	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922734	44922734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	118	160	0	ENST00000377967.4:c.1595C>T	p.Ser532Leu	p.S532L	ENST00000377967	NM_021140.2	532	tCa/tTa	16/29	0.372744160189173	2	FACETS	1	0.965	1			1	CLONAL	2	TRUE	NA	0.431705000567729	2		160	251	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779848	3779849	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	TA	TA	-	novel	NA	P-0032380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	68	619	0	ENST00000262367.5:c.5199_5200del	p.Tyr1733Ter	p.Y1733*	ENST00000262367	NM_004380.2	1733	taTAac/taac	31/31	0.262423203115684	1	FACETS	0.625	0.543	0.714	0.625	0.543	0.714	SUBCLONAL	1	TRUE	0	0.262423203115684	1		619	720	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577076	7577095	+	frameshift_variant	Frame_Shift_Del	DEL	TCTCTTCCTCTGTGCGCCGG	TCTCTTCCTCTGTGCGCCGG	-	novel	NA	P-0032380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	84	547	0	ENST00000269305.4:c.843_862del	p.Asp281GlufsTer18	p.D281Efs*18	ENST00000269305	NM_001126112.2	281	gaCCGGCGCACAGAGGAAGAGAat/gaat	8/11	0.262423203115684	1	FACETS	0.747	0.659	0.841	0.747	0.659	0.841	SUBCLONAL	1	TRUE	0	0.262423203115684	1		547	745	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156177	106156177	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	27	237	0	ENST00000380013.4:c.1078T>A	p.Leu360Met	p.L360M	ENST00000380013	NM_001127208.2	360	Ttg/Atg	3/11	0.262423203115684	1	FACETS	0.545	0.434	0.672	0.545	0.434	0.672	SUBCLONAL	1	TRUE	0	0.262423203115684	1		237	328	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0032383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	59	596	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.925	0.801	1	1	0.977	1	CLONAL	2	TRUE	1	0.205814712101298	2		596	310	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0032383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	15	173	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	1	0.783	1	1	0.783	1	CLONAL	1	TRUE	1	0.205814712101298	2		173	136	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900353	3900353	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	48	439	0	ENST00000262367.5:c.743del	p.Pro248ArgfsTer3	p.P248Rfs*3	ENST00000262367	NM_004380.2	248	cCg/cg	2/31	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.205814712101298	2		439	440	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0032384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	90	292	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.575501005488083	1	FACETS	0.804	0.723	0.888	0.804	0.723	0.888	CLONAL	1	TRUE	0	0.575501005488083	1		292	277	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663346	227663346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024227751	NA	P-0032384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	114	394	0	ENST00000305123.5:c.109G>A	p.Glu37Lys	p.E37K	ENST00000305123	NM_005544.2	37	Gag/Aag	1/2	1	2	FACETS	0.939	0.852	1	0.939	0.852	1	CLONAL	1	TRUE	1	0.575501005488083	2		394	422	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86676366	86676366	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	60	218	0	ENST00000274376.6:c.2644C>T	p.Gln882Ter	p.Q882*	ENST00000274376	NM_002890.2	882	Cag/Tag	20/25	0.540159501021679	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.575501005488083	1		218	135	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673793	37673793	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	130	440	0	ENST00000447079.4:c.2947C>T	p.Arg983Ter	p.R983*	ENST00000447079	NM_015083.1	983	Cga/Tga	10/14	1	2	FACETS	0.869	0.792	0.949	0.869	0.792	0.949	CLONAL	1	TRUE	1	0.575501005488083	2		440	520	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495438	56495438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	125	459	0	ENST00000267101.3:c.3628C>T	p.His1210Tyr	p.H1210Y	ENST00000267101	NM_001982.3	1210	Cat/Tat	28/28	1	2	FACETS	0.848	0.772	0.928	0.848	0.772	0.928	CLONAL	1	TRUE	1	0.575501005488083	2		459	512	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041159	29041159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	136	522	0	ENST00000282397.4:c.269G>A	p.Ser90Asn	p.S90N	ENST00000282397	NM_002019.4	90	aGt/aAt	3/30	1	2	FACETS	0.845	0.772	0.922	0.845	0.772	0.922	CLONAL	1	TRUE	1	0.575501005488083	2		522	559	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120554	2120554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555505178	NA	P-0032384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	178	649	0	ENST00000219476.3:c.1814C>T	p.Pro605Leu	p.P605L	ENST00000219476	NM_000548.3	605	cCa/cTa	17/42	1	2	FACETS	0.869	0.803	0.937	0.869	0.803	0.937	CLONAL	1	TRUE	1	0.575501005488083	2		649	712	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528481	29528481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	67	337	0	ENST00000356175.3:c.1238C>T	p.Ser413Leu	p.S413L	ENST00000356175	NM_000267.3	413	tCa/tTa	11/57	1	2	FACETS	0.721	0.631	0.817	0.721	0.631	0.817	SUBCLONAL	1	TRUE	1	0.575501005488083	2		337	323	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39567815	39567815	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	57	197	0	ENST00000262039.4:c.571G>A	p.Asp191Asn	p.D191N	ENST00000262039	NM_002647.2	191	Gat/Aat	5/25	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.575501005488083	2		197	177	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266477	41266477	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	97	262	0	ENST00000349496.5:c.274C>T	p.Gln92Ter	p.Q92*	ENST00000349496	NM_001904.3	92	Cag/Tag	4/15	0.540159501021679	1	FACETS	0.879	0.796	0.966	0.879	0.796	0.966	CLONAL	1	TRUE	0	0.575501005488083	1		262	273	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521063	187521066	+	frameshift_variant	Frame_Shift_Del	DEL	GACG	GACG	-	novel	NA	P-0032384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	85	269	0	ENST00000441802.2:c.12089_12092del	p.Pro4030HisfsTer15	p.P4030Hfs*15	ENST00000441802	NM_005245.3	4030	cCGTCa/ca	22/27	0.575501005488083	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.575501005488083	1		269	202	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939979	76939979	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	135	409	0	ENST00000373344.5:c.769A>T	p.Met257Leu	p.M257L	ENST00000373344	NM_000489.3	257	Atg/Ttg	9/35	1	2	FACETS	0.969	0.887	1	0.969	0.887	1	CLONAL	1	TRUE	1	0.575501005488083	2		409	484	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615599	100615599	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	152	447	0	ENST00000308731.7:c.733G>C	p.Glu245Gln	p.E245Q	ENST00000308731	NM_000061.2	245	Gag/Cag	8/19	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.575501005488083	2		447	481	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	2219	447	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.59161889236146	21	FACETS	0.985	0.976	0.994			1	CLONAL	20	TRUE	NA	0.59161889236146	21		447	2520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0032385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	327	906	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.59161889236146	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.59161889236146	1		906	699	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552732	18552732	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0032385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	39	496	0	ENST00000266497.5:c.2143A>T	p.Arg715Ter	p.R715*	ENST00000266497		715	Aga/Tga	14/31	0.349046701722851	1	FACETS	0.248	0.206	0.295	0.248	0.206	0.295	INDETERMINATE	1	TRUE	0	0.59161889236146	1		496	374	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647634	3647634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	72	791	0	ENST00000294008.3:c.1429G>A	p.Glu477Lys	p.E477K	ENST00000294008	NM_032444.2	477	Gaa/Aaa	7/15	0.337049607633997	2	FACETS	0.297	0.259	0.338	0.148	0.129	0.169	INDETERMINATE	1	TRUE	0	0.59161889236146	2		791	820	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878832	117878832	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0032385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	92	318	0	ENST00000297338.2:c.137C>G	p.Ser46Ter	p.S46*	ENST00000297338	NM_006265.2	46	tCa/tGa	2/14	0.59161889236146	1	FACETS	0.859	0.775	0.945	0.859	0.775	0.945	CLONAL	1	TRUE	0	0.59161889236146	1		318	255	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0032388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	36	314	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.12	2		314	526	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0032388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	13	212	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	1	2	FACETS	0.686	0.488	0.928	0.686	0.488	0.928	SUBCLONAL	1	TRUE	1	0.12	2		212	316	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0032388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	27	579	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	1	2	FACETS	0.529	0.419	0.656	0.529	0.419	0.656	SUBCLONAL	1	TRUE	1	0.12	2		579	851	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652140	3652140	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759447034	NA	P-0032388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	111	593	0	ENST00000294008.3:c.929G>A	p.Arg310Gln	p.R310Q	ENST00000294008	NM_032444.2	310	cGa/cAa	4/15	0.135294750844132	3	FACETS	0.898	0.805	0.996	0.898	0.805	0.996	CLONAL	2	TRUE	1	0.12	3		593	1092	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0032392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	239	319	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.521749569349933	3	FACETS	0.816	0.771	0.86	0.816	0.771	0.86	CLONAL	2	TRUE	1	0.868048670042823	3		319	484	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0032392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	164	410	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.868048670042823	2		410	294	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385256	4385256	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1019910889	NA	P-0032392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	296	502	0	ENST00000261254.3:c.281C>T	p.Pro94Leu	p.P94L	ENST00000261254	NM_001759.3	94	cCg/cTg	2/5	0.144669433099567	3	FACETS	0.82	0.78	0.861	0.82	0.78	0.861	INDETERMINATE	2	TRUE	1	0.868048670042823	3		502	596	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793483	18793483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267603405	NA	P-0032392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	137	323	0	ENST00000266497.5:c.4180G>A	p.Glu1394Lys	p.E1394K	ENST00000266497		1394	Gaa/Aaa	30/31	0.144669433099567	3	FACETS	1	0.988	1	0.714	0.66	0.769	INDETERMINATE	1	TRUE	1	0.868048670042823	3		323	317	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969813	81969813	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	147	476	0	ENST00000359376.3:c.2882C>G	p.Thr961Arg	p.T961R	ENST00000359376	NM_002661.3	961	aCg/aGg	27/33	0.526891323926017	1	FACETS	0.388	0.356	0.421	0.388	0.356	0.421	SUBCLONAL	1	TRUE	0	0.868048670042823	1		476	494	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17382427	17382427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	328	591	0	ENST00000359435.4:c.307G>A	p.Glu103Lys	p.E103K	ENST00000359435	NM_001033549.1	103	Gag/Aag	3/9	0.142503539587478	5	FACETS	0.928	0.88	0.978	0.464	0.44	0.489	INDETERMINATE	2	TRUE	1	0.868048670042823	5		591	937	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266946	18266946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	159	182	0	ENST00000222254.8:c.257C>T	p.Pro86Leu	p.P86L	ENST00000222254	NM_005027.3	86	cCc/cTc	2/16	0.142503539587478	5	FACETS	1	0.941	1	0.753	0.706	0.799	INDETERMINATE	3	TRUE	1	0.868048670042823	5		182	280	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794089	42794089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	228	441	2	ENST00000575354.2:c.1450C>T	p.Pro484Ser	p.P484S	ENST00000575354	NM_015125.3	484	Cca/Tca	9/20	0.142503539587478	5	FACETS	1	0.952	1	0.508	0.477	0.54	INDETERMINATE	2	TRUE	1	0.868048670042823	5		443	595	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157455	106157455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	130	293	0	ENST00000380013.4:c.2356C>T	p.His786Tyr	p.H786Y	ENST00000380013	NM_001127208.2	786	Cat/Tat	3/11	1	2	FACETS	0.902	0.83	0.976	0.902	0.83	0.976	CLONAL	1	TRUE	1	0.868048670042823	2		293	332	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247385	153247385	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0032392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	128	201	0	ENST00000281708.4:c.1419-2A>C		p.X473_splice	ENST00000281708	NM_033632.3	473			1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.868048670042823	2		201	289	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924546	131924546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201544462	NA	P-0032392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	80	376	0	ENST00000265335.6:c.1219G>A	p.Glu407Lys	p.E407K	ENST00000265335		407	Gaa/Aaa	8/25	1	2	FACETS	0.409	0.361	0.459	0.409	0.361	0.459	SUBCLONAL	1	TRUE	1	0.868048670042823	2		376	451	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715371	117715371	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	139	331	0	ENST00000368508.3:c.1118C>T	p.Ser373Phe	p.S373F	ENST00000368508	NM_002944.2	373	tCc/tTc	10/43	0.868048670042823	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.868048670042823	1		331	164	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	681	549	0	ENST00000356142.4:c.85C>G	p.Pro29Ala	p.P29A	ENST00000356142	NM_018890.3	29	Cct/Gct	2/7	0.667535779069223	4	FACETS	0.988	0.962	1	0.988	0.962	1	CLONAL	3	TRUE	1	0.868048670042823	4		549	989	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046393	69046393	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	181	542	0	ENST00000288368.4:c.3866T>C	p.Met1289Thr	p.M1289T	ENST00000288368	NM_024870.2	1289	aTg/aCg	32/40	1	2	FACETS	0.606	0.561	0.653	0.606	0.561	0.653	SUBCLONAL	1	TRUE	1	0.868048670042823	2		542	688	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93607792	93607792	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	152	353	0	ENST00000375746.1:c.494A>T	p.Lys165Ile	p.K165I	ENST00000375746	NM_001174167.1	165	aAa/aTa	3/14	1	2	FACETS	0.882	0.816	0.949	0.882	0.816	0.949	CLONAL	1	TRUE	1	0.868048670042823	2		353	397	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409833	63409833	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780867419	NA	P-0032392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	196	456	1	ENST00000330258.3:c.3334G>A	p.Glu1112Lys	p.E1112K	ENST00000330258	NM_152424.3	1112	Gag/Aag	2/2	1	2	FACETS	0.907	0.847	0.967	0.907	0.847	0.967	CLONAL	1	TRUE	1	0.868048670042823	2		457	498	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020225	123020225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	255	608	0	ENST00000355640.3:c.713G>A	p.Arg238Gln	p.R238Q	ENST00000355640		238	cGa/cAa	2/7	1	2	FACETS	0.877	0.826	0.929	0.877	0.826	0.929	CLONAL	1	TRUE	1	0.868048670042823	2		608	670	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247195	153247195	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	AA	novel	NA	P-0032392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	153	297	0	ENST00000281708.4:c.1607delinsTT	p.Thr536IlefsTer7	p.T536Ifs*7	ENST00000281708	NM_033632.3	536	aCg/aTTg	10/12	1	2	FACETS	0.886	0.82	0.953	0.886	0.82	0.953	CLONAL	1	TRUE	1	0.868048670042823	2		297	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0032393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	164	620	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.432867547811184	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.432867547811184	1		621	550	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0032393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	20	614	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.432867547811184	1	FACETS	0.111	0.084	0.143	0.111	0.084	0.143	SUBCLONAL	1	TRUE	0	0.432867547811184	1		616	652	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578476	7578476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767328513	NA	P-0032393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	30	873	1	ENST00000269305.4:c.454C>T	p.Pro152Ser	p.P152S	ENST00000269305	NM_001126112.2	152	Ccg/Tcg	5/11	0.432867547811184	1	FACETS	0.149	0.119	0.183	0.149	0.119	0.183	SUBCLONAL	1	TRUE	0	0.432867547811184	1		874	730	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	200	652	0	ENST00000267101.3:c.850G>C	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Cga	7/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.432867547811184	2		652	800	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196849	106196849	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	48	378	0	ENST00000380013.4:c.5182G>T	p.Glu1728Ter	p.E1728*	ENST00000380013	NM_001127208.2	1728	Gag/Tag	11/11	NA	2	FACETS	0.528	0.447	0.617			1	INDETERMINATE	1	TRUE	NA	0.432867547811184	2		378	420	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	80	325	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.937	0.826	1	0.937	0.826	1	CLONAL	1	TRUE	1	0.274884282999724	2		325	621	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0032394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	73	382	1	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.274884282999724	2		383	522	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0032394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	310	577	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	0.274884282999724	3	FACETS	0.892	0.843	0.942	0.892	0.843	0.942	CLONAL	3	TRUE	0	0.274884282999724	3		577	959	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853886	59853886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759142191	NA	P-0032394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	59	371	0	ENST00000259008.2:c.1973G>A	p.Arg658Gln	p.R658Q	ENST00000259008	NM_032043.2	658	cGg/cAg	14/20	1	2	FACETS	0.848	0.731	0.976	0.848	0.731	0.976	CLONAL	1	TRUE	1	0.274884282999724	2		371	506	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692830	89692830	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	77	160	1	ENST00000371953.3:c.314G>T	p.Cys105Phe	p.C105F	ENST00000371953	NM_000314.4	105	tGt/tTt	5/9	0.274884282999724	3	FACETS	0.904	0.806	1	0.904	0.806	1	CLONAL	3	TRUE	0	0.274884282999724	3		161	235	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692919	89692919	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782360	NA	P-0032394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	255	551	0	ENST00000371953.3:c.403A>G	p.Ile135Val	p.I135V	ENST00000371953	NM_000314.4	135	Ata/Gta	5/9	0.274884282999724	3	FACETS	0.981	0.923	1	0.981	0.923	1	CLONAL	3	TRUE	0	0.274884282999724	3		551	717	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508721	106508721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754275924	NA	P-0032394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	113	498	0	ENST00000359195.3:c.715G>A	p.Asp239Asn	p.D239N	ENST00000359195	NM_002649.2	239	Gac/Aac	2/11	0.260191610567477	3	FACETS	1	0.972	1	0.613	0.551	0.678	CLONAL	1	TRUE	1	0.274884282999724	3		498	763	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630605	187630605	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	239	762	0	ENST00000441802.2:c.377del	p.Asn126IlefsTer20	p.N126Ifs*20	ENST00000441802	NM_005245.3	126	aAt/at	2/27	0.274884282999724	3	FACETS	0.902	0.842	0.965	0.902	0.842	0.965	CLONAL	2	TRUE	1	0.274884282999724	3		762	1096	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589593	67589598	+	inframe_deletion	In_Frame_Del	DEL	TAACAC	TAACAC	-	novel	NA	P-0032394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	29	214	0	ENST00000274335.5:c.1357_1362del	p.Asn453_Thr454del	p.N453_T454del	ENST00000274335		452	taTAACACt/tat	10/15	1	2	FACETS	1	0.827	1	1	0.827	1	CLONAL	1	TRUE	1	0.274884282999724	2		214	206	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424178	49424178	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs886040960	NA	P-0032394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	92	466	0	ENST00000301067.7:c.13884del	p.Thr4629ProfsTer11	p.T4629Pfs*11	ENST00000301067	NM_003482.3	4628	ccC/cc	42/54	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.274884282999724	2		466	589	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101068	27101068	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	135	699	0	ENST00000324856.7:c.4354del	p.Gln1452ArgfsTer29	p.Q1452Rfs*29	ENST00000324856	NM_006015.4	1450	ggC/gg	18/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.274884282999724	2		699	881	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644874	67644874	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	89	426	0	ENST00000264010.4:c.143del	p.Gly48ValfsTer14	p.G48Vfs*14	ENST00000264010	NM_006565.3	47	Ggg/gg	3/12	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.274884282999724	2		426	567	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647662	2647662	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	111	516	0	ENST00000342085.4:c.1565C>A	p.Thr522Lys	p.T522K	ENST00000342085	NM_002613.4	522	aCg/aAg	14/14	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.274884282999724	2		516	703	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686985	37686985	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774869348	NA	P-0032394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	116	450	1	ENST00000447079.4:c.3889G>A	p.Val1297Met	p.V1297M	ENST00000447079	NM_015083.1	1297	Gtg/Atg	14/14	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.274884282999724	2		451	669	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023810	27023811	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0032394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	96	306	0	ENST00000324856.7:c.920dup	p.Tyr308LeufsTer92	p.Y308Lfs*92	ENST00000324856	NM_006015.4	306	cgg/cGgg	1/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.274884282999724	2		306	489	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267416	7267416	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	107	499	0	ENST00000302850.5:c.592G>A	p.Ala198Thr	p.A198T	ENST00000302850	NM_000208.2	198	Gcc/Acc	2/22	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.274884282999724	2		499	759	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178198	142178198	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778835776	NA	P-0032394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	42	340	0	ENST00000350721.4:c.7220G>A	p.Arg2407His	p.R2407H	ENST00000350721	NM_001184.3	2407	cGc/cAc	43/47	1	2	FACETS	0.802	0.671	0.947	0.802	0.671	0.947	CLONAL	1	TRUE	1	0.274884282999724	2		340	381	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518670	204518670	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	77	336	0	ENST00000367182.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000367182	NM_001278516.1	445	Cga/Tga	11/11	0.274029852121248	4	FACETS	1	0.954	1	0.394	0.346	0.446	CLONAL	1	TRUE	1	0.274884282999724	4		336	604	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659834	88659834	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1443649142	NA	P-0032394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	90	503	0	ENST00000372037.3:c.481G>A	p.Ala161Thr	p.A161T	ENST00000372037	NM_004329.2	161	Gct/Act	7/13	0.274884282999724	3	FACETS	0.965	0.856	1	0.322	0.285	0.361	CLONAL	1	TRUE	0	0.274884282999724	3		503	772	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434982	49434983	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0032394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	54	465	0	ENST00000301067.7:c.6570dup	p.Thr2191HisfsTer11	p.T2191Hfs*11	ENST00000301067	NM_003482.3	2190	-/C	31/54	1	2	FACETS	0.836	0.715	0.968	0.836	0.715	0.968	CLONAL	1	TRUE	1	0.274884282999724	2		465	470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579561	7579567	+	frameshift_variant	Frame_Shift_Del	DEL	ATCATCC	ATCATCC	-	novel	NA	P-0032394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	122	689	1	ENST00000269305.4:c.120_126del	p.Met40IlefsTer2	p.M40Ifs*2	ENST00000269305	NM_001126112.2	40	atGGATGAT/at	4/11	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.274884282999724	2		690	828	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228562	36228562	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	141	728	0	ENST00000222270.7:c.7576T>C	p.Phe2526Leu	p.F2526L	ENST00000222270	NM_014727.1	2526	Ttc/Ctc	34/37	1	2	FACETS	0.992	0.903	1	0.992	0.903	1	CLONAL	1	TRUE	1	0.274884282999724	2		728	1034	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607835	46607835	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs776667520	NA	P-0032394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	107	734	0	ENST00000263734.3:c.2024A>G	p.His675Arg	p.H675R	ENST00000263734	NM_001430.4	675	cAt/cGt	12/16	1	2	FACETS	0.941	0.844	1	0.941	0.844	1	CLONAL	1	TRUE	1	0.274884282999724	2		734	827	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722052	176722053	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	72	465	0	ENST00000439151.2:c.7683_7684insT	p.Gly2562TrpfsTer3	p.G2562Wfs*3	ENST00000439151	NM_022455.4	2561	-/T	23/23	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.274884282999724	2		465	510	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671508	30671508	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1562081241	NA	P-0032394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	139	771	0	ENST00000376406.3:c.5452A>G	p.Met1818Val	p.M1818V	ENST00000376406	NM_014641.2	1818	Atg/Gtg	10/15	1	2	FACETS	0.952	0.865	1	0.952	0.865	1	CLONAL	1	TRUE	1	0.274884282999724	2		771	1062	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6031642	6031642	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs537024768	NA	P-0032394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	89	365	0	ENST00000265849.7:c.950A>G	p.Gln317Arg	p.Q317R	ENST00000265849	NM_000535.5	317	cAg/cGg	9/15	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.274884282999724	2		365	624	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148544325	148544326	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0032394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	97	562	0	ENST00000320356.2:c.65_66del	p.Glu22ValfsTer14	p.E22Vfs*14	ENST00000320356	NM_004456.4	22	gAG/g	2/20	0.260191610567477	3	FACETS	0.767	0.682	0.857	0.383	0.341	0.429	SUBCLONAL	1	TRUE	1	0.274884282999724	3		562	1047	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	142	447	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.983	0.903	1	0.983	0.903	1	CLONAL	1	TRUE	1	0.632115638243876	2		447	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0032395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	323	620	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.632115638243876	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.632115638243876	1		621	634	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0032395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	27	363	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.486263771106498	1	FACETS	0.392	0.316	0.477	0.392	0.316	0.477	SUBCLONAL	1	TRUE	0	0.632115638243876	1		363	149	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0032395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	110	385	1	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	0.486263771106498	1	FACETS	0.788	0.718	0.86	0.788	0.718	0.86	SUBCLONAL	1	TRUE	0	0.632115638243876	1		386	302	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371633	55371633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs931390946	NA	P-0032395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	322	581	1	ENST00000297316.4:c.323C>T	p.Ala108Val	p.A108V	ENST00000297316	NM_022454.3	108	gCg/gTg	2/2	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.632115638243876	2		582	910	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40458460	40458460	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	585	813	0	ENST00000345506.4:c.1675A>G	p.Asn559Asp	p.N559D	ENST00000345506	NM_003152.3	559	Aac/Gac	14/20	0.632115638243876	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.632115638243876	2		813	920	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745096	41745096	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	149	581	0	ENST00000301178.4:c.1162G>T	p.Glu388Ter	p.E388*	ENST00000301178	NM_021913.4	388	Gag/Tag	9/20	0.486263771106498	1	FACETS	0.447	0.409	0.487	0.447	0.409	0.487	SUBCLONAL	1	TRUE	0	0.632115638243876	1		581	721	SUCCESS
APC	324	MSKCC	GRCh37	5	112102954	112102954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	74	346	0	ENST00000257430.4:c.289G>A	p.Gly97Arg	p.G97R	ENST00000257430	NM_000038.5	97	Gga/Aga	4/16	0.486263771106498	1	FACETS	0.356	0.312	0.402	0.356	0.312	0.402	SUBCLONAL	1	TRUE	0	0.632115638243876	1		346	450	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878743	151878743	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	62	352	0	ENST00000262189.6:c.6202T>C	p.Ser2068Pro	p.S2068P	ENST00000262189	NM_170606.2	2068	Tct/Cct	36/59	0.632115638243876	2	FACETS	0.436	0.377	0.499	0.218	0.188	0.25	SUBCLONAL	1	TRUE	0	0.632115638243876	2		352	450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0032403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	158	508	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.36236609868481	1	FACETS	0.953	0.875	1	0.953	0.875	1	CLONAL	1	TRUE	0	0.36236609868481	1		509	749	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0032403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	102	680	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.904	0.81	1	0.904	0.81	1	CLONAL	1	TRUE	1	0.36236609868481	2		680	623	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	125	476	4	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.36236609868481	2		480	685	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916929	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519931	NA	P-0032403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	89	391	0	ENST00000263967.3:c.316G>C	p.Gly106Arg	p.G106R	ENST00000263967	NM_006218.2	106	Ggc/Cgc	2/21	1	2	FACETS	0.887	0.788	0.992	0.887	0.788	0.992	CLONAL	1	TRUE	1	0.36236609868481	2		391	554	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604785	48604785	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	75	297	0	ENST00000342988.3:c.1607T>C	p.Leu536Pro	p.L536P	ENST00000342988	NM_005359.5	536	cTa/cCa	12/12	0.36236609868481	1	FACETS	0.947	0.835	1	0.947	0.835	1	CLONAL	1	TRUE	0	0.36236609868481	1		297	358	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57470682	57470683	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTTT	novel	NA	P-0032403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	86	275	0	ENST00000371085.3:c.156_157insTTTT	p.Lys53PhefsTer2	p.K53Ffs*2	ENST00000371085	NM_000516.4	52	ggt/ggTTTTt	2/13	1	2	FACETS	0.927	0.823	1	0.927	0.823	1	CLONAL	1	TRUE	1	0.36236609868481	2		275	512	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0032405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	235	789	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.661454469939265	2		789	680	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057874	27057874	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	229	663	0	ENST00000324856.7:c.1582C>T	p.Gln528Ter	p.Q528*	ENST00000324856	NM_006015.4	528	Cag/Tag	3/20	0.359803324417232	1	FACETS	0.724	0.679	0.77	0.724	0.679	0.77	INDETERMINATE	1	TRUE	0	0.661454469939265	1		663	640	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057835	27057835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	166	670	0	ENST00000324856.7:c.1543C>T	p.Gln515Ter	p.Q515*	ENST00000324856	NM_006015.4	515	Cag/Tag	3/20	0.359803324417232	1	FACETS	0.446	0.41	0.483	0.446	0.41	0.483	INDETERMINATE	1	TRUE	0	0.661454469939265	1		670	754	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	335	677	0	ENST00000397752.3:c.3028G>A	p.Asp1010Asn	p.D1010N	ENST00000397752	NM_000245.2	1010	Gat/Aat	14/21	0.325914791133789	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.390592584114691	2		677	852	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162807	47162807	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	48	358	0	ENST00000409792.3:c.3319G>T	p.Glu1107Ter	p.E1107*	ENST00000409792	NM_014159.6	1107	Gag/Tag	3/21	0.337744394548709	2	FACETS	0.482	0.407	0.564	0.241	0.203	0.282	SUBCLONAL	1	TRUE	0	0.390592584114691	2		358	510	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748583	40748583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444440253	NA	P-0032406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	31	310	0	ENST00000373198.4:c.2933C>T	p.Ala978Val	p.A978V	ENST00000373198	NM_133170.3	978	gCg/gTg	21/32	0.290393831533228	1	FACETS	0.4	0.324	0.486	0.4	0.324	0.486	SUBCLONAL	1	TRUE	0	0.390592584114691	1		310	319	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527459	29527459	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	45	329	0	ENST00000356175.3:c.908T>C	p.Leu303Pro	p.L303P	ENST00000356175	NM_000267.3	303	cTa/cCa	9/57	0.390592584114691	1	FACETS	0.465	0.391	0.546	0.465	0.391	0.546	SUBCLONAL	1	TRUE	0	0.390592584114691	1		329	399	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189938	66189938	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs757455898	NA	P-0032406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	30	251	0	ENST00000273854.3:c.3009-1G>A		p.X1003_splice	ENST00000273854	NM_004439.5	1003			1	2	FACETS	0.541	0.437	0.658	0.541	0.437	0.658	SUBCLONAL	1	TRUE	1	0.390592584114691	2		251	284	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971163	21971808	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGCAGCAGCAGCTCCGCCACTCGGGCGCTGCCCATCATCATGACCTGCCAGAGAGAACAGAATGGTCAGAGCCAGGGTGGGGGCCGGCATGACGGAAAGGAAGCTTGTGTAGAGCCCCCTCACCGCCAAGCAGACCCCCACACAAGCCCCAGGTGTCTAATTACCCCTACATTTGCTTCCAGTTTCCAATTTCCTTCTTGAGTTCTCTATCCATTCTTCAGTACACAATGAATTCCATTATATCCTCCGAACTTCTGCGGAGCTGTCGTCACAGGCAGAGAGCACTGTGAGGCACGGGCAAAATAGCAAAGGGGCAGGGACAGACTGACTTTTACTCCAGGCTAACTTCCTGTATTTCCCCTGAGATACAACTACTGAAATTTCTTCCTGAAATTATGTTAGGCCTGGAGATTTTTTTTTTTTTTTTTGTTCACTGCTGTATATCCAAGCGCAGAATGTGGTAATTGTTAAAAAGAGAAAACTTGTTTGTTTGTTAAAACAAATTCTCACAAAACTTTTAAGTTACACTTAGCTTCTGGGAATGTTGAACTTCAATTTCTTTTTCATTATATTAGTTTTAAAATTATATATTGGGATAGTACAGTTGTATATATTTATGTGGTACAATATGAAGTTATGATCTTT	GAGCAGCAGCAGCTCCGCCACTCGGGCGCTGCCCATCATCATGACCTGCCAGAGAGAACAGAATGGTCAGAGCCAGGGTGGGGGCCGGCATGACGGAAAGGAAGCTTGTGTAGAGCCCCCTCACCGCCAAGCAGACCCCCACACAAGCCCCAGGTGTCTAATTACCCCTACATTTGCTTCCAGTTTCCAATTTCCTTCTTGAGTTCTCTATCCATTCTTCAGTACACAATGAATTCCATTATATCCTCCGAACTTCTGCGGAGCTGTCGTCACAGGCAGAGAGCACTGTGAGGCACGGGCAAAATAGCAAAGGGGCAGGGACAGACTGACTTTTACTCCAGGCTAACTTCCTGTATTTCCCCTGAGATACAACTACTGAAATTTCTTCCTGAAATTATGTTAGGCCTGGAGATTTTTTTTTTTTTTTTTGTTCACTGCTGTATATCCAAGCGCAGAATGTGGTAATTGTTAAAAAGAGAAAACTTGTTTGTTTGTTAAAACAAATTCTCACAAAACTTTTAAGTTACACTTAGCTTCTGGGAATGTTGAACTTCAATTTCTTTTTCATTATATTAGTTTTAAAATTATATATTGGGATAGTACAGTTGTATATATTTATGTGGTACAATATGAAGTTATGATCTTT	-	novel	NA	P-0032406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	20	283	0	ENST00000304494.5:c.151-601_195del		p.X51_splice	ENST00000304494	NM_000077.4	51		2/3	0.390592584114691	1	FACETS	0.418	0.321	0.531	0.418	0.321	0.531	SUBCLONAL	1	TRUE	0	0.390592584114691	1		283	197	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164505	47164505	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	44	372	0	ENST00000409792.3:c.1621C>T	p.Arg541Ter	p.R541*	ENST00000409792	NM_014159.6	541	Cga/Tga	3/21	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.244697879492951	2		372	342	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0032408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	123	485	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.82	0.744	0.899	0.82	0.744	0.899	CLONAL	1	TRUE	1	0.531185078439342	2		485	565	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248998	55248999	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCCAGCG	rs727504263	NA	P-0032408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	182	394	0	ENST00000275493.2:c.2300_2308dup	p.Ala767_Val769dup	p.A767_V769dup	ENST00000275493	NM_005228.3	767	atg/aTGGCCAGCGtg	20/28	0.513614365766855	3	FACETS	0.812	0.755	0.871	0.812	0.755	0.871	CLONAL	2	TRUE	1	0.531185078439342	3		394	534	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0032408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	119	241	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	0.334718215365995	3	FACETS	1	0.976	1	0.615	0.559	0.674	CLONAL	1	TRUE	1	0.531185078439342	3		241	461	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0032408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	147	228	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.513614365766855	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.531185078439342	3		228	321	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858237	27858238	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs763163035	NA	P-0032408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	141	446	0	ENST00000359303.2:c.333_334del	p.Ala112TyrfsTer11	p.A112Yfs*11	ENST00000359303	NM_003535.2	111	tgTGct/tgct	1/1	1	2	FACETS	0.978	0.895	1	0.978	0.895	1	CLONAL	1	TRUE	1	0.531185078439342	2		446	543	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717715	89717715	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs1057519368	NA	P-0032408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	133	325	0	ENST00000371953.3:c.740T>G	p.Leu247Ter	p.L247*	ENST00000371953	NM_000314.4	247	tTa/tGa	7/9	0.513614365766855	3	FACETS	1	0.966	1	0.559	0.51	0.61	CLONAL	1	TRUE	1	0.531185078439342	3		325	567	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1555525585	NA	P-0032411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	468	473	0	ENST00000269305.4:c.673-2A>G		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.424419769867744	4	FACETS	0.954	0.92	0.988	0.954	0.92	0.988	CLONAL	4	TRUE	0	0.443721318178383	4		473	798	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506257	120506257	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782493871	NA	P-0032411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	153	313	0	ENST00000256646.2:c.1855G>A	p.Asp619Asn	p.D619N	ENST00000256646	NM_024408.3	619	Gat/Aat	11/34	0.347097698935899	4	FACETS	0.98	0.903	1	0.98	0.903	1	CLONAL	2	TRUE	2	0.443721318178383	4		313	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1555525585	NA	P-0032411-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	149	473	0	ENST00000269305.4:c.673-2A>G		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.169501143530172	5	FACETS	1	0.97	1	0.889	0.818	0.962	CLONAL	4	TRUE	0	0.169501143530172	5		473	496	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506257	120506257	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782493871	NA	P-0032411-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	39	313	0	ENST00000256646.2:c.1855G>A	p.Asp619Asn	p.D619N	ENST00000256646	NM_024408.3	619	Gat/Aat	11/34	0.132600752316424	4	FACETS	1	0.925	1	0.612	0.507	0.728	CLONAL	1	TRUE	2	0.169501143530172	4		313	440	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1555525585	NA	P-0032411-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	200	473	0	ENST00000269305.4:c.673-2A>G		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.583213684227326	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.583213684227326	2		473	304	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506257	120506257	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782493871	NA	P-0032411-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	98	313	0	ENST00000256646.2:c.1855G>A	p.Asp619Asn	p.D619N	ENST00000256646	NM_024408.3	619	Gat/Aat	11/34	0.209271883473405	3	FACETS	0.762	0.689	0.836	0.762	0.689	0.836	INDETERMINATE	2	TRUE	1	0.583213684227326	3		313	285	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0032427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	342	391	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.375033228026779	7	FACETS	1	0.99	1	1	0.996	1	CLONAL	7	TRUE	2	0.375033228026779	7		391	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579344	7579351	+	frameshift_variant	Frame_Shift_Del	DEL	GCAAGAAG	GCAAGAAG	-	novel	NA	P-0032427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	312	494	0	ENST00000269305.4:c.336_343del	p.Leu114TrpfsTer32	p.L114Wfs*32	ENST00000269305	NM_001126112.2	112	ggCTTCTTGCat/ggat	4/11	0.375033228026779	2	FACETS	1	0.986	1	1	0.997	1	CLONAL	4	TRUE	0	0.375033228026779	2		494	402	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656789	45656789	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	232	438	0	ENST00000407780.3:c.367C>A	p.Gln123Lys	p.Q123K	ENST00000407780	NM_001283052.1	123	Cag/Aag	3/7	0.227686679260957	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	0	0.375033228026779	3		438	452	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651663	48651803	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCGTGTGCAATGCCTGCGGCCTCTACTACAAGCTACACCAGGTGACGCCCTGCCCCTTGGAGCCACCCCTCTGCTTTCCCTGTCTTCATGCCACACTGCCCCCCACTCTGTTCCTGTTCTACCTCTCTCTTCCCCCACAA	CCCGTGTGCAATGCCTGCGGCCTCTACTACAAGCTACACCAGGTGACGCCCTGCCCCTTGGAGCCACCCCTCTGCTTTCCCTGTCTTCATGCCACACTGCCCCCCACTCTGTTCCTGTTCTACCTCTCTCTTCCCCCACAA	-	novel	NA	P-0032427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	94	502	0	ENST00000376670.3:c.832_870+102del		p.X278_splice	ENST00000376670	NM_002049.3	278		5/6	1	2	FACETS	0.902	0.804	1	0.902	0.804	1	CLONAL	1	TRUE	1	0.375033228026779	2		502	556	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094293	27094294	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0032429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	93	342	0	ENST00000324856.7:c.3002_3003del	p.Ser1001TyrfsTer5	p.S1001Yfs*5	ENST00000324856	NM_006015.4	1001	TCt/t	11/20	1	2	FACETS	0.9	0.802	1	0.9	0.802	1	CLONAL	1	TRUE	1	0.38	2		342	544	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221642	36221642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471498012	NA	P-0032429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	170	676	0	ENST00000222270.7:c.5311C>T	p.Arg1771Trp	p.R1771W	ENST00000222270	NM_014727.1	1771	Cgg/Tgg	26/37	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.38	2		676	801	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983035	201983035	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757948712	NA	P-0032432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	341	736	0	ENST00000359651.3:c.884G>A	p.Trp295Ter	p.W295*	ENST00000359651		295	tGg/tAg	7/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.814229911803614	2		736	767	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651921	36651930	+	frameshift_variant	Frame_Shift_Del	DEL	AGCAAGGCCT	AGCAAGGCCT	GGCAGGCCA	novel	NA	P-0032432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	388	599	1	ENST00000244741.5:c.43_52delinsGGCAGGCCA	p.Ser15GlyfsTer16	p.S15Gfs*16	ENST00000244741	NM_000389.4	15	AGCAAGGCCTgc/GGCAGGCCAgc	2/3	0.814229911803614	2	FACETS	0.951	0.923	0.978	0.951	0.923	0.978	CLONAL	2	TRUE	0	0.814229911803614	2		600	501	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137323776	137323785	+	frameshift_variant	Frame_Shift_Del	DEL	ATGCGGGACA	ATGCGGGACA	-	novel	NA	P-0032432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	79	735	0	ENST00000481739.1:c.1069_1078del	p.Met357CysfsTer33	p.M357Cfs*33	ENST00000481739	NM_002957.4	357	ATGCGGGACAtg/tg	8/10	0.601593134942704	1	FACETS	0.21	0.185	0.237	0.21	0.185	0.237	SUBCLONAL	1	TRUE	0	0.814229911803614	1		735	548	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	91	258	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.903	1	1	0.99	1	CLONAL	3	FALSE	1	0.241431411397002	2		258	251	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0032435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	231	583	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	3	FALSE	1	0.241431411397002	2		583	550	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410700	32410700	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	141	431	3	ENST00000332351.3:c.1458G>A	p.Trp486Ter	p.W486*	ENST00000332351	NM_024426.4	486	tgG/tgA	10/10	1	2	FACETS	1	0.971	1	1	0.993	1	CLONAL	3	FALSE	1	0.241431411397002	2		434	351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0032438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	175	574	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.256754157981778	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.260797330368016	2		574	591	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589168	67589168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	65	305	0	ENST00000274335.5:c.1156C>T	p.Arg386Ter	p.R386*	ENST00000274335		386	Cga/Tga	9/15	0.260797330368016	3	FACETS	1	0.968	1	0.468	0.408	0.534	CLONAL	1	TRUE	0	0.260797330368016	3		305	401	SUCCESS
APC	324	MSKCC	GRCh37	5	112173299	112173299	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0032438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	96	222	0	ENST00000257430.4:c.2008A>T	p.Lys670Ter	p.K670*	ENST00000257430	NM_000038.5	670	Aaa/Taa	16/16	0.260797330368016	3	FACETS	0.904	0.815	0.996	0.904	0.815	0.996	CLONAL	3	TRUE	0	0.260797330368016	3		222	307	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015350	176015350	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	45	377	0	ENST00000367669.3:c.1388C>T	p.Pro463Leu	p.P463L	ENST00000367669	NM_022457.5	463	cCt/cTt	12/20	0.237016175068841	3	FACETS	0.887	0.746	1	0.443	0.373	0.521	CLONAL	1	TRUE	1	0.260797330368016	3		377	440	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226567	1226567	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	155	506	0	ENST00000326873.7:c.1223G>A	p.Gly408Asp	p.G408D	ENST00000326873	NM_000455.4	408	gGc/gAc	9/10	0.032783951954261	3	FACETS	1	0.974	1	1	0.974	1	INDETERMINATE	2	TRUE	1	0.260797330368016	3		506	588	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0032439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	38	369	1	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.667	0.556	0.789	0.667	0.556	0.789	SUBCLONAL	1	FALSE	1	0.50882905471218	2		370	224	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	170	591	0	ENST00000269305.4:c.613dup	p.Tyr205LeufsTer4	p.Y205Lfs*4	ENST00000269305	NM_001126112.2	205	tat/tTat	6/11	0.456398914711244	1	FACETS	0.79	0.729	0.852	0.79	0.729	0.852	SUBCLONAL	1	FALSE	0	0.50882905471218	1		591	631	SUCCESS
APC	324	MSKCC	GRCh37	5	112175735	112175751	+	frameshift_variant	Frame_Shift_Del	DEL	CTTCCAGATGCTGATAC	CTTCCAGATGCTGATAC	-	novel	NA	P-0032439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	45	339	0	ENST00000257430.4:c.4444_4460del	p.Leu1482PhefsTer26	p.L1482Ffs*26	ENST00000257430	NM_000038.5	1482	CTTCCAGATGCTGATACt/t	16/16	1	2	FACETS	0.551	0.465	0.645	0.551	0.465	0.645	SUBCLONAL	1	FALSE	1	0.50882905471218	2		339	321	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90971001	90971001	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	117	433	1	ENST00000265433.3:c.1076A>T	p.Asn359Ile	p.N359I	ENST00000265433	NM_002485.4	359	aAc/aTc	9/16	1	2	FACETS	0.619	0.558	0.683	0.619	0.558	0.683	SUBCLONAL	1	FALSE	1	0.50882905471218	2		434	743	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0032439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	97	369	1	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.825	0.741	0.912	0.825	0.741	0.912	CLONAL	1	TRUE	1	0.627264058979086	2		370	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	271	591	0	ENST00000269305.4:c.613dup	p.Tyr205LeufsTer4	p.Y205Lfs*4	ENST00000269305	NM_001126112.2	205	tat/tTat	6/11	0.627264058979086	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.627264058979086	1		591	550	SUCCESS
APC	324	MSKCC	GRCh37	5	112175735	112175751	+	frameshift_variant	Frame_Shift_Del	DEL	CTTCCAGATGCTGATAC	CTTCCAGATGCTGATAC	-	novel	NA	P-0032439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	85	339	0	ENST00000257430.4:c.4444_4460del	p.Leu1482PhefsTer26	p.L1482Ffs*26	ENST00000257430	NM_000038.5	1482	CTTCCAGATGCTGATACt/t	16/16	1	2	FACETS	0.759	0.676	0.846	0.759	0.676	0.846	SUBCLONAL	1	TRUE	1	0.627264058979086	2		339	357	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90971001	90971001	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	112	433	1	ENST00000265433.3:c.1076A>T	p.Asn359Ile	p.N359I	ENST00000265433	NM_002485.4	359	aAc/aTc	9/16	0.627264058979086	3	FACETS	0.484	0.434	0.536	0.242	0.217	0.268	SUBCLONAL	1	TRUE	1	0.627264058979086	3		434	970	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420081	49420081	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs779303083	NA	P-0032439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	78	499	0	ENST00000301067.7:c.15668A>G	p.Asn5223Ser	p.N5223S	ENST00000301067	NM_003482.3	5223	aAt/aGt	48/54	1	2	FACETS	0.415	0.365	0.469	0.415	0.365	0.469	SUBCLONAL	1	TRUE	1	0.627264058979086	2		499	599	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866356	37866356	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	68	550	0	ENST00000269571.5:c.661G>T	p.Ala221Ser	p.A221S	ENST00000269571		221	Gcc/Tcc	6/27	1	2	FACETS	0.33	0.286	0.376	0.33	0.286	0.376	SUBCLONAL	1	TRUE	1	0.627264058979086	2		550	658	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	131	447	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.819	0.746	0.895	0.819	0.746	0.895	CLONAL	1	TRUE	1	0.556139675032983	2		447	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0032440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	440	650	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.556139675032983	2		650	745	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	114	229	0	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	0.556139675032983	2	FACETS	0.82	0.753	0.887	0.82	0.753	0.887	CLONAL	2	TRUE	0	0.556139675032983	2		229	250	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591931	48591931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	141	500	0	ENST00000342988.3:c.1094G>A	p.Gly365Asp	p.G365D	ENST00000342988	NM_005359.5	365	gGt/gAt	9/12	0.556139675032983	1	FACETS	0.92	0.847	0.994	0.92	0.847	0.994	CLONAL	1	TRUE	0	0.556139675032983	1		500	398	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134823	41134823	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	525	475	0	ENST00000379561.5:c.805C>T	p.Arg269Ter	p.R269*	ENST00000379561	NM_002015.3	269	Cga/Tga	2/3	0.540373583543828	5	FACETS	0.947	0.915	0.979	0.947	0.915	0.979	CLONAL	4	TRUE	1	0.556139675032983	5		475	914	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182213	99182213	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs984538193	NA	P-0032440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	196	571	0	ENST00000074304.5:c.2278G>A	p.Val760Ile	p.V760I	ENST00000074304	NM_001134224.1	760	Gtc/Atc	21/26	1	2	FACETS	0.997	0.926	1	0.997	0.926	1	CLONAL	1	TRUE	1	0.556139675032983	2		571	707	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391103	89391103	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	167	621	3	ENST00000336596.2:c.1169C>A	p.Thr390Asn	p.T390N	ENST00000336596	NM_005233.5	390	aCc/aAc	5/17	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.556139675032983	2		624	559	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859707	57859707	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	95	321	0	ENST00000228682.2:c.761A>G	p.His254Arg	p.H254R	ENST00000228682	NM_005269.2	254	cAc/cGc	7/12	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.556139675032983	2		321	318	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325332	1325332	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	149	445	0	ENST00000400841.2:c.343T>G	p.Tyr115Asp	p.Y115D	ENST00000400841		115	Tat/Gat	3/6	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.556139675032983	2		445	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0032442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	124	703	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	0.191221839517829	2	FACETS	0.77	0.698	0.845	0.77	0.698	0.845	SUBCLONAL	2	TRUE	0	0.264041583869571	2		703	610	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211517	46211545	+	frameshift_variant	Frame_Shift_Del	DEL	GGTGCTTTCACTGTTATCTGGACTCCCAA	GGTGCTTTCACTGTTATCTGGACTCCCAA	-	novel	NA	P-0032442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	87	351	1	ENST00000334344.6:c.483_511del	p.Val162Ter	p.V162*	ENST00000334344	NM_152641.2	161	ttGGTGCTTTCACTGTTATCTGGACTCCCAAat/ttat	5/21	0.191221839517829	2	FACETS	1	0.977	1	0.704	0.626	0.787	CLONAL	1	TRUE	0	0.264041583869571	2		352	468	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440732	56440734	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0032442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	112	563	0	ENST00000407977.2:c.484_486del	p.Val162del	p.V162del	ENST00000407977		162	GTG/-	5/10	0.264041583869571	2	FACETS	0.859	0.776	0.945	0.859	0.776	0.945	CLONAL	2	TRUE	0	0.264041583869571	2		563	494	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440741	56440741	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	113	545	0	ENST00000407977.2:c.477G>C	p.Trp159Cys	p.W159C	ENST00000407977		159	tgG/tgC	5/10	0.264041583869571	2	FACETS	0.947	0.857	1	0.947	0.857	1	CLONAL	2	TRUE	0	0.264041583869571	2		545	452	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129361	152129361	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs975546721	NA	P-0032442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	42	422	0	ENST00000206249.3:c.314C>T	p.Pro105Leu	p.P105L	ENST00000206249	NM_000125.3	105	cCg/cTg	1/8	0.191221839517829	2	FACETS	0.961	0.805	1	0.481	0.402	0.567	CLONAL	1	TRUE	0	0.264041583869571	2		422	331	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0032444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	52	594	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		594	513	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94163078	94163078	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	37	390	2	ENST00000323929.3:c.2069A>G	p.Glu690Gly	p.E690G	ENST00000323929	NM_005591.3	690	gAg/gGg	19/20	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		392	542	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0032445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	142	778	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.213405436796617	3	FACETS	0.994	0.907	1	0.994	0.907	1	CLONAL	2	TRUE	1	0.213405436796617	3		779	741	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431665	431665	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs754467075	NA	P-0032445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	44	485	0	ENST00000399788.2:c.2344C>T	p.Arg782Ter	p.R782*	ENST00000399788	NM_001042603.1	782	Cga/Tga	17/28	NA	2	FACETS	0.522	0.436	0.617			1	INDETERMINATE	1	TRUE	NA	0.213405436796617	2		485	790	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932064	36932064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371426547	NA	P-0032445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	27	435	0	ENST00000361632.4:c.2405C>T	p.Thr802Ile	p.T802I	ENST00000361632		802	aCc/aTc	16/16	1	2	FACETS	0.538	0.428	0.666	0.538	0.428	0.666	SUBCLONAL	1	TRUE	1	0.213405436796617	2		435	470	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938263	36938263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138558210	NA	P-0032445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	50	580	0	ENST00000361632.4:c.698G>A	p.Arg233Gln	p.R233Q	ENST00000361632		233	cGg/cAg	6/16	1	2	FACETS	0.7	0.593	0.819	0.7	0.593	0.819	SUBCLONAL	1	TRUE	1	0.213405436796617	2		580	669	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612656	228612656	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	48	556	0	ENST00000366696.1:c.371A>G	p.Asp124Gly	p.D124G	ENST00000366696	NM_003493.2	124	gAc/gGc	1/1	1	2	FACETS	0.648	0.547	0.76	0.648	0.547	0.76	SUBCLONAL	1	TRUE	1	0.213405436796617	2		556	694	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096108	178096108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	31	443	0	ENST00000397062.3:c.1223C>T	p.Ser408Leu	p.S408L	ENST00000397062	NM_006164.4	408	tCa/tTa	5/5	0.0348881257930409	3	FACETS	0.616	0.497	0.751	0.308	0.248	0.376	INDETERMINATE	1	TRUE	1	0.213405436796617	3		443	522	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	384	354	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.652544620973489	4	FACETS	1	0.994	1	0.854	0.826	0.88	CLONAL	3	TRUE	0	0.747080334453381	4		354	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934573	NA	P-0032446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	629	577	0	ENST00000269305.4:c.722C>A	p.Ser241Tyr	p.S241Y	ENST00000269305	NM_001126112.2	241	tCc/tAc	7/11	0.652544620973489	4	FACETS	0.907	0.886	0.927	0.907	0.886	0.927	CLONAL	4	TRUE	0	0.747080334453381	4		577	811	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201815	66201815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764665078	NA	P-0032446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	315	413	1	ENST00000273854.3:c.2687G>A	p.Arg896His	p.R896H	ENST00000273854	NM_004439.5	896	cGt/cAt	16/18	0.634460063648322	3	FACETS	0.854	0.822	0.885	0.854	0.822	0.885	CLONAL	3	TRUE	0	0.747080334453381	3		414	452	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29686011	29686011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1170836879	NA	P-0032446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	204	389	0	ENST00000356175.3:c.8075G>A	p.Arg2692Gln	p.R2692Q	ENST00000356175	NM_000267.3	2692	cGg/cAg	55/57	0.641615875796821	4	FACETS	0.811	0.757	0.866	0.406	0.378	0.433	CLONAL	2	TRUE	0	0.747080334453381	4		389	588	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339328	70339328	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0032446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	280	395	0	ENST00000374080.3:c.204+1G>A		p.X68_splice	ENST00000374080		68			0.67890724985917	4	FACETS	0.947	0.904	0.989	0.947	0.904	0.989	CLONAL	3	TRUE	1	0.747080334453381	4		395	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0032449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	426	712	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.827300090906216	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	4	TRUE	0	0.827300090906216	4		712	465	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030410	49030410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	222	416	0	ENST00000267163.4:c.1885G>A	p.Glu629Lys	p.E629K	ENST00000267163	NM_000321.2	629	Gag/Aag	19/27	0.827300090906216	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.827300090906216	2		416	253	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609582	81609582	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	100	498	0	ENST00000298171.2:c.1180G>A	p.Glu394Lys	p.E394K	ENST00000298171	NM_000369.2	394	Gaa/Aaa	10/10	0.288028651631217	3	FACETS	1	0.984	1	0.727	0.662	0.793	INDETERMINATE	1	TRUE	1	0.827300090906216	3		498	235	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609386	81609386	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1231925448	NA	P-0032449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	103	417	0	ENST00000298171.2:c.984G>C	p.Glu328Asp	p.E328D	ENST00000298171	NM_000369.2	328	gaG/gaC	10/10	0.288028651631217	3	FACETS	1	0.985	1	0.727	0.663	0.792	INDETERMINATE	1	TRUE	1	0.827300090906216	3		417	242	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969438	44969438	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	195	485	0	ENST00000377967.4:c.4120G>T	p.Val1374Leu	p.V1374L	ENST00000377967	NM_021140.2	1374	Gtg/Ttg	28/29	0.827300090906216	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.827300090906216	1		485	219	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577587	7577587	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	382	539	0	ENST00000269305.4:c.694A>T	p.Ile232Phe	p.I232F	ENST00000269305	NM_001126112.2	232	Atc/Ttc	7/11	0.598029739532915	2	FACETS	0.947	0.91	0.984	0.947	0.91	0.984	CLONAL	2	TRUE	0	0.632175713727003	2		539	638	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439769	220439769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111982983	NA	P-0032455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	114	640	0	ENST00000243786.2:c.622C>T	p.Arg208Trp	p.R208W	ENST00000243786	NM_002191.3	208	Cgg/Tgg	2/2	NA	2	FACETS	0.495	0.446	0.547			1	INDETERMINATE	1	TRUE	NA	0.632175713727003	2		640	728	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746055	162746056	+	missense_variant	Missense_Mutation	DNP	AG	AG	TT	novel	NA	P-0032455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	113	374	0	ENST00000367921.3:c.2178_2179delinsTT	p.Ala727Ser	p.A727S	ENST00000367921	NM_006182.2	726	atAGct/atTTct	16/18	1	2	FACETS	0.876	0.795	0.961	0.876	0.795	0.961	CLONAL	1	TRUE	1	0.632175713727003	2		374	408	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012328	176012328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	149	383	0	ENST00000367669.3:c.1606G>A	p.Ala536Thr	p.A536T	ENST00000367669	NM_022457.5	536	Gca/Aca	14/20	1	2	FACETS	0.803	0.737	0.872	0.803	0.737	0.872	CLONAL	1	TRUE	1	0.632175713727003	2		383	587	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005335	29005335	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	96	651	0	ENST00000282397.4:c.926A>G	p.Tyr309Cys	p.Y309C	ENST00000282397	NM_002019.4	309	tAt/tGt	7/30	0.326098264656719	1	FACETS	0.337	0.3	0.375	0.337	0.3	0.375	INDETERMINATE	1	TRUE	0	0.632175713727003	1		651	617	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602263	10602276	+	frameshift_variant	Frame_Shift_Del	DEL	TGTTGTGGTGGATG	TGTTGTGGTGGATG	-	novel	NA	P-0032455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	302	542	0	ENST00000171111.5:c.1302_1315del	p.Cys434TrpfsTer6	p.C434Wfs*6	ENST00000171111	NM_203500.1	434	tgCATCCACCACAACAgt/tggt	3/6	0.594816936283099	2	FACETS	0.853	0.813	0.893	0.853	0.813	0.893	CLONAL	2	TRUE	0	0.632175713727003	2		542	560	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198264976	198264976	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	67	343	0	ENST00000335508.6:c.2901G>T	p.Glu967Asp	p.E967D	ENST00000335508	NM_012433.2	967	gaG/gaT	19/25	0.24717828490798	3	FACETS	0.64	0.558	0.728	0.213	0.186	0.243	INDETERMINATE	1	TRUE	0	0.632175713727003	3		343	436	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116272	209116272	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	58	260	0	ENST00000345146.2:c.4T>G	p.Ser2Ala	p.S2A	ENST00000345146	NM_005896.2	2	Tcc/Gcc	3/10	0.24717828490798	3	FACETS	0.651	0.562	0.747	0.217	0.187	0.249	INDETERMINATE	1	TRUE	0	0.632175713727003	3		260	371	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022479	31022479	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	43	227	0	ENST00000375687.4:c.1964C>A	p.Thr655Asn	p.T655N	ENST00000375687	NM_015338.5	655	aCc/aAc	13/13	0.632175713727003	3	FACETS	0.487	0.408	0.573	0.243	0.204	0.287	SUBCLONAL	1	TRUE	1	0.632175713727003	3		227	368	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656908	45656908	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	86	581	0	ENST00000407780.3:c.248G>A	p.Arg83Gln	p.R83Q	ENST00000407780	NM_001283052.1	83	cGa/cAa	3/7	0.56959428602304	3	FACETS	0.369	0.326	0.416	0.123	0.108	0.139	SUBCLONAL	1	TRUE	0	0.632175713727003	3		581	970	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147546	47147546	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0032455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	138	422	0	ENST00000409792.3:c.4780A>T	p.Lys1594Ter	p.K1594*	ENST00000409792	NM_014159.6	1594	Aag/Tag	6/21	0.159953165643082	2	FACETS	0.723	0.66	0.788	0.361	0.33	0.394	INDETERMINATE	1	TRUE	0	0.632175713727003	2		422	604	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156968	89156968	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	91	443	0	ENST00000336596.2:c.71del	p.Pro24ArgfsTer59	p.P24Rfs*59	ENST00000336596	NM_005233.5	24	Ccg/cg	1/17	0.159953165643082	2	FACETS	0.623	0.556	0.694	0.312	0.278	0.347	INDETERMINATE	1	TRUE	0	0.632175713727003	2		443	462	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664690	138664690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1382669559	NA	P-0032455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	179	79	0	ENST00000330315.3:c.875C>T	p.Pro292Leu	p.P292L	ENST00000330315	NM_023067.3	292	cCg/cTg	1/1	0.278950524936082	4	FACETS	0.917	0.872	0.96	0.917	0.872	0.96	INDETERMINATE	4	TRUE	0	0.632175713727003	4		79	252	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955575	55955575	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	225	550	0	ENST00000263923.4:c.3370A>G	p.Arg1124Gly	p.R1124G	ENST00000263923	NM_002253.2	1124	Aga/Gga	25/30	0.386349984576018	3	FACETS	1	0.979	1	0.558	0.52	0.596	CLONAL	1	TRUE	1	0.632175713727003	3		550	840	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564675	86564675	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs769463654	NA	P-0032455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	108	655	0	ENST00000274376.6:c.407C>G	p.Pro136Arg	p.P136R	ENST00000274376	NM_002890.2	136	cCt/cGt	1/25	0.248187437556829	3	FACETS	0.593	0.532	0.658	0.198	0.177	0.22	INDETERMINATE	1	TRUE	0	0.632175713727003	3		655	758	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	122	325	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.909	0.829	0.992	1	0.992	1	CLONAL	3	TRUE	1	0.215080555549071	2		325	416	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0032456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	114	632	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.99	0.901	1	1	0.991	1	CLONAL	3	TRUE	1	0.215080555549071	2		636	357	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366939	15366939	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	193	810	3	ENST00000263377.2:c.1687del	p.Ser563AlafsTer21	p.S563Afs*21	ENST00000263377	NM_058243.2	563	Agc/gc	9/20	1	2	FACETS	1	0.941	1	1	0.995	1	CLONAL	3	TRUE	1	0.215080555549071	2		813	591	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913476	NA	P-0032456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	187	711	0	ENST00000358487.5:c.1647T>G	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaG	12/18	1	2	FACETS	0.894	0.834	0.956	1	0.995	1	CLONAL	4	TRUE	1	0.215080555549071	2		711	486	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0032456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	147	571	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.871	0.8	0.945	1	0.993	1	CLONAL	3	TRUE	1	0.215080555549071	2		571	523	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692911	89692911	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121909241	NA	P-0032456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	115	609	0	ENST00000371953.3:c.395G>T	p.Gly132Val	p.G132V	ENST00000371953	NM_000314.4	132	gGt/gTt	5/9	1	2	FACETS	1	0.947	1	1	0.992	1	CLONAL	3	TRUE	1	0.215080555549071	2		609	338	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0032456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	72	723	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	1	0.94	1	1	0.987	1	CLONAL	3	TRUE	1	0.215080555549071	2		723	205	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188164	11188164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777893	NA	P-0032456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	172	511	0	ENST00000361445.4:c.5930C>T	p.Thr1977Ile	p.T1977I	ENST00000361445	NM_004958.3	1977	aCa/aTa	43/58	1	2	FACETS	0.962	0.891	1	1	0.994	1	CLONAL	3	TRUE	1	0.215080555549071	2		511	554	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123246935	123246935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113014479	NA	P-0032456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	116	391	2	ENST00000358487.5:c.1990C>T	p.Arg664Trp	p.R664W	ENST00000358487	NM_000141.4	664	Cgg/Tgg	15/18	1	2	FACETS	1	0.97	1	1	0.992	1	CLONAL	3	TRUE	1	0.215080555549071	2		393	315	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612911	228612911	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	139	542	1	ENST00000366696.1:c.116C>T	p.Pro39Leu	p.P39L	ENST00000366696	NM_003493.2	39	cCg/cTg	1/1	1	2	FACETS	0.997	0.916	1	1	0.993	1	CLONAL	3	TRUE	1	0.215080555549071	2		543	432	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307280	65307283	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0032456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	128	374	0	ENST00000342505.4:c.2405_2408del	p.Lys802ArgfsTer11	p.K802Rfs*11	ENST00000342505	NM_002227.2	802	aAAGAg/ag	18/25	1	2	FACETS	1	0.946	1	1	0.992	1	CLONAL	3	TRUE	1	0.215080555549071	2		374	380	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057666	27057666	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	201	703	0	ENST00000324856.7:c.1377del	p.Ser460AlafsTer159	p.S460Afs*159	ENST00000324856	NM_006015.4	458	ggC/gg	3/20	1	2	FACETS	0.903	0.84	0.967	1	0.995	1	CLONAL	3	TRUE	1	0.215080555549071	2		703	690	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200107	138200107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746331032	NA	P-0032456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	128	460	1	ENST00000237289.4:c.1525G>A	p.Ala509Thr	p.A509T	ENST00000237289	NM_001270507.1	509	Gcc/Acc	7/9	NA	3	FACETS	1	0.964	1	1	0.989	1	INDETERMINATE	3	TRUE	1	0.215080555549071	3		461	399	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136097	11136097	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0032456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	188	574	0	ENST00000358026.2:c.3082-1G>A		p.X1028_splice	ENST00000358026	NM_001128849.1	1028			1	2	FACETS	1	0.969	1	1	0.995	1	CLONAL	3	TRUE	1	0.215080555549071	2		574	543	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	221	892	3	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	0.995	1	CLONAL	3	TRUE	1	0.215080555549071	2		895	648	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645382	215645382	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs377153250	NA	P-0032456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	146	728	0	ENST00000260947.4:c.1216C>T	p.Arg406Ter	p.R406*	ENST00000260947	NM_000465.2	406	Cga/Tga	4/11	1	2	FACETS	0.988	0.909	1	1	0.993	1	CLONAL	3	TRUE	1	0.215080555549071	2		728	458	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825518	50825519	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1219062549	NA	P-0032456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	51	525	2	ENST00000398568.2:c.2156dup	p.Asn719LysfsTer2	p.N719Kfs*2	ENST00000398568	NM_001042412.1	717	gaa/gAaa	14/18	1	2	FACETS	0.994	0.862	1	1	0.981	1	CLONAL	3	TRUE	1	0.215080555549071	2		527	159	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490839	56490839	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	188	509	0	ENST00000267101.3:c.2285C>T	p.Ala762Val	p.A762V	ENST00000267101	NM_001982.3	762	gCc/gTc	20/28	0.0582497814597505	4	FACETS	1	0.958	1	1	0.994	1	INDETERMINATE	4	TRUE	2	0.215080555549071	4		509	512	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690848	89690848	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0032456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	54	382	0	ENST00000371953.3:c.253+2T>G		p.X85_splice	ENST00000371953	NM_000314.4	85			1	2	FACETS	0.951	0.827	1	1	0.982	1	CLONAL	3	TRUE	1	0.215080555549071	2		382	176	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998799	100998799	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	154	647	0	ENST00000325455.5:c.1003del	p.Ala335LeufsTer21	p.A335Lfs*21	ENST00000325455	NM_001202474.3	335	Gct/ct	1/8	1	2	FACETS	0.974	0.898	1	1	0.993	1	CLONAL	3	TRUE	1	0.215080555549071	2		647	490	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218333	133218333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373272795	NA	P-0032456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	221	760	0	ENST00000320574.5:c.5278G>A	p.Val1760Met	p.V1760M	ENST00000320574	NM_006231.2	1760	Gtg/Atg	39/49	1	2	FACETS	1	0.984	1	1	0.996	1	CLONAL	3	TRUE	1	0.215080555549071	2		760	597	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135255	2135255	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886041919	NA	P-0032456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	260	876	1	ENST00000219476.3:c.4594C>T	p.Gln1532Ter	p.Q1532*	ENST00000219476	NM_000548.3	1532	Cag/Tag	36/42	0.215080555549071	2	FACETS	1	0.973	1	1	0.994	1	CLONAL	3	TRUE	0	0.215080555549071	2		877	761	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655389	67655390	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	141	655	0	ENST00000264010.4:c.1255dup	p.Ser419LysfsTer25	p.S419Kfs*25	ENST00000264010	NM_006565.3	418	caa/cAaa	7/12	1	2	FACETS	1	0.936	1	1	0.993	1	CLONAL	3	TRUE	1	0.215080555549071	2		655	428	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744434	41744434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	190	779	0	ENST00000301178.4:c.1054C>T	p.His352Tyr	p.H352Y	ENST00000301178	NM_021913.4	352	Cat/Tat	8/20	1	2	FACETS	0.914	0.849	0.981	1	0.994	1	CLONAL	3	TRUE	1	0.215080555549071	2		779	644	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286160	66286160	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	46	386	0	ENST00000273854.3:c.1526A>T	p.Lys509Met	p.K509M	ENST00000273854	NM_004439.5	509	aAg/aTg	6/18	1	2	FACETS	0.914	0.792	1	1	0.981	1	CLONAL	4	TRUE	1	0.215080555549071	2		386	117	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100044	157100049	+	inframe_deletion	In_Frame_Del	DEL	AGGAGC	AGGAGC	-	rs747438636	NA	P-0032456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	12	100	0	ENST00000346085.5:c.992_997del	p.Ala331_Gly332del	p.A331_G332del	ENST00000346085	NM_020732.3	327	ggAGGAGCa/gga	1/20	NA	3	FACETS	1	0.812	1	0.606	0.43	0.817	INDETERMINATE	1	TRUE	1	0.215080555549071	3		100	102	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457088	5457088	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	32	301	0	ENST00000381577.3:c.62T>C	p.Val21Ala	p.V21A	ENST00000381577	NM_014143.3	21	gTc/gCc	3/7	1	2	FACETS	0.918	0.755	1	1	0.959	1	CLONAL	2	TRUE	1	0.215080555549071	2		301	162	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128420079	128420079	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0032456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	114	639	0	ENST00000265960.3:c.350-1G>A		p.X117_splice	ENST00000265960	NM_001006617.1	117			1	2	FACETS	0.886	0.804	0.97	1	0.991	1	CLONAL	3	TRUE	1	0.215080555549071	2		639	399	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0032457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	65	410	0				ENST00000310581	NM_198253.2	-/1132			0.116150878881228	3	FACETS	1	0.968	1	0.701	0.611	0.799	INDETERMINATE	1	TRUE	1	0.263573320583045	3		410	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577518	7577518	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519995	NA	P-0032457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	117	644	0	ENST00000269305.4:c.763A>T	p.Ile255Phe	p.I255F	ENST00000269305	NM_001126112.2	255	Atc/Ttc	7/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.263573320583045	2		644	759	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43749791	43749791	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866329410	NA	P-0032457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	58	409	0	ENST00000523873.1:c.644C>T	p.Ala215Val	p.A215V	ENST00000523873		215	gCg/gTg	7/8	1	2	FACETS	0.746	0.641	0.861	0.746	0.641	0.861	SUBCLONAL	1	TRUE	1	0.263573320583045	2		409	590	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	42	258	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.464	0.388	0.547	0.464	0.388	0.547	SUBCLONAL	1	TRUE	1	0.534347659573867	2		258	339	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11554273	NA	P-0032460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	50	547	0	ENST00000371085.3:c.601C>A	p.Arg201Ser	p.R201S	ENST00000371085	NM_000516.4	201	Cgt/Agt	8/13	1	2	FACETS	0.309	0.262	0.362	0.309	0.262	0.362	SUBCLONAL	1	TRUE	1	0.534347659573867	2		547	605	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416941	416941	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	65	412	0	ENST00000399788.2:c.3609G>A	p.Trp1203Ter	p.W1203*	ENST00000399788	NM_001042603.1	1203	tgG/tgA	23/28	1	2	FACETS	0.451	0.391	0.515	0.451	0.391	0.515	SUBCLONAL	1	TRUE	1	0.534347659573867	2		412	540	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212402	5212402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769362751	NA	P-0032460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	111	668	0	ENST00000357368.4:c.4715G>A	p.Arg1572Gln	p.R1572Q	ENST00000357368	NM_002850.3	1572	cGg/cAg	31/38	1	2	FACETS	0.592	0.532	0.655	0.592	0.532	0.655	SUBCLONAL	1	TRUE	1	0.534347659573867	2		668	702	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518529	69518529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	164	468	0	ENST00000294312.3:c.116G>A	p.Gly39Asp	p.G39D	ENST00000294312	NM_005117.2	39	gGc/gAc	1/3	1	2	FACETS	0.861	0.793	0.931	0.861	0.793	0.931	CLONAL	1	TRUE	1	0.588716259332456	2		468	647	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518557	69518557	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	160	521	2	ENST00000294312.3:c.88G>A	p.Ala30Thr	p.A30T	ENST00000294312	NM_005117.2	30	Gcg/Acg	1/3	1	2	FACETS	0.829	0.762	0.897	0.829	0.762	0.897	CLONAL	1	TRUE	1	0.588716259332456	2		523	656	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435871	49435871	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0032461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	237	827	1	ENST00000301067.7:c.6109+1G>A		p.X2037_splice	ENST00000301067	NM_003482.3	2037			1	2	FACETS	0.979	0.917	1	0.979	0.917	1	CLONAL	1	TRUE	1	0.588716259332456	2		828	822	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312632	30312632	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	228	602	0	ENST00000262643.3:c.613A>G	p.Ile205Val	p.I205V	ENST00000262643	NM_001238.2	205	Atc/Gtc	8/12	1	2	FACETS	0.992	0.927	1	0.992	0.927	1	CLONAL	1	TRUE	1	0.588716259332456	2		602	781	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0032463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	410	720	4	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.273193169996743	3	FACETS	0.874	0.834	0.915	0.874	0.834	0.915	CLONAL	3	TRUE	0	0.3370678830045	3		724	1084	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845086	128845086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761395599	NA	P-0032463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1600	141	658	0	ENST00000249373.3:c.580G>A	p.Glu194Lys	p.E194K	ENST00000249373	NM_005631.4	194	Gaa/Aaa	3/12	0.3370678830045	6	FACETS	0.804	0.73	0.884			1	CLONAL	1	TRUE	NA	0.3370678830045	6		658	1741	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191448	185191448	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1012339817	NA	P-0032463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	114	639	1	ENST00000265026.3:c.2329G>A	p.Glu777Lys	p.E777K	ENST00000265026	NM_004721.4	777	Gaa/Aaa	11/14	0.268988467882615	3	FACETS	0.82	0.737	0.908	0.41	0.368	0.454	CLONAL	1	TRUE	1	0.3370678830045	3		640	964	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881511	48881511	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	144	364	0	ENST00000267163.4:c.233G>A	p.Trp78Ter	p.W78*	ENST00000267163	NM_000321.2	78	tGg/tAg	2/27	0.273215874885715	2	FACETS	0.781	0.716	0.848	0.781	0.716	0.848	SUBCLONAL	2	TRUE	0	0.3370678830045	2		364	547	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150549885	150549885	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	73	341	0	ENST00000369026.2:c.1019G>C	p.Gly340Ala	p.G340A	ENST00000369026	NM_021960.4	340	gGa/gCa	3/3	0.3370678830045	4	FACETS	0.864	0.756	0.982	0.288	0.252	0.328	CLONAL	1	TRUE	1	0.3370678830045	4		341	670	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948248	71948248	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1195	130	814	0	ENST00000298229.2:c.2960A>G	p.Tyr987Cys	p.Y987C	ENST00000298229	NM_001567.3	987	tAc/tGc	26/28	0.268988467882615	3	FACETS	0.68	0.615	0.749	0.34	0.307	0.375	SUBCLONAL	1	TRUE	1	0.3370678830045	3		814	1325	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880991	37880992	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCCAGCGTGGCTGGTG	novel	NA	P-0032463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	339	692	0	ENST00000269571.5:c.2324_2325insCAGCGTGGCTGGTGTGGC	p.Ala775_Gly776insSerValAlaGlyValAla	p.A775_G776insSVAGVA	ENST00000269571		774	atg/aTGGCCAGCGTGGCTGGTGtg	20/27	0.3370678830045	3	FACETS	0.964	0.912	1	0.964	0.912	1	CLONAL	2	TRUE	1	0.3370678830045	3		692	1219	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484852	57484852	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	74	432	0	ENST00000371085.3:c.832A>C	p.Asn278His	p.N278H	ENST00000371085	NM_000516.4	278	Aac/Cac	10/13	0.268988467882615	3	FACETS	0.741	0.649	0.841	0.371	0.324	0.421	SUBCLONAL	1	TRUE	1	0.3370678830045	3		432	692	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786896	135786896	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203474	NA	P-0032463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	172	406	0	ENST00000298552.3:c.973C>T	p.Gln325Ter	p.Q325*	ENST00000298552	NM_001162426.1	325	Cag/Tag	10/23	0.157344565651237	4	FACETS	0.823	0.758	0.891	0.823	0.758	0.891	INDETERMINATE	2	TRUE	2	0.3370678830045	4		406	829	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0032464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	226	620	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.518980306521447	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.518980306521447	1		621	544	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0032464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	150	535	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.875	0.802	0.95	0.875	0.802	0.95	CLONAL	1	TRUE	1	0.518980306521447	2		535	661	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215339	5215339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs114545401	NA	P-0032464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	121	531	0	ENST00000357368.4:c.4279G>A	p.Ala1427Thr	p.A1427T	ENST00000357368	NM_002850.3	1427	Gcc/Acc	28/38	0.518980306521447	2	FACETS	0.585	0.528	0.645	0.293	0.264	0.323	SUBCLONAL	1	TRUE	0	0.518980306521447	2		531	797	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482369	56482369	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	239	560	2	ENST00000267101.3:c.917C>G	p.Pro306Arg	p.P306R	ENST00000267101	NM_001982.3	306	cCt/cGt	8/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.518980306521447	2		562	803	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828054	3828054	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555483689	NA	P-0032464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	109	557	1	ENST00000262367.5:c.2071C>T	p.Gln691Ter	p.Q691*	ENST00000262367	NM_004380.2	691	Cag/Tag	10/31	0.22962582492541	2	FACETS	0.518	0.465	0.574	0.259	0.232	0.287	INDETERMINATE	1	TRUE	0	0.518980306521447	2		558	811	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261131	16261131	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	86	360	1	ENST00000375759.3:c.8396A>T	p.Asp2799Val	p.D2799V	ENST00000375759	NM_015001.2	2799	gAc/gTc	11/15	0.431120400968066	1	FACETS	0.493	0.437	0.552	0.493	0.437	0.552	SUBCLONAL	1	TRUE	0	0.518980306521447	1		361	498	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161906	47161907	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	160	408	1	ENST00000409792.3:c.4219dup	p.Arg1407LysfsTer8	p.R1407Kfs*8	ENST00000409792	NM_014159.6	1407	agg/aAgg	3/21	0.518980306521447	1	FACETS	0.897	0.828	0.968	0.897	0.828	0.968	CLONAL	1	TRUE	0	0.518980306521447	1		409	509	SUCCESS
APC	324	MSKCC	GRCh37	5	112175558	112175558	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	213	250	4	ENST00000257430.4:c.4267del	p.Leu1423PhefsTer50	p.L1423Ffs*50	ENST00000257430	NM_000038.5	1423	Ctt/tt	16/16	0.518980306521447	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.518980306521447	2		254	404	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647356	23647356	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	215	721	0	ENST00000261584.4:c.511T>G	p.Leu171Val	p.L171V	ENST00000261584	NM_024675.3	171	Ttg/Gtg	4/13	0.404541728544779	1	FACETS	0.893	0.831	0.958	0.893	0.831	0.958	CLONAL	1	TRUE	0	0.404541728544779	1		721	949	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949924	44950016	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTGGTACTTTGGGTTGCTTTATAACTGTTTTTTTTTTTCCTAGCCTGCCAGTATAAATTGGCAGTGGAACGGTACGAATGGAACAAATTGCA	TTTGGTACTTTGGGTTGCTTTATAACTGTTTTTTTTTTTCCTAGCCTGCCAGTATAAATTGGCAGTGGAACGGTACGAATGGAACAAATTGCA	-	novel	NA	P-0032465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	100	190	0	ENST00000377967.4:c.3737-44_3785del		p.X1246_splice	ENST00000377967	NM_021140.2	1246		26/29	0.380186914978504	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.404541728544779	1		190	307	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579334	7579344	+	frameshift_variant	Frame_Shift_Del	DEL	GTCCCAGAATG	GTCCCAGAATG	C	novel	NA	P-0032465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	168	521	0	ENST00000269305.4:c.343_353delinsG	p.His115GlufsTer5	p.H115Efs*5	ENST00000269305	NM_001126112.2	115	CATTCTGGGACa/Ga	4/11	0.404541728544779	1	FACETS	0.893	0.822	0.966	0.893	0.822	0.966	CLONAL	1	TRUE	0	0.404541728544779	1		521	742	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0032467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	98	1011	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.214490202578402	2		1012	898	SUCCESS
APC	324	MSKCC	GRCh37	5	112175198	112175198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	49	226	0	ENST00000257430.4:c.3907C>T	p.Gln1303Ter	p.Q1303*	ENST00000257430	NM_000038.5	1303	Caa/Taa	16/16	0.197020549945584	2	FACETS	0.892	0.762	1	0.892	0.762	1	CLONAL	2	TRUE	0	0.214490202578402	2		226	256	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0032467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	46	349	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	0.881	0.742	1	0.881	0.742	1	CLONAL	1	TRUE	1	0.214490202578402	2		349	487	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300486	11300486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	84	693	0	ENST00000361445.4:c.1660C>T	p.His554Tyr	p.H554Y	ENST00000361445	NM_004958.3	554	Cac/Tac	11/58	1	2	FACETS	0.823	0.725	0.928	0.823	0.725	0.928	CLONAL	1	TRUE	1	0.214490202578402	2		693	952	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804303	46804303	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	84	632	0	ENST00000290295.7:c.704A>C	p.Tyr235Ser	p.Y235S	ENST00000290295	NM_006361.5	235	tAt/tCt	2/2	0.138910419310805	4	FACETS	1	0.946	1	0.565	0.498	0.637	CLONAL	1	TRUE	2	0.214490202578402	4		632	842	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0032473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	37	391	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.71	0.587	0.849	0.71	0.587	0.849	SUBCLONAL	1	TRUE	1	0.28	2		391	372	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0032473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	42	571	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.607	0.507	0.719	0.607	0.507	0.719	SUBCLONAL	1	TRUE	1	0.28	2		571	494	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0032473-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	63	391	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.911	0.79	1	0.911	0.79	1	CLONAL	1	FALSE	1	0.305361664386596	2		391	453	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0032473-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	57	571	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.745	0.64	0.86	0.745	0.64	0.86	SUBCLONAL	1	FALSE	1	0.305361664386596	2		571	501	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468442	89468442	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	56	351	0	ENST00000336596.2:c.1976A>C	p.Tyr659Ser	p.Y659S	ENST00000336596	NM_005233.5	659	tAc/tCc	11/17	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.306225101669948	2		351	327	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226022	226065	+	frameshift_variant	Frame_Shift_Del	DEL	AGCAGAACTGAAGATGGGAAGATTTATCAGCGTGCATTTGGTGG	AGCAGAACTGAAGATGGGAAGATTTATCAGCGTGCATTTGGTGG	-	novel	NA	P-0032476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	18	96	0	ENST00000264932.6:c.482_525del	p.Ser161ThrfsTer19	p.S161Tfs*19	ENST00000264932	NM_004168.2	161	AGCAGAACTGAAGATGGGAAGATTTATCAGCGTGCATTTGGTGGa/a	5/15	1	2	FACETS	0.964	0.734	1	0.964	0.734	1	CLONAL	1	TRUE	1	0.306225101669948	2		96	122	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412039	116412057	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGAAGGTATATTTCAGTTT	AGAAGGTATATTTCAGTTT	-	novel	NA	P-0032476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	130	900	0	ENST00000397752.3:c.3025_3028+15del		p.X1009_splice	ENST00000397752	NM_000245.2	1009		14/21	0.306225101669948	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.306225101669948	1		900	679	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578551	7578551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	88	737	0	ENST00000269305.4:c.379T>C	p.Ser127Pro	p.S127P	ENST00000269305	NM_001126112.2	127	Tcc/Ccc	5/11	0.426340977709474	1	FACETS	0.993	0.889	1	0.993	0.889	1	CLONAL	1	TRUE	0	0.426340977709474	1		737	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579356	7579356	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	109	625	0	ENST00000269305.4:c.331C>A	p.Leu111Met	p.L111M	ENST00000269305	NM_001126112.2	111	Ctg/Atg	4/11	0.426340977709474	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.426340977709474	1		625	320	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431943	49431943	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	113	809	0	ENST00000301067.7:c.9196T>G	p.Phe3066Val	p.F3066V	ENST00000301067	NM_003482.3	3066	Ttc/Gtc	34/54	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.426340977709474	2		809	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578545	7578546	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0032478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	89	760	3	ENST00000269305.4:c.384_385delinsCT	p.Ala129Ser	p.A129S	ENST00000269305	NM_001126112.2	128	ccTGcc/ccCTcc	5/11	0.426340977709474	1	FACETS	0.955	0.854	1	0.955	0.854	1	CLONAL	1	TRUE	0	0.426340977709474	1		763	344	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932171	39932171	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555918056	NA	P-0032481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	23	425	0	ENST00000378444.4:c.2428C>T	p.Arg810Ter	p.R810*	ENST00000378444	NM_001123385.1	810	Cga/Tga	4/15	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		425	442	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0032482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	204	447	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.493895017420984	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.493895017420984	1		447	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0032482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	288	769	0	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	0.493895017420984	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.493895017420984	1		769	859	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115451	115115451	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0032482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	54	663	0	ENST00000257566.3:c.875T>G	p.Leu292Ter	p.L292*	ENST00000257566	NM_016569.3	292	tTa/tGa	5/8	1	2	FACETS	0.271	0.231	0.315	0.271	0.231	0.315	SUBCLONAL	1	TRUE	1	0.493895017420984	2		663	807	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0032483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	119	391	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.226875685681634	1	FACETS	1	0.962	1	1	0.993	1	CLONAL	5	FALSE	0	0.226839222326295	1		391	179	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0032483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	65	518	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.842	0.74	0.948	1	0.984	1	CLONAL	3	FALSE	1	0.226839222326295	2		518	227	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0032483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	91	327	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.88	0.796	0.965	1	0.99	1	CLONAL	4	FALSE	1	0.226839222326295	2		327	228	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0032483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	92	332	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	1	0.931	1	1	0.99	1	CLONAL	3	FALSE	1	0.226839222326295	2		332	260	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0032483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	145	348	0	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	0.918	0.845	0.994	1	0.993	1	CLONAL	3	FALSE	1	0.226839222326295	2		348	464	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087533	27087533	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	241	708	0	ENST00000324856.7:c.2109del	p.Ala704ProfsTer38	p.A704Pfs*38	ENST00000324856	NM_006015.4	703	Ccc/cc	5/20	1	2	FACETS	1	0.976	1	1	0.996	1	CLONAL	3	FALSE	1	0.226839222326295	2		708	660	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311650	15311650	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	16	48	0	ENST00000263388.2:c.67C>G	p.Pro23Ala	p.P23A	ENST00000263388	NM_000435.2	23	Ccc/Gcc	1/33	1	2	FACETS	1	0.858	1	1	0.937	1	CLONAL	2	FALSE	1	0.226839222326295	2		48	59	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578179	7578179	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	186	623	0	ENST00000269305.4:c.670G>T	p.Glu224Ter	p.E224*	ENST00000269305	NM_001126112.2	224	Gag/Tag	6/11	0.465797643643095	3	FACETS	0.935	0.879	0.991			1	CLONAL	3	TRUE	NA	0.465797643643095	3		623	351	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115383	115115383	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0032493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	126	554	0	ENST00000257566.3:c.941+2T>A		p.X314_splice	ENST00000257566	NM_016569.3	314			0.465797643643095	3	FACETS	0.836	0.764	0.91	0.836	0.764	0.91	CLONAL	2	TRUE	1	0.465797643643095	3		554	399	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909677	76909680	+	frameshift_variant	Frame_Shift_Del	DEL	CTTT	CTTT	-	novel	NA	P-0032493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	119	258	0	ENST00000373344.5:c.4225_4228del	p.Lys1409GlnfsTer80	p.K1409Qfs*80	ENST00000373344	NM_000489.3	1409	AAAGca/ca	14/35	0.357381386879713	2	FACETS	1	0.978	1			1	CLONAL	2	TRUE	NA	0.465797643643095	2		258	220	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146051	38146051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777371681	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	235	763	0	ENST00000317025.8:c.3455C>T	p.Thr1152Met	p.T1152M	ENST00000317025	NM_023034.1	1152	aCg/aTg	19/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.534538103810543	2		763	752	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	45	325	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.336	0.282	0.396	0.336	0.282	0.396	SUBCLONAL	1	TRUE	1	0.534538103810543	2		325	501	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	132	340	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.534538103810543	2		340	429	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	100	327	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.534538103810543	2		327	372	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	102	470	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.881	0.793	0.974	0.881	0.793	0.974	CLONAL	1	TRUE	1	0.534538103810543	2		471	433	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247516	123247516	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519795	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	163	556	0	ENST00000358487.5:c.1975A>G	p.Lys659Glu	p.K659E	ENST00000358487	NM_000141.4	659	Aag/Gag	14/18	1	2	FACETS	0.935	0.862	1	0.935	0.862	1	CLONAL	1	TRUE	1	0.534538103810543	2		556	652	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	142	600	3	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.534538103810543	2		603	508	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	114	540	7	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.908	0.822	0.997	0.908	0.822	0.997	CLONAL	1	TRUE	1	0.534538103810543	2		547	470	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968322	2968323	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs762770988	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	113	521	2	ENST00000396946.4:c.1663dup	p.Arg555ProfsTer38	p.R555Pfs*38	ENST00000396946	NM_032415.4	555	cgg/cCgg	13/25	1	2	FACETS	0.802	0.725	0.883	0.802	0.725	0.883	CLONAL	1	TRUE	1	0.534538103810543	2		523	527	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878069	48878069	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	32	91	0	ENST00000267163.4:c.25del	p.Thr9ArgfsTer56	p.T9Rfs*56	ENST00000267163	NM_000321.2	7	cgA/cg	1/27	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.534538103810543	2		91	98	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900884	3900884	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	181	611	0	ENST00000262367.5:c.212C>T	p.Ser71Leu	p.S71L	ENST00000262367	NM_004380.2	71	tCg/tTg	2/31	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.534538103810543	2		611	647	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255883	16255883	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	46	414	0	ENST00000375759.3:c.3154del	p.Ile1052SerfsTer40	p.I1052Sfs*40	ENST00000375759	NM_015001.2	1050	Aaa/aa	11/15	1	2	FACETS	0.438	0.369	0.513	0.438	0.369	0.513	SUBCLONAL	1	TRUE	1	0.534538103810543	2		414	393	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671654	67671655	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	118	498	1	ENST00000264010.4:c.2070dup	p.Glu691ArgfsTer5	p.E691Rfs*5	ENST00000264010	NM_006565.3	688	gta/gtAa	12/12	1	2	FACETS	0.914	0.829	1	0.914	0.829	1	CLONAL	1	TRUE	1	0.534538103810543	2		499	483	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991757	72991758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760959844	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	84	322	1	ENST00000268489.5:c.2287dup	p.Glu763GlyfsTer26	p.E763Gfs*26	ENST00000268489	NM_006885.3	763	gag/gGag	2/10	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.534538103810543	2		323	303	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	63	673	1	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	0.352	0.304	0.405	0.352	0.304	0.405	SUBCLONAL	1	TRUE	1	0.534538103810543	2		674	669	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102196076	102196076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	119	428	1	ENST00000263464.3:c.836C>T	p.Ala279Val	p.A279V	ENST00000263464	NM_001165.4	279	gCg/gTg	2/9	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.534538103810543	2		429	398	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498235	498235	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	22	193	1	ENST00000399788.2:c.23del	p.Gly8AlafsTer58	p.G8Afs*58	ENST00000399788	NM_001042603.1	8	gGc/gc	1/28	1	2	FACETS	0.452	0.353	0.566	0.452	0.353	0.566	SUBCLONAL	1	TRUE	1	0.534538103810543	2		194	182	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088770	27088770	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	72	571	1	ENST00000324856.7:c.2382del	p.Ser795AlafsTer38	p.S795Afs*38	ENST00000324856	NM_006015.4	793	atG/at	7/20	1	2	FACETS	0.504	0.44	0.571	0.504	0.44	0.571	SUBCLONAL	1	TRUE	1	0.534538103810543	2		572	535	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119780	70119781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	40	508	0	ENST00000245479.2:c.788dup	p.Arg264GlnfsTer32	p.R264Qfs*32	ENST00000245479	NM_000346.3	261	gag/gaGg	3/3	1	2	FACETS	0.358	0.298	0.425	0.358	0.298	0.425	SUBCLONAL	1	TRUE	1	0.534538103810543	2		508	418	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	173	614	2	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	0.988	1	CLONAL	1	TRUE	1	0.534538103810543	2		616	488	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24134057	24134057	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	72	338	0	ENST00000263121.7:c.214del	p.Thr72GlnfsTer13	p.T72Qfs*13	ENST00000263121	NM_003073.3	70	Aaa/aa	2/9	1	2	FACETS	0.73	0.642	0.824	0.73	0.642	0.824	SUBCLONAL	1	TRUE	1	0.534538103810543	2		338	369	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437711	49437713	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs886049482	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	190	693	0	ENST00000301067.7:c.5257_5259del	p.Lys1753del	p.K1753del	ENST00000301067	NM_003482.3	1753	AAG/-	22/54	1	2	FACETS	0.959	0.889	1	0.959	0.889	1	CLONAL	1	TRUE	1	0.534538103810543	2		693	741	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852113	63852113	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	54	498	0	ENST00000279873.7:c.2891G>T	p.Gly964Val	p.G964V	ENST00000279873	NM_032199.2	964	gGc/gTc	10/10	1	2	FACETS	0.39	0.333	0.452	0.39	0.333	0.452	SUBCLONAL	1	TRUE	1	0.534538103810543	2		498	518	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720873	89720884	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGGTCAGTTAA	AAGGTCAGTTAA	-	novel	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	30	287	0	ENST00000371953.3:c.1025_1026+10del		p.X342_splice	ENST00000371953	NM_000314.4	342		8/9	1	2	FACETS	0.537	0.436	0.65	0.537	0.436	0.65	SUBCLONAL	1	TRUE	1	0.534538103810543	2		287	209	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402304	402304	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs753191754	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	187	568	1	ENST00000399788.2:c.4487T>C	p.Val1496Ala	p.V1496A	ENST00000399788	NM_001042603.1	1496	gTg/gCg	27/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.534538103810543	2		569	578	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954341	48954341	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	130	428	0	ENST00000267163.4:c.1462G>C	p.Ala488Pro	p.A488P	ENST00000267163	NM_000321.2	488	Gcg/Ccg	16/27	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.534538103810543	2		428	436	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060967	38060967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	98	332	0	ENST00000250448.2:c.1022C>T	p.Thr341Met	p.T341M	ENST00000250448	NM_004496.3	341	aCg/aTg	2/2	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.534538103810543	2		332	292	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474342	40474342	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	168	513	1	ENST00000264657.5:c.2059T>C	p.Cys687Arg	p.C687R	ENST00000264657	NM_139276.2	687	Tgt/Cgt	21/24	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.534538103810543	2		514	560	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532673	63532673	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs978837790	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	124	506	1	ENST00000307078.5:c.1908-2A>G		p.X636_splice	ENST00000307078	NM_004655.3	636			1	2	FACETS	0.961	0.874	1	0.961	0.874	1	CLONAL	1	TRUE	1	0.534538103810543	2		507	483	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277940	18277940	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1293969169	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	103	381	1	ENST00000222254.8:c.1560G>T	p.Arg520Ser	p.R520S	ENST00000222254	NM_005027.3	520	agG/agT	13/16	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.534538103810543	2		382	360	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223951	36223952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	114	727	0	ENST00000222270.7:c.6505dup	p.Ala2169GlyfsTer14	p.A2169Gfs*14	ENST00000222270	NM_014727.1	2167	-/G	28/37	1	2	FACETS	0.738	0.666	0.813	0.738	0.666	0.813	SUBCLONAL	1	TRUE	1	0.534538103810543	2		727	578	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40747858	40747858	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	121	606	0	ENST00000392038.2:c.560T>G	p.Val187Gly	p.V187G	ENST00000392038	NM_001626.4	187	gTc/gGc	6/14	1	2	FACETS	0.866	0.786	0.949	0.866	0.786	0.949	CLONAL	1	TRUE	1	0.534538103810543	2		606	523	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871887	45871887	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	136	515	0	ENST00000391945.4:c.360+1G>A		p.X120_splice	ENST00000391945	NM_000400.3	120			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.534538103810543	2		515	447	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605215	46605215	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1407435090	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	45	281	7	ENST00000263734.3:c.1432A>T	p.Ser478Cys	p.S478C	ENST00000263734	NM_001430.4	478	Agc/Tgc	10/16	1	2	FACETS	0.941	0.802	1	0.941	0.802	1	CLONAL	1	TRUE	1	0.534538103810543	2		288	179	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38943038	38943038	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	101	366	0	ENST00000357387.3:c.4949T>C	p.Ile1650Thr	p.I1650T	ENST00000357387	NM_152756.3	1650	aTa/aCa	37/38	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.534538103810543	2		366	366	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591070	67591070	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	52	284	0	ENST00000274335.5:c.1663G>T	p.Glu555Ter	p.E555*	ENST00000274335		555	Gag/Tag	12/15	1	2	FACETS	0.763	0.655	0.879	0.763	0.655	0.879	SUBCLONAL	1	TRUE	1	0.534538103810543	2		284	255	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591129	67591130	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATC	novel	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	80	335	0	ENST00000274335.5:c.1723_1724insTCA	p.Arg574_Lys575insIle	p.R574_K575insI	ENST00000274335		574	-/ATC	12/15	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.534538103810543	2		335	287	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053225	180053225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	64	743	2	ENST00000261937.6:c.1144C>T	p.His382Tyr	p.H382Y	ENST00000261937	NM_182925.4	382	Cat/Tat	9/30	1	2	FACETS	0.408	0.353	0.467	0.408	0.353	0.467	SUBCLONAL	1	TRUE	1	0.534538103810543	2		745	587	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778195	27778195	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	29	554	0	ENST00000369163.2:c.344C>A	p.Ala115Asp	p.A115D	ENST00000369163	NM_003536.2	115	gCc/gAc	1/1	1	2	FACETS	0.205	0.164	0.252	0.205	0.164	0.252	SUBCLONAL	1	TRUE	1	0.534538103810543	2		554	529	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100310	157100310	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1392553148	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	11	171	0	ENST00000346085.5:c.1250del	p.Pro417ArgfsTer13	p.P417Rfs*13	ENST00000346085	NM_020732.3	416	aCc/ac	1/20	1	2	FACETS	0.288	0.199	0.397	0.288	0.199	0.397	SUBCLONAL	1	TRUE	1	0.534538103810543	2		171	143	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859859	151859859	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	128	401	1	ENST00000262189.6:c.10803del	p.Lys3604ArgfsTer26	p.K3604Rfs*26	ENST00000262189	NM_170606.2	3601	aaA/aa	43/59	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.534538103810543	2		402	424	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046467	69046467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	77	567	0	ENST00000288368.4:c.3940G>A	p.Ala1314Thr	p.A1314T	ENST00000288368	NM_024870.2	1314	Gca/Aca	32/40	1	2	FACETS	0.441	0.387	0.499	0.441	0.387	0.499	SUBCLONAL	1	TRUE	1	0.534538103810543	2		567	654	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265814	16265814	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	54	679	0	ENST00000375759.3:c.10889del	p.Pro3630ArgfsTer29	p.P3630Rfs*29	ENST00000375759	NM_015001.2	3629	ttC/tt	15/15	1	2	FACETS	0.588	0.502	0.682	0.588	0.502	0.682	SUBCLONAL	1	TRUE	1	0.329295338460041	2		679	558	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859467	151859488	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTGGCCTGGGCAGGACTCTG	TCTTGGCCTGGGCAGGACTCTG	-	novel	NA	P-0032499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	43	601	0	ENST00000262189.6:c.11174_11195del	p.Thr3725ArgfsTer13	p.T3725Rfs*13	ENST00000262189	NM_170606.2	3725	aCAGAGTCCTGCCCAGGCCAAGAg/ag	43/59	1	2	FACETS	0.472	0.395	0.558	0.472	0.395	0.558	SUBCLONAL	1	TRUE	1	0.329295338460041	2		601	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs786201057	NA	P-0032500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	261	603	2	ENST00000269305.4:c.374C>A	p.Thr125Lys	p.T125K	ENST00000269305	NM_001126112.2	125	aCg/aAg	4/11	0.757299771087861	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.757299771087861	1		605	402	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134514496	134514496	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1245944825	NA	P-0032500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	208	435	1	ENST00000398015.3:c.23T>C	p.Leu8Pro	p.L8P	ENST00000398015	NM_004441.4	8	cTg/cCg	1/16	1	2	FACETS	0.995	0.931	1	0.995	0.931	1	CLONAL	1	TRUE	1	0.757299771087861	2		436	552	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711939	89711965	+	inframe_deletion	In_Frame_Del	DEL	TGGATTATAGACCAGTGGCACTGTTGT	TGGATTATAGACCAGTGGCACTGTTGT	-	novel	NA	P-0032500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	313	631	2	ENST00000371953.3:c.558_584del	p.Asp187_Phe195del	p.D187_F195del	ENST00000371953	NM_000314.4	186	cTGGATTATAGACCAGTGGCACTGTTGTtt/ctt	6/9	1	2	FACETS	0.807	0.773	0.841	1	0.996	1	CLONAL	2	TRUE	1	0.757299771087861	2		633	512	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967092	25967092	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	289	615	0	ENST00000435504.4:c.2114G>T	p.Gly705Val	p.G705V	ENST00000435504		705	gGt/gTt	13/13	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.757299771087861	2		615	734	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39772522	39772522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	349	674	1	ENST00000288319.7:c.719C>T	p.Ala240Val	p.A240V	ENST00000288319	NM_182918.3	240	gCt/gTt	6/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.757299771087861	2		675	904	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0032504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	35	391	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	TRUE	1	0.16	2		391	418	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0032504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	24	319	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.716	0.561	0.896	0.716	0.561	0.896	SUBCLONAL	1	TRUE	1	0.16	2		319	419	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0032504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	52	410	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.16	2		410	649	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0032504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	59	585	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	1	2	FACETS	0.861	0.739	0.994	0.861	0.739	0.994	CLONAL	1	TRUE	1	0.16	2		585	857	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0032505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	66	460	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.923	0.801	1	0.923	0.801	1	CLONAL	1	TRUE	1	0.228488803488984	2		460	626	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0032505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	53	461	1	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.228488803488984	1	FACETS	0.817	0.697	0.948	0.817	0.697	0.948	CLONAL	1	TRUE	0	0.228488803488984	1		462	503	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0032505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	32	281	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	0.228488803488984	1	FACETS	0.725	0.59	0.878	0.725	0.59	0.878	SUBCLONAL	1	TRUE	0	0.228488803488984	1		281	342	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443864	52443864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	113	817	1	ENST00000460680.1:c.31G>A	p.Asp11Asn	p.D11N	ENST00000460680	NM_004656.3	11	Gac/Aac	1/17	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.228488803488984	2		818	936	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122567	108122567	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	61	388	0	ENST00000278616.4:c.1611del	p.Ala538GlnfsTer5	p.A538Qfs*5	ENST00000278616	NM_000051.3	537	ccT/cc	11/63	0.228488803488984	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.228488803488984	1		388	416	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215227	142215238	+	inframe_deletion	In_Frame_Del	DEL	TTCCACGTACAG	TTCCACGTACAG	-	novel	NA	P-0032505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	49	410	0	ENST00000350721.4:c.5863_5874del	p.Leu1955_Glu1958del	p.L1955_E1958del	ENST00000350721	NM_001184.3	1955	CTGTACGTGGAA/-	34/47	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.228488803488984	2		410	427	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066813	30066813	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	123	294	1	ENST00000331968.5:c.2318T>A	p.Ile773Asn	p.I773N	ENST00000331968	NM_002742.2	773	aTc/aAc	16/18	0.341996684640842	4	FACETS	0.765	0.695	0.838	0.765	0.695	0.838	SUBCLONAL	2	FALSE	2	0.441793353792794	4		295	525	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0032508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	96	391	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.289819808760055	3	FACETS	0.95	0.853	1	0.95	0.853	1	CLONAL	2	TRUE	1	0.289819808760055	3		391	399	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624404	140624415	+	inframe_deletion	In_Frame_Del	DEL	CGGCGCCGGCGC	CGGCGCCGGCGC	-	rs397507458	NA	P-0032508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	49	161	1	ENST00000288602.6:c.89_100del	p.Gly30_Ala33del	p.G30_A33del	ENST00000288602	NM_004333.4	30	gGCGCCGGCGCCGcg/gcg	1/18	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.289819808760055	2		162	263	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099452	27099453	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0032508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	58	410	0	ENST00000324856.7:c.3690_3691dup	p.Asp1231GlyfsTer7	p.D1231Gfs*7	ENST00000324856	NM_006015.4	1230	aag/aaGGg	14/20	0.260438130654568	1	FACETS	0.752	0.648	0.866	0.752	0.648	0.866	SUBCLONAL	1	TRUE	0	0.289819808760055	1		410	455	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482826	140482826	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	69	452	0	ENST00000288602.6:c.1309C>G	p.Arg437Gly	p.R437G	ENST00000288602	NM_004333.4	437	Cga/Gga	10/18	1	2	FACETS	0.841	0.733	0.958	0.841	0.733	0.958	CLONAL	1	TRUE	1	0.289819808760055	2		452	566	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0032510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	185	367	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.903	0.839	0.97	0.903	0.839	0.97	CLONAL	1	TRUE	1	0.690668182877144	2		367	593	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115952	8115953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0032510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	136	292	0	ENST00000346208.3:c.1300dup	p.His434ProfsTer73	p.H434Pfs*73	ENST00000346208		433	cac/caCc	6/6	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.690668182877144	2		292	391	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860667	151860667	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0032510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	209	478	0	ENST00000262189.6:c.9995T>A	p.Leu3332Ter	p.L3332*	ENST00000262189	NM_170606.2	3332	tTa/tAa	43/59	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.690668182877144	2		478	594	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0032513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	86	460	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.145716689473961	3	FACETS	1	0.977	1	0.723	0.641	0.81	INDETERMINATE	1	TRUE	1	0.25270990000565	3		460	530	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783226	9783226	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	39	436	0	ENST00000377346.4:c.2470C>G	p.Leu824Val	p.L824V	ENST00000377346	NM_005026.3	824	Ctc/Gtc	20/24	1	2	FACETS	0.588	0.487	0.701	0.588	0.487	0.701	SUBCLONAL	1	TRUE	1	0.25270990000565	2		436	525	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813048	89813051	+	frameshift_variant	Frame_Shift_Del	DEL	CGAC	CGAC	-	novel	NA	P-0032513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	41	561	0	ENST00000389301.3:c.3454_3457del	p.Val1152ThrfsTer13	p.V1152Tfs*13	ENST00000389301	NM_000135.2	1152	GTCGac/ac	35/43	0.120429603089072	0	FACETS	0.409	0.34	0.486			1	INDETERMINATE	1	TRUE	0	0.25270990000565	0		561	593	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602802	10602814	+	frameshift_variant	Frame_Shift_Del	DEL	TGTTCGCAGTCGT	TGTTCGCAGTCGT	-	novel	NA	P-0032513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	144	836	0	ENST00000171111.5:c.764_776del	p.Tyr255CysfsTer18	p.Y255Cfs*18	ENST00000171111	NM_203500.1	255	tACGACTGCGAACAg/tg	3/6	0.25270990000565	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.25270990000565	1		836	925	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910603	50910603	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	77	679	0	ENST00000440232.2:c.1706T>C	p.Leu569Pro	p.L569P	ENST00000440232	NM_002691.3	569	cTg/cCg	14/27	0.25270990000565	1	FACETS	0.779	0.684	0.882	0.779	0.684	0.882	SUBCLONAL	1	TRUE	0	0.25270990000565	1		679	683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578463	7578463	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371524413	NA	P-0032514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	92	686	0	ENST00000269305.4:c.467G>C	p.Arg156Pro	p.R156P	ENST00000269305	NM_001126112.2	156	cGc/cCc	5/11	1	2	FACETS	0.925	0.82	1	0.925	0.82	1	CLONAL	1	TRUE	1	0.19	2		686	1047	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40490814	40490814	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	57	300	0	ENST00000264657.5:c.485T>G	p.Met162Arg	p.M162R	ENST00000264657	NM_139276.2	162	aTg/aGg	6/24	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.19	2		300	524	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884469	151884469	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	43	287	0	ENST00000262189.6:c.4886T>C	p.Met1629Thr	p.M1629T	ENST00000262189	NM_170606.2	1629	aTg/aCg	33/59	1	2	FACETS	0.9	0.753	1	0.9	0.753	1	CLONAL	1	TRUE	1	0.19	2		287	503	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905524	50905524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1295943468	NA	P-0032518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1350	117	904	1	ENST00000440232.2:c.652C>T	p.Arg218Cys	p.R218C	ENST00000440232	NM_002691.3	218	Cgc/Tgc	6/27	0.176175624071908	4	FACETS	0.856	0.769	0.949	0.428	0.384	0.475	CLONAL	1	TRUE	2	0.228978253329304	4		905	1467	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945469	151945469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1568	127	1119	0	ENST00000262189.6:c.2050C>T	p.Pro684Ser	p.P684S	ENST00000262189	NM_170606.2	684	Cct/Tct	14/59	0.222047154616103	4	FACETS	0.804	0.725	0.888	0.402	0.362	0.444	CLONAL	1	TRUE	2	0.228978253329304	4		1119	1695	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0032520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	252	427	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.499280622411139	4	FACETS	0.939	0.881	0.998	0.939	0.881	0.998	CLONAL	2	TRUE	2	0.499280622411139	4		427	806	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0032520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	334	524	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	2	TRUE	NA	0.499280622411139	2		524	649	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028657	12028657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	188	374	1	ENST00000353533.5:c.860G>A	p.Arg287His	p.R287H	ENST00000353533	NM_003010.3	287	cGc/cAc	8/11	0.499280622411139	2	FACETS	0.905	0.847	0.963	0.905	0.847	0.963	CLONAL	2	TRUE	0	0.499280622411139	2		375	416	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937602	76937603	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	351	403	1	ENST00000373344.5:c.3145dup	p.Ile1049AsnfsTer4	p.I1049Nfs*4	ENST00000373344	NM_000489.3	1049	ata/aAta	9/35	0.499280622411139	5	FACETS	0.952	0.906	0.999			1	CLONAL	3	TRUE	NA	0.499280622411139	5		404	861	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209390	98209390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571030658	NA	P-0032520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	126	448	0	ENST00000331920.6:c.4148C>T	p.Pro1383Leu	p.P1383L	ENST00000331920	NM_000264.3	1383	cCg/cTg	23/24	0.499280622411139	3	FACETS	0.99	0.899	1	0.495	0.449	0.543	CLONAL	1	TRUE	1	0.499280622411139	3		448	637	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225564	2225564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763780388	NA	P-0032520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	396	685	0	ENST00000326181.6:c.1567G>A	p.Val523Met	p.V523M	ENST00000326181	NM_032271.2	523	Gtg/Atg	17/21	0.499280622411139	4	FACETS	1	0.983	1	0.532	0.507	0.558	CLONAL	2	TRUE	0	0.499280622411139	4		685	1117	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288417	15288417	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	137	521	2	ENST00000263388.2:c.4322G>T	p.Arg1441Leu	p.R1441L	ENST00000263388	NM_000435.2	1441	cGc/cTc	24/33	1	2	FACETS	0.872	0.796	0.952	0.872	0.796	0.952	CLONAL	1	TRUE	1	0.499280622411139	2		523	629	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1064795203	NA	P-0032521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	179	688	0	ENST00000269305.4:c.532C>G	p.His178Asp	p.H178D	ENST00000269305	NM_001126112.2	178	Cac/Gac	5/11	0.38244733969479	1	FACETS	0.973	0.899	1	0.973	0.899	1	CLONAL	1	TRUE	0	0.38244733969479	1		688	778	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124241	2124241	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567474646	NA	P-0032521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	209	834	2	ENST00000219476.3:c.2396G>A	p.Arg799His	p.R799H	ENST00000219476	NM_000548.3	799	cGc/cAc	22/42	1	2	FACETS	0.874	0.81	0.94	0.874	0.81	0.94	CLONAL	1	TRUE	1	0.38244733969479	2		836	1251	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939028	48939028	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0032521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	75	260	0	ENST00000267163.4:c.862-2A>T		p.X288_splice	ENST00000267163	NM_000321.2	288			0.38244733969479	1	FACETS	0.955	0.844	1	0.955	0.844	1	CLONAL	1	TRUE	0	0.38244733969479	1		260	332	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778209	3778209	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781438241	NA	P-0032521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	82	789	0	ENST00000262367.5:c.6839G>A	p.Gly2280Glu	p.G2280E	ENST00000262367	NM_004380.2	2280	gGg/gAg	31/31	1	2	FACETS	0.433	0.381	0.49	0.433	0.381	0.49	SUBCLONAL	1	TRUE	1	0.38244733969479	2		789	990	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217398	7217398	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0032521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	151	561	1	ENST00000380728.2:c.397+1G>A		p.X133_splice	ENST00000380728		133			0.38244733969479	1	FACETS	0.898	0.823	0.977	0.898	0.823	0.977	CLONAL	1	TRUE	0	0.38244733969479	1		562	711	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573312	41573312	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs763290593	NA	P-0032521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	71	803	0	ENST00000263253.7:c.5597C>G	p.Pro1866Arg	p.P1866R	ENST00000263253	NM_001429.3	1866	cCg/cGg	31/31	0.38244733969479	1	FACETS	0.316	0.275	0.361	0.316	0.275	0.361	SUBCLONAL	1	TRUE	0	0.38244733969479	1		803	949	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515399	149515399	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	118	526	0	ENST00000261799.4:c.83A>G	p.Gln28Arg	p.Q28R	ENST00000261799	NM_002609.3	28	cAg/cGg	3/23	0.320933339320617	2	FACETS	0.767	0.691	0.846	0.383	0.345	0.423	SUBCLONAL	1	TRUE	0	0.38244733969479	2		526	805	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285906	38285906	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	128	580	0	ENST00000425967.3:c.505T>C	p.Ser169Pro	p.S169P	ENST00000425967	NM_001174067.1	169	Tca/Cca	5/19	0.38244733969479	1	FACETS	0.678	0.614	0.744	0.678	0.614	0.744	SUBCLONAL	1	TRUE	0	0.38244733969479	1		580	799	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	134	258	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		258	422	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	355	354	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.409765195673762	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.635366349098736	1		354	596	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0032523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	672	906	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.637035989940727	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.635366349098736	2		906	991	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467823	50467823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	45	483	1	ENST00000331340.3:c.1058C>T	p.Pro353Leu	p.P353L	ENST00000331340	NM_006060.4	353	cCg/cTg	8/8	0.637035989940727	3	FACETS	0.45	0.378	0.528	0.225	0.189	0.264	SUBCLONAL	1	TRUE	1	0.635366349098736	3		484	415	SUCCESS
ATR	545	MSKCC	GRCh37	3	142168389	142168389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199948706	NA	P-0032523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	102	505	0	ENST00000350721.4:c.7817G>A	p.Arg2606Gln	p.R2606Q	ENST00000350721	NM_001184.3	2606	cGa/cAa	47/47	0.336634261013328	4	FACETS	0.807	0.722	0.896	0.403	0.361	0.448	INDETERMINATE	1	TRUE	2	0.635366349098736	4		505	651	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043407	180043407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757396801	NA	P-0032523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	341	866	0	ENST00000261937.6:c.3179G>A	p.Arg1060Gln	p.R1060Q	ENST00000261937	NM_182925.4	1060	cGg/cAg	23/30	0.637035989940727	3	FACETS	0.918	0.874	0.963	0.918	0.874	0.963	CLONAL	2	TRUE	1	0.635366349098736	3		866	770	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598383	28598383	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0032523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	183	713	0	ENST00000253063.3:c.354+1G>A		p.X118_splice	ENST00000253063	NM_031459.4	118			0.32790548306067	3	FACETS	1	0.93	1	0.503	0.465	0.542	INDETERMINATE	1	TRUE	1	0.635366349098736	3		713	755	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100598	8100598	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	121	717	0	ENST00000346208.3:c.572C>T	p.Pro191Leu	p.P191L	ENST00000346208		191	cCc/cTc	3/6	0.635366349098736	2	FACETS	0.769	0.699	0.843	0.385	0.349	0.422	SUBCLONAL	1	TRUE	0	0.635366349098736	2		717	495	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130153	143130153	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	48	584	0	ENST00000262992.4:c.863A>G	p.Glu288Gly	p.E288G	ENST00000262992	NM_001101669.1	288	gAg/gGg	11/24	0.386726991812543	5	FACETS	0.488	0.412	0.572	0.163	0.137	0.191	SUBCLONAL	1	TRUE	2	0.635366349098736	5		584	605	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584725	187584725	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	60	420	0	ENST00000441802.2:c.3308C>T	p.Ser1103Phe	p.S1103F	ENST00000441802	NM_005245.3	1103	tCc/tTc	3/27	0.386726991812543	5	FACETS	0.688	0.593	0.791	0.229	0.197	0.264	SUBCLONAL	1	TRUE	2	0.635366349098736	5		420	536	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39074458	39074458	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1205555082	NA	P-0032523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	348	520	0	ENST00000357387.3:c.22C>G	p.Arg8Gly	p.R8G	ENST00000357387	NM_152756.3	8	Cgc/Ggc	1/38	0.333118972280871	6	FACETS	1	0.983	1	0.545	0.516	0.574	INDETERMINATE	2	TRUE	2	0.635366349098736	6		520	1142	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910644	29910645	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0032523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	149	1045	0	ENST00000376809.5:c.185dup	p.Ser62ArgfsTer37	p.S62Rfs*37	ENST00000376809	NM_002116.7	62	agc/aGgc	2/8	0.338142289205022	6	FACETS	1	0.98	1	0.309	0.282	0.337	INDETERMINATE	1	TRUE	2	0.635366349098736	6		1045	861	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322895	31322896	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCCT	novel	NA	P-0032523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	74	685	0	ENST00000412585.2:c.997_1000dup	p.Arg334LysfsTer25	p.R334Kfs*25	ENST00000412585	NM_005514.6	334	agg/aAGGAgg	5/8	0.338142289205022	6	FACETS	0.73	0.638	0.828	0.182	0.159	0.207	INDETERMINATE	1	TRUE	2	0.635366349098736	6		685	725	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0032526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	337	619	1	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.704628259728974	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	FALSE	0	0.704628259728974	2		620	443	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73350221	73350221	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	17	271	0	ENST00000377767.4:c.664G>C	p.Glu222Gln	p.E222Q	ENST00000377767	NM_014953.3	222	Gaa/Caa	5/21	0.682417311813831	2	FACETS	0.231	0.172	0.3	0.115	0.086	0.15	SUBCLONAL	1	FALSE	0	0.704628259728974	2		271	209	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578268	+	frameshift_variant	Frame_Shift_Del	DEL	CGGATAA	CGGATAA	-	novel	NA	P-0032526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	340	626	1	ENST00000269305.4:c.581_587del	p.Leu194GlnfsTer51	p.L194Qfs*51	ENST00000269305	NM_001126112.2	194	cTTATCCGa/ca	6/11	0.704628259728974	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	FALSE	0	0.704628259728974	2		627	441	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29686004	29686004	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	324	348	0	ENST00000356175.3:c.8069del	p.Leu2690CysfsTer28	p.L2690Cfs*28	ENST00000356175	NM_000267.3	2690	Ttg/tg	55/57	0.688845749422383	4	FACETS	1	0.986	1			1	CLONAL	2	FALSE	NA	0.704628259728974	4		348	716	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59937165	59937165	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	192	286	0	ENST00000259008.2:c.197C>G	p.Ser66Cys	p.S66C	ENST00000259008	NM_032043.2	66	tCt/tGt	3/20	0.563112688000521	4	FACETS	0.851	0.793	0.91	0.851	0.793	0.91	CLONAL	2	FALSE	2	0.704628259728974	4		286	546	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31020719	31020719	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	168	221	0	ENST00000375687.4:c.1016A>G	p.Gln339Arg	p.Q339R	ENST00000375687	NM_015338.5	339	cAg/cGg	11/13	0.704628259728974	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	FALSE	2	0.704628259728974	4		221	376	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0032532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	23	680	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.707	0.55	0.889	0.707	0.55	0.889	SUBCLONAL	1	TRUE	1	0.14	2		680	465	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0032532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	24	499	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.799	0.626	1	0.799	0.626	1	CLONAL	1	TRUE	1	0.14	2		499	429	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144591	119144591	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	21	407	0	ENST00000264033.4:c.604T>C	p.Trp202Arg	p.W202R	ENST00000264033	NM_005188.3	202	Tgg/Cgg	4/16	1	2	FACETS	0.971	0.748	1	0.971	0.748	1	CLONAL	1	TRUE	1	0.14	2		407	309	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678217	58678217	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1176152587	NA	P-0032532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	29	616	0	ENST00000305921.3:c.442G>T	p.Ala148Ser	p.A148S	ENST00000305921	NM_003620.3	148	Gct/Tct	1/6	1	2	FACETS	0.979	0.786	1	0.979	0.786	1	CLONAL	1	TRUE	1	0.14	2		616	423	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143219	30143219	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1321334043	NA	P-0032532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	15	329	0	ENST00000389048.3:c.307G>T	p.Gly103Trp	p.G103W	ENST00000389048	NM_004304.4	103	Ggg/Tgg	1/29	1	2	FACETS	1	0.734	1	1	0.734	1	CLONAL	1	TRUE	1	0.14	2		329	214	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460458	149460458	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1308547474	NA	P-0032532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	22	718	1	ENST00000286301.3:c.179T>C	p.Leu60Pro	p.L60P	ENST00000286301	NM_005211.3	60	cTg/cCg	3/22	1	2	FACETS	0.772	0.597	0.976	0.772	0.597	0.976	CLONAL	1	TRUE	1	0.14	2		719	407	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523291	176523291	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	23	621	0	ENST00000292408.4:c.1948C>A	p.Arg650Ser	p.R650S	ENST00000292408	NM_213647.1	650	Cgc/Agc	15/18	1	2	FACETS	0.853	0.665	1	0.853	0.665	1	CLONAL	1	TRUE	1	0.14	2		621	385	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0032533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	94	410	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.68	2		410	264	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573894	18573894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759658584	NA	P-0032533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	151	517	1	ENST00000266497.5:c.2212C>T	p.Arg738Cys	p.R738C	ENST00000266497		738	Cgt/Tgt	15/31	0.133927416993085	1	FACETS	0.58	0.534	0.628	0.58	0.534	0.628	INDETERMINATE	1	TRUE	0	0.68	1		518	505	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453145	140453146	+	missense_variant	Missense_Mutation	DNP	AG	AG	GA	rs121913368	NA	P-0032533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	611	441	0	ENST00000288602.6:c.1789_1790delinsTC	p.Leu597Ser	p.L597S	ENST00000288602	NM_004333.4	597	CTa/TCa	15/18	0.677690295322896	5	FACETS	0.945	0.924	0.966	0.945	0.924	0.966	CLONAL	5	TRUE	0	0.68	5		441	768	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134239	11134239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	212	628	2	ENST00000358026.2:c.2905C>T	p.His969Tyr	p.H969Y	ENST00000358026	NM_001128849.1	969	Cac/Tac	20/36	1	2	FACETS	0.974	0.91	1	0.974	0.91	1	CLONAL	1	TRUE	1	0.68	2		630	640	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950397	15950397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs190623603	NA	P-0032533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	189	586	0	ENST00000268712.3:c.6547C>T	p.Arg2183Cys	p.R2183C	ENST00000268712	NM_006311.3	2183	Cgc/Tgc	42/46	0.677690295322896	1	FACETS	0.968	0.909	1	0.968	0.909	1	CLONAL	1	TRUE	0	0.68	1		586	379	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36217254	36217254	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	232	588	0	ENST00000222270.7:c.4003G>A	p.Gly1335Arg	p.G1335R	ENST00000222270	NM_014727.1	1335	Gga/Aga	14/37	1	2	FACETS	0.999	0.936	1	0.999	0.936	1	CLONAL	1	TRUE	1	0.68	2		588	683	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640715	3640715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs114472821	NA	P-0032533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	292	708	0	ENST00000294008.3:c.2924C>T	p.Pro975Leu	p.P975L	ENST00000294008	NM_032444.2	975	cCg/cTg	12/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.68	2		708	795	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964400	93964400	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1051471746	NA	P-0032533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	139	562	1	ENST00000369303.4:c.2497G>A	p.Gly833Arg	p.G833R	ENST00000369303	NM_004440.3	833	Gga/Aga	14/17	1	2	FACETS	0.848	0.777	0.921	0.848	0.777	0.921	CLONAL	1	TRUE	1	0.68	2		563	482	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589677	69589677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	42	72	0	ENST00000168712.1:c.176C>T	p.Pro59Leu	p.P59L	ENST00000168712	NM_002007.2	59	cCg/cTg	1/3	1	2	FACETS	0.772	0.675	0.868	1	0.97	1	SUBCLONAL	2	TRUE	1	0.68	2		72	80	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27183498	27183498	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779939521	NA	P-0032533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	145	490	0	ENST00000380036.4:c.1072C>T	p.His358Tyr	p.H358Y	ENST00000380036	NM_000459.3	358	Cat/Tat	8/23	0.677690295322896	1	FACETS	0.914	0.849	0.979	0.914	0.849	0.979	CLONAL	1	TRUE	0	0.68	1		490	308	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404530	70404530	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	169	479	0	ENST00000373644.4:c.2044G>A	p.Glu682Lys	p.E682K	ENST00000373644	NM_030625.2	682	Gaa/Aaa	4/12	1	2	FACETS	0.967	0.896	1	0.967	0.896	1	CLONAL	1	TRUE	1	0.68	2		479	514	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992163	72992163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564027629	NA	P-0032533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	253	626	0	ENST00000268489.5:c.1882G>A	p.Glu628Lys	p.E628K	ENST00000268489	NM_006885.3	628	Gag/Aag	2/10	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.68	2		626	726	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934270	81934270	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	204	657	0	ENST00000359376.3:c.1247A>C	p.His416Pro	p.H416P	ENST00000359376	NM_002661.3	416	cAc/cCc	14/33	1	2	FACETS	0.889	0.828	0.951	0.889	0.828	0.951	CLONAL	1	TRUE	1	0.68	2		657	675	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144497	11144497	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	271	604	0	ENST00000358026.2:c.3829C>T	p.Pro1277Ser	p.P1277S	ENST00000358026	NM_001128849.1	1277	Ccg/Tcg	27/36	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.68	2		604	700	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210431	36210431	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs748888652	NA	P-0032533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	229	563	0	ENST00000222270.7:c.424C>T	p.Arg142Ter	p.R142*	ENST00000222270	NM_014727.1	142	Cga/Tga	2/37	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.68	2		563	658	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224142	36224142	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	191	515	0	ENST00000222270.7:c.6692C>T	p.Ser2231Phe	p.S2231F	ENST00000222270	NM_014727.1	2231	tCc/tTc	28/37	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.68	2		515	532	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486221	8486221	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	180	520	1	ENST00000356435.5:c.2596G>A	p.Glu866Lys	p.E866K	ENST00000356435		866	Gag/Aag	17/35	0.677690295322896	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.68	1		521	327	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87475988	87475988	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	275	861	0	ENST00000277120.3:c.1430C>T	p.Ser477Leu	p.S477L	ENST00000277120		477	tCa/tTa	13/19	1	2	FACETS	0.922	0.868	0.978	0.922	0.868	0.978	CLONAL	1	TRUE	1	0.68	2		861	877	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058549	42058551	+	missense_variant	Missense_Mutation	TNP	AAA	AAA	GAT	novel	NA	P-0032533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	126	454	0	ENST00000219905.7:c.8269_8271delinsGAT	p.Lys2757Asp	p.K2757D	ENST00000219905	NM_001164273.1	2757	AAA/GAT	24/24	1	2	FACETS	0.874	0.798	0.953	0.874	0.798	0.953	CLONAL	1	TRUE	1	0.68	2		454	424	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	161	447	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.912	0.839	0.987	1	0.991	1	CLONAL	2	TRUE	1	0.27	2		447	654	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691003	NA	P-0032534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	25	499	0	ENST00000269305.4:c.96+1G>T		p.X32_splice	ENST00000269305	NM_001126112.2	32			1	2	FACETS	0.431	0.339	0.537	0.431	0.339	0.537	SUBCLONAL	1	TRUE	1	0.27	2		499	430	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12043879	12043879	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	38	411	0	ENST00000396373.4:c.1258A>T	p.Met420Leu	p.M420L	ENST00000396373	NM_001987.4	420	Atg/Ttg	8/8	1	2	FACETS	0.8	0.663	0.952	0.8	0.663	0.952	CLONAL	1	TRUE	1	0.27	2		411	352	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211694	36211694	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	53	599	2	ENST00000222270.7:c.1445G>T	p.Arg482Leu	p.R482L	ENST00000222270	NM_014727.1	482	cGg/cTg	3/37	1	2	FACETS	0.85	0.726	0.985	0.85	0.726	0.985	CLONAL	1	TRUE	1	0.27	2		601	462	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971006	55971006	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	50	668	0	ENST00000263923.4:c.1791G>C	p.Glu597Asp	p.E597D	ENST00000263923	NM_002253.2	597	gaG/gaC	13/30	1	2	FACETS	0.529	0.448	0.619	0.529	0.448	0.619	SUBCLONAL	1	TRUE	1	0.27	2		668	700	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518845	187518845	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	27	458	0	ENST00000441802.2:c.12359G>T	p.Arg4120Met	p.R4120M	ENST00000441802	NM_005245.3	4120	aGg/aTg	24/27	1	2	FACETS	0.419	0.333	0.518	0.419	0.333	0.518	SUBCLONAL	1	TRUE	1	0.27	2		458	477	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435393	18435393	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	30	400	0	ENST00000266497.5:c.378G>T	p.Trp126Cys	p.W126C	ENST00000266497		126	tgG/tgT	1/31	1	2	FACETS	0.311	0.25	0.38	0.311	0.25	0.38	SUBCLONAL	1	NA	1	0.47481284958986	2		400	406	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553300	106553300	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	49	445	0	ENST00000369096.4:c.1265G>T	p.Cys422Phe	p.C422F	ENST00000369096	NM_001198.3	422	tGt/tTt	5/7	1	2	FACETS	0.46	0.39	0.537	0.46	0.39	0.537	SUBCLONAL	1	NA	1	0.47481284958986	2		445	449	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0032537-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	77	814	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.23	2		814	544	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045025	47045025	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032537-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	116	859	0	ENST00000377604.3:c.2351A>T	p.His784Leu	p.H784L	ENST00000377604	NM_001204468.1	784	cAc/cTc	20/24	NA	2	FACETS	0.807	0.729	0.889			1	INDETERMINATE	2	TRUE	NA	0.23	2		859	625	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0032537-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	17	634	1	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.26	0.193	0.341	0.26	0.193	0.341	SUBCLONAL	1	TRUE	1	0.233711810704208	2		635	559	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0032537-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	101	814	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.233711810704208	2		814	685	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577524	7577524	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032537-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	90	776	0	ENST00000269305.4:c.757A>C	p.Thr253Pro	p.T253P	ENST00000269305	NM_001126112.2	253	Acc/Ccc	7/11	0.231755179523161	1	FACETS	0.911	0.808	1	0.911	0.808	1	CLONAL	1	TRUE	0	0.233711810704208	1		776	747	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341142	8341142	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032537-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	54	563	0	ENST00000356435.5:c.5074C>T	p.Arg1692Cys	p.R1692C	ENST00000356435		1692	Cgt/Tgt	30/35	1	2	FACETS	0.887	0.758	1	0.887	0.758	1	CLONAL	1	TRUE	1	0.233711810704208	2		563	521	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400842	72400842	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032537-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	42	489	0	ENST00000357731.5:c.329T>G	p.Val110Gly	p.V110G	ENST00000357731	NM_173808.2	110	gTg/gGg	2/7	1	2	FACETS	0.645	0.538	0.765	0.645	0.538	0.765	SUBCLONAL	1	TRUE	1	0.233711810704208	2		489	557	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344225	70344225	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032537-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	17	346	1	ENST00000374080.3:c.1961G>T	p.Ser654Ile	p.S654I	ENST00000374080		654	aGc/aTc	13/45	0.20676692513118	1	FACETS	0.41	0.306	0.535	0.41	0.306	0.535	SUBCLONAL	1	TRUE	0	0.233711810704208	1		347	313	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152092	55152103	+	inframe_deletion	In_Frame_Del	DEL	GACATCATGCAT	GACATCATGCAT	-	rs1553906053	NA	P-0032539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	218	709	0	ENST00000257290.5:c.2526_2537del	p.Ile843_Asp846del	p.I843_D846del	ENST00000257290	NM_006206.4	842	GACATCATGCAT/-	18/23	1	2	FACETS	0.943	0.881	1	0.943	0.881	1	CLONAL	1	TRUE	1	0.65484351927196	2		709	706	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0032546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	89	518	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	0.987	1	CLONAL	2	TRUE	1	0.18	2		518	445	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159754	20159754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	43	364	0	ENST00000379607.5:c.5C>T	p.Pro2Leu	p.P2L	ENST00000379607	NM_001412.3	2	cCc/cTc	1/7	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.18	2		364	440	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592159	67592160	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	GCTCTGTAGTGTA	novel	NA	P-0032546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	31	238	0	ENST00000274335.5:c.1976_1985+3dup		p.C659CSVV*X	ENST00000274335		659	tgc/tGCTCTGTAGTGTAgc	14/15	1	2	FACETS	1	0.823	1	1	0.823	1	CLONAL	1	TRUE	1	0.18	2		238	339	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400107	139400107	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	80	729	0	ENST00000277541.6:c.4241G>A	p.Cys1414Tyr	p.C1414Y	ENST00000277541	NM_017617.3	1414	tGc/tAc	25/34	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.18	2		729	876	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	16	447	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.345	0.254	0.454	0.345	0.254	0.454	SUBCLONAL	1	TRUE	1	0.21	2		447	442	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522740	67522741	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	22	255	0	ENST00000274335.5:c.244dup	p.Ile82AsnfsTer24	p.I82Nfs*24	ENST00000274335		79	-/A	1/15	1	2	FACETS	0.797	0.619	1	0.797	0.619	1	CLONAL	1	TRUE	1	0.21	2		255	263	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073997	8073997	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	44	494	0	ENST00000377482.5:c.662A>C	p.Asp221Ala	p.D221A	ENST00000377482	NM_018948.3	221	gAt/gCt	4/4	1	2	FACETS	0.991	0.832	1	0.991	0.832	1	CLONAL	1	TRUE	1	0.21	2		494	423	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075630	8075630	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	61	534	0	ENST00000377482.5:c.50C>A	p.Thr17Asn	p.T17N	ENST00000377482	NM_018948.3	17	aCt/aAt	2/4	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.21	2		534	550	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587777894	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	38	695	2	ENST00000361445.4:c.6644C>A	p.Ser2215Tyr	p.S2215Y	ENST00000361445	NM_004958.3	2215	tCt/tAt	47/58	1	2	FACETS	0.49	0.403	0.587	0.49	0.403	0.587	SUBCLONAL	1	TRUE	1	0.21	2		697	739	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254623	16254623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749814808	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	45	607	0	ENST00000375759.3:c.1888C>T	p.Arg630Cys	p.R630C	ENST00000375759	NM_015001.2	630	Cgt/Tgt	11/15	1	2	FACETS	0.908	0.763	1	0.908	0.763	1	CLONAL	1	TRUE	1	0.21	2		607	472	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17350472	17350473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	43	562	0	ENST00000375499.3:c.637dup	p.Met213AsnfsTer9	p.M213Nfs*9	ENST00000375499	NM_003000.2	213	atg/aAtg	6/8	1	2	FACETS	0.687	0.574	0.813	0.687	0.574	0.813	SUBCLONAL	1	TRUE	1	0.21	2		562	596	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106355	27106355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773909963	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	44	590	0	ENST00000324856.7:c.5966G>A	p.Arg1989Gln	p.R1989Q	ENST00000324856	NM_006015.4	1989	cGa/cAa	20/20	1	2	FACETS	0.791	0.663	0.932	0.791	0.663	0.932	CLONAL	1	TRUE	1	0.21	2		590	530	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076716	72076716	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	38	530	0	ENST00000357731.5:c.781G>T	p.Glu261Ter	p.E261*	ENST00000357731	NM_173808.2	261	Gag/Tag	5/7	1	2	FACETS	0.659	0.544	0.788	0.659	0.544	0.788	SUBCLONAL	1	TRUE	1	0.21	2		530	549	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748026	72748026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	41	598	0	ENST00000357731.5:c.152G>A	p.Arg51Lys	p.R51K	ENST00000357731	NM_173808.2	51	aGa/aAa	1/7	1	2	FACETS	0.615	0.511	0.731	0.615	0.511	0.731	SUBCLONAL	1	TRUE	1	0.21	2		598	635	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166001	118166001	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147179158	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	33	540	0	ENST00000369448.3:c.511G>A	p.Asp171Asn	p.D171N	ENST00000369448	NM_017709.3	171	Gac/Aac	2/2	1	2	FACETS	0.604	0.491	0.732	0.604	0.491	0.732	SUBCLONAL	1	TRUE	1	0.21	2		540	520	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480581	120480581	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	41	582	0	ENST00000256646.2:c.3236T>C	p.Val1079Ala	p.V1079A	ENST00000256646	NM_024408.3	1079	gTt/gCt	20/34	1	2	FACETS	0.727	0.605	0.863	0.727	0.605	0.863	SUBCLONAL	1	TRUE	1	0.21	2		582	537	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491669	120491669	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	40	352	0	ENST00000256646.2:c.2560T>G	p.Phe854Val	p.F854V	ENST00000256646	NM_024408.3	854	Ttt/Gtt	16/34	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.21	2		352	329	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156836757	156836757	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	45	584	0	ENST00000524377.1:c.415T>C	p.Ser139Pro	p.S139P	ENST00000524377	NM_002529.3	139	Tcc/Ccc	4/17	1	2	FACETS	0.672	0.563	0.792	0.672	0.563	0.792	SUBCLONAL	1	TRUE	1	0.21	2		584	638	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837936	156837936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141629165	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	46	694	1	ENST00000524377.1:c.469C>T	p.Arg157Cys	p.R157C	ENST00000524377	NM_002529.3	157	Cgc/Tgc	5/17	1	2	FACETS	0.662	0.556	0.779	0.662	0.556	0.779	SUBCLONAL	1	TRUE	1	0.21	2		695	662	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091397	193091397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	31	411	0	ENST00000367435.3:c.67G>A	p.Asp23Asn	p.D23N	ENST00000367435	NM_024529.4	23	Gac/Aac	1/17	1	2	FACETS	0.674	0.545	0.821	0.674	0.545	0.821	SUBCLONAL	1	TRUE	1	0.21	2		411	438	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716094	243716094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	47	596	0	ENST00000263826.5:c.1100G>A	p.Arg367Gln	p.R367Q	ENST00000263826	NM_005465.4	367	cGa/cAa	10/13	1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	1	0.21	2		596	446	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852557	63852557	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	39	557	0	ENST00000279873.7:c.3335T>G	p.Leu1112Arg	p.L1112R	ENST00000279873	NM_032199.2	1112	cTt/cGt	10/10	1	2	FACETS	0.75	0.622	0.894	0.75	0.622	0.894	SUBCLONAL	1	TRUE	1	0.21	2		557	495	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70411605	70411605	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs868611128	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	21	348	0	ENST00000373644.4:c.4279C>T	p.Arg1427Ter	p.R1427*	ENST00000373644	NM_030625.2	1427	Cga/Tga	5/12	1	2	FACETS	0.635	0.489	0.805	0.635	0.489	0.805	SUBCLONAL	1	TRUE	1	0.21	2		348	315	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625317	69625317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554980341	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	57	658	0	ENST00000334134.2:c.476G>A	p.Gly159Asp	p.G159D	ENST00000334134	NM_005247.2	159	gGc/gAc	3/3	1	2	FACETS	0.959	0.823	1	0.959	0.823	1	CLONAL	1	TRUE	1	0.21	2		658	566	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922251	100922251	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	28	454	0	ENST00000325455.5:c.2261C>A	p.Ser754Tyr	p.S754Y	ENST00000325455	NM_001202474.3	754	tCt/tAt	5/8	1	2	FACETS	0.852	0.682	1	0.852	0.682	1	CLONAL	1	TRUE	1	0.21	2		454	313	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922264	100922264	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	25	419	0	ENST00000325455.5:c.2248C>T	p.Leu750Phe	p.L750F	ENST00000325455	NM_001202474.3	750	Ctc/Ttc	5/8	1	2	FACETS	0.81	0.639	1	0.81	0.639	1	CLONAL	1	TRUE	1	0.21	2		419	294	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115600	108115600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772821016	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	43	593	1	ENST00000278616.4:c.748C>T	p.Arg250Ter	p.R250*	ENST00000278616	NM_000051.3	250	Cga/Tga	7/63	1	2	FACETS	0.996	0.835	1	0.996	0.835	1	CLONAL	1	TRUE	1	0.21	2		594	411	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203493	108203493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140263969	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	25	299	0	ENST00000278616.4:c.7793G>A	p.Arg2598Gln	p.R2598Q	ENST00000278616	NM_000051.3	2598	cGa/cAa	53/63	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.21	2		299	181	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111958593	111958593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555186772	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	61	570	0	ENST00000375549.3:c.65G>A	p.Arg22Gln	p.R22Q	ENST00000375549	NM_003002.3	22	cGa/cAa	2/4	1	2	FACETS	0.954	0.823	1	0.954	0.823	1	CLONAL	1	TRUE	1	0.21	2		570	609	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118368660	118368660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555044474	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	38	415	0	ENST00000534358.1:c.5674C>T	p.Arg1892Cys	p.R1892C	ENST00000534358	NM_005933.3	1892	Cgt/Tgt	21/36	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.21	2		415	324	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373428	118373428	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	36	435	0	ENST00000534358.1:c.6821T>C	p.Val2274Ala	p.V2274A	ENST00000534358	NM_005933.3	2274	gTt/gCt	27/36	1	2	FACETS	0.917	0.755	1	0.917	0.755	1	CLONAL	1	TRUE	1	0.21	2		435	374	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863433	57863433	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149817893	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	31	593	0	ENST00000228682.2:c.1528C>T	p.Arg510Trp	p.R510W	ENST00000228682	NM_005269.2	510	Cgg/Tgg	11/12	1	2	FACETS	0.508	0.41	0.62	0.508	0.41	0.62	SUBCLONAL	1	TRUE	1	0.21	2		593	581	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864202	57864202	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780728258	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	36	560	0	ENST00000228682.2:c.1679C>T	p.Ser560Phe	p.S560F	ENST00000228682	NM_005269.2	560	tCc/tTc	12/12	1	2	FACETS	0.694	0.57	0.833	0.694	0.57	0.833	SUBCLONAL	1	TRUE	1	0.21	2		560	494	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120717	115120717	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	38	623	1	ENST00000257566.3:c.289G>T	p.Glu97Ter	p.E97*	ENST00000257566	NM_016569.3	97	Gaa/Taa	1/8	1	2	FACETS	0.629	0.519	0.753	0.629	0.519	0.753	SUBCLONAL	1	TRUE	1	0.21	2		624	575	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226360	133226360	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201738371	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	47	660	0	ENST00000320574.5:c.3698G>A	p.Arg1233Gln	p.R1233Q	ENST00000320574	NM_006231.2	1233	cGa/cAa	30/49	1	2	FACETS	0.641	0.54	0.754	0.641	0.54	0.754	SUBCLONAL	1	TRUE	1	0.21	2		660	698	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	26	479	0	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	1	2	FACETS	0.628	0.497	0.779	0.628	0.497	0.779	SUBCLONAL	1	TRUE	1	0.21	2		479	394	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256623	133256623	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555230189	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	20	493	0	ENST00000320574.5:c.340C>T	p.Arg114Ter	p.R114*	ENST00000320574	NM_006231.2	114	Cga/Tga	5/49	1	2	FACETS	0.508	0.388	0.649	0.508	0.388	0.649	SUBCLONAL	1	TRUE	1	0.21	2		493	375	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578253	28578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	59	550	0	ENST00000241453.7:c.2918G>T	p.Arg973Leu	p.R973L	ENST00000241453	NM_004119.2	973	cGa/cTa	24/24	1	2	FACETS	0.892	0.767	1	0.892	0.767	1	CLONAL	1	TRUE	1	0.21	2		550	630	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589808	28589808	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568745490	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	37	493	0	ENST00000241453.7:c.2572G>A	p.Glu858Lys	p.E858K	ENST00000241453	NM_004119.2	858	Gaa/Aaa	21/24	1	2	FACETS	0.92	0.76	1	0.92	0.76	1	CLONAL	1	TRUE	1	0.21	2		493	383	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893667	28893667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753623232	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	25	387	0	ENST00000282397.4:c.3179G>A	p.Arg1060Gln	p.R1060Q	ENST00000282397	NM_002019.4	1060	cGa/cAa	24/30	1	2	FACETS	0.589	0.464	0.734	0.589	0.464	0.734	SUBCLONAL	1	TRUE	1	0.21	2		387	404	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913823	32913823	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	41	466	0	ENST00000380152.3:c.5331G>T	p.Lys1777Asn	p.K1777N	ENST00000380152		1777	aaG/aaT	11/27	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.21	2		466	314	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936691	32936691	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	27	470	0	ENST00000380152.3:c.7837A>C	p.Lys2613Gln	p.K2613Q	ENST00000380152		2613	Aag/Cag	17/27	1	2	FACETS	0.671	0.534	0.828	0.671	0.534	0.828	SUBCLONAL	1	TRUE	1	0.21	2		470	383	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134998	41134998	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	19	331	0	ENST00000379561.5:c.631-1G>T		p.X211_splice	ENST00000379561	NM_002015.3	211			1	2	FACETS	0.704	0.535	0.902	0.704	0.535	0.902	CLONAL	1	TRUE	1	0.21	2		331	257	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515141	103515141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770246574	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	32	364	1	ENST00000355739.4:c.1642G>A	p.Glu548Lys	p.E548K	ENST00000355739	NM_000123.3	548	Gaa/Aaa	8/15	1	2	FACETS	0.958	0.78	1	0.958	0.78	1	CLONAL	1	TRUE	1	0.21	2		365	318	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515302	103515302	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	30	373	0	ENST00000355739.4:c.1803A>C	p.Glu601Asp	p.E601D	ENST00000355739	NM_000123.3	601	gaA/gaC	8/15	1	2	FACETS	0.925	0.747	1	0.925	0.747	1	CLONAL	1	TRUE	1	0.21	2		373	309	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093456	30093456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1008608681	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	34	432	0	ENST00000331968.5:c.1807C>T	p.Arg603Cys	p.R603C	ENST00000331968	NM_002742.2	603	Cgt/Tgt	13/18	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.21	2		432	309	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987100	36987100	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	45	551	1	ENST00000354822.5:c.589C>T	p.Leu197Phe	p.L197F	ENST00000354822	NM_001079668.2	197	Ctc/Ttc	3/3	1	2	FACETS	0.797	0.669	0.938	0.797	0.669	0.938	CLONAL	1	TRUE	1	0.21	2		552	538	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572489	95572489	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	34	460	0	ENST00000393063.1:c.2876A>C	p.Lys959Thr	p.K959T	ENST00000393063	NM_030621.3	959	aAa/aCa	19/28	1	2	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	TRUE	1	0.21	2		460	308	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95596406	95596406	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	30	357	0	ENST00000393063.1:c.562G>T	p.Glu188Ter	p.E188*	ENST00000393063	NM_030621.3	188	Gaa/Taa	6/28	1	2	FACETS	1	0.835	1	1	0.835	1	CLONAL	1	TRUE	1	0.21	2		357	276	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070635	67070635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753519175	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	22	230	0	ENST00000412916.2:c.259G>A	p.Asp87Asn	p.D87N	ENST00000412916		87	Gac/Aac	3/6	1	2	FACETS	0.68	0.527	0.858	0.68	0.527	0.858	SUBCLONAL	1	TRUE	1	0.21	2		230	308	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993411	72993411	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	42	729	0	ENST00000268489.5:c.634G>A	p.Asp212Asn	p.D212N	ENST00000268489	NM_006885.3	212	Gac/Aac	2/10	1	2	FACETS	0.605	0.504	0.718	0.605	0.504	0.718	SUBCLONAL	1	TRUE	1	0.21	2		729	661	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946288	81946288	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	49	591	1	ENST00000359376.3:c.2021G>A	p.Arg674Gln	p.R674Q	ENST00000359376	NM_002661.3	674	cGa/cAa	19/33	1	2	FACETS	0.788	0.667	0.922	0.788	0.667	0.922	CLONAL	1	TRUE	1	0.21	2		592	592	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953114	81953114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764736362	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	27	358	0	ENST00000359376.3:c.2080C>T	p.Arg694Cys	p.R694C	ENST00000359376	NM_002661.3	694	Cgc/Tgc	20/33	1	2	FACETS	0.606	0.482	0.749	0.606	0.482	0.749	SUBCLONAL	1	TRUE	1	0.21	2		358	424	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813297	89813297	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	32	476	0	ENST00000389301.3:c.3350G>T	p.Arg1117Ile	p.R1117I	ENST00000389301	NM_000135.2	1117	aGa/aTa	34/43	1	2	FACETS	0.646	0.523	0.784	0.646	0.523	0.784	SUBCLONAL	1	TRUE	1	0.21	2		476	472	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434943	56434943	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775335997	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	70	628	1	ENST00000407977.2:c.2194C>T	p.Arg732Cys	p.R732C	ENST00000407977		732	Cgc/Tgc	9/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.21	2		629	581	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821942	59821942	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	43	397	0	ENST00000259008.2:c.2108A>C	p.Lys703Thr	p.K703T	ENST00000259008	NM_032043.2	703	aAa/aCa	15/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.21	2		397	300	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63537626	63537626	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	38	623	0	ENST00000307078.5:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000307078	NM_004655.3	336	Gaa/Taa	4/11	1	2	FACETS	0.659	0.544	0.788	0.659	0.544	0.788	SUBCLONAL	1	TRUE	1	0.21	2		623	549	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39570468	39570468	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs267605182	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	18	351	0	ENST00000262039.4:c.664C>T	p.Arg222Ter	p.R222*	ENST00000262039	NM_002647.2	222	Cga/Tga	6/25	1	2	FACETS	0.749	0.565	0.965	0.749	0.565	0.965	CLONAL	1	TRUE	1	0.21	2		351	229	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39623696	39623696	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	18	328	0	ENST00000262039.4:c.2104-1G>T		p.X702_splice	ENST00000262039	NM_002647.2	702			1	2	FACETS	0.755	0.57	0.973	0.755	0.57	0.973	CLONAL	1	TRUE	1	0.21	2		328	227	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267653	7267653	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs929761465	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	46	685	0	ENST00000302850.5:c.355G>A	p.Ala119Thr	p.A119T	ENST00000302850	NM_000208.2	119	Gcg/Acg	2/22	1	2	FACETS	0.586	0.492	0.691	0.586	0.492	0.691	SUBCLONAL	1	TRUE	1	0.21	2		685	747	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295174	15295174	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	52	827	0	ENST00000263388.2:c.2498T>G	p.Phe833Cys	p.F833C	ENST00000263388	NM_000435.2	833	tTc/tGc	16/33	1	2	FACETS	0.74	0.629	0.862	0.74	0.629	0.862	SUBCLONAL	1	TRUE	1	0.21	2		827	669	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940461	29940461	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	21	345	0	ENST00000389048.3:c.770C>A	p.Ser257Tyr	p.S257Y	ENST00000389048	NM_004304.4	257	tCt/tAt	2/29	1	2	FACETS	0.704	0.543	0.892	0.704	0.543	0.892	SUBCLONAL	1	TRUE	1	0.21	2		345	284	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635547	47635547	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	41	368	2	ENST00000233146.2:c.219G>T	p.Lys73Asn	p.K73N	ENST00000233146	NM_000251.2	73	aaG/aaT	2/16	1	2	FACETS	0.974	0.812	1	0.974	0.812	1	CLONAL	1	TRUE	1	0.21	2		370	401	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703539	47703539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1203462814	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	48	604	0	ENST00000233146.2:c.2039G>A	p.Arg680Gln	p.R680Q	ENST00000233146	NM_000251.2	680	cGa/cAa	13/16	1	2	FACETS	0.872	0.737	1	0.872	0.737	1	CLONAL	1	TRUE	1	0.21	2		604	524	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026224	48026224	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	22	423	0	ENST00000234420.5:c.1102G>T	p.Glu368Ter	p.E368*	ENST00000234420	NM_000179.2	368	Gaa/Taa	4/10	1	2	FACETS	0.568	0.44	0.717	0.568	0.44	0.717	SUBCLONAL	1	TRUE	1	0.21	2		423	369	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61711210	61711210	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	35	446	0	ENST00000401558.2:c.2539A>C	p.Asn847His	p.N847H	ENST00000401558	NM_003400.3	847	Aac/Cac	21/25	1	2	FACETS	0.903	0.741	1	0.903	0.741	1	CLONAL	1	TRUE	1	0.21	2		446	369	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038130	128038130	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	32	504	0	ENST00000285398.2:c.1420G>T	p.Asp474Tyr	p.D474Y	ENST00000285398	NM_000122.1	474	Gat/Tat	9/15	1	2	FACETS	0.538	0.436	0.655	0.538	0.436	0.655	SUBCLONAL	1	TRUE	1	0.21	2		504	566	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044527	128044527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772229792	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	42	566	1	ENST00000285398.2:c.1094G>A	p.Gly365Asp	p.G365D	ENST00000285398	NM_000122.1	365	gGc/gAc	8/15	1	2	FACETS	0.758	0.632	0.897	0.758	0.632	0.897	SUBCLONAL	1	TRUE	1	0.21	2		567	528	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190742103	190742103	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	21	505	0	ENST00000441310.2:c.2740G>T	p.Glu914Ter	p.E914*	ENST00000441310	NM_000534.4	914	Gag/Tag	13/13	1	2	FACETS	0.514	0.395	0.653	0.514	0.395	0.653	SUBCLONAL	1	TRUE	1	0.21	2		505	389	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295755	212295755	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	43	620	0	ENST00000342788.4:c.2558C>A	p.Ser853Tyr	p.S853Y	ENST00000342788	NM_005235.2	853	tCt/tAt	21/28	1	2	FACETS	0.961	0.805	1	0.961	0.805	1	CLONAL	1	TRUE	1	0.21	2		620	426	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646149	215646149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881412	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	42	567	0	ENST00000260947.4:c.449G>A	p.Arg150Gln	p.R150Q	ENST00000260947	NM_000465.2	150	cGa/cAa	4/11	1	2	FACETS	0.84	0.702	0.994	0.84	0.702	0.994	CLONAL	1	TRUE	1	0.21	2		567	476	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376235	225376235	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	26	530	0	ENST00000264414.4:c.719G>T	p.Arg240Ile	p.R240I	ENST00000264414	NM_003590.4	240	aGa/aTa	6/16	1	2	FACETS	0.561	0.444	0.697	0.561	0.444	0.697	SUBCLONAL	1	TRUE	1	0.21	2		530	441	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39690084	39690084	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	21	289	0	ENST00000361337.2:c.109G>T	p.Glu37Ter	p.E37*	ENST00000361337	NM_003286.2	37	Gaa/Taa	3/21	1	2	FACETS	0.625	0.481	0.793	0.625	0.481	0.793	SUBCLONAL	1	TRUE	1	0.21	2		289	320	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39745020	39745020	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	29	560	0	ENST00000361337.2:c.1810G>A	p.Glu604Lys	p.E604K	ENST00000361337	NM_003286.2	604	Gaa/Aaa	17/21	1	2	FACETS	0.508	0.406	0.623	0.508	0.406	0.623	SUBCLONAL	1	TRUE	1	0.21	2		560	544	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770576	40770576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	38	547	0	ENST00000373198.4:c.2806C>T	p.Arg936Ter	p.R936*	ENST00000373198	NM_133170.3	936	Cga/Tga	19/32	1	2	FACETS	0.731	0.604	0.873	0.731	0.604	0.873	SUBCLONAL	1	TRUE	1	0.21	2		547	495	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466870	57466870	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	14	230	0	ENST00000371085.3:c.89T>G	p.Leu30Arg	p.L30R	ENST00000371085	NM_000516.4	30	cTg/cGg	1/13	1	2	FACETS	0.519	0.375	0.693	0.519	0.375	0.693	SUBCLONAL	1	TRUE	1	0.21	2		230	257	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268766	41268766	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	29	508	0	ENST00000349496.5:c.1004A>C	p.Lys335Thr	p.K335T	ENST00000349496	NM_001904.3	335	aAa/aCa	7/15	1	2	FACETS	0.696	0.558	0.852	0.696	0.558	0.852	SUBCLONAL	1	TRUE	1	0.21	2		508	397	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014076	70014076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759306986	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	43	545	1	ENST00000394351.3:c.937C>T	p.Arg313Trp	p.R313W	ENST00000394351	NM_000248.3	313	Cgg/Tgg	9/9	1	2	FACETS	0.767	0.641	0.906	0.767	0.641	0.906	CLONAL	1	TRUE	1	0.21	2		546	534	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457278	89457278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	48	470	0	ENST00000336596.2:c.1759C>T	p.His587Tyr	p.H587Y	ENST00000336596	NM_005233.5	587	Cat/Tat	9/17	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.21	2		470	378	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468357	89468357	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	11	213	0	ENST00000336596.2:c.1891G>T	p.Glu631Ter	p.E631*	ENST00000336596	NM_005233.5	631	Gaa/Taa	11/17	1	2	FACETS	0.526	0.364	0.728	0.526	0.364	0.728	SUBCLONAL	1	TRUE	1	0.21	2		213	199	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480466	89480466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446890859	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	22	422	0	ENST00000336596.2:c.2303C>T	p.Ser768Leu	p.S768L	ENST00000336596	NM_005233.5	768	tCg/tTg	13/17	1	2	FACETS	0.536	0.415	0.677	0.536	0.415	0.677	SUBCLONAL	1	TRUE	1	0.21	2		422	391	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453486	138453486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451809865	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	35	406	0	ENST00000289153.2:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000289153	NM_006219.2	321	cGa/cAa	5/22	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.21	2		406	313	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178199	142178199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746049210	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	20	357	0	ENST00000350721.4:c.7219C>T	p.Arg2407Cys	p.R2407C	ENST00000350721	NM_001184.3	2407	Cgc/Tgc	43/47	1	2	FACETS	0.777	0.596	0.989	0.777	0.596	0.989	CLONAL	1	TRUE	1	0.21	2		357	245	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281186	142281186	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	40	442	0	ENST00000350721.4:c.1058T>C	p.Phe353Ser	p.F353S	ENST00000350721	NM_001184.3	353	tTc/tCc	4/47	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.21	2		442	344	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149243898	149243898	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767747431	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	31	550	0	ENST00000360632.3:c.920C>T	p.Ser307Leu	p.S307L	ENST00000360632	NM_015472.4	307	tCg/tTg	6/7	1	2	FACETS	0.534	0.431	0.651	0.534	0.431	0.651	SUBCLONAL	1	TRUE	1	0.21	2		550	553	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181377	185181377	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	29	345	0	ENST00000265026.3:c.1318A>G	p.Ile440Val	p.I440V	ENST00000265026	NM_004721.4	440	Atc/Gtc	8/14	1	2	FACETS	0.787	0.632	0.963	0.787	0.632	0.963	CLONAL	1	TRUE	1	0.21	2		345	351	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356406	66356406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	34	421	1	ENST00000273854.3:c.1091C>T	p.Ala364Val	p.A364V	ENST00000273854	NM_004439.5	364	gCc/gTc	5/18	1	2	FACETS	0.912	0.747	1	0.912	0.747	1	CLONAL	1	TRUE	1	0.21	2		422	355	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143029297	143029297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757219824	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	34	375	0	ENST00000262992.4:c.2323G>A	p.Glu775Lys	p.E775K	ENST00000262992	NM_001101669.1	775	Gaa/Aaa	21/24	1	2	FACETS	0.925	0.757	1	0.925	0.757	1	CLONAL	1	TRUE	1	0.21	2		375	350	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143352352	143352352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150489920	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	37	665	0	ENST00000262992.4:c.61G>A	p.Ala21Thr	p.A21T	ENST00000262992	NM_001101669.1	21	Gcc/Acc	2/24	1	2	FACETS	0.669	0.551	0.801	0.669	0.551	0.801	SUBCLONAL	1	TRUE	1	0.21	2		665	527	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	43	522	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	0.71	0.593	0.839	0.71	0.593	0.839	SUBCLONAL	1	TRUE	1	0.21	2		522	577	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539951	187539951	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs777631605	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	40	477	0	ENST00000441802.2:c.7789C>T	p.Arg2597Ter	p.R2597*	ENST00000441802	NM_005245.3	2597	Cga/Tga	10/27	1	2	FACETS	0.872	0.725	1	0.872	0.725	1	CLONAL	1	TRUE	1	0.21	2		477	437	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449442	31449442	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766022493	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	45	587	0	ENST00000344624.3:c.2767C>T	p.Arg923Trp	p.R923W	ENST00000344624		923	Cgg/Tgg	19/33	1	2	FACETS	0.8	0.672	0.941	0.8	0.672	0.941	CLONAL	1	TRUE	1	0.21	2		587	536	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950689	38950689	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	23	405	0	ENST00000357387.3:c.3261C>A	p.Phe1087Leu	p.F1087L	ENST00000357387	NM_152756.3	1087	ttC/ttA	31/38	1	2	FACETS	0.846	0.661	1	0.846	0.661	1	CLONAL	1	TRUE	1	0.21	2		405	259	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961018	79961018	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	51	560	0	ENST00000265081.6:c.415G>T	p.Glu139Ter	p.E139*	ENST00000265081	NM_002439.4	139	Gaa/Taa	3/24	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.21	2		560	431	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064749	80064749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148896355	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	28	494	0	ENST00000265081.6:c.2180G>A	p.Arg727Gln	p.R727Q	ENST00000265081	NM_002439.4	727	cGa/cAa	15/24	1	2	FACETS	0.771	0.616	0.946	0.771	0.616	0.946	CLONAL	1	TRUE	1	0.21	2		494	346	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670680	86670680	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	14	322	0	ENST00000274376.6:c.1958G>T	p.Arg653Ile	p.R653I	ENST00000274376	NM_002890.2	653	aGa/aTa	15/25	1	2	FACETS	0.481	0.347	0.644	0.481	0.347	0.644	SUBCLONAL	1	TRUE	1	0.21	2		322	277	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670721	86670721	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	12	233	0	ENST00000274376.6:c.1999G>T	p.Asp667Tyr	p.D667Y	ENST00000274376	NM_002890.2	667	Gat/Tat	15/25	1	2	FACETS	0.628	0.442	0.856	0.628	0.442	0.856	SUBCLONAL	1	TRUE	1	0.21	2		233	182	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045858	26045858	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs774188493	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	44	503	0	ENST00000540144.1:c.220G>T	p.Glu74Ter	p.E74*	ENST00000540144	NM_003531.2	74	Gaa/Taa	1/1	1	2	FACETS	0.993	0.834	1	0.993	0.834	1	CLONAL	1	TRUE	1	0.21	2		503	422	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673064	30673064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144657716	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	46	699	1	ENST00000376406.3:c.3896G>A	p.Arg1299Gln	p.R1299Q	ENST00000376406	NM_014641.2	1299	cGa/cAa	10/15	1	2	FACETS	0.687	0.577	0.808	0.687	0.577	0.808	SUBCLONAL	1	TRUE	1	0.21	2		700	638	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288366	33288366	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs758422357	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	23	446	0	ENST00000374542.5:c.1042G>A	p.Val348Ile	p.V348I	ENST00000374542	NM_001141970.1	348	Gtt/Att	4/8	1	2	FACETS	0.64	0.499	0.804	0.64	0.499	0.804	SUBCLONAL	1	TRUE	1	0.21	2		446	342	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93973581	93973581	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	32	371	0	ENST00000369303.4:c.1795C>A	p.His599Asn	p.H599N	ENST00000369303	NM_004440.3	599	Cat/Aat	9/17	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.21	2		371	290	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109314067	109314067	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs557313505	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	25	566	0	ENST00000436639.2:c.1156C>T	p.Arg386Cys	p.R386C	ENST00000436639	NM_014454.2	386	Cgt/Tgt	7/10	1	2	FACETS	0.601	0.473	0.749	0.601	0.473	0.749	SUBCLONAL	1	TRUE	1	0.21	2		566	396	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983108	111983108	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	35	503	1	ENST00000368678.4:c.1439A>G	p.Tyr480Cys	p.Y480C	ENST00000368678		480	tAc/tGc	13/13	1	2	FACETS	0.756	0.619	0.909	0.756	0.619	0.909	CLONAL	1	TRUE	1	0.21	2		504	441	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674297	117674297	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	48	598	0	ENST00000368508.3:c.4177G>T	p.Asp1393Tyr	p.D1393Y	ENST00000368508	NM_002944.2	1393	Gat/Tat	26/43	1	2	FACETS	0.992	0.839	1	0.992	0.839	1	CLONAL	1	TRUE	1	0.21	2		598	461	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265323	152265323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866869178	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	18	346	0	ENST00000206249.3:c.776G>A	p.Arg259Gln	p.R259Q	ENST00000206249	NM_000125.3	259	cGa/cAa	4/8	1	2	FACETS	0.546	0.411	0.706	0.546	0.411	0.706	SUBCLONAL	1	TRUE	1	0.21	2		346	314	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148526850	148526850	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	49	500	0	ENST00000320356.2:c.454A>C	p.Asn152His	p.N152H	ENST00000320356	NM_004456.4	152	Aat/Cat	5/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.21	2		500	324	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860908	151860908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	55	451	2	ENST00000262189.6:c.9754C>T	p.Arg3252Cys	p.R3252C	ENST00000262189	NM_170606.2	3252	Cgt/Tgt	43/59	1	2	FACETS	0.761	0.654	0.877	1	0.968	1	SUBCLONAL	2	TRUE	1	0.21	2		453	344	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031690	69031690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371787029	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	43	548	0	ENST00000288368.4:c.3445C>T	p.Arg1149Cys	p.R1149C	ENST00000288368	NM_024870.2	1149	Cgc/Tgc	28/40	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.21	2		548	384	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70967540	70967540	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	48	553	0	ENST00000276594.2:c.1483A>G	p.Thr495Ala	p.T495A	ENST00000276594	NM_024504.3	495	Act/Gct	7/8	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.21	2		553	421	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70971059	70971059	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	55	656	0	ENST00000276594.2:c.1202G>T	p.Arg401Ile	p.R401I	ENST00000276594	NM_024504.3	401	aGa/aTa	6/8	1	2	FACETS	0.822	0.703	0.953	0.822	0.703	0.953	CLONAL	1	TRUE	1	0.21	2		656	637	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069038	5069038	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	18	293	0	ENST00000381652.3:c.1343A>C	p.Glu448Ala	p.E448A	ENST00000381652	NM_004972.3	448	gAa/gCa	11/25	1	2	FACETS	0.861	0.651	1	0.861	0.651	1	CLONAL	1	TRUE	1	0.21	2		293	199	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636794	8636794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	35	514	0	ENST00000356435.5:c.115G>A	p.Gly39Arg	p.G39R	ENST00000356435		39	Gga/Aga	2/35	1	2	FACETS	0.661	0.541	0.796	0.661	0.541	0.796	SUBCLONAL	1	TRUE	1	0.21	2		514	504	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36846873	36846873	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749063137	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	33	461	1	ENST00000358127.4:c.1066G>A	p.Asp356Asn	p.D356N	ENST00000358127	NM_001280556.1	356	Gac/Aac	9/10	1	2	FACETS	0.697	0.567	0.843	0.697	0.567	0.843	SUBCLONAL	1	TRUE	1	0.21	2		462	451	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98009789	98009789	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	40	359	0	ENST00000289081.3:c.175A>G	p.Thr59Ala	p.T59A	ENST00000289081	NM_000136.2	59	Aca/Gca	3/15	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.21	2		359	279	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231389	98231389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559293815	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	57	650	0	ENST00000331920.6:c.1894G>A	p.Asp632Asn	p.D632N	ENST00000331920	NM_000264.3	632	Gac/Aac	14/24	1	2	FACETS	0.869	0.745	1	0.869	0.745	1	CLONAL	1	TRUE	1	0.21	2		650	625	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242854	98242854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs925067209	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	35	420	2	ENST00000331920.6:c.763C>T	p.Arg255Trp	p.R255W	ENST00000331920	NM_000264.3	255	Cgg/Tgg	6/24	1	2	FACETS	0.866	0.71	1	0.866	0.71	1	CLONAL	1	TRUE	1	0.21	2		422	385	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933085	39933085	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	52	765	0	ENST00000378444.4:c.1514C>A	p.Ala505Asp	p.A505D	ENST00000378444	NM_001123385.1	505	gCt/gAt	4/15	1	2	FACETS	0.675	0.573	0.787	0.675	0.573	0.787	SUBCLONAL	1	TRUE	1	0.21	2		765	734	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426731	47426731	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1452639448	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	44	670	0	ENST00000377045.4:c.976C>T	p.Arg326Ter	p.R326*	ENST00000377045	NM_001654.4	326	Cga/Tga	10/16	1	2	FACETS	0.637	0.533	0.752	0.637	0.533	0.752	SUBCLONAL	1	TRUE	1	0.21	2		670	658	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340905	70340905	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	51	601	0	ENST00000374080.3:c.638G>A	p.Gly213Glu	p.G213E	ENST00000374080		213	gGg/gAg	5/45	1	2	FACETS	0.752	0.638	0.877	0.752	0.638	0.877	SUBCLONAL	1	TRUE	1	0.21	2		601	646	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344662	70344662	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	58	655	0	ENST00000374080.3:c.2023C>A	p.Leu675Ile	p.L675I	ENST00000374080		675	Ctc/Atc	14/45	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.21	2		655	538	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348535	70348535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	46	661	0	ENST00000374080.3:c.3442C>T	p.Arg1148Cys	p.R1148C	ENST00000374080		1148	Cgc/Tgc	24/45	1	2	FACETS	0.704	0.592	0.829	0.704	0.592	0.829	SUBCLONAL	1	TRUE	1	0.21	2		661	622	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352988	70352988	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	35	634	2	ENST00000374080.3:c.4543C>T	p.Arg1515Ter	p.R1515*	ENST00000374080		1515	Cga/Tga	33/45	1	2	FACETS	0.663	0.542	0.798	0.663	0.542	0.798	SUBCLONAL	1	TRUE	1	0.21	2		636	503	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778843	76778843	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	42	650	1	ENST00000373344.5:c.6736G>T	p.Glu2246Ter	p.E2246*	ENST00000373344	NM_000489.3	2246	Gaa/Taa	31/35	1	2	FACETS	0.913	0.763	1	0.913	0.763	1	CLONAL	1	TRUE	1	0.21	2		651	438	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76919037	76919038	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	18	358	0	ENST00000373344.5:c.3953dup	p.Asn1318LysfsTer6	p.N1318Kfs*6	ENST00000373344	NM_000489.3	1318	aat/aaAt	12/35	1	2	FACETS	0.557	0.419	0.72	0.557	0.419	0.72	SUBCLONAL	1	TRUE	1	0.21	2		358	308	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938218	76938218	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs142601264	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	52	743	0	ENST00000373344.5:c.2530A>G	p.Thr844Ala	p.T844A	ENST00000373344	NM_000489.3	844	Aca/Gca	9/35	1	2	FACETS	0.861	0.733	1	0.861	0.733	1	CLONAL	1	TRUE	1	0.21	2		743	575	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938325	76938325	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782181535	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	29	713	0	ENST00000373344.5:c.2423G>A	p.Arg808Gln	p.R808Q	ENST00000373344	NM_000489.3	808	cGa/cAa	9/35	1	2	FACETS	0.499	0.4	0.613	0.499	0.4	0.613	SUBCLONAL	1	TRUE	1	0.21	2		713	553	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215312	123215312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1214610561	NA	P-0032548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	44	600	0	ENST00000218089.9:c.2858G>A	p.Arg953Gln	p.R953Q	ENST00000218089	NM_001042749.1	953	cGa/cAa	28/35	1	2	FACETS	0.84	0.704	0.99	0.84	0.704	0.99	CLONAL	1	TRUE	1	0.21	2		600	499	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	97	258	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.67	2		258	289	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0032549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	81	319	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.822	0.733	0.917	0.822	0.733	0.917	CLONAL	1	TRUE	1	0.67	2		319	294	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0032550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	41	314	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.225362942722849	3	FACETS	0.799	0.665	0.947	0.399	0.332	0.474	CLONAL	1	FALSE	1	0.225362942722849	3		314	507	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38957801	38957801	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	54	371	0	ENST00000357387.3:c.2452C>G	p.Leu818Val	p.L818V	ENST00000357387	NM_152756.3	818	Ctg/Gtg	25/38	1	2	FACETS	0.966	0.826	1	0.966	0.826	1	CLONAL	1	FALSE	1	0.225362942722849	2		371	496	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056498	26056498	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	47	295	0	ENST00000343677.2:c.159G>T	p.Glu53Asp	p.E53D	ENST00000343677	NM_005319.3	53	gaG/gaT	1/1	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	FALSE	1	0.225362942722849	2		295	395	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150470	157150470	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	57	545	0	ENST00000346085.5:c.1652G>C	p.Gly551Ala	p.G551A	ENST00000346085	NM_020732.3	551	gGc/gCc	2/20	0.225362942722849	2	FACETS	0.918	0.788	1	0.459	0.394	0.53	CLONAL	1	FALSE	0	0.225362942722849	2		545	551	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	166	258	0				ENST00000310581	NM_198253.2	-/1132			0.886200769814817	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.886200769814817	1		258	206	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0032551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	501	659	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.886200769814817	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.886200769814817	1		659	607	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278159	41278160	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0032551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	47	502	0	ENST00000349496.5:c.2037dup	p.Ser680GlnfsTer13	p.S680Qfs*13	ENST00000349496	NM_001904.3	679	acc/aCcc	13/15	0.886200769814817	1	FACETS	0.141	0.118	0.165	0.141	0.118	0.165	SUBCLONAL	1	TRUE	0	0.886200769814817	1		502	420	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440371	52440387	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGATGTCGTGGTAGG	GCGGATGTCGTGGTAGG	-	novel	NA	P-0032551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	317	474	0	ENST00000460680.1:c.665_681del	p.Pro222LeufsTer15	p.P222Lfs*15	ENST00000460680	NM_004656.3	222	cCCTACCACGACATCCGC/c	9/17	0.886200769814817	1	FACETS	0.951	0.919	0.982	0.951	0.919	0.982	CLONAL	1	TRUE	0	0.886200769814817	1		474	419	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0032552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	103	314	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.896	0.805	0.991	0.896	0.805	0.991	CLONAL	1	TRUE	1	0.446648142614771	2		314	515	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382152	152382154	+	inframe_deletion	In_Frame_Del	DEL	TGG	TGG	-	novel	NA	P-0032552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	159	493	0	ENST00000206249.3:c.1265_1267del	p.Val422del	p.V422del	ENST00000206249	NM_000125.3	421	aTGGtg/atg	6/8	1	2	FACETS	0.936	0.859	1	0.936	0.859	1	CLONAL	1	TRUE	1	0.446648142614771	2		493	761	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160759	56160759	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	117	351	0	ENST00000399503.3:c.1033C>T	p.Gln345Ter	p.Q345*	ENST00000399503	NM_005921.1	345	Cag/Tag	4/20	1	2	FACETS	0.944	0.854	1	0.944	0.854	1	CLONAL	1	TRUE	1	0.446648142614771	2		351	555	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157119	106157119	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1352624446	NA	P-0032552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	196	467	2	ENST00000380013.4:c.2020C>T	p.Gln674Ter	p.Q674*	ENST00000380013	NM_001127208.2	674	Cag/Tag	3/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.446648142614771	2		469	847	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805369	32805369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	179	468	0	ENST00000374899.4:c.553G>A	p.Asp185Asn	p.D185N	ENST00000374899	NM_018833.2	185	Gac/Aac	3/12	1	2	FACETS	0.94	0.867	1	0.94	0.867	1	CLONAL	1	TRUE	1	0.446648142614771	2		468	853	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553529	29553536	+	frameshift_variant	Frame_Shift_Del	DEL	TGTTTCTG	TGTTTCTG	-	novel	NA	P-0032552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	73	380	0	ENST00000356175.3:c.2080_2087del	p.Phe694GlufsTer3	p.F694Efs*3	ENST00000356175	NM_000267.3	693	aTGTTTCTG/a	18/57	0.446648142614771	1	FACETS	0.532	0.467	0.603	0.532	0.467	0.603	SUBCLONAL	1	TRUE	0	0.446648142614771	1		380	477	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576084	29576085	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCTCCTC	novel	NA	P-0032552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	67	580	0	ENST00000356175.3:c.4058_4064dup	p.Glu1356LeufsTer20	p.E1356Lfs*20	ENST00000356175	NM_000267.3	1353	tcc/tCCTCCTCcc	30/57	0.446648142614771	1	FACETS	0.306	0.265	0.35	0.306	0.265	0.35	SUBCLONAL	1	TRUE	0	0.446648142614771	1		580	761	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619125	1619125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375278992	NA	P-0032552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	156	536	0	ENST00000344749.5:c.1435C>T	p.Pro479Ser	p.P479S	ENST00000344749	NM_001136139.2	479	Ccc/Tcc	16/19	1	2	FACETS	0.844	0.773	0.917	0.844	0.773	0.917	CLONAL	1	TRUE	1	0.446648142614771	2		536	828	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218360	36218360	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0032552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	227	713	0	ENST00000222270.7:c.4139C>G	p.Ser1380Ter	p.S1380*	ENST00000222270	NM_014727.1	1380	tCa/tGa	16/37	1	2	FACETS	0.88	0.819	0.943	0.88	0.819	0.943	CLONAL	1	TRUE	1	0.446648142614771	2		713	1155	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752659	128752659	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	68	235	0	ENST00000377970.2:c.820G>T	p.Glu274Ter	p.E274*	ENST00000377970	NM_002467.4	274	Gag/Tag	3/3	1	2	FACETS	0.735	0.642	0.835	0.735	0.642	0.835	SUBCLONAL	1	TRUE	1	0.446648142614771	2		235	414	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310909	123310929	+	inframe_deletion	In_Frame_Del	DEL	GTTGGCCGCAGGCACAGCATG	GTTGGCCGCAGGCACAGCATG	-	novel	NA	P-0032563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	287	670	2	ENST00000358487.5:c.499_519del	p.His167_Asn173del	p.H167_N173del	ENST00000358487	NM_000141.4	167	CATGCTGTGCCTGCGGCCAAC/-	5/18	0.400832545204404	2	FACETS	0.985	0.931	1	0.985	0.931	1	CLONAL	2	TRUE	0	0.400832545204404	2		672	727	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651531	52651531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	148	609	0	ENST00000394830.3:c.1565G>A	p.Arg522Gln	p.R522Q	ENST00000394830	NM_018313.4	522	cGa/cAa	15/30	0.400832545204404	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.400832545204404	1		609	580	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0032564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	21	322	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.333	0.255	0.424	0.333	0.255	0.424	SUBCLONAL	1	FALSE	1	0.25438916963378	2		322	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0032564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	43	711	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	1	2	FACETS	0.453	0.378	0.537	0.453	0.378	0.537	SUBCLONAL	1	FALSE	1	0.25438916963378	2		711	746	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753233	42753233	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377467874	NA	P-0032564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	53	849	0	ENST00000222329.4:c.1031G>A	p.Arg344His	p.R344H	ENST00000222329	NM_006494.2	344	cGc/cAc	4/4	1	2	FACETS	0.55	0.468	0.641	0.55	0.468	0.641	SUBCLONAL	1	FALSE	1	0.25438916963378	2		849	757	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711913	89711913	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0032565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	77	621	0	ENST00000371953.3:c.531T>A	p.Tyr177Ter	p.Y177*	ENST00000371953	NM_000314.4	177	taT/taA	6/9	0.361796535042685	1	FACETS	0.541	0.474	0.612	0.541	0.474	0.612	SUBCLONAL	1	TRUE	0	0.361796535042685	1		621	645	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864158	57864158	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	44	593	0	ENST00000228682.2:c.1635C>A	p.Ser545Arg	p.S545R	ENST00000228682	NM_005269.2	545	agC/agA	12/12	0.216726122872056	1	FACETS	0.248	0.207	0.294	0.248	0.207	0.294	INDETERMINATE	1	TRUE	0	0.361796535042685	1		593	803	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	75	801	0	ENST00000269305.4:c.455C>G	p.Pro152Arg	p.P152R	ENST00000269305	NM_001126112.2	152	cCg/cGg	5/11	0.21247390941098	1	FACETS	0.903	0.791	1	0.903	0.791	1	CLONAL	1	FALSE	0	0.21247390941098	1		801	699	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420493	49420493	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs727503979	NA	P-0032566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	77	622	0	ENST00000301067.7:c.15256C>T	p.Arg5086Ter	p.R5086*	ENST00000301067	NM_003482.3	5086	Cga/Tga	48/54	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.21247390941098	2		622	557	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934155	48934155	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	33	301	1	ENST00000267163.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000267163	NM_000321.2	204	Gaa/Taa	7/27	0.21247390941098	1	FACETS	0.731	0.595	0.883	0.731	0.595	0.883	SUBCLONAL	1	FALSE	0	0.21247390941098	1		302	380	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087480	27087480	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	75	666	0	ENST00000324856.7:c.2054C>G	p.Thr685Ser	p.T685S	ENST00000324856	NM_006015.4	685	aCc/aGc	5/20	1	2	FACETS	0.983	0.861	1	0.983	0.861	1	CLONAL	1	FALSE	1	0.21247390941098	2		666	718	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929126	32929126	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	67	426	0	ENST00000380152.3:c.7136G>C	p.Gly2379Ala	p.G2379A	ENST00000380152		2379	gGa/gCa	14/27	0.21247390941098	1	FACETS	0.959	0.833	1	0.959	0.833	1	CLONAL	1	FALSE	0	0.21247390941098	1		426	588	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371731	89371731	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	58	515	0	ENST00000301030.4:c.109A>T	p.Thr37Ser	p.T37S	ENST00000301030	NM_001256183.1	37	Acc/Tcc	4/13	0.21247390941098	1	FACETS	0.886	0.761	1	0.886	0.761	1	CLONAL	1	FALSE	0	0.21247390941098	1		515	551	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461563	138461563	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	90	475	0	ENST00000289153.2:c.458del	p.Arg153ProfsTer20	p.R153Pfs*20	ENST00000289153	NM_006219.2	153	cGc/cc	3/22	0.21247390941098	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	0	0.21247390941098	1		475	709	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55987285	55987285	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	51	469	0	ENST00000263923.4:c.140C>A	p.Thr47Lys	p.T47K	ENST00000263923	NM_002253.2	47	aCa/aAa	2/30	0.21247390941098	1	FACETS	0.733	0.623	0.855	0.733	0.623	0.855	SUBCLONAL	1	FALSE	0	0.21247390941098	1		469	585	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046328	180046328	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	63	503	0	ENST00000261937.6:c.2686del	p.Glu896SerfsTer30	p.E896Sfs*30	ENST00000261937	NM_182925.4	896	Gag/ag	19/30	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.21247390941098	2		503	473	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975390	13975390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	50	403	0	ENST00000405192.2:c.497C>T	p.Pro166Leu	p.P166L	ENST00000405192	NM_001163147.1	166	cCa/cTa	7/12	1	2	FACETS	0.762	0.645	0.89	0.762	0.645	0.89	SUBCLONAL	1	FALSE	1	0.21247390941098	2		403	618	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	357	258	0				ENST00000310581	NM_198253.2	-/1132			0.599985973273485	3	FACETS	0.949	0.92	0.976	0.949	0.92	0.976	CLONAL	3	TRUE	0	0.75199196988416	3		258	459	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797414	45797414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	475	866	0	ENST00000450313.1:c.1105G>A	p.Glu369Lys	p.E369K	ENST00000450313	NM_012222.2	369	Gag/Aag	12/16	0.605375797684329	3	FACETS	0.851	0.817	0.885	0.851	0.817	0.885	CLONAL	2	TRUE	1	0.75199196988416	3		866	1021	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0032586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	415	720	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.749049492190839	3	FACETS	0.831	0.795	0.867	0.831	0.795	0.867	CLONAL	2	TRUE	1	0.75199196988416	3		720	914	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276369	115276369	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	140	617	0	ENST00000438362.2:c.959T>A	p.Val320Glu	p.V320E	ENST00000438362	NM_001242891.1	320	gTa/gAa	9/20	0.749049492190839	3	FACETS	0.638	0.581	0.698	0.319	0.29	0.349	SUBCLONAL	1	TRUE	1	0.75199196988416	3		617	803	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939849	71939850	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0032586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2389	770	856	1	ENST00000298229.2:c.476_477delinsTT	p.Pro159Leu	p.P159L	ENST00000298229	NM_001567.3	159	cCC/cTT	4/28	0.75199196988416	8	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.75199196988416	8		857	3159	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94926647	94926647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	241	565	0	ENST00000536441.1:c.118C>T	p.Pro40Ser	p.P40S	ENST00000536441	NM_144665.3	40	Cca/Tca	2/10	0.601192045947163	2	FACETS	1	0.993	1	0.691	0.654	0.727	CLONAL	1	TRUE	0	0.75199196988416	2		565	464	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233099	69233099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1221150148	NA	P-0032586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	200	376	0	ENST00000462284.1:c.964C>T	p.Pro322Ser	p.P322S	ENST00000462284	NM_002392.5	322	Cca/Tca	11/11	0.605375797684329	3	FACETS	0.878	0.825	0.931	0.878	0.825	0.931	CLONAL	2	TRUE	1	0.75199196988416	3		376	417	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536737	120536737	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	204	679	0	ENST00000229340.5:c.355G>A	p.Gly119Ser	p.G119S	ENST00000229340	NM_006861.6	119	Ggt/Agt	5/6	0.605375797684329	3	FACETS	0.771	0.715	0.829	0.386	0.357	0.415	SUBCLONAL	1	TRUE	1	0.75199196988416	3		679	968	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784118	120784118	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	284	991	0	ENST00000257552.2:c.867C>G	p.His289Gln	p.H289Q	ENST00000257552	NM_002442.3	289	caC/caG	13/15	0.605375797684329	3	FACETS	0.808	0.758	0.859	0.404	0.379	0.43	CLONAL	1	TRUE	1	0.75199196988416	3		991	1287	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28631597	28631598	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0032586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	152	362	0	ENST00000241453.7:c.370_371delinsAA	p.Gly124Lys	p.G124K	ENST00000241453	NM_004119.2	124	GGa/AAa	4/24	0.543405307909618	4	FACETS	1	0.988	1	0.715	0.659	0.774	CLONAL	1	TRUE	2	0.75199196988416	4		362	495	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347911	73347911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146500302	NA	P-0032586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	163	316	0	ENST00000377767.4:c.1150C>T	p.Arg384Cys	p.R384C	ENST00000377767	NM_014953.3	384	Cgc/Tgc	8/21	0.543405307909618	4	FACETS	1	0.989	1	0.745	0.688	0.802	CLONAL	1	TRUE	2	0.75199196988416	4		316	510	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422175	81422175	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	309	479	0	ENST00000298171.2:c.151C>T	p.Pro51Ser	p.P51S	ENST00000298171	NM_000369.2	51	Ccg/Tcg	1/10	0.605375797684329	3	FACETS	0.827	0.785	0.868	0.827	0.785	0.868	CLONAL	2	TRUE	1	0.75199196988416	3		479	684	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007814	45007814	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0032586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	151	449	0	ENST00000558401.1:c.261C>G	p.Tyr87Ter	p.Y87*	ENST00000558401	NM_004048.2	87	taC/taG	2/4	0.611469761604432	1	FACETS	0.816	0.76	0.873	0.816	0.76	0.873	CLONAL	1	TRUE	0	0.75199196988416	1		449	307	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726689	88726689	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	125	503	1	ENST00000360948.2:c.355C>T	p.Gln119Ter	p.Q119*	ENST00000360948	NM_001012338.2	119	Cag/Tag	4/19	0.75199196988416	6	FACETS	0.728	0.657	0.803	0.146	0.131	0.161	SUBCLONAL	1	TRUE	1	0.75199196988416	6		504	1144	SUCCESS
BLM	641	MSKCC	GRCh37	15	91352491	91352491	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1555424890	NA	P-0032586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	101	320	0	ENST00000355112.3:c.3874+2T>C		p.X1292_splice	ENST00000355112	NM_000057.2	1292			0.75199196988416	6	FACETS	0.786	0.702	0.875	0.157	0.14	0.175	SUBCLONAL	1	TRUE	1	0.75199196988416	6		320	856	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633287	3633287	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149726415	NA	P-0032586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	324	1139	0	ENST00000294008.3:c.4964G>A	p.Arg1655Lys	p.R1655K	ENST00000294008	NM_032444.2	1655	aGg/aAg	14/15	0.538292585494175	3	FACETS	0.861	0.812	0.911	0.431	0.406	0.456	CLONAL	1	TRUE	1	0.75199196988416	3		1139	1377	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044471	12044471	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	218	336	0	ENST00000353533.5:c.1094C>T	p.Pro365Leu	p.P365L	ENST00000353533	NM_003010.3	365	cCc/cTc	11/11	0.601192045947163	2	FACETS	0.835	0.794	0.876	0.835	0.794	0.876	CLONAL	2	TRUE	0	0.75199196988416	2		336	347	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220096	5220096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	363	621	0	ENST00000357368.4:c.3619C>T	p.Pro1207Ser	p.P1207S	ENST00000357368	NM_002850.3	1207	Ccc/Tcc	22/38	0.543405307909618	4	FACETS	0.839	0.797	0.881	0.839	0.797	0.881	CLONAL	2	TRUE	2	0.75199196988416	4		621	1008	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376365	15376365	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1217	674	1211	0	ENST00000263377.2:c.649C>T	p.Pro217Ser	p.P217S	ENST00000263377	NM_058243.2	217	Cct/Tct	5/20	0.543405307909618	4	FACETS	0.83	0.8	0.861	0.83	0.8	0.861	CLONAL	2	TRUE	2	0.75199196988416	4		1211	1891	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61712946	61712946	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	147	585	0	ENST00000401558.2:c.2465T>A	p.Ile822Lys	p.I822K	ENST00000401558	NM_003400.3	822	aTa/aAa	20/25	0.605375797684329	3	FACETS	0.721	0.659	0.786	0.361	0.329	0.393	SUBCLONAL	1	TRUE	1	0.75199196988416	3		585	746	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719454	190719454	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	68	224	0	ENST00000441310.2:c.1456G>A	p.Gly486Ser	p.G486S	ENST00000441310	NM_000534.4	486	Ggt/Agt	9/13	0.654066231652365	3	FACETS	0.912	0.801	1	0.456	0.4	0.514	CLONAL	1	TRUE	1	0.75199196988416	3		224	273	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426786	212426786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866491191	NA	P-0032586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	134	466	0	ENST00000342788.4:c.2329C>T	p.His777Tyr	p.H777Y	ENST00000342788	NM_005235.2	777	Cat/Tat	20/28	0.654066231652365	3	FACETS	0.811	0.739	0.885	0.405	0.369	0.443	CLONAL	1	TRUE	1	0.75199196988416	3		466	605	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570052	212570052	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	243	537	0	ENST00000342788.4:c.1189G>A	p.Glu397Lys	p.E397K	ENST00000342788	NM_005235.2	397	Gag/Aag	10/28	0.654066231652365	3	FACETS	0.781	0.737	0.827	0.781	0.737	0.827	SUBCLONAL	2	TRUE	1	0.75199196988416	3		537	569	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547004	9547004	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	81	300	0	ENST00000353224.5:c.1018C>T	p.Leu340Phe	p.L340F	ENST00000353224	NM_177990.2	340	Ctc/Ttc	5/10	0.599173055316375	4	FACETS	0.769	0.679	0.864	0.256	0.226	0.288	SUBCLONAL	1	TRUE	1	0.75199196988416	4		300	491	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931589	NA	P-0032586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	320	304	0	ENST00000349496.5:c.101G>A	p.Gly34Glu	p.G34E	ENST00000349496	NM_001904.3	34	gGa/gAa	3/15	0.720317094351501	4	FACETS	0.926	0.886	0.965	0.926	0.886	0.965	CLONAL	3	TRUE	1	0.75199196988416	4		304	537	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163857	47163857	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	558	577	0	ENST00000409792.3:c.2269C>T	p.Gln757Ter	p.Q757*	ENST00000409792	NM_014159.6	757	Caa/Taa	3/21	0.720317094351501	4	FACETS	0.869	0.84	0.898	0.869	0.84	0.898	CLONAL	3	TRUE	1	0.75199196988416	4		577	997	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181392	185181392	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1422857669	NA	P-0032586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	99	370	0	ENST00000265026.3:c.1333A>G	p.Thr445Ala	p.T445A	ENST00000265026	NM_004721.4	445	Act/Gct	8/14	0.720317094351501	4	FACETS	0.755	0.675	0.84	0.252	0.225	0.28	SUBCLONAL	1	TRUE	1	0.75199196988416	4		370	611	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444561	187444561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1248764498	NA	P-0032586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	224	672	0	ENST00000232014.4:c.1666C>T	p.Arg556Cys	p.R556C	ENST00000232014	NM_001130845.1	556	Cgc/Tgc	7/10	0.720317094351501	4	FACETS	0.896	0.833	0.961	0.299	0.277	0.321	CLONAL	1	TRUE	1	0.75199196988416	4		672	1165	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197443	106197443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1452689450	NA	P-0032586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	91	291	0	ENST00000380013.4:c.5776C>T	p.Arg1926Cys	p.R1926C	ENST00000380013	NM_001127208.2	1926	Cgt/Tgt	11/11	1	2	FACETS	0.887	0.798	0.978	0.887	0.798	0.978	CLONAL	1	TRUE	1	0.75199196988416	2		291	273	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081584	143081584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	172	595	0	ENST00000262992.4:c.1490C>T	p.Pro497Leu	p.P497L	ENST00000262992	NM_001101669.1	497	cCc/cTc	15/24	1	2	FACETS	0.818	0.758	0.881	0.818	0.758	0.881	CLONAL	1	TRUE	1	0.75199196988416	2		595	559	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453150	140453150	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913341	NA	P-0032586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	99	325	0	ENST00000288602.6:c.1785T>G	p.Phe595Leu	p.F595L	ENST00000288602	NM_004333.4	595	ttT/ttG	15/18	0.651434206438267	4	FACETS	0.786	0.703	0.874	0.262	0.234	0.292	SUBCLONAL	1	TRUE	1	0.75199196988416	4		325	587	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376627	8376627	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	461	479	0	ENST00000356435.5:c.4486C>T	p.Arg1496Ter	p.R1496*	ENST00000356435		1496	Cga/Tga	27/35	0.601176021221366	4	FACETS	1	0.996	1	0.866	0.841	0.89	CLONAL	3	TRUE	0	0.75199196988416	4		479	620	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0032592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	325	620	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.392938378820339	2	FACETS	0.987	0.937	1	0.987	0.937	1	CLONAL	2	TRUE	0	0.413230372059408	2		621	797	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0032592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	36	213	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	0.204418483585177	2	FACETS	1	0.843	1	0.507	0.422	0.599	INDETERMINATE	1	TRUE	0	0.413230372059408	2		213	172	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371782	55371782	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	112	286	0	ENST00000297316.4:c.472G>A	p.Gly158Ser	p.G158S	ENST00000297316	NM_022454.3	158	Ggc/Agc	2/2	0.254661092103523	4	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	2	0.413230372059408	4		286	372	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145051	58145052	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0032592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	148	580	0	ENST00000257904.6:c.292dup	p.Gln98ProfsTer61	p.Q98Pfs*61	ENST00000257904	NM_000075.3	98	cag/cCag	3/8	0.413230372059408	3	FACETS	0.986	0.9	1	0.329	0.3	0.359	CLONAL	1	TRUE	0	0.413230372059408	3		580	877	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40679355	40679370	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTAGGCAAATGAAAG	CCTAGGCAAATGAAAG	-	novel	NA	P-0032592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	79	420	1	ENST00000249776.8:c.438-4_449del		p.X146_splice	ENST00000249776	NM_033286.3	146		4/9	1	2	FACETS	0.835	0.737	0.939	0.835	0.737	0.939	CLONAL	1	TRUE	1	0.413230372059408	2		421	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0032599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	193	620	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.303131357911523	2	FACETS	0.803	0.747	0.861	0.803	0.747	0.861	CLONAL	2	TRUE	0	0.383777996267911	2		621	626	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294283	1294283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	47	448	1	ENST00000310581.5:c.718C>T	p.Arg240Cys	p.R240C	ENST00000310581	NM_198253.2	240	Cgt/Tgt	2/16	0.145261097555447	2	FACETS	0.398	0.335	0.467	0.199	0.167	0.234	INDETERMINATE	1	TRUE	0	0.383777996267911	2		449	616	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724597	724597	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	54	494	1	ENST00000314574.4:c.1459C>T	p.Arg487Ter	p.R487*	ENST00000314574	NM_005433.3	487	Cga/Tga	12/12	0.133475523424048	5	FACETS	0.681	0.581	0.791	0.227	0.193	0.264	INDETERMINATE	1	TRUE	2	0.383777996267911	5		495	651	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219955	5219955	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1405757941	NA	P-0032599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	86	497	0	ENST00000357368.4:c.3760G>A	p.Glu1254Lys	p.E1254K	ENST00000357368	NM_002850.3	1254	Gag/Aag	22/38	0.303131357911523	2	FACETS	0.803	0.712	0.9	0.402	0.356	0.45	CLONAL	1	TRUE	0	0.383777996267911	2		497	558	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	89	317	0	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	1	2	FACETS	0.864	0.771	0.963	0.864	0.771	0.963	CLONAL	1	TRUE	1	0.5	2		317	412	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	115	427	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	0.5	2		427	357	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052632	42052632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779811318	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	60	505	1	ENST00000219905.7:c.7303C>T	p.Arg2435Trp	p.R2435W	ENST00000219905	NM_001164273.1	2435	Cgg/Tgg	20/24	1	2	FACETS	0.282	0.242	0.326	0.282	0.242	0.326	SUBCLONAL	1	TRUE	1	0.5	2		506	850	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	204	654	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.927	0.861	0.996	0.927	0.861	0.996	CLONAL	1	TRUE	1	0.5	2		657	880	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	50	525	2	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	0.26	0.22	0.305	0.26	0.22	0.305	SUBCLONAL	1	TRUE	1	0.5	2		527	769	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	19	358	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.328	0.249	0.42	0.328	0.249	0.42	SUBCLONAL	1	TRUE	1	0.5	2		358	232	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243923	5243923	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778260386	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	151	454	0	ENST00000357368.4:c.1559C>T	p.Thr520Met	p.T520M	ENST00000357368	NM_002850.3	520	aCg/aTg	11/38	1	2	FACETS	0.965	0.885	1	0.965	0.885	1	CLONAL	1	TRUE	1	0.5	2		454	626	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023327	27023327	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	24	113	0	ENST00000324856.7:c.437del	p.Pro146GlnfsTer86	p.P146Qfs*86	ENST00000324856	NM_006015.4	145	Ccc/cc	1/20	1	2	FACETS	0.623	0.494	0.77	0.623	0.494	0.77	SUBCLONAL	1	TRUE	1	0.5	2		113	154	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	253	771	0	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	1	2	FACETS	0.962	0.9	1	0.962	0.9	1	CLONAL	1	TRUE	1	0.5	2		771	1052	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	221	556	0	ENST00000206249.3:c.1607T>C	p.Leu536Pro	p.L536P	ENST00000206249	NM_000125.3	536	cTc/cCc	8/8	1	2	FACETS	0.974	0.907	1	0.974	0.907	1	CLONAL	1	TRUE	1	0.5	2		556	908	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	264	671	4	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.989	0.927	1	0.989	0.927	1	CLONAL	1	TRUE	1	0.5	2		675	1068	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610674	52610674	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	58	481	0	ENST00000394830.3:c.3499del	p.Tyr1167MetfsTer26	p.Y1167Mfs*26	ENST00000394830	NM_018313.4	1167	Tat/at	23/30	1	2	FACETS	0.756	0.654	0.865	0.756	0.654	0.865	SUBCLONAL	1	TRUE	1	0.5	2		481	307	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	36	427	2	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.282	0.232	0.339	0.282	0.232	0.339	SUBCLONAL	1	TRUE	1	0.5	2		429	510	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309776	104309776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202247756	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	237	697	0	ENST00000369902.3:c.367C>T	p.Arg123Cys	p.R123C	ENST00000369902	NM_016169.3	123	Cgt/Tgt	3/12	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.5	2		697	947	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199804	108199804	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	48	273	0	ENST00000278616.4:c.7150del	p.Met2384Ter	p.M2384*	ENST00000278616	NM_000051.3	2382	ggA/gg	49/63	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.5	2		273	167	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399351	139399351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779195962	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	337	788	0	ENST00000277541.6:c.4792C>T	p.Arg1598Cys	p.R1598C	ENST00000277541	NM_017617.3	1598	Cgc/Tgc	26/34	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.5	2		788	1206	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711894	89711894	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786204865	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	79	594	0	ENST00000371953.3:c.512A>G	p.Gln171Arg	p.Q171R	ENST00000371953	NM_000314.4	171	cAg/cGg	6/9	1	2	FACETS	0.84	0.744	0.943	0.84	0.744	0.943	CLONAL	1	TRUE	1	0.5	2		594	376	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354152	15354152	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs868796773	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	172	599	0	ENST00000263377.2:c.2728del	p.Gln910LysfsTer39	p.Q910Kfs*39	ENST00000263377	NM_058243.2	910	Caa/aa	14/20	1	2	FACETS	0.847	0.781	0.917	0.847	0.781	0.917	CLONAL	1	TRUE	1	0.5	2		599	812	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405954	157405954	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	40	550	1	ENST00000346085.5:c.2201del	p.Gly734AlafsTer11	p.G734Afs*11	ENST00000346085	NM_020732.3	732	ccG/cc	6/20	1	2	FACETS	0.219	0.181	0.262	0.219	0.181	0.262	SUBCLONAL	1	TRUE	1	0.5	2		551	730	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	316	740	1	ENST00000397062.3:c.246A>C	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaC	2/5	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.5	2		741	853	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966551	36966551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768417029	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	62	659	0	ENST00000358127.4:c.775G>A	p.Glu259Lys	p.E259K	ENST00000358127	NM_001280556.1	259	Gag/Aag	6/10	1	2	FACETS	0.264	0.227	0.304	0.264	0.227	0.304	SUBCLONAL	1	TRUE	1	0.5	2		659	939	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	194	568	2	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	1	2	FACETS	0.89	0.824	0.958	0.89	0.824	0.958	CLONAL	1	TRUE	1	0.5	2		570	872	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300040	137300040	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	256	749	5	ENST00000481739.1:c.331del	p.Leu111TrpfsTer57	p.L111Wfs*57	ENST00000481739	NM_002957.4	109	Ccc/cc	3/10	1	2	FACETS	0.872	0.816	0.93	0.872	0.816	0.93	CLONAL	1	TRUE	1	0.5	2		754	1174	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190747	11190747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759603938	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	68	790	1	ENST00000361445.4:c.5452C>T	p.Arg1818Cys	p.R1818C	ENST00000361445	NM_004958.3	1818	Cgt/Tgt	39/58	1	2	FACETS	0.22	0.19	0.252	0.22	0.19	0.252	SUBCLONAL	1	TRUE	1	0.5	2		791	1238	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554345	141554345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748399150	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	319	831	5	ENST00000220592.5:c.1806del	p.Ala603ProfsTer92	p.A603Pfs*92	ENST00000220592	NM_012154.3	602	ccC/cc	14/19	1	2	FACETS	0.968	0.913	1	0.968	0.913	1	CLONAL	1	TRUE	1	0.5	2		836	1318	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31372576	31372576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868507905	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	162	458	0	ENST00000328111.2:c.217G>A	p.Asp73Asn	p.D73N	ENST00000328111	NM_006892.3	73	Gat/Aat	4/23	1	2	FACETS	0.918	0.844	0.994	0.918	0.844	0.994	CLONAL	1	TRUE	1	0.5	2		458	706	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40476849	40476850	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	184	490	1	ENST00000264657.5:c.1479dup	p.Thr494TyrfsTer55	p.T494Yfs*55	ENST00000264657	NM_139276.2	493	-/T	17/24	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.5	2		491	662	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158131	27158131	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772321726	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	84	348	1	ENST00000380036.4:c.355C>T	p.Arg119Cys	p.R119C	ENST00000380036	NM_000459.3	119	Cgt/Tgt	2/23	1	2	FACETS	0.787	0.698	0.881	0.787	0.698	0.881	SUBCLONAL	1	TRUE	1	0.5	2		349	427	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692783	89692783	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	53	452	0	ENST00000371953.3:c.270del	p.Phe90LeufsTer9	p.F90Lfs*9	ENST00000371953	NM_000314.4	89	ccT/cc	5/9	1	2	FACETS	0.955	0.824	1	0.955	0.824	1	CLONAL	1	TRUE	1	0.5	2		452	222	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466554	120466554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	198	611	0	ENST00000256646.2:c.4565G>A	p.Cys1522Tyr	p.C1522Y	ENST00000256646	NM_024408.3	1522	tGc/tAc	26/34	1	2	FACETS	0.958	0.888	1	0.958	0.888	1	CLONAL	1	TRUE	1	0.5	2		611	827	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984362	201984375	+	protein_altering_variant	In_Frame_Del	DEL	GAACGGGTGGATGG	GAACGGGTGGATGG	AC	novel	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	220	542	2	ENST00000359651.3:c.1027_1040delinsAC	p.Glu343_Gly347delinsThr	p.E343_G347delinsT	ENST00000359651		343	GAACGGGTGGATGGc/ACc	8/8	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.5	2		544	870	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246490528	246490528	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	108	634	0	ENST00000388985.4:c.506T>C	p.Phe169Ser	p.F169S	ENST00000388985		169	tTt/tCt	5/12	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.5	2		634	411	SUCCESS
EED	8726	MSKCC	GRCh37	11	85968606	85968606	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	39	424	0	ENST00000263360.6:c.602G>C	p.Arg201Thr	p.R201T	ENST00000263360	NM_003797.3	201	aGa/aCa	6/12	1	2	FACETS	0.65	0.543	0.768	0.65	0.543	0.768	SUBCLONAL	1	TRUE	1	0.5	2		424	240	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912720	100912720	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	108	541	0	ENST00000325455.5:c.2602C>T	p.Gln868Ter	p.Q868*	ENST00000325455	NM_001202474.3	868	Cag/Tag	7/8	1	2	FACETS	0.887	0.8	0.978	0.887	0.8	0.978	CLONAL	1	TRUE	1	0.5	2		541	487	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206571	108206571	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	36	273	1	ENST00000278616.4:c.8152-1G>T		p.X2718_splice	ENST00000278616	NM_000051.3	2718			1	2	FACETS	0.563	0.465	0.67	0.563	0.465	0.67	SUBCLONAL	1	TRUE	1	0.5	2		274	256	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563293	21563293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367963331	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	342	802	1	ENST00000382592.4:c.626G>A	p.Arg209Gln	p.R209Q	ENST00000382592	NM_014572.2	209	cGg/cAg	4/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.5	2		803	1287	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437791	110437791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	68	605	0	ENST00000375856.3:c.610C>T	p.Pro204Ser	p.P204S	ENST00000375856	NM_003749.2	204	Ccc/Tcc	1/2	1	2	FACETS	0.299	0.259	0.342	0.299	0.259	0.342	SUBCLONAL	1	TRUE	1	0.5	2		605	910	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061776	38061777	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	215	617	0	ENST00000250448.2:c.212dup	p.Leu73ProfsTer154	p.L73Pfs*154	ENST00000250448	NM_004496.3	71	ccg/ccCg	2/2	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.5	2		617	857	SUCCESS
BLM	641	MSKCC	GRCh37	15	91334047	91334048	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGAC	novel	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	76	398	0	ENST00000355112.3:c.2993_2996dup	p.Arg1000AspfsTer24	p.R1000Dfs*24	ENST00000355112	NM_000057.2	998	gtg/gTGACtg	15/22	1	2	FACETS	0.95	0.841	1	0.95	0.841	1	CLONAL	1	TRUE	1	0.5	2		398	320	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781466	3781468	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs1555471931	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	88	342	0	ENST00000262367.5:c.4897_4899del	p.Phe1633del	p.F1633del	ENST00000262367	NM_004380.2	1633	TTC/-	30/31	0.151476659131843	3	FACETS	1	0.89	1	0.5	0.445	0.558	INDETERMINATE	1	TRUE	1	0.5	3		342	440	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592357	29592357	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1555619423	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	31	509	0	ENST00000356175.3:c.4772G>T	p.Arg1591Met	p.R1591M	ENST00000356175	NM_000267.3	1591	aGg/aTg	35/57	1	2	FACETS	0.418	0.338	0.506	0.418	0.338	0.506	SUBCLONAL	1	TRUE	1	0.5	2		509	297	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474395	40474395	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	28	581	0	ENST00000264657.5:c.2006C>A	p.Pro669Gln	p.P669Q	ENST00000264657	NM_139276.2	669	cCa/cAa	21/24	1	2	FACETS	0.207	0.164	0.255	0.207	0.164	0.255	SUBCLONAL	1	TRUE	1	0.5	2		581	542	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56787310	56787310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	68	667	0	ENST00000337432.4:c.796G>A	p.Ala266Thr	p.A266T	ENST00000337432	NM_058216.2	266	Gcc/Acc	5/9	1	2	FACETS	0.628	0.548	0.714	0.628	0.548	0.714	SUBCLONAL	1	TRUE	1	0.5	2		667	433	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120296	70120296	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1280	244	912	0	ENST00000245479.2:c.1298C>T	p.Pro433Leu	p.P433L	ENST00000245479	NM_000346.3	433	cCg/cTg	3/3	1	2	FACETS	0.64	0.597	0.686	0.64	0.597	0.686	SUBCLONAL	1	TRUE	1	0.5	2		912	1524	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226790	2226790	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	241	565	0	ENST00000398665.3:c.4270C>A	p.His1424Asn	p.H1424N	ENST00000398665	NM_032482.2	1424	Cac/Aac	27/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.5	2		565	903	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252726	10252726	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	217	530	1	ENST00000340748.4:c.3239C>A	p.Pro1080His	p.P1080H	ENST00000340748		1080	cCc/cAc	29/40	1	2	FACETS	0.99	0.922	1	0.99	0.922	1	CLONAL	1	TRUE	1	0.5	2		531	877	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211879	36211879	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777053465	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1394	85	1010	0	ENST00000222270.7:c.1630C>T	p.Arg544Trp	p.R544W	ENST00000222270	NM_014727.1	544	Cgg/Tgg	3/37	1	2	FACETS	0.23	0.202	0.26	0.23	0.202	0.26	SUBCLONAL	1	TRUE	1	0.5	2		1010	1479	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214711	36214724	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGGGGGGCGGGA	GCCGGGGGGCGGGA	-	novel	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	218	548	0	ENST00000222270.7:c.3139_3152del	p.Arg1047TrpfsTer36	p.R1047Wfs*36	ENST00000222270	NM_014727.1	1046	cGCCGGGGGGCGGGA/c	8/37	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.5	2		548	640	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753375	42753375	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	321	946	0	ENST00000222329.4:c.889T>A	p.Ser297Thr	p.S297T	ENST00000222329	NM_006494.2	297	Tca/Aca	4/4	1	2	FACETS	0.989	0.933	1	0.989	0.933	1	CLONAL	1	TRUE	1	0.5	2		946	1298	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753866	42753866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	312	874	2	ENST00000222329.4:c.398C>T	p.Pro133Leu	p.P133L	ENST00000222329	NM_006494.2	133	cCg/cTg	4/4	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.5	2		876	1156	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488732	212488732	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	135	578	0	ENST00000342788.4:c.2117A>G	p.Asn706Ser	p.N706S	ENST00000342788	NM_005235.2	706	aAt/aGt	18/28	1	2	FACETS	0.929	0.848	1	0.929	0.848	1	CLONAL	1	TRUE	1	0.5	2		578	581	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431008	181431008	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	292	602	3	ENST00000325404.1:c.860C>T	p.Ala287Val	p.A287V	ENST00000325404	NM_003106.3	287	gCc/gTc	1/1	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.5	2		605	859	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818234	32818234	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	232	652	0	ENST00000354258.4:c.1291C>A	p.Leu431Met	p.L431M	ENST00000354258	NM_000593.5	431	Ctg/Atg	5/11	1	2	FACETS	0.908	0.847	0.971	0.908	0.847	0.971	CLONAL	1	TRUE	1	0.5	2		652	1022	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946348	2946348	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	131	847	0	ENST00000396946.4:c.3389A>G	p.Glu1130Gly	p.E1130G	ENST00000396946	NM_032415.4	1130	gAg/gGg	25/25	1	2	FACETS	0.411	0.372	0.453	0.411	0.372	0.453	SUBCLONAL	1	TRUE	1	0.5	2		847	1274	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987269	2987269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	194	656	0	ENST00000396946.4:c.160G>A	p.Glu54Lys	p.E54K	ENST00000396946	NM_032415.4	54	Gag/Aag	3/25	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.5	2		656	774	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90996773	90996779	+	frameshift_variant	Frame_Shift_Del	DEL	GGCAGCA	GGCAGCA	-	novel	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	152	421	0	ENST00000265433.3:c.11_17del	p.Leu4ProfsTer14	p.L4Pfs*14	ENST00000265433	NM_002485.4	4	cTGCTGCCc/cc	1/16	1	2	FACETS	0.982	0.902	1	0.982	0.902	1	CLONAL	1	TRUE	1	0.5	2		421	619	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549451	5549451	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146333130	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	344	730	2	ENST00000397747.3:c.478G>A	p.Val160Ile	p.V160I	ENST00000397747	NM_025239.3	160	Gtt/Att	4/7	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.5	2		732	1078	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611167	100611167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	195	568	1	ENST00000308731.7:c.1439G>A	p.Gly480Asp	p.G480D	ENST00000308731	NM_000061.2	480	gGc/gAc	15/19	0.0806232325598	0	FACETS	0.478	0.443	0.514			1	INDETERMINATE	1	TRUE	0	0.5	0		569	816	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0032606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	28	651	1	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	1	2	FACETS	0.269	0.214	0.332	0.269	0.214	0.332	SUBCLONAL	1	TRUE	1	0.291565011046667	2		652	714	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952117	178952117	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	41	348	0	ENST00000263967.3:c.3172A>C	p.Ile1058Leu	p.I1058L	ENST00000263967	NM_006218.2	1058	Atc/Ctc	21/21	1	2	FACETS	0.847	0.708	1	0.847	0.708	1	CLONAL	1	TRUE	1	0.291565011046667	2		348	332	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0032606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	63	386	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.291565011046667	2		386	394	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0032606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	8	315	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	0.100300005027624	4	FACETS	0.254	0.163	0.373	0.085	0.054	0.125	INDETERMINATE	1	TRUE	1	0.291565011046667	4		315	279	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106483	27106484	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	80	652	0	ENST00000324856.7:c.6098dup	p.Glu2034GlyfsTer65	p.E2034Gfs*65	ENST00000324856	NM_006015.4	2032	gaa/gAaa	20/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.291565011046667	2		652	455	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249390	153249390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	90	708	0	ENST00000281708.4:c.1388C>T	p.Thr463Ile	p.T463I	ENST00000281708	NM_033632.3	463	aCt/aTt	9/12	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.291565011046667	2		708	573	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0032611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	353	314	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.739576027962593	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.739576027962593	3		314	618	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0032611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	422	604	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	0.739576027962593	3	FACETS	0.967	0.928	1	0.967	0.928	1	CLONAL	2	TRUE	1	0.739576027962593	3		604	808	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468089	120468089	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	112	688	0	ENST00000256646.2:c.4350G>T	p.Trp1450Cys	p.W1450C	ENST00000256646	NM_024408.3	1450	tgG/tgT	25/34	NA	2	FACETS	0.606	0.547	0.667			1	INDETERMINATE	1	TRUE	NA	0.739576027962593	2		688	500	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881428	37881428	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375637720	NA	P-0032611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	192	679	3	ENST00000269571.5:c.2620G>A	p.Glu874Lys	p.E874K	ENST00000269571		874	Gag/Aag	21/27	0.147742820791399	2	FACETS	1	0.973	1	0.539	0.503	0.575	INDETERMINATE	1	TRUE	0	0.739576027962593	2		682	482	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100597	67100597	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	106	563	0	ENST00000412916.2:c.295G>T	p.Ala99Ser	p.A99S	ENST00000412916		99	Gct/Tct	4/6	0.739576027962593	2	FACETS	0.704	0.636	0.775	0.352	0.318	0.388	SUBCLONAL	1	TRUE	0	0.739576027962593	2		563	407	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645141	67645141	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	23	597	0	ENST00000264010.4:c.406G>A	p.Gly136Arg	p.G136R	ENST00000264010	NM_006565.3	136	Ggg/Agg	3/12	0.739576027962593	2	FACETS	0.154	0.119	0.193	0.077	0.059	0.097	SUBCLONAL	1	TRUE	0	0.739576027962593	2		597	405	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023033	31023033	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	192	562	0	ENST00000375687.4:c.2518C>A	p.Pro840Thr	p.P840T	ENST00000375687	NM_015338.5	840	Cct/Act	13/13	0.739576027962593	3	FACETS	1	0.969	1	0.539	0.5	0.578	CLONAL	1	TRUE	1	0.739576027962593	3		562	660	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564566	41564566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	196	574	0	ENST00000263253.7:c.3988G>A	p.Asp1330Asn	p.D1330N	ENST00000263253	NM_001429.3	1330	Gac/Aac	24/31	0.361623885172823	5	FACETS	1	0.989	1	0.464	0.43	0.498	INDETERMINATE	1	TRUE	2	0.739576027962593	5		574	804	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032006	26032006	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	38	404	0	ENST00000244661.2:c.283G>C	p.Glu95Gln	p.E95Q	ENST00000244661	NM_003537.3	95	Gag/Cag	1/1	0.739576027962593	3	FACETS	0.301	0.248	0.359	0.15	0.124	0.18	SUBCLONAL	1	TRUE	1	0.739576027962593	3		404	468	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680515	30680515	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	369	664	1	ENST00000376406.3:c.1204A>G	p.Ser402Gly	p.S402G	ENST00000376406	NM_014641.2	402	Agc/Ggc	5/15	0.739576027962593	3	FACETS	0.948	0.907	0.989	0.948	0.907	0.989	CLONAL	2	TRUE	1	0.739576027962593	3		665	721	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190489	32190489	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	93	794	0	ENST00000375023.3:c.250C>G	p.Leu84Val	p.L84V	ENST00000375023	NM_004557.3	84	Ctt/Gtt	3/30	0.739576027962593	3	FACETS	0.509	0.453	0.569	0.254	0.226	0.285	SUBCLONAL	1	TRUE	1	0.739576027962593	3		794	677	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412733	139412733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	151	657	2	ENST00000277541.6:c.1111C>T	p.His371Tyr	p.H371Y	ENST00000277541	NM_017617.3	371	Cac/Tac	7/34	0.739576027962593	3	FACETS	0.955	0.877	1	0.477	0.438	0.518	CLONAL	1	TRUE	1	0.739576027962593	3		659	586	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027231	49027232	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	351	459	7	ENST00000267163.4:c.1798_1799insT	p.His600LeufsTer53	p.H600Lfs*53	ENST00000267163	NM_000321.2	600	cac/cTac	18/27	0.874973874528599	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.874973874528599	3		466	360	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574027	7574028	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	410	680	6	ENST00000269305.4:c.999dup	p.Gly334TrpfsTer3	p.G334Wfs*3	ENST00000269305	NM_001126112.2	333	-/T	10/11	0.874973874528599	3	FACETS	0.998	0.979	1	0.998	0.979	1	CLONAL	3	TRUE	0	0.874973874528599	3		686	450	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	108	258	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.933	0.849	1			1	INDETERMINATE	5	TRUE	NA	0.1513273938382	2		258	306	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs863224683	NA	P-0032619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	67	859	0	ENST00000269305.4:c.388C>G	p.Leu130Val	p.L130V	ENST00000269305	NM_001126112.2	130	Ctc/Gtc	5/11	0.3	3	FACETS	0.76	0.66	0.867	0.76	0.66	0.867	SUBCLONAL	2	TRUE	1	0.1513273938382	3		859	627	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974792	21974792	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs141798398	NA	P-0032619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	258	141	0	ENST00000304494.5:c.35C>A	p.Ser12Ter	p.S12*	ENST00000304494	NM_000077.4	12	tCg/tAg	1/3	0.3	3	FACETS	0.984	0.939	1	1	0.997	1	CLONAL	9	TRUE	1	0.1513273938382	3		141	414	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717609	89717609	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs876661024	NA	P-0032619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	43	411	2	ENST00000371953.3:c.635-1G>A		p.X212_splice	ENST00000371953	NM_000314.4	212			0.3	3	FACETS	1	0.898	1	1	0.898	1	CLONAL	2	TRUE	1	0.1513273938382	3		413	280	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667596	29667596	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0032619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	159	698	0	ENST00000356175.3:c.6932C>G	p.Ser2311Ter	p.S2311*	ENST00000356175	NM_000267.3	2311	tCa/tGa	46/57	0.3	3	FACETS	0.917	0.844	0.993	1	0.991	1	CLONAL	4	TRUE	1	0.1513273938382	3		698	616	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149387	61149387	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0032619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	59	453	0	ENST00000295025.8:c.1577C>G	p.Ser526Ter	p.S526*	ENST00000295025	NM_002908.2	526	tCa/tGa	11/11	0.1513273938382	2	FACETS	0.997	0.861	1	0.997	0.861	1	CLONAL	2	TRUE	0	0.1513273938382	2		453	391	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225367736	225367736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	30	493	0	ENST00000264414.4:c.1431G>A	p.Met477Ile	p.M477I	ENST00000264414	NM_003590.4	477	atG/atA	10/16	0.1513273938382	2	FACETS	0.762	0.617	0.926	0.762	0.617	0.926	CLONAL	2	TRUE	0	0.1513273938382	2		493	260	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609944	117609944	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779954823	NA	P-0032619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	38	446	0	ENST00000368508.3:c.6755G>A	p.Cys2252Tyr	p.C2252Y	ENST00000368508	NM_002944.2	2252	tGt/tAt	43/43	NA	2	FACETS	0.829	0.688	0.985			1	INDETERMINATE	2	TRUE	NA	0.1513273938382	2		446	303	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	127	354	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.888	0.809	0.971	0.888	0.809	0.971	CLONAL	1	TRUE	1	0.555430385024352	2		354	515	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0032620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	84	289	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.976	0.871	1	0.976	0.871	1	CLONAL	1	TRUE	1	0.555430385024352	2		289	310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579536	7579536	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567556930	NA	P-0032620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	221	764	0	ENST00000269305.4:c.151G>T	p.Glu51Ter	p.E51*	ENST00000269305	NM_001126112.2	51	Gaa/Taa	4/11	0.535897135196097	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.555430385024352	1		764	566	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253401	226253401	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	39	206	0	ENST00000366813.1:c.173C>T	p.Ser58Phe	p.S58F	ENST00000366813		58	tCc/tTc	2/3	1	2	FACETS	0.826	0.694	0.968	0.826	0.694	0.968	CLONAL	1	TRUE	1	0.555430385024352	2		206	170	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432581	49432581	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754988293	NA	P-0032620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	189	852	0	ENST00000301067.7:c.8558C>T	p.Pro2853Leu	p.P2853L	ENST00000301067	NM_003482.3	2853	cCg/cTg	34/54	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.555430385024352	2		852	674	SUCCESS
APC	324	MSKCC	GRCh37	5	112173766	112173766	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	69	449	0	ENST00000257430.4:c.2477del	p.Leu826Ter	p.L826*	ENST00000257430	NM_000038.5	825	taT/ta	16/16	1	2	FACETS	0.639	0.559	0.724	0.639	0.559	0.724	SUBCLONAL	1	TRUE	1	0.555430385024352	2		449	389	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223523	55223523	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	188	863	0	ENST00000275493.2:c.890G>A	p.Arg297His	p.R297H	ENST00000275493	NM_005228.3	297	cGt/cAt	8/28	1	2	FACETS	0.944	0.875	1	0.944	0.875	1	CLONAL	1	TRUE	1	0.555430385024352	2		863	717	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426043	47426043	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777037087	NA	P-0032620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	166	773	0	ENST00000377045.4:c.563G>A	p.Arg188His	p.R188H	ENST00000377045	NM_001654.4	188	cGc/cAc	7/16	1	2	FACETS	0.817	0.752	0.884	0.817	0.752	0.884	CLONAL	1	TRUE	1	0.555430385024352	2		773	732	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0032630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	71	372	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.138874909788668	3	FACETS	0.989	0.865	1	0.495	0.432	0.561	INDETERMINATE	1	TRUE	1	0.344912265576389	3		372	488	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247190	153247190	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	57	324	0	ENST00000281708.4:c.1612C>A	p.Gln538Lys	p.Q538K	ENST00000281708	NM_033632.3	538	Cag/Aag	10/12	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.344912265576389	2		324	329	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028828	47028855	+	frameshift_variant	Frame_Shift_Del	DEL	TCCTCGCGAGTATGGCAGCCAGGAGGGC	TCCTCGCGAGTATGGCAGCCAGGAGGGC	-	novel	NA	P-0032630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	134	693	0	ENST00000377604.3:c.132_159del	p.Tyr44Ter	p.Y44*	ENST00000377604	NM_001204468.1	44	taTCCTCGCGAGTATGGCAGCCAGGAGGGC/ta	3/24	1	2	FACETS	0.981	0.892	1	0.981	0.892	1	CLONAL	1	TRUE	1	0.344912265576389	2		693	792	SUCCESS
AR	367	MSKCC	GRCh37	X	66765779	66765779	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	70	1023	0	ENST00000374690.3:c.791G>T	p.Arg264Leu	p.R264L	ENST00000374690	NM_000044.3	264	cGg/cTg	1/8	1	2	FACETS	0.373	0.324	0.427	0.373	0.324	0.427	SUBCLONAL	1	TRUE	1	0.344912265576389	2		1023	1088	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0032635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	194	557	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.51394068083689	3	FACETS	0.88	0.821	0.941	0.88	0.821	0.941	CLONAL	2	TRUE	1	0.51394068083689	3		557	539	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0032635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	194	1222	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.51394068083689	1	FACETS	0.967	0.901	1	0.967	0.901	1	CLONAL	1	TRUE	0	0.51394068083689	1		1222	580	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243505	46243526	+	frameshift_variant	Frame_Shift_Del	DEL	TCTGTTGTTCGTGTTGATTCTG	TCTGTTGTTCGTGTTGATTCTG	-	novel	NA	P-0032635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	94	370	0	ENST00000334344.6:c.1859_1880del	p.Ser620PhefsTer20	p.S620Ffs*20	ENST00000334344	NM_152641.2	620	TCTGTTGTTCGTGTTGATTCTGtt/tt	14/21	0.51394068083689	1	FACETS	0.992	0.895	1	0.992	0.895	1	CLONAL	1	TRUE	0	0.51394068083689	1		370	274	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0032642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	471	620	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.330853641513739	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.379664533685406	3		621	944	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285666	46285666	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	94	469	0	ENST00000334344.6:c.5026C>T	p.Gln1676Ter	p.Q1676*	ENST00000334344	NM_152641.2	1676	Cag/Tag	17/21	0.379664533685406	1	FACETS	0.988	0.885	1	0.988	0.885	1	CLONAL	1	TRUE	0	0.379664533685406	1		469	406	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105554	27105560	+	frameshift_variant	Frame_Shift_Del	DEL	GATGCCT	GATGCCT	-	novel	NA	P-0032642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	93	492	0	ENST00000324856.7:c.5168_5174del	p.Cys1723LeufsTer7	p.C1723Lfs*7	ENST00000324856	NM_006015.4	1722	cGATGCCTg/cg	20/20	1	2	FACETS	0.961	0.857	1	0.961	0.857	1	CLONAL	1	TRUE	1	0.379664533685406	2		492	510	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632744	23632744	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	112	565	0	ENST00000261584.4:c.3052G>A	p.Glu1018Lys	p.E1018K	ENST00000261584	NM_024675.3	1018	Gag/Aag	10/13	0.379664533685406	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.379664533685406	1		565	450	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961862	15962884	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGACTTATCACCTCAATAGCATCGCTAGGTGTTTCATACCTGTGAGAAGATACTTTAAGAAAAGAAAATCTTATTTCAAAACTAATCCCAGGAAAAGTTTCTGAAGTCTAAGTTCTTCACACCTGTAGCATTTTTTCAATTCTGATCCACCATGTTCAAAGGTATTCCAGGTTAATGAGGGTTTTCTGAAGTTTTATGGGCTTTAAGACATGTTTTAGGCTGGGTGCAGTGGCTCATGGCTGTAATCCCAGCACTTTGGAAGGCCGAGGCAGGTGGATCACCTGAGGTCAGGGGTTTGAGACCAGCCTGACCAACGTGGAGAAACCCTGTCTCTACTAAAAAAAATACAAAATTAGTAGGGCGTGGTAGCTCATGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCCGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGTGGTGAGCTGAGATTGTGTCATTGCACTCCATTCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAGACATGTTTTAAAGCCCAATAATAAACACTGGAATGAGGCAGAACAGAGAACAGATTTATGATATTTTCCTGGGAGCTGGAAAAGAAATCACCAGGGAAACATTTATGGAAGAGGTTAATAAACAAATGAGGGAGTAGATCTCAATAACTGATTCCAATGATTCCAATTCTGTGGGACACTCTGTTCTTAGAAAAACGCTGAGGCTATAAAGCTGCTTCATTCACCACCATGATGATTTTAAAGCTATGGATTATATAACACTATATAATGATTTTCTCAAATAAATGGAGTATTGCTAACAAAACTTACTCCAAACATTAATAATTTTTTAGCACTGTGTTACATTGTGAAAATAACCAGAAATGGTAGAGAATGTCTGAAGGGAAGTATATTCCCAGAAAGGGAGGATGTCAACCAACTCTGGAGGATACCCACATCAGAAAAGGACCTCCTCTAAGACACAGTTCCCAAGTAAACAGAGGGCTATGCAGTG	GGACTTATCACCTCAATAGCATCGCTAGGTGTTTCATACCTGTGAGAAGATACTTTAAGAAAAGAAAATCTTATTTCAAAACTAATCCCAGGAAAAGTTTCTGAAGTCTAAGTTCTTCACACCTGTAGCATTTTTTCAATTCTGATCCACCATGTTCAAAGGTATTCCAGGTTAATGAGGGTTTTCTGAAGTTTTATGGGCTTTAAGACATGTTTTAGGCTGGGTGCAGTGGCTCATGGCTGTAATCCCAGCACTTTGGAAGGCCGAGGCAGGTGGATCACCTGAGGTCAGGGGTTTGAGACCAGCCTGACCAACGTGGAGAAACCCTGTCTCTACTAAAAAAAATACAAAATTAGTAGGGCGTGGTAGCTCATGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCCGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGTGGTGAGCTGAGATTGTGTCATTGCACTCCATTCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAGACATGTTTTAAAGCCCAATAATAAACACTGGAATGAGGCAGAACAGAGAACAGATTTATGATATTTTCCTGGGAGCTGGAAAAGAAATCACCAGGGAAACATTTATGGAAGAGGTTAATAAACAAATGAGGGAGTAGATCTCAATAACTGATTCCAATGATTCCAATTCTGTGGGACACTCTGTTCTTAGAAAAACGCTGAGGCTATAAAGCTGCTTCATTCACCACCATGATGATTTTAAAGCTATGGATTATATAACACTATATAATGATTTTCTCAAATAAATGGAGTATTGCTAACAAAACTTACTCCAAACATTAATAATTTTTTAGCACTGTGTTACATTGTGAAAATAACCAGAAATGGTAGAGAATGTCTGAAGGGAAGTATATTCCCAGAAAGGGAGGATGTCAACCAACTCTGGAGGATACCCACATCAGAAAAGGACCTCCTCTAAGACACAGTTCCCAAGTAAACAGAGGGCTATGCAGTG	-	novel	NA	P-0032642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	91	481	0	ENST00000268712.3:c.5882-971_5933del		p.X1961_splice	ENST00000268712	NM_006311.3	1961		38/46	0.330853641513739	3	FACETS	0.706	0.626	0.791	0.235	0.208	0.264	SUBCLONAL	1	TRUE	0	0.379664533685406	3		481	808	SUCCESS
YES1	7525	MSKCC	GRCh37	18	751744	751744	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	103	558	0	ENST00000314574.4:c.332C>T	p.Ser111Leu	p.S111L	ENST00000314574	NM_005433.3	111	tCa/tTa	3/12	0.355821248535593	2	FACETS	0.934	0.838	1	0.467	0.419	0.518	CLONAL	1	TRUE	0	0.379664533685406	2		558	581	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0032644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	126	697	1	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	0.916	0.832	1	0.916	0.832	1	CLONAL	1	TRUE	1	0.454620407488371	2		698	605	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248998	55248999	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCCAGCG	rs727504263	NA	P-0032644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	109	394	0	ENST00000275493.2:c.2300_2308dup	p.Ala767_Val769dup	p.A767_V769dup	ENST00000275493	NM_005228.3	767	atg/aTGGCCAGCGtg	20/28	0.426394889015365	3	FACETS	0.811	0.735	0.889	0.811	0.735	0.889	CLONAL	2	TRUE	1	0.454620407488371	3		394	363	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0032645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	48	814	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.967	0.819	1	0.967	0.819	1	CLONAL	1	FALSE	1	0.216652348214585	2		814	458	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044850	47044850	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	72	384	1	ENST00000377604.3:c.2176C>T	p.Arg726Ter	p.R726*	ENST00000377604	NM_001204468.1	726	Cga/Tga	20/24	1	1	FACETS	0.975	0.86	1	1	0.982	1	CLONAL	2	FALSE	0	0.216652348214585	1		385	304	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0032647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	100	363	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.798	0.72	0.88	1	0.984	1	SUBCLONAL	2	TRUE	1	0.35	2		363	358	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0032647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	165	508	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.3	2	FACETS	1	0.988	1	0.707	0.651	0.764	CLONAL	1	TRUE	0	0.35	2		509	667	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0032647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	119	651	1	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.3	2	FACETS	0.831	0.75	0.917	0.416	0.375	0.459	CLONAL	1	TRUE	0	0.35	2		652	818	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149511631	149511631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375122221	NA	P-0032647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	34	497	1	ENST00000261799.4:c.1154G>A	p.Arg385His	p.R385H	ENST00000261799	NM_002609.3	385	cGc/cAc	8/23	0.265097572935677	1	FACETS	0.349	0.285	0.422	0.349	0.285	0.422	SUBCLONAL	1	TRUE	0	0.35	1		498	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0032648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	660	614	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.610870324782568	3	FACETS	0.994	0.969	1	0.994	0.969	1	CLONAL	3	TRUE	0	0.643081556587885	3		616	910	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564511	86564511	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	320	589	4	ENST00000274376.6:c.248del	p.Gly83GlufsTer4	p.G83Efs*4	ENST00000274376	NM_002890.2	81	ctG/ct	1/25	0.643081556587885	2	FACETS	0.957	0.917	0.996	0.957	0.917	0.996	CLONAL	2	TRUE	0	0.643081556587885	2		593	520	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805562	46805562	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	228	876	0	ENST00000290295.7:c.394G>T	p.Gly132Ter	p.G132*	ENST00000290295	NM_006361.5	132	Gga/Tga	1/2	0.643081556587885	3	FACETS	0.762	0.709	0.818	0.381	0.354	0.409	SUBCLONAL	1	TRUE	1	0.643081556587885	3		876	1229	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65304246	65304246	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	421	458	0	ENST00000342505.4:c.2869G>T	p.Glu957Ter	p.E957*	ENST00000342505	NM_002227.2	957	Gaa/Taa	21/25	0.521503948136001	5	FACETS	0.888	0.849	0.926	0.888	0.849	0.926	CLONAL	3	TRUE	2	0.643081556587885	5		458	966	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942661	48942661	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0032648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	171	285	0	ENST00000267163.4:c.1050-2A>G		p.X350_splice	ENST00000267163	NM_000321.2	350			0.643081556587885	2	FACETS	0.94	0.885	0.993	0.94	0.885	0.993	CLONAL	2	TRUE	0	0.643081556587885	2		285	283	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868147	56868163	+	frameshift_variant	Frame_Shift_Del	DEL	CAGTACTTCTATTTCCT	CAGTACTTCTATTTCCT	-	novel	NA	P-0032648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	122	645	0	ENST00000308159.5:c.1648_1664del	p.Tyr550GlyfsTer2	p.Y550Gfs*2	ENST00000308159	NM_014669.4	549	CAGTACTTCTATTTCCTc/c	14/22	0.540458805134959	4	FACETS	0.621	0.56	0.685	0.31	0.28	0.343	SUBCLONAL	1	TRUE	2	0.643081556587885	4		645	1004	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0032670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	450	447	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.60861128492684	5	FACETS	1	0.972	1	1	0.972	1	CLONAL	4	TRUE	1	0.631505860010215	5		447	689	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0032670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	543	597	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.204420008477457	5	FACETS	1	0.995	1			1	INDETERMINATE	4	TRUE	NA	0.631505860010215	5		597	760	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007818	45007818	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	119	477	0	ENST00000558401.1:c.265G>T	p.Glu89Ter	p.E89*	ENST00000558401	NM_004048.2	89	Gaa/Taa	2/4	0.560151920079108	5	FACETS	0.945	0.853	1	0.315	0.284	0.347	CLONAL	1	TRUE	2	0.631505860010215	5		477	777	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197187	26197187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	107	614	0	ENST00000356476.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000356476		98	Gag/Aag	1/1	0.63161838880949	3	FACETS	0.937	0.845	1	0.468	0.422	0.517	CLONAL	1	TRUE	1	0.631505860010215	3		614	476	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39074437	39074437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1384811064	NA	P-0032670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	275	480	0	ENST00000357387.3:c.43G>A	p.Val15Ile	p.V15I	ENST00000357387	NM_152756.3	15	Gta/Ata	1/38	0.631505860010215	8	FACETS	1	0.988	1	0.346	0.324	0.367	CLONAL	2	TRUE	1	0.631505860010215	8		480	1042	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343250	118343250	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	69	363	0	ENST00000534358.1:c.1376C>G	p.Ser459Cys	p.S459C	ENST00000534358	NM_005933.3	459	tCt/tGt	3/36	0.429313074340463	3	FACETS	0.836	0.733	0.946			1	CLONAL	1	TRUE	NA	0.631505860010215	3		363	344	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343259	118343259	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	68	368	0	ENST00000534358.1:c.1385C>T	p.Ser462Leu	p.S462L	ENST00000534358	NM_005933.3	462	tCa/tTa	3/36	0.429313074340463	3	FACETS	0.833	0.73	0.944			1	CLONAL	1	TRUE	NA	0.631505860010215	3		368	340	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343271	118343271	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	64	368	1	ENST00000534358.1:c.1397del	p.Ser466PhefsTer101	p.S466Ffs*101	ENST00000534358	NM_005933.3	466	tCt/tt	3/36	0.429313074340463	3	FACETS	0.787	0.686	0.895			1	SUBCLONAL	1	TRUE	NA	0.631505860010215	3		369	339	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109708	115109709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0032670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	193	990	0	ENST00000257566.3:c.2168_2169dup	p.Ile724AlafsTer166	p.I724Afs*166	ENST00000257566	NM_016569.3	723	-/GC	8/8	0.617738957394386	5	FACETS	1	0.943	1	0.205	0.189	0.222	CLONAL	1	TRUE	0	0.631505860010215	5		990	1161	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657012	47657012	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	96	334	0	ENST00000233146.2:c.1208A>C	p.Asp403Ala	p.D403A	ENST00000233146	NM_000251.2	403	gAt/gCt	7/16	0.63161838880949	4	FACETS	0.891	0.796	0.991	0.297	0.265	0.331	CLONAL	1	TRUE	1	0.631505860010215	4		334	557	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719840	61719840	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	182	619	0	ENST00000401558.2:c.1428G>C	p.Met476Ile	p.M476I	ENST00000401558	NM_003400.3	476	atG/atC	14/25	0.63161838880949	4	FACETS	1	0.937	1	0.339	0.313	0.367	CLONAL	1	TRUE	1	0.631505860010215	4		619	924	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104718	209104718	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	68	320	0	ENST00000345146.2:c.860C>G	p.Ser287Cys	p.S287C	ENST00000345146	NM_005896.2	287	tCt/tGt	8/10	NA	2	FACETS	0.97	0.857	1			1	INDETERMINATE	1	TRUE	NA	0.631505860010215	2		320	222	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056240	26056240	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	157	628	0	ENST00000343677.2:c.417G>T	p.Lys139Asn	p.K139N	ENST00000343677	NM_005319.3	139	aaG/aaT	1/1	0.63161838880949	3	FACETS	1	0.949	1	0.522	0.48	0.565	CLONAL	1	TRUE	1	0.631505860010215	3		628	627	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774840	73774926	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGGGGAGCGGAAACCGCCCAGCCCTCCCCCGGCTCCAGGCCTTTGTCTTACCTGCAGCGCACCGATGGCTGCGCTCTGAAACCTCAG	CGGGGAGCGGAAACCGCCCAGCCCTCCCCCGGCTCCAGGCCTTTGTCTTACCTGCAGCGCACCGATGGCTGCGCTCTGAAACCTCAG	T	novel	NA	P-0032670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	128	790	0	ENST00000254810.4:c.247_283-36delinsA		p.X83_splice	ENST00000254810	NM_005324.3	83		3/4	0.63161838880949	3	FACETS	1	0.931	1	0.513	0.467	0.561	CLONAL	1	TRUE	1	0.631505860010215	3		790	520	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0032673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	322	447	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.437219456697811	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.482223169623323	3		447	746	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856020	68856020	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	73	583	0	ENST00000261769.5:c.1828C>T	p.Gln610Ter	p.Q610*	ENST00000261769	NM_004360.3	610	Cag/Tag	12/16	0.482223169623323	1	FACETS	0.444	0.388	0.503	0.444	0.388	0.503	SUBCLONAL	1	TRUE	0	0.482223169623323	1		583	518	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771344	68771344	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	30	271	0	ENST00000261769.5:c.26C>A	p.Ser9Ter	p.S9*	ENST00000261769	NM_004360.3	9	tCg/tAg	1/16	0.482223169623323	1	FACETS	0.397	0.321	0.481	0.397	0.321	0.481	SUBCLONAL	1	TRUE	0	0.482223169623323	1		271	238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578371	7578371	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs776167460	NA	P-0032673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	151	748	0	ENST00000269305.4:c.559G>A	p.Gly187Ser	p.G187S	ENST00000269305	NM_001126112.2	187	Ggt/Agt	5/11	0.482223169623323	1	FACETS	0.992	0.914	1	0.992	0.914	1	CLONAL	1	TRUE	0	0.482223169623323	1		748	479	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944614	32944614	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	93	764	1	ENST00000380152.3:c.8407C>A	p.Leu2803Met	p.L2803M	ENST00000380152		2803	Ctg/Atg	19/27	1	2	FACETS	0.43	0.382	0.482	0.43	0.382	0.482	SUBCLONAL	1	TRUE	1	0.482223169623323	2		765	896	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944624	32944624	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	100	746	0	ENST00000380152.3:c.8417C>A	p.Ser2806Ter	p.S2806*	ENST00000380152		2806	tCa/tAa	19/27	1	2	FACETS	0.468	0.417	0.522	0.468	0.417	0.522	SUBCLONAL	1	TRUE	1	0.482223169623323	2		746	887	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998913	11998913	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	81	263	1	ENST00000353533.5:c.415del	p.Glu139LysfsTer13	p.E139Kfs*13	ENST00000353533	NM_003010.3	139	Gaa/aa	4/11	0.482223169623323	1	FACETS	0.934	0.833	1	0.934	0.833	1	CLONAL	1	TRUE	0	0.482223169623323	1		264	273	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218849	36218849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753899619	NA	P-0032673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	169	750	0	ENST00000222270.7:c.4460G>A	p.Arg1487His	p.R1487H	ENST00000222270	NM_014727.1	1487	cGc/cAc	18/37	0.482223169623323	1	FACETS	0.892	0.825	0.962	0.892	0.825	0.962	CLONAL	1	TRUE	0	0.482223169623323	1		750	596	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138375052	138375052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	58	489	0	ENST00000289153.2:c.3007C>T	p.Leu1003Phe	p.L1003F	ENST00000289153	NM_006219.2	1003	Ctc/Ttc	21/22	1	2	FACETS	0.396	0.34	0.457	0.396	0.34	0.457	SUBCLONAL	1	TRUE	1	0.482223169623323	2		489	608	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250104	110250104	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	67	741	0	ENST00000374672.4:c.571A>T	p.Asn191Tyr	p.N191Y	ENST00000374672	NM_004235.4	191	Aac/Tac	3/5	0.437219456697811	3	FACETS	0.396	0.343	0.454	0.198	0.171	0.227	SUBCLONAL	1	TRUE	1	0.482223169623323	3		741	870	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184154	123184154	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	50	430	0	ENST00000218089.9:c.1012G>T	p.Asp338Tyr	p.D338Y	ENST00000218089	NM_001042749.1	338	Gat/Tat	11/35	1	2	FACETS	0.426	0.361	0.497	0.426	0.361	0.497	SUBCLONAL	1	TRUE	1	0.482223169623323	2		430	487	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	168	447	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.354106252810022	1	FACETS	0.798	0.74	0.858	1	0.991	1	SUBCLONAL	2	TRUE	0	0.354106252810022	1		447	489	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0032677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	134	726	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.354106252810022	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.354106252810022	1		726	588	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962529	100962529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767360879	NA	P-0032677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	90	557	1	ENST00000325455.5:c.1868G>A	p.Arg623His	p.R623H	ENST00000325455	NM_001202474.3	623	cGc/cAc	3/8	1	2	FACETS	0.782	0.694	0.875	0.782	0.694	0.875	SUBCLONAL	1	TRUE	1	0.354106252810022	2		558	650	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0032678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	325	712	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.439621252087209	3	FACETS	1	0.985	1	0.724	0.689	0.759	CLONAL	2	TRUE	0	0.544179893309384	3		712	700	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271870	15271870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528151296	NA	P-0032678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	392	855	2	ENST00000263388.2:c.6569C>T	p.Ala2190Val	p.A2190V	ENST00000263388	NM_000435.2	2190	gCg/gTg	33/33	0.403675261102819	5	FACETS	0.835	0.796	0.875	0.835	0.796	0.875	CLONAL	3	TRUE	2	0.544179893309384	5		857	1044	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589815	212589815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866956005	NA	P-0032678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	68	455	0	ENST00000342788.4:c.727G>A	p.Asp243Asn	p.D243N	ENST00000342788	NM_005235.2	243	Gac/Aac	6/28	0.456386420842516	4	FACETS	0.755	0.658	0.86	0.378	0.329	0.43	SUBCLONAL	1	TRUE	2	0.544179893309384	4		455	511	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190803	185190803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	113	692	0	ENST00000265026.3:c.1684G>A	p.Val562Met	p.V562M	ENST00000265026	NM_004721.4	562	Gtg/Atg	11/14	0.401765784200568	6	FACETS	0.866	0.778	0.959	0.216	0.194	0.24	CLONAL	1	TRUE	2	0.544179893309384	6		692	1002	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971169	21971170	+	missense_variant	Missense_Mutation	DNP	CA	CA	TG	novel	NA	P-0032678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	125	361	0	ENST00000304494.5:c.188_189inv	p.Leu63Pro	p.L63P	ENST00000304494	NM_000077.4	63	cTG/cCA	2/3	0.544179893309384	3	FACETS	0.849	0.778	0.922	0.566	0.519	0.615	CLONAL	2	TRUE	0	0.544179893309384	3		361	344	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217299	11217319	+	inframe_deletion	In_Frame_Del	DEL	AGGGCATCCTCCCACTCGTGC	AGGGCATCCTCCCACTCGTGC	-	novel	NA	P-0032679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	42	751	0	ENST00000361445.4:c.4359_4379del	p.His1454_Leu1460del	p.H1454_L1460del	ENST00000361445	NM_004958.3	1453	ctGCACGAGTGGGAGGATGCCCTt/ctt	30/58	1	2	FACETS	0.665	0.553	0.789	0.665	0.553	0.789	SUBCLONAL	1	TRUE	1	0.16	2		751	790	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0032680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	41	349	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.256082452246452	1	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	0	0.256082452246452	1		349	264	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0032680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	81	840	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	NA	2	FACETS	0.936	0.825	1			1	INDETERMINATE	1	TRUE	NA	0.256082452246452	2		840	676	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0032680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	1119	655	1	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.256082452246452	12	FACETS	0.968	0.948	0.989			1	CLONAL	12	TRUE	NA	0.256082452246452	12		656	1715	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604735	48604736	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0032680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	59	310	0	ENST00000342988.3:c.1558dup	p.Glu520GlyfsTer7	p.E520Gfs*7	ENST00000342988	NM_005359.5	519	-/G	12/12	0.256082452246452	1	FACETS	0.999	0.863	1	0.999	0.863	1	CLONAL	1	TRUE	0	0.256082452246452	1		310	402	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917634	178917634	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	41	299	0	ENST00000263967.3:c.509A>G	p.Asn170Ser	p.N170S	ENST00000263967	NM_006218.2	170	aAt/aGt	3/21	1	2	FACETS	0.887	0.741	1	0.887	0.741	1	CLONAL	1	TRUE	1	0.256082452246452	2		299	361	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268224	153268224	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0032680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	21	130	0	ENST00000281708.4:c.585-1G>A		p.X195_splice	ENST00000281708	NM_033632.3	195			1	2	FACETS	0.97	0.753	1	0.97	0.753	1	CLONAL	1	TRUE	1	0.256082452246452	2		130	169	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0032682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	97	297	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	1	2	FACETS	0.664	0.596	0.736	0.664	0.596	0.736	SUBCLONAL	1	TRUE	1	0.719155658832955	2		297	406	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345240	73345240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	135	273	0	ENST00000377767.4:c.1649C>T	p.Ser550Phe	p.S550F	ENST00000377767	NM_014953.3	550	tCc/tTc	12/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.719155658832955	2		273	341	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217652	7217654	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	novel	NA	P-0032682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	21	416	1	ENST00000380728.2:c.273_275del	p.Lys92del	p.K92del	ENST00000380728		91	aaGAAa/aaa	4/11	0.693825700638323	1	FACETS	0.093	0.071	0.118	0.093	0.071	0.118	SUBCLONAL	1	TRUE	0	0.719155658832955	1		417	404	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871599	35871599	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0032682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	53	259	0	ENST00000216797.5:c.906+1G>T		p.X302_splice	ENST00000216797	NM_020529.2	302			1	2	FACETS	0.49	0.42	0.565	0.49	0.42	0.565	SUBCLONAL	1	TRUE	1	0.719155658832955	2		259	301	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572926	7572935	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	GTCAGTCTGA	GTCAGTCTGA	-	novel	NA	P-0032682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	53	433	0	ENST00000269305.4:c.1174_*1del		p.*392*	ENST00000269305	NM_001126112.2	392		11/11	0.693825700638323	1	FACETS	0.237	0.202	0.274	0.237	0.202	0.274	SUBCLONAL	1	TRUE	0	0.719155658832955	1		433	399	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732265	74732265	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	94	227	0	ENST00000359995.5:c.644A>T	p.Glu215Val	p.E215V	ENST00000359995	NM_001195427.1	215	gAg/gTg	2/3	1	2	FACETS	0.947	0.855	1	0.947	0.855	1	CLONAL	1	TRUE	1	0.719155658832955	2		227	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0032683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	23	659	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	1	2	FACETS	0.648	0.503	0.817	0.648	0.503	0.817	SUBCLONAL	1	TRUE	1	0.11	2		659	645	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555526097	NA	P-0032685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	229	595	0	ENST00000269305.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000269305	NM_001126112.2	167	Cag/Tag	5/11	0.526203056884555	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.526203056884555	1		595	567	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5534921	5534921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	139	362	0	ENST00000397747.3:c.232G>A	p.Glu78Lys	p.E78K	ENST00000397747	NM_025239.3	78	Gag/Aag	3/7	0.526203056884555	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.526203056884555	1		362	339	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934189	48934189	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs768305224	NA	P-0032685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	139	395	0	ENST00000267163.4:c.644C>A	p.Ser215Ter	p.S215*	ENST00000267163	NM_000321.2	215	tCa/tAa	7/27	0.526203056884555	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.526203056884555	1		395	375	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217239	11217239	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs780930764	NA	P-0032685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	192	521	0	ENST00000361445.4:c.4439G>T	p.Arg1480Leu	p.R1480L	ENST00000361445	NM_004958.3	1480	cGc/cTc	30/58	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.526203056884555	2		521	702	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622151	43622151	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	179	428	0	ENST00000355710.3:c.3168G>C	p.Trp1056Cys	p.W1056C	ENST00000355710	NM_020975.4	1056	tgG/tgC	19/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.526203056884555	2		428	599	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426415	49426415	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	277	759	0	ENST00000301067.7:c.12073G>A	p.Glu4025Lys	p.E4025K	ENST00000301067	NM_003482.3	4025	Gaa/Aaa	39/54	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.526203056884555	2		759	1026	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457593	67457593	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	79	453	0	ENST00000327367.4:c.403C>A	p.Leu135Ile	p.L135I	ENST00000327367	NM_005902.3	135	Cta/Ata	3/9	0.418839830790713	1	FACETS	0.497	0.439	0.559	0.497	0.439	0.559	SUBCLONAL	1	TRUE	0	0.526203056884555	1		453	445	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251234	99251234	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	26	421	0	ENST00000268035.6:c.538G>T	p.Asp180Tyr	p.D180Y	ENST00000268035	NM_000875.3	180	Gac/Tac	2/21	0.526203056884555	1	FACETS	0.171	0.135	0.212	0.171	0.135	0.212	SUBCLONAL	1	TRUE	0	0.526203056884555	1		421	427	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251791	212251791	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	89	250	0	ENST00000342788.4:c.3268G>T	p.Glu1090Ter	p.E1090*	ENST00000342788	NM_005235.2	1090	Gaa/Taa	27/28	0.311233928919914	1	FACETS	0.667	0.595	0.741	0.667	0.595	0.741	INDETERMINATE	1	TRUE	0	0.526203056884555	1		250	374	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225367791	225367791	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0032685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	65	256	0	ENST00000264414.4:c.1378-2A>C		p.X460_splice	ENST00000264414	NM_003590.4	460			0.311233928919914	1	FACETS	0.662	0.58	0.749	0.662	0.58	0.749	INDETERMINATE	1	TRUE	0	0.526203056884555	1		256	275	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663433	227663433	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs745389011	NA	P-0032685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	66	235	0	ENST00000305123.5:c.22G>C	p.Asp8His	p.D8H	ENST00000305123	NM_005544.2	8	Gat/Cat	1/2	0.311233928919914	1	FACETS	0.725	0.637	0.818	0.725	0.637	0.818	INDETERMINATE	1	TRUE	0	0.526203056884555	1		235	255	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127933446	127933446	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	86	361	0	ENST00000373547.4:c.89A>G	p.Tyr30Cys	p.Y30C	ENST00000373547	NM_002721.4	30	tAc/tGc	2/7	0.173536825625473	3	FACETS	0.86	0.764	0.963	0.287	0.254	0.321	INDETERMINATE	1	TRUE	0	0.526203056884555	3		361	480	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770071	56770071	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	34	479	0	ENST00000337432.4:c.67G>T	p.Val23Leu	p.V23L	ENST00000337432	NM_058216.2	23	Gtg/Ttg	1/9	0.377859234558613	3	FACETS	0.468	0.382	0.565	0.156	0.127	0.189	SUBCLONAL	1	TRUE	0	0.381219745650401	3		479	454	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770083	56770083	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	33	480	0	ENST00000337432.4:c.79C>G	p.Leu27Val	p.L27V	ENST00000337432	NM_058216.2	27	Ctg/Gtg	1/9	0.377859234558613	3	FACETS	0.454	0.369	0.55	0.151	0.123	0.184	SUBCLONAL	1	TRUE	0	0.381219745650401	3		480	454	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287280	33287280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	52	501	1	ENST00000374542.5:c.1817G>A	p.Gly606Asp	p.G606D	ENST00000374542	NM_001141970.1	606	gGc/gAc	6/8	0.381219745650401	3	FACETS	0.766	0.654	0.889	0.383	0.327	0.445	SUBCLONAL	1	TRUE	1	0.381219745650401	3		502	424	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845334	76845334	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	34	388	0	ENST00000373344.5:c.6187G>C	p.Glu2063Gln	p.E2063Q	ENST00000373344	NM_000489.3	2063	Gaa/Caa	27/35	0.381219745650401	1	FACETS	0.665	0.548	0.795	0.665	0.548	0.795	SUBCLONAL	1	TRUE	0	0.381219745650401	1		388	217	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0032689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	87	569	1	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.232594503513546	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.232594503513546	1		570	551	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044901	47044901	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	108	863	0	ENST00000377604.3:c.2227G>T	p.Glu743Ter	p.E743*	ENST00000377604	NM_001204468.1	743	Gag/Tag	20/24	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.232594503513546	2		863	709	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056140	27056140	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0032689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	29	349	0	ENST00000324856.7:c.1138-2A>T		p.X380_splice	ENST00000324856	NM_006015.4	380			1	2	FACETS	0.823	0.662	1	0.823	0.662	1	CLONAL	1	TRUE	1	0.232594503513546	2		349	303	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163309260	163309260	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	34	318	0	ENST00000271452.3:c.599A>C	p.Gln200Pro	p.Q200P	ENST00000271452	NM_145697.2	200	cAa/cCa	8/14	0.118436937532821	3	FACETS	0.963	0.788	1	0.481	0.394	0.579	INDETERMINATE	1	TRUE	1	0.232594503513546	3		318	339	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156639	2156640	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0032689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	67	565	2	ENST00000434045.2:c.282_283delinsCT	p.Asp95Tyr	p.D95Y	ENST00000434045	NM_001127598.1	94	gtGGac/gtCTac	3/5	0.118436937532821	3	FACETS	1	0.959	1	0.632	0.55	0.72	INDETERMINATE	1	TRUE	1	0.232594503513546	3		567	509	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623550	28623550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	69	450	2	ENST00000241453.7:c.1007C>A	p.Pro336His	p.P336H	ENST00000241453	NM_004119.2	336	cCc/cAc	8/24	0.118436937532821	3	FACETS	1	0.97	1	0.708	0.618	0.804	INDETERMINATE	1	TRUE	1	0.232594503513546	3		452	468	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571442	95571442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	30	243	0	ENST00000393063.1:c.3235G>A	p.Gly1079Ser	p.G1079S	ENST00000393063	NM_030621.3	1079	Ggc/Agc	21/28	1	2	FACETS	0.931	0.753	1	0.931	0.753	1	CLONAL	1	TRUE	1	0.232594503513546	2		243	277	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119706	17119706	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	44	436	0	ENST00000285071.4:c.1288G>T	p.Val430Leu	p.V430L	ENST00000285071	NM_144997.5	430	Gtg/Ttg	11/14	0.232594503513546	1	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	0	0.232594503513546	1		436	316	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586483	189586483	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	52	359	0	ENST00000264731.3:c.1107G>T	p.Lys369Asn	p.K369N	ENST00000264731	NM_003722.4	369	aaG/aaT	8/14	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.232594503513546	2		359	346	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542629	187542629	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	34	503	1	ENST00000441802.2:c.5111G>T	p.Gly1704Val	p.G1704V	ENST00000441802	NM_005245.3	1704	gGa/gTa	10/27	1	2	FACETS	0.593	0.484	0.716	0.593	0.484	0.716	SUBCLONAL	1	TRUE	1	0.232594503513546	2		504	493	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589161	67589161	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	18	284	0	ENST00000274335.5:c.1149A>G	p.Ile383Met	p.I383M	ENST00000274335		383	atA/atG	9/15	1	2	FACETS	0.664	0.501	0.856	0.664	0.501	0.856	SUBCLONAL	1	TRUE	1	0.232594503513546	2		284	233	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207038	1207039	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	T	novel	NA	P-0032689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	80	618	0	ENST00000326873.7:c.126_127delinsT	p.Ala43ProfsTer8	p.A43Pfs*8	ENST00000326873	NM_000455.4	42	cgGGcc/cgTcc	1/10	0.232594503513546	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.232594503513546	1		618	502	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162077	47162078	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	51	341	0	ENST00000409792.3:c.4048dup	p.Ser1350PhefsTer6	p.S1350Ffs*6	ENST00000409792	NM_014159.6	1350	tca/tTca	3/21	1	2	FACETS	0.614	0.523	0.714	0.614	0.523	0.714	SUBCLONAL	1	TRUE	1	0.396255668460041	2		341	419	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	70	258	0				ENST00000310581	NM_198253.2	-/1132			0.105462475845465	3	FACETS	1	0.974	1	0.677	0.605	0.751	INDETERMINATE	1	TRUE	1	0.896161252329827	3		258	167	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0032693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	264	574	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.105462475845465	3	FACETS	1	0.994	1	0.739	0.699	0.779	INDETERMINATE	1	TRUE	1	0.896161252329827	3		574	577	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACAACCCCC	rs397517115	NA	P-0032693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	1301	441	0	ENST00000275493.2:c.2311_2319dup	p.Asn771_His773dup	p.N771_H773dup	ENST00000275493	NM_005228.3	771	gac/gACAACCCCCac	20/28	0.896161252329827	11	FACETS	0.97	0.95	0.991			1	CLONAL	7	TRUE	NA	0.896161252329827	11		441	2151	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577142	+	missense_variant	Missense_Mutation	DNP	CC	CC	GT	novel	NA	P-0032693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	219	547	0	ENST00000269305.4:c.796_797delinsAC	p.Gly266Thr	p.G266T	ENST00000269305	NM_001126112.2	266	GGa/ACa	8/11	0.105462475845465	3	FACETS	1	0.993	1	0.736	0.692	0.78	INDETERMINATE	1	TRUE	1	0.896161252329827	3		547	481	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	141	447	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.867	0.794	0.942	0.867	0.794	0.942	CLONAL	1	TRUE	1	0.616287152392635	2		447	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs967461896	NA	P-0032696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	243	622	0	ENST00000269305.4:c.526T>A	p.Cys176Ser	p.C176S	ENST00000269305	NM_001126112.2	176	Tgc/Agc	5/11	0.616287152392635	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.616287152392635	1		622	504	SUCCESS
BLM	641	MSKCC	GRCh37	15	91298115	91298115	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	116	330	0	ENST00000355112.3:c.1034C>A	p.Pro345His	p.P345H	ENST00000355112	NM_000057.2	345	cCt/cAt	5/22	0.475271389058125	1	FACETS	0.829	0.758	0.903	0.829	0.758	0.903	CLONAL	1	TRUE	0	0.616287152392635	1		330	314	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757401	40757401	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1240	181	616	0	ENST00000373198.4:c.2897A>G	p.Tyr966Cys	p.Y966C	ENST00000373198	NM_133170.3	966	tAc/tGc	20/32	0.616287152392635	5	FACETS	0.795	0.731	0.863	0.199	0.182	0.216	SUBCLONAL	1	TRUE	1	0.616287152392635	5		616	1421	SUCCESS
APC	324	MSKCC	GRCh37	5	112175749	112175750	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0032696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	93	334	0	ENST00000257430.4:c.4459_4460dup	p.Leu1489TyrfsTer19	p.L1489Yfs*19	ENST00000257430	NM_000038.5	1486	-/AC	16/16	1	2	FACETS	0.818	0.733	0.907	0.818	0.733	0.907	CLONAL	1	TRUE	1	0.616287152392635	2		334	369	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	117	447	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.989	0.898	1	0.989	0.898	1	CLONAL	1	TRUE	1	0.524773031331218	2		447	451	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0032702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	33	314	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.265	0.216	0.321	0.265	0.216	0.321	SUBCLONAL	1	TRUE	1	0.524773031331218	2		314	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0032702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	308	720	4	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.524773031331218	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.524773031331218	1		724	808	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0032702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	54	239	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.328476712911276	1	FACETS	0.635	0.548	0.728	0.635	0.548	0.728	SUBCLONAL	1	TRUE	0	0.524773031331218	1		239	239	SUCCESS
APC	324	MSKCC	GRCh37	5	112175761	112175761	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	79	313	0	ENST00000257430.4:c.4473del	p.Phe1491LeufsTer16	p.F1491Lfs*16	ENST00000257430	NM_000038.5	1490	caT/ca	16/16	0.328476712911276	1	FACETS	0.55	0.486	0.617	0.55	0.486	0.617	SUBCLONAL	1	TRUE	0	0.524773031331218	1		313	404	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552198	29552198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	28	442	0	ENST00000356175.3:c.1931C>T	p.Ser644Phe	p.S644F	ENST00000356175	NM_000267.3	644	tCc/tTc	17/57	NA	2	FACETS	0.244	0.195	0.301			1	INDETERMINATE	1	TRUE	NA	0.524773031331218	2		442	437	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450363	50450363	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1441542459	NA	P-0032702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	205	427	0	ENST00000331340.3:c.547C>T	p.Arg183Cys	p.R183C	ENST00000331340	NM_006060.4	183	Cgc/Tgc	5/8	0.357955392920631	3	FACETS	1	0.986	1	0.616	0.572	0.66	CLONAL	1	TRUE	1	0.524773031331218	3		427	801	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229244	36229245	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAATGCCGCCCGCTTCAT	novel	NA	P-0032702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	67	674	0	ENST00000222270.7:c.7938_7955dup	p.Ala2647_Asn2652dup	p.A2647_N2652dup	ENST00000222270	NM_014727.1	2647	ggc/ggCAATGCCGCCCGCTTCATc	37/37	0.220283167067323	3	FACETS	0.279	0.241	0.32	0.139	0.12	0.16	INDETERMINATE	1	TRUE	1	0.524773031331218	3		674	1157	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76856028	76856028	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	97	386	0	ENST00000373344.5:c.5572G>A	p.Gly1858Ser	p.G1858S	ENST00000373344	NM_000489.3	1858	Ggc/Agc	23/35	1	2	FACETS	0.848	0.76	0.94	0.848	0.76	0.94	CLONAL	1	TRUE	1	0.524773031331218	2		386	436	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0032751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	175	361	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	1	2	FACETS	0.922	0.859	0.986	1	0.994	1	CLONAL	3	FALSE	1	0.294925467611347	2		361	429	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0032751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	214	443	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	1	0.969	1	1	0.995	1	CLONAL	3	FALSE	1	0.294925467611347	2		443	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0032755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	256	535	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.3068004015304	3	FACETS	0.857	0.805	0.909	0.857	0.805	0.909	CLONAL	3	TRUE	0	0.3068004015304	3		535	749	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968867	15968867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772605440	NA	P-0032755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	103	443	0	ENST00000268712.3:c.4883G>A	p.Arg1628His	p.R1628H	ENST00000268712	NM_006311.3	1628	cGt/cAt	33/46	0.3068004015304	3	FACETS	1	0.958	1	0.379	0.339	0.421	CLONAL	1	TRUE	0	0.3068004015304	3		443	681	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086205	16086205	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	31	352	0	ENST00000281043.3:c.1381G>T	p.Ala461Ser	p.A461S	ENST00000281043	NM_005378.4	461	Gct/Tct	3/3	0.177242482136813	3	FACETS	0.56	0.453	0.682	0.28	0.226	0.341	INDETERMINATE	1	TRUE	1	0.3068004015304	3		352	416	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201565	133201565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765125852	NA	P-0032755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	136	490	0	ENST00000320574.5:c.6673C>T	p.Arg2225Cys	p.R2225C	ENST00000320574	NM_006231.2	2225	Cgc/Tgc	48/49	0.3068004015304	3	FACETS	0.844	0.77	0.921	0.562	0.513	0.614	CLONAL	2	TRUE	0	0.3068004015304	3		490	606	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667552	29667552	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	111	484	0	ENST00000356175.3:c.6888G>T	p.Trp2296Cys	p.W2296C	ENST00000356175	NM_000267.3	2296	tgG/tgT	46/57	0.3068004015304	3	FACETS	1	0.976	1	0.642	0.578	0.71	CLONAL	1	TRUE	1	0.3068004015304	3		484	650	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273279	198273279	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	43	390	0	ENST00000335508.6:c.931G>C	p.Ala311Pro	p.A311P	ENST00000335508	NM_012433.2	311	Gct/Cct	8/25	0.177242482136813	3	FACETS	0.613	0.513	0.725	0.307	0.256	0.363	INDETERMINATE	1	TRUE	1	0.3068004015304	3		390	527	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587152	212587152	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	61	450	0	ENST00000342788.4:c.849C>A	p.Tyr283Ter	p.Y283*	ENST00000342788	NM_005235.2	283	taC/taA	7/28	0.177242482136813	3	FACETS	0.958	0.828	1	0.479	0.414	0.549	INDETERMINATE	1	TRUE	1	0.3068004015304	3		450	479	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204655	128204655	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	66	480	0	ENST00000341105.2:c.786C>A	p.Ser262Arg	p.S262R	ENST00000341105	NM_032638.4	262	agC/agA	3/6	0.204794124100592	2	FACETS	0.722	0.627	0.825	0.361	0.313	0.413	SUBCLONAL	1	TRUE	0	0.3068004015304	2		480	596	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495468	149495468	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	143	639	0	ENST00000261799.4:c.3179G>A	p.Cys1060Tyr	p.C1060Y	ENST00000261799	NM_002609.3	1060	tGt/tAt	23/23	0.204794124100592	2	FACETS	1	0.982	1	0.65	0.594	0.709	CLONAL	1	TRUE	0	0.3068004015304	2		639	717	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43745355	43745355	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	138	506	0	ENST00000523873.1:c.268G>T	p.Glu90Ter	p.E90*	ENST00000523873		90	Gag/Tag	3/8	0.3068004015304	4	FACETS	1	0.985	1	0.47	0.427	0.514	CLONAL	1	TRUE	1	0.3068004015304	4		506	834	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393703	139393703	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	32	459	0	ENST00000277541.6:c.5943C>G	p.Ile1981Met	p.I1981M	ENST00000277541	NM_017617.3	1981	atC/atG	32/34	1	2	FACETS	0.383	0.31	0.465	0.383	0.31	0.465	SUBCLONAL	1	TRUE	1	0.3068004015304	2		459	545	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348454	70348454	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	35	479	0	ENST00000374080.3:c.3361G>T	p.Asp1121Tyr	p.D1121Y	ENST00000374080		1121	Gac/Tac	24/45	1	2	FACETS	0.444	0.363	0.535	0.444	0.363	0.535	SUBCLONAL	1	TRUE	1	0.3068004015304	2		479	514	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303273	11303276	+	missense_variant	Missense_Mutation	ONP	AGGG	AGGG	CGGC	novel	NA	P-0032755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	64	497	0	ENST00000361445.4:c.1307_1310delinsGCCG	p.Ala436_Leu437delinsGlyArg	p.A436_L437delinsGR	ENST00000361445	NM_004958.3	436	gCCCTg/gGCCGg	9/58	0.177242482136813	3	FACETS	0.801	0.693	0.917	0.4	0.346	0.459	INDETERMINATE	1	TRUE	1	0.3068004015304	3		497	601	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061854	38061862	+	inframe_deletion	In_Frame_Del	DEL	GTTCATGGA	GTTCATGGA	-	novel	NA	P-0032757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	109	575	0	ENST00000250448.2:c.127_135del	p.Ser43_Asn45del	p.S43_N45del	ENST00000250448	NM_004496.3	43	TCCATGAAC/-	2/2	1	2	FACETS	0.786	0.708	0.867	0.786	0.708	0.867	SUBCLONAL	1	TRUE	1	0.517736040802487	2		575	536	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061232	38061234	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0032757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	109	392	0	ENST00000250448.2:c.755_757del	p.Asn252del	p.N252del	ENST00000250448	NM_004496.3	252	aACAtg/atg	2/2	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.517736040802487	2		392	383	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222501	2222501	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	113	547	0	ENST00000326181.6:c.695G>C	p.Arg232Pro	p.R232P	ENST00000326181	NM_032271.2	232	cGg/cCg	9/21	1	2	FACETS	0.957	0.867	1	0.957	0.867	1	CLONAL	1	TRUE	1	0.517736040802487	2		547	456	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19261498	19261498	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	117	483	0	ENST00000162023.5:c.47A>T	p.Asn16Ile	p.N16I	ENST00000162023		16	aAt/aTt	6/13	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.517736040802487	2		483	423	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745212	41745212	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	85	416	0	ENST00000301178.4:c.1278G>T	p.Trp426Cys	p.W426C	ENST00000301178	NM_021913.4	426	tgG/tgT	9/20	1	2	FACETS	0.89	0.792	0.993	0.89	0.792	0.993	CLONAL	1	TRUE	1	0.517736040802487	2		416	369	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375181	31375181	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	99	480	0	ENST00000328111.2:c.578A>T	p.Gln193Leu	p.Q193L	ENST00000328111	NM_006892.3	193	cAg/cTg	6/23	1	2	FACETS	0.846	0.759	0.937	0.846	0.759	0.937	CLONAL	1	TRUE	1	0.517736040802487	2		480	452	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155571	56155571	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	67	284	0	ENST00000399503.3:c.663T>G	p.Asp221Glu	p.D221E	ENST00000399503	NM_005921.1	221	gaT/gaG	3/20	1	2	FACETS	0.911	0.8	1	0.911	0.8	1	CLONAL	1	TRUE	1	0.517736040802487	2		284	284	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120509066	120509066	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	235	412	0	ENST00000256646.2:c.1500C>A	p.Ser500Arg	p.S500R	ENST00000256646	NM_024408.3	500	agC/agA	9/34	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.930643901853816	2		412	496	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0032780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	38	410	0				ENST00000310581	NM_198253.2	-/1132			0.202986550823623	0	FACETS	0.562	0.471	0.661			1	INDETERMINATE	1	FALSE	0	0.437214174759194	0		410	174	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0032780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	222	609	0	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	0.437214174759194	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	0	0.437214174759194	1		609	703	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453145	140453145	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913366	NA	P-0032780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	66	277	0	ENST00000288602.6:c.1790T>A	p.Leu597Gln	p.L597Q	ENST00000288602	NM_004333.4	597	cTa/cAa	15/18	1	2	FACETS	0.812	0.708	0.922	0.812	0.708	0.922	CLONAL	1	FALSE	1	0.437214174759194	2		277	372	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077580	30077580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	63	277	0	ENST00000338641.4:c.1727C>T	p.Thr576Ile	p.T576I	ENST00000338641	NM_000268.3	576	aCc/aTc	15/16	1	2	FACETS	0.898	0.782	1	0.898	0.782	1	CLONAL	1	FALSE	1	0.437214174759194	2		277	321	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279569	1279569	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	54	558	2	ENST00000310581.5:c.1967C>T	p.Ser656Leu	p.S656L	ENST00000310581	NM_198253.2	656	tCg/tTg	5/16	0.202986550823623	0	FACETS	0.396	0.34	0.457			1	INDETERMINATE	1	FALSE	0	0.437214174759194	0		560	351	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39214711	39214711	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	132	323	0	ENST00000402219.2:c.3413T>C	p.Ile1138Thr	p.I1138T	ENST00000402219	NM_005633.3	1138	aTa/aCa	22/23	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.437214174759194	2		323	531	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981534	70981534	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	93	661	0	ENST00000276594.2:c.562G>A	p.Glu188Lys	p.E188K	ENST00000276594	NM_024504.3	188	Gaa/Aaa	2/8	0.437214174759194	1	FACETS	0.694	0.62	0.773	0.694	0.62	0.773	SUBCLONAL	1	FALSE	0	0.437214174759194	1		661	479	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156737	20156737	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	108	410	0	ENST00000379607.5:c.20A>G	p.Lys7Arg	p.K7R	ENST00000379607	NM_001412.3	7	aAa/aGa	2/7	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.785717393227134	2		410	250	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229002	36229009	+	frameshift_variant	Frame_Shift_Del	DEL	CATCGACG	CATCGACG	-	novel	NA	P-0032782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	122	638	0	ENST00000222270.7:c.7783_7790del	p.Ile2595GlyfsTer18	p.I2595Gfs*18	ENST00000222270	NM_014727.1	2594	aaCATCGACGcg/aacg	36/37	0.416621470732866	5	FACETS	0.942	0.85	1	0.236	0.212	0.26	CLONAL	1	TRUE	1	0.416621470732866	5		638	1010	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933278	100933279	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	36	536	0	ENST00000325455.5:c.2111dup	p.Asp704GlufsTer6	p.D704Efs*6	ENST00000325455	NM_001202474.3	704	gac/gaAc	4/8	0.62340321657619	1	FACETS	0.138	0.112	0.166	0.138	0.112	0.166	SUBCLONAL	1	TRUE	0	0.62340321657619	1		536	578	SUCCESS
APC	324	MSKCC	GRCh37	5	112174096	112174096	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs137854575	NA	P-0032784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	93	276	0	ENST00000257430.4:c.2805C>G	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	taC/taG	16/16	0.253530325188168	2	FACETS	0.958	0.858	1	0.958	0.858	1	CLONAL	2	TRUE	0	0.253530325188168	2		276	383	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248153	110248153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	58	384	0	ENST00000374672.4:c.1319C>T	p.Ser440Leu	p.S440L	ENST00000374672	NM_004235.4	440	tCa/tTa	5/5	1	2	FACETS	0.883	0.76	1	0.883	0.76	1	CLONAL	1	TRUE	1	0.253530325188168	2		384	518	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446282	70446282	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs371499355	NA	P-0032784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	128	376	0	ENST00000373644.4:c.5222G>T	p.Arg1741Leu	p.R1741L	ENST00000373644	NM_030625.2	1741	cGc/cTc	11/12	0.230473920577219	3	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	1	0.253530325188168	3		376	535	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967262	38967262	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0032784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	31	172	0	ENST00000357387.3:c.1218+1G>T		p.X406_splice	ENST00000357387	NM_152756.3	406			0.253530325188168	3	FACETS	0.977	0.793	1	0.489	0.396	0.592	CLONAL	1	TRUE	1	0.253530325188168	3		172	282	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78811796	78811796	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	54	364	0	ENST00000306801.3:c.1212+1del		p.R404fs	ENST00000306801	NM_020761.2	404	cGg/cg	10/34	0.192932866562839	4	FACETS	0.955	0.816	1	0.478	0.408	0.554	CLONAL	1	TRUE	2	0.253530325188168	4		364	559	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220380	1220380	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	124	443	1	ENST00000326873.7:c.473del	p.Cys158PhefsTer3	p.C158Ffs*3	ENST00000326873	NM_000455.4	158	tGt/tt	4/10	0.253530325188168	2	FACETS	0.855	0.776	0.937	0.855	0.776	0.937	CLONAL	2	TRUE	0	0.253530325188168	2		444	572	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222462	39222462	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs886041814	NA	P-0032784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	60	575	0	ENST00000402219.2:c.3148A>G	p.Met1050Val	p.M1050V	ENST00000402219	NM_005633.3	1050	Atg/Gtg	20/23	0.230473920577219	3	FACETS	0.68	0.585	0.785	0.34	0.292	0.393	SUBCLONAL	1	TRUE	1	0.253530325188168	3		575	784	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352982	70352982	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	53	409	0	ENST00000374080.3:c.4537A>G	p.Asn1513Asp	p.N1513D	ENST00000374080		1513	Aat/Gat	33/45	0.230473920577219	3	FACETS	0.756	0.644	0.879	0.378	0.322	0.44	SUBCLONAL	1	TRUE	1	0.253530325188168	3		409	623	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	171	258	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.974	1	1	0.994	1	CLONAL	2	TRUE	1	0.403549962656957	2		258	389	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	83	378	0	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	0.381516119656352	0	FACETS	0.879	0.786	0.977			1	CLONAL	1	TRUE	0	0.403549962656957	0		378	279	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600634	43600634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1564491460	NA	P-0032876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	220	487	0	ENST00000355710.3:c.860G>A	p.Arg287Gln	p.R287Q	ENST00000355710	NM_020975.4	287	cGg/cAg	4/20	1	2	FACETS	0.921	0.863	0.98	1	0.994	1	CLONAL	2	TRUE	1	0.403549962656957	2		487	592	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087944	27087944	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0000120-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	204	596	0	ENST00000324856.7:c.2231C>G	p.Ser744Ter	p.S744*	ENST00000324856	NM_006015.4	744	tCa/tGa	6/20	1	2	FACETS	0.926	0.86	0.994	0.926	0.86	0.994	CLONAL	1	TRUE	1	0.520987299516808	2		596	846	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686863	37686863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000120-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	185	428	0	ENST00000447079.4:c.3767C>T	p.Pro1256Leu	p.P1256L	ENST00000447079	NM_015083.1	1256	cCt/cTt	14/14	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.520987299516808	2		428	672	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866328	42866328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150389990	NA	P-0000120-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	243	640	0	ENST00000398585.3:c.304G>A	p.Val102Ile	p.V102I	ENST00000398585	NM_001135099.1	102	Gtc/Atc	3/14	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.520987299516808	2		640	897	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122880	2122880	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45517222	NA	P-0000120-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	237	659	1	ENST00000219476.3:c.2251C>T	p.Arg751Ter	p.R751*	ENST00000219476	NM_000548.3	751	Cga/Tga	21/42	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.520987299516808	2		660	848	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437399	110437399	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000120-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	65	187	0	ENST00000375856.3:c.1002C>G	p.Ser334Arg	p.S334R	ENST00000375856	NM_003749.2	334	agC/agG	1/2	0.520987299516808	4	FACETS	0.83	0.722	0.947			1	CLONAL	1	TRUE	NA	0.520987299516808	4		187	457	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62303963	62303963	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000120-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	220	578	0	ENST00000360203.5:c.754G>C	p.Ala252Pro	p.A252P	ENST00000360203	NM_001283009.1	252	Gct/Cct	9/35	0.520987299516808	3	FACETS	1	0.975	1	0.55	0.512	0.59	CLONAL	1	TRUE	1	0.520987299516808	3		578	967	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948755	55948781	+	inframe_deletion	In_Frame_Del	DEL	TTTACACTCACAGGCCGGCTCTTTCGC	TTTACACTCACAGGCCGGCTCTTTCGC	-	novel	NA	P-0000120-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	72	498	0	ENST00000263923.4:c.3684_3710del	p.Arg1229_Lys1237del	p.R1229_K1237del	ENST00000263923	NM_002253.2	1228	aaGCGAAAGAGCCGGCCTGTGAGTGTAAAa/aaa	28/30	1	2	FACETS	0.399	0.348	0.454	0.399	0.348	0.454	SUBCLONAL	1	TRUE	1	0.520987299516808	2		498	693	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294541	1294541	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000120-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	62	279	0	ENST00000310581.5:c.460G>C	p.Ala154Pro	p.A154P	ENST00000310581	NM_198253.2	154	Gca/Cca	2/16	0.520987299516808	3	FACETS	0.647	0.56	0.741	0.323	0.28	0.371	SUBCLONAL	1	TRUE	1	0.520987299516808	3		279	464	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971315	13971315	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000120-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	151	466	0	ENST00000405192.2:c.614G>C	p.Arg205Thr	p.R205T	ENST00000405192	NM_001163147.1	205	aGg/aCg	8/12	0.520987299516808	1	FACETS	0.916	0.844	0.99	0.916	0.844	0.99	CLONAL	1	TRUE	0	0.520987299516808	1		466	468	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435769	110435769	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs745351480	NA	P-0000120-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	15	59	0	ENST00000375856.3:c.2632G>C	p.Glu878Gln	p.E878Q	ENST00000375856	NM_003749.2	878	Gag/Cag	1/2	0.520987299516808	4	FACETS	0.554	0.407	0.729			1	SUBCLONAL	1	TRUE	NA	0.520987299516808	4		59	158	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0000122-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	473	835	0	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	0.805284323482304	1	FACETS	0.963	0.931	0.994	0.963	0.931	0.994	CLONAL	1	TRUE	0	0.805284323482304	1		835	729	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437341	121437341	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000122-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	99	825	0	ENST00000257555.6:c.1679C>T	p.Ser560Phe	p.S560F	ENST00000257555		560	tCt/tTt	9/10	1	2	FACETS	0.209	0.186	0.234	0.209	0.186	0.234	SUBCLONAL	1	TRUE	1	0.805284323482304	2		825	1176	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925083	81925083	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000122-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	337	605	0	ENST00000359376.3:c.874A>T	p.Thr292Ser	p.T292S	ENST00000359376	NM_002661.3	292	Acg/Tcg	11/33	0.805284323482304	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.805284323482304	1		605	493	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62316910	62316926	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGTTCCCCAGCAGGG	CTGGTTCCCCAGCAGGG	-	novel	NA	P-0000122-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	348	778	0	ENST00000360203.5:c.1230_1246del	p.Ser411GlyfsTer6	p.S411Gfs*6	ENST00000360203	NM_001283009.1	409	cCTGGTTCCCCAGCAGGG/c	15/35	0.289828456325034	1	FACETS	0.534	0.507	0.562	0.534	0.507	0.562	INDETERMINATE	1	TRUE	0	0.805284323482304	1		778	966	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343003	70343008	+	frameshift_variant	Frame_Shift_Ins	INS	AGCGTT	AGCGTT	TTCACAG	novel	NA	P-0000122-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	378	746	1	ENST00000374080.3:c.1544_1549delinsTTCACAG	p.Lys515IlefsTer23	p.K515Ifs*23	ENST00000374080		515	aAGCGTTct/aTTCACAGct	11/45	0.805284323482304	1	FACETS	0.91	0.875	0.945	0.91	0.875	0.945	CLONAL	1	TRUE	0	0.805284323482304	1		747	616	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431021	49431021	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000202-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	190	514	0	ENST00000301067.7:c.10118C>A	p.Ser3373Ter	p.S3373*	ENST00000301067	NM_003482.3	3373	tCa/tAa	34/54	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		514	395	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44896901	44896904	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TCAA	TCAA	-	novel	NA	P-0000202-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	700	472	0	ENST00000377967.4:c.622_625del	p.Gln208PhefsTer33	p.Q208Ffs*33	ENST00000377967	NM_021140.2	207	atTCAA/at	8/29	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		472	844	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397700	139397700	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000374-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	147	227	0	ENST00000277541.6:c.5101G>C	p.Ala1701Pro	p.A1701P	ENST00000277541	NM_017617.3	1701	Gca/Cca	27/34	0.261765893877326	5	FACETS	1	0.958	1	1	0.992	1	CLONAL	4	TRUE	3	0.261765893877326	5		227	371	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390864	139390876	+	frameshift_variant	Frame_Shift_Del	DEL	CGTCTGCCTGGCT	CGTCTGCCTGGCT	-	novel	NA	P-0000374-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	93	257	0	ENST00000277541.6:c.7315_7327del	p.Ser2439CysfsTer34	p.S2439Cfs*34	ENST00000277541	NM_017617.3	2439	AGCCAGGCAGACGtg/tg	34/34	0.261765893877326	5	FACETS	1	0.92	1	1	0.983	1	CLONAL	3	TRUE	3	0.261765893877326	5		257	321	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098895	47098895	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000434-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	141	208	0	ENST00000409792.3:c.6379C>T	p.Gln2127Ter	p.Q2127*	ENST00000409792	NM_014159.6	2127	Caa/Taa	15/21	1	2	FACETS	0.8	0.735	0.866	1	0.989	1	SUBCLONAL	2	TRUE	1	0.401634605097795	2		208	439	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807513	1807513	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000434-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	121	302	0	ENST00000260795.2:c.1682G>C	p.Gly561Ala	p.G561A	ENST00000260795		561	gGt/gCt	12/17	0.266007715144384	0	FACETS	0.996	0.91	1			1	CLONAL	1	TRUE	0	0.401634605097795	0		302	362	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544630	65544630	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs786203385	NA	P-0000434-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	152	227	0	ENST00000358664.4:c.295+1G>A		p.X99_splice	ENST00000358664	NM_002382.4	99			0.329954180018069	0	FACETS	0.733	0.683	0.783			1	SUBCLONAL	2	TRUE	0	0.401634605097795	0		227	309	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508643	38508643	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000434-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	179	241	0	ENST00000254066.5:c.691C>G	p.Leu231Val	p.L231V	ENST00000254066	NM_000964.3	231	Ctc/Gtc	6/9	0.148563255105964	6	FACETS	0.924	0.857	0.993			1	INDETERMINATE	3	TRUE	NA	0.401634605097795	6		241	580	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259228	36259229	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0000434-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	277	159	0	ENST00000300305.3:c.262dup	p.Glu88GlyfsTer50	p.E88Gfs*50	ENST00000300305		88	gag/gGag	3/8	0.196956445486896	3	FACETS	1	0.977	1	1	0.977	1	INDETERMINATE	2	TRUE	1	0.401634605097795	3		159	777	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086160	16086160	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000507-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	193	294	0	ENST00000281043.3:c.1336A>G	p.Lys446Glu	p.K446E	ENST00000281043	NM_005378.4	446	Aaa/Gaa	3/3	1	2	FACETS	0.987	0.916	1	0.987	0.916	1	CLONAL	1	TRUE	1	0.54	2		294	724	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71008502	71008502	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000507-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	141	537	0	ENST00000318789.4:c.1930G>T	p.Glu644Ter	p.E644*	ENST00000318789	NM_032682.5	644	Gaa/Taa	21/21	1	2	FACETS	0.426	0.386	0.467	0.426	0.386	0.467	SUBCLONAL	1	TRUE	1	0.54	2		537	1227	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685310	86685310	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000507-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	57	225	0	ENST00000274376.6:c.3026T>G	p.Leu1009Arg	p.L1009R	ENST00000274376	NM_002890.2	1009	cTt/cGt	24/25	0.149773385323976	4	FACETS	0.58	0.497	0.669	0.29	0.248	0.335	INDETERMINATE	1	TRUE	2	0.54	4		225	561	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589159	67589160	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TATT	novel	NA	P-0000507-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1323	101	435	0	ENST00000274335.5:c.1149_1152dup	p.His385IlefsTer11	p.H385Ifs*11	ENST00000274335		383	ata/aTATTta	9/15	0.149773385323976	4	FACETS	0.405	0.36	0.452	0.202	0.18	0.226	INDETERMINATE	1	TRUE	2	0.54	4		435	1424	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760514	133760514	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000507-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	80	486	0	ENST00000318560.5:c.2838del	p.Lys947SerfsTer122	p.K947Sfs*122	ENST00000318560	NM_005157.4	946	gCc/gc	11/11	NA	2	FACETS	0.353	0.31	0.4			1	INDETERMINATE	1	TRUE	NA	0.54	2		486	839	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913189	44913189	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000507-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1338	418	742	3	ENST00000377967.4:c.866del	p.Phe289SerfsTer36	p.F289Sfs*36	ENST00000377967	NM_021140.2	288	taT/ta	10/29	NA	2	FACETS	0.882	0.837	0.927			1	INDETERMINATE	1	TRUE	NA	0.54	2		745	1756	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263754	16263754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747098120	NA	P-0000524-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	110	360	0	ENST00000375759.3:c.10123G>A	p.Gly3375Ser	p.G3375S	ENST00000375759	NM_015001.2	3375	Ggt/Agt	12/15	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.733099855504462	NA		360	277	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390874	139390877	+	frameshift_variant	Frame_Shift_Del	DEL	GCTC	GCTC	-	novel	NA	P-0000524-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	56	287	0	ENST00000277541.6:c.7314_7317del	p.Ser2439ArgfsTer37	p.S2439Rfs*37	ENST00000277541	NM_017617.3	2438	ccGAGC/cc	34/34	0.733099855504462	1	FACETS	0.949	0.848	1	0.949	0.848	1	CLONAL	1	TRUE	0	0.733099855504462	1		287	102	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413113	139413115	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	novel	NA	P-0000524-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	90	408	0	ENST00000277541.6:c.1027_1029del	p.Ala343del	p.A343del	ENST00000277541	NM_017617.3	343	GCC/-	6/34	0.733099855504462	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.733099855504462	1		408	143	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123722	11123722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1263140481	NA	P-0000618-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	26	370	0	ENST00000358026.2:c.2372C>T	p.Ala791Val	p.A791V	ENST00000358026	NM_001128849.1	791	gCg/gTg	16/36	1	2	FACETS	0.277	0.219	0.344	0.277	0.219	0.344	SUBCLONAL	1	TRUE	1	0.489642008776856	2		370	383	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022913	27022938	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGCCGCCGCCAGCAGCCTGGGCAA	CCCGCCGCCGCCAGCAGCCTGGGCAA	-	rs797045262	NA	P-0000618-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	38	96	0	ENST00000324856.7:c.31_56del	p.Ser11AlafsTer91	p.S11Afs*91	ENST00000324856	NM_006015.4	7	CCCGCCGCCGCCAGCAGCCTGGGCAAc/c	1/20	0.335161508780831	4	FACETS	0.876	0.739	1			1	CLONAL	2	TRUE	NA	0.489642008776856	4		96	132	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390792	139390792	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0000618-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	69	262	0	ENST00000277541.6:c.7399del	p.Ser2467ArgfsTer10	p.S2467Rfs*10	ENST00000277541	NM_017617.3	2467	Tcg/cg	34/34	0.166823067941299	4	FACETS	1	0.924	1	1	0.924	1	INDETERMINATE	2	TRUE	2	0.489642008776856	4		262	199	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949081	44949082	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	C	novel	NA	P-0000618-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	232	341	0	ENST00000377967.4:c.3642_3643delinsC	p.Gly1215GlufsTer6	p.G1215Efs*6	ENST00000377967	NM_021140.2	1214	ccTGga/ccCga	25/29	1	1	FACETS	0.868	0.823	0.913	1	0.995	1	CLONAL	2	TRUE	0	0.489642008776856	1		341	412	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371770	116371770	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000623-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	26	365	0	ENST00000397752.3:c.1249C>G	p.Arg417Gly	p.R417G	ENST00000397752	NM_000245.2	417	Cga/Gga	3/21	1	2	FACETS	0.241	0.19	0.299	0.241	0.19	0.299	SUBCLONAL	1	FALSE	1	0.465427410376627	2		365	464	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949064	44949064	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000623-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	34	587	1	ENST00000377967.4:c.3625A>G	p.Arg1209Gly	p.R1209G	ENST00000377967	NM_021140.2	1209	Agg/Ggg	25/29	0.34314983431666	0	FACETS	0.169	0.138	0.204			1	SUBCLONAL	1	FALSE	0	0.465427410376627	0		588	462	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106553	27106554	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0000623-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	208	531	0	ENST00000324856.7:c.6165dup	p.Leu2056AlafsTer43	p.L2056Afs*43	ENST00000324856	NM_006015.4	2055	atg/atGg	20/20	1	2	FACETS	0.814	0.762	0.867	1	0.993	1	CLONAL	2	FALSE	1	0.465427410376627	2		531	549	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106553	27106554	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0000623-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	169	531	0	ENST00000324856.7:c.6165dup	p.Leu2056AlafsTer43	p.L2056Afs*43	ENST00000324856	NM_006015.4	2055	atg/atGg	20/20	0.186362424100297	1	FACETS	0.51	0.473	0.549	0.51	0.473	0.549	INDETERMINATE	1	TRUE	0	0.8	1		531	497	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030342	49030342	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000790-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	126	215	0	ENST00000267163.4:c.1817A>G	p.Tyr606Cys	p.Y606C	ENST00000267163	NM_000321.2	606	tAt/tGt	19/27	0.123922743269706	4	FACETS	1	0.976	1	1	0.976	1	INDETERMINATE	2	TRUE	2	0.403717042977051	4		215	369	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206772	36206776	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGT	GGCGT	-	novel	NA	P-0000790-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	13	121	0	ENST00000300305.3:c.736_740del	p.Thr246GlnfsTer13	p.T246Qfs*13	ENST00000300305		246	ACGCCc/c	6/8	0.123922743269706	4	FACETS	0.473	0.338	0.638	0.237	0.169	0.319	INDETERMINATE	1	TRUE	2	0.403717042977051	4		121	191	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928997	44928998	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0000792-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	299	456	0	ENST00000377967.4:c.2098dup	p.Ser700PhefsTer30	p.S700Ffs*30	ENST00000377967	NM_021140.2	699	-/T	17/29	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		456	1065	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937720	44937721	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0000948-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	33	427	0	ENST00000377967.4:c.2909_2910del	p.Ile970ThrfsTer8	p.I970Tfs*8	ENST00000377967	NM_021140.2	970	ATa/a	19/29	0.626462557367927	1	FACETS	0.21	0.171	0.253	0.21	0.171	0.253	SUBCLONAL	1	TRUE	0	0.75200866697415	1		427	261	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301138	65301138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1477623179	NA	P-0000980-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	90	259	0	ENST00000342505.4:c.3310C>T	p.Leu1104Phe	p.L1104F	ENST00000342505	NM_002227.2	1104	Ctt/Ttt	24/25	0.0948029342917255	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		259	874	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675669	86675669	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0000980-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	199	131	0	ENST00000274376.6:c.2603+2T>A		p.X868_splice	ENST00000274376	NM_002890.2	868			0.3	5	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	5		131	554	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530381	187530382	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0000980-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	334	270	0	ENST00000441802.2:c.10161dup	p.Val3388ArgfsTer27	p.V3388Rfs*27	ENST00000441802	NM_005245.3	3387	-/C	16/27	0.219691771689302	4	FACETS		NA	1			1	NA	NA	FALSE	2	NA	4		270	943	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409941	139409942	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0000980-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	78	220	0	ENST00000277541.6:c.1896dup	p.Thr633AspfsTer12	p.T633Dfs*12	ENST00000277541	NM_017617.3	632	-/G	11/34	0.3	4	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	4		220	651	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933446	39933447	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGGGAACT	novel	NA	P-0000980-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	249	143	0	ENST00000378444.4:c.1145_1152dup	p.Ala385SerfsTer60	p.A385Sfs*60	ENST00000378444	NM_001123385.1	384	-/AGTTCCCC	4/15	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		143	497	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982440	25982440	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001201-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	51	362	0	ENST00000435504.4:c.850C>T	p.Arg284Ter	p.R284*	ENST00000435504		284	Cga/Tga	9/13	1	2	FACETS	0.465	0.394	0.543	0.465	0.394	0.543	SUBCLONAL	1	TRUE	1	0.31	2		362	708	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198262721	198262721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001201-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	208	451	0	ENST00000335508.6:c.3254C>T	p.Ala1085Val	p.A1085V	ENST00000335508	NM_012433.2	1085	gCa/gTa	22/25	1	2	FACETS	1	0.968	1	1	0.994	1	CLONAL	2	TRUE	1	0.31	2		451	632	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425038	49425038	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783690	NA	P-0001201-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	46	582	2	ENST00000301067.7:c.13450C>T	p.Arg4484Ter	p.R4484*	ENST00000301067	NM_003482.3	4484	Cga/Tga	39/54	1	2	FACETS	0.477	0.401	0.561	0.477	0.401	0.561	SUBCLONAL	1	TRUE	1	0.31	2		584	622	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926885	112926885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507544	NA	P-0001201-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	52	434	0	ENST00000351677.2:c.1505C>T	p.Ser502Leu	p.S502L	ENST00000351677	NM_002834.3	502	tCa/tTa	13/16	1	2	FACETS	0.634	0.54	0.738	0.634	0.54	0.738	SUBCLONAL	1	TRUE	1	0.31	2		434	529	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86681188	86681189	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0001201-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	179	352	0	ENST00000274376.6:c.2830dup	p.Val944GlyfsTer6	p.V944Gfs*6	ENST00000274376	NM_002890.2	943	-/G	22/25	0.3	4	FACETS	1	0.972	1			1	CLONAL	2	TRUE	NA	0.31	4		352	686	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930340	39930341	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0001201-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	265	812	1	ENST00000378444.4:c.3123dup	p.Glu1042ArgfsTer37	p.E1042Rfs*37	ENST00000378444	NM_001123385.1	1041	-/C	6/15	0.3	1	FACETS	0.949	0.894	1	1	0.995	1	CLONAL	2	TRUE	0	0.31	1		813	761	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413072	139413076	+	missense_variant	Missense_Mutation	ONP	AAGGA	AAGGA	GAGGC	novel	NA	P-0001201-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	164	431	0	ENST00000277541.6:c.1066_1070delinsGCCTC	p.Ser356_Phe357delinsAlaSer	p.S356_F357delinsAS	ENST00000277541	NM_017617.3	356	TCCTTc/GCCTCc	6/34	0.443270599459399	4	FACETS	0.956	0.88	1	0.956	0.88	1	CLONAL	2	TRUE	2	0.31	4		431	725	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148516749	148516749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001327-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	216	287	0	ENST00000320356.2:c.938G>A	p.Arg313Gln	p.R313Q	ENST00000320356	NM_004456.4	313	cGg/cAg	9/20	1	2	FACETS	0.869	0.811	0.93	0.869	0.811	0.93	CLONAL	1	TRUE	1	0.657199377958776	2		287	756	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0001363-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	20	361	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.209735668968902	4	FACETS	0.617	0.474	0.781	0.308	0.237	0.391	INDETERMINATE	1	TRUE	2	0.54	4		361	185	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636171	87636171	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001363-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	53	278	0	ENST00000277120.3:c.2336T>C	p.Ile779Thr	p.I779T	ENST00000277120		779	aTa/aCa	19/19	0.290226516596251	4	FACETS	1	0.925	1	0.56	0.481	0.644	INDETERMINATE	1	TRUE	2	0.54	4		278	270	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911562	32911562	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659687	NA	P-0001363-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	70	239	0	ENST00000380152.3:c.3070A>G	p.Ile1024Val	p.I1024V	ENST00000380152		1024	Att/Gtt	11/27	0.414492072650771	4	FACETS	1	0.956	1	0.601	0.528	0.679	CLONAL	1	TRUE	2	0.54	4		239	332	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390792	139390792	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001451-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	111	262	0	ENST00000277541.6:c.7399del	p.Ser2467ArgfsTer10	p.S2467Rfs*10	ENST00000277541	NM_017617.3	2467	Tcg/cg	34/34	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.63	2		262	284	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106045	27106045	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001451-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	123	137	0	ENST00000324856.7:c.5656G>T	p.Glu1886Ter	p.E1886*	ENST00000324856	NM_006015.4	1886	Gag/Tag	20/20	0.185678388737745	3	FACETS	1	0.984	1	1	0.984	1	INDETERMINATE	2	TRUE	1	0.63	3		137	211	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188115	108188115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555114568	NA	P-0001451-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	159	343	0	ENST00000278616.4:c.6214G>A	p.Gly2072Arg	p.G2072R	ENST00000278616	NM_000051.3	2072	Gga/Aga	43/63	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.63	2		343	480	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418413	139418414	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0001451-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	23	81	0	ENST00000277541.6:c.158_159del	p.Val53GlyfsTer89	p.V53Gfs*89	ENST00000277541	NM_017617.3	53	gTG/g	3/34	1	2	FACETS	0.723	0.575	0.887	0.723	0.575	0.887	SUBCLONAL	1	TRUE	1	0.63	2		81	101	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922974	44922975	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0001451-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	152	435	0	ENST00000377967.4:c.1838dup	p.Asn613LysfsTer8	p.N613Kfs*8	ENST00000377967	NM_021140.2	612	cga/cgAa	16/29	0.313592310501917	0	FACETS	0.469	0.434	0.504			1	INDETERMINATE	1	TRUE	0	0.63	0		435	381	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022913	27022938	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGCCGCCGCCAGCAGCCTGGGCAA	CCCGCCGCCGCCAGCAGCCTGGGCAA	-	rs797045262	NA	P-0001585-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	23	96	0	ENST00000324856.7:c.31_56del	p.Ser11AlafsTer91	p.S11Afs*91	ENST00000324856	NM_006015.4	7	CCCGCCGCCGCCAGCAGCCTGGGCAAc/c	1/20	1	2	FACETS	1	0.804	1	1	0.804	1	CLONAL	1	FALSE	1	0.3	2		96	150	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931669	39931670	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATCGGTCACCCACGTAC	novel	NA	P-0001585-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	73	735	0	ENST00000378444.4:c.2929_2930insGTACGTGGGTGACCGAT	p.Phe977CysfsTer50	p.F977Cfs*50	ENST00000378444	NM_001123385.1	977	ttc/tGTACGTGGGTGACCGATtc	4/15	0.220087326795341	1	FACETS	0.467	0.407	0.531	0.467	0.407	0.531	SUBCLONAL	1	FALSE	0	0.3	1		735	886	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164601	36164601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002214-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	79	234	0	ENST00000300305.3:c.1274C>T	p.Pro425Leu	p.P425L	ENST00000300305		425	cCg/cTg	8/8	1	2	FACETS	0.323	0.284	0.365	0.323	0.284	0.365	SUBCLONAL	1	TRUE	1	0.769648903823086	2		234	635	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0003061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	89	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.865	0.767	0.969	0.865	0.767	0.969	CLONAL	1	TRUE	1	0.320171553291289	2		336	643	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0003111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	182	264	1	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.788462946319497	2		265	451	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0003327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	267	463	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.972	0.917	1	0.972	0.917	1	CLONAL	1	TRUE	1	0.805931750197777	2		463	682	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450366	50450366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	194	325	0	ENST00000331340.3:c.550C>T	p.Arg184Trp	p.R184W	ENST00000331340	NM_006060.4	184	Cgg/Tgg	5/8	1	2	FACETS	0.995	0.93	1	0.995	0.93	1	CLONAL	1	TRUE	1	0.805931750197777	2		325	484	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440404	49440404	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	183	330	0	ENST00000301067.7:c.4406G>A	p.Trp1469Ter	p.W1469*	ENST00000301067	NM_003482.3	1469	tGg/tAg	15/54	1	2	FACETS	0.897	0.835	0.961	0.897	0.835	0.961	CLONAL	1	TRUE	1	0.805931750197777	2		330	506	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459336	99459337	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACCGGCACAATTACTGCTCCAAAG	novel	NA	P-0003327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	273	389	0	ENST00000268035.6:c.1973_1996dup	p.Arg659_Asp666dup	p.R659_D666dup	ENST00000268035	NM_000875.3	659	tac/tACCGGCACAATTACTGCTCCAAAGac	9/21	0.378844067842614	2	FACETS	1	0.945	1	0.5	0.472	0.529	INDETERMINATE	1	TRUE	0	0.805931750197777	2		389	677	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390734	139390735	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGGGGGGC	novel	NA	P-0003327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	177	334	0	ENST00000277541.6:c.7449_7456dup	p.Ser2486CysfsTer106	p.S2486Cfs*106	ENST00000277541	NM_017617.3	2486	tcg/tGCCCCCCTcg	34/34	0.805931750197777	2	FACETS	1	0.991	1	0.691	0.649	0.732	CLONAL	1	TRUE	0	0.805931750197777	2		334	318	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287157	33287157	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003469-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	189	233	0	ENST00000374542.5:c.1940G>C	p.Ser647Thr	p.S647T	ENST00000374542	NM_001141970.1	647	aGc/aCc	6/8	0.910831955801513	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.910831955801513	1		233	225	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727889	78727889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003469-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	280	431	0	ENST00000306801.3:c.734C>T	p.Ala245Val	p.A245V	ENST00000306801	NM_020761.2	245	gCc/gTc	6/34	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.910831955801513	2		431	615	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577260	64577266	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGATA	GAGGATA	-	novel	NA	P-0003469-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	230	367	0	ENST00000312049.6:c.316_322del	p.Tyr106GlufsTer11	p.Y106Efs*11	ENST00000312049	NM_130799.2	106	TATCCTCga/ga	2/10	0.910831955801513	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.910831955801513	1		367	263	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247373	153247373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	140	263	0	ENST00000281708.4:c.1429G>A	p.Gly477Ser	p.G477S	ENST00000281708	NM_033632.3	477	Ggt/Agt	10/12	1	2	FACETS	0.97	0.891	1	0.97	0.891	1	CLONAL	1	TRUE	1	0.63	2		263	458	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247373	153247373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003532-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	168	263	0	ENST00000281708.4:c.1429G>A	p.Gly477Ser	p.G477S	ENST00000281708	NM_033632.3	477	Ggt/Agt	10/12	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.38	2		263	837	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911573	39911573	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	76	315	0	ENST00000378444.4:c.5057del	p.Asn1686ThrfsTer39	p.N1686Tfs*39	ENST00000378444	NM_001123385.1	1686	aAc/ac	15/15	1	1	FACETS	0.944	0.842	1	1	0.984	1	CLONAL	2	FALSE	0	0.3	1		315	228	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279971	18279971	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	162	538	0	ENST00000222254.8:c.2054T>G	p.Leu685Arg	p.L685R	ENST00000222254	NM_005027.3	685	cTg/cGg	16/16	1	2	FACETS	0.882	0.81	0.956	0.882	0.81	0.956	CLONAL	1	TRUE	1	0.481549010281153	2		538	763	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578229	7578237	+	inframe_deletion	In_Frame_Del	DEL	TCCAAATAC	TCCAAATAC	-	novel	NA	P-0003678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	199	703	0	ENST00000269305.4:c.612_620del	p.Glu204_Leu206del	p.E204_L206del	ENST00000269305	NM_001126112.2	204	gaGTATTTGGAt/gat	6/11	0.481549010281153	1	FACETS	0.909	0.846	0.975	0.909	0.846	0.975	CLONAL	1	TRUE	0	0.481549010281153	1		703	690	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117639384	117639384	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	62	579	0	ENST00000368508.3:c.5972A>C	p.Lys1991Thr	p.K1991T	ENST00000368508	NM_002944.2	1991	aAg/aCg	37/43	0.238202500818201	1	FACETS	0.298	0.257	0.343	0.298	0.257	0.343	INDETERMINATE	1	TRUE	0	0.481549010281153	1		579	655	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964491	70964491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1447674775	NA	P-0003678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	53	664	1	ENST00000276594.2:c.1537G>A	p.Gly513Arg	p.G513R	ENST00000276594	NM_024504.3	513	Ggg/Agg	8/8	0.357480472201989	1	FACETS	0.223	0.19	0.26	0.223	0.19	0.26	SUBCLONAL	1	TRUE	0	0.481549010281153	1		665	748	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134566	41134566	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	63	530	1	ENST00000379561.5:c.1062G>T	p.Lys354Asn	p.K354N	ENST00000379561	NM_002015.3	354	aaG/aaT	2/3	1	2	FACETS	0.417	0.36	0.478	0.417	0.36	0.478	SUBCLONAL	1	TRUE	1	0.481549010281153	2		531	628	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217441	7217441	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	59	578	0	ENST00000380728.2:c.355A>T	p.Ser119Cys	p.S119C	ENST00000380728		119	Agc/Tgc	5/11	0.481549010281153	1	FACETS	0.305	0.262	0.352	0.305	0.262	0.352	SUBCLONAL	1	TRUE	0	0.481549010281153	1		578	609	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754651	41754651	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	61	686	0	ENST00000301178.4:c.1637A>T	p.Glu546Val	p.E546V	ENST00000301178	NM_021913.4	546	gAg/gTg	14/20	1	2	FACETS	0.318	0.273	0.366	0.318	0.273	0.366	SUBCLONAL	1	TRUE	1	0.481549010281153	2		686	797	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295711	212295711	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	55	575	0	ENST00000342788.4:c.2602T>G	p.Leu868Val	p.L868V	ENST00000342788	NM_005235.2	868	Ttg/Gtg	21/28	1	2	FACETS	0.346	0.295	0.402	0.346	0.295	0.402	SUBCLONAL	1	TRUE	1	0.481549010281153	2		575	660	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376641	8376641	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	48	587	0	ENST00000356435.5:c.4472C>A	p.Ala1491Asp	p.A1491D	ENST00000356435		1491	gCc/gAc	27/35	1	2	FACETS	0.252	0.212	0.296	0.252	0.212	0.296	SUBCLONAL	1	TRUE	1	0.481549010281153	2		587	792	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	428	654	0	ENST00000206249.3:c.1607T>C	p.Leu536Pro	p.L536P	ENST00000206249	NM_000125.3	536	cTc/cCc	8/8	0.849653257983844	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.849653257983844	1		654	561	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500868	149500868	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1320275282	NA	P-0003751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	419	623	0	ENST00000261799.4:c.2362C>T	p.Arg788Ter	p.R788*	ENST00000261799	NM_002609.3	788	Cga/Tga	17/23	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.849653257983844	2		623	913	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061450	38061450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	266	451	0	ENST00000250448.2:c.539C>T	p.Thr180Ile	p.T180I	ENST00000250448	NM_004496.3	180	aCc/aTc	2/2	1	2	FACETS	0.956	0.903	1	0.956	0.903	1	CLONAL	1	TRUE	1	0.849653257983844	2		451	655	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112764363	112764363	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0003751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	207	390	0	ENST00000369452.4:c.973-1G>C		p.X325_splice	ENST00000369452	NM_007373.3	325			0.849653257983844	1	FACETS	0.97	0.926	1	0.97	0.926	1	CLONAL	1	TRUE	0	0.849653257983844	1		390	289	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55269476	55269476	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0003751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	587	908	0	ENST00000275493.2:c.3162+1G>C		p.X1054_splice	ENST00000275493	NM_005228.3	1054			1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.849653257983844	2		908	1260	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	33	270	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		270	106	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166323	118166323	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	301	459	0	ENST00000369448.3:c.833T>A	p.Phe278Tyr	p.F278Y	ENST00000369448	NM_017709.3	278	tTc/tAc	2/2	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.91108096722785	2		459	650	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946194	13946194	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	47	313	0	ENST00000405192.2:c.902G>T	p.Arg301Leu	p.R301L	ENST00000405192	NM_001163147.1	301	cGg/cTg	10/12	0.91108096722785	4	FACETS	0.324	0.273	0.38	0.162	0.136	0.19	SUBCLONAL	1	TRUE	2	0.91108096722785	4		313	609	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526658	106526658	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	277	422	0	ENST00000359195.3:c.2951C>A	p.Pro984Gln	p.P984Q	ENST00000359195	NM_002649.2	984	cCa/cAa	10/11	0.91108096722785	4	FACETS	0.981	0.92	1	0.49	0.46	0.522	CLONAL	1	TRUE	2	0.91108096722785	4		422	1185	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313484	30313484	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	295	429	0	ENST00000262643.3:c.1084A>G	p.Thr362Ala	p.T362A	ENST00000262643	NM_001238.2	362	Acc/Gcc	11/12	0.91108096722785	3	FACETS	1	0.962	1	0.513	0.484	0.543	CLONAL	1	TRUE	1	0.91108096722785	3		429	919	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391219	139391246	+	frameshift_variant	Frame_Shift_Del	DEL	GTTGTATTGGTTCGGCACCATGCCGCTC	GTTGTATTGGTTCGGCACCATGCCGCTC	-	novel	NA	P-0004371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	1102	399	0	ENST00000277541.6:c.6945_6972del	p.Gln2315HisfsTer12	p.Q2315Hfs*12	ENST00000277541	NM_017617.3	2315	caGAGCGGCATGGTGCCGAACCAATACAAC/ca	34/34	0.91108096722785	6	FACETS	1	0.992	1	0.845	0.831	0.858	CLONAL	5	TRUE	0	0.91108096722785	6		399	1347	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397636	139397637	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAG	novel	NA	P-0004371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	680	385	0	ENST00000277541.6:c.5164_5165insCTC	p.Val1721_Gln1722insPro	p.V1721_Q1722insP	ENST00000277541	NM_017617.3	1722	cag/cCTCag	27/34	0.91108096722785	6	FACETS	0.992	0.959	1	0.496	0.479	0.512	CLONAL	3	TRUE	0	0.91108096722785	6		385	1416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0004887-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	126	651	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.212478592030994	1	FACETS	0.759	0.689	0.834	1	0.986	1	SUBCLONAL	2	TRUE	0	0.212478592030994	1		651	698	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0004887-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	71	702	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	0.212478592030994	1	FACETS	0.882	0.77	1	0.882	0.77	1	CLONAL	1	TRUE	0	0.212478592030994	1		702	677	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106525	27106525	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004887-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	51	861	0	ENST00000324856.7:c.6136G>C	p.Val2046Leu	p.V2046L	ENST00000324856	NM_006015.4	2046	Gtg/Ctg	20/20	0.212478592030994	1	FACETS	0.453	0.384	0.53	0.453	0.384	0.53	SUBCLONAL	1	TRUE	0	0.212478592030994	1		861	947	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55963919	55963919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41469552	NA	P-0004887-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	41	554	0	ENST00000263923.4:c.2524C>T	p.Arg842Cys	p.R842C	ENST00000263923	NM_002253.2	842	Cgt/Tgt	18/30	0.114168288720278	0	FACETS	0.395	0.328	0.47			1	INDETERMINATE	1	TRUE	0	0.212478592030994	0		554	770	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843278	128843278	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004887-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	49	802	0	ENST00000249373.3:c.385G>C	p.Val129Leu	p.V129L	ENST00000249373	NM_005631.4	129	Gta/Cta	2/12	0.204826129481987	1	FACETS	0.568	0.48	0.665	0.568	0.48	0.665	SUBCLONAL	1	TRUE	0	0.212478592030994	1		802	726	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772939	135772939	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004887-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	73	558	0	ENST00000298552.3:c.2684T>A	p.Val895Asp	p.V895D	ENST00000298552	NM_001162426.1	895	gTt/gAt	21/23	0.193388226094826	0	FACETS	0.722	0.631	0.821			1	SUBCLONAL	1	TRUE	0	0.212478592030994	0		558	749	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998198	100998198	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004887-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	58	626	0	ENST00000325455.5:c.1604C>G	p.Pro535Arg	p.P535R	ENST00000325455	NM_001202474.3	535	cCg/cGg	1/8	0.212478592030994	3	FACETS	1	0.878	1			1	CLONAL	1	TRUE	NA	0.212478592030994	3		626	590	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124247	2124247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004887-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	70	725	1	ENST00000219476.3:c.2402C>T	p.Ala801Val	p.A801V	ENST00000219476	NM_000548.3	801	gCc/gTc	22/42	0.212478592030994	0	FACETS	1	0.928	1			1	CLONAL	1	TRUE	0	0.212478592030994	0		726	476	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120455	70120455	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004887-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	47	739	0	ENST00000245479.2:c.1457T>A	p.Val486Asp	p.V486D	ENST00000245479	NM_000346.3	486	gTc/gAc	3/3	0.212478592030994	2	FACETS	0.608	0.511	0.714	0.304	0.255	0.357	SUBCLONAL	1	TRUE	0	0.212478592030994	2		739	728	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205045	123205045	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004887-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	51	328	0	ENST00000218089.9:c.2405T>G	p.Ile802Ser	p.I802S	ENST00000218089	NM_001042749.1	802	aTt/aGt	25/35	0.133663867262124	0	FACETS	0.69	0.586	0.804			1	SUBCLONAL	1	TRUE	NA	0.212478592030994	0		328	548	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005361-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	82	270	0				ENST00000310581	NM_198253.2	-/1132			0.162583989039655	0	FACETS	0.423	0.379	0.469			1	INDETERMINATE	1	TRUE	0	0.621455366974733	0		270	236	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653807	89653807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554893782	NA	P-0005361-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	115	352	0	ENST00000371953.3:c.105G>A	p.Met35Ile	p.M35I	ENST00000371953	NM_000314.4	35	atG/atA	2/9	0.621455366974733	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.621455366974733	1		352	233	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281250	15281250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184522923	NA	P-0005361-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	239	617	0	ENST00000263388.2:c.5006G>A	p.Arg1669His	p.R1669H	ENST00000263388	NM_000435.2	1669	cGc/cAc	27/33	0.621455366974733	3	FACETS	1	0.961	1	0.52	0.485	0.555	CLONAL	1	TRUE	1	0.621455366974733	3		617	970	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572404	41572404	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs139310551	NA	P-0005361-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	282	560	0	ENST00000263253.7:c.4933C>T	p.Arg1645Ter	p.R1645*	ENST00000263253	NM_001429.3	1645	Cga/Tga	30/31	0.621455366974733	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.621455366974733	1		560	557	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953940	131953940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005361-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	129	363	0	ENST00000265335.6:c.3343G>A	p.Glu1115Lys	p.E1115K	ENST00000265335		1115	Gaa/Aaa	21/25	1	2	FACETS	0.86	0.784	0.938	0.86	0.784	0.938	CLONAL	1	TRUE	1	0.621455366974733	2		363	483	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702410	47702410	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs267607986	NA	P-0005361-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	88	201	1	ENST00000233146.2:c.2005+1G>A		p.X669_splice	ENST00000233146	NM_000251.2	669			1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.621455366974733	2		202	259	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209110138	209110138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1315254690	NA	P-0005361-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	147	361	0	ENST00000345146.2:c.425C>T	p.Thr142Ile	p.T142I	ENST00000345146	NM_005896.2	142	aCt/aTt	5/10	0.105861059082175	3	FACETS	1	0.984	1	0.649	0.597	0.702	INDETERMINATE	1	TRUE	1	0.621455366974733	3		361	478	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105236688	105236688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005361-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	243	535	3	ENST00000349310.3:c.1433G>A	p.Gly478Asp	p.G478D	ENST00000349310	NM_001014432.1	478	gGc/gAc	15/15	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.621455366974733	2		538	738	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257116	19257116	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1283878180	NA	P-0005361-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	150	446	0	ENST00000162023.5:c.847G>A	p.Gly283Ser	p.G283S	ENST00000162023		283	Ggt/Agt	12/13	0.621455366974733	3	FACETS	0.914	0.838	0.994	0.457	0.419	0.497	CLONAL	1	TRUE	1	0.621455366974733	3		446	692	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257363	19257363	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0005361-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	232	616	0	ENST00000162023.5:c.769+1G>A		p.X257_splice	ENST00000162023		257			0.621455366974733	3	FACETS	1	0.936	1	0.502	0.468	0.537	CLONAL	1	TRUE	1	0.621455366974733	3		616	975	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873110	136873110	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005361-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	137	317	0	ENST00000241393.3:c.388A>G	p.Ile130Val	p.I130V	ENST00000241393	NM_003467.2	130	Atc/Gtc	2/2	0.105861059082175	3	FACETS	1	0.979	1	0.61	0.558	0.663	INDETERMINATE	1	TRUE	1	0.621455366974733	3		317	474	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422521	225422521	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005361-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	100	416	0	ENST00000264414.4:c.119C>T	p.Ala40Val	p.A40V	ENST00000264414	NM_003590.4	40	gCa/gTa	2/16	NA	2	FACETS	0.879	0.792	0.97			1	INDETERMINATE	1	TRUE	NA	0.621455366974733	2		416	366	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808231	99808231	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005361-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	217	594	0	ENST00000280892.6:c.458C>T	p.Thr153Ile	p.T153I	ENST00000280892	NM_001130678.1	153	aCa/aTa	5/7	0.105861059082175	3	FACETS	1	0.965	1	0.528	0.491	0.565	INDETERMINATE	1	TRUE	1	0.621455366974733	3		594	867	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98002930	98002930	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1175257797	NA	P-0005361-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	101	382	0	ENST00000289081.3:c.345+1G>A		p.X115_splice	ENST00000289081	NM_000136.2	115			1	2	FACETS	0.923	0.833	1	0.923	0.833	1	CLONAL	1	TRUE	1	0.621455366974733	2		382	352	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044556	47044556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005361-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	217	683	2	ENST00000377604.3:c.2053C>T	p.Arg685Trp	p.R685W	ENST00000377604	NM_001204468.1	685	Cgg/Tgg	18/24	1	2	FACETS	0.855	0.797	0.915	0.855	0.797	0.915	CLONAL	1	TRUE	1	0.621455366974733	2		685	817	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937393	76937393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005361-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	133	400	0	ENST00000373344.5:c.3355G>A	p.Glu1119Lys	p.E1119K	ENST00000373344	NM_000489.3	1119	Gaa/Aaa	9/35	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.621455366974733	2		400	402	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918596	44918597	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0005392-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	392	233	0	ENST00000377967.4:c.1083_1084del	p.Tyr362Ter	p.Y362*	ENST00000377967	NM_021140.2	360	aCT/a	12/29	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.884269741189449	1		233	465	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399409	139399411	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	rs761020817	NA	P-0005392-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	365	426	6	ENST00000277541.6:c.4732_4734del	p.Val1578del	p.V1578del	ENST00000277541	NM_017617.3	1578	GTG/-	26/34	NA	2	FACETS	0.868	0.826	0.911			1	INDETERMINATE	1	TRUE	NA	0.884269741189449	2		432	951	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169375	11169375	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519915	NA	P-0005392-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	44	596	0	ENST00000361445.4:c.7500T>G	p.Ile2500Met	p.I2500M	ENST00000361445	NM_004958.3	2500	atT/atG	56/58	0.870949457095294	1	FACETS	0.098	0.081	0.116	0.098	0.081	0.116	SUBCLONAL	1	TRUE	0	0.884269741189449	1		596	569	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250569	26250569	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005392-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	804	1011	0	ENST00000446824.2:c.265G>T	p.Ala89Ser	p.A89S	ENST00000446824	NM_021018.2	89	Gct/Tct	1/1	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.884269741189449	2		1011	1768	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907099	32907101	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0005392-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	251	360	0	ENST00000380152.3:c.1488_1490del	p.Ser497del	p.S497del	ENST00000380152		495	gCTTct/gct	10/27	0.113600150332849	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.884269741189449	0		360	646	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0005624-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	518	435	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.271251903140257	2	FACETS	1	0.997	1	0.744	0.718	0.77	INDETERMINATE	1	TRUE	0	0.75	2		435	928	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717739	89717739	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005624-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	85	296	0	ENST00000371953.3:c.764T>C	p.Val255Ala	p.V255A	ENST00000371953	NM_000314.4	255	gTa/gCa	7/9	1	2	FACETS	0.372	0.329	0.418	0.372	0.329	0.418	SUBCLONAL	1	TRUE	1	0.75	2		296	609	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949177	44949177	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs793888510	NA	P-0005624-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	218	408	0	ENST00000377967.4:c.3736+2T>C		p.X1246_splice	ENST00000377967	NM_021140.2	1246			1	2	FACETS	0.746	0.696	0.798	0.746	0.696	0.798	SUBCLONAL	1	TRUE	1	0.75	2		408	779	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003010	42003011	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005624-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	617	984	0	ENST00000219905.7:c.2548dup	p.Thr850AsnfsTer11	p.T850Nfs*11	ENST00000219905	NM_001164273.1	849	-/A	8/24	1	2	FACETS	0.987	0.95	1	0.987	0.95	1	CLONAL	1	TRUE	1	0.75	2		984	1667	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	219	270	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.922	0.867	0.978	1	0.996	1	CLONAL	6	FALSE	1	0.161198174514321	2		270	491	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788606	3788606	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	420	445	0	ENST00000262367.5:c.4348T>A	p.Tyr1450Asn	p.Y1450N	ENST00000262367	NM_004380.2	1450	Tac/Aac	26/31	1	2	FACETS	0.948	0.908	0.989	1	0.998	1	CLONAL	6	FALSE	1	0.161198174514321	2		445	916	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066482	94066482	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs542602078	NA	P-0006032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	452	578	0	ENST00000369303.4:c.1277G>T	p.Arg426Leu	p.R426L	ENST00000369303	NM_004440.3	426	cGa/cTa	5/17	0.161960926006377	3	FACETS	0.971	0.925	1	1	0.997	1	CLONAL	4	FALSE	1	0.161198174514321	3		578	1561	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32931894	32931894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358990	NA	P-0006032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	317	320	0	ENST00000380152.3:c.7633G>A	p.Val2545Ile	p.V2545I	ENST00000380152		2545	Gtt/Att	16/27	0.161960926006377	1	FACETS	0.984	0.935	1	1	0.997	1	CLONAL	5	FALSE	0	0.161198174514321	1		320	735	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578466	7578466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006047-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	110	686	0	ENST00000269305.4:c.464C>T	p.Thr155Ile	p.T155I	ENST00000269305	NM_001126112.2	155	aCc/aTc	5/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.2	2		686	943	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39607452	39607452	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006047-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	44	403	0	ENST00000262039.4:c.1530T>A	p.Asp510Glu	p.D510E	ENST00000262039	NM_002647.2	510	gaT/gaA	14/25	1	2	FACETS	0.833	0.698	0.983	0.833	0.698	0.983	CLONAL	1	TRUE	1	0.2	2		403	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0006482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	236	526	3	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.605262570902433	1	FACETS	0.964	0.908	1	0.964	0.908	1	CLONAL	1	TRUE	0	0.605262570902433	1		529	564	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	127	564	2	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.419	0.379	0.461	0.419	0.379	0.461	SUBCLONAL	1	TRUE	1	0.605262570902433	2		566	1002	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0006482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	246	617	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	0.898	0.841	0.957	0.898	0.841	0.957	CLONAL	1	TRUE	1	0.605262570902433	2		617	905	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0006482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	65	381	3	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.659	0.575	0.748	0.659	0.575	0.748	SUBCLONAL	1	TRUE	1	0.605262570902433	2		384	326	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602797	10602797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	172	822	0	ENST00000171111.5:c.781C>T	p.Arg261Trp	p.R261W	ENST00000171111	NM_203500.1	261	Cgg/Tgg	3/6	1	2	FACETS	0.465	0.426	0.505	0.465	0.426	0.505	SUBCLONAL	1	TRUE	1	0.605262570902433	2		822	1223	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443612	29443612	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	126	603	0	ENST00000389048.3:c.3605del	p.Gly1202GlufsTer56	p.G1202Efs*56	ENST00000389048	NM_004304.4	1202	gGa/ga	23/29	0.605262570902433	1	FACETS	0.453	0.411	0.497	0.453	0.411	0.497	SUBCLONAL	1	TRUE	0	0.605262570902433	1		603	641	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300040	137300040	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	133	692	1	ENST00000481739.1:c.331del	p.Leu111TrpfsTer57	p.L111Wfs*57	ENST00000481739	NM_002957.4	109	Ccc/cc	3/10	0.605262570902433	1	FACETS	0.43	0.391	0.471	0.43	0.391	0.471	SUBCLONAL	1	TRUE	0	0.605262570902433	1		693	713	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211138	36211138	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	409	869	2	ENST00000222270.7:c.889C>T	p.Arg297Ter	p.R297*	ENST00000222270	NM_014727.1	297	Cga/Tga	3/37	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.605262570902433	2		871	1328	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820202	32820202	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	298	602	1	ENST00000354258.4:c.856C>T	p.Arg286Ter	p.R286*	ENST00000354258	NM_000593.5	286	Cga/Tga	2/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.605262570902433	2		603	928	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289953	15289953	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772172068	NA	P-0006482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	291	762	1	ENST00000263388.2:c.3601C>T	p.Arg1201Cys	p.R1201C	ENST00000263388	NM_000435.2	1201	Cgc/Tgc	22/33	1	2	FACETS	0.879	0.827	0.932	0.879	0.827	0.932	CLONAL	1	TRUE	1	0.605262570902433	2		763	1094	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259739	16259739	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	110	559	0	ENST00000375759.3:c.7004C>G	p.Thr2335Arg	p.T2335R	ENST00000375759	NM_015001.2	2335	aCa/aGa	11/15	0.288319318845668	2	FACETS	0.441	0.395	0.488	0.22	0.197	0.244	INDETERMINATE	1	TRUE	0	0.605262570902433	2		559	825	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023482	27023482	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	136	567	0	ENST00000324856.7:c.591del	p.Gln199SerfsTer33	p.Q199Sfs*33	ENST00000324856	NM_006015.4	196	gcG/gc	1/20	0.288319318845668	2	FACETS	0.501	0.455	0.549	0.25	0.227	0.275	INDETERMINATE	1	TRUE	0	0.605262570902433	2		567	897	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200104	67200104	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	193	500	0	ENST00000312629.5:c.491G>A	p.Gly164Asp	p.G164D	ENST00000312629	NM_003952.2	164	gGc/gAc	6/15	1	2	FACETS	0.93	0.863	0.998	0.93	0.863	0.998	CLONAL	1	TRUE	1	0.605262570902433	2		500	686	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420642	49420642	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	234	534	0	ENST00000301067.7:c.15107A>G	p.His5036Arg	p.H5036R	ENST00000301067	NM_003482.3	5036	cAt/cGt	48/54	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.605262570902433	2		534	761	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003382	42003383	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAG	rs565548940	NA	P-0006482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	92	515	0	ENST00000219905.7:c.2931_2933dup	p.Gln981dup	p.Q981dup	ENST00000219905	NM_001164273.1	981	-/CAG	8/24	0.31343305787299	1	FACETS	0.364	0.324	0.407	0.364	0.324	0.407	INDETERMINATE	1	TRUE	0	0.605262570902433	1		515	582	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640786	3640786	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	246	601	0	ENST00000294008.3:c.2853G>T	p.Glu951Asp	p.E951D	ENST00000294008	NM_032444.2	951	gaG/gaT	12/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.605262570902433	2		601	767	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849638	68849639	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0006482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	229	500	0	ENST00000261769.5:c.1544_1545del	p.Thr515IlefsTer21	p.T515Ifs*21	ENST00000261769	NM_004360.3	514	gAC/g	10/16	0.605262570902433	1	FACETS	0.999	0.941	1	0.999	0.941	1	CLONAL	1	TRUE	0	0.605262570902433	1		500	528	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685596	29685596	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	201	548	1	ENST00000356175.3:c.8006A>G	p.Tyr2669Cys	p.Y2669C	ENST00000356175	NM_000267.3	2669	tAc/tGc	54/57	1	2	FACETS	0.953	0.887	1	0.953	0.887	1	CLONAL	1	TRUE	1	0.605262570902433	2		549	697	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793160	42793160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	186	748	0	ENST00000575354.2:c.1052G>A	p.Arg351Gln	p.R351Q	ENST00000575354	NM_015125.3	351	cGg/cAg	7/20	1	2	FACETS	0.555	0.512	0.6	0.555	0.512	0.6	SUBCLONAL	1	TRUE	1	0.605262570902433	2		748	1107	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794933	42794933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	266	626	0	ENST00000575354.2:c.2013G>A	p.Met671Ile	p.M671I	ENST00000575354	NM_015125.3	671	atG/atA	10/20	1	2	FACETS	0.985	0.926	1	0.985	0.926	1	CLONAL	1	TRUE	1	0.605262570902433	2		626	892	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690202	47690225	+	inframe_deletion	In_Frame_Del	DEL	ATTTGATCCTAATCTCAGTGAATT	ATTTGATCCTAATCTCAGTGAATT	-	novel	NA	P-0006482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	156	420	0	ENST00000233146.2:c.1420_1443del	p.Phe474_Leu481del	p.F474_L481del	ENST00000233146	NM_000251.2	473	tcATTTGATCCTAATCTCAGTGAATTa/tca	9/16	0.605262570902433	1	FACETS	0.899	0.833	0.966	0.899	0.833	0.966	CLONAL	1	TRUE	0	0.605262570902433	1		420	400	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660849	227660849	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	194	517	0	ENST00000305123.5:c.2606G>T	p.Ser869Ile	p.S869I	ENST00000305123	NM_005544.2	869	aGc/aTc	1/2	1	2	FACETS	0.957	0.889	1	0.957	0.889	1	CLONAL	1	TRUE	1	0.605262570902433	2		517	670	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139464	47139464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	171	445	1	ENST00000409792.3:c.5123G>A	p.Arg1708Gln	p.R1708Q	ENST00000409792	NM_014159.6	1708	cGa/cAa	9/21	1	2	FACETS	0.973	0.9	1	0.973	0.9	1	CLONAL	1	TRUE	1	0.605262570902433	2		446	581	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165677	47165677	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1293708012	NA	P-0006482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	166	470	0	ENST00000409792.3:c.449A>G	p.His150Arg	p.H150R	ENST00000409792	NM_014159.6	150	cAt/cGt	3/21	1	2	FACETS	0.925	0.854	0.998	0.925	0.854	0.998	CLONAL	1	TRUE	1	0.605262570902433	2		470	593	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932907	49932907	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	261	653	0	ENST00000296474.3:c.3037T>G	p.Ser1013Ala	p.S1013A	ENST00000296474	NM_002447.2	1013	Tcg/Gcg	13/20	1	2	FACETS	0.894	0.838	0.951	0.894	0.838	0.951	CLONAL	1	TRUE	1	0.605262570902433	2		653	965	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197829	66197829	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	52	257	0	ENST00000273854.3:c.2870C>T	p.Ala957Val	p.A957V	ENST00000273854	NM_004439.5	957	gCa/gTa	17/18	0.244743516029864	5	FACETS	0.644	0.548	0.749			1	INDETERMINATE	1	TRUE	NA	0.605262570902433	5		257	509	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536269	106536269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1427730094	NA	P-0006482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	80	356	1	ENST00000369096.4:c.236C>T	p.Ala79Val	p.A79V	ENST00000369096	NM_001198.3	79	gCg/gTg	2/7	1	2	FACETS	0.486	0.428	0.547	0.486	0.428	0.547	SUBCLONAL	1	TRUE	1	0.605262570902433	2		357	544	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508800	106508800	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	47	475	0	ENST00000359195.3:c.794A>T	p.Gln265Leu	p.Q265L	ENST00000359195	NM_002649.2	265	cAa/cTa	2/11	1	2	FACETS	0.221	0.186	0.26	0.221	0.186	0.26	SUBCLONAL	1	TRUE	1	0.605262570902433	2		475	703	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650295	48650295	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	95	634	0	ENST00000376670.3:c.269del	p.Gly90AlafsTer47	p.G90Afs*47	ENST00000376670	NM_002049.3	89	Ggg/gg	3/6	1	2	FACETS	0.38	0.337	0.425	0.38	0.337	0.425	SUBCLONAL	1	TRUE	1	0.605262570902433	2		634	827	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0006518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	193	378	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	0.490823814243347	2		378	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577123	7577123	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876660333	NA	P-0006518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	27	648	0	ENST00000269305.4:c.815T>A	p.Val272Glu	p.V272E	ENST00000269305	NM_001126112.2	272	gTg/gAg	8/11	0.490823814243347	1	FACETS	0.087	0.068	0.108	0.087	0.068	0.108	SUBCLONAL	1	TRUE	0	0.490823814243347	1		648	956	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396911	139396911	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1208976166	NA	P-0006518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	178	275	1	ENST00000277541.6:c.5197C>T	p.Gln1733Ter	p.Q1733*	ENST00000277541	NM_017617.3	1733	Cag/Tag	28/34	1	2	FACETS	0.992	0.917	1	0.992	0.917	1	CLONAL	1	TRUE	1	0.490823814243347	2		276	731	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42053937	42053937	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	282	608	1	ENST00000219905.7:c.7399G>T	p.Ala2467Ser	p.A2467S	ENST00000219905	NM_001164273.1	2467	Gcc/Tcc	21/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.490823814243347	2		609	1019	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928373	69928373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770693882	NA	P-0006690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	34	435	1	ENST00000352241.4:c.193C>T	p.Arg65Cys	p.R65C	ENST00000352241	NM_198159.2	65	Cgt/Tgt	2/10	0.203100789819575	4	FACETS	0.457	0.373	0.552			1	INDETERMINATE	1	TRUE	NA	0.407054923678869	4		436	514	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933142	39933143	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0006690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	196	237	0	ENST00000378444.4:c.1455_1456dup	p.Thr486LysfsTer43	p.T486Kfs*43	ENST00000378444	NM_001123385.1	486	aca/aAAca	4/15	0.257158418824372	2	FACETS	1	0.99	1			1	CLONAL	3	TRUE	NA	0.407054923678869	2		237	276	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399836	139399836	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs41309766	NA	P-0006690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	20	484	0	ENST00000277541.6:c.4512del	p.Cys1505ValfsTer75	p.C1505Vfs*75	ENST00000277541	NM_017617.3	1504	caC/ca	25/34	0.293450986667811	3	FACETS	0.315	0.241	0.403	0.158	0.12	0.202	SUBCLONAL	1	TRUE	1	0.407054923678869	3		484	375	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945516	151945516	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006939-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	197	137	0	ENST00000262189.6:c.2003del	p.Gln668ArgfsTer3	p.Q668Rfs*3	ENST00000262189	NM_170606.2	668	cAg/cg	14/59	0.261890437684616	3	FACETS	1	0.97	1	1	0.994	1	CLONAL	4	TRUE	1	0.261890437684616	3		137	404	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390794	139390794	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006939-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	342	497	0	ENST00000277541.6:c.7397del	p.Thr2466SerfsTer11	p.T2466Sfs*11	ENST00000277541	NM_017617.3	2466	aCg/ag	34/34	1	2	FACETS	0.928	0.881	0.976	1	0.997	1	CLONAL	3	TRUE	1	0.261890437684616	2		497	938	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0007096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	323	361	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.432815055432813	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.432815055432813	2		361	722	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482369	56482369	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	461	314	0	ENST00000267101.3:c.917C>G	p.Pro306Arg	p.P306R	ENST00000267101	NM_001982.3	306	cCt/cGt	8/28	0.432815055432813	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	TRUE	1	0.432815055432813	4		314	994	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528558	89528558	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	34	210	0	ENST00000336596.2:c.2858A>T	p.Lys953Met	p.K953M	ENST00000336596	NM_005233.5	953	aAg/aTg	17/17	0.432815055432813	3	FACETS	0.347	0.283	0.419	0.173	0.141	0.21	SUBCLONAL	1	TRUE	1	0.432815055432813	3		210	551	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	459909	459909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	151	310	0	ENST00000399788.2:c.1186C>T	p.Arg396Trp	p.R396W	ENST00000399788	NM_001042603.1	396	Cgg/Tgg	10/28	0.294061553492891	5	FACETS	1	0.979	1	0.406	0.371	0.443	CLONAL	1	TRUE	2	0.432815055432813	5		310	944	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879831	37879831	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	311	355	0	ENST00000269571.5:c.2126A>T	p.Gln709Leu	p.Q709L	ENST00000269571		709	cAg/cTg	18/27	0.432815055432813	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.432815055432813	2		355	666	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860951	45860951	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	138	406	0	ENST00000391945.4:c.1244C>G	p.Thr415Ser	p.T415S	ENST00000391945	NM_000400.3	415	aCc/aGc	13/23	1	2	FACETS	0.832	0.758	0.91	0.832	0.758	0.91	CLONAL	1	TRUE	1	0.432815055432813	2		406	766	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0007102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	42	435	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.933	0.777	1	0.933	0.777	1	CLONAL	1	TRUE	1	0.12	2		435	750	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894228	NA	P-0007102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	54	355	0	ENST00000451590.1:c.37G>C	p.Gly13Arg	p.G13R	ENST00000451590	NM_001130442.1	13	Ggt/Cgt	2/5	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.12	2		355	785	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0007102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	23	351	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	1	2	FACETS	0.376	0.291	0.475	0.376	0.291	0.475	SUBCLONAL	1	TRUE	1	0.12	2		351	1019	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0007145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	408	377	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.874657233153725	2		377	918	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517445	157517445	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs773740590	NA	P-0007145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	446	344	0	ENST00000346085.5:c.4009C>T	p.Arg1337Ter	p.R1337*	ENST00000346085	NM_020732.3	1337	Cga/Tga	16/20	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.874657233153725	2		344	906	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412686	139412688	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	novel	NA	P-0007145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	498	582	0	ENST00000277541.6:c.1156_1158del	p.Asn386del	p.N386del	ENST00000277541	NM_017617.3	386	AAC/-	7/34	1	2	FACETS	0.951	0.912	0.99	0.951	0.912	0.99	CLONAL	1	TRUE	1	0.874657233153725	2		582	1198	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572256	41572257	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTTGTGATCCGCAA	novel	NA	P-0007145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	292	317	0	ENST00000263253.7:c.4797_4798insAATTTGTGATCCGC	p.Leu1600AsnfsTer3	p.L1600Nfs*3	ENST00000263253	NM_001429.3	1595	-/TTTGTGATCCGCAA	30/31	1	2	FACETS	0.833	0.787	0.879	0.833	0.787	0.879	CLONAL	1	TRUE	1	0.874657233153725	2		317	802	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740533	58740533	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs749097315	NA	P-0007145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	643	659	0	ENST00000305921.3:c.1440del	p.Ala481ProfsTer2	p.A481Pfs*2	ENST00000305921	NM_003620.3	480	Aaa/aa	6/6	1	2	FACETS	0.988	0.953	1	0.988	0.953	1	CLONAL	1	TRUE	1	0.874657233153725	2		659	1488	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390822	139390857	+	frameshift_variant	Frame_Shift_Del	DEL	GAATAGTGTGCACCGCCAGGCTGCTGGGGCCCAGTG	GAATAGTGTGCACCGCCAGGCTGCTGGGGCCCAGTG	CAATAGTA	novel	NA	P-0007145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	334	390	0	ENST00000277541.6:c.7334_7369delinsTACTATTG	p.Pro2445LeufsTer23	p.P2445Lfs*23	ENST00000277541	NM_017617.3	2445	cCACTGGGCCCCAGCAGCCTGGCGGTGCACACTATTCtg/cTACTATTGtg	34/34	1	2	FACETS	0.917	0.871	0.963	0.917	0.871	0.963	CLONAL	1	TRUE	1	0.874657233153725	2		390	833	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0007322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	174	491	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.216368778038396	5	FACETS	1	0.979	1	0.786	0.723	0.85	CLONAL	2	TRUE	2	0.216368778038396	5		491	904	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0007322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	52	504	6	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.216368778038396	2	FACETS	1	0.923	1	0.565	0.482	0.656	CLONAL	1	TRUE	0	0.216368778038396	2		510	425	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0007322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	50	214	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.216368778038396	2	FACETS	1	0.889	1	0.528	0.448	0.615	CLONAL	1	TRUE	0	0.216368778038396	2		214	438	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28601366	28601378	+	frameshift_variant	Frame_Shift_Del	DEL	CTGATCCAGCGGC	CTGATCCAGCGGC	GT	novel	NA	P-0007322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	67	530	2	ENST00000253063.3:c.1051_1063delinsGT	p.Leu351ValfsTer4	p.L351Vfs*4	ENST00000253063	NM_031459.4	351	CTGATCCAGCGGCtt/GTtt	8/10	0.216368778038396	5	FACETS	1	0.883	1	0.34	0.294	0.389	CLONAL	1	TRUE	2	0.216368778038396	5		532	805	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226356	2226361	+	inframe_deletion	In_Frame_Del	DEL	TTCTCA	TTCTCA	-	novel	NA	P-0007322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	118	629	0	ENST00000326181.6:c.1969_1974del	p.Phe657_Ser658del	p.F657_S658del	ENST00000326181	NM_032271.2	657	TTCTCA/-	20/21	0.216368778038396	5	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.216368778038396	5		629	1040	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647921	3647921	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146021821	NA	P-0007322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	83	669	2	ENST00000294008.3:c.1243G>A	p.Glu415Lys	p.E415K	ENST00000294008	NM_032444.2	415	Gag/Aag	6/15	0.216368778038396	6	FACETS	1	0.895	1	0.34	0.299	0.384	CLONAL	1	TRUE	3	0.216368778038396	6		671	1079	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86658465	86658465	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	34	245	0	ENST00000274376.6:c.1430A>G	p.Lys477Arg	p.K477R	ENST00000274376	NM_002890.2	477	aAg/aGg	10/25	0.210436408239685	4	FACETS	1	0.888	1	0.561	0.459	0.674	CLONAL	1	TRUE	2	0.216368778038396	4		245	341	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90971001	90971001	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs768886664	NA	P-0007322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	47	357	0	ENST00000265433.3:c.1076A>G	p.Asn359Ser	p.N359S	ENST00000265433	NM_002485.4	359	aAc/aGc	9/16	0.210436408239685	4	FACETS	1	0.887	1	0.532	0.448	0.623	CLONAL	1	TRUE	2	0.216368778038396	4		357	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0007369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	767	712	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.694560646959604	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.694560646959604	2		712	1095	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACAACCCCC	rs397517115	NA	P-0007369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	1111	629	15	ENST00000275493.2:c.2311_2319dup	p.Asn771_His773dup	p.N771_H773dup	ENST00000275493	NM_005228.3	771	gac/gACAACCCCCac	20/28	0.694560646959604	7	FACETS	1	0.995	1	0.857	0.836	0.878	CLONAL	4	TRUE	2	0.694560646959604	7		644	2043	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633569	69633569	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782297586	NA	P-0007369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	105	247	6	ENST00000334134.2:c.133C>T	p.Arg45Cys	p.R45C	ENST00000334134	NM_005247.2	45	Cgc/Tgc	1/3	0.694560646959604	2	FACETS	1	0.944	1	0.527	0.479	0.576	CLONAL	1	TRUE	0	0.694560646959604	2		253	287	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134003	41134003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145453868	NA	P-0007369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	302	535	6	ENST00000379561.5:c.1625C>T	p.Thr542Met	p.T542M	ENST00000379561	NM_002015.3	542	aCg/aTg	2/3	0.694560646959604	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.694560646959604	1		541	484	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356098	66356098	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	186	490	3	ENST00000273854.3:c.1399G>T	p.Ala467Ser	p.A467S	ENST00000273854	NM_004439.5	467	Gca/Tca	5/18	0.694560646959604	2	FACETS	0.885	0.822	0.95	0.443	0.411	0.475	CLONAL	1	TRUE	0	0.694560646959604	2		493	605	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680071	30680071	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	283	742	0	ENST00000376406.3:c.1648C>T	p.Gln550Ter	p.Q550*	ENST00000376406	NM_014641.2	550	Caa/Taa	5/15	0.694560646959604	3	FACETS	0.946	0.888	1	0.473	0.444	0.502	CLONAL	1	TRUE	1	0.694560646959604	3		742	1161	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918596	44918597	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0007499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	305	233	0	ENST00000377967.4:c.1083_1084del	p.Tyr362Ter	p.Y362*	ENST00000377967	NM_021140.2	360	aCT/a	12/29	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	0	NA	2		233	533	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469898	157469898	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	267	303	0	ENST00000346085.5:c.2692del	p.Arg898GlufsTer16	p.R898Efs*16	ENST00000346085	NM_020732.3	898	Cga/ga	9/20	0.135296641916934	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		303	864	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087395	27087396	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0007499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	320	414	0	ENST00000324856.7:c.1970_1971insTT	p.Ser658Ter	p.S658*	ENST00000324856	NM_006015.4	657	ctg/cTTtg	5/20	0.3	3	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	3		414	1133	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0007699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	92	307	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	1	2	FACETS	0.834	0.743	0.932	1	0.983	1	CLONAL	2	TRUE	1	0.193762877892549	2		307	569	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331643	8331643	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	103	460	0	ENST00000356435.5:c.5473G>C	p.Gly1825Arg	p.G1825R	ENST00000356435		1825	Ggc/Cgc	33/35	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.193762877892549	2		460	1035	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570418	87570418	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	38	409	0	ENST00000277120.3:c.2158A>T	p.Thr720Ser	p.T720S	ENST00000277120		720	Act/Tct	17/19	1	2	FACETS	0.544	0.448	0.652	0.544	0.448	0.652	SUBCLONAL	1	TRUE	1	0.193762877892549	2		409	721	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0007699-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	393	307	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.74104122070018	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	0	0.74104122070018	3		307	482	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331643	8331643	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007699-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	270	460	0	ENST00000356435.5:c.5473G>C	p.Gly1825Arg	p.G1825R	ENST00000356435		1825	Ggc/Cgc	33/35	0.74104122070018	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.74104122070018	3		460	487	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570418	87570418	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007699-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	104	409	0	ENST00000277120.3:c.2158A>T	p.Thr720Ser	p.T720S	ENST00000277120		720	Act/Tct	17/19	0.74104122070018	3	FACETS	0.827	0.745	0.914	0.414	0.372	0.457	CLONAL	1	TRUE	1	0.74104122070018	3		409	465	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465638	8465638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781067774	NA	P-0007699-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	25	409	0	ENST00000356435.5:c.3542G>A	p.Arg1181His	p.R1181H	ENST00000356435		1181	cGt/cAt	21/35	0.74104122070018	3	FACETS	0.263	0.207	0.328	0.132	0.103	0.164	SUBCLONAL	1	TRUE	1	0.74104122070018	3		409	351	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534794	18534794	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007699-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	25	323	0	ENST00000266497.5:c.1852C>G	p.Pro618Ala	p.P618A	ENST00000266497		618	Cca/Gca	12/31	0.74104122070018	2	FACETS	0.195	0.153	0.243	0.098	0.076	0.122	SUBCLONAL	1	TRUE	0	0.74104122070018	2		323	346	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353939	15353947	+	inframe_deletion	In_Frame_Del	DEL	GGGGTGGTG	GGGGTGGTG	-	rs758265124	NA	P-0007699-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	43	64	0	ENST00000263377.2:c.2933_2941del	p.Pro978_Pro980del	p.P978_P980del	ENST00000263377	NM_058243.2	978	cCACCACCCCag/cag	14/20	0.74104122070018	4	FACETS	1	0.929	1			1	CLONAL	1	TRUE	NA	0.74104122070018	4		64	173	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492927	8492927	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1455	872	512	0	ENST00000356435.5:c.2402C>A	p.Thr801Lys	p.T801K	ENST00000356435		801	aCa/aAa	16/35	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.749773922147835	2		512	2327	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0007849-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	89	193	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	0.660718033766814	2		193	218	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492927	8492927	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007849-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	203	512	0	ENST00000356435.5:c.2402C>A	p.Thr801Lys	p.T801K	ENST00000356435		801	aCa/aAa	16/35	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.660718033766814	2		512	614	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949142	44949143	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0007849-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	181	283	0	ENST00000377967.4:c.3705_3706dup	p.Asn1236ThrfsTer30	p.N1236Tfs*30	ENST00000377967	NM_021140.2	1235	aac/aACac	25/29	0.266838875307208	0	FACETS	0.634	0.599	0.669			1	INDETERMINATE	1	TRUE	NA	0.660718033766814	0		283	293	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444600	187444630	+	frameshift_variant	Frame_Shift_Del	DEL	CACTGTGGGTCTGCAGCGTGTGCCTCTTGAG	CACTGTGGGTCTGCAGCGTGTGCCTCTTGAG	-	novel	NA	P-0008045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	136	276	0	ENST00000232014.4:c.1597_1627del	p.Leu533ThrfsTer47	p.L533Tfs*47	ENST00000232014	NM_001130845.1	533	CTCAAGAGGCACACGCTGCAGACCCACAGTGac/ac	7/10	0.23647644300793	5	FACETS	1	0.958	1	1	0.987	1	CLONAL	4	TRUE	2	0.23647644300793	5		276	366	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105586	27105586	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	686	490	0	ENST00000324856.7:c.5197G>T	p.Glu1733Ter	p.E1733*	ENST00000324856	NM_006015.4	1733	Gag/Tag	20/20	0.778942071353131	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.817180639853204	1		490	977	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0008068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	154	381	3	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	0.697656105985266	4	FACETS	1	0.985	1	0.808	0.754	0.863	CLONAL	2	TRUE	1	0.697656105985266	4		384	309	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0008068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	338	625	1	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.615412951563036	2	FACETS	0.821	0.786	0.856	0.821	0.786	0.856	CLONAL	2	TRUE	0	0.697656105985266	2		626	590	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0008068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	189	377	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	0.864	0.803	0.927	0.864	0.803	0.927	CLONAL	1	TRUE	1	0.697656105985266	2		377	627	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791533	42791533	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	211	717	0	ENST00000575354.2:c.514C>T	p.Gln172Ter	p.Q172*	ENST00000575354	NM_015125.3	172	Cag/Tag	4/20	1	2	FACETS	0.75	0.699	0.804	0.75	0.699	0.804	SUBCLONAL	1	TRUE	1	0.697656105985266	2		717	806	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	540	811	1	ENST00000269305.4:c.430del	p.Gln144SerfsTer26	p.Q144Sfs*26	ENST00000269305	NM_001126112.2	144	Cag/ag	5/11	0.621181910539602	2	FACETS	0.884	0.855	0.912	0.884	0.855	0.912	CLONAL	2	TRUE	0	0.697656105985266	2		812	876	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821734	72821734	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	45	462	0	ENST00000268489.5:c.10441A>G	p.Arg3481Gly	p.R3481G	ENST00000268489	NM_006885.3	3481	Agg/Ggg	10/10	0.259979506473987	3	FACETS	0.319	0.268	0.376	0.106	0.089	0.126	INDETERMINATE	1	TRUE	0	0.697656105985266	3		462	545	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140366	50140366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	173	611	1	ENST00000246792.3:c.175G>A	p.Asp59Asn	p.D59N	ENST00000246792	NM_006270.3	59	Gac/Aac	2/6	1	2	FACETS	0.785	0.725	0.846	0.785	0.725	0.846	SUBCLONAL	1	TRUE	1	0.697656105985266	2		612	632	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874524	155874524	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	273	613	0	ENST00000368323.3:c.235C>G	p.Gln79Glu	p.Q79E	ENST00000368323	NM_006912.5	79	Cag/Gag	4/6	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.67152723210893	2		613	804	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99472802	99472802	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	398	552	0	ENST00000268035.6:c.2798T>G	p.Phe933Cys	p.F933C	ENST00000268035	NM_000875.3	933	tTc/tGc	14/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.67152723210893	2		552	1104	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850781	63850782	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0008151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	445	685	1	ENST00000279873.7:c.1560dup	p.Asp521ArgfsTer7	p.D521Rfs*7	ENST00000279873	NM_032199.2	520	aca/acAa	10/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.67152723210893	2		686	1292	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410452	139410453	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs864622059	NA	P-0008385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	402	440	0	ENST00000277541.6:c.1649dup	p.Tyr550Ter	p.Y550*	ENST00000277541	NM_017617.3	550	tac/taAc	10/34	0.164858121276703	5	FACETS	1	0.96	1	1	0.997	1	CLONAL	7	FALSE	3	0.164858121276703	5		440	866	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139184	37139184	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	125	161	0	ENST00000373509.5:c.524T>C	p.Ile175Thr	p.I175T	ENST00000373509	NM_002648.3	175	aTc/aCc	4/6	0.164858121276703	5	FACETS	0.993	0.921	1			1	CLONAL	8	FALSE	NA	0.164858121276703	5		161	238	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807902	3807902	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	319	392	0	ENST00000262367.5:c.3517C>G	p.Arg1173Gly	p.R1173G	ENST00000262367	NM_004380.2	1173	Cga/Gga	18/31	NA	2	FACETS	0.954	0.908	1			1	INDETERMINATE	6	FALSE	NA	0.164858121276703	2		392	676	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0008688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	25	435	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.757	0.605	0.927	1	0.934	1	CLONAL	2	FALSE	1	0.250050087655318	2		435	132	SUCCESS
BLM	641	MSKCC	GRCh37	15	91328261	91328261	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	48	439	0	ENST00000355112.3:c.2773T>C	p.Ser925Pro	p.S925P	ENST00000355112	NM_000057.2	925	Tct/Cct	14/22	0.250050087655318	3	FACETS	1	0.921	1	1	0.972	1	CLONAL	3	FALSE	1	0.250050087655318	3		439	132	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164544	36164545	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGTT	novel	NA	P-0008688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	37	294	0	ENST00000300305.3:c.1327_1330dup	p.Pro444GlnfsTer157	p.P444Qfs*157	ENST00000300305		444	ccc/cAACCcc	8/8	0.0604979053831967	4	FACETS	1	0.904	1	1	0.904	1	INDETERMINATE	2	FALSE	2	0.250050087655318	4		294	165	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350902	89350902	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	57	1565	0	ENST00000301030.4:c.2048del	p.Lys683SerfsTer2	p.K683Sfs*2	ENST00000301030	NM_001256183.1	683	aAg/ag	9/13	0.250050087655318	1	FACETS	0.831	0.721	0.948	1	0.974	1	CLONAL	2	FALSE	0	0.250050087655318	1		1565	240	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0008768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	255	403	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.959	0.898	1	0.959	0.898	1	CLONAL	1	TRUE	1	0.505040678222255	2		403	1053	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777894	NA	P-0008768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	67	535	0	ENST00000361445.4:c.6644C>T	p.Ser2215Phe	p.S2215F	ENST00000361445	NM_004958.3	2215	tCt/tTt	47/58	0.483318685017498	1	FACETS	0.223	0.193	0.255	0.223	0.193	0.255	SUBCLONAL	1	TRUE	0	0.505040678222255	1		535	891	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716329	52716329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863225094	NA	P-0008768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	38	403	0	ENST00000322088.6:c.773G>A	p.Arg258His	p.R258H	ENST00000322088	NM_014225.5	258	cGc/cAc	6/15	1	2	FACETS	0.131	0.107	0.157	0.131	0.107	0.157	SUBCLONAL	1	TRUE	1	0.505040678222255	2		403	1153	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390866	139390867	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CTGCCTGGCTCGGCTCTCCACTCAGGAAGCTC	novel	NA	P-0008768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	276	343	0	ENST00000277541.6:c.7293_7324dup	p.Asp2442GlyfsTer4	p.D2442Gfs*4	ENST00000277541	NM_017617.3	2442	gac/gGAGCTTCCTGAGTGGAGAGCCGAGCCAGGCAGac	34/34	0.505040678222255	3	FACETS	1	0.974	1	0.536	0.502	0.571	CLONAL	1	TRUE	1	0.505040678222255	3		343	1277	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779056	3779056	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756378412	NA	P-0009150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	204	571	0	ENST00000262367.5:c.5992G>A	p.Val1998Met	p.V1998M	ENST00000262367	NM_004380.2	1998	Gtg/Atg	31/31	0.634713448389147	3	FACETS	1	0.981	1	0.575	0.535	0.615	CLONAL	1	TRUE	1	0.701010118323682	3		571	684	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245909	16245909	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	183	358	0	ENST00000375759.3:c.1532G>T	p.Gly511Val	p.G511V	ENST00000375759	NM_015001.2	511	gGa/gTa	8/15	0.379690033240202	1	FACETS	0.879	0.823	0.935	0.879	0.823	0.935	INDETERMINATE	1	TRUE	0	0.701010118323682	1		358	386	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0009317-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	56	328	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.276069491253399	3	FACETS	1	0.958	1	0.661	0.569	0.76	CLONAL	1	TRUE	1	0.28	3		328	345	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879574	151879574	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009317-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	19	252	0	ENST00000262189.6:c.5371C>T	p.Gln1791Ter	p.Q1791*	ENST00000262189	NM_170606.2	1791	Cag/Tag	36/59	0.3	4	FACETS	0.706	0.537	0.904	0.353	0.268	0.452	CLONAL	1	TRUE	2	0.28	4		252	246	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673703	37673703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009401-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	393	648	0	ENST00000447079.4:c.2857G>A	p.Gly953Ser	p.G953S	ENST00000447079	NM_015083.1	953	Ggt/Agt	10/14	0.625197828264199	3	FACETS	1	0.983	1			1	CLONAL	1	FALSE	NA	0.807691243969101	3		648	1274	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944841	31944842	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0009401-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	407	754	0	ENST00000340398.3:c.259_260del	p.Ala87SerfsTer9	p.A87Sfs*9	ENST00000340398	NM_001013699.2	87	GCa/a	1/1	1	2	FACETS	0.71	0.675	0.746	0.71	0.675	0.746	SUBCLONAL	1	FALSE	1	0.807691243969101	2		754	1419	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618989	37618990	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0009401-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	738	737	0	ENST00000447079.4:c.670dup	p.His224ProfsTer6	p.H224Pfs*6	ENST00000447079	NM_015083.1	222	agc/agCc	1/14	0.625197828264199	3	FACETS	0.912	0.885	0.94			1	CLONAL	2	FALSE	NA	0.807691243969101	3		737	1406	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274768	123274768	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	53	381	0	ENST00000358487.5:c.1150G>C	p.Gly384Arg	p.G384R	ENST00000358487	NM_000141.4	384	Ggg/Cgg	9/18	0.3	5	FACETS	0.725	0.616	0.845			1	SUBCLONAL	1	TRUE	NA	0.18	5		381	1032	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112212	115112212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	101	209	1	ENST00000257566.3:c.1528C>T	p.Gln510Ter	p.Q510*	ENST00000257566	NM_016569.3	510	Caa/Taa	7/8	0.3	7	FACETS	1	0.951	1			1	CLONAL	3	TRUE	NA	0.18	7		210	493	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914723	39914723	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	32	314	0	ENST00000378444.4:c.4639del	p.Arg1547AspfsTer21	p.R1547Dfs*21	ENST00000378444	NM_001123385.1	1547	Cga/ga	12/15	0.3	2	FACETS	0.682	0.553	0.829			1	SUBCLONAL	1	TRUE	NA	0.18	2		314	521	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0009534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	15	193	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		193	445	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759488	133759488	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	615	525	0	ENST00000318560.5:c.1811T>A	p.Ile604Asn	p.I604N	ENST00000318560	NM_005157.4	604	aTc/aAc	11/11	1	2	FACETS	0.931	0.896	0.966	0.931	0.896	0.966	CLONAL	1	TRUE	1	0.825485041147675	2		525	1601	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459326	99459327	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCTACCTTTACCGGCACAATTACTGCTCCAAAGGT	novel	NA	P-0009832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1192	319	369	0	ENST00000268035.6:c.1963_1996+2dup		p.G655_G666dup	ENST00000268035	NM_000875.3	655	-/GGCTACCTTTACCGGCACAATTACTGCTCCAAAGGT	9/21	1	2	FACETS	0.512	0.481	0.542	0.512	0.481	0.542	SUBCLONAL	1	TRUE	1	0.825485041147675	2		369	1511	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0010508-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	2863	435	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.805449088957568	21	FACETS	0.999	0.991	1			1	CLONAL	19	TRUE	NA	0.805449088957568	21		435	3240	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010508-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	184	613	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.805449088957568	4	FACETS	0.964	0.89	1	0.482	0.445	0.52	CLONAL	1	TRUE	2	0.805449088957568	4		613	856	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864645	57864645	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010508-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	416	702	0	ENST00000228682.2:c.2122G>T	p.Glu708Ter	p.E708*	ENST00000228682	NM_005269.2	708	Gaa/Taa	12/12	0.805449088957568	4	FACETS	0.976	0.934	1	0.976	0.934	1	CLONAL	2	TRUE	2	0.805449088957568	4		702	955	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070596	67070596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010508-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	250	305	0	ENST00000412916.2:c.220C>T	p.Gln74Ter	p.Q74*	ENST00000412916		74	Cag/Tag	3/6	0.805449088957568	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.805449088957568	2		305	292	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111475	8111476	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0010508-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	269	594	0	ENST00000346208.3:c.962_963insAA	p.Thr322ArgfsTer34	p.T322Rfs*34	ENST00000346208		321	cag/cAAag	5/6	0.805449088957568	3	FACETS	1	0.971	1	0.527	0.495	0.559	CLONAL	1	TRUE	1	0.805449088957568	3		594	889	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577271	64577272	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACA	novel	NA	P-0010508-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	447	706	0	ENST00000312049.6:c.308_310dup	p.Leu103dup	p.L103dup	ENST00000312049	NM_130799.2	103	tcc/tTGTcc	2/10	NA	2	FACETS	0.954	0.927	0.979			1	INDETERMINATE	2	TRUE	NA	0.805449088957568	2		706	582	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261080	16261121	+	protein_altering_variant	In_Frame_Del	DEL	ACAGTCGGTTCCACCCAGGGTCCATGCCTGTGATCGACGATC	ACAGTCGGTTCCACCCAGGGTCCATGCCTGTGATCGACGATC	TGA	novel	NA	P-0010508-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	152	541	2	ENST00000375759.3:c.8345_8386delinsTGA	p.Asn2782_Arg2796delinsMetSer	p.N2782_R2796delinsMS	ENST00000375759	NM_015001.2	2782	aACAGTCGGTTCCACCCAGGGTCCATGCCTGTGATCGACGATCgt/aTGAgt	11/15	0.19299891026999	3	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.805449088957568	3		543	407	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010654-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	449	270	0				ENST00000310581	NM_198253.2	-/1132			0.216950370927732	1	FACETS	0.655	0.629	0.682	0.655	0.629	0.682	INDETERMINATE	1	TRUE	0	0.84738231148598	1		270	932	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380254	25380254	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010654-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	647	537	0	ENST00000311936.3:c.204G>C	p.Arg68Ser	p.R68S	ENST00000311936	NM_004985.3	68	agG/agC	3/5	NA	2	FACETS	0.962	0.928	0.997			1	INDETERMINATE	1	TRUE	NA	0.84738231148598	2		537	1587	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309887	65309887	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1304838920	NA	P-0010654-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	552	376	1	ENST00000342505.4:c.2263C>T	p.Arg755Ter	p.R755*	ENST00000342505	NM_002227.2	755	Cga/Tga	17/25	0.84738231148598	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.84738231148598	1		377	741	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931847	39931848	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTAA	novel	NA	P-0010654-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	698	224	0	ENST00000378444.4:c.2751_2752insTTAC	p.Gln918LeufsTer29	p.Q918Lfs*29	ENST00000378444	NM_001123385.1	917	-/TTAC	4/15	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.84738231148598	1		224	876	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0010663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	183	451	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	1	2	FACETS	0.837	0.774	0.903	0.837	0.774	0.903	CLONAL	1	TRUE	1	0.525397239812519	2		451	832	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910764	114910764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	433	892	3	ENST00000543371.1:c.883C>T	p.Pro295Ser	p.P295S	ENST00000543371	NM_001198531.1	295	Ccc/Tcc	9/14	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.525397239812519	2		895	1552	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572921	41572921	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	229	546	1	ENST00000263253.7:c.5206C>T	p.Gln1736Ter	p.Q1736*	ENST00000263253	NM_001429.3	1736	Cag/Tag	31/31	1	2	FACETS	0.883	0.823	0.945	0.883	0.823	0.945	CLONAL	1	TRUE	1	0.525397239812519	2		547	987	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010992-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	252	562	3	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.77770036175583	3	FACETS	1	0.971	1	0.529	0.496	0.562	CLONAL	1	TRUE	1	0.783355430962518	3		565	847	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936983	48936983	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690863	NA	P-0010992-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	885	571	0	ENST00000267163.4:c.751C>T	p.Arg251Ter	p.R251*	ENST00000267163	NM_000321.2	251	Cga/Tga	8/27	0.783355430962518	4	FACETS	1	0.996	1	1	0.996	1	CLONAL	4	TRUE	0	0.783355430962518	4		571	983	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098816	178098816	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011205-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	256	642	0	ENST00000397062.3:c.229G>T	p.Asp77Tyr	p.D77Y	ENST00000397062	NM_006164.4	77	Gat/Tat	2/5	0.307912322411771	3	FACETS	1	0.986	1	0.591	0.554	0.629	INDETERMINATE	1	TRUE	1	0.56519985584484	3		642	983	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264416	46264416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011205-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	90	537	0	ENST00000371998.3:c.1463G>A	p.Gly488Glu	p.G488E	ENST00000371998		488	gGg/gAg	11/23	1	2	FACETS	0.455	0.403	0.51	0.455	0.403	0.51	SUBCLONAL	1	TRUE	1	0.56519985584484	2		537	700	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961751	55961751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011205-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	92	517	0	ENST00000263923.4:c.2810C>T	p.Pro937Leu	p.P937L	ENST00000263923	NM_002253.2	937	cCc/cTc	20/30	1	2	FACETS	0.518	0.461	0.58	0.518	0.461	0.58	SUBCLONAL	1	TRUE	1	0.56519985584484	2		517	628	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214368	55214368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761795138	NA	P-0011205-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	108	628	3	ENST00000275493.2:c.494G>A	p.Arg165Gln	p.R165Q	ENST00000275493	NM_005228.3	165	cGg/cAg	4/28	1	2	FACETS	0.472	0.424	0.524	0.472	0.424	0.524	SUBCLONAL	1	TRUE	1	0.56519985584484	2		631	809	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0011309-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	61	548	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.118841463439257	3	FACETS	0.846	0.73	0.973	0.282	0.243	0.325	INDETERMINATE	1	FALSE	0	0.269980818414782	3		548	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577119	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0011309-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	58	532	0	ENST00000269305.4:c.819dup	p.Val274CysfsTer32	p.V274Cfs*32	ENST00000269305	NM_001126112.2	273	-/T	8/11	1	2	FACETS	0.54	0.463	0.624	0.54	0.463	0.624	SUBCLONAL	1	FALSE	1	0.269980818414782	2		532	796	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117799	108117799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202160435	NA	P-0011474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	24	355	1	ENST00000278616.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000278616	NM_000051.3	337	cGt/cAt	8/63	0.215877583845042	1	FACETS	0.507	0.397	0.635	0.507	0.397	0.635	SUBCLONAL	1	TRUE	0	0.215877583845042	1		356	391	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845759	151845759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	69	598	1	ENST00000262189.6:c.13253G>A	p.Arg4418Lys	p.R4418K	ENST00000262189	NM_170606.2	4418	aGg/aAg	52/59	0.146063845501119	3	FACETS	0.619	0.537	0.708	0.309	0.268	0.354	SUBCLONAL	1	TRUE	1	0.215877583845042	3		599	1145	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058967	42058967	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1210	73	876	0	ENST00000219905.7:c.8687C>A	p.Ser2896Tyr	p.S2896Y	ENST00000219905	NM_001164273.1	2896	tCt/tAt	24/24	0.214828741527775	0	FACETS	0.413	0.36	0.471			1	SUBCLONAL	1	TRUE	0	0.215877583845042	0		876	1283	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456347	99456347	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	56	436	0	ENST00000268035.6:c.1664A>G	p.Asp555Gly	p.D555G	ENST00000268035	NM_000875.3	555	gAc/gGc	8/21	1	2	FACETS	0.673	0.575	0.78	0.673	0.575	0.78	SUBCLONAL	1	TRUE	1	0.215877583845042	2		436	771	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933047	39933047	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	58	337	0	ENST00000378444.4:c.1552G>T	p.Glu518Ter	p.E518*	ENST00000378444	NM_001123385.1	518	Gaa/Taa	4/15	0.181022578767472	0	FACETS	0.705	0.605	0.813			1	SUBCLONAL	1	TRUE	NA	0.215877583845042	0		337	598	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247559	53247559	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	51	379	1	ENST00000375401.3:c.250A>C	p.Asn84His	p.N84H	ENST00000375401	NM_004187.3	84	Aac/Cac	3/26	1	1	FACETS	0.631	0.535	0.736	0.631	0.535	0.736	SUBCLONAL	1	TRUE	0	0.215877583845042	1		380	668	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395219	139395220	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0011474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	154	503	0	ENST00000277541.6:c.5718_5719del	p.Pro1907GlyfsTer35	p.P1907Gfs*35	ENST00000277541	NM_017617.3	1906	gcGCcg/gccg	31/34	0.185750854666128	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.215877583845042	1		503	858	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231424	46231425	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0011474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	131	385	0	ENST00000334344.6:c.1265dup	p.Tyr423IlefsTer38	p.Y423Ifs*38	ENST00000334344	NM_152641.2	422	cta/cTta	10/21	1	2	FACETS	0.954	0.868	1	1	0.99	1	CLONAL	2	TRUE	1	0.215877583845042	2		385	636	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436083	49436083	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	13	126	0	ENST00000301067.7:c.5898del	p.Gly1967ValfsTer80	p.G1967Vfs*80	ENST00000301067	NM_003482.3	1966	ccC/cc	28/54	0.214493691058147	0	FACETS	0.569	0.407	0.765			1	SUBCLONAL	1	TRUE	0	0.215877583845042	0		126	166	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056160	27056160	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	75	283	0	ENST00000324856.7:c.1156C>T	p.Gln386Ter	p.Q386*	ENST00000324856	NM_006015.4	386	Cag/Tag	2/20	1	2	FACETS	0.344	0.301	0.391	0.344	0.301	0.391	SUBCLONAL	1	TRUE	1	0.544704211100739	2		283	801	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552838	106552838	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367766895	NA	P-0012051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1461	184	528	0	ENST00000369096.4:c.803G>A	p.Arg268His	p.R268H	ENST00000369096	NM_001198.3	268	cGt/cAt	5/7	1	2	FACETS	0.411	0.377	0.446	0.411	0.377	0.446	SUBCLONAL	1	TRUE	1	0.544704211100739	2		528	1645	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435733	116435733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	238	311	0	ENST00000397752.3:c.3823G>A	p.Glu1275Lys	p.E1275K	ENST00000397752	NM_000245.2	1275	Gag/Aag	20/21	1	2	FACETS	0.98	0.916	1	0.98	0.916	1	CLONAL	1	TRUE	1	0.544704211100739	2		311	892	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115684	108115685	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCATTATTGAATTATTTCAACTGCAAATTTATATCCATCATCCGAAAGGAGCCAA	novel	NA	P-0012051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	57	228	0	ENST00000278616.4:c.833_887dup	p.Lys296AsnfsTer4	p.K296Nfs*4	ENST00000278616	NM_000051.3	278	gtc/gTCATTATTGAATTATTTCAACTGCAAATTTATATCCATCATCCGAAAGGAGCCAAtc	7/63	1	2	FACETS	0.284	0.243	0.329	0.284	0.243	0.329	SUBCLONAL	1	TRUE	1	0.544704211100739	2		228	736	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390736	139390736	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	473	810	1	ENST00000277541.6:c.7455del	p.Ser2486ArgfsTer103	p.S2486Rfs*103	ENST00000277541	NM_017617.3	2485	ccC/cc	34/34	NA	2	FACETS	0.931	0.902	0.959			1	INDETERMINATE	2	TRUE	NA	0.742997494712622	2		811	684	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922282	39922282	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	173	272	0	ENST00000378444.4:c.3890C>A	p.Ser1297Ter	p.S1297*	ENST00000378444	NM_001123385.1	1297	tCa/tAa	9/15	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.742997494712622	1		272	252	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176684087	176684087	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	411	479	0	ENST00000439151.2:c.4901G>C	p.Arg1634Pro	p.R1634P	ENST00000439151	NM_022455.4	1634	cGg/cCg	13/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.673897329987511	2		479	1184	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397654	139397654	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	590	360	0	ENST00000277541.6:c.5147A>C	p.Tyr1716Ser	p.Y1716S	ENST00000277541	NM_017617.3	1716	tAc/tCc	27/34	0.673897329987511	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.673897329987511	2		360	845	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870230	44870230	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	465	297	0	ENST00000377967.4:c.409G>C	p.Gly137Arg	p.G137R	ENST00000377967	NM_021140.2	137	Ggt/Cgt	5/29	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.673897329987511	1		297	729	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390905	139390906	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	GGTGGCCGCTGGCTGCTGAGCTCACGCCAAGGTGCGGCTGTGGTGGT	novel	NA	P-0012652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	211	290	0	ENST00000277541.6:c.7239_7285dup	p.Leu2429HisfsTer9	p.L2429Hfs*9	ENST00000277541	NM_017617.3	2429	ctg/cACCACCACAGCCGCACCTTGGCGTGAGCTCAGCAGCCAGCGGCCACCtg	34/34	0.673897329987511	2	FACETS	0.527	0.489	0.567	0.264	0.244	0.284	SUBCLONAL	1	TRUE	0	0.673897329987511	2		290	1188	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256020	16256021	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0012652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	618	336	0	ENST00000375759.3:c.3287_3288del	p.Val1096GlyfsTer25	p.V1096Gfs*25	ENST00000375759	NM_015001.2	1095	tcTGtg/tctg	11/15	0.673897329987511	2	FACETS	0.964	0.937	0.992	0.964	0.937	0.992	CLONAL	2	TRUE	0	0.673897329987511	2		336	951	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274734	123274734	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	531	533	0	ENST00000358487.5:c.1184T>A	p.Val395Asp	p.V395D	ENST00000358487	NM_000141.4	395	gTc/gAc	9/18	0.635322032312497	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.635322032312497	2		533	813	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130570	29130570	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	548	503	0	ENST00000328354.6:c.140C>G	p.Pro47Arg	p.P47R	ENST00000328354	NM_007194.3	47	cCa/cGa	2/15	0.351504430596225	5	FACETS	0.885	0.851	0.919	0.885	0.851	0.919	INDETERMINATE	3	TRUE	2	0.635322032312497	5		503	1269	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396878	139396879	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCGGCCGCCGCCACGTACATGAAGTGCAGCTGCGCCGGCGGGGGCGGCTCCACGGT	novel	NA	P-0013084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	58	285	0	ENST00000277541.6:c.5173_5229dup	p.Thr1725_Ala1743dup	p.T1725_A1743dup	ENST00000277541	NM_017617.3	1725	-/ACCGTGGAGCCGCCCCCGCCGGCGCAGCTGCACTTCATGTACGTGGCGGCGGCCGCC	28/34	0.528266393077812	3	FACETS	0.4	0.343	0.461	0.2	0.171	0.231	SUBCLONAL	1	TRUE	1	0.635322032312497	3		285	602	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578217	+	inframe_deletion	In_Frame_Del	DEL	TATGTCGAAAAG	TATGTCGAAAAG	-	novel	NA	P-0013084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	583	732	0	ENST00000269305.4:c.632_643del	p.Thr211_His214del	p.T211_H214del	ENST00000269305	NM_001126112.2	211	aCTTTTCGACATAgt/agt	6/11	0.635322032312497	2	FACETS	0.989	0.959	1	0.989	0.959	1	CLONAL	2	TRUE	0	0.635322032312497	2		732	928	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041454	42041455	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0013084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1295	788	928	0	ENST00000219905.7:c.5651dup	p.Ser1885IlefsTer8	p.S1885Ifs*8	ENST00000219905	NM_001164273.1	1883	-/C	17/24	0.623551526513863	4	FACETS	0.974	0.941	1	0.974	0.941	1	CLONAL	2	TRUE	2	0.635322032312497	4		928	2083	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0013620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	108	498	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.776	0.7	0.856	0.776	0.7	0.856	SUBCLONAL	1	TRUE	1	0.570185655549836	2		498	488	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0013620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	61	355	0	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	0.267330255291347	1	FACETS	0.305	0.263	0.35	0.305	0.263	0.35	INDETERMINATE	1	TRUE	0	0.570185655549836	1		355	502	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141515	11141515	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	226	670	0	ENST00000358026.2:c.3492C>G	p.Asn1164Lys	p.N1164K	ENST00000358026	NM_001128849.1	1164	aaC/aaG	25/36	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.570185655549836	2		670	757	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397639	139397639	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	369	520	0	ENST00000277541.6:c.5162T>G	p.Val1721Gly	p.V1721G	ENST00000277541	NM_017617.3	1721	gTg/gGg	27/34	1	2	FACETS	0.944	0.901	0.987	0.944	0.901	0.987	CLONAL	1	TRUE	1	0.954563810190935	2		520	819	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268138	153268138	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1406877044	NA	P-0013838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	526	594	0	ENST00000281708.4:c.670C>T	p.Arg224Ter	p.R224*	ENST00000281708	NM_033632.3	224	Cga/Tga	4/12	1	2	FACETS	0.937	0.901	0.973	0.937	0.901	0.973	CLONAL	1	TRUE	1	0.954563810190935	2		594	1176	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161298206	161298206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148566767	NA	P-0013838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	550	630	2	ENST00000367975.2:c.98C>T	p.Thr33Met	p.T33M	ENST00000367975	NM_003001.3	33	aCg/aTg	3/6	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.954563810190935	2		632	1140	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760377	133760378	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0013838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	342	507	2	ENST00000318560.5:c.2705dup	p.Pro903ThrfsTer37	p.P903Tfs*37	ENST00000318560	NM_005157.4	900	-/C	11/11	1	2	FACETS	0.978	0.932	1	0.978	0.932	1	CLONAL	1	TRUE	1	0.954563810190935	2		509	733	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390843	139390844	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCTGGGGCCCAGTG	novel	NA	P-0013838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	213	472	0	ENST00000277541.6:c.7334_7347dup	p.Ser2450HisfsTer32	p.S2450Hfs*32	ENST00000277541	NM_017617.3	2449	-/CACTGGGCCCCAGC	34/34	1	2	FACETS	0.609	0.568	0.651	0.609	0.568	0.651	SUBCLONAL	1	TRUE	1	0.954563810190935	2		472	733	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0014382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	113	470	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.48	0.432	0.531	0.48	0.432	0.531	SUBCLONAL	1	TRUE	1	0.64	2		471	736	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0014382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	28	389	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	1	2	FACETS	0.116	0.092	0.143	0.116	0.092	0.143	SUBCLONAL	1	TRUE	1	0.64	2		389	755	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0014382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	47	243	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.267	0.225	0.314	0.267	0.225	0.314	SUBCLONAL	1	TRUE	1	0.64	2		243	550	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166282	7166282	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	74	680	0	ENST00000302850.5:c.1744G>T	p.Gly582Cys	p.G582C	ENST00000302850	NM_000208.2	582	Ggt/Tgt	8/22	1	2	FACETS	0.18	0.157	0.205	0.18	0.157	0.205	SUBCLONAL	1	TRUE	1	0.64	2		680	1285	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346337	73346337	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	74	395	0	ENST00000377767.4:c.1463A>G	p.Asp488Gly	p.D488G	ENST00000377767	NM_014953.3	488	gAt/gGt	10/21	1	2	FACETS	0.383	0.335	0.434	0.383	0.335	0.434	SUBCLONAL	1	TRUE	1	0.64	2		395	604	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820762	3820762	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1706	246	984	2	ENST00000262367.5:c.2689C>T	p.Gln897Ter	p.Q897*	ENST00000262367	NM_004380.2	897	Cag/Tag	14/31	1	2	FACETS	0.394	0.366	0.423	0.394	0.366	0.423	SUBCLONAL	1	TRUE	1	0.64	2		986	1952	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670886	30670886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1171	130	600	0	ENST00000376406.3:c.5860C>T	p.His1954Tyr	p.H1954Y	ENST00000376406	NM_014641.2	1954	Cat/Tat	12/15	1	2	FACETS	0.312	0.282	0.344	0.312	0.282	0.344	SUBCLONAL	1	TRUE	1	0.64	2		600	1301	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942756	44942756	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	123	662	0	ENST00000377967.4:c.3336del	p.Val1113TyrfsTer7	p.V1113Yfs*7	ENST00000377967	NM_021140.2	1112	gtC/gt	23/29	1	2	FACETS	0.376	0.339	0.415	0.376	0.339	0.415	SUBCLONAL	1	TRUE	1	0.64	2		662	1023	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399421	139399423	+	inframe_deletion	In_Frame_Del	DEL	CAG	CAG	-	novel	NA	P-0014405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	894	588	4	ENST00000277541.6:c.4720_4722del	p.Leu1574del	p.L1574del	ENST00000277541	NM_017617.3	1574	CTG/-	26/34	0.914131770746941	3	FACETS	1	0.998	1	0.833	0.817	0.849	CLONAL	2	TRUE	0	0.914131770746941	3		592	1140	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974715	21974732	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCCCCCGCCTCCA	GCAGCGCCCCCGCCTCCA	-	novel	NA	P-0014472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	45	314	0	ENST00000304494.5:c.95_112del	p.Leu32_Leu37del	p.L32_L37del	ENST00000304494	NM_000077.4	32	cTGGAGGCGGGGGCGCTGCcc/ccc	1/3	0.186328644118768	1	FACETS	0.102	0.085	0.12	0.102	0.085	0.12	INDETERMINATE	1	TRUE	0	0.84	1		314	611	SUCCESS
ATM	472	MSKCC	GRCh37	11	108099987	108099988	+	missense_variant	Missense_Mutation	DNP	AG	AG	GT	novel	NA	P-0014472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	68	391	1	ENST00000278616.4:c.268_269delinsGT	p.Arg90Val	p.R90V	ENST00000278616	NM_000051.3	90	AGg/GTg	4/63	1	2	FACETS	0.209	0.181	0.239	0.209	0.181	0.239	SUBCLONAL	1	TRUE	1	0.84	2		392	774	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266041	41266041	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	47	286	0	ENST00000349496.5:c.39del	p.Met14TrpfsTer33	p.M14Wfs*33	ENST00000349496	NM_001904.3	13	gCc/gc	3/15	1	2	FACETS	0.204	0.172	0.239	0.204	0.172	0.239	SUBCLONAL	1	TRUE	1	0.84	2		286	549	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44894216	44894225	+	frameshift_variant	Frame_Shift_Del	DEL	TGTCCAATGC	TGTCCAATGC	-	novel	NA	P-0014472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	63	462	0	ENST00000377967.4:c.607_616del	p.Ser203LysfsTer36	p.S203Kfs*36	ENST00000377967	NM_021140.2	202	tTGTCCAATGCt/tt	7/29	0.203334749572464	1	FACETS	0.126	0.109	0.145	0.126	0.109	0.145	INDETERMINATE	1	TRUE	0	0.84	1		462	689	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255092	16255093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0014709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	210	490	1	ENST00000375759.3:c.2363dup	p.Asn788LysfsTer2	p.N788Kfs*2	ENST00000375759	NM_015001.2	786	aca/acAa	11/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.442400330924641	2		491	903	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171600	36171600	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0014709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	27	283	0	ENST00000300305.3:c.965C>G	p.Ser322Ter	p.S322*	ENST00000300305		322	tCa/tGa	7/8	1	2	FACETS	0.239	0.189	0.296	0.239	0.189	0.296	SUBCLONAL	1	TRUE	1	0.442400330924641	2		283	511	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555639	21555640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0014709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	112	637	0	ENST00000382592.4:c.2630dup	p.Asn878LysfsTer18	p.N878Kfs*18	ENST00000382592	NM_014572.2	877	cca/ccCa	6/8	1	2	FACETS	0.5	0.448	0.554	0.5	0.448	0.554	SUBCLONAL	1	TRUE	1	0.442400330924641	2		637	1013	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992589	72992589	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	249	539	0	ENST00000268489.5:c.1456G>T	p.Glu486Ter	p.E486*	ENST00000268489	NM_006885.3	486	Gag/Tag	2/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.442400330924641	2		539	1020	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484617	57484617	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	139	466	0	ENST00000371085.3:c.701G>A	p.Trp234Ter	p.W234*	ENST00000371085	NM_000516.4	234	tGg/tAg	9/13	1	2	FACETS	0.719	0.654	0.787	0.719	0.654	0.787	SUBCLONAL	1	TRUE	1	0.442400330924641	2		466	874	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206817	36206817	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	172	454	0	ENST00000300305.3:c.695G>T	p.Arg232Leu	p.R232L	ENST00000300305		232	cGg/cTg	6/8	1	2	FACETS	0.895	0.824	0.969	0.895	0.824	0.969	CLONAL	1	TRUE	1	0.442400330924641	2		454	869	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252856	36252857	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0014709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	91	366	0	ENST00000300305.3:c.504_505dup	p.Arg169LysfsTer8	p.R169Kfs*8	ENST00000300305		169	aga/aAAga	4/8	1	2	FACETS	0.589	0.523	0.659	0.589	0.523	0.659	SUBCLONAL	1	TRUE	1	0.442400330924641	2		366	699	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566474	41566474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	147	534	0	ENST00000263253.7:c.4351C>T	p.His1451Tyr	p.H1451Y	ENST00000263253	NM_001429.3	1451	Cat/Tat	27/31	1	2	FACETS	0.7	0.639	0.765	0.7	0.639	0.765	SUBCLONAL	1	TRUE	1	0.442400330924641	2		534	949	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259284	89259284	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	153	414	0	ENST00000336596.2:c.428T>C	p.Ile143Thr	p.I143T	ENST00000336596	NM_005233.5	143	aTt/aCt	3/17	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.442400330924641	2		414	674	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196490	106196491	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0014709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	149	454	0	ENST00000380013.4:c.4825_4826dup	p.Leu1609PhefsTer2	p.L1609Ffs*2	ENST00000380013	NM_001127208.2	1608	tat/taTTt	11/11	1	2	FACETS	0.925	0.847	1	0.925	0.847	1	CLONAL	1	TRUE	1	0.442400330924641	2		454	728	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0014961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	109	470	1				ENST00000310581	NM_198253.2	-/1132			0.765717397087684	1	FACETS	0.616	0.562	0.672	0.616	0.562	0.672	SUBCLONAL	1	FALSE	0	0.765717397087684	1		471	285	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101138	27101138	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1476360310	NA	P-0014961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	323	664	0	ENST00000324856.7:c.4420C>T	p.Gln1474Ter	p.Q1474*	ENST00000324856	NM_006015.4	1474	Caa/Taa	18/20	0.152213488819396	4	FACETS	0.945	0.897	0.994	0.945	0.897	0.994	INDETERMINATE	2	FALSE	2	0.765717397087684	4		664	788	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106751	27106751	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	266	577	0	ENST00000324856.7:c.6364del	p.Leu2122SerfsTer13	p.L2122Sfs*13	ENST00000324856	NM_006015.4	2121	aCc/ac	20/20	0.152213488819396	4	FACETS	0.909	0.858	0.961	0.909	0.858	0.961	INDETERMINATE	2	FALSE	2	0.765717397087684	4		577	675	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572265	41572265	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	276	571	0	ENST00000263253.7:c.4795del	p.Arg1599AlafsTer25	p.R1599Afs*25	ENST00000263253	NM_001429.3	1598	atC/at	30/31	NA	2	FACETS	1	0.966	1			1	INDETERMINATE	1	FALSE	NA	0.765717397087684	2		571	700	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390867	139390870	+	frameshift_variant	Frame_Shift_Del	DEL	CTGC	CTGC	-	novel	NA	P-0014961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	454	595	0	ENST00000277541.6:c.7321_7324del	p.Ala2441ThrfsTer35	p.A2441Tfs*35	ENST00000277541	NM_017617.3	2441	GCAGac/ac	34/34	NA	2	FACETS	0.977	0.949	1			1	INDETERMINATE	2	FALSE	NA	0.765717397087684	2		595	607	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0015475-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	20	456	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.25734495440491	3	FACETS	0.724	0.555	0.92	0.362	0.277	0.46	CLONAL	1	TRUE	1	0.28	3		456	225	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416567	49416567	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015961-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	124	790	0	ENST00000301067.7:c.16144del	p.His5382ThrfsTer36	p.H5382Tfs*36	ENST00000301067	NM_003482.3	5382	Cac/ac	51/54	1	2	FACETS	0.802	0.724	0.884	0.802	0.724	0.884	CLONAL	1	TRUE	1	0.283012261674817	2		790	1093	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	64	520	0	ENST00000308159.5:c.43C>G	p.Gln15Glu	p.Q15E	ENST00000308159	NM_014669.4	15	Cag/Gag	2/22	1	2	FACETS	0.948	0.821	1	0.948	0.821	1	CLONAL	1	TRUE	1	0.22	2		520	614	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221930	98221930	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	79	614	0	ENST00000331920.6:c.2839G>T	p.Glu947Ter	p.E947*	ENST00000331920	NM_000264.3	947	Gaa/Taa	17/24	1	2	FACETS	0.992	0.872	1	0.992	0.872	1	CLONAL	1	TRUE	1	0.22	2		614	724	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345800	152345800	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730882047	NA	P-0016379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	48	482	0	ENST00000359321.1:c.770C>T	p.Ser257Leu	p.S257L	ENST00000359321	NM_005431.1	257	tCa/tTa	3/3	1	2	FACETS	0.629	0.53	0.738	0.629	0.53	0.738	SUBCLONAL	1	TRUE	1	0.22	2		482	694	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337618	73337618	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754638163	NA	P-0016379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	48	378	0	ENST00000377767.4:c.2098G>A	p.Glu700Lys	p.E700K	ENST00000377767	NM_014953.3	700	Gaa/Aaa	16/21	1	2	FACETS	0.831	0.703	0.973	0.831	0.703	0.973	CLONAL	1	TRUE	1	0.22	2		378	525	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10287981	10287981	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	77	687	0	ENST00000340748.4:c.508C>G	p.His170Asp	p.H170D	ENST00000340748		170	Cat/Gat	5/40	1	2	FACETS	0.765	0.67	0.868	0.765	0.67	0.868	SUBCLONAL	1	TRUE	1	0.22	2		687	915	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958777	38958777	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	47	375	0	ENST00000357387.3:c.2335G>A	p.Glu779Lys	p.E779K	ENST00000357387	NM_152756.3	779	Gaa/Aaa	23/38	1	2	FACETS	0.794	0.67	0.931	0.794	0.67	0.931	CLONAL	1	TRUE	1	0.22	2		375	538	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891214	151891214	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0016379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	84	618	0	ENST00000262189.6:c.4541-1G>A		p.X1514_splice	ENST00000262189	NM_170606.2	1514			1	2	FACETS	0.896	0.79	1	0.896	0.79	1	CLONAL	1	TRUE	1	0.22	2		618	852	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70355045	70355045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	98	751	0	ENST00000374080.3:c.4967C>T	p.Ser1656Phe	p.S1656F	ENST00000374080		1656	tCc/tTc	36/45	1	2	FACETS	0.979	0.872	1	0.979	0.872	1	CLONAL	1	TRUE	1	0.22	2		751	910	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0017174-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3390	612	728	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.219540824342102	29	FACETS	0.92	0.88	0.962	0.19	0.182	0.199	CLONAL	6	TRUE	0	0.219540824342102	29		728	4002	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0017174-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	2471	548	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.219540824342102	29	FACETS	0.996	0.984	1	0.962	0.95	0.973	CLONAL	28	TRUE	0	0.219540824342102	29		548	3200	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462860	120462860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755747980	NA	P-0017174-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	23	282	1	ENST00000256646.2:c.5471G>A	p.Arg1824His	p.R1824H	ENST00000256646	NM_024408.3	1824	cGt/cAt	30/34	1	2	FACETS	0.529	0.412	0.665	0.529	0.412	0.665	SUBCLONAL	1	TRUE	1	0.219540824342102	2		283	396	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355087	73355087	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017174-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	73	600	0	ENST00000377767.4:c.283C>G	p.Leu95Val	p.L95V	ENST00000377767	NM_014953.3	95	Ctt/Gtt	2/21	0.219540824342102	1	FACETS	0.753	0.658	0.856	0.753	0.658	0.856	SUBCLONAL	1	TRUE	0	0.219540824342102	1		600	786	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0017174-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	117	632	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.219540824342102	2		632	1052	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30956886	30956889	+	frameshift_variant	Frame_Shift_Del	DEL	TTTA	TTTA	-	novel	NA	P-0017174-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	127	530	0	ENST00000375687.4:c.213_216del	p.Phe71LeufsTer48	p.F71Lfs*48	ENST00000375687	NM_015338.5	71	tTTTAt/tt	4/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.219540824342102	2		530	882	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249091	55249091	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519861	NA	P-0017174-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3635	597	749	0	ENST00000275493.2:c.2389T>A	p.Cys797Ser	p.C797S	ENST00000275493	NM_005228.3	797	Tgc/Agc	20/28	0.219540824342102	29	FACETS	1	0.97	1	0.176	0.167	0.184	CLONAL	5	TRUE	0	0.219540824342102	29		749	4232	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873297	151873297	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017174-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	30	344	0	ENST00000262189.6:c.9241G>C	p.Glu3081Gln	p.E3081Q	ENST00000262189	NM_170606.2	3081	Gaa/Caa	38/59	0.2186802973815	1	FACETS	0.491	0.394	0.6	0.491	0.394	0.6	SUBCLONAL	1	TRUE	0	0.219540824342102	1		344	496	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032579	47032579	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017174-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	449	335	0	ENST00000377604.3:c.485del	p.Met162SerfsTer104	p.M162Sfs*104	ENST00000377604	NM_001204468.1	162	aTg/ag	5/24	0.219540824342102	4	FACETS	0.974	0.936	1			1	CLONAL	6	TRUE	NA	0.219540824342102	4		335	854	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577523	7577524	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018480-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	72	731	0	ENST00000269305.4:c.757dup	p.Thr253AsnfsTer11	p.T253Nfs*11	ENST00000269305	NM_001126112.2	253	acc/aAcc	7/11	1	2	FACETS	0.497	0.434	0.566	0.497	0.434	0.566	SUBCLONAL	1	TRUE	1	0.369234979175899	2		731	784	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257776	16257776	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018480-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	42	607	0	ENST00000375759.3:c.5041G>A	p.Glu1681Lys	p.E1681K	ENST00000375759	NM_015001.2	1681	Gaa/Aaa	11/15	1	2	FACETS	0.309	0.257	0.367	0.309	0.257	0.367	SUBCLONAL	1	TRUE	1	0.369234979175899	2		607	737	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174404	11174418	+	inframe_deletion	In_Frame_Del	DEL	TCATAGACAAAGGCT	TCATAGACAAAGGCT	-	novel	NA	P-0018480-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	41	674	0	ENST00000361445.4:c.7257_7271del	p.Glu2419_Tyr2423del	p.E2419_Y2423del	ENST00000361445	NM_004958.3	2419	gaAGCCTTTGTCTATGAc/gac	53/58	1	2	FACETS	0.278	0.231	0.331	0.278	0.231	0.331	SUBCLONAL	1	TRUE	1	0.369234979175899	2		674	798	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727451	66727465	+	inframe_deletion	In_Frame_Del	DEL	AGAAGCAGAAGGTGG	AGAAGCAGAAGGTGG	-	novel	NA	P-0018480-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	40	555	0	ENST00000307102.5:c.167_181del	p.Gln56_Gly61delinsArg	p.Q56_G61delinsR	ENST00000307102	NM_002755.3	56	cAGAAGCAGAAGGTGGga/cga	2/11	1	2	FACETS	0.357	0.296	0.425	0.357	0.296	0.425	SUBCLONAL	1	TRUE	1	0.369234979175899	2		555	607	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40379693	40379693	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755543502	NA	P-0018480-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	46	667	0	ENST00000293328.3:c.139G>A	p.Asp47Asn	p.D47N	ENST00000293328	NM_012448.3	47	Gat/Aat	3/19	1	2	FACETS	0.375	0.315	0.441	0.375	0.315	0.441	SUBCLONAL	1	TRUE	1	0.369234979175899	2		667	665	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018544-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	70	270	0				ENST00000310581	NM_198253.2	-/1132			0.684372946727549	3	FACETS	1	0.944	1	0.56	0.494	0.628	CLONAL	1	TRUE	1	0.689481144171874	3		270	244	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0018544-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	438	595	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.689481144171874	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.689481144171874	3		595	822	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572935	7572938	+	frameshift_variant	Frame_Shift_Del	DEL	AGTC	AGTC	-	novel	NA	P-0018544-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	162	556	0	ENST00000269305.4:c.1171_1174del	p.Asp391GlnfsTer30	p.D391Qfs*30	ENST00000269305	NM_001126112.2	391	GACTca/ca	11/11	0.689481144171874	3	FACETS	0.821	0.754	0.89	0.41	0.377	0.445	CLONAL	1	TRUE	1	0.689481144171874	3		556	770	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575507	67575507	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018544-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	173	356	0	ENST00000274335.5:c.581del	p.Pro194GlnfsTer13	p.P194Qfs*13	ENST00000274335		194	Cca/ca	4/15	1	2	FACETS	0.779	0.731	0.827	1	0.992	1	SUBCLONAL	2	TRUE	1	0.689481144171874	2		356	322	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743502	46743502	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018544-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	22	532	0	ENST00000371975.4:c.1883A>G	p.Glu628Gly	p.E628G	ENST00000371975	NM_003579.3	628	gAg/gGg	17/18	1	2	FACETS	0.167	0.129	0.211	0.167	0.129	0.211	SUBCLONAL	1	TRUE	1	0.689481144171874	2		532	383	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	153	728	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.285358918755369	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.285358918755369	1		728	764	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491662	120491663	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs312262800	NA	P-0019136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	49	429	0	ENST00000256646.2:c.2566_2567del	p.Ser856LeufsTer17	p.S856Lfs*17	ENST00000256646	NM_024408.3	856	AGt/t	16/34	0.188585898559563	3	FACETS	0.644	0.545	0.754	0.322	0.272	0.377	SUBCLONAL	1	TRUE	1	0.285358918755369	3		429	609	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335693	81335693	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	53	633	1	ENST00000222390.5:c.1667G>C	p.Arg556Thr	p.R556T	ENST00000222390	NM_000601.4	556	aGa/aCa	15/18	0.188585898559563	3	FACETS	0.686	0.584	0.797	0.343	0.292	0.399	SUBCLONAL	1	TRUE	1	0.285358918755369	3		634	619	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433896	49433896	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	258	886	0	ENST00000301067.7:c.7657C>T	p.Gln2553Ter	p.Q2553*	ENST00000301067	NM_003482.3	2553	Cag/Tag	31/54	1	2	FACETS	0.764	0.715	0.815	1	0.993	1	SUBCLONAL	2	TRUE	1	0.285358918755369	2		886	1183	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40761168	40761168	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	190	652	1	ENST00000392038.2:c.184C>A	p.Leu62Met	p.L62M	ENST00000392038	NM_001626.4	62	Ctg/Atg	4/14	0.157950479490117	2	FACETS	1	0.987	1	0.666	0.615	0.719	INDETERMINATE	1	TRUE	0	0.285358918755369	2		653	1000	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265921	16265921	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0019136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	53	514	0	ENST00000375759.3:c.10994G>C	p.Ter3665SerextTer9	p.*3665Sext*9	ENST00000375759	NM_015001.2	3665	tGa/tCa	15/15	1	2	FACETS	0.51	0.433	0.593	0.51	0.433	0.593	SUBCLONAL	1	TRUE	1	0.285358918755369	2		514	729	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804280	43804280	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	93	635	0	ENST00000372470.3:c.280C>A	p.Gln94Lys	p.Q94K	ENST00000372470	NM_005373.2	94	Cag/Aag	3/12	1	2	FACETS	0.81	0.719	0.906	0.81	0.719	0.906	CLONAL	1	TRUE	1	0.285358918755369	2		635	805	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606842	43606842	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs763617146	NA	P-0019136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	197	857	1	ENST00000355710.3:c.1451T>C	p.Met484Thr	p.M484T	ENST00000355710	NM_020975.4	484	aTg/aCg	7/20	0.285358918755369	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.285358918755369	1		858	999	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786152	3786152	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	136	819	0	ENST00000262367.5:c.4613C>G	p.Pro1538Arg	p.P1538R	ENST00000262367	NM_004380.2	1538	cCc/cGc	28/31	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.285358918755369	2		819	951	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231591	5231591	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	91	267	0	ENST00000357368.4:c.1885A>G	p.Ser629Gly	p.S629G	ENST00000357368	NM_002850.3	629	Agc/Ggc	14/38	0.285358918755369	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.285358918755369	1		267	410	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665057	138665057	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	48	151	0	ENST00000330315.3:c.508G>T	p.Gly170Ter	p.G170*	ENST00000330315	NM_023067.3	170	Gga/Tga	1/1	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.285358918755369	2		151	258	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622162	162622162	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0019136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	79	347	0	ENST00000366898.1:c.534+1G>T		p.X178_splice	ENST00000366898	NM_004562.2	178			0.188585898559563	3	FACETS	1	0.969	1	0.656	0.579	0.739	CLONAL	1	TRUE	1	0.285358918755369	3		347	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577508	7577508	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060501201	NA	P-0019357-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	462	575	0	ENST00000269305.4:c.773A>G	p.Glu258Gly	p.E258G	ENST00000269305	NM_001126112.2	258	gAa/gGa	7/11	0.70074765577625	2	FACETS	0.884	0.855	0.912	0.884	0.855	0.912	CLONAL	2	TRUE	0	0.746959118811411	2		575	700	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019711-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	74	435	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.31	2		435	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0019711-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	126	621	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.211898472637887	2	FACETS	1	0.976	1	0.615	0.558	0.675	CLONAL	1	TRUE	0	0.31	2		624	661	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0019711-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	59	259	1	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	0.275354184814023	1	FACETS	0.978	0.846	1	0.978	0.846	1	CLONAL	1	TRUE	0	0.31	1		260	329	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385221	41385221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375454640	NA	P-0019711-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	55	581	0	ENST00000373198.4:c.740G>A	p.Arg247His	p.R247H	ENST00000373198	NM_133170.3	247	cGc/cAc	6/32	0.299466538006766	3	FACETS	0.42	0.358	0.489	0.21	0.179	0.245	SUBCLONAL	1	TRUE	1	0.31	3		581	975	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943806	9943806	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019711-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	92	343	0	ENST00000330684.3:c.1135G>A	p.Glu379Lys	p.E379K	ENST00000330684	NM_001134407.1	379	Gag/Aag	5/13	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.31	2		343	486	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0019711-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	165	524	2	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	0.299466538006766	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.31	1		526	679	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953214	81953214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369516453	NA	P-0019711-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	86	324	0	ENST00000359376.3:c.2180G>A	p.Arg727Gln	p.R727Q	ENST00000359376	NM_002661.3	727	cGa/cAa	20/33	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.31	2		324	481	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016634	12016634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019711-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	89	327	0	ENST00000353533.5:c.770C>T	p.Ser257Phe	p.S257F	ENST00000353533	NM_003010.3	257	tCt/tTt	7/11	0.211898472637887	2	FACETS	1	0.971	1	0.639	0.569	0.713	CLONAL	1	TRUE	0	0.31	2		327	449	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650377	48650377	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1557020191	NA	P-0019711-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	45	695	0	ENST00000376670.3:c.347C>G	p.Ser116Cys	p.S116C	ENST00000376670	NM_002049.3	116	tCt/tGt	3/6	1	2	FACETS	0.349	0.292	0.413	0.349	0.292	0.413	SUBCLONAL	1	TRUE	1	0.31	2		695	831	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528094	157528094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021983-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	191	483	0	ENST00000346085.5:c.5819C>T	p.Ser1940Leu	p.S1940L	ENST00000346085	NM_020732.3	1940	tCg/tTg	20/20	0.613890638046337	4	FACETS	1	0.988	1	0.449	0.416	0.483	CLONAL	1	TRUE	1	0.613890638046337	4		483	746	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685283	89685283	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1554897262	NA	P-0021983-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	28	368	0	ENST00000371953.3:c.178A>T	p.Lys60Ter	p.K60*	ENST00000371953	NM_000314.4	60	Aag/Tag	3/9	0.613890638046337	1	FACETS	0.68	0.558	0.811	0.68	0.558	0.811	SUBCLONAL	1	TRUE	0	0.613890638046337	1		368	93	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046701	42046701	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021983-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	115	659	1	ENST00000219905.7:c.7075T>A	p.Ser2359Thr	p.S2359T	ENST00000219905	NM_001164273.1	2359	Tca/Aca	18/24	0.613890638046337	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.613890638046337	1		660	213	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72863707	72863707	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1313136028	NA	P-0021983-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	159	604	0	ENST00000268489.5:c.3500A>C	p.Glu1167Ala	p.E1167A	ENST00000268489	NM_006885.3	1167	gAg/gCg	5/10	0.269064473779806	3	FACETS	1	0.987	1	0.67	0.619	0.723	INDETERMINATE	1	TRUE	1	0.613890638046337	3		604	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579359	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGAAA	novel	NA	P-0021983-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	413	757	0	ENST00000269305.4:c.324_328dup	p.Arg110LeufsTer15	p.R110Lfs*15	ENST00000269305	NM_001126112.2	110	cgt/cTTTCCgt	4/11	0.613890638046337	3	FACETS	0.868	0.836	0.9	0.868	0.836	0.9	CLONAL	3	TRUE	0	0.613890638046337	3		757	675	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248569	10248569	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021983-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	143	712	0	ENST00000340748.4:c.4184G>T	p.Trp1395Leu	p.W1395L	ENST00000340748		1395	tGg/tTg	35/40	0.532518164500177	4	FACETS	0.863	0.787	0.943	0.288	0.262	0.315	CLONAL	1	TRUE	1	0.613890638046337	4		712	871	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451758	29451758	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1340992656	NA	P-0021983-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	116	637	0	ENST00000389048.3:c.2807G>T	p.Gly936Val	p.G936V	ENST00000389048	NM_004304.4	936	gGa/gTa	16/29	0.613890638046337	3	FACETS	0.885	0.801	0.974	0.443	0.4	0.487	CLONAL	1	TRUE	1	0.613890638046337	3		637	558	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916661	178916661	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021983-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	34	461	4	ENST00000263967.3:c.48G>A	p.Met16Ile	p.M16I	ENST00000263967	NM_006218.2	16	atG/atA	2/21	0.613890638046337	3	FACETS	0.613	0.504	0.734	0.204	0.168	0.245	SUBCLONAL	1	TRUE	0	0.613890638046337	3		465	236	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163276	32163276	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021983-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	249	822	2	ENST00000375023.3:c.5950G>T	p.Asp1984Tyr	p.D1984Y	ENST00000375023	NM_004557.3	1984	Gac/Tac	30/30	0.613890638046337	3	FACETS	0.953	0.89	1	0.476	0.445	0.509	CLONAL	1	TRUE	1	0.613890638046337	3		824	1113	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115923	8115924	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0021983-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	157	401	0	ENST00000346208.3:c.1270_1271del	p.Pro424AlafsTer82	p.P424Afs*82	ENST00000346208		423	caCCcg/cacg	6/6	0.386680968324379	2	FACETS	0.458	0.418	0.499	0.229	0.209	0.25	SUBCLONAL	1	TRUE	0	0.613890638046337	2		401	1117	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571997	64571997	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021983-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	403	712	0	ENST00000312049.6:c.1642G>T	p.Gly548Cys	p.G548C	ENST00000312049	NM_130799.2	548	Ggt/Tgt	10/10	0.613890638046337	3	FACETS	1	0.994	1	0.645	0.613	0.677	CLONAL	1	TRUE	1	0.613890638046337	3		712	1330	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712914	43712914	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs200611664	NA	P-0021983-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	101	616	1	ENST00000382044.4:c.4270C>G	p.Pro1424Ala	p.P1424A	ENST00000382044	NM_001141980.1	1424	Ccc/Gcc	21/28	0.613890638046337	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.613890638046337	1		617	180	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47079200	47079200	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021983-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	89	659	0	ENST00000409792.3:c.7306G>C	p.Glu2436Gln	p.E2436Q	ENST00000409792	NM_014159.6	2436	Gag/Cag	18/21	0.613890638046337	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.613890638046337	1		659	173	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443695	29443695	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs863225281	NA	P-0121444-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	497	532	0	ENST00000389048.3:c.3522C>G	p.Phe1174Leu	p.F1174L	ENST00000389048	NM_004304.4	1174	ttC/ttG	23/29	0.828242217932852	4	FACETS	0.85	0.821	0.879	0.638	0.616	0.66	CLONAL	3	NA	0	0.863532904605531	4		532	841	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914127	32914127	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs55996097	NA	P-0121444-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	589	573	1	ENST00000380152.3:c.5635G>T	p.Glu1879Ter	p.E1879*	ENST00000380152		1879	Gag/Tag	11/27	0.863532904605531	4	FACETS	0.973	0.937	1	0.648	0.625	0.672	CLONAL	2	NA	1	0.863532904605531	4		574	1307	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353783	15353783	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0121444-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	52	647	0	ENST00000263377.2:c.3097C>G	p.Pro1033Ala	p.P1033A	ENST00000263377	NM_058243.2	1033	Cct/Gct	14/20	0.851588542675844	2	FACETS	0.218	0.185	0.254	0.109	0.092	0.127	SUBCLONAL	1	NA	0	0.863532904605531	2		647	553	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212689	36212689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0121444-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	53	756	2	ENST00000222270.7:c.2440G>A	p.Val814Met	p.V814M	ENST00000222270	NM_014727.1	814	Gtg/Atg	3/37	0.564126828942571	4	FACETS	0.232	0.197	0.271	0.077	0.065	0.091	SUBCLONAL	1	NA	1	0.863532904605531	4		758	986	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356816	70356816	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0121444-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	51	773	0	ENST00000374080.3:c.5488A>G	p.Thr1830Ala	p.T1830A	ENST00000374080		1830	Aca/Gca	38/45	0.852960721637295	1	FACETS	0.146	0.124	0.17	0.146	0.124	0.17	SUBCLONAL	1	NA	0	0.863532904605531	1		773	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs11575997	NA	P-0022584-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	301	652	0	ENST00000269305.4:c.993+1G>T		p.X331_splice	ENST00000269305	NM_001126112.2	331			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		652	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0023276-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	505	616	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.666442946951288	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.67083257422484	2		616	729	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961688	41961688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023276-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	205	591	5	ENST00000219905.7:c.596G>A	p.Arg199His	p.R199H	ENST00000219905	NM_001164273.1	199	cGt/cAt	2/24	1	2	FACETS	0.995	0.929	1	0.995	0.929	1	CLONAL	1	TRUE	1	0.67083257422484	2		596	614	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372103	45372103	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023276-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	409	666	6	ENST00000262160.6:c.1066T>G	p.Phe356Val	p.F356V	ENST00000262160	NM_005901.5	356	Ttt/Gtt	9/11	0.67083257422484	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.67083257422484	2		672	591	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477191	67477191	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023627-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	30	418	0	ENST00000327367.4:c.998A>C	p.Lys333Thr	p.K333T	ENST00000327367	NM_005902.3	333	aAg/aCg	7/9	0.431132011926315	3	FACETS	0.298	0.239	0.364	0.149	0.119	0.182	SUBCLONAL	1	TRUE	1	0.445994226858549	3		418	553	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170015159	170015159	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023627-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	126	525	0	ENST00000295797.4:c.1565T>C	p.Phe522Ser	p.F522S	ENST00000295797	NM_002740.5	522	tTc/tCc	16/18	0.331071344703303	4	FACETS	0.984	0.891	1	0.492	0.445	0.541	CLONAL	1	TRUE	2	0.445994226858549	4		525	830	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106543578	106543578	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023627-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	72	339	0	ENST00000369096.4:c.380C>A	p.Pro127His	p.P127H	ENST00000369096	NM_001198.3	127	cCt/cAt	3/7	0.431132011926315	3	FACETS	0.872	0.764	0.987	0.436	0.382	0.494	CLONAL	1	TRUE	1	0.445994226858549	3		339	453	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126395	5126395	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023627-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	21	371	0	ENST00000381652.3:c.3240A>C	p.Glu1080Asp	p.E1080D	ENST00000381652	NM_004972.3	1080	gaA/gaC	24/25	0.187688721055414	2	FACETS	0.288	0.221	0.366	0.144	0.11	0.183	INDETERMINATE	1	TRUE	0	0.445994226858549	2		371	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0023805-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	137	430	2	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	0.625153635707423	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.625153635707423	1		432	293	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258894	16258894	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs779191752	NA	P-0023805-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	27	578	1	ENST00000375759.3:c.6159C>A	p.Asn2053Lys	p.N2053K	ENST00000375759	NM_015001.2	2053	aaC/aaA	11/15	0.320674042762054	1	FACETS	0.11	0.087	0.137	0.11	0.087	0.137	INDETERMINATE	1	TRUE	0	0.625153635707423	1		579	538	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244971	41244971	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023805-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	69	492	1	ENST00000357654.3:c.2577T>G	p.Asn859Lys	p.N859K	ENST00000357654	NM_007294.3	859	aaT/aaG	10/23	0.223210082726705	1	FACETS	0.271	0.236	0.309	0.271	0.236	0.309	INDETERMINATE	1	TRUE	0	0.625153635707423	1		493	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577567	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1567549651	NA	P-0024181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	636	537	0	ENST00000269305.4:c.714dup	p.Asn239Ter	p.N239*	ENST00000269305	NM_001126112.2	238	-/T	7/11	0.644341093553708	2	FACETS	0.967	0.938	0.995	0.967	0.938	0.995	CLONAL	2	TRUE	0	0.644341093553708	2		537	1021	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351367	89351367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	251	718	0	ENST00000301030.4:c.1583G>A	p.Ser528Asn	p.S528N	ENST00000301030	NM_001256183.1	528	aGc/aAc	9/13	1	2	FACETS	0.779	0.729	0.83	0.779	0.729	0.83	SUBCLONAL	1	TRUE	1	0.644341093553708	2		718	1000	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404612	8404612	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	47	356	0	ENST00000356435.5:c.4135G>T	p.Val1379Leu	p.V1379L	ENST00000356435		1379	Gta/Tta	25/35	0.424453169099031	1	FACETS	0.272	0.23	0.319	0.272	0.23	0.319	SUBCLONAL	1	TRUE	0	0.644341093553708	1		356	363	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128419953	128419953	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1288547228	NA	P-0024181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	211	585	3	ENST00000265960.3:c.475G>A	p.Glu159Lys	p.E159K	ENST00000265960	NM_001006617.1	159	Gag/Aag	4/12	1	2	FACETS	0.712	0.662	0.764	0.712	0.662	0.764	SUBCLONAL	1	TRUE	1	0.644341093553708	2		588	920	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845393	76845393	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	239	334	0	ENST00000373344.5:c.6128C>T	p.Ser2043Phe	p.S2043F	ENST00000373344	NM_000489.3	2043	tCc/tTc	27/35	0.668194745037326	4	FACETS	0.929	0.874	0.985	0.929	0.874	0.985	CLONAL	2	TRUE	2	0.728989090406224	4		334	610	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911998	32911998	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1194031580	NA	P-0024224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	212	647	0	ENST00000380152.3:c.3506A>G	p.Asn1169Ser	p.N1169S	ENST00000380152		1169	aAt/aGt	11/27	1	2	FACETS	0.998	0.933	1	0.998	0.933	1	CLONAL	1	TRUE	1	0.728989090406224	2		647	583	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711879	89711879	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1554900515	NA	P-0024954-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	99	482	0	ENST00000371953.3:c.497T>A	p.Val166Glu	p.V166E	ENST00000371953	NM_000314.4	166	gTa/gAa	6/9	0.3	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.35	1		482	426	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665157	29665157	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024954-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	211	636	0	ENST00000356175.3:c.6756G>C	p.Lys2252Asn	p.K2252N	ENST00000356175	NM_000267.3	2252	aaG/aaC	44/57	0.297887503586042	2	FACETS	0.892	0.832	0.953	0.892	0.832	0.953	CLONAL	2	TRUE	0	0.35	2		636	676	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	GAAC	novel	NA	P-0025155-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	152	634	0	ENST00000275493.2:c.2239_2248delinsGAAC	p.Leu747_Ala750delinsGluPro	p.L747_A750delinsEP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/GAACca	19/28	0.495563656841998	4	FACETS	1	0.987	1	0.708	0.651	0.768	CLONAL	1	TRUE	2	0.564108133060138	4		634	595	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094880	11094880	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060502087	NA	P-0025756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	75	914	0	ENST00000358026.2:c.53C>T	p.Pro18Leu	p.P18L	ENST00000358026	NM_001128849.1	18	cCg/cTg	2/36	0.225050088814826	3	FACETS	0.857	0.75	0.973	0.429	0.375	0.487	CLONAL	1	FALSE	1	0.225050088814826	3		914	865	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0026115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	34	155	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	0.76	0.624	0.91	0.76	0.624	0.91	CLONAL	1	TRUE	1	0.363772541978753	2		155	246	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17947979	17947979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368885175	NA	P-0026115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	70	437	0	ENST00000458235.1:c.1745G>A	p.Arg582Gln	p.R582Q	ENST00000458235	NM_000215.3	582	cGg/cAg	13/24	1	2	FACETS	0.559	0.487	0.637	0.559	0.487	0.637	SUBCLONAL	1	TRUE	1	0.363772541978753	2		437	688	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628412	86628412	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	16	137	0	ENST00000274376.6:c.781T>A	p.Cys261Ser	p.C261S	ENST00000274376	NM_002890.2	261	Tgt/Agt	3/25	1	2	FACETS	0.619	0.461	0.805	0.619	0.461	0.805	SUBCLONAL	1	TRUE	1	0.363772541978753	2		137	142	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040989	47040989	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	109	194	0	ENST00000377604.3:c.1519del	p.Ile507SerfsTer197	p.I507Sfs*197	ENST00000377604	NM_001204468.1	507	Atc/tc	14/24	1	1	FACETS	0.793	0.722	0.867	1	0.986	1	SUBCLONAL	2	TRUE	0	0.363772541978753	1		194	309	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0026120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	111	505	4	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.2546775179178	3	FACETS	1	0.972	1	0.797	0.722	0.875	CLONAL	2	TRUE	0	0.2546775179178	3		509	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782177	NA	P-0026120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	165	406	0	ENST00000269305.4:c.644G>T	p.Ser215Ile	p.S215I	ENST00000269305	NM_001126112.2	215	aGt/aTt	6/11	NA	2	FACETS	1	0.961	1			1	INDETERMINATE	2	TRUE	NA	0.2546775179178	2		406	608	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690576	88690576	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	80	284	0	ENST00000360948.2:c.454C>A	p.Leu152Ile	p.L152I	ENST00000360948	NM_001012338.2	152	Ctt/Att	5/19	0.21779500265092	2	FACETS	1	0.973	1	0.686	0.606	0.771	CLONAL	1	TRUE	0	0.2546775179178	2		284	458	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983164	7983164	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	114	303	0	ENST00000319144.4:c.850C>G	p.Pro284Ala	p.P284A	ENST00000319144	NM_001139.2	284	Cca/Gca	7/15	NA	2	FACETS	0.979	0.887	1			1	INDETERMINATE	2	TRUE	NA	0.2546775179178	2		303	457	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528456	29528456	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782233	NA	P-0026120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	23	256	0	ENST00000356175.3:c.1213A>G	p.Thr405Ala	p.T405A	ENST00000356175	NM_000267.3	405	Aca/Gca	11/57	0.205253532172699	3	FACETS	0.587	0.457	0.737	0.293	0.228	0.369	SUBCLONAL	1	TRUE	1	0.2546775179178	3		256	347	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348415	56348415	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	31	118	0	ENST00000348428.3:c.223G>T	p.Glu75Ter	p.E75*	ENST00000348428	NM_006785.3	75	Gag/Tag	2/17	0.171953609068852	3	FACETS	1	0.936	1	0.693	0.565	0.835	CLONAL	1	TRUE	1	0.2546775179178	3		118	198	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213513	36213513	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	115	470	0	ENST00000222270.7:c.2615G>T	p.Cys872Phe	p.C872F	ENST00000222270	NM_014727.1	872	tGc/tTc	5/37	0.123131124052899	6	FACETS	0.801	0.721	0.885	0.4	0.36	0.443	INDETERMINATE	2	TRUE	2	0.2546775179178	6		470	851	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279758	46279758	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs753862970	NA	P-0026120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	206	282	0	ENST00000371998.3:c.3684A>T	p.Gln1228His	p.Q1228H	ENST00000371998		1228	caA/caT	20/23	0.2546775179178	5	FACETS	1	0.944	1	1	0.944	1	CLONAL	4	TRUE	1	0.2546775179178	5		282	553	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983112	111983112	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	27	215	0	ENST00000368678.4:c.1435G>T	p.Gly479Cys	p.G479C	ENST00000368678		479	Ggc/Tgc	13/13	1	2	FACETS	0.688	0.549	0.848	0.688	0.549	0.848	SUBCLONAL	1	TRUE	1	0.2546775179178	2		215	308	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426520	47426521	+	missense_variant	Missense_Mutation	DNP	AG	AG	TA	novel	NA	P-0026120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	48	335	0	ENST00000377045.4:c.863_864delinsTA	p.Lys288Ile	p.K288I	ENST00000377045	NM_001654.4	288	aAG/aTA	9/16	0.2546775179178	1	FACETS	0.818	0.693	0.955	0.818	0.693	0.955	CLONAL	1	TRUE	0	0.2546775179178	1		335	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577129	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519986	NA	P-0026121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	190	378	0	ENST00000269305.4:c.809T>G	p.Phe270Cys	p.F270C	ENST00000269305	NM_001126112.2	270	tTt/tGt	8/11	0.348816807801882	2	FACETS	0.976	0.908	1	0.976	0.908	1	CLONAL	2	TRUE	0	0.351529256129463	2		378	554	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716229	52716229	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	99	300	0	ENST00000322088.6:c.673G>T	p.Val225Leu	p.V225L	ENST00000322088	NM_014225.5	225	Gtg/Ttg	6/15	0.351529256129463	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.351529256129463	1		300	355	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967174	25967174	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	50	180	2	ENST00000435504.4:c.2032G>T	p.Ala678Ser	p.A678S	ENST00000435504		678	Gcc/Tcc	13/13	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.351529256129463	2		182	227	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542228	187542229	+	stop_gained	Nonsense_Mutation	DNP	CA	CA	AT	novel	NA	P-0026121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	36	250	0	ENST00000441802.2:c.5511_5512delinsAT	p.Tyr1837_Glu1838delinsTer	p.Y1837_E1838delins*	ENST00000441802	NM_005245.3	1837	taTGaa/taATaa	10/27	0.348816807801882	2	FACETS	0.619	0.51	0.74	0.309	0.255	0.37	SUBCLONAL	1	TRUE	0	0.351529256129463	2		250	331	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0026124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	215	562	3	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.632332490568234	4	FACETS	0.876	0.819	0.934	0.876	0.819	0.934	CLONAL	2	TRUE	2	0.662149431324307	4		565	616	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0026124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	399	477	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.662149431324307	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.662149431324307	2		478	564	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411678	63411678	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	376	210	1	ENST00000330258.3:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000330258	NM_152424.3	497	Cga/Tga	2/2	0.635750800812324	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.662149431324307	2		211	477	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508234	38508234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367821941	NA	P-0026124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	140	273	0	ENST00000254066.5:c.542C>T	p.Thr181Met	p.T181M	ENST00000254066	NM_000964.3	181	aCg/aTg	5/9	0.662149431324307	2	FACETS	0.99	0.91	1	0.495	0.455	0.537	CLONAL	1	TRUE	0	0.662149431324307	2		273	427	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982087	93982087	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1448138791	NA	P-0026124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	120	227	2	ENST00000369303.4:c.1378G>A	p.Glu460Lys	p.E460K	ENST00000369303	NM_004440.3	460	Gag/Aag	6/17	0.662149431324307	3	FACETS	1	0.956	1	0.542	0.493	0.593	CLONAL	1	TRUE	1	0.662149431324307	3		229	445	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119762	70119763	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0026124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	364	352	3	ENST00000245479.2:c.767_768dup	p.Arg257GlyfsTer23	p.R257Gfs*23	ENST00000245479	NM_000346.3	255	gag/gaGGg	3/3	0.662149431324307	2	FACETS	0.946	0.91	0.982	0.946	0.91	0.982	CLONAL	2	TRUE	0	0.662149431324307	2		355	581	SUCCESS
APC	324	MSKCC	GRCh37	5	112174411	112174411	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	127	138	0	ENST00000257430.4:c.3120G>T	p.Arg1040Ser	p.R1040S	ENST00000257430	NM_000038.5	1040	agG/agT	16/16	0.662149431324307	3	FACETS	0.997	0.923	1	0.997	0.923	1	CLONAL	2	TRUE	1	0.662149431324307	3		138	256	SUCCESS
APC	324	MSKCC	GRCh37	5	112174551	112174551	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	192	260	1	ENST00000257430.4:c.3260del	p.Leu1087ProfsTer39	p.L1087Pfs*39	ENST00000257430	NM_000038.5	1087	cTc/cc	16/16	0.662149431324307	3	FACETS	0.963	0.903	1	0.963	0.903	1	CLONAL	2	TRUE	1	0.662149431324307	3		261	401	SUCCESS
APC	324	MSKCC	GRCh37	5	112175980	112175981	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0026124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	64	147	1	ENST00000257430.4:c.4691dup	p.Leu1564PhefsTer3	p.L1564Ffs*3	ENST00000257430	NM_000038.5	1563	-/T	16/16	0.662149431324307	3	FACETS	0.916	0.8	1	0.458	0.4	0.519	CLONAL	1	TRUE	1	0.662149431324307	3		148	281	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739803	41739803	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	135	266	0	ENST00000242208.4:c.170C>G	p.Ala57Gly	p.A57G	ENST00000242208	NM_002192.2	57	gCc/gGc	2/3	0.632332490568234	4	FACETS	0.978	0.891	1	0.489	0.445	0.535	CLONAL	1	TRUE	2	0.662149431324307	4		266	693	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930216	39930234	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTTTACTTACATCTCTCAC	GTTTACTTACATCTCTCAC	-	novel	NA	P-0026124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	189	101	2	ENST00000378444.4:c.3230_3238+10del		p.X1077_splice	ENST00000378444	NM_001123385.1	1077		6/15	0.635750800812324	2	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.662149431324307	2		103	241	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026326-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	223	270	0				ENST00000310581	NM_198253.2	-/1132			0.331232567687816	2	FACETS	0.755	0.712	0.798	0.755	0.712	0.798	INDETERMINATE	2	TRUE	0	0.65213310985847	2		270	453	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0026326-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	436	477	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.65213310985847	2		477	957	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878115	48878117	+	inframe_deletion	In_Frame_Del	DEL	CCG	CCG	-	rs587778823	NA	P-0026326-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	10	42	0	ENST00000267163.4:c.78_80del	p.Pro29del	p.P29del	ENST00000267163	NM_000321.2	23	CCG/-	1/27	0.364611408114439	3	FACETS	0.241	0.163	0.338	0.12	0.081	0.169	INDETERMINATE	1	TRUE	1	0.65213310985847	3		42	169	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259262	89259262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770780950	NA	P-0026326-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	102	386	0	ENST00000336596.2:c.406C>T	p.Arg136Ter	p.R136*	ENST00000336596	NM_005233.5	136	Cga/Tga	3/17	0.315792654347846	3	FACETS	0.63	0.564	0.7	0.21	0.188	0.234	INDETERMINATE	1	TRUE	0	0.65213310985847	3		386	658	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245411	153245411	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026326-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	230	475	0	ENST00000281708.4:c.1780C>T	p.Leu594Phe	p.L594F	ENST00000281708	NM_033632.3	594	Ctt/Ttt	11/12	0.382510643086578	1	FACETS	0.788	0.74	0.837	0.788	0.74	0.837	INDETERMINATE	1	TRUE	0	0.65213310985847	1		475	603	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243979	41243979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755209182	NA	P-0026326-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	409	495	0	ENST00000357654.3:c.3569C>T	p.Pro1190Leu	p.P1190L	ENST00000357654	NM_007294.3	1190	cCt/cTt	10/23	0.364611408114439	3	FACETS	0.867	0.829	0.906	0.867	0.829	0.906	INDETERMINATE	2	TRUE	1	0.65213310985847	3		495	959	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910350	29910350	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026326-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1607	108	645	1	ENST00000376809.5:c.20G>A	p.Arg7Gln	p.R7Q	ENST00000376809	NM_002116.7	7	cGa/cAa	1/8	0.65213310985847	4	FACETS	0.319	0.285	0.356	0.106	0.095	0.119	SUBCLONAL	1	TRUE	1	0.65213310985847	4		646	1715	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014170	70014170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769488988	NA	P-0026326-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	172	474	2	ENST00000394351.3:c.1031C>T	p.Thr344Met	p.T344M	ENST00000394351	NM_000248.3	344	aCg/aTg	9/9	0.315792654347846	3	FACETS	0.599	0.55	0.651	0.2	0.183	0.217	INDETERMINATE	1	TRUE	0	0.65213310985847	3		476	1167	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444317	50444317	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026326-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	257	316	1	ENST00000331340.3:c.247C>T	p.Arg83Ter	p.R83*	ENST00000331340	NM_006060.4	83	Cga/Tga	4/8	0.315396620722908	3	FACETS	0.806	0.76	0.853	0.806	0.76	0.853	INDETERMINATE	2	TRUE	1	0.65213310985847	3		317	648	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435049	49435050	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0026326-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	233	458	1	ENST00000301067.7:c.6503_6504delinsTT	p.Pro2168Leu	p.P2168L	ENST00000301067	NM_003482.3	2168	cCC/cTT	31/54	0.442463582873519	1	FACETS	0.799	0.75	0.848	0.799	0.75	0.848	SUBCLONAL	1	TRUE	0	0.65213310985847	1		459	603	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445809	49445809	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772559303	NA	P-0026326-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	224	712	1	ENST00000301067.7:c.1657C>T	p.Pro553Ser	p.P553S	ENST00000301067	NM_003482.3	553	Cct/Tct	10/54	0.442463582873519	1	FACETS	0.449	0.417	0.481	0.449	0.417	0.481	SUBCLONAL	1	TRUE	0	0.65213310985847	1		713	1032	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123880969	123880970	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0026326-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	174	277	0	ENST00000330479.4:c.587_588delinsTT	p.Ala196Val	p.A196V	ENST00000330479	NM_020382.3	196	gCC/gTT	5/9	0.442463582873519	1	FACETS	0.825	0.768	0.883	0.825	0.768	0.883	CLONAL	1	TRUE	0	0.65213310985847	1		277	436	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28971138	28971138	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026326-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	255	319	0	ENST00000282397.4:c.1619A>G	p.Lys540Arg	p.K540R	ENST00000282397	NM_002019.4	540	aAa/aGa	12/30	0.364611408114439	3	FACETS	0.871	0.823	0.921	0.871	0.823	0.921	INDETERMINATE	2	TRUE	1	0.65213310985847	3		319	595	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40874903	40874903	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026326-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	241	516	0	ENST00000428826.2:c.397C>T	p.Pro133Ser	p.P133S	ENST00000428826		133	Ccc/Tcc	6/21	0.364611408114439	3	FACETS	1	0.961	1	0.52	0.486	0.555	INDETERMINATE	1	TRUE	1	0.65213310985847	3		516	943	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086124	16086124	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026326-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	411	465	0	ENST00000281043.3:c.1300C>T	p.Gln434Ter	p.Q434*	ENST00000281043	NM_005378.4	434	Cag/Tag	3/3	0.331232567687816	2	FACETS	1	0.996	1	0.708	0.678	0.739	INDETERMINATE	1	TRUE	0	0.65213310985847	2		465	890	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400169	41400169	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026326-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	259	407	0	ENST00000373198.4:c.590G>A	p.Arg197Gln	p.R197Q	ENST00000373198	NM_133170.3	197	cGa/cAa	5/32	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.65213310985847	2		407	779	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972936	55972936	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026326-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	167	478	0	ENST00000263923.4:c.1454G>A	p.Trp485Ter	p.W485*	ENST00000263923	NM_002253.2	485	tGg/tAg	11/30	0.382510643086578	1	FACETS	0.706	0.654	0.759	0.706	0.654	0.759	INDETERMINATE	1	TRUE	0	0.65213310985847	1		478	489	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183092	32183092	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026326-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1438	328	563	0	ENST00000375023.3:c.1932A>T	p.Lys644Asn	p.K644N	ENST00000375023	NM_004557.3	644	aaA/aaT	12/30	0.65213310985847	4	FACETS	0.941	0.886	0.998	0.314	0.295	0.333	CLONAL	1	TRUE	1	0.65213310985847	4		563	1766	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981789	70981789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs889703632	NA	P-0026326-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	147	564	0	ENST00000276594.2:c.307C>T	p.Pro103Ser	p.P103S	ENST00000276594	NM_024504.3	103	Cca/Tca	2/8	0.65213310985847	3	FACETS	0.471	0.429	0.516	0.236	0.214	0.258	SUBCLONAL	1	TRUE	1	0.65213310985847	3		564	1268	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636815	8636815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026326-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	382	398	0	ENST00000356435.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000356435		32	Gat/Aat	2/35	0.65213310985847	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.65213310985847	1		398	636	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0026599-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	46	562	3	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.702	0.59	0.826	0.702	0.59	0.826	SUBCLONAL	1	TRUE	1	0.2	2		565	655	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974695	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691187	NA	P-0026599-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	37	344	0	ENST00000304494.5:c.132del	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	taC/ta	1/3	0.155320663419228	1	FACETS	0.713	0.588	0.853	0.713	0.588	0.853	SUBCLONAL	1	TRUE	0	0.2	1		344	467	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220691	1220691	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs878853247	NA	P-0026599-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	70	575	0	ENST00000326873.7:c.709G>T	p.Asp237Tyr	p.D237Y	ENST00000326873	NM_000455.4	237	Gac/Tac	5/10	0.155320663419228	1	FACETS	0.801	0.697	0.913	0.801	0.697	0.913	CLONAL	1	TRUE	0	0.2	1		575	787	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602757	10602757	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026599-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	70	638	0	ENST00000171111.5:c.821A>G	p.His274Arg	p.H274R	ENST00000171111	NM_203500.1	274	cAc/cGc	3/6	0.155320663419228	1	FACETS	0.723	0.629	0.825	0.723	0.629	0.825	SUBCLONAL	1	TRUE	0	0.2	1		638	871	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129670	11129670	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026599-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	68	571	0	ENST00000358026.2:c.2476G>C	p.Ala826Pro	p.A826P	ENST00000358026	NM_001128849.1	826	Gcc/Ccc	17/36	0.155320663419228	1	FACETS	0.775	0.673	0.885	0.775	0.673	0.885	SUBCLONAL	1	TRUE	0	0.2	1		571	790	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935516	13935516	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026599-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	47	296	0	ENST00000405192.2:c.1340C>T	p.Pro447Leu	p.P447L	ENST00000405192	NM_001163147.1	447	cCc/cTc	12/12	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.2	2		296	455	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259123	16259123	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026657-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	60	535	0	ENST00000375759.3:c.6388G>C	p.Glu2130Gln	p.E2130Q	ENST00000375759	NM_015001.2	2130	Gag/Cag	11/15	0.437717973928223	5	FACETS	0.428	0.367	0.494	0.143	0.122	0.165	SUBCLONAL	1	TRUE	2	0.437717973928223	5		535	1062	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263811	16263811	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1263979988	NA	P-0026657-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	63	462	0	ENST00000375759.3:c.10180G>A	p.Gly3394Arg	p.G3394R	ENST00000375759	NM_015001.2	3394	Ggg/Agg	12/15	0.437717973928223	5	FACETS	0.514	0.443	0.592	0.171	0.147	0.198	SUBCLONAL	1	TRUE	2	0.437717973928223	5		462	927	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247804	59247804	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026657-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	139	572	0	ENST00000371222.2:c.939G>T	p.Met313Ile	p.M313I	ENST00000371222	NM_002228.3	313	atG/atT	1/1	0.437717973928223	3	FACETS	1	0.915	1	0.502	0.457	0.549	CLONAL	1	TRUE	1	0.437717973928223	3		572	771	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719934	18719934	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1296146485	NA	P-0026657-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	94	429	0	ENST00000266497.5:c.3831C>G	p.Phe1277Leu	p.F1277L	ENST00000266497		1277	ttC/ttG	27/31	0.234360440606443	2	FACETS	0.954	0.854	1	0.477	0.427	0.531	INDETERMINATE	1	TRUE	0	0.437717973928223	2		429	450	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039441	49039441	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026657-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	104	441	0	ENST00000267163.4:c.2426T>G	p.Leu809Arg	p.L809R	ENST00000267163	NM_000321.2	809	cTg/cGg	23/27	0.430200529595784	1	FACETS	0.89	0.803	0.982	0.89	0.803	0.982	CLONAL	1	TRUE	0	0.437717973928223	1		441	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0026657-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	227	395	0	ENST00000269305.4:c.673-1G>C		p.X225_splice	ENST00000269305	NM_001126112.2	225			1	2	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	1	0.437717973928223	2		395	452	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122730	7122730	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026657-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	142	524	0	ENST00000302850.5:c.3424G>A	p.Glu1142Lys	p.E1142K	ENST00000302850	NM_000208.2	1142	Gag/Aag	19/22	0.437717973928223	4	FACETS	1	0.964	1	0.555	0.505	0.606	CLONAL	1	TRUE	2	0.437717973928223	4		524	841	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921110	50921110	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026657-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	52	435	0	ENST00000440232.2:c.3230C>G	p.Pro1077Arg	p.P1077R	ENST00000440232	NM_002691.3	1077	cCc/cGc	27/27	0.437717973928223	3	FACETS	0.368	0.312	0.429	0.184	0.156	0.215	SUBCLONAL	1	TRUE	1	0.437717973928223	3		435	787	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190742112	190742112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026657-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	98	437	0	ENST00000441310.2:c.2749C>T	p.His917Tyr	p.H917Y	ENST00000441310	NM_000534.4	917	Cat/Tat	13/13	1	2	FACETS	0.869	0.778	0.966	0.869	0.778	0.966	CLONAL	1	TRUE	1	0.437717973928223	2		437	515	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0026657-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	90	332	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.384898918392081	3	FACETS	1	0.932	1	0.531	0.473	0.592	CLONAL	1	TRUE	1	0.437717973928223	3		332	472	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963866	2963866	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0026657-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	103	421	0	ENST00000396946.4:c.1940+1G>C		p.X647_splice	ENST00000396946	NM_032415.4	647			0.250748701610641	5	FACETS	1	0.966	1	0.397	0.355	0.441	INDETERMINATE	1	TRUE	2	0.437717973928223	5		421	655	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252059	226252059	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026843-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	146	247	0	ENST00000366813.1:c.7C>G	p.Arg3Gly	p.R3G	ENST00000366813		3	Cgt/Ggt	1/3	0.684825322639315	5	FACETS	0.854	0.792	0.917	0.854	0.792	0.917	CLONAL	3	TRUE	2	0.712106885176127	5		247	331	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572567	64572571	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGT	GGCGT	-	novel	NA	P-0026843-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	211	517	0	ENST00000312049.6:c.1285_1289del	p.Thr429CysfsTer18	p.T429Cfs*18	ENST00000312049	NM_130799.2	429	ACGCCt/t	9/10	0.695032461979069	2	FACETS	0.814	0.771	0.857	0.814	0.771	0.857	CLONAL	2	TRUE	0	0.712106885176127	2		517	364	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396711	396712	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0026843-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	176	460	0	ENST00000262320.3:c.314_315del	p.Phe105SerfsTer26	p.F105Sfs*26	ENST00000262320	NM_003502.3	105	tTC/t	2/11	0.694660103315241	2	FACETS	0.919	0.87	0.966	0.919	0.87	0.966	CLONAL	2	TRUE	0	0.712106885176127	2		460	269	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66525009	66525009	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0026843-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	154	231	0	ENST00000358598.2:c.770-2A>C		p.X257_splice	ENST00000358598	NM_212471.2	257			0.68720654215005	3	FACETS	0.997	0.952	1	0.997	0.952	1	CLONAL	3	TRUE	0	0.712106885176127	3		231	196	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0027024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	603	616	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.725627127259057	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.737973972405316	2		616	797	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022465	12022465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	301	812	1	ENST00000396373.4:c.571C>T	p.Arg191Trp	p.R191W	ENST00000396373	NM_001987.4	191	Cgg/Tgg	5/8	0.723845952887312	3	FACETS	0.978	0.921	1	0.489	0.46	0.518	CLONAL	1	TRUE	1	0.737973972405316	3		813	1142	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584585	189584585	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	221	454	0	ENST00000264731.3:c.881A>T	p.Gln294Leu	p.Q294L	ENST00000264731	NM_003722.4	294	cAg/cTg	6/14	0.737973972405316	3	FACETS	1	0.944	1	0.507	0.473	0.542	CLONAL	1	TRUE	1	0.737973972405316	3		454	809	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0027024-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	407	616	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.493114188983783	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.493114188983783	2		616	792	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022465	12022465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027024-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	160	812	1	ENST00000396373.4:c.571C>T	p.Arg191Trp	p.R191W	ENST00000396373	NM_001987.4	191	Cgg/Tgg	5/8	0.493114188983783	3	FACETS	0.751	0.688	0.818	0.376	0.344	0.409	SUBCLONAL	1	TRUE	1	0.493114188983783	3		813	1077	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584585	189584585	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027024-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	95	454	0	ENST00000264731.3:c.881A>T	p.Gln294Leu	p.Q294L	ENST00000264731	NM_003722.4	294	cAg/cTg	6/14	0.493114188983783	3	FACETS	0.883	0.788	0.983	0.441	0.394	0.492	CLONAL	1	TRUE	1	0.493114188983783	3		454	544	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0027418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	415	377	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.491464236510268	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.491464236510268	3		377	947	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579701	7579702	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0027418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	237	528	0	ENST00000269305.4:c.94_95del	p.Leu32ValfsTer10	p.L32Vfs*10	ENST00000269305	NM_001126112.2	32	CTg/g	3/11	0.491464236510268	1	FACETS	0.958	0.898	1	0.958	0.898	1	CLONAL	1	TRUE	0	0.491464236510268	1		528	759	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974773	21974777	+	frameshift_variant	Frame_Shift_Del	DEL	CGTGG	CGTGG	-	rs1554656525	NA	P-0027418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	130	188	0	ENST00000304494.5:c.50_54del	p.Ala17GlyfsTer25	p.A17Gfs*25	ENST00000304494	NM_000077.4	17	gCCACG/g	1/3	0.491464236510268	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.491464236510268	1		188	350	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0027536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	162	280	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.416445840199037	3	FACETS	1	0.985	1	0.804	0.75	0.859	CLONAL	2	TRUE	0	0.487015051603946	3		280	343	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578189	7578189	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1567551150	NA	P-0027536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	851	646	14	ENST00000269305.4:c.660T>A	p.Tyr220Ter	p.Y220*	ENST00000269305	NM_001126112.2	220	taT/taA	6/11	0.448954723641935	4	FACETS	1	0.993	1			1	CLONAL	4	TRUE	NA	0.487015051603946	4		660	1249	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056092	26056092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	147	363	2	ENST00000343677.2:c.565G>A	p.Ala189Thr	p.A189T	ENST00000343677	NM_005319.3	189	Gct/Act	1/1	0.487015051603946	6	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.487015051603946	6		365	909	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372259	55372270	+	inframe_deletion	In_Frame_Del	DEL	CACCAGCACCAG	CACCAGCACCAG	-	rs564144826	NA	P-0027536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	202	543	2	ENST00000297316.4:c.966_977del	p.Gln322_His325del	p.Q322_H325del	ENST00000297316	NM_022454.3	317	CACCAGCACCAG/-	2/2	0.487015051603946	3	FACETS	1	0.979	1	0.382	0.354	0.411	CLONAL	1	TRUE	0	0.487015051603946	3		545	900	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0027549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	111	332	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.265507992189101	3	FACETS	0.899	0.815	0.986	0.899	0.815	0.986	CLONAL	2	TRUE	1	0.376360098298817	3		332	390	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0027549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	87	437	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.376360098298817	2	FACETS	1	0.89	1	0.5	0.445	0.559	CLONAL	1	TRUE	0	0.376360098298817	2		437	462	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	68	319	0	ENST00000342988.3:c.1610A>T	p.Asp537Val	p.D537V	ENST00000342988	NM_005359.5	537	gAc/gTc	12/12	0.343372777925085	1	FACETS	0.717	0.627	0.814	0.717	0.627	0.814	SUBCLONAL	1	TRUE	0	0.376360098298817	1		319	409	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748481	162748481	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	48	275	0	ENST00000367921.3:c.2395G>A	p.Glu799Lys	p.E799K	ENST00000367921	NM_006182.2	799	Gag/Aag	17/18	1	2	FACETS	0.669	0.567	0.781	0.669	0.567	0.781	SUBCLONAL	1	TRUE	1	0.376360098298817	2		275	381	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765640	41765640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	99	534	0	ENST00000301178.4:c.2516G>A	p.Gly839Glu	p.G839E	ENST00000301178	NM_021913.4	839	gGa/gAa	20/20	1	2	FACETS	0.912	0.816	1	0.912	0.816	1	CLONAL	1	TRUE	1	0.376360098298817	2		534	577	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350068	89350068	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750887042	NA	P-0027549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	90	525	1	ENST00000301030.4:c.2882G>A	p.Arg961His	p.R961H	ENST00000301030	NM_001256183.1	961	cGc/cAc	9/13	1	2	FACETS	0.789	0.701	0.883	0.789	0.701	0.883	SUBCLONAL	1	TRUE	1	0.376360098298817	2		526	606	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268382	198268382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	81	383	1	ENST00000335508.6:c.1646G>A	p.Arg549His	p.R549H	ENST00000335508	NM_012433.2	549	cGt/cAt	12/25	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.376360098298817	2		384	374	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770612	40770612	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159847	NA	P-0027549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	54	332	0	ENST00000373198.4:c.2770G>A	p.Asp924Asn	p.D924N	ENST00000373198	NM_133170.3	924	Gac/Aac	19/32	0.265507992189101	3	FACETS	0.71	0.607	0.823	0.355	0.303	0.412	SUBCLONAL	1	TRUE	1	0.376360098298817	3		332	480	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912580	NA	P-0027619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	332	388	0	ENST00000342988.3:c.1157G>A	p.Gly386Asp	p.G386D	ENST00000342988	NM_005359.5	386	gGt/gAt	10/12	0.484638879175012	2	FACETS	0.957	0.912	1	0.957	0.912	1	CLONAL	2	TRUE	0	0.511663098332065	2		388	678	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102132	27102132	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	502	596	0	ENST00000324856.7:c.5058G>A	p.Trp1686Ter	p.W1686*	ENST00000324856	NM_006015.4	1686	tgG/tgA	19/20	0.484638879175012	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.511663098332065	2		596	978	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574262	95574263	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTTAAATTCTAGTGCAGGTTT	novel	NA	P-0027619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	77	382	0	ENST00000393063.1:c.2584_2604dup	p.Lys862_Lys868dup	p.K862_K868dup	ENST00000393063	NM_030621.3	862	-/AAACCTGCACTAGAATTTAAA	17/28	1	2	FACETS	0.44	0.386	0.498	0.44	0.386	0.498	SUBCLONAL	1	TRUE	1	0.511663098332065	2		382	684	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842471	68842471	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1131690808	NA	P-0027619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	209	518	0	ENST00000261769.5:c.531+1G>T		p.X177_splice	ENST00000261769	NM_004360.3	177			0.511663098332065	1	FACETS	0.94	0.877	1	0.94	0.877	1	CLONAL	1	TRUE	0	0.511663098332065	1		518	647	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490288	29490288	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs876659418	NA	P-0027619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	217	441	0	ENST00000356175.3:c.373C>G	p.Arg125Gly	p.R125G	ENST00000356175	NM_000267.3	125	Cgt/Ggt	4/57	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.511663098332065	2		441	809	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523719	41523719	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	258	705	0	ENST00000263253.7:c.1135A>G	p.Met379Val	p.M379V	ENST00000263253	NM_001429.3	379	Atg/Gtg	4/31	1	2	FACETS	0.821	0.767	0.875	0.821	0.767	0.875	CLONAL	1	TRUE	1	0.511663098332065	2		705	1229	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859308	151859309	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0027619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	119	300	0	ENST00000262189.6:c.11353_11354del	p.Lys3785ValfsTer10	p.K3785Vfs*10	ENST00000262189	NM_170606.2	3785	AAg/g	43/59	0.505523672833041	1	FACETS	0.807	0.734	0.883	0.807	0.734	0.883	CLONAL	1	TRUE	0	0.511663098332065	1		300	429	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941189	71941189	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	691	794	1	ENST00000298229.2:c.964G>A	p.Asp322Asn	p.D322N	ENST00000298229	NM_001567.3	322	Gac/Aac	9/28	0.868175780754277	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.868175780754277	1		795	852	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579569	7579581	+	frameshift_variant	Frame_Shift_Del	DEL	TTGCTTGGGACGG	TTGCTTGGGACGG	-	novel	NA	P-0027622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	646	649	0	ENST00000269305.4:c.106_118del	p.Pro36TrpfsTer4	p.P36Wfs*4	ENST00000269305	NM_001126112.2	36	CCGTCCCAAGCAAtg/tg	4/11	NA	2	FACETS	0.931	0.911	0.95			1	INDETERMINATE	2	TRUE	NA	0.868175780754277	2		649	799	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140837	37140837	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	500	594	0	ENST00000373509.5:c.673G>T	p.Val225Phe	p.V225F	ENST00000373509	NM_002648.3	225	Gtc/Ttc	5/6	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.868175780754277	2		594	1119	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970990	21971194	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCCCAGCTCCTCAGCCAGGTCCACGGGCAGACGGCCCCAGGCATCGCGCACGTCCAGCCGCGCCCCGGCCCGGTGCAGCACCACCAGCGTGTCCAGGAAGCCCTCCCGGGCAGCGTCGTGCACGGGTCGGGTGAGAGTGGCGGGGTCGGCGCAGTTGGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCTGC	TGGCCCAGCTCCTCAGCCAGGTCCACGGGCAGACGGCCCCAGGCATCGCGCACGTCCAGCCGCGCCCCGGCCCGGTGCAGCACCACCAGCGTGTCCAGGAAGCCCTCCCGGGCAGCGTCGTGCACGGGTCGGGTGAGAGTGGCGGGGTCGGCGCAGTTGGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCTGC	-	novel	NA	P-0027622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	421	616	0	ENST00000304494.5:c.164_368del	p.Gly55ValfsTer23	p.G55Vfs*23	ENST00000304494	NM_000077.4	55	gGCAGCGCCCGAGTGGCGGAGCTGCTGCTGCTCCACGGCGCGGAGCCCAACTGCGCCGACCCCGCCACTCTCACCCGACCCGTGCACGACGCTGCCCGGGAGGGCTTCCTGGACACGCTGGTGGTGCTGCACCGGGCCGGGGCGCGGCTGGACGTGCGCGATGCCTGGGGCCGTCTGCCCGTGGACCTGGCTGAGGAGCTGGGCCAt/gt	2/3	0.868175780754277	1	FACETS	0.987	0.958	1	0.987	0.958	1	CLONAL	1	TRUE	0	0.868175780754277	1		616	556	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	192	384	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.269369037058501	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.269369037058501	3		384	758	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033968	49033968	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	88	440	0	ENST00000267163.4:c.2105A>T	p.Gln702Leu	p.Q702L	ENST00000267163	NM_000321.2	702	cAa/cTa	20/27	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.269369037058501	2		440	646	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219359	1219360	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AT	novel	NA	P-0027684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	136	737	3	ENST00000326873.7:c.411_412delinsAT	p.Glu138Ter	p.E138*	ENST00000326873	NM_000455.4	137	caGGaa/caATaa	3/10	0.245016662935387	2	FACETS	1	0.98	1	0.637	0.58	0.698	CLONAL	1	TRUE	0	0.269369037058501	2		740	792	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602490	10602490	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	151	480	0	ENST00000171111.5:c.1088G>C	p.Ser363Thr	p.S363T	ENST00000171111	NM_203500.1	363	aGc/aCc	3/6	0.245016662935387	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	2	TRUE	0	0.269369037058501	2		480	559	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170515	11170516	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	198	724	0	ENST00000358026.2:c.4818_4819insT	p.Ser1607Ter	p.S1607*	ENST00000358026	NM_001128849.1	1606	-/T	34/36	0.245016662935387	2	FACETS	0.981	0.912	1	0.981	0.912	1	CLONAL	2	TRUE	0	0.269369037058501	2		724	749	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820994	36820994	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs145487256	NA	P-0027691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	124	798	1	ENST00000373129.3:c.383G>T	p.Arg128Leu	p.R128L	ENST00000373129	NM_032017.1	128	cGg/cTg	6/12	0.281368422381191	3	FACETS	0.537	0.485	0.592	0.179	0.161	0.198	INDETERMINATE	1	TRUE	0	0.580135762767329	3		799	1027	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023170	1023170	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	268	712	0	ENST00000358495.3:c.1085A>T	p.Asn362Ile	p.N362I	ENST00000358495	NM_134424.2	362	aAc/aTc	11/12	0.303930554682987	3	FACETS	1	0.98	1	0.553	0.518	0.588	INDETERMINATE	1	TRUE	1	0.580135762767329	3		712	1078	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865568	57865568	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	744	764	2	ENST00000228682.2:c.3045G>T	p.Glu1015Asp	p.E1015D	ENST00000228682	NM_005269.2	1015	gaG/gaT	12/12	0.580135762767329	4	FACETS	0.926	0.897	0.954	0.926	0.897	0.954	CLONAL	3	TRUE	1	0.580135762767329	4		766	1459	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28599044	28599044	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	368	701	0	ENST00000241453.7:c.2244C>A	p.Asp748Glu	p.D748E	ENST00000241453	NM_004119.2	748	gaC/gaA	18/24	0.52399760423144	2	FACETS	0.931	0.892	0.971	0.931	0.892	0.971	CLONAL	2	TRUE	0	0.580135762767329	2		701	681	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358526	67358526	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1390289135	NA	P-0027691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	166	483	0	ENST00000327367.4:c.34G>T	p.Val12Leu	p.V12L	ENST00000327367	NM_005902.3	12	Gtg/Ttg	1/9	1	2	FACETS	0.937	0.864	1	0.937	0.864	1	CLONAL	1	TRUE	1	0.580135762767329	2		483	611	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81922790	81922790	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	244	451	0	ENST00000359376.3:c.779A>T	p.Gln260Leu	p.Q260L	ENST00000359376	NM_002661.3	260	cAg/cTg	10/33	0.29168023783501	2	FACETS	0.782	0.738	0.826	0.782	0.738	0.826	INDETERMINATE	2	TRUE	0	0.580135762767329	2		451	538	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0027691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	618	792	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.580135762767329	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.580135762767329	2		792	1028	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770037	56770037	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	387	571	2	ENST00000337432.4:c.33G>T	p.Gln11His	p.Q11H	ENST00000337432	NM_058216.2	11	caG/caT	1/9	0.346411823686079	4	FACETS	1	0.982	1	1	0.982	1	INDETERMINATE	2	TRUE	2	0.580135762767329	4		573	993	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625692	1625692	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	355	879	0	ENST00000344749.5:c.382G>C	p.Gly128Arg	p.G128R	ENST00000344749	NM_001136139.2	128	Ggc/Cgc	7/19	0.580135762767329	2	FACETS	1	0.985	1	0.55	0.521	0.579	CLONAL	1	TRUE	0	0.580135762767329	2		879	1113	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170492	11170492	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	677	903	0	ENST00000358026.2:c.4795G>T	p.Glu1599Ter	p.E1599*	ENST00000358026	NM_001128849.1	1599	Gag/Tag	34/36	0.580135762767329	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.580135762767329	2		903	1115	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027101	71027102	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	444	634	0	ENST00000318789.4:c.1225dup	p.Thr409AsnfsTer52	p.T409Nfs*52	ENST00000318789	NM_032682.5	409	acc/aAcc	15/21	0.564505083276529	2	FACETS	0.98	0.943	1	0.98	0.943	1	CLONAL	2	TRUE	0	0.580135762767329	2		634	781	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201747	66201747	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs146343247	NA	P-0027691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	218	581	0	ENST00000273854.3:c.2755C>T	p.Arg919Ter	p.R919*	ENST00000273854	NM_004439.5	919	Cga/Tga	16/18	0.555055760082475	4	FACETS	1	0.932	1	0.502	0.466	0.539	CLONAL	1	TRUE	2	0.580135762767329	4		581	1183	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201786	66201786	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	404	607	0	ENST00000273854.3:c.2716G>T	p.Ala906Ser	p.A906S	ENST00000273854	NM_004439.5	906	Gct/Tct	16/18	0.555055760082475	4	FACETS	0.957	0.912	1	0.957	0.912	1	CLONAL	2	TRUE	2	0.580135762767329	4		607	1150	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549745	187549745	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	92	432	0	ENST00000441802.2:c.4496C>A	p.Pro1499Gln	p.P1499Q	ENST00000441802	NM_005245.3	1499	cCa/cAa	8/27	0.535323465470635	3	FACETS	0.506	0.449	0.567	0.169	0.149	0.189	SUBCLONAL	1	TRUE	0	0.580135762767329	3		432	809	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120476	94120476	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	237	452	0	ENST00000369303.4:c.575G>C	p.Cys192Ser	p.C192S	ENST00000369303	NM_004440.3	192	tGc/tCc	3/17	0.29168023783501	2	FACETS	0.774	0.729	0.818	0.774	0.729	0.818	INDETERMINATE	2	TRUE	0	0.580135762767329	2		452	528	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38157081	38157081	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	862	845	2	ENST00000317025.8:c.2639C>A	p.Pro880His	p.P880H	ENST00000317025	NM_023034.1	880	cCc/cAc	15/24	0.541887175825891	4	FACETS	0.908	0.882	0.934			1	CLONAL	3	TRUE	NA	0.580135762767329	4		847	1724	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129930	69129930	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	165	405	2	ENST00000288368.4:c.4684G>T	p.Ala1562Ser	p.A1562S	ENST00000288368	NM_024870.2	1562	Gct/Tct	38/40	0.317198981499794	1	FACETS	1	0.929	1	1	0.929	1	INDETERMINATE	1	TRUE	0	0.580135762767329	1		407	404	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518007	8518007	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303346936	NA	P-0027691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	61	546	3	ENST00000356435.5:c.1384C>T	p.His462Tyr	p.H462Y	ENST00000356435		462	Cat/Tat	10/35	0.52399760423144	2	FACETS	0.388	0.335	0.446	0.194	0.167	0.223	SUBCLONAL	1	TRUE	0	0.580135762767329	2		549	542	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0027742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	44	562	3	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	0.1	2		565	688	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860829	151860829	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	28	279	0	ENST00000262189.6:c.9833C>A	p.Pro3278His	p.P3278H	ENST00000262189	NM_170606.2	3278	cCt/cAt	43/59	1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	1	0.1	2		279	524	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	74	270	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.33	2		270	339	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788600	3788600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	115	494	2	ENST00000262367.5:c.4354G>A	p.Glu1452Lys	p.E1452K	ENST00000262367	NM_004380.2	1452	Gag/Aag	26/31	0.226116773403358	2	FACETS	1	0.944	1	0.534	0.481	0.589	CLONAL	1	TRUE	0	0.33	2		496	653	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652035	36652035	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	889	710	0	ENST00000244741.5:c.159del	p.Phe53LeufsTer95	p.F53Lfs*95	ENST00000244741	NM_000389.4	53	Ttt/tt	2/3	0.3	11	FACETS	1	0.979	1			1	CLONAL	8	TRUE	NA	0.33	11		710	1661	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748424	162748424	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	59	392	0	ENST00000367921.3:c.2338A>G	p.Thr780Ala	p.T780A	ENST00000367921	NM_006182.2	780	Act/Gct	17/18	0.3	7	FACETS	0.681	0.584	0.788	0.114	0.097	0.132	SUBCLONAL	1	TRUE	1	0.33	7		392	958	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954299	48954299	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0027838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	51	286	0	ENST00000267163.4:c.1422-2A>G		p.X474_splice	ENST00000267163	NM_000321.2	474			1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.33	2		286	287	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021477	42021477	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	70	572	0	ENST00000219905.7:c.3773C>A	p.Ser1258Tyr	p.S1258Y	ENST00000219905	NM_001164273.1	1258	tCc/tAc	11/24	1	2	FACETS	0.628	0.547	0.715	0.628	0.547	0.715	SUBCLONAL	1	TRUE	1	0.33	2		572	676	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786706	3786706	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	113	627	0	ENST00000262367.5:c.4505G>C	p.Trp1502Ser	p.W1502S	ENST00000262367	NM_004380.2	1502	tGg/tCg	27/31	0.226116773403358	2	FACETS	0.933	0.84	1	0.467	0.42	0.516	CLONAL	1	TRUE	0	0.33	2		627	734	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786779	3786779	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	59	415	0	ENST00000262367.5:c.4432G>A	p.Glu1478Lys	p.E1478K	ENST00000262367	NM_004380.2	1478	Gaa/Aaa	27/31	0.226116773403358	2	FACETS	0.753	0.649	0.866	0.376	0.324	0.433	SUBCLONAL	1	TRUE	0	0.33	2		415	475	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578279	7578280	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0027838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	171	606	0	ENST00000269305.4:c.569dup	p.Pro191SerfsTer18	p.P191Sfs*18	ENST00000269305	NM_001126112.2	190	cct/ccCt	6/11	0.251761407393905	3	FACETS	0.889	0.821	0.96	0.593	0.547	0.64	CLONAL	2	TRUE	0	0.33	3		606	679	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132418	11132418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753447676	NA	P-0027838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	64	717	0	ENST00000358026.2:c.2634G>A	p.Met878Ile	p.M878I	ENST00000358026	NM_001128849.1	878	atG/atA	19/36	1	2	FACETS	0.547	0.473	0.628	0.547	0.473	0.628	SUBCLONAL	1	TRUE	1	0.33	2		717	709	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627571	14627571	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	63	513	0	ENST00000254322.2:c.499G>T	p.Asp167Tyr	p.D167Y	ENST00000254322	NM_006145.1	167	Gac/Tac	2/3	1	2	FACETS	0.65	0.563	0.746	0.65	0.563	0.746	SUBCLONAL	1	TRUE	1	0.33	2		513	587	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295758	15295758	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	146	849	0	ENST00000263388.2:c.2369del	p.Pro790LeufsTer70	p.P790Lfs*70	ENST00000263388	NM_000435.2	790	cCt/ct	15/33	1	2	FACETS	0.976	0.89	1	0.976	0.89	1	CLONAL	1	TRUE	1	0.33	2		849	907	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0027930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	362	505	4	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.823048440830505	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.823048440830505	3		509	613	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100438	8100438	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs774820359	NA	P-0027930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	208	692	1	ENST00000346208.3:c.412T>A	p.Ser138Thr	p.S138T	ENST00000346208		138	Tcc/Acc	3/6	0.823048440830505	3	FACETS	0.581	0.539	0.626	0.291	0.269	0.313	SUBCLONAL	1	TRUE	1	0.823048440830505	3		693	1227	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94153299	94153299	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0027930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	254	464	1	ENST00000323929.3:c.2119A>T	p.Arg707Ter	p.R707*	ENST00000323929	NM_005591.3	707	Aga/Tga	20/20	0.823048440830505	3	FACETS	0.972	0.924	1	0.972	0.924	1	CLONAL	2	TRUE	1	0.823048440830505	3		465	448	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423603	88423603	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	210	438	0	ENST00000360948.2:c.2232C>A	p.Tyr744Ter	p.Y744*	ENST00000360948	NM_001012338.2	744	taC/taA	18/19	0.823048440830505	3	FACETS	0.954	0.889	1	0.477	0.444	0.511	CLONAL	1	TRUE	1	0.823048440830505	3		438	755	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81927370	81927370	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	646	624	0	ENST00000359376.3:c.1043G>T	p.Cys348Phe	p.C348F	ENST00000359376	NM_002661.3	348	tGc/tTc	12/33	0.823048440830505	4	FACETS	0.959	0.925	0.993	0.959	0.925	0.993	CLONAL	2	TRUE	2	0.823048440830505	4		624	1492	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221338	1221627	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTGGGAGCCTCATCCCTCTGCCCGCAGCCCCAGGGAGGCGGGGCTTTTGTGCAGAAATGTAGGGTTGGGGGTGTCAGGTGGGGGGCTATTGGCCCCGAGACCCCAGCAGGCATTGAGAGGACTGAGTGGAGAGGCCGACCTCCCCGCAGGGCCTGGTTTGCCAGGTCCCTCAGCTCCACCCTGCTTCTGGGCCCTGTTCACCCTCCGAACTCCCACCCCAGAGGGCAGTGCTGCCCTGCGCCTCCCCCAGCCCCACCCTCGGGGGCTCCCTGGCTTGCAGGGTCTGTC	AGGTGGGAGCCTCATCCCTCTGCCCGCAGCCCCAGGGAGGCGGGGCTTTTGTGCAGAAATGTAGGGTTGGGGGTGTCAGGTGGGGGGCTATTGGCCCCGAGACCCCAGCAGGCATTGAGAGGACTGAGTGGAGAGGCCGACCTCCCCGCAGGGCCTGGTTTGCCAGGTCCCTCAGCTCCACCCTGCTTCTGGGCCCTGTTCACCCTCCGAACTCCCACCCCAGAGGGCAGTGCTGCCCTGCGCCTCCCCCAGCCCCACCCTCGGGGGCTCCCTGGCTTGCAGGGTCTGTC	-	novel	NA	P-0027930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	465	510	0	ENST00000326873.7:c.862+2_862+291del		p.X288_splice	ENST00000326873	NM_000455.4	288		6/10	0.823048440830505	2	FACETS	0.922	0.896	0.946	0.922	0.896	0.946	CLONAL	2	TRUE	0	0.823048440830505	2		510	613	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2185863	2185891	+	frameshift_variant	Frame_Shift_Del	DEL	TGAAGAAATCCCGGATCTCAAGCTCGCTA	TGAAGAAATCCCGGATCTCAAGCTCGCTA	-	novel	NA	P-0027930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	451	628	0	ENST00000398665.3:c.137_165del	p.Glu46GlyfsTer7	p.E46Gfs*7	ENST00000398665	NM_032482.2	45	tgTGAAGAAATCCCGGATCTCAAGCTCGCTAtg/tgtg	3/28	0.823048440830505	2	FACETS	0.951	0.926	0.976	0.951	0.926	0.976	CLONAL	2	TRUE	0	0.823048440830505	2		628	576	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600395	10600395	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	798	728	0	ENST00000171111.5:c.1460C>G	p.Ala487Gly	p.A487G	ENST00000171111	NM_203500.1	487	gCt/gGt	4/6	0.823048440830505	2	FACETS	0.987	0.969	1	0.987	0.969	1	CLONAL	2	TRUE	0	0.823048440830505	2		728	982	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306776	41306776	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	147	303	0	ENST00000373198.4:c.883C>A	p.Pro295Thr	p.P295T	ENST00000373198	NM_133170.3	295	Cca/Aca	7/32	0.823048440830505	3	FACETS	0.896	0.822	0.972	0.448	0.411	0.486	CLONAL	1	TRUE	1	0.823048440830505	3		303	563	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231763	66231763	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	94	340	0	ENST00000273854.3:c.1937G>T	p.Gly646Val	p.G646V	ENST00000273854	NM_004439.5	646	gGa/gTa	11/18	0.823048440830505	3	FACETS	0.827	0.741	0.917	0.413	0.37	0.459	CLONAL	1	TRUE	1	0.823048440830505	3		340	390	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279390	38279390	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	342	628	0	ENST00000425967.3:c.1099G>C	p.Ala367Pro	p.A367P	ENST00000425967	NM_001174067.1	367	Gca/Cca	9/19	0.433319467490902	3	FACETS	1	0.991	1	0.598	0.568	0.63	INDETERMINATE	1	TRUE	1	0.823048440830505	3		628	980	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69039645	69039645	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	275	374	0	ENST00000288368.4:c.3757G>T	p.Glu1253Ter	p.E1253*	ENST00000288368	NM_024870.2	1253	Gaa/Taa	31/40	0.487154764603374	4	FACETS	0.857	0.817	0.896	0.857	0.817	0.896	INDETERMINATE	3	TRUE	1	0.823048440830505	4		374	474	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319833	8319833	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	126	280	0	ENST00000356435.5:c.5668G>T	p.Glu1890Ter	p.E1890*	ENST00000356435		1890	Gag/Tag	34/35	0.823048440830505	3	FACETS	0.94	0.857	1	0.47	0.428	0.513	CLONAL	1	TRUE	1	0.823048440830505	3		280	460	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787713	135787713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	475	504	0	ENST00000298552.3:c.869C>T	p.Ala290Val	p.A290V	ENST00000298552	NM_001162426.1	290	gCc/gTc	9/23	0.823048440830505	3	FACETS	0.949	0.915	0.984	0.949	0.915	0.984	CLONAL	2	TRUE	1	0.823048440830505	3		504	858	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185069	123185069	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	204	493	0	ENST00000218089.9:c.1116G>T	p.Lys372Asn	p.K372N	ENST00000218089	NM_001042749.1	372	aaG/aaT	12/35	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.823048440830505	2		493	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0027944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	225	727	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.352341635665968	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	3	TRUE	0	0.352341635665968	3		727	497	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017552	112017552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373817482	NA	P-0027944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	56	507	1	ENST00000368678.4:c.961G>A	p.Asp321Asn	p.D321N	ENST00000368678		321	Gac/Aac	9/13	0.352341635665968	4	FACETS	0.917	0.787	1	0.306	0.262	0.353	CLONAL	1	TRUE	1	0.352341635665968	4		508	469	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971142	21971142	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	69	442	1	ENST00000304494.5:c.216C>A	p.Cys72Ter	p.C72*	ENST00000304494	NM_000077.4	72	tgC/tgA	2/3	0.352341635665968	2	FACETS	1	0.965	1	0.644	0.566	0.727	CLONAL	1	TRUE	0	0.352341635665968	2		443	304	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176085770	176085770	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	127	492	1	ENST00000367669.3:c.1016G>A	p.Gly339Asp	p.G339D	ENST00000367669	NM_022457.5	339	gGc/gAc	9/20	0.352341635665968	6	FACETS	1	0.965	1	0.749	0.681	0.819	CLONAL	2	TRUE	3	0.352341635665968	6		493	547	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719971	18719971	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	106	481	0	ENST00000266497.5:c.3868G>C	p.Val1290Leu	p.V1290L	ENST00000266497		1290	Gta/Cta	27/31	0.352341635665968	6	FACETS	1	0.932	1	0.522	0.47	0.577	CLONAL	2	TRUE	2	0.352341635665968	6		481	491	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9928076	9928076	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	72	417	0	ENST00000330684.3:c.1663G>T	p.Ala555Ser	p.A555S	ENST00000330684	NM_001134407.1	555	Gcc/Tcc	8/13	0.250443739662492	4	FACETS	0.883	0.778	0.994			1	CLONAL	2	TRUE	NA	0.352341635665968	4		417	313	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993684	72993684	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	68	532	2	ENST00000268489.5:c.361del	p.Asp121ThrfsTer27	p.D121Tfs*27	ENST00000268489	NM_006885.3	121	Gac/ac	2/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.352341635665968	2		534	315	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541547	29541547	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	53	659	0	ENST00000356175.3:c.1471T>C	p.Tyr491His	p.Y491H	ENST00000356175	NM_000267.3	491	Tat/Cat	13/57	0.327036924616817	2	FACETS	0.88	0.754	1	0.44	0.377	0.508	CLONAL	1	TRUE	0	0.352341635665968	2		659	342	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775209	73775209	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	129	568	0	ENST00000254810.4:c.47C>A	p.Ala16Asp	p.A16D	ENST00000254810	NM_005324.3	16	gCc/gAc	2/4	0.352341635665968	5	FACETS	0.953	0.868	1			1	CLONAL	2	TRUE	NA	0.352341635665968	5		568	587	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17389834	17389834	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	66	823	0	ENST00000359435.4:c.967A>T	p.Ile323Phe	p.I323F	ENST00000359435	NM_001033549.1	323	Att/Ttt	9/9	0.352341635665968	5	FACETS	0.716	0.62	0.82	0.239	0.206	0.274	SUBCLONAL	1	TRUE	2	0.352341635665968	5		823	800	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523701	176523701	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	60	687	2	ENST00000292408.4:c.2112G>T	p.Glu704Asp	p.E704D	ENST00000292408	NM_213647.1	704	gaG/gaT	16/18	0.352341635665968	3	FACETS	0.784	0.676	0.901	0.392	0.338	0.451	CLONAL	1	TRUE	1	0.352341635665968	3		689	511	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225783	26225783	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	120	418	0	ENST00000360408.1:c.401A>T	p.Glu134Val	p.E134V	ENST00000360408	NM_003532.2	134	gAg/gTg	1/1	0.352341635665968	6	FACETS	0.847	0.77	0.927			1	CLONAL	3	TRUE	NA	0.352341635665968	6		418	457	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346570	81346571	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0027944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	39	375	1	ENST00000222390.5:c.1382_1383delinsAT	p.Trp461Tyr	p.W461Y	ENST00000222390	NM_000601.4	461	tGG/tAT	11/18	1	2	FACETS	0.731	0.608	0.866	0.731	0.608	0.866	SUBCLONAL	1	TRUE	1	0.352341635665968	2		376	303	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636251	87636251	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	136	522	0	ENST00000277120.3:c.2416T>A	p.Trp806Arg	p.W806R	ENST00000277120		806	Tgg/Agg	19/19	0.352341635665968	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.352341635665968	2		522	346	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028816	47028816	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	152	759	0	ENST00000377604.3:c.120C>A	p.Asp40Glu	p.D40E	ENST00000377604	NM_001204468.1	40	gaC/gaA	3/24	0.250443739662492	4	FACETS	0.898	0.823	0.974			1	CLONAL	2	TRUE	NA	0.352341635665968	4		759	650	SUCCESS
AR	367	MSKCC	GRCh37	X	66765686	66765686	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	86	934	1	ENST00000374690.3:c.698C>A	p.Ser233Tyr	p.S233Y	ENST00000374690	NM_000044.3	233	tCt/tAt	1/8	0.250443739662492	4	FACETS	0.887	0.785	0.997			1	CLONAL	1	TRUE	NA	0.352341635665968	4		935	744	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210181	123210181	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0027944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	134	549	0	ENST00000218089.9:c.2534-1G>A		p.X845_splice	ENST00000218089	NM_001042749.1	845			NA	2	FACETS	1	0.962	1			1	INDETERMINATE	2	TRUE	NA	0.352341635665968	2		549	353	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425208	49425209	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	G	novel	NA	P-0027944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	498	862	0	ENST00000301067.7:c.13279_13280delinsC	p.Gly4427GlnfsTer5	p.G4427Qfs*5	ENST00000301067	NM_003482.3	4427	GGa/Ca	39/54	0.352341635665968	9	FACETS	0.966	0.93	1			1	CLONAL	7	TRUE	NA	0.352341635665968	9		862	934	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0027957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	127	242	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.507176624347113	3	FACETS	0.966	0.877	1	0.322	0.292	0.353	CLONAL	1	FALSE	0	0.507176624347113	3		242	650	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577595	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0027957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	702	605	1	ENST00000269305.4:c.686_687del	p.Cys229TyrfsTer10	p.C229Yfs*10	ENST00000269305	NM_001126112.2	229	tGT/t	7/11	0.507176624347113	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	4	FALSE	0	0.507176624347113	4		606	1041	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650599	18650599	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	164	489	0	ENST00000266497.5:c.2810A>C	p.Gln937Pro	p.Q937P	ENST00000266497		937	cAa/cCa	20/31	0.823338198302045	7	FACETS	1	0.925	1	0.202	0.185	0.22	CLONAL	1	TRUE	2	0.823338198302045	7		489	1206	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678354	88678354	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs765400907	NA	P-0027993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	231	687	0	ENST00000360948.2:c.1182C>G	p.His394Gln	p.H394Q	ENST00000360948	NM_001012338.2	394	caC/caG	9/19	0.823338198302045	3	FACETS	0.694	0.647	0.744	0.231	0.215	0.248	SUBCLONAL	1	TRUE	0	0.823338198302045	3		687	1141	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577514	7577515	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	699	552	1	ENST00000269305.4:c.766dup	p.Thr256AsnfsTer8	p.T256Nfs*8	ENST00000269305	NM_001126112.2	256	aca/aAca	7/11	0.369614006804705	4	FACETS	0.999	0.984	1			1	INDETERMINATE	4	TRUE	NA	0.823338198302045	4		553	775	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753692	42753693	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CACTACAGTCACTGACTGAGCCTCG	novel	NA	P-0027993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	526	789	0	ENST00000222329.4:c.547_571dup	p.Asp191AlafsTer6	p.D191Afs*6	ENST00000222329	NM_006494.2	191	gat/gCGAGGCTCAGTCAGTGACTGTAGTGat	4/4	0.823338198302045	4	FACETS	0.907	0.871	0.944	0.605	0.581	0.629	CLONAL	2	TRUE	1	0.823338198302045	4		789	1284	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523657	41523657	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	249	725	0	ENST00000263253.7:c.1073A>G	p.Asn358Ser	p.N358S	ENST00000263253	NM_001429.3	358	aAt/aGt	4/31	1	2	FACETS	0.966	0.91	1	0.966	0.91	1	CLONAL	1	TRUE	1	0.823338198302045	2		725	626	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595534	55595534	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	121	416	0	ENST00000288135.5:c.2024A>T	p.Tyr675Phe	p.Y675F	ENST00000288135	NM_000222.2	675	tAt/tTt	14/21	0.823338198302045	3	FACETS	0.967	0.881	1	0.484	0.44	0.529	CLONAL	1	TRUE	1	0.823338198302045	3		416	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578258	7578259	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0028007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	41	654	1	ENST00000269305.4:c.590dup	p.Glu198GlyfsTer11	p.E198Gfs*11	ENST00000269305	NM_001126112.2	197	gtg/gtTg	6/11	1	2	FACETS	0.946	0.787	1	0.946	0.787	1	CLONAL	1	TRUE	1	0.14	2		655	619	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410675	63410675	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	23	405	0	ENST00000330258.3:c.2492A>T	p.Asp831Val	p.D831V	ENST00000330258	NM_152424.3	831	gAt/gTt	2/2	1	1	FACETS	0.918	0.716	1	0.918	0.716	1	CLONAL	1	TRUE	0	0.14	1		405	333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577541	7577541	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201762	NA	P-0028017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	430	532	1	ENST00000269305.4:c.740A>T	p.Asn247Ile	p.N247I	ENST00000269305	NM_001126112.2	247	aAc/aTc	7/11	0.861805988442282	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.861805988442282	1		533	554	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489817	2489817	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	449	616	5	ENST00000355716.4:c.214G>T	p.Gly72Cys	p.G72C	ENST00000355716	NM_003820.2	72	Ggc/Tgc	3/8	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.861805988442282	2		621	941	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916850	48916850	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs1131690843	NA	P-0028017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	249	323	1	ENST00000267163.4:c.380G>C	p.Ser127Thr	p.S127T	ENST00000267163	NM_000321.2	127	aGt/aCt	3/27	0.861805988442282	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.861805988442282	1		324	305	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675064	40675064	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	490	643	3	ENST00000249776.8:c.28G>T	p.Asp10Tyr	p.D10Y	ENST00000249776	NM_033286.3	10	Gac/Tac	1/9	0.861805988442282	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.861805988442282	1		646	639	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593423	215593423	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	135	252	0	ENST00000260947.4:c.2311G>T	p.Glu771Ter	p.E771*	ENST00000260947	NM_000465.2	771	Gag/Tag	11/11	1	2	FACETS	0.847	0.779	0.916	0.847	0.779	0.916	CLONAL	1	TRUE	1	0.861805988442282	2		252	370	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27213483	27213483	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	244	402	1	ENST00000380036.4:c.2879T>A	p.Phe960Tyr	p.F960Y	ENST00000380036	NM_000459.3	960	tTt/tAt	18/23	1	2	FACETS	0.961	0.906	1	0.961	0.906	1	CLONAL	1	TRUE	1	0.861805988442282	2		403	589	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845348	76845348	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	357	379	0	ENST00000373344.5:c.6173G>T	p.Ser2058Ile	p.S2058I	ENST00000373344	NM_000489.3	2058	aGt/aTt	27/35	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.861805988442282	2		379	743	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937643	76937643	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	249	365	2	ENST00000373344.5:c.3105T>G	p.Ile1035Met	p.I1035M	ENST00000373344	NM_000489.3	1035	atT/atG	9/35	1	2	FACETS	0.917	0.864	0.971	0.917	0.864	0.971	CLONAL	1	TRUE	1	0.861805988442282	2		367	630	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819655	81819655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	112	652	1	ENST00000359376.3:c.61G>A	p.Ala21Thr	p.A21T	ENST00000359376	NM_002661.3	21	Gcc/Acc	2/33	1	2	FACETS	0.839	0.754	0.929	0.839	0.754	0.929	CLONAL	1	TRUE	1	0.313486612136359	2		653	852	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442069	52442069	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	118	551	0	ENST00000460680.1:c.280C>G	p.His94Asp	p.H94D	ENST00000460680	NM_004656.3	94	Cat/Gat	5/17	0.313486612136359	1	FACETS	0.887	0.801	0.977	0.887	0.801	0.977	CLONAL	1	TRUE	0	0.313486612136359	1		551	716	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165690	47165690	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0028115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	78	443	0	ENST00000409792.3:c.436A>T	p.Lys146Ter	p.K146*	ENST00000409792	NM_014159.6	146	Aaa/Taa	3/21	0.313486612136359	1	FACETS	0.744	0.655	0.84	0.744	0.655	0.84	SUBCLONAL	1	TRUE	0	0.313486612136359	1		443	564	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52621392	52621392	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0028115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	114	515	0	ENST00000394830.3:c.3025A>T	p.Lys1009Ter	p.K1009*	ENST00000394830	NM_018313.4	1009	Aag/Tag	20/30	0.313486612136359	1	FACETS	0.749	0.674	0.828	0.749	0.674	0.828	SUBCLONAL	1	TRUE	0	0.313486612136359	1		515	819	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0028197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	579	712	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	1	2	FACETS	0.967	0.931	1	0.967	0.931	1	CLONAL	1	TRUE	1	0.93	2		712	1288	SUCCESS
AR	367	MSKCC	GRCh37	X	66942741	66942741	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs9332969	NA	P-0028197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	331	641	1	ENST00000374690.3:c.2522G>A	p.Arg841His	p.R841H	ENST00000374690	NM_000044.3	841	cGt/cAt	7/8	1	2	FACETS	0.729	0.69	0.768	0.729	0.69	0.768	SUBCLONAL	1	TRUE	1	0.93	2		642	977	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980397	1980397	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	665	1037	1	ENST00000382891.5:c.3859G>T	p.Val1287Leu	p.V1287L	ENST00000382891	NM_133335.3	1287	Gtg/Ttg	22/22	1	2	FACETS	0.901	0.869	0.933	0.901	0.869	0.933	CLONAL	1	TRUE	1	0.93	2		1038	1587	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	74	486	0	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	0.339717149024767	2		486	361	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781146	161781146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531247345	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	128	602	0	ENST00000366898.1:c.1259G>A	p.Arg420His	p.R420H	ENST00000366898	NM_004562.2	420	cGc/cAc	11/12	0.333105427876071	2	FACETS	0.959	0.869	1	0.479	0.434	0.527	CLONAL	1	TRUE	0	0.339717149024767	2		602	786	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398279	25398279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894365	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	47	507	0	ENST00000311936.3:c.40G>A	p.Val14Ile	p.V14I	ENST00000311936	NM_004985.3	14	Gta/Ata	2/5	1	2	FACETS	0.775	0.656	0.905	0.775	0.656	0.905	CLONAL	1	TRUE	1	0.339717149024767	2		507	357	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	93	834	1	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	0.134164891952205	4	FACETS	0.594	0.526	0.667	0.198	0.175	0.223	INDETERMINATE	1	TRUE	1	0.339717149024767	4		835	1235	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	47	459	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.773	0.654	0.903	0.773	0.654	0.903	CLONAL	1	TRUE	1	0.339717149024767	2		459	358	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120013	70120013	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	32	137	0	ENST00000245479.2:c.1015C>T	p.Gln339Ter	p.Q339*	ENST00000245479	NM_000346.3	339	Cag/Tag	3/3	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.339717149024767	2		137	164	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247947	10247947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	59	533	0	ENST00000340748.4:c.4255G>A	p.Ala1419Thr	p.A1419T	ENST00000340748		1419	Gca/Aca	36/40	1	2	FACETS	0.509	0.437	0.588	0.509	0.437	0.588	SUBCLONAL	1	TRUE	1	0.339717149024767	2		533	682	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372092	55372093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	99	433	0	ENST00000297316.4:c.788dup	p.Glu264GlyfsTer101	p.E264Gfs*101	ENST00000297316	NM_022454.3	261	ggc/ggCc	2/2	0.291595568936391	3	FACETS	1	0.931	1	0.528	0.471	0.587	CLONAL	1	TRUE	1	0.339717149024767	3		433	646	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237692	133237692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753759783	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	146	624	2	ENST00000320574.5:c.2923C>T	p.Arg975Cys	p.R975C	ENST00000320574	NM_006231.2	975	Cgc/Tgc	25/49	1	2	FACETS	0.977	0.891	1	0.977	0.891	1	CLONAL	1	TRUE	1	0.339717149024767	2		626	880	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235390	235390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878854625	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	147	622	0	ENST00000264932.6:c.1196C>T	p.Pro399Leu	p.P399L	ENST00000264932	NM_004168.2	399	cCg/cTg	9/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.339717149024767	2		622	778	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32814930	32814930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1458831913	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	73	719	1	ENST00000354258.4:c.2135C>T	p.Ala712Val	p.A712V	ENST00000354258	NM_000593.5	712	gCg/gTg	10/11	0.333105427876071	2	FACETS	0.422	0.368	0.481	0.211	0.184	0.241	SUBCLONAL	1	TRUE	0	0.339717149024767	2		720	1018	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713727	30713727	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs869025537	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	99	452	0	ENST00000295754.5:c.1052G>A	p.Gly351Asp	p.G351D	ENST00000295754	NM_003242.5	351	gGc/gAc	4/7	1	2	FACETS	0.988	0.884	1	0.988	0.884	1	CLONAL	1	TRUE	1	0.339717149024767	2		452	590	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427983	49427983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866777837	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	132	663	0	ENST00000301067.7:c.10607G>A	p.Arg3536His	p.R3536H	ENST00000301067	NM_003482.3	3536	cGc/cAc	38/54	1	2	FACETS	0.935	0.849	1	0.935	0.849	1	CLONAL	1	TRUE	1	0.339717149024767	2		663	831	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972955	68972955	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141759315	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	121	521	1	ENST00000288368.4:c.1280G>A	p.Arg427Lys	p.R427K	ENST00000288368	NM_024870.2	427	aGg/aAg	11/40	0.291595568936391	3	FACETS	0.806	0.732	0.884	0.806	0.732	0.884	CLONAL	2	TRUE	1	0.339717149024767	3		522	517	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045854	180045854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1400281005	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	142	616	0	ENST00000261937.6:c.2917C>T	p.Arg973Trp	p.R973W	ENST00000261937	NM_182925.4	973	Cgg/Tgg	21/30	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.339717149024767	2		616	747	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515612	31515613	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	42	490	0	ENST00000344624.3:c.1006dup	p.Glu336GlyfsTer4	p.E336Gfs*4	ENST00000344624		336	gag/gGag	4/33	1	2	FACETS	0.488	0.407	0.578	0.488	0.407	0.578	SUBCLONAL	1	TRUE	1	0.339717149024767	2		490	507	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426444	47426444	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1439786171	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	174	398	0	ENST00000377045.4:c.787G>A	p.Val263Met	p.V263M	ENST00000377045	NM_001654.4	263	Gtg/Atg	9/16	1	1	FACETS	0.847	0.786	0.909	1	0.992	1	CLONAL	2	TRUE	0	0.339717149024767	1		398	502	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216188	36216188	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	154	672	0	ENST00000222270.7:c.3596G>C	p.Gly1199Ala	p.G1199A	ENST00000222270	NM_014727.1	1199	gGc/gCc	11/37	0.134164891952205	4	FACETS	1	0.975	1	0.392	0.358	0.428	INDETERMINATE	1	TRUE	1	0.339717149024767	4		672	1033	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023715	27023716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	81	392	0	ENST00000324856.7:c.827dup	p.Gly277ArgfsTer123	p.G277Rfs*123	ENST00000324856	NM_006015.4	274	atg/atGg	1/20	1	2	FACETS	0.914	0.807	1	0.914	0.807	1	CLONAL	1	TRUE	1	0.339717149024767	2		392	522	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466284	120466284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	80	455	0	ENST00000256646.2:c.4835G>A	p.Gly1612Asp	p.G1612D	ENST00000256646	NM_024408.3	1612	gGt/gAt	26/34	1	2	FACETS	0.823	0.726	0.928	0.823	0.726	0.928	CLONAL	1	TRUE	1	0.339717149024767	2		455	572	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667470	241667470	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	50	341	0	ENST00000366560.3:c.980C>A	p.Ala327Asp	p.A327D	ENST00000366560	NM_000143.3	327	gCc/gAc	7/10	1	2	FACETS	0.716	0.609	0.833	0.716	0.609	0.833	SUBCLONAL	1	TRUE	1	0.339717149024767	2		341	411	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948713	71948713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779810240	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	146	713	0	ENST00000298229.2:c.3425G>A	p.Arg1142His	p.R1142H	ENST00000298229	NM_001567.3	1142	cGc/cAc	26/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.339717149024767	2		713	718	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204804	94204804	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	32	518	0	ENST00000323929.3:c.781T>G	p.Phe261Val	p.F261V	ENST00000323929	NM_005591.3	261	Ttt/Gtt	8/20	1	2	FACETS	0.508	0.412	0.615	0.508	0.412	0.615	SUBCLONAL	1	TRUE	1	0.339717149024767	2		518	371	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111959690	111959690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200255724	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	89	355	2	ENST00000375549.3:c.269C>T	p.Ala90Val	p.A90V	ENST00000375549	NM_003002.3	90	gCg/gTg	3/4	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.339717149024767	2		357	491	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641538	18641538	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	45	447	0	ENST00000266497.5:c.2537A>C	p.Lys846Thr	p.K846T	ENST00000266497		846	aAg/aCg	17/31	0.339717149024767	1	FACETS	0.707	0.597	0.828	0.707	0.597	0.828	SUBCLONAL	1	TRUE	0	0.339717149024767	1		447	311	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437409	121437409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853239	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	166	703	1	ENST00000257555.6:c.1747C>T	p.Arg583Trp	p.R583W	ENST00000257555		583	Cgg/Tgg	9/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.339717149024767	2		704	730	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781225	3781225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	196	827	0	ENST00000262367.5:c.5140G>A	p.Val1714Met	p.V1714M	ENST00000262367	NM_004380.2	1714	Gtg/Atg	30/31	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.339717149024767	2		827	1113	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943819	9943819	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	89	382	0	ENST00000330684.3:c.1123-1G>A		p.X375_splice	ENST00000330684	NM_001134407.1	375			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.339717149024767	2		382	461	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984594	72984594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	200	703	2	ENST00000268489.5:c.2990C>T	p.Ala997Val	p.A997V	ENST00000268489	NM_006885.3	997	gCc/gTc	3/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.339717149024767	2		705	1007	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40456448	40456448	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	58	778	1	ENST00000345506.4:c.1257+1G>A		p.X419_splice	ENST00000345506	NM_003152.3	419			1	2	FACETS	0.379	0.324	0.438	0.379	0.324	0.438	SUBCLONAL	1	TRUE	1	0.339717149024767	2		779	902	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55693419	55693419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759162213	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	145	673	1	ENST00000284073.2:c.626C>T	p.Ala209Val	p.A209V	ENST00000284073	NM_138962.2	209	gCg/gTg	9/14	1	2	FACETS	0.875	0.797	0.956	0.875	0.797	0.956	CLONAL	1	TRUE	1	0.339717149024767	2		674	976	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581303	48581303	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs199809905	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	136	516	0	ENST00000342988.3:c.607C>A	p.Pro203Thr	p.P203T	ENST00000342988	NM_005359.5	203	Cca/Aca	5/12	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.339717149024767	2		516	780	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217051	2217051	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	170	756	0	ENST00000398665.3:c.2509del	p.Ala837ProfsTer14	p.A837Pfs*14	ENST00000398665	NM_032482.2	836	Ggg/gg	21/28	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.339717149024767	2		756	886	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953881	17953881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767865565	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	86	739	1	ENST00000458235.1:c.521C>T	p.Ala174Val	p.A174V	ENST00000458235	NM_000215.3	174	gCg/gTg	5/24	1	2	FACETS	0.471	0.415	0.531	0.471	0.415	0.531	SUBCLONAL	1	TRUE	1	0.339717149024767	2		740	1075	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965946	18965946	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	145	700	0	ENST00000262803.5:c.1439A>C	p.Lys480Thr	p.K480T	ENST00000262803	NM_002911.3	480	aAg/aCg	11/24	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.339717149024767	2		700	842	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256638	19256638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	73	600	1	ENST00000162023.5:c.1075C>T	p.Arg359Trp	p.R359W	ENST00000162023		359	Cgg/Tgg	13/13	1	2	FACETS	0.579	0.506	0.658	0.579	0.506	0.658	SUBCLONAL	1	TRUE	1	0.339717149024767	2		601	742	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753594	42753594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1320701373	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	172	791	0	ENST00000222329.4:c.670C>T	p.Arg224Cys	p.R224C	ENST00000222329	NM_006494.2	224	Cgc/Tgc	4/4	0.134164891952205	4	FACETS	1	0.971	1	0.374	0.343	0.406	INDETERMINATE	1	TRUE	1	0.339717149024767	4		791	1210	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025775	48025776	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	32	260	0	ENST00000234420.5:c.655_656del	p.Ser219Ter	p.S219*	ENST00000234420	NM_000179.2	218	aAG/a	4/10	0.339717149024767	1	FACETS	0.81	0.664	0.972	0.81	0.664	0.972	CLONAL	1	TRUE	0	0.339717149024767	1		260	193	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22153344	22153344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	75	473	0	ENST00000215832.6:c.566C>T	p.Ala189Val	p.A189V	ENST00000215832	NM_002745.4	189	gCc/gTc	4/9	1	2	FACETS	0.721	0.632	0.817	0.721	0.632	0.817	SUBCLONAL	1	TRUE	1	0.339717149024767	2		473	612	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12653516	12653516	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	142	592	0	ENST00000251849.4:c.253G>T	p.Ala85Ser	p.A85S	ENST00000251849	NM_002880.3	85	Gca/Tca	3/17	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.339717149024767	2		592	808	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441235	52441235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910211860	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	101	522	0	ENST00000460680.1:c.535C>T	p.Arg179Trp	p.R179W	ENST00000460680	NM_004656.3	179	Cgg/Tgg	7/17	1	2	FACETS	0.854	0.764	0.95	0.854	0.764	0.95	CLONAL	1	TRUE	1	0.339717149024767	2		522	696	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268325	142268325	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	14	352	0	ENST00000350721.4:c.3167T>C	p.Leu1056Pro	p.L1056P	ENST00000350721	NM_001184.3	1056	cTg/cCg	15/47	1	2	FACETS	0.336	0.243	0.45	0.336	0.243	0.45	SUBCLONAL	1	TRUE	1	0.339717149024767	2		352	245	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917494	178917494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	29	339	0	ENST00000263967.3:c.369G>A	p.Met123Ile	p.M123I	ENST00000263967	NM_006218.2	123	atG/atA	3/21	1	2	FACETS	0.79	0.638	0.961	0.79	0.638	0.961	CLONAL	1	TRUE	1	0.339717149024767	2		339	216	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361127	66361127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1400810776	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	43	368	0	ENST00000273854.3:c.1045C>T	p.Pro349Ser	p.P349S	ENST00000273854	NM_004439.5	349	Cca/Tca	4/18	1	2	FACETS	0.641	0.537	0.755	0.641	0.537	0.755	SUBCLONAL	1	TRUE	1	0.339717149024767	2		368	395	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542567	187542567	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	76	573	0	ENST00000441802.2:c.5173C>A	p.Leu1725Met	p.L1725M	ENST00000441802	NM_005245.3	1725	Ctg/Atg	10/27	1	2	FACETS	0.946	0.832	1	0.946	0.832	1	CLONAL	1	TRUE	1	0.339717149024767	2		573	473	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38968099	38968099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	45	500	0	ENST00000357387.3:c.1006C>T	p.Arg336Cys	p.R336C	ENST00000357387	NM_152756.3	336	Cgt/Tgt	12/38	0.339717149024767	1	FACETS	0.57	0.48	0.669	0.57	0.48	0.669	SUBCLONAL	1	TRUE	0	0.339717149024767	1		500	386	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671772	30671772	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1237536606	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	81	695	0	ENST00000376406.3:c.5188C>A	p.Pro1730Thr	p.P1730T	ENST00000376406	NM_014641.2	1730	Cct/Act	10/15	0.333105427876071	2	FACETS	0.562	0.494	0.635	0.281	0.247	0.318	SUBCLONAL	1	TRUE	0	0.339717149024767	2		695	848	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948260	31948260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs534517982	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	333	710	0	ENST00000375333.2:c.848G>A	p.Arg283Gln	p.R283Q	ENST00000375333	NM_032454.1	283	cGa/cAa	6/8	0.333105427876071	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.339717149024767	2		710	927	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815347	32815347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	341	775	2	ENST00000354258.4:c.2026G>A	p.Ala676Thr	p.A676T	ENST00000354258	NM_000593.5	676	Gca/Aca	9/11	0.333105427876071	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.339717149024767	2		777	953	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554937	106554937	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs565965311	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	137	526	0	ENST00000369096.4:c.2054G>A	p.Arg685Gln	p.R685Q	ENST00000369096	NM_001198.3	685	cGg/cAg	7/7	0.333105427876071	2	FACETS	1	0.971	1	0.575	0.524	0.629	CLONAL	1	TRUE	0	0.339717149024767	2		526	701	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196092	138196092	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200740561	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	186	366	0	ENST00000237289.4:c.406C>T	p.Arg136Cys	p.R136C	ENST00000237289	NM_001270507.1	136	Cgc/Tgc	3/9	0.333105427876071	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.339717149024767	2		366	532	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129240	152129240	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1172047540	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	88	733	1	ENST00000206249.3:c.193G>A	p.Ala65Thr	p.A65T	ENST00000206249	NM_000125.3	65	Gcg/Acg	1/8	0.333105427876071	2	FACETS	0.624	0.552	0.701	0.312	0.276	0.351	SUBCLONAL	1	TRUE	0	0.339717149024767	2		734	830	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141557661	141557661	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759579021	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	195	844	0	ENST00000220592.5:c.1654G>A	p.Val552Met	p.V552M	ENST00000220592	NM_012154.3	552	Gtg/Atg	13/19	0.291595568936391	3	FACETS	1	0.966	1	0.541	0.499	0.584	CLONAL	1	TRUE	1	0.339717149024767	3		844	1242	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133748291	133748291	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	123	610	0	ENST00000318560.5:c.952A>G	p.Met318Val	p.M318V	ENST00000318560	NM_005157.4	318	Atg/Gtg	6/11	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.339717149024767	2		610	723	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133756021	133756021	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1271393830	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	145	557	0	ENST00000318560.5:c.1648A>G	p.Met550Val	p.M550V	ENST00000318560	NM_005157.4	550	Atg/Gtg	10/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.339717149024767	2		557	698	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403498	139403498	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756840659	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	184	769	1	ENST00000277541.6:c.2995G>A	p.Val999Met	p.V999M	ENST00000277541	NM_017617.3	999	Gtg/Atg	19/34	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.339717149024767	2		770	937	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841081	15841081	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	80	356	0	ENST00000307771.7:c.1165T>C	p.Tyr389His	p.Y389H	ENST00000307771	NM_005089.3	389	Tac/Cac	11/11	1	1	FACETS	0.852	0.753	0.957	0.852	0.753	0.957	CLONAL	1	TRUE	0	0.339717149024767	1		356	459	SUCCESS
APC	324	MSKCC	GRCh37	5	112175570	112175571	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	G	novel	NA	P-0028274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	83	398	0	ENST00000257430.4:c.4279_4280delinsG	p.Pro1427ValfsTer46	p.P1427Vfs*46	ENST00000257430	NM_000038.5	1427	CCt/Gt	16/16	0.339717149024767	1	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	0	0.339717149024767	1		398	404	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653867	89653867	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1554893835	NA	P-0028290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	158	292	0	ENST00000371953.3:c.164+1G>T		p.X55_splice	ENST00000371953	NM_000314.4	55			NA	2	FACETS	0.999	0.946	1			1	INDETERMINATE	2	TRUE	NA	0.706236119428814	2		292	224	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48921986	48921986	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	60	299	0	ENST00000267163.4:c.526C>T	p.Gln176Ter	p.Q176*	ENST00000267163	NM_000321.2	176	Caa/Taa	5/27	0.706236119428814	1	FACETS	0.833	0.74	0.927	0.833	0.74	0.927	CLONAL	1	TRUE	0	0.706236119428814	1		299	132	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579408	7579460	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTG	CAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTG	-	rs1555526610	NA	P-0028293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	285	367	2	ENST00000269305.4:c.227_279del	p.Ala76ValfsTer55	p.A76Vfs*55	ENST00000269305	NM_001126112.2	76	gCACCAGCAGCTCCTACACCGGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTG/g	4/11	0.814138595468058	2	FACETS	0.994	0.963	1	0.994	0.963	1	CLONAL	2	TRUE	0	0.814138595468058	2		369	352	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272029	15272030	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0028293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	207	315	0	ENST00000263388.2:c.6409_6410del	p.Leu2137GlyfsTer104	p.L2137Gfs*104	ENST00000263388	NM_000435.2	2137	CTg/g	33/33	0.814138595468058	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.814138595468058	2		315	249	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718675	190718675	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	186	238	0	ENST00000441310.2:c.833A>G	p.His278Arg	p.H278R	ENST00000441310	NM_000534.4	278	cAt/cGt	8/13	0.759144037582379	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.814138595468058	4		238	359	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs863224499	NA	P-0028307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	710	790	2	ENST00000269305.4:c.672+1G>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.619498617047358	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.619498617047358	2		792	1111	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871625	35871625	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	248	320	0	ENST00000216797.5:c.881A>G	p.Glu294Gly	p.E294G	ENST00000216797	NM_020529.2	294	gAg/gGg	5/6	0.606022111061379	2	FACETS	0.972	0.925	1	0.972	0.925	1	CLONAL	2	TRUE	0	0.619498617047358	2		320	412	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849551	68849551	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	163	679	0	ENST00000261769.5:c.1454T>A	p.Ile485Asn	p.I485N	ENST00000261769	NM_004360.3	485	aTc/aAc	10/16	0.619498617047358	1	FACETS	0.529	0.486	0.573	0.529	0.486	0.573	SUBCLONAL	1	TRUE	0	0.619498617047358	1		679	687	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295810	212295810	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	87	636	0	ENST00000342788.4:c.2503G>T	p.Glu835Ter	p.E835*	ENST00000342788	NM_005235.2	835	Gaa/Taa	21/28	0.619498617047358	1	FACETS	0.317	0.28	0.356	0.317	0.28	0.356	SUBCLONAL	1	TRUE	0	0.619498617047358	1		636	612	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566719	212566719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1229970702	NA	P-0028307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	45	430	0	ENST00000342788.4:c.1462C>T	p.Arg488Trp	p.R488W	ENST00000342788	NM_005235.2	488	Cgg/Tgg	12/28	0.619498617047358	1	FACETS	0.181	0.152	0.214	0.181	0.152	0.214	SUBCLONAL	1	TRUE	0	0.619498617047358	1		430	553	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0028309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	199	435	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.803650863332157	2		435	460	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0028309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	159	377	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.803650863332157	2		377	389	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046488	69046488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	226	458	3	ENST00000288368.4:c.3961C>T	p.Gln1321Ter	p.Q1321*	ENST00000288368	NM_024870.2	1321	Cag/Tag	32/40	0.690248533377313	3	FACETS	0.992	0.926	1	0.496	0.463	0.53	CLONAL	1	TRUE	1	0.803650863332157	3		461	795	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216506	36216506	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs956016804	NA	P-0028309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	76	682	4	ENST00000222270.7:c.3769C>T	p.Arg1257Cys	p.R1257C	ENST00000222270	NM_014727.1	1257	Cgc/Tgc	12/37	0.803650863332157	3	FACETS	0.22	0.192	0.25	0.11	0.096	0.125	SUBCLONAL	1	TRUE	1	0.803650863332157	3		686	1206	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259688	16259688	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs761621829	NA	P-0028309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	293	469	5	ENST00000375759.3:c.6953C>G	p.Ser2318Cys	p.S2318C	ENST00000375759	NM_015001.2	2318	tCt/tGt	11/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.803650863332157	2		474	708	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56477579	56477579	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	291	510	13	ENST00000267101.3:c.127G>T	p.Glu43Ter	p.E43*	ENST00000267101	NM_001982.3	43	Gag/Tag	2/28	0.690248533377313	3	FACETS	0.986	0.928	1	0.493	0.464	0.522	CLONAL	1	TRUE	1	0.803650863332157	3		523	1030	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89383389	89383389	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	319	618	0	ENST00000301030.4:c.39A>T	p.Glu13Asp	p.E13D	ENST00000301030	NM_001256183.1	13	gaA/gaT	3/13	NA	2	FACETS	0.909	0.861	0.958			1	INDETERMINATE	1	TRUE	NA	0.803650863332157	2		618	873	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264375	30264375	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	201	248	3	ENST00000322652.5:c.110C>A	p.Ser37Ter	p.S37*	ENST00000322652	NM_015355.2	37	tCg/tAg	1/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.803650863332157	2		251	460	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18956861	18956861	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	322	598	12	ENST00000262803.5:c.304G>C	p.Glu102Gln	p.E102Q	ENST00000262803	NM_002911.3	102	Gag/Cag	2/24	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.803650863332157	2		610	726	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916728	178916728	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	132	378	7	ENST00000263967.3:c.115G>C	p.Glu39Gln	p.E39Q	ENST00000263967	NM_006218.2	39	Gag/Cag	2/21	1	2	FACETS	0.925	0.851	1	0.925	0.851	1	CLONAL	1	TRUE	1	0.803650863332157	2		385	355	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907115	101907115	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	28	418	0	ENST00000374994.4:c.1075G>A	p.Asp359Asn	p.D359N	ENST00000374994	NM_004612.2	359	Gat/Aat	6/9	1	2	FACETS	0.186	0.149	0.229	0.186	0.149	0.229	SUBCLONAL	1	TRUE	1	0.803650863332157	2		418	374	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0028448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	99	384	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.731	0.653	0.814	0.731	0.653	0.814	SUBCLONAL	1	TRUE	1	0.381361194668406	2		384	710	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0028448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	106	503	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.977	0.878	1	0.977	0.878	1	CLONAL	1	TRUE	1	0.381361194668406	2		503	569	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0028448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	64	372	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	1	2	FACETS	0.653	0.566	0.747	0.653	0.566	0.747	SUBCLONAL	1	TRUE	1	0.381361194668406	2		372	514	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023008	27023010	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs587779737	NA	P-0028452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	10	39	0	ENST00000324856.7:c.126_128del	p.Ala45del	p.A45del	ENST00000324856	NM_006015.4	38	gaGGCg/gag	1/20	0.49276211845243	1	FACETS	0.276	0.188	0.385	0.276	0.188	0.385	SUBCLONAL	1	TRUE	0	0.498735946590559	1		39	109	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104359302	104359302	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0028452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	207	483	0	ENST00000369902.3:c.1022+1G>T		p.X341_splice	ENST00000369902	NM_016169.3	341			1	2	FACETS	0.899	0.835	0.966	0.899	0.835	0.966	CLONAL	1	TRUE	1	0.498735946590559	2		483	923	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557420	21557420	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	227	469	0	ENST00000382592.4:c.2425G>C	p.Asp809His	p.D809H	ENST00000382592	NM_014572.2	809	Gat/Cat	5/8	0.49276211845243	1	FACETS	0.96	0.898	1	0.96	0.898	1	CLONAL	1	TRUE	0	0.498735946590559	1		469	712	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526165	63526165	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1273	80	679	1	ENST00000307078.5:c.2461A>G	p.Ile821Val	p.I821V	ENST00000307078	NM_004655.3	821	Atc/Gtc	11/11	1	2	FACETS	0.237	0.208	0.269	0.237	0.208	0.269	SUBCLONAL	1	TRUE	1	0.498735946590559	2		680	1353	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439930	52439930	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0028452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	199	373	0	ENST00000460680.1:c.784-2A>G		p.X262_splice	ENST00000460680	NM_004656.3	262			0.49276211845243	1	FACETS	0.997	0.929	1	0.997	0.929	1	CLONAL	1	TRUE	0	0.498735946590559	1		373	601	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300819	137300819	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1389	75	723	0	ENST00000481739.1:c.464G>C	p.Cys155Ser	p.C155S	ENST00000481739	NM_002957.4	155	tGc/tCc	4/10	0.483152225505837	2	FACETS	0.205	0.179	0.234	0.103	0.089	0.117	SUBCLONAL	1	TRUE	0	0.498735946590559	2		723	1464	SUCCESS
AR	367	MSKCC	GRCh37	X	66766223	66766223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762550472	NA	P-0028452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	187	408	1	ENST00000374690.3:c.1235C>T	p.Ala412Val	p.A412V	ENST00000374690	NM_000044.3	412	gCg/gTg	1/8	1	2	FACETS	0.985	0.912	1	0.985	0.912	1	CLONAL	1	TRUE	1	0.498735946590559	2		409	761	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0028524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	21	588	1	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	0.538253191462894	1	FACETS	0.12	0.092	0.153	0.12	0.092	0.153	SUBCLONAL	1	TRUE	0	0.538253191462894	1		589	475	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0028524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	256	836	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.538253191462894	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.538253191462894	1		836	669	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112940006	112940006	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148176616	NA	P-0028524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	234	694	0	ENST00000351677.2:c.1658C>T	p.Thr553Met	p.T553M	ENST00000351677	NM_002834.3	553	aCg/aTg	14/16	0.538253191462894	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.538253191462894	1		694	626	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936983	48936983	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690863	NA	P-0028524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	212	571	0	ENST00000267163.4:c.751C>T	p.Arg251Ter	p.R251*	ENST00000267163	NM_000321.2	251	Cga/Tga	8/27	0.538253191462894	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.538253191462894	1		571	576	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935606	13935606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326846768	NA	P-0028524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	154	509	0	ENST00000405192.2:c.1250G>A	p.Arg417His	p.R417H	ENST00000405192	NM_001163147.1	417	cGt/cAt	12/12	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.538253191462894	2		509	556	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0028524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	173	407	16	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	0.538253191462894	1	FACETS	0.88	0.815	0.946	0.88	0.815	0.946	CLONAL	1	TRUE	0	0.538253191462894	1		423	534	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120493	2120493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370324876	NA	P-0028524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	30	763	1	ENST00000219476.3:c.1753C>T	p.Arg585Cys	p.R585C	ENST00000219476	NM_000548.3	585	Cgt/Tgt	17/42	0.538253191462894	1	FACETS	0.157	0.126	0.192	0.157	0.126	0.192	SUBCLONAL	1	TRUE	0	0.538253191462894	1		764	520	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536242	106536242	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	167	571	0	ENST00000369096.4:c.209G>A	p.Gly70Asp	p.G70D	ENST00000369096	NM_001198.3	70	gGt/gAt	2/7	0.538253191462894	1	FACETS	0.922	0.854	0.991	0.922	0.854	0.991	CLONAL	1	TRUE	0	0.538253191462894	1		571	492	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971312	15971312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1441094420	NA	P-0028524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	26	648	0	ENST00000268712.3:c.4637C>T	p.Pro1546Leu	p.P1546L	ENST00000268712	NM_006311.3	1546	cCg/cTg	32/46	0.538253191462894	1	FACETS	0.137	0.108	0.17	0.137	0.108	0.17	SUBCLONAL	1	TRUE	0	0.538253191462894	1		648	517	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47600710	47600710	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs866758817	NA	P-0028524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	93	500	0	ENST00000263735.4:c.184+1G>A		p.X62_splice	ENST00000263735	NM_002354.2	62			0.538253191462894	1	FACETS	0.489	0.436	0.545	0.489	0.436	0.545	SUBCLONAL	1	TRUE	0	0.538253191462894	1		500	517	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9786991	9786993	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0028524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	27	559	0	ENST00000377346.4:c.3029_3031del	p.Glu1010del	p.E1010del	ENST00000377346	NM_005026.3	1008	GAG/-	24/24	0.538253191462894	1	FACETS	0.143	0.113	0.178	0.143	0.113	0.178	SUBCLONAL	1	TRUE	0	0.538253191462894	1		559	512	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32182003	32182003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780829867	NA	P-0028524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	243	822	0	ENST00000375023.3:c.2051C>T	p.Thr684Met	p.T684M	ENST00000375023	NM_004557.3	684	aCg/aTg	13/30	0.538253191462894	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.538253191462894	1		822	621	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103398	2103398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200045926	NA	P-0028524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	105	849	0	ENST00000219476.3:c.281C>T	p.Pro94Leu	p.P94L	ENST00000219476	NM_000548.3	94	cCg/cTg	4/42	0.538253191462894	1	FACETS	0.603	0.543	0.666	0.603	0.543	0.666	SUBCLONAL	1	TRUE	0	0.538253191462894	1		849	473	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293589	1293589	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	196	775	0	ENST00000310581.5:c.1412G>A	p.Arg471Gln	p.R471Q	ENST00000310581	NM_198253.2	471	cGg/cAg	2/16	0.538253191462894	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.538253191462894	1		775	479	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166506	118166506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753542382	NA	P-0028524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	100	441	0	ENST00000369448.3:c.1016G>A	p.Arg339His	p.R339H	ENST00000369448	NM_017709.3	339	cGt/cAt	2/2	0.538253191462894	1	FACETS	0.684	0.616	0.756	0.684	0.616	0.756	SUBCLONAL	1	TRUE	0	0.538253191462894	1		441	397	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601854	43601854	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	163	610	1	ENST00000355710.3:c.898G>A	p.Asp300Asn	p.D300N	ENST00000355710	NM_020975.4	300	Gat/Aat	5/20	0.538253191462894	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.538253191462894	1		611	412	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203782	94203782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	90	362	0	ENST00000323929.3:c.872G>A	p.Gly291Glu	p.G291E	ENST00000323929	NM_005591.3	291	gGg/gAg	9/20	0.538253191462894	1	FACETS	0.858	0.771	0.948	0.858	0.771	0.948	CLONAL	1	TRUE	0	0.538253191462894	1		362	285	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562246	21562246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745371213	NA	P-0028524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	34	788	1	ENST00000382592.4:c.1673G>A	p.Arg558His	p.R558H	ENST00000382592	NM_014572.2	558	cGc/cAc	4/8	0.538253191462894	1	FACETS	0.162	0.132	0.196	0.162	0.132	0.196	SUBCLONAL	1	TRUE	0	0.538253191462894	1		789	569	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028600	42028600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	217	771	0	ENST00000219905.7:c.4138C>T	p.Arg1380Ter	p.R1380*	ENST00000219905	NM_001164273.1	1380	Cga/Tga	13/24	0.538253191462894	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.538253191462894	1		771	537	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884286	37884286	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs36085723	NA	P-0028524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	148	589	1	ENST00000269571.5:c.3757G>A	p.Val1253Met	p.V1253M	ENST00000269571		1253	Gtg/Atg	27/27	0.538253191462894	1	FACETS	0.92	0.848	0.994	0.92	0.848	0.994	CLONAL	1	TRUE	0	0.538253191462894	1		590	437	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533584	63533584	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	211	781	1	ENST00000307078.5:c.1570G>A	p.Val524Ile	p.V524I	ENST00000307078	NM_004655.3	524	Gtc/Atc	6/11	0.538253191462894	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.538253191462894	1		782	513	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890186	76890186	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	31	248	0	ENST00000373344.5:c.4708T>A	p.Phe1570Ile	p.F1570I	ENST00000373344	NM_000489.3	1570	Ttt/Att	17/35	1	1	FACETS	0.207	0.167	0.252	0.207	0.167	0.252	SUBCLONAL	1	TRUE	0	0.538253191462894	1		248	407	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	62	270	0				ENST00000310581	NM_198253.2	-/1132			0.338726029822533	3	FACETS	1	0.959	1	0.626	0.547	0.711	CLONAL	1	TRUE	1	0.465714805470745	3		270	262	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870519	40870519	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	98	660	0	ENST00000428826.2:c.884A>G	p.His295Arg	p.H295R	ENST00000428826		295	cAc/cGc	9/21	0.308409031780042	3	FACETS	0.747	0.666	0.832	0.373	0.333	0.416	SUBCLONAL	1	TRUE	1	0.465714805470745	3		660	695	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163841	47163841	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	130	589	0	ENST00000409792.3:c.2285C>A	p.Ser762Tyr	p.S762Y	ENST00000409792	NM_014159.6	762	tCt/tAt	3/21	0.355857662262406	2	FACETS	1	0.983	1	0.665	0.608	0.723	CLONAL	1	TRUE	0	0.465714805470745	2		589	420	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974370	93974370	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	143	613	2	ENST00000369303.4:c.1684G>A	p.Ala562Thr	p.A562T	ENST00000369303	NM_004440.3	562	Gct/Act	8/17	0.22302699333799	4	FACETS	1	0.98	1	0.622	0.568	0.679	INDETERMINATE	1	TRUE	2	0.465714805470745	4		615	723	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	48	270	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.521331206913037	2		270	146	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916614	178916614	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0028527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	107	483	0	ENST00000263967.3:c.1A>G	p.Met1?	p.M1?	ENST00000263967	NM_006218.2	1	Atg/Gtg	2/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.521331206913037	2		483	348	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653856	89653856	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	87	459	0	ENST00000371953.3:c.154del	p.Asp52MetfsTer2	p.D52Mfs*2	ENST00000371953	NM_000314.4	52	Gat/at	2/9	0.521331206913037	1	FACETS	0.894	0.802	0.99	0.894	0.802	0.99	CLONAL	1	TRUE	0	0.521331206913037	1		459	276	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537142	80537142	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	76	531	0	ENST00000286548.4:c.256G>A	p.Ala86Thr	p.A86T	ENST00000286548	NM_002072.3	86	Gcc/Acc	2/7	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.521331206913037	2		531	259	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0028529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	31	533	0	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	1	2	FACETS	0.616	0.5	0.747	0.616	0.5	0.747	SUBCLONAL	1	TRUE	1	0.34	2		533	296	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579592	7579592	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs879254212	NA	P-0028529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	38	593	0	ENST00000269305.4:c.97-2A>G		p.X33_splice	ENST00000269305	NM_001126112.2	33			1	2	FACETS	0.86	0.715	1	0.86	0.715	1	CLONAL	1	TRUE	1	0.34	2		593	260	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829040	128829042	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	rs570242755	NA	P-0028541-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	13	52	0	ENST00000249373.3:c.67_69del	p.Leu23del	p.L23del	ENST00000249373	NM_005631.4	16	ggGCTg/ggg	1/12	0.489900745887877	6	FACETS	0.498	0.355	0.672	0.124	0.088	0.168	SUBCLONAL	1	TRUE	2	0.489900745887877	6		52	211	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771545	112771545	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028541-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	126	594	0	ENST00000369452.4:c.1718A>T	p.Lys573Met	p.K573M	ENST00000369452	NM_007373.3	573	aAg/aTg	9/9	0.486344166650559	3	FACETS	0.808	0.731	0.888	0.404	0.365	0.444	CLONAL	1	TRUE	1	0.489900745887877	3		594	793	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443679	29443679	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028541-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	136	798	0	ENST00000389048.3:c.3538G>C	p.Val1180Leu	p.V1180L	ENST00000389048	NM_004304.4	1180	Gtt/Ctt	23/29	0.434675668646234	4	FACETS	0.734	0.666	0.806	0.183	0.166	0.202	SUBCLONAL	1	TRUE	0	0.489900745887877	4		798	1127	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841818	151841818	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028541-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	80	380	0	ENST00000262189.6:c.14323C>A	p.Leu4775Met	p.L4775M	ENST00000262189	NM_170606.2	4775	Ctg/Atg	55/59	0.489900745887877	6	FACETS	0.834	0.734	0.943	0.209	0.183	0.236	CLONAL	1	TRUE	2	0.489900745887877	6		380	775	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0028671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	32	470	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.673	0.545	0.819	0.673	0.545	0.819	SUBCLONAL	1	TRUE	1	0.17	2		471	559	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137360	202137360	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0028671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	35	279	0	ENST00000358485.4:c.589-1G>A		p.X197_splice	ENST00000358485	NM_001080125.1	197			1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.17	2		279	329	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230604	46230604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	26	340	2	ENST00000334344.6:c.853C>T	p.Arg285Trp	p.R285W	ENST00000334344	NM_152641.2	285	Cgg/Tgg	8/21	1	2	FACETS	0.695	0.55	0.862	0.695	0.55	0.862	SUBCLONAL	1	TRUE	1	0.17	2		342	440	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491126	120491126	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	40	469	0	ENST00000256646.2:c.2663G>T	p.Cys888Phe	p.C888F	ENST00000256646	NM_024408.3	888	tGc/tTc	17/34	1	2	FACETS	0.769	0.638	0.916	0.769	0.638	0.916	CLONAL	1	TRUE	1	0.17	2		469	612	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850628	63850628	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0028671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	18	240	0	ENST00000279873.7:c.1406C>G	p.Ser469Ter	p.S469*	ENST00000279873	NM_032199.2	469	tCa/tGa	10/10	1	2	FACETS	0.699	0.526	0.903	0.699	0.526	0.903	SUBCLONAL	1	TRUE	1	0.17	2		240	303	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287244	46287244	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	36	378	0	ENST00000334344.6:c.5192del	p.Lys1731ArgfsTer4	p.K1731Rfs*4	ENST00000334344	NM_152641.2	1730	cAa/ca	19/21	1	2	FACETS	0.864	0.71	1	0.864	0.71	1	CLONAL	1	TRUE	1	0.17	2		378	490	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994791	73994791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375871029	NA	P-0028671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	50	564	0	ENST00000318443.5:c.275G>A	p.Arg92His	p.R92H	ENST00000318443	NM_001024736.1	92	cGc/cAc	3/10	1	2	FACETS	0.938	0.795	1	0.938	0.795	1	CLONAL	1	TRUE	1	0.17	2		564	627	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36217200	36217200	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	139	789	0	ENST00000222270.7:c.3949G>T	p.Glu1317Ter	p.E1317*	ENST00000222270	NM_014727.1	1317	Gag/Tag	14/37	1	2	FACETS	0.87	0.791	0.953	1	0.989	1	CLONAL	2	TRUE	1	0.17	2		789	940	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199809	138199809	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	42	480	0	ENST00000237289.4:c.1227G>C	p.Glu409Asp	p.E409D	ENST00000237289	NM_001270507.1	409	gaG/gaC	7/9	1	2	FACETS	0.907	0.756	1	0.907	0.756	1	CLONAL	1	TRUE	1	0.17	2		480	545	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395008	139395008	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	40	388	0	ENST00000277541.6:c.5930del	p.Phe1977SerfsTer4	p.F1977Sfs*4	ENST00000277541	NM_017617.3	1977	tTc/tc	31/34	1	2	FACETS	0.974	0.809	1	0.974	0.809	1	CLONAL	1	TRUE	1	0.17	2		388	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0028676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	48	607	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.992	0.842	1	0.992	0.842	1	CLONAL	1	TRUE	1	0.281179941446754	2		607	344	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0028676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	53	538	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.281179941446754	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.281179941446754	1		538	220	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593387	48593387	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0028676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	18	246	1	ENST00000342988.3:c.1140-2A>T		p.X380_splice	ENST00000342988	NM_005359.5	380			1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.281179941446754	2		247	98	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042101	42042107	+	frameshift_variant	Frame_Shift_Del	DEL	AAAATTT	AAAATTT	-	novel	NA	P-0028676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	38	573	0	ENST00000219905.7:c.6298_6304del	p.Asn2100ValfsTer11	p.N2100Vfs*11	ENST00000219905	NM_001164273.1	2099	cAAAATTTa/ca	17/24	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.281179941446754	2		573	233	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042118	42042118	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	38	558	1	ENST00000219905.7:c.6313C>T	p.Gln2105Ter	p.Q2105*	ENST00000219905	NM_001164273.1	2105	Cag/Tag	17/24	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.281179941446754	2		559	242	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3842075	3842075	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1302427305	NA	P-0028693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	200	360	0	ENST00000262367.5:c.1237C>T	p.Arg413Ter	p.R413*	ENST00000262367	NM_004380.2	413	Cga/Tga	5/31	1	2	FACETS	0.932	0.872	0.993	0.932	0.872	0.993	CLONAL	1	TRUE	1	0.863137690307229	2		360	497	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801726	3801726	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs587783483	NA	P-0028693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	308	506	0	ENST00000262367.5:c.3779+1G>A		p.X1260_splice	ENST00000262367	NM_004380.2	1260			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.863137690307229	2		506	679	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949128	44949129	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	316	484	0	ENST00000377967.4:c.3690dup	p.Ile1231TyrfsTer20	p.I1231Yfs*20	ENST00000377967	NM_021140.2	1230	gct/gcTt	25/29	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.863137690307229	2		484	705	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035295	42035301	+	frameshift_variant	Frame_Shift_Del	DEL	CCAACTT	CCAACTT	-	novel	NA	P-0028693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	305	530	0	ENST00000219905.7:c.5138_5144del	p.Pro1713HisfsTer19	p.P1713Hfs*19	ENST00000219905	NM_001164273.1	1713	CCAACTTca/ca	15/24	1	2	FACETS	0.93	0.881	0.979	0.93	0.881	0.979	CLONAL	1	TRUE	1	0.863137690307229	2		530	760	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523614	41523616	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0028693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	685	651	0	ENST00000263253.7:c.1032_1034del	p.Leu346del	p.L346del	ENST00000263253	NM_001429.3	344	CTC/-	4/31	0.753398488898627	2	FACETS	0.964	0.946	0.982	0.964	0.946	0.982	CLONAL	2	TRUE	0	0.863137690307229	2		651	823	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266061	41266062	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0028693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	188	346	0	ENST00000349496.5:c.59dup	p.Ala21GlyfsTer3	p.A21Gfs*3	ENST00000349496	NM_001904.3	20	gcg/gCcg	3/15	1	2	FACETS	0.929	0.867	0.991	0.929	0.867	0.991	CLONAL	1	TRUE	1	0.863137690307229	2		346	469	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900122	151900122	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	152	253	0	ENST00000262189.6:c.3989del	p.Leu1330Ter	p.L1330*	ENST00000262189	NM_170606.2	1330	tTa/ta	26/59	1	2	FACETS	0.917	0.849	0.986	0.917	0.849	0.986	CLONAL	1	TRUE	1	0.863137690307229	2		253	384	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132824	152132842	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCGGCGGCTGCGGCTGC	TGGCGGCGGCTGCGGCTGC	-	novel	NA	P-0028693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	33	524	0	ENST00000262189.6:c.30_48del	p.Glu10AspfsTer89	p.E10Dfs*89	ENST00000262189	NM_170606.2	10	gaGCAGCCGCAGCCGCCGCCA/ga	1/59	1	2	FACETS	0.178	0.145	0.216	0.178	0.145	0.216	SUBCLONAL	1	TRUE	1	0.863137690307229	2		524	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0028989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	635	523	1	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.734289113052621	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.734289113052621	1		524	1004	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342446	118342446	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0028989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	295	374	0	ENST00000534358.1:c.572C>G	p.Ser191Ter	p.S191*	ENST00000534358	NM_005933.3	191	tCa/tGa	3/36	0.734289113052621	1	FACETS	0.938	0.894	0.982	0.938	0.894	0.982	CLONAL	1	TRUE	0	0.734289113052621	1		374	542	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781210	3781210	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	576	600	0	ENST00000262367.5:c.5155C>A	p.His1719Asn	p.H1719N	ENST00000262367	NM_004380.2	1719	Cac/Aac	30/31	0.734289113052621	1	FACETS	0.971	0.939	1	0.971	0.939	1	CLONAL	1	TRUE	0	0.734289113052621	1		600	1022	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799188	42799188	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1376	563	522	0	ENST00000575354.2:c.4672G>T	p.Asp1558Tyr	p.D1558Y	ENST00000575354	NM_015125.3	1558	Gac/Tac	20/20	0.583405463421391	3	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.734289113052621	3		522	1939	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139794970	139794970	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	534	556	0	ENST00000247668.2:c.364G>T	p.Glu122Ter	p.E122*	ENST00000247668	NM_021138.3	122	Gag/Tag	4/11	0.734289113052621	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.734289113052621	1		556	869	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0029180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	96	459	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.338367386392026	1	FACETS	0.83	0.741	0.924	0.83	0.741	0.924	CLONAL	1	TRUE	0	0.338367386392026	1		459	568	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0029180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	170	734	0	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.338367386392026	2		734	927	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139163	108139163	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	90	685	0	ENST00000278616.4:c.2665del	p.Tyr889IlefsTer10	p.Y889Ifs*10	ENST00000278616	NM_000051.3	889	Tat/at	18/63	1	2	FACETS	0.767	0.68	0.859	0.767	0.68	0.859	SUBCLONAL	1	TRUE	1	0.338367386392026	2		685	694	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865164	57865164	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	176	929	1	ENST00000228682.2:c.2641C>A	p.Leu881Met	p.L881M	ENST00000228682	NM_005269.2	881	Ctg/Atg	12/12	1	2	FACETS	0.962	0.885	1	0.962	0.885	1	CLONAL	1	TRUE	1	0.338367386392026	2		930	1081	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654605	29654605	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1555533569	NA	P-0029180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	95	391	0	ENST00000356175.3:c.5294C>A	p.Ser1765Ter	p.S1765*	ENST00000356175	NM_000267.3	1765	tCg/tAg	37/57	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.338367386392026	2		391	510	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223230	36223230	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs372039999	NA	P-0029180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	147	892	0	ENST00000222270.7:c.5780G>T	p.Arg1927Leu	p.R1927L	ENST00000222270	NM_014727.1	1927	cGg/cTg	28/37	1	2	FACETS	0.686	0.624	0.751	0.686	0.624	0.751	SUBCLONAL	1	TRUE	1	0.338367386392026	2		892	1267	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470611	25470611	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	160	637	0	ENST00000264709.3:c.863G>T	p.Arg288Leu	p.R288L	ENST00000264709	NM_175629.2	288	cGg/cTg	8/23	1	2	FACETS	0.969	0.888	1	0.969	0.888	1	CLONAL	1	TRUE	1	0.338367386392026	2		637	976	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279253	142279253	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	114	589	0	ENST00000350721.4:c.1393G>T	p.Ala465Ser	p.A465S	ENST00000350721	NM_001184.3	465	Gca/Tca	6/47	0.338367386392026	1	FACETS	0.85	0.766	0.937	0.85	0.766	0.937	CLONAL	1	TRUE	0	0.338367386392026	1		589	659	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790710	89790710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	147	907	1	ENST00000336032.3:c.97C>T	p.Pro33Ser	p.P33S	ENST00000336032	NM_006813.2	33	Ccg/Tcg	1/2	1	2	FACETS	0.77	0.701	0.842	0.77	0.701	0.842	SUBCLONAL	1	TRUE	1	0.338367386392026	2		908	1129	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0029180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	206	459	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.222694803343816	3	FACETS	0.837	0.778	0.898	0.837	0.778	0.898	CLONAL	2	TRUE	1	0.354991224089573	3		459	816	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139163	108139163	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	128	685	0	ENST00000278616.4:c.2665del	p.Tyr889IlefsTer10	p.Y889Ifs*10	ENST00000278616	NM_000051.3	889	Tat/at	18/63	0.354991224089573	3	FACETS	1	0.95	1	0.536	0.486	0.589	CLONAL	1	TRUE	1	0.354991224089573	3		685	792	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865164	57865164	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1210	83	929	1	ENST00000228682.2:c.2641C>A	p.Leu881Met	p.L881M	ENST00000228682	NM_005269.2	881	Ctg/Atg	12/12	0.222694803343816	3	FACETS	0.426	0.374	0.482	0.213	0.187	0.241	SUBCLONAL	1	TRUE	1	0.354991224089573	3		930	1293	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654605	29654605	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1555533569	NA	P-0029180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	59	391	0	ENST00000356175.3:c.5294C>A	p.Ser1765Ter	p.S1765*	ENST00000356175	NM_000267.3	1765	tCg/tAg	37/57	1	2	FACETS	0.652	0.561	0.75	0.652	0.561	0.75	SUBCLONAL	1	TRUE	1	0.354991224089573	2		391	510	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223230	36223230	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs372039999	NA	P-0029180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	178	892	0	ENST00000222270.7:c.5780G>T	p.Arg1927Leu	p.R1927L	ENST00000222270	NM_014727.1	1927	cGg/cTg	28/37	1	2	FACETS	0.711	0.653	0.772	0.711	0.653	0.772	SUBCLONAL	1	TRUE	1	0.354991224089573	2		892	1410	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470611	25470611	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	101	637	0	ENST00000264709.3:c.863G>T	p.Arg288Leu	p.R288L	ENST00000264709	NM_175629.2	288	cGg/cTg	8/23	1	2	FACETS	0.61	0.544	0.68	0.61	0.544	0.68	SUBCLONAL	1	TRUE	1	0.354991224089573	2		637	933	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279253	142279253	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	131	589	0	ENST00000350721.4:c.1393G>T	p.Ala465Ser	p.A465S	ENST00000350721	NM_001184.3	465	Gca/Tca	6/47	0.18693344053054	1	FACETS	0.887	0.807	0.972	0.887	0.807	0.972	INDETERMINATE	1	TRUE	0	0.354991224089573	1		589	684	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790710	89790710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1201	82	907	1	ENST00000336032.3:c.97C>T	p.Pro33Ser	p.P33S	ENST00000336032	NM_006813.2	33	Ccg/Tcg	1/2	1	2	FACETS	0.36	0.316	0.408	0.36	0.316	0.408	SUBCLONAL	1	TRUE	1	0.354991224089573	2		908	1283	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439597	51439597	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1348544322	NA	P-0029180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	89	419	0	ENST00000262662.1:c.162G>C	p.Arg54Ser	p.R54S	ENST00000262662		54	agG/agC	4/4	1	2	FACETS	0.717	0.636	0.804	0.717	0.636	0.804	SUBCLONAL	1	TRUE	1	0.354991224089573	2		419	699	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	401962	401962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	182	408	1	ENST00000399788.2:c.4829G>A	p.Cys1610Tyr	p.C1610Y	ENST00000399788	NM_001042603.1	1610	tGc/tAc	27/28	0.354991224089573	3	FACETS	0.801	0.74	0.863	0.534	0.493	0.576	CLONAL	2	TRUE	0	0.354991224089573	3		409	754	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779844	3779844	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793090	NA	P-0029180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	74	799	0	ENST00000262367.5:c.5204C>T	p.Thr1735Met	p.T1735M	ENST00000262367	NM_004380.2	1735	aCg/aTg	31/31	1	2	FACETS	0.376	0.328	0.429	0.376	0.328	0.429	SUBCLONAL	1	TRUE	1	0.354991224089573	2		799	1108	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774098	56774098	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	61	698	0	ENST00000337432.4:c.449G>C	p.Gly150Ala	p.G150A	ENST00000337432	NM_058216.2	150	gGa/gCa	3/9	1	2	FACETS	0.304	0.261	0.351	0.304	0.261	0.351	SUBCLONAL	1	TRUE	1	0.354991224089573	2		698	1130	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741023	40741023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	67	815	2	ENST00000392038.2:c.1295C>T	p.Ser432Phe	p.S432F	ENST00000392038	NM_001626.4	432	tCc/tTc	13/14	1	2	FACETS	0.331	0.286	0.38	0.331	0.286	0.38	SUBCLONAL	1	TRUE	1	0.354991224089573	2		817	1141	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724294	52724294	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	68	706	0	ENST00000322088.6:c.1426G>C	p.Glu476Gln	p.E476Q	ENST00000322088	NM_014225.5	476	Gag/Cag	12/15	1	2	FACETS	0.382	0.331	0.437	0.382	0.331	0.437	SUBCLONAL	1	TRUE	1	0.354991224089573	2		706	1003	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546761	9546761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768724288	NA	P-0029180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	74	331	0	ENST00000353224.5:c.1261G>A	p.Asp421Asn	p.D421N	ENST00000353224	NM_177990.2	421	Gac/Aac	5/10	0.206106750501756	3	FACETS	1	0.918	1	0.353	0.309	0.399	INDETERMINATE	1	TRUE	0	0.354991224089573	3		331	464	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568626	41568626	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	46	636	0	ENST00000263253.7:c.4576G>C	p.Glu1526Gln	p.E1526Q	ENST00000263253	NM_001429.3	1526	Gag/Cag	28/31	0.18693344053054	1	FACETS	0.24	0.201	0.283	0.24	0.201	0.283	INDETERMINATE	1	TRUE	0	0.354991224089573	1		636	889	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163189	47163189	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	29	485	0	ENST00000409792.3:c.2937C>G	p.Ile979Met	p.I979M	ENST00000409792	NM_014159.6	979	atC/atG	3/21	0.206106750501756	3	FACETS	0.335	0.268	0.412	0.112	0.089	0.138	INDETERMINATE	1	TRUE	0	0.354991224089573	3		485	574	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190906	185190906	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	221	841	0	ENST00000265026.3:c.1787G>C	p.Arg596Thr	p.R596T	ENST00000265026	NM_004721.4	596	aGa/aCa	11/14	0.18693344053054	1	FACETS	0.878	0.816	0.943	0.878	0.816	0.943	INDETERMINATE	1	TRUE	0	0.354991224089573	1		841	1166	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170827176	170827176	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029180-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	32	549	0	ENST00000296930.5:c.544G>C	p.Asp182His	p.D182H	ENST00000296930	NM_002520.6	182	Gat/Cat	7/11	1	2	FACETS	0.298	0.241	0.362	0.298	0.241	0.362	SUBCLONAL	1	TRUE	1	0.354991224089573	2		549	606	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0029609-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	53	504	6	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.177148544159825	2		510	476	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030485-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	217	270	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.974	0.913	1	0.974	0.913	1	CLONAL	1	TRUE	1	0.791698762862022	2		270	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0030485-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	692	795	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	1	2	FACETS	0.928	0.906	0.949	1	0.998	1	CLONAL	2	TRUE	1	0.791698762862022	2		795	942	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692901	89692901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786204929	NA	P-0030485-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	228	576	0	ENST00000371953.3:c.385G>A	p.Gly129Arg	p.G129R	ENST00000371953	NM_000314.4	129	Gga/Aga	5/9	0.791698762862022	1	FACETS	0.897	0.851	0.942	0.897	0.851	0.942	CLONAL	1	TRUE	0	0.791698762862022	1		576	388	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430005	78430005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030485-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	143	395	0	ENST00000370768.2:c.874G>A	p.Gly292Arg	p.G292R	ENST00000370768	NM_003902.3	292	Gga/Aga	11/20	1	2	FACETS	0.85	0.782	0.92	0.85	0.782	0.92	CLONAL	1	TRUE	1	0.791698762862022	2		395	425	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175916347	175916347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030485-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	188	462	1	ENST00000367669.3:c.2162G>A	p.Ser721Asn	p.S721N	ENST00000367669	NM_022457.5	721	aGt/aAt	19/20	1	2	FACETS	0.865	0.805	0.926	0.865	0.805	0.926	CLONAL	1	TRUE	1	0.791698762862022	2		463	549	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039353	49039354	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0030485-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	164	724	0	ENST00000267163.4:c.2339dup	p.Pro781ThrfsTer14	p.P781Tfs*14	ENST00000267163	NM_000321.2	780	tca/tCca	23/27	0.791698762862022	1	FACETS	0.48	0.444	0.518	0.48	0.444	0.518	SUBCLONAL	1	TRUE	0	0.791698762862022	1		724	521	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0030545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	282	435	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.56026202067636	3	FACETS	0.926	0.884	0.967	0.926	0.884	0.967	CLONAL	3	TRUE	0	0.56026202067636	3		435	464	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	130	654	0	ENST00000206249.3:c.1607T>C	p.Leu536Pro	p.L536P	ENST00000206249	NM_000125.3	536	cTc/cCc	8/8	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.56026202067636	2		654	449	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060780	38060797	+	inframe_deletion	In_Frame_Del	DEL	GTTGATGGAGAACGGGTG	GTTGATGGAGAACGGGTG	-	novel	NA	P-0030545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	218	614	2	ENST00000250448.2:c.1192_1209del	p.His398_Asn403del	p.H398_N403del	ENST00000250448	NM_004496.3	398	CACCCGTTCTCCATCAAC/-	2/2	0.56026202067636	3	FACETS	0.884	0.821	0.949	0.442	0.41	0.475	CLONAL	1	TRUE	1	0.56026202067636	3		616	1127	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727084	243727084	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	115	343	0	ENST00000263826.5:c.886G>C	p.Gly296Arg	p.G296R	ENST00000263826	NM_005465.4	296	Ggg/Cgg	9/13	0.481477274822421	5	FACETS	0.93	0.838	1			1	CLONAL	1	TRUE	NA	0.56026202067636	5		343	812	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219510	133219510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	131	432	1	ENST00000320574.5:c.4624G>A	p.Gly1542Ser	p.G1542S	ENST00000320574	NM_006231.2	1542	Ggc/Agc	36/49	0.334674443654154	4	FACETS	0.985	0.895	1	0.492	0.447	0.54	INDETERMINATE	1	TRUE	2	0.56026202067636	4		433	741	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793488	89793488	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	62	270	0	ENST00000336032.3:c.557T>A	p.Met186Lys	p.M186K	ENST00000336032	NM_006813.2	186	aTg/aAg	2/2	1	2	FACETS	0.838	0.732	0.952	0.838	0.732	0.952	CLONAL	1	TRUE	1	0.56026202067636	2		270	264	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435481	110435481	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	101	353	1	ENST00000375856.3:c.2920C>A	p.Pro974Thr	p.P974T	ENST00000375856	NM_003749.2	974	Ccg/Acg	1/2	1	2	FACETS	0.934	0.842	1	0.934	0.842	1	CLONAL	1	TRUE	1	0.56026202067636	2		354	386	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934578	NA	P-0030660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	213	590	0	ENST00000269305.4:c.524G>T	p.Arg175Leu	p.R175L	ENST00000269305	NM_001126112.2	175	cGc/cTc	5/11	0.389277512494259	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.432114866533505	2		590	477	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116175	209116175	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1253479303	NA	P-0030660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	65	421	0	ENST00000345146.2:c.101A>G	p.Tyr34Cys	p.Y34C	ENST00000345146	NM_005896.2	34	tAc/tGc	3/10	0.397990538432291	3	FACETS	0.945	0.823	1	0.473	0.411	0.538	CLONAL	1	TRUE	1	0.432114866533505	3		421	387	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041164	29041164	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	90	620	1	ENST00000282397.4:c.264C>A	p.Phe88Leu	p.F88L	ENST00000282397	NM_002019.4	88	ttC/ttA	3/30	0.432114866533505	2	FACETS	1	0.927	1	0.525	0.468	0.584	CLONAL	1	TRUE	0	0.432114866533505	2		621	397	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294537	1294537	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	131	274	1	ENST00000310581.5:c.464G>A	p.Arg155His	p.R155H	ENST00000310581	NM_198253.2	155	cGc/cAc	2/16	0.432114866533505	6	FACETS	0.985	0.897	1	0.492	0.448	0.538	CLONAL	2	TRUE	2	0.432114866533505	6		275	574	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873219	71873219	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	54	445	3	ENST00000357731.5:c.975C>A	p.Ser325Arg	p.S325R	ENST00000357731	NM_173808.2	325	agC/agA	7/7	1	2	FACETS	0.755	0.648	0.871	0.755	0.648	0.871	SUBCLONAL	1	TRUE	1	0.432114866533505	2		448	331	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737108	162737108	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	91	492	0	ENST00000367921.3:c.1252A>T	p.Ile418Phe	p.I418F	ENST00000367921	NM_006182.2	418	Atc/Ttc	11/18	0.374491439781367	3	FACETS	1	0.92	1	0.519	0.463	0.579	CLONAL	1	TRUE	1	0.432114866533505	3		492	493	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508760	38508760	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0030660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	178	472	1	ENST00000254066.5:c.807+1G>T		p.X269_splice	ENST00000254066	NM_000964.3	269			0.343584511965177	4	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	2	0.432114866533505	4		473	583	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600364	10600364	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	234	655	0	ENST00000171111.5:c.1491del	p.Trp497CysfsTer3	p.W497Cfs*3	ENST00000171111	NM_203500.1	497	tgG/tg	4/6	0.432114866533505	2	FACETS	0.994	0.936	1	0.994	0.936	1	CLONAL	2	TRUE	0	0.432114866533505	2		655	545	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732527	190732527	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	30	344	0	ENST00000441310.2:c.2345T>G	p.Leu782Arg	p.L782R	ENST00000441310	NM_000534.4	782	cTt/cGt	11/13	0.397990538432291	3	FACETS	0.903	0.734	1	0.451	0.367	0.546	CLONAL	1	TRUE	1	0.432114866533505	3		344	187	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089163	37089163	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	63	423	2	ENST00000231790.2:c.1885G>T	p.Glu629Ter	p.E629*	ENST00000231790	NM_000249.3	629	Gaa/Taa	16/19	0.432114866533505	2	FACETS	0.938	0.817	1	0.469	0.408	0.533	CLONAL	1	TRUE	0	0.432114866533505	2		425	311	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180627	32180627	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	184	515	0	ENST00000375023.3:c.2500A>G	p.Thr834Ala	p.T834A	ENST00000375023	NM_004557.3	834	Act/Gct	16/30	0.411941115050178	4	FACETS	1	0.968	1	0.716	0.665	0.768	CLONAL	2	TRUE	1	0.432114866533505	4		515	568	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967876	93967876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	70	578	0	ENST00000369303.4:c.2051G>A	p.Ser684Asn	p.S684N	ENST00000369303	NM_004440.3	684	aGc/aAc	11/17	1	2	FACETS	0.893	0.783	1	0.893	0.783	1	CLONAL	1	TRUE	1	0.432114866533505	2		578	363	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332824	152332824	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	74	517	0	ENST00000206249.3:c.1130A>T	p.His377Leu	p.H377L	ENST00000206249	NM_000125.3	377	cAc/cTc	5/8	1	2	FACETS	0.874	0.769	0.985	0.874	0.769	0.985	CLONAL	1	TRUE	1	0.432114866533505	2		517	392	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521276	8521276	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0030660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	129	298	0	ENST00000356435.5:c.961+1G>T		p.X321_splice	ENST00000356435		321			0.432114866533505	3	FACETS	0.984	0.913	1	0.984	0.913	1	CLONAL	3	TRUE	0	0.432114866533505	3		298	246	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399541	139399541	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	157	449	0	ENST00000277541.6:c.4602G>T	p.Gln1534His	p.Q1534H	ENST00000277541	NM_017617.3	1534	caG/caT	26/34	0.179876787577509	5	FACETS	1	0.978	1	0.775	0.715	0.837	INDETERMINATE	2	TRUE	2	0.432114866533505	5		449	515	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227970	53227970	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	200	683	0	ENST00000375401.3:c.2344G>T	p.Glu782Ter	p.E782*	ENST00000375401	NM_004187.3	782	Gag/Tag	16/26	0.432114866533505	1	FACETS	0.797	0.748	0.848	1	0.993	1	SUBCLONAL	2	TRUE	0	0.432114866533505	1		683	455	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354597	70354597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767396596	NA	P-0030712-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	130	565	0	ENST00000374080.3:c.4762G>A	p.Val1588Met	p.V1588M	ENST00000374080		1588	Gtg/Atg	35/45	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.875028505959622	2		565	295	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31424571	31424571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1186040397	NA	P-0030712-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	357	670	0	ENST00000344624.3:c.3224G>A	p.Arg1075His	p.R1075H	ENST00000344624		1075	cGc/cAc	25/33	1	2	FACETS	0.974	0.927	1	0.974	0.927	1	CLONAL	1	TRUE	1	0.875028505959622	2		670	838	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573990	7573991	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CATTCAGCTCTCGGAA	novel	NA	P-0030712-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	160	719	0	ENST00000269305.4:c.1021_1036dup	p.Glu346ValfsTer6	p.E346Vfs*6	ENST00000269305	NM_001126112.2	346	gag/gTTCCGAGAGCTGAATGag	10/11	0.875028505959622	2	FACETS	1	0.985	1	0.6	0.56	0.638	CLONAL	1	TRUE	0	0.875028505959622	2		719	305	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152288	99152288	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030712-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	123	566	0	ENST00000074304.5:c.367A>G	p.Lys123Glu	p.K123E	ENST00000074304	NM_001134224.1	123	Aaa/Gaa	6/26	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.875028505959622	2		566	265	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410855	31410855	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030712-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	301	513	0	ENST00000344624.3:c.3665A>C	p.Glu1222Ala	p.E1222A	ENST00000344624		1222	gAa/gCa	28/33	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.875028505959622	2		513	650	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099403	157099414	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAG	CAGCAGCAGCAG	-	rs587779743	NA	P-0030713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	14	204	0	ENST00000346085.5:c.351_362del	p.Gln128_Gln131del	p.Q128_Q131del	ENST00000346085	NM_020732.3	114	CAGCAGCAGCAG/-	1/20	0.234910680728108	3	FACETS	0.364	0.264	0.485	0.182	0.132	0.243	INDETERMINATE	1	TRUE	1	0.571442056110221	3		204	173	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099403	157099414	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAG	CAGCAGCAGCAG	-	rs587779743	NA	P-0030713-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	14	204	0	ENST00000346085.5:c.351_362del	p.Gln128_Gln131del	p.Q128_Q131del	ENST00000346085	NM_020732.3	114	CAGCAGCAGCAG/-	1/20	0.354082707007656	3	FACETS	0.19	0.137	0.255	0.095	0.068	0.128	INDETERMINATE	1	TRUE	1	0.658842119621118	3		204	297	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103717	47103717	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1205330893	NA	P-0030782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	44	533	2	ENST00000409792.3:c.6229C>T	p.Arg2077Ter	p.R2077*	ENST00000409792	NM_014159.6	2077	Cga/Tga	14/21	1	2	FACETS	0.345	0.288	0.409	0.345	0.288	0.409	SUBCLONAL	1	TRUE	1	0.31	2		535	822	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272308	38272308	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs869320694	NA	P-0030782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	207	551	0	ENST00000425967.3:c.2059A>G	p.Lys687Glu	p.K687E	ENST00000425967	NM_001174067.1	687	Aag/Gag	15/19	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.31	2		551	1060	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273561	38273561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	123	420	0	ENST00000425967.3:c.1774G>A	p.Val592Met	p.V592M	ENST00000425967	NM_001174067.1	592	Gtg/Atg	14/19	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.31	2		420	716	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0030850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	226	361	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.373286496158411	4	FACETS	1	0.985	1	0.822	0.781	0.862	CLONAL	3	TRUE	0	0.58649734253727	4		361	372	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247516	123247516	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	813	439	0	ENST00000358487.5:c.1975A>C	p.Lys659Gln	p.K659Q	ENST00000358487	NM_000141.4	659	Aag/Cag	14/18	0.58649734253727	14	FACETS	0.964	0.941	0.986			1	CLONAL	11	TRUE	NA	0.58649734253727	14		439	1182	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426751	49426751	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	37	255	0	ENST00000301067.7:c.11737C>A	p.Gln3913Lys	p.Q3913K	ENST00000301067	NM_003482.3	3913	Cag/Aag	39/54	0.58649734253727	3	FACETS	0.837	0.697	0.989	0.418	0.348	0.495	CLONAL	1	TRUE	1	0.58649734253727	3		255	195	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50916702	50916702	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	80	454	1	ENST00000440232.2:c.2174G>A	p.Arg725His	p.R725H	ENST00000440232	NM_002691.3	725	cGt/cAt	18/27	0.534297869140478	4	FACETS	0.984	0.87	1	0.328	0.29	0.369	CLONAL	1	TRUE	1	0.58649734253727	4		455	440	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981561	70981561	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	141	745	0	ENST00000276594.2:c.535G>C	p.Glu179Gln	p.E179Q	ENST00000276594	NM_024504.3	179	Gag/Cag	2/8	0.551547686590461	5	FACETS	1	0.98	1	0.249	0.227	0.273	CLONAL	1	TRUE	0	0.58649734253727	5		745	725	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0030876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	221	332	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.694787940125625	3	FACETS	1	0.978	1	0.556	0.519	0.594	CLONAL	1	TRUE	1	0.694787940125625	3		332	771	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0030876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	21	235	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.694787940125625	3	FACETS	0.127	0.097	0.162	0.064	0.048	0.081	SUBCLONAL	1	TRUE	1	0.694787940125625	3		235	641	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044449	5044449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371826393	NA	P-0030876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	220	374	0	ENST00000381652.3:c.397C>T	p.Arg133Trp	p.R133W	ENST00000381652	NM_004972.3	133	Cgg/Tgg	5/25	0.694787940125625	1	FACETS	0.986	0.932	1	0.986	0.932	1	CLONAL	1	TRUE	0	0.694787940125625	1		374	419	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856008	111856008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1222585515	NA	P-0030876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	146	152	0	ENST00000341259.2:c.59C>T	p.Ala20Val	p.A20V	ENST00000341259	NM_005475.2	20	gCg/gTg	2/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.694787940125625	2		152	354	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142447	119142447	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs199739868	NA	P-0030876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	185	289	0	ENST00000264033.4:c.446G>A	p.Arg149Gln	p.R149Q	ENST00000264033	NM_005188.3	149	cGa/cAa	3/16	0.694787940125625	1	FACETS	0.987	0.928	1	0.987	0.928	1	CLONAL	1	TRUE	0	0.694787940125625	1		289	352	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40998378	40998378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	53	292	0	ENST00000267868.3:c.229G>A	p.Glu77Lys	p.E77K	ENST00000267868	NM_002875.4	77	Gag/Aag	4/10	1	2	FACETS	0.247	0.21	0.287	0.247	0.21	0.287	SUBCLONAL	1	TRUE	1	0.694787940125625	2		292	618	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0030880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	690	505	4	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.437895594897654	6	FACETS	1	0.99	1	1	0.99	1	CLONAL	5	TRUE	1	0.437895594897654	6		509	1138	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783832	50783832	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	280	676	2	ENST00000398568.2:c.223C>G	p.Leu75Val	p.L75V	ENST00000398568	NM_001042412.1	75	Cta/Gta	3/18	0.326425809345241	4	FACETS	0.948	0.892	1	0.948	0.892	1	CLONAL	2	TRUE	2	0.437895594897654	4		678	970	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579584	7579585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0030880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	259	557	0	ENST00000269305.4:c.102dup	p.Pro36AlafsTer7	p.P36Afs*7	ENST00000269305	NM_001126112.2	34	-/C	4/11	NA	2	FACETS	1	0.952	1			1	INDETERMINATE	2	TRUE	NA	0.437895594897654	2		557	587	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594094	55594094	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs794726675	NA	P-0030880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	83	389	1	ENST00000288135.5:c.1879+1G>A		p.X627_splice	ENST00000288135	NM_000222.2	627			0.181684659578958	0	FACETS	0.516	0.458	0.578			1	INDETERMINATE	1	TRUE	0	0.437895594897654	0		390	413	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247172	153247172	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	73	346	2	ENST00000281708.4:c.1630G>T	p.Val544Phe	p.V544F	ENST00000281708	NM_033632.3	544	Gtc/Ttc	10/12	1	2	FACETS	0.848	0.746	0.958	0.848	0.746	0.958	CLONAL	1	TRUE	1	0.437895594897654	2		348	393	SUCCESS
APC	324	MSKCC	GRCh37	5	112175753	112175760	+	frameshift_variant	Frame_Shift_Del	DEL	TTATTACA	TTATTACA	-	novel	NA	P-0030880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	186	379	2	ENST00000257430.4:c.4464_4471del	p.Leu1488PhefsTer23	p.L1488Ffs*23	ENST00000257430	NM_000038.5	1488	TTATTACAt/t	16/16	0.437895594897654	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.437895594897654	2		381	416	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0030884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	119	377	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.27	2		377	767	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	73	322	0	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	0.3	1	FACETS	0.886	0.776	1	0.886	0.776	1	CLONAL	1	TRUE	0	0.27	1		322	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0030884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	92	502	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.3	1	FACETS	0.984	0.876	1	0.984	0.876	1	CLONAL	1	TRUE	0	0.27	1		502	599	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337261	89337261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	74	406	0	ENST00000301030.4:c.7770G>A	p.Trp2590Ter	p.W2590*	ENST00000301030	NM_001256183.1	2590	tgG/tgA	12/13	1	2	FACETS	0.965	0.846	1	0.965	0.846	1	CLONAL	1	TRUE	1	0.27	2		406	568	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628936	187628936	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	121	518	0	ENST00000441802.2:c.2046G>T	p.Met682Ile	p.M682I	ENST00000441802	NM_005245.3	682	atG/atT	2/27	0.3	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.27	1		518	732	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243967	41243971	+	missense_variant	Missense_Mutation	ONP	GTGAA	GTGAA	TTGAG	novel	NA	P-0030884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	76	521	0	ENST00000357654.3:c.3577_3581delinsCTCAA	p.Phe1193_Thr1194delinsLeuAsn	p.F1193_T1194delinsLN	ENST00000357654	NM_007294.3	1193	TTCACc/CTCAAc	10/23	1	2	FACETS	0.763	0.668	0.865	0.763	0.668	0.865	SUBCLONAL	1	TRUE	1	0.27	2		521	738	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0030886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	124	366	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.894	0.811	0.981	0.894	0.811	0.981	CLONAL	1	TRUE	1	0.439737555046494	2		366	631	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590533	95590533	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	110	241	0	ENST00000393063.1:c.1376G>A	p.Arg459Lys	p.R459K	ENST00000393063	NM_030621.3	459	aGa/aAa	9/28	0.277712413538351	1	FACETS	0.664	0.603	0.728	0.664	0.603	0.728	INDETERMINATE	1	TRUE	0	0.639753103980876	1		241	352	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657450	29657450	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs62070718	NA	P-0030890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	50	484	0	ENST00000356175.3:c.5683G>C	p.Ala1895Pro	p.A1895P	ENST00000356175	NM_000267.3	1895	Gca/Cca	38/57	0.476567351274681	0	FACETS	0.124	0.105	0.145			1	SUBCLONAL	1	TRUE	0	0.639753103980876	0		484	454	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096983	11096983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	177	517	0	ENST00000358026.2:c.478del	p.Gln160ArgfsTer143	p.Q160Rfs*143	ENST00000358026	NM_001128849.1	158	gaC/ga	4/36	1	2	FACETS	0.7	0.646	0.756	0.7	0.646	0.756	SUBCLONAL	1	TRUE	1	0.639753103980876	2		517	791	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578188	7578188	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201592	NA	P-0030900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	89	534	1	ENST00000269305.4:c.661G>T	p.Glu221Ter	p.E221*	ENST00000269305	NM_001126112.2	221	Gag/Tag	6/11	0.307293209967394	1	FACETS	0.804	0.713	0.9	0.804	0.713	0.9	CLONAL	1	TRUE	0	0.307293209967394	1		535	610	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78831591	78831591	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	61	337	1	ENST00000306801.3:c.1400C>T	p.Ala467Val	p.A467V	ENST00000306801	NM_020761.2	467	gCc/gTc	13/34	0.307293209967394	3	FACETS	0.977	0.844	1	0.488	0.422	0.56	CLONAL	1	TRUE	1	0.307293209967394	3		338	469	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	125	270	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.943	0.868	1	0.943	0.868	1	CLONAL	1	TRUE	1	0.904414369520069	2		270	293	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0030906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	150	512	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	NA	2	FACETS	0.697	0.642	0.754			1	INDETERMINATE	1	TRUE	NA	0.904414369520069	2		512	476	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0030906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	253	617	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	1	2	FACETS	0.971	0.917	1	0.971	0.917	1	CLONAL	1	TRUE	1	0.904414369520069	2		617	576	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218052	108218052	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1064794840	NA	P-0030906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	264	624	0	ENST00000278616.4:c.8631G>C	p.Leu2877Phe	p.L2877F	ENST00000278616	NM_000051.3	2877	ttG/ttC	59/63	1	2	FACETS	0.943	0.891	0.996	0.943	0.891	0.996	CLONAL	1	TRUE	1	0.904414369520069	2		624	619	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426751	49426751	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	118	335	0	ENST00000301067.7:c.11737C>T	p.Gln3913Ter	p.Q3913*	ENST00000301067	NM_003482.3	3913	Cag/Tag	39/54	1	2	FACETS	0.974	0.895	1	0.974	0.895	1	CLONAL	1	TRUE	1	0.904414369520069	2		335	268	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445170	49445170	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	337	821	0	ENST00000301067.7:c.2296G>T	p.Glu766Ter	p.E766*	ENST00000301067	NM_003482.3	766	Gag/Tag	10/54	1	2	FACETS	0.941	0.895	0.987	0.941	0.895	0.987	CLONAL	1	TRUE	1	0.904414369520069	2		821	792	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439578	51439578	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	243	467	0	ENST00000262662.1:c.143G>T	p.Gly48Val	p.G48V	ENST00000262662		48	gGa/gTa	4/4	1	2	FACETS	0.981	0.925	1	0.981	0.925	1	CLONAL	1	TRUE	1	0.904414369520069	2		467	548	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321655	30321655	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	323	739	1	ENST00000322652.5:c.1510C>T	p.Gln504Ter	p.Q504*	ENST00000322652	NM_015355.2	504	Cag/Tag	13/16	1	2	FACETS	0.922	0.875	0.968	0.922	0.875	0.968	CLONAL	1	TRUE	1	0.904414369520069	2		740	775	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322609	30322609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	300	656	0	ENST00000322652.5:c.1622C>T	p.Ser541Phe	p.S541F	ENST00000322652	NM_015355.2	541	tCt/tTt	14/16	1	2	FACETS	0.915	0.867	0.963	0.915	0.867	0.963	CLONAL	1	TRUE	1	0.904414369520069	2		656	725	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091759	29091759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	218	462	1	ENST00000328354.6:c.1198G>A	p.Gly400Arg	p.G400R	ENST00000328354	NM_007194.3	400	Ggg/Agg	11/15	1	2	FACETS	0.982	0.923	1	0.982	0.923	1	CLONAL	1	TRUE	1	0.904414369520069	2		463	491	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188035	151188035	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	189	527	0	ENST00000262187.5:c.118G>C	p.Glu40Gln	p.E40Q	ENST00000262187	NM_005614.3	40	Gaa/Caa	2/8	1	2	FACETS	0.767	0.714	0.821	0.767	0.714	0.821	SUBCLONAL	1	TRUE	1	0.904414369520069	2		527	545	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151866270	151866270	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0030906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	314	578	0	ENST00000262189.6:c.9517+1G>T		p.X3173_splice	ENST00000262189	NM_170606.2	3173			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.904414369520069	2		578	673	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989482	85989482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	114	510	0	ENST00000263360.6:c.1241G>A	p.Arg414Gln	p.R414Q	ENST00000263360	NM_003797.3	414	cGa/cAa	12/12	1	2	FACETS	0.777	0.701	0.856	0.777	0.701	0.856	SUBCLONAL	1	TRUE	1	0.485120552076865	2		510	605	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717704	89717705	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0030907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	125	561	1	ENST00000371953.3:c.730_731del	p.Pro244SerfsTer8	p.P244Sfs*8	ENST00000371953	NM_000314.4	243	ttCCct/ttct	7/9	0.485120552076865	1	FACETS	0.869	0.793	0.949	0.869	0.793	0.949	CLONAL	1	TRUE	0	0.485120552076865	1		562	449	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030705	48030705	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779415187	NA	P-0030907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	120	483	0	ENST00000234420.5:c.3319G>A	p.Asp1107Asn	p.D1107N	ENST00000234420	NM_000179.2	1107	Gat/Aat	5/10	1	2	FACETS	0.925	0.839	1	0.925	0.839	1	CLONAL	1	TRUE	1	0.485120552076865	2		483	535	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227897	123227897	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	71	531	1	ENST00000218089.9:c.3608A>T	p.Asp1203Val	p.D1203V	ENST00000218089	NM_001042749.1	1203	gAt/gTt	33/35	1	2	FACETS	0.681	0.596	0.771	0.681	0.596	0.771	SUBCLONAL	1	TRUE	1	0.485120552076865	2		532	430	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0030909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	88	361	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.203188314499121	2	FACETS	1	0.972	1	0.646	0.575	0.721	CLONAL	1	TRUE	0	0.318209219468481	2		361	428	SUCCESS
APC	324	MSKCC	GRCh37	5	112175525	112175525	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	49	436	1	ENST00000257430.4:c.4234G>T	p.Gly1412Ter	p.G1412*	ENST00000257430	NM_000038.5	1412	Gga/Tga	16/16	0.138716404768536	3	FACETS	0.949	0.807	1	0.475	0.403	0.553	INDETERMINATE	1	TRUE	1	0.318209219468481	3		437	376	SUCCESS
ALK	238	MSKCC	GRCh37	2	29420420	29420420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	55	656	0	ENST00000389048.3:c.4061G>A	p.Cys1354Tyr	p.C1354Y	ENST00000389048	NM_004304.4	1354	tGc/tAc	27/29	0.227205323875889	3	FACETS	0.821	0.703	0.95	0.411	0.351	0.475	CLONAL	1	TRUE	1	0.318209219468481	3		656	488	SUCCESS
APC	324	MSKCC	GRCh37	5	112128198	112128199	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0030909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	86	645	0	ENST00000257430.4:c.703_704del	p.Leu235ThrfsTer16	p.L235Tfs*16	ENST00000257430	NM_000038.5	234	cTT/c	7/16	0.138716404768536	3	FACETS	0.996	0.882	1	0.498	0.441	0.559	INDETERMINATE	1	TRUE	1	0.318209219468481	3		645	629	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737702	145737728	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCACACCTGCCGGAAAGCATGTCAGAT	GCACACCTGCCGGAAAGCATGTCAGAT	-	novel	NA	P-0030909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	85	713	0	ENST00000428558.2:c.3056-21_3061del		p.X1019_splice	ENST00000428558	NM_004260.3	1019		19/22	0.318209219468481	12	FACETS	1	0.976	1			1	CLONAL	1	TRUE	NA	0.318209219468481	12		713	955	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902306	151902307	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	T	novel	NA	P-0030909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	28	247	0	ENST00000262189.6:c.3845_3846delinsA	p.Ile1282LysfsTer21	p.I1282Kfs*21	ENST00000262189	NM_170606.2	1282	aTT/aA	25/59	0.318209219468481	5	FACETS	1	0.817	1	0.34	0.272	0.416	CLONAL	1	TRUE	2	0.318209219468481	5		247	255	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415040	116415040	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	248	739	0	ENST00000397752.3:c.3134C>A	p.Pro1045Gln	p.P1045Q	ENST00000397752	NM_000245.2	1045	cCa/cAa	15/21	0.604149554913576	1	FACETS	0.908	0.856	0.962	0.908	0.856	0.962	CLONAL	1	TRUE	0	0.614914509506793	1		739	615	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259287	89259287	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	325	502	0	ENST00000336596.2:c.431A>C	p.Asp144Ala	p.D144A	ENST00000336596	NM_005233.5	144	gAc/gCc	3/17	1	2	FACETS	0.895	0.85	0.941	0.895	0.85	0.941	CLONAL	1	TRUE	1	0.889864165210598	2		502	816	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063718	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0030920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	111	233	0	ENST00000412916.2:c.165+2dup		p.X55_splice	ENST00000412916		55			0.635958644608278	1	FACETS	0.879	0.807	0.951	0.879	0.807	0.951	CLONAL	1	TRUE	0	0.689700621142989	1		233	240	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928060	178928086	+	inframe_deletion	In_Frame_Del	DEL	GCCAGTACCTCATGGATTAGAAGATTT	GCCAGTACCTCATGGATTAGAAGATTT	-	novel	NA	P-0030920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	358	668	0	ENST00000263967.3:c.1340_1366del	p.Pro447_Leu455del	p.P447_L455del	ENST00000263967	NM_006218.2	446	tgGCCAGTACCTCATGGATTAGAAGATTTg/tgg	8/21	0.62707271605702	3	FACETS	1	0.993	1			1	CLONAL	1	TRUE	NA	0.689700621142989	3		668	1069	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111556	8111556	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	581	607	0	ENST00000346208.3:c.1042C>A	p.His348Asn	p.H348N	ENST00000346208		348	Cac/Aac	5/6	0.66584642515974	3	FACETS	0.99	0.956	1	0.99	0.956	1	CLONAL	2	TRUE	1	0.689700621142989	3		607	1144	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161785	56161800	+	frameshift_variant	Frame_Shift_Del	DEL	ACGTCTAGTTCAGAAA	ACGTCTAGTTCAGAAA	-	novel	NA	P-0030920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	165	567	0	ENST00000399503.3:c.1284_1299del	p.Ser429AlafsTer2	p.S429Afs*2	ENST00000399503	NM_005921.1	428	ACGTCTAGTTCAGAAAac/ac	6/20	1	2	FACETS	0.601	0.553	0.652	0.601	0.553	0.652	SUBCLONAL	1	TRUE	1	0.689700621142989	2		567	796	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56171112	56171116	+	frameshift_variant	Frame_Shift_Del	DEL	TCTAC	TCTAC	-	novel	NA	P-0030920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	126	373	0	ENST00000399503.3:c.1940_1944del	p.Val647GlufsTer48	p.V647Efs*48	ENST00000399503	NM_005921.1	647	gTCTAC/g	10/20	1	2	FACETS	0.704	0.641	0.77	0.704	0.641	0.77	SUBCLONAL	1	TRUE	1	0.689700621142989	2		373	519	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0030922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	107	562	3	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.231260310131804	3	FACETS	0.968	0.873	1	0.484	0.436	0.534	INDETERMINATE	1	TRUE	1	0.58857275374537	3		565	486	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	158	270	0				ENST00000310581	NM_198253.2	-/1132			0.200196623013732	4	FACETS	0.927	0.857	0.999	0.927	0.857	0.999	INDETERMINATE	2	TRUE	2	0.58857275374537	4		270	460	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001374	150001374	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	92	661	3	ENST00000253339.5:c.2230C>T	p.Arg744Ter	p.R744*	ENST00000253339		744	Cga/Tga	4/7	0.169931242081265	2	FACETS	0.744	0.665	0.828	0.372	0.332	0.414	INDETERMINATE	1	TRUE	0	0.58857275374537	2		664	420	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0030922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	241	768	10	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	0.971	0.91	1	0.971	0.91	1	CLONAL	1	TRUE	1	0.58857275374537	2		778	843	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781374	3781374	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	233	726	1	ENST00000262367.5:c.4991G>A	p.Arg1664His	p.R1664H	ENST00000262367	NM_004380.2	1664	cGc/cAc	30/31	1	2	FACETS	0.956	0.894	1	0.956	0.894	1	CLONAL	1	TRUE	1	0.58857275374537	2		727	828	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982348	201982348	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	251	817	6	ENST00000359651.3:c.729del	p.Lys244SerfsTer10	p.K244Sfs*10	ENST00000359651		243	Ggg/gg	6/8	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.58857275374537	2		823	846	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176330	24176330	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	423	681	4	ENST00000263121.7:c.1121G>C	p.Arg374Pro	p.R374P	ENST00000263121	NM_003073.3	374	cGg/cCg	9/9	0.58857275374537	2	FACETS	0.956	0.919	0.992	0.956	0.919	0.992	CLONAL	2	TRUE	0	0.58857275374537	2		685	752	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645691	12645691	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1085307553	NA	P-0030922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	135	369	3	ENST00000251849.4:c.778A>C	p.Thr260Pro	p.T260P	ENST00000251849	NM_002880.3	260	Aca/Cca	7/17	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.58857275374537	2		372	442	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	108	270	0				ENST00000310581	NM_198253.2	-/1132			0.176752447155077	0	FACETS	0.384	0.349	0.42			1	INDETERMINATE	1	TRUE	0	0.641907575726908	0		270	314	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692829	89692829	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	115	247	0	ENST00000371953.3:c.313T>A	p.Cys105Ser	p.C105S	ENST00000371953	NM_000314.4	105	Tgt/Agt	5/9	0.641907575726908	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.641907575726908	1		247	179	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244009	46244009	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	212	662	0	ENST00000334344.6:c.2103del	p.Val702SerfsTer56	p.V702Sfs*56	ENST00000334344	NM_152641.2	701	acT/ac	15/21	1	2	FACETS	0.848	0.79	0.908	0.848	0.79	0.908	CLONAL	1	TRUE	1	0.641907575726908	2		662	779	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053110	180053110	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0030924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	138	690	0	ENST00000261937.6:c.1258+1G>A		p.X420_splice	ENST00000261937	NM_182925.4	420			0.235923128038115	0	FACETS	0.289	0.264	0.315			1	INDETERMINATE	1	TRUE	0	0.641907575726908	0		690	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0030927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	471	510	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.569511222676806	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.569511222676806	2		510	826	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119758	70119758	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	552	779	0	ENST00000245479.2:c.760C>T	p.Arg254Ter	p.R254*	ENST00000245479	NM_000346.3	254	Cga/Tga	3/3	0.511265602044496	5	FACETS	1	0.991	1	0.742	0.712	0.773	CLONAL	2	TRUE	2	0.569511222676806	5		779	1614	SUCCESS
APC	324	MSKCC	GRCh37	5	112175235	112175235	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0030927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	234	408	0	ENST00000257430.4:c.3944C>G	p.Ser1315Ter	p.S1315*	ENST00000257430	NM_000038.5	1315	tCa/tGa	16/16	0.502742858099418	3	FACETS	0.844	0.8	0.887	0.844	0.8	0.887	CLONAL	3	TRUE	0	0.569511222676806	3		408	417	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095038	11095038	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	590	908	0	ENST00000358026.2:c.211C>T	p.Gln71Ter	p.Q71*	ENST00000358026	NM_001128849.1	71	Cag/Tag	2/36	0.569511222676806	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.569511222676806	3		908	1277	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641916	12641916	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0030927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	155	443	0	ENST00000251849.4:c.835-2A>G		p.X279_splice	ENST00000251849	NM_002880.3	279			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.569511222676806	2		443	512	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786485	135786485	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	465	761	0	ENST00000298552.3:c.1045C>T	p.Pro349Ser	p.P349S	ENST00000298552	NM_001162426.1	349	Cca/Tca	11/23	0.569511222676806	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.569511222676806	3		761	1030	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937038	76937038	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0030927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	175	331	0	ENST00000373344.5:c.3710C>G	p.Ser1237Ter	p.S1237*	ENST00000373344	NM_000489.3	1237	tCa/tGa	9/35	0.569511222676806	2	FACETS	0.897	0.829	0.968			1	CLONAL	1	TRUE	NA	0.569511222676806	2		331	685	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	114	270	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.922	0.843	1	0.922	0.843	1	CLONAL	1	TRUE	1	0.83217093897727	2		270	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747342068	NA	P-0030929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	92	886	1	ENST00000269305.4:c.394A>G	p.Lys132Glu	p.K132E	ENST00000269305	NM_001126112.2	132	Aag/Gag	5/11	1	2	FACETS	0.201	0.178	0.226	0.201	0.178	0.226	SUBCLONAL	1	TRUE	1	0.83217093897727	2		887	1100	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711892	89711892	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	284	506	0	ENST00000371953.3:c.510T>G	p.Ser170Arg	p.S170R	ENST00000371953	NM_000314.4	170	agT/agG	6/9	0.83217093897727	1	FACETS	0.96	0.922	0.998	0.96	0.922	0.998	CLONAL	1	TRUE	0	0.83217093897727	1		506	415	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223604	55223604	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	317	615	1	ENST00000275493.2:c.971G>T	p.Arg324Leu	p.R324L	ENST00000275493	NM_005228.3	324	cGc/cTc	8/28	0.83217093897727	3	FACETS	1	0.976	1	0.529	0.5	0.559	CLONAL	1	TRUE	1	0.83217093897727	3		616	1020	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	76	245	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.259631154149843	2	FACETS	0.782	0.69	0.878	0.782	0.69	0.878	SUBCLONAL	2	TRUE	0	0.274632875333304	2		245	354	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939479	68939479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778971988	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	89	604	0	ENST00000288368.4:c.464G>A	p.Arg155Gln	p.R155Q	ENST00000288368	NM_024870.2	155	cGg/cAg	5/40	1	2	FACETS	0.942	0.836	1	0.942	0.836	1	CLONAL	1	TRUE	1	0.274632875333304	2		604	688	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	103	622	6	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.915	0.818	1	0.915	0.818	1	CLONAL	1	TRUE	1	0.274632875333304	2		628	820	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375120	31375120	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs906767301	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	145	784	0	ENST00000328111.2:c.517G>A	p.Asp173Asn	p.D173N	ENST00000328111	NM_006892.3	173	Gac/Aac	6/23	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.274632875333304	2		784	975	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	106	573	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.976	0.875	1	0.976	0.875	1	CLONAL	1	TRUE	1	0.274632875333304	2		573	791	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180207	38180207	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1300885784	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	149	563	1	ENST00000396334.3:c.55C>T	p.Pro19Ser	p.P19S	ENST00000396334	NM_002468.4	19	Ccc/Tcc	1/5	0.242288769461174	3	FACETS	0.85	0.778	0.925	0.85	0.778	0.925	CLONAL	2	TRUE	1	0.274632875333304	3		564	726	SUCCESS
AR	367	MSKCC	GRCh37	X	66766199	66766199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035114992	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	33	471	0	ENST00000374690.3:c.1211C>T	p.Ala404Val	p.A404V	ENST00000374690	NM_000044.3	404	gCg/gTg	1/8	1	2	FACETS	0.448	0.364	0.542	0.448	0.364	0.542	SUBCLONAL	1	TRUE	1	0.274632875333304	2		471	537	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958295	11958295	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	74	498	0	ENST00000353533.5:c.205C>T	p.Gln69Ter	p.Q69*	ENST00000353533	NM_003010.3	69	Caa/Taa	2/11	0.274632875333304	1	FACETS	0.947	0.831	1	0.947	0.831	1	CLONAL	1	TRUE	0	0.274632875333304	1		498	491	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061517	38061517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771653601	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	59	355	0	ENST00000250448.2:c.472G>A	p.Asp158Asn	p.D158N	ENST00000250448	NM_004496.3	158	Gac/Aac	2/2	1	2	FACETS	0.93	0.802	1	0.93	0.802	1	CLONAL	1	TRUE	1	0.274632875333304	2		355	462	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023042	48023042	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs63749873	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	56	386	0	ENST00000234420.5:c.467C>G	p.Ser156Ter	p.S156*	ENST00000234420	NM_000179.2	156	tCa/tGa	3/10	1	2	FACETS	0.731	0.626	0.845	0.731	0.626	0.845	SUBCLONAL	1	TRUE	1	0.274632875333304	2		386	558	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867304	45867304	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1372639983	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	126	744	1	ENST00000391945.4:c.889G>A	p.Ala297Thr	p.A297T	ENST00000391945	NM_000400.3	297	Gcc/Acc	10/23	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.274632875333304	2		745	878	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959106	2959106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs895214237	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	139	737	0	ENST00000396946.4:c.2410C>T	p.Arg804Cys	p.R804C	ENST00000396946	NM_032415.4	804	Cgt/Tgt	18/25	NA	2	FACETS	0.861	0.782	0.945			1	INDETERMINATE	1	TRUE	NA	0.274632875333304	2		737	1175	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790090	40790090	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	59	672	2	ENST00000373198.4:c.2641del	p.Arg881GlyfsTer20	p.R881Gfs*20	ENST00000373198	NM_133170.3	881	Cgg/gg	18/32	1	2	FACETS	0.465	0.398	0.537	0.465	0.398	0.537	SUBCLONAL	1	TRUE	1	0.274632875333304	2		674	925	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834561	156834561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1326	114	897	0	ENST00000524377.1:c.329C>T	p.Ala110Val	p.A110V	ENST00000524377	NM_002529.3	110	gCc/gTc	3/17	0.267010812531093	5	FACETS	0.814	0.73	0.903	0.204	0.182	0.226	CLONAL	1	TRUE	1	0.274632875333304	5		897	1440	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845366	151845366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	131	733	0	ENST00000262189.6:c.13646G>A	p.Arg4549His	p.R4549H	ENST00000262189	NM_170606.2	4549	cGc/cAc	52/59	0.274632875333304	2	FACETS	0.956	0.866	1	0.478	0.433	0.526	CLONAL	1	TRUE	0	0.274632875333304	2		733	998	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738172	133738172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755144370	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	66	546	0	ENST00000318560.5:c.572G>A	p.Arg191His	p.R191H	ENST00000318560	NM_005157.4	191	cGc/cAc	4/11	1	2	FACETS	0.672	0.583	0.769	0.672	0.583	0.769	SUBCLONAL	1	TRUE	1	0.274632875333304	2		546	715	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210432	2210432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761437945	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	101	749	0	ENST00000398665.3:c.1039C>T	p.Arg347Cys	p.R347C	ENST00000398665	NM_032482.2	347	Cgc/Tgc	13/28	1	2	FACETS	0.823	0.734	0.917	0.823	0.734	0.917	CLONAL	1	TRUE	1	0.274632875333304	2		749	894	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741517	17741517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	116	554	1	ENST00000250003.3:c.188C>T	p.Ser63Leu	p.S63L	ENST00000250003	NM_002478.4	63	tCg/tTg	1/3	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.274632875333304	2		555	664	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182095	11182095	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1365408542	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	133	704	3	ENST00000361445.4:c.6751C>T	p.Arg2251Trp	p.R2251W	ENST00000361445	NM_004958.3	2251	Cgg/Tgg	48/58	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.274632875333304	2		707	967	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783248	9783248	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	130	731	0	ENST00000377346.4:c.2492C>A	p.Ser831Ter	p.S831*	ENST00000377346	NM_005026.3	831	tCa/tAa	20/24	1	2	FACETS	0.882	0.799	0.971	0.882	0.799	0.971	CLONAL	1	TRUE	1	0.274632875333304	2		731	1073	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11273592	11273592	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	72	543	0	ENST00000361445.4:c.3149G>A	p.Ser1050Asn	p.S1050N	ENST00000361445	NM_004958.3	1050	aGc/aAc	21/58	1	2	FACETS	0.773	0.675	0.879	0.773	0.675	0.879	SUBCLONAL	1	TRUE	1	0.274632875333304	2		543	678	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023030	27023030	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	11	54	0	ENST00000324856.7:c.136G>T	p.Glu46Ter	p.E46*	ENST00000324856	NM_006015.4	46	Gag/Tag	1/20	1	2	FACETS	0.735	0.512	1	0.735	0.512	1	CLONAL	1	TRUE	1	0.274632875333304	2		54	109	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981599	101981599	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	29	180	0	ENST00000282441.5:c.20C>A	p.Pro7Gln	p.P7Q	ENST00000282441	NM_001130145.2	7	cCg/cAg	1/9	1	2	FACETS	0.788	0.635	0.961	0.788	0.635	0.961	CLONAL	1	TRUE	1	0.274632875333304	2		180	268	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100483	102100483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	111	687	1	ENST00000282441.5:c.1327G>A	p.Asp443Asn	p.D443N	ENST00000282441	NM_001130145.2	443	Gac/Aac	9/9	1	2	FACETS	0.837	0.751	0.928	0.837	0.751	0.928	CLONAL	1	TRUE	1	0.274632875333304	2		688	966	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343673	118343673	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	84	547	0	ENST00000534358.1:c.1799C>G	p.Ser600Cys	p.S600C	ENST00000534358	NM_005933.3	600	tCc/tGc	3/36	1	2	FACETS	0.856	0.755	0.963	0.856	0.755	0.963	CLONAL	1	TRUE	1	0.274632875333304	2		547	715	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912656	32912656	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80359433	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	129	726	1	ENST00000380152.3:c.4169del	p.Leu1390TrpfsTer20	p.L1390Wfs*20	ENST00000380152		1388	acT/ac	11/27	1	2	FACETS	0.946	0.857	1	0.946	0.857	1	CLONAL	1	TRUE	1	0.274632875333304	2		727	993	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849522	68849522	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	134	740	0	ENST00000261769.5:c.1426del	p.Asp476MetfsTer5	p.D476Mfs*5	ENST00000261769	NM_004360.3	475	gtG/gt	10/16	0.274632875333304	1	FACETS	0.923	0.838	1	0.923	0.838	1	CLONAL	1	TRUE	0	0.274632875333304	1		740	912	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828389	72828389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750838080	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	85	703	1	ENST00000268489.5:c.8192G>A	p.Arg2731Gln	p.R2731Q	ENST00000268489	NM_006885.3	2731	cGg/cAg	9/10	0.274632875333304	1	FACETS	0.799	0.707	0.899	0.799	0.707	0.899	SUBCLONAL	1	TRUE	0	0.274632875333304	1		704	668	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217917	7217917	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	81	463	0	ENST00000380728.2:c.95-1G>T		p.X32_splice	ENST00000380728		32			0.274632875333304	1	FACETS	0.863	0.761	0.971	0.863	0.761	0.971	CLONAL	1	TRUE	0	0.274632875333304	1		463	590	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265192	5265192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760753054	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	120	762	1	ENST00000357368.4:c.395C>T	p.Ser132Phe	p.S132F	ENST00000357368	NM_002850.3	132	tCt/tTt	5/38	1	2	FACETS	0.93	0.839	1	0.93	0.839	1	CLONAL	1	TRUE	1	0.274632875333304	2		763	940	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367953	15367953	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1285226583	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	125	797	1	ENST00000263377.2:c.1373C>T	p.Pro458Leu	p.P458L	ENST00000263377	NM_058243.2	458	cCg/cTg	8/20	1	2	FACETS	0.889	0.803	0.98	0.889	0.803	0.98	CLONAL	1	TRUE	1	0.274632875333304	2		798	1024	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99180041	99180041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	103	674	1	ENST00000074304.5:c.1984C>T	p.Pro662Ser	p.P662S	ENST00000074304	NM_001134224.1	662	Ccc/Tcc	19/26	1	2	FACETS	0.854	0.764	0.951	0.854	0.764	0.951	CLONAL	1	TRUE	1	0.274632875333304	2		675	878	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188302	10188302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780077	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	118	630	0	ENST00000256474.2:c.445G>A	p.Ala149Thr	p.A149T	ENST00000256474	NM_000551.3	149	Gcc/Acc	2/3	0.242288769461174	3	FACETS	0.931	0.838	1	0.465	0.419	0.515	CLONAL	1	TRUE	1	0.274632875333304	3		630	1050	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090425	37090425	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs755577490	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	113	675	0	ENST00000231790.2:c.2020G>C	p.Glu674Gln	p.E674Q	ENST00000231790	NM_000249.3	674	Gaa/Caa	18/19	0.242288769461174	3	FACETS	0.817	0.734	0.907	0.409	0.367	0.454	CLONAL	1	TRUE	1	0.274632875333304	3		675	1145	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940580	49940580	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776668243	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	92	725	0	ENST00000296474.3:c.463G>A	p.Val155Met	p.V155M	ENST00000296474	NM_002447.2	155	Gtg/Atg	1/20	0.242288769461174	3	FACETS	0.764	0.677	0.856	0.382	0.338	0.428	SUBCLONAL	1	TRUE	1	0.274632875333304	3		725	998	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586445	189586445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	109	621	1	ENST00000264731.3:c.1069G>A	p.Asp357Asn	p.D357N	ENST00000264731	NM_003722.4	357	Gat/Aat	8/14	0.242288769461174	3	FACETS	1	0.901	1	0.502	0.45	0.557	CLONAL	1	TRUE	1	0.274632875333304	3		622	899	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382214	152382215	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	103	631	2	ENST00000206249.3:c.1324_1325delinsAA	p.Gly442Lys	p.G442K	ENST00000206249	NM_000125.3	442	GGa/AAa	6/8	1	2	FACETS	0.804	0.718	0.895	0.804	0.718	0.895	CLONAL	1	TRUE	1	0.274632875333304	2		633	933	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55270273	55270273	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764780987	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	151	813	0	ENST00000275493.2:c.3226G>A	p.Ala1076Thr	p.A1076T	ENST00000275493	NM_005228.3	1076	Gcc/Acc	27/28	0.242288769461174	3	FACETS	1	0.915	1	0.501	0.457	0.548	CLONAL	1	TRUE	1	0.274632875333304	3		813	1247	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035947	47035952	+	inframe_deletion	In_Frame_Del	DEL	CCCAAG	CCCAAG	-	novel	NA	P-0030930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	128	792	0	ENST00000377604.3:c.631_636del	p.Pro211_Lys212del	p.P211_K212del	ENST00000377604	NM_001204468.1	209	CCCAAG/-	7/24	1	2	FACETS	0.897	0.812	0.988	0.897	0.812	0.988	CLONAL	1	TRUE	1	0.274632875333304	2		792	1039	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	690	651	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.703982178621292	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.703982178621292	2		651	870	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	713	800	3	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	0.703982178621292	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.703982178621292	2		803	864	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263973	104263974	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776579	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	83	236	0	ENST00000369902.3:c.71dup	p.Ala25GlyfsTer23	p.A25Gfs*23	ENST00000369902	NM_016169.3	22	gcc/gCcc	1/12	0.661577888073909	2	FACETS	0.486	0.43	0.546	0.243	0.215	0.273	SUBCLONAL	1	TRUE	0	0.703982178621292	2		236	485	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434367	121434367	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	193	782	2	ENST00000257555.6:c.1136del	p.Pro379LeufsTer5	p.P379Lfs*5	ENST00000257555		377	ctC/ct	6/10	0.703982178621292	2	FACETS	0.753	0.699	0.809	0.377	0.349	0.405	SUBCLONAL	1	TRUE	0	0.703982178621292	2		784	728	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575209	48575209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767326	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	102	460	0	ENST00000342988.3:c.403C>T	p.Arg135Ter	p.R135*	ENST00000342988	NM_005359.5	135	Cga/Tga	3/12	0.634159713697795	2	FACETS	0.894	0.83	0.957	0.894	0.83	0.957	CLONAL	2	TRUE	0	0.703982178621292	2		460	162	SUCCESS
AR	367	MSKCC	GRCh37	X	66765158	66765158	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs78686797	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	26	178	0	ENST00000374690.3:c.170T>A	p.Leu57Gln	p.L57Q	ENST00000374690	NM_000044.3	57	cTg/cAg	1/8	0.141552348352791	2	FACETS	1	0.85	1			1	INDETERMINATE	1	TRUE	NA	0.703982178621292	2		178	71	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828914	72828914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147043604	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	164	804	1	ENST00000268489.5:c.7667C>T	p.Ala2556Val	p.A2556V	ENST00000268489	NM_006885.3	2556	gCg/gTg	9/10	0.251061622321624	2	FACETS	0.522	0.479	0.567	0.261	0.239	0.284	INDETERMINATE	1	TRUE	0	0.703982178621292	2		805	893	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997697	149997697	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs145871963	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	173	546	0	ENST00000253339.5:c.2770C>T	p.Arg924Ter	p.R924*	ENST00000253339		924	Cga/Tga	5/7	0.693201728580694	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.703982178621292	1		546	296	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543660	9543660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	197	667	0	ENST00000353224.5:c.1494G>A	p.Met498Ile	p.M498I	ENST00000353224	NM_177990.2	498	atG/atA	6/10	0.561167455316325	4	FACETS	1	0.986	1	0.418	0.388	0.449	CLONAL	1	TRUE	1	0.703982178621292	4		667	760	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510166	149510166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747109578	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	255	800	1	ENST00000261799.4:c.1303C>T	p.Arg435Cys	p.R435C	ENST00000261799	NM_002609.3	435	Cgc/Tgc	9/23	0.240519533922453	2	FACETS	0.706	0.661	0.752	0.353	0.33	0.376	INDETERMINATE	1	TRUE	0	0.703982178621292	2		801	1026	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210703	5210703	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762760744	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	380	714	2	ENST00000357368.4:c.5348G>A	p.Arg1783Gln	p.R1783Q	ENST00000357368	NM_002850.3	1783	cGg/cAg	34/38	0.703982178621292	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.703982178621292	1		716	534	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149440497	149440497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs281860269	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	334	821	0	ENST00000286301.3:c.1897G>A	p.Glu633Lys	p.E633K	ENST00000286301	NM_005211.3	633	Gag/Aag	14/22	0.240519533922453	2	FACETS	1	0.995	1	0.685	0.652	0.717	INDETERMINATE	1	TRUE	0	0.703982178621292	2		821	693	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858216	27858216	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	186	693	0	ENST00000359303.2:c.355A>G	p.Thr119Ala	p.T119A	ENST00000359303	NM_003535.2	119	Act/Gct	1/1	0.703982178621292	2	FACETS	0.696	0.644	0.75	0.348	0.322	0.375	SUBCLONAL	1	TRUE	0	0.703982178621292	2		693	759	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953616	32953616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45469092	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	88	741	0	ENST00000380152.3:c.8917C>T	p.Arg2973Cys	p.R2973C	ENST00000380152		2973	Cgt/Tgt	22/27	0.693201728580694	1	FACETS	0.74	0.668	0.813	0.74	0.668	0.813	SUBCLONAL	1	TRUE	0	0.703982178621292	1		741	219	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262240	115262240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	457	624	3	ENST00000438362.2:c.2314C>T	p.Arg772Cys	p.R772C	ENST00000438362	NM_001242891.1	772	Cgc/Tgc	18/20	0.703982178621292	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.703982178621292	2		627	623	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904847	101904847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	78	488	0	ENST00000374994.4:c.835G>A	p.Val279Met	p.V279M	ENST00000374994	NM_004612.2	279	Gtg/Atg	5/9	0.703982178621292	2	FACETS	1	0.941	1	0.538	0.482	0.596	CLONAL	1	TRUE	0	0.703982178621292	2		488	206	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905074	50905074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1726801	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	619	734	1	ENST00000440232.2:c.356G>A	p.Arg119His	p.R119H	ENST00000440232	NM_002691.3	119	cGc/cAc	4/27	0.703982178621292	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.703982178621292	2		735	784	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691820	30691820	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs756999639	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	155	736	0	ENST00000295754.5:c.322T>C	p.Tyr108His	p.Y108H	ENST00000295754	NM_003242.5	108	Tac/Cac	3/7	0.703982178621292	2	FACETS	1	0.989	1	0.682	0.635	0.729	CLONAL	1	TRUE	0	0.703982178621292	2		736	323	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261988	16261988	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	144	615	0	ENST00000375759.3:c.9253A>G	p.Thr3085Ala	p.T3085A	ENST00000375759	NM_015001.2	3085	Acc/Gcc	11/15	0.703982178621292	2	FACETS	0.81	0.744	0.879	0.405	0.372	0.44	CLONAL	1	TRUE	0	0.703982178621292	2		615	505	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596143	43596143	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	549	747	0	ENST00000355710.3:c.310A>T	p.Ser104Cys	p.S104C	ENST00000355710	NM_020975.4	104	Agc/Tgc	2/20	0.703982178621292	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.703982178621292	2		747	687	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716329	18716329	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	85	519	0	ENST00000266497.5:c.3676A>T	p.Thr1226Ser	p.T1226S	ENST00000266497		1226	Aca/Tca	26/31	0.655986983233676	2	FACETS	1	0.914	1	0.509	0.458	0.563	CLONAL	1	TRUE	0	0.703982178621292	2		519	237	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431579	49431579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1435084589	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	182	762	1	ENST00000301067.7:c.9560C>T	p.Ala3187Val	p.A3187V	ENST00000301067	NM_003482.3	3187	gCc/gTc	34/54	0.655986983233676	2	FACETS	0.743	0.688	0.8	0.371	0.344	0.4	SUBCLONAL	1	TRUE	0	0.703982178621292	2		763	696	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864507	57864507	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	166	853	0	ENST00000228682.2:c.1984T>G	p.Cys662Gly	p.C662G	ENST00000228682	NM_005269.2	662	Tgt/Ggt	12/12	0.703982178621292	2	FACETS	0.756	0.697	0.816	0.378	0.348	0.408	SUBCLONAL	1	TRUE	0	0.703982178621292	2		853	624	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225519	133225519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143229302	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	331	700	2	ENST00000320574.5:c.4145G>A	p.Arg1382His	p.R1382H	ENST00000320574	NM_006231.2	1382	cGc/cAc	32/49	0.703982178621292	2	FACETS	1	0.995	1	0.71	0.677	0.743	CLONAL	1	TRUE	0	0.703982178621292	2		702	662	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355756	73355756	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	181	521	0	ENST00000377767.4:c.215T>C	p.Val72Ala	p.V72A	ENST00000377767	NM_014953.3	72	gTg/gCg	1/21	0.693201728580694	1	FACETS	0.581	0.539	0.624	0.581	0.539	0.624	SUBCLONAL	1	TRUE	0	0.703982178621292	1		521	574	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007691	45007691	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	122	535	0	ENST00000558401.1:c.138T>G	p.Tyr46Ter	p.Y46*	ENST00000558401	NM_004048.2	46	taT/taG	2/4	0.703982178621292	1	FACETS	0.867	0.8	0.935	0.867	0.8	0.935	CLONAL	1	TRUE	0	0.703982178621292	1		535	259	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465474	99465474	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs995287825	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	150	750	0	ENST00000268035.6:c.2299G>A	p.Asp767Asn	p.D767N	ENST00000268035	NM_000875.3	767	Gac/Aac	11/21	0.703982178621292	2	FACETS	0.624	0.572	0.678	0.312	0.286	0.339	SUBCLONAL	1	TRUE	0	0.703982178621292	2		750	683	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348235	348235	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	179	881	0	ENST00000262320.3:c.1271A>G	p.Asp424Gly	p.D424G	ENST00000262320	NM_003502.3	424	gAc/gGc	6/11	0.263064662730399	5	FACETS	0.946	0.871	1	0.189	0.174	0.205	INDETERMINATE	1	TRUE	0	0.703982178621292	5		881	1105	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900441	3900441	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	208	845	1	ENST00000262367.5:c.655G>T	p.Gly219Ter	p.G219*	ENST00000262367	NM_004380.2	219	Gga/Tga	2/31	0.263064662730399	5	FACETS	1	0.928	1	0.2	0.185	0.216	INDETERMINATE	1	TRUE	0	0.703982178621292	5		846	1213	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029480	14029480	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs765254949	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	126	619	0	ENST00000311895.7:c.1691A>G	p.Tyr564Cys	p.Y564C	ENST00000311895	NM_005236.2	564	tAt/tGt	8/11	0.263064662730399	5	FACETS	0.996	0.903	1	0.199	0.18	0.219	INDETERMINATE	1	TRUE	0	0.703982178621292	5		619	739	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993390	72993390	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	251	941	1	ENST00000268489.5:c.655T>C	p.Ser219Pro	p.S219P	ENST00000268489	NM_006885.3	219	Tca/Cca	2/10	0.251061622321624	2	FACETS	0.717	0.671	0.765	0.359	0.335	0.383	INDETERMINATE	1	TRUE	0	0.703982178621292	2		942	994	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044563	12044563	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1209244324	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	93	627	0	ENST00000353533.5:c.1186A>G	p.Met396Val	p.M396V	ENST00000353533	NM_003010.3	396	Atg/Gtg	11/11	0.703982178621292	2	FACETS	0.625	0.559	0.694	0.312	0.279	0.347	SUBCLONAL	1	TRUE	0	0.703982178621292	2		627	423	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805693	46805693	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	156	819	0	ENST00000290295.7:c.263A>G	p.Tyr88Cys	p.Y88C	ENST00000290295	NM_006361.5	88	tAc/tGc	1/2	0.703982178621292	2	FACETS	0.641	0.589	0.696	0.321	0.294	0.348	SUBCLONAL	1	TRUE	0	0.703982178621292	2		819	691	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257624	19257624	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1195649670	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	59	895	0	ENST00000162023.5:c.602A>G	p.Tyr201Cys	p.Y201C	ENST00000162023		201	tAc/tGc	10/13	0.703982178621292	2	FACETS	0.199	0.17	0.23	0.099	0.085	0.115	SUBCLONAL	1	TRUE	0	0.703982178621292	2		895	843	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729949	47729949	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	242	557	0	ENST00000449228.1:c.440G>T	p.Gly147Val	p.G147V	ENST00000449228	NM_001127240.2	147	gGg/gTg	3/4	0.703982178621292	2	FACETS	0.817	0.765	0.87	0.408	0.382	0.435	CLONAL	1	TRUE	0	0.703982178621292	2		557	842	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010522	48010549	+	frameshift_variant	Frame_Shift_Del	DEL	GAGCGAGGCTGGGCCTGGGCCCAGGCCC	GAGCGAGGCTGGGCCTGGGCCCAGGCCC	-	novel	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	263	422	0	ENST00000234420.5:c.150_177del	p.Trp50CysfsTer22	p.W50Cfs*22	ENST00000234420	NM_000179.2	50	tgGAGCGAGGCTGGGCCTGGGCCCAGGCCC/tg	1/10	0.703982178621292	2	FACETS	0.849	0.809	0.888	0.849	0.809	0.888	CLONAL	2	TRUE	0	0.703982178621292	2		422	440	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309606	30309606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757071036	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	912	838	2	ENST00000307677.4:c.416G>A	p.Arg139His	p.R139H	ENST00000307677	NM_138578.1	139	cGc/cAc	2/3	0.561167455316325	4	FACETS	0.904	0.88	0.928	0.904	0.88	0.928	CLONAL	3	TRUE	1	0.703982178621292	4		840	1628	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31393149	31393149	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	35	609	1	ENST00000328111.2:c.2237T>C	p.Val746Ala	p.V746A	ENST00000328111	NM_006892.3	746	gTg/gCg	21/23	0.561167455316325	4	FACETS	0.242	0.197	0.292	0.081	0.065	0.098	SUBCLONAL	1	TRUE	1	0.703982178621292	4		610	700	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728807	39728807	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	59	590	1	ENST00000361337.2:c.1087G>A	p.Gly363Ser	p.G363S	ENST00000361337	NM_003286.2	363	Ggc/Agc	12/21	0.561167455316325	4	FACETS	0.273	0.233	0.316	0.091	0.077	0.106	SUBCLONAL	1	TRUE	1	0.703982178621292	4		591	1048	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522476	157522476	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	193	859	0	ENST00000346085.5:c.4748T>G	p.Val1583Gly	p.V1583G	ENST00000346085	NM_020732.3	1583	gTc/gGc	18/20	0.693201728580694	1	FACETS	0.658	0.613	0.704	0.658	0.613	0.704	SUBCLONAL	1	TRUE	0	0.703982178621292	1		859	540	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5462972	5462972	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	534	519	0	ENST00000381577.3:c.533A>G	p.Lys178Arg	p.K178R	ENST00000381577	NM_014143.3	178	aAg/aGg	4/7	0.703982178621292	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.703982178621292	3		519	652	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864041	97864041	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	155	725	1	ENST00000289081.3:c.1625G>T	p.Arg542Ile	p.R542I	ENST00000289081	NM_000136.2	542	aGa/aTa	15/15	0.703982178621292	2	FACETS	0.722	0.664	0.782	0.361	0.332	0.391	SUBCLONAL	1	TRUE	0	0.703982178621292	2		726	610	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0030932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	389	629	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.577021255277132	5	FACETS	1	0.985	1	0.725	0.69	0.761	CLONAL	2	TRUE	2	0.577021255277132	5		629	1156	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0030932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	309	727	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.577021255277132	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.577021255277132	1		727	686	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161479	2161479	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	89	653	0	ENST00000434045.2:c.48A>T	p.Glu16Asp	p.E16D	ENST00000434045	NM_001127598.1	16	gaA/gaT	2/5	0.534344325363821	2	FACETS	0.325	0.287	0.366	0.163	0.143	0.183	SUBCLONAL	1	TRUE	0	0.577021255277132	2		653	949	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165832	47165832	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	92	669	0	ENST00000409792.3:c.294T>A	p.Ser98Arg	p.S98R	ENST00000409792	NM_014159.6	98	agT/agA	3/21	0.577021255277132	1	FACETS	0.356	0.317	0.398	0.356	0.317	0.398	SUBCLONAL	1	TRUE	0	0.577021255277132	1		669	637	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0030934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	320	701	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.418133345789811	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.418133345789811	2		701	738	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339072	225339072	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	108	483	1	ENST00000264414.4:c.2197C>T	p.Arg733Ter	p.R733*	ENST00000264414	NM_003590.4	733	Cga/Tga	16/16	0.402535638659159	3	FACETS	0.939	0.844	1	0.47	0.422	0.52	CLONAL	1	TRUE	1	0.418133345789811	3		484	665	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249012	55249013	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGG	novel	NA	P-0030934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	522	600	0	ENST00000275493.2:c.2310_2311insGGG	p.Asp770_Asn771insGly	p.D770_N771insG	ENST00000275493	NM_005228.3	770	-/GGG	20/28	0.418133345789811	7	FACETS	1	0.992	1	0.896	0.862	0.93	CLONAL	4	TRUE	2	0.418133345789811	7		600	1140	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625398	69625398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1408695395	NA	P-0030934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2375	129	741	4	ENST00000334134.2:c.395G>A	p.Arg132Gln	p.R132Q	ENST00000334134	NM_005247.2	132	cGg/cAg	3/3	0.418133345789811	14	FACETS	0.865	0.78	0.955			1	CLONAL	1	TRUE	NA	0.418133345789811	14		745	2504	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066842	77066842	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs887262054	NA	P-0030934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	121	460	0	ENST00000356341.3:c.643C>T	p.Arg215Trp	p.R215W	ENST00000356341	NM_002576.4	215	Cgg/Tgg	7/15	0.402535638659159	3	FACETS	1	0.963	1	0.562	0.508	0.617	CLONAL	1	TRUE	1	0.418133345789811	3		460	623	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	430224	430224	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	125	535	0	ENST00000399788.2:c.2478G>C	p.Leu826Phe	p.L826F	ENST00000399788	NM_001042603.1	826	ttG/ttC	18/28	0.354482428288477	3	FACETS	1	0.969	1			1	CLONAL	1	TRUE	NA	0.418133345789811	3		535	626	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2214534	2214536	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0030934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	155	720	0	ENST00000398665.3:c.1864_1866del	p.Glu622del	p.E622del	ENST00000398665	NM_032482.2	621	aAGGag/aag	19/28	0.337166997150614	4	FACETS	0.974	0.891	1	0.487	0.445	0.531	CLONAL	1	TRUE	2	0.418133345789811	4		720	1079	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462416	89462431	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTAACCACAATGACC	GGTAACCACAATGACC	-	novel	NA	P-0030934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	110	645	0	ENST00000336596.2:c.1888_1888+15del		p.X630_splice	ENST00000336596	NM_005233.5	630		10/17	0.418133345789811	2	FACETS	0.834	0.751	0.922	0.417	0.375	0.461	CLONAL	1	TRUE	0	0.418133345789811	2		645	631	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0030935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	162	846	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.176681815449597	6	FACETS	0.994	0.927	1			1	INDETERMINATE	4	TRUE	NA	0.447765219742256	6		846	345	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293449	1293449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs551522837	NA	P-0030935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	23	628	2	ENST00000310581.5:c.1552G>A	p.Ala518Thr	p.A518T	ENST00000310581	NM_198253.2	518	Gct/Act	2/16	0.358768551208002	3	FACETS	0.59	0.462	0.737	0.197	0.154	0.246	SUBCLONAL	1	TRUE	0	0.447765219742256	3		630	213	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746132	162746132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1374086542	NA	P-0030935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	27	380	0	ENST00000367921.3:c.2255G>A	p.Arg752His	p.R752H	ENST00000367921	NM_006182.2	752	cGc/cAc	16/18	0.449456858731516	3	FACETS	0.533	0.425	0.655	0.266	0.212	0.328	SUBCLONAL	1	TRUE	1	0.447765219742256	3		380	277	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21565467	21565467	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	43	756	0	ENST00000382592.4:c.419G>C	p.Gly140Ala	p.G140A	ENST00000382592	NM_014572.2	140	gGc/gCc	3/8	1	2	FACETS	0.756	0.637	0.886	0.756	0.637	0.886	SUBCLONAL	1	TRUE	1	0.447765219742256	2		756	254	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347505	91347505	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	62	727	0	ENST00000355112.3:c.3667A>G	p.Thr1223Ala	p.T1223A	ENST00000355112	NM_000057.2	1223	Aca/Gca	19/22	0.449456858731516	5	FACETS	1	0.942	1	0.388	0.336	0.443	CLONAL	1	TRUE	2	0.447765219742256	5		727	398	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350623	15350623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	36	799	0	ENST00000263377.2:c.3292G>A	p.Ala1098Thr	p.A1098T	ENST00000263377	NM_058243.2	1098	Gct/Act	16/20	0.343209134129164	4	FACETS	0.823	0.679	0.982	0.411	0.339	0.491	CLONAL	1	TRUE	2	0.447765219742256	4		799	283	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661797	227661797	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	21	743	0	ENST00000305123.5:c.1658A>T	p.Glu553Val	p.E553V	ENST00000305123	NM_005544.2	553	gAg/gTg	1/2	1	2	FACETS	0.447	0.345	0.564	0.447	0.345	0.564	SUBCLONAL	1	TRUE	1	0.447765219742256	2		743	210	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31437406	31437406	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0030935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	46	678	0	ENST00000344624.3:c.2883-1G>T		p.X961_splice	ENST00000344624		961			0.358768551208002	3	FACETS	0.85	0.719	0.991	0.283	0.239	0.331	CLONAL	1	TRUE	0	0.447765219742256	3		678	296	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	49	270	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.975	0.83	1	0.975	0.83	1	CLONAL	1	TRUE	1	0.3	2		270	335	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0030939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	112	689	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.892	0.802	0.988	0.892	0.802	0.988	CLONAL	1	TRUE	1	0.3	2		690	837	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381541	81381541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	76	404	0	ENST00000222390.5:c.520G>A	p.Glu174Lys	p.E174K	ENST00000222390	NM_000601.4	174	Gaa/Aaa	5/18	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.3	2		404	451	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735503	40735503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763584414	NA	P-0030939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	101	584	2	ENST00000373198.4:c.3370G>A	p.Glu1124Lys	p.E1124K	ENST00000373198	NM_133170.3	1124	Gag/Aag	25/32	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.3	2		586	667	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727443	66727443	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	82	513	0	ENST00000307102.5:c.159T>A	p.Phe53Leu	p.F53L	ENST00000307102	NM_002755.3	53	ttT/ttA	2/11	1	2	FACETS	0.849	0.749	0.956	0.849	0.749	0.956	CLONAL	1	TRUE	1	0.3	2		513	644	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274121	10274121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	67	599	0	ENST00000330684.3:c.148G>A	p.Glu50Lys	p.E50K	ENST00000330684	NM_001134407.1	50	Gaa/Aaa	2/13	1	2	FACETS	0.766	0.666	0.874	0.766	0.666	0.874	SUBCLONAL	1	TRUE	1	0.3	2		599	583	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193889	106193889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1395976555	NA	P-0030939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	80	472	0	ENST00000380013.4:c.4351C>T	p.Arg1451Trp	p.R1451W	ENST00000380013	NM_001127208.2	1451	Cgg/Tgg	10/11	1	2	FACETS	0.934	0.823	1	0.934	0.823	1	CLONAL	1	TRUE	1	0.3	2		472	571	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158134	47158134	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	127	681	0	ENST00000409792.3:c.4565A>G	p.Asn1522Ser	p.N1522S	ENST00000409792	NM_014159.6	1522	aAt/aGt	4/21	1	2	FACETS	0.867	0.784	0.954	0.867	0.784	0.954	CLONAL	1	TRUE	1	0.3	2		681	977	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499814	8499814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750362550	NA	P-0030939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	100	570	0	ENST00000356435.5:c.2155G>A	p.Glu719Lys	p.E719K	ENST00000356435		719	Gag/Aag	14/35	0.295216667207892	1	FACETS	0.923	0.826	1	0.923	0.826	1	CLONAL	1	TRUE	0	0.3	1		570	614	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913449	32913449	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782186	NA	P-0030939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	126	743	0	ENST00000380152.3:c.4957A>G	p.Thr1653Ala	p.T1653A	ENST00000380152		1653	Act/Gct	11/27	1	2	FACETS	0.896	0.811	0.987	0.896	0.811	0.987	CLONAL	1	TRUE	1	0.3	2		743	937	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986887	36986887	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	63	334	0	ENST00000354822.5:c.802G>A	p.Gly268Ser	p.G268S	ENST00000354822	NM_001079668.2	268	Ggc/Agc	3/3	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.3	2		334	322	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211154	36211154	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	148	983	1	ENST00000222270.7:c.905C>A	p.Pro302His	p.P302H	ENST00000222270	NM_014727.1	302	cCc/cAc	3/37	1	2	FACETS	0.961	0.876	1	0.961	0.876	1	CLONAL	1	TRUE	1	0.3	2		984	1027	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227887	36227887	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	91	779	1	ENST00000222270.7:c.7372G>A	p.Gly2458Arg	p.G2458R	ENST00000222270	NM_014727.1	2458	Gga/Aga	32/37	1	2	FACETS	0.81	0.719	0.907	0.81	0.719	0.907	CLONAL	1	TRUE	1	0.3	2		780	749	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39233650	39233650	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	100	597	0	ENST00000402219.2:c.2694del	p.Ile900PhefsTer2	p.I900Ffs*2	ENST00000402219	NM_005633.3	898	aaG/aa	17/23	1	2	FACETS	0.946	0.845	1	0.946	0.845	1	CLONAL	1	TRUE	1	0.3	2		597	705	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624937	9624937	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	84	433	0	ENST00000353224.5:c.40C>T	p.Pro14Ser	p.P14S	ENST00000353224	NM_177990.2	14	Ccg/Tcg	3/10	1	2	FACETS	0.976	0.863	1	0.976	0.863	1	CLONAL	1	TRUE	1	0.3	2		433	574	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513494	41513494	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	117	674	0	ENST00000263253.7:c.398C>A	p.Ser133Tyr	p.S133Y	ENST00000263253	NM_001429.3	133	tCt/tAt	2/31	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.3	2		674	769	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725555	117725555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	117	615	0	ENST00000368508.3:c.326C>T	p.Ser109Phe	p.S109F	ENST00000368508	NM_002944.2	109	tCc/tTc	5/43	0.295216667207892	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	0	0.3	1		615	661	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69032449	69032449	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	137	738	0	ENST00000288368.4:c.3523C>T	p.Leu1175Phe	p.L1175F	ENST00000288368	NM_024870.2	1175	Ctc/Ttc	29/40	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.3	2		738	886	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	500	695	8	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	0.423231416500863	3	FACETS	0.943	0.905	0.981	0.943	0.905	0.981	CLONAL	2	TRUE	1	0.591741204439712	3		703	1161	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0030940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	631	651	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.591741204439712	2	FACETS	0.986	0.956	1	0.986	0.956	1	CLONAL	2	TRUE	0	0.591741204439712	2		651	1081	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851354	156851354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1324983370	NA	P-0030940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	898	773	22	ENST00000524377.1:c.2311C>T	p.Arg771Cys	p.R771C	ENST00000524377	NM_002529.3	771	Cgc/Tgc	17/17	0.591741204439712	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	1	0.591741204439712	4		795	1545	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68984801	68984801	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	334	617	4	ENST00000288368.4:c.1565C>T	p.Ala522Val	p.A522V	ENST00000288368	NM_024870.2	522	gCa/gTa	14/40	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.591741204439712	2		621	879	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27220119	27220119	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	335	699	3	ENST00000380036.4:c.3176A>G	p.Lys1059Arg	p.K1059R	ENST00000380036	NM_000459.3	1059	aAg/aGg	21/23	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.591741204439712	2		702	1047	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229535	5229549	+	inframe_deletion	In_Frame_Del	DEL	CGGCGGCCCGCGGGC	CGGCGGCCCGCGGGC	-	novel	NA	P-0030941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	57	98	0	ENST00000357368.4:c.2302_2316del	p.Ala768_Pro772del	p.A768_P772del	ENST00000357368	NM_002850.3	768	GCCCGCGGGCCGCCG/-	15/38	0.249134606754556	3	FACETS	0.871	0.759	0.988	1	0.962	1	CLONAL	3	TRUE	1	0.249134606754556	3		98	197	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	194	459	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.315364695317339	5	FACETS	0.94	0.879	1			1	CLONAL	3	TRUE	NA	0.501076359972323	5		459	481	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	216	407	16	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	0.501076359972323	2	FACETS	0.982	0.925	1	0.982	0.925	1	CLONAL	2	TRUE	0	0.501076359972323	2		423	439	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	66	551	4	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	0.454759402878906	4	FACETS	0.786	0.684	0.897	0.393	0.342	0.449	SUBCLONAL	1	TRUE	2	0.501076359972323	4		555	503	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	170	622	6	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.881	0.822	0.941	1	0.992	1	CLONAL	2	TRUE	1	0.501076359972323	2		628	385	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	176	656	9	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	0.255762968813501	3	FACETS	0.818	0.759	0.879	0.545	0.506	0.586	INDETERMINATE	2	TRUE	0	0.501076359972323	3		665	537	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	67	581	1	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	0.136660163828535	5	FACETS	1	0.912	1	0.265	0.231	0.302	INDETERMINATE	1	TRUE	1	0.501076359972323	5		582	442	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354008	15354008	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	14	282	3	ENST00000263377.2:c.2872del	p.Leu958CysfsTer110	p.L958Cfs*110	ENST00000263377	NM_058243.2	958	Ctg/tg	14/20	1	2	FACETS	0.482	0.351	0.636	0.482	0.351	0.636	SUBCLONAL	1	TRUE	1	0.501076359972323	2		285	116	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468382	89468382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs570346631	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	95	231	0	ENST00000336596.2:c.1916G>A	p.Arg639His	p.R639H	ENST00000336596	NM_005233.5	639	cGc/cAc	11/17	0.403487016830073	3	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	1	0.501076359972323	3		231	221	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	78	282	2	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	0.219453789268328	0	FACETS	0.465	0.412	0.521			1	INDETERMINATE	1	TRUE	0	0.501076359972323	0		284	334	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255142	16255143	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	rs764595221	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	105	473	3	ENST00000375759.3:c.2417_2418del	p.Arg806ThrfsTer14	p.R806Tfs*14	ENST00000375759	NM_015001.2	803	GAg/g	11/15	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.501076359972323	2		476	413	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	74	468	1	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.874	0.771	0.983	0.874	0.771	0.983	CLONAL	1	TRUE	1	0.501076359972323	2		469	338	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133269	30133269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778826879	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	112	650	0	ENST00000263025.4:c.229G>A	p.Glu77Lys	p.E77K	ENST00000263025	NM_002746.2	77	Gaa/Aaa	2/9	1	2	FACETS	0.866	0.783	0.954	0.866	0.783	0.954	CLONAL	1	TRUE	1	0.501076359972323	2		650	516	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962854	2962854	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	62	725	3	ENST00000396946.4:c.2054del	p.Gly685AlafsTer31	p.G685Afs*31	ENST00000396946	NM_032415.4	685	gGc/gc	16/25	0.136660163828535	5	FACETS	1	0.898	1	0.26	0.225	0.298	INDETERMINATE	1	TRUE	1	0.501076359972323	5		728	416	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106926	11106928	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs876657378	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	34	658	0	ENST00000358026.2:c.1636_1638del	p.Lys546del	p.K546del	ENST00000358026	NM_001128849.1	544	cAGAag/cag	10/36	1	2	FACETS	0.239	0.194	0.289	0.239	0.194	0.289	SUBCLONAL	1	TRUE	1	0.501076359972323	2		658	568	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200629	67200629	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1034596803	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	83	687	0	ENST00000312629.5:c.740A>G	p.Asn247Ser	p.N247S	ENST00000312629	NM_003952.2	247	aAc/aGc	9/15	1	2	FACETS	0.706	0.626	0.792	0.706	0.626	0.792	SUBCLONAL	1	TRUE	1	0.501076359972323	2		687	469	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498235	498235	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	11	234	0	ENST00000399788.2:c.23del	p.Gly8AlafsTer58	p.G8Afs*58	ENST00000399788	NM_001042603.1	8	gGc/gc	1/28	0.136660163828535	5	FACETS	0.359	0.248	0.498	0.09	0.062	0.125	INDETERMINATE	1	TRUE	1	0.501076359972323	5		234	214	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965013	25965013	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs190294224	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	212	445	0	ENST00000435504.4:c.4193C>T	p.Ser1398Leu	p.S1398L	ENST00000435504		1398	tCg/tTg	13/13	0.501076359972323	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	0	0.501076359972323	2		445	420	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800902	120800903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs748469666	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	131	649	5	ENST00000257552.2:c.345dup	p.Leu116AlafsTer15	p.L116Afs*15	ENST00000257552	NM_002442.3	115	-/G	6/15	0.255762968813501	3	FACETS	0.886	0.805	0.971	0.295	0.268	0.324	INDETERMINATE	1	TRUE	0	0.501076359972323	3		654	738	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	187	643	6	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	0.499568590127095	4	FACETS	1	0.965	1	0.705	0.656	0.754	CLONAL	2	TRUE	1	0.501076359972323	4		649	530	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599271	28599271	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs770146088	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	41	718	0	ENST00000253063.3:c.722del	p.Pro241GlnfsTer6	p.P241Qfs*6	ENST00000253063	NM_031459.4	239	agC/ag	5/10	1	2	FACETS	0.279	0.232	0.332	0.279	0.232	0.332	SUBCLONAL	1	TRUE	1	0.501076359972323	2		718	586	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370686	225370686	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1232071537	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	32	394	1	ENST00000264414.4:c.1193del	p.Lys398ArgfsTer6	p.K398Rfs*6	ENST00000264414	NM_003590.4	398	aAg/ag	8/16	0.391185557675253	3	FACETS	0.668	0.545	0.805	0.223	0.181	0.269	SUBCLONAL	1	TRUE	0	0.501076359972323	3		395	239	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158764	26158764	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	52	683	0	ENST00000289316.2:c.367A>G	p.Thr123Ala	p.T123A	ENST00000289316	NM_138720.2	123	Acc/Gcc	1/2	0.502406606587131	4	FACETS	0.382	0.324	0.446	0.191	0.162	0.223	SUBCLONAL	1	TRUE	2	0.501076359972323	4		683	815	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780286	9780286	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	61	513	0	ENST00000377346.4:c.1456C>A	p.Pro486Thr	p.P486T	ENST00000377346	NM_005026.3	486	Ccc/Acc	11/24	1	2	FACETS	0.768	0.667	0.876	0.768	0.667	0.876	SUBCLONAL	1	TRUE	1	0.501076359972323	2		513	317	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943750	71943750	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780875030	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	109	697	0	ENST00000298229.2:c.1793G>A	p.Arg598His	p.R598H	ENST00000298229	NM_001567.3	598	cGt/cAt	15/28	1	2	FACETS	0.837	0.754	0.923	0.837	0.754	0.923	CLONAL	1	TRUE	1	0.501076359972323	2		697	520	SUCCESS
BLM	641	MSKCC	GRCh37	15	91308555	91308555	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	40	442	0	ENST00000355112.3:c.2104C>A	p.Pro702Thr	p.P702T	ENST00000355112	NM_000057.2	702	Cct/Act	9/22	1	2	FACETS	0.448	0.373	0.532	0.448	0.373	0.532	SUBCLONAL	1	TRUE	1	0.501076359972323	2		442	356	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223075	5223075	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1369452734	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	72	656	0	ENST00000357368.4:c.2728C>T	p.Arg910Cys	p.R910C	ENST00000357368	NM_002850.3	910	Cgc/Tgc	18/38	0.219453789268328	0	FACETS	0.441	0.388	0.497			1	INDETERMINATE	1	TRUE	0	0.501076359972323	0		656	325	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791730	42791730	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	102	577	1	ENST00000575354.2:c.616G>A	p.Ala206Thr	p.A206T	ENST00000575354	NM_015125.3	206	Gcc/Acc	5/20	1	2	FACETS	0.919	0.827	1	0.919	0.827	1	CLONAL	1	TRUE	1	0.501076359972323	2		578	443	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416436	29416436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765034301	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	230	690	0	ENST00000389048.3:c.4517C>T	p.Thr1506Met	p.T1506M	ENST00000389048	NM_004304.4	1506	aCg/aTg	29/29	0.501076359972323	2	FACETS	0.871	0.82	0.922	0.871	0.82	0.922	CLONAL	2	TRUE	0	0.501076359972323	2		690	527	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917788	29917788	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	206	651	0	ENST00000389048.3:c.880C>T	p.Pro294Ser	p.P294S	ENST00000389048	NM_004304.4	294	Ccc/Tcc	3/29	0.501076359972323	2	FACETS	0.936	0.88	0.993	0.936	0.88	0.993	CLONAL	2	TRUE	0	0.501076359972323	2		651	439	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665402	182665402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	39	396	0	ENST00000292782.4:c.539C>T	p.Ala180Val	p.A180V	ENST00000292782	NM_020640.2	180	gCc/gTc	5/7	0.403487016830073	3	FACETS	0.735	0.612	0.869	0.367	0.306	0.435	SUBCLONAL	1	TRUE	1	0.501076359972323	3		396	265	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38943062	38943062	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	51	326	0	ENST00000357387.3:c.4925A>C	p.Lys1642Thr	p.K1642T	ENST00000357387	NM_152756.3	1642	aAg/aCg	37/38	0.474992470154531	2	FACETS	0.942	0.811	1	0.471	0.405	0.542	CLONAL	1	TRUE	0	0.501076359972323	2		326	216	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80160684	80160684	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs973992111	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	86	700	0	ENST00000265081.6:c.3059del	p.Asn1020IlefsTer40	p.N1020Ifs*40	ENST00000265081	NM_002439.4	1018	gAa/ga	22/24	0.345990813406989	3	FACETS	0.958	0.852	1	0.319	0.284	0.357	CLONAL	1	TRUE	0	0.501076359972323	3		700	448	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405820	157405821	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	71	389	0	ENST00000346085.5:c.2063_2064del	p.Leu688ProfsTer74	p.L688Pfs*74	ENST00000346085	NM_020732.3	688	CTc/c	6/20	0.136660163828535	5	FACETS	0.771	0.678	0.869	0.385	0.339	0.435	INDETERMINATE	2	TRUE	1	0.501076359972323	5		389	322	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729663	41729663	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	45	502	0	ENST00000242208.4:c.866A>G	p.His289Arg	p.H289R	ENST00000242208	NM_002192.2	289	cAc/cGc	3/3	0.136660163828535	5	FACETS	0.835	0.703	0.979	0.209	0.175	0.245	INDETERMINATE	1	TRUE	1	0.501076359972323	5		502	377	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494142	140494142	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	181	759	0	ENST00000288602.6:c.1106T>C	p.Val369Ala	p.V369A	ENST00000288602	NM_004333.4	369	gTg/gCg	8/18	0.340422871586086	4	FACETS	0.96	0.891	1	0.96	0.891	1	CLONAL	2	TRUE	2	0.501076359972323	4		759	565	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993640	90993640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	89	367	0	ENST00000265433.3:c.283del	p.Asp95MetfsTer14	p.D95Mfs*14	ENST00000265433	NM_002485.4	95	Gat/at	3/16	0.491338351325236	4	FACETS	0.997	0.886	1	0.332	0.295	0.372	CLONAL	1	TRUE	1	0.501076359972323	4		367	535	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741658	145741658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770138627	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	102	656	0	ENST00000428558.2:c.845C>T	p.Ala282Val	p.A282V	ENST00000428558	NM_004260.3	282	gCt/gTt	5/22	0.491338351325236	4	FACETS	0.923	0.827	1	0.308	0.275	0.342	CLONAL	1	TRUE	1	0.501076359972323	4		656	662	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966718	44966718	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	161	315	0	ENST00000377967.4:c.3945del	p.Glu1316ArgfsTer40	p.E1316Rfs*40	ENST00000377967	NM_021140.2	1314	ggA/gg	27/29	0.502406606587131	2	FACETS	0.84	0.792	0.887			1	CLONAL	3	TRUE	NA	0.501076359972323	2		315	255	SUCCESS
AR	367	MSKCC	GRCh37	X	66765131	66765131	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	38	207	0	ENST00000374690.3:c.143C>T	p.Ala48Val	p.A48V	ENST00000374690	NM_000044.3	48	gCa/gTa	1/8	0.502406606587131	2	FACETS	1	0.924	1			1	CLONAL	1	TRUE	NA	0.501076359972323	2		207	130	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	179	270	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.543976209856907	2		270	648	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888210	112888210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121918464	NA	P-0030954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	197	564	0	ENST00000351677.2:c.226G>A	p.Glu76Lys	p.E76K	ENST00000351677	NM_002834.3	76	Gag/Aag	3/16	1	2	FACETS	0.819	0.759	0.881	0.819	0.759	0.881	CLONAL	1	TRUE	1	0.543976209856907	2		564	884	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670026	29670026	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0030954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	119	365	0	ENST00000356175.3:c.7000-1G>A		p.X2334_splice	ENST00000356175	NM_000267.3	2334			1	2	FACETS	0.9	0.817	0.987	0.9	0.817	0.987	CLONAL	1	TRUE	1	0.543976209856907	2		365	486	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685296	89685296	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	68	329	0	ENST00000371953.3:c.191A>C	p.His64Pro	p.H64P	ENST00000371953	NM_000314.4	64	cAt/cCt	3/9	0.543976209856907	1	FACETS	0.968	0.859	1	0.968	0.859	1	CLONAL	1	TRUE	0	0.543976209856907	1		329	188	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528505	29528505	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0030954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	125	448	0	ENST00000356175.3:c.1260+2T>C		p.X420_splice	ENST00000356175	NM_000267.3	420			1	2	FACETS	0.997	0.909	1	0.997	0.909	1	CLONAL	1	TRUE	1	0.543976209856907	2		448	461	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253767	153253769	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0030956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	61	324	0	ENST00000281708.4:c.964_966del	p.Arg322del	p.R322del	ENST00000281708	NM_033632.3	322	AGA/-	6/12	0.341346666185772	1	FACETS	0.823	0.714	0.941	0.823	0.714	0.941	CLONAL	1	TRUE	0	0.341346666185772	1		324	360	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564620	86564636	+	frameshift_variant	Frame_Shift_Del	DEL	AAACTGCCCACTTCGTT	AAACTGCCCACTTCGTT	-	novel	NA	P-0030956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	136	695	0	ENST00000274376.6:c.352_368del	p.Lys118AlafsTer3	p.K118Afs*3	ENST00000274376	NM_002890.2	118	AAACTGCCCACTTCGTTg/g	1/25	0.341346666185772	1	FACETS	0.948	0.864	1	0.948	0.864	1	CLONAL	1	TRUE	0	0.341346666185772	1		695	697	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0030957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	130	491	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.331359509283864	2		491	650	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0030958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	897	616	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.779022679288687	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.779138977427049	3		616	1040	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339535	81339535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1192583398	NA	P-0030958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	218	394	1	ENST00000222390.5:c.1469C>T	p.Thr490Met	p.T490M	ENST00000222390	NM_000601.4	490	aCg/aTg	13/18	0.321573036288723	5	FACETS	0.866	0.815	0.917	0.866	0.815	0.917	INDETERMINATE	3	TRUE	2	0.779138977427049	5		395	467	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533650	63533650	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	248	584	0	ENST00000307078.5:c.1504G>C	p.Gly502Arg	p.G502R	ENST00000307078	NM_004655.3	502	Ggc/Cgc	6/11	0.779022679288687	3	FACETS	0.995	0.932	1	0.332	0.31	0.354	CLONAL	1	TRUE	0	0.779138977427049	3		584	889	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009080	27009080	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	74	209	0	ENST00000335756.4:c.16C>G	p.Arg6Gly	p.R6G	ENST00000335756	NM_001809.3	6	Cgg/Ggg	1/5	1	2	FACETS	0.95	0.848	1	0.95	0.848	1	CLONAL	1	TRUE	1	0.779138977427049	2		209	200	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747916	41747916	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	191	439	0	ENST00000226382.2:c.853G>T	p.Asp285Tyr	p.D285Y	ENST00000226382	NM_003924.3	285	Gat/Tat	3/3	0.772539184233593	3	FACETS	0.738	0.683	0.796	0.369	0.341	0.398	SUBCLONAL	1	TRUE	1	0.779138977427049	3		439	923	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370817	55370817	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	132	575	0	ENST00000297316.4:c.119G>C	p.Gly40Ala	p.G40A	ENST00000297316	NM_022454.3	40	gGg/gCg	1/2	0.760430072431953	3	FACETS	0.674	0.612	0.738	0.337	0.306	0.369	SUBCLONAL	1	TRUE	1	0.779138977427049	3		575	699	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	54	193	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.74	0.633	0.858	0.74	0.633	0.858	SUBCLONAL	1	TRUE	1	0.282156230034043	2		193	517	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	79	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.282156230034043	2		336	516	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	82	610	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.959	0.847	1	0.959	0.847	1	CLONAL	1	TRUE	1	0.282156230034043	2		611	606	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	124	287	0	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	0.991	1	CLONAL	2	TRUE	1	0.282156230034043	2		287	407	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554345	141554345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748399150	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	113	719	4	ENST00000220592.5:c.1806del	p.Ala603ProfsTer92	p.A603Pfs*92	ENST00000220592	NM_012154.3	602	ccC/cc	14/19	1	2	FACETS	0.906	0.815	1	0.906	0.815	1	CLONAL	1	TRUE	1	0.282156230034043	2		723	884	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	89	468	1	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.282156230034043	2		469	559	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007620	45007620	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs111947448	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	37	223	0	ENST00000558401.1:c.68-1G>T		p.X23_splice	ENST00000558401	NM_004048.2	23			1	2	FACETS	0.914	0.757	1	0.914	0.757	1	CLONAL	1	TRUE	1	0.282156230034043	2		223	287	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023598	31023598	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200702600	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	77	563	0	ENST00000375687.4:c.3083C>T	p.Ser1028Leu	p.S1028L	ENST00000375687	NM_015338.5	1028	tCg/tTg	13/13	1	2	FACETS	0.861	0.756	0.974	0.861	0.756	0.974	CLONAL	1	TRUE	1	0.282156230034043	2		563	634	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	35	340	0	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	0.695	0.57	0.834	0.695	0.57	0.834	SUBCLONAL	1	TRUE	1	0.282156230034043	2		340	357	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753988	57753988	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	48	303	1	ENST00000274289.3:c.636del	p.Phe212LeufsTer8	p.F212Lfs*8	ENST00000274289	NM_006622.3	212	ttT/tt	5/14	1	2	FACETS	0.789	0.668	0.922	0.789	0.668	0.922	CLONAL	1	TRUE	1	0.282156230034043	2		304	431	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477184	67477184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1320208623	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	66	385	0	ENST00000327367.4:c.991G>A	p.Val331Ile	p.V331I	ENST00000327367	NM_005902.3	331	Gtc/Atc	7/9	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.282156230034043	2		385	421	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678783	52678784	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	54	298	0	ENST00000394830.3:c.835dup	p.Ile279AsnfsTer8	p.I279Nfs*8	ENST00000394830	NM_018313.4	279	ata/aAta	9/30	1	2	FACETS	0.804	0.688	0.931	0.804	0.688	0.931	CLONAL	1	TRUE	1	0.282156230034043	2		298	476	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938230	76938230	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	94	556	5	ENST00000373344.5:c.2518del	p.Arg840GlufsTer29	p.R840Efs*29	ENST00000373344	NM_000489.3	840	Aga/ga	9/35	1	2	FACETS	0.944	0.84	1	0.944	0.84	1	CLONAL	1	TRUE	1	0.282156230034043	2		561	706	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830859	3830859	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	64	477	0	ENST00000262367.5:c.1697C>T	p.Ser566Phe	p.S566F	ENST00000262367	NM_004380.2	566	tCc/tTc	8/31	1	2	FACETS	0.728	0.63	0.834	0.728	0.63	0.834	SUBCLONAL	1	TRUE	1	0.282156230034043	2		477	623	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007689	45007690	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	75	360	0	ENST00000558401.1:c.137_138del	p.Tyr46CysfsTer10	p.Y46Cfs*10	ENST00000558401	NM_004048.2	46	TAt/t	2/4	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.282156230034043	2		360	474	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928873	44928873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376210390	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	67	377	0	ENST00000377967.4:c.1973G>A	p.Arg658Gln	p.R658Q	ENST00000377967	NM_021140.2	658	cGa/cAa	17/29	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.282156230034043	2		377	469	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438238	56438238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	109	545	0	ENST00000407977.2:c.755G>A	p.Cys252Tyr	p.C252Y	ENST00000407977		252	tGc/tAc	7/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.282156230034043	2		545	544	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	359972	359972	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	83	536	0	ENST00000262320.3:c.1116+1G>A		p.X372_splice	ENST00000262320	NM_003502.3	372			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.282156230034043	2		536	490	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863054	56863054	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1266824391	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	90	545	2	ENST00000519728.1:c.327del	p.Glu110LysfsTer15	p.E110Kfs*15	ENST00000519728	NM_002350.3	107	acA/ac	5/13	1	2	FACETS	0.975	0.866	1	0.975	0.866	1	CLONAL	1	TRUE	1	0.282156230034043	2		547	654	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509883	187509883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769964561	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	34	305	0	ENST00000441802.2:c.13630G>A	p.Ala4544Thr	p.A4544T	ENST00000441802	NM_005245.3	4544	Gcc/Acc	27/27	1	2	FACETS	0.777	0.637	0.934	0.777	0.637	0.934	CLONAL	1	TRUE	1	0.282156230034043	2		305	310	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61213502	61213502	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778585796	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	87	423	3	ENST00000301761.2:c.460C>T	p.Arg154Cys	p.R154C	ENST00000301761	NM_017841.2	154	Cgt/Tgt	4/4	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.282156230034043	2		426	565	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970916	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	117	622	0	ENST00000265081.6:c.1147_1148del	p.Lys383GlyfsTer20	p.K383Gfs*20	ENST00000265081	NM_002439.4	381	AAa/a	7/24	1	2	FACETS	0.954	0.86	1	0.954	0.86	1	CLONAL	1	TRUE	1	0.282156230034043	2		622	869	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748488	162748488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs565955901	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	65	311	0	ENST00000367921.3:c.2402C>T	p.Thr801Ile	p.T801I	ENST00000367921	NM_006182.2	801	aCt/aTt	17/18	0.267767755493339	3	FACETS	1	0.941	1	0.574	0.499	0.655	CLONAL	1	TRUE	1	0.282156230034043	3		311	458	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253478	226253478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	48	289	1	ENST00000366813.1:c.250C>T	p.Arg84Cys	p.R84C	ENST00000366813		84	Cgc/Tgc	2/3	0.267767755493339	3	FACETS	0.995	0.844	1	0.498	0.422	0.581	CLONAL	1	TRUE	1	0.282156230034043	3		290	390	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680510	241680510	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	168	433	1	ENST00000366560.3:c.239A>T	p.Lys80Met	p.K80M	ENST00000366560	NM_000143.3	80	aAg/aTg	2/10	0.267767755493339	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.282156230034043	3		434	636	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533578	533578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1342261234	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	89	601	0	ENST00000451590.1:c.325G>A	p.Val109Met	p.V109M	ENST00000451590	NM_001130442.1	109	Gtg/Atg	4/5	1	2	FACETS	0.954	0.847	1	0.954	0.847	1	CLONAL	1	TRUE	1	0.282156230034043	2		601	661	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039408	49039408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374523971	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	106	570	1	ENST00000267163.4:c.2393G>A	p.Arg798Gln	p.R798Q	ENST00000267163	NM_000321.2	798	cGg/cAg	23/27	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.282156230034043	2		571	704	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713277	43713277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200691218	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	137	734	1	ENST00000382044.4:c.4196C>T	p.Thr1399Met	p.T1399M	ENST00000382044	NM_001141980.1	1399	aCg/aTg	20/28	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.282156230034043	2		735	838	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829866	72829866	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	109	633	0	ENST00000268489.5:c.6715T>C	p.Trp2239Arg	p.W2239R	ENST00000268489	NM_006885.3	2239	Tgg/Cgg	9/10	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.282156230034043	2		633	709	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337247	89337247	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	81	462	0	ENST00000301030.4:c.7784A>G	p.Asp2595Gly	p.D2595G	ENST00000301030	NM_001256183.1	2595	gAt/gGt	12/13	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.282156230034043	2		462	531	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346789	89346789	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	31	405	0	ENST00000301030.4:c.6161C>T	p.Ala2054Val	p.A2054V	ENST00000301030	NM_001256183.1	2054	gCt/gTt	9/13	1	2	FACETS	0.695	0.564	0.844	0.695	0.564	0.844	SUBCLONAL	1	TRUE	1	0.282156230034043	2		405	316	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89354986	89354986	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	103	614	1	ENST00000301030.4:c.694C>A	p.Leu232Ile	p.L232I	ENST00000301030	NM_001256183.1	232	Cta/Ata	7/13	1	2	FACETS	0.983	0.88	1	0.983	0.88	1	CLONAL	1	TRUE	1	0.282156230034043	2		615	743	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39570501	39570501	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs759533616	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	36	246	0	ENST00000262039.4:c.697A>G	p.Ile233Val	p.I233V	ENST00000262039	NM_002647.2	233	Att/Gtt	6/25	1	2	FACETS	0.931	0.769	1	0.931	0.769	1	CLONAL	1	TRUE	1	0.282156230034043	2		246	274	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267482	7267482	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	94	530	0	ENST00000302850.5:c.526A>G	p.Lys176Glu	p.K176E	ENST00000302850	NM_000208.2	176	Aaa/Gaa	2/22	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.282156230034043	2		530	637	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600462	10600462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	134	617	1	ENST00000171111.5:c.1393G>A	p.Val465Met	p.V465M	ENST00000171111	NM_203500.1	465	Gtg/Atg	4/6	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.282156230034043	2		618	686	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281176	15281176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	92	811	1	ENST00000263388.2:c.5080C>T	p.Arg1694Trp	p.R1694W	ENST00000263388	NM_000435.2	1694	Cgg/Tgg	27/33	1	2	FACETS	0.908	0.807	1	0.908	0.807	1	CLONAL	1	TRUE	1	0.282156230034043	2		812	718	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354212	15354212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201423321	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	93	681	1	ENST00000263377.2:c.2668G>A	p.Val890Met	p.V890M	ENST00000263377	NM_058243.2	890	Gtg/Atg	14/20	1	2	FACETS	0.939	0.835	1	0.939	0.835	1	CLONAL	1	TRUE	1	0.282156230034043	2		682	702	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384923	17384923	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	86	695	0	ENST00000359435.4:c.473G>A	p.Gly158Asp	p.G158D	ENST00000359435	NM_001033549.1	158	gGc/gAc	5/9	1	2	FACETS	0.921	0.815	1	0.921	0.815	1	CLONAL	1	TRUE	1	0.282156230034043	2		695	662	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634731	158634731	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748791232	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	65	346	0	ENST00000263640.3:c.455G>A	p.Arg152His	p.R152H	ENST00000263640	NM_001105.4	152	cGc/cAc	5/11	1	2	FACETS	0.982	0.854	1	0.982	0.854	1	CLONAL	1	TRUE	1	0.282156230034043	2		346	469	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542317	187542317	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1036641566	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	64	341	0	ENST00000441802.2:c.5423T>C	p.Val1808Ala	p.V1808A	ENST00000441802	NM_005245.3	1808	gTa/gCa	10/27	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.282156230034043	2		341	373	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628452	187628452	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs745890477	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	155	659	1	ENST00000441802.2:c.2530G>T	p.Val844Phe	p.V844F	ENST00000441802	NM_005245.3	844	Gtt/Ttt	2/27	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.282156230034043	2		660	916	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439417	149439417	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	82	516	0	ENST00000286301.3:c.1978C>G	p.Leu660Val	p.L660V	ENST00000286301	NM_005211.3	660	Ctg/Gtg	15/22	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.282156230034043	2		516	539	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41904993	41904993	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	79	495	0	ENST00000372991.4:c.554T>G	p.Phe185Cys	p.F185C	ENST00000372991	NM_001760.3	185	tTt/tGt	3/5	1	2	FACETS	0.94	0.827	1	0.94	0.827	1	CLONAL	1	TRUE	1	0.282156230034043	2		495	596	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511292	157511292	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	63	431	1	ENST00000346085.5:c.3810G>A	p.Met1270Ile	p.M1270I	ENST00000346085	NM_020732.3	1270	atG/atA	15/20	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.282156230034043	2		432	430	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527835	157527835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	44	461	0	ENST00000346085.5:c.5560G>A	p.Gly1854Ser	p.G1854S	ENST00000346085	NM_020732.3	1854	Ggt/Agt	20/20	1	2	FACETS	0.695	0.583	0.818	0.695	0.583	0.818	SUBCLONAL	1	TRUE	1	0.282156230034043	2		461	449	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509082	106509082	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs144565710	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	82	550	0	ENST00000359195.3:c.1076G>T	p.Arg359Leu	p.R359L	ENST00000359195	NM_002649.2	359	cGc/cTc	2/11	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.282156230034043	2		550	572	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606184	93606184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201301123	NA	P-0030960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	64	403	0	ENST00000375746.1:c.4G>A	p.Ala2Thr	p.A2T	ENST00000375746	NM_001174167.1	2	Gcc/Acc	2/14	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.282156230034043	2		403	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0030962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	419	701	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.597178786978984	2		701	655	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460504	8460504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148300682	NA	P-0030962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	264	502	1	ENST00000356435.5:c.3782C>T	p.Thr1261Met	p.T1261M	ENST00000356435		1261	aCg/aTg	22/35	0.282822142865862	5	FACETS	1	0.985	1	0.753	0.709	0.798	INDETERMINATE	2	TRUE	2	0.597178786978984	5		503	742	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294439	1294439	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	80	377	0	ENST00000310581.5:c.562C>G	p.Pro188Ala	p.P188A	ENST00000310581	NM_198253.2	188	Cca/Gca	2/16	1	2	FACETS	0.412	0.362	0.465	0.412	0.362	0.465	SUBCLONAL	1	TRUE	1	0.547579632169802	2		377	710	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797303	135797304	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0030963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	141	281	0	ENST00000298552.3:c.564_565dup	p.His189LeufsTer22	p.H189Lfs*22	ENST00000298552	NM_001162426.1	189	cat/cTCat	7/23	0.524386476421779	1	FACETS	0.85	0.781	0.921	0.85	0.781	0.921	CLONAL	1	TRUE	0	0.547579632169802	1		281	440	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0030964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	52	384	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.198340359802759	2		384	479	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560512	65560512	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	76	336	0	ENST00000358664.4:c.85A>G	p.Asn29Asp	p.N29D	ENST00000358664	NM_002382.4	29	Aat/Gat	3/5	0.198340359802759	2	FACETS	0.785	0.691	0.886	0.785	0.691	0.886	SUBCLONAL	2	TRUE	0	0.198340359802759	2		336	488	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859890	117859890	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	52	226	0	ENST00000297338.2:c.1745T>G	p.Leu582Arg	p.L582R	ENST00000297338	NM_006265.2	582	cTt/cGt	14/14	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.198340359802759	2		226	380	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045655	47045655	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0030964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	85	437	0	ENST00000377604.3:c.2538-2A>G		p.X846_splice	ENST00000377604	NM_001204468.1	846			0.19810905156284	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.198340359802759	1		437	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579417	7579418	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0030965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	204	493	0	ENST00000269305.4:c.268_269dup	p.Trp91ProfsTer33	p.W91Pfs*33	ENST00000269305	NM_001126112.2	90	tcc/tcTCc	4/11	0.485430890519171	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.485430890519171	1		493	606	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149595	202149595	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs768612301	NA	P-0030965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	134	346	0	ENST00000358485.4:c.1036T>C	p.Cys346Arg	p.C346R	ENST00000358485	NM_001080125.1	346	Tgc/Cgc	8/9	1	2	FACETS	0.993	0.906	1	0.993	0.906	1	CLONAL	1	TRUE	1	0.485430890519171	2		346	556	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288899	212288904	+	inframe_deletion	In_Frame_Del	DEL	AACGTC	AACGTC	-	novel	NA	P-0030965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	42	184	0	ENST00000342788.4:c.2842_2847del	p.Asp948_Val949del	p.D948_V949del	ENST00000342788	NM_005235.2	948	GACGTT/-	23/28	1	2	FACETS	0.809	0.682	0.946	0.809	0.682	0.946	CLONAL	1	TRUE	1	0.485430890519171	2		184	214	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645760	215645760	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	110	423	0	ENST00000260947.4:c.838T>G	p.Leu280Val	p.L280V	ENST00000260947	NM_000465.2	280	Tta/Gta	4/11	1	2	FACETS	0.857	0.773	0.945	0.857	0.773	0.945	CLONAL	1	TRUE	1	0.485430890519171	2		423	529	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520476	176520476	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	189	501	0	ENST00000292408.4:c.1321A>G	p.Ser441Gly	p.S441G	ENST00000292408	NM_213647.1	441	Agc/Ggc	10/18	0.485430890519171	1	FACETS	0.98	0.91	1	0.98	0.91	1	CLONAL	1	TRUE	0	0.485430890519171	1		501	602	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361159	66361159	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	13	272	0	ENST00000273854.3:c.1013G>T	p.Cys338Phe	p.C338F	ENST00000273854	NM_004439.5	338	tGt/tTt	4/18	0.274433475001529	1	FACETS	0.229	0.163	0.309	0.229	0.163	0.309	SUBCLONAL	1	TRUE	0	0.432219597157591	1		272	206	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0030966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	119	432	0	ENST00000269305.4:c.920-2A>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.432219597157591	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.432219597157591	1		432	338	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989443	85989443	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	57	237	0	ENST00000263360.6:c.1202G>T	p.Cys401Phe	p.C401F	ENST00000263360	NM_003797.3	401	tGt/tTt	12/12	NA	2	FACETS	0.945	0.818	1			1	INDETERMINATE	1	TRUE	NA	0.432219597157591	2		237	279	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075618	8075618	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs200259274	NA	P-0030966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	48	311	0	ENST00000377482.5:c.62A>G	p.His21Arg	p.H21R	ENST00000377482	NM_018948.3	21	cAt/cGt	2/4	0.274433475001529	1	FACETS	0.711	0.606	0.823	0.711	0.606	0.823	SUBCLONAL	1	TRUE	0	0.432219597157591	1		311	245	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797753	45797753	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs766638306	NA	P-0030966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	71	485	0	ENST00000450313.1:c.939G>T	p.Glu313Asp	p.E313D	ENST00000450313	NM_012222.2	313	gaG/gaT	11/16	1	2	FACETS	0.898	0.788	1	0.898	0.788	1	CLONAL	1	TRUE	1	0.432219597157591	2		485	366	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042472	42042472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	77	454	1	ENST00000219905.7:c.6667G>A	p.Asp2223Asn	p.D2223N	ENST00000219905	NM_001164273.1	2223	Gac/Aac	17/24	0.412853091000212	1	FACETS	0.94	0.834	1	0.94	0.834	1	CLONAL	1	TRUE	0	0.432219597157591	1		455	297	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007704	45007704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	55	292	0	ENST00000558401.1:c.151C>T	p.His51Tyr	p.H51Y	ENST00000558401	NM_004048.2	51	Cat/Tat	2/4	0.412853091000212	1	FACETS	0.964	0.836	1	0.964	0.836	1	CLONAL	1	TRUE	0	0.432219597157591	1		292	207	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805742	46805742	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	177	551	0	ENST00000290295.7:c.214G>T	p.Gly72Trp	p.G72W	ENST00000290295	NM_006361.5	72	Ggg/Tgg	1/2	0.423091233354423	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.432219597157591	2		551	385	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600327	10600327	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	80	407	0	ENST00000171111.5:c.1528del	p.Ala510GlnfsTer22	p.A510Qfs*22	ENST00000171111	NM_203500.1	510	Gca/ca	4/6	0.432219597157591	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.432219597157591	1		407	267	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022313	26022313	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	79	369	0	ENST00000435504.4:c.344G>T	p.Ser115Ile	p.S115I	ENST00000435504		115	aGc/aTc	5/13	1	2	FACETS	0.97	0.858	1	0.97	0.858	1	CLONAL	1	TRUE	1	0.432219597157591	2		369	377	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743952	40743952	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0030966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	43	265	0	ENST00000373198.4:c.3043A>T	p.Lys1015Ter	p.K1015*	ENST00000373198	NM_133170.3	1015	Aaa/Taa	23/32	0.188648152627719	2	FACETS	1	0.875	1	0.518	0.439	0.604	INDETERMINATE	1	TRUE	0	0.432219597157591	2		265	192	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523318	176523318	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	87	635	0	ENST00000292408.4:c.1975G>T	p.Glu659Ter	p.E659*	ENST00000292408	NM_213647.1	659	Gag/Tag	15/18	0.432219597157591	1	FACETS	0.879	0.784	0.978	0.879	0.784	0.978	CLONAL	1	TRUE	0	0.432219597157591	1		635	359	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622247	162622247	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	38	303	0	ENST00000366898.1:c.450C>A	p.Cys150Ter	p.C150*	ENST00000366898	NM_004562.2	150	tgC/tgA	4/12	0.432219597157591	1	FACETS	0.686	0.573	0.809	0.686	0.573	0.809	SUBCLONAL	1	TRUE	0	0.432219597157591	1		303	201	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971243	13971243	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	40	328	0	ENST00000405192.2:c.686A>G	p.Gln229Arg	p.Q229R	ENST00000405192	NM_001163147.1	229	cAg/cGg	8/12	0.432219597157591	4	FACETS	0.734	0.612	0.87	0.245	0.204	0.29	SUBCLONAL	1	TRUE	1	0.432219597157591	4		328	361	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140454023	140454023	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	19	204	0	ENST00000288602.6:c.1705G>C	p.Ala569Pro	p.A569P	ENST00000288602	NM_004333.4	569	Gcc/Ccc	14/18	0.274433475001529	1	FACETS	0.41	0.313	0.523	0.41	0.313	0.523	SUBCLONAL	1	TRUE	0	0.432219597157591	1		204	168	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945096	151945096	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	22	355	0	ENST00000262189.6:c.2423C>G	p.Ala808Gly	p.A808G	ENST00000262189	NM_170606.2	808	gCt/gGt	14/59	0.274433475001529	1	FACETS	0.328	0.255	0.413	0.328	0.255	0.413	SUBCLONAL	1	TRUE	0	0.432219597157591	1		355	243	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971163	21971164	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGC	novel	NA	P-0030966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	45	220	0	ENST00000304494.5:c.192_194dup	p.Leu65dup	p.L65dup	ENST00000304494	NM_000077.4	65	ctc/ctGCTc	2/3	0.432219597157591	1	FACETS	0.846	0.72	0.981	0.846	0.72	0.981	CLONAL	1	TRUE	0	0.432219597157591	1		220	193	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949017	44949017	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	47	190	0	ENST00000377967.4:c.3578G>T	p.Trp1193Leu	p.W1193L	ENST00000377967	NM_021140.2	1193	tGg/tTg	25/29	0.360988706255921	0	FACETS	0.864	0.745	0.988			1	CLONAL	1	TRUE	NA	0.432219597157591	0		190	143	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346090	89346090	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	12	47	0	ENST00000301030.4:c.6860G>T	p.Gly2287Val	p.G2287V	ENST00000301030	NM_001256183.1	2287	gGt/gTt	9/13	0.188648152627719	2	FACETS	1	0.818	1	0.591	0.429	0.774	INDETERMINATE	1	TRUE	0	0.432219597157591	2		47	47	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245720	46245720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	29	436	4	ENST00000334344.6:c.3814C>T	p.Arg1272Ter	p.R1272*	ENST00000334344	NM_152641.2	1272	Cga/Tga	15/21	1	2	FACETS	0.671	0.538	0.824	0.671	0.538	0.824	SUBCLONAL	1	TRUE	1	0.18	2		440	480	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106385	27106386	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0030967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	26	486	2	ENST00000324856.7:c.5996_5997insC	p.Glu2000Ter	p.E2000*	ENST00000324856	NM_006015.4	1999	ttt/ttCt	20/20	1	2	FACETS	0.672	0.531	0.833	0.672	0.531	0.833	SUBCLONAL	1	TRUE	1	0.18	2		488	430	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0030968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	80	562	3	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.828	0.736	0.924	0.828	0.736	0.924	CLONAL	1	TRUE	1	0.625605110380149	2		565	309	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0030968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	125	554	1	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.625605110380149	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.625605110380149	1		555	262	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0030968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	65	307	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.805	0.706	0.91	0.805	0.706	0.91	CLONAL	1	TRUE	1	0.625605110380149	2		307	258	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0030968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	46	272	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	0.625605110380149	1	FACETS	0.683	0.587	0.784	0.683	0.587	0.784	SUBCLONAL	1	TRUE	0	0.625605110380149	1		272	148	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481903	56481905	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0030968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	104	519	1	ENST00000267101.3:c.833_835del	p.Thr278del	p.T278del	ENST00000267101	NM_001982.3	277	caCACc/cac	7/28	1	2	FACETS	0.87	0.786	0.958	0.87	0.786	0.958	CLONAL	1	TRUE	1	0.625605110380149	2		520	382	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575666	48575667	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TC	TC	-	rs377767328	NA	P-0030968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	22	448	0	ENST00000342988.3:c.430_431del	p.Ser144ArgfsTer7	p.S144Rfs*7	ENST00000342988	NM_005359.5	142	gaTCtc/gatc	4/12	0.625605110380149	1	FACETS	0.348	0.272	0.433	0.348	0.272	0.433	SUBCLONAL	1	TRUE	0	0.625605110380149	1		448	139	SUCCESS
APC	324	MSKCC	GRCh37	5	112173560	112173560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	46	284	0	ENST00000257430.4:c.2269C>T	p.Gln757Ter	p.Q757*	ENST00000257430	NM_000038.5	757	Caa/Taa	16/16	1	2	FACETS	0.804	0.687	0.929	0.804	0.687	0.929	CLONAL	1	TRUE	1	0.625605110380149	2		284	183	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371747	45371748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	33	353	0	ENST00000262160.6:c.1243dup	p.Arg415LysfsTer25	p.R415Kfs*25	ENST00000262160	NM_005901.5	415	aga/aAga	10/11	0.625605110380149	1	FACETS	0.364	0.299	0.436	0.364	0.299	0.436	SUBCLONAL	1	TRUE	0	0.625605110380149	1		353	199	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638414	117638414	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	37	357	0	ENST00000368508.3:c.6027T>G	p.Ile2009Met	p.I2009M	ENST00000368508	NM_002944.2	2009	atT/atG	38/43	0.28009469411848	5	FACETS	0.744	0.613	0.892	0.248	0.204	0.298	SUBCLONAL	1	TRUE	2	0.28009469411848	5		357	504	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112334	115112334	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	11	66	0	ENST00000257566.3:c.1406A>T	p.Glu469Val	p.E469V	ENST00000257566	NM_016569.3	469	gAg/gTg	7/8	0.28009469411848	3	FACETS	0.953	0.665	1	0.476	0.332	0.651	CLONAL	1	TRUE	1	0.28009469411848	3		66	94	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	31	368	2	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	0.402295535011796	3	FACETS	0.42	0.339	0.511	0.21	0.169	0.256	SUBCLONAL	1	TRUE	1	0.402295535011796	3		370	441	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696450	47696450	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	133	389	0	ENST00000347630.2:c.373T>G	p.Phe125Val	p.F125V	ENST00000347630	NM_001007230.1	125	Ttt/Gtt	6/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.402295535011796	2		389	496	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0030973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	295	800	3	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	0.221099591403454	0	FACETS	0.93	0.892	0.967			1	CLONAL	5	FALSE	0	0.221099591403454	0		803	447	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056568	26056568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41266789	NA	P-0030973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	139	190	0	ENST00000343677.2:c.89G>A	p.Gly30Asp	p.G30D	ENST00000343677	NM_005319.3	30	gGt/gAt	1/1	1	2	FACETS	0.938	0.867	1	1	0.993	1	CLONAL	4	FALSE	1	0.221099591403454	2		190	335	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933771	39933772	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	311	223	0	ENST00000378444.4:c.827dup	p.Pro278AlafsTer23	p.P278Afs*23	ENST00000378444	NM_001123385.1	276	atc/atTc	4/15	0.131213048420719	0	FACETS	0.929	0.9	0.957			1	INDETERMINATE	6	FALSE	NA	0.221099591403454	0		223	393	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880257	37880257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	230	464	0	ENST00000269571.5:c.2301C>G	p.Ile767Met	p.I767M	ENST00000269571		767	atC/atG	19/27	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.538505663504269	2		464	854	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041061	112041061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	179	445	0	ENST00000368678.4:c.194G>A	p.Gly65Glu	p.G65E	ENST00000368678		65	gGa/gAa	3/13	1	2	FACETS	0.955	0.883	1	0.955	0.883	1	CLONAL	1	TRUE	1	0.538505663504269	2		445	696	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138575	55138575	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	197	490	0	ENST00000257290.5:c.1252C>G	p.Leu418Val	p.L418V	ENST00000257290	NM_006206.4	418	Ctg/Gtg	9/23	1	2	FACETS	0.967	0.897	1	0.967	0.897	1	CLONAL	1	TRUE	1	0.538505663504269	2		490	757	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343517	343517	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	534	648	0	ENST00000262320.3:c.2157G>C	p.Lys719Asn	p.K719N	ENST00000262320	NM_003502.3	719	aaG/aaC	8/11	1	2	FACETS	0.776	0.745	0.807	1	0.997	1	SUBCLONAL	2	TRUE	1	0.538505663504269	2		648	1278	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426235	49426235	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	275	724	0	ENST00000301067.7:c.12253C>T	p.Gln4085Ter	p.Q4085*	ENST00000301067	NM_003482.3	4085	Cag/Tag	39/54	1	2	FACETS	0.89	0.835	0.946	0.89	0.835	0.946	CLONAL	1	TRUE	1	0.538505663504269	2		724	1148	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26928010	26928010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	174	415	0	ENST00000381527.3:c.449G>A	p.Arg150Lys	p.R150K	ENST00000381527	NM_001260.1	150	aGa/aAa	4/13	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.538505663504269	2		415	610	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41242984	41242984	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	205	407	0	ENST00000357654.3:c.4162C>A	p.Gln1388Lys	p.Q1388K	ENST00000357654	NM_007294.3	1388	Cag/Aag	11/23	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.538505663504269	2		407	675	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244196	41244196	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397507215	NA	P-0030974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	224	562	1	ENST00000357654.3:c.3352C>T	p.Gln1118Ter	p.Q1118*	ENST00000357654	NM_007294.3	1118	Cag/Tag	10/23	1	2	FACETS	0.967	0.902	1	0.967	0.902	1	CLONAL	1	TRUE	1	0.538505663504269	2		563	860	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78765262	78765262	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs765785590	NA	P-0030974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	144	286	0	ENST00000306801.3:c.843G>C	p.Gln281His	p.Q281H	ENST00000306801	NM_020761.2	281	caG/caC	7/34	1	2	FACETS	0.857	0.784	0.933	0.857	0.784	0.933	CLONAL	1	TRUE	1	0.538505663504269	2		286	624	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021332	31021332	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373126831	NA	P-0030974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	263	482	0	ENST00000375687.4:c.1331C>T	p.Ser444Leu	p.S444L	ENST00000375687	NM_015338.5	444	tCa/tTa	12/13	0.537021868737708	3	FACETS	1	0.984	1	0.572	0.536	0.609	CLONAL	1	TRUE	1	0.538505663504269	3		482	1084	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022334	31022334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	151	387	0	ENST00000375687.4:c.1819G>A	p.Gly607Ser	p.G607S	ENST00000375687	NM_015338.5	607	Ggt/Agt	13/13	0.537021868737708	3	FACETS	0.961	0.88	1	0.48	0.44	0.523	CLONAL	1	TRUE	1	0.538505663504269	3		387	741	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645051	86645051	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	125	297	0	ENST00000274376.6:c.1123C>G	p.Leu375Val	p.L375V	ENST00000274376	NM_002890.2	375	Ctt/Gtt	8/25	1	2	FACETS	0.984	0.896	1	0.984	0.896	1	CLONAL	1	TRUE	1	0.538505663504269	2		297	472	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510157	149510157	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	276	575	0	ENST00000261799.4:c.1312G>C	p.Gly438Arg	p.G438R	ENST00000261799	NM_002609.3	438	Ggc/Cgc	9/23	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.538505663504269	2		575	927	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513324	149513324	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0030974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	179	454	0	ENST00000261799.4:c.760-1G>C		p.X254_splice	ENST00000261799	NM_002609.3	254			1	2	FACETS	0.944	0.873	1	0.944	0.873	1	CLONAL	1	TRUE	1	0.538505663504269	2		454	704	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202271	138202271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774778736	NA	P-0030974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	230	495	0	ENST00000237289.4:c.2188G>A	p.Glu730Lys	p.E730K	ENST00000237289	NM_001270507.1	730	Gag/Aag	9/9	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.538505663504269	2		495	786	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250507	26250507	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	47	608	1	ENST00000446824.2:c.327C>A	p.Asn109Lys	p.N109K	ENST00000446824	NM_021018.2	109	aaC/aaA	1/1	1	2	FACETS	0.207	0.174	0.244	0.207	0.174	0.244	SUBCLONAL	1	TRUE	1	0.538505663504269	2		609	843	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0030976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	150	214	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.972450350495611	2		214	287	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056352	27056352	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1557591264	NA	P-0030976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	122	217	0	ENST00000324856.7:c.1348C>T	p.Gln450Ter	p.Q450*	ENST00000324856	NM_006015.4	450	Cag/Tag	2/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.972450350495611	2		217	233	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307699	11307699	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	179	358	0	ENST00000361445.4:c.1208G>T	p.Arg403Leu	p.R403L	ENST00000361445	NM_004958.3	403	cGa/cTa	8/58	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.972450350495611	2		358	348	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	171	410	0	ENST00000347630.2:c.305T>C	p.Phe102Ser	p.F102S	ENST00000347630	NM_001007230.1	102	tTc/tCc	5/11	1	2	FACETS	0.921	0.859	0.983	0.921	0.859	0.983	CLONAL	1	TRUE	1	0.972450350495611	2		410	382	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274839	142274840	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGT	novel	NA	P-0030976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	187	428	0	ENST00000350721.4:c.2220_2221insACA	p.Leu740_Phe741insThr	p.L740_F741insT	ENST00000350721	NM_001184.3	740	-/ACA	10/47	1	2	FACETS	0.984	0.922	1	0.984	0.922	1	CLONAL	1	TRUE	1	0.972450350495611	2		428	391	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0030977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	72	435	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.213539478435319	5	FACETS	0.932	0.831	1	1	0.98	1	CLONAL	5	FALSE	2	0.213539478435319	5		435	191	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0030977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	86	329	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	0.213539478435319	3	FACETS	0.888	0.788	0.994	0.888	0.788	0.994	CLONAL	2	FALSE	1	0.213539478435319	3		329	502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352697	NA	P-0030977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	8	401	0	ENST00000269305.4:c.587G>A	p.Arg196Gln	p.R196Q	ENST00000269305	NM_001126112.2	196	cGa/cAa	6/11	0.213539478435319	1	FACETS	0.204	0.131	0.3	0.204	0.131	0.3	SUBCLONAL	1	FALSE	0	0.213539478435319	1		401	328	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646084	215646085	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs746325928	NA	P-0030977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	26	360	1	ENST00000260947.4:c.513dup	p.Asp172ArgfsTer10	p.D172Rfs*10	ENST00000260947	NM_000465.2	171	-/A	4/11	0.213539478435319	1	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	FALSE	0	0.213539478435319	1		361	177	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453531	138453531	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372119491	NA	P-0030977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	27	247	0	ENST00000289153.2:c.917G>A	p.Arg306Gln	p.R306Q	ENST00000289153	NM_006219.2	306	cGa/cAa	5/22	0.213539478435319	5	FACETS	0.856	0.686	1	0.571	0.457	0.698	CLONAL	2	FALSE	2	0.213539478435319	5		247	195	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916935	178916935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	8	295	0	ENST00000263967.3:c.322C>T	p.Arg108Cys	p.R108C	ENST00000263967	NM_006218.2	108	Cgt/Tgt	2/21	0.213539478435319	5	FACETS	0.338	0.216	0.496	0.113	0.072	0.166	SUBCLONAL	1	FALSE	2	0.213539478435319	5		295	293	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0030980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	282	479	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.356799667774908	2	FACETS	0.875	0.827	0.924	0.875	0.827	0.924	CLONAL	2	TRUE	0	0.43200083831554	2		479	746	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538257	9538257	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs746240534	NA	P-0030980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	34	382	0	ENST00000353224.5:c.1741C>T	p.Arg581Trp	p.R581W	ENST00000353224	NM_177990.2	581	Cgg/Tgg	7/10	0.387881354632175	1	FACETS	0.255	0.208	0.308	0.255	0.208	0.308	SUBCLONAL	1	TRUE	0	0.43200083831554	1		382	484	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032602	12032604	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GTG	GTG	-	novel	NA	P-0030980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	72	340	0	ENST00000353533.5:c.1040+1_1040+3del		p.LCdel	ENST00000353533	NM_003010.3	346	ttGTGc/ttc	9/11	0.356799667774908	2	FACETS	0.729	0.639	0.826	0.365	0.319	0.413	SUBCLONAL	1	TRUE	0	0.43200083831554	2		340	457	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266039	41266305	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAA	GGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAA	-	novel	NA	P-0030980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	31	180	0	ENST00000349496.5:c.37_241+62del		p.X13_splice	ENST00000349496	NM_001904.3	13		3/15	0.43200083831554	2	FACETS	1	0.835	1	0.509	0.418	0.609	CLONAL	1	TRUE	0	0.43200083831554	2		180	141	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38137179	38137187	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGGCATC	GCCGGCATC	A	novel	NA	P-0030980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	64	389	0	ENST00000317025.8:c.3631_3639delinsT	p.Asp1211SerfsTer14	p.D1211Sfs*14	ENST00000317025	NM_023034.1	1211	GATGCCGGC/T	21/24	0.27681349365348	3	FACETS	0.537	0.464	0.616	0.268	0.232	0.308	SUBCLONAL	1	TRUE	1	0.43200083831554	3		389	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	208	349	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.408495888165445	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.430650259947549	1		349	672	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437178	49437178	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	47	297	0	ENST00000301067.7:c.5501C>T	p.Ser1834Phe	p.S1834F	ENST00000301067	NM_003482.3	1834	tCc/tTc	24/54	0.358600508069127	3	FACETS	0.382	0.322	0.449	0.191	0.161	0.225	SUBCLONAL	1	TRUE	1	0.430650259947549	3		297	694	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954198	48954198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123331	NA	P-0030981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	72	157	1	ENST00000267163.4:c.1399C>T	p.Arg467Ter	p.R467*	ENST00000267163	NM_000321.2	467	Cga/Tga	15/27	0.409001500401654	2	FACETS	1	0.969	1	0.656	0.58	0.735	CLONAL	1	TRUE	0	0.430650259947549	2		158	255	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140123	50140177	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGCACGCATGTACTGCTCTCTCATGGCCCCGAACTCTTCCTGGCCCGCGGTGT	CCAGCACGCATGTACTGCTCTCTCATGGCCCCGAACTCTTCCTGGCCCGCGGTGT	-	novel	NA	P-0030981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	32	361	0	ENST00000246792.3:c.248_302del	p.Asp83AlafsTer133	p.D83Afs*133	ENST00000246792	NM_006270.3	83	gACACCGCGGGCCAGGAAGAGTTCGGGGCCATGAGAGAGCAGTACATGCGTGCTGGc/gc	3/6	1	2	FACETS	0.235	0.19	0.286	0.235	0.19	0.286	SUBCLONAL	1	TRUE	1	0.430650259947549	2		361	632	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72842176	72842176	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	23	175	0	ENST00000325599.8:c.1072G>C	p.Val358Leu	p.V358L	ENST00000325599	NM_018130.2	358	Gtt/Ctt	10/11	0.419207364167076	1	FACETS	0.357	0.279	0.446	0.357	0.279	0.446	SUBCLONAL	1	TRUE	0	0.430650259947549	1		175	235	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0030981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	96	208	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	0.389985528439081	1	FACETS	0.943	0.847	1	0.943	0.847	1	CLONAL	1	TRUE	0	0.430650259947549	1		208	371	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540718	187540718	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	84	178	0	ENST00000441802.2:c.7022T>G	p.Leu2341Arg	p.L2341R	ENST00000441802	NM_005245.3	2341	cTc/cGc	10/27	0.389985528439081	1	FACETS	0.903	0.804	1	0.903	0.804	1	CLONAL	1	TRUE	0	0.430650259947549	1		178	339	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55229252	55229252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	61	257	0	ENST00000275493.2:c.1559C>T	p.Pro520Leu	p.P520L	ENST00000275493	NM_005228.3	520	cCc/cTc	13/28	0.211945854265925	3	FACETS	0.629	0.543	0.723	0.315	0.271	0.362	INDETERMINATE	1	TRUE	1	0.430650259947549	3		257	547	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317896	8317896	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	80	200	0	ENST00000356435.5:c.5717G>T	p.Ser1906Ile	p.S1906I	ENST00000356435		1906	aGc/aTc	35/35	0.211945854265925	3	FACETS	0.965	0.852	1	0.482	0.426	0.543	INDETERMINATE	1	TRUE	1	0.430650259947549	3		200	468	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776183	135776183	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	44	217	0	ENST00000298552.3:c.2544G>C	p.Leu848Phe	p.L848F	ENST00000298552	NM_001162426.1	848	ttG/ttC	20/23	0.392955667026534	3	FACETS	0.441	0.369	0.521	0.147	0.123	0.174	SUBCLONAL	1	TRUE	0	0.430650259947549	3		217	563	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0030982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	14	384	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.787	0.568	1	0.787	0.568	1	CLONAL	1	TRUE	1	0.141250658052954	2		384	252	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0030982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	26	242	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.141250658052954	3	FACETS	0.88	0.7	1	0.88	0.7	1	CLONAL	2	TRUE	1	0.141250658052954	3		242	224	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577035	7577036	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0030982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	61	517	0	ENST00000269305.4:c.902dup	p.Gly302ArgfsTer4	p.G302Rfs*4	ENST00000269305	NM_001126112.2	301	cca/ccCa	8/11	0.141250658052954	3	FACETS	1	0.966	1	0.717	0.618	0.825	CLONAL	1	TRUE	1	0.141250658052954	3		517	645	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445404	49445404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371076182	NA	P-0030983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	79	659	0	ENST00000301067.7:c.2062C>T	p.Arg688Cys	p.R688C	ENST00000301067	NM_003482.3	688	Cgc/Tgc	10/54	0.751025225896345	7	FACETS	1	0.972	1			1	CLONAL	1	TRUE	NA	0.751025225896345	7		659	447	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274090	10274090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758117698	NA	P-0030983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	74	421	0	ENST00000330684.3:c.179C>T	p.Ala60Val	p.A60V	ENST00000330684	NM_001134407.1	60	gCg/gTg	2/13	0.751025225896345	7	FACETS	1	0.927	1	0.783	0.701	0.867	CLONAL	3	TRUE	3	0.751025225896345	7		421	181	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524102	187524102	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	14	363	1	ENST00000441802.2:c.11437A>G	p.Lys3813Glu	p.K3813E	ENST00000441802	NM_005245.3	3813	Aaa/Gaa	20/27	0.361321030835672	1	FACETS	0.216	0.157	0.285	0.216	0.157	0.285	INDETERMINATE	1	TRUE	0	0.751025225896345	1		364	108	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724340	117724340	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	66	410	0	ENST00000368508.3:c.539C>T	p.Ser180Phe	p.S180F	ENST00000368508	NM_002944.2	180	tCc/tTc	6/43	0.296843042286508	2	FACETS	1	0.956	1	0.574	0.512	0.638	INDETERMINATE	1	TRUE	0	0.751025225896345	2		410	153	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80646079	80646079	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	27	98	0	ENST00000286548.4:c.73A>G	p.Ile25Val	p.I25V	ENST00000286548	NM_002072.3	25	Atc/Gtc	1/7	0.361321030835672	1	FACETS	1	0.926	1	1	0.926	1	INDETERMINATE	1	TRUE	0	0.751025225896345	1		98	40	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0030985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	48	332	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.786	0.671	0.908	0.786	0.671	0.908	CLONAL	1	FALSE	1	0.552953054305521	2		332	221	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0030985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	150	621	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.515128924453791	1	FACETS	0.863	0.795	0.932	0.863	0.795	0.932	CLONAL	1	FALSE	0	0.552953054305521	1		624	455	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553656	29553659	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	TAAC	TAAC	ATA	novel	NA	P-0030985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	80	372	0	ENST00000356175.3:c.2205_2208delinsATA	p.Tyr735Ter	p.Y735*	ENST00000356175	NM_000267.3	735	taTAAC/taATA	18/57	0.552953054305521	1	FACETS	0.745	0.664	0.83	0.745	0.664	0.83	SUBCLONAL	1	FALSE	0	0.552953054305521	1		372	281	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0030986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	475	332	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.655112625301301	4	FACETS	0.962	0.927	0.996	0.962	0.927	0.996	CLONAL	3	TRUE	1	0.655112625301301	4		332	832	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217034	2217034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368118931	NA	P-0030986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	211	527	0	ENST00000398665.3:c.2489C>T	p.Pro830Leu	p.P830L	ENST00000398665	NM_032482.2	830	cCg/cTg	21/28	0.655112625301301	2	FACETS	0.924	0.862	0.988	0.462	0.431	0.494	CLONAL	1	TRUE	0	0.655112625301301	2		527	697	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868953	117868953	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	147	256	0	ENST00000297338.2:c.746C>T	p.Ser249Phe	p.S249F	ENST00000297338	NM_006265.2	249	tCt/tTt	7/14	0.655112625301301	4	FACETS	1	0.952	1	0.353	0.322	0.384	CLONAL	1	TRUE	1	0.655112625301301	4		256	702	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713877	30713877	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	171	366	0	ENST00000295754.5:c.1202C>T	p.Ser401Phe	p.S401F	ENST00000295754	NM_003242.5	401	tCc/tTc	4/7	0.655112625301301	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.655112625301301	1		366	339	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748312	41748312	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	239	545	0	ENST00000226382.2:c.457T>G	p.Phe153Val	p.F153V	ENST00000226382	NM_003924.3	153	Ttt/Gtt	3/3	1	2	FACETS	0.959	0.899	1	0.959	0.899	1	CLONAL	1	TRUE	1	0.655112625301301	2		545	761	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938326	76938326	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	229	178	0	ENST00000373344.5:c.2422C>T	p.Arg808Ter	p.R808*	ENST00000373344	NM_000489.3	808	Cga/Tga	9/35	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.819488061940668	1		178	280	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943658	9943658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	139	374	0	ENST00000330684.3:c.1283C>T	p.Thr428Met	p.T428M	ENST00000330684	NM_001134407.1	428	aCg/aTg	5/13	1	2	FACETS	0.705	0.646	0.766	0.705	0.646	0.766	SUBCLONAL	1	TRUE	1	0.819488061940668	2		374	481	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555297	106555297	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1296446700	NA	P-0030987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	59	379	0	ENST00000369096.4:c.2414G>C	p.Ser805Thr	p.S805T	ENST00000369096	NM_001198.3	805	aGc/aCc	7/7	1	2	FACETS	0.312	0.268	0.359	0.312	0.268	0.359	SUBCLONAL	1	TRUE	1	0.819488061940668	2		379	462	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	36	435	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.29	2		435	227	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216189	36216189	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	57	407	3	ENST00000222270.7:c.3602del	p.Pro1201ArgfsTer154	p.P1201Rfs*154	ENST00000222270	NM_014727.1	1199	ggC/gg	11/37	1	2	FACETS	0.762	0.654	0.879	0.762	0.654	0.879	SUBCLONAL	1	TRUE	1	0.29	2		410	516	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	57	610	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.765	0.657	0.883	0.765	0.657	0.883	SUBCLONAL	1	TRUE	1	0.29	2		611	514	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	34	503	1	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.837	0.687	1	0.837	0.687	1	CLONAL	1	TRUE	1	0.29	2		504	280	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	47	551	4	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	0.241552850215448	3	FACETS	0.869	0.735	1	0.435	0.367	0.509	CLONAL	1	TRUE	1	0.29	3		555	427	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	56	622	6	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.942	0.809	1	0.942	0.809	1	CLONAL	1	TRUE	1	0.29	2		628	410	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101268	27101268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	54	423	0	ENST00000324856.7:c.4555del	p.Gln1519ArgfsTer8	p.Q1519Rfs*8	ENST00000324856	NM_006015.4	1517	gCc/gc	18/20	1	2	FACETS	0.746	0.638	0.865	0.746	0.638	0.865	SUBCLONAL	1	TRUE	1	0.29	2		423	499	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	74	337	3	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.831	0.734	0.933	1	0.98	1	CLONAL	2	TRUE	1	0.29	2		340	307	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100425	8100425	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	48	535	2	ENST00000346208.3:c.404del	p.Pro135ArgfsTer60	p.P135Rfs*60	ENST00000346208		133	taC/ta	3/6	0.075974589546493	3	FACETS	0.644	0.543	0.754	0.322	0.271	0.377	INDETERMINATE	1	TRUE	1	0.29	3		537	589	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835780	68835781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	56	338	1	ENST00000261769.5:c.377dup	p.Pro127AlafsTer41	p.P127Afs*41	ENST00000261769	NM_004360.3	124	cgc/cgCc	3/16	1	2	FACETS	0.817	0.701	0.943	0.817	0.701	0.943	CLONAL	1	TRUE	1	0.29	2		339	473	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289107	33289107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760147301	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	69	414	0	ENST00000374542.5:c.445G>A	p.Ala149Thr	p.A149T	ENST00000374542	NM_001141970.1	149	Gcc/Acc	3/8	0.075974589546493	3	FACETS	1	0.875	1	0.502	0.437	0.571	INDETERMINATE	1	TRUE	1	0.29	3		414	543	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	76	403	0	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.993	0.872	1	0.993	0.872	1	CLONAL	1	TRUE	1	0.29	2		403	528	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923086	39923087	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	70	387	0	ENST00000378444.4:c.3621dup	p.Gln1208ThrfsTer8	p.Q1208Tfs*8	ENST00000378444	NM_001123385.1	1207	-/A	8/15	0.075974589546493	0	FACETS	0.647	0.565	0.735			1	INDETERMINATE	1	TRUE	0	0.29	0		387	530	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272337	15272337	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs771517374	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	83	523	6	ENST00000263388.2:c.6102del	p.Gly2035ValfsTer50	p.G2035Vfs*50	ENST00000263388	NM_000435.2	2034	ccC/cc	33/33	1	2	FACETS	0.866	0.764	0.975	0.866	0.764	0.975	CLONAL	1	TRUE	1	0.29	2		529	661	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222868	5222868	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1028304582	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	55	367	0	ENST00000357368.4:c.2935C>T	p.Arg979Ter	p.R979*	ENST00000357368	NM_002850.3	979	Cga/Tga	18/38	1	2	FACETS	0.841	0.721	0.972	0.841	0.721	0.972	CLONAL	1	TRUE	1	0.29	2		367	451	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448304	56448304	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	78	425	0	ENST00000407977.2:c.343del	p.Ala115ProfsTer43	p.A115Pfs*43	ENST00000407977		115	Gcc/cc	3/10	1	2	FACETS	0.892	0.785	1	0.892	0.785	1	CLONAL	1	TRUE	1	0.29	2		425	603	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100577	157100577	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1289149988	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	47	285	0	ENST00000346085.5:c.1518del	p.Gly507AspfsTer16	p.G507Dfs*16	ENST00000346085	NM_020732.3	505	aCc/ac	1/20	1	2	FACETS	0.833	0.705	0.974	0.833	0.705	0.974	CLONAL	1	TRUE	1	0.29	2		285	389	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434595	110434595	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs555841746	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	69	423	0	ENST00000375856.3:c.3806A>C	p.Gln1269Pro	p.Q1269P	ENST00000375856	NM_003749.2	1269	cAg/cCg	1/2	0.075974589546493	0	FACETS	0.655	0.571	0.745			1	INDETERMINATE	1	TRUE	0	0.29	0		423	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572991	7572991	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	54	250	0	ENST00000269305.4:c.1118del	p.Lys373ArgfsTer49	p.K373Rfs*49	ENST00000269305	NM_001126112.2	373	aAg/ag	11/11	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.29	2		250	359	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725019	47725019	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs762488821	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	86	587	3	ENST00000449228.1:c.725del	p.Gly242AlafsTer48	p.G242Afs*48	ENST00000449228	NM_001127240.2	242	gGc/gc	4/4	1	2	FACETS	0.858	0.759	0.964	0.858	0.759	0.964	CLONAL	1	TRUE	1	0.29	2		590	691	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724625	162724625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757919179	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	30	251	0	ENST00000367921.3:c.397C>T	p.Arg133Trp	p.R133W	ENST00000367921	NM_006182.2	133	Cgg/Tgg	5/18	1	2	FACETS	0.683	0.551	0.831	0.683	0.551	0.831	SUBCLONAL	1	TRUE	1	0.29	2		251	303	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78921083	78921083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755012671	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	66	385	0	ENST00000306801.3:c.3197G>A	p.Arg1066Gln	p.R1066Q	ENST00000306801	NM_020761.2	1066	cGg/cAg	27/34	1	2	FACETS	0.916	0.796	1	0.916	0.796	1	CLONAL	1	TRUE	1	0.29	2		385	497	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209593	98209593	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	52	359	2	ENST00000331920.6:c.3945del	p.Tyr1316ThrfsTer56	p.Y1316Tfs*56	ENST00000331920	NM_000264.3	1315	ccC/cc	23/24	0.241552850215448	3	FACETS	1	0.863	1	0.506	0.431	0.587	CLONAL	1	TRUE	1	0.29	3		361	406	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	89	464	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.075974589546493	3	FACETS	1	0.951	1	0.565	0.501	0.633	INDETERMINATE	1	TRUE	1	0.29	3		464	622	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411521	63411521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs937173075	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	88	513	0	ENST00000330258.3:c.1646G>A	p.Arg549Gln	p.R549Q	ENST00000330258	NM_152424.3	549	cGg/cAg	2/2	0.075974589546493	0	FACETS	0.734	0.651	0.822			1	INDETERMINATE	1	TRUE	0	0.29	0		513	587	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99181170	99181170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759905070	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	35	329	0	ENST00000074304.5:c.2111G>A	p.Arg704His	p.R704H	ENST00000074304	NM_001134224.1	704	cGc/cAc	20/26	1	2	FACETS	0.549	0.449	0.66	0.549	0.449	0.66	SUBCLONAL	1	TRUE	1	0.29	2		329	440	SUCCESS
APC	324	MSKCC	GRCh37	5	112174973	112174973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085227	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	23	146	0	ENST00000257430.4:c.3682C>T	p.Gln1228Ter	p.Q1228*	ENST00000257430	NM_000038.5	1228	Cag/Tag	16/16	1	2	FACETS	0.835	0.655	1	0.835	0.655	1	CLONAL	1	TRUE	1	0.29	2		146	190	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951811	2951811	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146334064	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	65	347	0	ENST00000396946.4:c.3139G>A	p.Ala1047Thr	p.A1047T	ENST00000396946	NM_032415.4	1047	Gcc/Acc	23/25	1	2	FACETS	0.948	0.824	1	0.948	0.824	1	CLONAL	1	TRUE	1	0.29	2		347	473	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831345	89831346	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs878853663	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	57	374	0	ENST00000389301.3:c.2730_2731del	p.Trp911AspfsTer31	p.W911Dfs*31	ENST00000389301	NM_000135.2	910	ctCTgg/ctgg	28/43	1	2	FACETS	0.681	0.584	0.787	0.681	0.584	0.787	SUBCLONAL	1	TRUE	1	0.29	2		374	577	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100619	8100619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	80	499	2	ENST00000346208.3:c.593C>T	p.Ser198Leu	p.S198L	ENST00000346208		198	tCg/tTg	3/6	0.075974589546493	3	FACETS	1	0.898	1	0.51	0.449	0.576	INDETERMINATE	1	TRUE	1	0.29	3		501	619	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77069962	77069962	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1221370333	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	66	279	0	ENST00000356341.3:c.578G>A	p.Arg193His	p.R193H	ENST00000356341	NM_002576.4	193	cGc/cAc	6/15	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.29	2		279	422	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920788	100920788	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	13	232	0	ENST00000325455.5:c.2360A>G	p.Gln787Arg	p.Q787R	ENST00000325455	NM_001202474.3	787	cAg/cGg	6/8	1	2	FACETS	0.684	0.491	0.916	0.684	0.491	0.916	SUBCLONAL	1	TRUE	1	0.29	2		232	131	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402112	402114	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs763675548	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	50	326	0	ENST00000399788.2:c.4677_4679del	p.Glu1560del	p.E1560del	ENST00000399788	NM_001042603.1	1559	gaAGAg/gag	27/28	1	2	FACETS	0.971	0.827	1	0.971	0.827	1	CLONAL	1	TRUE	1	0.29	2		326	355	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987028	36987028	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	52	368	0	ENST00000354822.5:c.661C>T	p.Arg221Cys	p.R221C	ENST00000354822	NM_001079668.2	221	Cgc/Tgc	3/3	1	2	FACETS	0.834	0.711	0.968	0.834	0.711	0.968	CLONAL	1	TRUE	1	0.29	2		368	430	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129197	2129197	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs397515302	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	85	488	0	ENST00000219476.3:c.3131G>T	p.Arg1044Met	p.R1044M	ENST00000219476	NM_000548.3	1044	aGg/aTg	27/42	1	2	FACETS	0.966	0.855	1	0.966	0.855	1	CLONAL	1	TRUE	1	0.29	2		488	607	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853250	68853250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224727	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	63	357	1	ENST00000261769.5:c.1633C>T	p.Arg545Trp	p.R545W	ENST00000261769	NM_004360.3	545	Cgg/Tgg	11/16	1	2	FACETS	0.859	0.744	0.983	0.859	0.744	0.983	CLONAL	1	TRUE	1	0.29	2		358	506	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554293	29554293	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	82	473	0	ENST00000356175.3:c.2309C>G	p.Thr770Ser	p.T770S	ENST00000356175	NM_000267.3	770	aCt/aGt	19/57	1	2	FACETS	0.994	0.878	1	0.994	0.878	1	CLONAL	1	TRUE	1	0.29	2		473	569	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40476746	40476746	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	57	313	0	ENST00000264657.5:c.1583T>C	p.Leu528Pro	p.L528P	ENST00000264657	NM_139276.2	528	cTg/cCg	17/24	1	2	FACETS	0.786	0.675	0.907	0.786	0.675	0.907	CLONAL	1	TRUE	1	0.29	2		313	500	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622410	1622410	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	71	399	0	ENST00000344749.5:c.554A>G	p.Tyr185Cys	p.Y185C	ENST00000344749	NM_001136139.2	185	tAc/tGc	9/19	1	2	FACETS	0.895	0.782	1	0.895	0.782	1	CLONAL	1	TRUE	1	0.29	2		399	547	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099312	4099312	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	78	538	2	ENST00000262948.5:c.806del	p.Pro269ArgfsTer58	p.P269Rfs*58	ENST00000262948	NM_030662.3	269	cCg/cg	7/11	1	2	FACETS	0.888	0.781	1	0.888	0.781	1	CLONAL	1	TRUE	1	0.29	2		540	606	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627722	14627722	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	75	406	2	ENST00000254322.2:c.348del	p.Phe116LeufsTer29	p.F116Lfs*29	ENST00000254322	NM_006145.1	116	ttT/tt	2/3	1	2	FACETS	0.855	0.75	0.968	0.855	0.75	0.968	CLONAL	1	TRUE	1	0.29	2		408	605	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379845	17379845	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	87	570	0	ENST00000359435.4:c.230C>A	p.Pro77Gln	p.P77Q	ENST00000359435	NM_001033549.1	77	cCg/cAg	2/9	1	2	FACETS	0.78	0.69	0.877	0.78	0.69	0.877	SUBCLONAL	1	TRUE	1	0.29	2		570	769	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210944	36210944	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	94	536	0	ENST00000222270.7:c.695G>A	p.Arg232Lys	p.R232K	ENST00000222270	NM_014727.1	232	aGg/aAg	3/37	1	2	FACETS	0.955	0.85	1	0.955	0.85	1	CLONAL	1	TRUE	1	0.29	2		536	679	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467481	25467481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	56	374	0	ENST00000264709.3:c.1595G>A	p.Gly532Asp	p.G532D	ENST00000264709	NM_175629.2	532	gGc/gAc	14/23	0.075974589546493	0	FACETS	0.553	0.474	0.639			1	INDETERMINATE	1	TRUE	0	0.29	0		374	496	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471041	25471041	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	64	475	0	ENST00000264709.3:c.720G>T	p.Glu240Asp	p.E240D	ENST00000264709	NM_175629.2	240	gaG/gaT	7/23	0.075974589546493	0	FACETS	0.554	0.48	0.634			1	INDETERMINATE	1	TRUE	0	0.29	0		475	566	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206730	36206730	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	61	405	1	ENST00000300305.3:c.782C>A	p.Pro261His	p.P261H	ENST00000300305		261	cCt/cAt	6/8	1	2	FACETS	0.769	0.664	0.883	0.769	0.664	0.883	SUBCLONAL	1	TRUE	1	0.29	2		406	547	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41521970	41521970	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	57	414	0	ENST00000263253.7:c.832A>C	p.Thr278Pro	p.T278P	ENST00000263253	NM_001429.3	278	Act/Cct	3/31	1	2	FACETS	0.959	0.825	1	0.959	0.825	1	CLONAL	1	TRUE	1	0.29	2		414	410	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374753	149374753	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	64	309	0	ENST00000360632.3:c.341G>A	p.Arg114His	p.R114H	ENST00000360632	NM_015472.4	114	cGc/cAc	2/7	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.29	2		309	436	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927471	178927471	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	13	221	0	ENST00000263967.3:c.1234C>T	p.Arg412Ter	p.R412*	ENST00000263967	NM_006218.2	412	Cga/Tga	7/21	1	2	FACETS	0.815	0.587	1	0.815	0.587	1	CLONAL	1	TRUE	1	0.29	2		221	110	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803700	1803700	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	100	559	0	ENST00000260795.2:c.878T>C	p.Val293Ala	p.V293A	ENST00000260795		293	gTg/gCg	6/17	0.3	2	FACETS	1	0.937	1			1	CLONAL	1	TRUE	NA	0.29	2		559	647	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31483732	31483732	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	29	164	0	ENST00000344624.3:c.2000C>A	p.Pro667His	p.P667H	ENST00000344624		667	cCt/cAt	13/33	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.29	2		164	151	SUCCESS
APC	324	MSKCC	GRCh37	5	112154839	112154839	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	40	341	0	ENST00000257430.4:c.1112del	p.Gly371GlufsTer83	p.G371Efs*83	ENST00000257430	NM_000038.5	370	ttG/tt	10/16	1	2	FACETS	0.668	0.556	0.793	0.668	0.556	0.793	SUBCLONAL	1	TRUE	1	0.29	2		341	413	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636733	176636733	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	48	289	0	ENST00000439151.2:c.1333G>T	p.Gly445Cys	p.G445C	ENST00000439151	NM_022455.4	445	Ggt/Tgt	5/23	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.29	2		289	315	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670632	30670634	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	51	324	0	ENST00000376406.3:c.5886_5888del	p.Phe1962del	p.F1962del	ENST00000376406	NM_014641.2	1962	ttCTTa/tta	13/15	0.075974589546493	3	FACETS	0.952	0.811	1	0.476	0.405	0.553	INDETERMINATE	1	TRUE	1	0.29	3		324	423	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820828	32820828	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	86	475	0	ENST00000354258.4:c.766C>A	p.Leu256Ile	p.L256I	ENST00000354258	NM_000593.5	256	Ctc/Atc	1/11	0.075974589546493	3	FACETS	1	0.916	1	0.522	0.461	0.586	INDETERMINATE	1	TRUE	1	0.29	3		475	651	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198324	138198324	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	35	207	0	ENST00000237289.4:c.917A>G	p.Tyr306Cys	p.Y306C	ENST00000237289	NM_001270507.1	306	tAc/tGc	6/9	1	2	FACETS	0.969	0.799	1	0.969	0.799	1	CLONAL	1	TRUE	1	0.29	2		207	249	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781156	161781156	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	56	366	0	ENST00000366898.1:c.1249C>T	p.Pro417Ser	p.P417S	ENST00000366898	NM_004562.2	417	Ccc/Tcc	11/12	1	2	FACETS	0.82	0.704	0.947	0.82	0.704	0.947	CLONAL	1	TRUE	1	0.29	2		366	471	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431638	6431638	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	52	244	0	ENST00000356142.4:c.191A>G	p.Tyr64Cys	p.Y64C	ENST00000356142	NM_018890.3	64	tAt/tGt	3/7	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.29	2		244	331	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508065	106508065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1326957848	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	15	131	0	ENST00000359195.3:c.59G>A	p.Arg20His	p.R20H	ENST00000359195	NM_002649.2	20	cGc/cAc	2/11	1	2	FACETS	0.598	0.439	0.787	0.598	0.439	0.787	SUBCLONAL	1	TRUE	1	0.29	2		131	173	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189055	38189055	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1250796714	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	43	378	0	ENST00000317025.8:c.959C>T	p.Ala320Val	p.A320V	ENST00000317025	NM_023034.1	320	gCg/gTg	5/24	1	2	FACETS	0.738	0.618	0.87	0.738	0.618	0.87	SUBCLONAL	1	TRUE	1	0.29	2		378	402	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413246	139413246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	69	460	0	ENST00000277541.6:c.896G>A	p.Cys299Tyr	p.C299Y	ENST00000277541	NM_017617.3	299	tGc/tAc	6/34	0.241552850215448	3	FACETS	0.745	0.648	0.85	0.373	0.324	0.425	SUBCLONAL	1	TRUE	1	0.29	3		460	731	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934426	39934426	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766556436	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	45	274	0	ENST00000378444.4:c.173C>T	p.Ala58Val	p.A58V	ENST00000378444	NM_001123385.1	58	gCg/gTg	4/15	0.075974589546493	0	FACETS	0.543	0.457	0.637			1	INDETERMINATE	1	TRUE	0	0.29	0		274	406	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855219	76855219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	30	373	0	ENST00000373344.5:c.5768G>A	p.Ser1923Asn	p.S1923N	ENST00000373344	NM_000489.3	1923	aGc/aAc	24/35	0.075974589546493	0	FACETS	0.765	0.622	0.925			1	INDETERMINATE	1	TRUE	0	0.29	0		373	192	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974792	21974792	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs141798398	NA	P-0030990-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	12	86	0	ENST00000304494.5:c.35C>A	p.Ser12Ter	p.S12*	ENST00000304494	NM_000077.4	12	tCg/tAg	1/3	1	2	FACETS	0.58	0.41	0.785	0.58	0.41	0.785	SUBCLONAL	1	TRUE	1	0.342243917462511	2		86	121	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504570	103504570	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030990-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	59	378	0	ENST00000355739.4:c.191A>T	p.Lys64Ile	p.K64I	ENST00000355739	NM_000123.3	64	aAa/aTa	2/15	1	2	FACETS	0.661	0.569	0.76	0.661	0.569	0.76	SUBCLONAL	1	TRUE	1	0.342243917462511	2		378	522	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0030996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	392	667	1	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.415315315312452	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	0	0.415315315312452	3		668	729	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911521	101911521	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	177	482	0	ENST00000374994.4:c.1446G>T	p.Arg482Ser	p.R482S	ENST00000374994	NM_004612.2	482	agG/agT	9/9	0.415315315312452	2	FACETS	0.993	0.926	1	0.993	0.926	1	CLONAL	2	TRUE	0	0.415315315312452	2		482	429	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259675	11259675	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	95	575	0	ENST00000361445.4:c.4030G>T	p.Ala1344Ser	p.A1344S	ENST00000361445	NM_004958.3	1344	Gcc/Tcc	27/58	0.415315315312452	5	FACETS	1	0.942	1	0.272	0.242	0.304	CLONAL	1	TRUE	1	0.415315315312452	5		575	682	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813409	102813409	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	117	497	0	ENST00000307046.8:c.280G>T	p.Glu94Ter	p.E94*	ENST00000307046	NM_001111285.1	94	Gag/Tag	3/4	0.415315315312452	4	FACETS	1	0.96	1	0.374	0.338	0.413	CLONAL	1	TRUE	1	0.415315315312452	4		497	710	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220632	1220640	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCTTTCC	CGGCTTTCC	GA	novel	NA	P-0030996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	195	527	1	ENST00000326873.7:c.650_658delinsGA	p.Pro217ArgfsTer68	p.P217Rfs*68	ENST00000326873	NM_000455.4	217	cCGGCTTTCCag/cGAag	5/10	0.415315315312452	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.415315315312452	2		528	456	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054433	13054433	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	210	593	0	ENST00000316448.5:c.1043G>T	p.Gly348Val	p.G348V	ENST00000316448	NM_004343.3	348	gGc/gTc	8/9	0.353021788373012	4	FACETS	0.98	0.914	1	0.98	0.914	1	CLONAL	2	TRUE	2	0.415315315312452	4		593	730	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361105	66361105	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0030996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	46	330	0	ENST00000273854.3:c.1066+1del		p.X356_splice	ENST00000273854	NM_004439.5	356			0.415315315312452	3	FACETS	0.762	0.644	0.892	0.381	0.322	0.446	SUBCLONAL	1	TRUE	1	0.415315315312452	3		330	351	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334737	81334737	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	92	555	0	ENST00000222390.5:c.1979G>A	p.Gly660Glu	p.G660E	ENST00000222390	NM_000601.4	660	gGg/gAg	17/18	1	2	FACETS	0.949	0.847	1	0.949	0.847	1	CLONAL	1	TRUE	1	0.415315315312452	2		555	467	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528762	8528762	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	148	409	0	ENST00000356435.5:c.370G>T	p.Gly124Cys	p.G124C	ENST00000356435		124	Ggc/Tgc	4/35	0.415315315312452	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.415315315312452	2		409	321	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87322805	87322805	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	141	477	0	ENST00000277120.3:c.406C>A	p.Arg136Ser	p.R136S	ENST00000277120		136	Cgt/Agt	5/19	0.298924647214977	1	FACETS	0.758	0.699	0.817	1	0.989	1	SUBCLONAL	2	TRUE	0	0.415315315312452	1		477	355	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760927	133760927	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	113	901	0	ENST00000318560.5:c.3250C>T	p.Arg1084Ter	p.R1084*	ENST00000318560	NM_005157.4	1084	Cga/Tga	11/11	0.415315315312452	2	FACETS	0.821	0.74	0.906	0.41	0.37	0.453	CLONAL	1	TRUE	0	0.415315315312452	2		901	663	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351402	70351402	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	238	688	0	ENST00000374080.3:c.4050C>G	p.Asn1350Lys	p.N1350K	ENST00000374080		1350	aaC/aaG	29/45	0.29838970330581	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.415315315312452	4		688	787	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907675	76907675	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	338	628	0	ENST00000373344.5:c.4486G>T	p.Ala1496Ser	p.A1496S	ENST00000373344	NM_000489.3	1496	Gct/Tct	15/35	0.415315315312452	5	FACETS	1	0.976	1			1	CLONAL	3	TRUE	NA	0.415315315312452	5		628	843	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	28	270	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.584029358421988	2		270	91	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955538	48955538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913303	NA	P-0030997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	46	355	0	ENST00000267163.4:c.1654C>T	p.Arg552Ter	p.R552*	ENST00000267163	NM_000321.2	552	Cga/Tga	17/27	0.490606958235649	1	FACETS	0.648	0.555	0.748	0.648	0.555	0.748	SUBCLONAL	1	TRUE	0	0.584029358421988	1		355	172	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577569	7577569	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519981	NA	P-0030997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	89	418	0	ENST00000269305.4:c.712T>A	p.Cys238Ser	p.C238S	ENST00000269305	NM_001126112.2	238	Tgt/Agt	7/11	0.523769265750438	1	FACETS	0.963	0.871	1	0.963	0.871	1	CLONAL	1	TRUE	0	0.584029358421988	1		418	224	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846307	156846307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762542314	NA	P-0030997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	114	570	2	ENST00000524377.1:c.1748G>A	p.Arg583His	p.R583H	ENST00000524377	NM_002529.3	583	cGc/cAc	14/17	1	2	FACETS	0.969	0.88	1	0.969	0.88	1	CLONAL	1	TRUE	1	0.584029358421988	2		572	403	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435402	121435402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	95	555	0	ENST00000257555.6:c.1436del	p.Pro479LeufsTer6	p.P479Lfs*6	ENST00000257555		479	Cct/ct	7/10	1	2	FACETS	0.904	0.812	1	0.904	0.812	1	CLONAL	1	TRUE	1	0.584029358421988	2		555	360	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0030998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	219	491	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.167028618549288	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.253971044401045	4		491	995	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0030998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	56	546	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.253971044401045	1	FACETS	0.608	0.52	0.704	0.608	0.52	0.704	SUBCLONAL	1	TRUE	0	0.253971044401045	1		546	633	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909235	41909235	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	58	648	0	ENST00000372991.4:c.153G>C	p.Glu51Asp	p.E51D	ENST00000372991	NM_001760.3	51	gaG/gaC	1/5	0.253971044401045	3	FACETS	0.54	0.462	0.625	0.18	0.154	0.209	SUBCLONAL	1	TRUE	0	0.253971044401045	3		648	954	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144122	55144122	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	69	564	0	ENST00000257290.5:c.1951C>A	p.Leu651Met	p.L651M	ENST00000257290	NM_006206.4	651	Ctg/Atg	14/23	0.114152672217939	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.894892521579514	0		564	166	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214737	36214737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763123772	NA	P-0031000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	10	526	2	ENST00000222270.7:c.3163C>T	p.Arg1055Trp	p.R1055W	ENST00000222270	NM_014727.1	1055	Cgg/Tgg	8/37	1	2	FACETS	0.12	0.081	0.168	0.12	0.081	0.168	SUBCLONAL	1	FALSE	1	0.894892521579514	2		528	187	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578440	7578440	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs879254249	NA	P-0031001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	46	518	0	ENST00000269305.4:c.490A>G	p.Lys164Glu	p.K164E	ENST00000269305	NM_001126112.2	164	Aag/Gag	5/11	1	2	FACETS	0.15	0.126	0.178	0.15	0.126	0.178	SUBCLONAL	1	TRUE	1	0.723800185620467	2		518	845	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591102	67591102	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	160	288	0	ENST00000274335.5:c.1695C>A	p.Ser565Arg	p.S565R	ENST00000274335		565	agC/agA	12/15	1	2	FACETS	0.912	0.843	0.982	0.912	0.843	0.982	CLONAL	1	TRUE	1	0.723800185620467	2		288	485	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119673	108119673	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs775767808	NA	P-0031001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	79	148	0	ENST00000278616.4:c.1079A>G	p.Asp360Gly	p.D360G	ENST00000278616	NM_000051.3	360	gAt/gGt	9/63	0.723800185620467	1	FACETS	0.981	0.893	1	0.981	0.893	1	CLONAL	1	TRUE	0	0.723800185620467	1		148	142	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465451	99465451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	184	372	0	ENST00000268035.6:c.2276C>T	p.Ala759Val	p.A759V	ENST00000268035	NM_000875.3	759	gCc/gTc	11/21	1	2	FACETS	0.919	0.855	0.986	0.919	0.855	0.986	CLONAL	1	TRUE	1	0.723800185620467	2		372	553	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967622	90967622	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs370121348	NA	P-0031001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	160	272	0	ENST00000265433.3:c.1286A>G	p.Tyr429Cys	p.Y429C	ENST00000265433	NM_002485.4	429	tAt/tGt	10/16	0.570599873175866	3	FACETS	0.954	0.878	1			1	CLONAL	1	TRUE	NA	0.723800185620467	3		272	631	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0031003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	125	621	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.348434976983274	1	FACETS	0.953	0.865	1	0.953	0.865	1	CLONAL	1	TRUE	0	0.348434976983274	1		624	622	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	98	384	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.889	0.794	0.989	0.889	0.794	0.989	CLONAL	1	TRUE	1	0.348434976983274	2		384	633	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020754	37020754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	121	540	3	ENST00000358127.4:c.91C>T	p.Arg31Trp	p.R31W	ENST00000358127	NM_001280556.1	31	Cgg/Tgg	2/10	1	2	FACETS	0.974	0.881	1	0.974	0.881	1	CLONAL	1	TRUE	1	0.348434976983274	2		543	713	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492938	56492938	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0031003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	45	201	0	ENST00000407977.2:c.1A>G	p.Met1?	p.M1?	ENST00000407977		1	Atg/Gtg	2/10	0.348434976983274	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.348434976983274	1		201	187	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593602	55593610	+	inframe_deletion	In_Frame_Del	DEL	GTGGAAGGT	GTGGAAGGT	-	novel	NA	P-0031004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	202	493	0	ENST00000288135.5:c.1668_1676del	p.Gln556_Val559delinsHis	p.Q556_V559delinsH	ENST00000288135	NM_000222.2	556	caGTGGAAGGTt/cat	11/21	1	2	FACETS	0.844	0.786	0.904	0.844	0.786	0.904	CLONAL	1	TRUE	1	0.73398445902188	2		493	652	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1427441061	NA	P-0031005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	196	560	0	ENST00000269305.4:c.560-2A>G		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.226940863125097	2	FACETS	0.913	0.85	0.977	0.913	0.85	0.977	CLONAL	2	TRUE	0	0.355488075602617	2		560	604	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242481	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAGCAA	TTAAGAGAAGCAA	C	rs397509368	NA	P-0031005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	402	589	0	ENST00000275493.2:c.2239_2251delinsC	p.Leu747_Thr751delinsPro	p.L747_T751delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGCAAca/Cca	19/28	0.355488075602617	5	FACETS	0.876	0.836	0.916	0.876	0.836	0.916	CLONAL	4	TRUE	1	0.355488075602617	5		589	990	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860717	3860717	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs749031320	NA	P-0031005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	71	498	0	ENST00000262367.5:c.862A>G	p.Met288Val	p.M288V	ENST00000262367	NM_004380.2	288	Atg/Gtg	3/31	1	2	FACETS	0.591	0.515	0.673	0.591	0.515	0.673	SUBCLONAL	1	TRUE	1	0.355488075602617	2		498	676	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0031006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	463	633	1	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	0.35839810868206	2	FACETS	0.959	0.916	1	0.959	0.916	1	CLONAL	2	TRUE	0	0.35839810868206	2		634	1347	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045709	26045709	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	99	250	0	ENST00000540144.1:c.71A>G	p.Lys24Arg	p.K24R	ENST00000540144	NM_003531.2	24	aAa/aGa	1/1	0.35839810868206	4	FACETS	1	0.897	1	0.502	0.448	0.56	CLONAL	1	TRUE	2	0.35839810868206	4		250	747	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0031007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	156	440	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	0.259635345634928	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.259635345634928	2		440	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0031007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	195	691	0	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	0.259635345634928	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.259635345634928	1		691	953	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0031009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	59	477	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.237581339569567	2	FACETS	0.355	0.305	0.411	0.178	0.152	0.206	SUBCLONAL	1	TRUE	0	0.389316259678589	2		478	853	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0031009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	342	790	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.237581339569567	2	FACETS	0.877	0.831	0.923	0.877	0.831	0.923	CLONAL	2	TRUE	0	0.389316259678589	2		790	1002	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001340	150001340	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	148	630	0	ENST00000253339.5:c.2264A>G	p.Asp755Gly	p.D755G	ENST00000253339		755	gAt/gGt	4/7	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.389316259678589	2		630	713	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220074	36220075	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTGTA	novel	NA	P-0031009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	371	658	0	ENST00000222270.7:c.4795_4799dup	p.Ile1601CysfsTer47	p.I1601Cfs*47	ENST00000222270	NM_014727.1	1598	-/TTGTA	22/37	0.346407307520933	3	FACETS	0.885	0.844	0.926	0.885	0.844	0.926	CLONAL	3	TRUE	0	0.389316259678589	3		658	858	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218659	98218659	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	47	415	0	ENST00000331920.6:c.3205G>T	p.Gly1069Cys	p.G1069C	ENST00000331920	NM_000264.3	1069	Ggc/Tgc	19/24	1	2	FACETS	0.534	0.451	0.626	0.534	0.451	0.626	SUBCLONAL	1	TRUE	1	0.389316259678589	2		415	452	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891277	101891277	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	101	602	1	ENST00000374994.4:c.238C>T	p.Arg80Ter	p.R80*	ENST00000374994	NM_004612.2	80	Cga/Tga	2/9	0.501274647733555	1	FACETS	0.929	0.84	1	0.929	0.84	1	CLONAL	1	TRUE	0	0.501274647733555	1		603	325	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106957	27106965	+	inframe_deletion	In_Frame_Del	DEL	GGCAGTATC	GGCAGTATC	-	novel	NA	P-0031012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	89	473	0	ENST00000324856.7:c.6572_6580del	p.Ser2191_Gly2193del	p.S2191_G2193del	ENST00000324856	NM_006015.4	2190	GGCAGTATC/-	20/20	0.501274647733555	1	FACETS	0.971	0.873	1	0.971	0.873	1	CLONAL	1	TRUE	0	0.501274647733555	1		473	274	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353848	40353848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1489641088	NA	P-0031012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	107	508	0	ENST00000293328.3:c.2272G>A	p.Asp758Asn	p.D758N	ENST00000293328	NM_012448.3	758	Gat/Aat	19/19	0.501274647733555	3	FACETS	0.967	0.87	1	0.484	0.435	0.535	CLONAL	1	TRUE	1	0.501274647733555	3		508	552	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528075	157528075	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	93	506	0	ENST00000346085.5:c.5800A>T	p.Ile1934Phe	p.I1934F	ENST00000346085	NM_020732.3	1934	Atc/Ttc	20/20	1	2	FACETS	0.937	0.839	1	0.937	0.839	1	CLONAL	1	TRUE	1	0.501274647733555	2		506	396	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0031013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	34	572	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.874	0.713	1	0.874	0.713	1	CLONAL	1	TRUE	1	0.14	2		572	556	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0031013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	48	366	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.757	0.641	0.885	1	0.962	1	SUBCLONAL	2	TRUE	1	0.14	2		366	453	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0031013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	37	658	3	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.975	0.803	1	0.975	0.803	1	CLONAL	1	TRUE	1	0.14	2		661	542	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339328	70339328	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0031013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	23	468	0	ENST00000374080.3:c.204+1G>T		p.X68_splice	ENST00000374080		68			1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.14	2		468	276	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163866	152163866	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	55	481	0	ENST00000206249.3:c.587A>G	p.His196Arg	p.H196R	ENST00000206249	NM_000125.3	196	cAt/cGt	2/8	0.175430389144933	3	FACETS	0.81	0.693	0.937	0.81	0.693	0.937	CLONAL	2	TRUE	1	0.14	3		481	519	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828912	72828912	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	34	578	1	ENST00000268489.5:c.7669C>T	p.Gln2557Ter	p.Q2557*	ENST00000268489	NM_006885.3	2557	Cag/Tag	9/10	0.101595749582925	3	FACETS	0.858	0.703	1	0.858	0.703	1	CLONAL	2	TRUE	1	0.14	3		579	303	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622517	158622517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906588	NA	P-0031013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	35	515	0	ENST00000263640.3:c.982G>A	p.Gly328Arg	p.G328R	ENST00000263640	NM_001105.4	328	Ggg/Agg	8/11	1	2	FACETS	0.882	0.721	1	0.882	0.721	1	CLONAL	1	TRUE	1	0.14	2		515	567	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0031023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	221	435	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.413494909653452	4	FACETS	0.952	0.89	1	0.952	0.89	1	CLONAL	2	TRUE	2	0.500420872532146	4		435	696	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0031023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1318	99	648	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.413494909653452	4	FACETS	0.419	0.372	0.469	0.209	0.186	0.235	SUBCLONAL	1	TRUE	2	0.500420872532146	4		648	1417	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951089	17951089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750687910	NA	P-0031023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	250	662	1	ENST00000458235.1:c.1204C>T	p.Arg402Cys	p.R402C	ENST00000458235	NM_000215.3	402	Cgc/Tgc	9/24	1	2	FACETS	0.976	0.913	1	0.976	0.913	1	CLONAL	1	TRUE	1	0.500420872532146	2		663	1024	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962899	2962899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3735134	NA	P-0031023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	231	733	0	ENST00000396946.4:c.2009C>T	p.Thr670Met	p.T670M	ENST00000396946	NM_032415.4	670	aCg/aTg	16/25	1	2	FACETS	0.911	0.85	0.975	0.911	0.85	0.975	CLONAL	1	TRUE	1	0.500420872532146	2		733	1013	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	139	270	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.72163879304409	2		270	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0031024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	254	621	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.72163879304409	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.72163879304409	1		624	418	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184750	185184750	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs752255390	NA	P-0031024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	186	363	0	ENST00000265026.3:c.1642C>T	p.Arg548Trp	p.R548W	ENST00000265026	NM_004721.4	548	Cgg/Tgg	10/14	0.205377467992164	3	FACETS	0.767	0.716	0.819	0.767	0.716	0.819	INDETERMINATE	2	TRUE	1	0.72163879304409	3		363	457	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924952	49924952	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1397526390	NA	P-0031024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	238	523	3	ENST00000296474.3:c.3991C>T	p.Arg1331Ter	p.R1331*	ENST00000296474	NM_002447.2	1331	Cga/Tga	20/20	0.205377467992164	3	FACETS	1	0.992	1	0.701	0.659	0.745	INDETERMINATE	1	TRUE	1	0.72163879304409	3		526	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0031025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	164	701	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.28	2		701	1117	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	90	384	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	0.28	2		384	536	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729968	30729968	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs863223852	NA	P-0031025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	66	399	0	ENST00000295754.5:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000295754	NM_003242.5	497	Cga/Tga	6/7	1	2	FACETS	0.734	0.637	0.84	0.734	0.637	0.84	SUBCLONAL	1	TRUE	1	0.28	2		399	642	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281421	142281421	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	48	641	0	ENST00000350721.4:c.823G>T	p.Glu275Ter	p.E275*	ENST00000350721	NM_001184.3	275	Gaa/Taa	4/47	1	2	FACETS	0.528	0.446	0.62	0.528	0.446	0.62	SUBCLONAL	1	TRUE	1	0.28	2		641	649	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970953	21970992	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCGCAGCCGCGCGCAGGTACCGTGCGACATCGCGATGG	CCCCGCAGCCGCGCGCAGGTACCGTGCGACATCGCGATGG	-	novel	NA	P-0031025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	81	640	0	ENST00000304494.5:c.366_405del	p.His123AlafsTer10	p.H123Afs*10	ENST00000304494	NM_000077.4	122	ggCCATCGCGATGTCGCACGGTACCTGCGCGCGGCTGCGGGG/gg	2/3	0.20356082816636	1	FACETS	0.493	0.433	0.558	0.493	0.433	0.558	SUBCLONAL	1	TRUE	0	0.28	1		640	1009	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	247	384	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.290074412180482	6	FACETS	0.883	0.826	0.942			1	CLONAL	3	FALSE	NA	0.290074412180482	6		384	1016	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	227	270	0				ENST00000310581	NM_198253.2	-/1132			0.189978680960353	2	FACETS	0.911	0.85	0.974	0.455	0.425	0.487	INDETERMINATE	1	TRUE	0	0.547151792600879	2		270	911	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0031027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	184	332	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	0.547151792600879	2		332	596	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0031027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1501	216	651	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.290764194996617	3	FACETS	0.586	0.542	0.631	0.293	0.271	0.316	INDETERMINATE	1	TRUE	1	0.547151792600879	3		651	1717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572928	7572928	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	novel	NA	P-0031027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	503	525	0	ENST00000269305.4:c.1181G>C	p.Ter394SerextTer9	p.*394Sext*9	ENST00000269305	NM_001126112.2	394	tGa/tCa	11/11	0.547151792600879	1	FACETS	0.779	0.752	0.806	1	0.997	1	SUBCLONAL	2	TRUE	0	0.547151792600879	1		525	857	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536229	41536229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	335	643	0	ENST00000263253.7:c.1846G>A	p.Glu616Lys	p.E616K	ENST00000263253	NM_001429.3	616	Gaa/Aaa	9/31	0.433585082448343	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.547151792600879	1		643	862	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023696	27023696	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	352	559	0	ENST00000324856.7:c.802C>T	p.Gln268Ter	p.Q268*	ENST00000324856	NM_006015.4	268	Cag/Tag	1/20	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.547151792600879	2		559	1066	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120457930	120457930	+	stop_lost	Nonstop_Mutation	SNP	C	C	A	novel	NA	P-0031027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	41	382	0	ENST00000256646.2:c.7415G>T	p.Ter2472LeuextTer7	p.*2472Lext*7	ENST00000256646	NM_024408.3	2472	tGa/tTa	34/34	1	2	FACETS	0.196	0.163	0.234	0.196	0.163	0.234	SUBCLONAL	1	TRUE	1	0.547151792600879	2		382	764	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830734	156830734	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	68	114	0	ENST00000524377.1:c.8G>C	p.Arg3Pro	p.R3P	ENST00000524377	NM_002529.3	3	cGa/cCa	1/17	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.547151792600879	2		114	196	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943312	71943312	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	227	656	0	ENST00000298229.2:c.1644C>A	p.Phe548Leu	p.F548L	ENST00000298229	NM_001567.3	548	ttC/ttA	14/28	0.194927226414507	2	FACETS	0.598	0.555	0.642	0.299	0.277	0.321	INDETERMINATE	1	TRUE	0	0.547151792600879	2		656	1388	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941720	48941720	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	113	370	0	ENST00000267163.4:c.1030C>A	p.Gln344Lys	p.Q344K	ENST00000267163	NM_000321.2	344	Cag/Aag	10/27	0.547151792600879	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.547151792600879	1		370	276	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051240	13051240	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs938433963	NA	P-0031027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	292	459	0	ENST00000316448.5:c.676G>A	p.Asp226Asn	p.D226N	ENST00000316448	NM_004343.3	226	Gat/Aat	5/9	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.547151792600879	2		459	859	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721073	61721073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	261	546	0	ENST00000401558.2:c.1201G>A	p.Asp401Asn	p.D401N	ENST00000401558	NM_003400.3	401	Gat/Aat	12/25	0.290764194996617	3	FACETS	1	0.987	1	0.596	0.559	0.635	INDETERMINATE	1	TRUE	1	0.547151792600879	3		546	1019	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947495	38947495	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	57	321	0	ENST00000357387.3:c.4185G>C	p.Leu1395Phe	p.L1395F	ENST00000357387	NM_152756.3	1395	ttG/ttC	32/38	0.189978680960353	2	FACETS	0.487	0.419	0.561	0.243	0.209	0.281	INDETERMINATE	1	TRUE	0	0.547151792600879	2		321	428	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652005	36652005	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	252	703	0	ENST00000244741.5:c.127C>T	p.Gln43Ter	p.Q43*	ENST00000244741	NM_000389.4	43	Cag/Tag	2/3	0.333932430462203	1	FACETS	0.553	0.517	0.591	0.553	0.517	0.591	SUBCLONAL	1	TRUE	0	0.547151792600879	1		703	1210	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350071	81350071	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	52	432	0	ENST00000222390.5:c.1261G>C	p.Asp421His	p.D421H	ENST00000222390	NM_000601.4	421	Gac/Cac	10/18	1	2	FACETS	0.386	0.328	0.448	0.386	0.328	0.448	SUBCLONAL	1	TRUE	1	0.547151792600879	2		432	493	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938818	76938818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	41	329	0	ENST00000373344.5:c.1930G>A	p.Val644Ile	p.V644I	ENST00000373344	NM_000489.3	644	Gtt/Att	9/35	0.519175393657345	2	FACETS	0.338	0.281	0.4			1	SUBCLONAL	1	TRUE	NA	0.547151792600879	2		329	444	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81968086	81968086	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	123	563	1	ENST00000359376.3:c.2792C>A	p.Ser931Tyr	p.S931Y	ENST00000359376	NM_002661.3	931	tCt/tAt	26/33	0.41957745419263	2	FACETS	0.931	0.845	1	0.466	0.422	0.511	CLONAL	1	TRUE	0	0.463420388480324	2		564	570	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604665	48604665	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	216	260	0	ENST00000342988.3:c.1487G>C	p.Arg496Pro	p.R496P	ENST00000342988	NM_005359.5	496	cGt/cCt	12/12	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	2	TRUE	NA	0.849050357705789	2		260	248	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106178	27106178	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	396	524	0	ENST00000324856.7:c.5789C>A	p.Ser1930Ter	p.S1930*	ENST00000324856	NM_006015.4	1930	tCa/tAa	20/20	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.849050357705789	2		524	453	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248245	59248245	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	18	25	0	ENST00000371222.2:c.498G>C	p.Glu166Asp	p.E166D	ENST00000371222	NM_002228.3	166	gaG/gaC	1/1	0.829523066991055	4	FACETS	1	0.843	1	1	0.843	1	CLONAL	2	TRUE	2	0.849050357705789	4		25	37	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577064	7577065	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0031030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	433	664	0	ENST00000269305.4:c.873_874del	p.Lys292ArgfsTer13	p.K292Rfs*13	ENST00000269305	NM_001126112.2	291	aaGAaa/aaaa	8/11	0.840809914887223	2	FACETS	0.932	0.907	0.956	0.932	0.907	0.956	CLONAL	2	TRUE	0	0.849050357705789	2		664	547	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939769	76939769	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	303	422	0	ENST00000373344.5:c.979G>T	p.Glu327Ter	p.E327*	ENST00000373344	NM_000489.3	327	Gaa/Taa	9/35	0.753294544482994	4	FACETS	0.868	0.822	0.915	0.868	0.822	0.915	CLONAL	2	TRUE	2	0.849050357705789	4		422	760	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863356	57863356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	437	894	0	ENST00000228682.2:c.1451G>A	p.Gly484Glu	p.G484E	ENST00000228682	NM_005269.2	484	gGa/gAa	11/12	0.849050357705789	6	FACETS	0.913	0.87	0.957	0.457	0.435	0.479	CLONAL	2	TRUE	2	0.849050357705789	6		894	1521	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226490	2226490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780810017	NA	P-0031030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	519	800	2	ENST00000398665.3:c.3970G>A	p.Ala1324Thr	p.A1324T	ENST00000398665	NM_032482.2	1324	Gcg/Acg	27/28	0.849050357705789	2	FACETS	0.992	0.971	1	0.992	0.971	1	CLONAL	2	TRUE	0	0.849050357705789	2		802	616	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218809	5218809	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	330	516	0	ENST00000357368.4:c.3924C>G	p.Asn1308Lys	p.N1308K	ENST00000357368	NM_002850.3	1308	aaC/aaG	24/38	0.849050357705789	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.849050357705789	2		516	386	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141570518	141570518	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1547	224	587	0	ENST00000220592.5:c.610C>T	p.Gln204Ter	p.Q204*	ENST00000220592	NM_012154.3	204	Cag/Tag	5/19	0.849050357705789	8	FACETS	1	0.962	1	0.176	0.163	0.19	CLONAL	1	TRUE	2	0.849050357705789	8		587	1771	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0031038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	271	836	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.494318162767129	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.501069708032708	1		836	768	SUCCESS
APC	324	MSKCC	GRCh37	5	112175271	112175271	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	184	234	1	ENST00000257430.4:c.3980C>A	p.Ser1327Ter	p.S1327*	ENST00000257430	NM_000038.5	1327	tCa/tAa	16/16	0.495679726704267	2	FACETS	0.984	0.923	1	0.984	0.923	1	CLONAL	2	TRUE	0	0.501069708032708	2		235	373	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211109	36211109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756303519	NA	P-0031038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	273	879	1	ENST00000222270.7:c.860G>A	p.Arg287His	p.R287H	ENST00000222270	NM_014727.1	287	cGt/cAt	3/37	1	2	FACETS	0.933	0.875	0.992	0.933	0.875	0.992	CLONAL	1	TRUE	1	0.501069708032708	2		880	1168	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145623	11145623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878854219	NA	P-0031038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	235	712	0	ENST00000358026.2:c.3985C>T	p.Arg1329Cys	p.R1329C	ENST00000358026	NM_001128849.1	1329	Cgc/Tgc	29/36	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.501069708032708	2		712	890	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0031040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	360	562	1	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.326598945513926	3	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.387196689220793	3		563	953	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562482	21562483	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGGCG	rs550642106	NA	P-0031040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	12	139	0	ENST00000382592.4:c.1431_1436dup	p.Pro479_Ala480dup	p.P479_A480dup	ENST00000382592	NM_014572.2	479	ccg/ccCGCCCCg	4/8	0.274726559804088	2	FACETS	0.544	0.385	0.735	0.272	0.192	0.368	SUBCLONAL	1	TRUE	0	0.387196689220793	2		139	114	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435666	18435666	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	19	251	0	ENST00000266497.5:c.651G>C	p.Trp217Cys	p.W217C	ENST00000266497		217	tgG/tgC	1/31	0.236021238809894	1	FACETS	0.247	0.187	0.318	0.247	0.187	0.318	SUBCLONAL	1	TRUE	0	0.387196689220793	1		251	320	SUCCESS
AR	367	MSKCC	GRCh37	X	66937409	66937409	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	147	243	0	ENST00000374690.3:c.2263T>G	p.Phe755Val	p.F755V	ENST00000374690	NM_000044.3	755	Ttc/Gtc	5/8	0.202240783053329	2	FACETS	0.869	0.8	0.939			1	INDETERMINATE	2	TRUE	NA	0.387196689220793	2		243	437	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	214	568	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.744	0.691	0.799	0.744	0.691	0.799	SUBCLONAL	1	TRUE	1	0.517321814350736	2		570	1112	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	151	233	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.517321814350736	2		233	407	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	171	734	4	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.514	0.471	0.559	0.514	0.471	0.559	SUBCLONAL	1	TRUE	1	0.517321814350736	2		738	1286	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027087	71027087	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	177	460	1	ENST00000318789.4:c.1240del	p.Leu414Ter	p.L414*	ENST00000318789	NM_032682.5	414	Ctg/tg	15/21	1	2	FACETS	0.785	0.723	0.848	0.785	0.723	0.848	SUBCLONAL	1	TRUE	1	0.517321814350736	2		461	872	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498235	498235	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	27	234	0	ENST00000399788.2:c.23del	p.Gly8AlafsTer58	p.G8Afs*58	ENST00000399788	NM_001042603.1	8	gGc/gc	1/28	1	2	FACETS	0.242	0.192	0.299	0.242	0.192	0.299	SUBCLONAL	1	TRUE	1	0.517321814350736	2		234	431	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	307	488	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.517321814350736	2		488	904	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793663	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	330	613	0	ENST00000263967.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000263967	NM_006218.2	93	cGg/cAg	2/21	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.517321814350736	2		613	971	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023904	27023904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1232964733	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	61	154	0	ENST00000324856.7:c.1015del	p.Ala339LeufsTer24	p.A339Lfs*24	ENST00000324856	NM_006015.4	337	tGg/tg	1/20	1	2	FACETS	0.947	0.826	1	0.947	0.826	1	CLONAL	1	TRUE	1	0.517321814350736	2		154	249	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	254	467	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.517321814350736	2		467	791	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	208	637	5	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	0.665	0.616	0.715	0.665	0.616	0.715	SUBCLONAL	1	TRUE	1	0.517321814350736	2		642	1210	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845553	63845553	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	138	420	0	ENST00000279873.7:c.1295del	p.Asn432MetfsTer47	p.N432Mfs*47	ENST00000279873	NM_032199.2	431	gAa/ga	9/10	1	2	FACETS	0.702	0.639	0.768	0.702	0.639	0.768	SUBCLONAL	1	TRUE	1	0.517321814350736	2		420	760	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884218	37884218	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	69	569	2	ENST00000269571.5:c.3694del	p.Ala1232LeufsTer70	p.A1232Lfs*70	ENST00000269571		1230	cGg/cg	27/27	1	2	FACETS	0.257	0.223	0.294	0.257	0.223	0.294	SUBCLONAL	1	TRUE	1	0.517321814350736	2		571	1039	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630626	158630626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912678	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	208	261	0	ENST00000263640.3:c.617G>A	p.Arg206His	p.R206H	ENST00000263640	NM_001105.4	206	cGc/cAc	6/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.517321814350736	2		261	587	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	246	610	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	0.517321814350736	2		613	1258	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1358	83	739	1	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.223	0.195	0.252	0.223	0.195	0.252	SUBCLONAL	1	TRUE	1	0.517321814350736	2		740	1441	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221756	36221756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377420237	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	238	678	1	ENST00000222270.7:c.5425G>A	p.Ala1809Thr	p.A1809T	ENST00000222270	NM_014727.1	1809	Gcc/Acc	26/37	1	2	FACETS	0.799	0.745	0.854	0.799	0.745	0.854	SUBCLONAL	1	TRUE	1	0.517321814350736	2		679	1152	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830778	72830778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781579217	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	174	483	3	ENST00000268489.5:c.5803C>T	p.Arg1935Cys	p.R1935C	ENST00000268489	NM_006885.3	1935	Cgc/Tgc	9/10	1	2	FACETS	0.778	0.716	0.841	0.778	0.716	0.841	SUBCLONAL	1	TRUE	1	0.517321814350736	2		486	865	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874836	151874836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs992402398	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	170	242	0	ENST00000262189.6:c.7702G>A	p.Gly2568Arg	p.G2568R	ENST00000262189	NM_170606.2	2568	Gga/Aga	38/59	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.517321814350736	2		242	512	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120457941	120457941	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	109	350	0	ENST00000256646.2:c.7404G>T	p.Gln2468His	p.Q2468H	ENST00000256646	NM_024408.3	2468	caG/caT	34/34	1	2	FACETS	0.599	0.538	0.663	0.599	0.538	0.663	SUBCLONAL	1	TRUE	1	0.517321814350736	2		350	704	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023437	27023455	+	frameshift_variant	Frame_Shift_Del	DEL	GGCAGCGCTGCAGAGCGGC	GGCAGCGCTGCAGAGCGGC	-	novel	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	369	549	0	ENST00000324856.7:c.546_564del	p.Leu184GlyfsTer42	p.L184Gfs*42	ENST00000324856	NM_006015.4	181	ctGGCAGCGCTGCAGAGCGGC/ct	1/20	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.517321814350736	2		549	986	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984430	201984430	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	56	550	0	ENST00000359651.3:c.1095G>T	p.Glu365Asp	p.E365D	ENST00000359651		365	gaG/gaT	8/8	1	2	FACETS	0.203	0.173	0.236	0.203	0.173	0.236	SUBCLONAL	1	TRUE	1	0.517321814350736	2		550	1066	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720771	89720772	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTGCAGATAATGACAAGGAATATCTA	novel	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	68	171	0	ENST00000371953.3:c.925_950dup	p.Leu318GlnfsTer8	p.L318Qfs*8	ENST00000371953	NM_000314.4	308	cgt/cGTGCAGATAATGACAAGGAATATCTAgt	8/9	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.517321814350736	2		171	261	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724619	112724619	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	295	409	0	ENST00000369452.4:c.503T>C	p.Leu168Ser	p.L168S	ENST00000369452	NM_007373.3	168	tTg/tCg	2/9	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.517321814350736	2		409	831	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999121	100999122	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	237	577	0	ENST00000325455.5:c.680_681del	p.Ser227Ter	p.S227*	ENST00000325455	NM_001202474.3	227	tCT/t	1/8	1	2	FACETS	0.835	0.779	0.893	0.835	0.779	0.893	CLONAL	1	TRUE	1	0.517321814350736	2		577	1097	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	463270	463270	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	51	499	0	ENST00000399788.2:c.1001A>C	p.Asp334Ala	p.D334A	ENST00000399788	NM_001042603.1	334	gAc/gCc	8/28	1	2	FACETS	0.211	0.179	0.247	0.211	0.179	0.247	SUBCLONAL	1	TRUE	1	0.517321814350736	2		499	933	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929185	32929185	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs80358948	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	235	550	0	ENST00000380152.3:c.7195A>G	p.Thr2399Ala	p.T2399A	ENST00000380152		2399	Aca/Gca	14/27	1	2	FACETS	0.883	0.824	0.944	0.883	0.824	0.944	CLONAL	1	TRUE	1	0.517321814350736	2		550	1029	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36989283	36989283	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	196	491	0	ENST00000354822.5:c.52G>A	p.Gly18Arg	p.G18R	ENST00000354822	NM_001079668.2	18	Ggg/Agg	1/3	1	2	FACETS	0.817	0.757	0.88	0.817	0.757	0.88	CLONAL	1	TRUE	1	0.517321814350736	2		491	927	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609518	81609518	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs768939158	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	104	387	0	ENST00000298171.2:c.1120del	p.Gln374ArgfsTer38	p.Q374Rfs*38	ENST00000298171	NM_000369.2	372	aaC/aa	10/10	1	2	FACETS	0.503	0.45	0.559	0.503	0.45	0.559	SUBCLONAL	1	TRUE	1	0.517321814350736	2		387	800	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354328	354328	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	113	483	0	ENST00000262320.3:c.1230G>T	p.Glu410Asp	p.E410D	ENST00000262320	NM_003502.3	410	gaG/gaT	5/11	1	2	FACETS	0.453	0.407	0.502	0.453	0.407	0.502	SUBCLONAL	1	TRUE	1	0.517321814350736	2		483	964	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992651	72992651	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	49	332	0	ENST00000268489.5:c.1394A>C	p.Glu465Ala	p.E465A	ENST00000268489	NM_006885.3	465	gAg/gCg	2/10	1	2	FACETS	0.275	0.232	0.322	0.275	0.232	0.322	SUBCLONAL	1	TRUE	1	0.517321814350736	2		332	690	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81922853	81922853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749902171	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	216	444	0	ENST00000359376.3:c.842C>T	p.Ala281Val	p.A281V	ENST00000359376	NM_002661.3	281	gCt/gTt	10/33	1	2	FACETS	0.857	0.797	0.919	0.857	0.797	0.919	CLONAL	1	TRUE	1	0.517321814350736	2		444	974	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52722997	52722998	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	219	515	1	ENST00000322088.6:c.1182_1183delinsAT	p.Ile395Phe	p.I395F	ENST00000322088	NM_014225.5	394	gtGAtt/gtATtt	10/15	1	2	FACETS	0.8	0.744	0.858	0.8	0.744	0.858	SUBCLONAL	1	TRUE	1	0.517321814350736	2		516	1058	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561223	9561223	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs34280805	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	167	356	0	ENST00000353224.5:c.559C>A	p.Pro187Thr	p.P187T	ENST00000353224	NM_177990.2	187	Cct/Act	4/10	1	2	FACETS	0.891	0.82	0.964	0.891	0.82	0.964	CLONAL	1	TRUE	1	0.517321814350736	2		356	725	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031668	36031668	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	86	566	0	ENST00000358208.4:c.1497C>A	p.Cys499Ter	p.C499*	ENST00000358208		499	tgC/tgA	12/12	1	2	FACETS	0.296	0.261	0.334	0.296	0.261	0.334	SUBCLONAL	1	TRUE	1	0.517321814350736	2		566	1124	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728733	39728733	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs761702126	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	160	388	0	ENST00000361337.2:c.1013A>G	p.Tyr338Cys	p.Y338C	ENST00000361337	NM_003286.2	338	tAt/tGt	12/21	1	2	FACETS	0.839	0.771	0.91	0.839	0.771	0.91	CLONAL	1	TRUE	1	0.517321814350736	2		388	737	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730774	40730774	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	114	447	0	ENST00000373198.4:c.3761C>T	p.Ala1254Val	p.A1254V	ENST00000373198	NM_133170.3	1254	gCa/gTa	27/32	1	2	FACETS	0.541	0.487	0.599	0.541	0.487	0.599	SUBCLONAL	1	TRUE	1	0.517321814350736	2		447	814	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383998	84383998	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780076912	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	198	488	0	ENST00000321945.7:c.854G>A	p.Arg285Gln	p.R285Q	ENST00000321945	NM_139076.2	285	cGg/cAg	9/9	1	2	FACETS	0.769	0.712	0.829	0.769	0.712	0.829	SUBCLONAL	1	TRUE	1	0.517321814350736	2		488	995	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31424570	31424571	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	126	674	0	ENST00000344624.3:c.3224dup	p.Glu1076ArgfsTer19	p.E1076Rfs*19	ENST00000344624		1075	cgc/cgGc	25/33	1	2	FACETS	0.414	0.374	0.457	0.414	0.374	0.457	SUBCLONAL	1	TRUE	1	0.517321814350736	2		674	1176	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371869	116371869	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	45	392	0	ENST00000397752.3:c.1348C>A	p.Leu450Ile	p.L450I	ENST00000397752	NM_000245.2	450	Ctc/Atc	3/21	1	2	FACETS	0.238	0.199	0.281	0.238	0.199	0.281	SUBCLONAL	1	TRUE	1	0.517321814350736	2		392	732	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852149	128852149	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1306	82	766	0	ENST00000249373.3:c.2221C>A	p.Pro741Thr	p.P741T	ENST00000249373	NM_005631.4	741	Ccc/Acc	12/12	1	2	FACETS	0.228	0.2	0.259	0.228	0.2	0.259	SUBCLONAL	1	TRUE	1	0.517321814350736	2		766	1388	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38135865	38135865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	114	485	1	ENST00000317025.8:c.3826G>A	p.Gly1276Arg	p.G1276R	ENST00000317025	NM_023034.1	1276	Gga/Aga	22/24	0.264727208203321	3	FACETS	0.5	0.449	0.554	0.167	0.149	0.185	INDETERMINATE	1	TRUE	0	0.517321814350736	3		486	1110	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981896	70981896	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	77	612	0	ENST00000276594.2:c.200C>A	p.Pro67His	p.P67H	ENST00000276594	NM_024504.3	67	cCc/cAc	2/8	0.517321814350736	3	FACETS	0.303	0.265	0.345	0.101	0.088	0.115	SUBCLONAL	1	TRUE	0	0.517321814350736	3		612	1236	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732907	44732907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	301	464	2	ENST00000377967.4:c.110C>T	p.Ala37Val	p.A37V	ENST00000377967	NM_021140.2	37	gCg/gTg	1/29	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.517321814350736	2		466	853	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412944	63412944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	256	698	0	ENST00000330258.3:c.223G>A	p.Gly75Arg	p.G75R	ENST00000330258	NM_152424.3	75	Ggg/Agg	2/2	1	2	FACETS	0.825	0.772	0.881	0.825	0.772	0.881	CLONAL	1	TRUE	1	0.517321814350736	2		698	1199	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	117	384	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.946	0.865	1	0.946	0.865	1	CLONAL	1	TRUE	1	0.777700364379688	2		384	318	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175481	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0031043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	89	253	0	ENST00000257430.4:c.4192_4193del	p.Arg1399PhefsTer9	p.R1399Ffs*9	ENST00000257430	NM_000038.5	1397	GAg/g	16/16	1	2	FACETS	0.86	0.774	0.95	0.86	0.774	0.95	CLONAL	1	TRUE	1	0.777700364379688	2		253	266	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0031043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	129	351	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.746855193852246	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.777700364379688	1		351	201	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0031043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	101	458	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.777700364379688	2		458	256	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109311998	109311998	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	195	574	0	ENST00000436639.2:c.1274G>A	p.Arg425His	p.R425H	ENST00000436639	NM_014454.2	425	cGc/cAc	8/10	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.777700364379688	2		574	495	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300899	137300899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765850979	NA	P-0031043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	144	634	2	ENST00000481739.1:c.544C>T	p.Arg182Trp	p.R182W	ENST00000481739	NM_002957.4	182	Cgg/Tgg	4/10	1	2	FACETS	0.884	0.814	0.955	0.884	0.814	0.955	CLONAL	1	TRUE	1	0.777700364379688	2		636	419	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73046207	73046207	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	84	507	0	ENST00000356692.5:c.19C>T	p.Gln7Ter	p.Q7*	ENST00000356692		7	Cag/Tag	1/9	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.2	2		507	694	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0031046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	131	491	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.964	0.875	1	0.964	0.875	1	CLONAL	1	TRUE	1	0.310488940019194	2		491	875	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0031046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	132	595	0	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.310488940019194	2		595	809	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0031047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	158	332	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.352078655178099	2		332	764	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0031047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	220	403	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.352078655178099	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.352078655178099	1		403	860	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	113	695	8	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	0.149003184063201	0	FACETS	0.577	0.519	0.638			1	INDETERMINATE	1	TRUE	0	0.352078655178099	0		703	721	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	190	367	8	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.494355067285515	2		375	622	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	136	404	2	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.849	0.774	0.927	0.849	0.774	0.927	CLONAL	1	TRUE	1	0.494355067285515	2		406	648	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	104	280	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.985	0.888	1	0.985	0.888	1	CLONAL	1	TRUE	1	0.494355067285515	2		280	427	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	141	610	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.749	0.683	0.818	0.749	0.683	0.818	SUBCLONAL	1	TRUE	1	0.494355067285515	2		611	762	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111467	8111467	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759044265	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	207	489	2	ENST00000346208.3:c.953C>T	p.Ala318Val	p.A318V	ENST00000346208		318	gCg/gTg	5/6	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.494355067285515	2		491	793	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	89	287	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.791	0.705	0.883	0.791	0.705	0.883	SUBCLONAL	1	TRUE	1	0.494355067285515	2		287	455	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280160	115280160	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	172	403	0	ENST00000438362.2:c.472T>G	p.Leu158Val	p.L158V	ENST00000438362	NM_001242891.1	158	Tta/Gta	5/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.494355067285515	2		403	632	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70360793	70360793	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	39	300	0	ENST00000373644.4:c.1968+2T>C		p.X656_splice	ENST00000373644	NM_030625.2	656			1	2	FACETS	0.336	0.279	0.401	0.336	0.279	0.401	SUBCLONAL	1	TRUE	1	0.494355067285515	2		300	469	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	61	233	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	0.599	0.518	0.686	0.599	0.518	0.686	SUBCLONAL	1	TRUE	1	0.494355067285515	2		233	412	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742865	17742865	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	216	636	0	ENST00000250003.3:c.773G>A	p.Arg258His	p.R258H	ENST00000250003	NM_002478.4	258	cGc/cAc	3/3	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.494355067285515	2		636	847	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196604	67196604	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	89	457	0	ENST00000312629.5:c.133T>C	p.Tyr45His	p.Y45H	ENST00000312629	NM_003952.2	45	Tat/Cat	3/15	1	2	FACETS	0.537	0.477	0.602	0.537	0.477	0.602	SUBCLONAL	1	TRUE	1	0.494355067285515	2		457	670	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202569	67202569	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369452492	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	223	597	1	ENST00000312629.5:c.1378G>A	p.Ala460Thr	p.A460T	ENST00000312629	NM_003952.2	460	Gcc/Acc	15/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.494355067285515	2		598	850	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	156	462	0	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	0.868	0.797	0.943	0.868	0.797	0.943	CLONAL	1	TRUE	1	0.494355067285515	2		462	727	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	117	450	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	1	2	FACETS	0.885	0.801	0.972	0.885	0.801	0.972	CLONAL	1	TRUE	1	0.494355067285515	2		450	535	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	246	734	4	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.494355067285515	2		738	901	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478777	56478777	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	175	409	0	ENST00000267101.3:c.235-2A>C		p.X79_splice	ENST00000267101	NM_001982.3	79			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.494355067285515	2		409	644	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884621	111884621	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	108	458	0	ENST00000341259.2:c.797T>C	p.Leu266Pro	p.L266P	ENST00000341259	NM_005475.2	266	cTt/cCt	3/8	1	2	FACETS	0.641	0.575	0.71	0.641	0.575	0.71	SUBCLONAL	1	TRUE	1	0.494355067285515	2		458	682	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43738624	43738624	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	195	537	0	ENST00000382044.4:c.3001A>T	p.Thr1001Ser	p.T1001S	ENST00000382044	NM_001141980.1	1001	Act/Tct	14/28	1	2	FACETS	0.941	0.873	1	0.941	0.873	1	CLONAL	1	TRUE	1	0.494355067285515	2		537	838	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096132	2096133	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs763525759	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	132	496	0	ENST00000219066.1:c.374dup	p.Val127GlyfsTer43	p.V127Gfs*43	ENST00000219066	NM_002528.5	125	cca/ccCa	2/6	1	2	FACETS	0.832	0.757	0.91	0.832	0.757	0.91	CLONAL	1	TRUE	1	0.494355067285515	2		496	642	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649273	23649273	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs200048921	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	117	335	0	ENST00000261584.4:c.109C>T	p.Arg37Cys	p.R37C	ENST00000261584	NM_024675.3	37	Cgt/Tgt	3/13	1	2	FACETS	0.921	0.834	1	0.921	0.834	1	CLONAL	1	TRUE	1	0.494355067285515	2		335	514	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011137	12011137	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	112	380	0	ENST00000353533.5:c.544T>C	p.Ser182Pro	p.S182P	ENST00000353533	NM_003010.3	182	Tct/Cct	5/11	1	2	FACETS	0.912	0.824	1	0.912	0.824	1	CLONAL	1	TRUE	1	0.494355067285515	2		380	497	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857641	59857641	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	117	292	0	ENST00000259008.2:c.1916A>G	p.His639Arg	p.H639R	ENST00000259008	NM_032043.2	639	cAt/cGt	13/20	1	2	FACETS	0.928	0.841	1	0.928	0.841	1	CLONAL	1	TRUE	1	0.494355067285515	2		292	510	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56381342	56381342	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	78	262	0	ENST00000348428.3:c.985+1G>C		p.X329_splice	ENST00000348428	NM_006785.3	329			1	2	FACETS	0.923	0.817	1	0.923	0.817	1	CLONAL	1	TRUE	1	0.494355067285515	2		262	342	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1650237	1650237	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757916399	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	221	611	1	ENST00000344749.5:c.11C>T	p.Pro4Leu	p.P4L	ENST00000344749	NM_001136139.2	4	cCg/cTg	2/19	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.494355067285515	2		612	889	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212055	5212055	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749770933	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	185	639	3	ENST00000357368.4:c.4976G>A	p.Arg1659His	p.R1659H	ENST00000357368	NM_002850.3	1659	cGc/cAc	32/38	1	2	FACETS	0.956	0.884	1	0.956	0.884	1	CLONAL	1	TRUE	1	0.494355067285515	2		642	783	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130286	11130286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	175	478	0	ENST00000358026.2:c.2525G>A	p.Arg842Gln	p.R842Q	ENST00000358026	NM_001128849.1	842	cGg/cAg	18/36	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.494355067285515	2		478	690	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211549	36211549	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	59	552	0	ENST00000222270.7:c.1304del	p.Pro435GlnfsTer40	p.P435Qfs*40	ENST00000222270	NM_014727.1	434	Ccc/cc	3/37	1	2	FACETS	0.375	0.322	0.432	0.375	0.322	0.432	SUBCLONAL	1	TRUE	1	0.494355067285515	2		552	637	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224339	36224340	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	204	744	0	ENST00000222270.7:c.6895dup	p.Arg2299ProfsTer4	p.R2299Pfs*4	ENST00000222270	NM_014727.1	2297	gcc/gCcc	28/37	1	2	FACETS	0.814	0.755	0.875	0.814	0.755	0.875	CLONAL	1	TRUE	1	0.494355067285515	2		744	1014	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137404	202137404	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	30	377	0	ENST00000358485.4:c.632T>C	p.Leu211Pro	p.L211P	ENST00000358485	NM_001080125.1	211	cTg/cCg	4/9	1	2	FACETS	0.221	0.177	0.271	0.221	0.177	0.271	SUBCLONAL	1	TRUE	1	0.494355067285515	2		377	549	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793431	242793431	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376257658	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	168	588	0	ENST00000334409.5:c.646G>A	p.Val216Met	p.V216M	ENST00000334409	NM_005018.2	216	Gtg/Atg	5/5	1	2	FACETS	0.912	0.84	0.987	0.912	0.84	0.987	CLONAL	1	TRUE	1	0.494355067285515	2		588	745	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321659	62321659	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	51	541	0	ENST00000360203.5:c.2278G>C	p.Ala760Pro	p.A760P	ENST00000360203	NM_001283009.1	760	Gcc/Ccc	26/35	1	2	FACETS	0.27	0.229	0.316	0.27	0.229	0.316	SUBCLONAL	1	TRUE	1	0.494355067285515	2		541	764	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572357	41572357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	188	553	1	ENST00000263253.7:c.4886C>T	p.Ala1629Val	p.A1629V	ENST00000263253	NM_001429.3	1629	gCg/gTg	30/31	1	2	FACETS	0.993	0.92	1	0.993	0.92	1	CLONAL	1	TRUE	1	0.494355067285515	2		554	766	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261565	142261565	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	63	466	0	ENST00000350721.4:c.3392del	p.Leu1131TrpfsTer9	p.L1131Wfs*9	ENST00000350721	NM_001184.3	1131	tTg/tg	17/47	1	2	FACETS	0.359	0.31	0.413	0.359	0.31	0.413	SUBCLONAL	1	TRUE	1	0.494355067285515	2		466	709	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963105	38963105	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	37	301	0	ENST00000357387.3:c.1439A>G	p.His480Arg	p.H480R	ENST00000357387	NM_152756.3	480	cAt/cGt	17/38	1	2	FACETS	0.41	0.338	0.49	0.41	0.338	0.49	SUBCLONAL	1	TRUE	1	0.494355067285515	2		301	365	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	108	343	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	0.877	0.791	0.968	0.877	0.791	0.968	CLONAL	1	TRUE	1	0.494355067285515	2		343	498	SUCCESS
APC	324	MSKCC	GRCh37	5	112164663	112164664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	88	284	0	ENST00000257430.4:c.1742dup	p.Glu582GlyfsTer20	p.E582Gfs*20	ENST00000257430	NM_000038.5	579	-/A	14/16	1	2	FACETS	0.795	0.707	0.887	0.795	0.707	0.887	SUBCLONAL	1	TRUE	1	0.494355067285515	2		284	448	SUCCESS
APC	324	MSKCC	GRCh37	5	112170861	112170861	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1114167580	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	125	459	0	ENST00000257430.4:c.1957A>G	p.Arg653Gly	p.R653G	ENST00000257430	NM_000038.5	653	Agg/Ggg	15/16	1	2	FACETS	0.875	0.795	0.959	0.875	0.795	0.959	CLONAL	1	TRUE	1	0.494355067285515	2		459	578	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671396	30671396	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	177	514	0	ENST00000376406.3:c.5562+2T>C		p.X1854_splice	ENST00000376406	NM_014641.2	1854			1	2	FACETS	0.993	0.918	1	0.993	0.918	1	CLONAL	1	TRUE	1	0.494355067285515	2		514	721	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112035565	112035565	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	98	337	0	ENST00000368678.4:c.329A>G	p.Gln110Arg	p.Q110R	ENST00000368678		110	cAa/cGa	4/13	1	2	FACETS	0.738	0.661	0.82	0.738	0.661	0.82	SUBCLONAL	1	TRUE	1	0.494355067285515	2		337	537	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043355	6043355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188006077	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	155	188	4	ENST00000265849.7:c.319C>T	p.Arg107Trp	p.R107W	ENST00000265849	NM_000535.5	107	Cgg/Tgg	4/15	0.489232276956328	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	1	0.494355067285515	3		192	373	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453150	140453150	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913341	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	108	426	0	ENST00000288602.6:c.1785T>G	p.Phe595Leu	p.F595L	ENST00000288602	NM_004333.4	595	ttT/ttG	15/18	0.489232276956328	3	FACETS	0.784	0.704	0.869	0.392	0.352	0.435	SUBCLONAL	1	TRUE	1	0.494355067285515	3		426	695	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187222	38187222	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	214	802	2	ENST00000317025.8:c.1255del	p.Thr419ProfsTer8	p.T419Pfs*8	ENST00000317025	NM_023034.1	419	Acc/cc	6/24	1	2	FACETS	0.734	0.681	0.789	0.734	0.681	0.789	SUBCLONAL	1	TRUE	1	0.494355067285515	2		804	1179	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372206	55372206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	134	390	2	ENST00000297316.4:c.896C>T	p.Ala299Val	p.A299V	ENST00000297316	NM_022454.3	299	gCg/gTg	2/2	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.494355067285515	2		392	451	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	172	599	2	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	0.917	0.845	0.991	0.917	0.845	0.991	CLONAL	1	TRUE	1	0.494355067285515	2		601	759	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56879458	56879458	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	95	513	0	ENST00000519728.1:c.973+2T>C		p.X325_splice	ENST00000519728	NM_002350.3	325			1	2	FACETS	0.556	0.495	0.621	0.556	0.495	0.621	SUBCLONAL	1	TRUE	1	0.494355067285515	2		513	691	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	221	772	0	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	1	2	FACETS	0.843	0.784	0.904	0.843	0.784	0.904	CLONAL	1	TRUE	1	0.494355067285515	2		772	1061	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932804	39932804	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	234	327	0	ENST00000378444.4:c.1795G>T	p.Gly599Cys	p.G599C	ENST00000378444	NM_001123385.1	599	Ggc/Tgc	4/15	1	1	FACETS	0.792	0.749	0.835	1	0.994	1	SUBCLONAL	2	TRUE	0	0.494355067285515	1		327	450	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099982	157099987	+	inframe_deletion	In_Frame_Del	DEL	GGCGGC	GGCGGC	-	rs587779747	NA	P-0031050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	56	266	0	ENST00000346085.5:c.939_944del	p.Gly318_Gly319del	p.G318_G319del	ENST00000346085	NM_020732.3	307	GGCGGC/-	1/20	1	2	FACETS	0.662	0.57	0.762	0.662	0.57	0.762	SUBCLONAL	1	TRUE	1	0.494355067285515	2		266	342	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	98	384	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.211862138574832	3	FACETS	0.657	0.585	0.734			1	INDETERMINATE	1	TRUE	NA	0.377913210810889	3		384	938	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0031051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	131	616	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.647	0.586	0.712	0.647	0.586	0.712	SUBCLONAL	1	TRUE	1	0.377913210810889	2		616	1071	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448310	56448310	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567880628	NA	P-0031051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	181	596	5	ENST00000407977.2:c.337C>T	p.Arg113Ter	p.R113*	ENST00000407977		113	Cga/Tga	3/10	1	2	FACETS	0.854	0.787	0.925	0.854	0.787	0.925	CLONAL	1	TRUE	1	0.377913210810889	2		601	1121	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0031054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	265	377	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	0.94	0.889	0.992	0.94	0.889	0.992	CLONAL	1	TRUE	1	0.943949950536878	2		377	597	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55143660	55143660	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0031054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	187	258	0	ENST00000257290.5:c.1891+1G>T		p.X631_splice	ENST00000257290	NM_006206.4	631			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.943949950536878	2		258	371	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	95	270	0				ENST00000310581	NM_198253.2	-/1132			0.335715687701504	1	FACETS	0.563	0.503	0.626	0.563	0.503	0.626	SUBCLONAL	1	TRUE	0	0.517000163049604	1		270	484	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0031055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	186	477	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.975	0.903	1	0.975	0.903	1	CLONAL	1	TRUE	1	0.517000163049604	2		477	738	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0031055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	352	510	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.517000163049604	2	FACETS	0.975	0.932	1	0.975	0.932	1	CLONAL	2	TRUE	0	0.517000163049604	2		510	698	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	239	384	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.36938921533738	4	FACETS	1	0.95	1	1	0.95	1	CLONAL	3	TRUE	1	0.36938921533738	4		384	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0031056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	294	651	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.363335218766194	2	FACETS	0.966	0.913	1	0.966	0.913	1	CLONAL	2	TRUE	0	0.36938921533738	2		651	824	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864700	68864700	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	103	402	1	ENST00000288368.4:c.71G>A	p.Arg24His	p.R24H	ENST00000288368	NM_024870.2	24	cGc/cAc	1/40	0.184317100799255	2	FACETS	0.776	0.694	0.862	0.388	0.347	0.431	INDETERMINATE	1	TRUE	0	0.36938921533738	2		403	719	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71947005	71947023	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCGGGAGGAGCCCTTGA	CCCCGGGAGGAGCCCTTGA	-	novel	NA	P-0031056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	59	720	0	ENST00000298229.2:c.2858_2876del	p.Arg953ProfsTer3	p.R953Pfs*3	ENST00000298229	NM_001567.3	952	CCCCGGGAGGAGCCCTTGAcc/cc	25/28	0.363335218766194	2	FACETS	0.271	0.232	0.314	0.135	0.116	0.157	SUBCLONAL	1	TRUE	0	0.36938921533738	2		720	1179	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15943759	15943759	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	123	343	0	ENST00000268712.3:c.6729del	p.Ser2244GlnfsTer49	p.S2244Qfs*49	ENST00000268712	NM_006311.3	2243	acG/ac	43/46	0.363335218766194	2	FACETS	0.76	0.693	0.83	0.76	0.693	0.83	SUBCLONAL	2	TRUE	0	0.36938921533738	2		343	438	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573591	48573610	+	frameshift_variant	Frame_Shift_Del	DEL	ACAGCTATAACTACAAATGG	ACAGCTATAACTACAAATGG	-	novel	NA	P-0031056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	53	325	0	ENST00000342988.3:c.176_195del	p.Thr59SerfsTer4	p.T59Sfs*4	ENST00000342988	NM_005359.5	59	ACAGCTATAACTACAAATGGa/a	2/12	0.36938921533738	1	FACETS	0.955	0.823	1	0.955	0.823	1	CLONAL	1	TRUE	0	0.36938921533738	1		325	245	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485280	8485280	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	74	508	0	ENST00000356435.5:c.3100G>T	p.Val1034Leu	p.V1034L	ENST00000356435		1034	Gtg/Ttg	18/35	1	2	FACETS	0.737	0.646	0.834	0.737	0.646	0.834	SUBCLONAL	1	TRUE	1	0.36938921533738	2		508	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0031057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	429	541	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	0.50799104916898	2	FACETS	0.997	0.957	1	0.997	0.957	1	CLONAL	2	TRUE	0	0.50799104916898	2		541	847	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435619	18435619	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1164190418	NA	P-0031057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	75	251	0	ENST00000266497.5:c.604G>A	p.Glu202Lys	p.E202K	ENST00000266497		202	Gaa/Aaa	1/31	0.457349816399809	6	FACETS	0.951	0.834	1	0.238	0.208	0.27	CLONAL	1	TRUE	2	0.50799104916898	6		251	626	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0031058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	181	377	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.429876366277296	1	FACETS	0.855	0.794	0.918	0.855	0.794	0.918	CLONAL	1	FALSE	0	0.561605625112652	1		377	542	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0031058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	67	284	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	FALSE	1	0.561605625112652	2		284	219	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0031058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	330	558	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.561605625112652	1	FACETS	0.931	0.883	0.98	0.931	0.883	0.98	CLONAL	1	FALSE	0	0.561605625112652	1		558	908	SUCCESS
APC	324	MSKCC	GRCh37	5	112174388	112174388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	19	223	0	ENST00000257430.4:c.3097G>A	p.Asp1033Asn	p.D1033N	ENST00000257430	NM_000038.5	1033	Gat/Aat	16/16	1	2	FACETS	0.47	0.36	0.597	0.47	0.36	0.597	SUBCLONAL	1	FALSE	1	0.561605625112652	2		223	144	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341317	89341317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555523386	NA	P-0031058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	52	209	0	ENST00000301030.4:c.7618C>T	p.Arg2540Trp	p.R2540W	ENST00000301030	NM_001256183.1	2540	Cgg/Tgg	11/13	0.384015112614968	3	FACETS	0.78	0.668	0.901	0.39	0.334	0.451	CLONAL	1	FALSE	1	0.561605625112652	3		209	304	SUCCESS
APC	324	MSKCC	GRCh37	5	112175890	112175890	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	23	200	0	ENST00000257430.4:c.4599del	p.Asn1533LysfsTer32	p.N1533Kfs*32	ENST00000257430	NM_000038.5	1533	aaT/aa	16/16	1	2	FACETS	0.402	0.314	0.501	0.402	0.314	0.501	SUBCLONAL	1	FALSE	1	0.561605625112652	2		200	204	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2966384	2966384	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	151	538	0	ENST00000396946.4:c.1796T>C	p.Leu599Ser	p.L599S	ENST00000396946	NM_032415.4	599	tTa/tCa	14/25	0.186413874845206	0	FACETS	0.361	0.331	0.392			1	INDETERMINATE	1	FALSE	0	0.561605625112652	0		538	653	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0031060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	59	332	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.896	0.774	1	0.896	0.774	1	CLONAL	1	TRUE	1	0.342206906097419	2		332	385	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	47	384	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.609	0.514	0.713	0.609	0.514	0.713	SUBCLONAL	1	TRUE	1	0.342206906097419	2		384	451	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473779	67473779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906850	NA	P-0031060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	104	426	0	ENST00000327367.4:c.859C>T	p.Arg287Trp	p.R287W	ENST00000327367	NM_005902.3	287	Cgg/Tgg	6/9	1	2	FACETS	0.795	0.711	0.883	0.795	0.711	0.883	SUBCLONAL	1	TRUE	1	0.342206906097419	2		426	765	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981167	201981168	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0031060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	349	682	0	ENST00000359651.3:c.248dup	p.Asn83LysfsTer9	p.N83Kfs*9	ENST00000359651		82	-/A	2/8	0.330126934386592	3	FACETS	0.835	0.79	0.882	0.835	0.79	0.882	CLONAL	2	TRUE	1	0.342206906097419	3		682	1430	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690624	88690624	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	86	394	0	ENST00000360948.2:c.406A>G	p.Ser136Gly	p.S136G	ENST00000360948	NM_001012338.2	136	Agt/Ggt	5/19	1	2	FACETS	0.787	0.696	0.883	0.787	0.696	0.883	SUBCLONAL	1	TRUE	1	0.342206906097419	2		394	639	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223397	2223399	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TTT	TTT	-	novel	NA	P-0031060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	121	505	0	ENST00000326181.6:c.1009_1011del	p.Phe337del	p.F337del	ENST00000326181	NM_032271.2	337	TTT/-	10/21	1	2	FACETS	0.891	0.805	0.981	0.891	0.805	0.981	CLONAL	1	TRUE	1	0.342206906097419	2		505	794	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665125	138665125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	45	418	1	ENST00000330315.3:c.440G>A	p.Arg147His	p.R147H	ENST00000330315	NM_023067.3	147	cGc/cAc	1/1	1	2	FACETS	0.338	0.283	0.4	0.338	0.283	0.4	SUBCLONAL	1	TRUE	1	0.342206906097419	2		419	777	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339251	70339252	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGG	novel	NA	P-0031060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	167	255	0	ENST00000374080.3:c.129_131dup	p.Gly44dup	p.G44dup	ENST00000374080		44	caa/caAGGa	2/45	1	1	FACETS	0.801	0.742	0.862	1	0.991	1	CLONAL	2	TRUE	0	0.342206906097419	1		255	505	SUCCESS
APC	324	MSKCC	GRCh37	5	112176063	112176064	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0031062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	48	321	0	ENST00000257430.4:c.4778dup	p.Pro1594AlafsTer38	p.P1594Afs*38	ENST00000257430	NM_000038.5	1591	gca/gcAa	16/16	0.520914926075727	1	FACETS	0.262	0.221	0.307	0.262	0.221	0.307	SUBCLONAL	1	TRUE	0	0.520914926075727	1		321	521	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436026	56436026	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771831816	NA	P-0031062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	38	322	1	ENST00000407977.2:c.1111C>T	p.Arg371Ter	p.R371*	ENST00000407977		371	Cga/Tga	9/10	1	2	FACETS	0.301	0.249	0.36	0.301	0.249	0.36	SUBCLONAL	1	TRUE	1	0.520914926075727	2		323	484	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258163	16258163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144013241	NA	P-0031062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	324	489	0	ENST00000375759.3:c.5428C>T	p.Pro1810Ser	p.P1810S	ENST00000375759	NM_015001.2	1810	Cca/Tca	11/15	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.520914926075727	2		489	1025	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434508	110434508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	217	408	1	ENST00000375856.3:c.3893G>A	p.Gly1298Asp	p.G1298D	ENST00000375856	NM_003749.2	1298	gGc/gAc	1/2	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.520914926075727	2		409	815	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383182	42383182	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782657641	NA	P-0031062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	254	536	0	ENST00000221972.3:c.202C>T	p.Arg68Cys	p.R68C	ENST00000221972	NM_021601.3	68	Cgc/Tgc	2/5	1	2	FACETS	0.997	0.934	1	0.997	0.934	1	CLONAL	1	TRUE	1	0.520914926075727	2		536	978	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0031065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	17	384	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	1	2	FACETS	0.564	0.419	0.737	0.564	0.419	0.737	SUBCLONAL	1	TRUE	1	0.13	2		384	464	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120612013	120612014	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0031065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	11	63	1	ENST00000256646.2:c.7_8delinsTT	p.Ala3Phe	p.A3F	ENST00000256646	NM_024408.3	3	GCc/TTc	1/34	1	2	FACETS	0.863	0.602	1	1	0.878	1	CLONAL	2	TRUE	1	0.13	2		64	98	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519998	NA	P-0031065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	43	520	0	ENST00000269305.4:c.581T>C	p.Leu194Pro	p.L194P	ENST00000269305	NM_001126112.2	194	cTt/cCt	6/11	1	2	FACETS	0.82	0.684	0.971	0.82	0.684	0.971	CLONAL	1	TRUE	1	0.13	2		520	807	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097654	27097655	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0031065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	51	519	0	ENST00000324856.7:c.3245_3246del	p.Val1082GlyfsTer22	p.V1082Gfs*22	ENST00000324856	NM_006015.4	1081	aaTGtg/aatg	12/20	1	2	FACETS	0.92	0.78	1	0.92	0.78	1	CLONAL	1	TRUE	1	0.13	2		519	853	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983105	201983105	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	56	532	0	ENST00000359651.3:c.954G>C	p.Lys318Asn	p.K318N	ENST00000359651		318	aaG/aaC	7/8	1	2	FACETS	0.965	0.824	1	0.965	0.824	1	CLONAL	1	TRUE	1	0.13	2		532	893	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971172	21971175	+	frameshift_variant	Frame_Shift_Del	DEL	CAGC	CAGC	-	novel	NA	P-0031065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	44	344	0	ENST00000304494.5:c.183_186del	p.Glu61AspfsTer84	p.E61Dfs*84	ENST00000304494	NM_000077.4	61	gaGCTG/ga	2/3	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.13	2		344	520	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0031071-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	95	170	1	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.512843844739986	2		171	306	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222986	1222986	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs864622488	NA	P-0031071-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	172	357	0	ENST00000326873.7:c.923G>T	p.Trp308Leu	p.W308L	ENST00000326873	NM_000455.4	308	tGg/tTg	8/10	0.512843844739986	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.512843844739986	1		357	375	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438583	49438583	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031071-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	188	520	0	ENST00000301067.7:c.4907G>T	p.Gly1636Val	p.G1636V	ENST00000301067	NM_003482.3	1636	gGc/gTc	19/54	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.512843844739986	2		520	581	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346378	89346378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749486628	NA	P-0031071-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	122	384	0	ENST00000301030.4:c.6572C>T	p.Pro2191Leu	p.P2191L	ENST00000301030	NM_001256183.1	2191	cCt/cTt	9/13	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.512843844739986	2		384	463	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210796	2210797	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0031071-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	162	389	0	ENST00000398665.3:c.1293_1294del	p.Ala432ThrfsTer121	p.A432Tfs*121	ENST00000398665	NM_032482.2	431	acTGca/acca	14/28	0.512843844739986	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.512843844739986	1		389	408	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602452	10602452	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031071-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	188	426	0	ENST00000171111.5:c.1126G>C	p.Ala376Pro	p.A376P	ENST00000171111	NM_203500.1	376	Gcc/Ccc	3/6	0.512843844739986	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.512843844739986	1		426	408	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138480	11138480	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031071-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	128	299	0	ENST00000358026.2:c.3236C>G	p.Ser1079Trp	p.S1079W	ENST00000358026	NM_001128849.1	1079	tCg/tGg	24/36	0.512843844739986	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.512843844739986	1		299	318	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876137	35876137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031071-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	125	247	0	ENST00000303115.3:c.929G>A	p.Arg310Lys	p.R310K	ENST00000303115	NM_002185.3	310	aGg/aAg	8/8	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.512843844739986	2		247	405	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730099	41730099	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031071-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	115	181	0	ENST00000242208.4:c.430G>T	p.Gly144Cys	p.G144C	ENST00000242208	NM_002192.2	144	Ggc/Tgc	3/3	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.512843844739986	2		181	386	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274018	10274018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1354238435	NA	P-0031076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	168	613	4	ENST00000330684.3:c.251C>T	p.Thr84Met	p.T84M	ENST00000330684	NM_001134407.1	84	aCg/aTg	2/13	0.590541414689576	3	FACETS	1	0.959	1	0.531	0.49	0.575	CLONAL	1	TRUE	1	0.6057292722745	3		617	680	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198262742	198262742	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	308	362	0	ENST00000335508.6:c.3233T>G	p.Val1078Gly	p.V1078G	ENST00000335508	NM_012433.2	1078	gTc/gGc	22/25	0.6057292722745	3	FACETS	0.948	0.91	0.985	0.948	0.91	0.985	CLONAL	3	TRUE	0	0.6057292722745	3		362	466	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545877	41545877	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	196	609	0	ENST00000263253.7:c.2492C>A	p.Ser831Ter	p.S831*	ENST00000263253	NM_001429.3	831	tCa/tAa	14/31	0.601749740297877	2	FACETS	0.991	0.922	1	0.496	0.461	0.531	CLONAL	1	TRUE	0	0.6057292722745	2		609	653	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412027	116412042	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AGCTACTTTTCCAGAA	AGCTACTTTTCCAGAA	-	novel	NA	P-0031076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	875	565	0	ENST00000397752.3:c.3012_3027del	p.Ala1005IlefsTer19	p.A1005Ifs*19	ENST00000397752	NM_000245.2	1004	cgAGCTACTTTTCCAGAA/cg	14/21	0.597630192971382	5	FACETS	0.982	0.963	1	0.982	0.963	1	CLONAL	5	TRUE	0	0.6057292722745	5		565	1123	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	95	270	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.648344510286345	2		270	287	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651879	36651879	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0031079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	316	359	0	ENST00000244741.5:c.1A>G	p.Met1?	p.M1?	ENST00000244741	NM_000389.4	1	Atg/Gtg	2/3	0.648344510286345	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.648344510286345	2		359	476	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376227	225376227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	124	364	0	ENST00000264414.4:c.727G>A	p.Glu243Lys	p.E243K	ENST00000264414	NM_003590.4	243	Gaa/Aaa	6/16	1	2	FACETS	0.917	0.837	1	0.917	0.837	1	CLONAL	1	TRUE	1	0.648344510286345	2		364	417	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039462	49039462	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0031079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	199	445	0	ENST00000267163.4:c.2447C>G	p.Ser816Ter	p.S816*	ENST00000267163	NM_000321.2	816	tCa/tGa	23/27	0.648344510286345	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.648344510286345	1		445	389	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376218	225376218	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	133	399	0	ENST00000264414.4:c.736G>C	p.Glu246Gln	p.E246Q	ENST00000264414	NM_003590.4	246	Gaa/Caa	6/16	1	2	FACETS	0.937	0.858	1	0.937	0.858	1	CLONAL	1	TRUE	1	0.648344510286345	2		399	438	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436684	52436684	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	206	490	0	ENST00000460680.1:c.1990G>A	p.Asp664Asn	p.D664N	ENST00000460680	NM_004656.3	664	Gac/Aac	16/17	0.648344510286345	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.648344510286345	1		490	400	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593609	55593611	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	rs121913685	NA	P-0031080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	242	346	0	ENST00000288135.5:c.1679_1681del	p.Val560del	p.V560del	ENST00000288135	NM_000222.2	559	GTT/-	11/21	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.874563117316707	2		346	552	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0031081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	220	491	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.274701613210359	3	FACETS	0.853	0.797	0.91	0.853	0.797	0.91	CLONAL	2	TRUE	1	0.438628590004052	3		491	717	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919295	48919295	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0031081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	68	189	0	ENST00000267163.4:c.460A>T	p.Lys154Ter	p.K154*	ENST00000267163	NM_000321.2	154	Aag/Tag	4/27	0.438628590004052	1	FACETS	0.802	0.703	0.906	0.802	0.703	0.906	CLONAL	1	TRUE	0	0.438628590004052	1		189	302	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050781	5050781	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	117	389	1	ENST00000381652.3:c.564A>T	p.Arg188Ser	p.R188S	ENST00000381652	NM_004972.3	188	agA/agT	6/25	1	2	FACETS	0.825	0.745	0.908	0.825	0.745	0.908	CLONAL	1	TRUE	1	0.438628590004052	2		390	647	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	74	270	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.480085090841833	2		270	284	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681777	78681777	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	89	464	0	ENST00000306801.3:c.485G>A	p.Gly162Glu	p.G162E	ENST00000306801	NM_020761.2	162	gGg/gAg	4/34	1	2	FACETS	0.544	0.483	0.61	0.544	0.483	0.61	SUBCLONAL	1	TRUE	1	0.480085090841833	2		464	681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574002	7574002	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	283	496	0	ENST00000269305.4:c.1025del	p.Arg342GlnfsTer3	p.R342Qfs*3	ENST00000269305	NM_001126112.2	342	cGa/ca	10/11	0.44039096557121	2	FACETS	0.913	0.864	0.961	0.913	0.864	0.961	CLONAL	2	TRUE	0	0.480085090841833	2		496	646	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200023	123200023	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0031082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	67	170	0	ENST00000218089.9:c.2097-2A>G		p.X699_splice	ENST00000218089	NM_001042749.1	699			1	2	FACETS	0.797	0.708	0.889	1	0.979	1	SUBCLONAL	2	TRUE	1	0.480085090841833	2		170	175	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609720	28609720	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745828241	NA	P-0031082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	86	498	0	ENST00000241453.7:c.1509G>A	p.Met503Ile	p.M503I	ENST00000241453	NM_004119.2	503	atG/atA	12/24	0.381003908787977	1	FACETS	0.476	0.422	0.534	0.476	0.422	0.534	SUBCLONAL	1	TRUE	0	0.480085090841833	1		498	572	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56363669	56363669	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	62	367	0	ENST00000348428.3:c.448G>A	p.Ala150Thr	p.A150T	ENST00000348428	NM_006785.3	150	Gca/Aca	3/17	1	2	FACETS	0.678	0.588	0.775	0.678	0.588	0.775	SUBCLONAL	1	TRUE	1	0.480085090841833	2		367	381	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1206893	1206913	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	TCCAGGACCCTGGGTCCAGCA	TCCAGGACCCTGGGTCCAGCA	-	novel	NA	P-0031082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	90	324	0	ENST00000326873.7:c.-19_2del		p.*7*	ENST00000326873	NM_000455.4	?-1/433		1/10	1	2	FACETS	0.992	0.887	1	0.992	0.887	1	CLONAL	1	TRUE	1	0.480085090841833	2		324	378	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228079	36228079	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	102	557	0	ENST00000222270.7:c.7465A>C	p.Lys2489Gln	p.K2489Q	ENST00000222270	NM_014727.1	2489	Aag/Cag	33/37	0.228537981447494	3	FACETS	0.641	0.573	0.714	0.214	0.191	0.238	INDETERMINATE	1	TRUE	0	0.480085090841833	3		557	822	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45873425	45873425	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	65	492	0	ENST00000391945.4:c.71A>T	p.Tyr24Phe	p.Y24F	ENST00000391945	NM_000400.3	24	tAc/tTc	2/23	0.381003908787977	1	FACETS	0.466	0.405	0.531	0.466	0.405	0.531	SUBCLONAL	1	TRUE	0	0.480085090841833	1		492	442	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940479	29940479	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	92	368	0	ENST00000389048.3:c.752A>T	p.Asp251Val	p.D251V	ENST00000389048	NM_004304.4	251	gAc/gTc	2/29	0.450759944834251	3	FACETS	1	0.897	1	0.335	0.299	0.373	CLONAL	1	TRUE	0	0.480085090841833	3		368	473	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950718	79950718	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs148550291	NA	P-0031082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	14	58	1	ENST00000265081.6:c.172G>C	p.Ala58Pro	p.A58P	ENST00000265081	NM_002439.4	58	Gca/Cca	1/24	0.124431334231236	3	FACETS	0.438	0.318	0.583			1	INDETERMINATE	1	TRUE	NA	0.480085090841833	3		59	165	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391877	139391891	+	inframe_deletion	In_Frame_Del	DEL	ATGCGCTCCTGTGCG	ATGCGCTCCTGTGCG	-	novel	NA	P-0031082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	188	490	0	ENST00000277541.6:c.6300_6314del	p.Ile2100_Arg2104del	p.I2100_R2104del	ENST00000277541	NM_017617.3	2100	atCGCACAGGAGCGCATg/atg	34/34	0.480085090841833	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.480085090841833	1		490	446	SUCCESS
AR	367	MSKCC	GRCh37	X	66765076	66765076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761416673	NA	P-0031082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	75	519	2	ENST00000374690.3:c.88G>A	p.Val30Met	p.V30M	ENST00000374690	NM_000044.3	30	Gtg/Atg	1/8	1	2	FACETS	0.427	0.373	0.484	0.427	0.373	0.484	SUBCLONAL	1	TRUE	1	0.480085090841833	2		521	732	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	99	384	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.319039840656177	3	FACETS	0.972	0.876	1	0.972	0.876	1	CLONAL	2	TRUE	1	0.328280165158879	3		384	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579383	7579383	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	211	548	0	ENST00000269305.4:c.304del	p.Thr102ProfsTer21	p.T102Pfs*21	ENST00000269305	NM_001126112.2	102	Acc/cc	4/11	0.295765322431388	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.328280165158879	2		548	611	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0031085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	180	586	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.264075390010943	2	FACETS	0.781	0.723	0.84	0.781	0.723	0.84	SUBCLONAL	2	TRUE	0	0.367805461993815	2		586	627	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198878	67198878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753540467	NA	P-0031085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	38	348	0	ENST00000312629.5:c.349C>T	p.Arg117Trp	p.R117W	ENST00000312629	NM_003952.2	117	Cgg/Tgg	5/15	0.171512392647727	3	FACETS	0.566	0.468	0.676	0.283	0.234	0.338	INDETERMINATE	1	TRUE	1	0.367805461993815	3		348	432	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430543	181430543	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	14	219	0	ENST00000325404.1:c.395T>C	p.Leu132Pro	p.L132P	ENST00000325404	NM_003106.3	132	cTg/cCg	1/1	0.367805461993815	5	FACETS	0.428	0.309	0.573	0.107	0.077	0.144	SUBCLONAL	1	TRUE	1	0.367805461993815	5		219	276	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503792	186503798	+	frameshift_variant	Frame_Shift_Del	DEL	GTTGGTA	GTTGGTA	-	novel	NA	P-0031086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	42	429	0	ENST00000323963.5:c.469_475del	p.Val157HisfsTer9	p.V157Hfs*9	ENST00000323963		157	GTTGGTAca/ca	5/11	1	2	FACETS	0.901	0.751	1	0.901	0.751	1	CLONAL	1	TRUE	1	0.14	2		429	666	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0031088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	384	477	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.445885904949008	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.445885904949008	2		478	799	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0031088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	128	459	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.301734544301888	3	FACETS	0.775	0.707	0.845	0.775	0.707	0.845	SUBCLONAL	2	TRUE	1	0.445885904949008	3		459	453	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004217	150004217	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1431439182	NA	P-0031088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	71	232	0	ENST00000253339.5:c.2008C>T	p.Arg670Trp	p.R670W	ENST00000253339		670	Cgg/Tgg	3/7	0.445885904949008	3	FACETS	0.934	0.819	1	0.467	0.409	0.529	CLONAL	1	TRUE	1	0.445885904949008	3		232	417	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416659	29416659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	102	307	0	ENST00000389048.3:c.4294C>T	p.Arg1432Trp	p.R1432W	ENST00000389048	NM_004304.4	1432	Cgg/Tgg	29/29	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.445885904949008	2		307	434	SUCCESS
APC	324	MSKCC	GRCh37	5	112170865	112170865	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	T	rs879254032	NA	P-0031088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	151	321	0	ENST00000257430.4:c.1958+3A>T		p.X653_splice	ENST00000257430	NM_000038.5	653			0.323332225667104	2	FACETS	0.758	0.699	0.818	0.758	0.699	0.818	SUBCLONAL	2	TRUE	0	0.445885904949008	2		321	447	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0031090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	48	505	4	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.255278032332278	1	FACETS	0.85	0.72	0.992	0.85	0.72	0.992	CLONAL	1	TRUE	0	0.255278032332278	1		509	386	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850342	128850342	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	75	486	0	ENST00000249373.3:c.1605G>T	p.Trp535Cys	p.W535C	ENST00000249373	NM_005631.4	535	tgG/tgT	9/12	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.255278032332278	2		486	540	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377019	118377019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	53	283	0	ENST00000534358.1:c.10412C>T	p.Ser3471Phe	p.S3471F	ENST00000534358	NM_005933.3	3471	tCc/tTc	27/36	0.255278032332278	1	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	0	0.255278032332278	1		283	339	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490235	29490235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567817857	NA	P-0031090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	31	279	0	ENST00000356175.3:c.320C>T	p.Thr107Met	p.T107M	ENST00000356175	NM_000267.3	107	aCg/aTg	4/57	1	2	FACETS	0.565	0.456	0.688	0.565	0.456	0.688	SUBCLONAL	1	TRUE	1	0.255278032332278	2		279	430	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937142	39937142	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	89	506	0	ENST00000378444.4:c.41G>T	p.Trp14Leu	p.W14L	ENST00000378444	NM_001123385.1	14	tGg/tTg	2/15	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.255278032332278	2		506	621	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	137	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.55246299887372	3	FACETS	0.994	0.907	1	0.497	0.453	0.543	CLONAL	1	TRUE	1	0.55246299887372	3		336	637	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	164	426	1	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	0.98	0.904	1	0.98	0.904	1	CLONAL	1	TRUE	1	0.55246299887372	2		427	606	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	142	498	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.989	0.906	1	0.989	0.906	1	CLONAL	1	TRUE	1	0.55246299887372	2		498	520	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	177	564	2	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	0.55246299887372	3	FACETS	1	0.931	1	0.505	0.466	0.546	CLONAL	1	TRUE	1	0.55246299887372	3		566	810	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	360	610	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.977	0.935	1	1	0.997	1	CLONAL	2	TRUE	1	0.55246299887372	2		611	667	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	25	350	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.223	0.175	0.278	0.223	0.175	0.278	SUBCLONAL	1	TRUE	1	0.55246299887372	2		351	406	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	128	337	3	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.929	0.846	1	0.929	0.846	1	CLONAL	1	TRUE	1	0.55246299887372	2		340	499	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793433	242793433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs2227982	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	155	537	1	ENST00000334409.5:c.644C>T	p.Ala215Val	p.A215V	ENST00000334409	NM_005018.2	215	gCc/gTc	5/5	1	2	FACETS	0.978	0.899	1	0.978	0.899	1	CLONAL	1	TRUE	1	0.55246299887372	2		538	574	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	134	346	1	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	1	2	FACETS	0.915	0.836	0.998	0.915	0.836	0.998	CLONAL	1	TRUE	1	0.55246299887372	2		347	530	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1023835002	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	105	287	0	ENST00000558401.1:c.1A>G	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Gtg	1/4	1	2	FACETS	0.967	0.874	1	0.967	0.874	1	CLONAL	1	TRUE	1	0.55246299887372	2		287	393	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141584	202141584	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	181	386	0	ENST00000358485.4:c.872C>A	p.Pro291His	p.P291H	ENST00000358485	NM_001080125.1	291	cCt/cAt	7/9	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.55246299887372	2		386	632	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296358	15296358	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	384	655	4	ENST00000263388.2:c.2084del	p.Pro695ArgfsTer165	p.P695Rfs*165	ENST00000263388	NM_000435.2	695	cCg/cg	13/33	1	2	FACETS	1	0.987	1	1	0.997	1	CLONAL	2	TRUE	1	0.55246299887372	2		659	654	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	122	408	0	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	1	2	FACETS	0.898	0.816	0.983	0.898	0.816	0.983	CLONAL	1	TRUE	1	0.55246299887372	2		408	492	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	145	656	9	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.804	0.735	0.875	0.804	0.735	0.875	CLONAL	1	TRUE	1	0.55246299887372	2		665	653	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828768	3828768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	165	407	0	ENST00000262367.5:c.1874G>A	p.Arg625His	p.R625H	ENST00000262367	NM_004380.2	625	cGc/cAc	9/31	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.55246299887372	2		407	588	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	301	581	1	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	0.55246299887372	3	FACETS	0.945	0.895	0.995	0.945	0.895	0.995	CLONAL	2	TRUE	1	0.55246299887372	3		582	736	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147533	47147533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	123	386	0	ENST00000409792.3:c.4793G>A	p.Arg1598Gln	p.R1598Q	ENST00000409792	NM_014159.6	1598	cGa/cAa	6/21	1	2	FACETS	0.875	0.795	0.958	0.875	0.795	0.958	CLONAL	1	TRUE	1	0.55246299887372	2		386	509	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007332	143007332	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	107	338	0	ENST00000262992.4:c.2452del	p.Arg818GlufsTer4	p.R818Efs*4	ENST00000262992	NM_001101669.1	818	Aga/ga	22/24	1	2	FACETS	0.905	0.817	0.997	0.905	0.817	0.997	CLONAL	1	TRUE	1	0.55246299887372	2		338	428	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	178	517	5	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.55246299887372	2		522	588	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944382	131944382	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs748536322	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	155	364	4	ENST00000265335.6:c.2801del	p.Asn934IlefsTer6	p.N934Ifs*6	ENST00000265335		932	Aaa/aa	17/25	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.55246299887372	2		368	501	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629033	14629035	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs764800868	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	107	405	0	ENST00000254322.2:c.127_129del	p.Glu43del	p.E43del	ENST00000254322	NM_006145.1	43	GAG/-	1/3	1	2	FACETS	0.888	0.802	0.979	0.888	0.802	0.979	CLONAL	1	TRUE	1	0.55246299887372	2		405	436	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347983	347983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760961378	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	394	551	8	ENST00000262320.3:c.1523del	p.Gly508ValfsTer197	p.G508Vfs*197	ENST00000262320	NM_003502.3	508	gGt/gt	6/11	1	2	FACETS	1	0.988	1	1	0.997	1	CLONAL	2	TRUE	1	0.55246299887372	2		559	669	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480110	50480110	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376164103	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	167	420	0	ENST00000394963.4:c.344C>T	p.Ala115Val	p.A115V	ENST00000394963	NM_003076.4	115	gCg/gTg	2/13	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.55246299887372	2		420	560	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733513	85733513	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs387906350	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	143	389	2	ENST00000370580.1:c.499del	p.Ser167LeufsTer6	p.S167Lfs*6	ENST00000370580	NM_003921.4	167	Tct/ct	3/3	1	2	FACETS	0.915	0.838	0.994	0.915	0.838	0.994	CLONAL	1	TRUE	1	0.55246299887372	2		391	566	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245024	133245024	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs752846614	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	182	526	1	ENST00000320574.5:c.2091del	p.Leu698CysfsTer94	p.L698Cfs*94	ENST00000320574	NM_006231.2	697	ccC/cc	19/49	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.55246299887372	2		527	638	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510102	187510102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368666671	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	167	348	0	ENST00000441802.2:c.13411G>A	p.Ala4471Thr	p.A4471T	ENST00000441802	NM_005245.3	4471	Gcg/Acg	27/27	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.55246299887372	2		348	483	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401384	139401384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766198119	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	197	572	1	ENST00000277541.6:c.3685G>A	p.Val1229Ile	p.V1229I	ENST00000277541	NM_017617.3	1229	Gtt/Att	23/34	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.55246299887372	2		573	695	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238356	98238356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	109	384	0	ENST00000331920.6:c.1688C>T	p.Ala563Val	p.A563V	ENST00000331920	NM_000264.3	563	gCg/gTg	12/24	1	2	FACETS	0.893	0.807	0.982	0.893	0.807	0.982	CLONAL	1	TRUE	1	0.55246299887372	2		384	442	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725018	47725019	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs762488821	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	227	681	0	ENST00000449228.1:c.725dup	p.Arg243GlnfsTer7	p.R243Qfs*7	ENST00000449228	NM_001127240.2	242	ggc/ggGc	4/4	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.55246299887372	2		681	790	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530163	63530163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145007501	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	146	388	0	ENST00000307078.5:c.2272G>A	p.Ala758Thr	p.A758T	ENST00000307078	NM_004655.3	758	Gcg/Acg	10/11	1	2	FACETS	0.99	0.909	1	0.99	0.909	1	CLONAL	1	TRUE	1	0.55246299887372	2		388	534	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256501	16256501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	209	572	0	ENST00000375759.3:c.3766G>A	p.Glu1256Lys	p.E1256K	ENST00000375759	NM_015001.2	1256	Gaa/Aaa	11/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.55246299887372	2		572	694	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546787	9546787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	94	227	0	ENST00000353224.5:c.1235C>T	p.Pro412Leu	p.P412L	ENST00000353224	NM_177990.2	412	cCg/cTg	5/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.55246299887372	2		227	287	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213961	2213961	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs753146456	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	200	572	4	ENST00000326181.6:c.45del	p.Ser17AlafsTer111	p.S17Afs*111	ENST00000326181	NM_032271.2	14	Ggg/gg	2/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.55246299887372	2		576	685	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395053	139395053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1484525055	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	141	491	2	ENST00000277541.6:c.5885G>A	p.Arg1962His	p.R1962H	ENST00000277541	NM_017617.3	1962	cGc/cAc	31/34	1	2	FACETS	0.98	0.898	1	0.98	0.898	1	CLONAL	1	TRUE	1	0.55246299887372	2		493	521	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519504	137519505	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	79	266	2	ENST00000367739.4:c.1132_1133dup	p.Ser378ArgfsTer6	p.S378Rfs*6	ENST00000367739	NM_000416.2	378	agt/agAGt	7/7	1	2	FACETS	0.717	0.634	0.805	0.717	0.634	0.805	SUBCLONAL	1	TRUE	1	0.55246299887372	2		268	399	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27016049	27016049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756721845	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	160	472	0	ENST00000335756.4:c.325G>A	p.Ala109Thr	p.A109T	ENST00000335756	NM_001809.3	109	Gcc/Acc	4/5	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.55246299887372	2		472	480	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257832	198257832	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	183	414	0	ENST00000335508.6:c.3620C>T	p.Ser1207Leu	p.S1207L	ENST00000335508	NM_012433.2	1207	tCg/tTg	24/25	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.55246299887372	2		414	594	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950344	17950344	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	217	652	0	ENST00000458235.1:c.1383del	p.Leu462CysfsTer3	p.L462Cfs*3	ENST00000458235	NM_000215.3	461	ggG/gg	10/24	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.55246299887372	2		652	766	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346961	89346961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775491352	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	85	272	0	ENST00000301030.4:c.5989G>A	p.Ala1997Thr	p.A1997T	ENST00000301030	NM_001256183.1	1997	Gcg/Acg	9/13	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.55246299887372	2		272	291	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945048	151945048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780852959	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	41	413	0	ENST00000262189.6:c.2471G>A	p.Gly824Asp	p.G824D	ENST00000262189	NM_170606.2	824	gGc/gAc	14/59	0.55246299887372	3	FACETS	0.292	0.243	0.348	0.146	0.121	0.174	SUBCLONAL	1	TRUE	1	0.55246299887372	3		413	648	SUCCESS
BLM	641	MSKCC	GRCh37	15	91306294	91306294	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	122	330	0	ENST00000355112.3:c.1986del	p.Lys662AsnfsTer12	p.K662Nfs*12	ENST00000355112	NM_000057.2	661	Aaa/aa	8/22	1	2	FACETS	0.999	0.91	1	0.999	0.91	1	CLONAL	1	TRUE	1	0.55246299887372	2		330	442	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099578	157099579	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	16	43	0	ENST00000346085.5:c.521dup	p.Pro177AlafsTer55	p.P177Afs*55	ENST00000346085	NM_020732.3	172	gac/gaCc	1/20	1	2	FACETS	0.674	0.507	0.865	0.674	0.507	0.865	SUBCLONAL	1	TRUE	1	0.55246299887372	2		43	86	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664882	138664882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	51	57	1	ENST00000330315.3:c.683C>T	p.Ala228Val	p.A228V	ENST00000330315	NM_023067.3	228	gCa/gTa	1/1	1	2	FACETS	0.932	0.825	1	1	0.979	1	CLONAL	2	TRUE	1	0.55246299887372	2		58	99	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288772	11288772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	93	429	0	ENST00000361445.4:c.2983C>T	p.Pro995Ser	p.P995S	ENST00000361445	NM_004958.3	995	Ccc/Tcc	19/58	1	2	FACETS	0.606	0.54	0.675	0.606	0.54	0.675	SUBCLONAL	1	TRUE	1	0.55246299887372	2		429	556	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111006	193111006	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	87	218	0	ENST00000367435.3:c.544del	p.Ile182LeufsTer20	p.I182Lfs*20	ENST00000367435	NM_024529.4	180	gAa/ga	7/17	1	2	FACETS	0.885	0.79	0.985	0.885	0.79	0.985	CLONAL	1	TRUE	1	0.55246299887372	2		218	356	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724562	112724562	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1175428649	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	165	432	1	ENST00000369452.4:c.446T>C	p.Met149Thr	p.M149T	ENST00000369452	NM_007373.3	149	aTg/aCg	2/9	1	2	FACETS	0.968	0.893	1	0.968	0.893	1	CLONAL	1	TRUE	1	0.55246299887372	2		433	617	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410704	32410704	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139893274	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	101	260	0	ENST00000332351.3:c.1454G>A	p.Arg485Gln	p.R485Q	ENST00000332351	NM_024426.4	485	cGg/cAg	10/10	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.55246299887372	2		260	360	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200228	67200228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770979132	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	160	487	0	ENST00000312629.5:c.536C>T	p.Thr179Met	p.T179M	ENST00000312629	NM_003952.2	179	aCg/aTg	7/15	1	2	FACETS	0.936	0.862	1	0.936	0.862	1	CLONAL	1	TRUE	1	0.55246299887372	2		487	619	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94963954	94963954	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	61	199	0	ENST00000536441.1:c.71T>C	p.Leu24Pro	p.L24P	ENST00000536441	NM_144665.3	24	cTg/cCg	1/10	1	2	FACETS	0.964	0.843	1	0.964	0.843	1	CLONAL	1	TRUE	1	0.55246299887372	2		199	229	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998717	100998717	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	121	484	1	ENST00000325455.5:c.1085C>T	p.Ala362Val	p.A362V	ENST00000325455	NM_001202474.3	362	gCg/gTg	1/8	1	2	FACETS	0.644	0.583	0.709	0.644	0.583	0.709	SUBCLONAL	1	TRUE	1	0.55246299887372	2		485	680	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428217	49428217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	225	558	1	ENST00000301067.7:c.10483C>T	p.Pro3495Ser	p.P3495S	ENST00000301067	NM_003482.3	3495	Ccc/Tcc	37/54	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.55246299887372	2		559	713	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109836	115109836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756448415	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	91	260	0	ENST00000257566.3:c.2042C>T	p.Pro681Leu	p.P681L	ENST00000257566	NM_016569.3	681	cCg/cTg	8/8	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.55246299887372	2		260	310	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972803	32972803	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507261	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	148	401	0	ENST00000380152.3:c.10153C>T	p.Arg3385Cys	p.R3385C	ENST00000380152		3385	Cgt/Tgt	27/27	0.508679303207143	3	FACETS	0.99	0.906	1	0.495	0.453	0.539	CLONAL	1	TRUE	1	0.55246299887372	3		401	691	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434973	110434973	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	111	371	0	ENST00000375856.3:c.3428del	p.Gly1143AlafsTer116	p.G1143Afs*116	ENST00000375856	NM_003749.2	1143	gGc/gc	1/2	0.508679303207143	3	FACETS	0.865	0.779	0.955	0.432	0.389	0.478	CLONAL	1	TRUE	1	0.55246299887372	3		371	593	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872481	35872481	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	156	378	0	ENST00000216797.5:c.422A>G	p.Asp141Gly	p.D141G	ENST00000216797	NM_020529.2	141	gAc/gGc	3/6	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.55246299887372	2		378	525	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701200	43701200	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	201	452	0	ENST00000382044.4:c.5495C>T	p.Ser1832Phe	p.S1832F	ENST00000382044	NM_001141980.1	1832	tCt/tTt	26/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.55246299887372	2		452	656	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2645837	2645837	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1441301361	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	151	440	0	ENST00000342085.4:c.1387G>A	p.Val463Met	p.V463M	ENST00000342085	NM_002613.4	463	Gtg/Atg	12/14	1	2	FACETS	0.939	0.863	1	0.939	0.863	1	CLONAL	1	TRUE	1	0.55246299887372	2		440	582	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858705	9858705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759145938	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	87	280	0	ENST00000330684.3:c.2696G>A	p.Arg899Gln	p.R899Q	ENST00000330684	NM_001134407.1	899	cGg/cAg	13/13	1	2	FACETS	0.833	0.743	0.928	0.833	0.743	0.928	CLONAL	1	TRUE	1	0.55246299887372	2		280	378	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349196	11349196	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs985283832	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	21	11	0	ENST00000332029.2:c.140C>T	p.Ala47Val	p.A47V	ENST00000332029	NM_003745.1	47	gCc/gTc	2/2	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.55246299887372	2		11	55	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133298	30133298	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772578869	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	168	466	0	ENST00000263025.4:c.200G>A	p.Arg67His	p.R67H	ENST00000263025	NM_002746.2	67	cGc/cAc	2/9	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.55246299887372	2		466	579	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671680	67671680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201916739	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	181	404	0	ENST00000264010.4:c.2089G>A	p.Ala697Thr	p.A697T	ENST00000264010	NM_006565.3	697	Gca/Aca	12/12	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.55246299887372	2		404	614	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993624	72993624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs997674247	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	137	469	0	ENST00000268489.5:c.421G>A	p.Ala141Thr	p.A141T	ENST00000268489	NM_006885.3	141	Gcg/Acg	2/10	1	2	FACETS	0.978	0.895	1	0.978	0.895	1	CLONAL	1	TRUE	1	0.55246299887372	2		469	507	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877156	89877156	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	190	473	0	ENST00000389301.3:c.481T>C	p.Phe161Leu	p.F161L	ENST00000389301	NM_000135.2	161	Ttc/Ctc	5/43	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.55246299887372	2		473	647	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434890	56434891	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	173	487	0	ENST00000407977.2:c.2246_2247del	p.Ser749Ter	p.S749*	ENST00000407977		749	tCT/t	9/10	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.55246299887372	2		487	620	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736897	736897	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	208	544	1	ENST00000314574.4:c.1202A>C	p.Asn401Thr	p.N401T	ENST00000314574	NM_005433.3	401	aAt/aCt	10/12	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.55246299887372	2		545	745	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379697	17379697	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	63	571	0	ENST00000359435.4:c.82C>A	p.Arg28Ser	p.R28S	ENST00000359435	NM_001033549.1	28	Cgc/Agc	2/9	1	2	FACETS	0.405	0.35	0.465	0.405	0.35	0.465	SUBCLONAL	1	TRUE	1	0.55246299887372	2		571	563	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47730007	47730007	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	61	190	0	ENST00000449228.1:c.382T>G	p.Ser128Ala	p.S128A	ENST00000449228	NM_001127240.2	128	Tca/Gca	3/4	1	2	FACETS	0.818	0.712	0.93	0.818	0.712	0.93	CLONAL	1	TRUE	1	0.55246299887372	2		190	270	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707840	47707840	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	113	266	0	ENST00000233146.2:c.2464T>G	p.Cys822Gly	p.C822G	ENST00000233146	NM_000251.2	822	Tgt/Ggt	15/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.55246299887372	2		266	383	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050348	37050349	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs63749959	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	147	376	0	ENST00000231790.2:c.503dup	p.Asn168LysfsTer4	p.N168Kfs*4	ENST00000231790	NM_000249.3	166	tta/ttAa	6/19	1	2	FACETS	0.985	0.905	1	0.985	0.905	1	CLONAL	1	TRUE	1	0.55246299887372	2		376	540	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924799	49924799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	222	633	0	ENST00000296474.3:c.4144C>T	p.Pro1382Ser	p.P1382S	ENST00000296474	NM_002447.2	1382	Ccc/Tcc	20/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.55246299887372	2		633	731	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916747	178916747	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	169	362	0	ENST00000263967.3:c.134T>C	p.Ile45Thr	p.I45T	ENST00000263967	NM_006218.2	45	aTa/aCa	2/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.55246299887372	2		362	521	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803576	1803576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	133	311	1	ENST00000260795.2:c.754C>T	p.Arg252Trp	p.R252W	ENST00000260795		252	Cgg/Tgg	6/17	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.55246299887372	2		312	378	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518033	187518033	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	177	414	1	ENST00000441802.2:c.12661C>A	p.Leu4221Met	p.L4221M	ENST00000441802	NM_005245.3	4221	Ctg/Atg	25/27	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.55246299887372	2		415	606	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542414	187542414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	118	308	0	ENST00000441802.2:c.5326G>A	p.Glu1776Lys	p.E1776K	ENST00000441802	NM_005245.3	1776	Gaa/Aaa	10/27	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.55246299887372	2		308	407	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636791	176636791	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	179	438	0	ENST00000439151.2:c.1391C>A	p.Pro464His	p.P464H	ENST00000439151	NM_022455.4	464	cCt/cAt	5/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.55246299887372	2		438	558	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180049730	180049730	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	132	409	0	ENST00000261937.6:c.1657+1G>A		p.X553_splice	ENST00000261937	NM_182925.4	553			1	2	FACETS	0.887	0.809	0.968	0.887	0.809	0.968	CLONAL	1	TRUE	1	0.55246299887372	2		409	539	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858400	27858401	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	101	402	0	ENST00000359303.2:c.170dup	p.Ser58ValfsTer3	p.S58Vfs*3	ENST00000359303	NM_003535.2	57	aag/aaAg	1/1	1	2	FACETS	0.844	0.759	0.934	0.844	0.759	0.934	CLONAL	1	TRUE	1	0.55246299887372	2		402	433	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120713	94120713	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	118	334	0	ENST00000369303.4:c.338C>A	p.Pro113His	p.P113H	ENST00000369303	NM_004440.3	113	cCt/cAt	3/17	1	2	FACETS	0.913	0.829	1	0.913	0.829	1	CLONAL	1	TRUE	1	0.55246299887372	2		334	468	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041092	112041092	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376211530	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	152	366	0	ENST00000368678.4:c.163G>A	p.Ala55Thr	p.A55T	ENST00000368678		55	Gca/Aca	3/13	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.55246299887372	2		366	474	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117645553	117645553	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	173	462	0	ENST00000368508.3:c.5583T>G	p.Ser1861Arg	p.S1861R	ENST00000368508	NM_002944.2	1861	agT/agG	34/43	1	2	FACETS	0.932	0.861	1	0.932	0.861	1	CLONAL	1	TRUE	1	0.55246299887372	2		462	672	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467922	50467922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	62	350	0	ENST00000331340.3:c.1157G>A	p.Arg386His	p.R386H	ENST00000331340	NM_006060.4	386	cGc/cAc	8/8	0.55246299887372	3	FACETS	0.518	0.448	0.594	0.259	0.224	0.297	SUBCLONAL	1	TRUE	1	0.55246299887372	3		350	553	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334789	81334789	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	130	385	0	ENST00000222390.5:c.1927A>G	p.Ser643Gly	p.S643G	ENST00000222390	NM_000601.4	643	Agc/Ggc	17/18	0.55246299887372	3	FACETS	0.933	0.848	1	0.466	0.424	0.511	CLONAL	1	TRUE	1	0.55246299887372	3		385	644	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540396	23540396	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs768668734	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	27	58	0	ENST00000380871.4:c.7A>G	p.Arg3Gly	p.R3G	ENST00000380871	NM_006167.3	3	Agg/Ggg	1/2	1	2	FACETS	0.897	0.728	1	0.897	0.728	1	CLONAL	1	TRUE	1	0.55246299887372	2		58	109	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68993058	68993058	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	124	368	0	ENST00000288368.4:c.1865del	p.Gly622AspfsTer22	p.G622Dfs*22	ENST00000288368	NM_024870.2	621	aaG/aa	17/40	1	2	FACETS	0.795	0.721	0.871	0.795	0.721	0.871	SUBCLONAL	1	TRUE	1	0.55246299887372	2		368	565	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128347850	128347850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771286674	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	35	468	0	ENST00000265960.3:c.655C>T	p.Arg219Trp	p.R219W	ENST00000265960	NM_001006617.1	219	Cgg/Tgg	5/12	1	2	FACETS	0.24	0.196	0.289	0.24	0.196	0.289	SUBCLONAL	1	TRUE	1	0.55246299887372	2		468	529	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137313568	137313568	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	236	693	0	ENST00000481739.1:c.827T>C	p.Leu276Pro	p.L276P	ENST00000481739	NM_002957.4	276	cTt/cCt	6/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.55246299887372	2		693	836	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841259	15841259	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766374131	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	89	189	0	ENST00000307771.7:c.1343G>A	p.Arg448His	p.R448H	ENST00000307771	NM_005089.3	448	cGc/cAc	11/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.55246299887372	2		189	247	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346845	70346845	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	158	399	0	ENST00000374080.3:c.2712G>T	p.Glu904Asp	p.E904D	ENST00000374080		904	gaG/gaT	20/45	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.55246299887372	2		399	554	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940474	76940474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	187	417	0	ENST00000373344.5:c.619G>A	p.Asp207Asn	p.D207N	ENST00000373344	NM_000489.3	207	Gat/Aat	8/35	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.55246299887372	2		417	620	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0031092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	236	836	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.326475734990639	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.326475734990639	2		836	702	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994665	73994665	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	125	711	1	ENST00000318443.5:c.149G>A	p.Cys50Tyr	p.C50Y	ENST00000318443	NM_001024736.1	50	tGc/tAc	3/10	0.326475734990639	2	FACETS	1	0.926	1	0.513	0.464	0.564	CLONAL	1	TRUE	0	0.326475734990639	2		712	747	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273132	55273132	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	110	504	0	ENST00000275493.2:c.3455A>G	p.Asp1152Gly	p.D1152G	ENST00000275493	NM_005228.3	1152	gAc/gGc	28/28	0.326475734990639	4	FACETS	1	0.938	1	0.531	0.477	0.589	CLONAL	1	TRUE	2	0.326475734990639	4		504	841	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0031093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	349	403	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.745736678950593	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.745736678950593	1		403	545	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073835	8073835	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	148	287	0	ENST00000377482.5:c.824del	p.Asn275ThrfsTer20	p.N275Tfs*20	ENST00000377482	NM_018948.3	275	aAc/ac	4/4	0.37875400502111	1	FACETS	0.816	0.759	0.873	0.816	0.759	0.873	INDETERMINATE	1	TRUE	0	0.745736678950593	1		287	305	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729468	41729468	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	294	500	0	ENST00000242208.4:c.1061G>A	p.Cys354Tyr	p.C354Y	ENST00000242208	NM_002192.2	354	tGc/tAc	3/3	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.745736678950593	2		500	758	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	141	367	8	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.49991216628557	2	FACETS	1	0.965	1	0.55	0.504	0.598	CLONAL	1	TRUE	0	0.49991216628557	2		375	513	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	101	350	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.9	0.809	0.995	0.9	0.809	0.995	CLONAL	1	TRUE	1	0.49991216628557	2		351	449	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007332	143007332	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	111	338	0	ENST00000262992.4:c.2452del	p.Arg818GlufsTer4	p.R818Efs*4	ENST00000262992	NM_001101669.1	818	Aga/ga	22/24	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.49991216628557	2		338	373	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	86	282	2	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	0.864	0.769	0.965	0.864	0.769	0.965	CLONAL	1	TRUE	1	0.49991216628557	2		284	398	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	28	324	0	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.247	0.197	0.304	0.247	0.197	0.304	SUBCLONAL	1	TRUE	1	0.49991216628557	2		324	454	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	69	243	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.49991216628557	2	FACETS	0.914	0.803	1	0.457	0.401	0.516	CLONAL	1	TRUE	0	0.49991216628557	2		243	302	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	168	491	0	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.49991216628557	2		491	621	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105841	27105841	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	119	398	0	ENST00000324856.7:c.5452C>T	p.Gln1818Ter	p.Q1818*	ENST00000324856	NM_006015.4	1818	Cag/Tag	20/20	1	2	FACETS	0.952	0.864	1	0.952	0.864	1	CLONAL	1	TRUE	1	0.49991216628557	2		398	500	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456425	32456425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1201988298	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	141	454	0	ENST00000332351.3:c.467G>A	p.Cys156Tyr	p.C156Y	ENST00000332351	NM_024426.4	156	tGc/tAc	1/10	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.49991216628557	2		454	529	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686901	37686901	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	59	418	2	ENST00000447079.4:c.3810del	p.Gly1271AspfsTer23	p.G1271Dfs*23	ENST00000447079	NM_015083.1	1269	Ccc/cc	14/14	1	2	FACETS	0.477	0.411	0.549	0.477	0.411	0.549	SUBCLONAL	1	TRUE	1	0.49991216628557	2		420	495	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618715	37618716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	93	495	0	ENST00000447079.4:c.397dup	p.Ser133LysfsTer24	p.S133Kfs*24	ENST00000447079	NM_015083.1	131	gaa/gAaa	1/14	1	2	FACETS	0.558	0.496	0.623	0.558	0.496	0.623	SUBCLONAL	1	TRUE	1	0.49991216628557	2		495	667	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043349	6043349	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781716	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	80	240	0	ENST00000265849.7:c.325del	p.Glu109LysfsTer3	p.E109Kfs*3	ENST00000265849	NM_000535.5	109	Gaa/aa	4/15	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.49991216628557	2		240	275	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151290	202151290	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	127	409	0	ENST00000358485.4:c.1596del	p.Lys532AsnfsTer73	p.K532Nfs*73	ENST00000358485	NM_001080125.1	530	agA/ag	9/9	1	2	FACETS	0.992	0.904	1	0.992	0.904	1	CLONAL	1	TRUE	1	0.49991216628557	2		409	512	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307280	65307283	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	91	332	0	ENST00000342505.4:c.2405_2408del	p.Lys802ArgfsTer11	p.K802Rfs*11	ENST00000342505	NM_002227.2	802	aAAGAg/ag	18/25	1	2	FACETS	0.924	0.826	1	0.924	0.826	1	CLONAL	1	TRUE	1	0.49991216628557	2		332	394	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310935	123310935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1171095092	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	108	355	1	ENST00000358487.5:c.493C>T	p.Arg165Trp	p.R165W	ENST00000358487	NM_000141.4	165	Cgg/Tgg	5/18	0.49991216628557	2	FACETS	0.929	0.839	1	0.465	0.419	0.512	CLONAL	1	TRUE	0	0.49991216628557	2		356	465	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076785	72076785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576347795	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	154	437	0	ENST00000357731.5:c.712G>A	p.Gly238Arg	p.G238R	ENST00000357731	NM_173808.2	238	Gga/Aga	5/7	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.49991216628557	2		437	579	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052635	42052635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	69	415	0	ENST00000219905.7:c.7306C>T	p.Arg2436Cys	p.R2436C	ENST00000219905	NM_001164273.1	2436	Cgt/Tgt	20/24	1	2	FACETS	0.463	0.403	0.528	0.463	0.403	0.528	SUBCLONAL	1	TRUE	1	0.49991216628557	2		415	596	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815712	32815712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1374606443	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	144	622	0	ENST00000354258.4:c.1904G>A	p.Arg635His	p.R635H	ENST00000354258	NM_000593.5	635	cGc/cAc	8/11	1	2	FACETS	0.935	0.856	1	0.935	0.856	1	CLONAL	1	TRUE	1	0.49991216628557	2		622	616	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561430	141561430	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	97	376	0	ENST00000220592.5:c.1375del	p.Gln459SerfsTer9	p.Q459Sfs*9	ENST00000220592	NM_012154.3	459	Cag/ag	11/19	1	2	FACETS	0.982	0.882	1	0.982	0.882	1	CLONAL	1	TRUE	1	0.49991216628557	2		376	395	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856208	111856208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1342201193	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	45	142	1	ENST00000341259.2:c.259C>T	p.Arg87Cys	p.R87C	ENST00000341259	NM_005475.2	87	Cgc/Tgc	2/8	1	2	FACETS	0.963	0.82	1	0.963	0.82	1	CLONAL	1	TRUE	1	0.49991216628557	2		143	187	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27093013	27093015	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	novel	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	95	376	0	ENST00000324856.7:c.2949_2951del	p.Asn983del	p.N983del	ENST00000324856	NM_006015.4	982	AAC/-	10/20	1	2	FACETS	0.821	0.734	0.912	0.821	0.734	0.912	CLONAL	1	TRUE	1	0.49991216628557	2		376	463	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981297	201981297	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs756079277	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	45	575	1	ENST00000359651.3:c.376C>T	p.Arg126Ter	p.R126*	ENST00000359651		126	Cga/Tga	2/8	1	2	FACETS	0.32	0.268	0.377	0.32	0.268	0.377	SUBCLONAL	1	TRUE	1	0.49991216628557	2		576	563	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720732	89720733	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	rs587780006	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	30	127	0	ENST00000371953.3:c.884_885insTT	p.Cys296TyrfsTer12	p.C296Yfs*12	ENST00000371953	NM_000314.4	295	cta/cTTta	8/9	0.49991216628557	2	FACETS	1	0.88	1	0.546	0.449	0.65	CLONAL	1	TRUE	0	0.49991216628557	2		127	110	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316075	14316075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs566703225	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	17	297	0	ENST00000256196.4:c.350G>A	p.Arg117His	p.R117H	ENST00000256196		117	cGt/cAt	4/6	1	2	FACETS	0.216	0.161	0.282	0.216	0.161	0.282	SUBCLONAL	1	TRUE	1	0.49991216628557	2		297	315	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913323	28913323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751180218	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	170	504	0	ENST00000282397.4:c.2470C>T	p.Arg824Trp	p.R824W	ENST00000282397	NM_002019.4	824	Cgg/Tgg	17/30	1	2	FACETS	0.962	0.887	1	0.962	0.887	1	CLONAL	1	TRUE	1	0.49991216628557	2		504	707	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632632	3632632	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1238019311	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	221	611	2	ENST00000294008.3:c.5216A>G	p.Glu1739Gly	p.E1739G	ENST00000294008	NM_032444.2	1739	gAg/gGg	15/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.49991216628557	2		613	792	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821200	72821200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	167	550	1	ENST00000268489.5:c.10975G>T	p.Asp3659Tyr	p.D3659Y	ENST00000268489	NM_006885.3	3659	Gac/Tac	10/10	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.49991216628557	2		551	668	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221439	36221439	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	193	639	0	ENST00000222270.7:c.5198G>A	p.Gly1733Asp	p.G1733D	ENST00000222270	NM_014727.1	1733	gGt/gAt	25/37	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.49991216628557	2		639	728	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99169298	99169299	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	138	490	0	ENST00000074304.5:c.1230_1231del	p.Arg410SerfsTer35	p.R410Sfs*35	ENST00000074304	NM_001134224.1	410	AGa/a	15/26	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.49991216628557	2		490	514	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99180093	99180093	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	97	442	0	ENST00000074304.5:c.2036G>A	p.Cys679Tyr	p.C679Y	ENST00000074304	NM_001134224.1	679	tGc/tAc	19/26	1	2	FACETS	0.807	0.722	0.896	0.807	0.722	0.896	CLONAL	1	TRUE	1	0.49991216628557	2		442	481	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99204022	99204022	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	87	328	0	ENST00000074304.5:c.2885C>A	p.Pro962His	p.P962H	ENST00000074304	NM_001134224.1	962	cCc/cAc	26/26	1	2	FACETS	0.983	0.878	1	0.983	0.878	1	CLONAL	1	TRUE	1	0.49991216628557	2		328	354	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732718	204732718	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	111	335	0	ENST00000302823.3:c.53G>T	p.Arg18Met	p.R18M	ENST00000302823	NM_005214.4	18	aGg/aTg	1/4	1	2	FACETS	0.982	0.889	1	0.982	0.889	1	CLONAL	1	TRUE	1	0.49991216628557	2		335	452	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845342	42845343	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCCAGG	novel	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	44	605	0	ENST00000398585.3:c.914_919dup	p.Pro305_Trp306dup	p.P305_W306dup	ENST00000398585	NM_001135099.1	305	cag/cCCTGGCag	9/14	1	2	FACETS	0.252	0.211	0.298	0.252	0.211	0.298	SUBCLONAL	1	TRUE	1	0.49991216628557	2		605	698	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067433	37067433	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	127	487	1	ENST00000231790.2:c.1348del	p.Asp450IlefsTer41	p.D450Ifs*41	ENST00000231790	NM_000249.3	448	gaG/ga	12/19	1	2	FACETS	0.863	0.784	0.945	0.863	0.784	0.945	CLONAL	1	TRUE	1	0.49991216628557	2		488	589	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696245	52696245	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	149	469	0	ENST00000394830.3:c.432C>G	p.Tyr144Ter	p.Y144*	ENST00000394830	NM_018313.4	144	taC/taG	5/30	1	2	FACETS	0.921	0.844	1	0.921	0.844	1	CLONAL	1	TRUE	1	0.49991216628557	2		469	647	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430536	181430536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	85	233	0	ENST00000325404.1:c.388G>A	p.Gly130Arg	p.G130R	ENST00000325404	NM_003106.3	130	Ggg/Agg	1/1	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.49991216628557	2		233	327	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638068	176638072	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTC	TTCTC	-	rs1131691754	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	100	524	0	ENST00000439151.2:c.2672_2676del	p.Ser891CysfsTer3	p.S891Cfs*3	ENST00000439151	NM_022455.4	890	TTCTCt/t	5/23	1	2	FACETS	0.717	0.642	0.796	0.717	0.642	0.796	SUBCLONAL	1	TRUE	1	0.49991216628557	2		524	558	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138197298	138197298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1340493697	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	44	176	1	ENST00000237289.4:c.800G>A	p.Gly267Glu	p.G267E	ENST00000237289	NM_001270507.1	267	gGg/gAg	5/9	1	2	FACETS	0.759	0.642	0.885	0.759	0.642	0.885	SUBCLONAL	1	TRUE	1	0.49991216628557	2		177	232	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527703	157527703	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554237318	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	162	479	0	ENST00000346085.5:c.5428C>T	p.Gln1810Ter	p.Q1810*	ENST00000346085	NM_020732.3	1810	Cag/Tag	20/20	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.49991216628557	2		479	640	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935520	13935520	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	75	263	0	ENST00000405192.2:c.1336del	p.His446ThrfsTer47	p.H446Tfs*47	ENST00000405192	NM_001163147.1	446	Cac/ac	12/12	1	2	FACETS	0.901	0.796	1	0.901	0.796	1	CLONAL	1	TRUE	1	0.49991216628557	2		263	333	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128246785	128246785	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	161	605	2	ENST00000265960.3:c.1144C>T	p.His382Tyr	p.H382Y	ENST00000265960	NM_001006617.1	382	Cat/Tat	9/12	1	2	FACETS	0.927	0.852	1	0.927	0.852	1	CLONAL	1	TRUE	1	0.49991216628557	2		607	695	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413907	139413907	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	53	526	0	ENST00000277541.6:c.853C>T	p.Pro285Ser	p.P285S	ENST00000277541	NM_017617.3	285	Cca/Tca	5/34	1	2	FACETS	0.315	0.268	0.367	0.315	0.268	0.367	SUBCLONAL	1	TRUE	1	0.49991216628557	2		526	673	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841247	15841247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1180602444	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	66	174	0	ENST00000307771.7:c.1331G>A	p.Arg444Gln	p.R444Q	ENST00000307771	NM_005089.3	444	cGg/cAg	11/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.49991216628557	2		174	183	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424212	47424212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	142	505	0	ENST00000377045.4:c.217G>A	p.Ala73Thr	p.A73T	ENST00000377045	NM_001654.4	73	Gcc/Acc	4/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.49991216628557	2		505	542	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0031096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	62	505	4	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.218159577470035	1	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	0	0.221943767300368	1		509	476	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0031096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	73	496	0	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.221943767300368	1	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	0	0.221943767300368	1		496	577	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014039	14014039	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	51	356	0	ENST00000311895.7:c.17C>T	p.Pro6Leu	p.P6L	ENST00000311895	NM_005236.2	6	cCg/cTg	1/11	1	2	FACETS	0.995	0.847	1	0.995	0.847	1	CLONAL	1	TRUE	1	0.221943767300368	2		356	462	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662703	117662703	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	72	347	0	ENST00000368508.3:c.4762A>G	p.Lys1588Glu	p.K1588E	ENST00000368508	NM_002944.2	1588	Aaa/Gaa	29/43	0.221943767300368	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.221943767300368	1		347	479	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608978	100608978	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0031096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	59	360	0	ENST00000308731.7:c.1632-2A>T		p.X544_splice	ENST00000308731	NM_000061.2	544			1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.221943767300368	2		360	505	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0031096-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	77	472	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.22	2		472	650	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249029	55249029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs483352806	NA	P-0031096-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	58	394	0	ENST00000275493.2:c.2327G>A	p.Arg776His	p.R776H	ENST00000275493	NM_005228.3	776	cGc/cAc	20/28	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.22	2		394	527	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850885	128850885	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031096-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	64	563	1	ENST00000249373.3:c.1732G>T	p.Glu578Ter	p.E578*	ENST00000249373	NM_005631.4	578	Gag/Tag	10/12	1	2	FACETS	0.926	0.802	1	0.926	0.802	1	CLONAL	1	TRUE	1	0.22	2		564	628	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0031097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	146	728	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.207524680072065	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.207524680072065	3		728	695	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0031097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	156	491	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.207524680072065	3	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	1	0.207524680072065	3		491	811	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0031097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	42	417	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.692	0.577	0.82	0.692	0.577	0.82	SUBCLONAL	1	TRUE	1	0.207524680072065	2		419	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519975	NA	P-0031097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	79	716	0	ENST00000269305.4:c.403T>C	p.Cys135Arg	p.C135R	ENST00000269305	NM_001126112.2	135	Tgc/Cgc	5/11	1	2	FACETS	0.832	0.73	0.942	0.832	0.73	0.942	CLONAL	1	TRUE	1	0.207524680072065	2		716	915	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265579	198265579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	25	405	0	ENST00000335508.6:c.2578G>A	p.Glu860Lys	p.E860K	ENST00000335508	NM_012433.2	860	Gaa/Aaa	18/25	1	2	FACETS	0.55	0.433	0.685	0.55	0.433	0.685	SUBCLONAL	1	TRUE	1	0.207524680072065	2		405	438	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627941	187627941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	42	522	0	ENST00000441802.2:c.3041C>T	p.Ser1014Phe	p.S1014F	ENST00000441802	NM_005245.3	1014	tCt/tTt	2/27	1	2	FACETS	0.632	0.527	0.75	0.632	0.527	0.75	SUBCLONAL	1	TRUE	1	0.207524680072065	2		522	640	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710744	117710744	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1375443218	NA	P-0031097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	31	303	0	ENST00000368508.3:c.1528C>T	p.Leu510Phe	p.L510F	ENST00000368508	NM_002944.2	510	Ctt/Ttt	12/43	1	2	FACETS	0.743	0.601	0.904	0.743	0.601	0.904	CLONAL	1	TRUE	1	0.207524680072065	2		303	402	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239895	53239895	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	53	518	0	ENST00000375401.3:c.1546G>C	p.Glu516Gln	p.E516Q	ENST00000375401	NM_004187.3	516	Gag/Cag	11/26	1	2	FACETS	0.692	0.589	0.806	0.692	0.589	0.806	SUBCLONAL	1	TRUE	1	0.207524680072065	2		518	738	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138550	11138550	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	46	566	0	ENST00000358026.2:c.3306C>A	p.Phe1102Leu	p.F1102L	ENST00000358026	NM_001128849.1	1102	ttC/ttA	24/36	1	2	FACETS	0.617	0.519	0.727	0.617	0.519	0.727	SUBCLONAL	1	TRUE	1	0.207524680072065	2		566	718	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396856	396856	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs574168909	NA	P-0031097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	39	531	0	ENST00000262320.3:c.170C>T	p.Ser57Leu	p.S57L	ENST00000262320	NM_003502.3	57	tCg/tTg	2/11	1	2	FACETS	0.486	0.401	0.581	0.486	0.401	0.581	SUBCLONAL	1	TRUE	1	0.207524680072065	2		531	774	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607661	43607661	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	60	724	0	ENST00000355710.3:c.1637G>A	p.Gly546Glu	p.G546E	ENST00000355710	NM_020975.4	546	gGa/gAa	8/20	1	2	FACETS	0.688	0.592	0.794	0.688	0.592	0.794	SUBCLONAL	1	TRUE	1	0.207524680072065	2		724	840	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142465	119142465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1262627997	NA	P-0031097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	26	365	0	ENST00000264033.4:c.464C>T	p.Ser155Phe	p.S155F	ENST00000264033	NM_005188.3	155	tCc/tTc	3/16	0.18412253199113	2	FACETS	0.569	0.45	0.707	0.285	0.225	0.354	SUBCLONAL	1	TRUE	0	0.207524680072065	2		365	440	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427927	49427927	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	51	511	0	ENST00000301067.7:c.10663G>C	p.Glu3555Gln	p.E3555Q	ENST00000301067	NM_003482.3	3555	Gag/Cag	38/54	0.207524680072065	2	FACETS	0.786	0.668	0.917	0.393	0.334	0.459	CLONAL	1	TRUE	0	0.207524680072065	2		511	625	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349135	89349135	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	74	804	0	ENST00000301030.4:c.3815G>C	p.Arg1272Thr	p.R1272T	ENST00000301030	NM_001256183.1	1272	aGa/aCa	9/13	1	2	FACETS	0.633	0.552	0.72	0.633	0.552	0.72	SUBCLONAL	1	TRUE	1	0.207524680072065	2		804	1127	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89807223	89807223	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs759514393	NA	P-0031097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	57	466	0	ENST00000389301.3:c.3817C>G	p.Leu1273Val	p.L1273V	ENST00000389301	NM_000135.2	1273	Ctg/Gtg	38/43	1	2	FACETS	0.913	0.783	1	0.913	0.783	1	CLONAL	1	TRUE	1	0.207524680072065	2		466	602	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016603	12016603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	28	354	0	ENST00000353533.5:c.739G>A	p.Asp247Asn	p.D247N	ENST00000353533	NM_003010.3	247	Gac/Aac	7/11	1	2	FACETS	0.862	0.69	1	0.862	0.69	1	CLONAL	1	TRUE	1	0.207524680072065	2		354	313	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57569890	57569890	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	23	231	0	ENST00000316660.6:c.70G>C	p.Glu24Gln	p.E24Q	ENST00000316660	NM_021127.2	24	Gag/Cag	2/2	1	2	FACETS	0.693	0.54	0.869	0.693	0.54	0.869	SUBCLONAL	1	TRUE	1	0.207524680072065	2		231	320	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353909	15353909	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	46	337	1	ENST00000263377.2:c.2971C>T	p.Gln991Ter	p.Q991*	ENST00000263377	NM_058243.2	991	Cag/Tag	14/20	1	2	FACETS	0.974	0.821	1	0.974	0.821	1	CLONAL	1	TRUE	1	0.207524680072065	2		338	455	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974993	18974993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	50	398	0	ENST00000262803.5:c.2790G>A	p.Met930Ile	p.M930I	ENST00000262803	NM_002911.3	930	atG/atA	20/24	0.207524680072065	5	FACETS	0.799	0.676	0.935			1	CLONAL	1	TRUE	NA	0.207524680072065	5		398	791	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808955	1808955	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768644781	NA	P-0031097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	95	461	0	ENST00000260795.2:c.2387C>T	p.Pro796Leu	p.P796L	ENST00000260795		796	cCg/cTg	17/17	1	2	FACETS	0.825	0.736	0.919	1	0.983	1	CLONAL	2	TRUE	1	0.207524680072065	2		461	555	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197119	26197119	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	32	446	0	ENST00000356476.2:c.360C>G	p.Ile120Met	p.I120M	ENST00000356476		120	atC/atG	1/1	1	2	FACETS	0.559	0.452	0.679	0.559	0.452	0.679	SUBCLONAL	1	TRUE	1	0.207524680072065	2		446	552	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041662	47041663	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0031097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	108	627	0	ENST00000377604.3:c.1891dup	p.Ala631GlyfsTer42	p.A631Gfs*42	ENST00000377604	NM_001204468.1	629	-/G	17/24	0.144836810390117	3	FACETS	1	0.976	1	0.657	0.589	0.73	CLONAL	1	TRUE	1	0.207524680072065	3		627	874	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239703	53239703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	49	521	1	ENST00000375401.3:c.1639G>A	p.Glu547Lys	p.E547K	ENST00000375401	NM_004187.3	547	Gaa/Aaa	12/26	1	2	FACETS	0.609	0.514	0.713	0.609	0.514	0.713	SUBCLONAL	1	TRUE	1	0.207524680072065	2		522	776	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944501	71944501	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	152	532	0	ENST00000298229.2:c.2057C>T	p.Pro686Leu	p.P686L	ENST00000298229	NM_001567.3	686	cCc/cTc	18/28	0.554766589019295	2	FACETS	1	0.99	1	0.722	0.674	0.771	CLONAL	1	TRUE	0	0.718109898796615	2		532	293	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098953	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	109	326	0	ENST00000397062.3:c.92G>C	p.Gly31Ala	p.G31A	ENST00000397062	NM_006164.4	31	gGa/gCa	2/5	0.36690731038652	3	FACETS	1	0.984	1	0.499	0.452	0.548	CLONAL	1	TRUE	0	0.498288294608291	3		326	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0031099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	251	574	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	0.356583178111823	2	FACETS	1	0.992	1	0.684	0.643	0.727	CLONAL	1	TRUE	0	0.498288294608291	2		574	736	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717661	89717661	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0031099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	182	422	0	ENST00000371953.3:c.686C>G	p.Ser229Ter	p.S229*	ENST00000371953	NM_000314.4	229	tCa/tGa	7/9	0.356583178111823	2	FACETS	1	0.991	1	0.744	0.692	0.796	CLONAL	1	TRUE	0	0.498288294608291	2		422	491	SUCCESS
ATR	545	MSKCC	GRCh37	3	142259767	142259767	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs762440684	NA	P-0031099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	69	405	0	ENST00000350721.4:c.3560A>G	p.Asp1187Gly	p.D1187G	ENST00000350721	NM_001184.3	1187	gAt/gGt	18/47	0.498288294608291	6	FACETS	0.612	0.531	0.699	0.102	0.088	0.117	SUBCLONAL	1	TRUE	0	0.498288294608291	6		405	904	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076731	72076731	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1320611514	NA	P-0031099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	216	457	3	ENST00000357731.5:c.766G>C	p.Glu256Gln	p.E256Q	ENST00000357731	NM_173808.2	256	Gaa/Caa	5/7	0.356583178111823	2	FACETS	0.807	0.757	0.858	0.807	0.757	0.858	CLONAL	2	TRUE	0	0.498288294608291	2		460	537	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193202178	193202178	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	143	330	0	ENST00000367435.3:c.1210C>G	p.Leu404Val	p.L404V	ENST00000367435	NM_024529.4	404	Cta/Gta	14/17	0.498288294608291	3	FACETS	1	0.984	1	0.444	0.407	0.483	CLONAL	1	TRUE	0	0.498288294608291	3		330	538	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425119	49425119	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	204	626	0	ENST00000301067.7:c.13369G>T	p.Glu4457Ter	p.E4457*	ENST00000301067	NM_003482.3	4457	Gaa/Taa	39/54	0.264621637395863	3	FACETS	1	0.963	1	0.53	0.491	0.57	INDETERMINATE	1	TRUE	1	0.498288294608291	3		626	965	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622494	28622494	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	175	498	2	ENST00000241453.7:c.1123G>A	p.Ala375Thr	p.A375T	ENST00000241453	NM_004119.2	375	Gcc/Acc	9/24	0.356583178111823	2	FACETS	1	0.991	1	0.744	0.692	0.798	CLONAL	1	TRUE	0	0.498288294608291	2		500	472	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050979	49050979	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1555295354	NA	P-0031099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	129	283	1	ENST00000267163.4:c.2663G>A	p.Ser888Asn	p.S888N	ENST00000267163	NM_000321.2	888	aGt/aAt	25/27	0.356583178111823	2	FACETS	0.806	0.742	0.872	0.806	0.742	0.872	CLONAL	2	TRUE	0	0.498288294608291	2		284	321	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108097	30108097	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	92	471	0	ENST00000331968.5:c.710C>T	p.Ser237Leu	p.S237L	ENST00000331968	NM_002742.2	237	tCa/tTa	5/18	1	2	FACETS	0.786	0.701	0.875	0.786	0.701	0.875	SUBCLONAL	1	TRUE	1	0.498288294608291	2		471	470	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554161	63554161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	196	559	0	ENST00000307078.5:c.578C>T	p.Ser193Phe	p.S193F	ENST00000307078	NM_004655.3	193	tCt/tTt	2/11	0.211243630269099	5	FACETS	0.76	0.704	0.818	0.507	0.469	0.546	INDETERMINATE	2	TRUE	2	0.498288294608291	5		559	904	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169977831	169977831	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	119	457	0	ENST00000295797.4:c.298G>C	p.Glu100Gln	p.E100Q	ENST00000295797	NM_002740.5	100	Gaa/Caa	3/18	0.498288294608291	6	FACETS	0.857	0.772	0.947	0.143	0.128	0.158	CLONAL	1	TRUE	0	0.498288294608291	6		457	1113	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505322	186505322	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	242	319	0	ENST00000323963.5:c.948G>A	p.Met316Ile	p.M316I	ENST00000323963		316	atG/atA	9/11	0.498288294608291	6	FACETS	1	0.985	1	0.389	0.364	0.415	CLONAL	2	TRUE	0	0.498288294608291	6		319	831	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067107	143067107	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	131	322	0	ENST00000262992.4:c.1606A>T	p.Ile536Phe	p.I536F	ENST00000262992	NM_001101669.1	536	Att/Ttt	16/24	0.356583178111823	2	FACETS	1	0.982	1	0.638	0.584	0.694	CLONAL	1	TRUE	0	0.498288294608291	2		322	412	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912386	29912420	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGCTCAGGTGGAGAAGGGGTGAAGGGTGGGGTCT	GAGCTCAGGTGGAGAAGGGGTGAAGGGTGGGGTCT	-	novel	NA	P-0031099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	296	417	0	ENST00000376809.5:c.1008_1012+30del		p.X336_splice	ENST00000376809	NM_002116.7	336		5/8	0.497180195941974	2	FACETS	0.814	0.771	0.857	0.814	0.771	0.857	CLONAL	2	TRUE	0	0.498288294608291	2		417	730	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166449	32166449	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	442	579	2	ENST00000375023.3:c.4594G>C	p.Glu1532Gln	p.E1532Q	ENST00000375023	NM_004557.3	1532	Gag/Cag	25/30	0.497180195941974	2	FACETS	0.904	0.866	0.942	0.904	0.866	0.942	CLONAL	2	TRUE	0	0.498288294608291	2		581	981	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852035	128852035	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs777762925	NA	P-0031099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	274	654	0	ENST00000249373.3:c.2107C>T	p.Arg703Ter	p.R703*	ENST00000249373	NM_005631.4	703	Cga/Tga	12/12	0.356583178111823	2	FACETS	1	0.992	1	0.661	0.622	0.7	CLONAL	1	TRUE	0	0.498288294608291	2		654	832	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209270	98209270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	158	554	0	ENST00000331920.6:c.4268G>A	p.Arg1423Lys	p.R1423K	ENST00000331920	NM_000264.3	1423	aGg/aAg	23/24	0.111730070746398	4	FACETS	1	0.97	1	0.562	0.515	0.611	INDETERMINATE	1	TRUE	2	0.498288294608291	4		554	846	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0031100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	90	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.91	0.812	1	0.91	0.812	1	CLONAL	1	TRUE	1	0.443296127172774	2		336	446	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0031100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	46	294	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	0.555	0.468	0.65	0.555	0.468	0.65	SUBCLONAL	1	TRUE	1	0.443296127172774	2		294	374	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344186	70344186	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	104	340	0	ENST00000374080.3:c.1922C>A	p.Ala641Asp	p.A641D	ENST00000374080		641	gCc/gAc	13/45	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.443296127172774	2		340	437	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845757	68845757	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587780784	NA	P-0031101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	57	278	0	ENST00000261769.5:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000261769	NM_004360.3	335	Cga/Tga	7/16	0.254681508713338	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.254681508713338	1		278	327	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189448	56189448	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	98	402	1	ENST00000399503.3:c.4480C>T	p.Gln1494Ter	p.Q1494*	ENST00000399503	NM_005921.1	1494	Cag/Tag	20/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.254681508713338	2		403	545	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912133	50912133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768773535	NA	P-0031101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	84	645	1	ENST00000440232.2:c.1867C>T	p.Arg623Trp	p.R623W	ENST00000440232	NM_002691.3	623	Cgg/Tgg	15/27	0.254681508713338	3	FACETS	0.854	0.753	0.962	0.427	0.376	0.481	CLONAL	1	TRUE	1	0.254681508713338	3		646	871	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434181	49434181	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	130	728	1	ENST00000301067.7:c.7372C>T	p.Gln2458Ter	p.Q2458*	ENST00000301067	NM_003482.3	2458	Cag/Tag	31/54	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.254681508713338	2		729	982	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638911	176638911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367790484	NA	P-0031101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	116	503	0	ENST00000439151.2:c.3511C>T	p.Arg1171Cys	p.R1171C	ENST00000439151	NM_022455.4	1171	Cgt/Tgt	5/23	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.254681508713338	2		503	718	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626656	12626656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	62	414	0	ENST00000251849.4:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000251849	NM_002880.3	545	Gag/Aag	15/17	1	2	FACETS	0.866	0.749	0.994	0.866	0.749	0.994	CLONAL	1	TRUE	1	0.254681508713338	2		414	562	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097808	27097808	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	73	284	0	ENST00000324856.7:c.3397C>G	p.Pro1133Ala	p.P1133A	ENST00000324856	NM_006015.4	1133	Ccc/Gcc	12/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.254681508713338	2		284	414	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161310403	161310403	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	68	313	0	ENST00000367975.2:c.199A>G	p.Met67Val	p.M67V	ENST00000367975	NM_003001.3	67	Atg/Gtg	4/6	0.254681508713338	3	FACETS	1	0.872	1	0.501	0.436	0.571	CLONAL	1	TRUE	1	0.254681508713338	3		313	601	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805325	89805325	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139478274	NA	P-0031101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	84	432	1	ENST00000389301.3:c.4225C>T	p.Arg1409Trp	p.R1409W	ENST00000389301	NM_000135.2	1409	Cgg/Tgg	42/43	0.254681508713338	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.254681508713338	1		433	545	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217635	7217635	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	59	318	0	ENST00000380728.2:c.292G>T	p.Glu98Ter	p.E98*	ENST00000380728		98	Gaa/Taa	4/11	0.254681508713338	1	FACETS	0.97	0.837	1	0.97	0.837	1	CLONAL	1	TRUE	0	0.254681508713338	1		318	417	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428294	33428294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	83	401	0	ENST00000345365.6:c.829C>T	p.Leu277Phe	p.L277F	ENST00000345365	NM_002878.3	277	Ctc/Ttc	9/10	0.254681508713338	3	FACETS	1	0.957	1	0.591	0.522	0.665	CLONAL	1	TRUE	1	0.254681508713338	3		401	622	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033771	48033771	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	80	256	0	ENST00000234420.5:c.3982C>T	p.Gln1328Ter	p.Q1328*	ENST00000234420	NM_000179.2	1328	Cag/Tag	9/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.254681508713338	2		256	478	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627262	12627262	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	53	364	0	ENST00000251849.4:c.1454G>T	p.Gly485Val	p.G485V	ENST00000251849	NM_002880.3	485	gGa/gTa	14/17	1	2	FACETS	0.704	0.6	0.818	0.704	0.6	0.818	SUBCLONAL	1	TRUE	1	0.254681508713338	2		364	591	SUCCESS
ATR	545	MSKCC	GRCh37	3	142180814	142180814	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	49	318	0	ENST00000350721.4:c.7160G>C	p.Arg2387Thr	p.R2387T	ENST00000350721	NM_001184.3	2387	aGa/aCa	42/47	1	2	FACETS	0.725	0.614	0.847	0.725	0.614	0.847	SUBCLONAL	1	TRUE	1	0.254681508713338	2		318	531	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189442	56189442	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	96	405	2	ENST00000399503.3:c.4474C>A	p.Gln1492Lys	p.Q1492K	ENST00000399503	NM_005921.1	1492	Caa/Aaa	20/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.254681508713338	2		407	556	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575513	67575513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1418066079	NA	P-0031101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	66	294	0	ENST00000274335.5:c.586C>T	p.Pro196Ser	p.P196S	ENST00000274335		196	Cct/Tct	4/15	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.254681508713338	2		294	479	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520725	176520725	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	92	457	2	ENST00000292408.4:c.1468G>A	p.Asp490Asn	p.D490N	ENST00000292408	NM_213647.1	490	Gac/Aac	11/18	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.254681508713338	2		459	616	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858279	27858279	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	75	487	0	ENST00000359303.2:c.292G>C	p.Glu98Gln	p.E98Q	ENST00000359303	NM_003535.2	98	Gag/Cag	1/1	1	2	FACETS	0.886	0.776	1	0.886	0.776	1	CLONAL	1	TRUE	1	0.254681508713338	2		487	665	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519513	137519513	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	61	263	0	ENST00000367739.4:c.1125G>C	p.Glu375Asp	p.E375D	ENST00000367739	NM_000416.2	375	gaG/gaC	7/7	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.254681508713338	2		263	404	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851496	151851496	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	76	303	0	ENST00000262189.6:c.11995G>C	p.Asp3999His	p.D3999H	ENST00000262189	NM_170606.2	3999	Gac/Cac	47/59	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.254681508713338	2		303	442	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517901	8517901	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0031101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	60	266	0	ENST00000356435.5:c.1490C>G	p.Ser497Ter	p.S497*	ENST00000356435		497	tCa/tGa	10/35	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.254681508713338	2		266	348	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759824	133759824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	64	469	0	ENST00000318560.5:c.2147C>T	p.Ser716Phe	p.S716F	ENST00000318560	NM_005157.4	716	tCt/tTt	11/11	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.254681508713338	2		469	469	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443695	29443695	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs863225281	NA	P-0121612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	253	397	0	ENST00000389048.3:c.3522C>A	p.Phe1174Leu	p.F1174L	ENST00000389048	NM_004304.4	1174	ttC/ttA	23/29	0.690271410222894	4	FACETS	0.905	0.851	0.959	0.603	0.567	0.639	CLONAL	2	NA	1	0.693448891065944	4		397	683	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38504690	38504691	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0121612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	163	479	0	ENST00000254066.5:c.303_304del	p.Val102GlnfsTer4	p.V102Qfs*4	ENST00000254066	NM_000964.3	101	GGg/g	3/9	0.673560969197023	5	FACETS	0.987	0.905	1	0.329	0.301	0.358	CLONAL	1	NA	2	0.693448891065944	5		479	972	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557642	95557642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	359	658	1	ENST00000393063.1:c.5425G>A	p.Gly1809Arg	p.G1809R	ENST00000393063	NM_030621.3	1809	Ggg/Agg	26/28	1	2	FACETS	0.937	0.894	0.981	0.937	0.894	0.981	CLONAL	1	TRUE	1	0.949124786606769	2		659	807	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553703	29553703	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1555613843	NA	P-0031106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	335	642	0	ENST00000356175.3:c.2251+1G>A		p.X751_splice	ENST00000356175	NM_000267.3	751			0.949124786606769	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.949124786606769	1		642	353	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262270	16262270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	112	222	0	ENST00000375759.3:c.9535G>A	p.Val3179Ile	p.V3179I	ENST00000375759	NM_015001.2	3179	Gtc/Atc	11/15	0.46292138338412	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.949124786606769	0		222	120	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124656	108124656	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	270	541	0	ENST00000278616.4:c.2014G>T	p.Glu672Ter	p.E672*	ENST00000278616	NM_000051.3	672	Gaa/Taa	13/63	0.949124786606769	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.949124786606769	1		541	296	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95563051	95563051	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0031106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	136	250	0	ENST00000393063.1:c.4207-1G>A		p.X1403_splice	ENST00000393063	NM_030621.3	1403			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.949124786606769	2		250	262	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121293	29121293	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	344	773	0	ENST00000328354.6:c.382C>G	p.Pro128Ala	p.P128A	ENST00000328354	NM_007194.3	128	Cca/Gca	3/15	0.486020558532516	1	FACETS	0.602	0.575	0.628	0.602	0.575	0.628	INDETERMINATE	1	TRUE	0	0.949124786606769	1		773	633	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098953	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	84	326	0	ENST00000397062.3:c.92G>C	p.Gly31Ala	p.G31A	ENST00000397062	NM_006164.4	31	gGa/gCa	2/5	1	2	FACETS	0.979	0.874	1	0.979	0.874	1	CLONAL	1	TRUE	1	0.58	2		326	296	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266088	41266099	+	inframe_deletion	In_Frame_Del	DEL	TCTTACCTGGAC	TCTTACCTGGAC	-	novel	NA	P-0031130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	101	324	0	ENST00000349496.5:c.88_99del	p.Tyr30_Ser33del	p.Y30_S33del	ENST00000349496	NM_001904.3	29	TCTTACCTGGAC/-	3/15	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.58	2		324	346	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0031132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	56	568	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.752	0.643	0.871	1	0.966	1	SUBCLONAL	2	TRUE	1	0.11	2		570	677	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0031132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	14	437	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.433	0.311	0.582	0.433	0.311	0.582	SUBCLONAL	1	TRUE	1	0.11	2		437	588	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711891	89711891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	21	418	0	ENST00000371953.3:c.509G>A	p.Ser170Asn	p.S170N	ENST00000371953	NM_000314.4	170	aGt/aAt	6/9	1	2	FACETS	0.656	0.503	0.836	0.656	0.503	0.836	SUBCLONAL	1	TRUE	1	0.11	2		418	582	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991949	72991949	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs753977275	NA	P-0031132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	30	436	0	ENST00000268489.5:c.2096del	p.Gly699AlafsTer125	p.G699Afs*125	ENST00000268489	NM_006885.3	699	gGc/gc	2/10	1	2	FACETS	0.944	0.759	1	0.944	0.759	1	CLONAL	1	TRUE	1	0.11	2		436	578	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102189	27102190	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0031132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	24	408	0	ENST00000324856.7:c.5117_5118dup	p.Gln1708ValfsTer7	p.Q1708Vfs*7	ENST00000324856	NM_006015.4	1705	-/CT	19/20	1	2	FACETS	0.913	0.714	1	0.913	0.714	1	CLONAL	1	TRUE	1	0.11	2		408	478	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805420	1805420	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs761527653	NA	P-0031132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	28	421	1	ENST00000260795.2:c.932C>T	p.Thr311Met	p.T311M	ENST00000260795		311	aCg/aTg	7/17	1	2	FACETS	0.914	0.729	1	0.914	0.729	1	CLONAL	1	TRUE	1	0.11	2		422	557	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0031133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	1404	435	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.683711006880958	8	FACETS	0.998	0.983	1			1	CLONAL	7	TRUE	NA	0.683711006880958	8		435	1794	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578532	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	392	743	0	ENST00000269305.4:c.398T>A	p.Met133Lys	p.M133K	ENST00000269305	NM_001126112.2	133	aTg/aAg	5/11	0.683711006880958	1	FACETS	0.941	0.901	0.982	0.941	0.901	0.982	CLONAL	1	TRUE	0	0.683711006880958	1		743	802	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685281	89685281	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1060500116	NA	P-0031133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	97	268	0	ENST00000371953.3:c.176C>G	p.Ser59Ter	p.S59*	ENST00000371953	NM_000314.4	59	tCa/tGa	3/9	0.683711006880958	1	FACETS	0.988	0.905	1	0.988	0.905	1	CLONAL	1	TRUE	0	0.683711006880958	1		268	189	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187947	32187947	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771104755	NA	P-0031133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	115	622	0	ENST00000375023.3:c.1274C>T	p.Ser425Leu	p.S425L	ENST00000375023	NM_004557.3	425	tCg/tTg	7/30	1	2	FACETS	0.359	0.323	0.398	0.359	0.323	0.398	SUBCLONAL	1	TRUE	1	0.683711006880958	2		622	937	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032099	10032099	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	282	608	0	ENST00000330684.3:c.724G>A	p.Glu242Lys	p.E242K	ENST00000330684	NM_001134407.1	242	Gag/Aag	3/13	1	2	FACETS	0.975	0.919	1	0.975	0.919	1	CLONAL	1	TRUE	1	0.683711006880958	2		608	846	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029509	14029509	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	71	391	0	ENST00000311895.7:c.1720G>A	p.Glu574Lys	p.E574K	ENST00000311895	NM_005236.2	574	Gag/Aag	8/11	1	2	FACETS	0.337	0.294	0.383	0.337	0.294	0.383	SUBCLONAL	1	TRUE	1	0.683711006880958	2		391	617	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133161	30133161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs976845326	NA	P-0031133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	75	372	0	ENST00000263025.4:c.337G>A	p.Glu113Lys	p.E113K	ENST00000263025	NM_002746.2	113	Gaa/Aaa	2/9	1	2	FACETS	0.392	0.343	0.444	0.392	0.343	0.444	SUBCLONAL	1	TRUE	1	0.683711006880958	2		372	560	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40447652	40447652	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1636	141	458	0	ENST00000345506.4:c.391G>A	p.Gly131Arg	p.G131R	ENST00000345506	NM_003152.3	131	Ggg/Agg	6/20	0.683711006880958	6	FACETS	0.549	0.498	0.604			1	SUBCLONAL	1	TRUE	NA	0.683711006880958	6		458	1777	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71008424	71008424	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	58	282	1	ENST00000318789.4:c.2008G>A	p.Glu670Lys	p.E670K	ENST00000318789	NM_032682.5	670	Gaa/Aaa	21/21	1	2	FACETS	0.334	0.287	0.385	0.334	0.287	0.385	SUBCLONAL	1	TRUE	1	0.683711006880958	2		283	508	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921486	178921486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1734	179	514	2	ENST00000263967.3:c.968C>T	p.Ser323Phe	p.S323F	ENST00000263967	NM_006218.2	323	tCt/tTt	5/21	0.683711006880958	8	FACETS	0.835	0.766	0.907			1	CLONAL	1	TRUE	NA	0.683711006880958	8		516	1913	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149450034	149450034	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	149	548	2	ENST00000286301.3:c.1183G>A	p.Glu395Lys	p.E395K	ENST00000286301	NM_005211.3	395	Gag/Aag	8/22	0.152803640961956	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.683711006880958	0		550	673	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983281	149983281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749247753	NA	P-0031133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	248	551	0	ENST00000253339.5:c.2977G>A	p.Glu993Lys	p.E993K	ENST00000253339		993	Gaa/Aaa	7/7	1	2	FACETS	0.869	0.815	0.924	0.869	0.815	0.924	CLONAL	1	TRUE	1	0.683711006880958	2		551	835	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207435	29207435	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1440390437	NA	P-0031133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	66	438	0	ENST00000240100.2:c.361G>A	p.Asp121Asn	p.D121N	ENST00000240100	NM_001394.6	121	Gac/Aac	1/4	0.683711006880958	1	FACETS	0.331	0.288	0.377	0.331	0.288	0.377	SUBCLONAL	1	TRUE	0	0.683711006880958	1		438	384	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0031136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	53	503	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.16606023597583	2		503	559	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962846	2962846	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	43	575	0	ENST00000396946.4:c.2062C>T	p.Arg688Ter	p.R688*	ENST00000396946	NM_032415.4	688	Cga/Tga	16/25	1	2	FACETS	0.631	0.526	0.748	0.631	0.526	0.748	SUBCLONAL	1	TRUE	1	0.16606023597583	2		575	821	SUCCESS
APC	324	MSKCC	GRCh37	5	112175246	112175246	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1057517558	NA	P-0031136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	21	245	0	ENST00000257430.4:c.3956del	p.Pro1319LeufsTer2	p.P1319Lfs*2	ENST00000257430	NM_000038.5	1319	Cct/ct	16/16	1	2	FACETS	0.667	0.513	0.848	0.667	0.513	0.848	SUBCLONAL	1	TRUE	1	0.16606023597583	2		245	379	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038879	12038879	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	220	439	1	ENST00000396373.4:c.1172A>G	p.Tyr391Cys	p.Y391C	ENST00000396373	NM_001987.4	391	tAt/tGt	7/8	1	2	FACETS	0.972	0.913	1	0.972	0.913	1	CLONAL	1	TRUE	1	0.839507124919109	2		440	539	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061232	38061232	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1486264414	NA	P-0031137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	52	510	0	ENST00000250448.2:c.757A>G	p.Met253Val	p.M253V	ENST00000250448	NM_004496.3	253	Atg/Gtg	2/2	1	2	FACETS	0.19	0.161	0.222	0.19	0.161	0.222	SUBCLONAL	1	TRUE	1	0.839507124919109	2		510	652	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729084	66729100	+	protein_altering_variant	In_Frame_Del	DEL	CTAATTCATCTGGAGAT	CTAATTCATCTGGAGAT	GAGAG	novel	NA	P-0031137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	198	568	1	ENST00000307102.5:c.292_308delinsGAGAG	p.Leu98_Ile103delinsGluSer	p.L98_I103delinsES	ENST00000307102	NM_002755.3	98	CTAATTCATCTGGAGATc/GAGAGc	3/11	1	2	FACETS	0.825	0.769	0.882	0.825	0.769	0.882	CLONAL	1	TRUE	1	0.839507124919109	2		569	572	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0031139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	59	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.928	0.799	1	0.928	0.799	1	CLONAL	1	TRUE	1	0.24	2		336	530	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547874	41547874	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0031139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	45	438	0	ENST00000263253.7:c.2855C>G	p.Ser952Ter	p.S952*	ENST00000263253	NM_001429.3	952	tCa/tGa	15/31	1	2	FACETS	0.642	0.539	0.756	0.642	0.539	0.756	SUBCLONAL	1	TRUE	1	0.24	2		438	584	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103717	47103717	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1205330893	NA	P-0031139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	56	533	2	ENST00000409792.3:c.6229C>T	p.Arg2077Ter	p.R2077*	ENST00000409792	NM_014159.6	2077	Cga/Tga	14/21	1	2	FACETS	0.763	0.653	0.883	0.763	0.653	0.883	SUBCLONAL	1	TRUE	1	0.24	2		535	612	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246445	105246445	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	53	589	0	ENST00000349310.3:c.155T>G	p.Leu52Arg	p.L52R	ENST00000349310	NM_001014432.1	52	cTc/cGc	4/15	1	2	FACETS	0.509	0.432	0.593	0.509	0.432	0.593	SUBCLONAL	1	TRUE	1	0.24	2		589	868	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094347	27094347	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	37	500	0	ENST00000324856.7:c.3055G>C	p.Glu1019Gln	p.E1019Q	ENST00000324856	NM_006015.4	1019	Gag/Cag	11/20	1	2	FACETS	0.427	0.351	0.513	0.427	0.351	0.513	SUBCLONAL	1	TRUE	1	0.24	2		500	722	SUCCESS
EED	8726	MSKCC	GRCh37	11	85977198	85977198	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0031139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	25	449	0	ENST00000263360.6:c.800C>G	p.Ser267Ter	p.S267*	ENST00000263360	NM_003797.3	267	tCa/tGa	8/12	1	2	FACETS	0.42	0.33	0.524	0.42	0.33	0.524	SUBCLONAL	1	TRUE	1	0.24	2		449	496	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223316	36223316	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	94	895	0	ENST00000222270.7:c.5866G>T	p.Gly1956Trp	p.G1956W	ENST00000222270	NM_014727.1	1956	Ggg/Tgg	28/37	1	2	FACETS	0.682	0.605	0.765	0.682	0.605	0.765	SUBCLONAL	1	TRUE	1	0.24	2		895	1148	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0031140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	66	193	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.691472463341396	3	FACETS	1	0.941	1	0.558	0.491	0.629	CLONAL	1	TRUE	1	0.691472463341396	3		193	230	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	206	384	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.280987819238492	4	FACETS	1	0.985	1	0.767	0.721	0.813	INDETERMINATE	2	TRUE	1	0.691472463341396	4		384	438	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0031140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	43	387	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	0.691472463341396	3	FACETS	0.895	0.759	1	0.448	0.379	0.521	CLONAL	1	TRUE	1	0.691472463341396	3		387	187	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920402	114920402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs927089403	NA	P-0031140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	163	549	0	ENST00000543371.1:c.1343G>A	p.Arg448Gln	p.R448Q	ENST00000543371	NM_001198531.1	448	cGg/cAg	13/14	0.691472463341396	2	FACETS	0.99	0.938	1	0.99	0.938	1	CLONAL	2	TRUE	0	0.691472463341396	2		549	238	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912195	114912195	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs866960970	NA	P-0031140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	143	539	0	ENST00000543371.1:c.1265A>G	p.Asn422Ser	p.N422S	ENST00000543371	NM_001198531.1	422	aAc/aGc	11/14	0.691472463341396	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.691472463341396	2		539	195	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822385	72822385	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	75	833	1	ENST00000268489.5:c.9790G>A	p.Ala3264Thr	p.A3264T	ENST00000268489	NM_006885.3	3264	Gcc/Acc	10/10	0.573863984829143	4	FACETS	1	0.962	1	0.607	0.537	0.681	CLONAL	1	TRUE	2	0.691472463341396	4		834	302	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554198	63554198	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	146	680	0	ENST00000307078.5:c.541G>T	p.Val181Leu	p.V181L	ENST00000307078	NM_004655.3	181	Gtg/Ttg	2/11	0.379949261129551	6	FACETS	0.782	0.716	0.851	0.522	0.477	0.568	INDETERMINATE	2	TRUE	3	0.691472463341396	6		680	643	SUCCESS
APC	324	MSKCC	GRCh37	5	112174843	112174844	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0031140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	67	357	0	ENST00000257430.4:c.3554_3555del	p.Thr1185ArgfsTer22	p.T1185Rfs*22	ENST00000257430	NM_000038.5	1184	gcCAca/gcca	16/16	0.691472463341396	3	FACETS	0.881	0.788	0.976	0.881	0.788	0.976	CLONAL	2	TRUE	1	0.691472463341396	3		357	148	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044901	47044901	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	116	741	0	ENST00000377604.3:c.2227G>T	p.Glu743Ter	p.E743*	ENST00000377604	NM_001204468.1	743	Gag/Tag	20/24	1	2	FACETS	0.568	0.511	0.628	0.568	0.511	0.628	SUBCLONAL	1	TRUE	1	0.47	2		741	869	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235404	235404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769936006	NA	P-0031141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	243	535	0	ENST00000264932.6:c.1210C>T	p.Pro404Ser	p.P404S	ENST00000264932	NM_004168.2	404	Ccc/Tcc	9/15	0.3	6	FACETS	0.85	0.793	0.909	0.34	0.317	0.364	CLONAL	2	TRUE	1	0.47	6		535	1180	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0031141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	115	551	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	1	2	FACETS	0.598	0.538	0.661	0.598	0.538	0.661	SUBCLONAL	1	TRUE	1	0.47	2		551	819	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0031142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	296	332	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.466039422526053	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	1	0.466039422526053	3		332	783	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210795	133210795	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	192	641	0	ENST00000320574.5:c.5981A>T	p.Asn1994Ile	p.N1994I	ENST00000320574	NM_006231.2	1994	aAc/aTc	43/49	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.466039422526053	2		641	724	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441972	40441972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	228	744	0	ENST00000345506.4:c.217G>A	p.Glu73Lys	p.E73K	ENST00000345506	NM_003152.3	73	Gag/Aag	4/20	NA	2	FACETS	1	0.957	1			1	INDETERMINATE	1	TRUE	NA	0.466039422526053	2		744	945	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197316	26197316	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	203	551	1	ENST00000356476.2:c.163T>A	p.Tyr55Asn	p.Y55N	ENST00000356476		55	Tac/Aac	1/1	0.223429757280305	4	FACETS	0.864	0.804	0.926	0.864	0.804	0.926	INDETERMINATE	2	TRUE	2	0.466039422526053	4		552	739	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845116	151845116	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0031142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	153	461	0	ENST00000262189.6:c.13894+2T>C		p.X4632_splice	ENST00000262189	NM_170606.2	4632			NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.466039422526053	2		461	522	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0031143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	61	562	3	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.18	2		565	625	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288996	33288996	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773506568	NA	P-0031143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	70	490	2	ENST00000374542.5:c.556C>T	p.Arg186Trp	p.R186W	ENST00000374542	NM_001141970.1	186	Cgg/Tgg	3/8	1	2	FACETS	0.954	0.831	1	0.954	0.831	1	CLONAL	1	TRUE	1	0.18	2		492	815	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591132	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	rs1057519842	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	68	364	0	ENST00000274335.5:c.1727_1729del	p.Thr576del	p.T576del	ENST00000274335		575	aaGACg/aag	12/15	0.38916501939395	2	FACETS	0.822	0.718	0.934	0.411	0.359	0.467	CLONAL	1	TRUE	0	0.38916501939395	2		364	425	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084146	47084146	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	106	445	1	ENST00000409792.3:c.7143del	p.Ser2382LeufsTer29	p.S2382Lfs*29	ENST00000409792	NM_014159.6	2381	ccC/cc	17/21	1	2	FACETS	0.809	0.726	0.897	0.809	0.726	0.897	CLONAL	1	TRUE	1	0.38916501939395	2		446	673	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245587	41245587	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357522	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	153	730	3	ENST00000357654.3:c.1961del	p.Lys654SerfsTer47	p.K654Sfs*47	ENST00000357654	NM_007294.3	654	aAg/ag	10/23	1	2	FACETS	0.894	0.817	0.973	0.894	0.817	0.973	CLONAL	1	TRUE	1	0.38916501939395	2		733	880	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	285	367	8	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	0.996	1	CLONAL	2	TRUE	1	0.38916501939395	2		375	711	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057937	27057937	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	152	594	1	ENST00000324856.7:c.1650del	p.Tyr551ThrfsTer68	p.Y551Tfs*68	ENST00000324856	NM_006015.4	549	Ccc/cc	3/20	1	2	FACETS	0.974	0.892	1	0.974	0.892	1	CLONAL	1	TRUE	1	0.38916501939395	2		595	802	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446270	187446270	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	124	569	0	ENST00000232014.4:c.1418del	p.Pro473ArgfsTer117	p.P473Rfs*117	ENST00000232014	NM_001130845.1	473	cCg/cg	6/10	1	2	FACETS	0.793	0.717	0.872	0.793	0.717	0.872	SUBCLONAL	1	TRUE	1	0.38916501939395	2		569	804	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	313	426	1	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	1	0.963	1	1	0.996	1	CLONAL	2	TRUE	1	0.38916501939395	2		427	789	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366309	15366309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	115	509	0	ENST00000263377.2:c.1846C>T	p.Arg616Trp	p.R616W	ENST00000263377	NM_058243.2	616	Cgg/Tgg	10/20	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.38916501939395	2		509	590	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630605	187630605	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	155	651	0	ENST00000441802.2:c.377del	p.Asn126IlefsTer20	p.N126Ifs*20	ENST00000441802	NM_005245.3	126	aAt/at	2/27	1	2	FACETS	0.879	0.805	0.957	0.879	0.805	0.957	CLONAL	1	TRUE	1	0.38916501939395	2		651	906	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276861	15276861	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	161	704	1	ENST00000263388.2:c.5404del	p.Ala1802LeufsTer23	p.A1802Lfs*23	ENST00000263388	NM_000435.2	1802	Gct/ct	30/33	1	2	FACETS	0.932	0.855	1	0.932	0.855	1	CLONAL	1	TRUE	1	0.38916501939395	2		705	888	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522741	67522741	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	93	319	0	ENST00000274335.5:c.244del	p.Ile82SerfsTer32	p.I82Sfs*32	ENST00000274335		80	Aaa/aa	1/15	0.38916501939395	2	FACETS	1	0.946	1	0.547	0.489	0.608	CLONAL	1	TRUE	0	0.38916501939395	2		319	437	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829075	128829075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1247591045	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	13	26	0	ENST00000249373.3:c.88del	p.Ala30ArgfsTer25	p.A30Rfs*25	ENST00000249373	NM_005631.4	28	cGg/cg	1/12	1	2	FACETS	1	0.759	1	1	0.759	1	CLONAL	1	TRUE	1	0.38916501939395	2		26	64	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	186	619	2	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.38916501939395	2		621	930	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216712	36216712	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780411851	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	112	435	1	ENST00000222270.7:c.3878G>A	p.Arg1293His	p.R1293H	ENST00000222270	NM_014727.1	1293	cGc/cAc	13/37	1	2	FACETS	0.971	0.875	1	0.971	0.875	1	CLONAL	1	TRUE	1	0.38916501939395	2		436	593	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614463	38614463	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	91	451	0	ENST00000299084.4:c.234del	p.Asp79ThrfsTer42	p.D79Tfs*42	ENST00000299084	NM_152594.2	77	Aaa/aa	3/7	1	2	FACETS	0.96	0.856	1	0.96	0.856	1	CLONAL	1	TRUE	1	0.38916501939395	2		451	487	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	104	818	5	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	1	2	FACETS	0.557	0.498	0.621	0.557	0.498	0.621	SUBCLONAL	1	TRUE	1	0.38916501939395	2		823	959	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201692	66201692	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753118521	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	118	510	0	ENST00000273854.3:c.2810G>A	p.Arg937His	p.R937H	ENST00000273854	NM_004439.5	937	cGt/cAt	16/18	1	2	FACETS	0.807	0.729	0.89	0.807	0.729	0.89	CLONAL	1	TRUE	1	0.38916501939395	2		510	751	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216189	36216189	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	159	407	3	ENST00000222270.7:c.3602del	p.Pro1201ArgfsTer154	p.P1201Rfs*154	ENST00000222270	NM_014727.1	1199	ggC/gg	11/37	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.38916501939395	2		410	752	SUCCESS
APC	324	MSKCC	GRCh37	5	112174188	112174189	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	199	482	0	ENST00000257430.4:c.2898dup	p.Val967CysfsTer3	p.V967Cfs*3	ENST00000257430	NM_000038.5	966	agt/agTt	16/16	0.38916501939395	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.38916501939395	2		482	470	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220184	36220184	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	134	527	1	ENST00000222270.7:c.4904G>A	p.Arg1635Gln	p.R1635Q	ENST00000222270	NM_014727.1	1635	cGa/cAa	22/37	1	2	FACETS	0.922	0.839	1	0.922	0.839	1	CLONAL	1	TRUE	1	0.38916501939395	2		528	747	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226052	226052	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776193478	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	64	97	0	ENST00000264932.6:c.511C>T	p.Arg171Cys	p.R171C	ENST00000264932	NM_004168.2	171	Cgt/Tgt	5/15	0.117150519796221	0	FACETS	0.975	0.858	1			1	INDETERMINATE	1	TRUE	0	0.38916501939395	0		97	206	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100399	8100399	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs535492085	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	183	720	1	ENST00000346208.3:c.373G>A	p.Gly125Ser	p.G125S	ENST00000346208		125	Ggc/Agc	3/6	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.38916501939395	2		721	928	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435156	49435156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781460562	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	99	451	0	ENST00000301067.7:c.6397G>A	p.Ala2133Thr	p.A2133T	ENST00000301067	NM_003482.3	2133	Gcc/Acc	31/54	1	2	FACETS	0.935	0.837	1	0.935	0.837	1	CLONAL	1	TRUE	1	0.38916501939395	2		451	544	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40860051	40860051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772252090	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	201	596	0	ENST00000428826.2:c.1585C>T	p.Arg529Cys	p.R529C	ENST00000428826		529	Cgc/Tgc	15/21	1	2	FACETS	0.942	0.872	1	0.942	0.872	1	CLONAL	1	TRUE	1	0.38916501939395	2		596	1097	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115000	3115000	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	219	712	1	ENST00000078429.4:c.535G>A	p.Val179Met	p.V179M	ENST00000078429	NM_002067.2	179	Gtg/Atg	4/7	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.38916501939395	2		713	1075	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143964	11143964	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	129	455	1	ENST00000358026.2:c.3547-2A>G		p.X1183_splice	ENST00000358026	NM_001128849.1	1183			1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.38916501939395	2		456	653	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266718	18266718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1371555508	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	185	617	1	ENST00000222254.8:c.29G>A	p.Arg10His	p.R10H	ENST00000222254	NM_005027.3	10	cGc/cAc	2/16	1	2	FACETS	0.93	0.858	1	0.93	0.858	1	CLONAL	1	TRUE	1	0.38916501939395	2		618	1022	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224257	36224273	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCCCGCCCCGCCAGG	CAGCCCGCCCCGCCAGG	-	novel	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	171	684	0	ENST00000222270.7:c.6808_6824del	p.Ser2270HisfsTer27	p.S2270Hfs*27	ENST00000222270	NM_014727.1	2269	gcCAGCCCGCCCCGCCAGGcc/gccc	28/37	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.38916501939395	2		684	829	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793331	42793331	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1306910781	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	125	607	0	ENST00000575354.2:c.1135-2A>G		p.X379_splice	ENST00000575354	NM_015125.3	379			1	2	FACETS	0.939	0.852	1	0.939	0.852	1	CLONAL	1	TRUE	1	0.38916501939395	2		607	684	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921184	50921184	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	140	670	0	ENST00000440232.2:c.3304C>A	p.Pro1102Thr	p.P1102T	ENST00000440232	NM_002691.3	1102	Cct/Act	27/27	1	2	FACETS	0.842	0.766	0.92	0.842	0.766	0.92	CLONAL	1	TRUE	1	0.38916501939395	2		670	855	SUCCESS
ATR	545	MSKCC	GRCh37	3	142177831	142177831	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	98	397	0	ENST00000350721.4:c.7472T>C	p.Val2491Ala	p.V2491A	ENST00000350721	NM_001184.3	2491	gTa/gCa	44/47	1	2	FACETS	0.976	0.874	1	0.976	0.874	1	CLONAL	1	TRUE	1	0.38916501939395	2		397	516	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430630	181430630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	126	509	0	ENST00000325404.1:c.482C>T	p.Ala161Val	p.A161V	ENST00000325404	NM_003106.3	161	gCg/gTg	1/1	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.38916501939395	2		509	563	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807803	1807803	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913113	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	145	722	0	ENST00000260795.2:c.1862G>A	p.Arg621His	p.R621H	ENST00000260795		621	cGc/cAc	13/17	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.38916501939395	2		722	724	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158109	106158109	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1217499559	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	101	396	0	ENST00000380013.4:c.3014del	p.Lys1005ArgfsTer2	p.K1005Rfs*2	ENST00000380013	NM_001127208.2	1004	Aaa/aa	3/11	1	2	FACETS	0.968	0.868	1	0.968	0.868	1	CLONAL	1	TRUE	1	0.38916501939395	2		396	536	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557322	187557322	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	193	580	0	ENST00000441802.2:c.4040C>A	p.Ser1347Tyr	p.S1347Y	ENST00000441802	NM_005245.3	1347	tCc/tAc	6/27	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.38916501939395	2		580	918	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515379	149515379	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568728923	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	342	649	1	ENST00000261799.4:c.103G>A	p.Val35Ile	p.V35I	ENST00000261799	NM_002609.3	35	Gtc/Atc	3/23	0.38916501939395	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.38916501939395	2		650	803	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197360	26197360	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	121	423	0	ENST00000356476.2:c.119A>C	p.His40Pro	p.H40P	ENST00000356476		40	cAc/cCc	1/1	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.38916501939395	2		423	521	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467928	50467928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	115	452	1	ENST00000331340.3:c.1163C>T	p.Ala388Val	p.A388V	ENST00000331340	NM_006060.4	388	gCg/gTg	8/8	1	2	FACETS	0.972	0.878	1	0.972	0.878	1	CLONAL	1	TRUE	1	0.38916501939395	2		453	608	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856144	151856144	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	76	407	0	ENST00000262189.6:c.11474C>A	p.Ala3825Asp	p.A3825D	ENST00000262189	NM_170606.2	3825	gCt/gAt	44/59	1	2	FACETS	0.781	0.687	0.882	0.781	0.687	0.882	SUBCLONAL	1	TRUE	1	0.38916501939395	2		407	500	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877053	151877054	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	104	462	0	ENST00000262189.6:c.7307dup	p.Pro2437ThrfsTer8	p.P2437Tfs*8	ENST00000262189	NM_170606.2	2436	cca/ccCa	37/59	1	2	FACETS	0.93	0.835	1	0.93	0.835	1	CLONAL	1	TRUE	1	0.38916501939395	2		462	575	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371694	55371694	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	145	598	0	ENST00000297316.4:c.384del	p.His128GlnfsTer18	p.H128Qfs*18	ENST00000297316	NM_022454.3	128	caC/ca	2/2	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.38916501939395	2		598	711	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185621	27185621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	135	580	0	ENST00000380036.4:c.1321G>A	p.Val441Ile	p.V441I	ENST00000380036	NM_000459.3	441	Gtt/Att	9/23	1	2	FACETS	0.836	0.76	0.916	0.836	0.76	0.916	CLONAL	1	TRUE	1	0.38916501939395	2		580	830	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87356833	87356833	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	95	444	0	ENST00000277120.3:c.1186A>C	p.Ile396Leu	p.I396L	ENST00000277120		396	Att/Ctt	10/19	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.38916501939395	2		444	488	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0031147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	68	435	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.531878548329675	4	FACETS	1	0.951	1	1	0.951	1	CLONAL	3	TRUE	1	0.526345577086382	4		435	121	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0031147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	64	652	0	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	0.52634857510364	3	FACETS	0.906	0.817	0.993	0.906	0.817	0.993	CLONAL	3	TRUE	0	0.526345577086382	3		652	113	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0031148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	18	377	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.362	0.271	0.471	0.362	0.271	0.471	SUBCLONAL	1	TRUE	1	0.16	2		377	621	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0031148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	17	476	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.444	0.33	0.58	0.444	0.33	0.58	SUBCLONAL	1	TRUE	1	0.16	2		476	479	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0031149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	40	435	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.813	0.674	0.968	0.813	0.674	0.968	CLONAL	1	TRUE	1	0.15	2		435	656	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547287	106547287	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1020145708	NA	P-0031149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	46	437	0	ENST00000369096.4:c.524C>T	p.Ala175Val	p.A175V	ENST00000369096	NM_001198.3	175	gCg/gTg	4/7	0.300084602462482	3	FACETS	0.97	0.815	1			1	CLONAL	1	TRUE	NA	0.15	3		437	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0031150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	370	361	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.281773508017715	6	FACETS	0.987	0.942	1			1	CLONAL	5	TRUE	NA	0.281773508017715	6		361	832	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198415	108198415	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	64	509	0	ENST00000278616.4:c.7019T>A	p.Val2340Asp	p.V2340D	ENST00000278616	NM_000051.3	2340	gTt/gAt	48/63	0.281773508017715	6	FACETS	0.833	0.719	0.956	0.208	0.179	0.239	CLONAL	1	TRUE	2	0.281773508017715	6		509	853	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627913	37627913	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0031150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	147	510	0	ENST00000447079.4:c.1828A>T	p.Lys610Ter	p.K610*	ENST00000447079	NM_015083.1	610	Aag/Tag	2/14	0.275086291830686	2	FACETS	0.795	0.728	0.865	0.795	0.728	0.865	SUBCLONAL	2	TRUE	0	0.281773508017715	2		510	656	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90990484	90990484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	41	482	0	ENST00000265433.3:c.548C>T	p.Ala183Val	p.A183V	ENST00000265433	NM_002485.4	183	gCa/gTa	5/16	0.281773508017715	5	FACETS	0.544	0.452	0.647	0.181	0.15	0.216	SUBCLONAL	1	TRUE	2	0.281773508017715	5		482	761	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0031153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	408	538	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.363530651311802	6	FACETS	1	0.984	1			1	CLONAL	4	TRUE	NA	0.541022790755452	6		538	750	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0031153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	89	546	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.541022790755452	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.541022790755452	1		546	236	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690572	88690600	+	frameshift_variant	Frame_Shift_Del	DEL	CGAAGACTCAGCGTCTGGAAGAGCTGCCA	CGAAGACTCAGCGTCTGGAAGAGCTGCCA	-	novel	NA	P-0031153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	73	459	0	ENST00000360948.2:c.430_458del	p.Trp144GlyfsTer14	p.W144Gfs*14	ENST00000360948	NM_001012338.2	144	TGGCAGCTCTTCCAGACGCTGAGTCTTCGg/g	5/19	1	2	FACETS	0.927	0.819	1	0.927	0.819	1	CLONAL	1	TRUE	1	0.541022790755452	2		459	291	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	44	270	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.419	0.351	0.496	0.419	0.351	0.496	SUBCLONAL	1	TRUE	1	0.34	2		270	617	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447310	49447310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747495428	NA	P-0031155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	570	45	0	ENST00000301067.7:c.788G>A	p.Arg263His	p.R263H	ENST00000301067	NM_003482.3	263	cGc/cAc	6/54	1	2	FACETS	1	0.994	1	1	0.998	1	CLONAL	2	TRUE	1	0.34	2		45	1415	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103385	2103385	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45517099	NA	P-0031171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	359	721	0	ENST00000219476.3:c.268C>T	p.Gln90Ter	p.Q90*	ENST00000219476	NM_000548.3	90	Cag/Tag	4/42	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		721	1449	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136735	2136735	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	310	746	1	ENST00000219476.3:c.4852del	p.Val1618SerfsTer7	p.V1618Sfs*7	ENST00000219476	NM_000548.3	1618	Gtc/tc	38/42	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		747	1353	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0031177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	629	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.592318417083732	4	FACETS	0.939	0.915	0.962	0.939	0.915	0.962	CLONAL	4	TRUE	0	0.628565730986899	4		336	868	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0031177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	372	470	1				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.628565730986899	2		471	516	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494690	2494690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770694552	NA	P-0031177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	187	712	0	ENST00000355716.4:c.830C>T	p.Thr277Met	p.T277M	ENST00000355716	NM_003820.2	277	aCg/aTg	8/8	0.618871750791609	3	FACETS	0.981	0.908	1	0.491	0.454	0.529	CLONAL	1	TRUE	1	0.628565730986899	3		712	797	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0031177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	135	536	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.623142975554526	1	FACETS	0.816	0.751	0.882	0.816	0.751	0.882	CLONAL	1	TRUE	0	0.628565730986899	1		536	361	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95579443	95579443	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs878855246	NA	P-0031177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	254	469	0	ENST00000393063.1:c.2026C>T	p.Arg676Ter	p.R676*	ENST00000393063	NM_030621.3	676	Cga/Tga	13/28	0.415405057780713	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.628565730986899	4		469	575	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662554	227662554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866672328	NA	P-0031177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	177	521	2	ENST00000305123.5:c.901C>T	p.Arg301Cys	p.R301C	ENST00000305123	NM_005544.2	301	Cgc/Tgc	1/2	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.628565730986899	2		523	491	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100912	41100912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866253502	NA	P-0031177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	242	614	1	ENST00000373198.4:c.1444G>A	p.Glu482Lys	p.E482K	ENST00000373198	NM_133170.3	482	Gaa/Aaa	8/32	0.628565730986899	5	FACETS	0.758	0.708	0.809	0.505	0.472	0.539	SUBCLONAL	2	TRUE	2	0.628565730986899	5		615	987	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743845	46743845	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	181	718	0	ENST00000371975.4:c.2135A>C	p.Lys712Thr	p.K712T	ENST00000371975	NM_003579.3	712	aAg/aCg	18/18	0.628565730986899	3	FACETS	1	0.94	1	0.509	0.471	0.549	CLONAL	1	TRUE	1	0.628565730986899	3		718	743	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433032	49433032	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770978212	NA	P-0031177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	167	763	5	ENST00000301067.7:c.8339C>T	p.Thr2780Met	p.T2780M	ENST00000301067	NM_003482.3	2780	aCg/aTg	33/54	0.582022274146245	3	FACETS	0.881	0.81	0.954	0.44	0.405	0.477	CLONAL	1	TRUE	1	0.628565730986899	3		768	793	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434962	110435072	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGCGGCCCCCCTGCGGGTCTGCGCGGATGACCTTGGCGCCGCGGTGGGGGTCCGGGGGCTGGCTGGCCTGCAGGAAGGCCTCGACTCCCGACACCTGCTCCATGA	GGCGGCGGCGGCCCCCCTGCGGGTCTGCGCGGATGACCTTGGCGCCGCGGTGGGGGTCCGGGGGCTGGCTGGCCTGCAGGAAGGCCTCGACTCCCGACACCTGCTCCATGA	-	novel	NA	P-0031177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	199	817	0	ENST00000375856.3:c.3329_3439del	p.Leu1110_Arg1146del	p.L1110_R1146del	ENST00000375856	NM_003749.2	1110	cTCATGGAGCAGGTGTCGGGAGTCGAGGCCTTCCTGCAGGCCAGCCAGCCCCCGGACCCCCACCGCGGCGCCAAGGTCATCCGCGCAGACCCGCAGGGGGGCCGCCGCCGCCac/cac	1/2	0.628565730986899	4	FACETS	0.868	0.803	0.936	0.289	0.267	0.312	CLONAL	1	TRUE	1	0.628565730986899	4		817	1188	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512270	38512270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866777491	NA	P-0031177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	173	707	1	ENST00000254066.5:c.1181G>A	p.Arg394Gln	p.R394Q	ENST00000254066	NM_000964.3	394	cGg/cAg	9/9	0.628565730986899	3	FACETS	0.94	0.866	1	0.47	0.433	0.508	CLONAL	1	TRUE	1	0.628565730986899	3		708	770	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690238	47690238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659702	NA	P-0031177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	163	631	0	ENST00000233146.2:c.1455G>A	p.Met485Ile	p.M485I	ENST00000233146	NM_000251.2	485	atG/atA	9/16	1	2	FACETS	0.915	0.844	0.987	0.915	0.844	0.987	CLONAL	1	TRUE	1	0.628565730986899	2		631	567	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0031179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	206	526	3	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.290201472777113	2		529	1050	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	236	384	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.290201472777113	3	FACETS	0.88	0.821	0.941			1	CLONAL	2	FALSE	NA	0.290201472777113	3		384	1058	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0031182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	210	477	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.476522097379006	1	FACETS	0.913	0.851	0.978	0.913	0.851	0.978	CLONAL	1	TRUE	0	0.476522097379006	1		478	735	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0031182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	188	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.476522097379006	2		336	770	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0031182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	147	503	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.997	0.913	1	0.997	0.913	1	CLONAL	1	TRUE	1	0.476522097379006	2		503	619	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0031182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	105	280	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.839	0.755	0.928	0.839	0.755	0.928	CLONAL	1	TRUE	1	0.476522097379006	2		280	525	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0031182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	354	658	3	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.476522097379006	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.476522097379006	2		661	680	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278074	18278074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	216	924	1	ENST00000222254.8:c.1694C>T	p.Pro565Leu	p.P565L	ENST00000222254	NM_005027.3	565	cCg/cTg	13/16	1	2	FACETS	0.955	0.889	1	0.955	0.889	1	CLONAL	1	TRUE	1	0.476522097379006	2		925	949	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120708	115120708	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	212	931	0	ENST00000257566.3:c.298G>T	p.Glu100Ter	p.E100*	ENST00000257566	NM_016569.3	100	Gag/Tag	1/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.476522097379006	2		931	819	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419974	41419974	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	116	706	0	ENST00000373198.4:c.347G>T	p.Ser116Ile	p.S116I	ENST00000373198	NM_133170.3	116	aGc/aTc	3/32	1	2	FACETS	0.842	0.762	0.927	0.842	0.762	0.927	CLONAL	1	TRUE	1	0.476522097379006	2		706	578	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713813	30713849	+	protein_altering_variant	In_Frame_Del	DEL	CTCAAGAGCTCCAATATCCTCGTGAAGAACGACCTAA	CTCAAGAGCTCCAATATCCTCGTGAAGAACGACCTAA	GATG	novel	NA	P-0031182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	112	860	4	ENST00000295754.5:c.1138_1174delinsGATG	p.Leu380_Thr392delinsAspAla	p.L380_T392delinsDA	ENST00000295754	NM_003242.5	380	CTCAAGAGCTCCAATATCCTCGTGAAGAACGACCTAAcc/GATGcc	4/7	0.476522097379006	1	FACETS	0.606	0.546	0.669	0.606	0.546	0.669	SUBCLONAL	1	TRUE	0	0.476522097379006	1		864	591	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829221	128829221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	112	527	1	ENST00000249373.3:c.229G>A	p.Val77Met	p.V77M	ENST00000249373	NM_005631.4	77	Gtg/Atg	1/12	1	2	FACETS	0.889	0.802	0.979	0.889	0.802	0.979	CLONAL	1	TRUE	1	0.476522097379006	2		528	529	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630190	100630190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs128620185	NA	P-0031182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	293	790	0	ENST00000308731.7:c.83G>A	p.Arg28His	p.R28H	ENST00000308731	NM_000061.2	28	cGc/cAc	2/19	0.476522097379006	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.476522097379006	1		790	723	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0031186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	84	435	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.21	2		435	766	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	86	684	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.253169012153658	1	FACETS	0.926	0.818	1	0.926	0.818	1	CLONAL	1	TRUE	0	0.21	1		684	792	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061240	38061240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	102	591	0	ENST00000250448.2:c.749C>T	p.Ser250Phe	p.S250F	ENST00000250448	NM_004496.3	250	tCc/tTc	2/2	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.21	2		591	847	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0031186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	71	753	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	1	2	FACETS	0.736	0.641	0.839	0.736	0.641	0.839	SUBCLONAL	1	TRUE	1	0.21	2		753	919	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118924	115118925	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0031186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	66	338	0	ENST00000257566.3:c.416_417del	p.Arg139MetfsTer6	p.R139Mfs*6	ENST00000257566	NM_016569.3	139	aGA/a	2/8	1	2	FACETS	0.95	0.824	1	0.95	0.824	1	CLONAL	1	TRUE	1	0.21	2		338	662	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056172	26056172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772814824	NA	P-0031186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	38	485	0	ENST00000343677.2:c.485C>T	p.Ala162Val	p.A162V	ENST00000343677	NM_005319.3	162	gCc/gTc	1/1	0.166718584794346	3	FACETS	0.546	0.45	0.654	0.273	0.225	0.327	SUBCLONAL	1	TRUE	1	0.21	3		485	733	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0031188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	241	332	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	0.723285171534411	2		332	648	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0031188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	266	504	6	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.723285171534411	1	FACETS	0.926	0.879	0.973	0.926	0.879	0.973	CLONAL	1	TRUE	0	0.723285171534411	1		510	507	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0031188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	237	503	1	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.723285171534411	1	FACETS	0.982	0.931	1	0.982	0.931	1	CLONAL	1	TRUE	0	0.723285171534411	1		504	426	SUCCESS
APC	324	MSKCC	GRCh37	5	112170813	112170813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554083227	NA	P-0031188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	363	681	5	ENST00000257430.4:c.1909G>A	p.Gly637Arg	p.G637R	ENST00000257430	NM_000038.5	637	Ggg/Agg	15/16	0.723285171534411	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.723285171534411	1		686	621	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0031188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	541	617	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.723285171534411	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.723285171534411	3		617	959	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276974	123276974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918504	NA	P-0031188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	219	419	2	ENST00000358487.5:c.943G>A	p.Ala315Thr	p.A315T	ENST00000358487	NM_000141.4	315	Gcc/Acc	8/18	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.723285171534411	2		421	605	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120132	70120133	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0031188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	126	185	0	ENST00000245479.2:c.1137_1138dup	p.His380ArgfsTer4	p.H380Rfs*4	ENST00000245479	NM_000346.3	378	-/GC	3/3	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.723285171534411	2		185	348	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206715	102206715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759842920	NA	P-0031188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	261	463	4	ENST00000263464.3:c.1343G>A	p.Arg448Gln	p.R448Q	ENST00000263464	NM_001165.4	448	cGg/cAg	7/9	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.723285171534411	2		467	686	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619857	21619857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	720	488	3	ENST00000382592.4:c.309G>A	p.Met103Ile	p.M103I	ENST00000382592	NM_014572.2	103	atG/atA	2/8	0.627831972604555	5	FACETS	0.944	0.914	0.974	0.944	0.914	0.974	CLONAL	3	TRUE	2	0.723285171534411	5		491	1466	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436025	56436025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs929720505	NA	P-0031188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	266	497	3	ENST00000407977.2:c.1112G>A	p.Arg371Gln	p.R371Q	ENST00000407977		371	cGa/cAa	9/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.723285171534411	2		500	726	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119787	70119788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0031188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	461	688	6	ENST00000245479.2:c.790dup	p.Arg264LysfsTer32	p.R264Kfs*32	ENST00000245479	NM_000346.3	263	-/A	3/3	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.723285171534411	2		694	1201	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0031189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	645	795	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.820393984241093	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.820393984241093	2		795	786	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0031189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	95	381	3	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	0.793340226846937	3	FACETS	0.761	0.682	0.845	0.381	0.341	0.423	SUBCLONAL	1	TRUE	1	0.820393984241093	3		384	429	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0031189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	660	702	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	0.718331050246102	4	FACETS	0.982	0.948	1	0.982	0.948	1	CLONAL	2	TRUE	2	0.820393984241093	4		702	1491	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446140	70446140	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	316	600	0	ENST00000373644.4:c.5080C>A	p.Arg1694Ser	p.R1694S	ENST00000373644	NM_030625.2	1694	Cgc/Agc	11/12	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.820393984241093	2		600	758	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121860	2121873	+	frameshift_variant	Frame_Shift_Del	DEL	TGCAGGCCCCGCCG	TGCAGGCCCCGCCG	-	novel	NA	P-0031189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	310	501	0	ENST00000219476.3:c.2025_2038del	p.Gly676AlafsTer22	p.G676Afs*22	ENST00000219476	NM_000548.3	674	ccTGCAGGCCCCGCCGtg/cctg	19/42	0.820393984241093	3	FACETS	1	0.993	1			1	CLONAL	1	TRUE	NA	0.820393984241093	3		501	819	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633302	3633302	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	351	924	0	ENST00000294008.3:c.4949G>C	p.Gly1650Ala	p.G1650A	ENST00000294008	NM_032444.2	1650	gGa/gCa	14/15	0.820393984241093	2	FACETS	0.988	0.94	1	0.494	0.47	0.519	CLONAL	1	TRUE	0	0.820393984241093	2		924	866	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708087	117708087	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	369	710	0	ENST00000368508.3:c.2090G>T	p.Gly697Val	p.G697V	ENST00000368508	NM_002944.2	697	gGa/gTa	14/43	0.793340226846937	3	FACETS	1	0.981	1	0.534	0.506	0.562	CLONAL	1	TRUE	1	0.820393984241093	3		710	1188	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931899	68931899	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	304	718	0	ENST00000288368.4:c.329T>G	p.Leu110Arg	p.L110R	ENST00000288368	NM_024870.2	110	cTt/cGt	3/40	0.820393984241093	3	FACETS	0.912	0.859	0.966	0.456	0.429	0.483	CLONAL	1	TRUE	1	0.820393984241093	3		718	1146	SUCCESS
AR	367	MSKCC	GRCh37	X	66765268	66765268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2330	177	354	0	ENST00000374690.3:c.280G>A	p.Asp94Asn	p.D94N	ENST00000374690	NM_000044.3	94	Gat/Aat	1/8	0.820393984241093	8	FACETS	0.596	0.546	0.648			1	SUBCLONAL	1	TRUE	NA	0.820393984241093	8		354	2507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0031190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	264	836	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.232019933498592	2	FACETS	0.896	0.84	0.954	0.896	0.84	0.954	CLONAL	2	TRUE	0	0.267872011002301	2		836	1100	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974782	21974782	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs138677674	NA	P-0031190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	64	260	1	ENST00000304494.5:c.45G>A	p.Trp15Ter	p.W15*	ENST00000304494	NM_000077.4	15	tgG/tgA	1/3	0.267872011002301	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.267872011002301	1		261	287	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178941974	178942485	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTACTTTCTTGGGGGTTTCATTGATATATTTAAATAAATACCTTTTCTGGATAAAATCTTGAGAAAAGTAAAAATGTCTGTTATAATTAGAATGTTCAATAATTTATGCTTCTCTCTCTCATTCTCCTACCCTCAAAATAAGAGTAGTATATCTTAAGTTCAGTACTGCCTTTATTCAGAATGAGTTTTTACTACTTAAATAATACAGTTTAAAACCTTCTATGGCCAGAATTTCTGTTACCATAGGATAAGAAATGGAAATGTAATATCTGTAAAACTAATGATATATCTCTATATATTTGTTGGAAATTCATATGCAATTATATAACTTTTAAAACTTTTAGTTTTTTTTATACTCTTTAGGAATGGATTCCTAAATAAAAATTGAGGTGAAAGTTGTAAATCTTTGTAACACTTCAAAAAGCTATATTGTATTTATATTTTAAAATAAATTTCAGGGTAAAATAATAATAAAGCAAAGGTACCTAGTAAAGTTTTTAACTATTTTAA	AGGTACTTTCTTGGGGGTTTCATTGATATATTTAAATAAATACCTTTTCTGGATAAAATCTTGAGAAAAGTAAAAATGTCTGTTATAATTAGAATGTTCAATAATTTATGCTTCTCTCTCTCATTCTCCTACCCTCAAAATAAGAGTAGTATATCTTAAGTTCAGTACTGCCTTTATTCAGAATGAGTTTTTACTACTTAAATAATACAGTTTAAAACCTTCTATGGCCAGAATTTCTGTTACCATAGGATAAGAAATGGAAATGTAATATCTGTAAAACTAATGATATATCTCTATATATTTGTTGGAAATTCATATGCAATTATATAACTTTTAAAACTTTTAGTTTTTTTTATACTCTTTAGGAATGGATTCCTAAATAAAAATTGAGGTGAAAGTTGTAAATCTTTGTAACACTTCAAAAAGCTATATTGTATTTATATTTTAAAATAAATTTCAGGGTAAAATAATAATAAAGCAAAGGTACCTAGTAAAGTTTTTAACTATTTTAA	-	novel	NA	P-0031190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	110	499	0	ENST00000263967.3:c.2294+2_2295del		p.X765_splice	ENST00000263967	NM_006218.2	765		15/21	0.18171427756297	3	FACETS	1	0.942	1	0.536	0.481	0.594	CLONAL	1	TRUE	1	0.267872011002301	3		499	869	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178942609	178943631	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTAAGGAAGAGTATTAATGAGCTTATGATGCATGAATTTAGCTATCTTTTTATACACAGGATATTTATGAACCATGAAAACTACTGAAAGCCATTTAAGGAATATACACATGTGATAAAATATGTAATATTTATCAGATGTCTTGACCTTTGAAATATGCATGTATAATCAATGAAAAGAAAAGAAGTACTAGGTTTAGATCAGAAGTCCTGAAATCAGTTTTTTGTTTTTTCTTTTTCCTGTTCCCTGCCTCCAACCCCCCTCCCGTGGACCTGTGTAGAGAAGTATTTTTTGTTGTTGTTTTGGTTTTTTTTTTAATCAGTTTCTAATTATCATTTGCTTAGCTGTGTGAGTATCCATTCATTCCATAAATATTCTATGTGCTAGGCCCTGGGGTTTTAGCAGTGAAGAAAACAGAATCCCTGCCCTCTTGGAGCTTACAGCCTAACAGAGAAAAGAGGGACATTAAATGAATAATTACAAAAATAAAATTGCAAGCATGTTGCAAAGGAAGAGTGTAGTCTGCTCAGGAACCATATAAAAGAAGGTACTTATATGGAGGAAAAGGCTATGGGGGGAGTGAAGGAGGATCATGGATGGGTTTTCAATAGGAAATGACATTTCAGCAGTGAATTCTGTTGATCCCAATATTTTAATATAAACATGTGTTCAAATTTAAGGATTCAGAAAAATAATTACTATAAATGCTTTAATTAAAAATTTTTGTGAGATGCATGCTCACTTATCCTACATTGTTATTCAAATATGTTTATGCAAAGACTTTAAAAGTGGATTTAAGAATCAGAATATTAAGAGCCATTTGTAGTGGTGCATGCTTGTGATCCCAGTTGCTCTGGAGGATTACTTGAGCCCAGGAGTTTTAGACCAGCCTGGGCAACTTAGCAAGACCCCATCTCAAAAAATTATAAATACATTAATAAAGCTATGTAAAGGCTTTGAGTGGACATATACACTCATTTATAAATTTTTTGAAAAGAAATCAGAATATTGCTTTCCTGAAG	GGTAAGGAAGAGTATTAATGAGCTTATGATGCATGAATTTAGCTATCTTTTTATACACAGGATATTTATGAACCATGAAAACTACTGAAAGCCATTTAAGGAATATACACATGTGATAAAATATGTAATATTTATCAGATGTCTTGACCTTTGAAATATGCATGTATAATCAATGAAAAGAAAAGAAGTACTAGGTTTAGATCAGAAGTCCTGAAATCAGTTTTTTGTTTTTTCTTTTTCCTGTTCCCTGCCTCCAACCCCCCTCCCGTGGACCTGTGTAGAGAAGTATTTTTTGTTGTTGTTTTGGTTTTTTTTTTAATCAGTTTCTAATTATCATTTGCTTAGCTGTGTGAGTATCCATTCATTCCATAAATATTCTATGTGCTAGGCCCTGGGGTTTTAGCAGTGAAGAAAACAGAATCCCTGCCCTCTTGGAGCTTACAGCCTAACAGAGAAAAGAGGGACATTAAATGAATAATTACAAAAATAAAATTGCAAGCATGTTGCAAAGGAAGAGTGTAGTCTGCTCAGGAACCATATAAAAGAAGGTACTTATATGGAGGAAAAGGCTATGGGGGGAGTGAAGGAGGATCATGGATGGGTTTTCAATAGGAAATGACATTTCAGCAGTGAATTCTGTTGATCCCAATATTTTAATATAAACATGTGTTCAAATTTAAGGATTCAGAAAAATAATTACTATAAATGCTTTAATTAAAAATTTTTGTGAGATGCATGCTCACTTATCCTACATTGTTATTCAAATATGTTTATGCAAAGACTTTAAAAGTGGATTTAAGAATCAGAATATTAAGAGCCATTTGTAGTGGTGCATGCTTGTGATCCCAGTTGCTCTGGAGGATTACTTGAGCCCAGGAGTTTTAGACCAGCCTGGGCAACTTAGCAAGACCCCATCTCAAAAAATTATAAATACATTAATAAAGCTATGTAAAGGCTTTGAGTGGACATATACACTCATTTATAAATTTTTTGAAAAGAAATCAGAATATTGCTTTCCTGAAG	-	novel	NA	P-0031190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	60	497	0	ENST00000263967.3:c.2416_2417-119del		p.X806_splice	ENST00000263967	NM_006218.2	806		16/21	0.18171427756297	3	FACETS	0.691	0.594	0.797	0.346	0.297	0.399	SUBCLONAL	1	TRUE	1	0.267872011002301	3		497	735	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947231	178947791	+	splice_acceptor_variant,splice_donor_variant,intron_variant	Splice_Site	DEL	GTGAGTTGTATTATTCTTTCTTCCTATGTTAATCTAAGTTTTTGTTAGATGAGTCTGTCGGTGTTTGTGTATTCCTCTGAGTTAGAACAGAGAAAACAATTGTACTTTCTATGGAAAAAAATATGCTCAACCTTTGAAATATTTGATGTTAATGGATTTAAATGATTATAATTACTTTTAATTTGGTAAAATCTTAAACATTCATCTTATGTATTATCTAAAATGTATTGTTATTGCTTATTCTTTTTAAAACAAATGAATATTGCACATTCAAAATTTTATTTCTAATTCATTGTTAAAATGATTAGAAAAAAATAATTTTAATGACATGCTAAGTATTTTTTCACATGAAGAATTATGCTTTGGTCAGGGAACATCTGGAAATTTCCTTAGAAACCCATGAAAACTTCACAATCTCAAAATCTTTGGACATAATTTCCTTATTCGTTGTCAGTGATTGTTTTCATTGTTTAAATGGAAACTTGCACCCTGTTTTCTTTTCTCAAGTTGGCCTGAATCACTATATTTCCATACTACTCATGAGGTGTTTATTCTTTGTAG	GTGAGTTGTATTATTCTTTCTTCCTATGTTAATCTAAGTTTTTGTTAGATGAGTCTGTCGGTGTTTGTGTATTCCTCTGAGTTAGAACAGAGAAAACAATTGTACTTTCTATGGAAAAAAATATGCTCAACCTTTGAAATATTTGATGTTAATGGATTTAAATGATTATAATTACTTTTAATTTGGTAAAATCTTAAACATTCATCTTATGTATTATCTAAAATGTATTGTTATTGCTTATTCTTTTTAAAACAAATGAATATTGCACATTCAAAATTTTATTTCTAATTCATTGTTAAAATGATTAGAAAAAAATAATTTTAATGACATGCTAAGTATTTTTTCACATGAAGAATTATGCTTTGGTCAGGGAACATCTGGAAATTTCCTTAGAAACCCATGAAAACTTCACAATCTCAAAATCTTTGGACATAATTTCCTTATTCGTTGTCAGTGATTGTTTTCATTGTTTAAATGGAAACTTGCACCCTGTTTTCTTTTCTCAAGTTGGCCTGAATCACTATATTTCCATACTACTCATGAGGTGTTTATTCTTTGTAG	-	novel	NA	P-0031190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	60	278	0	ENST00000263967.3:c.2666+1_2667-1del		p.X889_splice	ENST00000263967	NM_006218.2	889			0.18171427756297	3	FACETS	0.871	0.751	1	0.436	0.375	0.502	CLONAL	1	TRUE	1	0.267872011002301	3		278	583	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947910	178948012	+	splice_acceptor_variant,splice_donor_variant,intron_variant	Splice_Site	DEL	GTAATGGTTTTCTCTGTTTAAAATGTTTTGGTGTTCTTAATTTATTCAAGACATTTTGTATCTGCATATATCAAACTATAACATAATTTCTTATTTTTGAAAG	GTAATGGTTTTCTCTGTTTAAAATGTTTTGGTGTTCTTAATTTATTCAAGACATTTTGTATCTGCATATATCAAACTATAACATAATTTCTTATTTTTGAAAG	-	novel	NA	P-0031190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	95	479	0	ENST00000263967.3:c.2784+1_2785-1del		p.X928_splice	ENST00000263967	NM_006218.2	928			0.18171427756297	3	FACETS	0.894	0.794	1	0.447	0.397	0.5	CLONAL	1	TRUE	1	0.267872011002301	3		479	900	SUCCESS
APC	324	MSKCC	GRCh37	5	112164663	112164664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAAAAGGTTAA	novel	NA	P-0031190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	137	446	0	ENST00000257430.4:c.1743+2_1743+3insTAAAAAAAGGT		p.-579fs	ENST00000257430	NM_000038.5	579	-/AAAAAGGTTAA	14/16	0.214057806500476	3	FACETS	0.801	0.73	0.876	0.534	0.486	0.584	CLONAL	2	TRUE	0	0.267872011002301	3		446	724	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0031191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	237	505	4	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.265517358952562	2	FACETS	1	0.992	1	0.695	0.652	0.738	INDETERMINATE	1	TRUE	0	0.52082603211355	2		509	655	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285455	38285455	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	77	563	0	ENST00000425967.3:c.698G>C	p.Arg233Thr	p.R233T	ENST00000425967	NM_001174067.1	233	aGa/aCa	6/19	0.243999095824366	3	FACETS	0.452	0.396	0.512	0.226	0.198	0.256	INDETERMINATE	1	TRUE	1	0.52082603211355	3		563	825	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040683	47040683	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	191	321	0	ENST00000377604.3:c.1318C>T	p.Gln440Ter	p.Q440*	ENST00000377604	NM_001204468.1	440	Cag/Tag	13/24	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.52082603211355	1		321	368	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741860	145741860	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs749049274	NA	P-0031191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	110	657	0	ENST00000428558.2:c.643G>C	p.Glu215Gln	p.E215Q	ENST00000428558	NM_004260.3	215	Gag/Cag	5/22	0.243999095824366	3	FACETS	0.65	0.584	0.72	0.325	0.292	0.36	INDETERMINATE	1	TRUE	1	0.52082603211355	3		657	819	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975422	26975422	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	67	401	0	ENST00000381527.3:c.1048C>G	p.Gln350Glu	p.Q350E	ENST00000381527	NM_001260.1	350	Caa/Gaa	11/13	0.305714881125734	1	FACETS	0.372	0.323	0.424	0.372	0.323	0.424	INDETERMINATE	1	TRUE	0	0.52082603211355	1		401	512	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33430490	33430490	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	251	655	0	ENST00000345365.6:c.650G>T	p.Gly217Val	p.G217V	ENST00000345365	NM_002878.3	217	gGa/gTa	7/10	0.243999095824366	3	FACETS	0.842	0.792	0.894	0.842	0.792	0.894	INDETERMINATE	2	TRUE	1	0.52082603211355	3		655	721	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419873	41419873	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	33	521	0	ENST00000373198.4:c.448G>C	p.Glu150Gln	p.E150Q	ENST00000373198	NM_133170.3	150	Gag/Cag	3/32	1	2	FACETS	0.209	0.17	0.254	0.209	0.17	0.254	SUBCLONAL	1	TRUE	1	0.52082603211355	2		521	606	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839810	42839810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	72	401	0	ENST00000398585.3:c.1429G>A	p.Asp477Asn	p.D477N	ENST00000398585	NM_001135099.1	477	Gac/Aac	13/14	0.305714881125734	1	FACETS	0.48	0.421	0.543	0.48	0.421	0.543	INDETERMINATE	1	TRUE	0	0.52082603211355	1		401	426	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217448	142217448	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	65	428	0	ENST00000350721.4:c.5549A>G	p.Tyr1850Cys	p.Y1850C	ENST00000350721	NM_001184.3	1850	tAt/tGt	32/47	1	2	FACETS	0.474	0.411	0.541	0.474	0.411	0.541	SUBCLONAL	1	TRUE	1	0.52082603211355	2		428	527	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374909	149374909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	109	519	0	ENST00000360632.3:c.185C>T	p.Ser62Leu	p.S62L	ENST00000360632	NM_015472.4	62	tCg/tTg	2/7	1	2	FACETS	0.613	0.551	0.678	0.613	0.551	0.678	SUBCLONAL	1	TRUE	1	0.52082603211355	2		519	683	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673448	30673448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	133	494	1	ENST00000376406.3:c.3512C>T	p.Ser1171Phe	p.S1171F	ENST00000376406	NM_014641.2	1171	tCc/tTc	10/15	1	2	FACETS	0.891	0.813	0.973	0.891	0.813	0.973	CLONAL	1	TRUE	1	0.52082603211355	2		495	573	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518003	8518003	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	265	404	0	ENST00000356435.5:c.1388T>A	p.Val463Asp	p.V463D	ENST00000356435		463	gTc/gAc	10/35	0.52082603211355	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.52082603211355	2		404	507	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321382	1321382	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	153	455	1	ENST00000400841.2:c.373G>T	p.Val125Leu	p.V125L	ENST00000400841		125	Gtg/Ttg	4/6	1	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.52082603211355	1		456	396	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913164	39913164	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	125	148	0	ENST00000378444.4:c.4951A>G	p.Asn1651Asp	p.N1651D	ENST00000378444	NM_001123385.1	1651	Aac/Gac	14/15	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.52082603211355	1		148	239	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615625	100615625	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	364	272	0	ENST00000308731.7:c.707G>T	p.Arg236Leu	p.R236L	ENST00000308731	NM_000061.2	236	cGg/cTg	8/19	0.43988530132633	2	FACETS	0.893	0.861	0.923			1	CLONAL	3	TRUE	NA	0.52082603211355	2		272	522	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0031192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	104	648	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	0.424314490718457	1	FACETS	0.607	0.544	0.674	0.607	0.544	0.674	SUBCLONAL	1	TRUE	0	0.424314490718457	1		648	636	SUCCESS
APC	324	MSKCC	GRCh37	5	112176042	112176046	+	frameshift_variant	Frame_Shift_Del	DEL	CAACA	CAACA	ACT	novel	NA	P-0031192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	75	510	1	ENST00000257430.4:c.4751_4755delinsACT	p.Pro1584HisfsTer2	p.P1584Hfs*2	ENST00000257430	NM_000038.5	1584	cCAACA/cACT	16/16	0.35613570355215	1	FACETS	0.649	0.571	0.732	0.649	0.571	0.732	SUBCLONAL	1	TRUE	0	0.424314490718457	1		511	429	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977918	131977918	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	88	615	0	ENST00000265335.6:c.3801C>G	p.Ile1267Met	p.I1267M	ENST00000265335		1267	atC/atG	25/25	0.35613570355215	1	FACETS	0.743	0.661	0.829	0.743	0.661	0.829	SUBCLONAL	1	TRUE	0	0.424314490718457	1		615	440	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992697	68992697	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	109	711	0	ENST00000288368.4:c.1662C>G	p.Phe554Leu	p.F554L	ENST00000288368	NM_024870.2	554	ttC/ttG	16/40	0.424314490718457	1	FACETS	0.835	0.753	0.92	0.835	0.753	0.92	CLONAL	1	TRUE	0	0.424314490718457	1		711	485	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248093	110248093	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	154	553	0	ENST00000374672.4:c.1379A>G	p.Lys460Arg	p.K460R	ENST00000374672	NM_004235.4	460	aAa/aGa	5/5	1	2	FACETS	0.838	0.767	0.912	0.838	0.767	0.912	CLONAL	1	TRUE	1	0.424314490718457	2		553	866	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	95	270	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.774	0.691	0.862	0.774	0.691	0.862	SUBCLONAL	1	TRUE	1	0.448894256680414	2		270	547	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916614	178916614	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0031193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2144	832	483	0	ENST00000263967.3:c.1A>G	p.Met1?	p.M1?	ENST00000263967	NM_006218.2	1	Atg/Gtg	2/21	0.448894256680414	15	FACETS	0.976	0.942	1			1	CLONAL	5	TRUE	NA	0.448894256680414	15		483	2976	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609894	117609894	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs202153378	NA	P-0031193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	242	630	0	ENST00000368508.3:c.6805C>T	p.Arg2269Ter	p.R2269*	ENST00000368508	NM_002944.2	2269	Cga/Tga	43/43	1	2	FACETS	0.933	0.87	0.997	0.933	0.87	0.997	CLONAL	1	TRUE	1	0.448894256680414	2		630	1156	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220274	55220274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1244	40	739	0	ENST00000275493.2:c.664C>T	p.Arg222Cys	p.R222C	ENST00000275493	NM_005228.3	222	Cgc/Tgc	6/28	1	2	FACETS	0.139	0.114	0.166	0.139	0.114	0.166	SUBCLONAL	1	TRUE	1	0.448894256680414	2		739	1284	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720803	89720804	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs786204892	NA	P-0031193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	71	228	0	ENST00000371953.3:c.955dup	p.Thr319AsnfsTer6	p.T319Nfs*6	ENST00000371953	NM_000314.4	318	-/A	8/9	0.448894256680414	1	FACETS	0.764	0.672	0.862	0.764	0.672	0.862	SUBCLONAL	1	TRUE	0	0.448894256680414	1		228	321	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976727	2976727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1298741148	NA	P-0031193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	170	647	0	ENST00000396946.4:c.1285G>A	p.Val429Ile	p.V429I	ENST00000396946	NM_032415.4	429	Gtc/Atc	9/25	1	2	FACETS	0.757	0.696	0.822	0.757	0.696	0.822	SUBCLONAL	1	TRUE	1	0.448894256680414	2		647	1000	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267710	198267710	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	126	564	0	ENST00000335508.6:c.1769G>C	p.Arg590Thr	p.R590T	ENST00000335508	NM_012433.2	590	aGa/aCa	13/25	1	2	FACETS	0.645	0.583	0.709	0.645	0.583	0.709	SUBCLONAL	1	TRUE	1	0.448894256680414	2		564	871	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715417	117715417	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	221	564	0	ENST00000368508.3:c.1072G>C	p.Asp358His	p.D358H	ENST00000368508	NM_002944.2	358	Gac/Cac	10/43	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.448894256680414	2		564	930	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921567	178921567	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553821144	NA	P-0031195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	89	442	0	ENST00000263967.3:c.1049A>G	p.Asp350Gly	p.D350G	ENST00000263967	NM_006218.2	350	gAc/gGc	5/21	1	2	FACETS	0.979	0.87	1	0.979	0.87	1	CLONAL	1	TRUE	1	0.34	2		442	535	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0031195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	148	632	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.34	2		632	852	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0031195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	99	287	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.938	0.839	1	0.938	0.839	1	CLONAL	1	TRUE	1	0.34	2		287	621	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	142	749	1	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.86	0.783	0.941	0.86	0.783	0.941	CLONAL	1	TRUE	1	0.34	2		750	971	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0031195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	128	537	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.92	0.834	1	0.92	0.834	1	CLONAL	1	TRUE	1	0.34	2		537	818	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653807	89653807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554893782	NA	P-0031195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	127	352	0	ENST00000371953.3:c.105G>A	p.Met35Ile	p.M35I	ENST00000371953	NM_000314.4	35	atG/atA	2/9	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.34	2		352	732	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257144	19257144	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	93	487	2	ENST00000162023.5:c.819del	p.Thr274ProfsTer?	p.T274Pfs*?	ENST00000162023		273	ccC/cc	12/13	1	2	FACETS	0.885	0.788	0.988	0.885	0.788	0.988	CLONAL	1	TRUE	1	0.34	2		489	618	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505443	157505443	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554231830	NA	P-0031195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	185	556	0	ENST00000346085.5:c.3428del	p.Lys1143SerfsTer68	p.K1143Sfs*68	ENST00000346085	NM_020732.3	1142	Aaa/aa	13/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.34	2		556	1014	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170949	56170949	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	82	329	0	ENST00000399503.3:c.1780del	p.Ala594ProfsTer62	p.A594Pfs*62	ENST00000399503	NM_005921.1	593	Ggg/gg	10/20	1	2	FACETS	0.869	0.768	0.977	0.869	0.768	0.977	CLONAL	1	TRUE	1	0.34	2		329	555	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027087	71027087	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	130	460	1	ENST00000318789.4:c.1240del	p.Leu414Ter	p.L414*	ENST00000318789	NM_032682.5	414	Ctg/tg	15/21	1	2	FACETS	0.8	0.725	0.879	0.8	0.725	0.879	SUBCLONAL	1	TRUE	1	0.34	2		461	956	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551952	150551952	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	152	526	0	ENST00000369026.2:c.55del	p.Ala19ProfsTer30	p.A19Pfs*30	ENST00000369026	NM_021960.4	19	Gcc/cc	1/3	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.34	2		526	852	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825519	50825519	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	134	576	6	ENST00000398568.2:c.2156del	p.Asn719MetfsTer13	p.N719Mfs*13	ENST00000398568	NM_001042412.1	717	gAa/ga	14/18	1	2	FACETS	0.926	0.841	1	0.926	0.841	1	CLONAL	1	TRUE	1	0.34	2		582	851	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098959	178098959	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519921	NA	P-0031195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	96	397	0	ENST00000397062.3:c.86A>G	p.Asp29Gly	p.D29G	ENST00000397062	NM_006164.4	29	gAt/gGt	2/5	1	2	FACETS	0.992	0.886	1	0.992	0.886	1	CLONAL	1	TRUE	1	0.34	2		397	569	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873205	136873205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	93	438	0	ENST00000241393.3:c.293C>T	p.Ala98Val	p.A98V	ENST00000241393	NM_003467.2	98	gCc/gTc	2/2	1	2	FACETS	0.909	0.809	1	0.909	0.809	1	CLONAL	1	TRUE	1	0.34	2		438	602	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214714	36214714	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	98	547	0	ENST00000222270.7:c.3145del	p.Ala1049ArgfsTer133	p.A1049Rfs*133	ENST00000222270	NM_014727.1	1047	cGg/cg	8/37	1	2	FACETS	0.895	0.8	0.997	0.895	0.8	0.997	CLONAL	1	TRUE	1	0.34	2		547	644	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11193214	11193214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	184	681	1	ENST00000361445.4:c.5287G>A	p.Gly1763Ser	p.G1763S	ENST00000361445	NM_004958.3	1763	Ggc/Agc	38/58	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.34	2		682	1034	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099119	27099120	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0031195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	118	462	0	ENST00000324856.7:c.3536dup	p.Met1179IlefsTer14	p.M1179Ifs*14	ENST00000324856	NM_006015.4	1179	atg/aTtg	13/20	1	2	FACETS	0.983	0.888	1	0.983	0.888	1	CLONAL	1	TRUE	1	0.34	2		462	706	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599194	28599194	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	169	809	0	ENST00000253063.3:c.640T>G	p.Cys214Gly	p.C214G	ENST00000253063	NM_031459.4	214	Tgt/Ggt	5/10	1	2	FACETS	0.909	0.834	0.987	0.909	0.834	0.987	CLONAL	1	TRUE	1	0.34	2		809	1094	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406673	70406673	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	65	641	0	ENST00000373644.4:c.4187A>G	p.Asn1396Ser	p.N1396S	ENST00000373644	NM_030625.2	1396	aAt/aGt	4/12	1	2	FACETS	0.392	0.338	0.45	0.392	0.338	0.45	SUBCLONAL	1	TRUE	1	0.34	2		641	976	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717689	89717689	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	182	518	1	ENST00000371953.3:c.714del	p.Phe238LeufsTer18	p.F238Lfs*18	ENST00000371953	NM_000314.4	238	ttC/tt	7/9	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.34	2		519	961	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883773	37883774	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs766671083	NA	P-0031195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	86	800	0	ENST00000269571.5:c.3391dup	p.Leu1131ProfsTer8	p.L1131Pfs*8	ENST00000269571		1129	gcc/gCcc	26/27	1	2	FACETS	0.455	0.401	0.513	0.455	0.401	0.513	SUBCLONAL	1	TRUE	1	0.34	2		800	1113	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120419	70120419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746125506	NA	P-0031195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	234	892	0	ENST00000245479.2:c.1421G>A	p.Arg474His	p.R474H	ENST00000245479	NM_000346.3	474	cGc/cAc	3/3	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.34	2		892	1323	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271796	15271796	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs774187286	NA	P-0031195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	134	768	0	ENST00000263388.2:c.6643C>A	p.Pro2215Thr	p.P2215T	ENST00000263388	NM_000435.2	2215	Cca/Aca	33/33	1	2	FACETS	0.786	0.713	0.863	0.786	0.713	0.863	SUBCLONAL	1	TRUE	1	0.34	2		768	1003	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223502	36223502	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	147	783	2	ENST00000222270.7:c.6056del	p.Gly2019AlafsTer21	p.G2019Afs*21	ENST00000222270	NM_014727.1	2018	Ggg/gg	28/37	1	2	FACETS	0.877	0.8	0.958	0.877	0.8	0.958	CLONAL	1	TRUE	1	0.34	2		785	986	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267330	198267330	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	154	675	0	ENST00000335508.6:c.2027G>C	p.Gly676Ala	p.G676A	ENST00000335508	NM_012433.2	676	gGc/gCc	14/25	1	2	FACETS	0.956	0.874	1	0.956	0.874	1	CLONAL	1	TRUE	1	0.34	2		675	948	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264146	46264146	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	98	402	0	ENST00000371998.3:c.1193T>C	p.Val398Ala	p.V398A	ENST00000371998		398	gTa/gCa	11/23	1	2	FACETS	0.931	0.832	1	0.931	0.832	1	CLONAL	1	TRUE	1	0.34	2		402	619	SUCCESS
ATR	545	MSKCC	GRCh37	3	142238541	142238541	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	65	357	0	ENST00000350721.4:c.4352G>T	p.Arg1451Leu	p.R1451L	ENST00000350721	NM_001184.3	1451	cGg/cTg	24/47	1	2	FACETS	0.608	0.527	0.696	0.608	0.527	0.696	SUBCLONAL	1	TRUE	1	0.34	2		357	629	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181807	56181807	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	114	497	0	ENST00000399503.3:c.4031C>A	p.Ser1344Ter	p.S1344*	ENST00000399503	NM_005921.1	1344	tCa/tAa	17/20	1	2	FACETS	0.851	0.766	0.941	0.851	0.766	0.941	CLONAL	1	TRUE	1	0.34	2		497	788	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858210	27858210	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs776524828	NA	P-0031195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	138	655	0	ENST00000359303.2:c.361A>G	p.Met121Val	p.M121V	ENST00000359303	NM_003535.2	121	Atg/Gtg	1/1	1	2	FACETS	0.905	0.823	0.991	0.905	0.823	0.991	CLONAL	1	TRUE	1	0.34	2		655	897	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231038	53231038	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	76	667	0	ENST00000375401.3:c.1864T>C	p.Trp622Arg	p.W622R	ENST00000375401	NM_004187.3	622	Tgg/Cgg	13/26	1	2	FACETS	0.459	0.401	0.521	0.459	0.401	0.521	SUBCLONAL	1	TRUE	1	0.34	2		667	975	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	150	619	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	1	2	FACETS	0.898	0.82	0.98	0.898	0.82	0.98	CLONAL	1	TRUE	1	0.343032123947287	2		619	974	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519980	NA	P-0031196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	147	695	0	ENST00000269305.4:c.528C>G	p.Cys176Trp	p.C176W	ENST00000269305	NM_001126112.2	176	tgC/tgG	5/11	0.343032123947287	1	FACETS	0.813	0.743	0.888	0.813	0.743	0.888	CLONAL	1	TRUE	0	0.343032123947287	1		695	873	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720650	89720650	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1257124719	NA	P-0031196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	65	211	0	ENST00000371953.3:c.802-1G>A		p.X268_splice	ENST00000371953	NM_000314.4	268			0.342056242705027	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.343032123947287	2		211	170	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606357	93606357	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	121	697	3	ENST00000375746.1:c.177G>T	p.Arg59Ser	p.R59S	ENST00000375746	NM_001174167.1	59	agG/agT	2/14	1	2	FACETS	0.842	0.76	0.928	0.842	0.76	0.928	CLONAL	1	TRUE	1	0.343032123947287	2		700	838	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435843	149435843	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs281860274	NA	P-0031197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	234	604	0	ENST00000286301.3:c.2381T>C	p.Ile794Thr	p.I794T	ENST00000286301	NM_005211.3	794	aTt/aCt	18/22	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		604	847	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0031198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	429	477	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.679131554001544	1	FACETS	0.977	0.937	1	0.977	0.937	1	CLONAL	1	TRUE	0	0.679131554001544	1		478	854	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0031199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	109	510	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.213364660636413	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.213364660636413	1		510	724	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486063	29486066	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	rs771115661	NA	P-0031199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	57	439	0	ENST00000356175.3:c.244_247del	p.Gln83Ter	p.Q83*	ENST00000356175	NM_000267.3	80	taTCTC/ta	3/57	0.213364660636413	1	FACETS	0.755	0.647	0.873	0.755	0.647	0.873	SUBCLONAL	1	TRUE	0	0.213364660636413	1		439	632	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	54	384	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.602	0.513	0.699	0.602	0.513	0.699	SUBCLONAL	1	TRUE	1	0.27	2		384	665	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578476	7578477	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGTGT	novel	NA	P-0031200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	60	759	0	ENST00000269305.4:c.453_454insACACC	p.Pro152ThrfsTer20	p.P152Tfs*20	ENST00000269305	NM_001126112.2	151	-/ACACC	5/11	1	2	FACETS	0.441	0.378	0.509	0.441	0.378	0.509	SUBCLONAL	1	TRUE	1	0.27	2		759	1008	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370799	225370799	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	93	593	0	ENST00000264414.4:c.1080C>G	p.Phe360Leu	p.F360L	ENST00000264414	NM_003590.4	360	ttC/ttG	8/16	NA	2	FACETS	1	0.954	1			1	INDETERMINATE	1	TRUE	NA	0.31	2		593	531	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191474	10191485	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	ATACTCTGAAAG	ATACTCTGAAAG	-	novel	NA	P-0031201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	87	439	0	ENST00000256474.2:c.468_479del	p.Tyr156_Glu160delinsTer	p.Y156_E160delins*	ENST00000256474	NM_000551.3	156	tATACTCTGAAAGag/tag	3/3	0.304495364244255	1	FACETS	0.912	0.81	1	0.912	0.81	1	CLONAL	1	TRUE	0	0.31	1		439	520	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440297	52440297	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	106	645	0	ENST00000460680.1:c.755G>C	p.Arg252Pro	p.R252P	ENST00000460680	NM_004656.3	252	cGt/cCt	9/17	0.304495364244255	1	FACETS	0.755	0.677	0.838	0.755	0.677	0.838	SUBCLONAL	1	TRUE	0	0.31	1		645	765	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0031202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	212	459	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.852	0.795	0.911	0.852	0.795	0.911	CLONAL	1	TRUE	1	0.706706559100001	2		459	704	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0031202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	351	361	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.648987748861332	1	FACETS	0.841	0.802	0.88	0.841	0.802	0.88	CLONAL	1	TRUE	0	0.706706559100001	1		361	764	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445091	89445091	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	198	441	2	ENST00000336596.2:c.1411G>A	p.Glu471Lys	p.E471K	ENST00000336596	NM_005233.5	471	Gag/Aag	6/17	1	2	FACETS	0.852	0.792	0.912	0.852	0.792	0.912	CLONAL	1	TRUE	1	0.706706559100001	2		443	658	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127460	55127460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779332376	NA	P-0031202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	428	593	1	ENST00000257290.5:c.248C>T	p.Thr83Met	p.T83M	ENST00000257290	NM_006206.4	83	aCg/aTg	3/23	1	2	FACETS	0.921	0.878	0.965	0.921	0.878	0.965	CLONAL	1	TRUE	1	0.706706559100001	2		594	1315	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509349	46509349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	351	518	0	ENST00000262741.5:c.1382G>A	p.Arg461Lys	p.R461K	ENST00000262741	NM_003629.3	461	aGa/aAa	10/10	1	2	FACETS	0.96	0.911	1	0.96	0.911	1	CLONAL	1	TRUE	1	0.706706559100001	2		518	1035	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266049	41266300	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACT	CCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACT	-	novel	NA	P-0031202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	26	344	0	ENST00000349496.5:c.46_241+56del		p.X16_splice	ENST00000349496	NM_001904.3	16		3/15	0.679088106155825	2	FACETS	0.293	0.233	0.362	0.147	0.116	0.181	SUBCLONAL	1	TRUE	0	0.706706559100001	2		344	251	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631837	90631837	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	165	585	0	ENST00000330062.3:c.516G>T	p.Arg172Ser	p.R172S	ENST00000330062	NM_002168.2	172	agG/agT	4/11	1	2	FACETS	0.893	0.821	0.969	0.893	0.821	0.969	CLONAL	1	TRUE	1	0.44611390834048	2		585	828	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984330	201984336	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CACCCAG	CACCCAG	-	novel	NA	P-0031204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	371	641	0	ENST00000359651.3:c.1002-7_1002-1del		p.X334_splice	ENST00000359651		334			0.44611390834048	2	FACETS	0.987	0.941	1	0.987	0.941	1	CLONAL	2	TRUE	0	0.44611390834048	2		641	843	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612036	43612036	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	217	831	0	ENST00000355710.3:c.2141A>C	p.Asp714Ala	p.D714A	ENST00000355710	NM_020975.4	714	gAt/gCt	12/20	1	2	FACETS	0.871	0.809	0.935	0.871	0.809	0.935	CLONAL	1	TRUE	1	0.44611390834048	2		831	1117	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0031205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	149	779	1	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.220541827075059	2		780	1200	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981292	201981292	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	162	648	0	ENST00000359651.3:c.371A>T	p.Gln124Leu	p.Q124L	ENST00000359651		124	cAg/cTg	2/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.220541827075059	2		648	1104	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32932028	32932033	+	inframe_deletion	In_Frame_Del	DEL	CTCCAA	CTCCAA	-	novel	NA	P-0031205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	90	467	0	ENST00000380152.3:c.7767_7772del	p.Ser2590_Asn2591del	p.S2590_N2591del	ENST00000380152		2589	ccCTCCAAt/cct	16/27	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.220541827075059	2		467	596	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149152	61149152	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0031205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	53	486	1	ENST00000295025.8:c.1342A>T	p.Arg448Ter	p.R448*	ENST00000295025	NM_002908.2	448	Aga/Tga	11/11	1	2	FACETS	0.646	0.55	0.752	0.646	0.55	0.752	SUBCLONAL	1	TRUE	1	0.220541827075059	2		487	744	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098935	178098935	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	98	391	0	ENST00000397062.3:c.110T>C	p.Phe37Ser	p.F37S	ENST00000397062	NM_006164.4	37	tTt/tCt	2/5	0.220541827075059	3	FACETS	1	0.963	1	0.395	0.352	0.441	CLONAL	1	TRUE	0	0.220541827075059	3		391	832	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149566	202149566	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	245	523	0	ENST00000358485.4:c.1007T>A	p.Leu336His	p.L336H	ENST00000358485	NM_001080125.1	336	cTt/cAt	8/9	0.220541827075059	3	FACETS	0.927	0.868	0.988	0.927	0.868	0.988	CLONAL	3	TRUE	0	0.220541827075059	3		523	887	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096085	71096093	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACGCATACC	ACGCATACC	-	novel	NA	P-0031205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	49	310	0	ENST00000318789.4:c.664_664+8del		p.X222_splice	ENST00000318789	NM_032682.5	222		10/21	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.220541827075059	2		310	420	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	99	568	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.658	0.592	0.727	0.658	0.592	0.727	SUBCLONAL	1	TRUE	1	0.759937916934422	2		570	396	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	231	610	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.927	0.886	0.965	1	0.995	1	CLONAL	2	TRUE	1	0.759937916934422	2		611	328	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051053	180051053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755736057	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	203	566	1	ENST00000261937.6:c.1430G>A	p.Arg477Gln	p.R477Q	ENST00000261937	NM_182925.4	477	cGg/cAg	11/30	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.759937916934422	2		567	514	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	84	457	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	1	2	FACETS	0.485	0.43	0.543	0.485	0.43	0.543	SUBCLONAL	1	TRUE	1	0.759937916934422	2		457	456	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247367	153247367	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	177	350	0	ENST00000281708.4:c.1435C>T	p.Arg479Ter	p.R479*	ENST00000281708	NM_033632.3	479	Cga/Tga	10/12	1	2	FACETS	0.924	0.859	0.991	0.924	0.859	0.991	CLONAL	1	TRUE	1	0.759937916934422	2		350	504	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	81	364	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	0.743	0.662	0.827	0.743	0.662	0.827	SUBCLONAL	1	TRUE	1	0.759937916934422	2		364	287	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732996	30732996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893809	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	148	462	1	ENST00000295754.5:c.1609C>T	p.Arg537Cys	p.R537C	ENST00000295754	NM_003242.5	537	Cgc/Tgc	7/7	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.759937916934422	2		463	379	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254510	1254510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918664	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	169	672	0	ENST00000310581.5:c.3268G>A	p.Val1090Met	p.V1090M	ENST00000310581	NM_198253.2	1090	Gtg/Atg	15/16	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.759937916934422	2		672	442	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053023	180053023	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	189	688	2	ENST00000261937.6:c.1267del	p.Gln423ArgfsTer70	p.Q423Rfs*70	ENST00000261937	NM_182925.4	423	Cag/ag	10/30	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.759937916934422	2		690	481	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	196	485	2	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.759937916934422	2		487	501	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007871	45007872	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	137	460	0	ENST00000558401.1:c.319_320del	p.Leu107ValfsTer7	p.L107Vfs*7	ENST00000558401	NM_004048.2	106	acTTtg/actg	2/4	1	2	FACETS	0.869	0.798	0.942	0.869	0.798	0.942	CLONAL	1	TRUE	1	0.759937916934422	2		460	415	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554345	141554345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748399150	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	51	719	4	ENST00000220592.5:c.1806del	p.Ala603ProfsTer92	p.A603Pfs*92	ENST00000220592	NM_012154.3	602	ccC/cc	14/19	0.309683569074849	3	FACETS	0.301	0.255	0.351	0.15	0.127	0.176	INDETERMINATE	1	TRUE	1	0.759937916934422	3		723	616	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588927	67588927	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	20	329	0	ENST00000274335.5:c.1020-2A>G		p.X340_splice	ENST00000274335		340			1	2	FACETS	0.162	0.123	0.207	0.162	0.123	0.207	SUBCLONAL	1	TRUE	1	0.759937916934422	2		329	325	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445203	49445203	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	75	671	1	ENST00000301067.7:c.2263del	p.Arg755GlyfsTer175	p.R755Gfs*175	ENST00000301067	NM_003482.3	755	Cgg/gg	10/54	0.759937916934422	2	FACETS	0.446	0.392	0.503	0.223	0.196	0.252	SUBCLONAL	1	TRUE	0	0.759937916934422	2		672	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572929	7572929	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	169	521	0	ENST00000269305.4:c.1180T>C	p.Ter394ArgextTer9	p.*394Rext*9	ENST00000269305	NM_001126112.2	394	Tga/Cga	11/11	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.759937916934422	2		521	444	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729609	41729609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	174	497	0	ENST00000242208.4:c.920G>A	p.Arg307Gln	p.R307Q	ENST00000242208	NM_002192.2	307	cGg/cAg	3/3	0.264540447943252	4	FACETS	1	0.99	1	0.727	0.674	0.782	INDETERMINATE	1	TRUE	2	0.759937916934422	4		497	554	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831936	72831936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs181722888	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	170	718	2	ENST00000268489.5:c.4645G>A	p.Val1549Ile	p.V1549I	ENST00000268489	NM_006885.3	1549	Gtc/Atc	9/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.759937916934422	2		720	395	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228119	36228119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201885107	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	168	605	0	ENST00000222270.7:c.7505C>T	p.Pro2502Leu	p.P2502L	ENST00000222270	NM_014727.1	2502	cCg/cTg	33/37	1	2	FACETS	0.923	0.856	0.992	0.923	0.856	0.992	CLONAL	1	TRUE	1	0.759937916934422	2		605	479	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45805916	45805916	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	28	542	0	ENST00000450313.1:c.11T>G	p.Leu4Arg	p.L4R	ENST00000450313	NM_012222.2	4	cTc/cGc	1/16	1	2	FACETS	0.148	0.118	0.183	0.148	0.118	0.183	SUBCLONAL	1	TRUE	1	0.759937916934422	2		542	498	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161326485	161326485	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	51	535	0	ENST00000367975.2:c.260T>C	p.Met87Thr	p.M87T	ENST00000367975	NM_003001.3	87	aTg/aCg	5/6	0.759410228301262	4	FACETS	0.309	0.262	0.361	0.103	0.087	0.121	SUBCLONAL	1	TRUE	1	0.759937916934422	4		535	765	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724750	112724750	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	157	519	1	ENST00000369452.4:c.638del	p.Asn213ThrfsTer33	p.N213Tfs*33	ENST00000369452	NM_007373.3	212	Aaa/aa	2/9	1	2	FACETS	0.864	0.798	0.932	0.864	0.798	0.932	CLONAL	1	TRUE	1	0.759937916934422	2		520	478	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398283	+	missense_variant	Missense_Mutation	DNP	CA	CA	GG	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	230	544	0	ENST00000311936.3:c.36_37delinsCC	p.Gly13Arg	p.G13R	ENST00000311936	NM_004985.3	12	ggTGgc/ggCCgc	2/5	1	2	FACETS	0.983	0.922	1	0.983	0.922	1	CLONAL	1	TRUE	1	0.759937916934422	2		544	616	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487946	56487946	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	63	638	0	ENST00000267101.3:c.1677G>A	p.Met559Ile	p.M559I	ENST00000267101	NM_001982.3	559	atG/atA	14/28	0.759937916934422	2	FACETS	0.379	0.328	0.433	0.189	0.164	0.217	SUBCLONAL	1	TRUE	0	0.759937916934422	2		638	438	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218407	133218407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1467058337	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	28	626	0	ENST00000320574.5:c.5204C>T	p.Ala1735Val	p.A1735V	ENST00000320574	NM_006231.2	1735	gCc/gTc	39/49	NA	2	FACETS	0.155	0.123	0.191			1	INDETERMINATE	1	TRUE	NA	0.759937916934422	2		626	476	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562955	21562955	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772459145	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	85	510	0	ENST00000382592.4:c.964G>A	p.Gly322Ser	p.G322S	ENST00000382592	NM_014572.2	322	Ggt/Agt	4/8	0.759937916934422	3	FACETS	0.417	0.368	0.47	0.209	0.184	0.235	SUBCLONAL	1	TRUE	1	0.759937916934422	3		510	740	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32890628	32890628	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80359393	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	22	397	1	ENST00000380152.3:c.36del	p.Phe12LeufsTer13	p.F12Lfs*13	ENST00000380152		11	Ttt/tt	2/27	0.759937916934422	3	FACETS	0.276	0.214	0.349	0.138	0.107	0.175	SUBCLONAL	1	TRUE	1	0.759937916934422	3		398	289	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878100	48878100	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	121	96	0	ENST00000267163.4:c.52G>A	p.Ala18Thr	p.A18T	ENST00000267163	NM_000321.2	18	Gcg/Acg	1/27	0.759937916934422	3	FACETS	0.977	0.905	1	0.977	0.905	1	CLONAL	2	TRUE	1	0.759937916934422	3		96	225	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2105401	2105401	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs45517110	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	125	519	0	ENST00000219476.3:c.482-2A>G		p.X161_splice	ENST00000219476	NM_000548.3	161			1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.759937916934422	2		519	327	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627608	37627608	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	183	669	0	ENST00000447079.4:c.1523T>C	p.Leu508Pro	p.L508P	ENST00000447079	NM_015083.1	508	cTg/cCg	2/14	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.759937916934422	2		669	436	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214636	5214636	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532712500	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	69	721	1	ENST00000357368.4:c.4430G>A	p.Arg1477His	p.R1477H	ENST00000357368	NM_002850.3	1477	cGt/cAt	29/38	1	2	FACETS	0.313	0.272	0.356	0.313	0.272	0.356	SUBCLONAL	1	TRUE	1	0.759937916934422	2		722	581	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215309	5215309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	87	515	0	ENST00000357368.4:c.4309C>T	p.Pro1437Ser	p.P1437S	ENST00000357368	NM_002850.3	1437	Ccc/Tcc	28/38	1	2	FACETS	0.487	0.433	0.545	0.487	0.433	0.545	SUBCLONAL	1	TRUE	1	0.759937916934422	2		515	470	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098482	11098482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1364450672	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	19	327	0	ENST00000358026.2:c.1000G>A	p.Gly334Arg	p.G334R	ENST00000358026	NM_001128849.1	334	Ggg/Agg	6/36	1	2	FACETS	0.152	0.115	0.195	0.152	0.115	0.195	SUBCLONAL	1	TRUE	1	0.759937916934422	2		327	330	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40747882	40747882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	186	608	0	ENST00000392038.2:c.536C>T	p.Ala179Val	p.A179V	ENST00000392038	NM_001626.4	179	gCc/gTc	6/14	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.759937916934422	2		608	467	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143058	30143058	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	25	601	0	ENST00000389048.3:c.468del	p.Glu160ArgfsTer26	p.E160Rfs*26	ENST00000389048	NM_004304.4	156	ggG/gg	1/29	1	2	FACETS	0.152	0.119	0.19	0.152	0.119	0.19	SUBCLONAL	1	TRUE	1	0.759937916934422	2		601	433	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662010	227662010	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	87	638	0	ENST00000305123.5:c.1445A>G	p.His482Arg	p.H482R	ENST00000305123	NM_005544.2	482	cAc/cGc	1/2	1	2	FACETS	0.741	0.663	0.822	0.741	0.663	0.822	SUBCLONAL	1	TRUE	1	0.759937916934422	2		638	309	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657087	45657087	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	33	343	0	ENST00000407780.3:c.69G>T	p.Lys23Asn	p.K23N	ENST00000407780	NM_001283052.1	23	aaG/aaT	3/7	1	2	FACETS	0.269	0.219	0.325	0.269	0.219	0.325	SUBCLONAL	1	TRUE	1	0.759937916934422	2		343	323	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191511	185191511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	46	616	0	ENST00000265026.3:c.2392C>T	p.Pro798Ser	p.P798S	ENST00000265026	NM_004721.4	798	Cct/Tct	11/14	1	2	FACETS	0.232	0.195	0.273	0.232	0.195	0.273	SUBCLONAL	1	TRUE	1	0.759937916934422	2		616	521	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356424	66356424	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	158	346	0	ENST00000273854.3:c.1073C>T	p.Pro358Leu	p.P358L	ENST00000273854	NM_004439.5	358	cCc/cTc	5/18	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.759937916934422	2		346	379	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271215	153271215	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	90	393	0	ENST00000281708.4:c.563G>A	p.Cys188Tyr	p.C188Y	ENST00000281708	NM_033632.3	188	tGc/tAc	3/12	1	2	FACETS	0.769	0.69	0.851	0.769	0.69	0.851	SUBCLONAL	1	TRUE	1	0.759937916934422	2		393	308	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168740	56168740	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	294	492	1	ENST00000399503.3:c.1594C>T	p.Arg532Ter	p.R532*	ENST00000399503	NM_005921.1	532	Cga/Tga	9/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.759937916934422	2		493	740	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502612	149502612	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	80	315	0	ENST00000261799.4:c.2176del	p.Leu726CysfsTer7	p.L726Cfs*7	ENST00000261799	NM_002609.3	726	Ctg/tg	15/23	1	2	FACETS	0.988	0.887	1	0.988	0.887	1	CLONAL	1	TRUE	1	0.759937916934422	2		315	213	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324916	31324917	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	147	471	0	ENST00000412585.2:c.19dup	p.Arg7ProfsTer92	p.R7Pfs*92	ENST00000412585	NM_005514.6	7	cga/cCga	1/8	1	2	FACETS	0.834	0.767	0.902	0.834	0.767	0.902	CLONAL	1	TRUE	1	0.759937916934422	2		471	464	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527947	157527947	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	68	575	0	ENST00000346085.5:c.5672A>G	p.Asp1891Gly	p.D1891G	ENST00000346085	NM_020732.3	1891	gAc/gGc	20/20	1	2	FACETS	0.387	0.338	0.441	0.387	0.338	0.441	SUBCLONAL	1	TRUE	1	0.759937916934422	2		575	462	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450364	50450364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	182	554	2	ENST00000331340.3:c.548G>A	p.Arg183His	p.R183H	ENST00000331340	NM_006060.4	183	cGc/cAc	5/8	0.264540447943252	4	FACETS	1	0.986	1	0.642	0.594	0.69	INDETERMINATE	1	TRUE	2	0.759937916934422	4		556	657	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468260	50468260	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	70	589	0	ENST00000331340.3:c.1495A>G	p.Ser499Gly	p.S499G	ENST00000331340	NM_006060.4	499	Agc/Ggc	8/8	0.264540447943252	4	FACETS	0.404	0.351	0.461	0.202	0.175	0.231	INDETERMINATE	1	TRUE	2	0.759937916934422	4		589	803	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534466	140534466	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	102	549	0	ENST00000288602.6:c.447del	p.Lys150SerfsTer32	p.K150Sfs*32	ENST00000288602	NM_004333.4	149	ccC/cc	3/18	0.264540447943252	4	FACETS	0.519	0.463	0.578	0.259	0.231	0.289	INDETERMINATE	1	TRUE	2	0.759937916934422	4		549	911	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874078	151874078	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	128	563	0	ENST00000262189.6:c.8460T>A	p.Asn2820Lys	p.N2820K	ENST00000262189	NM_170606.2	2820	aaT/aaA	38/59	0.264540447943252	4	FACETS	1	0.97	1	1	0.97	1	INDETERMINATE	2	TRUE	2	0.759937916934422	4		563	270	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126697	5126697	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	150	387	0	ENST00000381652.3:c.3305T>C	p.Met1102Thr	p.M1102T	ENST00000381652	NM_004972.3	1102	aTg/aCg	25/25	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.759937916934422	2		387	381	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933031	39933031	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	232	739	0	ENST00000378444.4:c.1568A>G	p.Lys523Arg	p.K523R	ENST00000378444	NM_001123385.1	523	aAa/aGa	4/15	0.74824170943877	1	FACETS	0.805	0.761	0.85	0.805	0.761	0.85	CLONAL	1	TRUE	0	0.759937916934422	1		739	470	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70353061	70353061	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	30	438	0	ENST00000374080.3:c.4616T>C	p.Leu1539Pro	p.L1539P	ENST00000374080		1539	cTg/cCg	33/45	0.74824170943877	1	FACETS	0.126	0.101	0.154	0.126	0.101	0.154	SUBCLONAL	1	TRUE	0	0.759937916934422	1		438	389	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855286	76855286	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	16	376	0	ENST00000373344.5:c.5701T>C	p.Tyr1901His	p.Y1901H	ENST00000373344	NM_000489.3	1901	Tat/Cat	24/35	0.74824170943877	1	FACETS	0.18	0.134	0.235	0.18	0.134	0.235	SUBCLONAL	1	TRUE	0	0.759937916934422	1		376	145	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0031208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	647	435	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.718443810470167	5	FACETS	1	0.972	1	0.754	0.729	0.778	CLONAL	3	TRUE	1	0.718443810470167	5		435	1241	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131976439	131976439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660400	NA	P-0031208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	271	690	0	ENST00000265335.6:c.3694G>A	p.Glu1232Lys	p.E1232K	ENST00000265335		1232	Gag/Aag	24/25	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.718443810470167	2		690	697	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844139	68844139	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	264	690	0	ENST00000261769.5:c.727G>C	p.Glu243Gln	p.E243Q	ENST00000261769	NM_004360.3	243	Gag/Cag	6/16	0.718443810470167	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.718443810470167	1		690	445	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94209488	94209488	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555014479	NA	P-0031208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	164	485	0	ENST00000323929.3:c.626C>T	p.Ser209Phe	p.S209F	ENST00000323929	NM_005591.3	209	tCt/tTt	7/20	1	2	FACETS	0.76	0.701	0.821	0.76	0.701	0.821	SUBCLONAL	1	TRUE	1	0.718443810470167	2		485	601	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982329	201982329	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1471	310	822	0	ENST00000359651.3:c.708G>C	p.Lys236Asn	p.K236N	ENST00000359651		236	aaG/aaC	6/8	0.718443810470167	5	FACETS	1	0.946	1	0.252	0.236	0.268	CLONAL	1	TRUE	1	0.718443810470167	5		822	1781	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253394	226253394	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	101	227	0	ENST00000366813.1:c.166C>G	p.Gln56Glu	p.Q56E	ENST00000366813		56	Cag/Gag	2/3	0.718443810470167	5	FACETS	1	0.904	1	0.252	0.226	0.28	CLONAL	1	TRUE	1	0.718443810470167	5		227	579	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906690	32906690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555281730	NA	P-0031208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	43	622	0	ENST00000380152.3:c.1075G>A	p.Glu359Lys	p.E359K	ENST00000380152		359	Gaa/Aaa	10/27	0.718443810470167	2	FACETS	0.175	0.146	0.207	0.087	0.072	0.104	SUBCLONAL	1	TRUE	0	0.718443810470167	2		622	685	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640164	3640164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	380	977	0	ENST00000294008.3:c.3475G>A	p.Glu1159Lys	p.E1159K	ENST00000294008	NM_032444.2	1159	Gag/Aag	12/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.718443810470167	2		977	1043	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50816324	50816324	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	223	609	0	ENST00000398568.2:c.1764G>C	p.Lys588Asn	p.K588N	ENST00000398568	NM_001042412.1	588	aaG/aaC	10/18	NA	2	FACETS	0.892	0.834	0.951			1	INDETERMINATE	1	TRUE	NA	0.718443810470167	2		609	696	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351830	89351830	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	67	918	0	ENST00000301030.4:c.1120G>C	p.Glu374Gln	p.E374Q	ENST00000301030	NM_001256183.1	374	Gaa/Caa	9/13	1	2	FACETS	0.183	0.158	0.21	0.183	0.158	0.21	SUBCLONAL	1	TRUE	1	0.718443810470167	2		918	1021	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351884	89351884	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	64	944	0	ENST00000301030.4:c.1066G>C	p.Asp356His	p.D356H	ENST00000301030	NM_001256183.1	356	Gac/Cac	9/13	1	2	FACETS	0.172	0.148	0.198	0.172	0.148	0.198	SUBCLONAL	1	TRUE	1	0.718443810470167	2		944	1037	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578456	7578465	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGACGCGG	GCGGACGCGG	-	novel	NA	P-0031208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	609	782	0	ENST00000269305.4:c.465_474del	p.Arg156ProfsTer11	p.R156Pfs*11	ENST00000269305	NM_001126112.2	155	acCCGCGTCCGC/ac	5/11	0.718443810470167	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.718443810470167	2		782	835	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3113385	3113385	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	63	702	0	ENST00000078429.4:c.379C>G	p.Gln127Glu	p.Q127E	ENST00000078429	NM_002067.2	127	Cag/Gag	3/7	0.718443810470167	3	FACETS	0.219	0.188	0.252	0.109	0.094	0.126	SUBCLONAL	1	TRUE	1	0.718443810470167	3		702	1090	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129691	47129691	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	243	537	0	ENST00000409792.3:c.5189C>G	p.Ser1730Cys	p.S1730C	ENST00000409792	NM_014159.6	1730	tCt/tGt	10/21	0.718443810470167	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.718443810470167	1		537	429	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269135	142269135	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	177	409	0	ENST00000350721.4:c.2815G>T	p.Glu939Ter	p.E939*	ENST00000350721	NM_001184.3	939	Gaa/Taa	14/47	0.718443810470167	5	FACETS	1	0.95	1	0.261	0.24	0.282	CLONAL	1	TRUE	1	0.718443810470167	5		409	982	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815305	32815305	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	334	816	0	ENST00000354258.4:c.2068C>A	p.Gln690Lys	p.Q690K	ENST00000354258	NM_000593.5	690	Cag/Aag	9/11	0.711242020403252	4	FACETS	1	0.977	1	0.356	0.335	0.377	CLONAL	1	TRUE	1	0.718443810470167	4		816	1497	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112035614	112035614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	164	538	0	ENST00000368678.4:c.280G>A	p.Glu94Lys	p.E94K	ENST00000368678		94	Gaa/Aaa	4/13	1	2	FACETS	0.698	0.643	0.755	0.698	0.643	0.755	SUBCLONAL	1	TRUE	1	0.718443810470167	2		538	654	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868444	117868444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	294	663	0	ENST00000297338.2:c.898G>A	p.Glu300Lys	p.E300K	ENST00000297338	NM_006265.2	300	Gag/Aag	8/14	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.718443810470167	2		663	717	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221645	22221647	+	stop_gained	Nonsense_Mutation	TNP	GAG	GAG	TAA	novel	NA	P-0031208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	111	296	1	ENST00000215832.6:c.84_86delinsTTA	p.Ser29Ter	p.S29*	ENST00000215832	NM_002745.4	28	ctCTCg/ctTTAg	1/9	0.718443810470167	2	FACETS	1	0.955	1	0.536	0.49	0.584	CLONAL	1	TRUE	0	0.718443810470167	2		297	288	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0031220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	54	505	4	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.883	0.752	1	0.883	0.752	1	CLONAL	1	TRUE	1	0.13	2		509	941	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0031221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	417	505	4	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.662104873358063	2	FACETS	0.936	0.903	0.969	0.936	0.903	0.969	CLONAL	2	TRUE	0	0.675978119700883	2		509	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0031221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	805	451	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.640061716941402	3	FACETS	0.984	0.962	1	0.984	0.962	1	CLONAL	3	TRUE	0	0.675978119700883	3		451	1080	SUCCESS
APC	324	MSKCC	GRCh37	5	112175419	112175419	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0031221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	386	336	0	ENST00000257430.4:c.4128T>A	p.Tyr1376Ter	p.Y1376*	ENST00000257430	NM_000038.5	1376	taT/taA	16/16	0.640061716941402	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	0	0.675978119700883	3		336	505	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137283	64137283	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	269	717	2	ENST00000334205.4:c.1715C>T	p.Thr572Met	p.T572M	ENST00000334205	NM_003942.2	572	aCg/aTg	14/17	1	2	FACETS	0.937	0.882	0.994	0.937	0.882	0.994	CLONAL	1	TRUE	1	0.675978119700883	2		719	849	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434863	49434864	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0031221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	510	904	0	ENST00000301067.7:c.6689dup	p.Pro2231ThrfsTer12	p.P2231Tfs*12	ENST00000301067	NM_003482.3	2230	cca/ccCa	31/54	0.675978119700883	3	FACETS	0.784	0.752	0.817			1	SUBCLONAL	2	TRUE	NA	0.675978119700883	3		904	1287	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185035	32185035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766255732	NA	P-0031221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	217	703	0	ENST00000375023.3:c.1633G>A	p.Gly545Ser	p.G545S	ENST00000375023	NM_004557.3	545	Ggc/Agc	10/30	0.583165905728896	4	FACETS	0.85	0.789	0.913	0.425	0.394	0.457	CLONAL	1	TRUE	2	0.675978119700883	4		703	1266	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741664	17741664	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	71	563	0	ENST00000250003.3:c.335A>G	p.Lys112Arg	p.K112R	ENST00000250003	NM_002478.4	112	aAg/aGg	1/3	0.683411285408222	1	FACETS	0.45	0.396	0.507	0.45	0.396	0.507	SUBCLONAL	1	TRUE	0	0.683411285408222	1		563	304	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637901	39637920	+	frameshift_variant	Frame_Shift_Del	DEL	TTCCTCCACCAATGAAGCTG	TTCCTCCACCAATGAAGCTG	-	novel	NA	P-0031222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	121	609	0	ENST00000262039.4:c.2318_2337del	p.Leu773GlnfsTer2	p.L773Qfs*2	ENST00000262039	NM_002647.2	773	cTTCCTCCACCAATGAAGCTG/c	22/25	0.386163199216227	1	FACETS	0.45	0.408	0.494	0.45	0.408	0.494	INDETERMINATE	1	TRUE	0	0.683411285408222	1		609	518	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0031223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	293	562	3	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.767	0.722	0.813	0.767	0.722	0.813	SUBCLONAL	1	TRUE	1	0.71915859228594	2		565	1062	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0031223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	211	503	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.705	0.656	0.756	0.705	0.656	0.756	SUBCLONAL	1	TRUE	1	0.71915859228594	2		503	832	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0031223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	15	328	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.095	0.068	0.126	0.095	0.068	0.126	SUBCLONAL	1	TRUE	1	0.71915859228594	2		328	441	SUCCESS
APC	324	MSKCC	GRCh37	5	112175651	112175651	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	197	467	0	ENST00000257430.4:c.4364del	p.Asn1455IlefsTer18	p.N1455Ifs*18	ENST00000257430	NM_000038.5	1454	Aaa/aa	16/16	1	2	FACETS	0.669	0.62	0.719	0.669	0.62	0.719	SUBCLONAL	1	TRUE	1	0.71915859228594	2		467	819	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939479	68939479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778971988	NA	P-0031223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	205	604	0	ENST00000288368.4:c.464G>A	p.Arg155Gln	p.R155Q	ENST00000288368	NM_024870.2	155	cGg/cAg	5/40	1	2	FACETS	0.744	0.692	0.798	0.744	0.692	0.798	SUBCLONAL	1	TRUE	1	0.71915859228594	2		604	766	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003496	42003496	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	281	634	0	ENST00000219905.7:c.3033del	p.Tyr1011Ter	p.Y1011*	ENST00000219905	NM_001164273.1	1011	taC/ta	8/24	1	2	FACETS	0.648	0.608	0.689	0.648	0.608	0.689	SUBCLONAL	1	TRUE	1	0.71915859228594	2		634	1206	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288541	15288541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	23	148	0	ENST00000263388.2:c.4198C>T	p.Arg1400Cys	p.R1400C	ENST00000263388	NM_000435.2	1400	Cgc/Tgc	24/33	1	2	FACETS	0.291	0.227	0.363	0.291	0.227	0.363	SUBCLONAL	1	TRUE	1	0.71915859228594	2		148	220	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922111	39922111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	71	430	1	ENST00000378444.4:c.4061G>A	p.Ser1354Asn	p.S1354N	ENST00000378444	NM_001123385.1	1354	aGc/aAc	9/15	1	1	FACETS	0.156	0.136	0.178	0.156	0.136	0.178	SUBCLONAL	1	TRUE	0	0.71915859228594	1		431	810	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092740	27092740	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1557611083	NA	P-0031227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	112	516	0	ENST00000324856.7:c.2765del	p.Gly922AlafsTer2	p.G922Afs*2	ENST00000324856	NM_006015.4	921	Ggg/gg	9/20	1	2	FACETS	0.837	0.754	0.925	0.837	0.754	0.925	CLONAL	1	TRUE	1	0.391113699158824	2		516	684	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098954	178098954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553488015	NA	P-0031227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	105	382	0	ENST00000397062.3:c.91G>A	p.Gly31Arg	p.G31R	ENST00000397062	NM_006164.4	31	Gga/Aga	2/5	0.391113699158824	3	FACETS	1	0.976	1	0.648	0.583	0.717	CLONAL	1	TRUE	1	0.391113699158824	3		382	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577537	7577538	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0031227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	361	822	3	ENST00000269305.4:c.743_744delinsTT	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGG/cTT	7/11	0.391113699158824	2	FACETS	0.976	0.928	1	0.976	0.928	1	CLONAL	2	TRUE	0	0.391113699158824	2		825	946	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294285	1294285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	377	672	0	ENST00000310581.5:c.716G>A	p.Arg239Lys	p.R239K	ENST00000310581	NM_198253.2	239	aGg/aAg	2/16	0.289337391177159	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.391113699158824	4		672	1190	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259667	16259667	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	186	715	1	ENST00000375759.3:c.6932C>A	p.Ser2311Ter	p.S2311*	ENST00000375759	NM_015001.2	2311	tCa/tAa	11/15	1	2	FACETS	0.96	0.886	1	0.96	0.886	1	CLONAL	1	TRUE	1	0.391113699158824	2		716	991	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176085797	176085798	+	missense_variant	Missense_Mutation	DNP	TC	TC	GA	novel	NA	P-0031227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	92	642	0	ENST00000367669.3:c.988_989inv	p.Glu330Ser	p.E330S	ENST00000367669	NM_022457.5	330	GAa/TCa	9/20	0.368948519638652	4	FACETS	0.942	0.837	1	0.314	0.279	0.351	CLONAL	1	TRUE	1	0.391113699158824	4		642	695	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112769486	112769486	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	73	638	0	ENST00000369452.4:c.1438A>G	p.Asn480Asp	p.N480D	ENST00000369452	NM_007373.3	480	Aac/Gac	8/9	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.391113699158824	2		638	359	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298165	123298165	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	163	642	0	ENST00000358487.5:c.689C>G	p.Thr230Ser	p.T230S	ENST00000358487	NM_000141.4	230	aCc/aGc	6/18	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.391113699158824	2		642	816	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492580	56492580	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	339	678	0	ENST00000267101.3:c.2730G>T	p.Glu910Asp	p.E910D	ENST00000267101	NM_001982.3	910	gaG/gaT	23/28	0.381406133410888	3	FACETS	0.984	0.932	1	0.984	0.932	1	CLONAL	2	TRUE	1	0.391113699158824	3		678	1053	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504612	103504612	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	105	341	0	ENST00000355739.4:c.233G>T	p.Gly78Val	p.G78V	ENST00000355739	NM_000123.3	78	gGg/gTg	2/15	0.391113699158824	2	FACETS	0.776	0.702	0.852	0.776	0.702	0.852	SUBCLONAL	2	TRUE	0	0.391113699158824	2		341	346	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288709	15288710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0031227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	48	101	0	ENST00000263388.2:c.4029dup	p.Cys1344LeufsTer219	p.C1344Lfs*219	ENST00000263388	NM_000435.2	1343	-/C	24/33	0.323269818325062	4	FACETS	1	0.964	1	0.746	0.637	0.863	CLONAL	1	TRUE	2	0.391113699158824	4		101	229	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190742106	190742106	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	199	668	0	ENST00000441310.2:c.2743T>A	p.Cys915Ser	p.C915S	ENST00000441310	NM_000534.4	915	Tgt/Agt	13/13	0.391113699158824	3	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	1	0.391113699158824	3		668	600	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499355	89499355	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	205	486	0	ENST00000336596.2:c.2525G>C	p.Arg842Pro	p.R842P	ENST00000336596	NM_005233.5	842	cGa/cCa	15/17	0.391113699158824	2	FACETS	0.929	0.868	0.991	0.929	0.868	0.991	CLONAL	2	TRUE	0	0.391113699158824	2		486	564	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864629	56864629	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	123	730	0	ENST00000519728.1:c.592C>G	p.Arg198Gly	p.R198G	ENST00000519728	NM_002350.3	198	Cga/Gga	7/13	0.166338227178994	3	FACETS	0.905	0.818	0.996	0.302	0.272	0.332	INDETERMINATE	1	TRUE	0	0.391113699158824	3		730	831	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971045	21971045	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	298	574	0	ENST00000304494.5:c.313del	p.Asp105ThrfsTer41	p.D105Tfs*41	ENST00000304494	NM_000077.4	105	Gac/ac	2/3	0.391113699158824	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.391113699158824	2		574	738	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	201	384	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	0.472165782277522	2		384	778	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0031228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	264	890	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.45770720150081	1	FACETS	0.959	0.901	1	0.959	0.901	1	CLONAL	1	TRUE	0	0.472165782277522	1		892	891	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435287	49435287	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	229	877	0	ENST00000301067.7:c.6266del	p.Lys2089ArgfsTer5	p.K2089Rfs*5	ENST00000301067	NM_003482.3	2089	aAg/ag	31/54	1	2	FACETS	0.83	0.773	0.89	0.83	0.773	0.89	CLONAL	1	TRUE	1	0.472165782277522	2		877	1168	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	65	270	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.803	0.696	0.918	0.803	0.696	0.918	CLONAL	1	TRUE	1	0.26	2		270	623	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419897	41419897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs577588058	NA	P-0031235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	131	525	0	ENST00000373198.4:c.424G>A	p.Val142Ile	p.V142I	ENST00000373198	NM_133170.3	142	Gtc/Atc	3/32	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.26	2		525	877	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11297916	11297916	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	48	506	0	ENST00000361445.4:c.2192G>A	p.Arg731His	p.R731H	ENST00000361445	NM_004958.3	731	cGc/cAc	13/58	0.3	1	FACETS	0.445	0.375	0.522	0.445	0.375	0.522	SUBCLONAL	1	TRUE	0	0.26	1		506	722	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42385043	42385043	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555844167	NA	P-0031235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	86	549	0	ENST00000221972.3:c.677C>T	p.Pro226Leu	p.P226L	ENST00000221972	NM_021601.3	226	cCg/cTg	5/5	1	2	FACETS	0.763	0.674	0.859	0.763	0.674	0.859	SUBCLONAL	1	TRUE	1	0.26	2		549	867	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38960046	38960046	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	36	341	0	ENST00000357387.3:c.1886A>G	p.Asp629Gly	p.D629G	ENST00000357387	NM_152756.3	629	gAt/gGt	21/38	1	2	FACETS	0.64	0.526	0.767	0.64	0.526	0.767	SUBCLONAL	1	TRUE	1	0.26	2		341	433	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505129	149505137	+	protein_altering_variant	In_Frame_Del	DEL	GTAACGTGG	GTAACGTGG	CAT	novel	NA	P-0031235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	97	589	2	ENST00000261799.4:c.1678_1686delinsATG	p.Pro560_Tyr562delinsMet	p.P560_Y562delinsM	ENST00000261799	NM_002609.3	560	CCACGTTAC/ATG	12/23	1	2	FACETS	0.933	0.831	1	0.933	0.831	1	CLONAL	1	TRUE	1	0.26	2		591	800	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397828	116397828	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	58	518	0	ENST00000397752.3:c.2102+1del		p.S701fs	ENST00000397752	NM_000245.2	701	aGt/at	8/21	NA	2	FACETS	0.658	0.565	0.76			1	INDETERMINATE	1	TRUE	NA	0.26	2		518	678	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	257	270	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.8	2		270	554	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0031236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	275	435	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.8	2		435	562	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0031236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	221	636	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	1	2	FACETS	0.871	0.816	0.928	0.871	0.816	0.928	CLONAL	1	TRUE	1	0.8	2		636	634	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519896	NA	P-0031236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	277	470	1	ENST00000281708.4:c.1514G>T	p.Arg505Leu	p.R505L	ENST00000281708	NM_033632.3	505	cGc/cTc	10/12	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.8	2		471	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579378	7579379	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0031237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	800	690	2	ENST00000269305.4:c.308dup	p.Tyr103Ter	p.Y103*	ENST00000269305	NM_001126112.2	103	tac/taAc	4/11	0.922885650720612	2	FACETS	0.913	0.897	0.929	0.913	0.897	0.929	CLONAL	2	TRUE	0	0.922885650720612	2		692	949	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0031238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	237	526	3	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.209204482393437	2	FACETS	0.925	0.863	0.989	0.925	0.863	0.989	CLONAL	2	TRUE	0	0.234895453296634	2		529	1091	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243222	123243223	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0031238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	266	693	2	ENST00000358487.5:c.2290dup	p.Thr764AsnfsTer4	p.T764Nfs*4	ENST00000358487	NM_000141.4	764	aca/aAca	17/18	0.177843935852427	2	FACETS	0.894	0.837	0.953	0.894	0.837	0.953	CLONAL	2	TRUE	0	0.234895453296634	2		695	1267	SUCCESS
APC	324	MSKCC	GRCh37	5	112111363	112111363	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	59	441	3	ENST00000257430.4:c.460G>T	p.Glu154Ter	p.E154*	ENST00000257430	NM_000038.5	154	Gaa/Taa	5/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.234895453296634	2		444	390	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87338542	87338542	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	121	592	4	ENST00000277120.3:c.638C>G	p.Ser213Cys	p.S213C	ENST00000277120		213	tCt/tGt	7/19	1	2	FACETS	0.936	0.844	1	0.936	0.844	1	CLONAL	1	TRUE	1	0.234895453296634	2		596	1101	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0031241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	331	505	4	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.730374091422004	2		509	879	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445271	49445271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200451733	NA	P-0031241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	412	724	1	ENST00000301067.7:c.2195C>T	p.Pro732Leu	p.P732L	ENST00000301067	NM_003482.3	732	cCg/cTg	10/54	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.730374091422004	2		725	1123	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060799	38060799	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1019963817	NA	P-0031241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	406	798	0	ENST00000250448.2:c.1190A>G	p.Asn397Ser	p.N397S	ENST00000250448	NM_004496.3	397	aAc/aGc	2/2	1	2	FACETS	0.931	0.887	0.976	0.931	0.887	0.976	CLONAL	1	TRUE	1	0.730374091422004	2		798	1194	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994907	73994907	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	48	77	0	ENST00000318443.5:c.391A>G	p.Ser131Gly	p.S131G	ENST00000318443	NM_001024736.1	131	Agc/Ggc	3/10	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.730374091422004	2		77	115	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251007	99251007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1335469497	NA	P-0031241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	266	468	0	ENST00000268035.6:c.311C>T	p.Thr104Met	p.T104M	ENST00000268035	NM_000875.3	104	aCg/aTg	2/21	1	2	FACETS	0.969	0.912	1	0.969	0.912	1	CLONAL	1	TRUE	1	0.730374091422004	2		468	752	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108663	8108663	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	335	540	1	ENST00000585124.1:c.732G>T	p.Met244Ile	p.M244I	ENST00000585124	NM_004217.3	244	atG/atT	8/9	0.710468702772565	3	FACETS	1	0.978	1	0.532	0.503	0.562	CLONAL	1	TRUE	1	0.730374091422004	3		541	1176	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761006	59761006	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	290	502	0	ENST00000259008.2:c.3401C>G	p.Pro1134Arg	p.P1134R	ENST00000259008	NM_032043.2	1134	cCt/cGt	20/20	0.710468702772565	3	FACETS	0.991	0.932	1	0.495	0.466	0.526	CLONAL	1	TRUE	1	0.730374091422004	3		502	1094	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610330	10610330	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	759	714	1	ENST00000171111.5:c.380G>T	p.Gly127Val	p.G127V	ENST00000171111	NM_203500.1	127	gGt/gTt	2/6	0.724971253142573	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.730374091422004	2		715	1038	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543638	29543638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772615782	NA	P-0031241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	308	549	0	ENST00000389048.3:c.1525G>A	p.Ala509Thr	p.A509T	ENST00000389048	NM_004304.4	509	Gcc/Acc	7/29	1	2	FACETS	0.927	0.876	0.978	0.927	0.876	0.978	CLONAL	1	TRUE	1	0.730374091422004	2		549	910	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520192	9520192	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	253	427	1	ENST00000353224.5:c.2077G>T	p.Glu693Ter	p.E693*	ENST00000353224	NM_177990.2	693	Gaa/Taa	10/10	1	2	FACETS	0.906	0.851	0.961	0.906	0.851	0.961	CLONAL	1	TRUE	1	0.730374091422004	2		428	765	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602910	55602910	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	492	368	0	ENST00000288135.5:c.2620C>A	p.Pro874Thr	p.P874T	ENST00000288135	NM_000222.2	874	Ccg/Acg	19/21	0.730374091422004	3	FACETS	1	0.97	1			1	CLONAL	2	TRUE	NA	0.730374091422004	3		368	913	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057520000	NA	P-0031242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	838	804	1	ENST00000269305.4:c.452C>A	p.Pro151His	p.P151H	ENST00000269305	NM_001126112.2	151	cCc/cAc	5/11	0.902823015687817	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.905283957351247	2		805	902	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182140	11182140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	375	723	1	ENST00000361445.4:c.6706C>T	p.Leu2236Phe	p.L2236F	ENST00000361445	NM_004958.3	2236	Ctc/Ttc	48/58	0.905283957351247	3	FACETS	0.99	0.94	1	0.495	0.47	0.521	CLONAL	1	TRUE	1	0.905283957351247	3		724	1216	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632761	23632761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761032954	NA	P-0031242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	287	627	0	ENST00000261584.4:c.3035C>T	p.Thr1012Ile	p.T1012I	ENST00000261584	NM_024675.3	1012	aCt/aTt	10/13	0.90286166392769	2	FACETS	0.919	0.87	0.968	0.459	0.435	0.484	CLONAL	1	TRUE	0	0.905283957351247	2		627	690	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475534	12475534	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	262	699	2	ENST00000287820.6:c.1408C>T	p.Leu470Phe	p.L470F	ENST00000287820	NM_015869.4	470	Ctc/Ttc	7/7	0.902823015687817	2	FACETS	0.844	0.795	0.893	0.422	0.397	0.447	CLONAL	1	TRUE	0	0.905283957351247	2		701	686	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0031248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	448	487	0	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.502892581288327	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.502892581288327	2		487	878	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0031248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	84	246	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.502892581288327	2	FACETS	0.848	0.766	0.931	0.848	0.766	0.931	CLONAL	2	TRUE	0	0.502892581288327	2		246	197	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530058	63530058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	320	597	0	ENST00000307078.5:c.2377G>T	p.Glu793Ter	p.E793*	ENST00000307078	NM_004655.3	793	Gag/Tag	10/11	0.502892581288327	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.502892581288327	2		597	606	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0031249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	90	332	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.256947264214296	3	FACETS	0.862	0.765	0.966	0.431	0.382	0.483	CLONAL	1	TRUE	1	0.33	3		332	737	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579367	7579367	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	278	788	0	ENST00000269305.4:c.320del	p.Tyr107SerfsTer16	p.Y107Sfs*16	ENST00000269305	NM_001126112.2	107	tAc/tc	4/11	0.291126502985869	2	FACETS	0.916	0.862	0.971	0.916	0.862	0.971	CLONAL	2	TRUE	0	0.33	2		788	920	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	134	270	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.941	0.865	1	0.941	0.865	1	CLONAL	1	TRUE	1	0.767763621771246	2		270	371	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0031250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	231	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.996	0.936	1	0.996	0.936	1	CLONAL	1	TRUE	1	0.767763621771246	2		336	604	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866297	42866297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61735793	NA	P-0031250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	51	614	0	ENST00000398585.3:c.335C>T	p.Thr112Ile	p.T112I	ENST00000398585	NM_001135099.1	112	aCa/aTa	3/14	1	2	FACETS	0.17	0.144	0.199	0.17	0.144	0.199	SUBCLONAL	1	TRUE	1	0.767763621771246	2		614	781	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023905	27023905	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	99	92	0	ENST00000324856.7:c.1011G>A	p.Trp337Ter	p.W337*	ENST00000324856	NM_006015.4	337	tgG/tgA	1/20	1	2	FACETS	1	0.964	1	1	0.991	1	CLONAL	4	FALSE	1	0.201493703152757	2		92	221	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0031253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	41	345	2	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.641207314868408	2	FACETS	1	0.918	1	0.556	0.476	0.64	CLONAL	1	TRUE	0	0.641207314868408	2		347	115	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	60	384	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.803	0.701	0.912	0.803	0.701	0.912	CLONAL	1	TRUE	1	0.641207314868408	2		384	233	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604790	48604790	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1568211615	NA	P-0031253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	62	419	1	ENST00000342988.3:c.1612G>T	p.Glu538Ter	p.E538*	ENST00000342988	NM_005359.5	538	Gaa/Taa	12/12	0.342941323129904	1	FACETS	0.848	0.75	0.947	0.848	0.75	0.947	INDETERMINATE	1	TRUE	0	0.641207314868408	1		420	155	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175481	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0031253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	43	253	0	ENST00000257430.4:c.4192_4193del	p.Arg1399PhefsTer9	p.R1399Ffs*9	ENST00000257430	NM_000038.5	1397	GAg/g	16/16	0.641207314868408	2	FACETS	1	0.886	1	0.52	0.445	0.598	CLONAL	1	TRUE	0	0.641207314868408	2		253	129	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982395	201982395	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	256	878	1	ENST00000359651.3:c.774G>A	p.Trp258Ter	p.W258*	ENST00000359651		258	tgG/tgA	6/8	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.641207314868408	2		879	787	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0031255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	76	562	3	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.203965915552665	2		565	653	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577599	7577600	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1567550002	NA	P-0031255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	57	600	1	ENST00000269305.4:c.681dup	p.Asp228Ter	p.D228*	ENST00000269305	NM_001126112.2	227	-/T	7/11	0.203965915552665	1	FACETS	0.904	0.776	1	0.904	0.776	1	CLONAL	1	TRUE	0	0.203965915552665	1		601	555	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584607	48584607	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	50	518	0	ENST00000342988.3:c.780C>A	p.Tyr260Ter	p.Y260*	ENST00000342988	NM_005359.5	260	taC/taA	6/12	0.203965915552665	1	FACETS	0.927	0.787	1	0.927	0.787	1	CLONAL	1	TRUE	0	0.203965915552665	1		518	475	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991668	25991668	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	59	459	1	ENST00000435504.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000435504		192	Cag/Tag	7/13	1	2	FACETS	0.977	0.841	1	0.977	0.841	1	CLONAL	1	TRUE	1	0.203965915552665	2		460	592	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115725	8115728	+	frameshift_variant	Frame_Shift_Del	DEL	GAAG	GAAG	-	novel	NA	P-0031261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	32	494	0	ENST00000346208.3:c.1076_1079del	p.Glu359AlafsTer44	p.E359Afs*44	ENST00000346208		357	aaGAAG/aa	6/6	0.257951268644444	1	FACETS	0.215	0.175	0.261	0.215	0.175	0.261	INDETERMINATE	1	TRUE	0	0.569540885611186	1		494	373	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374775	118374775	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	101	499	0	ENST00000534358.1:c.8168T>A	p.Val2723Asp	p.V2723D	ENST00000534358	NM_005933.3	2723	gTt/gAt	27/36	0.48075502465777	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.569540885611186	1		499	244	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11114017	11114017	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	67	626	0	ENST00000358026.2:c.1945T>A	p.Tyr649Asn	p.Y649N	ENST00000358026	NM_001128849.1	649	Tat/Aat	13/36	0.299434912117033	0	FACETS	0.302	0.264	0.343			1	INDETERMINATE	1	TRUE	0	0.569540885611186	0		626	335	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294033	1294033	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139342764	NA	P-0031261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	133	1048	1	ENST00000310581.5:c.968C>T	p.Pro323Leu	p.P323L	ENST00000310581	NM_198253.2	323	cCg/cTg	2/16	0.286222799819969	1	FACETS	0.404	0.367	0.444	0.404	0.367	0.444	INDETERMINATE	1	TRUE	0	0.569540885611186	1		1049	826	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846083	68846083	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	202	697	0	ENST00000261769.5:c.1055del	p.Gly352ValfsTer4	p.G352Vfs*4	ENST00000261769	NM_004360.3	352	Ggt/gt	8/16	0.381348917536984	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.381348917536984	1		697	757	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152864462	152864462	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	35	73	0	ENST00000406277.2:c.64G>C	p.Ala22Pro	p.A22P	ENST00000406277	NM_152274.4	22	Gcc/Ccc	3/7	0.356462848249593		FACETS		0.703	0.989				CLONAL	2	TRUE	1	0.381348917536984	3		73	130	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0031263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	49	562	3	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.879	0.75	1	0.879	0.75	1	CLONAL	1	TRUE	1	0.411564852155148	2		565	271	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971000	21971000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	64	571	0	ENST00000304494.5:c.358G>T	p.Glu120Ter	p.E120*	ENST00000304494	NM_000077.4	120	Gag/Tag	2/3	1	2	FACETS	0.957	0.835	1	0.957	0.835	1	CLONAL	1	TRUE	1	0.411564852155148	2		571	325	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578369	7578370	+	splice_donor_variant	Splice_Site	INS	-	-	CCATCGTTATCTGAGCAGCGCTCATGGTGGGGGCAGCGCCTCACAACCTCCG	novel	NA	P-0031263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	26	689	0	ENST00000269305.4:c.559+1_559+2insCGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAACGATGG		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.411564852155148	1	FACETS	0.315	0.249	0.389	0.315	0.249	0.389	SUBCLONAL	1	TRUE	0	0.411564852155148	1		689	319	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971035	21971036	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CG	novel	NA	P-0031263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	47	411	0	ENST00000304494.5:c.321_322dup	p.Asp108AlafsTer39	p.D108Afs*39	ENST00000304494	NM_000077.4	108	gat/gCGat	2/3	1				0.846	1				CLONAL	1	TRUE	1	0.411564852155148	2		411	230	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929443	44929452	+	frameshift_variant	Frame_Shift_Del	DEL	ACAGTGGGCT	ACAGTGGGCT	-	novel	NA	P-0031263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	55	820	0	ENST00000377967.4:c.2546_2555del	p.Ser849ThrfsTer15	p.S849Tfs*15	ENST00000377967	NM_021140.2	848	cACAGTGGGCTa/ca	17/29	1	2	FACETS	0.798	0.686	0.919	0.798	0.686	0.919	CLONAL	1	TRUE	1	0.411564852155148	2		820	335	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	368	270	0				ENST00000310581	NM_198253.2	-/1132			0.213087310573738	6	FACETS	1	0.99	1	1	0.996	1	INDETERMINATE	4	TRUE	3	0.470467430391915	6		270	686	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578266	7578266	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs942158624	NA	P-0031266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	164	623	0	ENST00000269305.4:c.583A>T	p.Ile195Phe	p.I195F	ENST00000269305	NM_001126112.2	195	Atc/Ttc	6/11	0.470467430391915	3	FACETS	1	0.963	1	0.542	0.498	0.587	CLONAL	1	TRUE	1	0.470467430391915	3		623	795	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938577	44938577	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0031266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	142	274	0	ENST00000377967.4:c.3125C>G	p.Ser1042Ter	p.S1042*	ENST00000377967	NM_021140.2	1042	tCa/tGa	20/29	0.363761966354694	2	FACETS	0.883	0.828	0.936			1	CLONAL	3	TRUE	NA	0.470467430391915	2		274	228	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319902	8319902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	76	401	0	ENST00000356435.5:c.5599G>A	p.Glu1867Lys	p.E1867K	ENST00000356435		1867	Gaa/Aaa	34/35	0.470467430391915	3	FACETS	0.869	0.765	0.981	0.435	0.382	0.491	CLONAL	1	TRUE	1	0.470467430391915	3		401	459	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714556	52714556	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1489963266	NA	P-0031266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	498	508	0	ENST00000322088.6:c.314G>A	p.Arg105Gln	p.R105Q	ENST00000322088	NM_014225.5	105	cGg/cAg	4/15	0.239713460039969	3	FACETS	1	0.99	1			1	INDETERMINATE	3	TRUE	NA	0.470467430391915	3		508	823	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847225	68847225	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782798	NA	P-0031266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	340	380	1	ENST00000261769.5:c.1147C>T	p.Gln383Ter	p.Q383*	ENST00000261769	NM_004360.3	383	Cag/Tag	9/16	0.470467430391915	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	3	TRUE	0	0.470467430391915	3		381	589	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039464	49039464	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	90	521	1	ENST00000267163.4:c.2449G>T	p.Glu817Ter	p.E817*	ENST00000267163	NM_000321.2	817	Gaa/Taa	23/27	0.373409720078737	0	FACETS	0.656	0.588	0.726			1	SUBCLONAL	1	TRUE	0	0.470467430391915	0		522	309	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012689	36012689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1406297899	NA	P-0031266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	66	24	0	ENST00000358208.4:c.133G>A	p.Asp45Asn	p.D45N	ENST00000358208		45	Gac/Aac	2/12	0.213087310573738	6	FACETS	1	0.936	1	1	0.936	1	INDETERMINATE	3	TRUE	3	0.470467430391915	6		24	168	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258616	16258616	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745908478	NA	P-0031266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	117	408	1	ENST00000375759.3:c.5881G>A	p.Asp1961Asn	p.D1961N	ENST00000375759	NM_015001.2	1961	Gat/Aat	11/15	0.213087310573738	6	FACETS	1	0.962	1	0.379	0.341	0.418	INDETERMINATE	1	TRUE	3	0.470467430391915	6		409	850	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736590	85736590	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0031266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	51	206	0	ENST00000370580.1:c.58-1G>A		p.X20_splice	ENST00000370580	NM_003921.4	20			0.213087310573738	6	FACETS	1	0.945	1	0.797	0.689	0.911	INDETERMINATE	2	TRUE	3	0.470467430391915	6		206	176	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99486250	99486250	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	295	551	0	ENST00000268035.6:c.3556G>A	p.Asp1186Asn	p.D1186N	ENST00000268035	NM_000875.3	1186	Gat/Aat	19/21	0.470467430391915	6	FACETS	0.969	0.911	1	0.484	0.455	0.514	CLONAL	2	TRUE	2	0.470467430391915	6		551	1256	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845689	68845689	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	498	555	1	ENST00000261769.5:c.935C>A	p.Pro312His	p.P312H	ENST00000261769	NM_004360.3	312	cCt/cAt	7/16	0.470467430391915	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	TRUE	0	0.470467430391915	3		556	867	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242470	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs397517097	NA	P-0031267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	102	617	0	ENST00000275493.2:c.2240T>C	p.Leu747Ser	p.L747S	ENST00000275493	NM_005228.3	747	tTa/tCa	19/28	0.19337835357081	3	FACETS	1	0.974	1	0.65	0.58	0.724	CLONAL	1	TRUE	1	0.199096046126308	3		617	867	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241706	55241707	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0031267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	90	747	1	ENST00000275493.2:c.2154_2155delinsTT	p.Gly719Cys	p.G719C	ENST00000275493	NM_005228.3	718	ctGGgc/ctTTgc	18/28	0.19337835357081	3	FACETS	1	0.965	1	0.613	0.543	0.688	CLONAL	1	TRUE	1	0.199096046126308	3		748	811	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972740	32972740	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	52	623	0	ENST00000380152.3:c.10090T>G	p.Ser3364Ala	p.S3364A	ENST00000380152		3364	Tct/Gct	27/27	1	2	FACETS	0.788	0.67	0.918	0.788	0.67	0.918	CLONAL	1	TRUE	1	0.199096046126308	2		623	663	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020983	26020983	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	50	456	0	ENST00000357647.3:c.266C>A	p.Ala89Asp	p.A89D	ENST00000357647	NM_003529.2	89	gCt/gAt	1/1	0.199096046126308	3	FACETS	1	0.874	1	0.517	0.439	0.603	CLONAL	1	TRUE	1	0.199096046126308	3		456	534	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0031270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	52	498	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.179856343366564	4	FACETS	0.826	0.709	0.953	0.826	0.709	0.953	CLONAL	2	FALSE	2	0.288528298400632	4		498	281	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508860	106508860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1251220989	NA	P-0031270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	49	649	1	ENST00000359195.3:c.854C>T	p.Thr285Met	p.T285M	ENST00000359195	NM_002649.2	285	aCg/aTg	2/11	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.288528298400632	2		650	265	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349488	73349488	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0031270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	50	550	0	ENST00000377767.4:c.848T>G	p.Leu283Ter	p.L283*	ENST00000377767	NM_014953.3	283	tTa/tGa	6/21	0.179856343366564	4	FACETS	1	0.929	1	0.58	0.493	0.674	CLONAL	1	FALSE	2	0.288528298400632	4		550	385	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060751	38060756	+	inframe_deletion	In_Frame_Del	DEL	TGCTGC	TGCTGC	-	novel	NA	P-0031270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	394	1138	0	ENST00000250448.2:c.1233_1238del	p.Gln411_Gln412del	p.Q411_Q412del	ENST00000250448	NM_004496.3	411	caGCAGCAt/cat	2/2	0.179856343366564	4	FACETS	0.879	0.835	0.923	1	0.994	1	CLONAL	3	FALSE	2	0.288528298400632	4		1138	1335	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324185	62324185	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	66	948	1	ENST00000360203.5:c.2680G>A	p.Asp894Asn	p.D894N	ENST00000360203	NM_001283009.1	894	Gac/Aac	29/35	0.215878240881956	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	0	0.288528298400632	1		949	331	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817460	39817460	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	215	674	0	ENST00000288319.7:c.103G>T	p.Ala35Ser	p.A35S	ENST00000288319	NM_182918.3	35	Gcg/Tcg	2/10	1	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	FALSE	1	0.288528298400632	2		674	603	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0031271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	114	435	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.952	1	1	0.992	1	CLONAL	4	FALSE	1	0.15513596161728	2		435	344	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863356	57863356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	224	894	0	ENST00000228682.2:c.1451G>A	p.Gly484Glu	p.G484E	ENST00000228682	NM_005269.2	484	gGa/gAa	11/12	1	2	FACETS	0.947	0.888	1	1	0.996	1	CLONAL	5	FALSE	1	0.15513596161728	2		894	610	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0031271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	183	610	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.951	1	1	0.995	1	CLONAL	4	FALSE	1	0.15513596161728	2		611	572	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0031271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	87	483	0	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS	0.97	0.87	1	1	0.99	1	CLONAL	4	FALSE	1	0.15513596161728	2		483	289	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0031271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	188	632	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.971	0.906	1	1	0.995	1	CLONAL	5	FALSE	1	0.15513596161728	2		632	499	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0031271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	96	287	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.931	0.842	1	1	0.991	1	CLONAL	5	FALSE	1	0.15513596161728	2		287	266	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70412302	70412302	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	141	509	0	ENST00000373644.4:c.4412A>G	p.Tyr1471Cys	p.Y1471C	ENST00000373644	NM_030625.2	1471	tAc/tGc	6/12	1	2	FACETS	1	0.961	1	1	0.994	1	CLONAL	4	FALSE	1	0.15513596161728	2		509	423	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0031271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	111	426	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	0.994	0.903	1	1	0.992	1	CLONAL	4	FALSE	1	0.15513596161728	2		426	360	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0031271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	109	372	3	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	0.912	0.827	1	1	0.991	1	CLONAL	4	FALSE	1	0.15513596161728	2		375	385	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059170	42059170	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs756744691	NA	P-0031271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	118	555	5	ENST00000219905.7:c.8895del	p.Thr2966ProfsTer4	p.T2966Pfs*4	ENST00000219905	NM_001164273.1	2964	Ccc/cc	24/24	1	2	FACETS	0.996	0.907	1	1	0.992	1	CLONAL	4	FALSE	1	0.15513596161728	2		560	382	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56855485	56855485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs79070284	NA	P-0031271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	135	555	0	ENST00000308159.5:c.634G>A	p.Val212Ile	p.V212I	ENST00000308159	NM_014669.4	212	Gtc/Atc	7/22	1	2	FACETS	0.912	0.835	0.992	1	0.993	1	CLONAL	4	FALSE	1	0.15513596161728	2		555	477	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251647	212251647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	104	518	0	ENST00000342788.4:c.3412G>A	p.Glu1138Lys	p.E1138K	ENST00000342788	NM_005235.2	1138	Gaa/Aaa	27/28	0.135597964578492	0	FACETS	1	0.933	1			1	CLONAL	3	FALSE	0	0.15513596161728	0		518	363	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319391	62319391	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760398738	NA	P-0031271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	260	867	2	ENST00000360203.5:c.1583C>T	p.Ala528Val	p.A528V	ENST00000360203	NM_001283009.1	528	gCg/gTg	18/35	0.135597964578492	0	FACETS	1	0.953	1			1	CLONAL	4	FALSE	0	0.15513596161728	0		869	699	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549713	187549713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	30	561	1	ENST00000441802.2:c.4528G>A	p.Ala1510Thr	p.A1510T	ENST00000441802	NM_005245.3	1510	Gca/Aca	8/27	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	FALSE	1	0.15513596161728	2		562	358	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134987	41134987	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	58	334	0	ENST00000379561.5:c.641G>A	p.Arg214His	p.R214H	ENST00000379561	NM_002015.3	214	cGt/cAt	2/3	1	2	FACETS	1	0.941	1	1	0.984	1	CLONAL	3	FALSE	1	0.15513596161728	2		334	217	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099090	27099091	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0031271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	156	698	0	ENST00000324856.7:c.3510_3511del	p.His1170GlnfsTer22	p.H1170Qfs*22	ENST00000324856	NM_006015.4	1169	cCA/c	13/20	1	2	FACETS	1	0.932	1	1	0.994	1	CLONAL	4	FALSE	1	0.15513596161728	2		698	497	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625302	69625302	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782573423	NA	P-0031271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	195	956	1	ENST00000334134.2:c.491G>A	p.Arg164His	p.R164H	ENST00000334134	NM_005247.2	164	cGc/cAc	3/3	1	2	FACETS	0.912	0.851	0.975	1	0.995	1	CLONAL	5	FALSE	1	0.15513596161728	2		957	551	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008044	29008044	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0031271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	107	472	0	ENST00000282397.4:c.725T>A	p.Leu242Ter	p.L242*	ENST00000282397	NM_002019.4	242	tTa/tAa	6/30	1	2	FACETS	1	0.96	1	1	0.992	1	CLONAL	4	FALSE	1	0.15513596161728	2		472	313	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435208	110435208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	204	565	1	ENST00000375856.3:c.3193G>A	p.Asp1065Asn	p.D1065N	ENST00000375856	NM_003749.2	1065	Gac/Aac	1/2	1	2	FACETS	0.948	0.886	1	1	0.996	1	CLONAL	5	FALSE	1	0.15513596161728	2		566	555	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829114	72829115	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0031271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	99	622	1	ENST00000268489.5:c.7466dup	p.Pro2490SerfsTer44	p.P2490Sfs*44	ENST00000268489	NM_006885.3	2489	cct/ccCt	9/10	1	2	FACETS	1	0.955	1	1	0.99	1	CLONAL	3	FALSE	1	0.15513596161728	2		623	383	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923808	72923808	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	167	779	0	ENST00000268489.5:c.3270C>A	p.Cys1090Ter	p.C1090*	ENST00000268489	NM_006885.3	1090	tgC/tgA	4/10	1	2	FACETS	1	0.974	1	1	0.995	1	CLONAL	4	FALSE	1	0.15513596161728	2		779	484	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298713	15298713	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	50	993	0	ENST00000263388.2:c.1585T>C	p.Tyr529His	p.Y529H	ENST00000263388	NM_000435.2	529	Tac/Cac	10/33	1	2	FACETS	0.846	0.716	0.989	0.846	0.716	0.989	CLONAL	1	FALSE	1	0.15513596161728	2		993	762	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905875	50905875	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	206	927	1	ENST00000440232.2:c.847C>T	p.Gln283Ter	p.Q283*	ENST00000440232	NM_002691.3	283	Cag/Tag	8/27	1	2	FACETS	1	0.978	1	1	0.996	1	CLONAL	4	FALSE	1	0.15513596161728	2		928	599	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266194	41266194	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1330746638	NA	P-0031271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	141	430	0	ENST00000349496.5:c.191A>G	p.Tyr64Cys	p.Y64C	ENST00000349496	NM_001904.3	64	tAt/tGt	3/15	1	2	FACETS	1	0.927	1	1	0.994	1	CLONAL	5	FALSE	1	0.15513596161728	2		430	362	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86642543	86642543	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0031271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	56	431	0	ENST00000274376.6:c.1102+2T>C		p.X368_splice	ENST00000274376	NM_002890.2	368			1	2	FACETS	0.963	0.833	1	1	0.982	1	CLONAL	3	FALSE	1	0.15513596161728	2		431	250	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339542	116339542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1203410917	NA	P-0031271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	83	446	0	ENST00000397752.3:c.404G>A	p.Ser135Asn	p.S135N	ENST00000397752	NM_000245.2	135	aGc/aAc	2/21	1	2	FACETS	0.918	0.824	1	1	0.99	1	CLONAL	5	FALSE	1	0.15513596161728	2		446	233	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842259	151842259	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	151	515	0	ENST00000262189.6:c.14153A>G	p.His4718Arg	p.H4718R	ENST00000262189	NM_170606.2	4718	cAt/cGt	54/59	1	2	FACETS	0.947	0.875	1	1	0.994	1	CLONAL	5	FALSE	1	0.15513596161728	2		515	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0031274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	263	595	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.320012275444799	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.320012275444799	2		595	701	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	82	354	0	ENST00000397062.3:c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	NM_006164.4	34	Cga/Gga	2/5	0.320012275444799	2	FACETS	1	0.97	1	0.645	0.572	0.723	CLONAL	1	TRUE	0	0.320012275444799	2		354	397	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852060	63852060	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	32	557	0	ENST00000279873.7:c.2838G>C	p.Gln946His	p.Q946H	ENST00000279873	NM_032199.2	946	caG/caC	10/10	1	2	FACETS	0.317	0.257	0.386	0.317	0.257	0.386	SUBCLONAL	1	TRUE	1	0.320012275444799	2		557	630	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060925	38060925	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0031274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	35	338	0	ENST00000250448.2:c.1064C>G	p.Ser355Ter	p.S355*	ENST00000250448	NM_004496.3	355	tCa/tGa	2/2	1	2	FACETS	0.588	0.482	0.706	0.588	0.482	0.706	SUBCLONAL	1	TRUE	1	0.320012275444799	2		338	372	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81534654	81534654	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0031274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	101	453	0	ENST00000298171.2:c.299T>A	p.Leu100Ter	p.L100*	ENST00000298171	NM_000369.2	100	tTg/tAg	3/10	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.320012275444799	2		453	555	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470572	25470572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	121	734	0	ENST00000264709.3:c.902G>A	p.Arg301Gln	p.R301Q	ENST00000264709	NM_175629.2	301	cGg/cAg	8/23	0.320012275444799	3	FACETS	0.959	0.865	1	0.479	0.432	0.529	CLONAL	1	TRUE	1	0.320012275444799	3		734	915	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076860	41076860	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	86	390	0	ENST00000373198.4:c.1560G>T	p.Glu520Asp	p.E520D	ENST00000373198	NM_133170.3	520	gaG/gaT	9/32	0.104912177357697	5	FACETS	1	0.976	1	0.356	0.315	0.399	INDETERMINATE	1	TRUE	1	0.320012275444799	5		390	559	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799975	72799975	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	127	289	0	ENST00000325599.8:c.1194G>T	p.Leu398Phe	p.L398F	ENST00000325599	NM_018130.2	398	ttG/ttT	11/11	0.320012275444799	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.320012275444799	2		289	337	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143226656	143226656	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1345451681	NA	P-0031274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	67	407	0	ENST00000262992.4:c.458G>A	p.Gly153Glu	p.G153E	ENST00000262992	NM_001101669.1	153	gGa/gAa	7/24	0.320012275444799	2	FACETS	0.81	0.705	0.923	0.405	0.352	0.462	CLONAL	1	TRUE	0	0.320012275444799	2		407	517	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517741	187517741	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758283398	NA	P-0031274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	46	200	0	ENST00000441802.2:c.12953C>T	p.Ser4318Phe	p.S4318F	ENST00000441802	NM_005245.3	4318	tCt/tTt	25/27	0.320012275444799	2	FACETS	1	0.923	1	0.573	0.486	0.667	CLONAL	1	TRUE	0	0.320012275444799	2		200	251	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32814973	32814973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	41	486	0	ENST00000354258.4:c.2092G>A	p.Glu698Lys	p.E698K	ENST00000354258	NM_000593.5	698	Gag/Aag	10/11	0.320012275444799	2	FACETS	0.5	0.416	0.594	0.25	0.208	0.297	SUBCLONAL	1	TRUE	0	0.320012275444799	2		486	512	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0031275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	126	562	3	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.161211883927322	0	FACETS	0.951	0.872	1			1	CLONAL	4	TRUE	0	0.16104031785834	0		565	345	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0031275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	481	651	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.161211883927322	0	FACETS	0.878	0.854	0.902			1	CLONAL	9	TRUE	0	0.16104031785834	0		651	634	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0031276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	85	193	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.743	0.659	0.832	0.743	0.659	0.832	SUBCLONAL	1	TRUE	1	0.482566600585192	2		193	474	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0031276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	176	470	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.482566600585192	2		471	522	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215865	133215865	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	143	328	0	ENST00000320574.5:c.5398G>C	p.Val1800Leu	p.V1800L	ENST00000320574	NM_006231.2	1800	Gtg/Ctg	40/49	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.482566600585192	2		328	503	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936085	178936085	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	90	462	0	ENST00000263967.3:c.1627A>T	p.Ile543Phe	p.I543F	ENST00000263967	NM_006218.2	543	Atc/Ttc	10/21	1	2	FACETS	0.757	0.674	0.844	0.757	0.674	0.844	SUBCLONAL	1	TRUE	1	0.482566600585192	2		462	493	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268642	55269477	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TATTTGAATCTCATGTAGGGGCTTTCAAGCATCAAAGGATGGTTCATGTTTTATTTTAAGGCACCCACATCATGTCATGAGGGGAGGCAGCTATAATTTAGAGAACCAAGGGGGATTTCATTATAACAAAATTGGCAAACACACAGGCACCTGCTGGCAATAGACCCCTGCTCCTATAGCCAAGAAGTGGAATAGCATCTCTACGGGCCATTCTAATAGCCTCAAAATCTCTGCACCAGGGGGATGAAAGAATGCATTTGCCAAGTCCTACAGACTCCAACTTCTACCGTGCCCTGATGGATGAAGAAGACATGGACGACGTGGTGGATGCCGACGAGTACCTCATCCCACAGCAGGGCTTCTTCAGCAGCCCCTCCACGTCACGGACTCCCCTCCTGAGCTCTCTGGTATGAAATCTCTGTCTCTCTCTCTCTCTCAAGCTGTGTCTACTCATTTGAACAAATTGAATTTTAGGGAAAATAACCATCTAGTGAAACTCACATGGATATGAAGTCAATTTTAACCAAATGGTAAAATCAAAATCAAAATAAATTAAGTGTATTAATTATTTTGTTGCATTGCAACAACTTGATTGTAAGCCTTTTAGGTCCACTATGGAATGTAATTAAATCAAAACTAAACCTAGTTGCTCTAAAACTAACGATTAAGACAAAAATTAAACACCTTCACAATATACCCTCCATGAGGCACACCACCTGCATTCAGGAAAAGTGGATGAGATGTGGTACAAGCATTCCATGGGCAACTTCTCTGTTTCTTTTTCAGAGTGCAACCAGCAACAATTCCACCGTGGCTTGCATTGATAGAAATGGGGT	TATTTGAATCTCATGTAGGGGCTTTCAAGCATCAAAGGATGGTTCATGTTTTATTTTAAGGCACCCACATCATGTCATGAGGGGAGGCAGCTATAATTTAGAGAACCAAGGGGGATTTCATTATAACAAAATTGGCAAACACACAGGCACCTGCTGGCAATAGACCCCTGCTCCTATAGCCAAGAAGTGGAATAGCATCTCTACGGGCCATTCTAATAGCCTCAAAATCTCTGCACCAGGGGGATGAAAGAATGCATTTGCCAAGTCCTACAGACTCCAACTTCTACCGTGCCCTGATGGATGAAGAAGACATGGACGACGTGGTGGATGCCGACGAGTACCTCATCCCACAGCAGGGCTTCTTCAGCAGCCCCTCCACGTCACGGACTCCCCTCCTGAGCTCTCTGGTATGAAATCTCTGTCTCTCTCTCTCTCTCAAGCTGTGTCTACTCATTTGAACAAATTGAATTTTAGGGAAAATAACCATCTAGTGAAACTCACATGGATATGAAGTCAATTTTAACCAAATGGTAAAATCAAAATCAAAATAAATTAAGTGTATTAATTATTTTGTTGCATTGCAACAACTTGATTGTAAGCCTTTTAGGTCCACTATGGAATGTAATTAAATCAAAACTAAACCTAGTTGCTCTAAAACTAACGATTAAGACAAAAATTAAACACCTTCACAATATACCCTCCATGAGGCACACCACCTGCATTCAGGAAAAGTGGATGAGATGTGGTACAAGCATTCCATGGGCAACTTCTCTGTTTCTTTTTCAGAGTGCAACCAGCAACAATTCCACCGTGGCTTGCATTGATAGAAATGGGGT	-	novel	NA	P-0031276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9416	13973	746	0	ENST00000275493.2:c.2947-239_3162+2del		p.X983_splice	ENST00000275493	NM_005228.3	983		25-26/28	0.482566600585192	39	FACETS	0.983	0.976	0.99	0.63	0.626	0.635	CLONAL	25	TRUE	0	0.482566600585192	39		746	23389	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0031277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	50	562	3	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.278107895378079	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.278107895378079	1		565	242	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577560	7577560	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520002	NA	P-0031277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	37	640	0	ENST00000269305.4:c.721T>C	p.Ser241Pro	p.S241P	ENST00000269305	NM_001126112.2	241	Tcc/Ccc	7/11	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.278107895378079	2		640	233	SUCCESS
APC	324	MSKCC	GRCh37	5	112175419	112175419	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0031277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	19	338	0	ENST00000257430.4:c.4128T>G	p.Tyr1376Ter	p.Y1376*	ENST00000257430	NM_000038.5	1376	taT/taG	16/16	1	2	FACETS	1	0.787	1	1	0.787	1	CLONAL	1	TRUE	1	0.278107895378079	2		338	133	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832095	72832095	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	11	525	0	ENST00000268489.5:c.4486G>C	p.Glu1496Gln	p.E1496Q	ENST00000268489	NM_006885.3	1496	Gag/Cag	9/10	1	2	FACETS	0.404	0.279	0.558	0.404	0.279	0.558	SUBCLONAL	1	TRUE	1	0.278107895378079	2		525	196	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554669	63554669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	19	459	0	ENST00000307078.5:c.70C>A	p.Pro24Thr	p.P24T	ENST00000307078	NM_004655.3	24	Ccc/Acc	2/11	1	2	FACETS	0.818	0.625	1	0.818	0.625	1	CLONAL	1	TRUE	1	0.278107895378079	2		459	167	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120192	70120193	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0031277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	15	550	0	ENST00000245479.2:c.1195_1196dup	p.Glu400ArgfsTer4	p.E400Rfs*4	ENST00000245479	NM_000346.3	398	-/AC	3/3	1	2	FACETS	0.459	0.336	0.607	0.459	0.336	0.607	SUBCLONAL	1	TRUE	1	0.278107895378079	2		550	235	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177626	56177626	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	18	396	0	ENST00000399503.3:c.2599G>T	p.Glu867Ter	p.E867*	ENST00000399503	NM_005921.1	867	Gaa/Taa	14/20	1	2	FACETS	0.748	0.566	0.96	0.748	0.566	0.96	CLONAL	1	TRUE	1	0.278107895378079	2		396	173	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0031281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	49	505	4	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.0324949618219983	3	FACETS	1	0.962	1	0.717	0.614	0.827	INDETERMINATE	1	FALSE	1	0.374039831425968	3		509	217	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0031281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	49	538	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.0324949618219983	3	FACETS	0.766	0.657	0.882	0.766	0.657	0.882	INDETERMINATE	2	FALSE	1	0.374039831425968	3		538	203	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	49	351	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	0.374039831425968	1	FACETS	0.959	0.822	1	0.959	0.822	1	CLONAL	1	FALSE	0	0.374039831425968	1		351	222	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591977	48591977	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0031281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	10	230	0	ENST00000342988.3:c.1139+1G>T		p.X380_splice	ENST00000342988	NM_005359.5	380			0.374039831425968	1	FACETS	0.58	0.398	0.8	0.58	0.398	0.8	SUBCLONAL	1	FALSE	0	0.374039831425968	1		230	75	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100988	27100988	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	42	565	0	ENST00000324856.7:c.4270C>T	p.Gln1424Ter	p.Q1424*	ENST00000324856	NM_006015.4	1424	Cag/Tag	18/20	1	2	FACETS	0.802	0.673	0.943	0.802	0.673	0.943	CLONAL	1	FALSE	1	0.374039831425968	2		565	280	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933303	100933303	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	17	528	0	ENST00000325455.5:c.2087C>T	p.Pro696Leu	p.P696L	ENST00000325455	NM_001202474.3	696	cCa/cTa	4/8	1	2	FACETS	0.417	0.312	0.541	0.417	0.312	0.541	SUBCLONAL	1	FALSE	1	0.374039831425968	2		528	218	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322633	30322633	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	35	527	0	ENST00000322652.5:c.1646G>T	p.Gly549Val	p.G549V	ENST00000322652	NM_015355.2	549	gGg/gTg	14/16	0.374039831425968	2	FACETS	0.965	0.799	1	0.482	0.399	0.574	CLONAL	1	FALSE	0	0.374039831425968	2		527	194	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302395	15302395	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	24	776	0	ENST00000263388.2:c.876C>G	p.Phe292Leu	p.F292L	ENST00000263388	NM_000435.2	292	ttC/ttG	6/33	1	2	FACETS	0.354	0.277	0.442	0.354	0.277	0.442	SUBCLONAL	1	FALSE	1	0.374039831425968	2		776	363	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793431	242793431	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	50	568	1	ENST00000334409.5:c.646G>T	p.Val216Leu	p.V216L	ENST00000334409	NM_005018.2	216	Gtg/Ttg	5/5	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	FALSE	1	0.374039831425968	2		569	257	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098368	47098368	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0031281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	33	449	0	ENST00000409792.3:c.6906T>A	p.Cys2302Ter	p.C2302*	ENST00000409792	NM_014159.6	2302	tgT/tgA	15/21	0.0324949618219983	3	FACETS	1	0.838	1	0.511	0.419	0.612	INDETERMINATE	1	FALSE	1	0.374039831425968	3		449	205	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164136	47164136	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0031281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	15	345	0	ENST00000409792.3:c.1990A>T	p.Arg664Ter	p.R664*	ENST00000409792	NM_014159.6	664	Aga/Tga	3/21	0.0324949618219983	3	FACETS	0.716	0.528	0.938	0.358	0.264	0.469	INDETERMINATE	1	FALSE	1	0.374039831425968	3		345	133	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507435	8507435	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0031281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	16	223	0	ENST00000356435.5:c.1544-1G>T		p.X515_splice	ENST00000356435		515			1	2	FACETS	0.92	0.691	1	0.92	0.691	1	CLONAL	1	FALSE	1	0.374039831425968	2		223	93	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0031284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	142	349	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.600844379653686	2		349	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs17849781	NA	P-0031284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	236	684	0	ENST00000269305.4:c.832C>A	p.Pro278Thr	p.P278T	ENST00000269305	NM_001126112.2	278	Cct/Act	8/11	1	2	FACETS	0.951	0.89	1	0.951	0.89	1	CLONAL	1	TRUE	1	0.600844379653686	2		684	826	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0031284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	119	329	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.600844379653686	2		329	389	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878077	48878108	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCCACCGCCGCCGCTGCCGCCGCGGAACCC	CCGCCACCGCCGCCGCTGCCGCCGCGGAACCC	-	novel	NA	P-0031284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	113	122	0	ENST00000267163.4:c.32_63del	p.Ala11GlyfsTer9	p.A11Gfs*9	ENST00000267163	NM_000321.2	10	gCCGCCACCGCCGCCGCTGCCGCCGCGGAACCC/g	1/27	0.600844379653686	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.600844379653686	1		122	216	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2206792	2206792	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	338	498	0	ENST00000398665.3:c.852G>T	p.Leu284Phe	p.L284F	ENST00000398665	NM_032482.2	284	ttG/ttT	10/28	0.453208727889556	2	FACETS	0.864	0.825	0.903	0.864	0.825	0.903	CLONAL	2	TRUE	0	0.600844379653686	2		498	651	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878080	48878080	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs899323337	NA	P-0031284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	19	110	0	ENST00000267163.4:c.32C>G	p.Ala11Gly	p.A11G	ENST00000267163	NM_000321.2	11	gCc/gGc	1/27	0.600844379653686	1	FACETS	0.221	0.168	0.283	0.221	0.168	0.283	SUBCLONAL	1	TRUE	0	0.600844379653686	1		110	200	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0031285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	382	487	0	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.957457667428943	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.957457667428943	1		487	395	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206941988	206941988	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376415487	NA	P-0031285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	171	232	0	ENST00000423557.1:c.530G>A	p.Arg177Gln	p.R177Q	ENST00000423557	NM_000572.2	177	cGa/cAa	5/5	0.957457667428943	3	FACETS	0.997	0.923	1	0.498	0.461	0.536	CLONAL	1	TRUE	1	0.957457667428943	3		232	530	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212851	27212851	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760084463	NA	P-0031285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	210	493	1	ENST00000380036.4:c.2833G>A	p.Ala945Thr	p.A945T	ENST00000380036	NM_000459.3	945	Gct/Act	17/23	1	2	FACETS	0.512	0.476	0.549	0.512	0.476	0.549	SUBCLONAL	1	TRUE	1	0.957457667428943	2		494	857	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447770	49447770	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	286	378	0	ENST00000301067.7:c.664G>T	p.Ala222Ser	p.A222S	ENST00000301067	NM_003482.3	222	Gca/Tca	5/54	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.957457667428943	2		378	596	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940565	29940565	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0031285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	269	382	0	ENST00000389048.3:c.668-2A>C		p.X223_splice	ENST00000389048	NM_004304.4	223			1	2	FACETS	0.949	0.899	1	0.949	0.899	1	CLONAL	1	TRUE	1	0.957457667428943	2		382	592	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790165	40790165	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	253	361	0	ENST00000373198.4:c.2566del	p.Glu856SerfsTer22	p.E856Sfs*22	ENST00000373198	NM_133170.3	856	Gag/ag	18/32	1	2	FACETS	0.973	0.92	1	0.973	0.92	1	CLONAL	1	TRUE	1	0.957457667428943	2		361	543	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448500	89448500	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	223	308	1	ENST00000336596.2:c.1464G>T	p.Arg488Ser	p.R488S	ENST00000336596	NM_005233.5	488	agG/agT	7/17	0.957457667428943	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.957457667428943	1		309	235	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825358	134825358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs995446201	NA	P-0031285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	259	329	0	ENST00000398015.3:c.874C>T	p.Arg292Cys	p.R292C	ENST00000398015	NM_004441.4	292	Cgc/Tgc	4/16	0.957457667428943	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.957457667428943	1		329	280	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484595	57484595	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs797045203	NA	P-0031287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	202	448	0	ENST00000371085.3:c.679C>A	p.Gln227Lys	p.Q227K	ENST00000371085	NM_000516.4	227	Cag/Aag	9/13	1	2	FACETS	0.985	0.917	1	0.985	0.917	1	CLONAL	1	TRUE	1	0.619638183142434	2		448	662	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420213	49420213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267607237	NA	P-0031287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	197	703	5	ENST00000301067.7:c.15536G>A	p.Arg5179His	p.R5179H	ENST00000301067	NM_003482.3	5179	cGt/cAt	48/54	1	2	FACETS	0.658	0.609	0.709	0.658	0.609	0.709	SUBCLONAL	1	TRUE	1	0.619638183142434	2		708	966	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436353	49436363	+	frameshift_variant	Frame_Shift_Del	DEL	AGGAACGGGGA	AGGAACGGGGA	TAC	novel	NA	P-0031287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	55	724	2	ENST00000301067.7:c.5848_5858delinsGTA	p.Ser1950ValfsTer4	p.S1950Vfs*4	ENST00000301067	NM_003482.3	1950	TCCCCGTTCCTg/GTAg	27/54	1	2	FACETS	0.195	0.166	0.227	0.195	0.166	0.227	SUBCLONAL	1	TRUE	1	0.619638183142434	2		726	911	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544682	65544683	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0031287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	199	721	0	ENST00000358664.4:c.242_243dup	p.Gln82ThrfsTer89	p.Q82Tfs*89	ENST00000358664	NM_002382.4	81	-/AC	4/5	1	2	FACETS	0.648	0.6	0.698	0.648	0.6	0.698	SUBCLONAL	1	TRUE	1	0.619638183142434	2		721	991	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81971363	81971363	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	106	416	0	ENST00000359376.3:c.3053A>G	p.Asp1018Gly	p.D1018G	ENST00000359376	NM_002661.3	1018	gAt/gGt	28/33	1	2	FACETS	0.637	0.573	0.705	0.637	0.573	0.705	SUBCLONAL	1	TRUE	1	0.619638183142434	2		416	537	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753385	42753386	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0031287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	59	854	0	ENST00000222329.4:c.878_879del	p.Gly293AlafsTer15	p.G293Afs*15	ENST00000222329	NM_006494.2	293	gGG/g	4/4	1	2	FACETS	0.174	0.149	0.201	0.174	0.149	0.201	SUBCLONAL	1	TRUE	1	0.619638183142434	2		854	1096	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0031293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	107	377	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.28065384521442	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.28065384521442	1		377	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0031293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	128	660	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.28065384521442	1	FACETS	0.989	0.897	1	0.989	0.897	1	CLONAL	1	TRUE	0	0.28065384521442	1		660	793	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983998	2983998	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	73	614	0	ENST00000396946.4:c.532G>C	p.Glu178Gln	p.E178Q	ENST00000396946	NM_032415.4	178	Gag/Cag	5/25	0.28065384521442	1	FACETS	0.477	0.416	0.543	0.477	0.416	0.543	SUBCLONAL	1	TRUE	0	0.28065384521442	1		614	938	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268991	115268991	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs181895470	NA	P-0031293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	115	458	0	ENST00000438362.2:c.1619G>A	p.Ser540Asn	p.S540N	ENST00000438362	NM_001242891.1	540	aGt/aAt	14/20	0.28065384521442	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.28065384521442	1		458	661	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690841	89690849	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCAGAGGTA	GCAGAGGTA	-	novel	NA	P-0031293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	71	490	0	ENST00000371953.3:c.249_253+4del		p.X83_splice	ENST00000371953	NM_000314.4	83		4/9	0.28065384521442	1	FACETS	0.935	0.819	1	0.935	0.819	1	CLONAL	1	TRUE	0	0.28065384521442	1		490	465	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948682	71948682	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	69	627	0	ENST00000298229.2:c.3394G>T	p.Glu1132Ter	p.E1132*	ENST00000298229	NM_001567.3	1132	Gag/Tag	26/28	0.28065384521442	1	FACETS	0.698	0.608	0.795	0.698	0.608	0.795	SUBCLONAL	1	TRUE	0	0.28065384521442	1		627	606	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527822	103527822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	123	546	0	ENST00000355739.4:c.3130G>A	p.Glu1044Lys	p.E1044K	ENST00000355739	NM_000123.3	1044	Gaa/Aaa	15/15	0.28065384521442	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.28065384521442	1		546	673	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350072	15350072	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	113	599	0	ENST00000263377.2:c.3580C>G	p.Leu1194Val	p.L1194V	ENST00000263377	NM_058243.2	1194	Ctg/Gtg	18/20	0.177805250092947	2	FACETS	1	0.944	1	0.535	0.482	0.592	CLONAL	1	TRUE	0	0.28065384521442	2		599	752	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39251251	39251251	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	133	607	0	ENST00000402219.2:c.1102G>C	p.Glu368Gln	p.E368Q	ENST00000402219	NM_005633.3	368	Gaa/Caa	9/23	0.28065384521442	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.28065384521442	1		607	662	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131498	202131498	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	115	583	0	ENST00000358485.4:c.466C>T	p.Gln156Ter	p.Q156*	ENST00000358485	NM_001080125.1	156	Caa/Taa	2/9	0.28065384521442	1	FACETS	0.946	0.852	1	0.946	0.852	1	CLONAL	1	TRUE	0	0.28065384521442	1		583	745	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533715	41533715	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	154	666	1	ENST00000263253.7:c.1681C>T	p.Gln561Ter	p.Q561*	ENST00000263253	NM_001429.3	561	Caa/Taa	8/31	0.28065384521442	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.28065384521442	1		667	895	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636685	176636685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	46	502	0	ENST00000439151.2:c.1285G>A	p.Glu429Lys	p.E429K	ENST00000439151	NM_022455.4	429	Gaa/Aaa	5/23	1	2	FACETS	0.477	0.401	0.562	0.477	0.401	0.562	SUBCLONAL	1	TRUE	1	0.28065384521442	2		502	687	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984166	2984166	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	27	321	0	ENST00000396946.4:c.364G>T	p.Glu122Ter	p.E122*	ENST00000396946	NM_032415.4	122	Gaa/Taa	5/25	0.28065384521442	1	FACETS	0.362	0.287	0.447	0.362	0.287	0.447	SUBCLONAL	1	TRUE	0	0.28065384521442	1		321	457	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224431	53224432	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0031293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	100	311	0	ENST00000375401.3:c.3281_3282del	p.Ser1094LeufsTer35	p.S1094Lfs*35	ENST00000375401	NM_004187.3	1094	tCT/t	21/26	1	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.28065384521442	1		311	412	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913381	NA	P-0031293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	41	292	0	ENST00000304494.5:c.322G>T	p.Asp108Tyr	p.D108Y	ENST00000304494	NM_000077.4	108	Gat/Tat	2/3	0.28574192997429	1	FACETS	0.703	0.587	0.831	0.703	0.587	0.831	SUBCLONAL	1	TRUE	0	0.28574192997429	1		292	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	82	372	0	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	0.28574192997429	1	FACETS	0.918	0.811	1	0.918	0.811	1	CLONAL	1	TRUE	0	0.28574192997429	1		372	536	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602863	10602863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	135	535	1	ENST00000171111.5:c.715G>A	p.Val239Met	p.V239M	ENST00000171111	NM_203500.1	239	Gtg/Atg	3/6	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.28574192997429	2		536	903	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911062	29911063	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0031293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	39	482	0	ENST00000376809.5:c.362dup	p.Met122AsnfsTer55	p.M122Nfs*55	ENST00000376809	NM_002116.7	121	ata/aTta	3/8	0.261742881613455	1	FACETS	0.32	0.264	0.382	0.32	0.264	0.382	SUBCLONAL	1	TRUE	0	0.28574192997429	1		482	732	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0031295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	311	463	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.789028142223055	2		463	738	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557629	95557629	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	592	698	0	ENST00000393063.1:c.5438A>G	p.Glu1813Gly	p.E1813G	ENST00000393063	NM_030621.3	1813	gAg/gGg	26/28	0.77424652149675	2	FACETS	0.971	0.947	0.993	0.971	0.947	0.993	CLONAL	2	TRUE	0	0.789028142223055	2		698	773	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274794	123274794	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913478	NA	P-0031295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	562	583	0	ENST00000358487.5:c.1124A>G	p.Tyr375Cys	p.Y375C	ENST00000358487	NM_000141.4	375	tAc/tGc	9/18	0.789028142223055	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.789028142223055	2		583	683	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0031295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	244	525	0	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	0.789028142223055	2		525	565	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740620	145740620	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	284	792	0	ENST00000428558.2:c.1397C>G	p.Pro466Arg	p.P466R	ENST00000428558	NM_004260.3	466	cCg/cGg	8/22	1	2	FACETS	0.989	0.935	1	0.989	0.935	1	CLONAL	1	TRUE	1	0.789028142223055	2		792	728	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582159	95582159	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0031295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	30	348	0	ENST00000393063.1:c.1753-1G>T		p.X585_splice	ENST00000393063	NM_030621.3	585			0.77424652149675	2	FACETS	0.17	0.137	0.208	0.085	0.068	0.104	SUBCLONAL	1	TRUE	0	0.789028142223055	2		348	447	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662427	67662427	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	452	758	0	ENST00000264010.4:c.1673C>G	p.Ser558Cys	p.S558C	ENST00000264010	NM_006565.3	558	tCt/tGt	9/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.789028142223055	2		758	1098	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267611	7267611	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	399	807	0	ENST00000302850.5:c.397C>G	p.Leu133Val	p.L133V	ENST00000302850	NM_000208.2	133	Ctc/Gtc	2/22	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.789028142223055	2		807	997	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99136555	99136555	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374377384	NA	P-0031295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	301	690	1	ENST00000074304.5:c.44G>A	p.Arg15His	p.R15H	ENST00000074304	NM_001134224.1	15	cGt/cAt	3/26	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.789028142223055	2		691	728	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247234	153247234	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	329	592	0	ENST00000281708.4:c.1568T>A	p.Val523Glu	p.V523E	ENST00000281708	NM_033632.3	523	gTa/gAa	10/12	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.789028142223055	2		592	748	SUCCESS
AR	367	MSKCC	GRCh37	X	66765398	66765398	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	281	684	0	ENST00000374690.3:c.410C>G	p.Ala137Gly	p.A137G	ENST00000374690	NM_000044.3	137	gCc/gGc	1/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.789028142223055	2		684	643	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427039	49427039	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	252	567	0	ENST00000301067.7:c.11449G>A	p.Ala3817Thr	p.A3817T	ENST00000301067	NM_003482.3	3817	Gct/Act	39/54	0.125673526327835	12	FACETS	1	0.963	1	0.829	0.778	0.88	CLONAL	8	TRUE	2	0.125673526327835	12		567	788	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392119	118392119	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	176	528	0	ENST00000534358.1:c.11630A>G	p.Tyr3877Cys	p.Y3877C	ENST00000534358	NM_005933.3	3877	tAt/tGt	35/36	1	2	FACETS	0.975	0.902	1	0.975	0.902	1	CLONAL	1	TRUE	1	0.538730882450691	2		528	670	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602354	28602354	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	203	648	0	ENST00000241453.7:c.2014G>C	p.Glu672Gln	p.E672Q	ENST00000241453	NM_004119.2	672	Gag/Cag	16/24	1	2	FACETS	0.997	0.927	1	0.997	0.927	1	CLONAL	1	TRUE	1	0.538730882450691	2		648	756	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346466	89346466	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	264	788	0	ENST00000301030.4:c.6484C>A	p.Pro2162Thr	p.P2162T	ENST00000301030	NM_001256183.1	2162	Cct/Act	9/13	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.538730882450691	2		788	938	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868282	37868282	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	542	715	0	ENST00000269571.5:c.1003A>T	p.Ser335Cys	p.S335C	ENST00000269571		335	Agc/Tgc	8/27	0.356170485303005	4	FACETS	0.948	0.913	0.982			1	CLONAL	3	TRUE	NA	0.538730882450691	4		715	1089	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610399	10610399	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	289	836	1	ENST00000171111.5:c.311G>T	p.Ser104Ile	p.S104I	ENST00000171111	NM_203500.1	104	aGc/aTc	2/6	0.538730882450691	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.538730882450691	1		837	753	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098381	11098382	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0031301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	233	551	1	ENST00000358026.2:c.900_901del	p.Lys301AlafsTer85	p.K301Afs*85	ENST00000358026	NM_001128849.1	300	cAG/c	6/36	0.538730882450691	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.538730882450691	1		552	534	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017563	112017563	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	207	646	0	ENST00000368678.4:c.950A>G	p.Lys317Arg	p.K317R	ENST00000368678		317	aAg/aGg	9/13	1	2	FACETS	0.962	0.895	1	0.962	0.895	1	CLONAL	1	TRUE	1	0.538730882450691	2		646	799	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900096	151900096	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	186	596	0	ENST00000262189.6:c.4015G>A	p.Glu1339Lys	p.E1339K	ENST00000262189	NM_170606.2	1339	Gaa/Aaa	26/59	1	2	FACETS	0.869	0.804	0.936	0.869	0.804	0.936	CLONAL	1	TRUE	1	0.538730882450691	2		596	795	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0031302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	502	604	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.645198218384359	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.645198218384359	2		604	735	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604704	48604704	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	190	466	0	ENST00000342988.3:c.1526G>A	p.Trp509Ter	p.W509*	ENST00000342988	NM_005359.5	509	tGg/tAg	12/12	0.645198218384359	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.645198218384359	1		466	360	SUCCESS
APC	324	MSKCC	GRCh37	5	112175173	112175173	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	121	308	0	ENST00000257430.4:c.3883del	p.Glu1295LysfsTer10	p.E1295Kfs*10	ENST00000257430	NM_000038.5	1294	caG/ca	16/16	1	2	FACETS	0.982	0.896	1	0.982	0.896	1	CLONAL	1	TRUE	1	0.645198218384359	2		308	382	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524175	187524176	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	GGGCACCTTCCCTCTTCATTCAAAGAGGGGAG	novel	NA	P-0031302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	109	464	0	ENST00000441802.2:c.11351-19_11363dup	p.Pro3789SerfsTer4	p.P3789Sfs*4	ENST00000441802	NM_005245.3	3788	cca/ccCTCCCCTCTTTGAATGAAGAGGGAAGGTGCCCa	20/27	1	2	FACETS	0.606	0.545	0.669	0.606	0.545	0.669	SUBCLONAL	1	TRUE	1	0.645198218384359	2		464	558	SUCCESS
APC	324	MSKCC	GRCh37	5	112116549	112116550	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs878853459	NA	P-0031302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	193	446	0	ENST00000257430.4:c.595dup	p.Ala199GlyfsTer53	p.A199Gfs*53	ENST00000257430	NM_000038.5	198	-/G	6/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.645198218384359	2		446	577	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953070	2953070	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	203	570	0	ENST00000396946.4:c.2870A>C	p.Asn957Thr	p.N957T	ENST00000396946	NM_032415.4	957	aAc/aCc	22/25	0.295243885078349	6	FACETS	1	0.987	1	0.43	0.398	0.463	INDETERMINATE	1	TRUE	3	0.645198218384359	6		570	1117	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968136	68968136	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	193	603	0	ENST00000288368.4:c.1165A>T	p.Met389Leu	p.M389L	ENST00000288368	NM_024870.2	389	Atg/Ttg	10/40	0.517650378877898	4	FACETS	0.912	0.843	0.984	0.456	0.421	0.492	CLONAL	1	TRUE	2	0.645198218384359	4		603	1079	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0031303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	437	332	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.694037475043192	2	FACETS	0.963	0.931	0.994	0.963	0.931	0.994	CLONAL	2	TRUE	0	0.694037475043192	2		332	654	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	268	384	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	0.694037475043192	2		384	724	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0031303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	179	214	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.694037475043192	2	FACETS	0.968	0.899	1	0.484	0.449	0.519	CLONAL	1	TRUE	0	0.694037475043192	2		214	533	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544655	65544655	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	541	567	0	ENST00000358664.4:c.271C>T	p.Gln91Ter	p.Q91*	ENST00000358664	NM_002382.4	91	Cag/Tag	4/5	0.694037475043192	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.694037475043192	2		567	760	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832398	72832398	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	223	552	0	ENST00000268489.5:c.4183G>C	p.Asp1395His	p.D1395H	ENST00000268489	NM_006885.3	1395	Gat/Cat	9/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.694037475043192	2		552	589	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255875	16255875	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	235	564	0	ENST00000375759.3:c.3140G>C	p.Arg1047Thr	p.R1047T	ENST00000375759	NM_015001.2	1047	aGa/aCa	11/15	1	2	FACETS	0.938	0.879	0.998	0.938	0.879	0.998	CLONAL	1	TRUE	1	0.694037475043192	2		564	722	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870224	155870224	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	585	724	0	ENST00000368323.3:c.615G>C	p.Lys205Asn	p.K205N	ENST00000368323	NM_006912.5	205	aaG/aaC	6/6	0.694037475043192	3	FACETS	0.971	0.937	1	0.971	0.937	1	CLONAL	2	TRUE	1	0.694037475043192	3		724	1169	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348903	11348903	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	145	322	0	ENST00000332029.2:c.433G>T	p.Asp145Tyr	p.D145Y	ENST00000332029	NM_003745.1	145	Gac/Tac	2/2	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.694037475043192	2		322	413	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128588	30128588	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	214	536	0	ENST00000263025.4:c.794C>T	p.Ser265Phe	p.S265F	ENST00000263025	NM_002746.2	265	tCc/tTc	6/9	1	2	FACETS	0.968	0.905	1	0.968	0.905	1	CLONAL	1	TRUE	1	0.694037475043192	2		536	637	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974932	15974932	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	222	578	0	ENST00000268712.3:c.3943C>G	p.Pro1315Ala	p.P1315A	ENST00000268712	NM_006311.3	1315	Ccc/Gcc	30/46	1	2	FACETS	0.922	0.862	0.983	0.922	0.862	0.983	CLONAL	1	TRUE	1	0.694037475043192	2		578	694	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974965	15974965	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	185	548	0	ENST00000268712.3:c.3910A>G	p.Thr1304Ala	p.T1304A	ENST00000268712	NM_006311.3	1304	Aca/Gca	30/46	1	2	FACETS	0.891	0.828	0.957	0.891	0.828	0.957	CLONAL	1	TRUE	1	0.694037475043192	2		548	598	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226464	41226464	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555581971	NA	P-0031303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	263	687	0	ENST00000357654.3:c.4559G>C	p.Arg1520Thr	p.R1520T	ENST00000357654	NM_007294.3	1520	aGa/aCa	14/23	1	2	FACETS	0.913	0.858	0.969	0.913	0.858	0.969	CLONAL	1	TRUE	1	0.694037475043192	2		687	830	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57567440	57567440	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	218	422	0	ENST00000316660.6:c.31C>T	p.Gln11Ter	p.Q11*	ENST00000316660	NM_021127.2	11	Caa/Taa	1/2	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.694037475043192	2		422	623	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157256	106157256	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	260	641	0	ENST00000380013.4:c.2157del	p.Leu719PhefsTer32	p.L719Ffs*32	ENST00000380013	NM_001127208.2	719	ttG/tt	3/11	1	2	FACETS	0.948	0.892	1	0.948	0.892	1	CLONAL	1	TRUE	1	0.694037475043192	2		641	790	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815823	32815823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	254	583	0	ENST00000354258.4:c.1793G>A	p.Gly598Glu	p.G598E	ENST00000354258	NM_000593.5	598	gGa/gAa	8/11	1	2	FACETS	0.962	0.904	1	0.962	0.904	1	CLONAL	1	TRUE	1	0.694037475043192	2		583	761	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359096	81359096	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0031303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	139	425	0	ENST00000222390.5:c.866-1G>T		p.X289_splice	ENST00000222390	NM_000601.4	289			1	2	FACETS	0.984	0.905	1	0.984	0.905	1	CLONAL	1	TRUE	1	0.694037475043192	2		425	407	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404376	139404376	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	280	735	0	ENST00000277541.6:c.2778C>G	p.Ile926Met	p.I926M	ENST00000277541	NM_017617.3	926	atC/atG	18/34	1	2	FACETS	0.953	0.898	1	0.953	0.898	1	CLONAL	1	TRUE	1	0.694037475043192	2		735	847	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0031304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	589	491	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.656906133120788	4	FACETS	0.9	0.87	0.931	0.9	0.87	0.931	CLONAL	3	TRUE	1	0.656906133120788	4		491	1100	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0031304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	285	733	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.656906133120788	1	FACETS	0.944	0.896	0.993	0.944	0.896	0.993	CLONAL	1	TRUE	0	0.656906133120788	1		733	617	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26046026	26046026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	179	458	1	ENST00000540144.1:c.388C>T	p.Arg130Cys	p.R130C	ENST00000540144	NM_003531.2	130	Cgc/Tgc	1/1	1	2	FACETS	0.985	0.915	1	0.985	0.915	1	CLONAL	1	TRUE	1	0.656906133120788	2		459	553	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939473	71939473	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	293	752	0	ENST00000298229.2:c.328G>C	p.Val110Leu	p.V110L	ENST00000298229	NM_001567.3	110	Gtg/Ctg	3/28	1	2	FACETS	0.89	0.839	0.943	0.89	0.839	0.943	CLONAL	1	TRUE	1	0.656906133120788	2		752	1002	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800822	18800822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	150	443	0	ENST00000266497.5:c.4198G>A	p.Glu1400Lys	p.E1400K	ENST00000266497		1400	Gaa/Aaa	31/31	NA	2	FACETS	0.934	0.86	1			1	INDETERMINATE	1	TRUE	NA	0.656906133120788	2		443	489	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223138	1223138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060499967	NA	P-0031304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	270	651	0	ENST00000326873.7:c.1075G>A	p.Asp359Asn	p.D359N	ENST00000326873	NM_000455.4	359	Gac/Aac	8/10	0.656906133120788	1	FACETS	0.989	0.938	1	0.989	0.938	1	CLONAL	1	TRUE	0	0.656906133120788	1		651	558	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106195611	106196633	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AACATTCCCGAATCTTACATAATAAATCTTATTTTAATTATTTAGCAAATTCCATTGCATGCCAGGCAATGAAGAAGTAAGTAAAATAAAACATTTTCCTTCCCATTTAGGAATTTACTTACCAGTGGGGGTGAAGAGAGGGCTAAAAACATAACTATAATACATTGTGAGTATTGCTTTATCAGATCTATCTTTGCAGTTGAGTATTACAAAAGCACTAGAAGATGAGGTCAAAGCGGTCCCTTGAGGAAGGGATGACTACACCAAGGAAGGATAGGGAGAGAGGGAGGAAAAGGGAGGCACTTCAAGCAGAGGCATGTTCAGAAGTTCCAAAGAACATTTTGCTCTCAATGGAATGGCTTTGGATGTTTATTACATTTTTTTTTTCACTAAGTTTTGTATTTCTAATGCCTTAGACAAAAAATTGTGCTGGACAATGATCAGAACCCTGACTTTGCTCTTATCTTTGCTTAATGGGTGTCGTATATCACTAGTGGAGTTTCTTACCTACATTTAAGTATCCTCACTAGCCTTCATAAAATAATCATCAACATCAAAGATACCTGTTTCTGTTCTCTCTTACCCTGTCCACAGAACTTTTGCGACTTTCAGGACCAGTCATGCAGCAGTCCCAGCAGCCCCAGCCTCTACAGAAGCAGCCACCACAGCCCCAGCAGCAGCAGAGACCCCAGCAGCAGCAGCCACATCACCCTCAGACAGAGTCTGTCAACTCTTATTCTGCTTCTGGATCCACCAATCCATACATGAGACGGCCCAATCCAGTTAGTCCTTATCCAAACTCTTCACACACTTCAGATATCTATGGAAGCACCAGCCCTATGAACTTCTATTCCACCTCATCTCAAGCTGCAGGTTCATATTTGAATTCTTCTAATCCCATGAACCCTTACCCTGGGCTTTTGAATCAGAATACCCAATATCCATCATATCAATGCAATGGAAACCTATCAGTGGACAACTGCTCCCCATATCTGGGTTCCTATTCTCCCCAGTCTCAGCCGA	AACATTCCCGAATCTTACATAATAAATCTTATTTTAATTATTTAGCAAATTCCATTGCATGCCAGGCAATGAAGAAGTAAGTAAAATAAAACATTTTCCTTCCCATTTAGGAATTTACTTACCAGTGGGGGTGAAGAGAGGGCTAAAAACATAACTATAATACATTGTGAGTATTGCTTTATCAGATCTATCTTTGCAGTTGAGTATTACAAAAGCACTAGAAGATGAGGTCAAAGCGGTCCCTTGAGGAAGGGATGACTACACCAAGGAAGGATAGGGAGAGAGGGAGGAAAAGGGAGGCACTTCAAGCAGAGGCATGTTCAGAAGTTCCAAAGAACATTTTGCTCTCAATGGAATGGCTTTGGATGTTTATTACATTTTTTTTTTCACTAAGTTTTGTATTTCTAATGCCTTAGACAAAAAATTGTGCTGGACAATGATCAGAACCCTGACTTTGCTCTTATCTTTGCTTAATGGGTGTCGTATATCACTAGTGGAGTTTCTTACCTACATTTAAGTATCCTCACTAGCCTTCATAAAATAATCATCAACATCAAAGATACCTGTTTCTGTTCTCTCTTACCCTGTCCACAGAACTTTTGCGACTTTCAGGACCAGTCATGCAGCAGTCCCAGCAGCCCCAGCCTCTACAGAAGCAGCCACCACAGCCCCAGCAGCAGCAGAGACCCCAGCAGCAGCAGCCACATCACCCTCAGACAGAGTCTGTCAACTCTTATTCTGCTTCTGGATCCACCAATCCATACATGAGACGGCCCAATCCAGTTAGTCCTTATCCAAACTCTTCACACACTTCAGATATCTATGGAAGCACCAGCCCTATGAACTTCTATTCCACCTCATCTCAAGCTGCAGGTTCATATTTGAATTCTTCTAATCCCATGAACCCTTACCCTGGGCTTTTGAATCAGAATACCCAATATCCATCATATCAATGCAATGGAAACCTATCAGTGGACAACTGCTCCCCATATCTGGGTTCCTATTCTCCCCAGTCTCAGCCGA	-	novel	NA	P-0031304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1	72	0	0	ENST00000380013.4:c.4538-594_4966del		p.X1513_splice	ENST00000380013	NM_001127208.2	1513		11/11	0.656906133120788	1	FACETS	1	0.982	1	1	0.99	1	CLONAL	2	TRUE	0	0.656906133120788	1		0	73	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0031305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	89	538	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.959	0.849	1	0.959	0.849	1	CLONAL	1	TRUE	1	0.223318159964776	2		538	831	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592132	67592132	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	41	382	0	ENST00000274335.5:c.1948G>C	p.Glu650Gln	p.E650Q	ENST00000274335		650	Gag/Cag	14/15	1	2	FACETS	0.628	0.522	0.746	0.628	0.522	0.746	SUBCLONAL	1	TRUE	1	0.223318159964776	2		382	585	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0031307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	187	377	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.946	0.876	1	0.946	0.876	1	CLONAL	1	TRUE	1	0.513615961627171	2		377	770	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0031307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	178	242	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.973	0.9	1	0.973	0.9	1	CLONAL	1	TRUE	1	0.513615961627171	2		242	712	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645693	12645693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397516827	NA	P-0031307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	134	367	0	ENST00000251849.4:c.776C>T	p.Ser259Phe	p.S259F	ENST00000251849	NM_002880.3	259	tCc/tTc	7/17	1	2	FACETS	0.985	0.899	1	0.985	0.899	1	CLONAL	1	TRUE	1	0.513615961627171	2		367	530	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604745	48604745	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	232	568	0	ENST00000342988.3:c.1567T>C	p.Cys523Arg	p.C523R	ENST00000342988	NM_005359.5	523	Tgc/Cgc	12/12	0.513615961627171	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.513615961627171	1		568	611	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107136	27107137	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0031307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	224	572	0	ENST00000324856.7:c.6749_6750del	p.Glu2250ValfsTer27	p.E2250Vfs*27	ENST00000324856	NM_006015.4	2249	tcAGag/tcag	20/20	0.513615961627171	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.513615961627171	1		572	621	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784041	9784041	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	242	687	0	ENST00000377346.4:c.2609G>C	p.Arg870Pro	p.R870P	ENST00000377346	NM_005026.3	870	cGa/cCa	21/24	0.513615961627171	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.513615961627171	1		687	691	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324105	31324105	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	87	257	0	ENST00000412585.2:c.458A>G	p.Asp153Gly	p.D153G	ENST00000412585	NM_005514.6	153	gAc/gGc	3/8	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.513615961627171	2		257	309	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324112	31324119	+	frameshift_variant	Frame_Shift_Del	DEL	TCAGGGCG	TCAGGGCG	-	novel	NA	P-0031307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	110	274	0	ENST00000412585.2:c.444_451del	p.Ala149ArgfsTer25	p.A149Rfs*25	ENST00000412585	NM_005514.6	148	atCGCCCTGAac/atac	3/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.513615961627171	2		274	319	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148657	20148657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	171	523	1	ENST00000379607.5:c.406G>A	p.Asp136Asn	p.D136N	ENST00000379607	NM_001412.3	136	Gat/Aat	6/7	1	2	FACETS	0.903	0.833	0.977	0.903	0.833	0.977	CLONAL	1	TRUE	1	0.513615961627171	2		524	737	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0031321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	132	264	1	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	1	2	FACETS	0.895	0.814	0.979	0.895	0.814	0.979	CLONAL	1	TRUE	1	0.441752488357476	2		265	668	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0031321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	147	638	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	0.913	0.835	0.994	0.913	0.835	0.994	CLONAL	1	TRUE	1	0.441752488357476	2		638	729	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597433	52597433	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	87	486	0	ENST00000394830.3:c.3877G>T	p.Glu1293Ter	p.E1293*	ENST00000394830	NM_018313.4	1293	Gag/Tag	25/30	0.431650537154757	1	FACETS	0.589	0.523	0.659	0.589	0.523	0.659	SUBCLONAL	1	TRUE	0	0.441752488357476	1		486	521	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	113	384	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.663	0.601	0.728	0.663	0.601	0.728	SUBCLONAL	1	TRUE	1	0.813097101025732	2		384	419	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570018	95570018	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	54	631	0	ENST00000393063.1:c.3715A>T	p.Ser1239Cys	p.S1239C	ENST00000393063	NM_030621.3	1239	Agt/Tgt	22/28	1	2	FACETS	0.861	0.735	0.999	0.861	0.735	0.999	CLONAL	1	TRUE	1	0.212230551363241	2		631	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578436	7578439	+	frameshift_variant	Frame_Shift_Del	DEL	TGCT	TGCT	-	novel	NA	P-0031323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	123	813	0	ENST00000269305.4:c.491_494del	p.Lys164SerfsTer5	p.K164Sfs*5	ENST00000269305	NM_001126112.2	164	aAGCAg/ag	5/11	0.212230551363241	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.212230551363241	1		813	839	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0031324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	1747	491	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.694793846245009	9	FACETS	0.954	0.938	0.97	0.954	0.938	0.97	CLONAL	7	TRUE	2	0.694793846245009	9		491	2584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0031324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	494	712	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.63059191524798	2	FACETS	0.834	0.804	0.863	0.834	0.804	0.863	CLONAL	2	TRUE	0	0.694793846245009	2		712	853	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720801	89720802	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0031324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	65	225	0	ENST00000371953.3:c.954dup	p.Thr319TyrfsTer6	p.T319Yfs*6	ENST00000371953	NM_000314.4	318	ctt/cTtt	8/9	0.5499605380972	2	FACETS	1	0.956	1	0.581	0.516	0.648	CLONAL	1	TRUE	0	0.694793846245009	2		225	161	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537256	80537263	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	CTGTCCCT	CTGTCCCT	-	novel	NA	P-0031324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	188	631	0	ENST00000286548.4:c.137-2_142del		p.X46_splice	ENST00000286548	NM_002072.3	46		2/7	0.614238394614751	2	FACETS	0.811	0.753	0.872	0.406	0.376	0.436	CLONAL	1	TRUE	0	0.694793846245009	2		631	667	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577530	7577530	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs730882007	NA	P-0031325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	85	606	0	ENST00000269305.4:c.751A>C	p.Ile251Leu	p.I251L	ENST00000269305	NM_001126112.2	251	Atc/Ctc	7/11	0.296827514447552	1	FACETS	0.826	0.733	0.925	0.826	0.733	0.925	CLONAL	1	TRUE	0	0.35	1		606	485	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81927400	81927400	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0031325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	189	591	1	ENST00000359376.3:c.1072+1G>A		p.X358_splice	ENST00000359376	NM_002661.3	358			0.3	3	FACETS	0.787	0.729	0.848	0.787	0.729	0.848	SUBCLONAL	2	TRUE	1	0.35	3		592	806	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662984	52662984	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	47	520	0	ENST00000394830.3:c.1369G>C	p.Glu457Gln	p.E457Q	ENST00000394830	NM_018313.4	457	Gaa/Caa	13/30	0.189347821467755	2	FACETS	0.535	0.451	0.627	0.268	0.225	0.314	INDETERMINATE	1	TRUE	0	0.35	2		520	502	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138197138	138197138	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	56	343	0	ENST00000237289.4:c.640A>T	p.Met214Leu	p.M214L	ENST00000237289	NM_001270507.1	214	Atg/Ttg	5/9	0.265802628051305	2	FACETS	0.7	0.601	0.808	0.35	0.3	0.404	SUBCLONAL	1	TRUE	0	0.35	2		343	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0031326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	58	625	2	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	1	2	FACETS	0.984	0.844	1	0.984	0.844	1	CLONAL	1	TRUE	1	0.15	2		627	786	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123695	46123695	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	18	206	0	ENST00000334344.6:c.76T>C	p.Phe26Leu	p.F26L	ENST00000334344	NM_152641.2	26	Ttc/Ctc	1/21	1	2	FACETS	0.741	0.557	0.958	0.741	0.557	0.958	CLONAL	1	TRUE	1	0.15	2		206	324	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	105	384	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.0770638837618671	3	FACETS	0.908	0.814	1	0.454	0.407	0.505	INDETERMINATE	1	TRUE	1	0.349486989027463	3		384	777	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576924	7576925	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0031328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	104	613	0	ENST00000269305.4:c.921dup	p.Leu308ThrfsTer29	p.L308Tfs*29	ENST00000269305	NM_001126112.2	307	-/A	9/11	0.349486989027463	1	FACETS	0.915	0.822	1	0.915	0.822	1	CLONAL	1	TRUE	0	0.349486989027463	1		613	537	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584546	48584546	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	78	469	0	ENST00000342988.3:c.719T>A	p.Ile240Lys	p.I240K	ENST00000342988	NM_005359.5	240	aTa/aAa	6/12	1	2	FACETS	0.994	0.877	1	0.994	0.877	1	CLONAL	1	TRUE	1	0.349486989027463	2		469	449	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584813	48584814	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0031328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	57	366	0	ENST00000342988.3:c.891_892insA	p.Pro298ThrfsTer10	p.P298Tfs*10	ENST00000342988	NM_005359.5	297	-/A	7/12	1	2	FACETS	0.782	0.673	0.901	0.782	0.673	0.901	CLONAL	1	TRUE	1	0.349486989027463	2		366	417	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710735	117710735	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	60	453	0	ENST00000368508.3:c.1537G>T	p.Asp513Tyr	p.D513Y	ENST00000368508	NM_002944.2	513	Gat/Tat	12/43	1	2	FACETS	0.848	0.733	0.972	0.848	0.733	0.972	CLONAL	1	TRUE	1	0.349486989027463	2		453	405	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845753	151845753	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	90	639	0	ENST00000262189.6:c.13259T>C	p.Leu4420Pro	p.L4420P	ENST00000262189	NM_170606.2	4420	cTc/cCc	52/59	0.349486989027463	1	FACETS	0.699	0.621	0.782	0.699	0.621	0.782	SUBCLONAL	1	TRUE	0	0.349486989027463	1		639	608	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	11	270	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.488	0.337	0.675	0.488	0.337	0.675	SUBCLONAL	1	TRUE	1	0.22	2		270	205	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335837	73335837	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372878316	NA	P-0031330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	52	413	1	ENST00000377767.4:c.2458C>T	p.Arg820Trp	p.R820W	ENST00000377767	NM_014953.3	820	Cgg/Tgg	18/21	1	2	FACETS	0.699	0.594	0.815	0.699	0.594	0.815	SUBCLONAL	1	TRUE	1	0.22	2		414	676	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220694	1220694	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	238	590	0	ENST00000326873.7:c.712A>T	p.Ile238Phe	p.I238F	ENST00000326873	NM_000455.4	238	Atc/Ttc	5/10	0.539435530933697	2	FACETS	0.904	0.854	0.954	0.904	0.854	0.954	CLONAL	2	TRUE	0	0.539435530933697	2		590	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573943	7573943	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	290	631	0	ENST00000269305.4:c.1084A>G	p.Ser362Gly	p.S362G	ENST00000269305	NM_001126112.2	362	Agc/Ggc	10/11	0.539435530933697	3	FACETS	0.991	0.938	1	0.991	0.938	1	CLONAL	2	TRUE	1	0.539435530933697	3		631	689	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601964	43601964	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	314	730	0	ENST00000355710.3:c.1008C>A	p.Asn336Lys	p.N336K	ENST00000355710	NM_020975.4	336	aaC/aaA	5/20	0.539435530933697	3	FACETS	0.942	0.893	0.991	0.942	0.893	0.991	CLONAL	2	TRUE	1	0.539435530933697	3		730	785	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913120	32913131	+	inframe_deletion	In_Frame_Del	DEL	AAAACCTTTTTG	AAAACCTTTTTG	-	novel	NA	P-0031331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	274	646	0	ENST00000380152.3:c.4629_4640del	p.Lys1543_Asp1547delinsAsn	p.K1543_D1547delinsN	ENST00000380152		1543	aAAAACCTTTTTGat/aat	11/27	0.539435530933697	3	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	1	0.539435530933697	3		646	641	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058693	42058693	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779061413	NA	P-0031331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	81	369	0	ENST00000219905.7:c.8413G>T	p.Asp2805Tyr	p.D2805Y	ENST00000219905	NM_001164273.1	2805	Gat/Tat	24/24	1	2	FACETS	0.856	0.76	0.957	0.856	0.76	0.957	CLONAL	1	TRUE	1	0.539435530933697	2		369	351	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664439	29664439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	247	551	0	ENST00000356175.3:c.6421del	p.Tyr2141ThrfsTer38	p.Y2141Tfs*38	ENST00000356175	NM_000267.3	2140	Ttt/tt	42/57	0.539435530933697	3	FACETS	0.972	0.916	1	0.972	0.916	1	CLONAL	2	TRUE	1	0.539435530933697	3		551	598	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664876	29664876	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	107	443	0	ENST00000356175.3:c.6619C>T	p.Gln2207Ter	p.Q2207*	ENST00000356175	NM_000267.3	2207	Cag/Tag	43/57	0.539435530933697	3	FACETS	0.984	0.886	1	0.492	0.443	0.543	CLONAL	1	TRUE	1	0.539435530933697	3		443	512	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45377675	45377675	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1204398491	NA	P-0031331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	83	368	0	ENST00000262160.6:c.754A>G	p.Thr252Ala	p.T252A	ENST00000262160	NM_005901.5	252	Act/Gct	7/11	1	2	FACETS	0.999	0.891	1	0.999	0.891	1	CLONAL	1	TRUE	1	0.539435530933697	2		368	308	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213595	2213595	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	327	754	0	ENST00000398665.3:c.1615C>T	p.Gln539Ter	p.Q539*	ENST00000398665	NM_032482.2	539	Cag/Tag	17/28	0.539435530933697	2	FACETS	0.997	0.952	1	0.997	0.952	1	CLONAL	2	TRUE	0	0.539435530933697	2		754	608	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600363	10600363	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	314	728	0	ENST00000171111.5:c.1492C>T	p.Arg498Ter	p.R498*	ENST00000171111	NM_203500.1	498	Cga/Tga	4/6	0.539435530933697	2	FACETS	0.954	0.91	0.999	0.954	0.91	0.999	CLONAL	2	TRUE	0	0.539435530933697	2		728	610	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609164	46609178	+	inframe_deletion	In_Frame_Del	DEL	GAACCTCAGGGGTGG	GAACCTCAGGGGTGG	-	novel	NA	P-0031331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	45	732	0	ENST00000263734.3:c.2225_2239del	p.Asn742_Gly746del	p.N742_G746del	ENST00000263734	NM_001430.4	741	aaGAACCTCAGGGGTGGg/aag	14/16	0.539435530933697	3	FACETS	0.293	0.245	0.346	0.147	0.122	0.173	SUBCLONAL	1	TRUE	1	0.539435530933697	3		732	723	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504374	8504375	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATG	novel	NA	P-0031331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	45	573	0	ENST00000356435.5:c.1706_1708dup	p.Ser569dup	p.S569dup	ENST00000356435		569	tat/tCATat	12/35	0.539435530933697	2	FACETS	0.37	0.311	0.435	0.185	0.155	0.218	SUBCLONAL	1	TRUE	0	0.539435530933697	2		573	451	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937166	39937166	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	160	617	0	ENST00000378444.4:c.17C>T	p.Pro6Leu	p.P6L	ENST00000378444	NM_001123385.1	6	cCc/cTc	2/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.539435530933697	2		617	552	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0031333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	53	193	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.555	0.474	0.644	0.555	0.474	0.644	SUBCLONAL	1	TRUE	1	0.384254562112396	2		193	497	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29497003	29497003	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397514641	NA	P-0031333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	56	344	0	ENST00000356175.3:c.574C>T	p.Arg192Ter	p.R192*	ENST00000356175	NM_000267.3	192	Cga/Tga	5/57	1	2	FACETS	0.656	0.563	0.758	0.656	0.563	0.758	SUBCLONAL	1	TRUE	1	0.384254562112396	2		344	444	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546040	29546058	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCGAAACCCAAGGCAGT	GCCCGAAACCCAAGGCAGT	-	novel	NA	P-0031333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	43	507	0	ENST00000356175.3:c.1545_1563del	p.Pro516GlnfsTer4	p.P516Qfs*4	ENST00000356175	NM_000267.3	515	ggGCCCGAAACCCAAGGCAGT/gg	14/57	1	2	FACETS	0.333	0.277	0.394	0.333	0.277	0.394	SUBCLONAL	1	TRUE	1	0.384254562112396	2		507	673	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181834	56181835	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0031333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	48	525	0	ENST00000399503.3:c.4059dup	p.Leu1354ThrfsTer9	p.L1354Tfs*9	ENST00000399503	NM_005921.1	1353	tta/ttAa	17/20	1	2	FACETS	0.421	0.355	0.493	0.421	0.355	0.493	SUBCLONAL	1	TRUE	1	0.384254562112396	2		525	594	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189435	56189461	+	inframe_deletion	In_Frame_Del	DEL	AGAACTTCAACCTCAGGACAGACCTCC	AGAACTTCAACCTCAGGACAGACCTCC	-	novel	NA	P-0031333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	40	554	0	ENST00000399503.3:c.4468_4494del	p.Glu1490_Pro1498del	p.E1490_P1498del	ENST00000399503	NM_005921.1	1489	ttAGAACTTCAACCTCAGGACAGACCTCCa/tta	20/20	1	2	FACETS	0.326	0.27	0.388	0.326	0.27	0.388	SUBCLONAL	1	TRUE	1	0.384254562112396	2		554	639	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284906	15284906	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1469453455	NA	P-0031334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	106	633	1	ENST00000263388.2:c.4709G>A	p.Arg1570His	p.R1570H	ENST00000263388	NM_000435.2	1570	cGt/cAt	25/33	0.389723468154501	1	FACETS	0.781	0.707	0.859	0.781	0.707	0.859	SUBCLONAL	1	TRUE	0	0.533528918871315	1		634	373	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533586	533586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730880462	NA	P-0031334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	74	673	1	ENST00000451590.1:c.317C>T	p.Ser106Leu	p.S106L	ENST00000451590	NM_001130442.1	106	tCg/tTg	4/5	1	2	FACETS	0.583	0.512	0.659	0.583	0.512	0.659	SUBCLONAL	1	TRUE	1	0.533528918871315	2		674	476	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354131	15354131	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	88	506	0	ENST00000263377.2:c.2749G>C	p.Glu917Gln	p.E917Q	ENST00000263377	NM_058243.2	917	Gag/Cag	14/20	0.389723468154501	1	FACETS	0.826	0.74	0.914	0.826	0.74	0.914	CLONAL	1	TRUE	0	0.533528918871315	1		506	293	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216477	36216477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778306717	NA	P-0031334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	75	765	1	ENST00000222270.7:c.3740G>A	p.Arg1247His	p.R1247H	ENST00000222270	NM_014727.1	1247	cGt/cAt	12/37	0.389723468154501	1	FACETS	0.493	0.434	0.556	0.493	0.434	0.556	SUBCLONAL	1	TRUE	0	0.533528918871315	1		766	418	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732584	190732584	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	17	578	0	ENST00000441310.2:c.2402G>C	p.Arg801Thr	p.R801T	ENST00000441310	NM_000534.4	801	aGa/aCa	11/13	0.389723468154501	1	FACETS	0.29	0.218	0.375	0.29	0.218	0.375	SUBCLONAL	1	TRUE	0	0.533528918871315	1		578	161	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532905	187532905	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	77	422	0	ENST00000441802.2:c.9488C>T	p.Ser3163Leu	p.S3163L	ENST00000441802	NM_005245.3	3163	tCa/tTa	14/27	0.198803054698072	3	FACETS	1	0.975	1	0.698	0.62	0.779	INDETERMINATE	1	TRUE	1	0.533528918871315	3		422	262	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0031337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	94	526	3	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.377004263061023	3	FACETS	0.901	0.81	0.995	0.901	0.81	0.995	CLONAL	2	FALSE	1	0.377004263061023	3		529	329	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221313	1221314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs121913321	NA	P-0031337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	91	575	1	ENST00000326873.7:c.842dup	p.Leu282AlafsTer3	p.L282Afs*3	ENST00000326873	NM_000455.4	279	ggc/ggCc	6/10	0.30766884703475	3	FACETS	1	0.971	1	0.42	0.375	0.468	CLONAL	1	FALSE	0	0.377004263061023	3		576	455	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62297356	62297356	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0031337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	51	451	0	ENST00000360203.5:c.539-1G>C		p.X180_splice	ENST00000360203	NM_001283009.1	180			0.377004263061023	12	FACETS	1	0.899	1	0.12	0.101	0.14	CLONAL	1	FALSE	3	0.377004263061023	12		451	723	SUCCESS
EED	8726	MSKCC	GRCh37	11	85975306	85975306	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0031337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	10	345	0	ENST00000263360.6:c.726+1G>C		p.X242_splice	ENST00000263360	NM_003797.3	242			0.282764330029861	1	FACETS	0.957	0.668	1	0.957	0.668	1	CLONAL	1	FALSE	0	0.377004263061023	1		345	45	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986689	36986690	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0031337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	20	13	0	ENST00000354822.5:c.999_1000insT	p.Ile334TyrfsTer105	p.I334Yfs*105	ENST00000354822	NM_001079668.2	333	-/T	3/3	0.182092206690273	2	FACETS	1	0.829	1	1	0.829	1	INDETERMINATE	2	FALSE	0	0.377004263061023	2		13	51	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0031342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	213	701	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.194547823493434	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.210018520191906	2		701	932	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0031342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	24	245	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.199340819118487	3	FACETS	0.815	0.639	1	0.407	0.319	0.509	CLONAL	1	TRUE	1	0.210018520191906	3		245	310	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720876	89720876	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0031342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	53	363	0	ENST00000371953.3:c.1026+1G>T		p.X342_splice	ENST00000371953	NM_000314.4	342			0.199340819118487	3	FACETS	0.953	0.813	1	0.477	0.406	0.554	CLONAL	1	TRUE	1	0.210018520191906	3		363	585	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807296	3807296	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	109	488	0	ENST00000262367.5:c.3691C>T	p.Gln1231Ter	p.Q1231*	ENST00000262367	NM_004380.2	1231	Cag/Tag	19/31	1	2	FACETS	0.834	0.751	0.923	1	0.986	1	CLONAL	2	TRUE	1	0.210018520191906	2		488	622	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371849	55371850	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0031342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	21	81	0	ENST00000297316.4:c.541dup	p.Leu181ProfsTer184	p.L181Pfs*184	ENST00000297316	NM_022454.3	180	ggc/ggCc	2/2	0.114832360812297	4	FACETS	1	0.828	1	1	0.828	1	INDETERMINATE	2	TRUE	2	0.210018520191906	4		81	113	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0031350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	174	692	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	0.258266241976308	2	FACETS	0.858	0.793	0.926	0.858	0.793	0.926	CLONAL	2	FALSE	0	0.3	2		692	676	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	160	480	1	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	0.102555877551169	4	FACETS	1	0.942	1	1	0.942	1	INDETERMINATE	2	FALSE	2	0.3	4		481	674	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31493360	31493360	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	79	472	0	ENST00000344624.3:c.1796A>T	p.Tyr599Phe	p.Y599F	ENST00000344624		599	tAt/tTt	10/33	1	2	FACETS	0.882	0.777	0.995	0.882	0.777	0.995	CLONAL	1	FALSE	1	0.3	2		472	597	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357219	70357219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	143	752	0	ENST00000374080.3:c.5734C>T	p.Arg1912Cys	p.R1912C	ENST00000374080		1912	Cgc/Tgc	39/45	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.392786037888807	2		752	683	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643768	52643768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	41	763	1	ENST00000394830.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000394830	NM_018313.4	710	Cga/Tga	17/30	1	2	FACETS	0.278	0.23	0.331	0.278	0.23	0.331	SUBCLONAL	1	TRUE	1	0.392786037888807	2		764	752	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587119	189587119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765502786	NA	P-0031351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	139	485	0	ENST00000264731.3:c.1136G>A	p.Arg379His	p.R379H	ENST00000264731	NM_003722.4	379	cGt/cAt	9/14	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.392786037888807	2		485	533	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380334	14380334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	23	310	0	ENST00000256196.4:c.83C>T	p.Ser28Leu	p.S28L	ENST00000256196		28	tCg/tTg	1/6	1	2	FACETS	0.397	0.31	0.498	0.397	0.31	0.498	SUBCLONAL	1	TRUE	1	0.392786037888807	2		310	295	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842702	68842702	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	153	750	0	ENST00000261769.5:c.638G>A	p.Trp213Ter	p.W213*	ENST00000261769	NM_004360.3	213	tGg/tAg	5/16	1	2	FACETS	0.973	0.891	1	0.973	0.891	1	CLONAL	1	TRUE	1	0.392786037888807	2		750	801	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842746	68842746	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	110	540	0	ENST00000261769.5:c.682T>A	p.Tyr228Asn	p.Y228N	ENST00000261769	NM_004360.3	228	Tac/Aac	5/16	1	2	FACETS	0.945	0.851	1	0.945	0.851	1	CLONAL	1	TRUE	1	0.392786037888807	2		540	593	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120164	70120165	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0031351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	98	489	0	ENST00000245479.2:c.1169dup	p.Gln391ProfsTer187	p.Q391Pfs*187	ENST00000245479	NM_000346.3	389	ccg/ccGg	3/3	1	2	FACETS	0.984	0.881	1	0.984	0.881	1	CLONAL	1	TRUE	1	0.392786037888807	2		489	507	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229294	36229294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	297	812	0	ENST00000222270.7:c.7984C>T	p.Arg2662Trp	p.R2662W	ENST00000222270	NM_014727.1	2662	Cgg/Tgg	37/37	0.39189902722846	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.392786037888807	3		812	875	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623094	52623094	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	122	517	0	ENST00000394830.3:c.2957A>T	p.Asp986Val	p.D986V	ENST00000394830	NM_018313.4	986	gAt/gTt	19/30	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.392786037888807	2		517	580	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891137	101891137	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	54	347	0	ENST00000374994.4:c.98C>A	p.Ala33Glu	p.A33E	ENST00000374994	NM_004612.2	33	gCg/gAg	2/9	0.392786037888807	1	FACETS	0.678	0.582	0.781	0.678	0.582	0.781	SUBCLONAL	1	TRUE	0	0.392786037888807	1		347	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0031355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	450	691	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.404605790131766	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.404605790131766	2		691	986	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-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	111	237	0	ENST00000394830.3:c.1778_1818+45del		p.X593_splice	ENST00000394830	NM_018313.4	593		15/30	0.404605790131766	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.404605790131766	1		237	298	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0031356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	214	332	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.659352425351924	3	FACETS	1	0.968	1	0.533	0.496	0.571	CLONAL	1	TRUE	1	0.659352425351924	3		332	810	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0031356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	697	562	1	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.659352425351924	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.659352425351924	2		563	872	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0031356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	361	706	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.525077039607396	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.659352425351924	1		706	517	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050906	49050906	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	632	623	0	ENST00000267163.4:c.2590G>T	p.Glu864Ter	p.E864*	ENST00000267163	NM_000321.2	864	Gaa/Taa	25/27	0.659352425351924	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.659352425351924	3		623	817	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412905	49412905	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519951	NA	P-0031356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	559	854	0	ENST00000418115.1:c.118G>C	p.Glu40Gln	p.E40Q	ENST00000418115	NM_001664.2	40	Gag/Cag	2/5	0.659352425351924	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.659352425351924	2		854	792	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101327	27101327	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	404	789	0	ENST00000324856.7:c.4609C>T	p.Gln1537Ter	p.Q1537*	ENST00000324856	NM_006015.4	1537	Cag/Tag	18/20	0.659296555352615	3	FACETS	0.969	0.927	1	0.969	0.927	1	CLONAL	2	TRUE	1	0.659352425351924	3		789	841	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436821	52436821	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	468	705	1	ENST00000460680.1:c.1957G>A	p.Glu653Lys	p.E653K	ENST00000460680	NM_004656.3	653	Gag/Aag	15/17	0.659352425351924	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.659352425351924	2		706	661	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845644	68845693	+	frameshift_variant	Frame_Shift_Del	DEL	ATGCCGCCATCGCTTACACCATCCTCAGCCAAGATCCTGAGCTCCCTGAC	ATGCCGCCATCGCTTACACCATCCTCAGCCAAGATCCTGAGCTCCCTGAC	-	novel	NA	P-0031356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	303	769	0	ENST00000261769.5:c.891_940del	p.Asn297LysfsTer7	p.N297Kfs*7	ENST00000261769	NM_004360.3	297	aATGCCGCCATCGCTTACACCATCCTCAGCCAAGATCCTGAGCTCCCTGAC/a	7/16	0.659352425351924	2	FACETS	0.879	0.839	0.917	0.879	0.839	0.917	CLONAL	2	TRUE	0	0.659352425351924	2		769	523	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379718	17379718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1193352612	NA	P-0031356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	204	888	0	ENST00000359435.4:c.103G>A	p.Glu35Lys	p.E35K	ENST00000359435	NM_001033549.1	35	Gag/Aag	2/9	1	2	FACETS	0.864	0.804	0.926	0.864	0.804	0.926	CLONAL	1	TRUE	1	0.659352425351924	2		888	716	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961435	1961470	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGGGCCTGGTCGCCAAGAGGGACATCAGAAAGGTA	TGGGGCCTGGTCGCCAAGAGGGACATCAGAAAGGTA	-	novel	NA	P-0031356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	144	658	0	ENST00000382891.5:c.3225_3255+5del		p.X1075_splice	ENST00000382891	NM_133335.3	1075		17/22	1	2	FACETS	0.812	0.744	0.882	0.812	0.744	0.882	CLONAL	1	TRUE	1	0.659352425351924	2		658	538	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0031358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	79	361	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.874	0.768	0.988	0.874	0.768	0.988	CLONAL	1	TRUE	1	0.243577514882336	2		361	742	SUCCESS
BLM	641	MSKCC	GRCh37	15	91295052	91295052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	35	412	0	ENST00000355112.3:c.835G>A	p.Glu279Lys	p.E279K	ENST00000355112	NM_000057.2	279	Gaa/Aaa	4/22	1	2	FACETS	0.567	0.464	0.683	0.567	0.464	0.683	SUBCLONAL	1	TRUE	1	0.243577514882336	2		412	507	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265194	46265194	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	44	390	0	ENST00000371998.3:c.2064G>C	p.Leu688Phe	p.L688F	ENST00000371998		688	ttG/ttC	12/23	1	2	FACETS	0.836	0.702	0.984	0.836	0.702	0.984	CLONAL	1	TRUE	1	0.243577514882336	2		390	432	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793566	89793569	+	frameshift_variant	Frame_Shift_Del	DEL	ACAG	ACAG	-	novel	NA	P-0031358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	25	364	2	ENST00000336032.3:c.640_643del	p.Gln214LysfsTer8	p.Q214Kfs*8	ENST00000336032	NM_006813.2	212	aACAGa/aa	2/2	1	2	FACETS	0.432	0.34	0.539	0.432	0.34	0.539	SUBCLONAL	1	TRUE	1	0.243577514882336	2		366	475	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882084	36882084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	70	711	0	ENST00000358127.4:c.929C>T	p.Thr310Met	p.T310M	ENST00000358127	NM_001280556.1	310	aCg/aTg	8/10	1	2	FACETS	0.368	0.32	0.42	0.368	0.32	0.42	SUBCLONAL	1	TRUE	1	0.430677564230732	2		711	884	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0031360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	205	690	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.430677564230732	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.430677564230732	1		690	698	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741577	17741577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758659312	NA	P-0031360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	89	369	1	ENST00000250003.3:c.248C>T	p.Ala83Val	p.A83V	ENST00000250003	NM_002478.4	83	gCg/gTg	1/3	1	2	FACETS	0.796	0.708	0.89	0.796	0.708	0.89	SUBCLONAL	1	TRUE	1	0.430677564230732	2		370	519	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0031360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	159	318	1	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	0.430677564230732	2	FACETS	0.964	0.895	1	0.964	0.895	1	CLONAL	2	TRUE	0	0.430677564230732	2		319	383	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574323	41574323	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1233278896	NA	P-0031360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	84	737	1	ENST00000263253.7:c.6608C>T	p.Pro2203Leu	p.P2203L	ENST00000263253	NM_001429.3	2203	cCt/cTt	31/31	1	2	FACETS	0.385	0.339	0.435	0.385	0.339	0.435	SUBCLONAL	1	TRUE	1	0.430677564230732	2		738	1012	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519388	137519388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	72	322	0	ENST00000367739.4:c.1250G>A	p.Ser417Asn	p.S417N	ENST00000367739	NM_000416.2	417	aGc/aAc	7/7	1	2	FACETS	0.694	0.608	0.786	0.694	0.608	0.786	SUBCLONAL	1	TRUE	1	0.430677564230732	2		322	482	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	20	384	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.25540058613712	1	FACETS	0.776	0.597	0.983	0.776	0.597	0.983	CLONAL	1	TRUE	0	0.25540058613712	1		384	176	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422612	49422612	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	44	534	0	ENST00000301067.7:c.14381A>G	p.Lys4794Arg	p.K4794R	ENST00000301067	NM_003482.3	4794	aAg/aGg	45/54	0.137007925175724	3	FACETS	0.941	0.79	1	0.47	0.395	0.554	INDETERMINATE	1	TRUE	1	0.25540058613712	3		534	413	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0031371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	510	621	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.531496448422958	3	FACETS	1	0.996	1	0.805	0.778	0.832	CLONAL	2	FALSE	0	0.651886999287282	3		624	859	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481915	56481915	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	276	616	3	ENST00000267101.3:c.843G>T	p.Gln281His	p.Q281H	ENST00000267101	NM_001982.3	281	caG/caT	7/28	0.487681343864251	3	FACETS	1	0.988	1	0.744	0.708	0.78	CLONAL	2	FALSE	0	0.651886999287282	3		619	503	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120806057	120806057	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	241	573	0	ENST00000257552.2:c.120C>A	p.Phe40Leu	p.F40L	ENST00000257552	NM_002442.3	40	ttC/ttA	3/15	0.487681343864251	3	FACETS	0.784	0.731	0.839	0.261	0.243	0.28	SUBCLONAL	1	FALSE	0	0.651886999287282	3		573	1251	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719903	52719914	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	AGCTGAAGGATG	AGCTGAAGGATG	-	novel	NA	P-0031371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	223	560	0	ENST00000322088.6:c.1117_1128del	p.Leu373_Glu376del	p.L373_E376del	ENST00000322088	NM_014225.5	372	cAGCTGAAGGATGag/cag	9/15	0.625020188648044	4	FACETS	0.805	0.753	0.858	0.805	0.753	0.858	CLONAL	2	FALSE	2	0.651886999287282	4		560	702	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178941872	178941872	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	38	318	0	ENST00000263967.3:c.2191C>A	p.Gln731Lys	p.Q731K	ENST00000263967	NM_006218.2	731	Cag/Aag	15/21	0.625020188648044	4	FACETS	1	0.956	1	0.735	0.62	0.857	CLONAL	1	FALSE	2	0.651886999287282	4		318	131	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589157	67589161	+	protein_altering_variant	In_Frame_Del	DEL	AAATA	AAATA	TT	novel	NA	P-0031371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	46	331	1	ENST00000274335.5:c.1145_1149delinsTT	p.Lys382del	p.K382del	ENST00000274335		382	aAAATA/aTT	9/15	0.617872619215778	2	FACETS	0.882	0.781	0.981	0.882	0.781	0.981	CLONAL	2	FALSE	0	0.651886999287282	2		332	80	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468013	50468013	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	244	508	0	ENST00000331340.3:c.1248C>A	p.Asn416Lys	p.N416K	ENST00000331340	NM_006060.4	416	aaC/aaA	8/8	0.492172522101667	3	FACETS	0.962	0.899	1	0.481	0.449	0.514	CLONAL	1	FALSE	1	0.651886999287282	3		508	1032	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856110	151856110	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	167	397	0	ENST00000262189.6:c.11508G>T	p.Gln3836His	p.Q3836H	ENST00000262189	NM_170606.2	3836	caG/caT	44/59	0.290104508959576	6	FACETS	1	0.973	1	0.813	0.758	0.868	INDETERMINATE	3	FALSE	2	0.651886999287282	6		397	363	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206770	27206770	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	104	502	0	ENST00000380036.4:c.2555C>G	p.Ala852Gly	p.A852G	ENST00000380036	NM_000459.3	852	gCt/gGt	15/23	0.213231892905732	5	FACETS	0.896	0.803	0.995	0.299	0.267	0.332	INDETERMINATE	1	FALSE	2	0.651886999287282	5		502	704	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0031373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	75	505	4	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.24	2		509	603	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316107	11316108	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0031373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	67	600	1	ENST00000361445.4:c.646dup	p.Cys216LeufsTer9	p.C216Lfs*9	ENST00000361445	NM_004958.3	216	tgt/tTgt	5/58	1	2	FACETS	0.882	0.766	1	0.882	0.766	1	CLONAL	1	TRUE	1	0.24	2		601	633	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996800	100996800	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	105	650	0	ENST00000325455.5:c.1727G>T	p.Gly576Val	p.G576V	ENST00000325455	NM_001202474.3	576	gGc/gTc	2/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.24	2		650	612	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112127	115112127	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	85	693	0	ENST00000257566.3:c.1613G>T	p.Gly538Val	p.G538V	ENST00000257566	NM_016569.3	538	gGc/gTc	7/8	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.24	2		693	666	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254209	133254209	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	42	583	0	ENST00000320574.5:c.675T>A	p.Asp225Glu	p.D225E	ENST00000320574	NM_006231.2	225	gaT/gaA	7/49	1	2	FACETS	0.528	0.44	0.626	0.528	0.44	0.626	SUBCLONAL	1	TRUE	1	0.24	2		583	663	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748404	43748404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555405105	NA	P-0031373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	57	813	0	ENST00000382044.4:c.2402C>T	p.Pro801Leu	p.P801L	ENST00000382044	NM_001141980.1	801	cCa/cTa	12/28	1	2	FACETS	0.586	0.501	0.678	0.586	0.501	0.678	SUBCLONAL	1	TRUE	1	0.24	2		813	811	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199918	128199918	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	41	469	0	ENST00000341105.2:c.1387T>A	p.Ser463Thr	p.S463T	ENST00000341105	NM_032638.4	463	Tcc/Acc	6/6	1	2	FACETS	0.785	0.655	0.931	0.785	0.655	0.931	CLONAL	1	TRUE	1	0.24	2		469	435	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679762	30679762	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	61	599	0	ENST00000376406.3:c.1957G>A	p.Asp653Asn	p.D653N	ENST00000376406	NM_014641.2	653	Gac/Aac	5/15	1	2	FACETS	0.919	0.793	1	0.919	0.793	1	CLONAL	1	TRUE	1	0.24	2		599	553	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242488	55242488	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	76	595	0	ENST00000275493.2:c.2258C>A	p.Pro753Gln	p.P753Q	ENST00000275493	NM_005228.3	753	cCg/cAg	19/28	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.24	2		595	630	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5064952	5064952	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	61	500	0	ENST00000381652.3:c.1126A>T	p.Thr376Ser	p.T376S	ENST00000381652	NM_004972.3	376	Act/Tct	9/25	0.3	1	FACETS	0.779	0.672	0.896	0.779	0.672	0.896	SUBCLONAL	1	TRUE	0	0.24	1		500	574	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499745	8499745	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	59	558	0	ENST00000356435.5:c.2224G>T	p.Gly742Cys	p.G742C	ENST00000356435		742	Ggc/Tgc	14/35	0.3	1	FACETS	0.745	0.641	0.858	0.745	0.641	0.858	SUBCLONAL	1	TRUE	0	0.24	1		558	581	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409993	63409994	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0031373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	22	539	1	ENST00000330258.3:c.3173_3174delinsAA	p.Pro1058Gln	p.P1058Q	ENST00000330258	NM_152424.3	1058	cCC/cAA	2/2	0.3	1	FACETS	0.369	0.285	0.467	0.369	0.285	0.467	SUBCLONAL	1	TRUE	0	0.24	1		540	437	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178622	56178622	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	104	310	0	ENST00000399503.3:c.3595C>T	p.Gln1199Ter	p.Q1199*	ENST00000399503	NM_005921.1	1199	Cag/Tag	14/20	1	2	FACETS	1	0.966	1	1	0.989	1	CLONAL	2	FALSE	1	0.216819040463887	2		310	412	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0031376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	159	483	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			0.216819040463887	1	FACETS	1	0.983	1	1	0.993	1	CLONAL	2	FALSE	0	0.216819040463887	1		483	532	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180556	56180560	+	frameshift_variant	Frame_Shift_Del	DEL	AAGAA	AAGAA	-	novel	NA	P-0031376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	82	446	0	ENST00000399503.3:c.3885_3889del	p.Arg1296AspfsTer11	p.R1296Dfs*11	ENST00000399503	NM_005921.1	1295	atAAGAAtg/attg	16/20	1	2	FACETS	0.995	0.883	1	1	0.985	1	CLONAL	2	FALSE	1	0.216819040463887	2		446	380	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859583	151859599	+	frameshift_variant	Frame_Shift_Del	DEL	AGTTGCTTGTGAGAAAT	AGTTGCTTGTGAGAAAT	-	novel	NA	P-0031376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	142	507	0	ENST00000262189.6:c.11063_11079del	p.Asp3688AlafsTer31	p.D3688Afs*31	ENST00000262189	NM_170606.2	3688	gATTTCTCACAAGCAACT/g	43/59	0.216819040463887	1	FACETS	1	0.978	1	1	0.992	1	CLONAL	2	FALSE	0	0.216819040463887	1		507	492	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820570	44820570	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	153	596	0	ENST00000377967.4:c.270del	p.Val91TrpfsTer9	p.V91Wfs*9	ENST00000377967	NM_021140.2	89	ggA/gg	3/29	1	2	FACETS	1	0.98	1	1	0.993	1	CLONAL	2	FALSE	1	0.216819040463887	2		596	582	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0031378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	291	701	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.560758175576931	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.560758175576931	1		701	670	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0031378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	282	377	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.78	0.738	0.821	1	0.995	1	SUBCLONAL	2	TRUE	1	0.560758175576931	2		377	645	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296323	15296323	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1378515982	NA	P-0031378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	239	761	3	ENST00000263388.2:c.2119G>A	p.Gly707Ser	p.G707S	ENST00000263388	NM_000435.2	707	Ggc/Agc	13/33	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.560758175576931	2		764	828	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143029273	143029273	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	103	360	0	ENST00000262992.4:c.2347A>T	p.Ile783Leu	p.I783L	ENST00000262992	NM_001101669.1	783	Ata/Tta	21/24	0.560758175576931	1	FACETS	0.965	0.877	1	0.965	0.877	1	CLONAL	1	TRUE	0	0.560758175576931	1		360	274	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0031379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	200	551	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.541113278994502	2		551	737	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913400	NA	P-0031379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	119	361	0	ENST00000349496.5:c.98C>A	p.Ser33Tyr	p.S33Y	ENST00000349496	NM_001904.3	33	tCt/tAt	3/15	1	2	FACETS	0.932	0.846	1	0.932	0.846	1	CLONAL	1	TRUE	1	0.541113278994502	2		361	472	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0031379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	231	610	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.966	0.902	1	0.966	0.902	1	CLONAL	1	TRUE	1	0.541113278994502	2		611	884	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0031379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	592	572	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.53505673145628	3	FACETS	0.994	0.965	1	0.994	0.965	1	CLONAL	3	TRUE	0	0.541113278994502	3		572	932	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0031379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	264	648	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.541113278994502	2		648	928	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0031379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	216	609	10	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	1	2	FACETS	0.955	0.89	1	0.955	0.89	1	CLONAL	1	TRUE	1	0.541113278994502	2		619	836	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097625	11097625	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	260	848	3	ENST00000358026.2:c.810del	p.Met272CysfsTer31	p.M272Cfs*31	ENST00000358026	NM_001128849.1	269	Ccc/cc	5/36	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.541113278994502	2		851	958	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096048	11096048	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	256	770	3	ENST00000358026.2:c.326del	p.Pro109ArgfsTer194	p.P109Rfs*194	ENST00000358026	NM_001128849.1	108	Ccc/cc	3/36	1	2	FACETS	0.94	0.88	1	0.94	0.88	1	CLONAL	1	TRUE	1	0.541113278994502	2		773	1007	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413710	138413710	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	73	466	1	ENST00000289153.2:c.1810del	p.Arg604GlyfsTer4	p.R604Gfs*4	ENST00000289153	NM_006219.2	604	Cgg/gg	12/22	1	2	FACETS	0.399	0.348	0.453	0.399	0.348	0.453	SUBCLONAL	1	TRUE	1	0.541113278994502	2		467	677	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741552	17741552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	153	464	2	ENST00000250003.3:c.223G>A	p.Ala75Thr	p.A75T	ENST00000250003	NM_002478.4	75	Gca/Aca	1/3	1	2	FACETS	0.906	0.832	0.983	0.906	0.832	0.983	CLONAL	1	TRUE	1	0.541113278994502	2		466	624	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433005	49433005	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1208681909	NA	P-0031379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	62	648	1	ENST00000301067.7:c.8366G>A	p.Arg2789Gln	p.R2789Q	ENST00000301067	NM_003482.3	2789	cGg/cAg	33/54	1	2	FACETS	0.281	0.242	0.324	0.281	0.242	0.324	SUBCLONAL	1	TRUE	1	0.541113278994502	2		649	815	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591712	38591713	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0031379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	169	523	0	ENST00000299084.4:c.177dup	p.Ile60TyrfsTer18	p.I60Yfs*18	ENST00000299084	NM_152594.2	57	-/T	2/7	1	2	FACETS	0.891	0.822	0.963	0.891	0.822	0.963	CLONAL	1	TRUE	1	0.541113278994502	2		523	701	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441955	40441955	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	77	701	0	ENST00000345506.4:c.200A>G	p.Glu67Gly	p.E67G	ENST00000345506	NM_003152.3	67	gAg/gGg	4/20	1	2	FACETS	0.319	0.279	0.362	0.319	0.279	0.362	SUBCLONAL	1	TRUE	1	0.541113278994502	2		701	893	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097149	11097149	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	261	735	0	ENST00000358026.2:c.640C>T	p.Gln214Ter	p.Q214*	ENST00000358026	NM_001128849.1	214	Cag/Tag	4/36	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.541113278994502	2		735	920	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214714	36214714	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774265693	NA	P-0031379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	181	544	0	ENST00000222270.7:c.3140G>A	p.Arg1047Gln	p.R1047Q	ENST00000222270	NM_014727.1	1047	cGg/cAg	8/37	1	2	FACETS	0.938	0.868	1	0.938	0.868	1	CLONAL	1	TRUE	1	0.541113278994502	2		544	713	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54956607	54956607	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	178	487	0	ENST00000312783.6:c.587T>C	p.Leu196Pro	p.L196P	ENST00000312783	NM_198436.1	196	cTg/cCg	7/10	1	2	FACETS	0.956	0.884	1	0.956	0.884	1	CLONAL	1	TRUE	1	0.541113278994502	2		487	688	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139069	37139069	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	201	564	0	ENST00000373509.5:c.409G>T	p.Gly137Ter	p.G137*	ENST00000373509	NM_002648.3	137	Gga/Tga	4/6	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.541113278994502	2		564	735	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978799	13978799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	277	626	0	ENST00000405192.2:c.308G>A	p.Cys103Tyr	p.C103Y	ENST00000405192	NM_001163147.1	103	tGc/tAc	6/12	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.541113278994502	2		626	864	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0031380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	385	498	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.822	0.789	0.855	1	0.996	1	CLONAL	2	TRUE	1	0.683730333939715	2		498	685	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070577	67070577	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	123	306	0	ENST00000412916.2:c.201G>T	p.Gln67His	p.Q67H	ENST00000412916		67	caG/caT	3/6	0.654868590948911	1	FACETS	0.688	0.63	0.748	0.688	0.63	0.748	SUBCLONAL	1	TRUE	0	0.683730333939715	1		306	344	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591931	48591931	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	151	447	0	ENST00000342988.3:c.1094G>T	p.Gly365Val	p.G365V	ENST00000342988	NM_005359.5	365	gGt/gTt	9/12	0.654868590948911	1	FACETS	0.714	0.66	0.77	0.714	0.66	0.77	SUBCLONAL	1	TRUE	0	0.683730333939715	1		447	407	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15827432	15827432	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	210	596	0	ENST00000307771.7:c.548T>A	p.Phe183Tyr	p.F183Y	ENST00000307771	NM_005089.3	183	tTt/tAt	7/11	1	2	FACETS	0.827	0.77	0.885	0.827	0.77	0.885	CLONAL	1	TRUE	1	0.683730333939715	2		596	743	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	113	270	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.892	0.807	0.982	0.892	0.807	0.982	CLONAL	1	TRUE	1	0.504547212575785	2		270	502	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0031381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10551	1418	595	0	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.504547212575785	40	FACETS	0.994	0.965	1	0.124	0.12	0.128	CLONAL	5	TRUE	0	0.504547212575785	40		595	11969	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0031381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8461	1618	536	2	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.504547212575785	40	FACETS	0.962	0.936	0.989	0.168	0.163	0.173	CLONAL	7	TRUE	0	0.504547212575785	40		538	10079	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221722	55221722	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3284	5096	425	1	ENST00000275493.2:c.766G>T	p.Asp256Tyr	p.D256Y	ENST00000275493	NM_005228.3	256	Gac/Tac	7/28	0.504547212575785	40	FACETS	0.981	0.971	0.992	0.638	0.631	0.645	CLONAL	26	TRUE	0	0.504547212575785	40		426	8380	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590684	189590684	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1489154659	NA	P-0031381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	184	510	0	ENST00000264731.3:c.1249A>G	p.Ile417Val	p.I417V	ENST00000264731	NM_003722.4	417	Atc/Gtc	10/14	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.504547212575785	2		510	706	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0031385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	141	430	2	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	0.3014871641518	2	FACETS	0.946	0.872	1	0.946	0.872	1	CLONAL	2	TRUE	0	0.386962564620507	2		432	385	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99454561	99454561	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	118	501	0	ENST00000268035.6:c.1480C>G	p.His494Asp	p.H494D	ENST00000268035	NM_000875.3	494	Cat/Gat	7/21	0.165757547908201	2	FACETS	0.913	0.834	0.994	0.913	0.834	0.994	INDETERMINATE	2	TRUE	0	0.386962564620507	2		501	334	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139112	37139140	+	frameshift_variant	Frame_Shift_Del	DEL	TGCTGGAGGCCGTGCGGCACTGCCACAAC	TGCTGGAGGCCGTGCGGCACTGCCACAAC	-	novel	NA	P-0031385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	76	513	0	ENST00000373509.5:c.455_483del	p.Leu152ArgfsTer47	p.L152Rfs*47	ENST00000373509	NM_002648.3	151	gTGCTGGAGGCCGTGCGGCACTGCCACAAC/g	4/6	0.386962564620507	7	FACETS	0.851	0.749	0.96	0.426	0.374	0.48	CLONAL	2	TRUE	3	0.386962564620507	7		513	454	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0031386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	158	491	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.194427370156915	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	1	0.236360995223041	3		491	717	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727451	66727451	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519729	NA	P-0031386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	16	414	0	ENST00000307102.5:c.167A>C	p.Gln56Pro	p.Q56P	ENST00000307102	NM_002755.3	56	cAg/cCg	2/11	1	2	FACETS	0.264	0.194	0.349	0.264	0.194	0.349	SUBCLONAL	1	TRUE	1	0.236360995223041	2		414	512	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649111	37649111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	60	413	0	ENST00000447079.4:c.2216G>A	p.Gly739Asp	p.G739D	ENST00000447079	NM_015083.1	739	gGc/gAc	4/14	1	2	FACETS	0.897	0.773	1	0.897	0.773	1	CLONAL	1	TRUE	1	0.236360995223041	2		413	566	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259441	55259442	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0031386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	120	420	1	ENST00000275493.2:c.2499_2500delinsTT	p.Leu833_Val834delinsPheLeu	p.L833_V834delinsFL	ENST00000275493	NM_005228.3	833	ttGGtg/ttTTtg	21/28	0.194427370156915	3	FACETS	1	0.919	1	1	0.919	1	CLONAL	2	TRUE	1	0.236360995223041	3		421	559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0031387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	152	890	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.445713356553771	3	FACETS	0.806	0.742	0.872	0.806	0.742	0.872	CLONAL	2	TRUE	1	0.442875247429073	3		892	520	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0031387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	33	258	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	0.166218666564298	4	FACETS	0.991	0.813	1	0.495	0.406	0.594	INDETERMINATE	1	TRUE	2	0.442875247429073	4		258	217	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0031387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	28	483	0	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	0.166218666564298	4	FACETS	0.612	0.49	0.751	0.306	0.245	0.376	INDETERMINATE	1	TRUE	2	0.442875247429073	4		483	298	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481417	140481417	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913348	NA	P-0031387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	42	383	1	ENST00000288602.6:c.1391G>T	p.Gly464Val	p.G464V	ENST00000288602	NM_004333.4	464	gGa/gTa	11/18	NA	2	FACETS	0.568	0.476	0.669			1	INDETERMINATE	1	TRUE	NA	0.442875247429073	2		384	334	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952076	178952076	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1064793838	NA	P-0031387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	31	461	0	ENST00000263967.3:c.3131A>G	p.Asn1044Ser	p.N1044S	ENST00000263967	NM_006218.2	1044	aAt/aGt	21/21	0.166218666564298	4	FACETS	0.527	0.427	0.641	0.264	0.213	0.321	INDETERMINATE	1	TRUE	2	0.442875247429073	4		461	383	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0031389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	121	170	1	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.632227830116584	6	FACETS	1	0.976	1	0.597	0.545	0.65	CLONAL	2	TRUE	2	0.632227830116584	6		171	363	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0031389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	144	538	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	0.632227830116584	3	FACETS	1	0.969	1	0.559	0.513	0.607	CLONAL	1	TRUE	1	0.632227830116584	3		538	536	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9779982	9779982	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587777390	NA	P-0031389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	287	516	0	ENST00000377346.4:c.1246T>C	p.Cys416Arg	p.C416R	ENST00000377346	NM_005026.3	416	Tgc/Cgc	10/24	0.632227830116584	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.632227830116584	3		516	565	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0031391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	172	498	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.517662143463437	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.524905167730825	1		498	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578509	7578510	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGTCTT	novel	NA	P-0031391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	213	944	0	ENST00000269305.4:c.415_420dup	p.Lys139_Thr140dup	p.K139_T140dup	ENST00000269305	NM_001126112.2	139	-/AAGACC	5/11	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.524905167730825	2		944	685	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061235	38061235	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1428644047	NA	P-0031392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	285	602	0	ENST00000250448.2:c.754A>C	p.Asn252His	p.N252H	ENST00000250448	NM_004496.3	252	Aac/Cac	2/2	0.187013577907098	6	FACETS	1	0.955	1	1	0.991	1	CLONAL	5	FALSE	2	0.187013577907098	6		602	826	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0031394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	220	459	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.141584629861209	3	FACETS	1	0.982	1	0.582	0.542	0.625	INDETERMINATE	1	TRUE	1	0.46	3		459	1010	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577035	7577036	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0031394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	66	517	0	ENST00000269305.4:c.902dup	p.Gly302ArgfsTer4	p.G302Rfs*4	ENST00000269305	NM_001126112.2	301	cca/ccCa	8/11	1	2	FACETS	0.368	0.319	0.422	0.368	0.319	0.422	SUBCLONAL	1	TRUE	1	0.46	2		517	780	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593478	48593479	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs730881952	NA	P-0031394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	43	397	0	ENST00000342988.3:c.1231_1232del	p.Ser411LeufsTer17	p.S411Lfs*17	ENST00000342988	NM_005359.5	410	cAG/c	10/12	1	2	FACETS	0.321	0.268	0.38	0.321	0.268	0.38	SUBCLONAL	1	TRUE	1	0.46	2		397	583	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445404	49445404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371076182	NA	P-0031394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	112	659	0	ENST00000301067.7:c.2062C>T	p.Arg688Cys	p.R688C	ENST00000301067	NM_003482.3	688	Cgc/Tgc	10/54	0.141584629861209	3	FACETS	0.603	0.541	0.669	0.302	0.27	0.335	INDETERMINATE	1	TRUE	1	0.46	3		659	993	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201881	67201881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146762475	NA	P-0031394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	73	652	0	ENST00000312629.5:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000312629	NM_003952.2	361	Cgc/Tgc	13/15	1	2	FACETS	0.386	0.336	0.439	0.386	0.336	0.439	SUBCLONAL	1	TRUE	1	0.46	2		652	823	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845153	151845154	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0031394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	49	534	0	ENST00000262189.6:c.13858dup	p.His4620ProfsTer2	p.H4620Pfs*2	ENST00000262189	NM_170606.2	4620	cat/cCat	52/59	0.141584629861209	3	FACETS	0.322	0.272	0.378	0.161	0.136	0.189	INDETERMINATE	1	TRUE	1	0.46	3		534	814	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039824	47039824	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	88	703	0	ENST00000377604.3:c.1168del	p.Ala390ProfsTer95	p.A390Pfs*95	ENST00000377604	NM_001204468.1	389	atG/at	12/24	1	2	FACETS	0.5	0.443	0.562	0.5	0.443	0.562	SUBCLONAL	1	TRUE	1	0.46	2		703	765	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115955	8115956	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0031404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	39	336	0	ENST00000346208.3:c.1305dup	p.Ser436LeufsTer71	p.S436Lfs*71	ENST00000346208		434	cac/caCc	6/6	0.341177416991854	3	FACETS	0.405	0.335	0.482	0.135	0.111	0.161	SUBCLONAL	1	TRUE	0	0.551277058131428	3		336	446	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459340	99459340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45451896	NA	P-0031404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	23	384	0	ENST00000268035.6:c.1976G>A	p.Arg659Gln	p.R659Q	ENST00000268035	NM_000875.3	659	cGg/cAg	9/21	0.235453390870732	2	FACETS	0.189	0.147	0.238	0.095	0.073	0.119	INDETERMINATE	1	TRUE	0	0.551277058131428	2		384	441	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588842	69588842	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	101	703	0	ENST00000168712.1:c.394G>T	p.Ala132Ser	p.A132S	ENST00000168712	NM_002007.2	132	Gcc/Tcc	2/3	0.287045751466962	5	FACETS	0.627	0.559	0.7	0.209	0.186	0.234	INDETERMINATE	1	TRUE	2	0.551277058131428	5		703	1067	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50490711	50490711	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	209	526	0	ENST00000394963.4:c.1348G>C	p.Gly450Arg	p.G450R	ENST00000394963	NM_003076.4	450	Ggt/Cgt	11/13	0.480913594829061	3	FACETS	1	0.988	1	0.649	0.604	0.695	CLONAL	1	TRUE	1	0.551277058131428	3		526	745	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30099980	30099980	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1775	182	426	0	ENST00000331968.5:c.1640G>T	p.Gly547Val	p.G547V	ENST00000331968	NM_002742.2	547	gGc/gTc	10/18	0.551277058131428	13	FACETS	1	0.986	1	0.124	0.113	0.135	CLONAL	1	TRUE	2	0.551277058131428	13		426	1957	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234442	41234442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	23	553	0	ENST00000357654.3:c.4336G>A	p.Glu1446Lys	p.E1446K	ENST00000357654	NM_007294.3	1446	Gaa/Aaa	12/23	0.551277058131428	1	FACETS	0.14	0.108	0.176	0.14	0.108	0.176	SUBCLONAL	1	TRUE	0	0.551277058131428	1		553	432	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325680	87325680	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	76	469	1	ENST00000277120.3:c.557T>C	p.Leu186Pro	p.L186P	ENST00000277120		186	cTg/cCg	6/19	0.453823209663858	5	FACETS	0.614	0.538	0.697	0.205	0.179	0.233	SUBCLONAL	1	TRUE	2	0.551277058131428	5		470	820	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0031405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	22	562	3	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.622	0.48	0.788	0.622	0.48	0.788	SUBCLONAL	1	TRUE	1	0.11	2		565	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579442	7579442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	37	713	0	ENST00000269305.4:c.245del	p.Pro82ArgfsTer41	p.P82Rfs*41	ENST00000269305	NM_001126112.2	82	cCg/cg	4/11	1	2	FACETS	0.989	0.814	1	0.989	0.814	1	CLONAL	1	TRUE	1	0.11	2		713	680	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891173	101891173	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	31	351	0	ENST00000374994.4:c.134A>T	p.Asn45Ile	p.N45I	ENST00000374994	NM_004612.2	45	aAt/aTt	2/9	1	2	FACETS	1	0.826	1	1	0.826	1	CLONAL	1	TRUE	1	0.11	2		351	550	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1427441061	NA	P-0031406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	310	560	0	ENST00000269305.4:c.560-2A>G		p.X187_splice	ENST00000269305	NM_001126112.2	187			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		560	699	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0031407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	331	912	0	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	0.561857437281918	1	FACETS	0.981	0.932	1	0.981	0.932	1	CLONAL	1	TRUE	0	0.595471120659815	1		912	796	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156603	55156603	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200676118	NA	P-0031407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	175	619	1	ENST00000257290.5:c.3004G>T	p.Asp1002Tyr	p.D1002Y	ENST00000257290	NM_006206.4	1002	Gac/Tac	22/23	0.461789247454061	1	FACETS	0.729	0.676	0.784	0.729	0.676	0.784	SUBCLONAL	1	TRUE	0	0.595471120659815	1		620	566	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964316	55964316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1224362892	NA	P-0031407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	51	468	0	ENST00000263923.4:c.2497C>T	p.Arg833Trp	p.R833W	ENST00000263923	NM_002253.2	833	Cgg/Tgg	17/30	0.461789247454061	1	FACETS	0.353	0.301	0.409	0.353	0.301	0.409	SUBCLONAL	1	TRUE	0	0.595471120659815	1		468	341	SUCCESS
APC	324	MSKCC	GRCh37	5	112173627	112173627	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs1561576302	NA	P-0031407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	73	410	0	ENST00000257430.4:c.2336T>G	p.Leu779Ter	p.L779*	ENST00000257430	NM_000038.5	779	tTa/tGa	16/16	0.461789247454061	1	FACETS	0.498	0.438	0.561	0.498	0.438	0.561	SUBCLONAL	1	TRUE	0	0.595471120659815	1		410	346	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	167	384	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.672552029624062	2	FACETS	0.941	0.891	0.989	0.941	0.891	0.989	CLONAL	2	TRUE	0	0.718488454546321	2		384	247	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0031409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	101	503	1	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.329785596005536	3	FACETS	1	0.976	1	0.629	0.569	0.69	INDETERMINATE	1	TRUE	1	0.718488454546321	3		504	304	SUCCESS
APC	324	MSKCC	GRCh37	5	112174112	112174112	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	61	425	0	ENST00000257430.4:c.2821G>T	p.Glu941Ter	p.E941*	ENST00000257430	NM_000038.5	941	Gaa/Taa	16/16	0.329785596005536	3	FACETS	0.986	0.862	1	0.493	0.431	0.559	INDETERMINATE	1	TRUE	1	0.718488454546321	3		425	234	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717609	89717609	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs876661024	NA	P-0031412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	242	327	0	ENST00000371953.3:c.635-1G>C		p.X212_splice	ENST00000371953	NM_000314.4	212			0.690871526034241	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.690871526034241	1		327	388	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440844	52440844	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0031412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	253	499	0	ENST00000460680.1:c.659+1G>T		p.X220_splice	ENST00000460680	NM_004656.3	220			0.690871526034241	1	FACETS	0.993	0.941	1	0.993	0.941	1	CLONAL	1	TRUE	0	0.690871526034241	1		499	483	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43745252	43745311	+	inframe_deletion	In_Frame_Del	DEL	CGAGACCCTGGTGGACATCTTCCAGGAGTACCCTGATGAGATCGAGTACATCTTCAAGCC	CGAGACCCTGGTGGACATCTTCCAGGAGTACCCTGATGAGATCGAGTACATCTTCAAGCC	-	novel	NA	P-0031412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	255	579	0	ENST00000523873.1:c.165_224del	p.Glu56_Pro75del	p.E56_P75del	ENST00000523873		55	atCGAGACCCTGGTGGACATCTTCCAGGAGTACCCTGATGAGATCGAGTACATCTTCAAGCCa/ata	3/8	1	2	FACETS	0.879	0.825	0.934	0.879	0.825	0.934	CLONAL	1	TRUE	1	0.690871526034241	2		579	840	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0031413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	301	477	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	NA	2	FACETS	0.961	0.909	1			1	INDETERMINATE	2	TRUE	NA	0.380478361064174	2		478	823	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0031413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	227	548	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.380478361064174	3	FACETS	0.977	0.914	1	0.977	0.914	1	CLONAL	2	TRUE	1	0.380478361064174	3		548	727	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732907	74732908	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0031413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	97	221	0	ENST00000359995.5:c.335dup	p.Gly113ArgfsTer11	p.G113Rfs*11	ENST00000359995	NM_001195427.1	112	ggc/ggGc	1/3	0.380478361064174	4	FACETS	0.805	0.722	0.893	0.403	0.361	0.447	CLONAL	2	TRUE	0	0.380478361064174	4		221	437	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728602	190728602	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	121	575	0	ENST00000441310.2:c.1990C>T	p.Gln664Ter	p.Q664*	ENST00000441310	NM_000534.4	664	Cag/Tag	10/13	1	2	FACETS	0.896	0.81	0.986	0.896	0.81	0.986	CLONAL	1	TRUE	1	0.380478361064174	2		575	710	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467919	66467919	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	65	328	0	ENST00000273854.3:c.350G>T	p.Trp117Leu	p.W117L	ENST00000273854	NM_004439.5	117	tGg/tTg	3/18	0.255302302991322	3	FACETS	0.704	0.61	0.805			1	SUBCLONAL	1	TRUE	NA	0.380478361064174	3		328	578	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0031417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	280	477	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.285120534134593	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.285120534134593	3		477	920	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0031417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	230	737	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.285120534134593	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.285120534134593	2		737	768	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604673	48604673	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060500738	NA	P-0031417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	79	485	0	ENST00000342988.3:c.1495T>C	p.Cys499Arg	p.C499R	ENST00000342988	NM_005359.5	499	Tgc/Cgc	12/12	0.285120534134593	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.285120534134593	1		485	416	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011200	12011200	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	69	394	0	ENST00000353533.5:c.607G>T	p.Glu203Ter	p.E203*	ENST00000353533	NM_003010.3	203	Gaa/Taa	5/11	0.285120534134593	2	FACETS	0.886	0.78	0.998	0.886	0.78	0.998	CLONAL	2	TRUE	0	0.285120534134593	2		394	273	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	90	745	0	ENST00000397062.3:c.246A>T	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaT	2/5	0.101409642844943	2	FACETS	0.974	0.863	1	0.974	0.863	1	CLONAL	2	TRUE	0	0.101409642844943	2		745	911	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0031418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	152	706	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.101264905437162	5	FACETS	1	0.938	1	1	0.938	1	CLONAL	4	TRUE	1	0.101409642844943	5		706	838	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820696	3820696	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1231	66	1061	1	ENST00000262367.5:c.2755C>T	p.Gln919Ter	p.Q919*	ENST00000262367	NM_004380.2	919	Cag/Tag	14/31	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.101409642844943	2		1062	1297	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106975	27106991	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGGCTTCCTAGAGGA	CTGGGCTTCCTAGAGGA	-	novel	NA	P-0031418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	34	529	0	ENST00000324856.7:c.6587_6603del	p.Leu2196GlnfsTer23	p.L2196Qfs*23	ENST00000324856	NM_006015.4	2196	CTGGGCTTCCTAGAGGAc/c	20/20	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.101409642844943	2		529	618	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590440	67590441	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0031418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	26	326	0	ENST00000274335.5:c.1505_1506dup	p.Arg503SerfsTer8	p.R503Sfs*8	ENST00000274335		501	caa/caAGa	11/15	1	2	FACETS	1	0.83	1	1	0.83	1	CLONAL	1	TRUE	1	0.101409642844943	2		326	485	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805684	46805713	+	inframe_deletion	In_Frame_Del	DEL	CGGCAGGAGTAGTACCCGCCTCCAAAGTAA	CGGCAGGAGTAGTACCCGCCTCCAAAGTAA	-	novel	NA	P-0031419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	425	866	0	ENST00000290295.7:c.243_272del	p.Tyr82_Arg91del	p.Y82_R91del	ENST00000290295	NM_006361.5	81	ggTTACTTTGGAGGCGGGTACTACTCCTGCCGa/gga	1/2	1	2	FACETS	0.861	0.822	0.901	0.861	0.822	0.901	CLONAL	1	TRUE	1	0.886842084102081	2		866	1113	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165153	47165153	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	197	358	0	ENST00000409792.3:c.973G>A	p.Glu325Lys	p.E325K	ENST00000409792	NM_014159.6	325	Gaa/Aaa	3/21	1	2	FACETS	0.92	0.86	0.98	0.92	0.86	0.98	CLONAL	1	TRUE	1	0.886842084102081	2		358	483	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445082	89445082	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	295	536	0	ENST00000336596.2:c.1402T>A	p.Leu468Met	p.L468M	ENST00000336596	NM_005233.5	468	Ttg/Atg	6/17	1	2	FACETS	0.98	0.929	1	0.98	0.929	1	CLONAL	1	TRUE	1	0.886842084102081	2		536	679	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467759	50467759	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	51	689	0	ENST00000331340.3:c.994C>T	p.Gln332Ter	p.Q332*	ENST00000331340	NM_006060.4	332	Cag/Tag	8/8	1	2	FACETS	0.14	0.119	0.164	0.14	0.119	0.164	SUBCLONAL	1	TRUE	1	0.886842084102081	2		689	819	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231375	5231375	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs757257991	NA	P-0031424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	82	738	0	ENST00000357368.4:c.2101G>C	p.Glu701Gln	p.E701Q	ENST00000357368	NM_002850.3	701	Gag/Cag	14/38	0.14465153720491	4	FACETS	0.803	0.707	0.906	0.401	0.353	0.453	INDETERMINATE	1	TRUE	2	0.340611703734044	4		738	804	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351737	89351737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1385566000	NA	P-0031424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	276	921	0	ENST00000301030.4:c.1213C>T	p.Arg405Cys	p.R405C	ENST00000301030	NM_001256183.1	405	Cgt/Tgt	9/13	0.287398657073831	3	FACETS	0.893	0.839	0.949	0.595	0.559	0.633	CLONAL	2	TRUE	0	0.340611703734044	3		921	1062	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032069	26032069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	51	473	0	ENST00000244661.2:c.220G>A	p.Glu74Lys	p.E74K	ENST00000244661	NM_003537.3	74	Gaa/Aaa	1/1	1	2	FACETS	0.713	0.607	0.829	0.713	0.607	0.829	SUBCLONAL	1	TRUE	1	0.340611703734044	2		473	420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579503	7579503	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567556752	NA	P-0031424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	195	899	0	ENST00000269305.4:c.184G>T	p.Glu62Ter	p.E62*	ENST00000269305	NM_001126112.2	62	Gaa/Taa	4/11	0.253785228714967	2	FACETS	0.814	0.756	0.874	0.814	0.756	0.874	CLONAL	2	TRUE	0	0.340611703734044	2		899	703	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101393	27101393	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	138	501	2	ENST00000324856.7:c.4675G>T	p.Ala1559Ser	p.A1559S	ENST00000324856	NM_006015.4	1559	Gcc/Tcc	18/20	0.253785228714967	2	FACETS	0.887	0.813	0.962	0.887	0.813	0.962	CLONAL	2	TRUE	0	0.340611703734044	2		503	457	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909912	100909912	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	54	446	0	ENST00000325455.5:c.2737A>T	p.Ile913Phe	p.I913F	ENST00000325455	NM_001202474.3	913	Att/Ttt	8/8	0.33856567138119	2	FACETS	0.701	0.6	0.812	0.351	0.3	0.406	SUBCLONAL	1	TRUE	0	0.340611703734044	2		446	452	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392030	118392030	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	221	504	0	ENST00000534358.1:c.11541C>A	p.Phe3847Leu	p.F3847L	ENST00000534358	NM_005933.3	3847	ttC/ttA	35/36	0.272458593223327		FACETS		0.876	0.996				CLONAL	3	TRUE	NA	0.340611703734044	4		504	620	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156016	119156016	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1246882963	NA	P-0031424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	91	783	0	ENST00000264033.4:c.1681C>G	p.Gln561Glu	p.Q561E	ENST00000264033	NM_005188.3	561	Caa/Gaa	11/16	0.272458593223327	4	FACETS	0.764	0.677	0.857			1	SUBCLONAL	1	TRUE	NA	0.340611703734044	4		783	938	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006442	12006442	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	88	769	1	ENST00000396373.4:c.410G>C	p.Gly137Ala	p.G137A	ENST00000396373	NM_001987.4	137	gGa/gCa	4/8	0.226714763009855	4	FACETS	0.784	0.693	0.881	0.392	0.346	0.441	SUBCLONAL	1	TRUE	2	0.340611703734044	4		770	884	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443745	49443745	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	121	835	0	ENST00000301067.7:c.3626C>G	p.Ser1209Cys	p.S1209C	ENST00000301067	NM_003482.3	1209	tCt/tGt	11/54	0.292357588668217	3	FACETS	0.927	0.837	1	0.463	0.418	0.511	CLONAL	1	TRUE	1	0.340611703734044	3		835	897	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913983	32913983	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	146	613	0	ENST00000380152.3:c.5491A>C	p.Ile1831Leu	p.I1831L	ENST00000380152		1831	Ata/Cta	11/27	0.253785228714967	2	FACETS	0.886	0.814	0.959	0.886	0.814	0.959	CLONAL	2	TRUE	0	0.340611703734044	2		613	484	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955223	17955223	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	205	860	0	ENST00000458235.1:c.4del	p.Ala2HisfsTer9	p.A2Hfs*9	ENST00000458235	NM_000215.3	2	Gca/ca	2/24	0.226714763009855	4	FACETS	0.871	0.809	0.936	0.871	0.809	0.936	CLONAL	2	TRUE	2	0.340611703734044	4		860	926	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098953	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	93	381	0	ENST00000397062.3:c.92G>T	p.Gly31Val	p.G31V	ENST00000397062	NM_006164.4	31	gGa/gTa	2/5	0.292357588668217	3	FACETS	0.759	0.679	0.843	0.759	0.679	0.843	SUBCLONAL	2	TRUE	1	0.340611703734044	3		381	421	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30682855	30682855	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	82	632	2	ENST00000376406.3:c.98G>T	p.Arg33Leu	p.R33L	ENST00000376406	NM_014641.2	33	cGg/cTg	2/15	1	2	FACETS	0.756	0.667	0.851	0.756	0.667	0.851	SUBCLONAL	1	TRUE	1	0.340611703734044	2		634	637	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971060	21971071	+	inframe_deletion	In_Frame_Del	DEL	CCCGGTGCAGCA	CCCGGTGCAGCA	-	novel	NA	P-0031424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	158	500	0	ENST00000304494.5:c.287_298del	p.Val96_Arg99del	p.V96_R99del	ENST00000304494	NM_000077.4	96	gTGCTGCACCGGGcc/gcc	2/3	0.289257396053963	2	FACETS	0.987	0.912	1	0.987	0.912	1	CLONAL	2	TRUE	0	0.340611703734044	2		500	470	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0031426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	40	381	3	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.416	0.347	0.492	0.416	0.347	0.492	SUBCLONAL	1	TRUE	1	0.637184232282372	2		384	302	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481403	140481403	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913357	NA	P-0031426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	416	528	0	ENST00000288602.6:c.1405G>C	p.Gly469Arg	p.G469R	ENST00000288602	NM_004333.4	469	Gga/Cga	11/18	0.637184232282372	3	FACETS	0.98	0.939	1	0.98	0.939	1	CLONAL	2	TRUE	1	0.637184232282372	3		528	878	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271198	153271198	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs202191840	NA	P-0031426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	107	265	15	ENST00000281708.4:c.580A>G	p.Thr194Ala	p.T194A	ENST00000281708	NM_033632.3	194	Aca/Gca	3/12	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.637184232282372	2		280	330	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836758	151836758	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0031426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	332	476	0	ENST00000262189.6:c.14460+2T>G		p.X4820_splice	ENST00000262189	NM_170606.2	4820			0.637184232282372	3	FACETS	0.871	0.828	0.914	0.871	0.828	0.914	CLONAL	2	TRUE	1	0.637184232282372	3		476	789	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032264	10032264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751692867	NA	P-0031429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	13	444	0	ENST00000330684.3:c.559G>A	p.Val187Ile	p.V187I	ENST00000330684	NM_001134407.1	187	Gtc/Atc	3/13	0.106862400716072	3	FACETS	0.965	0.69	1	0.482	0.345	0.649	CLONAL	1	TRUE	1	0.17	3		444	172	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17350532	17350532	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	68	470	0	ENST00000375499.3:c.578G>C	p.Ser193Thr	p.S193T	ENST00000375499	NM_003000.2	193	aGc/aCc	6/8	0.287498956904921	4	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	2	0.17	4		470	430	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245456	46245456	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	10	336	0	ENST00000334344.6:c.3550C>A	p.Pro1184Thr	p.P1184T	ENST00000334344	NM_152641.2	1184	Cct/Act	15/21	0.444834941790528	4	FACETS	0.819	0.556	1	0.41	0.278	0.575	CLONAL	1	TRUE	2	0.17	4		336	168	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695830	117695830	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	10	448	0	ENST00000369458.3:c.607T>C	p.Ser203Pro	p.S203P	ENST00000369458	NM_024626.3	203	Tct/Cct	4/6	0.287498956904921	4	FACETS	0.99	0.673	1	0.495	0.336	0.693	CLONAL	1	TRUE	2	0.17	4		448	139	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245298	46245298	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	17	343	0	ENST00000334344.6:c.3392C>A	p.Pro1131Gln	p.P1131Q	ENST00000334344	NM_152641.2	1131	cCa/cAa	15/21	0.444834941790528	4	FACETS	0.907	0.677	1	0.453	0.338	0.59	CLONAL	1	TRUE	2	0.17	4		343	258	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245315	46245315	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	12	338	0	ENST00000334344.6:c.3409T>A	p.Ser1137Thr	p.S1137T	ENST00000334344	NM_152641.2	1137	Tca/Aca	15/21	0.444834941790528	4	FACETS	0.779	0.548	1	0.39	0.274	0.532	CLONAL	1	TRUE	2	0.17	4		338	212	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246399	46246399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762564588	NA	P-0031429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	10	313	0	ENST00000334344.6:c.4493C>T	p.Ala1498Val	p.A1498V	ENST00000334344	NM_152641.2	1498	gCc/gTc	15/21	0.444834941790528	4	FACETS	1	0.796	1	0.626	0.427	0.872	CLONAL	1	TRUE	2	0.17	4		313	110	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032277	10032277	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	12	433	0	ENST00000330684.3:c.546A>C	p.Glu182Asp	p.E182D	ENST00000330684	NM_001134407.1	182	gaA/gaC	3/13	0.106862400716072	3	FACETS	0.875	0.616	1	0.438	0.308	0.596	CLONAL	1	TRUE	1	0.17	3		433	175	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782171	56782171	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	11	252	0	ENST00000308159.5:c.12G>T	p.Glu4Asp	p.E4D	ENST00000308159	NM_014669.4	4	gaG/gaT	2/22	0.106862400716072	3	FACETS	0.955	0.662	1	0.478	0.331	0.658	CLONAL	1	TRUE	1	0.17	3		252	147	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553541	29553541	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	13	280	0	ENST00000356175.3:c.2090A>G	p.Asn697Ser	p.N697S	ENST00000356175	NM_000267.3	697	aAc/aGc	18/57	0.173440308098744	3	FACETS	0.802	0.572	1	0.401	0.286	0.541	CLONAL	1	TRUE	1	0.17	3		280	207	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682123	37682123	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1388586586	NA	P-0031429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	11	325	0	ENST00000447079.4:c.3314C>G	p.Ala1105Gly	p.A1105G	ENST00000447079	NM_015083.1	1105	gCt/gGt	13/14	0.173440308098744	3	FACETS	0.728	0.503	1	0.364	0.251	0.503	CLONAL	1	TRUE	1	0.17	3		325	193	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713609	52713609	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs529388126	NA	P-0031429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	10	363	0	ENST00000394830.3:c.119A>G	p.Asn40Ser	p.N40S	ENST00000394830	NM_018313.4	40	aAt/aGt	2/30	1	2	FACETS	0.692	0.469	0.971	0.692	0.469	0.971	SUBCLONAL	1	TRUE	1	0.17	2		363	170	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38173489	38173489	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	11	419	0	ENST00000317025.8:c.1927A>G	p.Thr643Ala	p.T643A	ENST00000317025	NM_023034.1	643	Act/Gct	10/24	1	2	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	TRUE	1	0.17	2		419	91	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867495	101867495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564120661	NA	P-0031429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	14	42	0	ENST00000374994.4:c.8C>T	p.Ala3Val	p.A3V	ENST00000374994	NM_004612.2	3	gCg/gTg	1/9	0.106862400716072	3	FACETS	0.757	0.547	1	0.379	0.273	0.506	CLONAL	1	TRUE	1	0.17	3		42	236	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361142	70361142	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	18	245	0	ENST00000374080.3:c.6330A>C	p.Gln2110His	p.Q2110H	ENST00000374080		2110	caA/caC	43/45	0.3	2	FACETS	0.679	0.511	0.878	0.339	0.255	0.439	SUBCLONAL	1	TRUE	0	0.17	2		245	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0031430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	42	660	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		660	654	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469672	NA	P-0031430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	36	580	0	ENST00000374080.3:c.131G>A	p.Gly44Asp	p.G44D	ENST00000374080		44	gGt/gAt	2/45	0.0780536131330872	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		580	711	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928089	178928089	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	42	471	0	ENST00000263967.3:c.1367T>G	p.Leu456Arg	p.L456R	ENST00000263967	NM_006218.2	456	cTg/cGg	8/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		471	451	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0031433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	88	538	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.35	2		538	503	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0031433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	75	391	1	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.35	2		392	416	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781315	3781315	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587783503	NA	P-0031433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	33	590	1	ENST00000262367.5:c.5050T>C	p.Ser1684Pro	p.S1684P	ENST00000262367	NM_004380.2	1684	Tcc/Ccc	30/31	1	2	FACETS	0.315	0.255	0.382	0.315	0.255	0.382	SUBCLONAL	1	TRUE	1	0.35	2		591	599	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922364	178922364	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397514565	NA	P-0031433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	15	357	0	ENST00000263967.3:c.1133G>A	p.Cys378Tyr	p.C378Y	ENST00000263967	NM_006218.2	378	tGt/tAt	6/21	1	2	FACETS	0.2	0.146	0.266	0.2	0.146	0.266	SUBCLONAL	1	TRUE	1	0.35	2		357	428	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	236	619	2	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	1	2	FACETS	0.928	0.87	0.988	1	0.994	1	CLONAL	2	TRUE	1	0.354569133107574	2		621	717	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	114	568	2	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	0.354569133107574	2		570	561	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	157	350	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.988	0.914	1	1	0.992	1	CLONAL	2	TRUE	1	0.354569133107574	2		351	448	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	107	520	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.354569133107574	2		520	600	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	105	479	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.354569133107574	2		479	565	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	125	436	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.77	0.701	0.841	1	0.987	1	SUBCLONAL	2	TRUE	1	0.354569133107574	2		436	458	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711927	89711928	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554900593	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	99	452	0	ENST00000371953.3:c.548dup	p.Asn184GlufsTer6	p.N184Efs*6	ENST00000371953	NM_000314.4	182	tta/ttAa	6/9	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.354569133107574	2		452	466	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690847	89690847	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776667	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	65	392	0	ENST00000371953.3:c.253+1G>A		p.X85_splice	ENST00000371953	NM_000314.4	85			1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.354569133107574	2		392	346	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913255	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	129	565	0	ENST00000369535.4:c.183A>C	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caC	3/7	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.354569133107574	2		565	674	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	124	597	15	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.354569133107574	2		612	525	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161939	47161939	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	57	338	1	ENST00000409792.3:c.4187del	p.Asn1396MetfsTer16	p.N1396Mfs*16	ENST00000409792	NM_014159.6	1396	aAt/at	3/21	1	2	FACETS	0.775	0.667	0.892	0.775	0.667	0.892	SUBCLONAL	1	TRUE	1	0.354569133107574	2		339	415	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945008	31945008	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	39	646	1	ENST00000340398.3:c.93del	p.Ser32LeufsTer5	p.S32Lfs*5	ENST00000340398	NM_001013699.2	31	ccC/cc	1/1	1	2	FACETS	0.283	0.233	0.338	0.283	0.233	0.338	SUBCLONAL	1	TRUE	1	0.354569133107574	2		647	778	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156719	20156719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	136	455	0	ENST00000379607.5:c.38G>A	p.Arg13His	p.R13H	ENST00000379607	NM_001412.3	13	cGc/cAc	2/7	1	2	FACETS	0.814	0.746	0.885	1	0.989	1	CLONAL	2	TRUE	1	0.354569133107574	2		455	471	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673759	176673759	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	116	495	0	ENST00000439151.2:c.4463del	p.Asn1488MetfsTer15	p.N1488Mfs*15	ENST00000439151	NM_022455.4	1487	Aaa/aa	10/23	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.354569133107574	2		495	591	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431873	49431874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1333678798	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	89	649	1	ENST00000301067.7:c.9265dup	p.Val3089GlyfsTer9	p.V3089Gfs*9	ENST00000301067	NM_003482.3	3089	gtg/gGtg	34/54	1	2	FACETS	0.901	0.801	1	0.901	0.801	1	CLONAL	1	TRUE	1	0.354569133107574	2		650	557	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495715	56495715	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	24	446	0	ENST00000267101.3:c.3910del	p.His1304MetfsTer7	p.H1304Mfs*7	ENST00000267101	NM_001982.3	1302	gCc/gc	28/28	1	2	FACETS	0.323	0.253	0.405	0.323	0.253	0.405	SUBCLONAL	1	TRUE	1	0.354569133107574	2		446	419	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115385	115115386	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	90	536	0	ENST00000257566.3:c.940dup	p.Arg314LysfsTer13	p.R314Kfs*13	ENST00000257566	NM_016569.3	314	aga/aAga	5/8	1	2	FACETS	0.925	0.822	1	0.925	0.822	1	CLONAL	1	TRUE	1	0.354569133107574	2		536	549	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286238	66286238	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	75	421	1	ENST00000273854.3:c.1448del	p.Asn483ThrfsTer18	p.N483Tfs*18	ENST00000273854	NM_004439.5	483	aAc/ac	6/18	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.354569133107574	2		422	354	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134451	30134452	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	101	505	0	ENST00000263025.4:c.79dup	p.Glu27GlyfsTer35	p.E27Gfs*35	ENST00000263025	NM_002746.2	27	gag/gGag	1/9	1	2	FACETS	0.989	0.886	1	0.989	0.886	1	CLONAL	1	TRUE	1	0.354569133107574	2		505	576	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752763	42752763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760204780	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	158	700	1	ENST00000222329.4:c.1501G>A	p.Ala501Thr	p.A501T	ENST00000222329	NM_006494.2	501	Gct/Act	4/4	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.354569133107574	2		701	728	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092980	27092980	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	30	400	0	ENST00000324856.7:c.2914del	p.Asp972MetfsTer2	p.D972Mfs*2	ENST00000324856	NM_006015.4	971	Ggg/gg	10/20	1	2	FACETS	0.411	0.331	0.502	0.411	0.331	0.502	SUBCLONAL	1	TRUE	1	0.354569133107574	2		400	412	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41525977	41525977	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	114	539	0	ENST00000263253.7:c.1256del	p.Asn419MetfsTer12	p.N419Mfs*12	ENST00000263253	NM_001429.3	418	Aaa/aa	5/31	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.354569133107574	2		539	571	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217306	11217306	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	126	602	0	ENST00000361445.4:c.4372G>C	p.Asp1458His	p.D1458H	ENST00000361445	NM_004958.3	1458	Gat/Cat	30/58	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.354569133107574	2		602	664	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272530	11272530	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	72	367	0	ENST00000361445.4:c.3400G>A	p.Ala1134Thr	p.A1134T	ENST00000361445	NM_004958.3	1134	Gca/Aca	23/58	1	2	FACETS	0.981	0.861	1	0.981	0.861	1	CLONAL	1	TRUE	1	0.354569133107574	2		367	414	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023624	27023660	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGCGGCTGCCGGCTCCAAGCCGCCTCCCTCCTCCA	GCGGCGGCTGCCGGCTCCAAGCCGCCTCCCTCCTCCA	-	novel	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	93	446	0	ENST00000324856.7:c.733_769del	p.Ala245ProfsTer106	p.A245Pfs*106	ENST00000324856	NM_006015.4	244	GCGGCGGCTGCCGGCTCCAAGCCGCCTCCCTCCTCCAgc/gc	1/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.354569133107574	2		446	451	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101565	27101565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	119	679	3	ENST00000324856.7:c.4847C>T	p.Ala1616Val	p.A1616V	ENST00000324856	NM_006015.4	1616	gCa/gTa	18/20	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.354569133107574	2		682	670	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162742039	162742039	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	62	446	2	ENST00000367921.3:c.1728+2T>C		p.X576_splice	ENST00000367921	NM_006182.2	576			0.354569133107574	3	FACETS	0.754	0.652	0.865	0.377	0.326	0.433	SUBCLONAL	1	TRUE	1	0.354569133107574	3		448	546	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112745407	112745407	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	86	544	1	ENST00000369452.4:c.725C>T	p.Thr242Met	p.T242M	ENST00000369452	NM_007373.3	242	aCg/aTg	3/9	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.354569133107574	2		545	484	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944732	71944732	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	167	708	1	ENST00000298229.2:c.2160del	p.Val721CysfsTer37	p.V721Cfs*37	ENST00000298229	NM_001567.3	719	tCc/tc	19/28	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.354569133107574	2		709	856	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94225948	94225948	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	100	384	0	ENST00000323929.3:c.20T>C	p.Leu7Pro	p.L7P	ENST00000323929	NM_005591.3	7	cTt/cCt	2/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.354569133107574	2		384	492	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175510	108175510	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	101	410	2	ENST00000278616.4:c.5609del	p.Phe1870SerfsTer47	p.F1870Sfs*47	ENST00000278616	NM_000051.3	1869	Ttt/tt	37/63	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.354569133107574	2		412	497	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50490745	50490745	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	106	526	1	ENST00000394963.4:c.1384del	p.Asp462ThrfsTer5	p.D462Tfs*5	ENST00000394963	NM_003076.4	461	aGg/ag	11/13	1	2	FACETS	0.917	0.823	1	0.917	0.823	1	CLONAL	1	TRUE	1	0.354569133107574	2		527	652	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042588	42042588	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	110	469	1	ENST00000219905.7:c.6787del	p.Ser2263AlafsTer72	p.S2263Afs*72	ENST00000219905	NM_001164273.1	2261	gcA/gc	17/24	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.354569133107574	2		470	503	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647625	3647625	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	120	801	0	ENST00000294008.3:c.1438G>T	p.Gly480Cys	p.G480C	ENST00000294008	NM_032444.2	480	Ggc/Tgc	7/15	1	2	FACETS	0.794	0.717	0.876	0.794	0.717	0.876	SUBCLONAL	1	TRUE	1	0.354569133107574	2		801	852	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341601	89341601	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1555523580	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	27	396	0	ENST00000301030.4:c.7471-2A>G		p.X2491_splice	ENST00000301030	NM_001256183.1	2491			1	2	FACETS	0.338	0.268	0.417	0.338	0.268	0.417	SUBCLONAL	1	TRUE	1	0.354569133107574	2		396	451	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29563004	29563004	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	81	465	0	ENST00000356175.3:c.3939T>A	p.Asp1313Glu	p.D1313E	ENST00000356175	NM_000267.3	1313	gaT/gaA	29/57	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.354569133107574	2		465	435	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219957	36219957	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	84	616	0	ENST00000222270.7:c.4759T>C	p.Tyr1587His	p.Y1587H	ENST00000222270	NM_014727.1	1587	Tac/Cac	21/37	1	2	FACETS	0.788	0.697	0.886	0.788	0.697	0.886	SUBCLONAL	1	TRUE	1	0.354569133107574	2		616	601	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800555	32800555	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	157	686	0	ENST00000374899.4:c.992T>C	p.Val331Ala	p.V331A	ENST00000374899	NM_018833.2	331	gTg/gCg	6/12	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.354569133107574	2		686	862	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509345	106509345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	37	487	1	ENST00000359195.3:c.1339G>A	p.Ala447Thr	p.A447T	ENST00000359195	NM_002649.2	447	Gca/Aca	2/11	1	2	FACETS	0.382	0.314	0.458	0.382	0.314	0.458	SUBCLONAL	1	TRUE	1	0.354569133107574	2		488	546	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481382	140481382	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	43	330	0	ENST00000288602.6:c.1426T>C	p.Trp476Arg	p.W476R	ENST00000288602	NM_004333.4	476	Tgg/Cgg	11/18	1	2	FACETS	0.795	0.669	0.934	0.795	0.669	0.934	CLONAL	1	TRUE	1	0.354569133107574	2		330	305	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859953	151859953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	24	351	1	ENST00000262189.6:c.10709G>A	p.Cys3570Tyr	p.C3570Y	ENST00000262189	NM_170606.2	3570	tGt/tAt	43/59	1	2	FACETS	0.367	0.287	0.459	0.367	0.287	0.459	SUBCLONAL	1	TRUE	1	0.354569133107574	2		352	369	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238372	98238372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	122	512	0	ENST00000331920.6:c.1672G>A	p.Ala558Thr	p.A558T	ENST00000331920	NM_000264.3	558	Gcc/Acc	12/24	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.354569133107574	2		512	530	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413097	139413097	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	134	625	0	ENST00000277541.6:c.1045A>T	p.Thr349Ser	p.T349S	ENST00000277541	NM_017617.3	349	Acc/Tcc	6/34	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.354569133107574	2		625	720	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413136	139413136	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	185	699	0	ENST00000277541.6:c.1006A>T	p.Ile336Phe	p.I336F	ENST00000277541	NM_017617.3	336	Att/Ttt	6/34	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.354569133107574	2		699	862	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426783	47426783	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	29	476	0	ENST00000377045.4:c.1028C>A	p.Pro343His	p.P343H	ENST00000377045	NM_001654.4	343	cCc/cAc	10/16	1	2	FACETS	0.304	0.243	0.374	0.304	0.243	0.374	SUBCLONAL	1	TRUE	1	0.354569133107574	2		476	538	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184118	123184118	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	75	413	0	ENST00000218089.9:c.976G>A	p.Asp326Asn	p.D326N	ENST00000218089	NM_001042749.1	326	Gac/Aac	11/35	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.354569133107574	2		413	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0031438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	343	403	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.226790949851937	3	FACETS	0.954	0.907	1	0.954	0.907	1	CLONAL	3	TRUE	0	0.327781893917911	3		403	851	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597850	43597850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138265837	NA	P-0031438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	68	624	2	ENST00000355710.3:c.398G>A	p.Arg133His	p.R133H	ENST00000355710	NM_020975.4	133	cGt/cAt	3/20	0.327781893917911	2	FACETS	0.435	0.377	0.498	0.218	0.188	0.249	SUBCLONAL	1	TRUE	0	0.327781893917911	2		626	953	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50811777	50811777	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	88	429	0	ENST00000398568.2:c.1057del	p.Tyr353IlefsTer3	p.Y353Ifs*3	ENST00000398568	NM_001042412.1	352	Ttt/tt	7/18	0.284748702458902	3	FACETS	0.845	0.748	0.948	0.422	0.374	0.474	CLONAL	1	TRUE	1	0.327781893917911	3		429	740	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0031439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	236	435	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.525667747964597	6	FACETS	0.99	0.933	1	0.99	0.933	1	CLONAL	3	TRUE	3	0.742688062916075	6		435	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579410	7579410	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567556123	NA	P-0031439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	264	617	0	ENST00000269305.4:c.277del	p.Leu93CysfsTer30	p.L93Cfs*30	ENST00000269305	NM_001126112.2	93	Ctg/tg	4/11	0.735563439053279	2	FACETS	0.99	0.952	1	0.99	0.952	1	CLONAL	2	TRUE	0	0.742688062916075	2		617	359	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123505237	123505237	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	169	262	0	ENST00000371139.4:c.383C>A	p.Pro128Gln	p.P128Q	ENST00000371139	NM_001114937.2	128	cCa/cAa	4/4	0.451170020642791	4	FACETS	1	0.99	1	0.737	0.682	0.794	CLONAL	1	TRUE	2	0.742688062916075	4		262	538	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359437	118359437	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	159	306	0	ENST00000534358.1:c.4441T>A	p.Phe1481Ile	p.F1481I	ENST00000534358	NM_005933.3	1481	Ttc/Atc	11/36	0.54750603267504	4	FACETS	0.844	0.781	0.908			1	CLONAL	2	TRUE	NA	0.742688062916075	4		306	442	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585498	29585498	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	19	182	0	ENST00000356175.3:c.4250del	p.Gly1417AlafsTer2	p.G1417Afs*2	ENST00000356175	NM_000267.3	1416	aGg/ag	31/57	0.725044140511374	2	FACETS	0.283	0.215	0.361	0.141	0.107	0.181	SUBCLONAL	1	TRUE	0	0.742688062916075	2		182	181	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0031441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	68	435	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.921	0.805	1	0.921	0.805	1	CLONAL	1	TRUE	1	0.35832602580439	2		435	412	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155721	56155722	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0031441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	58	355	0	ENST00000399503.3:c.816_817del	p.Arg273SerfsTer27	p.R273Sfs*27	ENST00000399503	NM_005921.1	271	agAAaa/agaa	3/20	1	2	FACETS	0.631	0.543	0.727	0.631	0.543	0.727	SUBCLONAL	1	TRUE	1	0.35832602580439	2		355	513	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177920	56177920	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	116	409	1	ENST00000399503.3:c.2893C>T	p.Gln965Ter	p.Q965*	ENST00000399503	NM_005921.1	965	Cag/Tag	14/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.35832602580439	2		410	572	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207088	1207088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	115	602	1	ENST00000326873.7:c.176C>T	p.Ser59Phe	p.S59F	ENST00000326873	NM_000455.4	59	tCt/tTt	1/10	1	2	FACETS	0.879	0.793	0.971	0.879	0.793	0.971	CLONAL	1	TRUE	1	0.35832602580439	2		603	730	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609467	81609467	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	36	439	0	ENST00000298171.2:c.1065C>A	p.Phe355Leu	p.F355L	ENST00000298171	NM_000369.2	355	ttC/ttA	10/10	1	2	FACETS	0.593	0.486	0.712	0.593	0.486	0.712	SUBCLONAL	1	TRUE	1	0.241586971463676	2		439	503	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143043375	143043375	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	56	336	0	ENST00000262992.4:c.2041G>T	p.Asp681Tyr	p.D681Y	ENST00000262992	NM_001101669.1	681	Gac/Tac	19/24	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.241586971463676	2		336	442	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845360	42845360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775494034	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	78	531	0	ENST00000398585.3:c.902C>T	p.Pro301Leu	p.P301L	ENST00000398585	NM_001135099.1	301	cCg/cTg	9/14	1	2	FACETS	0.987	0.868	1	0.987	0.868	1	CLONAL	1	TRUE	1	0.241586971463676	2		531	654	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211157	55211157	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	142	470	0	ENST00000275493.2:c.400G>T	p.Glu134Ter	p.E134*	ENST00000275493	NM_005228.3	134	Gag/Tag	3/28	0.241586971463676	5	FACETS	1	0.979	1	0.821	0.751	0.895	CLONAL	2	TRUE	2	0.241586971463676	5		470	650	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	138	533	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.241586971463676	2	FACETS	0.992	0.906	1	0.992	0.906	1	CLONAL	2	TRUE	0	0.241586971463676	2		533	576	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979269	93979269	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs986768697	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	41	392	0	ENST00000369303.4:c.1559C>A	p.Ala520Asp	p.A520D	ENST00000369303	NM_004440.3	520	gCt/gAt	7/17	0.172307822044687	2	FACETS	0.782	0.652	0.927	0.391	0.326	0.464	CLONAL	1	TRUE	0	0.241586971463676	2		392	434	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430160	181430160	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	17	121	0	ENST00000325404.1:c.12G>T	p.Met4Ile	p.M4I	ENST00000325404	NM_003106.3	4	atG/atT	1/1	1	2	FACETS	0.926	0.696	1	0.926	0.696	1	CLONAL	1	TRUE	1	0.241586971463676	2		121	152	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576121	88576121	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	60	573	0	ENST00000360948.2:c.1552C>A	p.Arg518Ser	p.R518S	ENST00000360948	NM_001012338.2	518	Cgt/Agt	13/19	1	2	FACETS	0.809	0.697	0.931	0.809	0.697	0.931	CLONAL	1	TRUE	1	0.241586971463676	2		573	614	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850951	128850951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767352128	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	43	403	0	ENST00000249373.3:c.1798G>A	p.Val600Met	p.V600M	ENST00000249373	NM_005631.4	600	Gtg/Atg	10/12	0.12297455967238	3	FACETS	0.79	0.661	0.933	0.263	0.22	0.311	INDETERMINATE	1	TRUE	0	0.241586971463676	3		403	505	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188548	11188548	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	41	427	0	ENST00000361445.4:c.5873A>T	p.His1958Leu	p.H1958L	ENST00000361445	NM_004958.3	1958	cAc/cTc	42/58	1	2	FACETS	0.722	0.602	0.856	0.722	0.602	0.856	SUBCLONAL	1	TRUE	1	0.241586971463676	2		427	470	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468261	120468261	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	44	519	0	ENST00000256646.2:c.4178G>C	p.Arg1393Pro	p.R1393P	ENST00000256646	NM_024408.3	1393	cGc/cCc	25/34	1	2	FACETS	0.72	0.604	0.849	0.72	0.604	0.849	SUBCLONAL	1	TRUE	1	0.241586971463676	2		519	506	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653396	206653396	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	63	563	0	ENST00000367120.3:c.1280G>T	p.Arg427Leu	p.R427L	ENST00000367120	NM_014002.3	427	cGg/cTg	12/22	1	2	FACETS	0.789	0.682	0.906	0.789	0.682	0.906	CLONAL	1	TRUE	1	0.241586971463676	2		563	661	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333188	70333188	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	109	570	2	ENST00000373644.4:c.1093C>A	p.Leu365Ile	p.L365I	ENST00000373644	NM_030625.2	365	Cta/Ata	2/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.241586971463676	2		572	645	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333822	70333822	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	65	419	0	ENST00000373644.4:c.1727A>T	p.Tyr576Phe	p.Y576F	ENST00000373644	NM_030625.2	576	tAt/tTt	2/12	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.241586971463676	2		419	457	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410674	32410674	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	41	379	0	ENST00000332351.3:c.1484G>C	p.Arg495Pro	p.R495P	ENST00000332351	NM_024426.4	495	cGg/cCg	10/10	1	2	FACETS	0.672	0.559	0.797	0.672	0.559	0.797	SUBCLONAL	1	TRUE	1	0.241586971463676	2		379	505	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998657	100998657	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	48	638	0	ENST00000325455.5:c.1145del	p.Pro382ArgfsTer4	p.P382Rfs*4	ENST00000325455	NM_001202474.3	382	cCg/cg	1/8	1	2	FACETS	0.623	0.526	0.73	0.623	0.526	0.73	SUBCLONAL	1	TRUE	1	0.241586971463676	2		638	638	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999032	100999032	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs746902021	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	34	538	0	ENST00000325455.5:c.770C>G	p.Pro257Arg	p.P257R	ENST00000325455	NM_001202474.3	257	cCg/cGg	1/8	1	2	FACETS	0.646	0.527	0.779	0.646	0.527	0.779	SUBCLONAL	1	TRUE	1	0.241586971463676	2		538	436	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438196	438196	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	26	286	0	ENST00000399788.2:c.1774-1G>A		p.X592_splice	ENST00000399788	NM_001042603.1	592			0.241586971463676	3	FACETS	0.615	0.487	0.763			1	SUBCLONAL	1	TRUE	NA	0.241586971463676	3		286	392	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244309	46244310	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	73	405	0	ENST00000334344.6:c.2406dup	p.Gly803TrpfsTer38	p.G803Wfs*38	ENST00000334344	NM_152641.2	801	-/T	15/21	0.177081153541268	2	FACETS	1	0.975	1	0.744	0.654	0.841	CLONAL	1	TRUE	0	0.241586971463676	2		405	406	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433541	49433541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	129	752	1	ENST00000301067.7:c.8012G>A	p.Gly2671Asp	p.G2671D	ENST00000301067	NM_003482.3	2671	gGc/gAc	31/54	0.177081153541268	2	FACETS	1	0.985	1	0.732	0.665	0.804	CLONAL	1	TRUE	0	0.241586971463676	2		753	729	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112939999	112939999	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	50	435	0	ENST00000351677.2:c.1651G>T	p.Asp551Tyr	p.D551Y	ENST00000351677	NM_002834.3	551	Gac/Tac	14/16	0.172307822044687	2	FACETS	0.692	0.587	0.808	0.346	0.293	0.404	SUBCLONAL	1	TRUE	0	0.241586971463676	2		435	598	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434381	121434381	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	97	591	0	ENST00000257555.6:c.1145C>G	p.Thr382Ser	p.T382S	ENST00000257555		382	aCc/aGc	6/10	0.172307822044687	2	FACETS	1	0.976	1	0.673	0.601	0.749	CLONAL	1	TRUE	0	0.241586971463676	2		591	597	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100220	30100220	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	40	357	0	ENST00000331968.5:c.1400C>A	p.Pro467His	p.P467H	ENST00000331968	NM_002742.2	467	cCt/cAt	10/18	1	2	FACETS	0.814	0.677	0.965	0.814	0.677	0.965	CLONAL	1	TRUE	1	0.241586971463676	2		357	407	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061532	38061532	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	25	270	0	ENST00000250448.2:c.457G>T	p.Ala153Ser	p.A153S	ENST00000250448	NM_004496.3	153	Gcg/Tcg	2/2	1	2	FACETS	0.69	0.544	0.857	0.69	0.544	0.857	SUBCLONAL	1	TRUE	1	0.241586971463676	2		270	300	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058261	42058261	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	36	331	0	ENST00000219905.7:c.7981G>T	p.Gly2661Ter	p.G2661*	ENST00000219905	NM_001164273.1	2661	Gga/Tga	24/24	0.241586971463676	1	FACETS	0.943	0.779	1	0.943	0.779	1	CLONAL	1	TRUE	0	0.241586971463676	1		331	278	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472534	88472534	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	34	530	0	ENST00000360948.2:c.2021A>T	p.His674Leu	p.H674L	ENST00000360948	NM_001012338.2	674	cAc/cTc	16/19	1	2	FACETS	0.517	0.422	0.625	0.517	0.422	0.625	SUBCLONAL	1	TRUE	1	0.241586971463676	2		530	544	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678566	88678566	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	19	314	0	ENST00000360948.2:c.970G>T	p.Val324Leu	p.V324L	ENST00000360948	NM_001012338.2	324	Gtg/Ttg	9/19	1	2	FACETS	0.558	0.423	0.716	0.558	0.423	0.716	SUBCLONAL	1	TRUE	1	0.241586971463676	2		314	282	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50811781	50811781	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	100	480	0	ENST00000398568.2:c.1058A>G	p.Tyr353Cys	p.Y353C	ENST00000398568	NM_001042412.1	353	tAt/tGt	7/18	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.241586971463676	2		480	592	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89862370	89862370	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	63	537	0	ENST00000389301.3:c.950A>G	p.Lys317Arg	p.K317R	ENST00000389301	NM_000135.2	317	aAg/aGg	11/43	1	2	FACETS	0.788	0.681	0.904	0.788	0.681	0.904	CLONAL	1	TRUE	1	0.241586971463676	2		537	662	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89862409	89862409	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs745451374	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	52	486	0	ENST00000389301.3:c.911G>T	p.Gly304Val	p.G304V	ENST00000389301	NM_000135.2	304	gGa/gTa	11/43	1	2	FACETS	0.692	0.589	0.806	0.692	0.589	0.806	SUBCLONAL	1	TRUE	1	0.241586971463676	2		486	622	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527523	29527523	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	81	512	0	ENST00000356175.3:c.972T>G	p.Cys324Trp	p.C324W	ENST00000356175	NM_000267.3	324	tgT/tgG	9/57	0.241586971463676	3	FACETS	1	0.923	1	0.532	0.468	0.6	CLONAL	1	TRUE	1	0.241586971463676	3		512	707	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354443	40354443	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	183	650	0	ENST00000293328.3:c.2152G>T	p.Ala718Ser	p.A718S	ENST00000293328	NM_012448.3	718	Gcc/Tcc	18/19	0.241586971463676	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.241586971463676	3		650	754	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780679	56780679	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	60	427	0	ENST00000337432.4:c.694G>T	p.Glu232Ter	p.E232*	ENST00000337432	NM_058216.2	232	Gaa/Taa	4/9	0.241586971463676	3	FACETS	0.844	0.726	0.972	0.422	0.363	0.486	CLONAL	1	TRUE	1	0.241586971463676	3		427	660	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120356	70120356	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768237701	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	251	744	0	ENST00000245479.2:c.1358G>A	p.Ser453Asn	p.S453N	ENST00000245479	NM_000346.3	453	aGc/aAc	3/3	0.241586971463676	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.241586971463676	3		744	1114	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971160	18971160	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	137	651	0	ENST00000262803.5:c.2213A>T	p.Gln738Leu	p.Q738L	ENST00000262803	NM_002911.3	738	cAg/cTg	16/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.241586971463676	2		651	791	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867535	45867535	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	125	672	0	ENST00000391945.4:c.773G>T	p.Arg258Leu	p.R258L	ENST00000391945	NM_000400.3	258	cGg/cTg	9/23	0.213443768480768	2	FACETS	1	0.984	1	0.722	0.654	0.793	CLONAL	1	TRUE	0	0.241586971463676	2		672	717	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991682	25991682	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	38	368	0	ENST00000435504.4:c.560C>A	p.Ser187Tyr	p.S187Y	ENST00000435504		187	tCc/tAc	7/13	1	2	FACETS	0.649	0.536	0.775	0.649	0.536	0.775	SUBCLONAL	1	TRUE	1	0.241586971463676	2		368	485	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190717379	190717379	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	52	288	0	ENST00000441310.2:c.700-2A>T		p.X234_splice	ENST00000441310	NM_000534.4	234			0.1397263839565	3	FACETS	1	0.953	1	0.652	0.557	0.755	INDETERMINATE	1	TRUE	1	0.241586971463676	3		288	370	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384614	31384614	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	65	540	0	ENST00000328111.2:c.1316G>T	p.Gly439Val	p.G439V	ENST00000328111	NM_006892.3	439	gGc/gTc	13/23	1	2	FACETS	0.76	0.658	0.871	0.76	0.658	0.871	SUBCLONAL	1	TRUE	1	0.241586971463676	2		540	708	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306735	41306735	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	23	422	0	ENST00000373198.4:c.924G>T	p.Lys308Asn	p.K308N	ENST00000373198	NM_133170.3	308	aaG/aaT	7/32	1	2	FACETS	0.424	0.33	0.534	0.424	0.33	0.534	SUBCLONAL	1	TRUE	1	0.241586971463676	2		422	449	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408860	41408860	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	28	407	0	ENST00000373198.4:c.566G>T	p.Cys189Phe	p.C189F	ENST00000373198	NM_133170.3	189	tGc/tTc	4/32	1	2	FACETS	0.492	0.393	0.606	0.492	0.393	0.606	SUBCLONAL	1	TRUE	1	0.241586971463676	2		407	471	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845358	42845360	+	frameshift_variant	Frame_Shift_Del	DEL	CCG	CCG	AA	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	78	538	1	ENST00000398585.3:c.902_904delinsTT	p.Pro301LeufsTer29	p.P301Lfs*29	ENST00000398585	NM_001135099.1	301	cCGGgg/cTTgg	9/14	1	2	FACETS	0.974	0.856	1	0.974	0.856	1	CLONAL	1	TRUE	1	0.241586971463676	2		539	663	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434218	12434218	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	37	417	0	ENST00000287820.6:c.586C>A	p.Gln196Lys	p.Q196K	ENST00000287820	NM_015869.4	196	Cag/Aag	4/7	1	2	FACETS	0.511	0.421	0.613	0.511	0.421	0.613	SUBCLONAL	1	TRUE	1	0.241586971463676	2		417	599	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125873	47125873	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	35	127	0	ENST00000409792.3:c.5398-1G>T		p.X1800_splice	ENST00000409792	NM_014159.6	1800			1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.241586971463676	2		127	206	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72891443	72891443	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1349397292	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	37	387	0	ENST00000325599.8:c.319G>C	p.Val107Leu	p.V107L	ENST00000325599	NM_018130.2	107	Gtg/Ctg	3/11	1	2	FACETS	0.608	0.5	0.728	0.608	0.5	0.728	SUBCLONAL	1	TRUE	1	0.241586971463676	2		387	504	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73113233	73113233	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	31	156	1	ENST00000356692.5:c.574G>T	p.Gly192Trp	p.G192W	ENST00000356692		192	Ggg/Tgg	7/9	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.241586971463676	2		157	215	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114261	73114261	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	26	276	0	ENST00000356692.5:c.897G>C	p.Glu299Asp	p.E299D	ENST00000356692		299	gaG/gaC	8/9	1	2	FACETS	0.568	0.45	0.704	0.568	0.45	0.704	SUBCLONAL	1	TRUE	1	0.241586971463676	2		276	379	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480480	89480480	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	44	284	0	ENST00000336596.2:c.2317G>T	p.Asp773Tyr	p.D773Y	ENST00000336596	NM_005233.5	773	Gat/Tat	13/17	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.241586971463676	2		284	344	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499331	89499331	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	28	297	0	ENST00000336596.2:c.2501T>G	p.Ile834Ser	p.I834S	ENST00000336596	NM_005233.5	834	aTt/aGt	15/17	1	2	FACETS	0.639	0.51	0.784	0.639	0.51	0.784	SUBCLONAL	1	TRUE	1	0.241586971463676	2		297	363	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521612	89521612	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	33	286	0	ENST00000336596.2:c.2691-2A>T		p.X897_splice	ENST00000336596	NM_005233.5	897			1	2	FACETS	0.719	0.586	0.869	0.719	0.586	0.869	SUBCLONAL	1	TRUE	1	0.241586971463676	2		286	380	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665527	138665527	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	93	465	0	ENST00000330315.3:c.38G>T	p.Gly13Val	p.G13V	ENST00000330315	NM_023067.3	13	gGg/gTg	1/1	1	2	FACETS	0.804	0.718	0.895	1	0.983	1	CLONAL	2	TRUE	1	0.241586971463676	2		465	479	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274718	142274718	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	48	275	0	ENST00000350721.4:c.2341+1G>T		p.X781_splice	ENST00000350721	NM_001184.3	781			1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.241586971463676	2		275	331	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170020887	170020887	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	22	154	0	ENST00000295797.4:c.1763T>C	p.Leu588Pro	p.L588P	ENST00000295797	NM_002740.5	588	cTt/cCt	18/18	1	2	FACETS	0.82	0.638	1	0.82	0.638	1	CLONAL	1	TRUE	1	0.241586971463676	2		154	222	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430227	181430229	+	inframe_deletion	In_Frame_Del	DEL	GCG	GCG	-	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	23	324	0	ENST00000325404.1:c.87_89del	p.Ala30del	p.A30del	ENST00000325404	NM_003106.3	27	GCG/-	1/1	1	2	FACETS	0.53	0.413	0.666	0.53	0.413	0.666	SUBCLONAL	1	TRUE	1	0.241586971463676	2		324	359	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587170	189587170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1038188765	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	47	401	0	ENST00000264731.3:c.1187C>T	p.Pro396Leu	p.P396L	ENST00000264731	NM_003722.4	396	cCa/cTa	9/14	1	2	FACETS	0.876	0.74	1	0.876	0.74	1	CLONAL	1	TRUE	1	0.241586971463676	2		401	444	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197750	66197751	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	37	423	0	ENST00000273854.3:c.2948_2949del	p.Thr983ArgfsTer65	p.T983Rfs*65	ENST00000273854	NM_004439.5	983	aCA/a	17/18	1	2	FACETS	0.676	0.557	0.809	0.676	0.557	0.809	SUBCLONAL	1	TRUE	1	0.241586971463676	2		423	453	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356143	66356143	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	35	398	1	ENST00000273854.3:c.1354C>A	p.Pro452Thr	p.P452T	ENST00000273854	NM_004439.5	452	Cca/Aca	5/18	1	2	FACETS	0.618	0.506	0.744	0.618	0.506	0.744	SUBCLONAL	1	TRUE	1	0.241586971463676	2		399	469	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518876	187518876	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	65	483	0	ENST00000441802.2:c.12328G>T	p.Gly4110Cys	p.G4110C	ENST00000441802	NM_005245.3	4110	Ggc/Tgc	24/27	1	2	FACETS	0.812	0.703	0.929	0.812	0.703	0.929	CLONAL	1	TRUE	1	0.241586971463676	2		483	663	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541193	187541193	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	52	291	0	ENST00000441802.2:c.6547G>T	p.Glu2183Ter	p.E2183*	ENST00000441802	NM_005245.3	2183	Gaa/Taa	10/27	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.241586971463676	2		291	344	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295322	1295322	+	upstream_gene_variant	5'Flank	DEL	G	G	-	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	121	429	0				ENST00000310581	NM_198253.2	-/1132			0.194545565423928	5	FACETS	0.897	0.815	0.983	0.897	0.815	0.983	CLONAL	3	TRUE	2	0.241586971463676	5		429	507	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871314	35871314	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs200751605	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	62	338	2	ENST00000303115.3:c.536C>A	p.Thr179Lys	p.T179K	ENST00000303115	NM_002185.3	179	aCg/aAg	4/8	0.194545565423928	5	FACETS	1	0.969	1	0.491	0.425	0.562	CLONAL	1	TRUE	2	0.241586971463676	5		340	475	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225392	26225392	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1426545521	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	17	226	0	ENST00000360408.1:c.10A>T	p.Thr4Ser	p.T4S	ENST00000360408	NM_003532.2	4	Act/Tct	1/1	0.172307822044687	2	FACETS	0.69	0.516	0.895	0.345	0.258	0.448	SUBCLONAL	1	TRUE	0	0.241586971463676	2		226	204	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515129	148515129	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	80	349	0	ENST00000320356.2:c.1080A>T	p.Arg360Ser	p.R360S	ENST00000320356	NM_004456.4	360	agA/agT	10/20	0.12297455967238	3	FACETS	0.783	0.692	0.88	0.522	0.461	0.587	INDETERMINATE	2	TRUE	0	0.241586971463676	3		349	474	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279318	38279319	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	47	621	0	ENST00000425967.3:c.1170_1171delinsTT	p.Glu391Ter	p.E391*	ENST00000425967	NM_001174067.1	390	ctGGaa/ctTTaa	9/19	0.172307822044687	2	FACETS	0.642	0.541	0.754	0.321	0.27	0.377	SUBCLONAL	1	TRUE	0	0.241586971463676	2		621	606	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981662	70981662	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	76	753	0	ENST00000276594.2:c.434G>T	p.Gly145Val	p.G145V	ENST00000276594	NM_024504.3	145	gGa/gTa	2/8	1	2	FACETS	0.784	0.686	0.889	0.784	0.686	0.889	SUBCLONAL	1	TRUE	1	0.241586971463676	2		753	803	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549569	5549569	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	126	554	0	ENST00000397747.3:c.596T>A	p.Val199Glu	p.V199E	ENST00000397747	NM_025239.3	199	gTg/gAg	4/7	0.241586971463676	2	FACETS	1	0.984	1	0.722	0.655	0.793	CLONAL	1	TRUE	0	0.241586971463676	2		554	722	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340441	8340441	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1355211431	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	113	331	0	ENST00000356435.5:c.5155G>T	p.Gly1719Trp	p.G1719W	ENST00000356435		1719	Ggg/Tgg	31/35	0.241586971463676	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	0	0.241586971463676	2		331	453	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484156	8484156	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	57	435	0	ENST00000356435.5:c.3376G>T	p.Val1126Leu	p.V1126L	ENST00000356435		1126	Gtg/Ttg	19/35	0.241586971463676	2	FACETS	0.863	0.74	0.996	0.431	0.37	0.498	CLONAL	1	TRUE	0	0.241586971463676	2		435	547	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499690	8499690	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	134	401	0	ENST00000356435.5:c.2279A>T	p.Lys760Met	p.K760M	ENST00000356435		760	aAg/aTg	14/35	0.241586971463676	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.241586971463676	2		401	480	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101895023	101895023	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	58	203	0	ENST00000374994.4:c.574+2T>A		p.X192_splice	ENST00000374994	NM_004612.2	192			0.241586971463676	2	FACETS	0.972	0.844	1	0.972	0.844	1	CLONAL	2	TRUE	0	0.241586971463676	2		203	247	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760285	133760285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763746423	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	133	456	0	ENST00000318560.5:c.2608G>A	p.Ala870Thr	p.A870T	ENST00000318560	NM_005157.4	870	Gcc/Acc	11/11	0.241586971463676	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.241586971463676	2		456	490	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390837	139390837	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	122	670	1	ENST00000277541.6:c.7354G>T	p.Ala2452Ser	p.A2452S	ENST00000277541	NM_017617.3	2452	Gcg/Tcg	34/34	0.241586971463676	2	FACETS	1	0.984	1	0.731	0.661	0.804	CLONAL	1	TRUE	0	0.241586971463676	2		671	691	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402562	139402562	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	153	604	0	ENST00000277541.6:c.3355G>T	p.Gly1119Ter	p.G1119*	ENST00000277541	NM_017617.3	1119	Gga/Tga	21/34	0.241586971463676	2	FACETS	0.948	0.87	1	0.948	0.87	1	CLONAL	2	TRUE	0	0.241586971463676	2		604	668	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139438502	139438502	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	204	663	0	ENST00000277541.6:c.114A>T	p.Glu38Asp	p.E38D	ENST00000277541	NM_017617.3	38	gaA/gaT	2/34	0.241586971463676	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.241586971463676	2		663	779	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70353052	70353052	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	45	229	0	ENST00000374080.3:c.4607G>T	p.Arg1536Leu	p.R1536L	ENST00000374080		1536	cGg/cTg	33/45	0.241586971463676	2	FACETS	1	0.954	1			1	CLONAL	1	TRUE	NA	0.241586971463676	2		229	270	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845355	42845355	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	75	542	0	ENST00000398585.3:c.907del	p.Ala303ProfsTer27	p.A303Pfs*27	ENST00000398585	NM_001135099.1	303	Gcc/cc	9/14	1	2	FACETS	0.957	0.838	1	0.957	0.838	1	CLONAL	1	TRUE	1	0.241586971463676	2		542	649	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475459	12475464	+	missense_variant	Missense_Mutation	ONP	CTGGAG	CTGGAG	ATGGAC	novel	NA	P-0031442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	66	552	0	ENST00000287820.6:c.1333_1338delinsATGGAC	p.Leu445_Glu446delinsMetAsp	p.L445_E446delinsMD	ENST00000287820	NM_015869.4	445	CTGGAG/ATGGAC	7/7	1	2	FACETS	0.752	0.652	0.86	0.752	0.652	0.86	SUBCLONAL	1	TRUE	1	0.241586971463676	2		552	727	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	137	270	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.465870094748458	2		270	514	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054650	13054658	+	inframe_deletion	In_Frame_Del	DEL	GAGGATGAG	GAGGATGAG	-	rs550353351	NA	P-0031444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	104	509	0	ENST00000316448.5:c.1191_1199del	p.Glu398_Asp400del	p.E398_D400del	ENST00000316448	NM_004343.3	393	GAGGATGAG/-	9/9	0.399502125749601	3	FACETS	0.66	0.59	0.734	0.33	0.295	0.367	SUBCLONAL	1	TRUE	1	0.465870094748458	3		509	834	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888163	112888163	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397507509	NA	P-0031444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	14	581	0	ENST00000351677.2:c.179G>T	p.Gly60Val	p.G60V	ENST00000351677	NM_002834.3	60	gGt/gTt	3/16	1	2	FACETS	0.093	0.067	0.126	0.093	0.067	0.126	SUBCLONAL	1	TRUE	1	0.465870094748458	2		581	644	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141557610	141557610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1226849588	NA	P-0031444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	220	740	1	ENST00000220592.5:c.1705G>A	p.Val569Ile	p.V569I	ENST00000220592	NM_012154.3	569	Gtc/Atc	13/19	1	2	FACETS	0.883	0.821	0.947	0.883	0.821	0.947	CLONAL	1	TRUE	1	0.465870094748458	2		741	1070	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436101	51436102	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0031445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	164	364	0	ENST00000262662.1:c.63dup	p.Thr22TyrfsTer2	p.T22Yfs*2	ENST00000262662		21	ctt/cTtt	3/4	0.77105145773894	1	FACETS	0.986	0.929	1	0.986	0.929	1	CLONAL	1	TRUE	0	0.77105145773894	1		364	265	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866457	56866457	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	229	624	0	ENST00000519728.1:c.704G>A	p.Trp235Ter	p.W235*	ENST00000519728	NM_002350.3	235	tGg/tAg	8/13	1	2	FACETS	0.919	0.862	0.978	0.919	0.862	0.978	CLONAL	1	TRUE	1	0.77105145773894	2		624	646	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	120	270	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.904	0.828	0.983	0.904	0.828	0.983	CLONAL	1	TRUE	1	0.819234866055981	2		270	324	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0031446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	212	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.819234866055981	2		336	468	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495375	56495377	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs780883720	NA	P-0031450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	83	568	0	ENST00000267101.3:c.3573_3575del	p.Glu1191del	p.E1191del	ENST00000267101	NM_001982.3	1189	GAA/-	28/28	0.303694168582764	3	FACETS	0.936	0.826	1	0.468	0.413	0.527	CLONAL	1	TRUE	1	0.303694168582764	3		568	673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0031450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	203	616	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.300001433081041	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.303694168582764	2		616	598	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435581	56435581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200166143	NA	P-0031450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	206	665	0	ENST00000407977.2:c.1556G>A	p.Arg519Gln	p.R519Q	ENST00000407977		519	cGa/cAa	9/10	0.303694168582764	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.303694168582764	3		665	751	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713485	40713485	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	52	553	0	ENST00000373198.4:c.4030C>T	p.Pro1344Ser	p.P1344S	ENST00000373198	NM_133170.3	1344	Cca/Tca	30/32	0.303694168582764	6	FACETS	0.701	0.595	0.818	0.175	0.148	0.205	SUBCLONAL	1	TRUE	2	0.303694168582764	6		553	785	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189873	66189873	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1032457637	NA	P-0031450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	47	386	0	ENST00000273854.3:c.3073G>T	p.Glu1025Ter	p.E1025*	ENST00000273854	NM_004439.5	1025	Gaa/Taa	18/18	1	2	FACETS	0.853	0.722	0.996	0.853	0.722	0.996	CLONAL	1	TRUE	1	0.303694168582764	2		386	363	SUCCESS
APC	324	MSKCC	GRCh37	5	112175488	112175488	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	60	310	0	ENST00000257430.4:c.4198del	p.Ser1400ArgfsTer15	p.S1400Rfs*15	ENST00000257430	NM_000038.5	1399	cgT/cg	16/16	0.231605855232199	2	FACETS	1	0.96	1	0.65	0.564	0.742	CLONAL	1	TRUE	0	0.303694168582764	2		310	304	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982002	70982002	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	170	771	0	ENST00000276594.2:c.94C>A	p.Pro32Thr	p.P32T	ENST00000276594	NM_024504.3	32	Cct/Act	2/8	0.303694168582764	5	FACETS	1	0.988	1	0.364	0.334	0.396	CLONAL	1	TRUE	1	0.303694168582764	5		771	1119	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400978	139400978	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0031450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	63	481	0	ENST00000277541.6:c.4014+1G>A		p.X1338_splice	ENST00000277541	NM_017617.3	1338			0.300001433081041	2	FACETS	0.932	0.809	1	0.466	0.404	0.533	CLONAL	1	TRUE	0	0.303694168582764	2		481	445	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913396	NA	P-0031452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	145	265	0	ENST00000349496.5:c.95A>C	p.Asp32Ala	p.D32A	ENST00000349496	NM_001904.3	32	gAc/gCc	3/15	0.191981349051921	6	FACETS	1	0.931	1			1	CLONAL	3	TRUE	NA	0.3	6		265	508	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0031453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	118	562	3	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.64049452398734	2	FACETS	0.97	0.904	1	0.97	0.904	1	CLONAL	2	TRUE	0	0.64049452398734	2		565	190	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579585	7579591	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GGGGGAC	GGGGGAC	TGGGAA	novel	NA	P-0031453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	74	458	1	ENST00000269305.4:c.97-1_102delinsTTCCCA		p.X33_splice	ENST00000269305	NM_001126112.2	33		4/11	0.64049452398734	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.64049452398734	1		459	147	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492730	56492730	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	13	465	1	ENST00000407977.2:c.209C>T	p.Ala70Val	p.A70V	ENST00000407977		70	gCt/gTt	2/10	0.64049452398734	1	FACETS	0.129	0.092	0.174	0.129	0.092	0.174	SUBCLONAL	1	TRUE	0	0.64049452398734	1		466	214	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584825	48584825	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	61	240	0	ENST00000342988.3:c.903C>A	p.Tyr301Ter	p.Y301*	ENST00000342988	NM_005359.5	301	taC/taA	7/12	0.64049452398734	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.64049452398734	1		240	119	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170039	32170052	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGCATCGCAGGC	CCAGCATCGCAGGC	-	novel	NA	P-0031453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	106	675	0	ENST00000375023.3:c.3556_3569del	p.Ala1186LeufsTer44	p.A1186Lfs*44	ENST00000375023	NM_004557.3	1186	GCCTGCGATGCTGGc/c	21/30	0.64049452398734	1	FACETS	0.926	0.847	1	0.926	0.847	1	CLONAL	1	TRUE	0	0.64049452398734	1		675	243	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0031459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	53	728	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.150478399126182	4	FACETS	0.768	0.653	0.895	0.384	0.326	0.448	SUBCLONAL	1	TRUE	2	0.17	4		728	950	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0031459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	113	491	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.150478399126182	4	FACETS	0.882	0.793	0.976	0.882	0.793	0.976	CLONAL	2	TRUE	2	0.17	4		491	882	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0031459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	91	795	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.209483439247335	3	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.17	3		795	778	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46527695	46527695	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	28	435	0	ENST00000262741.5:c.670A>C	p.Lys224Gln	p.K224Q	ENST00000262741	NM_003629.3	224	Aaa/Caa	6/10	1	2	FACETS	0.589	0.47	0.726	0.589	0.47	0.726	SUBCLONAL	1	TRUE	1	0.17	2		435	559	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55260498	55260498	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	102	597	0	ENST00000275493.2:c.2665A>G	p.Arg889Gly	p.R889G	ENST00000275493	NM_005228.3	889	Aga/Gga	22/28	0.150478399126182	4	FACETS	0.873	0.78	0.972	0.873	0.78	0.972	CLONAL	2	TRUE	2	0.17	4		597	804	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0031461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	15	332	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.205762446990736	3	FACETS	0.465	0.34	0.616	0.233	0.17	0.308	SUBCLONAL	1	TRUE	1	0.27	3		332	271	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0031461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	17	235	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.205762446990736	3	FACETS	0.276	0.205	0.362	0.138	0.102	0.181	SUBCLONAL	1	TRUE	1	0.27	3		235	517	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023702	31023702	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1311033207	NA	P-0031461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	70	625	0	ENST00000375687.4:c.3187C>T	p.Gln1063Ter	p.Q1063*	ENST00000375687	NM_015338.5	1063	Cag/Tag	13/13	1	2	FACETS	0.544	0.473	0.621	0.544	0.473	0.621	SUBCLONAL	1	TRUE	1	0.27	2		625	953	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520017	NA	P-0031461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	137	708	1	ENST00000326873.7:c.647C>T	p.Ser216Phe	p.S216F	ENST00000326873	NM_000455.4	216	tCc/tTc	5/10	0.269406125683171	1	FACETS	0.886	0.805	0.971	0.886	0.805	0.971	CLONAL	1	TRUE	0	0.27	1		709	991	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259262	89259262	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	28	361	0	ENST00000336596.2:c.406C>G	p.Arg136Gly	p.R136G	ENST00000336596	NM_005233.5	136	Cga/Gga	3/17	0.205762446990736	3	FACETS	0.46	0.367	0.567	0.23	0.183	0.284	SUBCLONAL	1	TRUE	1	0.27	3		361	512	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131647	2131647	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	74	707	0	ENST00000219476.3:c.3662C>G	p.Ser1221Trp	p.S1221W	ENST00000219476	NM_000548.3	1221	tCg/tGg	31/42	0.269406125683171	1	FACETS	0.486	0.424	0.553	0.486	0.424	0.553	SUBCLONAL	1	TRUE	0	0.27	1		707	975	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829347	72829347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	68	542	0	ENST00000268489.5:c.7234G>A	p.Glu2412Lys	p.E2412K	ENST00000268489	NM_006885.3	2412	Gag/Aag	9/10	1	2	FACETS	0.523	0.454	0.599	0.523	0.454	0.599	SUBCLONAL	1	TRUE	1	0.27	2		542	963	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942062	17942062	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1203084402	NA	P-0031461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	162	679	0	ENST00000458235.1:c.2953G>A	p.Glu985Lys	p.E985K	ENST00000458235	NM_000215.3	985	Gag/Aag	21/24	1	2	FACETS	0.987	0.903	1	0.987	0.903	1	CLONAL	1	TRUE	1	0.27	2		679	1216	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136839	69136840	+	missense_variant	Missense_Mutation	DNP	CG	CG	AA	novel	NA	P-0031461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	34	374	1	ENST00000288368.4:c.4753_4754delinsAA	p.Arg1585Lys	p.R1585K	ENST00000288368	NM_024870.2	1585	CGg/AAg	39/40	0.3	3	FACETS	0.451	0.367	0.545			1	SUBCLONAL	1	TRUE	NA	0.27	3		375	634	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820547	44820548	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0031461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	14	255	0	ENST00000377967.4:c.247_248del	p.Leu83AsnfsTer5	p.L83Nfs*5	ENST00000377967	NM_021140.2	82	TCt/t	3/29	1	1	FACETS	0.78	0.569	1	0.78	0.569	1	CLONAL	1	TRUE	0	0.27	1		255	115	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720808	89720808	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	133	268	0	ENST00000371953.3:c.959T>C	p.Leu320Ser	p.L320S	ENST00000371953	NM_000314.4	320	tTa/tCa	8/9	0.661901782314211	2	FACETS	0.957	0.896	1	0.957	0.896	1	CLONAL	2	TRUE	0	0.661901782314211	2		268	210	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0031462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	304	541	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.304433890436908	6	FACETS	0.937	0.888	0.987	0.937	0.888	0.987	INDETERMINATE	3	TRUE	3	0.661901782314211	6		541	759	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576853	7576853	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs11575996	NA	P-0031462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	320	568	0	ENST00000269305.4:c.993G>T	p.Gln331His	p.Q331H	ENST00000269305	NM_001126112.2	331	caG/caT	9/11	0.304433890436908	6	FACETS	0.982	0.932	1	0.982	0.932	1	INDETERMINATE	3	TRUE	3	0.661901782314211	6		568	763	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420213	49420213	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	327	555	2	ENST00000301067.7:c.15536G>T	p.Arg5179Leu	p.R5179L	ENST00000301067	NM_003482.3	5179	cGt/cTt	48/54	0.661901782314211	3	FACETS	0.999	0.953	1	0.999	0.953	1	CLONAL	2	TRUE	1	0.661901782314211	3		557	658	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288754	11288754	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	228	477	0	ENST00000361445.4:c.3001A>G	p.Ile1001Val	p.I1001V	ENST00000361445	NM_004958.3	1001	Att/Gtt	19/58	0.661901782314211	2	FACETS	0.973	0.927	1	0.973	0.927	1	CLONAL	2	TRUE	0	0.661901782314211	2		477	354	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981875	201981875	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370916337	NA	P-0031462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	429	716	0	ENST00000359651.3:c.586G>A	p.Val196Ile	p.V196I	ENST00000359651		196	Gtc/Atc	4/8	0.661901782314211	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.661901782314211	3		716	760	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16005051	16005051	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	284	519	0	ENST00000268712.3:c.2203G>T	p.Glu735Ter	p.E735*	ENST00000268712	NM_006311.3	735	Gag/Tag	20/46	0.304433890436908	6	FACETS	0.961	0.909	1	0.961	0.909	1	INDETERMINATE	3	TRUE	3	0.661901782314211	6		519	692	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610275	10610275	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	386	751	0	ENST00000171111.5:c.435C>G	p.Ile145Met	p.I145M	ENST00000171111	NM_203500.1	145	atC/atG	2/6	0.661901782314211	3	FACETS	0.998	0.955	1	0.998	0.955	1	CLONAL	2	TRUE	1	0.661901782314211	3		751	778	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969942	161969942	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	259	504	0	ENST00000366898.1:c.1027C>A	p.Pro343Thr	p.P343T	ENST00000366898	NM_004562.2	343	Ccg/Acg	9/12	0.661901782314211	3	FACETS	0.994	0.942	1	0.994	0.942	1	CLONAL	2	TRUE	1	0.661901782314211	3		504	524	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238954	5238956	+	missense_variant	Missense_Mutation	TNP	CCA	CCA	ACC	novel	NA	P-0031462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	172	482	0	ENST00000357368.4:c.1823_1825delinsGGT	p.Val608_Val609delinsGlyLeu	p.V608_V609delinsGL	ENST00000357368	NM_002850.3	608	gTGGtg/gGGTtg	13/38	0.661901782314211	3	FACETS	0.917	0.856	0.979	0.917	0.856	0.979	CLONAL	2	TRUE	1	0.661901782314211	3		482	377	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	193	384	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.281909265426723	3	FACETS	0.994	0.927	1	0.994	0.927	1	CLONAL	3	TRUE	0	0.28	3		384	527	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0031463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	138	536	0	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.207166780335301	2	FACETS	0.779	0.711	0.85	0.779	0.711	0.85	SUBCLONAL	2	TRUE	0	0.28	2		536	633	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231403	46231403	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	22	463	0	ENST00000334344.6:c.1243G>C	p.Val415Leu	p.V415L	ENST00000334344	NM_152641.2	415	Gta/Cta	10/21	1	2	FACETS	0.504	0.39	0.635	0.504	0.39	0.635	SUBCLONAL	1	TRUE	1	0.28	2		463	312	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233128	66233128	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	30	379	1	ENST00000273854.3:c.1871G>T	p.Ser624Ile	p.S624I	ENST00000273854	NM_004439.5	624	aGc/aTc	10/18	1	2	FACETS	0.561	0.452	0.684	0.561	0.452	0.684	SUBCLONAL	1	TRUE	1	0.28	2		380	382	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0031464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	63	562	3	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.888	1	1	0.982	1	CLONAL	2	TRUE	1	0.403070882511932	2		565	156	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	26	632	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	1	2	FACETS	0.768	0.626	0.92	1	0.943	1	CLONAL	2	TRUE	1	0.403070882511932	2		632	84	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81574756	81574756	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	51	445	0	ENST00000298171.2:c.652A>G	p.Lys218Glu	p.K218E	ENST00000298171	NM_000369.2	218	Aaa/Gaa	8/10	0.403070882511932	6	FACETS	1	0.925	1	0.557	0.48	0.64	CLONAL	2	TRUE	2	0.403070882511932	6		445	205	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0031466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	245	759	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.193848722761529	2	FACETS	0.822	0.768	0.877	0.822	0.768	0.877	CLONAL	2	TRUE	0	0.294551571385937	2		759	1012	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412690	139412690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	191	802	0	ENST00000277541.6:c.1154C>T	p.Ser385Phe	p.S385F	ENST00000277541	NM_017617.3	385	tCc/tTc	7/34	0.193848722761529	2	FACETS	1	0.988	1	0.681	0.63	0.734	CLONAL	1	TRUE	0	0.294551571385937	2		802	952	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0031466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	199	368	0	ENST00000374080.3:c.3670C>T	p.Leu1224Phe	p.L1224F	ENST00000374080		1224	Ctc/Ttc	26/45	0.228519273387705	2	FACETS	1	0.981	1			1	CLONAL	2	TRUE	NA	0.294551571385937	2		368	592	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447709	187447709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	74	523	0	ENST00000232014.4:c.484G>A	p.Val162Met	p.V162M	ENST00000232014	NM_001130845.1	162	Gtg/Atg	5/10	0.294551571385937	4	FACETS	0.722	0.631	0.821	0.241	0.21	0.274	SUBCLONAL	1	TRUE	1	0.294551571385937	4		523	901	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405253	70405253	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	120	564	0	ENST00000373644.4:c.2767A>G	p.Thr923Ala	p.T923A	ENST00000373644	NM_030625.2	923	Aca/Gca	4/12	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.294551571385937	2		564	771	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405272	70405272	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	110	566	0	ENST00000373644.4:c.2786G>T	p.Ser929Ile	p.S929I	ENST00000373644	NM_030625.2	929	aGc/aTc	4/12	1	2	FACETS	0.944	0.848	1	0.944	0.848	1	CLONAL	1	TRUE	1	0.294551571385937	2		566	791	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120751	115120751	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	71	673	0	ENST00000257566.3:c.255del	p.His86IlefsTer2	p.H86Ifs*2	ENST00000257566	NM_016569.3	85	gcG/gc	1/8	1	2	FACETS	0.513	0.446	0.585	0.513	0.446	0.585	SUBCLONAL	1	TRUE	1	0.294551571385937	2		673	940	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610509	215610509	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	113	507	0	ENST00000260947.4:c.1747A>G	p.Lys583Glu	p.K583E	ENST00000260947	NM_000465.2	583	Aaa/Gaa	8/11	0.239324103267101	1	FACETS	0.918	0.826	1	0.918	0.826	1	CLONAL	1	TRUE	0	0.294551571385937	1		507	713	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628022	187628022	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	138	601	0	ENST00000441802.2:c.2960del	p.Gln987ArgfsTer15	p.Q987Rfs*15	ENST00000441802	NM_005245.3	987	cAg/cg	2/27	0.190350427065699	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.294551571385937	1		601	729	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129495	152129495	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	18	173	0	ENST00000206249.3:c.448T>G	p.Tyr150Asp	p.Y150D	ENST00000206249	NM_000125.3	150	Tac/Gac	1/8	1	2	FACETS	0.529	0.399	0.682	0.529	0.399	0.682	SUBCLONAL	1	TRUE	1	0.294551571385937	2		173	231	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971147	21971151	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGC	TGGGC	-	novel	NA	P-0031466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	84	462	0	ENST00000304494.5:c.207_211del	p.Pro70LeufsTer48	p.P70Lfs*48	ENST00000304494	NM_000077.4	69	gaGCCCAac/gaac	2/3	0.239324103267101	1	FACETS	0.923	0.817	1	0.923	0.817	1	CLONAL	1	TRUE	0	0.294551571385937	1		462	527	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413274	139413274	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	182	642	0	ENST00000277541.6:c.868C>T	p.Gln290Ter	p.Q290*	ENST00000277541	NM_017617.3	290	Cag/Tag	6/34	0.193848722761529	2	FACETS	1	0.989	1	0.729	0.673	0.787	CLONAL	1	TRUE	0	0.294551571385937	2		642	848	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436011	116436011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1258671501	NA	P-0031468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	228	697	2	ENST00000397752.3:c.4006C>T	p.Arg1336Trp	p.R1336W	ENST00000397752	NM_000245.2	1336	Cgg/Tgg	21/21	1	2	FACETS	0.888	0.83	0.947	0.888	0.83	0.947	CLONAL	1	TRUE	1	0.66784742777516	2		699	769	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032846	30032846	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	170	425	0	ENST00000338641.4:c.221G>A	p.Trp74Ter	p.W74*	ENST00000338641	NM_000268.3	74	tGg/tAg	2/16	0.66784742777516	1	FACETS	0.953	0.89	1	0.953	0.89	1	CLONAL	1	TRUE	0	0.66784742777516	1		425	356	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	34	270	0				ENST00000310581	NM_198253.2	-/1132			0.320521066894352	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		270	146	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0031469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	140	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.217832244520632	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		336	428	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003217	143003217	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	61	372	0	ENST00000262992.4:c.2609A>G	p.Asp870Gly	p.D870G	ENST00000262992	NM_001101669.1	870	gAc/gGc	23/24	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		372	276	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781147	161781147	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145135117	NA	P-0031469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	46	484	0	ENST00000366898.1:c.1258C>T	p.Arg420Cys	p.R420C	ENST00000366898	NM_004562.2	420	Cgc/Tgc	11/12	0.217832244520632	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		484	351	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0031470-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	98	491	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	0.223836632944552	2		491	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0031470-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	123	890	2	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	0.223836632944552	2		892	765	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360630	70360630	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031470-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	50	280	0	ENST00000374080.3:c.6190C>T	p.Gln2064Ter	p.Q2064*	ENST00000374080		2064	Cag/Tag	42/45	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.223836632944552	2		280	316	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554374	81554374	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0031470-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	24	349	0	ENST00000298171.2:c.392+2T>A		p.X131_splice	ENST00000298171	NM_000369.2	131			1	2	FACETS	0.664	0.521	0.829	0.664	0.521	0.829	SUBCLONAL	1	TRUE	1	0.223836632944552	2		349	323	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925134	81925134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768664050	NA	P-0031470-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	65	553	0	ENST00000359376.3:c.925G>A	p.Val309Met	p.V309M	ENST00000359376	NM_002661.3	309	Gtg/Atg	11/33	1	2	FACETS	0.845	0.732	0.968	0.845	0.732	0.968	CLONAL	1	TRUE	1	0.223836632944552	2		553	687	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860329	42860329	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031470-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	52	526	0	ENST00000398585.3:c.548A>G	p.Asn183Ser	p.N183S	ENST00000398585	NM_001135099.1	183	aAt/aGt	5/14	0.0615491489251341	4	FACETS	0.741	0.63	0.864	0.371	0.315	0.432	INDETERMINATE	1	TRUE	2	0.223836632944552	4		526	767	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235281	235281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031470-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	26	409	0	ENST00000264932.6:c.1087C>T	p.His363Tyr	p.H363Y	ENST00000264932	NM_004168.2	363	Cac/Tac	9/15	0.0218707946170813	3	FACETS	0.519	0.41	0.644			1	INDETERMINATE	1	TRUE	NA	0.223836632944552	3		409	498	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039288	47039288	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031470-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	120	774	0	ENST00000377604.3:c.911T>C	p.Leu304Ser	p.L304S	ENST00000377604	NM_001204468.1	304	tTg/tCg	10/24	1	2	FACETS	0.765	0.691	0.842	1	0.985	1	SUBCLONAL	2	TRUE	1	0.223836632944552	2		774	701	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039297	47039297	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031470-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	125	799	0	ENST00000377604.3:c.920T>G	p.Leu307Arg	p.L307R	ENST00000377604	NM_001204468.1	307	cTg/cGg	10/24	1	2	FACETS	0.77	0.698	0.846	1	0.986	1	SUBCLONAL	2	TRUE	1	0.223836632944552	2		799	725	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578192	7578193	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCACCACCACACTATGTCGAAAAGTGTTTCTGTCATCCAAATACTCCACACGCAAATTTCCTTCCACTCGGATA	novel	NA	P-0031473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	68	640	0	ENST00000269305.4:c.582_656dup	p.Ile195_Pro219dup	p.I195_P219dup	ENST00000269305	NM_001126112.2	195	ccc/ccTATCCGAGTGGAAGGAAATTTGCGTGTGGAGTATTTGGATGACAGAAACACTTTTCGACATAGTGTGGTGGTGCCc	6/11	0.711548081001972	1	FACETS	0.175	0.152	0.201	0.175	0.152	0.201	SUBCLONAL	1	TRUE	0	0.711548081001972	1		640	702	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412016	63412016	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	195	276	0	ENST00000330258.3:c.1151A>T	p.Glu384Val	p.E384V	ENST00000330258	NM_152424.3	384	gAg/gTg	2/2	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.711548081001972	1		276	254	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0031476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	298	435	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.596740131198352	3	FACETS	0.998	0.947	1	0.998	0.947	1	CLONAL	2	TRUE	1	0.596740131198352	3		435	650	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578433	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	290	583	2	ENST00000269305.4:c.497C>A	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	166	tCa/tAa	5/11	0.596740131198352	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.596740131198352	1		585	616	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177681	56177682	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCAG	novel	NA	P-0031476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	137	356	0	ENST00000399503.3:c.2654_2655insCCAG	p.Leu885PhefsTer20	p.L885Ffs*20	ENST00000399503	NM_005921.1	885	ttg/ttCCAGg	14/20	1	2	FACETS	0.906	0.829	0.985	0.906	0.829	0.985	CLONAL	1	TRUE	1	0.596740131198352	2		356	507	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611808	100611808	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	197	424	0	ENST00000308731.7:c.1313C>A	p.Ser438Tyr	p.S438Y	ENST00000308731	NM_000061.2	438	tCt/tAt	14/19	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.596740131198352	2		424	615	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0031477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	239	594	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.795049628894695	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.795049628894695	1		594	326	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117388	115117389	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTACA	novel	NA	P-0031477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	145	450	0	ENST00000257566.3:c.785_786insTGTAA	p.Lys262AsnfsTer22	p.K262Nfs*22	ENST00000257566	NM_016569.3	262	aaa/aaTGTAAa	4/8	1	2	FACETS	0.962	0.889	1	0.962	0.889	1	CLONAL	1	TRUE	1	0.795049628894695	2		450	379	SUCCESS
BLM	641	MSKCC	GRCh37	15	91337488	91337488	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	38	397	0	ENST00000355112.3:c.3111G>T	p.Arg1037Ser	p.R1037S	ENST00000355112	NM_000057.2	1037	agG/agT	16/22	0.158752872830609	3	FACETS	0.766	0.631	0.916	0.383	0.315	0.458	CLONAL	1	FALSE	1	0.158752872830609	3		397	675	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579503	7579503	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	50	540	0	ENST00000269305.4:c.184del	p.Glu62LysfsTer61	p.E62Kfs*61	ENST00000269305	NM_001126112.2	62	Gaa/aa	4/11	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	1	0.158752872830609	2		540	534	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913517	NA	P-0031480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	163	526	0	ENST00000288135.5:c.1676T>G	p.Val559Gly	p.V559G	ENST00000288135	NM_000222.2	559	gTt/gGt	11/21	1	2	FACETS	0.998	0.924	1	0.998	0.924	1	CLONAL	1	TRUE	1	0.693686825949578	2		526	471	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46603793	46603793	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1396288218	NA	P-0031481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	43	584	0	ENST00000263734.3:c.1150G>C	p.Glu384Gln	p.E384Q	ENST00000263734	NM_001430.4	384	Gag/Cag	9/16	0.192689499188851	3	FACETS	1	0.94	1	0.631	0.531	0.739	CLONAL	1	TRUE	1	0.291542093294302	3		584	268	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245846	41245846	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	19	480	0	ENST00000357654.3:c.1702C>G	p.Pro568Ala	p.P568A	ENST00000357654	NM_007294.3	568	Cct/Gct	10/23	1	2	FACETS	0.519	0.395	0.665	0.519	0.395	0.665	SUBCLONAL	1	TRUE	1	0.291542093294302	2		480	251	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044359	128044359	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	32	594	0	ENST00000285398.2:c.1262G>A	p.Trp421Ter	p.W421*	ENST00000285398	NM_000122.1	421	tGg/tAg	8/15	0.192689499188851	3	FACETS	1	0.881	1	0.554	0.452	0.667	CLONAL	1	TRUE	1	0.291542093294302	3		594	227	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520416	176520416	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777668601	NA	P-0031481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	16	613	0	ENST00000292408.4:c.1261G>A	p.Glu421Lys	p.E421K	ENST00000292408	NM_213647.1	421	Gag/Aag	10/18	0.192689499188851	3	FACETS	0.501	0.37	0.657	0.251	0.185	0.329	SUBCLONAL	1	TRUE	1	0.291542093294302	3		613	251	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001083	150001083	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	39	413	0	ENST00000253339.5:c.2521C>T	p.His841Tyr	p.H841Y	ENST00000253339		841	Cat/Tat	4/7	1	2	FACETS	0.91	0.758	1	0.91	0.758	1	CLONAL	1	TRUE	1	0.291542093294302	2		413	294	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617557	100617557	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	15	514	0	ENST00000308731.7:c.512G>T	p.Arg171Met	p.R171M	ENST00000308731	NM_000061.2	171	aGg/aTg	6/19	0.149868093116391	0	FACETS	0.401	0.294	0.528			1	INDETERMINATE	1	TRUE	0	0.291542093294302	0		514	182	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0031483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	632	566	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.916369912726074	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.916369912726074	2		566	669	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589612	67589613	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAAGTCGAGAATATG	novel	NA	P-0031484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	244	319	0	ENST00000274335.5:c.1377_1391dup	p.Tyr463_Asp464insGluSerArgGluTyr	p.Y463_D464insESREY	ENST00000274335		459	aaa/aAAAGTCGAGAATATGaa	10/15	0.463231562845209	4	FACETS	0.854	0.805	0.903	0.64	0.603	0.678	CLONAL	3	TRUE	0	0.494235767516943	4		319	576	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	121	270	0				ENST00000310581	NM_198253.2	-/1132			0.42047169006592	1	FACETS	0.876	0.799	0.955	0.876	0.799	0.955	CLONAL	1	TRUE	0	0.535398672007889	1		270	378	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	106	384	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	0.535398672007889	2		384	331	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2185868	2185868	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	185	693	0	ENST00000398665.3:c.140A>T	p.Glu47Val	p.E47V	ENST00000398665	NM_032482.2	47	gAa/gTa	3/28	0.502778629474266	0	FACETS	0.421	0.39	0.454			1	SUBCLONAL	1	TRUE	0	0.535398672007889	0		693	762	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270593	98270595	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	rs756897237	NA	P-0031487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	10	34	0	ENST00000331920.6:c.49_51del	p.Gly17del	p.G17del	ENST00000331920	NM_000264.3	17	GGC/-	1/24	0.42047169006592	1	FACETS	0.33	0.226	0.456	0.33	0.226	0.456	SUBCLONAL	1	TRUE	0	0.535398672007889	1		34	83	SUCCESS
APC	324	MSKCC	GRCh37	5	112175772	112175772	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	59	330	0	ENST00000257430.4:c.4483del	p.Ser1495ValfsTer12	p.S1495Vfs*12	ENST00000257430	NM_000038.5	1494	gAa/ga	16/16	0.42047169006592	1	FACETS	0.585	0.507	0.667	0.585	0.507	0.667	SUBCLONAL	1	TRUE	0	0.535398672007889	1		330	276	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186757	108186757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs864622251	NA	P-0031487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	108	511	0	ENST00000278616.4:c.6115G>A	p.Glu2039Lys	p.E2039K	ENST00000278616	NM_000051.3	2039	Gaa/Aaa	42/63	1	2	FACETS	0.868	0.783	0.956	0.868	0.783	0.956	CLONAL	1	TRUE	1	0.535398672007889	2		511	465	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241912	72241912	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	22	429	0	ENST00000357731.5:c.478T>A	p.Cys160Ser	p.C160S	ENST00000357731	NM_173808.2	160	Tgt/Agt	3/7	1	2	FACETS	0.254	0.196	0.32	0.254	0.196	0.32	SUBCLONAL	1	TRUE	1	0.535398672007889	2		429	324	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106562	108106562	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0031487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	44	345	0	ENST00000278616.4:c.496+1G>T		p.X166_splice	ENST00000278616	NM_000051.3	166			1	2	FACETS	0.604	0.51	0.707	0.604	0.51	0.707	SUBCLONAL	1	TRUE	1	0.535398672007889	2		345	272	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331719	68331719	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs751355274	NA	P-0031487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	10	106	0	ENST00000487270.1:c.316-1G>C		p.X106_splice	ENST00000487270	NM_133509.3	106			0.535398672007889	1	FACETS	0.391	0.269	0.538	0.391	0.269	0.538	SUBCLONAL	1	TRUE	0	0.535398672007889	1		106	70	SUCCESS
APC	324	MSKCC	GRCh37	5	112174215	112174218	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	novel	NA	P-0031487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	38	455	0	ENST00000257430.4:c.2925_2928del	p.Arg976ValfsTer3	p.R976Vfs*3	ENST00000257430	NM_000038.5	975	aAAAGa/aa	16/16	0.42047169006592	1	FACETS	0.371	0.308	0.441	0.371	0.308	0.441	SUBCLONAL	1	TRUE	0	0.535398672007889	1		455	280	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519922	NA	P-0031489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	266	621	0	ENST00000397062.3:c.235G>A	p.Glu79Lys	p.E79K	ENST00000397062	NM_006164.4	79	Gag/Aag	2/5	0.307748106789581	5	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.626167275986878	5		621	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577056	7577056	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	986	748	0	ENST00000269305.4:c.882del	p.Glu294AspfsTer51	p.E294Dfs*51	ENST00000269305	NM_001126112.2	294	gaG/ga	8/11	0.58858678756648	5	FACETS	0.992	0.975	1	0.992	0.975	1	CLONAL	5	TRUE	0	0.626167275986878	5		748	1231	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27204919	27204919	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs759108843	NA	P-0031489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	62	366	0	ENST00000380036.4:c.2220C>A	p.Asp740Glu	p.D740E	ENST00000380036	NM_000459.3	740	gaC/gaA	14/23	0.626167275986878	2	FACETS	0.498	0.431	0.569	0.249	0.215	0.285	SUBCLONAL	1	TRUE	0	0.626167275986878	2		366	398	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918318	44918318	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	141	249	0	ENST00000377967.4:c.943G>T	p.Glu315Ter	p.E315*	ENST00000377967	NM_021140.2	315	Gaa/Taa	11/29	0.626167275986878	2	FACETS	1	0.967	1			1	CLONAL	2	TRUE	NA	0.626167275986878	2		249	216	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720709	89720709	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs863224909	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	131	93	0	ENST00000371953.3:c.860C>G	p.Ser287Ter	p.S287*	ENST00000371953	NM_000314.4	287	tCa/tGa	8/9	0.667218901314092	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.667218901314092	2		93	174	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257434	16257434	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	310	485	0	ENST00000375759.3:c.4699G>A	p.Glu1567Lys	p.E1567K	ENST00000375759	NM_015001.2	1567	Gag/Aag	11/15	0.658050004555961	4	FACETS	0.878	0.845	0.91			1	CLONAL	4	TRUE	NA	0.667218901314092	4		485	441	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256750	16256750	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760134992	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	323	507	0	ENST00000375759.3:c.4015C>T	p.Arg1339Cys	p.R1339C	ENST00000375759	NM_015001.2	1339	Cgt/Tgt	11/15	0.658050004555961	4	FACETS	0.879	0.847	0.911			1	CLONAL	4	TRUE	NA	0.667218901314092	4		507	459	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255496	16255496	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	324	543	0	ENST00000375759.3:c.2761C>T	p.Gln921Ter	p.Q921*	ENST00000375759	NM_015001.2	921	Cag/Tag	11/15	0.658050004555961	4	FACETS	0.89	0.857	0.921			1	CLONAL	4	TRUE	NA	0.667218901314092	4		543	455	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254522	1254522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	359	824	2	ENST00000310581.5:c.3256C>T	p.Arg1086Cys	p.R1086C	ENST00000310581	NM_198253.2	1086	Cgt/Tgt	15/16	0.667218901314092	6	FACETS	1	0.984	1			1	CLONAL	2	TRUE	NA	0.667218901314092	6		826	1151	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259043	16259043	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	542	680	0	ENST00000375759.3:c.6313del	p.Ala2105LeufsTer33	p.A2105Lfs*33	ENST00000375759	NM_015001.2	2103	aGg/ag	11/15	0.658050004555961	4	FACETS	0.91	0.885	0.934			1	CLONAL	4	TRUE	NA	0.667218901314092	4		680	744	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259893	16259893	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	638	627	0	ENST00000375759.3:c.7158G>C	p.Gln2386His	p.Q2386H	ENST00000375759	NM_015001.2	2386	caG/caC	11/15	0.658050004555961	4	FACETS	1	0.994	1			1	CLONAL	4	TRUE	NA	0.667218901314092	4		627	767	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255934	16255934	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	282	569	0	ENST00000375759.3:c.3199C>T	p.Gln1067Ter	p.Q1067*	ENST00000375759	NM_015001.2	1067	Cag/Tag	11/15	0.658050004555961	4	FACETS	1	0.99	1			1	CLONAL	3	TRUE	NA	0.667218901314092	4		569	425	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259068	16259068	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1172519195	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	595	677	0	ENST00000375759.3:c.6333G>C	p.Glu2111Asp	p.E2111D	ENST00000375759	NM_015001.2	2111	gaG/gaC	11/15	0.658050004555961	4	FACETS	0.998	0.975	1			1	CLONAL	4	TRUE	NA	0.667218901314092	4		677	745	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255220	16255220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1482043812	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	295	496	0	ENST00000375759.3:c.2485C>T	p.His829Tyr	p.H829Y	ENST00000375759	NM_015001.2	829	Cac/Tac	11/15	0.658050004555961	4	FACETS	0.882	0.848	0.914			1	CLONAL	4	TRUE	NA	0.667218901314092	4		496	418	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123685	11123685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	239	609	3	ENST00000358026.2:c.2335G>A	p.Asp779Asn	p.D779N	ENST00000358026	NM_001128849.1	779	Gac/Aac	16/36	0.589481264472473	4	FACETS	0.813	0.762	0.864	0.813	0.762	0.864	CLONAL	2	TRUE	2	0.667218901314092	4		612	735	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256568	16256568	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	311	529	0	ENST00000375759.3:c.3833C>A	p.Ser1278Tyr	p.S1278Y	ENST00000375759	NM_015001.2	1278	tCc/tAc	11/15	0.658050004555961	4	FACETS	1	0.992	1			1	CLONAL	3	TRUE	NA	0.667218901314092	4		529	460	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257014	16257014	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	309	495	0	ENST00000375759.3:c.4279G>C	p.Glu1427Gln	p.E1427Q	ENST00000375759	NM_015001.2	1427	Gaa/Caa	11/15	0.658050004555961	4	FACETS	1	0.992	1			1	CLONAL	3	TRUE	NA	0.667218901314092	4		495	454	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257102	16257102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	343	500	0	ENST00000375759.3:c.4367C>T	p.Ser1456Leu	p.S1456L	ENST00000375759	NM_015001.2	1456	tCa/tTa	11/15	0.658050004555961	4	FACETS	1	0.993	1			1	CLONAL	3	TRUE	NA	0.667218901314092	4		500	496	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257797	16257797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	302	512	0	ENST00000375759.3:c.5062G>A	p.Glu1688Lys	p.E1688K	ENST00000375759	NM_015001.2	1688	Gaa/Aaa	11/15	0.658050004555961	4	FACETS	1	0.991	1			1	CLONAL	3	TRUE	NA	0.667218901314092	4		512	450	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257971	16257971	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444111349	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	251	540	0	ENST00000375759.3:c.5236G>A	p.Glu1746Lys	p.E1746K	ENST00000375759	NM_015001.2	1746	Gag/Aag	11/15	0.658050004555961	4	FACETS	0.886	0.849	0.921			1	CLONAL	4	TRUE	NA	0.667218901314092	4		540	354	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257975	16257975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768562805	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	251	524	0	ENST00000375759.3:c.5240G>A	p.Ser1747Asn	p.S1747N	ENST00000375759	NM_015001.2	1747	aGc/aAc	11/15	0.658050004555961	4	FACETS	0.891	0.854	0.926			1	CLONAL	4	TRUE	NA	0.667218901314092	4		524	352	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258091	16258091	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	248	491	0	ENST00000375759.3:c.5356G>A	p.Asp1786Asn	p.D1786N	ENST00000375759	NM_015001.2	1786	Gat/Aat	11/15	0.658050004555961	4	FACETS	1	0.987	1			1	CLONAL	3	TRUE	NA	0.667218901314092	4		491	378	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258820	16258820	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	648	701	1	ENST00000375759.3:c.6085G>T	p.Glu2029Ter	p.E2029*	ENST00000375759	NM_015001.2	2029	Gaa/Taa	11/15	0.658050004555961	4	FACETS	0.97	0.947	0.991			1	CLONAL	4	TRUE	NA	0.667218901314092	4		702	835	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258869	16258869	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	705	720	0	ENST00000375759.3:c.6134G>C	p.Arg2045Thr	p.R2045T	ENST00000375759	NM_015001.2	2045	aGa/aCa	11/15	0.658050004555961	4	FACETS	0.964	0.942	0.984			1	CLONAL	4	TRUE	NA	0.667218901314092	4		720	914	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259573	16259573	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1461527382	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	578	543	0	ENST00000375759.3:c.6838G>C	p.Glu2280Gln	p.E2280Q	ENST00000375759	NM_015001.2	2280	Gaa/Caa	11/15	0.658050004555961	4	FACETS	1	0.994	1			1	CLONAL	4	TRUE	NA	0.667218901314092	4		543	691	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259654	16259654	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	706	615	0	ENST00000375759.3:c.6919G>A	p.Glu2307Lys	p.E2307K	ENST00000375759	NM_015001.2	2307	Gaa/Aaa	11/15	0.658050004555961	4	FACETS	1	0.995	1			1	CLONAL	4	TRUE	NA	0.667218901314092	4		615	848	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260485	16260485	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	423	471	0	ENST00000375759.3:c.7750del	p.Glu2584LysfsTer7	p.E2584Kfs*7	ENST00000375759	NM_015001.2	2584	Gaa/aa	11/15	0.658050004555961	4	FACETS	0.968	0.941	0.994			1	CLONAL	4	TRUE	NA	0.667218901314092	4		471	546	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260485	16260491	+	frameshift_variant	Frame_Shift_Del	DEL	GAAAAAA	GAAAAAA	AAAAAC	novel	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	428	487	0	ENST00000375759.3:c.7750_7756delinsAAAAAC	p.Glu2584LysfsTer7	p.E2584Kfs*7	ENST00000375759	NM_015001.2	2584	GAAAAAAca/AAAAACca	11/15	0.658050004555961	4	FACETS	0.953	0.926	0.98			1	CLONAL	4	TRUE	NA	0.667218901314092	4		487	561	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260491	16260491	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	428	487	0	ENST00000375759.3:c.7756A>C	p.Thr2586Pro	p.T2586P	ENST00000375759	NM_015001.2	2586	Aca/Cca	11/15	0.658050004555961	4	FACETS	0.976	0.949	1			1	CLONAL	4	TRUE	NA	0.667218901314092	4		487	548	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260546	16260546	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	582	576	0	ENST00000375759.3:c.7811C>A	p.Ala2604Asp	p.A2604D	ENST00000375759	NM_015001.2	2604	gCt/gAt	11/15	0.658050004555961	4	FACETS	1	0.984	1			1	CLONAL	4	TRUE	NA	0.667218901314092	4		576	721	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264028	16264028	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	942	864	1	ENST00000375759.3:c.10397G>A	p.Ser3466Asn	p.S3466N	ENST00000375759	NM_015001.2	3466	aGc/aAc	12/15	0.658050004555961	4	FACETS	1	0.992	1			1	CLONAL	4	TRUE	NA	0.667218901314092	4		865	1157	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852551	63852551	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	1479	467	0	ENST00000279873.7:c.3329C>G	p.Thr1110Ser	p.T1110S	ENST00000279873	NM_032199.2	1110	aCt/aGt	10/10	0.667218901314092	14	FACETS	0.998	0.99	1			1	CLONAL	14	TRUE	NA	0.667218901314092	14		467	1587	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527783	103527783	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	225	397	0	ENST00000355739.4:c.3091G>T	p.Ala1031Ser	p.A1031S	ENST00000355739	NM_000123.3	1031	Gcc/Tcc	15/15	NA	2	FACETS	0.953	0.906	0.998			1	INDETERMINATE	2	TRUE	NA	0.667218901314092	2		397	354	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873653	35873653	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	166	358	0	ENST00000216797.5:c.198G>A	p.Trp66Ter	p.W66*	ENST00000216797	NM_020529.2	66	tgG/tgA	1/6	0.667218901314092	2	FACETS	0.953	0.9	1	0.953	0.9	1	CLONAL	2	TRUE	0	0.667218901314092	2		358	261	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961164	41961164	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	181	335	0	ENST00000219905.7:c.72C>G	p.Phe24Leu	p.F24L	ENST00000219905	NM_001164273.1	24	ttC/ttG	2/24	0.589481264472473	4	FACETS	0.996	0.929	1	0.996	0.929	1	CLONAL	2	TRUE	2	0.667218901314092	4		335	454	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714084	43714084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	295	700	0	ENST00000382044.4:c.4069C>T	p.Pro1357Ser	p.P1357S	ENST00000382044	NM_001141980.1	1357	Ccc/Tcc	19/28	0.589481264472473	4	FACETS	0.956	0.904	1	0.956	0.904	1	CLONAL	2	TRUE	2	0.667218901314092	4		700	771	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211387	36211387	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	390	821	0	ENST00000222270.7:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000222270	NM_014727.1	380	Gag/Cag	3/37	0.667218901314092	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.667218901314092	2		821	575	SUCCESS
REL	5966	MSKCC	GRCh37	2	61144012	61144013	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	180	287	0	ENST00000295025.8:c.395_396insG	p.Glu134Ter	p.E134*	ENST00000295025	NM_002908.2	132	gtc/gtGc	5/11	0.667218901314092	4	FACETS	0.947	0.882	1	0.947	0.882	1	CLONAL	2	TRUE	2	0.667218901314092	4		287	475	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371721	225371721	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	216	368	0	ENST00000264414.4:c.884-1G>C		p.X295_splice	ENST00000264414	NM_003590.4	295			0.360817715210155	5	FACETS	1	0.98	1	0.741	0.694	0.789	INDETERMINATE	2	TRUE	2	0.667218901314092	5		368	583	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679009	117679009	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	254	296	0	ENST00000368508.3:c.3812G>A	p.Arg1271Lys	p.R1271K	ENST00000368508	NM_002944.2	1271	aGg/aAg	24/43	0.667218901314092	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.667218901314092	4		296	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578533	7578553	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TCTTGTTGAGGGCAGGGGAGT	TCTTGTTGAGGGCAGGGGAGT	-	novel	NA	P-0031490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	323	897	0	ENST00000269305.4:c.377_397del	p.Tyr126_Met133delinsLeu	p.Y126_M133delinsL	ENST00000269305	NM_001126112.2	126	tACTCCCCTGCCCTCAACAAGAtg/ttg	5/11	0.655862688509594	2	FACETS	0.919	0.88	0.956	0.919	0.88	0.956	CLONAL	2	TRUE	0	0.667218901314092	2		897	527	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0031491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	89	621	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.206853807806626	2	FACETS	0.926	0.822	1	0.926	0.822	1	CLONAL	2	TRUE	0	0.16	2		624	601	SUCCESS
APC	324	MSKCC	GRCh37	5	112174922	112174923	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTCT	novel	NA	P-0031491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	17	301	0	ENST00000257430.4:c.3633_3637dup	p.Ser1213CysfsTer54	p.S1213Cfs*54	ENST00000257430	NM_000038.5	1211	atg/aTGTCTtg	16/16	0.3	1	FACETS	0.889	0.672	1	1	0.921	1	CLONAL	2	TRUE	0	0.16	1		301	110	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026099	71026099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	43	387	0	ENST00000318789.4:c.1523C>T	p.Thr508Met	p.T508M	ENST00000318789	NM_032682.5	508	aCg/aTg	17/21	0.165229563716316	4	FACETS	0.888	0.746	1	0.888	0.746	1	CLONAL	2	TRUE	2	0.16	4		387	351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0031493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	42	574	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	1	2	FACETS	0.654	0.545	0.776	0.654	0.545	0.776	SUBCLONAL	1	TRUE	1	0.2	2		574	642	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974742	21974742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554656382	NA	P-0031493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	28	282	0	ENST00000304494.5:c.85C>T	p.Arg29Trp	p.R29W	ENST00000304494	NM_000077.4	29	Cgg/Tgg	1/3	1	2	FACETS	1	0.818	1	1	0.818	1	CLONAL	1	TRUE	1	0.2	2		282	274	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0031498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	1081	701	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.732793492062923	7	FACETS	0.997	0.985	1			1	CLONAL	7	TRUE	NA	0.732793492062923	7		701	1197	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435300	110435302	+	inframe_deletion	In_Frame_Del	DEL	GGT	GGT	-	rs765493638	NA	P-0031498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	11	111	1	ENST00000375856.3:c.3099_3101del	p.Pro1036del	p.P1036del	ENST00000375856	NM_003749.2	1033	ccACCg/ccg	1/2	0.732793492062923	6	FACETS	0.404	0.28	0.559	0.101	0.07	0.14	SUBCLONAL	1	TRUE	2	0.732793492062923	6		112	183	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729496	41729496	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	129	661	0	ENST00000242208.4:c.1033T>A	p.Tyr345Asn	p.Y345N	ENST00000242208	NM_002192.2	345	Tat/Aat	3/3	0.258439087306134	6	FACETS	1	0.985	1	0.49	0.445	0.536	INDETERMINATE	1	TRUE	3	0.732793492062923	6		661	591	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592616	28592626	+	frameshift_variant	Frame_Shift_Del	DEL	AACATAGTTGG	AACATAGTTGG	-	novel	NA	P-0031498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	115	496	0	ENST00000241453.7:c.2519_2529del	p.Ser840CysfsTer19	p.S840Cfs*19	ENST00000241453	NM_004119.2	840	tCCAACTATGTT/t	20/24	0.732793492062923	6	FACETS	0.963	0.867	1	0.241	0.216	0.266	CLONAL	1	TRUE	2	0.732793492062923	6		496	804	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217458	142217458	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	29	417	0	ENST00000350721.4:c.5539G>C	p.Gly1847Arg	p.G1847R	ENST00000350721	NM_001184.3	1847	Gga/Cga	32/47	0.732793492062923	3	FACETS	0.238	0.191	0.292	0.079	0.063	0.098	SUBCLONAL	1	TRUE	0	0.732793492062923	3		417	454	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860483	151860484	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0031498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	117	605	0	ENST00000262189.6:c.10178_10179insT	p.Glu3393AspfsTer9	p.E3393Dfs*9	ENST00000262189	NM_170606.2	3393	gaa/gaTa	43/59	0.451225560180025	5	FACETS	1	0.959	1	0.371	0.335	0.409	CLONAL	1	TRUE	2	0.732793492062923	5		605	602	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	232	349	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.64170580895674	1	FACETS	0.909	0.856	0.963	0.909	0.856	0.963	CLONAL	1	TRUE	0	0.64170580895674	1		349	540	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165756	108165756	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886039592	NA	P-0031500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	65	439	0	ENST00000278616.4:c.4879C>T	p.Gln1627Ter	p.Q1627*	ENST00000278616	NM_000051.3	1627	Cag/Tag	32/63	0.339497562854088	1	FACETS	0.334	0.29	0.381	0.334	0.29	0.381	INDETERMINATE	1	TRUE	0	0.64170580895674	1		439	412	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010631	48010631	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1064793939	NA	P-0031500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	126	319	0	ENST00000234420.5:c.259A>G	p.Ser87Gly	p.S87G	ENST00000234420	NM_000179.2	87	Agt/Ggt	1/10	0.356197452065768	1	FACETS	0.799	0.733	0.866	0.799	0.733	0.866	INDETERMINATE	1	TRUE	0	0.64170580895674	1		319	334	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169988209	169988209	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	40	313	0	ENST00000295797.4:c.451C>T	p.Arg151Cys	p.R151C	ENST00000295797	NM_002740.5	151	Cgt/Tgt	6/18	0.25128579978815	3	FACETS	0.449	0.373	0.532	0.224	0.186	0.266	INDETERMINATE	1	TRUE	1	0.64170580895674	3		313	367	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179064	123179064	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	74	337	0	ENST00000218089.9:c.513C>G	p.Phe171Leu	p.F171L	ENST00000218089	NM_001042749.1	171	ttC/ttG	8/35	0.429555913564917	2	FACETS	0.485	0.425	0.548			1	SUBCLONAL	1	TRUE	NA	0.64170580895674	2		337	476	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0031506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	66	562	3	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.764	0.664	0.873	0.764	0.664	0.873	SUBCLONAL	1	TRUE	1	0.31	2		565	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0031506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	95	820	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	1	2	FACETS	0.798	0.71	0.892	0.798	0.71	0.892	SUBCLONAL	1	TRUE	1	0.31	2		820	768	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492871	56492889	+	frameshift_variant	Frame_Shift_Del	DEL	GCCTGCAGGGTAGCCATCA	GCCTGCAGGGTAGCCATCA	-	novel	NA	P-0031506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	42	358	0	ENST00000407977.2:c.50_68del	p.Leu17GlnfsTer28	p.L17Qfs*28	ENST00000407977		17	cTGATGGCTACCCTGCAGGCa/ca	2/10	NA	2	FACETS	0.877	0.735	1			1	INDETERMINATE	1	TRUE	NA	0.31	2		358	309	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	149	384	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	0.452324814441746	2		384	574	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0031508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	108	363	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	0.979	0.883	1	0.979	0.883	1	CLONAL	1	TRUE	1	0.452324814441746	2		363	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0031508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	348	661	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.435830361127014	2	FACETS	0.956	0.91	1	0.956	0.91	1	CLONAL	2	TRUE	0	0.452324814441746	2		661	805	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94923096	94923096	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	47	497	0	ENST00000536441.1:c.372A>C	p.Leu124Phe	p.L124F	ENST00000536441	NM_144665.3	124	ttA/ttC	4/10	1	2	FACETS	0.329	0.277	0.387	0.329	0.277	0.387	SUBCLONAL	1	TRUE	1	0.452324814441746	2		497	631	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102198829	102198829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141069802	NA	P-0031508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	118	415	0	ENST00000263464.3:c.1000G>A	p.Val334Ile	p.V334I	ENST00000263464	NM_001165.4	334	Gtt/Att	4/9	1	2	FACETS	0.973	0.882	1	0.973	0.882	1	CLONAL	1	TRUE	1	0.452324814441746	2		415	536	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481622	56481622	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	172	628	3	ENST00000267101.3:c.657T>A	p.Phe219Leu	p.F219L	ENST00000267101	NM_001982.3	219	ttT/ttA	6/28	0.434840898294331	3	FACETS	1	0.959	1	0.532	0.489	0.576	CLONAL	1	TRUE	1	0.452324814441746	3		631	877	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149794	202149794	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	157	553	0	ENST00000358485.4:c.1235A>T	p.Lys412Ile	p.K412I	ENST00000358485	NM_001080125.1	412	aAa/aTa	8/9	0.340284615621034	3	FACETS	1	0.962	1	0.541	0.496	0.588	CLONAL	1	TRUE	1	0.452324814441746	3		553	786	SUCCESS
AR	367	MSKCC	GRCh37	X	66765979	66765979	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	228	769	0	ENST00000374690.3:c.991G>A	p.Ala331Thr	p.A331T	ENST00000374690	NM_000044.3	331	Gct/Act	1/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.452324814441746	2		769	892	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302845	15302845	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767539048	NA	P-0031508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	173	766	0	ENST00000263388.2:c.605C>T	p.Ala202Val	p.A202V	ENST00000263388	NM_000435.2	202	gCa/gTa	4/33	1	2	FACETS	0.876	0.807	0.948	0.876	0.807	0.948	CLONAL	1	TRUE	1	0.452324814441746	2		766	873	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226146	2226146	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	118	632	0	ENST00000326181.6:c.1843A>C	p.Lys615Gln	p.K615Q	ENST00000326181	NM_032271.2	615	Aaa/Caa	19/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		632	401	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0031510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	202	550	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.521639570291046	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.521639570291046	1		550	564	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0031510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	28	98	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	1	2	FACETS	0.617	0.498	0.75	0.617	0.498	0.75	SUBCLONAL	1	TRUE	1	0.521639570291046	2		98	174	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559195	29559209	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	AGTTATTTCTTAAGT	AGTTATTTCTTAAGT	-	novel	NA	P-0031510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	132	408	0	ENST00000356175.3:c.3303_3314+3del		p.X1101_splice	ENST00000356175	NM_000267.3	1101		25/57	0.46738518976537	2	FACETS	1	0.939	1	0.517	0.473	0.564	CLONAL	1	TRUE	0	0.521639570291046	2		408	489	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223595	55223595	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	176	477	0	ENST00000275493.2:c.962A>G	p.Asp321Gly	p.D321G	ENST00000275493	NM_005228.3	321	gAc/gGc	8/28	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.521639570291046	2		477	662	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0031515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	93	498	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.882	0.794	0.973	0.882	0.794	0.973	CLONAL	1	TRUE	1	0.700761046171363	2		498	301	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439808	52439808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	150	555	0	ENST00000460680.1:c.904C>T	p.Pro302Ser	p.P302S	ENST00000460680	NM_004656.3	302	Cct/Tct	10/17	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.700761046171363	2		555	417	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443600	52443600	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	109	582	0	ENST00000460680.1:c.92A>C	p.Glu31Ala	p.E31A	ENST00000460680	NM_004656.3	31	gAg/gCg	3/17	1	2	FACETS	0.943	0.857	1	0.943	0.857	1	CLONAL	1	TRUE	1	0.700761046171363	2		582	330	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	171	270	0				ENST00000310581	NM_198253.2	-/1132			0.499204699129144	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.499204699129144	3		270	376	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0031516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	91	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.499204699129144	2		336	355	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850678	63850678	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	41	417	0	ENST00000279873.7:c.1456G>A	p.Glu486Lys	p.E486K	ENST00000279873	NM_032199.2	486	Gag/Aag	10/10	1	2	FACETS	0.467	0.39	0.552	0.467	0.39	0.552	SUBCLONAL	1	TRUE	1	0.499204699129144	2		417	352	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181801	56181801	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs751446450	NA	P-0031516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	36	360	0	ENST00000399503.3:c.4025A>G	p.Lys1342Arg	p.K1342R	ENST00000399503	NM_005921.1	1342	aAa/aGa	17/20	1	2	FACETS	0.424	0.349	0.508	0.424	0.349	0.508	SUBCLONAL	1	TRUE	1	0.499204699129144	2		360	340	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0031517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	48	257	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.423188987741316	0	FACETS	0.532	0.454	0.617			1	SUBCLONAL	1	FALSE	0	0.423188987741316	0		257	246	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710664	114710665	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0031517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	103	542	0	ENST00000543371.1:c.149_150del	p.Asn50ArgfsTer46	p.N50Rfs*46	ENST00000543371	NM_001198531.1	50	aAT/a	1/14	0.423188987741316	0	FACETS	0.568	0.511	0.629			1	SUBCLONAL	1	FALSE	0	0.423188987741316	0		542	494	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436023	49436037	+	inframe_deletion	In_Frame_Del	DEL	GGTTGTGGGGGTGGA	GGTTGTGGGGGTGGA	-	novel	NA	P-0031517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	67	561	0	ENST00000301067.7:c.5944_5958del	p.Ser1982_Thr1986del	p.S1982_T1986del	ENST00000301067	NM_003482.3	1982	TCCACCCCCACAACC/-	28/54	0.423188987741316	0	FACETS	0.445	0.388	0.507			1	SUBCLONAL	1	FALSE	0	0.423188987741316	0		561	410	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206770	36206774	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGC	TGGGC	-	novel	NA	P-0031517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	140	688	0	ENST00000300305.3:c.738_742del	p.Asn248SerfsTer11	p.N248Sfs*11	ENST00000300305		246	acGCCCAac/acac	6/8	0.423188987741316	0	FACETS	0.571	0.521	0.623			1	SUBCLONAL	1	FALSE	0	0.423188987741316	0		688	668	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0031521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	225	505	4	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.325676576085702	4	FACETS	0.876	0.82	0.934	0.876	0.82	0.934	CLONAL	3	TRUE	1	0.325676576085702	4		509	697	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0031521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	49	229	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	1	2	FACETS	0.912	0.776	1	0.912	0.776	1	CLONAL	1	TRUE	1	0.325676576085702	2		229	330	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857046	9857046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774039446	NA	P-0031521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	29	242	0	ENST00000330684.3:c.4355G>A	p.Arg1452His	p.R1452H	ENST00000330684	NM_001134407.1	1452	cGc/cAc	13/13	1	2	FACETS	0.481	0.386	0.589	0.481	0.386	0.589	SUBCLONAL	1	TRUE	1	0.325676576085702	2		242	370	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136051	64136051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	51	489	0	ENST00000334205.4:c.1312G>A	p.Ala438Thr	p.A438T	ENST00000334205	NM_003942.2	438	Gca/Aca	11/17	0.325676576085702	1	FACETS	0.427	0.362	0.498	0.427	0.362	0.498	SUBCLONAL	1	TRUE	0	0.325676576085702	1		489	614	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609993	81609993	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs139892516	NA	P-0031521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	46	245	0	ENST00000298171.2:c.1591C>G	p.Arg531Gly	p.R531G	ENST00000298171	NM_000369.2	531	Cgg/Ggg	10/10	0.293978479633233	1	FACETS	0.815	0.691	0.951	0.815	0.691	0.951	CLONAL	1	TRUE	0	0.325676576085702	1		245	290	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858412	9858412	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1555482789	NA	P-0031521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	34	430	0	ENST00000330684.3:c.2989G>T	p.Glu997Ter	p.E997*	ENST00000330684	NM_001134407.1	997	Gag/Tag	13/13	1	2	FACETS	0.395	0.322	0.478	0.395	0.322	0.478	SUBCLONAL	1	TRUE	1	0.325676576085702	2		430	528	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862827	9862827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	119	594	1	ENST00000330684.3:c.2476G>A	p.Ala826Thr	p.A826T	ENST00000330684	NM_001134407.1	826	Gcc/Acc	12/13	1	2	FACETS	0.879	0.794	0.97	0.879	0.794	0.97	CLONAL	1	TRUE	1	0.325676576085702	2		595	831	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319908	62319908	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	282	661	0	ENST00000360203.5:c.1750G>T	p.Ala584Ser	p.A584S	ENST00000360203	NM_001283009.1	584	Gcg/Tcg	21/35	0.312868561472867	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.325676576085702	2		661	810	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193847	106193847	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	59	356	0	ENST00000380013.4:c.4309G>T	p.Glu1437Ter	p.E1437*	ENST00000380013	NM_001127208.2	1437	Gag/Tag	10/11	1	2	FACETS	0.774	0.667	0.89	0.774	0.667	0.89	SUBCLONAL	1	TRUE	1	0.325676576085702	2		356	468	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958430	90958430	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0031521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	83	309	0	ENST00000265433.3:c.2008A>T	p.Arg670Ter	p.R670*	ENST00000265433	NM_002485.4	670	Aga/Tga	13/16	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.325676576085702	2		309	506	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0031522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	115	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.953	0.864	1	0.953	0.864	1	CLONAL	1	TRUE	1	0.49637659916057	2		336	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578266	7578266	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs942158624	NA	P-0031522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	119	623	0	ENST00000269305.4:c.583A>T	p.Ile195Phe	p.I195F	ENST00000269305	NM_001126112.2	195	Atc/Ttc	6/11	0.49637659916057	1	FACETS	0.959	0.874	1	0.959	0.874	1	CLONAL	1	TRUE	0	0.49637659916057	1		623	376	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636948	176636948	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	100	611	0	ENST00000439151.2:c.1548A>G	p.Ile516Met	p.I516M	ENST00000439151	NM_022455.4	516	atA/atG	5/23	1	2	FACETS	0.75	0.672	0.833	0.75	0.672	0.833	SUBCLONAL	1	TRUE	1	0.49637659916057	2		611	537	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56477655	56477655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142735651	NA	P-0031522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	129	572	5	ENST00000267101.3:c.203C>T	p.Thr68Met	p.T68M	ENST00000267101	NM_001982.3	68	aCg/aTg	2/28	1	2	FACETS	0.937	0.853	1	0.937	0.853	1	CLONAL	1	TRUE	1	0.49637659916057	2		577	555	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025927	1025927	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	117	580	0	ENST00000358495.3:c.603G>T	p.Glu201Asp	p.E201D	ENST00000358495	NM_134424.2	201	gaG/gaT	8/12	NA	2	FACETS	0.857	0.776	0.942			1	INDETERMINATE	1	TRUE	NA	0.49637659916057	2		580	550	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438233	56438233	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	121	597	0	ENST00000407977.2:c.760C>T	p.Gln254Ter	p.Q254*	ENST00000407977		254	Cag/Tag	7/10	0.49637659916057	1	FACETS	0.996	0.91	1	0.996	0.91	1	CLONAL	1	TRUE	0	0.49637659916057	1		597	368	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101074	41101074	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs747194630	NA	P-0031522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	82	612	0	ENST00000373198.4:c.1282T>C	p.Tyr428His	p.Y428H	ENST00000373198	NM_133170.3	428	Tat/Cat	8/32	0.41658645881462	1	FACETS	0.704	0.625	0.786	0.704	0.625	0.786	SUBCLONAL	1	TRUE	0	0.49637659916057	1		612	353	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041122	180041122	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	148	933	0	ENST00000261937.6:c.3277A>T	p.Thr1093Ser	p.T1093S	ENST00000261937	NM_182925.4	1093	Acg/Tcg	24/30	1	2	FACETS	0.865	0.792	0.942	0.865	0.792	0.942	CLONAL	1	TRUE	1	0.49637659916057	2		933	689	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0031524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	123	651	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.326462189968048	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.326462189968048	1		651	525	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0031526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	105	505	4	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	0.308493539258868	2		509	624	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79965965	79965965	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	100	593	0	ENST00000265081.6:c.629A>C	p.His210Pro	p.H210P	ENST00000265081	NM_002439.4	210	cAt/cCt	4/24	1	2	FACETS	0.76	0.678	0.847	0.76	0.678	0.847	SUBCLONAL	1	TRUE	1	0.308493539258868	2		593	853	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	158	384	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.338946572071829	3	FACETS	0.882	0.812	0.955	0.882	0.812	0.955	CLONAL	2	TRUE	1	0.348880210006787	3		384	603	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0031527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	90	246	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.338946572071829	3	FACETS	0.826	0.738	0.917	0.826	0.738	0.917	CLONAL	2	TRUE	1	0.348880210006787	3		246	367	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	36	322	0	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	0.348880210006787	1	FACETS	0.492	0.405	0.589	0.492	0.405	0.589	SUBCLONAL	1	TRUE	0	0.348880210006787	1		322	346	SUCCESS
APC	324	MSKCC	GRCh37	5	112157650	112157650	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1060503333	NA	P-0031527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	108	411	0	ENST00000257430.4:c.1370C>A	p.Ser457Ter	p.S457*	ENST00000257430	NM_000038.5	457	tCa/tAa	11/16	0.338946572071829	3	FACETS	1	0.907	1	0.505	0.453	0.56	CLONAL	1	TRUE	1	0.348880210006787	3		411	720	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057520007	NA	P-0031527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	338	687	0	ENST00000269305.4:c.614A>T	p.Tyr205Phe	p.Y205F	ENST00000269305	NM_001126112.2	205	tAt/tTt	6/11	0.347612868877353	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.348880210006787	2		687	913	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528972	157528972	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs766971912	NA	P-0031527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	73	384	0	ENST00000346085.5:c.6697T>A	p.Ser2233Thr	p.S2233T	ENST00000346085	NM_020732.3	2233	Tct/Act	20/20	0.143760175113643	3	FACETS	0.784	0.686	0.89	0.261	0.228	0.297	INDETERMINATE	1	TRUE	0	0.348880210006787	3		384	627	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	73	684	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.3	1	FACETS	0.402	0.351	0.456	0.402	0.351	0.456	SUBCLONAL	1	TRUE	0	0.49	1		684	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs17849781	NA	P-0031528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	109	556	0	ENST00000269305.4:c.832C>G	p.Pro278Ala	p.P278A	ENST00000269305	NM_001126112.2	278	Cct/Gct	8/11	1	2	FACETS	0.604	0.543	0.67	0.604	0.543	0.67	SUBCLONAL	1	TRUE	1	0.49	2		556	736	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0031529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	502	701	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.362153637350059	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.372200601419317	3		701	975	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245738	46245738	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	104	536	0	ENST00000334344.6:c.3832A>T	p.Thr1278Ser	p.T1278S	ENST00000334344	NM_152641.2	1278	Acc/Tcc	15/21	0.329786131376373	1	FACETS	0.794	0.713	0.879	0.794	0.713	0.879	SUBCLONAL	1	TRUE	0	0.372200601419317	1		536	573	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630694	90630694	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	102	638	0	ENST00000330062.3:c.792C>A	p.Asp264Glu	p.D264E	ENST00000330062	NM_002168.2	264	gaC/gaA	6/11	0.372200601419317	5	FACETS	0.837	0.747	0.933	0.167	0.149	0.187	CLONAL	1	TRUE	0	0.372200601419317	5		638	1020	SUCCESS
ATR	545	MSKCC	GRCh37	3	142284974	142284974	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1335528590	NA	P-0031529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	162	474	0	ENST00000350721.4:c.281G>C	p.Gly94Ala	p.G94A	ENST00000350721	NM_001184.3	94	gGc/gCc	3/47	0.282092077472107	4	FACETS	0.771	0.708	0.836	0.514	0.472	0.557	SUBCLONAL	2	TRUE	1	0.372200601419317	4		474	775	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197115	106197115	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs202035674	NA	P-0031529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	55	338	0	ENST00000380013.4:c.5448A>T	p.Leu1816Phe	p.L1816F	ENST00000380013	NM_001127208.2	1816	ttA/ttT	11/11	0.152282804820173	2	FACETS	0.79	0.679	0.911	0.395	0.339	0.456	INDETERMINATE	1	TRUE	0	0.372200601419317	2		338	374	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	103	384	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.439120556658699	2	FACETS	0.965	0.881	1	0.965	0.881	1	CLONAL	2	TRUE	0	0.439120556658699	2		384	243	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882019	NA	P-0031531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	131	709	3	ENST00000269305.4:c.455dup	p.Pro153AlafsTer28	p.P153Afs*28	ENST00000269305	NM_001126112.2	152	ccg/ccCg	5/11	0.298466601200585	3	FACETS	0.994	0.913	1	0.663	0.608	0.718	CLONAL	2	TRUE	0	0.439120556658699	3		712	366	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123789	11123789	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1555774786	NA	P-0031531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	66	420	0	ENST00000358026.2:c.2438+1G>A		p.X813_splice	ENST00000358026	NM_001128849.1	813			0.412453691893685	3	FACETS	1	0.932	1	0.552	0.482	0.627	CLONAL	1	TRUE	1	0.439120556658699	3		420	332	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111048	193111048	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	196	286	3	ENST00000367435.3:c.581G>T	p.Arg194Ile	p.R194I	ENST00000367435	NM_024529.4	194	aGa/aTa	7/17	0.439120556658699	6	FACETS	1	0.949	1	1	0.949	1	CLONAL	5	TRUE	1	0.439120556658699	6		289	334	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111467	8111467	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759044265	NA	P-0031531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	110	489	2	ENST00000346208.3:c.953C>T	p.Ala318Val	p.A318V	ENST00000346208		318	gCg/gTg	5/6	0.439120556658699	3	FACETS	0.819	0.743	0.898	0.819	0.743	0.898	CLONAL	2	TRUE	1	0.439120556658699	3		491	373	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827327	72827327	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	124	594	2	ENST00000268489.5:c.9254A>T	p.Lys3085Ile	p.K3085I	ENST00000268489	NM_006885.3	3085	aAa/aTa	9/10	0.376888905264319	4	FACETS	0.816	0.742	0.893	0.816	0.742	0.893	CLONAL	2	TRUE	2	0.439120556658699	4		596	498	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492917	56492917	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	94	207	0	ENST00000407977.2:c.22C>T	p.Gln8Ter	p.Q8*	ENST00000407977		8	Cag/Tag	2/10	0.439120556658699	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.439120556658699	2		207	186	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740710	58740710	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	128	599	0	ENST00000305921.3:c.1615G>C	p.Glu539Gln	p.E539Q	ENST00000305921	NM_003620.3	539	Gaa/Caa	6/6	0.439120556658699	2	FACETS	0.962	0.886	1	0.962	0.886	1	CLONAL	2	TRUE	0	0.439120556658699	2		599	303	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902283	50902283	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	113	771	0	ENST00000440232.2:c.175C>T	p.Gln59Ter	p.Q59*	ENST00000440232	NM_002691.3	59	Cag/Tag	2/27	0.412453691893685	3	FACETS	0.789	0.716	0.864	0.789	0.716	0.864	SUBCLONAL	2	TRUE	1	0.439120556658699	3		771	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0031532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	335	701	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.45280691863274	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.45280691863274	1		701	768	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246509	41246509	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs749508254	NA	P-0031532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	169	600	0	ENST00000357654.3:c.1039del	p.Leu347CysfsTer27	p.L347Cfs*27	ENST00000357654	NM_007294.3	347	Ctg/tg	10/23	0.45280691863274	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.45280691863274	1		600	558	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339776	116339776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367722737	NA	P-0031532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	79	391	0	ENST00000397752.3:c.638C>T	p.Ser213Leu	p.S213L	ENST00000397752	NM_000245.2	213	tCg/tTg	2/21	0.420979842357439	3	FACETS	0.814	0.717	0.917	0.271	0.239	0.306	CLONAL	1	TRUE	0	0.45280691863274	3		391	526	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775936	9775936	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	107	612	2	ENST00000377346.4:c.400C>A	p.Pro134Thr	p.P134T	ENST00000377346	NM_005026.3	134	Cca/Aca	5/24	0.162700533793946	2	FACETS	0.655	0.588	0.727	0.328	0.294	0.364	INDETERMINATE	1	TRUE	0	0.45280691863274	2		614	721	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405437	70405437	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0031532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	93	675	0	ENST00000373644.4:c.2951C>G	p.Ser984Ter	p.S984*	ENST00000373644	NM_030625.2	984	tCa/tGa	4/12	0.162700533793946	2	FACETS	0.541	0.481	0.606	0.271	0.24	0.303	INDETERMINATE	1	TRUE	0	0.45280691863274	2		675	759	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435978	110435978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762132376	NA	P-0031532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	106	616	0	ENST00000375856.3:c.2423G>A	p.Arg808His	p.R808H	ENST00000375856	NM_003749.2	808	cGc/cAc	1/2	NA	2	FACETS	0.613	0.549	0.68			1	INDETERMINATE	1	TRUE	NA	0.45280691863274	2		616	764	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820767	3820767	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	303	813	0	ENST00000262367.5:c.2684C>G	p.Ser895Cys	p.S895C	ENST00000262367	NM_004380.2	895	tCc/tGc	14/31	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.45280691863274	2		813	960	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753855	42753855	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	132	757	0	ENST00000222329.4:c.409T>C	p.Ser137Pro	p.S137P	ENST00000222329	NM_006494.2	137	Tcg/Ccg	4/4	1	2	FACETS	0.803	0.73	0.88	0.803	0.73	0.88	CLONAL	1	TRUE	1	0.45280691863274	2		757	726	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873420	136873431	+	inframe_deletion	In_Frame_Del	DEL	TTCCTTCATGGA	TTCCTTCATGGA	-	novel	NA	P-0031532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	54	407	0	ENST00000241393.3:c.67_78del	p.Ser23_Glu26del	p.S23_E26del	ENST00000241393	NM_003467.2	23	TCCATGAAGGAA/-	2/2	0.311931404955158	1	FACETS	0.497	0.426	0.574	0.497	0.426	0.574	SUBCLONAL	1	TRUE	0	0.45280691863274	1		407	371	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911424	134911424	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	61	433	0	ENST00000398015.3:c.1889T>A	p.Phe630Tyr	p.F630Y	ENST00000398015	NM_004441.4	630	tTt/tAt	11/16	0.45280691863274	3	FACETS	0.492	0.424	0.567	0.246	0.212	0.284	SUBCLONAL	1	TRUE	1	0.45280691863274	3		433	671	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430402	181430402	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	99	547	0	ENST00000325404.1:c.254C>G	p.Thr85Arg	p.T85R	ENST00000325404	NM_003106.3	85	aCg/aGg	1/1	0.45280691863274	3	FACETS	0.745	0.665	0.83	0.372	0.332	0.415	SUBCLONAL	1	TRUE	1	0.45280691863274	3		547	720	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850224	128850224	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	94	561	0	ENST00000249373.3:c.1487T>A	p.Ile496Asn	p.I496N	ENST00000249373	NM_005631.4	496	aTc/aAc	9/12	0.420979842357439	3	FACETS	0.725	0.645	0.81	0.242	0.215	0.27	SUBCLONAL	1	TRUE	0	0.45280691863274	3		561	702	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965645	90965645	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs876659451	NA	P-0031532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	68	419	0	ENST00000265433.3:c.1672A>C	p.Ile558Leu	p.I558L	ENST00000265433	NM_002485.4	558	Ata/Cta	11/16	0.296216585672997	3	FACETS	0.737	0.642	0.839	0.246	0.214	0.28	SUBCLONAL	1	TRUE	0	0.45280691863274	3		419	500	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933926	39933926	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	303	686	0	ENST00000378444.4:c.673C>T	p.Gln225Ter	p.Q225*	ENST00000378444	NM_001123385.1	225	Cag/Tag	4/15	NA	2	FACETS	0.993	0.943	1			1	INDETERMINATE	2	TRUE	NA	0.45280691863274	2		686	674	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0031537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	188	578	0	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	0.311416611954201	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.311416611954201	1		578	847	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0031537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	92	470	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.828	0.735	0.926	0.828	0.735	0.926	CLONAL	1	TRUE	1	0.311416611954201	2		470	714	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610503	81610503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137908024	NA	P-0031537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	91	409	0	ENST00000298171.2:c.2101C>T	p.Arg701Cys	p.R701C	ENST00000298171	NM_000369.2	701	Cgc/Tgc	10/10	0.311416611954201	1	FACETS	0.979	0.872	1	0.979	0.872	1	CLONAL	1	TRUE	0	0.311416611954201	1		409	504	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175217	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0031537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	47	253	0	ENST00000257430.4:c.3929dup	p.Ile1311AspfsTer4	p.I1311Dfs*4	ENST00000257430	NM_000038.5	1309	gaa/gAaa	16/16	1	2	FACETS	0.865	0.732	1	0.865	0.732	1	CLONAL	1	TRUE	1	0.311416611954201	2		253	349	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520747	176520747	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	114	464	0	ENST00000292408.4:c.1490C>A	p.Ala497Asp	p.A497D	ENST00000292408	NM_213647.1	497	gCc/gAc	11/18	1	2	FACETS	0.941	0.847	1	0.941	0.847	1	CLONAL	1	TRUE	1	0.311416611954201	2		464	778	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0031538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	108	345	2	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.824	0.742	0.909	0.824	0.742	0.909	CLONAL	1	TRUE	1	0.506275712277297	2		347	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0031538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	241	890	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.947	0.885	1	0.947	0.885	1	CLONAL	1	TRUE	1	0.506275712277297	2		892	1005	SUCCESS
APC	324	MSKCC	GRCh37	5	112175417	112175418	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	rs1554085533	NA	P-0031538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	113	297	0	ENST00000257430.4:c.4127_4128del	p.Tyr1376CysfsTer9	p.Y1376Cfs*9	ENST00000257430	NM_000038.5	1376	TAt/t	16/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.506275712277297	2		297	411	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713383	40713383	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs773803715	NA	P-0031538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	335	557	1	ENST00000373198.4:c.4132C>T	p.Arg1378Ter	p.R1378*	ENST00000373198	NM_133170.3	1378	Cga/Tga	30/32	0.150096448594045	6	FACETS	1	0.991	1	0.803	0.76	0.847	INDETERMINATE	2	TRUE	3	0.506275712277297	6		558	1106	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711903	89711904	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0031538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	126	496	0	ENST00000371953.3:c.522dup	p.Val175CysfsTer5	p.V175Cfs*5	ENST00000371953	NM_000314.4	174	tat/taTt	6/9	0.506275712277297	1	FACETS	0.768	0.7	0.839	0.768	0.7	0.839	SUBCLONAL	1	TRUE	0	0.506275712277297	1		496	484	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811751	102811751	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	53	629	0	ENST00000307046.8:c.433A>C	p.Lys145Gln	p.K145Q	ENST00000307046	NM_001111285.1	145	Aag/Cag	4/4	1	2	FACETS	0.288	0.245	0.336	0.288	0.245	0.336	SUBCLONAL	1	TRUE	1	0.506275712277297	2		629	726	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056285	180056285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762045883	NA	P-0031538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	199	636	2	ENST00000261937.6:c.959G>A	p.Arg320Gln	p.R320Q	ENST00000261937	NM_182925.4	320	cGg/cAg	7/30	0.480950601640717	3	FACETS	0.96	0.889	1	0.48	0.444	0.517	CLONAL	1	TRUE	1	0.506275712277297	3		638	1026	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471043	8471043	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	101	384	0	ENST00000356435.5:c.3456del	p.Lys1153AsnfsTer14	p.K1153Nfs*14	ENST00000356435		1152	ggG/gg	20/35	1	2	FACETS	0.854	0.768	0.946	0.854	0.768	0.946	CLONAL	1	TRUE	1	0.506275712277297	2		384	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0031552-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	196	504	0	ENST00000269305.4:c.97-1G>A		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.49202880887431	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.49202880887431	1		504	598	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246490592	246490592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031552-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	260	543	0	ENST00000388985.4:c.442G>T	p.Val148Leu	p.V148L	ENST00000388985		148	Gta/Tta	5/12	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.49202880887431	2		543	936	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350354	89350354	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031552-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	309	662	0	ENST00000301030.4:c.2596A>G	p.Arg866Gly	p.R866G	ENST00000301030	NM_001256183.1	866	Agg/Ggg	9/13	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.49202880887431	2		662	1174	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872064	37872064	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs373192991	NA	P-0031552-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	264	637	1	ENST00000269571.5:c.1385G>T	p.Gly462Val	p.G462V	ENST00000269571		462	gGc/gTc	12/27	1	2	FACETS	0.978	0.917	1	0.978	0.917	1	CLONAL	1	TRUE	1	0.49202880887431	2		638	1097	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223436	2223436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031552-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	192	455	0	ENST00000398665.3:c.3547C>T	p.Leu1183Phe	p.L1183F	ENST00000398665	NM_032482.2	1183	Ctc/Ttc	25/28	0.338098052410121	1	FACETS	0.893	0.829	0.958	0.893	0.829	0.958	CLONAL	1	TRUE	0	0.49202880887431	1		455	659	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568895	212568895	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031552-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	138	523	0	ENST00000342788.4:c.1223C>G	p.Pro408Arg	p.P408R	ENST00000342788	NM_005235.2	408	cCa/cGa	11/28	1	2	FACETS	0.872	0.796	0.952	0.872	0.796	0.952	CLONAL	1	TRUE	1	0.49202880887431	2		523	643	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	221	270	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.89	2		270	494	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805404	32805404	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	412	745	0	ENST00000374899.4:c.518C>G	p.Ser173Cys	p.S173C	ENST00000374899	NM_018833.2	173	tCt/tGt	3/12	1	2	FACETS	0.954	0.912	0.997	0.954	0.912	0.997	CLONAL	1	TRUE	1	0.89	2		745	970	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0031554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	248	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.89	2		336	513	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0031555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	175	470	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.974	1	1	0.995	1	CLONAL	3	FALSE	1	0.286865314977406	2		471	375	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0031555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	331	512	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.993	1	1	0.997	1	CLONAL	6	FALSE	1	0.286865314977406	2		512	369	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947827	178947827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	11	376	0	ENST00000263967.3:c.2702G>T	p.Cys901Phe	p.C901F	ENST00000263967	NM_006218.2	901	tGt/tTt	19/21	1	2	FACETS	0.198	0.136	0.275	0.198	0.136	0.275	SUBCLONAL	1	FALSE	1	0.286865314977406	2		376	388	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652009	36652010	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0031555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	119	709	0	ENST00000244741.5:c.133dup	p.Ala45GlyfsTer3	p.A45Gfs*3	ENST00000244741	NM_000389.4	44	gag/gaGg	2/3	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	FALSE	1	0.286865314977406	2		709	803	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797306	135797313	+	frameshift_variant	Frame_Shift_Del	DEL	AAGAGTGC	AAGAGTGC	-	novel	NA	P-0031555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	40	430	0	ENST00000298552.3:c.556_563del	p.Ala186SerfsTer29	p.A186Sfs*29	ENST00000298552	NM_001162426.1	186	GCACTCTTt/t	7/23	0.286865314977406	0	FACETS	0.888	0.744	1			1	CLONAL	1	FALSE	0	0.286865314977406	0		430	224	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949085	44949085	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	273	269	0	ENST00000377967.4:c.3646G>C	p.Asp1216His	p.D1216H	ENST00000377967	NM_021140.2	1216	Gat/Cat	25/29	1	1	FACETS	1	0.995	1	1	0.997	1	CLONAL	5	FALSE	0	0.286865314977406	1		269	299	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044886	47044887	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0031555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	325	381	0	ENST00000377604.3:c.2212_2213del	p.Ser738Ter	p.S738*	ENST00000377604	NM_001204468.1	738	AGt/t	20/24	1	1	FACETS	1	0.987	1	1	0.997	1	CLONAL	5	FALSE	0	0.286865314977406	1		381	379	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288967	212288967	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs537458255	NA	P-0031556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	201	613	0	ENST00000342788.4:c.2779C>T	p.Arg927Ter	p.R927*	ENST00000342788	NM_005235.2	927	Cga/Tga	23/28	0.691406618230302	1	FACETS	0.758	0.709	0.807	0.758	0.709	0.807	SUBCLONAL	1	TRUE	0	0.691406618230302	1		613	502	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11177077	11177077	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	193	627	0	ENST00000361445.4:c.7000T>G	p.Leu2334Val	p.L2334V	ENST00000361445	NM_004958.3	2334	Tta/Gta	50/58	0.691406618230302	1	FACETS	0.747	0.698	0.797	0.747	0.698	0.797	SUBCLONAL	1	TRUE	0	0.691406618230302	1		627	489	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42026718	42026718	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1298380126	NA	P-0031556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	36	570	1	ENST00000219905.7:c.3844-2A>G		p.X1282_splice	ENST00000219905	NM_001164273.1	1282			0.691406618230302	1	FACETS	0.142	0.116	0.17	0.142	0.116	0.17	SUBCLONAL	1	TRUE	0	0.691406618230302	1		571	481	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287175	33287175	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0031556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	33	517	0	ENST00000374542.5:c.1922C>G	p.Ser641Ter	p.S641*	ENST00000374542	NM_001141970.1	641	tCa/tGa	6/8	0.690936717181577	1	FACETS	0.101	0.082	0.123	0.101	0.082	0.123	SUBCLONAL	1	TRUE	0	0.691406618230302	1		517	617	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288563	33288563	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	226	518	0	ENST00000374542.5:c.989T>C	p.Leu330Pro	p.L330P	ENST00000374542	NM_001141970.1	330	cTc/cCc	3/8	0.690936717181577	1	FACETS	0.788	0.74	0.836	0.788	0.74	0.836	SUBCLONAL	1	TRUE	0	0.691406618230302	1		518	543	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0031557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	134	332	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.317780781221989	3	FACETS	1	0.982	1	0.669	0.609	0.733	CLONAL	1	TRUE	1	0.317780781221989	3		332	730	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535364	187535364	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	246	543	0	ENST00000441802.2:c.9210C>G	p.Phe3070Leu	p.F3070L	ENST00000441802	NM_005245.3	3070	ttC/ttG	12/27	0.317780781221989	5	FACETS	1	0.935	1	0.667	0.623	0.713	CLONAL	2	TRUE	2	0.317780781221989	5		543	1142	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111517	8111518	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACCC	novel	NA	P-0031557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	156	710	0	ENST00000346208.3:c.1004_1007dup	p.Val337ProfsTer16	p.V337Pfs*16	ENST00000346208		335	gac/gACCCac	5/6	0.317780781221989	3	FACETS	1	0.965	1	0.553	0.506	0.603	CLONAL	1	TRUE	1	0.317780781221989	3		710	1029	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115952	8115953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCAC	novel	NA	P-0031557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	76	402	0	ENST00000346208.3:c.1301_1304dup	p.Ser436ProfsTer72	p.S436Pfs*72	ENST00000346208		433	cac/caCCACc	6/6	0.317780781221989	3	FACETS	0.938	0.823	1	0.469	0.411	0.531	CLONAL	1	TRUE	1	0.317780781221989	3		402	591	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210503	5210503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	146	761	0	ENST00000357368.4:c.5464G>A	p.Glu1822Lys	p.E1822K	ENST00000357368	NM_002850.3	1822	Gag/Aag	35/38	0.317780781221989	3	FACETS	1	0.949	1	0.529	0.482	0.579	CLONAL	1	TRUE	1	0.317780781221989	3		761	1006	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288982	212288982	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1339233847	NA	P-0031557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	123	745	0	ENST00000342788.4:c.2764G>C	p.Asp922His	p.D922H	ENST00000342788	NM_005235.2	922	Gat/Cat	23/28	0.317780781221989	3	FACETS	1	0.961	1	0.56	0.506	0.617	CLONAL	1	TRUE	1	0.317780781221989	3		745	801	SUCCESS
ATR	545	MSKCC	GRCh37	3	142180806	142180806	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	115	486	0	ENST00000350721.4:c.7168C>A	p.Leu2390Met	p.L2390M	ENST00000350721	NM_001184.3	2390	Ctg/Atg	42/47	0.317780781221989	3	FACETS	1	0.964	1	0.575	0.518	0.635	CLONAL	1	TRUE	1	0.317780781221989	3		486	729	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126395	5126396	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0031557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	89	462	0	ENST00000381652.3:c.3240_3241del	p.Glu1080AspfsTer5	p.E1080Dfs*5	ENST00000381652	NM_004972.3	1080	gaACtt/gatt	24/25	0.282953410229757	4	FACETS	0.934	0.828	1	0.467	0.414	0.524	CLONAL	1	TRUE	2	0.317780781221989	4		462	790	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0031558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	132	505	4	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.22	2		509	1187	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023008	27023010	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs587779737	NA	P-0031558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	14	39	0	ENST00000324856.7:c.126_128del	p.Ala45del	p.A45del	ENST00000324856	NM_006015.4	38	gaGGCg/gag	1/20	1	2	FACETS	0.511	0.369	0.683	0.511	0.369	0.683	SUBCLONAL	1	TRUE	1	0.22	2		39	249	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038831	47038831	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	95	746	0	ENST00000377604.3:c.838G>T	p.Gly280Ter	p.G280*	ENST00000377604	NM_001204468.1	280	Gga/Tga	9/24	0.268517481394845	1	FACETS	0.916	0.815	1	0.916	0.815	1	CLONAL	1	TRUE	0	0.22	1		746	839	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460581	149460581	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	85	668	0	ENST00000286301.3:c.56G>T	p.Gly19Val	p.G19V	ENST00000286301	NM_005211.3	19	gGa/gTa	3/22	1	2	FACETS	0.929	0.82	1	0.929	0.82	1	CLONAL	1	TRUE	1	0.22	2		668	832	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874674	151874674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1416721225	NA	P-0031558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	70	516	0	ENST00000262189.6:c.7864C>T	p.His2622Tyr	p.H2622Y	ENST00000262189	NM_170606.2	2622	Cac/Tac	38/59	1	2	FACETS	0.726	0.631	0.828	0.726	0.631	0.828	SUBCLONAL	1	TRUE	1	0.22	2		516	877	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449731	8449731	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	70	594	0	ENST00000356435.5:c.3982del	p.Thr1328HisfsTer22	p.T1328Hfs*22	ENST00000356435		1328	Aca/ca	23/35	1	2	FACETS	0.713	0.62	0.814	0.713	0.62	0.814	SUBCLONAL	1	TRUE	1	0.22	2		594	892	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717704	89717704	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	115	445	1	ENST00000371953.3:c.731del	p.Pro244LeufsTer12	p.P244Lfs*12	ENST00000371953	NM_000314.4	243	ttC/tt	7/9	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.21	2		446	800	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0031562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	286	562	3	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.302556829221321	5	FACETS	0.837	0.789	0.887	0.837	0.789	0.887	CLONAL	3	TRUE	2	0.385244316062875	5		565	933	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0031562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	361	804	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.376196965082823	2	FACETS	0.972	0.924	1	0.972	0.924	1	CLONAL	2	TRUE	0	0.385244316062875	2		804	964	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0031562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	207	345	2	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.27243049349256	2	FACETS	0.885	0.827	0.945	0.885	0.827	0.945	CLONAL	2	TRUE	0	0.385244316062875	2		347	607	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670598	134670598	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs563780078	NA	P-0031562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	241	918	1	ENST00000398015.3:c.509G>A	p.Arg170Gln	p.R170Q	ENST00000398015	NM_004441.4	170	cGg/cAg	3/16	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.385244316062875	2		919	1057	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45423009	45423009	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	112	470	0	ENST00000262160.6:c.119G>A	p.Trp40Ter	p.W40*	ENST00000262160	NM_005901.5	40	tGg/tAg	2/11	0.385244316062875	1	FACETS	0.881	0.795	0.97	0.881	0.795	0.97	CLONAL	1	TRUE	0	0.385244316062875	1		470	533	SUCCESS
APC	324	MSKCC	GRCh37	5	112175193	112175196	+	frameshift_variant	Frame_Shift_Del	DEL	CCCT	CCCT	-	novel	NA	P-0031562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	26	309	0	ENST00000257430.4:c.3902_3905del	p.Thr1301SerfsTer3	p.T1301Sfs*3	ENST00000257430	NM_000038.5	1301	aCCCTg/ag	16/16	0.27243049349256	2	FACETS	0.347	0.274	0.43	0.173	0.137	0.215	SUBCLONAL	1	TRUE	0	0.385244316062875	2		309	389	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934387	39934387	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	196	358	0	ENST00000378444.4:c.212G>A	p.Ser71Asn	p.S71N	ENST00000378444	NM_001123385.1	71	aGc/aAc	4/15	0.353256864792381	2	FACETS	0.786	0.731	0.843			1	SUBCLONAL	2	TRUE	NA	0.385244316062875	2		358	647	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0031563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	78	505	4	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.624	0.548	0.707	0.624	0.548	0.707	SUBCLONAL	1	TRUE	1	0.31	2		509	806	SUCCESS
FH	2271	MSKCC	GRCh37	1	241672012	241672012	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	89	622	1	ENST00000366560.3:c.629G>T	p.Gly210Val	p.G210V	ENST00000366560	NM_000143.3	210	gGa/gTa	5/10	0.301541857790836	4	FACETS	0.672	0.594	0.755	0.224	0.198	0.252	SUBCLONAL	1	TRUE	1	0.31	4		623	1120	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533785	533785	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	94	784	0	ENST00000451590.1:c.271G>C	p.Glu91Gln	p.E91Q	ENST00000451590	NM_001130442.1	91	Gag/Cag	3/5	1	2	FACETS	0.596	0.529	0.668	0.596	0.529	0.668	SUBCLONAL	1	TRUE	1	0.31	2		784	1017	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533885	533885	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	98	799	0	ENST00000451590.1:c.171T>G	p.Asp57Glu	p.D57E	ENST00000451590	NM_001130442.1	57	gaT/gaG	3/5	1	2	FACETS	0.616	0.548	0.689	0.616	0.548	0.689	SUBCLONAL	1	TRUE	1	0.31	2		799	1026	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285865	46285865	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	73	635	0	ENST00000334344.6:c.5133G>C	p.Gln1711His	p.Q1711H	ENST00000334344	NM_152641.2	1711	caG/caC	18/21	1	2	FACETS	0.577	0.504	0.657	0.577	0.504	0.657	SUBCLONAL	1	TRUE	1	0.31	2		635	816	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426686	121426686	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	104	677	0	ENST00000257555.6:c.377A>G	p.His126Arg	p.H126R	ENST00000257555		126	cAc/cGc	2/10	1	2	FACETS	0.707	0.632	0.787	0.707	0.632	0.787	SUBCLONAL	1	TRUE	1	0.31	2		677	949	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271966	15271966	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1167807322	NA	P-0031563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	115	746	0	ENST00000263388.2:c.6473T>G	p.Leu2158Arg	p.L2158R	ENST00000263388	NM_000435.2	2158	cTc/cGc	33/33	0.25703133502336	3	FACETS	0.754	0.678	0.836	0.377	0.339	0.418	SUBCLONAL	1	TRUE	1	0.31	3		746	1136	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437213	220437213	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	236	911	2	ENST00000243786.2:c.117T>A	p.Asp39Glu	p.D39E	ENST00000243786	NM_002191.3	39	gaT/gaA	1/2	0.25703133502336	3	FACETS	1	0.991	1	0.703	0.655	0.753	CLONAL	1	TRUE	1	0.31	3		913	1250	SUCCESS
ATR	545	MSKCC	GRCh37	3	142238614	142238614	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	34	354	0	ENST00000350721.4:c.4279A>G	p.Ile1427Val	p.I1427V	ENST00000350721	NM_001184.3	1427	Att/Gtt	24/47	1	2	FACETS	0.492	0.402	0.593	0.492	0.402	0.593	SUBCLONAL	1	TRUE	1	0.31	2		354	446	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201809	66201809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	62	700	2	ENST00000273854.3:c.2693C>T	p.Pro898Leu	p.P898L	ENST00000273854	NM_004439.5	898	cCa/cTa	16/18	1	2	FACETS	0.484	0.417	0.557	0.484	0.417	0.557	SUBCLONAL	1	TRUE	1	0.31	2		702	827	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522506	187522506	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	103	684	0	ENST00000441802.2:c.11557A>G	p.Met3853Val	p.M3853V	ENST00000441802	NM_005245.3	3853	Atg/Gtg	21/27	1	2	FACETS	0.686	0.612	0.764	0.686	0.612	0.764	SUBCLONAL	1	TRUE	1	0.31	2		684	969	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871233	35871233	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	94	556	0	ENST00000303115.3:c.455C>T	p.Thr152Ile	p.T152I	ENST00000303115	NM_002185.3	152	aCa/aTa	4/8	0.279840146062528	5	FACETS	0.801	0.711	0.898	0.2	0.177	0.225	CLONAL	1	TRUE	1	0.31	5		556	1109	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467655	50467655	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	69	579	0	ENST00000331340.3:c.890C>A	p.Ala297Asp	p.A297D	ENST00000331340	NM_006060.4	297	gCc/gAc	8/8	0.25703133502336	3	FACETS	0.603	0.524	0.689	0.301	0.262	0.345	SUBCLONAL	1	TRUE	1	0.31	3		579	853	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1331482	1331483	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0031563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	85	756	1	ENST00000400841.2:c.45_46delinsTT	p.Gly16Ter	p.G16*	ENST00000400841		15	ctGGga/ctTTga	1/6	1	1	FACETS	0.446	0.393	0.504	0.446	0.393	0.504	SUBCLONAL	1	TRUE	0	0.31	1		757	1038	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0031573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	969	779	1	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.753360187906589	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.753360187906589	2		780	1228	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350772	89350775	+	frameshift_variant	Frame_Shift_Del	DEL	TTTG	TTTG	-	rs886039734	NA	P-0031573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	330	700	0	ENST00000301030.4:c.2175_2178del	p.Asn725LysfsTer23	p.N725Kfs*23	ENST00000301030	NM_001256183.1	725	aaCAAA/aa	9/13	1	2	FACETS	0.825	0.78	0.87	0.825	0.78	0.87	CLONAL	1	TRUE	1	0.753360187906589	2		700	1062	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443586	52443586	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	230	456	1	ENST00000460680.1:c.106C>T	p.Gln36Ter	p.Q36*	ENST00000460680	NM_004656.3	36	Cag/Tag	3/17	0.753360187906589	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.753360187906589	1		457	371	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0031575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	147	498	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.434944222249433	2		498	673	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099325	27099325	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	154	532	1	ENST00000324856.7:c.3562C>T	p.Gln1188Ter	p.Q1188*	ENST00000324856	NM_006015.4	1188	Cag/Tag	14/20	0.434944222249433	1	FACETS	0.913	0.839	0.99	0.913	0.839	0.99	CLONAL	1	TRUE	0	0.434944222249433	1		533	607	SUCCESS
APC	324	MSKCC	GRCh37	5	112164619	112164619	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	130	364	1	ENST00000257430.4:c.1693G>T	p.Glu565Ter	p.E565*	ENST00000257430	NM_000038.5	565	Gaa/Taa	14/16	0.434944222249433	1	FACETS	0.966	0.882	1	0.966	0.882	1	CLONAL	1	TRUE	0	0.434944222249433	1		365	484	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0031576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	18	389	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	1	2	FACETS	0.465	0.348	0.603	0.465	0.348	0.603	SUBCLONAL	1	TRUE	1	0.13	2		389	596	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	55	745	0	ENST00000397062.3:c.246A>T	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaT	2/5	1	2	FACETS	0.922	0.786	1	0.922	0.786	1	CLONAL	1	TRUE	1	0.13	2		745	918	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510611	38510611	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	48	542	0	ENST00000254066.5:c.865G>A	p.Gly289Arg	p.G289R	ENST00000254066	NM_000964.3	289	Ggg/Agg	7/9	1	2	FACETS	0.781	0.658	0.918	0.781	0.658	0.918	CLONAL	1	TRUE	1	0.13	2		542	945	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0031576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	32	283	1	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.9	0.729	1	0.9	0.729	1	CLONAL	1	TRUE	1	0.13	2		284	547	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199469672	NA	P-0031576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	24	559	0	ENST00000374080.3:c.131G>T	p.Gly44Val	p.G44V	ENST00000374080		44	gGt/gTt	2/45	1	2	FACETS	0.35	0.272	0.44	0.35	0.272	0.44	SUBCLONAL	1	TRUE	1	0.13	2		559	1056	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0031576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	45	568	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.913	0.766	1	0.913	0.766	1	CLONAL	1	TRUE	1	0.13	2		570	758	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0031576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	64	682	4	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	1	2	FACETS	0.904	0.78	1	0.904	0.78	1	CLONAL	1	TRUE	1	0.13	2		686	1089	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200675	67200675	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1160033493	NA	P-0031576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	46	586	0	ENST00000312629.5:c.786G>A	p.Met262Ile	p.M262I	ENST00000312629	NM_003952.2	262	atG/atA	9/15	1	2	FACETS	0.911	0.765	1	0.911	0.765	1	CLONAL	1	TRUE	1	0.13	2		586	777	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939233	71939233	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0031576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	53	499	0	ENST00000298229.2:c.183-1G>T		p.X61_splice	ENST00000298229	NM_001567.3	61			1	2	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	TRUE	1	0.13	2		499	813	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865726	57865726	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	46	612	0	ENST00000228682.2:c.3206del	p.Gly1069AlafsTer20	p.G1069Afs*20	ENST00000228682	NM_005269.2	1068	cGg/cg	12/12	1	2	FACETS	0.786	0.66	0.927	0.786	0.66	0.927	CLONAL	1	TRUE	1	0.13	2		612	900	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296204	15296204	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0031576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	63	632	0	ENST00000263388.2:c.2160T>A	p.Cys720Ter	p.C720*	ENST00000263388	NM_000435.2	720	tgT/tgA	14/33	1	2	FACETS	0.931	0.803	1	0.931	0.803	1	CLONAL	1	TRUE	1	0.13	2		632	1041	SUCCESS
ATR	545	MSKCC	GRCh37	3	142212030	142212030	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs148465901	NA	P-0031576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	45	463	0	ENST00000350721.4:c.6022C>T	p.Arg2008Ter	p.R2008*	ENST00000350721	NM_001184.3	2008	Cga/Tga	35/47	1	2	FACETS	0.856	0.717	1	0.856	0.717	1	CLONAL	1	TRUE	1	0.13	2		463	809	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604298	189604298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138832017	NA	P-0031576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	40	479	0	ENST00000264731.3:c.1465G>A	p.Ala489Thr	p.A489T	ENST00000264731	NM_003722.4	489	Gcc/Acc	11/14	1	2	FACETS	0.854	0.707	1	0.854	0.707	1	CLONAL	1	TRUE	1	0.13	2		479	721	SUCCESS
APC	324	MSKCC	GRCh37	5	112177449	112177449	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	40	350	0	ENST00000257430.4:c.6158C>A	p.Pro2053His	p.P2053H	ENST00000257430	NM_000038.5	2053	cCt/cAt	16/16	1	2	FACETS	0.931	0.772	1	0.931	0.772	1	CLONAL	1	TRUE	1	0.13	2		350	661	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047908	180047908	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	59	636	0	ENST00000261937.6:c.2267G>A	p.Cys756Tyr	p.C756Y	ENST00000261937	NM_182925.4	756	tGc/tAc	15/30	1	2	FACETS	0.943	0.809	1	0.943	0.809	1	CLONAL	1	TRUE	1	0.13	2		636	963	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057006	180057006	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	71	679	0	ENST00000261937.6:c.613C>T	p.Gln205Ter	p.Q205*	ENST00000261937	NM_182925.4	205	Cag/Tag	5/30	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.13	2		679	1067	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0031578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	100	562	3	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.892	0.799	0.992	1	0.985	1	CLONAL	2	TRUE	1	0.184927347496442	2		565	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0031578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	154	477	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.184927347496442	2	FACETS	0.926	0.848	1	0.926	0.848	1	CLONAL	2	TRUE	0	0.184927347496442	2		478	899	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0031578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	35	246	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.184927347496442	2		246	363	SUCCESS
APC	324	MSKCC	GRCh37	5	112173590	112173590	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561575998	NA	P-0031578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	61	403	0	ENST00000257430.4:c.2299C>T	p.Gln767Ter	p.Q767*	ENST00000257430	NM_000038.5	767	Cag/Tag	16/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.184927347496442	2		403	498	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251937	153251937	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0031578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	70	653	0	ENST00000281708.4:c.1069A>T	p.Arg357Ter	p.R357*	ENST00000281708	NM_033632.3	357	Aga/Tga	7/12	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.184927347496442	2		653	526	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707798	176707798	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	80	489	0	ENST00000439151.2:c.5855G>A	p.Arg1952Gln	p.R1952Q	ENST00000439151	NM_022455.4	1952	cGg/cAg	18/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.184927347496442	2		489	646	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394926	394926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	115	534	0	ENST00000380956.4:c.322G>A	p.Glu108Lys	p.E108K	ENST00000380956	NM_001195286.1	108	Gag/Aag	3/9	1	2	FACETS	0.845	0.762	0.933	1	0.986	1	CLONAL	2	TRUE	1	0.184927347496442	2		534	736	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0031581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	97	614	1	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	1	2	FACETS	0.725	0.645	0.81	0.725	0.645	0.81	SUBCLONAL	1	TRUE	1	0.28	2		615	956	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913233	NA	P-0031581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	209	648	2	ENST00000451590.1:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000451590	NM_001130442.1	61	cAg/cTg	3/5	0.193785249365195	3	FACETS	1	0.989	1	0.682	0.632	0.735	CLONAL	1	TRUE	1	0.28	3		650	1247	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670728	67670728	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	109	548	1	ENST00000264010.4:c.1973G>T	p.Arg658Ile	p.R658I	ENST00000264010	NM_006565.3	658	aGa/aTa	11/12	1	2	FACETS	0.822	0.737	0.913	0.822	0.737	0.913	CLONAL	1	TRUE	1	0.28	2		549	947	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945719	17945719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140655992	NA	P-0031583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	140	638	4	ENST00000458235.1:c.2141C>T	p.Thr714Met	p.T714M	ENST00000458235	NM_000215.3	714	aCg/aTg	16/24	0.660602910935356	3	FACETS	0.884	0.808	0.963	0.442	0.404	0.482	CLONAL	1	TRUE	1	0.733881433680055	3		642	590	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-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	267	698	0	ENST00000269305.4:c.376-11_379del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	0.721770416911559	2	FACETS	0.912	0.873	0.95	0.912	0.873	0.95	CLONAL	2	TRUE	0	0.733881433680055	2		698	399	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49413009	49413009	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519953	NA	P-0031583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	122	613	0	ENST00000418115.1:c.14G>T	p.Arg5Leu	p.R5L	ENST00000418115	NM_001664.2	5	cGg/cTg	2/5	0.733881433680055	3	FACETS	0.9	0.818	0.986	0.3	0.272	0.329	CLONAL	1	TRUE	0	0.733881433680055	3		613	505	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502855	186502856	+	inframe_insertion	In_Frame_Ins	INS	-	-	TAG	novel	NA	P-0031583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	122	504	0	ENST00000323963.5:c.316_318dup	p.Val106dup	p.V106dup	ENST00000323963		106	cta/cTAGta	4/11	0.733881433680055	3	FACETS	0.862	0.783	0.945	0.287	0.261	0.315	CLONAL	1	TRUE	0	0.733881433680055	3		504	527	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0031584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	92	835	0	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	0.266099918220325	1	FACETS	0.433	0.385	0.485	0.433	0.385	0.485	SUBCLONAL	1	TRUE	0	0.433650331924114	1		835	767	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591125	67591125	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	144	438	0	ENST00000274335.5:c.1718T>C	p.Leu573Pro	p.L573P	ENST00000274335		573	cTg/cCg	12/15	0.405317614571436	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.433650331924114	1		438	467	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020769	37020769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	41	591	0	ENST00000358127.4:c.76del	p.Val26PhefsTer3	p.V26Ffs*3	ENST00000358127	NM_001280556.1	26	Gtt/tt	2/10	1	2	FACETS	0.242	0.2	0.288	0.242	0.2	0.288	SUBCLONAL	1	TRUE	1	0.433650331924114	2		591	782	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052636	42052636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1054243525	NA	P-0031584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	91	523	0	ENST00000219905.7:c.7307G>A	p.Arg2436His	p.R2436H	ENST00000219905	NM_001164273.1	2436	cGt/cAt	20/24	0.314990691547663	1	FACETS	0.485	0.43	0.543	0.485	0.43	0.543	SUBCLONAL	1	TRUE	0	0.433650331924114	1		523	678	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604668	48604668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	128	378	0	ENST00000342988.3:c.1490G>A	p.Arg497His	p.R497H	ENST00000342988	NM_005359.5	497	cGc/cAc	12/12	0.433650331924114	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.433650331924114	1		378	432	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94211962	94211962	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	95	621	0	ENST00000323929.3:c.483G>C	p.Lys161Asn	p.K161N	ENST00000323929	NM_005591.3	161	aaG/aaC	6/20	0.266099918220325	1	FACETS	0.431	0.383	0.481	0.431	0.383	0.481	SUBCLONAL	1	TRUE	0	0.433650331924114	1		621	797	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119925	70119926	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0031584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	125	503	0	ENST00000245479.2:c.928dup	p.His310ProfsTer268	p.H310Pfs*268	ENST00000245479	NM_000346.3	309	-/C	3/3	0.266099918220325	1	FACETS	0.805	0.731	0.882	0.805	0.731	0.882	CLONAL	1	TRUE	0	0.433650331924114	1		503	561	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39613862	39613862	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	172	533	0	ENST00000262039.4:c.1780C>A	p.Pro594Thr	p.P594T	ENST00000262039	NM_002647.2	594	Cct/Act	16/25	0.433650331924114	1	FACETS	0.968	0.894	1	0.968	0.894	1	CLONAL	1	TRUE	0	0.433650331924114	1		533	642	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266024	41266592	+	splice_donor_variant,splice_acceptor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	GATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACA	GATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACA	-	novel	NA	P-0031584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	98	236	0	ENST00000349496.5:c.25_393del		p.X9_splice	ENST00000349496	NM_001904.3	9	ttGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAg/ttg	3-4/15	0.266099918220325	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.433650331924114	1		236	323	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	50	270	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.89	0.759	1	0.89	0.759	1	CLONAL	1	TRUE	1	0.327539058407425	2		270	343	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0031585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	159	404	2	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.215701117106331	2	FACETS	0.884	0.815	0.955	0.884	0.815	0.955	CLONAL	2	TRUE	0	0.327539058407425	2		406	549	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	116	714	2	ENST00000269305.4:c.166G>T	p.Glu56Ter	p.E56*	ENST00000269305	NM_001126112.2	56	Gaa/Taa	4/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.327539058407425	2		716	644	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247367	153247367	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747241612	NA	P-0031585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	55	342	0	ENST00000281708.4:c.1435C>G	p.Arg479Gly	p.R479G	ENST00000281708	NM_033632.3	479	Cga/Gga	10/12	1	2	FACETS	0.7	0.599	0.809	0.7	0.599	0.809	SUBCLONAL	1	TRUE	1	0.327539058407425	2		342	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579566	7579566	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	120	661	0	ENST00000269305.4:c.121G>C	p.Asp41His	p.D41H	ENST00000269305	NM_001126112.2	41	Gat/Cat	4/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.327539058407425	2		661	636	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001390	150001390	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	38	602	0	ENST00000253339.5:c.2214G>C	p.Lys738Asn	p.K738N	ENST00000253339		738	aaG/aaC	4/7	1	2	FACETS	0.427	0.352	0.51	0.427	0.352	0.51	SUBCLONAL	1	TRUE	1	0.327539058407425	2		602	544	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592283	29592283	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	86	290	0	ENST00000356175.3:c.4698G>C	p.Leu1566Phe	p.L1566F	ENST00000356175	NM_000267.3	1566	ttG/ttC	35/57	1	2	FACETS	0.834	0.745	0.926	1	0.983	1	CLONAL	2	TRUE	1	0.327539058407425	2		290	315	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489566	56489566	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	49	477	0	ENST00000267101.3:c.2031G>C	p.Met677Ile	p.M677I	ENST00000267101	NM_001982.3	677	atG/atC	17/28	1	2	FACETS	0.461	0.39	0.54	0.461	0.39	0.54	SUBCLONAL	1	TRUE	1	0.327539058407425	2		477	649	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115269681	115269681	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	115	512	0	ENST00000438362.2:c.1525G>A	p.Asp509Asn	p.D509N	ENST00000438362	NM_001242891.1	509	Gac/Aac	13/20	0.215701117106331	2	FACETS	1	0.983	1	0.705	0.638	0.775	CLONAL	1	TRUE	0	0.327539058407425	2		512	498	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667387	241667387	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	131	551	0	ENST00000366560.3:c.1063G>C	p.Glu355Gln	p.E355Q	ENST00000366560	NM_000143.3	355	Gaa/Caa	7/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.327539058407425	2		551	677	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436060	49436060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777415982	NA	P-0031585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	45	388	1	ENST00000301067.7:c.5921C>T	p.Thr1974Met	p.T1974M	ENST00000301067	NM_003482.3	1974	aCg/aTg	28/54	1	2	FACETS	0.753	0.634	0.883	0.753	0.634	0.883	SUBCLONAL	1	TRUE	1	0.327539058407425	2		389	365	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133236080	133236080	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	68	443	0	ENST00000320574.5:c.3076G>C	p.Asp1026His	p.D1026H	ENST00000320574	NM_006231.2	1026	Gac/Cac	26/49	1	2	FACETS	0.885	0.772	1	0.885	0.772	1	CLONAL	1	TRUE	1	0.327539058407425	2		443	469	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349811	89349811	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	150	744	0	ENST00000301030.4:c.3139C>G	p.Gln1047Glu	p.Q1047E	ENST00000301030	NM_001256183.1	1047	Cag/Gag	9/13	1	2	FACETS	0.949	0.867	1	0.949	0.867	1	CLONAL	1	TRUE	1	0.327539058407425	2		744	965	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961304	15961304	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	134	572	0	ENST00000268712.3:c.6085C>T	p.Gln2029Ter	p.Q2029*	ENST00000268712	NM_006311.3	2029	Cag/Tag	39/46	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.327539058407425	2		572	580	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627877	37627877	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	129	548	1	ENST00000447079.4:c.1792C>T	p.Gln598Ter	p.Q598*	ENST00000447079	NM_015083.1	598	Cag/Tag	2/14	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.327539058407425	2		549	697	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196866	106196866	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	68	380	0	ENST00000380013.4:c.5199C>G	p.Phe1733Leu	p.F1733L	ENST00000380013	NM_001127208.2	1733	ttC/ttG	11/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.327539058407425	2		380	355	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138644	37138644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318584789	NA	P-0031585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	87	644	1	ENST00000373509.5:c.178G>A	p.Asp60Asn	p.D60N	ENST00000373509	NM_002648.3	60	Gac/Aac	2/6	1	2	FACETS	0.864	0.766	0.969	0.864	0.766	0.969	CLONAL	1	TRUE	1	0.327539058407425	2		645	615	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001578	150001578	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	27	336	0	ENST00000253339.5:c.2026G>C	p.Asp676His	p.D676H	ENST00000253339		676	Gat/Cat	4/7	1	2	FACETS	0.472	0.376	0.583	0.472	0.376	0.583	SUBCLONAL	1	TRUE	1	0.327539058407425	2		336	349	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404540	8404540	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	58	266	0	ENST00000356435.5:c.4207G>C	p.Glu1403Gln	p.E1403Q	ENST00000356435		1403	Gaa/Caa	25/35	0.327539058407425	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.327539058407425	1		266	268	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391059	139391059	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	115	717	0	ENST00000277541.6:c.7132C>A	p.His2378Asn	p.H2378N	ENST00000277541	NM_017617.3	2378	Cac/Aac	34/34	0.327539058407425	1	FACETS	0.966	0.872	1	0.966	0.872	1	CLONAL	1	TRUE	0	0.327539058407425	1		717	608	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0031611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	112	621	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.419646079054301	1	FACETS	0.889	0.808	0.972	0.889	0.808	0.972	CLONAL	1	TRUE	0	0.529293518452192	1		624	350	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921567	178921567	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553821144	NA	P-0031611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	62	442	0	ENST00000263967.3:c.1049A>G	p.Asp350Gly	p.D350G	ENST00000263967	NM_006218.2	350	gAc/gGc	5/21	1	2	FACETS	0.734	0.639	0.837	0.734	0.639	0.837	SUBCLONAL	1	TRUE	1	0.529293518452192	2		442	319	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78435632	78435632	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	123	437	0	ENST00000370768.2:c.188A>G	p.Gln63Arg	p.Q63R	ENST00000370768	NM_003902.3	63	cAa/cGa	2/20	1	2	FACETS	0.815	0.74	0.894	0.815	0.74	0.894	CLONAL	1	TRUE	1	0.529293518452192	2		437	570	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614780	23614780	+	stop_lost	Nonstop_Mutation	SNP	T	T	A	novel	NA	P-0031611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	118	390	0	ENST00000261584.4:c.3561A>T	p.Ter1187TyrextTer5	p.*1187Yext*5	ENST00000261584	NM_024675.3	1187	taA/taT	13/13	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.529293518452192	2		390	418	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389375	8389375	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	115	386	0	ENST00000356435.5:c.4243T>A	p.Tyr1415Asn	p.Y1415N	ENST00000356435		1415	Tac/Aac	26/35	1	2	FACETS	0.941	0.853	1	0.941	0.853	1	CLONAL	1	TRUE	1	0.529293518452192	2		386	462	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139565447	139565447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	216	521	0	ENST00000308874.7:c.617G>A	p.Arg206Lys	p.R206K	ENST00000308874		206	aGg/aAg	8/10	0.406006532005374	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.529293518452192	1		521	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0031616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	314	621	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.741029015146285	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.753465088324812	2		624	410	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	367	376	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	0.741029015146285	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.753465088324812	2		376	445	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918527	94918527	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	128	467	0	ENST00000536441.1:c.655G>C	p.Glu219Gln	p.E219Q	ENST00000536441	NM_144665.3	219	Gaa/Caa	5/10	0.733004627215963	3	FACETS	0.908	0.828	0.992	0.454	0.414	0.496	CLONAL	1	TRUE	1	0.753465088324812	3		467	515	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125479	7125479	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	204	548	0	ENST00000302850.5:c.3073C>G	p.Leu1025Val	p.L1025V	ENST00000302850	NM_000208.2	1025	Ctc/Gtc	17/22	0.753465088324812	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.753465088324812	1		548	319	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397205	397205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372869810	NA	P-0031616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	89	371	1	ENST00000380956.4:c.590C>T	p.Thr197Met	p.T197M	ENST00000380956	NM_001195286.1	197	aCg/aTg	5/9	0.733004627215963	3	FACETS	0.945	0.846	1	0.473	0.423	0.525	CLONAL	1	TRUE	1	0.753465088324812	3		372	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0031617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	215	558	2	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.416365035014431	2	FACETS	0.923	0.865	0.982	0.923	0.865	0.982	CLONAL	2	TRUE	0	0.422616188263988	2		560	551	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106533	27106533	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	449	629	0	ENST00000324856.7:c.6144G>A	p.Trp2048Ter	p.W2048*	ENST00000324856	NM_006015.4	2048	tgG/tgA	20/20	0.411849289862992	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	0	0.422616188263988	3		629	836	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326739	62326740	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0031617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	138	651	0	ENST00000360203.5:c.3559_3560del	p.Gln1187GlufsTer11	p.Q1187Efs*11	ENST00000360203	NM_001283009.1	1186	agACag/agag	34/35	0.394009747446751	4	FACETS	0.925	0.841	1	0.463	0.42	0.507	CLONAL	1	TRUE	2	0.422616188263988	4		651	1004	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	118	470	1				ENST00000310581	NM_198253.2	-/1132			0.235024013662131	1	FACETS	0.874	0.794	0.956	0.874	0.794	0.956	INDETERMINATE	1	TRUE	0	0.476420701500147	1		471	432	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873199	71873199	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866639633	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	412	466	1	ENST00000357731.5:c.995G>T	p.Cys332Phe	p.C332F	ENST00000357731	NM_173808.2	332	tGc/tTc	7/7	0.476420701500147	3	FACETS	0.899	0.862	0.936	0.899	0.862	0.936	CLONAL	3	TRUE	0	0.476420701500147	3		467	794	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256530	+	missense_variant	Missense_Mutation	DNP	TG	TG	AA	novel	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	502	565	3	ENST00000369535.4:c.181_182delinsTT	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	CAa/TTa	3/7	0.476420701500147	3	FACETS	0.899	0.865	0.932	0.899	0.865	0.932	CLONAL	3	TRUE	0	0.476420701500147	3		568	968	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625453	69625453	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147952743	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	188	551	0	ENST00000334134.2:c.340G>A	p.Glu114Lys	p.E114K	ENST00000334134	NM_005247.2	114	Gag/Aag	3/3	1	2	FACETS	0.958	0.886	1	0.958	0.886	1	CLONAL	1	TRUE	1	0.476420701500147	2		551	824	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998306	100998306	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1255934976	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	20	64	0	ENST00000325455.5:c.1496C>T	p.Ser499Phe	p.S499F	ENST00000325455	NM_001202474.3	499	tCc/tTc	1/8	1	2	FACETS	0.807	0.628	1	0.807	0.628	1	CLONAL	1	TRUE	1	0.476420701500147	2		64	104	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359464	118359465	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	101	313	0	ENST00000534358.1:c.4469dup	p.Ala1491GlyfsTer9	p.A1491Gfs*9	ENST00000534358	NM_005933.3	1490	cag/cAag	11/36	0.442772601803819	1	FACETS	0.807	0.727	0.892	0.807	0.727	0.892	CLONAL	1	TRUE	0	0.476420701500147	1		313	400	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148882	119148882	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	88	357	0	ENST00000264033.4:c.1102T>A	p.Tyr368Asn	p.Y368N	ENST00000264033	NM_005188.3	368	Tat/Aat	8/16	0.442772601803819	1	FACETS	0.802	0.716	0.891	0.802	0.716	0.891	CLONAL	1	TRUE	0	0.476420701500147	1		357	351	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435190	18435190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	66	381	1	ENST00000266497.5:c.175G>A	p.Asp59Asn	p.D59N	ENST00000266497		59	Gat/Aat	1/31	0.235024013662131	1	FACETS	0.429	0.373	0.49	0.429	0.373	0.49	INDETERMINATE	1	TRUE	0	0.476420701500147	1		382	492	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715780	18715780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745816756	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	58	340	0	ENST00000266497.5:c.3611C>T	p.Ser1204Leu	p.S1204L	ENST00000266497		1204	tCg/tTg	25/31	0.235024013662131	1	FACETS	0.397	0.342	0.458	0.397	0.342	0.458	INDETERMINATE	1	TRUE	0	0.476420701500147	1		340	467	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241909	133241909	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs755607339	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	88	476	0	ENST00000320574.5:c.2447A>G	p.Tyr816Cys	p.Y816C	ENST00000320574	NM_006231.2	816	tAt/tGt	21/49	0.235024013662131	1	FACETS	0.394	0.349	0.443	0.394	0.349	0.443	INDETERMINATE	1	TRUE	0	0.476420701500147	1		476	714	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910512	32910512	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879255439	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	123	386	0	ENST00000380152.3:c.2020G>A	p.Glu674Lys	p.E674K	ENST00000380152		674	Gaa/Aaa	11/27	1	2	FACETS	0.846	0.768	0.929	0.846	0.768	0.929	CLONAL	1	TRUE	1	0.476420701500147	2		386	610	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95583017	95583017	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886037672	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	98	262	0	ENST00000393063.1:c.1525C>T	p.Arg509Ter	p.R509*	ENST00000393063	NM_030621.3	509	Cga/Tga	11/28	1	2	FACETS	0.948	0.851	1	0.948	0.851	1	CLONAL	1	TRUE	1	0.476420701500147	2		262	434	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923459	9923460	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	133	485	1	ENST00000330684.3:c.1827_1828delinsAA	p.Trp609_Gly610delinsTer	p.W609_G610delins*	ENST00000330684	NM_001134407.1	609	tgGGgc/tgAAgc	9/13	1	2	FACETS	0.771	0.701	0.844	0.771	0.701	0.844	SUBCLONAL	1	TRUE	1	0.476420701500147	2		486	724	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032197	10032197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774932381	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	203	553	1	ENST00000330684.3:c.626C>T	p.Ser209Phe	p.S209F	ENST00000330684	NM_001134407.1	209	tCc/tTc	3/13	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.476420701500147	2		554	799	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81922807	81922807	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs530712899	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	133	380	1	ENST00000359376.3:c.796C>T	p.Arg266Cys	p.R266C	ENST00000359376	NM_002661.3	266	Cgt/Tgt	10/33	1	2	FACETS	0.836	0.761	0.914	0.836	0.761	0.914	CLONAL	1	TRUE	1	0.476420701500147	2		381	668	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968169	18968169	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	170	556	0	ENST00000262803.5:c.2009T>G	p.Val670Gly	p.V670G	ENST00000262803	NM_002911.3	670	gTg/gGg	15/24	1	2	FACETS	0.91	0.838	0.985	0.91	0.838	0.985	CLONAL	1	TRUE	1	0.476420701500147	2		556	784	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799290	42799290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	121	402	0	ENST00000575354.2:c.4774C>T	p.Pro1592Ser	p.P1592S	ENST00000575354	NM_015125.3	1592	Ccc/Tcc	20/20	1	2	FACETS	0.882	0.799	0.968	0.882	0.799	0.968	CLONAL	1	TRUE	1	0.476420701500147	2		402	576	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714697	52714697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267605629	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	130	515	2	ENST00000322088.6:c.455C>T	p.Ser152Phe	p.S152F	ENST00000322088	NM_014225.5	152	tCc/tTc	4/15	1	2	FACETS	0.718	0.652	0.788	0.718	0.652	0.788	SUBCLONAL	1	TRUE	1	0.476420701500147	2		517	760	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462599	29462599	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766666105	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	310	595	0	ENST00000389048.3:c.2302G>A	p.Asp768Asn	p.D768N	ENST00000389048	NM_004304.4	768	Gat/Aat	13/29	0.249194568647182	3	FACETS	0.824	0.778	0.87	0.824	0.778	0.87	INDETERMINATE	2	TRUE	1	0.476420701500147	3		595	978	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551282	29551282	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	162	643	1	ENST00000389048.3:c.1348C>T	p.Gln450Ter	p.Q450*	ENST00000389048	NM_004304.4	450	Cag/Tag	6/29	0.249194568647182	3	FACETS	0.994	0.913	1	0.497	0.456	0.54	INDETERMINATE	1	TRUE	1	0.476420701500147	3		644	847	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547022	9547022	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs58486349	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	58	214	0	ENST00000353224.5:c.1000G>A	p.Asp334Asn	p.D334N	ENST00000353224	NM_177990.2	334	Gat/Aat	5/10	1	2	FACETS	0.747	0.646	0.856	0.747	0.646	0.856	SUBCLONAL	1	TRUE	1	0.476420701500147	2		214	326	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39729929	39729929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	188	513	0	ENST00000361337.2:c.1244C>T	p.Ser415Phe	p.S415F	ENST00000361337	NM_003286.2	415	tCc/tTc	13/21	1	2	FACETS	0.976	0.903	1	0.976	0.903	1	CLONAL	1	TRUE	1	0.476420701500147	2		513	809	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714415	40714415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765339833	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	172	400	1	ENST00000373198.4:c.3982G>A	p.Asp1328Asn	p.D1328N	ENST00000373198	NM_133170.3	1328	Gac/Aac	29/32	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.476420701500147	2		401	706	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733252	40733252	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	179	498	1	ENST00000373198.4:c.3554T>C	p.Leu1185Pro	p.L1185P	ENST00000373198	NM_133170.3	1185	cTg/cCg	26/32	1	2	FACETS	0.966	0.892	1	0.966	0.892	1	CLONAL	1	TRUE	1	0.476420701500147	2		499	778	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101050	41101050	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs192944843	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	173	571	0	ENST00000373198.4:c.1306G>A	p.Glu436Lys	p.E436K	ENST00000373198	NM_133170.3	436	Gag/Aag	8/32	1	2	FACETS	0.979	0.903	1	0.979	0.903	1	CLONAL	1	TRUE	1	0.476420701500147	2		571	742	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091213	29091213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	43	88	0	ENST00000328354.6:c.1277C>T	p.Pro426Leu	p.P426L	ENST00000328354	NM_007194.3	426	cCt/cTt	12/15	0.314460301906162	4	FACETS	0.877	0.747	1	0.877	0.747	1	CLONAL	2	TRUE	2	0.476420701500147	4		88	152	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032867	30032867	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	205	350	0	ENST00000338641.4:c.240+2T>C		p.X80_splice	ENST00000338641	NM_000268.3	80			0.314460301906162	4	FACETS	0.897	0.835	0.961	0.897	0.835	0.961	CLONAL	2	TRUE	2	0.476420701500147	4		350	708	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713513	30713513	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	65	449	1	ENST00000295754.5:c.838C>G	p.Pro280Ala	p.P280A	ENST00000295754	NM_003242.5	280	Ccc/Gcc	4/7	0.235024013662131	1	FACETS	0.33	0.286	0.378	0.33	0.286	0.378	INDETERMINATE	1	TRUE	0	0.476420701500147	1		450	630	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521624	89521624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	113	406	0	ENST00000336596.2:c.2701C>T	p.Leu901Phe	p.L901F	ENST00000336596	NM_005233.5	901	Ctt/Ttt	16/17	1	2	FACETS	0.951	0.86	1	0.951	0.86	1	CLONAL	1	TRUE	1	0.476420701500147	2		406	499	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189585721	189585721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	115	386	1	ENST00000264731.3:c.982G>A	p.Glu328Lys	p.E328K	ENST00000264731	NM_003722.4	328	Gaa/Aaa	7/14	1	2	FACETS	0.867	0.784	0.954	0.867	0.784	0.954	CLONAL	1	TRUE	1	0.476420701500147	2		387	557	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604319	189604319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	133	359	0	ENST00000264731.3:c.1486C>T	p.Pro496Ser	p.P496S	ENST00000264731	NM_003722.4	496	Cct/Tct	11/14	1	2	FACETS	0.889	0.81	0.972	0.889	0.81	0.972	CLONAL	1	TRUE	1	0.476420701500147	2		359	628	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612085	189612085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868285317	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	144	474	1	ENST00000264731.3:c.1837C>T	p.Pro613Ser	p.P613S	ENST00000264731	NM_003722.4	613	Cct/Tct	14/14	1	2	FACETS	0.856	0.782	0.933	0.856	0.782	0.933	CLONAL	1	TRUE	1	0.476420701500147	2		475	706	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973926	55973926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746838678	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	152	450	0	ENST00000263923.4:c.1390G>A	p.Glu464Lys	p.E464K	ENST00000263923	NM_002253.2	464	Gaa/Aaa	10/30	1	2	FACETS	0.992	0.911	1	0.992	0.911	1	CLONAL	1	TRUE	1	0.476420701500147	2		450	643	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439326	149439326	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	82	571	2	ENST00000286301.3:c.2069G>A	p.Gly690Asp	p.G690D	ENST00000286301	NM_005211.3	690	gGc/gAc	15/22	0.235024013662131	1	FACETS	0.347	0.306	0.392	0.347	0.306	0.392	INDETERMINATE	1	TRUE	0	0.476420701500147	1		573	755	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519758	176519758	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	177	624	0	ENST00000292408.4:c.1030C>T	p.Gln344Ter	p.Q344*	ENST00000292408	NM_213647.1	344	Cag/Tag	8/18	0.235024013662131	1	FACETS	0.739	0.682	0.798	0.739	0.682	0.798	INDETERMINATE	1	TRUE	0	0.476420701500147	1		624	766	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176618984	176618984	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	91	535	0	ENST00000439151.2:c.1027T>A	p.Ser343Thr	p.S343T	ENST00000439151	NM_022455.4	343	Tct/Act	3/23	0.235024013662131	1	FACETS	0.404	0.359	0.453	0.404	0.359	0.453	INDETERMINATE	1	TRUE	0	0.476420701500147	1		535	720	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180310	32180310	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	88	505	0	ENST00000375023.3:c.2621G>A	p.Trp874Ter	p.W874*	ENST00000375023	NM_004557.3	874	tGg/tAg	17/30	0.476420701500147	3	FACETS	0.45	0.397	0.506	0.225	0.198	0.253	SUBCLONAL	1	TRUE	1	0.476420701500147	3		505	1017	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631415	117631415	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	50	348	0	ENST00000368508.3:c.6263C>T	p.Ser2088Phe	p.S2088F	ENST00000368508	NM_002944.2	2088	tCc/tTc	40/43	0.235024013662131	1	FACETS	0.37	0.314	0.431	0.37	0.314	0.431	INDETERMINATE	1	TRUE	0	0.476420701500147	1		348	432	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367272	50367273	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	110	386	1	ENST00000331340.3:c.79_80delinsAA	p.Gly27Asn	p.G27N	ENST00000331340	NM_006060.4	27	GGc/AAc	3/8	0.249194568647182	3	FACETS	0.852	0.767	0.942	0.426	0.383	0.471	INDETERMINATE	1	TRUE	1	0.476420701500147	3		387	671	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259417	55259417	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	147	325	0	ENST00000275493.2:c.2475G>A	p.Met825Ile	p.M825I	ENST00000275493	NM_005228.3	825	atG/atA	21/28	0.249194568647182	3	FACETS	0.758	0.697	0.821	0.758	0.697	0.821	INDETERMINATE	2	TRUE	1	0.476420701500147	3		325	504	SUCCESS
MET	4233	MSKCC	GRCh37	7	116417463	116417463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913244	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	139	336	0	ENST00000397752.3:c.3280C>T	p.His1094Tyr	p.H1094Y	ENST00000397752	NM_000245.2	1094	Cat/Tat	16/21	0.249194568647182	3	FACETS	1	0.984	1	0.663	0.606	0.722	INDETERMINATE	1	TRUE	1	0.476420701500147	3		336	545	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956759	68956759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777080876	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	187	567	1	ENST00000288368.4:c.877C>T	p.Arg293Trp	p.R293W	ENST00000288368	NM_024870.2	293	Cgg/Tgg	8/40	1	2	FACETS	0.899	0.831	0.97	0.899	0.831	0.97	CLONAL	1	TRUE	1	0.476420701500147	2		568	873	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	121	349	1	ENST00000304494.5:c.143C>T	p.Pro48Leu	p.P48L	ENST00000304494	NM_000077.4	48	cCg/cTg	1/3	0.476420701500147	1	FACETS	0.958	0.873	1	0.958	0.873	1	CLONAL	1	TRUE	0	0.476420701500147	1		350	404	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359975	87359976	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	67	358	0	ENST00000277120.3:c.1283_1284delinsAA	p.Arg428Gln	p.R428Q	ENST00000277120		428	cGG/cAA	11/19	0.235024013662131	1	FACETS	0.474	0.413	0.54	0.474	0.413	0.54	INDETERMINATE	1	TRUE	0	0.476420701500147	1		358	452	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396841	139396841	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	170	541	2	ENST00000277541.6:c.5267T>C	p.Leu1756Pro	p.L1756P	ENST00000277541	NM_017617.3	1756	cTg/cCg	28/34	0.235024013662131	1	FACETS	0.727	0.67	0.786	0.727	0.67	0.786	INDETERMINATE	1	TRUE	0	0.476420701500147	1		543	748	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938492	44938493	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	143	271	0	ENST00000377967.4:c.3040_3041delinsTT	p.Pro1014Phe	p.P1014F	ENST00000377967	NM_021140.2	1014	CCc/TTc	20/29	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.476420701500147	1		271	366	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858029	152858030	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AT	novel	NA	P-0031640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	96	170	0	ENST00000406277.2:c.585_586delinsAT	p.Tyr195Ter	p.Y195*	ENST00000406277	NM_152274.4	195	taCCtg/taATtg	6/7	1	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.476420701500147	1		170	221	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631171	176631171	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	197	554	0	ENST00000439151.2:c.1114C>T	p.Pro372Ser	p.P372S	ENST00000439151	NM_022455.4	372	Cct/Tct	4/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.475015248972462	2		554	761	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11308150	11308150	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs757384321	NA	P-0031642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	157	389	1	ENST00000361445.4:c.842G>A	p.Arg281His	p.R281H	ENST00000361445	NM_004958.3	281	cGt/cAt	7/58	0.475015248972462	3	FACETS	1	0.966	1	0.549	0.504	0.596	CLONAL	1	TRUE	1	0.475015248972462	3		390	745	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874964	151874965	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	GCCTAGGCATATCTACAGAT	novel	NA	P-0031642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	90	281	0	ENST00000262189.6:c.7554_7573dup	p.Pro2525HisfsTer3	p.P2525Hfs*3	ENST00000262189	NM_170606.2	2525	cct/cATCTGTAGATATGCCTAGGCct	38/59	0.475015248972462	2	FACETS	0.818	0.729	0.913	0.409	0.364	0.457	CLONAL	1	TRUE	0	0.475015248972462	2		281	463	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	128	270	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.902	0.82	0.988	0.902	0.82	0.988	CLONAL	1	TRUE	1	0.444158739398277	2		270	639	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457158	25457158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1459396018	NA	P-0031644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	150	578	0	ENST00000264709.3:c.2729C>T	p.Ala910Val	p.A910V	ENST00000264709	NM_175629.2	910	gCg/gTg	23/23	1	2	FACETS	0.916	0.839	0.997	0.916	0.839	0.997	CLONAL	1	TRUE	1	0.444158739398277	2		578	737	SUCCESS
MET	4233	MSKCC	GRCh37	7	116399482	116399482	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	147	541	0	ENST00000397752.3:c.2302A>C	p.Asn768His	p.N768H	ENST00000397752	NM_000245.2	768	Aat/Cat	10/21	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.444158739398277	2		541	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0031645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	63	701	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	0.585	0.506	0.671	0.585	0.506	0.671	SUBCLONAL	1	FALSE	1	0.38712270270652	2		701	556	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251288	99251288	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	59	541	0	ENST00000268035.6:c.592A>C	p.Asn198His	p.N198H	ENST00000268035	NM_000875.3	198	Aac/Cac	2/21	0.38712270270652	3	FACETS	0.62	0.533	0.714	0.31	0.266	0.357	SUBCLONAL	1	FALSE	1	0.38712270270652	3		541	587	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124271	2124314	+	frameshift_variant	Frame_Shift_Del	DEL	CCATCTGCAGCGTGGAGATGCCTGACATCATCATCAAGGCGCTG	CCATCTGCAGCGTGGAGATGCCTGACATCATCATCAAGGCGCTG	-	novel	NA	P-0031645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	63	783	1	ENST00000219476.3:c.2428_2471del	p.Ile810CysfsTer58	p.I810Cfs*58	ENST00000219476	NM_000548.3	809	tCCATCTGCAGCGTGGAGATGCCTGACATCATCATCAAGGCGCTG/t	22/42	1	2	FACETS	0.643	0.557	0.737	0.643	0.557	0.737	SUBCLONAL	1	FALSE	1	0.38712270270652	2		784	506	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450367	50450367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs869312885	NA	P-0031645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	19	522	0	ENST00000331340.3:c.551G>A	p.Arg184Gln	p.R184Q	ENST00000331340	NM_006060.4	184	cGg/cAg	5/8	1	2	FACETS	0.29	0.219	0.372	0.29	0.219	0.372	SUBCLONAL	1	FALSE	1	0.38712270270652	2		522	339	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509079	106509079	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	53	594	0	ENST00000359195.3:c.1073A>G	p.Asp358Gly	p.D358G	ENST00000359195	NM_002649.2	358	gAc/gGc	2/11	0.205391395124111	5	FACETS	0.873	0.745	1	0.291	0.248	0.338	INDETERMINATE	1	FALSE	2	0.38712270270652	5		594	496	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457213	89457215	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CCA	CCA	-	novel	NA	P-0031645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	28	387	0	ENST00000336596.2:c.1698-4_1698-2del		p.X566_splice	ENST00000336596	NM_005233.5	566			0.308734279288239	3	FACETS	0.591	0.474	0.725	0.296	0.237	0.363	SUBCLONAL	1	FALSE	1	0.38712270270652	3		387	292	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928072	178928098	+	inframe_deletion	In_Frame_Del	DEL	TGGATTAGAAGATTTGCTGAACCCTAT	TGGATTAGAAGATTTGCTGAACCCTAT	-	novel	NA	P-0031647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	168	555	0	ENST00000263967.3:c.1353_1379del	p.Leu452_Gly460del	p.L452_G460del	ENST00000263967	NM_006218.2	450	caTGGATTAGAAGATTTGCTGAACCCTATt/cat	8/21	0.432789873717214	5	FACETS	1	0.987	1	0.352	0.323	0.382	CLONAL	1	TRUE	1	0.432789873717214	5		555	910	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615113	100615113	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	259	524	0	ENST00000308731.7:c.802T>A	p.Tyr268Asn	p.Y268N	ENST00000308731	NM_000061.2	268	Tat/Aat	9/19	0.432789873717214	1	FACETS	0.909	0.861	0.956	1	0.995	1	CLONAL	2	TRUE	0	0.432789873717214	1		524	516	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050374	176050377	+	frameshift_variant	Frame_Shift_Del	DEL	GGAC	GGAC	-	novel	NA	P-0031647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	100	488	0	ENST00000367669.3:c.1188_1191del	p.Lys398LeufsTer10	p.K398Lfs*10	ENST00000367669	NM_022457.5	396	ttGTCC/tt	11/20	0.432789873717214	4	FACETS	0.688	0.613	0.767	0.172	0.153	0.192	SUBCLONAL	1	TRUE	0	0.432789873717214	4		488	963	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373307	118373307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782272214	NA	P-0031647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	224	540	0	ENST00000534358.1:c.6700G>A	p.Gly2234Arg	p.G2234R	ENST00000534358	NM_005933.3	2234	Ggg/Agg	27/36	0.370340959336322	0	FACETS	0.809	0.769	0.848			1	CLONAL	2	TRUE	0	0.432789873717214	0		540	363	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21626547	21626547	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	120	471	0	ENST00000421138.2:c.1385T>G	p.Phe462Cys	p.F462C	ENST00000421138		462	tTt/tGt	13/16	0.38421569914843	0	FACETS	0.754	0.687	0.824			1	SUBCLONAL	1	TRUE	0	0.432789873717214	0		471	417	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396479	396479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	304	878	1	ENST00000262320.3:c.547G>A	p.Asp183Asn	p.D183N	ENST00000262320	NM_003502.3	183	Gac/Aac	2/11	0.432789873717214	3	FACETS	0.773	0.728	0.818	0.773	0.728	0.818	SUBCLONAL	2	TRUE	1	0.432789873717214	3		879	1106	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649137	37649137	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	113	461	0	ENST00000447079.4:c.2242G>C	p.Asp748His	p.D748H	ENST00000447079	NM_015083.1	748	Gac/Cac	4/14	1	2	FACETS	0.998	0.902	1	0.998	0.902	1	CLONAL	1	TRUE	1	0.432789873717214	2		461	523	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155043	55155043	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	200	481	1	ENST00000257290.5:c.2752C>A	p.Pro918Thr	p.P918T	ENST00000257290	NM_006206.4	918	Cct/Act	20/23	1	2	FACETS	0.915	0.856	0.975	1	0.994	1	CLONAL	2	TRUE	1	0.432789873717214	2		482	505	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652011	36652011	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	133	724	0	ENST00000244741.5:c.133G>T	p.Ala45Ser	p.A45S	ENST00000244741	NM_000389.4	45	Gcc/Tcc	2/3	0.159916054500327	5	FACETS	1	0.946	1			1	INDETERMINATE	1	TRUE	NA	0.432789873717214	5		724	956	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231381	98231382	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0031649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	209	549	0	ENST00000331920.6:c.1901_1902del	p.His634ArgfsTer19	p.H634Rfs*19	ENST00000331920	NM_000264.3	634	cAC/c	14/24	1	2	FACETS	0.961	0.895	1	0.961	0.895	1	CLONAL	1	TRUE	1	0.591212905363667	2		549	736	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98247989	98247999	+	frameshift_variant	Frame_Shift_Del	DEL	CACGGCTGGCC	CACGGCTGGCC	-	novel	NA	P-0031649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	151	401	0	ENST00000331920.6:c.552_562del	p.Gln184HisfsTer64	p.Q184Hfs*64	ENST00000331920	NM_000264.3	184	caGGCCAGCCGTGtc/catc	3/24	1	2	FACETS	0.93	0.855	1	0.93	0.855	1	CLONAL	1	TRUE	1	0.591212905363667	2		401	549	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	84	672	0	ENST00000269305.4:c.313G>T	p.Gly105Cys	p.G105C	ENST00000269305	NM_001126112.2	105	Ggc/Tgc	4/11	0.218025916816075	1	FACETS	0.893	0.788	1	0.893	0.788	1	CLONAL	1	TRUE	0	0.218025916816075	1		672	769	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856208	111856208	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	42	205	0	ENST00000341259.2:c.259C>A	p.Arg87Ser	p.R87S	ENST00000341259	NM_005475.2	87	Cgc/Agc	2/8	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.218025916816075	2		205	326	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50815286	50815286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	79	519	0	ENST00000398568.2:c.1639C>T	p.Pro547Ser	p.P547S	ENST00000398568	NM_001042412.1	547	Ccg/Tcg	9/18	0.218025916816075	1	FACETS	0.84	0.738	0.949	0.84	0.738	0.949	CLONAL	1	TRUE	0	0.218025916816075	1		519	769	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509591	29509596	+	stop_gained	Nonsense_Mutation	ONP	GTTTGG	GTTTGG	TTTTGA	novel	NA	P-0031651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	78	563	0	ENST00000356175.3:c.796_801delinsTTTTGA	p.Val266_Trp267delinsPheTer	p.V266_W267delinsF*	ENST00000356175	NM_000267.3	266	GTTTGG/TTTTGA	8/57	0.218025916816075	1	FACETS	0.817	0.717	0.925	0.817	0.717	0.925	CLONAL	1	TRUE	0	0.218025916816075	1		563	780	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268120	153268120	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	38	291	0	ENST00000281708.4:c.688C>G	p.Pro230Ala	p.P230A	ENST00000281708	NM_033632.3	230	Cca/Gca	4/12	1	2	FACETS	0.706	0.583	0.843	0.706	0.583	0.843	SUBCLONAL	1	TRUE	1	0.218025916816075	2		291	494	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589147	67589151	+	frameshift_variant	Frame_Shift_Del	DEL	AAATT	AAATT	-	novel	NA	P-0031651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	42	311	0	ENST00000274335.5:c.1137_1141del	p.Lys379AsnfsTer14	p.K379Nfs*14	ENST00000274335		379	AAATTa/a	9/15	0.218025916816075	1	FACETS	0.878	0.734	1	0.878	0.734	1	CLONAL	1	TRUE	0	0.218025916816075	1		311	391	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672318	86672318	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	73	454	1	ENST00000274376.6:c.2120G>T	p.Arg707Leu	p.R707L	ENST00000274376	NM_002890.2	707	cGt/cTt	16/25	0.218025916816075	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	0	0.218025916816075	1		455	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0031655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	135	621	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.31945830171468	1	FACETS	0.906	0.824	0.992	0.906	0.824	0.992	CLONAL	1	TRUE	0	0.31945830171468	1		624	784	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	272	384	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.259250207113825	3	FACETS	1	0.983	1	0.742	0.698	0.787	CLONAL	2	TRUE	0	0.31945830171468	3		384	887	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438481	52438481	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	51	549	0	ENST00000460680.1:c.1238A>G	p.Asn413Ser	p.N413S	ENST00000460680	NM_004656.3	413	aAc/aGc	12/17	1	2	FACETS	0.475	0.403	0.555	0.475	0.403	0.555	SUBCLONAL	1	TRUE	1	0.31945830171468	2		549	672	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575103	48575103	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs876660079	NA	P-0031655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	112	452	0	ENST00000342988.3:c.297G>A	p.Trp99Ter	p.W99*	ENST00000342988	NM_005359.5	99	tgG/tgA	3/12	0.31945830171468	1	FACETS	0.969	0.874	1	0.969	0.874	1	CLONAL	1	TRUE	0	0.31945830171468	1		452	608	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802625	139802625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149585522	NA	P-0031657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	211	642	0	ENST00000247668.2:c.470C>T	p.Pro157Leu	p.P157L	ENST00000247668	NM_021138.3	157	cCg/cTg	5/11	1	2	FACETS	0.914	0.851	0.979	0.914	0.851	0.979	CLONAL	1	TRUE	1	0.559700472082453	2		642	825	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0031657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	193	631	0	ENST00000269305.4:c.97-1G>T		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.559700472082453	1	FACETS	0.976	0.911	1	0.976	0.911	1	CLONAL	1	TRUE	0	0.559700472082453	1		631	509	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103382	2103400	+	frameshift_variant	Frame_Shift_Del	DEL	TTGCAGCCGGAGCGGCCGC	TTGCAGCCGGAGCGGCCGC	-	novel	NA	P-0031657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	268	745	0	ENST00000219476.3:c.266_284del	p.Leu89TrpfsTer11	p.L89Wfs*11	ENST00000219476	NM_000548.3	89	TTGCAGCCGGAGCGGCCGCtg/tg	4/42	0.559700472082453	1	FACETS	0.965	0.91	1	0.965	0.91	1	CLONAL	1	TRUE	0	0.559700472082453	1		745	715	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992100	72992100	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	209	642	0	ENST00000268489.5:c.1945C>G	p.Leu649Val	p.L649V	ENST00000268489	NM_006885.3	649	Ctg/Gtg	2/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.559700472082453	2		642	716	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688734	47688734	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	195	498	1	ENST00000347630.2:c.566A>T	p.Glu189Val	p.E189V	ENST00000347630	NM_001007230.1	189	gAg/gTg	7/11	1	2	FACETS	0.955	0.886	1	0.955	0.886	1	CLONAL	1	TRUE	1	0.559700472082453	2		499	730	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095938	178095938	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	161	515	0	ENST00000397062.3:c.1393C>G	p.His465Asp	p.H465D	ENST00000397062	NM_006164.4	465	Cat/Gat	5/5	1	2	FACETS	0.925	0.852	1	0.925	0.852	1	CLONAL	1	TRUE	1	0.559700472082453	2		515	622	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752371	57752371	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1245544149	NA	P-0031657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	320	405	0	ENST00000274289.3:c.1202A>G	p.Asp401Gly	p.D401G	ENST00000274289	NM_006622.3	401	gAt/gGt	9/14	0.559313974447585	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.559700472082453	2		405	524	SUCCESS
APC	324	MSKCC	GRCh37	5	112176627	112176627	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	172	464	0	ENST00000257430.4:c.5336T>G	p.Ile1779Arg	p.I1779R	ENST00000257430	NM_000038.5	1779	aTa/aGa	16/16	0.559313974447585	2	FACETS	0.807	0.744	0.872	0.403	0.372	0.436	CLONAL	1	TRUE	0	0.559700472082453	2		464	762	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577575	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782289	NA	P-0031658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	481	586	0	ENST00000269305.4:c.706T>C	p.Tyr236His	p.Y236H	ENST00000269305	NM_001126112.2	236	Tac/Cac	7/11	0.629776845139805	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.629776845139805	2		586	734	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288893	33288893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	333	434	0	ENST00000374542.5:c.659C>T	p.Ser220Phe	p.S220F	ENST00000374542	NM_001141970.1	220	tCc/tTc	3/8	0.629776845139805	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.629776845139805	2		434	516	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0031659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	131	377	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.492018133644285	2		377	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0031659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	138	660	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.481010667883834	1	FACETS	0.938	0.86	1	0.938	0.86	1	CLONAL	1	TRUE	0	0.492018133644285	1		660	451	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0031659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	64	452	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.492018133644285	2		452	204	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405970	70405970	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	153	732	0	ENST00000373644.4:c.3484A>G	p.Lys1162Glu	p.K1162E	ENST00000373644	NM_030625.2	1162	Aag/Gag	4/12	1	2	FACETS	0.96	0.881	1	0.96	0.881	1	CLONAL	1	TRUE	1	0.492018133644285	2		732	648	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479252	50479252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	152	472	0	ENST00000394963.4:c.100C>T	p.Pro34Ser	p.P34S	ENST00000394963	NM_003076.4	34	Ccg/Tcg	1/13	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.492018133644285	2		472	524	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849552	68849552	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	163	664	0	ENST00000261769.5:c.1455C>G	p.Ile485Met	p.I485M	ENST00000261769	NM_004360.3	485	atC/atG	10/16	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.492018133644285	2		664	634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0031660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	27	361	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.158	0.125	0.196	0.158	0.125	0.196	SUBCLONAL	1	TRUE	1	0.45	2		361	761	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	149	270	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.671893556109362	2		270	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0031663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	37	771	1	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	1	2	FACETS	0.111	0.091	0.134	0.111	0.091	0.134	SUBCLONAL	1	TRUE	1	0.671893556109362	2		772	994	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0031663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5223	4053	774	3	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.671893556109362	21	FACETS	0.96	0.946	0.974			1	CLONAL	10	TRUE	NA	0.671893556109362	21		777	9276	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817489	39817489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763409220	NA	P-0031663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	260	636	0	ENST00000288319.7:c.74C>T	p.Thr25Met	p.T25M	ENST00000288319	NM_182918.3	25	aCg/aTg	2/10	1	2	FACETS	0.983	0.925	1	0.983	0.925	1	CLONAL	1	TRUE	1	0.671893556109362	2		636	787	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255700	16255700	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	38	554	0	ENST00000375759.3:c.2965G>T	p.Ala989Ser	p.A989S	ENST00000375759	NM_015001.2	989	Gca/Tca	11/15	1	2	FACETS	0.179	0.147	0.215	0.179	0.147	0.215	SUBCLONAL	1	TRUE	1	0.671893556109362	2		554	631	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115269685	115269685	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0031663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	49	516	0	ENST00000438362.2:c.1521T>G	p.Tyr507Ter	p.Y507*	ENST00000438362	NM_001242891.1	507	taT/taG	13/20	1	2	FACETS	0.219	0.185	0.257	0.219	0.185	0.257	SUBCLONAL	1	TRUE	1	0.671893556109362	2		516	665	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104352440	104352440	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	237	634	2	ENST00000369902.3:c.556C>T	p.Gln186Ter	p.Q186*	ENST00000369902	NM_016169.3	186	Cag/Tag	4/12	0.671893556109362	1	FACETS	0.937	0.885	0.989	0.937	0.885	0.989	CLONAL	1	TRUE	0	0.671893556109362	1		636	500	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805303	89805303	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	218	627	0	ENST00000389301.3:c.4247C>T	p.Ser1416Leu	p.S1416L	ENST00000389301	NM_000135.2	1416	tCa/tTa	42/43	1	2	FACETS	0.947	0.885	1	0.947	0.885	1	CLONAL	1	TRUE	1	0.671893556109362	2		627	685	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0002221-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	230	350	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.994	0.936	1	0.994	0.936	1	CLONAL	1	TRUE	1	0.866633535307304	2		350	534	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002221-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	198	454	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.866633535307304	2		454	427	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0002221-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	186	299	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	1	2	FACETS	0.956	0.893	1	0.956	0.893	1	CLONAL	1	TRUE	1	0.866633535307304	2		299	449	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720839	176720839	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002221-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	200	332	0	ENST00000439151.2:c.6470G>A	p.Trp2157Ter	p.W2157*	ENST00000439151	NM_022455.4	2157	tGg/tAg	23/23	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.866633535307304	2		332	457	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673161	30673161	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002221-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	248	523	0	ENST00000376406.3:c.3799C>T	p.Gln1267Ter	p.Q1267*	ENST00000376406	NM_014641.2	1267	Cag/Tag	10/15	1	2	FACETS	0.858	0.807	0.91	0.858	0.807	0.91	CLONAL	1	TRUE	1	0.866633535307304	2		523	667	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574572	64574572	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0002221-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	332	529	1	ENST00000312049.6:c.825-2A>T		p.X275_splice	ENST00000312049	NM_130799.2	275			0.866633535307304	1	FACETS	0.989	0.956	1	0.989	0.956	1	CLONAL	1	TRUE	0	0.866633535307304	1		530	439	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670847	134670847	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002375-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	201	435	0	ENST00000398015.3:c.758G>T	p.Cys253Phe	p.C253F	ENST00000398015	NM_004441.4	253	tGc/tTc	3/16	0.262500363648894	4	FACETS	0.908	0.844	0.973	1	0.989	1	CLONAL	3	TRUE	2	0.262500363648894	4		435	710	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456348	32456348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002375-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	92	628	0	ENST00000332351.3:c.544C>T	p.Pro182Ser	p.P182S	ENST00000332351	NM_024426.4	182	Cct/Tct	1/10	0.25633373904598	3	FACETS	0.869	0.77	0.974	0.434	0.385	0.487	CLONAL	1	TRUE	1	0.262500363648894	3		628	913	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456366	32456366	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002375-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	88	631	0	ENST00000332351.3:c.526C>G	p.Arg176Gly	p.R176G	ENST00000332351	NM_024426.4	176	Cgc/Ggc	1/10	0.25633373904598	3	FACETS	0.854	0.755	0.96	0.427	0.377	0.48	CLONAL	1	TRUE	1	0.262500363648894	3		631	888	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347972	347972	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002375-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	92	717	1	ENST00000262320.3:c.1534G>T	p.Gly512Trp	p.G512W	ENST00000262320	NM_003502.3	512	Ggg/Tgg	6/11	0.262500363648894	5	FACETS	0.86	0.762	0.965	0.215	0.19	0.242	CLONAL	1	TRUE	1	0.262500363648894	5		718	1136	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456679	32456680	+	missense_variant	Missense_Mutation	DNP	GG	GG	TA	novel	NA	P-0002375-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	60	298	0	ENST00000332351.3:c.212_213delinsTA	p.Ser71Leu	p.S71L	ENST00000332351	NM_024426.4	71	tCC/tTA	1/10	0.25633373904598	3	FACETS	0.915	0.789	1	0.458	0.394	0.527	CLONAL	1	TRUE	1	0.262500363648894	3		298	565	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456322	32456323	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0002375-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	92	610	2	ENST00000332351.3:c.569_570delinsTT	p.Ser190Phe	p.S190F	ENST00000332351	NM_024426.4	190	tCC/tTT	1/10	0.25633373904598	3	FACETS	0.842	0.747	0.944	0.421	0.373	0.472	CLONAL	1	TRUE	1	0.262500363648894	3		612	942	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256929	16256929	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002375-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	72	658	0	ENST00000375759.3:c.4194A>C	p.Leu1398Phe	p.L1398F	ENST00000375759	NM_015001.2	1398	ttA/ttC	11/15	0.235287946730465	4	FACETS	0.756	0.659	0.861	0.378	0.329	0.431	SUBCLONAL	1	TRUE	2	0.262500363648894	4		658	916	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435401	18435401	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002375-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	67	400	2	ENST00000266497.5:c.386C>G	p.Pro129Arg	p.P129R	ENST00000266497		129	cCc/cGc	1/31	0.25633373904598	3	FACETS	1	0.95	1	0.595	0.518	0.678	CLONAL	1	TRUE	1	0.262500363648894	3		402	485	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0002841-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	37	712	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	0.459050536276469	2		712	135	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002841-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	8	433	0	ENST00000263967.3:c.333G>T	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaT	2/21	1	2	FACETS	0.236	0.152	0.344	0.236	0.152	0.344	SUBCLONAL	1	TRUE	1	0.459050536276469	2		433	148	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213538	2213538	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002841-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	20	531	2	ENST00000398665.3:c.1558G>A	p.Glu520Lys	p.E520K	ENST00000398665	NM_032482.2	520	Gag/Aag	17/28	1	2	FACETS	0.239	0.182	0.305	0.239	0.182	0.305	SUBCLONAL	1	TRUE	1	0.459050536276469	2		533	365	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216503	108216503	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002841-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	13	325	0	ENST00000278616.4:c.8452G>A	p.Glu2818Lys	p.E2818K	ENST00000278616	NM_000051.3	2818	Gaa/Aaa	58/63	0.459050536276469	1	FACETS	0.474	0.343	0.63	0.474	0.343	0.63	SUBCLONAL	1	TRUE	0	0.459050536276469	1		325	92	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790180	40790180	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002841-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	15	371	0	ENST00000373198.4:c.2551G>C	p.Asp851His	p.D851H	ENST00000373198	NM_133170.3	851	Gat/Cat	18/32	1	2	FACETS	0.245	0.179	0.324	0.245	0.179	0.324	SUBCLONAL	1	TRUE	1	0.459050536276469	2		371	267	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687366	37687366	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002841-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	301	461	0	ENST00000447079.4:c.4270G>A	p.Glu1424Lys	p.E1424K	ENST00000447079	NM_015083.1	1424	Gag/Aag	14/14	0.459050536276469	10	FACETS	1	0.947	1			1	CLONAL	4	TRUE	NA	0.459050536276469	10		461	927	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667874	37667874	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002841-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	52	397	0	ENST00000447079.4:c.2759G>C	p.Trp920Ser	p.W920S	ENST00000447079	NM_015083.1	920	tGg/tCg	8/14	0.459050536276469	10	FACETS	0.837	0.715	0.97			1	CLONAL	2	TRUE	NA	0.459050536276469	10		397	384	SUCCESS
ATR	545	MSKCC	GRCh37	3	142218528	142218528	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002841-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	12	382	0	ENST00000350721.4:c.5321G>A	p.Arg1774Lys	p.R1774K	ENST00000350721	NM_001184.3	1774	aGa/aAa	31/47	1	2	FACETS	0.224	0.157	0.307	0.224	0.157	0.307	SUBCLONAL	1	TRUE	1	0.459050536276469	2		382	233	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781296	9781296	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763994711	NA	P-0002901-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	80	456	0	ENST00000377346.4:c.1801C>T	p.Arg601Trp	p.R601W	ENST00000377346	NM_005026.3	601	Cgg/Tgg	14/24	0.572849422474734	2	FACETS	0.995	0.886	1	0.497	0.443	0.554	CLONAL	1	TRUE	0	0.572461525603153	2		456	281	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608116	28608116	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002901-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	75	591	1	ENST00000241453.7:c.1850G>T	p.Gly617Val	p.G617V	ENST00000241453	NM_004119.2	617	gGa/gTa	15/24	0.389795114388547	3	FACETS	0.892	0.786	1	0.446	0.393	0.502	CLONAL	1	TRUE	1	0.572461525603153	3		592	378	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0003274-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	21	673	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.171187574094398	3	FACETS	0.135	0.103	0.172	0.067	0.051	0.086	INDETERMINATE	1	TRUE	1	0.366810837884471	3		673	1006	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0003274-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	481	594	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.366810837884471	4	FACETS	1	0.978	1			1	CLONAL	2	TRUE	NA	0.366810837884471	4		594	1726	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0003274-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	25	514	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.171187574094398	3	FACETS	0.147	0.115	0.184	0.073	0.057	0.092	INDETERMINATE	1	TRUE	1	0.366810837884471	3		514	1099	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0003274-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	26	609	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.145	0.114	0.181	0.145	0.114	0.181	SUBCLONAL	1	TRUE	1	0.366810837884471	2		610	977	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515133	148515133	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003274-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	55	450	0	ENST00000320356.2:c.1076G>T	p.Arg359Ile	p.R359I	ENST00000320356	NM_004456.4	359	aGa/aTa	10/20	0.171187574094398	3	FACETS	0.499	0.426	0.579	0.25	0.213	0.29	INDETERMINATE	1	TRUE	1	0.366810837884471	3		450	711	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0004288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	325	431	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	NA	2	FACETS	0.837	0.802	0.871			1	INDETERMINATE	3	TRUE	NA	0.482130405637156	2		431	537	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913499	NA	P-0004288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	92	234	0	ENST00000345146.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000345146	NM_005896.2	132	Cgt/Ggt	4/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.482130405637156	2		234	282	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138612	55138612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202072966	NA	P-0004288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1403	1509	432	0	ENST00000257290.5:c.1289G>A	p.Gly430Glu	p.G430E	ENST00000257290	NM_006206.4	430	gGa/gAa	9/23	0.482130405637156	24	FACETS	0.968	0.947	0.989			1	CLONAL	14	TRUE	NA	0.482130405637156	24		432	2912	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881488	48881489	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0004288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	72	256	0	ENST00000267163.4:c.219_220dup	p.Ala74GlufsTer4	p.A74Efs*4	ENST00000267163	NM_000321.2	70	-/AG	2/27	NA	2	FACETS	1	0.957	1			1	INDETERMINATE	1	TRUE	NA	0.482130405637156	2		256	254	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061341	38061341	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	116	453	0	ENST00000250448.2:c.648C>A	p.Asn216Lys	p.N216K	ENST00000250448	NM_004496.3	216	aaC/aaA	2/2	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.482130405637156	2		453	465	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524590	187524590	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1560924328	NA	P-0004288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	246	519	0	ENST00000441802.2:c.11090T>C	p.Phe3697Ser	p.F3697S	ENST00000441802	NM_005245.3	3697	tTt/tCt	19/27	0.31723820983078	3	FACETS	0.884	0.831	0.939	0.884	0.831	0.939	CLONAL	2	TRUE	1	0.482130405637156	3		519	716	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353822	40353824	+	missense_variant	Missense_Mutation	TNP	CGC	CGC	AAT	novel	NA	P-0004288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	68	510	1	ENST00000293328.3:c.2296_2298delinsATT	p.Ala766Ile	p.A766I	ENST00000293328	NM_012448.3	766	GCG/ATT	19/19	0.482130405637156	3	FACETS	0.569	0.495	0.649	0.285	0.247	0.325	SUBCLONAL	1	TRUE	1	0.482130405637156	3		511	615	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138664	55138664	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	1174	341	0	ENST00000257290.5:c.1341G>T	p.Trp447Cys	p.W447C	ENST00000257290	NM_006206.4	447	tgG/tgT	9/23	0.482130405637156	24	FACETS	1	0.99	1			1	CLONAL	13	TRUE	NA	0.482130405637156	24		341	2301	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138791	55139773	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGGTGTGATAGCTTCAGGGTGTGTATCTTTTGTCATGAATAGCTGTGAGAAGAAGGTCCAGGGCTCTCATTAGACCTTCAAAATGTCTCCAATCTAAAAACAAGAGTGAATTTTAAGAACCACTGTTCTAAGAAGATTTTTACTACCCTGGCTCACATATCTTATTTGGTGAACTTTGTTTGGTAGTCGGACTGCATGTAAACATAAATGTGACTGCTTAGTCCCTTATCTGCCCACCTGCTGTTTGGTGGGTTAATTCGCCATTCCCTCCTCCCTCCCCCGAGTCCTCAGCCTTCTTAAATGGGCACATGAGCAATGTGTTTACACTTCATCCATGGTAACTGGTTGTGTTCAGAAGCCTCAGTTGTTTCTTCCTCTAGACAGAGACTCCTCATCTTAACTTCTAGGGCTAAGAACAGACTTGGATGTTGACTGGGGTTTCTAGTAGATTCCAGTGTGGAGCAGGATTCTAGGTCTTATAACTCAATCTGAGGATCATCGCAACCCTAGTGACACCCTAGGGGCTCTTCCCAGTGTGAGTGTTGAGAAGGGAGGGCTCCAGGCCTTTTTGAAGGGGTGGGAGATTGAGATCATTAAATATGGTTGAAGTTGAACTGTTCAGTTTGCTCATAGGTTCAAGATTGGGGAATGGTAGTCATATTTTATTAAACTTGATTATCTCTGCCTGCTATGTAAACACTTAGCTTTCAGTTGTTCATGTGTGAGTTATTCCCTCTTCAGCACATGCAGACAAGTTTTAATGTTCATCTGCATGTAAAATAAATCAGTGTGTATTGCCCCGAAATGCAGACAAGGTCCCAACTCCTTGCCATCTTAGAGTGTTCCCGTGGCTCCACTCATTGCCATGACTCTCAGGAATTGGCCCTATACTTAGGCCCTTTTTCTCTCTAGATGTAATAATGAAACTTCCTGGACTATTTTGGCCAACAATGTCTCAAACATCATCACGGAGATCCACTCC	TGGGTGTGATAGCTTCAGGGTGTGTATCTTTTGTCATGAATAGCTGTGAGAAGAAGGTCCAGGGCTCTCATTAGACCTTCAAAATGTCTCCAATCTAAAAACAAGAGTGAATTTTAAGAACCACTGTTCTAAGAAGATTTTTACTACCCTGGCTCACATATCTTATTTGGTGAACTTTGTTTGGTAGTCGGACTGCATGTAAACATAAATGTGACTGCTTAGTCCCTTATCTGCCCACCTGCTGTTTGGTGGGTTAATTCGCCATTCCCTCCTCCCTCCCCCGAGTCCTCAGCCTTCTTAAATGGGCACATGAGCAATGTGTTTACACTTCATCCATGGTAACTGGTTGTGTTCAGAAGCCTCAGTTGTTTCTTCCTCTAGACAGAGACTCCTCATCTTAACTTCTAGGGCTAAGAACAGACTTGGATGTTGACTGGGGTTTCTAGTAGATTCCAGTGTGGAGCAGGATTCTAGGTCTTATAACTCAATCTGAGGATCATCGCAACCCTAGTGACACCCTAGGGGCTCTTCCCAGTGTGAGTGTTGAGAAGGGAGGGCTCCAGGCCTTTTTGAAGGGGTGGGAGATTGAGATCATTAAATATGGTTGAAGTTGAACTGTTCAGTTTGCTCATAGGTTCAAGATTGGGGAATGGTAGTCATATTTTATTAAACTTGATTATCTCTGCCTGCTATGTAAACACTTAGCTTTCAGTTGTTCATGTGTGAGTTATTCCCTCTTCAGCACATGCAGACAAGTTTTAATGTTCATCTGCATGTAAAATAAATCAGTGTGTATTGCCCCGAAATGCAGACAAGGTCCCAACTCCTTGCCATCTTAGAGTGTTCCCGTGGCTCCACTCATTGCCATGACTCTCAGGAATTGGCCCTATACTTAGGCCCTTTTTCTCTCTAGATGTAATAATGAAACTTCCTGGACTATTTTGGCCAACAATGTCTCAAACATCATCACGGAGATCCACTCC	-	novel	NA	P-0004288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	139	89	0	ENST00000257290.5:c.1364+104_1434del		p.X455_splice	ENST00000257290	NM_006206.4	455		10/23	0.482130405637156	24	FACETS	1	0.947	1			1	CLONAL	6	TRUE	NA	0.482130405637156	24		89	577	SUCCESS
APC	324	MSKCC	GRCh37	5	112176345	112176345	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004339-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	60	391	0	ENST00000257430.4:c.5058del	p.Lys1686AsnfsTer23	p.K1686Nfs*23	ENST00000257430	NM_000038.5	1685	gAa/ga	16/16	0.192935490949762	3	FACETS	0.695	0.599	0.799	0.347	0.299	0.4	INDETERMINATE	1	TRUE	1	0.369211256396659	3		391	554	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165695	118165695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745917069	NA	P-0004339-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	53	356	0	ENST00000369448.3:c.205G>A	p.Val69Ile	p.V69I	ENST00000369448	NM_017709.3	69	Gtc/Atc	2/2	1	2	FACETS	0.593	0.506	0.688	0.593	0.506	0.688	SUBCLONAL	1	TRUE	1	0.369211256396659	2		356	484	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164591	47164591	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0004339-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	110	326	0	ENST00000409792.3:c.1535C>G	p.Ser512Ter	p.S512*	ENST00000409792	NM_014159.6	512	tCa/tGa	3/21	0.369211256396659	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.369211256396659	1		326	337	SUCCESS
APC	324	MSKCC	GRCh37	5	112176386	112176386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004339-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	76	368	0	ENST00000257430.4:c.5095G>A	p.Glu1699Lys	p.E1699K	ENST00000257430	NM_000038.5	1699	Gag/Aag	16/16	0.192935490949762	3	FACETS	0.954	0.839	1	0.477	0.419	0.539	INDETERMINATE	1	TRUE	1	0.369211256396659	3		368	511	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437836	110437836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004339-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	64	378	1	ENST00000375856.3:c.565C>T	p.Pro189Ser	p.P189S	ENST00000375856	NM_003749.2	189	Ccc/Tcc	1/2	1	2	FACETS	0.709	0.615	0.81	0.709	0.615	0.81	SUBCLONAL	1	TRUE	1	0.369211256396659	2		379	489	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591895	48591895	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs377767346	NA	P-0004339-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	135	448	0	ENST00000342988.3:c.1058A>G	p.Tyr353Cys	p.Y353C	ENST00000342988	NM_005359.5	353	tAc/tGc	9/12	0.307975742530817	2	FACETS	0.783	0.717	0.851	0.783	0.717	0.851	SUBCLONAL	2	TRUE	0	0.369211256396659	2		448	467	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010560	48010560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004339-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	90	391	0	ENST00000234420.5:c.188C>T	p.Ser63Phe	p.S63F	ENST00000234420	NM_000179.2	63	tCc/tTc	1/10	0.192935490949762	3	FACETS	0.911	0.809	1	0.455	0.404	0.51	INDETERMINATE	1	TRUE	1	0.369211256396659	3		391	634	SUCCESS
APC	324	MSKCC	GRCh37	5	112176357	112176386	+	inframe_deletion	In_Frame_Del	DEL	CCATTCCTACAGAAGGCAGAAGTACAGATG	CCATTCCTACAGAAGGCAGAAGTACAGATG	-	novel	NA	P-0004339-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	54	389	0	ENST00000257430.4:c.5066_5095del	p.Thr1689_Glu1699delinsLys	p.T1689_E1699delinsK	ENST00000257430	NM_000038.5	1689	aCCATTCCTACAGAAGGCAGAAGTACAGATGag/aag	16/16	0.192935490949762	3	FACETS	0.665	0.568	0.771	0.333	0.284	0.386	INDETERMINATE	1	TRUE	1	0.369211256396659	3		389	521	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397639	139397639	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	128	683	0	ENST00000277541.6:c.5162T>G	p.Val1721Gly	p.V1721G	ENST00000277541	NM_017617.3	1721	gTg/gGg	27/34	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.29	2		683	751	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219367	1219367	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555737790	NA	P-0004606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	155	788	0	ENST00000326873.7:c.419T>C	p.Leu140Pro	p.L140P	ENST00000326873	NM_000455.4	140	cTg/cCg	3/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.29	2		788	992	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123788	11123788	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1064795105	NA	P-0004606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	81	555	1	ENST00000358026.2:c.2438C>T	p.Ser813Leu	p.S813L	ENST00000358026	NM_001128849.1	813	tCa/tTa	16/36	1	2	FACETS	0.895	0.789	1	0.895	0.789	1	CLONAL	1	TRUE	1	0.29	2		556	624	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390758	139390776	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGTCACGGGTGGGACCA	GCGGTCACGGGTGGGACCA	-	novel	NA	P-0004606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	139	900	0	ENST00000277541.6:c.7415_7433del	p.Leu2472GlnfsTer5	p.L2472Qfs*5	ENST00000277541	NM_017617.3	2472	cTGGTCCCACCCGTGACCGCa/ca	34/34	1	2	FACETS	0.909	0.826	0.996	0.909	0.826	0.996	CLONAL	1	TRUE	1	0.29	2		900	1055	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0005940-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	383	833	1	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.757648274485468	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.757648274485468	1		834	571	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559126	29559126	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0005940-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	141	264	0	ENST00000356175.3:c.3233C>G	p.Ser1078Ter	p.S1078*	ENST00000356175	NM_000267.3	1078	tCa/tGa	25/57	0.757648274485468	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.757648274485468	1		264	223	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37863278	37863278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005940-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	5039	566	0	ENST00000269571.5:c.109G>A	p.Ala37Thr	p.A37T	ENST00000269571		37	Gcc/Acc	2/27	0.757648274485468	14	FACETS	1	0.999	1			1	CLONAL	14	TRUE	NA	0.757648274485468	14		566	5171	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171600	36171600	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0005940-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	266	250	0	ENST00000300305.3:c.965C>G	p.Ser322Ter	p.S322*	ENST00000300305		322	tCa/tGa	7/8	0.749201900739	3	FACETS	0.968	0.92	1	0.968	0.92	1	CLONAL	2	TRUE	1	0.757648274485468	3		250	500	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589592	67589593	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTT	novel	NA	P-0005940-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	459	314	0	ENST00000274335.5:c.1356_1357insTTT	p.Tyr452_Asn453insPhe	p.Y452_N453insF	ENST00000274335		452	tat/taTTTt	10/15	0.757648274485468	4	FACETS	0.91	0.877	0.943			1	CLONAL	3	TRUE	NA	0.757648274485468	4		314	780	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246752	41246752	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005940-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	181	468	0	ENST00000357654.3:c.796G>C	p.Val266Leu	p.V266L	ENST00000357654	NM_007294.3	266	Gtt/Ctt	10/23	0.757648274485468	3	FACETS	0.877	0.811	0.946	0.292	0.27	0.316	CLONAL	1	TRUE	0	0.757648274485468	3		468	751	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656960	47656960	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005940-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	143	379	0	ENST00000233146.2:c.1156G>C	p.Asp386His	p.D386H	ENST00000233146	NM_000251.2	386	Gat/Cat	7/16	1	2	FACETS	0.876	0.806	0.948	0.876	0.806	0.948	CLONAL	1	TRUE	1	0.757648274485468	2		379	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0006781-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	332	685	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.518906353800783	3	FACETS	0.895	0.858	0.932			1	CLONAL	3	TRUE	NA	0.58950127575977	3		685	543	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149996	202149996	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006781-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	172	373	0	ENST00000358485.4:c.1437G>A	p.Trp479Ter	p.W479*	ENST00000358485	NM_001080125.1	479	tgG/tgA	8/9	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.58950127575977	2		373	443	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572348	41572348	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006781-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	173	471	0	ENST00000263253.7:c.4877G>T	p.Gly1626Val	p.G1626V	ENST00000263253	NM_001429.3	1626	gGt/gTt	30/31	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.58950127575977	2		471	491	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872115	76872116	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	TT	novel	NA	P-0006781-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	173	202	0	ENST00000373344.5:c.5531_5532delinsAA	p.Cys1844Ter	p.C1844*	ENST00000373344	NM_000489.3	1844	tGC/tAA	22/35	0.58950127575977	2	FACETS	1	0.986	1			1	CLONAL	2	TRUE	NA	0.58950127575977	2		202	259	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992720	68992721	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs764112302	NA	P-0006781-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	148	483	7	ENST00000288368.4:c.1693dup	p.Ser565PhefsTer3	p.S565Ffs*3	ENST00000288368	NM_024870.2	562	cgt/cgTt	16/40	0.107403939661379	5	FACETS	0.967	0.89	1	0.484	0.445	0.524	INDETERMINATE	2	TRUE	1	0.58950127575977	5		490	489	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81960731	81960731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006781-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	79	423	1	ENST00000359376.3:c.2462C>T	p.Ser821Phe	p.S821F	ENST00000359376	NM_002661.3	821	tCc/tTc	23/33	0.512632969616829	2	FACETS	0.567	0.5	0.638	0.283	0.25	0.319	SUBCLONAL	1	TRUE	0	0.58950127575977	2		424	473	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007594-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	653	537	0	ENST00000206249.3:c.1610A>G	p.Tyr537Cys	p.Y537C	ENST00000206249	NM_000125.3	537	tAt/tGt	8/8	0.728249699944144	2	FACETS	0.973	0.948	0.996	0.973	0.948	0.996	CLONAL	2	TRUE	0	0.74678142197571	2		537	899	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123107	5123107	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs774539976	NA	P-0007594-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	154	362	0	ENST00000381652.3:c.3163A>G	p.Lys1055Glu	p.K1055E	ENST00000381652	NM_004972.3	1055	Aaa/Gaa	23/25	0.74678142197571	1	FACETS	0.741	0.688	0.794	0.741	0.688	0.794	SUBCLONAL	1	TRUE	0	0.74678142197571	1		362	349	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099360	193099360	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007594-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	205	366	0	ENST00000367435.3:c.294del	p.Asn99MetfsTer10	p.N99Mfs*10	ENST00000367435	NM_024529.4	98	ctC/ct	3/17	0.74678142197571	3	FACETS	0.937	0.871	1	0.468	0.435	0.503	CLONAL	1	TRUE	1	0.74678142197571	3		366	805	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098949	178098951	+	inframe_deletion	In_Frame_Del	DEL	TAC	TAC	-	novel	NA	P-0007594-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	129	229	0	ENST00000397062.3:c.94_96del	p.Val32del	p.V32del	ENST00000397062	NM_006164.4	32	GTA/-	2/5	1	2	FACETS	0.855	0.783	0.93	0.855	0.783	0.93	CLONAL	1	TRUE	1	0.74678142197571	2		229	404	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859689	151859690	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0007594-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	165	269	0	ENST00000262189.6:c.10972dup	p.Gln3658ProfsTer30	p.Q3658Pfs*30	ENST00000262189	NM_170606.2	3658	caa/cCaa	43/59	0.744743140874371	1	FACETS	0.968	0.91	1	0.968	0.91	1	CLONAL	1	TRUE	0	0.74678142197571	1		269	286	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274737	123274737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs971411400	NA	P-0007922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	23374	471	0	ENST00000358487.5:c.1181C>T	p.Thr394Ile	p.T394I	ENST00000358487	NM_000141.4	394	aCa/aTa	9/18	0.678388543614375	89	FACETS	1	0.998	1			1	CLONAL	88	TRUE	NA	0.678388543614375	89		471	23902	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817493	39817493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755303168	NA	P-0007922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	121	450	0	ENST00000288319.7:c.70G>A	p.Gly24Arg	p.G24R	ENST00000288319	NM_182918.3	24	Gga/Aga	2/10	0.577134270514154	6	FACETS	0.888	0.801	0.98	0.222	0.2	0.245	CLONAL	1	TRUE	2	0.678388543614375	6		450	947	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274763	123274768	+	missense_variant	Missense_Mutation	ONP	GACCCC	GACCCC	AACCCT	novel	NA	P-0007922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	21960	472	1	ENST00000358487.5:c.1150_1155delinsAGGGTT	p.Gly384Arg	p.G384R	ENST00000358487	NM_000141.4	384	GGGGTC/AGGGTT	9/18	0.678388543614375	89	FACETS	0.998	0.997	1			1	CLONAL	88	TRUE	NA	0.678388543614375	89		473	22484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0010343-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	538	803	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.549566612962034	2	FACETS	0.89	0.858	0.921	0.89	0.858	0.921	CLONAL	2	TRUE	0	0.602926699681862	2		803	1003	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144897	47144898	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	GAGTGGCATCTATTATCTGGGAGAAGAGGATC	novel	NA	P-0010343-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	82	470	0	ENST00000409792.3:c.4840-16_4855dup	p.Gln1619ArgfsTer7	p.Q1619Rfs*7	ENST00000409792	NM_014159.6	1619	caa/cGATCCTCTTCTCCCAGATAATAGATGCCACTCaa	7/21	0.602926699681862	1	FACETS	0.515	0.457	0.576	0.515	0.457	0.576	SUBCLONAL	1	TRUE	0	0.602926699681862	1		470	369	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122931	2122931	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010343-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	59	875	0	ENST00000219476.3:c.2302C>G	p.Pro768Ala	p.P768A	ENST00000219476	NM_000548.3	768	Cca/Gca	21/42	0.54315276558484	2	FACETS	0.191	0.164	0.222	0.096	0.082	0.111	SUBCLONAL	1	TRUE	0	0.602926699681862	2		875	1023	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604696	48604699	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	GAAA	GAAA	TTGAT	novel	NA	P-0010343-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	249	501	1	ENST00000342988.3:c.1518_1521delinsTTGAT	p.Lys507Ter	p.K507*	ENST00000342988	NM_005359.5	506	gtGAAA/gtTTGAT	12/12	0.527270526894659	2	FACETS	0.839	0.795	0.884	0.839	0.795	0.884	CLONAL	2	TRUE	0	0.602926699681862	2		502	492	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112910835	112910835	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397507529	NA	P-0010920-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	47	485	2	ENST00000351677.2:c.844A>G	p.Ile282Val	p.I282V	ENST00000351677	NM_002834.3	282	Atc/Gtc	7/16	1	2	FACETS	0.398	0.335	0.468	0.398	0.335	0.468	SUBCLONAL	1	TRUE	1	0.351731870274504	2		487	671	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123880935	123880935	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010920-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	52	373	0	ENST00000330479.4:c.553T>G	p.Tyr185Asp	p.Y185D	ENST00000330479	NM_020382.3	185	Tac/Gac	5/9	1	2	FACETS	0.566	0.482	0.659	0.566	0.482	0.659	SUBCLONAL	1	TRUE	1	0.351731870274504	2		373	522	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52661328	52661328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010920-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	29	389	0	ENST00000394830.3:c.1502C>T	p.Ser501Phe	p.S501F	ENST00000394830	NM_018313.4	501	tCt/tTt	14/30	1	2	FACETS	0.341	0.273	0.418	0.341	0.273	0.418	SUBCLONAL	1	TRUE	1	0.351731870274504	2		389	484	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841271	15841271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768133914	NA	P-0010920-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	62	259	0	ENST00000307771.7:c.1355G>A	p.Arg452His	p.R452H	ENST00000307771	NM_005089.3	452	cGc/cAc	11/11	1	1	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	0	0.351731870274504	1		259	275	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476376	88476376	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	73	523	0	ENST00000360948.2:c.1756C>A	p.Gln586Lys	p.Q586K	ENST00000360948	NM_001012338.2	586	Cag/Aag	15/19	1	2	FACETS	0.779	0.681	0.885	1	0.975	1	SUBCLONAL	2	TRUE	1	0.13	2		523	721	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426127	47426127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	64	729	0	ENST00000377045.4:c.647C>T	p.Pro216Leu	p.P216L	ENST00000377045	NM_001654.4	216	cCc/cTc	7/16	1	2	FACETS	0.997	0.86	1	0.997	0.86	1	CLONAL	1	TRUE	1	0.13	2		729	988	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	110	545	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.380056116126439	3	FACETS	1	0.955	1	0.552	0.497	0.611	CLONAL	1	TRUE	1	0.387788549382883	3		545	613	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947827	178947827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	93	322	0	ENST00000263967.3:c.2702G>T	p.Cys901Phe	p.C901F	ENST00000263967	NM_006218.2	901	tGt/tTt	19/21	0.380056116126439	3	FACETS	0.958	0.862	1	0.958	0.862	1	CLONAL	2	TRUE	1	0.387788549382883	3		322	299	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260644	1260644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1278994586	NA	P-0011193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	136	562	0	ENST00000310581.5:c.2915G>A	p.Arg972His	p.R972H	ENST00000310581	NM_198253.2	972	cGc/cAc	12/16	0.348216606698679	4	FACETS	1	0.966	1	0.564	0.513	0.618	CLONAL	1	TRUE	2	0.387788549382883	4		562	863	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519988	NA	P-0012630-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	491	677	0	ENST00000269305.4:c.808T>C	p.Phe270Leu	p.F270L	ENST00000269305	NM_001126112.2	270	Ttt/Ctt	8/11	0.656720676182665	2	FACETS	0.985	0.954	1	0.985	0.954	1	CLONAL	2	TRUE	0	0.675622567154239	2		677	738	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354369	354369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012630-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	254	682	0	ENST00000262320.3:c.1189G>A	p.Glu397Lys	p.E397K	ENST00000262320	NM_003502.3	397	Gag/Aag	5/11	0.675622567154239	3	FACETS	0.979	0.916	1	0.489	0.458	0.522	CLONAL	1	TRUE	1	0.675622567154239	3		682	1028	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905098	50905098	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013299-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1753	262	1077	1	ENST00000440232.2:c.380C>T	p.Ala127Val	p.A127V	ENST00000440232	NM_002691.3	127	gCc/gTc	4/27	NA	2	FACETS	0.483	0.451	0.517			1	INDETERMINATE	1	TRUE	NA	0.538220622444061	2		1078	2015	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579524	7579540	+	frameshift_variant	Frame_Shift_Del	DEL	TGAACCATTGTTCAATA	TGAACCATTGTTCAATA	-	novel	NA	P-0013299-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	249	616	0	ENST00000269305.4:c.147_163del	p.Ile50Ter	p.I50*	ENST00000269305	NM_001126112.2	49	gaTATTGAACAATGGTTCAct/gact	4/11	0.377657335018529	0	FACETS	0.675	0.636	0.715			1	SUBCLONAL	1	TRUE	0	0.538220622444061	0		616	633	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844244	68844244	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs943875725	NA	P-0013539-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	65	552	0	ENST00000261769.5:c.832G>C	p.Gly278Arg	p.G278R	ENST00000261769	NM_004360.3	278	Gga/Cga	6/16	0.181862212416306	1	FACETS	0.94	0.815	1	0.94	0.815	1	CLONAL	1	TRUE	0	0.181862212416306	1		552	691	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645935	67645935	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	268	190	0	ENST00000264010.4:c.863A>G	p.His288Arg	p.H288R	ENST00000264010	NM_006565.3	288	cAc/cGc	4/12	0.70500273537619	1	FACETS	0.9	0.854	0.947	0.9	0.854	0.947	CLONAL	1	FALSE	0	0.714918563006533	1		190	535	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111547	8111565	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TACAAGCTTCACAATGTAA	TACAAGCTTCACAATGTAA	-	novel	NA	P-0014121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	160	243	0	ENST00000346208.3:c.1033_1047+4del		p.X345_splice	ENST00000346208		345		5/6	1	2	FACETS	0.65	0.597	0.704	0.65	0.597	0.704	SUBCLONAL	1	FALSE	1	0.714918563006533	2		243	689	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274172	10274172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567354612	NA	P-0014121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	163	215	1	ENST00000330684.3:c.97G>A	p.Ala33Thr	p.A33T	ENST00000330684	NM_001134407.1	33	Gcg/Acg	2/13	0.714918563006533	4	FACETS	0.979	0.899	1	0.326	0.299	0.354	CLONAL	1	FALSE	1	0.714918563006533	4		216	799	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0014259-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	11	485	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.568562717417845	1	FACETS	0.769	0.556	1	0.769	0.556	1	CLONAL	1	TRUE	0	0.568562717417845	1		485	36	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119666144	119666144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775155403	NA	P-0014259-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	11	465	0	ENST00000316626.5:c.337C>T	p.Arg113Cys	p.R113C	ENST00000316626		113	Cgt/Tgt	3/12	0.414806536169635	4	FACETS	0.759	0.545	1	0.759	0.545	1	CLONAL	2	TRUE	2	0.568562717417845	4		465	40	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870904	12870904	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs748854742	NA	P-0014464-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	73	481	0	ENST00000228872.4:c.131A>G	p.Asp44Gly	p.D44G	ENST00000228872	NM_004064.3	44	gAc/gGc	1/3	1	2	FACETS	0.935	0.821	1	0.935	0.821	1	CLONAL	1	TRUE	1	0.374594036331824	2		481	417	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717732	89717749	+	inframe_deletion	In_Frame_Del	DEL	ATCAAAGTAGAGTTCTTC	ATCAAAGTAGAGTTCTTC	-	novel	NA	P-0014477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	182	389	0	ENST00000371953.3:c.757_774del	p.Ile253_Phe258del	p.I253_F258del	ENST00000371953	NM_000314.4	253	ATCAAAGTAGAGTTCTTC/-	7/9	0.656748260807382	1	FACETS	0.87	0.812	0.928	0.87	0.812	0.928	CLONAL	1	TRUE	0	0.656748260807382	1		389	428	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115897	8115900	+	protein_altering_variant	In_Frame_Del	DEL	ATGC	ATGC	G	novel	NA	P-0014477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	168	449	0	ENST00000346208.3:c.1243_1246delinsG	p.Met415_Leu416delinsVal	p.M415_L416delinsV	ENST00000346208		415	ATGCtg/Gtg	6/6	0.274144479371148	1	FACETS	0.717	0.665	0.771	0.717	0.665	0.771	INDETERMINATE	1	TRUE	0	0.656748260807382	1		449	479	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591125	67591267	+	splice_donor_variant,splice_acceptor_variant,stop_lost,protein_altering_variant,intron_variant	Splice_Site	DEL	TGAGAAAGACGAGAGACCAATACTTGATGTAAGTATTTGAAATGGAATCCTATACATGAATAATTGGTGATTGCTACAATTCAGGATGAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGGTTGACTCAAAAAGGTG	TGAGAAAGACGAGAGACCAATACTTGATGTAAGTATTTGAAATGGAATCCTATACATGAATAATTGGTGATTGCTACAATTCAGGATGAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGGTTGACTCAAAAAGGTG	-	novel	NA	P-0014628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	48	322	0	ENST00000274335.5:c.1719_1766del		p.X573_splice	ENST00000274335		573	cTGAGAAAGACGAGAGACCAATACTTGATGTAAGTATTTGAAATGGAATCCTATACATGAATAATTGGTGATTGCTACAATTCAGGATGAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGGTTGACTCAAAAAGGTGtt/ctt	12-13/15	1	2	FACETS	0.807	0.681	0.946	0.807	0.681	0.946	CLONAL	1	FALSE	1	0.183901603904086	2		322	647	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061238	38061239	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGAGTCCGGGTGCAGCGTCCAGTA	novel	NA	P-0014829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	126	885	0	ENST00000250448.2:c.727_750dup	p.Tyr243_Ser250dup	p.Y243_S250dup	ENST00000250448	NM_004496.3	243	-/TACTGGACGCTGCACCCGGACTCC	2/2	0.260589788260999	6	FACETS	0.978	0.886	1	0.652	0.591	0.717	CLONAL	2	TRUE	3	0.260589788260999	6		885	752	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	137	712	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.195961761388024	4	FACETS	1	0.958	1	1	0.989	1	CLONAL	3	TRUE	2	0.260589788260999	4		712	414	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857311	68857312	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	98	625	0	ENST00000261769.5:c.1947dup	p.Ile650TyrfsTer13	p.I650Yfs*13	ENST00000261769	NM_004360.3	649	tct/tcTt	13/16	0.260589788260999	1	FACETS	1	0.969	1	1	0.989	1	CLONAL	2	TRUE	0	0.260589788260999	1		625	279	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206722	36206722	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	211	1131	0	ENST00000300305.3:c.790C>T	p.Gln264Ter	p.Q264*	ENST00000300305		264	Cag/Tag	6/8	0.210228053436904	3	FACETS	0.861	0.802	0.92	1	0.989	1	CLONAL	3	TRUE	1	0.260589788260999	3		1131	709	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117425	115117450	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTGGTATTTGTGCATGGAGTTCAA	GGCTGGTATTTGTGCATGGAGTTCAA	C	novel	NA	P-0014829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	101	669	0	ENST00000257566.3:c.724_749delinsG	p.Leu242AlafsTer6	p.L242Afs*6	ENST00000257566	NM_016569.3	242	TTGAACTCCATGCACAAATACCAGCCc/Gc	4/8	0.167598416438659	4	FACETS	0.958	0.86	1	0.958	0.86	1	CLONAL	2	TRUE	2	0.260589788260999	4		669	510	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645920	67645920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567609067	NA	P-0014829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	79	945	1	ENST00000264010.4:c.848G>A	p.Arg283His	p.R283H	ENST00000264010	NM_006565.3	283	cGt/cAt	4/12	0.260589788260999	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.260589788260999	1		946	434	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015040-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	231	532	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.928	0.868	0.988	0.928	0.868	0.988	CLONAL	1	TRUE	1	0.67951022930277	2		533	733	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577595	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0015040-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	273	389	0	ENST00000269305.4:c.686_687del	p.Cys229TyrfsTer10	p.C229Yfs*10	ENST00000269305	NM_001126112.2	229	tGT/t	7/11	0.67951022930277	1	FACETS	0.956	0.907	1	0.956	0.907	1	CLONAL	1	TRUE	0	0.67951022930277	1		389	555	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339864	116339864	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015040-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	293	369	0	ENST00000397752.3:c.726A>T	p.Arg242Ser	p.R242S	ENST00000397752	NM_000245.2	242	agA/agT	2/21	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.67951022930277	2		369	793	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121522	2121522	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015043-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	87	596	0	ENST00000219476.3:c.1852del	p.Leu618CysfsTer80	p.L618Cfs*80	ENST00000219476	NM_000548.3	617	ttC/tt	18/42	0.75212069567379	1	FACETS	0.159	0.14	0.179	0.159	0.14	0.179	SUBCLONAL	1	TRUE	0	0.75212069567379	1		596	907	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288967	33288969	+	inframe_deletion	In_Frame_Del	DEL	CAG	CAG	-	novel	NA	P-0015043-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	305	383	0	ENST00000374542.5:c.583_585del	p.Leu195del	p.L195del	ENST00000374542	NM_001141970.1	195	CTG/-	3/8	0.75212069567379	1	FACETS	0.899	0.857	0.94	0.899	0.857	0.94	CLONAL	1	TRUE	0	0.75212069567379	1		383	563	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136298	2136299	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015043-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	473	712	0	ENST00000219476.3:c.4767_4768insT	p.Asp1590Ter	p.D1590*	ENST00000219476	NM_000548.3	1589	-/T	37/42	0.75212069567379	1	FACETS	0.786	0.755	0.818	0.786	0.755	0.818	SUBCLONAL	1	TRUE	0	0.75212069567379	1		712	998	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0015149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	367	597	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.47440465655307	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.47440465655307	2		597	687	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101125	41101125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756719404	NA	P-0015149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	48	543	1	ENST00000373198.4:c.1231G>A	p.Gly411Ser	p.G411S	ENST00000373198	NM_133170.3	411	Ggc/Agc	8/32	0.396851890284414	4	FACETS	0.314	0.264	0.369	0.157	0.132	0.185	SUBCLONAL	1	TRUE	2	0.47440465655307	4		544	951	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439913	56439914	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0015149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	436	584	0	ENST00000407977.2:c.678_679del	p.His226GlnfsTer32	p.H226Qfs*32	ENST00000407977		226	caCAgc/cagc	6/10	0.47440465655307	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.47440465655307	2		584	803	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	84	532	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.698	0.616	0.787	0.698	0.616	0.787	SUBCLONAL	1	TRUE	1	0.27	2		533	891	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602662	10602662	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1457377196	NA	P-0015556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	105	689	0	ENST00000171111.5:c.916G>T	p.Glu306Ter	p.E306*	ENST00000171111	NM_203500.1	306	Gag/Tag	3/6	0.227369517864003	1	FACETS	0.664	0.594	0.739	0.664	0.594	0.739	SUBCLONAL	1	TRUE	0	0.27	1		689	1013	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503787	186503789	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs1560084666	NA	P-0015556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	102	611	11	ENST00000323963.5:c.470_472del	p.Val157del	p.V157del	ENST00000323963		155	aTTGtt/att	5/11	1	2	FACETS	0.715	0.638	0.797	0.715	0.638	0.797	SUBCLONAL	1	TRUE	1	0.27	2		622	1057	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056429	26056429	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	43	339	0	ENST00000343677.2:c.228del	p.Asn76LysfsTer13	p.N76Kfs*13	ENST00000343677	NM_005319.3	76	aaC/aa	1/1	1	2	FACETS	0.563	0.47	0.666	0.563	0.47	0.666	SUBCLONAL	1	TRUE	1	0.27	2		339	566	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023100	150023100	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	129	633	0	ENST00000253339.5:c.163A>T	p.Ser55Cys	p.S55C	ENST00000253339		55	Agt/Tgt	1/7	1	2	FACETS	0.869	0.787	0.957	0.869	0.787	0.957	CLONAL	1	TRUE	1	0.27	2		633	1099	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255972	16255972	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015619-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	56	492	0	ENST00000375759.3:c.3237G>T	p.Arg1079Ser	p.R1079S	ENST00000375759	NM_015001.2	1079	agG/agT	11/15	1	2	FACETS	0.305	0.261	0.353	0.305	0.261	0.353	SUBCLONAL	1	TRUE	1	0.7	2		492	524	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3824569	3824569	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0015619-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	204	270	0	ENST00000262367.5:c.2283+1del		p.X761_splice	ENST00000262367	NM_004380.2	761			0.685979241247041	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.7	2		270	280	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122774	7122774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752500268	NA	P-0015619-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	169	482	0	ENST00000302850.5:c.3380G>A	p.Gly1127Asp	p.G1127D	ENST00000302850	NM_000208.2	1127	gGc/gAc	19/22	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.7	2		482	458	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117874166	117874166	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015619-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	42	227	0	ENST00000297338.2:c.288del	p.Pro97LeufsTer28	p.P97Lfs*28	ENST00000297338	NM_006265.2	96	ctG/ct	4/14	1	2	FACETS	0.316	0.264	0.373	0.316	0.264	0.373	SUBCLONAL	1	TRUE	1	0.7	2		227	380	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061313	38061313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1204900727	NA	P-0015960-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	102	714	0	ENST00000250448.2:c.676G>A	p.Asp226Asn	p.D226N	ENST00000250448	NM_004496.3	226	Gac/Aac	2/2	0.319461702938713	5	FACETS	0.817	0.735	0.904	0.545	0.49	0.603	CLONAL	2	TRUE	2	0.45113176148304	5		714	464	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589606	67589611	+	inframe_deletion	In_Frame_Del	DEL	CAAGAA	CAAGAA	-	novel	NA	P-0015960-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	75	366	0	ENST00000274335.5:c.1369_1374del	p.Gln457_Glu458del	p.Q457_E458del	ENST00000274335		457	CAAGAA/-	10/15	0.286136113560802	3	FACETS	1	0.909	1	0.679	0.607	0.754	CLONAL	2	TRUE	0	0.45113176148304	3		366	200	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202925	27202925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749958421	NA	P-0015960-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	72	561	0	ENST00000380036.4:c.2017C>T	p.Arg673Cys	p.R673C	ENST00000380036	NM_000459.3	673	Cgt/Tgt	13/23	0.45113176148304	7	FACETS	0.836	0.73	0.952	0.167	0.146	0.191	CLONAL	1	TRUE	2	0.45113176148304	7		561	812	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352464	118352464	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015960-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	38	522	0	ENST00000534358.1:c.3669T>A	p.Ser1223Arg	p.S1223R	ENST00000534358	NM_005933.3	1223	agT/agA	7/36	0.45113176148304	3	FACETS	0.554	0.458	0.66	0.277	0.229	0.33	SUBCLONAL	1	TRUE	1	0.45113176148304	3		522	373	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0016054-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	207	641	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.234816126951681	4	FACETS	0.921	0.853	0.991	0.921	0.853	0.991	CLONAL	2	TRUE	2	0.234765218240521	4		641	1182	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272410	38272410	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121909628	NA	P-0016054-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	77	393	0	ENST00000425967.3:c.1957C>T	p.Arg653Ter	p.R653*	ENST00000425967	NM_001174067.1	653	Cga/Tga	15/19	0.196804812098469	2	FACETS	0.948	0.832	1	0.474	0.416	0.537	CLONAL	1	TRUE	0	0.234765218240521	2		393	692	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45422926	45422926	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016054-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	116	396	0	ENST00000262160.6:c.202C>T	p.Gln68Ter	p.Q68*	ENST00000262160	NM_005901.5	68	Caa/Taa	2/11	0.199763435434619	3	FACETS	0.969	0.876	1	0.969	0.876	1	CLONAL	2	TRUE	1	0.234765218240521	3		396	570	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392173	81392173	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016054-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	73	294	0	ENST00000222390.5:c.104G>C	p.Arg35Thr	p.R35T	ENST00000222390	NM_000601.4	35	aGa/aCa	2/18	0.234816126951681	4	FACETS	0.765	0.67	0.866	0.765	0.67	0.866	SUBCLONAL	2	TRUE	2	0.234765218240521	4		294	502	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226125	53226125	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016054-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	72	573	0	ENST00000375401.3:c.2724del	p.Arg909GlyfsTer26	p.R909Gfs*26	ENST00000375401	NM_004187.3	908	ggG/gg	19/26	1	2	FACETS	0.612	0.533	0.698	0.612	0.533	0.698	SUBCLONAL	1	TRUE	1	0.234765218240521	2		573	1002	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783767	50783767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375455772	NA	P-0016054-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	109	742	0	ENST00000398568.2:c.158G>A	p.Arg53His	p.R53H	ENST00000398568	NM_001042412.1	53	cGt/cAt	3/18	0.234816126951681	3	FACETS	0.836	0.748	0.93			1	CLONAL	1	TRUE	NA	0.234765218240521	3		742	1241	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180479	38180489	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCCGCGACG	GGGCCGCGACG	-	novel	NA	P-0016054-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	60	499	0	ENST00000396334.3:c.327_337del	p.Gly110ArgfsTer10	p.G110Rfs*10	ENST00000396334	NM_002468.4	109	ctGGGCCGCGACGac/ctac	1/5	0.234816126951681	3	FACETS	0.612	0.526	0.707	0.306	0.263	0.354	SUBCLONAL	1	TRUE	1	0.234765218240521	3		499	933	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0016549-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	232	673	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.526813443883132	5	FACETS	1	0.991	1	0.468	0.436	0.502	CLONAL	1	TRUE	2	0.526813443883132	5		673	1122	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0016549-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	573	576	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.526813443883132	5	FACETS	0.991	0.954	1	0.991	0.954	1	CLONAL	3	TRUE	2	0.526813443883132	5		576	1310	SUCCESS
APC	324	MSKCC	GRCh37	5	112102960	112102960	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139196838	NA	P-0016549-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	160	472	0	ENST00000257430.4:c.295C>T	p.Arg99Trp	p.R99W	ENST00000257430	NM_000038.5	99	Cgg/Tgg	4/16	0.362645814665005	3	FACETS	1	0.925	1	0.504	0.462	0.547	CLONAL	1	TRUE	1	0.526813443883132	3		472	762	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931589	NA	P-0016549-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	86	363	0	ENST00000349496.5:c.101G>A	p.Gly34Glu	p.G34E	ENST00000349496	NM_001904.3	34	gGa/gAa	3/15	1	2	FACETS	0.668	0.593	0.747	0.668	0.593	0.747	SUBCLONAL	1	TRUE	1	0.526813443883132	2		363	489	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088759	27088759	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016549-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	208	571	1	ENST00000324856.7:c.2368C>T	p.Gln790Ter	p.Q790*	ENST00000324856	NM_006015.4	790	Cag/Tag	7/20	0.303651230272235	1	FACETS	0.86	0.802	0.92	0.86	0.802	0.92	INDETERMINATE	1	TRUE	0	0.526813443883132	1		572	676	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274175	18274175	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016549-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	222	672	0	ENST00000222254.8:c.1393G>A	p.Glu465Lys	p.E465K	ENST00000222254	NM_005027.3	465	Gaa/Aaa	11/16	1	2	FACETS	0.981	0.915	1	0.981	0.915	1	CLONAL	1	TRUE	1	0.526813443883132	2		672	859	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0017322-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	50	367	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.16	2		367	572	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11273560	11273560	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017322-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	61	422	0	ENST00000361445.4:c.3181G>T	p.Val1061Leu	p.V1061L	ENST00000361445	NM_004958.3	1061	Gta/Tta	21/58	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.16	2		422	597	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041897	42041897	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs760287422	NA	P-0017322-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	55	319	0	ENST00000219905.7:c.6092A>T	p.His2031Leu	p.H2031L	ENST00000219905	NM_001164273.1	2031	cAt/cTt	17/24	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.16	2		319	599	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528847	157528847	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017322-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	74	472	0	ENST00000346085.5:c.6572del	p.Ser2191ThrfsTer2	p.S2191Tfs*2	ENST00000346085	NM_020732.3	2191	aGc/ac	20/20	1	2	FACETS	0.823	0.721	0.932	1	0.978	1	CLONAL	2	TRUE	1	0.16	2		472	562	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863304	56863304	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017322-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	75	448	0	ENST00000519728.1:c.448G>C	p.Ala150Pro	p.A150P	ENST00000519728	NM_002350.3	150	Gct/Cct	6/13	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.16	2		448	843	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356425	70356425	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017322-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	71	629	1	ENST00000374080.3:c.5320G>T	p.Ala1774Ser	p.A1774S	ENST00000374080		1774	Gct/Tct	37/45	0.259007612542608	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.16	1		630	650	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495796	56495796	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017627-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	17	359	0	ENST00000267101.3:c.3986G>A	p.Trp1329Ter	p.W1329*	ENST00000267101	NM_001982.3	1329	tGg/tAg	28/28	1	2	FACETS	0.383	0.285	0.501	0.383	0.285	0.501	SUBCLONAL	1	TRUE	1	0.212255054254976	2		359	418	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048253	180048253	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0017627-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	14	617	0	ENST00000261937.6:c.2021-1G>T		p.X674_splice	ENST00000261937	NM_182925.4	674			0.119014948963955	5	FACETS	0.204	0.146	0.275	0.051	0.036	0.069	INDETERMINATE	1	TRUE	1	0.212255054254976	5		617	853	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242487	+	protein_altering_variant	In_Frame_Del	DEL	GAATTAAGAGAAGCAACATCTC	GAATTAAGAGAAGCAACATCTC	CTCT	novel	NA	P-0017627-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	41	502	2	ENST00000275493.2:c.2236_2257delinsCTCT	p.Glu746_Pro753delinsLeuSer	p.E746_P753delinsLS	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCAACATCTCcg/CTCTcg	19/28	1	2	FACETS	0.656	0.545	0.779	0.656	0.545	0.779	SUBCLONAL	1	TRUE	1	0.212255054254976	2		504	589	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740325	145740328	+	frameshift_variant	Frame_Shift_Del	DEL	CATC	CATC	-	novel	NA	P-0017627-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	42	670	0	ENST00000428558.2:c.1612_1615del	p.Asp538ThrfsTer19	p.D538Tfs*19	ENST00000428558	NM_004260.3	538	GATGac/ac	9/22	0.212255054254976	3	FACETS	0.492	0.409	0.585	0.246	0.204	0.293	SUBCLONAL	1	TRUE	1	0.212255054254976	3		670	889	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0018142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	186	283	0				ENST00000310581	NM_198253.2	-/1132			0.579831087249362	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.579831087249362	3		283	352	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197842	123197842	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	280	349	0	ENST00000218089.9:c.1966C>T	p.Gln656Ter	p.Q656*	ENST00000218089	NM_001042749.1	656	Caa/Taa	20/35	0.565411824206213	2	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.579831087249362	2		349	400	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582195	189582195	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	78	463	0	ENST00000264731.3:c.754G>A	p.Glu252Lys	p.E252K	ENST00000264731	NM_003722.4	252	Gaa/Aaa	5/14	0.579831087249362	6	FACETS	0.763	0.669	0.863	0.254	0.223	0.288	SUBCLONAL	1	TRUE	3	0.579831087249362	6		463	762	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982403	201982404	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0018142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	809	881	0	ENST00000359651.3:c.783dup	p.Glu262ArgfsTer39	p.E262Rfs*39	ENST00000359651		261	ctc/ctCc	6/8	0.579831087249362	4	FACETS	0.988	0.966	1	0.988	0.966	1	CLONAL	4	TRUE	0	0.579831087249362	4		881	1115	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409107	4409107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3217921	NA	P-0018142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	118	527	0	ENST00000261254.3:c.802G>A	p.Gly268Arg	p.G268R	ENST00000261254	NM_001759.3	268	Gga/Aga	5/5	0.54958727512715	4	FACETS	0.936	0.846	1	0.468	0.423	0.516	CLONAL	1	TRUE	2	0.579831087249362	4		527	687	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003254	42003254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	174	744	0	ENST00000219905.7:c.2791C>T	p.His931Tyr	p.H931Y	ENST00000219905	NM_001164273.1	931	Cat/Tat	8/24	0.567886736739656	3	FACETS	1	0.932	1	0.505	0.466	0.546	CLONAL	1	TRUE	1	0.579831087249362	3		744	766	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059086	42059086	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	244	422	2	ENST00000219905.7:c.8806G>T	p.Asp2936Tyr	p.D2936Y	ENST00000219905	NM_001164273.1	2936	Gat/Tat	24/24	0.567886736739656	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.579831087249362	3		424	491	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892152	9892152	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	150	724	4	ENST00000330684.3:c.2338C>A	p.Leu780Ile	p.L780I	ENST00000330684	NM_001134407.1	780	Ctt/Att	11/13	0.54958727512715	4	FACETS	0.974	0.891	1	0.487	0.445	0.531	CLONAL	1	TRUE	2	0.579831087249362	4		728	839	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56872979	56872979	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs1292577738	NA	P-0018142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	168	251	0	ENST00000308159.5:c.2134G>C	p.Asp712His	p.D712H	ENST00000308159	NM_014669.4	712	Gat/Cat	19/22	0.54958727512715	4	FACETS	0.845	0.789	0.902	1	0.987	1	CLONAL	3	TRUE	2	0.579831087249362	4		251	361	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145770	11145770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	154	758	1	ENST00000358026.2:c.4132G>A	p.Asp1378Asn	p.D1378N	ENST00000358026	NM_001128849.1	1378	Gac/Aac	29/36	0.579831087249362	4	FACETS	0.874	0.799	0.952	0.219	0.199	0.238	CLONAL	1	TRUE	0	0.579831087249362	4		759	960	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212120	36212120	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	37	523	0	ENST00000222270.7:c.1871C>A	p.Ala624Asp	p.A624D	ENST00000222270	NM_014727.1	624	gCc/gAc	3/37	0.579831087249362	4	FACETS	0.313	0.257	0.376	0.078	0.064	0.094	SUBCLONAL	1	TRUE	0	0.579831087249362	4		523	644	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61753572	61753572	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	282	658	2	ENST00000401558.2:c.211C>A	p.Gln71Lys	p.Q71K	ENST00000401558	NM_003400.3	71	Cag/Aag	3/25	0.567886736739656	3	FACETS	0.841	0.794	0.888	0.841	0.794	0.888	CLONAL	2	TRUE	1	0.579831087249362	3		660	746	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030918	36030918	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	149	700	0	ENST00000358208.4:c.1197G>C	p.Glu399Asp	p.E399D	ENST00000358208		399	gaG/gaC	10/12	0.567886736739656	3	FACETS	0.971	0.889	1	0.485	0.444	0.528	CLONAL	1	TRUE	1	0.579831087249362	3		700	683	SUCCESS
APC	324	MSKCC	GRCh37	5	112178786	112178786	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs33941929	NA	P-0018142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	230	534	0	ENST00000257430.4:c.7495G>C	p.Val2499Leu	p.V2499L	ENST00000257430	NM_000038.5	2499	Gtt/Ctt	16/16	0.567886736739656	3	FACETS	0.967	0.911	1	0.967	0.911	1	CLONAL	2	TRUE	1	0.579831087249362	3		534	529	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721105	176721105	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	77	506	0	ENST00000439151.2:c.6736C>T	p.Gln2246Ter	p.Q2246*	ENST00000439151	NM_022455.4	2246	Cag/Tag	23/23	0.579831087249362	3	FACETS	0.779	0.686	0.877	0.389	0.343	0.439	SUBCLONAL	1	TRUE	1	0.579831087249362	3		506	440	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631349	117631349	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs763571645	NA	P-0018142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	124	523	0	ENST00000368508.3:c.6329A>C	p.Tyr2110Ser	p.Y2110S	ENST00000368508	NM_002944.2	2110	tAt/tCt	40/43	0.300275430821183	5	FACETS	1	0.977	1	0.416	0.377	0.457	INDETERMINATE	1	TRUE	2	0.579831087249362	5		523	641	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201851	152201851	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	139	579	0	ENST00000206249.3:c.705G>C	p.Lys235Asn	p.K235N	ENST00000206249	NM_000125.3	235	aaG/aaC	3/8	0.300275430821183	5	FACETS	1	0.984	1	0.448	0.409	0.489	INDETERMINATE	1	TRUE	2	0.579831087249362	5		579	667	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157256609	157256609	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	107	409	0	ENST00000346085.5:c.1936C>G	p.Gln646Glu	p.Q646E	ENST00000346085	NM_020732.3	646	Cag/Gag	5/20	0.300275430821183	5	FACETS	1	0.971	1	0.406	0.365	0.449	INDETERMINATE	1	TRUE	2	0.579831087249362	5		409	567	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931901	68931901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	185	725	0	ENST00000288368.4:c.331C>T	p.His111Tyr	p.H111Y	ENST00000288368	NM_024870.2	111	Cac/Tac	3/40	0.54958727512715	4	FACETS	1	0.943	1	0.513	0.473	0.554	CLONAL	1	TRUE	2	0.579831087249362	4		725	983	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0018666-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	728	350	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.45501770906784	2	FACETS	0.844	0.825	0.862	0.844	0.825	0.862	INDETERMINATE	2	TRUE	0	0.89859521382946	2		350	960	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117870639	117870639	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1360712011	NA	P-0018666-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	271	355	0	ENST00000297338.2:c.433A>C	p.Met145Leu	p.M145L	ENST00000297338	NM_006265.2	145	Atg/Ctg	5/14	1	2	FACETS	0.847	0.799	0.896	0.847	0.799	0.896	CLONAL	1	TRUE	1	0.89859521382946	2		355	712	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0018882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	585	601	7	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.740678147451705	2	FACETS	0.968	0.943	0.991	0.968	0.943	0.991	CLONAL	2	TRUE	0	0.781183828439384	2		608	774	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835596	68835596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587783047	NA	P-0018882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	266	516	1	ENST00000261769.5:c.187C>T	p.Arg63Ter	p.R63*	ENST00000261769	NM_004360.3	63	Cga/Tga	3/16	0.781183828439384	1	FACETS	0.993	0.949	1	0.993	0.949	1	CLONAL	1	TRUE	0	0.781183828439384	1		517	418	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409944	63409944	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	263	469	0	ENST00000330258.3:c.3223G>C	p.Ala1075Pro	p.A1075P	ENST00000330258	NM_152424.3	1075	Gcc/Ccc	2/2	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.781183828439384	2		469	637	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974722	15974722	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0018882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	338	450	0	ENST00000268712.3:c.4152+1del		p.X1384_splice	ENST00000268712	NM_006311.3	1384			0.740678147451705	2	FACETS	0.974	0.943	1	0.974	0.943	1	CLONAL	2	TRUE	0	0.781183828439384	2		450	444	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206728	36206728	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	348	648	0	ENST00000300305.3:c.784C>T	p.Gln262Ter	p.Q262*	ENST00000300305		262	Cag/Tag	6/8	0.326549957411352	3	FACETS	0.757	0.721	0.794	0.757	0.721	0.794	INDETERMINATE	2	TRUE	1	0.781183828439384	3		648	818	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375483	118375483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	51	268	0	ENST00000534358.1:c.8876G>A	p.Gly2959Glu	p.G2959E	ENST00000534358	NM_005933.3	2959	gGg/gAg	27/36	0.629749721991607	3	FACETS	0.808	0.694	0.932	0.269	0.231	0.311	CLONAL	1	TRUE	0	0.697343153643311	3		268	244	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170454	11170454	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	35	593	0	ENST00000358026.2:c.4757A>T	p.Gln1586Leu	p.Q1586L	ENST00000358026	NM_001128849.1	1586	cAg/cTg	34/36	0.697343153643311	3	FACETS	0.202	0.165	0.244	0.101	0.082	0.122	SUBCLONAL	1	TRUE	1	0.697343153643311	3		593	669	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600464	10600464	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019765-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	1700	659	1	ENST00000171111.5:c.1391G>T	p.Gly464Val	p.G464V	ENST00000171111	NM_203500.1	464	gGc/gTc	4/6	0.664998938112831	3	FACETS	0.955	0.941	0.969	0.955	0.941	0.969	CLONAL	3	TRUE	0	0.698586728604546	3		660	2292	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974799	21974799	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019765-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	183	71	0	ENST00000304494.5:c.28G>T	p.Glu10Ter	p.E10*	ENST00000304494	NM_000077.4	10	Gag/Tag	1/3	0.635381292341162	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.698586728604546	2		71	254	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677765	47677765	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019765-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	170	476	2	ENST00000347630.2:c.1100del	p.Pro367HisfsTer5	p.P367Hfs*5	ENST00000347630	NM_001007230.1	367	cCa/ca	11/11	0.321902932617249	2	FACETS	0.482	0.443	0.523	0.241	0.221	0.262	INDETERMINATE	1	TRUE	0	0.698586728604546	2		478	1010	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258581	16258581	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019765-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	1202	595	0	ENST00000375759.3:c.5846G>T	p.Arg1949Leu	p.R1949L	ENST00000375759	NM_015001.2	1949	cGg/cTg	11/15	0.629434779229541	3	FACETS	0.931	0.913	0.948	0.931	0.913	0.948	CLONAL	3	TRUE	0	0.698586728604546	3		595	1663	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731181	162731181	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019765-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	581	424	0	ENST00000367921.3:c.1036A>T	p.Ile346Phe	p.I346F	ENST00000367921	NM_006182.2	346	Atc/Ttc	9/18	0.416072468512644	4	FACETS	1	0.986	1	1	0.986	1	INDETERMINATE	2	TRUE	2	0.698586728604546	4		424	1347	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944122	71944122	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019765-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	2090	613	0	ENST00000298229.2:c.1955A>T	p.Glu652Val	p.E652V	ENST00000298229	NM_001567.3	652	gAg/gTg	17/28	0.697188322641445	4	FACETS	1	0.996	1	1	0.996	1	CLONAL	4	TRUE	0	0.698586728604546	4		613	2503	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117430	115117430	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0019765-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	219	476	0	ENST00000257566.3:c.744C>G	p.Tyr248Ter	p.Y248*	ENST00000257566	NM_016569.3	248	taC/taG	4/8	0.698586728604546	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.698586728604546	1		476	407	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478604	99478604	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019765-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	615	558	0	ENST00000268035.6:c.3246G>T	p.Met1082Ile	p.M1082I	ENST00000268035	NM_000875.3	1082	atG/atT	17/21	0.326881832024273	3	FACETS	1	0.995	1	0.756	0.733	0.78	INDETERMINATE	2	TRUE	0	0.698586728604546	3		558	1047	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577542	7577561	+	frameshift_variant	Frame_Shift_Del	DEL	TCATGCCGCCCATGCAGGAA	TCATGCCGCCCATGCAGGAA	-	novel	NA	P-0019765-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	395	653	0	ENST00000269305.4:c.720_739del	p.Ser240ArgfsTer17	p.S240Rfs*17	ENST00000269305	NM_001126112.2	240	agTTCCTGCATGGGCGGCATGAac/agac	7/11	0.698586728604546	1	FACETS	0.878	0.84	0.916	0.878	0.84	0.916	CLONAL	1	TRUE	0	0.698586728604546	1		653	838	SUCCESS
YES1	7525	MSKCC	GRCh37	18	739749	739749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019765-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	678	560	0	ENST00000314574.4:c.1123G>A	p.Asp375Asn	p.D375N	ENST00000314574	NM_005433.3	375	Gat/Aat	9/12	0.698586728604546	3	FACETS	0.994	0.972	1	0.994	0.972	1	CLONAL	3	TRUE	0	0.698586728604546	3		560	878	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288740	15288741	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0019765-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	150	29	0	ENST00000263388.2:c.3998_3999delinsTT	p.Gly1333Val	p.G1333V	ENST00000263388	NM_000435.2	1333	gGG/gTT	24/33	0.664998938112831	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.698586728604546	3		29	181	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379718	17379718	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019765-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	1953	821	1	ENST00000359435.4:c.103G>T	p.Glu35Ter	p.E35*	ENST00000359435	NM_001033549.1	35	Gag/Tag	2/9	0.664998938112831	3	FACETS	0.969	0.956	0.982	0.969	0.956	0.982	CLONAL	3	TRUE	0	0.698586728604546	3		822	2595	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36217207	36217207	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019765-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3049	308	755	0	ENST00000222270.7:c.3956C>G	p.Ser1319Cys	p.S1319C	ENST00000222270	NM_014727.1	1319	tCt/tGt	14/37	0.698586728604546	3	FACETS	0.354	0.332	0.378	0.177	0.166	0.189	SUBCLONAL	1	TRUE	1	0.698586728604546	3		755	3357	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047393	128047393	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019765-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	268	357	1	ENST00000285398.2:c.529G>T	p.Val177Phe	p.V177F	ENST00000285398	NM_000122.1	177	Gtt/Ttt	5/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.698586728604546	2		358	742	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39772532	39772532	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019765-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	262	601	0	ENST00000288319.7:c.709T>C	p.Tyr237His	p.Y237H	ENST00000288319	NM_182918.3	237	Tat/Cat	6/10	0.698586728604546	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.698586728604546	1		601	457	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37622769	37622769	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019765-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	1096	692	1	ENST00000249071.6:c.523G>T	p.Ala175Ser	p.A175S	ENST00000249071	NM_002872.4	175	Gcc/Tcc	6/7	0.628350397403341	2	FACETS	0.944	0.924	0.964	0.944	0.924	0.964	CLONAL	2	TRUE	0	0.698586728604546	2		693	1662	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683507	182683507	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019765-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	82	516	0	ENST00000292782.4:c.38G>T	p.Arg13Leu	p.R13L	ENST00000292782	NM_020640.2	13	cGt/cTt	2/7	0.422198637100254	3	FACETS	0.438	0.386	0.494	0.146	0.128	0.165	SUBCLONAL	1	TRUE	0	0.698586728604546	3		516	723	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946270	55946270	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019765-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	510	294	0	ENST00000263923.4:c.3909C>G	p.Ser1303Arg	p.S1303R	ENST00000263923	NM_002253.2	1303	agC/agG	30/30	0.52293714116681	3	FACETS	0.883	0.856	0.909			1	CLONAL	3	TRUE	NA	0.698586728604546	3		294	744	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818363	170818363	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs11551576	NA	P-0019765-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	177	382	0	ENST00000296930.5:c.193A>G	p.Met65Val	p.M65V	ENST00000296930	NM_002520.6	65	Atg/Gtg	3/11	0.698586728604546	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.698586728604546	1		382	301	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976825	2976825	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019765-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1859	474	729	0	ENST00000396946.4:c.1187G>T	p.Cys396Phe	p.C396F	ENST00000396946	NM_032415.4	396	tGc/tTc	9/25	0.582126439686059	4	FACETS	0.988	0.94	1	0.329	0.313	0.346	CLONAL	1	TRUE	1	0.698586728604546	4		729	2333	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381516	81381516	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019765-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	38	345	0	ENST00000222390.5:c.545G>T	p.Gly182Val	p.G182V	ENST00000222390	NM_000601.4	182	gGg/gTg	5/18	0.416072468512644	4	FACETS	0.893	0.745	1	0.446	0.372	0.527	INDETERMINATE	1	TRUE	2	0.698586728604546	4		345	207	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319966	8319966	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019765-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	55	260	0	ENST00000356435.5:c.5535C>A	p.Ser1845Arg	p.S1845R	ENST00000356435		1845	agC/agA	34/35	0.635381292341162	2	FACETS	1	0.97	1	0.685	0.606	0.764	CLONAL	1	TRUE	0	0.698586728604546	2		260	115	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650616	48650617	+	missense_variant	Missense_Mutation	DNP	CT	CT	AA	novel	NA	P-0019765-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1537	167	650	0	ENST00000376670.3:c.586_587delinsAA	p.Leu196Lys	p.L196K	ENST00000376670	NM_002049.3	196	CTg/AAg	3/6	0.274546674626854	4	FACETS	0.477	0.436	0.519			1	INDETERMINATE	1	TRUE	NA	0.698586728604546	4		650	1704	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652384	48652384	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019765-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2426	331	822	1	ENST00000376670.3:c.1055G>T	p.Gly352Val	p.G352V	ENST00000376670	NM_002049.3	352	gGc/gTc	6/6	0.274546674626854	4	FACETS	0.584	0.549	0.62			1	INDETERMINATE	1	TRUE	NA	0.698586728604546	4		823	2757	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650823	37650823	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019819-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	116	595	0	ENST00000447079.4:c.2297del	p.Gly766AlafsTer16	p.G766Afs*16	ENST00000447079	NM_015083.1	765	gaG/ga	5/14	1	2	FACETS	0.908	0.817	1	0.908	0.817	1	CLONAL	1	TRUE	1	0.25692301488478	2		595	994	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748470	40748470	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019819-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	104	568	1	ENST00000392038.2:c.412G>T	p.Val138Leu	p.V138L	ENST00000392038	NM_001626.4	138	Gtg/Ttg	5/14	0.148617081048266	1	FACETS	0.924	0.827	1	0.924	0.827	1	INDETERMINATE	1	TRUE	0	0.25692301488478	1		569	764	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39713141	39713141	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0019819-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	77	338	1	ENST00000361337.2:c.547A>T	p.Lys183Ter	p.K183*	ENST00000361337	NM_003286.2	183	Aaa/Taa	8/21	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.25692301488478	2		339	573	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227685	53227685	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781782813	NA	P-0019819-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	80	255	0	ENST00000375401.3:c.2503G>A	p.Gly835Ser	p.G835S	ENST00000375401	NM_004187.3	835	Ggc/Agc	17/26	0.25692301488478	2	FACETS	1	0.964	1			1	CLONAL	1	TRUE	NA	0.25692301488478	2		255	503	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067131	143067131	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019857-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	124	466	1	ENST00000262992.4:c.1582G>A	p.Val528Met	p.V528M	ENST00000262992	NM_001101669.1	528	Gtg/Atg	16/24	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.31	2		467	669	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0019857-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	212	618	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.301982418815442	2	FACETS	0.801	0.745	0.858	0.801	0.745	0.858	CLONAL	2	TRUE	0	0.31	2		618	854	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0019948-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	370	442	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	0.825704004519342	4	FACETS	1	0.956	1			1	CLONAL	2	TRUE	NA	0.825704004519342	4		442	817	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052601	42052601	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0019948-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	314	440	0	ENST00000219905.7:c.7272T>G	p.Tyr2424Ter	p.Y2424*	ENST00000219905	NM_001164273.1	2424	taT/taG	20/24	0.825704004519342	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.825704004519342	2		440	367	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519938	NA	P-0020383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	53	335	0	ENST00000263967.3:c.1034A>T	p.Asn345Ile	p.N345I	ENST00000263967	NM_006218.2	345	aAt/aTt	5/21	1	2	FACETS	0.86	0.748	0.976	0.86	0.748	0.976	CLONAL	1	TRUE	1	0.780434721471446	2		335	158	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0020383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	105	443	2	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.975	0.887	1	0.975	0.887	1	CLONAL	1	TRUE	1	0.780434721471446	2		445	276	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913250	NA	P-0020383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	114	331	0	ENST00000369535.4:c.34G>T	p.Gly12Cys	p.G12C	ENST00000369535	NM_002524.4	12	Ggt/Tgt	2/7	0.780434721471446	1	FACETS	0.825	0.762	0.887	0.825	0.762	0.887	CLONAL	1	TRUE	0	0.780434721471446	1		331	216	SUCCESS
APC	324	MSKCC	GRCh37	5	112173835	112173838	+	frameshift_variant	Frame_Shift_Del	DEL	AGAT	AGAT	-	rs398123118	NA	P-0020383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	91	372	0	ENST00000257430.4:c.2547_2550del	p.Asp849GlufsTer11	p.D849Efs*11	ENST00000257430	NM_000038.5	848	aaAGAT/aa	16/16	0.780434721471446	1	FACETS	0.948	0.873	1	0.948	0.873	1	CLONAL	1	TRUE	0	0.780434721471446	1		372	150	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711272	114711273	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	275	347	0	ENST00000543371.1:c.291dup	p.Pro98AlafsTer47	p.P98Afs*47	ENST00000543371	NM_001198531.1	96	aag/aaGg	3/14	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.780434721471446	2		347	646	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120783407	120783407	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	281	647	0	ENST00000257552.2:c.1076A>G	p.Asn359Ser	p.N359S	ENST00000257552	NM_002442.3	359	aAt/aGt	14/15	1	2	FACETS	0.94	0.887	0.994	0.94	0.887	0.994	CLONAL	1	TRUE	1	0.780434721471446	2		647	766	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020500-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	49	546	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.1606950111328	1	FACETS	0.844	0.722	0.974	1	0.97	1	CLONAL	2	TRUE	0	0.225940720856366	1		546	228	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0020500-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	24	622	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.225940720856366	2		622	173	SUCCESS
APC	324	MSKCC	GRCh37	5	112175246	112175246	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1057517558	NA	P-0020500-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	26	247	0	ENST00000257430.4:c.3956del	p.Pro1319LeufsTer2	p.P1319Lfs*2	ENST00000257430	NM_000038.5	1319	Cct/ct	16/16	0.129438250795064	4	FACETS	1	0.904	1	0.627	0.499	0.772	INDETERMINATE	1	TRUE	2	0.225940720856366	4		247	225	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0020500-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	36	456	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	0.129438250795064	4	FACETS	1	0.942	1	0.69	0.57	0.824	INDETERMINATE	1	TRUE	2	0.225940720856366	4		456	283	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903763	114903763	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020500-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	28	494	0	ENST00000543371.1:c.767C>T	p.Pro256Leu	p.P256L	ENST00000543371	NM_001198531.1	256	cCg/cTg	7/14	1	2	FACETS	0.789	0.632	0.968	0.789	0.632	0.968	CLONAL	1	TRUE	1	0.225940720856366	2		494	314	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376191	118376191	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147412214	NA	P-0020500-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	39	550	4	ENST00000534358.1:c.9584C>T	p.Pro3195Leu	p.P3195L	ENST00000534358	NM_005933.3	3195	cCg/cTg	27/36	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.225940720856366	2		554	279	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351461	70351461	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020500-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	36	583	0	ENST00000374080.3:c.4109C>A	p.Thr1370Asn	p.T1370N	ENST00000374080		1370	aCc/aAc	29/45	0.141055447622199	1	FACETS	0.849	0.7	1	0.849	0.7	1	CLONAL	1	TRUE	0	0.225940720856366	1		583	333	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020836-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	108	532	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.85	0.767	0.938	0.85	0.767	0.938	CLONAL	1	TRUE	1	0.517280730048257	2		533	491	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266611	198266611	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs755415626	NA	P-0020836-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	196	404	0	ENST00000335508.6:c.2225G>A	p.Gly742Asp	p.G742D	ENST00000335508	NM_012433.2	742	gGt/gAt	16/25	0.517280730048257	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.517280730048257	2		404	374	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937664	44937665	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020836-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	75	240	0	ENST00000377967.4:c.2855dup	p.Phe953LeufsTer26	p.F953Lfs*26	ENST00000377967	NM_021140.2	951	gct/gcTt	19/29	1	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.517280730048257	1		240	184	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023372	27023373	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020836-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	128	192	0	ENST00000324856.7:c.480dup	p.Val161ArgfsTer239	p.V161Rfs*239	ENST00000324856	NM_006015.4	160	gcc/gCcc	1/20	0.517280730048257	2	FACETS	0.903	0.834	0.972	0.903	0.834	0.972	CLONAL	2	TRUE	0	0.517280730048257	2		192	274	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396319	396319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020836-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	126	673	0	ENST00000262320.3:c.707G>A	p.Gly236Glu	p.G236E	ENST00000262320	NM_003502.3	236	gGa/gAa	2/11	1	2	FACETS	0.988	0.9	1	0.988	0.9	1	CLONAL	1	TRUE	1	0.517280730048257	2		673	493	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781192	3781192	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0020836-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	118	509	0	ENST00000262367.5:c.5172+1G>A		p.X1724_splice	ENST00000262367	NM_004380.2	1724			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.517280730048257	2		509	418	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	124	454	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.972	0.892	1	0.972	0.892	1	CLONAL	1	TRUE	1	0.80260767713703	2		454	318	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0021526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	582	465	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.80260767713703	4	FACETS	1	0.989	1			1	CLONAL	3	TRUE	NA	0.80260767713703	4		465	844	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708999	117708999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34203286	NA	P-0021526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	161	393	0	ENST00000368508.3:c.1958C>T	p.Ser653Phe	p.S653F	ENST00000368508	NM_002944.2	653	tCt/tTt	13/43	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.80260767713703	2		393	356	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0021526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	185	402	0	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	1	2	FACETS	0.922	0.88	0.962	1	0.995	1	CLONAL	2	TRUE	1	0.80260767713703	2		402	250	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538897	23538897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1200957711	NA	P-0021526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	192	399	1	ENST00000380871.4:c.542G>A	p.Arg181Gln	p.R181Q	ENST00000380871	NM_006167.3	181	cGa/cAa	2/2	0.338267695682207	1	FACETS	0.668	0.625	0.71	0.668	0.625	0.71	INDETERMINATE	1	TRUE	0	0.80260767713703	1		400	429	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134255	11134255	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	209	483	0	ENST00000358026.2:c.2921C>T	p.Pro974Leu	p.P974L	ENST00000358026	NM_001128849.1	974	cCc/cTc	20/36	0.80260767713703	3	FACETS	1	0.963	1	0.525	0.489	0.562	CLONAL	1	TRUE	1	0.80260767713703	3		483	695	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169552	27169552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	250	489	1	ENST00000380036.4:c.553G>A	p.Asp185Asn	p.D185N	ENST00000380036	NM_000459.3	185	Gat/Aat	4/23	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.80260767713703	2		490	563	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980355	201980355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764832150	NA	P-0021526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	244	618	1	ENST00000359651.3:c.91C>T	p.Pro31Ser	p.P31S	ENST00000359651		31	Cct/Tct	1/8	0.80260767713703	4	FACETS	0.867	0.809	0.927	0.289	0.269	0.309	CLONAL	1	TRUE	1	0.80260767713703	4		619	1264	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359404	118359404	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	192	288	0	ENST00000534358.1:c.4408C>T	p.Gln1470Ter	p.Q1470*	ENST00000534358	NM_005933.3	1470	Cag/Tag	11/36	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.80260767713703	2		288	401	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699332	18699332	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	81	330	0	ENST00000266497.5:c.3433G>T	p.Asp1145Tyr	p.D1145Y	ENST00000266497		1145	Gac/Tac	24/31	1	2	FACETS	0.87	0.779	0.964	0.87	0.779	0.964	CLONAL	1	TRUE	1	0.80260767713703	2		330	232	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49054143	49054143	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1432581053	NA	P-0021526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	82	263	0	ENST00000267163.4:c.2723G>A	p.Arg908Gln	p.R908Q	ENST00000267163	NM_000321.2	908	cGa/cAa	27/27	1	2	FACETS	0.968	0.871	1	0.968	0.871	1	CLONAL	1	TRUE	1	0.80260767713703	2		263	211	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5258075	5258075	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	208	414	1	ENST00000357368.4:c.659A>G	p.Asn220Ser	p.N220S	ENST00000357368	NM_002850.3	220	aAc/aGc	8/38	0.80260767713703	5	FACETS	1	0.957	1	0.261	0.242	0.281	CLONAL	1	TRUE	1	0.80260767713703	5		415	1094	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223418	36223418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	608	713	1	ENST00000222270.7:c.5968G>A	p.Asp1990Asn	p.D1990N	ENST00000222270	NM_014727.1	1990	Gac/Aac	28/37	0.80260767713703	3	FACETS	1	0.996	1			1	CLONAL	1	TRUE	NA	0.80260767713703	3		714	1677	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224559	36224559	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	652	764	0	ENST00000222270.7:c.7021G>T	p.Gly2341Trp	p.G2341W	ENST00000222270	NM_014727.1	2341	Ggg/Tgg	29/37	0.80260767713703	3	FACETS	1	0.996	1			1	CLONAL	1	TRUE	NA	0.80260767713703	3		764	1708	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858010	45858010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	916	543	0	ENST00000391945.4:c.1643C>T	p.Thr548Ile	p.T548I	ENST00000391945	NM_000400.3	548	aCc/aTc	17/23	0.80260767713703	5	FACETS	1	0.989	1	1	0.989	1	CLONAL	4	TRUE	1	0.80260767713703	5		543	1239	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881389	111881389	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	185	385	0	ENST00000393256.3:c.67G>A	p.Glu23Lys	p.E23K	ENST00000393256	NM_006538.4	23	Gag/Aag	2/4	1	2	FACETS	0.973	0.907	1	0.973	0.907	1	CLONAL	1	TRUE	1	0.80260767713703	2		385	474	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309925	30309925	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	165	404	0	ENST00000307677.4:c.97A>T	p.Asn33Tyr	p.N33Y	ENST00000307677	NM_138578.1	33	Aac/Tac	2/3	1	2	FACETS	0.958	0.89	1	0.958	0.89	1	CLONAL	1	TRUE	1	0.80260767713703	2		404	429	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932690	49932690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	311	597	0	ENST00000296474.3:c.3181G>A	p.Asp1061Asn	p.D1061N	ENST00000296474	NM_002447.2	1061	Gac/Aac	14/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.80260767713703	2		597	715	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498473	89498473	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	100	259	0	ENST00000336596.2:c.2445G>A	p.Trp815Ter	p.W815*	ENST00000336596	NM_005233.5	815	tgG/tgA	14/17	1	2	FACETS	0.913	0.828	1	0.913	0.828	1	CLONAL	1	TRUE	1	0.80260767713703	2		259	273	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446330	187446330	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	143	367	0	ENST00000232014.4:c.1358C>T	p.Ser453Phe	p.S453F	ENST00000232014	NM_001130845.1	453	tCc/tTc	6/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.80260767713703	2		367	328	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541690	187541690	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	138	310	0	ENST00000441802.2:c.6050T>A	p.Leu2017His	p.L2017H	ENST00000441802	NM_005245.3	2017	cTc/cAc	10/27	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.80260767713703	2		310	289	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876497	35876497	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	190	451	0	ENST00000303115.3:c.1289C>T	p.Pro430Leu	p.P430L	ENST00000303115	NM_002185.3	430	cCa/cTa	8/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.80260767713703	2		451	439	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048898	180048898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	230	596	1	ENST00000261937.6:c.1664C>T	p.Pro555Leu	p.P555L	ENST00000261937	NM_182925.4	555	cCc/cTc	13/30	1	2	FACETS	0.901	0.845	0.958	0.901	0.845	0.958	CLONAL	1	TRUE	1	0.80260767713703	2		597	636	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671853	30671853	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	273	563	0	ENST00000376406.3:c.5107C>T	p.Pro1703Ser	p.P1703S	ENST00000376406	NM_014641.2	1703	Cct/Tct	10/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.80260767713703	2		563	633	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372151	55372151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	193	415	0	ENST00000297316.4:c.841C>T	p.Pro281Ser	p.P281S	ENST00000297316	NM_022454.3	281	Ccc/Tcc	2/2	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.80260767713703	2		415	426	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022040	5022040	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	115	420	0	ENST00000381652.3:c.53C>T	p.Ser18Phe	p.S18F	ENST00000381652	NM_004972.3	18	tCt/tTt	3/25	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.80260767713703	2		420	282	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430405	47430406	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	179	408	1	ENST00000377045.4:c.1680_1681delinsTT	p.Pro561Ser	p.P561S	ENST00000377045	NM_001654.4	560	ttCCcc/ttTTcc	15/16	0.80260767713703	3	FACETS	0.975	0.903	1	0.488	0.451	0.525	CLONAL	1	TRUE	1	0.80260767713703	3		409	641	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148504797	148504797	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	137	319	0	ENST00000320356.2:c.2197T>C	p.Tyr733His	p.Y733H	ENST00000320356	NM_004456.4	733	Tac/Cac	20/20	1	2	FACETS	0.956	0.881	1	0.956	0.881	1	CLONAL	1	TRUE	1	0.80260767713703	2		319	357	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021595-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	77	454	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.753	0.665	0.847	1	0.977	1	SUBCLONAL	2	TRUE	1	0.25487802117745	2		454	401	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192042	108192042	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021595-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	83	419	0	ENST00000278616.4:c.6467A>G	p.Glu2156Gly	p.E2156G	ENST00000278616	NM_000051.3	2156	gAa/gGa	45/63	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.25487802117745	2		419	651	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947576	48947576	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021595-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	112	467	1	ENST00000267163.4:c.1166del	p.Leu389Ter	p.L389*	ENST00000267163	NM_000321.2	388	aTt/at	12/27	0.25487802117745	1	FACETS	0.779	0.704	0.858	1	0.985	1	SUBCLONAL	2	TRUE	0	0.25487802117745	1		468	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578470	7578470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852789	NA	P-0021595-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	247	640	1	ENST00000269305.4:c.460G>A	p.Gly154Ser	p.G154S	ENST00000269305	NM_001126112.2	154	Ggc/Agc	5/11	0.25487802117745	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.25487802117745	2		641	836	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622252	162622252	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs781548251	NA	P-0021595-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	77	380	0	ENST00000366898.1:c.445T>C	p.Tyr149His	p.Y149H	ENST00000366898	NM_004562.2	149	Tat/Cat	4/12	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.25487802117745	2		380	551	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342999	225342999	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021595-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	68	546	0	ENST00000264414.4:c.2093A>G	p.Asp698Gly	p.D698G	ENST00000264414	NM_003590.4	698	gAc/gGc	15/16	1	2	FACETS	0.645	0.56	0.738	0.645	0.56	0.738	SUBCLONAL	1	TRUE	1	0.25487802117745	2		546	827	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953191	17953191	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs778908329	NA	P-0121419-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	263	629	1	ENST00000458235.1:c.795C>A	p.His265Gln	p.H265Q	ENST00000458235	NM_000215.3	265	caC/caA	6/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	NA	1	0.847330263939728	2		630	561	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40682114	40682114	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121419-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	245	445	0	ENST00000249776.8:c.669C>A	p.Ser223Arg	p.S223R	ENST00000249776	NM_033286.3	223	agC/agA	6/9	NA	2	FACETS	0.995	0.938	1			1	INDETERMINATE	1	NA	NA	0.847330263939728	2		445	581	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115697	8115703	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTAGAT	TTTAGAT	-	novel	NA	P-0023160-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	85	381	1	ENST00000346208.3:c.1048-4_1050del		p.X350_splice	ENST00000346208		350		6/6	1	2	FACETS	0.976	0.867	1	0.976	0.867	1	CLONAL	1	TRUE	1	0.403355616467262	2		382	432	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063676	67063676	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023160-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	95	342	1	ENST00000412916.2:c.125del	p.Ala42AspfsTer47	p.A42Dfs*47	ENST00000412916		42	gCa/ga	2/6	0.403355616467262	1	FACETS	0.995	0.893	1	0.995	0.893	1	CLONAL	1	TRUE	0	0.403355616467262	1		343	378	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415574	152415574	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023160-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	39	619	0	ENST00000206249.3:c.1424T>G	p.Ile475Ser	p.I475S	ENST00000206249	NM_000125.3	475	aTc/aGc	7/8	1	2	FACETS	0.284	0.235	0.34	0.284	0.235	0.34	SUBCLONAL	1	TRUE	1	0.403355616467262	2		619	680	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	100	454	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.993	0.905	1	0.993	0.905	1	CLONAL	1	TRUE	1	0.860915095444169	2		454	234	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0024039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	237	338	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.988	0.931	1	0.988	0.931	1	CLONAL	1	TRUE	1	0.860915095444169	2		338	557	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	280	622	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.999	0.946	1	0.999	0.946	1	CLONAL	1	TRUE	1	0.860915095444169	2		622	651	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0024039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	178	461	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.860915095444169	2		461	413	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285938	38285938	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913473	NA	P-0024039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	188	498	1	ENST00000425967.3:c.473C>T	p.Ser158Leu	p.S158L	ENST00000425967	NM_001174067.1	158	tCg/tTg	5/19	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.860915095444169	2		499	433	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923060	44923060	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	265	546	0	ENST00000377967.4:c.1921C>T	p.Gln641Ter	p.Q641*	ENST00000377967	NM_021140.2	641	Cag/Tag	16/29	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.860915095444169	2		546	598	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115963	8115964	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0024039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	126	282	0	ENST00000346208.3:c.1310_1311dup	p.Met438AlafsTer38	p.M438Afs*38	ENST00000346208		437	agc/aGCgc	6/6	1	2	FACETS	0.829	0.76	0.9	0.829	0.76	0.9	CLONAL	1	TRUE	1	0.860915095444169	2		282	353	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748660	43748660	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	309	786	0	ENST00000382044.4:c.2146G>C	p.Glu716Gln	p.E716Q	ENST00000382044	NM_001141980.1	716	Gaa/Caa	12/28	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.860915095444169	2		786	717	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748786	43748786	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	275	712	0	ENST00000382044.4:c.2020G>C	p.Glu674Gln	p.E674Q	ENST00000382044	NM_001141980.1	674	Gag/Cag	12/28	1	2	FACETS	0.892	0.842	0.943	0.892	0.842	0.943	CLONAL	1	TRUE	1	0.860915095444169	2		712	716	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439427	220439427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	91	309	0	ENST00000243786.2:c.280G>A	p.Glu94Lys	p.E94K	ENST00000243786	NM_002191.3	94	Gag/Aag	2/2	0.860915095444169	1	FACETS	0.933	0.869	0.994	0.933	0.869	0.994	CLONAL	1	TRUE	0	0.860915095444169	1		309	129	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180462	38180462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	219	454	1	ENST00000396334.3:c.310G>A	p.Glu104Lys	p.E104K	ENST00000396334	NM_002468.4	104	Gag/Aag	1/5	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.860915095444169	2		455	449	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651941	36651942	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	412	519	0	ENST00000244741.5:c.65dup	p.Gly23ArgfsTer13	p.G23Rfs*13	ENST00000244741	NM_000389.4	21	-/T	2/3	0.845785778550068	2	FACETS	0.981	0.957	1	0.981	0.957	1	CLONAL	2	TRUE	0	0.860915095444169	2		519	488	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154344	2154344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369452652	NA	P-0024039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	55	766	0	ENST00000434045.2:c.584G>A	p.Gly195Asp	p.G195D	ENST00000434045	NM_001127598.1	195	gGt/gAt	5/5	0.860915095444169	1	FACETS	0.202	0.173	0.233	0.202	0.173	0.233	SUBCLONAL	1	TRUE	0	0.860915095444169	1		766	361	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983263	149983264	+	missense_variant	Missense_Mutation	DNP	TC	TC	CG	novel	NA	P-0024039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	37	573	0	ENST00000253339.5:c.2994_2995delinsCG	p.Lys998_Asn999delinsAsnAsp	p.K998_N999delinsND	ENST00000253339		998	aaGAat/aaCGat	7/7	1	2	FACETS	0.136	0.112	0.164	0.136	0.112	0.164	SUBCLONAL	1	TRUE	1	0.860915095444169	2		573	630	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024039-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	149	454	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.801130981713517	2		454	349	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0024039-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	289	338	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	0.801130981713517	2		338	705	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024039-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	341	622	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.801130981713517	2		622	831	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0024039-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	161	461	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.901	0.835	0.969	0.901	0.835	0.969	CLONAL	1	TRUE	1	0.801130981713517	2		461	446	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285938	38285938	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913473	NA	P-0024039-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	161	498	1	ENST00000425967.3:c.473C>T	p.Ser158Leu	p.S158L	ENST00000425967	NM_001174067.1	158	tCg/tTg	5/19	1	2	FACETS	0.853	0.789	0.919	0.853	0.789	0.919	CLONAL	1	TRUE	1	0.801130981713517	2		499	471	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923060	44923060	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024039-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	313	546	0	ENST00000377967.4:c.1921C>T	p.Gln641Ter	p.Q641*	ENST00000377967	NM_021140.2	641	Cag/Tag	16/29	NA	2	FACETS	0.985	0.934	1			1	INDETERMINATE	1	TRUE	NA	0.801130981713517	2		546	793	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115963	8115964	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0024039-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	101	282	0	ENST00000346208.3:c.1310_1311dup	p.Met438AlafsTer38	p.M438Afs*38	ENST00000346208		437	agc/aGCgc	6/6	1	2	FACETS	0.79	0.715	0.869	0.79	0.715	0.869	SUBCLONAL	1	TRUE	1	0.801130981713517	2		282	319	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748660	43748660	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024039-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	360	786	0	ENST00000382044.4:c.2146G>C	p.Glu716Gln	p.E716Q	ENST00000382044	NM_001141980.1	716	Gaa/Caa	12/28	1	2	FACETS	0.987	0.939	1	0.987	0.939	1	CLONAL	1	TRUE	1	0.801130981713517	2		786	911	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748786	43748786	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024039-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	285	712	0	ENST00000382044.4:c.2020G>C	p.Glu674Gln	p.E674Q	ENST00000382044	NM_001141980.1	674	Gag/Cag	12/28	1	2	FACETS	0.901	0.85	0.952	0.901	0.85	0.952	CLONAL	1	TRUE	1	0.801130981713517	2		712	790	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439427	220439427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024039-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	103	309	0	ENST00000243786.2:c.280G>A	p.Glu94Lys	p.E94K	ENST00000243786	NM_002191.3	94	Gag/Aag	2/2	0.801130981713517	1	FACETS	0.934	0.866	1	0.934	0.866	1	CLONAL	1	TRUE	0	0.801130981713517	1		309	165	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180462	38180462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024039-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	185	454	1	ENST00000396334.3:c.310G>A	p.Glu104Lys	p.E104K	ENST00000396334	NM_002468.4	104	Gag/Aag	1/5	1	2	FACETS	0.876	0.815	0.939	0.876	0.815	0.939	CLONAL	1	TRUE	1	0.801130981713517	2		455	527	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651941	36651942	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024039-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	379	519	0	ENST00000244741.5:c.65dup	p.Gly23ArgfsTer13	p.G23Rfs*13	ENST00000244741	NM_000389.4	21	-/T	2/3	0.781256589027208	2	FACETS	0.935	0.906	0.963	0.935	0.906	0.963	CLONAL	2	TRUE	0	0.801130981713517	2		519	506	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024054-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	205	622	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.398358416487403	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.4023484960402	2		622	450	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727441	66727441	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519728	NA	P-0024054-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	18	503	0	ENST00000307102.5:c.157T>G	p.Phe53Val	p.F53V	ENST00000307102	NM_002755.3	53	Ttt/Gtt	2/11	1	2	FACETS	0.184	0.138	0.239	0.184	0.138	0.239	SUBCLONAL	1	TRUE	1	0.4023484960402	2		503	486	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138857	64138857	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779234584	NA	P-0024054-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	150	592	1	ENST00000334205.4:c.2224C>T	p.Arg742Cys	p.R742C	ENST00000334205	NM_003942.2	742	Cgc/Tgc	17/17	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.4023484960402	2		593	589	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911071	29911072	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	TATA	novel	NA	P-0024054-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	119	619	0	ENST00000376809.5:c.370_371insTATA	p.Gly124ValfsTer2	p.G124Vfs*2	ENST00000376809	NM_002116.7	124	ggc/gTATAgc	3/8	0.209872850316396	3	FACETS	1	0.969	1	0.584	0.529	0.643	INDETERMINATE	1	TRUE	1	0.4023484960402	3		619	608	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990400	81990400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370547009	NA	P-0024054-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	114	622	1	ENST00000359376.3:c.3671G>A	p.Arg1224His	p.R1224H	ENST00000359376	NM_002661.3	1224	cGc/cAc	32/33	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.4023484960402	2		623	491	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101385	27101392	+	frameshift_variant	Frame_Shift_Del	DEL	GTCCCTCT	GTCCCTCT	-	novel	NA	P-0024054-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	48	527	0	ENST00000324856.7:c.4668_4675del	p.Ser1558CysfsTer11	p.S1558Cfs*11	ENST00000324856	NM_006015.4	1556	gGTCCCTCT/g	18/20	1	2	FACETS	0.555	0.47	0.648	0.555	0.47	0.648	SUBCLONAL	1	TRUE	1	0.4023484960402	2		527	430	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604785	48604798	+	frameshift_variant	Frame_Shift_Del	DEL	TAGACGAAGTACTT	TAGACGAAGTACTT	-	novel	NA	P-0024054-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	56	429	0	ENST00000342988.3:c.1607_1620del	p.Leu536ProfsTer36	p.L536Pfs*36	ENST00000342988	NM_005359.5	536	cTAGACGAAGTACTT/c	12/12	0.4023484960402	1	FACETS	0.904	0.783	1	0.904	0.783	1	CLONAL	1	TRUE	0	0.4023484960402	1		429	246	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619281	37619281	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0024076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	174	390	0	ENST00000447079.4:c.957C>G	p.Tyr319Ter	p.Y319*	ENST00000447079	NM_015083.1	319	taC/taG	1/14	1	2	FACETS	0.906	0.84	0.973	0.906	0.84	0.973	CLONAL	1	FALSE	1	0.724975387701665	2		390	530	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618522	37618523	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0024076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	249	502	1	ENST00000447079.4:c.199dup	p.Ile67AsnfsTer8	p.I67Nfs*8	ENST00000447079	NM_015083.1	66	-/A	1/14	1	2	FACETS	0.959	0.902	1	0.959	0.902	1	CLONAL	1	FALSE	1	0.724975387701665	2		503	716	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606439	93606439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201177148	NA	P-0024076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	331	618	1	ENST00000375746.1:c.259G>A	p.Asp87Asn	p.D87N	ENST00000375746	NM_001174167.1	87	Gac/Aac	2/14	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.724975387701665	2		619	793	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0024568-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	62	369	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.658	0.569	0.755	0.658	0.569	0.755	SUBCLONAL	1	TRUE	1	0.349649984428997	2		369	539	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070639	67070639	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0024568-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	49	263	1	ENST00000412916.2:c.263T>G	p.Leu88Ter	p.L88*	ENST00000412916		88	tTa/tGa	3/6	1	2	FACETS	0.81	0.689	0.942	0.81	0.689	0.942	CLONAL	1	TRUE	1	0.349649984428997	2		264	346	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-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	39	261	1	ENST00000346208.3:c.1048-5_1071del		p.X350_splice	ENST00000346208		350		6/6	1	2	FACETS	0.632	0.525	0.751	0.632	0.525	0.751	SUBCLONAL	1	TRUE	1	0.349649984428997	2		262	353	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662292	67662292	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024568-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	29	358	0	ENST00000264010.4:c.1538A>G	p.His513Arg	p.H513R	ENST00000264010	NM_006565.3	513	cAc/cGc	9/12	1	2	FACETS	0.372	0.298	0.456	0.372	0.298	0.456	SUBCLONAL	1	TRUE	1	0.349649984428997	2		358	446	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0024677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	268	654	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.480675537788693	2	FACETS	0.973	0.922	1	0.973	0.922	1	CLONAL	2	TRUE	0	0.480675537788693	2		654	573	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0024677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	188	324	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	0.480675537788693	5	FACETS	1	0.932	1	0.67	0.621	0.72	CLONAL	2	TRUE	2	0.480675537788693	5		324	670	SUCCESS
MET	4233	MSKCC	GRCh37	7	116417463	116417463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913244	NA	P-0024677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	231	213	1	ENST00000397752.3:c.3280C>T	p.His1094Tyr	p.H1094Y	ENST00000397752	NM_000245.2	1094	Cat/Tat	16/21	0.480675537788693	9	FACETS	1	0.946	1			1	CLONAL	4	TRUE	NA	0.480675537788693	9		214	639	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281360	49281360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201503697	NA	P-0024677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	298	517	0	ENST00000282018.3:c.407G>A	p.Arg136His	p.R136H	ENST00000282018	NM_020377.2	136	cGt/cAt	1/1	NA	2	FACETS	0.902	0.856	0.949			1	INDETERMINATE	2	TRUE	NA	0.480675537788693	2		517	687	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800946	243800946	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	90	308	0	ENST00000263826.5:c.528G>C	p.Met176Ile	p.M176I	ENST00000263826	NM_005465.4	176	atG/atC	5/13	0.20532894313275	4	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.480675537788693	4		308	495	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643678	52643678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	83	334	1	ENST00000394830.3:c.2218G>A	p.Glu740Lys	p.E740K	ENST00000394830	NM_018313.4	740	Gag/Aag	17/30	0.345869924535948	3	FACETS	0.852	0.754	0.956	0.426	0.377	0.478	CLONAL	1	TRUE	1	0.480675537788693	3		335	503	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0025185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	238	655	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	0.756	0.707	0.805	1	0.993	1	SUBCLONAL	2	FALSE	1	0.384553200102879	2		655	819	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919758	50919758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750457028	NA	P-0025185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1402	321	591	0	ENST00000440232.2:c.2926G>A	p.Glu976Lys	p.E976K	ENST00000440232	NM_002691.3	976	Gag/Aag	23/27	0.384553200102879	9	FACETS	1	0.985	1			1	CLONAL	2	FALSE	NA	0.384553200102879	9		591	1723	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919689	50919689	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1711	396	699	0	ENST00000440232.2:c.2857G>C	p.Asp953His	p.D953H	ENST00000440232	NM_002691.3	953	Gac/Cac	23/27	0.384553200102879	9	FACETS	1	0.989	1			1	CLONAL	2	FALSE	NA	0.384553200102879	9		699	2107	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919707	50919707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1411727570	NA	P-0025185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1660	397	680	1	ENST00000440232.2:c.2875G>A	p.Glu959Lys	p.E959K	ENST00000440232	NM_002691.3	959	Gag/Aag	23/27	0.384553200102879	9	FACETS	1	0.99	1			1	CLONAL	2	FALSE	NA	0.384553200102879	9		681	2057	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919872	50919872	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs985679759	NA	P-0025185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1359	319	646	0	ENST00000440232.2:c.2959G>A	p.Asp987Asn	p.D987N	ENST00000440232	NM_002691.3	987	Gac/Aac	24/27	0.384553200102879	9	FACETS	1	0.987	1			1	CLONAL	2	FALSE	NA	0.384553200102879	9		646	1678	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0025528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	71	712	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.57845307234568	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	1	0.57845307234568	3		712	140	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587118	189587118	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761885185	NA	P-0025528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	10	284	0	ENST00000264731.3:c.1135C>T	p.Arg379Cys	p.R379C	ENST00000264731	NM_003722.4	379	Cgt/Tgt	9/14	0.57845307234568	3	FACETS	0.279	0.189	0.391	0.139	0.094	0.196	SUBCLONAL	1	TRUE	1	0.57845307234568	3		284	160	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561352	9561352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773981325	NA	P-0025528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	8	342	0	ENST00000353224.5:c.430G>A	p.Glu144Lys	p.E144K	ENST00000353224	NM_177990.2	144	Gaa/Aaa	4/10	0.418209241557304	3	FACETS	0.207	0.133	0.303	0.104	0.066	0.152	SUBCLONAL	1	TRUE	1	0.57845307234568	3		342	172	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936096	178936096	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	56	494	0	ENST00000263967.3:c.1638G>C	p.Gln546His	p.Q546H	ENST00000263967	NM_006218.2	546	caG/caC	10/21	0.57845307234568	3	FACETS	1	0.904	1	0.527	0.456	0.602	CLONAL	1	TRUE	1	0.57845307234568	3		494	237	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061208	38061208	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	118	345	1	ENST00000250448.2:c.781C>A	p.Arg261Ser	p.R261S	ENST00000250448	NM_004496.3	261	Cgc/Agc	2/2	0.172239282303844	1	FACETS	0.909	0.831	0.989	0.909	0.831	0.989	INDETERMINATE	1	TRUE	0	0.57845307234568	1		346	319	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49280981	49280981	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs201474852	NA	P-0025528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	28	463	0	ENST00000282018.3:c.28C>A	p.Pro10Thr	p.P10T	ENST00000282018	NM_020377.2	10	Cca/Aca	1/1	1	2	FACETS	0.88	0.718	1	0.88	0.718	1	CLONAL	1	TRUE	1	0.57845307234568	2		463	110	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267383	198267383	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	42	409	0	ENST00000335508.6:c.1974G>T	p.Trp658Cys	p.W658C	ENST00000335508	NM_012433.2	658	tgG/tgT	14/25	1	2	FACETS	0.643	0.541	0.753	0.643	0.541	0.753	SUBCLONAL	1	TRUE	1	0.57845307234568	2		409	226	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6038902	6038902	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs863224681	NA	P-0025528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	42	337	0	ENST00000265849.7:c.542A>T	p.Tyr181Phe	p.Y181F	ENST00000265849	NM_000535.5	181	tAt/tTt	6/15	0.23645171676128	1	FACETS	0.765	0.652	0.883	0.765	0.652	0.883	INDETERMINATE	1	TRUE	0	0.57845307234568	1		337	135	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11114030	11114030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774927302	NA	P-0025528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	10	481	0	ENST00000358026.2:c.1958C>T	p.Pro653Leu	p.P653L	ENST00000358026	NM_001128849.1	653	cCg/cTg	13/36	1	2	FACETS	0.176	0.119	0.248	0.176	0.119	0.248	SUBCLONAL	1	TRUE	1	0.57845307234568	2		481	196	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0025975-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	705	338	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.924448230890576	3	FACETS	0.976	0.949	1	0.651	0.633	0.669	CLONAL	2	TRUE	0	0.924448230890576	3		338	1142	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0025975-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	182	576	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.509737327057728	1	FACETS	0.366	0.34	0.394	0.366	0.34	0.394	INDETERMINATE	1	TRUE	0	0.924448230890576	1		576	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578517	7578517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750600586	NA	P-0025975-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	1194	945	0	ENST00000269305.4:c.413C>T	p.Ala138Val	p.A138V	ENST00000269305	NM_001126112.2	138	gCc/gTc	5/11	0.924448230890576	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.924448230890576	2		945	1270	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792753	33792753	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs867463920	NA	P-0025975-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	10	51	0	ENST00000498907.2:c.568T>C	p.Ser190Pro	p.S190P	ENST00000498907	NM_004364.3	190	Tcg/Ccg	1/1	0.479188385675456	3	FACETS	0.422	0.29	0.582	0.141	0.096	0.194	INDETERMINATE	1	TRUE	0	0.924448230890576	3		51	75	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947514	48947568	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACATTTTCCTATTTTTATCCCCTCTAGGACTGTTATGAACACTATCCAACAATTA	ACATTTTCCTATTTTTATCCCCTCTAGGACTGTTATGAACACTATCCAACAATTA	-	novel	NA	P-0025975-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	251	361	1	ENST00000267163.4:c.1128-26_1156del		p.X376_splice	ENST00000267163	NM_000321.2	376		12/27	0.924448230890576	2	FACETS	0.966	0.941	0.989	0.966	0.941	0.989	CLONAL	2	TRUE	0	0.924448230890576	2		362	281	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007327	143007327	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025975-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	156	407	0	ENST00000262992.4:c.2457G>C	p.Lys819Asn	p.K819N	ENST00000262992	NM_001101669.1	819	aaG/aaC	22/24	0.472672491367483	2	FACETS	0.558	0.513	0.604	0.279	0.256	0.302	INDETERMINATE	1	TRUE	0	0.924448230890576	2		407	605	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426725	47426725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773318953	NA	P-0025975-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	213	729	2	ENST00000377045.4:c.970G>A	p.Val324Met	p.V324M	ENST00000377045	NM_001654.4	324	Gtg/Atg	10/16	0.150638127368675	3	FACETS	0.628	0.583	0.675	0.209	0.194	0.225	INDETERMINATE	1	TRUE	0	0.924448230890576	3		731	1073	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0025982-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	333	369	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.387714412068401	4	FACETS	0.959	0.913	1	0.959	0.913	1	CLONAL	3	TRUE	1	0.464409427989605	4		369	730	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574030	7574030	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025982-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	214	415	0	ENST00000269305.4:c.997del	p.Arg333ValfsTer12	p.R333Vfs*12	ENST00000269305	NM_001126112.2	333	Cgt/gt	10/11	0.464409427989605	2	FACETS	0.904	0.848	0.96	0.904	0.848	0.96	CLONAL	2	TRUE	0	0.464409427989605	2		415	510	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663871	241663871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1131691244	NA	P-0025982-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	100	288	0	ENST00000366560.3:c.1256C>T	p.Ser419Leu	p.S419L	ENST00000366560	NM_000143.3	419	tCa/tTa	9/10	1	2	FACETS	0.981	0.882	1	0.981	0.882	1	CLONAL	1	TRUE	1	0.464409427989605	2		288	439	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115849	8115850	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026026-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	96	537	0	ENST00000346208.3:c.1196dup	p.His399GlnfsTer108	p.H399Qfs*108	ENST00000346208		399	cac/cAac	6/6	0.495191436772342	3	FACETS	0.806	0.72	0.898	0.403	0.36	0.449	CLONAL	1	TRUE	1	0.514491425674865	3		537	582	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540336	187540336	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026026-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	198	466	0	ENST00000441802.2:c.7404del	p.Asp2469MetfsTer12	p.D2469Mfs*12	ENST00000441802	NM_005245.3	2468	tcT/tc	10/27	0.486257394737931	4	FACETS	0.908	0.845	0.972	0.908	0.845	0.972	CLONAL	2	TRUE	2	0.514491425674865	4		466	642	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0026525-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	46	555	3	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	1	2	FACETS	0.754	0.634	0.887	0.754	0.634	0.887	SUBCLONAL	1	TRUE	1	0.2	2		558	610	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038783	47038783	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026525-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	62	318	0	ENST00000377604.3:c.790G>T	p.Glu264Ter	p.E264*	ENST00000377604	NM_001204468.1	264	Gag/Tag	9/24	1	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.2	1		318	416	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458078	120458078	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026525-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	43	507	0	ENST00000256646.2:c.7267G>T	p.Asp2423Tyr	p.D2423Y	ENST00000256646	NM_024408.3	2423	Gac/Tac	34/34	1	2	FACETS	0.691	0.577	0.818	0.691	0.577	0.818	SUBCLONAL	1	TRUE	1	0.2	2		507	622	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866665	117866665	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026525-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	28	460	0	ENST00000297338.2:c.980A>G	p.Asp327Gly	p.D327G	ENST00000297338	NM_006265.2	327	gAc/gGc	9/14	1	2	FACETS	0.569	0.454	0.701	0.569	0.454	0.701	SUBCLONAL	1	TRUE	1	0.2	2		460	492	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866539	117866542	+	missense_variant	Missense_Mutation	ONP	ACTC	ACTC	TCTA	novel	NA	P-0026525-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	29	437	0	ENST00000297338.2:c.1103_1106delinsTAGA	p.Gly368_Val369delinsValGlu	p.G368_V369delinsVE	ENST00000297338	NM_006265.2	368	gGAGTa/gTAGAa	9/14	1	2	FACETS	0.594	0.476	0.729	0.594	0.476	0.729	SUBCLONAL	1	TRUE	1	0.2	2		437	488	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711873	89711873	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs587781784	NA	P-0027193-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	148	331	2	ENST00000371953.3:c.493-2A>G		p.X165_splice	ENST00000371953	NM_000314.4	165			1	2	FACETS	0.754	0.701	0.806	1	0.99	1	SUBCLONAL	2	TRUE	1	0.659022559478289	2		333	298	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37863257	37863261	+	frameshift_variant	Frame_Shift_Del	DEL	GACAT	GACAT	-	novel	NA	P-0027193-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	363	498	13	ENST00000269571.5:c.90_94del	p.Asp30GlufsTer78	p.D30Efs*78	ENST00000269571		30	GACATg/g	2/27	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.659022559478289	2		511	781	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438288	56438289	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0027193-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	199	461	7	ENST00000407977.2:c.704_705del	p.Arg235AsnfsTer23	p.R235Nfs*23	ENST00000407977		235	aGA/a	7/10	1	2	FACETS	0.764	0.719	0.81	1	0.993	1	SUBCLONAL	2	TRUE	1	0.659022559478289	2		468	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs786201838	NA	P-0027259-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	170	528	0	ENST00000269305.4:c.578A>C	p.His193Pro	p.H193P	ENST00000269305	NM_001126112.2	193	cAt/cCt	6/11	0.226698667552547	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	0	0.24	2		528	690	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957419	1957419	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0027259-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	57	277	0	ENST00000382891.5:c.2523del		p.X841_splice	ENST00000382891	NM_133335.3	841			1	2	FACETS	0.973	0.836	1	0.973	0.836	1	CLONAL	1	TRUE	1	0.24	2		277	488	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285039	15285039	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027259-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	102	523	0	ENST00000263388.2:c.4576C>A	p.Arg1526Ser	p.R1526S	ENST00000263388	NM_000435.2	1526	Cgt/Agt	25/33	0.226698667552547	2	FACETS	1	0.94	1	0.538	0.481	0.599	CLONAL	1	TRUE	0	0.24	2		523	790	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233268	46233268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027259-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	90	248	0	ENST00000334344.6:c.1487C>T	p.Ala496Val	p.A496V	ENST00000334344	NM_152641.2	496	gCa/gTa	11/21	0.3	9	FACETS	0.777	0.688	0.872			1	SUBCLONAL	2	TRUE	NA	0.24	9		248	888	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438272	49438272	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027259-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	189	406	0	ENST00000301067.7:c.4997T>G	p.Leu1666Arg	p.L1666R	ENST00000301067	NM_003482.3	1666	cTg/cGg	20/54	0.217736912213029	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.24	2		406	717	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445059	49445059	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027259-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	71	477	0	ENST00000301067.7:c.2407G>T	p.Glu803Ter	p.E803*	ENST00000301067	NM_003482.3	803	Gaa/Taa	10/54	0.217736912213029	2	FACETS	0.811	0.707	0.923	0.405	0.353	0.462	CLONAL	1	TRUE	0	0.24	2		477	730	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109822	115109822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762726425	NA	P-0027259-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	46	405	0	ENST00000257566.3:c.2056G>A	p.Val686Met	p.V686M	ENST00000257566	NM_016569.3	686	Gtg/Atg	8/8	0.3	3	FACETS	0.755	0.635	0.887	0.377	0.317	0.444	SUBCLONAL	1	TRUE	1	0.24	3		405	569	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28644651	28644651	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027259-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	116	458	0	ENST00000241453.7:c.142G>C	p.Gly48Arg	p.G48R	ENST00000241453	NM_004119.2	48	Ggg/Cgg	2/24	0.217736912213029	2	FACETS	1	0.983	1	0.733	0.662	0.809	CLONAL	1	TRUE	0	0.24	2		458	659	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667552	29667552	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027259-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	161	407	0	ENST00000356175.3:c.6888G>A	p.Trp2296Ter	p.W2296*	ENST00000356175	NM_000267.3	2296	tgG/tgA	46/57	0.226698667552547	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.24	2		407	630	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276699	15276699	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0027259-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	200	593	1	ENST00000263388.2:c.5566A>T	p.Lys1856Ter	p.K1856*	ENST00000263388	NM_000435.2	1856	Aag/Tag	30/33	0.226698667552547	2	FACETS	0.961	0.892	1	0.961	0.892	1	CLONAL	2	TRUE	0	0.24	2		594	867	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712615	52712615	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0027259-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	90	226	0	ENST00000394830.3:c.139-2A>T		p.X47_splice	ENST00000394830	NM_018313.4	47			0.226698667552547	2	FACETS	0.982	0.877	1	0.982	0.877	1	CLONAL	2	TRUE	0	0.24	2		226	382	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158482	106158482	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027259-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	58	219	0	ENST00000380013.4:c.3383A>G	p.Tyr1128Cys	p.Y1128C	ENST00000380013	NM_001127208.2	1128	tAt/tGt	3/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.24	2		219	377	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557740	187557740	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs777497306	NA	P-0027259-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	83	211	0	ENST00000441802.2:c.3971C>T	p.Ser1324Leu	p.S1324L	ENST00000441802	NM_005245.3	1324	tCa/tTa	5/27	1	2	FACETS	0.955	0.849	1	1	0.984	1	CLONAL	2	TRUE	1	0.24	2		211	362	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627199	86627200	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027259-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	57	186	0	ENST00000274376.6:c.576dup	p.Glu193ArgfsTer18	p.E193Rfs*18	ENST00000274376	NM_002890.2	192	gaa/gAaa	2/25	0.226698667552547	2	FACETS	0.89	0.77	1	0.89	0.77	1	CLONAL	2	TRUE	0	0.24	2		186	267	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486253	8486253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1256737547	NA	P-0027259-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	51	251	0	ENST00000356435.5:c.2564G>A	p.Gly855Asp	p.G855D	ENST00000356435		855	gGc/gAc	17/35	0.3	1	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	0	0.24	1		251	371	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321407	1321407	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0027259-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	52	277	0	ENST00000400841.2:c.350-2A>T		p.X117_splice	ENST00000400841		117			1	1	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	0	0.24	1		277	363	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409198	31409198	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027259-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	69	376	0	ENST00000344624.3:c.3819G>T	p.Arg1273Ser	p.R1273S	ENST00000344624		1273	agG/agT	30/33	0.258223306570311	3	FACETS	0.974	0.848	1	0.487	0.424	0.556	CLONAL	1	TRUE	1	0.24	3		376	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782177	NA	P-0027746-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	164	640	0	ENST00000269305.4:c.644G>T	p.Ser215Ile	p.S215I	ENST00000269305	NM_001126112.2	215	aGt/aTt	6/11	0.264709883848215	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.264709883848215	1		640	829	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0027746-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	87	521	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.264709883848215	2		521	615	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180312	38180312	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027746-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	81	572	0	ENST00000396334.3:c.160A>G	p.Thr54Ala	p.T54A	ENST00000396334	NM_002468.4	54	Aca/Gca	1/5	1	2	FACETS	0.882	0.777	0.995	0.882	0.777	0.995	CLONAL	1	TRUE	1	0.264709883848215	2		572	694	SUCCESS
APC	324	MSKCC	GRCh37	5	112174833	112174833	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1554085102	NA	P-0027746-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	47	434	0	ENST00000257430.4:c.3542T>A	p.Leu1181Ter	p.L1181*	ENST00000257430	NM_000038.5	1181	tTa/tAa	16/16	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.264709883848215	2		434	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578466	7578466	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786202752	NA	P-0027801-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	389	682	0	ENST00000269305.4:c.464C>A	p.Thr155Asn	p.T155N	ENST00000269305	NM_001126112.2	155	aCc/aAc	5/11	0.433344080116567	4	FACETS	0.893	0.858	0.927	0.893	0.858	0.927	CLONAL	4	TRUE	0	0.503164813070197	4		682	651	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs199469669	NA	P-0027801-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	225	541	0	ENST00000374080.3:c.130G>C	p.Gly44Arg	p.G44R	ENST00000374080		44	Ggt/Cgt	2/45	0.380593828466925	3	FACETS	1	0.973	1			1	CLONAL	2	TRUE	NA	0.503164813070197	3		541	528	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274255	10274255	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027801-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	77	238	0	ENST00000330684.3:c.14G>C	p.Gly5Ala	p.G5A	ENST00000330684	NM_001134407.1	5	gGc/gCc	2/13	0.49911031114034	3	FACETS	0.908	0.812	1	0.605	0.541	0.671	CLONAL	2	TRUE	0	0.503164813070197	3		238	211	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17129529	17129529	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027801-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	69	513	0	ENST00000285071.4:c.357C>G	p.Ser119Arg	p.S119R	ENST00000285071	NM_144997.5	119	agC/agG	5/14	0.433344080116567	4	FACETS	0.706	0.615	0.804	0.176	0.153	0.201	SUBCLONAL	1	TRUE	0	0.503164813070197	4		513	584	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211733	5211733	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027801-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	62	625	0	ENST00000357368.4:c.5102A>C	p.Asn1701Thr	p.N1701T	ENST00000357368	NM_002850.3	1701	aAt/aCt	33/38	0.49911031114034	3	FACETS	0.586	0.507	0.673	0.195	0.169	0.225	SUBCLONAL	1	TRUE	0	0.503164813070197	3		625	526	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732648	190732648	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027801-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	25	319	0	ENST00000441310.2:c.2466G>C	p.Leu822Phe	p.L822F	ENST00000441310	NM_000534.4	822	ttG/ttC	11/13	NA	2	FACETS	0.286	0.225	0.356			1	INDETERMINATE	1	TRUE	NA	0.503164813070197	2		319	347	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028013-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	105	454	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		454	335	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0028640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	111	338	0	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	FALSE	1	0.376492863048234	2		338	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0028640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	229	545	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.201174915871314	3	FACETS	0.785	0.732	0.839	0.785	0.732	0.839	INDETERMINATE	2	FALSE	1	0.376492863048234	3		545	921	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28934577	NA	P-0028640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	205	483	0	ENST00000269305.4:c.770T>C	p.Leu257Pro	p.L257P	ENST00000269305	NM_001126112.2	257	cTg/cCg	7/11	0.201174915871314	3	FACETS	1	0.988	1	0.666	0.617	0.716	INDETERMINATE	1	FALSE	1	0.376492863048234	3		483	972	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144612	119144612	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs767162260	NA	P-0028640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	133	396	0	ENST00000264033.4:c.625C>G	p.Leu209Val	p.L209V	ENST00000264033	NM_005188.3	209	Cta/Gta	4/16	0.183625648110503	3	FACETS	1	0.98	1	0.642	0.584	0.702	INDETERMINATE	1	FALSE	1	0.376492863048234	3		396	654	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644489	3644489	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	210	607	0	ENST00000294008.3:c.2125G>T	p.Val709Leu	p.V709L	ENST00000294008	NM_032444.2	709	Gtg/Ttg	10/15	0.376492863048234	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	0	0.376492863048234	1		607	854	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912329	97912329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	101	417	0	ENST00000289081.3:c.562G>A	p.Val188Ile	p.V188I	ENST00000289081	NM_000136.2	188	Gtc/Atc	7/15	0.361396893640174	1	FACETS	0.695	0.622	0.772	0.695	0.622	0.772	SUBCLONAL	1	FALSE	0	0.376492863048234	1		417	627	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591948	48591969	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CACAGGACAGAAGCCATTGAGA	CACAGGACAGAAGCCATTGAGA	AGATAGTTACTTTAAAAAATT	novel	NA	P-0028640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	42	355	1	ENST00000342988.3:c.1111_1132delinsAGATAGTTACTTTAAAAAATT	p.His371ArgfsTer2	p.H371Rfs*2	ENST00000342988	NM_005359.5	371	CACAGGACAGAAGCCATTGAGAga/AGATAGTTACTTTAAAAAATTga	9/12	0.376492863048234	1	FACETS	0.412	0.344	0.487	0.412	0.344	0.487	SUBCLONAL	1	FALSE	0	0.376492863048234	1		356	440	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0028641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	74	546	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.8	0.7	0.907	0.8	0.7	0.907	CLONAL	1	TRUE	1	0.280445721690188	2		546	660	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0028641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	97	685	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.280445721690188	1	FACETS	0.845	0.753	0.942	0.845	0.753	0.942	CLONAL	1	TRUE	0	0.280445721690188	1		685	704	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971177	21971177	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913382	NA	P-0028641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	99	451	0	ENST00000304494.5:c.181G>T	p.Glu61Ter	p.E61*	ENST00000304494	NM_000077.4	61	Gag/Tag	2/3	0.280445721690188	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.280445721690188	1		451	488	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515211	103515211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759628522	NA	P-0028641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	63	463	0	ENST00000355739.4:c.1712C>T	p.Pro571Leu	p.P571L	ENST00000355739	NM_000123.3	571	cCg/cTg	8/15	1	2	FACETS	0.811	0.702	0.929	0.811	0.702	0.929	CLONAL	1	TRUE	1	0.280445721690188	2		463	554	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597355	10597355	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	110	599	0	ENST00000171111.5:c.1848G>C	p.Gln616His	p.Q616H	ENST00000171111	NM_203500.1	616	caG/caC	6/6	1	2	FACETS	0.874	0.784	0.969	0.874	0.784	0.969	CLONAL	1	TRUE	1	0.280445721690188	2		599	898	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001581	150001581	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	55	320	0	ENST00000253339.5:c.2023C>A	p.Gln675Lys	p.Q675K	ENST00000253339		675	Caa/Aaa	4/7	1	2	FACETS	0.874	0.749	1	0.874	0.749	1	CLONAL	1	TRUE	1	0.280445721690188	2		320	449	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0028641-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	67	546	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.569	0.494	0.65	0.569	0.494	0.65	SUBCLONAL	1	TRUE	1	0.35	2		546	673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0028641-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	71	685	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	1	2	FACETS	0.467	0.406	0.532	0.467	0.406	0.532	SUBCLONAL	1	TRUE	1	0.35	2		685	869	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971177	21971177	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913382	NA	P-0028641-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	43	451	0	ENST00000304494.5:c.181G>T	p.Glu61Ter	p.E61*	ENST00000304494	NM_000077.4	61	Gag/Tag	2/3	1	2	FACETS	0.428	0.358	0.506	0.428	0.358	0.506	SUBCLONAL	1	TRUE	1	0.35	2		451	574	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515211	103515211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759628522	NA	P-0028641-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	32	463	0	ENST00000355739.4:c.1712C>T	p.Pro571Leu	p.P571L	ENST00000355739	NM_000123.3	571	cCg/cTg	8/15	1	2	FACETS	0.392	0.318	0.477	0.392	0.318	0.477	SUBCLONAL	1	TRUE	1	0.35	2		463	466	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	38	454	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.697	0.576	0.832	0.697	0.576	0.832	SUBCLONAL	1	TRUE	1	0.242926140473081	2		454	449	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0028642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	152	429	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.223499978032783	2	FACETS	0.889	0.815	0.966	0.889	0.815	0.966	CLONAL	2	TRUE	0	0.242926140473081	2		429	704	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0028642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	57	232	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.238546903369643	1	FACETS	0.898	0.772	1	0.898	0.772	1	CLONAL	1	TRUE	0	0.242926140473081	1		232	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0028642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	146	517	0	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.242926140473081	2		517	1015	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724322	112724322	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs781645815	NA	P-0028642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	140	517	0	ENST00000369452.4:c.206A>G	p.Asp69Gly	p.D69G	ENST00000369452	NM_007373.3	69	gAc/gGc	2/9	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.242926140473081	2		517	1097	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851306	156851306	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	125	477	1	ENST00000524377.1:c.2263G>T	p.Glu755Ter	p.E755*	ENST00000524377	NM_002529.3	755	Gag/Tag	17/17	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.242926140473081	2		478	943	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741825	17741825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs548800810	NA	P-0028642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	49	131	0	ENST00000250003.3:c.496G>A	p.Asp166Asn	p.D166N	ENST00000250003	NM_002478.4	166	Gac/Aac	1/3	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.242926140473081	2		131	356	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119668	70119685	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTTTATTGTCCACAGGG	CTTTTATTGTCCACAGGG	-	novel	NA	P-0028642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	89	366	0	ENST00000245479.2:c.686-15_688del		p.X229_splice	ENST00000245479	NM_000346.3	229		3/3	1	2	FACETS	0.996	0.883	1	0.996	0.883	1	CLONAL	1	TRUE	1	0.242926140473081	2		366	736	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188284	10188284	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs372757722	NA	P-0028642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	86	474	0	ENST00000256474.2:c.427G>C	p.Asp143His	p.D143H	ENST00000256474	NM_000551.3	143	Gac/Cac	2/3	1	2	FACETS	0.725	0.64	0.816	0.725	0.64	0.816	SUBCLONAL	1	TRUE	1	0.242926140473081	2		474	977	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0028643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	118	281	1	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.301487383869118	1	FACETS	0.796	0.726	0.869	0.796	0.726	0.869	INDETERMINATE	1	TRUE	0	0.573057812375165	1		282	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0028643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	492	664	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.573057812375165	2		664	805	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0028643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	700	496	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.573057812375165	3	FACETS	1	0.991	1			1	CLONAL	3	TRUE	NA	0.573057812375165	3		496	1012	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845757	68845757	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587780784	NA	P-0028643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	169	292	0	ENST00000261769.5:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000261769	NM_004360.3	335	Cga/Tga	7/16	0.546144506687543	1	FACETS	0.915	0.849	0.982	0.915	0.849	0.982	CLONAL	1	TRUE	0	0.573057812375165	1		292	460	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433950	49433950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780306423	NA	P-0028643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	235	612	0	ENST00000301067.7:c.7603C>T	p.Arg2535Cys	p.R2535C	ENST00000301067	NM_003482.3	2535	Cgt/Tgt	31/54	1	2	FACETS	0.981	0.918	1	0.981	0.918	1	CLONAL	1	TRUE	1	0.573057812375165	2		612	836	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481806	56481806	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	217	464	0	ENST00000267101.3:c.734C>G	p.Ala245Gly	p.A245G	ENST00000267101	NM_001982.3	245	gCc/gGc	7/28	0.573057812375165	3	FACETS	1	0.956	1			1	CLONAL	1	TRUE	NA	0.573057812375165	3		464	940	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296488	15296488	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	246	644	2	ENST00000263388.2:c.1954C>A	p.Pro652Thr	p.P652T	ENST00000263388	NM_000435.2	652	Ccc/Acc	13/33	0.301487383869118	1	FACETS	0.81	0.76	0.861	0.81	0.76	0.861	INDETERMINATE	1	TRUE	0	0.573057812375165	1		646	756	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0028644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	403	605	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.535225839790143	2	FACETS	0.964	0.924	1	0.964	0.924	1	CLONAL	2	TRUE	0	0.535225839790143	2		607	781	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0028644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	244	227	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.535225839790143	2	FACETS	0.995	0.944	1	0.995	0.944	1	CLONAL	2	TRUE	0	0.535225839790143	2		227	458	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0028644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	230	227	0	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	0.532314650995608	2	FACETS	0.881	0.831	0.931	0.881	0.831	0.931	CLONAL	2	TRUE	0	0.535225839790143	2		227	488	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495022	56495022	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763808045	NA	P-0028644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	342	572	1	ENST00000267101.3:c.3379C>T	p.Arg1127Cys	p.R1127C	ENST00000267101	NM_001982.3	1127	Cgc/Tgc	27/28	0.532314650995608	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.535225839790143	2		573	629	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544748	65544748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	265	371	1	ENST00000358664.4:c.178C>T	p.Arg60Trp	p.R60W	ENST00000358664	NM_002382.4	60	Cgg/Tgg	4/5	0.532314650995608	2	FACETS	0.984	0.935	1	0.984	0.935	1	CLONAL	2	TRUE	0	0.535225839790143	2		372	503	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662939	52662939	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	370	461	0	ENST00000394830.3:c.1414C>T	p.Arg472Ter	p.R472*	ENST00000394830	NM_018313.4	472	Cga/Tga	13/30	0.535225839790143	2	FACETS	0.96	0.919	1	0.96	0.919	1	CLONAL	2	TRUE	0	0.535225839790143	2		461	720	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665110	29665110	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658541	NA	P-0028644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	449	530	1	ENST00000356175.3:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000356175	NM_000267.3	2237	Cga/Tga	44/57	0.535225839790143	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.535225839790143	2		531	819	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59793411	59793411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375082407	NA	P-0028644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	292	368	0	ENST00000259008.2:c.2393G>A	p.Arg798Gln	p.R798Q	ENST00000259008	NM_032043.2	798	cGa/cAa	17/20	0.535225839790143	2	FACETS	0.962	0.916	1	0.962	0.916	1	CLONAL	2	TRUE	0	0.535225839790143	2		368	567	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155399	99155399	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1559033620	NA	P-0028644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	314	433	0	ENST00000074304.5:c.625C>T	p.Arg209Ter	p.R209*	ENST00000074304	NM_001134224.1	209	Cga/Tga	9/26	NA	2	FACETS	0.991	0.945	1			1	INDETERMINATE	2	TRUE	NA	0.535225839790143	2		433	592	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445178	49445178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771291128	NA	P-0028644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	341	640	0	ENST00000301067.7:c.2288C>T	p.Pro763Leu	p.P763L	ENST00000301067	NM_003482.3	763	cCg/cTg	10/54	0.532314650995608	2	FACETS	0.941	0.898	0.984	0.941	0.898	0.984	CLONAL	2	TRUE	0	0.535225839790143	2		640	677	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804370	43804370	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	671	457	0	ENST00000372470.3:c.370G>A	p.Val124Ile	p.V124I	ENST00000372470	NM_005373.2	124	Gtc/Atc	3/12	0.535225839790143	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	4	TRUE	0	0.535225839790143	4		457	953	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849828	156849828	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121964868	NA	P-0028644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	300	470	1	ENST00000524377.1:c.2084C>T	p.Pro695Leu	p.P695L	ENST00000524377	NM_002529.3	695	cCg/cTg	16/17	0.535225839790143	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.535225839790143	2		471	542	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204506581	204506581	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145156544	NA	P-0028644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	364	463	0	ENST00000367182.3:c.367G>A	p.Ala123Thr	p.A123T	ENST00000367182	NM_001278516.1	123	Gca/Aca	6/11	0.535225839790143	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.535225839790143	2		463	679	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497721	125497721	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	123	379	0	ENST00000428830.2:c.285A>T	p.Arg95Ser	p.R95S	ENST00000428830	NM_001114121.2	95	agA/agT	3/14	0.535225839790143	2	FACETS	0.778	0.705	0.853	0.389	0.352	0.427	SUBCLONAL	1	TRUE	0	0.535225839790143	2		379	591	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958211	11958211	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	252	300	0	ENST00000353533.5:c.121C>T	p.Arg41Cys	p.R41C	ENST00000353533	NM_003010.3	41	Cgc/Tgc	2/11	0.535225839790143	2	FACETS	0.949	0.899	0.999	0.949	0.899	0.999	CLONAL	2	TRUE	0	0.535225839790143	2		300	496	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58700977	58700977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375732384	NA	P-0028644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	427	597	2	ENST00000305921.3:c.568G>A	p.Val190Ile	p.V190I	ENST00000305921	NM_003620.3	190	Gta/Ata	2/6	0.535225839790143	2	FACETS	0.987	0.948	1	0.987	0.948	1	CLONAL	2	TRUE	0	0.535225839790143	2		599	808	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	DEL	C	C	-	rs1567550969	NA	P-0028646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	333	660	0	ENST00000269305.4:c.672+1del		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.39686317522396	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.39686317522396	2		660	784	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588177	69588177	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	165	665	0	ENST00000168712.1:c.521A>T	p.Tyr174Phe	p.Y174F	ENST00000168712	NM_002007.2	174	tAc/tTc	3/3	0.39686317522396	2	FACETS	1	0.974	1	0.567	0.522	0.614	CLONAL	1	TRUE	0	0.39686317522396	2		665	733	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974331	93974331	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	151	585	0	ENST00000369303.4:c.1723G>T	p.Gly575Cys	p.G575C	ENST00000369303	NM_004440.3	575	Ggc/Tgc	8/17	0.39686317522396	3	FACETS	0.778	0.715	0.844	0.778	0.715	0.844	SUBCLONAL	2	TRUE	1	0.39686317522396	3		585	586	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	146	454	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.962	0.891	1	0.962	0.891	1	CLONAL	1	TRUE	1	0.884907069064278	2		454	343	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311619	15311621	+	inframe_deletion	In_Frame_Del	DEL	AGC	AGC	-	rs746497955	NA	P-0028647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	10	75	0	ENST00000263388.2:c.96_98del	p.Leu33del	p.L33del	ENST00000263388	NM_000435.2	32	ctGCTa/cta	1/33	1	2	FACETS	0.165	0.112	0.231	0.165	0.112	0.231	SUBCLONAL	1	TRUE	1	0.884907069064278	2		75	137	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015023	27015023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202063570	NA	P-0028647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	247	324	0	ENST00000335756.4:c.125G>A	p.Arg42Gln	p.R42Q	ENST00000335756	NM_001809.3	42	cGg/cAg	2/5	1	2	FACETS	0.899	0.847	0.952	0.899	0.847	0.952	CLONAL	1	TRUE	1	0.884907069064278	2		324	621	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801119	1801119	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	604	524	0	ENST00000260795.2:c.248C>G	p.Pro83Arg	p.P83R	ENST00000260795		83	cCc/cGc	2/17	1	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	1	0.884907069064278	2		524	996	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	45	454	0				ENST00000310581	NM_198253.2	-/1132			0.111340882455535	3	FACETS	0.982	0.827	1	0.982	0.827	1	CLONAL	2	TRUE	1	0.125195079785774	3		454	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876659675	NA	P-0028652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	72	550	0	ENST00000269305.4:c.764T>A	p.Ile255Asn	p.I255N	ENST00000269305	NM_001126112.2	255	aTc/aAc	7/11	1	2	FACETS	0.91	0.795	1	1	0.98	1	CLONAL	2	TRUE	1	0.125195079785774	2		550	632	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560043	29560043	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs868450405	NA	P-0028652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	68	281	1	ENST00000356175.3:c.3520C>T	p.Gln1174Ter	p.Q1174*	ENST00000356175	NM_000267.3	1174	Cag/Tag	27/57	0.125195079785774	3	FACETS	1	0.891	1	1	0.891	1	CLONAL	3	TRUE	0	0.125195079785774	3		282	377	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762237	43762237	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	60	559	0	ENST00000382044.4:c.1208C>G	p.Ser403Cys	p.S403C	ENST00000382044	NM_001141980.1	403	tCt/tGt	11/28	0.111340882455535	3	FACETS	1	0.965	1	0.712	0.613	0.821	CLONAL	1	TRUE	1	0.125195079785774	3		559	715	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420206	88420206	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	40	441	0	ENST00000360948.2:c.2480del	p.Leu827TrpfsTer20	p.L827Wfs*20	ENST00000360948	NM_001012338.2	827	tTg/tg	19/19	0.111340882455535	3	FACETS	1	0.938	1	0.65	0.54	0.774	CLONAL	1	TRUE	1	0.125195079785774	3		441	522	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121536	2121536	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	134	622	1	ENST00000219476.3:c.1865G>T	p.Arg622Leu	p.R622L	ENST00000219476	NM_000548.3	622	cGg/cTg	18/42	0.125195079785774	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	3	TRUE	0	0.125195079785774	3		623	687	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39620697	39620697	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	27	267	0	ENST00000262039.4:c.2095A>T	p.Ser699Cys	p.S699C	ENST00000262039	NM_002647.2	699	Agc/Tgc	19/25	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.125195079785774	2		267	383	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420080	41420080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	15	292	0	ENST00000373198.4:c.241G>A	p.Gly81Arg	p.G81R	ENST00000373198	NM_133170.3	81	Ggg/Agg	3/32	0.125195079785774	0	FACETS	0.788	0.576	1			1	CLONAL	1	TRUE	0	0.125195079785774	0		292	266	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514493	41514493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	57	494	0	ENST00000373198.4:c.168G>T	p.Gln56His	p.Q56H	ENST00000373198	NM_133170.3	56	caG/caT	2/32	0.125195079785774	0	FACETS	1	0.958	1			1	CLONAL	1	TRUE	0	0.125195079785774	0		494	598	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531013	187531013	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	27	405	0	ENST00000441802.2:c.10010A>G	p.Gln3337Arg	p.Q3337R	ENST00000441802	NM_005245.3	3337	cAa/cGa	15/27	1	2	FACETS	0.844	0.67	1	0.844	0.67	1	CLONAL	1	TRUE	1	0.125195079785774	2		405	511	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674287	86674288	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0028652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	29	369	0	ENST00000274376.6:c.2422_2423del	p.Gln808ValfsTer21	p.Q808Vfs*21	ENST00000274376	NM_002890.2	807	ACa/a	18/25	0.111340882455535	3	FACETS	1	0.889	1	0.585	0.469	0.717	CLONAL	1	TRUE	1	0.125195079785774	3		369	421	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13949311	13949311	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0028652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	34	255	1	ENST00000405192.2:c.817A>T	p.Lys273Ter	p.K273*	ENST00000405192	NM_001163147.1	273	Aag/Tag	9/12	0.0825064468666372	4	FACETS	0.881	0.721	1	0.881	0.721	1	CLONAL	2	TRUE	2	0.125195079785774	4		256	347	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842313	151842313	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	41	314	0	ENST00000262189.6:c.14099del	p.Pro4700LeufsTer16	p.P4700Lfs*16	ENST00000262189	NM_170606.2	4700	cCt/ct	54/59	0.0825064468666372	4	FACETS	0.903	0.753	1	0.903	0.753	1	CLONAL	2	TRUE	2	0.125195079785774	4		314	408	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465651	8465651	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	27	386	0	ENST00000356435.5:c.3529C>G	p.Arg1177Gly	p.R1177G	ENST00000356435		1177	Cgc/Ggc	21/35	0.125195079785774	1	FACETS	1	0.831	1	1	0.831	1	CLONAL	1	TRUE	0	0.125195079785774	1		386	385	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240688	53240688	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	54	516	0	ENST00000375401.3:c.1392del	p.Glu465LysfsTer12	p.E465Kfs*12	ENST00000375401	NM_004187.3	464	ccC/cc	10/26	1	2	FACETS	0.794	0.679	0.921	1	0.968	1	CLONAL	2	TRUE	1	0.125195079785774	2		516	543	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0028654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	148	493	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	0.93	0.851	1	0.93	0.851	1	CLONAL	1	TRUE	1	0.4154617306835	2		493	766	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035253	6035253	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	98	313	0	ENST00000265849.7:c.815T>G	p.Phe272Cys	p.F272C	ENST00000265849	NM_000535.5	272	tTc/tGc	8/15	0.150514131930644	3	FACETS	0.946	0.846	1	0.473	0.423	0.527	INDETERMINATE	1	TRUE	1	0.4154617306835	3		313	602	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331912	81331912	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1396522967	NA	P-0028654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	19	217	1	ENST00000222390.5:c.2172G>T	p.Lys724Asn	p.K724N	ENST00000222390	NM_000601.4	724	aaG/aaT	18/18	0.159401411484242	5	FACETS	0.526	0.4	0.675	0.175	0.133	0.225	INDETERMINATE	1	TRUE	2	0.4154617306835	5		218	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0028657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	297	605	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.399474971038299	2	FACETS	0.913	0.866	0.961	0.913	0.866	0.961	CLONAL	2	TRUE	0	0.470057813307856	2		607	692	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120805842	120805842	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	118	656	1	ENST00000257552.2:c.236C>T	p.Ala79Val	p.A79V	ENST00000257552	NM_002442.3	79	gCg/gTg	4/15	0.135319882536539	3	FACETS	0.876	0.791	0.965	0.292	0.263	0.322	INDETERMINATE	1	TRUE	0	0.470057813307856	3		657	708	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678430	88678430	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	114	669	0	ENST00000360948.2:c.1106C>A	p.Thr369Asn	p.T369N	ENST00000360948	NM_001012338.2	369	aCc/aAc	9/19	0.470057813307856	5	FACETS	0.655	0.588	0.726	0.164	0.147	0.182	SUBCLONAL	1	TRUE	1	0.470057813307856	5		669	1263	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821692	72821692	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	48	247	0	ENST00000268489.5:c.10483G>T	p.Val3495Leu	p.V3495L	ENST00000268489	NM_006885.3	3495	Gtg/Ttg	10/10	0.135319882536539	3	FACETS	0.907	0.772	1	0.302	0.257	0.352	INDETERMINATE	1	TRUE	0	0.470057813307856	3		247	278	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714667	52714667	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	172	529	0	ENST00000322088.6:c.425C>A	p.Thr142Asn	p.T142N	ENST00000322088	NM_014225.5	142	aCc/aAc	4/15	0.399474971038299	2	FACETS	0.822	0.764	0.881	0.822	0.764	0.881	CLONAL	2	TRUE	0	0.470057813307856	2		529	445	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587155	212587155	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	216	416	0	ENST00000342788.4:c.846G>C	p.Lys282Asn	p.K282N	ENST00000342788	NM_005235.2	282	aaG/aaC	7/28	0.440327849733988	2	FACETS	0.986	0.928	1	0.986	0.928	1	CLONAL	2	TRUE	0	0.470057813307856	2		416	466	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971139	21971186	+	inframe_deletion	In_Frame_Del	DEL	GGCGCAGTTGGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCG	GGCGCAGTTGGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCG	-	novel	NA	P-0028657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	112	448	0	ENST00000304494.5:c.172_219del	p.Arg58_Ala73del	p.R58_A73del	ENST00000304494	NM_000077.4	58	CGAGTGGCGGAGCTGCTGCTGCTCCACGGCGCGGAGCCCAACTGCGCC/-	2/3	0.470057813307856	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.470057813307856	1		448	303	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857569	9857569	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	54	326	0	ENST00000330684.3:c.3832C>A	p.Gln1278Lys	p.Q1278K	ENST00000330684	NM_001134407.1	1278	Caa/Aaa	13/13	0.324436230973918	2	FACETS	1	0.912	1	0.539	0.464	0.619	CLONAL	1	TRUE	0	0.388364369165655	2		326	258	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602788	10602788	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	85	638	0	ENST00000171111.5:c.790G>T	p.Val264Phe	p.V264F	ENST00000171111	NM_203500.1	264	Gtc/Ttc	3/6	0.324436230973918	2	FACETS	0.706	0.625	0.793	0.353	0.312	0.397	SUBCLONAL	1	TRUE	0	0.388364369165655	2		638	620	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39318145	39318145	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	61	386	0	ENST00000373001.3:c.657T>A	p.Ser219Arg	p.S219R	ENST00000373001	NM_022157.3	219	agT/agA	4/7	0.341378238341792	2	FACETS	1	0.892	1	0.515	0.447	0.587	CLONAL	1	TRUE	0	0.388364369165655	2		386	305	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680776	88680776	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	110	448	0	ENST00000360948.2:c.481T>G	p.Phe161Val	p.F161V	ENST00000360948	NM_001012338.2	161	Ttt/Gtt	6/19	0.239576651786506	5	FACETS	0.774	0.697	0.855	0.516	0.465	0.57	SUBCLONAL	2	TRUE	2	0.388364369165655	5		448	579	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680785	88680785	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	109	423	0	ENST00000360948.2:c.472G>T	p.Glu158Ter	p.E158*	ENST00000360948	NM_001012338.2	158	Gag/Tag	6/19	0.239576651786506	5	FACETS	0.796	0.717	0.879	0.531	0.478	0.586	SUBCLONAL	2	TRUE	2	0.388364369165655	5		423	558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574001	7574001	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	173	604	0	ENST00000269305.4:c.1026del	p.Glu343SerfsTer2	p.E343Sfs*2	ENST00000269305	NM_001126112.2	342	cgA/cg	10/11	0.341378238341792	2	FACETS	0.772	0.715	0.831	0.772	0.715	0.831	SUBCLONAL	2	TRUE	0	0.388364369165655	2		604	577	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484266	57484266	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	44	291	0	ENST00000371085.3:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000371085	NM_000516.4	194	Gat/Tat	7/13	0.388364369165655	6	FACETS	0.697	0.583	0.822	0.174	0.145	0.206	SUBCLONAL	1	TRUE	2	0.388364369165655	6		291	578	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164761	36164761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	77	577	0	ENST00000300305.3:c.1114G>A	p.Gly372Ser	p.G372S	ENST00000300305		372	Ggc/Agc	8/8	1	2	FACETS	0.658	0.578	0.743	0.658	0.578	0.743	SUBCLONAL	1	TRUE	1	0.388364369165655	2		577	603	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552845	106552845	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	100	591	1	ENST00000369096.4:c.810C>A	p.Asn270Lys	p.N270K	ENST00000369096	NM_001198.3	270	aaC/aaA	5/7	0.234473879269057	3	FACETS	0.948	0.848	1	0.316	0.282	0.352	CLONAL	1	TRUE	0	0.388364369165655	3		592	649	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92462536	92462536	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	64	484	0	ENST00000265734.4:c.102G>T	p.Lys34Asn	p.K34N	ENST00000265734	NM_001259.6	34	aaG/aaT	2/8	0.239576651786506	5	FACETS	0.906	0.784	1	0.302	0.261	0.346	CLONAL	1	TRUE	2	0.388364369165655	5		484	576	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399987	139399987	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	29	553	0	ENST00000277541.6:c.4361G>T	p.Cys1454Phe	p.C1454F	ENST00000277541	NM_017617.3	1454	tGc/tTc	25/34	1	2	FACETS	0.287	0.229	0.352	0.287	0.229	0.352	SUBCLONAL	1	TRUE	1	0.388364369165655	2		553	521	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936093	178936093	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913275	NA	P-0028661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	584	423	0	ENST00000263967.3:c.1635G>C	p.Glu545Asp	p.E545D	ENST00000263967	NM_006218.2	545	gaG/gaC	10/21	0.577769852337741	4	FACETS	0.881	0.855	0.907	1	0.996	1	CLONAL	4	TRUE	1	0.577769852337741	4		423	905	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0028661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	74	311	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.862	0.762	0.968	0.862	0.762	0.968	CLONAL	1	TRUE	1	0.577769852337741	2		312	297	SUCCESS
APC	324	MSKCC	GRCh37	5	112173830	112173831	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0028661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	162	263	0	ENST00000257430.4:c.2544dup	p.Asp849ArgfsTer2	p.D849Rfs*2	ENST00000257430	NM_000038.5	847	gaa/gAaa	16/16	0.534728427570767	3	FACETS	0.833	0.772	0.895			1	CLONAL	2	TRUE	NA	0.577769852337741	3		263	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876660825	NA	P-0028661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	301	452	0	ENST00000269305.4:c.569C>G	p.Pro190Arg	p.P190R	ENST00000269305	NM_001126112.2	190	cCt/cGt	6/11	1	2	FACETS	0.959	0.915	1	1	0.996	1	CLONAL	2	TRUE	1	0.577769852337741	2		452	543	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981564	201981564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	562	548	0	ENST00000359651.3:c.478G>A	p.Asp160Asn	p.D160N	ENST00000359651		160	Gac/Aac	3/8	0.561271802096142	4	FACETS	0.947	0.914	0.98	0.947	0.914	0.98	CLONAL	3	TRUE	1	0.577769852337741	4		548	1080	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354795	40354795	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	283	423	0	ENST00000293328.3:c.2109G>T	p.Gln703His	p.Q703H	ENST00000293328	NM_012448.3	703	caG/caT	17/19	0.568416824997598	3	FACETS	0.935	0.885	0.986	0.624	0.59	0.657	CLONAL	2	TRUE	0	0.577769852337741	3		423	675	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481618	40481618	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	323	383	0	ENST00000264657.5:c.1187T>C	p.Met396Thr	p.M396T	ENST00000264657	NM_139276.2	396	aTg/aCg	13/24	0.568416824997598	3	FACETS	0.949	0.902	0.997	0.633	0.601	0.665	CLONAL	2	TRUE	0	0.577769852337741	3		383	759	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488730	212488730	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	251	320	0	ENST00000342788.4:c.2119C>A	p.Gln707Lys	p.Q707K	ENST00000342788	NM_005235.2	707	Caa/Aaa	18/28	0.577769852337741	5	FACETS	0.897	0.841	0.955	0.598	0.56	0.637	CLONAL	2	TRUE	2	0.577769852337741	5		320	904	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589572	67589580	+	inframe_deletion	In_Frame_Del	DEL	AGGGAAAAA	AGGGAAAAA	-	novel	NA	P-0028661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	139	209	0	ENST00000274335.5:c.1336_1344del	p.Gly446_Lys448del	p.G446_K448del	ENST00000274335		445	gtAGGGAAAAAa/gta	10/15	0.536180576619589	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.577769852337741	2		209	235	SUCCESS
APC	324	MSKCC	GRCh37	5	112175768	112175784	+	frameshift_variant	Frame_Shift_Del	DEL	ACGGAAAGTACTCCAGA	ACGGAAAGTACTCCAGA	C	novel	NA	P-0028661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	76	209	0	ENST00000257430.4:c.4477_4493delinsC	p.Thr1493LeufsTer9	p.T1493Lfs*9	ENST00000257430	NM_000038.5	1493	ACGGAAAGTACTCCAGAt/Ct	16/16	0.534728427570767	3	FACETS	0.939	0.829	1			1	CLONAL	1	TRUE	NA	0.577769852337741	3		209	361	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0028670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	1698	622	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.506461710917154	13	FACETS	1	0.995	1			1	CLONAL	11	TRUE	NA	0.506461710917154	13		622	2258	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578482	7578482	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	388	764	0	ENST00000269305.4:c.448del	p.Thr150HisfsTer20	p.T150Hfs*20	ENST00000269305	NM_001126112.2	150	Aca/ca	5/11	0.506461710917154	2	FACETS	0.94	0.899	0.981	0.94	0.899	0.981	CLONAL	2	TRUE	0	0.506461710917154	2		764	815	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84403325	84403325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	142	445	0	ENST00000321945.7:c.160G>A	p.Glu54Lys	p.E54K	ENST00000321945	NM_139076.2	54	Gaa/Aaa	2/9	0.506461710917154	5	FACETS	0.795	0.723	0.872			1	SUBCLONAL	1	TRUE	NA	0.506461710917154	5		445	1241	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777667	9777667	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765798990	NA	P-0028670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	77	649	1	ENST00000377346.4:c.1003G>A	p.Ala335Thr	p.A335T	ENST00000377346	NM_005026.3	335	Gcc/Acc	8/24	0.424595201130858	3	FACETS	0.49	0.429	0.555	0.245	0.214	0.278	SUBCLONAL	1	TRUE	1	0.506461710917154	3		650	778	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506997	186506997	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	33	229	0	ENST00000323963.5:c.1163T>C	p.Ile388Thr	p.I388T	ENST00000323963		388	aTt/aCt	11/11	0.338742038419382	4	FACETS	0.572	0.467	0.691	0.286	0.233	0.346	SUBCLONAL	1	TRUE	2	0.506461710917154	4		229	343	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967584	90967584	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1554559097	NA	P-0028670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	532	289	0	ENST00000265433.3:c.1324A>G	p.Ser442Gly	p.S442G	ENST00000265433	NM_002485.4	442	Agt/Ggt	10/16	0.506461710917154	8	FACETS	1	0.985	1	1	0.985	1	CLONAL	6	TRUE	2	0.506461710917154	8		289	857	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0028672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	44	411	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.837	0.702	0.986	0.837	0.702	0.986	CLONAL	1	TRUE	1	0.22	2		411	478	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0028672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	25	552	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.367	0.288	0.458	0.367	0.288	0.458	SUBCLONAL	1	TRUE	1	0.22	2		552	620	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0028672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	40	459	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.705	0.585	0.838	0.705	0.585	0.838	SUBCLONAL	1	TRUE	1	0.22	2		459	516	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0028672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	42	220	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.22	2		220	296	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693010	89693010	+	splice_donor_variant	Splice_Site	DEL	T	T	-	rs1060500124	NA	P-0028672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	29	377	0	ENST00000371953.3:c.492+2del		p.X164_splice	ENST00000371953	NM_000314.4	164			1	2	FACETS	0.859	0.691	1	0.859	0.691	1	CLONAL	1	TRUE	1	0.22	2		377	307	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692941	89692941	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	40	568	0	ENST00000371953.3:c.428del	p.Gly143AlafsTer4	p.G143Afs*4	ENST00000371953	NM_000314.4	142	cGg/cg	5/9	1	2	FACETS	0.726	0.603	0.863	0.726	0.603	0.863	SUBCLONAL	1	TRUE	1	0.22	2		568	501	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104359298	104359298	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	37	443	0	ENST00000369902.3:c.1022del	p.Pro341ArgfsTer20	p.P341Rfs*20	ENST00000369902	NM_016169.3	340	gCc/gc	8/12	1	2	FACETS	0.656	0.54	0.785	0.656	0.54	0.785	SUBCLONAL	1	TRUE	1	0.22	2		443	513	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026963	48026963	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs730881825	NA	P-0028672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	44	281	0	ENST00000234420.5:c.1842del	p.Cys615ValfsTer7	p.C615Vfs*7	ENST00000234420	NM_000179.2	614	tCc/tc	4/10	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.22	2		281	357	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176710828	176710828	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	28	376	0	ENST00000439151.2:c.6050G>T	p.Arg2017Leu	p.R2017L	ENST00000439151	NM_022455.4	2017	cGg/cTg	20/23	1	2	FACETS	0.588	0.469	0.723	0.588	0.469	0.723	SUBCLONAL	1	TRUE	1	0.22	2		376	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0028673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	285	609	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.340289437017475	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.361381451355652	2		610	697	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519934	NA	P-0028673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	143	436	0	ENST00000263967.3:c.333G>C	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaC	2/21	0.311308633237235	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.361381451355652	4		436	489	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106535	27106535	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	216	711	0	ENST00000324856.7:c.6146G>A	p.Trp2049Ter	p.W2049*	ENST00000324856	NM_006015.4	2049	tGg/tAg	20/20	0.311308633237235	4	FACETS	0.916	0.853	0.982	0.916	0.853	0.982	CLONAL	2	TRUE	2	0.361381451355652	4		711	888	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541322	187541322	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	53	307	0	ENST00000441802.2:c.6418C>T	p.Gln2140Ter	p.Q2140*	ENST00000441802	NM_005245.3	2140	Caa/Taa	10/27	0.138102049873601	5	FACETS	1	0.927	1	0.285	0.243	0.33	INDETERMINATE	1	TRUE	1	0.361381451355652	5		307	397	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370892	55370892	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	87	651	0	ENST00000297316.4:c.194A>C	p.Glu65Ala	p.E65A	ENST00000297316	NM_022454.3	65	gAg/gCg	1/2	NA	2	FACETS	0.961	0.854	1			1	INDETERMINATE	1	TRUE	NA	0.361381451355652	2		651	501	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202788	133202788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201165149	NA	P-0028675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	83	558	1	ENST00000320574.5:c.6446G>A	p.Arg2149His	p.R2149H	ENST00000320574	NM_006231.2	2149	cGc/cAc	46/49	0.317442544486738	3	FACETS	0.57	0.503	0.642	0.19	0.167	0.214	SUBCLONAL	1	TRUE	0	0.512958500781056	3		559	713	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36934823	36934823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145256322	NA	P-0028675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	153	472	0	ENST00000361632.4:c.1510G>A	p.Val504Met	p.V504M	ENST00000361632		504	Gtg/Atg	11/16	0.51358656175209	2	FACETS	1	0.978	1	0.584	0.537	0.631	CLONAL	1	TRUE	0	0.512958500781056	2		472	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578474	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	342	668	0	ENST00000269305.4:c.456del	p.Gly154AlafsTer16	p.G154Afs*16	ENST00000269305	NM_001126112.2	152	ccG/cc	5/11	0.51358656175209	2	FACETS	0.923	0.88	0.967	0.923	0.88	0.967	CLONAL	2	TRUE	0	0.512958500781056	2		668	722	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55478746	55478746	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	62	431	0	ENST00000284073.2:c.319A>G	p.Thr107Ala	p.T107A	ENST00000284073	NM_138962.2	107	Aca/Gca	6/14	0.512958500781056	5	FACETS	0.515	0.444	0.593			1	SUBCLONAL	1	TRUE	NA	0.512958500781056	5		431	830	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026757	6026758	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs863224498	NA	P-0028675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	56	183	0	ENST00000265849.7:c.1638_1639del	p.Ser547ArgfsTer14	p.S547Rfs*14	ENST00000265849	NM_000535.5	546	ttTTca/ttca	11/15	0.257075296082033	4	FACETS	1	0.962	1	0.334	0.289	0.383	INDETERMINATE	1	TRUE	0	0.512958500781056	4		183	247	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0028677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	71	532	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.822	0.718	0.935	0.822	0.718	0.935	CLONAL	1	TRUE	1	0.288707507056891	2		533	598	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030343	49030343	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs137853297	NA	P-0028677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	59	242	0	ENST00000267163.4:c.1818T>A	p.Tyr606Ter	p.Y606*	ENST00000267163	NM_000321.2	606	taT/taA	19/27	0.217720521945696	1	FACETS	0.988	0.854	1	0.988	0.854	1	CLONAL	1	TRUE	0	0.288707507056891	1		242	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1555525429	NA	P-0028677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	123	561	0	ENST00000269305.4:c.782+1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.217720521945696	1	FACETS	0.892	0.807	0.983	0.892	0.807	0.983	CLONAL	1	TRUE	0	0.288707507056891	1		561	817	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	138	454	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.972	0.898	1	0.972	0.898	1	CLONAL	1	TRUE	1	0.874001193348662	2		454	325	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0028679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	209	461	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.874001193348662	2		461	383	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0028679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	20	487	1	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.076	0.058	0.098	0.076	0.058	0.098	SUBCLONAL	1	TRUE	1	0.874001193348662	2		488	599	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119789	70119789	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	286	627	0	ENST00000245479.2:c.791G>C	p.Arg264Thr	p.R264T	ENST00000245479	NM_000346.3	264	aGa/aCa	3/3	1	2	FACETS	0.987	0.935	1	0.987	0.935	1	CLONAL	1	TRUE	1	0.874001193348662	2		627	663	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185061	123185061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	14	261	0	ENST00000218089.9:c.1108C>T	p.Arg370Trp	p.R370W	ENST00000218089	NM_001042749.1	370	Cgg/Tgg	12/35	1	1	FACETS	0.055	0.039	0.075	0.055	0.039	0.075	SUBCLONAL	1	TRUE	0	0.874001193348662	1		261	326	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628335	187628335	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	311	546	0	ENST00000441802.2:c.2647C>A	p.Leu883Met	p.L883M	ENST00000441802	NM_005245.3	883	Ctg/Atg	2/27	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.874001193348662	2		546	696	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373293	118373293	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	262	368	1	ENST00000534358.1:c.6686C>A	p.Ser2229Ter	p.S2229*	ENST00000534358	NM_005933.3	2229	tCa/tAa	27/36	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.874001193348662	2		369	537	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266019	41266019	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	51	165	0	ENST00000349496.5:c.16G>A	p.Asp6Asn	p.D6N	ENST00000349496	NM_001904.3	6	Gat/Aat	3/15	1	2	FACETS	0.459	0.394	0.53	0.459	0.394	0.53	SUBCLONAL	1	TRUE	1	0.874001193348662	2		165	254	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665463	176665463	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	195	336	0	ENST00000439151.2:c.4147C>G	p.Pro1383Ala	p.P1383A	ENST00000439151	NM_022455.4	1383	Cca/Gca	7/23	0.843503198485616	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.874001193348662	1		336	249	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884510	151884510	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	192	361	1	ENST00000262189.6:c.4845G>C	p.Trp1615Cys	p.W1615C	ENST00000262189	NM_170606.2	1615	tgG/tgC	33/59	1	2	FACETS	0.976	0.913	1	0.976	0.913	1	CLONAL	1	TRUE	1	0.874001193348662	2		362	450	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0028680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	312	546	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.630746103226519	5	FACETS	1	0.992	1	0.874	0.835	0.912	CLONAL	3	TRUE	1	0.630746103226519	5		546	551	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044970	47044970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	653	610	0	ENST00000377604.3:c.2296C>T	p.Arg766Cys	p.R766C	ENST00000377604	NM_001204468.1	766	Cgc/Tgc	20/24	0.301900062801435	5	FACETS	1	0.995	1	0.799	0.77	0.828	INDETERMINATE	2	TRUE	2	0.630746103226519	5		610	1681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578369	7578369	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0028680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	713	386	3	ENST00000269305.4:c.559+2T>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.630858817967356	3	FACETS	1	0.986	1			1	CLONAL	3	TRUE	NA	0.630746103226519	3		389	977	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248726	212248726	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	62	308	0	ENST00000342788.4:c.3541C>G	p.Gln1181Glu	p.Q1181E	ENST00000342788	NM_005235.2	1181	Caa/Gaa	28/28	0.32541035003472	5	FACETS	0.926	0.803	1	0.309	0.267	0.353	INDETERMINATE	1	TRUE	2	0.630746103226519	5		308	413	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867471	35867471	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	45	316	0	ENST00000303115.3:c.285G>C	p.Glu95Asp	p.E95D	ENST00000303115	NM_002185.3	95	gaG/gaC	3/8	0.587223685153497	5	FACETS	0.62	0.521	0.729	0.207	0.173	0.243	SUBCLONAL	1	TRUE	2	0.630746103226519	5		316	448	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43745213	43745213	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	69	379	1	ENST00000523873.1:c.126G>T	p.Lys42Asn	p.K42N	ENST00000523873		42	aaG/aaT	3/8	0.28226235093258	5	FACETS	0.452	0.392	0.517	0.151	0.13	0.173	INDETERMINATE	1	TRUE	2	0.630746103226519	5		380	942	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055730	152055730	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	93	469	0	ENST00000262189.6:c.192del	p.Asp65MetfsTer40	p.D65Mfs*40	ENST00000262189	NM_170606.2	64	gaA/ga	2/59	0.49235175696469	3	FACETS	0.908	0.812	1	0.454	0.406	0.505	CLONAL	1	TRUE	1	0.630746103226519	3		469	427	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0028684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	201	688	1	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	0.176877284346525	3	FACETS	1	0.926	1	0.5	0.463	0.539	INDETERMINATE	1	TRUE	1	0.42	3		689	1158	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846130	68846131	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0028684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	223	673	1	ENST00000261769.5:c.1102dup	p.Thr368AsnfsTer4	p.T368Nfs*4	ENST00000261769	NM_004360.3	367	-/A	8/16	0.3	1	FACETS	0.975	0.91	1	0.975	0.91	1	CLONAL	1	TRUE	0	0.42	1		674	860	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589770	55589771	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0028684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	88	374	0	ENST00000288135.5:c.1253dup	p.Tyr418Ter	p.Y418*	ENST00000288135	NM_000222.2	418	tac/tAac	8/21	0.145094620770593	0	FACETS	0.609	0.543	0.679			1	INDETERMINATE	1	TRUE	0	0.42	0		374	399	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177771	56177772	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0028684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	62	295	0	ENST00000399503.3:c.2745_2746del	p.Ala917TyrfsTer12	p.A917Yfs*12	ENST00000399503	NM_005921.1	915	tTA/t	14/20	0.0975754668973918	3	FACETS	0.772	0.668	0.884	0.386	0.334	0.442	INDETERMINATE	1	TRUE	1	0.42	3		295	463	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519896	NA	P-0028689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	402	407	0	ENST00000281708.4:c.1514G>T	p.Arg505Leu	p.R505L	ENST00000281708	NM_033632.3	505	cGc/cTc	10/12	0.567650889043554	5	FACETS	1	0.986	1	1	0.986	1	CLONAL	4	FALSE	1	0.63838697792795	5		407	593	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46725681	46725681	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	174	526	0	ENST00000371975.4:c.317G>C	p.Arg106Pro	p.R106P	ENST00000371975	NM_003579.3	106	cGc/cCc	5/18	0.63838697792795	4	FACETS	1	0.989	1	0.705	0.652	0.76	CLONAL	1	FALSE	2	0.63838697792795	4		526	633	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176132097	176132097	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1322	285	512	0	ENST00000367669.3:c.670G>C	p.Asp224His	p.D224H	ENST00000367669	NM_022457.5	224	Gat/Cat	5/20	0.63838697792795	12	FACETS	1	0.986	1			1	CLONAL	2	FALSE	NA	0.63838697792795	12		512	1607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579813	7579843	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTGCCCTTCCAATGGATCCACTCACAGTTT	CCTGCCCTTCCAATGGATCCACTCACAGTTT	-	novel	NA	P-0028689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	150	587	0	ENST00000269305.4:c.70_74+26del		p.X24_splice	ENST00000269305	NM_001126112.2	24		2/11	NA	2	FACETS	0.873	0.817	0.929			1	INDETERMINATE	2	FALSE	NA	0.63838697792795	2		587	269	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492686	56492686	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0028689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	212	391	0	ENST00000407977.2:c.252+1G>T		p.X84_splice	ENST00000407977		84			0.475222806862026	4	FACETS	0.937	0.886	0.989	1	0.993	1	CLONAL	3	FALSE	2	0.63838697792795	4		391	387	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96931098	96931098	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	26	53	0	ENST00000258439.3:c.22G>A	p.Gly8Arg	p.G8R	ENST00000258439	NM_001193304.2	8	Ggg/Agg	2/4	0.63838697792795	4	FACETS	1	0.922	1	1	0.922	1	CLONAL	2	FALSE	2	0.63838697792795	4		53	55	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411875	116411898	+	splice_region_variant,intron_variant	Splice_Region	DEL	CAAGCTCTTTCTTTCTCTCTGTTT	CAAGCTCTTTCTTTCTCTCTGTTT	-	novel	NA	P-0028694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	90	909	0	ENST00000397752.3:c.2888-28_2888-5del		p.X963_splice	ENST00000397752	NM_000245.2	963			1	2	FACETS	0.668	0.591	0.75	0.668	0.591	0.75	SUBCLONAL	1	TRUE	1	0.280729688083414	2		909	960	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039279	47039279	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	50	829	0	ENST00000377604.3:c.903del	p.Ile302SerfsTer6	p.I302Sfs*6	ENST00000377604	NM_001204468.1	301	aCc/ac	10/24	0.280729688083414	1	FACETS	0.424	0.359	0.496	0.424	0.359	0.496	SUBCLONAL	1	TRUE	0	0.280729688083414	1		829	722	SUCCESS
BTK	695	MSKCC	GRCh37	X	100629553	100629553	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	41	643	0	ENST00000308731.7:c.211A>C	p.Lys71Gln	p.K71Q	ENST00000308731	NM_000061.2	71	Aaa/Caa	3/19	0.280729688083414	1	FACETS	0.354	0.294	0.421	0.354	0.294	0.421	SUBCLONAL	1	TRUE	0	0.280729688083414	1		643	709	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0028695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	137	671	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.571811188359767	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.556931928254842	2		671	222	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711960	89711962	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0028695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	47	534	0	ENST00000371953.3:c.582_584del	p.Leu194del	p.L194del	ENST00000371953	NM_000314.4	193	cTGTtg/ctg	6/9	0.571811188359767	2	FACETS	0.532	0.451	0.621	0.266	0.225	0.311	SUBCLONAL	1	TRUE	0	0.556931928254842	2		534	317	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510216	149510216	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	35	602	0	ENST00000261799.4:c.1253G>C	p.Arg418Pro	p.R418P	ENST00000261799	NM_002609.3	418	cGa/cCa	9/23	0.353897150272337	1	FACETS	0.357	0.294	0.427	0.357	0.294	0.427	SUBCLONAL	1	TRUE	0	0.556931928254842	1		602	254	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000036	30000036	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0028697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	200	504	0	ENST00000338641.4:c.49A>T	p.Lys17Ter	p.K17*	ENST00000338641	NM_000268.3	17	Aag/Tag	1/16	0.745306192660474	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.745306192660474	1		504	313	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834552	156834552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540521894	NA	P-0028700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	76	747	1	ENST00000524377.1:c.320C>T	p.Ala107Val	p.A107V	ENST00000524377	NM_002529.3	107	gCg/gTg	3/17	0.256006132691977	5	FACETS	0.688	0.601	0.781	0.229	0.2	0.261	SUBCLONAL	1	TRUE	2	0.314780460612712	5		748	1034	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455097	50455097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	57	434	0	ENST00000331340.3:c.644C>T	p.Ser215Phe	p.S215F	ENST00000331340	NM_006060.4	215	tCt/tTt	6/8	0.256006132691977	5	FACETS	0.922	0.791	1	0.307	0.263	0.355	CLONAL	1	TRUE	2	0.314780460612712	5		434	578	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	28	278	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.419	0.335	0.515	0.419	0.335	0.515	SUBCLONAL	1	TRUE	1	0.348037020038518	2		278	384	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	77	826	3	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	0.348037020038518	3	FACETS	0.543	0.476	0.617	0.272	0.238	0.309	SUBCLONAL	1	TRUE	1	0.348037020038518	3		829	956	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651264	45651264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772294235	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	90	607	0	ENST00000407780.3:c.761C>T	p.Ala254Val	p.A254V	ENST00000407780	NM_001283052.1	254	gCg/gTg	5/7	1	2	FACETS	0.654	0.58	0.733	0.654	0.58	0.733	SUBCLONAL	1	TRUE	1	0.348037020038518	2		607	791	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	54	333	1	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	1	FACETS	0.737	0.632	0.85	0.737	0.632	0.85	SUBCLONAL	1	TRUE	0	0.348037020038518	1		334	348	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276755	15276755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138265894	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	80	748	0	ENST00000263388.2:c.5510G>A	p.Arg1837His	p.R1837H	ENST00000263388	NM_000435.2	1837	cGt/cAt	30/33	1	2	FACETS	0.657	0.578	0.742	0.657	0.578	0.742	SUBCLONAL	1	TRUE	1	0.348037020038518	2		748	700	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	24	518	1	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	1	2	FACETS	0.263	0.205	0.33	0.263	0.205	0.33	SUBCLONAL	1	TRUE	1	0.348037020038518	2		519	525	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979563	7979563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1221632429	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	76	570	0	ENST00000319144.4:c.1462C>T	p.Arg488Cys	p.R488C	ENST00000319144	NM_001139.2	488	Cgt/Tgt	11/15	1	2	FACETS	0.65	0.57	0.736	0.65	0.57	0.736	SUBCLONAL	1	TRUE	1	0.348037020038518	2		570	672	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138570	2138570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45517423	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	67	587	2	ENST00000219476.3:c.5383C>T	p.Arg1795Cys	p.R1795C	ENST00000219476	NM_000548.3	1795	Cgc/Tgc	42/42	1	2	FACETS	0.611	0.531	0.698	0.611	0.531	0.698	SUBCLONAL	1	TRUE	1	0.348037020038518	2		589	630	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662224	227662224	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	77	734	2	ENST00000305123.5:c.1231C>T	p.Arg411Ter	p.R411*	ENST00000305123	NM_005544.2	411	Cga/Tga	1/2	1	2	FACETS	0.602	0.528	0.682	0.602	0.528	0.682	SUBCLONAL	1	TRUE	1	0.348037020038518	2		736	735	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204842	128204842	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs768767517	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	70	787	2	ENST00000341105.2:c.599del	p.Gly200ValfsTer18	p.G200Vfs*18	ENST00000341105	NM_032638.4	200	gGt/gt	3/6	1	2	FACETS	0.568	0.495	0.648	0.568	0.495	0.648	SUBCLONAL	1	TRUE	1	0.348037020038518	2		789	708	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467699	50467699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	66	669	1	ENST00000331340.3:c.934G>A	p.Asp312Asn	p.D312N	ENST00000331340	NM_006060.4	312	Gac/Aac	8/8	1	2	FACETS	0.54	0.468	0.618	0.54	0.468	0.618	SUBCLONAL	1	TRUE	1	0.348037020038518	2		670	702	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317422	1317422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759127718	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	58	489	0	ENST00000400841.2:c.643C>T	p.Arg215Trp	p.R215W	ENST00000400841		215	Cgg/Tgg	5/6	1	1	FACETS	0.557	0.479	0.642	0.557	0.479	0.642	SUBCLONAL	1	TRUE	0	0.348037020038518	1		489	494	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149917	202149917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	45	609	3	ENST00000358485.4:c.1358C>T	p.Pro453Leu	p.P453L	ENST00000358485	NM_001080125.1	453	cCg/cTg	8/9	1	2	FACETS	0.391	0.327	0.461	0.391	0.327	0.461	SUBCLONAL	1	TRUE	1	0.348037020038518	2		612	662	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411291	63411291	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1408150272	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	67	387	0	ENST00000330258.3:c.1876C>T	p.Arg626Ter	p.R626*	ENST00000330258	NM_152424.3	626	Cga/Tga	2/2	1	1	FACETS	0.93	0.813	1	0.93	0.813	1	CLONAL	1	TRUE	0	0.348037020038518	1		387	342	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820602	3820602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749011678	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	78	682	0	ENST00000262367.5:c.2849C>T	p.Thr950Met	p.T950M	ENST00000262367	NM_004380.2	950	aCg/aTg	14/31	1	2	FACETS	0.607	0.532	0.686	0.607	0.532	0.686	SUBCLONAL	1	TRUE	1	0.348037020038518	2		682	739	SUCCESS
APC	324	MSKCC	GRCh37	5	112175952	112175952	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587783031	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	39	303	0	ENST00000257430.4:c.4666del	p.Thr1556LeufsTer9	p.T1556Lfs*9	ENST00000257430	NM_000038.5	1554	gAa/ga	16/16	1	2	FACETS	0.661	0.549	0.785	0.661	0.549	0.785	SUBCLONAL	1	TRUE	1	0.348037020038518	2		303	339	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954273	32954273	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359752	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	47	397	0	ENST00000380152.3:c.9253del	p.Thr3085GlnfsTer19	p.T3085Qfs*19	ENST00000380152		3083	Aaa/aa	24/27	1	2	FACETS	0.491	0.414	0.576	0.491	0.414	0.576	SUBCLONAL	1	TRUE	1	0.348037020038518	2		397	550	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176666775	176666775	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776547552	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	53	457	0	ENST00000439151.2:c.4211G>A	p.Arg1404His	p.R1404H	ENST00000439151	NM_022455.4	1404	cGt/cAt	8/23	1	2	FACETS	0.498	0.425	0.58	0.498	0.425	0.58	SUBCLONAL	1	TRUE	1	0.348037020038518	2		457	611	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522741	67522741	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	38	284	1	ENST00000274335.5:c.244del	p.Ile82SerfsTer32	p.I82Sfs*32	ENST00000274335		80	Aaa/aa	1/15	1	2	FACETS	0.652	0.54	0.776	0.652	0.54	0.776	SUBCLONAL	1	TRUE	1	0.348037020038518	2		285	335	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874197	155874197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375724784	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	78	667	0	ENST00000368323.3:c.334C>T	p.Arg112Cys	p.R112C	ENST00000368323	NM_006912.5	112	Cgt/Tgt	5/6	1	2	FACETS	0.529	0.463	0.599	0.529	0.463	0.599	SUBCLONAL	1	TRUE	1	0.348037020038518	2		667	848	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119780	70119781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	63	627	0	ENST00000245479.2:c.788dup	p.Arg264GlnfsTer32	p.R264Qfs*32	ENST00000245479	NM_000346.3	261	gag/gaGg	3/3	1	2	FACETS	0.593	0.513	0.681	0.593	0.513	0.681	SUBCLONAL	1	TRUE	1	0.348037020038518	2		627	610	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145611	11145611	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	67	591	2	ENST00000358026.2:c.3973C>T	p.Arg1325Cys	p.R1325C	ENST00000358026	NM_001128849.1	1325	Cgc/Tgc	29/36	1	2	FACETS	0.608	0.528	0.695	0.608	0.528	0.695	SUBCLONAL	1	TRUE	1	0.348037020038518	2		593	633	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	187	754	0	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	0.348037020038518	3	FACETS	1	0.985	1	0.638	0.589	0.689	CLONAL	1	TRUE	1	0.348037020038518	3		754	988	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428327	33428327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781813	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	64	552	0	ENST00000345365.6:c.796C>T	p.Arg266Cys	p.R266C	ENST00000345365	NM_002878.3	266	Cgc/Tgc	9/10	1	2	FACETS	0.596	0.516	0.683	0.596	0.516	0.683	SUBCLONAL	1	TRUE	1	0.348037020038518	2		552	617	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444543	187444543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs77733730	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	54	495	0	ENST00000232014.4:c.1684G>A	p.Ala562Thr	p.A562T	ENST00000232014	NM_001130845.1	562	Gcc/Acc	7/10	1	2	FACETS	0.531	0.453	0.617	0.531	0.453	0.617	SUBCLONAL	1	TRUE	1	0.348037020038518	2		495	584	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43733757	43733757	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	63	408	0	ENST00000382044.4:c.3065del	p.Asn1022MetfsTer20	p.N1022Mfs*20	ENST00000382044	NM_001141980.1	1022	aAt/at	15/28	1	2	FACETS	0.546	0.472	0.627	0.546	0.472	0.627	SUBCLONAL	1	TRUE	1	0.348037020038518	2		408	663	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984559	72984559	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770062973	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	69	675	0	ENST00000268489.5:c.3025G>A	p.Val1009Met	p.V1009M	ENST00000268489	NM_006885.3	1009	Gtg/Atg	3/10	1	2	FACETS	0.535	0.465	0.611	0.535	0.465	0.611	SUBCLONAL	1	TRUE	1	0.348037020038518	2		675	741	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41197783	41197783	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs273902776	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	93	579	0	ENST00000357654.3:c.5504G>A	p.Arg1835Gln	p.R1835Q	ENST00000357654	NM_007294.3	1835	cGa/cAa	23/23	1	2	FACETS	0.689	0.612	0.771	0.689	0.612	0.771	SUBCLONAL	1	TRUE	1	0.348037020038518	2		579	776	SUCCESS
APC	324	MSKCC	GRCh37	5	112174213	112174214	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554084587	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	36	405	0	ENST00000257430.4:c.2926dup	p.Arg976LysfsTer9	p.R976Kfs*9	ENST00000257430	NM_000038.5	974	-/A	16/16	1	2	FACETS	0.389	0.319	0.467	0.389	0.319	0.467	SUBCLONAL	1	TRUE	1	0.348037020038518	2		405	532	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324513	62324513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123018	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	117	743	0	ENST00000360203.5:c.2869C>T	p.Arg957Trp	p.R957W	ENST00000360203	NM_001283009.1	957	Cgg/Tgg	30/35	1	2	FACETS	0.785	0.708	0.868	0.785	0.708	0.868	SUBCLONAL	1	TRUE	1	0.348037020038518	2		743	856	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182662919	182662919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451035070	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	57	551	1	ENST00000292782.4:c.743G>A	p.Arg248His	p.R248H	ENST00000292782	NM_020640.2	248	cGc/cAc	7/7	1	2	FACETS	0.463	0.396	0.535	0.463	0.396	0.535	SUBCLONAL	1	TRUE	1	0.348037020038518	2		552	708	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260103	19260103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369287078	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	84	676	0	ENST00000162023.5:c.190C>T	p.Arg64Cys	p.R64C	ENST00000162023		64	Cgt/Tgt	7/13	1	2	FACETS	0.619	0.546	0.697	0.619	0.546	0.697	SUBCLONAL	1	TRUE	1	0.348037020038518	2		676	780	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260447	16260447	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	30	476	0	ENST00000375759.3:c.7715del	p.Pro2572ArgfsTer11	p.P2572Rfs*11	ENST00000375759	NM_015001.2	2571	gCc/gc	11/15	1	2	FACETS	0.313	0.252	0.384	0.313	0.252	0.384	SUBCLONAL	1	TRUE	1	0.348037020038518	2		476	550	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088655	27088655	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	80	738	1	ENST00000324856.7:c.2264G>T	p.Arg755Met	p.R755M	ENST00000324856	NM_006015.4	755	aGg/aTg	7/20	1	2	FACETS	0.59	0.519	0.667	0.59	0.519	0.667	SUBCLONAL	1	TRUE	1	0.348037020038518	2		739	779	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546330	46546330	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	47	389	0	ENST00000262741.5:c.199T>C	p.Trp67Arg	p.W67R	ENST00000262741	NM_003629.3	67	Tgg/Cgg	2/10	1	2	FACETS	0.555	0.468	0.65	0.555	0.468	0.65	SUBCLONAL	1	TRUE	1	0.348037020038518	2		389	487	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439919	51439919	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	18	236	0	ENST00000262662.1:c.488del	p.Gly163GlufsTer24	p.G163Efs*24	ENST00000262662		162	Ggg/gg	4/4	1	2	FACETS	0.358	0.269	0.463	0.358	0.269	0.463	SUBCLONAL	1	TRUE	1	0.348037020038518	2		236	289	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332824	65332824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773295622	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	47	352	0	ENST00000342505.4:c.715C>T	p.Arg239Trp	p.R239W	ENST00000342505	NM_002227.2	239	Cgg/Tgg	7/25	1	2	FACETS	0.578	0.488	0.678	0.578	0.488	0.678	SUBCLONAL	1	TRUE	1	0.348037020038518	2		352	467	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226566919	226566919	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	58	486	0	ENST00000366794.5:c.1669del	p.Gly558AlafsTer38	p.G558Afs*38	ENST00000366794	NM_001618.3	557	Ctt/tt	12/23	1	2	FACETS	0.593	0.509	0.684	0.593	0.509	0.684	SUBCLONAL	1	TRUE	1	0.348037020038518	2		486	562	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612975	228612975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs551314787	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	42	377	0	ENST00000366696.1:c.52C>T	p.Arg18Cys	p.R18C	ENST00000366696	NM_003493.2	18	Cgc/Tgc	1/1	1	2	FACETS	0.69	0.577	0.813	0.69	0.577	0.813	SUBCLONAL	1	TRUE	1	0.348037020038518	2		377	350	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692783	89692783	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	44	410	0	ENST00000371953.3:c.270del	p.Phe90LeufsTer9	p.F90Lfs*9	ENST00000371953	NM_000314.4	89	ccT/cc	5/9	1	2	FACETS	0.504	0.422	0.594	0.504	0.422	0.594	SUBCLONAL	1	TRUE	1	0.348037020038518	2		410	502	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154869	2154869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	86	741	1	ENST00000434045.2:c.352C>T	p.Arg118Cys	p.R118C	ENST00000434045	NM_001127598.1	118	Cgc/Tgc	4/5	1	2	FACETS	0.741	0.656	0.832	0.741	0.656	0.832	SUBCLONAL	1	TRUE	1	0.348037020038518	2		742	667	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047243	77047243	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	47	532	0	ENST00000356341.3:c.1301A>G	p.Glu434Gly	p.E434G	ENST00000356341	NM_002576.4	434	gAg/gGg	13/15	1	2	FACETS	0.45	0.379	0.529	0.45	0.379	0.529	SUBCLONAL	1	TRUE	1	0.348037020038518	2		532	600	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023135	1023135	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776952629	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	37	546	1	ENST00000358495.3:c.1120G>A	p.Val374Ile	p.V374I	ENST00000358495	NM_134424.2	374	Gtt/Att	11/12	NA	2	FACETS	0.312	0.256	0.374			1	INDETERMINATE	1	TRUE	NA	0.348037020038518	2		547	682	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420732	49420732	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	61	561	0	ENST00000301067.7:c.15017A>C	p.Glu5006Ala	p.E5006A	ENST00000301067	NM_003482.3	5006	gAg/gCg	48/54	1	2	FACETS	0.584	0.504	0.672	0.584	0.504	0.672	SUBCLONAL	1	TRUE	1	0.348037020038518	2		561	600	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437555	49437557	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	54	551	0	ENST00000301067.7:c.5328_5330del	p.Phe1777del	p.F1777del	ENST00000301067	NM_003482.3	1776	ttCTTt/ttt	23/54	1	2	FACETS	0.563	0.481	0.653	0.563	0.481	0.653	SUBCLONAL	1	TRUE	1	0.348037020038518	2		551	551	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112283	115112283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1018135320	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	24	173	0	ENST00000257566.3:c.1457C>T	p.Thr486Met	p.T486M	ENST00000257566	NM_016569.3	486	aCg/aTg	7/8	1	2	FACETS	0.758	0.598	0.939	0.758	0.598	0.939	CLONAL	1	TRUE	1	0.348037020038518	2		173	182	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896972	28896972	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1033990749	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	39	435	0	ENST00000282397.4:c.2908G>A	p.Gly970Ser	p.G970S	ENST00000282397	NM_002019.4	970	Ggc/Agc	21/30	0.331568536692628	1	FACETS	0.283	0.234	0.339	0.283	0.234	0.339	SUBCLONAL	1	TRUE	0	0.348037020038518	1		435	653	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242059	105242059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746934495	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	81	691	0	ENST00000349310.3:c.365C>T	p.Ser122Leu	p.S122L	ENST00000349310	NM_001014432.1	122	tCg/tTg	6/15	1	2	FACETS	0.653	0.575	0.737	0.653	0.575	0.737	SUBCLONAL	1	TRUE	1	0.348037020038518	2		691	713	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99482559	99482559	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	51	495	0	ENST00000268035.6:c.3427G>T	p.Val1143Leu	p.V1143L	ENST00000268035	NM_000875.3	1143	Gta/Tta	18/21	1	2	FACETS	0.459	0.39	0.536	0.459	0.39	0.536	SUBCLONAL	1	TRUE	1	0.348037020038518	2		495	638	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820668	3820668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768030911	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	110	796	1	ENST00000262367.5:c.2783C>T	p.Pro928Leu	p.P928L	ENST00000262367	NM_004380.2	928	cCg/cTg	14/31	1	2	FACETS	0.719	0.645	0.797	0.719	0.645	0.797	SUBCLONAL	1	TRUE	1	0.348037020038518	2		797	879	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23635330	23635330	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	70	607	0	ENST00000261584.4:c.2834G>A	p.Arg945Lys	p.R945K	ENST00000261584	NM_024675.3	945	aGg/aAg	8/13	1	2	FACETS	0.563	0.49	0.641	0.563	0.49	0.641	SUBCLONAL	1	TRUE	1	0.348037020038518	2		607	715	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969947	81969947	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	52	492	0	ENST00000359376.3:c.3016G>A	p.Gly1006Ser	p.G1006S	ENST00000359376	NM_002661.3	1006	Ggt/Agt	27/33	1	2	FACETS	0.566	0.482	0.658	0.566	0.482	0.658	SUBCLONAL	1	TRUE	1	0.348037020038518	2		492	528	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681003	37681003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1225789669	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	63	500	0	ENST00000447079.4:c.3172G>A	p.Glu1058Lys	p.E1058K	ENST00000447079	NM_015083.1	1058	Gaa/Aaa	12/14	1	2	FACETS	0.524	0.452	0.602	0.524	0.452	0.602	SUBCLONAL	1	TRUE	1	0.348037020038518	2		500	691	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512369	38512370	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	37	635	0	ENST00000254066.5:c.1286dup	p.Gly430TrpfsTer16	p.G430Wfs*16	ENST00000254066	NM_000964.3	427	ccg/ccGg	9/9	1	2	FACETS	0.36	0.296	0.432	0.36	0.296	0.432	SUBCLONAL	1	TRUE	1	0.348037020038518	2		635	591	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10264989	10264989	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763570334	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	32	380	1	ENST00000340748.4:c.1951C>T	p.Arg651Trp	p.R651W	ENST00000340748		651	Cgg/Tgg	21/40	1	2	FACETS	0.481	0.391	0.584	0.481	0.391	0.584	SUBCLONAL	1	TRUE	1	0.348037020038518	2		381	382	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296304	15296304	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	64	680	0	ENST00000263388.2:c.2138C>A	p.Pro713His	p.P713H	ENST00000263388	NM_000435.2	713	cCt/cAt	13/33	1	2	FACETS	0.629	0.544	0.72	0.629	0.544	0.72	SUBCLONAL	1	TRUE	1	0.348037020038518	2		680	585	SUCCESS
AXL	558	MSKCC	GRCh37	19	41737112	41737112	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	51	765	0	ENST00000301178.4:c.692T>G	p.Leu231Arg	p.L231R	ENST00000301178	NM_021913.4	231	cTc/cGc	6/20	0.348037020038518	3	FACETS	0.382	0.324	0.447	0.191	0.162	0.224	SUBCLONAL	1	TRUE	1	0.348037020038518	3		765	900	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867053	45867053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1285451320	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	48	586	1	ENST00000391945.4:c.1066G>A	p.Ala356Thr	p.A356T	ENST00000391945	NM_000400.3	356	Gcc/Acc	11/23	0.348037020038518	3	FACETS	0.457	0.385	0.536	0.228	0.192	0.268	SUBCLONAL	1	TRUE	1	0.348037020038518	3		587	709	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637396	47637396	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	67	574	0	ENST00000233146.2:c.531del	p.Glu177AspfsTer37	p.E177Dfs*37	ENST00000233146	NM_000251.2	177	gAa/ga	3/16	1	2	FACETS	0.517	0.448	0.591	0.517	0.448	0.591	SUBCLONAL	1	TRUE	1	0.348037020038518	2		574	745	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257847	198257847	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	66	490	0	ENST00000335508.6:c.3605T>C	p.Phe1202Ser	p.F1202S	ENST00000335508	NM_012433.2	1202	tTt/tCt	24/25	1	2	FACETS	0.569	0.494	0.651	0.569	0.494	0.651	SUBCLONAL	1	TRUE	1	0.348037020038518	2		490	666	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657162	215657162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	29	237	0	ENST00000260947.4:c.223G>A	p.Val75Ile	p.V75I	ENST00000260947	NM_000465.2	75	Gta/Ata	3/11	1	2	FACETS	0.45	0.361	0.551	0.45	0.361	0.551	SUBCLONAL	1	TRUE	1	0.348037020038518	2		237	370	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379425	225379425	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	66	597	1	ENST00000264414.4:c.443G>A	p.Arg148Gln	p.R148Q	ENST00000264414	NM_003590.4	148	cGa/cAa	4/16	1	2	FACETS	0.456	0.395	0.523	0.456	0.395	0.523	SUBCLONAL	1	TRUE	1	0.348037020038518	2		598	831	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017790	31017790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564841799	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	66	559	0	ENST00000375687.4:c.652C>T	p.Arg218Cys	p.R218C	ENST00000375687	NM_015338.5	218	Cgt/Tgt	8/13	1	2	FACETS	0.649	0.564	0.742	0.649	0.564	0.742	SUBCLONAL	1	TRUE	1	0.348037020038518	2		559	584	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419863	41419863	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	55	542	0	ENST00000373198.4:c.458T>C	p.Ile153Thr	p.I153T	ENST00000373198	NM_133170.3	153	aTc/aCc	3/32	0.348037020038518	0	FACETS	0.407	0.348	0.471			1	SUBCLONAL	1	TRUE	0	0.348037020038518	0		542	506	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319048	62319048	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779627326	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	94	741	1	ENST00000360203.5:c.1406G>A	p.Arg469His	p.R469H	ENST00000360203	NM_001283009.1	469	cGc/cAc	17/35	1	2	FACETS	0.723	0.643	0.808	0.723	0.643	0.808	SUBCLONAL	1	TRUE	1	0.348037020038518	2		742	747	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42879925	42879925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	44	209	0	ENST00000398585.3:c.7C>T	p.Pro3Ser	p.P3S	ENST00000398585	NM_001135099.1	3	Cct/Tct	1/14	1	2	FACETS	0.744	0.626	0.873	0.744	0.626	0.873	SUBCLONAL	1	TRUE	1	0.348037020038518	2		209	340	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438586	52438586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1466585782	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	41	367	0	ENST00000460680.1:c.1133C>T	p.Ala378Val	p.A378V	ENST00000460680	NM_004656.3	378	gCg/gTg	12/17	1	2	FACETS	0.542	0.451	0.642	0.542	0.451	0.642	SUBCLONAL	1	TRUE	1	0.348037020038518	2		367	435	SUCCESS
ATR	545	MSKCC	GRCh37	3	142177876	142177876	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777776233	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	44	558	0	ENST00000350721.4:c.7427G>A	p.Arg2476His	p.R2476H	ENST00000350721	NM_001184.3	2476	cGt/cAt	44/47	1	2	FACETS	0.399	0.334	0.471	0.399	0.334	0.471	SUBCLONAL	1	TRUE	1	0.348037020038518	2		558	634	SUCCESS
ATR	545	MSKCC	GRCh37	3	142238584	142238584	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1366497648	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	40	281	0	ENST00000350721.4:c.4309G>A	p.Gly1437Ser	p.G1437S	ENST00000350721	NM_001184.3	1437	Ggc/Agc	24/47	1	2	FACETS	0.588	0.489	0.697	0.588	0.489	0.697	SUBCLONAL	1	TRUE	1	0.348037020038518	2		281	391	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612243	189612243	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	39	397	0	ENST00000264731.3:c.1995G>T	p.Met665Ile	p.M665I	ENST00000264731	NM_003722.4	665	atG/atT	14/14	1	2	FACETS	0.506	0.419	0.602	0.506	0.419	0.602	SUBCLONAL	1	TRUE	1	0.348037020038518	2		397	443	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509115	66509115	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1398953167	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	29	414	0	ENST00000273854.3:c.212G>A	p.Gly71Glu	p.G71E	ENST00000273854	NM_004439.5	71	gGg/gAg	2/18	1	2	FACETS	0.347	0.278	0.426	0.347	0.278	0.426	SUBCLONAL	1	TRUE	1	0.348037020038518	2		414	480	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500479	149500479	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1218819598	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	72	595	0	ENST00000261799.4:c.2558G>A	p.Arg853Gln	p.R853Q	ENST00000261799	NM_002609.3	853	cGg/cAg	18/23	1	2	FACETS	0.631	0.551	0.717	0.631	0.551	0.717	SUBCLONAL	1	TRUE	1	0.348037020038518	2		595	656	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638455	176638455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1460977537	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	86	678	0	ENST00000439151.2:c.3055C>T	p.Arg1019Cys	p.R1019C	ENST00000439151	NM_022455.4	1019	Cgc/Tgc	5/23	1	2	FACETS	0.606	0.536	0.682	0.606	0.536	0.682	SUBCLONAL	1	TRUE	1	0.348037020038518	2		678	815	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983060	111983060	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	58	592	0	ENST00000368678.4:c.1487T>C	p.Met496Thr	p.M496T	ENST00000368678		496	aTg/aCg	13/13	1	2	FACETS	0.548	0.471	0.633	0.548	0.471	0.633	SUBCLONAL	1	TRUE	1	0.348037020038518	2		592	608	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129337	152129338	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	50	471	2	ENST00000206249.3:c.296dup	p.Leu100ThrfsTer57	p.L100Tfs*57	ENST00000206249	NM_000125.3	97	ttc/ttCc	1/8	1	2	FACETS	0.614	0.521	0.715	0.614	0.521	0.715	SUBCLONAL	1	TRUE	1	0.348037020038518	2		473	468	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527742	157527742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1315767745	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	63	478	0	ENST00000346085.5:c.5467G>A	p.Gly1823Arg	p.G1823R	ENST00000346085	NM_020732.3	1823	Ggg/Agg	20/20	1	2	FACETS	0.636	0.55	0.729	0.636	0.55	0.729	SUBCLONAL	1	TRUE	1	0.348037020038518	2		478	569	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343444	70343444	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1209035119	NA	P-0028701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	14	239	2	ENST00000374080.3:c.1618C>T	p.Arg540Cys	p.R540C	ENST00000374080		540	Cgt/Tgt	12/45	1	1	FACETS	0.255	0.184	0.341	0.255	0.184	0.341	SUBCLONAL	1	TRUE	0	0.348037020038518	1		241	261	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577586	7577586	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587781589	NA	P-0028704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	161	539	0	ENST00000269305.4:c.695T>C	p.Ile232Thr	p.I232T	ENST00000269305	NM_001126112.2	232	aTc/aCc	7/11	0.236959904807221	2	FACETS	0.773	0.711	0.838	0.773	0.711	0.838	SUBCLONAL	2	TRUE	0	0.289635534362379	2		539	719	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935636	15935636	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532511938	NA	P-0028704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	44	307	0	ENST00000268712.3:c.7297G>A	p.Glu2433Lys	p.E2433K	ENST00000268712	NM_006311.3	2433	Gag/Aag	46/46	0.236959904807221	2	FACETS	0.806	0.677	0.947	0.403	0.338	0.474	CLONAL	1	TRUE	0	0.289635534362379	2		307	377	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94128989	94128989	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	64	374	0	ENST00000369303.4:c.71C>T	p.Thr24Ile	p.T24I	ENST00000369303	NM_004440.3	24	aCa/aTa	1/17	0.271145293092017	3	FACETS	0.845	0.731	0.967	0.422	0.365	0.484	CLONAL	1	TRUE	1	0.289635534362379	3		374	599	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	37	454	0				ENST00000310581	NM_198253.2	-/1132			0.267469313686868	0	FACETS	0.749	0.639	0.862			1	SUBCLONAL	3	TRUE	0	0.267938832057588	0		454	90	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598345	28598366	+	frameshift_variant	Frame_Shift_Del	DEL	CCTTGGCCAGCTCCTGGCGCCA	CCTTGGCCAGCTCCTGGCGCCA	-	novel	NA	P-0028705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	74	707	0	ENST00000253063.3:c.318_339del	p.Leu107ThrfsTer16	p.L107Tfs*16	ENST00000253063	NM_031459.4	106	cCCTTGGCCAGCTCCTGGCGCCAc/cc	3/10	0.267938832057588	5	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	3	0.267938832057588	5		707	325	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750420	41750420	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1242397056	NA	P-0028705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	25	502	1	ENST00000226382.2:c.208C>T	p.Leu70Phe	p.L70F	ENST00000226382	NM_003924.3	70	Ctc/Ttc	1/3	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.267938832057588	2		503	156	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971146	55971146	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	28	567	1	ENST00000263923.4:c.1651C>A	p.Pro551Thr	p.P551T	ENST00000263923	NM_002253.2	551	Cct/Act	13/30	1	2	FACETS	0.933	0.75	1	0.933	0.75	1	CLONAL	1	TRUE	1	0.267938832057588	2		568	224	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875640	35875640	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	38	446	0	ENST00000303115.3:c.827T>C	p.Leu276Pro	p.L276P	ENST00000303115	NM_002185.3	276	cTc/cCc	7/8	0.267938832057588	9	FACETS	1	0.874	1	0.424	0.353	0.503	CLONAL	2	TRUE	4	0.267938832057588	9		446	259	SUCCESS
APC	324	MSKCC	GRCh37	5	112179488	112179488	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1429919728	NA	P-0028705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	21	486	0	ENST00000257430.4:c.8197C>G	p.Gln2733Glu	p.Q2733E	ENST00000257430	NM_000038.5	2733	Caa/Gaa	16/16	0.267938832057588	7	FACETS	0.855	0.659	1	0.214	0.164	0.271	CLONAL	1	TRUE	3	0.267938832057588	7		486	306	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002874	69002874	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	53	357	0	ENST00000288368.4:c.2174T>A	p.Ile725Asn	p.I725N	ENST00000288368	NM_024870.2	725	aTc/aAc	20/40	0.234067034717164	3	FACETS	0.768	0.66	0.885	0.768	0.66	0.885	SUBCLONAL	2	TRUE	1	0.267938832057588	3		357	292	SUCCESS
BLM	641	MSKCC	GRCh37	15	91352421	91352423	+	frameshift_variant	Frame_Shift_Del	DEL	ACA	ACA	G	novel	NA	P-0028705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	36	438	0	ENST00000355112.3:c.3806_3808delinsG	p.Asp1269GlyfsTer18	p.D1269Gfs*18	ENST00000355112	NM_000057.2	1269	gACAaa/gGaa	20/22	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.267938832057588	2		438	206	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0028708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	190	532	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.309365582798956	3	FACETS	0.774	0.717	0.832			1	SUBCLONAL	2	TRUE	NA	0.406359968491444	3		533	727	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578260	7578260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204041	NA	P-0028708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	208	781	0	ENST00000269305.4:c.589G>A	p.Val197Met	p.V197M	ENST00000269305	NM_001126112.2	197	Gtg/Atg	6/11	0.406359968491444	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.406359968491444	1		781	802	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244401	46244401	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	149	637	0	ENST00000334344.6:c.2495C>T	p.Ser832Leu	p.S832L	ENST00000334344	NM_152641.2	832	tCa/tTa	15/21	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.406359968491444	2		637	719	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974683	21974684	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0028708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	263	483	0	ENST00000304494.5:c.142_143dup	p.Ile49ArgfsTer5	p.I49Rfs*5	ENST00000304494	NM_000077.4	48	ccg/ccCCg	1/3	0.406359968491444	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.406359968491444	2		483	624	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0028710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	80	546	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.922	0.82	1	0.922	0.82	1	CLONAL	1	TRUE	1	0.590288658624481	2		546	294	SUCCESS
APC	324	MSKCC	GRCh37	5	112175246	112175246	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1057517558	NA	P-0028710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	71	247	0	ENST00000257430.4:c.3956del	p.Pro1319LeufsTer2	p.P1319Lfs*2	ENST00000257430	NM_000038.5	1319	Cct/ct	16/16	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.590288658624481	2		247	226	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593466	48593466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064796102	NA	P-0028710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	92	371	0	ENST00000342988.3:c.1217C>T	p.Ala406Val	p.A406V	ENST00000342988	NM_005359.5	406	gCg/gTg	10/12	0.590288658624481	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.590288658624481	1		371	213	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916644	178916644	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	85	421	0	ENST00000263967.3:c.31T>G	p.Trp11Gly	p.W11G	ENST00000263967	NM_006218.2	11	Tgg/Ggg	2/21	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.590288658624481	2		421	275	SUCCESS
APC	324	MSKCC	GRCh37	5	112175251	112175255	+	frameshift_variant	Frame_Shift_Del	DEL	GAGCG	GAGCG	-	novel	NA	P-0028710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	66	246	0	ENST00000257430.4:c.3960_3964del	p.Glu1322SerfsTer8	p.E1322Sfs*8	ENST00000257430	NM_000038.5	1320	gtGAGCGaa/gtaa	16/16	1	2	FACETS	0.981	0.864	1	0.981	0.864	1	CLONAL	1	TRUE	1	0.590288658624481	2		246	228	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0028712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	193	545	1	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	0.755795566822996	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.755795566822996	1		546	281	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17743021	17743021	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	124	673	0	ENST00000250003.3:c.929G>T	p.Gly310Val	p.G310V	ENST00000250003	NM_002478.4	310	gGt/gTt	3/3	0.318707719820749	1	FACETS	0.762	0.702	0.821	0.762	0.702	0.821	INDETERMINATE	1	TRUE	0	0.755795566822996	1		673	268	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570070	212570070	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs745408040	NA	P-0028712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	74	387	0	ENST00000342788.4:c.1171G>T	p.Val391Phe	p.V391F	ENST00000342788	NM_005235.2	391	Gtc/Ttc	10/28	0.246258679268462	3	FACETS	0.745	0.657	0.84	0.373	0.328	0.42	INDETERMINATE	1	TRUE	1	0.755795566822996	3		387	362	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105973	27105973	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0028712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	71	457	0	ENST00000324856.7:c.5584A>T	p.Lys1862Ter	p.K1862*	ENST00000324856	NM_006015.4	1862	Aag/Tag	20/20	0.331157874163844	4	FACETS	0.76	0.666	0.861	0.38	0.333	0.431	INDETERMINATE	1	TRUE	2	0.755795566822996	4		457	434	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332390	70332390	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	154	525	0	ENST00000373644.4:c.295T>A	p.Cys99Ser	p.C99S	ENST00000373644	NM_030625.2	99	Tgc/Agc	2/12	NA	2	FACETS	1	0.944	1			1	INDETERMINATE	1	TRUE	NA	0.755795566822996	2		525	398	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111958623	111958623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	132	355	0	ENST00000375549.3:c.95C>T	p.Ser32Leu	p.S32L	ENST00000375549	NM_003002.3	32	tCa/tTa	2/4	0.264645467165244	4	FACETS	0.774	0.71	0.841	0.774	0.71	0.841	INDETERMINATE	2	TRUE	2	0.755795566822996	4		355	396	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484327	50484328	+	missense_variant	Missense_Mutation	DNP	GC	GC	AT	novel	NA	P-0028712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	111	460	3	ENST00000394963.4:c.1087_1088delinsAT	p.Ala363Ile	p.A363I	ENST00000394963	NM_003076.4	363	GCc/ATc	9/13	0.688830568734074	2	FACETS	1	0.956	1	0.536	0.49	0.583	CLONAL	1	TRUE	0	0.755795566822996	2		463	274	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434783	110434783	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	165	746	1	ENST00000375856.3:c.3618G>T	p.Gln1206His	p.Q1206H	ENST00000375856	NM_003749.2	1206	caG/caT	1/2	0.727721250127508	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.755795566822996	1		747	257	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89846317	89846317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201323171	NA	P-0028712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	133	644	0	ENST00000389301.3:c.1675G>A	p.Glu559Lys	p.E559K	ENST00000389301	NM_000135.2	559	Gag/Aag	18/43	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.755795566822996	2		644	346	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510593	38510593	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	131	652	0	ENST00000254066.5:c.847A>C	p.Thr283Pro	p.T283P	ENST00000254066	NM_000964.3	283	Acc/Ccc	7/9	0.321976125226803	1	FACETS	0.492	0.45	0.536	0.492	0.45	0.536	INDETERMINATE	1	TRUE	0	0.755795566822996	1		652	438	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796039	78796039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	167	598	0	ENST00000306801.3:c.929G>A	p.Gly310Asp	p.G310D	ENST00000306801	NM_020761.2	310	gGt/gAt	8/34	0.321976125226803	1	FACETS	0.584	0.541	0.627	0.584	0.541	0.627	INDETERMINATE	1	TRUE	0	0.755795566822996	1		598	471	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17389793	17389793	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	222	836	0	ENST00000359435.4:c.926G>T	p.Ser309Ile	p.S309I	ENST00000359435	NM_001033549.1	309	aGc/aTc	9/9	0.755795566822996	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.755795566822996	1		836	322	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128030511	128030511	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	113	533	0	ENST00000285398.2:c.1757A>C	p.Gln586Pro	p.Q586P	ENST00000285398	NM_000122.1	586	cAg/cCg	11/15	0.321976125226803	1	FACETS	1	0.957	1	1	0.957	1	INDETERMINATE	1	TRUE	0	0.755795566822996	1		533	179	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566833	212566833	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	51	287	0	ENST00000342788.4:c.1348C>A	p.Leu450Met	p.L450M	ENST00000342788	NM_005235.2	450	Ctg/Atg	12/28	0.246258679268462	3	FACETS	0.721	0.618	0.832	0.36	0.309	0.416	INDETERMINATE	1	TRUE	1	0.755795566822996	3		287	258	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368527	225368527	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	16	206	0	ENST00000264414.4:c.1219G>T	p.Glu407Ter	p.E407*	ENST00000264414	NM_003590.4	407	Gaa/Taa	9/16	0.246258679268462	3	FACETS	0.298	0.22	0.389	0.149	0.11	0.195	INDETERMINATE	1	TRUE	1	0.755795566822996	3		206	196	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790084	40790085	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AT	novel	NA	P-0028712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	116	575	0	ENST00000373198.4:c.2646_2647delinsAT	p.Asp882_Gln883delinsGluTer	p.D882_Q883delinsE*	ENST00000373198	NM_133170.3	882	gaCCag/gaATag	18/32	0.407695117814506	3	FACETS	0.732	0.662	0.805	0.244	0.22	0.269	INDETERMINATE	1	TRUE	0	0.755795566822996	3		575	578	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72861859	72861859	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	145	560	0	ENST00000325599.8:c.1023G>A	p.Met341Ile	p.M341I	ENST00000325599	NM_018130.2	341	atG/atA	9/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.755795566822996	2		560	337	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205121	128205121	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	127	557	0	ENST00000341105.2:c.320C>A	p.Ala107Asp	p.A107D	ENST00000341105	NM_032638.4	107	gCc/gAc	3/6	1	2	FACETS	0.911	0.834	0.989	0.911	0.834	0.989	CLONAL	1	TRUE	1	0.755795566822996	2		557	369	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447565	187447565	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	83	542	0	ENST00000232014.4:c.628G>T	p.Asp210Tyr	p.D210Y	ENST00000232014	NM_001130845.1	210	Gat/Tat	5/10	1	2	FACETS	0.6	0.533	0.671	0.6	0.533	0.671	SUBCLONAL	1	TRUE	1	0.755795566822996	2		542	366	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155245	55155245	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	98	505	0	ENST00000257290.5:c.2844G>T	p.Glu948Asp	p.E948D	ENST00000257290	NM_006206.4	948	gaG/gaT	21/23	1	2	FACETS	0.882	0.797	0.97	0.882	0.797	0.97	CLONAL	1	TRUE	1	0.755795566822996	2		505	294	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405809	157405809	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	117	334	0	ENST00000346085.5:c.2051C>T	p.Ser684Phe	p.S684F	ENST00000346085	NM_020732.3	684	tCc/tTc	6/20	0.755795566822996	1	FACETS	0.958	0.89	1	0.958	0.89	1	CLONAL	1	TRUE	0	0.755795566822996	1		334	201	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93640032	93640032	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	50	267	0	ENST00000375746.1:c.1361G>A	p.Gly454Asp	p.G454D	ENST00000375746	NM_001174167.1	454	gGt/gAt	10/14	0.499648462797837	1	FACETS	0.392	0.336	0.451	0.392	0.336	0.451	SUBCLONAL	1	TRUE	0	0.755795566822996	1		267	210	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911461	101911461	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs1249384165	NA	P-0028712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	46	232	0	ENST00000374994.4:c.1387-1G>T		p.X463_splice	ENST00000374994	NM_004612.2	463			0.499648462797837	1	FACETS	0.765	0.668	0.863	0.765	0.668	0.863	SUBCLONAL	1	TRUE	0	0.755795566822996	1		232	99	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0028714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	619	609	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.943	0.922	0.962	1	0.998	1	CLONAL	3	TRUE	1	0.572314045215392	2		610	765	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913499	NA	P-0028714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	112	240	0	ENST00000345146.2:c.394C>A	p.Arg132Ser	p.R132S	ENST00000345146	NM_005896.2	132	Cgt/Agt	4/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.572314045215392	2		240	278	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0028714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	32	609	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	1	2	FACETS	0.152	0.123	0.186	0.152	0.123	0.186	SUBCLONAL	1	TRUE	1	0.572314045215392	2		609	734	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912129	76912129	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	13	168	0	ENST00000373344.5:c.4135del	p.Ser1379GlnfsTer111	p.S1379Qfs*111	ENST00000373344	NM_000489.3	1379	Tca/ca	13/35	1	1	FACETS	0.131	0.093	0.177	0.131	0.093	0.177	SUBCLONAL	1	TRUE	0	0.572314045215392	1		168	248	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944404	76944407	+	frameshift_variant	Frame_Shift_Del	DEL	CCCA	CCCA	-	novel	NA	P-0028714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	248	241	0	ENST00000373344.5:c.498_501del	p.His166GlnfsTer3	p.H166Qfs*3	ENST00000373344	NM_000489.3	166	caTGGG/ca	7/35	1	1	FACETS	0.949	0.913	0.983	1	0.996	1	CLONAL	2	TRUE	0	0.572314045215392	1		241	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0028715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	342	590	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.363408582208593	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.380250950745582	2		590	831	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916940	178916948	+	inframe_deletion	In_Frame_Del	DEL	AGAAAAGAT	AGAAAAGAT	-	novel	NA	P-0028715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	74	383	0	ENST00000263967.3:c.327_335del	p.Glu109_Ile112delinsAsp	p.E109_I112delinsD	ENST00000263967	NM_006218.2	109	gaAGAAAAGATc/gac	2/21	0.255514950755956	3	FACETS	0.833	0.737	0.934	0.833	0.737	0.934	CLONAL	2	TRUE	1	0.380250950745582	3		383	278	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885995	59885995	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752309409	NA	P-0028715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	140	437	0	ENST00000259008.2:c.751C>T	p.Arg251Cys	p.R251C	ENST00000259008	NM_032043.2	251	Cgc/Tgc	7/20	0.380250950745582	2	FACETS	0.889	0.818	0.963	0.889	0.818	0.963	CLONAL	2	TRUE	0	0.380250950745582	2		437	414	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663780	29663780	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	146	483	0	ENST00000356175.3:c.6212A>G	p.Asn2071Ser	p.N2071S	ENST00000356175	NM_000267.3	2071	aAt/aGt	41/57	1	2	FACETS	0.937	0.858	1	0.937	0.858	1	CLONAL	1	TRUE	1	0.49012656755987	2		483	636	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547883	41547883	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	134	432	0	ENST00000263253.7:c.2864C>G	p.Pro955Arg	p.P955R	ENST00000263253	NM_001429.3	955	cCa/cGa	15/31	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.49012656755987	2		432	523	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953832	55953832	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs145493938	NA	P-0028716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	121	437	0	ENST00000263923.4:c.3604A>G	p.Met1202Val	p.M1202V	ENST00000263923	NM_002253.2	1202	Atg/Gtg	27/30	1	2	FACETS	0.869	0.788	0.954	0.869	0.788	0.954	CLONAL	1	TRUE	1	0.49012656755987	2		437	568	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143215	30143215	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	72	459	0	ENST00000389048.3:c.311C>A	p.Pro104Gln	p.P104Q	ENST00000389048	NM_004304.4	104	cCg/cAg	1/29	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		459	582	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0028720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	148	576	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.310198092723525	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.310198092723525	3		576	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882025	NA	P-0028720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	136	548	0	ENST00000269305.4:c.646G>T	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ttg	6/11	0.274902413225365	2	FACETS	0.848	0.775	0.923	0.848	0.775	0.923	CLONAL	2	TRUE	0	0.310198092723525	2		548	517	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760836	59760836	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs761405340	NA	P-0028720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	146	534	0	ENST00000259008.2:c.3571A>G	p.Ile1191Val	p.I1191V	ENST00000259008	NM_032043.2	1191	Ata/Gta	20/20	0.290157305599533	4	FACETS	0.876	0.801	0.954	0.876	0.801	0.954	CLONAL	2	TRUE	2	0.310198092723525	4		534	704	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0028721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	583	498	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.846260359119631	2	FACETS	0.973	0.952	0.992	0.973	0.952	0.992	CLONAL	2	TRUE	0	0.857526109731286	2		498	699	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111554	8111554	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	278	502	0	ENST00000346208.3:c.1040T>G	p.Leu347Arg	p.L347R	ENST00000346208		347	cTt/cGt	5/6	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.857526109731286	2		502	645	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542785	187542785	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	29	377	0	ENST00000441802.2:c.4955C>T	p.Ser1652Phe	p.S1652F	ENST00000441802	NM_005245.3	1652	tCt/tTt	10/27	1	2	FACETS	0.141	0.113	0.174	0.141	0.113	0.174	SUBCLONAL	1	TRUE	1	0.857526109731286	2		377	479	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852054	63852057	+	frameshift_variant	Frame_Shift_Del	DEL	CAGC	CAGC	-	novel	NA	P-0028721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	266	497	0	ENST00000279873.7:c.2835_2838del	p.Ser945ArgfsTer15	p.S945Rfs*15	ENST00000279873	NM_032199.2	944	ggCAGC/gg	10/10	1	2	FACETS	0.949	0.896	1	0.949	0.896	1	CLONAL	1	TRUE	1	0.857526109731286	2		497	654	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402127	402127	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	276	474	0	ENST00000399788.2:c.4664T>G	p.Leu1555Arg	p.L1555R	ENST00000399788	NM_001042603.1	1555	cTa/cGa	27/28	0.672227133082131	3	FACETS	1	0.946	1			1	CLONAL	1	TRUE	NA	0.857526109731286	3		474	915	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555625	21555625	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	216	527	0	ENST00000382592.4:c.2645C>T	p.Pro882Leu	p.P882L	ENST00000382592	NM_014572.2	882	cCc/cTc	6/8	0.857526109731286	1	FACETS	0.827	0.785	0.868	0.827	0.785	0.868	CLONAL	1	TRUE	0	0.857526109731286	1		527	348	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273261	18273261	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	84	507	0	ENST00000222254.8:c.1054T>G	p.Phe352Val	p.F352V	ENST00000222254	NM_005027.3	352	Ttc/Gtc	9/16	0.857526109731286	1	FACETS	0.324	0.289	0.362	0.324	0.289	0.362	SUBCLONAL	1	TRUE	0	0.857526109731286	1		507	345	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026807	71026807	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	111	250	0	ENST00000318789.4:c.1415C>G	p.Ser472Cys	p.S472C	ENST00000318789	NM_032682.5	472	tCt/tGt	16/21	0.857526109731286	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.857526109731286	1		250	144	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929331	44929331	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	319	652	0	ENST00000377967.4:c.2431A>T	p.Thr811Ser	p.T811S	ENST00000377967	NM_021140.2	811	Act/Tct	17/29	1	2	FACETS	0.883	0.837	0.929	0.883	0.837	0.929	CLONAL	1	TRUE	1	0.857526109731286	2		652	843	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0028722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	62	383	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.839	0.732	0.954	0.839	0.732	0.954	CLONAL	1	TRUE	1	0.523830378163163	2		383	282	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950393	17950393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777849274	NA	P-0028722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	155	626	1	ENST00000458235.1:c.1334G>A	p.Arg445Gln	p.R445Q	ENST00000458235	NM_000215.3	445	cGa/cAa	10/24	0.434899483634678	4	FACETS	0.943	0.863	1	0.472	0.431	0.514	CLONAL	1	TRUE	2	0.523830378163163	4		627	956	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578266	7578266	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs942158624	NA	P-0028722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	325	589	0	ENST00000269305.4:c.583A>T	p.Ile195Phe	p.I195F	ENST00000269305	NM_001126112.2	195	Atc/Ttc	6/11	0.523830378163163	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.523830378163163	2		589	563	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168682	32168682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs935064991	NA	P-0028722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	333	598	0	ENST00000375023.3:c.4241C>T	p.Ala1414Val	p.A1414V	ENST00000375023	NM_004557.3	1414	gCg/gTg	23/30	0.508394536807257	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	2	0.523830378163163	4		598	806	SUCCESS
ATM	472	MSKCC	GRCh37	11	108099978	108099978	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	147	307	0	ENST00000278616.4:c.259C>T	p.Gln87Ter	p.Q87*	ENST00000278616	NM_000051.3	87	Caa/Taa	4/63	0.523830378163163	4	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	2	0.523830378163163	4		307	423	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727899	41727899	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	294	668	0	ENST00000301178.4:c.524A>C	p.Gln175Pro	p.Q175P	ENST00000301178	NM_021913.4	175	cAg/cCg	4/20	0.434899483634678	4	FACETS	0.945	0.892	0.999	0.945	0.892	0.999	CLONAL	2	TRUE	2	0.523830378163163	4		668	905	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755839	39755839	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	149	215	0	ENST00000288319.7:c.926G>T	p.Gly309Val	p.G309V	ENST00000288319	NM_182918.3	309	gGc/gTc	10/10	1	2	FACETS	0.996	0.924	1	0.996	0.924	1	CLONAL	1	TRUE	1	0.874644827088244	2		215	342	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	151	557	0	ENST00000347630.2:c.397T>C	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	Ttc/Ctc	6/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.498694162454678	2		557	567	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913396	NA	P-0028741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	225	294	0	ENST00000349496.5:c.95A>C	p.Asp32Ala	p.D32A	ENST00000349496	NM_001904.3	32	gAc/gCc	3/15	0.498694162454678	4	FACETS	0.886	0.833	0.938	0.886	0.833	0.938	CLONAL	3	TRUE	1	0.498694162454678	4		294	509	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969369	44969369	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1318649487	NA	P-0028741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	75	240	0	ENST00000377967.4:c.4051C>T	p.Arg1351Ter	p.R1351*	ENST00000377967	NM_021140.2	1351	Cga/Tga	28/29	1	1	FACETS	0.706	0.624	0.792	0.706	0.624	0.792	SUBCLONAL	1	TRUE	0	0.498694162454678	1		240	320	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451223	70451223	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	133	568	0	ENST00000373644.4:c.6063G>C	p.Glu2021Asp	p.E2021D	ENST00000373644	NM_030625.2	2021	gaG/gaC	12/12	1	2	FACETS	0.841	0.766	0.92	0.841	0.766	0.92	CLONAL	1	TRUE	1	0.498694162454678	2		568	634	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164723	36164724	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGC	novel	NA	P-0028741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	41	643	0	ENST00000300305.3:c.1149_1151dup	p.Pro384dup	p.P384dup	ENST00000300305		384	ccc/ccGCCc	8/8	0.376128858740988	3	FACETS	0.294	0.244	0.35	0.147	0.122	0.175	SUBCLONAL	1	TRUE	1	0.498694162454678	3		643	699	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913517	NA	P-0028742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	92	424	0	ENST00000288135.5:c.1676T>C	p.Val559Ala	p.V559A	ENST00000288135	NM_000222.2	559	gTt/gCt	11/21	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.568701982888518	2		424	305	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487559	38487559	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	88	588	1	ENST00000254066.5:c.89C>T	p.Pro30Leu	p.P30L	ENST00000254066	NM_000964.3	30	cCt/cTt	2/9	1	2	FACETS	0.57	0.506	0.638	0.57	0.506	0.638	SUBCLONAL	1	TRUE	1	0.568701982888518	2		589	543	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0028743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	152	350	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.350224697850406	4	FACETS	1	0.985	1	0.664	0.609	0.721	CLONAL	1	TRUE	2	0.548057717410654	4		350	647	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46714262	46714262	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	98	358	0	ENST00000371975.4:c.82G>T	p.Gly28Cys	p.G28C	ENST00000371975	NM_003579.3	28	Ggc/Tgc	2/18	1	2	FACETS	0.747	0.669	0.828	0.747	0.669	0.828	SUBCLONAL	1	TRUE	1	0.548057717410654	2		358	479	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515263	103515263	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	68	330	0	ENST00000355739.4:c.1764C>A	p.Ser588Arg	p.S588R	ENST00000355739	NM_000123.3	588	agC/agA	8/15	1	2	FACETS	0.701	0.614	0.794	0.701	0.614	0.794	SUBCLONAL	1	TRUE	1	0.548057717410654	2		330	354	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631837	90631837	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	123	431	0	ENST00000330062.3:c.516G>T	p.Arg172Ser	p.R172S	ENST00000330062	NM_002168.2	172	agG/agT	4/11	1	2	FACETS	0.922	0.838	1	0.922	0.838	1	CLONAL	1	TRUE	1	0.548057717410654	2		431	487	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138572	11138572	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	116	532	0	ENST00000358026.2:c.3328A>G	p.Thr1110Ala	p.T1110A	ENST00000358026	NM_001128849.1	1110	Acc/Gcc	24/36	1	2	FACETS	0.764	0.691	0.841	0.764	0.691	0.841	SUBCLONAL	1	TRUE	1	0.548057717410654	2		532	554	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719125	52719125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771769470	NA	P-0028743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	129	528	0	ENST00000322088.6:c.901G>A	p.Ala301Thr	p.A301T	ENST00000322088	NM_014225.5	301	Gca/Aca	7/15	1	2	FACETS	0.969	0.884	1	0.969	0.884	1	CLONAL	1	TRUE	1	0.548057717410654	2		528	486	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570377	87570377	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	139	552	1	ENST00000277120.3:c.2117T>C	p.Val706Ala	p.V706A	ENST00000277120		706	gTg/gCg	17/19	1	2	FACETS	0.899	0.822	0.979	0.899	0.822	0.979	CLONAL	1	TRUE	1	0.548057717410654	2		553	564	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0028744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	51	556	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.15502279645215	2	FACETS	0.795	0.677	0.923	0.795	0.677	0.923	CLONAL	2	TRUE	0	0.15502279645215	2		556	414	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0028744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	78	427	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.15502279645215	2	FACETS	0.883	0.777	0.996	0.883	0.777	0.996	CLONAL	2	TRUE	0	0.15502279645215	2		427	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0028744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	92	664	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.15502279645215	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	2	TRUE	0	0.15502279645215	2		664	571	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205070	128205070	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569301892	NA	P-0028744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	80	660	1	ENST00000341105.2:c.371C>T	p.Thr124Met	p.T124M	ENST00000341105	NM_032638.4	124	aCg/aTg	3/6	1	2	FACETS	0.907	0.8	1	1	0.982	1	CLONAL	2	TRUE	1	0.15502279645215	2		661	569	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836833	151836841	+	inframe_deletion	In_Frame_Del	DEL	ATGGTGTGT	ATGGTGTGT	-	novel	NA	P-0028744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	40	518	0	ENST00000262189.6:c.14379_14387del	p.His4794_Met4796del	p.H4794_M4796del	ENST00000262189	NM_170606.2	4793	aaACACACCATg/aag	56/59	0.15502279645215	3	FACETS	0.888	0.737	1	0.444	0.368	0.529	CLONAL	1	TRUE	1	0.15502279645215	3		518	626	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129631	11129631	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0028745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	107	551	0	ENST00000358026.2:c.2439-2A>G		p.X813_splice	ENST00000358026	NM_001128849.1	813			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		551	408	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0028746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	105	514	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.24	2		514	625	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813492	32813492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	39	588	0	ENST00000354258.4:c.2291G>A	p.Ser764Asn	p.S764N	ENST00000354258	NM_000593.5	764	aGc/aAc	11/11	1	2	FACETS	0.487	0.402	0.581	0.487	0.402	0.581	SUBCLONAL	1	TRUE	1	0.24	2		588	668	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0028751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	187	543	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.378559856579155	1	FACETS	0.973	0.901	1	0.973	0.901	1	CLONAL	1	TRUE	0	0.393731757422133	1		543	784	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692887	89692887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660535	NA	P-0028751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	303	263	0	ENST00000371953.3:c.371G>A	p.Cys124Tyr	p.C124Y	ENST00000371953	NM_000314.4	124	tGt/tAt	5/9	0.393731757422133	3	FACETS	0.939	0.892	0.986	0.939	0.892	0.986	CLONAL	3	TRUE	0	0.393731757422133	3		263	654	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161405	185161405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	134	387	0	ENST00000265026.3:c.832C>T	p.Arg278Cys	p.R278C	ENST00000265026	NM_004721.4	278	Cgt/Tgt	4/14	0.362073610420986	4	FACETS	0.95	0.862	1	0.237	0.215	0.261	CLONAL	1	TRUE	0	0.393731757422133	4		387	999	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432095	49432095	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	369	574	0	ENST00000301067.7:c.9044G>A	p.Gly3015Asp	p.G3015D	ENST00000301067	NM_003482.3	3015	gGt/gAt	34/54	0.362350162180459	3	FACETS	0.917	0.87	0.965	0.917	0.87	0.965	CLONAL	2	TRUE	1	0.393731757422133	3		574	1223	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974740	15974740	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	113	360	0	ENST00000268712.3:c.4135G>C	p.Glu1379Gln	p.E1379Q	ENST00000268712	NM_006311.3	1379	Gag/Cag	30/46	0.389434265489633	4	FACETS	0.824	0.74	0.913	0.275	0.246	0.305	CLONAL	1	TRUE	1	0.393731757422133	4		360	971	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157838	27157838	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	113	366	0	ENST00000380036.4:c.62A>G	p.Glu21Gly	p.E21G	ENST00000380036	NM_000459.3	21	gAa/gGa	2/23	0.393731757422133	1	FACETS	0.947	0.856	1	0.947	0.856	1	CLONAL	1	TRUE	0	0.393731757422133	1		366	487	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595880	52595881	+	frameshift_variant	Frame_Shift_Ins	INS	AA	AA	CAG	novel	NA	P-0028751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	166	527	0	ENST00000394830.3:c.4034_4035delinsCTG	p.Ile1345ThrfsTer25	p.I1345Tfs*25	ENST00000394830	NM_018313.4	1345	aTT/aCTG	26/30	0.373113568261316	4	FACETS	0.983	0.902	1	0.492	0.451	0.535	CLONAL	1	TRUE	2	0.393731757422133	4		527	1195	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0028754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	492	532	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.484641884950124	4	FACETS	0.912	0.878	0.946	0.912	0.878	0.946	CLONAL	3	TRUE	1	0.593158096330037	4		533	966	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555687605	NA	P-0028754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	221	413	3	ENST00000342988.3:c.1610A>G	p.Asp537Gly	p.D537G	ENST00000342988	NM_005359.5	537	gAc/gGc	12/12	0.593158096330037	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.593158096330037	1		416	462	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932136	36932136	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759549054	NA	P-0028754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	184	524	0	ENST00000361632.4:c.2333C>T	p.Ala778Val	p.A778V	ENST00000361632		778	gCg/gTg	16/16	0.542903885481585	3	FACETS	0.91	0.841	0.982	0.455	0.42	0.491	CLONAL	1	TRUE	1	0.593158096330037	3		524	884	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576991	7577353	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCACCGCTTCTTGTCCTGCTTGCTTACCTCGCTTAGTGCTCCCTGGGGGCAGCTCGTGGTGAGGCTCCCCTTTCTTGCGGAGATTCTCTTCCTCTGTGCGCCGGTCTCTCCCAGGACAGGCACAAACACGCACCTCAAAGCTGTTCCGTCCCAGTAGATTACCACTACTCAGGATAGGAAAAGAGAAGCAAGAGGCAGTAAGGAAATCAGGTCCTACCTGTCCCATTTAAAAAACCAGGCTCCATCTACTCCCAACCACCCTTGTCCTTTCTGGAGCCTAAGCTCCAGCTCCAGGTAGGTGGAGGAGAAGCCACAGGTTAAGAGGTCCCAAAGCCAGAGAAAAGAAAACTGAGTGGGAGCAG	TCCACCGCTTCTTGTCCTGCTTGCTTACCTCGCTTAGTGCTCCCTGGGGGCAGCTCGTGGTGAGGCTCCCCTTTCTTGCGGAGATTCTCTTCCTCTGTGCGCCGGTCTCTCCCAGGACAGGCACAAACACGCACCTCAAAGCTGTTCCGTCCCAGTAGATTACCACTACTCAGGATAGGAAAAGAGAAGCAAGAGGCAGTAAGGAAATCAGGTCCTACCTGTCCCATTTAAAAAACCAGGCTCCATCTACTCCCAACCACCCTTGTCCTTTCTGGAGCCTAAGCTCCAGCTCCAGGTAGGTGGAGGAGAAGCCACAGGTTAAGAGGTCCCAAAGCCAGAGAAAAGAAAACTGAGTGGGAGCAG	-	novel	NA	P-0028754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	248	536	2	ENST00000269305.4:c.782+146_919+28del		p.X261_splice	ENST00000269305	NM_001126112.2	261		8/11	0.528666021444789	2	FACETS	1	0.993	1	0.705	0.665	0.746	CLONAL	1	TRUE	0	0.593158096330037	2		538	593	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61710126	61710126	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1441467096	NA	P-0028754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	50	428	0	ENST00000401558.2:c.2778C>G	p.Ile926Met	p.I926M	ENST00000401558	NM_003400.3	926	atC/atG	22/25	0.593158096330037	3	FACETS	0.258	0.218	0.302	0.086	0.072	0.101	SUBCLONAL	1	TRUE	0	0.593158096330037	3		428	848	SUCCESS
APC	324	MSKCC	GRCh37	5	112175828	112175829	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0028754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	121	298	3	ENST00000257430.4:c.4538_4539del	p.Glu1513AlafsTer19	p.E1513Afs*19	ENST00000257430	NM_000038.5	1513	GAg/g	16/16	0.522244756869518	1	FACETS	0.883	0.809	0.959	0.883	0.809	0.959	CLONAL	1	TRUE	0	0.593158096330037	1		301	325	SUCCESS
APC	324	MSKCC	GRCh37	5	112175411	112175411	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	59	248	0	ENST00000257430.4:c.4120G>T	p.Glu1374Ter	p.E1374*	ENST00000257430	NM_000038.5	1374	Gaa/Taa	16/16	0.306530783366107	3	FACETS	0.733	0.633	0.841	0.366	0.316	0.421	INDETERMINATE	1	TRUE	1	0.516860821289437	3		248	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0028793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	66	536	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.3233362532619	1	FACETS	0.291	0.252	0.334	0.291	0.252	0.334	SUBCLONAL	1	TRUE	0	0.516860821289437	1		536	650	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851754	134851754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56396912	NA	P-0028793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	98	442	3	ENST00000398015.3:c.1160C>T	p.Thr387Met	p.T387M	ENST00000398015	NM_004441.4	387	aCg/aTg	5/16	1	2	FACETS	0.608	0.543	0.677	0.608	0.543	0.677	SUBCLONAL	1	TRUE	1	0.516860821289437	2		445	624	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356452	70356454	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0028793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	82	367	0	ENST00000374080.3:c.5353_5355del	p.Lys1785del	p.K1785del	ENST00000374080		1783	AAG/-	37/45	0.313881110413369	2	FACETS	0.469	0.413	0.528			1	SUBCLONAL	1	TRUE	NA	0.516860821289437	2		367	677	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822609	72822609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771122441	NA	P-0028793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	130	521	1	ENST00000268489.5:c.9566C>T	p.Ala3189Val	p.A3189V	ENST00000268489	NM_006885.3	3189	gCg/gTg	10/10	1	2	FACETS	0.72	0.654	0.789	0.72	0.654	0.789	SUBCLONAL	1	TRUE	1	0.516860821289437	2		522	699	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43738583	43738583	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0028793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	94	414	0	ENST00000382044.4:c.3040+2T>C		p.X1014_splice	ENST00000382044	NM_001141980.1	1014			1	2	FACETS	0.616	0.549	0.688	0.616	0.549	0.688	SUBCLONAL	1	TRUE	1	0.516860821289437	2		414	590	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879598	37879598	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	412	723	0	ENST00000269571.5:c.1973T>G	p.Val658Gly	p.V658G	ENST00000269571		658	gTg/gGg	17/27	0.516860821289437	3	FACETS	0.814	0.775	0.853	0.814	0.775	0.853	CLONAL	2	TRUE	1	0.516860821289437	3		723	1233	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494218	140494218	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	179	856	0	ENST00000288602.6:c.1030C>T	p.Gln344Ter	p.Q344*	ENST00000288602	NM_004333.4	344	Cag/Tag	8/18	0.306530783366107	3	FACETS	0.647	0.595	0.702	0.324	0.297	0.351	INDETERMINATE	1	TRUE	1	0.516860821289437	3		856	1347	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0028897-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	410	367	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.374212742859117	3	FACETS	0.958	0.917	1	1	0.996	1	CLONAL	3	TRUE	1	0.374212742859117	3		367	905	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207146	1207146	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028897-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	350	741	0	ENST00000326873.7:c.234G>T	p.Lys78Asn	p.K78N	ENST00000326873	NM_000455.4	78	aaG/aaT	1/10	0.369029835481729	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.374212742859117	2		741	914	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11264660	11264660	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028897-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	123	549	0	ENST00000361445.4:c.3902G>T	p.Arg1301Leu	p.R1301L	ENST00000361445	NM_004958.3	1301	cGc/cTc	26/58	1	2	FACETS	0.936	0.848	1	0.936	0.848	1	CLONAL	1	TRUE	1	0.374212742859117	2		549	702	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793440	242793440	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028897-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	219	560	1	ENST00000334409.5:c.637C>G	p.Pro213Ala	p.P213A	ENST00000334409	NM_005018.2	213	Ccc/Gcc	5/5	0.374212742859117	3	FACETS	0.915	0.854	0.978	0.915	0.854	0.978	CLONAL	2	TRUE	1	0.374212742859117	3		561	759	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217108	66217108	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028897-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	303	429	0	ENST00000273854.3:c.2507G>C	p.Arg836Thr	p.R836T	ENST00000273854	NM_004439.5	836	aGg/aCg	14/18	0.374212742859117	5	FACETS	0.94	0.888	0.992	0.94	0.888	0.992	CLONAL	3	TRUE	2	0.374212742859117	5		429	897	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15808651	15808651	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028897-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	138	625	0	ENST00000307771.7:c.33G>C	p.Glu11Asp	p.E11D	ENST00000307771	NM_005089.3	11	gaG/gaC	1/11	0.334021174991657	3	FACETS	1	0.922	1			1	CLONAL	1	TRUE	NA	0.374212742859117	3		625	863	SUCCESS
ATM	472	MSKCC	GRCh37	11	108168013	108168013	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0028897-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	139	297	0	ENST00000278616.4:c.4910-1G>A		p.X1637_splice	ENST00000278616	NM_000051.3	1637			0.337731908376216	2	FACETS	0.945	0.87	1	0.945	0.87	1	CLONAL	2	TRUE	0	0.374212742859117	2		297	393	SUCCESS
AXL	558	MSKCC	GRCh37	19	41736935	41736935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776682499	NA	P-0029291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	32	491	0	ENST00000301178.4:c.650G>A	p.Arg217His	p.R217H	ENST00000301178	NM_021913.4	217	cGc/cAc	5/20	1	2	FACETS	0.166	0.134	0.202	0.166	0.134	0.202	SUBCLONAL	1	TRUE	1	0.671159739335761	2		491	575	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390791	139390791	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	40	632	0	ENST00000277541.6:c.7400C>A	p.Ser2467Ter	p.S2467*	ENST00000277541	NM_017617.3	2467	tCg/tAg	34/34	1	2	FACETS	0.173	0.143	0.206	0.173	0.143	0.206	SUBCLONAL	1	TRUE	1	0.671159739335761	2		632	690	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390794	139390794	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	47	627	0	ENST00000277541.6:c.7397del	p.Thr2466SerfsTer11	p.T2466Sfs*11	ENST00000277541	NM_017617.3	2466	aCg/ag	34/34	1	2	FACETS	0.204	0.171	0.24	0.204	0.171	0.24	SUBCLONAL	1	TRUE	1	0.671159739335761	2		627	688	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089721	27089721	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	228	518	0	ENST00000324856.7:c.2680del	p.Thr894ProfsTer25	p.T894Pfs*25	ENST00000324856	NM_006015.4	893	Aaa/aa	8/20	0.361048847406959	2	FACETS	1	0.982	1	0.558	0.523	0.593	INDETERMINATE	1	TRUE	0	0.671159739335761	2		518	609	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857614	78857614	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	98	505	0	ENST00000306801.3:c.1684T>A	p.Cys562Ser	p.C562S	ENST00000306801	NM_020761.2	562	Tgc/Agc	16/34	1	2	FACETS	0.546	0.488	0.607	0.546	0.488	0.607	SUBCLONAL	1	TRUE	1	0.671159739335761	2		505	535	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053203	180053203	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	111	527	0	ENST00000261937.6:c.1166T>C	p.Val389Ala	p.V389A	ENST00000261937	NM_182925.4	389	gTg/gCg	9/30	1	2	FACETS	0.522	0.47	0.577	0.522	0.47	0.577	SUBCLONAL	1	TRUE	1	0.671159739335761	2		527	634	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878133	151878134	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	73	389	0	ENST00000262189.6:c.6811dup	p.Thr2271AsnfsTer7	p.T2271Nfs*7	ENST00000262189	NM_170606.2	2271	aca/aAca	36/59	1	2	FACETS	0.527	0.463	0.595	0.527	0.463	0.595	SUBCLONAL	1	TRUE	1	0.671159739335761	2		389	413	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390906	139390909	+	frameshift_variant	Frame_Shift_Del	DEL	GGTG	GGTG	CCT	novel	NA	P-0029291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	86	574	4	ENST00000277541.6:c.7282_7285delinsAGG	p.His2428ArgfsTer7	p.H2428Rfs*7	ENST00000277541	NM_017617.3	2428	CACCtg/AGGtg	34/34	1	2	FACETS	0.425	0.376	0.477	0.425	0.376	0.477	SUBCLONAL	1	TRUE	1	0.671159739335761	2		578	603	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396740	139396741	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTCGCCGAGGGGCT	novel	NA	P-0029291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	83	479	0	ENST00000277541.6:c.5354_5367dup	p.Asp1790SerfsTer13	p.D1790Sfs*13	ENST00000277541	NM_017617.3	1789	-/AGCCCCTCGGCGAG	28/34	1	2	FACETS	0.361	0.318	0.407	0.361	0.318	0.407	SUBCLONAL	1	TRUE	1	0.671159739335761	2		479	685	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0029328-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	142	712	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.154053346468294	2	FACETS	0.936	0.856	1	1	0.986	1	CLONAL	3	TRUE	0	0.16	2		712	632	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0029328-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	230	653	0	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	0.170104549205285	3	FACETS	0.995	0.928	1	0.995	0.928	1	CLONAL	3	TRUE	0	0.16	3		653	1040	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54948538	54948538	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029328-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	38	457	0	ENST00000312783.6:c.780G>T	p.Glu260Asp	p.E260D	ENST00000312783	NM_198436.1	260	gaG/gaT	8/10	1	2	FACETS	0.638	0.526	0.765	0.638	0.526	0.765	SUBCLONAL	1	TRUE	1	0.16	2		457	744	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0029428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	33	601	7	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.987	0.802	1	0.987	0.802	1	CLONAL	1	TRUE	1	0.11	2		608	608	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243926	41243926	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0029428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	30	595	1	ENST00000357654.3:c.3622A>T	p.Lys1208Ter	p.K1208*	ENST00000357654	NM_007294.3	1208	Aaa/Taa	10/23	1	2	FACETS	0.969	0.779	1	0.969	0.779	1	CLONAL	1	TRUE	1	0.11	2		596	563	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267393	198267393	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	66	599	0	ENST00000335508.6:c.1964A>G	p.Lys655Arg	p.K655R	ENST00000335508	NM_012433.2	655	aAg/aGg	14/25	0.3	3	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	3		599	1100	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411882	116411898	+	splice_region_variant,intron_variant	Splice_Region	DEL	TTTCTTTCTCTCTGTTT	TTTCTTTCTCTCTGTTT	-	novel	NA	P-0029472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	244	902	0	ENST00000397752.3:c.2888-20_2888-4del		p.X963_splice	ENST00000397752	NM_000245.2	963			1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		902	1316	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	75	279	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.325527773954423	2		279	453	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	168	535	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.794	0.732	0.858	1	0.99	1	SUBCLONAL	2	TRUE	1	0.325527773954423	2		536	650	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675438	30675438	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780670990	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	252	456	1	ENST00000376406.3:c.2918C>T	p.Ala973Val	p.A973V	ENST00000376406	NM_014641.2	973	gCg/gTg	8/15	0.325527773954423	2	FACETS	0.932	0.88	0.983	1	0.993	1	CLONAL	3	TRUE	0	0.325527773954423	2		457	554	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268144	153268144	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs920052554	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	80	307	0	ENST00000281708.4:c.664C>T	p.Arg222Ter	p.R222*	ENST00000281708	NM_033632.3	222	Cga/Tga	4/12	1	2	FACETS	0.929	0.82	1	0.929	0.82	1	CLONAL	1	TRUE	1	0.325527773954423	2		307	529	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457242	25457242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147001633	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	130	504	1	ENST00000264709.3:c.2645G>A	p.Arg882His	p.R882H	ENST00000264709	NM_175629.2	882	cGc/cAc	23/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.325527773954423	2		505	622	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	105	402	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.325527773954423	2		402	546	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582168	189582168	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121908835	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	136	435	0	ENST00000264731.3:c.727C>T	p.Arg243Trp	p.R243W	ENST00000264731	NM_003722.4	243	Cgg/Tgg	5/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.325527773954423	2		435	656	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636818	8636818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146973770	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	112	391	0	ENST00000356435.5:c.91G>A	p.Val31Ile	p.V31I	ENST00000356435		31	Gtt/Att	2/35	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.325527773954423	2		391	582	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651264	45651264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772294235	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	155	607	0	ENST00000407780.3:c.761C>T	p.Ala254Val	p.A254V	ENST00000407780	NM_001283052.1	254	gCg/gTg	5/7	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.325527773954423	2		607	747	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627774	187627774	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1183516785	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	117	452	0	ENST00000441802.2:c.3208C>T	p.Arg1070Ter	p.R1070*	ENST00000441802	NM_005245.3	1070	Cga/Tga	2/27	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.325527773954423	2		452	692	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905516	50905516	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs993539085	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	123	694	2	ENST00000440232.2:c.644C>T	p.Ala215Val	p.A215V	ENST00000440232	NM_002691.3	215	gCg/gTg	6/27	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.325527773954423	2		696	683	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412898	49412898	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519954	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	160	618	0	ENST00000418115.1:c.125A>G	p.Tyr42Cys	p.Y42C	ENST00000418115	NM_001664.2	42	tAt/tGt	2/5	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.325527773954423	2		618	812	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793677	89793677	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	123	375	0	ENST00000336032.3:c.752del	p.Lys251SerfsTer14	p.K251Sfs*14	ENST00000336032	NM_006813.2	249	gAa/ga	2/2	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.325527773954423	2		375	648	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508401	106508401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760958737	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	52	260	0	ENST00000359195.3:c.395C>T	p.Pro132Leu	p.P132L	ENST00000359195	NM_002649.2	132	cCg/cTg	2/11	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.325527773954423	2		260	285	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120031	70120031	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	13	57	0	ENST00000245479.2:c.1037del	p.Pro346ArgfsTer37	p.P346Rfs*37	ENST00000245479	NM_000346.3	345	Ccc/cc	3/3	1	2	FACETS	1	0.806	1	1	0.806	1	CLONAL	1	TRUE	1	0.325527773954423	2		57	70	SUCCESS
APC	324	MSKCC	GRCh37	5	112173837	112173838	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	95	380	0	ENST00000257430.4:c.2547_2548del	p.Asp849GlufsTer62	p.D849Efs*62	ENST00000257430	NM_000038.5	849	gAT/g	16/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.325527773954423	2		380	485	SUCCESS
APC	324	MSKCC	GRCh37	5	112175696	112175696	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060503288	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	78	355	1	ENST00000257430.4:c.4405C>T	p.Gln1469Ter	p.Q1469*	ENST00000257430	NM_000038.5	1469	Caa/Taa	16/16	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.325527773954423	2		356	453	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253759	30253759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388146136	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	134	418	0	ENST00000307677.4:c.695G>A	p.Arg232Gln	p.R232Q	ENST00000307677	NM_138578.1	232	cGg/cAg	3/3	1	2	FACETS	0.806	0.736	0.878	1	0.988	1	CLONAL	2	TRUE	1	0.325527773954423	2		418	511	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456460	89456460	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1221318412	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	98	318	0	ENST00000336596.2:c.1636G>A	p.Ala546Thr	p.A546T	ENST00000336596	NM_005233.5	546	Gcc/Acc	8/17	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.325527773954423	2		318	532	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164863	36164863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	143	675	3	ENST00000300305.3:c.1012G>A	p.Ala338Thr	p.A338T	ENST00000300305		338	Gcg/Acg	8/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.325527773954423	2		678	753	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193850	106193850	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	82	358	0	ENST00000380013.4:c.4317del	p.Lys1439AsnfsTer9	p.K1439Nfs*9	ENST00000380013	NM_001127208.2	1438	Aaa/aa	10/11	1	2	FACETS	0.992	0.877	1	0.992	0.877	1	CLONAL	1	TRUE	1	0.325527773954423	2		358	508	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741761	145741761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540719285	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	135	623	0	ENST00000428558.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000428558	NM_004260.3	248	Cgt/Tgt	5/22	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.325527773954423	2		623	659	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433388	49433388	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555191598	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	151	645	1	ENST00000301067.7:c.8059C>T	p.Arg2687Ter	p.R2687*	ENST00000301067	NM_003482.3	2687	Cga/Tga	32/54	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.325527773954423	2		646	755	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	103	724	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.325527773954423	2		724	622	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943749	9943749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	114	486	1	ENST00000330684.3:c.1192G>A	p.Asp398Asn	p.D398N	ENST00000330684	NM_001134407.1	398	Gac/Aac	5/13	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.325527773954423	2		487	553	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932819	39932819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764515953	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	131	261	1	ENST00000378444.4:c.1780G>A	p.Val594Ile	p.V594I	ENST00000378444	NM_001123385.1	594	Gtt/Att	4/15	1	1	FACETS	0.954	0.877	1	1	0.991	1	CLONAL	2	TRUE	0	0.325527773954423	1		262	353	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2090156	2090156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148474733	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	147	645	3	ENST00000219066.1:c.793G>A	p.Ala265Thr	p.A265T	ENST00000219066	NM_002528.5	265	Gcc/Acc	5/6	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.325527773954423	2		648	761	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753149	42753151	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs199960550	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	102	616	7	ENST00000222329.4:c.1113_1115del	p.Ser373del	p.S373del	ENST00000222329	NM_006494.2	371	tcTTCc/tcc	4/4	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.325527773954423	2		623	581	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909730	50909730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426671575	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	139	678	0	ENST00000440232.2:c.1450G>A	p.Glu484Lys	p.E484K	ENST00000440232	NM_002691.3	484	Gag/Aag	12/27	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.325527773954423	2		678	746	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737400	145737400	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765087683	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	141	595	1	ENST00000428558.2:c.3287G>A	p.Arg1096His	p.R1096H	ENST00000428558	NM_004260.3	1096	cGc/cAc	20/22	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.325527773954423	2		596	674	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023778	27023778	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	110	343	0	ENST00000324856.7:c.884T>G	p.Leu295Arg	p.L295R	ENST00000324856	NM_006015.4	295	cTc/cGc	1/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.325527773954423	2		343	503	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954991	2954991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	116	491	1	ENST00000396946.4:c.2719G>A	p.Glu907Lys	p.E907K	ENST00000396946	NM_032415.4	907	Gag/Aag	21/25	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.325527773954423	2		492	547	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696748	47696748	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	88	249	0	ENST00000347630.2:c.201-1G>A		p.X67_splice	ENST00000347630	NM_001007230.1	67			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.325527773954423	2		249	373	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221294	1221294	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782199	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	149	618	1	ENST00000326873.7:c.817G>A	p.Ala273Thr	p.A273T	ENST00000326873	NM_000455.4	273	Gcc/Acc	6/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.325527773954423	2		619	715	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199618	16199618	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs953954789	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	111	390	0	ENST00000375759.3:c.391C>T	p.Arg131Trp	p.R131W	ENST00000375759	NM_015001.2	131	Cgg/Tgg	2/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.325527773954423	2		390	576	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128706	64128706	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561332088	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	133	508	0	ENST00000334205.4:c.563C>T	p.Thr188Met	p.T188M	ENST00000334205	NM_003942.2	188	aCg/aTg	5/17	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.325527773954423	2		508	611	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201736	67201736	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	107	482	0	ENST00000312629.5:c.1037G>T	p.Arg346Met	p.R346M	ENST00000312629	NM_003952.2	346	aGg/aTg	12/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.325527773954423	2		482	544	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377145	118377145	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	63	348	0	ENST00000534358.1:c.10538C>G	p.Thr3513Ser	p.T3513S	ENST00000534358	NM_005933.3	3513	aCc/aGc	27/36	1	2	FACETS	0.878	0.761	1	0.878	0.761	1	CLONAL	1	TRUE	1	0.325527773954423	2		348	441	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244479	46244479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	119	424	0	ENST00000334344.6:c.2573C>T	p.Ala858Val	p.A858V	ENST00000334344	NM_152641.2	858	gCa/gTa	15/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.325527773954423	2		424	634	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506134	103506134	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	116	355	0	ENST00000355739.4:c.292G>A	p.Ala98Thr	p.A98T	ENST00000355739	NM_000123.3	98	Gcg/Acg	3/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.325527773954423	2		355	550	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041327	42041327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771491619	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	94	438	0	ENST00000219905.7:c.5522G>A	p.Arg1841Gln	p.R1841Q	ENST00000219905	NM_001164273.1	1841	cGg/cAg	17/24	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.325527773954423	2		438	576	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348232	348232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	137	616	0	ENST00000262320.3:c.1274G>A	p.Gly425Asp	p.G425D	ENST00000262320	NM_003502.3	425	gGc/gAc	6/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.325527773954423	2		616	663	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632393	3632393	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	144	690	0	ENST00000294008.3:c.5455C>T	p.Gln1819Ter	p.Q1819*	ENST00000294008	NM_032444.2	1819	Cag/Tag	15/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.325527773954423	2		690	718	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656526	3656526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199912910	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	162	586	1	ENST00000294008.3:c.709C>T	p.Arg237Trp	p.R237W	ENST00000294008	NM_032444.2	237	Cgg/Tgg	3/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.325527773954423	2		587	852	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779692	3779692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555471394	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	90	501	1	ENST00000262367.5:c.5356C>T	p.Arg1786Cys	p.R1786C	ENST00000262367	NM_004380.2	1786	Cgc/Tgc	31/31	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.325527773954423	2		502	540	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56875731	56875731	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs77860880	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	120	397	0	ENST00000308159.5:c.2335G>A	p.Glu779Lys	p.E779K	ENST00000308159	NM_014669.4	779	Gag/Aag	21/22	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.325527773954423	2		397	550	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946260	81946260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519831	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	116	588	0	ENST00000359376.3:c.1993C>T	p.Arg665Trp	p.R665W	ENST00000359376	NM_002661.3	665	Cgg/Tgg	19/33	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.325527773954423	2		588	595	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346855	89346855	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746355740	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	57	298	0	ENST00000301030.4:c.6095C>T	p.Pro2032Leu	p.P2032L	ENST00000301030	NM_001256183.1	2032	cCg/cTg	9/13	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.325527773954423	2		298	268	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58711219	58711219	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	126	400	0	ENST00000305921.3:c.707T>C	p.Met236Thr	p.M236T	ENST00000305921	NM_003620.3	236	aTg/aCg	3/6	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.325527773954423	2		400	756	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936325	78936325	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762913188	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	116	602	0	ENST00000306801.3:c.3757G>A	p.Val1253Met	p.V1253M	ENST00000306801	NM_020761.2	1253	Gtg/Atg	32/34	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.325527773954423	2		602	585	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17389780	17389780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs575115485	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	150	711	1	ENST00000359435.4:c.913C>T	p.Arg305Trp	p.R305W	ENST00000359435	NM_001033549.1	305	Cgg/Tgg	9/9	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.325527773954423	2		712	718	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228119	36228119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201885107	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	138	606	1	ENST00000222270.7:c.7505C>T	p.Pro2502Leu	p.P2502L	ENST00000222270	NM_014727.1	2502	cCg/cTg	33/37	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.325527773954423	2		607	695	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027688	48027691	+	frameshift_variant	Frame_Shift_Del	DEL	ATTG	ATTG	-	rs587779243	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	67	152	0	ENST00000234420.5:c.2569_2572del	p.Asp857PhefsTer10	p.D857Ffs*10	ENST00000234420	NM_000179.2	856	ATTGat/at	4/10	1	2	FACETS	0.931	0.822	1	1	0.981	1	CLONAL	2	TRUE	1	0.325527773954423	2		152	221	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189367	99189367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	128	509	0	ENST00000074304.5:c.2623G>A	p.Asp875Asn	p.D875N	ENST00000074304	NM_001134224.1	875	Gac/Aac	24/26	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.325527773954423	2		509	709	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275753	41275753	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	106	454	0	ENST00000349496.5:c.1648C>T	p.Arg550Cys	p.R550C	ENST00000349496	NM_001904.3	550	Cgt/Tgt	10/15	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.325527773954423	2		454	642	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190866	185190866	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1178695004	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	145	579	2	ENST00000265026.3:c.1747C>T	p.Arg583Ter	p.R583*	ENST00000265026	NM_004721.4	583	Cga/Tga	11/14	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.325527773954423	2		581	788	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526115	189526115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375508394	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	133	511	0	ENST00000264731.3:c.379G>A	p.Gly127Ser	p.G127S	ENST00000264731	NM_003722.4	127	Ggc/Agc	4/14	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.325527773954423	2		511	769	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1956969	1956969	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	131	553	0	ENST00000382891.5:c.2420C>T	p.Ala807Val	p.A807V	ENST00000382891	NM_133335.3	807	gCc/gTc	13/22	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.325527773954423	2		553	588	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170877	56170877	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	58	270	0	ENST00000399503.3:c.1705G>A	p.Val569Ile	p.V569I	ENST00000399503	NM_005921.1	569	Gtt/Att	10/20	1	2	FACETS	0.907	0.782	1	0.907	0.782	1	CLONAL	1	TRUE	1	0.325527773954423	2		270	393	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80088584	80088585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	122	369	0	ENST00000265081.6:c.2582dup	p.Asn861LysfsTer8	p.N861Kfs*8	ENST00000265081	NM_002439.4	859	ata/atAa	19/24	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.325527773954423	2		369	687	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681924	30681924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754781804	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	201	370	0	ENST00000376406.3:c.173G>A	p.Arg58Gln	p.R58Q	ENST00000376406	NM_014641.2	58	cGa/cAa	3/15	0.325527773954423	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.325527773954423	2		370	525	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32814921	32814921	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769612391	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	301	551	0	ENST00000354258.4:c.2144G>A	p.Arg715Gln	p.R715Q	ENST00000354258	NM_000593.5	715	cGa/cAa	10/11	0.325527773954423	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.325527773954423	2		551	827	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222613	157222613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1296046545	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	109	454	0	ENST00000346085.5:c.1880C>T	p.Ala627Val	p.A627V	ENST00000346085	NM_020732.3	627	gCg/gTg	4/20	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.325527773954423	2		454	643	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38314898	38314898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	90	411	0	ENST00000425967.3:c.166C>T	p.Pro56Ser	p.P56S	ENST00000425967	NM_001174067.1	56	Ccg/Tcg	3/19	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.325527773954423	2		411	461	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046377	69046377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	96	453	0	ENST00000288368.4:c.3850G>A	p.Ala1284Thr	p.A1284T	ENST00000288368	NM_024870.2	1284	Gcg/Acg	32/40	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.325527773954423	2		453	580	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137313595	137313595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759850724	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	133	728	1	ENST00000481739.1:c.854G>A	p.Arg285Gln	p.R285Q	ENST00000481739	NM_002957.4	285	cGg/cAg	6/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.325527773954423	2		729	706	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357061	70357061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763700798	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	132	341	2	ENST00000374080.3:c.5576G>A	p.Arg1859His	p.R1859H	ENST00000374080		1859	cGt/cAt	39/45	1	1	FACETS	0.877	0.805	0.952	1	0.99	1	CLONAL	2	TRUE	0	0.325527773954423	1		343	387	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360599	70360600	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCAGCAA	rs762261992	NA	P-0029495-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	19	166	0	ENST00000374080.3:c.6174_6182dup	p.Gln2074_Gln2076dup	p.Q2074_Q2076dup	ENST00000374080		2074	-/CAGCAGCAA	42/45	1	1	FACETS	0.459	0.349	0.587	0.459	0.349	0.587	SUBCLONAL	1	TRUE	0	0.325527773954423	1		166	213	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0029609-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	57	286	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.205396584019735	2		286	534	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0029719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	201	532	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.218796832287129	5	FACETS	0.896	0.836	0.958			1	INDETERMINATE	3	TRUE	NA	0.406829540052344	5		533	592	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508614	106508614	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377001952	NA	P-0029719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	80	537	1	ENST00000359195.3:c.608C>T	p.Thr203Met	p.T203M	ENST00000359195	NM_002649.2	203	aCg/aTg	2/11	0.406829540052344	3	FACETS	0.893	0.788	1	0.446	0.394	0.503	CLONAL	1	TRUE	1	0.406829540052344	3		538	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0029719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	94	579	0	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.406829540052344	1	FACETS	0.86	0.77	0.955	0.86	0.77	0.955	CLONAL	1	TRUE	0	0.406829540052344	1		579	428	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633556	69633556	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs281860300	NA	P-0029719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	26	257	0	ENST00000334134.2:c.146A>G	p.Tyr49Cys	p.Y49C	ENST00000334134	NM_005247.2	49	tAc/tGc	1/3	1	2	FACETS	0.578	0.46	0.712	0.578	0.46	0.712	SUBCLONAL	1	TRUE	1	0.406829540052344	2		257	221	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409382	31409382	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1233387563	NA	P-0029846-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	98	395	0	ENST00000344624.3:c.3725A>G	p.Asn1242Ser	p.N1242S	ENST00000344624		1242	aAt/aGt	29/33	1	2	FACETS	0.79	0.705	0.88	0.79	0.705	0.88	SUBCLONAL	1	TRUE	1	0.34472115504794	2		395	720	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041244	47041245	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0029846-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	168	322	0	ENST00000377604.3:c.1672_1673del	p.Gln558GlyfsTer18	p.Q558Gfs*18	ENST00000377604	NM_001204468.1	558	CAg/g	15/24	1	1	FACETS	0.789	0.731	0.849	1	0.991	1	SUBCLONAL	2	TRUE	0	0.34472115504794	1		322	511	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411866	116411893	+	intron_variant	Intron	DEL	CGTCTTTAACAAGCTCTTTCTTTCTCTC	CGTCTTTAACAAGCTCTTTCTTTCTCTC	G	novel	NA	P-0029846-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	249	786	0	ENST00000397752.3:c.2888-37_2888-10delinsG		p.*963*	ENST00000397752	NM_000245.2	-/1390			0.34472115504794	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.34472115504794	1		786	1031	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748450	162748451	+	inframe_insertion	In_Frame_Ins	INS	-	-	TAT	novel	NA	P-0029892-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	63	397	0	ENST00000367921.3:c.2366_2368dup	p.Tyr789dup	p.Y789dup	ENST00000367921	NM_006182.2	789	-/TAT	17/18	0.277150076982896	7	FACETS	0.84	0.728	0.961			1	CLONAL	2	TRUE	NA	0.277150076982896	7		397	458	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982979	201982979	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029892-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	112	714	0	ENST00000359651.3:c.828G>A	p.Trp276Ter	p.W276*	ENST00000359651		276	tgG/tgA	7/8	0.267819914454684	4	FACETS	1	0.983	1	0.737	0.664	0.815	CLONAL	1	TRUE	2	0.277150076982896	4		714	700	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606749	43606749	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029892-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	29	653	0	ENST00000355710.3:c.1358G>A	p.Gly453Glu	p.G453E	ENST00000355710	NM_020975.4	453	gGg/gAg	7/20	0.210699321054285	3	FACETS	0.505	0.404	0.619	0.252	0.202	0.31	SUBCLONAL	1	TRUE	1	0.277150076982896	3		653	472	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425371	49425371	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs531287935	NA	P-0029892-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	63	770	0	ENST00000301067.7:c.13117G>T	p.Gly4373Cys	p.G4373C	ENST00000301067	NM_003482.3	4373	Ggt/Tgt	39/54	0.277150076982896	3	FACETS	0.926	0.801	1	0.463	0.4	0.531	CLONAL	1	TRUE	1	0.277150076982896	3		770	559	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917057	50917057	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029892-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	52	713	0	ENST00000440232.2:c.2309A>G	p.Glu770Gly	p.E770G	ENST00000440232	NM_002691.3	770	gAg/gGg	19/27	0.277150076982896	3	FACETS	0.927	0.79	1	0.309	0.263	0.359	CLONAL	1	TRUE	0	0.277150076982896	3		713	461	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166915	32166917	+	missense_variant	Missense_Mutation	TNP	AGG	AGG	CAT	novel	NA	P-0029892-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	56	803	1	ENST00000375023.3:c.4321_4323delinsATG	p.Pro1441Met	p.P1441M	ENST00000375023	NM_004557.3	1441	CCT/ATG	24/30	0.277150076982896	2	FACETS	0.797	0.683	0.921	0.399	0.341	0.461	CLONAL	1	TRUE	0	0.277150076982896	2		804	507	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111982971	111982971	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029892-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	41	561	0	ENST00000368678.4:c.1576C>G	p.Pro526Ala	p.P526A	ENST00000368678		526	Ccc/Gcc	13/13	0.277150076982896	3	FACETS	0.685	0.57	0.812	0.342	0.285	0.406	SUBCLONAL	1	TRUE	1	0.277150076982896	3		561	492	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5462959	5462959	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029892-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	37	389	0	ENST00000381577.3:c.520G>A	p.Val174Ile	p.V174I	ENST00000381577	NM_014143.3	174	Gtc/Atc	4/7	0.277150076982896	1	FACETS	1	0.845	1	1	0.845	1	CLONAL	1	TRUE	0	0.277150076982896	1		389	226	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0029943-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	130	398	0	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.185678151283816	4	FACETS	0.911	0.829	0.996	0.911	0.829	0.996	CLONAL	3	TRUE	1	0.189590821805362	4		398	597	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225365164	225365164	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029943-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	20	286	2	ENST00000264414.4:c.1526C>T	p.Thr509Met	p.T509M	ENST00000264414	NM_003590.4	509	aCg/aTg	11/16	0.189590821805362	2	FACETS	0.624	0.477	0.797	0.312	0.238	0.399	SUBCLONAL	1	TRUE	0	0.189590821805362	2		288	338	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99163148	99163148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029943-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	80	283	0	ENST00000074304.5:c.1154C>T	p.Thr385Ile	p.T385I	ENST00000074304	NM_001134224.1	385	aCc/aTc	13/26	0.168757286154863	3	FACETS	1	0.895	1	1	0.895	1	CLONAL	2	TRUE	1	0.189590821805362	3		283	456	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841523	156841523	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029943-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	101	501	0	ENST00000524377.1:c.826G>T	p.Val276Phe	p.V276F	ENST00000524377	NM_002529.3	276	Gtc/Ttc	7/17	0.189590821805362	5	FACETS	0.891	0.796	0.992	0.594	0.531	0.661	CLONAL	2	TRUE	2	0.189590821805362	5		501	768	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332142	70332142	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029943-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	27	209	0	ENST00000373644.4:c.47A>C	p.Glu16Ala	p.E16A	ENST00000373644	NM_030625.2	16	gAa/gCa	2/12	0.185678151283816	4	FACETS	1	0.926	1	0.467	0.373	0.573	CLONAL	1	TRUE	1	0.189590821805362	4		209	242	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94163142	94163142	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029943-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	42	283	0	ENST00000323929.3:c.2005A>C	p.Thr669Pro	p.T669P	ENST00000323929	NM_005591.3	669	Aca/Cca	19/20	0.168757286154863	3	FACETS	1	0.944	1	0.661	0.553	0.78	CLONAL	1	TRUE	1	0.189590821805362	3		283	367	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951170	48951170	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs1555286250	NA	P-0029943-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	34	301	0	ENST00000267163.4:c.1332G>C	p.Gln444His	p.Q444H	ENST00000267163	NM_000321.2	444	caG/caC	13/27	0.189590821805362	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.189590821805362	1		301	230	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560308	95560308	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029943-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	65	307	0	ENST00000393063.1:c.5281G>T	p.Val1761Phe	p.V1761F	ENST00000393063	NM_030621.3	1761	Gtc/Ttc	25/28	0.168757286154863	3	FACETS	0.865	0.752	0.986	0.865	0.752	0.986	CLONAL	2	TRUE	1	0.189590821805362	3		307	434	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457628	67457628	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029943-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	53	461	0	ENST00000327367.4:c.438C>G	p.Ile146Met	p.I146M	ENST00000327367	NM_005902.3	146	atC/atG	3/9	0.189590821805362	2	FACETS	1	0.894	1	0.529	0.451	0.615	CLONAL	1	TRUE	0	0.189590821805362	2		461	528	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828163	50828163	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029943-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	51	291	1	ENST00000398568.2:c.2501C>A	p.Pro834Gln	p.P834Q	ENST00000398568	NM_001042412.1	834	cCa/cAa	17/18	0.0524370739661006	4	FACETS	1	0.96	1	0.713	0.607	0.829	INDETERMINATE	1	TRUE	2	0.189590821805362	4		292	449	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289675	15289675	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029943-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	145	534	0	ENST00000263388.2:c.3796G>C	p.Gly1266Arg	p.G1266R	ENST00000263388	NM_000435.2	1266	Ggt/Cgt	23/33	0.189590821805362	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.189590821805362	2		534	670	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17382459	17382459	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029943-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	33	407	0	ENST00000359435.4:c.339C>G	p.Phe113Leu	p.F113L	ENST00000359435	NM_001033549.1	113	ttC/ttG	3/9	0.189590821805362	2	FACETS	0.56	0.454	0.679	0.28	0.227	0.34	SUBCLONAL	1	TRUE	0	0.189590821805362	2		407	622	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295826	212295826	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0029943-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	66	283	0	ENST00000342788.4:c.2488-1G>T		p.X830_splice	ENST00000342788	NM_005235.2	830			0.189590821805362	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	0	0.189590821805362	2		283	307	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520158	9520159	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0029943-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	28	307	1	ENST00000353224.5:c.2110_2111delinsCT	p.Gly704Leu	p.G704L	ENST00000353224	NM_177990.2	704	GGt/CTt	10/10	0.189590821805362	6	FACETS	0.821	0.655	1	0.205	0.163	0.253	CLONAL	1	TRUE	2	0.189590821805362	6		308	496	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143029272	143029272	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029943-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	52	227	0	ENST00000262992.4:c.2348T>C	p.Ile783Thr	p.I783T	ENST00000262992	NM_001101669.1	783	aTa/aCa	21/24	0.189590821805362	2	FACETS	0.896	0.768	1	0.896	0.768	1	CLONAL	2	TRUE	0	0.189590821805362	2		227	306	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205120	123205121	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029943-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	33	389	0	ENST00000218089.9:c.2480_2481insA	p.Ser827ArgfsTer10	p.S827Rfs*10	ENST00000218089	NM_001042749.1	827	agc/agAc	25/35	0.189590821805362	3	FACETS	1	0.898	1	0.579	0.473	0.699	CLONAL	1	TRUE	1	0.189590821805362	3		389	329	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0029962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	190	654	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.37407918672783	NA		654	511	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400777	72400777	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	51	303	0	ENST00000357731.5:c.394C>T	p.His132Tyr	p.H132Y	ENST00000357731	NM_173808.2	132	Cat/Tat	2/7	0.320835610371395	3	FACETS	1	0.891	1	0.525	0.449	0.608	CLONAL	1	TRUE	1	0.37407918672783	3		303	308	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0029965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	488	545	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.726624003927036	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.726624003927036	2		545	642	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0029965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	83	193	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.726624003927036	2		193	209	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132833	64132833	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1447050686	NA	P-0029965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	483	539	0	ENST00000334205.4:c.967C>T	p.Arg323Cys	p.R323C	ENST00000334205	NM_003942.2	323	Cgc/Tgc	9/17	0.505909334907097	4	FACETS	0.958	0.918	0.998	0.958	0.918	0.998	CLONAL	2	TRUE	2	0.726624003927036	4		539	1198	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190744	11190744	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148876562	NA	P-0029965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	50	522	0	ENST00000361445.4:c.5455C>T	p.His1819Tyr	p.H1819Y	ENST00000361445	NM_004958.3	1819	Cat/Tat	39/58	0.726624003927036	2	FACETS	0.177	0.149	0.207	0.088	0.074	0.104	SUBCLONAL	1	TRUE	0	0.726624003927036	2		522	778	SUCCESS
APC	324	MSKCC	GRCh37	5	112174620	112174620	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0029965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	99	346	0	ENST00000257430.4:c.3329C>G	p.Ser1110Ter	p.S1110*	ENST00000257430	NM_000038.5	1110	tCa/tGa	16/16	1	2	FACETS	0.849	0.766	0.934	0.849	0.766	0.934	CLONAL	1	TRUE	1	0.726624003927036	2		346	321	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995526	68995526	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	384	507	0	ENST00000288368.4:c.1930G>T	p.Val644Phe	p.V644F	ENST00000288368	NM_024870.2	644	Gtt/Ttt	18/40	0.70594854306829	5	FACETS	0.91	0.876	0.943	0.91	0.876	0.943	CLONAL	4	TRUE	1	0.726624003927036	5		507	607	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087944	27087944	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	106	494	0	ENST00000324856.7:c.2231C>G	p.Ser744Ter	p.S744*	ENST00000324856	NM_006015.4	744	tCa/tGa	6/20	0.410139146248958	3	FACETS	0.641	0.573	0.713	0.32	0.286	0.357	SUBCLONAL	1	TRUE	1	0.410139146248958	3		494	972	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092809	27092809	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	115	479	0	ENST00000324856.7:c.2830C>T	p.Gln944Ter	p.Q944*	ENST00000324856	NM_006015.4	944	Cag/Tag	9/20	0.410139146248958	3	FACETS	0.727	0.654	0.804	0.363	0.327	0.402	SUBCLONAL	1	TRUE	1	0.410139146248958	3		479	930	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430824	78430824	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	163	449	0	ENST00000370768.2:c.565G>T	p.Glu189Ter	p.E189*	ENST00000370768	NM_003902.3	189	Gaa/Taa	8/20	0.410139146248958	3	FACETS	1	0.925	1	0.504	0.462	0.548	CLONAL	1	TRUE	1	0.410139146248958	3		449	950	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999521	100999521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780296630	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	271	734	0	ENST00000325455.5:c.281G>A	p.Arg94Lys	p.R94K	ENST00000325455	NM_001202474.3	94	aGg/aAg	1/8	0.362988987938537	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.410139146248958	1		734	874	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142036	108142036	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	139	461	0	ENST00000278616.4:c.2980G>C	p.Val994Leu	p.V994L	ENST00000278616	NM_000051.3	994	Gtc/Ctc	20/63	0.362988987938537	1	FACETS	0.883	0.807	0.963	0.883	0.807	0.963	CLONAL	1	TRUE	0	0.410139146248958	1		461	610	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170263	119170263	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	92	272	0	ENST00000264033.4:c.2493C>G	p.Ile831Met	p.I831M	ENST00000264033	NM_005188.3	831	atC/atG	16/16	0.362988987938537	1	FACETS	0.977	0.875	1	0.977	0.875	1	CLONAL	1	TRUE	0	0.410139146248958	1		272	365	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383225	4383225	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	93	309	0	ENST00000261254.3:c.19G>C	p.Glu7Gln	p.E7Q	ENST00000261254	NM_001759.3	7	Gag/Cag	1/5	1	2	FACETS	0.977	0.873	1	0.977	0.873	1	CLONAL	1	TRUE	1	0.410139146248958	2		309	464	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440430	49440431	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	194	558	0	ENST00000301067.7:c.4379dup	p.Leu1461ThrfsTer30	p.L1461Tfs*30	ENST00000301067	NM_003482.3	1460	cca/ccCa	15/54	1	2	FACETS	0.978	0.905	1	0.978	0.905	1	CLONAL	1	TRUE	1	0.410139146248958	2		558	967	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518091	103518091	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	61	344	0	ENST00000355739.4:c.2029C>G	p.Pro677Ala	p.P677A	ENST00000355739	NM_000123.3	677	Ccc/Gcc	9/15	0.410139146248958	1	FACETS	0.575	0.498	0.659	0.575	0.498	0.659	SUBCLONAL	1	TRUE	0	0.410139146248958	1		344	411	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871608	35871608	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	20	193	0	ENST00000216797.5:c.898G>C	p.Glu300Gln	p.E300Q	ENST00000216797	NM_020529.2	300	Gag/Cag	5/6	1	2	FACETS	0.268	0.204	0.343	0.268	0.204	0.343	SUBCLONAL	1	TRUE	1	0.410139146248958	2		193	364	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42049996	42049996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	62	326	0	ENST00000219905.7:c.7150C>T	p.His2384Tyr	p.H2384Y	ENST00000219905	NM_001164273.1	2384	Cac/Tac	19/24	1	2	FACETS	0.641	0.554	0.734	0.641	0.554	0.734	SUBCLONAL	1	TRUE	1	0.410139146248958	2		326	472	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054533	42054533	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs759572856	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	96	314	2	ENST00000219905.7:c.7717C>G	p.Leu2573Val	p.L2573V	ENST00000219905	NM_001164273.1	2573	Ctt/Gtt	22/24	1	2	FACETS	0.862	0.77	0.959	0.862	0.77	0.959	CLONAL	1	TRUE	1	0.410139146248958	2		316	543	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701865	43701865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	87	257	0	ENST00000382044.4:c.5380G>A	p.Glu1794Lys	p.E1794K	ENST00000382044	NM_001141980.1	1794	Gaa/Aaa	25/28	1	2	FACETS	0.956	0.85	1	0.956	0.85	1	CLONAL	1	TRUE	1	0.410139146248958	2		257	444	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134616	2134616	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1425542648	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	193	625	3	ENST00000219476.3:c.4393G>A	p.Asp1465Asn	p.D1465N	ENST00000219476	NM_000548.3	1465	Gac/Aac	34/42	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.410139146248958	2		628	894	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133263	30133263	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	96	478	0	ENST00000263025.4:c.235C>G	p.Gln79Glu	p.Q79E	ENST00000263025	NM_002746.2	79	Cag/Gag	2/9	1	2	FACETS	0.569	0.506	0.636	0.569	0.506	0.636	SUBCLONAL	1	TRUE	1	0.410139146248958	2		478	823	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671689	67671689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	155	485	0	ENST00000264010.4:c.2098G>A	p.Glu700Lys	p.E700K	ENST00000264010	NM_006565.3	700	Gag/Aag	12/12	1	2	FACETS	0.993	0.911	1	0.993	0.911	1	CLONAL	1	TRUE	1	0.410139146248958	2		485	761	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830412	72830412	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	93	269	0	ENST00000268489.5:c.6169C>T	p.Gln2057Ter	p.Q2057*	ENST00000268489	NM_006885.3	2057	Cag/Tag	9/10	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.410139146248958	2		269	434	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349620	89349620	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	207	657	0	ENST00000301030.4:c.3330G>C	p.Glu1110Asp	p.E1110D	ENST00000301030	NM_001256183.1	1110	gaG/gaC	9/13	1	2	FACETS	0.966	0.896	1	0.966	0.896	1	CLONAL	1	TRUE	1	0.410139146248958	2		657	1045	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223192	41223192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357411	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	155	479	0	ENST00000357654.3:c.4739C>T	p.Ser1580Phe	p.S1580F	ENST00000357654	NM_007294.3	1580	tCt/tTt	15/23	NA	2	FACETS	0.997	0.914	1			1	INDETERMINATE	1	TRUE	NA	0.410139146248958	2		479	758	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732266	74732266	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	82	243	0	ENST00000359995.5:c.643G>C	p.Glu215Gln	p.E215Q	ENST00000359995	NM_001195427.1	215	Gag/Cag	2/3	0.410139146248958	3	FACETS	1	0.886	1	0.501	0.443	0.563	CLONAL	1	TRUE	1	0.410139146248958	3		243	481	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575667	48575667	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1568203595	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	86	443	0	ENST00000342988.3:c.427C>T	p.Leu143Phe	p.L143F	ENST00000342988	NM_005359.5	143	Ctc/Ttc	4/12	1	2	FACETS	0.708	0.627	0.795	0.708	0.627	0.795	SUBCLONAL	1	TRUE	1	0.410139146248958	2		443	592	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765576	41765576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763066660	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	160	565	0	ENST00000301178.4:c.2452G>A	p.Glu818Lys	p.E818K	ENST00000301178	NM_021913.4	818	Gaa/Aaa	20/20	1	2	FACETS	0.894	0.82	0.971	0.894	0.82	0.971	CLONAL	1	TRUE	1	0.410139146248958	2		565	873	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765672	41765672	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	175	502	0	ENST00000301178.4:c.2548G>C	p.Asp850His	p.D850H	ENST00000301178	NM_021913.4	850	Gat/Cat	20/20	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.410139146248958	2		502	848	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383359	42383359	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1555843599	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	126	396	0	ENST00000221972.3:c.379C>T	p.Gln127Ter	p.Q127*	ENST00000221972	NM_021601.3	127	Cag/Tag	2/5	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.410139146248958	2		396	592	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082231	16082231	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	172	683	0	ENST00000281043.3:c.45G>C	p.Lys15Asn	p.K15N	ENST00000281043	NM_005378.4	15	aaG/aaC	2/3	1	2	FACETS	0.813	0.747	0.881	0.813	0.747	0.881	CLONAL	1	TRUE	1	0.410139146248958	2		683	1032	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46603721	46603721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	194	539	1	ENST00000263734.3:c.1078G>A	p.Glu360Lys	p.E360K	ENST00000263734	NM_001430.4	360	Gaa/Aaa	9/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.410139146248958	2		540	868	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660645	190660645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	77	306	0	ENST00000441310.2:c.283G>A	p.Glu95Lys	p.E95K	ENST00000441310	NM_000534.4	95	Gaa/Aaa	3/13	0.328447166681375	4	FACETS	0.759	0.666	0.859	0.253	0.222	0.287	SUBCLONAL	1	TRUE	1	0.410139146248958	4		306	698	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270084	198270084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777705664	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	334	391	0	ENST00000335508.6:c.1352G>A	p.Arg451Gln	p.R451Q	ENST00000335508	NM_012433.2	451	cGa/cAa	10/25	0.328447166681375	4	FACETS	1	0.991	1	0.808	0.766	0.851	CLONAL	2	TRUE	1	0.410139146248958	4		391	947	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626746	12626746	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	90	382	0	ENST00000251849.4:c.1543G>C	p.Glu515Gln	p.E515Q	ENST00000251849	NM_002880.3	515	Gag/Cag	15/17	0.220893914332742	3	FACETS	0.816	0.725	0.914			1	INDETERMINATE	1	TRUE	NA	0.410139146248958	3		382	648	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089049	37089049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	106	306	0	ENST00000231790.2:c.1771G>A	p.Asp591Asn	p.D591N	ENST00000231790	NM_000249.3	591	Gat/Aat	16/19	1	2	FACETS	0.955	0.86	1	0.955	0.86	1	CLONAL	1	TRUE	1	0.410139146248958	2		306	541	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651527	52651527	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	66	402	0	ENST00000394830.3:c.1569del	p.Met523IlefsTer46	p.M523Ifs*46	ENST00000394830	NM_018313.4	523	atG/at	15/30	1	2	FACETS	0.532	0.462	0.608	0.532	0.462	0.608	SUBCLONAL	1	TRUE	1	0.410139146248958	2		402	605	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916728	178916728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	177	329	1	ENST00000263967.3:c.115G>A	p.Glu39Lys	p.E39K	ENST00000263967	NM_006218.2	39	Gag/Aag	2/21	0.335421562500082	5	FACETS	0.811	0.747	0.876	0.405	0.373	0.438	CLONAL	2	TRUE	1	0.410139146248958	5		330	860	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1941483	1941483	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	94	372	0	ENST00000382891.5:c.1859C>G	p.Ser620Cys	p.S620C	ENST00000382891	NM_133335.3	620	tCt/tGt	9/22	1	2	FACETS	0.811	0.724	0.904	0.811	0.724	0.904	CLONAL	1	TRUE	1	0.410139146248958	2		372	565	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230909	66230909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	59	264	0	ENST00000273854.3:c.2062G>A	p.Glu688Lys	p.E688K	ENST00000273854	NM_004439.5	688	Gaa/Aaa	12/18	1	2	FACETS	0.78	0.674	0.894	0.78	0.674	0.894	SUBCLONAL	1	TRUE	1	0.410139146248958	2		264	369	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196561	106196561	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1283023309	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	76	349	1	ENST00000380013.4:c.4894C>G	p.Gln1632Glu	p.Q1632E	ENST00000380013	NM_001127208.2	1632	Caa/Gaa	11/11	1	2	FACETS	0.722	0.635	0.816	0.722	0.635	0.816	SUBCLONAL	1	TRUE	1	0.410139146248958	2		350	513	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549865	187549865	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs750386635	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	89	367	0	ENST00000441802.2:c.4376C>G	p.Ser1459Ter	p.S1459*	ENST00000441802	NM_005245.3	1459	tCa/tGa	8/27	1	2	FACETS	0.755	0.67	0.845	0.755	0.67	0.845	SUBCLONAL	1	TRUE	1	0.410139146248958	2		367	575	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38981983	38981983	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	86	358	0	ENST00000357387.3:c.739G>C	p.Asp247His	p.D247H	ENST00000357387	NM_152756.3	247	Gat/Cat	8/38	1	2	FACETS	0.697	0.617	0.782	0.697	0.617	0.782	SUBCLONAL	1	TRUE	1	0.410139146248958	2		358	602	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163317	32163318	+	missense_variant	Missense_Mutation	DNP	GG	GG	TA	novel	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	226	681	0	ENST00000375023.3:c.5908_5909delinsTA	p.Pro1970Tyr	p.P1970Y	ENST00000375023	NM_004557.3	1970	CCt/TAt	30/30	0.410139146248958	2	FACETS	1	0.933	1	0.501	0.466	0.537	CLONAL	1	TRUE	0	0.410139146248958	2		681	1100	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199621	138199621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	69	371	0	ENST00000237289.4:c.1039G>A	p.Glu347Lys	p.E347K	ENST00000237289	NM_001270507.1	347	Gaa/Aaa	7/9	1	2	FACETS	0.632	0.551	0.72	0.632	0.551	0.72	SUBCLONAL	1	TRUE	1	0.410139146248958	2		371	532	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163803	152163803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	126	386	1	ENST00000206249.3:c.524C>T	p.Ala175Val	p.A175V	ENST00000206249	NM_000125.3	175	gCt/gTt	2/8	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.410139146248958	2		387	604	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845762	151845762	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	609	510	0	ENST00000262189.6:c.13250C>T	p.Ala4417Val	p.A4417V	ENST00000262189	NM_170606.2	4417	gCa/gTa	52/59	0.410139146248958	4	FACETS	1	0.991	1			1	CLONAL	3	TRUE	NA	0.410139146248958	4		510	1296	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152009018	152009018	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	60	294	0	ENST00000262189.6:c.604C>T	p.Gln202Ter	p.Q202*	ENST00000262189	NM_170606.2	202	Cag/Tag	5/59	0.410139146248958	4	FACETS	0.625	0.538	0.72			1	SUBCLONAL	1	TRUE	NA	0.410139146248958	4		294	660	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022105	5022105	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1183427218	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	71	399	0	ENST00000381652.3:c.118C>T	p.Gln40Ter	p.Q40*	ENST00000381652	NM_004972.3	40	Cag/Tag	3/25	0.382606195083081	1	FACETS	0.503	0.44	0.572	0.503	0.44	0.572	SUBCLONAL	1	TRUE	0	0.410139146248958	1		399	547	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760786	133760786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1330364358	NA	P-0029967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	164	511	2	ENST00000318560.5:c.3109G>A	p.Glu1037Lys	p.E1037K	ENST00000318560	NM_005157.4	1037	Gag/Aag	11/11	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.410139146248958	2		513	780	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0029974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	46	555	3	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	1	2	FACETS	0.909	0.766	1	0.909	0.766	1	CLONAL	1	TRUE	1	0.21	2		558	482	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007461	62007461	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	52	523	0	ENST00000392795.3:c.406G>T	p.Gly136Cys	p.G136C	ENST00000392795	NM_001039933.1	136	Ggc/Tgc	3/6	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.21	2		523	478	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221983	1221991	+	inframe_deletion	In_Frame_Del	DEL	ATCCGGCAG	ATCCGGCAG	-	novel	NA	P-0029974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	43	646	0	ENST00000326873.7:c.907_915del	p.Ile303_Gln305del	p.I303_Q305del	ENST00000326873	NM_000455.4	300	ATCCGGCAG/-	7/10	0.167595862158262	1	FACETS	0.795	0.666	0.938	0.795	0.666	0.938	CLONAL	1	TRUE	0	0.21	1		646	461	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610405	10610405	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	54	764	0	ENST00000171111.5:c.305C>A	p.Ser102Ter	p.S102*	ENST00000171111	NM_203500.1	102	tCa/tAa	2/6	0.167595862158262	1	FACETS	0.809	0.691	0.938	0.809	0.691	0.938	CLONAL	1	TRUE	0	0.21	1		764	569	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117630084	117630084	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	21	353	0	ENST00000368508.3:c.6442G>T	p.Gly2148Ter	p.G2148*	ENST00000368508	NM_002944.2	2148	Gga/Tga	41/43	1	2	FACETS	0.667	0.514	0.845	0.667	0.514	0.845	SUBCLONAL	1	TRUE	1	0.21	2		353	300	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398675	116398675	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0029974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	14	370	1	ENST00000397752.3:c.2264+1G>T		p.X755_splice	ENST00000397752	NM_000245.2	755			0.3	1	FACETS	0.44	0.318	0.589	0.44	0.318	0.589	SUBCLONAL	1	TRUE	0	0.21	1		371	271	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411762	63411762	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	50	373	0	ENST00000330258.3:c.1405G>T	p.Glu469Ter	p.E469*	ENST00000330258	NM_152424.3	469	Gaa/Taa	2/2	1	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.21	1		373	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0029988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	406	485	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.492003804822093	2	FACETS	0.988	0.946	1	0.988	0.946	1	CLONAL	2	TRUE	0	0.493419986976246	2		485	833	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434986	110434986	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	204	472	0	ENST00000375856.3:c.3415G>T	p.Asp1139Tyr	p.D1139Y	ENST00000375856	NM_003749.2	1139	Gac/Tac	1/2	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.493419986976246	2		472	701	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110615	4110615	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	178	507	0	ENST00000262948.5:c.342G>C	p.Gln114His	p.Q114H	ENST00000262948	NM_030662.3	114	caG/caC	3/11	0.357949211211257	5	FACETS	1	0.982	1	0.405	0.373	0.439	CLONAL	1	TRUE	2	0.493419986976246	5		507	1033	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11018745	11018745	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	202	579	0	ENST00000327064.4:c.377C>T	p.Thr126Ile	p.T126I	ENST00000327064	NM_199141.1	126	aCc/aTc	3/16	0.493419986976246	5	FACETS	1	0.942	1	0.34	0.314	0.368	CLONAL	1	TRUE	2	0.493419986976246	5		579	1395	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129227	152129227	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0029988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	140	560	2	ENST00000206249.3:c.180C>G	p.Tyr60Ter	p.Y60*	ENST00000206249	NM_000125.3	60	taC/taG	1/8	0.493098781298118	3	FACETS	0.825	0.751	0.902			1	CLONAL	1	TRUE	NA	0.493419986976246	3		562	858	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332030	81332030	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	167	346	0	ENST00000222390.5:c.2054G>C	p.Arg685Thr	p.R685T	ENST00000222390	NM_000601.4	685	aGa/aCa	18/18	0.307815389555322	5	FACETS	1	0.958	1	0.702	0.649	0.757	CLONAL	2	TRUE	2	0.493419986976246	5		346	559	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0030083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	46	356	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	FALSE	1	0.212713790888056	2		356	424	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0030083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	52	338	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	FALSE	1	0.212713790888056	2		338	489	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0030083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	26	283	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.815	0.647	1	0.815	0.647	1	CLONAL	1	FALSE	1	0.212713790888056	2		283	300	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0030083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	40	298	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	FALSE	1	0.212713790888056	2		298	343	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0030083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	22	231	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	1	2	FACETS	0.799	0.62	1	0.799	0.62	1	CLONAL	1	FALSE	1	0.212713790888056	2		231	259	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023768	27023769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0030083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	31	395	0	ENST00000324856.7:c.879dup	p.Thr294HisfsTer106	p.T294Hfs*106	ENST00000324856	NM_006015.4	292	acc/aCcc	1/20	1	2	FACETS	0.775	0.627	0.942	0.775	0.627	0.942	CLONAL	1	FALSE	1	0.212713790888056	2		395	376	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491052	120491052	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	13	229	0	ENST00000256646.2:c.2737G>C	p.Asp913His	p.D913H	ENST00000256646	NM_024408.3	913	Gat/Cat	17/34	1	2	FACETS	0.525	0.374	0.708	0.525	0.374	0.708	SUBCLONAL	1	FALSE	1	0.212713790888056	2		229	233	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8246198	8246198	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	39	454	0	ENST00000335790.3:c.436C>A	p.Gln146Lys	p.Q146K	ENST00000335790	NM_002315.2	146	Cag/Aag	4/4	1	2	FACETS	0.82	0.68	0.977	0.82	0.68	0.977	CLONAL	1	FALSE	1	0.212713790888056	2		454	447	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41201161	41201161	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854958	NA	P-0030083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	62	577	1	ENST00000357654.3:c.5383C>T	p.Leu1795Phe	p.L1795F	ENST00000357654	NM_007294.3	1795	Ctt/Ttt	21/23	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	FALSE	1	0.212713790888056	2		578	528	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713360	40713360	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	56	473	0	ENST00000373198.4:c.4155G>C	p.Gln1385His	p.Q1385H	ENST00000373198	NM_133170.3	1385	caG/caC	30/32	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	FALSE	1	0.212713790888056	2		473	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0030086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	573	645	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.561585923350924	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.926652408783012	1		645	609	SUCCESS
ALK	238	MSKCC	GRCh37	2	29450536	29450536	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs372008367	NA	P-0030086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	247	567	0	ENST00000389048.3:c.2818G>A	p.Gly940Ser	p.G940S	ENST00000389048	NM_004304.4	940	Ggc/Agc	17/29	1	2	FACETS	0.942	0.889	0.996	0.942	0.889	0.996	CLONAL	1	TRUE	1	0.926652408783012	2		567	566	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0030088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	128	622	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.468836194102377	2		622	522	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402543	139402543	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200871631	NA	P-0030088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	86	458	0	ENST00000277541.6:c.3374C>T	p.Ala1125Val	p.A1125V	ENST00000277541	NM_017617.3	1125	gCg/gTg	21/34	NA	2	FACETS	0.589	0.521	0.661			1	INDETERMINATE	1	TRUE	NA	0.468836194102377	2		458	623	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0030088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	214	541	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.468836194102377	1	FACETS	0.929	0.867	0.994	0.929	0.867	0.994	CLONAL	1	TRUE	0	0.468836194102377	1		541	752	SUCCESS
APC	324	MSKCC	GRCh37	5	112170683	112170683	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554083132	NA	P-0030088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	122	288	0	ENST00000257430.4:c.1779G>A	p.Trp593Ter	p.W593*	ENST00000257430	NM_000038.5	593	tgG/tgA	15/16	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.468836194102377	2		288	510	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129416	64129417	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCGATTGAGAC	novel	NA	P-0030088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	94	496	0	ENST00000334205.4:c.855_856insAGACGCGATTG	p.Gly286ArgfsTer93	p.G286Rfs*93	ENST00000334205	NM_003942.2	283	aag/aaGCGATTGAGACg	8/17	1	2	FACETS	0.598	0.532	0.667	0.598	0.532	0.667	SUBCLONAL	1	TRUE	1	0.468836194102377	2		496	671	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129460	64129460	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	111	489	0	ENST00000334205.4:c.892C>A	p.His298Asn	p.H298N	ENST00000334205	NM_003942.2	298	Cat/Aat	8/17	1	2	FACETS	0.689	0.62	0.762	0.689	0.62	0.762	SUBCLONAL	1	TRUE	1	0.468836194102377	2		489	687	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88428944	88428944	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	35	128	0	ENST00000360948.2:c.2156A>G	p.Asp719Gly	p.D719G	ENST00000360948	NM_001012338.2	719	gAt/gGt	17/19	1	2	FACETS	0.574	0.473	0.687	0.574	0.473	0.687	SUBCLONAL	1	TRUE	1	0.468836194102377	2		128	260	SUCCESS
BLM	641	MSKCC	GRCh37	15	91306366	91306367	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0030088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	48	253	0	ENST00000355112.3:c.2054_2055del	p.Cys685PhefsTer10	p.C685Ffs*10	ENST00000355112	NM_000057.2	685	TGt/t	8/22	1	2	FACETS	0.489	0.414	0.571	0.489	0.414	0.571	SUBCLONAL	1	TRUE	1	0.468836194102377	2		253	419	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705582	47705582	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	127	250	0	ENST00000233146.2:c.2382A>G	p.Ile794Met	p.I794M	ENST00000233146	NM_000251.2	794	atA/atG	14/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.468836194102377	2		250	463	SUCCESS
APC	324	MSKCC	GRCh37	5	112175419	112175420	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATAG	novel	NA	P-0030088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	50	255	0	ENST00000257430.4:c.4128_4129insATAG	p.Val1377IlefsTer10	p.V1377Ifs*10	ENST00000257430	NM_000038.5	1376	-/ATAG	16/16	1	2	FACETS	0.711	0.607	0.824	0.711	0.607	0.824	SUBCLONAL	1	TRUE	1	0.468836194102377	2		255	300	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038648	14038648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	168	340	0	ENST00000311895.7:c.1973G>A	p.Arg658Lys	p.R658K	ENST00000311895	NM_005236.2	658	aGa/aAa	10/11	1	2	FACETS	0.887	0.82	0.956	0.887	0.82	0.956	CLONAL	1	TRUE	1	0.676108416359395	2		340	560	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791797	42791797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	268	626	1	ENST00000575354.2:c.683G>A	p.Arg228Gln	p.R228Q	ENST00000575354	NM_015125.3	228	cGg/cAg	5/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.676108416359395	2		627	738	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	40	724	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.548239281352222	1	FACETS	0.137	0.113	0.164	0.137	0.113	0.164	SUBCLONAL	1	TRUE	0	0.676108416359395	1		724	571	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271898	15271898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	257	754	0	ENST00000263388.2:c.6541C>T	p.Pro2181Ser	p.P2181S	ENST00000263388	NM_000435.2	2181	Cca/Tca	33/33	1	2	FACETS	0.968	0.91	1	0.968	0.91	1	CLONAL	1	TRUE	1	0.676108416359395	2		754	785	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775925	9775926	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	249	597	0	ENST00000377346.4:c.389_390delinsTT	p.Ser130Phe	p.S130F	ENST00000377346	NM_005026.3	130	tCC/tTT	5/24	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.676108416359395	2		597	733	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190824	11190824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868040471	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	172	334	0	ENST00000361445.4:c.5375C>T	p.Ala1792Val	p.A1792V	ENST00000361445	NM_004958.3	1792	gCg/gTg	39/58	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.676108416359395	2		334	473	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255832	16255832	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	172	426	0	ENST00000375759.3:c.3097G>A	p.Gly1033Arg	p.G1033R	ENST00000375759	NM_015001.2	1033	Gga/Aga	11/15	1	2	FACETS	0.94	0.871	1	0.94	0.871	1	CLONAL	1	TRUE	1	0.676108416359395	2		426	541	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17359629	17359629	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	168	321	0	ENST00000375499.3:c.212T>C	p.Met71Thr	p.M71T	ENST00000375499	NM_003000.2	71	aTg/aCg	3/8	1	2	FACETS	0.869	0.803	0.937	0.869	0.803	0.937	CLONAL	1	TRUE	1	0.676108416359395	2		321	572	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100857	27100857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	198	440	0	ENST00000324856.7:c.4139C>T	p.Pro1380Leu	p.P1380L	ENST00000324856	NM_006015.4	1380	cCt/cTt	18/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.676108416359395	2		440	566	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058545	72058545	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	196	369	0	ENST00000357731.5:c.895G>A	p.Ala299Thr	p.A299T	ENST00000357731	NM_173808.2	299	Gct/Act	6/7	1	2	FACETS	0.966	0.9	1	0.966	0.9	1	CLONAL	1	TRUE	1	0.676108416359395	2		369	600	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241963	72241963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	130	233	0	ENST00000357731.5:c.427G>A	p.Asp143Asn	p.D143N	ENST00000357731	NM_173808.2	143	Gac/Aac	3/7	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.676108416359395	2		233	351	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256595	115256595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139287106	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	159	336	0	ENST00000369535.4:c.116C>T	p.Ser39Phe	p.S39F	ENST00000369535	NM_002524.4	39	tCt/tTt	3/7	1	2	FACETS	0.913	0.843	0.986	0.913	0.843	0.986	CLONAL	1	TRUE	1	0.676108416359395	2		336	515	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461978	120461979	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	168	404	0	ENST00000256646.2:c.5737_5738delinsTT	p.Pro1913Leu	p.P1913L	ENST00000256646	NM_024408.3	1913	CCa/TTa	31/34	1	2	FACETS	0.961	0.89	1	0.961	0.89	1	CLONAL	1	TRUE	1	0.676108416359395	2		404	517	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851415	156851415	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	253	694	0	ENST00000524377.1:c.2372A>G	p.Tyr791Cys	p.Y791C	ENST00000524377	NM_002529.3	791	tAc/tGc	17/17	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.676108416359395	2		694	738	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667423	241667423	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913122	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	228	432	2	ENST00000366560.3:c.1027C>T	p.Arg343Ter	p.R343*	ENST00000366560	NM_000143.3	343	Cga/Tga	7/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.676108416359395	2		434	660	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852436	63852436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	227	475	0	ENST00000279873.7:c.3214C>T	p.Pro1072Ser	p.P1072S	ENST00000279873	NM_032199.2	1072	Ccc/Tcc	10/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.676108416359395	2		475	649	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332857	70332857	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	267	567	1	ENST00000373644.4:c.762A>T	p.Gln254His	p.Q254H	ENST00000373644	NM_030625.2	254	caA/caT	2/12	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.676108416359395	2		568	761	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70432771	70432771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	190	309	0	ENST00000373644.4:c.4793G>A	p.Arg1598Lys	p.R1598K	ENST00000373644	NM_030625.2	1598	aGa/aAa	8/12	1	2	FACETS	0.85	0.789	0.913	0.85	0.789	0.913	CLONAL	1	TRUE	1	0.676108416359395	2		309	661	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903742	114903742	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	220	471	0	ENST00000543371.1:c.746C>T	p.Thr249Ile	p.T249I	ENST00000543371	NM_001198531.1	249	aCc/aTc	7/14	1	2	FACETS	0.913	0.853	0.974	0.913	0.853	0.974	CLONAL	1	TRUE	1	0.676108416359395	2		471	713	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123353276	123353276	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760903123	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	273	541	0	ENST00000358487.5:c.56C>T	p.Ser19Phe	p.S19F	ENST00000358487	NM_000141.4	19	tCc/tTc	2/18	1	2	FACETS	0.998	0.94	1	0.998	0.94	1	CLONAL	1	TRUE	1	0.676108416359395	2		541	809	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533854	533854	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	228	643	0	ENST00000451590.1:c.202C>T	p.Arg68Trp	p.R68W	ENST00000451590	NM_001130442.1	68	Cgg/Tgg	3/5	1	2	FACETS	0.822	0.768	0.878	0.822	0.768	0.878	CLONAL	1	TRUE	1	0.676108416359395	2		643	820	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943950	71943950	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	268	671	0	ENST00000298229.2:c.1883T>G	p.Phe628Cys	p.F628C	ENST00000298229	NM_001567.3	628	tTt/tGt	16/28	1	2	FACETS	0.987	0.929	1	0.987	0.929	1	CLONAL	1	TRUE	1	0.676108416359395	2		671	803	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115615	108115615	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770911662	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	176	281	0	ENST00000278616.4:c.763G>A	p.Gly255Arg	p.G255R	ENST00000278616	NM_000051.3	255	Gga/Aga	7/63	1	2	FACETS	0.855	0.791	0.92	0.855	0.791	0.92	CLONAL	1	TRUE	1	0.676108416359395	2		281	609	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153542	108153542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334793787	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	137	148	0	ENST00000278616.4:c.3682G>A	p.Glu1228Lys	p.E1228K	ENST00000278616	NM_000051.3	1228	Gaa/Aaa	25/63	1	2	FACETS	0.954	0.875	1	0.954	0.875	1	CLONAL	1	TRUE	1	0.676108416359395	2		148	425	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118370615	118370615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	109	220	0	ENST00000534358.1:c.6145C>T	p.Pro2049Ser	p.P2049S	ENST00000534358	NM_005933.3	2049	Cct/Tct	24/36	1	2	FACETS	0.998	0.908	1	0.998	0.908	1	CLONAL	1	TRUE	1	0.676108416359395	2		220	323	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374067	118374067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	168	374	0	ENST00000534358.1:c.7460C>T	p.Ser2487Phe	p.S2487F	ENST00000534358	NM_005933.3	2487	tCt/tTt	27/36	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.676108416359395	2		374	486	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390430	118390431	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	177	556	1	ENST00000534358.1:c.11244_11245delinsTT	p.Arg3749Cys	p.R3749C	ENST00000534358	NM_005933.3	3748	ttCCgt/ttTTgt	32/36	1	2	FACETS	0.849	0.786	0.913	0.849	0.786	0.913	CLONAL	1	TRUE	1	0.676108416359395	2		557	617	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	165	347	2	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	NA	2	FACETS	0.965	0.893	1			1	INDETERMINATE	1	TRUE	NA	0.676108416359395	2		349	506	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	465691	465691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	161	382	0	ENST00000399788.2:c.685G>A	p.Asp229Asn	p.D229N	ENST00000399788	NM_001042603.1	229	Gat/Aat	6/28	NA	2	FACETS	0.763	0.703	0.826			1	INDETERMINATE	1	TRUE	NA	0.676108416359395	2		382	624	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385196	4385196	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	174	378	0	ENST00000261254.3:c.221A>T	p.Glu74Val	p.E74V	ENST00000261254	NM_001759.3	74	gAa/gTa	2/5	NA	2	FACETS	0.996	0.924	1			1	INDETERMINATE	1	TRUE	NA	0.676108416359395	2		378	517	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21639444	21639444	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766866319	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	176	184	0	ENST00000421138.2:c.470C>T	p.Ser157Leu	p.S157L	ENST00000421138		157	tCa/tTa	6/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.676108416359395	2		184	486	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945069	31945069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371692293	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	221	525	0	ENST00000340398.3:c.32C>T	p.Ser11Phe	p.S11F	ENST00000340398	NM_001013699.2	11	tCc/tTc	1/1	1	2	FACETS	0.967	0.904	1	0.967	0.904	1	CLONAL	1	TRUE	1	0.676108416359395	2		525	676	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245297	46245297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775722505	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	201	410	0	ENST00000334344.6:c.3391C>T	p.Pro1131Ser	p.P1131S	ENST00000334344	NM_152641.2	1131	Cca/Tca	15/21	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.676108416359395	2		410	574	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431228	49431230	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	31	487	0	ENST00000301067.7:c.9909_9911del	p.Pro3304del	p.P3304del	ENST00000301067	NM_003482.3	3303	tcTCCc/tcc	34/54	0.548239281352222	1	FACETS	0.126	0.101	0.154	0.126	0.101	0.154	SUBCLONAL	1	TRUE	0	0.676108416359395	1		487	482	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433142	49433142	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	33	536	0	ENST00000301067.7:c.8230-1G>A		p.X2744_splice	ENST00000301067	NM_003482.3	2744			0.548239281352222	1	FACETS	0.141	0.114	0.171	0.141	0.114	0.171	SUBCLONAL	1	TRUE	0	0.676108416359395	1		536	459	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433357	49433357	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774178055	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	37	580	1	ENST00000301067.7:c.8090G>A	p.Arg2697His	p.R2697H	ENST00000301067	NM_003482.3	2697	cGc/cAc	32/54	0.548239281352222	1	FACETS	0.148	0.121	0.177	0.148	0.121	0.177	SUBCLONAL	1	TRUE	0	0.676108416359395	1		581	491	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433632	49433632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	76	789	0	ENST00000301067.7:c.7921C>T	p.Pro2641Ser	p.P2641S	ENST00000301067	NM_003482.3	2641	Cct/Tct	31/54	0.548239281352222	1	FACETS	0.212	0.186	0.241	0.212	0.186	0.241	SUBCLONAL	1	TRUE	0	0.676108416359395	1		789	701	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440431	49440431	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1240601136	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	267	597	0	ENST00000301067.7:c.4379del	p.Pro1460HisfsTer46	p.P1460Hfs*46	ENST00000301067	NM_003482.3	1460	cCa/ca	15/54	0.548239281352222	1	FACETS	0.889	0.841	0.937	0.889	0.841	0.937	CLONAL	1	TRUE	0	0.676108416359395	1		597	588	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444256	49444256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542933613	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	369	858	0	ENST00000301067.7:c.3115C>T	p.Pro1039Ser	p.P1039S	ENST00000301067	NM_003482.3	1039	Cct/Tct	11/54	0.548239281352222	1	FACETS	0.98	0.937	1	0.98	0.937	1	CLONAL	1	TRUE	0	0.676108416359395	1		858	737	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445430	49445431	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	50	854	3	ENST00000301067.7:c.2035_2036delinsTT	p.Pro679Phe	p.P679F	ENST00000301067	NM_003482.3	679	CCc/TTc	10/54	0.548239281352222	1	FACETS	0.131	0.111	0.154	0.131	0.111	0.154	SUBCLONAL	1	TRUE	0	0.676108416359395	1		857	745	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864754	57864754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	45	613	0	ENST00000228682.2:c.2231G>A	p.Gly744Glu	p.G744E	ENST00000228682	NM_005269.2	744	gGa/gAa	12/12	0.548239281352222	1	FACETS	0.179	0.15	0.211	0.179	0.15	0.211	SUBCLONAL	1	TRUE	0	0.676108416359395	1		613	493	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222560	69222560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764554024	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	196	228	0	ENST00000462284.1:c.533C>T	p.Ser178Leu	p.S178L	ENST00000462284	NM_002392.5	178	tCa/tTa	8/11	1	2	FACETS	0.759	0.714	0.804	1	0.993	1	SUBCLONAL	2	TRUE	1	0.676108416359395	2		228	382	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601228	28601228	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772146579	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	178	360	1	ENST00000241453.7:c.2204C>T	p.Ser735Phe	p.S735F	ENST00000241453	NM_004119.2	735	tCc/tTc	17/24	0.676108416359395	1	FACETS	0.947	0.887	1	0.947	0.887	1	CLONAL	1	TRUE	0	0.676108416359395	1		361	368	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281881	49281881	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	253	544	0	ENST00000282018.3:c.928G>T	p.Glu310Ter	p.E310*	ENST00000282018	NM_020377.2	310	Gag/Tag	1/1	0.676108416359395	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.676108416359395	1		544	490	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435811	110435811	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	131	313	0	ENST00000375856.3:c.2590C>T	p.Pro864Ser	p.P864S	ENST00000375856	NM_003749.2	864	Cct/Tct	1/2	0.676108416359395	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.676108416359395	1		313	254	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135385	30135385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	25	388	0	ENST00000331968.5:c.433C>T	p.Arg145Cys	p.R145C	ENST00000331968	NM_002742.2	145	Cgt/Tgt	3/18	0.57062559103748	1	FACETS	0.117	0.091	0.146	0.117	0.091	0.146	SUBCLONAL	1	TRUE	0	0.676108416359395	1		388	420	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061045	38061045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	102	286	0	ENST00000250448.2:c.944G>A	p.Gly315Glu	p.G315E	ENST00000250448	NM_004496.3	315	gGg/gAg	2/2	0.57062559103748	1	FACETS	0.799	0.728	0.872	0.799	0.728	0.872	SUBCLONAL	1	TRUE	0	0.676108416359395	1		286	250	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582079	95582079	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	140	305	0	ENST00000393063.1:c.1832T>G	p.Phe611Cys	p.F611C	ENST00000393063	NM_030621.3	611	tTc/tGc	12/28	1	2	FACETS	0.993	0.913	1	0.993	0.913	1	CLONAL	1	TRUE	1	0.676108416359395	2		305	417	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472644	88472644	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	107	277	0	ENST00000360948.2:c.1911G>A	p.Met637Ile	p.M637I	ENST00000360948	NM_001012338.2	637	atG/atA	16/19	1	2	FACETS	0.998	0.907	1	0.998	0.907	1	CLONAL	1	TRUE	1	0.676108416359395	2		277	317	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339518	339519	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	251	698	1	ENST00000262320.3:c.2383_2384delinsTT	p.Pro795Phe	p.P795F	ENST00000262320	NM_003502.3	795	CCc/TTc	10/11	1	2	FACETS	0.888	0.833	0.944	0.888	0.833	0.944	CLONAL	1	TRUE	1	0.676108416359395	2		699	836	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343668	343668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774921991	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	306	724	0	ENST00000262320.3:c.2006C>T	p.Ser669Phe	p.S669F	ENST00000262320	NM_003502.3	669	tCc/tTc	8/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.676108416359395	2		724	886	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396789	396790	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	212	538	1	ENST00000262320.3:c.236_237delinsTT	p.Thr79Ile	p.T79I	ENST00000262320	NM_003502.3	79	aCC/aTT	2/11	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.676108416359395	2		539	627	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2114317	2114317	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs137854346	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	123	682	0	ENST00000219476.3:c.1491del	p.Glu498ArgfsTer37	p.E498Rfs*37	ENST00000219476	NM_000548.3	496	atC/at	15/42	1	2	FACETS	0.424	0.383	0.467	0.424	0.383	0.467	SUBCLONAL	1	TRUE	1	0.676108416359395	2		682	858	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135027	2135027	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	219	621	0	ENST00000219476.3:c.4569G>T	p.Glu1523Asp	p.E1523D	ENST00000219476	NM_000548.3	1523	gaG/gaT	35/42	1	2	FACETS	0.995	0.931	1	0.995	0.931	1	CLONAL	1	TRUE	1	0.676108416359395	2		621	651	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222305	2222305	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	243	648	0	ENST00000326181.6:c.589A>T	p.Ser197Cys	p.S197C	ENST00000326181	NM_032271.2	197	Agc/Tgc	8/21	1	2	FACETS	0.981	0.92	1	0.981	0.92	1	CLONAL	1	TRUE	1	0.676108416359395	2		648	733	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857284	9857284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	179	449	1	ENST00000330684.3:c.4117G>A	p.Asp1373Asn	p.D1373N	ENST00000330684	NM_001134407.1	1373	Gat/Aat	13/13	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.676108416359395	2		450	529	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632746	23632746	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	240	428	0	ENST00000261584.4:c.3050del	p.Ala1017ValfsTer16	p.A1017Vfs*16	ENST00000261584	NM_024675.3	1017	gCt/gt	10/13	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.676108416359395	2		428	686	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128078	30128078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	272	611	0	ENST00000263025.4:c.1051G>A	p.Glu351Lys	p.E351K	ENST00000263025	NM_002746.2	351	Gag/Aag	8/9	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.676108416359395	2		611	773	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835618	68835618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	229	501	0	ENST00000261769.5:c.209C>T	p.Ser70Phe	p.S70F	ENST00000261769	NM_004360.3	70	tCc/tTc	3/16	0.676108416359395	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.676108416359395	1		501	443	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984765	72984765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769225828	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	210	511	0	ENST00000268489.5:c.2819C>T	p.Pro940Leu	p.P940L	ENST00000268489	NM_006885.3	940	cCg/cTg	3/10	0.676108416359395	1	FACETS	0.935	0.879	0.99	0.935	0.879	0.99	CLONAL	1	TRUE	0	0.676108416359395	1		511	440	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357423	89357424	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	138	457	0	ENST00000301030.4:c.394_395delinsTT	p.Pro132Leu	p.P132L	ENST00000301030	NM_001256183.1	132	CCa/TTa	5/13	0.676108416359395	1	FACETS	0.919	0.852	0.987	0.919	0.852	0.987	CLONAL	1	TRUE	0	0.676108416359395	1		457	294	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816261	89816262	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	209	491	1	ENST00000389301.3:c.3115_3116delinsAA	p.Gly1039Asn	p.G1039N	ENST00000389301	NM_000135.2	1039	GGc/AAc	32/43	0.676108416359395	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.676108416359395	1		492	388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579700	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	521	566	0	ENST00000269305.4:c.96_96+1delinsAA		p.X32_splice	ENST00000269305	NM_001126112.2	32		3/11	NA	2	FACETS	0.957	0.927	0.987			1	INDETERMINATE	2	TRUE	NA	0.676108416359395	2		566	805	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16062178	16062178	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs201746136	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	189	414	0	ENST00000268712.3:c.628G>C	p.Glu210Gln	p.E210Q	ENST00000268712	NM_006311.3	210	Gaa/Caa	6/46	1	2	FACETS	0.905	0.841	0.971	0.905	0.841	0.971	CLONAL	1	TRUE	1	0.676108416359395	2		414	618	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068451	16068451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	10	94	0	ENST00000268712.3:c.460G>A	p.Glu154Lys	p.E154K	ENST00000268712	NM_006311.3	154	Gaa/Aaa	5/46	1	2	FACETS	0.152	0.102	0.214	0.152	0.102	0.214	SUBCLONAL	1	TRUE	1	0.676108416359395	2		94	195	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576085	29576085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555617346	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	217	473	0	ENST00000356175.3:c.4058C>T	p.Ser1353Phe	p.S1353F	ENST00000356175	NM_000267.3	1353	tCc/tTc	30/57	1	2	FACETS	0.871	0.813	0.931	0.871	0.813	0.931	CLONAL	1	TRUE	1	0.676108416359395	2		473	737	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664523	29664523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	208	449	0	ENST00000356175.3:c.6502C>T	p.Pro2168Ser	p.P2168S	ENST00000356175	NM_000267.3	2168	Cct/Tct	42/57	1	2	FACETS	0.909	0.847	0.972	0.909	0.847	0.972	CLONAL	1	TRUE	1	0.676108416359395	2		449	677	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475020	40475020	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	154	380	0	ENST00000264657.5:c.1888+2T>C		p.X630_splice	ENST00000264657	NM_139276.2	630			1	2	FACETS	0.878	0.809	0.949	0.878	0.809	0.949	CLONAL	1	TRUE	1	0.676108416359395	2		380	519	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40500530	40500530	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	216	381	0	ENST00000264657.5:c.5C>T	p.Ala2Val	p.A2V	ENST00000264657	NM_139276.2	2	gCc/gTc	2/24	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.676108416359395	2		381	608	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870597	40870597	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	234	503	0	ENST00000428826.2:c.806T>C	p.Leu269Pro	p.L269P	ENST00000428826		269	cTt/cCt	9/21	1	2	FACETS	0.94	0.881	1	0.94	0.881	1	CLONAL	1	TRUE	1	0.676108416359395	2		503	736	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435554	56435554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	225	587	0	ENST00000407977.2:c.1583C>T	p.Ser528Phe	p.S528F	ENST00000407977		528	tCt/tTt	9/10	1	2	FACETS	0.926	0.866	0.987	0.926	0.866	0.987	CLONAL	1	TRUE	1	0.676108416359395	2		587	719	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120457	70120457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	386	770	0	ENST00000245479.2:c.1459C>T	p.Pro487Ser	p.P487S	ENST00000245479	NM_000346.3	487	Cct/Tct	3/3	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.676108416359395	2		770	1137	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118624	11118624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878854203	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	219	513	0	ENST00000358026.2:c.2048C>T	p.Pro683Leu	p.P683L	ENST00000358026	NM_001128849.1	683	cCc/cTc	14/36	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.676108416359395	2		513	635	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272138	15272138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	249	625	2	ENST00000263388.2:c.6301C>T	p.Pro2101Ser	p.P2101S	ENST00000263388	NM_000435.2	2101	Ccc/Tcc	33/33	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.676108416359395	2		627	706	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281173	15281173	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	294	686	0	ENST00000263388.2:c.5083G>T	p.Glu1695Ter	p.E1695*	ENST00000263388	NM_000435.2	1695	Gaa/Taa	27/33	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.676108416359395	2		686	857	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210419	36210419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs567944243	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	47	502	0	ENST00000222270.7:c.412C>T	p.Arg138Cys	p.R138C	ENST00000222270	NM_014727.1	138	Cgc/Tgc	2/37	1	2	FACETS	0.199	0.167	0.234	0.199	0.167	0.234	SUBCLONAL	1	TRUE	1	0.676108416359395	2		502	698	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791808	42791808	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	264	642	0	ENST00000575354.2:c.694A>G	p.Lys232Glu	p.K232E	ENST00000575354	NM_015125.3	232	Aag/Gag	5/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.676108416359395	2		642	726	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796539	42796539	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	228	680	0	ENST00000575354.2:c.3096del	p.Tyr1032Ter	p.Y1032*	ENST00000575354	NM_015125.3	1032	taC/ta	13/20	1	2	FACETS	0.926	0.867	0.987	0.926	0.867	0.987	CLONAL	1	TRUE	1	0.676108416359395	2		680	728	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798339	42798339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762473510	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	225	645	0	ENST00000575354.2:c.4210C>T	p.Pro1404Ser	p.P1404S	ENST00000575354	NM_015125.3	1404	Ccc/Tcc	18/20	1	2	FACETS	0.958	0.896	1	0.958	0.896	1	CLONAL	1	TRUE	1	0.676108416359395	2		645	695	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719873	52719873	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	255	535	0	ENST00000322088.6:c.1085T>A	p.Ile362Asn	p.I362N	ENST00000322088	NM_014225.5	362	aTc/aAc	9/15	1	2	FACETS	0.934	0.877	0.992	0.934	0.877	0.992	CLONAL	1	TRUE	1	0.676108416359395	2		535	808	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085773	16085773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	183	429	0	ENST00000281043.3:c.949G>A	p.Glu317Lys	p.E317K	ENST00000281043	NM_005378.4	317	Gag/Aag	3/3	NA	2	FACETS	0.975	0.906	1			1	INDETERMINATE	1	TRUE	NA	0.676108416359395	2		429	555	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443615	29443615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	265	585	0	ENST00000389048.3:c.3602G>A	p.Gly1201Glu	p.G1201E	ENST00000389048	NM_004304.4	1201	gGg/gAg	23/29	0.676108416359395	3	FACETS	1	0.96	1	0.516	0.484	0.549	CLONAL	1	TRUE	1	0.676108416359395	3		585	1017	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027654	48027654	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	123	271	0	ENST00000234420.5:c.2532G>C	p.Met844Ile	p.M844I	ENST00000234420	NM_000179.2	844	atG/atC	4/10	0.2733631259681	3	FACETS	1	0.979	1	0.618	0.564	0.674	INDETERMINATE	1	TRUE	1	0.676108416359395	3		271	394	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593635	215593635	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1553612184	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	113	304	0	ENST00000260947.4:c.2099del	p.Gly700AlafsTer14	p.G700Afs*14	ENST00000260947	NM_000465.2	700	gGc/gc	11/11	1	2	FACETS	0.741	0.671	0.814	0.741	0.671	0.814	SUBCLONAL	1	TRUE	1	0.676108416359395	2		304	451	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440183	220440184	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	255	670	1	ENST00000243786.2:c.1036_1037delinsAA	p.Gly346Lys	p.G346K	ENST00000243786	NM_002191.3	346	GGa/AAa	2/2	1	2	FACETS	0.931	0.875	0.989	0.931	0.875	0.989	CLONAL	1	TRUE	1	0.676108416359395	2		671	810	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661350	227661351	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	234	554	0	ENST00000305123.5:c.2104_2105delinsAA	p.Gly702Lys	p.G702K	ENST00000305123	NM_005544.2	702	GGg/AAg	1/2	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.676108416359395	2		554	674	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624936	9624936	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	147	299	0	ENST00000353224.5:c.41C>A	p.Pro14Gln	p.P14Q	ENST00000353224	NM_177990.2	14	cCg/cAg	3/10	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.676108416359395	2		299	428	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024885	31024885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	190	526	0	ENST00000375687.4:c.4370C>T	p.Ser1457Phe	p.S1457F	ENST00000375687	NM_015338.5	1457	tCc/tTc	13/13	1	2	FACETS	0.84	0.78	0.902	0.84	0.78	0.902	CLONAL	1	TRUE	1	0.676108416359395	2		526	669	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031679	36031680	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	251	661	2	ENST00000358208.4:c.1508_1509delinsAA	p.Arg503Gln	p.R503Q	ENST00000358208		503	cGG/cAA	12/12	1	2	FACETS	0.991	0.931	1	0.991	0.931	1	CLONAL	1	TRUE	1	0.676108416359395	2		663	749	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40828006	40828007	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	115	324	0	ENST00000373198.4:c.2421_2422delinsAA	p.Glu808Lys	p.E808K	ENST00000373198	NM_133170.3	807	aaGGag/aaAAag	17/32	1	2	FACETS	0.891	0.81	0.974	0.891	0.81	0.974	CLONAL	1	TRUE	1	0.676108416359395	2		324	382	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899064	40899065	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	179	514	1	ENST00000373198.4:c.2205_2206delinsAT	p.Gly736Trp	p.G736W	ENST00000373198	NM_133170.3	735	ccGGgg/ccATgg	14/32	1	2	FACETS	0.961	0.892	1	0.961	0.892	1	CLONAL	1	TRUE	1	0.676108416359395	2		515	551	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264097	46264097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772695646	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	102	312	0	ENST00000371998.3:c.1144C>T	p.Pro382Ser	p.P382S	ENST00000371998		382	Cct/Tct	11/23	1	2	FACETS	0.788	0.71	0.869	0.788	0.71	0.869	SUBCLONAL	1	TRUE	1	0.676108416359395	2		312	383	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264865	46264865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	180	351	0	ENST00000371998.3:c.1735C>T	p.Pro579Ser	p.P579S	ENST00000371998		579	Cca/Tca	12/23	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.676108416359395	2		351	504	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292792	62292792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	142	364	0	ENST00000360203.5:c.244C>T	p.Pro82Ser	p.P82S	ENST00000360203	NM_001283009.1	82	Ccg/Tcg	3/35	1	2	FACETS	0.975	0.896	1	0.975	0.896	1	CLONAL	1	TRUE	1	0.676108416359395	2		364	431	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324263	62324263	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	299	749	1	ENST00000360203.5:c.2758C>A	p.Gln920Lys	p.Q920K	ENST00000360203	NM_001283009.1	920	Cag/Aag	29/35	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.676108416359395	2		750	849	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171604	36171604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	106	233	0	ENST00000300305.3:c.961C>T	p.Leu321Phe	p.L321F	ENST00000300305		321	Ctc/Ttc	7/8	1	2	FACETS	0.925	0.838	1	0.925	0.838	1	CLONAL	1	TRUE	1	0.676108416359395	2		233	339	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42843805	42843805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	192	434	0	ENST00000398585.3:c.1114C>T	p.Pro372Ser	p.P372S	ENST00000398585	NM_001135099.1	372	Cca/Tca	10/14	1	2	FACETS	0.943	0.878	1	0.943	0.878	1	CLONAL	1	TRUE	1	0.676108416359395	2		434	602	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715621	30715621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863223850	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	95	237	1	ENST00000295754.5:c.1279C>T	p.Pro427Ser	p.P427S	ENST00000295754	NM_003242.5	427	Cca/Tca	5/7	0.676108416359395	1	FACETS	0.925	0.844	1	0.925	0.844	1	CLONAL	1	TRUE	0	0.676108416359395	1		238	201	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042469	37042469	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	176	216	0	ENST00000231790.2:c.231T>G	p.Cys77Trp	p.C77W	ENST00000231790	NM_000249.3	77	tgT/tgG	3/19	0.676108416359395	1	FACETS	0.921	0.862	0.982	0.921	0.862	0.982	CLONAL	1	TRUE	0	0.676108416359395	1		216	374	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162327	47162327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	137	321	0	ENST00000409792.3:c.3799C>T	p.Pro1267Ser	p.P1267S	ENST00000409792	NM_014159.6	1267	Cct/Tct	3/21	0.676108416359395	1	FACETS	0.955	0.886	1	0.955	0.886	1	CLONAL	1	TRUE	0	0.676108416359395	1		321	281	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441265	52441266	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	199	455	0	ENST00000460680.1:c.504_505delinsTT	p.His169Tyr	p.H169Y	ENST00000460680	NM_004656.3	168	ttCCac/ttTTac	7/17	0.676108416359395	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.676108416359395	1		455	372	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445067	89445067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	177	431	0	ENST00000336596.2:c.1387C>T	p.Pro463Ser	p.P463S	ENST00000336596	NM_005233.5	463	Cct/Tct	6/17	0.676108416359395	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.676108416359395	1		431	346	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582364	119582364	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	129	278	0	ENST00000316626.5:c.1037A>G	p.Glu346Gly	p.E346G	ENST00000316626		346	gAa/gGa	10/12	0.615040548020509	3	FACETS	0.864	0.786	0.945	0.432	0.393	0.473	CLONAL	1	TRUE	1	0.676108416359395	3		278	591	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967173	134967173	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370164002	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	138	360	2	ENST00000398015.3:c.2512G>A	p.Glu838Lys	p.E838K	ENST00000398015	NM_004441.4	838	Gag/Aag	14/16	0.615040548020509	3	FACETS	0.953	0.871	1	0.477	0.435	0.52	CLONAL	1	TRUE	1	0.676108416359395	3		362	573	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977925	134977925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	248	517	0	ENST00000398015.3:c.2918G>A	p.Arg973Lys	p.R973K	ENST00000398015	NM_004441.4	973	aGg/aAg	16/16	0.615040548020509	3	FACETS	0.963	0.901	1	0.482	0.45	0.514	CLONAL	1	TRUE	1	0.676108416359395	3		517	1019	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170015153	170015153	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770998502	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	219	438	0	ENST00000295797.4:c.1559C>T	p.Pro520Leu	p.P520L	ENST00000295797	NM_002740.5	520	cCg/cTg	16/18	0.615040548020509	3	FACETS	0.893	0.831	0.957	0.446	0.415	0.479	CLONAL	1	TRUE	1	0.676108416359395	3		438	971	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502237	186502237	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757324676	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	107	216	0	ENST00000323963.5:c.46G>A	p.Glu16Lys	p.E16K	ENST00000323963		16	Gag/Aag	2/11	0.615040548020509	3	FACETS	0.921	0.831	1	0.46	0.415	0.508	CLONAL	1	TRUE	1	0.676108416359395	3		216	460	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607273	189607273	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	211	495	0	ENST00000264731.3:c.1652G>T	p.Ser551Ile	p.S551I	ENST00000264731	NM_003722.4	551	aGt/aTt	12/14	0.615040548020509	3	FACETS	0.988	0.92	1	0.494	0.46	0.53	CLONAL	1	TRUE	1	0.676108416359395	3		495	845	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127318	55127318	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	191	433	0	ENST00000257290.5:c.106G>A	p.Glu36Lys	p.E36K	ENST00000257290	NM_006206.4	36	Gaa/Aaa	3/23	1	2	FACETS	0.967	0.9	1	0.967	0.9	1	CLONAL	1	TRUE	1	0.676108416359395	2		433	584	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602770	55602770	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	140	310	0	ENST00000288135.5:c.2591C>T	p.Ser864Phe	p.S864F	ENST00000288135	NM_000222.2	864	tCt/tTt	18/21	1	2	FACETS	0.845	0.775	0.918	0.845	0.775	0.918	CLONAL	1	TRUE	1	0.676108416359395	2		310	490	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201816	66201816	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556854839	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	178	399	1	ENST00000273854.3:c.2686C>T	p.Arg896Cys	p.R896C	ENST00000273854	NM_004439.5	896	Cgt/Tgt	16/18	1	2	FACETS	0.908	0.842	0.976	0.908	0.842	0.976	CLONAL	1	TRUE	1	0.676108416359395	2		400	580	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155524	106155524	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs752891551	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	181	375	0	ENST00000380013.4:c.425C>A	p.Ser142Tyr	p.S142Y	ENST00000380013	NM_001127208.2	142	tCc/tAc	3/11	1	2	FACETS	0.99	0.919	1	0.99	0.919	1	CLONAL	1	TRUE	1	0.676108416359395	2		375	541	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541201	187541201	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	130	313	0	ENST00000441802.2:c.6539C>T	p.Pro2180Leu	p.P2180L	ENST00000441802	NM_005245.3	2180	cCt/cTt	10/27	1	2	FACETS	0.976	0.894	1	0.976	0.894	1	CLONAL	1	TRUE	1	0.676108416359395	2		313	394	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628251	187628251	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	237	565	0	ENST00000441802.2:c.2731del	p.Val911SerfsTer3	p.V911Sfs*3	ENST00000441802	NM_005245.3	911	Gtc/tc	2/27	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.676108416359395	2		565	687	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628763	187628763	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	276	515	0	ENST00000441802.2:c.2219A>G	p.Asn740Ser	p.N740S	ENST00000441802	NM_005245.3	740	aAc/aGc	2/27	1	2	FACETS	0.997	0.939	1	0.997	0.939	1	CLONAL	1	TRUE	1	0.676108416359395	2		515	819	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278850	1278850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	244	484	0	ENST00000310581.5:c.2192G>A	p.Ser731Asn	p.S731N	ENST00000310581	NM_198253.2	731	aGc/aAc	6/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.676108416359395	2		484	649	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294672	1294672	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	169	442	0	ENST00000310581.5:c.329G>C	p.Gly110Ala	p.G110A	ENST00000310581	NM_198253.2	110	gGc/gCc	2/16	1	2	FACETS	0.934	0.865	1	0.934	0.865	1	CLONAL	1	TRUE	1	0.676108416359395	2		442	535	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295204	1295204	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs2735943	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	139	274	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.676108416359395	2		274	391	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31437349	31437349	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	255	489	0	ENST00000344624.3:c.2939C>A	p.Thr980Asn	p.T980N	ENST00000344624		980	aCc/aAc	21/33	1	2	FACETS	0.833	0.781	0.886	0.833	0.781	0.886	CLONAL	1	TRUE	1	0.676108416359395	2		489	906	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31485041	31485041	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	152	107	0	ENST00000344624.3:c.1943T>C	p.Phe648Ser	p.F648S	ENST00000344624		648	tTt/tCt	12/33	1	2	FACETS	0.986	0.91	1	0.986	0.91	1	CLONAL	1	TRUE	1	0.676108416359395	2		107	456	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576786	67576786	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	170	206	0	ENST00000274335.5:c.868A>T	p.Ile290Leu	p.I290L	ENST00000274335		290	Ata/Tta	6/15	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.676108416359395	2		206	485	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86667993	86667993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	108	247	0	ENST00000274376.6:c.1757C>T	p.Ser586Phe	p.S586F	ENST00000274376	NM_002890.2	586	tCc/tTc	13/25	1	2	FACETS	0.772	0.698	0.849	0.772	0.698	0.849	SUBCLONAL	1	TRUE	1	0.676108416359395	2		247	414	SUCCESS
APC	324	MSKCC	GRCh37	5	112102944	112102945	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	139	321	2	ENST00000257430.4:c.279_280delinsTT	p.Arg94Cys	p.R94C	ENST00000257430	NM_000038.5	93	ctCCgt/ctTTgt	4/16	1	2	FACETS	0.848	0.777	0.921	0.848	0.777	0.921	CLONAL	1	TRUE	1	0.676108416359395	2		323	485	SUCCESS
APC	324	MSKCC	GRCh37	5	112179530	112179530	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	132	341	0	ENST00000257430.4:c.8239C>T	p.Pro2747Ser	p.P2747S	ENST00000257430	NM_000038.5	2747	Cct/Tct	16/16	1	2	FACETS	0.896	0.82	0.974	0.896	0.82	0.974	CLONAL	1	TRUE	1	0.676108416359395	2		341	436	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707714	176707714	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	174	432	1	ENST00000439151.2:c.5771T>A	p.Val1924Glu	p.V1924E	ENST00000439151	NM_022455.4	1924	gTg/gAg	18/23	1	2	FACETS	0.921	0.853	0.99	0.921	0.853	0.99	CLONAL	1	TRUE	1	0.676108416359395	2		433	559	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401645	401645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	185	458	1	ENST00000380956.4:c.967G>A	p.Gly323Arg	p.G323R	ENST00000380956	NM_001195286.1	323	Ggg/Agg	7/9	NA	2	FACETS	1	0.949	1			1	INDETERMINATE	1	TRUE	NA	0.676108416359395	2		459	534	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056149	26056149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750380165	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	183	337	0	ENST00000343677.2:c.508G>A	p.Val170Met	p.V170M	ENST00000343677	NM_005319.3	170	Gtg/Atg	1/1	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.676108416359395	2		337	539	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778137	27778137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	155	557	0	ENST00000369163.2:c.286G>A	p.Ala96Thr	p.A96T	ENST00000369163	NM_003536.2	96	Gca/Aca	1/1	1	2	FACETS	0.849	0.782	0.918	0.849	0.782	0.918	CLONAL	1	TRUE	1	0.676108416359395	2		557	540	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778157	27778158	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	153	596	0	ENST00000369163.2:c.306_307delinsAA	p.Gly103Arg	p.G103R	ENST00000369163	NM_003536.2	102	gtGGgg/gtAAgg	1/1	1	2	FACETS	0.771	0.709	0.836	0.771	0.709	0.836	SUBCLONAL	1	TRUE	1	0.676108416359395	2		596	587	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911058	29911059	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	87	552	1	ENST00000376809.5:c.357_358delinsTT	p.Gln120Ter	p.Q120*	ENST00000376809	NM_002116.7	119	atCCag/atTTag	3/8	1	2	FACETS	0.45	0.399	0.504	0.45	0.399	0.504	SUBCLONAL	1	TRUE	1	0.676108416359395	2		553	572	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324097	31324097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs72558116	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	143	320	0	ENST00000412585.2:c.466T>C	p.Ser156Pro	p.S156P	ENST00000412585	NM_005514.6	156	Tcc/Ccc	3/8	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.676108416359395	2		320	386	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31939793	31939793	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1186398625	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	300	669	0	ENST00000375333.2:c.20C>T	p.Ala7Val	p.A7V	ENST00000375333	NM_032454.1	7	gCt/gTt	1/8	1	2	FACETS	0.957	0.904	1	0.957	0.904	1	CLONAL	1	TRUE	1	0.676108416359395	2		669	927	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140939	37140939	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1480448252	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	112	285	0	ENST00000373509.5:c.775G>A	p.Val259Ile	p.V259I	ENST00000373509	NM_002648.3	259	Gtc/Atc	5/6	1	2	FACETS	0.87	0.789	0.953	0.87	0.789	0.953	CLONAL	1	TRUE	1	0.676108416359395	2		285	381	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956699	93956699	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs538121970	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	124	280	0	ENST00000369303.4:c.2537T>C	p.Ile846Thr	p.I846T	ENST00000369303	NM_004440.3	846	aTa/aCa	15/17	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.676108416359395	2		280	359	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969189	93969189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868510824	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	130	232	0	ENST00000369303.4:c.1807C>T	p.Pro603Ser	p.P603S	ENST00000369303	NM_004440.3	603	Cca/Tca	10/17	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.676108416359395	2		232	375	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979219	93979219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1009626356	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	125	261	0	ENST00000369303.4:c.1609G>A	p.Glu537Lys	p.E537K	ENST00000369303	NM_004440.3	537	Gaa/Aaa	7/17	1	2	FACETS	0.876	0.8	0.955	0.876	0.8	0.955	CLONAL	1	TRUE	1	0.676108416359395	2		261	422	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120377	94120377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	141	271	0	ENST00000369303.4:c.674C>T	p.Ser225Phe	p.S225F	ENST00000369303	NM_004440.3	225	tCc/tTc	3/17	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.676108416359395	2		271	372	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120620	94120620	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	139	343	0	ENST00000369303.4:c.431T>A	p.Val144Glu	p.V144E	ENST00000369303	NM_004440.3	144	gTa/gAa	3/17	1	2	FACETS	0.862	0.79	0.936	0.862	0.79	0.936	CLONAL	1	TRUE	1	0.676108416359395	2		343	477	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983139	111983140	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	140	368	0	ENST00000368678.4:c.1407_1408delinsTT	p.Arg470Trp	p.R470W	ENST00000368678		469	aaCCgg/aaTTgg	13/13	1	2	FACETS	0.933	0.857	1	0.933	0.857	1	CLONAL	1	TRUE	1	0.676108416359395	2		368	444	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609838	117609839	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	212	491	0	ENST00000368508.3:c.6860dup	p.Ser2288ValfsTer2	p.S2288Vfs*2	ENST00000368508	NM_002944.2	2287	aag/aaAg	43/43	1	2	FACETS	0.87	0.811	0.93	0.87	0.811	0.93	CLONAL	1	TRUE	1	0.676108416359395	2		491	721	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117645576	117645576	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	165	274	0	ENST00000368508.3:c.5560G>A	p.Asp1854Asn	p.D1854N	ENST00000368508	NM_002944.2	1854	Gat/Aat	34/43	1	2	FACETS	0.852	0.786	0.919	0.852	0.786	0.919	CLONAL	1	TRUE	1	0.676108416359395	2		274	573	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700228	117700228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	175	337	0	ENST00000368508.3:c.2591G>A	p.Gly864Glu	p.G864E	ENST00000368508	NM_002944.2	864	gGa/gAa	17/43	1	2	FACETS	0.924	0.857	0.994	0.924	0.857	0.994	CLONAL	1	TRUE	1	0.676108416359395	2		337	560	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117737457	117737457	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	214	297	0	ENST00000368508.3:c.192G>T	p.Trp64Cys	p.W64C	ENST00000368508	NM_002944.2	64	tgG/tgT	3/43	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.676108416359395	2		297	620	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200032	138200033	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	139	418	1	ENST00000237289.4:c.1450_1451delinsTT	p.Pro484Phe	p.P484F	ENST00000237289	NM_001270507.1	484	CCc/TTc	7/9	1	2	FACETS	0.95	0.872	1	0.95	0.872	1	CLONAL	1	TRUE	1	0.676108416359395	2		419	433	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997781	149997781	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777307051	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	171	416	0	ENST00000253339.5:c.2686C>T	p.Arg896Trp	p.R896W	ENST00000253339		896	Cgg/Tgg	5/7	1	2	FACETS	0.949	0.879	1	0.949	0.879	1	CLONAL	1	TRUE	1	0.676108416359395	2		416	533	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004239	150004239	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	145	152	0	ENST00000253339.5:c.1986del	p.Lys662AsnfsTer3	p.K662Nfs*3	ENST00000253339		662	aaA/aa	3/7	1	2	FACETS	0.968	0.891	1	0.968	0.891	1	CLONAL	1	TRUE	1	0.676108416359395	2		152	443	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864395	162864396	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	161	419	0	ENST00000366898.1:c.117_118delinsTT	p.Gln40Ter	p.Q40*	ENST00000366898	NM_004562.2	39	gaCCag/gaTTag	2/12	0.676108416359395	2	FACETS	0.907	0.838	0.979	0.454	0.419	0.49	CLONAL	1	TRUE	0	0.676108416359395	2		419	525	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985538	2985538	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1407244585	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	234	461	0	ENST00000396946.4:c.273C>A	p.Phe91Leu	p.F91L	ENST00000396946	NM_032415.4	91	ttC/ttA	4/25	1	2	FACETS	0.997	0.935	1	0.997	0.935	1	CLONAL	1	TRUE	1	0.676108416359395	2		461	694	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386572	81386572	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	168	344	0	ENST00000222390.5:c.415A>C	p.Thr139Pro	p.T139P	ENST00000222390	NM_000601.4	139	Aca/Cca	4/18	1	2	FACETS	0.864	0.799	0.932	0.864	0.799	0.932	CLONAL	1	TRUE	1	0.676108416359395	2		344	575	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81399215	81399215	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	213	510	0	ENST00000222390.5:c.73G>A	p.Ala25Thr	p.A25T	ENST00000222390	NM_000601.4	25	Gcc/Acc	1/18	1	2	FACETS	0.827	0.771	0.885	0.827	0.771	0.885	CLONAL	1	TRUE	1	0.676108416359395	2		510	762	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523478	106523478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1302712513	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	107	204	0	ENST00000359195.3:c.2630G>A	p.Gly877Glu	p.G877E	ENST00000359195	NM_002649.2	877	gGa/gAa	8/11	1	2	FACETS	0.956	0.868	1	0.956	0.868	1	CLONAL	1	TRUE	1	0.676108416359395	2		204	331	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397714	116397716	+	frameshift_variant	Frame_Shift_Del	DEL	CGC	CGC	TG	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	218	392	1	ENST00000397752.3:c.1988_1990delinsTG	p.Ser663LeufsTer15	p.S663Lfs*15	ENST00000397752	NM_000245.2	663	tCGCcg/tTGcg	8/21	1	2	FACETS	0.925	0.864	0.988	0.925	0.864	0.988	CLONAL	1	TRUE	1	0.676108416359395	2		393	697	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412025	116412025	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs766865557	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	295	457	0	ENST00000397752.3:c.3010C>T	p.Arg1004Ter	p.R1004*	ENST00000397752	NM_000245.2	1004	Cga/Tga	14/21	1	2	FACETS	0.936	0.883	0.99	0.936	0.883	0.99	CLONAL	1	TRUE	1	0.676108416359395	2		457	932	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859881	151859881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	126	293	0	ENST00000262189.6:c.10781C>T	p.Ser3594Phe	p.S3594F	ENST00000262189	NM_170606.2	3594	tCt/tTt	43/59	1	2	FACETS	0.934	0.854	1	0.934	0.854	1	CLONAL	1	TRUE	1	0.676108416359395	2		293	399	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878310	151878310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	206	477	0	ENST00000262189.6:c.6635C>T	p.Pro2212Leu	p.P2212L	ENST00000262189	NM_170606.2	2212	cCt/cTt	36/59	1	2	FACETS	0.961	0.897	1	0.961	0.897	1	CLONAL	1	TRUE	1	0.676108416359395	2		477	634	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884350	151884350	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	81	170	0	ENST00000262189.6:c.5005C>T	p.Pro1669Ser	p.P1669S	ENST00000262189	NM_170606.2	1669	Cct/Tct	33/59	1	2	FACETS	0.911	0.814	1	0.911	0.814	1	CLONAL	1	TRUE	1	0.676108416359395	2		170	263	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346145	152346145	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	234	452	0	ENST00000359321.1:c.425C>A	p.Ser142Tyr	p.S142Y	ENST00000359321	NM_005431.1	142	tCt/tAt	3/3	1	2	FACETS	0.993	0.931	1	0.993	0.931	1	CLONAL	1	TRUE	1	0.676108416359395	2		452	697	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133386	38133386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	114	299	0	ENST00000317025.8:c.4087C>T	p.Pro1363Ser	p.P1363S	ENST00000317025	NM_023034.1	1363	Ccg/Tcg	24/24	1	2	FACETS	0.961	0.875	1	0.961	0.875	1	CLONAL	1	TRUE	1	0.676108416359395	2		299	351	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271802	38271802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	231	412	0	ENST00000425967.3:c.2147C>T	p.Ser716Phe	p.S716F	ENST00000425967	NM_001174067.1	716	tCt/tTt	17/19	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.676108416359395	2		412	625	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275777	38275777	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	248	571	0	ENST00000425967.3:c.1492G>C	p.Glu498Gln	p.E498Q	ENST00000425967	NM_001174067.1	498	Gaa/Caa	11/19	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.676108416359395	2		571	720	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863054	56863054	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1266824391	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	237	406	0	ENST00000519728.1:c.327del	p.Glu110LysfsTer15	p.E110Kfs*15	ENST00000519728	NM_002350.3	107	acA/ac	5/13	1	2	FACETS	0.916	0.858	0.976	0.916	0.858	0.976	CLONAL	1	TRUE	1	0.676108416359395	2		406	765	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56879420	56879420	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	232	532	0	ENST00000519728.1:c.937G>A	p.Glu313Lys	p.E313K	ENST00000519728	NM_002350.3	313	Gag/Aag	9/13	1	2	FACETS	0.896	0.838	0.955	0.896	0.838	0.955	CLONAL	1	TRUE	1	0.676108416359395	2		532	766	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956766	68956766	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	228	539	1	ENST00000288368.4:c.884T>C	p.Leu295Pro	p.L295P	ENST00000288368	NM_024870.2	295	cTt/cCt	8/40	1	2	FACETS	0.839	0.784	0.895	0.839	0.784	0.895	CLONAL	1	TRUE	1	0.676108416359395	2		540	804	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956771	68956771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774302685	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	219	539	0	ENST00000288368.4:c.889C>T	p.Arg297Cys	p.R297C	ENST00000288368	NM_024870.2	297	Cgt/Tgt	8/40	1	2	FACETS	0.831	0.775	0.888	0.831	0.775	0.888	CLONAL	1	TRUE	1	0.676108416359395	2		539	780	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104721	69104721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750905811	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	182	363	0	ENST00000288368.4:c.4565G>A	p.Gly1522Asp	p.G1522D	ENST00000288368	NM_024870.2	1522	gGc/gAc	37/40	1	2	FACETS	0.979	0.909	1	0.979	0.909	1	CLONAL	1	TRUE	1	0.676108416359395	2		363	550	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970886	70970887	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	142	412	1	ENST00000276594.2:c.1374_1375delinsTT	p.Arg459Trp	p.R459W	ENST00000276594	NM_024504.3	458	caCCgg/caTTgg	6/8	1	2	FACETS	0.849	0.779	0.921	0.849	0.779	0.921	CLONAL	1	TRUE	1	0.676108416359395	2		413	495	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486007	8486007	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	181	381	0	ENST00000356435.5:c.2810T>C	p.Leu937Ser	p.L937S	ENST00000356435		937	tTa/tCa	17/35	0.676108416359395	1	FACETS	0.987	0.926	1	0.987	0.926	1	CLONAL	1	TRUE	0	0.676108416359395	1		381	359	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128246755	128246755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	478	476	0	ENST00000265960.3:c.1174C>T	p.His392Tyr	p.H392Y	ENST00000265960	NM_001006617.1	392	Cac/Tac	9/12	0.676108416359395	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.676108416359395	3		476	931	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391340	139391340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1341934554	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	599	750	0	ENST00000277541.6:c.6851C>T	p.Thr2284Ile	p.T2284I	ENST00000277541	NM_017617.3	2284	aCc/aTc	34/34	0.676108416359395	3	FACETS	0.99	0.956	1	0.99	0.956	1	CLONAL	2	TRUE	1	0.676108416359395	3		750	1197	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397721	139397721	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	260	622	0	ENST00000277541.6:c.5080C>T	p.Gln1694Ter	p.Q1694*	ENST00000277541	NM_017617.3	1694	Cag/Tag	27/34	0.676108416359395	3	FACETS	1	0.971	1	0.529	0.496	0.563	CLONAL	1	TRUE	1	0.676108416359395	3		622	973	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399130	139399131	+	missense_variant	Missense_Mutation	DNP	GA	GA	AC	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	230	594	2	ENST00000277541.6:c.5012_5013delinsGT	p.Val1671Gly	p.V1671G	ENST00000277541	NM_017617.3	1671	gTC/gGT	26/34	0.676108416359395	3	FACETS	0.976	0.91	1	0.488	0.455	0.522	CLONAL	1	TRUE	1	0.676108416359395	3		596	933	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399967	139399967	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	553	609	0	ENST00000277541.6:c.4381A>T	p.Lys1461Ter	p.K1461*	ENST00000277541	NM_017617.3	1461	Aag/Tag	25/34	0.676108416359395	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.676108416359395	3		609	1090	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139565401	139565401	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	476	595	0	ENST00000308874.7:c.572-1G>A		p.X191_splice	ENST00000308874		191			0.676108416359395	3	FACETS	0.98	0.942	1	0.98	0.942	1	CLONAL	2	TRUE	1	0.676108416359395	3		595	961	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148671	20148671	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	232	93	0	ENST00000379607.5:c.392T>C	p.Phe131Ser	p.F131S	ENST00000379607	NM_001412.3	131	tTt/tCt	6/7	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.676108416359395	1		93	332	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938110	76938110	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	266	226	1	ENST00000373344.5:c.2638G>A	p.Glu880Lys	p.E880K	ENST00000373344	NM_000489.3	880	Gaa/Aaa	9/35	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.676108416359395	1		227	414	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117737457	117737457	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	181	297	0	ENST00000368508.3:c.192G>A	p.Trp64Ter	p.W64*	ENST00000368508	NM_002944.2	64	tgG/tgA	3/43	1	2	FACETS	0.864	0.8	0.929	0.864	0.8	0.929	CLONAL	1	TRUE	1	0.676108416359395	2		297	620	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816262	89816262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773260958	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	208	490	0	ENST00000389301.3:c.3115G>A	p.Gly1039Ser	p.G1039S	ENST00000389301	NM_000135.2	1039	Ggc/Agc	32/43	0.676108416359395	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.676108416359395	1		490	388	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816261	89816261	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	209	492	0	ENST00000389301.3:c.3116G>A	p.Gly1039Asp	p.G1039D	ENST00000389301	NM_000135.2	1039	gGc/gAc	32/43	0.676108416359395	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.676108416359395	1		492	388	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123837	46123837	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0030091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	27	273	0	ENST00000334344.6:c.103A>T	p.Lys35Ter	p.K35*	ENST00000334344	NM_152641.2	35	Aaa/Taa	2/21	1	2	FACETS	0.838	0.669	1	0.838	0.669	1	CLONAL	1	TRUE	1	0.24788537942511	2		273	260	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578476	7578476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767328513	NA	P-0030091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	98	668	0	ENST00000269305.4:c.454C>T	p.Pro152Ser	p.P152S	ENST00000269305	NM_001126112.2	152	Ccg/Tcg	5/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.24788537942511	2		668	714	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114748	108114748	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	21	322	0	ENST00000278616.4:c.565A>G	p.Arg189Gly	p.R189G	ENST00000278616	NM_000051.3	189	Aga/Gga	6/63	1	2	FACETS	0.974	0.755	1	0.974	0.755	1	CLONAL	1	TRUE	1	0.24788537942511	2		322	174	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915487	112915487	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	24	439	0	ENST00000351677.2:c.886G>T	p.Asp296Tyr	p.D296Y	ENST00000351677	NM_002834.3	296	Gat/Tat	8/16	1	2	FACETS	0.846	0.666	1	0.846	0.666	1	CLONAL	1	TRUE	1	0.24788537942511	2		439	229	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056347	180056347	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs138606846	NA	P-0030091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	78	660	0	ENST00000261937.6:c.897C>A	p.Asn299Lys	p.N299K	ENST00000261937	NM_182925.4	299	aaC/aaA	7/30	0.24788537942511	1	FACETS	0.931	0.819	1	0.931	0.819	1	CLONAL	1	TRUE	0	0.24788537942511	1		660	592	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	215	454	0				ENST00000310581	NM_198253.2	-/1132			0.315628545065294	5	FACETS	1	0.988	1	0.819	0.766	0.873	CLONAL	2	TRUE	2	0.514192060869822	5		454	603	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047507	49047507	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0030092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	93	90	0	ENST00000267163.4:c.2501C>G	p.Ser834Ter	p.S834*	ENST00000267163	NM_000321.2	834	tCa/tGa	24/27	0.514192060869822	1	FACETS	0.977	0.881	1	0.977	0.881	1	CLONAL	1	TRUE	0	0.514192060869822	1		90	275	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577575	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587782289	NA	P-0030092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	471	571	0	ENST00000269305.4:c.706T>A	p.Tyr236Asn	p.Y236N	ENST00000269305	NM_001126112.2	236	Tac/Aac	7/11	0.302205801671288	3	FACETS	1	0.969	1			1	INDETERMINATE	3	TRUE	NA	0.514192060869822	3		571	765	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953560	32953560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	223	503	0	ENST00000380152.3:c.8861C>T	p.Ser2954Phe	p.S2954F	ENST00000380152		2954	tCt/tTt	22/27	0.514192060869822	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.514192060869822	1		503	545	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41222959	41222959	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	185	551	0	ENST00000357654.3:c.4972A>G	p.Thr1658Ala	p.T1658A	ENST00000357654	NM_007294.3	1658	Acc/Gcc	15/23	0.494150898689444	3	FACETS	1	0.958	1	0.527	0.487	0.569	CLONAL	1	TRUE	1	0.514192060869822	3		551	858	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389381	8389381	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	93	348	0	ENST00000356435.5:c.4237G>A	p.Ala1413Thr	p.A1413T	ENST00000356435		1413	Gcc/Acc	26/35	0.482045434015291	2	FACETS	0.87	0.778	0.966	0.435	0.389	0.483	CLONAL	1	TRUE	0	0.514192060869822	2		348	416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0030103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	194	498	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	1	2	FACETS	0.973	0.907	1	0.973	0.907	1	CLONAL	1	TRUE	1	0.736078052922144	2		498	542	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0030103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	215	501	1	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	1	2	FACETS	0.911	0.852	0.972	0.911	0.852	0.972	CLONAL	1	TRUE	1	0.736078052922144	2		502	641	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781408	3781408	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	221	490	1	ENST00000262367.5:c.4957G>T	p.Asp1653Tyr	p.D1653Y	ENST00000262367	NM_004380.2	1653	Gac/Tac	30/31	NA	2	FACETS	0.993	0.93	1			1	INDETERMINATE	1	TRUE	NA	0.736078052922144	2		491	605	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110086	115110086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1314719430	NA	P-0030103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	323	638	2	ENST00000257566.3:c.1792G>A	p.Gly598Arg	p.G598R	ENST00000257566	NM_016569.3	598	Gga/Aga	8/8	0.736078052922144	3	FACETS	1	0.989	1	0.582	0.55	0.615	CLONAL	1	TRUE	1	0.736078052922144	3		640	1031	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097648	8097648	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	206	219	0	ENST00000346208.3:c.30G>T	p.Trp10Cys	p.W10C	ENST00000346208		10	tgG/tgT	2/6	0.610781001186883	4	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	2	0.736078052922144	4		219	478	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427398	49427401	+	frameshift_variant	Frame_Shift_Del	DEL	CCTG	CCTG	-	novel	NA	P-0030103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	736	583	0	ENST00000301067.7:c.11087_11090del	p.Ser3696TrpfsTer52	p.S3696Wfs*52	ENST00000301067	NM_003482.3	3696	tCAGGg/tg	39/54	0.736078052922144	5	FACETS	1	0.98	1			1	CLONAL	3	TRUE	NA	0.736078052922144	5		583	1383	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687524	29687524	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1453592264	NA	P-0030103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	134	321	0	ENST00000356175.3:c.8117A>G	p.Tyr2706Cys	p.Y2706C	ENST00000356175	NM_000267.3	2706	tAt/tGt	56/57	0.736078052922144	3	FACETS	0.924	0.844	1	0.462	0.422	0.504	CLONAL	1	TRUE	1	0.736078052922144	3		321	539	SUCCESS
REL	5966	MSKCC	GRCh37	2	61121548	61121548	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	117	293	0	ENST00000295025.8:c.170G>T	p.Gly57Val	p.G57V	ENST00000295025	NM_002908.2	57	gGa/gTa	3/11	0.736078052922144	4	FACETS	0.923	0.835	1	0.308	0.278	0.339	CLONAL	1	TRUE	1	0.736078052922144	4		293	598	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231710	66231710	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	216	363	0	ENST00000273854.3:c.1990del	p.His664ThrfsTer7	p.H664Tfs*7	ENST00000273854	NM_004439.5	664	Cac/ac	11/18	0.667759969922675	3	FACETS	0.936	0.882	0.989	0.936	0.882	0.989	CLONAL	2	TRUE	1	0.736078052922144	3		363	429	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674212	86674212	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0030103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	188	219	0	ENST00000274376.6:c.2345-1G>T		p.X782_splice	ENST00000274376	NM_002890.2	782			0.730831101172645	2	FACETS	0.975	0.929	1	0.975	0.929	1	CLONAL	2	TRUE	0	0.736078052922144	2		219	262	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468116	50468116	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	110	385	0	ENST00000331340.3:c.1351G>A	p.Val451Met	p.V451M	ENST00000331340	NM_006060.4	451	Gtg/Atg	8/8	0.610781001186883	4	FACETS	0.86	0.775	0.951	0.43	0.387	0.476	CLONAL	1	TRUE	2	0.736078052922144	4		385	603	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900297	101900297	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	268	293	2	ENST00000374994.4:c.731G>T	p.Arg244Leu	p.R244L	ENST00000374994	NM_004612.2	244	cGt/cTt	4/9	0.729817500925842	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.736078052922144	2		295	359	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395093	139395093	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	691	503	3	ENST00000277541.6:c.5845G>T	p.Glu1949Ter	p.E1949*	ENST00000277541	NM_017617.3	1949	Gag/Tag	31/34	0.736078052922144	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	0	0.736078052922144	3		506	848	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395250	139395250	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	732	572	4	ENST00000277541.6:c.5688G>C	p.Glu1896Asp	p.E1896D	ENST00000277541	NM_017617.3	1896	gaG/gaC	31/34	0.736078052922144	3	FACETS	0.993	0.973	1	0.993	0.973	1	CLONAL	3	TRUE	0	0.736078052922144	3		576	913	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045189	47045190	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	TT	novel	NA	P-0030103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	198	473	1	ENST00000377604.3:c.2430_2430+1delinsTT		p.X810_splice	ENST00000377604	NM_001204468.1	810		21/24	NA	2	FACETS	0.947	0.883	1			1	INDETERMINATE	1	TRUE	NA	0.736078052922144	2		474	568	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0030104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	102	576	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.894	0.799	0.995	0.894	0.799	0.995	CLONAL	1	TRUE	1	0.287750444165903	2		576	793	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0030104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	78	588	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.701	0.616	0.794	0.701	0.616	0.794	SUBCLONAL	1	TRUE	1	0.287750444165903	2		588	773	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0030104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	77	668	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	1	2	FACETS	0.786	0.69	0.889	0.786	0.69	0.889	SUBCLONAL	1	TRUE	1	0.287750444165903	2		668	681	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	80	454	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.805673768707672	2		454	193	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0030105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	11	622	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.121	0.083	0.168	0.121	0.083	0.168	SUBCLONAL	1	TRUE	1	0.805673768707672	2		622	226	SUCCESS
ATR	545	MSKCC	GRCh37	3	142204114	142204114	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755650081	NA	P-0030105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	73	474	0	ENST00000350721.4:c.6089C>T	p.Ala2030Val	p.A2030V	ENST00000350721	NM_001184.3	2030	gCg/gTg	36/47	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.805673768707672	2		474	173	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0030105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	126	461	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	0.805673768707672	2		461	287	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171455	123171455	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	56	198	0	ENST00000218089.9:c.367C>T	p.Gln123Ter	p.Q123*	ENST00000218089	NM_001042749.1	123	Cag/Tag	6/35	0.413473947365187	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.805673768707672	2		198	94	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562409	21562409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs538663790	NA	P-0030105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	164	510	1	ENST00000382592.4:c.1510G>A	p.Val504Met	p.V504M	ENST00000382592	NM_014572.2	504	Gtg/Atg	4/8	0.224408753076234	4	FACETS	1	0.972	1	1	0.972	1	INDETERMINATE	2	TRUE	2	0.805673768707672	4		511	341	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431006	49431006	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	65	523	0	ENST00000301067.7:c.10133C>A	p.Ser3378Ter	p.S3378*	ENST00000301067	NM_003482.3	3378	tCa/tAa	34/54	0.224408753076234	4	FACETS	1	0.901	1	0.517	0.452	0.585	INDETERMINATE	1	TRUE	2	0.805673768707672	4		523	282	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431102	49431102	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	72	620	0	ENST00000301067.7:c.10037C>G	p.Ser3346Cys	p.S3346C	ENST00000301067	NM_003482.3	3346	tCc/tGc	34/54	0.224408753076234	4	FACETS	1	0.915	1	0.524	0.462	0.59	INDETERMINATE	1	TRUE	2	0.805673768707672	4		620	308	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431130	49431130	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	88	594	0	ENST00000301067.7:c.10009C>G	p.His3337Asp	p.H3337D	ENST00000301067	NM_003482.3	3337	Cat/Gat	34/54	0.224408753076234	4	FACETS	1	0.942	1	0.542	0.484	0.603	INDETERMINATE	1	TRUE	2	0.805673768707672	4		594	364	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433896	49433896	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	100	891	1	ENST00000301067.7:c.7657C>T	p.Gln2553Ter	p.Q2553*	ENST00000301067	NM_003482.3	2553	Cag/Tag	31/54	0.224408753076234	4	FACETS	1	0.973	1	0.621	0.56	0.685	INDETERMINATE	1	TRUE	2	0.805673768707672	4		892	361	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434201	49434201	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	119	987	1	ENST00000301067.7:c.7352C>T	p.Ser2451Phe	p.S2451F	ENST00000301067	NM_003482.3	2451	tCt/tTt	31/54	0.224408753076234	4	FACETS	0.982	0.89	1	0.491	0.445	0.54	INDETERMINATE	1	TRUE	2	0.805673768707672	4		988	543	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434283	49434283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	145	981	0	ENST00000301067.7:c.7270C>T	p.Pro2424Ser	p.P2424S	ENST00000301067	NM_003482.3	2424	Cca/Tca	31/54	0.224408753076234	4	FACETS	1	0.962	1	0.544	0.498	0.592	INDETERMINATE	1	TRUE	2	0.805673768707672	4		981	597	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434289	49434289	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	147	977	0	ENST00000301067.7:c.7264C>T	p.Gln2422Ter	p.Q2422*	ENST00000301067	NM_003482.3	2422	Cag/Tag	31/54	0.224408753076234	4	FACETS	1	0.964	1	0.546	0.501	0.594	INDETERMINATE	1	TRUE	2	0.805673768707672	4		977	603	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434618	49434618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs949690934	NA	P-0030105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	78	760	0	ENST00000301067.7:c.6935C>T	p.Ser2312Leu	p.S2312L	ENST00000301067	NM_003482.3	2312	tCa/tTa	31/54	0.224408753076234	4	FACETS	1	0.976	1	0.696	0.621	0.776	INDETERMINATE	1	TRUE	2	0.805673768707672	4		760	251	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434627	49434627	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762743834	NA	P-0030105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	74	766	1	ENST00000301067.7:c.6926C>T	p.Ser2309Leu	p.S2309L	ENST00000301067	NM_003482.3	2309	tCa/tTa	31/54	0.224408753076234	4	FACETS	1	0.971	1	0.658	0.584	0.736	INDETERMINATE	1	TRUE	2	0.805673768707672	4		767	252	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346752	225346752	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	19	399	0	ENST00000264414.4:c.1886G>C	p.Arg629Thr	p.R629T	ENST00000264414	NM_003590.4	629	aGa/aCa	14/16	0.128196926180575	4	FACETS	0.432	0.329	0.552	0.216	0.164	0.276	INDETERMINATE	1	TRUE	2	0.805673768707672	4		399	197	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652144	36652145	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGGA	novel	NA	P-0030105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	164	599	0	ENST00000244741.5:c.269_272dup	p.Gly92ArgfsTer38	p.G92Rfs*38	ENST00000244741	NM_000389.4	89	ttg/ttGGGAg	2/3	0.224408753076234	4	FACETS	0.888	0.824	0.952	0.888	0.824	0.952	INDETERMINATE	2	TRUE	2	0.805673768707672	4		599	414	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781225	135781225	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	27	558	0	ENST00000298552.3:c.1740C>G	p.Ile580Met	p.I580M	ENST00000298552	NM_001162426.1	580	atC/atG	15/23	0.805673768707672	1	FACETS	0.28	0.225	0.34	0.28	0.225	0.34	SUBCLONAL	1	TRUE	0	0.805673768707672	1		558	143	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786421	135786421	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0030105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	12	600	0	ENST00000298552.3:c.1109C>G	p.Ser370Ter	p.S370*	ENST00000298552	NM_001162426.1	370	tCa/tGa	11/23	0.805673768707672	1	FACETS	0.187	0.133	0.253	0.187	0.133	0.253	SUBCLONAL	1	TRUE	0	0.805673768707672	1		600	95	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0030109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	36	237	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.391002741082645	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.391002741082645	1		237	121	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458330	12458330	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	166	558	0	ENST00000287820.6:c.947G>C	p.Arg316Pro	p.R316P	ENST00000287820	NM_015869.4	316	cGc/cCc	6/7	0.234440870497938	3	FACETS	1	0.987	1	0.695	0.64	0.753	INDETERMINATE	1	TRUE	1	0.391002741082645	3		558	730	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749902	162749902	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	87	332	0	ENST00000367921.3:c.2434A>G	p.Thr812Ala	p.T812A	ENST00000367921	NM_006182.2	812	Act/Gct	18/18	0.337174169353898	15	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.337174169353898	15		332	1114	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0030123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	28	367	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.164844207810392	2	FACETS	1	0.92	1	0.618	0.508	0.736	INDETERMINATE	1	TRUE	0	0.514522036919544	2		367	88	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879580	37879580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	57	498	1	ENST00000269571.5:c.1955C>T	p.Thr652Met	p.T652M	ENST00000269571		652	aCg/aTg	17/27	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.514522036919544	2		499	186	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231773	36231773	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1569061762	NA	P-0030123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	10	558	0	ENST00000300305.3:c.611G>A	p.Arg204Gln	p.R204Q	ENST00000300305		204	cGa/cAa	5/8	0.142162663695431	0	FACETS	0.072	0.048	0.102			1	INDETERMINATE	1	TRUE	0	0.514522036919544	0		558	262	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954586	17954586	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs774202259	NA	P-0030123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	12	631	0	ENST00000458235.1:c.308G>A	p.Arg103His	p.R103H	ENST00000458235	NM_000215.3	103	cGc/cAc	3/24	0.456099956012195	3	FACETS	0.277	0.194	0.378	0.138	0.097	0.189	SUBCLONAL	1	TRUE	1	0.514522036919544	3		631	212	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138602	11138602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373590049	NA	P-0030123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	10	499	0	ENST00000358026.2:c.3358G>A	p.Gly1120Ser	p.G1120S	ENST00000358026	NM_001128849.1	1120	Ggc/Agc	24/36	0.456099956012195	3	FACETS	0.317	0.215	0.445	0.159	0.107	0.223	SUBCLONAL	1	TRUE	1	0.514522036919544	3		499	154	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0030125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	30	429	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.98	0.794	1	0.98	0.794	1	CLONAL	1	TRUE	1	0.24	2		429	255	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0030127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	12	311	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.233	0.163	0.32	0.233	0.163	0.32	SUBCLONAL	1	TRUE	1	0.28	2		312	368	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226579987	226579987	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	54	492	0	ENST00000366794.5:c.315G>T	p.Lys105Asn	p.K105N	ENST00000366794	NM_001618.3	105	aaG/aaT	3/23	1	2	FACETS	0.65	0.555	0.755	0.65	0.555	0.755	SUBCLONAL	1	TRUE	1	0.28	2		492	593	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342056	70342056	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	28	174	0	ENST00000374080.3:c.1108C>G	p.Leu370Val	p.L370V	ENST00000374080		370	Ctc/Gtc	8/45	1	1	FACETS	0.664	0.533	0.813	0.664	0.533	0.813	SUBCLONAL	1	TRUE	0	0.28	1		174	259	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0030128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	512	498	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.776930577269068	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.776930577269068	2		498	658	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988585	41988585	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	49	469	0	ENST00000219905.7:c.1377C>G	p.Phe459Leu	p.F459L	ENST00000219905	NM_001164273.1	459	ttC/ttG	3/24	0.229165881339426	3	FACETS	0.267	0.225	0.312	0.133	0.112	0.156	INDETERMINATE	1	TRUE	1	0.776930577269068	3		469	657	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819730	170819731	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0030128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	54	166	0	ENST00000296930.5:c.371_372del	p.Glu124ValfsTer4	p.E124Vfs*4	ENST00000296930	NM_002520.6	123	gcAGag/gcag	5/11	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.776930577269068	2		166	125	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0030129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	230	367	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.663757814838903	2	FACETS	0.949	0.904	0.994	0.949	0.904	0.994	CLONAL	2	TRUE	0	0.663757814838903	2		367	365	SUCCESS
APC	324	MSKCC	GRCh37	5	112174112	112174112	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	114	336	0	ENST00000257430.4:c.2821G>T	p.Glu941Ter	p.E941*	ENST00000257430	NM_000038.5	941	Gaa/Taa	16/16	0.663757814838903	3	FACETS	0.99	0.897	1	0.495	0.448	0.544	CLONAL	1	TRUE	1	0.663757814838903	3		336	462	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	174	318	0	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	0.663757814838903	3	FACETS	0.957	0.894	1	0.957	0.894	1	CLONAL	2	TRUE	1	0.663757814838903	3		318	365	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0030129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	106	428	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.663757814838903	3	FACETS	0.861	0.776	0.951	0.431	0.388	0.476	CLONAL	1	TRUE	1	0.663757814838903	3		428	494	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636820	8636820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369741244	NA	P-0030129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	248	341	0	ENST00000356435.5:c.89C>T	p.Pro30Leu	p.P30L	ENST00000356435		30	cCc/cTc	2/35	0.663757814838903	3	FACETS	0.876	0.827	0.926	0.876	0.827	0.926	CLONAL	2	TRUE	1	0.663757814838903	3		341	568	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101118	41101118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751886972	NA	P-0030129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	541	450	0	ENST00000373198.4:c.1238C>T	p.Ala413Val	p.A413V	ENST00000373198	NM_133170.3	413	gCg/gTg	8/32	0.663757814838903	6	FACETS	1	0.964	1	0.752	0.723	0.782	CLONAL	3	TRUE	2	0.663757814838903	6		450	1261	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577115	7577128	+	frameshift_variant	Frame_Shift_Del	DEL	AAACACGCACCTCA	AAACACGCACCTCA	-	novel	NA	P-0030129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	332	654	0	ENST00000269305.4:c.810_823del	p.Phe270LeufsTer31	p.F270Lfs*31	ENST00000269305	NM_001126112.2	270	ttTGAGGTGCGTGTTTgt/ttgt	8/11	0.663757814838903	2	FACETS	0.874	0.837	0.911	0.874	0.837	0.911	CLONAL	2	TRUE	0	0.663757814838903	2		654	572	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556208	29556208	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	58	219	0	ENST00000356175.3:c.2575G>T	p.Gly859Cys	p.G859C	ENST00000356175	NM_000267.3	859	Ggc/Tgc	21/57	0.663757814838903	2	FACETS	0.753	0.655	0.858	0.377	0.327	0.429	SUBCLONAL	1	TRUE	0	0.663757814838903	2		219	232	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41818322	41818322	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	22	28	0	ENST00000373198.4:c.52C>T	p.Pro18Ser	p.P18S	ENST00000373198	NM_133170.3	18	Ccg/Tcg	1/32	0.663757814838903	6	FACETS	0.964	0.768	1	0.482	0.384	0.59	CLONAL	2	TRUE	2	0.663757814838903	6		28	80	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115874	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752977342	NA	P-0030133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	112	480	0	ENST00000346208.3:c.1220C>T	p.Ser407Leu	p.S407L	ENST00000346208		407	tCg/tTg	6/6	1	2	FACETS	0.996	0.897	1	0.996	0.897	1	CLONAL	1	TRUE	1	0.348746982925395	2		480	645	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0030133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	132	295	0				ENST00000310581	NM_198253.2	-/1132			0.104218728829018	3	FACETS	1	0.95	1			1	INDETERMINATE	2	TRUE	NA	0.348746982925395	3		295	422	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162742035	162742035	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	64	294	0	ENST00000367921.3:c.1726G>A	p.Glu576Lys	p.E576K	ENST00000367921	NM_006182.2	576	Gag/Aag	13/18	1	2	FACETS	0.751	0.651	0.858	0.751	0.651	0.858	SUBCLONAL	1	TRUE	1	0.348746982925395	2		294	489	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482363	56482363	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	109	398	0	ENST00000267101.3:c.911C>T	p.Ala304Val	p.A304V	ENST00000267101	NM_001982.3	304	gCc/gTc	8/28	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.348746982925395	2		398	608	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218952	133218952	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	119	642	0	ENST00000320574.5:c.4984G>C	p.Glu1662Gln	p.E1662Q	ENST00000320574	NM_006231.2	1662	Gag/Cag	38/49	1	2	FACETS	0.823	0.743	0.908	0.823	0.743	0.908	CLONAL	1	TRUE	1	0.348746982925395	2		642	829	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332930	152332930	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0030133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	43	228	0	ENST00000206249.3:c.1235+1G>T		p.X412_splice	ENST00000206249	NM_000125.3	412			1	2	FACETS	0.865	0.728	1	0.865	0.728	1	CLONAL	1	TRUE	1	0.348746982925395	2		228	285	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929354	44929354	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	131	329	0	ENST00000377967.4:c.2454del	p.Pro819HisfsTer48	p.P819Hfs*48	ENST00000377967	NM_021140.2	818	tcA/tc	17/29	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.348746982925395	1		329	425	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733356	85733356	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	48	530	1	ENST00000370580.1:c.656G>T	p.Ser219Ile	p.S219I	ENST00000370580	NM_003921.4	219	aGt/aTt	3/3	1	2	FACETS	0.272	0.23	0.319	0.272	0.23	0.319	SUBCLONAL	1	TRUE	1	0.732080748139559	2		531	482	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514934	103514934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757867311	NA	P-0030134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	119	320	0	ENST00000355739.4:c.1435G>A	p.Val479Ile	p.V479I	ENST00000355739	NM_000123.3	479	Gtt/Att	8/15	0.233663937726406	4	FACETS	0.86	0.777	0.946	0.43	0.388	0.473	INDETERMINATE	1	TRUE	2	0.732080748139559	4		320	655	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0030134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	463	573	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.686044121884241	2	FACETS	0.914	0.884	0.943	0.914	0.884	0.943	CLONAL	2	TRUE	0	0.732080748139559	2		573	692	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220596	1220602	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCGGA	CGGCGGA	-	novel	NA	P-0030134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	429	642	0	ENST00000326873.7:c.616_622del	p.Ala206ThrfsTer79	p.A206Tfs*79	ENST00000326873	NM_000455.4	205	gCGGCGGAc/gc	5/10	0.732080748139559	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.732080748139559	1		642	675	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457743	149457743	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	219	602	0	ENST00000286301.3:c.661C>T	p.Gln221Ter	p.Q221*	ENST00000286301	NM_005211.3	221	Cag/Tag	5/22	0.41147462151664	1	FACETS	0.44	0.409	0.471	0.44	0.409	0.471	INDETERMINATE	1	TRUE	0	0.732080748139559	1		602	863	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021810	69021810	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	134	562	0	ENST00000288368.4:c.3098T>G	p.Leu1033Arg	p.L1033R	ENST00000288368	NM_024870.2	1033	cTt/cGt	25/40	1	2	FACETS	0.575	0.523	0.628	0.575	0.523	0.628	SUBCLONAL	1	TRUE	1	0.732080748139559	2		562	637	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0030135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	239	350	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.273532828607765	6	FACETS	1	0.984	1	0.835	0.787	0.882	INDETERMINATE	3	TRUE	2	0.585211855270711	6		350	531	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	104	454	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.585211855270711	2		454	294	SUCCESS
CBL	867	MSKCC	GRCh37	11	119167635	119167635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	111	427	0	ENST00000264033.4:c.2044C>T	p.Pro682Ser	p.P682S	ENST00000264033	NM_005188.3	682	Cct/Tct	13/16	0.563096157165003	1	FACETS	0.958	0.876	1	0.958	0.876	1	CLONAL	1	TRUE	0	0.585211855270711	1		427	280	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350062	81350062	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs759145490	NA	P-0030135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	83	337	0	ENST00000222390.5:c.1270C>T	p.Arg424Cys	p.R424C	ENST00000222390	NM_000601.4	424	Cgt/Tgt	10/18	0.109504185797754	4	FACETS	0.762	0.68	0.848	0.762	0.68	0.848	INDETERMINATE	2	TRUE	2	0.585211855270711	4		337	295	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953820	55953820	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	119	528	0	ENST00000263923.4:c.3616G>A	p.Glu1206Lys	p.E1206K	ENST00000263923	NM_002253.2	1206	Gaa/Aaa	27/30	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.585211855270711	2		528	349	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351685	89351685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	231	729	0	ENST00000301030.4:c.1265C>T	p.Thr422Ile	p.T422I	ENST00000301030	NM_001256183.1	422	aCa/aTa	9/13	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.585211855270711	2		729	671	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435925	110435925	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	123	708	0	ENST00000375856.3:c.2476A>T	p.Met826Leu	p.M826L	ENST00000375856	NM_003749.2	826	Atg/Ttg	1/2	0.244147151569976	3	FACETS	1	0.958	1	0.546	0.496	0.597	INDETERMINATE	1	TRUE	1	0.585211855270711	3		708	498	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993746	72993746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	27	487	0	ENST00000268489.5:c.299C>T	p.Pro100Leu	p.P100L	ENST00000268489	NM_006885.3	100	cCc/cTc	2/10	1	2	FACETS	0.322	0.256	0.396	0.322	0.256	0.396	SUBCLONAL	1	TRUE	1	0.585211855270711	2		487	287	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031182	11031182	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	190	760	0	ENST00000327064.4:c.1267C>T	p.Gln423Ter	p.Q423*	ENST00000327064	NM_199141.1	423	Cag/Tag	11/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.585211855270711	2		760	562	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555057	106555057	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs940196192	NA	P-0030135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	138	532	0	ENST00000369096.4:c.2174G>T	p.Arg725Leu	p.R725L	ENST00000369096	NM_001198.3	725	cGa/cTa	7/7	0.244147151569976	3	FACETS	1	0.982	1	0.636	0.583	0.692	INDETERMINATE	1	TRUE	1	0.585211855270711	3		532	479	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937250	76937250	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	31	510	0	ENST00000373344.5:c.3498A>T	p.Lys1166Asn	p.K1166N	ENST00000373344	NM_000489.3	1166	aaA/aaT	9/35	0.25441688283195	2	FACETS	0.329	0.266	0.4	0.165	0.133	0.2	INDETERMINATE	1	TRUE	0	0.585211855270711	2		510	322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0030138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	395	545	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.787116908456454	3	FACETS	1	0.988	1	1	0.997	1	CLONAL	3	TRUE	1	0.787116908456454	3		545	458	SUCCESS
APC	324	MSKCC	GRCh37	5	112173656	112173656	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123117	NA	P-0030138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	220	397	1	ENST00000257430.4:c.2365C>T	p.Gln789Ter	p.Q789*	ENST00000257430	NM_000038.5	789	Cag/Tag	16/16	0.787116908456454	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.787116908456454	2		398	274	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974314	18974314	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	328	635	0	ENST00000262803.5:c.2668A>G	p.Asn890Asp	p.N890D	ENST00000262803	NM_002911.3	890	Aac/Gac	19/24	0.787116908456454	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.787116908456454	3		635	567	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014047	70014047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369552358	NA	P-0030138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	136	473	1	ENST00000394351.3:c.908C>T	p.Thr303Met	p.T303M	ENST00000394351	NM_000248.3	303	aCg/aTg	9/9	0.780766896134619	2	FACETS	1	0.962	1	0.535	0.494	0.577	CLONAL	1	TRUE	0	0.787116908456454	2		474	323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0030140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	256	654	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	NA	2	FACETS	0.798	0.757	0.839			1	INDETERMINATE	2	TRUE	NA	0.656020814055465	2		654	489	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0030140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	138	375	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.656020814055465	3	FACETS	0.87	0.804	0.937	0.87	0.804	0.937	CLONAL	2	TRUE	1	0.656020814055465	3		375	321	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878115	48878117	+	inframe_deletion	In_Frame_Del	DEL	CCG	CCG	-	rs587778823	NA	P-0030140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	14	115	0	ENST00000267163.4:c.78_80del	p.Pro29del	p.P29del	ENST00000267163	NM_000321.2	23	CCG/-	1/27	1	2	FACETS	0.171	0.123	0.229	0.171	0.123	0.229	SUBCLONAL	1	TRUE	1	0.656020814055465	2		115	249	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70360793	70360793	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0030140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	43	193	0	ENST00000373644.4:c.1968+2T>C		p.X656_splice	ENST00000373644	NM_030625.2	656			1	2	FACETS	0.874	0.745	1	0.874	0.745	1	CLONAL	1	TRUE	1	0.656020814055465	2		193	150	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652129	36652129	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	213	585	0	ENST00000244741.5:c.251G>C	p.Arg84Pro	p.R84P	ENST00000244741	NM_000389.4	84	cGa/cCa	2/3	0.225051546506623	3	FACETS	1	0.99	1	0.659	0.616	0.704	INDETERMINATE	1	TRUE	1	0.656020814055465	3		585	654	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0030141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	66	464	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	0.695590089617339	1	FACETS	0.628	0.555	0.704	0.628	0.555	0.704	SUBCLONAL	1	TRUE	0	0.695590089617339	1		464	197	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913499	NA	P-0030141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	81	240	0	ENST00000345146.2:c.394C>A	p.Arg132Ser	p.R132S	ENST00000345146	NM_005896.2	132	Cgt/Agt	4/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.695590089617339	2		240	206	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577128	7577128	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519987	NA	P-0030141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	534	638	0	ENST00000269305.4:c.810T>G	p.Phe270Leu	p.F270L	ENST00000269305	NM_001126112.2	270	ttT/ttG	8/11	0.695590089617339	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.695590089617339	2		638	689	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938271	76938272	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0030141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	124	262	0	ENST00000373344.5:c.2476_2477del	p.Lys826GlufsTer4	p.K826Efs*4	ENST00000373344	NM_000489.3	826	AAg/g	9/35	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.695590089617339	1		262	201	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0030142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	263	367	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.3	3	FACETS	1	0.968	1			1	CLONAL	4	TRUE	NA	0.19	3		367	729	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520017	NA	P-0030142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	51	757	0	ENST00000326873.7:c.647C>T	p.Ser216Phe	p.S216F	ENST00000326873	NM_000455.4	216	tCc/tTc	5/10	1	2	FACETS	0.694	0.588	0.81	0.694	0.588	0.81	SUBCLONAL	1	TRUE	1	0.19	2		757	774	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602443	10602443	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	50	692	0	ENST00000171111.5:c.1135G>T	p.Gly379Cys	p.G379C	ENST00000171111	NM_203500.1	379	Ggc/Tgc	3/6	1	2	FACETS	0.765	0.648	0.894	0.765	0.648	0.894	SUBCLONAL	1	TRUE	1	0.19	2		692	688	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115844	8115844	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	87	576	1	ENST00000346208.3:c.1190C>G	p.Ser397Cys	p.S397C	ENST00000346208		397	tCc/tGc	6/6	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.19	2		577	753	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333017	70333017	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	57	735	1	ENST00000373644.4:c.922G>T	p.Asp308Tyr	p.D308Y	ENST00000373644	NM_030625.2	308	Gac/Tac	2/12	1	2	FACETS	0.726	0.621	0.84	0.726	0.621	0.84	SUBCLONAL	1	TRUE	1	0.19	2		736	827	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202759	108202759	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	37	370	0	ENST00000278616.4:c.7783del	p.Asp2595MetfsTer11	p.D2595Mfs*11	ENST00000278616	NM_000051.3	2595	Gat/at	52/63	1	2	FACETS	0.787	0.648	0.942	0.787	0.648	0.942	CLONAL	1	TRUE	1	0.19	2		370	495	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719128	190719128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	33	283	0	ENST00000441310.2:c.1130G>A	p.Gly377Glu	p.G377E	ENST00000441310	NM_000534.4	377	gGa/gAa	9/13	1	2	FACETS	1	0.824	1	1	0.824	1	CLONAL	1	TRUE	1	0.19	2		283	344	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713325	40713325	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	31	547	0	ENST00000373198.4:c.4190G>C	p.Cys1397Ser	p.C1397S	ENST00000373198	NM_133170.3	1397	tGc/tCc	30/32	1	2	FACETS	0.589	0.475	0.718	0.589	0.475	0.718	SUBCLONAL	1	TRUE	1	0.19	2		547	554	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125413	47125413	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	27	385	0	ENST00000409792.3:c.5857G>T	p.Glu1953Ter	p.E1953*	ENST00000409792	NM_014159.6	1953	Gaa/Taa	12/21	1	2	FACETS	0.567	0.45	0.702	0.567	0.45	0.702	SUBCLONAL	1	TRUE	1	0.19	2		385	501	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873057	134873057	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	36	594	0	ENST00000398015.3:c.1361G>A	p.Trp454Ter	p.W454*	ENST00000398015	NM_004441.4	454	tGg/tAg	6/16	1	2	FACETS	0.56	0.459	0.674	0.56	0.459	0.674	SUBCLONAL	1	TRUE	1	0.19	2		594	677	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435833	149435833	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	63	678	0	ENST00000286301.3:c.2391C>A	p.Phe797Leu	p.F797L	ENST00000286301	NM_005211.3	797	ttC/ttA	18/22	1	2	FACETS	0.871	0.752	1	0.871	0.752	1	CLONAL	1	TRUE	1	0.19	2		678	761	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979286	93979286	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	40	404	0	ENST00000369303.4:c.1542G>T	p.Gln514His	p.Q514H	ENST00000369303	NM_004440.3	514	caG/caT	7/17	1	2	FACETS	0.977	0.812	1	0.977	0.812	1	CLONAL	1	TRUE	1	0.19	2		404	431	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974759	21974759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064794292	NA	P-0030142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	22	287	0	ENST00000304494.5:c.68G>A	p.Gly23Asp	p.G23D	ENST00000304494	NM_000077.4	23	gGt/gAt	1/3	1	2	FACETS	0.785	0.609	0.989	0.785	0.609	0.989	CLONAL	1	TRUE	1	0.19	2		287	295	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570229	87570229	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	18	336	0	ENST00000277120.3:c.1969G>C	p.Glu657Gln	p.E657Q	ENST00000277120		657	Gag/Cag	17/19	1	2	FACETS	0.543	0.408	0.703	0.543	0.408	0.703	SUBCLONAL	1	TRUE	1	0.19	2		336	349	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209530	98209530	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	78	572	0	ENST00000331920.6:c.4008G>T	p.Arg1336Ser	p.R1336S	ENST00000331920	NM_000264.3	1336	agG/agT	23/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.19	2		572	598	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410597	63410598	+	missense_variant	Missense_Mutation	DNP	CG	CG	AA	novel	NA	P-0030142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	53	343	2	ENST00000330258.3:c.2569_2570delinsTT	p.Arg857Leu	p.R857L	ENST00000330258	NM_152424.3	857	CGa/TTa	2/2	1	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.19	1		345	388	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526719	31526719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	115	692	1	ENST00000344624.3:c.321G>A	p.Met107Ile	p.M107I	ENST00000344624		107	atG/atA	2/33	0.47153155461392	3	FACETS	0.98	0.885	1	0.49	0.442	0.54	CLONAL	1	TRUE	1	0.47153155461392	3		693	615	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138591	11138591	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	102	525	3	ENST00000358026.2:c.3347T>C	p.Phe1116Ser	p.F1116S	ENST00000358026	NM_001128849.1	1116	tTt/tCt	24/36	0.266682808321766	1	FACETS	1	0.947	1	1	0.947	1	INDETERMINATE	1	TRUE	0	0.47153155461392	1		528	310	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515096	103515096	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	36	303	4	ENST00000355739.4:c.1597del	p.Val533CysfsTer57	p.V533Cfs*57	ENST00000355739	NM_000123.3	533	Gtg/tg	8/15	1	2	FACETS	0.863	0.718	1	0.863	0.718	1	CLONAL	1	TRUE	1	0.47153155461392	2		307	177	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061250	38061250	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	548	548	7	ENST00000250448.2:c.739C>A	p.His247Asn	p.H247N	ENST00000250448	NM_004496.3	247	Cac/Aac	2/2	0.47153155461392	9	FACETS	1	0.975	1			1	CLONAL	7	TRUE	NA	0.47153155461392	9		555	874	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7163209	7163209	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1469593224	NA	P-0030143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	39	358	0	ENST00000302850.5:c.1863C>A	p.Asn621Lys	p.N621K	ENST00000302850	NM_000208.2	621	aaC/aaA	9/22	0.266682808321766	1	FACETS	0.583	0.487	0.687	0.583	0.487	0.687	INDETERMINATE	1	TRUE	0	0.47153155461392	1		358	217	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0030144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	82	532	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.816	0.723	0.914	0.816	0.723	0.914	CLONAL	1	TRUE	1	0.482076039265507	2		533	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0030144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	82	478	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.452779671291162	1	FACETS	0.766	0.681	0.855	0.766	0.681	0.855	SUBCLONAL	1	TRUE	0	0.482076039265507	1		479	337	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0030144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	91	588	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.699	0.622	0.781	0.699	0.622	0.781	SUBCLONAL	1	TRUE	1	0.482076039265507	2		588	540	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057736	27057736	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	112	819	3	ENST00000324856.7:c.1444C>T	p.Gln482Ter	p.Q482*	ENST00000324856	NM_006015.4	482	Cag/Tag	3/20	0.493376844170289	0	FACETS	0.491	0.444	0.541			1	SUBCLONAL	1	TRUE	0	0.482076039265507	0		822	490	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120941	115120941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	70	531	0	ENST00000257566.3:c.65C>T	p.Pro22Leu	p.P22L	ENST00000257566	NM_016569.3	22	cCt/cTt	1/8	1	2	FACETS	0.825	0.724	0.933	0.825	0.724	0.933	CLONAL	1	TRUE	1	0.482076039265507	2		531	352	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482870	67482870	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	82	326	0	ENST00000327367.4:c.1274C>A	p.Ser425Tyr	p.S425Y	ENST00000327367	NM_005902.3	425	tCt/tAt	9/9	0.330632531161709	2	FACETS	1	0.895	1	0.503	0.447	0.562	CLONAL	1	TRUE	0	0.482076039265507	2		326	338	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375496	40375496	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121908502	NA	P-0030144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	96	577	0	ENST00000293328.3:c.454C>T	p.Arg152Ter	p.R152*	ENST00000293328	NM_012448.3	152	Cga/Tga	5/19	1	2	FACETS	0.844	0.755	0.937	0.844	0.755	0.937	CLONAL	1	TRUE	1	0.482076039265507	2		577	472	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604743	48604744	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	20	429	0	ENST00000342988.3:c.1567dup	p.Cys523LeufsTer4	p.C523Lfs*4	ENST00000342988	NM_005359.5	522	cct/ccTt	12/12	0.485680072767837	1	FACETS	0.204	0.155	0.26	0.204	0.155	0.26	SUBCLONAL	1	TRUE	0	0.482076039265507	1		429	309	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023534	27023535	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCTA	novel	NA	P-0030145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	252	447	0	ENST00000324856.7:c.642_645dup	p.Tyr216LeufsTer185	p.Y216Lfs*185	ENST00000324856	NM_006015.4	214	tcc/tCCTAcc	1/20	1	2	FACETS	0.983	0.926	1	0.983	0.926	1	CLONAL	1	TRUE	1	0.785367832054376	2		447	653	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214312	55214332	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCGTGCGGTTCAGCAACAA	CGCCGTGCGGTTCAGCAACAA	G	novel	NA	P-0030145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	33	456	0	ENST00000275493.2:c.438_458delinsG	p.Ala147ProfsTer18	p.A147Pfs*18	ENST00000275493	NM_005228.3	146	ggCGCCGTGCGGTTCAGCAACAAc/ggGc	4/28	1	2	FACETS	0.162	0.131	0.197	0.162	0.131	0.197	SUBCLONAL	1	TRUE	1	0.785367832054376	2		456	519	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0030146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	163	618	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.208013262427684	5	FACETS	0.99	0.912	1	0.743	0.684	0.804	CLONAL	3	TRUE	1	0.208013262427684	5		618	692	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	166	870	0	ENST00000269305.4:c.403del	p.Cys135AlafsTer35	p.C135Afs*35	ENST00000269305	NM_001126112.2	135	Tgc/gc	5/11	0.153253078459334	2	FACETS	0.848	0.779	0.92	0.848	0.779	0.92	CLONAL	2	TRUE	0	0.208013262427684	2		870	941	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95595946	95595946	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0030146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	41	528	0	ENST00000393063.1:c.597T>A	p.Cys199Ter	p.C199*	ENST00000393063	NM_030621.3	199	tgT/tgA	7/28	1	2	FACETS	0.696	0.579	0.827	0.696	0.579	0.827	SUBCLONAL	1	TRUE	1	0.208013262427684	2		528	566	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952048	178952048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	91	410	1	ENST00000263967.3:c.3103G>A	p.Ala1035Thr	p.A1035T	ENST00000263967	NM_006218.2	1035	Gct/Act	21/21	0.156424552292697	4	FACETS	0.944	0.84	1	0.944	0.84	1	CLONAL	2	TRUE	2	0.208013262427684	4		411	560	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772219	68772225	+	protein_altering_variant	In_Frame_Del	DEL	AGGAGCC	AGGAGCC	G	novel	NA	P-0030146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	93	676	0	ENST00000261769.5:c.68_74delinsG	p.Gln23_Pro25delinsArg	p.Q23_P25delinsR	ENST00000261769	NM_004360.3	23	cAGGAGCCg/cGg	2/16	0.208013262427684	2	FACETS	1	0.959	1	0.583	0.518	0.652	CLONAL	1	TRUE	0	0.208013262427684	2		676	767	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0030147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	281	622	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.289612953587014	5	FACETS	1	0.972	1	1	0.993	1	CLONAL	4	TRUE	2	0.289612953587014	5		622	668	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0030147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	231	601	7	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.286392367932085	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.289612953587014	2		608	748	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0030147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	35	179	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.289612953587014	3	FACETS	0.862	0.709	1	0.431	0.354	0.517	CLONAL	1	TRUE	1	0.289612953587014	3		179	321	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0030147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	74	193	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	0.289612953587014	3	FACETS	0.917	0.81	1	0.917	0.81	1	CLONAL	2	TRUE	1	0.289612953587014	3		193	319	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015010	37015010	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762649232	NA	P-0030147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	144	358	0	ENST00000358127.4:c.394G>A	p.Val132Ile	p.V132I	ENST00000358127	NM_001280556.1	132	Gtc/Atc	3/10	0.289612953587014	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	1	0.289612953587014	3		358	546	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117625	4117625	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	110	529	0	ENST00000262948.5:c.95C>A	p.Ala32Glu	p.A32E	ENST00000262948	NM_030662.3	32	gCa/gAa	2/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.289612953587014	2		529	668	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660252	227660252	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	49	556	0	ENST00000305123.5:c.3203G>T	p.Gly1068Val	p.G1068V	ENST00000305123	NM_005544.2	1068	gGc/gTc	1/2	NA	2	FACETS	0.483	0.408	0.566			1	INDETERMINATE	1	TRUE	NA	0.289612953587014	2		556	700	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0030150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	134	324	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.610362095103483	1	FACETS	0.903	0.832	0.975	0.903	0.832	0.975	CLONAL	1	TRUE	0	0.610362095103483	1		324	338	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99482442	99482442	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	105	373	0	ENST00000268035.6:c.3310C>G	p.Leu1104Val	p.L1104V	ENST00000268035	NM_000875.3	1104	Cta/Gta	18/21	1	2	FACETS	0.908	0.82	0.999	0.908	0.82	0.999	CLONAL	1	TRUE	1	0.610362095103483	2		373	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579356	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0030150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	238	671	0	ENST00000269305.4:c.331_332del	p.Leu111GlyfsTer37	p.L111Gfs*37	ENST00000269305	NM_001126112.2	111	CTg/g	4/11	0.610362095103483	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.610362095103483	1		671	464	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260152	10260152	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	179	525	1	ENST00000340748.4:c.2515C>T	p.Pro839Ser	p.P839S	ENST00000340748		839	Ccc/Tcc	25/40	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.610362095103483	2		526	577	SUCCESS
APC	324	MSKCC	GRCh37	5	112175173	112175173	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	153	238	0	ENST00000257430.4:c.3883del	p.Glu1295LysfsTer10	p.E1295Kfs*10	ENST00000257430	NM_000038.5	1294	caG/ca	16/16	0.610362095103483	2	FACETS	0.987	0.927	1	0.987	0.927	1	CLONAL	2	TRUE	0	0.610362095103483	2		238	254	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030154-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	52	454	0				ENST00000310581	NM_198253.2	-/1132			0.114191656118883	5	FACETS	1	0.885	1	1	0.885	1	INDETERMINATE	3	TRUE	2	0.228711916966796	5		454	198	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0030154-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	157	605	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.228711916966796	2	FACETS	0.982	0.902	1	0.982	0.902	1	CLONAL	2	TRUE	0	0.228711916966796	2		607	699	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020354	69020354	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030154-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	91	390	0	ENST00000288368.4:c.2726T>C	p.Val909Ala	p.V909A	ENST00000288368	NM_024870.2	909	gTa/gCa	24/40	0.206772217428661	2	FACETS	1	0.979	1	0.73	0.65	0.815	CLONAL	1	TRUE	0	0.228711916966796	2		390	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0030161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	31	546	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.278334380557016	1	FACETS	0.416	0.336	0.506	0.416	0.336	0.506	SUBCLONAL	1	TRUE	0	0.307796485342324	1		547	410	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845416	156845416	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	49	704	1	ENST00000524377.1:c.1459C>T	p.Gln487Ter	p.Q487*	ENST00000524377	NM_002529.3	487	Caa/Taa	12/17	0.193909526948126	3	FACETS	0.736	0.624	0.86	0.368	0.312	0.43	SUBCLONAL	1	TRUE	1	0.307796485342324	3		705	499	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350107	81350107	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	71	379	0	ENST00000222390.5:c.1225G>T	p.Gly409Ter	p.G409*	ENST00000222390	NM_000601.4	409	Gga/Tga	10/18	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.307796485342324	2		379	340	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934218	48934222	+	frameshift_variant	Frame_Shift_Del	DEL	TATTT	TATTT	-	novel	NA	P-0030161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	14	516	0	ENST00000267163.4:c.677_681del	p.Phe226Ter	p.F226*	ENST00000267163	NM_000321.2	225	TATTTt/t	7/27	0.304870738637086	1	FACETS	0.282	0.203	0.377	0.282	0.203	0.377	SUBCLONAL	1	TRUE	0	0.307796485342324	1		516	273	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176055009	176055009	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	88	482	0	ENST00000367669.3:c.1044G>T	p.Trp348Cys	p.W348C	ENST00000367669	NM_022457.5	348	tgG/tgT	10/20	NA	2	FACETS	1	0.972	1			1	INDETERMINATE	1	TRUE	NA	0.307796485342324	2		482	439	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945324	71945324	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0030161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	44	635	0	ENST00000298229.2:c.2213-1G>T		p.X738_splice	ENST00000298229	NM_001567.3	738			1	2	FACETS	0.654	0.549	0.77	0.654	0.549	0.77	SUBCLONAL	1	TRUE	1	0.307796485342324	2		635	437	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954309	48954329	+	inframe_deletion	In_Frame_Del	DEL	TGAATGACAACATTTTTCATA	TGAATGACAACATTTTTCATA	-	novel	NA	P-0030161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	50	312	0	ENST00000267163.4:c.1432_1452del	p.Asn478_Met484del	p.N478_M484del	ENST00000267163	NM_000321.2	477	cTGAATGACAACATTTTTCATAtg/ctg	16/27	0.304870738637086	1	FACETS	0.954	0.815	1	0.954	0.815	1	CLONAL	1	TRUE	0	0.307796485342324	1		312	288	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644462	3644462	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	25	670	0	ENST00000294008.3:c.2152A>G	p.Ile718Val	p.I718V	ENST00000294008	NM_032444.2	718	Atc/Gtc	10/15	1	2	FACETS	0.357	0.281	0.445	0.357	0.281	0.445	SUBCLONAL	1	TRUE	1	0.307796485342324	2		670	455	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4097336	4097336	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs377755503	NA	P-0030161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	44	520	0	ENST00000262948.5:c.925G>T	p.Gly309Trp	p.G309W	ENST00000262948	NM_030662.3	309	Ggg/Tgg	8/11	0.278334380557016	1	FACETS	0.564	0.473	0.664	0.564	0.473	0.664	SUBCLONAL	1	TRUE	0	0.307796485342324	1		520	429	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187934	32187934	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	21	618	0	ENST00000375023.3:c.1287C>A	p.Cys429Ter	p.C429*	ENST00000375023	NM_004557.3	429	tgC/tgA	7/30	0.278334380557016	1	FACETS	0.275	0.211	0.35	0.275	0.211	0.35	SUBCLONAL	1	TRUE	0	0.307796485342324	1		618	420	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821212	32821212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	36	727	0	ENST00000354258.4:c.382C>T	p.Leu128Phe	p.L128F	ENST00000354258	NM_000593.5	128	Ctc/Ttc	1/11	1	2	FACETS	0.538	0.442	0.645	0.538	0.442	0.645	SUBCLONAL	1	TRUE	1	0.307796485342324	2		727	435	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528707	8528707	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	49	388	0	ENST00000356435.5:c.425C>A	p.Thr142Lys	p.T142K	ENST00000356435		142	aCg/aAg	4/35	0.193909526948126	3	FACETS	0.993	0.844	1	0.496	0.422	0.578	CLONAL	1	TRUE	1	0.307796485342324	3		388	370	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417944	32417944	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	34	448	0	ENST00000332351.3:c.1108C>A	p.Arg370Ser	p.R370S	ENST00000332351	NM_024426.4	370	Cgt/Agt	7/10	1	2	FACETS	0.659	0.54	0.793	0.659	0.54	0.793	SUBCLONAL	1	TRUE	1	0.307796485342324	2		448	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0030164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	172	711	0	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	0.261584516925029	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.261584516925029	1		711	954	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476310	88476310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760692815	NA	P-0030164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	53	705	0	ENST00000360948.2:c.1822G>A	p.Gly608Ser	p.G608S	ENST00000360948	NM_001012338.2	608	Ggc/Agc	15/19	0.213978105898939	1	FACETS	0.445	0.378	0.518	0.445	0.378	0.518	SUBCLONAL	1	TRUE	0	0.261584516925029	1		705	792	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307229	118307229	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0030164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	26	152	0	ENST00000534358.1:c.2T>C	p.Met1?	p.M1?	ENST00000534358	NM_005933.3	1	aTg/aCg	1/36	1	2	FACETS	0.552	0.437	0.684	0.552	0.437	0.684	SUBCLONAL	1	TRUE	1	0.261584516925029	2		152	360	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786176	3786176	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	68	639	0	ENST00000262367.5:c.4589G>C	p.Arg1530Thr	p.R1530T	ENST00000262367	NM_004380.2	1530	aGg/aCg	28/31	0.197377256609145	1	FACETS	0.575	0.499	0.657	0.575	0.499	0.657	SUBCLONAL	1	TRUE	0	0.261584516925029	1		639	786	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215617260	215617260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760144724	NA	P-0030164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	32	395	0	ENST00000260947.4:c.1588C>T	p.Pro530Ser	p.P530S	ENST00000260947	NM_000465.2	530	Cct/Tct	7/11	1	2	FACETS	0.516	0.418	0.627	0.516	0.418	0.627	SUBCLONAL	1	TRUE	1	0.261584516925029	2		395	474	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0030165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	321	281	1	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.536932187693592	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.536932187693592	3		282	719	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0030165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	225	284	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	0.536932187693592	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.536932187693592	3		284	498	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958241	11958242	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0030165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	108	436	0	ENST00000353533.5:c.153_154dup	p.Pro52HisfsTer11	p.P52Hfs*11	ENST00000353533	NM_003010.3	51	cca/cCAca	2/11	0.536932187693592	1	FACETS	0.9	0.817	0.985	0.9	0.817	0.985	CLONAL	1	TRUE	0	0.536932187693592	1		436	327	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0030168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	71	622	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.15	2		622	693	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112602	115112602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs865915137	NA	P-0030168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	71	635	2	ENST00000257566.3:c.1138G>A	p.Glu380Lys	p.E380K	ENST00000257566	NM_016569.3	380	Gag/Aag	7/8	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.15	2		637	935	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729757	162729757	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	42	448	0	ENST00000367921.3:c.843C>G	p.Phe281Leu	p.F281L	ENST00000367921	NM_006182.2	281	ttC/ttG	8/18	0.187463614197683	3	FACETS	0.744	0.619	0.884	0.372	0.309	0.442	SUBCLONAL	1	TRUE	1	0.15	3		448	809	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112745494	112745494	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	53	461	0	ENST00000369452.4:c.812A>G	p.Asn271Ser	p.N271S	ENST00000369452	NM_007373.3	271	aAt/aGt	3/9	1	2	FACETS	0.958	0.815	1	0.958	0.815	1	CLONAL	1	TRUE	1	0.15	2		461	738	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69210685	69210685	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	31	370	0	ENST00000462284.1:c.268G>T	p.Asp90Tyr	p.D90Y	ENST00000462284	NM_002392.5	90	Gat/Tat	4/11	1	2	FACETS	0.724	0.584	0.883	0.724	0.584	0.883	SUBCLONAL	1	TRUE	1	0.15	2		370	571	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845698	68845698	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	93	497	0	ENST00000261769.5:c.944A>G	p.Asn315Ser	p.N315S	ENST00000261769	NM_004360.3	315	aAt/aGt	7/16	0.203638485567785	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.15	1		497	833	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618649	37618649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	42	445	0	ENST00000447079.4:c.325C>T	p.His109Tyr	p.H109Y	ENST00000447079	NM_015083.1	109	Cac/Tac	1/14	1	2	FACETS	0.707	0.588	0.84	0.707	0.588	0.84	SUBCLONAL	1	TRUE	1	0.15	2		445	792	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777862	27777862	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1297719047	NA	P-0030168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	24	261	0	ENST00000369163.2:c.11C>T	p.Thr4Met	p.T4M	ENST00000369163	NM_003536.2	4	aCg/aTg	1/1	1	2	FACETS	0.882	0.691	1	0.882	0.691	1	CLONAL	1	TRUE	1	0.15	2		261	363	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631935	90631935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267606870	NA	P-0030170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	8	715	0	ENST00000330062.3:c.418C>T	p.Arg140Trp	p.R140W	ENST00000330062	NM_002168.2	140	Cgg/Tgg	4/11	0.114236811033103	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.76	0		715	353	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225896	2225896	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	122	761	0	ENST00000326181.6:c.1688A>G	p.Tyr563Cys	p.Y563C	ENST00000326181	NM_032271.2	563	tAc/tGc	18/21	1	2	FACETS	0.931	0.851	1	0.931	0.851	1	CLONAL	1	TRUE	1	0.76	2		761	345	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554279	106554279	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	15	458	0	ENST00000369096.4:c.1807T>G	p.Phe603Val	p.F603V	ENST00000369096	NM_001198.3	603	Ttc/Gtc	6/7	0.158079343217471	3	FACETS	0.2	0.145	0.265	0.1	0.072	0.133	INDETERMINATE	1	TRUE	1	0.76	3		458	273	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961336	15961336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200722329	NA	P-0030175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	104	449	0	ENST00000268712.3:c.6053G>A	p.Arg2018Gln	p.R2018Q	ENST00000268712	NM_006311.3	2018	cGa/cAa	39/46	0.440465912655378	2	FACETS	1	0.948	1	0.54	0.487	0.596	CLONAL	1	TRUE	0	0.440465912655378	2		449	437	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115947	8115965	+	frameshift_variant	Frame_Shift_Del	DEL	ACCACACCACCCCTCCAGC	ACCACACCACCCCTCCAGC	-	novel	NA	P-0030175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	56	308	0	ENST00000346208.3:c.1294_1312del	p.Pro432TrpfsTer37	p.P432Wfs*37	ENST00000346208		431	ggACCACACCACCCCTCCAGC/gg	6/6	0.165143136964033	3	FACETS	0.976	0.841	1	0.325	0.28	0.374	INDETERMINATE	1	TRUE	0	0.440465912655378	3		308	318	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884617	111884617	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	169	520	0	ENST00000341259.2:c.793C>G	p.Arg265Gly	p.R265G	ENST00000341259	NM_005475.2	265	Cgg/Ggg	3/8	0.429410275569107	4	FACETS	0.897	0.829	0.968	0.598	0.552	0.646	CLONAL	2	TRUE	1	0.440465912655378	4		520	616	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936036	178936036	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	19	77	0	ENST00000263967.3:c.1578T>A	p.Asn526Lys	p.N526K	ENST00000263967	NM_006218.2	526	aaT/aaA	10/21	0.440465912655378	3	FACETS	1	0.857	1	0.578	0.448	0.726	CLONAL	1	TRUE	1	0.440465912655378	3		77	91	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372047	55372047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	218	358	0	ENST00000297316.4:c.737C>T	p.Pro246Leu	p.P246L	ENST00000297316	NM_022454.3	246	cCg/cTg	2/2	0.440465912655378	5	FACETS	0.868	0.812	0.925	0.868	0.812	0.925	CLONAL	3	TRUE	2	0.440465912655378	5		358	631	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578530	7578530	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	302	693	0	ENST00000269305.4:c.400T>G	p.Phe134Val	p.F134V	ENST00000269305	NM_001126112.2	134	Ttt/Gtt	5/11	0.531310306783225	1	FACETS	0.957	0.909	1	0.957	0.909	1	CLONAL	1	TRUE	0	0.663475490265948	1		693	636	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610227	81610227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs763679435	NA	P-0030184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	32	379	0	ENST00000298171.2:c.1825C>T	p.Arg609Ter	p.R609*	ENST00000298171	NM_000369.2	609	Cga/Tga	10/10	1	2	FACETS	0.245	0.199	0.298	0.245	0.199	0.298	SUBCLONAL	1	TRUE	1	0.663475490265948	2		379	393	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753567	42753567	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	190	700	0	ENST00000222329.4:c.697C>T	p.Arg233Ter	p.R233*	ENST00000222329	NM_006494.2	233	Cga/Tga	4/4	0.411330581305741	1	FACETS	0.736	0.686	0.787	0.736	0.686	0.787	SUBCLONAL	1	TRUE	0	0.663475490265948	1		700	520	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0030186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	140	322	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.103359764807347	3	FACETS	0.898	0.828	0.97	0.599	0.552	0.647	INDETERMINATE	2	TRUE	0	0.528325255517002	3		322	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577567	7577567	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920789	NA	P-0030186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	147	427	0	ENST00000269305.4:c.714T>G	p.Cys238Trp	p.C238W	ENST00000269305	NM_001126112.2	238	tgT/tgG	7/11	0.528325255517002	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.528325255517002	1		427	357	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211834	2211834	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	27	569	0	ENST00000398665.3:c.1550A>T	p.Gln517Leu	p.Q517L	ENST00000398665	NM_032482.2	517	cAg/cTg	16/28	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		569	436	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293485	1293485	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	98	748	0	ENST00000310581.5:c.1516C>A	p.Gln506Lys	p.Q506K	ENST00000310581	NM_198253.2	506	Cag/Aag	2/16	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		748	399	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0030188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	135	367	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	0.43811099612466	2		367	595	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521468	8521468	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	156	461	0	ENST00000356435.5:c.770G>C	p.Cys257Ser	p.C257S	ENST00000356435		257	tGt/tCt	9/35	1	2	FACETS	0.907	0.832	0.986	0.907	0.832	0.986	CLONAL	1	TRUE	1	0.43811099612466	2		461	785	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123688	11123688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	174	538	0	ENST00000358026.2:c.2338G>A	p.Glu780Lys	p.E780K	ENST00000358026	NM_001128849.1	780	Gag/Aag	16/36	0.43811099612466	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.43811099612466	1		538	597	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500562	99500562	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	147	474	0	ENST00000268035.6:c.3995G>T	p.Gly1332Val	p.G1332V	ENST00000268035	NM_000875.3	1332	gGg/gTg	21/21	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.43811099612466	2		474	664	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774218	56774218	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	83	264	0	ENST00000337432.4:c.569A>G	p.Glu190Gly	p.E190G	ENST00000337432	NM_058216.2	190	gAg/gGg	3/9	1	2	FACETS	0.926	0.822	1	0.926	0.822	1	CLONAL	1	TRUE	1	0.43811099612466	2		264	409	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610475	10610475	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	194	507	0	ENST00000171111.5:c.235G>T	p.Val79Phe	p.V79F	ENST00000171111	NM_203500.1	79	Gtc/Ttc	2/6	0.43811099612466	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.43811099612466	1		507	672	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223650	36223650	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs758571377	NA	P-0030188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	238	736	0	ENST00000222270.7:c.6200G>T	p.Gly2067Val	p.G2067V	ENST00000222270	NM_014727.1	2067	gGc/gTc	28/37	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.43811099612466	2		736	974	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510230	187510230	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	134	426	0	ENST00000441802.2:c.13283G>T	p.Gly4428Val	p.G4428V	ENST00000441802	NM_005245.3	4428	gGc/gTc	27/27	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.43811099612466	2		426	601	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319946	8319946	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	65	236	0	ENST00000356435.5:c.5555G>T	p.Gly1852Val	p.G1852V	ENST00000356435		1852	gGa/gTa	34/35	1	2	FACETS	0.834	0.727	0.948	0.834	0.727	0.948	CLONAL	1	TRUE	1	0.43811099612466	2		236	356	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028778	47028778	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	211	346	0	ENST00000377604.3:c.82G>T	p.Glu28Ter	p.E28*	ENST00000377604	NM_001204468.1	28	Gag/Tag	3/24	1	1	FACETS	0.788	0.741	0.837	1	0.993	1	SUBCLONAL	2	TRUE	0	0.43811099612466	1		346	477	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0030189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	215	569	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.232366480142427	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.232366480142427	2		569	897	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397714	116397714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376459715	NA	P-0030189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	123	429	0	ENST00000397752.3:c.1988C>T	p.Ser663Leu	p.S663L	ENST00000397752	NM_000245.2	663	tCg/tTg	8/21	0.162065915720076	4	FACETS	0.937	0.849	1	0.937	0.849	1	CLONAL	2	TRUE	2	0.232366480142427	4		429	696	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784397	9784397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	187	517	0	ENST00000377346.4:c.2782G>A	p.Glu928Lys	p.E928K	ENST00000377346	NM_005026.3	928	Gag/Aag	22/24	0.231989262794662	3	FACETS	0.905	0.835	0.977	0.905	0.835	0.977	CLONAL	2	TRUE	1	0.232366480142427	3		517	993	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36022602	36022602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769358602	NA	P-0030189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	300	520	1	ENST00000358208.4:c.475C>T	p.Arg159Trp	p.R159W	ENST00000358208		159	Cgg/Tgg	5/12	0.232366480142427	5	FACETS	0.986	0.929	1	0.986	0.929	1	CLONAL	3	TRUE	2	0.232366480142427	5		521	1177	SUCCESS
APC	324	MSKCC	GRCh37	5	112175009	112175030	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	AGTGGTCAGCCTCAAAAGGCTG	AGTGGTCAGCCTCAAAAGGCTG	TGAGGCTGA	novel	NA	P-0030189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	40	217	1	ENST00000257430.4:c.3718_3739delinsTGAGGCTGA	p.Ser1240Ter	p.S1240*	ENST00000257430	NM_000038.5	1240	AGTGGTCAGCCTCAAAAGGCTGcc/TGAGGCTGAcc	16/16	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.232366480142427	2		218	324	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913492	NA	P-0030190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	52	440	0	ENST00000286548.4:c.626A>G	p.Gln209Arg	p.Q209R	ENST00000286548	NM_002072.3	209	cAa/cGa	5/7	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		440	526	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0030191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	62	429	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.315195653047963	2		429	273	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0030191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	22	337	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.629	0.489	0.79	0.629	0.489	0.79	SUBCLONAL	1	FALSE	1	0.315195653047963	2		337	222	SUCCESS
APC	324	MSKCC	GRCh37	5	112175755	112175755	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	13	273	0	ENST00000257430.4:c.4464del	p.Leu1488PhefsTer19	p.L1488Ffs*19	ENST00000257430	NM_000038.5	1488	ttA/tt	16/16	1	2	FACETS	0.425	0.304	0.573	0.425	0.304	0.573	SUBCLONAL	1	FALSE	1	0.315195653047963	2		273	194	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0030191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	51	560	0	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	1	2	FACETS	0.807	0.688	0.937	0.807	0.688	0.937	CLONAL	1	FALSE	1	0.315195653047963	2		560	401	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913517	NA	P-0030194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	205	373	0	ENST00000288135.5:c.1676T>A	p.Val559Asp	p.V559D	ENST00000288135	NM_000222.2	559	gTt/gAt	11/21	1	2	FACETS	0.962	0.899	1	0.962	0.899	1	CLONAL	1	TRUE	1	0.782260757475014	2		373	545	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332297	70332297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780528931	NA	P-0030196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	30	422	0	ENST00000373644.4:c.202G>A	p.Val68Met	p.V68M	ENST00000373644	NM_030625.2	68	Gtg/Atg	2/12	0.269849038928729	5	FACETS	0.408	0.328	0.499	0.136	0.109	0.167	SUBCLONAL	1	FALSE	2	0.420056426946292	5		422	571	SUCCESS
APC	324	MSKCC	GRCh37	5	112173600	112173600	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1060503310	NA	P-0030196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	97	343	0	ENST00000257430.4:c.2309C>G	p.Ser770Ter	p.S770*	ENST00000257430	NM_000038.5	770	tCa/tGa	16/16	0.105695058846939	4	FACETS	0.868	0.78	0.959	0.868	0.78	0.959	INDETERMINATE	2	FALSE	2	0.420056426946292	4		343	378	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1623981	1623981	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	196	499	0	ENST00000344749.5:c.518del	p.Val173AlafsTer111	p.V173Afs*111	ENST00000344749	NM_001136139.2	173	gTc/gc	8/19	0.257532402860388	4	FACETS	0.962	0.894	1	0.962	0.894	1	CLONAL	2	FALSE	2	0.420056426946292	4		499	689	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266129	41266143	+	inframe_deletion	In_Frame_Del	DEL	AGCTCCTTCTCTGAG	AGCTCCTTCTCTGAG	-	novel	NA	P-0030201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	100	264	0	ENST00000349496.5:c.126_140del	p.Ala43_Ser47del	p.A43_S47del	ENST00000349496	NM_001904.3	42	acAGCTCCTTCTCTGAGt/act	3/15	1	2	FACETS	0.975	0.88	1	1	0.988	1	CLONAL	2	TRUE	1	0.3	2		264	342	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0030202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	53	325	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.750218263848407	3	FACETS	0.778	0.67	0.893	0.389	0.335	0.447	SUBCLONAL	1	TRUE	1	0.77059566999971	3		325	245	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444762	49444762	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	85	700	0	ENST00000301067.7:c.2704G>T	p.Glu902Ter	p.E902*	ENST00000301067	NM_003482.3	902	Gag/Tag	10/54	1	2	FACETS	0.549	0.488	0.613	0.549	0.488	0.613	SUBCLONAL	1	TRUE	1	0.77059566999971	2		700	402	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879016	151879016	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	97	463	0	ENST00000262189.6:c.5929del	p.Gln1977AsnfsTer13	p.Q1977Nfs*13	ENST00000262189	NM_170606.2	1977	Caa/aa	36/59	0.750218263848407	3	FACETS	0.901	0.81	0.997	0.451	0.405	0.499	CLONAL	1	TRUE	1	0.77059566999971	3		463	387	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	195	454	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.903442682967697	2		454	393	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118914	70118915	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0030203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	410	461	0	ENST00000245479.2:c.488_489dup	p.Gln164CysfsTer20	p.Q164Cfs*20	ENST00000245479	NM_000346.3	162	-/GT	2/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.903442682967697	2		461	874	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0030204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	215	712	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.352752662439086	3	FACETS	0.904	0.848	0.96	1	0.991	1	CLONAL	3	TRUE	1	0.352752662439086	3		712	529	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852590	63852590	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	76	347	0	ENST00000279873.7:c.3368C>G	p.Ser1123Trp	p.S1123W	ENST00000279873	NM_032199.2	1123	tCg/tGg	10/10	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.352752662439086	2		347	406	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69039621	69039621	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	89	362	0	ENST00000288368.4:c.3733T>C	p.Cys1245Arg	p.C1245R	ENST00000288368	NM_024870.2	1245	Tgt/Cgt	31/40	1	2	FACETS	0.95	0.845	1	0.95	0.845	1	CLONAL	1	TRUE	1	0.352752662439086	2		362	531	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0030208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	289	283	0				ENST00000310581	NM_198253.2	-/1132			0.716880516694794	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.729638618504496	4		283	618	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755612	39755612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776452839	NA	P-0030208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	329	480	0	ENST00000288319.7:c.1153C>T	p.Arg385Cys	p.R385C	ENST00000288319	NM_182918.3	385	Cgc/Tgc	10/10	0.716880516694794	4	FACETS	0.889	0.843	0.936	0.889	0.843	0.936	CLONAL	2	TRUE	2	0.729638618504496	4		480	877	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266007	41266170	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGA	GTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGA	-	novel	NA	P-0030208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	54	189	0	ENST00000349496.5:c.14-10_167del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.716880516694794	4	FACETS	0.694	0.595	0.801	0.347	0.297	0.401	SUBCLONAL	1	TRUE	2	0.729638618504496	4		189	369	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55270264	55270264	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	475	746	0	ENST00000275493.2:c.3217C>T	p.Pro1073Ser	p.P1073S	ENST00000275493	NM_005228.3	1073	Ccc/Tcc	27/28	0.716880516694794	4	FACETS	0.986	0.945	1	0.986	0.945	1	CLONAL	2	TRUE	2	0.729638618504496	4		746	1142	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	78	454	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.258917293478161	2		454	499	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266713	198266713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776846119	NA	P-0030209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	109	483	0	ENST00000335508.6:c.2219G>A	p.Gly740Glu	p.G740E	ENST00000335508	NM_012433.2	740	gGa/gAa	15/25	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.258917293478161	2		483	736	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100720	8100720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	86	621	1	ENST00000346208.3:c.694G>A	p.Gly232Arg	p.G232R	ENST00000346208		232	Gga/Aga	3/6	1	2	FACETS	0.841	0.743	0.946	0.841	0.743	0.946	CLONAL	1	TRUE	1	0.258917293478161	2		622	790	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401005	139401005	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1249540119	NA	P-0030209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	105	577	0	ENST00000277541.6:c.3988C>T	p.Arg1330Cys	p.R1330C	ENST00000277541	NM_017617.3	1330	Cgc/Tgc	24/34	0.19506454672334	3	FACETS	0.956	0.855	1	0.478	0.427	0.532	CLONAL	1	TRUE	1	0.258917293478161	3		577	958	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533256	29533256	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0030209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	39	249	0	ENST00000356175.3:c.1261-2A>T		p.X421_splice	ENST00000356175	NM_000267.3	421			1	2	FACETS	0.819	0.68	0.973	0.819	0.68	0.973	CLONAL	1	TRUE	1	0.258917293478161	2		249	368	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354255	70354255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	122	316	0	ENST00000374080.3:c.4666G>A	p.Glu1556Lys	p.E1556K	ENST00000374080		1556	Gag/Aag	34/45	1	1	FACETS	0.95	0.865	1	1	0.989	1	CLONAL	2	TRUE	0	0.258917293478161	1		316	432	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023123	33023123	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	95	404	2	ENST00000300177.4:c.232C>T	p.Gln78Ter	p.Q78*	ENST00000300177	NM_001191322.1	78	Caa/Taa	2/2	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.258917293478161	2		406	645	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528166	29528166	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	107	542	0	ENST00000356175.3:c.1174C>T	p.Gln392Ter	p.Q392*	ENST00000356175	NM_000267.3	392	Caa/Taa	10/57	1	2	FACETS	0.983	0.881	1	0.983	0.881	1	CLONAL	1	TRUE	1	0.258917293478161	2		542	841	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559213	141559213	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	74	456	0	ENST00000220592.5:c.1588G>A	p.Ala530Thr	p.A530T	ENST00000220592	NM_012154.3	530	Gcc/Acc	12/19	1	2	FACETS	0.881	0.771	0.999	0.881	0.771	0.999	CLONAL	1	TRUE	1	0.258917293478161	2		456	649	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055892	180055892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369919880	NA	P-0030209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	78	474	1	ENST00000261937.6:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000261937	NM_182925.4	365	Gag/Aag	8/30	1	2	FACETS	0.913	0.802	1	0.913	0.802	1	CLONAL	1	TRUE	1	0.258917293478161	2		475	660	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599107	28599107	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	159	625	0	ENST00000253063.3:c.553G>T	p.Gly185Cys	p.G185C	ENST00000253063	NM_031459.4	185	Ggc/Tgc	5/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.258917293478161	2		625	913	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248738	59248738	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	138	627	0	ENST00000371222.2:c.5C>T	p.Thr2Ile	p.T2I	ENST00000371222	NM_002228.3	2	aCt/aTt	1/1	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.258917293478161	2		627	1031	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843712	156843712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	157	768	0	ENST00000524377.1:c.1138G>A	p.Asp380Asn	p.D380N	ENST00000524377	NM_002529.3	380	Gac/Aac	8/17	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.258917293478161	2		768	1068	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215785	133215786	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0030209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	97	566	1	ENST00000320574.5:c.5477_5478delinsAA	p.Arg1826Gln	p.R1826Q	ENST00000320574	NM_006231.2	1826	cGG/cAA	40/49	1	2	FACETS	0.868	0.773	0.97	0.868	0.773	0.97	CLONAL	1	TRUE	1	0.258917293478161	2		567	863	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337669	73337669	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	62	245	0	ENST00000377767.4:c.2047T>G	p.Ser683Ala	p.S683A	ENST00000377767	NM_014953.3	683	Tct/Gct	16/21	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.258917293478161	2		245	437	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993672	72993672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	114	497	0	ENST00000268489.5:c.373G>A	p.Asp125Asn	p.D125N	ENST00000268489	NM_006885.3	125	Gac/Aac	2/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.258917293478161	2		497	698	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490319	29490320	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0030209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	66	397	0	ENST00000356175.3:c.404_405delinsAA	p.Arg135Gln	p.R135Q	ENST00000356175	NM_000267.3	135	cGG/cAA	4/57	1	2	FACETS	0.826	0.717	0.944	0.826	0.717	0.944	CLONAL	1	TRUE	1	0.258917293478161	2		397	617	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872667	37872667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	139	727	1	ENST00000269571.5:c.1627G>A	p.Glu543Lys	p.E543K	ENST00000269571		543	Gaa/Aaa	13/27	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.258917293478161	2		728	991	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226823	2226823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	61	356	0	ENST00000398665.3:c.4303C>T	p.Pro1435Ser	p.P1435S	ENST00000398665	NM_032482.2	1435	Ccc/Tcc	27/28	1	2	FACETS	0.994	0.859	1	0.994	0.859	1	CLONAL	1	TRUE	1	0.258917293478161	2		356	474	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097626	11097626	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	149	713	0	ENST00000358026.2:c.806C>G	p.Pro269Arg	p.P269R	ENST00000358026	NM_001128849.1	269	cCc/cGc	5/36	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.258917293478161	2		713	977	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125691	47125691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1482913329	NA	P-0030209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	112	360	0	ENST00000409792.3:c.5579C>T	p.Pro1860Leu	p.P1860L	ENST00000409792	NM_014159.6	1860	cCt/cTt	12/21	0.19506454672334	3	FACETS	0.793	0.715	0.875	0.793	0.715	0.875	SUBCLONAL	2	TRUE	1	0.258917293478161	3		360	616	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939931	49939931	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1340049565	NA	P-0030209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	102	632	0	ENST00000296474.3:c.1112T>C	p.Ile371Thr	p.I371T	ENST00000296474	NM_002447.2	371	aTt/aCt	1/20	0.19506454672334	3	FACETS	0.76	0.678	0.848	0.38	0.339	0.424	SUBCLONAL	1	TRUE	1	0.258917293478161	3		632	1171	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587169	189587169	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	158	423	0	ENST00000264731.3:c.1186C>T	p.Pro396Ser	p.P396S	ENST00000264731	NM_003722.4	396	Cca/Tca	9/14	0.214751214755911	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.258917293478161	4		423	712	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612161	189612161	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	134	456	0	ENST00000264731.3:c.1913T>G	p.Val638Gly	p.V638G	ENST00000264731	NM_003722.4	638	gTt/gGt	14/14	0.214751214755911	4	FACETS	0.754	0.685	0.827	0.754	0.685	0.827	SUBCLONAL	2	TRUE	2	0.258917293478161	4		456	864	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99802237	99802237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	32	138	0	ENST00000280892.6:c.656C>T	p.Ser219Phe	p.S219F	ENST00000280892	NM_001130678.1	219	tCc/tTc	7/7	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.258917293478161	2		138	213	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499042	149499042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	124	460	0	ENST00000261799.4:c.2786C>T	p.Ala929Val	p.A929V	ENST00000261799	NM_002609.3	929	gCc/gTc	20/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.258917293478161	2		460	714	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510223	149510223	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	113	466	0	ENST00000261799.4:c.1246C>T	p.Pro416Ser	p.P416S	ENST00000261799	NM_002609.3	416	Cct/Tct	9/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.258917293478161	2		466	707	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527925	157527925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377877762	NA	P-0030209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	105	502	0	ENST00000346085.5:c.5650C>T	p.Arg1884Trp	p.R1884W	ENST00000346085	NM_020732.3	1884	Cgg/Tgg	20/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.258917293478161	2		502	718	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492939	8492939	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	79	489	0	ENST00000356435.5:c.2390C>T	p.Ser797Phe	p.S797F	ENST00000356435		797	tCc/tTc	16/35	0.258917293478161	1	FACETS	0.907	0.798	1	0.907	0.798	1	CLONAL	1	TRUE	0	0.258917293478161	1		489	586	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504279	8504279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753412640	NA	P-0030209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	76	394	1	ENST00000356435.5:c.1804G>A	p.Ala602Thr	p.A602T	ENST00000356435		602	Gct/Act	12/35	0.258917293478161	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.258917293478161	1		395	476	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889188	76889188	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	87	265	0	ENST00000373344.5:c.4822C>T	p.Leu1608Phe	p.L1608F	ENST00000373344	NM_000489.3	1608	Ctt/Ttt	18/35	1	1	FACETS	0.841	0.75	0.935	1	0.983	1	CLONAL	2	TRUE	0	0.258917293478161	1		265	348	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0030210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	353	430	0	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	2	TRUE	NA	0.43063348465382	2		430	751	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572612	64572612	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446518998	NA	P-0030210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	77	643	0	ENST00000312049.6:c.1244G>A	p.Arg415Gln	p.R415Q	ENST00000312049	NM_130799.2	415	cGa/cAa	9/10	1	2	FACETS	0.404	0.353	0.458	0.404	0.353	0.458	SUBCLONAL	1	TRUE	1	0.43063348465382	2		643	886	SUCCESS
MET	4233	MSKCC	GRCh37	7	116381023	116381023	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	333	479	0	ENST00000397752.3:c.1645G>C	p.Glu549Gln	p.E549Q	ENST00000397752	NM_000245.2	549	Gag/Cag	5/21	0.43190872365823	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.43063348465382	1		479	835	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579347	7579358	+	inframe_deletion	In_Frame_Del	DEL	AGAAGCCCAGAC	AGAAGCCCAGAC	-	novel	NA	P-0030210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	176	585	0	ENST00000269305.4:c.329_340del	p.Arg110_Phe113del	p.R110_F113del	ENST00000269305	NM_001126112.2	110	cGTCTGGGCTTCTtg/ctg	4/11	0.43190872365823	1	FACETS	0.92	0.85	0.993	0.92	0.85	0.993	CLONAL	1	TRUE	0	0.43063348465382	1		585	697	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3634827	3634827	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs543847606	NA	P-0030210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	92	588	1	ENST00000294008.3:c.4682C>T	p.Thr1561Met	p.T1561M	ENST00000294008	NM_032444.2	1561	aCg/aTg	13/15	0.0718777206077457	3	FACETS	0.51	0.452	0.572			1	INDETERMINATE	1	TRUE	NA	0.43063348465382	3		589	1019	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849948	156849948	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	257	540	0	ENST00000524377.1:c.2204A>T	p.Glu735Val	p.E735V	ENST00000524377	NM_002529.3	735	gAg/gTg	16/17	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.43063348465382	2		540	887	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588221	69588221	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	58	455	0	ENST00000168712.1:c.477G>C	p.Glu159Asp	p.E159D	ENST00000168712	NM_002007.2	159	gaG/gaC	3/3	1	2	FACETS	0.345	0.295	0.399	0.345	0.295	0.399	SUBCLONAL	1	TRUE	1	0.43063348465382	2		455	781	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46240671	46240671	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	36	335	0	ENST00000334344.6:c.1531C>A	p.Pro511Thr	p.P511T	ENST00000334344	NM_152641.2	511	Cca/Aca	12/21	1	2	FACETS	0.314	0.257	0.377	0.314	0.257	0.377	SUBCLONAL	1	TRUE	1	0.43063348465382	2		335	533	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487652	56487652	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	77	397	2	ENST00000267101.3:c.1585T>C	p.Cys529Arg	p.C529R	ENST00000267101	NM_001982.3	529	Tgt/Cgt	13/28	0.43190872365823	1	FACETS	0.481	0.422	0.543	0.481	0.422	0.543	SUBCLONAL	1	TRUE	0	0.43063348465382	1		399	584	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589379	28589379	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	57	426	0	ENST00000241453.7:c.2668C>T	p.Pro890Ser	p.P890S	ENST00000241453	NM_004119.2	890	Cct/Tct	22/24	0.43190872365823	1	FACETS	0.385	0.33	0.444	0.385	0.33	0.444	SUBCLONAL	1	TRUE	0	0.43063348465382	1		426	540	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41023350	41023350	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1263727210	NA	P-0030210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	294	438	0	ENST00000267868.3:c.994G>C	p.Asp332His	p.D332H	ENST00000267868	NM_002875.4	332	Gat/Cat	10/10	NA	2	FACETS	0.78	0.737	0.825			1	INDETERMINATE	2	TRUE	NA	0.43063348465382	2		438	875	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554057	63554057	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	50	572	0	ENST00000307078.5:c.682T>A	p.Leu228Met	p.L228M	ENST00000307078	NM_004655.3	228	Ttg/Atg	2/11	0.43190872365823	1	FACETS	0.287	0.243	0.336	0.287	0.243	0.336	SUBCLONAL	1	TRUE	0	0.43063348465382	1		572	634	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78923284	78923284	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	71	563	0	ENST00000306801.3:c.3307G>T	p.Glu1103Ter	p.E1103*	ENST00000306801	NM_020761.2	1103	Gaa/Taa	28/34	0.43190872365823	3	FACETS	0.367	0.319	0.419	0.122	0.106	0.14	SUBCLONAL	1	TRUE	0	0.43063348465382	3		563	1092	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281158	46281158	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	73	396	1	ENST00000371998.3:c.3955C>T	p.Gln1319Ter	p.Q1319*	ENST00000371998		1319	Caa/Taa	21/23	NA	2	FACETS	0.452	0.395	0.514			1	INDETERMINATE	1	TRUE	NA	0.43063348465382	2		397	750	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485860	57485860	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	58	307	0	ENST00000371085.3:c.1161C>G	p.His387Gln	p.H387Q	ENST00000371085	NM_000516.4	387	caC/caG	13/13	0.43190872365823	3	FACETS	0.481	0.412	0.555			1	SUBCLONAL	1	TRUE	NA	0.43063348465382	3		307	681	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62298891	62298891	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0030210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	67	543	1	ENST00000360203.5:c.684C>G	p.Tyr228Ter	p.Y228*	ENST00000360203	NM_001283009.1	228	taC/taG	8/35	0.43190872365823	1	FACETS	0.309	0.267	0.353	0.309	0.267	0.353	SUBCLONAL	1	TRUE	0	0.43063348465382	1		544	791	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623161	52623161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756858926	NA	P-0030210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	41	470	1	ENST00000394830.3:c.2890G>A	p.Val964Ile	p.V964I	ENST00000394830	NM_018313.4	964	Gtc/Atc	19/30	0.43190872365823	1	FACETS	0.228	0.189	0.271	0.228	0.189	0.271	SUBCLONAL	1	TRUE	0	0.43063348465382	1		471	655	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664779	138664779	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	49	240	0	ENST00000330315.3:c.786G>C	p.Gln262His	p.Q262H	ENST00000330315	NM_023067.3	262	caG/caC	1/1	NA	2	FACETS	0.561	0.476	0.653			1	INDETERMINATE	1	TRUE	NA	0.43063348465382	2		240	406	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806624	1806624	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	108	662	0	ENST00000260795.2:c.1340A>C	p.Glu447Ala	p.E447A	ENST00000260795		447	gAg/gCg	9/17	0.43190872365823	1	FACETS	0.501	0.449	0.555	0.501	0.449	0.555	SUBCLONAL	1	TRUE	0	0.43063348465382	1		662	786	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383715	84383715	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	90	612	0	ENST00000321945.7:c.1137A>T	p.Gln379His	p.Q379H	ENST00000321945	NM_139076.2	379	caA/caT	9/9	0.43190872365823	2	FACETS	0.399	0.353	0.448	0.199	0.176	0.224	SUBCLONAL	1	TRUE	0	0.43063348465382	2		612	1048	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753041	57753874	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAAACTGGGACGATCCTCTGGGTTTTTGGACAACATACTAGCAATTAAGTGCTTGGCAGGAGCCAGCAATGAGGACGGCATTGTATACCTTGCTTCCCTTATGCACCTATAAGTTTCTTTGAGATTTGTAGTTTCAAATGGGGGCCTCCCTAGTAACATTGTATACCTGTGTGCAAAGAAACACATCTTTAGCAATGGTCATAAAGCAACTCTTTTCAAGTGTTAAAATCTAAATCCGAATTTGCTTTTTAATTATTCTGCTGCATTTACTTACATTACACAGCCCAGGGCCCAAATGTCTGATTCACAGCCATGTCCTTGTTTGTTGAGGACTTCAGGAGAGAGATAATTTGGGGTACCACATATCGTTCTGGAAAGACAAAATATTGAGATCGTGTTAGGAACTATTCCACTACTTAAACTTGGTTCTCTTGACATGACTTGATGGGAGACAAAATCTTAAACAAAATCTTAAAATCTATACTGAATTTCTATTTGGAAACATTTGACTTTTGGCATCTGAAAATTCAATTGAGATCTGACCAAATGAGTTTTGGTAATTTTTAAAAATGCACACACGTTGTTTTAGCCCACATGCAAAGTGTTGTTAACCAACTAAAGCCAGGGACGTCGTGGCATTTTATACATTTTAAGCCAAGAAAAGACTTCATTGACTGCTTTCATAATCAATTTAGAGGCACAGGGTGCTCTGTCTAGTCCATAGTGGGCATTTAATAAGTATTTCTTTAAATTAACATTGCTATGATTTATAGATTTTATTACCGGACCTCTGAAACATTAAATGCAAAATAATGAAGGCATATTTGGTCTCCA	CAAACTGGGACGATCCTCTGGGTTTTTGGACAACATACTAGCAATTAAGTGCTTGGCAGGAGCCAGCAATGAGGACGGCATTGTATACCTTGCTTCCCTTATGCACCTATAAGTTTCTTTGAGATTTGTAGTTTCAAATGGGGGCCTCCCTAGTAACATTGTATACCTGTGTGCAAAGAAACACATCTTTAGCAATGGTCATAAAGCAACTCTTTTCAAGTGTTAAAATCTAAATCCGAATTTGCTTTTTAATTATTCTGCTGCATTTACTTACATTACACAGCCCAGGGCCCAAATGTCTGATTCACAGCCATGTCCTTGTTTGTTGAGGACTTCAGGAGAGAGATAATTTGGGGTACCACATATCGTTCTGGAAAGACAAAATATTGAGATCGTGTTAGGAACTATTCCACTACTTAAACTTGGTTCTCTTGACATGACTTGATGGGAGACAAAATCTTAAACAAAATCTTAAAATCTATACTGAATTTCTATTTGGAAACATTTGACTTTTGGCATCTGAAAATTCAATTGAGATCTGACCAAATGAGTTTTGGTAATTTTTAAAAATGCACACACGTTGTTTTAGCCCACATGCAAAGTGTTGTTAACCAACTAAAGCCAGGGACGTCGTGGCATTTTATACATTTTAAGCCAAGAAAAGACTTCATTGACTGCTTTCATAATCAATTTAGAGGCACAGGGTGCTCTGTCTAGTCCATAGTGGGCATTTAATAAGTATTTCTTTAAATTAACATTGCTATGATTTATAGATTTTATTACCGGACCTCTGAAACATTAAATGCAAAATAATGAAGGCATATTTGGTCTCCA	-	novel	NA	P-0030210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	119	376	0	ENST00000274289.3:c.713+37_975del		p.X238_splice	ENST00000274289	NM_006622.3	238		6-7/14	0.347961324020108	1	FACETS	0.88	0.798	0.965	0.88	0.798	0.965	CLONAL	1	TRUE	0	0.43063348465382	1		376	493	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129420	152129420	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	46	331	0	ENST00000206249.3:c.373G>C	p.Gly125Arg	p.G125R	ENST00000206249	NM_000125.3	125	Ggc/Cgc	1/8	0.285008518399775	1	FACETS	0.422	0.356	0.495	0.422	0.356	0.495	SUBCLONAL	1	TRUE	0	0.43063348465382	1		331	397	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033171	69033171	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	70	468	0	ENST00000288368.4:c.3611T>C	p.Met1204Thr	p.M1204T	ENST00000288368	NM_024870.2	1204	aTg/aCg	30/40	0.276144107989513	5	FACETS	0.504	0.438	0.576			1	SUBCLONAL	1	TRUE	NA	0.43063348465382	5		468	1061	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971066	21971100	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGCACCACCAGCGTGTCCAGGAAGCCCTCCCGG	GCAGCACCACCAGCGTGTCCAGGAAGCCCTCCCGG	-	novel	NA	P-0030210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	208	393	0	ENST00000304494.5:c.258_292del	p.Arg87ProfsTer21	p.R87Pfs*21	ENST00000304494	NM_000077.4	86	gcCCGGGAGGGCTTCCTGGACACGCTGGTGGTGCTGCac/gcac	2/3	0.43190872365823	3	FACETS	0.962	0.899	1	0.642	0.599	0.685	CLONAL	2	TRUE	0	0.43063348465382	3		393	610	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402444	139402444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	261	670	0	ENST00000277541.6:c.3473C>T	p.Ala1158Val	p.A1158V	ENST00000277541	NM_017617.3	1158	gCc/gTc	21/34	0.43190872365823	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.43063348465382	1		670	817	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340799	70340855	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTTTTTCCCTCTTTCCTCCAGAATGGACTCAGATCATCACCAAGTACTTATGGGAG	CCTTTTTCCCTCTTTCCTCCAGAATGGACTCAGATCATCACCAAGTACTTATGGGAG	-	novel	NA	P-0030210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	150	309	0	ENST00000374080.3:c.554-21_589del		p.X185_splice	ENST00000374080		185		5/45	0.43190872365823	3	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.43063348465382	3		309	651	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348273	70348273	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	62	519	0	ENST00000374080.3:c.3337C>G	p.Leu1113Val	p.L1113V	ENST00000374080		1113	Ctc/Gtc	23/45	0.43190872365823	3	FACETS	0.305	0.262	0.352			1	SUBCLONAL	1	TRUE	NA	0.43063348465382	3		519	1148	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0030211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	60	286	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.268905954117165	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.286292525966378	1		286	331	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166214	118166214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	42	403	3	ENST00000369448.3:c.724G>A	p.Gly242Arg	p.G242R	ENST00000369448	NM_017709.3	242	Ggg/Agg	2/2	1	2	FACETS	0.868	0.727	1	0.868	0.727	1	CLONAL	1	TRUE	1	0.286292525966378	2		406	338	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829549	72829549	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs575480618	NA	P-0030211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	76	626	1	ENST00000268489.5:c.7032C>G	p.Ile2344Met	p.I2344M	ENST00000268489	NM_006885.3	2344	atC/atG	9/10	0.268905954117165	1	FACETS	0.944	0.83	1	0.944	0.83	1	CLONAL	1	TRUE	0	0.286292525966378	1		627	482	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970993	70970993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	79	755	5	ENST00000276594.2:c.1268C>T	p.Pro423Leu	p.P423L	ENST00000276594	NM_024504.3	423	cCc/cTc	6/8	0.166272281894619	1	FACETS	0.73	0.642	0.824	0.73	0.642	0.824	INDETERMINATE	1	TRUE	0	0.286292525966378	1		760	648	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563036	21563036	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	85	803	3	ENST00000382592.4:c.883G>T	p.Gly295Ter	p.G295*	ENST00000382592	NM_014572.2	295	Gga/Tga	4/8	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.286292525966378	2		806	516	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628550	90628550	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	67	744	5	ENST00000330062.3:c.1037C>T	p.Ala346Val	p.A346V	ENST00000330062	NM_002168.2	346	gCc/gTc	8/11	1	2	FACETS	0.814	0.708	0.929	0.814	0.708	0.929	CLONAL	1	TRUE	1	0.286292525966378	2		749	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578418	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-	novel	NA	P-0030211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	85	672	4	ENST00000269305.4:c.512_514del	p.Glu171del	p.E171del	ENST00000269305	NM_001126112.2	171	gAGGtt/gtt	5/11	0.268905954117165	1	FACETS	0.977	0.866	1	0.977	0.866	1	CLONAL	1	TRUE	0	0.286292525966378	1		676	521	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0030217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	209	427	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.556605346013631	3	FACETS	0.912	0.854	0.97	0.912	0.854	0.97	CLONAL	2	TRUE	1	0.567055247400104	3		427	519	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236087	108236087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781894	NA	P-0030217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	440	522	0	ENST00000278616.4:c.9023G>A	p.Arg3008His	p.R3008H	ENST00000278616	NM_000051.3	3008	cGt/cAt	63/63	0.551037889257194	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	TRUE	0	0.567055247400104	3		522	663	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48586262	48586262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658694	NA	P-0030217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	101	436	0	ENST00000342988.3:c.931C>T	p.Gln311Ter	p.Q311*	ENST00000342988	NM_005359.5	311	Cag/Tag	8/12	0.567055247400104	1	FACETS	0.945	0.858	1	0.945	0.858	1	CLONAL	1	TRUE	0	0.567055247400104	1		436	270	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793362	242793362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137861407	NA	P-0030217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	228	831	4	ENST00000334409.5:c.715G>A	p.Val239Met	p.V239M	ENST00000334409	NM_005018.2	239	Gtg/Atg	5/5	1	2	FACETS	0.878	0.819	0.939	0.878	0.819	0.939	CLONAL	1	TRUE	1	0.567055247400104	2		835	916	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521663	89521663	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs549868478	NA	P-0030217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	152	454	1	ENST00000336596.2:c.2740C>T	p.Arg914Cys	p.R914C	ENST00000336596	NM_005233.5	914	Cgc/Tgc	16/17	1	2	FACETS	0.984	0.905	1	0.984	0.905	1	CLONAL	1	TRUE	1	0.567055247400104	2		455	545	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0030218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	40	546	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.741	0.614	0.882	0.741	0.614	0.882	SUBCLONAL	1	TRUE	1	0.18	2		546	600	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591798	48591798	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	34	309	0	ENST00000342988.3:c.961G>T	p.Glu321Ter	p.E321*	ENST00000342988	NM_005359.5	321	Gag/Tag	9/12	1	2	FACETS	0.91	0.744	1	0.91	0.744	1	CLONAL	1	TRUE	1	0.18	2		309	415	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14303251	14303253	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0030218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	66	579	0	ENST00000256196.4:c.422_424del	p.Glu141del	p.E141del	ENST00000256196		141	gAAGga/gga	5/6	1	2	FACETS	0.982	0.851	1	0.982	0.851	1	CLONAL	1	TRUE	1	0.18	2		579	747	SUCCESS
APC	324	MSKCC	GRCh37	5	112176146	112176146	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	40	397	0	ENST00000257430.4:c.4856del	p.Pro1619HisfsTer31	p.P1619Hfs*31	ENST00000257430	NM_000038.5	1619	Cca/ca	16/16	1	2	FACETS	0.911	0.757	1	0.911	0.757	1	CLONAL	1	TRUE	1	0.18	2		397	488	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752847	42752848	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0030220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	281	618	2	ENST00000222329.4:c.1416dup	p.Gly473ArgfsTer13	p.G473Rfs*13	ENST00000222329	NM_006494.2	472	-/C	4/4	1	2	FACETS	1	0.963	1	1	0.995	1	CLONAL	2	TRUE	1	0.261732978657154	2		620	1039	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0030225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	10	356	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	0.374527403400094	5	FACETS	0.535	0.363	0.749			1	SUBCLONAL	1	TRUE	NA	0.374527403400094	5		356	156	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777927	27777927	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	57	393	1	ENST00000369163.2:c.76G>A	p.Ala26Thr	p.A26T	ENST00000369163	NM_003536.2	26	Gct/Act	1/1	0.374527403400094	7	FACETS	0.636	0.544	0.737	0.159	0.136	0.185	SUBCLONAL	1	TRUE	3	0.374527403400094	7		394	927	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204511966	204511966	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	21	477	0	ENST00000367182.3:c.566G>C	p.Gly189Ala	p.G189A	ENST00000367182	NM_001278516.1	189	gGa/gCa	8/11	0.280429769428628	4	FACETS	0.759	0.587	0.958	0.38	0.293	0.479	CLONAL	1	TRUE	2	0.374527403400094	4		477	203	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042542	42042542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	50	536	0	ENST00000219905.7:c.6737G>A	p.Arg2246Lys	p.R2246K	ENST00000219905	NM_001164273.1	2246	aGg/aAg	17/24	0.139958018972604	4	FACETS	0.866	0.736	1	0.433	0.368	0.504	INDETERMINATE	1	TRUE	2	0.374527403400094	4		536	424	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735353	204735354	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0030225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	32	263	1	ENST00000302823.3:c.154_155delinsTT	p.Gly52Phe	p.G52F	ENST00000302823	NM_005214.4	52	GGc/TTc	2/4	1	2	FACETS	0.416	0.337	0.504	0.416	0.337	0.504	SUBCLONAL	1	TRUE	1	0.374527403400094	2		264	411	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288188	33288189	+	missense_variant	Missense_Mutation	DNP	TC	TC	AG	novel	NA	P-0030225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	68	392	1	ENST00000374542.5:c.1219_1220delinsCT	p.Asp407Leu	p.D407L	ENST00000374542	NM_001141970.1	407	GAc/CTc	4/8	0.374527403400094	5	FACETS	0.572	0.496	0.654			1	SUBCLONAL	1	TRUE	NA	0.374527403400094	5		393	992	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851148	151851148	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	35	410	0	ENST00000262189.6:c.12223C>A	p.Pro4075Thr	p.P4075T	ENST00000262189	NM_170606.2	4075	Ccc/Acc	48/59	0.229797527861693	3	FACETS	0.725	0.596	0.869	0.363	0.298	0.435	SUBCLONAL	1	TRUE	1	0.374527403400094	3		410	306	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	355	454	0				ENST00000310581	NM_198253.2	-/1132			0.237979992118092	2	FACETS	0.802	0.764	0.841	0.802	0.764	0.841	INDETERMINATE	2	TRUE	0	0.534999143913377	2		454	827	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467924	50467924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	92	383	0	ENST00000331340.3:c.1159G>A	p.Glu387Lys	p.E387K	ENST00000331340	NM_006060.4	387	Gag/Aag	8/8	0.241906702171218	3	FACETS	0.634	0.563	0.709	0.317	0.281	0.355	INDETERMINATE	1	TRUE	1	0.534999143913377	3		383	688	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882019	NA	P-0030226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	545	732	0	ENST00000269305.4:c.455del	p.Pro152ArgfsTer18	p.P152Rfs*18	ENST00000269305	NM_001126112.2	152	cCg/cg	5/11	0.500135805133967	2	FACETS	0.886	0.853	0.919	0.886	0.853	0.919	CLONAL	2	TRUE	0	0.534999143913377	2		732	1150	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944947	31944947	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868835690	NA	P-0030226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	90	340	0	ENST00000340398.3:c.154C>T	p.Arg52Cys	p.R52C	ENST00000340398	NM_001013699.2	52	Cgt/Tgt	1/1	NA	2	FACETS	0.456	0.404	0.511			1	INDETERMINATE	1	TRUE	NA	0.534999143913377	2		340	738	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224604	108224604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555142909	NA	P-0030226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	58	238	0	ENST00000278616.4:c.8783G>A	p.Arg2928Lys	p.R2928K	ENST00000278616	NM_000051.3	2928	aGa/aAa	60/63	0.237979992118092	2	FACETS	0.475	0.409	0.547	0.238	0.204	0.274	INDETERMINATE	1	TRUE	0	0.534999143913377	2		238	456	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843748	151843748	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778512	NA	P-0030226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	114	386	0	ENST00000262189.6:c.13967C>T	p.Ala4656Val	p.A4656V	ENST00000262189	NM_170606.2	4656	gCg/gTg	53/59	0.195019872100117	2	FACETS	0.583	0.525	0.644	0.291	0.262	0.322	INDETERMINATE	1	TRUE	0	0.534999143913377	2		386	731	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578119	226578119	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	33	347	0	ENST00000366794.5:c.609G>C	p.Lys203Asn	p.K203N	ENST00000366794	NM_001618.3	203	aaG/aaC	4/23	0.28977010339659	1	FACETS	0.152	0.123	0.185	0.152	0.123	0.185	INDETERMINATE	1	TRUE	0	0.534999143913377	1		347	593	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863430	57863430	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	331	577	0	ENST00000228682.2:c.1525C>T	p.Leu509Phe	p.L509F	ENST00000228682	NM_005269.2	509	Ctc/Ttc	11/12	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.534999143913377	2		577	978	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961360	41961360	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777880782	NA	P-0030226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	58	405	1	ENST00000219905.7:c.268C>T	p.His90Tyr	p.H90Y	ENST00000219905	NM_001164273.1	90	Cat/Tat	2/24	0.337407396044632	1	FACETS	0.296	0.254	0.341	0.296	0.254	0.341	SUBCLONAL	1	TRUE	0	0.534999143913377	1		406	537	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945705	54945705	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	283	374	1	ENST00000312783.6:c.865C>T	p.Leu289Phe	p.L289F	ENST00000312783	NM_198436.1	289	Ctc/Ttc	9/10	0.241906702171218	3	FACETS	0.836	0.789	0.884	0.836	0.789	0.884	INDETERMINATE	2	TRUE	1	0.534999143913377	3		375	802	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72891437	72891437	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	94	418	0	ENST00000325599.8:c.325G>C	p.Glu109Gln	p.E109Q	ENST00000325599	NM_018130.2	109	Gaa/Caa	3/11	0.534999143913377	1	FACETS	0.623	0.558	0.692	0.623	0.558	0.692	SUBCLONAL	1	TRUE	0	0.534999143913377	1		418	413	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176671236	176671236	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	107	368	0	ENST00000439151.2:c.4343C>G	p.Ser1448Cys	p.S1448C	ENST00000439151	NM_022455.4	1448	tCt/tGt	9/23	1	2	FACETS	0.481	0.431	0.535	0.481	0.431	0.535	SUBCLONAL	1	TRUE	1	0.534999143913377	2		368	831	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411623	116411623	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1361155132	NA	P-0030226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	115	476	0	ENST00000397752.3:c.2802G>C	p.Leu934Phe	p.L934F	ENST00000397752	NM_000245.2	934	ttG/ttC	13/21	0.302460037488891	1	FACETS	0.44	0.396	0.486	0.44	0.396	0.486	INDETERMINATE	1	TRUE	0	0.534999143913377	1		476	716	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69032438	69032438	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	127	616	0	ENST00000288368.4:c.3512C>A	p.Ser1171Ter	p.S1171*	ENST00000288368	NM_024870.2	1171	tCa/tAa	29/40	0.291469499604546	2	FACETS	0.465	0.42	0.512	0.232	0.21	0.256	INDETERMINATE	1	TRUE	0	0.534999143913377	2		616	1022	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528600	8528600	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	179	307	0	ENST00000356435.5:c.532T>A	p.Leu178Ile	p.L178I	ENST00000356435		178	Tta/Ata	4/35	0.534999143913377	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.534999143913377	1		307	482	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410436	139410436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	197	541	1	ENST00000277541.6:c.1666G>A	p.Glu556Lys	p.E556K	ENST00000277541	NM_017617.3	556	Gaa/Aaa	10/34	0.534999143913377	1	FACETS	0.577	0.534	0.621	0.577	0.534	0.621	SUBCLONAL	1	TRUE	0	0.534999143913377	1		542	935	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	120	299	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.748	0.679	0.821	0.748	0.679	0.821	SUBCLONAL	1	TRUE	1	0.615561483559429	2		299	521	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0030227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	102	249	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	0.85	0.766	0.937	0.85	0.766	0.937	CLONAL	1	TRUE	1	0.615561483559429	2		249	390	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650770	67650770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1363179074	NA	P-0030227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	48	459	1	ENST00000264010.4:c.1075G>A	p.Ala359Thr	p.A359T	ENST00000264010	NM_006565.3	359	Gcc/Acc	5/12	1	2	FACETS	0.203	0.171	0.238	0.203	0.171	0.238	SUBCLONAL	1	TRUE	1	0.615561483559429	2		460	769	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685307	89685307	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123317	NA	P-0030227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	130	290	0	ENST00000371953.3:c.202T>C	p.Tyr68His	p.Y68H	ENST00000371953	NM_000314.4	68	Tac/Cac	3/9	0.122637002942349	3	FACETS	1	0.967	1	0.561	0.512	0.612	INDETERMINATE	1	TRUE	1	0.615561483559429	3		290	492	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390606	139390606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1052013977	NA	P-0030227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	104	762	0	ENST00000277541.6:c.7585G>A	p.Val2529Ile	p.V2529I	ENST00000277541	NM_017617.3	2529	Gtc/Atc	34/34	1	2	FACETS	0.291	0.259	0.324	0.291	0.259	0.324	SUBCLONAL	1	TRUE	1	0.615561483559429	2		762	1162	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602341	10602341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1178941219	NA	P-0030227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	198	643	2	ENST00000171111.5:c.1237C>T	p.Arg413Cys	p.R413C	ENST00000171111	NM_203500.1	413	Cgt/Tgt	3/6	1	2	FACETS	0.644	0.596	0.694	0.644	0.596	0.694	SUBCLONAL	1	TRUE	1	0.615561483559429	2		645	999	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368387	225368388	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	94	337	2	ENST00000264414.4:c.1358dup	p.Asn453LysfsTer5	p.N453Kfs*5	ENST00000264414	NM_003590.4	453	aac/aaAc	9/16	1	2	FACETS	0.576	0.514	0.642	0.576	0.514	0.642	SUBCLONAL	1	TRUE	1	0.615561483559429	2		339	530	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717714	89717714	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167662	NA	P-0030227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	170	419	1	ENST00000371953.3:c.740del	p.Leu247TyrfsTer9	p.L247Yfs*9	ENST00000371953	NM_000314.4	247	Tta/ta	7/9	0.122637002942349	3	FACETS	1	0.975	1	0.567	0.523	0.612	INDETERMINATE	1	TRUE	1	0.615561483559429	3		420	637	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420204	49420204	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	148	496	0	ENST00000301067.7:c.15545del	p.Gly5182AlafsTer61	p.G5182Afs*61	ENST00000301067	NM_003482.3	5182	gGc/gc	48/54	1	2	FACETS	0.609	0.556	0.663	0.609	0.556	0.663	SUBCLONAL	1	TRUE	1	0.615561483559429	2		496	790	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023581	27023582	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0030227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	127	471	0	ENST00000324856.7:c.690_691del	p.Leu231GlufsTer168	p.L231Efs*168	ENST00000324856	NM_006015.4	229	taCGcg/tacg	1/20	1	2	FACETS	0.59	0.535	0.648	0.59	0.535	0.648	SUBCLONAL	1	TRUE	1	0.615561483559429	2		471	699	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107224	27107225	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	76	315	0	ENST00000324856.7:c.6836dup	p.Phe2280ValfsTer105	p.F2280Vfs*105	ENST00000324856	NM_006015.4	2279	ctg/cTtg	20/20	1	2	FACETS	0.491	0.431	0.555	0.491	0.431	0.555	SUBCLONAL	1	TRUE	1	0.615561483559429	2		315	503	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500401	99500403	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs779842858	NA	P-0030227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	155	632	0	ENST00000268035.6:c.3836_3838del	p.Phe1279del	p.F1279del	ENST00000268035	NM_000875.3	1278	tcCTTc/tcc	21/21	1	2	FACETS	0.665	0.61	0.723	0.665	0.61	0.723	SUBCLONAL	1	TRUE	1	0.615561483559429	2		632	757	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831337	72831338	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCTGGGCCAGCGTTTGTGCTTGTTGTTGTTGTTGTTGTTGTT	novel	NA	P-0030227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	24	223	0	ENST00000268489.5:c.5201_5243dup	p.Gln1749ThrfsTer39	p.Q1749Tfs*39	ENST00000268489	NM_006885.3	1748	gcc/gcAACAACAACAACAACAACAACAAGCACAAACGCTGGCCCAGGCc	9/10	1	2	FACETS	0.209	0.163	0.262	0.209	0.163	0.262	SUBCLONAL	1	TRUE	1	0.615561483559429	2		223	373	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164748	36164749	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCGTG	novel	NA	P-0030227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	212	576	0	ENST00000300305.3:c.1122_1126dup	p.Arg376ProfsTer220	p.R376Pfs*220	ENST00000300305		376	cgc/cCACGCgc	8/8	1	2	FACETS	0.811	0.755	0.87	0.811	0.755	0.87	CLONAL	1	TRUE	1	0.615561483559429	2		576	849	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589596	67589608	+	protein_altering_variant	In_Frame_Del	DEL	CACTCAGTTTCAA	CACTCAGTTTCAA	AACT	novel	NA	P-0030227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	121	334	3	ENST00000274335.5:c.1359_1371delinsAACT	p.Asn453_Gln457delinsLysThr	p.N453_Q457delinsKT	ENST00000274335		453	aaCACTCAGTTTCAA/aaAACT	10/15	1	2	FACETS	0.804	0.73	0.881	0.804	0.73	0.881	CLONAL	1	TRUE	1	0.615561483559429	2		337	489	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591050	67591051	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTTGAAGAAGC	novel	NA	P-0030227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	64	269	0	ENST00000274335.5:c.1644_1654dup	p.Gln552ProfsTer2	p.Q552Pfs*2	ENST00000274335		548	gac/gaCTTGAAGAAGCc	12/15	1	2	FACETS	0.547	0.476	0.624	0.547	0.476	0.624	SUBCLONAL	1	TRUE	1	0.615561483559429	2		269	380	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413893	139413893	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1164392989	NA	P-0030227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	142	410	0	ENST00000277541.6:c.865+2C>T		p.X289_splice	ENST00000277541	NM_017617.3	289			1	2	FACETS	0.697	0.637	0.76	0.697	0.637	0.76	SUBCLONAL	1	TRUE	1	0.615561483559429	2		410	662	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061334	38061334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	290	656	1	ENST00000250448.2:c.655C>A	p.Arg219Ser	p.R219S	ENST00000250448	NM_004496.3	219	Cgc/Agc	2/2	1	2	FACETS	0.97	0.914	1	0.97	0.914	1	CLONAL	1	TRUE	1	0.585920783732995	2		657	1020	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0030229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	754	465	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.636411149956847	4	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	FALSE	1	0.636411149956847	4		465	1146	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839787	27839787	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	111	515	0	ENST00000328488.2:c.307G>A	p.Gly103Arg	p.G103R	ENST00000328488	NM_003533.2	103	Ggg/Agg	1/1	0.466972656188768	6	FACETS	1	0.97	1			1	CLONAL	1	FALSE	NA	0.636411149956847	6		515	658	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0030229-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	560	465	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.668692519671663	3	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.668692519671663	3		465	1000	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0030230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	146	545	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.303661689530641	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.31	1		545	712	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0030230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	94	359	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.31	2		359	540	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0030230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	41	179	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.809	0.676	0.955	0.809	0.676	0.955	CLONAL	1	TRUE	1	0.31	2		179	327	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0030230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	151	543	2	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.31	2		545	777	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965472	68965472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200682883	NA	P-0030230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	358	757	0	ENST00000288368.4:c.1084C>T	p.Arg362Trp	p.R362W	ENST00000288368	NM_024870.2	362	Cgg/Tgg	9/40	0.237708993417605	4	FACETS	0.84	0.796	0.884	0.84	0.796	0.884	CLONAL	3	TRUE	1	0.31	4		757	1201	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0030231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	168	350	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.44467291473121	3	FACETS	1	0.971	1	0.557	0.512	0.604	CLONAL	1	TRUE	1	0.44467291473121	3		350	829	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0030231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	157	241	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.219644079112648	3	FACETS	0.819	0.755	0.885	0.819	0.755	0.885	INDETERMINATE	2	TRUE	1	0.44467291473121	3		241	527	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757274881	NA	P-0030231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	429	696	0	ENST00000269305.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	144	Cag/Tag	5/11	NA	2	FACETS	0.922	0.882	0.963			1	INDETERMINATE	2	TRUE	NA	0.44467291473121	2		696	1046	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0030231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	89	232	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.219644079112648	3	FACETS	1	0.901	1	0.507	0.451	0.566	INDETERMINATE	1	TRUE	1	0.44467291473121	3		232	483	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0030231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	180	311	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.44467291473121	2		312	685	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593505	48593505	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	36	240	0	ENST00000342988.3:c.1256G>T	p.Gly419Val	p.G419V	ENST00000342988	NM_005359.5	419	gGg/gTg	10/12	0.444417438000191	1	FACETS	0.395	0.325	0.472	0.395	0.325	0.472	SUBCLONAL	1	TRUE	0	0.44467291473121	1		240	319	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855029	76855029	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1557085898	NA	P-0030231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	8	177	1	ENST00000373344.5:c.5807A>G	p.Lys1936Arg	p.K1936R	ENST00000373344	NM_000489.3	1936	aAg/aGg	25/35	0.44467291473121	2	FACETS	0.103	0.066	0.152			1	SUBCLONAL	1	TRUE	NA	0.44467291473121	2		178	348	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121912580	NA	P-0030231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	37	298	0	ENST00000342988.3:c.1157G>C	p.Gly386Ala	p.G386A	ENST00000342988	NM_005359.5	386	gGt/gCt	10/12	0.444417438000191	1	FACETS	0.336	0.277	0.402	0.336	0.277	0.402	SUBCLONAL	1	TRUE	0	0.44467291473121	1		298	385	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850813	63850813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779891226	NA	P-0030231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	43	401	0	ENST00000279873.7:c.1591G>A	p.Glu531Lys	p.E531K	ENST00000279873	NM_032199.2	531	Gag/Aag	10/10	0.444417438000191	1	FACETS	0.336	0.281	0.397	0.336	0.281	0.397	SUBCLONAL	1	TRUE	0	0.44467291473121	1		401	447	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29686031	29686043	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGGTAAGAAAAT	AAGGTAAGAAAAT	-	novel	NA	P-0030231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	26	232	0	ENST00000356175.3:c.8096_8097+11del		p.X2699_splice	ENST00000356175	NM_000267.3	2699		55/57	0.44467291473121	2	FACETS	0.276	0.218	0.342	0.138	0.109	0.171	SUBCLONAL	1	TRUE	0	0.44467291473121	2		232	424	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742552	145742552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	153	515	0	ENST00000428558.2:c.236G>A	p.Gly79Glu	p.G79E	ENST00000428558	NM_004260.3	79	gGg/gAg	4/22	0.44467291473121	4	FACETS	1	0.974	1	0.387	0.354	0.421	CLONAL	1	TRUE	1	0.44467291473121	4		515	857	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0030232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	139	502	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	1	2	FACETS	0.85	0.774	0.93	0.85	0.774	0.93	CLONAL	1	TRUE	1	0.39623968359747	2		502	825	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443870	52443870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	312	707	0	ENST00000460680.1:c.25G>A	p.Glu9Lys	p.E9K	ENST00000460680	NM_004656.3	9	Gag/Aag	1/17	0.283044797320384	2	FACETS	1	0.994	1	0.746	0.705	0.789	CLONAL	1	TRUE	0	0.39623968359747	2		707	1055	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578484	7578485	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1064793929	NA	P-0030233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	343	888	0	ENST00000269305.4:c.445dup	p.Ser149PhefsTer32	p.S149Ffs*32	ENST00000269305	NM_001126112.2	149	tcc/tTcc	5/11	0.235682768158163	2	FACETS	0.541	0.51	0.572	0.27	0.255	0.286	INDETERMINATE	1	TRUE	0	0.853463835553137	2		888	1487	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0030234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	26	237	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.429266882407477	1	FACETS	0.375	0.297	0.462	0.375	0.297	0.462	SUBCLONAL	1	TRUE	0	0.429266882407477	1		237	254	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027417	48027417	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	54	351	0	ENST00000234420.5:c.2295C>A	p.Cys765Ter	p.C765*	ENST00000234420	NM_000179.2	765	tgC/tgA	4/10	0.334643785394424	1	FACETS	0.433	0.37	0.502	0.433	0.37	0.502	SUBCLONAL	1	TRUE	0	0.429266882407477	1		351	456	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943727	71943727	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	TAA	novel	NA	P-0030234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	189	671	0	ENST00000298229.2:c.1770delinsTAA	p.Asn591LysfsTer31	p.N591Kfs*31	ENST00000298229	NM_001567.3	590	ctC/ctTAA	15/28	0.429266882407477	1	FACETS	0.906	0.84	0.975	0.906	0.84	0.975	CLONAL	1	TRUE	0	0.429266882407477	1		671	763	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714267	43714269	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	GTG	GTG	-	novel	NA	P-0030235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	67	701	0	ENST00000382044.4:c.3884_3886del	p.Ser1295_Gln1296delinsTer	p.S1295_Q1296delins*	ENST00000382044	NM_001141980.1	1295	tCACag/tag	19/28	0.191741484659036	4	FACETS	0.539	0.467	0.617	0.269	0.233	0.309	INDETERMINATE	1	TRUE	2	0.432965909529093	4		701	823	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526568	66526577	+	frameshift_variant	Frame_Shift_Del	DEL	GTTTTGTGTC	GTTTTGTGTC	-	novel	NA	P-0030235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	40	303	0	ENST00000358598.2:c.1124_1133del	p.Ser375AsnfsTer63	p.S375Nfs*63	ENST00000358598	NM_212471.2	375	aGTTTTGTGTCa/aa	11/11	1	2	FACETS	0.491	0.409	0.583	0.491	0.409	0.583	SUBCLONAL	1	TRUE	1	0.432965909529093	2		303	376	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	175	250	1	ENST00000257430.4:c.4199C>A	p.Ser1400Ter	p.S1400*	ENST00000257430	NM_000038.5	1400	tCg/tAg	16/16	0.448081465642558	2	FACETS	0.986	0.921	1	0.986	0.921	1	CLONAL	2	TRUE	0	0.448081465642558	2		251	396	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763251	59763251	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	176	607	0	ENST00000259008.2:c.2851del	p.Ile951LeufsTer34	p.I951Lfs*34	ENST00000259008	NM_032043.2	951	Att/tt	19/20	0.26535344577129	3	FACETS	0.8	0.741	0.861	0.8	0.741	0.861	INDETERMINATE	2	TRUE	1	0.448081465642558	3		607	601	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790026	40790026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1366458329	NA	P-0030236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	65	461	0	ENST00000373198.4:c.2705G>A	p.Arg902Lys	p.R902K	ENST00000373198	NM_133170.3	902	aGa/aAa	18/32	0.448081465642558	5	FACETS	0.434	0.375	0.499	0.109	0.093	0.125	SUBCLONAL	1	TRUE	1	0.448081465642558	5		461	1117	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	142	454	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		454	524	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0030238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	78	286	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.340374259207346	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.340374259207346	1		286	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0030238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	118	456	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.340374259207346	3	FACETS	1	0.98	1	0.666	0.602	0.733	CLONAL	1	TRUE	1	0.340374259207346	3		456	609	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0030238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	113	478	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.340374259207346	3	FACETS	1	0.974	1	0.621	0.56	0.685	CLONAL	1	TRUE	1	0.340374259207346	3		479	626	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0030238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	30	179	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.734	0.595	0.891	0.734	0.595	0.891	SUBCLONAL	1	TRUE	1	0.340374259207346	2		179	240	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0030238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	75	383	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.340374259207346	2		383	428	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120572	2120572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934872	NA	P-0030238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	325	517	0	ENST00000219476.3:c.1832G>A	p.Arg611Gln	p.R611Q	ENST00000219476	NM_000548.3	611	cGg/cAg	17/42	0.106242207408316	3	FACETS	1	0.981	1			1	INDETERMINATE	3	TRUE	NA	0.340374259207346	3		517	702	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710600	114710600	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	95	372	0	ENST00000543371.1:c.85G>T	p.Glu29Ter	p.E29*	ENST00000543371	NM_001198531.1	29	Gag/Tag	1/14	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.340374259207346	2		372	458	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509046	106509046	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	36	375	1	ENST00000359195.3:c.1040A>G	p.Glu347Gly	p.E347G	ENST00000359195	NM_002649.2	347	gAg/gGg	2/11	0.272627164647695	3	FACETS	0.459	0.377	0.552	0.23	0.188	0.276	SUBCLONAL	1	TRUE	1	0.340374259207346	3		376	539	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120820	115120821	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	75	367	0	ENST00000257566.3:c.185dup	p.Pro63AlafsTer48	p.P63Afs*48	ENST00000257566	NM_016569.3	62	aag/aaAg	1/8	0.227998483747015	4	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	2	0.2300965113189	4		367	347	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541523	29541523	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	27	447	0	ENST00000356175.3:c.1447G>T	p.Asp483Tyr	p.D483Y	ENST00000356175	NM_000267.3	483	Gac/Tac	13/57	0.2300965113189	5	FACETS	0.94	0.748	1	0.313	0.249	0.386	CLONAL	1	TRUE	2	0.2300965113189	5		447	336	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825395	134825395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371780361	NA	P-0030240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	78	411	0	ENST00000398015.3:c.911G>A	p.Arg304Gln	p.R304Q	ENST00000398015	NM_004441.4	304	cGg/cAg	4/16	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.2300965113189	2		411	612	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619281	37619281	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0030242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	221	390	0	ENST00000447079.4:c.957C>G	p.Tyr319Ter	p.Y319*	ENST00000447079	NM_015083.1	319	taC/taG	1/14	0.422225428804904	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.429665465128524	2		390	489	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577514	7577516	+	inframe_deletion	In_Frame_Del	DEL	GTG	GTG	-	novel	NA	P-0030242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	158	556	0	ENST00000269305.4:c.765_767del	p.Thr256del	p.T256del	ENST00000269305	NM_001126112.2	255	atCACa/ata	7/11	0.426291047416088	1	FACETS	0.987	0.909	1	0.987	0.909	1	CLONAL	1	TRUE	0	0.429665465128524	1		556	585	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60795898	60795898	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	125	452	0	ENST00000333681.4:c.680G>C	p.Gly227Ala	p.G227A	ENST00000333681		227	gGa/gCa	3/3	NA	2	FACETS	0.824	0.747	0.905			1	INDETERMINATE	1	TRUE	NA	0.429665465128524	2		452	706	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030639	11030639	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	126	410	0	ENST00000327064.4:c.1193C>T	p.Ser398Phe	p.S398F	ENST00000327064	NM_199141.1	398	tCc/tTc	10/16	NA	2	FACETS	1	0.911	1			1	INDETERMINATE	1	TRUE	NA	0.429665465128524	2		410	585	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912362	97912362	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs773272931	NA	P-0030242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	95	329	0	ENST00000289081.3:c.529C>G	p.Pro177Ala	p.P177A	ENST00000289081	NM_000136.2	177	Ccc/Gcc	7/15	1	2	FACETS	0.888	0.794	0.988	0.888	0.794	0.988	CLONAL	1	TRUE	1	0.429665465128524	2		329	498	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0030243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	125	712	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.390419606341696	3	FACETS	0.79	0.725	0.858	0.79	0.725	0.858	SUBCLONAL	2	TRUE	1	0.606123510098176	3		712	340	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100310	157100310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1309774100	NA	P-0030243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	61	277	0	ENST00000346085.5:c.1247C>T	p.Thr416Ile	p.T416I	ENST00000346085	NM_020732.3	416	aCc/aTc	1/20	0.350415511671378	2	FACETS	1	0.895	1	0.511	0.448	0.577	INDETERMINATE	1	TRUE	0	0.606123510098176	2		277	197	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772200	68772223	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GTCTCCTCTTGGCTCTGCCAGGAG	GTCTCCTCTTGGCTCTGCCAGGAG	A	novel	NA	P-0030243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	98	607	0	ENST00000261769.5:c.49_72delinsA	p.Val17ThrfsTer9	p.V17Tfs*9	ENST00000261769	NM_004360.3	17	GTCTCCTCTTGGCTCTGCCAGGAG/A	2/16	0.616943407426041	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.606123510098176	1		607	191	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	74	350	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.477	0.418	0.54	0.477	0.418	0.54	SUBCLONAL	1	TRUE	1	0.60838238368685	2		350	510	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	64	369	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.458	0.398	0.524	0.458	0.398	0.524	SUBCLONAL	1	TRUE	1	0.60838238368685	2		369	459	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	175	535	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.99	0.917	1	0.99	0.917	1	CLONAL	1	TRUE	1	0.60838238368685	2		536	581	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	149	507	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.546	0.499	0.596	0.546	0.499	0.596	SUBCLONAL	1	TRUE	1	0.60838238368685	2		511	897	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521525	46521525	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	117	426	0	ENST00000262741.5:c.883del	p.Met295Ter	p.M295*	ENST00000262741	NM_003629.3	295	Atg/tg	7/10	1	2	FACETS	0.475	0.428	0.525	0.475	0.428	0.525	SUBCLONAL	1	TRUE	1	0.60838238368685	2		426	809	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974721	21974721	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	55	242	0	ENST00000304494.5:c.106del	p.Ala36ArgfsTer17	p.A36Rfs*17	ENST00000304494	NM_000077.4	36	Gcg/cg	1/3	1	2	FACETS	0.58	0.499	0.667	0.58	0.499	0.667	SUBCLONAL	1	TRUE	1	0.60838238368685	2		242	312	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030585	47030585	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs377667483	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	81	611	1	ENST00000377604.3:c.360T>G	p.Asp120Glu	p.D120E	ENST00000377604	NM_001204468.1	120	gaT/gaG	4/24	1	2	FACETS	0.434	0.382	0.489	0.434	0.382	0.489	SUBCLONAL	1	TRUE	1	0.60838238368685	2		612	614	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	49	402	0	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	0.371	0.315	0.433	0.371	0.315	0.433	SUBCLONAL	1	TRUE	1	0.60838238368685	2		402	434	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459531	50459531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	64	282	0	ENST00000331340.3:c.820C>T	p.Arg274Cys	p.R274C	ENST00000331340	NM_006060.4	274	Cgt/Tgt	7/8	1	2	FACETS	0.41	0.355	0.469	0.41	0.355	0.469	SUBCLONAL	1	TRUE	1	0.60838238368685	2		282	513	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223131	5223131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375155482	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	113	591	1	ENST00000357368.4:c.2672C>T	p.Thr891Met	p.T891M	ENST00000357368	NM_002850.3	891	aCg/aTg	18/38	1	2	FACETS	0.561	0.506	0.62	0.561	0.506	0.62	SUBCLONAL	1	TRUE	1	0.60838238368685	2		592	662	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	134	527	7	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.63	0.573	0.69	0.63	0.573	0.69	SUBCLONAL	1	TRUE	1	0.60838238368685	2		534	699	SUCCESS
AR	367	MSKCC	GRCh37	X	66765159	66765194	+	inframe_deletion	In_Frame_Del	DEL	GCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA	GCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA	-	rs3032358	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	16	234	0	ENST00000374690.3:c.204_239del	p.Gln69_Gln80del	p.Q69_Q80del	ENST00000374690	NM_000044.3	57	ctGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAg/ctg	1/8	1	2	FACETS	0.216	0.159	0.283	0.216	0.159	0.283	SUBCLONAL	1	TRUE	1	0.60838238368685	2		234	244	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795187	42795187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377759151	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	60	638	0	ENST00000575354.2:c.2267C>T	p.Ala756Val	p.A756V	ENST00000575354	NM_015125.3	756	gCg/gTg	10/20	0.310275346930675	3	FACETS	0.329	0.282	0.379	0.164	0.141	0.19	INDETERMINATE	1	TRUE	1	0.60838238368685	3		638	783	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	109	455	0	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	1	2	FACETS	0.582	0.523	0.643	0.582	0.523	0.643	SUBCLONAL	1	TRUE	1	0.60838238368685	2		455	616	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966593	36966593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	79	436	0	ENST00000358127.4:c.733C>T	p.His245Tyr	p.H245Y	ENST00000358127	NM_001280556.1	245	Cac/Tac	6/10	1	2	FACETS	0.452	0.398	0.511	0.452	0.398	0.511	SUBCLONAL	1	TRUE	1	0.60838238368685	2		436	574	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403254	213403254	+	frameshift_variant,start_lost,start_retained_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	61	325	0	ENST00000342788.4:c.1del	p.Met1?	p.M1?	ENST00000342788	NM_005235.2	1	Atg/tg	1/28	1	2	FACETS	0.489	0.423	0.56	0.489	0.423	0.56	SUBCLONAL	1	TRUE	1	0.60838238368685	2		325	410	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166202	118166202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	68	378	0	ENST00000369448.3:c.712G>A	p.Glu238Lys	p.E238K	ENST00000369448	NM_017709.3	238	Gaa/Aaa	2/2	1	2	FACETS	0.49	0.428	0.558	0.49	0.428	0.558	SUBCLONAL	1	TRUE	1	0.60838238368685	2		378	456	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465301	120465301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758689134	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	62	363	0	ENST00000256646.2:c.4960G>A	p.Ala1654Thr	p.A1654T	ENST00000256646	NM_024408.3	1654	Gcc/Acc	27/34	1	2	FACETS	0.473	0.41	0.541	0.473	0.41	0.541	SUBCLONAL	1	TRUE	1	0.60838238368685	2		363	431	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514870	44514870	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	57	349	0	ENST00000291552.4:c.377C>T	p.Ala126Val	p.A126V	ENST00000291552	NM_006758.2	126	gCt/gTt	6/8	1	2	FACETS	0.356	0.305	0.411	0.356	0.305	0.411	SUBCLONAL	1	TRUE	1	0.60838238368685	2		349	527	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971139	21971139	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730881679	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	51	290	1	ENST00000579755.1:c.262C>T	p.Arg88Ter	p.R88*	ENST00000579755		88	Cga/Tga	2/3	1				0.371	0.506				SUBCLONAL	1	TRUE	1	0.60838238368685	2		291	385	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576486	67576487	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	68	393	0	ENST00000274335.5:c.770dup	p.Asn257LysfsTer10	p.N257Kfs*10	ENST00000274335		255	-/A	5/15	1	2	FACETS	0.439	0.383	0.5	0.439	0.383	0.5	SUBCLONAL	1	TRUE	1	0.60838238368685	2		393	509	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	80	515	1	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			0.310275346930675	3	FACETS	0.541	0.476	0.61	0.27	0.238	0.305	INDETERMINATE	1	TRUE	1	0.60838238368685	3		516	634	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925402	114925402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748822481	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	121	533	1	ENST00000543371.1:c.1485del	p.Ser496ProfsTer5	p.S496Pfs*5	ENST00000543371	NM_001198531.1	494	Ccc/cc	14/14	1	2	FACETS	0.553	0.5	0.609	0.553	0.5	0.609	SUBCLONAL	1	TRUE	1	0.60838238368685	2		534	719	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911005	94911007	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	109	580	0	ENST00000536441.1:c.1123_1125del	p.Leu375del	p.L375del	ENST00000536441	NM_144665.3	375	CTT/-	8/10	1	2	FACETS	0.475	0.427	0.527	0.475	0.427	0.527	SUBCLONAL	1	TRUE	1	0.60838238368685	2		580	754	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240657	133240657	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1337524033	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	90	482	1	ENST00000320574.5:c.2639C>T	p.Thr880Met	p.T880M	ENST00000320574	NM_006231.2	880	aCg/aTg	23/49	1	2	FACETS	0.483	0.429	0.541	0.483	0.429	0.541	SUBCLONAL	1	TRUE	1	0.60838238368685	2		483	612	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324463	31324463	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	85	407	0	ENST00000412585.2:c.343+2T>C		p.X115_splice	ENST00000412585	NM_005514.6	115			1	2	FACETS	0.523	0.463	0.587	0.523	0.463	0.587	SUBCLONAL	1	TRUE	1	0.60838238368685	2		407	534	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633565	69633565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	71	170	0	ENST00000334134.2:c.137G>A	p.Arg46His	p.R46H	ENST00000334134	NM_005247.2	46	cGc/cAc	1/3	1	2	FACETS	0.855	0.754	0.961	0.855	0.754	0.961	CLONAL	1	TRUE	1	0.60838238368685	2		170	273	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858037	9858037	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	63	472	0	ENST00000330684.3:c.3364G>A	p.Gly1122Ser	p.G1122S	ENST00000330684	NM_001134407.1	1122	Ggt/Agt	13/13	1	2	FACETS	0.409	0.354	0.469	0.409	0.354	0.469	SUBCLONAL	1	TRUE	1	0.60838238368685	2		472	506	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821673	72821673	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	43	177	0	ENST00000268489.5:c.10502T>C	p.Val3501Ala	p.V3501A	ENST00000268489	NM_006885.3	3501	gTg/gCg	10/10	1	2	FACETS	0.686	0.581	0.8	0.686	0.581	0.8	SUBCLONAL	1	TRUE	1	0.60838238368685	2		177	206	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976166	18976166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1010786745	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	112	563	0	ENST00000262803.5:c.2926G>A	p.Val976Met	p.V976M	ENST00000262803	NM_002911.3	976	Gtg/Atg	21/24	1	2	FACETS	0.467	0.42	0.517	0.467	0.42	0.517	SUBCLONAL	1	TRUE	1	0.60838238368685	2		563	788	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119717	70119717	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	96	600	2	ENST00000245479.2:c.723del	p.Thr243ProfsTer10	p.T243Pfs*10	ENST00000245479	NM_000346.3	240	aCc/ac	3/3	1	2	FACETS	0.46	0.41	0.513	0.46	0.41	0.513	SUBCLONAL	1	TRUE	1	0.60838238368685	2		602	686	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038935	12038935	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	73	359	0	ENST00000396373.4:c.1228G>T	p.Glu410Ter	p.E410*	ENST00000396373	NM_001987.4	410	Gag/Tag	7/8	0.167199441386367	4	FACETS	0.71	0.621	0.804	0.355	0.31	0.402	INDETERMINATE	1	TRUE	2	0.60838238368685	4		359	544	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986774	36986774	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1448653785	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	23	62	0	ENST00000354822.5:c.915del	p.Ala306ArgfsTer75	p.A306Rfs*75	ENST00000354822	NM_001079668.2	305	ccC/cc	3/3	1	2	FACETS	0.482	0.379	0.598	0.482	0.379	0.598	SUBCLONAL	1	TRUE	1	0.60838238368685	2		62	157	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21630862	21630862	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202110155	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	57	515	0	ENST00000421138.2:c.742G>A	p.Ala248Thr	p.A248T	ENST00000421138		248	Gca/Aca	8/16	1	2	FACETS	0.243	0.208	0.282	0.243	0.208	0.282	SUBCLONAL	1	TRUE	1	0.60838238368685	2		515	771	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664720	138664720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	23	165	0	ENST00000330315.3:c.845C>T	p.Ala282Val	p.A282V	ENST00000330315	NM_023067.3	282	gCc/gTc	1/1	1	2	FACETS	0.332	0.259	0.415	0.332	0.259	0.415	SUBCLONAL	1	TRUE	1	0.60838238368685	2		165	228	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775780	9775780	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765031777	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	91	584	0	ENST00000377346.4:c.323G>A	p.Arg108His	p.R108H	ENST00000377346	NM_005026.3	108	cGc/cAc	4/24	1	2	FACETS	0.448	0.398	0.501	0.448	0.398	0.501	SUBCLONAL	1	TRUE	1	0.60838238368685	2		584	668	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809860	36809860	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	84	454	0	ENST00000373129.3:c.745C>T	p.Pro249Ser	p.P249S	ENST00000373129	NM_032017.1	249	Ccg/Tcg	9/12	1	2	FACETS	0.504	0.446	0.566	0.504	0.446	0.566	SUBCLONAL	1	TRUE	1	0.60838238368685	2		454	548	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612752	228612752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	105	510	0	ENST00000366696.1:c.275C>T	p.Ala92Val	p.A92V	ENST00000366696	NM_003493.2	92	gCg/gTg	1/1	0.310275346930675	3	FACETS	0.563	0.504	0.626	0.282	0.252	0.313	INDETERMINATE	1	TRUE	1	0.60838238368685	3		510	799	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114901046	114901046	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	78	391	0	ENST00000543371.1:c.656A>G	p.His219Arg	p.H219R	ENST00000543371	NM_001198531.1	219	cAc/cGc	6/14	1	2	FACETS	0.435	0.383	0.492	0.435	0.383	0.492	SUBCLONAL	1	TRUE	1	0.60838238368685	2		391	589	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023179	1023179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	86	447	1	ENST00000358495.3:c.1076C>T	p.Ala359Val	p.A359V	ENST00000358495	NM_134424.2	359	gCc/gTc	11/12	NA	2	FACETS	0.43	0.38	0.483			1	INDETERMINATE	1	TRUE	NA	0.60838238368685	2		448	658	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435113	49435113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764604229	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	38	466	0	ENST00000301067.7:c.6440C>T	p.Ala2147Val	p.A2147V	ENST00000301067	NM_003482.3	2147	gCg/gTg	31/54	1	2	FACETS	0.282	0.233	0.337	0.282	0.233	0.337	SUBCLONAL	1	TRUE	1	0.60838238368685	2		466	443	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435993	110435993	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	128	656	0	ENST00000375856.3:c.2408A>G	p.Tyr803Cys	p.Y803C	ENST00000375856	NM_003749.2	803	tAc/tGc	1/2	0.607417418971832	3	FACETS	0.565	0.511	0.621	0.282	0.255	0.311	SUBCLONAL	1	TRUE	1	0.60838238368685	3		656	972	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988193	36988193	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1009176098	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	52	341	0	ENST00000354822.5:c.460G>A	p.Ala154Thr	p.A154T	ENST00000354822	NM_001079668.2	154	Gcc/Acc	2/3	1	2	FACETS	0.42	0.358	0.487	0.42	0.358	0.487	SUBCLONAL	1	TRUE	1	0.60838238368685	2		341	407	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483977	88483977	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	61	324	1	ENST00000360948.2:c.1593G>T	p.Gln531His	p.Q531H	ENST00000360948	NM_001012338.2	531	caG/caT	14/19	1	2	FACETS	0.426	0.368	0.489	0.426	0.368	0.489	SUBCLONAL	1	TRUE	1	0.60838238368685	2		325	471	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799380	88799380	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1397502133	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	37	244	0	ENST00000360948.2:c.5A>G	p.Asp2Gly	p.D2G	ENST00000360948	NM_001012338.2	2	gAt/gGt	2/19	1	2	FACETS	0.419	0.347	0.5	0.419	0.347	0.5	SUBCLONAL	1	TRUE	1	0.60838238368685	2		244	290	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99452071	99452071	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	28	372	0	ENST00000268035.6:c.1405A>G	p.Lys469Glu	p.K469E	ENST00000268035	NM_000875.3	469	Aaa/Gaa	6/21	1	2	FACETS	0.178	0.142	0.22	0.178	0.142	0.22	SUBCLONAL	1	TRUE	1	0.60838238368685	2		372	516	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632773	23632773	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	37	436	0	ENST00000261584.4:c.3023C>A	p.Pro1008His	p.P1008H	ENST00000261584	NM_024675.3	1008	cCc/cAc	10/13	1	2	FACETS	0.217	0.178	0.26	0.217	0.178	0.26	SUBCLONAL	1	TRUE	1	0.60838238368685	2		436	561	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40456407	40456407	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	104	506	0	ENST00000345506.4:c.1217A>G	p.His406Arg	p.H406R	ENST00000345506	NM_003152.3	406	cAc/cGc	11/20	1	2	FACETS	0.55	0.493	0.61	0.55	0.493	0.61	SUBCLONAL	1	TRUE	1	0.60838238368685	2		506	622	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621884	1621884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	81	582	1	ENST00000344749.5:c.908G>A	p.Gly303Asp	p.G303D	ENST00000344749	NM_001136139.2	303	gGc/gAc	11/19	1	2	FACETS	0.426	0.375	0.48	0.426	0.375	0.48	SUBCLONAL	1	TRUE	1	0.60838238368685	2		583	625	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383241	42383242	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	101	560	0	ENST00000221972.3:c.263dup	p.Asn88LysfsTer94	p.N88Kfs*94	ENST00000221972	NM_021601.3	87	-/A	2/5	0.310275346930675	3	FACETS	0.629	0.563	0.7	0.315	0.281	0.35	INDETERMINATE	1	TRUE	1	0.60838238368685	3		560	688	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918792	50918792	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	186	610	0	ENST00000440232.2:c.2662A>G	p.Thr888Ala	p.T888A	ENST00000440232	NM_002691.3	888	Acc/Gcc	21/27	0.310275346930675	3	FACETS	1	0.954	1	0.521	0.482	0.562	INDETERMINATE	1	TRUE	1	0.60838238368685	3		610	765	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919885	50919885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775264944	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	164	544	0	ENST00000440232.2:c.2972G>A	p.Cys991Tyr	p.C991Y	ENST00000440232	NM_002691.3	991	tGc/tAc	24/27	0.310275346930675	3	FACETS	0.969	0.891	1	0.484	0.445	0.525	INDETERMINATE	1	TRUE	1	0.60838238368685	3		544	726	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39347478	39347478	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1329641866	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	55	255	0	ENST00000402219.2:c.86del	p.Lys29ArgfsTer23	p.K29Rfs*23	ENST00000402219	NM_005633.3	29	aAg/ag	1/23	1	2	FACETS	0.45	0.386	0.519	0.45	0.386	0.519	SUBCLONAL	1	TRUE	1	0.60838238368685	2		255	402	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630454	47630454	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1553348804	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	87	577	0	ENST00000233146.2:c.124T>C	p.Phe42Leu	p.F42L	ENST00000233146	NM_000251.2	42	Ttc/Ctc	1/16	1	2	FACETS	0.454	0.402	0.509	0.454	0.402	0.509	SUBCLONAL	1	TRUE	1	0.60838238368685	2		577	630	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121317	29121317	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	47	528	1	ENST00000328354.6:c.358del	p.Ser120AlafsTer11	p.S120Afs*11	ENST00000328354	NM_007194.3	120	Agc/gc	3/15	1	2	FACETS	0.192	0.161	0.226	0.192	0.161	0.226	SUBCLONAL	1	TRUE	1	0.60838238368685	2		529	805	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573722	41573722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771512182	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	101	574	1	ENST00000263253.7:c.6007C>T	p.Pro2003Ser	p.P2003S	ENST00000263253	NM_001429.3	2003	Ccc/Tcc	31/31	1	2	FACETS	0.514	0.46	0.571	0.514	0.46	0.571	SUBCLONAL	1	TRUE	1	0.60838238368685	2		575	646	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713915	30713915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	78	356	0	ENST00000295754.5:c.1240G>A	p.Ala414Thr	p.A414T	ENST00000295754	NM_003242.5	414	Gct/Act	4/7	1	2	FACETS	0.611	0.539	0.687	0.611	0.539	0.687	SUBCLONAL	1	TRUE	1	0.60838238368685	2		356	420	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952087	178952087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	82	342	0	ENST00000263967.3:c.3142C>T	p.His1048Tyr	p.H1048Y	ENST00000263967	NM_006218.2	1048	Cat/Tat	21/21	1	2	FACETS	0.607	0.538	0.681	0.607	0.538	0.681	SUBCLONAL	1	TRUE	1	0.60838238368685	2		342	444	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139799	55139799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764214258	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	63	436	0	ENST00000257290.5:c.1460G>A	p.Arg487His	p.R487H	ENST00000257290	NM_006206.4	487	cGt/cAt	10/23	1	2	FACETS	0.349	0.301	0.4	0.349	0.301	0.4	SUBCLONAL	1	TRUE	1	0.60838238368685	2		436	594	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539619	187539619	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	59	280	0	ENST00000441802.2:c.8121C>A	p.Phe2707Leu	p.F2707L	ENST00000441802	NM_005245.3	2707	ttC/ttA	10/27	1	2	FACETS	0.499	0.43	0.572	0.499	0.43	0.572	SUBCLONAL	1	TRUE	1	0.60838238368685	2		280	389	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264630	1264630	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	90	558	0	ENST00000310581.5:c.2732A>G	p.Asp911Gly	p.D911G	ENST00000310581	NM_198253.2	911	gAc/gGc	11/16	1	2	FACETS	0.414	0.367	0.465	0.414	0.367	0.465	SUBCLONAL	1	TRUE	1	0.60838238368685	2		558	714	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518089	176518089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777645394	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	89	512	0	ENST00000292408.4:c.587G>A	p.Arg196His	p.R196H	ENST00000292408	NM_213647.1	196	cGc/cAc	5/18	1	2	FACETS	0.464	0.411	0.52	0.464	0.411	0.52	SUBCLONAL	1	TRUE	1	0.60838238368685	2		512	631	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528666	157528666	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	80	530	0	ENST00000346085.5:c.6391T>C	p.Ser2131Pro	p.S2131P	ENST00000346085	NM_020732.3	2131	Tcc/Ccc	20/20	1	2	FACETS	0.413	0.363	0.466	0.413	0.363	0.466	SUBCLONAL	1	TRUE	1	0.60838238368685	2		530	637	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418998	116418998	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	42	216	0	ENST00000397752.3:c.3509del	p.Arg1170GlnfsTer9	p.R1170Qfs*9	ENST00000397752	NM_000245.2	1170	cGa/ca	17/21	1	2	FACETS	0.525	0.441	0.617	0.525	0.441	0.617	SUBCLONAL	1	TRUE	1	0.60838238368685	2		216	263	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372062	55372062	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	62	335	0	ENST00000297316.4:c.752A>G	p.Tyr251Cys	p.Y251C	ENST00000297316	NM_022454.3	251	tAc/tGc	2/2	1	2	FACETS	0.459	0.397	0.526	0.459	0.397	0.526	SUBCLONAL	1	TRUE	1	0.60838238368685	2		335	444	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982704	90982704	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	84	279	0	ENST00000265433.3:c.784T>C	p.Phe262Leu	p.F262L	ENST00000265433	NM_002485.4	262	Ttc/Ctc	7/16	1	2	FACETS	0.479	0.424	0.539	0.479	0.424	0.539	SUBCLONAL	1	TRUE	1	0.60838238368685	2		279	576	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5055691	5055691	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	72	270	0	ENST00000381652.3:c.959T>C	p.Phe320Ser	p.F320S	ENST00000381652	NM_004972.3	320	tTt/tCt	8/25	1	2	FACETS	0.599	0.526	0.677	0.599	0.526	0.677	SUBCLONAL	1	TRUE	1	0.60838238368685	2		270	395	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080345	5080345	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	24	251	0	ENST00000381652.3:c.2248G>T	p.Gly750Ter	p.G750*	ENST00000381652	NM_004972.3	750	Gga/Tga	17/25	1	2	FACETS	0.199	0.156	0.25	0.199	0.156	0.25	SUBCLONAL	1	TRUE	1	0.60838238368685	2		251	396	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412517	80412517	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	76	271	0	ENST00000286548.4:c.524C>T	p.Thr175Met	p.T175M	ENST00000286548	NM_002072.3	175	aCg/aTg	4/7	1	2	FACETS	0.589	0.519	0.664	0.589	0.519	0.664	SUBCLONAL	1	TRUE	1	0.60838238368685	2		271	424	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612190	189612190	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	203	530	0	ENST00000264731.3:c.1942C>T	p.Gln648Ter	p.Q648*	ENST00000264731	NM_003722.4	648	Cag/Tag	14/14	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.641345608534204	2		530	630	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156863	106156863	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	184	526	0	ENST00000380013.4:c.1765del	p.Ile589PhefsTer12	p.I589Ffs*12	ENST00000380013	NM_001127208.2	588	tcA/tc	3/11	1	2	FACETS	0.864	0.801	0.929	0.864	0.801	0.929	CLONAL	1	TRUE	1	0.641345608534204	2		526	664	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0030248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	133	283	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.476662181884883	2		283	508	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0030248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	198	461	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.285511082639583	1	FACETS	0.968	0.9	1	0.968	0.9	1	INDETERMINATE	1	TRUE	0	0.476662181884883	1		461	654	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0030248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	72	336	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.514	0.449	0.584	0.514	0.449	0.584	SUBCLONAL	1	TRUE	1	0.476662181884883	2		336	588	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479322	50479322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	130	259	0	ENST00000394963.4:c.170C>T	p.Ala57Val	p.A57V	ENST00000394963	NM_003076.4	57	gCc/gTc	1/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.476662181884883	2		259	462	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615815	1615815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	171	323	0	ENST00000344749.5:c.1456G>A	p.Gly486Arg	p.G486R	ENST00000344749	NM_001136139.2	486	Ggg/Agg	17/19	0.298755570425831	3	FACETS	1	0.988	1	0.466	0.431	0.503	CLONAL	1	TRUE	0	0.476662181884883	3		323	635	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376338	15376338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	288	690	0	ENST00000263377.2:c.676C>T	p.Pro226Ser	p.P226S	ENST00000263377	NM_058243.2	226	Cct/Tct	5/20	0.298755570425831	3	FACETS	1	0.988	1	0.402	0.377	0.427	CLONAL	1	TRUE	0	0.476662181884883	3		690	1242	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443884	52443884	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1559593389	NA	P-0030248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	208	426	0	ENST00000460680.1:c.11del	p.Gly4AlafsTer68	p.G4Afs*68	ENST00000460680	NM_004656.3	4	gGc/gc	1/17	0.476662181884883	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.476662181884883	1		426	609	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0030249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	281	546	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.276811045636618	3	FACETS	1	0.955	1			1	CLONAL	2	TRUE	NA	0.388895521722904	3		546	850	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248151	110248151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	70	371	0	ENST00000374672.4:c.1321G>A	p.Asp441Asn	p.D441N	ENST00000374672	NM_004235.4	441	Gat/Aat	5/5	1	2	FACETS	0.629	0.549	0.716	0.629	0.549	0.716	SUBCLONAL	1	TRUE	1	0.388895521722904	2		371	572	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844155	68844155	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	86	600	0	ENST00000261769.5:c.743T>G	p.Ile248Ser	p.I248S	ENST00000261769	NM_004360.3	248	aTt/aGt	6/16	0.282337326176086	1	FACETS	0.545	0.482	0.612	0.545	0.482	0.612	SUBCLONAL	1	TRUE	0	0.388895521722904	1		600	654	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0030255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	39	283	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.782	0.647	0.933	0.782	0.647	0.933	CLONAL	1	TRUE	1	0.17	2		283	587	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256530	+	missense_variant	Missense_Mutation	DNP	TG	TG	CT	rs1057519834	NA	P-0030255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	20	663	1	ENST00000369535.4:c.181_182delinsAG	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	CAa/AGa	3/7	1	2	FACETS	0.332	0.253	0.426	0.332	0.253	0.426	SUBCLONAL	1	TRUE	1	0.17	2		664	708	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953742	48953742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1131690851	NA	P-0030255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	26	303	0	ENST00000267163.4:c.1345G>A	p.Gly449Arg	p.G449R	ENST00000267163	NM_000321.2	449	Gga/Aga	14/27	1	2	FACETS	0.892	0.707	1	0.892	0.707	1	CLONAL	1	TRUE	1	0.17	2		303	343	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	49	622	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.206576847892064	3	FACETS	0.82	0.694	0.96	0.41	0.347	0.48	CLONAL	1	TRUE	1	0.206576847892064	3		622	638	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	60	582	1	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.806	0.693	0.929	0.806	0.693	0.929	CLONAL	1	TRUE	1	0.206576847892064	2		583	721	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1403	161	714	0	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	1	2	FACETS	0.997	0.911	1	0.997	0.911	1	CLONAL	1	TRUE	1	0.206576847892064	2		714	1564	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878127	48878127	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1276653645	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	116	154	0	ENST00000267163.4:c.83del	p.Pro28LeufsTer37	p.P28Lfs*37	ENST00000267163	NM_000321.2	27	Ccc/cc	1/27	1	2	FACETS	0.808	0.729	0.891	1	0.986	1	CLONAL	2	TRUE	1	0.206576847892064	2		154	695	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33427997	33427997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	102	650	2	ENST00000345365.6:c.962C>T	p.Ala321Val	p.A321V	ENST00000345365	NM_002878.3	321	gCc/gTc	10/10	1	2	FACETS	0.822	0.733	0.918	0.822	0.733	0.918	CLONAL	1	TRUE	1	0.206576847892064	2		652	1201	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598066	55598066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201165084	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	58	488	0	ENST00000288135.5:c.2263G>A	p.Ala755Thr	p.A755T	ENST00000288135	NM_000222.2	755	Gcc/Acc	16/21	1	2	FACETS	0.677	0.58	0.783	0.677	0.58	0.783	SUBCLONAL	1	TRUE	1	0.206576847892064	2		488	830	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430901	181430901	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1749	531	781	1	ENST00000325404.1:c.758del	p.Pro253LeufsTer21	p.P253Lfs*21	ENST00000325404	NM_003106.3	251	agC/ag	1/1	0.206576847892064	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	1	0.206576847892064	3		782	2280	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138915	64138915	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1513	218	671	3	ENST00000334205.4:c.2287del	p.Arg763AlafsTer21	p.R763Afs*21	ENST00000334205	NM_003942.2	761	gCc/gc	17/17	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.206576847892064	2		674	1731	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458435	120458436	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs771237928	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	102	500	0	ENST00000256646.2:c.6909dup	p.Ile2304HisfsTer9	p.I2304Hfs*9	ENST00000256646	NM_024408.3	2303	-/C	34/34	1	2	FACETS	0.926	0.827	1	0.926	0.827	1	CLONAL	1	TRUE	1	0.206576847892064	2		500	1066	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115751	8115751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	95	584	0	ENST00000346208.3:c.1097G>A	p.Arg366Gln	p.R366Q	ENST00000346208		366	cGa/cAa	6/6	1	2	FACETS	0.852	0.756	0.954	0.852	0.756	0.954	CLONAL	1	TRUE	1	0.206576847892064	2		584	1080	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817414	39817414	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542019196	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	113	459	1	ENST00000288319.7:c.149G>A	p.Arg50His	p.R50H	ENST00000288319	NM_182918.3	50	cGc/cAc	2/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.206576847892064	2		460	959	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374909	149374909	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1638	232	589	0	ENST00000360632.3:c.185C>G	p.Ser62Trp	p.S62W	ENST00000360632	NM_015472.4	62	tCg/tGg	2/7	0.206576847892064	3	FACETS	1	0.989	1	0.663	0.615	0.712	CLONAL	1	TRUE	1	0.206576847892064	3		589	1870	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795061	242795061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1203794937	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1795	212	961	0	ENST00000334409.5:c.148G>A	p.Ala50Thr	p.A50T	ENST00000334409	NM_005018.2	50	Gcc/Acc	2/5	0.206576847892064	1	FACETS	0.917	0.848	0.989	0.917	0.848	0.989	CLONAL	1	TRUE	0	0.206576847892064	1		961	2007	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421039	49421039	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398123721	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	107	522	1	ENST00000301067.7:c.14710C>T	p.Arg4904Ter	p.R4904*	ENST00000301067	NM_003482.3	4904	Cga/Tga	48/54	1	2	FACETS	0.979	0.876	1	0.979	0.876	1	CLONAL	1	TRUE	1	0.206576847892064	2		523	1058	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245435	133245435	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs754925525	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1387	128	708	0	ENST00000320574.5:c.1885del	p.Ala629ProfsTer8	p.A629Pfs*8	ENST00000320574	NM_006231.2	629	Gcc/cc	17/49	0.202163039940014	3	FACETS	0.902	0.815	0.996	0.451	0.407	0.498	CLONAL	1	TRUE	1	0.206576847892064	3		708	1515	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158131	27158131	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772321726	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	79	494	0	ENST00000380036.4:c.355C>T	p.Arg119Cys	p.R119C	ENST00000380036	NM_000459.3	119	Cgt/Tgt	2/23	1	2	FACETS	0.867	0.761	0.981	0.867	0.761	0.981	CLONAL	1	TRUE	1	0.206576847892064	2		494	882	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100464	2100464	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767626323	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	80	641	5	ENST00000219476.3:c.202G>A	p.Ala68Thr	p.A68T	ENST00000219476	NM_000548.3	68	Gca/Aca	3/42	1	2	FACETS	0.656	0.576	0.744	0.656	0.576	0.744	SUBCLONAL	1	TRUE	1	0.206576847892064	2		646	1180	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643503	38643503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057518683	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	76	658	0	ENST00000299084.4:c.973C>T	p.Arg325Ter	p.R325*	ENST00000299084	NM_152594.2	325	Cga/Tga	7/7	1	2	FACETS	0.714	0.625	0.811	0.714	0.625	0.811	SUBCLONAL	1	TRUE	1	0.206576847892064	2		658	1030	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89791150	89791151	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	97	134	0	ENST00000336032.3:c.539_540del	p.Glu180GlyfsTer27	p.E180Gfs*27	ENST00000336032	NM_006813.2	179	aaAGag/aaag	1/2	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.206576847892064	2		134	727	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920586	96920586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750870974	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	75	354	1	ENST00000258439.3:c.394G>A	p.Ala132Thr	p.A132T	ENST00000258439	NM_001193304.2	132	Gcc/Acc	3/4	1	2	FACETS	0.977	0.856	1	0.977	0.856	1	CLONAL	1	TRUE	1	0.206576847892064	2		355	743	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305233	39305233	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780315074	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	119	484	1	ENST00000373001.3:c.1192G>A	p.Ala398Thr	p.A398T	ENST00000373001	NM_022157.3	398	Gcc/Acc	7/7	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.206576847892064	2		485	1037	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058517	72058517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372023233	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	65	409	0	ENST00000357731.5:c.923C>T	p.Ala308Val	p.A308V	ENST00000357731	NM_173808.2	308	gCg/gTg	6/7	1	2	FACETS	0.71	0.614	0.815	0.71	0.614	0.815	SUBCLONAL	1	TRUE	1	0.206576847892064	2		409	886	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112760182	112760182	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	38	503	0	ENST00000369452.4:c.851C>G	p.Ser284Cys	p.S284C	ENST00000369452	NM_007373.3	284	tCc/tGc	4/9	1	2	FACETS	0.689	0.569	0.823	0.689	0.569	0.823	SUBCLONAL	1	TRUE	1	0.206576847892064	2		503	534	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14317388	14317388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782670869	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	48	447	0	ENST00000256196.4:c.122C>T	p.Thr41Met	p.T41M	ENST00000256196		41	aCg/aTg	2/6	1	2	FACETS	0.754	0.637	0.884	0.754	0.637	0.884	SUBCLONAL	1	TRUE	1	0.206576847892064	2		447	616	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344836	118344836	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	40	387	0	ENST00000534358.1:c.2962A>C	p.Thr988Pro	p.T988P	ENST00000534358	NM_005933.3	988	Acc/Ccc	3/36	1	2	FACETS	0.558	0.462	0.665	0.558	0.462	0.665	SUBCLONAL	1	TRUE	1	0.206576847892064	2		387	694	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475260	475260	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	78	576	0	ENST00000399788.2:c.377G>A	p.Ser126Asn	p.S126N	ENST00000399788	NM_001042603.1	126	aGc/aAc	4/28	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.206576847892064	2		576	681	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856347	111856347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752374176	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	110	130	0	ENST00000341259.2:c.398G>A	p.Cys133Tyr	p.C133Y	ENST00000341259	NM_005475.2	133	tGc/tAc	2/8	0.202163039940014	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.206576847892064	3		130	487	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926932	112926932	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1488010874	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	91	540	0	ENST00000351677.2:c.1552G>T	p.Val518Phe	p.V518F	ENST00000351677	NM_002834.3	518	Gtc/Ttc	13/16	0.202163039940014	3	FACETS	0.902	0.799	1	0.451	0.399	0.506	CLONAL	1	TRUE	1	0.206576847892064	3		540	1078	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220564	133220564	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	86	475	0	ENST00000320574.5:c.4150-1G>T		p.X1384_splice	ENST00000320574	NM_006231.2	1384			0.202163039940014	3	FACETS	0.867	0.765	0.977	0.434	0.382	0.489	CLONAL	1	TRUE	1	0.206576847892064	3		475	1059	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001919	29001919	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	74	564	1	ENST00000282397.4:c.1246A>T	p.Lys416Ter	p.K416*	ENST00000282397	NM_002019.4	416	Aaa/Taa	9/30	1	2	FACETS	0.866	0.757	0.984	0.866	0.757	0.984	CLONAL	1	TRUE	1	0.206576847892064	2		565	827	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442843	99442843	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	90	515	0	ENST00000268035.6:c.1240C>A	p.Leu414Ile	p.L414I	ENST00000268035	NM_000875.3	414	Cta/Ata	5/21	1	2	FACETS	0.896	0.793	1	0.896	0.793	1	CLONAL	1	TRUE	1	0.206576847892064	2		515	973	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024693	14024693	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	39	496	1	ENST00000311895.7:c.919C>A	p.Leu307Ile	p.L307I	ENST00000311895	NM_005236.2	307	Ctt/Att	5/11	1	2	FACETS	0.654	0.541	0.781	0.654	0.541	0.781	SUBCLONAL	1	TRUE	1	0.206576847892064	2		497	577	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216642	36216642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1276578109	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1242	176	696	0	ENST00000222270.7:c.3808C>T	p.Arg1270Cys	p.R1270C	ENST00000222270	NM_014727.1	1270	Cgc/Tgc	13/37	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.206576847892064	2		696	1418	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919028	50919028	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1678	146	628	0	ENST00000440232.2:c.2765T>C	p.Val922Ala	p.V922A	ENST00000440232	NM_002691.3	922	gTc/gCc	22/27	1	2	FACETS	0.775	0.704	0.85	0.775	0.704	0.85	SUBCLONAL	1	TRUE	1	0.206576847892064	2		628	1824	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462638	29462638	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs925915337	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1490	165	767	1	ENST00000389048.3:c.2263C>A	p.His755Asn	p.H755N	ENST00000389048	NM_004304.4	755	Cac/Aac	13/29	0.206576847892064	2	FACETS	0.965	0.883	1	0.483	0.441	0.526	CLONAL	1	TRUE	0	0.206576847892064	2		768	1655	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513694	41513694	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	160	627	0	ENST00000263253.7:c.598C>T	p.Arg200Ter	p.R200*	ENST00000263253	NM_001429.3	200	Cga/Tga	2/31	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.206576847892064	2		627	1296	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014358	70014358	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	126	559	1	ENST00000394351.3:c.1219A>T	p.Arg407Trp	p.R407W	ENST00000394351	NM_000248.3	407	Agg/Tgg	9/9	0.206576847892064	2	FACETS	1	0.922	1	0.512	0.462	0.564	CLONAL	1	TRUE	0	0.206576847892064	2		560	1192	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430180	181430180	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	112	168	1	ENST00000325404.1:c.32C>A	p.Pro11Gln	p.P11Q	ENST00000325404	NM_003106.3	11	cCg/cAg	1/1	0.206576847892064	3	FACETS	0.825	0.743	0.912	0.825	0.743	0.912	CLONAL	2	TRUE	1	0.206576847892064	3		169	725	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517474	176517474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200344385	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1508	166	735	5	ENST00000292408.4:c.175C>T	p.Arg59Trp	p.R59W	ENST00000292408	NM_213647.1	59	Cgg/Tgg	3/18	1	2	FACETS	0.96	0.878	1	0.96	0.878	1	CLONAL	1	TRUE	1	0.206576847892064	2		740	1674	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910568	29910572	+	frameshift_variant	Frame_Shift_Del	DEL	GTCCC	GTCCC	-	novel	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1833	189	796	0	ENST00000376809.5:c.109_113del	p.Ser37AlafsTer60	p.S37Afs*60	ENST00000376809	NM_002116.7	36	gtGTCCCgg/gtgg	2/8	0.206576847892064	2	FACETS	0.905	0.832	0.981	0.452	0.416	0.491	CLONAL	1	TRUE	0	0.206576847892064	2		796	2022	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800483	32800483	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1824	219	903	0	ENST00000374899.4:c.1064A>T	p.Tyr355Phe	p.Y355F	ENST00000374899	NM_018833.2	355	tAt/tTt	6/12	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.206576847892064	2		903	2043	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137522040	137522041	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	24	342	0	ENST00000367739.4:c.838dup	p.Ser280LysfsTer22	p.S280Kfs*22	ENST00000367739	NM_000416.2	280	agc/aAgc	6/7	1	2	FACETS	0.495	0.387	0.621	0.495	0.387	0.621	SUBCLONAL	1	TRUE	1	0.206576847892064	2		342	469	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220334	55220334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1350	279	635	2	ENST00000275493.2:c.724G>T	p.Gly242Cys	p.G242C	ENST00000275493	NM_005228.3	242	Ggc/Tgc	6/28	0.202163039940014	3	FACETS	0.915	0.857	0.975	0.915	0.857	0.975	CLONAL	2	TRUE	1	0.206576847892064	3		637	1629	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55231458	55231458	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1349	116	600	0	ENST00000275493.2:c.1664G>A	p.Cys555Tyr	p.C555Y	ENST00000275493	NM_005228.3	555	tGc/tAc	14/28	0.202163039940014	3	FACETS	0.846	0.759	0.938	0.423	0.379	0.469	CLONAL	1	TRUE	1	0.206576847892064	3		600	1465	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271189	38271189	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771680156	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	136	489	0	ENST00000425967.3:c.2519G>A	p.Arg840Gln	p.R840Q	ENST00000425967	NM_001174067.1	840	cGa/cAa	19/19	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.206576847892064	2		489	1097	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372050	55372050	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1290	140	436	2	ENST00000297316.4:c.740C>T	p.Ala247Val	p.A247V	ENST00000297316	NM_022454.3	247	gCg/gTg	2/2	1	2	FACETS	0.948	0.86	1	0.948	0.86	1	CLONAL	1	TRUE	1	0.206576847892064	2		438	1430	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981732	70981732	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1764	150	818	2	ENST00000276594.2:c.364G>A	p.Ala122Thr	p.A122T	ENST00000276594	NM_024504.3	122	Gcg/Acg	2/8	1	2	FACETS	0.759	0.69	0.831	0.759	0.69	0.831	SUBCLONAL	1	TRUE	1	0.206576847892064	2		820	1914	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413959	139413959	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1543	187	848	0	ENST00000277541.6:c.801G>C	p.Lys267Asn	p.K267N	ENST00000277541	NM_017617.3	267	aaG/aaC	5/34	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.206576847892064	2		848	1730	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227872	123227872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	45	366	0	ENST00000218089.9:c.3583C>T	p.Arg1195Cys	p.R1195C	ENST00000218089	NM_001042749.1	1195	Cgt/Tgt	33/35	0.206576847892064	1	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	0	0.206576847892064	1		366	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0030258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	207	545	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.363510637052027	2	FACETS	0.991	0.928	1	0.991	0.928	1	CLONAL	2	TRUE	0	0.402363804461212	2		545	519	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465262	120465262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs17024517	NA	P-0030258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	90	232	0	ENST00000256646.2:c.4999G>A	p.Val1667Ile	p.V1667I	ENST00000256646	NM_024408.3	1667	Gtc/Atc	27/34	0.300418316970654	5	FACETS	0.991	0.886	1	0.661	0.591	0.734	CLONAL	2	TRUE	2	0.402363804461212	5		232	362	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99440093	99440093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	81	355	0	ENST00000268035.6:c.1061C>T	p.Thr354Ile	p.T354I	ENST00000268035	NM_000875.3	354	aCc/aTc	4/21	1	2	FACETS	0.93	0.823	1	0.93	0.823	1	CLONAL	1	TRUE	1	0.402363804461212	2		355	433	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280598	115280598	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	56	397	0	ENST00000438362.2:c.433C>T	p.Arg145Ter	p.R145*	ENST00000438362	NM_001242891.1	145	Cga/Tga	4/20	0.300418316970654	5	FACETS	0.675	0.578	0.782	0.225	0.192	0.261	SUBCLONAL	1	TRUE	2	0.402363804461212	5		397	661	SUCCESS
FH	2271	MSKCC	GRCh37	1	241683005	241683011	+	frameshift_variant	Frame_Shift_Del	DEL	CCGAAGT	CCGAAGT	-	novel	NA	P-0030258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	63	329	0	ENST00000366560.3:c.12_18del	p.Leu5SerfsTer16	p.L5Sfs*16	ENST00000366560	NM_000143.3	4	gcACTTCGG/gc	1/10	0.402363804461212	5	FACETS	0.815	0.705	0.935	0.272	0.235	0.312	CLONAL	1	TRUE	2	0.402363804461212	5		329	616	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098654	2098656	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0030258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	96	376	0	ENST00000219476.3:c.40_42del	p.Lys14del	p.K14del	ENST00000219476	NM_000548.3	13	gAGAag/gag	2/42	0.363510637052027	2	FACETS	0.984	0.88	1	0.492	0.44	0.547	CLONAL	1	TRUE	0	0.402363804461212	2		376	485	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878802	151878802	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	160	403	0	ENST00000262189.6:c.6143A>T	p.Gln2048Leu	p.Q2048L	ENST00000262189	NM_170606.2	2048	cAa/cTa	36/59	0.402363804461212	5	FACETS	0.93	0.855	1			1	CLONAL	2	TRUE	NA	0.402363804461212	5		403	686	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0030259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	52	546	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.895	0.763	1	0.895	0.763	1	CLONAL	1	FALSE	1	0.242099056673576	2		546	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0030259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	58	545	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.242099056673576	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	FALSE	0	0.242099056673576	1		545	371	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0030259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	23	167	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.722	0.564	0.904	0.722	0.564	0.904	CLONAL	1	FALSE	1	0.242099056673576	2		167	263	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0030259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	38	219	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	1	0.837	1	1	0.837	1	CLONAL	1	FALSE	1	0.242099056673576	2		219	311	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958497	175958497	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0030259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	55	284	1	ENST00000367669.3:c.1847+1G>A		p.X616_splice	ENST00000367669	NM_022457.5	616			1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	1	0.242099056673576	2		285	384	SUCCESS
APC	324	MSKCC	GRCh37	5	112173512	112173513	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0030259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	33	231	0	ENST00000257430.4:c.2224_2225dup	p.Met743LeufsTer19	p.M743Lfs*19	ENST00000257430	NM_000038.5	741	aat/aATat	16/16	1	2	FACETS	0.94	0.768	1	0.94	0.768	1	CLONAL	1	FALSE	1	0.242099056673576	2		231	290	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608219	28608219	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	35	392	0	ENST00000241453.7:c.1837G>T	p.Gly613Trp	p.G613W	ENST00000241453	NM_004119.2	613	Ggg/Tgg	14/24	0.242099056673576	4	FACETS	0.522	0.426	0.63	0.261	0.213	0.315	SUBCLONAL	1	FALSE	2	0.242099056673576	4		392	688	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007624	45007624	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	TAT	novel	NA	P-0030259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	32	178	0	ENST00000558401.1:c.71delinsTAT	p.Thr24IlefsTer21	p.T24Ifs*21	ENST00000558401	NM_004048.2	24	aCt/aTATt	2/4	0.242099056673576	1	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	FALSE	0	0.242099056673576	1		178	205	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	244	535	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.89	0.843	0.936	1	0.995	1	CLONAL	2	TRUE	1	0.6	2		536	457	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	117	368	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.785	0.711	0.861	0.785	0.711	0.861	SUBCLONAL	1	TRUE	1	0.6	2		368	497	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380346	14380346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	101	231	0	ENST00000256196.4:c.71G>A	p.Gly24Asp	p.G24D	ENST00000256196		24	gGc/gAc	1/6	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.6	2		231	320	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	155	526	2	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.9	0.828	0.975	0.9	0.828	0.975	CLONAL	1	TRUE	1	0.6	2		528	574	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	201	299	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.779	0.732	0.827	1	0.993	1	SUBCLONAL	2	TRUE	1	0.6	2		299	430	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	152	478	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.897	0.824	0.972	0.897	0.824	0.972	CLONAL	1	TRUE	1	0.6	2		479	565	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979987	7979987	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746723399	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	153	527	2	ENST00000319144.4:c.1350del	p.Leu451SerfsTer16	p.L451Sfs*16	ENST00000319144	NM_001139.2	450	ggG/gg	10/15	1	2	FACETS	0.821	0.754	0.891	0.821	0.754	0.891	CLONAL	1	TRUE	1	0.6	2		529	621	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs79184941	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	84	254	0	ENST00000358487.5:c.755C>T	p.Ser252Leu	p.S252L	ENST00000358487	NM_000141.4	252	tCg/tTg	7/18	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.6	2		254	264	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743932	41743933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs778012871	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	171	667	0	ENST00000301178.4:c.874dup	p.His292ProfsTer47	p.H292Pfs*47	ENST00000301178	NM_021913.4	289	-/C	7/20	1	2	FACETS	0.818	0.754	0.883	0.818	0.754	0.883	CLONAL	1	TRUE	1	0.6	2		667	697	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	119	582	1	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.908	0.825	0.993	0.908	0.825	0.993	CLONAL	1	TRUE	1	0.6	2		583	437	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	143	488	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.844	0.773	0.917	0.844	0.773	0.917	CLONAL	1	TRUE	1	0.6	2		488	565	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871932	45871932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	201	478	0	ENST00000391945.4:c.316G>A	p.Gly106Arg	p.G106R	ENST00000391945	NM_000400.3	106	Gga/Aga	5/23	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.6	2		478	661	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553478	29553478	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781807	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	190	510	2	ENST00000356175.3:c.2033del	p.Pro678ArgfsTer10	p.P678Rfs*10	ENST00000356175	NM_000267.3	676	aCc/ac	18/57	1	2	FACETS	0.802	0.743	0.863	0.802	0.743	0.863	CLONAL	1	TRUE	1	0.6	2		512	790	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	114	442	1	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	0.856	0.776	0.939	0.856	0.776	0.939	CLONAL	1	TRUE	1	0.6	2		443	444	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023769	27023769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	124	380	0	ENST00000324856.7:c.879del	p.Thr294ProfsTer69	p.T294Pfs*69	ENST00000324856	NM_006015.4	292	aCc/ac	1/20	1	2	FACETS	0.916	0.835	1	0.916	0.835	1	CLONAL	1	TRUE	1	0.6	2		380	451	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	148	573	4	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	0.673	0.616	0.733	0.673	0.616	0.733	SUBCLONAL	1	TRUE	1	0.6	2		577	733	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346153	89346153	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748996527	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	56	217	0	ENST00000301030.4:c.6797C>T	p.Ala2266Val	p.A2266V	ENST00000301030	NM_001256183.1	2266	gCg/gTg	9/13	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.6	2		217	150	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439839	220439839	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761479412	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	177	540	1	ENST00000243786.2:c.692G>A	p.Arg231Gln	p.R231Q	ENST00000243786	NM_002191.3	231	cGa/cAa	2/2	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.6	2		541	564	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105892	27105892	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	139	353	0	ENST00000324856.7:c.5503C>T	p.Gln1835Ter	p.Q1835*	ENST00000324856	NM_006015.4	1835	Cag/Tag	20/20	1	2	FACETS	0.916	0.839	0.995	0.916	0.839	0.995	CLONAL	1	TRUE	1	0.6	2		353	506	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748296	41748296	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	205	523	1	ENST00000226382.2:c.473G>A	p.Arg158His	p.R158H	ENST00000226382	NM_003924.3	158	cGc/cAc	3/3	1	2	FACETS	0.987	0.92	1	0.987	0.92	1	CLONAL	1	TRUE	1	0.6	2		524	692	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856623	111856623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	104	257	0	ENST00000341259.2:c.674G>A	p.Arg225His	p.R225H	ENST00000341259	NM_005475.2	225	cGc/cAc	2/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.6	2		257	275	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661395	227661396	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGC	rs138975702	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	68	410	0	ENST00000305123.5:c.2057_2059dup	p.Ser686dup	p.S686dup	ENST00000305123	NM_005544.2	686	aac/aGCAac	1/2	1	2	FACETS	0.501	0.437	0.57	0.501	0.437	0.57	SUBCLONAL	1	TRUE	1	0.6	2		410	452	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466018	69466018	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	156	572	0	ENST00000227507.2:c.856A>G	p.Thr286Ala	p.T286A	ENST00000227507	NM_053056.2	286	Aca/Gca	5/5	1	2	FACETS	0.917	0.844	0.992	0.917	0.844	0.992	CLONAL	1	TRUE	1	0.6	2		572	567	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673711	176673711	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs570278338	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	116	360	0	ENST00000439151.2:c.4411C>T	p.Arg1471Ter	p.R1471*	ENST00000439151	NM_022455.4	1471	Cga/Tga	10/23	1	2	FACETS	0.865	0.785	0.949	0.865	0.785	0.949	CLONAL	1	TRUE	1	0.6	2		360	447	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197713	66197713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238493512	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	127	285	0	ENST00000273854.3:c.2986G>A	p.Ala996Thr	p.A996T	ENST00000273854	NM_004439.5	996	Gct/Act	17/18	1	2	FACETS	0.96	0.876	1	0.96	0.876	1	CLONAL	1	TRUE	1	0.6	2		285	441	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633229	12633229	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	181	444	0	ENST00000251849.4:c.1171A>G	p.Arg391Gly	p.R391G	ENST00000251849	NM_002880.3	391	Agg/Ggg	11/17	1	2	FACETS	0.986	0.914	1	0.986	0.914	1	CLONAL	1	TRUE	1	0.6	2		444	612	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11175494	11175494	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	133	424	1	ENST00000361445.4:c.7048A>T	p.Ser2350Cys	p.S2350C	ENST00000361445	NM_004958.3	2350	Agt/Tgt	51/58	1	2	FACETS	0.937	0.857	1	0.937	0.857	1	CLONAL	1	TRUE	1	0.6	2		425	473	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717662	89717663	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	161	431	1	ENST00000371953.3:c.689dup	p.Pro231ThrfsTer12	p.P231Tfs*12	ENST00000371953	NM_000314.4	229	-/G	7/9	1	2	FACETS	0.979	0.904	1	0.979	0.904	1	CLONAL	1	TRUE	1	0.6	2		432	548	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376116	118376116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	30	388	0	ENST00000534358.1:c.9509C>T	p.Ala3170Val	p.A3170V	ENST00000534358	NM_005933.3	3170	gCa/gTa	27/36	1	2	FACETS	0.217	0.175	0.266	0.217	0.175	0.266	SUBCLONAL	1	TRUE	1	0.6	2		388	460	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514420	125514420	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	83	284	1	ENST00000428830.2:c.1115G>A	p.Arg372Gln	p.R372Q	ENST00000428830	NM_001114121.2	372	cGg/cAg	11/14	1	2	FACETS	0.777	0.691	0.868	0.777	0.691	0.868	SUBCLONAL	1	TRUE	1	0.6	2		285	356	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624017	21624017	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	63	175	0	ENST00000421138.2:c.1683del	p.Phe561LeufsTer10	p.F561Lfs*10	ENST00000421138		561	ttT/tt	15/16	1	2	FACETS	0.913	0.8	1	0.913	0.8	1	CLONAL	1	TRUE	1	0.6	2		175	230	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435164	49435168	+	frameshift_variant	Frame_Shift_Del	DEL	GTGGG	GTGGG	-	novel	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	79	428	0	ENST00000301067.7:c.6385_6389del	p.Pro2129TyrfsTer24	p.P2129Yfs*24	ENST00000301067	NM_003482.3	2129	CCCACt/t	31/54	1	2	FACETS	0.766	0.678	0.857	0.766	0.678	0.857	SUBCLONAL	1	TRUE	1	0.6	2		428	344	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133238270	133238270	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	rs1555226066	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	89	263	0	ENST00000320574.5:c.2707G>T	p.Glu903Ter	p.E903*	ENST00000320574	NM_006231.2	903	Gaa/Taa	24/49	1	2	FACETS	0.948	0.849	1	0.948	0.849	1	CLONAL	1	TRUE	1	0.6	2		263	313	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592647	28592647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	92	427	0	ENST00000241453.7:c.2498C>T	p.Ala833Val	p.A833V	ENST00000241453	NM_004119.2	833	gCt/gTt	20/24	1	2	FACETS	0.565	0.503	0.63	0.565	0.503	0.63	SUBCLONAL	1	TRUE	1	0.6	2		427	543	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128041	30128041	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	148	506	0	ENST00000263025.4:c.1088T>G	p.Leu363Arg	p.L363R	ENST00000263025	NM_002746.2	363	cTc/cGc	8/9	1	2	FACETS	0.886	0.813	0.961	0.886	0.813	0.961	CLONAL	1	TRUE	1	0.6	2		506	557	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59924581	59924581	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	63	240	0	ENST00000259008.2:c.508A>C	p.Ile170Leu	p.I170L	ENST00000259008	NM_032043.2	170	Att/Ctt	6/20	1	2	FACETS	0.729	0.636	0.828	0.729	0.636	0.828	SUBCLONAL	1	TRUE	1	0.6	2		240	288	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758333	41758333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs537492526	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	139	419	1	ENST00000301178.4:c.1789G>A	p.Val597Ile	p.V597I	ENST00000301178	NM_021913.4	597	Gtc/Atc	15/20	1	2	FACETS	0.894	0.819	0.973	0.894	0.819	0.973	CLONAL	1	TRUE	1	0.6	2		420	518	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918708	50918708	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768799892	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	103	366	0	ENST00000440232.2:c.2578G>A	p.Ala860Thr	p.A860T	ENST00000440232	NM_002691.3	860	Gcg/Acg	21/27	1	2	FACETS	0.987	0.892	1	0.987	0.892	1	CLONAL	1	TRUE	1	0.6	2		366	348	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131250	202131250	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	35	379	0	ENST00000358485.4:c.218T>C	p.Leu73Pro	p.L73P	ENST00000358485	NM_001080125.1	73	cTg/cCg	2/9	1	2	FACETS	0.214	0.175	0.259	0.214	0.175	0.259	SUBCLONAL	1	TRUE	1	0.6	2		379	544	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728731	39728732	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	139	320	0	ENST00000361337.2:c.1013_1014del	p.Tyr338TrpfsTer7	p.Y338Wfs*7	ENST00000361337	NM_003286.2	337	gaATat/gaat	12/21	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.6	2		320	444	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37056026	37056029	+	frameshift_variant	Frame_Shift_Del	DEL	TTCA	TTCA	-	novel	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	96	323	0	ENST00000231790.2:c.782_785del	p.Phe261SerfsTer6	p.F261Sfs*6	ENST00000231790	NM_000249.3	261	TTCAtc/tc	9/19	1	2	FACETS	0.724	0.649	0.803	0.724	0.649	0.803	SUBCLONAL	1	TRUE	1	0.6	2		323	442	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37092123	37092123	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs267607893	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	142	304	0	ENST00000231790.2:c.2250C>G	p.Tyr750Ter	p.Y750*	ENST00000231790	NM_000249.3	750	taC/taG	19/19	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.6	2		304	438	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099357	157099362	+	inframe_deletion	In_Frame_Del	DEL	CCACCT	CCACCT	-	novel	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	18	238	0	ENST00000346085.5:c.299_304del	p.Leu100_His101del	p.L100_H101del	ENST00000346085	NM_020732.3	98	caCCACCTc/cac	1/20	1	2	FACETS	0.278	0.209	0.358	0.278	0.209	0.358	SUBCLONAL	1	TRUE	1	0.6	2		238	216	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129916	69129916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1243836474	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	113	244	0	ENST00000288368.4:c.4670G>A	p.Arg1557His	p.R1557H	ENST00000288368	NM_024870.2	1557	cGt/cAt	38/40	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.6	2		244	342	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720857	89720858	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CT	CT	A	novel	NA	P-0030260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	111	254	0	ENST00000371953.3:c.1008_1009delinsA	p.Tyr336Ter	p.Y336*	ENST00000371953	NM_000314.4	336	taCTtt/taAtt	8/9	1	2	FACETS	0.905	0.82	0.993	0.905	0.82	0.993	CLONAL	1	TRUE	1	0.6	2		254	409	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0030261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	20	622	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.254	0.193	0.326	0.254	0.193	0.326	SUBCLONAL	1	FALSE	1	0.248920588810893	2		622	632	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0030262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	154	532	1	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	0.478258416082365	2		533	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0030262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	229	485	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.245384276261721	1	FACETS	1	0.988	1	1	0.988	1	INDETERMINATE	1	TRUE	0	0.478258416082365	1		485	602	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0030262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	56	192	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	0.478258416082365	1	FACETS	0.963	0.839	1	0.963	0.839	1	CLONAL	1	TRUE	0	0.478258416082365	1		192	185	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9927977	9927977	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	43	269	0	ENST00000330684.3:c.1762T>G	p.Leu588Val	p.L588V	ENST00000330684	NM_001134407.1	588	Tta/Gta	8/13	0.227077061442554	3	FACETS	0.589	0.494	0.694	0.196	0.164	0.232	INDETERMINATE	1	TRUE	0	0.478258416082365	3		269	378	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794923	242794923	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1188302181	NA	P-0030262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	72	573	1	ENST00000334409.5:c.286C>T	p.Arg96Cys	p.R96C	ENST00000334409	NM_005018.2	96	Cgt/Tgt	2/5	0.237121802942734	2	FACETS	0.464	0.405	0.527	0.232	0.202	0.264	INDETERMINATE	1	TRUE	0	0.478258416082365	2		574	649	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797216	32797216	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	98	498	0	ENST00000374899.4:c.1893T>A	p.Asp631Glu	p.D631E	ENST00000374899	NM_018833.2	631	gaT/gaA	11/12	0.41110201457307	2	FACETS	0.664	0.593	0.739	0.332	0.296	0.37	SUBCLONAL	1	TRUE	0	0.478258416082365	2		498	617	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0030264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	230	532	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.560815805349481	5	FACETS	0.9	0.841	0.961	0.6	0.56	0.641	CLONAL	2	TRUE	2	0.560815805349481	5		533	839	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261554	142261555	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1043355995	NA	P-0030264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	257	425	2	ENST00000350721.4:c.3402dup	p.Asn1135Ter	p.N1135*	ENST00000350721	NM_001184.3	1134	-/T	17/47	0.443146196023654	4	FACETS	0.886	0.833	0.941	0.886	0.833	0.941	CLONAL	2	TRUE	2	0.560815805349481	4		427	807	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578418	7578418	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	127	589	0	ENST00000269305.4:c.512A>G	p.Glu171Gly	p.E171G	ENST00000269305	NM_001126112.2	171	gAg/gGg	5/11	0.526099102159699	2	FACETS	0.936	0.868	1	0.936	0.868	1	CLONAL	2	TRUE	0	0.560815805349481	2		589	242	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38148175	38148175	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	357	315	0	ENST00000317025.8:c.2936G>A	p.Cys979Tyr	p.C979Y	ENST00000317025	NM_023034.1	979	tGc/tAc	17/24	0.3	20	FACETS	0.952	0.9	1			1	INDETERMINATE	5	TRUE	NA	0.8	20		315	1537	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0030269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	33	546	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.749	0.613	0.901	0.749	0.613	0.901	CLONAL	1	TRUE	1	0.33364434918394	2		546	264	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0030269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	57	712	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.32137577180732	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.33364434918394	1		712	252	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0030269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	46	241	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.783	0.662	0.916	0.783	0.662	0.916	CLONAL	1	TRUE	1	0.33364434918394	2		241	352	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0030269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	48	219	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	0.872	0.74	1	0.872	0.74	1	CLONAL	1	TRUE	1	0.33364434918394	2		219	330	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943631	9943631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770071260	NA	P-0030269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	63	331	0	ENST00000330684.3:c.1310G>A	p.Arg437Gln	p.R437Q	ENST00000330684	NM_001134407.1	437	cGg/cAg	5/13	1	2	FACETS	0.763	0.661	0.873	0.763	0.661	0.873	SUBCLONAL	1	TRUE	1	0.33364434918394	2		331	495	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575077	48575077	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	48	243	0	ENST00000342988.3:c.271C>A	p.Pro91Thr	p.P91T	ENST00000342988	NM_005359.5	91	Cct/Act	3/12	0.33364434918394	1	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	0	0.33364434918394	1		243	220	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246091255	246091255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	73	282	0	ENST00000388985.4:c.680G>T	p.Arg227Leu	p.R227L	ENST00000388985		227	cGa/cTa	7/12	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.33364434918394	2		282	425	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624275	89624276	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	79	237	0	ENST00000371953.3:c.51dup	p.Glu18ArgfsTer26	p.E18Rfs*26	ENST00000371953	NM_000314.4	17	caa/cAaa	1/9	0.33364434918394	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.33364434918394	1		237	292	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042757	42042757	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	26	289	0	ENST00000219905.7:c.6952G>T	p.Glu2318Ter	p.E2318*	ENST00000219905	NM_001164273.1	2318	Gaa/Taa	17/24	0.32137577180732	1	FACETS	0.451	0.358	0.557	0.451	0.358	0.557	SUBCLONAL	1	TRUE	0	0.33364434918394	1		289	288	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78831653	78831653	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758599889	NA	P-0030269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	63	333	0	ENST00000306801.3:c.1462C>T	p.Arg488Trp	p.R488W	ENST00000306801	NM_020761.2	488	Cgg/Tgg	13/34	1	2	FACETS	0.652	0.564	0.748	0.652	0.564	0.748	SUBCLONAL	1	TRUE	1	0.33364434918394	2		333	579	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374844	45374844	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0030269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	55	278	0	ENST00000262160.6:c.997+2T>C		p.X333_splice	ENST00000262160	NM_005901.5	333			0.33364434918394	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.33364434918394	1		278	253	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	33	372	1	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	1	2	FACETS	0.355	0.288	0.431	0.355	0.288	0.431	SUBCLONAL	1	FALSE	1	0.314603816610718	2		373	591	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952139	178952139	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1560150596	NA	P-0030271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	88	245	0	ENST00000263967.3:c.3194A>T	p.His1065Leu	p.H1065L	ENST00000263967	NM_006218.2	1065	cAt/cTt	21/21	0.314603816610718	1	FACETS	1	0.915	1	1	0.987	1	CLONAL	2	FALSE	0	0.314603816610718	1		245	232	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011228	12011228	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0030271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	82	288	0	ENST00000353533.5:c.633+2T>G		p.X211_splice	ENST00000353533	NM_003010.3	211			0.314603816610718	0	FACETS	0.916	0.826	1			1	CLONAL	2	FALSE	0	0.314603816610718	0		288	195	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	140	557	0	ENST00000347630.2:c.397T>C	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	Ttc/Ctc	6/11	0.158133457210897	4	FACETS	0.922	0.845	1	0.922	0.845	1	INDETERMINATE	2	FALSE	2	0.437602406271572	4		557	499	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163710	47163711	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	40	512	0	ENST00000409792.3:c.2415dup	p.Asn806Ter	p.N806*	ENST00000409792	NM_014159.6	805	-/T	3/21	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	1	0.437602406271572	2		512	142	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835896	151835897	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0030288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	133	435	0	ENST00000262189.6:c.14627_14628delinsAA	p.Ile4876Lys	p.I4876K	ENST00000262189	NM_170606.2	4876	aTC/aAA	58/59	0.437602406271572	5	FACETS	1	0.98	1	0.819	0.75	0.889	CLONAL	2	FALSE	2	0.437602406271572	5		435	410	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0030291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	478	350	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.70798095517202	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.70798095517202	3		350	870	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518160	8518160	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	213	475	0	ENST00000356435.5:c.1231C>G	p.Gln411Glu	p.Q411E	ENST00000356435		411	Caa/Gaa	10/35	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.70798095517202	2		475	532	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854945	76854945	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	337	375	0	ENST00000373344.5:c.5891del	p.Gly1964GlufsTer18	p.G1964Efs*18	ENST00000373344	NM_000489.3	1964	gGa/ga	25/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.70798095517202	1		375	439	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	147	454	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.99	0.917	1	0.99	0.917	1	CLONAL	1	TRUE	1	0.871242608628131	2		454	341	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0030292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	301	465	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	0.871242608628131	2		465	634	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463541	25463541	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs367909007	NA	P-0030292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	295	650	0	ENST00000264709.3:c.2141C>G	p.Ser714Cys	p.S714C	ENST00000264709	NM_175629.2	714	tCc/tGc	18/23	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.871242608628131	2		650	561	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858107	40858107	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	317	699	0	ENST00000428826.2:c.1757G>T	p.Cys586Phe	p.C586F	ENST00000428826		586	tGt/tTt	16/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.871242608628131	2		699	678	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	139	454	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.578182539958248	2		454	455	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0030294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	120	167	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.578182539958248	2		167	384	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807889	1807889	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs78311289	NA	P-0030294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	236	596	0	ENST00000260795.2:c.1948A>G	p.Lys650Glu	p.K650E	ENST00000260795		650	Aag/Gag	13/17	1	2	FACETS	0.954	0.892	1	0.954	0.892	1	CLONAL	1	TRUE	1	0.578182539958248	2		596	856	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962553	100962553	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778032418	NA	P-0030294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	234	493	0	ENST00000325455.5:c.1844G>A	p.Arg615His	p.R615H	ENST00000325455	NM_001202474.3	615	cGc/cAc	3/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.578182539958248	2		493	773	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478549	99478549	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372138082	NA	P-0030294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	147	290	0	ENST00000268035.6:c.3191G>A	p.Arg1064Gln	p.R1064Q	ENST00000268035	NM_000875.3	1064	cGa/cAa	17/21	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.578182539958248	2		290	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0030296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	210	594	0	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	0.62282350686835	1	FACETS	0.487	0.452	0.523	0.487	0.452	0.523	SUBCLONAL	1	TRUE	0	0.62282350686835	1		594	953	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0030296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	48	611	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	0.62282350686835	1	FACETS	0.136	0.114	0.16	0.136	0.114	0.16	SUBCLONAL	1	TRUE	0	0.62282350686835	1		613	779	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653796	89653798	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs1554893765	NA	P-0030296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	261	442	1	ENST00000371953.3:c.97_99del	p.Ile33del	p.I33del	ENST00000371953	NM_000314.4	32	ATT/-	2/9	0.62282350686835	1	FACETS	0.998	0.944	1	0.998	0.944	1	CLONAL	1	TRUE	0	0.62282350686835	1		443	578	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114817	108114817	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786204543	NA	P-0030296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	163	507	4	ENST00000278616.4:c.640del	p.Ser214ProfsTer16	p.S214Pfs*16	ENST00000278616	NM_000051.3	212	Ttt/tt	6/63	0.62282350686835	1	FACETS	0.399	0.366	0.434	0.399	0.366	0.434	SUBCLONAL	1	TRUE	0	0.62282350686835	1		511	903	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523009	25523009	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	133	536	4	ENST00000264709.3:c.176del	p.Pro59ArgfsTer13	p.P59Rfs*13	ENST00000264709	NM_175629.2	59	cCg/cg	3/23	0.62282350686835	1	FACETS	0.365	0.332	0.401	0.365	0.332	0.401	SUBCLONAL	1	TRUE	0	0.62282350686835	1		540	805	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0030296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	224	690	3	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	0.62282350686835	1	FACETS	0.443	0.412	0.476	0.443	0.412	0.476	SUBCLONAL	1	TRUE	0	0.62282350686835	1		693	1117	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986752	36986752	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	70	71	0	ENST00000354822.5:c.937C>A	p.Gln313Lys	p.Q313K	ENST00000354822	NM_001079668.2	313	Caa/Aaa	3/3	0.62282350686835	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.62282350686835	1		71	143	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670036	29670046	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGTATTTAT	GAAGTATTTAT	-	novel	NA	P-0030296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	273	396	0	ENST00000356175.3:c.7010_7020del	p.Glu2337GlyfsTer24	p.E2337Gfs*24	ENST00000356175	NM_000267.3	2337	GAAGTATTTATg/g	47/57	0.62282350686835	1	FACETS	0.988	0.935	1	0.988	0.935	1	CLONAL	1	TRUE	0	0.62282350686835	1		396	611	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37081734	37081734	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs267607843	NA	P-0030296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	327	452	0	ENST00000231790.2:c.1616C>A	p.Ala539Asp	p.A539D	ENST00000231790	NM_000249.3	539	gCc/gAc	14/19	0.62282350686835	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.62282350686835	1		452	711	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65323437	65323437	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1240783724	NA	P-0030296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	76	446	0	ENST00000342505.4:c.1360C>T	p.Arg454Trp	p.R454W	ENST00000342505	NM_002227.2	454	Cgg/Tgg	10/25	0.62282350686835	1	FACETS	0.219	0.192	0.249	0.219	0.192	0.249	SUBCLONAL	1	TRUE	0	0.62282350686835	1		446	767	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778785	76778787	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs1557042392	NA	P-0030296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	208	291	2	ENST00000373344.5:c.6792_6794del	p.Glu2265del	p.E2265del	ENST00000373344	NM_000489.3	2264	gaAGAg/gag	31/35	1	1	FACETS	0.647	0.603	0.692	0.647	0.603	0.692	SUBCLONAL	1	TRUE	0	0.62282350686835	1		293	711	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499355	89499355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758183213	NA	P-0030296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	62	377	0	ENST00000336596.2:c.2525G>A	p.Arg842Gln	p.R842Q	ENST00000336596	NM_005233.5	842	cGa/cAa	15/17	0.62282350686835	1	FACETS	0.209	0.18	0.241	0.209	0.18	0.241	SUBCLONAL	1	TRUE	0	0.62282350686835	1		377	655	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675662	30675662	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	213	766	0	ENST00000376406.3:c.2694G>T	p.Glu898Asp	p.E898D	ENST00000376406	NM_014641.2	898	gaG/gaT	8/15	0.62282350686835	1	FACETS	0.403	0.374	0.433	0.403	0.374	0.433	SUBCLONAL	1	TRUE	0	0.62282350686835	1		766	1169	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099578	157099579	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0030296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	21	125	0	ENST00000346085.5:c.521dup	p.Pro177AlafsTer55	p.P177Afs*55	ENST00000346085	NM_020732.3	172	gac/gaCc	1/20	0.62282350686835	1	FACETS	0.209	0.161	0.265	0.209	0.161	0.265	SUBCLONAL	1	TRUE	0	0.62282350686835	1		125	222	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740708	145740708	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0030296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	62	522	0	ENST00000428558.2:c.1390+2T>C		p.X464_splice	ENST00000428558	NM_004260.3	464			0.62282350686835	1	FACETS	0.169	0.145	0.194	0.169	0.145	0.194	SUBCLONAL	1	TRUE	0	0.62282350686835	1		522	813	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653796	89653798	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs1554893765	NA	P-0030296-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	108	442	1	ENST00000371953.3:c.97_99del	p.Ile33del	p.I33del	ENST00000371953	NM_000314.4	32	ATT/-	2/9	0.528456385785376	1	FACETS	0.952	0.865	1	0.952	0.865	1	CLONAL	1	TRUE	0	0.528456385785376	1		443	316	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101267	27101268	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0030296-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	38	578	0	ENST00000324856.7:c.4555dup	p.Gln1519ProfsTer13	p.Q1519Pfs*13	ENST00000324856	NM_006015.4	1517	gcc/gCcc	18/20	0.528456385785376	1	FACETS	0.19	0.156	0.227	0.19	0.156	0.227	SUBCLONAL	1	TRUE	0	0.528456385785376	1		578	557	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114817	108114817	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786204543	NA	P-0030296-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	132	507	4	ENST00000278616.4:c.640del	p.Ser214ProfsTer16	p.S214Pfs*16	ENST00000278616	NM_000051.3	212	Ttt/tt	6/63	0.528456385785376	1	FACETS	0.875	0.802	0.951	0.875	0.802	0.951	CLONAL	1	TRUE	0	0.528456385785376	1		511	420	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523009	25523009	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030296-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	188	536	4	ENST00000264709.3:c.176del	p.Pro59ArgfsTer13	p.P59Rfs*13	ENST00000264709	NM_175629.2	59	cCg/cg	3/23	0.528456385785376	1	FACETS	0.873	0.811	0.936	0.873	0.811	0.936	CLONAL	1	TRUE	0	0.528456385785376	1		540	600	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030296-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	105	713	2	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	0.528456385785376	1	FACETS	0.38	0.34	0.422	0.38	0.34	0.422	SUBCLONAL	1	TRUE	0	0.528456385785376	1		715	770	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0030296-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	117	507	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.528456385785376	1	FACETS	0.539	0.487	0.593	0.539	0.487	0.593	SUBCLONAL	1	TRUE	0	0.528456385785376	1		511	605	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0030296-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	227	690	3	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	0.528456385785376	1	FACETS	0.889	0.832	0.947	0.889	0.832	0.947	CLONAL	1	TRUE	0	0.528456385785376	1		693	711	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599271	28599271	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs770146088	NA	P-0030296-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	39	585	0	ENST00000253063.3:c.722del	p.Pro241GlnfsTer6	p.P241Qfs*6	ENST00000253063	NM_031459.4	239	agC/ag	5/10	0.528456385785376	1	FACETS	0.156	0.128	0.186	0.156	0.128	0.186	SUBCLONAL	1	TRUE	0	0.528456385785376	1		585	698	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986752	36986752	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030296-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	45	71	0	ENST00000354822.5:c.937C>A	p.Gln313Lys	p.Q313K	ENST00000354822	NM_001079668.2	313	Caa/Aaa	3/3	0.528456385785376	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.528456385785376	1		71	101	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670036	29670046	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGTATTTAT	GAAGTATTTAT	-	novel	NA	P-0030296-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	105	396	0	ENST00000356175.3:c.7010_7020del	p.Glu2337GlyfsTer24	p.E2337Gfs*24	ENST00000356175	NM_000267.3	2337	GAAGTATTTATg/g	47/57	0.528456385785376	1	FACETS	0.949	0.862	1	0.949	0.862	1	CLONAL	1	TRUE	0	0.528456385785376	1		396	308	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37081734	37081734	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs267607843	NA	P-0030296-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	163	452	0	ENST00000231790.2:c.1616C>A	p.Ala539Asp	p.A539D	ENST00000231790	NM_000249.3	539	gCc/gAc	14/19	0.528456385785376	1	FACETS	0.827	0.763	0.892	0.827	0.763	0.892	CLONAL	1	TRUE	0	0.528456385785376	1		452	549	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941944	71941944	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0030296-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	32	593	0	ENST00000298229.2:c.1300+2T>G		p.X434_splice	ENST00000298229	NM_001567.3	434			0.528456385785376	1	FACETS	0.164	0.133	0.2	0.164	0.133	0.2	SUBCLONAL	1	TRUE	0	0.528456385785376	1		593	542	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257130	198257130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030296-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	48	459	0	ENST00000335508.6:c.3812C>T	p.Ser1271Phe	p.S1271F	ENST00000335508	NM_012433.2	1271	tCc/tTc	25/25	0.528456385785376	1	FACETS	0.309	0.261	0.361	0.309	0.261	0.361	SUBCLONAL	1	TRUE	0	0.528456385785376	1		459	433	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322949	31322949	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030296-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	119	717	2	ENST00000412585.2:c.947C>T	p.Ala316Val	p.A316V	ENST00000412585	NM_005514.6	316	gCt/gTt	5/8	0.526651688137411	1	FACETS	0.392	0.354	0.433	0.392	0.354	0.433	SUBCLONAL	1	TRUE	0	0.528456385785376	1		719	845	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006189	22006189	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030296-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	28	522	1	ENST00000276925.6:c.214C>T	p.Pro72Ser	p.P72S	ENST00000276925	NM_004936.3	72	Ccc/Tcc	2/2	0.528456385785376	1	FACETS	0.14	0.112	0.174	0.14	0.112	0.174	SUBCLONAL	1	TRUE	0	0.528456385785376	1		523	555	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577148	7577148	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1060501194	NA	P-0030297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	302	545	0	ENST00000269305.4:c.790del	p.Leu264TyrfsTer81	p.L264Yfs*81	ENST00000269305	NM_001126112.2	264	Cta/ta	8/11	0.397411281157216	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.41375084362756	2		545	644	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120169	70120169	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	413	277	1	ENST00000245479.2:c.1171C>T	p.Gln391Ter	p.Q391*	ENST00000245479	NM_000346.3	391	Cag/Tag	3/3	0.41375084362756	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	4	TRUE	0	0.41375084362756	4		278	658	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915739	112915740	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGAAT	novel	NA	P-0030297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	101	493	0	ENST00000351677.2:c.1013_1017dup	p.Asp340Ter	p.D340*	ENST00000351677	NM_002834.3	338	gtg/gTGAATtg	9/16	0.391394270443758	3	FACETS	0.757	0.677	0.843	0.379	0.338	0.422	SUBCLONAL	1	TRUE	1	0.41375084362756	3		493	778	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561134	9561134	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	97	492	0	ENST00000353224.5:c.648G>C	p.Lys216Asn	p.K216N	ENST00000353224	NM_177990.2	216	aaG/aaC	4/10	0.317312418324943	4	FACETS	0.968	0.863	1	0.484	0.431	0.54	CLONAL	1	TRUE	2	0.41375084362756	4		492	685	SUCCESS
APC	324	MSKCC	GRCh37	5	112136974	112136975	+	splice_acceptor_variant	Splice_Site	DEL	AG	AG	-	rs387906228	NA	P-0030297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	184	421	0	ENST00000257430.4:c.730_731del		p.X244_splice	ENST00000257430	NM_000038.5	244			0.397411281157216	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.41375084362756	2		421	416	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0030300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	23	381	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.717	0.557	0.902	0.717	0.557	0.902	CLONAL	1	TRUE	1	0.12	2		381	535	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0030300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	23	453	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.761	0.591	0.958	0.761	0.591	0.958	CLONAL	1	TRUE	1	0.12	2		453	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577543	7577543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1019340046	NA	P-0030300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	59	597	0	ENST00000269305.4:c.738G>A	p.Met246Ile	p.M246I	ENST00000269305	NM_001126112.2	246	atG/atA	7/11	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.12	2		597	857	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086157	16086157	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	50	592	1	ENST00000281043.3:c.1333G>A	p.Glu445Lys	p.E445K	ENST00000281043	NM_005378.4	445	Gaa/Aaa	3/3	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.12	2		593	822	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874011	123874013	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs780061449	NA	P-0030300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	12	35	0	ENST00000330479.4:c.62_64del	p.Ala21del	p.A21del	ENST00000330479	NM_020382.3	14	gaGGCg/gag	2/9	1	2	FACETS	1	0.775	1	1	0.925	1	CLONAL	3	TRUE	1	0.12	2		35	61	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0030302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	441	695	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.64474270612428	2	FACETS	0.99	0.957	1	0.99	0.957	1	CLONAL	2	TRUE	0	0.65579057501371	2		695	679	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469943	25469956	+	frameshift_variant	Frame_Shift_Del	DEL	TGCGGTACATGGGC	TGCGGTACATGGGC	-	novel	NA	P-0030302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	52	609	0	ENST00000264709.3:c.1086_1099del	p.Pro363SerfsTer25	p.P363Sfs*25	ENST00000264709	NM_175629.2	362	caGCCCATGTACCGCAaa/caaa	9/23	0.65579057501371	2	FACETS	0.271	0.23	0.316	0.136	0.115	0.158	SUBCLONAL	1	TRUE	0	0.65579057501371	2		609	585	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102098222	102098222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	40	525	0	ENST00000282441.5:c.1186G>A	p.Glu396Lys	p.E396K	ENST00000282441	NM_001130145.2	396	Gag/Aag	8/9	0.176047204597664	2	FACETS	0.473	0.392	0.564	0.237	0.196	0.282	SUBCLONAL	1	TRUE	0	0.219590268278814	2		525	770	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147512	47147512	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	63	576	0	ENST00000409792.3:c.4814A>G	p.Tyr1605Cys	p.Y1605C	ENST00000409792	NM_014159.6	1605	tAt/tGt	6/21	0.205940968200508	1	FACETS	0.854	0.739	0.979	0.854	0.739	0.979	CLONAL	1	TRUE	0	0.219590268278814	1		576	598	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679274	29679274	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0030303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	135	342	0	ENST00000356175.3:c.7395-1G>T		p.X2465_splice	ENST00000356175	NM_000267.3	2465			0.189976730741517	3	FACETS	0.866	0.792	0.944			1	CLONAL	3	TRUE	NA	0.219590268278814	3		342	525	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241974	72241974	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	64	299	0	ENST00000357731.5:c.416del	p.Pro139LeufsTer10	p.P139Lfs*10	ENST00000357731	NM_173808.2	139	cCt/ct	3/7	0.176047204597664	2	FACETS	0.771	0.671	0.879	0.771	0.671	0.879	SUBCLONAL	2	TRUE	0	0.219590268278814	2		299	378	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214715	133214715	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	64	515	0	ENST00000320574.5:c.5563G>A	p.Glu1855Lys	p.E1855K	ENST00000320574	NM_006231.2	1855	Gag/Aag	41/49	0.211236455719583	2	FACETS	0.691	0.597	0.794	0.346	0.298	0.397	SUBCLONAL	1	TRUE	0	0.219590268278814	2		515	843	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799024	42799024	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	140	823	0	ENST00000575354.2:c.4508C>G	p.Ser1503Cys	p.S1503C	ENST00000575354	NM_015125.3	1503	tCc/tGc	20/20	0.219590268278814	3	FACETS	1	0.945	1	0.352	0.319	0.387	CLONAL	1	TRUE	0	0.219590268278814	3		823	1340	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993102	90993102	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	76	397	0	ENST00000265433.3:c.340del	p.Val114LeufsTer7	p.V114Lfs*7	ENST00000265433	NM_002485.4	114	Gtt/tt	4/16	0.176400932899205	3	FACETS	1	0.955	1	0.776	0.686	0.871	CLONAL	2	TRUE	0	0.219590268278814	3		397	330	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518229	8518229	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs368577359	NA	P-0030303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	143	467	0	ENST00000356435.5:c.1162G>T	p.Asp388Tyr	p.D388Y	ENST00000356435		388	Gat/Tat	10/35	0.176047204597664	2	FACETS	0.956	0.874	1	0.956	0.874	1	CLONAL	2	TRUE	0	0.219590268278814	2		467	681	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198374	108198374	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	30	452	0	ENST00000278616.4:c.6978C>A	p.Asn2326Lys	p.N2326K	ENST00000278616	NM_000051.3	2326	aaC/aaA	48/63	0.176047204597664	2	FACETS	0.505	0.406	0.618	0.253	0.203	0.309	SUBCLONAL	1	TRUE	0	0.219590268278814	2		452	541	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0030307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	59	546	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.2	2		546	508	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0030307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	46	584	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.983	0.828	1	0.983	0.828	1	CLONAL	1	TRUE	1	0.2	2		584	468	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	71	714	0	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	1	2	FACETS	0.72	0.627	0.822	0.72	0.627	0.822	SUBCLONAL	1	TRUE	1	0.2	2		714	986	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087890	27087911	+	frameshift_variant	Frame_Shift_Del	DEL	CTCGGCCACCCAGTGGCCAGTC	CTCGGCCACCCAGTGGCCAGTC	TG	novel	NA	P-0030307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	93	609	3	ENST00000324856.7:c.2177_2198delinsTG	p.Pro726LeufsTer84	p.P726Lfs*84	ENST00000324856	NM_006015.4	726	cCTCGGCCACCCAGTGGCCAGTCg/cTGg	6/20	1	2	FACETS	0.963	0.854	1	0.963	0.854	1	CLONAL	1	TRUE	1	0.2	2		612	966	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480121	50480121	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	55	469	0	ENST00000394963.4:c.355C>T	p.Arg119Ter	p.R119*	ENST00000394963	NM_003076.4	119	Cga/Tga	2/13	1	2	FACETS	0.682	0.582	0.792	0.682	0.582	0.792	SUBCLONAL	1	TRUE	1	0.2	2		469	806	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371960	55371961	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0030307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	46	323	0	ENST00000297316.4:c.653dup	p.Leu219ValfsTer146	p.L219Vfs*146	ENST00000297316	NM_022454.3	217	tac/taCc	2/2	1	2	FACETS	0.69	0.58	0.812	0.69	0.58	0.812	SUBCLONAL	1	TRUE	1	0.2	2		323	667	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	86	454	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.906	0.804	1			1	INDETERMINATE	1	TRUE	NA	0.393206731999032	2		454	483	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0030310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3772	144	643	0	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.393206731999032	26	FACETS	1	0.949	1			1	CLONAL	1	TRUE	NA	0.393206731999032	26		643	3916	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933217	36933217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1287134931	NA	P-0030310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	152	647	1	ENST00000361632.4:c.1900G>A	p.Gly634Ser	p.G634S	ENST00000361632		634	Ggc/Agc	14/16	1	2	FACETS	0.851	0.778	0.927	0.851	0.778	0.927	CLONAL	1	TRUE	1	0.393206731999032	2		648	909	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522491	157522657	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCACATCCCAGGTCACCGGGCCACCACCCCAACCACCCCCAATCAGAAGGGAGATCACCTTTCCTCCTGGCTCAGTAGAAGCATCACAACCAGTCTTGAAACAAAGGCGAAAGATTACCTCCAAAGATATCGGTAAGAATTCCAAAGCTTTCATTCTGAAATGAATT	CCACATCCCAGGTCACCGGGCCACCACCCCAACCACCCCCAATCAGAAGGGAGATCACCTTTCCTCCTGGCTCAGTAGAAGCATCACAACCAGTCTTGAAACAAAGGCGAAAGATTACCTCCAAAGATATCGGTAAGAATTCCAAAGCTTTCATTCTGAAATGAATT	-	novel	NA	P-0030310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	83	711	0	ENST00000346085.5:c.4766_4894+38del		p.X1589_splice	ENST00000346085	NM_020732.3	1589		18/20	0.370674282182592	3	FACETS	0.527	0.464	0.595	0.264	0.232	0.298	SUBCLONAL	1	TRUE	1	0.393206731999032	3		711	958	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs587781702	NA	P-0030323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	119	598	0	ENST00000269305.4:c.920-1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.25	2		598	887	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398255	25398255	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913236	NA	P-0030323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	123	576	0	ENST00000311936.3:c.64C>A	p.Gln22Lys	p.Q22K	ENST00000311936	NM_004985.3	22	Cag/Aag	2/5	0.175346897153907	2	FACETS	1	0.978	1	0.64	0.579	0.704	CLONAL	1	TRUE	0	0.25	2		576	769	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431109	49431109	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	139	604	2	ENST00000301067.7:c.10030G>T	p.Ala3344Ser	p.A3344S	ENST00000301067	NM_003482.3	3344	Gct/Tct	34/54	0.175346897153907	2	FACETS	1	0.976	1	0.606	0.551	0.664	CLONAL	1	TRUE	0	0.25	2		606	917	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112569	115112569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180836314	NA	P-0030323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	96	646	0	ENST00000257566.3:c.1171G>A	p.Asp391Asn	p.D391N	ENST00000257566	NM_016569.3	391	Gac/Aac	7/8	1	2	FACETS	0.834	0.742	0.932	0.834	0.742	0.932	CLONAL	1	TRUE	1	0.25	2		646	921	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120791115	120791116	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0030323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	143	619	1	ENST00000257552.2:c.719_720delinsAA	p.Thr240Lys	p.T240K	ENST00000257552	NM_002442.3	240	aCC/aAA	10/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.25	2		620	898	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805789	46805789	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	72	596	1	ENST00000290295.7:c.167C>A	p.Ser56Ter	p.S56*	ENST00000290295	NM_006361.5	56	tCg/tAg	1/2	0.232472873215441	3	FACETS	0.624	0.543	0.711	0.312	0.271	0.356	SUBCLONAL	1	TRUE	1	0.25	3		597	1039	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210638	2210638	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	65	590	0	ENST00000398665.3:c.1135G>T	p.Glu379Ter	p.E379*	ENST00000398665	NM_032482.2	379	Gag/Tag	14/28	0.3	1	FACETS	0.598	0.517	0.685	0.598	0.517	0.685	SUBCLONAL	1	TRUE	0	0.25	1		590	761	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729872	47729872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	153	426	0	ENST00000449228.1:c.517G>A	p.Gly173Ser	p.G173S	ENST00000449228	NM_001127240.2	173	Ggc/Agc	3/4	0.212939957396782	4	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.25	4		426	1081	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702390	47702390	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	46	340	0	ENST00000233146.2:c.1986G>T	p.Gln662His	p.Q662H	ENST00000233146	NM_000251.2	662	caG/caT	12/16	1	2	FACETS	0.797	0.671	0.935	0.797	0.671	0.935	CLONAL	1	TRUE	1	0.25	2		340	462	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566778	212566778	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	56	391	0	ENST00000342788.4:c.1403A>G	p.Tyr468Cys	p.Y468C	ENST00000342788	NM_005235.2	468	tAt/tGt	12/28	1	2	FACETS	0.7	0.599	0.81	0.7	0.599	0.81	SUBCLONAL	1	TRUE	1	0.25	2		391	640	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944516	40944516	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	86	577	0	ENST00000373198.4:c.1986C>G	p.His662Gln	p.H662Q	ENST00000373198	NM_133170.3	662	caC/caG	12/32	0.229784182826759	1	FACETS	0.716	0.632	0.805	0.716	0.632	0.805	SUBCLONAL	1	TRUE	0	0.25	1		577	841	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539051	187539051	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1169115609	NA	P-0030323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	50	613	0	ENST00000441802.2:c.8689C>T	p.Gln2897Ter	p.Q2897*	ENST00000441802	NM_005245.3	2897	Cag/Tag	10/27	1	2	FACETS	0.455	0.385	0.533	0.455	0.385	0.533	SUBCLONAL	1	TRUE	1	0.25	2		613	879	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729475	41729475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	96	614	0	ENST00000242208.4:c.1054G>A	p.Gly352Ser	p.G352S	ENST00000242208	NM_002192.2	352	Ggt/Agt	3/3	1	2	FACETS	0.78	0.693	0.872	0.78	0.693	0.872	SUBCLONAL	1	TRUE	1	0.25	2		614	985	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371820	55371820	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	18	74	0	ENST00000297316.4:c.510G>T	p.Glu170Asp	p.E170D	ENST00000297316	NM_022454.3	170	gaG/gaT	2/2	1	2	FACETS	0.986	0.749	1	0.986	0.749	1	CLONAL	1	TRUE	1	0.25	2		74	146	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404653	8404653	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	24	308	0	ENST00000356435.5:c.4094A>T	p.Asp1365Val	p.D1365V	ENST00000356435		1365	gAc/gTc	25/35	0.229784182826759	1	FACETS	0.49	0.384	0.612	0.49	0.384	0.612	SUBCLONAL	1	TRUE	0	0.25	1		308	343	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521534	8521534	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	82	523	0	ENST00000356435.5:c.704del	p.Pro235HisfsTer33	p.P235Hfs*33	ENST00000356435		235	cCa/ca	9/35	0.229784182826759	1	FACETS	0.759	0.669	0.856	0.759	0.669	0.856	SUBCLONAL	1	TRUE	0	0.25	1		523	756	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875919	76875919	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	119	256	0	ENST00000373344.5:c.5216G>T	p.Arg1739Leu	p.R1739L	ENST00000373344	NM_000489.3	1739	cGa/cTa	20/35	0.227180287917679	2	FACETS	1	0.961	1			1	CLONAL	2	TRUE	NA	0.25	2		256	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0030331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	146	546	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.199796110001706	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.213953434425592	2		547	622	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0030331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	108	461	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.180598476847705	3	FACETS	0.898	0.808	0.994	0.898	0.808	0.994	CLONAL	2	TRUE	1	0.213953434425592	3		461	622	SUCCESS
APC	324	MSKCC	GRCh37	5	112174784	112174784	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0030331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	64	372	0	ENST00000257430.4:c.3493A>T	p.Lys1165Ter	p.K1165*	ENST00000257430	NM_000038.5	1165	Aaa/Taa	16/16	0.199796110001706	2	FACETS	0.981	0.856	1	0.981	0.856	1	CLONAL	2	TRUE	0	0.213953434425592	2		372	305	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925328	114925328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	113	526	0	ENST00000543371.1:c.1406G>A	p.Cys469Tyr	p.C469Y	ENST00000543371	NM_001198531.1	469	tGc/tAc	14/14	0.206568102872983	3	FACETS	0.963	0.869	1	0.963	0.869	1	CLONAL	2	TRUE	1	0.213953434425592	3		526	607	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850820	63850820	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746755575	NA	P-0030331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	56	795	0	ENST00000279873.7:c.1598C>T	p.Ala533Val	p.A533V	ENST00000279873	NM_032199.2	533	gCg/gTg	10/10	0.206568102872983	3	FACETS	0.756	0.646	0.876	0.378	0.323	0.438	SUBCLONAL	1	TRUE	1	0.213953434425592	3		795	767	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332760	70332760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749194238	NA	P-0030331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	38	605	1	ENST00000373644.4:c.665G>A	p.Arg222His	p.R222H	ENST00000373644	NM_030625.2	222	cGc/cAc	2/12	0.206568102872983	3	FACETS	0.746	0.616	0.892	0.373	0.308	0.446	SUBCLONAL	1	TRUE	1	0.213953434425592	3		606	527	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572112	95572112	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	74	366	0	ENST00000393063.1:c.2996T>C	p.Leu999Pro	p.L999P	ENST00000393063	NM_030621.3	999	cTt/cCt	20/28	0.213953434425592	5	FACETS	1	0.907	1	0.692	0.608	0.782	CLONAL	2	TRUE	2	0.213953434425592	5		366	440	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095854	29095854	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780194	NA	P-0030331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	54	574	0	ENST00000328354.6:c.980A>G	p.Tyr327Cys	p.Y327C	ENST00000328354	NM_007194.3	327	tAt/tGt	9/15	1	2	FACETS	0.791	0.675	0.919	0.791	0.675	0.919	CLONAL	1	TRUE	1	0.213953434425592	2		574	638	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572465	41572465	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	55	752	1	ENST00000263253.7:c.4994G>A	p.Arg1665His	p.R1665H	ENST00000263253	NM_001429.3	1665	cGc/cAc	30/31	1	2	FACETS	0.642	0.548	0.745	0.642	0.548	0.745	SUBCLONAL	1	TRUE	1	0.213953434425592	2		753	801	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0030332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	46	712	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.19	2		712	439	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174867	56174868	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0030332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	45	401	0	ENST00000399503.3:c.2026_2027del	p.Leu676SerfsTer20	p.L676Sfs*20	ENST00000399503	NM_005921.1	676	CTt/t	11/20	1	2	FACETS	0.861	0.723	1	0.861	0.723	1	CLONAL	1	TRUE	1	0.19	2		401	550	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041017	42041020	+	frameshift_variant	Frame_Shift_Del	DEL	AACT	AACT	-	novel	NA	P-0030333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	375	608	0	ENST00000219905.7:c.5395_5398del	p.Asn1799TyrfsTer38	p.N1799Yfs*38	ENST00000219905	NM_001164273.1	1799	AACTta/ta	16/24	0.416951384568415	1	FACETS	0.764	0.73	0.798	0.764	0.73	0.798	INDETERMINATE	1	TRUE	0	0.770759118062946	1		608	783	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0030338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	127	815	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.283036113213826	1	FACETS	0.82	0.742	0.902	0.82	0.742	0.902	CLONAL	1	TRUE	0	0.283036113213826	1		815	940	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63537656	63537656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201387209	NA	P-0030338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	122	529	0	ENST00000307078.5:c.976C>T	p.Arg326Cys	p.R326C	ENST00000307078	NM_004655.3	326	Cgt/Tgt	4/11	0.283036113213826	3	FACETS	1	0.979	1	0.65	0.588	0.716	CLONAL	1	TRUE	1	0.283036113213826	3		529	757	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280028	66280028	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	70	313	0	ENST00000273854.3:c.1661G>A	p.Arg554Lys	p.R554K	ENST00000273854	NM_004439.5	554	aGa/aAa	7/18	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.283036113213826	2		313	493	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602763	10602763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774469695	NA	P-0030338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	176	845	1	ENST00000171111.5:c.815G>A	p.Arg272His	p.R272H	ENST00000171111	NM_203500.1	272	cGc/cAc	3/6	0.283036113213826	1	FACETS	0.986	0.907	1	0.986	0.907	1	CLONAL	1	TRUE	0	0.283036113213826	1		846	1083	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229256	36229256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	154	728	0	ENST00000222270.7:c.7946G>A	p.Arg2649His	p.R2649H	ENST00000222270	NM_014727.1	2649	cGc/cAc	37/37	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.283036113213826	2		728	933	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741897	17741897	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752898631	NA	P-0030338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	18	169	0	ENST00000250003.3:c.568G>A	p.Gly190Ser	p.G190S	ENST00000250003	NM_002478.4	190	Ggc/Agc	1/3	0.283036113213826	1	FACETS	0.639	0.483	0.819	0.639	0.483	0.819	SUBCLONAL	1	TRUE	0	0.283036113213826	1		169	171	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969796	81969796	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	100	629	0	ENST00000359376.3:c.2865C>G	p.Ile955Met	p.I955M	ENST00000359376	NM_002661.3	955	atC/atG	27/33	0.283036113213826	1	FACETS	0.908	0.812	1	0.908	0.812	1	CLONAL	1	TRUE	0	0.283036113213826	1		629	668	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923159	48923159	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	58	282	0	ENST00000267163.4:c.607+1del		p.G203fs	ENST00000267163	NM_000321.2	203	Ggg/gg	6/27	0.69045769213552	2	FACETS	0.903	0.816	0.987	0.903	0.816	0.987	CLONAL	2	TRUE	0	0.69045769213552	2		282	93	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264049	16264049	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	221	667	0	ENST00000375759.3:c.10418T>C	p.Leu3473Pro	p.L3473P	ENST00000375759	NM_015001.2	3473	cTg/cCg	12/15	0.229873840035562	4	FACETS	0.852	0.791	0.915	0.426	0.395	0.458	INDETERMINATE	1	TRUE	2	0.69045769213552	4		667	1270	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828107	243828107	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	108	424	0	ENST00000263826.5:c.251A>G	p.Glu84Gly	p.E84G	ENST00000263826	NM_005465.4	84	gAg/gGg	3/13	0.395354963233553	5	FACETS	1	0.982	1	0.475	0.429	0.523	INDETERMINATE	1	TRUE	2	0.69045769213552	5		424	447	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633561	69633561	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1317320809	NA	P-0030339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	85	192	0	ENST00000334134.2:c.141G>T	p.Lys47Asn	p.K47N	ENST00000334134	NM_005247.2	47	aaG/aaT	1/3	0.264852030236779	4	FACETS	1	0.911	1	0.257	0.228	0.287	INDETERMINATE	1	TRUE	0	0.69045769213552	4		192	405	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202715	133202716	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs774417192	NA	P-0030339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	161	452	0	ENST00000320574.5:c.6518_6519del	p.Ser2173PhefsTer130	p.S2173Ffs*130	ENST00000320574	NM_006231.2	2173	tCT/t	46/49	0.579481417635277	4	FACETS	1	0.929	1	0.337	0.31	0.366	CLONAL	1	TRUE	1	0.69045769213552	4		452	779	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240697	133240697	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	124	548	0	ENST00000320574.5:c.2599G>T	p.Val867Phe	p.V867F	ENST00000320574	NM_006231.2	867	Gtc/Ttc	23/49	0.579481417635277	4	FACETS	0.604	0.545	0.666	0.201	0.181	0.222	SUBCLONAL	1	TRUE	1	0.69045769213552	4		548	1006	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578188	7578200	+	frameshift_variant	Frame_Shift_Del	DEL	CATAGGGCACCAC	CATAGGGCACCAC	-	novel	NA	P-0030339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	601	598	0	ENST00000269305.4:c.649_661del	p.Val217SerfsTer26	p.V217Sfs*26	ENST00000269305	NM_001126112.2	217	GTGGTGCCCTATGag/ag	6/11	0.69045769213552	4	FACETS	0.958	0.928	0.988	0.718	0.696	0.741	CLONAL	3	TRUE	0	0.69045769213552	4		598	1024	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634750	158634750	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	36	394	0	ENST00000263640.3:c.436C>G	p.Leu146Val	p.L146V	ENST00000263640	NM_001105.4	146	Ctc/Gtc	5/11	0.264852030236779	4	FACETS	0.263	0.215	0.316	0.066	0.053	0.079	INDETERMINATE	1	TRUE	0	0.69045769213552	4		394	671	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293832	1293832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	94	681	2	ENST00000310581.5:c.1169G>A	p.Arg390Gln	p.R390Q	ENST00000310581	NM_198253.2	390	cGg/cAg	2/16	0.69045769213552	3	FACETS	0.346	0.307	0.388	0.115	0.102	0.13	SUBCLONAL	1	TRUE	0	0.69045769213552	3		683	1059	SUCCESS
APC	324	MSKCC	GRCh37	5	112176777	112176777	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs767612847	NA	P-0030339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	246	329	0	ENST00000257430.4:c.5486A>G	p.Asn1829Ser	p.N1829S	ENST00000257430	NM_000038.5	1829	aAt/aGt	16/16	0.69045769213552	3	FACETS	1	0.973	1	0.693	0.657	0.729	CLONAL	2	TRUE	0	0.69045769213552	3		329	461	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349972	70349972	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs901783069	NA	P-0030339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	253	605	1	ENST00000374080.3:c.3955C>T	p.Arg1319Cys	p.R1319C	ENST00000374080		1319	Cgc/Tgc	28/45	0.24783416779022	3	FACETS	1	0.977	1	0.362	0.339	0.385	INDETERMINATE	1	TRUE	0	0.69045769213552	3		606	909	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938440	76938440	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	29	534	0	ENST00000373344.5:c.2308C>G	p.Gln770Glu	p.Q770E	ENST00000373344	NM_000489.3	770	Cag/Gag	9/35	0.24783416779022	3	FACETS	0.197	0.157	0.243	0.066	0.052	0.081	INDETERMINATE	1	TRUE	0	0.69045769213552	3		534	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0030340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	90	622	1	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	1	2	FACETS	0.871	0.775	0.974	0.871	0.775	0.974	CLONAL	1	TRUE	1	0.356738169016663	2		623	579	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10277332	10277332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1430311136	NA	P-0030340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	100	630	2	ENST00000340748.4:c.785C>T	p.Pro262Leu	p.P262L	ENST00000340748		262	cCg/cTg	10/40	0.356738169016663	1	FACETS	0.602	0.538	0.671	0.602	0.538	0.671	SUBCLONAL	1	TRUE	0	0.356738169016663	1		632	765	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860276	151860296	+	inframe_deletion	In_Frame_Del	DEL	AAAATCACAAGGTAAGTCGGA	AAAATCACAAGGTAAGTCGGA	-	novel	NA	P-0030340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	41	530	0	ENST00000262189.6:c.10366_10386del	p.Ser3456_Phe3462del	p.S3456_F3462del	ENST00000262189	NM_170606.2	3456	TCCGACTTACCTTGTGATTTT/-	43/59	0.201433214059808	4	FACETS	0.618	0.514	0.733	0.309	0.257	0.367	INDETERMINATE	1	TRUE	2	0.356738169016663	4		530	505	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740627	145740627	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0030340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	432	756	0	ENST00000428558.2:c.1391-1G>C		p.X464_splice	ENST00000428558	NM_004260.3	464			0.356738169016663	5	FACETS	0.875	0.837	0.914	0.875	0.837	0.914	CLONAL	4	TRUE	1	0.356738169016663	5		756	1062	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484210	8484210	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	143	587	0	ENST00000356435.5:c.3322T>G	p.Leu1108Val	p.L1108V	ENST00000356435		1108	Tta/Gta	19/35	0.356738169016663	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.356738169016663	1		587	624	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0030341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	384	622	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.494894572319646	4	FACETS	0.954	0.918	0.989	0.954	0.918	0.989	CLONAL	4	TRUE	0	0.494894572319646	4		622	608	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271898	15271898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	314	754	0	ENST00000263388.2:c.6541C>T	p.Pro2181Ser	p.P2181S	ENST00000263388	NM_000435.2	2181	Cca/Tca	33/33	0.477527866680047	3	FACETS	0.965	0.915	1	0.965	0.915	1	CLONAL	2	TRUE	1	0.494894572319646	3		754	820	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610695	52610695	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	219	354	0	ENST00000394830.3:c.3478C>T	p.Arg1160Ter	p.R1160*	ENST00000394830	NM_018313.4	1160	Cga/Tga	23/30	0.494894572319646	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.494894572319646	2		354	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0030341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	553	676	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.494894572319646	3	FACETS	0.944	0.913	0.976	0.944	0.913	0.976	CLONAL	3	TRUE	0	0.494894572319646	3		676	984	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058505	72058505	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	122	374	0	ENST00000357731.5:c.935T>G	p.Leu312Arg	p.L312R	ENST00000357731	NM_173808.2	312	cTt/cGt	6/7	0.477527866680047	3	FACETS	1	0.932	1	0.517	0.468	0.568	CLONAL	1	TRUE	1	0.494894572319646	3		374	595	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893421	32893430	+	frameshift_variant	Frame_Shift_Del	DEL	AATCTCCTGT	AATCTCCTGT	-	novel	NA	P-0030341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	97	438	0	ENST00000380152.3:c.277_286del	p.Ser93LysfsTer3	p.S93Kfs*3	ENST00000380152		92	cAATCTCCTGTa/ca	3/27	0.351519740239411	6	FACETS	1	0.957	1	0.286	0.255	0.32	CLONAL	1	TRUE	2	0.494894572319646	6		438	681	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982743	7982743	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764382022	NA	P-0030341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	121	454	0	ENST00000319144.4:c.1042G>A	p.Glu348Lys	p.E348K	ENST00000319144	NM_001139.2	348	Gag/Aag	8/15	0.494894572319646	3	FACETS	1	0.929	1	0.343	0.311	0.378	CLONAL	1	TRUE	0	0.494894572319646	3		454	592	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906830	50906841	+	inframe_deletion	In_Frame_Del	DEL	CATCTCTCGGGC	CATCTCTCGGGC	-	novel	NA	P-0030341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	76	506	0	ENST00000440232.2:c.1219_1230del	p.Ile407_Ala410del	p.I407_A410del	ENST00000440232	NM_002691.3	406	ctCATCTCTCGGGCc/ctc	10/27	0.477527866680047	3	FACETS	0.543	0.476	0.616	0.272	0.238	0.308	SUBCLONAL	1	TRUE	1	0.494894572319646	3		506	705	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115888	8115889	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0030342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	83	427	0	ENST00000346208.3:c.1236dup	p.Ser413GlnfsTer94	p.S413Qfs*94	ENST00000346208		412	tcc/tCcc	6/6	0.21937641313215	3	FACETS	1	0.953	1	0.58	0.511	0.653	CLONAL	1	TRUE	1	0.21937641313215	3		427	724	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426712	121426712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	89	557	2	ENST00000257555.6:c.403G>A	p.Asp135Asn	p.D135N	ENST00000257555		135	Gat/Aat	2/10	0.21937641313215	3	FACETS	1	0.894	1			1	CLONAL	1	TRUE	NA	0.21937641313215	3		559	891	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577068	7577071	+	frameshift_variant	Frame_Shift_Del	DEL	GCGG	GCGG	-	novel	NA	P-0030342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	163	561	0	ENST00000269305.4:c.867_870del	p.Lys292GlyfsTer52	p.K292Gfs*52	ENST00000269305	NM_001126112.2	289	ctCCGC/ct	8/11	0.21937641313215	2	FACETS	0.863	0.792	0.937	0.863	0.792	0.937	CLONAL	2	TRUE	0	0.21937641313215	2		561	861	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0030345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	104	505	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	1	2	FACETS	0.918	0.829	1	0.918	0.829	1	CLONAL	1	TRUE	1	0.568989383983846	2		505	398	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872894	136872894	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	261	450	0	ENST00000241393.3:c.604C>A	p.Gln202Lys	p.Q202K	ENST00000241393	NM_003467.2	202	Cag/Aag	2/2	0.540014590064226	3	FACETS	0.963	0.909	1	0.963	0.909	1	CLONAL	2	TRUE	1	0.568989383983846	3		450	612	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577120	+	missense_variant	Missense_Mutation	TNP	CAC	CAC	AAA	novel	NA	P-0030345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	343	593	0	ENST00000269305.4:c.818_820delinsTTT	p.Arg273_Val274delinsLeuPhe	p.R273_V274delinsLF	ENST00000269305	NM_001126112.2	273	cGTGtt/cTTTtt	8/11	0.568989383983846	2	FACETS	0.898	0.858	0.939	0.898	0.858	0.939	CLONAL	2	TRUE	0	0.568989383983846	2		593	671	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	245	454	0				ENST00000310581	NM_198253.2	-/1132			0.46919982505317	5	FACETS	1	0.946	1	1	0.946	1	CLONAL	3	TRUE	2	0.468882523414123	5		454	591	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223166	41223166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357002	NA	P-0030346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	144	547	0	ENST00000357654.3:c.4765C>T	p.Arg1589Cys	p.R1589C	ENST00000357654	NM_007294.3	1589	Cgt/Tgt	15/23	0.468882523414123	6	FACETS	0.928	0.844	1	0.186	0.168	0.204	CLONAL	1	TRUE	1	0.468882523414123	6		547	1282	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107224	27107225	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0030346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	202	422	0	ENST00000324856.7:c.6835_6836del	p.Leu2279ValfsTer105	p.L2279Vfs*105	ENST00000324856	NM_006015.4	2279	CTg/g	20/20	0.462984854852591	3	FACETS	0.892	0.832	0.954	0.892	0.832	0.954	CLONAL	2	TRUE	1	0.468882523414123	3		422	596	SUCCESS
AR	367	MSKCC	GRCh37	X	66766421	66766421	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs760558682	NA	P-0030346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	41	169	0	ENST00000374690.3:c.1433T>C	p.Val478Ala	p.V478A	ENST00000374690	NM_000044.3	478	gTa/gCa	1/8	1	2	FACETS	0.795	0.668	0.933	0.795	0.668	0.933	CLONAL	1	TRUE	1	0.468882523414123	2		169	220	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0030347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	759	565	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	0.908749531897193	3	FACETS	0.99	0.978	1	0.99	0.978	1	CLONAL	3	TRUE	0	0.908749531897193	3		565	818	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0030347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	88	464	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	0.889656686066746	3	FACETS	0.798	0.713	0.887	0.399	0.356	0.444	SUBCLONAL	1	TRUE	1	0.908749531897193	3		464	353	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023151	27023179	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	-	novel	NA	P-0030347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	173	66	1	ENST00000324856.7:c.267_295del	p.Ser90ProfsTer11	p.S90Pfs*11	ENST00000324856	NM_006015.4	86	gGCGGAGCCGGCAGCGGCGGCGGGCCCGGC/g	1/20	0.157324739903523	3	FACETS	1	0.984	1	1	0.984	1	INDETERMINATE	2	TRUE	1	0.908749531897193	3		67	251	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720858	89720858	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1564568660	NA	P-0030347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	294	319	0	ENST00000371953.3:c.1012del	p.Ser338LeufsTer6	p.S338Lfs*6	ENST00000371953	NM_000314.4	337	Ttt/tt	8/9	0.908749531897193	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.908749531897193	3		319	311	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101702	27101703	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0030347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	321	605	0	ENST00000324856.7:c.4985_4986del	p.Lys1662ArgfsTer35	p.K1662Rfs*35	ENST00000324856	NM_006015.4	1662	AAa/a	18/20	0.157324739903523	3	FACETS	1	0.993	1	0.646	0.613	0.68	INDETERMINATE	1	TRUE	1	0.908749531897193	3		605	795	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945145	44945146	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0030347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	86	488	0	ENST00000377967.4:c.3470_3471del	p.Ile1157LysfsTer6	p.I1157Kfs*6	ENST00000377967	NM_021140.2	1157	ATa/a	24/29	0.880491480172389	1	FACETS	0.861	0.8	0.917	0.861	0.8	0.917	CLONAL	1	TRUE	0	0.908749531897193	1		488	120	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	38	454	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.894	0.74	1	0.894	0.74	1	CLONAL	1	TRUE	1	0.215856408481495	2		454	394	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0030348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	56	717	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	0.676	0.578	0.784	0.676	0.578	0.784	SUBCLONAL	1	TRUE	1	0.215856408481495	2		717	767	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106162495	106162495	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0030348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	30	298	0	ENST00000380013.4:c.3410-1G>C		p.X1137_splice	ENST00000380013	NM_001127208.2	1137			1	2	FACETS	0.847	0.684	1	0.847	0.684	1	CLONAL	1	TRUE	1	0.215856408481495	2		298	328	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524475	44524475	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	112	360	0	ENST00000291552.4:c.82C>T	p.Arg28Cys	p.R28C	ENST00000291552	NM_006758.2	28	Cgt/Tgt	2/8	0.215856408481495	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.215856408481495	3		360	521	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253969	133253969	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	70	655	0	ENST00000320574.5:c.781G>A	p.Asp261Asn	p.D261N	ENST00000320574	NM_006231.2	261	Gat/Aat	8/49	1	2	FACETS	0.981	0.855	1	0.981	0.855	1	CLONAL	1	TRUE	1	0.215856408481495	2		655	661	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21639499	21639499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	36	390	0	ENST00000421138.2:c.415C>T	p.Pro139Ser	p.P139S	ENST00000421138		139	Cca/Tca	6/16	1	2	FACETS	0.828	0.681	0.992	0.828	0.681	0.992	CLONAL	1	TRUE	1	0.215856408481495	2		390	403	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437296	121437296	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0030348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	84	740	0	ENST00000257555.6:c.1634C>G	p.Ser545Ter	p.S545*	ENST00000257555		545	tCa/tGa	9/10	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.215856408481495	2		740	746	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274154	10274154	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	43	477	0	ENST00000330684.3:c.115A>G	p.Met39Val	p.M39V	ENST00000330684	NM_001134407.1	39	Atg/Gtg	2/13	1	2	FACETS	0.724	0.606	0.856	0.724	0.606	0.856	SUBCLONAL	1	TRUE	1	0.215856408481495	2		477	550	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422838	12422838	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	97	493	0	ENST00000287820.6:c.328C>T	p.Pro110Ser	p.P110S	ENST00000287820	NM_015869.4	110	Cct/Tct	3/7	0.103522280868636	4	FACETS	0.846	0.755	0.942	0.846	0.755	0.942	INDETERMINATE	2	TRUE	2	0.215856408481495	4		493	646	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495670	72495676	+	frameshift_variant	Frame_Shift_Del	DEL	ATCGCAG	ATCGCAG	-	novel	NA	P-0030348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	43	339	0	ENST00000477973.2:c.394_400del	p.Ile132MetfsTer2	p.I132Mfs*2	ENST00000477973	NM_012234.5	132	atCTGCGAT/at	1/4	0.103522280868636	4	FACETS	0.963	0.806	1	0.482	0.403	0.569	INDETERMINATE	1	TRUE	2	0.215856408481495	4		339	503	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139894	55139894	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	41	299	0	ENST00000257290.5:c.1555C>T	p.Pro519Ser	p.P519S	ENST00000257290	NM_006206.4	519	Ccc/Tcc	10/23	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.215856408481495	2		299	366	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922825	44922826	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCAG	novel	NA	P-0030348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	66	211	0	ENST00000377967.4:c.1686_1687insGCAG	p.Pro563AlafsTer19	p.P563Afs*19	ENST00000377967	NM_021140.2	562	-/GCAG	16/29	0.182741142789015	2	FACETS	1	0.886	1			1	CLONAL	2	TRUE	NA	0.215856408481495	2		211	302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0030357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	840	590	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.421000749674799	8	FACETS	0.974	0.952	0.995			1	CLONAL	8	TRUE	NA	0.421000749674799	8		590	1159	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0030357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	142	311	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.421000749674799	2	FACETS	0.956	0.883	1	0.956	0.883	1	CLONAL	2	TRUE	0	0.421000749674799	2		312	353	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0030358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	27	532	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.552	0.446	0.67	0.552	0.446	0.67	SUBCLONAL	1	TRUE	1	0.735102595145869	2		533	133	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221995	1221995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201090	NA	P-0030358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	326	376	0	ENST00000326873.7:c.910C>T	p.Arg304Trp	p.R304W	ENST00000326873	NM_000455.4	304	Cgg/Tgg	7/10	0.735102595145869	1	FACETS	0.961	0.918	1	0.961	0.918	1	CLONAL	1	TRUE	0	0.735102595145869	1		376	584	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359091	81359091	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	31	212	0	ENST00000222390.5:c.870C>A	p.Asp290Glu	p.D290E	ENST00000222390	NM_000601.4	290	gaC/gaA	8/18	1	2	FACETS	1	0.839	1	1	0.839	1	CLONAL	1	TRUE	1	0.735102595145869	2		212	84	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400780	72400781	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0030358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	31	158	0	ENST00000357731.5:c.390_391delinsTT	p.Gln130_Val131delinsHisLeu	p.Q130_V131delinsHL	ENST00000357731	NM_173808.2	130	caGGtg/caTTtg	2/7	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.735102595145869	2		158	81	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253211	133253211	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	182	321	1	ENST00000320574.5:c.830A>T	p.Glu277Val	p.E277V	ENST00000320574	NM_006231.2	277	gAg/gTg	9/49	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.735102595145869	2		322	449	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530122	63530122	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0030358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	165	331	0	ENST00000307078.5:c.2313T>A	p.Cys771Ter	p.C771*	ENST00000307078	NM_004655.3	771	tgT/tgA	10/11	0.174096691214024	1	FACETS	0.567	0.524	0.61	0.567	0.524	0.61	INDETERMINATE	1	TRUE	0	0.735102595145869	1		331	501	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067069	143067069	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	68	231	0	ENST00000262992.4:c.1644del	p.Ser549ValfsTer16	p.S549Vfs*16	ENST00000262992	NM_001101669.1	548	ggC/gg	16/24	1	2	FACETS	0.865	0.764	0.969	0.865	0.764	0.969	CLONAL	1	TRUE	1	0.735102595145869	2		231	214	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289271	33289271	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	208	246	0	ENST00000374542.5:c.281G>T	p.Arg94Leu	p.R94L	ENST00000374542	NM_001141970.1	94	cGt/cTt	3/8	1	2	FACETS	0.938	0.877	1	0.938	0.877	1	CLONAL	1	TRUE	1	0.735102595145869	2		246	603	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851608	128851608	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	234	339	0	ENST00000249373.3:c.1933C>A	p.Pro645Thr	p.P645T	ENST00000249373	NM_005631.4	645	Cca/Aca	11/12	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.735102595145869	2		339	611	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648218	206648218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782466362	NA	P-0030362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	185	307	0	ENST00000367120.3:c.239G>A	p.Arg80Gln	p.R80Q	ENST00000367120	NM_014002.3	80	cGg/cAg	5/22	1	2	FACETS	0.965	0.902	1	0.965	0.902	1	CLONAL	1	TRUE	1	0.891992071762971	2		307	430	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894228	NA	P-0030362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	559	435	0	ENST00000451590.1:c.37G>C	p.Gly13Arg	p.G13R	ENST00000451590	NM_001130442.1	13	Ggt/Cgt	2/5	1	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	1	0.891992071762971	2		435	913	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138199	64138199	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0030362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	353	528	0	ENST00000334205.4:c.2121+1G>T		p.X707_splice	ENST00000334205	NM_003942.2	707			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.891992071762971	2		528	769	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639821	3639821	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	316	540	0	ENST00000294008.3:c.3818C>G	p.Thr1273Ser	p.T1273S	ENST00000294008	NM_032444.2	1273	aCc/aGc	12/15	1	2	FACETS	0.913	0.866	0.96	0.913	0.866	0.96	CLONAL	1	TRUE	1	0.891992071762971	2		540	776	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0030362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	678	436	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.885319797067298	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.891992071762971	2		436	754	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227048	2227048	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	373	456	1	ENST00000398665.3:c.4528G>T	p.Val1510Leu	p.V1510L	ENST00000398665	NM_032482.2	1510	Gtg/Ttg	27/28	0.891992071762971	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.891992071762971	1		457	445	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292489	15292489	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	438	554	0	ENST00000263388.2:c.2690G>T	p.Gly897Val	p.G897V	ENST00000263388	NM_000435.2	897	gGc/gTc	17/33	0.891992071762971	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.891992071762971	1		554	523	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188405	32188406	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0030362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	251	364	1	ENST00000375023.3:c.935_936delinsTT	p.Ser312Phe	p.S312F	ENST00000375023	NM_004557.3	312	tCC/tTT	6/30	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.891992071762971	2		365	534	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287157	33287157	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	206	325	0	ENST00000374542.5:c.1940G>T	p.Ser647Ile	p.S647I	ENST00000374542	NM_001141970.1	647	aGc/aTc	6/8	1	2	FACETS	0.948	0.889	1	0.948	0.889	1	CLONAL	1	TRUE	1	0.891992071762971	2		325	487	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641078	117641079	+	missense_variant	Missense_Mutation	DNP	CT	CT	AG	novel	NA	P-0030362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	214	413	0	ENST00000368508.3:c.5892_5893inv	p.Val1965Leu	p.V1965L	ENST00000368508	NM_002944.2	1964	gcAGtg/gcCTtg	36/43	1	2	FACETS	0.919	0.862	0.977	0.919	0.862	0.977	CLONAL	1	TRUE	1	0.891992071762971	2		413	522	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376701	8376701	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	236	361	0	ENST00000356435.5:c.4412G>T	p.Ser1471Ile	p.S1471I	ENST00000356435		1471	aGc/aTc	27/35	1	2	FACETS	0.943	0.888	0.999	0.943	0.888	0.999	CLONAL	1	TRUE	1	0.891992071762971	2		361	561	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	213	625	0	ENST00000269305.4:c.470T>G	p.Val157Gly	p.V157G	ENST00000269305	NM_001126112.2	157	gTc/gGc	5/11	0.564300127148461	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.564300127148461	1		625	500	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517201	NA	P-0030363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	145	554	0	ENST00000263967.3:c.1637A>C	p.Gln546Pro	p.Q546P	ENST00000263967	NM_006218.2	546	cAg/cCg	10/21	0.538607072918274	3	FACETS	1	0.929	1	0.508	0.465	0.554	CLONAL	1	TRUE	1	0.564300127148461	3		554	648	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0030364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	188	546	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.375071793634662	4	FACETS	0.788	0.73	0.847	0.788	0.73	0.847	SUBCLONAL	2	TRUE	2	0.515001762490493	4		546	702	SUCCESS
ATM	472	MSKCC	GRCh37	11	108181032	108181032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781722	NA	P-0030364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	152	208	0	ENST00000278616.4:c.5908C>T	p.Gln1970Ter	p.Q1970*	ENST00000278616	NM_000051.3	1970	Caa/Taa	39/63	0.457570881786161	2	FACETS	0.811	0.752	0.871	0.811	0.752	0.871	CLONAL	2	TRUE	0	0.515001762490493	2		208	364	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748914	43748914	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	384	565	0	ENST00000382044.4:c.1892A>C	p.Gln631Pro	p.Q631P	ENST00000382044	NM_001141980.1	631	cAg/cCg	12/28	0.375071793634662	4	FACETS	0.861	0.817	0.905	0.861	0.817	0.905	CLONAL	2	TRUE	2	0.515001762490493	4		565	1312	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921188	50921188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415038504	NA	P-0030364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	183	505	0	ENST00000440232.2:c.3308G>A	p.Gly1103Glu	p.G1103E	ENST00000440232	NM_002691.3	1103	gGa/gAa	27/27	0.388735288039331	3	FACETS	0.95	0.877	1	0.475	0.438	0.513	CLONAL	1	TRUE	1	0.515001762490493	3		505	941	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715621	30715621	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	126	192	0	ENST00000295754.5:c.1279C>A	p.Pro427Thr	p.P427T	ENST00000295754	NM_003242.5	427	Cca/Aca	5/7	0.457570881786161	2	FACETS	0.896	0.827	0.966	0.896	0.827	0.966	CLONAL	2	TRUE	0	0.515001762490493	2		192	273	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076782	72076782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373419972	NA	P-0030365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	60	404	0	ENST00000357731.5:c.715C>T	p.Arg239Cys	p.R239C	ENST00000357731	NM_173808.2	239	Cgc/Tgc	5/7	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		404	388	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932711	39932712	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0030366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	304	264	0	ENST00000378444.4:c.1887_1888insAA	p.Glu630LysfsTer40	p.E630Kfs*40	ENST00000378444	NM_001123385.1	629	-/AA	4/15	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.686626374955449	1		264	485	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879976	44879976	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0030366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	115	203	0	ENST00000377967.4:c.564+1G>C		p.X188_splice	ENST00000377967	NM_021140.2	188			1	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.686626374955449	1		203	189	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372478	55372478	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	109	672	0	ENST00000297316.4:c.1168G>A	p.Asp390Asn	p.D390N	ENST00000297316	NM_022454.3	390	Gac/Aac	2/2	1	2	FACETS	0.857	0.769	0.951	0.857	0.769	0.951	CLONAL	1	TRUE	1	0.28	2		672	908	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120169	70120169	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	95	277	1	ENST00000245479.2:c.1171C>T	p.Gln391Ter	p.Q391*	ENST00000245479	NM_000346.3	391	Cag/Tag	3/3	0.25746012970446	2	FACETS	0.945	0.849	1	0.945	0.849	1	CLONAL	2	TRUE	0	0.28	2		278	359	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0030367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	88	461	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.892	0.79	1	0.892	0.79	1	CLONAL	1	TRUE	1	0.28	2		461	705	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0030367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	75	916	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.28	2		916	517	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100175	27100176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0030367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	47	325	0	ENST00000324856.7:c.3977dup	p.Gln1327AlafsTer11	p.Q1327Afs*11	ENST00000324856	NM_006015.4	1324	tac/taCc	16/20	1	2	FACETS	0.637	0.537	0.747	0.637	0.537	0.747	SUBCLONAL	1	TRUE	1	0.28	2		325	527	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0030367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	38	383	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.601	0.496	0.717	0.601	0.496	0.717	SUBCLONAL	1	TRUE	1	0.28	2		383	452	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	35	175	0	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	1	2	FACETS	0.784	0.644	0.939	0.784	0.644	0.939	CLONAL	1	TRUE	1	0.28	2		175	319	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455090	50455090	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	63	313	1	ENST00000331340.3:c.637C>T	p.Arg213Ter	p.R213*	ENST00000331340	NM_006060.4	213	Cga/Tga	6/8	0.261346554242972	3	FACETS	0.977	0.846	1	0.489	0.423	0.56	CLONAL	1	TRUE	1	0.28	3		314	525	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710645	114710645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	76	343	1	ENST00000543371.1:c.130G>T	p.Val44Phe	p.V44F	ENST00000543371	NM_001198531.1	44	Gtc/Ttc	1/14	1	2	FACETS	0.983	0.864	1	0.983	0.864	1	CLONAL	1	TRUE	1	0.28	2		344	552	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737419	145737419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756401653	NA	P-0030367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	88	497	0	ENST00000428558.2:c.3268G>A	p.Glu1090Lys	p.E1090K	ENST00000428558	NM_004260.3	1090	Gag/Aag	20/22	1	2	FACETS	0.835	0.739	0.937	0.835	0.739	0.937	CLONAL	1	TRUE	1	0.28	2		497	753	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648470	30648470	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0030367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	63	357	1	ENST00000295754.5:c.94+1G>A		p.X32_splice	ENST00000295754	NM_003242.5	32			1	2	FACETS	0.932	0.807	1	0.932	0.807	1	CLONAL	1	TRUE	1	0.28	2		358	483	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088760	27088760	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	67	475	0	ENST00000324856.7:c.2369del	p.Gln790ArgfsTer43	p.Q790Rfs*43	ENST00000324856	NM_006015.4	790	cAg/cg	7/20	1	2	FACETS	0.719	0.624	0.821	0.719	0.624	0.821	SUBCLONAL	1	TRUE	1	0.28	2		475	666	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983123	201983123	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	97	477	0	ENST00000359651.3:c.972G>A	p.Met324Ile	p.M324I	ENST00000359651		324	atG/atA	7/8	1	2	FACETS	0.96	0.856	1	0.96	0.856	1	CLONAL	1	TRUE	1	0.28	2		477	722	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727844	41727844	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	113	580	0	ENST00000301178.4:c.469A>G	p.Asn157Asp	p.N157D	ENST00000301178	NM_021913.4	157	Aac/Gac	4/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.28	2		580	758	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	79	454	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.287871288719891	2		454	524	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109692	115109692	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	129	628	0	ENST00000257566.3:c.2186G>T	p.Ser729Ile	p.S729I	ENST00000257566	NM_016569.3	729	aGc/aTc	8/8	1	2	FACETS	0.821	0.743	0.903	0.821	0.743	0.903	CLONAL	1	TRUE	1	0.287871288719891	2		628	1092	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819174	3819174	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0030369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	71	333	0	ENST00000262367.5:c.3060+1G>A		p.X1020_splice	ENST00000262367	NM_004380.2	1020			1	2	FACETS	0.793	0.692	0.902	0.793	0.692	0.902	CLONAL	1	TRUE	1	0.287871288719891	2		333	622	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29422353	29422353	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567786829	NA	P-0030369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	141	569	0	ENST00000356175.3:c.26G>A	p.Trp9Ter	p.W9*	ENST00000356175	NM_000267.3	9	tGg/tAg	1/57	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.287871288719891	2		569	946	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164181	32164182	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	T	novel	NA	P-0030369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	97	369	0	ENST00000375023.3:c.5217_5218delinsA	p.His1739GlnfsTer6	p.H1739Qfs*6	ENST00000375023	NM_004557.3	1739	caCTgg/caAgg	29/30	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.287871288719891	2		369	661	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471812	120471812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	48	344	0	ENST00000256646.2:c.3679G>A	p.Asp1227Asn	p.D1227N	ENST00000256646	NM_024408.3	1227	Gat/Aat	23/34	0.397114334544637	5	FACETS	0.416	0.35	0.488			1	SUBCLONAL	1	TRUE	NA	0.628490629558091	5		344	714	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639971	3639971	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376133540	NA	P-0030371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	83	526	0	ENST00000294008.3:c.3668C>T	p.Pro1223Leu	p.P1223L	ENST00000294008	NM_032444.2	1223	cCg/cTg	12/15	0.397114334544637	5	FACETS	0.454	0.4	0.514			1	SUBCLONAL	1	TRUE	NA	0.628490629558091	5		526	1129	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578259	7578259	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	76	566	0	ENST00000269305.4:c.590T>G	p.Val197Gly	p.V197G	ENST00000269305	NM_001126112.2	197	gTg/gGg	6/11	0.255946257996254	1	FACETS	0.755	0.662	0.855	0.755	0.662	0.855	SUBCLONAL	1	TRUE	0	0.255946257996254	1		566	686	SUCCESS
ATR	545	MSKCC	GRCh37	3	142185352	142185384	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAATGTGGAACTACTTCCATCAACCTGAAAAAA	TAATGTGGAACTACTTCCATCAACCTGAAAAAA	-	novel	NA	P-0030374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	49	349	0	ENST00000350721.4:c.6688-9_6711del		p.X2230_splice	ENST00000350721	NM_001184.3	2230		40/47	1	2	FACETS	0.685	0.58	0.801	0.685	0.58	0.801	SUBCLONAL	1	TRUE	1	0.255946257996254	2		349	559	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940032	76940056	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGCATTATGGCAAAAGTCACAAC	AAAGCATTATGGCAAAAGTCACAAC	-	novel	NA	P-0030374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	55	543	0	ENST00000373344.5:c.692_716del	p.Cys231SerfsTer18	p.C231Sfs*18	ENST00000373344	NM_000489.3	231	tGTTGTGACTTTTGCCATAATGCTTTc/tc	9/35	0.255946257996254	1	FACETS	0.455	0.388	0.529	0.455	0.388	0.529	SUBCLONAL	1	TRUE	0	0.255946257996254	1		543	823	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0030375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	269	645	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	NA	2	FACETS	0.906	0.853	0.961			1	INDETERMINATE	2	TRUE	NA	0.356418638439003	2		645	833	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368202	45368202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	47	310	0	ENST00000262160.6:c.1400C>T	p.Ser467Leu	p.S467L	ENST00000262160	NM_005901.5	467	tCa/tTa	11/11	0.169047928406908	3	FACETS	0.747	0.631	0.874	0.373	0.315	0.437	INDETERMINATE	1	TRUE	1	0.356418638439003	3		310	416	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056425	26056427	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	rs774779034	NA	P-0030375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	37	247	0	ENST00000343677.2:c.230_232del	p.Asn77del	p.N77del	ENST00000343677	NM_005319.3	77	aACAgc/agc	1/1	1	2	FACETS	0.731	0.605	0.87	0.731	0.605	0.87	SUBCLONAL	1	TRUE	1	0.356418638439003	2		247	284	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846037	68846037	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0030375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	75	460	0	ENST00000261769.5:c.1009-1G>C		p.X337_splice	ENST00000261769	NM_004360.3	337			1	2	FACETS	0.75	0.658	0.849	0.75	0.658	0.849	SUBCLONAL	1	TRUE	1	0.356418638439003	2		460	561	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305381	65305381	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	81	398	0	ENST00000342505.4:c.2747G>T	p.Gly916Val	p.G916V	ENST00000342505	NM_002227.2	916	gGt/gTt	20/25	0.303518800808167	3	FACETS	0.821	0.724	0.926	0.411	0.362	0.463	CLONAL	1	TRUE	1	0.356418638439003	3		398	652	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562634	21562634	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	41	265	0	ENST00000382592.4:c.1285C>A	p.Pro429Thr	p.P429T	ENST00000382592	NM_014572.2	429	Ccc/Acc	4/8	1	2	FACETS	0.514	0.428	0.609	0.514	0.428	0.609	SUBCLONAL	1	TRUE	1	0.356418638439003	2		265	448	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913991	32913992	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	64	478	0	ENST00000380152.3:c.5500dup	p.Ser1834LysfsTer2	p.S1834Kfs*2	ENST00000380152		1833	-/A	11/27	1	2	FACETS	0.517	0.447	0.594	0.517	0.447	0.594	SUBCLONAL	1	TRUE	1	0.356418638439003	2		478	694	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216349	7216349	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	69	402	0	ENST00000380728.2:c.899A>G	p.Lys300Arg	p.K300R	ENST00000380728		300	aAg/aGg	10/11	NA	2	FACETS	0.672	0.586	0.765			1	INDETERMINATE	1	TRUE	NA	0.356418638439003	2		402	576	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752631	42752631	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs754180432	NA	P-0030375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	77	375	0	ENST00000222329.4:c.1633C>G	p.His545Asp	p.H545D	ENST00000222329	NM_006494.2	545	Cac/Gac	4/4	0.314606915116452	2	FACETS	0.898	0.791	1	0.449	0.395	0.507	CLONAL	1	TRUE	0	0.356418638439003	2		375	481	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339771	116339771	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	151	334	0	ENST00000397752.3:c.633G>T	p.Leu211Phe	p.L211F	ENST00000397752	NM_000245.2	211	ttG/ttT	2/21	0.356418638439003	4	FACETS	0.826	0.757	0.898	0.413	0.378	0.449	CLONAL	2	TRUE	0	0.356418638439003	4		334	696	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696433	47696433	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	257	478	0	ENST00000347630.2:c.390C>G	p.Asp130Glu	p.D130E	ENST00000347630	NM_001007230.1	130	gaC/gaG	6/11	1	2	FACETS	0.99	0.932	1	0.99	0.932	1	CLONAL	1	TRUE	1	0.749508487838037	2		478	693	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191587	10191599	+	frameshift_variant	Frame_Shift_Del	DEL	GTGCAGAAAGACC	GTGCAGAAAGACC	-	novel	NA	P-0030377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	341	473	0	ENST00000256474.2:c.580_592del	p.Val194TrpfsTer4	p.V194Wfs*4	ENST00000256474	NM_000551.3	194	GTGCAGAAAGACCtg/tg	3/3	0.749508487838037	2	FACETS	0.964	0.93	0.996	0.964	0.93	0.996	CLONAL	2	TRUE	0	0.749508487838037	2		473	472	SUCCESS
APC	324	MSKCC	GRCh37	5	112175969	112175969	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	168	264	0	ENST00000257430.4:c.4678G>T	p.Glu1560Ter	p.E1560*	ENST00000257430	NM_000038.5	1560	Gaa/Taa	16/16	0.857867250770988	1	FACETS	0.985	0.938	1	0.985	0.938	1	CLONAL	1	TRUE	0	0.857867250770988	1		264	227	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114116	115114116	+	splice_donor_variant	Splice_Site	DEL	A	A	-	novel	NA	P-0030381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	266	374	0	ENST00000257566.3:c.1099+2del		p.X367_splice	ENST00000257566	NM_016569.3	367			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.857867250770988	2		374	599	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061847	38061848	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTAG	novel	NA	P-0030381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	373	744	0	ENST00000250448.2:c.138_141dup	p.Met48LeufsTer180	p.M48Lfs*180	ENST00000250448	NM_004496.3	47	-/CTAC	2/2	1	2	FACETS	0.881	0.838	0.924	0.881	0.838	0.924	CLONAL	1	TRUE	1	0.857867250770988	2		744	987	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0030382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	296	601	7	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.381613777641329	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.381613777641329	2		608	774	SUCCESS
APC	324	MSKCC	GRCh37	5	112174204	112174204	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	170	416	0	ENST00000257430.4:c.2913del	p.Asp971GlufsTer9	p.D971Efs*9	ENST00000257430	NM_000038.5	971	gaT/ga	16/16	0.373650838141467	3	FACETS	0.899	0.831	0.969	0.899	0.831	0.969	CLONAL	2	TRUE	1	0.381613777641329	3		416	590	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815623	139815623	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	124	562	3	ENST00000247668.2:c.1094G>T	p.Arg365Leu	p.R365L	ENST00000247668	NM_021138.3	365	cGc/cTc	9/11	0.373650838141467	3	FACETS	1	0.941	1	0.526	0.477	0.579	CLONAL	1	TRUE	1	0.381613777641329	3		565	735	SUCCESS
APC	324	MSKCC	GRCh37	5	112103086	112103111	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTAACTTTTCTTCATATAGTAAAC	AGGTAACTTTTCTTCATATAGTAAAC	-	novel	NA	P-0030386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	23	194	0	ENST00000257430.4:c.422_422+25del		p.X141_splice	ENST00000257430	NM_000038.5	141		4/16	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		194	164	SUCCESS
REL	5966	MSKCC	GRCh37	2	61121593	61121593	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	143	412	0	ENST00000295025.8:c.215A>T	p.Tyr72Phe	p.Y72F	ENST00000295025	NM_002908.2	72	tAt/tTt	3/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.454341191755208	2		412	570	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	101	454	0				ENST00000310581	NM_198253.2	-/1132			0.336938605346729	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.336938605346729	1		454	352	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	293	613	0	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	0.336938605346729	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.336938605346729	3		613	841	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047507	49047507	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0030389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	101	90	0	ENST00000267163.4:c.2501C>G	p.Ser834Ter	p.S834*	ENST00000267163	NM_000321.2	834	tCa/tGa	24/27	0.336938605346729	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.336938605346729	1		90	355	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0030389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	85	398	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.302754427144414	3	FACETS	1	0.963	1	0.605	0.537	0.678	CLONAL	1	TRUE	1	0.336938605346729	3		398	487	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670433	88670433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	37	331	0	ENST00000360948.2:c.1253C>T	p.Pro418Leu	p.P418L	ENST00000360948	NM_001012338.2	418	cCt/cTt	11/19	1	2	FACETS	0.56	0.462	0.67	0.56	0.462	0.67	SUBCLONAL	1	TRUE	1	0.336938605346729	2		331	392	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549884	187549884	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756351356	NA	P-0030389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	54	344	3	ENST00000441802.2:c.4357C>T	p.Arg1453Cys	p.R1453C	ENST00000441802	NM_005245.3	1453	Cgt/Tgt	8/27	0.152980343786991	3	FACETS	0.723	0.618	0.838	0.241	0.206	0.28	INDETERMINATE	1	TRUE	0	0.336938605346729	3		347	518	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453179	140453179	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913340	NA	P-0030389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	108	304	2	ENST00000288602.6:c.1756G>A	p.Glu586Lys	p.E586K	ENST00000288602	NM_004333.4	586	Gaa/Aaa	15/18	0.302754427144414	3	FACETS	0.779	0.702	0.859	0.779	0.702	0.859	SUBCLONAL	2	TRUE	1	0.336938605346729	3		306	481	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866707	37866707	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	161	587	0	ENST00000269571.5:c.874G>C	p.Gly292Arg	p.G292R	ENST00000269571		292	Ggc/Cgc	7/27	0.223522302620021	3	FACETS	1	0.987	1	0.701	0.644	0.761	CLONAL	1	TRUE	1	0.336938605346729	3		587	796	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831324	72831324	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	33	284	0	ENST00000268489.5:c.5257C>T	p.Gln1753Ter	p.Q1753*	ENST00000268489	NM_006885.3	1753	Caa/Taa	9/10	1	2	FACETS	0.556	0.454	0.672	0.556	0.454	0.672	SUBCLONAL	1	TRUE	1	0.336938605346729	2		284	352	SUCCESS
APC	324	MSKCC	GRCh37	5	112179500	112179500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	55	350	0	ENST00000257430.4:c.8209G>A	p.Glu2737Lys	p.E2737K	ENST00000257430	NM_000038.5	2737	Gag/Aag	16/16	0.131204254070681	3	FACETS	0.718	0.615	0.832	0.359	0.307	0.416	INDETERMINATE	1	TRUE	1	0.336938605346729	3		350	531	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206941996	206941996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	86	311	0	ENST00000423557.1:c.522G>A	p.Met174Ile	p.M174I	ENST00000423557	NM_000572.2	174	atG/atA	5/5	0.287682745378918	5	FACETS	1	0.976	1	0.473	0.42	0.531	CLONAL	1	TRUE	2	0.336938605346729	5		311	541	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41199660	41199660	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs80357212	NA	P-0030389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	91	550	0	ENST00000357654.3:c.5467G>A	p.Ala1823Thr	p.A1823T	ENST00000357654	NM_007294.3	1823	Gca/Aca	22/23	0.223522302620021	3	FACETS	0.748	0.663	0.838	0.374	0.331	0.419	SUBCLONAL	1	TRUE	1	0.336938605346729	3		550	844	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097595	27097610	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTTTGGTTATACAGG	GGTTTGGTTATACAGG	-	novel	NA	P-0030389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	191	377	0	ENST00000324856.7:c.3199-15_3199del		p.X1067_splice	ENST00000324856	NM_006015.4	1067		12/20	0.336938605346729	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.336938605346729	3		377	609	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366765	40366781	+	protein_altering_variant	In_Frame_Del	DEL	AGCGAGCCGGTCGCTCA	AGCGAGCCGGTCGCTCA	CT	novel	NA	P-0030389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	66	434	2	ENST00000397332.2:c.416_432delinsAG	p.Val139_Ala144delinsGlu	p.V139_A144delinsE	ENST00000397332	NM_001033082.2	139	gTGAGCGACCGGCTCGCT/gAG	2/3	0.336938605346729	3	FACETS	0.787	0.683	0.899	0.393	0.341	0.45	SUBCLONAL	1	TRUE	1	0.336938605346729	3		436	582	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252059	226252059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	27	246	0	ENST00000366813.1:c.7C>T	p.Arg3Cys	p.R3C	ENST00000366813		3	Cgt/Tgt	1/3	0.287682745378918	5	FACETS	0.591	0.47	0.73	0.197	0.156	0.244	SUBCLONAL	1	TRUE	2	0.336938605346729	5		246	408	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622099	43622099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs79853121	NA	P-0030389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	68	429	1	ENST00000355710.3:c.3116C>T	p.Pro1039Leu	p.P1039L	ENST00000355710	NM_020975.4	1039	cCg/cTg	19/20	0.226012640316527	2	FACETS	0.695	0.605	0.792	0.347	0.302	0.396	SUBCLONAL	1	TRUE	0	0.336938605346729	2		430	581	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348736	89348736	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs977735530	NA	P-0030389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	77	783	0	ENST00000301030.4:c.4214C>G	p.Ser1405Cys	p.S1405C	ENST00000301030	NM_001256183.1	1405	tCt/tGt	9/13	1	2	FACETS	0.492	0.431	0.558	0.492	0.431	0.558	SUBCLONAL	1	TRUE	1	0.336938605346729	2		783	929	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351863	89351863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	123	761	2	ENST00000301030.4:c.1087G>A	p.Asp363Asn	p.D363N	ENST00000301030	NM_001256183.1	363	Gac/Aac	9/13	1	2	FACETS	0.864	0.781	0.952	0.864	0.781	0.952	CLONAL	1	TRUE	1	0.336938605346729	2		763	845	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836363	89836371	+	inframe_deletion	In_Frame_Del	DEL	ACCTGGACT	ACCTGGACT	-	novel	NA	P-0030389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	75	538	0	ENST00000389301.3:c.2378_2386del	p.Glu793_Ser796delinsAla	p.E793_S796delinsA	ENST00000389301	NM_000135.2	793	gAGTCCAGGTct/gct	26/43	1	2	FACETS	0.677	0.593	0.767	0.677	0.593	0.767	SUBCLONAL	1	TRUE	1	0.336938605346729	2		538	658	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006636	62006636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369201285	NA	P-0030389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	75	499	2	ENST00000392795.3:c.643C>T	p.Arg215Trp	p.R215W	ENST00000392795	NM_001039933.1	215	Cgg/Tgg	6/6	0.223522302620021	3	FACETS	0.748	0.655	0.849	0.374	0.327	0.425	SUBCLONAL	1	TRUE	1	0.336938605346729	3		501	695	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464475	25464475	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0030389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	73	454	0	ENST00000264709.3:c.2038A>T	p.Lys680Ter	p.K680*	ENST00000264709	NM_175629.2	680	Aag/Tag	17/23	0.336938605346729	3	FACETS	0.749	0.655	0.851	0.374	0.327	0.426	SUBCLONAL	1	TRUE	1	0.336938605346729	3		454	676	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012689	36012689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1406297899	NA	P-0030389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	28	134	3	ENST00000358208.4:c.133G>A	p.Asp45Asn	p.D45N	ENST00000358208		45	Gac/Aac	2/12	0.336938605346729	3	FACETS	0.833	0.67	1	0.417	0.335	0.509	CLONAL	1	TRUE	1	0.336938605346729	3		137	233	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628296	187628296	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	162	545	0	ENST00000441802.2:c.2686G>A	p.Glu896Lys	p.E896K	ENST00000441802	NM_005245.3	896	Gag/Aag	2/27	0.152980343786991	3	FACETS	0.819	0.753	0.887	0.546	0.502	0.591	INDETERMINATE	2	TRUE	0	0.336938605346729	3		545	686	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288314	33288314	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	50	406	0	ENST00000374542.5:c.1094G>T	p.Arg365Leu	p.R365L	ENST00000374542	NM_001141970.1	365	cGg/cTg	4/8	0.268042553807337	3	FACETS	0.597	0.506	0.697			1	SUBCLONAL	1	TRUE	NA	0.336938605346729	3		406	581	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38148058	38148058	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	171	634	0	ENST00000317025.8:c.3053C>G	p.Pro1018Arg	p.P1018R	ENST00000317025	NM_023034.1	1018	cCt/cGt	17/24	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.336938605346729	2		634	912	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111510	8111511	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	99	557	0	ENST00000346208.3:c.998dup	p.Asn333LysfsTer19	p.N333Kfs*19	ENST00000346208		332	-/A	5/6	0.318656156766772	3	FACETS	0.912	0.816	1	0.456	0.408	0.507	CLONAL	1	TRUE	1	0.432047358824376	3		557	611	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0030394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	224	338	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.976	0.916	1	0.976	0.916	1	CLONAL	1	TRUE	1	0.824283643406547	2		338	557	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0030394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	512	283	0				ENST00000310581	NM_198253.2	-/1132			0.824283643406547	4	FACETS	0.99	0.96	1	0.99	0.96	1	CLONAL	3	TRUE	1	0.824283643406547	4		283	763	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0030394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	154	461	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.907	0.839	0.976	0.907	0.839	0.976	CLONAL	1	TRUE	1	0.824283643406547	2		461	412	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487641	56487641	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771536549	NA	P-0030394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	197	442	2	ENST00000267101.3:c.1574G>A	p.Arg525Gln	p.R525Q	ENST00000267101	NM_001982.3	525	cGa/cAa	13/28	1	2	FACETS	0.864	0.806	0.924	0.864	0.806	0.924	CLONAL	1	TRUE	1	0.824283643406547	2		444	553	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094386	27094386	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	229	450	0	ENST00000324856.7:c.3094G>T	p.Glu1032Ter	p.E1032*	ENST00000324856	NM_006015.4	1032	Gag/Tag	11/20	1	2	FACETS	0.98	0.921	1	0.98	0.921	1	CLONAL	1	TRUE	1	0.824283643406547	2		450	567	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651963	36651963	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	393	459	0	ENST00000244741.5:c.85C>T	p.Gln29Ter	p.Q29*	ENST00000244741	NM_000389.4	29	Cag/Tag	2/3	0.805369260698191	2	FACETS	0.987	0.961	1	0.987	0.961	1	CLONAL	2	TRUE	0	0.824283643406547	2		459	483	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796985	42796985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758868794	NA	P-0030394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	300	672	1	ENST00000575354.2:c.3443C>T	p.Pro1148Leu	p.P1148L	ENST00000575354	NM_015125.3	1148	cCg/cTg	14/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.824283643406547	2		673	683	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981550	201981551	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0030394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	328	651	0	ENST00000359651.3:c.467dup	p.Gly157ArgfsTer4	p.G157Rfs*4	ENST00000359651		155	gac/gaCc	3/8	1	2	FACETS	0.937	0.889	0.986	0.937	0.889	0.986	CLONAL	1	TRUE	1	0.824283643406547	2		651	849	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623584	43623584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	167	349	0	ENST00000355710.3:c.3212G>A	p.Gly1071Glu	p.G1071E	ENST00000355710	NM_020975.4	1071	gGa/gAa	20/20	1	2	FACETS	0.909	0.843	0.975	0.909	0.843	0.975	CLONAL	1	TRUE	1	0.824283643406547	2		349	446	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18439817	18439817	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	142	400	0	ENST00000266497.5:c.715C>G	p.Gln239Glu	p.Q239E	ENST00000266497		239	Caa/Gaa	2/31	1	2	FACETS	0.756	0.694	0.819	0.756	0.694	0.819	SUBCLONAL	1	TRUE	1	0.824283643406547	2		400	456	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478935	56478935	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	272	542	0	ENST00000267101.3:c.391C>G	p.Leu131Val	p.L131V	ENST00000267101	NM_001982.3	131	Ctg/Gtg	3/28	1	2	FACETS	0.994	0.939	1	0.994	0.939	1	CLONAL	1	TRUE	1	0.824283643406547	2		542	664	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906942	32906942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507579	NA	P-0030394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	180	423	0	ENST00000380152.3:c.1327G>A	p.Glu443Lys	p.E443K	ENST00000380152		443	Gag/Aag	10/27	1	2	FACETS	0.91	0.847	0.974	0.91	0.847	0.974	CLONAL	1	TRUE	1	0.824283643406547	2		423	480	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3795316	3795316	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	198	470	0	ENST00000262367.5:c.3876G>C	p.Gln1292His	p.Q1292H	ENST00000262367	NM_004380.2	1292	caG/caC	22/31	1	2	FACETS	0.867	0.809	0.926	0.867	0.809	0.926	CLONAL	1	TRUE	1	0.824283643406547	2		470	554	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863674	68863674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200894246	NA	P-0030394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	194	411	1	ENST00000261769.5:c.2413G>A	p.Asp805Asn	p.D805N	ENST00000261769	NM_004360.3	805	Gat/Aat	15/16	1	2	FACETS	0.987	0.923	1	0.987	0.923	1	CLONAL	1	TRUE	1	0.824283643406547	2		412	477	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170750	7170750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	268	540	1	ENST00000302850.5:c.1281C>A	p.Phe427Leu	p.F427L	ENST00000302850	NM_000208.2	427	ttC/ttA	6/22	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.824283643406547	2		541	628	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175861	24175861	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1568963037	NA	P-0030394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	200	458	0	ENST00000263121.7:c.1089G>T	p.Lys363Asn	p.K363N	ENST00000263121	NM_003073.3	363	aaG/aaT	8/9	1	2	FACETS	0.924	0.864	0.986	0.924	0.864	0.986	CLONAL	1	TRUE	1	0.824283643406547	2		458	525	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569659	41569659	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	119	297	0	ENST00000263253.7:c.4650G>T	p.Lys1550Asn	p.K1550N	ENST00000263253	NM_001429.3	1550	aaG/aaT	29/31	1	2	FACETS	0.8	0.73	0.872	0.8	0.73	0.872	SUBCLONAL	1	TRUE	1	0.824283643406547	2		297	361	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569713	41569716	+	frameshift_variant	Frame_Shift_Del	DEL	GAAG	GAAG	AAA	novel	NA	P-0030394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	173	408	1	ENST00000263253.7:c.4704_4707delinsAAA	p.Lys1570AsnfsTer28	p.K1570Nfs*28	ENST00000263253	NM_001429.3	1568	aaGAAG/aaAAA	29/31	1	2	FACETS	0.874	0.812	0.938	0.874	0.812	0.938	CLONAL	1	TRUE	1	0.824283643406547	2		409	480	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569773	41569773	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	143	328	0	ENST00000263253.7:c.4764G>T	p.Met1588Ile	p.M1588I	ENST00000263253	NM_001429.3	1588	atG/atT	29/31	1	2	FACETS	0.923	0.852	0.995	0.923	0.852	0.995	CLONAL	1	TRUE	1	0.824283643406547	2		328	376	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573438	41573438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1284977519	NA	P-0030394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	226	592	0	ENST00000263253.7:c.5723C>T	p.Pro1908Leu	p.P1908L	ENST00000263253	NM_001429.3	1908	cCa/cTa	31/31	1	2	FACETS	0.911	0.855	0.968	0.911	0.855	0.968	CLONAL	1	TRUE	1	0.824283643406547	2		592	602	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573636	41573636	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	206	592	0	ENST00000263253.7:c.5921G>C	p.Arg1974Thr	p.R1974T	ENST00000263253	NM_001429.3	1974	aGa/aCa	31/31	1	2	FACETS	0.899	0.841	0.958	0.899	0.841	0.958	CLONAL	1	TRUE	1	0.824283643406547	2		592	556	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574326	41574326	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	294	601	3	ENST00000263253.7:c.6611G>T	p.Gly2204Val	p.G2204V	ENST00000263253	NM_001429.3	2204	gGa/gTa	31/31	1	2	FACETS	0.985	0.933	1	0.985	0.933	1	CLONAL	1	TRUE	1	0.824283643406547	2		604	724	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564578	55564578	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	239	501	0	ENST00000288135.5:c.466C>T	p.Leu156Phe	p.L156F	ENST00000288135	NM_000222.2	156	Ctt/Ttt	3/21	1	2	FACETS	0.995	0.936	1	0.995	0.936	1	CLONAL	1	TRUE	1	0.824283643406547	2		501	583	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700313	117700313	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	211	340	0	ENST00000368508.3:c.2506C>G	p.Leu836Val	p.L836V	ENST00000368508	NM_002944.2	836	Cta/Gta	17/43	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.824283643406547	2		340	465	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889176	76889176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	219	240	0	ENST00000373344.5:c.4834C>T	p.Leu1612Phe	p.L1612F	ENST00000373344	NM_000489.3	1612	Ctt/Ttt	18/35	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.824283643406547	1		240	265	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0030407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	54	427	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.694	0.59	0.808	0.694	0.59	0.808	SUBCLONAL	1	TRUE	1	0.16	2		427	973	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0030407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	67	558	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	1	2	FACETS	0.781	0.677	0.895	0.781	0.677	0.895	SUBCLONAL	1	TRUE	1	0.16	2		558	1072	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28605709	28605709	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	63	665	0	ENST00000253063.3:c.1313G>C	p.Arg438Thr	p.R438T	ENST00000253063	NM_031459.4	438	aGa/aCa	9/10	1	2	FACETS	0.64	0.551	0.737	0.64	0.551	0.737	SUBCLONAL	1	TRUE	1	0.16	2		665	1230	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241275	105241276	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0030407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	72	530	0	ENST00000349310.3:c.632_633del	p.Thr211SerfsTer45	p.T211Sfs*45	ENST00000349310	NM_001014432.1	211	aCA/a	8/15	1	2	FACETS	0.847	0.738	0.966	0.847	0.738	0.966	CLONAL	1	TRUE	1	0.16	2		530	1062	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0030408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	400	645	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.885334569238065	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.885334569238065	1		645	474	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	244	587	1	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.885334569238065	2		588	550	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456470	89456470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147450955	NA	P-0030408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	281	379	3	ENST00000336596.2:c.1646C>T	p.Ala549Val	p.A549V	ENST00000336596	NM_005233.5	549	gCg/gTg	8/17	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.885334569238065	2		382	628	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310470	65310470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	333	510	0	ENST00000342505.4:c.2218C>T	p.Pro740Ser	p.P740S	ENST00000342505	NM_002227.2	740	Ccc/Tcc	16/25	0.885334569238065	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.885334569238065	1		510	410	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591259	67591261	+	inframe_deletion	In_Frame_Del	DEL	AAA	AAA	-	novel	NA	P-0030408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	312	473	0	ENST00000274335.5:c.1759_1761del	p.Lys587del	p.K587del	ENST00000274335		586	cAAAaa/caa	13/15	1	2	FACETS	0.889	0.842	0.936	0.889	0.842	0.936	CLONAL	1	TRUE	1	0.885334569238065	2		473	793	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0030409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	655	556	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.703859887913237	3	FACETS	0.893	0.863	0.923	0.893	0.863	0.923	CLONAL	2	TRUE	1	0.728455822832387	3		556	1374	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809854	36809854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749198474	NA	P-0030409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	167	485	0	ENST00000373129.3:c.751C>T	p.Arg251Cys	p.R251C	ENST00000373129	NM_032017.1	251	Cgt/Tgt	9/12	0.400196778029246	1	FACETS	0.409	0.377	0.443	0.409	0.377	0.443	INDETERMINATE	1	TRUE	0	0.728455822832387	1		485	712	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004813	16004813	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	30	534	0	ENST00000268712.3:c.2441del	p.Pro814HisfsTer13	p.P814Hfs*13	ENST00000268712	NM_006311.3	814	cCa/ca	20/46	0.728455822832387	1	FACETS	0.092	0.074	0.113	0.092	0.074	0.113	SUBCLONAL	1	TRUE	0	0.728455822832387	1		534	568	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112182	115112182	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	302	463	0	ENST00000257566.3:c.1558del	p.Leu520CysfsTer112	p.L520Cfs*112	ENST00000257566	NM_016569.3	520	Ctg/tg	7/8	0.724364162301882	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.728455822832387	1		463	496	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863701	68863701	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0030409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	201	289	0	ENST00000261769.5:c.2439+1G>A		p.X813_splice	ENST00000261769	NM_004360.3	813			0.728455822832387	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.728455822832387	1		289	322	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189442	56189443	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	174	442	0	ENST00000399503.3:c.4476dup	p.Pro1493ThrfsTer30	p.P1493Tfs*30	ENST00000399503	NM_005921.1	1492	caa/cAaa	20/20	1	2	FACETS	0.606	0.559	0.655	0.606	0.559	0.655	SUBCLONAL	1	TRUE	1	0.728455822832387	2		442	788	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163744	152163744	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	40	359	0	ENST00000206249.3:c.465T>A	p.Asp155Glu	p.D155E	ENST00000206249	NM_000125.3	155	gaT/gaA	2/8	1	2	FACETS	0.17	0.141	0.203	0.17	0.141	0.203	SUBCLONAL	1	TRUE	1	0.728455822832387	2		359	645	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266112	41266112	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913228	NA	P-0030410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	12	316	0	ENST00000349496.5:c.109T>C	p.Ser37Pro	p.S37P	ENST00000349496	NM_001904.3	37	Tct/Cct	3/15	1	2	FACETS	0.08	0.056	0.111	0.08	0.056	0.111	SUBCLONAL	1	TRUE	1	0.513817721909882	2		316	582	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191485	185191485	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	284	693	0	ENST00000265026.3:c.2368del	p.Leu790SerfsTer34	p.L790Sfs*34	ENST00000265026	NM_004721.4	789	tCc/tc	11/14	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.513817721909882	2		693	1030	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949983	44949996	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCAGTGGAACGG	TGGCAGTGGAACGG	-	novel	NA	P-0030410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	17	255	0	ENST00000377967.4:c.3753_3766del	p.Ala1252ArgfsTer34	p.A1252Rfs*34	ENST00000377967	NM_021140.2	1251	tTGGCAGTGGAACGG/t	26/29	1	1	FACETS	0.231	0.172	0.3	0.231	0.172	0.3	SUBCLONAL	1	TRUE	0	0.513817721909882	1		255	213	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0030411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	68	532	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.0881095156848046	3	FACETS	1	0.948	1	0.594	0.516	0.678	INDETERMINATE	1	TRUE	1	0.1723372039581	3		533	722	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0030411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	117	664	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.154122772522615	2	FACETS	0.936	0.845	1	0.936	0.845	1	CLONAL	2	TRUE	0	0.1723372039581	2		664	725	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028490	42028490	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	116	467	0	ENST00000219905.7:c.4028A>T	p.Asn1343Ile	p.N1343I	ENST00000219905	NM_001164273.1	1343	aAc/aTc	13/24	0.1723372039581	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.1723372039581	2		467	629	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690568	88690571	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TTCC	TTCC	-	novel	NA	P-0030411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	41	507	0	ENST00000360948.2:c.459_462del	p.Glu154CysfsTer48	p.E154Cfs*48	ENST00000360948	NM_001012338.2	153	cgGGAA/cg	5/19	0.0881095156848046	3	FACETS	0.669	0.555	0.795	0.334	0.277	0.398	INDETERMINATE	1	TRUE	1	0.1723372039581	3		507	773	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069392	30069392	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	124	623	0	ENST00000338641.4:c.1258del	p.Glu420ArgfsTer6	p.E420Rfs*6	ENST00000338641	NM_000268.3	419	acG/ac	12/16	0.154122772522615	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	0	0.1723372039581	2		623	688	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0030412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	202	241	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.977	0.909	1	1	0.994	1	CLONAL	2	TRUE	1	0.289440143319032	2		241	714	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0030412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	333	564	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.289440143319032	2		564	989	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028657	12028657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	146	505	0	ENST00000353533.5:c.860G>A	p.Arg287His	p.R287H	ENST00000353533	NM_003010.3	287	cGc/cAc	8/11	0.274181741650663	0	FACETS	0.687	0.63	0.745			1	SUBCLONAL	2	TRUE	0	0.289440143319032	0		505	522	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578260	7578260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204041	NA	P-0030412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	346	781	0	ENST00000269305.4:c.589G>A	p.Val197Met	p.V197M	ENST00000269305	NM_001126112.2	197	Gtg/Atg	6/11	0.274181741650663	0	FACETS	0.709	0.675	0.743			1	SUBCLONAL	3	TRUE	0	0.289440143319032	0		781	799	SUCCESS
APC	324	MSKCC	GRCh37	5	112175788	112175788	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	185	365	0	ENST00000257430.4:c.4497del	p.Ser1501LeufsTer6	p.S1501Lfs*6	ENST00000257430	NM_000038.5	1499	ggA/gg	16/16	1	2	FACETS	1	0.966	1	1	0.994	1	CLONAL	2	TRUE	1	0.289440143319032	2		365	599	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222726	5222726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779918003	NA	P-0030412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	340	617	0	ENST00000357368.4:c.3077G>A	p.Arg1026His	p.R1026H	ENST00000357368	NM_002850.3	1026	cGc/cAc	18/38	1	2	FACETS	0.894	0.849	0.939	1	0.997	1	CLONAL	3	TRUE	1	0.289440143319032	2		617	876	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411777	63411777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767567473	NA	P-0030412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	242	781	0	ENST00000330258.3:c.1390G>A	p.Ala464Thr	p.A464T	ENST00000330258	NM_152424.3	464	Gcc/Acc	2/2	0.289440143319032	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.289440143319032	1		781	1075	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259244	89259244	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	131	459	0	ENST00000336596.2:c.388G>T	p.Asp130Tyr	p.D130Y	ENST00000336596	NM_005233.5	130	Gat/Tat	3/17	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.289440143319032	2		459	741	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877349	40877349	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs747289224	NA	P-0030412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	435	409	0	ENST00000373198.4:c.2347G>C	p.Val783Leu	p.V783L	ENST00000373198	NM_133170.3	783	Gtg/Ctg	15/32	0.221244865980955	4	FACETS	1	0.988	1	1	0.996	1	CLONAL	4	TRUE	1	0.289440143319032	4		409	899	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0030414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	390	609	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.303257275577631	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	3	TRUE	0	0.29	3		610	1012	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098944	178098944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	75	313	0	ENST00000397062.3:c.101G>A	p.Arg34Gln	p.R34Q	ENST00000397062	NM_006164.4	34	cGa/cAa	2/5	0.303257275577631	3	FACETS	1	0.922	1	0.535	0.469	0.605	CLONAL	1	TRUE	1	0.29	3		313	554	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0030414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	56	311	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.303257275577631	3	FACETS	0.884	0.758	1	0.442	0.379	0.511	CLONAL	1	TRUE	1	0.29	3		311	500	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944512	40944512	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	153	499	0	ENST00000373198.4:c.1990T>C	p.Phe664Leu	p.F664L	ENST00000373198	NM_133170.3	664	Ttt/Ctt	12/32	0.303257275577631	4	FACETS	0.852	0.78	0.927	0.852	0.78	0.927	CLONAL	2	TRUE	2	0.29	4		499	799	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107135	27107136	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	190	465	0	ENST00000324856.7:c.6747dup	p.Glu2250ArgfsTer28	p.E2250Rfs*28	ENST00000324856	NM_006015.4	2249	tca/tcAa	20/20	0.303257275577631	2	FACETS	0.954	0.885	1	0.954	0.885	1	CLONAL	2	TRUE	0	0.29	2		465	687	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717609	89717609	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs876661024	NA	P-0030414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	163	364	0	ENST00000371953.3:c.635-1G>A		p.X212_splice	ENST00000371953	NM_000314.4	212			0.303257275577631	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	2	0.29	4		364	658	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539056	23539056	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	93	425	0	ENST00000380871.4:c.383G>A	p.Arg128Gln	p.R128Q	ENST00000380871	NM_006167.3	128	cGa/cAa	2/2	0.303257275577631	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.29	1		425	490	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919734	50919734	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878854545	NA	P-0030414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	57	589	0	ENST00000440232.2:c.2902C>T	p.Arg968Cys	p.R968C	ENST00000440232	NM_002691.3	968	Cgc/Tgc	23/27	0.29269430972694	2	FACETS	0.478	0.409	0.554	0.239	0.204	0.277	SUBCLONAL	1	TRUE	0	0.29	2		589	822	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372037	55372037	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1217255052	NA	P-0030414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	163	355	1	ENST00000297316.4:c.727G>A	p.Gly243Arg	p.G243R	ENST00000297316	NM_022454.3	243	Ggg/Agg	2/2	0.303257275577631	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.29	3		356	548	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998718	100998718	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	139	601	1	ENST00000325455.5:c.1084G>A	p.Ala362Thr	p.A362T	ENST00000325455	NM_001202474.3	362	Gcg/Acg	1/8	0.303257275577631	3	FACETS	1	0.966	1	0.563	0.512	0.617	CLONAL	1	TRUE	1	0.29	3		602	975	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149996	202149996	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	177	373	0	ENST00000358485.4:c.1437G>A	p.Trp479Ter	p.W479*	ENST00000358485	NM_001080125.1	479	tgG/tgA	8/9	0.303257275577631	3	FACETS	0.868	0.801	0.938	0.868	0.801	0.938	CLONAL	2	TRUE	1	0.29	3		373	805	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426590	49426590	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1459162950	NA	P-0030414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	277	651	0	ENST00000301067.7:c.11898T>G	p.Phe3966Leu	p.F3966L	ENST00000301067	NM_003482.3	3966	ttT/ttG	39/54	0.303257275577631	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.29	3		651	1025	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335624	81335624	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	178	450	0	ENST00000222390.5:c.1736T>C	p.Leu579Pro	p.L579P	ENST00000222390	NM_000601.4	579	cTg/cCg	15/18	0.303257275577631	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	2	0.29	4		450	753	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0030417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	37	576	0	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	1	2	FACETS	0.244	0.2	0.293	0.244	0.2	0.293	SUBCLONAL	1	TRUE	1	0.409709431745887	2		576	740	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247894	10247894	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	72	535	0	ENST00000340748.4:c.4308G>A	p.Trp1436Ter	p.W1436*	ENST00000340748		1436	tgG/tgA	36/40	0.28104221823084	3	FACETS	0.5	0.437	0.568	0.25	0.218	0.284	INDETERMINATE	1	TRUE	1	0.589245290809034	3		535	633	SUCCESS
AXL	558	MSKCC	GRCh37	19	41759593	41759593	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	47	582	0	ENST00000301178.4:c.2016C>A	p.Asp672Glu	p.D672E	ENST00000301178	NM_021913.4	672	gaC/gaA	17/20	0.589245290809034	3	FACETS	0.289	0.243	0.34	0.144	0.121	0.17	SUBCLONAL	1	TRUE	1	0.589245290809034	3		582	715	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835596	68835596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587783047	NA	P-0030420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	205	516	1	ENST00000261769.5:c.187C>T	p.Arg63Ter	p.R63*	ENST00000261769	NM_004360.3	63	Cga/Tga	3/16	0.661991345414126	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.661991345414126	1		517	384	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962594	100962594	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0030420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	197	374	0	ENST00000325455.5:c.1803C>G	p.Tyr601Ter	p.Y601*	ENST00000325455	NM_001202474.3	601	taC/taG	3/8	0.661991345414126	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.661991345414126	1		374	370	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793046	42793046	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	113	455	0	ENST00000575354.2:c.938C>T	p.Ser313Phe	p.S313F	ENST00000575354	NM_015125.3	313	tCt/tTt	7/20	1	2	FACETS	0.565	0.51	0.624	0.565	0.51	0.624	SUBCLONAL	1	TRUE	1	0.661991345414126	2		455	604	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029521	14029521	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202186213	NA	P-0030438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	104	381	0	ENST00000311895.7:c.1732G>A	p.Val578Met	p.V578M	ENST00000311895	NM_005236.2	578	Gtg/Atg	8/11	1	2	FACETS	0.996	0.901	1	0.996	0.901	1	CLONAL	1	TRUE	1	0.60550224073878	2		381	345	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696638	47696638	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	119	553	0	ENST00000347630.2:c.310T>A	p.Phe104Ile	p.F104I	ENST00000347630	NM_001007230.1	104	Ttc/Atc	5/11	0.403685313715784	1	FACETS	0.675	0.614	0.738	0.675	0.614	0.738	SUBCLONAL	1	TRUE	0	0.60550224073878	1		553	406	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588255	69588255	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0030438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	38	397	0	ENST00000168712.1:c.445-2A>T		p.X149_splice	ENST00000168712	NM_002007.2	149			0.403685313715784	1	FACETS	0.774	0.657	0.898	0.774	0.657	0.898	SUBCLONAL	1	TRUE	0	0.60550224073878	1		397	113	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832015	72832015	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	211	637	0	ENST00000268489.5:c.4566del	p.Arg1523GlufsTer17	p.R1523Efs*17	ENST00000268489	NM_006885.3	1522	aaG/aa	9/10	0.60550224073878	3	FACETS	0.985	0.926	1			1	CLONAL	2	TRUE	NA	0.60550224073878	3		637	461	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945146	44945146	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	170	299	0	ENST00000377967.4:c.3470T>G	p.Ile1157Arg	p.I1157R	ENST00000377967	NM_021140.2	1157	aTa/aGa	24/29	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.60550224073878	1		299	276	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0030439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	204	622	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.289570112397966	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.26	3		622	824	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0030439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	269	606	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.25005471282439	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.26	2		606	851	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944315	81944315	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367884906	NA	P-0030439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	113	500	0	ENST00000359376.3:c.1924G>A	p.Glu642Lys	p.E642K	ENST00000359376	NM_002661.3	642	Gag/Aag	18/33	0.275240662942502	2	FACETS	1	0.972	1	0.612	0.551	0.676	CLONAL	1	TRUE	0	0.26	2		500	710	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919473	78919473	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752129121	NA	P-0030439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1210	139	548	1	ENST00000306801.3:c.3032C>T	p.Thr1011Met	p.T1011M	ENST00000306801	NM_020761.2	1011	aCg/aTg	26/34	0.3	6	FACETS	1	0.975	1	0.241	0.218	0.265	CLONAL	1	TRUE	1	0.26	6		549	1349	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164751	106164751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	83	319	0	ENST00000380013.4:c.3619G>A	p.Glu1207Lys	p.E1207K	ENST00000380013	NM_001127208.2	1207	Gag/Aag	6/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.26	2		319	556	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199655	138199655	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	97	522	0	ENST00000237289.4:c.1073A>C	p.Glu358Ala	p.E358A	ENST00000237289	NM_001270507.1	358	gAa/gCa	7/9	1	2	FACETS	0.984	0.877	1	0.984	0.877	1	CLONAL	1	TRUE	1	0.26	2		522	758	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829252	128829648	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCACCTCCACACTGCTGGCCGGAGACTCGGACTCCCAGGAGGAAGCGCACGGCAAGCTCGTGCTCTGGTCGGGTAAGTGCGGCGGAGCCGGGTCTGGGGGGCGGGAGGTGCCGCGGTAAGATGGGGGCACCCTTGGAAAGAACAGGCTCAGGCCTGAGTTTTGGAGAGGGCGGGGACAGCACCCGGGAGAGTTGGAGGGACAGATCCCGAAACTTTGGGGGCAGGTTACGTGCAGGATGGGACCCTCGGTCATGGGAAAAGGAGGGCAAGGAAGTTGACGAAGCGGGTCACAAAGGGCCTGAGCTGGTGGGTGAGCAAAGGATGGCGGGGATGAGGGGCCCGTGAGGAGGTGGCTCTAAGCCACGGGAAAAGACATTTTGTAAGAAGAGGAGATGCT	CCACCTCCACACTGCTGGCCGGAGACTCGGACTCCCAGGAGGAAGCGCACGGCAAGCTCGTGCTCTGGTCGGGTAAGTGCGGCGGAGCCGGGTCTGGGGGGCGGGAGGTGCCGCGGTAAGATGGGGGCACCCTTGGAAAGAACAGGCTCAGGCCTGAGTTTTGGAGAGGGCGGGGACAGCACCCGGGAGAGTTGGAGGGACAGATCCCGAAACTTTGGGGGCAGGTTACGTGCAGGATGGGACCCTCGGTCATGGGAAAAGGAGGGCAAGGAAGTTGACGAAGCGGGTCACAAAGGGCCTGAGCTGGTGGGTGAGCAAAGGATGGCGGGGATGAGGGGCCCGTGAGGAGGTGGCTCTAAGCCACGGGAAAAGACATTTTGTAAGAAGAGGAGATGCT	-	novel	NA	P-0030439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	49	497	0	ENST00000249373.3:c.266_331+331del		p.X89_splice	ENST00000249373	NM_005631.4	89		1/12	1	2	FACETS	0.445	0.376	0.522	0.445	0.376	0.522	SUBCLONAL	1	TRUE	1	0.26	2		497	847	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0030439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	220	622	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.332557154888162	1	FACETS	0.819	0.769	0.869	0.819	0.769	0.869	INDETERMINATE	1	TRUE	0	0.670303687787072	1		622	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0030439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	309	606	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.670303687787072	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.670303687787072	1		606	488	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919473	78919473	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752129121	NA	P-0030439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	151	548	1	ENST00000306801.3:c.3032C>T	p.Thr1011Met	p.T1011M	ENST00000306801	NM_020761.2	1011	aCg/aTg	26/34	0.670303687787072	3	FACETS	0.531	0.485	0.58	0.177	0.161	0.194	SUBCLONAL	1	TRUE	0	0.670303687787072	3		549	1132	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199655	138199655	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	80	522	0	ENST00000237289.4:c.1073A>C	p.Glu358Ala	p.E358A	ENST00000237289	NM_001270507.1	358	gAa/gCa	7/9	0.236745268289149	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.670303687787072	0		522	531	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829252	128829648	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCACCTCCACACTGCTGGCCGGAGACTCGGACTCCCAGGAGGAAGCGCACGGCAAGCTCGTGCTCTGGTCGGGTAAGTGCGGCGGAGCCGGGTCTGGGGGGCGGGAGGTGCCGCGGTAAGATGGGGGCACCCTTGGAAAGAACAGGCTCAGGCCTGAGTTTTGGAGAGGGCGGGGACAGCACCCGGGAGAGTTGGAGGGACAGATCCCGAAACTTTGGGGGCAGGTTACGTGCAGGATGGGACCCTCGGTCATGGGAAAAGGAGGGCAAGGAAGTTGACGAAGCGGGTCACAAAGGGCCTGAGCTGGTGGGTGAGCAAAGGATGGCGGGGATGAGGGGCCCGTGAGGAGGTGGCTCTAAGCCACGGGAAAAGACATTTTGTAAGAAGAGGAGATGCT	CCACCTCCACACTGCTGGCCGGAGACTCGGACTCCCAGGAGGAAGCGCACGGCAAGCTCGTGCTCTGGTCGGGTAAGTGCGGCGGAGCCGGGTCTGGGGGGCGGGAGGTGCCGCGGTAAGATGGGGGCACCCTTGGAAAGAACAGGCTCAGGCCTGAGTTTTGGAGAGGGCGGGGACAGCACCCGGGAGAGTTGGAGGGACAGATCCCGAAACTTTGGGGGCAGGTTACGTGCAGGATGGGACCCTCGGTCATGGGAAAAGGAGGGCAAGGAAGTTGACGAAGCGGGTCACAAAGGGCCTGAGCTGGTGGGTGAGCAAAGGATGGCGGGGATGAGGGGCCCGTGAGGAGGTGGCTCTAAGCCACGGGAAAAGACATTTTGTAAGAAGAGGAGATGCT	-	novel	NA	P-0030439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	142	497	0	ENST00000249373.3:c.266_331+331del		p.X89_splice	ENST00000249373	NM_005631.4	89		1/12	1	2	FACETS	0.48	0.437	0.525	0.48	0.437	0.525	SUBCLONAL	1	TRUE	1	0.670303687787072	2		497	882	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980872	40980872	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	95	498	0	ENST00000373198.4:c.1614G>C	p.Gln538His	p.Q538H	ENST00000373198	NM_133170.3	538	caG/caC	10/32	0.249883249027277	2	FACETS	0.345	0.306	0.386	0.172	0.153	0.193	INDETERMINATE	1	TRUE	0	0.670303687787072	2		498	822	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871715	35871716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0030440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	102	501	0	ENST00000216797.5:c.790dup	p.Arg264ProfsTer21	p.R264Pfs*21	ENST00000216797	NM_020529.2	264	cgg/cCgg	5/6	1	2	FACETS	0.925	0.828	1	0.925	0.828	1	CLONAL	1	TRUE	1	0.326096919121697	2		501	676	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0030441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	60	286	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.550738444215349	1	FACETS	0.661	0.576	0.75	0.661	0.576	0.75	SUBCLONAL	1	TRUE	0	0.550738444215349	1		286	239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579378	7579378	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	134	707	0	ENST00000269305.4:c.309C>A	p.Tyr103Ter	p.Y103*	ENST00000269305	NM_001126112.2	103	taC/taA	4/11	NA	2	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.550738444215349	2		707	406	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366335	15366335	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	67	508	0	ENST00000263377.2:c.1820G>A	p.Cys607Tyr	p.C607Y	ENST00000263377	NM_058243.2	607	tGc/tAc	10/20	1	2	FACETS	0.742	0.649	0.84	0.742	0.649	0.84	SUBCLONAL	1	TRUE	1	0.550738444215349	2		508	328	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73350197	73350197	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	29	401	0	ENST00000377767.4:c.688G>C	p.Glu230Gln	p.E230Q	ENST00000377767	NM_014953.3	230	Gag/Cag	5/21	0.307404062793827	3	FACETS	0.602	0.486	0.733	0.301	0.243	0.367	INDETERMINATE	1	TRUE	1	0.550738444215349	3		401	223	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845764	68845764	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1060501237	NA	P-0030441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	71	428	0	ENST00000261769.5:c.1008+2T>C		p.X336_splice	ENST00000261769	NM_004360.3	336			0.47904003534066	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.550738444215349	1		428	172	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39575912	39575912	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	34	450	0	ENST00000262039.4:c.845C>G	p.Ser282Cys	p.S282C	ENST00000262039	NM_002647.2	282	tCt/tGt	8/25	0.550738444215349	1	FACETS	0.215	0.175	0.259	0.215	0.175	0.259	SUBCLONAL	1	TRUE	0	0.550738444215349	1		450	417	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797118	42797118	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	40	835	0	ENST00000575354.2:c.3480G>T	p.Met1160Ile	p.M1160I	ENST00000575354	NM_015125.3	1160	atG/atT	15/20	1	2	FACETS	0.261	0.216	0.311	0.261	0.216	0.311	SUBCLONAL	1	TRUE	1	0.550738444215349	2		835	557	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795476	39795476	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	205	521	0	ENST00000288319.7:c.244C>A	p.Pro82Thr	p.P82T	ENST00000288319	NM_182918.3	82	Cct/Act	3/10	0.550738444215349	3	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	1	0.550738444215349	3		521	470	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927976	178927984	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	ACACTGTCC	ACACTGTCC	-	novel	NA	P-0030441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	103	305	0	ENST00000263967.3:c.1255_1263del	p.His419_Pro421del	p.H419_P421del	ENST00000263967	NM_006218.2	418	gaACACTGTCCa/gaa	8/21	0.478709302772207	3	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	1	0.550738444215349	3		305	233	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714456	117714456	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0030441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	11	453	0	ENST00000368508.3:c.1193C>G	p.Ser398Ter	p.S398*	ENST00000368508	NM_002944.2	398	tCa/tGa	11/43	0.456955644612105	1	FACETS	0.148	0.102	0.206	0.148	0.102	0.206	SUBCLONAL	1	TRUE	0	0.550738444215349	1		453	195	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860107	151860107	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	85	471	0	ENST00000262189.6:c.10555del	p.Ser3519HisfsTer14	p.S3519Hfs*14	ENST00000262189	NM_170606.2	3519	Tca/ca	43/59	0.307404062793827	3	FACETS	1	0.976	1	0.681	0.609	0.756	INDETERMINATE	1	TRUE	1	0.550738444215349	3		471	289	SUCCESS
AR	367	MSKCC	GRCh37	X	66765038	66765038	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	68	840	1	ENST00000374690.3:c.50A>G	p.Lys17Arg	p.K17R	ENST00000374690	NM_000044.3	17	aAg/aGg	1/8	1	2	FACETS	0.426	0.371	0.486	0.426	0.371	0.486	SUBCLONAL	1	TRUE	1	0.550738444215349	2		841	579	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0030442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	361	427	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.604314560388933	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.604314560388933	2		427	579	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579348	7579349	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	312	647	0	ENST00000269305.4:c.338dup	p.His115AlafsTer34	p.H115Afs*34	ENST00000269305	NM_001126112.2	113	ttc/ttTc	4/11	0.58925149960281	1	FACETS	0.987	0.937	1	0.987	0.937	1	CLONAL	1	TRUE	0	0.604314560388933	1		647	730	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972909	55972909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	242	624	1	ENST00000263923.4:c.1481G>T	p.Gly494Val	p.G494V	ENST00000263923	NM_002253.2	494	gGa/gTa	11/30	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.604314560388933	2		625	744	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759622	133759623	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0030442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	300	709	0	ENST00000318560.5:c.1950dup	p.Asp652GlyfsTer4	p.D652Gfs*4	ENST00000318560	NM_005157.4	649	acc/aCcc	11/11	1	2	FACETS	0.899	0.847	0.953	0.899	0.847	0.953	CLONAL	1	TRUE	1	0.604314560388933	2		709	1104	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696425	47696425	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519967	NA	P-0030445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	85	515	0	ENST00000347630.2:c.398T>C	p.Phe133Ser	p.F133S	ENST00000347630	NM_001007230.1	133	tTc/tCc	6/11	1	2	FACETS	0.882	0.779	0.993	0.882	0.779	0.993	CLONAL	1	TRUE	1	0.23977693041735	2		515	804	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366578	118366578	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	58	447	0	ENST00000534358.1:c.5528del	p.Pro1843LeufsTer10	p.P1843Lfs*10	ENST00000534358	NM_005933.3	1843	Cct/ct	19/36	1	2	FACETS	0.757	0.65	0.874	0.757	0.65	0.874	SUBCLONAL	1	TRUE	1	0.23977693041735	2		447	639	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0030449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	24	532	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.438	0.343	0.549	0.438	0.343	0.549	SUBCLONAL	1	TRUE	1	0.23867218094147	2		533	459	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0030449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	41	622	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.801	0.668	0.949	0.801	0.668	0.949	CLONAL	1	TRUE	1	0.23867218094147	2		622	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0030449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	86	622	1	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.23867218094147	2		623	598	SUCCESS
APC	324	MSKCC	GRCh37	5	112174112	112174112	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	42	336	0	ENST00000257430.4:c.2821G>T	p.Glu941Ter	p.E941*	ENST00000257430	NM_000038.5	941	Gaa/Taa	16/16	1	2	FACETS	0.896	0.749	1	0.896	0.749	1	CLONAL	1	TRUE	1	0.23867218094147	2		336	393	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713589	30713589	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1553630174	NA	P-0030449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	97	380	2	ENST00000295754.5:c.914T>G	p.Leu305Arg	p.L305R	ENST00000295754	NM_003242.5	305	cTc/cGc	4/7	1	2	FACETS	0.819	0.733	0.91	1	0.984	1	CLONAL	2	TRUE	1	0.23867218094147	2		382	496	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199502	16199502	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	46	402	0	ENST00000375759.3:c.275A>C	p.Asp92Ala	p.D92A	ENST00000375759	NM_015001.2	92	gAt/gCt	2/15	1	2	FACETS	0.81	0.682	0.95	0.81	0.682	0.95	CLONAL	1	TRUE	1	0.23867218094147	2		402	476	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975681	26975681	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	45	436	0	ENST00000381527.3:c.1189C>T	p.Gln397Ter	p.Q397*	ENST00000381527	NM_001260.1	397	Cag/Tag	12/13	1	2	FACETS	0.766	0.644	0.902	0.766	0.644	0.902	CLONAL	1	TRUE	1	0.23867218094147	2		436	492	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223228	5223228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1224185745	NA	P-0030449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	86	623	1	ENST00000357368.4:c.2575G>A	p.Ala859Thr	p.A859T	ENST00000357368	NM_002850.3	859	Gcg/Acg	18/38	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.23867218094147	2		624	673	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249504	153249504	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	85	491	2	ENST00000281708.4:c.1274G>A	p.Trp425Ter	p.W425*	ENST00000281708	NM_033632.3	425	tGg/tAg	9/12	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.23867218094147	2		493	542	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0030450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	47	338	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.329	0.277	0.386	0.329	0.277	0.386	SUBCLONAL	1	TRUE	1	0.524154090148641	2		338	545	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0030450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	190	546	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.524154090148641	2		546	619	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0030450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	36	336	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.234	0.192	0.282	0.234	0.192	0.282	SUBCLONAL	1	TRUE	1	0.524154090148641	2		336	587	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555687605	NA	P-0030450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	46	413	3	ENST00000342988.3:c.1610A>G	p.Asp537Gly	p.D537G	ENST00000342988	NM_005359.5	537	gAc/gGc	12/12	0.524154090148641	1	FACETS	0.342	0.288	0.4	0.342	0.288	0.4	SUBCLONAL	1	TRUE	0	0.524154090148641	1		416	379	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391214	89391214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs530556931	NA	P-0030450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	110	320	3	ENST00000336596.2:c.1280C>T	p.Ala427Val	p.A427V	ENST00000336596	NM_005233.5	427	gCg/gTg	5/17	1	2	FACETS	0.933	0.843	1	0.933	0.843	1	CLONAL	1	TRUE	1	0.524154090148641	2		323	450	SUCCESS
APC	324	MSKCC	GRCh37	5	112175358	112175358	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	156	218	0	ENST00000257430.4:c.4067C>A	p.Ser1356Ter	p.S1356*	ENST00000257430	NM_000038.5	1356	tCa/tAa	16/16	0.524154090148641	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.524154090148641	2		218	284	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604656	48604656	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	21	265	0	ENST00000342988.3:c.1478A>T	p.Asp493Val	p.D493V	ENST00000342988	NM_005359.5	493	gAt/gTt	12/12	0.524154090148641	1	FACETS	0.189	0.145	0.24	0.189	0.145	0.24	SUBCLONAL	1	TRUE	0	0.524154090148641	1		265	313	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911575	114911575	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	210	575	0	ENST00000543371.1:c.1093A>G	p.Arg365Gly	p.R365G	ENST00000543371	NM_001198531.1	365	Aga/Gga	10/14	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.524154090148641	2		575	780	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143287	108143287	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	210	411	0	ENST00000278616.4:c.3107del	p.Phe1036SerfsTer3	p.F1036Sfs*3	ENST00000278616	NM_000051.3	1036	Ttc/tc	21/63	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.524154090148641	2		411	622	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40461409	40461409	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	52	592	0	ENST00000345506.4:c.2129C>A	p.Ser710Tyr	p.S710Y	ENST00000345506	NM_003152.3	710	tCt/tAt	19/20	1	2	FACETS	0.266	0.226	0.31	0.266	0.226	0.31	SUBCLONAL	1	TRUE	1	0.524154090148641	2		592	746	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297736	15297736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs530073028	NA	P-0030450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	118	686	0	ENST00000263388.2:c.1904G>A	p.Arg635His	p.R635H	ENST00000263388	NM_000435.2	635	cGt/cAt	12/33	0.195624191237169	3	FACETS	0.577	0.52	0.638	0.289	0.26	0.319	INDETERMINATE	1	TRUE	1	0.524154090148641	3		686	984	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210874	36210874	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1002774016	NA	P-0030450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	310	705	1	ENST00000222270.7:c.625C>T	p.Arg209Trp	p.R209W	ENST00000222270	NM_014727.1	209	Cgg/Tgg	3/37	0.195624191237169	3	FACETS	0.817	0.772	0.862	0.817	0.772	0.862	INDETERMINATE	2	TRUE	1	0.524154090148641	3		706	914	SUCCESS
AR	367	MSKCC	GRCh37	X	66765771	66765771	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	236	783	0	ENST00000374690.3:c.783A>C	p.Glu261Asp	p.E261D	ENST00000374690	NM_000044.3	261	gaA/gaC	1/8	0.342747082200137	1	FACETS	0.692	0.646	0.739	0.692	0.646	0.739	SUBCLONAL	1	TRUE	0	0.524154090148641	1		783	960	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119809	70119817	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGACGTG	CGCGACGTG	T	novel	NA	P-0030450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	202	583	0	ENST00000245479.2:c.811_819delinsT	p.Arg271Ter	p.R271*	ENST00000245479	NM_000346.3	271	CGCGACGTG/T	3/3	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.524154090148641	2		583	737	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0030451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	184	712	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.907	0.842	0.973	0.907	0.842	0.973	CLONAL	1	TRUE	1	0.687888529247076	2		712	590	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0030451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	295	552	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.864	0.814	0.914	0.864	0.814	0.914	CLONAL	1	TRUE	1	0.687888529247076	2		552	993	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273045	18273045	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1397761287	NA	P-0030451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	344	721	1	ENST00000222254.8:c.935C>T	p.Ala312Val	p.A312V	ENST00000222254	NM_005027.3	312	gCc/gTc	8/16	1	2	FACETS	0.953	0.903	1	0.953	0.903	1	CLONAL	1	TRUE	1	0.687888529247076	2		722	1050	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517697	187517697	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	11	127	0	ENST00000441802.2:c.12997G>T	p.Asp4333Tyr	p.D4333Y	ENST00000441802	NM_005245.3	4333	Gac/Tac	25/27	1	2	FACETS	0.458	0.317	0.631	0.458	0.317	0.631	SUBCLONAL	1	TRUE	1	0.320234373375752	2		127	150	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39744979	39744979	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	29	436	0	ENST00000361337.2:c.1769G>A	p.Arg590His	p.R590H	ENST00000361337	NM_003286.2	590	cGt/cAt	17/21	0.266165826441451	2	FACETS	0.35	0.28	0.429	0.175	0.14	0.215	SUBCLONAL	1	TRUE	0	0.323295000081824	2		436	513	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579363	7579364	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0030454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	190	601	0	ENST00000269305.4:c.323dup	p.Arg110ProfsTer39	p.R110Pfs*39	ENST00000269305	NM_001126112.2	108	ggt/ggGt	4/11	0.266165826441451	2	FACETS	0.928	0.863	0.996	0.928	0.863	0.996	CLONAL	2	TRUE	0	0.323295000081824	2		601	633	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0030455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	232	601	7	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.509701621292914	2		608	849	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0030455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	189	521	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.509701621292914	2		521	708	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222419	2222419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778985752	NA	P-0030455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	123	445	0	ENST00000398665.3:c.3251G>A	p.Arg1084His	p.R1084H	ENST00000398665	NM_032482.2	1084	cGc/cAc	24/28	0.509701621292914	2	FACETS	0.977	0.889	1	0.488	0.444	0.535	CLONAL	1	TRUE	0	0.509701621292914	2		445	494	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412031	116412031	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	57	742	0	ENST00000397752.3:c.3016A>C	p.Thr1006Pro	p.T1006P	ENST00000397752	NM_000245.2	1006	Act/Cct	14/21	0.339648537808028	5	FACETS	0.405	0.346	0.47	0.135	0.115	0.157	SUBCLONAL	1	TRUE	2	0.509701621292914	5		742	974	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717615	89717615	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909227	NA	P-0030456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	241	390	1	ENST00000371953.3:c.640C>T	p.Gln214Ter	p.Q214*	ENST00000371953	NM_000314.4	214	Cag/Tag	7/9	0.719868202421786	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.719868202421786	1		391	375	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589556	67589591	+	inframe_deletion	In_Frame_Del	DEL	ATAATATTGAAGCTGTAGGGAAAAAATTACATGAAT	ATAATATTGAAGCTGTAGGGAAAAAATTACATGAAT	-	novel	NA	P-0030456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	32	241	0	ENST00000274335.5:c.1323_1358del	p.Ile442_Asn453del	p.I442_N453del	ENST00000274335		440	gATAATATTGAAGCTGTAGGGAAAAAATTACATGAATat/gat	10/15	0.407478450950424	1	FACETS	0.213	0.173	0.258	0.213	0.173	0.258	INDETERMINATE	1	TRUE	0	0.719868202421786	1		241	267	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914928	32914941	+	frameshift_variant	Frame_Shift_Del	DEL	AATCACTCTATTAA	AATCACTCTATTAA	-	novel	NA	P-0030456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	36	451	0	ENST00000380152.3:c.6437_6450del	p.Asn2146SerfsTer25	p.N2146Sfs*25	ENST00000380152		2146	AATCACTCTATTAAa/a	11/27	0.408605511920588	1	FACETS	0.227	0.187	0.271	0.227	0.187	0.271	INDETERMINATE	1	TRUE	0	0.719868202421786	1		451	282	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040940	42040940	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	274	517	0	ENST00000219905.7:c.5318C>T	p.Thr1773Ile	p.T1773I	ENST00000219905	NM_001164273.1	1773	aCt/aTt	16/24	1	2	FACETS	0.985	0.929	1	0.985	0.929	1	CLONAL	1	TRUE	1	0.719868202421786	2		517	773	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707614	176707614	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	275	428	0	ENST00000439151.2:c.5671G>C	p.Glu1891Gln	p.E1891Q	ENST00000439151	NM_022455.4	1891	Gaa/Caa	18/23	0.407478450950424	1	FACETS	0.84	0.797	0.884	0.84	0.797	0.884	INDETERMINATE	1	TRUE	0	0.719868202421786	1		428	582	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0030457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	181	594	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.217736335596464	3	FACETS	0.945	0.871	1			1	CLONAL	2	TRUE	NA	0.23	3		594	929	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0030457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	59	513	5	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	1	2	FACETS	0.706	0.606	0.815	0.706	0.606	0.815	SUBCLONAL	1	TRUE	1	0.23	2		518	727	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896442	151896442	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	41	421	0	ENST00000262189.6:c.4195A>G	p.Met1399Val	p.M1399V	ENST00000262189	NM_170606.2	1399	Atg/Gtg	27/59	1	2	FACETS	0.569	0.473	0.676	0.569	0.473	0.676	SUBCLONAL	1	TRUE	1	0.23	2		421	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0030458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	51	545	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.170276781108295	2		545	548	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057970	27057971	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0030458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	45	341	1	ENST00000324856.7:c.1679dup	p.Tyr560Ter	p.Y560*	ENST00000324856	NM_006015.4	560	tac/tAac	3/20	1	2	FACETS	0.931	0.781	1	0.931	0.781	1	CLONAL	1	TRUE	1	0.170276781108295	2		342	568	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0030459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	108	350	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.328083112267278	3	FACETS	1	0.96	1	0.567	0.51	0.627	CLONAL	1	TRUE	1	0.395564773164003	3		350	577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0030459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	75	605	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.406	0.355	0.462	0.406	0.355	0.462	SUBCLONAL	1	TRUE	1	0.395564773164003	2		607	933	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0030459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	94	338	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.395564773164003	2		338	464	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0030459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	117	286	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.395564773164003	2		286	563	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0030459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	113	311	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.951	0.858	1	0.951	0.858	1	CLONAL	1	TRUE	1	0.395564773164003	2		312	601	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243045	105243045	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	58	711	0	ENST00000349310.3:c.238T>C	p.Trp80Arg	p.W80R	ENST00000349310	NM_001014432.1	80	Tgg/Cgg	5/15	1	2	FACETS	0.294	0.252	0.341	0.294	0.252	0.341	SUBCLONAL	1	TRUE	1	0.395564773164003	2		711	996	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575209	48575209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767326	NA	P-0030459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	61	274	1	ENST00000342988.3:c.403C>T	p.Arg135Ter	p.R135*	ENST00000342988	NM_005359.5	135	Cga/Tga	3/12	1	2	FACETS	0.881	0.764	1	0.881	0.764	1	CLONAL	1	TRUE	1	0.395564773164003	2		275	350	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371801	55371801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746536924	NA	P-0030459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	53	89	1	ENST00000297316.4:c.491C>T	p.Ala164Val	p.A164V	ENST00000297316	NM_022454.3	164	gCg/gTg	2/2	1	2	FACETS	0.924	0.807	1	1	0.977	1	CLONAL	2	TRUE	1	0.395564773164003	2		90	145	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793382	18793382	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs77070108	NA	P-0030459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	84	408	0	ENST00000266497.5:c.4079C>T	p.Ala1360Val	p.A1360V	ENST00000266497		1360	gCg/gTg	30/31	0.395564773164003	1	FACETS	0.752	0.667	0.842	0.752	0.667	0.842	SUBCLONAL	1	TRUE	0	0.395564773164003	1		408	453	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322718	30322718	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	146	530	0	ENST00000322652.5:c.1731A>T	p.Gln577His	p.Q577H	ENST00000322652	NM_015355.2	577	caA/caT	14/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.395564773164003	2		530	666	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94128980	94128980	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	77	350	1	ENST00000369303.4:c.80C>T	p.Ala27Val	p.A27V	ENST00000369303	NM_004440.3	27	gCg/gTg	1/17	1	2	FACETS	0.782	0.688	0.882	0.782	0.688	0.882	SUBCLONAL	1	TRUE	1	0.395564773164003	2		351	498	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	153	454	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.655879553963589	2		454	449	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0030460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	437	461	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.119196714296805	5	FACETS	0.927	0.888	0.966			1	INDETERMINATE	3	TRUE	NA	0.655879553963589	5		461	951	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807901	3807901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	61	489	0	ENST00000262367.5:c.3518G>A	p.Arg1173Gln	p.R1173Q	ENST00000262367	NM_004380.2	1173	cGa/cAa	18/31	1	2	FACETS	0.204	0.175	0.235	0.204	0.175	0.235	SUBCLONAL	1	TRUE	1	0.655879553963589	2		489	914	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753158	42753158	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	342	566	0	ENST00000222329.4:c.1106C>G	p.Ser369Cys	p.S369C	ENST00000222329	NM_006494.2	369	tCt/tGt	4/4	1	2	FACETS	0.937	0.887	0.988	0.937	0.887	0.988	CLONAL	1	TRUE	1	0.655879553963589	2		566	1113	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022373	26022373	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0030460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	415	401	0	ENST00000435504.4:c.284C>G	p.Ser95Ter	p.S95*	ENST00000435504		95	tCa/tGa	5/13	0.655879553963589	2	FACETS	0.925	0.891	0.959	0.925	0.891	0.959	CLONAL	2	TRUE	0	0.655879553963589	2		401	684	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569772	41569772	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057521737	NA	P-0030460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	408	326	0	ENST00000263253.7:c.4763T>C	p.Met1588Thr	p.M1588T	ENST00000263253	NM_001429.3	1588	aTg/aCg	29/31	0.628309254829892	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.655879553963589	2		326	615	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942820	44942821	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	264	555	0	ENST00000377967.4:c.3401dup	p.Tyr1135IlefsTer16	p.Y1135Ifs*16	ENST00000377967	NM_021140.2	1134	cta/cTta	23/29	1	2	FACETS	0.998	0.938	1	0.998	0.938	1	CLONAL	1	TRUE	1	0.655879553963589	2		555	807	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0030462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	265	493	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	0.638989512746288	3	FACETS	0.871	0.816	0.928			1	CLONAL	1	TRUE	NA	0.717349124188958	3		493	1152	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0030462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	183	532	1	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	0.88	0.817	0.944	0.88	0.817	0.944	CLONAL	1	TRUE	1	0.717349124188958	2		533	580	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7978948	7978948	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1174637390	NA	P-0030462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	216	526	0	ENST00000319144.4:c.1619T>C	p.Ile540Thr	p.I540T	ENST00000319144	NM_001139.2	540	aTa/aCa	12/15	1	2	FACETS	0.91	0.85	0.971	0.91	0.85	0.971	CLONAL	1	TRUE	1	0.717349124188958	2		526	662	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40761126	40761127	+	inframe_insertion	In_Frame_Ins	INS	-	-	TATGACAAAGGTGTTGGGTCGCGGCCTCTCGGTCTTCATCAGCTT	novel	NA	P-0030462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	140	746	0	ENST00000392038.2:c.225_226insAAGCTGATGAAGACCGAGAGGCCGCGACCCAACACCTTTGTCATA	p.Ile75_Arg76insLysLeuMetLysThrGluArgProArgProAsnThrPheValIle	p.I75_R76insKLMKTERPRPNTFVI	ENST00000392038	NM_001626.4	75	-/AAGCTGATGAAGACCGAGAGGCCGCGACCCAACACCTTTGTCATA	4/14	1	2	FACETS	0.374	0.34	0.41	0.374	0.34	0.41	SUBCLONAL	1	TRUE	1	0.717349124188958	2		746	1043	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742998	145742998	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	41	57	0	ENST00000428558.2:c.106G>A	p.Glu36Lys	p.E36K	ENST00000428558	NM_004260.3	36	Gag/Aag	2/22	0.70100403642768	3	FACETS	0.822	0.693	0.961	0.411	0.346	0.481	CLONAL	1	TRUE	1	0.717349124188958	3		57	189	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0030463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	167	298	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.375710351545036	3	FACETS	0.96	0.888	1	0.96	0.888	1	CLONAL	2	TRUE	1	0.409403432345382	3		298	512	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412095	63412095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852217	NA	P-0030463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	472	649	3	ENST00000330258.3:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000330258	NM_152424.3	358	Cga/Tga	2/2	0.409403432345382	5	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	2	0.409403432345382	5		652	1211	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572971	7572971	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	282	413	0	ENST00000269305.4:c.1138del	p.His380IlefsTer42	p.H380Ifs*42	ENST00000269305	NM_001126112.2	380	Cat/at	11/11	0.3856154127007	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.409403432345382	2		413	598	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637946	39637946	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	138	490	0	ENST00000262039.4:c.2363G>A	p.Gly788Glu	p.G788E	ENST00000262039	NM_002647.2	788	gGg/gAg	22/25	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.409403432345382	2		490	623	SUCCESS
APC	324	MSKCC	GRCh37	5	112174154	112174154	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	67	405	0	ENST00000257430.4:c.2863G>T	p.Glu955Ter	p.E955*	ENST00000257430	NM_000038.5	955	Gaa/Taa	16/16	0.375710351545036	3	FACETS	0.85	0.74	0.967	0.425	0.37	0.484	CLONAL	1	TRUE	1	0.409403432345382	3		405	464	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0030464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	39	283	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.25	2		283	249	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589599	67589604	+	inframe_deletion	In_Frame_Del	DEL	TCAGTT	TCAGTT	-	novel	NA	P-0030464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	64	415	0	ENST00000274335.5:c.1365_1370del	p.Phe456_Gln457del	p.F456_Q457del	ENST00000274335		454	acTCAGTTt/act	10/15	1	2	FACETS	0.835	0.723	0.957	0.835	0.723	0.957	CLONAL	1	TRUE	1	0.25	2		415	613	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249001	55249002	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCAGCGTGGACAACC	novel	NA	P-0030464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	28	469	0	ENST00000275493.2:c.2302_2316dup	p.Ser768_Pro772dup	p.S768_P772dup	ENST00000275493	NM_005228.3	768	gcc/gCCAGCGTGGACAACCcc	20/28	0.193096440366758	3	FACETS	0.434	0.345	0.535	0.217	0.172	0.268	SUBCLONAL	1	TRUE	1	0.25	3		469	581	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578250	7578250	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1131691011	NA	P-0030466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	50	689	0	ENST00000269305.4:c.599del	p.Asn200IlefsTer47	p.N200Ifs*47	ENST00000269305	NM_001126112.2	200	aAt/at	6/11	1	2	FACETS	0.868	0.734	1	0.868	0.734	1	CLONAL	1	TRUE	1	0.14	2		689	823	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380346	14380346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	178	231	0	ENST00000256196.4:c.71G>A	p.Gly24Asp	p.G24D	ENST00000256196		24	gGc/gAc	1/6	0.3	4	FACETS	0.994	0.925	1	1	0.993	1	CLONAL	6	TRUE	1	0.14	4		231	486	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149290752	149290752	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	54	553	0	ENST00000360632.3:c.467G>A	p.Arg156Lys	p.R156K	ENST00000360632	NM_015472.4	156	aGg/aAg	3/7	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.14	2		553	661	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467578	66467578	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	31	427	1	ENST00000273854.3:c.691A>G	p.Lys231Glu	p.K231E	ENST00000273854	NM_004439.5	231	Aaa/Gaa	3/18	1	2	FACETS	0.886	0.715	1	0.886	0.715	1	CLONAL	1	TRUE	1	0.14	2		428	500	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165657	118165657	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs565811357	NA	P-0030467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	126	437	0	ENST00000369448.3:c.167G>A	p.Arg56His	p.R56H	ENST00000369448	NM_017709.3	56	cGc/cAc	2/2	0.598922362824677	5	FACETS	0.996	0.902	1	0.249	0.225	0.274	CLONAL	1	TRUE	1	0.598922362824677	5		437	802	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70411644	70411644	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	182	610	0	ENST00000373644.4:c.4318C>T	p.Leu1440Phe	p.L1440F	ENST00000373644	NM_030625.2	1440	Ctt/Ttt	5/12	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.598922362824677	2		610	593	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340947	70340947	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	198	337	0	ENST00000374080.3:c.680A>G	p.Glu227Gly	p.E227G	ENST00000374080		227	gAg/gGg	5/45	0.531567467427025	2	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.598922362824677	2		337	551	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18975016	18975016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761111860	NA	P-0030469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	46	353	1	ENST00000262803.5:c.2813G>A	p.Arg938Gln	p.R938Q	ENST00000262803	NM_002911.3	938	cGg/cAg	20/24	1	2	FACETS	0.445	0.374	0.522	0.445	0.374	0.522	SUBCLONAL	1	TRUE	1	0.454807485052726	2		354	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578467	7578476	+	protein_altering_variant	In_Frame_Del	DEL	TGCCGGGCGG	TGCCGGGCGG	CGCC	novel	NA	P-0030469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	88	597	2	ENST00000269305.4:c.454_463delinsGGCG	p.Pro152_Thr155delinsGlyAla	p.P152_T155delinsGA	ENST00000269305	NM_001126112.2	152	CCGCCCGGCAcc/GGCGcc	5/11	1	2	FACETS	0.442	0.391	0.497	0.442	0.391	0.497	SUBCLONAL	1	TRUE	1	0.454807485052726	2		599	876	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0030470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	57	545	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.587	0.504	0.677	0.587	0.504	0.677	SUBCLONAL	1	TRUE	1	0.400494924245121	2		545	485	SUCCESS
APC	324	MSKCC	GRCh37	5	112175174	112175174	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	16	233	0	ENST00000257430.4:c.3883G>T	p.Glu1295Ter	p.E1295*	ENST00000257430	NM_000038.5	1295	Gaa/Taa	16/16	1	2	FACETS	0.398	0.294	0.52	0.398	0.294	0.52	SUBCLONAL	1	TRUE	1	0.400494924245121	2		233	201	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061191	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	14	307	0	ENST00000250448.2:c.798C>G	p.Phe266Leu	p.F266L	ENST00000250448	NM_004496.3	266	ttC/ttG	2/2	0.0800731523530887	3	FACETS	0.84	0.608	1	0.42	0.304	0.561	INDETERMINATE	1	TRUE	1	0.16	3		307	225	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435971	49435971	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	37	664	2	ENST00000301067.7:c.6010C>T	p.Gln2004Ter	p.Q2004*	ENST00000301067	NM_003482.3	2004	Cag/Tag	28/54	1	2	FACETS	0.964	0.794	1	0.964	0.794	1	CLONAL	1	TRUE	1	0.16	2		666	480	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158499	106158501	+	frameshift_variant	Frame_Shift_Del	DEL	AGA	AGA	GT	novel	NA	P-0030472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	18	371	1	ENST00000380013.4:c.3400_3402delinsGT	p.Arg1134ValfsTer3	p.R1134Vfs*3	ENST00000380013	NM_001127208.2	1134	AGA/GT	3/11	1	2	FACETS	0.726	0.546	0.938	0.726	0.546	0.938	CLONAL	1	TRUE	1	0.16	2		372	310	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0030473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	158	655	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.31847500786109	2		655	855	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912229	97912229	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	130	523	0	ENST00000289081.3:c.662A>T	p.Glu221Val	p.E221V	ENST00000289081	NM_000136.2	221	gAg/gTg	7/15	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.31847500786109	2		523	790	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0030475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	137	283	0				ENST00000310581	NM_198253.2	-/1132			0.369206540584668	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.383493848600927	3		283	393	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032481	12032481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	167	301	0	ENST00000353533.5:c.917C>T	p.Pro306Leu	p.P306L	ENST00000353533	NM_003010.3	306	cCt/cTt	9/11	0.357674311305201	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	3	TRUE	0	0.383493848600927	3		301	340	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369299	40369299	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	195	415	0	ENST00000293328.3:c.1259C>T	p.Ser420Phe	p.S420F	ENST00000293328	NM_012448.3	420	tCc/tTc	11/19	0.376788211540157	2	FACETS	0.831	0.773	0.89	0.831	0.773	0.89	CLONAL	2	TRUE	0	0.383493848600927	2		415	612	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149241	119149241	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867564832	NA	P-0030475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	122	486	1	ENST00000264033.4:c.1249C>T	p.Pro417Ser	p.P417S	ENST00000264033	NM_005188.3	417	Cct/Tct	9/16	0.383493848600927	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.383493848600927	1		487	496	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560883	9560883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	80	458	0	ENST00000353224.5:c.899G>A	p.Gly300Glu	p.G300E	ENST00000353224	NM_177990.2	300	gGa/gAa	4/10	0.338913898584287	3	FACETS	0.921	0.812	1	0.46	0.406	0.519	CLONAL	1	TRUE	1	0.383493848600927	3		458	540	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849500	68849501	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0030475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	124	493	2	ENST00000261769.5:c.1403_1404delinsTT	p.Thr468Ile	p.T468I	ENST00000261769	NM_004360.3	468	aCC/aTT	10/16	1	2	FACETS	0.986	0.894	1	0.986	0.894	1	CLONAL	1	TRUE	1	0.383493848600927	2		495	656	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248538	212248538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	219	456	1	ENST00000342788.4:c.3729G>A	p.Trp1243Ter	p.W1243*	ENST00000342788	NM_005235.2	1243	tgG/tgA	28/28	0.383493848600927	2	FACETS	0.953	0.893	1	0.953	0.893	1	CLONAL	2	TRUE	0	0.383493848600927	2		457	599	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246091297	246091297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758081490	NA	P-0030475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	325	486	2	ENST00000388985.4:c.638C>T	p.Ser213Leu	p.S213L	ENST00000388985		213	tCg/tTg	7/12	0.383493848600927	3	FACETS	1	0.992	1	0.814	0.773	0.856	CLONAL	2	TRUE	0	0.383493848600927	3		488	827	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246116	46246116	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	120	346	1	ENST00000334344.6:c.4210C>T	p.Gln1404Ter	p.Q1404*	ENST00000334344	NM_152641.2	1404	Caa/Taa	15/21	0.376788211540157	2	FACETS	0.984	0.901	1	0.984	0.901	1	CLONAL	2	TRUE	0	0.383493848600927	2		347	318	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054631	5054631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760174050	NA	P-0030475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	120	332	0	ENST00000381652.3:c.683G>A	p.Arg228Gln	p.R228Q	ENST00000381652	NM_004972.3	228	cGa/cAa	7/25	0.338913898584287	3	FACETS	0.964	0.879	1	0.964	0.879	1	CLONAL	2	TRUE	1	0.383493848600927	3		332	387	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120493437	120493437	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	160	389	0	ENST00000256646.2:c.2389G>A	p.Asp797Asn	p.D797N	ENST00000256646	NM_024408.3	797	Gat/Aat	15/34	0.369206540584668	3	FACETS	0.921	0.849	0.994	0.921	0.849	0.994	CLONAL	2	TRUE	1	0.383493848600927	3		389	540	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518557	69518557	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	94	356	3	ENST00000294312.3:c.88G>A	p.Ala30Thr	p.A30T	ENST00000294312	NM_005117.2	30	Gcg/Acg	1/3	0.369206540584668	3	FACETS	1	0.946	1	0.549	0.49	0.612	CLONAL	1	TRUE	1	0.383493848600927	3		359	532	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909851	100909851	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	120	175	0	ENST00000325455.5:c.2798A>T	p.Lys933Met	p.K933M	ENST00000325455	NM_001202474.3	933	aAg/aTg	8/8	0.383493848600927	6	FACETS	0.863	0.786	0.944			1	CLONAL	3	TRUE	NA	0.383493848600927	6		175	427	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006381	12006381	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765265003	NA	P-0030475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	78	333	0	ENST00000396373.4:c.349C>T	p.Leu117Phe	p.L117F	ENST00000396373	NM_001987.4	117	Ctt/Ttt	4/8	0.338913898584287	3	FACETS	0.951	0.837	1	0.475	0.418	0.536	CLONAL	1	TRUE	1	0.383493848600927	3		333	510	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448351	49448351	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	285	587	0	ENST00000301067.7:c.360C>G	p.Phe120Leu	p.F120L	ENST00000301067	NM_003482.3	120	ttC/ttG	3/54	0.376788211540157	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.383493848600927	2		587	709	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43769857	43769857	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	199	526	2	ENST00000382044.4:c.889C>T	p.Gln297Ter	p.Q297*	ENST00000382044	NM_001141980.1	297	Cag/Tag	8/28	0.369206540584668	3	FACETS	0.851	0.791	0.913	0.851	0.791	0.913	CLONAL	2	TRUE	1	0.383493848600927	3		528	727	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347466	91347466	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	194	508	1	ENST00000355112.3:c.3628C>T	p.Gln1210Ter	p.Q1210*	ENST00000355112	NM_000057.2	1210	Cag/Tag	19/22	0.369206540584668	3	FACETS	0.864	0.802	0.927	0.864	0.802	0.927	CLONAL	2	TRUE	1	0.383493848600927	3		509	698	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274147	10274147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	111	492	0	ENST00000330684.3:c.122G>A	p.Gly41Asp	p.G41D	ENST00000330684	NM_001134407.1	41	gGt/gAt	2/13	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.383493848600927	2		492	538	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745846	745846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	64	538	0	ENST00000314574.4:c.586C>T	p.Leu196Phe	p.L196F	ENST00000314574	NM_005433.3	196	Ctt/Ttt	6/12	0.212075726126097	3	FACETS	0.945	0.821	1			1	INDETERMINATE	1	TRUE	NA	0.383493848600927	3		538	421	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212395	36212395	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0030475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	146	682	1	ENST00000222270.7:c.2146A>T	p.Lys716Ter	p.K716*	ENST00000222270	NM_014727.1	716	Aag/Tag	3/37	0.373183682807668	4	FACETS	0.87	0.792	0.952	0.29	0.264	0.318	CLONAL	1	TRUE	1	0.383493848600927	4		683	1211	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241948	39241948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	99	440	0	ENST00000402219.2:c.1898C>T	p.Ser633Phe	p.S633F	ENST00000402219	NM_005633.3	633	tCc/tTc	11/23	0.369206540584668	3	FACETS	0.801	0.721	0.885	0.801	0.721	0.885	CLONAL	2	TRUE	1	0.383493848600927	3		440	384	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488747	212488747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	196	424	1	ENST00000342788.4:c.2102G>A	p.Ser701Asn	p.S701N	ENST00000342788	NM_005235.2	701	aGt/aAt	18/28	0.383493848600927	2	FACETS	0.897	0.836	0.959	0.897	0.836	0.959	CLONAL	2	TRUE	0	0.383493848600927	2		425	570	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866441	42866441	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770444484	NA	P-0030475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	328	802	0	ENST00000398585.3:c.191C>T	p.Pro64Leu	p.P64L	ENST00000398585	NM_001135099.1	64	cCc/cTc	3/14	0.338913898584287	3	FACETS	0.776	0.733	0.821	0.776	0.733	0.821	SUBCLONAL	2	TRUE	1	0.383493848600927	3		802	1313	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641665	12641665	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	179	427	0	ENST00000251849.4:c.976G>A	p.Glu326Lys	p.E326K	ENST00000251849	NM_002880.3	326	Gag/Aag	9/17	0.338913898584287	3	FACETS	0.894	0.828	0.962	0.894	0.828	0.962	CLONAL	2	TRUE	1	0.383493848600927	3		427	622	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515191	149515191	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	140	556	0	ENST00000261799.4:c.291A>C	p.Glu97Asp	p.E97D	ENST00000261799	NM_002609.3	97	gaA/gaC	3/23	0.369206540584668	3	FACETS	0.997	0.908	1	0.498	0.454	0.545	CLONAL	1	TRUE	1	0.383493848600927	3		556	873	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748512	43748512	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	129	485	0	ENST00000523873.1:c.466A>G	p.Lys156Glu	p.K156E	ENST00000523873		156	Aag/Gag	6/8	0.373183682807668	4	FACETS	1	0.958	1	0.367	0.332	0.403	CLONAL	1	TRUE	1	0.383493848600927	4		485	846	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622250	117622250	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	108	477	0	ENST00000368508.3:c.6620C>T	p.Thr2207Ile	p.T2207I	ENST00000368508	NM_002944.2	2207	aCt/aTt	42/43	0.376788211540157	2	FACETS	0.802	0.728	0.88	0.802	0.728	0.88	CLONAL	2	TRUE	0	0.383493848600927	2		477	351	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527847	157527847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	199	432	0	ENST00000346085.5:c.5572G>A	p.Glu1858Lys	p.E1858K	ENST00000346085	NM_020732.3	1858	Gag/Aag	20/20	0.376788211540157	2	FACETS	0.943	0.881	1	0.943	0.881	1	CLONAL	2	TRUE	0	0.383493848600927	2		432	550	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022079	5022079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	87	456	0	ENST00000381652.3:c.92C>T	p.Ser31Phe	p.S31F	ENST00000381652	NM_004972.3	31	tCt/tTt	3/25	0.338913898584287	3	FACETS	1	0.933	1	0.535	0.475	0.599	CLONAL	1	TRUE	1	0.383493848600927	3		456	505	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0030476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	160	283	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		283	357	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579433	7579434	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0030478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	147	632	0	ENST00000269305.4:c.253_254del	p.Pro85CysfsTer63	p.P85Cfs*63	ENST00000269305	NM_001126112.2	85	CCt/t	4/11	0.248604840225719	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.248604840225719	1		632	1000	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715351	117715351	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	49	325	0	ENST00000368508.3:c.1138del	p.Arg380GlufsTer15	p.R380Efs*15	ENST00000368508	NM_002944.2	380	Aga/ga	10/43	0.248604840225719	3	FACETS	0.835	0.707	0.975	0.417	0.353	0.488	CLONAL	1	TRUE	1	0.248604840225719	3		325	531	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200131	138200131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140357085	NA	P-0030478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	95	385	0	ENST00000237289.4:c.1549G>A	p.Asp517Asn	p.D517N	ENST00000237289	NM_001270507.1	517	Gat/Aat	7/9	0.248604840225719	3	FACETS	1	0.937	1	0.539	0.479	0.603	CLONAL	1	TRUE	1	0.248604840225719	3		385	797	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0030483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	202	545	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.325625908108838	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.338915790880276	1		545	668	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424164	49424164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373146997	NA	P-0030483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	109	475	1	ENST00000301067.7:c.13898C>T	p.Ser4633Leu	p.S4633L	ENST00000301067	NM_003482.3	4633	tCg/tTg	42/54	0.12658426310827	3	FACETS	1	0.944	1			1	INDETERMINATE	1	TRUE	NA	0.338915790880276	3		476	699	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831414	72831414	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	127	426	0	ENST00000268489.5:c.5167C>A	p.Gln1723Lys	p.Q1723K	ENST00000268489	NM_006885.3	1723	Cag/Aag	9/10	0.195231517334919	5	FACETS	0.893	0.811	0.979	0.595	0.54	0.653	INDETERMINATE	2	TRUE	2	0.338915790880276	5		426	633	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492911	56492942	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	CCAGCTGCAGCTGGTGGCCACCACTCATGCTA	CCAGCTGCAGCTGGTGGCCACCACTCATGCTA	-	novel	NA	P-0030483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	129	214	0	ENST00000407977.2:c.-4_28del		p.*2*	ENST00000407977		?-10/783		2/10	0.338915790880276	3	FACETS	0.927	0.853	1	0.927	0.853	1	CLONAL	3	TRUE	0	0.338915790880276	3		214	320	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63545652	63545652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	97	445	1	ENST00000307078.5:c.942G>A	p.Met314Ile	p.M314I	ENST00000307078	NM_004655.3	314	atG/atA	3/11	0.338915790880276	3	FACETS	0.926	0.826	1	0.309	0.275	0.345	CLONAL	1	TRUE	0	0.338915790880276	3		446	723	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	289	454	0				ENST00000310581	NM_198253.2	-/1132			0.755653678493003	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.808136620169539	3		454	449	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777894	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	278	693	0	ENST00000361445.4:c.6644C>T	p.Ser2215Phe	p.S2215F	ENST00000361445	NM_004958.3	2215	tCt/tTt	47/58	1	2	FACETS	0.833	0.785	0.882	0.833	0.785	0.882	CLONAL	1	TRUE	1	0.808136620169539	2		693	826	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	329	664	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	1	2	FACETS	0.95	0.902	0.999	0.95	0.902	0.999	CLONAL	1	TRUE	1	0.808136620169539	2		664	857	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591247	67591249	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GGT	GGT	-	rs1131692243	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	456	505	0	ENST00000274335.5:c.1748_1750del		p.X583_splice	ENST00000274335		583		13/15	0.808136620169539	3	FACETS	0.917	0.882	0.952	0.917	0.882	0.952	CLONAL	2	TRUE	1	0.808136620169539	3		505	864	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149710	202149710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	241	714	0	ENST00000358485.4:c.1151G>A	p.Gly384Asp	p.G384D	ENST00000358485	NM_001080125.1	384	gGc/gAc	8/9	1	2	FACETS	0.872	0.819	0.926	0.872	0.819	0.926	CLONAL	1	TRUE	1	0.808136620169539	2		714	684	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129722	47129722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	163	426	0	ENST00000409792.3:c.5158G>A	p.Glu1720Lys	p.E1720K	ENST00000409792	NM_014159.6	1720	Gaa/Aaa	10/21	1	2	FACETS	0.864	0.8	0.929	0.864	0.8	0.929	CLONAL	1	TRUE	1	0.808136620169539	2		426	467	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033352	48033352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750949	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	287	572	0	ENST00000234420.5:c.3656C>T	p.Thr1219Ile	p.T1219I	ENST00000234420	NM_000179.2	1219	aCt/aTt	8/10	1	2	FACETS	0.955	0.903	1	0.955	0.903	1	CLONAL	1	TRUE	1	0.808136620169539	2		572	744	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155201	108155201	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs200196781	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	160	507	0	ENST00000278616.4:c.3993+1G>A		p.X1331_splice	ENST00000278616	NM_000051.3	1331			1	2	FACETS	0.753	0.695	0.813	0.753	0.695	0.813	SUBCLONAL	1	TRUE	1	0.808136620169539	2		507	526	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104658	209104658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	191	545	0	ENST00000345146.2:c.920C>T	p.Ala307Val	p.A307V	ENST00000345146	NM_005896.2	307	gCt/gTt	8/10	1	2	FACETS	0.804	0.748	0.861	0.804	0.748	0.861	CLONAL	1	TRUE	1	0.808136620169539	2		545	588	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320282	30320282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748955039	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	290	461	0	ENST00000322652.5:c.1223C>T	p.Thr408Ile	p.T408I	ENST00000322652	NM_015355.2	408	aCa/aTa	11/16	1	2	FACETS	0.903	0.853	0.953	0.903	0.853	0.953	CLONAL	1	TRUE	1	0.808136620169539	2		461	795	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644448	18644448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751457593	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	228	624	0	ENST00000266497.5:c.2626C>T	p.Leu876Phe	p.L876F	ENST00000266497		876	Ctt/Ttt	18/31	1	2	FACETS	0.856	0.802	0.911	0.856	0.802	0.911	CLONAL	1	TRUE	1	0.808136620169539	2		624	659	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729917	47729917	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	20	296	3	ENST00000449228.1:c.472C>T	p.Pro158Ser	p.P158S	ENST00000449228	NM_001127240.2	158	Ccc/Tcc	3/4	1	2	FACETS	0.125	0.095	0.16	0.125	0.095	0.16	SUBCLONAL	1	TRUE	1	0.808136620169539	2		299	397	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158442	108158442	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	185	436	0	ENST00000278616.4:c.4109G>A	p.Gly1370Glu	p.G1370E	ENST00000278616	NM_000051.3	1370	gGg/gAg	27/63	1	2	FACETS	0.731	0.679	0.786	0.731	0.679	0.786	SUBCLONAL	1	TRUE	1	0.808136620169539	2		436	626	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514211	69514211	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	301	845	0	ENST00000294312.3:c.470G>A	p.Arg157Lys	p.R157K	ENST00000294312	NM_005117.2	157	aGa/aAa	3/3	1	2	FACETS	0.863	0.816	0.911	0.863	0.816	0.911	CLONAL	1	TRUE	1	0.808136620169539	2		845	863	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794433	42794433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	480	1160	2	ENST00000575354.2:c.1513C>T	p.His505Tyr	p.H505Y	ENST00000575354	NM_015125.3	505	Cac/Tac	10/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.808136620169539	2		1162	1144	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573988	7573988	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	342	867	1	ENST00000269305.4:c.1039G>A	p.Ala347Thr	p.A347T	ENST00000269305	NM_001126112.2	347	Gcc/Acc	10/11	1	2	FACETS	0.841	0.797	0.885	0.841	0.797	0.885	CLONAL	1	TRUE	1	0.808136620169539	2		868	1007	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288835	11288835	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	274	669	1	ENST00000361445.4:c.2920G>A	p.Ala974Thr	p.A974T	ENST00000361445	NM_004958.3	974	Gcc/Acc	19/58	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.808136620169539	2		670	662	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088670	27088670	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	390	909	0	ENST00000324856.7:c.2279C>T	p.Pro760Leu	p.P760L	ENST00000324856	NM_006015.4	760	cCc/cTc	7/20	1	2	FACETS	0.952	0.907	0.997	0.952	0.907	0.997	CLONAL	1	TRUE	1	0.808136620169539	2		909	1014	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430005	78430005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	198	482	0	ENST00000370768.2:c.874G>A	p.Gly292Arg	p.G292R	ENST00000370768	NM_003902.3	292	Gga/Aga	11/20	1	2	FACETS	0.863	0.805	0.922	0.863	0.805	0.922	CLONAL	1	TRUE	1	0.808136620169539	2		482	568	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510715	120510715	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782797463	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	282	739	0	ENST00000256646.2:c.1249G>A	p.Asp417Asn	p.D417N	ENST00000256646	NM_024408.3	417	Gat/Aat	7/34	1	2	FACETS	0.85	0.802	0.899	0.85	0.802	0.899	CLONAL	1	TRUE	1	0.808136620169539	2		739	821	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175916347	175916347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	233	528	0	ENST00000367669.3:c.2162G>A	p.Ser721Asn	p.S721N	ENST00000367669	NM_022457.5	721	aGt/aAt	19/20	1	2	FACETS	0.969	0.911	1	0.969	0.911	1	CLONAL	1	TRUE	1	0.808136620169539	2		528	595	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578292	226578292	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	242	695	0	ENST00000366794.5:c.436C>T	p.Pro146Ser	p.P146S	ENST00000366794	NM_001618.3	146	Ccg/Tcg	4/23	1	2	FACETS	0.869	0.816	0.923	0.869	0.816	0.923	CLONAL	1	TRUE	1	0.808136620169539	2		695	689	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115736	108115736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	130	288	0	ENST00000278616.4:c.884C>T	p.Ala295Val	p.A295V	ENST00000278616	NM_000051.3	295	gCc/gTc	7/63	1	2	FACETS	0.889	0.816	0.964	0.889	0.816	0.964	CLONAL	1	TRUE	1	0.808136620169539	2		288	362	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793475	18793475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	229	484	0	ENST00000266497.5:c.4172C>T	p.Thr1391Ile	p.T1391I	ENST00000266497		1391	aCt/aTt	30/31	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.808136620169539	2		484	546	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944899	31944899	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	164	354	0	ENST00000340398.3:c.202C>T	p.Gln68Ter	p.Q68*	ENST00000340398	NM_001013699.2	68	Cag/Tag	1/1	1	2	FACETS	0.927	0.859	0.995	0.927	0.859	0.995	CLONAL	1	TRUE	1	0.808136620169539	2		354	438	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233111	46233111	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	60	196	0	ENST00000334344.6:c.1331-1G>A		p.X444_splice	ENST00000334344	NM_152641.2	444			1	2	FACETS	0.474	0.411	0.542	0.474	0.411	0.542	SUBCLONAL	1	TRUE	1	0.808136620169539	2		196	313	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245226	46245226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	210	557	0	ENST00000334344.6:c.3320C>T	p.Ala1107Val	p.A1107V	ENST00000334344	NM_152641.2	1107	gCa/gTa	15/21	1	2	FACETS	0.964	0.903	1	0.964	0.903	1	CLONAL	1	TRUE	1	0.808136620169539	2		557	539	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424774	49424774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1173696978	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	321	734	0	ENST00000301067.7:c.13573G>A	p.Val4525Ile	p.V4525I	ENST00000301067	NM_003482.3	4525	Gta/Ata	40/54	1	2	FACETS	0.935	0.886	0.984	0.935	0.886	0.984	CLONAL	1	TRUE	1	0.808136620169539	2		734	850	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425176	49425176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1356221709	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	394	977	0	ENST00000301067.7:c.13312G>A	p.Glu4438Lys	p.E4438K	ENST00000301067	NM_003482.3	4438	Gag/Aag	39/54	1	2	FACETS	0.997	0.951	1	0.997	0.951	1	CLONAL	1	TRUE	1	0.808136620169539	2		977	978	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479238	50479238	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	102	273	0	ENST00000394963.4:c.86G>A	p.Gly29Asp	p.G29D	ENST00000394963	NM_003076.4	29	gGc/gAc	1/13	1	2	FACETS	0.565	0.508	0.624	0.565	0.508	0.624	SUBCLONAL	1	TRUE	1	0.808136620169539	2		273	447	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489073	56489073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	266	675	0	ENST00000267101.3:c.1892G>A	p.Gly631Glu	p.G631E	ENST00000267101	NM_001982.3	631	gGa/gAa	16/28	1	2	FACETS	0.894	0.843	0.947	0.894	0.843	0.947	CLONAL	1	TRUE	1	0.808136620169539	2		675	736	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145370	58145370	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	276	672	0	ENST00000257904.6:c.131G>A	p.Gly44Glu	p.G44E	ENST00000257904	NM_000075.3	44	gGa/gAa	2/8	1	2	FACETS	0.852	0.803	0.901	0.852	0.803	0.901	CLONAL	1	TRUE	1	0.808136620169539	2		672	802	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123873998	123873998	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	28	58	0	ENST00000330479.4:c.29C>T	p.Pro10Leu	p.P10L	ENST00000330479	NM_020382.3	10	cCc/cTc	2/9	1	2	FACETS	0.877	0.725	1	0.877	0.725	1	CLONAL	1	TRUE	1	0.808136620169539	2		58	79	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134904	41134904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	158	469	0	ENST00000379561.5:c.724G>A	p.Glu242Lys	p.E242K	ENST00000379561	NM_002015.3	242	Gag/Aag	2/3	0.711477477163603	1	FACETS	0.801	0.749	0.852	0.801	0.749	0.852	CLONAL	1	TRUE	0	0.808136620169539	1		469	291	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95595923	95595923	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	236	599	1	ENST00000393063.1:c.620C>T	p.Ala207Val	p.A207V	ENST00000393063	NM_030621.3	207	gCt/gTt	7/28	1	2	FACETS	0.816	0.765	0.868	0.816	0.765	0.868	CLONAL	1	TRUE	1	0.808136620169539	2		600	716	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639590	3639590	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	304	1026	2	ENST00000294008.3:c.4049G>A	p.Gly1350Asp	p.G1350D	ENST00000294008	NM_032444.2	1350	gGc/gAc	12/15	1	2	FACETS	0.81	0.765	0.856	0.81	0.765	0.856	CLONAL	1	TRUE	1	0.808136620169539	2		1028	929	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958206	11958206	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	166	421	0	ENST00000353533.5:c.116G>A	p.Gly39Asp	p.G39D	ENST00000353533	NM_003010.3	39	gGt/gAt	2/11	1	2	FACETS	0.761	0.703	0.82	0.761	0.703	0.82	SUBCLONAL	1	TRUE	1	0.808136620169539	2		421	540	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2164259	2164259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	299	695	0	ENST00000398665.3:c.76G>A	p.Val26Ile	p.V26I	ENST00000398665	NM_032482.2	26	Gtc/Atc	1/28	1	2	FACETS	0.871	0.823	0.919	0.871	0.823	0.919	CLONAL	1	TRUE	1	0.808136620169539	2		695	850	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5207932	5207932	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	259	783	0	ENST00000357368.4:c.5778+1G>A		p.X1926_splice	ENST00000357368	NM_002850.3	1926			1	2	FACETS	0.825	0.776	0.875	0.825	0.776	0.875	CLONAL	1	TRUE	1	0.808136620169539	2		783	777	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626783	14626783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	300	685	0	ENST00000254322.2:c.992G>A	p.Arg331Lys	p.R331K	ENST00000254322	NM_006145.1	331	aGa/aAa	3/3	1	2	FACETS	0.858	0.811	0.906	0.858	0.811	0.906	CLONAL	1	TRUE	1	0.808136620169539	2		685	865	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367020	15367020	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	40	461	0	ENST00000263377.2:c.1606C>T	p.Pro536Ser	p.P536S	ENST00000263377	NM_058243.2	536	Cca/Tca	9/20	1	2	FACETS	0.228	0.189	0.271	0.228	0.189	0.271	SUBCLONAL	1	TRUE	1	0.808136620169539	2		461	435	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229088	36229088	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	244	748	0	ENST00000222270.7:c.7868G>A	p.Gly2623Glu	p.G2623E	ENST00000222270	NM_014727.1	2623	gGg/gAg	36/37	1	2	FACETS	0.828	0.777	0.88	0.828	0.777	0.88	CLONAL	1	TRUE	1	0.808136620169539	2		748	729	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794977	42794977	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	304	830	0	ENST00000575354.2:c.2057T>C	p.Ile686Thr	p.I686T	ENST00000575354	NM_015125.3	686	aTc/aCc	10/20	1	2	FACETS	0.911	0.862	0.961	0.911	0.862	0.961	CLONAL	1	TRUE	1	0.808136620169539	2		830	826	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729991	47729991	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	165	395	0	ENST00000449228.1:c.398C>T	p.Ala133Val	p.A133V	ENST00000449228	NM_001127240.2	133	gCt/gTt	3/4	1	2	FACETS	0.968	0.899	1	0.968	0.899	1	CLONAL	1	TRUE	1	0.808136620169539	2		395	422	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827915	40827915	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	193	665	1	ENST00000373198.4:c.2513G>A	p.Gly838Asp	p.G838D	ENST00000373198	NM_133170.3	838	gGc/gAc	17/32	1	2	FACETS	0.751	0.698	0.805	0.751	0.698	0.805	SUBCLONAL	1	TRUE	1	0.808136620169539	2		666	636	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980804	40980804	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	249	665	1	ENST00000373198.4:c.1682C>T	p.Thr561Ile	p.T561I	ENST00000373198	NM_133170.3	561	aCc/aTc	10/32	1	2	FACETS	0.884	0.831	0.938	0.884	0.831	0.938	CLONAL	1	TRUE	1	0.808136620169539	2		666	697	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513313	44513313	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	405	924	0	ENST00000291552.4:c.622G>A	p.Asp208Asn	p.D208N	ENST00000291552	NM_006758.2	208	Gac/Aac	8/8	1	2	FACETS	0.908	0.865	0.951	0.908	0.865	0.951	CLONAL	1	TRUE	1	0.808136620169539	2		924	1104	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574754	41574754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	411	987	1	ENST00000263253.7:c.7039C>T	p.Pro2347Ser	p.P2347S	ENST00000263253	NM_001429.3	2347	Cca/Tca	31/31	1	2	FACETS	0.975	0.931	1	0.975	0.931	1	CLONAL	1	TRUE	1	0.808136620169539	2		988	1043	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163952	47163952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	186	391	0	ENST00000409792.3:c.2174G>A	p.Ser725Asn	p.S725N	ENST00000409792	NM_014159.6	725	aGt/aAt	3/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.808136620169539	2		391	440	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437458	52437458	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	232	630	0	ENST00000460680.1:c.1703G>A	p.Gly568Glu	p.G568E	ENST00000460680	NM_004656.3	568	gGg/gAg	13/17	1	2	FACETS	0.809	0.757	0.861	0.809	0.757	0.861	CLONAL	1	TRUE	1	0.808136620169539	2		630	710	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439852	52439852	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1270986936	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	285	625	0	ENST00000460680.1:c.860C>T	p.Ser287Leu	p.S287L	ENST00000460680	NM_004656.3	287	tCa/tTa	10/17	1	2	FACETS	0.97	0.917	1	0.97	0.917	1	CLONAL	1	TRUE	1	0.808136620169539	2		625	727	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990460	69990460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	204	461	0	ENST00000394351.3:c.419C>T	p.Pro140Leu	p.P140L	ENST00000394351	NM_000248.3	140	cCt/cTt	4/9	1	2	FACETS	0.826	0.771	0.883	0.826	0.771	0.883	CLONAL	1	TRUE	1	0.808136620169539	2		461	611	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430984	181430984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	375	819	0	ENST00000325404.1:c.836C>T	p.Pro279Leu	p.P279L	ENST00000325404	NM_003106.3	279	cCc/cTc	1/1	1	2	FACETS	0.946	0.901	0.992	0.946	0.901	0.992	CLONAL	1	TRUE	1	0.808136620169539	2		819	981	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902962	1902962	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	227	665	0	ENST00000382891.5:c.581G>A	p.Ser194Asn	p.S194N	ENST00000382891	NM_133335.3	194	aGt/aAt	2/22	1	2	FACETS	0.772	0.722	0.823	0.772	0.722	0.823	SUBCLONAL	1	TRUE	1	0.808136620169539	2		665	728	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532710	187532710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	238	596	0	ENST00000441802.2:c.9683C>T	p.Pro3228Leu	p.P3228L	ENST00000441802	NM_005245.3	3228	cCt/cTt	14/27	1	2	FACETS	0.839	0.787	0.892	0.839	0.787	0.892	CLONAL	1	TRUE	1	0.808136620169539	2		596	702	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176594	56176594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	213	601	0	ENST00000399503.3:c.2144G>A	p.Gly715Glu	p.G715E	ENST00000399503	NM_005921.1	715	gGa/gAa	12/20	0.755653678493003	3	FACETS	0.746	0.693	0.801	0.373	0.346	0.401	SUBCLONAL	1	TRUE	1	0.808136620169539	3		601	992	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633790	86633790	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	93	249	0	ENST00000274376.6:c.900-1G>A		p.X300_splice	ENST00000274376	NM_002890.2	300			0.808136620169539	3	FACETS	0.695	0.621	0.773	0.347	0.31	0.387	SUBCLONAL	1	TRUE	1	0.808136620169539	3		249	465	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180629	32180629	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1278741655	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	228	708	0	ENST00000375023.3:c.2498C>T	p.Pro833Leu	p.P833L	ENST00000375023	NM_004557.3	833	cCc/cTc	16/30	1	2	FACETS	0.812	0.76	0.865	0.812	0.76	0.865	CLONAL	1	TRUE	1	0.808136620169539	2		708	695	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821110	32821110	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	400	946	0	ENST00000354258.4:c.484G>A	p.Ala162Thr	p.A162T	ENST00000354258	NM_000593.5	162	Gca/Aca	1/11	1	2	FACETS	0.971	0.927	1	0.971	0.927	1	CLONAL	1	TRUE	1	0.808136620169539	2		946	1019	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686784	117686784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	224	553	0	ENST00000368508.3:c.2933G>A	p.Gly978Asp	p.G978D	ENST00000368508	NM_002944.2	978	gGt/gAt	19/43	1	2	FACETS	0.857	0.802	0.912	0.857	0.802	0.912	CLONAL	1	TRUE	1	0.808136620169539	2		553	647	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200389	138200389	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	291	655	0	ENST00000237289.4:c.1807G>A	p.Gly603Arg	p.G603R	ENST00000237289	NM_001270507.1	603	Ggg/Agg	7/9	1	2	FACETS	0.917	0.867	0.969	0.917	0.867	0.969	CLONAL	1	TRUE	1	0.808136620169539	2		655	785	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431673	6431673	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	394	976	0	ENST00000356142.4:c.225+1G>A		p.X75_splice	ENST00000356142	NM_018890.3	75			1	2	FACETS	0.984	0.938	1	0.984	0.938	1	CLONAL	1	TRUE	1	0.808136620169539	2		976	991	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739639	41739639	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	280	841	0	ENST00000242208.4:c.334G>A	p.Glu112Lys	p.E112K	ENST00000242208	NM_002192.2	112	Gaa/Aaa	2/3	0.808136620169539	4	FACETS	0.852	0.799	0.908	0.284	0.266	0.303	CLONAL	1	TRUE	1	0.808136620169539	4		841	1470	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371852	116371852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	215	545	2	ENST00000397752.3:c.1331C>T	p.Thr444Ile	p.T444I	ENST00000397752	NM_000245.2	444	aCc/aTc	3/21	0.808136620169539	4	FACETS	0.797	0.74	0.857	0.266	0.246	0.286	SUBCLONAL	1	TRUE	1	0.808136620169539	4		547	1207	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845532	128845532	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1212	263	765	0	ENST00000249373.3:c.829G>A	p.Gly277Ser	p.G277S	ENST00000249373	NM_005631.4	277	Ggc/Agc	4/12	0.808136620169539	4	FACETS	0.798	0.746	0.852	0.266	0.248	0.284	SUBCLONAL	1	TRUE	1	0.808136620169539	4		765	1475	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859780	151859780	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	188	354	0	ENST00000262189.6:c.10882G>A	p.Asp3628Asn	p.D3628N	ENST00000262189	NM_170606.2	3628	Gat/Aat	43/59	0.808136620169539	4	FACETS	1	0.976	1	0.375	0.347	0.404	CLONAL	1	TRUE	1	0.808136620169539	4		354	747	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127920624	127920624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756846788	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	283	639	1	ENST00000373547.4:c.275C>T	p.Thr92Ile	p.T92I	ENST00000373547	NM_002721.4	92	aCc/aTc	4/7	1	2	FACETS	0.822	0.775	0.87	0.822	0.775	0.87	CLONAL	1	TRUE	1	0.808136620169539	2		640	852	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354654	70354654	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	355	364	0	ENST00000374080.3:c.4819G>A	p.Glu1607Lys	p.E1607K	ENST00000374080		1607	Gag/Aag	35/45	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.808136620169539	1		364	503	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937945	76937945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	266	278	0	ENST00000373344.5:c.2803G>A	p.Glu935Lys	p.E935K	ENST00000373344	NM_000489.3	935	Gaa/Aaa	9/35	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.808136620169539	1		278	367	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913403	NA	P-0030486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	101	285	0	ENST00000349496.5:c.110C>A	p.Ser37Tyr	p.S37Y	ENST00000349496	NM_001904.3	37	tCt/tAt	3/15	1	2	FACETS	0.545	0.489	0.604	0.545	0.489	0.604	SUBCLONAL	1	TRUE	1	0.753428988393973	2		285	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0030486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	291	625	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	0.576690608611929	1	FACETS	0.702	0.665	0.739	0.702	0.665	0.739	SUBCLONAL	1	TRUE	0	0.753428988393973	1		625	686	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264361	46264361	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	186	344	0	ENST00000371998.3:c.1408A>G	p.Ser470Gly	p.S470G	ENST00000371998		470	Agt/Ggt	11/23	1	2	FACETS	0.754	0.699	0.81	0.754	0.699	0.81	SUBCLONAL	1	TRUE	1	0.753428988393973	2		344	655	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0030491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	336	597	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.492229858604254	2	FACETS	0.969	0.924	1	0.969	0.924	1	CLONAL	2	TRUE	0	0.510867692418743	2		597	679	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807481	36807481	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	194	562	0	ENST00000373129.3:c.1183G>T	p.Ala395Ser	p.A395S	ENST00000373129	NM_032017.1	395	Gcc/Tcc	12/12	0.47226336199706	3	FACETS	0.955	0.884	1	0.478	0.442	0.515	CLONAL	1	TRUE	1	0.510867692418743	3		562	998	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982800	7982800	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780035905	NA	P-0030493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	1068	679	0	ENST00000319144.4:c.985C>T	p.Leu329Phe	p.L329F	ENST00000319144	NM_001139.2	329	Ctc/Ttc	8/15	0.70823045293381	3	FACETS	1	0.992	1			1	CLONAL	3	TRUE	NA	0.734739478942958	3		679	1307	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720947	119720947	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	198	470	0	ENST00000316626.5:c.228T>G	p.Cys76Trp	p.C76W	ENST00000316626		76	tgT/tgG	2/12	0.70823045293381	3	FACETS	0.887	0.823	0.953			1	CLONAL	1	TRUE	NA	0.734739478942958	3		470	831	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112025256	112025257	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	novel	NA	P-0030493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	208	457	0	ENST00000368678.4:c.492_493delinsAA	p.Ser165Thr	p.S165T	ENST00000368678		164	ttGTcc/ttAAcc	6/13	0.719273206002988	3	FACETS	0.88	0.818	0.944	0.44	0.409	0.472	CLONAL	1	TRUE	1	0.734739478942958	3		457	880	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0030496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	306	546	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.380685216170258	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.428758033467034	2		547	668	SUCCESS
APC	324	MSKCC	GRCh37	5	112173968	112173968	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs199740875	NA	P-0030496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	172	359	0	ENST00000257430.4:c.2677G>T	p.Glu893Ter	p.E893*	ENST00000257430	NM_000038.5	893	Gaa/Taa	16/16	0.380685216170258	2	FACETS	0.974	0.907	1	0.974	0.907	1	CLONAL	2	TRUE	0	0.428758033467034	2		359	412	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0030496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	50	325	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	0.428758033467034	3	FACETS	0.583	0.495	0.679	0.291	0.247	0.34	SUBCLONAL	1	TRUE	1	0.428758033467034	3		325	486	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332916	153332916	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1362274408	NA	P-0030496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	78	270	1	ENST00000281708.4:c.40C>T	p.Arg14Ter	p.R14*	ENST00000281708	NM_033632.3	14	Cga/Tga	2/12	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.428758033467034	2		271	363	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573889	18573889	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	164	399	0	ENST00000266497.5:c.2209del	p.Ile737PhefsTer9	p.I737Ffs*9	ENST00000266497		736	gAa/ga	15/31	0.428758033467034	3	FACETS	0.986	0.913	1	0.986	0.913	1	CLONAL	2	TRUE	1	0.428758033467034	3		399	471	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829647	72829647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750069782	NA	P-0030496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	240	531	1	ENST00000268489.5:c.6934C>T	p.Arg2312Trp	p.R2312W	ENST00000268489	NM_006885.3	2312	Cgg/Tgg	9/10	0.380685216170258	2	FACETS	0.975	0.918	1	0.975	0.918	1	CLONAL	2	TRUE	0	0.428758033467034	2		532	574	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660462	227660462	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143760685	NA	P-0030496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	43	410	0	ENST00000305123.5:c.2993G>A	p.Arg998His	p.R998H	ENST00000305123	NM_005544.2	998	cGt/cAt	1/2	0.428758033467034	3	FACETS	0.456	0.381	0.539	0.228	0.19	0.27	SUBCLONAL	1	TRUE	1	0.428758033467034	3		410	534	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247337	153247337	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	85	311	0	ENST00000281708.4:c.1465G>T	p.Glu489Ter	p.E489*	ENST00000281708	NM_033632.3	489	Gag/Tag	10/12	1	2	FACETS	0.96	0.853	1	0.96	0.853	1	CLONAL	1	TRUE	1	0.428758033467034	2		311	413	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0030497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	258	606	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.379952969412647	2		606	1075	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs28934577	NA	P-0030497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	130	620	0	ENST00000269305.4:c.770T>A	p.Leu257Gln	p.L257Q	ENST00000269305	NM_001126112.2	257	cTg/cAg	7/11	1	2	FACETS	0.676	0.612	0.743	0.676	0.612	0.743	SUBCLONAL	1	TRUE	1	0.379952969412647	2		620	1013	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900635	32900635	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs81002849	NA	P-0030497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	97	329	1	ENST00000380152.3:c.517-1G>T		p.X173_splice	ENST00000380152		173			1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.379952969412647	2		330	492	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66522048	66522048	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	91	226	0	ENST00000358598.2:c.703C>T	p.Leu235Phe	p.L235F	ENST00000358598	NM_212471.2	235	Ctc/Ttc	7/11	1	2	FACETS	0.95	0.847	1	0.95	0.847	1	CLONAL	1	TRUE	1	0.379952969412647	2		226	504	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266564	115266564	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	211	608	0	ENST00000438362.2:c.1951del	p.Leu651Ter	p.L651*	ENST00000438362	NM_001242891.1	651	Ctg/tg	16/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.379952969412647	2		608	999	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406269	406269	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	313	501	1	ENST00000399788.2:c.4172G>T	p.Trp1391Leu	p.W1391L	ENST00000399788	NM_001042603.1	1391	tGg/tTg	25/28	0.318275670565318	4	FACETS	1	0.982	1			1	CLONAL	2	TRUE	NA	0.379952969412647	4		502	1045	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592687	28592687	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	174	630	0	ENST00000241453.7:c.2458A>C	p.Thr820Pro	p.T820P	ENST00000241453	NM_004119.2	820	Acc/Ccc	20/24	1	2	FACETS	0.921	0.847	0.997	0.921	0.847	0.997	CLONAL	1	TRUE	1	0.379952969412647	2		630	995	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288876	15288876	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1255319596	NA	P-0030497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	91	201	0	ENST00000263388.2:c.3863G>T	p.Arg1288Leu	p.R1288L	ENST00000263388	NM_000435.2	1288	cGg/cTg	24/33	0.107243266986535	4	FACETS	1	0.979	1	0.731	0.652	0.815	INDETERMINATE	1	TRUE	2	0.379952969412647	4		201	452	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085908	16085908	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	46	571	0	ENST00000281043.3:c.1084G>T	p.Val362Phe	p.V362F	ENST00000281043	NM_005378.4	362	Gtc/Ttc	3/3	0.379952969412647	1	FACETS	0.277	0.233	0.327	0.277	0.233	0.327	SUBCLONAL	1	TRUE	0	0.379952969412647	1		571	707	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935545	49935545	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	301	711	0	ENST00000296474.3:c.1819C>A	p.His607Asn	p.H607N	ENST00000296474	NM_002447.2	607	Cat/Aat	5/20	0.379952969412647	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.379952969412647	1		711	979	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259595	89259595	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	115	326	0	ENST00000336596.2:c.739G>T	p.Glu247Ter	p.E247*	ENST00000336596	NM_005233.5	247	Gaa/Taa	3/17	NA	2	FACETS	1	0.972	1			1	INDETERMINATE	1	TRUE	NA	0.379952969412647	2		326	504	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729441	41729441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	59	528	0	ENST00000242208.4:c.1088G>A	p.Gly363Glu	p.G363E	ENST00000242208	NM_002192.2	363	gGg/gAg	3/3	0.379952969412647	2	FACETS	0.366	0.314	0.423	0.183	0.157	0.212	SUBCLONAL	1	TRUE	0	0.379952969412647	2		528	848	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630236	100630236	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	149	179	0	ENST00000308731.7:c.37C>G	p.Arg13Gly	p.R13G	ENST00000308731	NM_000061.2	13	Cga/Gga	2/19	1	1	FACETS	0.829	0.767	0.893	1	0.991	1	CLONAL	2	TRUE	0	0.379952969412647	1		179	383	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0030505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	77	456	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.498431582867321	3	FACETS	0.72	0.633	0.813	0.36	0.316	0.407	SUBCLONAL	1	FALSE	1	0.495983779591345	3		456	538	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958788	55958788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780764266	NA	P-0030505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	45	576	1	ENST00000263923.4:c.3065G>A	p.Arg1022Gln	p.R1022Q	ENST00000263923	NM_002253.2	1022	cGa/cAa	22/30	NA	2	FACETS	0.438	0.369	0.515			1	INDETERMINATE	1	FALSE	NA	0.495983779591345	2		577	414	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627970	187627972	+	inframe_deletion	In_Frame_Del	DEL	TTT	TTT	-	novel	NA	P-0030505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	100	588	0	ENST00000441802.2:c.3010_3012del	p.Lys1004del	p.K1004del	ENST00000441802	NM_005245.3	1004	AAA/-	2/27	0.26880963686427	2	FACETS	0.867	0.779	0.96	0.434	0.389	0.48	INDETERMINATE	1	FALSE	0	0.495983779591345	2		588	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0030509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	444	590	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.375387232621563	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.378249281042164	2		590	1159	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0030509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	312	546	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.378249281042164	3	FACETS	0.888	0.843	0.934	1	0.993	1	CLONAL	3	TRUE	1	0.378249281042164	3		546	736	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652128	36652128	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs781404776	NA	P-0030509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	178	554	5	ENST00000244741.5:c.250C>T	p.Arg84Ter	p.R84*	ENST00000244741	NM_000389.4	84	Cga/Tga	2/3	0.375387232621563	2	FACETS	1	0.938	1	0.51	0.47	0.552	CLONAL	1	TRUE	0	0.378249281042164	2		559	922	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665362	138665362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	220	516	5	ENST00000330315.3:c.203G>A	p.Arg68His	p.R68H	ENST00000330315	NM_023067.3	68	cGc/cAc	1/1	0.378249281042164	3	FACETS	1	0.98	1	0.573	0.533	0.616	CLONAL	1	TRUE	1	0.378249281042164	3		521	1206	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864889	117864889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1162798324	NA	P-0030509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	120	436	3	ENST00000297338.2:c.1220G>A	p.Gly407Glu	p.G407E	ENST00000297338	NM_006265.2	407	gGa/gAa	10/14	0.378249281042164	3	FACETS	0.92	0.831	1	0.46	0.415	0.507	CLONAL	1	TRUE	1	0.378249281042164	3		439	820	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	173	454	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.946	1			1	INDETERMINATE	1	TRUE	NA	0.666651163075017	2		454	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577102	7577102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793881	NA	P-0030520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	602	696	0	ENST00000269305.4:c.836G>A	p.Gly279Glu	p.G279E	ENST00000269305	NM_001126112.2	279	gGg/gAg	8/11	0.666651163075017	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.666651163075017	1		696	971	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097665	27097665	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0030520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	437	785	0	ENST00000324856.7:c.3254C>G	p.Ser1085Ter	p.S1085*	ENST00000324856	NM_006015.4	1085	tCa/tGa	12/20	0.318299275087429	2	FACETS	1	0.991	1	0.567	0.541	0.592	INDETERMINATE	1	TRUE	0	0.666651163075017	2		785	1157	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048118	180048118	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	299	862	0	ENST00000261937.6:c.2155G>C	p.Glu719Gln	p.E719Q	ENST00000261937	NM_182925.4	719	Gag/Cag	14/30	0.420040695444131	1	FACETS	0.64	0.604	0.677	0.64	0.604	0.677	SUBCLONAL	1	TRUE	0	0.666651163075017	1		862	934	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264106	16264106	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1263	158	901	0	ENST00000375759.3:c.10475C>T	p.Ser3492Phe	p.S3492F	ENST00000375759	NM_015001.2	3492	tCc/tTc	12/15	NA	2	FACETS	0.334	0.304	0.364			1	INDETERMINATE	1	TRUE	NA	0.666651163075017	2		901	1421	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240676	133240676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	347	647	1	ENST00000320574.5:c.2620G>A	p.Glu874Lys	p.E874K	ENST00000320574	NM_006231.2	874	Gaa/Aaa	23/49	0.414502532997486	1	FACETS	0.783	0.744	0.823	0.783	0.744	0.823	SUBCLONAL	1	TRUE	0	0.666651163075017	1		648	886	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351675	89351675	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	92	830	0	ENST00000301030.4:c.1275G>C	p.Lys425Asn	p.K425N	ENST00000301030	NM_001256183.1	425	aaG/aaC	9/13	0.420040695444131	1	FACETS	0.171	0.151	0.192	0.171	0.151	0.192	SUBCLONAL	1	TRUE	0	0.666651163075017	1		830	1075	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575111	48575111	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	36	386	0	ENST00000342988.3:c.305C>G	p.Pro102Arg	p.P102R	ENST00000342988	NM_005359.5	102	cCt/cGt	3/12	1	2	FACETS	0.179	0.147	0.216	0.179	0.147	0.216	SUBCLONAL	1	TRUE	1	0.666651163075017	2		386	603	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223033	1223421	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCGAGCCCAGACACCAAGGACCGGTGGCGCAGCATGACTGTGGTGCCGTACTTGGAGGACCTGCACGGCGCGGACGAGGACGAGGACCTCTTCGACATCGAGGATGACATCATCTACACTCAGGACTTCACGGTGCCCGGTGAGTCTGGCGGGGGCCCCTGCCCGGCTCTGCTGACTCGGCCAGGATGTCCCACGGGAGCAGGGTGCCTGCCTGTCTGCAACAAGGACAGCTTCTGCCCTCTGGTGGCCAATCCCACGTCCCCAAAGCCTCCAGCCCACCTGCAGGCTGCCTCCGCCCTGCGGGCCGCTGGGACATGGCTGAAAGGTGTGGGGTCAGCGGGGGCACCAGCCCAGGCCTGTCTGGCCAGGAGGGTTCCTCAGGCGTCTCT	CCGAGCCCAGACACCAAGGACCGGTGGCGCAGCATGACTGTGGTGCCGTACTTGGAGGACCTGCACGGCGCGGACGAGGACGAGGACCTCTTCGACATCGAGGATGACATCATCTACACTCAGGACTTCACGGTGCCCGGTGAGTCTGGCGGGGGCCCCTGCCCGGCTCTGCTGACTCGGCCAGGATGTCCCACGGGAGCAGGGTGCCTGCCTGTCTGCAACAAGGACAGCTTCTGCCCTCTGGTGGCCAATCCCACGTCCCCAAAGCCTCCAGCCCACCTGCAGGCTGCCTCCGCCCTGCGGGCCGCTGGGACATGGCTGAAAGGTGTGGGGTCAGCGGGGGCACCAGCCCAGGCCTGTCTGGCCAGGAGGGTTCCTCAGGCGTCTCT	-	novel	NA	P-0030520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	237	795	0	ENST00000326873.7:c.973_1108+253del		p.X325_splice	ENST00000326873	NM_000455.4	325		8/10	1	2	FACETS	0.683	0.637	0.73	0.683	0.637	0.73	SUBCLONAL	1	TRUE	1	0.666651163075017	2		795	1041	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741878	40741879	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0030520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1217	128	769	0	ENST00000392038.2:c.1093_1094delinsTT	p.Glu365Leu	p.E365L	ENST00000392038	NM_001626.4	365	GAa/TTa	11/14	0.152217146247169	3	FACETS	0.381	0.344	0.42	0.19	0.172	0.21	INDETERMINATE	1	TRUE	1	0.666651163075017	3		769	1345	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99162467	99162467	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	369	481	0	ENST00000074304.5:c.985A>G	p.Lys329Glu	p.K329E	ENST00000074304	NM_001134224.1	329	Aaa/Gaa	12/26	0.372257620035374	3	FACETS	1	0.995	1	0.739	0.703	0.775	INDETERMINATE	1	TRUE	1	0.666651163075017	3		481	999	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231792	36231792	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	453	745	0	ENST00000300305.3:c.592G>C	p.Asp198His	p.D198H	ENST00000300305		198	Gat/Cat	5/8	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.666651163075017	2		745	1200	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31451648	31451648	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	350	426	0	ENST00000344624.3:c.2674C>G	p.Leu892Val	p.L892V	ENST00000344624		892	Ctg/Gtg	18/33	0.200591854349249	6	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.666651163075017	6		426	1017	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681642	30681642	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	186	520	0	ENST00000376406.3:c.455G>C	p.Arg152Thr	p.R152T	ENST00000376406	NM_014641.2	152	aGa/aCa	3/15	0.385970848324495	1	FACETS	0.508	0.47	0.547	0.508	0.47	0.547	INDETERMINATE	1	TRUE	0	0.666651163075017	1		520	732	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2949757	2949757	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	391	798	0	ENST00000396946.4:c.3187G>C	p.Asp1063His	p.D1063H	ENST00000396946	NM_032415.4	1063	Gac/Cac	24/25	NA	2	FACETS	0.89	0.845	0.935			1	INDETERMINATE	1	TRUE	NA	0.666651163075017	2		798	1318	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944379	76944379	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	28	303	0	ENST00000373344.5:c.526C>G	p.Gln176Glu	p.Q176E	ENST00000373344	NM_000489.3	176	Caa/Gaa	7/35	1	1	FACETS	0.119	0.095	0.147	0.119	0.095	0.147	SUBCLONAL	1	TRUE	0	0.666651163075017	1		303	469	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0030522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	185	283	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.837595811504429	2		283	412	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921551	178921551	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519939	NA	P-0030522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	189	413	0	ENST00000263967.3:c.1033A>C	p.Asn345His	p.N345H	ENST00000263967	NM_006218.2	345	Aat/Cat	5/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.837595811504429	2		413	435	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923506	9923507	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0030522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	229	446	0	ENST00000330684.3:c.1780_1781delinsTT	p.Pro594Phe	p.P594F	ENST00000330684	NM_001134407.1	594	CCc/TTc	9/13	1	2	FACETS	0.966	0.908	1	0.966	0.908	1	CLONAL	1	TRUE	1	0.837595811504429	2		446	566	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740623	58740623	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs372024236	NA	P-0030522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	351	609	1	ENST00000305921.3:c.1528C>T	p.Gln510Ter	p.Q510*	ENST00000305921	NM_003620.3	510	Caa/Taa	6/6	1	2	FACETS	0.983	0.935	1	0.983	0.935	1	CLONAL	1	TRUE	1	0.837595811504429	2		610	853	SUCCESS
ATR	545	MSKCC	GRCh37	3	142285038	142285038	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	268	521	0	ENST00000350721.4:c.217C>T	p.Gln73Ter	p.Q73*	ENST00000350721	NM_001184.3	73	Cag/Tag	3/47	1	2	FACETS	0.978	0.924	1	0.978	0.924	1	CLONAL	1	TRUE	1	0.837595811504429	2		521	654	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940497	31940497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	462	677	0	ENST00000375333.2:c.530G>A	p.Ser177Asn	p.S177N	ENST00000375333	NM_032454.1	177	aGc/aAc	3/8	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.837595811504429	2		677	1003	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93636963	93636963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56071116	NA	P-0030522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	401	418	0	ENST00000375746.1:c.1013G>A	p.Arg338Lys	p.R338K	ENST00000375746	NM_001174167.1	338	aGa/aAa	9/14	0.837595811504429	2	FACETS	0.977	0.951	1	0.977	0.951	1	CLONAL	2	TRUE	0	0.837595811504429	2		418	490	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239079	98239081	+	frameshift_variant	Frame_Shift_Del	DEL	AGG	AGG	GA	novel	NA	P-0030522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	429	457	1	ENST00000331920.6:c.1562_1564delinsTC	p.Ala521ValfsTer21	p.A521Vfs*21	ENST00000331920	NM_000264.3	521	gCCTtc/gTCtc	11/24	0.837595811504429	2	FACETS	0.923	0.897	0.948	0.923	0.897	0.948	CLONAL	2	TRUE	0	0.837595811504429	2		458	555	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328340	137328341	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCTCTGCGCTCCATCGGGCTCAAATGCCTGGAACATCTCTTCTTCTTCAA	novel	NA	P-0030522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	141	650	0	ENST00000481739.1:c.1274_1323dup	p.Ile442CysfsTer37	p.I442Cfs*37	ENST00000481739	NM_002957.4	423	-/GCTCTGCGCTCCATCGGGCTCAAATGCCTGGAACATCTCTTCTTCTTCAA	10/10	0.837595811504429	3	FACETS	0.366	0.332	0.401	0.122	0.11	0.134	SUBCLONAL	1	TRUE	0	0.837595811504429	3		650	1306	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0030524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	846	556	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.72513518790626	6	FACETS	0.976	0.949	1	0.976	0.949	1	CLONAL	4	TRUE	2	0.72513518790626	6		556	1465	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0030524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	258	375	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.72513518790626	4	FACETS	0.911	0.858	0.964	0.911	0.858	0.964	CLONAL	2	TRUE	2	0.72513518790626	4		375	674	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0030524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	432	419	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.72513518790626	3	FACETS	0.997	0.97	1	0.997	0.97	1	CLONAL	3	TRUE	0	0.72513518790626	3		419	543	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842408	68842408	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	385	643	1	ENST00000261769.5:c.469G>T	p.Val157Phe	p.V157F	ENST00000261769	NM_004360.3	157	Gtt/Ttt	4/16	0.72513518790626	2	FACETS	0.969	0.936	1	0.969	0.936	1	CLONAL	2	TRUE	0	0.72513518790626	2		644	548	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110047	115110047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766569858	NA	P-0030524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	243	762	2	ENST00000257566.3:c.1831G>A	p.Ala611Thr	p.A611T	ENST00000257566	NM_016569.3	611	Gcg/Acg	8/8	0.680124343748455	4	FACETS	1	0.934	1	0.5	0.467	0.535	CLONAL	1	TRUE	2	0.72513518790626	4		764	1156	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099090	27099091	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0030524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	135	469	0	ENST00000324856.7:c.3510_3511del	p.His1170GlnfsTer22	p.H1170Qfs*22	ENST00000324856	NM_006015.4	1169	cCA/c	13/20	1	2	FACETS	0.933	0.857	1	0.933	0.857	1	CLONAL	1	TRUE	1	0.72513518790626	2		469	399	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570197	95570197	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	236	380	0	ENST00000393063.1:c.3536C>T	p.Ser1179Phe	p.S1179F	ENST00000393063	NM_030621.3	1179	tCt/tTt	22/28	0.72513518790626	5	FACETS	0.895	0.838	0.953			1	CLONAL	2	TRUE	NA	0.72513518790626	5		380	759	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867199	68867199	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555518211	NA	P-0030524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	283	419	0	ENST00000261769.5:c.2446A>G	p.Lys816Glu	p.K816E	ENST00000261769	NM_004360.3	816	Aaa/Gaa	16/16	0.72513518790626	2	FACETS	0.978	0.94	1	0.978	0.94	1	CLONAL	2	TRUE	0	0.72513518790626	2		419	399	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15943760	15943760	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	118	319	0	ENST00000268712.3:c.6728C>A	p.Thr2243Lys	p.T2243K	ENST00000268712	NM_006311.3	2243	aCg/aAg	43/46	0.72513518790626	2	FACETS	1	0.926	1	0.507	0.463	0.552	CLONAL	1	TRUE	0	0.72513518790626	2		319	321	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945234	54945249	+	frameshift_variant	Frame_Shift_Del	DEL	ATTCTTTGTTTTGGCA	ATTCTTTGTTTTGGCA	-	novel	NA	P-0030524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1254	160	516	0	ENST00000312783.6:c.1177_1192del	p.Cys393GlnfsTer29	p.C393Qfs*29	ENST00000312783	NM_198436.1	393	TGCCAAAACAAAGAATca/ca	10/10	0.72513518790626	8	FACETS	0.991	0.906	1	0.198	0.181	0.217	CLONAL	1	TRUE	3	0.72513518790626	8		516	1414	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970880	70970880	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	365	446	0	ENST00000276594.2:c.1381C>G	p.His461Asp	p.H461D	ENST00000276594	NM_024504.3	461	Cac/Gac	6/8	0.679602753060233	5	FACETS	1	0.988	1	0.743	0.707	0.779	CLONAL	2	TRUE	2	0.72513518790626	5		446	943	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527504	29527505	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0030525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	320	596	0	ENST00000356175.3:c.954_955del	p.Ser319CysfsTer10	p.S319Cfs*10	ENST00000356175	NM_000267.3	318	gAA/g	9/57	0.735462254034034	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.735462254034034	1		596	523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0030527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	366	478	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.494959661448947	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.494959661448947	2		479	735	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0030527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	163	324	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.494959661448947	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.494959661448947	3		324	394	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654615	67654615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	237	461	0	ENST00000264010.4:c.1102C>T	p.Arg368Cys	p.R368C	ENST00000264010	NM_006565.3	368	Cgt/Tgt	6/12	0.494959661448947	3	FACETS	0.925	0.868	0.982	0.925	0.868	0.982	CLONAL	2	TRUE	1	0.494959661448947	3		461	646	SUCCESS
APC	324	MSKCC	GRCh37	5	112175594	112175594	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	124	361	0	ENST00000257430.4:c.4303del	p.Arg1435GlufsTer38	p.R1435Efs*38	ENST00000257430	NM_000038.5	1435	Aga/ga	16/16	0.494959661448947	3	FACETS	1	0.958	1	0.547	0.497	0.6	CLONAL	1	TRUE	1	0.494959661448947	3		361	571	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671543	30671543	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	225	662	0	ENST00000376406.3:c.5417A>C	p.Lys1806Thr	p.K1806T	ENST00000376406	NM_014641.2	1806	aAg/aCg	10/15	0.494959661448947	5	FACETS	1	0.985	1	0.407	0.378	0.437	CLONAL	1	TRUE	2	0.494959661448947	5		662	1298	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348233	348233	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs116350678	NA	P-0030529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	51	734	0	ENST00000262320.3:c.1273G>A	p.Gly425Ser	p.G425S	ENST00000262320	NM_003502.3	425	Ggc/Agc	6/11	0.340291273967279	1	FACETS	0.62	0.53	0.716	0.62	0.53	0.716	SUBCLONAL	1	FALSE	0	0.453070569222422	1		734	281	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs760043106	NA	P-0030529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	70	616	0	ENST00000269305.4:c.584T>G	p.Ile195Ser	p.I195S	ENST00000269305	NM_001126112.2	195	aTc/aGc	6/11	0.378690993150476	3	FACETS	1	0.952	1	0.585	0.514	0.66	CLONAL	1	FALSE	1	0.453070569222422	3		616	324	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0030541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	239	369	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.356000035140575	1	FACETS	0.875	0.824	0.926	1	0.994	1	CLONAL	2	FALSE	0	0.391149500807427	1		369	562	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0030541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	206	388	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.848	0.791	0.906	1	0.993	1	CLONAL	2	FALSE	1	0.391149500807427	2		388	621	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033653	48033656	+	frameshift_variant	Frame_Shift_Del	DEL	ATTC	ATTC	-	novel	NA	P-0030541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	65	492	0	ENST00000234420.5:c.3867_3870del	p.Phe1289LeufsTer37	p.F1289Lfs*37	ENST00000234420	NM_000179.2	1288	aaATTC/aa	9/10	0.391149500807427	1	FACETS	0.643	0.559	0.732	0.643	0.559	0.732	SUBCLONAL	1	FALSE	0	0.391149500807427	1		492	416	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0030542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	180	514	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.305099167545921	3	FACETS	0.863	0.799	0.93			1	CLONAL	2	TRUE	NA	0.359161600842578	3		514	685	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910647	29910647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	69	725	0	ENST00000376809.5:c.187G>A	p.Asp63Asn	p.D63N	ENST00000376809	NM_002116.7	63	Gac/Aac	2/8	1	2	FACETS	0.41	0.356	0.468	0.41	0.356	0.468	SUBCLONAL	1	TRUE	1	0.359161600842578	2		725	938	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614484	38614484	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	51	417	0	ENST00000299084.4:c.251del	p.Lys84ArgfsTer37	p.K84Rfs*37	ENST00000299084	NM_152594.2	84	Aag/ag	3/7	1	2	FACETS	0.805	0.687	0.933	0.805	0.687	0.933	CLONAL	1	TRUE	1	0.359161600842578	2		417	353	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122248	2122248	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	54	445	0	ENST00000219476.3:c.2104G>C	p.Asp702His	p.D702H	ENST00000219476	NM_000548.3	702	Gac/Cac	20/42	1	2	FACETS	0.477	0.406	0.553	0.477	0.406	0.553	SUBCLONAL	1	TRUE	1	0.359161600842578	2		445	631	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910661	29910661	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs199474396	NA	P-0030542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	73	755	0	ENST00000376809.5:c.201G>C	p.Gln67His	p.Q67H	ENST00000376809	NM_002116.7	67	caG/caC	2/8	1	2	FACETS	0.421	0.367	0.48	0.421	0.367	0.48	SUBCLONAL	1	TRUE	1	0.359161600842578	2		755	965	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019935	123019935	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	63	521	0	ENST00000355640.3:c.423G>C	p.Leu141Phe	p.L141F	ENST00000355640		141	ttG/ttC	2/7	1	2	FACETS	0.503	0.434	0.577	0.503	0.434	0.577	SUBCLONAL	1	TRUE	1	0.359161600842578	2		521	698	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508176	106508176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752039271	NA	P-0030544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	57	222	0	ENST00000359195.3:c.170C>T	p.Ala57Val	p.A57V	ENST00000359195	NM_002649.2	57	gCg/gTg	2/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.373548014406961	2		222	248	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56867319	56867319	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs138909849	NA	P-0030544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	73	313	0	ENST00000308159.5:c.1537+1G>A		p.X513_splice	ENST00000308159	NM_014669.4	513			1	2	FACETS	0.937	0.823	1	0.937	0.823	1	CLONAL	1	TRUE	1	0.373548014406961	2		313	417	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647245	2647245	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	114	531	0	ENST00000342085.4:c.1523C>T	p.Ala508Val	p.A508V	ENST00000342085	NM_002613.4	508	gCc/gTc	13/14	1	2	FACETS	0.82	0.739	0.906	0.82	0.739	0.906	CLONAL	1	TRUE	1	0.373548014406961	2		531	744	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069966	5069966	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	54	359	0	ENST00000381652.3:c.1555G>A	p.Asp519Asn	p.D519N	ENST00000381652	NM_004972.3	519	Gat/Aat	12/25	0.103738105925246	3	FACETS	1	0.908	1	0.359	0.308	0.413	INDETERMINATE	1	TRUE	0	0.373548014406961	3		359	319	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0030545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	208	712	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.700365387338105	6	FACETS	1	0.991	1	1	0.991	1	CLONAL	6	TRUE	0	0.700365387338105	6		712	227	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060780	38060797	+	inframe_deletion	In_Frame_Del	DEL	GTTGATGGAGAACGGGTG	GTTGATGGAGAACGGGTG	-	novel	NA	P-0030545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	169	672	0	ENST00000250448.2:c.1192_1209del	p.His398_Asn403del	p.H398_N403del	ENST00000250448	NM_004496.3	398	CACCCGTTCTCCATCAAC/-	2/2	0.537731920511801	5	FACETS	1	0.927	1	0.666	0.618	0.716	CLONAL	2	TRUE	2	0.700365387338105	5		672	495	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727084	243727084	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	21	402	0	ENST00000263826.5:c.886G>C	p.Gly296Arg	p.G296R	ENST00000263826	NM_005465.4	296	Ggg/Cgg	9/13	0.524496774642159	6	FACETS	0.911	0.708	1			1	CLONAL	1	TRUE	NA	0.700365387338105	6		402	158	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219510	133219510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	46	591	0	ENST00000320574.5:c.4624G>A	p.Gly1542Ser	p.G1542S	ENST00000320574	NM_006231.2	1542	Ggc/Agc	36/49	0.438804799282199	6	FACETS	1	0.947	1	0.426	0.361	0.495	CLONAL	1	TRUE	3	0.700365387338105	6		591	247	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793488	89793488	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	42	272	0	ENST00000336032.3:c.557T>A	p.Met186Lys	p.M186K	ENST00000336032	NM_006813.2	186	aTg/aAg	2/2	0.700365387338105	5	FACETS	1	0.945	1	0.429	0.363	0.501	CLONAL	1	TRUE	2	0.700365387338105	5		272	191	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0030546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	62	526	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.16	2		526	533	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230641	46230641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	42	476	1	ENST00000334344.6:c.890C>T	p.Ser297Phe	p.S297F	ENST00000334344	NM_152641.2	297	tCc/tTc	8/21	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.16	2		477	481	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658469	117658469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	32	579	0	ENST00000368508.3:c.5114C>T	p.Ser1705Leu	p.S1705L	ENST00000368508	NM_002944.2	1705	tCa/tTa	31/43	1	2	FACETS	0.794	0.643	0.964	0.794	0.643	0.964	CLONAL	1	TRUE	1	0.16	2		579	504	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244982	123244982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	35	554	1	ENST00000358487.5:c.2122C>T	p.Pro708Ser	p.P708S	ENST00000358487	NM_000141.4	708	Ccc/Tcc	16/18	1	2	FACETS	0.73	0.597	0.88	0.73	0.597	0.88	SUBCLONAL	1	TRUE	1	0.16	2		555	599	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481408	140481408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867748453	NA	P-0030546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	41	373	0	ENST00000288602.6:c.1400C>T	p.Ser467Leu	p.S467L	ENST00000288602	NM_004333.4	467	tCa/tTa	11/18	0.131145422903347	3	FACETS	1	0.947	1	0.688	0.574	0.815	CLONAL	1	TRUE	1	0.16	3		373	402	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389107	31389107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749860839	NA	P-0030546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	24	455	0	ENST00000328111.2:c.2020G>A	p.Glu674Lys	p.E674K	ENST00000328111	NM_006892.3	674	Gaa/Aaa	19/23	1	2	FACETS	0.699	0.547	0.875	0.699	0.547	0.875	SUBCLONAL	1	TRUE	1	0.16	2		455	429	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976644	55976644	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	37	486	0	ENST00000263923.4:c.1181G>A	p.Gly394Glu	p.G394E	ENST00000263923	NM_002253.2	394	gGa/gAa	9/30	1	2	FACETS	0.823	0.677	0.986	0.823	0.677	0.986	CLONAL	1	TRUE	1	0.16	2		486	562	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469139	25469139	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	43	631	0	ENST00000264709.3:c.1319G>T	p.Trp440Leu	p.W440L	ENST00000264709	NM_175629.2	440	tGg/tTg	11/23	1	2	FACETS	0.733	0.612	0.869	0.733	0.612	0.869	SUBCLONAL	1	TRUE	1	0.16	2		631	733	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196487	106196487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	22	370	0	ENST00000380013.4:c.4820C>T	p.Ser1607Leu	p.S1607L	ENST00000380013	NM_001127208.2	1607	tCa/tTa	11/11	1	2	FACETS	0.814	0.63	1	0.814	0.63	1	CLONAL	1	TRUE	1	0.16	2		370	338	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480014	120480014	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173598104	NA	P-0030546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	62	526	0	ENST00000256646.2:c.3413C>T	p.Pro1138Leu	p.P1138L	ENST00000256646	NM_024408.3	1138	cCc/cTc	21/34	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.16	2		526	646	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385262	4385262	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	41	487	0	ENST00000261254.3:c.287C>T	p.Ser96Phe	p.S96F	ENST00000261254	NM_001759.3	96	tCc/tTc	2/5	0.131145422903347	1	FACETS	0.893	0.743	1	0.893	0.743	1	CLONAL	1	TRUE	0	0.16	1		487	528	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784490	43784490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	44	509	0	ENST00000382044.4:c.184C>T	p.Pro62Ser	p.P62S	ENST00000382044	NM_001141980.1	62	Cct/Tct	2/28	1	2	FACETS	0.89	0.745	1	0.89	0.745	1	CLONAL	1	TRUE	1	0.16	2		509	618	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628610	90628610	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	39	746	1	ENST00000330062.3:c.977C>T	p.Ser326Phe	p.S326F	ENST00000330062	NM_002168.2	326	tCc/tTc	8/11	1	2	FACETS	0.729	0.602	0.87	0.729	0.602	0.87	SUBCLONAL	1	TRUE	1	0.16	2		747	669	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29563032	29563032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	29	315	0	ENST00000356175.3:c.3967C>T	p.Pro1323Ser	p.P1323S	ENST00000356175	NM_000267.3	1323	Cct/Tct	29/57	1	2	FACETS	1	0.829	1	1	0.829	1	CLONAL	1	TRUE	1	0.16	2		315	350	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664540	29664540	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	53	475	0	ENST00000356175.3:c.6519del	p.Glu2174ArgfsTer5	p.E2174Rfs*5	ENST00000356175	NM_000267.3	2173	agA/ag	42/57	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.16	2		475	544	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123733	11123735	+	frameshift_variant	Frame_Shift_Del	DEL	TAC	TAC	CA	novel	NA	P-0030546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	60	610	2	ENST00000358026.2:c.2383_2385delinsCA	p.Tyr795HisfsTer36	p.Y795Hfs*36	ENST00000358026	NM_001128849.1	795	TAC/CA	16/36	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.16	2		612	606	SUCCESS
ALK	238	MSKCC	GRCh37	2	29497983	29497983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1469128263	NA	P-0030546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	30	440	0	ENST00000389048.3:c.2023C>T	p.Pro675Ser	p.P675S	ENST00000389048	NM_004304.4	675	Ccc/Tcc	11/29	1	2	FACETS	0.673	0.541	0.824	0.673	0.541	0.824	SUBCLONAL	1	TRUE	1	0.16	2		440	557	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212615381	212615381	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	42	501	0	ENST00000342788.4:c.605A>G	p.Glu202Gly	p.E202G	ENST00000342788	NM_005235.2	202	gAa/gGa	5/28	1	2	FACETS	0.825	0.688	0.979	0.825	0.688	0.979	CLONAL	1	TRUE	1	0.16	2		501	636	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546653	9546653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	22	394	0	ENST00000353224.5:c.1369G>A	p.Glu457Lys	p.E457K	ENST00000353224	NM_177990.2	457	Gaa/Aaa	5/10	1	2	FACETS	0.65	0.503	0.822	0.65	0.503	0.822	SUBCLONAL	1	TRUE	1	0.16	2		394	423	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627277	37627277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	47	816	1	ENST00000249071.6:c.442G>A	p.Glu148Lys	p.E148K	ENST00000249071	NM_002872.4	148	Gag/Aag	5/7	1	2	FACETS	0.692	0.582	0.814	0.692	0.582	0.814	SUBCLONAL	1	TRUE	1	0.16	2		817	849	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541765	187541765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	24	422	0	ENST00000441802.2:c.5975C>T	p.Ser1992Phe	p.S1992F	ENST00000441802	NM_005245.3	1992	tCc/tTc	10/27	1	2	FACETS	0.714	0.559	0.894	0.714	0.559	0.894	SUBCLONAL	1	TRUE	1	0.16	2		422	420	SUCCESS
APC	324	MSKCC	GRCh37	5	112179035	112179035	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1451906942	NA	P-0030546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	21	360	0	ENST00000257430.4:c.7744G>A	p.Glu2582Lys	p.E2582K	ENST00000257430	NM_000038.5	2582	Gaa/Aaa	16/16	1	2	FACETS	0.698	0.537	0.887	0.698	0.537	0.887	SUBCLONAL	1	TRUE	1	0.16	2		360	376	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641099	117641099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs986549979	NA	P-0030546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	52	559	0	ENST00000368508.3:c.5872G>A	p.Glu1958Lys	p.E1958K	ENST00000368508	NM_002944.2	1958	Gaa/Aaa	36/43	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.16	2		559	582	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681075	117681075	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	32	556	0	ENST00000368508.3:c.3545G>A	p.Arg1182Lys	p.R1182K	ENST00000368508	NM_002944.2	1182	aGa/aAa	23/43	1	2	FACETS	0.66	0.534	0.803	0.66	0.534	0.803	SUBCLONAL	1	TRUE	1	0.16	2		556	606	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710528	117710528	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	15	221	0	ENST00000368508.3:c.1744C>T	p.Leu582Phe	p.L582F	ENST00000368508	NM_002944.2	582	Ctt/Ttt	12/43	1	2	FACETS	0.952	0.698	1	0.952	0.698	1	CLONAL	1	TRUE	1	0.16	2		221	197	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846143	128846143	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	71	684	1	ENST00000249373.3:c.1073C>T	p.Ser358Phe	p.S358F	ENST00000249373	NM_005631.4	358	tCc/tTc	5/12	0.131145422903347	3	FACETS	1	0.969	1	0.697	0.608	0.793	CLONAL	1	TRUE	1	0.16	3		685	688	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88676924	88676926	+	missense_variant	Missense_Mutation	TNP	GTC	GTC	TTT	novel	NA	P-0030546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	38	404	0	ENST00000372037.3:c.709_711delinsTTT	p.Val237Phe	p.V237F	ENST00000372037	NM_004329.2	237	GTC/TTT	9/13	1	2	FACETS	0.93	0.768	1	0.93	0.768	1	CLONAL	1	TRUE	1	0.16	2		404	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577569	7577569	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519981	NA	P-0030548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	102	500	0	ENST00000269305.4:c.712T>C	p.Cys238Arg	p.C238R	ENST00000269305	NM_001126112.2	238	Tgt/Cgt	7/11	0.328905370884708	1	FACETS	0.985	0.884	1	0.985	0.884	1	CLONAL	1	TRUE	0	0.328905370884708	1		500	526	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0030549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	127	369	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.337242119344992	1	FACETS	0.892	0.814	0.973	0.892	0.814	0.973	CLONAL	1	TRUE	0	0.471853134866448	1		369	461	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440328	52440328	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	182	591	0	ENST00000460680.1:c.724G>T	p.Glu242Ter	p.E242*	ENST00000460680	NM_004656.3	242	Gag/Tag	9/17	0.471853134866448	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.471853134866448	1		591	586	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518437	204518437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201947927	NA	P-0030549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	106	448	0	ENST00000367182.3:c.1100C>T	p.Ser367Leu	p.S367L	ENST00000367182	NM_001278516.1	367	tCg/tTg	11/11	0.286261930800808	3	FACETS	0.978	0.879	1	0.489	0.439	0.541	CLONAL	1	TRUE	1	0.471853134866448	3		448	568	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974675	21974695	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ACCTGGATCGGCCTCCGACCG	ACCTGGATCGGCCTCCGACCG	-	novel	NA	P-0030549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	104	471	0	ENST00000304494.5:c.132_150+2del		p.X44_splice	ENST00000304494	NM_000077.4	44		1/3	0.471853134866448	1	FACETS	0.81	0.73	0.893	0.81	0.73	0.893	CLONAL	1	TRUE	0	0.471853134866448	1		471	416	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637013	93637013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	150	364	0	ENST00000375746.1:c.1063C>T	p.Pro355Ser	p.P355S	ENST00000375746	NM_001174167.1	355	Ccc/Tcc	9/14	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.514348846062934	2		364	577	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867234	68867234	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0030553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	193	394	0	ENST00000261769.5:c.2481T>A	p.Tyr827Ter	p.Y827*	ENST00000261769	NM_004360.3	827	taT/taA	16/16	0.514348846062934	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.514348846062934	1		394	495	SUCCESS
APC	324	MSKCC	GRCh37	5	112178747	112178747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768537235	NA	P-0030555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	224	383	0	ENST00000257430.4:c.7456C>T	p.Pro2486Ser	p.P2486S	ENST00000257430	NM_000038.5	2486	Cct/Tct	16/16	1	2	FACETS	0.981	0.916	1	0.981	0.916	1	CLONAL	1	TRUE	1	0.581577215303637	2		383	785	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035196	30035196	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	181	441	1	ENST00000338641.4:c.359del	p.Leu120TyrfsTer3	p.L120Yfs*3	ENST00000338641	NM_000268.3	120	Tta/ta	3/16	0.57363043113288	1	FACETS	0.813	0.755	0.872	0.813	0.755	0.872	CLONAL	1	TRUE	0	0.581577215303637	1		442	543	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805537	32805537	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	427	730	16	ENST00000374899.4:c.474C>A	p.Phe158Leu	p.F158L	ENST00000374899	NM_018833.2	158	ttC/ttA	2/12	0.57363043113288	1	FACETS	0.933	0.891	0.976	0.933	0.891	0.976	CLONAL	1	TRUE	0	0.581577215303637	1		746	1116	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0030557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	110	622	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.873	0.798	0.949	0.873	0.798	0.949	CLONAL	1	TRUE	1	0.951434173392767	2		622	265	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	1022	538	0	ENST00000269305.4:c.503A>C	p.His168Pro	p.H168P	ENST00000269305	NM_001126112.2	168	cAc/cCc	5/11	0.944082831655115	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.951434173392767	2		538	1063	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513317	149513317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147568171	NA	P-0030557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	363	415	1	ENST00000261799.4:c.766C>T	p.Arg256Trp	p.R256W	ENST00000261799	NM_002609.3	256	Cgg/Tgg	6/23	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.951434173392767	2		416	692	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458902	120458902	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	477	576	1	ENST00000256646.2:c.6443del	p.Leu2148TyrfsTer7	p.L2148Yfs*7	ENST00000256646	NM_024408.3	2148	tTa/ta	34/34	0.948269760913728	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.951434173392767	1		577	523	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145418	58145419	+	missense_variant	Missense_Mutation	DNP	CT	CT	TG	novel	NA	P-0030557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	346	376	0	ENST00000257904.6:c.82_83delinsCA	p.Ser28His	p.S28H	ENST00000257904	NM_000075.3	28	AGt/CAt	2/8	1	2	FACETS	0.938	0.894	0.983	0.938	0.894	0.983	CLONAL	1	TRUE	1	0.951434173392767	2		376	775	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0030559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	106	546	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.445076712474115	1	FACETS	0.89	0.818	0.962	1	0.989	1	CLONAL	2	TRUE	0	0.445076712474115	1		546	208	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577520	7577520	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	156	451	0	ENST00000269305.4:c.761T>A	p.Ile254Asn	p.I254N	ENST00000269305	NM_001126112.2	254	aTc/aAc	7/11	0.445076712474115	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.445076712474115	1		451	463	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105809	27105810	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	69	349	0	ENST00000324856.7:c.5421dup	p.Lys1808Ter	p.K1808*	ENST00000324856	NM_006015.4	1807	agt/agTt	20/20	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.445076712474115	2		349	284	SUCCESS
YES1	7525	MSKCC	GRCh37	18	742978	742978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	33	353	0	ENST00000314574.4:c.1000C>T	p.Pro334Ser	p.P334S	ENST00000314574	NM_005433.3	334	Cca/Tca	8/12	0.445076712474115	1	FACETS	0.854	0.708	1	0.854	0.708	1	CLONAL	1	TRUE	0	0.445076712474115	1		353	135	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0030560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	81	673	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.296680531836282	3	FACETS	1	0.944	1	0.56	0.494	0.63	CLONAL	1	TRUE	1	0.296680531836282	3		673	560	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0030560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	158	576	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.296680531836282	3	FACETS	0.998	0.918	1	0.998	0.918	1	CLONAL	2	TRUE	1	0.296680531836282	3		576	613	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0030560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	178	528	1	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	0.296680531836282	2	FACETS	0.912	0.844	0.982	0.912	0.844	0.982	CLONAL	2	TRUE	0	0.296680531836282	2		529	658	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149574	61149574	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	105	368	0	ENST00000295025.8:c.1764T>A	p.Ser588Arg	p.S588R	ENST00000295025	NM_002908.2	588	agT/agA	11/11	0.296680531836282	3	FACETS	0.907	0.818	1	0.907	0.818	1	CLONAL	2	TRUE	1	0.296680531836282	3		368	448	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155460	106155460	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	72	376	0	ENST00000380013.4:c.361G>T	p.Glu121Ter	p.E121*	ENST00000380013	NM_001127208.2	121	Gaa/Taa	3/11	0.296680531836282	2	FACETS	1	0.946	1	0.572	0.502	0.648	CLONAL	1	TRUE	0	0.296680531836282	2		376	424	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041399	47041399	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	217	655	1	ENST00000377604.3:c.1743C>A	p.Tyr581Ter	p.Y581*	ENST00000377604	NM_001204468.1	581	taC/taA	16/24	0.296680531836282	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.296680531836282	2		656	679	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28929495	NA	P-0030562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	211	490	2	ENST00000275493.2:c.2155G>T	p.Gly719Cys	p.G719C	ENST00000275493	NM_005228.3	719	Ggc/Tgc	18/28	0.166100757353524	2	FACETS	0.928	0.866	0.99	0.928	0.866	0.99	INDETERMINATE	2	TRUE	0	0.357607987239474	2		492	636	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0030562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	170	431	2	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.166100757353524	2	FACETS	0.882	0.816	0.949	0.882	0.816	0.949	INDETERMINATE	2	TRUE	0	0.357607987239474	2		433	539	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578283	7578283	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	160	570	0	ENST00000269305.4:c.566C>A	p.Ala189Asp	p.A189D	ENST00000269305	NM_001126112.2	189	gCc/gAc	6/11	0.203982196990433	2	FACETS	0.789	0.727	0.853	0.789	0.727	0.853	INDETERMINATE	2	TRUE	0	0.357607987239474	2		570	567	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249808	133249808	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	73	516	0	ENST00000320574.5:c.1415A>C	p.Lys472Thr	p.K472T	ENST00000320574	NM_006231.2	472	aAg/aCg	14/49	1	2	FACETS	0.657	0.575	0.746	0.657	0.575	0.746	SUBCLONAL	1	TRUE	1	0.357607987239474	2		516	621	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578484	7578484	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	287	760	0	ENST00000269305.4:c.446C>A	p.Ser149Tyr	p.S149Y	ENST00000269305	NM_001126112.2	149	tCc/tAc	5/11	0.203982196990433	2	FACETS	0.785	0.739	0.833	0.785	0.739	0.833	INDETERMINATE	2	TRUE	0	0.357607987239474	2		760	1022	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131361	17131361	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	204	693	0	ENST00000285071.4:c.91C>T	p.Gln31Ter	p.Q31*	ENST00000285071	NM_144997.5	31	Caa/Taa	4/14	0.203982196990433	2	FACETS	0.832	0.774	0.89	0.832	0.774	0.89	INDETERMINATE	2	TRUE	0	0.357607987239474	2		693	686	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961000	55961000	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	61	441	0	ENST00000263923.4:c.2940G>T	p.Glu980Asp	p.E980D	ENST00000263923	NM_002253.2	980	gaG/gaT	21/30	1	2	FACETS	0.682	0.589	0.783	0.682	0.589	0.783	SUBCLONAL	1	TRUE	1	0.357607987239474	2		441	500	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38946648	38946648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776169234	NA	P-0030562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	28	302	0	ENST00000357387.3:c.4321G>A	p.Asp1441Asn	p.D1441N	ENST00000357387	NM_152756.3	1441	Gat/Aat	33/38	0.357607987239474	7	FACETS	1	0.805	1	0.168	0.134	0.206	CLONAL	1	TRUE	1	0.357607987239474	7		302	295	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545714	106545714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	91	594	1	ENST00000359195.3:c.3191C>T	p.Ala1064Val	p.A1064V	ENST00000359195	NM_002649.2	1064	gCt/gTt	11/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.357607987239474	2		595	401	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0030563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	13	367	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.918	0.655	1	0.918	0.655	1	CLONAL	1	TRUE	1	0.12	2		367	236	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291546	15291546	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1179899018	NA	P-0030564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	62	621	1	ENST00000263388.2:c.3088G>A	p.Gly1030Arg	p.G1030R	ENST00000263388	NM_000435.2	1030	Gga/Aga	19/33	NA	2	FACETS	0.302	0.26	0.347			1	INDETERMINATE	1	TRUE	NA	0.585538885357622	2		622	702	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0030566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	480	545	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.653786053801661	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.653786053801661	2		545	652	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0030566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	99	250	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.653786053801661	2		250	274	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0030566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	43	528	1	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	1	2	FACETS	0.248	0.207	0.293	0.248	0.207	0.293	SUBCLONAL	1	TRUE	1	0.653786053801661	2		529	531	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115272911	115272911	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs945873992	NA	P-0030566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	39	485	0	ENST00000438362.2:c.1462A>G	p.Lys488Glu	p.K488E	ENST00000438362	NM_001242891.1	488	Aaa/Gaa	12/20	1	2	FACETS	0.197	0.162	0.235	0.197	0.162	0.235	SUBCLONAL	1	TRUE	1	0.653786053801661	2		485	607	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433053	49433054	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0030566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	55	624	0	ENST00000301067.7:c.8317_8318del	p.Ser2773ProfsTer71	p.S2773Pfs*71	ENST00000301067	NM_003482.3	2773	TCc/c	33/54	1	2	FACETS	0.206	0.176	0.24	0.206	0.176	0.24	SUBCLONAL	1	TRUE	1	0.653786053801661	2		624	816	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589580	67589582	+	inframe_deletion	In_Frame_Del	DEL	AAT	AAT	-	novel	NA	P-0030566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	38	258	0	ENST00000274335.5:c.1343_1345del	p.Lys448_Leu449delinsIle	p.K448_L449delinsI	ENST00000274335		448	aAATta/ata	10/15	1	2	FACETS	0.471	0.391	0.558	0.471	0.391	0.558	SUBCLONAL	1	TRUE	1	0.653786053801661	2		258	247	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057520005	NA	P-0030567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	55	527	0	ENST00000269305.4:c.820G>T	p.Val274Phe	p.V274F	ENST00000269305	NM_001126112.2	274	Gtt/Ttt	8/11	1	2	FACETS	0.926	0.79	1	0.926	0.79	1	CLONAL	1	TRUE	1	0.155118779482973	2		527	766	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100356	27100356	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	57	502	0	ENST00000324856.7:c.4069del	p.Gln1357SerfsTer124	p.Q1357Sfs*124	ENST00000324856	NM_006015.4	1356	agC/ag	17/20	1	2	FACETS	0.992	0.849	1	0.992	0.849	1	CLONAL	1	TRUE	1	0.155118779482973	2		502	741	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922185	100922185	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	53	371	0	ENST00000325455.5:c.2327T>A	p.Leu776Gln	p.L776Q	ENST00000325455	NM_001202474.3	776	cTg/cAg	5/8	1	2	FACETS	0.976	0.836	1	1	0.975	1	CLONAL	2	TRUE	1	0.155118779482973	2		371	350	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81968090	81968090	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	34	438	0	ENST00000359376.3:c.2796C>A	p.Asp932Glu	p.D932E	ENST00000359376	NM_002661.3	932	gaC/gaA	26/33	1	2	FACETS	0.667	0.544	0.807	0.667	0.544	0.807	SUBCLONAL	1	TRUE	1	0.155118779482973	2		438	657	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965566	15965566	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	22	186	0	ENST00000268712.3:c.5240G>T	p.Arg1747Leu	p.R1747L	ENST00000268712	NM_006311.3	1747	cGa/cTa	36/46	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.155118779482973	2		186	248	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006836	62006836	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0030567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	49	456	1	ENST00000392795.3:c.553-1G>T		p.X185_splice	ENST00000392795	NM_001039933.1	185			1	2	FACETS	0.989	0.836	1	0.989	0.836	1	CLONAL	1	TRUE	1	0.155118779482973	2		457	639	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733233	74733233	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	51	407	0	ENST00000359995.5:c.10G>T	p.Gly4Cys	p.G4C	ENST00000359995	NM_001195427.1	4	Ggc/Tgc	1/3	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.155118779482973	2		407	573	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411898	116411904	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTAAGAT	TTAAGAT	AA	novel	NA	P-0030567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	243	699	1	ENST00000397752.3:c.2888-5_2889delinsAA		p.X963_splice	ENST00000397752	NM_000245.2	963		14/21	0.155118779482973	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	0	0.155118779482973	3		700	1012	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852092	128852092	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	97	715	0	ENST00000249373.3:c.2164G>C	p.Gly722Arg	p.G722R	ENST00000249373	NM_005631.4	722	Ggg/Cgg	12/12	0.155118779482973	3	FACETS	1	0.977	1	0.465	0.413	0.519	CLONAL	1	TRUE	0	0.155118779482973	3		715	967	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0030568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	453	410	1	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	0.830685953834166	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.830685953834166	2		411	540	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562676	95562677	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	27	269	0	ENST00000393063.1:c.4580dup	p.Trp1528LeufsTer11	p.W1528Lfs*11	ENST00000393063	NM_030621.3	1527	ttc/ttTc	24/28	0.830685953834166	2	FACETS	0.145	0.115	0.18	0.073	0.057	0.09	SUBCLONAL	1	TRUE	0	0.830685953834166	2		269	448	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562683	95562685	+	missense_variant	Missense_Mutation	TNP	ACC	ACC	CCA	novel	NA	P-0030568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	30	259	0	ENST00000393063.1:c.4572_4574delinsTGG	p.Val1525Gly	p.V1525G	ENST00000393063	NM_030621.3	1524	gtGGTg/gtTGGg	24/28	0.830685953834166	2	FACETS	0.163	0.131	0.199	0.081	0.065	0.1	SUBCLONAL	1	TRUE	0	0.830685953834166	2		259	444	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597830	43597830	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	228	735	1	ENST00000355710.3:c.378C>A	p.Phe126Leu	p.F126L	ENST00000355710	NM_020975.4	126	ttC/ttA	3/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.574699880436421	2		736	773	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240996	53240996	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	143	273	0	ENST00000375401.3:c.1215A>C	p.Lys405Asn	p.K405N	ENST00000375401	NM_004187.3	405	aaA/aaC	9/26	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.574699880436421	1		273	284	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38506115	38506115	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	128	548	0	ENST00000254066.5:c.407C>G	p.Thr136Ser	p.T136S	ENST00000254066	NM_000964.3	136	aCc/aGc	4/9	0.541106123243908	3	FACETS	0.884	0.803	0.969	0.442	0.401	0.485	CLONAL	1	TRUE	1	0.541106123243908	3		548	680	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976672	55976672	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	122	529	0	ENST00000263923.4:c.1153A>G	p.Ile385Val	p.I385V	ENST00000263923	NM_002253.2	385	Att/Gtt	9/30	0.429931346447783	4	FACETS	0.942	0.852	1	0.471	0.426	0.518	CLONAL	1	TRUE	2	0.541106123243908	4		529	738	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0030584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	217	410	1	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	0.315855696130652	2	FACETS	0.843	0.788	0.9	0.843	0.788	0.9	CLONAL	2	TRUE	0	0.37242886788722	2		411	691	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446129	70446129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1333809107	NA	P-0030584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	40	361	0	ENST00000373644.4:c.5069G>A	p.Arg1690Gln	p.R1690Q	ENST00000373644	NM_030625.2	1690	cGa/cAa	11/12	0.180360932873424	2	FACETS	0.536	0.446	0.636	0.268	0.223	0.318	INDETERMINATE	1	TRUE	0	0.37242886788722	2		361	401	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27228229	27228229	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757379347	NA	P-0030584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	35	525	1	ENST00000380036.4:c.3226C>T	p.Arg1076Trp	p.R1076W	ENST00000380036	NM_000459.3	1076	Cgg/Tgg	22/23	0.245518692578616	3	FACETS	0.382	0.313	0.461	0.191	0.156	0.231	SUBCLONAL	1	TRUE	1	0.37242886788722	3		526	583	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050932	49050933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	53	466	0	ENST00000267163.4:c.2622dup	p.Leu875ThrfsTer4	p.L875Tfs*4	ENST00000267163	NM_000321.2	872	-/A	25/27	0.37242886788722	4	FACETS	0.586	0.499	0.681	0.195	0.166	0.227	SUBCLONAL	1	TRUE	1	0.37242886788722	4		466	667	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281793	49281793	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	87	585	0	ENST00000282018.3:c.840A>C	p.Lys280Asn	p.K280N	ENST00000282018	NM_020377.2	280	aaA/aaC	1/1	0.37242886788722	4	FACETS	0.654	0.578	0.736	0.218	0.192	0.246	SUBCLONAL	1	TRUE	1	0.37242886788722	4		585	980	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730897	40730897	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	156	511	1	ENST00000373198.4:c.3638G>A	p.Cys1213Tyr	p.C1213Y	ENST00000373198	NM_133170.3	1213	tGc/tAc	27/32	0.140376549194894	6	FACETS	1	0.986	1	0.472	0.431	0.514	INDETERMINATE	1	TRUE	3	0.37242886788722	6		512	1033	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963018	38963018	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	18	254	0	ENST00000357387.3:c.1526A>C	p.Asp509Ala	p.D509A	ENST00000357387	NM_152756.3	509	gAt/gCt	17/38	0.370842680001724	3	FACETS	0.425	0.32	0.549	0.142	0.106	0.183	SUBCLONAL	1	TRUE	0	0.37242886788722	3		254	270	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459840	149459840	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761316359	NA	P-0030584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	139	604	2	ENST00000286301.3:c.367G>A	p.Ala123Thr	p.A123T	ENST00000286301	NM_005211.3	123	Gca/Aca	4/22	0.295726971891005	2	FACETS	1	0.939	1	0.518	0.472	0.566	CLONAL	1	TRUE	0	0.37242886788722	2		606	720	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129388	152129388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	41	370	2	ENST00000206249.3:c.341C>T	p.Pro114Leu	p.P114L	ENST00000206249	NM_000125.3	114	cCg/cTg	1/8	0.180360932873424	2	FACETS	0.413	0.344	0.491	0.207	0.172	0.246	INDETERMINATE	1	TRUE	0	0.37242886788722	2		372	533	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845190	151845190	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764910946	NA	P-0030584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	106	444	1	ENST00000262189.6:c.13822C>T	p.Arg4608Cys	p.R4608C	ENST00000262189	NM_170606.2	4608	Cgc/Tgc	52/59	0.139236030857942	3	FACETS	1	0.935	1	0.352	0.315	0.39	INDETERMINATE	1	TRUE	0	0.37242886788722	3		445	640	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404619	8404619	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	28	249	0	ENST00000356435.5:c.4128C>A	p.Asn1376Lys	p.N1376K	ENST00000356435		1376	aaC/aaA	25/35	0.245518692578616	3	FACETS	0.803	0.646	0.981	0.402	0.323	0.491	CLONAL	1	TRUE	1	0.37242886788722	3		249	222	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0030591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	377	576	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.623179851785564	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.623179851785564	2		576	591	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0030591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	89	250	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.623179851785564	2		250	277	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0030592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	72	532	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.242207784833046	5	FACETS	1	0.905	1	1	0.905	1	CLONAL	4	TRUE	1	0.242207784833046	5		533	199	SUCCESS
ATM	472	MSKCC	GRCh37	11	108099946	108099946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565346853	NA	P-0030592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	12	266	0	ENST00000278616.4:c.227G>A	p.Arg76Lys	p.R76K	ENST00000278616	NM_000051.3	76	aGa/aAa	4/63	0.211881575312273	3	FACETS	1	0.78	1	0.561	0.398	0.756	CLONAL	1	TRUE	1	0.242207784833046	3		266	99	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218071	108218071	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	24	288	0	ENST00000278616.4:c.8650G>C	p.Glu2884Gln	p.E2884Q	ENST00000278616	NM_000051.3	2884	Gaa/Caa	59/63	0.211881575312273	3	FACETS	0.958	0.763	1	0.958	0.763	1	CLONAL	2	TRUE	1	0.242207784833046	3		288	116	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210771	133210771	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0030592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	82	342	0	ENST00000320574.5:c.6004+1G>T		p.X2002_splice	ENST00000320574	NM_006231.2	2002			0.211881575312273	3	FACETS	1	0.977	1	0.738	0.653	0.83	CLONAL	1	TRUE	1	0.242207784833046	3		342	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0030592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	113	574	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	0.997	0.896	1	0.997	0.896	1	CLONAL	1	TRUE	1	0.242207784833046	2		574	936	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161300	185161300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1363166292	NA	P-0030592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	31	536	0	ENST00000265026.3:c.727G>A	p.Glu243Lys	p.E243K	ENST00000265026	NM_004721.4	243	Gag/Aag	4/14	0.211881575312273	3	FACETS	0.528	0.426	0.643	0.264	0.213	0.322	SUBCLONAL	1	TRUE	1	0.242207784833046	3		536	544	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541622	187541622	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	22	288	0	ENST00000441802.2:c.6118G>T	p.Asp2040Tyr	p.D2040Y	ENST00000441802	NM_005245.3	2040	Gat/Tat	10/27	1	2	FACETS	0.426	0.33	0.539	0.426	0.33	0.539	SUBCLONAL	1	TRUE	1	0.242207784833046	2		288	426	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044901	47044901	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	81	767	1	ENST00000377604.3:c.2227G>T	p.Glu743Ter	p.E743*	ENST00000377604	NM_001204468.1	743	Gag/Tag	20/24	1	2	FACETS	0.643	0.565	0.728	0.643	0.565	0.728	SUBCLONAL	1	TRUE	1	0.242207784833046	2		768	1040	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0030593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	201	324	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.238614056602362	6	FACETS	0.912	0.852	0.973			1	CLONAL	5	TRUE	NA	0.238614056602362	6		324	546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876659802	NA	P-0030593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	149	540	0	ENST00000269305.4:c.833C>A	p.Pro278His	p.P278H	ENST00000269305	NM_001126112.2	278	cCt/cAt	8/11	0.238614056602362	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.238614056602362	2		540	572	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571423	95571423	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	22	191	0	ENST00000393063.1:c.3254T>A	p.Leu1085His	p.L1085H	ENST00000393063	NM_030621.3	1085	cTt/cAt	21/28	1	2	FACETS	0.917	0.715	1	0.917	0.715	1	CLONAL	1	TRUE	1	0.238614056602362	2		191	201	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799820	72799820	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	59	394	0	ENST00000325599.8:c.1349C>G	p.Ser450Cys	p.S450C	ENST00000325599	NM_018130.2	450	tCc/tGc	11/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.238614056602362	2		394	369	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163726	32163726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	125	323	0	ENST00000375023.3:c.5500G>A	p.Gly1834Ser	p.G1834S	ENST00000375023	NM_004557.3	1834	Ggc/Agc	30/30	0.238614056602362	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	1	0.238614056602362	4		323	382	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0030594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	177	645	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.26746003205695	3	FACETS	0.958	0.884	1	0.958	0.884	1	CLONAL	2	TRUE	1	0.268365730016804	3		645	781	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0030594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	99	578	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.26746003205695	3	FACETS	1	0.932	1	0.53	0.472	0.591	CLONAL	1	TRUE	1	0.268365730016804	3		578	790	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16041492	16041492	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	59	253	0	ENST00000268712.3:c.1387G>T	p.Ala463Ser	p.A463S	ENST00000268712	NM_006311.3	463	Gca/Tca	13/46	0.26746003205695	3	FACETS	1	0.959	1	0.654	0.565	0.751	CLONAL	1	TRUE	1	0.268365730016804	3		253	381	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606709	29606709	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	126	422	0	ENST00000389048.3:c.1171G>T	p.Gly391Ter	p.G391*	ENST00000389048	NM_004304.4	391	Gga/Tga	5/29	0.232262226931253	4	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	2	0.268365730016804	4		422	580	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182264	38182264	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	111	426	0	ENST00000396334.3:c.700G>T	p.Val234Leu	p.V234L	ENST00000396334	NM_002468.4	234	Gtg/Ttg	4/5	0.264366730403436	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	2	TRUE	0	0.268365730016804	2		426	413	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694608	176694608	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	51	357	0	ENST00000439151.2:c.5192G>T	p.Arg1731Leu	p.R1731L	ENST00000439151	NM_022455.4	1731	cGt/cTt	15/23	0.26746003205695	3	FACETS	0.925	0.787	1	0.463	0.393	0.538	CLONAL	1	TRUE	1	0.268365730016804	3		357	466	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642438	117642438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	131	557	0	ENST00000368508.3:c.5761G>A	p.Ala1921Thr	p.A1921T	ENST00000368508	NM_002944.2	1921	Gcc/Acc	35/43	0.193660221766101	4	FACETS	0.813	0.738	0.891	0.813	0.738	0.891	CLONAL	2	TRUE	2	0.268365730016804	4		557	762	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388034	81388034	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	74	434	0	ENST00000222390.5:c.341A>T	p.His114Leu	p.H114L	ENST00000222390	NM_000601.4	114	cAt/cTt	3/18	0.26746003205695	3	FACETS	1	0.962	1	0.624	0.548	0.706	CLONAL	1	TRUE	1	0.268365730016804	3		434	501	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0030594-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	75	645	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	0.76	0.666	0.863	0.76	0.666	0.863	SUBCLONAL	1	TRUE	1	0.268411146480013	2		645	735	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0030594-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	53	578	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	1	2	FACETS	0.51	0.433	0.593	0.51	0.433	0.593	SUBCLONAL	1	TRUE	1	0.268411146480013	2		578	775	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16041492	16041492	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030594-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	21	253	0	ENST00000268712.3:c.1387G>T	p.Ala463Ser	p.A463S	ENST00000268712	NM_006311.3	463	Gca/Tca	13/46	1	2	FACETS	0.433	0.333	0.551	0.433	0.333	0.551	SUBCLONAL	1	TRUE	1	0.268411146480013	2		253	361	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606709	29606709	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030594-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	53	422	0	ENST00000389048.3:c.1171G>T	p.Gly391Ter	p.G391*	ENST00000389048	NM_004304.4	391	Gga/Tga	5/29	1	2	FACETS	0.868	0.741	1	0.868	0.741	1	CLONAL	1	TRUE	1	0.268411146480013	2		422	455	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182264	38182264	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030594-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	89	426	0	ENST00000396334.3:c.700G>T	p.Val234Leu	p.V234L	ENST00000396334	NM_002468.4	234	Gtg/Ttg	4/5	0.170560944832411	2	FACETS	1	0.975	1	0.674	0.6	0.753	CLONAL	1	TRUE	0	0.268411146480013	2		426	492	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694608	176694608	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030594-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	55	357	0	ENST00000439151.2:c.5192G>T	p.Arg1731Leu	p.R1731L	ENST00000439151	NM_022455.4	1731	cGt/cTt	15/23	1	2	FACETS	0.866	0.742	1	0.866	0.742	1	CLONAL	1	TRUE	1	0.268411146480013	2		357	473	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642438	117642438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030594-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	52	557	0	ENST00000368508.3:c.5761G>A	p.Ala1921Thr	p.A1921T	ENST00000368508	NM_002944.2	1921	Gcc/Acc	35/43	0.268411146480013	1	FACETS	0.52	0.442	0.606	0.52	0.442	0.606	SUBCLONAL	1	TRUE	0	0.268411146480013	1		557	645	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388034	81388034	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030594-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	24	434	0	ENST00000222390.5:c.341A>T	p.His114Leu	p.H114L	ENST00000222390	NM_000601.4	114	cAt/cTt	3/18	1	2	FACETS	0.479	0.375	0.599	0.479	0.375	0.599	SUBCLONAL	1	TRUE	1	0.268411146480013	2		434	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0030595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	90	495	0	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	0.261242967534723	1	FACETS	0.756	0.671	0.847	0.756	0.671	0.847	SUBCLONAL	1	TRUE	0	0.284822817190453	1		495	717	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936093	178936093	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913275	NA	P-0030595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	356	423	0	ENST00000263967.3:c.1635G>C	p.Glu545Asp	p.E545D	ENST00000263967	NM_006218.2	545	gaG/gaC	10/21	0.284822817190453	6	FACETS	1	0.983	1			1	CLONAL	4	TRUE	NA	0.284822817190453	6		423	913	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313029	30313029	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	35	343	0	ENST00000262643.3:c.832A>G	p.Ile278Val	p.I278V	ENST00000262643	NM_001238.2	278	Att/Gtt	9/12	1	2	FACETS	0.444	0.363	0.536	0.444	0.363	0.536	SUBCLONAL	1	TRUE	1	0.284822817190453	2		343	553	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917036	50917036	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	75	485	0	ENST00000440232.2:c.2288T>A	p.Phe763Tyr	p.F763Y	ENST00000440232	NM_002691.3	763	tTc/tAc	19/27	1	2	FACETS	0.702	0.615	0.797	0.702	0.615	0.797	SUBCLONAL	1	TRUE	1	0.284822817190453	2		485	750	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206841	36206842	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCTCGGAAAAGGACAA	novel	NA	P-0030595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	61	300	0	ENST00000300305.3:c.655_670dup	p.Arg224LeufsTer9	p.R224Lfs*9	ENST00000300305		224	cgg/cTTGTCCTTTTCCGAGCgg	6/8	1	2	FACETS	0.776	0.67	0.891	0.776	0.67	0.891	SUBCLONAL	1	TRUE	1	0.284822817190453	2		300	552	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36253011	36253011	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0030595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	28	286	0	ENST00000300305.3:c.352-1G>C		p.X118_splice	ENST00000300305		118			1	2	FACETS	0.417	0.332	0.513	0.417	0.332	0.513	SUBCLONAL	1	TRUE	1	0.284822817190453	2		286	472	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526684	106526684	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs749697128	NA	P-0030595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	37	364	0	ENST00000359195.3:c.2977T>C	p.Phe993Leu	p.F993L	ENST00000359195	NM_002649.2	993	Ttt/Ctt	10/11	1	2	FACETS	0.422	0.347	0.507	0.422	0.347	0.507	SUBCLONAL	1	TRUE	1	0.284822817190453	2		364	615	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	132	454	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.918	0.844	0.993	0.918	0.844	0.993	CLONAL	1	TRUE	1	0.841052276559187	2		454	342	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509660	106509660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757849968	NA	P-0030596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	270	444	0	ENST00000359195.3:c.1654C>T	p.Arg552Cys	p.R552C	ENST00000359195	NM_002649.2	552	Cgc/Tgc	2/11	0.841052276559187	3	FACETS	1	0.971	1	0.527	0.495	0.559	CLONAL	1	TRUE	1	0.841052276559187	3		444	866	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519912	NA	P-0030597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	150	288	0	ENST00000374080.3:c.3670C>G	p.Leu1224Val	p.L1224V	ENST00000374080		1224	Ctc/Gtc	26/45	1	1	FACETS	0.796	0.736	0.857	1	0.99	1	SUBCLONAL	2	TRUE	0	0.386908633368292	1		288	393	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041031	42041031	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	146	505	0	ENST00000219905.7:c.5411del	p.Pro1804LeufsTer34	p.P1804Lfs*34	ENST00000219905	NM_001164273.1	1803	caC/ca	16/24	1	2	FACETS	0.966	0.883	1	0.966	0.883	1	CLONAL	1	TRUE	1	0.386908633368292	2		505	781	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0030611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	184	622	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.215954294150423	3	FACETS	0.867	0.811	0.923	0.867	0.811	0.923	INDETERMINATE	2	TRUE	1	0.712156457760674	3		622	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786201059	NA	P-0030611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	235	538	0	ENST00000269305.4:c.856G>C	p.Glu286Gln	p.E286Q	ENST00000269305	NM_001126112.2	286	Gaa/Caa	8/11	0.712156457760674	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.712156457760674	1		538	410	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467924	50467924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	152	383	0	ENST00000331340.3:c.1159G>A	p.Glu387Lys	p.E387K	ENST00000331340	NM_006060.4	387	Gag/Aag	8/8	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.712156457760674	2		383	399	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262096	10262096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	170	447	0	ENST00000340748.4:c.2195C>T	p.Ser732Phe	p.S732F	ENST00000340748		732	tCt/tTt	23/40	1	2	FACETS	0.951	0.882	1	0.951	0.882	1	CLONAL	1	TRUE	1	0.712156457760674	2		447	502	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007747	45007747	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1279144545	NA	P-0030611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	146	343	0	ENST00000558401.1:c.194G>C	p.Arg65Thr	p.R65T	ENST00000558401	NM_004048.2	65	aGa/aCa	2/4	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.712156457760674	2		343	391	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576105	29576105	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555617368	NA	P-0030611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	189	395	0	ENST00000356175.3:c.4078C>T	p.Gln1360Ter	p.Q1360*	ENST00000356175	NM_000267.3	1360	Caa/Taa	30/57	0.712156457760674	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.712156457760674	1		395	307	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273164	115273164	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	206	457	0	ENST00000438362.2:c.1294C>T	p.His432Tyr	p.H432Y	ENST00000438362	NM_001242891.1	432	Cat/Tat	11/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.712156457760674	2		457	541	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578115	226578115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	157	355	0	ENST00000366794.5:c.613G>A	p.Glu205Lys	p.E205K	ENST00000366794	NM_001618.3	205	Gaa/Aaa	4/23	0.552212091552078	6	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.712156457760674	6		355	876	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143274	108143274	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	101	315	0	ENST00000278616.4:c.3093G>C	p.Glu1031Asp	p.E1031D	ENST00000278616	NM_000051.3	1031	gaG/gaC	21/63	1	2	FACETS	0.842	0.76	0.926	0.842	0.76	0.926	CLONAL	1	TRUE	1	0.712156457760674	2		315	337	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845617	68845618	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0030611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	151	464	0	ENST00000261769.5:c.863_864del	p.Asp288GlyfsTer4	p.D288Gfs*4	ENST00000261769	NM_004360.3	288	gAC/g	7/16	0.712156457760674	1	FACETS	0.867	0.807	0.927	0.867	0.807	0.927	CLONAL	1	TRUE	0	0.712156457760674	1		464	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577065	7577065	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	246	520	0	ENST00000269305.4:c.873G>T	p.Lys291Asn	p.K291N	ENST00000269305	NM_001126112.2	291	aaG/aaT	8/11	0.712156457760674	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.712156457760674	1		520	436	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220993	36220993	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	253	451	0	ENST00000222270.7:c.5043C>G	p.Phe1681Leu	p.F1681L	ENST00000222270	NM_014727.1	1681	ttC/ttG	23/37	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.712156457760674	2		451	606	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519430	137519430	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	114	232	0	ENST00000367739.4:c.1208C>A	p.Ser403Tyr	p.S403Y	ENST00000367739	NM_000416.2	403	tCt/tAt	7/7	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.712156457760674	2		232	295	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206807	162206807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	161	385	0	ENST00000366898.1:c.868G>A	p.Val290Met	p.V290M	ENST00000366898	NM_004562.2	290	Gtg/Atg	7/12	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.712156457760674	NA		385	441	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977615	2977615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	246	624	0	ENST00000396946.4:c.1069G>A	p.Asp357Asn	p.D357N	ENST00000396946	NM_032415.4	357	Gac/Aac	8/25	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.712156457760674	2		624	648	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361131	70361131	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1407030192	NA	P-0030611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	34	529	1	ENST00000374080.3:c.6319C>T	p.Gln2107Ter	p.Q2107*	ENST00000374080		2107	Cag/Tag	43/45	1	2	FACETS	0.159	0.129	0.192	0.159	0.129	0.192	SUBCLONAL	1	TRUE	1	0.712156457760674	2		530	602	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0030612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	1012	645	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.648011128377209	3	FACETS	1	0.998	1	1	0.998	1	CLONAL	3	TRUE	0	0.648011128377209	3		645	1246	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610123	10610123	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	1760	622	0	ENST00000171111.5:c.587G>T	p.Cys196Phe	p.C196F	ENST00000171111	NM_203500.1	196	tGt/tTt	2/6	0.648011128377209	3	FACETS	1	0.999	1	1	0.999	1	CLONAL	3	TRUE	0	0.648011128377209	3		622	2137	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253371	226253371	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	35	206	0	ENST00000366813.1:c.143C>T	p.Ala48Val	p.A48V	ENST00000366813		48	gCg/gTg	2/3	0.648011128377209	2	FACETS	0.75	0.643	0.857	0.75	0.643	0.857	SUBCLONAL	2	TRUE	0	0.648011128377209	2		206	72	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220579	1220579	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0030612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	2032	536	1	ENST00000326873.7:c.598-1G>T		p.X200_splice	ENST00000326873	NM_000455.4	200			0.648011128377209	3	FACETS	1	0.999	1	1	0.999	1	CLONAL	3	TRUE	0	0.648011128377209	3		537	2385	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259279	16259279	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142392560	NA	P-0030612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	124	309	0	ENST00000375759.3:c.6544G>A	p.Ala2182Thr	p.A2182T	ENST00000375759	NM_015001.2	2182	Gct/Act	11/15	0.332899906533224	5	FACETS	1	0.92	1	0.339	0.307	0.373	INDETERMINATE	1	TRUE	2	0.648011128377209	5		309	742	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797840	45797840	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0030612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	583	463	0	ENST00000450313.1:c.931A>T	p.Arg311Ter	p.R311*	ENST00000450313	NM_012222.2	311	Aga/Tga	10/16	0.332899906533224	5	FACETS	0.838	0.806	0.87	0.838	0.806	0.87	INDETERMINATE	3	TRUE	2	0.648011128377209	5		463	1412	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120457941	120457941	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	145	424	0	ENST00000256646.2:c.7404G>T	p.Gln2468His	p.Q2468H	ENST00000256646	NM_024408.3	2468	caG/caT	34/34	0.332899906533224	5	FACETS	0.968	0.89	1	0.645	0.593	0.698	INDETERMINATE	2	TRUE	2	0.648011128377209	5		424	456	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416075	49416075	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	325	503	0	ENST00000301067.7:c.16400G>T	p.Gly5467Val	p.G5467V	ENST00000301067	NM_003482.3	5467	gGc/gTc	52/54	0.648011128377209	4	FACETS	0.947	0.898	0.997			1	CLONAL	2	TRUE	NA	0.648011128377209	4		503	873	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118814	115118814	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	375	429	0	ENST00000257566.3:c.527C>A	p.Ala176Asp	p.A176D	ENST00000257566	NM_016569.3	176	gCc/gAc	2/8	0.336700068208818	4	FACETS	0.993	0.946	1	0.993	0.946	1	INDETERMINATE	2	TRUE	2	0.648011128377209	4		429	960	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549504	21549504	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0030612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	381	384	0	ENST00000382592.4:c.2773-1G>T		p.X925_splice	ENST00000382592	NM_014572.2	925			0.648011128377209	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	TRUE	0	0.648011128377209	3		384	515	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620098	21620098	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	652	526	0	ENST00000382592.4:c.68G>T	p.Arg23Leu	p.R23L	ENST00000382592	NM_014572.2	23	cGt/cTt	2/8	0.648011128377209	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.648011128377209	3		526	836	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779217	3779217	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751146607	NA	P-0030612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	211	348	0	ENST00000262367.5:c.5831C>T	p.Ala1944Val	p.A1944V	ENST00000262367	NM_004380.2	1944	gCc/gTc	31/31	0.648011128377209	3	FACETS	1	0.942	1	0.338	0.314	0.363	CLONAL	1	TRUE	0	0.648011128377209	3		348	850	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89842183	89842183	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	312	509	2	ENST00000389301.3:c.1867C>T	p.Gln623Ter	p.Q623*	ENST00000389301	NM_000135.2	623	Cag/Tag	21/43	0.648011128377209	5	FACETS	1	0.992	1	0.437	0.411	0.464	CLONAL	1	TRUE	2	0.648011128377209	5		511	1447	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7218309	7218309	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1534	493	440	0	ENST00000380728.2:c.63C>G	p.His21Gln	p.H21Q	ENST00000380728		21	caC/caG	2/11	0.648011128377209	3	FACETS	0.994	0.948	1	0.331	0.316	0.347	CLONAL	1	TRUE	0	0.648011128377209	3		440	2027	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63537670	63537670	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	17	436	1	ENST00000307078.5:c.962G>T	p.Gly321Val	p.G321V	ENST00000307078	NM_004655.3	321	gGa/gTa	4/11	0.648011128377209	3	FACETS	0.243	0.181	0.317	0.081	0.06	0.106	SUBCLONAL	1	TRUE	0	0.648011128377209	3		437	286	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138560	11138560	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	408	570	0	ENST00000358026.2:c.3316A>G	p.Thr1106Ala	p.T1106A	ENST00000358026	NM_001128849.1	1106	Acc/Gcc	24/36	0.648011128377209	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.648011128377209	3		570	521	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009122	27009122	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	265	152	0	ENST00000335756.4:c.58C>T	p.Pro20Ser	p.P20S	ENST00000335756	NM_001809.3	20	Ccg/Tcg	1/5	0.648011128377209	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.648011128377209	3		152	531	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193459	99193459	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1370	769	476	0	ENST00000074304.5:c.2654G>T	p.Arg885Leu	p.R885L	ENST00000074304	NM_001134224.1	885	cGc/cTc	25/26	0.259004323642441	6	FACETS	0.849	0.82	0.879	0.637	0.615	0.659	INDETERMINATE	3	TRUE	2	0.648011128377209	6		476	2139	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176671269	176671269	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs779660692	NA	P-0030612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	43	286	0	ENST00000439151.2:c.4376G>T	p.Gly1459Val	p.G1459V	ENST00000439151	NM_022455.4	1459	gGa/gTa	9/23	0.648011128377209	5	FACETS	0.884	0.78	0.985	0.707	0.624	0.788	CLONAL	4	TRUE	0	0.648011128377209	5		286	74	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032189	26032189	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	1007	258	0	ENST00000244661.2:c.100G>A	p.Gly34Ser	p.G34S	ENST00000244661	NM_003537.3	34	Ggc/Agc	1/1	0.648011128377209	4	FACETS	1	0.997	1	1	0.997	1	CLONAL	4	TRUE	0	0.648011128377209	4		258	1200	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163893	152163893	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	138	449	0	ENST00000206249.3:c.614G>T	p.Cys205Phe	p.C205F	ENST00000206249	NM_000125.3	205	tGc/tTc	2/8	0.626613558823496	3	FACETS	0.835	0.782	0.887	0.835	0.782	0.887	CLONAL	3	TRUE	0	0.648011128377209	3		449	225	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959038	2959038	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	670	509	0	ENST00000396946.4:c.2478C>G	p.Asp826Glu	p.D826E	ENST00000396946	NM_032415.4	826	gaC/gaG	18/25	0.648011128377209	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.648011128377209	3		509	1319	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331979	81331979	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763933267	NA	P-0030612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	11	335	0	ENST00000222390.5:c.2105G>T	p.Arg702Leu	p.R702L	ENST00000222390	NM_000601.4	702	cGt/cTt	18/18	0.648011128377209	3	FACETS	0.661	0.465	0.894	0.331	0.232	0.447	SUBCLONAL	1	TRUE	1	0.648011128377209	3		335	68	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545625	106545625	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	25	476	0	ENST00000359195.3:c.3102G>T	p.Met1034Ile	p.M1034I	ENST00000359195	NM_002649.2	1034	atG/atT	11/11	0.648011128377209	3	FACETS	0.831	0.665	1	0.415	0.332	0.507	CLONAL	1	TRUE	1	0.648011128377209	3		476	123	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370886	55370886	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	1896	469	2	ENST00000297316.4:c.188A>T	p.Lys63Met	p.K63M	ENST00000297316	NM_022454.3	63	aAg/aTg	1/2	0.648011128377209	4	FACETS	1	0.998	1	1	0.998	1	CLONAL	3	TRUE	1	0.648011128377209	4		471	2950	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs763804037	NA	P-0030612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	718	353	0	ENST00000304494.5:c.143C>G	p.Pro48Arg	p.P48R	ENST00000304494	NM_000077.4	48	cCg/cGg	1/3	0.648011128377209	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.648011128377209	2		353	1048	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602620	10602620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	344	508	2	ENST00000171111.5:c.958C>T	p.Arg320Trp	p.R320W	ENST00000171111	NM_203500.1	320	Cgg/Tgg	3/6	0.584405220493716	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.584405220493716	2		510	571	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579582	7579583	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	377	501	0	ENST00000269305.4:c.104dup	p.Leu35PhefsTer8	p.L35Ffs*8	ENST00000269305	NM_001126112.2	35	ttg/ttTg	4/11	0.584405220493716	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.584405220493716	2		501	579	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937094	48937094	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0030614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	149	233	1	ENST00000267163.4:c.861+1G>A		p.X287_splice	ENST00000267163	NM_000321.2	287			0.584405220493716	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	0	0.584405220493716	2		234	252	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667399	241667399	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	128	392	0	ENST00000366560.3:c.1051T>C	p.Ser351Pro	p.S351P	ENST00000366560	NM_000143.3	351	Tca/Cca	7/10	0.546930150022639	4	FACETS	0.919	0.834	1	0.46	0.417	0.505	CLONAL	1	TRUE	2	0.584405220493716	4		392	755	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111965561	111965561	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	98	176	0	ENST00000375549.3:c.347A>G	p.His116Arg	p.H116R	ENST00000375549	NM_003002.3	116	cAt/cGt	4/4	0.584405220493716	2	FACETS	0.921	0.846	0.996	0.921	0.846	0.996	CLONAL	2	TRUE	0	0.584405220493716	2		176	182	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037400	12037400	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	331	516	0	ENST00000396373.4:c.1031A>G	p.Tyr344Cys	p.Y344C	ENST00000396373	NM_001987.4	344	tAc/tGc	6/8	0.584405220493716	4	FACETS	0.934	0.885	0.984	0.934	0.885	0.984	CLONAL	2	TRUE	2	0.584405220493716	4		516	961	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336101	73336101	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	179	218	0	ENST00000377767.4:c.2302G>C	p.Ala768Pro	p.A768P	ENST00000377767	NM_014953.3	768	Gcg/Ccg	17/21	0.584405220493716	2	FACETS	0.969	0.912	1	0.969	0.912	1	CLONAL	2	TRUE	0	0.584405220493716	2		218	316	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041662	42041662	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0030614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	286	476	0	ENST00000219905.7:c.5857A>T	p.Lys1953Ter	p.K1953*	ENST00000219905	NM_001164273.1	1953	Aag/Tag	17/24	0.584405220493716	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.584405220493716	2		476	476	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720315	43720315	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	329	485	1	ENST00000382044.4:c.3727C>A	p.Arg1243Ser	p.R1243S	ENST00000382044	NM_001141980.1	1243	Cgt/Agt	18/28	0.546930150022639	4	FACETS	0.967	0.917	1	0.967	0.917	1	CLONAL	2	TRUE	2	0.584405220493716	4		486	922	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680727	88680727	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	319	531	0	ENST00000360948.2:c.530A>T	p.Gln177Leu	p.Q177L	ENST00000360948	NM_001012338.2	177	cAg/cTg	6/19	0.584405220493716	5	FACETS	1	0.974	1	0.699	0.661	0.738	CLONAL	2	TRUE	2	0.584405220493716	5		531	977	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348794	11348794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	78	173	0	ENST00000332029.2:c.542G>A	p.Arg181His	p.R181H	ENST00000332029	NM_003745.1	181	cGc/cAc	2/2	0.582983566088151	3	FACETS	1	0.971	1	0.651	0.579	0.726	CLONAL	1	TRUE	1	0.584405220493716	3		173	265	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190742095	190742095	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	130	432	0	ENST00000441310.2:c.2732A>C	p.Glu911Ala	p.E911A	ENST00000441310	NM_000534.4	911	gAa/gCa	13/13	0.582983566088151	3	FACETS	0.914	0.831	1	0.457	0.415	0.5	CLONAL	1	TRUE	1	0.584405220493716	3		432	629	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098910	47098910	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	310	534	0	ENST00000409792.3:c.6364C>G	p.Arg2122Gly	p.R2122G	ENST00000409792	NM_014159.6	2122	Cgg/Ggg	15/21	0.584405220493716	2	FACETS	0.956	0.913	0.999	0.956	0.913	0.999	CLONAL	2	TRUE	0	0.584405220493716	2		534	555	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134885815	134885815	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1223	152	427	0	ENST00000398015.3:c.1726A>T	p.Ser576Cys	p.S576C	ENST00000398015	NM_004441.4	576	Agc/Tgc	9/16	0.584405220493716	9	FACETS	1	0.971	1	0.165	0.15	0.18	CLONAL	1	TRUE	2	0.584405220493716	9		427	1375	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933311	39933311	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	190	589	0	ENST00000378444.4:c.1288C>A	p.Gln430Lys	p.Q430K	ENST00000378444	NM_001123385.1	430	Cag/Aag	4/15	0.584405220493716	3	FACETS	1	0.926	1	0.5	0.463	0.539	CLONAL	1	TRUE	1	0.584405220493716	3		589	840	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340976	70340976	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	150	436	0	ENST00000374080.3:c.709G>T	p.Glu237Ter	p.E237*	ENST00000374080		237	Gag/Tag	5/45	0.584405220493716	3	FACETS	0.932	0.853	1	0.466	0.426	0.507	CLONAL	1	TRUE	1	0.584405220493716	3		436	712	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939495	76939495	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	267	474	0	ENST00000373344.5:c.1253G>T	p.Arg418Leu	p.R418L	ENST00000373344	NM_000489.3	418	cGa/cTa	9/35	0.54937882766912	4	FACETS	0.929	0.875	0.985			1	CLONAL	2	TRUE	NA	0.584405220493716	4		474	779	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	150	545	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.315818129855906	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.334192617341909	1		545	696	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	89	712	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	0.334192617341909	2		712	460	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	114	405	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.97	0.875	1	0.97	0.875	1	CLONAL	1	TRUE	1	0.334192617341909	2		405	703	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	75	386	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.727	0.638	0.824	0.727	0.638	0.824	SUBCLONAL	1	TRUE	1	0.334192617341909	2		388	617	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	110	407	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.954	0.858	1	0.954	0.858	1	CLONAL	1	TRUE	1	0.334192617341909	2		408	690	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	176	401	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.299074775088576	3	FACETS	0.987	0.913	1	0.987	0.913	1	CLONAL	2	TRUE	1	0.334192617341909	3		402	623	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023327	27023327	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	19	72	0	ENST00000324856.7:c.437del	p.Pro146GlnfsTer86	p.P146Qfs*86	ENST00000324856	NM_006015.4	145	Ccc/cc	1/20	1	2	FACETS	1	0.829	1	1	0.829	1	CLONAL	1	TRUE	1	0.334192617341909	2		72	104	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528105	157528105	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1028186690	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	111	428	0	ENST00000346085.5:c.5830C>T	p.Arg1944Ter	p.R1944*	ENST00000346085	NM_020732.3	1944	Cga/Tga	20/20	1	2	FACETS	0.895	0.805	0.991	0.895	0.805	0.991	CLONAL	1	TRUE	1	0.334192617341909	2		428	742	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	67	264	1	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	0.315818129855906	1	FACETS	0.861	0.752	0.978	0.861	0.752	0.978	CLONAL	1	TRUE	0	0.334192617341909	1		265	388	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666635	206666635	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1430127416	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	117	523	2	ENST00000367120.3:c.1969C>T	p.Arg657Ter	p.R657*	ENST00000367120	NM_014002.3	657	Cga/Tga	20/22	1	2	FACETS	0.912	0.822	1	0.912	0.822	1	CLONAL	1	TRUE	1	0.334192617341909	2		525	768	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276860	15276861	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs753725730	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	113	591	2	ENST00000263388.2:c.5404dup	p.Ala1802GlyfsTer8	p.A1802Gfs*8	ENST00000263388	NM_000435.2	1802	gct/gGct	30/33	1	2	FACETS	0.737	0.663	0.817	0.737	0.663	0.817	SUBCLONAL	1	TRUE	1	0.334192617341909	2		593	917	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564530	86564530	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	128	470	0	ENST00000274376.6:c.266del	p.Gly89GlufsTer7	p.G89Efs*7	ENST00000274376	NM_002890.2	88	Ggg/gg	1/25	0.334192617341909	1	FACETS	0.995	0.904	1	0.995	0.904	1	CLONAL	1	TRUE	0	0.334192617341909	1		470	641	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749374	41749374	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	75	256	0	ENST00000226382.2:c.421C>T	p.Arg141Ter	p.R141*	ENST00000226382	NM_003924.3	141	Cga/Tga	2/3	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.334192617341909	2		256	398	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257102	19257102	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	116	545	1	ENST00000162023.5:c.861del	p.Ala288ProfsTer?	p.A288Pfs*?	ENST00000162023		287	ccC/cc	12/13	1	2	FACETS	0.851	0.767	0.94	0.851	0.767	0.94	CLONAL	1	TRUE	1	0.334192617341909	2		546	816	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154241	2154242	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755455183	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	141	565	0	ENST00000434045.2:c.686dup	p.Glu230ArgfsTer50	p.E230Rfs*50	ENST00000434045	NM_001127598.1	229	cca/ccCa	5/5	1	2	FACETS	0.968	0.882	1	0.968	0.882	1	CLONAL	1	TRUE	1	0.334192617341909	2		565	872	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920173	76920173	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	96	220	0	ENST00000373344.5:c.3904del	p.Arg1302GlufsTer44	p.R1302Efs*44	ENST00000373344	NM_000489.3	1302	Aga/ga	11/35	1	1	FACETS	0.848	0.767	0.933	1	0.986	1	CLONAL	2	TRUE	0	0.334192617341909	1		220	282	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918720	50918720	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765437818	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	107	509	0	ENST00000440232.2:c.2590G>A	p.Ala864Thr	p.A864T	ENST00000440232	NM_002691.3	864	Gca/Aca	21/27	1	2	FACETS	0.915	0.821	1	0.915	0.821	1	CLONAL	1	TRUE	1	0.334192617341909	2		509	700	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246532	41246532	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357569	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	111	577	4	ENST00000357654.3:c.1016del	p.Lys339ArgfsTer2	p.K339Rfs*2	ENST00000357654	NM_007294.3	339	aAg/ag	10/23	1	2	FACETS	0.88	0.791	0.974	0.88	0.791	0.974	CLONAL	1	TRUE	1	0.334192617341909	2		581	755	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521525	46521525	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	114	426	0	ENST00000262741.5:c.883del	p.Met295Ter	p.M295*	ENST00000262741	NM_003629.3	295	Atg/tg	7/10	1	2	FACETS	0.851	0.766	0.941	0.851	0.766	0.941	CLONAL	1	TRUE	1	0.334192617341909	2		426	802	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413710	138413710	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	94	369	2	ENST00000289153.2:c.1810del	p.Arg604GlyfsTer4	p.R604Gfs*4	ENST00000289153	NM_006219.2	604	Cgg/gg	12/22	1	2	FACETS	0.921	0.821	1	0.921	0.821	1	CLONAL	1	TRUE	1	0.334192617341909	2		371	611	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31468080	31468080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1458058411	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	113	537	1	ENST00000344624.3:c.2332C>T	p.Arg778Cys	p.R778C	ENST00000344624		778	Cgc/Tgc	15/33	1	2	FACETS	0.893	0.804	0.988	0.893	0.804	0.988	CLONAL	1	TRUE	1	0.334192617341909	2		538	757	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224124	36224124	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	126	560	0	ENST00000222270.7:c.6678del	p.Thr2227ArgfsTer34	p.T2227Rfs*34	ENST00000222270	NM_014727.1	2225	tCc/tc	28/37	1	2	FACETS	0.849	0.768	0.934	0.849	0.768	0.934	CLONAL	1	TRUE	1	0.334192617341909	2		560	888	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830778	72830778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781579217	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	120	408	0	ENST00000268489.5:c.5803C>T	p.Arg1935Cys	p.R1935C	ENST00000268489	NM_006885.3	1935	Cgc/Tgc	9/10	1	2	FACETS	0.981	0.887	1	0.981	0.887	1	CLONAL	1	TRUE	1	0.334192617341909	2		408	732	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206638	108206638	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs866402530	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	74	410	0	ENST00000278616.4:c.8218C>T	p.Gln2740Ter	p.Q2740*	ENST00000278616	NM_000051.3	2740	Cag/Tag	56/63	1	2	FACETS	0.819	0.718	0.927	0.819	0.718	0.927	CLONAL	1	TRUE	1	0.334192617341909	2		410	541	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233619	233619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457666982	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	57	262	0	ENST00000264932.6:c.923C>T	p.Thr308Met	p.T308M	ENST00000264932	NM_004168.2	308	aCg/aTg	8/15	1	2	FACETS	0.907	0.782	1	0.907	0.782	1	CLONAL	1	TRUE	1	0.334192617341909	2		262	376	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346631	81346631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	120	281	0	ENST00000222390.5:c.1322G>A	p.Arg441Gln	p.R441Q	ENST00000222390	NM_000601.4	441	cGa/cAa	11/18	0.299074775088576	3	FACETS	0.903	0.821	0.989	0.903	0.821	0.989	CLONAL	2	TRUE	1	0.334192617341909	3		281	464	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100090	27100090	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	125	587	1	ENST00000324856.7:c.3886C>T	p.Pro1296Ser	p.P1296S	ENST00000324856	NM_006015.4	1296	Cct/Tct	16/20	1	2	FACETS	0.783	0.707	0.862	0.783	0.707	0.862	SUBCLONAL	1	TRUE	1	0.334192617341909	2		588	956	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699295	117699295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773228516	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	103	412	1	ENST00000369458.3:c.346C>T	p.Arg116Trp	p.R116W	ENST00000369458	NM_024626.3	116	Cgg/Tgg	3/6	1	2	FACETS	0.997	0.894	1	0.997	0.894	1	CLONAL	1	TRUE	1	0.334192617341909	2		413	618	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651153	206651153	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	128	622	1	ENST00000367120.3:c.763G>T	p.Gly255Trp	p.G255W	ENST00000367120	NM_014002.3	255	Ggg/Tgg	8/22	1	2	FACETS	0.788	0.713	0.867	0.788	0.713	0.867	SUBCLONAL	1	TRUE	1	0.334192617341909	2		623	972	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670416	246670416	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	125	467	0	ENST00000388985.4:c.104C>A	p.Pro35His	p.P35H	ENST00000388985		35	cCc/cAc	1/12	1	2	FACETS	0.979	0.887	1	0.979	0.887	1	CLONAL	1	TRUE	1	0.334192617341909	2		467	764	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998658	100998658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	138	548	0	ENST00000325455.5:c.1144C>T	p.Pro382Ser	p.P382S	ENST00000325455	NM_001202474.3	382	Ccg/Tcg	1/8	1	2	FACETS	0.926	0.842	1	0.926	0.842	1	CLONAL	1	TRUE	1	0.334192617341909	2		548	892	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434247	49434247	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1235	174	841	0	ENST00000301067.7:c.7306del	p.Cys2436AlafsTer49	p.C2436Afs*49	ENST00000301067	NM_003482.3	2436	Tgc/gc	31/54	1	2	FACETS	0.739	0.678	0.803	0.739	0.678	0.803	SUBCLONAL	1	TRUE	1	0.334192617341909	2		841	1409	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120535059	120535059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	89	377	0	ENST00000229340.5:c.596G>A	p.Arg199His	p.R199H	ENST00000229340	NM_006861.6	199	cGc/cAc	6/6	1	2	FACETS	0.904	0.803	1	0.904	0.803	1	CLONAL	1	TRUE	1	0.334192617341909	2		377	589	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202741	133202741	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369549727	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	107	472	0	ENST00000320574.5:c.6493C>T	p.Arg2165Cys	p.R2165C	ENST00000320574	NM_006231.2	2165	Cgc/Tgc	46/49	1	2	FACETS	0.877	0.787	0.973	0.877	0.787	0.973	CLONAL	1	TRUE	1	0.334192617341909	2		472	730	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42057141	42057141	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	113	511	0	ENST00000219905.7:c.7802A>G	p.Gln2601Arg	p.Q2601R	ENST00000219905	NM_001164273.1	2601	cAa/cGa	23/24	1	2	FACETS	0.811	0.729	0.897	0.811	0.729	0.897	CLONAL	1	TRUE	1	0.334192617341909	2		511	834	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996134	73996134	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	179	746	0	ENST00000318443.5:c.868A>G	p.Thr290Ala	p.T290A	ENST00000318443	NM_001024736.1	290	Acc/Gcc	5/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.334192617341909	2		746	1026	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778038	3778038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373607295	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	205	779	0	ENST00000262367.5:c.7010C>T	p.Thr2337Met	p.T2337M	ENST00000262367	NM_004380.2	2337	aCg/aTg	31/31	1	2	FACETS	0.987	0.914	1	0.987	0.914	1	CLONAL	1	TRUE	1	0.334192617341909	2		779	1243	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831476	89831476	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	79	485	0	ENST00000389301.3:c.2602-2A>G		p.X868_splice	ENST00000389301	NM_000135.2	868			1	2	FACETS	0.679	0.597	0.768	0.679	0.597	0.768	SUBCLONAL	1	TRUE	1	0.334192617341909	2		485	696	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044510	12044510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	83	322	0	ENST00000353533.5:c.1133C>T	p.Ala378Val	p.A378V	ENST00000353533	NM_003010.3	378	gCa/gTa	11/11	0.315818129855906	1	FACETS	0.932	0.826	1	0.932	0.826	1	CLONAL	1	TRUE	0	0.334192617341909	1		322	444	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884044	37884045	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	147	665	0	ENST00000269571.5:c.3520_3521del	p.Ser1174ProfsTer102	p.S1174Pfs*102	ENST00000269571		1172	aCT/a	27/27	1	2	FACETS	0.837	0.763	0.915	0.837	0.763	0.915	CLONAL	1	TRUE	1	0.334192617341909	2		665	1051	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222799	5222799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	97	389	0	ENST00000357368.4:c.3004C>T	p.Pro1002Ser	p.P1002S	ENST00000357368	NM_002850.3	1002	Ccc/Tcc	18/38	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.334192617341909	2		389	556	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7132210	7132210	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	173	606	0	ENST00000302850.5:c.2801G>A	p.Gly934Asp	p.G934D	ENST00000302850	NM_000208.2	934	gGc/gAc	14/22	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.334192617341909	2		606	951	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18975015	18975015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1296944526	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	82	396	0	ENST00000262803.5:c.2812C>T	p.Arg938Trp	p.R938W	ENST00000262803	NM_002911.3	938	Cgg/Tgg	20/24	1	2	FACETS	0.891	0.787	1	0.891	0.787	1	CLONAL	1	TRUE	1	0.334192617341909	2		396	551	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967180	25967180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374101562	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	68	326	2	ENST00000435504.4:c.2026G>A	p.Ala676Thr	p.A676T	ENST00000435504		676	Gct/Act	13/13	1	2	FACETS	0.923	0.806	1	0.923	0.806	1	CLONAL	1	TRUE	1	0.334192617341909	2		328	441	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138409876	138409876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760002387	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	92	417	0	ENST00000289153.2:c.2002C>T	p.Arg668Trp	p.R668W	ENST00000289153	NM_006219.2	668	Cgg/Tgg	13/22	1	2	FACETS	0.978	0.871	1	0.978	0.871	1	CLONAL	1	TRUE	1	0.334192617341909	2		417	563	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191353	185191353	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	139	524	0	ENST00000265026.3:c.2234T>C	p.Ile745Thr	p.I745T	ENST00000265026	NM_004721.4	745	aTa/aCa	11/14	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.334192617341909	2		524	781	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189843	66189843	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758487170	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	75	334	0	ENST00000273854.3:c.3103G>A	p.Val1035Met	p.V1035M	ENST00000273854	NM_004439.5	1035	Gtg/Atg	18/18	1	2	FACETS	0.918	0.807	1	0.918	0.807	1	CLONAL	1	TRUE	1	0.334192617341909	2		334	489	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526201	31526201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	135	661	0	ENST00000344624.3:c.839G>A	p.Ser280Asn	p.S280N	ENST00000344624		280	aGc/aAc	2/33	1	2	FACETS	0.86	0.781	0.944	0.86	0.781	0.944	CLONAL	1	TRUE	1	0.334192617341909	2		661	939	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839930	27839930	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	114	459	0	ENST00000328488.2:c.164A>G	p.Tyr55Cys	p.Y55C	ENST00000328488	NM_003533.2	55	tAc/tGc	1/1	1	2	FACETS	0.872	0.786	0.964	0.872	0.786	0.964	CLONAL	1	TRUE	1	0.334192617341909	2		459	782	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964504	93964504	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	66	348	0	ENST00000369303.4:c.2393T>A	p.Ile798Asn	p.I798N	ENST00000369303	NM_004440.3	798	aTt/aAt	14/17	1	2	FACETS	0.859	0.747	0.979	0.859	0.747	0.979	CLONAL	1	TRUE	1	0.334192617341909	2		348	460	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969135	93969135	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	60	324	0	ENST00000369303.4:c.1861G>T	p.Val621Phe	p.V621F	ENST00000369303	NM_004440.3	621	Gtc/Ttc	10/17	1	2	FACETS	0.722	0.623	0.83	0.722	0.623	0.83	SUBCLONAL	1	TRUE	1	0.334192617341909	2		324	497	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355311	81355311	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	56	230	0	ENST00000222390.5:c.1063C>T	p.Arg355Ter	p.R355*	ENST00000222390	NM_000601.4	355	Cga/Tga	9/18	0.299074775088576	3	FACETS	0.983	0.845	1	0.491	0.422	0.566	CLONAL	1	TRUE	1	0.334192617341909	3		230	398	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980495	70980495	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1563442788	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	131	592	0	ENST00000276594.2:c.882G>T	p.Lys294Asn	p.K294N	ENST00000276594	NM_024504.3	294	aaG/aaT	4/8	1	2	FACETS	0.839	0.761	0.922	0.839	0.761	0.922	CLONAL	1	TRUE	1	0.334192617341909	2		592	934	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740788	145740790	+	inframe_deletion	In_Frame_Del	DEL	GTG	GTG	-	novel	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	131	665	0	ENST00000428558.2:c.1310_1312del	p.Pro437del	p.P437del	ENST00000428558	NM_004260.3	437	cCACaa/caa	7/22	1	2	FACETS	0.722	0.654	0.794	0.722	0.654	0.794	SUBCLONAL	1	TRUE	1	0.334192617341909	2		665	1086	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492970	8492970	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	67	370	0	ENST00000356435.5:c.2359A>G	p.Ile787Val	p.I787V	ENST00000356435		787	Att/Gtt	16/35	1	2	FACETS	0.728	0.633	0.83	0.728	0.633	0.83	SUBCLONAL	1	TRUE	1	0.334192617341909	2		370	551	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137323750	137323750	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs79625644	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	114	580	0	ENST00000481739.1:c.1044-1G>T		p.X348_splice	ENST00000481739	NM_002957.4	348			1	2	FACETS	0.792	0.713	0.877	0.792	0.713	0.877	SUBCLONAL	1	TRUE	1	0.334192617341909	2		580	861	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321393	1321393	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265666508	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	82	360	0	ENST00000400841.2:c.362C>T	p.Ser121Phe	p.S121F	ENST00000400841		121	tCc/tTc	4/6	1	1	FACETS	0.715	0.631	0.804	0.715	0.631	0.804	SUBCLONAL	1	TRUE	0	0.334192617341909	1		360	572	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841186	15841186	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	85	166	0	ENST00000307771.7:c.1270G>T	p.Gly424Ter	p.G424*	ENST00000307771	NM_005089.3	424	Gga/Tga	11/11	1	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.334192617341909	1		166	304	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044732	47044732	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	150	356	0	ENST00000377604.3:c.2132T>C	p.Met711Thr	p.M711T	ENST00000377604	NM_001204468.1	711	aTg/aCg	19/24	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.334192617341909	1		356	515	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196768	123196770	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0030615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	58	158	0	ENST00000218089.9:c.1661_1663del	p.Lys554del	p.K554del	ENST00000218089	NM_001042749.1	552	gAGAag/gag	18/35	1	1	FACETS	0.831	0.728	0.938	1	0.976	1	CLONAL	2	TRUE	0	0.334192617341909	1		158	174	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552891	106552891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771056895	NA	P-0030616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	77	795	2	ENST00000369096.4:c.856C>T	p.Arg286Cys	p.R286C	ENST00000369096	NM_001198.3	286	Cgt/Tgt	5/7	0.217482289950659	2	FACETS	0.853	0.748	0.967	0.427	0.374	0.484	CLONAL	1	TRUE	0	0.217482289950659	2		797	830	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0030616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	242	815	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.199525426124575	3	FACETS	0.894	0.836	0.953	0.894	0.836	0.953	CLONAL	3	TRUE	0	0.217482289950659	3		815	920	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350251	15350251	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	88	701	0	ENST00000263377.2:c.3528C>G	p.Asp1176Glu	p.D1176E	ENST00000263377	NM_058243.2	1176	gaC/gaG	17/20	0.217482289950659	2	FACETS	1	0.95	1	0.565	0.5	0.634	CLONAL	1	TRUE	0	0.217482289950659	2		701	716	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115873	8115874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0030617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	205	478	0	ENST00000346208.3:c.1220dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tCcg	6/6	1	2	FACETS	0.954	0.889	1	0.954	0.889	1	CLONAL	1	TRUE	1	0.638537966641572	2		478	673	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906916	32906919	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	rs80359277	NA	P-0030617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	158	450	0	ENST00000380152.3:c.1310_1313del	p.Lys437IlefsTer22	p.K437Ifs*22	ENST00000380152		434	aAAAGa/aa	10/27	0.633891976301472	1	FACETS	0.836	0.775	0.898	0.836	0.775	0.898	CLONAL	1	TRUE	0	0.638537966641572	1		450	403	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397163	397163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	158	365	0	ENST00000380956.4:c.548C>T	p.Pro183Leu	p.P183L	ENST00000380956	NM_001195286.1	183	cCg/cTg	5/9	1	2	FACETS	0.963	0.888	1	0.963	0.888	1	CLONAL	1	TRUE	1	0.638537966641572	2		365	514	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561076	9561076	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	121	322	0	ENST00000353224.5:c.706C>A	p.Pro236Thr	p.P236T	ENST00000353224	NM_177990.2	236	Cct/Act	4/10	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.638537966641572	2		322	379	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038473	180038473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	186	628	0	ENST00000261937.6:c.3544G>A	p.Glu1182Lys	p.E1182K	ENST00000261937	NM_182925.4	1182	Gag/Aag	27/30	1	2	FACETS	0.805	0.745	0.866	0.805	0.745	0.866	CLONAL	1	TRUE	1	0.638537966641572	2		628	724	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933244	36933244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	190	578	0	ENST00000361632.4:c.1873G>A	p.Glu625Lys	p.E625K	ENST00000361632		625	Gag/Aag	14/16	0.779867601696021	2	FACETS	1	0.955	1	0.513	0.479	0.547	CLONAL	1	FALSE	0	0.822938026386178	2		578	450	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502462	186502462	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	77	252	0	ENST00000323963.5:c.185G>C	p.Arg62Thr	p.R62T	ENST00000323963		62	aGa/aCa	3/11	0.732463537944577	4	FACETS	0.682	0.6	0.77	0.341	0.3	0.385	SUBCLONAL	1	FALSE	2	0.822938026386178	4		252	500	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929164	44929164	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	186	290	0	ENST00000377967.4:c.2264C>G	p.Thr755Arg	p.T755R	ENST00000377967	NM_021140.2	755	aCg/aGg	17/29	0.636570814124625	2	FACETS	0.996	0.93	1			1	CLONAL	1	FALSE	NA	0.822938026386178	2		290	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	144	455	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.188683823170044	5	FACETS	1	0.969	1	0.879	0.811	0.949	CLONAL	4	TRUE	0	0.22	5		455	396	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581157	48581157	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1555685624	NA	P-0030620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	42	235	0	ENST00000342988.3:c.461C>G	p.Ser154Ter	p.S154*	ENST00000342988	NM_005359.5	154	tCa/tGa	5/12	0.242143037092369	4	FACETS	1	0.875	1			1	CLONAL	2	TRUE	NA	0.22	4		235	223	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690847	89690847	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776667	NA	P-0030620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	31	280	0	ENST00000371953.3:c.253+1G>A		p.X85_splice	ENST00000371953	NM_000314.4	85			0.249312181450396	3	FACETS	1	0.9	1	0.767	0.63	0.916	CLONAL	2	TRUE	0	0.22	3		280	136	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213800	66213800	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	26	378	0	ENST00000273854.3:c.2630G>A	p.Arg877Lys	p.R877K	ENST00000273854	NM_004439.5	877	aGa/aAa	15/18	0.139883083518485	3	FACETS	1	0.904	1	1	0.904	1	CLONAL	2	TRUE	1	0.22	3		378	108	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106072	27106072	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	100	397	1	ENST00000324856.7:c.5683G>T	p.Glu1895Ter	p.E1895*	ENST00000324856	NM_006015.4	1895	Gag/Tag	20/20	0.3	4	FACETS	0.97	0.874	1	0.97	0.874	1	CLONAL	3	TRUE	1	0.22	4		398	381	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372774	81372774	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	79	308	0	ENST00000222390.5:c.760G>A	p.Gly254Ser	p.G254S	ENST00000222390	NM_000601.4	254	Ggc/Agc	7/18	0.155308190128806	4	FACETS	0.951	0.845	1	1	0.976	1	CLONAL	3	TRUE	2	0.22	4		308	307	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724462	724462	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	55	572	0	ENST00000314574.4:c.1594G>T	p.Ala532Ser	p.A532S	ENST00000314574	NM_005433.3	532	Gct/Tct	12/12	0.3	8	FACETS	0.833	0.714	0.964			1	CLONAL	2	TRUE	NA	0.22	8		572	498	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609334	39609334	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	43	317	0	ENST00000262039.4:c.1636C>T	p.Gln546Ter	p.Q546*	ENST00000262039	NM_002647.2	546	Cag/Tag	15/25	0.242143037092369	4	FACETS	0.969	0.818	1			1	CLONAL	2	TRUE	NA	0.22	4		317	246	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155268	55155268	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	46	391	0	ENST00000257290.5:c.2867G>T	p.Gly956Val	p.G956V	ENST00000257290	NM_006206.4	956	gGa/gTa	21/23	0.139883083518485	3	FACETS	1	0.959	1	0.732	0.619	0.855	CLONAL	1	TRUE	1	0.22	3		391	317	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356248	66356248	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	75	464	0	ENST00000273854.3:c.1249C>G	p.Arg417Gly	p.R417G	ENST00000273854	NM_004439.5	417	Cgg/Ggg	5/18	0.139883083518485	3	FACETS	0.996	0.878	1	0.996	0.878	1	CLONAL	2	TRUE	1	0.22	3		464	380	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382185	152382185	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0030620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	62	361	0	ENST00000206249.3:c.1295C>G	p.Ser432Ter	p.S432*	ENST00000206249	NM_000125.3	432	tCa/tGa	6/8	0.234653869099475	5	FACETS	1	0.951	1	0.803	0.699	0.915	CLONAL	2	TRUE	2	0.22	5		361	311	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931823	68931823	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	56	434	0	ENST00000288368.4:c.253A>G	p.Lys85Glu	p.K85E	ENST00000288368	NM_024870.2	85	Aaa/Gaa	3/40	0.119655465962665	3	FACETS	0.945	0.815	1	0.945	0.815	1	INDETERMINATE	2	TRUE	1	0.22	3		434	299	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974701	21974701	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	57	300	0	ENST00000304494.5:c.126T>A	p.Asn42Lys	p.N42K	ENST00000304494	NM_000077.4	42	aaT/aaA	1/3	0.3	1	FACETS	0.754	0.651	0.864	1	0.969	1	SUBCLONAL	2	TRUE	0	0.22	1		300	306	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224719	123224719	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	65	223	0	ENST00000218089.9:c.3483G>A	p.Trp1161Ter	p.W1161*	ENST00000218089	NM_001042749.1	1161	tgG/tgA	32/35	0.3	2	FACETS	1	0.95	1			1	CLONAL	3	TRUE	NA	0.22	2		223	173	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0030623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	317	548	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.799956255455658	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.799956255455658	1		548	460	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510811	157510811	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554232934	NA	P-0030623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	244	384	0	ENST00000346085.5:c.3586C>T	p.Gln1196Ter	p.Q1196*	ENST00000346085	NM_020732.3	1196	Cag/Tag	14/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.799956255455658	2		384	591	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610089	43610089	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	219	552	1	ENST00000355710.3:c.2041C>A	p.Gln681Lys	p.Q681K	ENST00000355710	NM_020975.4	681	Cag/Aag	11/20	1	2	FACETS	0.922	0.864	0.981	0.922	0.864	0.981	CLONAL	1	TRUE	1	0.799956255455658	2		553	594	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620458	52621480	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTCTTCAGCTCGACTGTCCTCTGAGTTGTCTGTATTCTTCTCATCATCACCTTTATCTGCATTTGCAAATACAGAGGCCACGCGAACCACAGGCAGAGGCACATCCCGAGGGACAAACCTGACTGAGCTGATGGGCATGGTCCACAGTTTAATTTTCTTAAAAGATTTGGTTTTGGCAGAATACCGTGATTCACAGACAAAAACATCCTCATCTCGGAAGTTTTCTGGGCATAACTTAAAGTATTCCTGGGGGGTGGGGAGGGCATAAGAATAAAACTAGTTAGGTGAATTTTCTGAAAATCAATCAAAAAAAAAAAAAAAAAAAGCAAATAACCAACCAACCAAACAAAAGCTGAACTGATTACAGACTTTCTGGCAGTTAACAAAAAATAATAAATGACCAGAGATTTAGAAGTATTTCTTTGGCTACGGAATGGACTTATTATATACACACCCTTTAAATTATAAAAACAAATAATTCCATTTAGCTTACAATTGCTCTTTGAAAACATATGAACATTTCATATAGCTATAATGTTCCTTAAAGCTTTGAAGAGGGCTTGTGTGTGTGTATCAGACAGACACACAAAAGCACACATTATTACCTAAAAAACAAACTGAAAATTTGTAATGATTATCCTTAAAAAAACATCATACTTAAAAATTAGCCTGGCAATATTAAAAACTTAACCTAACTGCATTATAGCCAAATAGTGTAAGCAGCAAGTGGTCTTTCACAACGAAGTTCAGGTTAATTTCTTCCCAAATCTTTTCATATAGCTATATAGACACGGCTTAAAAAATAGCTTAAAACAGAGTTCCTAATTTTGTAAACATCGATTATTTTCTGTGTTTTAAAATTTTATTCCTAGGGAATGAGTGAGACTTTGGGATTTAATGAGTTTCTTACCTTGACAAACATGACCACACACTTGCCTAGAATTTTACTAACTGGAACTTTGTTGTAATAGTCACTCTTAAAAACTTCTTTTTCTAGAAATTTTCGTGTAGCCAGGTGGAAT	TGTCTTCAGCTCGACTGTCCTCTGAGTTGTCTGTATTCTTCTCATCATCACCTTTATCTGCATTTGCAAATACAGAGGCCACGCGAACCACAGGCAGAGGCACATCCCGAGGGACAAACCTGACTGAGCTGATGGGCATGGTCCACAGTTTAATTTTCTTAAAAGATTTGGTTTTGGCAGAATACCGTGATTCACAGACAAAAACATCCTCATCTCGGAAGTTTTCTGGGCATAACTTAAAGTATTCCTGGGGGGTGGGGAGGGCATAAGAATAAAACTAGTTAGGTGAATTTTCTGAAAATCAATCAAAAAAAAAAAAAAAAAAAGCAAATAACCAACCAACCAAACAAAAGCTGAACTGATTACAGACTTTCTGGCAGTTAACAAAAAATAATAAATGACCAGAGATTTAGAAGTATTTCTTTGGCTACGGAATGGACTTATTATATACACACCCTTTAAATTATAAAAACAAATAATTCCATTTAGCTTACAATTGCTCTTTGAAAACATATGAACATTTCATATAGCTATAATGTTCCTTAAAGCTTTGAAGAGGGCTTGTGTGTGTGTATCAGACAGACACACAAAAGCACACATTATTACCTAAAAAACAAACTGAAAATTTGTAATGATTATCCTTAAAAAAACATCATACTTAAAAATTAGCCTGGCAATATTAAAAACTTAACCTAACTGCATTATAGCCAAATAGTGTAAGCAGCAAGTGGTCTTTCACAACGAAGTTCAGGTTAATTTCTTCCCAAATCTTTTCATATAGCTATATAGACACGGCTTAAAAAATAGCTTAAAACAGAGTTCCTAATTTTGTAAACATCGATTATTTTCTGTGTTTTAAAATTTTATTCCTAGGGAATGAGTGAGACTTTGGGATTTAATGAGTTTCTTACCTTGACAAACATGACCACACACTTGCCTAGAATTTTACTAACTGGAACTTTGTTGTAATAGTCACTCTTAAAAACTTCTTTTTCTAGAAATTTTCGTGTAGCCAGGTGGAAT	-	novel	NA	P-0030623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	17	378	0	ENST00000394830.3:c.2966-26_3298del		p.X989_splice	ENST00000394830	NM_018313.4	989		20-21/30	0.799956255455658	1	FACETS	0.245	0.185	0.314	0.245	0.185	0.314	SUBCLONAL	1	TRUE	0	0.799956255455658	1		378	104	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593606	55593650	+	inframe_deletion	In_Frame_Del	DEL	AAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGAC	AAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGAC	-	novel	NA	P-0030623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	139	375	0	ENST00000288135.5:c.1672_1716del	p.Lys558_Asp572del	p.K558_D572del	ENST00000288135	NM_000222.2	558	AAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGAC/-	11/21	1	2	FACETS	0.769	0.705	0.834	0.769	0.705	0.834	SUBCLONAL	1	TRUE	1	0.799956255455658	2		375	452	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117875409	117875410	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0030623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	148	338	0	ENST00000297338.2:c.233_234del	p.Cys78Ter	p.C78*	ENST00000297338	NM_006265.2	78	tGT/t	3/14	0.799956255455658	3	FACETS	0.812	0.744	0.883	0.271	0.248	0.295	CLONAL	1	TRUE	0	0.799956255455658	3		338	638	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950028	44950028	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0030623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	209	228	0	ENST00000377967.4:c.3797C>G	p.Ser1266Ter	p.S1266*	ENST00000377967	NM_021140.2	1266	tCa/tGa	26/29	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.799956255455658	1		228	268	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061243	38061243	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	173	395	0	ENST00000250448.2:c.746A>T	p.Asp249Val	p.D249V	ENST00000250448	NM_004496.3	249	gAc/gTc	2/2	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.762976109771704	2		395	449	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748995	43748996	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TACTAATGTCATCCCTGGTGTCTGTATCATCTCCC	novel	NA	P-0030625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	178	612	1	ENST00000382044.4:c.1776_1810dup	p.Ile604ArgfsTer14	p.I604Rfs*14	ENST00000382044	NM_001141980.1	604	att/aGGGAGATGATACAGACACCAGGGATGACATTAGTAtt	12/28	1	2	FACETS	0.565	0.521	0.61	0.565	0.521	0.61	SUBCLONAL	1	TRUE	1	0.762976109771704	2		613	826	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696688	47696688	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519971	NA	P-0030625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	326	404	0	ENST00000347630.2:c.260A>G	p.Tyr87Cys	p.Y87C	ENST00000347630	NM_001007230.1	87	tAc/tGc	5/11	0.759993422976209	3	FACETS	0.896	0.854	0.938	0.896	0.854	0.938	CLONAL	2	TRUE	1	0.762976109771704	3		404	659	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931463	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622007	NA	P-0030625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	210	209	0	ENST00000374690.3:c.2105T>A	p.Leu702His	p.L702H	ENST00000374690	NM_000044.3	702	cTc/cAc	4/8	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.762976109771704	1		209	263	SUCCESS
AR	367	MSKCC	GRCh37	X	66943543	66943543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852581	NA	P-0030625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	120	170	0	ENST00000374690.3:c.2623C>T	p.His875Tyr	p.H875Y	ENST00000374690	NM_000044.3	875	Cat/Tat	8/8	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.762976109771704	1		170	156	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0030626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	25	381	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.457	0.36	0.569	0.457	0.36	0.569	SUBCLONAL	1	TRUE	1	0.284310381135206	2		381	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578446	7578446	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	63	594	0	ENST00000269305.4:c.484A>T	p.Ile162Phe	p.I162F	ENST00000269305	NM_001126112.2	162	Atc/Ttc	5/11	1	2	FACETS	0.741	0.641	0.85	0.741	0.641	0.85	SUBCLONAL	1	TRUE	1	0.284310381135206	2		594	598	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032069	26032069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	24	379	0	ENST00000244661.2:c.220G>A	p.Glu74Lys	p.E74K	ENST00000244661	NM_003537.3	74	Gaa/Aaa	1/1	1	2	FACETS	0.448	0.351	0.56	0.448	0.351	0.56	SUBCLONAL	1	TRUE	1	0.284310381135206	2		379	377	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857250	9857250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866228360	NA	P-0030626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	41	453	0	ENST00000330684.3:c.4151C>T	p.Ser1384Leu	p.S1384L	ENST00000330684	NM_001134407.1	1384	tCg/tTg	13/13	1	2	FACETS	0.631	0.526	0.748	0.631	0.526	0.748	SUBCLONAL	1	TRUE	1	0.284310381135206	2		453	457	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602859	10602859	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	65	778	1	ENST00000171111.5:c.719G>T	p.Arg240Leu	p.R240L	ENST00000171111	NM_203500.1	240	cGc/cTc	3/6	0.23055544396994	1	FACETS	0.509	0.441	0.584	0.509	0.441	0.584	SUBCLONAL	1	TRUE	0	0.284310381135206	1		779	770	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376352	15376352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776261114	NA	P-0030626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	90	824	1	ENST00000263377.2:c.662C>T	p.Thr221Met	p.T221M	ENST00000263377	NM_058243.2	221	aCg/aTg	5/20	0.23055544396994	1	FACETS	0.676	0.599	0.758	0.676	0.599	0.758	SUBCLONAL	1	TRUE	0	0.284310381135206	1		825	804	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012340	176012340	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	46	396	0	ENST00000367669.3:c.1594G>T	p.Gly532Cys	p.G532C	ENST00000367669	NM_022457.5	532	Ggt/Tgt	14/20	0.284310381135206	3	FACETS	0.716	0.603	0.841	0.358	0.301	0.421	SUBCLONAL	1	TRUE	1	0.284310381135206	3		396	516	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450603	70450603	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	44	440	0	ENST00000373644.4:c.5443G>T	p.Glu1815Ter	p.E1815*	ENST00000373644	NM_030625.2	1815	Gaa/Taa	12/12	1	2	FACETS	0.585	0.49	0.69	0.585	0.49	0.69	SUBCLONAL	1	TRUE	1	0.284310381135206	2		440	529	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32449523	32449524	+	missense_variant	Missense_Mutation	DNP	AG	AG	CT	novel	NA	P-0030626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	52	604	1	ENST00000332351.3:c.850_851inv	p.Leu284Arg	p.L284R	ENST00000332351	NM_024426.4	284	CTg/AGg	3/10	0.23055544396994	1	FACETS	0.611	0.52	0.71	0.611	0.52	0.71	SUBCLONAL	1	TRUE	0	0.284310381135206	1		605	514	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949170	71949171	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	rs1484650919	NA	P-0030626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	56	726	0	ENST00000298229.2:c.3638_3639del	p.Tyr1213Ter	p.Y1213*	ENST00000298229	NM_001567.3	1213	TAt/t	27/28	0.23055544396994	1	FACETS	0.555	0.475	0.642	0.555	0.475	0.642	SUBCLONAL	1	TRUE	0	0.284310381135206	1		726	609	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865095	57865095	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	64	753	1	ENST00000228682.2:c.2572C>T	p.Gln858Ter	p.Q858*	ENST00000228682	NM_005269.2	858	Caa/Taa	12/12	1	2	FACETS	0.612	0.529	0.702	0.612	0.529	0.702	SUBCLONAL	1	TRUE	1	0.284310381135206	2		754	736	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120785269	120785269	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	44	490	0	ENST00000257552.2:c.839C>G	p.Ala280Gly	p.A280G	ENST00000257552	NM_002442.3	280	gCg/gGg	12/15	1	2	FACETS	0.645	0.541	0.76	0.645	0.541	0.76	SUBCLONAL	1	TRUE	1	0.284310381135206	2		490	480	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900402	32900402	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	31	361	0	ENST00000380152.3:c.499A>T	p.Thr167Ser	p.T167S	ENST00000380152		167	Aca/Tca	6/27	1	2	FACETS	0.52	0.421	0.633	0.52	0.421	0.633	SUBCLONAL	1	TRUE	1	0.284310381135206	2		361	419	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003736	45003752	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	CGGGCCGAGATGTCTCG	CGGGCCGAGATGTCTCG	-	novel	NA	P-0030626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	32	291	0	ENST00000558401.1:c.-8_9del		p.*3*	ENST00000558401	NM_004048.2	?-3/119		1/4	0.284310381135206	1	FACETS	0.718	0.585	0.866	0.718	0.585	0.866	SUBCLONAL	1	TRUE	0	0.284310381135206	1		291	269	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828694	72828694	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	56	464	0	ENST00000268489.5:c.7887C>G	p.Asn2629Lys	p.N2629K	ENST00000268489	NM_006885.3	2629	aaC/aaG	9/10	1	2	FACETS	0.685	0.587	0.793	0.685	0.587	0.793	SUBCLONAL	1	TRUE	1	0.284310381135206	2		464	575	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091794	29091794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	55	508	0	ENST00000328354.6:c.1163C>T	p.Pro388Leu	p.P388L	ENST00000328354	NM_007194.3	388	cCc/cTc	11/15	1	2	FACETS	0.635	0.543	0.736	0.635	0.543	0.736	SUBCLONAL	1	TRUE	1	0.284310381135206	2		508	609	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143044568	143044568	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	21	291	0	ENST00000262992.4:c.1894C>A	p.Leu632Ile	p.L632I	ENST00000262992	NM_001101669.1	632	Ctt/Att	18/24	1	2	FACETS	0.473	0.364	0.601	0.473	0.364	0.601	SUBCLONAL	1	TRUE	1	0.284310381135206	2		291	312	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79965916	79965916	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	42	390	1	ENST00000265081.6:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000265081	NM_002439.4	194	Gac/Tac	4/24	1	2	FACETS	0.767	0.642	0.906	0.767	0.642	0.906	CLONAL	1	TRUE	1	0.284310381135206	2		391	385	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925496	131925496	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	29	331	0	ENST00000265335.6:c.1419G>C	p.Arg473Ser	p.R473S	ENST00000265335		473	agG/agC	9/25	1	2	FACETS	0.487	0.39	0.597	0.487	0.39	0.597	SUBCLONAL	1	TRUE	1	0.284310381135206	2		331	419	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672375	30672375	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	99	563	0	ENST00000376406.3:c.4585A>G	p.Thr1529Ala	p.T1529A	ENST00000376406	NM_014641.2	1529	Aca/Gca	10/15	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.284310381135206	2		563	623	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188949	32188950	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0030626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	93	636	2	ENST00000375023.3:c.604_605delinsAA	p.Pro202Lys	p.P202K	ENST00000375023	NM_004557.3	202	CCa/AAa	4/30	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.284310381135206	2		638	604	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468024	50468024	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	35	391	0	ENST00000331340.3:c.1259C>A	p.Pro420Gln	p.P420Q	ENST00000331340	NM_006060.4	420	cCg/cAg	8/8	1	2	FACETS	0.573	0.469	0.689	0.573	0.469	0.689	SUBCLONAL	1	TRUE	1	0.284310381135206	2		391	430	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015065	37015065	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	31	483	0	ENST00000358127.4:c.339G>T	p.Glu113Asp	p.E113D	ENST00000358127	NM_001280556.1	113	gaG/gaT	3/10	1	2	FACETS	0.426	0.344	0.519	0.426	0.344	0.519	SUBCLONAL	1	TRUE	1	0.284310381135206	2		483	512	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11193180	11193180	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1216317039	NA	P-0030628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	103	472	0	ENST00000361445.4:c.5321A>G	p.Gln1774Arg	p.Q1774R	ENST00000361445	NM_004958.3	1774	cAg/cGg	38/58	1	2	FACETS	0.885	0.795	0.98	0.885	0.795	0.98	CLONAL	1	TRUE	1	0.450128907970045	2		472	517	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252095	226252095	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	24	124	0	ENST00000366813.1:c.43A>C	p.Lys15Gln	p.K15Q	ENST00000366813		15	Aaa/Caa	1/3	0.450128907970045	3	FACETS	0.832	0.659	1	0.416	0.329	0.514	CLONAL	1	TRUE	1	0.450128907970045	3		124	157	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424788	49424788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374531508	NA	P-0030628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	193	504	3	ENST00000301067.7:c.13559C>T	p.Pro4520Leu	p.P4520L	ENST00000301067	NM_003482.3	4520	cCg/cTg	40/54	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.450128907970045	2		507	643	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493638	56493638	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770800582	NA	P-0030628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	130	372	0	ENST00000267101.3:c.2954G>A	p.Gly985Glu	p.G985E	ENST00000267101	NM_001982.3	985	gGa/gAa	25/28	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.450128907970045	2		372	436	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871854	35871854	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	132	420	0	ENST00000216797.5:c.652C>T	p.Arg218Trp	p.R218W	ENST00000216797	NM_020529.2	218	Cgg/Tgg	5/6	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.450128907970045	2		420	493	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562362	95562362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	51	358	0	ENST00000393063.1:c.4895C>T	p.Ser1632Phe	p.S1632F	ENST00000393063	NM_030621.3	1632	tCt/tTt	24/28	1	2	FACETS	0.619	0.528	0.718	0.619	0.528	0.718	SUBCLONAL	1	TRUE	1	0.450128907970045	2		358	366	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347005	89347005	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	109	415	0	ENST00000301030.4:c.5945A>C	p.Lys1982Thr	p.K1982T	ENST00000301030	NM_001256183.1	1982	aAg/aCg	9/13	0.273257046946595	4	FACETS	1	0.959	1	0.563	0.506	0.622	CLONAL	1	TRUE	2	0.450128907970045	4		415	624	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348556	89348589	+	frameshift_variant	Frame_Shift_Del	DEL	TGTTTCTCTCTCTTCTTCTTCTCTTTTAGGATGT	TGTTTCTCTCTCTTCTTCTTCTCTTTTAGGATGT	-	novel	NA	P-0030628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	83	668	0	ENST00000301030.4:c.4361_4394del	p.Asn1454ThrfsTer66	p.N1454Tfs*66	ENST00000301030	NM_001256183.1	1454	aACATCCTAAAAGAGAAGAAGAAGAGAGAGAAACAc/ac	9/13	0.273257046946595	4	FACETS	0.498	0.438	0.563	0.249	0.219	0.282	SUBCLONAL	1	TRUE	2	0.450128907970045	4		668	1074	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	271	515	0	ENST00000269305.4:c.542G>C	p.Arg181Pro	p.R181P	ENST00000269305	NM_001126112.2	181	cGc/cCc	5/11	0.450128907970045	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.450128907970045	2		515	571	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627295	14627295	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs748486862	NA	P-0030628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	418	777	0	ENST00000254322.2:c.775A>G	p.Arg259Gly	p.R259G	ENST00000254322	NM_006145.1	259	Agg/Ggg	2/3	0.450128907970045	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.450128907970045	2		777	883	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047329	128047329	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748503195	NA	P-0030628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	76	396	0	ENST00000285398.2:c.593G>A	p.Arg198His	p.R198H	ENST00000285398	NM_000122.1	198	cGc/cAc	5/15	0.450128907970045	3	FACETS	0.799	0.702	0.902	0.399	0.351	0.451	CLONAL	1	TRUE	1	0.450128907970045	3		396	518	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71161698	71161699	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0030628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	192	364	0	ENST00000318789.4:c.269_270dup	p.Pro91AsnfsTer12	p.P91Nfs*12	ENST00000318789	NM_032682.5	90	-/AA	7/21	0.399459109792087	3	FACETS	0.893	0.839	0.948	0.893	0.839	0.948	CLONAL	3	TRUE	0	0.450128907970045	3		364	390	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916645	178916645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	536	374	0	ENST00000263967.3:c.32G>T	p.Trp11Leu	p.W11L	ENST00000263967	NM_006218.2	11	tGg/tTg	2/21	0.450128907970045	14	FACETS	1	0.969	1			1	CLONAL	7	TRUE	NA	0.450128907970045	14		374	1247	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133788	55133788	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	400	440	0	ENST00000257290.5:c.1001A>G	p.His334Arg	p.H334R	ENST00000257290	NM_006206.4	334	cAt/cGt	7/23	0.355143767151259	5	FACETS	0.876	0.838	0.914			1	CLONAL	4	TRUE	NA	0.450128907970045	5		440	850	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631299	117631299	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1321959715	NA	P-0030628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	225	396	0	ENST00000368508.3:c.6379T>G	p.Trp2127Gly	p.W2127G	ENST00000368508	NM_002944.2	2127	Tgg/Ggg	40/43	0.450128907970045	3	FACETS	0.981	0.92	1	0.981	0.92	1	CLONAL	2	TRUE	1	0.450128907970045	3		396	624	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265636	152265636	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	103	331	0	ENST00000206249.3:c.1089G>T	p.Arg363Ser	p.R363S	ENST00000206249	NM_000125.3	363	agG/agT	4/8	0.450128907970045	3	FACETS	1	0.959	1	0.566	0.509	0.627	CLONAL	1	TRUE	1	0.450128907970045	3		331	495	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194620	29194620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	173	678	0	ENST00000240100.2:c.1108G>A	p.Val370Ile	p.V370I	ENST00000240100	NM_001394.6	370	Gtc/Atc	4/4	0.450128907970045	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.450128907970045	1		678	576	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507436	8507436	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0030628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	72	249	0	ENST00000356435.5:c.1544-2A>T		p.X515_splice	ENST00000356435		515			0.415257770047924	2	FACETS	0.851	0.759	0.945	0.851	0.759	0.945	CLONAL	2	TRUE	0	0.450128907970045	2		249	188	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918870	76918870	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0030628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	97	229	1	ENST00000373344.5:c.4120+1G>A		p.X1374_splice	ENST00000373344	NM_000489.3	1374			1	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.450128907970045	1		230	224	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725247	49725247	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	23	31	0	ENST00000449682.2:c.178T>C	p.Trp60Arg	p.W60R	ENST00000449682	NM_020998.3	60	Tgg/Cgg	2/18	0.399459109792087	3	FACETS	0.907	0.75	1	0.907	0.75	1	CLONAL	3	TRUE	0	0.450128907970045	3		31	46	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0030630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	179	350	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.578643479808279	3	FACETS	1	0.991	1	0.749	0.695	0.804	CLONAL	1	TRUE	1	0.579371863294984	3		350	532	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0030630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	47	232	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.571	0.485	0.665	0.571	0.485	0.665	SUBCLONAL	1	TRUE	1	0.579371863294984	2		232	284	SUCCESS
APC	324	MSKCC	GRCh37	5	112174096	112174096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs137854575	NA	P-0030630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	36	280	0	ENST00000257430.4:c.2805C>A	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	taC/taA	16/16	1	2	FACETS	0.395	0.325	0.472	0.395	0.325	0.472	SUBCLONAL	1	TRUE	1	0.579371863294984	2		280	315	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827892	40827892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs573377632	NA	P-0030630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	75	327	0	ENST00000373198.4:c.2536G>A	p.Val846Ile	p.V846I	ENST00000373198	NM_133170.3	846	Gtc/Atc	17/32	1	2	FACETS	0.547	0.481	0.618	0.547	0.481	0.618	SUBCLONAL	1	TRUE	1	0.579371863294984	2		327	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0030630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	68	403	0	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.386405849457166	1	FACETS	0.395	0.345	0.449	0.395	0.345	0.449	SUBCLONAL	1	TRUE	0	0.579371863294984	1		403	422	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998516	100998516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749208871	NA	P-0030630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	74	411	2	ENST00000325455.5:c.1286C>T	p.Ala429Val	p.A429V	ENST00000325455	NM_001202474.3	429	gCg/gTg	1/8	1	2	FACETS	0.548	0.481	0.62	0.548	0.481	0.62	SUBCLONAL	1	TRUE	1	0.579371863294984	2		413	466	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026322	48026322	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	52	357	0	ENST00000234420.5:c.1201del	p.Asp401IlefsTer10	p.D401Ifs*10	ENST00000234420	NM_000179.2	400	gaG/ga	4/10	1	2	FACETS	0.525	0.449	0.607	0.525	0.449	0.607	SUBCLONAL	1	TRUE	1	0.579371863294984	2		357	342	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0030631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	100	587	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.280535720636839	1	FACETS	0.768	0.686	0.854	0.768	0.686	0.854	SUBCLONAL	1	TRUE	0	0.320253920679488	1		587	683	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0030631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	63	281	1	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.946	0.821	1	0.946	0.821	1	CLONAL	1	TRUE	1	0.320253920679488	2		282	416	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249348	110249348	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	157	742	0	ENST00000374672.4:c.1225A>C	p.Lys409Gln	p.K409Q	ENST00000374672	NM_004235.4	409	Aag/Cag	4/5	0.320253920679488	1	FACETS	0.95	0.87	1	0.95	0.87	1	CLONAL	1	TRUE	0	0.320253920679488	1		742	867	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862158	68862168	+	frameshift_variant	Frame_Shift_Del	DEL	GGGACAACGTT	GGGACAACGTT	-	novel	NA	P-0030631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	95	457	0	ENST00000261769.5:c.2246_2256del	p.Arg749LeufsTer4	p.R749Lfs*4	ENST00000261769	NM_004360.3	749	cGGGACAACGTT/c	14/16	0.320253920679488	1	FACETS	0.843	0.752	0.94	0.843	0.752	0.94	CLONAL	1	TRUE	0	0.320253920679488	1		457	591	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972786	32972786	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1412762465	NA	P-0030632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	93	313	0	ENST00000380152.3:c.10136A>G	p.Tyr3379Cys	p.Y3379C	ENST00000380152		3379	tAt/tGt	27/27	0.494568029744898	3	FACETS	1	0.979	1	0.467	0.419	0.517	CLONAL	1	TRUE	0	0.49407766997726	3		313	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578270	7578274	+	frameshift_variant	Frame_Shift_Del	DEL	ATGCT	ATGCT	-	novel	NA	P-0030632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	276	415	0	ENST00000269305.4:c.575_579del	p.Gln192ProfsTer15	p.Q192Pfs*15	ENST00000269305	NM_001126112.2	192	cAGCAT/c	6/11	0.460438011400162	4	FACETS	1	0.985	1	0.818	0.778	0.858	CLONAL	3	TRUE	0	0.49407766997726	4		415	510	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	56	622	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.416059341523767	2	FACETS	1	0.894	1	0.52	0.449	0.595	CLONAL	1	TRUE	0	0.416059341523767	2		622	259	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	128	545	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	0.416059341523767	2		545	571	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	79	507	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.753	0.664	0.849	0.753	0.664	0.849	SUBCLONAL	1	TRUE	1	0.416059341523767	2		511	504	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	62	319	0	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	1	2	FACETS	0.961	0.837	1	0.961	0.837	1	CLONAL	1	TRUE	1	0.416059341523767	2		319	310	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433673	149433673	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1467770819	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	141	465	1	ENST00000286301.3:c.2878G>A	p.Ala960Thr	p.A960T	ENST00000286301	NM_005211.3	960	Gcc/Acc	22/22	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.416059341523767	2		466	649	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	91	368	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.83	0.739	0.926	0.83	0.739	0.926	CLONAL	1	TRUE	1	0.416059341523767	2		368	527	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	121	446	2	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.993	0.9	1	0.993	0.9	1	CLONAL	1	TRUE	1	0.416059341523767	2		448	586	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294703	1294703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	77	285	1	ENST00000310581.5:c.298G>A	p.Gly100Ser	p.G100S	ENST00000310581	NM_198253.2	100	Ggc/Agc	2/16	1	2	FACETS	0.984	0.87	1	0.984	0.87	1	CLONAL	1	TRUE	1	0.416059341523767	2		286	376	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648383	30648383	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1281085856	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	77	289	1	ENST00000295754.5:c.12del	p.Leu5CysfsTer32	p.L5Cfs*32	ENST00000295754	NM_003242.5	3	cGg/cg	1/7	0.416059341523767	2	FACETS	0.871	0.768	0.98	0.435	0.384	0.49	CLONAL	1	TRUE	0	0.416059341523767	2		290	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578397	7578398	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	93	480	0	ENST00000269305.4:c.532dup	p.His178ProfsTer3	p.H178Pfs*3	ENST00000269305	NM_001126112.2	178	cac/cCac	5/11	1	2	FACETS	0.819	0.73	0.913	0.819	0.73	0.913	CLONAL	1	TRUE	1	0.416059341523767	2		480	546	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	125	464	1	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.855	0.775	0.939	0.855	0.775	0.939	CLONAL	1	TRUE	1	0.416059341523767	2		465	703	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346550	81346550	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs148293411	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	55	272	0	ENST00000222390.5:c.1403G>A	p.Arg468His	p.R468H	ENST00000222390	NM_000601.4	468	cGt/cAt	11/18	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.416059341523767	2		272	255	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19261529	19261529	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	116	437	1	ENST00000162023.5:c.16del	p.Ile6SerfsTer14	p.I6Sfs*14	ENST00000162023		6	Atc/tc	6/13	1	2	FACETS	0.896	0.81	0.988	0.896	0.81	0.988	CLONAL	1	TRUE	1	0.416059341523767	2		438	622	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390736	139390736	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	374	584	0	ENST00000277541.6:c.7455del	p.Ser2486ArgfsTer103	p.S2486Rfs*103	ENST00000277541	NM_017617.3	2485	ccC/cc	34/34	0.416059341523767	2	FACETS	0.987	0.94	1	0.987	0.94	1	CLONAL	2	TRUE	0	0.416059341523767	2		584	911	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61711074	61711074	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs755621083	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	53	279	0	ENST00000401558.2:c.2675C>T	p.Thr892Met	p.T892M	ENST00000401558	NM_003400.3	892	aCg/aTg	21/25	1	2	FACETS	0.87	0.747	1	0.87	0.747	1	CLONAL	1	TRUE	1	0.416059341523767	2		279	293	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345768	152345769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs759063323	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	19	252	0	ENST00000359321.1:c.801dup	p.His268ThrfsTer11	p.H268Tfs*11	ENST00000359321	NM_005431.1	267	-/A	3/3	1	2	FACETS	0.322	0.244	0.413	0.322	0.244	0.413	SUBCLONAL	1	TRUE	1	0.416059341523767	2		252	284	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276861	15276861	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	53	495	1	ENST00000263388.2:c.5404del	p.Ala1802LeufsTer23	p.A1802Lfs*23	ENST00000263388	NM_000435.2	1802	Gct/ct	30/33	1	2	FACETS	0.38	0.324	0.443	0.38	0.324	0.443	SUBCLONAL	1	TRUE	1	0.416059341523767	2		496	670	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137761	64137761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	159	595	1	ENST00000334205.4:c.1862C>T	p.Ala621Val	p.A621V	ENST00000334205	NM_003942.2	621	gCg/gTg	15/17	1	2	FACETS	0.93	0.853	1	0.93	0.853	1	CLONAL	1	TRUE	1	0.416059341523767	2		596	822	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348561	56348561	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	55	229	0	ENST00000348428.3:c.374del	p.Pro125GlnfsTer3	p.P125Qfs*3	ENST00000348428	NM_006785.3	123	agC/ag	2/17	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.416059341523767	2		229	247	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453531	138453531	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372119491	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	55	293	0	ENST00000289153.2:c.917G>A	p.Arg306Gln	p.R306Q	ENST00000289153	NM_006219.2	306	cGa/cAa	5/22	0.416059341523767	2	FACETS	0.987	0.851	1	0.493	0.425	0.566	CLONAL	1	TRUE	0	0.416059341523767	2		293	268	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435160	56435161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	96	501	0	ENST00000407977.2:c.1975_1976dup	p.Pro660ValfsTer41	p.P660Vfs*41	ENST00000407977		659	ggt/ggGGt	9/10	1	2	FACETS	0.794	0.709	0.885	0.794	0.709	0.885	SUBCLONAL	1	TRUE	1	0.416059341523767	2		501	581	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	71	826	3	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.41	0.357	0.467	0.41	0.357	0.467	SUBCLONAL	1	TRUE	1	0.416059341523767	2		829	833	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858195	9858195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777249842	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	34	374	0	ENST00000330684.3:c.3206C>T	p.Thr1069Met	p.T1069M	ENST00000330684	NM_001134407.1	1069	aCg/aTg	13/13	1	2	FACETS	0.358	0.292	0.432	0.358	0.292	0.432	SUBCLONAL	1	TRUE	1	0.416059341523767	2		374	457	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260978	16260978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774527727	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	31	306	0	ENST00000375759.3:c.8243C>T	p.Ala2748Val	p.A2748V	ENST00000375759	NM_015001.2	2748	gCt/gTt	11/15	1	2	FACETS	0.372	0.3	0.452	0.372	0.3	0.452	SUBCLONAL	1	TRUE	1	0.416059341523767	2		306	401	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228979	36228979	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555734923	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	116	472	0	ENST00000222270.7:c.7759C>T	p.Arg2587Ter	p.R2587*	ENST00000222270	NM_014727.1	2587	Cga/Tga	36/37	1	2	FACETS	0.902	0.815	0.994	0.902	0.815	0.994	CLONAL	1	TRUE	1	0.416059341523767	2		472	618	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967090	18967091	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	150	494	0	ENST00000262803.5:c.1814_1815dup	p.Leu606SerfsTer3	p.L606Sfs*3	ENST00000262803	NM_002911.3	602	gca/gcAGa	13/24	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.416059341523767	2		494	670	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210725	36210725	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	157	551	0	ENST00000222270.7:c.481del	p.Leu161PhefsTer6	p.L161Ffs*6	ENST00000222270	NM_014727.1	159	aCc/ac	3/37	1	2	FACETS	0.926	0.849	1	0.926	0.849	1	CLONAL	1	TRUE	1	0.416059341523767	2		551	815	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372478	55372478	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	194	672	0	ENST00000297316.4:c.1168G>A	p.Asp390Asn	p.D390N	ENST00000297316	NM_022454.3	390	Gac/Aac	2/2	0.416059341523767	2	FACETS	1	0.966	1	0.536	0.496	0.577	CLONAL	1	TRUE	0	0.416059341523767	2		672	870	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439811	51439811	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	75	264	0	ENST00000262662.1:c.376A>G	p.Thr126Ala	p.T126A	ENST00000262662		126	Acg/Gcg	4/4	1	2	FACETS	0.967	0.852	1	0.967	0.852	1	CLONAL	1	TRUE	1	0.416059341523767	2		264	373	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058616	72058616	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	76	287	0	ENST00000357731.5:c.824A>C	p.Asn275Thr	p.N275T	ENST00000357731	NM_173808.2	275	aAt/aCt	6/7	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.416059341523767	2		287	350	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663760	241663760	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	105	411	0	ENST00000366560.3:c.1367T>C	p.Val456Ala	p.V456A	ENST00000366560	NM_000143.3	456	gTg/gCg	9/10	0.363333769996193	4	FACETS	1	0.957	1	0.375	0.336	0.416	CLONAL	1	TRUE	1	0.416059341523767	4		411	636	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122636	108122636	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	23	343	0	ENST00000278616.4:c.1680G>T	p.Glu560Asp	p.E560D	ENST00000278616	NM_000051.3	560	gaG/gaT	11/63	1	2	FACETS	0.324	0.252	0.407	0.324	0.252	0.407	SUBCLONAL	1	TRUE	1	0.416059341523767	2		343	341	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870850	12870851	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	48	159	0	ENST00000228872.4:c.79_80dup	p.Ala28ArgfsTer15	p.A28Rfs*15	ENST00000228872	NM_004064.3	26	ccc/ccCTc	1/3	0.416059341523767	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.416059341523767	1		159	167	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339542	339542	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	44	609	0	ENST00000262320.3:c.2360A>G	p.Tyr787Cys	p.Y787C	ENST00000262320	NM_003502.3	787	tAc/tGc	10/11	1	2	FACETS	0.277	0.232	0.328	0.277	0.232	0.328	SUBCLONAL	1	TRUE	1	0.416059341523767	2		609	763	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131697	2131697	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	58	534	0	ENST00000219476.3:c.3712G>A	p.Ala1238Thr	p.A1238T	ENST00000219476	NM_000548.3	1238	Gct/Act	31/42	1	2	FACETS	0.401	0.344	0.464	0.401	0.344	0.464	SUBCLONAL	1	TRUE	1	0.416059341523767	2		534	695	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222519	2222519	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	156	580	1	ENST00000326181.6:c.713G>T	p.Ser238Ile	p.S238I	ENST00000326181	NM_032271.2	238	aGc/aTc	9/21	1	2	FACETS	0.985	0.904	1	0.985	0.904	1	CLONAL	1	TRUE	1	0.416059341523767	2		581	761	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10271082	10271082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1361695976	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	104	411	0	ENST00000340748.4:c.973C>T	p.Arg325Cys	p.R325C	ENST00000340748		325	Cgc/Tgc	13/40	1	2	FACETS	0.901	0.809	0.997	0.901	0.809	0.997	CLONAL	1	TRUE	1	0.416059341523767	2		411	555	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40740961	40740961	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1278736092	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	52	558	0	ENST00000392038.2:c.1357C>A	p.Pro453Thr	p.P453T	ENST00000392038	NM_001626.4	453	Cct/Act	13/14	1	2	FACETS	0.336	0.285	0.391	0.336	0.285	0.391	SUBCLONAL	1	TRUE	1	0.416059341523767	2		558	745	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589910	212589910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771486473	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	40	330	0	ENST00000342788.4:c.632C>T	p.Thr211Met	p.T211M	ENST00000342788	NM_005235.2	211	aCg/aTg	6/28	1	2	FACETS	0.434	0.361	0.516	0.434	0.361	0.516	SUBCLONAL	1	TRUE	1	0.416059341523767	2		330	443	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397745	49397746	+	stop_gained	Nonsense_Mutation	INS	-	-	AACACT	novel	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	226	405	0	ENST00000418115.1:c.473_478dup	p.Cys159_Ser160insTer	p.C159_S160ins*	ENST00000418115	NM_001664.2	160	tca/tAGTGTTca	5/5	0.416059341523767	2	FACETS	0.836	0.783	0.89	0.836	0.783	0.89	CLONAL	2	TRUE	0	0.416059341523767	2		405	650	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526556	31526556	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	52	540	1	ENST00000344624.3:c.484C>T	p.Gln162Ter	p.Q162*	ENST00000344624		162	Cag/Tag	2/33	1	2	FACETS	0.388	0.329	0.452	0.388	0.329	0.452	SUBCLONAL	1	TRUE	1	0.416059341523767	2		541	645	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163854	32163855	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	86	349	0	ENST00000375023.3:c.5371dup	p.Ala1791GlyfsTer21	p.A1791Gfs*21	ENST00000375023	NM_004557.3	1791	gca/gGca	30/30	0.397014617263304	3	FACETS	0.831	0.736	0.932	0.415	0.368	0.466	CLONAL	1	TRUE	1	0.416059341523767	3		349	601	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178634	32178635	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	139	545	0	ENST00000375023.3:c.2759dup	p.Gly921TrpfsTer15	p.G921Wfs*15	ENST00000375023	NM_004557.3	920	cct/ccCt	18/30	0.397014617263304	3	FACETS	0.926	0.843	1	0.463	0.421	0.507	CLONAL	1	TRUE	1	0.416059341523767	3		545	872	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180626	32180626	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	117	371	0	ENST00000375023.3:c.2501C>T	p.Thr834Ile	p.T834I	ENST00000375023	NM_004557.3	834	aCt/aTt	16/30	0.397014617263304	3	FACETS	1	0.94	1	0.527	0.476	0.581	CLONAL	1	TRUE	1	0.416059341523767	3		371	644	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903779	41903780	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	112	446	0	ENST00000372991.4:c.777_778del	p.Gln260AspfsTer63	p.Q260Dfs*63	ENST00000372991	NM_001760.3	259	tcTCag/tcag	5/5	0.397014617263304	3	FACETS	0.895	0.805	0.989	0.447	0.402	0.495	CLONAL	1	TRUE	1	0.416059341523767	3		446	727	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845426	151845426	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1342954023	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	106	426	0	ENST00000262189.6:c.13586G>A	p.Arg4529His	p.R4529H	ENST00000262189	NM_170606.2	4529	cGt/cAt	52/59	1	2	FACETS	0.811	0.729	0.899	0.811	0.729	0.899	CLONAL	1	TRUE	1	0.416059341523767	2		426	628	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271146	38271146	+	stop_lost	Nonstop_Mutation	SNP	T	T	C	novel	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	37	321	0	ENST00000425967.3:c.2562A>G	p.Ter854TrpextTer105	p.*854Wext*105	ENST00000425967	NM_001174067.1	854	tgA/tgG	19/19	0.416059341523767	2	FACETS	0.411	0.338	0.492	0.205	0.169	0.246	SUBCLONAL	1	TRUE	0	0.416059341523767	2		321	433	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864841	117864841	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	25	337	0	ENST00000297338.2:c.1268C>A	p.Pro423Gln	p.P423Q	ENST00000297338	NM_006265.2	423	cCa/cAa	10/14	0.416059341523767	2	FACETS	0.26	0.204	0.324	0.13	0.102	0.162	SUBCLONAL	1	TRUE	0	0.416059341523767	2		337	463	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411380	63411380	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	109	471	0	ENST00000330258.3:c.1787G>T	p.Arg596Met	p.R596M	ENST00000330258	NM_152424.3	596	aGg/aTg	2/2	1	2	FACETS	0.949	0.855	1	0.949	0.855	1	CLONAL	1	TRUE	1	0.416059341523767	2		471	552	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087513	27087513	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	199	603	0	ENST00000324856.7:c.2090del	p.Pro697ArgfsTer45	p.P697Rfs*45	ENST00000324856	NM_006015.4	696	tCc/tc	5/20	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.375956905724618	2		603	723	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089581	27089581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	65	591	0	ENST00000324856.7:c.2537G>A	p.Gly846Asp	p.G846D	ENST00000324856	NM_006015.4	846	gGc/gAc	8/20	1	2	FACETS	0.755	0.656	0.861	0.755	0.656	0.861	SUBCLONAL	1	TRUE	1	0.375956905724618	2		591	458	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092747	27092747	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	93	417	0	ENST00000324856.7:c.2768T>C	p.Met923Thr	p.M923T	ENST00000324856	NM_006015.4	923	aTg/aCg	9/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.375956905724618	2		417	341	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097737	27097737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	71	567	1	ENST00000324856.7:c.3326G>A	p.Arg1109Gln	p.R1109Q	ENST00000324856	NM_006015.4	1109	cGg/cAg	12/20	1	2	FACETS	0.8	0.7	0.907	0.8	0.7	0.907	CLONAL	1	TRUE	1	0.375956905724618	2		568	472	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598375	28598375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148862241	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	67	522	0	ENST00000253063.3:c.347C>T	p.Ala116Val	p.A116V	ENST00000253063	NM_031459.4	116	gCc/gTc	3/10	1	2	FACETS	0.704	0.613	0.803	0.704	0.613	0.803	SUBCLONAL	1	TRUE	1	0.375956905724618	2		522	506	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653796	89653798	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs1554893765	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	36	442	1	ENST00000371953.3:c.97_99del	p.Ile33del	p.I33del	ENST00000371953	NM_000314.4	32	ATT/-	2/9	1	2	FACETS	0.829	0.687	0.986	0.829	0.687	0.986	CLONAL	1	TRUE	1	0.375956905724618	2		443	231	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	23	295	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.644	0.505	0.802	0.644	0.505	0.802	SUBCLONAL	1	TRUE	1	0.375956905724618	2		295	190	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	59	278	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.785	0.686	0.889	1	0.974	1	SUBCLONAL	2	TRUE	1	0.375956905724618	2		278	200	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	99	442	4	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.841	0.76	0.925	1	0.986	1	CLONAL	2	TRUE	1	0.375956905724618	2		446	313	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571820	64571820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770686655	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	203	745	0	ENST00000312049.6:c.1819C>T	p.Arg607Cys	p.R607C	ENST00000312049	NM_130799.2	607	Cgc/Tgc	10/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.375956905724618	2		745	818	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948205	71948205	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	113	775	0	ENST00000298229.2:c.2917G>T	p.Ala973Ser	p.A973S	ENST00000298229	NM_001567.3	973	Gcg/Tcg	26/28	1	2	FACETS	0.908	0.818	1	0.908	0.818	1	CLONAL	1	TRUE	1	0.375956905724618	2		775	662	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342633	118342634	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1565278132	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	21	325	0	ENST00000534358.1:c.766dup	p.Ile256AsnfsTer2	p.I256Nfs*2	ENST00000534358	NM_005933.3	253	-/A	3/36	1	2	FACETS	0.535	0.413	0.675	0.535	0.413	0.675	SUBCLONAL	1	TRUE	1	0.375956905724618	2		325	209	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	61	572	1	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	1	2	FACETS	0.66	0.57	0.757	0.66	0.57	0.757	SUBCLONAL	1	TRUE	1	0.375956905724618	2		573	492	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416952	416953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs771545848	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	51	371	4	ENST00000399788.2:c.3597dup	p.Gly1200ArgfsTer7	p.G1200Rfs*7	ENST00000399788	NM_001042603.1	1199	-/A	23/28	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.375956905724618	2		375	253	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856439	111856439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	110	182	0	ENST00000341259.2:c.490G>A	p.Gly164Arg	p.G164R	ENST00000341259	NM_005475.2	164	Ggg/Agg	2/8	1	2	FACETS	0.903	0.821	0.987	1	0.988	1	CLONAL	2	TRUE	1	0.375956905724618	2		182	324	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123880971	123880971	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1433378503	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	38	290	1	ENST00000330479.4:c.589G>A	p.Glu197Lys	p.E197K	ENST00000330479	NM_020382.3	197	Gag/Aag	5/9	1	2	FACETS	0.766	0.637	0.908	0.766	0.637	0.908	CLONAL	1	TRUE	1	0.375956905724618	2		291	264	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	37	479	2	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	1	2	FACETS	0.613	0.507	0.731	0.613	0.507	0.731	SUBCLONAL	1	TRUE	1	0.375956905724618	2		481	321	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281629	49281629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749662416	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	164	633	0	ENST00000282018.3:c.676C>T	p.Arg226Trp	p.R226W	ENST00000282018	NM_020377.2	226	Cgg/Tgg	1/1	1	2	FACETS	0.811	0.749	0.874	1	0.991	1	CLONAL	2	TRUE	1	0.375956905724618	2		633	538	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	116	405	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.768	0.698	0.84	1	0.986	1	SUBCLONAL	2	TRUE	1	0.375956905724618	2		405	402	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127678	2127678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780981335	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	94	583	1	ENST00000219476.3:c.2917G>A	p.Glu973Lys	p.E973K	ENST00000219476	NM_000548.3	973	Gag/Aag	26/42	1	2	FACETS	0.865	0.771	0.965	0.865	0.771	0.965	CLONAL	1	TRUE	1	0.375956905724618	2		584	578	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857428	9857428	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	41	381	0	ENST00000330684.3:c.3973del	p.Tyr1325ThrfsTer72	p.Y1325Tfs*72	ENST00000330684	NM_001134407.1	1325	Tac/ac	13/13	1	2	FACETS	0.779	0.652	0.918	0.779	0.652	0.918	CLONAL	1	TRUE	1	0.375956905724618	2		381	280	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993832	72993832	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	84	359	1	ENST00000268489.5:c.213del	p.Ser72ProfsTer37	p.S72Pfs*37	ENST00000268489	NM_006885.3	71	ccC/cc	2/10	1	2	FACETS	0.757	0.676	0.842	1	0.98	1	SUBCLONAL	2	TRUE	1	0.375956905724618	2		360	295	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805672	89805672	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs17227396	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	128	538	0	ENST00000389301.3:c.4036G>A	p.Ala1346Thr	p.A1346T	ENST00000389301	NM_000135.2	1346	Gcg/Acg	41/43	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.375956905724618	2		538	466	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	93	427	5	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.375956905724618	2		432	361	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127424	17127424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372918705	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	179	551	1	ENST00000285071.4:c.430G>A	p.Gly144Arg	p.G144R	ENST00000285071	NM_144997.5	144	Gga/Aga	6/14	1	2	FACETS	0.928	0.862	0.995	1	0.993	1	CLONAL	2	TRUE	1	0.375956905724618	2		552	513	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453399	40453399	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs759027671	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	189	736	9	ENST00000345506.4:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000345506	NM_003152.3	366	Ccc/cc	10/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.375956905724618	2		745	679	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	150	535	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.804	0.74	0.87	1	0.99	1	CLONAL	2	TRUE	1	0.375956905724618	2		536	496	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119910	70119910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1297203260	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	82	452	3	ENST00000245479.2:c.916del	p.Val306CysfsTer77	p.V306Cfs*77	ENST00000245479	NM_000346.3	304	ccG/cc	3/3	1	2	FACETS	0.961	0.851	1	0.961	0.851	1	CLONAL	1	TRUE	1	0.375956905724618	2		455	454	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575096	48575096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555685159	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	28	345	0	ENST00000342988.3:c.290G>A	p.Arg97His	p.R97H	ENST00000342988	NM_005359.5	97	cGt/cAt	3/12	1	2	FACETS	0.662	0.532	0.808	0.662	0.532	0.808	SUBCLONAL	1	TRUE	1	0.375956905724618	2		345	225	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1623966	1623966	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756584024	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	167	577	0	ENST00000344749.5:c.533C>T	p.Pro178Leu	p.P178L	ENST00000344749	NM_001136139.2	178	cCg/cTg	8/19	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.375956905724618	2		577	597	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030669	48030669	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376243329	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	27	427	1	ENST00000234420.5:c.3283C>T	p.Arg1095Cys	p.R1095C	ENST00000234420	NM_000179.2	1095	Cgc/Tgc	5/10	1	2	FACETS	0.455	0.362	0.56	0.455	0.362	0.56	SUBCLONAL	1	TRUE	1	0.375956905724618	2		428	316	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215633966	215633966	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	38	490	0	ENST00000260947.4:c.1385G>T	p.Trp462Leu	p.W462L	ENST00000260947	NM_000465.2	462	tGg/tTg	5/11	1	2	FACETS	0.646	0.536	0.768	0.646	0.536	0.768	SUBCLONAL	1	TRUE	1	0.375956905724618	2		490	313	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44520605	44520605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	105	338	0	ENST00000291552.4:c.157C>T	p.Arg53Cys	p.R53C	ENST00000291552	NM_006758.2	53	Cgt/Tgt	3/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.375956905724618	2		338	383	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998127	169998128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs753143066	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	145	648	11	ENST00000295797.4:c.826dup	p.Thr276AsnfsTer16	p.T276Nfs*16	ENST00000295797	NM_002740.5	273	tta/ttAa	9/18	1	2	FACETS	0.759	0.697	0.823	1	0.988	1	SUBCLONAL	2	TRUE	1	0.375956905724618	2		659	508	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749415085	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	59	404	1	ENST00000263967.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000263967	NM_006218.2	38	Cgt/Tgt	2/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.375956905724618	2		405	216	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447061	187447061	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	105	655	0	ENST00000232014.4:c.1132T>C	p.Tyr378His	p.Y378H	ENST00000232014	NM_001130845.1	378	Tac/Cac	5/10	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.375956905724618	2		655	531	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280142	66280142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1327931544	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	34	281	1	ENST00000273854.3:c.1547C>T	p.Thr516Met	p.T516M	ENST00000273854	NM_004439.5	516	aCg/aTg	7/18	1	2	FACETS	0.957	0.79	1	0.957	0.79	1	CLONAL	1	TRUE	1	0.375956905724618	2		282	189	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467629	66467629	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	64	358	0	ENST00000273854.3:c.640T>C	p.Phe214Leu	p.F214L	ENST00000273854	NM_004439.5	214	Ttt/Ctt	3/18	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.375956905724618	2		358	236	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193806	106193807	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	40	318	0	ENST00000380013.4:c.4271_4272del	p.Ser1424Ter	p.S1424*	ENST00000380013	NM_001127208.2	1423	gTC/g	10/11	1	2	FACETS	0.736	0.615	0.87	0.736	0.615	0.87	SUBCLONAL	1	TRUE	1	0.375956905724618	2		318	289	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	68	313	6	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.76	0.67	0.854	1	0.976	1	SUBCLONAL	2	TRUE	1	0.375956905724618	2		319	238	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755776	57755776	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	23	469	0	ENST00000274289.3:c.11del	p.Leu4CysfsTer96	p.L4Cfs*96	ENST00000274289	NM_006622.3	4	tTg/tg	1/14	1	2	FACETS	0.304	0.236	0.382	0.304	0.236	0.382	SUBCLONAL	1	TRUE	1	0.375956905724618	2		469	403	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564366	86564366	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	95	337	0	ENST00000274376.6:c.98T>C	p.Val33Ala	p.V33A	ENST00000274376	NM_002890.2	33	gTg/gCg	1/25	1	2	FACETS	0.909	0.821	1	1	0.987	1	CLONAL	2	TRUE	1	0.375956905724618	2		337	278	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	60	360	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.375956905724618	2		360	226	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	27	231	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.375956905724618	2		231	127	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020848	26020848	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	57	374	0	ENST00000357647.3:c.131C>A	p.Pro44Gln	p.P44Q	ENST00000357647	NM_003529.2	44	cCg/cAg	1/1	0.375956905724618	2	FACETS	0.717	0.617	0.826	0.358	0.308	0.413	SUBCLONAL	1	TRUE	0	0.375956905724618	2		374	423	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798201	32798201	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	179	598	0	ENST00000374899.4:c.1478T>C	p.Leu493Pro	p.L493P	ENST00000374899	NM_018833.2	493	cTa/cCa	9/12	0.375956905724618	2	FACETS	1	0.99	1	0.75	0.694	0.807	CLONAL	1	TRUE	0	0.375956905724618	2		598	635	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800223	32800225	+	inframe_deletion	In_Frame_Del	DEL	CCC	CCC	-	novel	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	36	368	0	ENST00000374899.4:c.1157_1159del	p.Gly386del	p.G386del	ENST00000374899	NM_018833.2	386	gGGGtg/gtg	7/12	0.375956905724618	2	FACETS	0.612	0.504	0.731	0.306	0.252	0.366	SUBCLONAL	1	TRUE	0	0.375956905724618	2		368	313	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803041	32803041	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	80	618	0	ENST00000374899.4:c.835del	p.Val279TrpfsTer26	p.V279Wfs*26	ENST00000374899	NM_018833.2	279	Gtg/tg	5/12	0.375956905724618	2	FACETS	0.779	0.687	0.878	0.39	0.343	0.439	SUBCLONAL	1	TRUE	0	0.375956905724618	2		618	546	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	251	673	2	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	0.375956905724618	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.375956905724618	2		675	619	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100260	157100260	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1554248082	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	45	103	0	ENST00000346085.5:c.1202del	p.Gly401AlafsTer29	p.G401Afs*29	ENST00000346085	NM_020732.3	399	gcG/gc	1/20	0.134716936242798	3	FACETS	0.756	0.644	0.876			1	INDETERMINATE	2	TRUE	NA	0.375956905724618	3		103	188	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	129	564	2	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	0.375956905724618	2		566	458	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026514	6026514	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs63750451	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	28	572	0	ENST00000265849.7:c.1882C>T	p.Arg628Ter	p.R628*	ENST00000265849	NM_000535.5	628	Cga/Tga	11/15	1	2	FACETS	0.401	0.321	0.494	0.401	0.321	0.494	SUBCLONAL	1	TRUE	1	0.375956905724618	2		572	371	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240762	55240762	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768336804	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	168	689	0	ENST00000275493.2:c.2006G>A	p.Arg669Gln	p.R669Q	ENST00000275493	NM_005228.3	669	cGa/cAa	17/28	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.375956905724618	2		689	615	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146944	38146945	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	141	762	1	ENST00000317025.8:c.3197dup	p.Asn1066LysfsTer14	p.N1066Kfs*14	ENST00000317025	NM_023034.1	1066	aac/aaAc	18/24	1	2	FACETS	0.775	0.711	0.841	1	0.988	1	SUBCLONAL	2	TRUE	1	0.375956905724618	2		763	484	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740379	145740379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555407951	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	196	768	1	ENST00000428558.2:c.1561C>T	p.Arg521Trp	p.R521W	ENST00000428558	NM_004260.3	521	Cgg/Tgg	9/22	1	2	FACETS	0.79	0.734	0.847	1	0.992	1	SUBCLONAL	2	TRUE	1	0.375956905724618	2		769	660	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760790	133760790	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	72	530	0	ENST00000318560.5:c.3113C>A	p.Ala1038Glu	p.A1038E	ENST00000318560	NM_005157.4	1038	gCg/gAg	11/11	1	2	FACETS	0.878	0.77	0.994	0.878	0.77	0.994	CLONAL	1	TRUE	1	0.375956905724618	2		530	436	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	86	475	0	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	0.375956905724618	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.375956905724618	1		475	313	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215320	123215320	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	95	504	1	ENST00000218089.9:c.2866G>A	p.Ala956Thr	p.A956T	ENST00000218089	NM_001042749.1	956	Gct/Act	28/35	0.375956905724618	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.375956905724618	1		505	289	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0030637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	42	324	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.16	2		324	436	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0030637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	11	381	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.3	2	FACETS	0.43	0.296	0.597			1	SUBCLONAL	1	TRUE	NA	0.16	2		381	320	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0030637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	29	456	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	1	2	FACETS	0.944	0.758	1	0.944	0.758	1	CLONAL	1	TRUE	1	0.16	2		456	384	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716326	52716326	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	46	463	0	ENST00000322088.6:c.770G>C	p.Trp257Ser	p.W257S	ENST00000322088	NM_014225.5	257	tGg/tCg	6/15	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.16	NA		463	439	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247403	71247403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540360773	NA	P-0030637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	26	390	2	ENST00000318789.4:c.130G>A	p.Val44Met	p.V44M	ENST00000318789	NM_032682.5	44	Gtg/Atg	6/21	1	2	FACETS	0.804	0.637	0.997	0.804	0.637	0.997	CLONAL	1	TRUE	1	0.16	2		392	404	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564794	86564798	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCC	CCTCC	-	novel	NA	P-0030637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	36	604	0	ENST00000274376.6:c.526_530del	p.Pro176AsnfsTer2	p.P176Nfs*2	ENST00000274376	NM_002890.2	176	CCTCCa/a	1/25	1	2	FACETS	0.728	0.597	0.876	0.728	0.597	0.876	SUBCLONAL	1	TRUE	1	0.16	2		604	618	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0030639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	378	601	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.663813249021211	2	FACETS	1	0.994	1	0.637	0.608	0.666	CLONAL	1	TRUE	0	0.699905415793956	2		601	848	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922321	178922321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	117	471	0	ENST00000263967.3:c.1090G>A	p.Gly364Arg	p.G364R	ENST00000263967	NM_006218.2	364	Gga/Aga	6/21	0.193306564138881	3	FACETS	0.503	0.453	0.556	0.252	0.226	0.278	INDETERMINATE	1	TRUE	1	0.699905415793956	3		471	897	SUCCESS
APC	324	MSKCC	GRCh37	5	112137082	112137082	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0030639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	254	314	0	ENST00000257430.4:c.834+2T>C		p.X278_splice	ENST00000257430	NM_000038.5	278			0.699905415793956	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.699905415793956	1		314	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs878854073	NA	P-0030639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	285	454	0	ENST00000269305.4:c.673-1G>A		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.699905415793956	1	FACETS	0.997	0.949	1	0.997	0.949	1	CLONAL	1	TRUE	0	0.699905415793956	1		454	531	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922221	100922221	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	315	474	0	ENST00000325455.5:c.2291G>T	p.Gly764Val	p.G764V	ENST00000325455	NM_001202474.3	764	gGa/gTa	5/8	0.699905415793956	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.699905415793956	1		474	520	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861791	57861791	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	151	468	0	ENST00000228682.2:c.1092del	p.Cys364Ter	p.C364*	ENST00000228682	NM_005269.2	364	tgT/tg	10/12	0.366506333538134	1	FACETS	0.393	0.36	0.428	0.393	0.36	0.428	INDETERMINATE	1	TRUE	0	0.699905415793956	1		468	713	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870956	12870962	+	frameshift_variant	Frame_Shift_Del	DEL	TTTCGAT	TTTCGAT	-	novel	NA	P-0030640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	137	311	0	ENST00000228872.4:c.187_193del	p.Asp63ArgfsTer6	p.D63Rfs*6	ENST00000228872	NM_004064.3	61	aaTTTCGAT/aa	1/3	0.340624905931431	4	FACETS	1	0.969	1	0.746	0.684	0.811	CLONAL	2	FALSE	1	0.348938581819912	4		311	473	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943658	9943658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	62	511	1	ENST00000330684.3:c.1283C>T	p.Thr428Met	p.T428M	ENST00000330684	NM_001134407.1	428	aCg/aTg	5/13	NA	2	FACETS	0.725	0.627	0.831			1	INDETERMINATE	1	FALSE	NA	0.348938581819912	2		512	490	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916663	178916663	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	156	293	0	ENST00000263967.3:c.50C>A	p.Pro17His	p.P17H	ENST00000263967	NM_006218.2	17	cCc/cAc	2/21	0.348938581819912	6	FACETS	1	0.938	1	1	0.938	1	CLONAL	4	FALSE	2	0.348938581819912	6		293	375	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212782	27212782	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	60	583	0	ENST00000380036.4:c.2764A>T	p.Thr922Ser	p.T922S	ENST00000380036	NM_000459.3	922	Acg/Tcg	17/23	0.348938581819912	1	FACETS	0.554	0.478	0.637	0.554	0.478	0.637	SUBCLONAL	1	FALSE	0	0.348938581819912	1		583	512	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117684026	117684026	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	93	286	0	ENST00000368508.3:c.3121C>A	p.Pro1041Thr	p.P1041T	ENST00000368508	NM_002944.2	1041	Cca/Aca	21/43	0.461740383436471	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.461740383436471	2		286	186	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	107	454	0				ENST00000310581	NM_198253.2	-/1132			0.316841189500928	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	TRUE	1	0.316841189500928	4		454	257	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579321	7579322	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs587780067	NA	P-0030644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	102	435	0	ENST00000269305.4:c.365_366del	p.Val122AspfsTer26	p.V122Dfs*26	ENST00000269305	NM_001126112.2	122	gTG/g	4/11	0.24757071620095	2	FACETS	0.856	0.772	0.944	0.856	0.772	0.944	CLONAL	2	TRUE	0	0.316841189500928	2		435	376	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244233	153244233	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	84	323	0	ENST00000281708.4:c.1924G>A	p.Asp642Asn	p.D642N	ENST00000281708	NM_033632.3	642	Gat/Aat	12/12	1	2	FACETS	0.927	0.829	1	1	0.985	1	CLONAL	2	TRUE	1	0.316841189500928	2		323	286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577496	7577501	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GACCTG	GACCTG	-	novel	NA	P-0030652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	59	518	0	ENST00000269305.4:c.780_782+3del		p.X260_splice	ENST00000269305	NM_001126112.2	260		7/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		518	840	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098944	178098944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	79	313	0	ENST00000397062.3:c.101G>A	p.Arg34Gln	p.R34Q	ENST00000397062	NM_006164.4	34	cGa/cAa	2/5	1	2	FACETS	0.77	0.677	0.869	0.77	0.677	0.869	SUBCLONAL	1	TRUE	1	0.324750100594587	2		313	632	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032069	26032069	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	91	482	0	ENST00000244661.2:c.220G>C	p.Glu74Gln	p.E74Q	ENST00000244661	NM_003537.3	74	Gaa/Caa	1/1	1	2	FACETS	0.795	0.706	0.89	0.795	0.706	0.89	SUBCLONAL	1	TRUE	1	0.324750100594587	2		482	705	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096912	11096912	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs150949949	NA	P-0030654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	144	810	0	ENST00000358026.2:c.403C>G	p.Pro135Ala	p.P135A	ENST00000358026	NM_001128849.1	135	Cca/Gca	4/36	1	2	FACETS	0.773	0.703	0.846	0.773	0.703	0.846	SUBCLONAL	1	TRUE	1	0.324750100594587	2		810	1148	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs587781702	NA	P-0030654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	135	598	0	ENST00000269305.4:c.920-1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.272516336228354	1	FACETS	0.823	0.748	0.902	0.823	0.748	0.902	CLONAL	1	TRUE	0	0.324750100594587	1		598	846	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436102	49436102	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	62	402	2	ENST00000301067.7:c.5879del	p.Gly1960AlafsTer87	p.G1960Afs*87	ENST00000301067	NM_003482.3	1960	gGc/gc	28/54	1	2	FACETS	0.718	0.62	0.823	0.718	0.62	0.823	SUBCLONAL	1	TRUE	1	0.324750100594587	2		404	532	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11291480	11291480	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	101	528	0	ENST00000361445.4:c.2526G>T	p.Trp842Cys	p.W842C	ENST00000361445	NM_004958.3	842	tgG/tgT	17/58	0.324750100594587	1	FACETS	0.789	0.706	0.878	0.789	0.706	0.878	SUBCLONAL	1	TRUE	0	0.324750100594587	1		528	660	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100608	8100608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	65	719	0	ENST00000346208.3:c.582G>A	p.Met194Ile	p.M194I	ENST00000346208		194	atG/atA	3/6	1	2	FACETS	0.414	0.357	0.475	0.414	0.357	0.475	SUBCLONAL	1	TRUE	1	0.324750100594587	2		719	968	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435060	49435060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1340260705	NA	P-0030654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	135	640	0	ENST00000301067.7:c.6493C>T	p.Pro2165Ser	p.P2165S	ENST00000301067	NM_003482.3	2165	Ccc/Tcc	31/54	1	2	FACETS	0.915	0.831	1	0.915	0.831	1	CLONAL	1	TRUE	1	0.324750100594587	2		640	909	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749238	43749238	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	135	742	0	ENST00000382044.4:c.1568C>T	p.Ser523Phe	p.S523F	ENST00000382044	NM_001141980.1	523	tCt/tTt	12/28	1	2	FACETS	0.845	0.767	0.927	0.845	0.767	0.927	CLONAL	1	TRUE	1	0.324750100594587	2		742	984	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010427	48010427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	83	450	1	ENST00000234420.5:c.55G>A	p.Asp19Asn	p.D19N	ENST00000234420	NM_000179.2	19	Gat/Aat	1/10	0.237646762157208	4	FACETS	0.727	0.64	0.821			1	SUBCLONAL	1	TRUE	NA	0.324750100594587	4		451	931	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1956926	1956926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	152	725	0	ENST00000382891.5:c.2377C>T	p.His793Tyr	p.H793Y	ENST00000382891	NM_133335.3	793	Cac/Tac	13/22	0.324750100594587	1	FACETS	0.875	0.8	0.954	0.875	0.8	0.954	CLONAL	1	TRUE	0	0.324750100594587	1		725	896	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117629979	117629979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767792683	NA	P-0030654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	83	452	0	ENST00000368508.3:c.6547C>T	p.Pro2183Ser	p.P2183S	ENST00000368508	NM_002944.2	2183	Cca/Tca	41/43	1	2	FACETS	0.837	0.739	0.941	0.837	0.739	0.941	CLONAL	1	TRUE	1	0.324750100594587	2		452	611	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224324	55224324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	95	583	0	ENST00000275493.2:c.1105C>T	p.Leu369Phe	p.L369F	ENST00000275493	NM_005228.3	369	Ctc/Ttc	9/28	1	2	FACETS	0.743	0.661	0.831	0.743	0.661	0.831	SUBCLONAL	1	TRUE	1	0.324750100594587	2		583	787	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345222	70345222	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	83	644	0	ENST00000374080.3:c.2248T>C	p.Cys750Arg	p.C750R	ENST00000374080		750	Tgc/Cgc	16/45	0.324750100594587	1	FACETS	0.516	0.455	0.583	0.516	0.455	0.583	SUBCLONAL	1	TRUE	0	0.324750100594587	1		644	829	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417869	32417871	+	missense_variant	Missense_Mutation	TNP	AAG	AAG	TAA	novel	NA	P-0030654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	85	590	0	ENST00000332351.3:c.1181_1183delinsTTA	p.Ala394_Tyr395delinsValAsn	p.A394_Y395delinsVN	ENST00000332351	NM_024426.4	394	gCTTac/gTTAac	7/10	0.20418208666078	1	FACETS	0.559	0.493	0.629	0.559	0.493	0.629	SUBCLONAL	1	TRUE	0	0.324750100594587	1		590	785	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0030655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	629	546	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.878538298451412	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.878538298451412	2		547	683	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444143	49444143	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	147	772	1	ENST00000301067.7:c.3228G>T	p.Glu1076Asp	p.E1076D	ENST00000301067	NM_003482.3	1076	gaG/gaT	11/54	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.270284050893292	2		773	1010	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134168	41134168	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	78	452	0	ENST00000379561.5:c.1460C>A	p.Pro487His	p.P487H	ENST00000379561	NM_002015.3	487	cCc/cAc	2/3	0.21470441564079	4	FACETS	0.892	0.783	1			1	CLONAL	1	TRUE	NA	0.270284050893292	4		452	822	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348538	56348538	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs764958277	NA	P-0030656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	167	369	0	ENST00000348428.3:c.346A>G	p.Thr116Ala	p.T116A	ENST00000348428	NM_006785.3	116	Act/Gct	2/17	1	2	FACETS	1	0.96	1	1	0.993	1	CLONAL	2	TRUE	1	0.270284050893292	2		369	583	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218138	36218138	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1415208819	NA	P-0030656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	190	494	2	ENST00000222270.7:c.4085A>G	p.His1362Arg	p.H1362R	ENST00000222270	NM_014727.1	1362	cAc/cGc	15/37	1	2	FACETS	1	0.953	1	1	0.993	1	CLONAL	2	TRUE	1	0.270284050893292	2		496	679	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673001	30673001	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	134	759	1	ENST00000376406.3:c.3959A>G	p.Lys1320Arg	p.K1320R	ENST00000376406	NM_014641.2	1320	aAg/aGg	10/15	0.270284050893292	1	FACETS	0.968	0.879	1	0.968	0.879	1	CLONAL	1	TRUE	0	0.270284050893292	1		760	886	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816825	32816825	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	143	795	0	ENST00000354258.4:c.1499G>T	p.Ser500Ile	p.S500I	ENST00000354258	NM_000593.5	500	aGc/aTc	6/11	0.270284050893292	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.270284050893292	1		795	878	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410248	63410249	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0030656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	292	772	1	ENST00000330258.3:c.2918_2919delinsTT	p.Ala973Val	p.A973V	ENST00000330258	NM_152424.3	973	gCC/gTT	2/2	0.270284050893292	2	FACETS	1	0.957	1	1	0.994	1	CLONAL	3	TRUE	0	0.270284050893292	2		773	712	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0030657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	178	546	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	0.629162537859309	2		546	550	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0030657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	141	232	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.629162537859309	1	FACETS	0.994	0.921	1	0.994	0.921	1	CLONAL	1	TRUE	0	0.629162537859309	1		232	309	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0030657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	195	337	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.629162537859309	1	FACETS	0.972	0.911	1	0.972	0.911	1	CLONAL	1	TRUE	0	0.629162537859309	1		337	437	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117790	70117790	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	289	587	0	ENST00000245479.2:c.258G>A	p.Trp86Ter	p.W86*	ENST00000245479	NM_000346.3	86	tgG/tgA	1/3	0.629162537859309	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.629162537859309	1		587	553	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411411	63411411	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	247	665	0	ENST00000330258.3:c.1756C>T	p.Arg586Ter	p.R586*	ENST00000330258	NM_152424.3	586	Cga/Tga	2/2	1	2	FACETS	0.967	0.907	1	0.967	0.907	1	CLONAL	1	TRUE	1	0.629162537859309	2		665	812	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21627910	21627910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1176731657	NA	P-0030657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	149	490	0	ENST00000421138.2:c.1220G>A	p.Arg407Gln	p.R407Q	ENST00000421138		407	cGa/cAa	12/16	1	2	FACETS	0.906	0.833	0.981	0.906	0.833	0.981	CLONAL	1	TRUE	1	0.629162537859309	2		490	523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	255	523	2	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.200563497978305	3	FACETS	1	0.979	1			1	CLONAL	2	TRUE	NA	0.323966178471644	3		525	835	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954223	48954223	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	T	novel	NA	P-0030662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	93	262	0	ENST00000267163.4:c.1421+3A>T		p.X474_splice	ENST00000267163	NM_000321.2	474			0.21617610665558	2	FACETS	1	0.972	1	0.638	0.57	0.71	CLONAL	1	TRUE	0	0.323966178471644	2		262	450	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117712762	117712762	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	146	522	1	ENST00000369458.3:c.64G>T	p.Ala22Ser	p.A22S	ENST00000369458	NM_024626.3	22	Gca/Tca	2/6	0.323966178471644	5	FACETS	0.764	0.697	0.834	0.509	0.464	0.556	SUBCLONAL	2	TRUE	2	0.323966178471644	5		523	877	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026084	48026084	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	49	480	0	ENST00000234420.5:c.962C>T	p.Ser321Leu	p.S321L	ENST00000234420	NM_000179.2	321	tCa/tTa	4/10	0.232580567279563	3	FACETS	0.516	0.436	0.604	0.172	0.145	0.202	SUBCLONAL	1	TRUE	0	0.323966178471644	3		480	681	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680558	30680558	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	57	542	0	ENST00000376406.3:c.1161G>T	p.Gln387His	p.Q387H	ENST00000376406	NM_014641.2	387	caG/caT	5/15	0.304987591978961	4	FACETS	0.593	0.507	0.686	0.148	0.126	0.172	SUBCLONAL	1	TRUE	0	0.323966178471644	4		542	786	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111475	8111476	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	249	567	0	ENST00000346208.3:c.962dup	p.Thr322AspfsTer30	p.T322Dfs*30	ENST00000346208		321	cag/cAag	5/6	0.257155153098567	3	FACETS	1	0.993	1	0.734	0.688	0.781	INDETERMINATE	1	TRUE	1	0.493387782487371	3		567	857	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641388	18641389	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1229278001	NA	P-0030664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	165	265	0	ENST00000266497.5:c.2393dup	p.Asn798LysfsTer5	p.N798Kfs*5	ENST00000266497		796	cta/ctAa	17/31	0.483755621962392	3	FACETS	0.902	0.836	0.97	0.902	0.836	0.97	CLONAL	2	TRUE	1	0.493387782487371	3		265	462	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17941419	17941419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	100	600	2	ENST00000458235.1:c.2989G>A	p.Glu997Lys	p.E997K	ENST00000458235	NM_000215.3	997	Gaa/Aaa	22/24	0.489908361484316	1	FACETS	0.491	0.439	0.546	0.491	0.439	0.546	SUBCLONAL	1	TRUE	0	0.493387782487371	1		602	622	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139760	55139760	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751618661	NA	P-0030664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	97	535	2	ENST00000257290.5:c.1421C>T	p.Thr474Met	p.T474M	ENST00000257290	NM_006206.4	474	aCg/aTg	10/23	0.242238813967154	2	FACETS	0.532	0.474	0.594	0.266	0.237	0.297	INDETERMINATE	1	TRUE	0	0.493387782487371	2		537	739	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128999	30128999	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	141	492	0	ENST00000263025.4:c.767A>G	p.His256Arg	p.H256R	ENST00000263025	NM_002746.2	256	cAc/cGc	5/9	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.462624070794875	2		492	601	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000088	30000088	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	163	599	0	ENST00000338641.4:c.101del	p.Glu34GlyfsTer6	p.E34Gfs*6	ENST00000338641	NM_000268.3	34	gAg/gg	1/16	0.462624070794875	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.462624070794875	1		599	522	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443570	52443570	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	107	450	0	ENST00000460680.1:c.122G>T	p.Gly41Val	p.G41V	ENST00000460680	NM_004656.3	41	gGc/gTc	3/17	0.462624070794875	1	FACETS	0.876	0.792	0.964	0.876	0.792	0.964	CLONAL	1	TRUE	0	0.462624070794875	1		450	406	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798848	135798848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514784	NA	P-0030665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	22	343	0	ENST00000298552.3:c.395G>A	p.Gly132Asp	p.G132D	ENST00000298552	NM_001162426.1	132	gGc/gAc	6/23	0.462624070794875	1	FACETS	0.224	0.173	0.282	0.224	0.173	0.282	SUBCLONAL	1	TRUE	0	0.462624070794875	1		343	327	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508490	106508490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	20	231	0	ENST00000359195.3:c.484G>A	p.Val162Ile	p.V162I	ENST00000359195	NM_002649.2	162	Gtc/Atc	2/11	1	2	FACETS	0.85	0.656	1	1	0.928	1	CLONAL	2	TRUE	1	0.16	2		231	147	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138423304	138423304	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs902854177	NA	P-0030666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	34	411	0	ENST00000289153.2:c.1562G>A	p.Ser521Asn	p.S521N	ENST00000289153	NM_006219.2	521	aGt/aAt	10/22	1	2	FACETS	0.977	0.798	1	0.977	0.798	1	CLONAL	1	TRUE	1	0.16	2		411	435	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841488	156841488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1023556915	NA	P-0030666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	14	547	0	ENST00000524377.1:c.791C>T	p.Thr264Met	p.T264M	ENST00000524377	NM_002529.3	264	aCg/aTg	7/17	1	2	FACETS	0.407	0.293	0.546	0.407	0.293	0.546	SUBCLONAL	1	TRUE	1	0.16	2		547	430	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435378	18435378	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	13	307	0	ENST00000266497.5:c.363T>A	p.Asn121Lys	p.N121K	ENST00000266497		121	aaT/aaA	1/31	1	2	FACETS	0.749	0.534	1	0.749	0.534	1	CLONAL	1	TRUE	1	0.16	2		307	217	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913196	44913196	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	13	224	0	ENST00000377967.4:c.871G>T	p.Gly291Ter	p.G291*	ENST00000377967	NM_021140.2	291	Gga/Tga	10/29	1	1	FACETS	0.817	0.584	1	0.817	0.584	1	CLONAL	1	TRUE	0	0.16	1		224	183	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900302	3900329	+	frameshift_variant	Frame_Shift_Del	DEL	GCCATGCCTCCTGCCTGTGCGGTGTTCA	GCCATGCCTCCTGCCTGTGCGGTGTTCA	-	novel	NA	P-0121483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	105	437	0	ENST00000262367.5:c.767_794del	p.Leu256ProfsTer5	p.L256Pfs*5	ENST00000262367	NM_004380.2	256	cTGAACACCGCACAGGCAGGAGGCATGGCc/cc	2/31	0.281336430476347	1	FACETS	0.532	0.481	0.584	0.532	0.481	0.584	INDETERMINATE	1	NA	0	0.725187501283461	1		437	347	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990625	7990625	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	149	439	0	ENST00000319144.4:c.136G>T	p.Ala46Ser	p.A46S	ENST00000319144	NM_001139.2	46	Gca/Tca	1/15	1	2	FACETS	0.993	0.916	1	0.993	0.916	1	CLONAL	1	NA	1	0.725187501283461	2		439	414	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024130	112024130	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	112	475	0	ENST00000368678.4:c.655G>T	p.Ala219Ser	p.A219S	ENST00000368678		219	Gcc/Tcc	7/13	1	2	FACETS	0.504	0.454	0.556	0.504	0.454	0.556	SUBCLONAL	1	NA	1	0.725187501283461	2		475	613	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538906	23538906	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0121483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	149	494	0	ENST00000380871.4:c.533del	p.Lys178ArgfsTer23	p.K178Rfs*23	ENST00000380871	NM_006167.3	178	aAg/ag	2/2	1	2	FACETS	0.96	0.886	1	0.96	0.886	1	CLONAL	1	NA	1	0.725187501283461	2		494	428	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002921	69002921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1273873699	NA	P-0121483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	187	293	1	ENST00000288368.4:c.2221G>A	p.Ala741Thr	p.A741T	ENST00000288368	NM_024870.2	741	Gcc/Acc	20/40	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	NA	1	0.725187501283461	2		294	468	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50810135	50810135	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0030668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	183	556	0	ENST00000398568.2:c.959C>G	p.Ser320Ter	p.S320*	ENST00000398568	NM_001042412.1	320	tCa/tGa	6/18	0.690455330151048	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.690455330151048	1		556	346	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	41	454	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.934	1			1	INDETERMINATE	1	TRUE	NA	0.505466006640279	2		454	136	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24133959	24133959	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398122368	NA	P-0030673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	59	319	0	ENST00000263121.7:c.110G>A	p.Arg37His	p.R37H	ENST00000263121	NM_003073.3	37	cGt/cAt	2/9	1	2	FACETS	0.941	0.819	1	0.941	0.819	1	CLONAL	1	TRUE	1	0.505466006640279	2		319	248	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543898	41543898	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	267	472	0	ENST00000263253.7:c.2189C>A	p.Thr730Asn	p.T730N	ENST00000263253	NM_001429.3	730	aCc/aAc	12/31	1	2	FACETS	0.908	0.857	0.959	1	0.996	1	CLONAL	3	FALSE	1	0.288801483533895	2		472	679	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764146326	NA	P-0030675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	102	472	0	ENST00000269305.4:c.841G>T	p.Asp281Tyr	p.D281Y	ENST00000269305	NM_001126112.2	281	Gac/Tac	8/11	0.195007677252961	3	FACETS	1	0.982	1	0.738	0.663	0.817	INDETERMINATE	1	FALSE	1	0.327459583793878	3		472	491	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921551	178921551	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	18	285	0	ENST00000263967.3:c.1033A>T	p.Asn345Tyr	p.N345Y	ENST00000263967	NM_006218.2	345	Aat/Tat	5/21	0.327459583793878	3	FACETS	0.319	0.239	0.414	0.16	0.119	0.207	SUBCLONAL	1	FALSE	1	0.327459583793878	3		285	401	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620061	21620359	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	CTGAACCGAAGACTTGGATGGCTGTTTTAACCCCTCACGAATCTCTTGCAGTCGCTGCCGGCTATTTCCAGAATAAGTCGTGGCAGGAAAAGTCTTTGGCCTCATTGTTAGTCCAGTTTCCTTTTACCATAAATACAATCTTCTTAAAGTGTTTTATTATTTAAAAAAAAAAACTGTCAATAGTATCAGTTTGTTGTAAACATACTTTCAAAATAATTTCCTTTTGAAAATGTTCTTTCCTTCCATTTTTGTAGTTCCTATAGAGAACCTAAAATTTTCCAAAGTCTTCATTTTGAAGA	CTGAACCGAAGACTTGGATGGCTGTTTTAACCCCTCACGAATCTCTTGCAGTCGCTGCCGGCTATTTCCAGAATAAGTCGTGGCAGGAAAAGTCTTTGGCCTCATTGTTAGTCCAGTTTCCTTTTACCATAAATACAATCTTCTTAAAGTGTTTTATTATTTAAAAAAAAAAACTGTCAATAGTATCAGTTTGTTGTAAACATACTTTCAAAATAATTTCCTTTTGAAAATGTTCTTTCCTTCCATTTTTGTAGTTCCTATAGAGAACCTAAAATTTTCCAAAGTCTTCATTTTGAAGA	-	novel	NA	P-0030675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	232	442	0	ENST00000382592.4:c.-194_105del		p.*65*	ENST00000382592	NM_014572.2	?-35/1088		2/8	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.327459583793878	NA		442	805	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060688	38060688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561930261	NA	P-0030675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	95	493	0	ENST00000250448.2:c.1301C>T	p.Pro434Leu	p.P434L	ENST00000250448	NM_004496.3	434	cCc/cTc	2/2	0.195007677252961	3	FACETS	1	0.951	1	0.558	0.498	0.622	INDETERMINATE	1	FALSE	1	0.327459583793878	3		493	605	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027997	48027997	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751973865	NA	P-0030675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	47	241	0	ENST00000234420.5:c.2875C>T	p.Arg959Cys	p.R959C	ENST00000234420	NM_000179.2	959	Cgc/Tgc	4/10	0.106798217958962	4	FACETS	0.99	0.837	1	0.495	0.418	0.579	INDETERMINATE	1	FALSE	2	0.327459583793878	4		241	385	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600016	10600019	+	frameshift_variant	Frame_Shift_Del	DEL	ATAG	ATAG	-	novel	NA	P-0030683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	220	716	0	ENST00000171111.5:c.1557_1560del	p.Ile519MetfsTer12	p.I519Mfs*12	ENST00000171111	NM_203500.1	519	atCTAT/at	5/6	0.713018051935532	1	FACETS	0.834	0.785	0.883	0.834	0.785	0.883	CLONAL	1	TRUE	0	0.713018051935532	1		716	476	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0030684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	67	546	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	0.22	2		546	484	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433847	78433848	+	splice_donor_variant	Splice_Site	DEL	AC	AC	-	rs1477051807	NA	P-0030684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	28	404	0	ENST00000370768.2:c.250+1_250+2del		p.X84_splice	ENST00000370768	NM_003902.3	84			1	2	FACETS	0.629	0.502	0.773	0.629	0.502	0.773	SUBCLONAL	1	TRUE	1	0.22	2		404	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0030684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	66	685	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.22	2		685	496	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573563	48573564	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs786203560	NA	P-0030684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	43	391	0	ENST00000342988.3:c.153dup	p.Asp52ArgfsTer2	p.D52Rfs*2	ENST00000342988	NM_005359.5	49	-/A	2/12	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.22	2		391	264	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0030685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	75	594	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.18	2		594	768	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0030685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	31	609	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.478	0.385	0.584	0.478	0.385	0.584	SUBCLONAL	1	TRUE	1	0.18	2		610	721	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510612	38510612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	103	498	0	ENST00000254066.5:c.866G>A	p.Gly289Glu	p.G289E	ENST00000254066	NM_000964.3	289	gGg/gAg	7/9	1	2	FACETS	0.764	0.684	0.849	1	0.982	1	SUBCLONAL	2	TRUE	1	0.18	2		498	749	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324665	31324665	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	36	238	1	ENST00000412585.2:c.143C>T	p.Ser48Leu	p.S48L	ENST00000412585	NM_005514.6	48	tCa/tTa	2/8	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.18	2		239	352	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575108	48575153	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCTGATCTTCACAAAAATGAACTAAAACATGTTAAATATTGTCA	GGCCTGATCTTCACAAAAATGAACTAAAACATGTTAAATATTGTCA	-	novel	NA	P-0030685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	30	342	0	ENST00000342988.3:c.303_348del	p.Trp101CysfsTer6	p.W101Cfs*6	ENST00000342988	NM_005359.5	101	tGGCCTGATCTTCACAAAAATGAACTAAAACATGTTAAATATTGTCAg/tg	3/12	1	2	FACETS	0.651	0.524	0.796	0.651	0.524	0.796	SUBCLONAL	1	TRUE	1	0.18	2		342	512	SUCCESS
MET	4233	MSKCC	GRCh37	7	116409842	116409842	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs757811101	NA	P-0030685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	33	262	0	ENST00000397752.3:c.2727A>G	p.Ile909Met	p.I909M	ENST00000397752	NM_000245.2	909	atA/atG	12/21	1	2	FACETS	0.764	0.621	0.925	0.764	0.621	0.925	CLONAL	1	TRUE	1	0.18	2		262	480	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0030686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	63	369	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	NA	2	FACETS	0.911	0.789	1			1	INDETERMINATE	1	TRUE	NA	0.29	2		369	477	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0030686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	62	388	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.824	0.712	0.945	0.824	0.712	0.945	CLONAL	1	TRUE	1	0.29	2		388	519	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165642	118165642	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	53	410	0	ENST00000369448.3:c.152T>A	p.Ile51Asn	p.I51N	ENST00000369448	NM_017709.3	51	aTc/aAc	2/2	1	2	FACETS	0.967	0.828	1	0.967	0.828	1	CLONAL	1	TRUE	1	0.29	2		410	378	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857640	9857640	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	60	377	0	ENST00000330684.3:c.3761T>C	p.Leu1254Pro	p.L1254P	ENST00000330684	NM_001134407.1	1254	cTt/cCt	13/13	0.29206537327152	3	FACETS	1	0.902	1	0.528	0.455	0.606	CLONAL	1	TRUE	1	0.29	3		377	449	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371680	89371680	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs749607205	NA	P-0030686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	189	611	0	ENST00000301030.4:c.160C>T	p.Arg54Ter	p.R54*	ENST00000301030	NM_001256183.1	54	Cga/Tga	4/13	0.3	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.29	2		611	632	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54959339	54959339	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	88	396	0	ENST00000312783.6:c.361G>A	p.Glu121Lys	p.E121K	ENST00000312783	NM_198436.1	121	Gaa/Aaa	5/10	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.29	2		396	603	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564671	139564671	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	43	696	0	ENST00000308874.7:c.460A>G	p.Asn154Asp	p.N154D	ENST00000308874		154	Aac/Gac	7/10	1	2	FACETS	0.412	0.344	0.489	0.412	0.344	0.489	SUBCLONAL	1	TRUE	1	0.29	2		696	719	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0030689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	85	476	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.195175684713952	2		476	655	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463247	25463247	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs34843713	NA	P-0030689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	86	509	1	ENST00000264709.3:c.2246G>A	p.Arg749His	p.R749H	ENST00000264709	NM_175629.2	749	cGc/cAc	19/23	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.195175684713952	2		510	628	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044970	47044970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	89	610	0	ENST00000377604.3:c.2296C>T	p.Arg766Cys	p.R766C	ENST00000377604	NM_001204468.1	766	Cgc/Tgc	20/24	0.0806950575407988	3	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.195175684713952	3		610	748	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220504	1220504	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	80	519	0	ENST00000326873.7:c.597G>C	p.Glu199Asp	p.E199D	ENST00000326873	NM_000455.4	199	gaG/gaC	4/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.195175684713952	2		519	577	SUCCESS
APC	324	MSKCC	GRCh37	5	112173975	112173975	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	240	402	0	ENST00000257430.4:c.2684C>A	p.Ser895Ter	p.S895*	ENST00000257430	NM_000038.5	895	tCa/tAa	16/16	0.896355612879363	1	FACETS	0.922	0.887	0.955	0.922	0.887	0.955	CLONAL	1	TRUE	0	0.909527402164149	1		402	312	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843547	3843547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	719	566	0	ENST00000262367.5:c.1056del	p.Lys352AsnfsTer2	p.K352Nfs*2	ENST00000262367	NM_004380.2	352	aaA/aa	4/31	0.873225007670035	2	FACETS	0.947	0.93	0.962	0.947	0.93	0.962	CLONAL	2	TRUE	0	0.909527402164149	2		566	835	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265281	10265281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	267	503	0	ENST00000340748.4:c.1765G>A	p.Gly589Arg	p.G589R	ENST00000340748		589	Ggg/Agg	20/40	1	2	FACETS	0.93	0.879	0.982	0.93	0.879	0.982	CLONAL	1	TRUE	1	0.909527402164149	2		503	631	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663039	227663039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs529797752	NA	P-0030690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	221	491	0	ENST00000305123.5:c.416G>A	p.Ser139Asn	p.S139N	ENST00000305123	NM_005544.2	139	aGc/aAc	1/2	1	2	FACETS	0.822	0.771	0.875	0.822	0.771	0.875	CLONAL	1	TRUE	1	0.909527402164149	2		491	591	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076943	41076943	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1293077894	NA	P-0030690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	237	506	0	ENST00000373198.4:c.1477A>G	p.Ile493Val	p.I493V	ENST00000373198	NM_133170.3	493	Atc/Gtc	9/32	1	2	FACETS	0.834	0.784	0.885	0.834	0.784	0.885	CLONAL	1	TRUE	1	0.909527402164149	2		506	625	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573363	55573363	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	297	563	0	ENST00000288135.5:c.1025A>G	p.Lys342Arg	p.K342R	ENST00000288135	NM_000222.2	342	aAa/aGa	6/21	1	2	FACETS	0.975	0.925	1	0.975	0.925	1	CLONAL	1	TRUE	1	0.909527402164149	2		563	670	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056497	26056497	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs557734913	NA	P-0030690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	130	272	1	ENST00000343677.2:c.160C>T	p.Arg54Cys	p.R54C	ENST00000343677	NM_005319.3	54	Cgt/Tgt	1/1	1	2	FACETS	0.896	0.825	0.968	0.896	0.825	0.968	CLONAL	1	TRUE	1	0.909527402164149	2		273	319	SUCCESS
MET	4233	MSKCC	GRCh37	7	116422152	116422152	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0030693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	38	484	0	ENST00000397752.3:c.3632+1G>A		p.X1211_splice	ENST00000397752	NM_000245.2	1211			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		484	478	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0030696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	84	473	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	1	2	FACETS	0.423	0.374	0.475	0.423	0.374	0.475	SUBCLONAL	1	TRUE	1	0.721051905590235	2		473	551	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115725	8115728	+	frameshift_variant	Frame_Shift_Del	DEL	GAAG	GAAG	-	novel	NA	P-0030696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	59	411	0	ENST00000346208.3:c.1076_1079del	p.Glu359AlafsTer44	p.E359Afs*44	ENST00000346208		357	aaGAAG/aa	6/6	1	2	FACETS	0.299	0.257	0.345	0.299	0.257	0.345	SUBCLONAL	1	TRUE	1	0.721051905590235	2		411	547	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061450	38061450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	58	564	0	ENST00000250448.2:c.539C>T	p.Thr180Ile	p.T180I	ENST00000250448	NM_004496.3	180	aCc/aTc	2/2	1	2	FACETS	0.29	0.249	0.335	0.29	0.249	0.335	SUBCLONAL	1	TRUE	1	0.721051905590235	2		564	555	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100919	27100919	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	87	532	0	ENST00000324856.7:c.4201C>T	p.Gln1401Ter	p.Q1401*	ENST00000324856	NM_006015.4	1401	Cag/Tag	18/20	1	2	FACETS	0.405	0.359	0.454	0.405	0.359	0.454	SUBCLONAL	1	TRUE	1	0.721051905590235	2		532	596	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167767	56167768	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0030696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	71	438	0	ENST00000399503.3:c.1333_1334insCA	p.Ile445ThrfsTer43	p.I445Tfs*43	ENST00000399503	NM_005921.1	444	-/AC	7/20	1	2	FACETS	0.357	0.312	0.406	0.357	0.312	0.406	SUBCLONAL	1	TRUE	1	0.721051905590235	2		438	551	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178672	56178673	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	46	259	0	ENST00000399503.3:c.3646dup	p.Ile1216AsnfsTer23	p.I1216Nfs*23	ENST00000399503	NM_005921.1	1215	-/A	14/20	1	2	FACETS	0.367	0.31	0.429	0.367	0.31	0.429	SUBCLONAL	1	TRUE	1	0.721051905590235	2		259	348	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0030698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	225	712	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.559672731862228	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.559672731862228	3		712	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577501	7577501	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	rs1427471466	NA	P-0030698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	389	492	0	ENST00000269305.4:c.780del	p.Ser261ValfsTer84	p.S261Vfs*84	ENST00000269305	NM_001126112.2	260	tcC/tc	7/11	0.559672731862228	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.559672731862228	2		492	634	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55597532	55597532	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	112	458	0	ENST00000288135.5:c.2180G>T	p.Gly727Val	p.G727V	ENST00000288135	NM_000222.2	727	gGa/gTa	15/21	0.41629741168632	4	FACETS	0.913	0.822	1	0.456	0.411	0.504	CLONAL	1	TRUE	2	0.559672731862228	4		458	684	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0030699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	300	655	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.691250081944315	2		655	844	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106412	27106412	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	223	690	0	ENST00000324856.7:c.6023T>G	p.Leu2008Arg	p.L2008R	ENST00000324856	NM_006015.4	2008	cTg/cGg	20/20	1	2	FACETS	0.979	0.916	1	0.979	0.916	1	CLONAL	1	TRUE	1	0.691250081944315	2		690	659	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0030700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	90	546	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.121174932302436	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		546	472	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829039	128829040	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs570242755	NA	P-0030700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	15	24	0	ENST00000249373.3:c.67_69dup	p.Leu23dup	p.L23dup	ENST00000249373	NM_005631.4	23	ggg/ggGCTg	1/12	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		24	74	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0030703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	139	493	0	ENST00000269305.4:c.97-1G>A		p.X33_splice	ENST00000269305	NM_001126112.2	33			1	2	FACETS	0.884	0.809	0.962	1	0.99	1	CLONAL	2	TRUE	1	0.290164041280836	2		493	542	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739340	46739340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540912131	NA	P-0030703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	80	474	0	ENST00000371975.4:c.1531C>T	p.Arg511Cys	p.R511C	ENST00000371975	NM_003579.3	511	Cgt/Tgt	14/18	1	2	FACETS	0.784	0.69	0.886	0.784	0.69	0.886	SUBCLONAL	1	TRUE	1	0.290164041280836	2		474	703	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165073	47165073	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	64	337	0	ENST00000409792.3:c.1053T>G	p.Phe351Leu	p.F351L	ENST00000409792	NM_014159.6	351	ttT/ttG	3/21	0.246291610401357	3	FACETS	0.925	0.802	1	0.463	0.401	0.53	CLONAL	1	TRUE	1	0.290164041280836	3		337	546	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541447	187541447	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	81	525	0	ENST00000441802.2:c.6293A>T	p.His2098Leu	p.H2098L	ENST00000441802	NM_005245.3	2098	cAt/cTt	10/27	1	2	FACETS	0.879	0.775	0.991	0.879	0.775	0.991	CLONAL	1	TRUE	1	0.290164041280836	2		525	635	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217400	123217400	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0030703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	147	362	0	ENST00000218089.9:c.3053+1G>T		p.X1018_splice	ENST00000218089	NM_001042749.1	1018			0.246291610401357	3	FACETS	0.832	0.762	0.906	0.832	0.762	0.906	CLONAL	2	TRUE	1	0.290164041280836	3		362	697	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981838	70981838	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	190	688	0	ENST00000276594.2:c.258G>C	p.Arg86Ser	p.R86S	ENST00000276594	NM_024504.3	86	agG/agC	2/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.312872520229441	2		688	908	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0030706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1380	1869	546	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.548991407279445	17	FACETS	0.975	0.957	0.993	1	0.997	1	CLONAL	11	FALSE	7	0.548991407279445	17		546	3249	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757274881	NA	P-0030706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	535	696	0	ENST00000269305.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	144	Cag/Tag	5/11	0.495109691910785	3	FACETS	0.895	0.865	0.925	0.895	0.865	0.925	CLONAL	3	FALSE	0	0.548991407279445	3		696	925	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518279	187518279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779582047	NA	P-0030706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	71	302	0	ENST00000441802.2:c.12415G>A	p.Gly4139Arg	p.G4139R	ENST00000441802	NM_005245.3	4139	Ggg/Agg	25/27	0.548991407279445	3	FACETS	0.785	0.688	0.889	0.392	0.344	0.445	SUBCLONAL	1	FALSE	1	0.548991407279445	3		302	420	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0030707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	138	465	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		465	705	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782329	NA	P-0030709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	205	648	0	ENST00000269305.4:c.746G>C	p.Arg249Thr	p.R249T	ENST00000269305	NM_001126112.2	249	aGg/aCg	7/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.405778778503755	2		648	743	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829765	76829800	+	frameshift_variant	Frame_Shift_Del	DEL	TGCAGTAGTGGAACCATCTAAACGGTAATAGTCAAT	TGCAGTAGTGGAACCATCTAAACGGTAATAGTCAAT	AC	novel	NA	P-0030709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	106	799	2	ENST00000373344.5:c.6241_6276delinsGT	p.Ile2081ValfsTer17	p.I2081Vfs*17	ENST00000373344	NM_000489.3	2081	ATTGACTATTACCGTTTAGATGGTTCCACTACTGCA/GT	28/35	0.209517786593563	3	FACETS	0.778	0.697	0.864	0.389	0.348	0.432	INDETERMINATE	1	TRUE	1	0.405778778503755	3		801	808	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0030717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	386	338	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.676734500165767	9	FACETS	1	0.96	1	0.506	0.48	0.532	CLONAL	3	TRUE	3	0.676734500165767	9		338	1266	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140487359	140487359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs577372072	NA	P-0030717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	231	693	0	ENST00000288602.6:c.1166G>A	p.Arg389His	p.R389H	ENST00000288602	NM_004333.4	389	cGt/cAt	9/18	0.558660459015769	5	FACETS	1	0.98	1	0.377	0.351	0.404	CLONAL	1	TRUE	2	0.676734500165767	5		693	1216	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884478	151884478	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	47	461	0	ENST00000262189.6:c.4877A>C	p.Asn1626Thr	p.N1626T	ENST00000262189	NM_170606.2	1626	aAt/aCt	33/59	0.558660459015769	5	FACETS	0.4	0.336	0.47	0.133	0.112	0.157	SUBCLONAL	1	TRUE	2	0.676734500165767	5		461	700	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0030719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	167	546	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.112844415203478	3	FACETS	1	0.938	1	1	0.938	1	INDETERMINATE	3	TRUE	0	0.202695559845772	3		546	594	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182148	11182148	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	139	549	0	ENST00000361445.4:c.6698A>T	p.Asn2233Ile	p.N2233I	ENST00000361445	NM_004958.3	2233	aAc/aTc	48/58	0.195049375959548	3	FACETS	0.902	0.822	0.987	0.902	0.822	0.987	CLONAL	2	TRUE	1	0.202695559845772	3		549	837	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610129	43610129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141185224	NA	P-0030719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	67	623	0	ENST00000355710.3:c.2081G>A	p.Arg694Gln	p.R694Q	ENST00000355710	NM_020975.4	694	cGg/cAg	11/20	0.195049375959548	3	FACETS	1	0.876	1	0.505	0.438	0.577	CLONAL	1	TRUE	1	0.202695559845772	3		623	721	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111959708	111959708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	107	432	0	ENST00000375549.3:c.287C>T	p.Ala96Val	p.A96V	ENST00000375549	NM_003002.3	96	gCt/gTt	3/4	0.180205194809118	2	FACETS	0.967	0.87	1	0.967	0.87	1	CLONAL	2	TRUE	0	0.202695559845772	2		432	546	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434465	49434467	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	rs758375281	NA	P-0030719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	100	789	0	ENST00000301067.7:c.7086_7088del	p.Pro2363del	p.P2363del	ENST00000301067	NM_003482.3	2362	ccTCCa/cca	31/54	0.112844415203478	3	FACETS	0.778	0.696	0.866	0.519	0.464	0.578	INDETERMINATE	2	TRUE	0	0.202695559845772	3		789	698	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747342068	NA	P-0030719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	148	704	0	ENST00000269305.4:c.394A>G	p.Lys132Glu	p.K132E	ENST00000269305	NM_001126112.2	132	Aag/Gag	5/11	0.195049375959548	3	FACETS	0.838	0.764	0.915	0.838	0.764	0.915	CLONAL	2	TRUE	1	0.202695559845772	3		704	960	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600005	10600005	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	145	605	0	ENST00000171111.5:c.1571G>T	p.Gly524Val	p.G524V	ENST00000171111	NM_203500.1	524	gGc/gTc	5/6	0.180205194809118	2	FACETS	0.916	0.836	0.999	0.916	0.836	0.999	CLONAL	2	TRUE	0	0.202695559845772	2		605	781	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024624	11024625	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0030719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	87	534	0	ENST00000327064.4:c.743_744del	p.Pro248ArgfsTer43	p.P248Rfs*43	ENST00000327064	NM_199141.1	247	ctCCcc/ctcc	6/16	0.180205194809118	2	FACETS	1	0.978	1	0.734	0.651	0.822	CLONAL	1	TRUE	0	0.202695559845772	2		534	585	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130579	29130579	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	65	536	0	ENST00000328354.6:c.131G>T	p.Ser44Ile	p.S44I	ENST00000328354	NM_007194.3	44	aGc/aTc	2/15	0.112844415203478	3	FACETS	1	0.912	1	0.356	0.308	0.408	INDETERMINATE	1	TRUE	0	0.202695559845772	3		536	661	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670844	134670844	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	49	423	0	ENST00000398015.3:c.755G>C	p.Arg252Pro	p.R252P	ENST00000398015	NM_004441.4	252	cGa/cCa	3/16	0.195049375959548	3	FACETS	1	0.884	1	0.526	0.446	0.615	CLONAL	1	TRUE	1	0.202695559845772	3		423	506	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155631	106155631	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	79	468	0	ENST00000380013.4:c.532G>T	p.Glu178Ter	p.E178*	ENST00000380013	NM_001127208.2	178	Gag/Tag	3/11	0.180205194809118	2	FACETS	0.76	0.67	0.856	0.76	0.67	0.856	SUBCLONAL	2	TRUE	0	0.202695559845772	2		468	513	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1258758	1258758	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	124	581	1	ENST00000310581.5:c.2987C>A	p.Thr996Lys	p.T996K	ENST00000310581	NM_198253.2	996	aCg/aAg	13/16	0.0816731299392204	4	FACETS	0.852	0.77	0.938	0.852	0.77	0.938	INDETERMINATE	2	TRUE	2	0.202695559845772	4		582	864	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79966126	79966126	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	rs766997264	NA	P-0030719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	69	419	1	ENST00000265081.6:c.790G>T	p.Glu264Ter	p.E264*	ENST00000265081	NM_002439.4	264	Gag/Tag	4/24	0.195225752560092	2	FACETS	1	0.973	1	0.737	0.643	0.837	CLONAL	1	TRUE	0	0.202695559845772	2		420	462	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099054	157099226	+	coding_sequence_variant,5_prime_UTR_variant	Frame_Shift_Del	DEL	CGAACTCAACATGGCCCATAACGCGGGCGCCGCGGCCGCCGCCGGCACCCACAGCGCCAAGAGCGGCGGCTCCGAGGCGGCTCTCAAGGAGGGTGGAAGCGCCGCCGCGCTGTCCTCCTCCTCCTCCTCCTCCGCGGCGGCAGCGGCGGCATCCTCTTCCTCCTCGTCGGGCC	CGAACTCAACATGGCCCATAACGCGGGCGCCGCGGCCGCCGCCGGCACCCACAGCGCCAAGAGCGGCGGCTCCGAGGCGGCTCTCAAGGAGGGTGGAAGCGCCGCCGCGCTGTCCTCCTCCTCCTCCTCCTCCGCGGCGGCAGCGGCGGCATCCTCTTCCTCCTCGTCGGGCC	-	novel	NA	P-0030719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	151	18	0				ENST00000346085	NM_020732.3	?-55/2249		1/20	0.195225752560092	2	FACETS	1	0.97	1	1	0.993	1	CLONAL	4	TRUE	0	0.202695559845772	2		18	343	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376695	8376695	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	63	483	0	ENST00000356435.5:c.4418G>C	p.Gly1473Ala	p.G1473A	ENST00000356435		1473	gGc/gCc	27/35	0.202695559845772	3	FACETS	0.912	0.787	1	0.456	0.393	0.524	CLONAL	1	TRUE	1	0.202695559845772	3		483	751	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521468	8521468	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	55	461	0	ENST00000356435.5:c.770G>C	p.Cys257Ser	p.C257S	ENST00000356435		257	tGt/tCt	9/35	0.202695559845772	3	FACETS	0.717	0.611	0.832	0.358	0.305	0.416	SUBCLONAL	1	TRUE	1	0.202695559845772	3		461	834	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900226	101900226	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1013629735	NA	P-0030719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	53	451	0	ENST00000374994.4:c.660G>T	p.Trp220Cys	p.W220C	ENST00000374994	NM_004612.2	220	tgG/tgT	4/9	1	2	FACETS	0.934	0.796	1	0.934	0.796	1	CLONAL	1	TRUE	1	0.202695559845772	2		451	560	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815530	139815530	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528114067	NA	P-0030719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	77	652	0	ENST00000247668.2:c.1001C>T	p.Ala334Val	p.A334V	ENST00000247668	NM_021138.3	334	gCg/gTg	9/11	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.202695559845772	2		652	704	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921616	39921616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	48	511	0	ENST00000378444.4:c.4204G>A	p.Glu1402Lys	p.E1402K	ENST00000378444	NM_001123385.1	1402	Gag/Aag	10/15	1	2	FACETS	0.78	0.659	0.914	0.78	0.659	0.914	CLONAL	1	TRUE	1	0.202695559845772	2		511	607	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210244	123210244	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	45	517	0	ENST00000218089.9:c.2596G>T	p.Ala866Ser	p.A866S	ENST00000218089	NM_001042749.1	866	Gca/Tca	26/35	1	2	FACETS	0.771	0.647	0.908	0.771	0.647	0.908	CLONAL	1	TRUE	1	0.202695559845772	2		517	576	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220572	123220572	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	53	533	0	ENST00000218089.9:c.3229C>A	p.Pro1077Thr	p.P1077T	ENST00000218089	NM_001042749.1	1077	Cca/Aca	30/35	1	2	FACETS	0.752	0.641	0.875	0.752	0.641	0.875	SUBCLONAL	1	TRUE	1	0.202695559845772	2		533	695	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420145	420145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs564426386	NA	P-0030720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	222	489	0	ENST00000399788.2:c.3122C>T	p.Pro1041Leu	p.P1041L	ENST00000399788	NM_001042603.1	1041	cCg/cTg	21/28	1	2	FACETS	0.992	0.929	1	0.992	0.929	1	CLONAL	1	TRUE	1	0.719656962899391	2		489	622	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0030721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	241	532	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.478644119173294	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.562642763839882	3		533	519	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0030721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	67	622	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.499165185269905	3	FACETS	0.957	0.838	1	0.478	0.419	0.542	CLONAL	1	TRUE	1	0.562642763839882	3		622	319	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791797	42791797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	479	626	1	ENST00000575354.2:c.683G>A	p.Arg228Gln	p.R228Q	ENST00000575354	NM_015125.3	228	cGg/cAg	5/20	0.512967599652335	5	FACETS	0.973	0.933	1	0.973	0.933	1	CLONAL	3	TRUE	2	0.562642763839882	5		627	1076	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046944	128046946	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs761456808	NA	P-0030721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	222	513	8	ENST00000285398.2:c.789_791del	p.Glu264del	p.E264del	ENST00000285398	NM_000122.1	263	gaAGAg/gag	6/15	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.562642763839882	2		521	604	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052633	42052633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	126	420	0	ENST00000219905.7:c.7304G>A	p.Arg2435Gln	p.R2435Q	ENST00000219905	NM_001164273.1	2435	cGg/cAg	20/24	1	2	FACETS	0.828	0.753	0.906	0.828	0.753	0.906	CLONAL	1	TRUE	1	0.562642763839882	2		420	541	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101194	41101194	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200107921	NA	P-0030721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	72	504	0	ENST00000373198.4:c.1162C>A	p.His388Asn	p.H388N	ENST00000373198	NM_133170.3	388	Cat/Aat	8/32	NA	2	FACETS	0.595	0.522	0.674			1	INDETERMINATE	1	TRUE	NA	0.562642763839882	2		504	430	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0030723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	113	712	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.913	0.825	1	0.913	0.825	1	CLONAL	1	TRUE	1	0.43488401386512	2		712	569	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589219	67589219	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	36	408	0	ENST00000274335.5:c.1207G>A	p.Glu403Lys	p.E403K	ENST00000274335		403	Gaa/Aaa	9/15	1	2	FACETS	0.342	0.281	0.411	0.342	0.281	0.411	SUBCLONAL	1	TRUE	1	0.43488401386512	2		408	484	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589102	67589182	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATACCTTTATTTTTATATTGTTTTTACAGGAAAGGGGGAAATAACAAATTAATCAAAATATTTCATCGAGATGGGAAATAT	ATACCTTTATTTTTATATTGTTTTTACAGGAAAGGGGGAAATAACAAATTAATCAAAATATTTCATCGAGATGGGAAATAT	-	novel	NA	P-0030723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	28	254	0	ENST00000274335.5:c.1119-29_1170del		p.X373_splice	ENST00000274335		373		9/15	1	2	FACETS	0.428	0.342	0.525	0.428	0.342	0.525	SUBCLONAL	1	TRUE	1	0.43488401386512	2		254	301	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841908	151841908	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	69	345	0	ENST00000262189.6:c.14233G>C	p.Glu4745Gln	p.E4745Q	ENST00000262189	NM_170606.2	4745	Gaa/Caa	55/59	0.43488401386512	1	FACETS	0.627	0.549	0.711	0.627	0.549	0.711	SUBCLONAL	1	TRUE	0	0.43488401386512	1		345	396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0030726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	46	601	7	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.160534273131694	4	FACETS	0.888	0.765	1	0.888	0.765	1	INDETERMINATE	2	FALSE	2	0.601121497083154	4		608	138	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0030726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	33	695	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.160534273131694	4	FACETS	1	0.93	1	0.632	0.524	0.75	INDETERMINATE	1	FALSE	2	0.601121497083154	4		695	139	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872686	136872686	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1203148711	NA	P-0030726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	16	479	0	ENST00000241393.3:c.812A>G	p.Lys271Arg	p.K271R	ENST00000241393	NM_003467.2	271	aAg/aGg	2/2	1	2	FACETS	0.527	0.395	0.68	0.527	0.395	0.68	SUBCLONAL	1	FALSE	1	0.601121497083154	2		479	101	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0030727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	407	546	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.762298921507142	5	FACETS	1	0.992	1	1	0.992	1	CLONAL	4	TRUE	1	0.762298921507142	5		546	535	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	165	587	1	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.705339068927822	5	FACETS	1	0.961	1	0.703	0.652	0.755	CLONAL	2	TRUE	2	0.762298921507142	5		588	440	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0030727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	377	569	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.762298921507142	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.762298921507142	3		569	426	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916793	48916793	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	23	616	0	ENST00000267163.4:c.323T>A	p.Val108Asp	p.V108D	ENST00000267163	NM_000321.2	108	gTt/gAt	3/27	0.762298921507142	2	FACETS	0.227	0.177	0.284	0.113	0.088	0.142	SUBCLONAL	1	TRUE	0	0.762298921507142	2		616	266	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916803	48916823	+	inframe_deletion	In_Frame_Del	DEL	TGAGATGTCGTTCACTTTTAC	TGAGATGTCGTTCACTTTTAC	-	novel	NA	P-0030727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	18	587	0	ENST00000267163.4:c.337_357del	p.Met113_Glu119del	p.M113_E119del	ENST00000267163	NM_000321.2	111	gaTGAGATGTCGTTCACTTTTACt/gat	3/27	0.762298921507142	2	FACETS	0.188	0.141	0.243	0.094	0.07	0.122	SUBCLONAL	1	TRUE	0	0.762298921507142	2		587	251	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591137	67591138	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGACCA	novel	NA	P-0030727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	135	499	0	ENST00000274335.5:c.1732_1737dup	p.Asp578_Gln579dup	p.D578_Q579dup	ENST00000274335		578	aga/agAGACCAa	12/15	0.409486543860104	5	FACETS	0.981	0.901	1	0.654	0.601	0.709	INDETERMINATE	2	TRUE	2	0.762298921507142	5		499	387	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0030728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	47	556	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.231629580154226	2	FACETS	1	0.849	1	0.501	0.424	0.586	CLONAL	1	TRUE	0	0.261878977941504	2		556	358	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0030728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	175	671	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.255733597008047	2	FACETS	0.867	0.8	0.936	0.867	0.8	0.936	CLONAL	2	TRUE	0	0.261878977941504	2		671	771	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273278	55273278	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369585356	NA	P-0030728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	90	605	0	ENST00000275493.2:c.3601G>A	p.Ala1201Thr	p.A1201T	ENST00000275493	NM_005228.3	1201	Gcg/Acg	28/28	0.135739634148864	5	FACETS	1	0.931	1	0.357	0.316	0.401	INDETERMINATE	1	TRUE	2	0.261878977941504	5		605	894	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261243	16261243	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	97	598	0	ENST00000375759.3:c.8508G>C	p.Gln2836His	p.Q2836H	ENST00000375759	NM_015001.2	2836	caG/caC	11/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.261878977941504	2		598	571	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965122	15965122	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	64	454	0	ENST00000268712.3:c.5474T>C	p.Val1825Ala	p.V1825A	ENST00000268712	NM_006311.3	1825	gTg/gCg	37/46	0.255733597008047	2	FACETS	0.981	0.851	1	0.491	0.425	0.561	CLONAL	1	TRUE	0	0.261878977941504	2		454	498	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19261517	19261518	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0030728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	117	636	0	ENST00000162023.5:c.27_28del	p.Arg10HisfsTer24	p.R10Hfs*24	ENST00000162023		9	tcCCgc/tcgc	6/13	0.255733597008047	2	FACETS	0.948	0.853	1	0.474	0.426	0.524	CLONAL	1	TRUE	0	0.261878977941504	2		636	943	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460396	149460396	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	93	607	0	ENST00000286301.3:c.241A>T	p.Thr81Ser	p.T81S	ENST00000286301	NM_005211.3	81	Acc/Tcc	3/22	0.255733597008047	2	FACETS	1	0.916	1	0.518	0.46	0.579	CLONAL	1	TRUE	0	0.261878977941504	2		607	686	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044916	47044916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	104	806	0	ENST00000377604.3:c.2242G>A	p.Glu748Lys	p.E748K	ENST00000377604	NM_001204468.1	748	Gag/Aag	20/24	0.133078206233443	5	FACETS	1	0.953	1			1	INDETERMINATE	1	TRUE	NA	0.261878977941504	5		806	988	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720805	89720808	+	frameshift_variant	Frame_Shift_Del	DEL	CTTT	CTTT	-	rs398123330	NA	P-0030730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	41	288	0	ENST00000371953.3:c.956_959del	p.Thr319LysfsTer24	p.T319Kfs*24	ENST00000371953	NM_000314.4	319	aCTTTa/aa	8/9	0.128964991268446	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		288	220	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696430	47696430	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	61	673	0	ENST00000347630.2:c.393G>C	p.Trp131Cys	p.W131C	ENST00000347630	NM_001007230.1	131	tgG/tgC	6/11	0.128964991268446	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		673	585	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112593	115112593	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	78	757	0	ENST00000257566.3:c.1147G>T	p.Glu383Ter	p.E383*	ENST00000257566	NM_016569.3	383	Gag/Tag	7/8	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		757	777	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0030732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	536	712	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.513373207340606	6	FACETS	0.985	0.954	1	1	0.996	1	CLONAL	5	TRUE	2	0.513373207340606	6		712	859	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658955	3658955	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	635	476	0	ENST00000294008.3:c.11G>A	p.Ser4Asn	p.S4N	ENST00000294008	NM_032444.2	4	aGt/aAt	2/15	0.513373207340606	8	FACETS	1	0.992	1			1	CLONAL	5	TRUE	NA	0.513373207340606	8		476	1167	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577144	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	307	523	0	ENST00000269305.4:c.794T>A	p.Leu265Gln	p.L265Q	ENST00000269305	NM_001126112.2	265	cTg/cAg	8/11	0.510806402112534	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.513373207340606	2		523	570	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1919962	1919962	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	163	643	0	ENST00000382891.5:c.1022A>G	p.Lys341Arg	p.K341R	ENST00000382891	NM_133335.3	341	aAa/aGa	5/22	0.329429730717959	5	FACETS	1	0.98	1	0.404	0.371	0.439	CLONAL	1	TRUE	2	0.513373207340606	5		643	927	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959938	38959938	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	14	379	0	ENST00000357387.3:c.1994C>A	p.Thr665Lys	p.T665K	ENST00000357387	NM_152756.3	665	aCa/aAa	21/38	0.321300006874011	3	FACETS	0.254	0.183	0.34	0.127	0.091	0.17	SUBCLONAL	1	TRUE	1	0.513373207340606	3		379	270	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0030736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	71	428	1	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	0.417	0.364	0.474	0.417	0.364	0.474	SUBCLONAL	1	TRUE	1	0.625700288769065	2		429	544	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0030736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	221	656	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	0.985	0.921	1	0.985	0.921	1	CLONAL	1	TRUE	1	0.625700288769065	2		656	717	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356171	70356171	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	144	410	0	ENST00000374080.3:c.5066A>G	p.Asp1689Gly	p.D1689G	ENST00000374080		1689	gAt/gGt	37/45	1	1	FACETS	0.54	0.494	0.587	0.54	0.494	0.587	SUBCLONAL	1	TRUE	0	0.625700288769065	1		410	586	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0030737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	172	350	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.755786645446245	2		350	443	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	127	454	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.755786645446245	2		454	297	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359421	118359421	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs781871743	NA	P-0030737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	150	612	0	ENST00000534358.1:c.4425T>G	p.Cys1475Trp	p.C1475W	ENST00000534358	NM_005933.3	1475	tgT/tgG	11/36	1	2	FACETS	0.91	0.84	0.983	0.91	0.84	0.983	CLONAL	1	TRUE	1	0.755786645446245	2		612	436	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0030745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	180	532	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.408563684787784	4	FACETS	0.904	0.837	0.974	0.904	0.837	0.974	CLONAL	2	TRUE	2	0.419209592927697	4		533	674	SUCCESS
APC	324	MSKCC	GRCh37	5	112170652	112170652	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0030745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	111	230	0	ENST00000257430.4:c.1748C>G	p.Ser583Ter	p.S583*	ENST00000257430	NM_000038.5	583	tCa/tGa	15/16	0.419209592927697	2	FACETS	0.82	0.746	0.895	0.82	0.746	0.895	CLONAL	2	TRUE	0	0.419209592927697	2		230	323	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604715	55604715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373152714	NA	P-0030745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	73	237	0	ENST00000288135.5:c.2923G>A	p.Asp975Asn	p.D975N	ENST00000288135	NM_000222.2	975	Gat/Aat	21/21	1	2	FACETS	0.946	0.833	1	0.946	0.833	1	CLONAL	1	TRUE	1	0.419209592927697	2		237	368	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989671	68989671	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147538692	NA	P-0030745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	101	407	0	ENST00000288368.4:c.1609G>A	p.Val537Ile	p.V537I	ENST00000288368	NM_024870.2	537	Gtt/Att	15/40	0.417084967228796	3	FACETS	0.878	0.785	0.976	0.439	0.392	0.488	CLONAL	1	TRUE	1	0.419209592927697	3		407	664	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710518	114710518	+	start_lost	Translation_Start_Site	SNP	G	G	T	novel	NA	P-0030745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	119	252	0	ENST00000543371.1:c.3G>T	p.Met1?	p.M1?	ENST00000543371	NM_001198531.1	1	atG/atT	1/14	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.419209592927697	2		252	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0030745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	233	352	0	ENST00000269305.4:c.375+1G>C		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.270373888995621	2	FACETS	0.905	0.85	0.961	0.905	0.85	0.961	CLONAL	2	TRUE	0	0.419209592927697	2		352	614	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0030747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	362	505	1	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.674954799195038	1	FACETS	0.995	0.952	1	0.995	0.952	1	CLONAL	1	TRUE	0	0.674954799195038	1		506	714	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692902	89692902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909218	NA	P-0030747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	203	355	0	ENST00000371953.3:c.386G>A	p.Gly129Glu	p.G129E	ENST00000371953	NM_000314.4	129	gGa/gAa	5/9	0.674954799195038	1	FACETS	0.942	0.886	0.999	0.942	0.886	0.999	CLONAL	1	TRUE	0	0.674954799195038	1		355	423	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271491	26271491	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	143	276	0	ENST00000305910.3:c.122G>C	p.Arg41Pro	p.R41P	ENST00000305910	NM_003534.2	41	cGc/cCc	1/1	1	2	FACETS	0.879	0.807	0.953	0.879	0.807	0.953	CLONAL	1	TRUE	1	0.674954799195038	2		276	482	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263421	123263421	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	206	296	0	ENST00000358487.5:c.1322A>G	p.Asn441Ser	p.N441S	ENST00000358487	NM_000141.4	441	aAc/aGc	10/18	0.674954799195038	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.674954799195038	1		296	382	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416557	49416557	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0030747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	195	356	0	ENST00000301067.7:c.16154C>G	p.Ser5385Ter	p.S5385*	ENST00000301067	NM_003482.3	5385	tCa/tGa	51/54	1	2	FACETS	0.801	0.744	0.86	0.801	0.744	0.86	CLONAL	1	TRUE	1	0.674954799195038	2		356	721	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425755	49425755	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	282	487	0	ENST00000301067.7:c.12733G>T	p.Glu4245Ter	p.E4245*	ENST00000301067	NM_003482.3	4245	Gag/Tag	39/54	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.674954799195038	2		487	826	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562258	21562258	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	373	598	0	ENST00000382592.4:c.1661G>T	p.Gly554Val	p.G554V	ENST00000382592	NM_014572.2	554	gGc/gTc	4/8	0.674954799195038	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.674954799195038	1		598	717	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690612	88690612	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	202	321	0	ENST00000360948.2:c.418A>T	p.Thr140Ser	p.T140S	ENST00000360948	NM_001012338.2	140	Acc/Tcc	5/19	1	2	FACETS	0.901	0.839	0.965	0.901	0.839	0.965	CLONAL	1	TRUE	1	0.674954799195038	2		321	664	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158626964	158626964	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	201	339	0	ENST00000263640.3:c.706A>G	p.Ile236Val	p.I236V	ENST00000263640	NM_001105.4	236	Atc/Gtc	7/11	1	2	FACETS	0.929	0.866	0.994	0.929	0.866	0.994	CLONAL	1	TRUE	1	0.674954799195038	2		339	641	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728598	190728599	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0030747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	234	432	1	ENST00000441310.2:c.1986_1987delinsTT	p.Leu662_Ala663delinsPheSer	p.L662_A663delinsFS	ENST00000441310	NM_000534.4	662	ttGGcc/ttTTcc	10/13	1	2	FACETS	0.889	0.832	0.947	0.889	0.832	0.947	CLONAL	1	TRUE	1	0.674954799195038	2		433	780	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436345	52436345	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1451498951	NA	P-0030747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	294	411	0	ENST00000460680.1:c.2149C>T	p.Arg717Trp	p.R717W	ENST00000460680	NM_004656.3	717	Cgg/Tgg	17/17	0.668639065430956	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.674954799195038	1		411	540	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561896	55561896	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs867439564	NA	P-0030747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	128	199	0	ENST00000288135.5:c.286A>G	p.Thr96Ala	p.T96A	ENST00000288135	NM_000222.2	96	Acg/Gcg	2/21	1	2	FACETS	0.951	0.87	1	0.951	0.87	1	CLONAL	1	TRUE	1	0.674954799195038	2		199	399	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539912	187539912	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	209	255	0	ENST00000441802.2:c.7828G>T	p.Ala2610Ser	p.A2610S	ENST00000441802	NM_005245.3	2610	Gct/Tct	10/27	0.674954799195038	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.674954799195038	1		255	395	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662752	117662752	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	140	246	0	ENST00000368508.3:c.4713C>G	p.Asp1571Glu	p.D1571E	ENST00000368508	NM_002944.2	1571	gaC/gaG	29/43	1	2	FACETS	0.945	0.868	1	0.945	0.868	1	CLONAL	1	TRUE	1	0.674954799195038	2		246	439	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481581	40481581	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	209	383	0	ENST00000264657.5:c.1224C>G	p.Phe408Leu	p.F408L	ENST00000264657	NM_139276.2	408	ttC/ttG	13/24	0.117163607574172	5	FACETS	1	0.985	1			1	INDETERMINATE	2	TRUE	NA	0.436127596982275	5		383	660	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289247	33289247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1455644209	NA	P-0030748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	117	369	1	ENST00000374542.5:c.305C>T	p.Ser102Leu	p.S102L	ENST00000374542	NM_001141970.1	102	tCg/tTg	3/8	0.436127596982275	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.436127596982275	1		370	413	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332548	65332548	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0030748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	75	197	0	ENST00000342505.4:c.990+1G>A		p.X330_splice	ENST00000342505	NM_002227.2	330			1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.436127596982275	2		197	337	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406246	406246	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	250	353	0	ENST00000399788.2:c.4195G>C	p.Glu1399Gln	p.E1399Q	ENST00000399788	NM_001042603.1	1399	Gag/Cag	25/28	0.138818334207194	6	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.436127596982275	6		353	914	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917504	178917504	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	62	286	0	ENST00000263967.3:c.379G>A	p.Glu127Lys	p.E127K	ENST00000263967	NM_006218.2	127	Gaa/Aaa	3/21	1	2	FACETS	0.817	0.71	0.932	0.817	0.71	0.932	CLONAL	1	TRUE	1	0.436127596982275	2		286	348	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123011	5123011	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	30	232	0	ENST00000381652.3:c.3067C>G	p.Pro1023Ala	p.P1023A	ENST00000381652	NM_004972.3	1023	Cca/Gca	23/25	0.436127596982275	1	FACETS	0.384	0.31	0.467	0.384	0.31	0.467	SUBCLONAL	1	TRUE	0	0.436127596982275	1		232	280	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0030749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	98	546	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.345755798920955	3	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	1	0.345755798920955	3		546	320	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876659675	NA	P-0030749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	153	550	0	ENST00000269305.4:c.764T>A	p.Ile255Asn	p.I255N	ENST00000269305	NM_001126112.2	255	aTc/aAc	7/11	0.302468147650597	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.345755798920955	2		550	424	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374365	31374365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768468807	NA	P-0030749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	52	420	0	ENST00000328111.2:c.364C>T	p.Arg122Cys	p.R122C	ENST00000328111	NM_006892.3	122	Cgt/Tgt	5/23	0.314455925072104	3	FACETS	0.834	0.712	0.968	0.417	0.356	0.484	CLONAL	1	TRUE	1	0.345755798920955	3		420	423	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881339	111881340	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGAT	novel	NA	P-0030750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	110	281	0	ENST00000393256.3:c.18_21dup	p.Val8Ter	p.V8*	ENST00000393256	NM_006538.4	6	tct/tcTGATt	2/4	1	2	FACETS	0.394	0.354	0.436	0.394	0.354	0.436	SUBCLONAL	1	TRUE	1	0.848905456830568	2		281	658	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119634935	119634935	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	188	221	0	ENST00000316626.5:c.564G>C	p.Leu188Phe	p.L188F	ENST00000316626		188	ttG/ttC	5/12	NA	2	FACETS	0.904	0.843	0.966			1	INDETERMINATE	1	TRUE	NA	0.848905456830568	2		221	490	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522635	106522635	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	224	270	0	ENST00000359195.3:c.2612C>A	p.Ser871Ter	p.S871*	ENST00000359195	NM_002649.2	871	tCa/tAa	7/11	NA	2	FACETS	0.814	0.763	0.867			1	INDETERMINATE	1	TRUE	NA	0.848905456830568	2		270	648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0030753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	407	485	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA	2	FACETS	0.932	0.897	0.966			1	INDETERMINATE	2	TRUE	NA	0.649935788066312	2		485	672	SUCCESS
APC	324	MSKCC	GRCh37	5	112175174	112175174	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	65	233	0	ENST00000257430.4:c.3883G>T	p.Glu1295Ter	p.E1295*	ENST00000257430	NM_000038.5	1295	Gaa/Taa	16/16	0.61401467578926	2	FACETS	0.833	0.75	0.916	0.833	0.75	0.916	CLONAL	2	TRUE	0	0.649935788066312	2		233	120	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109888	115109888	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	251	467	2	ENST00000257566.3:c.1990G>T	p.Ala664Ser	p.A664S	ENST00000257566	NM_016569.3	664	Gcg/Tcg	8/8	0.0619879197559681	4	FACETS	0.934	0.879	0.99	0.934	0.879	0.99	INDETERMINATE	2	TRUE	2	0.649935788066312	4		469	682	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117789	70117789	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	241	476	0	ENST00000245479.2:c.257G>A	p.Trp86Ter	p.W86*	ENST00000245479	NM_000346.3	86	tGg/tAg	1/3	0.61401467578926	2	FACETS	1	0.989	1	0.605	0.569	0.641	CLONAL	1	TRUE	0	0.649935788066312	2		476	613	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183595	185183595	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0030753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	141	313	0	ENST00000265026.3:c.1449C>G	p.Tyr483Ter	p.Y483*	ENST00000265026	NM_004721.4	483	taC/taG	9/14	0.640815557918314	2	FACETS	0.982	0.902	1	0.491	0.451	0.532	CLONAL	1	TRUE	0	0.649935788066312	2		313	442	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182032	38182032	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	56	363	0	ENST00000396334.3:c.656C>G	p.Ser219Cys	p.S219C	ENST00000396334	NM_002468.4	219	tCt/tGt	3/5	1	2	FACETS	0.936	0.803	1	0.936	0.803	1	CLONAL	1	TRUE	1	0.23	2		363	520	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337696	73337696	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	27	170	0	ENST00000377767.4:c.2020G>C	p.Val674Leu	p.V674L	ENST00000377767	NM_014953.3	674	Gtt/Ctt	16/21	1	2	FACETS	0.745	0.594	0.918	0.745	0.594	0.918	CLONAL	1	TRUE	1	0.23	2		170	315	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30061051	30061052	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0030755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	63	297	0	ENST00000338641.4:c.884_885insTT	p.Ile296Ter	p.I296*	ENST00000338641	NM_000268.3	295	ctg/cTTtg	9/16	0.281684905342474	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.23	1		297	398	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129616	47129616	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	71	310	0	ENST00000409792.3:c.5264T>G	p.Leu1755Arg	p.L1755R	ENST00000409792	NM_014159.6	1755	cTg/cGg	10/21	0.264171017760222	1	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	0	0.23	1		310	516	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325871	65325873	+	missense_variant	Missense_Mutation	TNP	TGC	TGC	AAA	novel	NA	P-0030756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	236	411	1	ENST00000342505.4:c.1249_1251delinsTTT	p.Ala417Phe	p.A417F	ENST00000342505	NM_002227.2	417	GCA/TTT	9/25	0.219527666717678	3	FACETS	0.959	0.901	1	0.64	0.6	0.679	INDETERMINATE	2	TRUE	0	0.471251878837366	3		412	645	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622425	28622425	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	142	298	1	ENST00000241453.7:c.1192G>A	p.Asp398Asn	p.D398N	ENST00000241453	NM_004119.2	398	Gat/Aat	9/24	1	2	FACETS	0.942	0.869	1	0.942	0.869	1	CLONAL	1	TRUE	1	0.806237803016131	2		299	374	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178643	56178643	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	156	190	0	ENST00000399503.3:c.3617del	p.Pro1206LeufsTer39	p.P1206Lfs*39	ENST00000399503	NM_005921.1	1206	Cct/ct	14/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.806237803016131	2		190	339	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061463	38061463	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	170	341	0	ENST00000250448.2:c.526A>T	p.Ile176Phe	p.I176F	ENST00000250448	NM_004496.3	176	Atc/Ttc	2/2	1	2	FACETS	0.901	0.836	0.967	0.901	0.836	0.967	CLONAL	1	TRUE	1	0.806237803016131	2		341	468	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570177	95570177	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	144	262	0	ENST00000393063.1:c.3556A>G	p.Asn1186Asp	p.N1186D	ENST00000393063	NM_030621.3	1186	Aat/Gat	22/28	1	2	FACETS	0.96	0.887	1	0.96	0.887	1	CLONAL	1	TRUE	1	0.806237803016131	2		262	372	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835736	68835736	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	252	408	0	ENST00000261769.5:c.327del	p.Lys109AsnfsTer8	p.K109Nfs*8	ENST00000261769	NM_004360.3	109	aaG/aa	3/16	0.806237803016131	1	FACETS	0.969	0.926	1	0.969	0.926	1	CLONAL	1	TRUE	0	0.806237803016131	1		408	385	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0030758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	187	429	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	0.772385244024956	2		429	464	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130342	2130342	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	90	479	0	ENST00000219476.3:c.3574C>A	p.Gln1192Lys	p.Q1192K	ENST00000219476	NM_000548.3	1192	Cag/Aag	30/42	1	2	FACETS	0.351	0.311	0.393	0.351	0.311	0.393	SUBCLONAL	1	TRUE	1	0.772385244024956	2		479	664	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267537	198267537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	123	260	0	ENST00000335508.6:c.1820C>T	p.Ala607Val	p.A607V	ENST00000335508	NM_012433.2	607	gCt/gTt	14/25	1	2	FACETS	0.887	0.811	0.965	0.887	0.811	0.965	CLONAL	1	TRUE	1	0.772385244024956	2		260	359	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0030768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	167	532	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.35920871657042	2	FACETS	0.899	0.833	0.966	0.899	0.833	0.966	CLONAL	2	TRUE	0	0.383941856769115	2		533	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0030768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	270	578	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.315668719423784	2	FACETS	0.869	0.818	0.921	0.869	0.818	0.921	CLONAL	2	TRUE	0	0.383941856769115	2		578	809	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0030768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	25	241	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.177892996369562	2	FACETS	0.312	0.245	0.388	0.156	0.122	0.194	INDETERMINATE	1	TRUE	0	0.383941856769115	2		241	418	SUCCESS
APC	324	MSKCC	GRCh37	5	112175648	112175648	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	110	332	0	ENST00000257430.4:c.4358del	p.Pro1453LeufsTer20	p.P1453Lfs*20	ENST00000257430	NM_000038.5	1453	Cct/ct	16/16	0.177892996369562	2	FACETS	1	0.972	1	0.603	0.545	0.664	INDETERMINATE	1	TRUE	0	0.383941856769115	2		332	475	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198843	67198843	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	42	331	0	ENST00000312629.5:c.314A>C	p.Lys105Thr	p.K105T	ENST00000312629	NM_003952.2	105	aAa/aCa	5/15	1	2	FACETS	0.473	0.394	0.559	0.473	0.394	0.559	SUBCLONAL	1	TRUE	1	0.383941856769115	2		331	463	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939330	76939330	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	171	310	0	ENST00000373344.5:c.1418A>C	p.His473Pro	p.H473P	ENST00000373344	NM_000489.3	473	cAc/cCc	9/35	0.27963051276422	2	FACETS	1	0.977	1			1	CLONAL	2	TRUE	NA	0.383941856769115	2		310	401	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0030773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	109	569	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.437899747529406	1	FACETS	0.815	0.736	0.898	0.815	0.736	0.898	CLONAL	1	TRUE	0	0.446553744589537	1		569	465	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0030773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	103	426	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	1	2	FACETS	0.919	0.826	1	0.919	0.826	1	CLONAL	1	TRUE	1	0.446553744589537	2		426	502	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575675	48575676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	77	381	0	ENST00000342988.3:c.437dup	p.Leu146PhefsTer6	p.L146Ffs*6	ENST00000342988	NM_005359.5	145	-/T	4/12	0.437899747529406	1	FACETS	0.971	0.862	1	0.971	0.862	1	CLONAL	1	TRUE	0	0.446553744589537	1		381	276	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799021	42799021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1171990316	NA	P-0030773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	309	768	0	ENST00000575354.2:c.4505C>T	p.Pro1502Leu	p.P1502L	ENST00000575354	NM_015125.3	1502	cCc/cTc	20/20	0.446553744589537	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.446553744589537	1		768	921	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799306	42799306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	115	413	1	ENST00000575354.2:c.4790C>T	p.Pro1597Leu	p.P1597L	ENST00000575354	NM_015125.3	1597	cCa/cTa	20/20	0.446553744589537	1	FACETS	0.953	0.865	1	0.953	0.865	1	CLONAL	1	TRUE	0	0.446553744589537	1		414	420	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971155	21971156	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	A	novel	NA	P-0030773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	107	302	0	ENST00000304494.5:c.202_203delinsT	p.Ala68TrpfsTer78	p.A68Wfs*78	ENST00000304494	NM_000077.4	68	GCg/Tg	2/3	0.342283396031038	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.446553744589537	1		302	333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0030775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	451	590	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.70427380631922	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.70427380631922	1		590	716	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0030775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	169	241	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.350315395795628	1	FACETS	0.791	0.737	0.846	0.791	0.737	0.846	INDETERMINATE	1	TRUE	0	0.70427380631922	1		241	393	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0030775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	118	334	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.70427380631922	2		334	290	SUCCESS
APC	324	MSKCC	GRCh37	5	112175513	112175513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	98	258	0	ENST00000257430.4:c.4222G>T	p.Glu1408Ter	p.E1408*	ENST00000257430	NM_000038.5	1408	Gaa/Taa	16/16	0.350315395795628	1	FACETS	0.485	0.436	0.536	0.485	0.436	0.536	INDETERMINATE	1	TRUE	0	0.70427380631922	1		258	372	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587780070	NA	P-0030778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	220	458	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	0.56537241005591	2		458	755	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2137898	2137898	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45483392	NA	P-0030778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	291	530	1	ENST00000219476.3:c.5024C>T	p.Pro1675Leu	p.P1675L	ENST00000219476	NM_000548.3	1675	cCg/cTg	39/42	0.56537241005591	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.56537241005591	1		531	686	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574642	64574653	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTACTGACCTT	TCTACTGACCTT	-	novel	NA	P-0030778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	227	438	0	ENST00000312049.6:c.822_824+9del		p.X274_splice	ENST00000312049	NM_130799.2	274		5/10	0.56537241005591	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.56537241005591	1		438	574	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244586	46244586	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	207	374	0	ENST00000334344.6:c.2680C>G	p.Gln894Glu	p.Q894E	ENST00000334344	NM_152641.2	894	Cag/Gag	15/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.56537241005591	2		374	691	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820810	3820810	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	338	722	0	ENST00000262367.5:c.2641C>T	p.Gln881Ter	p.Q881*	ENST00000262367	NM_004380.2	881	Cag/Tag	14/31	0.56537241005591	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.56537241005591	1		722	819	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980596	1980596	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1379056879	NA	P-0030778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	225	446	0	ENST00000382891.5:c.4058G>A	p.Arg1353Gln	p.R1353Q	ENST00000382891	NM_133335.3	1353	cGg/cAg	22/22	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.56537241005591	2		446	764	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750823	57750823	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	159	328	0	ENST00000274289.3:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000274289	NM_006622.3	594	gAt/gGt	13/14	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.56537241005591	2		328	555	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288796	33288805	+	frameshift_variant	Frame_Shift_Del	DEL	GACACGGCCG	GACACGGCCG	-	novel	NA	P-0030778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	134	312	0	ENST00000374542.5:c.747_756del	p.Gly250Ter	p.G250*	ENST00000374542	NM_001141970.1	249	acCGGCCGTGTC/ac	3/8	0.56537241005591	1	FACETS	0.81	0.742	0.879	0.81	0.742	0.879	CLONAL	1	TRUE	0	0.56537241005591	1		312	420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0030779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	513	663	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.707093030772862	2	FACETS	0.938	0.911	0.966	0.938	0.911	0.966	CLONAL	2	TRUE	0	0.741696496586139	2		663	737	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907246	32907252	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTTTG	CTGTTTG	-	novel	NA	P-0030779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	162	367	0	ENST00000380152.3:c.1633_1639del	p.Val545HisfsTer11	p.V545Hfs*11	ENST00000380152		544	aCTGTTTGc/ac	10/27	0.707093030772862	2	FACETS	1	0.99	1	0.689	0.644	0.734	CLONAL	1	TRUE	0	0.741696496586139	2		367	317	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911147	29911147	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	213	451	0	ENST00000376809.5:c.446C>A	p.Ala149Asp	p.A149D	ENST00000376809	NM_002116.7	149	gCc/gAc	3/8	0.590254894715309	3	FACETS	0.818	0.769	0.868	0.818	0.769	0.868	CLONAL	2	TRUE	1	0.741696496586139	3		451	481	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934571	NA	P-0030780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	54	422	0	ENST00000269305.4:c.747G>C	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agC	7/11	0.16265765742248	0	FACETS	1	0.906	1			1	CLONAL	1	TRUE	0	0.219344932590173	0		422	358	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938911	76938911	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	70	497	0	ENST00000373344.5:c.1837G>T	p.Asp613Tyr	p.D613Y	ENST00000373344	NM_000489.3	613	Gat/Tat	9/35	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.219344932590173	2		497	616	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625144	69625144	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	108	646	0	ENST00000334134.2:c.649C>A	p.Pro217Thr	p.P217T	ENST00000334134	NM_005247.2	217	Ccg/Acg	3/3	1	2	FACETS	0.853	0.765	0.947	0.853	0.765	0.947	CLONAL	1	TRUE	1	0.291060848512869	2		646	870	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348803	11348803	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	44	225	0	ENST00000332029.2:c.533G>T	p.Cys178Phe	p.C178F	ENST00000332029	NM_003745.1	178	tGc/tTc	2/2	0.291060848512869	1	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	0	0.291060848512869	1		225	239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0030783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	103	511	0	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.291060848512869	1	FACETS	0.969	0.869	1	0.969	0.869	1	CLONAL	1	TRUE	0	0.291060848512869	1		511	624	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533351	29533351	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555611590	NA	P-0030783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	31	290	0	ENST00000356175.3:c.1354C>T	p.Gln452Ter	p.Q452*	ENST00000356175	NM_000267.3	452	Caa/Taa	12/57	0.291060848512869	1	FACETS	0.613	0.497	0.743	0.613	0.497	0.743	SUBCLONAL	1	TRUE	0	0.291060848512869	1		290	297	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602314	10602314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	147	758	0	ENST00000171111.5:c.1264G>A	p.Asp422Asn	p.D422N	ENST00000171111	NM_203500.1	422	Gat/Aat	3/6	0.291060848512869	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.291060848512869	1		758	827	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402752	20402752	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs767586218	NA	P-0030783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	22	382	0	ENST00000346618.3:c.289A>G	p.Ser97Gly	p.S97G	ENST00000346618	NM_001949.4	97	Agc/Ggc	1/7	0.291060848512869	1	FACETS	0.336	0.259	0.424	0.336	0.259	0.424	SUBCLONAL	1	TRUE	0	0.291060848512869	1		382	385	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121913370	NA	P-0030783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	48	333	0	ENST00000288602.6:c.1742A>G	p.Asn581Ser	p.N581S	ENST00000288602	NM_004333.4	581	aAt/aGt	15/18	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.291060848512869	2		333	317	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69050740	69050740	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	49	370	0	ENST00000288368.4:c.4075C>A	p.Pro1359Thr	p.P1359T	ENST00000288368	NM_024870.2	1359	Cct/Act	33/40	0.152306461795672	3	FACETS	0.962	0.817	1	0.481	0.408	0.561	INDETERMINATE	1	TRUE	1	0.291060848512869	3		370	401	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971078	21971087	+	frameshift_variant	Frame_Shift_Del	DEL	GCGTGTCCAG	GCGTGTCCAG	-	novel	NA	P-0030783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	81	446	0	ENST00000304494.5:c.271_280del	p.Leu91TrpfsTer52	p.L91Wfs*52	ENST00000304494	NM_000077.4	91	CTGGACACGCtg/tg	2/3	0.291060848512869	1	FACETS	0.987	0.872	1	0.987	0.872	1	CLONAL	1	TRUE	0	0.291060848512869	1		446	482	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99460015	99460015	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	102	526	0	ENST00000268035.6:c.2111A>C	p.Lys704Thr	p.K704T	ENST00000268035	NM_000875.3	704	aAa/aCa	10/21	0.116834826174686	3	FACETS	0.948	0.848	1			1	INDETERMINATE	1	TRUE	NA	0.360973638702983	3		526	704	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729821	47729821	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	253	723	0	ENST00000449228.1:c.568G>T	p.Glu190Ter	p.E190*	ENST00000449228	NM_001127240.2	190	Gag/Tag	3/4	0.342003483660475	3	FACETS	0.936	0.878	0.996	0.624	0.585	0.664	CLONAL	2	TRUE	0	0.360973638702983	3		723	884	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0030788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	152	495	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	NA	2	FACETS	0.836	0.766	0.91			1	INDETERMINATE	1	TRUE	NA	0.472196353795409	2		495	770	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691039	NA	P-0030788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	203	612	0	ENST00000269305.4:c.919+1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.472196353795409	1	FACETS	0.948	0.882	1	0.948	0.882	1	CLONAL	1	TRUE	0	0.472196353795409	1		612	693	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877430	40877430	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	146	511	0	ENST00000373198.4:c.2266C>A	p.Pro756Thr	p.P756T	ENST00000373198	NM_133170.3	756	Cca/Aca	15/32	1	2	FACETS	0.782	0.714	0.853	0.782	0.714	0.853	SUBCLONAL	1	TRUE	1	0.472196353795409	2		511	791	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190890	185190890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs979026761	NA	P-0030788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	222	661	1	ENST00000265026.3:c.1771C>T	p.Arg591Cys	p.R591C	ENST00000265026	NM_004721.4	591	Cgc/Tgc	11/14	1	2	FACETS	0.806	0.749	0.865	0.806	0.749	0.865	CLONAL	1	TRUE	1	0.472196353795409	2		662	1167	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144788	58144788	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	180	481	0	ENST00000257904.6:c.440T>C	p.Leu147Pro	p.L147P	ENST00000257904	NM_000075.3	147	cTg/cCg	4/8	0.472196353795409	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.472196353795409	1		481	582	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349079	89349079	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	58	790	0	ENST00000301030.4:c.3871G>T	p.Glu1291Ter	p.E1291*	ENST00000301030	NM_001256183.1	1291	Gag/Tag	9/13	0.472196353795409	1	FACETS	0.184	0.157	0.213	0.184	0.157	0.213	SUBCLONAL	1	TRUE	0	0.472196353795409	1		790	1021	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591143	67591155	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AATACTTGATGTA	AATACTTGATGTA	-	novel	NA	P-0030788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	28	343	0	ENST00000274335.5:c.1737_1745+4del		p.X579_splice	ENST00000274335		579		12/15	0.472196353795409	1	FACETS	0.2	0.159	0.246	0.2	0.159	0.246	SUBCLONAL	1	TRUE	0	0.472196353795409	1		343	454	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404320	139404322	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0030788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	64	700	0	ENST00000277541.6:c.2832_2834del	p.Glu944del	p.E944del	ENST00000277541	NM_017617.3	944	gaGGAc/gac	18/34	0.438422839673286	1	FACETS	0.228	0.197	0.262	0.228	0.197	0.262	SUBCLONAL	1	TRUE	0	0.472196353795409	1		700	908	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918966	76918966	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782802388	NA	P-0030788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	152	502	1	ENST00000373344.5:c.4025G>A	p.Arg1342Gln	p.R1342Q	ENST00000373344	NM_000489.3	1342	cGg/cAg	12/35	1	2	FACETS	0.889	0.815	0.967	0.889	0.815	0.967	CLONAL	1	TRUE	1	0.472196353795409	2		503	724	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2221594	2221594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766294780	NA	P-0030791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	315	847	0	ENST00000326181.6:c.463G>A	p.Ala155Thr	p.A155T	ENST00000326181	NM_032271.2	155	Gcc/Acc	7/21	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.787630020684244	2		847	789	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579359	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0030791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	634	858	0	ENST00000269305.4:c.327_328dup	p.Arg110ProfsTer14	p.R110Pfs*14	ENST00000269305	NM_001126112.2	110	cgt/cCCgt	4/11	0.778579788274109	2	FACETS	0.946	0.923	0.968	0.946	0.923	0.968	CLONAL	2	TRUE	0	0.787630020684244	2		858	851	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258831	16258831	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	528	787	0	ENST00000375759.3:c.6096del	p.Ala2033LeufsTer31	p.A2033Lfs*31	ENST00000375759	NM_015001.2	2032	gcT/gc	11/15	0.77865687461574	3	FACETS	0.936	0.903	0.97	0.936	0.903	0.97	CLONAL	2	TRUE	1	0.787630020684244	3		787	998	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205807	108205807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782719	NA	P-0030792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	123	509	0	ENST00000278616.4:c.8122G>A	p.Asp2708Asn	p.D2708N	ENST00000278616	NM_000051.3	2708	Gat/Aat	55/63	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.287138345780369	2		509	817	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104377138	104377138	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	78	719	1	ENST00000369902.3:c.1249T>G	p.Phe417Val	p.F417V	ENST00000369902	NM_016169.3	417	Ttt/Gtt	10/12	1	2	FACETS	0.515	0.451	0.585	0.515	0.451	0.585	SUBCLONAL	1	TRUE	1	0.287138345780369	2		720	1054	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054048	42054048	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	83	326	0	ENST00000219905.7:c.7510G>C	p.Gly2504Arg	p.G2504R	ENST00000219905	NM_001164273.1	2504	Ggt/Cgt	21/24	1	2	FACETS	0.951	0.84	1	0.951	0.84	1	CLONAL	1	TRUE	1	0.287138345780369	2		326	608	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0030793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	205	369	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	0.400663160862424	2		369	726	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0030793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	136	556	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.400663160862424	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.400663160862424	1		556	534	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727441	66727441	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519728	NA	P-0030793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	19	458	0	ENST00000307102.5:c.157T>C	p.Phe53Leu	p.F53L	ENST00000307102	NM_002755.3	53	Ttt/Ctt	2/11	0.199458215110671	3	FACETS	0.146	0.11	0.189	0.049	0.036	0.063	INDETERMINATE	1	TRUE	0	0.400663160862424	3		458	781	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	99	398	0	ENST00000256196.4:c.68G>T	p.Gly23Val	p.G23V	ENST00000256196		23	gGc/gTc	1/6	1	2	FACETS	0.848	0.758	0.942	0.848	0.758	0.942	CLONAL	1	TRUE	1	0.400663160862424	2		398	583	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659844	227659844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	136	368	0	ENST00000305123.5:c.3611C>T	p.Pro1204Leu	p.P1204L	ENST00000305123	NM_005544.2	1204	cCc/cTc	1/2	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.400663160862424	2		368	551	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520132	9520132	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs985653551	NA	P-0030793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	107	374	0	ENST00000353224.5:c.2137A>G	p.Met713Val	p.M713V	ENST00000353224	NM_177990.2	713	Atg/Gtg	10/10	1	2	FACETS	0.91	0.818	1	0.91	0.818	1	CLONAL	1	TRUE	1	0.400663160862424	2		374	587	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021682	31021682	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	333	571	2	ENST00000375687.4:c.1681C>T	p.Gln561Ter	p.Q561*	ENST00000375687	NM_015338.5	561	Cag/Tag	12/13	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.864552830172187	2		573	759	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0030801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	78	654	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.228307577272269	0	FACETS	0.76	0.667	0.859			1	SUBCLONAL	1	FALSE	0	0.228307577272269	0		654	694	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139816	55139816	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	58	522	1	ENST00000257290.5:c.1477G>A	p.Val493Met	p.V493M	ENST00000257290	NM_006206.4	493	Gtg/Atg	10/23	1	2	FACETS	0.656	0.563	0.759	0.656	0.563	0.759	SUBCLONAL	1	FALSE	1	0.228307577272269	2		523	774	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310920	123310920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	104	450	1	ENST00000358487.5:c.508C>T	p.Pro170Ser	p.P170S	ENST00000358487	NM_000141.4	170	Cct/Tct	5/18	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.228307577272269	2		451	768	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0030802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	130	594	0	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	0.344109679653154	1	FACETS	0.929	0.846	1	0.929	0.846	1	CLONAL	1	TRUE	0	0.367163939651433	1		594	622	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727454	66727454	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519909	NA	P-0030802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	74	549	0	ENST00000307102.5:c.170A>C	p.Lys57Thr	p.K57T	ENST00000307102	NM_002755.3	57	aAg/aCg	2/11	1	2	FACETS	0.765	0.671	0.866	0.765	0.671	0.866	SUBCLONAL	1	TRUE	1	0.367163939651433	2		549	527	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	81	486	0	ENST00000342988.3:c.1067C>G	p.Pro356Arg	p.P356R	ENST00000342988	NM_005359.5	356	cCt/cGt	9/12	0.28301643519648	1	FACETS	0.892	0.79	0.999	0.892	0.79	0.999	CLONAL	1	TRUE	0	0.367163939651433	1		486	404	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604769	48604769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766833269	NA	P-0030802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	80	519	0	ENST00000342988.3:c.1591C>T	p.Arg531Trp	p.R531W	ENST00000342988	NM_005359.5	531	Cgg/Tgg	12/12	0.28301643519648	1	FACETS	0.929	0.823	1	0.929	0.823	1	CLONAL	1	TRUE	0	0.367163939651433	1		519	383	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413578	32413578	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121907909	NA	P-0030802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	51	493	1	ENST00000332351.3:c.1372C>T	p.Arg458Ter	p.R458*	ENST00000332351	NM_024426.4	458	Cga/Tga	9/10	1	2	FACETS	0.7	0.596	0.813	0.7	0.596	0.813	SUBCLONAL	1	TRUE	1	0.367163939651433	2		494	397	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	153	454	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.289964663786035	2		454	858	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0030803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	277	876	1	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.289964663786035	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.289964663786035	1		877	1497	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268363	46268363	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs191706244	NA	P-0030803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	142	441	0	ENST00000371998.3:c.2750C>T	p.Ser917Leu	p.S917L	ENST00000371998		917	tCa/tTa	15/23	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.289964663786035	2		441	862	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696719	47696719	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	133	423	0	ENST00000347630.2:c.229G>C	p.Asp77His	p.D77H	ENST00000347630	NM_001007230.1	77	Gat/Cat	5/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.289964663786035	2		423	819	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562856	95562856	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	76	340	0	ENST00000393063.1:c.4401C>G	p.Ile1467Met	p.I1467M	ENST00000393063	NM_030621.3	1467	atC/atG	24/28	1	2	FACETS	0.839	0.736	0.949	0.839	0.736	0.949	CLONAL	1	TRUE	1	0.289964663786035	2		340	625	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033906	49033906	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	59	541	0	ENST00000267163.4:c.2043G>A	p.Trp681Ter	p.W681*	ENST00000267163	NM_000321.2	681	tgG/tgA	20/27	0.289964663786035	1	FACETS	0.406	0.348	0.469	0.406	0.348	0.469	SUBCLONAL	1	TRUE	0	0.289964663786035	1		541	857	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870966	12870966	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	112	414	0	ENST00000228872.4:c.193C>T	p.Gln65Ter	p.Q65*	ENST00000228872	NM_004064.3	65	Cag/Tag	1/3	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.289964663786035	2		414	754	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332739	70332739	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	76	520	1	ENST00000373644.4:c.644C>T	p.Pro215Leu	p.P215L	ENST00000373644	NM_030625.2	215	cCt/cTt	2/12	0.289964663786035	1	FACETS	0.535	0.469	0.608	0.535	0.469	0.608	SUBCLONAL	1	TRUE	0	0.289964663786035	1		521	837	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562404	95562404	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0030803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	101	456	0	ENST00000393063.1:c.4853C>G	p.Ser1618Ter	p.S1618*	ENST00000393063	NM_030621.3	1618	tCa/tGa	24/28	1	2	FACETS	0.9	0.804	1	0.9	0.804	1	CLONAL	1	TRUE	1	0.289964663786035	2		456	774	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562907	95562907	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	86	316	0	ENST00000393063.1:c.4350C>G	p.Ile1450Met	p.I1450M	ENST00000393063	NM_030621.3	1450	atC/atG	24/28	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.289964663786035	2		316	593	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042383	42042383	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	185	771	0	ENST00000219905.7:c.6578del	p.Cys2193LeufsTer9	p.C2193Lfs*9	ENST00000219905	NM_001164273.1	2193	tGt/tt	17/24	1	2	FACETS	0.944	0.87	1	0.944	0.87	1	CLONAL	1	TRUE	1	0.289964663786035	2		771	1351	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682823	190682823	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	131	506	0	ENST00000441310.2:c.499G>C	p.Asp167His	p.D167H	ENST00000441310	NM_000534.4	167	Gat/Cat	5/13	1	2	FACETS	0.873	0.791	0.96	0.873	0.791	0.96	CLONAL	1	TRUE	1	0.289964663786035	2		506	1035	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339017	225339017	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	119	549	0	ENST00000264414.4:c.2252G>C	p.Arg751Thr	p.R751T	ENST00000264414	NM_003590.4	751	aGa/aCa	16/16	0.241489554918689	1	FACETS	0.749	0.675	0.827	0.749	0.675	0.827	SUBCLONAL	1	TRUE	0	0.289964663786035	1		549	937	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109415101	109415101	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1280	190	836	1	ENST00000436639.2:c.176C>T	p.Ser59Leu	p.S59L	ENST00000436639	NM_014454.2	59	tCg/tTg	1/10	1	2	FACETS	0.891	0.822	0.965	0.891	0.822	0.965	CLONAL	1	TRUE	1	0.289964663786035	2		837	1470	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109415104	109415104	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1294	191	857	0	ENST00000436639.2:c.173C>T	p.Ser58Phe	p.S58F	ENST00000436639	NM_014454.2	58	tCt/tTt	1/10	1	2	FACETS	0.887	0.818	0.96	0.887	0.818	0.96	CLONAL	1	TRUE	1	0.289964663786035	2		857	1485	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500435	99500435	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	187	777	0	ENST00000268035.6:c.3868C>T	p.Pro1290Ser	p.P1290S	ENST00000268035	NM_000875.3	1290	Ccg/Tcg	21/21	0.401899569323827	1	FACETS	0.866	0.801	0.933	0.866	0.801	0.933	CLONAL	1	TRUE	0	0.408770447179122	1		777	841	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178943755	178943755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200671228	NA	P-0030808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	139	450	1	ENST00000263967.3:c.2422C>T	p.Arg808Trp	p.R808W	ENST00000263967	NM_006218.2	808	Cgg/Tgg	17/21	0.408770447179122	2	FACETS	1	0.953	1	0.533	0.486	0.582	CLONAL	1	TRUE	0	0.408770447179122	2		451	638	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443923	49443924	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0030808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	217	922	0	ENST00000301067.7:c.3446_3447dup	p.Gly1150LysfsTer15	p.G1150Kfs*15	ENST00000301067	NM_003482.3	1149	-/AA	11/54	0.408770447179122	2	FACETS	0.958	0.89	1	0.479	0.445	0.515	CLONAL	1	TRUE	0	0.408770447179122	2		922	1108	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546959	9546959	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	100	442	0	ENST00000353224.5:c.1063G>A	p.Ala355Thr	p.A355T	ENST00000353224	NM_177990.2	355	Gcc/Acc	5/10	0.408770447179122	1	FACETS	0.918	0.825	1	0.918	0.825	1	CLONAL	1	TRUE	0	0.408770447179122	1		442	424	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196889	106196889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	94	409	0	ENST00000380013.4:c.5222C>T	p.Pro1741Leu	p.P1741L	ENST00000380013	NM_001127208.2	1741	cCa/cTa	11/11	0.408770447179122	4	FACETS	0.956	0.851	1	0.319	0.283	0.356	CLONAL	1	TRUE	1	0.408770447179122	4		409	678	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256576	16256576	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	21	552	0	ENST00000375759.3:c.3841del	p.Leu1281TyrfsTer4	p.L1281Yfs*4	ENST00000375759	NM_015001.2	1281	Cta/ta	11/15	1	2	FACETS	0.439	0.338	0.556	0.439	0.338	0.556	SUBCLONAL	1	TRUE	1	0.366613977726981	2		552	261	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640008	3640008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202032197	NA	P-0030809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	24	801	1	ENST00000294008.3:c.3631G>A	p.Glu1211Lys	p.E1211K	ENST00000294008	NM_032444.2	1211	Gaa/Aaa	12/15	0.305164232210443	3	FACETS	0.523	0.411	0.653	0.262	0.205	0.327	SUBCLONAL	1	TRUE	1	0.366613977726981	3		802	296	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878094	151878094	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	40	413	0	ENST00000262189.6:c.6851C>A	p.Ser2284Ter	p.S2284*	ENST00000262189	NM_170606.2	2284	tCa/tAa	36/59	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.366613977726981	2		413	168	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0030811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	154	367	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.282382666113308	3	FACETS	0.933	0.856	1	0.933	0.856	1	CLONAL	2	TRUE	1	0.282382666113308	3		367	667	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0030811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	129	605	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.282382666113308	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.282382666113308	1		607	748	SUCCESS
AR	367	MSKCC	GRCh37	X	66766450	66766450	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	52	168	0	ENST00000374690.3:c.1462C>G	p.Gln488Glu	p.Q488E	ENST00000374690	NM_000044.3	488	Cag/Gag	1/8	1	1	FACETS	0.947	0.822	1	1	0.976	1	CLONAL	2	TRUE	0	0.282382666113308	1		168	167	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509448	149509449	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0030811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	110	623	0	ENST00000261799.4:c.1450dup	p.Glu484GlyfsTer7	p.E484Gfs*7	ENST00000261799	NM_002609.3	484	gag/gGag	10/23	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.282382666113308	2		623	738	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066583	94066583	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	60	430	0	ENST00000369303.4:c.1176G>T	p.Gln392His	p.Q392H	ENST00000369303	NM_004440.3	392	caG/caT	5/17	1	2	FACETS	0.832	0.717	0.956	0.832	0.717	0.956	CLONAL	1	TRUE	1	0.282382666113308	2		430	511	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864341	162864341	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0030811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	31	335	0	ENST00000366898.1:c.171+1G>T		p.X57_splice	ENST00000366898	NM_004562.2	57			0.282382666113308	1	FACETS	0.593	0.48	0.72	0.593	0.48	0.72	SUBCLONAL	1	TRUE	0	0.282382666113308	1		335	318	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393382	139393384	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	novel	NA	P-0030811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	108	640	0	ENST00000277541.6:c.6147_6149del	p.Lys2049del	p.K2049del	ENST00000277541	NM_017617.3	2049	aaGAAc/aac	33/34	0.282382666113308	1	FACETS	0.84	0.754	0.931	0.84	0.754	0.931	CLONAL	1	TRUE	0	0.282382666113308	1		640	782	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514495	NA	P-0030812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	127	686	1	ENST00000269305.4:c.542G>A	p.Arg181His	p.R181H	ENST00000269305	NM_001126112.2	181	cGc/cAc	5/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.395693755663052	2		687	521	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134606	2134606	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs397514977	NA	P-0030812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	196	855	0	ENST00000219476.3:c.4383C>G	p.Tyr1461Ter	p.Y1461*	ENST00000219476	NM_000548.3	1461	taC/taG	34/42	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.395693755663052	2		855	685	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919264	178919264	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	66	287	0	ENST00000263967.3:c.749A>G	p.Tyr250Cys	p.Y250C	ENST00000263967	NM_006218.2	250	tAt/tGt	4/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.395693755663052	2		287	245	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574493	64574493	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	302	626	0	ENST00000312049.6:c.902T>G	p.Leu301Arg	p.L301R	ENST00000312049	NM_130799.2	301	cTc/cGc	6/10	0.826806802912537	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.826806802912537	1		626	422	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389155	31389155	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	316	496	0	ENST00000328111.2:c.2068C>T	p.Arg690Trp	p.R690W	ENST00000328111	NM_006892.3	690	Cgg/Tgg	19/23	0.826806802912537	2	FACETS	1	0.974	1	0.519	0.493	0.546	CLONAL	1	TRUE	0	0.826806802912537	2		496	736	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0030815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	17	270	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	0.210455424443548	3	FACETS	0.757	0.563	0.987	0.378	0.281	0.494	CLONAL	1	TRUE	1	0.12	3		270	397	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0030815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	13	411	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.0934062346421385	3	FACETS	0.477	0.339	0.648	0.239	0.169	0.324	SUBCLONAL	1	TRUE	1	0.12	3		411	481	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0030815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	30	611	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	0.0934062346421385	3	FACETS	1	0.889	1	0.58	0.467	0.709	CLONAL	1	TRUE	1	0.12	3		613	457	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210893	36210893	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	33	686	3	ENST00000222270.7:c.649del	p.Arg217GlyfsTer22	p.R217Gfs*22	ENST00000222270	NM_014727.1	215	aCc/ac	3/37	1	2	FACETS	0.979	0.796	1	0.979	0.796	1	CLONAL	1	TRUE	1	0.12	2		689	562	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164716	36164716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1285485702	NA	P-0030815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	43	579	0	ENST00000300305.3:c.1159G>A	p.Gly387Ser	p.G387S	ENST00000300305		387	Ggc/Agc	8/8	0.0934062346421385	0	FACETS	0.964	0.805	1			1	CLONAL	1	TRUE	0	0.12	0		579	654	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073487	8073487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767822347	NA	P-0030815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	22	341	0	ENST00000377482.5:c.1172C>T	p.Ser391Leu	p.S391L	ENST00000377482	NM_018948.3	391	tCa/tTa	4/4	1	2	FACETS	0.962	0.745	1	0.962	0.745	1	CLONAL	1	TRUE	1	0.12	2		341	381	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727976	78727976	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	17	295	0	ENST00000306801.3:c.821C>T	p.Ala274Val	p.A274V	ENST00000306801	NM_020761.2	274	gCc/gTc	6/34	1	2	FACETS	0.885	0.66	1	0.885	0.66	1	CLONAL	1	TRUE	1	0.12	2		295	320	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141583	202141583	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	28	389	0	ENST00000358485.4:c.871C>A	p.Pro291Thr	p.P291T	ENST00000358485	NM_001080125.1	291	Cct/Act	7/9	0.0934062346421385	3	FACETS	0.885	0.706	1	0.442	0.353	0.546	CLONAL	1	TRUE	1	0.12	3		389	559	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612269	189612269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34713855	NA	P-0030815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	30	327	0	ENST00000264731.3:c.2021G>A	p.Arg674His	p.R674H	ENST00000264731	NM_003722.4	674	cGc/cAc	14/14	0.0934062346421385	3	FACETS	1	0.933	1	0.71	0.573	0.867	CLONAL	1	TRUE	1	0.12	3		327	373	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460435	8460435	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	21	327	0	ENST00000356435.5:c.3851T>C	p.Val1284Ala	p.V1284A	ENST00000356435		1284	gTc/gCc	22/35	1	2	FACETS	0.839	0.645	1	0.839	0.645	1	CLONAL	1	TRUE	1	0.12	2		327	417	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395102	139395102	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1440167765	NA	P-0030815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	26	552	2	ENST00000277541.6:c.5836C>T	p.Arg1946Cys	p.R1946C	ENST00000277541	NM_017617.3	1946	Cgc/Tgc	31/34	1	2	FACETS	0.883	0.698	1	0.883	0.698	1	CLONAL	1	TRUE	1	0.12	2		554	491	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0030816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	64	350	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.174737864629483	3	FACETS	1	0.924	1	0.547	0.475	0.626	CLONAL	1	TRUE	1	0.28	3		350	476	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0030816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	49	367	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.3	0	FACETS	1	0.918	1			1	CLONAL	1	TRUE	0	0.28	0		367	227	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968149	68968149	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	50	516	0	ENST00000288368.4:c.1178G>A	p.Gly393Glu	p.G393E	ENST00000288368	NM_024870.2	393	gGa/gAa	10/40	1	2	FACETS	0.743	0.63	0.865	0.743	0.63	0.865	SUBCLONAL	1	TRUE	1	0.28	2		516	481	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117630083	117630083	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	33	270	0	ENST00000368508.3:c.6443G>A	p.Gly2148Glu	p.G2148E	ENST00000368508	NM_002944.2	2148	gGa/gAa	41/43	1	2	FACETS	0.95	0.778	1	0.95	0.778	1	CLONAL	1	TRUE	1	0.28	2		270	248	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035319	42035319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	42	398	1	ENST00000219905.7:c.5161C>T	p.Pro1721Ser	p.P1721S	ENST00000219905	NM_001164273.1	1721	Cct/Tct	15/24	1	2	FACETS	0.826	0.692	0.975	0.826	0.692	0.975	CLONAL	1	TRUE	1	0.28	2		399	363	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876527	35876527	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	19	441	0	ENST00000303115.3:c.1319C>T	p.Ser440Phe	p.S440F	ENST00000303115	NM_002185.3	440	tCc/tTc	8/8	1	2	FACETS	0.429	0.326	0.552	0.429	0.326	0.552	SUBCLONAL	1	TRUE	1	0.28	2		441	316	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0030823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	309	338	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.174046156683037	5	FACETS	1	0.982	1			1	INDETERMINATE	3	TRUE	NA	0.532226214534976	5		338	653	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0030823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	16	712	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	0.532226214534976	1	FACETS	0.084	0.061	0.111	0.084	0.061	0.111	SUBCLONAL	1	TRUE	0	0.532226214534976	1		712	528	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184558	11184558	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	39	492	0	ENST00000361445.4:c.6659T>G	p.Leu2220Arg	p.L2220R	ENST00000361445	NM_004958.3	2220	cTc/cGc	47/58	0.532226214534976	1	FACETS	0.263	0.218	0.313	0.263	0.218	0.313	SUBCLONAL	1	TRUE	0	0.532226214534976	1		492	409	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528484	29528484	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	143	531	1	ENST00000356175.3:c.1241T>A	p.Leu414His	p.L414H	ENST00000356175	NM_000267.3	414	cTc/cAc	11/57	0.532226214534976	1	FACETS	0.909	0.836	0.983	0.909	0.836	0.983	CLONAL	1	TRUE	0	0.532226214534976	1		532	434	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505038	186505038	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	84	273	0	ENST00000323963.5:c.894C>A	p.Phe298Leu	p.F298L	ENST00000323963		298	ttC/ttA	8/11	1	2	FACETS	0.884	0.787	0.987	0.884	0.787	0.987	CLONAL	1	TRUE	1	0.532226214534976	2		273	357	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938673	76938676	+	frameshift_variant	Frame_Shift_Del	DEL	GATA	GATA	-	novel	NA	P-0030823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	158	571	0	ENST00000373344.5:c.2072_2075del	p.Leu691GlnfsTer4	p.L691Qfs*4	ENST00000373344	NM_000489.3	691	cTATCa/ca	9/35	1	2	FACETS	0.938	0.863	1	0.938	0.863	1	CLONAL	1	TRUE	1	0.532226214534976	2		571	633	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0030824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	55	427	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	0.16	2		427	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578528	7578528	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	73	810	0	ENST00000269305.4:c.402T>G	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	ttT/ttG	5/11	1	2	FACETS	0.986	0.861	1	0.986	0.861	1	CLONAL	1	TRUE	1	0.16	2		810	925	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686407	30686424	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTAAGCAAGCCTTTTAA	GGTAAGCAAGCCTTTTAA	-	novel	NA	P-0030824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	24	290	0	ENST00000295754.5:c.263+1_263+18del		p.X88_splice	ENST00000295754	NM_003242.5	88		2/7	1	2	FACETS	0.867	0.68	1	0.867	0.68	1	CLONAL	1	TRUE	1	0.16	2		290	346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0030826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	202	485	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.363306305298075	2	FACETS	0.899	0.84	0.959	0.899	0.84	0.959	CLONAL	2	FALSE	0	0.411599962323212	2		485	546	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0030826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	215	546	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.775	0.724	0.827	1	0.992	1	SUBCLONAL	2	FALSE	1	0.411599962323212	2		546	674	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604764	48604765	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs377767376	NA	P-0030826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	159	459	0	ENST00000342988.3:c.1587dup	p.His530ThrfsTer47	p.H530Tfs*47	ENST00000342988	NM_005359.5	529	tta/ttAa	12/12	0.35889827940903	2	FACETS	0.836	0.773	0.901	0.836	0.773	0.901	CLONAL	2	FALSE	0	0.411599962323212	2		459	462	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665185	138665185	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	107	672	0	ENST00000330315.3:c.380A>G	p.Tyr127Cys	p.Y127C	ENST00000330315	NM_023067.3	127	tAc/tGc	1/1	1	2	FACETS	0.922	0.829	1	0.922	0.829	1	CLONAL	1	FALSE	1	0.411599962323212	2		672	564	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974735	21974735	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	51	327	0	ENST00000304494.5:c.92del	p.Leu31ArgfsTer22	p.L31Rfs*22	ENST00000304494	NM_000077.4	31	cTg/cg	1/3	0.411599962323212	1	FACETS	0.891	0.766	1	0.891	0.766	1	CLONAL	1	FALSE	0	0.411599962323212	1		327	221	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0030832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	129	283	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.707675453960872	2		283	302	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888189	112888189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507511	NA	P-0030832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	176	632	0	ENST00000351677.2:c.205G>A	p.Glu69Lys	p.E69K	ENST00000351677	NM_002834.3	69	Gag/Aag	3/16	NA	2	FACETS	1	0.972	1			1	INDETERMINATE	1	TRUE	NA	0.707675453960872	2		632	458	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0030832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	130	227	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.707675453960872	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.707675453960872	1		227	227	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967614	26967614	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	42	405	0	ENST00000381527.3:c.757G>T	p.Asp253Tyr	p.D253Y	ENST00000381527	NM_001260.1	253	Gac/Tac	7/13	0.707675453960872	1	FACETS	0.298	0.251	0.351	0.298	0.251	0.351	SUBCLONAL	1	TRUE	0	0.707675453960872	1		405	257	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564437	86564437	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	158	562	0	ENST00000274376.6:c.169G>T	p.Val57Leu	p.V57L	ENST00000274376	NM_002890.2	57	Gtg/Ttg	1/25	1	2	FACETS	0.956	0.884	1	0.956	0.884	1	CLONAL	1	TRUE	1	0.707675453960872	2		562	467	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0030835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	168	286	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.633479197440161	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.644553257177707	1		286	343	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	280	372	1	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.644553257177707	2		373	805	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057877	27057877	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	338	826	1	ENST00000324856.7:c.1585C>T	p.Gln529Ter	p.Q529*	ENST00000324856	NM_006015.4	529	Cag/Tag	3/20	0.644553257177707	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.644553257177707	1		827	675	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922156	100922156	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1165724245	NA	P-0030835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	102	429	0	ENST00000325455.5:c.2356G>A	p.Glu786Lys	p.E786K	ENST00000325455	NM_001202474.3	786	Gaa/Aaa	5/8	1	2	FACETS	0.746	0.672	0.824	0.746	0.672	0.824	SUBCLONAL	1	TRUE	1	0.644553257177707	2		429	424	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070408	37070408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750746	NA	P-0030835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	152	359	0	ENST00000231790.2:c.1543G>A	p.Glu515Lys	p.E515K	ENST00000231790	NM_000249.3	515	Gag/Aag	13/19	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.644553257177707	2		359	470	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222653	53222653	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	343	885	0	ENST00000375401.3:c.4283C>A	p.Pro1428His	p.P1428H	ENST00000375401	NM_004187.3	1428	cCc/cAc	25/26	0.644553257177707	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.644553257177707	1		885	707	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0030841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	113	427	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.281071758253104	2	FACETS	1	0.907	1	0.503	0.453	0.556	CLONAL	1	TRUE	0	0.34017909360213	2		427	660	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913385	NA	P-0030841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	154	476	0	ENST00000304494.5:c.247C>G	p.His83Asp	p.H83D	ENST00000304494	NM_000077.4	83	Cac/Gac	2/3	0.296186820250763	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.34017909360213	1		476	655	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579400	7579401	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	182	756	2	ENST00000269305.4:c.286dup	p.Ser96PhefsTer53	p.S96Ffs*53	ENST00000269305	NM_001126112.2	96	tct/tTct	4/11	0.34017909360213	1	FACETS	0.975	0.9	1	0.975	0.9	1	CLONAL	1	TRUE	0	0.34017909360213	1		758	911	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584784	48584785	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	96	525	0	ENST00000342988.3:c.864dup	p.Gln289SerfsTer19	p.Q289Sfs*19	ENST00000342988	NM_005359.5	288	ctt/cTtt	7/12	0.284522618503783	1	FACETS	0.551	0.49	0.616	0.551	0.49	0.616	SUBCLONAL	1	TRUE	0	0.34017909360213	1		525	850	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591919	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0030841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	35	426	0	ENST00000342988.3:c.1082_1083del	p.Arg361LeufsTer16	p.R361Lfs*16	ENST00000342988	NM_005359.5	361	CGc/c	9/12	0.284522618503783	1	FACETS	0.294	0.24	0.355	0.294	0.24	0.355	SUBCLONAL	1	TRUE	0	0.34017909360213	1		426	581	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0030842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	33	237	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.671847396090084	1	FACETS	0.53	0.441	0.627	0.53	0.441	0.627	SUBCLONAL	1	TRUE	0	0.671847396090084	1		237	123	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577095	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519984	NA	P-0030842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	670	711	0	ENST00000269305.4:c.843C>G	p.Asp281Glu	p.D281E	ENST00000269305	NM_001126112.2	281	gaC/gaG	8/11	0.671847396090084	2	FACETS	0.991	0.965	1	0.991	0.965	1	CLONAL	2	TRUE	0	0.671847396090084	2		711	1006	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061238	38061239	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGAGTCCGGGTGCAGCGTCCAGTA	novel	NA	P-0030842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	279	885	0	ENST00000250448.2:c.727_750dup	p.Tyr243_Ser250dup	p.Y243_S250dup	ENST00000250448	NM_004496.3	243	-/TACTGGACGCTGCACCCGGACTCC	2/2	1	2	FACETS	0.695	0.652	0.739	0.695	0.652	0.739	SUBCLONAL	1	TRUE	1	0.671847396090084	2		885	1195	SUCCESS
APC	324	MSKCC	GRCh37	5	112177045	112177045	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	229	584	0	ENST00000257430.4:c.5756del	p.Asn1919IlefsTer51	p.N1919Ifs*51	ENST00000257430	NM_000038.5	1918	atA/at	16/16	0.671847396090084	1	FACETS	0.935	0.882	0.989	0.935	0.882	0.989	CLONAL	1	TRUE	0	0.671847396090084	1		584	484	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845678	151845678	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	153	453	0	ENST00000262189.6:c.13334del	p.Gly4445ValfsTer3	p.G4445Vfs*3	ENST00000262189	NM_170606.2	4445	gGt/gt	52/59	0.671847396090084	3	FACETS	0.711	0.65	0.774	0.355	0.325	0.387	SUBCLONAL	1	TRUE	1	0.671847396090084	3		453	856	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270504	98270504	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	80	549	0	ENST00000331920.6:c.140G>A	p.Arg47Gln	p.R47Q	ENST00000331920	NM_000264.3	47	cGg/cAg	1/24	1	2	FACETS	0.998	0.878	1	0.998	0.878	1	CLONAL	1	TRUE	1	0.22	2		549	729	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	70	613	0	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	1	2	FACETS	0.855	0.745	0.975	0.855	0.745	0.975	CLONAL	1	TRUE	1	0.22	2		613	744	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438535	52438535	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0030843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	72	564	0	ENST00000460680.1:c.1184C>G	p.Ser395Ter	p.S395*	ENST00000460680	NM_004656.3	395	tCa/tGa	12/17	1	2	FACETS	0.793	0.692	0.903	0.793	0.692	0.903	CLONAL	1	TRUE	1	0.22	2		564	825	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982987	201982987	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	156	676	0	ENST00000359651.3:c.836T>C	p.Ile279Thr	p.I279T	ENST00000359651		279	aTc/aCc	7/8	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.22	2		676	974	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431689	49431699	+	frameshift_variant	Frame_Shift_Del	DEL	AAGGGAATTGG	AAGGGAATTGG	-	novel	NA	P-0030843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	49	682	0	ENST00000301067.7:c.9440_9450del	p.Ala3147GlyfsTer25	p.A3147Gfs*25	ENST00000301067	NM_003482.3	3147	gCCAATTCCCTT/g	34/54	1	2	FACETS	0.612	0.517	0.717	0.612	0.517	0.717	SUBCLONAL	1	TRUE	1	0.22	2		682	728	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995336	15995336	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1240475793	NA	P-0030843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	34	365	0	ENST00000268712.3:c.2857C>G	p.Pro953Ala	p.P953A	ENST00000268712	NM_006311.3	953	Cca/Gca	22/46	1	2	FACETS	0.461	0.375	0.557	0.461	0.375	0.557	SUBCLONAL	1	TRUE	1	0.22	2		365	671	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092976	29092976	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0030843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	86	406	0	ENST00000328354.6:c.1009-1G>C		p.X337_splice	ENST00000328354	NM_007194.3	337			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.22	2		406	595	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443593	52443593	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	52	493	0	ENST00000460680.1:c.99C>A	p.Tyr33Ter	p.Y33*	ENST00000460680	NM_004656.3	33	taC/taA	3/17	1	2	FACETS	0.696	0.592	0.811	0.696	0.592	0.811	SUBCLONAL	1	TRUE	1	0.22	2		493	679	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874403	151874403	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0030843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	60	354	0	ENST00000262189.6:c.8135T>A	p.Leu2712Ter	p.L2712*	ENST00000262189	NM_170606.2	2712	tTa/tAa	38/59	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.22	2		354	540	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44970639	44970663	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	CCATCCGCCTCATCTTGATATTGTT	CCATCCGCCTCATCTTGATATTGTT	-	novel	NA	P-0030843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	27	258	0	ENST00000377967.4:c.4193_*11del		p.*1398*	ENST00000377967	NM_021140.2	1397		29/29	1	1	FACETS	0.639	0.509	0.787	0.639	0.509	0.787	SUBCLONAL	1	TRUE	0	0.22	1		258	342	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0030847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	136	532	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.629366871161341	3	FACETS	0.993	0.907	1	0.497	0.453	0.542	CLONAL	1	TRUE	1	0.629366871161341	3		533	572	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0030847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	164	622	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.981	0.907	1	0.981	0.907	1	CLONAL	1	TRUE	1	0.629366871161341	2		622	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0030847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	274	545	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.629366871161341	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.629366871161341	1		545	509	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160488	108160488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730881369	NA	P-0030847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	180	550	0	ENST00000278616.4:c.4396C>T	p.Arg1466Ter	p.R1466*	ENST00000278616	NM_000051.3	1466	Cga/Tga	29/63	1	2	FACETS	0.898	0.832	0.966	0.898	0.832	0.966	CLONAL	1	TRUE	1	0.629366871161341	2		550	637	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410700	32410700	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	189	387	0	ENST00000332351.3:c.1458G>C	p.Trp486Cys	p.W486C	ENST00000332351	NM_024426.4	486	tgG/tgC	10/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.629366871161341	2		387	557	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950052	44950052	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	160	274	0	ENST00000377967.4:c.3822del	p.Trp1275GlyfsTer17	p.W1275Gfs*17	ENST00000377967	NM_021140.2	1274	tCc/tc	26/29	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.629366871161341	1		274	241	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0030849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	277	532	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.326901070637661	4	FACETS	0.931	0.878	0.985	0.931	0.878	0.985	CLONAL	3	TRUE	1	0.326901070637661	4		533	805	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0030849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	266	876	1	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.326901070637661	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.326901070637661	1		877	1275	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057894	27057894	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	217	603	0	ENST00000324856.7:c.1602C>A	p.Tyr534Ter	p.Y534*	ENST00000324856	NM_006015.4	534	taC/taA	3/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.326901070637661	2		603	1197	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	157	520	1	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS	0.959	0.877	1	0.959	0.877	1	CLONAL	1	TRUE	1	0.326901070637661	2		521	1002	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618613	37618613	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	128	463	0	ENST00000447079.4:c.289G>C	p.Asp97His	p.D97H	ENST00000447079	NM_015083.1	97	Gac/Cac	1/14	1	2	FACETS	0.908	0.823	0.999	0.908	0.823	0.999	CLONAL	1	TRUE	1	0.326901070637661	2		463	862	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024602	11024602	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	143	614	0	ENST00000327064.4:c.719G>T	p.Gly240Val	p.G240V	ENST00000327064	NM_199141.1	240	gGc/gTc	6/16	1	2	FACETS	0.841	0.766	0.921	0.841	0.766	0.921	CLONAL	1	TRUE	1	0.326901070637661	2		614	1040	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306758	41306759	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0030849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	81	376	1	ENST00000373198.4:c.900_901delinsTA	p.Gly301Arg	p.G301R	ENST00000373198	NM_133170.3	300	gtGGgg/gtTAgg	7/32	1	2	FACETS	0.803	0.708	0.905	0.803	0.708	0.905	CLONAL	1	TRUE	1	0.326901070637661	2		377	617	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1941467	1941467	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	122	506	2	ENST00000382891.5:c.1846del	p.Ser616ValfsTer8	p.S616Vfs*8	ENST00000382891	NM_133335.3	615	Aaa/aa	9/22	1	2	FACETS	0.859	0.776	0.947	0.859	0.776	0.947	CLONAL	1	TRUE	1	0.326901070637661	2		508	869	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345324	70345324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	162	346	0	ENST00000374080.3:c.2350C>T	p.Arg784Cys	p.R784C	ENST00000374080		784	Cgc/Tgc	16/45	1	1	FACETS	0.8	0.739	0.863	1	0.99	1	SUBCLONAL	2	TRUE	0	0.326901070637661	1		346	518	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0030863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	126	227	0	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	0.625292952926218	1	FACETS	0.998	0.923	1	0.998	0.923	1	CLONAL	1	TRUE	0	0.662371208930465	1		227	255	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs863224499	NA	P-0030863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	250	583	0	ENST00000269305.4:c.672+1G>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.597305578950452	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.662371208930465	2		583	368	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36821033	36821033	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	104	411	0	ENST00000373129.3:c.344A>G	p.Asp115Gly	p.D115G	ENST00000373129	NM_032017.1	115	gAc/gGc	6/12	NA	2	FACETS	1	0.91	1			1	INDETERMINATE	1	TRUE	NA	0.662371208930465	2		411	313	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11114071	11114071	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	111	417	1	ENST00000358026.2:c.1999G>T	p.Glu667Ter	p.E667*	ENST00000358026	NM_001128849.1	667	Gag/Tag	13/36	0.662375027471463	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.662371208930465	1		418	195	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541457	187541457	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	101	383	0	ENST00000441802.2:c.6283del	p.Glu2095ArgfsTer12	p.E2095Rfs*12	ENST00000441802	NM_005245.3	2095	Gag/ag	10/27	0.55393967780232	2	FACETS	1	0.979	1	0.641	0.584	0.698	CLONAL	1	TRUE	0	0.662371208930465	2		383	238	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325487	1325487	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	85	427	0	ENST00000400841.2:c.188A>G	p.Asn63Ser	p.N63S	ENST00000400841		63	aAc/aGc	3/6	1	1	FACETS	0.493	0.439	0.55	0.493	0.439	0.55	SUBCLONAL	1	TRUE	0	0.662371208930465	1		427	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0030865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	143	708	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.39	2		709	642	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0030865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	84	429	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.3	0	FACETS	0.811	0.723	0.903			1	CLONAL	1	TRUE	0	0.39	0		429	324	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843613	156843613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561243137	NA	P-0030865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	54	619	2	ENST00000524377.1:c.1039C>T	p.Arg347Cys	p.R347C	ENST00000524377	NM_002529.3	347	Cgc/Tgc	8/17	0.221945134896763	3	FACETS	0.361	0.307	0.42	0.18	0.153	0.21	INDETERMINATE	1	TRUE	1	0.39	3		621	917	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	27	279	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	0.618	0.494	0.758	0.618	0.494	0.758	SUBCLONAL	1	TRUE	1	0.39	2		279	224	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193940	106193940	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0030865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	79	327	0	ENST00000380013.4:c.4402A>T	p.Lys1468Ter	p.K1468*	ENST00000380013	NM_001127208.2	1468	Aaa/Taa	10/11	1	2	FACETS	0.809	0.713	0.911	0.809	0.713	0.911	CLONAL	1	TRUE	1	0.39	2		327	501	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038648	14038648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	73	340	0	ENST00000311895.7:c.1973G>A	p.Arg658Lys	p.R658K	ENST00000311895	NM_005236.2	658	aGa/aAa	10/11	0.132837014930559	5	FACETS	1	0.924	1	0.36	0.314	0.409	INDETERMINATE	1	TRUE	2	0.297843958947688	5		340	657	SUCCESS
FH	2271	MSKCC	GRCh37	1	241669318	241669318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1245254230	NA	P-0030867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	73	385	0	ENST00000366560.3:c.889G>A	p.Val297Met	p.V297M	ENST00000366560	NM_000143.3	297	Gtg/Atg	6/10	0.297843958947688	6	FACETS	0.95	0.83	1	0.238	0.207	0.271	CLONAL	1	TRUE	2	0.297843958947688	6		385	823	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675139	40675139	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	80	613	0	ENST00000249776.8:c.103C>A	p.Leu35Ile	p.L35I	ENST00000249776	NM_033286.3	35	Cta/Ata	1/9	0.297843958947688	2	FACETS	0.854	0.752	0.963	0.427	0.376	0.482	CLONAL	1	TRUE	0	0.297843958947688	2		613	629	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578238	7578238	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	295	584	0	ENST00000269305.4:c.611del	p.Glu204GlyfsTer43	p.E204Gfs*43	ENST00000269305	NM_001126112.2	204	gAg/gg	6/11	0.291621399848174	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	0	0.297843958947688	3		584	704	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280045	18280045	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1463551736	NA	P-0030867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	37	187	0	ENST00000222254.8:c.2128G>A	p.Val710Ile	p.V710I	ENST00000222254	NM_005027.3	710	Gtc/Atc	16/16	0.0671973873982155	3	FACETS	1	0.949	1			1	INDETERMINATE	1	TRUE	NA	0.297843958947688	3		187	201	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211179	55211179	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	77	436	0	ENST00000275493.2:c.422A>T	p.Gln141Leu	p.Q141L	ENST00000275493	NM_005228.3	141	cAg/cTg	3/28	0.132837014930559	5	FACETS	1	0.967	1	0.434	0.382	0.491	INDETERMINATE	1	TRUE	2	0.297843958947688	5		436	574	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242279	98242279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	58	474	0	ENST00000331920.6:c.1039G>A	p.Val347Ile	p.V347I	ENST00000331920	NM_000264.3	347	Gtc/Atc	7/24	0.297843958947688	3	FACETS	0.736	0.632	0.849	0.368	0.316	0.425	SUBCLONAL	1	TRUE	1	0.297843958947688	3		474	608	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	58	454	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.935	0.816	1	0.935	0.816	1	CLONAL	1	TRUE	1	0.63	2		454	197	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0030868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	214	465	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.986	0.92	1	0.986	0.92	1	CLONAL	1	TRUE	1	0.63	2		465	689	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156719	20156719	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	159	195	0	ENST00000379607.5:c.38G>C	p.Arg13Pro	p.R13P	ENST00000379607	NM_001412.3	13	cGc/cCc	2/7	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.63	1		195	283	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749221	43749221	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	188	597	0	ENST00000382044.4:c.1585C>T	p.Gln529Ter	p.Q529*	ENST00000382044	NM_001141980.1	529	Cag/Tag	12/28	1	2	FACETS	0.917	0.851	0.985	0.917	0.851	0.985	CLONAL	1	TRUE	1	0.63	2		597	651	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0030869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	84	429	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	FALSE	1	0.219531046500418	2		429	716	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574032	7574032	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	43	318	0	ENST00000269305.4:c.995T>A	p.Ile332Asn	p.I332N	ENST00000269305	NM_001126112.2	332	aTc/aAc	10/11	0.219531046500418	1	FACETS	0.576	0.481	0.682	0.576	0.481	0.682	SUBCLONAL	1	FALSE	0	0.219531046500418	1		318	605	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245460	16245460	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	55	314	0	ENST00000375759.3:c.1435G>T	p.Ala479Ser	p.A479S	ENST00000375759	NM_015001.2	479	Gcg/Tcg	7/15	1	2	FACETS	0.692	0.591	0.803	0.692	0.591	0.803	SUBCLONAL	1	FALSE	1	0.219531046500418	2		314	724	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007798	45007798	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	58	282	0	ENST00000558401.1:c.245T>C	p.Phe82Ser	p.F82S	ENST00000558401	NM_004048.2	82	tTc/tCc	2/4	0.219531046500418	1	FACETS	0.71	0.609	0.819	0.71	0.609	0.819	SUBCLONAL	1	FALSE	0	0.219531046500418	1		282	663	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476247	88476247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	49	371	0	ENST00000360948.2:c.1885C>T	p.Leu629Phe	p.L629F	ENST00000360948	NM_001012338.2	629	Ctc/Ttc	15/19	0.219531046500418	1	FACETS	0.701	0.593	0.82	0.701	0.593	0.82	SUBCLONAL	1	FALSE	0	0.219531046500418	1		371	567	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028883	47028883	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	44	339	0	ENST00000377604.3:c.187G>T	p.Glu63Ter	p.E63*	ENST00000377604	NM_001204468.1	63	Gag/Tag	3/24	1	2	FACETS	0.728	0.61	0.858	0.728	0.61	0.858	SUBCLONAL	1	FALSE	1	0.219531046500418	2		339	551	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346284	70346284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	49	438	0	ENST00000374080.3:c.2635C>T	p.Leu879Phe	p.L879F	ENST00000374080		879	Ctc/Ttc	19/45	1	2	FACETS	0.638	0.539	0.747	0.638	0.539	0.747	SUBCLONAL	1	FALSE	1	0.219531046500418	2		438	700	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	20	454	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.742	0.567	0.946	0.742	0.567	0.946	CLONAL	1	TRUE	1	0.18157860955973	2		454	297	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231825	36231825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1429953108	NA	P-0030871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	61	496	0	ENST00000300305.3:c.559G>A	p.Ala187Thr	p.A187T	ENST00000300305		187	Gcc/Acc	5/8	1	2	FACETS	0.746	0.642	0.86	0.746	0.642	0.86	SUBCLONAL	1	TRUE	1	0.18157860955973	2		496	901	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720660	89720660	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	10	177	0	ENST00000371953.3:c.811T>G	p.Phe271Val	p.F271V	ENST00000371953	NM_000314.4	271	Ttt/Gtt	8/9	0.18157860955973	1	FACETS	0.759	0.516	1	0.759	0.516	1	CLONAL	1	TRUE	0	0.18157860955973	1		177	132	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0030872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	12	622	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.201	0.14	0.276	0.201	0.14	0.276	SUBCLONAL	1	TRUE	1	0.215549167809956	2		622	555	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0030872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	72	472	1	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	1	2	FACETS	0.921	0.804	1	0.921	0.804	1	CLONAL	1	TRUE	1	0.215549167809956	2		473	725	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340214	116340214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201274041	NA	P-0030872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	49	307	0	ENST00000397752.3:c.1076G>A	p.Arg359Gln	p.R359Q	ENST00000397752	NM_000245.2	359	cGa/cAa	2/21	1	2	FACETS	0.911	0.772	1	0.911	0.772	1	CLONAL	1	TRUE	1	0.215549167809956	2		307	499	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043925	180043925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	85	560	0	ENST00000261937.6:c.3071G>A	p.Gly1024Glu	p.G1024E	ENST00000261937	NM_182925.4	1024	gGg/gAg	22/30	1	2	FACETS	0.936	0.826	1	0.936	0.826	1	CLONAL	1	TRUE	1	0.215549167809956	2		560	843	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0030878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	74	283	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.526386052043815	2		283	279	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0030878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	810	465	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.526386052043815	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	0	0.526386052043815	3		465	1275	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856500	111856500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	64	175	0	ENST00000341259.2:c.551C>T	p.Pro184Leu	p.P184L	ENST00000341259	NM_005475.2	184	cCc/cTc	2/8	1	2	FACETS	0.935	0.819	1	0.935	0.819	1	CLONAL	1	TRUE	1	0.526386052043815	2		175	260	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0030892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	190	356	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	0.552667594080474	3	FACETS	0.982	0.93	1			1	CLONAL	3	FALSE	NA	0.552667594080474	3		356	298	SUCCESS
APC	324	MSKCC	GRCh37	5	112175328	112175328	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0030892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	122	272	0	ENST00000257430.4:c.4037C>G	p.Ser1346Ter	p.S1346*	ENST00000257430	NM_000038.5	1346	tCa/tGa	16/16	0.16478923415156	6	FACETS	1	0.974	1	0.786	0.717	0.858	INDETERMINATE	2	FALSE	3	0.552667594080474	6		272	394	SUCCESS
APC	324	MSKCC	GRCh37	5	112173299	112173299	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0030892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	105	237	0	ENST00000257430.4:c.2008A>T	p.Lys670Ter	p.K670*	ENST00000257430	NM_000038.5	670	Aaa/Taa	16/16	0.16478923415156	6	FACETS	0.995	0.906	1	0.995	0.906	1	INDETERMINATE	3	FALSE	3	0.552667594080474	6		237	268	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0030892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	327	486	0	ENST00000269305.4:c.559+1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.552667594080474	2	FACETS	0.999	0.955	1	0.999	0.955	1	CLONAL	2	FALSE	0	0.552667594080474	2		486	592	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604721	48604721	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs121912579	NA	P-0030892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	114	430	0	ENST00000342988.3:c.1543A>T	p.Arg515Ter	p.R515*	ENST00000342988	NM_005359.5	515	Aga/Tga	12/12	0.552667594080474	1	FACETS	0.839	0.763	0.917	0.839	0.763	0.917	CLONAL	1	FALSE	0	0.552667594080474	1		430	356	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675644	86675644	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	90	269	0	ENST00000274376.6:c.2580C>A	p.Phe860Leu	p.F860L	ENST00000274376	NM_002890.2	860	ttC/ttA	19/25	NA	2	FACETS	0.876	0.797	0.954			1	INDETERMINATE	2	FALSE	NA	0.552667594080474	2		269	186	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0030894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	136	532	1	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	0.350558358899008	2		533	738	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0030894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	163	645	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.350558358899008	1	FACETS	0.918	0.844	0.997	0.918	0.844	0.997	CLONAL	1	TRUE	0	0.350558358899008	1		645	835	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549458	187549458	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	60	456	0	ENST00000441802.2:c.4660G>C	p.Asp1554His	p.D1554H	ENST00000441802	NM_005245.3	1554	Gac/Cac	9/27	0.350558358899008	1	FACETS	0.398	0.342	0.458	0.398	0.342	0.458	SUBCLONAL	1	TRUE	0	0.350558358899008	1		456	710	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937711	36937711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752325760	NA	P-0030894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	152	503	1	ENST00000361632.4:c.1027C>T	p.Arg343Trp	p.R343W	ENST00000361632		343	Cgg/Tgg	8/16	1	2	FACETS	0.899	0.821	0.98	0.899	0.821	0.98	CLONAL	1	TRUE	1	0.350558358899008	2		504	965	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716164	243716164	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	62	533	0	ENST00000263826.5:c.1030T>A	p.Leu344Ile	p.L344I	ENST00000263826	NM_005465.4	344	Tta/Ata	10/13	1	2	FACETS	0.387	0.333	0.445	0.387	0.333	0.445	SUBCLONAL	1	TRUE	1	0.350558358899008	2		533	915	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727075	243727075	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	54	459	0	ENST00000263826.5:c.895G>T	p.Asp299Tyr	p.D299Y	ENST00000263826	NM_005465.4	299	Gat/Tat	9/13	1	2	FACETS	0.377	0.321	0.438	0.377	0.321	0.438	SUBCLONAL	1	TRUE	1	0.350558358899008	2		459	818	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218051	108218051	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	53	413	0	ENST00000278616.4:c.8630T>G	p.Leu2877Trp	p.L2877W	ENST00000278616	NM_000051.3	2877	tTg/tGg	59/63	0.350558358899008	3	FACETS	0.478	0.407	0.557	0.239	0.203	0.279	SUBCLONAL	1	TRUE	1	0.350558358899008	3		413	743	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641505	18641505	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	154	439	0	ENST00000266497.5:c.2504T>C	p.Ile835Thr	p.I835T	ENST00000266497		835	aTc/aCc	17/31	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.350558358899008	2		439	803	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245954	46245958	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	novel	NA	P-0030894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	106	453	0	ENST00000334344.6:c.4048_4052del	p.Lys1350Ter	p.K1350*	ENST00000334344	NM_152641.2	1350	AAAAGt/t	15/21	1	2	FACETS	0.88	0.79	0.976	0.88	0.79	0.976	CLONAL	1	TRUE	1	0.350558358899008	2		453	687	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112250	115112250	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	10	93	0	ENST00000257566.3:c.1490C>A	p.Pro497His	p.P497H	ENST00000257566	NM_016569.3	497	cCc/cAc	7/8	1	2	FACETS	0.468	0.318	0.653	0.468	0.318	0.653	SUBCLONAL	1	TRUE	1	0.350558358899008	2		93	122	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549233	21549233	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	113	692	0	ENST00000382592.4:c.3043A>T	p.Ser1015Cys	p.S1015C	ENST00000382592	NM_014572.2	1015	Agc/Tgc	8/8	1	2	FACETS	0.523	0.469	0.581	0.523	0.469	0.581	SUBCLONAL	1	TRUE	1	0.350558358899008	2		692	1232	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727454	88727454	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0030894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	122	463	0	ENST00000360948.2:c.323+2T>G		p.X108_splice	ENST00000360948	NM_001012338.2	108			0.252719409036952	5	FACETS	0.953	0.86	1	0.318	0.286	0.351	CLONAL	1	TRUE	2	0.350558358899008	5		463	1114	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917054	50917054	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	168	603	0	ENST00000440232.2:c.2306C>G	p.Ala769Gly	p.A769G	ENST00000440232	NM_002691.3	769	gCt/gGt	19/27	1	2	FACETS	0.897	0.824	0.974	0.897	0.824	0.974	CLONAL	1	TRUE	1	0.350558358899008	2		603	1068	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880993	134880993	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	143	464	1	ENST00000398015.3:c.1556G>T	p.Gly519Val	p.G519V	ENST00000398015	NM_004441.4	519	gGc/gTc	7/16	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.350558358899008	2		465	759	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56910947	56910947	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	187	560	0	ENST00000519728.1:c.1093C>G	p.His365Asp	p.H365D	ENST00000519728	NM_002350.3	365	Cac/Gac	11/13	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.350558358899008	2		560	999	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101910019	101910019	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	93	343	0	ENST00000374994.4:c.1339G>T	p.Glu447Ter	p.E447*	ENST00000374994	NM_004612.2	447	Gaa/Taa	8/9	0.350558358899008	1	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	0	0.350558358899008	1		343	432	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143994	11143994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	186	484	3	ENST00000358026.2:c.3575G>A	p.Arg1192His	p.R1192H	ENST00000358026	NM_001128849.1	1192	cGc/cAc	26/36	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.462364794745263	2		487	614	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0030897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	306	590	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.45384227680919	2	FACETS	0.954	0.905	1	0.954	0.905	1	CLONAL	2	TRUE	0	0.462364794745263	2		590	694	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974727	21974744	+	inframe_deletion	In_Frame_Del	DEL	CCTCCAGCAGCGCCCGCA	CCTCCAGCAGCGCCCGCA	-	novel	NA	P-0030897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	65	241	0	ENST00000304494.5:c.83_100del	p.Val28_Glu33del	p.V28_E33del	ENST00000304494	NM_000077.4	28	gTGCGGGCGCTGCTGGAGGcg/gcg	1/3	1	2	FACETS	0.95	0.831	1	0.95	0.831	1	CLONAL	1	TRUE	1	0.462364794745263	2		241	296	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248599	212248599	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1281587425	NA	P-0030897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	121	430	0	ENST00000342788.4:c.3668A>G	p.Lys1223Arg	p.K1223R	ENST00000342788	NM_005235.2	1223	aAg/aGg	28/28	1	2	FACETS	0.831	0.752	0.913	0.831	0.752	0.913	CLONAL	1	TRUE	1	0.462364794745263	2		430	630	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727114	243727114	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	68	435	0	ENST00000263826.5:c.856A>G	p.Lys286Glu	p.K286E	ENST00000263826	NM_005465.4	286	Aaa/Gaa	9/13	0.214717033675357	2	FACETS	0.42	0.364	0.479	0.21	0.182	0.24	INDETERMINATE	1	TRUE	0	0.462364794745263	2		435	701	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864492	56864492	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771130377	NA	P-0030897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	125	487	0	ENST00000308159.5:c.980G>A	p.Arg327His	p.R327H	ENST00000308159	NM_014669.4	327	cGc/cAc	10/22	0.462364794745263	1	FACETS	0.72	0.654	0.79	0.72	0.654	0.79	SUBCLONAL	1	TRUE	0	0.462364794745263	1		487	577	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983066	149983066	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	157	556	0	ENST00000253339.5:c.3192G>A	p.Trp1064Ter	p.W1064*	ENST00000253339		1064	tgG/tgA	7/7	0.393722392113814	1	FACETS	0.769	0.706	0.834	0.769	0.706	0.834	SUBCLONAL	1	TRUE	0	0.462364794745263	1		556	679	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69011939	69011939	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	193	614	1	ENST00000288368.4:c.2576G>T	p.Ser859Ile	p.S859I	ENST00000288368	NM_024870.2	859	aGt/aTt	23/40	0.462364794745263	3	FACETS	0.836	0.771	0.903	0.418	0.385	0.452	CLONAL	1	TRUE	1	0.462364794745263	3		615	1230	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868498	117868498	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	60	322	0	ENST00000297338.2:c.844G>A	p.Asp282Asn	p.D282N	ENST00000297338	NM_006265.2	282	Gat/Aat	8/14	0.462364794745263	3	FACETS	0.437	0.375	0.503	0.218	0.187	0.252	SUBCLONAL	1	TRUE	1	0.462364794745263	3		322	732	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0030899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	95	367	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	0.979	1	CLONAL	1	TRUE	1	0.205568189173409	2		367	636	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346338	73346338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	81	407	0	ENST00000377767.4:c.1462G>A	p.Asp488Asn	p.D488N	ENST00000377767	NM_014953.3	488	Gat/Aat	10/21	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.205568189173409	2		407	652	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683719	162683719	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	92	441	0	ENST00000366898.1:c.250G>T	p.Gly84Ter	p.G84*	ENST00000366898	NM_004562.2	84	Gga/Tga	3/12	1	2	FACETS	0.795	0.708	0.887	1	0.982	1	SUBCLONAL	2	TRUE	1	0.205568189173409	2		441	563	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039294	47039294	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	109	557	1	ENST00000377604.3:c.917A>T	p.Asn306Ile	p.N306I	ENST00000377604	NM_001204468.1	306	aAc/aTc	10/24	1	2	FACETS	0.793	0.713	0.877	1	0.984	1	SUBCLONAL	2	TRUE	1	0.205568189173409	2		558	669	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281669	49281669	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	96	591	0	ENST00000282018.3:c.718del	p.Val240PhefsTer7	p.V240Ffs*7	ENST00000282018	NM_020377.2	239	cGg/cg	1/1	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.205568189173409	2		591	726	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696432	47696432	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519968	NA	P-0030902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	102	492	0	ENST00000347630.2:c.391T>G	p.Trp131Gly	p.W131G	ENST00000347630	NM_001007230.1	131	Tgg/Ggg	6/11	1	2	FACETS	0.987	0.884	1	0.987	0.884	1	CLONAL	1	TRUE	1	0.3106972474408	2		492	665	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714619	52714619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs527266620	NA	P-0030902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	88	527	1	ENST00000322088.6:c.377C>T	p.Ala126Val	p.A126V	ENST00000322088	NM_014225.5	126	gCg/gTg	4/15	1	2	FACETS	0.844	0.748	0.947	0.844	0.748	0.947	CLONAL	1	TRUE	1	0.3106972474408	2		528	671	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907690	111907691	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0030902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	103	412	0	ENST00000393256.3:c.464_465insC	p.Gly156TrpfsTer5	p.G156Wfs*5	ENST00000393256	NM_006538.4	155	att/atCt	3/4	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.3106972474408	2		412	590	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787840	135787840	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	243	329	0	ENST00000298552.3:c.742A>G	p.Lys248Glu	p.K248E	ENST00000298552	NM_001162426.1	248	Aag/Gag	9/23	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		329	541	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0028755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	115	483	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	TRUE	1	0.364261253487814	2		483	610	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029445	16029446	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	112	406	0	ENST00000268712.3:c.1584dup	p.Glu529ArgfsTer7	p.E529Rfs*7	ENST00000268712	NM_006311.3	528	-/A	15/46	1	2	FACETS	0.842	0.758	0.932	0.842	0.758	0.932	CLONAL	1	TRUE	1	0.364261253487814	2		406	730	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259153	36259153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	116	567	0	ENST00000300305.3:c.338C>T	p.Pro113Leu	p.P113L	ENST00000300305		113	cCc/cTc	3/8	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.364261253487814	2		567	616	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	38	295	0	ENST00000256196.4:c.68G>A	p.Gly23Asp	p.G23D	ENST00000256196		23	gGc/gAc	1/6	1	2	FACETS	0.707	0.587	0.84	0.707	0.587	0.84	SUBCLONAL	1	TRUE	1	0.364261253487814	2		295	295	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252862	36252862	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	90	325	0	ENST00000300305.3:c.500G>A	p.Ser167Asn	p.S167N	ENST00000300305		167	aGt/aAt	4/8	1	2	FACETS	0.98	0.873	1	0.98	0.873	1	CLONAL	1	TRUE	1	0.364261253487814	2		325	504	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183342	56183342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	92	348	0	ENST00000399503.3:c.4252C>T	p.Pro1418Ser	p.P1418S	ENST00000399503	NM_005921.1	1418	Cct/Tct	18/20	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.364261253487814	2		348	476	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878416	151878416	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs867724616	NA	P-0028755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	130	681	1	ENST00000262189.6:c.6529C>T	p.Gln2177Ter	p.Q2177*	ENST00000262189	NM_170606.2	2177	Cag/Tag	36/59	1	2	FACETS	0.963	0.875	1	0.963	0.875	1	CLONAL	1	TRUE	1	0.364261253487814	2		682	741	SUCCESS
APC	324	MSKCC	GRCh37	5	112175235	112175235	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	143	245	0	ENST00000257430.4:c.3944C>A	p.Ser1315Ter	p.S1315*	ENST00000257430	NM_000038.5	1315	tCa/tAa	16/16	0.41324102377871	2	FACETS	1	0.986	1	0.681	0.627	0.737	CLONAL	1	TRUE	0	0.50579377598591	2		245	415	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920437	114920437	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	244	543	1	ENST00000543371.1:c.1378T>C	p.Cys460Arg	p.C460R	ENST00000543371	NM_001198531.1	460	Tgc/Cgc	13/14	0.194862456843189	2	FACETS	1	0.967	1	0.526	0.492	0.561	INDETERMINATE	1	TRUE	0	0.50579377598591	2		544	917	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275717	41275717	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	170	534	0	ENST00000349496.5:c.1612C>A	p.Gln538Lys	p.Q538K	ENST00000349496	NM_001904.3	538	Cag/Aag	10/15	1	2	FACETS	0.806	0.742	0.873	0.806	0.742	0.873	CLONAL	1	TRUE	1	0.50579377598591	2		534	834	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047500	49047500	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	43	392	0	ENST00000267163.4:c.2494T>G	p.Leu832Val	p.L832V	ENST00000267163	NM_000321.2	832	Tta/Gta	24/27	0.50579377598591	3	FACETS	0.269	0.224	0.319	0.09	0.074	0.107	SUBCLONAL	1	TRUE	0	0.50579377598591	3		392	791	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656648	3656648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	283	824	2	ENST00000294008.3:c.587C>T	p.Ala196Val	p.A196V	ENST00000294008	NM_032444.2	196	gCa/gTa	3/15	NA	2	FACETS	0.847	0.795	0.901			1	INDETERMINATE	1	TRUE	NA	0.50579377598591	2		826	1321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579538	7579539	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TATCG	novel	NA	P-0028759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	361	676	0	ENST00000269305.4:c.144_148dup	p.Ile50ThrfsTer75	p.I50Tfs*75	ENST00000269305	NM_001126112.2	50	att/aCGATAtt	4/11	0.41324102377871	2	FACETS	1	0.993	1	0.652	0.619	0.686	CLONAL	1	TRUE	0	0.50579377598591	2		676	1095	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376319	15376319	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1332	84	830	0	ENST00000263377.2:c.695T>G	p.Leu232Arg	p.L232R	ENST00000263377	NM_058243.2	232	cTc/cGc	5/20	0.247376496547796	3	FACETS	0.294	0.258	0.332	0.147	0.129	0.166	INDETERMINATE	1	TRUE	1	0.50579377598591	3		830	1416	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80109497	80109497	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	66	650	1	ENST00000265081.6:c.2750A>T	p.Gln917Leu	p.Q917L	ENST00000265081	NM_002439.4	917	cAg/cTg	20/24	0.41324102377871	2	FACETS	0.257	0.222	0.295	0.129	0.111	0.148	SUBCLONAL	1	TRUE	0	0.50579377598591	2		651	1015	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577479	64577479	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	183	574	1	ENST00000312049.6:c.103del	p.Val35CysfsTer84	p.V35Cfs*84	ENST00000312049	NM_130799.2	35	Gtg/tg	2/10	0.638768476816722	1	FACETS	0.961	0.898	1	0.961	0.898	1	CLONAL	1	TRUE	0	0.638768476816722	1		575	406	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0028761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	46	325	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.225	0.189	0.264	0.225	0.189	0.264	SUBCLONAL	1	TRUE	1	0.745684927252935	2		325	549	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912664	NA	P-0028761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	195	634	0	ENST00000269305.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000269305	NM_001126112.2	337	cGc/cAc	10/11	0.352436924844332	1	FACETS	0.461	0.428	0.495	0.461	0.428	0.495	INDETERMINATE	1	TRUE	0	0.745684927252935	1		634	712	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87322770	87322770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781137734	NA	P-0028761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	130	469	0	ENST00000277120.3:c.371G>A	p.Arg124Gln	p.R124Q	ENST00000277120		124	cGa/cAa	5/19	0.503007321395646	1	FACETS	0.679	0.625	0.734	0.679	0.625	0.734	SUBCLONAL	1	TRUE	0	0.745684927252935	1		469	322	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100041	157100055	+	inframe_deletion	In_Frame_Del	DEL	AGGAGGAGCAGGAGC	AGGAGGAGCAGGAGC	-	rs773423003	NA	P-0028761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	12	80	2	ENST00000346085.5:c.993_1007del	p.Gly333_Gly337del	p.G333_G337del	ENST00000346085	NM_020732.3	326	ggAGGAGGAGCAGGAGCa/gga	1/20	0.745684927252935	1	FACETS	0.326	0.234	0.433	0.326	0.234	0.433	SUBCLONAL	1	TRUE	0	0.745684927252935	1		82	62	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574000	7574013	+	frameshift_variant	Frame_Shift_Del	DEL	CTCGGAACATCTCG	CTCGGAACATCTCG	-	novel	NA	P-0028761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	326	706	1	ENST00000269305.4:c.1014_1027del	p.Phe338LeufsTer4	p.F338Lfs*4	ENST00000269305	NM_001126112.2	338	ttCGAGATGTTCCGAGag/ttag	10/11	0.352436924844332	1	FACETS	0.761	0.723	0.798	0.761	0.723	0.798	INDETERMINATE	1	TRUE	0	0.745684927252935	1		707	721	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554654	63554654	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	131	518	0	ENST00000307078.5:c.85G>A	p.Glu29Lys	p.E29K	ENST00000307078	NM_004655.3	29	Gaa/Aaa	2/11	0.352436924844332	1	FACETS	0.421	0.384	0.46	0.421	0.384	0.46	INDETERMINATE	1	TRUE	0	0.745684927252935	1		518	523	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	56	404	0				ENST00000310581	NM_198253.2	-/1132			0.208336386218961	2	FACETS	1	0.89	1	1	0.974	1	CLONAL	3	FALSE	0	0.259344593522227	2		404	142	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458005	120458005	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	100	485	3	ENST00000256646.2:c.7340del	p.Gly2447ValfsTer43	p.G2447Vfs*43	ENST00000256646	NM_024408.3	2447	gGt/gt	34/34	1	2	FACETS	1	0.951	1	1	0.988	1	CLONAL	2	FALSE	1	0.259344593522227	2		488	354	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511619	66511620	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0028762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	316	468	0	ENST00000358598.2:c.79_80del	p.Ile27SerfsTer17	p.I27Sfs*17	ENST00000358598	NM_212471.2	27	ATt/t	2/11	0.259344593522227	1	FACETS	0.985	0.936	1	1	0.997	1	CLONAL	3	FALSE	0	0.259344593522227	1		468	718	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0028772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	238	581	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.640714955232871	3	FACETS	0.956	0.915	0.996	0.956	0.915	0.996	CLONAL	3	TRUE	0	0.640714955232871	3		581	342	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0028772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	344	747	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	NA	2	FACETS	0.983	0.945	1			1	INDETERMINATE	2	TRUE	NA	0.640714955232871	2		750	546	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0028772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	117	370	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.640714955232871	2		370	364	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0028772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	124	369	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.956	0.872	1	0.956	0.872	1	CLONAL	1	TRUE	1	0.640714955232871	2		369	405	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412095	63412095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852217	NA	P-0028772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	383	563	1	ENST00000330258.3:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000330258	NM_152424.3	358	Cga/Tga	2/2	0.624990889174324	2	FACETS	0.947	0.911	0.983	0.947	0.911	0.983	CLONAL	2	TRUE	0	0.640714955232871	2		564	631	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486254	8486254	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	201	280	0	ENST00000356435.5:c.2563G>T	p.Gly855Cys	p.G855C	ENST00000356435		855	Ggc/Tgc	17/35	0.89872450010242	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.89872450010242	1		280	239	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144144	55144144	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519812	NA	P-0028773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	164	474	0	ENST00000257290.5:c.1973T>C	p.Val658Ala	p.V658A	ENST00000257290	NM_006206.4	658	gTa/gCa	14/23	NA	2	FACETS	0.607	0.56	0.656			1	INDETERMINATE	1	TRUE	NA	0.89872450010242	2		474	601	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152104	55152104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121908588	NA	P-0028773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	598	554	0	ENST00000257290.5:c.2536G>T	p.Asp846Tyr	p.D846Y	ENST00000257290	NM_006206.4	846	Gat/Tat	18/23	NA	2	FACETS	0.977	0.96	0.993			1	INDETERMINATE	2	TRUE	NA	0.89872450010242	2		554	681	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486254	8486254	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028773-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	270	280	0	ENST00000356435.5:c.2563G>T	p.Gly855Cys	p.G855C	ENST00000356435		855	Ggc/Tgc	17/35	0.962164151507832	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.962164151507832	1		280	284	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144144	55144144	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519812	NA	P-0028773-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	233	474	0	ENST00000257290.5:c.1973T>C	p.Val658Ala	p.V658A	ENST00000257290	NM_006206.4	658	gTa/gCa	14/23	NA	2	FACETS	0.701	0.657	0.746			1	INDETERMINATE	1	TRUE	NA	0.962164151507832	2		474	691	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152104	55152104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121908588	NA	P-0028773-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	657	554	0	ENST00000257290.5:c.2536G>T	p.Asp846Tyr	p.D846Y	ENST00000257290	NM_006206.4	846	Gat/Tat	18/23	NA	2	FACETS	1	0.997	1			1	INDETERMINATE	2	TRUE	NA	0.962164151507832	2		554	674	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0028774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	120	242	0	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.72760571412864	2		242	316	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812574	43812574	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200454070	NA	P-0028774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	146	359	2	ENST00000372470.3:c.1277G>A	p.Arg426Gln	p.R426Q	ENST00000372470	NM_005373.2	426	cGa/cAa	8/12	1	2	FACETS	0.942	0.868	1	0.942	0.868	1	CLONAL	1	TRUE	1	0.72760571412864	2		361	426	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624297	89624297	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs797044910	NA	P-0028774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	114	350	2	ENST00000371953.3:c.71A>G	p.Asp24Gly	p.D24G	ENST00000371953	NM_000314.4	24	gAc/gGc	1/9	1	2	FACETS	0.895	0.815	0.978	0.895	0.815	0.978	CLONAL	1	TRUE	1	0.72760571412864	2		352	350	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0028774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	106	494	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.72760571412864	2		494	272	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0028774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	96	282	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.72760571412864	2		282	250	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94923020	94923020	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	17	446	0	ENST00000536441.1:c.448C>T	p.Gln150Ter	p.Q150*	ENST00000536441	NM_144665.3	150	Caa/Taa	4/10	1	2	FACETS	0.166	0.123	0.216	0.166	0.123	0.216	SUBCLONAL	1	TRUE	1	0.72760571412864	2		446	282	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0028774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	181	471	6	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.925	0.859	0.992	0.925	0.859	0.992	CLONAL	1	TRUE	1	0.72760571412864	2		477	538	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001395	29001395	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	24	262	0	ENST00000282397.4:c.1337T>C	p.Leu446Pro	p.L446P	ENST00000282397	NM_002019.4	446	cTg/cCg	10/30	1	2	FACETS	0.203	0.159	0.254	0.203	0.159	0.254	SUBCLONAL	1	TRUE	1	0.72760571412864	2		262	325	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955550	48955550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913304	NA	P-0028774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	36	330	0	ENST00000267163.4:c.1666C>T	p.Arg556Ter	p.R556*	ENST00000267163	NM_000321.2	556	Cga/Tga	17/27	0.711533283603026	1	FACETS	0.348	0.289	0.412	0.348	0.289	0.412	SUBCLONAL	1	TRUE	0	0.72760571412864	1		330	181	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705513	43705514	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0028774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	176	398	0	ENST00000382044.4:c.5108_5109del	p.Glu1703ValfsTer6	p.E1703Vfs*6	ENST00000382044	NM_001141980.1	1703	gAG/g	24/28	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.72760571412864	2		398	474	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119710	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0028774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	100	260	0	ENST00000285071.4:c.1284_1285del	p.His429ArgfsTer26	p.H429Rfs*26	ENST00000285071	NM_144997.5	428	ccCCac/ccac	11/14	1	2	FACETS	0.864	0.781	0.951	0.864	0.781	0.951	CLONAL	1	TRUE	1	0.72760571412864	2		260	318	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58700941	58700941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	35	377	0	ENST00000305921.3:c.532G>A	p.Val178Ile	p.V178I	ENST00000305921	NM_003620.3	178	Gtc/Atc	2/6	1	2	FACETS	0.195	0.159	0.235	0.195	0.159	0.235	SUBCLONAL	1	TRUE	1	0.72760571412864	2		377	494	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245820	5245820	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746218785	NA	P-0028774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	46	445	1	ENST00000357368.4:c.955G>A	p.Val319Ile	p.V319I	ENST00000357368	NM_002850.3	319	Gtc/Atc	10/38	1	2	FACETS	0.256	0.216	0.301	0.256	0.216	0.301	SUBCLONAL	1	TRUE	1	0.72760571412864	2		446	493	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354008	15354008	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	37	153	0	ENST00000263377.2:c.2872del	p.Leu958CysfsTer110	p.L958Cfs*110	ENST00000263377	NM_058243.2	958	Ctg/tg	14/20	1	2	FACETS	0.585	0.488	0.689	0.585	0.488	0.689	SUBCLONAL	1	TRUE	1	0.72760571412864	2		153	174	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736166	204736166	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	97	322	0	ENST00000302823.3:c.529del	p.Tyr177IlefsTer10	p.Y177Ifs*10	ENST00000302823	NM_005214.4	175	Ttt/tt	3/4	1	2	FACETS	0.901	0.814	0.991	0.901	0.814	0.991	CLONAL	1	TRUE	1	0.72760571412864	2		322	296	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662809	227662809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	173	398	1	ENST00000305123.5:c.646C>T	p.His216Tyr	p.H216Y	ENST00000305123	NM_005544.2	216	Cac/Tac	1/2	1	2	FACETS	0.991	0.92	1	0.991	0.92	1	CLONAL	1	TRUE	1	0.72760571412864	2		399	480	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0028774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	69	228	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.72760571412864	3	FACETS	1	0.964	1	0.616	0.545	0.689	CLONAL	1	TRUE	1	0.72760571412864	3		228	210	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1978262	1978262	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	204	493	4	ENST00000382891.5:c.3682C>T	p.Arg1228Cys	p.R1228C	ENST00000382891	NM_133335.3	1228	Cgc/Tgc	21/22	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.72760571412864	2		497	523	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007331	143007332	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs772784869	NA	P-0028774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	41	273	0	ENST00000262992.4:c.2452dup	p.Arg818LysfsTer26	p.R818Kfs*26	ENST00000262992	NM_001101669.1	818	aga/aAga	22/24	1	2	FACETS	0.4	0.334	0.471	0.4	0.334	0.471	SUBCLONAL	1	TRUE	1	0.72760571412864	2		273	282	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851941	128851943	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs767361434	NA	P-0028774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	29	397	0	ENST00000249373.3:c.2021_2023del	p.Lys674del	p.K674del	ENST00000249373	NM_005631.4	671	cgGAAg/cgg	12/12	1	2	FACETS	0.164	0.131	0.202	0.164	0.131	0.202	SUBCLONAL	1	TRUE	1	0.72760571412864	2		397	485	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27192526	27192526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776631444	NA	P-0028774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	32	433	0	ENST00000380036.4:c.1529G>A	p.Arg510Gln	p.R510Q	ENST00000380036	NM_000459.3	510	cGg/cAg	11/23	1	2	FACETS	0.218	0.176	0.264	0.218	0.176	0.264	SUBCLONAL	1	TRUE	1	0.72760571412864	2		433	404	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209593	98209593	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	133	332	5	ENST00000331920.6:c.3945del	p.Tyr1316ThrfsTer56	p.Y1316Tfs*56	ENST00000331920	NM_000264.3	1315	ccC/cc	23/24	1	2	FACETS	0.896	0.822	0.973	0.896	0.822	0.973	CLONAL	1	TRUE	1	0.72760571412864	2		337	408	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0028774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	141	428	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.923	0.849	0.999	0.923	0.849	0.999	CLONAL	1	TRUE	1	0.72760571412864	2		428	420	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279814	46279815	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCA	rs3830810	NA	P-0028774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	45	258	1	ENST00000371998.3:c.3759_3761dup	p.Gln1276dup	p.Q1276dup	ENST00000371998		1276	atg/atGCAg	20/23	1	2	FACETS	0.35	0.295	0.411	0.35	0.295	0.411	SUBCLONAL	1	TRUE	1	0.72760571412864	2		259	353	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073548	8073548	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	40	216	0	ENST00000377482.5:c.1111G>T	p.Gly371Ter	p.G371*	ENST00000377482	NM_018948.3	371	Gga/Tga	4/4	1	2	FACETS	0.637	0.531	0.754	0.637	0.531	0.754	SUBCLONAL	1	TRUE	1	0.39	2		216	322	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074220	8074220	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	73	287	1	ENST00000377482.5:c.439G>T	p.Glu147Ter	p.E147*	ENST00000377482	NM_018948.3	147	Gaa/Taa	4/4	1	2	FACETS	0.767	0.673	0.868	0.767	0.673	0.868	SUBCLONAL	1	TRUE	1	0.39	2		288	488	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782347	9782347	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	110	363	0	ENST00000377346.4:c.2280G>A	p.Trp760Ter	p.W760*	ENST00000377346	NM_005026.3	760	tgG/tgA	18/24	1	2	FACETS	0.887	0.798	0.98	0.887	0.798	0.98	CLONAL	1	TRUE	1	0.39	2		363	636	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782592	9782592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1486776204	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	84	319	0	ENST00000377346.4:c.2354G>A	p.Arg785Gln	p.R785Q	ENST00000377346	NM_005026.3	785	cGg/cAg	19/24	1	2	FACETS	0.907	0.804	1	0.907	0.804	1	CLONAL	1	TRUE	1	0.39	2		319	475	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174381	11174381	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	84	304	0	ENST00000361445.4:c.7294A>G	p.Met2432Val	p.M2432V	ENST00000361445	NM_004958.3	2432	Atg/Gtg	53/58	1	2	FACETS	0.828	0.734	0.929	0.828	0.734	0.929	CLONAL	1	TRUE	1	0.39	2		304	520	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190761	11190761	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	105	333	0	ENST00000361445.4:c.5438A>G	p.Glu1813Gly	p.E1813G	ENST00000361445	NM_004958.3	1813	gAg/gGg	39/58	1	2	FACETS	0.9	0.809	0.997	0.9	0.809	0.997	CLONAL	1	TRUE	1	0.39	2		333	598	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199434	16199434	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	75	244	0	ENST00000375759.3:c.207G>T	p.Met69Ile	p.M69I	ENST00000375759	NM_015001.2	69	atG/atT	2/15	1	2	FACETS	0.934	0.822	1	0.934	0.822	1	CLONAL	1	TRUE	1	0.39	2		244	412	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255137	16255137	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	81	309	0	ENST00000375759.3:c.2402G>T	p.Arg801Ile	p.R801I	ENST00000375759	NM_015001.2	801	aGa/aTa	11/15	1	2	FACETS	0.829	0.733	0.932	0.829	0.733	0.932	CLONAL	1	TRUE	1	0.39	2		309	501	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259195	16259195	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	111	307	0	ENST00000375759.3:c.6460T>C	p.Ser2154Pro	p.S2154P	ENST00000375759	NM_015001.2	2154	Tct/Cct	11/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.39	2		307	485	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259759	16259759	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	105	324	0	ENST00000375759.3:c.7024C>T	p.Arg2342Ter	p.R2342*	ENST00000375759	NM_015001.2	2342	Cga/Tga	11/15	1	2	FACETS	0.852	0.765	0.944	0.852	0.765	0.944	CLONAL	1	TRUE	1	0.39	2		324	632	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260305	16260305	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	70	286	0	ENST00000375759.3:c.7570G>A	p.Ala2524Thr	p.A2524T	ENST00000375759	NM_015001.2	2524	Gcc/Acc	11/15	1	2	FACETS	0.847	0.741	0.96	0.847	0.741	0.96	CLONAL	1	TRUE	1	0.39	2		286	424	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261011	16261011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780025497	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	86	279	0	ENST00000375759.3:c.8276C>T	p.Thr2759Met	p.T2759M	ENST00000375759	NM_015001.2	2759	aCg/aTg	11/15	1	2	FACETS	0.826	0.732	0.925	0.826	0.732	0.925	CLONAL	1	TRUE	1	0.39	2		279	534	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261332	16261332	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	105	360	0	ENST00000375759.3:c.8597C>A	p.Pro2866His	p.P2866H	ENST00000375759	NM_015001.2	2866	cCt/cAt	11/15	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.39	2		360	521	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17371320	17371320	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs74315370	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	89	315	2	ENST00000375499.3:c.136C>T	p.Arg46Ter	p.R46*	ENST00000375499	NM_003000.2	46	Cga/Tga	2/8	1	2	FACETS	0.873	0.776	0.975	0.873	0.776	0.975	CLONAL	1	TRUE	1	0.39	2		317	523	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087905	27087905	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	133	387	0	ENST00000324856.7:c.2192G>A	p.Gly731Asp	p.G731D	ENST00000324856	NM_006015.4	731	gGc/gAc	6/20	1	2	FACETS	0.999	0.909	1	0.999	0.909	1	CLONAL	1	TRUE	1	0.39	2		387	683	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088694	27088694	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	166	388	0	ENST00000324856.7:c.2303G>A	p.Gly768Asp	p.G768D	ENST00000324856	NM_006015.4	768	gGc/gAc	7/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.39	2		388	683	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097631	27097631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	86	348	0	ENST00000324856.7:c.3220C>T	p.Arg1074Trp	p.R1074W	ENST00000324856	NM_006015.4	1074	Cgg/Tgg	12/20	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.39	2		348	429	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099972	27099972	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	96	348	0	ENST00000324856.7:c.3851C>A	p.Pro1284His	p.P1284H	ENST00000324856	NM_006015.4	1284	cCt/cAt	15/20	1	2	FACETS	0.989	0.884	1	0.989	0.884	1	CLONAL	1	TRUE	1	0.39	2		348	498	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	94	476	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.898	0.801	1	0.898	0.801	1	CLONAL	1	TRUE	1	0.39	2		476	537	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28605725	28605725	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	106	349	1	ENST00000253063.3:c.1329C>A	p.Phe443Leu	p.F443L	ENST00000253063	NM_031459.4	443	ttC/ttA	9/10	1	2	FACETS	0.92	0.827	1	0.92	0.827	1	CLONAL	1	TRUE	1	0.39	2		350	591	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820858	36820858	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	99	308	0	ENST00000373129.3:c.519G>T	p.Glu173Asp	p.E173D	ENST00000373129	NM_032017.1	173	gaG/gaT	6/12	1	2	FACETS	0.853	0.763	0.949	0.853	0.763	0.949	CLONAL	1	TRUE	1	0.39	2		308	595	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941085	36941085	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	113	361	0	ENST00000361632.4:c.254C>A	p.Ser85Tyr	p.S85Y	ENST00000361632		85	tCt/tAt	3/16	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.39	2		361	545	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805065	43805065	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	85	348	0	ENST00000372470.3:c.515G>A	p.Gly172Asp	p.G172D	ENST00000372470	NM_005373.2	172	gGc/gAc	4/12	1	2	FACETS	0.769	0.681	0.863	0.769	0.681	0.863	SUBCLONAL	1	TRUE	1	0.39	2		348	567	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332712	65332712	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	44	265	0	ENST00000342505.4:c.827C>A	p.Thr276Asn	p.T276N	ENST00000342505	NM_002227.2	276	aCt/aAt	7/25	1	2	FACETS	0.767	0.647	0.899	0.767	0.647	0.899	SUBCLONAL	1	TRUE	1	0.39	2		265	294	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733524	85733524	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370432633	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	33	295	2	ENST00000370580.1:c.488C>T	p.Thr163Met	p.T163M	ENST00000370580	NM_003921.4	163	aCg/aTg	3/3	1	2	FACETS	0.559	0.456	0.673	0.559	0.456	0.673	SUBCLONAL	1	TRUE	1	0.39	2		297	303	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115252260	115252260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779899354	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	70	287	0	ENST00000369535.4:c.380C>T	p.Thr127Ile	p.T127I	ENST00000369535	NM_002524.4	127	aCa/aTa	4/7	1	2	FACETS	0.867	0.759	0.983	0.867	0.759	0.983	CLONAL	1	TRUE	1	0.39	2		287	414	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263192	115263192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	74	367	0	ENST00000438362.2:c.2158C>T	p.Arg720Cys	p.R720C	ENST00000438362	NM_001242891.1	720	Cgc/Tgc	17/20	1	2	FACETS	0.796	0.698	0.9	0.796	0.698	0.9	SUBCLONAL	1	TRUE	1	0.39	2		367	477	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268917	115268917	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	50	319	0	ENST00000438362.2:c.1693C>A	p.Leu565Ile	p.L565I	ENST00000438362	NM_001242891.1	565	Ctc/Atc	14/20	1	2	FACETS	0.609	0.518	0.709	0.609	0.518	0.709	SUBCLONAL	1	TRUE	1	0.39	2		319	421	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844747	156844747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771342578	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	114	409	0	ENST00000524377.1:c.1301C>T	p.Thr434Met	p.T434M	ENST00000524377	NM_002529.3	434	aCg/aTg	11/17	1	2	FACETS	0.803	0.723	0.887	0.803	0.723	0.887	CLONAL	1	TRUE	1	0.39	2		409	728	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161326487	161326487	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	101	273	0	ENST00000367975.2:c.262T>C	p.Ser88Pro	p.S88P	ENST00000367975	NM_003001.3	88	Tcg/Ccg	5/6	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.39	2		273	434	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724598	162724598	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	86	289	0	ENST00000367921.3:c.370C>T	p.Arg124Trp	p.R124W	ENST00000367921	NM_006182.2	124	Cgg/Tgg	5/18	1	2	FACETS	0.889	0.789	0.995	0.889	0.789	0.995	CLONAL	1	TRUE	1	0.39	2		289	496	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741924	162741924	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	80	270	0	ENST00000367921.3:c.1615T>G	p.Ser539Ala	p.S539A	ENST00000367921	NM_006182.2	539	Tca/Gca	13/18	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.39	2		270	402	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163325222	163325222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	20	326	0	ENST00000271452.3:c.1358C>T	p.Ala453Val	p.A453V	ENST00000271452	NM_145697.2	453	gCt/gTt	14/14	1	2	FACETS	0.389	0.297	0.495	0.389	0.297	0.495	SUBCLONAL	1	TRUE	1	0.39	2		326	264	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050412	176050412	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	28	190	0	ENST00000367669.3:c.1153A>G	p.Thr385Ala	p.T385A	ENST00000367669	NM_022457.5	385	Act/Gct	11/20	1	2	FACETS	0.881	0.712	1	0.881	0.712	1	CLONAL	1	TRUE	1	0.39	2		190	163	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119485	193119485	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	48	233	0	ENST00000367435.3:c.880G>A	p.Asp294Asn	p.D294N	ENST00000367435	NM_024529.4	294	Gat/Aat	9/17	1	2	FACETS	0.733	0.622	0.853	0.733	0.622	0.853	SUBCLONAL	1	TRUE	1	0.39	2		233	336	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204501343	204501343	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	50	273	0	ENST00000367182.3:c.312G>T	p.Lys104Asn	p.K104N	ENST00000367182	NM_001278516.1	104	aaG/aaT	5/11	1	2	FACETS	0.953	0.815	1	0.953	0.815	1	CLONAL	1	TRUE	1	0.39	2		273	269	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567647	226567647	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	80	291	2	ENST00000366794.5:c.1519del	p.Ser507AlafsTer17	p.S507Afs*17	ENST00000366794	NM_001618.3	507	Agc/gc	10/23	1	2	FACETS	0.95	0.84	1	0.95	0.84	1	CLONAL	1	TRUE	1	0.39	2		293	432	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612954	228612954	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	32	218	0	ENST00000366696.1:c.73del	p.Val25TrpfsTer12	p.V25Wfs*12	ENST00000366696	NM_003493.2	25	Gtg/tg	1/1	1	2	FACETS	0.505	0.411	0.611	0.505	0.411	0.611	SUBCLONAL	1	TRUE	1	0.39	2		218	325	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246091238	246091238	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	74	269	0	ENST00000388985.4:c.697G>T	p.Glu233Ter	p.E233*	ENST00000388985		233	Gag/Tag	7/12	1	2	FACETS	0.757	0.665	0.857	0.757	0.665	0.857	SUBCLONAL	1	TRUE	1	0.39	2		269	501	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100645	8100645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1218595084	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	118	398	2	ENST00000346208.3:c.619G>A	p.Ala207Thr	p.A207T	ENST00000346208		207	Gcc/Acc	3/6	0.386904616141667	2	FACETS	0.894	0.808	0.985			1	CLONAL	1	TRUE	NA	0.39	2		400	677	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606811	43606811	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775842917	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	112	414	1	ENST00000355710.3:c.1420C>T	p.Arg474Trp	p.R474W	ENST00000355710	NM_020975.4	474	Cgg/Tgg	7/20	1	2	FACETS	0.872	0.785	0.963	0.872	0.785	0.963	CLONAL	1	TRUE	1	0.39	2		415	659	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759972	63759972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	69	205	0	ENST00000279873.7:c.625G>A	p.Ala209Thr	p.A209T	ENST00000279873	NM_032199.2	209	Gcc/Acc	4/10	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.39	2		205	325	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845634	63845634	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	31	181	0	ENST00000279873.7:c.1373C>A	p.Ala458Asp	p.A458D	ENST00000279873	NM_032199.2	458	gCc/gAc	9/10	1	2	FACETS	0.799	0.651	0.963	0.799	0.651	0.963	CLONAL	1	TRUE	1	0.39	2		181	199	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850713	63850713	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	53	265	0	ENST00000279873.7:c.1491A>G	p.Ile497Met	p.I497M	ENST00000279873	NM_032199.2	497	atA/atG	10/10	1	2	FACETS	0.717	0.614	0.83	0.717	0.614	0.83	SUBCLONAL	1	TRUE	1	0.39	2		265	379	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851224	63851224	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1262593085	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	103	357	1	ENST00000279873.7:c.2002G>A	p.Glu668Lys	p.E668K	ENST00000279873	NM_032199.2	668	Gag/Aag	10/10	1	2	FACETS	0.816	0.732	0.906	0.816	0.732	0.906	CLONAL	1	TRUE	1	0.39	2		358	647	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332605	70332605	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs781424040	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	55	288	1	ENST00000373644.4:c.510G>T	p.Glu170Asp	p.E170D	ENST00000373644	NM_030625.2	170	gaG/gaT	2/12	1	2	FACETS	0.766	0.658	0.884	0.766	0.658	0.884	SUBCLONAL	1	TRUE	1	0.39	2		289	368	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333498	70333498	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	53	298	0	ENST00000373644.4:c.1406del	p.Leu469CysfsTer23	p.L469Cfs*23	ENST00000373644	NM_030625.2	468	aTt/at	2/12	1	2	FACETS	0.713	0.61	0.825	0.713	0.61	0.825	SUBCLONAL	1	TRUE	1	0.39	2		298	381	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88678940	88678940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	44	233	0	ENST00000372037.3:c.880G>A	p.Ala294Thr	p.A294T	ENST00000372037	NM_004329.2	294	Gca/Aca	10/13	1	2	FACETS	0.892	0.754	1	0.892	0.754	1	CLONAL	1	TRUE	1	0.39	2		233	253	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692872	89692872	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1554898113	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	21	150	0	ENST00000371953.3:c.356T>G	p.Val119Gly	p.V119G	ENST00000371953	NM_000314.4	119	gTt/gGt	5/9	1	2	FACETS	0.913	0.713	1	0.913	0.713	1	CLONAL	1	TRUE	1	0.39	2		150	118	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	41	295	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	1	2	FACETS	0.883	0.742	1	0.883	0.742	1	CLONAL	1	TRUE	1	0.39	2		295	238	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717613	89717613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	35	212	0	ENST00000371953.3:c.638C>T	p.Pro213Leu	p.P213L	ENST00000371953	NM_000314.4	213	cCt/cTt	7/9	1	2	FACETS	0.739	0.609	0.882	0.739	0.609	0.882	SUBCLONAL	1	TRUE	1	0.39	2		212	243	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279653	123279653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	70	233	0	ENST00000358487.5:c.779C>T	p.Ala260Val	p.A260V	ENST00000358487	NM_000141.4	260	gCc/gTc	7/18	1	2	FACETS	0.9	0.788	1	0.9	0.788	1	CLONAL	1	TRUE	1	0.39	2		233	399	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128065	64128065	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1238025666	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	99	381	0	ENST00000334205.4:c.462+1G>A		p.X154_splice	ENST00000334205	NM_003942.2	154			1	2	FACETS	0.776	0.694	0.864	0.776	0.694	0.864	SUBCLONAL	1	TRUE	1	0.39	2		381	654	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132833	64132833	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1447050686	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	100	399	0	ENST00000334205.4:c.967C>T	p.Arg323Cys	p.R323C	ENST00000334205	NM_003942.2	323	Cgc/Tgc	9/17	1	2	FACETS	0.838	0.75	0.931	0.838	0.75	0.931	CLONAL	1	TRUE	1	0.39	2		399	612	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132927	64132927	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145356210	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	73	263	0	ENST00000334205.4:c.1061G>A	p.Arg354Gln	p.R354Q	ENST00000334205	NM_003942.2	354	cGa/cAa	9/17	1	2	FACETS	0.855	0.75	0.966	0.855	0.75	0.966	CLONAL	1	TRUE	1	0.39	2		263	438	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633523	69633523	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1049232873	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	110	251	0	ENST00000334134.2:c.179C>T	p.Pro60Leu	p.P60L	ENST00000334134	NM_005247.2	60	cCg/cTg	1/3	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.39	2		251	503	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942079	71942079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139442327	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	95	417	0	ENST00000298229.2:c.1343C>T	p.Ser448Leu	p.S448L	ENST00000298229	NM_001567.3	448	tCg/tTg	12/28	1	2	FACETS	0.809	0.722	0.902	0.809	0.722	0.902	CLONAL	1	TRUE	1	0.39	2		417	602	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911953	94911953	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	55	398	1	ENST00000536441.1:c.977G>T	p.Arg326Leu	p.R326L	ENST00000536441	NM_144665.3	326	cGa/cTa	7/10	1	2	FACETS	0.754	0.648	0.87	0.754	0.648	0.87	SUBCLONAL	1	TRUE	1	0.39	2		399	374	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100534	102100534	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	81	340	0	ENST00000282441.5:c.1378G>T	p.Gly460Ter	p.G460*	ENST00000282441	NM_001130145.2	460	Gga/Tga	9/9	1	2	FACETS	0.873	0.771	0.98	0.873	0.771	0.98	CLONAL	1	TRUE	1	0.39	2		340	476	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205756	108205756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531980488	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	42	267	0	ENST00000278616.4:c.8071C>T	p.Arg2691Cys	p.R2691C	ENST00000278616	NM_000051.3	2691	Cgc/Tgc	55/63	1	2	FACETS	0.89	0.749	1	0.89	0.749	1	CLONAL	1	TRUE	1	0.39	2		267	242	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371839	118371839	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	76	289	0	ENST00000534358.1:c.6296C>T	p.Ala2099Val	p.A2099V	ENST00000534358	NM_005933.3	2099	gCc/gTc	25/36	1	2	FACETS	0.792	0.697	0.894	0.792	0.697	0.894	SUBCLONAL	1	TRUE	1	0.39	2		289	492	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376310	118376310	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	72	353	0	ENST00000534358.1:c.9708del	p.Lys3236AsnfsTer20	p.K3236Nfs*20	ENST00000534358	NM_005933.3	3235	Aaa/aa	27/36	1	2	FACETS	0.863	0.757	0.976	0.863	0.757	0.976	CLONAL	1	TRUE	1	0.39	2		353	428	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103322	119103322	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	45	340	0	ENST00000264033.4:c.360G>T	p.Glu120Asp	p.E120D	ENST00000264033	NM_005188.3	120	gaG/gaT	2/16	1	2	FACETS	0.701	0.592	0.821	0.701	0.592	0.821	SUBCLONAL	1	TRUE	1	0.39	2		340	329	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156232	119156232	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	101	283	0	ENST00000264033.4:c.1897G>T	p.Asp633Tyr	p.D633Y	ENST00000264033	NM_005188.3	633	Gat/Tat	11/16	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.39	2		283	484	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514523	125514523	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	35	215	0	ENST00000428830.2:c.1218A>C	p.Lys406Asn	p.K406N	ENST00000428830	NM_001114121.2	406	aaA/aaC	11/14	1	2	FACETS	0.709	0.585	0.848	0.709	0.585	0.848	SUBCLONAL	1	TRUE	1	0.39	2		215	253	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905505	11905505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774396176	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	44	191	0	ENST00000396373.4:c.155C>T	p.Ala52Val	p.A52V	ENST00000396373	NM_001987.4	52	gCg/gTg	2/8	1	2	FACETS	0.686	0.577	0.805	0.686	0.577	0.805	SUBCLONAL	1	TRUE	1	0.39	2		191	329	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435472	18435472	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	21	151	0	ENST00000266497.5:c.460del	p.Ile154LeufsTer3	p.I154Lfs*3	ENST00000266497		153	Aaa/aa	1/31	1	2	FACETS	0.792	0.617	0.991	0.792	0.617	0.991	CLONAL	1	TRUE	1	0.39	2		151	136	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552631	18552631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766274056	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	42	271	2	ENST00000266497.5:c.2042G>A	p.Arg681His	p.R681H	ENST00000266497		681	cGc/cAc	14/31	1	2	FACETS	0.73	0.613	0.859	0.73	0.613	0.859	SUBCLONAL	1	TRUE	1	0.39	2		273	295	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21630862	21630862	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202110155	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	59	384	1	ENST00000421138.2:c.742G>A	p.Ala248Thr	p.A248T	ENST00000421138		248	Gca/Aca	8/16	1	2	FACETS	0.798	0.69	0.916	0.798	0.69	0.916	CLONAL	1	TRUE	1	0.39	2		385	379	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230544	46230544	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	32	224	0	ENST00000334344.6:c.793A>C	p.Ile265Leu	p.I265L	ENST00000334344	NM_152641.2	265	Att/Ctt	8/21	1	2	FACETS	0.797	0.652	0.957	0.797	0.652	0.957	CLONAL	1	TRUE	1	0.39	2		224	206	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230637	46230637	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	50	323	0	ENST00000334344.6:c.886C>T	p.Leu296Phe	p.L296F	ENST00000334344	NM_152641.2	296	Ctt/Ttt	8/21	1	2	FACETS	0.83	0.708	0.962	0.83	0.708	0.962	CLONAL	1	TRUE	1	0.39	2		323	309	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231352	46231352	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	37	258	0	ENST00000334344.6:c.1192G>A	p.Asp398Asn	p.D398N	ENST00000334344	NM_152641.2	398	Gat/Aat	10/21	1	2	FACETS	0.84	0.698	0.996	0.84	0.698	0.996	CLONAL	1	TRUE	1	0.39	2		258	226	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245103	46245103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1004162984	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	95	254	0	ENST00000334344.6:c.3197C>T	p.Pro1066Leu	p.P1066L	ENST00000334344	NM_152641.2	1066	cCg/cTg	15/21	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.39	2		254	477	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432651	49432651	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs727503983	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	119	447	0	ENST00000301067.7:c.8488C>T	p.Arg2830Ter	p.R2830*	ENST00000301067	NM_003482.3	2830	Cga/Tga	34/54	1	2	FACETS	0.854	0.771	0.94	0.854	0.771	0.94	CLONAL	1	TRUE	1	0.39	2		447	715	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448518	49448518	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1189364625	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	103	317	0	ENST00000301067.7:c.193C>T	p.Arg65Cys	p.R65C	ENST00000301067	NM_003482.3	65	Cgt/Tgt	3/54	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.39	2		317	521	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56477667	56477667	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	50	300	0	ENST00000267101.3:c.215C>T	p.Ala72Val	p.A72V	ENST00000267101	NM_001982.3	72	gCc/gTc	2/28	1	2	FACETS	0.412	0.349	0.481	0.412	0.349	0.481	SUBCLONAL	1	TRUE	1	0.39	2		300	623	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489468	56489468	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	68	233	0	ENST00000267101.3:c.1933G>A	p.Ala645Thr	p.A645T	ENST00000267101	NM_001982.3	645	Gct/Act	17/28	1	2	FACETS	0.948	0.829	1	0.948	0.829	1	CLONAL	1	TRUE	1	0.39	2		233	368	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495395	56495395	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	44	376	0	ENST00000267101.3:c.3585G>T	p.Glu1195Asp	p.E1195D	ENST00000267101	NM_001982.3	1195	gaG/gaT	28/28	1	2	FACETS	0.497	0.417	0.586	0.497	0.417	0.586	SUBCLONAL	1	TRUE	1	0.39	2		376	454	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861966	57861966	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1272008775	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	79	309	0	ENST00000228682.2:c.1267A>G	p.Ile423Val	p.I423V	ENST00000228682	NM_005269.2	423	Atc/Gtc	10/12	1	2	FACETS	0.869	0.767	0.978	0.869	0.767	0.978	CLONAL	1	TRUE	1	0.39	2		309	466	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863449	57863449	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781683841	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	68	302	0	ENST00000228682.2:c.1544G>A	p.Arg515Gln	p.R515Q	ENST00000228682	NM_005269.2	515	cGg/cAg	11/12	1	2	FACETS	0.723	0.631	0.823	0.723	0.631	0.823	SUBCLONAL	1	TRUE	1	0.39	2		302	482	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863451	57863451	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1565600997	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	99	293	0	ENST00000228682.2:c.1546G>T	p.Gly516Cys	p.G516C	ENST00000228682	NM_005269.2	516	Ggt/Tgt	11/12	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.39	2		293	478	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112893770	112893770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780911423	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	26	198	0	ENST00000351677.2:c.659G>A	p.Arg220His	p.R220H	ENST00000351677	NM_002834.3	220	cGt/cAt	6/16	1	2	FACETS	0.585	0.465	0.72	0.585	0.465	0.72	SUBCLONAL	1	TRUE	1	0.39	2		198	228	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112473	115112473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	51	305	0	ENST00000257566.3:c.1267del	p.Arg423GlyfsTer209	p.R423Gfs*209	ENST00000257566	NM_016569.3	423	Cgg/gg	7/8	1	2	FACETS	0.439	0.372	0.512	0.439	0.372	0.512	SUBCLONAL	1	TRUE	1	0.39	2		305	596	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118950	115118950	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	17	111	0	ENST00000257566.3:c.391C>T	p.Arg131Ter	p.R131*	ENST00000257566	NM_016569.3	131	Cga/Tga	2/8	1	2	FACETS	0.618	0.465	0.797	0.618	0.465	0.797	SUBCLONAL	1	TRUE	1	0.39	2		111	141	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434495	121434495	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	97	397	1	ENST00000257555.6:c.1259C>T	p.Ala420Val	p.A420V	ENST00000257555		420	gCc/gTc	6/10	1	2	FACETS	0.809	0.722	0.901	0.809	0.722	0.901	CLONAL	1	TRUE	1	0.39	2		398	615	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123875211	123875211	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	41	195	0	ENST00000330479.4:c.167C>T	p.Ser56Phe	p.S56F	ENST00000330479	NM_020382.3	56	tCc/tTc	3/9	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.39	2		195	207	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220131	133220131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764904030	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	99	374	1	ENST00000320574.5:c.4306C>T	p.Arg1436Trp	p.R1436W	ENST00000320574	NM_006231.2	1436	Cgg/Tgg	34/49	1	2	FACETS	0.781	0.698	0.869	0.781	0.698	0.869	SUBCLONAL	1	TRUE	1	0.39	2		375	650	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226047	133226047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753426630	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	44	370	0	ENST00000320574.5:c.3850C>T	p.Arg1284Trp	p.R1284W	ENST00000320574	NM_006231.2	1284	Cgg/Tgg	31/49	1	2	FACETS	0.341	0.285	0.404	0.341	0.285	0.404	SUBCLONAL	1	TRUE	1	0.39	2		370	661	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244149	133244149	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	122	326	1	ENST00000320574.5:c.2259C>A	p.Phe753Leu	p.F753L	ENST00000320574	NM_006231.2	753	ttC/ttA	20/49	1	2	FACETS	0.993	0.9	1	0.993	0.9	1	CLONAL	1	TRUE	1	0.39	2		327	630	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519943	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	91	327	0	ENST00000320574.5:c.857C>A	p.Pro286His	p.P286H	ENST00000320574	NM_006231.2	286	cCt/cAt	9/49	1	2	FACETS	0.911	0.812	1	0.911	0.812	1	CLONAL	1	TRUE	1	0.39	2		327	512	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256188	133256188	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	103	319	0	ENST00000320574.5:c.473A>G	p.His158Arg	p.H158R	ENST00000320574	NM_006231.2	158	cAc/cGc	6/49	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.39	2		319	472	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549116	21549116	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	64	310	0	ENST00000382592.4:c.3160C>T	p.Arg1054Ter	p.R1054*	ENST00000382592	NM_014572.2	1054	Cga/Tga	8/8	1	2	FACETS	0.72	0.625	0.822	0.72	0.625	0.822	SUBCLONAL	1	TRUE	1	0.39	2		310	456	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562486	21562486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	26	59	0	ENST00000382592.4:c.1433C>T	p.Ala478Val	p.A478V	ENST00000382592	NM_014572.2	478	gCc/gTc	4/8	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.39	2		59	93	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562609	21562609	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	63	162	0	ENST00000382592.4:c.1310C>T	p.Ala437Val	p.A437V	ENST00000382592	NM_014572.2	437	gCc/gTc	4/8	1	2	FACETS	0.833	0.723	0.95	0.833	0.723	0.95	CLONAL	1	TRUE	1	0.39	2		162	388	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619894	21619894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55842804	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	83	237	0	ENST00000382592.4:c.272C>T	p.Ser91Leu	p.S91L	ENST00000382592	NM_014572.2	91	tCg/tTg	2/8	1	2	FACETS	0.994	0.882	1	0.994	0.882	1	CLONAL	1	TRUE	1	0.39	2		237	428	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28599028	28599028	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	51	309	0	ENST00000241453.7:c.2260G>T	p.Gly754Trp	p.G754W	ENST00000241453	NM_004119.2	754	Ggg/Tgg	18/24	1	2	FACETS	0.858	0.733	0.992	0.858	0.733	0.992	CLONAL	1	TRUE	1	0.39	2		309	305	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919580	28919580	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	79	329	0	ENST00000282397.4:c.2355+2T>C		p.X785_splice	ENST00000282397	NM_002019.4	785			1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.39	2		329	378	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28979946	28979946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764045713	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	57	572	0	ENST00000282397.4:c.1522C>T	p.Arg508Cys	p.R508C	ENST00000282397	NM_002019.4	508	Cgc/Tgc	11/30	1	2	FACETS	0.965	0.834	1	0.965	0.834	1	CLONAL	1	TRUE	1	0.39	2		572	303	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893291	32893291	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs80358435	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	45	319	1	ENST00000380152.3:c.145G>T	p.Glu49Ter	p.E49*	ENST00000380152		49	Gaa/Taa	3/27	1	2	FACETS	0.845	0.715	0.987	0.845	0.715	0.987	CLONAL	1	TRUE	1	0.39	2		320	273	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912120	32912120	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	49	387	2	ENST00000380152.3:c.3628G>T	p.Asp1210Tyr	p.D1210Y	ENST00000380152		1210	Gat/Tat	11/27	1	2	FACETS	0.75	0.638	0.872	0.75	0.638	0.872	SUBCLONAL	1	TRUE	1	0.39	2		389	335	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134622	41134622	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1213192608	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	28	269	0	ENST00000379561.5:c.1006G>A	p.Asp336Asn	p.D336N	ENST00000379561	NM_002015.3	336	Gat/Aat	2/3	1	2	FACETS	0.515	0.412	0.631	0.515	0.412	0.631	SUBCLONAL	1	TRUE	1	0.39	2		269	279	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240107	41240107	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	19	70	0	ENST00000379561.5:c.243G>T	p.Glu81Asp	p.E81D	ENST00000379561	NM_002015.3	81	gaG/gaT	1/3	1	2	FACETS	0.946	0.73	1	0.946	0.73	1	CLONAL	1	TRUE	1	0.39	2		70	103	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039449	49039449	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	77	327	0	ENST00000267163.4:c.2434C>A	p.Pro812Thr	p.P812T	ENST00000267163	NM_000321.2	812	Cca/Aca	23/27	1	2	FACETS	0.995	0.878	1	0.995	0.878	1	CLONAL	1	TRUE	1	0.39	2		327	397	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103525619	103525619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs574826021	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	44	247	0	ENST00000355739.4:c.2890C>T	p.Arg964Trp	p.R964W	ENST00000355739	NM_000123.3	964	Cgg/Tgg	14/15	1	2	FACETS	0.865	0.73	1	0.865	0.73	1	CLONAL	1	TRUE	1	0.39	2		247	261	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435761	110435761	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	45	186	0	ENST00000375856.3:c.2640C>A	p.Phe880Leu	p.F880L	ENST00000375856	NM_003749.2	880	ttC/ttA	1/2	1	2	FACETS	0.81	0.685	0.946	0.81	0.685	0.946	CLONAL	1	TRUE	1	0.39	2		186	285	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046592	30046592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	81	292	0	ENST00000331968.5:c.2591G>T	p.Ser864Ile	p.S864I	ENST00000331968	NM_002742.2	864	aGt/aTt	18/18	1	2	FACETS	0.851	0.752	0.957	0.851	0.752	0.957	CLONAL	1	TRUE	1	0.39	2		292	488	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093411	30093411	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs201154555	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	41	317	0	ENST00000331968.5:c.1852C>T	p.Arg618Ter	p.R618*	ENST00000331968	NM_002742.2	618	Cga/Tga	13/18	1	2	FACETS	0.615	0.514	0.727	0.615	0.514	0.727	SUBCLONAL	1	TRUE	1	0.39	2		317	342	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396622	30396622	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200987283	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	28	123	1	ENST00000331968.5:c.97C>T	p.Pro33Ser	p.P33S	ENST00000331968	NM_002742.2	33	Ccc/Tcc	1/18	1	2	FACETS	0.772	0.622	0.94	0.772	0.622	0.94	CLONAL	1	TRUE	1	0.39	2		124	186	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873801	35873801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1347828578	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	68	244	0	ENST00000216797.5:c.50G>A	p.Arg17His	p.R17H	ENST00000216797	NM_020529.2	17	cGc/cAc	1/6	1	2	FACETS	0.872	0.762	0.99	0.872	0.762	0.99	CLONAL	1	TRUE	1	0.39	2		244	400	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610630	81610630	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	73	289	0	ENST00000298171.2:c.2231del	p.Asn744ThrfsTer4	p.N744Tfs*4	ENST00000298171	NM_000369.2	743	gAa/ga	10/10	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.39	2		289	372	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95599737	95599737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147660793	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	91	245	0	ENST00000393063.1:c.59C>T	p.Ala20Val	p.A20V	ENST00000393063	NM_030621.3	20	gCt/gTt	3/28	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.39	2		245	394	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40683715	40683715	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	72	397	1	ENST00000249776.8:c.707C>T	p.Ala236Val	p.A236V	ENST00000249776	NM_033286.3	236	gCa/gTa	7/9	1	2	FACETS	0.655	0.572	0.743	0.655	0.572	0.743	SUBCLONAL	1	TRUE	1	0.39	2		398	564	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989105	41989105	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	71	368	0	ENST00000219905.7:c.1897G>T	p.Gly633Ter	p.G633*	ENST00000219905	NM_001164273.1	633	Gga/Tga	3/24	1	2	FACETS	0.886	0.777	1	0.886	0.777	1	CLONAL	1	TRUE	1	0.39	2		368	411	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003414	42003414	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269317379	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	80	365	0	ENST00000219905.7:c.2951G>A	p.Arg984His	p.R984H	ENST00000219905	NM_001164273.1	984	cGc/cAc	8/24	1	2	FACETS	0.86	0.76	0.967	0.86	0.76	0.967	CLONAL	1	TRUE	1	0.39	2		365	477	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054444	42054444	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	38	266	0	ENST00000219905.7:c.7628G>T	p.Arg2543Ile	p.R2543I	ENST00000219905	NM_001164273.1	2543	aGa/aTa	22/24	1	2	FACETS	0.637	0.528	0.757	0.637	0.528	0.757	SUBCLONAL	1	TRUE	1	0.39	2		266	306	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43699735	43699735	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137879443	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	97	316	0	ENST00000382044.4:c.5780C>T	p.Thr1927Met	p.T1927M	ENST00000382044	NM_001141980.1	1927	aCg/aTg	28/28	1	2	FACETS	0.964	0.863	1	0.964	0.863	1	CLONAL	1	TRUE	1	0.39	2		316	516	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705524	43705525	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	114	345	0	ENST00000382044.4:c.5097_5098insT	p.Gly1700TrpfsTer10	p.G1700Wfs*10	ENST00000382044	NM_001141980.1	1699	-/T	24/28	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.39	2		345	575	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727452	66727452	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	85	282	0	ENST00000307102.5:c.168G>T	p.Gln56His	p.Q56H	ENST00000307102	NM_002755.3	56	caG/caT	2/11	1	2	FACETS	0.995	0.884	1	0.995	0.884	1	CLONAL	1	TRUE	1	0.39	2		282	438	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457244	67457244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	76	319	0	ENST00000327367.4:c.218G>A	p.Gly73Asp	p.G73D	ENST00000327367	NM_005902.3	73	gGc/gAc	2/9	1	2	FACETS	0.822	0.723	0.928	0.822	0.723	0.928	CLONAL	1	TRUE	1	0.39	2		319	474	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304140	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	42	345	0	ENST00000355112.3:c.1543_1544del	p.Asn515Ter	p.N515*	ENST00000355112	NM_000057.2	512	ggAAaa/ggaa	7/22	1	2	FACETS	0.728	0.61	0.856	0.728	0.61	0.856	SUBCLONAL	1	TRUE	1	0.39	2		345	296	SUCCESS
BLM	641	MSKCC	GRCh37	15	91341469	91341469	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	45	289	0	ENST00000355112.3:c.3260T>G	p.Phe1087Cys	p.F1087C	ENST00000355112	NM_000057.2	1087	tTt/tGt	17/22	1	2	FACETS	0.881	0.746	1	0.881	0.746	1	CLONAL	1	TRUE	1	0.39	2		289	262	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346930	91346930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324479116	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	22	281	1	ENST00000355112.3:c.3538G>A	p.Val1180Ile	p.V1180I	ENST00000355112	NM_000057.2	1180	Gta/Ata	18/22	1	2	FACETS	0.522	0.406	0.656	0.522	0.406	0.656	SUBCLONAL	1	TRUE	1	0.39	2		282	216	SUCCESS
BLM	641	MSKCC	GRCh37	15	91352442	91352442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760554566	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	42	229	0	ENST00000355112.3:c.3827C>T	p.Ala1276Val	p.A1276V	ENST00000355112	NM_000057.2	1276	gCg/gTg	20/22	1	2	FACETS	0.628	0.526	0.74	0.628	0.526	0.74	SUBCLONAL	1	TRUE	1	0.39	2		229	343	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99486166	99486166	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1287599859	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	79	263	0	ENST00000268035.6:c.3472C>T	p.Arg1158Ter	p.R1158*	ENST00000268035	NM_000875.3	1158	Cga/Tga	19/21	1	2	FACETS	0.976	0.863	1	0.976	0.863	1	CLONAL	1	TRUE	1	0.39	2		263	415	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103346	2103346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777459404	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	103	315	0	ENST00000219476.3:c.229G>A	p.Ala77Thr	p.A77T	ENST00000219476	NM_000548.3	77	Gca/Aca	4/42	1	2	FACETS	0.95	0.853	1	0.95	0.853	1	CLONAL	1	TRUE	1	0.39	2		315	556	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2224253	2224253	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1444259559	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	45	409	0	ENST00000326181.6:c.1265T>C	p.Val422Ala	p.V422A	ENST00000326181	NM_032271.2	422	gTg/gCg	14/21	1	2	FACETS	0.396	0.332	0.467	0.396	0.332	0.467	SUBCLONAL	1	TRUE	1	0.39	2		409	583	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3651050	3651050	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1218169126	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	113	336	1	ENST00000294008.3:c.1093del	p.Gln365SerfsTer32	p.Q365Sfs*32	ENST00000294008	NM_032444.2	365	Cag/ag	5/15	1	2	FACETS	0.913	0.823	1	0.913	0.823	1	CLONAL	1	TRUE	1	0.39	2		337	635	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778500	3778500	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779996604	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	113	476	0	ENST00000262367.5:c.6548C>T	p.Ala2183Val	p.A2183V	ENST00000262367	NM_004380.2	2183	gCg/gTg	31/31	1	2	FACETS	0.867	0.782	0.958	0.867	0.782	0.958	CLONAL	1	TRUE	1	0.39	2		476	668	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786671	3786671	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1471683943	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	137	361	0	ENST00000262367.5:c.4540C>T	p.Arg1514Trp	p.R1514W	ENST00000262367	NM_004380.2	1514	Cgg/Tgg	27/31	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.39	2		361	696	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3794900	3794900	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	46	281	0	ENST00000262367.5:c.3977C>T	p.Ala1326Val	p.A1326V	ENST00000262367	NM_004380.2	1326	gCt/gTt	23/31	1	2	FACETS	0.696	0.588	0.814	0.696	0.588	0.814	SUBCLONAL	1	TRUE	1	0.39	2		281	339	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808905	3808905	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	98	377	0	ENST00000262367.5:c.3319G>T	p.Glu1107Ter	p.E1107*	ENST00000262367	NM_004380.2	1107	Gag/Tag	17/31	1	2	FACETS	0.827	0.739	0.92	0.827	0.739	0.92	CLONAL	1	TRUE	1	0.39	2		377	608	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828783	3828783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	119	361	0	ENST00000262367.5:c.1859C>T	p.Ala620Val	p.A620V	ENST00000262367	NM_004380.2	620	gCt/gTt	9/31	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.39	2		361	557	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831224	3831224	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	46	300	0	ENST00000262367.5:c.1657A>G	p.Thr553Ala	p.T553A	ENST00000262367	NM_004380.2	553	Act/Gct	7/31	1	2	FACETS	0.698	0.59	0.816	0.698	0.59	0.816	SUBCLONAL	1	TRUE	1	0.39	2		300	338	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892199	9892199	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	91	307	1	ENST00000330684.3:c.2291C>T	p.Ala764Val	p.A764V	ENST00000330684	NM_001134407.1	764	gCc/gTc	11/13	1	2	FACETS	0.82	0.73	0.916	0.82	0.73	0.916	CLONAL	1	TRUE	1	0.39	2		308	569	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916172	9916172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1423127538	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	51	299	0	ENST00000330684.3:c.2117C>T	p.Thr706Ile	p.T706I	ENST00000330684	NM_001134407.1	706	aCc/aTc	10/13	1	2	FACETS	0.739	0.63	0.857	0.739	0.63	0.857	SUBCLONAL	1	TRUE	1	0.39	2		299	354	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614901	23614901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	66	332	1	ENST00000261584.4:c.3440G>A	p.Cys1147Tyr	p.C1147Y	ENST00000261584	NM_024675.3	1147	tGt/tAt	13/13	1	2	FACETS	0.868	0.757	0.987	0.868	0.757	0.987	CLONAL	1	TRUE	1	0.39	2		333	390	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637714	23637714	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	65	301	2	ENST00000261584.4:c.2591C>A	p.Pro864His	p.P864H	ENST00000261584	NM_024675.3	864	cCt/cAt	7/13	1	2	FACETS	0.773	0.673	0.882	0.773	0.673	0.882	SUBCLONAL	1	TRUE	1	0.39	2		303	431	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826586	50826586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	25	201	0	ENST00000398568.2:c.2311G>A	p.Glu771Lys	p.E771K	ENST00000398568	NM_001042412.1	771	Gaa/Aaa	15/18	1	2	FACETS	0.745	0.593	0.918	0.745	0.593	0.918	CLONAL	1	TRUE	1	0.39	2		201	172	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868281	56868281	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	28	156	0	ENST00000308159.5:c.1665-1G>T		p.X555_splice	ENST00000308159	NM_014669.4	555			1	2	FACETS	0.903	0.73	1	0.903	0.73	1	CLONAL	1	TRUE	1	0.39	2		156	159	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	47	470	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.662	0.56	0.774	0.662	0.56	0.774	SUBCLONAL	1	TRUE	1	0.39	2		470	364	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660508	67660508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	67	269	2	ENST00000264010.4:c.1408C>T	p.Arg470Cys	p.R470C	ENST00000264010	NM_006565.3	470	Cgt/Tgt	8/12	1	2	FACETS	0.853	0.744	0.969	0.853	0.744	0.969	CLONAL	1	TRUE	1	0.39	2		271	403	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844133	68844133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555515434	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	93	363	0	ENST00000261769.5:c.721G>A	p.Ala241Thr	p.A241T	ENST00000261769	NM_004360.3	241	Gca/Aca	6/16	1	2	FACETS	0.975	0.871	1	0.975	0.871	1	CLONAL	1	TRUE	1	0.39	2		363	489	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847252	68847252	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141864044	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	102	282	0	ENST00000261769.5:c.1174G>A	p.Val392Ile	p.V392I	ENST00000261769	NM_004360.3	392	Gta/Ata	9/16	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.39	2		282	511	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822391	72822391	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	146	478	0	ENST00000268489.5:c.9784G>T	p.Gly3262Ter	p.G3262*	ENST00000268489	NM_006885.3	3262	Gga/Tga	10/10	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.39	2		478	731	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828621	72828621	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	112	371	0	ENST00000268489.5:c.7960G>T	p.Glu2654Ter	p.E2654*	ENST00000268489	NM_006885.3	2654	Gaa/Taa	9/10	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.39	2		371	551	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828946	72828946	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	60	355	1	ENST00000268489.5:c.7635G>T	p.Trp2545Cys	p.W2545C	ENST00000268489	NM_006885.3	2545	tgG/tgT	9/10	1	2	FACETS	0.548	0.473	0.631	0.548	0.473	0.631	SUBCLONAL	1	TRUE	1	0.39	2		356	561	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829061	72829061	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	98	403	0	ENST00000268489.5:c.7520T>C	p.Leu2507Pro	p.L2507P	ENST00000268489	NM_006885.3	2507	cTg/cCg	9/10	1	2	FACETS	0.823	0.735	0.915	0.823	0.735	0.915	CLONAL	1	TRUE	1	0.39	2		403	611	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346225	89346225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372632879	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	41	139	0	ENST00000301030.4:c.6725C>T	p.Ala2242Val	p.A2242V	ENST00000301030	NM_001256183.1	2242	gCg/gTg	9/13	1	2	FACETS	0.973	0.819	1	0.973	0.819	1	CLONAL	1	TRUE	1	0.39	2		139	216	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813023	89813023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142833057	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	98	406	0	ENST00000389301.3:c.3482C>T	p.Thr1161Met	p.T1161M	ENST00000389301	NM_000135.2	1161	aCg/aTg	35/43	1	2	FACETS	0.793	0.708	0.882	0.793	0.708	0.882	SUBCLONAL	1	TRUE	1	0.39	2		406	634	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89865629	89865629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1010833101	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	88	384	0	ENST00000389301.3:c.838G>A	p.Ala280Thr	p.A280T	ENST00000389301	NM_000135.2	280	Gct/Act	10/43	1	2	FACETS	0.796	0.707	0.891	0.796	0.707	0.891	SUBCLONAL	1	TRUE	1	0.39	2		384	567	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882351	89882351	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	109	379	1	ENST00000389301.3:c.123G>T	p.Gln41His	p.Q41H	ENST00000389301	NM_000135.2	41	caG/caT	2/43	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.39	2		380	535	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587781525	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	18	424	0	ENST00000269305.4:c.842A>G	p.Asp281Gly	p.D281G	ENST00000269305	NM_001126112.2	281	gAc/gGc	8/11	1	2	FACETS	0.115	0.086	0.15	0.115	0.086	0.15	SUBCLONAL	1	TRUE	1	0.39	2		424	800	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108652	8108652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777705809	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	76	339	0	ENST00000585124.1:c.743G>A	p.Arg248His	p.R248H	ENST00000585124	NM_004217.3	248	cGc/cAc	8/9	1	2	FACETS	0.698	0.613	0.79	0.698	0.613	0.79	SUBCLONAL	1	TRUE	1	0.39	2		339	558	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110668	8110668	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	99	279	0	ENST00000585124.1:c.224A>G	p.Asp75Gly	p.D75G	ENST00000585124	NM_004217.3	75	gAt/gGt	5/9	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.39	2		279	478	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028632	12028632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753665559	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	47	262	0	ENST00000353533.5:c.835G>A	p.Ala279Thr	p.A279T	ENST00000353533	NM_003010.3	279	Gca/Aca	8/11	1	2	FACETS	0.828	0.703	0.964	0.828	0.703	0.964	CLONAL	1	TRUE	1	0.39	2		262	291	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971393	15971393	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759642635	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	63	321	0	ENST00000268712.3:c.4556C>T	p.Ser1519Leu	p.S1519L	ENST00000268712	NM_006311.3	1519	tCg/tTg	32/46	1	2	FACETS	0.696	0.604	0.796	0.696	0.604	0.796	SUBCLONAL	1	TRUE	1	0.39	2		321	464	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15976766	15976766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	54	411	1	ENST00000268712.3:c.3788C>T	p.Ser1263Phe	p.S1263F	ENST00000268712	NM_006311.3	1263	tCt/tTt	28/46	1	2	FACETS	0.789	0.677	0.91	0.789	0.677	0.91	CLONAL	1	TRUE	1	0.39	2		412	351	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983965	15983965	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	63	247	0	ENST00000268712.3:c.3254C>A	p.Ser1085Tyr	p.S1085Y	ENST00000268712	NM_006311.3	1085	tCt/tAt	24/46	1	2	FACETS	0.885	0.77	1	0.885	0.77	1	CLONAL	1	TRUE	1	0.39	2		247	365	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004872	16004872	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	101	293	2	ENST00000268712.3:c.2382G>T	p.Glu794Asp	p.E794D	ENST00000268712	NM_006311.3	794	gaG/gaT	20/46	1	2	FACETS	0.927	0.831	1	0.927	0.831	1	CLONAL	1	TRUE	1	0.39	2		295	559	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16040641	16040641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	39	292	1	ENST00000268712.3:c.1493G>A	p.Arg498His	p.R498H	ENST00000268712	NM_006311.3	498	cGc/cAc	14/46	1	2	FACETS	0.645	0.537	0.765	0.645	0.537	0.765	SUBCLONAL	1	TRUE	1	0.39	2		293	310	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29579995	29579996	+	intron_variant	Intron	INS	-	-	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	44	244	0	ENST00000356175.3:c.4110+3865dup		p.*1370*	ENST00000356175	NM_000267.3	1384/2839			1	2	FACETS	0.812	0.685	0.95	0.812	0.685	0.95	CLONAL	1	TRUE	1	0.39	2		244	278	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679429	29679429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768366978	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	53	220	0	ENST00000356175.3:c.7549C>T	p.Leu2517Phe	p.L2517F	ENST00000356175	NM_000267.3	2517	Ctt/Ttt	50/57	1	2	FACETS	0.9	0.773	1	0.9	0.773	1	CLONAL	1	TRUE	1	0.39	2		220	302	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320963	30320963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371166327	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	66	329	0	ENST00000322652.5:c.1373G>A	p.Arg458His	p.R458H	ENST00000322652	NM_015355.2	458	cGc/cAc	12/16	1	2	FACETS	0.863	0.753	0.982	0.863	0.753	0.982	CLONAL	1	TRUE	1	0.39	2		329	392	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	130	657	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.39	2		657	610	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511574	38511574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	115	339	0	ENST00000254066.5:c.1072G>A	p.Ala358Thr	p.A358T	ENST00000254066	NM_000964.3	358	Gcg/Acg	8/9	1	2	FACETS	0.998	0.902	1	0.998	0.902	1	CLONAL	1	TRUE	1	0.39	2		339	591	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512401	38512402	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs745553450	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	58	304	1	ENST00000254066.5:c.1319dup	p.Pro441AlafsTer5	p.P441Afs*5	ENST00000254066	NM_000964.3	438	gcc/gCcc	9/9	1	2	FACETS	0.713	0.615	0.82	0.713	0.615	0.82	SUBCLONAL	1	TRUE	1	0.39	2		305	417	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40447715	40447715	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	109	422	0	ENST00000345506.4:c.454C>T	p.Arg152Ter	p.R152*	ENST00000345506	NM_003152.3	152	Cga/Tga	6/20	1	2	FACETS	0.86	0.773	0.951	0.86	0.773	0.951	CLONAL	1	TRUE	1	0.39	2		422	650	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40478146	40478146	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	90	356	0	ENST00000264657.5:c.1353G>T	p.Lys451Asn	p.K451N	ENST00000264657	NM_139276.2	451	aaG/aaT	15/24	1	2	FACETS	0.827	0.736	0.924	0.827	0.736	0.924	CLONAL	1	TRUE	1	0.39	2		356	558	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870501	40870501	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768296055	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	123	302	0	ENST00000428826.2:c.902G>A	p.Arg301His	p.R301H	ENST00000428826		301	cGc/cAc	9/21	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.39	2		302	619	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41219675	41219675	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	72	271	0	ENST00000357654.3:c.5024C>A	p.Thr1675Asn	p.T1675N	ENST00000357654	NM_007294.3	1675	aCt/aAt	16/23	1	2	FACETS	0.849	0.744	0.96	0.849	0.744	0.96	CLONAL	1	TRUE	1	0.39	2		271	435	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435837	56435837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	23	243	0	ENST00000407977.2:c.1300C>T	p.Pro434Ser	p.P434S	ENST00000407977		434	Ccc/Tcc	9/10	1	2	FACETS	0.319	0.248	0.401	0.319	0.248	0.401	SUBCLONAL	1	TRUE	1	0.39	2		243	370	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448327	56448327	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	34	412	0	ENST00000407977.2:c.320T>A	p.Val107Asp	p.V107D	ENST00000407977		107	gTc/gAc	3/10	1	2	FACETS	0.262	0.213	0.317	0.262	0.213	0.317	SUBCLONAL	1	TRUE	1	0.39	2		412	665	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	106	394	1	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.836	0.751	0.927	0.836	0.751	0.927	CLONAL	1	TRUE	1	0.39	2		395	650	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534452	63534452	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755884266	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	141	343	1	ENST00000307078.5:c.1069C>T	p.Arg357Cys	p.R357C	ENST00000307078	NM_004655.3	357	Cgc/Tgc	5/11	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.39	2		344	701	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519896	66519896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	65	331	0	ENST00000358598.2:c.379G>A	p.Ala127Thr	p.A127T	ENST00000358598	NM_212471.2	127	Gct/Act	4/11	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.39	2		331	315	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732955	74732956	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs754601892	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	20	194	0	ENST00000359995.5:c.287dup	p.Asp97GlyfsTer27	p.D97Gfs*27	ENST00000359995	NM_001195427.1	96	ccg/ccCg	1/3	1	2	FACETS	0.333	0.254	0.425	0.333	0.254	0.425	SUBCLONAL	1	TRUE	1	0.39	2		194	308	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756770	756770	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	73	314	0	ENST00000314574.4:c.58A>G	p.Asn20Asp	p.N20D	ENST00000314574	NM_005433.3	20	Aat/Gat	2/12	1	2	FACETS	0.972	0.855	1	0.972	0.855	1	CLONAL	1	TRUE	1	0.39	2		314	385	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	33	373	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	0.629	0.515	0.757	0.629	0.515	0.757	SUBCLONAL	1	TRUE	1	0.39	2		373	269	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348505	56348505	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754296724	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	46	243	0	ENST00000348428.3:c.313G>A	p.Glu105Lys	p.E105K	ENST00000348428	NM_006785.3	105	Gaa/Aaa	2/17	1	2	FACETS	0.672	0.568	0.786	0.672	0.568	0.786	SUBCLONAL	1	TRUE	1	0.39	2		243	351	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56402535	56402535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	21	142	0	ENST00000348428.3:c.1577C>T	p.Thr526Ile	p.T526I	ENST00000348428	NM_006785.3	526	aCt/aTt	13/17	1	2	FACETS	0.695	0.54	0.872	0.695	0.54	0.872	SUBCLONAL	1	TRUE	1	0.39	2		142	155	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221313	1221314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs121913321	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	109	634	1	ENST00000326873.7:c.842dup	p.Leu282AlafsTer3	p.L282Afs*3	ENST00000326873	NM_000455.4	279	ggc/ggCc	6/10	1	2	FACETS	0.941	0.847	1	0.941	0.847	1	CLONAL	1	TRUE	1	0.39	2		635	594	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632351	1632351	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	124	451	0	ENST00000344749.5:c.199T>C	p.Ser67Pro	p.S67P	ENST00000344749	NM_001136139.2	67	Tcc/Ccc	4/19	1	2	FACETS	0.803	0.727	0.883	0.803	0.727	0.883	CLONAL	1	TRUE	1	0.39	2		451	792	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210735	2210735	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1238067958	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	154	592	2	ENST00000398665.3:c.1232G>A	p.Arg411His	p.R411H	ENST00000398665	NM_032482.2	411	cGc/cAc	14/28	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.39	2		594	690	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226796	2226796	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1358779949	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	112	302	1	ENST00000398665.3:c.4276C>T	p.Leu1426Phe	p.L1426F	ENST00000398665	NM_032482.2	1426	Ctc/Ttc	27/28	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.39	2		303	550	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212029	5212029	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	87	313	0	ENST00000357368.4:c.5002C>A	p.Leu1668Met	p.L1668M	ENST00000357368	NM_002850.3	1668	Ctg/Atg	32/38	1	2	FACETS	0.79	0.7	0.885	0.79	0.7	0.885	SUBCLONAL	1	TRUE	1	0.39	2		313	565	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222730	5222731	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs756013055	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	52	324	3	ENST00000357368.4:c.3072dup	p.Val1025ArgfsTer34	p.V1025Rfs*34	ENST00000357368	NM_002850.3	1024	-/C	18/38	1	2	FACETS	0.45	0.383	0.524	0.45	0.383	0.524	SUBCLONAL	1	TRUE	1	0.39	2		327	592	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243944	5243944	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	107	298	0	ENST00000357368.4:c.1538C>T	p.Ser513Leu	p.S513L	ENST00000357368	NM_002850.3	513	tCg/tTg	11/38	1	2	FACETS	0.925	0.832	1	0.925	0.832	1	CLONAL	1	TRUE	1	0.39	2		298	593	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117408	7117408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371841833	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	94	287	0	ENST00000302850.5:c.3808C>T	p.Arg1270Cys	p.R1270C	ENST00000302850	NM_000208.2	1270	Cgc/Tgc	22/22	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.39	2		287	442	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125295	7125295	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	78	283	0	ENST00000302850.5:c.3257T>G	p.Val1086Gly	p.V1086G	ENST00000302850	NM_000208.2	1086	gTg/gGg	17/22	1	2	FACETS	0.93	0.821	1	0.93	0.821	1	CLONAL	1	TRUE	1	0.39	2		283	430	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125371	7125371	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55882714	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	141	397	0	ENST00000302850.5:c.3181G>A	p.Glu1061Lys	p.E1061K	ENST00000302850	NM_000208.2	1061	Gag/Aag	17/22	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.39	2		397	719	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7141702	7141702	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1568440846	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	93	376	0	ENST00000302850.5:c.2668C>T	p.Arg890Ter	p.R890*	ENST00000302850	NM_000208.2	890	Cga/Tga	13/22	1	2	FACETS	0.869	0.774	0.969	0.869	0.774	0.969	CLONAL	1	TRUE	1	0.39	2		376	549	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7168022	7168022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	120	375	0	ENST00000302850.5:c.1567G>A	p.Asp523Asn	p.D523N	ENST00000302850	NM_000208.2	523	Gac/Aac	7/22	1	2	FACETS	0.889	0.804	0.979	0.889	0.804	0.979	CLONAL	1	TRUE	1	0.39	2		375	692	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11022908	11022908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768673985	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	139	405	0	ENST00000327064.4:c.607G>A	p.Ala203Thr	p.A203T	ENST00000327064	NM_199141.1	203	Gcc/Acc	5/16	1	2	FACETS	0.95	0.866	1	0.95	0.866	1	CLONAL	1	TRUE	1	0.39	2		405	750	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152145	11152145	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775399739	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	134	376	0	ENST00000358026.2:c.4429C>T	p.Arg1477Trp	p.R1477W	ENST00000358026	NM_001128849.1	1477	Cgg/Tgg	31/36	1	2	FACETS	0.857	0.779	0.939	0.857	0.779	0.939	CLONAL	1	TRUE	1	0.39	2		376	802	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272336	15272337	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs771517374	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	121	403	4	ENST00000263388.2:c.6102dup	p.Gly2035ArgfsTer60	p.G2035Rfs*60	ENST00000263388	NM_000435.2	2034	-/C	33/33	1	2	FACETS	0.868	0.785	0.955	0.868	0.785	0.955	CLONAL	1	TRUE	1	0.39	2		407	715	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276300	15276300	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	126	381	0	ENST00000263388.2:c.5694C>A	p.Asp1898Glu	p.D1898E	ENST00000263388	NM_000435.2	1898	gaC/gaA	31/33	1	2	FACETS	0.917	0.831	1	0.917	0.831	1	CLONAL	1	TRUE	1	0.39	2		381	705	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278191	15278191	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	62	348	1	ENST00000263388.2:c.5231C>T	p.Ala1744Val	p.A1744V	ENST00000263388	NM_000435.2	1744	gCt/gTt	29/33	1	2	FACETS	0.526	0.454	0.605	0.526	0.454	0.605	SUBCLONAL	1	TRUE	1	0.39	2		349	604	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290060	15290060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	34	378	0	ENST00000263388.2:c.3494G>A	p.Gly1165Asp	p.G1165D	ENST00000263388	NM_000435.2	1165	gGc/gAc	22/33	1	2	FACETS	0.268	0.218	0.324	0.268	0.218	0.324	SUBCLONAL	1	TRUE	1	0.39	2		378	651	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366939	15366939	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	114	499	1	ENST00000263377.2:c.1687del	p.Ser563AlafsTer21	p.S563Afs*21	ENST00000263377	NM_058243.2	563	Agc/gc	9/20	1	2	FACETS	0.856	0.772	0.945	0.856	0.772	0.945	CLONAL	1	TRUE	1	0.39	2		500	683	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942184	17942184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	106	284	0	ENST00000458235.1:c.2831G>A	p.Arg944His	p.R944H	ENST00000458235	NM_000215.3	944	cGc/cAc	21/24	1	2	FACETS	0.99	0.891	1	0.99	0.891	1	CLONAL	1	TRUE	1	0.39	2		284	549	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952455	17952455	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	76	355	0	ENST00000458235.1:c.978G>T	p.Gln326His	p.Q326H	ENST00000458235	NM_000215.3	326	caG/caT	7/24	1	2	FACETS	0.799	0.702	0.902	0.799	0.702	0.902	CLONAL	1	TRUE	1	0.39	2		355	488	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266816	18266816	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750768114	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	113	307	0	ENST00000222254.8:c.127G>A	p.Val43Met	p.V43M	ENST00000222254	NM_005027.3	43	Gtg/Atg	2/16	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.39	2		307	569	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965949	18965949	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	120	363	0	ENST00000262803.5:c.1442C>A	p.Thr481Asn	p.T481N	ENST00000262803	NM_002911.3	481	aCt/aAt	11/24	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.39	2		363	583	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256768	19256769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1202792889	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	68	622	1	ENST00000162023.5:c.944dup	p.Val316SerfsTer6	p.V316Sfs*6	ENST00000162023		315	cca/ccCa	13/13	1	2	FACETS	0.635	0.553	0.724	0.635	0.553	0.724	SUBCLONAL	1	TRUE	1	0.39	2		623	549	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30311657	30311657	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	38	280	0	ENST00000262643.3:c.511G>T	p.Asp171Tyr	p.D171Y	ENST00000262643	NM_001238.2	171	Gat/Tat	7/12	1	2	FACETS	0.645	0.535	0.767	0.645	0.535	0.767	SUBCLONAL	1	TRUE	1	0.39	2		280	302	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314633	30314640	+	frameshift_variant	Frame_Shift_Del	DEL	CACCCCGC	CACCCCGC	-	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	35	333	0	ENST00000262643.3:c.1185_1192del	p.Pro396GlufsTer3	p.P396Efs*3	ENST00000262643	NM_001238.2	394	ctCACCCCGCca/ctca	12/12	1	2	FACETS	0.28	0.228	0.337	0.28	0.228	0.337	SUBCLONAL	1	TRUE	1	0.39	2		333	642	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793175	33793175	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	31	151	0	ENST00000498907.2:c.146del	p.Pro49ArgfsTer111	p.P49Rfs*111	ENST00000498907	NM_004364.3	49	cCg/cg	1/1	1	2	FACETS	0.685	0.557	0.828	0.685	0.557	0.828	SUBCLONAL	1	TRUE	1	0.39	2		151	232	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211600	36211600	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	70	305	0	ENST00000222270.7:c.1351G>T	p.Glu451Ter	p.E451*	ENST00000222270	NM_014727.1	451	Gag/Tag	3/37	1	2	FACETS	0.88	0.771	0.997	0.88	0.771	0.997	CLONAL	1	TRUE	1	0.39	2		305	408	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214767	36214767	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	66	309	0	ENST00000222270.7:c.3193G>A	p.Glu1065Lys	p.E1065K	ENST00000222270	NM_014727.1	1065	Gag/Aag	8/37	1	2	FACETS	0.814	0.709	0.926	0.814	0.709	0.926	CLONAL	1	TRUE	1	0.39	2		309	416	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216461	36216461	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1002663544	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	147	434	0	ENST00000222270.7:c.3724G>A	p.Asp1242Asn	p.D1242N	ENST00000222270	NM_014727.1	1242	Gac/Aac	12/37	1	2	FACETS	0.942	0.861	1	0.942	0.861	1	CLONAL	1	TRUE	1	0.39	2		434	800	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223158	36223158	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	184	509	0	ENST00000222270.7:c.5708A>G	p.Asp1903Gly	p.D1903G	ENST00000222270	NM_014727.1	1903	gAc/gGc	28/37	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.39	2		509	761	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762362	41762362	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	79	261	0	ENST00000301178.4:c.2042A>G	p.Asn681Ser	p.N681S	ENST00000301178	NM_021913.4	681	aAt/aGt	18/20	1	2	FACETS	0.858	0.757	0.966	0.858	0.757	0.966	CLONAL	1	TRUE	1	0.39	2		261	472	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752816	42752816	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	136	394	1	ENST00000222329.4:c.1448G>A	p.Arg483His	p.R483H	ENST00000222329	NM_006494.2	483	cGc/cAc	4/4	1	2	FACETS	0.941	0.857	1	0.941	0.857	1	CLONAL	1	TRUE	1	0.39	2		395	741	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795725	42795725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	119	416	1	ENST00000575354.2:c.2714C>T	p.Pro905Leu	p.P905L	ENST00000575354	NM_015125.3	905	cCc/cTc	11/20	1	2	FACETS	0.882	0.797	0.971	0.882	0.797	0.971	CLONAL	1	TRUE	1	0.39	2		417	692	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798125	42798125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	103	314	0	ENST00000575354.2:c.4079C>T	p.Ala1360Val	p.A1360V	ENST00000575354	NM_015125.3	1360	gCt/gTt	17/20	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.39	2		314	479	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856559	45856559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	102	353	0	ENST00000391945.4:c.1699C>T	p.Leu567Phe	p.L567F	ENST00000391945	NM_000400.3	567	Ctc/Ttc	18/23	1	2	FACETS	0.882	0.791	0.979	0.882	0.791	0.979	CLONAL	1	TRUE	1	0.39	2		353	593	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45864858	45864858	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	154	496	0	ENST00000391945.4:c.1161G>T	p.Glu387Asp	p.E387D	ENST00000391945	NM_000400.3	387	gaG/gaT	12/23	1	2	FACETS	0.938	0.859	1	0.938	0.859	1	CLONAL	1	TRUE	1	0.39	2		496	842	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867316	45867316	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	133	373	0	ENST00000391945.4:c.877C>T	p.Arg293Trp	p.R293W	ENST00000391945	NM_000400.3	293	Cgg/Tgg	10/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.39	2		373	582	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918759	50918759	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555793039	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	114	411	0	ENST00000440232.2:c.2629G>A	p.Asp877Asn	p.D877N	ENST00000440232	NM_002691.3	877	Gat/Aat	21/27	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.39	2		411	565	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921125	50921125	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	97	335	0	ENST00000440232.2:c.3245G>T	p.Arg1082Leu	p.R1082L	ENST00000440232	NM_002691.3	1082	cGc/cTc	27/27	1	2	FACETS	0.926	0.828	1	0.926	0.828	1	CLONAL	1	TRUE	1	0.39	2		335	537	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719875	52719875	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751218909	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	110	388	1	ENST00000322088.6:c.1087G>A	p.Glu363Lys	p.E363K	ENST00000322088	NM_014225.5	363	Gag/Aag	9/15	1	2	FACETS	0.963	0.867	1	0.963	0.867	1	CLONAL	1	TRUE	1	0.39	2		389	586	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469540	25469540	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764880874	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	104	346	0	ENST00000264709.3:c.1228G>A	p.Ala410Thr	p.A410T	ENST00000264709	NM_175629.2	410	Gcc/Acc	10/23	1	2	FACETS	0.924	0.83	1	0.924	0.83	1	CLONAL	1	TRUE	1	0.39	2		346	577	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469984	25469984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1326972729	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	111	316	0	ENST00000264709.3:c.1058C>T	p.Ala353Val	p.A353V	ENST00000264709	NM_175629.2	353	gCg/gTg	9/23	1	2	FACETS	0.988	0.891	1	0.988	0.891	1	CLONAL	1	TRUE	1	0.39	2		316	576	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973038	25973038	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	70	263	0	ENST00000435504.4:c.1387C>T	p.Pro463Ser	p.P463S	ENST00000435504		463	Ccc/Tcc	12/13	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.39	2		263	325	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462643	29462643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs187200776	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	147	400	1	ENST00000389048.3:c.2258G>A	p.Arg753Gln	p.R753Q	ENST00000389048	NM_004304.4	753	cGg/cAg	13/29	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.39	2		401	716	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917817	29917817	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	93	433	0	ENST00000389048.3:c.851G>T	p.Arg284Met	p.R284M	ENST00000389048	NM_004304.4	284	aGg/aTg	3/29	1	2	FACETS	0.738	0.657	0.825	0.738	0.657	0.825	SUBCLONAL	1	TRUE	1	0.39	2		433	646	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39234215	39234215	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	55	378	2	ENST00000402219.2:c.2630C>A	p.Ala877Asp	p.A877D	ENST00000402219	NM_005633.3	877	gCt/gAt	16/23	1	2	FACETS	0.725	0.622	0.837	0.725	0.622	0.837	SUBCLONAL	1	TRUE	1	0.39	2		380	389	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607801	46607801	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	124	421	0	ENST00000263734.3:c.1990G>T	p.Ala664Ser	p.A664S	ENST00000263734	NM_001430.4	664	Gca/Tca	12/16	1	2	FACETS	0.969	0.879	1	0.969	0.879	1	CLONAL	1	TRUE	1	0.39	2		421	656	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607807	46607807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	129	413	0	ENST00000263734.3:c.1996C>T	p.Pro666Ser	p.P666S	ENST00000263734	NM_001430.4	666	Ccg/Tcg	12/16	1	2	FACETS	0.998	0.907	1	0.998	0.907	1	CLONAL	1	TRUE	1	0.39	2		413	663	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606170	47606170	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	35	260	1	ENST00000263735.4:c.634G>A	p.Val212Met	p.V212M	ENST00000263735	NM_002354.2	212	Gtg/Atg	6/9	1	2	FACETS	0.653	0.537	0.781	0.653	0.537	0.781	SUBCLONAL	1	TRUE	1	0.39	2		261	275	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637276	47637276	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	68	308	0	ENST00000233146.2:c.410G>A	p.Gly137Asp	p.G137D	ENST00000233146	NM_000251.2	137	gGt/gAt	3/16	1	2	FACETS	0.878	0.768	0.997	0.878	0.768	0.997	CLONAL	1	TRUE	1	0.39	2		308	397	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698180	47698180	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63751411	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	83	220	1	ENST00000233146.2:c.1738G>T	p.Glu580Ter	p.E580*	ENST00000233146	NM_000251.2	580	Gaa/Taa	11/16	1	2	FACETS	0.938	0.842	1	1	0.985	1	CLONAL	2	TRUE	1	0.39	2		221	227	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702235	47702235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369385048	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	42	411	0	ENST00000233146.2:c.1831G>A	p.Val611Met	p.V611M	ENST00000233146	NM_000251.2	611	Gtg/Atg	12/16	1	2	FACETS	0.626	0.524	0.738	0.626	0.524	0.738	SUBCLONAL	1	TRUE	1	0.39	2		411	344	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702274	47702275	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	73	391	0	ENST00000233146.2:c.1874dup	p.Leu625PhefsTer19	p.L625Ffs*19	ENST00000233146	NM_000251.2	624	att/aTtt	12/16	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.39	2		391	367	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023196	48023196	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1553411509	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	63	326	0	ENST00000234420.5:c.621G>T	p.Glu207Asp	p.E207D	ENST00000234420	NM_000179.2	207	gaG/gaT	3/10	1	2	FACETS	0.698	0.605	0.798	0.698	0.605	0.798	SUBCLONAL	1	TRUE	1	0.39	2		326	463	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028084	48028084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61753795	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	34	183	0	ENST00000234420.5:c.2962C>T	p.Arg988Cys	p.R988C	ENST00000234420	NM_000179.2	988	Cgc/Tgc	4/10	1	2	FACETS	0.73	0.6	0.873	0.73	0.6	0.873	SUBCLONAL	1	TRUE	1	0.39	2		183	239	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033421	48033421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750119	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	55	293	0	ENST00000234420.5:c.3725G>A	p.Arg1242His	p.R1242H	ENST00000234420	NM_000179.2	1242	cGt/cAt	8/10	1	2	FACETS	0.931	0.802	1	0.931	0.802	1	CLONAL	1	TRUE	1	0.39	2		293	303	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149365	61149365	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	37	227	0	ENST00000295025.8:c.1555C>A	p.Leu519Ile	p.L519I	ENST00000295025	NM_002908.2	519	Ctt/Att	11/11	1	2	FACETS	0.807	0.67	0.958	0.807	0.67	0.958	CLONAL	1	TRUE	1	0.39	2		227	235	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152220	99152220	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	25	199	0	ENST00000074304.5:c.299G>A	p.Ser100Asn	p.S100N	ENST00000074304	NM_001134224.1	100	aGt/aAt	6/26	1	2	FACETS	0.534	0.422	0.662	0.534	0.422	0.662	SUBCLONAL	1	TRUE	1	0.39	2		199	240	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99160439	99160439	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	65	309	0	ENST00000074304.5:c.918G>T	p.Gln306His	p.Q306H	ENST00000074304	NM_001134224.1	306	caG/caT	11/26	1	2	FACETS	0.683	0.593	0.78	0.683	0.593	0.78	SUBCLONAL	1	TRUE	1	0.39	2		309	488	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99163148	99163148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	45	278	0	ENST00000074304.5:c.1154C>T	p.Thr385Ile	p.T385I	ENST00000074304	NM_001134224.1	385	aCc/aTc	13/26	1	2	FACETS	0.486	0.408	0.571	0.486	0.408	0.571	SUBCLONAL	1	TRUE	1	0.39	2		278	475	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99180015	99180015	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	112	341	1	ENST00000074304.5:c.1958T>C	p.Val653Ala	p.V653A	ENST00000074304	NM_001134224.1	653	gTa/gCa	19/26	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.39	2		342	552	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128028921	128028921	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	82	275	0	ENST00000285398.2:c.1936G>T	p.Ala646Ser	p.A646S	ENST00000285398	NM_000122.1	646	Gct/Tct	12/15	1	2	FACETS	0.723	0.638	0.813	0.723	0.638	0.813	SUBCLONAL	1	TRUE	1	0.39	2		275	582	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050331	128050331	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755616510	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	79	294	0	ENST00000285398.2:c.326G>A	p.Arg109Gln	p.R109Q	ENST00000285398	NM_000122.1	109	cGa/cAa	3/15	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.39	2		294	393	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158626996	158626996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	56	210	0	ENST00000263640.3:c.674G>A	p.Gly225Asp	p.G225D	ENST00000263640	NM_001105.4	225	gGc/gAc	7/11	1	2	FACETS	0.783	0.673	0.901	0.783	0.673	0.901	CLONAL	1	TRUE	1	0.39	2		210	367	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095836	178095836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1328262363	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	48	304	0	ENST00000397062.3:c.1495C>T	p.Arg499Trp	p.R499W	ENST00000397062	NM_006164.4	499	Cgg/Tgg	5/5	1	2	FACETS	0.737	0.626	0.858	0.737	0.626	0.858	SUBCLONAL	1	TRUE	1	0.39	2		304	334	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098009	178098009	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749353894	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	65	280	0	ENST00000397062.3:c.371C>T	p.Ala124Val	p.A124V	ENST00000397062	NM_006164.4	124	gCg/gTg	3/5	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.39	2		280	316	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718969	190718969	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	22	121	0	ENST00000441310.2:c.971C>A	p.Ser324Tyr	p.S324Y	ENST00000441310	NM_000534.4	324	tCt/tAt	9/13	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.39	2		121	96	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198263242	198263242	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	44	280	0	ENST00000335508.6:c.3077A>T	p.Asn1026Ile	p.N1026I	ENST00000335508	NM_012433.2	1026	aAc/aTc	21/25	1	2	FACETS	0.728	0.613	0.853	0.728	0.613	0.853	SUBCLONAL	1	TRUE	1	0.39	2		280	310	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248450	212248450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1480034665	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	46	201	0	ENST00000342788.4:c.3817C>T	p.Arg1273Trp	p.R1273W	ENST00000342788	NM_005235.2	1273	Cgg/Tgg	28/28	1	2	FACETS	0.773	0.655	0.903	0.773	0.655	0.903	CLONAL	1	TRUE	1	0.39	2		201	305	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589887	212589887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757597004	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	97	318	1	ENST00000342788.4:c.655G>A	p.Gly219Ser	p.G219S	ENST00000342788	NM_005235.2	219	Ggc/Agc	6/28	1	2	FACETS	0.762	0.68	0.849	0.762	0.68	0.849	SUBCLONAL	1	TRUE	1	0.39	2		319	653	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646149	215646149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881412	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	26	242	1	ENST00000260947.4:c.449G>A	p.Arg150Gln	p.R150Q	ENST00000260947	NM_000465.2	150	cGa/cAa	4/11	1	2	FACETS	0.439	0.348	0.542	0.439	0.348	0.542	SUBCLONAL	1	TRUE	1	0.39	2		243	304	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793362	242793363	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	117	429	0	ENST00000334409.5:c.714dup	p.Val239ArgfsTer6	p.V239Rfs*6	ENST00000334409	NM_005018.2	238	-/C	5/5	1	2	FACETS	0.857	0.774	0.945	0.857	0.774	0.945	CLONAL	1	TRUE	1	0.39	2		429	700	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794488	242794488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	115	393	1	ENST00000334409.5:c.454C>T	p.Pro152Ser	p.P152S	ENST00000334409	NM_005018.2	152	Ccc/Tcc	3/5	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.39	2		394	573	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546618	9546618	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	60	351	0	ENST00000353224.5:c.1404G>T	p.Glu468Asp	p.E468D	ENST00000353224	NM_177990.2	468	gaG/gaT	5/10	1	2	FACETS	0.589	0.508	0.678	0.589	0.508	0.678	SUBCLONAL	1	TRUE	1	0.39	2		351	522	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624965	9624965	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	36	124	0	ENST00000353224.5:c.12G>T	p.Lys4Asn	p.K4N	ENST00000353224	NM_177990.2	4	aaG/aaT	3/10	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.39	2		124	151	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383297	31383297	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	98	356	2	ENST00000328111.2:c.1209C>A	p.Cys403Ter	p.C403*	ENST00000328111	NM_006892.3	403	tgC/tgA	11/23	1	2	FACETS	0.862	0.771	0.959	0.862	0.771	0.959	CLONAL	1	TRUE	1	0.39	2		358	583	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395677	31395677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1267164985	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	83	298	3	ENST00000328111.2:c.2530G>A	p.Ala844Thr	p.A844T	ENST00000328111	NM_006892.3	844	Gcc/Acc	23/23	1	2	FACETS	0.788	0.697	0.885	0.788	0.697	0.885	SUBCLONAL	1	TRUE	1	0.39	2		301	540	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739051	40739051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374135283	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	116	348	0	ENST00000373198.4:c.3233C>T	p.Ala1078Val	p.A1078V	ENST00000373198	NM_133170.3	1078	gCc/gTc	24/32	1	2	FACETS	0.914	0.825	1	0.914	0.825	1	CLONAL	1	TRUE	1	0.39	2		348	651	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279903	46279903	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	100	290	0	ENST00000371998.3:c.3829A>C	p.Thr1277Pro	p.T1277P	ENST00000371998		1277	Acc/Ccc	20/23	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.39	2		290	481	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54948613	54948613	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	31	228	0	ENST00000312783.6:c.706-1G>T		p.X236_splice	ENST00000312783	NM_198436.1	236			1	2	FACETS	0.783	0.638	0.944	0.783	0.638	0.944	CLONAL	1	TRUE	1	0.39	2		228	203	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466801	57466801	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	43	144	1	ENST00000371085.3:c.20G>T	p.Ser7Ile	p.S7I	ENST00000371085	NM_000516.4	7	aGt/aTt	1/13	1	2	FACETS	0.817	0.688	0.958	0.817	0.688	0.958	CLONAL	1	TRUE	1	0.39	2		145	270	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478781	57478781	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769546153	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	89	228	0	ENST00000371085.3:c.367G>A	p.Glu123Lys	p.E123K	ENST00000371085	NM_000516.4	123	Gag/Aag	5/13	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.39	2		228	452	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164703	36164703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	130	378	1	ENST00000300305.3:c.1172C>T	p.Ala391Val	p.A391V	ENST00000300305		391	gCg/gTg	8/8	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.39	2		379	637	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764352	39764352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1395772766	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	91	277	0	ENST00000288319.7:c.760C>T	p.Pro254Ser	p.P254S	ENST00000288319	NM_182918.3	254	Ccc/Tcc	7/10	1	2	FACETS	0.871	0.775	0.972	0.871	0.775	0.972	CLONAL	1	TRUE	1	0.39	2		277	536	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39774556	39774556	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	46	212	0	ENST00000288319.7:c.596C>A	p.Pro199His	p.P199H	ENST00000288319	NM_182918.3	199	cCt/cAt	5/10	1	2	FACETS	0.944	0.801	1	0.944	0.801	1	CLONAL	1	TRUE	1	0.39	2		212	250	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655277	45655277	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	115	374	0	ENST00000407780.3:c.575A>G	p.Asn192Ser	p.N192S	ENST00000407780	NM_001283052.1	192	aAc/aGc	4/7	1	2	FACETS	0.902	0.814	0.994	0.902	0.814	0.994	CLONAL	1	TRUE	1	0.39	2		374	654	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21272223	21272223	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	15	133	0	ENST00000354336.3:c.1A>G	p.Met1?	p.M1?	ENST00000354336	NM_005207.3	1	Atg/Gtg	1/3	1	2	FACETS	0.385	0.282	0.508	0.385	0.282	0.508	SUBCLONAL	1	TRUE	1	0.39	2		133	200	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288131	21288131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1344311195	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	58	350	0	ENST00000354336.3:c.376G>A	p.Glu126Lys	p.E126K	ENST00000354336	NM_005207.3	126	Gaa/Aaa	2/3	1	2	FACETS	0.793	0.684	0.911	0.793	0.684	0.911	CLONAL	1	TRUE	1	0.39	2		350	375	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162025	22162025	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	40	307	1	ENST00000215832.6:c.230G>A	p.Arg77His	p.R77H	ENST00000215832	NM_002745.4	77	cGc/cAc	2/9	1	2	FACETS	0.588	0.49	0.696	0.588	0.49	0.696	SUBCLONAL	1	TRUE	1	0.39	2		308	349	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091198	29091198	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555913504	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	18	109	0	ENST00000328354.6:c.1292G>T	p.Arg431Met	p.R431M	ENST00000328354	NM_007194.3	431	aGg/aTg	12/15	1	2	FACETS	0.847	0.647	1	0.847	0.647	1	CLONAL	1	TRUE	1	0.39	2		109	109	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064325	30064325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	38	171	0	ENST00000338641.4:c.889C>T	p.Leu297Phe	p.L297F	ENST00000338641	NM_000268.3	297	Ctc/Ttc	10/16	1	2	FACETS	0.906	0.756	1	0.906	0.756	1	CLONAL	1	TRUE	1	0.39	2		171	215	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573039	41573039	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	131	456	0	ENST00000263253.7:c.5324C>T	p.Thr1775Ile	p.T1775I	ENST00000263253	NM_001429.3	1775	aCc/aTc	31/31	1	2	FACETS	0.849	0.771	0.932	0.849	0.771	0.932	CLONAL	1	TRUE	1	0.39	2		456	791	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12393095	12393095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	48	288	0	ENST00000287820.6:c.4G>A	p.Gly2Ser	p.G2S	ENST00000287820	NM_015869.4	2	Ggt/Agt	1/7	1	2	FACETS	0.925	0.788	1	0.925	0.788	1	CLONAL	1	TRUE	1	0.39	2		288	266	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37058999	37058999	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs63751194	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	40	261	0	ENST00000231790.2:c.793C>T	p.Arg265Cys	p.R265C	ENST00000231790	NM_000249.3	265	Cgt/Tgt	10/19	1	2	FACETS	0.639	0.533	0.756	0.639	0.533	0.756	SUBCLONAL	1	TRUE	1	0.39	2		261	321	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180262	38180262	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	107	353	0	ENST00000396334.3:c.110C>A	p.Ala37Asp	p.A37D	ENST00000396334	NM_002468.4	37	gCt/gAt	1/5	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.39	2		353	514	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41279559	41279559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200308943	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	48	240	0	ENST00000349496.5:c.2129G>A	p.Arg710His	p.R710H	ENST00000349496	NM_001904.3	710	cGc/cAc	14/15	1	2	FACETS	0.87	0.74	1	0.87	0.74	1	CLONAL	1	TRUE	1	0.39	2		240	283	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059138	47059138	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	99	311	0	ENST00000409792.3:c.7523T>C	p.Leu2508Pro	p.L2508P	ENST00000409792	NM_014159.6	2508	cTg/cCg	20/21	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.39	2		311	496	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932747	49932747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144684048	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	133	425	2	ENST00000296474.3:c.3124G>A	p.Asp1042Asn	p.D1042N	ENST00000296474	NM_002447.2	1042	Gat/Aat	14/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.39	2		427	614	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934011	49934011	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1448216239	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	117	437	0	ENST00000296474.3:c.2401C>A	p.Leu801Met	p.L801M	ENST00000296474	NM_002447.2	801	Ctg/Atg	9/20	1	2	FACETS	0.958	0.866	1	0.958	0.866	1	CLONAL	1	TRUE	1	0.39	2		437	626	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439136	52439136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	85	363	0	ENST00000460680.1:c.1106C>T	p.Ser369Phe	p.S369F	ENST00000460680	NM_004656.3	369	tCc/tTc	11/17	1	2	FACETS	0.813	0.721	0.912	0.813	0.721	0.912	CLONAL	1	TRUE	1	0.39	2		363	536	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643935	52643935	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	13	258	0	ENST00000394830.3:c.1961A>G	p.Tyr654Cys	p.Y654C	ENST00000394830	NM_018313.4	654	tAc/tGc	17/30	1	2	FACETS	0.257	0.183	0.348	0.257	0.183	0.348	SUBCLONAL	1	TRUE	1	0.39	2		258	259	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73113153	73113153	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	16	42	0	ENST00000356692.5:c.495-1G>T		p.X165_splice	ENST00000356692		165			1	2	FACETS	0.76	0.582	0.956	1	0.909	1	CLONAL	2	TRUE	1	0.39	2		42	54	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259166	89259166	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	43	217	0	ENST00000336596.2:c.310C>T	p.Arg104Ter	p.R104*	ENST00000336596	NM_005233.5	104	Cga/Tga	3/17	1	2	FACETS	0.832	0.701	0.975	0.832	0.701	0.975	CLONAL	1	TRUE	1	0.39	2		217	265	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468517	89468517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372257039	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	42	252	0	ENST00000336596.2:c.2051G>A	p.Arg684Gln	p.R684Q	ENST00000336596	NM_005233.5	684	cGa/cAa	11/17	1	2	FACETS	0.851	0.716	0.999	0.851	0.716	0.999	CLONAL	1	TRUE	1	0.39	2		252	253	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480412	89480412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780417089	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	56	240	0	ENST00000336596.2:c.2249G>A	p.Arg750Gln	p.R750Q	ENST00000336596	NM_005233.5	750	cGg/cAg	13/17	1	2	FACETS	0.881	0.759	1	0.881	0.759	1	CLONAL	1	TRUE	1	0.39	2		240	326	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670598	134670598	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs563780078	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	93	434	0	ENST00000398015.3:c.509G>A	p.Arg170Gln	p.R170Q	ENST00000398015	NM_004441.4	170	cGg/cAg	3/16	1	2	FACETS	0.928	0.828	1	0.928	0.828	1	CLONAL	1	TRUE	1	0.39	2		434	514	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426057	138426057	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	26	292	0	ENST00000289153.2:c.1474C>T	p.His492Tyr	p.H492Y	ENST00000289153	NM_006219.2	492	Cat/Tat	9/22	1	2	FACETS	0.488	0.388	0.603	0.488	0.388	0.603	SUBCLONAL	1	TRUE	1	0.39	2		292	273	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665548	138665548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	77	261	0	ENST00000330315.3:c.17C>T	p.Pro6Leu	p.P6L	ENST00000330315	NM_023067.3	6	cCc/cTc	1/1	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.39	2		261	362	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188189	142188189	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	23	199	0	ENST00000350721.4:c.6542C>A	p.Ala2181Asp	p.A2181D	ENST00000350721	NM_001184.3	2181	gCt/gAt	38/47	1	2	FACETS	0.678	0.532	0.843	0.678	0.532	0.843	SUBCLONAL	1	TRUE	1	0.39	2		199	174	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275274	142275275	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1460933711	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	19	329	0	ENST00000350721.4:c.2028dup	p.Ile677TyrfsTer10	p.I677Yfs*10	ENST00000350721	NM_001184.3	676	-/T	9/47	1	2	FACETS	0.3	0.227	0.385	0.3	0.227	0.385	SUBCLONAL	1	TRUE	1	0.39	2		329	325	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919314	178919314	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	12	135	0	ENST00000263967.3:c.799C>A	p.Leu267Met	p.L267M	ENST00000263967	NM_006218.2	267	Ctg/Atg	4/21	1	2	FACETS	0.449	0.317	0.61	0.449	0.317	0.61	SUBCLONAL	1	TRUE	1	0.39	2		135	137	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178942545	178942545	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	39	238	0	ENST00000263967.3:c.2352G>T	p.Glu784Asp	p.E784D	ENST00000263967	NM_006218.2	784	gaG/gaT	16/21	1	2	FACETS	0.826	0.69	0.976	0.826	0.69	0.976	CLONAL	1	TRUE	1	0.39	2		238	242	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948079	178948079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	31	189	0	ENST00000263967.3:c.2851C>T	p.Arg951Cys	p.R951C	ENST00000263967	NM_006218.2	951	Cgt/Tgt	20/21	1	2	FACETS	0.713	0.58	0.861	0.713	0.58	0.861	SUBCLONAL	1	TRUE	1	0.39	2		189	223	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	39	440	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.913	0.764	1	0.913	0.764	1	CLONAL	1	TRUE	1	0.39	2		440	219	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504995	186504995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	46	216	0	ENST00000323963.5:c.851G>A	p.Arg284His	p.R284H	ENST00000323963		284	cGc/cAc	8/11	1	2	FACETS	0.708	0.599	0.828	0.708	0.599	0.828	SUBCLONAL	1	TRUE	1	0.39	2		216	333	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447080	187447080	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	131	427	0	ENST00000232014.4:c.1113A>C	p.Lys371Asn	p.K371N	ENST00000232014	NM_001130845.1	371	aaA/aaC	5/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.39	2		427	640	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586389	189586389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1029852196	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	61	206	0	ENST00000264731.3:c.1013G>A	p.Arg338His	p.R338H	ENST00000264731	NM_003722.4	338	cGc/cAc	8/14	1	2	FACETS	0.796	0.689	0.911	0.796	0.689	0.911	CLONAL	1	TRUE	1	0.39	2		206	393	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801067	1801067	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	40	385	2	ENST00000260795.2:c.196G>T	p.Gly66Cys	p.G66C	ENST00000260795		66	Ggt/Tgt	2/17	1	2	FACETS	0.33	0.273	0.393	0.33	0.273	0.393	SUBCLONAL	1	TRUE	1	0.39	2		387	622	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957874	1957874	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1157864395	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	66	331	2	ENST00000382891.5:c.2840G>A	p.Arg947His	p.R947H	ENST00000382891	NM_133335.3	947	cGc/cAc	15/22	1	2	FACETS	0.571	0.495	0.652	0.571	0.495	0.652	SUBCLONAL	1	TRUE	1	0.39	2		333	593	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161398	55161398	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752633017	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	92	277	1	ENST00000257290.5:c.3229G>A	p.Gly1077Ser	p.G1077S	ENST00000257290	NM_006206.4	1077	Ggc/Agc	23/23	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.39	2		278	458	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007392	143007392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139268004	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	32	151	0	ENST00000262992.4:c.2392G>A	p.Glu798Lys	p.E798K	ENST00000262992	NM_001101669.1	798	Gaa/Aaa	22/24	1	2	FACETS	1	0.822	1	1	0.822	1	CLONAL	1	TRUE	1	0.39	2		151	164	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244255	153244255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	19	225	0	ENST00000281708.4:c.1902G>T	p.Lys634Asn	p.K634N	ENST00000281708	NM_033632.3	634	aaG/aaT	12/12	1	2	FACETS	0.487	0.371	0.622	0.487	0.371	0.622	SUBCLONAL	1	TRUE	1	0.39	2		225	200	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	56	307	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.39	2		307	275	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519253	187519253	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	54	311	1	ENST00000441802.2:c.12130T>C	p.Tyr4044His	p.Y4044H	ENST00000441802	NM_005245.3	4044	Tac/Cac	23/27	1	2	FACETS	0.684	0.586	0.79	0.684	0.586	0.79	SUBCLONAL	1	TRUE	1	0.39	2		312	405	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538259	187538259	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	23	381	0	ENST00000441802.2:c.8975A>G	p.Tyr2992Cys	p.Y2992C	ENST00000441802	NM_005245.3	2992	tAc/tGc	11/27	1	2	FACETS	0.364	0.284	0.457	0.364	0.284	0.457	SUBCLONAL	1	TRUE	1	0.39	2		381	324	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540445	187540445	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	40	268	0	ENST00000441802.2:c.7295G>C	p.Gly2432Ala	p.G2432A	ENST00000441802	NM_005245.3	2432	gGc/gCc	10/27	1	2	FACETS	0.851	0.713	1	0.851	0.713	1	CLONAL	1	TRUE	1	0.39	2		268	241	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541691	187541691	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	28	231	0	ENST00000441802.2:c.6049C>A	p.Leu2017Ile	p.L2017I	ENST00000441802	NM_005245.3	2017	Ctc/Atc	10/27	1	2	FACETS	0.504	0.404	0.617	0.504	0.404	0.617	SUBCLONAL	1	TRUE	1	0.39	2		231	285	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549670	187549670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	41	265	0	ENST00000441802.2:c.4571C>T	p.Ala1524Val	p.A1524V	ENST00000441802	NM_005245.3	1524	gCt/gTt	8/27	1	2	FACETS	0.548	0.457	0.648	0.548	0.457	0.648	SUBCLONAL	1	TRUE	1	0.39	2		265	384	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294244	1294244	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	114	373	2	ENST00000310581.5:c.757C>T	p.Gln253Ter	p.Q253*	ENST00000310581	NM_198253.2	253	Cag/Tag	2/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.39	2		375	543	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515600	31515600	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	55	284	0	ENST00000344624.3:c.1019del	p.Asn340IlefsTer12	p.N340Ifs*12	ENST00000344624		340	aAt/at	4/33	1	2	FACETS	0.986	0.85	1	0.986	0.85	1	CLONAL	1	TRUE	1	0.39	2		284	286	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526997	31526997	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1196872143	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	85	343	0	ENST00000344624.3:c.43G>A	p.Gly15Arg	p.G15R	ENST00000344624		15	Gga/Aga	2/33	1	2	FACETS	0.833	0.739	0.934	0.833	0.739	0.934	CLONAL	1	TRUE	1	0.39	2		343	523	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39002716	39002716	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	47	304	1	ENST00000357387.3:c.313C>T	p.Arg105Ter	p.R105*	ENST00000357387	NM_152756.3	105	Cga/Tga	5/38	1	2	FACETS	0.746	0.633	0.87	0.746	0.633	0.87	SUBCLONAL	1	TRUE	1	0.39	2		305	323	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161221	56161221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781300314	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	55	244	0	ENST00000399503.3:c.1090C>T	p.Arg364Trp	p.R364W	ENST00000399503	NM_005921.1	364	Cgg/Tgg	5/20	1	2	FACETS	0.808	0.695	0.931	0.808	0.695	0.931	CLONAL	1	TRUE	1	0.39	2		244	349	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750454	57750454	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	56	291	1	ENST00000274289.3:c.2014C>T	p.Arg672Ter	p.R672*	ENST00000274289	NM_006622.3	672	Cga/Tga	14/14	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.39	2		292	277	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576529	67576529	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	34	254	0	ENST00000274335.5:c.808C>A	p.Pro270Thr	p.P270T	ENST00000274335		270	Cct/Act	5/15	1	2	FACETS	0.752	0.618	0.899	0.752	0.618	0.899	SUBCLONAL	1	TRUE	1	0.39	2		254	232	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589631	67589631	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	25	213	0	ENST00000274335.5:c.1394G>T	p.Arg465Ile	p.R465I	ENST00000274335		465	aGa/aTa	10/15	1	2	FACETS	0.697	0.553	0.859	0.697	0.553	0.859	SUBCLONAL	1	TRUE	1	0.39	2		213	184	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79974900	79974900	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	74	201	0	ENST00000265081.6:c.1328C>G	p.Ala443Gly	p.A443G	ENST00000265081	NM_002439.4	443	gCc/gGc	8/24	1	2	FACETS	0.988	0.87	1	0.988	0.87	1	CLONAL	1	TRUE	1	0.39	2		201	384	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80083424	80083424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757559592	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	48	375	1	ENST00000265081.6:c.2476C>T	p.His826Tyr	p.H826Y	ENST00000265081	NM_002439.4	826	Cat/Tat	18/24	1	2	FACETS	0.597	0.506	0.698	0.597	0.506	0.698	SUBCLONAL	1	TRUE	1	0.39	2		376	412	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649005	86649005	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	22	261	0	ENST00000274376.6:c.1285G>T	p.Glu429Ter	p.E429*	ENST00000274376	NM_002890.2	429	Gaa/Taa	9/25	1	2	FACETS	0.46	0.358	0.579	0.46	0.358	0.579	SUBCLONAL	1	TRUE	1	0.39	2		261	245	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672842	86672842	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	28	165	0	ENST00000274376.6:c.2329G>T	p.Glu777Ter	p.E777*	ENST00000274376	NM_002890.2	777	Gaa/Taa	17/25	1	2	FACETS	0.897	0.725	1	0.897	0.725	1	CLONAL	1	TRUE	1	0.39	2		165	160	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685284	86685284	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	37	154	0	ENST00000274376.6:c.3000G>T	p.Glu1000Asp	p.E1000D	ENST00000274376	NM_002890.2	1000	gaG/gaT	24/25	1	2	FACETS	0.724	0.6	0.861	0.724	0.6	0.861	SUBCLONAL	1	TRUE	1	0.39	2		154	262	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524653	176524654	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	106	350	0	ENST00000292408.4:c.2385_2386insA	p.Phe796IlefsTer18	p.F796Ifs*18	ENST00000292408	NM_213647.1	795	-/A	18/18	1	2	FACETS	0.882	0.793	0.977	0.882	0.793	0.977	CLONAL	1	TRUE	1	0.39	2		350	616	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030307	180030308	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs772530628	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	117	387	0	ENST00000261937.6:c.3976dup	p.Ala1326GlyfsTer118	p.A1326Gfs*118	ENST00000261937	NM_182925.4	1326	gcc/gGcc	30/30	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.39	2		387	580	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039567	180039567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	127	362	0	ENST00000261937.6:c.3476G>A	p.Arg1159Lys	p.R1159K	ENST00000261937	NM_182925.4	1159	aGa/aAa	26/30	1	2	FACETS	0.938	0.852	1	0.938	0.852	1	CLONAL	1	TRUE	1	0.39	2		362	694	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048656	180048656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	73	340	0	ENST00000261937.6:c.1906C>T	p.Leu636Phe	p.L636F	ENST00000261937	NM_182925.4	636	Ctc/Ttc	13/30	1	2	FACETS	0.705	0.618	0.799	0.705	0.618	0.799	SUBCLONAL	1	TRUE	1	0.39	2		340	531	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057729	180057729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202015753	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	87	321	0	ENST00000261937.6:c.226G>A	p.Glu76Lys	p.E76K	ENST00000261937	NM_182925.4	76	Gag/Aag	3/30	1	2	FACETS	0.787	0.698	0.882	0.787	0.698	0.882	SUBCLONAL	1	TRUE	1	0.39	2		321	567	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858563	27858563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376571568	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	39	150	0	ENST00000359303.2:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000359303	NM_003535.2	3	cGg/cAg	1/1	1	2	FACETS	0.943	0.789	1	0.943	0.789	1	CLONAL	1	TRUE	1	0.39	2		150	212	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679444	30679444	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	73	338	0	ENST00000376406.3:c.2128G>T	p.Ala710Ser	p.A710S	ENST00000376406	NM_014641.2	710	Gca/Tca	6/15	1	2	FACETS	0.902	0.792	1	0.902	0.792	1	CLONAL	1	TRUE	1	0.39	2		338	415	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163545	32163545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs899065646	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	99	333	0	ENST00000375023.3:c.5681A>G	p.Tyr1894Cys	p.Y1894C	ENST00000375023	NM_004557.3	1894	tAt/tGt	30/30	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.39	2		333	405	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166773	32166773	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1231739465	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	36	372	1	ENST00000375023.3:c.4465C>T	p.Arg1489Ter	p.R1489*	ENST00000375023	NM_004557.3	1489	Cga/Tga	24/30	1	2	FACETS	0.296	0.243	0.357	0.296	0.243	0.357	SUBCLONAL	1	TRUE	1	0.39	2		373	623	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188854	32188855	+	missense_variant	Missense_Mutation	DNP	GC	GC	AT	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	82	298	2	ENST00000375023.3:c.699_700delinsAT	p.Arg234Trp	p.R234W	ENST00000375023	NM_004557.3	233	ctGCgg/ctATgg	4/30	1	2	FACETS	0.88	0.778	0.988	0.88	0.778	0.988	CLONAL	1	TRUE	1	0.39	2		300	478	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797707	32797707	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	69	329	0	ENST00000374899.4:c.1795G>T	p.Asp599Tyr	p.D599Y	ENST00000374899	NM_018833.2	599	Gat/Tat	10/12	1	2	FACETS	0.699	0.61	0.795	0.699	0.61	0.795	SUBCLONAL	1	TRUE	1	0.39	2		329	506	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797867	32797867	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	52	223	0	ENST00000374899.4:c.1636-1G>T		p.X546_splice	ENST00000374899	NM_018833.2	546			1	2	FACETS	0.841	0.72	0.972	0.841	0.72	0.972	CLONAL	1	TRUE	1	0.39	2		223	317	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903745	41903745	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	113	345	0	ENST00000372991.4:c.812G>C	p.Arg271Pro	p.R271P	ENST00000372991	NM_001760.3	271	cGg/cCg	5/5	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.39	2		345	547	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748494	43748494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	89	294	0	ENST00000523873.1:c.448G>A	p.Gly150Arg	p.G150R	ENST00000523873		150	Ggg/Agg	6/8	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.39	2		294	417	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553533	106553533	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	68	214	0	ENST00000369096.4:c.1501del	p.Ala501ProfsTer5	p.A501Pfs*5	ENST00000369096	NM_001198.3	500	Ggg/gg	5/7	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.39	2		214	320	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710657	117710657	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	46	247	0	ENST00000368508.3:c.1615G>T	p.Glu539Ter	p.E539*	ENST00000368508	NM_002944.2	539	Gaa/Taa	12/43	1	2	FACETS	0.805	0.682	0.939	0.805	0.682	0.939	CLONAL	1	TRUE	1	0.39	2		247	293	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525525	137525525	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146687518	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	58	380	0	ENST00000367739.4:c.490G>A	p.Glu164Lys	p.E164K	ENST00000367739	NM_000416.2	164	Gaa/Aaa	4/7	1	2	FACETS	0.872	0.754	1	0.872	0.754	1	CLONAL	1	TRUE	1	0.39	2		380	341	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192537	138192537	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	72	268	0	ENST00000237289.4:c.173C>A	p.Pro58His	p.P58H	ENST00000237289	NM_001270507.1	58	cCt/cAt	2/9	1	2	FACETS	0.871	0.764	0.985	0.871	0.764	0.985	CLONAL	1	TRUE	1	0.39	2		268	424	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200145	138200145	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	90	274	1	ENST00000237289.4:c.1563C>A	p.Cys521Ter	p.C521*	ENST00000237289	NM_001270507.1	521	tgC/tgA	7/9	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.39	2		275	417	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001358	150001358	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	51	334	0	ENST00000253339.5:c.2246A>G	p.His749Arg	p.H749R	ENST00000253339		749	cAt/cGt	4/7	1	2	FACETS	0.769	0.657	0.891	0.769	0.657	0.891	SUBCLONAL	1	TRUE	1	0.39	2		334	340	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100367	157100367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	46	138	0	ENST00000346085.5:c.1304G>A	p.Gly435Asp	p.G435D	ENST00000346085	NM_020732.3	435	gGc/gAc	1/20	1	2	FACETS	0.947	0.805	1	0.947	0.805	1	CLONAL	1	TRUE	1	0.39	2		138	249	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469911	157469911	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	85	329	0	ENST00000346085.5:c.2705C>A	p.Ala902Asp	p.A902D	ENST00000346085	NM_020732.3	902	gCt/gAt	9/20	1	2	FACETS	0.893	0.792	1	0.893	0.792	1	CLONAL	1	TRUE	1	0.39	2		329	488	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521972	157521972	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs769118968	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	81	245	0	ENST00000346085.5:c.4244A>G	p.Asp1415Gly	p.D1415G	ENST00000346085	NM_020732.3	1415	gAc/gGc	18/20	1	2	FACETS	0.882	0.78	0.991	0.882	0.78	0.991	CLONAL	1	TRUE	1	0.39	2		245	471	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522496	157522496	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	118	418	0	ENST00000346085.5:c.4768T>G	p.Ser1590Ala	p.S1590A	ENST00000346085	NM_020732.3	1590	Tcc/Gcc	18/20	1	2	FACETS	0.962	0.87	1	0.962	0.87	1	CLONAL	1	TRUE	1	0.39	2		418	629	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528328	157528328	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	131	468	0	ENST00000346085.5:c.6053A>G	p.Glu2018Gly	p.E2018G	ENST00000346085	NM_020732.3	2018	gAg/gGg	20/20	1	2	FACETS	0.913	0.829	1	0.913	0.829	1	CLONAL	1	TRUE	1	0.39	2		468	736	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528349	157528349	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	121	474	0	ENST00000346085.5:c.6074T>C	p.Leu2025Ser	p.L2025S	ENST00000346085	NM_020732.3	2025	tTg/tCg	20/20	1	2	FACETS	0.875	0.792	0.963	0.875	0.792	0.963	CLONAL	1	TRUE	1	0.39	2		474	709	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161970006	161970006	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs767703008	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	107	346	0	ENST00000366898.1:c.963G>T	p.Glu321Asp	p.E321D	ENST00000366898	NM_004562.2	321	gaG/gaT	9/12	1	2	FACETS	0.948	0.852	1	0.948	0.852	1	CLONAL	1	TRUE	1	0.39	2		346	579	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935577	13935577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	62	273	0	ENST00000405192.2:c.1279C>T	p.Leu427Phe	p.L427F	ENST00000405192	NM_001163147.1	427	Ctt/Ttt	12/12	1	2	FACETS	0.941	0.818	1	0.941	0.818	1	CLONAL	1	TRUE	1	0.39	2		273	338	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946171	13946171	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	70	349	0	ENST00000405192.2:c.925C>T	p.Arg309Ter	p.R309*	ENST00000405192	NM_001163147.1	309	Cga/Tga	10/12	1	2	FACETS	0.772	0.675	0.876	0.772	0.675	0.876	SUBCLONAL	1	TRUE	1	0.39	2		349	465	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739661	41739661	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	129	471	1	ENST00000242208.4:c.312G>T	p.Glu104Asp	p.E104D	ENST00000242208	NM_002192.2	104	gaG/gaT	2/3	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.39	2		472	651	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467618	50467618	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	67	194	0	ENST00000331340.3:c.853G>A	p.Asp285Asn	p.D285N	ENST00000331340	NM_006060.4	285	Gac/Aac	8/8	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.39	2		194	282	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339547	81339547	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	43	280	0	ENST00000222390.5:c.1457C>A	p.Ser486Tyr	p.S486Y	ENST00000222390	NM_000601.4	486	tCt/tAt	13/18	1	2	FACETS	0.799	0.673	0.937	0.799	0.673	0.937	CLONAL	1	TRUE	1	0.39	2		280	276	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350062	81350062	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs759145490	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	35	216	0	ENST00000222390.5:c.1270C>T	p.Arg424Cys	p.R424C	ENST00000222390	NM_000601.4	424	Cgt/Tgt	10/18	1	2	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	TRUE	1	0.39	2		216	174	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358924	81358924	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	26	257	0	ENST00000222390.5:c.1037G>C	p.Cys346Ser	p.C346S	ENST00000222390	NM_000601.4	346	tGc/tCc	8/18	1	2	FACETS	0.551	0.438	0.679	0.551	0.438	0.679	SUBCLONAL	1	TRUE	1	0.39	2		257	242	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513171	106513171	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	33	164	0	ENST00000359195.3:c.2075G>T	p.Gly692Val	p.G692V	ENST00000359195	NM_002649.2	692	gGt/gTt	4/11	1	2	FACETS	0.746	0.611	0.895	0.746	0.611	0.895	SUBCLONAL	1	TRUE	1	0.39	2		164	227	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524705	106524705	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1487014289	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	35	201	0	ENST00000359195.3:c.2866G>A	p.Glu956Lys	p.E956K	ENST00000359195	NM_002649.2	956	Gag/Aag	9/11	1	2	FACETS	0.893	0.739	1	0.893	0.739	1	CLONAL	1	TRUE	1	0.39	2		201	201	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340242	116340243	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	32	226	0	ENST00000397752.3:c.1106_1107del	p.Tyr369CysfsTer26	p.Y369Cfs*26	ENST00000397752	NM_000245.2	368	aaATat/aaat	2/21	1	2	FACETS	0.654	0.533	0.788	0.654	0.533	0.788	SUBCLONAL	1	TRUE	1	0.39	2		226	251	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380071	116380071	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	61	357	0	ENST00000397752.3:c.1460C>A	p.Ser487Tyr	p.S487Y	ENST00000397752	NM_000245.2	487	tCt/tAt	4/21	1	2	FACETS	0.904	0.784	1	0.904	0.784	1	CLONAL	1	TRUE	1	0.39	2		357	346	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418998	116418998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369838973	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	33	162	1	ENST00000397752.3:c.3509G>A	p.Arg1170Gln	p.R1170Q	ENST00000397752	NM_000245.2	1170	cGa/cAa	17/21	1	2	FACETS	0.814	0.668	0.975	0.814	0.668	0.975	CLONAL	1	TRUE	1	0.39	2		163	208	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534548	140534548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	71	283	0	ENST00000288602.6:c.365C>T	p.Ser122Phe	p.S122F	ENST00000288602	NM_004333.4	122	tCt/tTt	3/18	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.39	2		283	326	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878698	151878698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	46	220	0	ENST00000262189.6:c.6247G>A	p.Asp2083Asn	p.D2083N	ENST00000262189	NM_170606.2	2083	Gat/Aat	36/59	1	2	FACETS	0.963	0.818	1	0.963	0.818	1	CLONAL	1	TRUE	1	0.39	2		220	245	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879111	151879111	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	74	349	1	ENST00000262189.6:c.5834G>T	p.Arg1945Met	p.R1945M	ENST00000262189	NM_170606.2	1945	aGg/aTg	36/59	1	2	FACETS	0.849	0.746	0.959	0.849	0.746	0.959	CLONAL	1	TRUE	1	0.39	2		350	447	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879590	151879590	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	57	208	0	ENST00000262189.6:c.5355A>T	p.Gln1785His	p.Q1785H	ENST00000262189	NM_170606.2	1785	caA/caT	36/59	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.39	2		208	274	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900027	151900027	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	39	238	0	ENST00000262189.6:c.4084T>C	p.Tyr1362His	p.Y1362H	ENST00000262189	NM_170606.2	1362	Tat/Cat	26/59	1	2	FACETS	0.639	0.531	0.758	0.639	0.531	0.758	SUBCLONAL	1	TRUE	1	0.39	2		238	313	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38157027	38157027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373265367	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	40	393	0	ENST00000317025.8:c.2693G>A	p.Arg898His	p.R898H	ENST00000317025	NM_023034.1	898	cGt/cAt	15/24	1	2	FACETS	0.595	0.495	0.704	0.595	0.495	0.704	SUBCLONAL	1	TRUE	1	0.39	2		393	345	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370805	55370805	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	70	320	1	ENST00000297316.4:c.107T>C	p.Leu36Pro	p.L36P	ENST00000297316	NM_022454.3	36	cTg/cCg	1/2	1	2	FACETS	0.886	0.776	1	0.886	0.776	1	CLONAL	1	TRUE	1	0.39	2		321	405	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922521	56922521	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465409982	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	87	347	0	ENST00000519728.1:c.1391G>A	p.Arg464His	p.R464H	ENST00000519728	NM_002350.3	464	cGt/cAt	13/13	1	2	FACETS	0.901	0.801	1	0.901	0.801	1	CLONAL	1	TRUE	1	0.39	2		347	495	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950493	68950493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760821149	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	44	253	0	ENST00000288368.4:c.805G>A	p.Asp269Asn	p.D269N	ENST00000288368	NM_024870.2	269	Gat/Aat	7/40	1	2	FACETS	0.809	0.682	0.947	0.809	0.682	0.947	CLONAL	1	TRUE	1	0.39	2		253	279	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030843	69030843	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	85	228	0	ENST00000288368.4:c.3385T>C	p.Cys1129Arg	p.C1129R	ENST00000288368	NM_024870.2	1129	Tgc/Cgc	27/40	1	2	FACETS	0.95	0.843	1	0.95	0.843	1	CLONAL	1	TRUE	1	0.39	2		228	459	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862863	117862863	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	33	282	0	ENST00000297338.2:c.1614G>T	p.Glu538Asp	p.E538D	ENST00000297338	NM_006265.2	538	gaG/gaT	12/14	1	2	FACETS	0.639	0.522	0.768	0.639	0.522	0.768	SUBCLONAL	1	TRUE	1	0.39	2		282	265	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866686	117866686	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	41	262	1	ENST00000297338.2:c.959G>T	p.Arg320Met	p.R320M	ENST00000297338	NM_006265.2	320	aGg/aTg	9/14	1	2	FACETS	0.883	0.742	1	0.883	0.742	1	CLONAL	1	TRUE	1	0.39	2		263	238	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141545574	141545574	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	127	408	0	ENST00000220592.5:c.2264G>T	p.Gly755Val	p.G755V	ENST00000220592	NM_012154.3	755	gGc/gTc	17/19	1	2	FACETS	0.974	0.884	1	0.974	0.884	1	CLONAL	1	TRUE	1	0.39	2		408	669	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566312	141566312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754710399	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	38	286	0	ENST00000220592.5:c.1100C>T	p.Ala367Val	p.A367V	ENST00000220592	NM_012154.3	367	gCg/gTg	9/19	1	2	FACETS	0.33	0.272	0.395	0.33	0.272	0.395	SUBCLONAL	1	TRUE	1	0.39	2		286	590	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737323	145737323	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369843844	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	99	341	0	ENST00000428558.2:c.3364G>A	p.Ala1122Thr	p.A1122T	ENST00000428558	NM_004260.3	1122	Gca/Aca	20/22	1	2	FACETS	0.824	0.737	0.917	0.824	0.737	0.917	CLONAL	1	TRUE	1	0.39	2		341	616	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738644	145738644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs571684398	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	126	312	0	ENST00000428558.2:c.2420G>A	p.Arg807His	p.R807H	ENST00000428558	NM_004260.3	807	cGt/cAt	15/22	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.39	2		312	510	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054752	5054752	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	24	245	0	ENST00000381652.3:c.804G>T	p.Glu268Asp	p.E268D	ENST00000381652	NM_004972.3	268	gaG/gaT	7/25	1	2	FACETS	0.542	0.427	0.674	0.542	0.427	0.674	SUBCLONAL	1	TRUE	1	0.39	2		245	227	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319853	8319853	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	48	287	0	ENST00000356435.5:c.5648G>A	p.Arg1883Gln	p.R1883Q	ENST00000356435		1883	cGa/cAa	34/35	1	2	FACETS	0.821	0.698	0.954	0.821	0.698	0.954	CLONAL	1	TRUE	1	0.39	2		287	300	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341941	8341941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	15	223	0	ENST00000356435.5:c.4699G>A	p.Asp1567Asn	p.D1567N	ENST00000356435		1567	Gat/Aat	29/35	1	2	FACETS	0.407	0.298	0.537	0.407	0.298	0.537	SUBCLONAL	1	TRUE	1	0.39	2		223	189	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341976	8341976	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs377463668	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	29	181	0	ENST00000356435.5:c.4664C>T	p.Ala1555Val	p.A1555V	ENST00000356435		1555	gCg/gTg	29/35	1	2	FACETS	0.966	0.785	1	0.966	0.785	1	CLONAL	1	TRUE	1	0.39	2		181	154	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499748	8499748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	88	310	0	ENST00000356435.5:c.2221C>T	p.His741Tyr	p.H741Y	ENST00000356435		741	Cat/Tat	14/35	1	2	FACETS	0.932	0.829	1	0.932	0.829	1	CLONAL	1	TRUE	1	0.39	2		310	484	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500865	8500865	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs748586269	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	67	363	1	ENST00000356435.5:c.2017C>A	p.Leu673Ile	p.L673I	ENST00000356435		673	Ctt/Att	13/35	1	2	FACETS	0.83	0.724	0.944	0.83	0.724	0.944	CLONAL	1	TRUE	1	0.39	2		364	414	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521544	8521544	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	78	267	0	ENST00000356435.5:c.694C>T	p.Arg232Cys	p.R232C	ENST00000356435		232	Cgc/Tgc	9/35	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.39	2		267	358	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8523519	8523519	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	50	239	0	ENST00000356435.5:c.685C>T	p.Arg229Ter	p.R229*	ENST00000356435		229	Cga/Tga	8/35	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.39	2		239	231	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633452	8633452	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	38	225	0	ENST00000356435.5:c.217G>T	p.Glu73Ter	p.E73*	ENST00000356435		73	Gag/Tag	3/35	1	2	FACETS	0.795	0.662	0.942	0.795	0.662	0.942	CLONAL	1	TRUE	1	0.39	2		225	245	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27168543	27168543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	52	395	1	ENST00000380036.4:c.415G>A	p.Val139Met	p.V139M	ENST00000380036	NM_000459.3	139	Gtg/Atg	3/23	1	2	FACETS	0.775	0.663	0.897	0.775	0.663	0.897	SUBCLONAL	1	TRUE	1	0.39	2		396	344	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206780	27206780	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	79	298	0	ENST00000380036.4:c.2565A>C	p.Lys855Asn	p.K855N	ENST00000380036	NM_000459.3	855	aaA/aaC	15/23	1	2	FACETS	0.904	0.799	1	0.904	0.799	1	CLONAL	1	TRUE	1	0.39	2		298	448	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002696	37002696	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	118	361	0	ENST00000358127.4:c.553C>A	p.Leu185Met	p.L185M	ENST00000358127	NM_001280556.1	185	Ctg/Atg	5/10	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.39	2		361	580	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317303	87317303	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303772589	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	55	299	0	ENST00000277120.3:c.328G>A	p.Ala110Thr	p.A110T	ENST00000277120		110	Gca/Aca	4/19	1	2	FACETS	0.769	0.66	0.886	0.769	0.66	0.886	SUBCLONAL	1	TRUE	1	0.39	2		299	367	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570318	87570318	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	119	332	0	ENST00000277120.3:c.2058G>T	p.Gln686His	p.Q686H	ENST00000277120		686	caG/caT	17/19	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.39	2		332	485	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864003	97864003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs370974124	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	83	259	0	ENST00000289081.3:c.1663C>T	p.Arg555Ter	p.R555*	ENST00000289081	NM_000136.2	555	Cga/Tga	15/15	1	2	FACETS	0.833	0.737	0.935	0.833	0.737	0.935	CLONAL	1	TRUE	1	0.39	2		259	511	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238396	98238396	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	81	313	2	ENST00000331920.6:c.1648C>A	p.Leu550Ile	p.L550I	ENST00000331920	NM_000264.3	550	Ctc/Atc	12/24	1	2	FACETS	0.88	0.778	0.989	0.88	0.778	0.989	CLONAL	1	TRUE	1	0.39	2		315	472	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98241306	98241306	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	93	341	0	ENST00000331920.6:c.1191G>T	p.Glu397Asp	p.E397D	ENST00000331920	NM_000264.3	397	gaG/gaT	8/24	1	2	FACETS	0.85	0.758	0.948	0.85	0.758	0.948	CLONAL	1	TRUE	1	0.39	2		341	561	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894974	101894974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745324433	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	36	196	0	ENST00000374994.4:c.527C>T	p.Thr176Met	p.T176M	ENST00000374994	NM_004612.2	176	aCg/aTg	3/9	1	2	FACETS	0.736	0.608	0.876	0.736	0.608	0.876	SUBCLONAL	1	TRUE	1	0.39	2		196	251	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911534	101911534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111426349	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	53	264	1	ENST00000374994.4:c.1459C>T	p.Arg487Trp	p.R487W	ENST00000374994	NM_004612.2	487	Cgg/Tgg	9/9	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.39	2		265	266	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127920582	127920582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140793926	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	62	662	1	ENST00000373547.4:c.317G>A	p.Arg106His	p.R106H	ENST00000373547	NM_002721.4	106	cGt/cAt	4/7	1	2	FACETS	0.891	0.773	1	0.891	0.773	1	CLONAL	1	TRUE	1	0.39	2		663	357	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128420047	128420047	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	27	373	4	ENST00000265960.3:c.381del	p.Lys127AsnfsTer20	p.K127Nfs*20	ENST00000265960	NM_001006617.1	127	aaA/aa	4/12	1	2	FACETS	0.405	0.322	0.499	0.405	0.322	0.499	SUBCLONAL	1	TRUE	1	0.39	2		377	342	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759844	133759844	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	107	334	0	ENST00000318560.5:c.2167C>A	p.Pro723Thr	p.P723T	ENST00000318560	NM_005157.4	723	Ccc/Acc	11/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.39	2		334	448	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760648	133760648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	133	450	1	ENST00000318560.5:c.2971G>A	p.Ala991Thr	p.A991T	ENST00000318560	NM_005157.4	991	Gcc/Acc	11/11	1	2	FACETS	0.914	0.831	1	0.914	0.831	1	CLONAL	1	TRUE	1	0.39	2		451	746	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391293	139391293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778573	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	40	414	0	ENST00000277541.6:c.6898G>A	p.Gly2300Arg	p.G2300R	ENST00000277541	NM_017617.3	2300	Ggg/Agg	34/34	1	2	FACETS	0.33	0.273	0.393	0.33	0.273	0.393	SUBCLONAL	1	TRUE	1	0.39	2		414	622	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409820	139409820	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238304834	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	41	428	0	ENST00000277541.6:c.1936G>A	p.Ala646Thr	p.A646T	ENST00000277541	NM_017617.3	646	Gcc/Acc	12/34	1	2	FACETS	0.269	0.223	0.321	0.269	0.223	0.321	SUBCLONAL	1	TRUE	1	0.39	2		428	781	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417614	139417614	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	175	375	0	ENST00000277541.6:c.430T>C	p.Cys144Arg	p.C144R	ENST00000277541	NM_017617.3	144	Tgc/Cgc	4/34	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.39	2		375	764	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139565413	139565413	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	80	322	0	ENST00000308874.7:c.583G>A	p.Ala195Thr	p.A195T	ENST00000308874		195	Gca/Aca	8/10	1	2	FACETS	0.758	0.669	0.854	0.758	0.669	0.854	SUBCLONAL	1	TRUE	1	0.39	2		322	541	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815584	139815584	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	57	392	0	ENST00000247668.2:c.1055G>T	p.Gly352Val	p.G352V	ENST00000247668	NM_021138.3	352	gGg/gTg	9/11	1	2	FACETS	0.449	0.385	0.519	0.449	0.385	0.519	SUBCLONAL	1	TRUE	1	0.39	2		392	651	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911517	39911517	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	68	369	0	ENST00000378444.4:c.5113C>A	p.Leu1705Ile	p.L1705I	ENST00000378444	NM_001123385.1	1705	Ctc/Atc	15/15	1	2	FACETS	0.725	0.632	0.825	0.725	0.632	0.825	SUBCLONAL	1	TRUE	1	0.39	2		369	481	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933065	39933065	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	87	366	0	ENST00000378444.4:c.1534C>T	p.Pro512Ser	p.P512S	ENST00000378444	NM_001123385.1	512	Ccc/Tcc	4/15	1	2	FACETS	0.791	0.702	0.886	0.791	0.702	0.886	SUBCLONAL	1	TRUE	1	0.39	2		366	564	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937723	44937723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	67	324	0	ENST00000377967.4:c.2911C>T	p.Arg971Cys	p.R971C	ENST00000377967	NM_021140.2	971	Cgt/Tgt	19/29	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.39	2		324	336	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030469	47030469	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556772646	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	107	365	0	ENST00000377604.3:c.244C>T	p.Arg82Trp	p.R82W	ENST00000377604	NM_001204468.1	82	Cgg/Tgg	4/24	1	2	FACETS	0.919	0.826	1	0.919	0.826	1	CLONAL	1	TRUE	1	0.39	2		365	597	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222451	53222451	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782614169	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	185	388	0	ENST00000375401.3:c.4381C>T	p.Arg1461Trp	p.R1461W	ENST00000375401	NM_004187.3	1461	Cgg/Tgg	26/26	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.39	2		388	808	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250074	53250074	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556854363	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	77	307	1	ENST00000375401.3:c.175G>A	p.Glu59Lys	p.E59K	ENST00000375401	NM_004187.3	59	Gaa/Aaa	2/26	1	2	FACETS	0.744	0.654	0.84	0.744	0.654	0.84	SUBCLONAL	1	TRUE	1	0.39	2		308	531	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411308	63411308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763577174	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	113	381	0	ENST00000330258.3:c.1859G>A	p.Gly620Asp	p.G620D	ENST00000330258	NM_152424.3	620	gGc/gAc	2/2	1	2	FACETS	0.913	0.823	1	0.913	0.823	1	CLONAL	1	TRUE	1	0.39	2		381	635	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344043	70344043	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	61	427	0	ENST00000374080.3:c.1779C>A	p.Phe593Leu	p.F593L	ENST00000374080		593	ttC/ttA	13/45	1	2	FACETS	0.551	0.475	0.633	0.551	0.475	0.633	SUBCLONAL	1	TRUE	1	0.39	2		427	568	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344137	70344137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318670088	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	74	331	0	ENST00000374080.3:c.1873G>A	p.Ala625Thr	p.A625T	ENST00000374080		625	Gcc/Acc	13/45	1	2	FACETS	0.684	0.599	0.774	0.684	0.599	0.774	SUBCLONAL	1	TRUE	1	0.39	2		331	555	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348165	70348165	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	74	280	0	ENST00000374080.3:c.3229C>A	p.Leu1077Met	p.L1077M	ENST00000374080		1077	Ctg/Atg	23/45	1	2	FACETS	0.799	0.701	0.903	0.799	0.701	0.903	CLONAL	1	TRUE	1	0.39	2		280	475	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356479	70356479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	131	365	0	ENST00000374080.3:c.5374C>T	p.Arg1792Cys	p.R1792C	ENST00000374080		1792	Cgc/Tgc	37/45	1	2	FACETS	0.928	0.843	1	0.928	0.843	1	CLONAL	1	TRUE	1	0.39	2		365	724	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937455	76937455	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	41	282	0	ENST00000373344.5:c.3293G>T	p.Gly1098Val	p.G1098V	ENST00000373344	NM_000489.3	1098	gGa/gTa	9/35	1	2	FACETS	0.725	0.607	0.855	0.725	0.607	0.855	SUBCLONAL	1	TRUE	1	0.39	2		282	290	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937744	76937744	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	44	299	0	ENST00000373344.5:c.3004G>A	p.Val1002Ile	p.V1002I	ENST00000373344	NM_000489.3	1002	Gta/Ata	9/35	1	2	FACETS	0.783	0.661	0.918	0.783	0.661	0.918	CLONAL	1	TRUE	1	0.39	2		299	288	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938556	76938556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	24	284	0	ENST00000373344.5:c.2192C>T	p.Ser731Phe	p.S731F	ENST00000373344	NM_000489.3	731	tCt/tTt	9/35	1	2	FACETS	0.631	0.498	0.783	0.631	0.498	0.783	SUBCLONAL	1	TRUE	1	0.39	2		284	195	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938788	76938788	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	48	374	1	ENST00000373344.5:c.1960C>T	p.Arg654Ter	p.R654*	ENST00000373344	NM_000489.3	654	Cga/Tga	9/35	1	2	FACETS	0.774	0.658	0.901	0.774	0.658	0.901	CLONAL	1	TRUE	1	0.39	2		375	318	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939016	76939016	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	49	352	0	ENST00000373344.5:c.1732A>G	p.Thr578Ala	p.T578A	ENST00000373344	NM_000489.3	578	Act/Gct	9/35	1	2	FACETS	0.931	0.794	1	0.931	0.794	1	CLONAL	1	TRUE	1	0.39	2		352	270	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939853	76939853	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	44	286	0	ENST00000373344.5:c.895A>C	p.Lys299Gln	p.K299Q	ENST00000373344	NM_000489.3	299	Aaa/Caa	9/35	1	2	FACETS	0.824	0.695	0.964	0.824	0.695	0.964	CLONAL	1	TRUE	1	0.39	2		286	274	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608898	100608898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	55	333	0	ENST00000308731.7:c.1710G>A	p.Met570Ile	p.M570I	ENST00000308731	NM_000061.2	570	atG/atA	17/19	1	2	FACETS	0.685	0.587	0.79	0.685	0.587	0.79	SUBCLONAL	1	TRUE	1	0.39	2		333	412	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019721	123019721	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	63	299	0	ENST00000355640.3:c.209T>C	p.Val70Ala	p.V70A	ENST00000355640		70	gTa/gCa	2/7	1	2	FACETS	0.91	0.792	1	0.91	0.792	1	CLONAL	1	TRUE	1	0.39	2		299	355	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176430	123176430	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150057715	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	29	235	0	ENST00000218089.9:c.397G>A	p.Ala133Thr	p.A133T	ENST00000218089	NM_001042749.1	133	Gca/Aca	7/35	1	2	FACETS	0.673	0.543	0.818	0.673	0.543	0.818	SUBCLONAL	1	TRUE	1	0.39	2		235	221	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176470	123176470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	30	264	0	ENST00000218089.9:c.437G>A	p.Arg146Gln	p.R146Q	ENST00000218089	NM_001042749.1	146	cGa/cAa	7/35	1	2	FACETS	0.615	0.498	0.747	0.615	0.498	0.747	SUBCLONAL	1	TRUE	1	0.39	2		264	250	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224502	123224502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	41	369	0	ENST00000218089.9:c.3355C>T	p.Pro1119Ser	p.P1119S	ENST00000218089	NM_001042749.1	1119	Cca/Tca	31/35	1	2	FACETS	0.591	0.493	0.698	0.591	0.493	0.698	SUBCLONAL	1	TRUE	1	0.39	2		369	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578254	7578254	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551821	NA	P-0028778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	212	404	0	ENST00000269305.4:c.595G>T	p.Gly199Ter	p.G199*	ENST00000269305	NM_001126112.2	199	Gga/Tga	6/11	0.464522801889391	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	FALSE	0	0.464522801889391	2		404	379	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403632	138403632	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74701669	NA	P-0028784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	319	443	0	ENST00000289153.2:c.2150A>G	p.Asn717Ser	p.N717S	ENST00000289153	NM_006219.2	717	aAt/aGt	15/22	1	2	FACETS	0.965	0.916	1	0.965	0.916	1	CLONAL	1	TRUE	1	0.833421846524437	2		443	793	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012100	16012100	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	317	430	0	ENST00000268712.3:c.2182G>C	p.Val728Leu	p.V728L	ENST00000268712	NM_006311.3	728	Gtt/Ctt	19/46	0.833421846524437	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.833421846524437	1		430	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0028787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	469	861	1	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.538785230144642	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.538785230144642	1		862	909	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0028787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	699	549	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.538785230144642	3	FACETS	0.846	0.82	0.872	1	0.997	1	CLONAL	3	TRUE	1	0.538785230144642	3		549	1298	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107136	27107137	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0028787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	250	600	0	ENST00000324856.7:c.6749_6750del	p.Glu2250ValfsTer27	p.E2250Vfs*27	ENST00000324856	NM_006015.4	2249	tcAGag/tcag	20/20	0.399349410707392	1	FACETS	0.857	0.804	0.911	0.857	0.804	0.911	CLONAL	1	TRUE	0	0.538785230144642	1		600	791	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570180	95570180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150514959	NA	P-0028787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	64	507	0	ENST00000393063.1:c.3553G>A	p.Ala1185Thr	p.A1185T	ENST00000393063	NM_030621.3	1185	Gcc/Acc	22/28	1	2	FACETS	0.317	0.274	0.364	0.317	0.274	0.364	SUBCLONAL	1	TRUE	1	0.538785230144642	2		507	750	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245528	153245528	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	208	514	0	ENST00000281708.4:c.1663G>T	p.Val555Leu	p.V555L	ENST00000281708	NM_033632.3	555	Gtg/Ttg	11/12	0.427624075018777	1	FACETS	0.936	0.874	0.998	0.936	0.874	0.998	CLONAL	1	TRUE	0	0.538785230144642	1		514	603	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542152	187542152	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	200	561	0	ENST00000441802.2:c.5588C>G	p.Ala1863Gly	p.A1863G	ENST00000441802	NM_005245.3	1863	gCg/gGg	10/27	0.427624075018777	1	FACETS	0.9	0.839	0.962	0.9	0.839	0.962	CLONAL	1	TRUE	0	0.538785230144642	1		561	603	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875048	151875048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531219111	NA	P-0028787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	71	259	0	ENST00000262189.6:c.7490G>A	p.Arg2497His	p.R2497H	ENST00000262189	NM_170606.2	2497	cGc/cAc	38/59	0.34497986512209	1	FACETS	0.561	0.493	0.634	0.561	0.493	0.634	SUBCLONAL	1	TRUE	0	0.538785230144642	1		259	343	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440334	52440334	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0028790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	322	697	0	ENST00000460680.1:c.718A>T	p.Lys240Ter	p.K240*	ENST00000460680	NM_004656.3	240	Aag/Tag	9/17	0.440843978052425	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.440843978052425	2		697	659	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917716	29917716	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs878854661	NA	P-0028790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	220	608	0	ENST00000389048.3:c.952G>A	p.Gly318Ser	p.G318S	ENST00000389048	NM_004304.4	318	Ggc/Agc	3/29	0.309599621858374	4	FACETS	0.891	0.831	0.953	0.891	0.831	0.953	CLONAL	2	TRUE	2	0.440843978052425	4		608	807	SUCCESS
AR	367	MSKCC	GRCh37	X	66863241	66863241	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs750677165	NA	P-0028790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	125	532	0	ENST00000374690.3:c.1760C>A	p.Ala587Asp	p.A587D	ENST00000374690	NM_000044.3	587	gCc/gAc	2/8	0.376023072453855	5	FACETS	0.966	0.873	1	0.322	0.291	0.355	CLONAL	1	TRUE	2	0.440843978052425	5		532	975	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578529	7578529	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	140	956	0	ENST00000269305.4:c.401T>C	p.Phe134Ser	p.F134S	ENST00000269305	NM_001126112.2	134	tTt/tCt	5/11	0.289607239979286	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.289607239979286	1		956	805	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576021	29576021	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	91	576	0	ENST00000356175.3:c.3994C>G	p.Leu1332Val	p.L1332V	ENST00000356175	NM_000267.3	1332	Ctt/Gtt	30/57	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.289607239979286	2		576	618	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0028802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	105	301	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.987	0.891	1	0.987	0.891	1	CLONAL	1	TRUE	1	0.51	2		301	417	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589149	67589151	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	novel	NA	P-0028802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	80	268	0	ENST00000274335.5:c.1138_1140del	p.Leu380del	p.L380del	ENST00000274335		379	aaATTa/aaa	9/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.51	2		268	249	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685297	89685297	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	74	338	0	ENST00000371953.3:c.193del	p.Tyr65ThrfsTer34	p.Y65Tfs*34	ENST00000371953	NM_000314.4	64	caT/ca	3/9	1	2	FACETS	0.789	0.695	0.888	0.789	0.695	0.888	SUBCLONAL	1	TRUE	1	0.51	2		338	368	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692851	89692851	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	42	142	0	ENST00000371953.3:c.335T>G	p.Leu112Arg	p.L112R	ENST00000371953	NM_000314.4	112	cTa/cGa	5/9	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.51	2		142	163	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0028803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	391	504	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.614554287694992	1	FACETS	0.99	0.946	1	0.99	0.946	1	CLONAL	1	TRUE	0	0.614554287694992	1		504	890	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0028803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	230	394	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.55589402315775	1	FACETS	0.705	0.66	0.752	0.705	0.66	0.752	SUBCLONAL	1	TRUE	0	0.614554287694992	1		394	735	SUCCESS
APC	324	MSKCC	GRCh37	5	112175606	112175606	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	239	465	0	ENST00000257430.4:c.4316del	p.Pro1439LeufsTer34	p.P1439Lfs*34	ENST00000257430	NM_000038.5	1439	Cct/ct	16/16	0.614554287694992	1	FACETS	0.983	0.927	1	0.983	0.927	1	CLONAL	1	TRUE	0	0.614554287694992	1		465	548	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374914	45374914	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	356	593	0	ENST00000262160.6:c.929G>C	p.Arg310Thr	p.R310T	ENST00000262160	NM_005901.5	310	aGg/aCg	8/11	0.614554287694992	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.614554287694992	1		593	719	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119971	70119971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	183	336	1	ENST00000245479.2:c.973G>A	p.Ala325Thr	p.A325T	ENST00000245479	NM_000346.3	325	Gcg/Acg	3/3	0.614554287694992	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.614554287694992	1		337	351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578551	7578551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	141	789	0	ENST00000269305.4:c.379T>C	p.Ser127Pro	p.S127P	ENST00000269305	NM_001126112.2	127	Tcc/Ccc	5/11	1	2	FACETS	0.771	0.701	0.844	1	0.987	1	SUBCLONAL	2	TRUE	1	0.18	2		789	1016	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170479	108170479	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121434217	NA	P-0028805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	33	399	1	ENST00000278616.4:c.5044G>C	p.Asp1682His	p.D1682H	ENST00000278616	NM_000051.3	1682	Gat/Cat	34/63	1	2	FACETS	0.661	0.537	0.801	0.661	0.537	0.801	SUBCLONAL	1	TRUE	1	0.18	2		400	555	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161285	185161285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	98	589	1	ENST00000265026.3:c.712C>T	p.His238Tyr	p.H238Y	ENST00000265026	NM_004721.4	238	Cat/Tat	4/14	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.18	2		590	940	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0028832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	173	591	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.994	0.924	1	0.994	0.924	1	CLONAL	1	TRUE	1	0.764824737608874	2		591	455	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0028832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	62	344	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.84	0.738	0.946	0.84	0.738	0.946	CLONAL	1	TRUE	1	0.764824737608874	2		345	193	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16097870	16097870	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs76145228	NA	P-0028832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	13	278	1	ENST00000268712.3:c.14G>T	p.Gly5Val	p.G5V	ENST00000268712	NM_006311.3	5	gGt/gTt	2/46	1	2	FACETS	0.148	0.105	0.2	0.148	0.105	0.2	SUBCLONAL	1	TRUE	1	0.764824737608874	2		279	230	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796777	42796777	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	183	373	1	ENST00000575354.2:c.3235C>T	p.Gln1079Ter	p.Q1079*	ENST00000575354	NM_015125.3	1079	Cag/Tag	14/20	0.764824737608874	1	FACETS	0.431	0.399	0.465	0.431	0.399	0.465	SUBCLONAL	1	TRUE	0	0.764824737608874	1		374	685	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797165	42797165	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	144	356	0	ENST00000575354.2:c.3532del	p.Gln1178ArgfsTer3	p.Q1178Rfs*3	ENST00000575354	NM_015125.3	1176	gCc/gc	15/20	0.764824737608874	1	FACETS	0.34	0.311	0.371	0.34	0.311	0.371	SUBCLONAL	1	TRUE	0	0.764824737608874	1		356	683	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287892	33287892	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	39	375	1	ENST00000374542.5:c.1361A>G	p.Glu454Gly	p.E454G	ENST00000374542	NM_001141970.1	454	gAa/gGa	5/8	1	2	FACETS	0.185	0.153	0.221	0.185	0.153	0.221	SUBCLONAL	1	TRUE	1	0.764824737608874	2		376	552	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0028834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	415	181	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.40260784917622	3	FACETS	0.912	0.873	0.95	0.912	0.873	0.95	INDETERMINATE	2	TRUE	1	0.70974929248398	3		181	869	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115914	8115915	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0028834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	511	469	5	ENST00000346208.3:c.1262dup	p.Met422AspfsTer85	p.M422Dfs*85	ENST00000346208		420	-/C	6/6	0.373168137287957	2	FACETS	1	0.997	1	0.748	0.72	0.775	INDETERMINATE	1	TRUE	0	0.70974929248398	2		474	963	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403190	213403190	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1300045748	NA	P-0028834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	221	457	1	ENST00000342788.4:c.65C>T	p.Pro22Leu	p.P22L	ENST00000342788	NM_005235.2	22	cCc/cTc	1/28	1	2	FACETS	0.602	0.56	0.646	0.602	0.56	0.646	SUBCLONAL	1	TRUE	1	0.70974929248398	2		458	1034	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518559	204518559	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	133	316	3	ENST00000367182.3:c.1222T>G	p.Ser408Ala	p.S408A	ENST00000367182	NM_001278516.1	408	Tca/Gca	11/11	0.414645632356152	4	FACETS	0.611	0.554	0.672	0.306	0.277	0.336	INDETERMINATE	1	TRUE	2	0.70974929248398	4		319	1048	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986838	36986838	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	141	152	3	ENST00000354822.5:c.851C>T	p.Ser284Leu	p.S284L	ENST00000354822	NM_001079668.2	284	tCg/tTg	3/3	NA	2	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.70974929248398	2		155	381	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984726	11984733	+	frameshift_variant	Frame_Shift_Del	DEL	CTGAACAA	CTGAACAA	-	novel	NA	P-0028834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	245	268	2	ENST00000353533.5:c.273_280del	p.Glu92LeufsTer37	p.E92Lfs*37	ENST00000353533	NM_003010.3	91	cCTGAACAA/c	3/11	0.70974929248398	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.70974929248398	1		270	401	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804218	46804218	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1904	234	774	4	ENST00000290295.7:c.789G>C	p.Trp263Cys	p.W263C	ENST00000290295	NM_006361.5	263	tgG/tgC	2/2	0.70974929248398	3	FACETS	0.418	0.388	0.449			1	SUBCLONAL	1	TRUE	NA	0.70974929248398	3		778	2138	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053330	37053330	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	302	482	3	ENST00000231790.2:c.565G>T	p.Gly189Cys	p.G189C	ENST00000231790	NM_000249.3	189	Ggc/Tgc	7/19	0.353270364266614	1	FACETS	0.685	0.648	0.722	0.685	0.648	0.722	INDETERMINATE	1	TRUE	0	0.70974929248398	1		485	802	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170016837	170016837	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	262	579	0	ENST00000295797.4:c.1642G>T	p.Gly548Cys	p.G548C	ENST00000295797	NM_002740.5	548	Ggt/Tgt	17/18	0.40260784917622	3	FACETS	0.68	0.636	0.727	0.34	0.318	0.364	INDETERMINATE	1	TRUE	1	0.70974929248398	3		579	1470	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55603375	55603375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553893575	NA	P-0028834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	151	448	2	ENST00000288135.5:c.2731C>T	p.Pro911Ser	p.P911S	ENST00000288135	NM_000222.2	911	Ccc/Tcc	20/21	0.353270364266614	1	FACETS	0.351	0.321	0.382	0.351	0.321	0.382	INDETERMINATE	1	TRUE	0	0.70974929248398	1		450	782	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160656	56160656	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	157	474	6	ENST00000399503.3:c.930A>C	p.Lys310Asn	p.K310N	ENST00000399503	NM_005921.1	310	aaA/aaC	4/20	NA	2	FACETS	0.502	0.46	0.546			1	INDETERMINATE	1	TRUE	NA	0.70974929248398	2		480	881	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839699	27839699	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	269	405	3	ENST00000328488.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000328488	NM_003533.2	132	cGa/cTa	1/1	1	2	FACETS	0.874	0.822	0.927	0.874	0.822	0.927	CLONAL	1	TRUE	1	0.70974929248398	2		408	867	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139107	37139107	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	194	419	1	ENST00000373509.5:c.447G>C	p.Trp149Cys	p.W149C	ENST00000373509	NM_002648.3	149	tgG/tgC	4/6	1	2	FACETS	0.569	0.527	0.614	0.569	0.527	0.614	SUBCLONAL	1	TRUE	1	0.70974929248398	2		420	960	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543680	148543680	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	121	306	3	ENST00000320356.2:c.128G>C	p.Ser43Thr	p.S43T	ENST00000320356	NM_004456.4	43	aGt/aCt	3/20	0.353270364266614	1	FACETS	0.404	0.367	0.444	0.404	0.367	0.444	INDETERMINATE	1	TRUE	0	0.70974929248398	1		309	544	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852563	63852578	+	frameshift_variant	Frame_Shift_Del	DEL	CACTCATGCAGCCCCT	CACTCATGCAGCCCCT	-	novel	NA	P-0028834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	263	404	3	ENST00000279873.7:c.3341_3356del	p.Pro1114ArgfsTer7	p.P1114Rfs*7	ENST00000279873	NM_032199.2	1114	cCACTCATGCAGCCCCTg/cg	10/10	NA	2	FACETS	0.96	0.903	1			1	INDETERMINATE	1	TRUE	NA	0.70974929248398	2		407	772	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0028837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	83	545	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.184156736505307	2	FACETS	0.853	0.754	0.959	0.427	0.377	0.48	INDETERMINATE	1	TRUE	0	0.325910847878658	2		545	597	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867546	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGC	GGCGGCGGC	-	rs11466445	NA	P-0028837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	10	17	0	ENST00000374994.4:c.70_78del	p.Ala24_Ala26del	p.A24_A26del	ENST00000374994	NM_004612.2	17	ctGGCGGCGGCg/ctg	1/9	0.118351049283084	5	FACETS	0.846	0.587	1	0.564	0.391	0.769	INDETERMINATE	2	TRUE	2	0.325910847878658	5		17	54	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041663	47041663	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	76	807	0	ENST00000377604.3:c.1891del	p.Ala631HisfsTer73	p.A631Hfs*73	ENST00000377604	NM_001204468.1	630	Ggg/gg	17/24	0.183684048798988	0	FACETS	0.678	0.596	0.764			1	INDETERMINATE	1	TRUE	0	0.325910847878658	0		807	464	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357045	70357045	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747305574	NA	P-0028837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	59	785	2	ENST00000374080.3:c.5560C>T	p.Arg1854Cys	p.R1854C	ENST00000374080		1854	Cgt/Tgt	39/45	0.183684048798988	0	FACETS	0.501	0.432	0.577			1	INDETERMINATE	1	TRUE	0	0.325910847878658	0		787	487	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034787	42034787	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	75	458	0	ENST00000219905.7:c.4629G>C	p.Met1543Ile	p.M1543I	ENST00000219905	NM_001164273.1	1543	atG/atC	15/24	0.186951292453613	5	FACETS	1	0.973	1	0.473	0.415	0.534	INDETERMINATE	1	TRUE	2	0.325910847878658	5		458	483	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640238	3640238	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	108	1071	0	ENST00000294008.3:c.3401C>A	p.Ser1134Ter	p.S1134*	ENST00000294008	NM_032444.2	1134	tCg/tAg	12/15	1	2	FACETS	0.845	0.759	0.937	0.845	0.759	0.937	CLONAL	1	TRUE	1	0.325910847878658	2		1071	784	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161298	55161298	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	18	391	2	ENST00000257290.5:c.3129G>T	p.Gln1043His	p.Q1043H	ENST00000257290	NM_006206.4	1043	caG/caT	23/23	1	2	FACETS	0.381	0.287	0.492	0.381	0.287	0.492	SUBCLONAL	1	TRUE	1	0.325910847878658	2		393	290	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258968	153258969	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0028837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	18	321	0	ENST00000281708.4:c.846_847del	p.Leu283AlafsTer3	p.L283Afs*3	ENST00000281708	NM_033632.3	282	tcATtg/tctg	5/12	0.270586612987773	4	FACETS	0.425	0.319	0.55			1	SUBCLONAL	1	TRUE	NA	0.325910847878658	4		321	345	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839804	27839804	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1561942570	NA	P-0028837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	114	571	0	ENST00000328488.2:c.290G>C	p.Cys97Ser	p.C97S	ENST00000328488	NM_003533.2	97	tGc/tCc	1/1	0.325910847878658	10	FACETS	1	0.948	1			1	CLONAL	2	TRUE	NA	0.325910847878658	10		571	745	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0028841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	163	532	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.354490154343551	2		532	717	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484302	8484302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	101	464	0	ENST00000356435.5:c.3230C>A	p.Pro1077His	p.P1077H	ENST00000356435		1077	cCt/cAt	19/35	1	2	FACETS	0.805	0.72	0.895	0.805	0.72	0.895	CLONAL	1	TRUE	1	0.354490154343551	2		464	708	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089725	27089725	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	50	615	0	ENST00000324856.7:c.2681C>G	p.Thr894Ser	p.T894S	ENST00000324856	NM_006015.4	894	aCc/aGc	8/20	1	2	FACETS	0.343	0.29	0.402	0.343	0.29	0.402	SUBCLONAL	1	TRUE	1	0.354490154343551	2		615	822	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112268	115112268	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	22	77	0	ENST00000257566.3:c.1472C>G	p.Ala491Gly	p.A491G	ENST00000257566	NM_016569.3	491	gCg/gGg	7/8	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.354490154343551	2		77	105	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675139	40675139	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	199	735	0	ENST00000249776.8:c.103C>G	p.Leu35Val	p.L35V	ENST00000249776	NM_033286.3	35	Cta/Gta	1/9	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.354490154343551	2		735	992	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476259	88476259	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	110	525	0	ENST00000360948.2:c.1873C>A	p.Leu625Met	p.L625M	ENST00000360948	NM_001012338.2	625	Ctg/Atg	15/19	1	2	FACETS	0.976	0.878	1	0.976	0.878	1	CLONAL	1	TRUE	1	0.354490154343551	2		525	636	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584465	187584465	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	24	302	1	ENST00000441802.2:c.3568C>T	p.His1190Tyr	p.H1190Y	ENST00000441802	NM_005245.3	1190	Cat/Tat	3/27	0.354490154343551	1	FACETS	0.325	0.254	0.406	0.325	0.254	0.406	SUBCLONAL	1	TRUE	0	0.354490154343551	1		303	343	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562505	176562505	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	115	648	0	ENST00000439151.2:c.401A>G	p.Asn134Ser	p.N134S	ENST00000439151	NM_022455.4	134	aAc/aGc	2/23	1	2	FACETS	0.667	0.6	0.738	0.667	0.6	0.738	SUBCLONAL	1	TRUE	1	0.354490154343551	2		648	973	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115961	8115961	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	173	314	0	ENST00000346208.3:c.1308del	p.Ser437AlafsTer38	p.S437Afs*38	ENST00000346208		436	tCc/tc	6/6	1	2	FACETS	0.911	0.845	0.979	0.911	0.845	0.979	CLONAL	1	TRUE	1	0.747297942257201	2		314	508	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061266	38061268	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	novel	NA	P-0028843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	435	809	0	ENST00000250448.2:c.721_723del	p.Gly241del	p.G241del	ENST00000250448	NM_004496.3	241	GGC/-	2/2	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.747297942257201	2		809	1126	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0028847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	238	670	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.957	0.896	1	1	0.996	1	CLONAL	4	TRUE	1	0.15	2		670	829	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0028858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	44	496	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	0.258621509174577	3	FACETS	0.74	0.621	0.871	0.37	0.31	0.436	SUBCLONAL	1	TRUE	1	0.31	3		496	443	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249091	55249091	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519861	NA	P-0028858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	32	569	0	ENST00000275493.2:c.2389T>A	p.Cys797Ser	p.C797S	ENST00000275493	NM_005228.3	797	Tgc/Agc	20/28	0.258621509174577	3	FACETS	0.411	0.333	0.5	0.206	0.166	0.25	SUBCLONAL	1	TRUE	1	0.31	3		569	580	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155432	99155432	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	27	331	0	ENST00000074304.5:c.658T>G	p.Leu220Val	p.L220V	ENST00000074304	NM_001134224.1	220	Ttg/Gtg	9/26	1	2	FACETS	0.456	0.363	0.563	0.456	0.363	0.563	SUBCLONAL	1	TRUE	1	0.31	2		331	382	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0028860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	272	591	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.947	0.896	0.998	0.947	0.896	0.998	CLONAL	1	TRUE	1	0.925480887387577	2		591	621	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144148	55144148	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519700	NA	P-0028860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	318	516	1	ENST00000257290.5:c.1977C>A	p.Asn659Lys	p.N659K	ENST00000257290	NM_006206.4	659	aaC/aaA	14/23	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.925480887387577	2		517	676	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717717	89717717	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	496	416	0	ENST00000371953.3:c.743del	p.Pro248LeufsTer8	p.P248Lfs*8	ENST00000371953	NM_000314.4	248	Cct/ct	7/9	0.925480887387577	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.925480887387577	2		416	536	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141012	55141012	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501502	NA	P-0028860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	62	272	0	ENST00000257290.5:c.1658C>T	p.Pro553Leu	p.P553L	ENST00000257290	NM_006206.4	553	cCg/cTg	12/23	1	2	FACETS	0.332	0.287	0.379	0.332	0.287	0.379	SUBCLONAL	1	TRUE	1	0.925480887387577	2		272	404	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221204	5221204	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	468	727	2	ENST00000357368.4:c.3262C>G	p.His1088Asp	p.H1088D	ENST00000357368	NM_002850.3	1088	Cac/Gac	20/38	1	2	FACETS	0.979	0.939	1	0.979	0.939	1	CLONAL	1	TRUE	1	0.925480887387577	2		729	1033	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144120	55144120	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	150	528	0	ENST00000257290.5:c.1949A>G	p.His650Arg	p.H650R	ENST00000257290	NM_006206.4	650	cAc/cGc	14/23	1	2	FACETS	0.462	0.423	0.502	0.462	0.423	0.502	SUBCLONAL	1	TRUE	1	0.925480887387577	2		528	702	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0028861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	289	504	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.51937654975342	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.51937654975342	1		504	822	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0028861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	103	591	0				ENST00000310581	NM_198253.2	-/1132			0.234966109863082	1	FACETS	0.643	0.578	0.71	0.643	0.578	0.71	INDETERMINATE	1	TRUE	0	0.51937654975342	1		591	457	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937001	48937005	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAA	CAGAA	-	rs1566192530	NA	P-0028861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	177	561	0	ENST00000267163.4:c.772_776del	p.Asn258GlufsTer11	p.N258Efs*11	ENST00000267163	NM_000321.2	257	CAGAAc/c	8/27	0.51937654975342	1	FACETS	0.957	0.889	1	0.957	0.889	1	CLONAL	1	TRUE	0	0.51937654975342	1		561	527	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0028861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6332	1456	843	1	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.51937654975342	20	FACETS	1	0.986	1			1	CLONAL	4	TRUE	NA	0.51937654975342	20		844	7788	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711876	89711876	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs786204863	NA	P-0028861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	12	363	0	ENST00000371953.3:c.494G>T	p.Gly165Val	p.G165V	ENST00000371953	NM_000314.4	165	gGa/gTa	6/9	0.51937654975342	1	FACETS	0.087	0.061	0.12	0.087	0.061	0.12	SUBCLONAL	1	TRUE	0	0.51937654975342	1		363	392	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	277	404	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.855872969293044	2		404	550	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0028862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	95	344	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.311066523627423	1	FACETS	0.623	0.567	0.678	0.623	0.567	0.678	INDETERMINATE	1	TRUE	0	0.855872969293044	1		345	204	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412375	139412375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1341448592	NA	P-0028862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	368	530	0	ENST00000277541.6:c.1270G>A	p.Glu424Lys	p.E424K	ENST00000277541	NM_017617.3	424	Gag/Aag	8/34	0.384304854629241	3	FACETS	0.767	0.732	0.802	0.511	0.488	0.535	INDETERMINATE	2	TRUE	0	0.855872969293044	3		530	801	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111049	193111049	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	52	255	0	ENST00000367435.3:c.582A>T	p.Arg194Ser	p.R194S	ENST00000367435	NM_024529.4	194	agA/agT	7/17	1	2	FACETS	0.617	0.533	0.706	0.617	0.533	0.706	SUBCLONAL	1	TRUE	1	0.855872969293044	2		255	197	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794759	42794759	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	163	671	0	ENST00000575354.2:c.1842del	p.Ser615GlnfsTer113	p.S615Qfs*113	ENST00000575354	NM_015125.3	613	ggC/gg	10/20	0.855872969293044	1	FACETS	0.515	0.478	0.553	0.515	0.478	0.553	SUBCLONAL	1	TRUE	0	0.855872969293044	1		671	423	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798426	42798426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	253	829	1	ENST00000575354.2:c.4297G>T	p.Glu1433Ter	p.E1433*	ENST00000575354	NM_015125.3	1433	Gag/Tag	18/20	0.855872969293044	1	FACETS	0.474	0.446	0.503	0.474	0.446	0.503	SUBCLONAL	1	TRUE	0	0.855872969293044	1		830	713	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067836	30067836	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315499	NA	P-0028863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	81	322	1	ENST00000338641.4:c.1021C>T	p.Arg341Ter	p.R341*	ENST00000338641	NM_000268.3	341	Cga/Tga	11/16	0.42428002920882	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.42428002920882	2		323	166	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591246	67591246	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0028863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	152	398	0	ENST00000274335.5:c.1746-2A>G		p.X582_splice	ENST00000274335		582			0.42428002920882	8	FACETS	0.879	0.811	0.95			1	CLONAL	4	TRUE	NA	0.42428002920882	8		398	463	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578426	7578427	+	missense_variant	Missense_Mutation	DNP	GT	GT	TC	novel	NA	P-0028863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	133	712	0	ENST00000269305.4:c.503_504delinsGA	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAC/cGA	5/11	0.42428002920882	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.42428002920882	2		712	295	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119992	70119992	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747845908	NA	P-0028863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	69	151	1	ENST00000245479.2:c.994G>A	p.Gly332Ser	p.G332S	ENST00000245479	NM_000346.3	332	Ggc/Agc	3/3	0.404295406859945	5	FACETS	0.934	0.83	1	0.934	0.83	1	CLONAL	3	TRUE	2	0.42428002920882	5		152	190	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0028864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	322	747	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.914	0.864	0.966	0.914	0.864	0.966	CLONAL	1	TRUE	1	0.618290969256887	2		750	1139	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0028864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	182	670	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.856	0.792	0.921	0.856	0.792	0.921	CLONAL	1	TRUE	1	0.618290969256887	2		670	688	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0028864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	431	737	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.618290969256887	2		737	1307	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0028864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	38	380	1	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	0.204	0.168	0.245	0.204	0.168	0.245	SUBCLONAL	1	TRUE	1	0.618290969256887	2		381	602	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604703	48604703	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	202	424	0	ENST00000342988.3:c.1525T>C	p.Trp509Arg	p.W509R	ENST00000342988	NM_005359.5	509	Tgg/Cgg	12/12	0.572913773093587	1	FACETS	0.933	0.874	0.992	0.933	0.874	0.992	CLONAL	1	TRUE	0	0.618290969256887	1		424	484	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944659	32944659	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs80359094	NA	P-0028864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	201	504	0	ENST00000380152.3:c.8452G>T	p.Val2818Phe	p.V2818F	ENST00000380152		2818	Gtt/Ttt	19/27	1	2	FACETS	0.775	0.719	0.832	0.775	0.719	0.832	SUBCLONAL	1	TRUE	1	0.618290969256887	2		504	839	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265886	41266210	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGA	TTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGA	-	novel	NA	P-0028864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	74	13	0	ENST00000349496.5:c.14-125_213del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.618290969256887	2	FACETS	0.985	0.94	1	1	0.989	1	CLONAL	3	TRUE	0	0.618290969256887	2		13	81	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618905	37618905	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028865-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	144	637	0	ENST00000447079.4:c.581A>G	p.His194Arg	p.H194R	ENST00000447079	NM_015083.1	194	cAc/cGc	1/14	0.428529384081324	4	FACETS	1	0.932	1	0.342	0.312	0.374	CLONAL	1	TRUE	1	0.428529384081324	4		637	935	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0028869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	50	498	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.801	0.683	0.929	0.801	0.683	0.929	CLONAL	1	TRUE	1	0.395007755368793	2		498	316	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0028869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	139	720	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.338974718432389	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.395007755368793	1		721	551	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612078	189612078	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs957895088	NA	P-0028869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	120	505	0	ENST00000264731.3:c.1830C>A	p.Phe610Leu	p.F610L	ENST00000264731	NM_003722.4	610	ttC/ttA	14/14	1	2	FACETS	0.928	0.839	1	0.928	0.839	1	CLONAL	1	TRUE	1	0.395007755368793	2		505	655	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073852	8073852	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	56	193	0	ENST00000377482.5:c.807A>G	p.Ile269Met	p.I269M	ENST00000377482	NM_018948.3	269	atA/atG	4/4	0.395007755368793	1	FACETS	0.948	0.821	1	0.948	0.821	1	CLONAL	1	TRUE	0	0.395007755368793	1		193	240	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213957	2213957	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373907303	NA	P-0028869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	71	538	3	ENST00000398665.3:c.1769G>A	p.Arg590His	p.R590H	ENST00000398665	NM_032482.2	590	cGc/cAc	18/28	0.148251262491471	0	FACETS	0.384	0.335	0.437			1	INDETERMINATE	1	TRUE	0	0.395007755368793	0		541	566	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0028870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	69	394	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.304988855690608	1	FACETS	0.754	0.66	0.855	0.754	0.66	0.855	SUBCLONAL	1	TRUE	0	0.364887053694458	1		394	410	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226187	53226187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376775932	NA	P-0028870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	99	255	1	ENST00000375401.3:c.2662C>T	p.Arg888Cys	p.R888C	ENST00000375401	NM_004187.3	888	Cgt/Tgt	19/26	1	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.364887053694458	1		256	309	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0028870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	90	434	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	NA	2	FACETS	0.929	0.827	1			1	INDETERMINATE	1	TRUE	NA	0.364887053694458	2		434	531	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858032	9858032	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	69	437	0	ENST00000330684.3:c.3369G>T	p.Glu1123Asp	p.E1123D	ENST00000330684	NM_001134407.1	1123	gaG/gaT	13/13	0.326213211802815	1	FACETS	0.889	0.779	1	0.889	0.779	1	CLONAL	1	TRUE	0	0.364887053694458	1		437	348	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971207	21971207	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	39	317	0	ENST00000304494.5:c.151G>T	p.Val51Phe	p.V51F	ENST00000304494	NM_000077.4	51	Gtc/Ttc	2/3	0.364887053694458	1	FACETS	0.517	0.43	0.614	0.517	0.43	0.614	SUBCLONAL	1	TRUE	0	0.364887053694458	1		317	338	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0028871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	90	354	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.435737717768487	2		354	366	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	61	591	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.224711309932276	2		591	473	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978935	25978935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	109	426	0	ENST00000435504.4:c.988G>A	p.Glu330Lys	p.E330K	ENST00000435504		330	Gaa/Aaa	10/13	0.224222457062956	2	FACETS	0.912	0.822	1	0.912	0.822	1	CLONAL	2	TRUE	0	0.224711309932276	2		426	532	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420082	41420082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	37	261	0	ENST00000373198.4:c.239C>T	p.Ser80Phe	p.S80F	ENST00000373198	NM_133170.3	80	tCt/tTt	3/32	1	2	FACETS	0.825	0.681	0.986	0.825	0.681	0.986	CLONAL	1	TRUE	1	0.224711309932276	2		261	399	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	177	728	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.224711309932276	2		728	1156	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754974	29754974	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	196	473	1	ENST00000389048.3:c.961C>T	p.Leu321Phe	p.L321F	ENST00000389048	NM_004304.4	321	Ctc/Ttc	4/29	0.224222457062956	2	FACETS	0.941	0.871	1	0.941	0.871	1	CLONAL	2	TRUE	0	0.224711309932276	2		474	927	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997433	149997433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	89	589	1	ENST00000253339.5:c.2846C>T	p.Pro949Leu	p.P949L	ENST00000253339		949	cCt/cTt	6/7	1	2	FACETS	0.881	0.78	0.99	0.881	0.78	0.99	CLONAL	1	TRUE	1	0.224711309932276	2		590	899	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712724	43712724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	93	684	2	ENST00000382044.4:c.4460C>T	p.Pro1487Leu	p.P1487L	ENST00000382044	NM_001141980.1	1487	cCa/cTa	21/28	1	2	FACETS	0.79	0.7	0.886	0.79	0.7	0.886	SUBCLONAL	1	TRUE	1	0.224711309932276	2		686	1048	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265824	16265824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	88	557	0	ENST00000375759.3:c.10897G>A	p.Glu3633Lys	p.E3633K	ENST00000375759	NM_015001.2	3633	Gag/Aag	15/15	1	2	FACETS	0.835	0.738	0.939	0.835	0.738	0.939	CLONAL	1	TRUE	1	0.224711309932276	2		557	938	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937039	36937040	+	missense_variant	Missense_Mutation	DNP	CT	CT	TA	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	46	425	0	ENST00000361632.4:c.1279_1280delinsTA	p.Ser427Tyr	p.S427Y	ENST00000361632		427	AGc/TAc	9/16	1	2	FACETS	0.659	0.554	0.776	0.659	0.554	0.776	SUBCLONAL	1	TRUE	1	0.224711309932276	2		425	621	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466441	120466442	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	155	509	2	ENST00000256646.2:c.4677_4678delinsTT	p.Gln1560Ter	p.Q1560*	ENST00000256646	NM_024408.3	1559	ctCCag/ctTTag	26/34	1	2	FACETS	0.911	0.835	0.99	1	0.991	1	CLONAL	2	TRUE	1	0.224711309932276	2		511	757	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163295896	163295896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748878165	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	36	539	0	ENST00000271452.3:c.55C>T	p.Arg19Cys	p.R19C	ENST00000271452	NM_145697.2	19	Cgc/Tgc	2/14	1	2	FACETS	0.585	0.48	0.703	0.585	0.48	0.703	SUBCLONAL	1	TRUE	1	0.224711309932276	2		539	548	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226558137	226558137	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	56	435	0	ENST00000366794.5:c.2152C>T	p.Gln718Ter	p.Q718*	ENST00000366794	NM_001618.3	718	Cag/Tag	15/23	1	2	FACETS	0.817	0.7	0.946	0.817	0.7	0.946	CLONAL	1	TRUE	1	0.224711309932276	2		435	610	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226564826	226564826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	45	415	0	ENST00000366794.5:c.1924G>A	p.Glu642Lys	p.E642K	ENST00000366794	NM_001618.3	642	Gag/Aag	13/23	1	2	FACETS	0.657	0.551	0.774	0.657	0.551	0.774	SUBCLONAL	1	TRUE	1	0.224711309932276	2		415	610	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910435	32910435	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886040398	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	38	305	0	ENST00000380152.3:c.1943C>T	p.Ser648Leu	p.S648L	ENST00000380152		648	tCa/tTa	11/27	1	2	FACETS	0.787	0.65	0.938	0.787	0.65	0.938	CLONAL	1	TRUE	1	0.224711309932276	2		305	430	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435200	110435202	+	missense_variant	Missense_Mutation	TNP	CCC	CCC	AGT	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	73	508	2	ENST00000375856.3:c.3199_3201delinsACT	p.Gly1067Thr	p.G1067T	ENST00000375856	NM_003749.2	1067	GGG/ACT	1/2	1	2	FACETS	0.728	0.636	0.829	0.728	0.636	0.829	SUBCLONAL	1	TRUE	1	0.224711309932276	2		510	892	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99440005	99440005	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	39	284	0	ENST00000268035.6:c.973G>A	p.Glu325Lys	p.E325K	ENST00000268035	NM_000875.3	325	Gaa/Aaa	4/21	1	2	FACETS	0.855	0.709	1	0.855	0.709	1	CLONAL	1	TRUE	1	0.224711309932276	2		284	406	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225935	2225936	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	52	617	0	ENST00000326181.6:c.1727_1728delinsTT	p.Thr576Ile	p.T576I	ENST00000326181	NM_032271.2	576	aCC/aTT	18/21	1	2	FACETS	0.554	0.47	0.647	0.554	0.47	0.647	SUBCLONAL	1	TRUE	1	0.224711309932276	2		617	835	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3824663	3824664	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	66	419	1	ENST00000262367.5:c.2189_2190delinsAA	p.Gly730Glu	p.G730E	ENST00000262367	NM_004380.2	730	gGG/gAA	12/31	1	2	FACETS	0.832	0.721	0.952	0.832	0.721	0.952	CLONAL	1	TRUE	1	0.224711309932276	2		420	706	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116155	67116155	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	73	364	1	ENST00000412916.2:c.439C>T	p.Arg147Trp	p.R147W	ENST00000412916		147	Cgg/Tgg	5/6	1	2	FACETS	0.939	0.821	1	0.939	0.821	1	CLONAL	1	TRUE	1	0.224711309932276	2		365	692	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16022791	16022791	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	33	387	0	ENST00000268712.3:c.1861G>A	p.Glu621Lys	p.E621K	ENST00000268712	NM_006311.3	621	Gag/Aag	17/46	1	2	FACETS	0.5	0.406	0.607	0.5	0.406	0.607	SUBCLONAL	1	TRUE	1	0.224711309932276	2		387	587	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453318	40453319	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	79	644	1	ENST00000345506.4:c.1015_1016delinsTT	p.Pro339Phe	p.P339F	ENST00000345506	NM_003152.3	339	CCt/TTt	10/20	1	2	FACETS	0.758	0.665	0.858	0.758	0.665	0.858	SUBCLONAL	1	TRUE	1	0.224711309932276	2		645	928	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485957	40485958	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	75	562	2	ENST00000264657.5:c.907_908delinsTT	p.Pro303Leu	p.P303L	ENST00000264657	NM_139276.2	303	CCg/TTg	9/24	1	2	FACETS	0.68	0.594	0.773	0.68	0.594	0.773	SUBCLONAL	1	TRUE	1	0.224711309932276	2		564	982	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489492	40489493	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	73	408	2	ENST00000264657.5:c.757_758delinsAA	p.Gly253Lys	p.G253K	ENST00000264657	NM_139276.2	253	GGa/AAa	8/24	1	2	FACETS	0.859	0.751	0.977	0.859	0.751	0.977	CLONAL	1	TRUE	1	0.224711309932276	2		410	756	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7141783	7141783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	47	547	0	ENST00000302850.5:c.2587G>A	p.Glu863Lys	p.E863K	ENST00000302850	NM_000208.2	863	Gag/Aag	13/22	1	2	FACETS	0.448	0.376	0.527	0.448	0.376	0.527	SUBCLONAL	1	TRUE	1	0.224711309932276	2		547	934	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7152768	7152768	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1403001456	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	115	652	0	ENST00000302850.5:c.2200G>A	p.Asp734Asn	p.D734N	ENST00000302850	NM_000208.2	734	Gat/Aat	10/22	1	2	FACETS	0.806	0.724	0.893	0.806	0.724	0.893	CLONAL	1	TRUE	1	0.224711309932276	2		652	1270	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250923	10250923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	60	502	0	ENST00000340748.4:c.3557T>G	p.Val1186Gly	p.V1186G	ENST00000340748		1186	gTg/gGg	32/40	1	2	FACETS	0.617	0.53	0.712	0.617	0.53	0.712	SUBCLONAL	1	TRUE	1	0.224711309932276	2		502	865	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214898	36214899	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	60	603	1	ENST00000222270.7:c.3324_3325delinsTT	p.Arg1109Ter	p.R1109*	ENST00000222270	NM_014727.1	1108	ccCCga/ccTTga	8/37	1	2	FACETS	0.533	0.458	0.616	0.533	0.458	0.616	SUBCLONAL	1	TRUE	1	0.224711309932276	2		604	1002	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498288	29498288	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	144	439	0	ENST00000389048.3:c.1892G>A	p.Ser631Asn	p.S631N	ENST00000389048	NM_004304.4	631	aGc/aAc	10/29	0.224222457062956	2	FACETS	0.901	0.824	0.982	0.901	0.824	0.982	CLONAL	2	TRUE	0	0.224711309932276	2		439	711	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346739	225346740	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	58	405	1	ENST00000264414.4:c.1898_1899delinsTT	p.Ser633Phe	p.S633F	ENST00000264414	NM_003590.4	633	tCC/tTT	14/16	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.224711309932276	2		406	475	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30955532	30955532	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs567076886	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	26	355	0	ENST00000375687.4:c.143G>A	p.Ser48Asn	p.S48N	ENST00000375687	NM_015338.5	48	aGt/aAt	3/13	1	2	FACETS	0.486	0.384	0.604	0.486	0.384	0.604	SUBCLONAL	1	TRUE	1	0.224711309932276	2		355	476	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30956904	30956904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	71	463	1	ENST00000375687.4:c.230G>A	p.Arg77Gln	p.R77Q	ENST00000375687	NM_015338.5	77	cGa/cAa	4/13	1	2	FACETS	0.924	0.806	1	0.924	0.806	1	CLONAL	1	TRUE	1	0.224711309932276	2		464	684	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376664	31376664	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773384575	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	42	375	0	ENST00000328111.2:c.659G>A	p.Gly220Glu	p.G220E	ENST00000328111	NM_006892.3	220	gGg/gAg	7/23	1	2	FACETS	0.591	0.492	0.7	0.591	0.492	0.7	SUBCLONAL	1	TRUE	1	0.224711309932276	2		375	633	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288306	21288306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	49	553	1	ENST00000354336.3:c.551C>T	p.Ser184Phe	p.S184F	ENST00000354336	NM_005207.3	184	tCc/tTc	2/3	1	2	FACETS	0.532	0.45	0.624	0.532	0.45	0.624	SUBCLONAL	1	TRUE	1	0.224711309932276	2		554	819	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934284	49934285	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	70	584	0	ENST00000296474.3:c.2222_2223delinsAA	p.Gly741Glu	p.G741E	ENST00000296474	NM_002447.2	741	gGG/gAA	8/20	1	2	FACETS	0.794	0.691	0.905	0.794	0.691	0.905	CLONAL	1	TRUE	1	0.224711309932276	2		584	785	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807180	1807181	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	127	684	1	ENST00000260795.2:c.1511_1512delinsTT	p.Thr504Ile	p.T504I	ENST00000260795		504	aCC/aTT	10/17	0.000209960449025104	3	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.224711309932276	3		685	994	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179484	56179484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	29	275	0	ENST00000399503.3:c.3797G>A	p.Gly1266Glu	p.G1266E	ENST00000399503	NM_005921.1	1266	gGa/gAa	15/20	1	2	FACETS	0.75	0.603	0.918	0.75	0.603	0.918	CLONAL	1	TRUE	1	0.224711309932276	2		275	344	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593299	67593300	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	48	276	0	ENST00000274335.5:c.2045_2046delinsTT	p.Ala682Val	p.A682V	ENST00000274335		682	gCC/gTT	15/15	1	2	FACETS	0.933	0.789	1	0.933	0.789	1	CLONAL	1	TRUE	1	0.224711309932276	2		276	458	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199981	138199982	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	52	360	0	ENST00000237289.4:c.1399_1400delinsTT	p.Pro467Phe	p.P467F	ENST00000237289	NM_001270507.1	467	CCt/TTt	7/9	1	2	FACETS	0.825	0.702	0.96	0.825	0.702	0.96	CLONAL	1	TRUE	1	0.224711309932276	2		360	561	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891186	151891187	+	missense_variant	Missense_Mutation	DNP	AA	AA	GG	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	194	437	1	ENST00000262189.6:c.4567_4568delinsCC	p.Leu1523Pro	p.L1523P	ENST00000262189	NM_170606.2	1523	TTa/CCa	31/59	0.224711309932276	5	FACETS	0.884	0.818	0.951	0.663	0.614	0.713	CLONAL	3	TRUE	1	0.224711309932276	5		438	871	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859888	117859888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	37	236	0	ENST00000297338.2:c.1747G>A	p.Glu583Lys	p.E583K	ENST00000297338	NM_006265.2	583	Gag/Aag	14/14	1	2	FACETS	0.786	0.648	0.94	0.786	0.648	0.94	CLONAL	1	TRUE	1	0.224711309932276	2		236	419	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402444	139402445	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1230	115	675	0	ENST00000277541.6:c.3472dup	p.Ala1158GlyfsTer25	p.A1158Gfs*25	ENST00000277541	NM_017617.3	1158	gcc/gGcc	21/34	0.20376051867323	4	FACETS	0.932	0.837	1	0.311	0.279	0.345	CLONAL	1	TRUE	1	0.224711309932276	4		675	1345	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15827351	15827351	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	58	501	0	ENST00000307771.7:c.467C>A	p.Pro156Gln	p.P156Q	ENST00000307771	NM_005089.3	156	cCa/cAa	7/11	1	2	FACETS	0.829	0.711	0.956	0.829	0.711	0.956	CLONAL	1	TRUE	1	0.224711309932276	2		501	623	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226022	53226023	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	84	685	3	ENST00000375401.3:c.2826_2827delinsTT	p.Arg943Ter	p.R943*	ENST00000375401	NM_004187.3	942	gcCCga/gcTTga	19/26	1	2	FACETS	0.787	0.694	0.888	0.787	0.694	0.888	SUBCLONAL	1	TRUE	1	0.224711309932276	2		688	950	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356729	70356729	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	63	441	0	ENST00000374080.3:c.5401G>A	p.Asp1801Asn	p.D1801N	ENST00000374080		1801	Gac/Aac	38/45	1	2	FACETS	0.796	0.688	0.915	0.796	0.688	0.915	CLONAL	1	TRUE	1	0.224711309932276	2		441	704	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937501	76937501	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	38	375	0	ENST00000373344.5:c.3247A>G	p.Lys1083Glu	p.K1083E	ENST00000373344	NM_000489.3	1083	Aag/Gag	9/35	1	2	FACETS	0.878	0.727	1	0.878	0.727	1	CLONAL	1	TRUE	1	0.224711309932276	2		375	385	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937775	76937775	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	37	471	1	ENST00000373344.5:c.2973A>T	p.Glu991Asp	p.E991D	ENST00000373344	NM_000489.3	991	gaA/gaT	9/35	1	2	FACETS	0.6	0.494	0.719	0.6	0.494	0.719	SUBCLONAL	1	TRUE	1	0.224711309932276	2		472	549	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0028875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	104	498	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.258047322360183	1	FACETS	0.949	0.85	1	0.949	0.85	1	CLONAL	1	TRUE	0	0.258047322360183	1		498	740	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579584	7579585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0028875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	127	511	0	ENST00000269305.4:c.102dup	p.Pro36AlafsTer7	p.P36Afs*7	ENST00000269305	NM_001126112.2	34	-/C	4/11	0.258047322360183	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.258047322360183	1		511	686	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521619	89521619	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	51	306	0	ENST00000336596.2:c.2696C>A	p.Ser899Ter	p.S899*	ENST00000336596	NM_005233.5	899	tCa/tAa	16/17	0.120910577977974	0	FACETS	0.526	0.446	0.613			1	INDETERMINATE	1	TRUE	0	0.258047322360183	0		306	558	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514360	148514379	+	frameshift_variant	Frame_Shift_Del	DEL	TTGTCATAGTAAGTGCCAAT	TTGTCATAGTAAGTGCCAAT	AGCGCCAAG	novel	NA	P-0028875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	68	419	2	ENST00000320356.2:c.1345_1364delinsCTTGGCGCT	p.Ile449LeufsTer9	p.I449Lfs*9	ENST00000320356	NM_004456.4	449	ATTGGCACTTACTATGACAAt/CTTGGCGCTt	11/20	1	2	FACETS	0.662	0.575	0.757	0.662	0.575	0.757	SUBCLONAL	1	TRUE	1	0.258047322360183	2		421	796	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0028876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	142	373	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.544403777650264	1	FACETS	0.904	0.832	0.978	0.904	0.832	0.978	CLONAL	1	TRUE	0	0.544403777650264	1		373	420	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0028876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	220	295	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.496694887376486	2	FACETS	0.914	0.862	0.966	0.914	0.862	0.966	CLONAL	2	TRUE	0	0.544403777650264	2		295	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203436	NA	P-0028876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	523	675	0	ENST00000269305.4:c.487T>C	p.Tyr163His	p.Y163H	ENST00000269305	NM_001126112.2	163	Tac/Cac	5/11	0.544403777650264	2	FACETS	0.993	0.958	1	0.993	0.958	1	CLONAL	2	TRUE	0	0.544403777650264	2		675	967	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134269	11134269	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	206	613	0	ENST00000358026.2:c.2935C>T	p.Arg979Ter	p.R979*	ENST00000358026	NM_001128849.1	979	Cga/Tga	20/36	0.544403777650264	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.544403777650264	1		613	545	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679546	86679546	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	144	342	0	ENST00000274376.6:c.2707C>G	p.Arg903Gly	p.R903G	ENST00000274376	NM_002890.2	903	Cga/Gga	21/25	0.544403777650264	1	FACETS	0.941	0.867	1	0.941	0.867	1	CLONAL	1	TRUE	0	0.544403777650264	1		342	409	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940078	31940078	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0028876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	234	584	0	ENST00000375333.2:c.221-1G>C		p.X74_splice	ENST00000375333	NM_032454.1	74			1	2	FACETS	0.985	0.92	1	0.985	0.92	1	CLONAL	1	TRUE	1	0.544403777650264	2		584	873	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0028878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	86	443	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.423	0.375	0.474	0.423	0.375	0.474	SUBCLONAL	1	TRUE	1	0.743210079005812	2		443	547	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603148	48603148	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1060500740	NA	P-0028878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	63	332	0	ENST00000342988.3:c.1447+2T>C		p.X483_splice	ENST00000342988	NM_005359.5	483			1	2	FACETS	0.384	0.332	0.439	0.384	0.332	0.439	SUBCLONAL	1	TRUE	1	0.743210079005812	2		332	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0028879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	245	906	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.298027692399308	2	FACETS	0.939	0.879	0.999	0.939	0.879	0.999	CLONAL	2	TRUE	0	0.306004535626587	2		906	853	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0028879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	67	338	1	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.795	0.691	0.907	0.795	0.691	0.907	CLONAL	1	TRUE	1	0.306004535626587	2		339	551	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457763	149457763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376495524	NA	P-0028879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	120	570	1	ENST00000286301.3:c.641G>A	p.Arg214Gln	p.R214Q	ENST00000286301	NM_005211.3	214	cGg/cAg	5/22	0.306004535626587	3	FACETS	1	0.914	1	0.507	0.457	0.559	CLONAL	1	TRUE	1	0.306004535626587	3		571	892	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641686	12641686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749989518	NA	P-0028879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	88	396	0	ENST00000251849.4:c.955G>A	p.Ala319Thr	p.A319T	ENST00000251849	NM_002880.3	319	Gca/Aca	9/17	0.306004535626587	3	FACETS	0.832	0.736	0.934	0.416	0.368	0.467	CLONAL	1	TRUE	1	0.306004535626587	3		396	797	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46527629	46527629	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0028879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	49	410	0	ENST00000262741.5:c.736A>T	p.Arg246Ter	p.R246*	ENST00000262741	NM_003629.3	246	Aga/Tga	6/10	0.218688065466071	2	FACETS	0.388	0.328	0.455	0.194	0.164	0.228	SUBCLONAL	1	TRUE	0	0.306004535626587	2		410	825	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461958	120461958	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	45	338	0	ENST00000256646.2:c.5758G>A	p.Ala1920Thr	p.A1920T	ENST00000256646	NM_024408.3	1920	Gct/Act	31/34	0.306004535626587	3	FACETS	0.535	0.449	0.631	0.267	0.224	0.316	SUBCLONAL	1	TRUE	1	0.306004535626587	3		338	634	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307643	118307643	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	51	474	0	ENST00000534358.1:c.416G>C	p.Gly139Ala	p.G139A	ENST00000534358	NM_005933.3	139	gGa/gCa	1/36	0.306004535626587	3	FACETS	0.456	0.386	0.533	0.228	0.193	0.267	SUBCLONAL	1	TRUE	1	0.306004535626587	3		474	843	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28908249	28908249	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	177	448	0	ENST00000282397.4:c.2506G>C	p.Gly836Arg	p.G836R	ENST00000282397	NM_002019.4	836	Ggg/Cgg	18/30	0.261166011515306	5	FACETS	0.871	0.802	0.943			1	CLONAL	2	TRUE	NA	0.306004535626587	5		448	969	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351127	89351127	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	64	460	0	ENST00000301030.4:c.1823A>G	p.Lys608Arg	p.K608R	ENST00000301030	NM_001256183.1	608	aAg/aGg	9/13	0.235798168093228	4	FACETS	0.612	0.529	0.704	0.204	0.176	0.235	SUBCLONAL	1	TRUE	1	0.306004535626587	4		460	892	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612239	189612239	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	93	381	0	ENST00000264731.3:c.1991A>T	p.Asp664Val	p.D664V	ENST00000264731	NM_003722.4	664	gAc/gTc	14/14	0.306004535626587	3	FACETS	1	0.934	1	0.534	0.475	0.597	CLONAL	1	TRUE	1	0.306004535626587	3		381	656	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294299	1294299	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	52	333	0	ENST00000310581.5:c.702G>T	p.Leu234Phe	p.L234F	ENST00000310581	NM_198253.2	234	ttG/ttT	2/16	0.306004535626587	3	FACETS	0.618	0.525	0.72	0.309	0.262	0.36	SUBCLONAL	1	TRUE	1	0.306004535626587	3		333	634	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455142	50455142	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	64	288	0	ENST00000331340.3:c.689T>A	p.Met230Lys	p.M230K	ENST00000331340	NM_006060.4	230	aTg/aAg	6/8	0.306004535626587	5	FACETS	0.855	0.739	0.98	0.285	0.246	0.327	CLONAL	1	TRUE	2	0.306004535626587	5		288	714	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0028880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	35	291	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.839	0.691	1	0.839	0.691	1	CLONAL	1	FALSE	1	0.3	2		291	278	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577571	7577571	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs765848205	NA	P-0028881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	295	538	0	ENST00000269305.4:c.710T>A	p.Met237Lys	p.M237K	ENST00000269305	NM_001126112.2	237	aTg/aAg	7/11	0.712211755482175	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.712211755482175	1		538	467	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295249	1295250	+	upstream_gene_variant	5'Flank	DNP	GG	GG	TA	novel	NA	P-0028881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	83	381	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.955	0.856	1	0.955	0.856	1	CLONAL	1	TRUE	1	0.712211755482175	2		381	244	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229346	5229346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761681941	NA	P-0028881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	216	691	1	ENST00000357368.4:c.2357C>T	p.Thr786Met	p.T786M	ENST00000357368	NM_002850.3	786	aCg/aTg	16/38	1	2	FACETS	0.978	0.915	1	0.978	0.915	1	CLONAL	1	TRUE	1	0.712211755482175	2		692	620	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111615	56111622	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTGCCT	AGCTGCCT	-	novel	NA	P-0028881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	72	172	0	ENST00000399503.3:c.215_222del	p.Gln72ArgfsTer89	p.Q72Rfs*89	ENST00000399503	NM_005921.1	72	cAGCTGCCT/c	1/20	1	2	FACETS	0.981	0.873	1	0.981	0.873	1	CLONAL	1	TRUE	1	0.712211755482175	2		172	206	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578181	7578181	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138983188	NA	P-0028884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	317	677	0	ENST00000269305.4:c.668C>T	p.Pro223Leu	p.P223L	ENST00000269305	NM_001126112.2	223	cCt/cTt	6/11	0.731126229119931	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.731126229119931	1		677	497	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631839	90631839	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519906	NA	P-0028884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	241	542	0	ENST00000330062.3:c.514A>G	p.Arg172Gly	p.R172G	ENST00000330062	NM_002168.2	172	Agg/Ggg	4/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.731126229119931	2		542	632	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772973	135772974	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0028885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	38	343	0	ENST00000298552.3:c.2649_2650del	p.Tyr884SerfsTer19	p.Y884Sfs*19	ENST00000298552	NM_001162426.1	883	gcCTat/gcat	21/23	1	2	FACETS	0.821	0.679	0.979	0.821	0.679	0.979	CLONAL	1	TRUE	1	0.21	2		343	441	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248633	59248634	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0028886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	243	714	0	ENST00000371222.2:c.109_110del	p.Ser37HisfsTer69	p.S37Hfs*69	ENST00000371222	NM_002228.3	37	AGc/c	1/1	0.227626327718145	2	FACETS	1	0.992	1	0.744	0.695	0.794	CLONAL	1	TRUE	0	0.327140031352412	2		714	999	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577508	7577508	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060501201	NA	P-0028886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	248	562	0	ENST00000269305.4:c.773A>G	p.Glu258Gly	p.E258G	ENST00000269305	NM_001126112.2	258	gAa/gGa	7/11	0.0914823457725289	3	FACETS	0.993	0.931	1			1	INDETERMINATE	2	TRUE	NA	0.327140031352412	3		562	888	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858279	27858279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	78	555	0	ENST00000359303.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000359303	NM_003535.2	98	Gag/Aag	1/1	0.327140031352412	3	FACETS	0.559	0.49	0.634	0.279	0.245	0.317	SUBCLONAL	1	TRUE	1	0.327140031352412	3		555	993	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748891	43748891	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1298603817	NA	P-0028886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	134	742	1	ENST00000382044.4:c.1915C>T	p.Arg639Ter	p.R639*	ENST00000382044	NM_001141980.1	639	Cga/Tga	12/28	1	2	FACETS	0.676	0.613	0.744	0.676	0.613	0.744	SUBCLONAL	1	TRUE	1	0.327140031352412	2		743	1211	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678559	88678559	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764882745	NA	P-0028886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	49	378	1	ENST00000360948.2:c.977G>A	p.Arg326His	p.R326H	ENST00000360948	NM_001012338.2	326	cGt/cAt	9/19	1	2	FACETS	0.663	0.562	0.773	0.663	0.562	0.773	SUBCLONAL	1	TRUE	1	0.327140031352412	2		379	452	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634744	158634744	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	132	346	0	ENST00000263640.3:c.442A>G	p.Lys148Glu	p.K148E	ENST00000263640	NM_001105.4	148	Aaa/Gaa	5/11	0.226670659452137	3	FACETS	1	0.986	1	0.744	0.677	0.814	CLONAL	1	TRUE	1	0.327140031352412	3		346	631	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916942	178916956	+	inframe_deletion	In_Frame_Del	DEL	AAAAGATCCTCAATC	AAAAGATCCTCAATC	-	novel	NA	P-0028886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	129	461	0	ENST00000263967.3:c.329_343del	p.Glu110_Arg115delinsGly	p.E110_R115delinsG	ENST00000263967	NM_006218.2	110	gAAAAGATCCTCAATCga/gga	2/21	0.227626327718145	2	FACETS	1	0.972	1	0.588	0.534	0.644	CLONAL	1	TRUE	0	0.327140031352412	2		461	671	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696435	47696435	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	168	517	0	ENST00000347630.2:c.388G>C	p.Asp130His	p.D130H	ENST00000347630	NM_001007230.1	130	Gac/Cac	6/11	0.231645144368044	1	FACETS	0.526	0.486	0.566	0.526	0.486	0.566	INDETERMINATE	1	TRUE	0	0.755095492439822	1		517	527	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499679	149499681	+	inframe_deletion	In_Frame_Del	DEL	AAA	AAA	-	novel	NA	P-0028887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	180	425	0	ENST00000261799.4:c.2592_2594del	p.Phe864del	p.F864del	ENST00000261799	NM_002609.3	864	ttTTTg/ttg	19/23	0.217680320519882	4	FACETS	1	0.989	1	0.701	0.65	0.753	INDETERMINATE	1	TRUE	2	0.755095492439822	4		425	597	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870909	12870909	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	313	384	2	ENST00000228872.4:c.136G>T	p.Glu46Ter	p.E46*	ENST00000228872	NM_004064.3	46	Gag/Tag	1/3	0.583657243684106	3	FACETS	0.888	0.853	0.921	0.888	0.853	0.921	CLONAL	3	TRUE	0	0.684285970545246	3		386	461	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184639	185184639	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	202	503	0	ENST00000265026.3:c.1531T>A	p.Tyr511Asn	p.Y511N	ENST00000265026	NM_004721.4	511	Tat/Aat	10/14	0.684285970545246	3	FACETS	1	0.93	1	0.5	0.465	0.537	CLONAL	1	TRUE	1	0.684285970545246	3		503	792	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912655	NA	P-0028890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	67	556	0	ENST00000269305.4:c.725G>C	p.Cys242Ser	p.C242S	ENST00000269305	NM_001126112.2	242	tGc/tCc	7/11	1	2	FACETS	0.88	0.763	1	0.88	0.763	1	CLONAL	1	TRUE	1	0.15	2		556	1015	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0028890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	79	490	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.15	2		490	934	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912655	NA	P-0028890-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	89	556	0	ENST00000269305.4:c.725G>C	p.Cys242Ser	p.C242S	ENST00000269305	NM_001126112.2	242	tGc/tCc	7/11	0.145115863555937	2	FACETS	1	0.958	1	0.586	0.52	0.657	CLONAL	1	TRUE	0	0.227235515358914	2		556	668	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0028890-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	121	490	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.227235515358914	3	FACETS	0.845	0.764	0.93	0.845	0.764	0.93	CLONAL	2	TRUE	1	0.227235515358914	3		490	702	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619289	37619289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028890-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	40	390	0	ENST00000447079.4:c.965G>A	p.Arg322Gln	p.R322Q	ENST00000447079	NM_015083.1	322	cGa/cAa	1/14	0.145115863555937	2	FACETS	0.554	0.46	0.66	0.277	0.23	0.33	SUBCLONAL	1	TRUE	0	0.227235515358914	2		390	635	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278343	39278343	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137852813	NA	P-0028890-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	73	636	0	ENST00000402219.2:c.806T>C	p.Met269Thr	p.M269T	ENST00000402219	NM_005633.3	269	aTg/aCg	6/23	1	2	FACETS	0.708	0.617	0.805	0.708	0.617	0.805	SUBCLONAL	1	TRUE	1	0.227235515358914	2		636	908	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28979946	28979946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764045713	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	130	572	0	ENST00000282397.4:c.1522C>T	p.Arg508Cys	p.R508C	ENST00000282397	NM_002019.4	508	Cgc/Tgc	11/30	1	2	FACETS	0.957	0.869	1	0.957	0.869	1	CLONAL	1	TRUE	1	0.373578613280391	2		572	727	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	73	291	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.92	0.808	1	0.92	0.808	1	CLONAL	1	TRUE	1	0.373578613280391	2		291	425	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703631	47703631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750636	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	137	450	0	ENST00000233146.2:c.2131C>T	p.Arg711Ter	p.R711*	ENST00000233146	NM_000251.2	711	Cga/Tga	13/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.373578613280391	2		450	624	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913837	32913837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359507	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	107	507	2	ENST00000380152.3:c.5351del	p.Asn1784ThrfsTer7	p.N1784Tfs*7	ENST00000380152		1782	cAa/ca	11/27	1	2	FACETS	0.849	0.762	0.94	0.849	0.762	0.94	CLONAL	1	TRUE	1	0.373578613280391	2		509	675	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	89	466	2	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.777	0.69	0.87	0.777	0.69	0.87	SUBCLONAL	1	TRUE	1	0.373578613280391	2		468	613	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	92	440	5	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.883	0.786	0.985	0.883	0.786	0.985	CLONAL	1	TRUE	1	0.373578613280391	2		445	558	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	201	768	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	0.373578613280391	2		768	738	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434367	121434367	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	158	666	2	ENST00000257555.6:c.1136del	p.Pro379LeufsTer5	p.P379Lfs*5	ENST00000257555		377	ctC/ct	6/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.373578613280391	2		668	723	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490980	56490980	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs931676601	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	134	588	0	ENST00000267101.3:c.2426A>G	p.Gln809Arg	p.Q809R	ENST00000267101	NM_001982.3	809	cAg/cGg	20/28	1	2	FACETS	0.93	0.846	1	0.93	0.846	1	CLONAL	1	TRUE	1	0.373578613280391	2		588	771	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164902	106164902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs937035385	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	70	348	1	ENST00000380013.4:c.3770C>T	p.Thr1257Met	p.T1257M	ENST00000380013	NM_001127208.2	1257	aCg/aTg	6/11	1	2	FACETS	0.756	0.66	0.858	0.756	0.66	0.858	SUBCLONAL	1	TRUE	1	0.373578613280391	2		349	496	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166607	118166607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752308622	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	68	292	0	ENST00000369448.3:c.1117G>A	p.Val373Ile	p.V373I	ENST00000369448	NM_017709.3	373	Gtt/Att	2/2	1	2	FACETS	0.966	0.845	1	0.966	0.845	1	CLONAL	1	TRUE	1	0.373578613280391	2		292	377	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	34	647	1	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.236	0.192	0.287	0.236	0.192	0.287	SUBCLONAL	1	TRUE	1	0.373578613280391	2		648	770	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788617	3788617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519884	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	174	397	1	ENST00000262367.5:c.4337G>A	p.Arg1446His	p.R1446H	ENST00000262367	NM_004380.2	1446	cGc/cAc	26/31	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.373578613280391	2		398	852	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	103	663	3	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	1	2	FACETS	0.752	0.673	0.836	0.752	0.673	0.836	SUBCLONAL	1	TRUE	1	0.373578613280391	2		666	733	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	216	757	1	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.373578613280391	2		758	1024	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	69	323	1	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.373578613280391	2		324	349	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118918	70118918	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	184	729	0	ENST00000245479.2:c.490C>T	p.Gln164Ter	p.Q164*	ENST00000245479	NM_000346.3	164	Cag/Tag	2/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.373578613280391	2		729	841	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104353441	104353441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	167	662	2	ENST00000369902.3:c.646G>A	p.Gly216Arg	p.G216R	ENST00000369902	NM_016169.3	216	Ggg/Agg	5/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.373578613280391	2		664	786	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	89	418	2	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.963	0.857	1	0.963	0.857	1	CLONAL	1	TRUE	1	0.373578613280391	2		420	495	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467637	50467637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1262982300	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	65	415	1	ENST00000331340.3:c.872C>T	p.Thr291Met	p.T291M	ENST00000331340	NM_006060.4	291	aCg/aTg	8/8	1	2	FACETS	0.753	0.655	0.859	0.753	0.655	0.859	SUBCLONAL	1	TRUE	1	0.373578613280391	2		416	462	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291083	10291084	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755889652	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	155	602	1	ENST00000340748.4:c.387dup	p.Lys130GlnfsTer19	p.K130Qfs*19	ENST00000340748		129	-/C	4/40	1	2	FACETS	0.939	0.859	1	0.939	0.859	1	CLONAL	1	TRUE	1	0.373578613280391	2		603	884	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480459	89480459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	90	319	0	ENST00000336596.2:c.2296G>A	p.Gly766Arg	p.G766R	ENST00000336596	NM_005233.5	766	Gga/Aga	13/17	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.373578613280391	2		319	473	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742547	145742547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1426829329	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	108	652	0	ENST00000428558.2:c.241del	p.His81IlefsTer2	p.H81Ifs*2	ENST00000428558	NM_004260.3	81	Cat/at	4/22	1	2	FACETS	0.906	0.815	1	0.906	0.815	1	CLONAL	1	TRUE	1	0.373578613280391	2		652	638	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395910	395910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755460615	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	94	468	0	ENST00000380956.4:c.467C>T	p.Thr156Met	p.T156M	ENST00000380956	NM_001195286.1	156	aCg/aTg	4/9	1	2	FACETS	0.953	0.851	1	0.953	0.851	1	CLONAL	1	TRUE	1	0.373578613280391	2		468	528	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007619	45007619	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs111482205	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	73	222	0	ENST00000558401.1:c.68-2A>G		p.X23_splice	ENST00000558401	NM_004048.2	23			0.373578613280391	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.373578613280391	1		222	281	SUCCESS
ATR	545	MSKCC	GRCh37	3	142177928	142177928	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762621866	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	122	490	0	ENST00000350721.4:c.7375C>T	p.Arg2459Cys	p.R2459C	ENST00000350721	NM_001184.3	2459	Cgt/Tgt	44/47	1	2	FACETS	0.97	0.879	1	0.97	0.879	1	CLONAL	1	TRUE	1	0.373578613280391	2		490	673	SUCCESS
APC	324	MSKCC	GRCh37	5	112177788	112177788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752091655	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	68	416	0	ENST00000257430.4:c.6497G>A	p.Arg2166Gln	p.R2166Q	ENST00000257430	NM_000038.5	2166	cGa/cAa	16/16	1	2	FACETS	0.682	0.594	0.777	0.682	0.594	0.777	SUBCLONAL	1	TRUE	1	0.373578613280391	2		416	534	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905055	50905055	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	108	516	3	ENST00000440232.2:c.342del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	113	Ggg/gg	4/27	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.373578613280391	2		519	529	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029193	26029195	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	100	406	0	ENST00000435504.4:c.155_157del	p.Pro52del	p.P52del	ENST00000435504		52	cCTCtt/ctt	4/13	1	2	FACETS	0.953	0.853	1	0.953	0.853	1	CLONAL	1	TRUE	1	0.373578613280391	2		406	562	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273456	5273456	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1054506328	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	155	667	0	ENST00000357368.4:c.376C>T	p.Arg126Ter	p.R126*	ENST00000357368	NM_002850.3	126	Cga/Tga	4/38	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.373578613280391	2		667	744	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8733794	8733794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs949202374	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	118	559	1	ENST00000356435.5:c.50G>A	p.Arg17His	p.R17H	ENST00000356435		17	cGc/cAc	1/35	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.373578613280391	2		560	590	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163554	32163554	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	97	511	1	ENST00000375023.3:c.5672del	p.Gly1891AlafsTer13	p.G1891Afs*13	ENST00000375023	NM_004557.3	1891	gGc/gc	30/30	1	2	FACETS	0.972	0.87	1	0.972	0.87	1	CLONAL	1	TRUE	1	0.373578613280391	2		512	534	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656969	47656969	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779075	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	143	419	1	ENST00000233146.2:c.1165C>T	p.Arg389Ter	p.R389*	ENST00000233146	NM_000251.2	389	Cga/Tga	7/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.373578613280391	2		420	686	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437606	56437606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886926322	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	114	525	0	ENST00000407977.2:c.856C>T	p.Arg286Trp	p.R286W	ENST00000407977		286	Cgg/Tgg	8/10	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.373578613280391	2		525	573	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5466787	5466787	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	64	222	0	ENST00000381577.3:c.813del	p.Lys271AsnfsTer44	p.K271Nfs*44	ENST00000381577	NM_014143.3	270	Aaa/aa	6/7	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.373578613280391	2		222	323	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510573	38510573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	29	540	0	ENST00000254066.5:c.827G>A	p.Arg276Gln	p.R276Q	ENST00000254066	NM_000964.3	276	cGg/cAg	7/9	1	2	FACETS	0.273	0.218	0.335	0.273	0.218	0.335	SUBCLONAL	1	TRUE	1	0.373578613280391	2		540	569	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238356	98238356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	115	507	1	ENST00000331920.6:c.1688C>T	p.Ala563Val	p.A563V	ENST00000331920	NM_000264.3	563	gCg/gTg	12/24	1	2	FACETS	0.988	0.892	1	0.988	0.892	1	CLONAL	1	TRUE	1	0.373578613280391	2		508	623	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166139	118166139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766689047	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	113	415	0	ENST00000369448.3:c.649G>A	p.Gly217Arg	p.G217R	ENST00000369448	NM_017709.3	217	Ggg/Agg	2/2	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.373578613280391	2		415	460	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210740	2210740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	168	686	1	ENST00000398665.3:c.1237C>T	p.Arg413Cys	p.R413C	ENST00000398665	NM_032482.2	413	Cgc/Tgc	14/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.373578613280391	2		687	800	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151254	202151254	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	115	478	0	ENST00000358485.4:c.1557del	p.Lys520AsnfsTer10	p.K520Nfs*10	ENST00000358485	NM_001080125.1	518	atG/at	9/9	1	2	FACETS	0.831	0.749	0.917	0.831	0.749	0.917	CLONAL	1	TRUE	1	0.373578613280391	2		478	741	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015040	37015040	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756345939	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	75	434	0	ENST00000358127.4:c.364C>T	p.Arg122Trp	p.R122W	ENST00000358127	NM_001280556.1	122	Cgg/Tgg	3/10	1	2	FACETS	0.668	0.586	0.757	0.668	0.586	0.757	SUBCLONAL	1	TRUE	1	0.373578613280391	2		434	601	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164862	36164862	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1273605678	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	199	744	0	ENST00000300305.3:c.1013C>T	p.Ala338Val	p.A338V	ENST00000300305		338	gCg/gTg	8/8	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.373578613280391	2		744	830	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964315	55964315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749143449	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	66	367	0	ENST00000263923.4:c.2498G>A	p.Arg833Gln	p.R833Q	ENST00000263923	NM_002253.2	833	cGg/cAg	17/30	1	2	FACETS	0.822	0.716	0.936	0.822	0.716	0.936	CLONAL	1	TRUE	1	0.373578613280391	2		367	430	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2952993	2952993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369115970	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	148	719	0	ENST00000396946.4:c.2947G>A	p.Val983Met	p.V983M	ENST00000396946	NM_032415.4	983	Gtg/Atg	22/25	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.373578613280391	2		719	787	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984839	11984839	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	125	466	0	ENST00000353533.5:c.385G>A	p.Ala129Thr	p.A129T	ENST00000353533	NM_003010.3	129	Gca/Aca	3/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.373578613280391	2		466	590	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966551	36966551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768417029	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	132	499	0	ENST00000358127.4:c.775G>A	p.Glu259Lys	p.E259K	ENST00000358127	NM_001280556.1	259	Gag/Aag	6/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.373578613280391	2		499	593	SUCCESS
AR	367	MSKCC	GRCh37	X	66905935	66905935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1218564193	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	89	435	0	ENST00000374690.3:c.1852C>T	p.Arg618Trp	p.R618W	ENST00000374690	NM_000044.3	618	Cgg/Tgg	3/8	0.373578613280391	1	FACETS	0.833	0.742	0.93	0.833	0.742	0.93	CLONAL	1	TRUE	0	0.373578613280391	1		435	465	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776087	9776087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755725121	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	143	632	1	ENST00000377346.4:c.551G>A	p.Arg184Gln	p.R184Q	ENST00000377346	NM_005026.3	184	cGg/cAg	5/24	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.373578613280391	2		633	717	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628529	90628529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1220662107	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	113	617	0	ENST00000330062.3:c.1058G>A	p.Arg353His	p.R353H	ENST00000330062	NM_002168.2	353	cGc/cAc	8/11	0.373578613280391	2	FACETS	0.87	0.784	0.962	0.435	0.392	0.481	CLONAL	1	TRUE	0	0.373578613280391	2		617	695	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673793	37673793	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	163	603	0	ENST00000447079.4:c.2947C>T	p.Arg983Ter	p.R983*	ENST00000447079	NM_015083.1	983	Cga/Tga	10/14	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.373578613280391	2		603	866	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	161	698	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.889	0.815	0.966	0.889	0.815	0.966	CLONAL	1	TRUE	1	0.373578613280391	2		704	970	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937355	32937355	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507952	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	124	493	3	ENST00000380152.3:c.8021del	p.Lys2674ArgfsTer2	p.K2674Rfs*2	ENST00000380152		2672	atA/at	18/27	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.373578613280391	2		496	659	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047888	180047888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	167	776	1	ENST00000261937.6:c.2287G>A	p.Val763Met	p.V763M	ENST00000261937	NM_182925.4	763	Gtg/Atg	15/30	1	2	FACETS	0.975	0.896	1	0.975	0.896	1	CLONAL	1	TRUE	1	0.373578613280391	2		777	917	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599234	28599234	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	45	743	1	ENST00000253063.3:c.685del	p.Gln229ArgfsTer18	p.Q229Rfs*18	ENST00000253063	NM_031459.4	227	gCc/gc	5/10	1	2	FACETS	0.309	0.259	0.365	0.309	0.259	0.365	SUBCLONAL	1	TRUE	1	0.373578613280391	2		744	779	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557912	21557912	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757472527	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	105	438	0	ENST00000382592.4:c.1933C>T	p.Arg645Trp	p.R645W	ENST00000382592	NM_014572.2	645	Cgg/Tgg	5/8	1	2	FACETS	0.968	0.869	1	0.968	0.869	1	CLONAL	1	TRUE	1	0.373578613280391	2		438	581	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	166	765	5	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	1	2	FACETS	0.935	0.859	1	0.935	0.859	1	CLONAL	1	TRUE	1	0.373578613280391	2		770	950	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481530	20481530	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	85	340	1	ENST00000346618.3:c.599G>T	p.Gly200Val	p.G200V	ENST00000346618	NM_001949.4	200	gGg/gTg	3/7	1	2	FACETS	0.977	0.867	1	0.977	0.867	1	CLONAL	1	TRUE	1	0.373578613280391	2		341	466	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230605	46230605	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303729294	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	113	472	1	ENST00000334344.6:c.854G>A	p.Arg285Gln	p.R285Q	ENST00000334344	NM_152641.2	285	cGg/cAg	8/21	1	2	FACETS	0.966	0.872	1	0.966	0.872	1	CLONAL	1	TRUE	1	0.373578613280391	2		473	626	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	149	694	9	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.373578613280391	2		703	794	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447773	49447773	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	68	501	0	ENST00000301067.7:c.661del	p.Ala221LeufsTer40	p.A221Lfs*40	ENST00000301067	NM_003482.3	221	Gct/ct	5/54	1	2	FACETS	0.534	0.464	0.61	0.534	0.464	0.61	SUBCLONAL	1	TRUE	1	0.373578613280391	2		501	682	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130306	11130306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	144	548	0	ENST00000358026.2:c.2545C>T	p.Arg849Trp	p.R849W	ENST00000358026	NM_001128849.1	849	Cgg/Tgg	18/36	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.373578613280391	2		548	703	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578184	7578184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146340390	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	177	679	0	ENST00000269305.4:c.665C>T	p.Pro222Leu	p.P222L	ENST00000269305	NM_001126112.2	222	cCg/cTg	6/11	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.373578613280391	2		679	940	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319934	8319934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764537367	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	34	318	1	ENST00000356435.5:c.5567C>T	p.Thr1856Met	p.T1856M	ENST00000356435		1856	aCg/aTg	34/35	1	2	FACETS	0.418	0.342	0.505	0.418	0.342	0.505	SUBCLONAL	1	TRUE	1	0.373578613280391	2		319	435	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448271	56448271	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	107	506	0	ENST00000407977.2:c.375+1G>A		p.X125_splice	ENST00000407977		125			1	2	FACETS	0.852	0.766	0.944	0.852	0.766	0.944	CLONAL	1	TRUE	1	0.373578613280391	2		506	672	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528630	157528630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771871664	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	160	657	0	ENST00000346085.5:c.6355G>A	p.Val2119Ile	p.V2119I	ENST00000346085	NM_020732.3	2119	Gtt/Att	20/20	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.373578613280391	2		657	835	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88676897	88676897	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782682	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	155	544	0	ENST00000372037.3:c.682C>T	p.Arg228Ter	p.R228*	ENST00000372037	NM_004329.2	228	Cga/Tga	9/13	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.373578613280391	2		544	768	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905543	50905543	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373001984	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	145	818	2	ENST00000440232.2:c.671G>A	p.Arg224His	p.R224H	ENST00000440232	NM_002691.3	224	cGc/cAc	6/27	1	2	FACETS	0.947	0.864	1	0.947	0.864	1	CLONAL	1	TRUE	1	0.373578613280391	2		820	820	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384765	17384765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754532648	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	166	744	0	ENST00000359435.4:c.397C>T	p.Arg133Trp	p.R133W	ENST00000359435	NM_001033549.1	133	Cgg/Tgg	4/9	1	2	FACETS	0.903	0.829	0.981	0.903	0.829	0.981	CLONAL	1	TRUE	1	0.373578613280391	2		744	984	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222520	39222520	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	138	477	1	ENST00000402219.2:c.3090del	p.Lys1030AsnfsTer6	p.K1030Nfs*6	ENST00000402219	NM_005633.3	1030	aaA/aa	20/23	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.373578613280391	2		478	681	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372287	55372288	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1170462661	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	98	470	0	ENST00000297316.4:c.983dup	p.Gly331ArgfsTer34	p.G331Rfs*34	ENST00000297316	NM_022454.3	326	cac/caCc	2/2	1	2	FACETS	0.922	0.825	1	0.922	0.825	1	CLONAL	1	TRUE	1	0.373578613280391	2		470	569	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672317	86672317	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	105	481	0	ENST00000274376.6:c.2119C>T	p.Arg707Cys	p.R707C	ENST00000274376	NM_002890.2	707	Cgt/Tgt	16/25	1	2	FACETS	0.914	0.821	1	0.914	0.821	1	CLONAL	1	TRUE	1	0.373578613280391	2		481	615	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716301	52716301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	157	562	1	ENST00000322088.6:c.745C>T	p.Arg249Cys	p.R249C	ENST00000322088	NM_014225.5	249	Cgc/Tgc	6/15	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.373578613280391	2		563	657	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022454	12022454	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753079378	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	168	802	1	ENST00000396373.4:c.560C>T	p.Thr187Met	p.T187M	ENST00000396373	NM_001987.4	187	aCg/aTg	5/8	0.205458721909203	3	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.373578613280391	3		803	966	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559360	141559360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	115	618	2	ENST00000220592.5:c.1441G>A	p.Ala481Thr	p.A481T	ENST00000220592	NM_012154.3	481	Gcc/Acc	12/19	1	2	FACETS	0.848	0.764	0.936	0.848	0.764	0.936	CLONAL	1	TRUE	1	0.373578613280391	2		620	726	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764303	39764303	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1414795545	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	141	580	0	ENST00000288319.7:c.809C>T	p.Ser270Leu	p.S270L	ENST00000288319	NM_182918.3	270	tCg/tTg	7/10	1	2	FACETS	0.843	0.768	0.923	0.843	0.768	0.923	CLONAL	1	TRUE	1	0.373578613280391	2		580	895	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489568	56489568	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	119	438	0	ENST00000267101.3:c.2033G>T	p.Arg678Met	p.R678M	ENST00000267101	NM_001982.3	678	aGg/aTg	17/28	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.373578613280391	2		438	604	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244068	5244068	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747170106	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	128	706	1	ENST00000357368.4:c.1414G>A	p.Val472Met	p.V472M	ENST00000357368	NM_002850.3	472	Gtg/Atg	11/38	1	2	FACETS	0.935	0.848	1	0.935	0.848	1	CLONAL	1	TRUE	1	0.373578613280391	2		707	733	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015228	128015228	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774571443	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	134	533	1	ENST00000285398.2:c.2293C>T	p.Arg765Trp	p.R765W	ENST00000285398	NM_000122.1	765	Cgg/Tgg	15/15	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.373578613280391	2		534	712	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017790	31017790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564841799	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	152	723	1	ENST00000375687.4:c.652C>T	p.Arg218Cys	p.R218C	ENST00000375687	NM_015338.5	218	Cgt/Tgt	8/13	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.373578613280391	2		724	684	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777608	9777608	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	139	593	0	ENST00000377346.4:c.944C>T	p.Ser315Phe	p.S315F	ENST00000377346	NM_005026.3	315	tCc/tTc	8/24	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.373578613280391	2		593	716	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258454	16258454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752378818	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	144	628	0	ENST00000375759.3:c.5719G>A	p.Val1907Ile	p.V1907I	ENST00000375759	NM_015001.2	1907	Gtc/Atc	11/15	1	2	FACETS	0.913	0.833	0.997	0.913	0.833	0.997	CLONAL	1	TRUE	1	0.373578613280391	2		628	844	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258928	16258928	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	177	776	0	ENST00000375759.3:c.6198del	p.Lys2066AsnfsTer20	p.K2066Nfs*20	ENST00000375759	NM_015001.2	2065	Aaa/aa	11/15	1	2	FACETS	0.93	0.856	1	0.93	0.856	1	CLONAL	1	TRUE	1	0.373578613280391	2		776	1019	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798843	45798843	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs372267274	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	124	601	0	ENST00000450313.1:c.389-1G>A		p.X130_splice	ENST00000450313	NM_012222.2	130			1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.373578613280391	2		601	620	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63816920	63816920	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	70	272	0	ENST00000279873.7:c.891C>A	p.Asn297Lys	p.N297K	ENST00000279873	NM_032199.2	297	aaC/aaA	6/10	1	2	FACETS	0.813	0.711	0.922	0.813	0.711	0.922	CLONAL	1	TRUE	1	0.373578613280391	2		272	461	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104375095	104375095	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	133	552	0	ENST00000369902.3:c.1093C>T	p.Gln365Ter	p.Q365*	ENST00000369902	NM_016169.3	365	Cag/Tag	9/12	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.373578613280391	2		552	686	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533485	533485	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	162	664	0	ENST00000451590.1:c.418C>A	p.Pro140Thr	p.P140T	ENST00000451590	NM_001130442.1	140	Ccc/Acc	4/5	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.373578613280391	2		664	774	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161499	2161499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	138	529	0	ENST00000434045.2:c.28G>A	p.Val10Met	p.V10M	ENST00000434045	NM_001127598.1	10	Gtg/Atg	2/5	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.373578613280391	2		529	707	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572637	64572637	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	134	699	0	ENST00000312049.6:c.1219C>A	p.Pro407Thr	p.P407T	ENST00000312049	NM_130799.2	407	Cct/Act	9/10	1	2	FACETS	0.847	0.769	0.928	0.847	0.769	0.928	CLONAL	1	TRUE	1	0.373578613280391	2		699	847	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998316	100998316	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	11	27	0	ENST00000325455.5:c.1486C>T	p.Pro496Ser	p.P496S	ENST00000325455	NM_001202474.3	496	Ccc/Tcc	1/8	1	2	FACETS	1	0.718	1	1	0.718	1	CLONAL	1	TRUE	1	0.373578613280391	2		27	58	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25368420	25368422	+	intron_variant	Intron	DEL	TTC	TTC	-	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	105	380	0	ENST00000311936.3:c.451-5577_451-5575del		p.*151*	ENST00000311936	NM_004985.3	175/189			1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.373578613280391	2		380	559	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420420	49420420	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	141	676	0	ENST00000301067.7:c.15329C>T	p.Pro5110Leu	p.P5110L	ENST00000301067	NM_003482.3	5110	cCc/cTc	48/54	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.373578613280391	2		676	716	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445499	49445500	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	116	807	0	ENST00000301067.7:c.1966dup	p.Leu656ProfsTer12	p.L656Pfs*12	ENST00000301067	NM_003482.3	656	ctg/cCtg	10/54	1	2	FACETS	0.755	0.68	0.834	0.755	0.68	0.834	SUBCLONAL	1	TRUE	1	0.373578613280391	2		807	823	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486587	56486587	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	135	592	0	ENST00000267101.3:c.1166C>T	p.Thr389Ile	p.T389I	ENST00000267101	NM_001982.3	389	aCa/aTa	10/28	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.373578613280391	2		592	722	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143021	58143021	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778188	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	129	684	0	ENST00000257904.6:c.763C>T	p.Arg255Cys	p.R255C	ENST00000257904	NM_000075.3	255	Cgc/Tgc	7/8	1	2	FACETS	0.822	0.745	0.903	0.822	0.745	0.903	CLONAL	1	TRUE	1	0.373578613280391	2		684	840	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924357	112924357	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1054802954	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	159	587	1	ENST00000351677.2:c.1303G>A	p.Val435Met	p.V435M	ENST00000351677	NM_002834.3	435	Gtg/Atg	11/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.373578613280391	2		588	696	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608311	28608311	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	148	576	0	ENST00000241453.7:c.1745C>T	p.Thr582Ile	p.T582I	ENST00000241453	NM_004119.2	582	aCc/aTc	14/24	1	2	FACETS	0.999	0.913	1	0.999	0.913	1	CLONAL	1	TRUE	1	0.373578613280391	2		576	793	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942724	48942725	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	84	327	0	ENST00000267163.4:c.1117_1118dup	p.Pro374LeufsTer7	p.P374Lfs*7	ENST00000267163	NM_000321.2	371	cca/cCAca	11/27	1	2	FACETS	0.923	0.818	1	0.923	0.818	1	CLONAL	1	TRUE	1	0.373578613280391	2		327	487	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951105	48951105	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	106	373	0	ENST00000267163.4:c.1267G>T	p.Gly423Ter	p.G423*	ENST00000267163	NM_000321.2	423	Gga/Tga	13/27	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.373578613280391	2		373	565	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396592	30396592	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	72	251	2	ENST00000331968.5:c.127G>A	p.Ala43Thr	p.A43T	ENST00000331968	NM_002742.2	43	Gcg/Acg	1/18	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.373578613280391	2		253	312	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034989	42034989	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	155	585	0	ENST00000219905.7:c.4831G>A	p.Ala1611Thr	p.A1611T	ENST00000219905	NM_001164273.1	1611	Gct/Act	15/24	0.373578613280391	1	FACETS	0.982	0.902	1	0.982	0.902	1	CLONAL	1	TRUE	0	0.373578613280391	1		585	687	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799218	88799219	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	87	617	0	ENST00000360948.2:c.166dup	p.Leu56ProfsTer82	p.L56Pfs*82	ENST00000360948	NM_001012338.2	56	ctc/cCtc	2/19	0.373578613280391	2	FACETS	0.771	0.684	0.865	0.386	0.342	0.433	SUBCLONAL	1	TRUE	0	0.373578613280391	2		617	604	SUCCESS
BLM	641	MSKCC	GRCh37	15	91306294	91306294	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	117	393	0	ENST00000355112.3:c.1986del	p.Lys662AsnfsTer12	p.K662Nfs*12	ENST00000355112	NM_000057.2	661	Aaa/aa	8/22	0.373578613280391	2	FACETS	0.973	0.879	1	0.486	0.439	0.536	CLONAL	1	TRUE	0	0.373578613280391	2		393	644	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121877	2121877	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756536921	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	119	740	0	ENST00000219476.3:c.2039G>A	p.Arg680Gln	p.R680Q	ENST00000219476	NM_000548.3	680	cGg/cAg	19/42	1	2	FACETS	0.824	0.744	0.909	0.824	0.744	0.909	CLONAL	1	TRUE	1	0.373578613280391	2		740	773	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129119	2129119	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	159	725	0	ENST00000219476.3:c.3053T>C	p.Leu1018Pro	p.L1018P	ENST00000219476	NM_000548.3	1018	cTc/cCc	27/42	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.373578613280391	2		725	815	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352576	89352576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762710349	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	119	405	0	ENST00000301030.4:c.763C>T	p.Arg255Trp	p.R255W	ENST00000301030	NM_001256183.1	255	Cgg/Tgg	8/13	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.373578613280391	2		405	538	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40457661	40457661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1307657759	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	148	549	1	ENST00000345506.4:c.1414G>A	p.Gly472Ser	p.G472S	ENST00000345506	NM_003152.3	472	Ggc/Agc	13/20	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.373578613280391	2		550	777	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936750	78936750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	165	725	0	ENST00000306801.3:c.3832G>A	p.Ala1278Thr	p.A1278T	ENST00000306801	NM_020761.2	1278	Gcc/Acc	33/34	1	2	FACETS	0.998	0.917	1	0.998	0.917	1	CLONAL	1	TRUE	1	0.373578613280391	2		725	885	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226875	2226875	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	41	210	0	ENST00000398665.3:c.4355G>A	p.Gly1452Asp	p.G1452D	ENST00000398665	NM_032482.2	1452	gGc/gAc	27/28	1	2	FACETS	0.754	0.631	0.889	0.754	0.631	0.889	SUBCLONAL	1	TRUE	1	0.373578613280391	2		210	291	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212221	5212221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377564137	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	120	615	1	ENST00000357368.4:c.4810G>A	p.Ala1604Thr	p.A1604T	ENST00000357368	NM_002850.3	1604	Gcc/Acc	32/38	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.373578613280391	2		616	637	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375495	15375495	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	166	824	1	ENST00000263377.2:c.932del	p.Pro311ArgfsTer18	p.P311Rfs*18	ENST00000263377	NM_058243.2	311	cCg/cg	6/20	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.373578613280391	2		825	851	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222965	36222965	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	189	811	0	ENST00000222270.7:c.5594T>C	p.Ile1865Thr	p.I1865T	ENST00000222270	NM_014727.1	1865	aTc/aCc	27/37	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.373578613280391	2		811	966	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228795	36228795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1193546654	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	145	710	1	ENST00000222270.7:c.7694G>A	p.Arg2565His	p.R2565H	ENST00000222270	NM_014727.1	2565	cGt/cAt	35/37	1	2	FACETS	0.903	0.824	0.986	0.903	0.824	0.986	CLONAL	1	TRUE	1	0.373578613280391	2		711	860	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716280	52716280	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	102	583	0	ENST00000322088.6:c.724G>A	p.Ala242Thr	p.A242T	ENST00000322088	NM_014225.5	242	Gcc/Acc	6/15	1	2	FACETS	0.825	0.739	0.916	0.825	0.739	0.916	CLONAL	1	TRUE	1	0.373578613280391	2		583	662	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660606	227660606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141295519	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	109	520	0	ENST00000305123.5:c.2849G>A	p.Arg950Gln	p.R950Q	ENST00000305123	NM_005544.2	950	cGg/cAg	1/2	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.373578613280391	2		520	574	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264834	46264834	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	131	487	0	ENST00000371998.3:c.1704del	p.Ser569ValfsTer69	p.S569Vfs*69	ENST00000371998		568	aaG/aa	12/23	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.373578613280391	2		487	653	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633229	12633229	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	119	536	0	ENST00000251849.4:c.1171A>G	p.Arg391Gly	p.R391G	ENST00000251849	NM_002880.3	391	Agg/Ggg	11/17	1	2	FACETS	0.778	0.702	0.858	0.778	0.702	0.858	SUBCLONAL	1	TRUE	1	0.373578613280391	2		536	819	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928927	49928927	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	164	742	0	ENST00000296474.3:c.3439A>G	p.Ile1147Val	p.I1147V	ENST00000296474	NM_002447.2	1147	Att/Gtt	16/20	1	2	FACETS	0.998	0.916	1	0.998	0.916	1	CLONAL	1	TRUE	1	0.373578613280391	2		742	880	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015044	71015044	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754297044	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	63	261	0	ENST00000318789.4:c.1886C>T	p.Ala629Val	p.A629V	ENST00000318789	NM_032682.5	629	gCc/gTc	20/21	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.373578613280391	2		261	327	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948792	55948792	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	119	370	0	ENST00000263923.4:c.3673C>T	p.Gln1225Ter	p.Q1225*	ENST00000263923	NM_002253.2	1225	Cag/Tag	28/30	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.373578613280391	2		370	637	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197435	106197435	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	66	384	0	ENST00000380013.4:c.5772del	p.Ala1925ProfsTer25	p.A1925Pfs*25	ENST00000380013	NM_001127208.2	1923	gAa/ga	11/11	1	2	FACETS	0.881	0.768	1	0.881	0.768	1	CLONAL	1	TRUE	1	0.373578613280391	2		384	401	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007314	143007314	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs750041873	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	99	354	0	ENST00000262992.4:c.2470A>G	p.Met824Val	p.M824V	ENST00000262992	NM_001101669.1	824	Atg/Gtg	22/24	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.373578613280391	2		354	525	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081595	143081595	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	99	469	0	ENST00000262992.4:c.1479G>T	p.Glu493Asp	p.E493D	ENST00000262992	NM_001101669.1	493	gaG/gaT	15/24	1	2	FACETS	0.941	0.843	1	0.941	0.843	1	CLONAL	1	TRUE	1	0.373578613280391	2		469	563	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541199	187541199	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs369172979	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	80	341	0	ENST00000441802.2:c.6541G>C	p.Val2181Leu	p.V2181L	ENST00000441802	NM_005245.3	2181	Gtg/Ctg	10/27	1	2	FACETS	0.939	0.83	1	0.939	0.83	1	CLONAL	1	TRUE	1	0.373578613280391	2		341	456	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155573	56155573	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1214852294	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	78	410	1	ENST00000399503.3:c.665G>T	p.Gly222Val	p.G222V	ENST00000399503	NM_005921.1	222	gGa/gTa	3/20	1	2	FACETS	0.703	0.618	0.794	0.703	0.618	0.794	SUBCLONAL	1	TRUE	1	0.373578613280391	2		411	594	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179445	56179445	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	88	353	0	ENST00000399503.3:c.3758C>T	p.Ala1253Val	p.A1253V	ENST00000399503	NM_005921.1	1253	gCa/gTa	15/20	1	2	FACETS	0.967	0.86	1	0.967	0.86	1	CLONAL	1	TRUE	1	0.373578613280391	2		353	487	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183314	56183314	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	65	500	0	ENST00000399503.3:c.4224A>C	p.Gln1408His	p.Q1408H	ENST00000399503	NM_005921.1	1408	caA/caC	18/20	1	2	FACETS	0.477	0.413	0.546	0.477	0.413	0.546	SUBCLONAL	1	TRUE	1	0.373578613280391	2		500	730	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514472	149514472	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	108	634	0	ENST00000261799.4:c.472G>A	p.Val158Met	p.V158M	ENST00000261799	NM_002609.3	158	Gtg/Atg	4/23	1	2	FACETS	0.809	0.726	0.896	0.809	0.726	0.896	CLONAL	1	TRUE	1	0.373578613280391	2		634	715	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045889	26045890	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	109	450	0	ENST00000540144.1:c.254dup	p.Gln86ProfsTer13	p.Q86Pfs*13	ENST00000540144	NM_003531.2	84	cgt/cgTt	1/1	1	2	FACETS	0.872	0.784	0.965	0.872	0.784	0.965	CLONAL	1	TRUE	1	0.373578613280391	2		450	669	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016259	150016259	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	141	489	0	ENST00000253339.5:c.447G>C	p.Glu149Asp	p.E149D	ENST00000253339		149	gaG/gaC	2/7	1	2	FACETS	0.988	0.901	1	0.988	0.901	1	CLONAL	1	TRUE	1	0.373578613280391	2		489	764	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884921	151884921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760955374	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	89	351	0	ENST00000262189.6:c.4672C>T	p.Arg1558Trp	p.R1558W	ENST00000262189	NM_170606.2	1558	Cgg/Tgg	32/59	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.373578613280391	2		351	463	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863088	56863088	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	143	595	1	ENST00000519728.1:c.355G>A	p.Ala119Thr	p.A119T	ENST00000519728	NM_002350.3	119	Gcc/Acc	5/13	1	2	FACETS	0.89	0.812	0.973	0.89	0.812	0.973	CLONAL	1	TRUE	1	0.373578613280391	2		596	860	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5081805	5081805	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373353534	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	71	353	0	ENST00000381652.3:c.2515C>T	p.Arg839Trp	p.R839W	ENST00000381652	NM_004972.3	839	Cgg/Tgg	19/25	1	2	FACETS	0.773	0.676	0.876	0.773	0.676	0.876	SUBCLONAL	1	TRUE	1	0.373578613280391	2		353	492	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486274	8486274	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	24	344	0	ENST00000356435.5:c.2543A>G	p.Asp848Gly	p.D848G	ENST00000356435		848	gAc/gGc	17/35	1	2	FACETS	0.293	0.229	0.367	0.293	0.229	0.367	SUBCLONAL	1	TRUE	1	0.373578613280391	2		344	439	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974789	21974789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745612549	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	38	145	1	ENST00000304494.5:c.38C>T	p.Ala13Val	p.A13V	ENST00000304494	NM_000077.4	13	gCt/gTt	1/3	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.373578613280391	2		146	141	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218572	98218572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748726158	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	49	457	3	ENST00000331920.6:c.3292G>A	p.Val1098Ile	p.V1098I	ENST00000331920	NM_000264.3	1098	Gtt/Att	19/24	1	2	FACETS	0.466	0.394	0.545	0.466	0.394	0.545	SUBCLONAL	1	TRUE	1	0.373578613280391	2		460	563	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760481	133760481	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143811852	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	170	724	1	ENST00000318560.5:c.2804C>T	p.Thr935Met	p.T935M	ENST00000318560	NM_005157.4	935	aCg/aTg	11/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.373578613280391	2		725	788	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413082	139413082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	126	608	0	ENST00000277541.6:c.1060G>A	p.Val354Met	p.V354M	ENST00000277541	NM_017617.3	354	Gtg/Atg	6/34	1	2	FACETS	0.947	0.859	1	0.947	0.859	1	CLONAL	1	TRUE	1	0.373578613280391	2		608	712	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914683	39914683	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762705967	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	42	562	2	ENST00000378444.4:c.4679C>T	p.Thr1560Met	p.T1560M	ENST00000378444	NM_001123385.1	1560	aCg/aTg	12/15	0.373578613280391	1	FACETS	0.266	0.221	0.316	0.266	0.221	0.316	SUBCLONAL	1	TRUE	0	0.373578613280391	1		564	687	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411003	63411003	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	151	600	0	ENST00000330258.3:c.2164T>G	p.Phe722Val	p.F722V	ENST00000330258	NM_152424.3	722	Ttc/Gtc	2/2	0.373578613280391	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.373578613280391	1		600	583	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106648	27106648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553153748	NA	P-0028892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	157	646	3	ENST00000324856.7:c.6259G>A	p.Gly2087Arg	p.G2087R	ENST00000324856	NM_006015.4	2087	Gga/Aga	20/20	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.402456545591168	2		649	760	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0028892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	85	351	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	0.402456545591168	2		351	391	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888799	76888799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	82	274	0	ENST00000373344.5:c.5030G>A	p.Gly1677Asp	p.G1677D	ENST00000373344	NM_000489.3	1677	gGt/gAt	19/35	0.343573003463834	2	FACETS	1	0.951	1			1	CLONAL	1	TRUE	NA	0.402456545591168	2		274	361	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023968	27023975	+	frameshift_variant	Frame_Shift_Del	DEL	CCACGCGC	CCACGCGC	-	novel	NA	P-0028892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	11	98	0	ENST00000324856.7:c.1077_1084del	p.Ala360GlufsTer37	p.A360Efs*37	ENST00000324856	NM_006015.4	358	caCCACGCGCcc/cacc	1/20	1	2	FACETS	0.48	0.333	0.658	0.48	0.333	0.658	SUBCLONAL	1	TRUE	1	0.402456545591168	2		98	114	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101030	4101030	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730880511	NA	P-0028892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	24	498	0	ENST00000262948.5:c.692G>T	p.Arg231Leu	p.R231L	ENST00000262948	NM_030662.3	231	cGc/cTc	6/11	1	2	FACETS	0.257	0.201	0.322	0.257	0.201	0.322	SUBCLONAL	1	TRUE	1	0.402456545591168	2		498	464	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023571	27023571	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	22	336	0	ENST00000324856.7:c.680del	p.Pro227ArgfsTer5	p.P227Rfs*5	ENST00000324856	NM_006015.4	226	gCc/gc	1/20	1	2	FACETS	0.27	0.209	0.341	0.27	0.209	0.341	SUBCLONAL	1	TRUE	1	0.402456545591168	2		336	405	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433844	49433844	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	211	908	2	ENST00000301067.7:c.7709C>A	p.Pro2570His	p.P2570H	ENST00000301067	NM_003482.3	2570	cCc/cAc	31/54	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.402456545591168	2		910	884	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811685	102811685	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	157	697	0	ENST00000307046.8:c.499G>A	p.Ala167Thr	p.A167T	ENST00000307046	NM_001111285.1	167	Gca/Aca	4/4	1	2	FACETS	0.886	0.811	0.963	0.886	0.811	0.963	CLONAL	1	TRUE	1	0.402456545591168	2		697	881	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790472	3790472	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	128	602	1	ENST00000262367.5:c.4061C>A	p.Ala1354Asp	p.A1354D	ENST00000262367	NM_004380.2	1354	gCc/gAc	24/31	1	2	FACETS	0.844	0.765	0.926	0.844	0.765	0.926	CLONAL	1	TRUE	1	0.402456545591168	2		603	754	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351780	89351780	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1486498219	NA	P-0028892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	221	889	0	ENST00000301030.4:c.1170T>G	p.Ser390Arg	p.S390R	ENST00000301030	NM_001256183.1	390	agT/agG	9/13	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.402456545591168	2		889	1066	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006596	62006596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	94	504	1	ENST00000392795.3:c.683G>A	p.Gly228Asp	p.G228D	ENST00000392795	NM_001039933.1	228	gGc/gAc	6/6	1	2	FACETS	0.934	0.834	1	0.934	0.834	1	CLONAL	1	TRUE	1	0.402456545591168	2		505	500	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646047	215646047	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	77	549	0	ENST00000260947.4:c.551C>A	p.Ser184Tyr	p.S184Y	ENST00000260947	NM_000465.2	184	tCc/tAc	4/11	0.402456545591168	3	FACETS	0.746	0.655	0.844	0.373	0.327	0.422	SUBCLONAL	1	TRUE	1	0.402456545591168	3		549	616	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495661	72495661	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	86	337	0	ENST00000477973.2:c.411A>T	p.Lys137Asn	p.K137N	ENST00000477973	NM_012234.5	137	aaA/aaT	1/4	1	2	FACETS	0.833	0.739	0.933	0.833	0.739	0.933	CLONAL	1	TRUE	1	0.402456545591168	2		337	513	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202822	128202822	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	80	625	0	ENST00000341105.2:c.898G>T	p.Ala300Ser	p.A300S	ENST00000341105	NM_032638.4	300	Gcc/Tcc	4/6	1	2	FACETS	0.554	0.488	0.626	0.554	0.488	0.626	SUBCLONAL	1	TRUE	1	0.402456545591168	2		625	717	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584582	189584582	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	31	409	1	ENST00000264731.3:c.878C>A	p.Pro293His	p.P293H	ENST00000264731	NM_003722.4	293	cCc/cAc	6/14	1	2	FACETS	0.342	0.276	0.417	0.342	0.276	0.417	SUBCLONAL	1	TRUE	1	0.402456545591168	2		410	450	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972092	55972092	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs765996740	NA	P-0028892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	87	423	0	ENST00000263923.4:c.1552G>T	p.Val518Phe	p.V518F	ENST00000263923	NM_002253.2	518	Gtt/Ttt	12/30	1	2	FACETS	0.868	0.771	0.971	0.868	0.771	0.971	CLONAL	1	TRUE	1	0.402456545591168	2		423	498	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250823	153250823	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1159697496	NA	P-0028892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	19	383	0	ENST00000281708.4:c.1236+1G>A		p.X412_splice	ENST00000281708	NM_033632.3	412			1	2	FACETS	0.266	0.201	0.342	0.266	0.201	0.342	SUBCLONAL	1	TRUE	1	0.402456545591168	2		383	355	SUCCESS
APC	324	MSKCC	GRCh37	5	112174771	112174771	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	75	361	0	ENST00000257430.4:c.3482del	p.Asn1161IlefsTer4	p.N1161Ifs*4	ENST00000257430	NM_000038.5	1160	acA/ac	16/16	1	2	FACETS	0.994	0.876	1	0.994	0.876	1	CLONAL	1	TRUE	1	0.402456545591168	2		361	375	SUCCESS
APC	324	MSKCC	GRCh37	5	112178105	112178105	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0028892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	113	396	0	ENST00000257430.4:c.6814A>T	p.Arg2272Ter	p.R2272*	ENST00000257430	NM_000038.5	2272	Aga/Tga	16/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.402456545591168	2		396	499	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974217	2974217	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	129	700	0	ENST00000396946.4:c.1388G>T	p.Gly463Val	p.G463V	ENST00000396946	NM_032415.4	463	gGg/gTg	10/25	1	2	FACETS	0.876	0.795	0.961	0.876	0.795	0.961	CLONAL	1	TRUE	1	0.402456545591168	2		700	732	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750547	128750547	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	141	582	0	ENST00000377970.2:c.84C>A	p.Asp28Glu	p.D28E	ENST00000377970	NM_002467.4	28	gaC/gaA	2/3	1	2	FACETS	0.965	0.881	1	0.965	0.881	1	CLONAL	1	TRUE	1	0.402456545591168	2		582	726	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180361	27180361	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373027386	NA	P-0028892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	70	353	0	ENST00000380036.4:c.1025G>A	p.Arg342Lys	p.R342K	ENST00000380036	NM_000459.3	342	aGa/aAa	7/23	1	2	FACETS	0.689	0.602	0.783	0.689	0.602	0.783	SUBCLONAL	1	TRUE	1	0.402456545591168	2		353	505	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390632	139390632	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	173	856	0	ENST00000277541.6:c.7559G>T	p.Trp2520Leu	p.W2520L	ENST00000277541	NM_017617.3	2520	tGg/tTg	34/34	1	2	FACETS	0.934	0.86	1	0.934	0.86	1	CLONAL	1	TRUE	1	0.402456545591168	2		856	920	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399786	139399786	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	132	592	0	ENST00000277541.6:c.4562G>C	p.Cys1521Ser	p.C1521S	ENST00000277541	NM_017617.3	1521	tGc/tCc	25/34	1	2	FACETS	0.914	0.831	1	0.914	0.831	1	CLONAL	1	TRUE	1	0.402456545591168	2		592	718	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841196	15841196	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	69	194	0	ENST00000307771.7:c.1280G>T	p.Arg427Met	p.R427M	ENST00000307771	NM_005089.3	427	aGg/aTg	11/11	0.343573003463834	2	FACETS	1	0.932	1			1	CLONAL	1	TRUE	NA	0.402456545591168	2		194	314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0028893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	86	581	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.143861154046111	3	FACETS	1	0.966	1	0.629	0.556	0.708	CLONAL	1	TRUE	1	0.183261266621581	3		581	814	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221243	1221243	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1057520606	NA	P-0028893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	135	715	0	ENST00000326873.7:c.766G>T	p.Glu256Ter	p.E256*	ENST00000326873	NM_000455.4	256	Gaa/Taa	6/10	0.183261266621581	2	FACETS	0.845	0.768	0.926	0.845	0.768	0.926	CLONAL	2	TRUE	0	0.183261266621581	2		715	872	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574027	7574027	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882028	NA	P-0028893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	65	624	1	ENST00000269305.4:c.1000G>T	p.Gly334Trp	p.G334W	ENST00000269305	NM_001126112.2	334	Ggg/Tgg	10/11	0.143861154046111	3	FACETS	0.883	0.764	1	0.441	0.382	0.507	CLONAL	1	TRUE	1	0.183261266621581	3		625	877	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155393	47155393	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	60	469	1	ENST00000409792.3:c.4688G>T	p.Gly1563Val	p.G1563V	ENST00000409792	NM_014159.6	1563	gGc/gTc	5/21	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.183261266621581	2		470	645	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800935	120800935	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	115	534	0	ENST00000257552.2:c.313del	p.Val105Ter	p.V105*	ENST00000257552	NM_002442.3	105	Gtg/tg	6/15	1	2	FACETS	0.86	0.775	0.949	1	0.987	1	CLONAL	2	TRUE	1	0.183261266621581	2		534	730	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223090	1223090	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	59	685	0	ENST00000326873.7:c.1027G>T	p.Asp343Tyr	p.D343Y	ENST00000326873	NM_000455.4	343	Gac/Tac	8/10	0.183261266621581	2	FACETS	0.709	0.608	0.82	0.355	0.304	0.41	SUBCLONAL	1	TRUE	0	0.183261266621581	2		685	908	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602328	10602328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	158	788	1	ENST00000171111.5:c.1250G>A	p.Gly417Glu	p.G417E	ENST00000171111	NM_203500.1	417	gGg/gAg	3/6	0.183261266621581	2	FACETS	0.913	0.837	0.994	0.913	0.837	0.994	CLONAL	2	TRUE	0	0.183261266621581	2		789	944	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233123	66233123	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	30	401	0	ENST00000273854.3:c.1876G>T	p.Ala626Ser	p.A626S	ENST00000273854	NM_004439.5	626	Gca/Tca	10/18	1	2	FACETS	0.589	0.473	0.721	0.589	0.473	0.721	SUBCLONAL	1	TRUE	1	0.183261266621581	2		401	556	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249507	153249507	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	99	552	0	ENST00000281708.4:c.1271T>C	p.Val424Ala	p.V424A	ENST00000281708	NM_033632.3	424	gTa/gCa	9/12	1	2	FACETS	0.782	0.698	0.87	1	0.982	1	SUBCLONAL	2	TRUE	1	0.183261266621581	2		552	691	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140508747	140508747	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	46	583	0	ENST00000288602.6:c.553C>A	p.Leu185Met	p.L185M	ENST00000288602	NM_004333.4	185	Ctg/Atg	4/18	0.143861154046111	3	FACETS	0.746	0.626	0.878	0.373	0.313	0.439	SUBCLONAL	1	TRUE	1	0.183261266621581	3		583	735	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551289	141551289	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	245	763	0	ENST00000220592.5:c.2008G>T	p.Gly670Cys	p.G670C	ENST00000220592	NM_012154.3	670	Ggt/Tgt	15/19	0.178464114927542	4	FACETS	0.842	0.785	0.9	0.842	0.785	0.9	CLONAL	3	TRUE	1	0.183261266621581	4		763	1253	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0028897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	57	532	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.17	2		532	587	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207146	1207146	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	91	761	0	ENST00000326873.7:c.234G>T	p.Lys78Asn	p.K78N	ENST00000326873	NM_000455.4	78	aaG/aaT	1/10	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.17	2		761	1053	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11264660	11264660	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	43	532	0	ENST00000361445.4:c.3902G>T	p.Arg1301Leu	p.R1301L	ENST00000361445	NM_004958.3	1301	cGc/cTc	26/58	1	2	FACETS	0.696	0.581	0.824	0.696	0.581	0.824	SUBCLONAL	1	TRUE	1	0.17	2		532	727	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793440	242793440	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	72	506	0	ENST00000334409.5:c.637C>G	p.Pro213Ala	p.P213A	ENST00000334409	NM_005018.2	213	Ccc/Gcc	5/5	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.17	2		506	791	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217108	66217108	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	54	299	0	ENST00000273854.3:c.2507G>C	p.Arg836Thr	p.R836T	ENST00000273854	NM_004439.5	836	aGg/aCg	14/18	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.17	2		299	505	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15808651	15808651	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	66	555	0	ENST00000307771.7:c.33G>C	p.Glu11Asp	p.E11D	ENST00000307771	NM_005089.3	11	gaG/gaC	1/11	0.3	2	FACETS	0.898	0.777	1			1	CLONAL	1	TRUE	NA	0.17	2		555	865	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107231	193107231	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	40	291	0	ENST00000367435.3:c.440G>T	p.Arg147Leu	p.R147L	ENST00000367435	NM_024529.4	147	cGc/cTc	6/17	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.202041667819132	2		291	336	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600605	43600605	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	47	475	0	ENST00000355710.3:c.831C>A	p.Asp277Glu	p.D277E	ENST00000355710	NM_020975.4	277	gaC/gaA	4/20	1	2	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	TRUE	1	0.202041667819132	2		475	464	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218321	133218321	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	56	606	1	ENST00000320574.5:c.5290G>T	p.Ala1764Ser	p.A1764S	ENST00000320574	NM_006231.2	1764	Gcc/Tcc	39/49	1	2	FACETS	0.916	0.785	1	0.916	0.785	1	CLONAL	1	TRUE	1	0.202041667819132	2		607	605	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0028899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	79	489	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.202041667819132	2		489	557	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212283	36212283	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	56	560	2	ENST00000222270.7:c.2034G>T	p.Glu678Asp	p.E678D	ENST00000222270	NM_014727.1	678	gaG/gaT	3/37	1	2	FACETS	0.868	0.743	1	0.868	0.743	1	CLONAL	1	TRUE	1	0.202041667819132	2		562	639	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244158	153244158	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	34	500	0	ENST00000281708.4:c.1999G>C	p.Gly667Arg	p.G667R	ENST00000281708	NM_033632.3	667	Ggg/Cgg	12/12	1	2	FACETS	0.594	0.484	0.717	0.594	0.484	0.717	SUBCLONAL	1	TRUE	1	0.202041667819132	2		500	567	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31464425	31464425	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	252	743	1	ENST00000344624.3:c.2492A>T	p.Lys831Met	p.K831M	ENST00000344624		831	aAg/aTg	17/33	0.202041667819132	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	TRUE	1	0.202041667819132	4		744	951	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249800	110249800	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763310984	NA	P-0028899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	73	650	0	ENST00000374672.4:c.875C>T	p.Pro292Leu	p.P292L	ENST00000374672	NM_004235.4	292	cCc/cTc	3/5	0.202041667819132	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.202041667819132	1		650	496	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944607	40944607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766880457	NA	P-0028900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	132	326	0	ENST00000373198.4:c.1895G>A	p.Arg632Gln	p.R632Q	ENST00000373198	NM_133170.3	632	cGa/cAa	12/32	1	2	FACETS	0.854	0.781	0.929	0.854	0.781	0.929	CLONAL	1	TRUE	1	0.672363141075649	2		326	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0028900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	504	650	1	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.67223963137105	2	FACETS	0.929	0.898	0.959	0.929	0.898	0.959	CLONAL	2	TRUE	0	0.672363141075649	2		651	807	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541542	29541542	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137854557	NA	P-0028900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	13	567	0	ENST00000356175.3:c.1466A>G	p.Tyr489Cys	p.Y489C	ENST00000356175	NM_000267.3	489	tAt/tGt	13/57	0.67223963137105	2	FACETS	0.186	0.132	0.251	0.093	0.066	0.126	SUBCLONAL	1	TRUE	0	0.672363141075649	2		567	208	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030416	49030416	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	148	468	1	ENST00000267163.4:c.1891C>T	p.Gln631Ter	p.Q631*	ENST00000267163	NM_000321.2	631	Caa/Taa	19/27	0.672363141075649	1	FACETS	0.958	0.891	1	0.958	0.891	1	CLONAL	1	TRUE	0	0.672363141075649	1		469	305	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870809	12870809	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	95	158	0	ENST00000228872.4:c.37del	p.Leu13TrpfsTer29	p.L13Wfs*29	ENST00000228872	NM_004064.3	12	agC/ag	1/3	0.672363141075649	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.672363141075649	1		158	156	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739027	40739027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749859329	NA	P-0028900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	244	470	1	ENST00000373198.4:c.3257G>A	p.Arg1086His	p.R1086H	ENST00000373198	NM_133170.3	1086	cGc/cAc	24/32	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.672363141075649	2		471	688	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891523	76891527	+	frameshift_variant	Frame_Shift_Del	DEL	GTGAA	GTGAA	-	novel	NA	P-0028900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	160	396	0	ENST00000373344.5:c.4578_4582del	p.Ser1527HisfsTer13	p.S1527Hfs*13	ENST00000373344	NM_000489.3	1526	gcTTCACcc/gccc	16/35	1	2	FACETS	0.842	0.777	0.91	0.842	0.777	0.91	CLONAL	1	TRUE	1	0.672363141075649	2		396	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0028903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	638	766	0	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	0.598797212225875	2	FACETS	0.993	0.964	1	0.993	0.964	1	CLONAL	2	TRUE	0	0.626244934709494	2		766	1026	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435422	18435422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	210	271	1	ENST00000266497.5:c.407C>T	p.Ala136Val	p.A136V	ENST00000266497		136	gCt/gTt	1/31	0.626244934709494	2	FACETS	0.981	0.93	1	0.981	0.93	1	CLONAL	2	TRUE	0	0.626244934709494	2		272	342	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144114	11144114	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	766	733	3	ENST00000358026.2:c.3695G>T	p.Gly1232Val	p.G1232V	ENST00000358026	NM_001128849.1	1232	gGc/gTc	26/36	0.626244934709494	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.626244934709494	2		736	1199	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029437	16029439	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	rs774778469	NA	P-0028903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	349	524	0	ENST00000268712.3:c.1591_1593del	p.Glu531del	p.E531del	ENST00000268712	NM_006311.3	531	GAA/-	15/46	0.601207581131241	4	FACETS	0.84	0.796	0.884			1	CLONAL	2	TRUE	NA	0.626244934709494	4		524	1079	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441342	149441342	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	103	586	2	ENST00000286301.3:c.1697C>A	p.Pro566His	p.P566H	ENST00000286301	NM_005211.3	566	cCc/cAc	12/22	0.394145977233151	2	FACETS	0.298	0.266	0.333	0.149	0.133	0.167	SUBCLONAL	1	TRUE	0	0.626244934709494	2		588	1103	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77043905	77043905	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	147	561	0	ENST00000356341.3:c.1421A>C	p.Tyr474Ser	p.Y474S	ENST00000356341	NM_002576.4	474	tAc/tCc	14/15	0.247280437953772	1	FACETS	0.484	0.443	0.527	0.484	0.443	0.527	INDETERMINATE	1	TRUE	0	0.626244934709494	1		561	666	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416612	121416612	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	250	568	0	ENST00000257555.6:c.41C>G	p.Ala14Gly	p.A14G	ENST00000257555		14	gCg/gGg	1/10	1	2	FACETS	0.991	0.93	1	0.991	0.93	1	CLONAL	1	TRUE	1	0.626244934709494	2		568	806	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28963993	28963993	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	21	334	0	ENST00000282397.4:c.1909A>G	p.Arg637Gly	p.R637G	ENST00000282397	NM_002019.4	637	Aga/Gga	13/30	0.557503897242299	2	FACETS	0.201	0.154	0.255	0.1	0.077	0.128	SUBCLONAL	1	TRUE	0	0.626244934709494	2		334	334	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38641714	38641714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	135	457	0	ENST00000299084.4:c.674C>T	p.Ser225Phe	p.S225F	ENST00000299084	NM_152594.2	225	tCc/tTc	6/7	1	2	FACETS	0.855	0.782	0.931	0.855	0.782	0.931	CLONAL	1	TRUE	1	0.626244934709494	2		457	504	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479751	67479751	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	211	450	1	ENST00000327367.4:c.1058C>A	p.Ala353Asp	p.A353D	ENST00000327367	NM_005902.3	353	gCc/gAc	8/9	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.626244934709494	2		451	666	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496953	29496953	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	298	342	0	ENST00000356175.3:c.524A>G	p.His175Arg	p.H175R	ENST00000356175	NM_000267.3	175	cAt/cGt	5/57	0.598797212225875	2	FACETS	0.926	0.884	0.967	0.926	0.884	0.967	CLONAL	2	TRUE	0	0.626244934709494	2		342	514	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223037	41223037	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs770193975	NA	P-0028903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	263	567	0	ENST00000357654.3:c.4894G>C	p.Val1632Leu	p.V1632L	ENST00000357654	NM_007294.3	1632	Gtg/Ctg	15/23	0.552073384775693	4	FACETS	0.998	0.933	1	0.333	0.311	0.355	CLONAL	1	TRUE	1	0.626244934709494	4		567	1369	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688664	47688664	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	221	341	0	ENST00000347630.2:c.636G>T	p.Gln212His	p.Q212H	ENST00000347630	NM_001007230.1	212	caG/caT	7/11	0.302561673228912	3	FACETS	0.761	0.713	0.81	0.761	0.713	0.81	INDETERMINATE	2	TRUE	1	0.626244934709494	3		341	609	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554704	63554704	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	139	465	0	ENST00000307078.5:c.35A>C	p.Asp12Ala	p.D12A	ENST00000307078	NM_004655.3	12	gAc/gCc	2/11	0.302561673228912	3	FACETS	0.96	0.877	1	0.48	0.438	0.524	INDETERMINATE	1	TRUE	1	0.626244934709494	3		465	607	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905380	50905380	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	285	779	0	ENST00000440232.2:c.588G>T	p.Glu196Asp	p.E196D	ENST00000440232	NM_002691.3	196	gaG/gaT	5/27	NA	2	FACETS	0.847	0.797	0.899			1	INDETERMINATE	1	TRUE	NA	0.626244934709494	2		779	1074	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251614	212251614	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs781436663	NA	P-0028903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	104	345	0	ENST00000342788.4:c.3445G>T	p.Gly1149Cys	p.G1149C	ENST00000342788	NM_005235.2	1149	Ggt/Tgt	27/28	0.0592164704769234	3	FACETS	0.853	0.767	0.944			1	INDETERMINATE	1	TRUE	NA	0.626244934709494	3		345	511	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101046	41101046	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	402	480	0	ENST00000373198.4:c.1310C>A	p.Ala437Asp	p.A437D	ENST00000373198	NM_133170.3	437	gCc/gAc	8/32	0.346333625392648	5	FACETS	1	0.99	1	0.761	0.726	0.798	INDETERMINATE	2	TRUE	2	0.626244934709494	5		480	1090	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139546	47139546	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	143	331	0	ENST00000409792.3:c.5041G>T	p.Gly1681Ter	p.G1681*	ENST00000409792	NM_014159.6	1681	Gga/Tga	9/21	1	2	FACETS	0.926	0.85	1	0.926	0.85	1	CLONAL	1	TRUE	1	0.626244934709494	2		331	493	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390122	89390122	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	169	330	1	ENST00000336596.2:c.871C>A	p.Pro291Thr	p.P291T	ENST00000336596	NM_005233.5	291	Ccg/Acg	4/17	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.626244934709494	2		331	504	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200148	128200148	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	205	586	0	ENST00000341105.2:c.1157T>A	p.Leu386Gln	p.L386Q	ENST00000341105	NM_032638.4	386	cTg/cAg	6/6	1	2	FACETS	0.891	0.829	0.954	0.891	0.829	0.954	CLONAL	1	TRUE	1	0.626244934709494	2		586	735	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134514486	134514486	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	162	439	0	ENST00000398015.3:c.13T>G	p.Tyr5Asp	p.Y5D	ENST00000398015	NM_004441.4	5	Tat/Gat	1/16	1	2	FACETS	0.883	0.814	0.954	0.883	0.814	0.954	CLONAL	1	TRUE	1	0.626244934709494	2		439	586	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134885806	134885806	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1166430396	NA	P-0028903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	182	471	0	ENST00000398015.3:c.1717G>T	p.Ala573Ser	p.A573S	ENST00000398015	NM_004441.4	573	Gct/Tct	9/16	1	2	FACETS	0.894	0.829	0.962	0.894	0.829	0.962	CLONAL	1	TRUE	1	0.626244934709494	2		471	650	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503956	186503956	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	82	241	0	ENST00000323963.5:c.521C>A	p.Pro174Gln	p.P174Q	ENST00000323963		174	cCa/cAa	6/11	0.626244934709494	3	FACETS	0.744	0.659	0.835	0.372	0.329	0.418	SUBCLONAL	1	TRUE	1	0.626244934709494	3		241	462	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440357	187440357	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	431	402	0	ENST00000232014.4:c.2010A>T	p.Lys670Asn	p.K670N	ENST00000232014	NM_001130845.1	670	aaA/aaT	10/10	0.626244934709494	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.626244934709494	3		402	872	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512391	149512391	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	78	648	0	ENST00000261799.4:c.1049G>C	p.Trp350Ser	p.W350S	ENST00000261799	NM_002609.3	350	tGg/tCg	7/23	0.394145977233151	2	FACETS	0.236	0.206	0.268	0.118	0.103	0.134	SUBCLONAL	1	TRUE	0	0.626244934709494	2		648	1057	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636893	176636893	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	370	423	0	ENST00000439151.2:c.1493G>T	p.Arg498Leu	p.R498L	ENST00000439151	NM_022455.4	498	cGa/cTa	5/23	0.626244934709494	2	FACETS	0.942	0.905	0.979	0.942	0.905	0.979	CLONAL	2	TRUE	0	0.626244934709494	2		423	627	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394996	394996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	209	428	0	ENST00000380956.4:c.392G>A	p.Gly131Glu	p.G131E	ENST00000380956	NM_001195286.1	131	gGa/gAa	3/9	0.388009118634409	1	FACETS	0.772	0.721	0.823	0.772	0.721	0.823	SUBCLONAL	1	TRUE	0	0.626244934709494	1		428	594	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420027	152420027	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	466	525	0	ENST00000206249.3:c.1714G>T	p.Gly572Cys	p.G572C	ENST00000206249	NM_000125.3	572	Ggc/Tgc	8/8	0.12729011462169	4	FACETS	1	0.982	1			1	INDETERMINATE	3	TRUE	NA	0.626244934709494	4		525	785	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012340	152012340	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	105	377	0	ENST00000262189.6:c.473G>T	p.Gly158Val	p.G158V	ENST00000262189	NM_170606.2	158	gGa/gTa	4/59	0.592848963039402	1	FACETS	0.758	0.688	0.83	0.758	0.688	0.83	SUBCLONAL	1	TRUE	0	0.626244934709494	1		377	304	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855214	76855214	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	261	267	0	ENST00000373344.5:c.5773G>T	p.Asp1925Tyr	p.D1925Y	ENST00000373344	NM_000489.3	1925	Gat/Tat	24/35	0.577331468182659	2	FACETS	1	0.99	1			1	CLONAL	2	TRUE	NA	0.626244934709494	2		267	375	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004366	150004367	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	A	novel	NA	P-0028903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	330	396	0	ENST00000253339.5:c.1858_1859delinsT	p.Asn620SerfsTer28	p.N620Sfs*28	ENST00000253339		620	AAc/Tc	3/7	0.12729011462169	4	FACETS	1	0.97	1			1	INDETERMINATE	3	TRUE	NA	0.626244934709494	4		396	562	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0028904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	93	498	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.288814312190572	2		498	643	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0028904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	141	665	0	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.288814312190572	2		665	803	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913351	NA	P-0028904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	88	369	0	ENST00000288602.6:c.1397G>A	p.Gly466Glu	p.G466E	ENST00000288602	NM_004333.4	466	gGa/gAa	11/18	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.288814312190572	2		369	589	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287446	46287446	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs774801990	NA	P-0028904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	93	409	2	ENST00000334344.6:c.5305C>T	p.Arg1769Ter	p.R1769*	ENST00000334344	NM_152641.2	1769	Cga/Tga	20/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.288814312190572	2		411	520	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950376	17950376	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs267605358	NA	P-0028904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	145	618	2	ENST00000458235.1:c.1351C>T	p.Arg451Ter	p.R451*	ENST00000458235	NM_000215.3	451	Cga/Tga	10/24	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.288814312190572	2		620	960	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206667267	206667267	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	222	410	0	ENST00000367120.3:c.2060G>T	p.Cys687Phe	p.C687F	ENST00000367120	NM_014002.3	687	tGc/tTc	21/22	0.288814312190572	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.288814312190572	3		410	757	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120502	2120502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	165	686	0	ENST00000219476.3:c.1762G>A	p.Glu588Lys	p.E588K	ENST00000219476	NM_000548.3	588	Gag/Aag	17/42	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.288814312190572	2		686	993	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492906	56492916	+	frameshift_variant	Frame_Shift_Del	DEL	GGCAGCCAGCT	GGCAGCCAGCT	-	novel	NA	P-0028904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	98	171	0	ENST00000407977.2:c.23_33del	p.Gln8ProfsTer28	p.Q8Pfs*28	ENST00000407977		8	cAGCTGGCTGCC/c	2/10	0.288814312190572	2	FACETS	0.901	0.818	0.986	1	0.981	1	CLONAL	3	TRUE	0	0.288814312190572	2		171	251	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267360	198267360	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs374250186	NA	P-0028905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	95	478	0	ENST00000335508.6:c.1997A>C	p.Lys666Thr	p.K666T	ENST00000335508	NM_012433.2	666	aAg/aCg	14/25	1	2	FACETS	0.943	0.839	1	0.943	0.839	1	CLONAL	1	TRUE	1	0.266612369855941	2		478	756	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482607	56482607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs993665271	NA	P-0028905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	157	565	0	ENST00000267101.3:c.1064C>T	p.Thr355Ile	p.T355I	ENST00000267101	NM_001982.3	355	aCc/aTc	9/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.266612369855941	2		565	896	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287500	46287500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457405698	NA	P-0028905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	67	419	0	ENST00000334344.6:c.5359C>T	p.Arg1787Cys	p.R1787C	ENST00000334344	NM_152641.2	1787	Cgc/Tgc	20/21	1	2	FACETS	0.785	0.682	0.897	0.785	0.682	0.897	SUBCLONAL	1	TRUE	1	0.266612369855941	2		419	640	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186602	108186602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	71	314	0	ENST00000278616.4:c.6059G>A	p.Gly2020Asp	p.G2020D	ENST00000278616	NM_000051.3	2020	gGc/gAc	41/63	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.266612369855941	2		314	489	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206605	108206605	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781967	NA	P-0028905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	78	323	0	ENST00000278616.4:c.8185C>T	p.Gln2729Ter	p.Q2729*	ENST00000278616	NM_000051.3	2729	Caa/Taa	56/63	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.266612369855941	2		323	582	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223166	1223166	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	91	394	1	ENST00000326873.7:c.1103T>A	p.Val368Glu	p.V368E	ENST00000326873	NM_000455.4	368	gTg/gAg	8/10	0.266612369855941	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.266612369855941	1		395	545	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099339	157099362	+	inframe_deletion	In_Frame_Del	DEL	CCACCACCACCATGCCCACCACCT	CCACCACCACCATGCCCACCACCT	-	rs1554247278	NA	P-0028905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	28	347	1	ENST00000346085.5:c.288_311del	p.His98_Ala105del	p.H98_A105del	ENST00000346085	NM_020732.3	92	caCCACCACCACCATGCCCACCACCTc/cac	1/20	1	2	FACETS	0.471	0.376	0.58	0.471	0.376	0.58	SUBCLONAL	1	TRUE	1	0.266612369855941	2		348	446	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0028907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	785	181	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.808658308372766	6	FACETS	1	0.986	1	1	0.986	1	CLONAL	5	TRUE	1	0.808658308372766	6		181	1007	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0028907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	149	529	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.808658308372766	6	FACETS	0.755	0.688	0.825	0.151	0.137	0.165	SUBCLONAL	1	TRUE	1	0.808658308372766	6		529	1278	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321626	30321626	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	228	472	0	ENST00000322652.5:c.1481G>T	p.Cys494Phe	p.C494F	ENST00000322652	NM_015355.2	494	tGt/tTt	13/16	0.808658308372766	2	FACETS	0.977	0.918	1	0.489	0.459	0.519	CLONAL	1	TRUE	0	0.808658308372766	2		472	577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579383	7579383	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	735	623	1	ENST00000269305.4:c.304del	p.Thr102ProfsTer21	p.T102Pfs*21	ENST00000269305	NM_001126112.2	102	Acc/cc	4/11	0.808658308372766	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.808658308372766	2		624	908	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	463266	463266	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	23	465	0	ENST00000399788.2:c.1005G>T	p.Trp335Cys	p.W335C	ENST00000399788	NM_001042603.1	335	tgG/tgT	8/28	0.808658308372766	1	FACETS	0.098	0.076	0.123	0.098	0.076	0.123	SUBCLONAL	1	TRUE	0	0.808658308372766	1		465	347	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325795	30325795	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	159	297	0	ENST00000322652.5:c.1993G>A	p.Asp665Asn	p.D665N	ENST00000322652	NM_015355.2	665	Gac/Aac	16/16	0.808658308372766	2	FACETS	0.923	0.855	0.992	0.462	0.427	0.496	CLONAL	1	TRUE	0	0.808658308372766	2		297	426	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300089	15300089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	275	475	0	ENST00000263388.2:c.1187C>T	p.Ser396Phe	p.S396F	ENST00000263388	NM_000435.2	396	tCt/tTt	7/33	0.670232215358865	3	FACETS	1	0.966	1			1	CLONAL	1	TRUE	NA	0.808658308372766	3		475	919	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799751	72799751	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0028907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	241	512	0	ENST00000325599.8:c.1418C>G	p.Ser473Ter	p.S473*	ENST00000325599	NM_018130.2	473	tCa/tGa	11/11	0.808658308372766	2	FACETS	1	0.972	1	0.526	0.495	0.556	CLONAL	1	TRUE	0	0.808658308372766	2		512	567	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155308	185155308	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	195	439	0	ENST00000265026.3:c.549C>G	p.Phe183Leu	p.F183L	ENST00000265026	NM_004721.4	183	ttC/ttG	3/14	0.808658308372766	6	FACETS	0.926	0.855	1	0.185	0.171	0.2	CLONAL	1	TRUE	1	0.808658308372766	6		439	1363	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155225	106155225	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs745818592	NA	P-0028907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	179	298	1	ENST00000380013.4:c.126G>C	p.Glu42Asp	p.E42D	ENST00000380013	NM_001127208.2	42	gaG/gaC	3/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.808658308372766	2		299	412	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155340	106155340	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	173	364	0	ENST00000380013.4:c.241G>C	p.Glu81Gln	p.E81Q	ENST00000380013	NM_001127208.2	81	Gaa/Caa	3/11	1	2	FACETS	0.918	0.853	0.984	0.918	0.853	0.984	CLONAL	1	TRUE	1	0.808658308372766	2		364	466	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143324101	143324101	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	120	229	0	ENST00000262992.4:c.362C>G	p.Ser121Cys	p.S121C	ENST00000262992	NM_001101669.1	121	tCt/tGt	5/24	1	2	FACETS	0.983	0.901	1	0.983	0.901	1	CLONAL	1	TRUE	1	0.808658308372766	2		229	302	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056830	180056830	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781159322	NA	P-0028907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	236	558	0	ENST00000261937.6:c.682G>A	p.Glu228Lys	p.E228K	ENST00000261937	NM_182925.4	228	Gag/Aag	6/30	0.743499449371316	4	FACETS	0.861	0.802	0.922	0.287	0.267	0.308	CLONAL	1	TRUE	1	0.808658308372766	4		558	1226	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555044	106555044	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766554111	NA	P-0028907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	404	376	0	ENST00000369096.4:c.2161G>A	p.Glu721Lys	p.E721K	ENST00000369096	NM_001198.3	721	Gaa/Aaa	7/7	0.808658308372766	3	FACETS	1	0.996	1	0.726	0.693	0.759	CLONAL	1	TRUE	1	0.808658308372766	3		376	966	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0028909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	127	850	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	0.244936826280865	2		850	745	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717777	89717777	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs786204873	NA	P-0028909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	41	282	0	ENST00000371953.3:c.801+1G>A		p.X267_splice	ENST00000371953	NM_000314.4	267			1	2	FACETS	0.881	0.735	1	0.881	0.735	1	CLONAL	1	TRUE	1	0.244936826280865	2		282	380	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659647	88659647	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	89	501	0	ENST00000372037.3:c.430G>T	p.Gly144Cys	p.G144C	ENST00000372037	NM_004329.2	144	Ggt/Tgt	6/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.244936826280865	2		501	597	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161390	2161390	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	80	450	0	ENST00000434045.2:c.137G>A	p.Arg46His	p.R46H	ENST00000434045	NM_001127598.1	46	cGc/cAc	2/5	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.244936826280865	2		450	520	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0028913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	144	466	2	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.848	0.779	0.919	0.848	0.779	0.919	CLONAL	1	TRUE	1	0.725855040511343	2		468	468	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	561	596	4	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	0.473262458980643	3	FACETS	0.99	0.956	1			1	CLONAL	2	TRUE	NA	0.725855040511343	3		600	1064	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481412	140481412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913353	NA	P-0028913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	145	404	1	ENST00000288602.6:c.1396G>A	p.Gly466Arg	p.G466R	ENST00000288602	NM_004333.4	466	Gga/Aga	11/18	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.725855040511343	2		405	393	SUCCESS
APC	324	MSKCC	GRCh37	5	112175358	112175358	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1554085480	NA	P-0028913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	70	237	0	ENST00000257430.4:c.4067C>G	p.Ser1356Ter	p.S1356*	ENST00000257430	NM_000038.5	1356	tCa/tGa	16/16	0.40371321130397	1	FACETS	0.564	0.499	0.631	0.564	0.499	0.631	INDETERMINATE	1	TRUE	0	0.725855040511343	1		237	218	SUCCESS
APC	324	MSKCC	GRCh37	5	112174658	112174658	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	19	380	1	ENST00000257430.4:c.3367C>T	p.Gln1123Ter	p.Q1123*	ENST00000257430	NM_000038.5	1123	Caa/Taa	16/16	0.40371321130397	1	FACETS	0.118	0.089	0.152	0.118	0.089	0.152	INDETERMINATE	1	TRUE	0	0.725855040511343	1		381	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577546	7577547	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0028913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	500	525	0	ENST00000269305.4:c.734dup	p.Met246HisfsTer18	p.M246Hfs*18	ENST00000269305	NM_001126112.2	245	ggc/ggGc	7/11	0.725855040511343	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.725855040511343	2		525	676	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295759	212295759	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	237	461	0	ENST00000342788.4:c.2554A>C	p.Lys852Gln	p.K852Q	ENST00000342788	NM_005235.2	852	Aaa/Caa	21/28	0.725855040511343	3	FACETS	1	0.974	1	0.539	0.505	0.575	CLONAL	1	TRUE	1	0.725855040511343	3		461	825	SUCCESS
ATR	545	MSKCC	GRCh37	3	142204013	142204013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	74	415	0	ENST00000350721.4:c.6190C>T	p.Leu2064Phe	p.L2064F	ENST00000350721	NM_001184.3	2064	Ctc/Ttc	36/47	0.725855040511343	3	FACETS	0.435	0.381	0.493	0.217	0.19	0.247	SUBCLONAL	1	TRUE	1	0.725855040511343	3		415	639	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181482	32181482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	113	578	0	ENST00000375023.3:c.2303C>T	p.Thr768Ile	p.T768I	ENST00000375023	NM_004557.3	768	aCt/aTt	14/30	1	2	FACETS	0.465	0.419	0.513	0.465	0.419	0.513	SUBCLONAL	1	TRUE	1	0.725855040511343	2		578	670	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0028914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	167	489	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.228289738624072	4	FACETS	0.779	0.716	0.844	0.779	0.716	0.844	SUBCLONAL	2	TRUE	2	0.345059004995117	4		489	836	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0028914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	183	614	0	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	0.228289738624072	4	FACETS	0.784	0.724	0.847	0.784	0.724	0.847	SUBCLONAL	2	TRUE	2	0.345059004995117	4		614	910	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718995	190718995	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	71	201	0	ENST00000441310.2:c.997A>T	p.Met333Leu	p.M333L	ENST00000441310	NM_000534.4	333	Atg/Ttg	9/13	0.265005781689029	3	FACETS	0.802	0.706	0.903	0.802	0.706	0.903	CLONAL	2	TRUE	1	0.345059004995117	3		201	301	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739096	40739096	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	129	458	0	ENST00000373198.4:c.3188T>A	p.Leu1063His	p.L1063H	ENST00000373198	NM_133170.3	1063	cTc/cAc	24/32	0.254680650183242	2	FACETS	1	0.985	1	0.715	0.651	0.781	CLONAL	1	TRUE	0	0.345059004995117	2		458	523	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8111076	8111076	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	69	527	0	ENST00000585124.1:c.131G>T	p.Arg44Leu	p.R44L	ENST00000585124	NM_004217.3	44	cGc/cTc	3/9	1	2	FACETS	0.854	0.745	0.971	0.854	0.745	0.971	CLONAL	1	TRUE	1	0.318676008194484	2		527	507	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927385	178927385	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	76	212	0	ENST00000263967.3:c.1148G>A	p.Trp383Ter	p.W383*	ENST00000263967	NM_006218.2	383	tGg/tAg	7/21	1	2	FACETS	1	0.896	1	1	0.984	1	CLONAL	2	TRUE	1	0.318676008194484	2		212	237	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788617	3788617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519884	NA	P-0028916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	25	397	1	ENST00000262367.5:c.4337G>A	p.Arg1446His	p.R1446H	ENST00000262367	NM_004380.2	1446	cGc/cAc	26/31	0.214601997781721	2	FACETS	0.368	0.288	0.459	0.184	0.144	0.23	SUBCLONAL	1	TRUE	0	0.225223182244809	2		398	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0028916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	162	598	1	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	1	2	FACETS	0.856	0.786	0.929	1	0.99	1	CLONAL	2	TRUE	1	0.225223182244809	2		599	840	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484596	57484596	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913494	NA	P-0028916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	135	391	0	ENST00000371085.3:c.680A>T	p.Gln227Leu	p.Q227L	ENST00000371085	NM_000516.4	227	cAg/cTg	9/13	1	2	FACETS	0.932	0.85	1	1	0.99	1	CLONAL	2	TRUE	1	0.225223182244809	2		391	643	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514515	41514515	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	45	496	0	ENST00000373198.4:c.146C>A	p.Thr49Asn	p.T49N	ENST00000373198	NM_133170.3	49	aCc/aAc	2/32	1	2	FACETS	0.585	0.491	0.69	0.585	0.491	0.69	SUBCLONAL	1	TRUE	1	0.225223182244809	2		496	683	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65323428	65323428	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	89	450	0	ENST00000342505.4:c.1369G>T	p.Gly457Ter	p.G457*	ENST00000342505	NM_002227.2	457	Gga/Tga	10/25	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.225223182244809	2		450	572	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495050	56495050	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758743468	NA	P-0028916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	92	527	0	ENST00000267101.3:c.3407G>A	p.Arg1136His	p.R1136H	ENST00000267101	NM_001982.3	1136	cGc/cAc	27/28	0.0291549127289636	3	FACETS	1	0.968	1	0.624	0.555	0.699	INDETERMINATE	1	TRUE	1	0.225223182244809	3		527	728	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864591	57864592	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0028916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	106	718	1	ENST00000228682.2:c.2068_2069delinsAT	p.Pro690Ile	p.P690I	ENST00000228682	NM_005269.2	690	CCc/ATc	12/12	0.0291549127289636	3	FACETS	1	0.976	1	0.653	0.585	0.725	INDETERMINATE	1	TRUE	1	0.225223182244809	3		719	802	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220433	1220433	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	92	621	0	ENST00000326873.7:c.526G>T	p.Asp176Tyr	p.D176Y	ENST00000326873	NM_000455.4	176	Gac/Tac	4/10	0.225223182244809	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.225223182244809	1		621	697	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342995	225342995	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	146	501	0	ENST00000264414.4:c.2097A>T	p.Arg699Ser	p.R699S	ENST00000264414	NM_003590.4	699	agA/agT	15/16	0.178086369274824	2	FACETS	0.988	0.905	1	0.988	0.905	1	CLONAL	2	TRUE	0	0.225223182244809	2		501	656	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509368	149509368	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	80	465	0	ENST00000261799.4:c.1531C>A	p.Arg511Ser	p.R511S	ENST00000261799	NM_002609.3	511	Cgc/Agc	10/23	0.178086369274824	2	FACETS	1	0.968	1	0.646	0.569	0.728	CLONAL	1	TRUE	0	0.225223182244809	2		465	550	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200032	123200032	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	21	236	0	ENST00000218089.9:c.2104G>T	p.Asp702Tyr	p.D702Y	ENST00000218089	NM_001042749.1	702	Gac/Tac	22/35	1	2	FACETS	0.876	0.677	1	0.876	0.677	1	CLONAL	1	TRUE	1	0.225223182244809	2		236	213	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275431	115275431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	23	310	0	ENST00000438362.2:c.982C>T	p.Pro328Ser	p.P328S	ENST00000438362	NM_001242891.1	328	Cca/Tca	10/20	1	2	FACETS	0.608	0.474	0.763	0.608	0.474	0.763	SUBCLONAL	1	TRUE	1	0.225223182244809	2		310	336	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458017	120458017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	92	425	0	ENST00000256646.2:c.7328C>T	p.Pro2443Leu	p.P2443L	ENST00000256646	NM_024408.3	2443	cCt/cTt	34/34	1	2	FACETS	0.795	0.708	0.886	1	0.982	1	SUBCLONAL	2	TRUE	1	0.225223182244809	2		425	514	SUCCESS
EED	8726	MSKCC	GRCh37	11	85968579	85968579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	24	282	0	ENST00000263360.6:c.575C>T	p.Ala192Val	p.A192V	ENST00000263360	NM_003797.3	192	gCt/gTt	6/12	1	2	FACETS	0.623	0.489	0.778	0.623	0.489	0.778	SUBCLONAL	1	TRUE	1	0.225223182244809	2		282	342	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975467	26975467	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	70	399	0	ENST00000381527.3:c.1093G>T	p.Asp365Tyr	p.D365Y	ENST00000381527	NM_001260.1	365	Gat/Tat	11/13	0.225223182244809	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.225223182244809	1		399	404	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66521938	66521938	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	33	327	1	ENST00000358598.2:c.593G>A	p.Gly198Glu	p.G198E	ENST00000358598	NM_212471.2	198	gGg/gAg	7/11	1	2	FACETS	0.713	0.581	0.862	0.713	0.581	0.862	SUBCLONAL	1	TRUE	1	0.225223182244809	2		328	411	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353804	15353804	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	27	439	0	ENST00000263377.2:c.3076del	p.Gln1026SerfsTer42	p.Q1026Sfs*42	ENST00000263377	NM_058243.2	1026	Cag/ag	14/20	0.225223182244809	1	FACETS	0.451	0.358	0.557	0.451	0.358	0.557	SUBCLONAL	1	TRUE	0	0.225223182244809	1		439	472	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954587	17954587	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs761583890	NA	P-0028916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	111	621	2	ENST00000458235.1:c.307C>A	p.Arg103Ser	p.R103S	ENST00000458235	NM_000215.3	103	Cgc/Agc	3/24	0.225223182244809	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.225223182244809	1		623	733	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940476	29940476	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs868525145	NA	P-0028916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	35	405	1	ENST00000389048.3:c.755C>A	p.Ser252Tyr	p.S252Y	ENST00000389048	NM_004304.4	252	tCc/tAc	2/29	1	2	FACETS	0.724	0.594	0.871	0.724	0.594	0.871	SUBCLONAL	1	TRUE	1	0.225223182244809	2		406	429	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271241	153271242	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0028916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	19	267	0	ENST00000281708.4:c.536_537delinsTT	p.Arg179Leu	p.R179L	ENST00000281708	NM_033632.3	179	cGC/cTT	3/12	1	2	FACETS	0.521	0.395	0.669	0.521	0.395	0.669	SUBCLONAL	1	TRUE	1	0.225223182244809	2		267	324	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913079	32913080	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs397507731	NA	P-0028918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	179	522	1	ENST00000380152.3:c.4593dup	p.Val1532SerfsTer2	p.V1532Sfs*2	ENST00000380152		1529	-/A	11/27	0.178481607238406	5	FACETS	0.964	0.89	1	0.643	0.593	0.694	INDETERMINATE	2	TRUE	2	0.360806991388826	5		523	793	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619446	1619446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs549395259	NA	P-0028918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	128	512	0	ENST00000344749.5:c.1195G>A	p.Glu399Lys	p.E399K	ENST00000344749	NM_001136139.2	399	Gag/Aag	15/19	1	2	FACETS	0.951	0.863	1	0.951	0.863	1	CLONAL	1	TRUE	1	0.360806991388826	2		512	746	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213923	2213923	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766949790	NA	P-0028918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	289	591	0	ENST00000398665.3:c.1735C>T	p.Arg579Trp	p.R579W	ENST00000398665	NM_032482.2	579	Cgg/Tgg	18/28	1	2	FACETS	0.967	0.913	1	1	0.995	1	CLONAL	2	TRUE	1	0.360806991388826	2		591	828	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271503	38271503	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	66	638	2	ENST00000425967.3:c.2318C>T	p.Ser773Leu	p.S773L	ENST00000425967	NM_001174067.1	773	tCa/tTa	18/19	0.265517378194386	5	FACETS	0.551	0.477	0.632	0.184	0.159	0.211	SUBCLONAL	1	TRUE	2	0.360806991388826	5		640	1023	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929041	44929041	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0028918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	224	498	0	ENST00000377967.4:c.2141T>G	p.Leu714Ter	p.L714*	ENST00000377967	NM_021140.2	714	tTa/tGa	17/29	0.360806991388826	2	FACETS	0.99	0.928	1	0.99	0.928	1	CLONAL	2	TRUE	0	0.360806991388826	2		498	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0028919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	94	740	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.628	0.558	0.702	0.628	0.558	0.702	SUBCLONAL	1	TRUE	1	0.363952778971197	2		741	823	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0028921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	289	657	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.936	0.884	0.988	0.936	0.884	0.988	CLONAL	1	TRUE	1	0.801227648912388	2		657	771	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101054	27101054	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	358	590	0	ENST00000324856.7:c.4336C>T	p.Arg1446Ter	p.R1446*	ENST00000324856	NM_006015.4	1446	Cga/Tga	18/20	0.801227648912388	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.801227648912388	1		590	482	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0028922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	46	354	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.18	2		354	493	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144731	58144731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	33	392	0	ENST00000257904.6:c.497G>A	p.Ser166Asn	p.S166N	ENST00000257904	NM_000075.3	166	aGc/aAc	4/8	1	2	FACETS	0.675	0.549	0.818	0.675	0.549	0.818	SUBCLONAL	1	TRUE	1	0.18	2		392	543	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061477	38061477	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	24	386	0	ENST00000250448.2:c.512C>G	p.Pro171Arg	p.P171R	ENST00000250448	NM_004496.3	171	cCg/cGg	2/2	1	2	FACETS	0.581	0.454	0.727	0.581	0.454	0.727	SUBCLONAL	1	TRUE	1	0.18	2		386	459	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063694	67063702	+	inframe_deletion	In_Frame_Del	DEL	GCCGCGACG	GCCGCGACG	-	novel	NA	P-0028922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	25	290	0	ENST00000412916.2:c.148_156del	p.Asp50_Arg52del	p.D50_R52del	ENST00000412916		48	tGCCGCGACGgc/tgc	2/6	1	2	FACETS	0.755	0.595	0.939	0.755	0.595	0.939	CLONAL	1	TRUE	1	0.18	2		290	368	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916923	178916923	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	48	534	0	ENST00000263967.3:c.310C>A	p.Pro104Thr	p.P104T	ENST00000263967	NM_006218.2	104	Cca/Aca	2/21	1	2	FACETS	0.749	0.632	0.879	0.749	0.632	0.879	SUBCLONAL	1	TRUE	1	0.18	2		534	712	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0028923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	63	504	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.27	2		504	340	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0028923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	59	498	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.304631846835723	3	FACETS	0.976	0.841	1	0.488	0.42	0.562	CLONAL	1	TRUE	1	0.27	3		498	508	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106608	27106609	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	72	565	0	ENST00000324856.7:c.6220dup	p.Ser2074PhefsTer25	p.S2074Ffs*25	ENST00000324856	NM_006015.4	2073	-/T	20/20	0.266508499062707	3	FACETS	0.992	0.875	1	0.992	0.875	1	CLONAL	2	TRUE	1	0.27	3		565	305	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825539	50825539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762650238	NA	P-0028923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	59	486	0	ENST00000398568.2:c.2170G>A	p.Val724Ile	p.V724I	ENST00000398568	NM_001042412.1	724	Gtt/Att	14/18	1	2	FACETS	0.967	0.834	1	0.967	0.834	1	CLONAL	1	TRUE	1	0.27	2		486	452	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974715	21974732	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCCCCCGCCTCCA	GCAGCGCCCCCGCCTCCA	-	novel	NA	P-0028923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	33	343	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	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.27	2		343	187	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105682	27105682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1164908440	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	132	288	0	ENST00000324856.7:c.5293G>A	p.Glu1765Lys	p.E1765K	ENST00000324856	NM_006015.4	1765	Gaa/Aaa	20/20	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.861302993357944	2		288	296	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107096	27107096	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	196	376	0	ENST00000324856.7:c.6707G>C	p.Arg2236Pro	p.R2236P	ENST00000324856	NM_006015.4	2236	cGc/cCc	20/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.861302993357944	2		376	426	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107130	27107130	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	171	410	0	ENST00000324856.7:c.6742del	p.His2248ThrfsTer19	p.H2248Tfs*19	ENST00000324856	NM_006015.4	2247	aaC/aa	20/20	1	2	FACETS	0.89	0.827	0.954	0.89	0.827	0.954	CLONAL	1	TRUE	1	0.861302993357944	2		410	446	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107183	27107183	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	32	418	0	ENST00000324856.7:c.6794C>A	p.Pro2265Gln	p.P2265Q	ENST00000324856	NM_006015.4	2265	cCg/cAg	20/20	1	2	FACETS	0.162	0.131	0.197	0.162	0.131	0.197	SUBCLONAL	1	TRUE	1	0.861302993357944	2		418	458	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624286	89624336	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTCGACTTAGACTTGACCTGTATCCATTTCTGCGGCTGCTCCTCTTTACC	ATTCGACTTAGACTTGACCTGTATCCATTTCTGCGGCTGCTCCTCTTTACC	-	novel	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	32	326	0	ENST00000371953.3:c.60_79+31del		p.X20_splice	ENST00000371953	NM_000314.4	20		1/9	0.861302993357944	3	FACETS	0.256	0.208	0.311	0.128	0.104	0.156	SUBCLONAL	1	TRUE	1	0.861302993357944	3		326	415	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	260	407	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.861302993357944	3	FACETS	0.97	0.924	1	0.97	0.924	1	CLONAL	2	TRUE	1	0.861302993357944	3		407	445	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	204	443	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	0.861302993357944	3	FACETS	1	0.963	1	0.525	0.489	0.561	CLONAL	1	TRUE	1	0.861302993357944	3		443	646	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135700	64135700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	57	464	0	ENST00000334205.4:c.1168C>T	p.Arg390Trp	p.R390W	ENST00000334205	NM_003942.2	390	Cgg/Tgg	10/17	1	2	FACETS	0.216	0.185	0.25	0.216	0.185	0.25	SUBCLONAL	1	TRUE	1	0.861302993357944	2		464	613	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	402	634	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.891	0.864	0.916	1	0.997	1	CLONAL	2	TRUE	1	0.861302993357944	2		637	524	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416644	416644	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	29	249	0	ENST00000399788.2:c.3906del	p.Ala1303GlnfsTer23	p.A1303Qfs*23	ENST00000399788	NM_001042603.1	1302	aaA/aa	23/28	0.861302993357944	3	FACETS	0.26	0.208	0.318	0.13	0.104	0.159	SUBCLONAL	1	TRUE	1	0.861302993357944	3		249	371	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	150	441	9	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	0.861302993357944	3	FACETS	0.975	0.897	1	0.488	0.448	0.528	CLONAL	1	TRUE	1	0.861302993357944	3		450	511	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025866	1025866	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	197	394	0	ENST00000358495.3:c.664G>A	p.Val222Met	p.V222M	ENST00000358495	NM_134424.2	222	Gtg/Atg	8/12	0.861302993357944	3	FACETS	1	0.949	1	0.512	0.476	0.549	CLONAL	1	TRUE	1	0.861302993357944	3		394	639	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	292	681	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.861302993357944	3	FACETS	1	0.977	1	0.533	0.503	0.564	CLONAL	1	TRUE	1	0.861302993357944	3		681	910	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440064	49440064	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	143	538	0	ENST00000301067.7:c.4562T>C	p.Ile1521Thr	p.I1521T	ENST00000301067	NM_003482.3	1521	aTc/aCc	16/54	0.861302993357944	3	FACETS	0.564	0.514	0.616	0.282	0.257	0.308	SUBCLONAL	1	TRUE	1	0.861302993357944	3		538	843	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495414	56495414	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758455948	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	214	494	0	ENST00000267101.3:c.3604C>T	p.Arg1202Trp	p.R1202W	ENST00000267101	NM_001982.3	1202	Cgg/Tgg	28/28	0.861302993357944	3	FACETS	0.985	0.919	1	0.492	0.459	0.526	CLONAL	1	TRUE	1	0.861302993357944	3		494	722	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246549	105246549	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	8	385	0	ENST00000349310.3:c.51G>T	p.Glu17Asp	p.E17D	ENST00000349310	NM_001014432.1	17	gaG/gaT	4/15	1	2	FACETS	0.047	0.03	0.069	0.047	0.03	0.069	SUBCLONAL	1	TRUE	1	0.861302993357944	2		385	396	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614463	38614463	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	18	352	1	ENST00000299084.4:c.234del	p.Asp79ThrfsTer42	p.D79Tfs*42	ENST00000299084	NM_152594.2	77	Aaa/aa	3/7	1	2	FACETS	0.225	0.17	0.289	0.225	0.17	0.289	SUBCLONAL	1	TRUE	1	0.861302993357944	2		353	186	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040903	42040903	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	185	442	0	ENST00000219905.7:c.5281C>T	p.Arg1761Ter	p.R1761*	ENST00000219905	NM_001164273.1	1761	Cga/Tga	16/24	1	2	FACETS	0.974	0.91	1	0.974	0.91	1	CLONAL	1	TRUE	1	0.861302993357944	2		442	441	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654664	67654664	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	213	405	0	ENST00000264010.4:c.1151G>A	p.Cys384Tyr	p.C384Y	ENST00000264010	NM_006565.3	384	tGc/tAc	6/12	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.861302993357944	2		405	470	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662450	67662450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	206	478	0	ENST00000264010.4:c.1696C>T	p.Arg566Cys	p.R566C	ENST00000264010	NM_006565.3	566	Cgt/Tgt	9/12	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.861302993357944	2		478	471	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853324	68853324	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	28	382	0	ENST00000261769.5:c.1707C>G	p.Asp569Glu	p.D569E	ENST00000261769	NM_004360.3	569	gaC/gaG	11/16	1	2	FACETS	0.15	0.119	0.185	0.15	0.119	0.185	SUBCLONAL	1	TRUE	1	0.861302993357944	2		382	433	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341532	89341532	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	173	398	0	ENST00000301030.4:c.7538del	p.Gly2513GlufsTer14	p.G2513Efs*14	ENST00000301030	NM_001256183.1	2513	gGa/ga	10/13	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.861302993357944	2		398	397	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627575	37627575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	158	503	0	ENST00000447079.4:c.1490C>T	p.Ala497Val	p.A497V	ENST00000447079	NM_015083.1	497	gCa/gTa	2/14	1	2	FACETS	0.986	0.916	1	0.986	0.916	1	CLONAL	1	TRUE	1	0.861302993357944	2		503	372	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63545705	63545705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751143605	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	204	397	1	ENST00000307078.5:c.889G>A	p.Ala297Thr	p.A297T	ENST00000307078	NM_004655.3	297	Gcc/Acc	3/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.861302993357944	2		398	450	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619323	1619323	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761667569	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	250	431	3	ENST00000344749.5:c.1318G>A	p.Ala440Thr	p.A440T	ENST00000344749	NM_001136139.2	440	Gca/Aca	15/19	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.861302993357944	2		434	494	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272114	15272114	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199995195	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	212	417	0	ENST00000263388.2:c.6325C>T	p.Arg2109Trp	p.R2109W	ENST00000263388	NM_000435.2	2109	Cgg/Tgg	33/33	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.861302993357944	2		417	487	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469629	25469629	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750837407	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	198	390	1	ENST00000264709.3:c.1139C>T	p.Ala380Val	p.A380V	ENST00000264709	NM_175629.2	380	gCg/gTg	10/23	1	2	FACETS	0.962	0.9	1	0.962	0.9	1	CLONAL	1	TRUE	1	0.861302993357944	2		391	478	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458638	12458640	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	novel	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	102	291	0	ENST00000287820.6:c.1258_1260del	p.Ile420del	p.I420del	ENST00000287820	NM_015869.4	419	ATT/-	6/7	0.861302993357944	3	FACETS	0.795	0.716	0.879	0.398	0.358	0.44	SUBCLONAL	1	TRUE	1	0.861302993357944	3		291	426	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	127	343	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.861302993357944	3	FACETS	0.988	0.903	1	0.494	0.451	0.538	CLONAL	1	TRUE	1	0.861302993357944	3		343	427	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437206	52437206	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35448940	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	252	455	2	ENST00000460680.1:c.1838C>T	p.Thr613Met	p.T613M	ENST00000460680	NM_004656.3	613	aCg/aTg	14/17	0.861302993357944	3	FACETS	1	0.971	1	0.529	0.496	0.562	CLONAL	1	TRUE	1	0.861302993357944	3		457	792	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202726	128202726	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	45	540	0	ENST00000341105.2:c.994C>T	p.Leu332Phe	p.L332F	ENST00000341105	NM_032638.4	332	Ctc/Ttc	4/6	0.861302993357944	3	FACETS	0.17	0.142	0.201	0.085	0.071	0.101	SUBCLONAL	1	TRUE	1	0.861302993357944	3		540	878	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	57	421	0	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	0.861302993357944	3	FACETS	0.842	0.731	0.959	0.421	0.365	0.48	CLONAL	1	TRUE	1	0.861302993357944	3		421	225	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913283	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	195	280	0	ENST00000263967.3:c.3129G>T	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atT	21/21	0.861302993357944	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.861302993357944	3		280	315	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803192	1803192	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	31	573	1	ENST00000260795.2:c.544C>A	p.Pro182Thr	p.P182T	ENST00000260795		182	Ccc/Acc	4/17	1	2	FACETS	0.129	0.103	0.157	0.129	0.103	0.157	SUBCLONAL	1	TRUE	1	0.861302993357944	2		574	560	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806180	1806181	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760502257	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	221	572	5	ENST00000260795.2:c.1206dup	p.Lys403GlnfsTer93	p.K403Qfs*93	ENST00000260795		400	agc/agCc	8/17	1	2	FACETS	0.804	0.753	0.857	0.804	0.753	0.857	CLONAL	1	TRUE	1	0.861302993357944	2		577	638	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007332	143007332	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	110	383	4	ENST00000262992.4:c.2452del	p.Arg818GlufsTer4	p.R818Efs*4	ENST00000262992	NM_001101669.1	818	Aga/ga	22/24	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.861302993357944	2		387	251	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526366	31526366	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	299	730	0	ENST00000344624.3:c.674T>C	p.Leu225Pro	p.L225P	ENST00000344624		225	cTg/cCg	2/33	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.861302993357944	2		730	684	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32189003	32189003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751063545	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	38	543	1	ENST00000375023.3:c.551C>T	p.Pro184Leu	p.P184L	ENST00000375023	NM_004557.3	184	cCg/cTg	4/30	0.861302993357944	3	FACETS	0.175	0.144	0.21	0.088	0.072	0.105	SUBCLONAL	1	TRUE	1	0.861302993357944	3		544	720	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288900	33288900	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	164	332	0	ENST00000374542.5:c.652C>A	p.Pro218Thr	p.P218T	ENST00000374542	NM_001141970.1	218	Cca/Aca	3/8	0.861302993357944	3	FACETS	1	0.985	1	0.626	0.581	0.673	CLONAL	1	TRUE	1	0.861302993357944	3		332	435	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199945	138199945	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	72	363	1	ENST00000237289.4:c.1368del	p.Pro457LeufsTer20	p.P457Lfs*20	ENST00000237289	NM_001270507.1	455	Ggg/gg	7/9	0.861302993357944	3	FACETS	0.512	0.449	0.58	0.256	0.224	0.29	SUBCLONAL	1	TRUE	1	0.861302993357944	3		364	467	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740564	145740564	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	265	535	0	ENST00000428558.2:c.1453C>T	p.Gln485Ter	p.Q485*	ENST00000428558	NM_004260.3	485	Cag/Tag	8/22	0.861302993357944	3	FACETS	1	0.945	1	0.503	0.473	0.534	CLONAL	1	TRUE	1	0.861302993357944	3		535	875	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073707	8073726	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGAGGCCTGTCTTCATCA	TGGGAGGCCTGTCTTCATCA	C	novel	NA	P-0028924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	127	277	0	ENST00000377482.5:c.933_952delinsG	p.Ser311ArgfsTer135	p.S311Rfs*135	ENST00000377482	NM_018948.3	311	agTGATGAAGACAGGCCTCCCAaa/agGaa	4/4	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.861302993357944	2		277	293	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0028926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	260	483	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.450466283691152	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.450466283691152	2		483	491	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0028926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	56	427	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.450466283691152	1	FACETS	0.461	0.396	0.532	0.461	0.396	0.532	SUBCLONAL	1	TRUE	0	0.450466283691152	1		427	418	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016647	12016648	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0028926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	72	338	0	ENST00000353533.5:c.783_784del	p.Asp263CysfsTer4	p.D263Cfs*4	ENST00000353533	NM_003010.3	261	acAAga/acga	7/11	0.450466283691152	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.450466283691152	1		338	238	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106081	8106083	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	novel	NA	P-0028926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	36	477	0	ENST00000346208.3:c.902_904del	p.Ile301del	p.I301del	ENST00000346208		301	ATT/-	4/6	0.450466283691152	2	FACETS	0.266	0.217	0.32	0.133	0.108	0.16	SUBCLONAL	1	TRUE	0	0.450466283691152	2		477	602	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215674280	215674280	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782499	NA	P-0028926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	97	483	0	ENST00000260947.4:c.14G>A	p.Arg5Gln	p.R5Q	ENST00000260947	NM_000465.2	5	cGg/cAg	1/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.450466283691152	2		483	388	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061209	38061209	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	107	442	1	ENST00000250448.2:c.780G>C	p.Leu260Phe	p.L260F	ENST00000250448	NM_004496.3	260	ttG/ttC	2/2	1	2	FACETS	0.875	0.788	0.967	0.875	0.788	0.967	CLONAL	1	TRUE	1	0.453803684177319	2		443	539	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0028927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	242	437	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.84	0.79	0.891	1	0.994	1	CLONAL	2	TRUE	1	0.453803684177319	2		437	635	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578400	7578400	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	177	547	0	ENST00000269305.4:c.530C>A	p.Pro177His	p.P177H	ENST00000269305	NM_001126112.2	177	cCc/cAc	5/11	0.453803684177319	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.453803684177319	1		547	556	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553594	29553594	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1336584572	NA	P-0028927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	77	247	0	ENST00000356175.3:c.2143G>T	p.Glu715Ter	p.E715*	ENST00000356175	NM_000267.3	715	Gag/Tag	18/57	0.453803684177319	1	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	0	0.453803684177319	1		247	260	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0028928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	648	440	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.695417786309	4	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	1	0.694734234012951	4		440	959	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258694	16258694	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	245	502	1	ENST00000375759.3:c.5959C>T	p.Gln1987Ter	p.Q1987*	ENST00000375759	NM_015001.2	1987	Cag/Tag	11/15	1	2	FACETS	0.947	0.889	1	0.947	0.889	1	CLONAL	1	TRUE	1	0.694734234012951	2		503	745	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057924	27057925	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0028928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	252	491	0	ENST00000324856.7:c.1635_1636del	p.Gln546GlufsTer76	p.Q546Efs*76	ENST00000324856	NM_006015.4	544	caCCcc/cacc	3/20	1	2	FACETS	0.918	0.862	0.976	0.918	0.862	0.976	CLONAL	1	TRUE	1	0.694734234012951	2		491	790	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	169	404	0				ENST00000310581	NM_198253.2	-/1132			0.239527998426322	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.931149747808071	0		404	318	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0028929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	198	440	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	1	0.931149747808071	2		440	423	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0028929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	272	276	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.832	0.803	0.86	1	0.996	1	CLONAL	2	FALSE	1	0.931149747808071	2		276	351	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729094	66729099	+	inframe_deletion	In_Frame_Del	DEL	TGGAGA	TGGAGA	-	novel	NA	P-0028929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	323	450	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	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.931149747808071	2		450	690	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169166	119169166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140725852	NA	P-0028929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	214	410	0	ENST00000264033.4:c.2350G>A	p.Val784Met	p.V784M	ENST00000264033	NM_005188.3	784	Gtg/Atg	15/16	1	2	FACETS	0.997	0.938	1	0.997	0.938	1	CLONAL	1	FALSE	1	0.931149747808071	2		410	461	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557393	95557393	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	213	387	0	ENST00000393063.1:c.5581G>T	p.Glu1861Ter	p.E1861*	ENST00000393063	NM_030621.3	1861	Gaa/Taa	27/28	0.154468208351905	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.931149747808071	0		387	499	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457653	67457653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs973219546	NA	P-0028929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	395	540	0	ENST00000327367.4:c.463G>A	p.Asp155Asn	p.D155N	ENST00000327367	NM_005902.3	155	Gac/Aac	3/9	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	1	0.931149747808071	2		540	755	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221280	36221280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555731980	NA	P-0028929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	321	599	1	ENST00000222270.7:c.5114G>A	p.Arg1705Gln	p.R1705Q	ENST00000222270	NM_014727.1	1705	cGa/cAa	24/37	0.214797020436272	3	FACETS	0.967	0.914	1	0.322	0.304	0.341	INDETERMINATE	1	FALSE	0	0.931149747808071	3		600	1045	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526692	106526692	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	200	358	0	ENST00000359195.3:c.2985G>T	p.Met995Ile	p.M995I	ENST00000359195	NM_002649.2	995	atG/atT	10/11	1	2	FACETS	0.976	0.916	1	0.976	0.916	1	CLONAL	1	FALSE	1	0.931149747808071	2		358	440	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411438	63411438	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	248	605	0	ENST00000330258.3:c.1729C>T	p.Gln577Ter	p.Q577*	ENST00000330258	NM_152424.3	577	Cag/Tag	2/2	0.597337622647421	1	FACETS	0.683	0.649	0.715	0.683	0.649	0.715	SUBCLONAL	1	FALSE	0	0.931149747808071	1		605	417	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0028930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	152	532	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.360795214217457	4	FACETS	0.984	0.905	1			1	CLONAL	2	TRUE	NA	0.385753224383267	4		532	555	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020768	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs926053251	NA	P-0028930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	37	443	0	ENST00000358127.4:c.77T>G	p.Val26Gly	p.V26G	ENST00000358127	NM_001280556.1	26	gTt/gGt	2/10	0.385753224383267	1	FACETS	0.33	0.272	0.395	0.33	0.272	0.395	SUBCLONAL	1	TRUE	0	0.385753224383267	1		443	469	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986588	36986601	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGCTGGCGGCGT	GGGGCTGGCGGCGT	-	novel	NA	P-0028930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	32	414	0	ENST00000354822.5:c.1088_1101del	p.His363ArgfsTer71	p.H363Rfs*71	ENST00000354822	NM_001079668.2	363	cACGCCGCCAGCCCC/c	3/3	1	2	FACETS	0.448	0.364	0.543	0.448	0.364	0.543	SUBCLONAL	1	TRUE	1	0.385753224383267	2		414	370	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986697	36986710	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGCCGCCTGCGC	GCCGCCGCCTGCGC	-	novel	NA	P-0028930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	12	25	0	ENST00000354822.5:c.979_992del	p.Ala327SerfsTer107	p.A327Sfs*107	ENST00000354822	NM_001079668.2	327	GCGCAGGCGGCGGCa/a	3/3	1	2	FACETS	0.943	0.676	1	0.943	0.676	1	CLONAL	1	TRUE	1	0.385753224383267	2		25	66	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678332	88678332	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	46	485	0	ENST00000360948.2:c.1204G>A	p.Glu402Lys	p.E402K	ENST00000360948	NM_001012338.2	402	Gag/Aag	9/19	0.328737205922664	3	FACETS	0.524	0.441	0.616	0.262	0.22	0.308	SUBCLONAL	1	TRUE	1	0.385753224383267	3		485	543	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943809	9943809	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	24	307	0	ENST00000330684.3:c.1132T>A	p.Trp378Arg	p.W378R	ENST00000330684	NM_001134407.1	378	Tgg/Agg	5/13	1	2	FACETS	0.358	0.28	0.447	0.358	0.28	0.447	SUBCLONAL	1	TRUE	1	0.385753224383267	2		307	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578412	7578414	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0028930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	88	542	0	ENST00000269305.4:c.516_518del	p.Val173del	p.V173del	ENST00000269305	NM_001126112.2	172	gtTGTg/gtg	5/11	0.368109596020322	1	FACETS	0.711	0.632	0.795	0.711	0.632	0.795	SUBCLONAL	1	TRUE	0	0.385753224383267	1		542	518	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134193	11134193	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1060502102	NA	P-0028930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	83	357	0	ENST00000358026.2:c.2860-1G>A		p.X954_splice	ENST00000358026	NM_001128849.1	954			0.368109596020322	1	FACETS	0.957	0.851	1	0.957	0.851	1	CLONAL	1	TRUE	0	0.385753224383267	1		357	363	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5534886	5534886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1420582774	NA	P-0028930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	83	485	0	ENST00000397747.3:c.197C>T	p.Thr66Ile	p.T66I	ENST00000397747	NM_025239.3	66	aCa/aTa	3/7	NA	2	FACETS	0.925	0.82	1			1	INDETERMINATE	1	TRUE	NA	0.385753224383267	2		485	465	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0028931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	89	354	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.369235225068075	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.369235225068075	1		354	332	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0028931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	136	691	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	0.201049690316932	2	FACETS	1	0.981	1	0.641	0.585	0.699	INDETERMINATE	1	TRUE	0	0.369235225068075	2		691	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577525	7577527	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0028931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	27	524	0	ENST00000269305.4:c.754_756del	p.Leu252del	p.L252del	ENST00000269305	NM_001126112.2	252	CTC/-	7/11	0.201049690316932	2	FACETS	0.275	0.218	0.34	0.137	0.109	0.17	INDETERMINATE	1	TRUE	0	0.369235225068075	2		524	532	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206908	102206909	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0028931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	86	320	0	ENST00000263464.3:c.1540_1541del	p.Leu514AlafsTer4	p.L514Afs*4	ENST00000263464	NM_001165.4	512	aaCTct/aact	7/9	0.2671144749012	4	FACETS	1	0.967	1	0.622	0.551	0.696	CLONAL	1	TRUE	2	0.369235225068075	4		320	513	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129647	11129647	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	122	491	0	ENST00000358026.2:c.2453G>A	p.Trp818Ter	p.W818*	ENST00000358026	NM_001128849.1	818	tGg/tAg	17/36	0.298336511236469	2	FACETS	1	0.984	1	0.703	0.639	0.769	CLONAL	1	TRUE	0	0.369235225068075	2		491	470	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264788	46264788	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	54	411	0	ENST00000371998.3:c.1658A>G	p.Asn553Ser	p.N553S	ENST00000371998		553	aAt/aGt	12/23	0.325122482112213	4	FACETS	0.614	0.524	0.713	0.307	0.262	0.357	SUBCLONAL	1	TRUE	2	0.369235225068075	4		411	652	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	218484	218484	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	48	176	0	ENST00000264932.6:c.14G>C	p.Arg5Pro	p.R5P	ENST00000264932	NM_004168.2	5	cGg/cCg	1/15	0.212082774019475	2	FACETS	1	0.946	1	0.619	0.529	0.715	INDETERMINATE	1	TRUE	0	0.369235225068075	2		176	210	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132738	152132738	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	20	295	0	ENST00000262189.6:c.134C>T	p.Ala45Val	p.A45V	ENST00000262189	NM_170606.2	45	gCt/gTt	1/59	0.201049690316932	2	FACETS	0.403	0.308	0.513	0.201	0.154	0.257	INDETERMINATE	1	TRUE	0	0.369235225068075	2		295	269	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508727	148508727	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	151	368	2	ENST00000320356.2:c.1937A>G	p.Tyr646Cys	p.Y646C	ENST00000320356	NM_004456.4	646	tAc/tGc	16/20	0.45025715685693	1	FACETS	0.341	0.313	0.37	0.341	0.313	0.37	INDETERMINATE	1	TRUE	0	0.890763702254777	1		370	551	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911607	114911607	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	208	540	0	ENST00000543371.1:c.1125A>T	p.Lys375Asn	p.K375N	ENST00000543371	NM_001198531.1	375	aaA/aaT	10/14	0.241546638810013	1	FACETS	0.301	0.279	0.323	0.301	0.279	0.323	INDETERMINATE	1	TRUE	0	0.890763702254777	1		540	861	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172260	38172260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	278	387	0	ENST00000317025.8:c.2147C>T	p.Pro716Leu	p.P716L	ENST00000317025	NM_023034.1	716	cCt/cTt	12/24	0.890763702254777	1	FACETS	0.978	0.945	1	0.978	0.945	1	CLONAL	1	TRUE	0	0.890763702254777	1		387	354	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0028934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	52	440	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.756	0.644	0.88	0.756	0.644	0.88	SUBCLONAL	1	TRUE	1	0.24	2		440	573	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464577	25464577	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0028934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	72	516	0	ENST00000264709.3:c.1937-1G>C		p.X646_splice	ENST00000264709	NM_175629.2	646			1	2	FACETS	0.935	0.817	1	0.935	0.817	1	CLONAL	1	TRUE	1	0.24	2		516	642	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0028935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	198	498	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.308199982513302	5	FACETS	0.958	0.89	1	0.638	0.593	0.685	CLONAL	2	TRUE	2	0.499610692206446	5		498	724	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0028935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	247	466	1	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.340391382098823	2	FACETS	1	0.993	1	0.737	0.693	0.782	CLONAL	1	TRUE	0	0.499610692206446	2		467	671	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804988	43804988	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	101	368	3	ENST00000372470.3:c.438G>T	p.Gln146His	p.Q146H	ENST00000372470	NM_005373.2	146	caG/caT	4/12	1	2	FACETS	0.797	0.716	0.884	0.797	0.716	0.884	SUBCLONAL	1	TRUE	1	0.499610692206446	2		371	507	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046637	30046637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771109503	NA	P-0028935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	78	398	0	ENST00000331968.5:c.2546G>A	p.Arg849Gln	p.R849Q	ENST00000331968	NM_002742.2	849	cGa/cAa	18/18	1	2	FACETS	0.563	0.495	0.635	0.563	0.495	0.635	SUBCLONAL	1	TRUE	1	0.499610692206446	2		398	555	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660837	227660837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200073898	NA	P-0028935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	105	411	0	ENST00000305123.5:c.2618G>A	p.Arg873Gln	p.R873Q	ENST00000305123	NM_005544.2	873	cGg/cAg	1/2	0.33667571374834	3	FACETS	0.861	0.773	0.954	0.431	0.386	0.477	CLONAL	1	TRUE	1	0.499610692206446	3		411	610	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265789	41266324	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTA	CAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTA	-	novel	NA	P-0028935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	48	39	0	ENST00000349496.5:c.13+217_241+80del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.389813179587809	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.499610692206446	2		39	79	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0028936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	48	516	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.676	0.57	0.792	0.676	0.57	0.792	SUBCLONAL	1	TRUE	1	0.206838080989866	2		516	687	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17117129	17117129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777826268	NA	P-0028936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	48	459	1	ENST00000285071.4:c.1580G>A	p.Arg527Gln	p.R527Q	ENST00000285071	NM_144997.5	527	cGa/cAa	14/14	1	2	FACETS	0.737	0.622	0.864	0.737	0.622	0.864	SUBCLONAL	1	TRUE	1	0.206838080989866	2		460	630	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045473	47045476	+	frameshift_variant	Frame_Shift_Del	DEL	TACC	TACC	-	novel	NA	P-0028936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	71	472	0	ENST00000377604.3:c.2440_2443del	p.Tyr814GlyfsTer32	p.Y814Gfs*32	ENST00000377604	NM_001204468.1	814	TACCgg/gg	22/24	1	2	FACETS	0.988	0.862	1	0.988	0.862	1	CLONAL	1	TRUE	1	0.206838080989866	2		472	695	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0028937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	61	402	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	0.424	0.365	0.489	0.424	0.365	0.489	SUBCLONAL	1	TRUE	1	0.325322734299599	2		402	884	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167577	NA	P-0028937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	27	277	0	ENST00000257430.4:c.4463del	p.Leu1488TyrfsTer19	p.L1488Yfs*19	ENST00000257430	NM_000038.5	1487	acT/ac	16/16	1	2	FACETS	0.351	0.278	0.434	0.351	0.278	0.434	SUBCLONAL	1	TRUE	1	0.325322734299599	2		277	473	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0028937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	40	347	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.399	0.331	0.476	0.399	0.331	0.476	SUBCLONAL	1	TRUE	1	0.325322734299599	2		347	616	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859478	57859478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	56	510	0	ENST00000228682.2:c.623A>C	p.Gln208Pro	p.Q208P	ENST00000228682	NM_005269.2	208	cAg/cCg	6/12	1	2	FACETS	0.425	0.363	0.493	0.425	0.363	0.493	SUBCLONAL	1	TRUE	1	0.325322734299599	2		510	810	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140758	55140758	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	61	468	0	ENST00000257290.5:c.1619T>A	p.Ile540Asn	p.I540N	ENST00000257290	NM_006206.4	540	aTc/aAc	11/23	NA	2	FACETS	0.415	0.357	0.479			1	INDETERMINATE	1	TRUE	NA	0.325322734299599	2		468	903	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0028938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	198	516	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.407574217327901	5	FACETS	1	0.978	1	0.288	0.266	0.311	CLONAL	1	FALSE	1	0.407574217327901	5		516	1359	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0028938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	273	591	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.255479840833559	2	FACETS	0.788	0.742	0.835	0.788	0.742	0.835	SUBCLONAL	2	FALSE	0	0.407574217327901	2		592	850	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0028939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	252	725	1	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.53186047607696	2	FACETS	1	0.992	1	1	0.996	1	CLONAL	3	TRUE	0	0.53186047607696	2		726	294	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246518365	246518365	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	245	442	0	ENST00000388985.4:c.196C>G	p.Arg66Gly	p.R66G	ENST00000388985		66	Cgc/Ggc	2/12	0.53186047607696	5	FACETS	1	0.981	1	1	0.994	1	CLONAL	5	TRUE	1	0.53186047607696	5		442	321	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103471	77103471	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	83	318	0	ENST00000356341.3:c.95G>T	p.Gly32Val	p.G32V	ENST00000356341	NM_002576.4	32	gGa/gTa	2/15	0.53186047607696	3	FACETS	1	0.977	1	0.703	0.628	0.781	CLONAL	1	TRUE	1	0.53186047607696	3		318	281	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577591	7577591	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	167	580	0	ENST00000269305.4:c.690del	p.Thr231ProfsTer16	p.T231Pfs*16	ENST00000269305	NM_001126112.2	230	acC/ac	7/11	1	2	FACETS	0.88	0.809	0.954	1	0.991	1	CLONAL	2	TRUE	1	0.22	2		580	863	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057520007	NA	P-0028940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	76	719	0	ENST00000269305.4:c.614A>C	p.Tyr205Ser	p.Y205S	ENST00000269305	NM_001126112.2	205	tAt/tCt	6/11	1	2	FACETS	0.634	0.554	0.72	0.634	0.554	0.72	SUBCLONAL	1	TRUE	1	0.22	2		719	1090	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106915	27106915	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	151	411	0	ENST00000324856.7:c.6526C>T	p.Gln2176Ter	p.Q2176*	ENST00000324856	NM_006015.4	2176	Cag/Tag	20/20	0.176286304443287	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.22	2		411	599	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17355219	17355219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121917755	NA	P-0028940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	44	426	0	ENST00000375499.3:c.299C>T	p.Ser100Phe	p.S100F	ENST00000375499	NM_003000.2	100	tCt/tTt	4/8	0.176286304443287	2	FACETS	0.538	0.45	0.636	0.269	0.225	0.318	SUBCLONAL	1	TRUE	0	0.22	2		426	744	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63661961	63661961	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	121	390	0	ENST00000279873.7:c.65A>T	p.Tyr22Phe	p.Y22F	ENST00000279873	NM_032199.2	22	tAc/tTc	2/10	1	2	FACETS	0.849	0.768	0.933	1	0.987	1	CLONAL	2	TRUE	1	0.22	2		390	648	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518211	103518211	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	25	310	0	ENST00000355739.4:c.2149G>T	p.Ala717Ser	p.A717S	ENST00000355739	NM_000123.3	717	Gct/Tct	9/15	1	2	FACETS	0.467	0.367	0.582	0.467	0.367	0.582	SUBCLONAL	1	TRUE	1	0.22	2		310	487	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438216	110438216	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	84	172	1	ENST00000375856.3:c.185C>A	p.Ala62Glu	p.A62E	ENST00000375856	NM_003749.2	62	gCg/gAg	1/2	1	2	FACETS	1	0.889	1	1	0.985	1	CLONAL	2	TRUE	1	0.22	2		173	382	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724513	43724513	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	248	907	0	ENST00000382044.4:c.3554A>G	p.Gln1185Arg	p.Q1185R	ENST00000382044	NM_001141980.1	1185	cAg/cGg	17/28	0.302201563533368	1	FACETS	0.853	0.797	0.911	1	0.994	1	CLONAL	2	TRUE	0	0.22	1		907	1176	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858447	9858447	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	93	470	0	ENST00000330684.3:c.2954C>A	p.Pro985His	p.P985H	ENST00000330684	NM_001134407.1	985	cCt/cAt	13/13	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.22	2		470	710	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644758	67644758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	159	526	0	ENST00000264010.4:c.24del	p.Ile9LeufsTer53	p.I9Lfs*53	ENST00000264010	NM_006565.3	8	gCc/gc	3/12	1	2	FACETS	0.821	0.753	0.893	1	0.99	1	CLONAL	2	TRUE	1	0.22	2		526	880	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835795	68835798	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	AGGT	AGGT	-	novel	NA	P-0028940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	43	499	0	ENST00000261769.5:c.387_387+3del		p.X129_splice	ENST00000261769	NM_004360.3	129		3/16	1	2	FACETS	0.504	0.42	0.597	0.504	0.42	0.597	SUBCLONAL	1	TRUE	1	0.22	2		499	776	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131409	17131409	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	151	605	1	ENST00000285071.4:c.43G>T	p.Gly15Cys	p.G15C	ENST00000285071	NM_144997.5	15	Ggc/Tgc	4/14	1	2	FACETS	0.767	0.701	0.836	1	0.988	1	SUBCLONAL	2	TRUE	1	0.22	2		606	895	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119695	70119695	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	60	741	0	ENST00000245479.2:c.697G>T	p.Gly233Cys	p.G233C	ENST00000245479	NM_000346.3	233	Ggc/Tgc	3/3	1	2	FACETS	0.488	0.419	0.564	0.488	0.419	0.564	SUBCLONAL	1	TRUE	1	0.22	2		741	1117	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295800	212295800	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	95	487	0	ENST00000342788.4:c.2513G>T	p.Arg838Leu	p.R838L	ENST00000342788	NM_005235.2	838	cGa/cTa	21/28	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.22	2		487	820	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661111	227661111	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	134	640	0	ENST00000305123.5:c.2344G>T	p.Glu782Ter	p.E782*	ENST00000305123	NM_005544.2	782	Gag/Tag	1/2	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.22	2		640	974	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36022674	36022674	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	79	551	0	ENST00000358208.4:c.547A>T	p.Thr183Ser	p.T183S	ENST00000358208		183	Acg/Tcg	5/12	1	2	FACETS	0.718	0.63	0.814	0.718	0.63	0.814	SUBCLONAL	1	TRUE	1	0.22	2		551	1000	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827904	40827904	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	144	528	0	ENST00000373198.4:c.2524A>C	p.Ser842Arg	p.S842R	ENST00000373198	NM_133170.3	842	Agt/Cgt	17/32	1	2	FACETS	0.779	0.711	0.851	1	0.988	1	SUBCLONAL	2	TRUE	1	0.22	2		528	840	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230906	66230906	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	20	275	0	ENST00000273854.3:c.2065G>T	p.Val689Phe	p.V689F	ENST00000273854	NM_004439.5	689	Gtt/Ttt	12/18	0.208288650647922	1	FACETS	0.442	0.337	0.565	0.442	0.337	0.565	SUBCLONAL	1	TRUE	0	0.22	1		275	366	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524759	187524759	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	104	597	1	ENST00000441802.2:c.10921C>A	p.His3641Asn	p.H3641N	ENST00000441802	NM_005245.3	3641	Cac/Aac	19/27	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.22	2		598	807	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554975	187554975	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	34	231	0	ENST00000441802.2:c.4186G>A	p.Gly1396Ser	p.G1396S	ENST00000441802	NM_005245.3	1396	Ggc/Agc	7/27	1	2	FACETS	0.849	0.695	1	0.849	0.695	1	CLONAL	1	TRUE	1	0.22	2		231	364	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946192	13946192	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	46	490	2	ENST00000405192.2:c.904G>T	p.Glu302Ter	p.E302*	ENST00000405192	NM_001163147.1	302	Gaa/Taa	10/12	0.193771634330689	3	FACETS	0.52	0.437	0.614	0.173	0.145	0.205	SUBCLONAL	1	TRUE	0	0.22	3		492	892	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528699	8528699	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	73	350	1	ENST00000356435.5:c.433A>T	p.Met145Leu	p.M145L	ENST00000356435		145	Atg/Ttg	4/35	0.302201563533368	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.22	1		351	491	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635161	87635161	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	101	402	0	ENST00000277120.3:c.2213C>T	p.Pro738Leu	p.P738L	ENST00000277120		738	cCa/cTa	18/19	0.302201563533368	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.22	1		402	589	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019994	123019994	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	113	365	0	ENST00000355640.3:c.482A>G	p.Tyr161Cys	p.Y161C	ENST00000355640		161	tAt/tGt	2/7	0.222235069610616	2	FACETS	0.819	0.739	0.904			1	CLONAL	2	TRUE	NA	0.22	2		365	627	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0028941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	418	498	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	0.42375104143019	NA		498	1005	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577599	7577600	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1567550002	NA	P-0028941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	223	474	0	ENST00000269305.4:c.681dup	p.Asp228Ter	p.D228*	ENST00000269305	NM_001126112.2	227	-/T	7/11	0.42375104143019	2	FACETS	0.881	0.826	0.937	0.881	0.826	0.937	CLONAL	2	TRUE	0	0.42375104143019	2		474	597	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699294	117699294	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767710032	NA	P-0028941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	40	354	0	ENST00000369458.3:c.347G>A	p.Arg116Gln	p.R116Q	ENST00000369458	NM_024626.3	116	cGg/cAg	3/6	0.23692136100204	4	FACETS	0.339	0.28	0.404			1	INDETERMINATE	1	TRUE	NA	0.42375104143019	4		354	794	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946161	71946161	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs1222699348	NA	P-0028942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	61	602	0	ENST00000298229.2:c.2417T>G	p.Leu806Arg	p.L806R	ENST00000298229	NM_001567.3	806	cTc/cGc	22/28	0.232056042302056	1	FACETS	0.801	0.691	0.921	0.801	0.691	0.921	CLONAL	1	TRUE	0	0.22	1		602	616	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719877	52719877	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	59	618	0	ENST00000322088.6:c.1089G>T	p.Glu363Asp	p.E363D	ENST00000322088	NM_014225.5	363	gaG/gaT	9/15	1	2	FACETS	0.709	0.608	0.818	0.709	0.608	0.818	SUBCLONAL	1	TRUE	1	0.22	2		618	757	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255980	16255980	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0028943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	165	592	0	ENST00000375759.3:c.3245C>G	p.Ser1082Ter	p.S1082*	ENST00000375759	NM_015001.2	1082	tCa/tGa	11/15	0.200670392877315	3	FACETS	0.619	0.568	0.671	0.206	0.189	0.224	INDETERMINATE	1	TRUE	0	0.914486117392965	3		592	850	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577528	7577529	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATGGGCCTCCGGTTC	novel	NA	P-0028943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	348	707	0	ENST00000269305.4:c.738_752dup	p.Met246_Pro250dup	p.M246_P250dup	ENST00000269305	NM_001126112.2	246	atc/atGAACCGGAGGCCCATc	7/11	0.851540485515838	1	FACETS	0.705	0.676	0.734	0.705	0.676	0.734	SUBCLONAL	1	TRUE	0	0.914486117392965	1		707	586	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913178	39913178	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	138	451	0	ENST00000378444.4:c.4937T>C	p.Leu1646Pro	p.L1646P	ENST00000378444	NM_001123385.1	1646	cTc/cCc	14/15	NA	2	FACETS	0.551	0.503	0.6			1	INDETERMINATE	1	TRUE	NA	0.914486117392965	2		451	548	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0028944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	308	532	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.615522630027573	3	FACETS	0.935	0.888	0.982	0.935	0.888	0.982	CLONAL	2	TRUE	1	0.615522630027573	3		532	700	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945129	32945129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80359104	NA	P-0028944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	129	399	0	ENST00000380152.3:c.8524C>T	p.Arg2842Cys	p.R2842C	ENST00000380152		2842	Cgc/Tgc	20/27	0.615522630027573	3	FACETS	0.838	0.762	0.918	0.419	0.381	0.459	CLONAL	1	TRUE	1	0.615522630027573	3		399	654	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739594	41739594	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	390	370	0	ENST00000242208.4:c.379G>T	p.Ala127Ser	p.A127S	ENST00000242208	NM_002192.2	127	Gcc/Tcc	2/3	0.576985531510128	5	FACETS	0.905	0.864	0.946	0.905	0.864	0.946	CLONAL	3	TRUE	2	0.615522630027573	5		370	898	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101631	27101631	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	267	763	0	ENST00000324856.7:c.4913del	p.Asp1638ValfsTer16	p.D1638Vfs*16	ENST00000324856	NM_006015.4	1638	gAt/gt	18/20	1	2	FACETS	0.978	0.919	1	0.978	0.919	1	CLONAL	1	TRUE	1	0.615522630027573	2		763	887	SUCCESS
RET	5979	MSKCC	GRCh37	10	43602018	43602018	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0028944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	192	598	0	ENST00000355710.3:c.1062T>A	p.Tyr354Ter	p.Y354*	ENST00000355710	NM_020975.4	354	taT/taA	5/20	0.576943415220691	5	FACETS	0.866	0.799	0.937			1	CLONAL	1	TRUE	NA	0.615522630027573	5		598	1385	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205835	108205835	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	267	370	0	ENST00000278616.4:c.8150A>C	p.Lys2717Thr	p.K2717T	ENST00000278616	NM_000051.3	2717	aAg/aCg	55/63	0.615522630027573	2	FACETS	0.921	0.877	0.965	0.921	0.877	0.965	CLONAL	2	TRUE	0	0.615522630027573	2		370	471	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263869	133263870	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0028944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	142	355	0	ENST00000320574.5:c.32_33del	p.Ala11GlyfsTer12	p.A11Gfs*12	ENST00000320574	NM_006231.2	11	gCG/g	1/49	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.615522630027573	NA		355	547	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609706	81609706	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	474	423	0	ENST00000298171.2:c.1304T>C	p.Val435Ala	p.V435A	ENST00000298171	NM_000369.2	435	gTc/gCc	10/10	0.593749994350337	4	FACETS	0.939	0.904	0.974	0.939	0.904	0.974	CLONAL	3	TRUE	1	0.615522630027573	4		423	883	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867572	78867572	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	246	600	0	ENST00000306801.3:c.2308G>T	p.Gly770Cys	p.G770C	ENST00000306801	NM_020761.2	770	Ggc/Tgc	20/34	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.615522630027573	2		600	745	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221298	1221308	+	frameshift_variant	Frame_Shift_Del	DEL	TCCCGGGCGAC	TCCCGGGCGAC	-	novel	NA	P-0028944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	610	614	0	ENST00000326873.7:c.822_832del	p.Ile274MetfsTer7	p.I274Mfs*7	ENST00000326873	NM_000455.4	274	aTCCCGGGCGAC/a	6/10	0.608468749524001	3	FACETS	0.944	0.918	0.971	0.944	0.918	0.971	CLONAL	3	TRUE	0	0.615522630027573	3		614	915	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390204	89390204	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	222	321	0	ENST00000336596.2:c.953C>A	p.Pro318Gln	p.P318Q	ENST00000336596	NM_005233.5	318	cCa/cAa	4/17	0.59343701249511	4	FACETS	0.962	0.901	1	0.962	0.901	1	CLONAL	2	TRUE	2	0.615522630027573	4		321	606	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540161	187540161	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	169	466	1	ENST00000441802.2:c.7579G>C	p.Val2527Leu	p.V2527L	ENST00000441802	NM_005245.3	2527	Gtt/Ctt	10/27	NA	2	FACETS	0.968	0.896	1			1	INDETERMINATE	1	TRUE	NA	0.615522630027573	2		467	567	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589225	67589225	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	277	373	0	ENST00000274335.5:c.1213A>G	p.Ile405Val	p.I405V	ENST00000274335		405	Ata/Gta	9/15	0.615522630027573	3	FACETS	0.983	0.931	1	0.983	0.931	1	CLONAL	2	TRUE	1	0.615522630027573	3		373	599	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346551	81346551	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	214	310	2	ENST00000222390.5:c.1402C>A	p.Arg468Ser	p.R468S	ENST00000222390	NM_000601.4	468	Cgt/Agt	11/18	0.615522630027573	3	FACETS	0.871	0.817	0.926	0.871	0.817	0.926	CLONAL	2	TRUE	1	0.615522630027573	3		312	522	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730915	40730915	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	AG	novel	NA	P-0028944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	248	487	0	ENST00000373198.4:c.3620delinsCT	p.Arg1207ProfsTer17	p.R1207Pfs*17	ENST00000373198	NM_133170.3	1207	cGt/cCTt	27/32	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.615522630027573	2		487	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0028946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	496	737	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	NA	2	FACETS	0.987	0.952	1			1	INDETERMINATE	2	TRUE	NA	0.583636663780533	2		737	861	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855917	76855962	+	frameshift_variant	Frame_Shift_Del	DEL	TAATGTAGTCTAGCTGCAAACACCAAGGATGAGTCCATATTCTACT	TAATGTAGTCTAGCTGCAAACACCAAGGATGAGTCCATATTCTACT	-	novel	NA	P-0028946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	134	471	0	ENST00000373344.5:c.5638_5683del	p.Ser1880AlafsTer17	p.S1880Afs*17	ENST00000373344	NM_000489.3	1880	AGTAGAATATGGACTCATCCTTGGTGTTTGCAGCTAGACTACATTAgc/gc	23/35	0.583636663780533	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.583636663780533	1		471	298	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	118	739	0	ENST00000397752.3:c.3028G>C	p.Asp1010His	p.D1010H	ENST00000397752	NM_000245.2	1010	Gat/Cat	14/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.25	2		739	825	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745529	162745529	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	26	491	0	ENST00000367921.3:c.1944C>A	p.Asp648Glu	p.D648E	ENST00000367921	NM_006182.2	648	gaC/gaA	15/18	1	2	FACETS	0.449	0.355	0.558	0.449	0.355	0.558	SUBCLONAL	1	TRUE	1	0.25	2		491	463	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340276	116340276	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	33	306	0	ENST00000397752.3:c.1142del	p.Asn381ThrfsTer3	p.N381Tfs*3	ENST00000397752	NM_000245.2	380	Aaa/aa	2/21	1	2	FACETS	0.657	0.535	0.794	0.657	0.535	0.794	SUBCLONAL	1	TRUE	1	0.25	2		306	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0028949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	393	906	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.413793029301832	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.413793029301832	2		906	872	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0028949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	207	256	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	0.413793029301832	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.413793029301832	2		256	454	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143128	30143128	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768229646	NA	P-0028949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	155	666	1	ENST00000389048.3:c.398G>A	p.Arg133His	p.R133H	ENST00000389048	NM_004304.4	133	cGc/cAc	1/29	0.403473317961258	3	FACETS	0.84	0.768	0.916	0.42	0.384	0.458	CLONAL	1	TRUE	1	0.413793029301832	3		667	1076	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878455	151878455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	204	663	0	ENST00000262189.6:c.6490G>A	p.Gly2164Arg	p.G2164R	ENST00000262189	NM_170606.2	2164	Gga/Aga	36/59	0.380964966946713	4	FACETS	1	0.961	1	0.529	0.489	0.571	CLONAL	1	TRUE	2	0.413793029301832	4		663	1317	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24133941	24133941	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0028950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	246	265	0	ENST00000263121.7:c.94-2A>T		p.X32_splice	ENST00000263121	NM_003073.3	32			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		265	449	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0028951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	121	532	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.175461002299838	4	FACETS	1	0.971	1	0.791	0.716	0.87	CLONAL	2	TRUE	1	0.175461002299838	4		532	683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0028951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	76	720	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.175461002299838	2		721	718	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974696	21974696	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	38	450	0	ENST00000304494.5:c.131del	p.Tyr44SerfsTer9	p.Y44Sfs*9	ENST00000304494	NM_000077.4	44	tAc/tc	1/3	0.175461002299838	1	FACETS	0.88	0.728	1	0.88	0.728	1	CLONAL	1	TRUE	0	0.175461002299838	1		450	449	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225362481	225362481	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	46	377	0	ENST00000264414.4:c.1696C>A	p.Pro566Thr	p.P566T	ENST00000264414	NM_003590.4	566	Cca/Aca	12/16	1	2	FACETS	0.941	0.792	1	0.941	0.792	1	CLONAL	1	TRUE	1	0.175461002299838	2		377	557	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	62	404	0				ENST00000310581	NM_198253.2	-/1132			0.31768868229709	1	FACETS	0.764	0.669	0.863	1	0.974	1	SUBCLONAL	2	FALSE	0	0.31768868229709	1		404	215	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0028953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	130	631	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.882	0.806	0.961	1	0.989	1	CLONAL	2	FALSE	1	0.31768868229709	2		632	464	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39321525	39321525	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	123	512	0	ENST00000373001.3:c.496A>G	p.Lys166Glu	p.K166E	ENST00000373001	NM_022157.3	166	Aaa/Gaa	3/7	1	2	FACETS	0.864	0.787	0.944	1	0.988	1	CLONAL	2	FALSE	1	0.31768868229709	2		512	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578444	+	missense_variant	Missense_Mutation	DNP	AG	AG	TA	novel	NA	P-0028953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	41	715	0	ENST00000269305.4:c.486_487delinsTA	p.Tyr163Asn	p.Y163N	ENST00000269305	NM_001126112.2	162	atCTac/atTAac	5/11	1	2	FACETS	0.564	0.469	0.668	0.564	0.469	0.668	SUBCLONAL	1	FALSE	1	0.31768868229709	2		715	458	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0028958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	92	301	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	0.448068084622663	1	FACETS	0.871	0.78	0.966	0.871	0.78	0.966	CLONAL	1	TRUE	0	0.448068084622663	1		301	366	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242484	+	inframe_deletion	In_Frame_Del	DEL	AATTAAGAGAAGCAACAT	AATTAAGAGAAGCAACAT	-	rs121913422	NA	P-0028958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	93	484	0	ENST00000275493.2:c.2237_2254del	p.Glu746_Ser752delinsAla	p.E746_S752delinsA	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATct/gct	19/28	0.448068084622663	3	FACETS	0.63	0.559	0.705	0.315	0.279	0.353	SUBCLONAL	1	TRUE	1	0.448068084622663	3		484	807	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0028960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	10	228	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.469	0.317	0.662	0.469	0.317	0.662	SUBCLONAL	1	TRUE	1	0.151639211993915	2		228	281	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0028960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	66	631	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.821	0.714	0.937	1	0.975	1	CLONAL	2	TRUE	1	0.151639211993915	2		632	530	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192065	108192065	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1317619286	NA	P-0028960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	14	417	0	ENST00000278616.4:c.6490G>C	p.Glu2164Gln	p.E2164Q	ENST00000278616	NM_000051.3	2164	Gag/Cag	45/63	1	2	FACETS	0.365	0.262	0.49	0.365	0.262	0.49	SUBCLONAL	1	TRUE	1	0.151639211993915	2		417	506	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681461	30681461	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	33	424	0	ENST00000376406.3:c.551C>T	p.Ser184Leu	p.S184L	ENST00000376406	NM_014641.2	184	tCa/tTa	4/15	1	2	FACETS	0.812	0.66	0.984	0.812	0.66	0.984	CLONAL	1	TRUE	1	0.151639211993915	2		424	536	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228252	53228252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	39	596	1	ENST00000375401.3:c.2150C>T	p.Ser717Leu	p.S717L	ENST00000375401	NM_004187.3	717	tCa/tTa	15/26	0.151639211993915	1	FACETS	0.715	0.591	0.854	0.715	0.591	0.854	SUBCLONAL	1	TRUE	0	0.151639211993915	1		597	665	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720732	89720732	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	10	148	0	ENST00000371953.3:c.883del	p.Leu295TyrfsTer12	p.L295Yfs*12	ENST00000371953	NM_000314.4	295	Cta/ta	8/9	0.151639211993915	2	FACETS	1	0.743	1	0.554	0.377	0.773	CLONAL	1	TRUE	0	0.151639211993915	2		148	119	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163315571	163315571	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	33	474	0	ENST00000271452.3:c.911C>T	p.Ser304Leu	p.S304L	ENST00000271452	NM_145697.2	304	tCa/tTa	11/14	0.151639211993915	3	FACETS	0.739	0.6	0.896	0.369	0.3	0.448	SUBCLONAL	1	TRUE	1	0.151639211993915	3		474	634	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716082	243716082	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0028960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	35	413	0	ENST00000263826.5:c.1112C>G	p.Ser371Ter	p.S371*	ENST00000263826	NM_005465.4	371	tCa/tGa	10/13	0.151639211993915	3	FACETS	0.724	0.592	0.873	0.362	0.296	0.437	SUBCLONAL	1	TRUE	1	0.151639211993915	3		413	686	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118875	115118876	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AATGTCC	novel	NA	P-0028960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	43	364	0	ENST00000257566.3:c.459_465dup	p.Ile156GlyfsTer6	p.I156Gfs*6	ENST00000257566	NM_016569.3	155	-/GGACATT	2/8	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.151639211993915	2		364	386	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936817	32936817	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397507395	NA	P-0028960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	24	336	0	ENST00000380152.3:c.7963C>T	p.Gln2655Ter	p.Q2655*	ENST00000380152		2655	Caa/Taa	17/27	1	2	FACETS	0.729	0.571	0.913	0.729	0.571	0.913	CLONAL	1	TRUE	1	0.151639211993915	2		336	434	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863692	68863698	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	ATTGATG	ATTGATG	-	novel	NA	P-0028960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	42	303	0	ENST00000261769.5:c.2432_2438del	p.Ile811LysfsTer3	p.I811Kfs*3	ENST00000261769	NM_004360.3	811	ATTGATGaa/aa	15/16	1	2	FACETS	0.829	0.695	0.977	1	0.963	1	CLONAL	2	TRUE	1	0.151639211993915	2		303	334	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71050209	71050209	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	22	225	0	ENST00000318789.4:c.976C>T	p.His326Tyr	p.H326Y	ENST00000318789	NM_032682.5	326	Cat/Tat	13/21	1	2	FACETS	1	0.782	1	1	0.782	1	CLONAL	1	TRUE	1	0.151639211993915	2		225	288	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951891	178951891	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	25	303	0	ENST00000263967.3:c.2946G>C	p.Glu982Asp	p.E982D	ENST00000263967	NM_006218.2	982	gaG/gaC	21/21	1	2	FACETS	0.802	0.632	0.999	0.802	0.632	0.999	CLONAL	1	TRUE	1	0.151639211993915	2		303	411	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557287	187557287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	60	485	0	ENST00000441802.2:c.4075G>A	p.Glu1359Lys	p.E1359K	ENST00000441802	NM_005245.3	1359	Gaa/Aaa	6/27	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.151639211993915	2		485	646	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0028966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	260	394	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.526776374868007	3	FACETS	1	0.986	1	0.751	0.71	0.791	CLONAL	2	TRUE	0	0.526652008953423	3		394	554	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs11575997	NA	P-0028966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	561	624	0	ENST00000269305.4:c.993+1G>T		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.486432348883088	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	0	0.526652008953423	3		624	889	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919665	96919665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200351681	NA	P-0028966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	266	372	0	ENST00000258439.3:c.598C>T	p.Pro200Ser	p.P200S	ENST00000258439	NM_001193304.2	200	Ccc/Tcc	4/4	0.417572833891316	4	FACETS	0.864	0.812	0.918	0.864	0.812	0.918	CLONAL	2	TRUE	2	0.526652008953423	4		372	892	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212252712	212252712	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	132	258	0	ENST00000342788.4:c.3141A>T	p.Glu1047Asp	p.E1047D	ENST00000342788	NM_005235.2	1047	gaA/gaT	26/28	0.493815288669791	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.526652008953423	2		258	238	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660741	227660741	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	224	615	0	ENST00000305123.5:c.2714A>T	p.Gln905Leu	p.Q905L	ENST00000305123	NM_005544.2	905	cAg/cTg	1/2	0.493815288669791	2	FACETS	0.908	0.846	0.972	0.454	0.423	0.486	CLONAL	1	TRUE	0	0.526652008953423	2		615	937	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149245658	149245658	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	507	713	0	ENST00000360632.3:c.870del	p.Ile291SerfsTer28	p.I291Sfs*28	ENST00000360632	NM_015472.4	290	tcC/tc	5/7	0.50953602893212	2	FACETS	0.966	0.93	1	0.966	0.93	1	CLONAL	2	TRUE	0	0.526652008953423	2		713	997	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151933020	151933020	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0028966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	84	108	0	ENST00000262189.6:c.2653-2A>T		p.X885_splice	ENST00000262189	NM_170606.2	885			0.417572833891316	4	FACETS	0.84	0.75	0.933	0.84	0.75	0.933	CLONAL	2	TRUE	2	0.526652008953423	4		108	290	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967752	90967752	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	56	195	0	ENST00000265433.3:c.1156G>A	p.Val386Ile	p.V386I	ENST00000265433	NM_002485.4	386	Gtc/Atc	10/16	0.443939317737351	4	FACETS	0.788	0.685	0.897	0.788	0.685	0.897	SUBCLONAL	2	TRUE	2	0.526652008953423	4		195	206	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518043	8518043	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	126	341	0	ENST00000356435.5:c.1348G>T	p.Gly450Ter	p.G450*	ENST00000356435		450	Gga/Tga	10/35	0.161537349558718	1	FACETS	0.693	0.63	0.757	0.693	0.63	0.757	INDETERMINATE	1	TRUE	0	0.526652008953423	1		341	509	SUCCESS
AR	367	MSKCC	GRCh37	X	66766352	66766352	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	46	114	0	ENST00000374690.3:c.1364G>C	p.Gly455Ala	p.G455A	ENST00000374690	NM_000044.3	455	gGt/gCt	1/8	0.158689684399071	0	FACETS	0.376	0.32	0.437			1	INDETERMINATE	1	TRUE	0	0.526652008953423	0		114	220	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	123	404	0				ENST00000310581	NM_198253.2	-/1132			0.138918016781569	4	FACETS	0.834	0.756	0.916	0.834	0.756	0.916	INDETERMINATE	2	TRUE	2	0.302342261372598	4		404	635	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0028969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	450	831	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	0.205526439701985	3	FACETS	0.887	0.847	0.927	0.887	0.847	0.927	CLONAL	3	TRUE	0	0.302342261372598	3		831	1288	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577555	7577556	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0028969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	149	668	2	ENST00000269305.4:c.725_726delinsTT	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGC/tTT	7/11	0.302342261372598	1	FACETS	0.997	0.911	1	0.997	0.911	1	CLONAL	1	TRUE	0	0.302342261372598	1		670	839	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148727	20148727	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0028969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	109	540	0	ENST00000379607.5:c.338-2A>T		p.X113_splice	ENST00000379607	NM_001412.3	113			1	2	FACETS	0.933	0.838	1	0.933	0.838	1	CLONAL	1	TRUE	1	0.302342261372598	2		540	773	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0028972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	227	747	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.456221566474453	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	0	0.456221566474453	1		750	611	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0028972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	90	631	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.202498492573995	3	FACETS	0.757	0.679	0.839	0.757	0.679	0.839	INDETERMINATE	2	FALSE	1	0.456221566474453	3		632	320	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0028972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	69	393	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.386350339363224	1	FACETS	0.797	0.701	0.899	0.797	0.701	0.899	SUBCLONAL	1	FALSE	0	0.456221566474453	1		393	293	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164928	47164928	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	38	237	1	ENST00000409792.3:c.1198C>T	p.Arg400Ter	p.R400*	ENST00000409792	NM_014159.6	400	Cga/Tga	3/21	0.217978636110321	1	FACETS	0.506	0.421	0.6	0.506	0.421	0.6	INDETERMINATE	1	FALSE	0	0.456221566474453	1		238	254	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829040	128829042	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	rs570242755	NA	P-0028972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	10	105	1	ENST00000249373.3:c.67_69del	p.Leu23del	p.L23del	ENST00000249373	NM_005631.4	16	ggGCTg/ggg	1/12	0.202498492573995	3	FACETS	0.544	0.371	0.756	0.272	0.185	0.378	INDETERMINATE	1	FALSE	1	0.456221566474453	3		106	99	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39251184	39251185	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	53	473	1	ENST00000402219.2:c.1168dup	p.Ile390AsnfsTer4	p.I390Nfs*4	ENST00000402219	NM_005633.3	390	ata/aAta	9/23	0.107620329325278	3	FACETS	0.681	0.582	0.789	0.227	0.194	0.263	INDETERMINATE	1	FALSE	0	0.456221566474453	3		474	419	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112910791	112910791	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	84	433	0	ENST00000351677.2:c.800A>T	p.Glu267Val	p.E267V	ENST00000351677	NM_002834.3	267	gAg/gTg	7/16	1	2	FACETS	0.909	0.808	1	0.909	0.808	1	CLONAL	1	FALSE	1	0.456221566474453	2		433	405	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576153	88576153	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140370971	NA	P-0028972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	120	542	0	ENST00000360948.2:c.1520G>A	p.Arg507His	p.R507H	ENST00000360948	NM_001012338.2	507	cGc/cAc	13/19	0.217978636110321	1	FACETS	0.675	0.611	0.741	0.675	0.611	0.741	INDETERMINATE	1	FALSE	0	0.456221566474453	1		542	602	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104637	69104637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746308010	NA	P-0028972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	100	506	2	ENST00000288368.4:c.4481G>A	p.Arg1494His	p.R1494H	ENST00000288368	NM_024870.2	1494	cGc/cAc	37/40	1	2	FACETS	0.686	0.614	0.763	0.686	0.614	0.763	SUBCLONAL	1	FALSE	1	0.456221566474453	2		508	639	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	100	404	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.837	0.755	0.924	0.837	0.755	0.924	CLONAL	1	TRUE	1	0.659685267302918	2		404	362	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781504	NA	P-0028976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	336	699	1	ENST00000269305.4:c.314G>A	p.Gly105Asp	p.G105D	ENST00000269305	NM_001126112.2	105	gGc/gAc	4/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.659685267302918	2		700	870	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577091	7577091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149633775	NA	P-0028976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	19	650	0	ENST00000269305.4:c.847C>T	p.Arg283Cys	p.R283C	ENST00000269305	NM_001126112.2	283	Cgc/Tgc	8/11	1	2	FACETS	0.067	0.05	0.087	0.067	0.05	0.087	SUBCLONAL	1	TRUE	1	0.659685267302918	2		650	858	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233037	55233037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1477025000	NA	P-0028976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5623	498	461	0	ENST00000275493.2:c.1787C>T	p.Pro596Leu	p.P596L	ENST00000275493	NM_005228.3	596	cCg/cTg	15/28	0.659685267302918	21	FACETS	0.896	0.851	0.943			1	CLONAL	2	TRUE	NA	0.659685267302918	21		461	6121	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578260	7578260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204041	NA	P-0028976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	300	600	1	ENST00000269305.4:c.589G>A	p.Val197Met	p.V197M	ENST00000269305	NM_001126112.2	197	Gtg/Atg	6/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.659685267302918	2		601	761	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683977	29683977	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0028976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	129	460	0	ENST00000356175.3:c.7676-1G>A		p.X2559_splice	ENST00000356175	NM_000267.3	2559			1	2	FACETS	0.534	0.484	0.585	0.534	0.484	0.585	SUBCLONAL	1	TRUE	1	0.659685267302918	2		460	733	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653860	89653860	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	250	449	0	ENST00000371953.3:c.158T>G	p.Val53Gly	p.V53G	ENST00000371953	NM_000314.4	53	gTa/gGa	2/9	0.659685267302918	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.659685267302918	1		449	411	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439570	51439570	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	196	318	0	ENST00000262662.1:c.135G>T	p.Met45Ile	p.M45I	ENST00000262662		45	atG/atT	4/4	0.360323804226406	3	FACETS	1	0.99	1	0.688	0.641	0.736	INDETERMINATE	1	TRUE	1	0.659685267302918	3		318	574	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409146	4409146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587777621	NA	P-0028976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	91	550	1	ENST00000261254.3:c.841C>T	p.Pro281Ser	p.P281S	ENST00000261254	NM_001759.3	281	Cct/Tct	5/5	1	2	FACETS	0.408	0.362	0.457	0.408	0.362	0.457	SUBCLONAL	1	TRUE	1	0.659685267302918	2		551	676	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490226	29490226	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs1057521097	NA	P-0028976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	80	318	0	ENST00000356175.3:c.311T>G	p.Leu104Ter	p.L104*	ENST00000356175	NM_000267.3	104	tTa/tGa	4/57	1	2	FACETS	0.418	0.368	0.472	0.418	0.368	0.472	SUBCLONAL	1	TRUE	1	0.659685267302918	2		318	580	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63531825	63531825	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	270	467	0	ENST00000307078.5:c.2156G>A	p.Ser719Asn	p.S719N	ENST00000307078	NM_004655.3	719	aGt/aAt	9/11	0.212483845761413	6	FACETS	0.99	0.93	1			1	INDETERMINATE	2	TRUE	NA	0.659685267302918	6		467	959	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106182964	106182964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	93	377	0	ENST00000380013.4:c.4003C>T	p.Pro1335Ser	p.P1335S	ENST00000380013	NM_001127208.2	1335	Cca/Tca	8/11	1	2	FACETS	0.386	0.343	0.432	0.386	0.343	0.432	SUBCLONAL	1	TRUE	1	0.659685267302918	2		377	730	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256768	19256769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1202792889	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	164	622	1	ENST00000162023.5:c.944dup	p.Val316SerfsTer6	p.V316Sfs*6	ENST00000162023		315	cca/ccCa	13/13	1	2	FACETS	0.704	0.647	0.762	0.704	0.647	0.762	SUBCLONAL	1	TRUE	1	0.636880224686339	2		623	732	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	227	768	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.826	0.771	0.883	0.826	0.771	0.883	CLONAL	1	TRUE	1	0.636880224686339	2		768	863	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007619	45007619	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs111482205	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	20	222	0	ENST00000558401.1:c.68-2A>G		p.X23_splice	ENST00000558401	NM_004048.2	23			0.636880224686339	1	FACETS	0.181	0.139	0.231	0.181	0.139	0.231	SUBCLONAL	1	TRUE	0	0.636880224686339	1		222	236	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	264	698	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.88	0.826	0.935	0.88	0.826	0.935	CLONAL	1	TRUE	1	0.636880224686339	2		704	942	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614463	38614463	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	222	352	1	ENST00000299084.4:c.234del	p.Asp79ThrfsTer42	p.D79Tfs*42	ENST00000299084	NM_152594.2	77	Aaa/aa	3/7	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.636880224686339	2		353	676	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	208	631	1	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	0.636880224686339	2		632	653	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2492096	2492097	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs772088410	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	254	638	1	ENST00000355716.4:c.500dup	p.Thr169AspfsTer65	p.T169Dfs*65	ENST00000355716	NM_003820.2	165	tgc/tgCc	5/8	1	2	FACETS	0.865	0.811	0.921	0.865	0.811	0.921	CLONAL	1	TRUE	1	0.636880224686339	2		639	922	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188177	11188177	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	49	456	0	ENST00000361445.4:c.5917A>G	p.Ile1973Val	p.I1973V	ENST00000361445	NM_004958.3	1973	Atc/Gtc	43/58	1	2	FACETS	0.243	0.205	0.284	0.243	0.205	0.284	SUBCLONAL	1	TRUE	1	0.636880224686339	2		456	634	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16247420	16247420	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs898876185	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	183	353	0	ENST00000375759.3:c.1691A>G	p.Tyr564Cys	p.Y564C	ENST00000375759	NM_015001.2	564	tAt/tGt	9/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.636880224686339	2		353	536	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366987	40366987	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	283	646	5	ENST00000397332.2:c.210del	p.Thr71ArgfsTer69	p.T71Rfs*69	ENST00000397332	NM_001033082.2	70	ccC/cc	2/3	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.636880224686339	2		651	827	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804952	43804953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	79	363	0	ENST00000372470.3:c.408dup	p.Ser137GlnfsTer27	p.S137Qfs*27	ENST00000372470	NM_005373.2	134	-/C	4/12	1	2	FACETS	0.636	0.563	0.714	0.636	0.563	0.714	SUBCLONAL	1	TRUE	1	0.636880224686339	2		363	390	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248118	59248120	+	inframe_deletion	In_Frame_Del	DEL	GCG	GCG	-	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	75	165	0	ENST00000371222.2:c.623_625del	p.Pro208del	p.P208del	ENST00000371222	NM_002228.3	208	cCGCac/cac	1/1	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.636880224686339	2		165	231	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464955	120464955	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	58	540	0	ENST00000256646.2:c.5117A>G	p.His1706Arg	p.H1706R	ENST00000256646	NM_024408.3	1706	cAt/cGt	28/34	1	2	FACETS	0.241	0.206	0.278	0.241	0.206	0.278	SUBCLONAL	1	TRUE	1	0.636880224686339	2		540	757	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880271	155880271	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	253	489	0	ENST00000368323.3:c.133C>T	p.Arg45Ter	p.R45*	ENST00000368323	NM_006912.5	45	Cga/Tga	3/6	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.636880224686339	2		489	752	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206667323	206667323	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs782670085	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	255	602	1	ENST00000367120.3:c.2116C>T	p.Arg706Trp	p.R706W	ENST00000367120	NM_014002.3	706	Cgg/Tgg	21/22	1	2	FACETS	0.975	0.916	1	0.975	0.916	1	CLONAL	1	TRUE	1	0.636880224686339	2		603	821	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226573330	226573330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781235145	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	180	512	1	ENST00000366794.5:c.886G>A	p.Glu296Lys	p.E296K	ENST00000366794	NM_001618.3	296	Gag/Aag	7/23	1	2	FACETS	0.768	0.71	0.828	0.768	0.71	0.828	SUBCLONAL	1	TRUE	1	0.636880224686339	2		513	736	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597885	43597885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1311922451	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	312	866	1	ENST00000355710.3:c.433G>A	p.Val145Ile	p.V145I	ENST00000355710	NM_020975.4	145	Gta/Ata	3/20	1	2	FACETS	0.938	0.886	0.992	0.938	0.886	0.992	CLONAL	1	TRUE	1	0.636880224686339	2		867	1044	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263973	104263974	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776579	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	65	220	0	ENST00000369902.3:c.71dup	p.Ala25GlyfsTer23	p.A25Gfs*23	ENST00000369902	NM_016169.3	22	gcc/gCcc	1/12	1	2	FACETS	0.63	0.55	0.715	0.63	0.55	0.715	SUBCLONAL	1	TRUE	1	0.636880224686339	2		220	324	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912739	100912739	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	210	496	1	ENST00000325455.5:c.2583del	p.Gly862GlufsTer31	p.G862Efs*31	ENST00000325455	NM_001202474.3	861	aaA/aa	7/8	1	2	FACETS	0.875	0.815	0.936	0.875	0.815	0.936	CLONAL	1	TRUE	1	0.636880224686339	2		497	754	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981613	101981614	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	56	145	0	ENST00000282441.5:c.40dup	p.Gln14ProfsTer98	p.Q14Pfs*98	ENST00000282441	NM_001130145.2	12	gcc/gCcc	1/9	1	2	FACETS	0.742	0.643	0.848	0.742	0.643	0.848	SUBCLONAL	1	TRUE	1	0.636880224686339	2		145	237	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150265	108150265	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	154	402	0	ENST00000278616.4:c.3332T>G	p.Leu1111Arg	p.L1111R	ENST00000278616	NM_000051.3	1111	cTt/cGt	23/63	1	2	FACETS	0.85	0.782	0.92	0.85	0.782	0.92	CLONAL	1	TRUE	1	0.636880224686339	2		402	569	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505403	125505404	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1565368022	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	184	345	0	ENST00000428830.2:c.700dup	p.Ile234AsnfsTer11	p.I234Nfs*11	ENST00000428830	NM_001114121.2	231	-/A	7/14	1	2	FACETS	0.911	0.845	0.979	0.911	0.845	0.979	CLONAL	1	TRUE	1	0.636880224686339	2		345	634	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438740	49438740	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	230	643	0	ENST00000301067.7:c.4750T>C	p.Tyr1584His	p.Y1584H	ENST00000301067	NM_003482.3	1584	Tac/Cac	19/54	1	2	FACETS	0.856	0.799	0.914	0.856	0.799	0.914	CLONAL	1	TRUE	1	0.636880224686339	2		643	844	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	208	810	1	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	1	2	FACETS	0.673	0.625	0.723	0.673	0.625	0.723	SUBCLONAL	1	TRUE	1	0.636880224686339	2		811	970	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856434	111856434	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs776317487	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	66	217	2	ENST00000341259.2:c.489del	p.Thr165ProfsTer32	p.T165Pfs*32	ENST00000341259	NM_005475.2	162	gCc/gc	2/8	1	2	FACETS	0.816	0.717	0.921	0.816	0.717	0.921	CLONAL	1	TRUE	1	0.636880224686339	2		219	254	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202765	133202765	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1172604164	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	55	627	0	ENST00000320574.5:c.6469A>G	p.Ile2157Val	p.I2157V	ENST00000320574	NM_006231.2	2157	Atc/Gtc	46/49	1	2	FACETS	0.229	0.195	0.267	0.229	0.195	0.267	SUBCLONAL	1	TRUE	1	0.636880224686339	2		627	753	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609744	28609744	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	314	641	0	ENST00000241453.7:c.1485G>T	p.Trp495Cys	p.W495C	ENST00000241453	NM_004119.2	495	tgG/tgT	12/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.636880224686339	2		641	949	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895700	28895700	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747063979	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	267	530	0	ENST00000282397.4:c.3074C>T	p.Ala1025Val	p.A1025V	ENST00000282397	NM_002019.4	1025	gCg/gTg	23/30	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.636880224686339	2		530	793	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281758	49281758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777488065	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	273	762	4	ENST00000282018.3:c.805G>A	p.Val269Ile	p.V269I	ENST00000282018	NM_020377.2	269	Gtc/Atc	1/1	1	2	FACETS	0.901	0.847	0.957	0.901	0.847	0.957	CLONAL	1	TRUE	1	0.636880224686339	2		766	951	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246445	105246445	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	188	662	0	ENST00000349310.3:c.155T>G	p.Leu52Arg	p.L52R	ENST00000349310	NM_001014432.1	52	cTc/cGc	4/15	1	2	FACETS	0.709	0.656	0.764	0.709	0.656	0.764	SUBCLONAL	1	TRUE	1	0.636880224686339	2		662	833	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	149	438	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	0.636880224686339	1	FACETS	0.776	0.716	0.837	0.776	0.716	0.837	SUBCLONAL	1	TRUE	0	0.636880224686339	1		438	411	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500333	99500333	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	119	678	0	ENST00000268035.6:c.3766A>G	p.Arg1256Gly	p.R1256G	ENST00000268035	NM_000875.3	1256	Agg/Ggg	21/21	1	2	FACETS	0.445	0.402	0.492	0.445	0.402	0.492	SUBCLONAL	1	TRUE	1	0.636880224686339	2		678	839	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126097	2126097	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	293	796	0	ENST00000219476.3:c.2668C>A	p.His890Asn	p.H890N	ENST00000219476	NM_000548.3	890	Cat/Aat	24/42	1	2	FACETS	0.948	0.893	1	0.948	0.893	1	CLONAL	1	TRUE	1	0.636880224686339	2		796	971	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134442	2134442	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45517332	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	341	797	1	ENST00000219476.3:c.4219G>A	p.Val1407Met	p.V1407M	ENST00000219476	NM_000548.3	1407	Gtg/Atg	34/42	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.636880224686339	2		798	946	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138239	2138239	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	237	768	0	ENST00000219476.3:c.5172G>T	p.Gln1724His	p.Q1724H	ENST00000219476	NM_000548.3	1724	caG/caT	41/42	1	2	FACETS	0.828	0.774	0.883	0.828	0.774	0.883	CLONAL	1	TRUE	1	0.636880224686339	2		768	899	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225116	2225116	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	322	776	0	ENST00000326181.6:c.1351A>G	p.Lys451Glu	p.K451E	ENST00000326181	NM_032271.2	451	Aaa/Gaa	15/21	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.636880224686339	2		776	997	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646980	23646981	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	291	654	1	ENST00000261584.4:c.886dup	p.Met296AsnfsTer7	p.M296Nfs*7	ENST00000261584	NM_024675.3	296	atg/aAtg	4/13	1	2	FACETS	0.872	0.821	0.924	0.872	0.821	0.924	CLONAL	1	TRUE	1	0.636880224686339	2		655	1048	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821959	72821960	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs762108866	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	97	326	5	ENST00000268489.5:c.10215dup	p.Gly3406ArgfsTer25	p.G3406Rfs*25	ENST00000268489	NM_006885.3	3405	-/C	10/10	1	2	FACETS	0.713	0.64	0.791	0.713	0.64	0.791	SUBCLONAL	1	TRUE	1	0.636880224686339	2		331	427	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439919	56439919	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	257	627	0	ENST00000407977.2:c.673del	p.Arg225AlafsTer194	p.R225Afs*194	ENST00000407977		225	Cgc/gc	6/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.636880224686339	2		627	756	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448297	56448298	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1567880599	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	212	655	2	ENST00000407977.2:c.349dup	p.Arg117ProfsTer8	p.R117Pfs*8	ENST00000407977		117	cgc/cCgc	3/10	1	2	FACETS	0.836	0.779	0.896	0.836	0.779	0.896	CLONAL	1	TRUE	1	0.636880224686339	2		657	796	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532465	63532465	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	279	685	0	ENST00000307078.5:c.2114C>T	p.Ala705Val	p.A705V	ENST00000307078	NM_004655.3	705	gCt/gTt	8/11	1	2	FACETS	0.989	0.931	1	0.989	0.931	1	CLONAL	1	TRUE	1	0.636880224686339	2		685	886	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	277	730	2	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.895	0.842	0.95	0.895	0.842	0.95	CLONAL	1	TRUE	1	0.636880224686339	2		732	972	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120376	70120377	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	384	920	0	ENST00000245479.2:c.1380dup	p.Gly461ArgfsTer117	p.G461Rfs*117	ENST00000245479	NM_000346.3	460	acc/aCcc	3/3	1	2	FACETS	0.95	0.902	0.998	0.95	0.902	0.998	CLONAL	1	TRUE	1	0.636880224686339	2		920	1270	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615697	1615698	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs757261438	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	229	772	2	ENST00000344749.5:c.1573dup	p.Arg525ProfsTer28	p.R525Pfs*28	ENST00000344749	NM_001136139.2	525	cgg/cCgg	17/19	1	2	FACETS	0.735	0.686	0.787	0.735	0.686	0.787	SUBCLONAL	1	TRUE	1	0.636880224686339	2		774	978	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152115	11152115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs796506759	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	265	643	0	ENST00000358026.2:c.4399G>A	p.Asp1467Asn	p.D1467N	ENST00000358026	NM_001128849.1	1467	Gac/Aac	31/36	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.636880224686339	2		643	815	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18975016	18975016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761111860	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	219	476	0	ENST00000262803.5:c.2813G>A	p.Arg938Gln	p.R938Q	ENST00000262803	NM_002911.3	938	cGg/cAg	20/24	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.636880224686339	2		476	615	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383185	42383185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782563209	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	297	569	1	ENST00000221972.3:c.205G>A	p.Val69Ile	p.V69I	ENST00000221972	NM_021601.3	69	Gtc/Atc	2/5	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.636880224686339	2		570	913	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	175	456	1	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	0.985	0.913	1	0.985	0.913	1	CLONAL	1	TRUE	1	0.636880224686339	2		457	558	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794424	42794424	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	204	863	0	ENST00000575354.2:c.1504T>A	p.Ser502Thr	p.S502T	ENST00000575354	NM_015125.3	502	Tcc/Acc	10/20	1	2	FACETS	0.551	0.51	0.593	0.551	0.51	0.593	SUBCLONAL	1	TRUE	1	0.636880224686339	2		863	1163	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867277	45867277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1403894013	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	241	737	0	ENST00000391945.4:c.916G>A	p.Ala306Thr	p.A306T	ENST00000391945	NM_000400.3	306	Gcc/Acc	10/23	1	2	FACETS	0.829	0.775	0.884	0.829	0.775	0.884	CLONAL	1	TRUE	1	0.636880224686339	2		737	913	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905983	50905983	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	262	745	0	ENST00000440232.2:c.955T>C	p.Cys319Arg	p.C319R	ENST00000440232	NM_002691.3	319	Tgc/Cgc	8/27	1	2	FACETS	0.982	0.923	1	0.982	0.923	1	CLONAL	1	TRUE	1	0.636880224686339	2		745	838	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46587776	46587776	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	194	401	0	ENST00000263734.3:c.455-1G>T		p.X152_splice	ENST00000263734	NM_001430.4	152			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.636880224686339	2		401	543	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158636987	158636987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370028017	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	230	569	0	ENST00000263640.3:c.193G>A	p.Val65Ile	p.V65I	ENST00000263640	NM_001105.4	65	Gtc/Atc	4/11	1	2	FACETS	0.984	0.921	1	0.984	0.921	1	CLONAL	1	TRUE	1	0.636880224686339	2		569	734	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719224	190719224	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	172	310	0	ENST00000441310.2:c.1226A>G	p.His409Arg	p.H409R	ENST00000441310	NM_000534.4	409	cAc/cGc	9/13	1	2	FACETS	0.943	0.872	1	0.943	0.872	1	CLONAL	1	TRUE	1	0.636880224686339	2		310	573	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660244	227660244	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750320720	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	216	723	1	ENST00000305123.5:c.3211G>A	p.Ala1071Thr	p.A1071T	ENST00000305123	NM_005544.2	1071	Gcc/Acc	1/2	1	2	FACETS	0.822	0.766	0.88	0.822	0.766	0.88	CLONAL	1	TRUE	1	0.636880224686339	2		724	825	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660190	12660190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs779001930	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	243	488	0	ENST00000251849.4:c.31A>G	p.Ile11Val	p.I11V	ENST00000251849	NM_002880.3	11	Atc/Gtc	2/17	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.636880224686339	2		488	738	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391075	89391075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs995238704	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	50	660	1	ENST00000336596.2:c.1141C>T	p.Arg381Cys	p.R381C	ENST00000336596	NM_005233.5	381	Cgc/Tgc	5/17	1	2	FACETS	0.177	0.149	0.208	0.177	0.149	0.208	SUBCLONAL	1	TRUE	1	0.636880224686339	2		661	887	SUCCESS
ATR	545	MSKCC	GRCh37	3	142285028	142285028	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	43	528	1	ENST00000350721.4:c.227T>A	p.Met76Lys	p.M76K	ENST00000350721	NM_001184.3	76	aTg/aAg	3/47	1	2	FACETS	0.182	0.151	0.216	0.182	0.151	0.216	SUBCLONAL	1	TRUE	1	0.636880224686339	2		529	742	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919087	178919089	+	inframe_deletion	In_Frame_Del	DEL	TAG	TAG	-	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	137	234	0	ENST00000263967.3:c.573_575del	p.Ile191_Val192delinsMet	p.I191_V192delinsM	ENST00000263967	NM_006218.2	191	aTAGtg/atg	4/21	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.636880224686339	2		234	428	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430206	181430208	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	134	325	3	ENST00000325404.1:c.67_69del	p.Gly23del	p.G23del	ENST00000325404	NM_003106.3	20	GGC/-	1/1	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.636880224686339	2		328	408	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430410	181430410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	269	676	2	ENST00000325404.1:c.262C>T	p.Arg88Trp	p.R88W	ENST00000325404	NM_003106.3	88	Cgg/Tgg	1/1	1	2	FACETS	0.893	0.839	0.948	0.893	0.839	0.948	CLONAL	1	TRUE	1	0.636880224686339	2		678	946	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447714	187447714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138532510	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	248	594	0	ENST00000232014.4:c.479G>A	p.Arg160His	p.R160H	ENST00000232014	NM_001130845.1	160	cGt/cAt	5/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.636880224686339	2		594	727	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127462	55127462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	229	586	0	ENST00000257290.5:c.250G>A	p.Val84Ile	p.V84I	ENST00000257290	NM_006206.4	84	Gtc/Atc	3/23	1	2	FACETS	0.935	0.874	0.997	0.935	0.874	0.997	CLONAL	1	TRUE	1	0.636880224686339	2		586	769	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557273	187557273	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	49	594	1	ENST00000441802.2:c.4089del	p.Phe1363LeufsTer5	p.F1363Lfs*5	ENST00000441802	NM_005245.3	1363	ttT/tt	6/27	1	2	FACETS	0.177	0.149	0.208	0.177	0.149	0.208	SUBCLONAL	1	TRUE	1	0.636880224686339	2		595	867	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228381	228381	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	109	470	0	ENST00000264932.6:c.703A>G	p.Ile235Val	p.I235V	ENST00000264932	NM_004168.2	235	Atc/Gtc	6/15	1	2	FACETS	0.595	0.536	0.658	0.595	0.536	0.658	SUBCLONAL	1	TRUE	1	0.636880224686339	2		470	575	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	256506	256506	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	46	356	0	ENST00000264932.6:c.1966A>G	p.Thr656Ala	p.T656A	ENST00000264932	NM_004168.2	656	Acc/Gcc	15/15	1	2	FACETS	0.31	0.261	0.364	0.31	0.261	0.364	SUBCLONAL	1	TRUE	1	0.636880224686339	2		356	466	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410924	31410924	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	79	699	0	ENST00000344624.3:c.3596A>G	p.Tyr1199Cys	p.Y1199C	ENST00000344624		1199	tAc/tGc	28/33	1	2	FACETS	0.283	0.248	0.321	0.283	0.248	0.321	SUBCLONAL	1	TRUE	1	0.636880224686339	2		699	876	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	184	484	7	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.963	0.894	1	0.963	0.894	1	CLONAL	1	TRUE	1	0.636880224686339	2		491	600	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80024669	80024669	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	173	316	0	ENST00000265081.6:c.1454-1G>T		p.X485_splice	ENST00000265081	NM_002439.4	485			1	2	FACETS	0.895	0.828	0.964	0.895	0.828	0.964	CLONAL	1	TRUE	1	0.636880224686339	2		316	607	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944382	131944382	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs748536322	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	188	291	3	ENST00000265335.6:c.2801del	p.Asn934IlefsTer6	p.N934Ifs*6	ENST00000265335		932	Aaa/aa	17/25	1	2	FACETS	0.951	0.883	1	0.951	0.883	1	CLONAL	1	TRUE	1	0.636880224686339	2		294	621	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048557	180048557	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	39	578	0	ENST00000261937.6:c.2005T>C	p.Tyr669His	p.Y669H	ENST00000261937	NM_182925.4	669	Tac/Cac	13/30	1	2	FACETS	0.173	0.143	0.208	0.173	0.143	0.208	SUBCLONAL	1	TRUE	1	0.636880224686339	2		578	706	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911072	29911072	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	188	736	0	ENST00000376809.5:c.371G>A	p.Gly124Asp	p.G124D	ENST00000376809	NM_002116.7	124	gGc/gAc	3/8	1	2	FACETS	0.68	0.629	0.733	0.68	0.629	0.733	SUBCLONAL	1	TRUE	1	0.636880224686339	2		736	868	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956526	93956526	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	131	291	0	ENST00000369303.4:c.2710C>A	p.Leu904Met	p.L904M	ENST00000369303	NM_004440.3	904	Ctg/Atg	15/17	1	2	FACETS	0.816	0.745	0.89	0.816	0.745	0.89	CLONAL	1	TRUE	1	0.636880224686339	2		291	504	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555345	106555345	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs763833695	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	190	453	0	ENST00000369096.4:c.2462A>G	p.Glu821Gly	p.E821G	ENST00000369096	NM_001198.3	821	gAa/gGa	7/7	1	2	FACETS	0.881	0.818	0.947	0.881	0.818	0.947	CLONAL	1	TRUE	1	0.636880224686339	2		453	677	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100021	157100021	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs201842850	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	37	179	0	ENST00000346085.5:c.958A>G	p.Ser320Gly	p.S320G	ENST00000346085	NM_020732.3	320	Agc/Ggc	1/20	1	2	FACETS	0.722	0.604	0.849	0.722	0.604	0.849	SUBCLONAL	1	TRUE	1	0.636880224686339	2		179	161	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521939	157521939	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs372833448	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	67	544	0	ENST00000346085.5:c.4211A>G	p.Tyr1404Cys	p.Y1404C	ENST00000346085	NM_020732.3	1404	tAc/tGc	18/20	1	2	FACETS	0.297	0.257	0.34	0.297	0.257	0.34	SUBCLONAL	1	TRUE	1	0.636880224686339	2		544	709	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935496	13935496	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	49	302	0	ENST00000405192.2:c.1360T>C	p.Tyr454His	p.Y454H	ENST00000405192	NM_001163147.1	454	Tat/Cat	12/12	1	2	FACETS	0.36	0.305	0.42	0.36	0.305	0.42	SUBCLONAL	1	TRUE	1	0.636880224686339	2		302	427	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370961	55370961	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	706	670	0	ENST00000297316.4:c.263A>G	p.Gln88Arg	p.Q88R	ENST00000297316	NM_022454.3	88	cAg/cGg	1/2	0.611232830029232	4	FACETS	0.972	0.943	1	0.972	0.943	1	CLONAL	3	TRUE	1	0.636880224686339	4		670	1244	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372068	55372068	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	173	488	0	ENST00000297316.4:c.758A>G	p.Tyr253Cys	p.Y253C	ENST00000297316	NM_022454.3	253	tAc/tGc	2/2	0.611232830029232	4	FACETS	0.965	0.888	1	0.322	0.296	0.348	CLONAL	1	TRUE	1	0.636880224686339	4		488	922	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964346	70964346	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	99	368	0	ENST00000276594.2:c.1682T>G	p.Phe561Cys	p.F561C	ENST00000276594	NM_024504.3	561	tTc/tGc	8/8	0.611232830029232	4	FACETS	0.727	0.649	0.81	0.242	0.216	0.27	SUBCLONAL	1	TRUE	1	0.636880224686339	4		368	700	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319959	8319959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745582718	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	122	232	0	ENST00000356435.5:c.5542G>A	p.Val1848Ile	p.V1848I	ENST00000356435		1848	Gtt/Att	34/35	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.636880224686339	2		232	369	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218617	98218617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202052415	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	35	508	0	ENST00000331920.6:c.3247G>A	p.Val1083Met	p.V1083M	ENST00000331920	NM_000264.3	1083	Gtg/Atg	19/24	1	2	FACETS	0.164	0.133	0.198	0.164	0.133	0.198	SUBCLONAL	1	TRUE	1	0.636880224686339	2		508	672	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391706	139391706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	336	793	1	ENST00000277541.6:c.6485G>A	p.Ser2162Asn	p.S2162N	ENST00000277541	NM_017617.3	2162	aGc/aAc	34/34	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.636880224686339	2		794	960	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245295	53245295	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	224	707	0	ENST00000375401.3:c.742C>A	p.Leu248Met	p.L248M	ENST00000375401	NM_004187.3	248	Ctg/Atg	6/26	1	2	FACETS	0.829	0.773	0.886	0.829	0.773	0.886	CLONAL	1	TRUE	1	0.636880224686339	2		707	849	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411071	63411071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750971248	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	233	572	0	ENST00000330258.3:c.2096G>A	p.Arg699His	p.R699H	ENST00000330258	NM_152424.3	699	cGt/cAt	2/2	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.636880224686339	2		572	670	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361116	70361121	+	inframe_deletion	In_Frame_Del	DEL	CAGCAA	CAGCAA	-	rs764789036	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	119	465	0	ENST00000374080.3:c.6315_6320del	p.Gln2114_Gln2115del	p.Q2114_Q2115del	ENST00000374080		2102	CAGCAA/-	43/45	1	2	FACETS	0.592	0.536	0.652	0.592	0.536	0.652	SUBCLONAL	1	TRUE	1	0.636880224686339	2		465	631	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937603	76937603	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	135	310	0	ENST00000373344.5:c.3145del	p.Ile1049Ter	p.I1049*	ENST00000373344	NM_000489.3	1049	Ata/ta	9/35	1	2	FACETS	0.768	0.701	0.837	0.768	0.701	0.837	SUBCLONAL	1	TRUE	1	0.636880224686339	2		310	552	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76949320	76949320	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	164	304	0	ENST00000373344.5:c.477del	p.Lys159AsnfsTer11	p.K159Nfs*11	ENST00000373344	NM_000489.3	159	aaA/aa	6/35	1	2	FACETS	0.858	0.792	0.927	0.858	0.792	0.927	CLONAL	1	TRUE	1	0.636880224686339	2		304	600	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034426	123034427	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	173	445	0	ENST00000355640.3:c.1189dup	p.Ile397AsnfsTer9	p.I397Nfs*9	ENST00000355640		395	gaa/gAaa	6/7	1	2	FACETS	0.709	0.654	0.767	0.709	0.654	0.767	SUBCLONAL	1	TRUE	1	0.636880224686339	2		445	766	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480553	123480553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	197	628	0	ENST00000371139.4:c.61C>T	p.Leu21Phe	p.L21F	ENST00000371139	NM_001114937.2	21	Ctt/Ttt	1/4	1	2	FACETS	0.833	0.773	0.894	0.833	0.773	0.894	CLONAL	1	TRUE	1	0.636880224686339	2		628	743	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0028979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	250	643	10	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.912	0.855	0.97	0.912	0.855	0.97	CLONAL	1	TRUE	1	0.636880224686339	2		653	861	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0028980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	106	369	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.249447929135085	1	FACETS	0.685	0.618	0.754	0.685	0.618	0.754	INDETERMINATE	1	TRUE	0	0.531366831932806	1		369	428	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0028980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	291	683	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.531366831932806	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.531366831932806	1		685	684	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584572	48584572	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	263	450	0	ENST00000342988.3:c.745C>T	p.Gln249Ter	p.Q249*	ENST00000342988	NM_005359.5	249	Cag/Tag	6/12	0.531366831932806	2	FACETS	0.898	0.851	0.946	0.898	0.851	0.946	CLONAL	2	TRUE	0	0.531366831932806	2		450	551	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368254	31368254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751741367	NA	P-0028980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	684	583	0	ENST00000328111.2:c.125G>A	p.Arg42His	p.R42H	ENST00000328111	NM_006892.3	42	cGc/cAc	2/23	0.531366831932806	6	FACETS	1	0.973	1	0.757	0.73	0.785	CLONAL	3	TRUE	2	0.531366831932806	6		583	1753	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266569	115266569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	203	589	0	ENST00000438362.2:c.1946G>A	p.Arg649His	p.R649H	ENST00000438362	NM_001242891.1	649	cGc/cAc	16/20	0.32412343863209	1	FACETS	0.906	0.845	0.969	0.906	0.845	0.969	CLONAL	1	TRUE	0	0.531366831932806	1		589	619	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631098	69631098	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	236	556	0	ENST00000334134.2:c.314T>C	p.Leu105Pro	p.L105P	ENST00000334134	NM_005247.2	105	cTc/cCc	2/3	0.519162572007549	3	FACETS	1	0.966	1	0.528	0.493	0.565	CLONAL	1	TRUE	1	0.531366831932806	3		556	1064	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182915	123182915	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	67	316	1	ENST00000218089.9:c.880G>T	p.Val294Leu	p.V294L	ENST00000218089	NM_001042749.1	294	Gta/Tta	10/35	0.158243368691855	3	FACETS	0.777	0.678	0.883	0.259	0.226	0.295	INDETERMINATE	1	TRUE	0	0.531366831932806	3		317	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578471	7578471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	1733	718	0	ENST00000269305.4:c.459del	p.Gly154AlafsTer16	p.G154Afs*16	ENST00000269305	NM_001126112.2	153	ccC/cc	5/11	0.736523072704449	4	FACETS	0.966	0.954	0.978	0.966	0.954	0.978	CLONAL	4	TRUE	0	0.744461067942577	4		718	2101	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781213	161781213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs571092914	NA	P-0028981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	199	513	0	ENST00000366898.1:c.1192G>A	p.Ala398Thr	p.A398T	ENST00000366898	NM_004562.2	398	Gcc/Acc	11/12	0.457238988438869	3	FACETS	0.701	0.649	0.755			1	SUBCLONAL	1	TRUE	NA	0.744461067942577	3		513	1047	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256463	115256463	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	21	511	0	ENST00000369535.4:c.248C>A	p.Ala83Asp	p.A83D	ENST00000369535	NM_002524.4	83	gCc/gAc	3/7	1	2	FACETS	0.189	0.145	0.24	0.189	0.145	0.24	SUBCLONAL	1	TRUE	1	0.744461067942577	2		511	298	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483237	120483237	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	199	425	0	ENST00000256646.2:c.3124G>A	p.Asp1042Asn	p.D1042N	ENST00000256646	NM_024408.3	1042	Gat/Aat	19/34	0.336720644933408	5	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.744461067942577	5		425	788	SUCCESS
RET	5979	MSKCC	GRCh37	10	43595959	43595960	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0028981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1536	472	756	1	ENST00000355710.3:c.126_127delinsAA	p.Asp43Asn	p.D43N	ENST00000355710	NM_020975.4	42	gtGGac/gtAAac	2/20	0.744461067942577	3	FACETS	0.867	0.825	0.909	0.289	0.275	0.303	CLONAL	1	TRUE	0	0.744461067942577	3		757	2008	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596079	43596079	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1235	461	683	0	ENST00000355710.3:c.246G>C	p.Glu82Asp	p.E82D	ENST00000355710	NM_020975.4	82	gaG/gaC	2/20	0.744461067942577	3	FACETS	1	0.955	1	0.334	0.318	0.35	CLONAL	1	TRUE	0	0.744461067942577	3		683	1696	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30956859	30956859	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	82	500	0	ENST00000375687.4:c.185C>A	p.Ser62Tyr	p.S62Y	ENST00000375687	NM_015338.5	62	tCc/tAc	4/13	0.744461067942577	7	FACETS	0.711	0.626	0.803	0.178	0.156	0.201	SUBCLONAL	1	TRUE	3	0.744461067942577	7		500	886	SUCCESS
APC	324	MSKCC	GRCh37	5	112179624	112179624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	244	407	1	ENST00000257430.4:c.8333C>T	p.Ala2778Val	p.A2778V	ENST00000257430	NM_000038.5	2778	gCt/gTt	16/16	0.665769756749918	2	FACETS	0.926	0.886	0.965	0.926	0.886	0.965	CLONAL	2	TRUE	0	0.744461067942577	2		408	354	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141582966	141582966	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	422	694	0	ENST00000220592.5:c.281T>C	p.Phe94Ser	p.F94S	ENST00000220592	NM_012154.3	94	tTt/tCt	3/19	0.744461067942577	3	FACETS	1	0.976	1	0.521	0.495	0.547	CLONAL	1	TRUE	1	0.744461067942577	3		694	1493	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0028987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	250	657	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	0.565933667147476	2	FACETS	0.991	0.929	1	0.495	0.464	0.527	CLONAL	1	TRUE	0	0.605127390775281	2		657	834	SUCCESS
AR	367	MSKCC	GRCh37	X	66765176	66765176	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs62636527	NA	P-0028987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	12	142	2	ENST00000374690.3:c.188A>T	p.Gln63Leu	p.Q63L	ENST00000374690	NM_000044.3	63	cAg/cTg	1/8	0.605127390775281	1	FACETS	0.199	0.14	0.27	0.199	0.14	0.27	SUBCLONAL	1	TRUE	0	0.605127390775281	1		144	139	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7132309	7132310	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0028987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	261	478	0	ENST00000302850.5:c.2701_2702del	p.Ser901ProfsTer97	p.S901Pfs*97	ENST00000302850	NM_000208.2	901	TCc/c	14/22	0.166168945770843	5	FACETS	1	0.954	1	0.678	0.637	0.72	INDETERMINATE	2	TRUE	2	0.605127390775281	5		478	809	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356359	66356359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199650353	NA	P-0028987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	101	488	0	ENST00000273854.3:c.1138C>T	p.Pro380Ser	p.P380S	ENST00000273854	NM_004439.5	380	Cct/Tct	5/18	0.264473214245788	4	FACETS	0.683	0.611	0.761	0.342	0.305	0.381	INDETERMINATE	1	TRUE	2	0.605127390775281	4		488	784	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	228	404	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.810940877544503	2		404	550	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362446	40362447	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1202978138	NA	P-0028992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	199	636	1	ENST00000293328.3:c.1749dup	p.His584ThrfsTer8	p.H584Tfs*8	ENST00000293328	NM_012448.3	583	-/A	14/19	1	2	FACETS	0.488	0.452	0.526	0.488	0.452	0.526	SUBCLONAL	1	TRUE	1	0.810940877544503	2		637	1006	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711915	89711915	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786204866	NA	P-0028992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	220	498	0	ENST00000371953.3:c.533A>G	p.Tyr178Cys	p.Y178C	ENST00000371953	NM_000314.4	178	tAt/tGt	6/9	0.810940877544503	1	FACETS	0.906	0.861	0.951	0.906	0.861	0.951	CLONAL	1	TRUE	0	0.810940877544503	1		498	356	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210077	55210077	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	15059	502	0	ENST00000275493.2:c.187G>C	p.Gly63Arg	p.G63R	ENST00000275493	NM_005228.3	63	Ggg/Cgg	2/28	0.810940877544503	19	FACETS	0.976	0.973	0.978			1	CLONAL	19	TRUE	NA	0.810940877544503	19		502	15815	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026176	48026176	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881787	NA	P-0028992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	238	396	1	ENST00000234420.5:c.1054G>A	p.Val352Ile	p.V352I	ENST00000234420	NM_000179.2	352	Gtt/Att	4/10	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.810940877544503	2		397	583	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145424	58145424	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7492	883	378	1	ENST00000257904.6:c.77C>T	p.Pro26Leu	p.P26L	ENST00000257904	NM_000075.3	26	cCc/cTc	2/8	NA	2	FACETS	0.26	0.25	0.27			1	INDETERMINATE	1	TRUE	NA	0.810940877544503	2		379	8375	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654742	29654742	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	160	367	0	ENST00000356175.3:c.5431G>A	p.Glu1811Lys	p.E1811K	ENST00000356175	NM_000267.3	1811	Gaa/Aaa	37/57	1	2	FACETS	0.603	0.555	0.654	0.603	0.555	0.654	SUBCLONAL	1	TRUE	1	0.810940877544503	2		367	654	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392033	81392033	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	177	343	0	ENST00000222390.5:c.244T>C	p.Phe82Leu	p.F82L	ENST00000222390	NM_000601.4	82	Ttc/Ctc	2/18	0.735306656498059	3	FACETS	0.953	0.882	1	0.476	0.441	0.513	CLONAL	1	TRUE	1	0.810940877544503	3		343	644	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0028993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	445	591	0				ENST00000310581	NM_198253.2	-/1132			0.410892283397418	5	FACETS	0.867	0.831	0.904	0.867	0.831	0.904	INDETERMINATE	3	TRUE	2	0.713028271969859	5		591	993	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0028993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	1405	512	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.713028271969859	9	FACETS	0.937	0.92	0.954			1	CLONAL	7	TRUE	NA	0.713028271969859	9		512	2100	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521711	89521711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	347	413	2	ENST00000336596.2:c.2788G>A	p.Glu930Lys	p.E930K	ENST00000336596	NM_005233.5	930	Gaa/Aaa	16/17	0.700673008877761	4	FACETS	0.939	0.892	0.986	0.939	0.892	0.986	CLONAL	2	TRUE	2	0.713028271969859	4		415	888	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333143	70333143	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767493807	NA	P-0028993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	262	530	1	ENST00000373644.4:c.1048G>A	p.Glu350Lys	p.E350K	ENST00000373644	NM_030625.2	350	Gaa/Aaa	2/12	0.710690073584313	3	FACETS	1	0.943	1	0.503	0.472	0.535	CLONAL	1	TRUE	1	0.713028271969859	3		531	991	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743272	743272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs188857712	NA	P-0028993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	209	636	0	ENST00000314574.4:c.868G>A	p.Glu290Lys	p.E290K	ENST00000314574	NM_005433.3	290	Gaa/Aaa	7/12	0.710690073584313	3	FACETS	0.817	0.759	0.878	0.409	0.379	0.439	CLONAL	1	TRUE	1	0.713028271969859	3		636	973	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755449	39755449	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	394	480	1	ENST00000288319.7:c.1316C>T	p.Pro439Leu	p.P439L	ENST00000288319	NM_182918.3	439	cCc/cTc	10/10	0.628098525020033	4	FACETS	0.949	0.905	0.994	0.949	0.905	0.994	CLONAL	2	TRUE	2	0.713028271969859	4		481	997	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790129	40790129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	459	533	1	ENST00000373198.4:c.2602C>T	p.Pro868Ser	p.P868S	ENST00000373198	NM_133170.3	868	Ccc/Tcc	18/32	0.628098525020033	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.713028271969859	4		534	1037	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422634	47422634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	451	259	1	ENST00000377045.4:c.106C>T	p.Arg36Trp	p.R36W	ENST00000377045	NM_001654.4	36	Cgg/Tgg	3/16	0.618809807890478	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.713028271969859	2		260	544	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939506	68939506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1309816810	NA	P-0028993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	191	546	2	ENST00000288368.4:c.491G>A	p.Gly164Glu	p.G164E	ENST00000288368	NM_024870.2	164	gGa/gAa	5/40	0.628098525020033	4	FACETS	0.918	0.856	0.98	0.918	0.856	0.98	CLONAL	2	TRUE	2	0.713028271969859	4		548	500	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727432	66727432	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	385	448	0	ENST00000307102.5:c.148C>T	p.Leu50Phe	p.L50F	ENST00000307102	NM_002755.3	50	Ctt/Ttt	2/11	0.628098525020033	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	2	0.713028271969859	4		448	925	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980352	201980352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1662	940	649	1	ENST00000359651.3:c.88C>T	p.Pro30Ser	p.P30S	ENST00000359651		30	Ccc/Tcc	1/8	0.713028271969859	8	FACETS	1	0.991	1	0.636	0.616	0.656	CLONAL	3	TRUE	3	0.713028271969859	8		650	2602	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912737	100912737	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	328	557	0	ENST00000325455.5:c.2585G>T	p.Gly862Val	p.G862V	ENST00000325455	NM_001202474.3	862	gGa/gTa	7/8	0.713028271969859	2	FACETS	0.948	0.912	0.984	0.948	0.912	0.984	CLONAL	2	TRUE	0	0.713028271969859	2		557	485	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436155	110436155	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	670	639	0	ENST00000375856.3:c.2246C>T	p.Ser749Phe	p.S749F	ENST00000375856	NM_003749.2	749	tCc/tTc	1/2	0.628098525020033	4	FACETS	0.992	0.957	1	0.992	0.957	1	CLONAL	2	TRUE	2	0.713028271969859	4		639	1622	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120042	70120092	+	inframe_deletion	In_Frame_Del	DEL	GCCCCCACAGGCCCCGCCGGCCCCGCAGGCGCCCCCGCAGCCGCAGGCGGC	GCCCCCACAGGCCCCGCCGGCCCCGCAGGCGCCCCCGCAGCCGCAGGCGGC	-	novel	NA	P-0028993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	70	44	0	ENST00000245479.2:c.1054_1104del	p.Ala352_Gln368del	p.A352_Q368del	ENST00000245479	NM_000346.3	348	caGCCCCCACAGGCCCCGCCGGCCCCGCAGGCGCCCCCGCAGCCGCAGGCGGCg/cag	3/3	0.710690073584313	3	FACETS	1	0.978	1	0.744	0.663	0.827	CLONAL	1	TRUE	1	0.713028271969859	3		44	179	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152224	11152224	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	232	588	0	ENST00000358026.2:c.4508A>G	p.Lys1503Arg	p.K1503R	ENST00000358026	NM_001128849.1	1503	aAg/aGg	31/36	0.710690073584313	3	FACETS	0.887	0.828	0.949	0.444	0.414	0.475	CLONAL	1	TRUE	1	0.713028271969859	3		588	995	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576808	212576808	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	173	510	0	ENST00000342788.4:c.1091G>A	p.Gly364Glu	p.G364E	ENST00000342788	NM_005235.2	364	gGg/gAg	9/28	0.628098525020033	4	FACETS	0.753	0.697	0.81	0.753	0.697	0.81	SUBCLONAL	2	TRUE	2	0.713028271969859	4		510	552	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612210	189612211	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0028993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	312	529	4	ENST00000264731.3:c.1962_1963delinsTT	p.Arg655Ter	p.R655*	ENST00000264731	NM_003722.4	654	ccCCga/ccTTga	14/14	0.700673008877761	4	FACETS	0.905	0.857	0.954	0.905	0.857	0.954	CLONAL	2	TRUE	2	0.713028271969859	4		533	828	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79968606	79968606	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	219	519	0	ENST00000265081.6:c.956G>A	p.Gly319Glu	p.G319E	ENST00000265081	NM_002439.4	319	gGa/gAa	6/24	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.713028271969859	2		519	582	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519347	137519347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747857191	NA	P-0028993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	92	306	0	ENST00000367739.4:c.1291C>T	p.Pro431Ser	p.P431S	ENST00000367739	NM_000416.2	431	Ccc/Tcc	7/7	0.710822176322301	3	FACETS	0.869	0.777	0.965	0.434	0.388	0.483	CLONAL	1	TRUE	1	0.713028271969859	3		306	403	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38173457	38173458	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0028993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	330	504	1	ENST00000317025.8:c.1958_1959delinsTT	p.Ser653Phe	p.S653F	ENST00000317025	NM_023034.1	653	tCC/tTT	10/24	0.628098525020033	4	FACETS	0.867	0.822	0.913	0.867	0.822	0.913	CLONAL	2	TRUE	2	0.713028271969859	4		505	914	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972677	76972678	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0028993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	305	278	1	ENST00000373344.5:c.63_64delinsTT	p.Leu22Phe	p.L22F	ENST00000373344	NM_000489.3	21	ttCCtt/ttTTtt	2/35	0.618809807890478	2	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.713028271969859	2		279	373	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256735	16256735	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	192	375	0	ENST00000375759.3:c.4000G>A	p.Glu1334Lys	p.E1334K	ENST00000375759	NM_015001.2	1334	Gaa/Aaa	11/15	0.3	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.27	1		375	860	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456384	32456384	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	226	285	0	ENST00000332351.3:c.508G>T	p.Gly170Cys	p.G170C	ENST00000332351	NM_024426.4	170	Ggc/Tgc	1/10	0.3	4	FACETS	0.854	0.794	0.916			1	CLONAL	2	TRUE	NA	0.27	4		285	1245	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366231	118366975	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTTGAGATATTTTTTAAAATATTGAGTTCTGTGTACTTCAGCAATTTTCAAACGCTGTGACTTGTTCTTATATTCTGTGAATGGCTCCTACATGGGGCAACAGGTGATATCAAGAATTTATTTTATACAGTTCTAGGTATACTGTAGGAGTTCAATAAATGCTTGTTGAATCAATTATTTTCAGCAGTGGGATGTTACCAAACGCAGTGCTTCCACCTTCACTTGACCATAATTATGCTCAGTGGCAGGAGCGAGAGGAAAACAGCCACACTGAGCAGCCTCCTTTAATGAAGAAAATCATTCCAGCTCCCAAACCCAAAGGTCCTGGAGAACCAGACTCACCAACTCCTCTGCATCCTCCTACACCACCAATTTTGAGTAAGCCACCAAAAGGAGAGTCGTCACCCATTTCCCTCTAGATGCAGATGATTGACTTCGTGAATCCAATTCACTAAAATTAGATATACTTGGATATCAGAAAGGAATTTTCAGGTCATCCTTAAATGTAATACCATCATTAATTTTGCTTCACTTGAGGTGTTAATGAGGACTTGATATAAATACTCTGGAGTATTGTAACATAGATGATGAGGTAGCGTAACTCTGAACACTTTTTGAAAAGTGGTTATTTTATAGGCTGTGGGCTATGTAAGCTGAATTATTTCTTTTTTCCTTGAAATCAGACATAGTATTGCCAATTTTAACTGGATCTCAAGGTATTGATGGGAGTCTTTTGGATTTCAAG	GTTGAGATATTTTTTAAAATATTGAGTTCTGTGTACTTCAGCAATTTTCAAACGCTGTGACTTGTTCTTATATTCTGTGAATGGCTCCTACATGGGGCAACAGGTGATATCAAGAATTTATTTTATACAGTTCTAGGTATACTGTAGGAGTTCAATAAATGCTTGTTGAATCAATTATTTTCAGCAGTGGGATGTTACCAAACGCAGTGCTTCCACCTTCACTTGACCATAATTATGCTCAGTGGCAGGAGCGAGAGGAAAACAGCCACACTGAGCAGCCTCCTTTAATGAAGAAAATCATTCCAGCTCCCAAACCCAAAGGTCCTGGAGAACCAGACTCACCAACTCCTCTGCATCCTCCTACACCACCAATTTTGAGTAAGCCACCAAAAGGAGAGTCGTCACCCATTTCCCTCTAGATGCAGATGATTGACTTCGTGAATCCAATTCACTAAAATTAGATATACTTGGATATCAGAAAGGAATTTTCAGGTCATCCTTAAATGTAATACCATCATTAATTTTGCTTCACTTGAGGTGTTAATGAGGACTTGATATAAATACTCTGGAGTATTGTAACATAGATGATGAGGTAGCGTAACTCTGAACACTTTTTGAAAAGTGGTTATTTTATAGGCTGTGGGCTATGTAAGCTGAATTATTTCTTTTTTCCTTGAAATCAGACATAGTATTGCCAATTTTAACTGGATCTCAAGGTATTGATGGGAGTCTTTTGGATTTCAAG	-	novel	NA	P-0028994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	116	7	0	ENST00000534358.1:c.5364-182_5559del		p.X1788_splice	ENST00000534358	NM_005933.3	1788		19/36	0.3	1	FACETS	1	0.985	1	1	0.993	1	CLONAL	5	TRUE	0	0.27	1		7	136	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825431	134825447	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	AAGTGGCATGCACTAGT	AAGTGGCATGCACTAGT	-	novel	NA	P-0028994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	50	226	0	ENST00000398015.3:c.952_961+7del		p.X318_splice	ENST00000398015	NM_004441.4	318		4/16	0.227720483864204	3	FACETS	0.46	0.389	0.539	0.23	0.194	0.27	SUBCLONAL	1	TRUE	1	0.27	3		226	913	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611880	100611880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	84	415	1	ENST00000308731.7:c.1241G>A	p.Gly414Glu	p.G414E	ENST00000308731	NM_000061.2	414	gGg/gAg	14/19	0.3	1	FACETS	0.524	0.461	0.591	0.524	0.461	0.591	SUBCLONAL	1	TRUE	0	0.27	1		416	1028	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0028995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	439	747	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	NA	2	FACETS	0.955	0.911	0.999			1	INDETERMINATE	2	TRUE	NA	0.365488668385477	2		750	1258	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0028995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	325	670	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.365488668385477	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.365488668385477	3		670	1038	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259335	89259335	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750779844	NA	P-0028995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	282	459	0	ENST00000336596.2:c.479G>A	p.Arg160His	p.R160H	ENST00000336596	NM_005233.5	160	cGt/cAt	3/17	0.365488668385477	2	FACETS	0.968	0.914	1	0.968	0.914	1	CLONAL	2	TRUE	0	0.365488668385477	2		459	797	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610129	43610129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141185224	NA	P-0028995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	201	670	0	ENST00000355710.3:c.2081G>A	p.Arg694Gln	p.R694Q	ENST00000355710	NM_020975.4	694	cGg/cAg	11/20	1	2	FACETS	0.956	0.885	1	0.956	0.885	1	CLONAL	1	TRUE	1	0.365488668385477	2		670	1150	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104686	209104686	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	283	373	0	ENST00000345146.2:c.892C>T	p.Pro298Ser	p.P298S	ENST00000345146	NM_005896.2	298	Cca/Tca	8/10	0.365488668385477	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.365488668385477	3		373	893	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306782	41306782	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	225	343	0	ENST00000373198.4:c.877G>T	p.Ala293Ser	p.A293S	ENST00000373198	NM_133170.3	293	Gct/Tct	7/32	0.365488668385477	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	1	0.365488668385477	3		343	719	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205283	38205283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372097319	NA	P-0028995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1342	335	877	0	ENST00000317025.8:c.407C>T	p.Pro136Leu	p.P136L	ENST00000317025	NM_023034.1	136	cCt/cTt	2/24	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.365488668385477	2		877	1677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0028996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1213	95	770	3	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	1	2	FACETS	0.29	0.257	0.326	0.29	0.257	0.326	SUBCLONAL	1	TRUE	1	0.500220967560955	2		773	1308	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264145	46264145	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	165	302	0	ENST00000371998.3:c.1192G>C	p.Val398Leu	p.V398L	ENST00000371998		398	Gta/Cta	11/23	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.817738282757161	2		302	389	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522087	157522087	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	253	442	0	ENST00000346085.5:c.4359G>T	p.Gln1453His	p.Q1453H	ENST00000346085	NM_020732.3	1453	caG/caT	18/20	0.817738282757161	1	FACETS	0.948	0.905	0.989	0.948	0.905	0.989	CLONAL	1	TRUE	0	0.817738282757161	1		442	386	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0029000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	214	415	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	0.801631928461207	3	FACETS	0.913	0.85	0.978	0.457	0.425	0.489	CLONAL	1	TRUE	1	0.801631928461207	3		415	819	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	470	785	1	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.801631928461207	2	FACETS	0.987	0.961	1	0.987	0.961	1	CLONAL	2	TRUE	0	0.801631928461207	2		786	594	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786031	135786031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766487204	NA	P-0029000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	288	687	2	ENST00000298552.3:c.1190C>T	p.Pro397Leu	p.P397L	ENST00000298552	NM_001162426.1	397	cCa/cTa	12/23	0.801631928461207	3	FACETS	1	0.968	1	0.347	0.326	0.367	CLONAL	1	TRUE	0	0.801631928461207	3		689	968	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446386	70446386	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0029000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	199	548	0	ENST00000373644.4:c.5326A>T	p.Lys1776Ter	p.K1776*	ENST00000373644	NM_030625.2	1776	Aaa/Taa	11/12	0.801631928461207	3	FACETS	0.903	0.839	0.97	0.452	0.419	0.485	CLONAL	1	TRUE	1	0.801631928461207	3		548	770	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272272	15272272	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	259	629	2	ENST00000263388.2:c.6167C>A	p.Ala2056Glu	p.A2056E	ENST00000263388	NM_000435.2	2056	gCa/gAa	33/33	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.801631928461207	2		631	644	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441275	52441275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	220	478	0	ENST00000460680.1:c.495G>A	p.Met165Ile	p.M165I	ENST00000460680	NM_004656.3	165	atG/atA	7/17	0.801631928461207	4	FACETS	0.991	0.922	1	0.495	0.461	0.531	CLONAL	1	TRUE	2	0.801631928461207	4		478	998	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513514	149513514	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	203	585	0	ENST00000261799.4:c.689A>T	p.Asn230Ile	p.N230I	ENST00000261799	NM_002609.3	230	aAc/aTc	5/23	0.801631928461207	5	FACETS	0.885	0.819	0.953	0.295	0.273	0.318	CLONAL	1	TRUE	2	0.801631928461207	5		585	1261	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0029014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	171	494	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.448863867471176	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.448863867471176	3		494	424	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829040	128829042	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	rs570242755	NA	P-0029014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	10	105	1	ENST00000249373.3:c.67_69del	p.Leu23del	p.L23del	ENST00000249373	NM_005631.4	16	ggGCTg/ggg	1/12	1	2	FACETS	0.299	0.203	0.419	0.299	0.203	0.419	SUBCLONAL	1	TRUE	1	0.448863867471176	2		106	149	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0029014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	224	428	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.448863867471176	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.448863867471176	3		428	373	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600042	10600042	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs148641376	NA	P-0029014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	207	756	0	ENST00000171111.5:c.1534G>A	p.Val512Ile	p.V512I	ENST00000171111	NM_203500.1	512	Gtc/Atc	5/6	1	2	FACETS	0.984	0.914	1	0.984	0.914	1	CLONAL	1	TRUE	1	0.448863867471176	2		756	937	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466019	69466019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	221	791	0	ENST00000227507.2:c.857C>T	p.Thr286Ile	p.T286I	ENST00000227507	NM_053056.2	286	aCa/aTa	5/5	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.448863867471176	2		791	954	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492938	56492938	+	start_lost	Translation_Start_Site	SNP	T	T	A	novel	NA	P-0029014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	50	197	0	ENST00000407977.2:c.1A>T	p.Met1?	p.M1?	ENST00000407977		1	Atg/Ttg	2/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.448863867471176	2		197	163	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111855990	111855990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201886863	NA	P-0029014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	171	613	3	ENST00000341259.2:c.41C>T	p.Ala14Val	p.A14V	ENST00000341259	NM_005475.2	14	gCg/gTg	2/8	1	2	FACETS	0.964	0.889	1	0.964	0.889	1	CLONAL	1	TRUE	1	0.448863867471176	2		616	790	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725059	89725059	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	30	243	0	ENST00000371953.3:c.1042A>C	p.Thr348Pro	p.T348P	ENST00000371953	NM_000314.4	348	Aca/Cca	9/9	0.448863867471176	3	FACETS	0.952	0.775	1	0.476	0.387	0.574	CLONAL	1	TRUE	1	0.448863867471176	3		243	172	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588109	69588109	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs200870263	NA	P-0029014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	188	601	0	ENST00000168712.1:c.589A>G	p.Met197Val	p.M197V	ENST00000168712	NM_002007.2	197	Atg/Gtg	3/3	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.448863867471176	2		601	796	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107215	27107224	+	frameshift_variant	Frame_Shift_Del	DEL	TGTGATGTAC	TGTGATGTAC	-	novel	NA	P-0029014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	270	477	1	ENST00000324856.7:c.6829_6838del	p.Asp2277PhefsTer2	p.D2277Ffs*2	ENST00000324856	NM_006015.4	2276	TGTGATGTACtg/tg	20/20	0.327682591822726	3	FACETS	1	0.99	1	0.802	0.759	0.846	CLONAL	2	TRUE	0	0.448863867471176	3		478	612	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828704	72828704	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	197	577	0	ENST00000268489.5:c.7877del	p.Pro2626LeufsTer19	p.P2626Lfs*19	ENST00000268489	NM_006885.3	2626	cCt/ct	9/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.448863867471176	2		577	771	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098892	47098892	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	166	756	2	ENST00000409792.3:c.6382G>T	p.Glu2128Ter	p.E2128*	ENST00000409792	NM_014159.6	2128	Gag/Tag	15/21	0.354678739683371	3	FACETS	0.863	0.791	0.937	0.431	0.395	0.469	CLONAL	1	TRUE	1	0.448863867471176	3		758	1050	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426709	49426712	+	stop_gained	Nonsense_Mutation	DEL	GAAG	GAAG	A	novel	NA	P-0029014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	56	257	0	ENST00000301067.7:c.11776_11779delinsT	p.Leu3926_Gln3927delinsTer	p.L3926_Q3927delins*	ENST00000301067	NM_003482.3	3926	CTTCag/Tag	39/54	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.448863867471176	2		257	193	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0029015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	44	483	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.394	0.33	0.465	0.394	0.33	0.465	SUBCLONAL	1	TRUE	1	0.351231908701514	2		483	636	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	99	404	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.933	0.835	1	0.933	0.835	1	CLONAL	1	TRUE	1	0.351231908701514	2		404	604	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0029015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	39	428	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.423	0.35	0.505	0.423	0.35	0.505	SUBCLONAL	1	TRUE	1	0.351231908701514	2		428	525	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	316	702	0	ENST00000269305.4:c.853G>T	p.Glu285Ter	p.E285*	ENST00000269305	NM_001126112.2	285	Gag/Tag	8/11	0.281122018693165	2	FACETS	0.835	0.788	0.882	0.835	0.788	0.882	CLONAL	2	TRUE	0	0.351231908701514	2		702	1078	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350074	81350074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	37	490	0	ENST00000222390.5:c.1258G>A	p.Glu420Lys	p.E420K	ENST00000222390	NM_000601.4	420	Gaa/Aaa	10/18	1	2	FACETS	0.36	0.296	0.432	0.36	0.296	0.432	SUBCLONAL	1	TRUE	1	0.351231908701514	2		490	585	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334750	81334750	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	53	583	0	ENST00000222390.5:c.1966G>A	p.Glu656Lys	p.E656K	ENST00000222390	NM_000601.4	656	Gaa/Aaa	17/18	1	2	FACETS	0.408	0.347	0.476	0.408	0.347	0.476	SUBCLONAL	1	TRUE	1	0.351231908701514	2		583	739	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0029016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	358	516	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.457237859662279	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	2	0.479524603599945	4		516	1095	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973560	15973560	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	136	434	0	ENST00000268712.3:c.4432G>C	p.Asp1478His	p.D1478H	ENST00000268712	NM_006311.3	1478	Gac/Cac	31/46	0.479524603599945	1	FACETS	0.673	0.613	0.735	0.673	0.613	0.735	SUBCLONAL	1	TRUE	0	0.479524603599945	1		434	641	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030622	47030637	+	frameshift_variant	Frame_Shift_Del	DEL	CTGAGGATGCTGCCAC	CTGAGGATGCTGCCAC	-	novel	NA	P-0029016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	145	808	0	ENST00000377604.3:c.397_412del	p.Leu133ArgfsTer24	p.L133Rfs*24	ENST00000377604	NM_001204468.1	133	CTGAGGATGCTGCCACag/ag	4/24	0.479524603599945	1	FACETS	0.874	0.802	0.949	0.874	0.802	0.949	CLONAL	1	TRUE	0	0.479524603599945	1		808	526	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0029018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	815	498	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.405344949634658	5	FACETS	1	0.997	1	0.897	0.877	0.917	CLONAL	4	TRUE	0	0.632150569318376	5		498	1120	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0029018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	711	731	1	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.632150569318376	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.632150569318376	2		732	926	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436716	110436716	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	850	766	2	ENST00000375856.3:c.1685A>T	p.Asp562Val	p.D562V	ENST00000375856	NM_003749.2	562	gAc/gTc	1/2	0.330589759445993	4	FACETS	0.896	0.875	0.916	0.896	0.875	0.916	INDETERMINATE	4	TRUE	0	0.632150569318376	4		768	1225	SUCCESS
APC	324	MSKCC	GRCh37	5	112176104	112176104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554086219	NA	P-0029018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	403	604	0	ENST00000257430.4:c.4813G>A	p.Val1605Met	p.V1605M	ENST00000257430	NM_000038.5	1605	Gtg/Atg	16/16	0.387424811412898	2	FACETS	0.89	0.855	0.925	0.89	0.855	0.925	CLONAL	2	TRUE	0	0.632150569318376	2		604	716	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741479	145741480	+	missense_variant	Missense_Mutation	DNP	AG	AG	GT	novel	NA	P-0029018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2267	476	962	1	ENST00000428558.2:c.1023_1024delinsAC	p.Phe342Leu	p.F342L	ENST00000428558	NM_004260.3	341	atCTtc/atACtc	5/22	0.632150569318376	7	FACETS	1	0.995	1	0.354	0.337	0.372	CLONAL	1	TRUE	3	0.632150569318376	7		963	2743	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	64	394	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.937	0.812	1	0.937	0.812	1	CLONAL	1	TRUE	1	0.233790589489345	2		394	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0029019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	130	489	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.888	0.803	0.978	0.888	0.803	0.978	CLONAL	1	TRUE	1	0.233790589489345	2		489	1252	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148500	119148513	+	frameshift_variant	Frame_Shift_Del	DEL	TGATCTGACTGGCT	TGATCTGACTGGCT	-	novel	NA	P-0029019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	101	513	0	ENST00000264033.4:c.1042_1055del	p.Asp348MetfsTer2	p.D348Mfs*2	ENST00000264033	NM_005188.3	347	ccTGATCTGACTGGCTta/ccta	7/16	0.233790589489345	2	FACETS	1	0.962	1	0.583	0.521	0.649	CLONAL	1	TRUE	0	0.233790589489345	2		513	741	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434325	49434326	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGAGAAAGGGTCGGAGGGCA	novel	NA	P-0029019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1641	90	789	0	ENST00000301067.7:c.7208_7227dup	p.Arg2410CysfsTer23	p.R2410Cfs*23	ENST00000301067	NM_003482.3	2409	-/TGCCCTCCGACCCTTTCTCC	31/54	1	2	FACETS	0.445	0.393	0.501	0.445	0.393	0.501	SUBCLONAL	1	TRUE	1	0.233790589489345	2		789	1731	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896473	28896473	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	53	462	0	ENST00000282397.4:c.2977C>T	p.Pro993Ser	p.P993S	ENST00000282397	NM_002019.4	993	Ccc/Tcc	22/30	0.233790589489345	2	FACETS	0.537	0.457	0.626	0.269	0.228	0.313	SUBCLONAL	1	TRUE	0	0.233790589489345	2		462	844	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356147	70356147	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1240	421	627	0	ENST00000374080.3:c.5042C>G	p.Thr1681Ser	p.T1681S	ENST00000374080		1681	aCc/aGc	37/45	0.211262848667177	4	FACETS	0.892	0.848	0.937			1	CLONAL	3	TRUE	NA	0.233790589489345	4		627	1661	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0029020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	176	399	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	0.917	0.848	0.989	0.917	0.848	0.989	CLONAL	1	TRUE	1	0.562772755000186	2		399	682	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0029020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	227	482	2	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.562772755000186	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.562772755000186	1		484	569	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033822	49033822	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0029020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	221	353	0	ENST00000267163.4:c.1961-2A>G		p.X654_splice	ENST00000267163	NM_000321.2	654			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.562772755000186	2		353	692	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900244	101900246	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs863223829	NA	P-0029020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	259	472	0	ENST00000374994.4:c.683_685del	p.Glu228del	p.E228del	ENST00000374994	NM_004612.2	226	ggAGAa/gga	4/9	0.562772755000186	1	FACETS	0.95	0.895	1	0.95	0.895	1	CLONAL	1	TRUE	0	0.562772755000186	1		472	696	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087426	27087426	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	391	705	0	ENST00000324856.7:c.2001del	p.Ser668AlafsTer74	p.S668Afs*74	ENST00000324856	NM_006015.4	667	tCc/tc	5/20	0.562772755000186	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.562772755000186	1		705	938	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853181	68853182	+	splice_acceptor_variant	Splice_Site	DEL	AG	AG	-	novel	NA	P-0029020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	202	456	0	ENST00000261769.5:c.1566-1_1566del		p.X522_splice	ENST00000261769	NM_004360.3	522			0.562772755000186	1	FACETS	0.876	0.817	0.936	0.876	0.817	0.936	CLONAL	1	TRUE	0	0.562772755000186	1		456	589	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0029021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	132	666	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.591	0.535	0.651	0.591	0.535	0.651	SUBCLONAL	1	TRUE	1	0.334509325020007	2		667	1335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587782272	NA	P-0029021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	80	642	0	ENST00000269305.4:c.994-1G>C		p.X332_splice	ENST00000269305	NM_001126112.2	332			1	2	FACETS	0.463	0.406	0.524	0.463	0.406	0.524	SUBCLONAL	1	TRUE	1	0.334509325020007	2		642	1034	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057935	27057935	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	137	669	0	ENST00000324856.7:c.1643del	p.Gln548ArgfsTer71	p.Q548Rfs*71	ENST00000324856	NM_006015.4	548	cAg/cg	3/20	1	2	FACETS	0.631	0.572	0.693	0.631	0.572	0.693	SUBCLONAL	1	TRUE	1	0.334509325020007	2		669	1298	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981139	201981159	+	inframe_deletion	In_Frame_Del	DEL	TGGACTGGATCAGCTACCAAG	TGGACTGGATCAGCTACCAAG	-	novel	NA	P-0029021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1262	81	712	0	ENST00000359651.3:c.222_242del	p.Asp74_Val80del	p.D74_V80del	ENST00000359651		73	cTGGACTGGATCAGCTACCAAGtg/ctg	2/8	1	2	FACETS	0.361	0.316	0.409	0.361	0.316	0.409	SUBCLONAL	1	TRUE	1	0.334509325020007	2		712	1343	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37081614	37081706	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGAAGTGGGGTTGGTAGGATTCTATTACTTACCTGTTTTTTGGTTTTATTTTTTGTTTTGCAGTTCTCCGGGAGATGTTGCATAACCACTCCT	TGAAGTGGGGTTGGTAGGATTCTATTACTTACCTGTTTTTTGGTTTTATTTTTTGTTTTGCAGTTCTCCGGGAGATGTTGCATAACCACTCCT	-	novel	NA	P-0029021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	16	116	0	ENST00000231790.2:c.1559-62_1589del		p.X520_splice	ENST00000231790	NM_000249.3	520		14/19	1	2	FACETS	0.336	0.248	0.441	0.336	0.248	0.441	SUBCLONAL	1	TRUE	1	0.334509325020007	2		116	285	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0029022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	96	498	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.924	0.823	1	0.924	0.823	1	CLONAL	1	TRUE	1	0.2753040482681	2		498	755	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216596	108216596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778080	NA	P-0029022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	85	354	0	ENST00000278616.4:c.8545C>T	p.Arg2849Ter	p.R2849*	ENST00000278616	NM_000051.3	2849	Cga/Tga	58/63	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.2753040482681	2		354	554	SUCCESS
APC	324	MSKCC	GRCh37	5	112154981	112154981	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	121	481	1	ENST00000257430.4:c.1252G>T	p.Glu418Ter	p.E418*	ENST00000257430	NM_000038.5	418	Gaa/Taa	10/16	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.2753040482681	2		482	852	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589553	67589612	+	inframe_deletion	In_Frame_Del	DEL	AAGATAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACACTCAGTTTCAAGAAA	AAGATAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACACTCAGTTTCAAGAAA	-	novel	NA	P-0029022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	50	325	0	ENST00000274335.5:c.1318_1377del	p.Asp440_Lys459del	p.D440_K459del	ENST00000274335		439	gAAGATAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACACTCAGTTTCAAGAAAaa/gaa	10/15	1	2	FACETS	0.716	0.608	0.835	0.716	0.608	0.835	SUBCLONAL	1	TRUE	1	0.2753040482681	2		325	507	SUCCESS
APC	324	MSKCC	GRCh37	5	112175865	112175867	+	frameshift_variant	Frame_Shift_Del	DEL	TGC	TGC	A	novel	NA	P-0029022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	46	292	0	ENST00000257430.4:c.4574_4576delinsA	p.Met1525AsnfsTer7	p.M1525Nfs*7	ENST00000257430	NM_000038.5	1525	aTGCct/aAct	16/16	1	2	FACETS	0.678	0.571	0.796	0.678	0.571	0.796	SUBCLONAL	1	TRUE	1	0.2753040482681	2		292	493	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	260	394	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.98	0.919	1	0.98	0.919	1	CLONAL	1	TRUE	1	0.530883457526472	2		394	999	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578537	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs879254214	NA	P-0029023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	780	800	0	ENST00000269305.4:c.393_395del	p.Asn131del	p.N131del	ENST00000269305	NM_001126112.2	131	aaCAAg/aag	5/11	0.520849271170533	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.530883457526472	2		800	1461	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95596457	95596457	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	225	570	0	ENST00000393063.1:c.511C>G	p.Leu171Val	p.L171V	ENST00000393063	NM_030621.3	171	Ctt/Gtt	6/28	NA	2	FACETS	0.914	0.852	0.978			1	INDETERMINATE	1	TRUE	NA	0.530883457526472	2		570	927	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965548	90965548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	189	479	0	ENST00000265433.3:c.1769G>A	p.Arg590Lys	p.R590K	ENST00000265433	NM_002485.4	590	aGa/aAa	11/16	1	2	FACETS	0.913	0.845	0.983	0.913	0.845	0.983	CLONAL	1	TRUE	1	0.530883457526472	2		479	780	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0029024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	160	489	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.222222476340623	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.222222476340623	1		489	875	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098528	108098528	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	59	341	0	ENST00000278616.4:c.98T>A	p.Leu33Gln	p.L33Q	ENST00000278616	NM_000051.3	33	cTg/cAg	3/63	1	2	FACETS	0.827	0.711	0.954	0.827	0.711	0.954	CLONAL	1	TRUE	1	0.222222476340623	2		341	642	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046509	69046509	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs557338072	NA	P-0029024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	123	384	0	ENST00000288368.4:c.3982T>G	p.Leu1328Val	p.L1328V	ENST00000288368	NM_024870.2	1328	Ttg/Gtg	32/40	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.222222476340623	2		384	807	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930087	68930087	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	40	496	0	ENST00000288368.4:c.148T>G	p.Leu50Val	p.L50V	ENST00000288368	NM_024870.2	50	Tta/Gta	2/40	1	2	FACETS	0.798	0.662	0.949	0.798	0.662	0.949	CLONAL	1	TRUE	1	0.18	2		496	557	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325847	30325847	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764103905	NA	P-0029025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	39	403	0	ENST00000322652.5:c.2045G>A	p.Arg682His	p.R682H	ENST00000322652	NM_015355.2	682	cGt/cAt	16/16	1	2	FACETS	0.98	0.813	1	0.98	0.813	1	CLONAL	1	TRUE	1	0.18	2		403	442	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660493	190660495	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGG	AGG	-	novel	NA	P-0029025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	28	221	0	ENST00000441310.2:c.133_135del		p.X45_splice	ENST00000441310	NM_000534.4	45		3/13	1	2	FACETS	1	0.835	1	1	0.835	1	CLONAL	1	TRUE	1	0.18	2		221	297	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210735	2210735	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1238067958	NA	P-0029026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	420	592	2	ENST00000398665.3:c.1232G>A	p.Arg411His	p.R411H	ENST00000398665	NM_032482.2	411	cGc/cAc	14/28	1	2	FACETS	0.95	0.906	0.995	0.95	0.906	0.995	CLONAL	1	TRUE	1	0.730556576099196	2		594	1210	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874012	151874013	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	272	499	0	ENST00000262189.6:c.8525dup	p.Asn2842LysfsTer2	p.N2842Kfs*2	ENST00000262189	NM_170606.2	2842	aat/aaAt	38/59	1	2	FACETS	0.84	0.791	0.891	0.84	0.791	0.891	CLONAL	1	TRUE	1	0.730556576099196	2		499	886	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247350	153247350	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	278	396	0	ENST00000281708.4:c.1452G>C	p.Arg484Ser	p.R484S	ENST00000281708	NM_033632.3	484	agG/agC	10/12	1	2	FACETS	0.962	0.907	1	0.962	0.907	1	CLONAL	1	TRUE	1	0.730556576099196	2		396	791	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911089	29911089	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	269	616	0	ENST00000376809.5:c.388G>T	p.Asp130Tyr	p.D130Y	ENST00000376809	NM_002116.7	130	Gac/Tac	3/8	0.730556576099196	1	FACETS	0.841	0.797	0.885	0.841	0.797	0.885	CLONAL	1	TRUE	0	0.730556576099196	1		616	556	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818912	32818912	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779306745	NA	P-0029026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	272	366	0	ENST00000354258.4:c.1039C>T	p.Arg347Trp	p.R347W	ENST00000354258	NM_000593.5	347	Cgg/Tgg	4/11	0.730556576099196	1	FACETS	0.979	0.932	1	0.979	0.932	1	CLONAL	1	TRUE	0	0.730556576099196	1		366	483	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068405	26068405	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	295	607	0	ENST00000435504.4:c.85A>G	p.Met29Val	p.M29V	ENST00000435504		29	Atg/Gtg	2/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.78	2		607	738	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	152	404	0				ENST00000310581	NM_198253.2	-/1132			0.481446077396929	3	FACETS	0.871	0.804	0.94	0.871	0.804	0.94	CLONAL	2	TRUE	1	0.483519641125216	3		404	448	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0029057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	163	631	1	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	0.483519641125216	2		632	458	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431441	121431441	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	40	515	0	ENST00000257555.6:c.645C>A	p.Phe215Leu	p.F215L	ENST00000257555		215	ttC/ttA	3/10	1	2	FACETS	0.274	0.227	0.327	0.274	0.227	0.327	SUBCLONAL	1	TRUE	1	0.483519641125216	2		515	603	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740842	58740842	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0029057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	193	452	0	ENST00000305921.3:c.1747A>T	p.Arg583Ter	p.R583*	ENST00000305921	NM_003620.3	583	Aga/Tga	6/6	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.483519641125216	2		452	621	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821895	59821895	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	149	424	0	ENST00000259008.2:c.2155T>A	p.Leu719Met	p.L719M	ENST00000259008	NM_032043.2	719	Ttg/Atg	15/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.483519641125216	2		424	453	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696466	47696466	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	231	361	0	ENST00000347630.2:c.357T>A	p.Ser119Arg	p.S119R	ENST00000347630	NM_001007230.1	119	agT/agA	6/11	0.327963190565785	3	FACETS	0.917	0.861	0.974	0.917	0.861	0.974	CLONAL	3	FALSE	0	0.327963190565785	3		361	596	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334852	81334852	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0029059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	91	320	0	ENST00000222390.5:c.1865-1G>A		p.X622_splice	ENST00000222390	NM_000601.4	622			0.232437386567975	4	FACETS	1	0.979	1	0.725	0.646	0.809	CLONAL	1	FALSE	2	0.327963190565785	4		320	508	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955550	48955550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913304	NA	P-0029060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	92	330	0	ENST00000267163.4:c.1666C>T	p.Arg556Ter	p.R556*	ENST00000267163	NM_000321.2	556	Cga/Tga	17/27	0.352432196105798	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.388892279929838	1		330	353	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0029060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	103	482	2	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.284151488177174	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.388892279929838	1		484	371	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0029060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	228	1069	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.388892279929838	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.388892279929838	1		1071	725	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637971	39637971	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	142	472	0	ENST00000262039.4:c.2388A>T	p.Gln796His	p.Q796H	ENST00000262039	NM_002647.2	796	caA/caT	22/25	0.284151488177174	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.388892279929838	1		472	571	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0029061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	575	516	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.438371825842648	5	FACETS	0.902	0.869	0.935	0.902	0.869	0.935	CLONAL	3	FALSE	2	0.699751655354802	5		516	1245	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0029061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	372	649	1	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.699751655354802	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	FALSE	0	0.699751655354802	1		650	603	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737419	145737419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756401653	NA	P-0029061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	120	619	0	ENST00000428558.2:c.3268G>A	p.Glu1090Lys	p.E1090K	ENST00000428558	NM_004260.3	1090	Gag/Aag	20/22	0.680775231730437	3	FACETS	0.547	0.494	0.604	0.182	0.164	0.202	SUBCLONAL	1	FALSE	0	0.699751655354802	3		619	846	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813525	32813525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1323308777	NA	P-0029061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	237	389	0	ENST00000354258.4:c.2258C>T	p.Ser753Phe	p.S753F	ENST00000354258	NM_000593.5	753	tCc/tTc	11/11	0.699751655354802	2	FACETS	1	0.992	1	0.663	0.625	0.7	CLONAL	1	FALSE	0	0.699751655354802	2		389	511	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472573	88472573	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	189	390	0	ENST00000360948.2:c.1982G>A	p.Ser661Asn	p.S661N	ENST00000360948	NM_001012338.2	661	aGt/aAt	16/19	0.699751655354802	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	0	0.699751655354802	1		390	350	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573542	48573542	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	182	312	0	ENST00000342988.3:c.128del	p.Leu43TrpfsTer2	p.L43Wfs*2	ENST00000342988	NM_005359.5	42	agT/ag	2/12	0.699751655354802	1	FACETS	0.989	0.929	1	0.989	0.929	1	CLONAL	1	FALSE	0	0.699751655354802	1		312	342	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138550	11138550	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	164	593	0	ENST00000358026.2:c.3306C>G	p.Phe1102Leu	p.F1102L	ENST00000358026	NM_001128849.1	1102	ttC/ttG	24/36	0.699751655354802	1	FACETS	0.491	0.452	0.531	0.491	0.452	0.531	SUBCLONAL	1	FALSE	0	0.699751655354802	1		593	621	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0029063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	259	428	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.546636251230056	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.546636251230056	3		428	539	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752411	57752412	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0029063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	91	146	0	ENST00000274289.3:c.1161_1162del	p.Arg387SerfsTer3	p.R387Sfs*3	ENST00000274289	NM_006622.3	387	agAGtg/agtg	9/14	0.546636251230056	6	FACETS	0.973	0.872	1	0.487	0.436	0.54	CLONAL	2	TRUE	2	0.546636251230056	6		146	358	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179455	56179457	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	novel	NA	P-0029063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	162	262	0	ENST00000399503.3:c.3770_3772del	p.Cys1257del	p.C1257del	ENST00000399503	NM_005921.1	1256	tcTTGt/tct	15/20	0.546636251230056	6	FACETS	1	0.966	1	0.542	0.5	0.586	CLONAL	2	TRUE	2	0.546636251230056	6		262	572	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177526	56177527	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0029063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	241	323	0	ENST00000399503.3:c.2502_2503dup	p.Ser835PhefsTer5	p.S835Ffs*5	ENST00000399503	NM_005921.1	833	-/TT	14/20	0.546636251230056	6	FACETS	1	0.971	1	0.787	0.741	0.834	CLONAL	3	TRUE	2	0.546636251230056	6		323	586	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0029064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	94	291	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.331958929878812	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.331958929878812	2		291	262	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0029064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	82	330	1	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.331958929878812	2	FACETS	0.898	0.802	0.999	0.898	0.802	0.999	CLONAL	2	TRUE	0	0.331958929878812	2		331	275	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844241	68844241	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	143	415	1	ENST00000261769.5:c.830del	p.Pro277GlnfsTer5	p.P277Qfs*5	ENST00000261769	NM_004360.3	277	Cca/ca	6/16	0.331958929878812	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	0	0.331958929878812	2		416	420	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961471	54961471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	63	289	1	ENST00000312783.6:c.161C>T	p.Ser54Phe	p.S54F	ENST00000312783	NM_198436.1	54	tCc/tTc	4/10	0.331958929878812	7	FACETS	1	0.897	1			1	CLONAL	1	TRUE	NA	0.331958929878812	7		290	665	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427369	49427369	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1565779294	NA	P-0029064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	90	597	0	ENST00000301067.7:c.11119C>T	p.Arg3707Ter	p.R3707*	ENST00000301067	NM_003482.3	3707	Cga/Tga	39/54	0.331958929878812	4	FACETS	0.915	0.812	1	0.458	0.406	0.513	CLONAL	1	TRUE	2	0.331958929878812	4		597	789	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058045	27058045	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	69	395	0	ENST00000324856.7:c.1753C>T	p.Gln585Ter	p.Q585*	ENST00000324856	NM_006015.4	585	Cag/Tag	3/20	0.331958929878812	2	FACETS	0.967	0.845	1	0.483	0.422	0.549	CLONAL	1	TRUE	0	0.331958929878812	2		395	430	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263854	16263854	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1225784551	NA	P-0029064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	50	586	0	ENST00000375759.3:c.10223C>T	p.Pro3408Leu	p.P3408L	ENST00000375759	NM_015001.2	3408	cCt/cTt	12/15	0.331958929878812	2	FACETS	0.481	0.408	0.562	0.241	0.204	0.281	SUBCLONAL	1	TRUE	0	0.331958929878812	2		586	626	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435877	110435877	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	35	525	0	ENST00000375856.3:c.2524C>T	p.Gln842Ter	p.Q842*	ENST00000375856	NM_003749.2	842	Cag/Tag	1/2	0.331958929878812	4	FACETS	0.415	0.339	0.501	0.208	0.169	0.251	SUBCLONAL	1	TRUE	2	0.331958929878812	4		525	676	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72833979	72833979	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	25	417	0	ENST00000268489.5:c.3914C>T	p.Ala1305Val	p.A1305V	ENST00000268489	NM_006885.3	1305	gCt/gTt	8/10	0.331958929878812	2	FACETS	0.383	0.302	0.477	0.192	0.151	0.239	SUBCLONAL	1	TRUE	0	0.331958929878812	2		417	393	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40879737	40879737	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	85	491	0	ENST00000428826.2:c.162G>T	p.Gln54His	p.Q54H	ENST00000428826		54	caG/caT	4/21	0.331958929878812	3	FACETS	1	0.915	1	0.52	0.46	0.584	CLONAL	1	TRUE	1	0.331958929878812	3		491	574	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387704	17387704	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	32	429	0	ENST00000359435.4:c.772G>C	p.Glu258Gln	p.E258Q	ENST00000359435	NM_001033549.1	258	Gag/Cag	8/9	0.331958929878812	3	FACETS	0.429	0.347	0.521	0.214	0.173	0.261	SUBCLONAL	1	TRUE	1	0.331958929878812	3		429	524	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703652	47703652	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587779139	NA	P-0029064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	35	379	0	ENST00000233146.2:c.2152C>G	p.Gln718Glu	p.Q718E	ENST00000233146	NM_000251.2	718	Caa/Gaa	13/16	0.331958929878812	3	FACETS	0.533	0.437	0.642	0.267	0.218	0.321	SUBCLONAL	1	TRUE	1	0.331958929878812	3		379	461	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1959731	1959731	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1416347752	NA	P-0029064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	28	244	0	ENST00000382891.5:c.2953G>A	p.Glu985Lys	p.E985K	ENST00000382891	NM_133335.3	985	Gag/Aag	16/22	0.331958929878812	4	FACETS	0.538	0.429	0.661			1	SUBCLONAL	1	TRUE	NA	0.331958929878812	4		244	418	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517974	8517974	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	33	339	0	ENST00000356435.5:c.1417G>C	p.Asp473His	p.D473H	ENST00000356435		473	Gac/Cac	10/35	0.331958929878812	3	FACETS	0.553	0.45	0.669	0.277	0.225	0.335	SUBCLONAL	1	TRUE	1	0.331958929878812	3		339	419	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969444	44969444	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	58	503	0	ENST00000377967.4:c.4126G>C	p.Glu1376Gln	p.E1376Q	ENST00000377967	NM_021140.2	1376	Gaa/Caa	28/29	0.325854255485918	4	FACETS	0.694	0.595	0.801	0.347	0.297	0.401	SUBCLONAL	1	TRUE	2	0.331958929878812	4		503	671	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039363	47039363	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	196	596	0	ENST00000377604.3:c.986C>A	p.Ser329Tyr	p.S329Y	ENST00000377604	NM_001204468.1	329	tCc/tAc	10/24	0.325854255485918	4	FACETS	0.998	0.926	1	0.998	0.926	1	CLONAL	2	TRUE	2	0.331958929878812	4		596	788	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972664	76972667	+	missense_variant	Missense_Mutation	ONP	GATG	GATG	AATA	novel	NA	P-0029064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	69	423	0	ENST00000373344.5:c.74_77delinsTATT	p.Ser25_Ser26delinsLeuLeu	p.S25_S26delinsLL	ENST00000373344	NM_000489.3	25	tCATCa/tTATTa	2/35	0.325854255485918	4	FACETS	0.956	0.834	1	0.478	0.417	0.545	CLONAL	1	TRUE	2	0.331958929878812	4		423	579	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	45	394	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.865	0.726	1	0.865	0.726	1	CLONAL	1	TRUE	1	0.17	2		394	612	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0029066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	54	523	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	1	2	FACETS	0.762	0.649	0.886	0.762	0.649	0.886	SUBCLONAL	1	TRUE	1	0.17	2		523	834	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138825	64138825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1388266879	NA	P-0029066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	71	521	0	ENST00000334205.4:c.2192G>A	p.Arg731Gln	p.R731Q	ENST00000334205	NM_003942.2	731	cGg/cAg	17/17	1	2	FACETS	0.891	0.776	1	0.891	0.776	1	CLONAL	1	TRUE	1	0.17	2		521	937	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464865	120464865	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	29	268	0	ENST00000256646.2:c.5207G>T	p.Gly1736Val	p.G1736V	ENST00000256646	NM_024408.3	1736	gGg/gTg	28/34	1	2	FACETS	0.735	0.589	0.902	0.735	0.589	0.902	CLONAL	1	TRUE	1	0.17	2		268	464	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406420	70406420	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	60	540	1	ENST00000373644.4:c.3934G>T	p.Val1312Leu	p.V1312L	ENST00000373644	NM_030625.2	1312	Gtg/Ttg	4/12	1	2	FACETS	0.82	0.705	0.946	0.82	0.705	0.946	CLONAL	1	TRUE	1	0.17	2		541	861	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377127	118377127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	34	263	0	ENST00000534358.1:c.10520C>T	p.Ala3507Val	p.A3507V	ENST00000534358	NM_005933.3	3507	gCt/gTt	27/36	1	2	FACETS	0.828	0.676	1	0.828	0.676	1	CLONAL	1	TRUE	1	0.17	2		263	483	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470615	25470615	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	48	525	0	ENST00000264709.3:c.859G>T	p.Gly287Cys	p.G287C	ENST00000264709	NM_175629.2	287	Ggc/Tgc	8/23	1	2	FACETS	0.622	0.524	0.731	0.622	0.524	0.731	SUBCLONAL	1	TRUE	1	0.17	2		525	908	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793450	242793450	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0029066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	82	415	0	ENST00000334409.5:c.628-1G>C		p.X210_splice	ENST00000334409	NM_005018.2	210			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.17	2		415	758	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807328	1807328	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	60	563	0	ENST00000260795.2:c.1577del	p.Met526ArgfsTer3	p.M526Rfs*3	ENST00000260795		526	aTg/ag	11/17	1	2	FACETS	0.723	0.621	0.835	0.723	0.621	0.835	SUBCLONAL	1	TRUE	1	0.17	2		563	976	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69000009	69000009	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	68	424	0	ENST00000288368.4:c.2078G>T	p.Gly693Val	p.G693V	ENST00000288368	NM_024870.2	693	gGa/gTa	19/40	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.17	2		424	791	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939205	76939205	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	51	499	0	ENST00000373344.5:c.1543A>T	p.Met515Leu	p.M515L	ENST00000373344	NM_000489.3	515	Atg/Ttg	9/35	1	2	FACETS	0.713	0.604	0.833	0.713	0.604	0.833	SUBCLONAL	1	TRUE	1	0.17	2		499	842	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439293	52439293	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	94	452	0	ENST00000460680.1:c.949del	p.Ala317LeufsTer18	p.A317Lfs*18	ENST00000460680	NM_004656.3	317	Gct/ct	11/17	0.487752787680613	1	FACETS	0.828	0.746	0.913	0.828	0.746	0.913	CLONAL	1	TRUE	0	0.54919781706366	1		452	300	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0029068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	121	272	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.587105715378993	2		272	408	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578538	7578538	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	325	722	0	ENST00000269305.4:c.392A>G	p.Asn131Ser	p.N131S	ENST00000269305	NM_001126112.2	131	aAc/aGc	5/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.587105715378993	2		722	1027	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073922	8073922	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0029068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	189	374	1	ENST00000377482.5:c.737T>A	p.Leu246Ter	p.L246*	ENST00000377482	NM_018948.3	246	tTa/tAa	4/4	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.587105715378993	2		375	551	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074336	8074337	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0029068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	90	336	0	ENST00000377482.5:c.322dup	p.Glu108GlyfsTer9	p.E108Gfs*9	ENST00000377482	NM_018948.3	108	gag/gGag	4/4	1	2	FACETS	0.618	0.55	0.69	0.618	0.55	0.69	SUBCLONAL	1	TRUE	1	0.587105715378993	2		336	496	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187719	11187719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767904339	NA	P-0029068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	255	501	0	ENST00000361445.4:c.6178C>T	p.Arg2060Trp	p.R2060W	ENST00000361445	NM_004958.3	2060	Cgg/Tgg	44/58	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.587105715378993	2		501	823	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876513	59876513	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1567829158	NA	P-0029068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	187	326	1	ENST00000259008.2:c.1288A>T	p.Ile430Leu	p.I430L	ENST00000259008	NM_032043.2	430	Ata/Tta	9/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.587105715378993	2		327	595	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117926	70117926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	155	335	0	ENST00000245479.2:c.394A>G	p.Asn132Asp	p.N132D	ENST00000245479	NM_000346.3	132	Aac/Gac	1/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.587105715378993	2		335	473	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291611	15291611	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	343	703	0	ENST00000263388.2:c.3023C>T	p.Pro1008Leu	p.P1008L	ENST00000263388	NM_000435.2	1008	cCt/cTt	19/33	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.587105715378993	2		703	1024	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069629	69069629	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	182	402	0	ENST00000288368.4:c.4304C>A	p.Ala1435Glu	p.A1435E	ENST00000288368	NM_024870.2	1435	gCa/gAa	35/40	0.511438966462664	4	FACETS	0.756	0.7	0.813	0.756	0.7	0.813	SUBCLONAL	2	TRUE	2	0.587105715378993	4		402	651	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0029069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	29	181	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.479	0.383	0.588	0.479	0.383	0.588	SUBCLONAL	1	TRUE	1	0.226783472102431	2		181	534	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	79	586	0	ENST00000269305.4:c.517G>C	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ctg	5/11	0.168001790728796	2	FACETS	0.928	0.815	1	0.464	0.407	0.525	CLONAL	1	TRUE	0	0.226783472102431	2		586	751	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346360	89346383	+	inframe_deletion	In_Frame_Del	DEL	GTGGAGGCCTGGTCAGGAGGCAGT	GTGGAGGCCTGGTCAGGAGGCAGT	-	novel	NA	P-0029069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	35	403	0	ENST00000301030.4:c.6567_6590del	p.Leu2190_Thr2197del	p.L2190_T2197del	ENST00000301030	NM_001256183.1	2189	gcACTGCCTCCTGACCAGGCCTCCACc/gcc	9/13	1	2	FACETS	0.539	0.441	0.649	0.539	0.441	0.649	SUBCLONAL	1	TRUE	1	0.226783472102431	2		403	573	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874188	151874188	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0029069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	116	229	0	ENST00000262189.6:c.8350A>T	p.Lys2784Ter	p.K2784*	ENST00000262189	NM_170606.2	2784	Aag/Tag	38/59	0.145403405784879	2	FACETS	0.883	0.799	0.972	0.883	0.799	0.972	CLONAL	2	TRUE	0	0.226783472102431	2		229	579	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	243	483	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	0.756474254701696	2		483	637	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	433	545	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.756474254701696	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.756474254701696	1		545	643	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10305520	10305520	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	63	467	0	ENST00000340748.4:c.56C>G	p.Ser19Trp	p.S19W	ENST00000340748		19	tCg/tGg	1/40	1	2	FACETS	0.201	0.173	0.232	0.201	0.173	0.232	SUBCLONAL	1	TRUE	1	0.756474254701696	2		467	828	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685281	89685281	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1060500116	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	81	223	0	ENST00000371953.3:c.176C>G	p.Ser59Ter	p.S59*	ENST00000371953	NM_000314.4	59	tCa/tGa	3/9	1	2	FACETS	0.871	0.779	0.966	0.871	0.779	0.966	CLONAL	1	TRUE	1	0.756474254701696	2		223	246	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604750	48604750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	203	482	1	ENST00000342988.3:c.1572G>T	p.Trp524Cys	p.W524C	ENST00000342988	NM_005359.5	524	tgG/tgT	12/12	0.756474254701696	1	FACETS	0.959	0.907	1	0.959	0.907	1	CLONAL	1	TRUE	0	0.756474254701696	1		483	348	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121909229	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	156	510	3	ENST00000371953.3:c.389G>T	p.Arg130Leu	p.R130L	ENST00000371953	NM_000314.4	130	cGa/cTa	5/9	1	2	FACETS	0.85	0.785	0.918	0.85	0.785	0.918	CLONAL	1	TRUE	1	0.756474254701696	2		513	485	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851515	63851515	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	263	425	0	ENST00000279873.7:c.2293G>C	p.Glu765Gln	p.E765Q	ENST00000279873	NM_032199.2	765	Gag/Cag	10/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.756474254701696	2		425	674	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874369	76874369	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	86	490	1	ENST00000373344.5:c.5353C>T	p.Gln1785Ter	p.Q1785*	ENST00000373344	NM_000489.3	1785	Caa/Taa	21/35	1	2	FACETS	0.486	0.431	0.544	0.486	0.431	0.544	SUBCLONAL	1	TRUE	1	0.756474254701696	2		491	468	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496932	29496932	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	148	271	0	ENST00000356175.3:c.503C>A	p.Ser168Ter	p.S168*	ENST00000356175	NM_000267.3	168	tCa/tAa	5/57	0.756474254701696	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.756474254701696	1		271	242	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933307	100933307	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	239	464	1	ENST00000325455.5:c.2083G>A	p.Glu695Lys	p.E695K	ENST00000325455	NM_001202474.3	695	Gaa/Aaa	4/8	1	2	FACETS	0.966	0.908	1	0.966	0.908	1	CLONAL	1	TRUE	1	0.756474254701696	2		465	654	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	210	320	0	ENST00000308159.5:c.40G>C	p.Glu14Gln	p.E14Q	ENST00000308159	NM_014669.4	14	Gaa/Caa	2/22	0.756474254701696	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.756474254701696	1		320	320	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280288	1280288	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	370	627	1	ENST00000310581.5:c.1935C>A	p.Phe645Leu	p.F645L	ENST00000310581	NM_198253.2	645	ttC/ttA	4/16	1	2	FACETS	0.907	0.861	0.952	0.907	0.861	0.952	CLONAL	1	TRUE	1	0.756474254701696	2		628	1079	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946152	55946152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1383334001	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	158	269	0	ENST00000263923.4:c.4027C>T	p.Leu1343Phe	p.L1343F	ENST00000263923	NM_002253.2	1343	Ctc/Ttc	30/30	1	2	FACETS	0.858	0.792	0.925	0.858	0.792	0.925	CLONAL	1	TRUE	1	0.756474254701696	2		269	487	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202762	108202762	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1555124747	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	141	330	0	ENST00000278616.4:c.7786G>A	p.Glu2596Lys	p.E2596K	ENST00000278616	NM_000051.3	2596	Gag/Aag	52/63	1	2	FACETS	0.894	0.822	0.967	0.894	0.822	0.967	CLONAL	1	TRUE	1	0.756474254701696	2		330	417	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21629923	21629923	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140033676	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	149	369	0	ENST00000421138.2:c.871C>T	p.Arg291Trp	p.R291W	ENST00000421138		291	Cgg/Tgg	9/16	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.756474254701696	2		369	387	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439896	49439896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	303	513	1	ENST00000301067.7:c.4645G>A	p.Glu1549Lys	p.E1549K	ENST00000301067	NM_003482.3	1549	Gaa/Aaa	17/54	1	2	FACETS	0.913	0.863	0.964	0.913	0.863	0.964	CLONAL	1	TRUE	1	0.756474254701696	2		514	877	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945104	32945104	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs558819788	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	102	288	0	ENST00000380152.3:c.8499G>C	p.Lys2833Asn	p.K2833N	ENST00000380152		2833	aaG/aaC	20/27	0.756474254701696	1	FACETS	0.947	0.874	1	0.947	0.874	1	CLONAL	1	TRUE	0	0.756474254701696	1		288	177	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701897	43701897	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	152	258	0	ENST00000382044.4:c.5348C>T	p.Ser1783Phe	p.S1783F	ENST00000382044	NM_001141980.1	1783	tCc/tTc	25/28	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.756474254701696	2		258	394	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632354	3632354	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	313	521	0	ENST00000294008.3:c.5494G>C	p.Glu1832Gln	p.E1832Q	ENST00000294008	NM_032444.2	1832	Gag/Cag	15/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.756474254701696	2		521	799	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273887	10273887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	307	611	1	ENST00000330684.3:c.382C>T	p.His128Tyr	p.H128Y	ENST00000330684	NM_001134407.1	128	Cat/Tat	2/13	1	2	FACETS	0.987	0.935	1	0.987	0.935	1	CLONAL	1	TRUE	1	0.756474254701696	2		612	822	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14021978	14021978	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	223	460	0	ENST00000311895.7:c.678G>C	p.Gln226His	p.Q226H	ENST00000311895	NM_005236.2	226	caG/caC	4/11	1	2	FACETS	0.998	0.936	1	0.998	0.936	1	CLONAL	1	TRUE	1	0.756474254701696	2		460	591	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844182	68844182	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	366	589	1	ENST00000261769.5:c.770A>T	p.Asp257Val	p.D257V	ENST00000261769	NM_004360.3	257	gAc/gTc	6/16	0.756474254701696	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.756474254701696	1		590	569	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16046984	16046984	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	208	356	0	ENST00000268712.3:c.1109C>G	p.Ser370Ter	p.S370*	ENST00000268712	NM_006311.3	370	tCa/tGa	11/46	0.756474254701696	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.756474254701696	1		356	325	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775135	73775135	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	137	401	0	ENST00000254810.4:c.121C>T	p.Arg41Cys	p.R41C	ENST00000254810	NM_005324.3	41	Cgc/Tgc	2/4	0.756474254701696	1	FACETS	0.585	0.538	0.633	0.585	0.538	0.633	SUBCLONAL	1	TRUE	0	0.756474254701696	1		401	385	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78519481	78519481	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	27	445	0	ENST00000306801.3:c.52G>A	p.Glu18Lys	p.E18K	ENST00000306801	NM_020761.2	18	Gag/Aag	1/34	0.756474254701696	1	FACETS	0.089	0.07	0.11	0.089	0.07	0.11	SUBCLONAL	1	TRUE	0	0.756474254701696	1		445	500	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661195	227661195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	365	605	0	ENST00000305123.5:c.2260G>A	p.Glu754Lys	p.E754K	ENST00000305123	NM_005544.2	754	Gag/Aag	1/2	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.756474254701696	2		605	943	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319716	62319716	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	387	594	0	ENST00000360203.5:c.1699G>A	p.Glu567Lys	p.E567K	ENST00000360203	NM_001283009.1	567	Gag/Aag	20/35	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.756474254701696	2		594	845	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162125	22162125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779189994	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	132	263	0	ENST00000215832.6:c.130G>A	p.Asp44Asn	p.D44N	ENST00000215832	NM_002745.4	44	Gat/Aat	2/9	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.756474254701696	2		263	335	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626066	12626066	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	233	325	0	ENST00000251849.4:c.1894G>A	p.Glu632Lys	p.E632K	ENST00000251849	NM_002880.3	632	Gag/Aag	17/17	1	2	FACETS	0.969	0.909	1	0.969	0.909	1	CLONAL	1	TRUE	1	0.756474254701696	2		325	636	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162504	47162504	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	145	296	0	ENST00000409792.3:c.3622G>T	p.Asp1208Tyr	p.D1208Y	ENST00000409792	NM_014159.6	1208	Gat/Tat	3/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.756474254701696	2		296	361	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164489	47164489	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	138	312	0	ENST00000409792.3:c.1637C>G	p.Ser546Cys	p.S546C	ENST00000409792	NM_014159.6	546	tCt/tGt	3/21	1	2	FACETS	0.931	0.856	1	0.931	0.856	1	CLONAL	1	TRUE	1	0.756474254701696	2		312	392	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164693	47164693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780072755	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	23	284	0	ENST00000409792.3:c.1433C>T	p.Ser478Phe	p.S478F	ENST00000409792	NM_014159.6	478	tCt/tTt	3/21	1	2	FACETS	0.159	0.124	0.2	0.159	0.124	0.2	SUBCLONAL	1	TRUE	1	0.756474254701696	2		284	382	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187558034	187558034	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	114	230	0	ENST00000441802.2:c.3677C>G	p.Ser1226Ter	p.S1226*	ENST00000441802	NM_005245.3	1226	tCa/tGa	5/27	1	2	FACETS	0.963	0.879	1	0.963	0.879	1	CLONAL	1	TRUE	1	0.756474254701696	2		230	313	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287897	33287898	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCC	rs762240849	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	126	398	0	ENST00000374542.5:c.1353_1355dup	p.Glu457dup	p.E457dup	ENST00000374542	NM_001141970.1	457	gaa/gaGGAa	5/8	1	2	FACETS	0.564	0.512	0.618	0.564	0.512	0.618	SUBCLONAL	1	TRUE	1	0.756474254701696	2		398	591	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522114	157522114	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	197	432	0	ENST00000346085.5:c.4386G>C	p.Gln1462His	p.Q1462H	ENST00000346085	NM_020732.3	1462	caG/caC	18/20	1	2	FACETS	0.928	0.866	0.992	0.928	0.866	0.992	CLONAL	1	TRUE	1	0.756474254701696	2		432	561	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444263	50444263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	179	295	0	ENST00000331340.3:c.193G>A	p.Glu65Lys	p.E65K	ENST00000331340	NM_006060.4	65	Gaa/Aaa	4/8	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.756474254701696	2		295	462	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476714	140476714	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	26	244	0	ENST00000288602.6:c.1692G>A	p.Met564Ile	p.M564I	ENST00000288602	NM_004333.4	564	atG/atA	13/18	1	2	FACETS	0.228	0.181	0.283	0.228	0.181	0.283	SUBCLONAL	1	TRUE	1	0.756474254701696	2		244	301	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874809	151874809	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	148	276	0	ENST00000262189.6:c.7729C>G	p.Pro2577Ala	p.P2577A	ENST00000262189	NM_170606.2	2577	Cca/Gca	38/59	1	2	FACETS	0.887	0.818	0.959	0.887	0.818	0.959	CLONAL	1	TRUE	1	0.756474254701696	2		276	441	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878676	151878676	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	165	370	0	ENST00000262189.6:c.6269C>G	p.Ser2090Ter	p.S2090*	ENST00000262189	NM_170606.2	2090	tCa/tGa	36/59	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.756474254701696	2		370	416	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345939	152345939	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	223	414	0	ENST00000359321.1:c.631C>G	p.His211Asp	p.H211D	ENST00000359321	NM_005431.1	211	Cat/Gat	3/3	1	2	FACETS	0.97	0.909	1	0.97	0.909	1	CLONAL	1	TRUE	1	0.756474254701696	2		414	608	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162233	38162233	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	36	405	0	ENST00000317025.8:c.2483C>G	p.Ser828Cys	p.S828C	ENST00000317025	NM_023034.1	828	tCt/tGt	14/24	1	2	FACETS	0.161	0.132	0.194	0.161	0.132	0.194	SUBCLONAL	1	TRUE	1	0.756474254701696	2		405	590	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484129	8484129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	148	309	0	ENST00000356435.5:c.3403G>A	p.Glu1135Lys	p.E1135K	ENST00000356435		1135	Gag/Aag	19/35	1	2	FACETS	0.866	0.797	0.936	0.866	0.797	0.936	CLONAL	1	TRUE	1	0.756474254701696	2		309	452	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650622	48650622	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557020273	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	38	503	0	ENST00000376670.3:c.592C>T	p.Pro198Ser	p.P198S	ENST00000376670	NM_002049.3	198	Ccc/Tcc	3/6	1	2	FACETS	0.151	0.124	0.181	0.151	0.124	0.181	SUBCLONAL	1	TRUE	1	0.756474254701696	2		503	666	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875916	76875916	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	44	406	0	ENST00000373344.5:c.5219C>G	p.Ser1740Ter	p.S1740*	ENST00000373344	NM_000489.3	1740	tCa/tGa	20/35	1	2	FACETS	0.225	0.189	0.266	0.225	0.189	0.266	SUBCLONAL	1	TRUE	1	0.756474254701696	2		406	516	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875940	76875940	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs782089856	NA	P-0029083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	35	409	0	ENST00000373344.5:c.5195C>G	p.Ser1732Cys	p.S1732C	ENST00000373344	NM_000489.3	1732	tCt/tGt	20/35	1	2	FACETS	0.187	0.153	0.225	0.187	0.153	0.225	SUBCLONAL	1	TRUE	1	0.756474254701696	2		409	495	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	245	483	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	0.985	1	CLONAL	1	TRUE	1	0.599250253718819	2		483	714	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	260	545	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.588403714159307	1	FACETS	0.96	0.906	1	0.96	0.906	1	CLONAL	1	TRUE	0	0.599250253718819	1		545	633	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685281	89685281	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1060500116	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	105	223	0	ENST00000371953.3:c.176C>G	p.Ser59Ter	p.S59*	ENST00000371953	NM_000314.4	59	tCa/tGa	3/9	1	2	FACETS	0.947	0.856	1	0.947	0.856	1	CLONAL	1	TRUE	1	0.599250253718819	2		223	370	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604750	48604750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	161	482	1	ENST00000342988.3:c.1572G>T	p.Trp524Cys	p.W524C	ENST00000342988	NM_005359.5	524	tgG/tgT	12/12	0.588403714159307	1	FACETS	0.9	0.835	0.967	0.9	0.835	0.967	CLONAL	1	TRUE	0	0.599250253718819	1		483	418	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121909229	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	186	510	3	ENST00000371953.3:c.389G>T	p.Arg130Leu	p.R130L	ENST00000371953	NM_000314.4	130	cGa/cTa	5/9	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.599250253718819	2		513	614	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851515	63851515	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	233	425	0	ENST00000279873.7:c.2293G>C	p.Glu765Gln	p.E765Q	ENST00000279873	NM_032199.2	765	Gag/Cag	10/10	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.599250253718819	2		425	766	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874369	76874369	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	218	490	1	ENST00000373344.5:c.5353C>T	p.Gln1785Ter	p.Q1785*	ENST00000373344	NM_000489.3	1785	Caa/Taa	21/35	0.398996801891848	1	FACETS	0.83	0.777	0.884	0.83	0.777	0.884	CLONAL	1	TRUE	0	0.599250253718819	1		491	614	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496932	29496932	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	145	271	0	ENST00000356175.3:c.503C>A	p.Ser168Ter	p.S168*	ENST00000356175	NM_000267.3	168	tCa/tAa	5/57	0.588403714159307	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.599250253718819	1		271	325	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933307	100933307	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	227	464	1	ENST00000325455.5:c.2083G>A	p.Glu695Lys	p.E695K	ENST00000325455	NM_001202474.3	695	Gaa/Aaa	4/8	1	2	FACETS	0.965	0.902	1	0.965	0.902	1	CLONAL	1	TRUE	1	0.599250253718819	2		465	785	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	161	320	0	ENST00000308159.5:c.40G>C	p.Glu14Gln	p.E14Q	ENST00000308159	NM_014669.4	14	Gaa/Caa	2/22	0.599250253718819	1	FACETS	0.925	0.858	0.992	0.925	0.858	0.992	CLONAL	1	TRUE	0	0.599250253718819	1		320	407	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280288	1280288	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	274	627	1	ENST00000310581.5:c.1935C>A	p.Phe645Leu	p.F645L	ENST00000310581	NM_198253.2	645	ttC/ttA	4/16	1	2	FACETS	0.915	0.86	0.972	0.915	0.86	0.972	CLONAL	1	TRUE	1	0.599250253718819	2		628	999	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946152	55946152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1383334001	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	144	269	0	ENST00000263923.4:c.4027C>T	p.Leu1343Phe	p.L1343F	ENST00000263923	NM_002253.2	1343	Ctc/Ttc	30/30	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.599250253718819	2		269	471	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202762	108202762	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1555124747	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	162	330	0	ENST00000278616.4:c.7786G>A	p.Glu2596Lys	p.E2596K	ENST00000278616	NM_000051.3	2596	Gag/Aag	52/63	1	2	FACETS	0.907	0.836	0.98	0.907	0.836	0.98	CLONAL	1	TRUE	1	0.599250253718819	2		330	596	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21629923	21629923	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140033676	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	167	369	0	ENST00000421138.2:c.871C>T	p.Arg291Trp	p.R291W	ENST00000421138		291	Cgg/Tgg	9/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.599250253718819	2		369	500	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439896	49439896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	214	513	1	ENST00000301067.7:c.4645G>A	p.Glu1549Lys	p.E1549K	ENST00000301067	NM_003482.3	1549	Gaa/Aaa	17/54	1	2	FACETS	0.929	0.866	0.994	0.929	0.866	0.994	CLONAL	1	TRUE	1	0.599250253718819	2		514	769	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945104	32945104	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs558819788	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	108	288	0	ENST00000380152.3:c.8499G>C	p.Lys2833Asn	p.K2833N	ENST00000380152		2833	aaG/aaC	20/27	0.599250253718819	1	FACETS	0.85	0.774	0.928	0.85	0.774	0.928	CLONAL	1	TRUE	0	0.599250253718819	1		288	297	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701897	43701897	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	142	258	0	ENST00000382044.4:c.5348C>T	p.Ser1783Phe	p.S1783F	ENST00000382044	NM_001141980.1	1783	tCc/tTc	25/28	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.599250253718819	2		258	464	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632354	3632354	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	213	521	0	ENST00000294008.3:c.5494G>C	p.Glu1832Gln	p.E1832Q	ENST00000294008	NM_032444.2	1832	Gag/Cag	15/15	1	2	FACETS	0.904	0.843	0.968	0.904	0.843	0.968	CLONAL	1	TRUE	1	0.599250253718819	2		521	786	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273887	10273887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	236	611	1	ENST00000330684.3:c.382C>T	p.His128Tyr	p.H128Y	ENST00000330684	NM_001134407.1	128	Cat/Tat	2/13	1	2	FACETS	0.956	0.894	1	0.956	0.894	1	CLONAL	1	TRUE	1	0.599250253718819	2		612	824	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14021978	14021978	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	188	460	0	ENST00000311895.7:c.678G>C	p.Gln226His	p.Q226H	ENST00000311895	NM_005236.2	226	caG/caC	4/11	1	2	FACETS	0.923	0.856	0.992	0.923	0.856	0.992	CLONAL	1	TRUE	1	0.599250253718819	2		460	680	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844182	68844182	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	243	589	1	ENST00000261769.5:c.770A>T	p.Asp257Val	p.D257V	ENST00000261769	NM_004360.3	257	gAc/gTc	6/16	0.599250253718819	1	FACETS	0.906	0.852	0.96	0.906	0.852	0.96	CLONAL	1	TRUE	0	0.599250253718819	1		590	627	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16046984	16046984	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	165	356	0	ENST00000268712.3:c.1109C>G	p.Ser370Ter	p.S370*	ENST00000268712	NM_006311.3	370	tCa/tGa	11/46	0.588403714159307	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.599250253718819	1		356	385	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775135	73775135	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	216	401	0	ENST00000254810.4:c.121C>T	p.Arg41Cys	p.R41C	ENST00000254810	NM_005324.3	41	Cgc/Tgc	2/4	0.588403714159307	1	FACETS	0.965	0.906	1	0.965	0.906	1	CLONAL	1	TRUE	0	0.599250253718819	1		401	523	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661195	227661195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	281	605	0	ENST00000305123.5:c.2260G>A	p.Glu754Lys	p.E754K	ENST00000305123	NM_005544.2	754	Gag/Aag	1/2	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.599250253718819	2		605	909	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319716	62319716	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	233	594	0	ENST00000360203.5:c.1699G>A	p.Glu567Lys	p.E567K	ENST00000360203	NM_001283009.1	567	Gag/Aag	20/35	1	2	FACETS	0.981	0.917	1	0.981	0.917	1	CLONAL	1	TRUE	1	0.599250253718819	2		594	793	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162125	22162125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779189994	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	139	263	0	ENST00000215832.6:c.130G>A	p.Asp44Asn	p.D44N	ENST00000215832	NM_002745.4	44	Gat/Aat	2/9	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.599250253718819	2		263	440	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626066	12626066	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	193	325	0	ENST00000251849.4:c.1894G>A	p.Glu632Lys	p.E632K	ENST00000251849	NM_002880.3	632	Gag/Aag	17/17	1	2	FACETS	0.996	0.925	1	0.996	0.925	1	CLONAL	1	TRUE	1	0.599250253718819	2		325	647	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162504	47162504	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	158	296	0	ENST00000409792.3:c.3622G>T	p.Asp1208Tyr	p.D1208Y	ENST00000409792	NM_014159.6	1208	Gat/Tat	3/21	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.599250253718819	2		296	476	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164489	47164489	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	125	312	0	ENST00000409792.3:c.1637C>G	p.Ser546Cys	p.S546C	ENST00000409792	NM_014159.6	546	tCt/tGt	3/21	1	2	FACETS	0.85	0.774	0.929	0.85	0.774	0.929	CLONAL	1	TRUE	1	0.599250253718819	2		312	491	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187558034	187558034	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	39	230	0	ENST00000441802.2:c.3677C>G	p.Ser1226Ter	p.S1226*	ENST00000441802	NM_005245.3	1226	tCa/tGa	5/27	0.337645080263562	1	FACETS	0.31	0.258	0.368	0.31	0.258	0.368	INDETERMINATE	1	TRUE	0	0.599250253718819	1		230	294	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287897	33287898	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCC	rs762240849	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	104	398	0	ENST00000374542.5:c.1353_1355dup	p.Glu457dup	p.E457dup	ENST00000374542	NM_001141970.1	457	gaa/gaGGAa	5/8	1	2	FACETS	0.55	0.493	0.61	0.55	0.493	0.61	SUBCLONAL	1	TRUE	1	0.599250253718819	2		398	631	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522114	157522114	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	201	432	0	ENST00000346085.5:c.4386G>C	p.Gln1462His	p.Q1462H	ENST00000346085	NM_020732.3	1462	caG/caC	18/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.599250253718819	2		432	609	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444263	50444263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	140	295	0	ENST00000331340.3:c.193G>A	p.Glu65Lys	p.E65K	ENST00000331340	NM_006060.4	65	Gaa/Aaa	4/8	1	2	FACETS	0.956	0.876	1	0.956	0.876	1	CLONAL	1	TRUE	1	0.599250253718819	2		295	489	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874809	151874809	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	143	276	0	ENST00000262189.6:c.7729C>G	p.Pro2577Ala	p.P2577A	ENST00000262189	NM_170606.2	2577	Cca/Gca	38/59	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.599250253718819	2		276	433	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878676	151878676	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	157	370	0	ENST00000262189.6:c.6269C>G	p.Ser2090Ter	p.S2090*	ENST00000262189	NM_170606.2	2090	tCa/tGa	36/59	1	2	FACETS	0.949	0.875	1	0.949	0.875	1	CLONAL	1	TRUE	1	0.599250253718819	2		370	552	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345939	152345939	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	159	414	0	ENST00000359321.1:c.631C>G	p.His211Asp	p.H211D	ENST00000359321	NM_005431.1	211	Cat/Gat	3/3	1	2	FACETS	0.782	0.718	0.847	0.782	0.718	0.847	SUBCLONAL	1	TRUE	1	0.599250253718819	2		414	679	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484129	8484129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	162	309	0	ENST00000356435.5:c.3403G>A	p.Glu1135Lys	p.E1135K	ENST00000356435		1135	Gag/Aag	19/35	1	2	FACETS	0.996	0.919	1	0.996	0.919	1	CLONAL	1	TRUE	1	0.599250253718819	2		309	543	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398262	25398262	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913538	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	156	412	0	ENST00000311936.3:c.57G>C	p.Leu19Phe	p.L19F	ENST00000311936	NM_004985.3	19	ttG/ttC	2/5	1	2	FACETS	0.928	0.855	1	0.928	0.855	1	CLONAL	1	TRUE	1	0.599250253718819	2		412	561	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023246	1023246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs184776294	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	81	365	0	ENST00000358495.3:c.1009G>A	p.Asp337Asn	p.D337N	ENST00000358495	NM_134424.2	337	Gat/Aat	11/12	1	2	FACETS	0.417	0.367	0.471	0.417	0.367	0.471	SUBCLONAL	1	TRUE	1	0.599250253718819	2		365	648	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2949706	2949706	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	235	582	0	ENST00000396946.4:c.3238G>C	p.Glu1080Gln	p.E1080Q	ENST00000396946	NM_032415.4	1080	Gag/Cag	24/25	1	2	FACETS	0.966	0.904	1	0.966	0.904	1	CLONAL	1	TRUE	1	0.599250253718819	2		582	812	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795601	42795601	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	52	612	0	ENST00000575354.2:c.2681C>G	p.Ser894Cys	p.S894C	ENST00000575354	NM_015125.3	894	tCc/tGc	10/20	0.168530679391257	3	FACETS	0.232	0.196	0.271	0.077	0.065	0.091	INDETERMINATE	1	TRUE	0	0.599250253718819	3		612	974	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197399	26197399	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	125	295	0	ENST00000356476.2:c.80G>C	p.Arg27Pro	p.R27P	ENST00000356476		27	cGa/cCa	1/1	0.207750588950574	3	FACETS	1	0.974	1	0.592	0.539	0.647	INDETERMINATE	1	TRUE	1	0.599250253718819	3		295	458	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106456	27106456	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	204	417	0	ENST00000324856.7:c.6067G>C	p.Glu2023Gln	p.E2023Q	ENST00000324856	NM_006015.4	2023	Gaa/Caa	20/20	1	2	FACETS	0.99	0.922	1	0.99	0.922	1	CLONAL	1	TRUE	1	0.599250253718819	2		417	688	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814638	43814638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	69	395	1	ENST00000372470.3:c.1433C>T	p.Ser478Leu	p.S478L	ENST00000372470	NM_005373.2	478	tCg/tTg	9/12	1	2	FACETS	0.371	0.323	0.423	0.371	0.323	0.423	SUBCLONAL	1	TRUE	1	0.599250253718819	2		396	620	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204513717	204513717	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	123	212	0	ENST00000367182.3:c.727G>C	p.Glu243Gln	p.E243Q	ENST00000367182	NM_001278516.1	243	Gag/Cag	9/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.599250253718819	2		212	387	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332663	70332663	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	95	418	0	ENST00000373644.4:c.568C>G	p.Gln190Glu	p.Q190E	ENST00000373644	NM_030625.2	190	Cag/Gag	2/12	1	2	FACETS	0.428	0.381	0.478	0.428	0.381	0.478	SUBCLONAL	1	TRUE	1	0.599250253718819	2		418	741	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77043864	77043864	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	136	527	0	ENST00000356341.3:c.1462G>C	p.Glu488Gln	p.E488Q	ENST00000356341	NM_002576.4	488	Gag/Cag	14/15	1	2	FACETS	0.482	0.438	0.529	0.482	0.438	0.529	SUBCLONAL	1	TRUE	1	0.599250253718819	2		527	941	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155108	108155108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	179	408	0	ENST00000278616.4:c.3901G>A	p.Glu1301Lys	p.E1301K	ENST00000278616	NM_000051.3	1301	Gag/Aag	26/63	1	2	FACETS	0.979	0.907	1	0.979	0.907	1	CLONAL	1	TRUE	1	0.599250253718819	2		408	610	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343925	118343925	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	170	339	0	ENST00000534358.1:c.2051C>G	p.Ser684Cys	p.S684C	ENST00000534358	NM_005933.3	684	tCt/tGt	3/36	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.599250253718819	2		339	512	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132987	30132987	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	220	419	0	ENST00000331968.5:c.614C>G	p.Ser205Ter	p.S205*	ENST00000331968	NM_002742.2	205	tCa/tGa	4/18	1	2	FACETS	0.87	0.811	0.931	0.87	0.811	0.931	CLONAL	1	TRUE	1	0.599250253718819	2		419	844	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68290300	68290300	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	67	337	0	ENST00000487270.1:c.40G>C	p.Glu14Gln	p.E14Q	ENST00000487270	NM_133509.3	14	Gag/Cag	2/11	1	2	FACETS	0.429	0.373	0.49	0.429	0.373	0.49	SUBCLONAL	1	TRUE	1	0.599250253718819	2		337	521	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993207	72993207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	315	615	0	ENST00000268489.5:c.838C>T	p.Pro280Ser	p.P280S	ENST00000268489	NM_006885.3	280	Ccc/Tcc	2/10	0.599250253718819	1	FACETS	0.964	0.915	1	0.964	0.915	1	CLONAL	1	TRUE	0	0.599250253718819	1		615	764	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57569975	57569975	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	69	254	0	ENST00000316660.6:c.155C>G	p.Ser52Ter	p.S52*	ENST00000316660	NM_021127.2	52	tCa/tGa	2/2	0.588403714159307	1	FACETS	0.468	0.41	0.529	0.468	0.41	0.529	SUBCLONAL	1	TRUE	0	0.599250253718819	1		254	345	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273487	5273489	+	frameshift_variant	Frame_Shift_Del	DEL	CTC	CTC	TT	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	200	577	3	ENST00000357368.4:c.343_345delinsAA	p.Glu115LysfsTer29	p.E115Kfs*29	ENST00000357368	NM_002850.3	115	GAG/AA	4/38	1	2	FACETS	0.81	0.752	0.87	0.81	0.752	0.87	CLONAL	1	TRUE	1	0.599250253718819	2		580	824	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223804	36223804	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	310	656	0	ENST00000222270.7:c.6354G>C	p.Leu2118Phe	p.L2118F	ENST00000222270	NM_014727.1	2118	ttG/ttC	28/37	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.599250253718819	2		656	1018	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149039	61149039	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	82	324	0	ENST00000295025.8:c.1229C>A	p.Ser410Ter	p.S410*	ENST00000295025	NM_002908.2	410	tCa/tAa	11/11	1	2	FACETS	0.457	0.403	0.514	0.457	0.403	0.514	SUBCLONAL	1	TRUE	1	0.599250253718819	2		324	599	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61706089	61706089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	189	402	0	ENST00000401558.2:c.3082G>A	p.Glu1028Lys	p.E1028K	ENST00000401558	NM_003400.3	1028	Gaa/Aaa	25/25	1	2	FACETS	0.986	0.915	1	0.986	0.915	1	CLONAL	1	TRUE	1	0.599250253718819	2		402	640	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659908	227659908	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	92	495	1	ENST00000305123.5:c.3547G>A	p.Asp1183Asn	p.D1183N	ENST00000305123	NM_005544.2	1183	Gat/Aat	1/2	1	2	FACETS	0.396	0.351	0.443	0.396	0.351	0.443	SUBCLONAL	1	TRUE	1	0.599250253718819	2		496	776	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012684	36012684	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1475181251	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	25	65	0	ENST00000358208.4:c.128C>G	p.Ser43Trp	p.S43W	ENST00000358208		43	tCg/tGg	2/12	1	2	FACETS	0.637	0.509	0.779	0.637	0.509	0.779	SUBCLONAL	1	TRUE	1	0.599250253718819	2		65	131	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514555	41514555	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	70	372	0	ENST00000373198.4:c.106G>C	p.Glu36Gln	p.E36Q	ENST00000373198	NM_133170.3	36	Gag/Cag	2/32	1	2	FACETS	0.352	0.307	0.402	0.352	0.307	0.402	SUBCLONAL	1	TRUE	1	0.599250253718819	2		372	663	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204614	128204614	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	130	520	0	ENST00000341105.2:c.827C>G	p.Ser276Cys	p.S276C	ENST00000341105	NM_032638.4	276	tCc/tGc	3/6	1	2	FACETS	0.522	0.473	0.573	0.522	0.473	0.573	SUBCLONAL	1	TRUE	1	0.599250253718819	2		520	831	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898743	134898743	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	72	293	0	ENST00000398015.3:c.1801G>C	p.Glu601Gln	p.E601Q	ENST00000398015	NM_004441.4	601	Gag/Cag	10/16	1	2	FACETS	0.502	0.439	0.569	0.502	0.439	0.569	SUBCLONAL	1	TRUE	1	0.599250253718819	2		293	479	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509136	66509149	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AATAAATTCACTGA	AATAAATTCACTGA	-	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	43	326	0	ENST00000273854.3:c.182-4_191del		p.X61_splice	ENST00000273854	NM_004439.5	61		2/18	1	2	FACETS	0.307	0.257	0.363	0.307	0.257	0.363	SUBCLONAL	1	TRUE	1	0.599250253718819	2		326	467	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970889	79970889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	129	510	0	ENST00000265081.6:c.1115C>T	p.Ser372Phe	p.S372F	ENST00000265081	NM_002439.4	372	tCt/tTt	7/24	1	2	FACETS	0.475	0.43	0.522	0.475	0.43	0.522	SUBCLONAL	1	TRUE	1	0.599250253718819	2		510	907	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339243	116339243	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs376244358	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	51	289	0	ENST00000397752.3:c.105G>C	p.Met35Ile	p.M35I	ENST00000397752	NM_000245.2	35	atG/atC	2/21	1	2	FACETS	0.337	0.286	0.393	0.337	0.286	0.393	SUBCLONAL	1	TRUE	1	0.599250253718819	2		289	505	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981679	70981679	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs760438283	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	112	704	0	ENST00000276594.2:c.417G>C	p.Glu139Asp	p.E139D	ENST00000276594	NM_024504.3	139	gaG/gaC	2/8	1	2	FACETS	0.388	0.348	0.43	0.388	0.348	0.43	SUBCLONAL	1	TRUE	1	0.599250253718819	2		704	963	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27192561	27192561	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1331501009	NA	P-0029083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	224	445	0	ENST00000380036.4:c.1564C>T	p.Arg522Cys	p.R522C	ENST00000380036	NM_000459.3	522	Cgt/Tgt	11/23	1	2	FACETS	0.935	0.872	0.998	0.935	0.872	0.998	CLONAL	1	TRUE	1	0.599250253718819	2		445	800	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0029084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	134	500	4	ENST00000269305.4:c.559+1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.337065255188703	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.384274413605558	2		504	332	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879617	123879617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	49	396	0	ENST00000330479.4:c.313G>A	p.Val105Ile	p.V105I	ENST00000330479	NM_020382.3	105	Gta/Ata	4/9	0.384274413605558	3	FACETS	0.861	0.732	1	0.287	0.244	0.334	CLONAL	1	TRUE	0	0.384274413605558	3		396	353	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913263	32913263	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	228	508	0	ENST00000380152.3:c.4771del	p.Cys1591ValfsTer26	p.C1591Vfs*26	ENST00000380152		1591	Tgt/gt	11/27	0.222985636003565	4	FACETS	0.939	0.882	0.997	0.704	0.661	0.748	INDETERMINATE	3	TRUE	0	0.384274413605558	4		508	583	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272078	15272078	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	73	592	0	ENST00000263388.2:c.6361T>G	p.Phe2121Val	p.F2121V	ENST00000263388	NM_000435.2	2121	Ttc/Gtc	33/33	0.374416685968224	3	FACETS	1	0.968	1	0.658	0.58	0.742	CLONAL	1	TRUE	1	0.384274413605558	3		592	344	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157256623	157256633	+	frameshift_variant	Frame_Shift_Del	DEL	AACTAGATCTC	AACTAGATCTC	-	novel	NA	P-0029084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	46	301	0	ENST00000346085.5:c.1953_1963del	p.Arg652SerfsTer8	p.R652Sfs*8	ENST00000346085	NM_020732.3	650	ggAACTAGATCTCaa/ggaa	5/20	0.374416685968224	3	FACETS	0.847	0.716	0.99	0.423	0.358	0.495	CLONAL	1	TRUE	1	0.384274413605558	3		301	337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0029087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	140	747	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.841	0.769	0.916	0.841	0.769	0.916	CLONAL	1	TRUE	1	0.55485175231067	2		750	600	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0029087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	168	665	0	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	1	2	FACETS	0.905	0.835	0.978	0.905	0.835	0.978	CLONAL	1	TRUE	1	0.55485175231067	2		665	669	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0029087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	93	393	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.552890605138984	1	FACETS	0.9	0.813	0.991	0.9	0.813	0.991	CLONAL	1	TRUE	0	0.55485175231067	1		393	269	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030613	48030613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779617676	NA	P-0029087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	101	423	1	ENST00000234420.5:c.3227G>A	p.Arg1076His	p.R1076H	ENST00000234420	NM_000179.2	1076	cGc/cAc	5/10	0.552890605138984	1	FACETS	0.84	0.76	0.923	0.84	0.76	0.923	CLONAL	1	TRUE	0	0.55485175231067	1		424	313	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696430	47696430	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	138	498	0	ENST00000347630.2:c.393G>C	p.Trp131Cys	p.W131C	ENST00000347630	NM_001007230.1	131	tgG/tgC	6/11	1	2	FACETS	0.856	0.782	0.933	0.856	0.782	0.933	CLONAL	1	TRUE	1	0.55485175231067	2		498	581	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925412	114925412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs573425555	NA	P-0029087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	83	661	0	ENST00000543371.1:c.1490C>T	p.Pro497Leu	p.P497L	ENST00000543371	NM_001198531.1	497	cCg/cTg	14/14	1	2	FACETS	0.432	0.381	0.486	0.432	0.381	0.486	SUBCLONAL	1	TRUE	1	0.55485175231067	2		661	693	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508733	106508733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1207051578	NA	P-0029087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	85	501	1	ENST00000359195.3:c.727G>A	p.Ala243Thr	p.A243T	ENST00000359195	NM_002649.2	243	Gcc/Acc	2/11	0.45428656407421	4	FACETS	0.623	0.55	0.701	0.311	0.275	0.351	SUBCLONAL	1	TRUE	2	0.55485175231067	4		502	765	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604769	48604769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766833269	NA	P-0029087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	57	360	0	ENST00000342988.3:c.1591C>T	p.Arg531Trp	p.R531W	ENST00000342988	NM_005359.5	531	Cgg/Tgg	12/12	1	2	FACETS	0.407	0.349	0.47	0.407	0.349	0.47	SUBCLONAL	1	TRUE	1	0.55485175231067	2		360	505	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933575	39933575	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs151177114	NA	P-0029087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	155	270	0	ENST00000378444.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000378444	NM_001123385.1	342	Cga/Tga	4/15	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.55485175231067	1		270	275	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432458	49432458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771221036	NA	P-0029087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	172	714	2	ENST00000301067.7:c.8681C>T	p.Pro2894Leu	p.P2894L	ENST00000301067	NM_003482.3	2894	cCg/cTg	34/54	1	2	FACETS	0.937	0.865	1	0.937	0.865	1	CLONAL	1	TRUE	1	0.55485175231067	2		716	662	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983295	15983295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1355823096	NA	P-0029087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	55	417	0	ENST00000268712.3:c.3484C>T	p.Arg1162Trp	p.R1162W	ENST00000268712	NM_006311.3	1162	Cgg/Tgg	26/46	1	2	FACETS	0.496	0.425	0.572	0.496	0.425	0.572	SUBCLONAL	1	TRUE	1	0.55485175231067	2		417	400	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310895	123310895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141796960	NA	P-0029087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	119	398	0	ENST00000358487.5:c.533G>A	p.Arg178His	p.R178H	ENST00000358487	NM_000141.4	178	cGc/cAc	5/18	1	2	FACETS	0.843	0.764	0.925	0.843	0.764	0.925	CLONAL	1	TRUE	1	0.55485175231067	2		398	509	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798112	45798112	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587782885	NA	P-0029087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	174	686	0	ENST00000450313.1:c.739C>T	p.Arg247Ter	p.R247*	ENST00000450313	NM_012222.2	247	Cga/Tga	9/16	1	2	FACETS	0.887	0.819	0.958	0.887	0.819	0.958	CLONAL	1	TRUE	1	0.55485175231067	2		686	707	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851510	63851510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766155061	NA	P-0029087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	111	478	0	ENST00000279873.7:c.2288C>T	p.Ser763Leu	p.S763L	ENST00000279873	NM_032199.2	763	tCg/tTg	10/10	1	2	FACETS	0.755	0.681	0.832	0.755	0.681	0.832	SUBCLONAL	1	TRUE	1	0.55485175231067	2		478	530	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911881	94911881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1489329660	NA	P-0029087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	113	487	1	ENST00000536441.1:c.1049G>A	p.Arg350Gln	p.R350Q	ENST00000536441	NM_144665.3	350	cGa/cAa	7/10	0.295601712379488	3	FACETS	0.944	0.853	1	0.472	0.426	0.52	INDETERMINATE	1	TRUE	1	0.55485175231067	3		488	551	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448147	49448147	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	179	579	0	ENST00000301067.7:c.453del	p.Gln152ArgfsTer56	p.Q152Rfs*56	ENST00000301067	NM_003482.3	151	ggG/gg	4/54	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.55485175231067	2		579	616	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456376	99456376	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747472047	NA	P-0029087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	31	478	1	ENST00000268035.6:c.1693G>A	p.Gly565Ser	p.G565S	ENST00000268035	NM_000875.3	565	Ggc/Agc	8/21	0.217788267643194	0	FACETS	0.107	0.086	0.131			1	INDETERMINATE	1	TRUE	0	0.55485175231067	0		479	464	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819704	81819704	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	152	591	1	ENST00000359376.3:c.114del	p.Glu39SerfsTer7	p.E39Sfs*7	ENST00000359376	NM_002661.3	37	aCc/ac	2/33	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.55485175231067	2		592	530	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953261	17953261	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1417493008	NA	P-0029087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	149	903	0	ENST00000458235.1:c.725T>G	p.Leu242Arg	p.L242R	ENST00000458235	NM_000215.3	242	cTg/cGg	6/24	1	2	FACETS	0.805	0.738	0.876	0.805	0.738	0.876	CLONAL	1	TRUE	1	0.55485175231067	2		903	667	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791238	42791238	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	92	781	0	ENST00000575354.2:c.298G>T	p.Ala100Ser	p.A100S	ENST00000575354	NM_015125.3	100	Gcc/Tcc	3/20	1	2	FACETS	0.492	0.437	0.55	0.492	0.437	0.55	SUBCLONAL	1	TRUE	1	0.55485175231067	2		781	674	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944584	40944584	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs531404437	NA	P-0029087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	133	391	0	ENST00000373198.4:c.1918G>T	p.Ala640Ser	p.A640S	ENST00000373198	NM_133170.3	640	Gct/Tct	12/32	0.142917039327856	0	FACETS	0.526	0.482	0.571			1	INDETERMINATE	1	TRUE	0	0.55485175231067	0		391	406	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815816	32815816	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	187	613	0	ENST00000354258.4:c.1800T>G	p.Asn600Lys	p.N600K	ENST00000354258	NM_000593.5	600	aaT/aaG	8/11	1	2	FACETS	0.904	0.837	0.972	0.904	0.837	0.972	CLONAL	1	TRUE	1	0.55485175231067	2		613	746	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017591	112017591	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	125	486	0	ENST00000368678.4:c.922T>C	p.Phe308Leu	p.F308L	ENST00000368678		308	Ttc/Ctc	9/13	0.552890605138984	1	FACETS	0.82	0.749	0.893	0.82	0.749	0.893	CLONAL	1	TRUE	0	0.55485175231067	1		486	397	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0029090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	40	591	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.832	0.69	0.991	0.832	0.69	0.991	CLONAL	1	TRUE	1	0.15	2		591	641	SUCCESS
APC	324	MSKCC	GRCh37	5	112176526	112176526	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	32	382	0	ENST00000257430.4:c.5235G>C	p.Lys1745Asn	p.K1745N	ENST00000257430	NM_000038.5	1745	aaG/aaC	16/16	1	2	FACETS	0.673	0.545	0.819	0.673	0.545	0.819	SUBCLONAL	1	TRUE	1	0.15	2		382	634	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103299	119103299	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	62	578	0	ENST00000264033.4:c.337G>C	p.Glu113Gln	p.E113Q	ENST00000264033	NM_005188.3	113	Gag/Cag	2/16	1	2	FACETS	0.927	0.799	1	0.927	0.799	1	CLONAL	1	TRUE	1	0.15	2		578	892	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656520	3656520	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	69	865	0	ENST00000294008.3:c.715G>C	p.Glu239Gln	p.E239Q	ENST00000294008	NM_032444.2	239	Gaa/Caa	3/15	1	2	FACETS	0.74	0.642	0.846	0.74	0.642	0.846	SUBCLONAL	1	TRUE	1	0.15	2		865	1244	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61724121	61724121	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	47	338	0	ENST00000401558.2:c.781C>T	p.Arg261Ter	p.R261*	ENST00000401558	NM_003400.3	261	Cga/Tga	10/25	0.146523689421661	3	FACETS	0.922	0.776	1	0.461	0.388	0.542	CLONAL	1	TRUE	1	0.15	3		338	731	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541797	187541857	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGGTAAACTTTAGGTGACTTTCTTTGCTTTCTTTCACATTAATTTTGACAGAGGTAAGG	CTGGGTAAACTTTAGGTGACTTTCTTTGCTTTCTTTCACATTAATTTTGACAGAGGTAAGG	-	novel	NA	P-0029090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	41	483	0	ENST00000441802.2:c.5883_5943del	p.Leu1962MetfsTer6	p.L1962Mfs*6	ENST00000441802	NM_005245.3	1961	ggCCTTACCTCTGTCAAAATTAATGTGAAAGAAAGCAAAGAAAGTCACCTAAAGTTTACCCAG/gg	10/27	1	2	FACETS	0.962	0.801	1	0.962	0.801	1	CLONAL	1	TRUE	1	0.15	2		483	568	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221806	55221806	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1157	82	830	0	ENST00000275493.2:c.852del	p.Lys284AsnfsTer9	p.K284Nfs*9	ENST00000275493	NM_005228.3	284	Aaa/aa	7/28	0.146523689421661	3	FACETS	0.949	0.834	1	0.474	0.417	0.537	CLONAL	1	TRUE	1	0.15	3		830	1239	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0029091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	154	301	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	0.771021187252078	2	FACETS	1	0.973	1	0.552	0.512	0.592	CLONAL	1	TRUE	0	0.771021187252078	2		301	362	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0029091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	25	768	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.771021187252078	2	FACETS	0.152	0.119	0.19	0.076	0.059	0.095	SUBCLONAL	1	TRUE	0	0.771021187252078	2		768	427	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412922	49412922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	701	719	0	ENST00000418115.1:c.101A>T	p.Tyr34Phe	p.Y34F	ENST00000418115	NM_001664.2	34	tAt/tTt	2/5	0.771021187252078	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.771021187252078	2		719	888	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351422	70351422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	599	699	1	ENST00000374080.3:c.4070G>A	p.Arg1357His	p.R1357H	ENST00000374080		1357	cGc/cAc	29/45	0.23314379572345	4	FACETS	0.915	0.887	0.944	0.687	0.665	0.708	INDETERMINATE	3	TRUE	0	0.771021187252078	4		700	1002	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426390	47426390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	582	555	1	ENST00000377045.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000377045	NM_001654.4	245	Ggt/Agt	9/16	0.23314379572345	4	FACETS	0.898	0.87	0.927	0.674	0.652	0.695	INDETERMINATE	3	TRUE	0	0.771021187252078	4		556	992	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748660	43748661	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	310	781	0	ENST00000382044.4:c.2145dup	p.Glu716ArgfsTer9	p.E716Rfs*9	ENST00000382044	NM_001141980.1	715	-/A	12/28	1	2	FACETS	0.914	0.865	0.964	0.914	0.865	0.964	CLONAL	1	TRUE	1	0.771021187252078	2		781	880	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118940	70118941	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	752	764	0	ENST00000245479.2:c.514dup	p.Tyr172LeufsTer80	p.Y172Lfs*80	ENST00000245479	NM_000346.3	171	gat/gaTt	2/3	0.771021187252078	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.771021187252078	2		764	921	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44894182	44894182	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	370	486	0	ENST00000377967.4:c.571C>T	p.Gln191Ter	p.Q191*	ENST00000377967	NM_021140.2	191	Cag/Tag	7/29	0.23314379572345	4	FACETS	0.858	0.823	0.894	0.644	0.617	0.67	INDETERMINATE	3	TRUE	0	0.771021187252078	4		486	660	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0029099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	335	498	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.327651742167235	4	FACETS	0.855	0.811	0.9	0.855	0.811	0.9	CLONAL	3	TRUE	1	0.371059280842332	4		498	965	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214618	5214618	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767215087	NA	P-0029099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	187	532	0	ENST00000357368.4:c.4448G>A	p.Arg1483Gln	p.R1483Q	ENST00000357368	NM_002850.3	1483	cGg/cAg	29/38	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.371059280842332	2		532	979	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0029102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	23	498	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.823	1	1	0.823	1	CLONAL	1	TRUE	1	0.11	2		498	392	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121909229	NA	P-0029102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	27	510	3	ENST00000371953.3:c.389G>T	p.Arg130Leu	p.R130L	ENST00000371953	NM_000314.4	130	cGa/cTa	5/9	1	2	FACETS	0.97	0.77	1	0.97	0.77	1	CLONAL	1	TRUE	1	0.11	2		513	506	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913403	NA	P-0029102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	21	273	0	ENST00000349496.5:c.110C>A	p.Ser37Tyr	p.S37Y	ENST00000349496	NM_001904.3	37	tCt/tAt	3/15	1	2	FACETS	0.736	0.565	0.936	0.736	0.565	0.936	CLONAL	1	TRUE	1	0.11	2		273	519	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0029103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	278	483	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.298099886520239	3	FACETS	0.804	0.758	0.852	0.804	0.758	0.852	INDETERMINATE	2	TRUE	1	0.512103267541887	3		483	848	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581229	48581229	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs377767331	NA	P-0029103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	205	444	0	ENST00000342988.3:c.533C>G	p.Ser178Ter	p.S178*	ENST00000342988	NM_005359.5	178	tCa/tGa	5/12	0.512103267541887	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.512103267541887	1		444	567	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030367	49030368	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	149	330	0	ENST00000267163.4:c.1848dup	p.Gly617ArgfsTer36	p.G617Rfs*36	ENST00000267163	NM_000321.2	614	-/A	19/27	0.512103267541887	1	FACETS	0.915	0.843	0.99	0.915	0.843	0.99	CLONAL	1	TRUE	0	0.512103267541887	1		330	473	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141493	11141493	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1229	298	607	2	ENST00000358026.2:c.3470G>A	p.Arg1157Gln	p.R1157Q	ENST00000358026	NM_001128849.1	1157	cGg/cAg	25/36	0.495379409014531	4	FACETS	1	0.986	1	0.384	0.361	0.409	CLONAL	1	TRUE	1	0.512103267541887	4		609	1527	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287204	46287204	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	300	295	0	ENST00000334344.6:c.5149C>T	p.Gln1717Ter	p.Q1717*	ENST00000334344	NM_152641.2	1717	Cag/Tag	19/21	0.512103267541887	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.512103267541887	2		295	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs863224499	NA	P-0029103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	261	513	0	ENST00000269305.4:c.672+1G>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.512103267541887	1	FACETS	0.944	0.888	1	0.944	0.888	1	CLONAL	1	TRUE	0	0.512103267541887	1		513	803	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602551	10602551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1240272074	NA	P-0029103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	250	572	0	ENST00000171111.5:c.1027G>A	p.Glu343Lys	p.E343K	ENST00000171111	NM_203500.1	343	Gag/Aag	3/6	0.512103267541887	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.512103267541887	1		572	719	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360547	70360547	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	294	605	0	ENST00000374080.3:c.6107A>G	p.Gln2036Arg	p.Q2036R	ENST00000374080		2036	cAg/cGg	42/45	1	2	FACETS	0.994	0.935	1	0.994	0.935	1	CLONAL	1	TRUE	1	0.512103267541887	2		605	1155	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	127	344	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.409726870567211	1	FACETS	0.361	0.329	0.394	0.361	0.329	0.394	INDETERMINATE	1	TRUE	0	0.899034662607578	1		345	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577571	7577571	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs765848205	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	411	538	0	ENST00000269305.4:c.710T>A	p.Met237Lys	p.M237K	ENST00000269305	NM_001126112.2	237	aTg/aAg	7/11	0.412424853483364	1	FACETS	0.574	0.549	0.599	0.574	0.549	0.599	INDETERMINATE	1	TRUE	0	0.899034662607578	1		538	877	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023057	150023057	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1326453282	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	113	666	0	ENST00000253339.5:c.206C>T	p.Pro69Leu	p.P69L	ENST00000253339		69	cCc/cTc	1/7	0.518825124358565	1	FACETS	0.127	0.114	0.141	0.127	0.114	0.141	INDETERMINATE	1	TRUE	0	0.899034662607578	1		666	1089	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156546	55156546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10543	619	573	0	ENST00000257290.5:c.2947G>A	p.Asp983Asn	p.D983N	ENST00000257290	NM_006206.4	983	Gac/Aac	22/23	0.899034662607578	17	FACETS	0.955	0.911	1	0.06	0.056	0.063	CLONAL	1	TRUE	1	0.899034662607578	17		573	11162	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578466	7578466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	526	708	0	ENST00000269305.4:c.464C>T	p.Thr155Ile	p.T155I	ENST00000269305	NM_001126112.2	155	aCc/aTc	5/11	0.412424853483364	1	FACETS	0.559	0.538	0.581	0.559	0.538	0.581	INDETERMINATE	1	TRUE	0	0.899034662607578	1		708	1152	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939666	76939669	+	frameshift_variant	Frame_Shift_Del	DEL	TCAA	TCAA	-	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	620	636	0	ENST00000373344.5:c.1079_1082del	p.Ile360ArgfsTer6	p.I360Rfs*6	ENST00000373344	NM_000489.3	360	aTTGAg/ag	9/35	0.511016147815964	1	FACETS	0.726	0.703	0.748	0.726	0.703	0.748	INDETERMINATE	1	TRUE	0	0.899034662607578	1		636	1046	SUCCESS
APC	324	MSKCC	GRCh37	5	112177010	112177010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	259	538	0	ENST00000257430.4:c.5719G>A	p.Ala1907Thr	p.A1907T	ENST00000257430	NM_000038.5	1907	Gct/Act	16/16	0.165865595372545	2	FACETS	0.576	0.54	0.613	0.288	0.27	0.307	INDETERMINATE	1	TRUE	0	0.899034662607578	2		538	1000	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513259	44513259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	33	429	0	ENST00000291552.4:c.676C>T	p.Arg226Cys	p.R226C	ENST00000291552	NM_006758.2	226	Cgt/Tgt	8/8	0.899034662607578	1	FACETS	0.069	0.056	0.085	0.069	0.056	0.085	SUBCLONAL	1	TRUE	0	0.899034662607578	1		429	582	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288925	11288925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	236	532	0	ENST00000361445.4:c.2830G>A	p.Asp944Asn	p.D944N	ENST00000361445	NM_004958.3	944	Gat/Aat	19/58	0.593996023253418	1	FACETS	0.355	0.332	0.379	0.355	0.332	0.379	SUBCLONAL	1	TRUE	0	0.899034662607578	1		532	813	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398050	4398050	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	199	545	0	ENST00000261254.3:c.614G>A	p.Gly205Glu	p.G205E	ENST00000261254	NM_001759.3	205	gGa/gAa	4/5	0.899034662607578	1	FACETS	0.482	0.45	0.514	0.482	0.45	0.514	SUBCLONAL	1	TRUE	0	0.899034662607578	1		545	506	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346963	89346963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768652993	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	128	410	0	ENST00000301030.4:c.5987C>T	p.Pro1996Leu	p.P1996L	ENST00000301030	NM_001256183.1	1996	cCc/cTc	9/13	1	2	FACETS	0.489	0.445	0.536	0.489	0.445	0.536	SUBCLONAL	1	TRUE	1	0.899034662607578	2		410	582	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136214	64136214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371615792	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	299	668	0	ENST00000334205.4:c.1373G>A	p.Arg458His	p.R458H	ENST00000334205	NM_003942.2	458	cGc/cAc	12/17	1	2	FACETS	0.515	0.484	0.547	0.515	0.484	0.547	SUBCLONAL	1	TRUE	1	0.899034662607578	2		668	1291	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856574	111856574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	118	190	0	ENST00000341259.2:c.625G>A	p.Ala209Thr	p.A209T	ENST00000341259	NM_005475.2	209	Gcc/Acc	2/8	1	2	FACETS	0.609	0.553	0.667	0.609	0.553	0.667	SUBCLONAL	1	TRUE	1	0.899034662607578	2		190	431	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11273614	11273614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	163	322	0	ENST00000361445.4:c.3127G>A	p.Val1043Ile	p.V1043I	ENST00000361445	NM_004958.3	1043	Gtc/Atc	21/58	0.593996023253418	1	FACETS	0.344	0.317	0.372	0.344	0.317	0.372	SUBCLONAL	1	TRUE	0	0.899034662607578	1		322	580	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261508	16261508	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	184	564	0	ENST00000375759.3:c.8773C>T	p.Gln2925Ter	p.Q2925*	ENST00000375759	NM_015001.2	2925	Cag/Tag	11/15	NA	2	FACETS	0.548	0.507	0.59			1	INDETERMINATE	1	TRUE	NA	0.899034662607578	2		564	747	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17349102	17349102	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	186	429	1	ENST00000375499.3:c.765+1G>A		p.X255_splice	ENST00000375499	NM_003000.2	255			0.593996023253418	1	FACETS	0.363	0.336	0.39	0.363	0.336	0.39	SUBCLONAL	1	TRUE	0	0.899034662607578	1		430	628	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39311713	39311713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	436	674	0	ENST00000373001.3:c.946G>A	p.Ala316Thr	p.A316T	ENST00000373001	NM_022157.3	316	Gca/Aca	6/7	0.593996023253418	1	FACETS	0.333	0.317	0.35	0.333	0.317	0.35	SUBCLONAL	1	TRUE	0	0.899034662607578	1		674	1604	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45800089	45800089	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876659408	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	288	504	1	ENST00000450313.1:c.131G>A	p.Ser44Asn	p.S44N	ENST00000450313	NM_012222.2	44	aGt/aAt	2/16	0.593996023253418	1	FACETS	0.401	0.378	0.424	0.401	0.378	0.424	SUBCLONAL	1	TRUE	0	0.899034662607578	1		505	880	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436161	51436161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	53	375	0	ENST00000262662.1:c.121G>A	p.Ala41Thr	p.A41T	ENST00000262662		41	Gcg/Acg	3/4	0.593996023253418	1	FACETS	0.106	0.09	0.124	0.106	0.09	0.124	SUBCLONAL	1	TRUE	0	0.899034662607578	1		375	613	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263198	115263198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	235	640	0	ENST00000438362.2:c.2152C>T	p.Pro718Ser	p.P718S	ENST00000438362	NM_001242891.1	718	Ccc/Tcc	17/20	1	2	FACETS	0.485	0.452	0.519	0.485	0.452	0.519	SUBCLONAL	1	TRUE	1	0.899034662607578	2		640	1078	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852116	63852116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	218	584	0	ENST00000279873.7:c.2894C>T	p.Pro965Leu	p.P965L	ENST00000279873	NM_032199.2	965	cCt/cTt	10/10	1	2	FACETS	0.46	0.428	0.494	0.46	0.428	0.494	SUBCLONAL	1	TRUE	1	0.899034662607578	2		584	1054	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154796	2154796	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748117121	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	101	813	1	ENST00000434045.2:c.425C>T	p.Thr142Ile	p.T142I	ENST00000434045	NM_001127598.1	142	aCc/aTc	4/5	0.899034662607578	1	FACETS	0.183	0.163	0.204	0.183	0.163	0.204	SUBCLONAL	1	TRUE	0	0.899034662607578	1		814	677	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100555	102100555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	99	565	1	ENST00000282441.5:c.1399G>A	p.Gly467Arg	p.G467R	ENST00000282441	NM_001130145.2	467	Gga/Aga	9/9	0.511016147815964	1	FACETS	0.142	0.126	0.159	0.142	0.126	0.159	INDETERMINATE	1	TRUE	0	0.899034662607578	1		566	854	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394680	394680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	209	577	0	ENST00000399788.2:c.5015C>T	p.Pro1672Leu	p.P1672L	ENST00000399788	NM_001042603.1	1672	cCt/cTt	28/28	0.899034662607578	1	FACETS	0.412	0.385	0.44	0.412	0.385	0.44	SUBCLONAL	1	TRUE	0	0.899034662607578	1		577	621	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944970	31944970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	231	552	0	ENST00000340398.3:c.131G>A	p.Gly44Glu	p.G44E	ENST00000340398	NM_001013699.2	44	gGg/gAg	1/1	1	2	FACETS	0.546	0.509	0.583	0.546	0.509	0.583	SUBCLONAL	1	TRUE	1	0.899034662607578	2		552	942	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246432	46246432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184036990	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	150	402	0	ENST00000334344.6:c.4526C>T	p.Thr1509Ile	p.T1509I	ENST00000334344	NM_152641.2	1509	aCa/aTa	15/21	1	2	FACETS	0.487	0.446	0.53	0.487	0.446	0.53	SUBCLONAL	1	TRUE	1	0.899034662607578	2		402	685	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420849	49420849	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	190	511	0	ENST00000301067.7:c.14900C>T	p.Pro4967Leu	p.P4967L	ENST00000301067	NM_003482.3	4967	cCc/cTc	48/54	1	2	FACETS	0.447	0.413	0.483	0.447	0.413	0.483	SUBCLONAL	1	TRUE	1	0.899034662607578	2		511	945	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432045	49432045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	331	760	0	ENST00000301067.7:c.9094G>A	p.Glu3032Lys	p.E3032K	ENST00000301067	NM_003482.3	3032	Gag/Aag	34/54	1	2	FACETS	0.539	0.509	0.571	0.539	0.509	0.571	SUBCLONAL	1	TRUE	1	0.899034662607578	2		760	1365	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437507	49437507	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	253	616	2	ENST00000301067.7:c.5378G>A	p.Gly1793Glu	p.G1793E	ENST00000301067	NM_003482.3	1793	gGg/gAg	23/54	1	2	FACETS	0.486	0.455	0.519	0.486	0.455	0.519	SUBCLONAL	1	TRUE	1	0.899034662607578	2		618	1157	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437773	49437773	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	170	478	0	ENST00000301067.7:c.5197G>A	p.Ala1733Thr	p.A1733T	ENST00000301067	NM_003482.3	1733	Gct/Act	22/54	1	2	FACETS	0.522	0.481	0.565	0.522	0.481	0.565	SUBCLONAL	1	TRUE	1	0.899034662607578	2		478	724	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50490640	50490640	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	473	440	0	ENST00000394963.4:c.1277A>G	p.Glu426Gly	p.E426G	ENST00000394963	NM_003076.4	426	gAg/gGg	11/13	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.899034662607578	2		440	994	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112455	115112455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	221	521	0	ENST00000257566.3:c.1285G>A	p.Asp429Asn	p.D429N	ENST00000257566	NM_016569.3	429	Gac/Aac	7/8	1	2	FACETS	0.504	0.469	0.54	0.504	0.469	0.54	SUBCLONAL	1	TRUE	1	0.899034662607578	2		521	976	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794720	120794720	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	85	567	0	ENST00000257552.2:c.637G>A	p.Gly213Ser	p.G213S	ENST00000257552	NM_002442.3	213	Ggc/Agc	9/15	1	2	FACETS	0.167	0.147	0.189	0.167	0.147	0.189	SUBCLONAL	1	TRUE	1	0.899034662607578	2		567	1132	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874001	123874001	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	31	36	0	ENST00000330479.4:c.32G>A	p.Arg11His	p.R11H	ENST00000330479	NM_020382.3	11	cGc/cAc	2/9	1	2	FACETS	0.639	0.528	0.757	0.639	0.528	0.757	SUBCLONAL	1	TRUE	1	0.899034662607578	2		36	108	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964203	28964203	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144651121	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	275	312	0	ENST00000282397.4:c.1699C>T	p.Pro567Ser	p.P567S	ENST00000282397	NM_002019.4	567	Ccg/Tcg	13/30	0.511016147815964	1	FACETS	0.707	0.674	0.74	0.707	0.674	0.74	INDETERMINATE	1	TRUE	0	0.899034662607578	1		312	476	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32968970	32968970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80359215	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	194	454	0	ENST00000380152.3:c.9401G>A	p.Gly3134Asp	p.G3134D	ENST00000380152		3134	gGc/gAc	25/27	0.511016147815964	1	FACETS	0.364	0.338	0.39	0.364	0.338	0.39	INDETERMINATE	1	TRUE	0	0.899034662607578	1		454	653	SUCCESS
BLM	641	MSKCC	GRCh37	15	91337588	91337588	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	118	229	0	ENST00000355112.3:c.3210+1G>A		p.X1070_splice	ENST00000355112	NM_000057.2	1070			1	2	FACETS	0.417	0.376	0.459	0.417	0.376	0.459	SUBCLONAL	1	TRUE	1	0.899034662607578	2		229	630	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779284	3779284	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	125	502	0	ENST00000262367.5:c.5764C>T	p.Pro1922Ser	p.P1922S	ENST00000262367	NM_004380.2	1922	Ccc/Tcc	31/31	1	2	FACETS	0.377	0.341	0.414	0.377	0.341	0.414	SUBCLONAL	1	TRUE	1	0.899034662607578	2		502	738	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863671	68863671	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	169	537	0	ENST00000261769.5:c.2410C>T	p.Pro804Ser	p.P804S	ENST00000261769	NM_004360.3	804	Ccc/Tcc	15/16	0.385596278555576	3	FACETS	0.483	0.443	0.524	0.241	0.221	0.262	INDETERMINATE	1	TRUE	1	0.899034662607578	3		537	1129	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828973	72828974	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	250	637	0	ENST00000268489.5:c.7607dup	p.Leu2537ValfsTer7	p.L2537Vfs*7	ENST00000268489	NM_006885.3	2536	aag/aaAg	9/10	0.385596278555576	3	FACETS	0.611	0.57	0.653	0.306	0.285	0.327	INDETERMINATE	1	TRUE	1	0.899034662607578	3		637	1319	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829049	72829049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	223	661	1	ENST00000268489.5:c.7532C>T	p.Pro2511Leu	p.P2511L	ENST00000268489	NM_006885.3	2511	cCc/cTc	9/10	0.385596278555576	3	FACETS	0.58	0.539	0.623	0.29	0.269	0.312	INDETERMINATE	1	TRUE	1	0.899034662607578	3		662	1239	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829668	72829668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	277	692	0	ENST00000268489.5:c.6913G>A	p.Gly2305Arg	p.G2305R	ENST00000268489	NM_006885.3	2305	Gga/Aga	9/10	0.385596278555576	3	FACETS	0.646	0.605	0.688	0.323	0.302	0.344	INDETERMINATE	1	TRUE	1	0.899034662607578	3		692	1383	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992925	72992925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1339	304	752	0	ENST00000268489.5:c.1120G>A	p.Glu374Lys	p.E374K	ENST00000268489	NM_006885.3	374	Gaa/Aaa	2/10	0.385596278555576	3	FACETS	0.597	0.56	0.634	0.298	0.28	0.317	INDETERMINATE	1	TRUE	1	0.899034662607578	3		752	1643	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89825109	89825109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1036643207	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	194	502	0	ENST00000389301.3:c.2857G>A	p.Asp953Asn	p.D953N	ENST00000389301	NM_000135.2	953	Gac/Aac	30/43	1	2	FACETS	0.52	0.482	0.56	0.52	0.482	0.56	SUBCLONAL	1	TRUE	1	0.899034662607578	2		502	830	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216970	7216970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1483985914	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	214	468	0	ENST00000380728.2:c.551C>T	p.Pro184Leu	p.P184L	ENST00000380728		184	cCt/cTt	7/11	0.412424853483364	1	FACETS	0.335	0.312	0.359	0.335	0.312	0.359	INDETERMINATE	1	TRUE	0	0.899034662607578	1		468	782	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976213	7976213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	190	499	0	ENST00000319144.4:c.1982G>A	p.Ser661Asn	p.S661N	ENST00000319144	NM_001139.2	661	aGc/aAc	15/15	0.412424853483364	1	FACETS	0.336	0.312	0.362	0.336	0.312	0.362	INDETERMINATE	1	TRUE	0	0.899034662607578	1		499	692	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984707	11984707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	67	259	0	ENST00000353533.5:c.253G>A	p.Gly85Arg	p.G85R	ENST00000353533	NM_003010.3	85	Gga/Aga	3/11	0.412424853483364	1	FACETS	0.189	0.165	0.216	0.189	0.165	0.216	INDETERMINATE	1	TRUE	0	0.899034662607578	1		259	433	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546041	29546041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	203	464	0	ENST00000356175.3:c.1546C>T	p.Pro516Ser	p.P516S	ENST00000356175	NM_000267.3	516	Ccc/Tcc	14/57	NA	2	FACETS	0.448	0.415	0.482			1	INDETERMINATE	1	TRUE	NA	0.899034662607578	2		464	1009	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41197705	41197705	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	257	625	1	ENST00000357654.3:c.5582G>A	p.Ser1861Asn	p.S1861N	ENST00000357654	NM_007294.3	1861	aGc/aAc	23/23	0.165865595372545	2	FACETS	0.539	0.504	0.574	0.269	0.252	0.287	INDETERMINATE	1	TRUE	0	0.899034662607578	2		626	1061	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246754	41246754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	99	475	0	ENST00000357654.3:c.794C>T	p.Ser265Phe	p.S265F	ENST00000357654	NM_007294.3	265	tCt/tTt	10/23	0.165865595372545	2	FACETS	0.215	0.192	0.241	0.108	0.096	0.121	INDETERMINATE	1	TRUE	0	0.899034662607578	2		475	1022	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256194	41256194	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1255	154	609	0	ENST00000357654.3:c.386G>A	p.Gly129Asp	p.G129D	ENST00000357654	NM_007294.3	129	gGc/gAc	6/23	0.165865595372545	2	FACETS	0.243	0.221	0.266	0.122	0.11	0.133	INDETERMINATE	1	TRUE	0	0.899034662607578	2		609	1409	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780691	56780691	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs876658644	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	102	411	0	ENST00000337432.4:c.705+1G>A		p.X235_splice	ENST00000337432	NM_058216.2	235			0.165865595372545	2	FACETS	0.192	0.171	0.214	0.096	0.085	0.107	INDETERMINATE	1	TRUE	0	0.899034662607578	2		411	1183	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519954	66519954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	109	439	0	ENST00000358598.2:c.437G>A	p.Arg146Lys	p.R146K	ENST00000358598	NM_212471.2	146	aGa/aAa	4/11	0.165865595372545	2	FACETS	0.254	0.227	0.282	0.127	0.113	0.141	INDETERMINATE	1	TRUE	0	0.899034662607578	2		439	955	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78935256	78935256	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	387	662	0	ENST00000306801.3:c.3668C>T	p.Pro1223Leu	p.P1223L	ENST00000306801	NM_020761.2	1223	cCc/cTc	31/34	0.165865595372545	2	FACETS	0.671	0.637	0.705	0.336	0.318	0.353	INDETERMINATE	1	TRUE	0	0.899034662607578	2		662	1283	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936378	78936378	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	74	531	0	ENST00000306801.3:c.3809+1G>A		p.X1270_splice	ENST00000306801	NM_020761.2	1270			0.165865595372545	2	FACETS	0.196	0.171	0.224	0.098	0.085	0.112	INDETERMINATE	1	TRUE	0	0.899034662607578	2		531	838	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39575920	39575920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777970706	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	203	430	0	ENST00000262039.4:c.853G>A	p.Asp285Asn	p.D285N	ENST00000262039	NM_002647.2	285	Gat/Aat	8/25	1	2	FACETS	0.482	0.447	0.519	0.482	0.447	0.519	SUBCLONAL	1	TRUE	1	0.899034662607578	2		430	936	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617778	39617778	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	174	338	1	ENST00000262039.4:c.1962G>A	p.Met654Ile	p.M654I	ENST00000262039	NM_002647.2	654	atG/atA	17/25	1	2	FACETS	0.455	0.419	0.492	0.455	0.419	0.492	SUBCLONAL	1	TRUE	1	0.899034662607578	2		339	851	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619807	1619807	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	267	751	1	ENST00000344749.5:c.1139C>T	p.Pro380Leu	p.P380L	ENST00000344749	NM_001136139.2	380	cCc/cTc	14/19	1	2	FACETS	0.503	0.471	0.536	0.503	0.471	0.536	SUBCLONAL	1	TRUE	1	0.899034662607578	2		752	1181	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213944	2213944	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	223	638	0	ENST00000398665.3:c.1756G>A	p.Glu586Lys	p.E586K	ENST00000398665	NM_032482.2	586	Gag/Aag	18/28	1	2	FACETS	0.464	0.432	0.498	0.464	0.432	0.498	SUBCLONAL	1	TRUE	1	0.899034662607578	2		638	1069	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251787	10251787	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	168	659	0	ENST00000340748.4:c.3340G>A	p.Gly1114Arg	p.G1114R	ENST00000340748		1114	Gga/Aga	30/40	1	2	FACETS	0.326	0.298	0.354	0.326	0.298	0.354	SUBCLONAL	1	TRUE	1	0.899034662607578	2		659	1148	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350024	15350024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	129	745	0	ENST00000263377.2:c.3628C>T	p.Pro1210Ser	p.P1210S	ENST00000263377	NM_058243.2	1210	Ccg/Tcg	18/20	1	2	FACETS	0.223	0.202	0.246	0.223	0.202	0.246	SUBCLONAL	1	TRUE	1	0.899034662607578	2		745	1285	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280054	18280054	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775677202	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	37	212	0	ENST00000222254.8:c.2137G>A	p.Ala713Thr	p.A713T	ENST00000222254	NM_005027.3	713	Gcg/Acg	16/16	1	2	FACETS	0.188	0.155	0.226	0.188	0.155	0.226	SUBCLONAL	1	TRUE	1	0.899034662607578	2		212	437	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211555	36211555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	64	501	0	ENST00000222270.7:c.1306G>A	p.Val436Met	p.V436M	ENST00000222270	NM_014727.1	436	Gtg/Atg	3/37	1	2	FACETS	0.193	0.166	0.222	0.193	0.166	0.222	SUBCLONAL	1	TRUE	1	0.899034662607578	2		501	738	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213953	36213953	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	298	809	0	ENST00000222270.7:c.2779G>A	p.Val927Met	p.V927M	ENST00000222270	NM_014727.1	927	Gtg/Atg	6/37	1	2	FACETS	0.495	0.465	0.526	0.495	0.465	0.526	SUBCLONAL	1	TRUE	1	0.899034662607578	2		809	1339	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752628	42752628	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	200	518	0	ENST00000222329.4:c.1636C>G	p.Arg546Gly	p.R546G	ENST00000222329	NM_006494.2	546	Cga/Gga	4/4	0.593996023253418	1	FACETS	0.329	0.306	0.353	0.329	0.306	0.353	SUBCLONAL	1	TRUE	0	0.899034662607578	1		518	744	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128036748	128036748	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	37	482	0	ENST00000285398.2:c.1730+1G>A		p.X577_splice	ENST00000285398	NM_000122.1	577			0.397230287025942	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.899034662607578	0		482	590	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137645	202137645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	215	410	0	ENST00000358485.4:c.752G>A	p.Ser251Asn	p.S251N	ENST00000358485	NM_001080125.1	251	aGt/aAt	5/9	0.409726870567211	1	FACETS	0.352	0.328	0.377	0.352	0.328	0.377	INDETERMINATE	1	TRUE	0	0.899034662607578	1		410	747	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645814	215645814	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	119	616	0	ENST00000260947.4:c.784G>A	p.Ala262Thr	p.A262T	ENST00000260947	NM_000465.2	262	Gca/Aca	4/11	1	2	FACETS	0.226	0.203	0.25	0.226	0.203	0.25	SUBCLONAL	1	TRUE	1	0.899034662607578	2		616	1173	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661600	227661600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762564505	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	184	556	0	ENST00000305123.5:c.1855G>A	p.Val619Met	p.V619M	ENST00000305123	NM_005544.2	619	Gtg/Atg	1/2	1	2	FACETS	0.443	0.409	0.479	0.443	0.409	0.479	SUBCLONAL	1	TRUE	1	0.899034662607578	2		556	923	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024615	31024615	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	57	545	0	ENST00000375687.4:c.4100T>A	p.Val1367Asp	p.V1367D	ENST00000375687	NM_015338.5	1367	gTc/gAc	13/13	1	2	FACETS	0.142	0.121	0.165	0.142	0.121	0.165	SUBCLONAL	1	TRUE	1	0.899034662607578	2		545	895	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386341	31386341	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	116	616	0	ENST00000328111.2:c.1566G>A	p.Trp522Ter	p.W522*	ENST00000328111	NM_006892.3	522	tgG/tgA	15/23	1	2	FACETS	0.262	0.236	0.29	0.262	0.236	0.29	SUBCLONAL	1	TRUE	1	0.899034662607578	2		616	984	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012654	36012654	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	104	170	0	ENST00000358208.4:c.98C>T	p.Pro33Leu	p.P33L	ENST00000358208		33	cCc/cTc	2/12	1	2	FACETS	0.574	0.518	0.633	0.574	0.518	0.633	SUBCLONAL	1	TRUE	1	0.899034662607578	2		170	403	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268404	46268404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	200	439	0	ENST00000371998.3:c.2791G>A	p.Glu931Lys	p.E931K	ENST00000371998		931	Gaa/Aaa	15/23	1	2	FACETS	0.501	0.464	0.539	0.501	0.464	0.539	SUBCLONAL	1	TRUE	1	0.899034662607578	2		439	888	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281239	46281239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	176	452	0	ENST00000371998.3:c.4036C>T	p.Pro1346Ser	p.P1346S	ENST00000371998		1346	Ccc/Tcc	21/23	1	2	FACETS	0.455	0.419	0.492	0.455	0.419	0.492	SUBCLONAL	1	TRUE	1	0.899034662607578	2		452	861	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326124	62326124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	242	648	1	ENST00000360203.5:c.3140C>T	p.Ser1047Phe	p.S1047F	ENST00000360203	NM_001283009.1	1047	tCt/tTt	32/35	0.899034662607578	1	FACETS	0.474	0.446	0.503	0.474	0.446	0.503	SUBCLONAL	1	TRUE	0	0.899034662607578	1		649	625	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37055976	37055976	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750303	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	253	463	0	ENST00000231790.2:c.731G>A	p.Gly244Asp	p.G244D	ENST00000231790	NM_000249.3	244	gGt/gAt	9/19	0.899034662607578	1	FACETS	0.868	0.832	0.902	0.868	0.832	0.902	CLONAL	1	TRUE	0	0.899034662607578	1		463	357	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721577	49721577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758285582	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	150	443	0	ENST00000449682.2:c.2062G>A	p.Val688Ile	p.V688I	ENST00000449682	NM_020998.3	688	Gtc/Atc	18/18	NA	2	FACETS	0.438	0.401	0.477			1	INDETERMINATE	1	TRUE	NA	0.899034662607578	2		443	762	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933255	49933255	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	186	725	0	ENST00000296474.3:c.2855G>A	p.Gly952Glu	p.G952E	ENST00000296474	NM_002447.2	952	gGg/gAg	12/20	NA	2	FACETS	0.36	0.332	0.39			1	INDETERMINATE	1	TRUE	NA	0.899034662607578	2		725	1148	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933402	49933402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781271350	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	181	610	0	ENST00000296474.3:c.2788C>T	p.Pro930Ser	p.P930S	ENST00000296474	NM_002447.2	930	Cca/Tca	11/20	NA	2	FACETS	0.517	0.477	0.558			1	INDETERMINATE	1	TRUE	NA	0.899034662607578	2		610	779	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933821	49933821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	175	617	1	ENST00000296474.3:c.2456C>T	p.Pro819Leu	p.P819L	ENST00000296474	NM_002447.2	819	cCa/cTa	10/20	NA	2	FACETS	0.438	0.403	0.474			1	INDETERMINATE	1	TRUE	NA	0.899034662607578	2		618	889	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940421	49940421	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	209	741	0	ENST00000296474.3:c.622G>A	p.Ala208Thr	p.A208T	ENST00000296474	NM_002447.2	208	Gct/Act	1/20	NA	2	FACETS	0.381	0.353	0.411			1	INDETERMINATE	1	TRUE	NA	0.899034662607578	2		741	1219	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49941039	49941039	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	62	487	0	ENST00000296474.3:c.4G>A	p.Glu2Lys	p.E2K	ENST00000296474	NM_002447.2	2	Gag/Aag	1/20	NA	2	FACETS	0.147	0.127	0.17			1	INDETERMINATE	1	TRUE	NA	0.899034662607578	2		487	936	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696180	52696180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	124	621	1	ENST00000394830.3:c.497G>A	p.Gly166Glu	p.G166E	ENST00000394830	NM_018313.4	166	gGg/gAg	5/30	0.899034662607578	1	FACETS	0.352	0.32	0.384	0.352	0.32	0.384	SUBCLONAL	1	TRUE	0	0.899034662607578	1		622	432	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799649	72799649	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142643189	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	111	635	0	ENST00000325599.8:c.1520G>A	p.Gly507Asp	p.G507D	ENST00000325599	NM_018130.2	507	gGt/gAt	11/11	0.381836604358756	2	FACETS	0.226	0.203	0.252	0.113	0.101	0.126	INDETERMINATE	1	TRUE	0	0.899034662607578	2		635	1091	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205753	128205753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	272	613	0	ENST00000341105.2:c.122C>T	p.Pro41Leu	p.P41L	ENST00000341105	NM_032638.4	41	cCt/cTt	2/6	0.641856012975396	1	FACETS	0.306	0.286	0.325	0.306	0.286	0.325	SUBCLONAL	1	TRUE	0	0.899034662607578	1		613	1090	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478014	138478014	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	194	447	1	ENST00000289153.2:c.171+1G>A		p.X57_splice	ENST00000289153	NM_006219.2	57			NA	2	FACETS	0.472	0.436	0.508			1	INDETERMINATE	1	TRUE	NA	0.899034662607578	2		448	915	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916783	178916783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	260	485	0	ENST00000263967.3:c.170C>T	p.Pro57Leu	p.P57L	ENST00000263967	NM_006218.2	57	cCc/cTc	2/21	0.470791843441474	1	FACETS	0.312	0.292	0.332	0.312	0.292	0.332	INDETERMINATE	1	TRUE	0	0.899034662607578	1		485	1022	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919113	178919113	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	159	262	0	ENST00000263967.3:c.598C>T	p.Pro200Ser	p.P200S	ENST00000263967	NM_006218.2	200	Cca/Tca	4/21	0.470791843441474	1	FACETS	0.357	0.329	0.386	0.357	0.329	0.386	INDETERMINATE	1	TRUE	0	0.899034662607578	1		262	546	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146517	185146517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779925776	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	188	486	0	ENST00000265026.3:c.148G>A	p.Gly50Arg	p.G50R	ENST00000265026	NM_004721.4	50	Ggg/Agg	2/14	0.470791843441474	1	FACETS	0.334	0.31	0.359	0.334	0.31	0.359	INDETERMINATE	1	TRUE	0	0.899034662607578	1		486	689	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502486	186502486	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	107	214	0	ENST00000323963.5:c.208+1G>A		p.X70_splice	ENST00000323963		70			0.470791843441474	1	FACETS	0.343	0.31	0.377	0.343	0.31	0.377	INDETERMINATE	1	TRUE	0	0.899034662607578	1		214	382	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138668	55138829	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATATGCAAAGATATTAAGAAGTATGGAAAACAGATGTGTCTTCTTCTTTCGTGGTCAGAATATTTCTCCCTTGACACAAATGATGTCAAATACATTTTACTTATTGACTATAAGATAGGGTTTTGGGTGTGATAGCTTCAGGGTGTGTATCTTTTGTCATGA	ATATGCAAAGATATTAAGAAGTATGGAAAACAGATGTGTCTTCTTCTTTCGTGGTCAGAATATTTCTCCCTTGACACAAATGATGTCAAATACATTTTACTTATTGACTATAAGATAGGGTTTTGGGTGTGATAGCTTCAGGGTGTGTATCTTTTGTCATGA	-	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1353	4953	387	0	ENST00000257290.5:c.1348_1364+145del		p.X450_splice	ENST00000257290	NM_006206.4	450		9/23	0.899034662607578	17	FACETS	0.966	0.958	0.974	0.846	0.838	0.853	CLONAL	14	TRUE	1	0.899034662607578	17		387	6306	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383635	84383635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	349	487	0	ENST00000321945.7:c.1217C>T	p.Ser406Phe	p.S406F	ENST00000321945	NM_139076.2	406	tCt/tTt	9/9	0.899034662607578	1	FACETS	0.544	0.518	0.571	0.544	0.518	0.571	SUBCLONAL	1	TRUE	0	0.899034662607578	1		487	785	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196972	106196972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs539389221	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	158	310	0	ENST00000380013.4:c.5305G>A	p.Ala1769Thr	p.A1769T	ENST00000380013	NM_001127208.2	1769	Gct/Act	11/11	0.899034662607578	1	FACETS	0.588	0.548	0.628	0.588	0.548	0.628	SUBCLONAL	1	TRUE	0	0.899034662607578	1		310	329	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279548	1279548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	275	781	0	ENST00000310581.5:c.1988G>A	p.Ser663Asn	p.S663N	ENST00000310581	NM_198253.2	663	aGc/aAc	5/16	0.392656501682314	1	FACETS	0.306	0.287	0.326	0.306	0.287	0.326	INDETERMINATE	1	TRUE	0	0.899034662607578	1		781	1099	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294285	1294285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	212	519	0	ENST00000310581.5:c.716G>A	p.Arg239Lys	p.R239K	ENST00000310581	NM_198253.2	239	aGg/aAg	2/16	0.392656501682314	1	FACETS	0.312	0.29	0.335	0.312	0.29	0.335	INDETERMINATE	1	TRUE	0	0.899034662607578	1		519	831	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953170	38953170	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	112	275	1	ENST00000357387.3:c.2814G>A	p.Trp938Ter	p.W938*	ENST00000357387	NM_152756.3	938	tgG/tgA	29/38	0.165865595372545	2	FACETS	0.441	0.398	0.486	0.22	0.199	0.244	INDETERMINATE	1	TRUE	0	0.899034662607578	2		276	565	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962444	38962444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	133	187	0	ENST00000357387.3:c.1688G>A	p.Arg563Lys	p.R563K	ENST00000357387	NM_152756.3	563	aGa/aAa	19/38	0.165865595372545	2	FACETS	0.493	0.449	0.539	0.247	0.224	0.27	INDETERMINATE	1	TRUE	0	0.899034662607578	2		187	600	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751867	57751867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	193	395	0	ENST00000274289.3:c.1370G>A	p.Ser457Asn	p.S457N	ENST00000274289	NM_006622.3	457	aGc/aAc	10/14	0.165865595372545	2	FACETS	0.62	0.575	0.665	0.31	0.287	0.333	INDETERMINATE	1	TRUE	0	0.899034662607578	2		395	693	SUCCESS
APC	324	MSKCC	GRCh37	5	112163647	112163647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1174962542	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	116	315	0	ENST00000257430.4:c.1570G>A	p.Gly524Ser	p.G524S	ENST00000257430	NM_000038.5	524	Ggc/Agc	13/16	0.165865595372545	2	FACETS	0.345	0.31	0.381	0.172	0.155	0.191	INDETERMINATE	1	TRUE	0	0.899034662607578	2		315	749	SUCCESS
APC	324	MSKCC	GRCh37	5	112175019	112175019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	79	228	0	ENST00000257430.4:c.3728C>T	p.Pro1243Leu	p.P1243L	ENST00000257430	NM_000038.5	1243	cCt/cTt	16/16	0.165865595372545	2	FACETS	0.407	0.359	0.458	0.203	0.179	0.229	INDETERMINATE	1	TRUE	0	0.899034662607578	2		228	432	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514342	149514342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	186	504	0	ENST00000261799.4:c.602C>T	p.Ser201Phe	p.S201F	ENST00000261799	NM_002609.3	201	tCt/tTt	4/23	0.899034662607578	1	FACETS	0.517	0.482	0.551	0.517	0.482	0.551	SUBCLONAL	1	TRUE	0	0.899034662607578	1		504	441	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176563024	176563024	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	106	372	0	ENST00000439151.2:c.920T>C	p.Leu307Ser	p.L307S	ENST00000439151	NM_022455.4	307	tTg/tCg	2/23	0.899034662607578	1	FACETS	0.199	0.179	0.221	0.199	0.179	0.221	SUBCLONAL	1	TRUE	0	0.899034662607578	1		372	651	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675496	30675496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	242	639	0	ENST00000376406.3:c.2860G>A	p.Gly954Arg	p.G954R	ENST00000376406	NM_014641.2	954	Ggg/Agg	8/15	1	2	FACETS	0.5	0.467	0.535	0.5	0.467	0.535	SUBCLONAL	1	TRUE	1	0.899034662607578	2		639	1076	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30676111	30676111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	108	319	0	ENST00000376406.3:c.2245G>A	p.Val749Ile	p.V749I	ENST00000376406	NM_014641.2	749	Gtc/Atc	8/15	1	2	FACETS	0.387	0.348	0.428	0.387	0.348	0.428	SUBCLONAL	1	TRUE	1	0.899034662607578	2		319	621	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163578	32163578	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1171367221	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	219	506	0	ENST00000375023.3:c.5648C>T	p.Ser1883Phe	p.S1883F	ENST00000375023	NM_004557.3	1883	tCc/tTc	30/30	1	2	FACETS	0.46	0.428	0.494	0.46	0.428	0.494	SUBCLONAL	1	TRUE	1	0.899034662607578	2		506	1059	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553543	106553543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	91	322	0	ENST00000369096.4:c.1508C>T	p.Ala503Val	p.A503V	ENST00000369096	NM_001198.3	503	gCc/gTc	5/7	0.518825124358565	1	FACETS	0.274	0.245	0.306	0.274	0.245	0.306	INDETERMINATE	1	TRUE	0	0.899034662607578	1		322	406	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641110	117641110	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752657920	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	199	633	0	ENST00000368508.3:c.5861G>A	p.Gly1954Glu	p.G1954E	ENST00000368508	NM_002944.2	1954	gGa/gAa	36/43	0.518825124358565	1	FACETS	0.307	0.285	0.33	0.307	0.285	0.33	INDETERMINATE	1	TRUE	0	0.899034662607578	1		633	793	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528318	157528318	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	279	704	0	ENST00000346085.5:c.6043G>A	p.Asp2015Asn	p.D2015N	ENST00000346085	NM_020732.3	2015	Gac/Aac	20/20	0.518825124358565	1	FACETS	0.349	0.328	0.371	0.349	0.328	0.371	INDETERMINATE	1	TRUE	0	0.899034662607578	1		704	978	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240707	55240707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1562783502	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	306	819	1	ENST00000275493.2:c.1951G>A	p.Val651Met	p.V651M	ENST00000275493	NM_005228.3	651	Gtg/Atg	17/28	0.511016147815964	1	FACETS	0.336	0.316	0.356	0.336	0.316	0.356	INDETERMINATE	1	TRUE	0	0.899034662607578	1		820	1116	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434506	140434506	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	173	352	0	ENST00000288602.6:c.2192C>T	p.Pro731Leu	p.P731L	ENST00000288602	NM_004333.4	731	cCc/cTc	18/18	0.899034662607578	1	FACETS	0.494	0.459	0.529	0.494	0.459	0.529	SUBCLONAL	1	TRUE	0	0.899034662607578	1		352	429	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859864	151859864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	56	314	0	ENST00000262189.6:c.10798G>A	p.Glu3600Lys	p.E3600K	ENST00000262189	NM_170606.2	3600	Gaa/Aaa	43/59	0.899034662607578	1	FACETS	0.193	0.165	0.222	0.193	0.165	0.222	SUBCLONAL	1	TRUE	0	0.899034662607578	1		314	356	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864421	151864421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	153	416	0	ENST00000262189.6:c.9560C>T	p.Thr3187Ile	p.T3187I	ENST00000262189	NM_170606.2	3187	aCc/aTc	42/59	0.899034662607578	1	FACETS	0.442	0.408	0.476	0.442	0.408	0.476	SUBCLONAL	1	TRUE	0	0.899034662607578	1		416	424	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70971066	70971066	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	301	638	0	ENST00000276594.2:c.1195G>A	p.Gly399Ser	p.G399S	ENST00000276594	NM_024504.3	399	Ggc/Agc	6/8	1	2	FACETS	0.456	0.428	0.485	0.456	0.428	0.485	SUBCLONAL	1	TRUE	1	0.899034662607578	2		638	1468	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342618	87342618	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	198	474	0	ENST00000277120.3:c.903G>A	p.Trp301Ter	p.W301*	ENST00000277120		301	tgG/tgA	9/19	0.511016147815964	1	FACETS	0.292	0.27	0.314	0.292	0.27	0.314	INDETERMINATE	1	TRUE	0	0.899034662607578	1		474	831	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759779	133759779	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	85	513	0	ENST00000318560.5:c.2102G>A	p.Gly701Asp	p.G701D	ENST00000318560	NM_005157.4	701	gGc/gAc	11/11	0.511016147815964	1	FACETS	0.208	0.184	0.234	0.208	0.184	0.234	INDETERMINATE	1	TRUE	0	0.899034662607578	1		513	500	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760097	133760097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1193093485	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	232	710	0	ENST00000318560.5:c.2420G>A	p.Gly807Asp	p.G807D	ENST00000318560	NM_005157.4	807	gGc/gAc	11/11	0.511016147815964	1	FACETS	0.363	0.339	0.387	0.363	0.339	0.387	INDETERMINATE	1	TRUE	0	0.899034662607578	1		710	783	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779058	135779058	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	148	407	0	ENST00000298552.3:c.2188G>A	p.Glu730Lys	p.E730K	ENST00000298552	NM_001162426.1	730	Gag/Aag	17/23	0.522095214346034	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.899034662607578	0		407	351	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040906	47040906	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	302	733	0	ENST00000377604.3:c.1436G>A	p.Gly479Asp	p.G479D	ENST00000377604	NM_001204468.1	479	gGt/gAt	14/24	0.511016147815964	1	FACETS	0.357	0.337	0.378	0.357	0.337	0.378	INDETERMINATE	1	TRUE	0	0.899034662607578	1		733	1035	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339236	70339236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	89	582	0	ENST00000374080.3:c.113C>T	p.Ala38Val	p.A38V	ENST00000374080		38	gCc/gTc	2/45	0.511016147815964	1	FACETS	0.11	0.097	0.124	0.11	0.097	0.124	INDETERMINATE	1	TRUE	0	0.899034662607578	1		582	988	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341238	70341238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754407926	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	172	536	1	ENST00000374080.3:c.797G>A	p.Arg266His	p.R266H	ENST00000374080		266	cGc/cAc	6/45	0.511016147815964	1	FACETS	0.285	0.262	0.308	0.285	0.262	0.308	INDETERMINATE	1	TRUE	0	0.899034662607578	1		537	740	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939187	76939187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782314240	NA	P-0029104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	255	587	0	ENST00000373344.5:c.1561C>T	p.Pro521Ser	p.P521S	ENST00000373344	NM_000489.3	521	Cct/Tct	9/35	0.511016147815964	1	FACETS	0.301	0.282	0.321	0.301	0.282	0.321	INDETERMINATE	1	TRUE	0	0.899034662607578	1		587	1036	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874264	155874264	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0029105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	313	558	1	ENST00000368323.3:c.267T>A	p.Tyr89Ter	p.Y89*	ENST00000368323	NM_006912.5	89	taT/taA	5/6	0.567229422963463	4	FACETS	0.921	0.871	0.971	0.921	0.871	0.971	CLONAL	2	TRUE	2	0.61380924830615	4		559	894	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	365	804	0	ENST00000269305.4:c.472del	p.Arg158AlafsTer12	p.R158Afs*12	ENST00000269305	NM_001126112.2	158	Cgc/gc	5/11	0.60693596615683	2	FACETS	0.908	0.87	0.945	0.908	0.87	0.945	CLONAL	2	TRUE	0	0.61380924830615	2		804	655	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029105-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	625	804	0	ENST00000269305.4:c.472del	p.Arg158AlafsTer12	p.R158Afs*12	ENST00000269305	NM_001126112.2	158	Cgc/gc	5/11	0.356774206022679	2	FACETS	0.933	0.914	0.951	1	0.998	1	CLONAL	5	TRUE	0	0.356773930212625	2		804	751	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846065	68846065	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029105-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	593	899	0	ENST00000261769.5:c.1036C>A	p.Gln346Lys	p.Q346K	ENST00000261769	NM_004360.3	346	Caa/Aaa	8/16	0.356773930212625	6	FACETS	1	0.992	1	1	0.997	1	CLONAL	4	TRUE	3	0.356773930212625	6		899	1303	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0029106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	208	490	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	1	2	FACETS	0.999	0.928	1	0.999	0.928	1	CLONAL	1	TRUE	1	0.451206734707882	2		490	923	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983938	15983938	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	145	344	0	ENST00000268712.3:c.3281A>C	p.Gln1094Pro	p.Q1094P	ENST00000268712	NM_006311.3	1094	cAg/cCg	24/46	1	2	FACETS	0.945	0.864	1	0.945	0.864	1	CLONAL	1	TRUE	1	0.451206734707882	2		344	680	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939901	76939901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057522580	NA	P-0029106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	115	290	0	ENST00000373344.5:c.847G>A	p.Val283Ile	p.V283I	ENST00000373344	NM_000489.3	283	Gta/Ata	9/35	1	1	FACETS	0.743	0.672	0.818	0.743	0.672	0.818	SUBCLONAL	1	TRUE	0	0.451206734707882	1		290	531	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0029107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	40	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	0.803	1	0.967	0.803	1	CLONAL	1	TRUE	1	0.16	2		440	517	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857532	68857532	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	C	novel	NA	P-0029107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	33	426	0	ENST00000261769.5:c.2164+3A>C		p.X722_splice	ENST00000261769	NM_004360.3	722			1	2	FACETS	1	0.823	1	1	0.823	1	CLONAL	1	TRUE	1	0.16	2		426	408	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0029109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	61	670	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.22	2		670	540	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971177	21971177	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913382	NA	P-0029109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	34	349	0	ENST00000304494.5:c.181G>T	p.Glu61Ter	p.E61*	ENST00000304494	NM_000077.4	61	Gag/Tag	2/3	0.277388448240255	1	FACETS	0.762	0.623	0.917	0.762	0.623	0.917	CLONAL	1	TRUE	0	0.22	1		349	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0029109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	35	507	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	1	2	FACETS	0.583	0.477	0.702	0.583	0.477	0.702	SUBCLONAL	1	TRUE	1	0.22	2		507	546	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs80338963	NA	P-0029109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	27	356	0	ENST00000342988.3:c.1081C>A	p.Arg361Ser	p.R361S	ENST00000342988	NM_005359.5	361	Cgc/Agc	9/12	1	2	FACETS	0.51	0.405	0.631	0.51	0.405	0.631	SUBCLONAL	1	TRUE	1	0.22	2		356	481	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42848533	42848533	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	52	562	0	ENST00000398585.3:c.809C>T	p.Ser270Leu	p.S270L	ENST00000398585	NM_001135099.1	270	tCa/tTa	8/14	1	2	FACETS	0.799	0.679	0.929	0.799	0.679	0.929	CLONAL	1	TRUE	1	0.22	2		562	592	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0029111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	147	344	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.837	0.774	0.902	1	0.993	1	CLONAL	3	FALSE	1	0.308031109457084	2		345	380	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0029111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	560	489	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.0580124750209832	3	FACETS	1	0.988	1			1	INDETERMINATE	5	FALSE	NA	0.308031109457084	3		489	814	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257249	133257249	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500889	NA	P-0029111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	134	577	1	ENST00000320574.5:c.229C>T	p.Arg77Cys	p.R77C	ENST00000320574	NM_006231.2	77	Cgc/Tgc	3/49	0.308031109457084	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	0	0.308031109457084	1		578	652	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	15	407	0	ENST00000263967.3:c.1034A>G	p.Asn345Ser	p.N345S	ENST00000263967	NM_006218.2	345	aAt/aGt	5/21	0.252227363306714	1	FACETS	0.155	0.113	0.207	0.155	0.113	0.207	SUBCLONAL	1	FALSE	0	0.308031109457084	1		407	530	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552660	18552660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758604951	NA	P-0029111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	115	637	0	ENST00000266497.5:c.2071C>T	p.Leu691Phe	p.L691F	ENST00000266497		691	Ctt/Ttt	14/31	0.308031109457084	1	FACETS	0.87	0.784	0.961	0.87	0.784	0.961	CLONAL	1	FALSE	0	0.308031109457084	1		637	726	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845386	76845387	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	162	231	0	ENST00000373344.5:c.6134dup	p.Ser2046IlefsTer6	p.S2046Ifs*6	ENST00000373344	NM_000489.3	2045	ata/atTa	27/35	0.308031109457084	0	FACETS	0.94	0.886	0.993			1	CLONAL	3	FALSE	NA	0.308031109457084	0		231	258	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0029113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	59	483	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	0.14	2		483	814	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0029113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	84	808	1	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.14	2		809	1054	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0029113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	28	300	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.8	0.638	0.985	0.8	0.638	0.985	CLONAL	1	TRUE	1	0.14	2		300	500	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023647	27023648	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCTC	novel	NA	P-0029113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	23	232	0	ENST00000324856.7:c.759_762dup	p.Ser255LeufsTer146	p.S255Lfs*146	ENST00000324856	NM_006015.4	251	-/CCTC	1/20	1	2	FACETS	0.773	0.602	0.972	0.773	0.602	0.972	CLONAL	1	TRUE	1	0.14	2		232	425	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720670	89720671	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	T	novel	NA	P-0029113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	25	200	0	ENST00000371953.3:c.821_822delinsT	p.Trp274LeufsTer2	p.W274Lfs*2	ENST00000371953	NM_000314.4	274	tGG/tT	8/9	1	2	FACETS	0.95	0.748	1	0.95	0.748	1	CLONAL	1	TRUE	1	0.14	2		200	376	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420134	420134	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	206	446	0	ENST00000399788.2:c.3133T>A	p.Ser1045Thr	p.S1045T	ENST00000399788	NM_001042603.1	1045	Tca/Aca	21/28	0.417110389182046	5	FACETS	0.827	0.767	0.889	0.551	0.511	0.593	CLONAL	2	FALSE	2	0.417110389182046	5		446	971	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0029117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	306	906	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.363187861828971	2	FACETS	0.848	0.802	0.894	0.848	0.802	0.894	CLONAL	2	TRUE	0	0.420290791547197	2		906	859	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716326	52716326	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	217	466	0	ENST00000322088.6:c.770G>T	p.Trp257Leu	p.W257L	ENST00000322088	NM_014225.5	257	tGg/tTg	6/15	0.199014893901172	5	FACETS	0.88	0.818	0.943	0.586	0.545	0.629	INDETERMINATE	2	TRUE	2	0.420290791547197	5		466	957	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380350	14380350	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	139	253	0	ENST00000256196.4:c.67G>T	p.Gly23Cys	p.G23C	ENST00000256196		23	Ggc/Tgc	1/6	0.276434145480642	3	FACETS	0.929	0.853	1	0.929	0.853	1	CLONAL	2	TRUE	1	0.420290791547197	3		253	431	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89176374	89176374	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0029117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	22	290	0	ENST00000336596.2:c.104C>G	p.Ser35Ter	p.S35*	ENST00000336596	NM_005233.5	35	tCa/tGa	2/17	0.203238681339651	4	FACETS	0.364	0.281	0.46	0.182	0.14	0.23	INDETERMINATE	1	TRUE	2	0.420290791547197	4		290	409	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589587	67589598	+	inframe_deletion	In_Frame_Del	DEL	TGAATATAACAC	TGAATATAACAC	-	novel	NA	P-0029117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	78	248	0	ENST00000274335.5:c.1351_1362del	p.Glu451_Thr454del	p.E451_T454del	ENST00000274335		450	caTGAATATAACACt/cat	10/15	0.420290791547197	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.420290791547197	1		248	252	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641147	93641147	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	115	621	0	ENST00000375746.1:c.1493G>C	p.Arg498Thr	p.R498T	ENST00000375746	NM_001174167.1	498	aGa/aCa	11/14	1	2	FACETS	0.823	0.742	0.908	0.823	0.742	0.908	CLONAL	1	TRUE	1	0.420290791547197	2		621	665	SUCCESS
AR	367	MSKCC	GRCh37	X	66765715	66765715	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	410	846	0	ENST00000374690.3:c.727G>C	p.Val243Leu	p.V243L	ENST00000374690	NM_000044.3	243	Gtg/Ctg	1/8	0.197024126059537	4	FACETS	0.95	0.903	0.997			1	INDETERMINATE	2	TRUE	NA	0.420290791547197	4		846	1459	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	154	404	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.81	2		404	370	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453136	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	rs397516897	NA	P-0029118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	136	486	0	ENST00000288602.6:c.1799_1801del	p.Val600_Lys601delinsGlu	p.V600_K601delinsE	ENST00000288602	NM_004333.4	600	gTGAaa/gaa	15/18	1	2	FACETS	0.996	0.919	1	0.996	0.919	1	CLONAL	1	TRUE	1	0.81	2		486	337	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151216587	151216587	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	29	136	0	ENST00000262187.5:c.11C>G	p.Ser4Cys	p.S4C	ENST00000262187	NM_005614.3	4	tCc/tGc	1/8	1	2	FACETS	0.307	0.248	0.374	0.307	0.248	0.374	SUBCLONAL	1	TRUE	1	0.81	2		136	233	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0029119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	180	631	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.285136193377535	3	FACETS	0.912	0.842	0.984	0.912	0.842	0.984	CLONAL	2	TRUE	1	0.285136193377535	3		632	791	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0029119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	81	412	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.983	0.867	1	0.983	0.867	1	CLONAL	1	TRUE	1	0.285136193377535	2		412	578	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175951	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1392778905	NA	P-0029119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	74	301	0	ENST00000257430.4:c.4660G>T	p.Glu1554Ter	p.E1554*	ENST00000257430	NM_000038.5	1554	Gaa/Taa	16/16	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.285136193377535	2		301	467	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685308	89685308	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876660634	NA	P-0029119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	74	309	1	ENST00000371953.3:c.203A>G	p.Tyr68Cys	p.Y68C	ENST00000371953	NM_000314.4	68	tAc/tGc	3/9	0.285136193377535	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.285136193377535	1		310	391	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732981	30732981	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	158	363	0	ENST00000295754.5:c.1594C>T	p.Gln532Ter	p.Q532*	ENST00000295754	NM_003242.5	532	Cag/Tag	7/7	0.285136193377535	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.285136193377535	2		363	507	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405962	49405962	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	118	598	0	ENST00000418115.1:c.176A>G	p.Asp59Gly	p.D59G	ENST00000418115	NM_001664.2	59	gAc/gGc	3/5	0.285136193377535	2	FACETS	0.957	0.863	1	0.478	0.431	0.528	CLONAL	1	TRUE	0	0.285136193377535	2		598	865	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466000	69466000	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	157	826	2	ENST00000227507.2:c.838G>T	p.Glu280Ter	p.E280*	ENST00000227507	NM_053056.2	280	Gag/Tag	5/5	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.285136193377535	2		828	862	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928358	69928358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774545277	NA	P-0029119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	66	444	0	ENST00000352241.4:c.178C>T	p.Arg60Cys	p.R60C	ENST00000352241	NM_198159.2	60	Cgc/Tgc	2/10	0.285136193377535	2	FACETS	0.985	0.857	1	0.492	0.428	0.562	CLONAL	1	TRUE	0	0.285136193377535	2		444	470	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404633	70404633	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	109	687	0	ENST00000373644.4:c.2147C>A	p.Ser716Ter	p.S716*	ENST00000373644	NM_030625.2	716	tCa/tAa	4/12	1	2	FACETS	0.835	0.749	0.926	0.835	0.749	0.926	CLONAL	1	TRUE	1	0.285136193377535	2		687	916	SUCCESS
BLM	641	MSKCC	GRCh37	15	91326125	91326125	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	80	478	0	ENST00000355112.3:c.2629G>T	p.Asp877Tyr	p.D877Y	ENST00000355112	NM_000057.2	877	Gat/Tat	13/22	1	2	FACETS	0.858	0.755	0.968	0.858	0.755	0.968	CLONAL	1	TRUE	1	0.285136193377535	2		478	654	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348962	89348962	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1468277012	NA	P-0029119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	139	737	1	ENST00000301030.4:c.3988G>A	p.Gly1330Arg	p.G1330R	ENST00000301030	NM_001256183.1	1330	Gga/Aga	9/13	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.285136193377535	2		738	873	SUCCESS
APC	324	MSKCC	GRCh37	5	112103078	112103081	+	frameshift_variant	Frame_Shift_Del	DEL	AGAA	AGAA	-	novel	NA	P-0029119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	46	322	0	ENST00000257430.4:c.416_419del	p.Lys139ArgfsTer30	p.K139Rfs*30	ENST00000257430	NM_000038.5	138	gAGAAa/ga	4/16	1	2	FACETS	0.747	0.63	0.876	0.747	0.63	0.876	SUBCLONAL	1	TRUE	1	0.285136193377535	2		322	432	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032747	30032749	+	frameshift_variant	Frame_Shift_Del	DEL	GGA	GGA	T	novel	NA	P-0029120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	51	280	0	ENST00000338641.4:c.122_124delinsT	p.Trp41LeufsTer7	p.W41Lfs*7	ENST00000338641	NM_000268.3	41	tGGAaa/tTaa	2/16	0.175825773688103	0	FACETS	0.867	0.755	0.982			1	CLONAL	4	FALSE	0	0.175730522143054	0		280	138	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0029121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	127	470	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.913	0.829	1	0.913	0.829	1	CLONAL	1	TRUE	1	0.393288571488786	2		470	707	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0029121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	129	498	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	0.393288571488786	2		498	587	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0029121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	217	698	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.393288571488786	2		704	1044	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0029121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	60	330	1	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	0.836	0.724	0.957	0.836	0.724	0.957	CLONAL	1	TRUE	1	0.393288571488786	2		331	365	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0029121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	99	255	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.978	0.876	1	0.978	0.876	1	CLONAL	1	TRUE	1	0.393288571488786	2		255	515	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0029121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	115	411	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.393288571488786	2		411	563	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056277	27056277	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	314	493	0	ENST00000324856.7:c.1273C>T	p.Gln425Ter	p.Q425*	ENST00000324856	NM_006015.4	425	Cag/Tag	2/20	0.393288571488786	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.393288571488786	2		493	710	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405953	157405954	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1554294674	NA	P-0029121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	134	481	0	ENST00000346085.5:c.2201dup	p.Ser736IlefsTer27	p.S736Ifs*27	ENST00000346085	NM_020732.3	732	ccg/ccGg	6/20	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.393288571488786	2		481	676	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508490	106508490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	61	247	0	ENST00000359195.3:c.484G>A	p.Val162Ile	p.V162I	ENST00000359195	NM_002649.2	162	Gtc/Atc	2/11	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.393288571488786	2		247	284	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830441	72830441	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	83	312	0	ENST00000268489.5:c.6140del	p.Pro2047LeufsTer54	p.P2047Lfs*54	ENST00000268489	NM_006885.3	2047	cCt/ct	9/10	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.393288571488786	2		312	407	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522190	157522190	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	143	528	0	ENST00000346085.5:c.4466del	p.Pro1489LeufsTer5	p.P1489Lfs*5	ENST00000346085	NM_020732.3	1488	Ccc/cc	18/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.393288571488786	2		528	660	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991949	72991949	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs753977275	NA	P-0029121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	129	505	2	ENST00000268489.5:c.2096del	p.Gly699AlafsTer125	p.G699Afs*125	ENST00000268489	NM_006885.3	699	gGc/gc	2/10	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.393288571488786	2		507	627	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214398	36214398	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs868041281	NA	P-0029121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	210	644	2	ENST00000222270.7:c.3057del	p.Gly1020AlafsTer4	p.G1020Afs*4	ENST00000222270	NM_014727.1	1018	Aaa/aa	7/37	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.393288571488786	2		646	1024	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554345	141554345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748399150	NA	P-0029121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	261	519	2	ENST00000220592.5:c.1806del	p.Ala603ProfsTer92	p.A603Pfs*92	ENST00000220592	NM_012154.3	602	ccC/cc	14/19	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.393288571488786	2		521	1302	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971053	21971053	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs137854598	NA	P-0029121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	187	388	0	ENST00000304494.5:c.305C>A	p.Ala102Glu	p.A102E	ENST00000304494	NM_000077.4	102	gCg/gAg	2/3	1	2	FACETS	0.782	0.726	0.839	1	0.991	1	SUBCLONAL	2	TRUE	1	0.393288571488786	2		388	608	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779220	3779220	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780545388	NA	P-0029121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	110	371	2	ENST00000262367.5:c.5828C>T	p.Pro1943Leu	p.P1943L	ENST00000262367	NM_004380.2	1943	cCg/cTg	31/31	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.393288571488786	2		373	448	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466025	69466026	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGA	novel	NA	P-0029121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	264	814	0	ENST00000227507.2:c.866_868dup	p.Asp289dup	p.D289dup	ENST00000227507	NM_053056.2	289	acc/acCGAc	5/5	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.393288571488786	2		814	1065	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948491	71948491	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1441023536	NA	P-0029121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	267	806	1	ENST00000298229.2:c.3203G>A	p.Ser1068Asn	p.S1068N	ENST00000298229	NM_001567.3	1068	aGc/aAc	26/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.393288571488786	2		807	1180	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141824	108141824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	144	424	0	ENST00000278616.4:c.2872G>A	p.Glu958Lys	p.E958K	ENST00000278616	NM_000051.3	958	Gag/Aag	19/63	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.393288571488786	2		424	636	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244794	46244794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	180	574	0	ENST00000334344.6:c.2888C>T	p.Thr963Ile	p.T963I	ENST00000334344	NM_152641.2	963	aCt/aTt	15/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.393288571488786	2		574	835	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285617	46285617	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	126	388	0	ENST00000334344.6:c.4980del	p.Asp1661MetfsTer40	p.D1661Mfs*40	ENST00000334344	NM_152641.2	1659	ggA/gg	17/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.393288571488786	2		388	599	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431998	49431998	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	248	750	0	ENST00000301067.7:c.9141del	p.Phe3047LeufsTer24	p.F3047Lfs*24	ENST00000301067	NM_003482.3	3047	ttT/tt	34/54	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.393288571488786	2		750	1188	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554200	63554200	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	210	570	0	ENST00000307078.5:c.539C>G	p.Ser180Trp	p.S180W	ENST00000307078	NM_004655.3	180	tCg/tGg	2/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.393288571488786	2		570	817	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622166	1622166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs916613545	NA	P-0029121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	44	656	1	ENST00000344749.5:c.709G>A	p.Gly237Arg	p.G237R	ENST00000344749	NM_001136139.2	237	Ggg/Agg	10/19	1	2	FACETS	0.266	0.222	0.315	0.266	0.222	0.315	SUBCLONAL	1	TRUE	1	0.393288571488786	2		657	841	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40742193	40742195	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0029121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	221	786	0	ENST00000392038.2:c.929_931del	p.Phe310del	p.F310del	ENST00000392038	NM_001626.4	310	tTCTgt/tgt	10/14	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.393288571488786	2		786	1028	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905775	50905775	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	245	758	0	ENST00000440232.2:c.823C>A	p.Leu275Met	p.L275M	ENST00000440232	NM_002691.3	275	Ctg/Atg	7/27	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.393288571488786	2		758	1076	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966157	25966157	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	171	540	1	ENST00000435504.4:c.3049C>T	p.Gln1017Ter	p.Q1017*	ENST00000435504		1017	Cag/Tag	13/13	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.393288571488786	2		541	818	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027887	48027887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752839086	NA	P-0029121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	106	382	0	ENST00000234420.5:c.2765G>A	p.Arg922Gln	p.R922Q	ENST00000234420	NM_000179.2	922	cGa/cAa	4/10	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.393288571488786	2		382	527	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871196	35871197	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0029121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	130	414	0	ENST00000303115.3:c.421dup	p.Glu141GlyfsTer5	p.E141Gfs*5	ENST00000303115	NM_002185.3	140	cgg/cGgg	4/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.393288571488786	2		414	539	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931451	131931452	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0029121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	61	381	1	ENST00000265335.6:c.2164_2165dup	p.Glu723ArgfsTer14	p.E723Rfs*14	ENST00000265335		719	cta/ctAAa	13/25	1	2	FACETS	0.514	0.444	0.592	0.514	0.444	0.592	SUBCLONAL	1	TRUE	1	0.393288571488786	2		382	603	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518795	176518795	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	221	719	0	ENST00000292408.4:c.713T>C	p.Leu238Pro	p.L238P	ENST00000292408	NM_213647.1	238	cTg/cCg	6/18	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.393288571488786	2		719	856	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555116	106555116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139718143	NA	P-0029121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	201	637	1	ENST00000369096.4:c.2233G>A	p.Val745Met	p.V745M	ENST00000369096	NM_001198.3	745	Gtg/Atg	7/7	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.393288571488786	2		638	945	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729529	41729529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138538132	NA	P-0029121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	154	624	0	ENST00000242208.4:c.1000G>A	p.Gly334Ser	p.G334S	ENST00000242208	NM_002192.2	334	Ggc/Agc	3/3	1	2	FACETS	0.957	0.877	1	0.957	0.877	1	CLONAL	1	TRUE	1	0.393288571488786	2		624	818	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929446	44929446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	201	666	0	ENST00000377967.4:c.2546G>A	p.Ser849Asn	p.S849N	ENST00000377967	NM_021140.2	849	aGt/aAt	17/29	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.393288571488786	2		666	1002	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371624	55371630	+	protein_altering_variant	In_Frame_Del	DEL	CGTGGAA	CGTGGAA	G	novel	NA	P-0029121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	169	567	0	ENST00000297316.4:c.314_320delinsG	p.Ser105_Lys107delinsTrp	p.S105_K107delinsW	ENST00000297316	NM_022454.3	105	tCGTGGAAg/tGg	2/2	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.393288571488786	2		567	728	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0029122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	157	478	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	0.26636292763549	3	FACETS	1	0.981	1	0.607	0.559	0.657	INDETERMINATE	1	TRUE	1	0.565126825480797	3		478	587	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784005	120784005	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	276	836	0	ENST00000257552.2:c.980C>T	p.Ser327Leu	p.S327L	ENST00000257552	NM_002442.3	327	tCg/tTg	13/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.565126825480797	2		836	904	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028627	12028628	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	141	370	0	ENST00000353533.5:c.832dup	p.Ser278LysfsTer8	p.S278Kfs*8	ENST00000353533	NM_003010.3	277	cca/ccAa	8/11	0.565126825480797	1	FACETS	0.937	0.864	1	0.937	0.864	1	CLONAL	1	TRUE	0	0.565126825480797	1		370	382	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709524	176709524	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	66	371	0	ENST00000439151.2:c.5951G>T	p.Arg1984Leu	p.R1984L	ENST00000439151	NM_022455.4	1984	cGa/cTa	19/23	1	2	FACETS	0.524	0.456	0.597	0.524	0.456	0.597	SUBCLONAL	1	TRUE	1	0.565126825480797	2		371	446	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935543	13935543	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763469375	NA	P-0029122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	113	272	0	ENST00000405192.2:c.1313C>T	p.Pro438Leu	p.P438L	ENST00000405192	NM_001163147.1	438	cCg/cTg	12/12	1	2	FACETS	0.975	0.885	1	0.975	0.885	1	CLONAL	1	TRUE	1	0.565126825480797	2		272	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0029123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	194	504	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.240131936494025	2	FACETS	0.983	0.91	1	0.983	0.91	1	CLONAL	2	TRUE	0	0.21	2		504	940	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575529	64575530	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0029123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	84	589	1	ENST00000312049.6:c.487_488delinsTT	p.Gly163Leu	p.G163L	ENST00000312049	NM_130799.2	163	GGg/TTg	3/10	0.282242578456405	3	FACETS	0.851	0.749	0.96			1	CLONAL	1	TRUE	NA	0.21	3		590	1039	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118353175	118353175	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	52	410	0	ENST00000534358.1:c.4051C>A	p.Pro1351Thr	p.P1351T	ENST00000534358	NM_005933.3	1351	Cca/Aca	8/36	0.213457488580424	2	FACETS	0.912	0.776	1	0.456	0.388	0.531	CLONAL	1	TRUE	0	0.21	2		410	543	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533659	63533659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	82	591	0	ENST00000307078.5:c.1495del	p.Leu499SerfsTer8	p.L499Sfs*8	ENST00000307078	NM_004655.3	499	Ctc/tc	6/11	0.234242490627687	0	FACETS	0.936	0.826	1			1	CLONAL	1	TRUE	0	0.21	0		591	659	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254620	10254620	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757550838	NA	P-0029123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	222	459	0	ENST00000340748.4:c.2890G>A	p.Val964Met	p.V964M	ENST00000340748		964	Gtg/Atg	28/40	1	2	FACETS	1	0.964	1	1	0.995	1	CLONAL	3	TRUE	1	0.21	2		459	674	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132515	11132515	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	340	741	0	ENST00000358026.2:c.2731G>A	p.Gly911Ser	p.G911S	ENST00000358026	NM_001128849.1	911	Ggc/Agc	19/36	1	2	FACETS	1	0.974	1	1	0.997	1	CLONAL	3	TRUE	1	0.21	2		741	1034	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248434	212248434	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	146	293	0	ENST00000342788.4:c.3833T>A	p.Val1278Glu	p.V1278E	ENST00000342788	NM_005235.2	1278	gTg/gAg	28/28	1	2	FACETS	1	0.956	1	1	0.993	1	CLONAL	3	TRUE	1	0.21	2		293	439	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572281	41572281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	182	660	0	ENST00000263253.7:c.4810C>T	p.Pro1604Ser	p.P1604S	ENST00000263253	NM_001429.3	1604	Cct/Tct	30/31	0.160291965149414	3	FACETS	0.9	0.83	0.974	0.9	0.83	0.974	CLONAL	2	TRUE	1	0.21	3		660	1064	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528472	29528472	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	29	374	0	ENST00000356175.3:c.1229del	p.Leu410ArgfsTer2	p.L410Rfs*2	ENST00000356175	NM_000267.3	410	cTg/cg	11/57	0.119634517758351	3	FACETS	0.674	0.541	0.825	0.225	0.18	0.275	INDETERMINATE	1	TRUE	0	0.265514258527444	3		374	367	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440889	56440889	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	188	654	0	ENST00000407977.2:c.448C>T	p.Gln150Ter	p.Q150*	ENST00000407977		150	Cag/Tag	4/10	0.240505435836979	1	FACETS	1	0.95	1	1	0.995	1	CLONAL	3	TRUE	0	0.265514258527444	1		654	403	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018252	48018252	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	83	444	0	ENST00000234420.5:c.447del	p.Lys149AsnfsTer25	p.K149Nfs*25	ENST00000234420	NM_000179.2	149	aaG/aa	2/10	0.165247782943877	4	FACETS	0.949	0.842	1	0.949	0.842	1	CLONAL	2	TRUE	2	0.265514258527444	4		444	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0029129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	540	747	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.652801140707329	3	FACETS	0.929	0.904	0.954	0.929	0.904	0.954	CLONAL	3	TRUE	0	0.710493641807486	3		750	739	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791751	42791751	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	111	578	0	ENST00000575354.2:c.637C>T	p.Arg213Trp	p.R213W	ENST00000575354	NM_015125.3	213	Cgg/Tgg	5/20	0.411302105774132	4	FACETS	0.813	0.732	0.899	0.407	0.366	0.45	INDETERMINATE	1	TRUE	2	0.710493641807486	4		578	657	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969969	81969969	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	149	402	0	ENST00000359376.3:c.3038A>G	p.Asn1013Ser	p.N1013S	ENST00000359376	NM_002661.3	1013	aAt/aGt	27/33	0.710493641807486	1	FACETS	0.749	0.694	0.805	0.749	0.694	0.805	SUBCLONAL	1	TRUE	0	0.710493641807486	1		402	361	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712580	52712580	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	100	385	0	ENST00000394830.3:c.172C>T	p.Arg58Ter	p.R58*	ENST00000394830	NM_018313.4	58	Cga/Tga	3/30	0.506455589860132	1	FACETS	0.896	0.81	0.986	0.896	0.81	0.986	CLONAL	1	TRUE	0	0.506455589860132	1		385	329	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475082	40475082	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	200	490	0	ENST00000264657.5:c.1828T>C	p.Phe610Leu	p.F610L	ENST00000264657	NM_139276.2	610	Ttc/Ctc	20/24	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.506455589860132	2		490	703	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183719	10183729	+	frameshift_variant	Frame_Shift_Del	DEL	TGCGCTCGGTG	TGCGCTCGGTG	-	novel	NA	P-0029131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	181	603	0	ENST00000256474.2:c.188_198del	p.Leu63GlnfsTer65	p.L63Qfs*65	ENST00000256474	NM_000551.3	63	cTGCGCTCGGTG/c	1/3	0.506455589860132	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.506455589860132	1		603	492	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23625369	23625369	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	134	476	0	ENST00000261584.4:c.3157G>T	p.Asp1053Tyr	p.D1053Y	ENST00000261584	NM_024675.3	1053	Gat/Tat	11/13	1	2	FACETS	0.55	0.499	0.603	0.55	0.499	0.603	SUBCLONAL	1	TRUE	1	0.55	2		476	886	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0029134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	422	308	1	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.68	2		309	930	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0029136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	65	483	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.913	0.796	1	0.913	0.796	1	CLONAL	1	FALSE	1	0.387853934098533	2		483	367	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0029136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	50	301	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	0.137651731525786	4	FACETS	0.947	0.806	1	0.473	0.403	0.55	INDETERMINATE	1	FALSE	2	0.387853934098533	4		301	378	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717661	89717661	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0029136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	199	693	1	ENST00000371953.3:c.686C>G	p.Ser229Ter	p.S229*	ENST00000371953	NM_000314.4	229	tCa/tGa	7/9	1	2	FACETS	0.928	0.866	0.991	1	0.993	1	CLONAL	2	FALSE	1	0.387853934098533	2		694	553	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654633	67654633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	109	399	0	ENST00000264010.4:c.1120A>G	p.Thr374Ala	p.T374A	ENST00000264010	NM_006565.3	374	Act/Gct	6/12	0.243172507600574	3	FACETS	1	0.977	1			1	CLONAL	1	FALSE	NA	0.387853934098533	3		399	521	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087443	27087443	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	123	526	0	ENST00000324856.7:c.2017C>T	p.Gln673Ter	p.Q673*	ENST00000324856	NM_006015.4	673	Cag/Tag	5/20	0.379621944548684	4	FACETS	1	0.978	1			1	CLONAL	1	FALSE	NA	0.387853934098533	4		526	688	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119936	70119937	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0029136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	102	367	0	ENST00000245479.2:c.939dup	p.Thr314HisfsTer264	p.T314Hfs*264	ENST00000245479	NM_000346.3	313	gtc/gtCc	3/3	0.127789027813211	4	FACETS	1	0.93	1	1	0.93	1	INDETERMINATE	2	FALSE	2	0.387853934098533	4		367	352	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0029138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	84	498	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.809	0.724	0.899	0.809	0.724	0.899	CLONAL	1	FALSE	1	0.736182307344305	2		498	282	SUCCESS
APC	324	MSKCC	GRCh37	5	112178000	112178000	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768922431	NA	P-0029138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	139	402	0	ENST00000257430.4:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000257430	NM_000038.5	2237	Cga/Tga	16/16	0.736182307344305	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	0	0.736182307344305	1		402	218	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207059	1207059	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	219	656	0	ENST00000326873.7:c.148del	p.Leu50Ter	p.L50*	ENST00000326873	NM_000455.4	49	taC/ta	1/10	0.736182307344305	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	0	0.736182307344305	1		656	358	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753374	42753374	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778567928	NA	P-0029138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	83	746	0	ENST00000222329.4:c.890C>T	p.Ser297Leu	p.S297L	ENST00000222329	NM_006494.2	297	tCa/tTa	4/4	1	2	FACETS	0.314	0.276	0.354	0.314	0.276	0.354	SUBCLONAL	1	FALSE	1	0.736182307344305	2		746	719	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022469	31022469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3746609	NA	P-0029139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	67	254	0	ENST00000375687.4:c.1954G>A	p.Gly652Ser	p.G652S	ENST00000375687	NM_015338.5	652	Ggc/Agc	13/13	0.25671712988898	5	FACETS	1	0.972	1	0.49	0.427	0.558	CLONAL	1	TRUE	2	0.308433069050932	5		254	432	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416800	121416800	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770695671	NA	P-0029139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	260	672	1	ENST00000257555.6:c.229G>A	p.Asp77Asn	p.D77N	ENST00000257555		77	Gat/Aat	1/10	0.308433069050932	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.308433069050932	3		673	874	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445125	49445125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs565042425	NA	P-0029139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	112	607	0	ENST00000301067.7:c.2341G>A	p.Ala781Thr	p.A781T	ENST00000301067	NM_003482.3	781	Gct/Act	10/54	0.308433069050932	3	FACETS	1	0.949	1	0.544	0.489	0.602	CLONAL	1	TRUE	1	0.308433069050932	3		607	771	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953186	81953186	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	149	318	0	ENST00000359376.3:c.2152A>T	p.Ser718Cys	p.S718C	ENST00000359376	NM_002661.3	718	Agt/Tgt	20/33	0.308433069050932	6	FACETS	1	0.976	1	0.589	0.54	0.641	CLONAL	2	TRUE	2	0.308433069050932	6		318	663	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254491	10254491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1256073808	NA	P-0029139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	89	421	0	ENST00000340748.4:c.3019G>A	p.Gly1007Ser	p.G1007S	ENST00000340748		1007	Ggc/Agc	28/40	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.308433069050932	2		421	548	SUCCESS
APC	324	MSKCC	GRCh37	5	112179614	112179614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1561622338	NA	P-0029139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	178	322	0	ENST00000257430.4:c.8323G>A	p.Gly2775Arg	p.G2775R	ENST00000257430	NM_000038.5	2775	Ggg/Agg	16/16	0.308433069050932	4	FACETS	1	0.942	1	1	0.942	1	CLONAL	3	TRUE	1	0.308433069050932	4		322	496	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346849	70346849	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	160	450	0	ENST00000374080.3:c.2716G>C	p.Glu906Gln	p.E906Q	ENST00000374080		906	Gag/Cag	20/45	0.308433069050932	6	FACETS	0.999	0.916	1	0.499	0.458	0.542	CLONAL	2	TRUE	2	0.308433069050932	6		450	840	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	534	779	2	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.738040250256053	2	FACETS	0.984	0.957	1	0.984	0.957	1	CLONAL	2	TRUE	0	0.738040250256053	2		781	735	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551295	141551295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	248	769	1	ENST00000220592.5:c.2002C>T	p.Arg668Cys	p.R668C	ENST00000220592	NM_012154.3	668	Cgc/Tgc	15/19	0.539126242191347	4	FACETS	0.831	0.775	0.889	0.415	0.387	0.445	CLONAL	1	TRUE	2	0.738040250256053	4		770	1406	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030378	49030378	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0029140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	143	338	0	ENST00000267163.4:c.1853C>G	p.Ser618Ter	p.S618*	ENST00000267163	NM_000321.2	618	tCa/tGa	19/27	0.737381345234145	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.738040250256053	2		338	193	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762511	41762511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200253980	NA	P-0029140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	85	297	0	ENST00000301178.4:c.2191G>A	p.Asp731Asn	p.D731N	ENST00000301178	NM_021913.4	731	Gat/Aat	18/20	0.304925394264621	3	FACETS	0.985	0.88	1	0.328	0.293	0.366	INDETERMINATE	1	TRUE	0	0.738040250256053	3		297	320	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31431696	31431696	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs776346705	NA	P-0029140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	74	399	0	ENST00000344624.3:c.3132T>G	p.Phe1044Leu	p.F1044L	ENST00000344624		1044	ttT/ttG	23/33	1	2	FACETS	0.76	0.673	0.85	0.76	0.673	0.85	SUBCLONAL	1	TRUE	1	0.738040250256053	2		399	264	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945702	151945702	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0029140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	86	286	0	ENST00000262189.6:c.1817C>G	p.Ser606Ter	p.S606*	ENST00000262189	NM_170606.2	606	tCa/tGa	14/59	0.738040250256053	2	FACETS	1	0.951	1	0.545	0.491	0.599	CLONAL	1	TRUE	0	0.738040250256053	2		286	214	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965627	90965627	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	93	290	0	ENST00000265433.3:c.1690G>T	p.Glu564Ter	p.E564*	ENST00000265433	NM_002485.4	564	Gaa/Taa	11/16	0.539126242191347	4	FACETS	0.873	0.789	0.959	0.873	0.789	0.959	CLONAL	2	TRUE	2	0.738040250256053	4		290	251	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771839	135771839	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs550526986	NA	P-0029140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	162	564	0	ENST00000298552.3:c.3278G>C	p.Arg1093Pro	p.R1093P	ENST00000298552	NM_001162426.1	1093	cGa/cCa	23/23	0.304925394264621	3	FACETS	0.933	0.859	1	0.311	0.286	0.337	INDETERMINATE	1	TRUE	0	0.738040250256053	3		564	644	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0029141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	114	465	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.187437771809413	3	FACETS	0.761	0.686	0.84	0.761	0.686	0.84	SUBCLONAL	2	TRUE	1	0.24	3		465	699	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508563	106508563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757016725	NA	P-0029141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	31	304	0	ENST00000359195.3:c.557C>T	p.Ala186Val	p.A186V	ENST00000359195	NM_002649.2	186	gCg/gTg	2/11	1	2	FACETS	0.644	0.521	0.784	0.644	0.521	0.784	SUBCLONAL	1	TRUE	1	0.24	2		304	401	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577531	7577531	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567549203	NA	P-0029141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	94	628	0	ENST00000269305.4:c.750del	p.Ile251SerfsTer94	p.I251Sfs*94	ENST00000269305	NM_001126112.2	250	ccC/cc	7/11	0.173602702643224	2	FACETS	1	0.938	1	0.539	0.48	0.603	CLONAL	1	TRUE	0	0.24	2		628	726	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838003	156838003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761633256	NA	P-0029141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	52	827	0	ENST00000524377.1:c.536G>A	p.Gly179Glu	p.G179E	ENST00000524377	NM_002529.3	179	gGg/gAg	5/17	0.187437771809413	3	FACETS	0.529	0.448	0.617	0.264	0.224	0.309	SUBCLONAL	1	TRUE	1	0.24	3		827	918	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302866	15302866	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	55	774	1	ENST00000263388.2:c.584A>T	p.Glu195Val	p.E195V	ENST00000263388	NM_000435.2	195	gAg/gTg	4/33	1	2	FACETS	0.64	0.547	0.743	0.64	0.547	0.743	SUBCLONAL	1	TRUE	1	0.24	2		775	716	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249002	55249003	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCGTGGA	rs397517109	NA	P-0029142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	222	578	0	ENST00000275493.2:c.2303_2311dup	p.Ser768_Asp770dup	p.S768_D770dup	ENST00000275493	NM_005228.3	768	gcc/gcCAGCGTGGAc	20/28	0.233664080349013	6	FACETS	1	0.978	1	0.833	0.777	0.89	CLONAL	3	TRUE	2	0.233664080349013	6		578	837	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039247	49039247	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	41	450	0	ENST00000267163.4:c.2325G>T	p.Arg775Ser	p.R775S	ENST00000267163	NM_000321.2	775	agG/agT	22/27	0.221626225386714	1	FACETS	0.597	0.497	0.709	0.597	0.497	0.709	SUBCLONAL	1	TRUE	0	0.233664080349013	1		450	519	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578571	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTGTAGGAAGAGGAAGG	ACTGTAGGAAGAGGAAGG	GCAGA	novel	NA	P-0029142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	150	727	1	ENST00000269305.4:c.376-17_376delinsTCTGC		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	0.197450269942115	2	FACETS	1	0.987	1	0.745	0.681	0.812	CLONAL	1	TRUE	0	0.233664080349013	2		728	862	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0029143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	201	489	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.654030053697343	3	FACETS	1	0.944	1	0.51	0.473	0.547	CLONAL	1	TRUE	1	0.654030053697343	3		489	800	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0029143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	485	614	0	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	0.654030053697343	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.654030053697343	3		614	978	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0029143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	79	195	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.654030053697343	2		195	226	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400138	41400138	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs755588862	NA	P-0029143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	361	484	0	ENST00000373198.4:c.621G>C	p.Gln207His	p.Q207H	ENST00000373198	NM_133170.3	207	caG/caC	5/32	0.654030053697343	6	FACETS	0.96	0.909	1	0.64	0.606	0.675	CLONAL	2	TRUE	3	0.654030053697343	6		484	1327	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432430	49432430	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	46	600	0	ENST00000301067.7:c.8709A>T	p.Arg2903Ser	p.R2903S	ENST00000301067	NM_003482.3	2903	agA/agT	34/54	0.654030053697343	2	FACETS	0.182	0.153	0.215	0.091	0.076	0.108	SUBCLONAL	1	TRUE	0	0.654030053697343	2		600	772	SUCCESS
APC	324	MSKCC	GRCh37	5	112174491	112174491	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	108	334	0	ENST00000257430.4:c.3201del	p.Gln1067HisfsTer59	p.Q1067Hfs*59	ENST00000257430	NM_000038.5	1067	cAa/ca	16/16	1	2	FACETS	0.966	0.876	1	0.966	0.876	1	CLONAL	1	TRUE	1	0.654030053697343	2		334	342	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928072	178928098	+	inframe_deletion	In_Frame_Del	DEL	TGGATTAGAAGATTTGCTGAACCCTAT	TGGATTAGAAGATTTGCTGAACCCTAT	-	novel	NA	P-0029146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	178	396	0	ENST00000263967.3:c.1353_1379del	p.Leu452_Gly460del	p.L452_G460del	ENST00000263967	NM_006218.2	450	caTGGATTAGAAGATTTGCTGAACCCTATt/cat	8/21	1	2	FACETS	0.706	0.655	0.759	0.706	0.655	0.759	SUBCLONAL	1	TRUE	1	0.887342683579431	2		396	568	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188164	11188164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777893	NA	P-0029146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	228	360	0	ENST00000361445.4:c.5930C>T	p.Thr1977Ile	p.T1977I	ENST00000361445	NM_004958.3	1977	aCa/aTa	43/58	0.887342683579431	1	FACETS	0.969	0.932	1	0.969	0.932	1	CLONAL	1	TRUE	0	0.887342683579431	1		360	295	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0029146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	303	644	0	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.887342683579431	2		644	666	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467677	66467677	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1343594860	NA	P-0029146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	212	321	0	ENST00000273854.3:c.592G>A	p.Glu198Lys	p.E198K	ENST00000273854	NM_004439.5	198	Gag/Aag	3/18	1	2	FACETS	0.887	0.831	0.943	0.887	0.831	0.943	CLONAL	1	TRUE	1	0.887342683579431	2		321	539	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0029148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	49	409	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.9	0.763	1	0.9	0.763	1	CLONAL	1	TRUE	1	0.22	2		409	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0029148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	116	559	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.169834797396227	2	FACETS	1	0.97	1	0.597	0.538	0.66	CLONAL	1	TRUE	0	0.22	2		559	883	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683984	29683985	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1135402907	NA	P-0029148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	33	393	0	ENST00000356175.3:c.7684_7685del	p.Arg2562AspfsTer12	p.R2562Dfs*12	ENST00000356175	NM_000267.3	2561	cAG/c	52/57	1	2	FACETS	0.47	0.382	0.571	0.47	0.382	0.571	SUBCLONAL	1	TRUE	1	0.22	2		393	638	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955472	48955473	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0029148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	50	390	0	ENST00000267163.4:c.1589_1590del	p.Lys530SerfsTer24	p.K530Sfs*24	ENST00000267163	NM_000321.2	530	AAa/a	17/27	1	2	FACETS	0.895	0.759	1	0.895	0.759	1	CLONAL	1	TRUE	1	0.22	2		390	508	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614536	38614536	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	57	509	0	ENST00000299084.4:c.303del	p.Thr102ArgfsTer19	p.T102Rfs*19	ENST00000299084	NM_152594.2	101	cTt/ct	3/7	1	2	FACETS	0.771	0.661	0.892	0.771	0.661	0.892	SUBCLONAL	1	TRUE	1	0.22	2		509	672	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003406	42003406	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	80	484	0	ENST00000219905.7:c.2945del	p.Gly982GlufsTer12	p.G982Efs*12	ENST00000219905	NM_001164273.1	981	caG/ca	8/24	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.22	2		484	681	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726703	88726703	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	39	400	0	ENST00000360948.2:c.341G>T	p.Gly114Val	p.G114V	ENST00000360948	NM_001012338.2	114	gGa/gTa	4/19	1	2	FACETS	0.608	0.503	0.726	0.608	0.503	0.726	SUBCLONAL	1	TRUE	1	0.22	2		400	583	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556192	29556193	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	CT	novel	NA	P-0029148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	19	153	0	ENST00000356175.3:c.2559_2560delinsCT	p.Gln853_Gln854delinsHisTer	p.Q853_Q854delinsH*	ENST00000356175	NM_000267.3	853	caGCag/caCTag	21/57	1	2	FACETS	0.868	0.662	1	0.868	0.662	1	CLONAL	1	TRUE	1	0.22	2		153	199	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170487	11170489	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs1375203306	NA	P-0029148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	86	621	0	ENST00000358026.2:c.4792_4794del	p.Lys1598del	p.K1598del	ENST00000358026	NM_001128849.1	1597	gAGAag/gag	34/36	1	2	FACETS	0.77	0.68	0.868	0.77	0.68	0.868	SUBCLONAL	1	TRUE	1	0.22	2		621	1015	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281554	15281554	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	96	669	0	ENST00000263388.2:c.4819G>T	p.Ala1607Ser	p.A1607S	ENST00000263388	NM_000435.2	1607	Gcc/Tcc	26/33	1	2	FACETS	0.849	0.755	0.95	0.849	0.755	0.95	CLONAL	1	TRUE	1	0.22	2		669	1028	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225400285	225400285	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	30	242	0	ENST00000264414.4:c.338A>T	p.Gln113Leu	p.Q113L	ENST00000264414	NM_003590.4	113	cAa/cTa	3/16	1	2	FACETS	0.781	0.63	0.953	0.781	0.63	0.953	CLONAL	1	TRUE	1	0.22	2		242	349	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586389	189586389	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	37	338	1	ENST00000264731.3:c.1013G>T	p.Arg338Leu	p.R338L	ENST00000264731	NM_003722.4	338	cGc/cTc	8/14	0.122539062355751	3	FACETS	0.812	0.669	0.971	0.406	0.334	0.486	INDETERMINATE	1	TRUE	1	0.22	3		339	460	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254594	1254594	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	177	559	1	ENST00000310581.5:c.3184G>T	p.Ala1062Ser	p.A1062S	ENST00000310581	NM_198253.2	1062	Gcc/Tcc	15/16	0.3	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.22	3		560	784	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80088596	80088596	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	49	422	0	ENST00000265081.6:c.2589del	p.Arg863SerfsTer4	p.R863Sfs*4	ENST00000265081	NM_002439.4	863	aGg/ag	19/24	1	2	FACETS	0.731	0.619	0.856	0.731	0.619	0.856	SUBCLONAL	1	TRUE	1	0.22	2		422	609	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441123	149441123	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	171	666	0	ENST00000286301.3:c.1789G>T	p.Val597Leu	p.V597L	ENST00000286301	NM_005211.3	597	Gtg/Ttg	13/22	0.169834797396227	2	FACETS	0.788	0.724	0.854	0.788	0.724	0.854	SUBCLONAL	2	TRUE	0	0.22	2		666	987	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514562	149514563	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	43	308	0	ENST00000261799.4:c.381_382insT	p.Leu128SerfsTer3	p.L128Sfs*3	ENST00000261799	NM_002609.3	127	-/T	4/23	0.169834797396227	2	FACETS	0.732	0.612	0.865	0.366	0.306	0.433	SUBCLONAL	1	TRUE	0	0.22	2		308	534	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6038846	6038846	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	58	501	0	ENST00000265849.7:c.598G>T	p.Val200Leu	p.V200L	ENST00000265849	NM_000535.5	200	Gta/Tta	6/15	0.122539062355751	3	FACETS	0.682	0.584	0.789	0.341	0.292	0.395	INDETERMINATE	1	TRUE	1	0.22	3		501	858	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845188	128845188	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	71	588	0	ENST00000249373.3:c.682C>A	p.Gln228Lys	p.Q228K	ENST00000249373	NM_005631.4	228	Cag/Aag	3/12	0.122539062355751	3	FACETS	0.856	0.746	0.976	0.428	0.373	0.488	INDETERMINATE	1	TRUE	1	0.22	3		588	837	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239666	53239666	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	92	304	0	ENST00000375401.3:c.1676G>T	p.Ser559Ile	p.S559I	ENST00000375401	NM_004187.3	559	aGc/aTc	12/26	1	1	FACETS	0.822	0.734	0.915	1	0.983	1	CLONAL	2	TRUE	0	0.22	1		304	453	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	58	404	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.934	1			1	INDETERMINATE	1	TRUE	NA	0.249070278050618	2		404	407	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0029149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	78	837	0	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	1	2	FACETS	0.729	0.639	0.826	0.729	0.639	0.826	SUBCLONAL	1	TRUE	1	0.249070278050618	2		837	859	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692871	89692871	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs139767111	NA	P-0029149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	36	297	0	ENST00000371953.3:c.355G>C	p.Val119Leu	p.V119L	ENST00000371953	NM_000314.4	119	Gtt/Ctt	5/9	0.249070278050618	1	FACETS	0.901	0.744	1	0.901	0.744	1	CLONAL	1	TRUE	0	0.249070278050618	1		297	281	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717727	89717727	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	60	449	0	ENST00000371953.3:c.752G>A	p.Gly251Asp	p.G251D	ENST00000371953	NM_000314.4	251	gGt/gAt	7/9	0.249070278050618	1	FACETS	0.805	0.694	0.925	0.805	0.694	0.925	CLONAL	1	TRUE	0	0.249070278050618	1		449	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578255	7578264	+	frameshift_variant	Frame_Shift_Del	DEL	TTCCACTCGG	TTCCACTCGG	-	novel	NA	P-0029149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	128	712	1	ENST00000269305.4:c.585_594del	p.Ile195MetfsTer49	p.I195Mfs*49	ENST00000269305	NM_001126112.2	195	atCCGAGTGGAA/at	6/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.249070278050618	2		713	763	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068018	94068018	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	42	342	0	ENST00000369303.4:c.944G>A	p.Gly315Glu	p.G315E	ENST00000369303	NM_004440.3	315	gGg/gAg	4/17	1	2	FACETS	0.63	0.526	0.747	0.63	0.526	0.747	SUBCLONAL	1	TRUE	1	0.249070278050618	2		342	535	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68984765	68984765	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	53	466	0	ENST00000288368.4:c.1529T>C	p.Val510Ala	p.V510A	ENST00000288368	NM_024870.2	510	gTg/gCg	14/40	1	2	FACETS	0.885	0.755	1	0.885	0.755	1	CLONAL	1	TRUE	1	0.249070278050618	2		466	481	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594221	55594221	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913512	NA	P-0029150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	31	327	0	ENST00000288135.5:c.1924A>G	p.Lys642Glu	p.K642E	ENST00000288135	NM_000222.2	642	Aaa/Gaa	13/21	0.639811787552312	1	FACETS	0.482	0.4	0.569	0.482	0.4	0.569	SUBCLONAL	1	TRUE	0	0.802372025341217	1		327	96	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292892	91292892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765089689	NA	P-0029150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	10	560	0	ENST00000355112.3:c.394C>T	p.Arg132Trp	p.R132W	ENST00000355112	NM_000057.2	132	Cgg/Tgg	3/22	0.802372025341217	1	FACETS	0.098	0.066	0.137	0.098	0.066	0.137	SUBCLONAL	1	TRUE	0	0.802372025341217	1		560	153	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808887	3808887	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398124144	NA	P-0029150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	11	494	0	ENST00000262367.5:c.3337C>T	p.Gln1113Ter	p.Q1113*	ENST00000262367	NM_004380.2	1113	Cag/Tag	17/31	0.358526436302904	1	FACETS	0.075	0.051	0.104	0.075	0.051	0.104	INDETERMINATE	1	TRUE	0	0.802372025341217	1		494	220	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36421183	36421183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	11	375	0	ENST00000300305.3:c.14G>A	p.Ser5Asn	p.S5N	ENST00000300305		5	aGc/aAc	1/8	0.802372025341217	3	FACETS	0.18	0.124	0.25	0.09	0.062	0.125	SUBCLONAL	1	TRUE	1	0.802372025341217	3		375	213	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593590	55593601	+	inframe_deletion	In_Frame_Del	DEL	GTATGAAGTACA	GTATGAAGTACA	-	novel	NA	P-0029150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	22	358	0	ENST00000288135.5:c.1658_1669del	p.Tyr553_Gln556del	p.Y553_Q556del	ENST00000288135	NM_000222.2	552	atGTATGAAGTACAg/atg	11/21	0.639811787552312	1	FACETS	0.438	0.349	0.534	0.438	0.349	0.534	SUBCLONAL	1	TRUE	0	0.802372025341217	1		358	75	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0029151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	213	415	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	1	2	FACETS	0.952	0.888	1	0.952	0.888	1	CLONAL	1	TRUE	1	0.625242719821677	2		415	716	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915524	112915524	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121918455	NA	P-0029151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	196	370	1	ENST00000351677.2:c.923A>G	p.Asn308Ser	p.N308S	ENST00000351677	NM_002834.3	308	aAt/aGt	8/16	0.625242719821677	3	FACETS	0.941	0.872	1	0.47	0.436	0.506	CLONAL	1	TRUE	1	0.625242719821677	3		371	875	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735533	40735533	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs777602624	NA	P-0029151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	160	423	0	ENST00000373198.4:c.3340A>G	p.Ile1114Val	p.I1114V	ENST00000373198	NM_133170.3	1114	Att/Gtt	25/32	0.625242719821677	3	FACETS	0.879	0.808	0.954	0.44	0.404	0.477	CLONAL	1	TRUE	1	0.625242719821677	3		423	764	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47679312	47679312	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371674237	NA	P-0029151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3507	189	344	0	ENST00000347630.2:c.895G>A	p.Val299Met	p.V299M	ENST00000347630	NM_001007230.1	299	Gtg/Atg	10/11	0.625242719821677	17	FACETS	0.931	0.855	1			1	CLONAL	1	TRUE	NA	0.625242719821677	17		344	3696	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0029152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	128	389	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	0.405608390847079	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.405608390847079	1		389	486	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220649	1220649	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	224	730	0	ENST00000326873.7:c.667G>T	p.Glu223Ter	p.E223*	ENST00000326873	NM_000455.4	223	Gag/Tag	5/10	0.405608390847079	1	FACETS	0.934	0.87	0.999	0.934	0.87	0.999	CLONAL	1	TRUE	0	0.405608390847079	1		730	943	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560425	65560425	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0029152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	67	264	0	ENST00000358664.4:c.171+1G>T		p.X57_splice	ENST00000358664	NM_002382.4	57			0.405608390847079	1	FACETS	0.887	0.777	1	0.887	0.777	1	CLONAL	1	TRUE	0	0.405608390847079	1		264	297	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244975	123244975	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	185	597	1	ENST00000358487.5:c.2129A>T	p.Glu710Val	p.E710V	ENST00000358487	NM_000141.4	710	gAg/gTg	16/18	0.405608390847079	1	FACETS	0.964	0.893	1	0.964	0.893	1	CLONAL	1	TRUE	0	0.405608390847079	1		598	754	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578315	7578493	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGCCTGGGGACCCTGGGCAACCAGCCCTGTCGTCTCTCCAGCCCCAGCTGCTCACCATCGCTATCTGAGCAGCGCTCATGGTGGGGGCAGCGCCTCACAACCTCCGTCATGTGCTGTGACTGCTTGTAGATGGCCATGGCGCGGACGCGGGTGCCGGGCGGGGGTGTGGAATCAACCC	AGGCCTGGGGACCCTGGGCAACCAGCCCTGTCGTCTCTCCAGCCCCAGCTGCTCACCATCGCTATCTGAGCAGCGCTCATGGTGGGGGCAGCGCCTCACAACCTCCGTCATGTGCTGTGACTGCTTGTAGATGGCCATGGCGCGGACGCGGGTGCCGGGCGGGGGTGTGGAATCAACCC	-	novel	NA	P-0029152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	224	495	0	ENST00000269305.4:c.437_560-26del		p.X146_splice	ENST00000269305	NM_001126112.2	146		5/11	0.405608390847079	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.405608390847079	1		495	672	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193884	106193885	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	104	358	0	ENST00000380013.4:c.4350dup	p.Arg1451SerfsTer27	p.R1451Sfs*27	ENST00000380013	NM_001127208.2	1449	tct/tcTt	10/11	0.405608390847079	1	FACETS	0.929	0.837	1	0.929	0.837	1	CLONAL	1	TRUE	0	0.405608390847079	1		358	440	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221313	1221314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs121913321	NA	P-0029153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	282	634	1	ENST00000326873.7:c.842dup	p.Leu282AlafsTer3	p.L282Afs*3	ENST00000326873	NM_000455.4	279	ggc/ggCc	6/10	0.482951665301249	2	FACETS	0.903	0.855	0.951	0.903	0.855	0.951	CLONAL	2	TRUE	0	0.48576997121316	2		635	643	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0029153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	199	670	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.48576997121316	3	FACETS	0.846	0.788	0.905	0.846	0.788	0.905	CLONAL	2	TRUE	1	0.48576997121316	3		670	602	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247804	59247805	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0029153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	183	714	0	ENST00000371222.2:c.937_938dup	p.Met313IlefsTer2	p.M313Ifs*2	ENST00000371222	NM_002228.3	313	atg/atATg	1/1	1	2	FACETS	0.897	0.829	0.968	0.897	0.829	0.968	CLONAL	1	TRUE	1	0.48576997121316	2		714	840	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644395	18644395	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	78	242	0	ENST00000266497.5:c.2573A>C	p.Lys858Thr	p.K858T	ENST00000266497		858	aAg/aCg	18/31	0.48576997121316	3	FACETS	0.926	0.817	1	0.463	0.408	0.521	CLONAL	1	TRUE	1	0.48576997121316	3		242	431	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46266401	46266401	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	105	318	0	ENST00000371998.3:c.2386G>T	p.Asp796Tyr	p.D796Y	ENST00000371998		796	Gac/Tac	13/23	0.436459007580072	4	FACETS	0.962	0.863	1	0.481	0.431	0.533	CLONAL	1	TRUE	2	0.48576997121316	4		318	668	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942753	68942753	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770289181	NA	P-0029153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	195	476	3	ENST00000288368.4:c.565C>T	p.Arg189Trp	p.R189W	ENST00000288368	NM_024870.2	189	Cgg/Tgg	6/40	0.469658012004528	4	FACETS	0.852	0.791	0.914	0.852	0.791	0.914	CLONAL	2	TRUE	2	0.48576997121316	4		479	700	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547022	9547022	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs58486349	NA	P-0029154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	128	206	0	ENST00000353224.5:c.1000G>A	p.Asp334Asn	p.D334N	ENST00000353224	NM_177990.2	334	Gat/Aat	5/10	0.738217834119436	8	FACETS	0.867	0.788	0.95			1	CLONAL	2	TRUE	NA	0.738217834119436	8		206	643	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127933411	127933411	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	343	546	1	ENST00000373547.4:c.124C>T	p.Gln42Ter	p.Q42*	ENST00000373547	NM_002721.4	42	Cag/Tag	2/7	0.713098582577394	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.738217834119436	3		547	625	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744450	41744450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775611992	NA	P-0029154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1483	607	652	0	ENST00000301178.4:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000301178	NM_021913.4	357	cGg/cAg	8/20	0.738217834119436	8	FACETS	0.843	0.809	0.878	0.422	0.404	0.439	CLONAL	3	TRUE	2	0.738217834119436	8		652	2090	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403254	116403254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	521	530	0	ENST00000397752.3:c.2515C>T	p.Pro839Ser	p.P839S	ENST00000397752	NM_000245.2	839	Cct/Tct	11/21	0.738217834119436	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	0	0.738217834119436	3		530	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577587	7577587	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	120	491	0	ENST00000269305.4:c.694A>T	p.Ile232Phe	p.I232F	ENST00000269305	NM_001126112.2	232	Atc/Ttc	7/11	0.201011533006952	2	FACETS	1	0.936	1	0.522	0.472	0.575	INDETERMINATE	1	TRUE	0	0.34435521178506	2		491	667	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0029155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	125	643	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.319923094744309	3	FACETS	1	0.982	1	0.674	0.612	0.74	CLONAL	1	TRUE	1	0.34435521178506	3		643	631	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278407	39278407	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	60	498	0	ENST00000402219.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000402219	NM_005633.3	248	Cgc/Tgc	6/23	1	2	FACETS	0.763	0.658	0.875	0.763	0.658	0.875	SUBCLONAL	1	TRUE	1	0.34435521178506	2		498	457	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738678	145738678	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746005466	NA	P-0029155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	57	604	1	ENST00000428558.2:c.2386G>A	p.Glu796Lys	p.E796K	ENST00000428558	NM_004260.3	796	Gag/Aag	15/22	0.34435521178506	3	FACETS	0.417	0.357	0.484	0.209	0.178	0.242	SUBCLONAL	1	TRUE	1	0.34435521178506	3		605	930	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578440	7578440	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	128	630	0	ENST00000269305.4:c.490A>C	p.Lys164Gln	p.K164Q	ENST00000269305	NM_001126112.2	164	Aag/Cag	5/11	0.201011533006952	2	FACETS	0.862	0.781	0.948	0.431	0.39	0.474	INDETERMINATE	1	TRUE	0	0.34435521178506	2		630	862	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152069	55152069	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	40	506	0	ENST00000257290.5:c.2501T>C	p.Ile834Thr	p.I834T	ENST00000257290	NM_006206.4	834	aTc/aCc	18/23	1	2	FACETS	0.377	0.312	0.449	0.377	0.312	0.449	SUBCLONAL	1	TRUE	1	0.34435521178506	2		506	617	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0029156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	119	498	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.951	0.861	1	0.951	0.861	1	CLONAL	1	TRUE	1	0.435946069898854	2		498	574	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971153	21971153	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913383	NA	P-0029156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	171	431	0	ENST00000304494.5:c.205G>T	p.Glu69Ter	p.E69*	ENST00000304494	NM_000077.4	69	Gag/Tag	2/3	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.435946069898854	2		431	723	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0029156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	50	250	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.675	0.575	0.783	0.675	0.575	0.783	SUBCLONAL	1	TRUE	1	0.435946069898854	2		250	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579567	7579580	+	frameshift_variant	Frame_Shift_Del	DEL	CATTGCTTGGGACG	CATTGCTTGGGACG	-	novel	NA	P-0029156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	151	669	0	ENST00000269305.4:c.107_120del	p.Pro36ArgfsTer2	p.P36Rfs*2	ENST00000269305	NM_001126112.2	36	cCGTCCCAAGCAATG/c	4/11	0.435946069898854	1	FACETS	0.785	0.72	0.853	0.785	0.72	0.853	SUBCLONAL	1	TRUE	0	0.435946069898854	1		669	690	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974770	21974795	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCGTGGCCAGCCAGTCAGCCGAAG	GGCCGTGGCCAGCCAGTCAGCCGAAG	-	novel	NA	P-0029156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	59	202	0	ENST00000304494.5:c.32_57del	p.Pro11ArgfsTer24	p.P11Rfs*24	ENST00000304494	NM_000077.4	11	cCTTCGGCTGACTGGCTGGCCACGGCC/c	1/3	1				0.767	1				CLONAL	1	TRUE	1	0.435946069898854	2		202	306	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	117	404	0				ENST00000310581	NM_198253.2	-/1132			0.264794770064215	1	FACETS	0.911	0.829	0.996	0.911	0.829	0.996	INDETERMINATE	1	TRUE	0	0.493378601743585	1		404	392	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562814	21562814	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	215	487	0	ENST00000382592.4:c.1105del	p.Gln369SerfsTer64	p.Q369Sfs*64	ENST00000382592	NM_014572.2	369	Cag/ag	4/8	0.493378601743585	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.493378601743585	1		487	595	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0029158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	25	400	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	0.788	0.62	0.983	0.788	0.62	0.983	CLONAL	1	TRUE	1	0.13	2		400	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0029158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	36	596	0	ENST00000269305.4:c.560-2A>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			1	2	FACETS	0.81	0.664	0.974	0.81	0.664	0.974	CLONAL	1	TRUE	1	0.13	2		596	684	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	166	404	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.987	0.916	1	0.987	0.916	1	CLONAL	1	TRUE	1	0.769888936990857	2		404	437	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74868172	74868172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1563677151	NA	P-0029159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	97	139	0	ENST00000284811.8:c.122C>T	p.Thr41Met	p.T41M	ENST00000284811		41	aCg/aTg	3/4	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.769888936990857	2		139	231	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162701	47162701	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	189	379	0	ENST00000409792.3:c.3425A>G	p.Glu1142Gly	p.E1142G	ENST00000409792	NM_014159.6	1142	gAa/gGa	3/21	1	2	FACETS	0.839	0.78	0.9	0.839	0.78	0.9	CLONAL	1	TRUE	1	0.769888936990857	2		379	585	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	111	404	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.936	0.855	1			1	INDETERMINATE	1	TRUE	NA	0.84129062590331	2		404	282	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164799	36164799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	301	740	1	ENST00000300305.3:c.1076C>T	p.Pro359Leu	p.P359L	ENST00000300305		359	cCg/cTg	8/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.84129062590331	2		741	651	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193205401	193205402	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTTTTTG	novel	NA	P-0029160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	222	370	0	ENST00000367435.3:c.1333_1339dup	p.Val447GlyfsTer19	p.V447Gfs*19	ENST00000367435	NM_024529.4	444	-/GTTTTTG	15/17	1	2	FACETS	0.901	0.845	0.958	0.901	0.845	0.958	CLONAL	1	TRUE	1	0.84129062590331	2		370	586	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858224	9858225	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGTG	novel	NA	P-0029160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	117	415	1	ENST00000330684.3:c.3172_3176dup	p.Asp1060ThrfsTer49	p.D1060Tfs*49	ENST00000330684	NM_001134407.1	1059	tct/tcCACTCt	13/13	1	2	FACETS	0.853	0.779	0.929	0.853	0.779	0.929	CLONAL	1	TRUE	1	0.84129062590331	2		416	326	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	18	394	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.17904116896978	0	FACETS	0.329	0.256	0.408			1	INDETERMINATE	1	TRUE	0	0.65	0		394	59	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0029162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	21	906	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.103418422816908	3	FACETS	0.8	0.626	0.995	0.4	0.313	0.498	INDETERMINATE	1	TRUE	1	0.65	3		906	107	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0029162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	31	462	1	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	0.973	0.808	1	0.973	0.808	1	CLONAL	1	TRUE	1	0.65	2		463	98	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0029162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	10	263	3	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.75	0.526	1	0.75	0.526	1	CLONAL	1	TRUE	1	0.65	2		266	41	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0029162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	21	306	7	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.65	2		313	58	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692896	89692896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123322	NA	P-0029162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	23	418	0	ENST00000371953.3:c.380G>A	p.Gly127Glu	p.G127E	ENST00000371953	NM_000314.4	127	gGa/gAa	5/9	1	2	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	TRUE	1	0.65	2		418	66	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193202211	193202211	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	16	434	0	ENST00000367435.3:c.1247del	p.Gly416AlafsTer12	p.G416Afs*12	ENST00000367435	NM_024529.4	415	Ggg/gg	14/17	0.935194830357782	3	FACETS	0.694	0.521	0.893	0.347	0.26	0.447	SUBCLONAL	1	TRUE	1	0.65	3		434	94	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922363	178922363	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	25	451	0	ENST00000263967.3:c.1132T>C	p.Cys378Arg	p.C378R	ENST00000263967	NM_006218.2	378	Tgt/Cgt	6/21	1	2	FACETS	0.999	0.812	1	0.999	0.812	1	CLONAL	1	TRUE	1	0.65	2		451	77	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0029162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	18	648	4	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.65	2		652	40	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492764	56492764	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	38	563	0	ENST00000407977.2:c.175G>T	p.Gly59Ter	p.G59*	ENST00000407977		59	Gga/Tga	2/10	0.103418422816908	3	FACETS	0.782	0.667	0.902	0.782	0.667	0.902	INDETERMINATE	2	TRUE	1	0.65	3		563	99	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692884	89692884	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	11	344	0	ENST00000371953.3:c.368A>T	p.His123Leu	p.H123L	ENST00000371953	NM_000314.4	123	cAc/cTc	5/9	1	2	FACETS	0.72	0.513	0.959	0.72	0.513	0.959	CLONAL	1	TRUE	1	0.65	2		344	47	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415846	49415846	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886041398	NA	P-0029162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	21	354	2	ENST00000301067.7:c.16501C>T	p.Arg5501Ter	p.R5501*	ENST00000301067	NM_003482.3	5501	Cga/Tga	53/54	0.239517447909551	4	FACETS	1	0.909	1	0.666	0.526	0.82	INDETERMINATE	1	TRUE	2	0.65	4		356	80	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78617605	78617605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	12	340	0	ENST00000306801.3:c.343C>T	p.Pro115Ser	p.P115S	ENST00000306801	NM_020761.2	115	Cca/Tca	3/34	0.103418422816908	3	FACETS	0.815	0.587	1	0.408	0.293	0.541	INDETERMINATE	1	TRUE	1	0.65	3		340	60	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132485	11132485	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	21	632	0	ENST00000358026.2:c.2701T>C	p.Tyr901His	p.Y901H	ENST00000358026	NM_001128849.1	901	Tat/Cat	19/36	1	2	FACETS	0.839	0.664	1	0.839	0.664	1	CLONAL	1	TRUE	1	0.65	2		632	77	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629155	14629167	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	TACCCATGACCCC	TACCCATGACCCC	-	novel	NA	P-0029162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	16	309	0	ENST00000254322.2:c.-6_7del		p.*2*	ENST00000254322	NM_006145.1	?-3/340		1/3	1	2	FACETS	0.693	0.525	0.884	0.693	0.525	0.884	SUBCLONAL	1	TRUE	1	0.65	2		309	71	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916624	178916624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749956691	NA	P-0029162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	13	298	0	ENST00000263967.3:c.11G>A	p.Arg4Gln	p.R4Q	ENST00000263967	NM_006218.2	4	cGa/cAa	2/21	1	2	FACETS	0.816	0.602	1	0.816	0.602	1	CLONAL	1	TRUE	1	0.65	2		298	49	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957865	1957865	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	28	499	0	ENST00000382891.5:c.2831G>C	p.Arg944Pro	p.R944P	ENST00000382891	NM_133335.3	944	cGg/cCg	15/22	1	2	FACETS	0.689	0.56	0.831	0.689	0.56	0.831	SUBCLONAL	1	TRUE	1	0.65	2		499	125	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878242	151878242	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs765851067	NA	P-0029162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	14	540	0	ENST00000262189.6:c.6703A>G	p.Arg2235Gly	p.R2235G	ENST00000262189	NM_170606.2	2235	Agg/Ggg	36/59	1	2	FACETS	0.538	0.396	0.704	0.538	0.396	0.704	SUBCLONAL	1	TRUE	1	0.65	2		540	80	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088754	27088754	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	28	548	0	ENST00000324856.7:c.2363del	p.Tyr788SerfsTer45	p.Y788Sfs*45	ENST00000324856	NM_006015.4	788	tAc/tc	7/20	0.351736983164288	4	FACETS	0.799	0.656	0.951	0.799	0.656	0.951	INDETERMINATE	2	TRUE	2	0.65	4		548	89	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	37	634	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.801	0.665	0.952	1	0.957	1	CLONAL	2	FALSE	1	0.183284917302258	2		637	252	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775611	9775611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1375117381	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	70	416	1	ENST00000377346.4:c.154C>T	p.Arg52Cys	p.R52C	ENST00000377346	NM_005026.3	52	Cgc/Tgc	4/24	0.146624823684121	0	FACETS	0.808	0.718	0.901			1	CLONAL	4	FALSE	0	0.183284917302258	0		417	193	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255142	16255143	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	rs764595221	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	159	483	10	ENST00000375759.3:c.2417_2418del	p.Arg806ThrfsTer14	p.R806Tfs*14	ENST00000375759	NM_015001.2	803	GAg/g	11/15	0.183284917302258	5	FACETS	1	0.943	1	1	0.993	1	CLONAL	5	FALSE	3	0.183284917302258	5		493	433	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258604	16258604	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1195174281	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	102	528	3	ENST00000375759.3:c.5869C>T	p.Arg1957Cys	p.R1957C	ENST00000375759	NM_015001.2	1957	Cgc/Tgc	11/15	0.183284917302258	5	FACETS	0.992	0.9	1	1	0.99	1	CLONAL	5	FALSE	3	0.183284917302258	5		531	286	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259043	16259043	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	96	584	1	ENST00000375759.3:c.6313del	p.Ala2105LeufsTer33	p.A2105Lfs*33	ENST00000375759	NM_015001.2	2103	aGg/ag	11/15	0.183284917302258	5	FACETS	1	0.912	1	1	0.989	1	CLONAL	5	FALSE	3	0.183284917302258	5		585	265	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105715	27105717	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs765246223	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	44	334	0	ENST00000324856.7:c.5334_5336del	p.Glu1780del	p.E1780del	ENST00000324856	NM_006015.4	1776	GAA/-	20/20	0.183284917302258	5	FACETS	1	0.901	1	1	0.966	1	CLONAL	3	FALSE	3	0.183284917302258	5		334	189	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812466	43812466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1298113648	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	59	414	0	ENST00000372470.3:c.1169G>A	p.Arg390His	p.R390H	ENST00000372470	NM_005373.2	390	cGc/cAc	8/12	1	2	FACETS	0.945	0.824	1	1	0.983	1	CLONAL	3	FALSE	1	0.183284917302258	2		414	227	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46738203	46738203	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	146	409	0	ENST00000371975.4:c.1235T>C	p.Val412Ala	p.V412A	ENST00000371975	NM_003579.3	412	gTt/gCt	11/18	1	2	FACETS	1	0.963	1	1	0.994	1	CLONAL	5	FALSE	1	0.183284917302258	2		409	302	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306996	65306997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	54	349	7	ENST00000342505.4:c.2580dup	p.Pro861ThrfsTer4	p.P861Tfs*4	ENST00000342505	NM_002227.2	860	-/A	19/25	1	2	FACETS	0.918	0.794	1	1	0.981	1	CLONAL	3	FALSE	1	0.183284917302258	2		356	214	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	70	467	3	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	1	2	FACETS	0.906	0.798	1	1	0.985	1	CLONAL	3	FALSE	1	0.183284917302258	2		470	281	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533595	533595	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	120	589	0	ENST00000451590.1:c.308T>C	p.Val103Ala	p.V103A	ENST00000451590	NM_001130442.1	103	gTg/gCg	4/5	1	2	FACETS	0.966	0.883	1	1	0.992	1	CLONAL	4	FALSE	1	0.183284917302258	2		589	339	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575419	64575419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	90	631	0	ENST00000312049.6:c.598G>A	p.Gly200Ser	p.G200S	ENST00000312049	NM_130799.2	200	Ggc/Agc	3/10	1	2	FACETS	0.986	0.883	1	1	0.989	1	CLONAL	3	FALSE	1	0.183284917302258	2		631	332	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443718	49443718	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	102	606	0	ENST00000301067.7:c.3653C>T	p.Ala1218Val	p.A1218V	ENST00000301067	NM_003482.3	1218	gCc/gTc	11/54	0.183284917302258	5	FACETS	1	0.917	1	1	0.98	1	CLONAL	4	FALSE	2	0.183284917302258	5		606	349	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133236020	133236020	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	95	497	0	ENST00000320574.5:c.3136T>C	p.Tyr1046His	p.Y1046H	ENST00000320574	NM_006231.2	1046	Tac/Cac	26/49	1	2	FACETS	0.949	0.858	1	1	0.991	1	CLONAL	4	FALSE	1	0.183284917302258	2		497	273	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953958	32953958	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	132	469	0	ENST00000380152.3:c.9025T>C	p.Tyr3009His	p.Y3009H	ENST00000380152		3009	Tat/Cat	23/27	0.183284917302258	3	FACETS	1	0.968	1	1	0.992	1	CLONAL	4	FALSE	1	0.183284917302258	3		469	355	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396579	30396580	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	62	278	0	ENST00000331968.5:c.139_140insT	p.Gly47ValfsTer14	p.G47Vfs*14	ENST00000331968	NM_002742.2	47	ggg/gTgg	1/18	0.183284917302258	4	FACETS	0.878	0.768	0.993	1	0.978	1	CLONAL	4	FALSE	2	0.183284917302258	4		278	228	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105238733	105238733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	93	643	1	ENST00000349310.3:c.1229G>A	p.Gly410Asp	p.G410D	ENST00000349310	NM_001014432.1	410	gGt/gAt	13/15	0.183284917302258	4	FACETS	0.893	0.802	0.989	1	0.985	1	CLONAL	4	FALSE	2	0.183284917302258	4		644	336	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343543	343543	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150504240	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	146	664	1	ENST00000262320.3:c.2131C>T	p.Arg711Cys	p.R711C	ENST00000262320	NM_003502.3	711	Cgc/Tgc	8/11	1	2	FACETS	0.948	0.879	1	1	0.994	1	CLONAL	5	FALSE	1	0.183284917302258	2		665	336	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346178	89346178	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	23	240	0	ENST00000301030.4:c.6772del	p.Ala2258LeufsTer79	p.A2258Lfs*79	ENST00000301030	NM_001256183.1	2258	Gct/ct	9/13	1	2	FACETS	1	0.84	1	1	0.95	1	CLONAL	2	FALSE	1	0.183284917302258	2		240	117	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950317	15950319	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	121	653	1	ENST00000268712.3:c.6625_6627del	p.Lys2209del	p.K2209del	ENST00000268712	NM_006311.3	2209	AAG/-	42/46	1	2	FACETS	1	0.938	1	1	0.993	1	CLONAL	4	FALSE	1	0.183284917302258	2		654	321	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858053	40858053	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	150	585	0	ENST00000428826.2:c.1811del	p.Asn604ThrfsTer26	p.N604Tfs*26	ENST00000428826		604	aAc/ac	16/21	1	2	FACETS	1	0.962	1	1	0.994	1	CLONAL	4	FALSE	1	0.183284917302258	2		585	385	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248608	10248608	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375225009	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	67	547	1	ENST00000340748.4:c.4145C>T	p.Ser1382Leu	p.S1382L	ENST00000340748		1382	tCg/tTg	35/40	1	2	FACETS	1	0.958	1	1	0.984	1	CLONAL	2	FALSE	1	0.183284917302258	2		548	299	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051081	13051081	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	142	430	0	ENST00000316448.5:c.517A>G	p.Thr173Ala	p.T173A	ENST00000316448	NM_004343.3	173	Aca/Gca	5/9	1	2	FACETS	1	0.961	1	1	0.994	1	CLONAL	4	FALSE	1	0.183284917302258	2		430	364	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279340	18279340	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	90	565	0	ENST00000222254.8:c.1796del	p.Asn599MetfsTer38	p.N599Mfs*38	ENST00000222254	NM_005027.3	598	Aaa/aa	14/16	1	2	FACETS	1	0.925	1	1	0.989	1	CLONAL	3	FALSE	1	0.183284917302258	2		565	315	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752695	42752695	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1366176199	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	67	588	4	ENST00000222329.4:c.1569del	p.Leu525SerfsTer6	p.L525Sfs*6	ENST00000222329	NM_006494.2	523	ggG/gg	4/4	1	2	FACETS	1	0.959	1	1	0.984	1	CLONAL	2	FALSE	1	0.183284917302258	2		592	297	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	143	790	0	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.958	0.883	1	1	0.994	1	CLONAL	4	FALSE	1	0.183284917302258	2		790	407	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143462	30143462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	40	280	0	ENST00000389048.3:c.64G>A	p.Gly22Arg	p.G22R	ENST00000389048	NM_004304.4	22	Ggg/Agg	1/29	0.183284917302258	0	FACETS	0.958	0.815	1			1	CLONAL	3	FALSE	0	0.183284917302258	0		280	124	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690193	47690193	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1553365719	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	140	400	0	ENST00000233146.2:c.1413del	p.Lys471AsnfsTer11	p.K471Nfs*11	ENST00000233146	NM_000251.2	470	gtA/gt	9/16	0.183284917302258	0	FACETS	0.878	0.828	0.926			1	CLONAL	7	FALSE	0	0.183284917302258	0		400	203	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084146	47084146	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	132	462	1	ENST00000409792.3:c.7143del	p.Ser2382LeufsTer29	p.S2382Lfs*29	ENST00000409792	NM_014159.6	2381	ccC/cc	17/21	1	2	FACETS	0.973	0.894	1	1	0.993	1	CLONAL	4	FALSE	1	0.183284917302258	2		463	370	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936594	49936594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	79	672	0	ENST00000296474.3:c.1333C>T	p.Pro445Ser	p.P445S	ENST00000296474	NM_002447.2	445	Cca/Tca	2/20	1	2	FACETS	0.925	0.827	1	1	0.989	1	CLONAL	4	FALSE	1	0.183284917302258	2		672	233	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437444	52437444	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	66	467	0	ENST00000460680.1:c.1717C>A	p.Leu573Met	p.L573M	ENST00000460680	NM_004656.3	573	Ctg/Atg	13/17	1	2	FACETS	0.909	0.798	1	1	0.985	1	CLONAL	3	FALSE	1	0.183284917302258	2		467	264	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916935	178916935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	151	523	1	ENST00000263967.3:c.322C>T	p.Arg108Cys	p.R108C	ENST00000263967	NM_006218.2	108	Cgt/Tgt	2/21	1	2	FACETS	1	0.973	1	1	0.994	1	CLONAL	4	FALSE	1	0.183284917302258	2		524	371	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443307	187443307	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	55	274	1	ENST00000232014.4:c.1819T>C	p.Cys607Arg	p.C607R	ENST00000232014	NM_001130845.1	607	Tgc/Cgc	8/10	1	2	FACETS	1	0.903	1	1	0.983	1	CLONAL	3	FALSE	1	0.183284917302258	2		275	191	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629475	187629475	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765412973	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	81	579	0	ENST00000441802.2:c.1507G>A	p.Ala503Thr	p.A503T	ENST00000441802	NM_005245.3	503	Gca/Aca	2/27	0.183284917302258	3	FACETS	0.911	0.809	1	1	0.974	1	CLONAL	3	FALSE	1	0.183284917302258	3		579	353	SUCCESS
APC	324	MSKCC	GRCh37	5	112175770	112175771	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	54	273	0	ENST00000257430.4:c.4479_4480del	p.Glu1494LysfsTer19	p.E1494Kfs*19	ENST00000257430	NM_000038.5	1493	acGGaa/acaa	16/16	0.183284917302258	3	FACETS	0.946	0.823	1	1	0.977	1	CLONAL	4	FALSE	1	0.183284917302258	3		273	170	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638435	176638435	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs112500609	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	107	621	1	ENST00000439151.2:c.3035G>A	p.Arg1012His	p.R1012H	ENST00000439151	NM_022455.4	1012	cGt/cAt	5/23	0.166582390798526	3	FACETS	1	0.929	1			1	CLONAL	3	FALSE	NA	0.183284917302258	3		622	411	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157488275	157488275	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377351099	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	61	348	0	ENST00000346085.5:c.2981C>T	p.Ala994Val	p.A994V	ENST00000346085	NM_020732.3	994	gCg/gTg	10/20	1	2	FACETS	0.977	0.855	1	1	0.984	1	CLONAL	3	FALSE	1	0.183284917302258	2		348	227	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371798	116371798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs986139438	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	122	371	1	ENST00000397752.3:c.1277G>A	p.Arg426His	p.R426H	ENST00000397752	NM_000245.2	426	cGc/cAc	3/21	1	2	FACETS	0.909	0.835	0.984	1	0.993	1	CLONAL	5	FALSE	1	0.183284917302258	2		372	293	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624475	140624480	+	inframe_deletion	In_Frame_Del	DEL	CCACCA	CCACCA	-	novel	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	50	80	0	ENST00000288602.6:c.24_29del	p.Gly10_Gly11del	p.G10_G11del	ENST00000288602	NM_004333.4	8	ggTGGTGGc/ggc	1/18	1	2	FACETS	1	0.91	1	1	0.983	1	CLONAL	4	FALSE	1	0.183284917302258	2		80	129	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741719	145741719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781314533	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	186	567	2	ENST00000428558.2:c.784C>T	p.Arg262Trp	p.R262W	ENST00000428558	NM_004260.3	262	Cgg/Tgg	5/22	1	2	FACETS	0.955	0.893	1	1	0.995	1	CLONAL	5	FALSE	1	0.183284917302258	2		569	425	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741892	145741892	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs757780731	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	57	623	0	ENST00000428558.2:c.611C>G	p.Ala204Gly	p.A204G	ENST00000428558	NM_004260.3	204	gCc/gGc	5/22	1	2	FACETS	0.777	0.669	0.895	1	0.97	1	SUBCLONAL	2	FALSE	1	0.183284917302258	2		623	400	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636191	87636191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	59	308	0	ENST00000277120.3:c.2356C>T	p.Arg786Ter	p.R786*	ENST00000277120		786	Cga/Tga	19/19	0.183284917302258	1	FACETS	0.898	0.784	1	1	0.983	1	CLONAL	3	FALSE	0	0.183284917302258	1		308	217	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760903	133760903	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	73	691	0	ENST00000318560.5:c.3226C>T	p.Gln1076Ter	p.Q1076*	ENST00000318560	NM_005157.4	1076	Caa/Taa	11/11	0.183284917302258	1	FACETS	1	0.954	1	1	0.985	1	CLONAL	2	FALSE	0	0.183284917302258	1		691	309	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139565405	139565405	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	42	547	0	ENST00000308874.7:c.575del	p.Val192GlyfsTer5	p.V192Gfs*5	ENST00000308874		192	gTg/gg	8/10	0.183284917302258	1	FACETS	0.89	0.749	1	1	0.967	1	CLONAL	2	FALSE	0	0.183284917302258	1		547	234	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615676	100615676	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	15	309	0	ENST00000308731.7:c.656T>C	p.Val219Ala	p.V219A	ENST00000308731	NM_000061.2	219	gTt/gCt	8/19	0.183284917302258	2	FACETS	1	0.816	1			1	CLONAL	1	FALSE	NA	0.183284917302258	2		309	143	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0029165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	127	532	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.923	0.838	1	0.923	0.838	1	CLONAL	1	TRUE	1	0.412060589672175	2		532	668	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241978	133241978	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1422986795	NA	P-0029165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	185	560	0	ENST00000320574.5:c.2378G>T	p.Arg793Leu	p.R793L	ENST00000320574	NM_006231.2	793	cGc/cTc	21/49	1	2	FACETS	0.975	0.9	1	0.975	0.9	1	CLONAL	1	TRUE	1	0.412060589672175	2		560	921	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220493	1220497	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGT	GGCGT	-	novel	NA	P-0029165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	207	703	0	ENST00000326873.7:c.589_593del	p.Val197ArgfsTer67	p.V197Rfs*67	ENST00000326873	NM_000455.4	196	GGCGTg/g	4/10	0.412060589672175	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.412060589672175	1		703	788	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3094695	3094695	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0029165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	109	309	0	ENST00000078429.4:c.46A>T	p.Lys16Ter	p.K16*	ENST00000078429	NM_002067.2	16	Aag/Tag	1/7	0.412060589672175	1	FACETS	0.929	0.84	1	0.929	0.84	1	CLONAL	1	TRUE	0	0.412060589672175	1		309	452	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602620	10602620	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	197	680	0	ENST00000171111.5:c.958del	p.Arg320GlyfsTer8	p.R320Gfs*8	ENST00000171111	NM_203500.1	320	Cgg/gg	3/6	0.412060589672175	1	FACETS	0.947	0.878	1	0.947	0.878	1	CLONAL	1	TRUE	0	0.412060589672175	1		680	802	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802655	139802655	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	164	499	0	ENST00000247668.2:c.500G>T	p.Arg167Leu	p.R167L	ENST00000247668	NM_021138.3	167	cGg/cTg	5/11	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.412060589672175	2		499	789	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342362	70342362	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	182	531	0	ENST00000374080.3:c.1253G>T	p.Arg418Leu	p.R418L	ENST00000374080		418	cGt/cTt	9/45	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.412060589672175	2		531	818	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	77	768	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.914	1	1	0.984	1	CLONAL	2	TRUE	1	0.14	2		768	525	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007332	143007332	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	33	383	4	ENST00000262992.4:c.2452del	p.Arg818GlufsTer4	p.R818Efs*4	ENST00000262992	NM_001101669.1	818	Aga/ga	22/24	1	2	FACETS	0.937	0.762	1	0.937	0.762	1	CLONAL	1	TRUE	1	0.14	2		387	503	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	50	730	2	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.14	2		732	616	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	44	462	1	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.14	2		463	475	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	19	416	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.634	0.48	0.816	0.634	0.48	0.816	SUBCLONAL	1	TRUE	1	0.14	2		416	428	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512383	38512383	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1188389540	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	22	469	1	ENST00000254066.5:c.1294C>T	p.Arg432Trp	p.R432W	ENST00000254066	NM_000964.3	432	Cgg/Tgg	9/9	1	2	FACETS	0.875	0.678	1	0.875	0.678	1	CLONAL	1	TRUE	1	0.14	2		470	359	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417921	138417921	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs866345647	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	40	456	0	ENST00000289153.2:c.1598del	p.Lys533SerfsTer6	p.K533Sfs*6	ENST00000289153	NM_006219.2	533	aAg/ag	11/22	1	2	FACETS	0.972	0.806	1	0.972	0.806	1	CLONAL	1	TRUE	1	0.14	2		456	588	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641389	18641389	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1229278001	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	33	283	0	ENST00000266497.5:c.2393del	p.Asn798MetfsTer16	p.N798Mfs*16	ENST00000266497		796	ctA/ct	17/31	1	2	FACETS	0.924	0.757	1	1	0.959	1	CLONAL	2	TRUE	1	0.14	2		283	255	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849663	68849663	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587780113	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	35	462	0	ENST00000261769.5:c.1565+1G>A		p.X522_splice	ENST00000261769	NM_004360.3	522			1	2	FACETS	1	0.824	1	1	0.824	1	CLONAL	1	TRUE	1	0.14	2		462	497	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521664	89521664	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17801309	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	31	513	0	ENST00000336596.2:c.2741G>A	p.Arg914His	p.R914H	ENST00000336596	NM_005233.5	914	cGc/cAc	16/17	1	2	FACETS	0.798	0.644	0.973	0.798	0.644	0.973	CLONAL	1	TRUE	1	0.14	2		513	555	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573505	48573506	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	27	395	0	ENST00000342988.3:c.94_95del	p.Ser32Ter	p.S32*	ENST00000342988	NM_005359.5	30	gGA/g	2/12	1	2	FACETS	0.959	0.763	1	0.959	0.763	1	CLONAL	1	TRUE	1	0.14	2		395	402	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055897	180055897	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	43	590	0	ENST00000261937.6:c.1088del	p.Pro363ArgfsTer27	p.P363Rfs*27	ENST00000261937	NM_182925.4	363	cCg/cg	8/30	0.3	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.14	1		590	475	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508535	106508535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	19	295	0	ENST00000359195.3:c.529C>T	p.Arg177Cys	p.R177C	ENST00000359195	NM_002649.2	177	Cgc/Tgc	2/11	1	2	FACETS	1	0.831	1	1	0.831	1	CLONAL	1	TRUE	1	0.14	2		295	242	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	84	601	0	ENST00000311936.3:c.180_181delinsAA	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggAAaa	3/5	1	2	FACETS	0.897	0.792	1	1	0.982	1	CLONAL	2	TRUE	1	0.14	2		601	669	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143052	30143052	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1244823020	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	37	717	1	ENST00000389048.3:c.474del	p.Glu160ArgfsTer26	p.E160Rfs*26	ENST00000389048	NM_004304.4	158	ccC/cc	1/29	1	2	FACETS	0.844	0.695	1	0.844	0.695	1	CLONAL	1	TRUE	1	0.14	2		718	626	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	57	787	0	ENST00000269305.4:c.388del	p.Leu130SerfsTer40	p.L130Sfs*40	ENST00000269305	NM_001126112.2	130	Ctc/tc	5/11	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.14	2		787	776	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663406	67663406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775874494	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	33	426	0	ENST00000264010.4:c.1807C>T	p.Arg603Cys	p.R603C	ENST00000264010	NM_006565.3	603	Cgc/Tgc	10/12	1	2	FACETS	0.875	0.711	1	0.875	0.711	1	CLONAL	1	TRUE	1	0.14	2		426	539	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	43	544	3	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.792	0.66	0.938	0.792	0.66	0.938	CLONAL	1	TRUE	1	0.14	2		547	776	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433388	49433388	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555191598	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	34	702	2	ENST00000301067.7:c.8059C>T	p.Arg2687Ter	p.R2687*	ENST00000301067	NM_003482.3	2687	Cga/Tga	32/54	1	2	FACETS	0.746	0.608	0.902	0.746	0.608	0.902	CLONAL	1	TRUE	1	0.14	2		704	651	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862845	9862845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764289741	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	34	613	0	ENST00000330684.3:c.2458G>A	p.Val820Ile	p.V820I	ENST00000330684	NM_001134407.1	820	Gta/Ata	12/13	1	2	FACETS	0.885	0.722	1	0.885	0.722	1	CLONAL	1	TRUE	1	0.14	2		613	549	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38139044	38139044	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	51	606	1	ENST00000317025.8:c.3559C>T	p.Arg1187Ter	p.R1187*	ENST00000317025	NM_023034.1	1187	Cga/Tga	20/24	1	2	FACETS	0.869	0.737	1	0.869	0.737	1	CLONAL	1	TRUE	1	0.14	2		607	838	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743940	46743940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372007047	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	41	428	1	ENST00000371975.4:c.2230C>T	p.Arg744Trp	p.R744W	ENST00000371975	NM_003579.3	744	Cgg/Tgg	18/18	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.14	2		429	420	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146944	38146945	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	77	725	2	ENST00000317025.8:c.3197dup	p.Asn1066LysfsTer14	p.N1066Kfs*14	ENST00000317025	NM_023034.1	1066	aac/aaAc	18/24	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.14	2		727	926	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052635	42052635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	58	532	1	ENST00000219905.7:c.7306C>T	p.Arg2436Cys	p.R2436C	ENST00000219905	NM_001164273.1	2436	Cgt/Tgt	20/24	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.14	2		533	749	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148544344	148544344	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	45	571	0	ENST00000320356.2:c.47G>A	p.Arg16Gln	p.R16Q	ENST00000320356	NM_004456.4	16	cGg/cAg	2/20	1	2	FACETS	0.936	0.785	1	0.936	0.785	1	CLONAL	1	TRUE	1	0.14	2		571	687	SUCCESS
AR	367	MSKCC	GRCh37	X	66941680	66941680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137852572	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	32	536	0	ENST00000374690.3:c.2324G>A	p.Arg775His	p.R775H	ENST00000374690	NM_000044.3	775	cGc/cAc	6/8	1	2	FACETS	0.853	0.691	1	0.853	0.691	1	CLONAL	1	TRUE	1	0.14	2		536	536	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70411605	70411605	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs868611128	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	32	401	1	ENST00000373644.4:c.4279C>T	p.Arg1427Ter	p.R1427*	ENST00000373644	NM_030625.2	1427	Cga/Tga	5/12	1	2	FACETS	0.969	0.785	1	0.969	0.785	1	CLONAL	1	TRUE	1	0.14	2		402	472	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649874	88649875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	23	411	0	ENST00000372037.3:c.128dup	p.Ser44ValfsTer27	p.S44Vfs*27	ENST00000372037	NM_004329.2	41	-/A	4/13	1	2	FACETS	0.815	0.635	1	0.815	0.635	1	CLONAL	1	TRUE	1	0.14	2		411	403	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911057	94911057	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	43	639	0	ENST00000536441.1:c.1073del	p.Asn358IlefsTer7	p.N358Ifs*7	ENST00000536441	NM_144665.3	358	aAt/at	8/10	1	2	FACETS	1	0.845	1	1	0.845	1	CLONAL	1	TRUE	1	0.14	2		639	607	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999138	100999138	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	40	632	0	ENST00000325455.5:c.664G>A	p.Glu222Lys	p.E222K	ENST00000325455	NM_001202474.3	222	Gag/Aag	1/8	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.14	2		632	533	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343443	118343445	+	inframe_deletion	In_Frame_Del	DEL	TAA	TAA	-	novel	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	24	444	0	ENST00000534358.1:c.1570_1572del	p.Asn524del	p.N524del	ENST00000534358	NM_005933.3	523	agTAAt/agt	3/36	1	2	FACETS	0.75	0.587	0.939	0.75	0.587	0.939	CLONAL	1	TRUE	1	0.14	2		444	457	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988573	36988573	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	56	705	0	ENST00000354822.5:c.80G>A	p.Arg27His	p.R27H	ENST00000354822	NM_001079668.2	27	cGc/cAc	2/3	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.14	2		705	733	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658691	3658691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	80	815	0	ENST00000294008.3:c.275G>A	p.Arg92Lys	p.R92K	ENST00000294008	NM_032444.2	92	aGg/aAg	2/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.14	2		815	910	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984790	72984790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374019817	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	34	543	1	ENST00000268489.5:c.2794G>A	p.Glu932Lys	p.E932K	ENST00000268489	NM_006885.3	932	Gag/Aag	3/10	1	2	FACETS	0.943	0.77	1	0.943	0.77	1	CLONAL	1	TRUE	1	0.14	2		544	515	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7141797	7141797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201466857	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	56	643	1	ENST00000302850.5:c.2573C>T	p.Thr858Met	p.T858M	ENST00000302850	NM_000208.2	858	aCg/aTg	13/22	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.14	2		644	628	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211183	36211183	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	77	899	0	ENST00000222270.7:c.939del	p.Val314Ter	p.V314*	ENST00000222270	NM_014727.1	312	Aaa/aa	3/37	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.14	2		899	923	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101152	41101153	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	34	571	0	ENST00000373198.4:c.1203dup	p.Gln402AlafsTer18	p.Q402Afs*18	ENST00000373198	NM_133170.3	401	-/G	8/32	1	2	FACETS	0.83	0.677	1	0.83	0.677	1	CLONAL	1	TRUE	1	0.14	2		571	585	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268420	142268420	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	37	458	0	ENST00000350721.4:c.3072T>G	p.Asn1024Lys	p.N1024K	ENST00000350721	NM_001184.3	1024	aaT/aaG	15/47	1	2	FACETS	0.973	0.801	1	0.973	0.801	1	CLONAL	1	TRUE	1	0.14	2		458	543	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540533	187540533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770573765	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	31	378	0	ENST00000441802.2:c.7207G>A	p.Ala2403Thr	p.A2403T	ENST00000441802	NM_005245.3	2403	Gcc/Acc	10/27	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.14	2		378	377	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526393	31526393	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	54	972	0	ENST00000344624.3:c.647C>A	p.Pro216His	p.P216H	ENST00000344624		216	cCc/cAc	2/33	1	2	FACETS	0.809	0.688	0.941	0.809	0.688	0.941	CLONAL	1	TRUE	1	0.14	2		972	954	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057717	180057717	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	47	646	0	ENST00000261937.6:c.238del	p.Val80TrpfsTer53	p.V80Wfs*53	ENST00000261937	NM_182925.4	80	Gtg/tg	3/30	0.3	1	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	0	0.14	1		646	616	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681423	30681423	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	30	425	0	ENST00000376406.3:c.587+2T>C		p.X196_splice	ENST00000376406	NM_014641.2	196			1	2	FACETS	0.871	0.701	1	0.871	0.701	1	CLONAL	1	TRUE	1	0.14	2		425	492	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181986	32181986	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	52	741	0	ENST00000375023.3:c.2068G>T	p.Ala690Ser	p.A690S	ENST00000375023	NM_004557.3	690	Gca/Tca	13/30	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.14	2		741	656	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200189	138200189	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	29	481	0	ENST00000237289.4:c.1607G>A	p.Cys536Tyr	p.C536Y	ENST00000237289	NM_001270507.1	536	tGc/tAc	7/9	1	2	FACETS	0.78	0.625	0.958	0.78	0.625	0.958	CLONAL	1	TRUE	1	0.14	2		481	531	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221972	98221972	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373120584	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	35	456	1	ENST00000331920.6:c.2797G>A	p.Ala933Thr	p.A933T	ENST00000331920	NM_000264.3	933	Gcg/Acg	17/24	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.14	2		457	458	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907789	76907789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	19	306	0	ENST00000373344.5:c.4372G>A	p.Glu1458Lys	p.E1458K	ENST00000373344	NM_000489.3	1458	Gag/Aag	15/35	1	2	FACETS	0.724	0.548	0.931	0.724	0.548	0.931	CLONAL	1	TRUE	1	0.14	2		306	375	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938055	76938055	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	54	635	0	ENST00000373344.5:c.2693A>G	p.Asp898Gly	p.D898G	ENST00000373344	NM_000489.3	898	gAc/gGc	9/35	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.14	2		635	680	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27093025	27093026	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	285	422	0	ENST00000324856.7:c.2957dup	p.Asp986GlufsTer21	p.D986Efs*21	ENST00000324856	NM_006015.4	986	gat/gAat	10/20	1	2	FACETS	0.924	0.873	0.977	0.924	0.873	0.977	CLONAL	1	TRUE	1	0.784647955805487	2		422	786	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577112	7577112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	432	647	0	ENST00000269305.4:c.826G>A	p.Ala276Thr	p.A276T	ENST00000269305	NM_001126112.2	276	Gcc/Acc	8/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.784647955805487	2		647	1087	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2193775	2193775	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	326	535	0	ENST00000398665.3:c.581A>G	p.Tyr194Cys	p.Y194C	ENST00000398665	NM_032482.2	194	tAt/tGt	6/28	1	2	FACETS	0.919	0.871	0.968	0.919	0.871	0.968	CLONAL	1	TRUE	1	0.784647955805487	2		535	904	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0029171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	189	437	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.958	0.893	1	0.958	0.893	1	CLONAL	1	TRUE	1	0.775403660322855	2		437	509	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115809	8115831	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCAAGAACAGCTCGTTTAACC	CCCCAAGAACAGCTCGTTTAACC	-	novel	NA	P-0029171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	107	529	0	ENST00000346208.3:c.1156_1178del	p.Pro386GlyfsTer113	p.P386Gfs*113	ENST00000346208		385	ttCCCCAAGAACAGCTCGTTTAACCcg/ttcg	6/6	1	2	FACETS	0.44	0.395	0.488	0.44	0.395	0.488	SUBCLONAL	1	TRUE	1	0.775403660322855	2		529	627	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376178	118376178	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	188	402	0	ENST00000534358.1:c.9571G>T	p.Val3191Phe	p.V3191F	ENST00000534358	NM_005933.3	3191	Gtt/Ttt	27/36	0.775403660322855	1	FACETS	0.848	0.798	0.898	0.848	0.798	0.898	CLONAL	1	TRUE	0	0.775403660322855	1		402	350	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829770	72829770	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	218	675	0	ENST00000268489.5:c.6811G>A	p.Glu2271Lys	p.E2271K	ENST00000268489	NM_006885.3	2271	Gaa/Aaa	9/10	1	2	FACETS	0.802	0.749	0.856	0.802	0.749	0.856	CLONAL	1	TRUE	1	0.775403660322855	2		675	701	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722336	176722336	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	236	484	0	ENST00000439151.2:c.7967A>G	p.Gln2656Arg	p.Q2656R	ENST00000439151	NM_022455.4	2656	cAg/cGg	23/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.775403660322855	2		484	555	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578529	7578529	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs780442292	NA	P-0029172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	287	763	0	ENST00000269305.4:c.401T>G	p.Phe134Cys	p.F134C	ENST00000269305	NM_001126112.2	134	tTt/tGt	5/11	0.203623229958858	3	FACETS	0.888	0.835	0.943	0.888	0.835	0.943	CLONAL	3	TRUE	0	0.215299721129155	3		763	1108	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851492	63851493	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	65	485	1	ENST00000279873.7:c.2273dup	p.Arg759GlnfsTer13	p.R759Qfs*13	ENST00000279873	NM_032199.2	757	agt/agTt	10/10	0.215299721129155	3	FACETS	0.945	0.818	1	0.472	0.409	0.541	CLONAL	1	TRUE	1	0.215299721129155	3		486	708	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096112	71096115	+	frameshift_variant	Frame_Shift_Del	DEL	GGGA	GGGA	TT	novel	NA	P-0029172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	72	252	1	ENST00000318789.4:c.642_645delinsAA	p.Pro215ThrfsTer79	p.P215Tfs*79	ENST00000318789	NM_032682.5	214	ctTCCC/ctAA	10/21	0.159968847617352	4	FACETS	0.835	0.731	0.946	0.835	0.731	0.946	CLONAL	2	TRUE	2	0.215299721129155	4		253	487	SUCCESS
APC	324	MSKCC	GRCh37	5	112173902	112173902	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	103	365	0	ENST00000257430.4:c.2611G>T	p.Gly871Ter	p.G871*	ENST00000257430	NM_000038.5	871	Gga/Tga	16/16	0.215299721129155	2	FACETS	0.94	0.845	1	0.94	0.845	1	CLONAL	2	TRUE	0	0.215299721129155	2		365	509	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200048	123200048	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	32	171	0	ENST00000218089.9:c.2120A>G	p.Asp707Gly	p.D707G	ENST00000218089	NM_001042749.1	707	gAt/gGt	22/35	0.190032416898463	2	FACETS	0.826	0.677	0.99			1	CLONAL	2	TRUE	NA	0.215299721129155	2		171	180	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119793	70119793	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	AT	novel	NA	P-0029172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	124	544	2	ENST00000245479.2:c.795delinsAT	p.Pro266SerfsTer30	p.P266Sfs*30	ENST00000245479	NM_000346.3	265	caG/caAT	3/3	0.203623229958858	3	FACETS	0.907	0.822	0.997	0.605	0.548	0.665	CLONAL	2	TRUE	0	0.215299721129155	3		546	703	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0029173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	285	512	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.406830914182188	1	FACETS	0.791	0.75	0.832	0.791	0.75	0.832	INDETERMINATE	1	TRUE	0	0.728596868129648	1		512	629	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653851	89653851	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	235	494	0	ENST00000371953.3:c.150del	p.Ile50MetfsTer4	p.I50Mfs*4	ENST00000371953	NM_000314.4	50	aTt/at	2/9	0.728596868129648	1	FACETS	0.919	0.87	0.968	0.919	0.87	0.968	CLONAL	1	TRUE	0	0.728596868129648	1		494	446	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037444	12037444	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs141938078	NA	P-0029174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	426	479	0	ENST00000396373.4:c.1075C>T	p.Arg359Ter	p.R359*	ENST00000396373	NM_001987.4	359	Cga/Tga	6/8	0.450356321950817	2	FACETS	0.987	0.947	1	0.987	0.947	1	CLONAL	2	TRUE	0	0.498217422122735	2		479	866	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573627	48573627	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	185	318	0	ENST00000342988.3:c.211T>C	p.Cys71Arg	p.C71R	ENST00000342988	NM_005359.5	71	Tgt/Cgt	2/12	0.498217422122735	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.498217422122735	1		318	477	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106932	11106932	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	247	639	0	ENST00000358026.2:c.1637A>G	p.Lys546Arg	p.K546R	ENST00000358026	NM_001128849.1	546	aAg/aGg	10/36	1	2	FACETS	0.964	0.901	1	0.964	0.901	1	CLONAL	1	TRUE	1	0.498217422122735	2		639	1029	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274734	142274734	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs766122444	NA	P-0029174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	159	336	0	ENST00000350721.4:c.2326A>G	p.Ser776Gly	p.S776G	ENST00000350721	NM_001184.3	776	Agt/Ggt	10/47	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.498217422122735	2		336	592	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274749	142274749	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	142	355	1	ENST00000350721.4:c.2311A>G	p.Lys771Glu	p.K771E	ENST00000350721	NM_001184.3	771	Aaa/Gaa	10/47	1	2	FACETS	0.955	0.874	1	0.955	0.874	1	CLONAL	1	TRUE	1	0.498217422122735	2		356	597	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246392	53246392	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	280	604	0	ENST00000375401.3:c.590del	p.Leu197HisfsTer37	p.L197Hfs*37	ENST00000375401	NM_004187.3	197	cTa/ca	5/26	0.498217422122735	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.498217422122735	1		604	778	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913396	NA	P-0029175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	224	254	0	ENST00000349496.5:c.95A>T	p.Asp32Val	p.D32V	ENST00000349496	NM_001904.3	32	gAc/gTc	3/15	0.764576612955087	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.764576612955087	3		254	390	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097810	27097811	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0029175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	220	355	0	ENST00000324856.7:c.3402_3403del	p.Pro1135CysfsTer57	p.P1135Cfs*57	ENST00000324856	NM_006015.4	1133	ccCTct/ccct	12/20	0.764576612955087	2	FACETS	0.905	0.864	0.944	0.905	0.864	0.944	CLONAL	2	TRUE	0	0.764576612955087	2		355	318	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912859	50912859	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	242	703	0	ENST00000440232.2:c.2090C>T	p.Ala697Val	p.A697V	ENST00000440232	NM_002691.3	697	gCc/gTc	17/27	0.764576612955087	3	FACETS	1	0.971	1	0.53	0.497	0.565	CLONAL	1	TRUE	1	0.764576612955087	3		703	825	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109311921	109311921	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs749534099	NA	P-0029175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	173	626	0	ENST00000436639.2:c.1351A>G	p.Met451Val	p.M451V	ENST00000436639	NM_014454.2	451	Atg/Gtg	8/10	0.764576612955087	3	FACETS	0.827	0.763	0.894	0.414	0.381	0.447	CLONAL	1	TRUE	1	0.764576612955087	3		626	756	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031885	26031885	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	71	219	0	ENST00000244661.2:c.404G>C	p.Arg135Thr	p.R135T	ENST00000244661	NM_003537.3	135	aGa/aCa	1/1	0.287515031536023	4	FACETS	1	0.97	1	0.461	0.403	0.523	CLONAL	1	TRUE	1	0.287515031536023	4		219	460	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575049	64575049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs386134259	NA	P-0029177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	114	487	0	ENST00000312049.6:c.758C>T	p.Ser253Leu	p.S253L	ENST00000312049	NM_130799.2	253	tCg/tTg	4/10	0.287515031536023	7	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.287515031536023	7		487	1073	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557891	187557891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200242253	NA	P-0029177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	39	452	0	ENST00000441802.2:c.3820G>A	p.Val1274Ile	p.V1274I	ENST00000441802	NM_005245.3	1274	Gtc/Atc	5/27	0.287515031536023	3	FACETS	0.431	0.356	0.515	0.215	0.178	0.258	SUBCLONAL	1	TRUE	1	0.287515031536023	3		452	720	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856020	111856020	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1263604332	NA	P-0029177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	119	575	0	ENST00000341259.2:c.71G>A	p.Arg24Gln	p.R24Q	ENST00000341259	NM_005475.2	24	cGg/cAg	2/8	0.287515031536023	5	FACETS	1	0.96	1	0.281	0.253	0.311	CLONAL	1	TRUE	1	0.287515031536023	5		575	1053	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	472168	472168	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	110	563	0	ENST00000399788.2:c.633G>A	p.Met211Ile	p.M211I	ENST00000399788	NM_001042603.1	211	atG/atA	5/28	0.287515031536023	6	FACETS	1	0.916	1	0.205	0.183	0.228	CLONAL	1	TRUE	1	0.287515031536023	6		563	1175	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636329	21636329	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	81	538	0	ENST00000421138.2:c.681G>A	p.Trp227Ter	p.W227*	ENST00000421138		227	tgG/tgA	7/16	1	2	FACETS	0.813	0.716	0.917	0.813	0.716	0.917	CLONAL	1	TRUE	1	0.287515031536023	2		538	693	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021503	31021503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	99	538	0	ENST00000375687.4:c.1502C>T	p.Ser501Phe	p.S501F	ENST00000375687	NM_015338.5	501	tCt/tTt	12/13	0.287515031536023	5	FACETS	0.893	0.795	0.998	0.298	0.265	0.333	CLONAL	1	TRUE	2	0.287515031536023	5		538	1104	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62320457	62320457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	102	660	0	ENST00000360203.5:c.1850C>T	p.Ala617Val	p.A617V	ENST00000360203	NM_001283009.1	617	gCc/gTc	22/35	0.255314363519253	4	FACETS	0.845	0.754	0.942	0.423	0.377	0.471	CLONAL	1	TRUE	2	0.287515031536023	4		660	1081	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204689	128204689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	314	797	2	ENST00000341105.2:c.752C>T	p.Ser251Phe	p.S251F	ENST00000341105	NM_032638.4	251	tCc/tTc	3/6	0.287515031536023	4	FACETS	1	0.976	1	0.71	0.669	0.752	CLONAL	2	TRUE	1	0.287515031536023	4		799	1321	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286179	66286179	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	38	362	1	ENST00000273854.3:c.1507G>C	p.Glu503Gln	p.E503Q	ENST00000273854	NM_004439.5	503	Gaa/Caa	6/18	0.287515031536023	3	FACETS	0.638	0.527	0.762	0.319	0.263	0.381	SUBCLONAL	1	TRUE	1	0.287515031536023	3		363	474	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717661	89717661	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0029178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	632	693	1	ENST00000371953.3:c.686C>G	p.Ser229Ter	p.S229*	ENST00000371953	NM_000314.4	229	tCa/tGa	7/9	0.682156074414767	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.682156074414767	2		694	922	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0029178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	693	837	0	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	NA	2	FACETS	0.97	0.944	0.996			1	INDETERMINATE	2	TRUE	NA	0.682156074414767	2		837	1047	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0029178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	694	558	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	0.680132284249217	3	FACETS	0.994	0.963	1	0.994	0.963	1	CLONAL	2	TRUE	1	0.682156074414767	3		558	1372	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095722	178095722	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	472	493	0	ENST00000397062.3:c.1609G>C	p.Glu537Gln	p.E537Q	ENST00000397062	NM_006164.4	537	Gaa/Caa	5/5	0.680132284249217	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.682156074414767	3		493	888	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165755	118165755	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	181	492	0	ENST00000369448.3:c.265A>G	p.Lys89Glu	p.K89E	ENST00000369448	NM_017709.3	89	Aaa/Gaa	2/2	1	2	FACETS	0.936	0.869	1	0.936	0.869	1	CLONAL	1	TRUE	1	0.682156074414767	2		492	567	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226573204	226573204	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs766655023	NA	P-0029178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	268	533	36	ENST00000366794.5:c.1011+1G>T		p.X337_splice	ENST00000366794	NM_001618.3	337			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.682156074414767	2		569	727	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442929	49442929	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	313	764	0	ENST00000301067.7:c.3979del	p.Ala1327ProfsTer3	p.A1327Pfs*3	ENST00000301067	NM_003482.3	1327	Gcc/cc	12/54	1	2	FACETS	0.929	0.878	0.981	0.929	0.878	0.981	CLONAL	1	TRUE	1	0.682156074414767	2		764	988	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579445	7579463	+	frameshift_variant	Frame_Shift_Del	DEL	GTAGGAGCTGCTGGTGCAG	GTAGGAGCTGCTGGTGCAG	-	novel	NA	P-0029178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	748	898	0	ENST00000269305.4:c.224_242del	p.Pro75HisfsTer42	p.P75Hfs*42	ENST00000269305	NM_001126112.2	75	cCTGCACCAGCAGCTCCTACa/ca	4/11	NA	2	FACETS	0.973	0.948	0.998			1	INDETERMINATE	2	TRUE	NA	0.682156074414767	2		898	1127	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667636	29667655	+	frameshift_variant	Frame_Shift_Del	DEL	AGATAGTCTCCGTATATTCA	AGATAGTCTCCGTATATTCA	-	novel	NA	P-0029178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	404	627	0	ENST00000356175.3:c.6973_6992del	p.Asp2325Ter	p.D2325*	ENST00000356175	NM_000267.3	2324	ttAGATAGTCTCCGTATATTCAat/ttat	46/57	0.682156074414767	2	FACETS	0.9	0.867	0.933	0.9	0.867	0.933	CLONAL	2	TRUE	0	0.682156074414767	2		627	658	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370818	225370818	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs983814335	NA	P-0029178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	473	590	2	ENST00000264414.4:c.1061G>T	p.Arg354Leu	p.R354L	ENST00000264414	NM_003590.4	354	cGc/cTc	8/16	0.239851285473162	5	FACETS	0.947	0.909	0.984			1	INDETERMINATE	3	TRUE	NA	0.682156074414767	5		592	988	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	351	394	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	0.997	1	CLONAL	3	TRUE	1	0.290807214384422	2		394	728	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	105	773	0	ENST00000269305.4:c.859G>T	p.Glu287Ter	p.E287*	ENST00000269305	NM_001126112.2	287	Gag/Tag	8/11	1	2	FACETS	0.944	0.846	1	0.944	0.846	1	CLONAL	1	TRUE	1	0.290807214384422	2		773	765	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26911754	26911754	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	22	554	0	ENST00000381527.3:c.179C>G	p.Ser60Cys	p.S60C	ENST00000381527	NM_001260.1	60	tCt/tGt	2/13	1	2	FACETS	0.362	0.28	0.458	0.362	0.28	0.458	SUBCLONAL	1	TRUE	1	0.290807214384422	2		554	418	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193172944	193172944	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	51	430	0	ENST00000367435.3:c.992A>T	p.Lys331Met	p.K331M	ENST00000367435	NM_024529.4	331	aAg/aTg	11/17	1	2	FACETS	0.913	0.779	1	0.913	0.779	1	CLONAL	1	TRUE	1	0.290807214384422	2		430	384	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204851	94204851	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	59	487	2	ENST00000323929.3:c.734A>G	p.His245Arg	p.H245R	ENST00000323929	NM_005591.3	245	cAt/cGt	8/20	1	2	FACETS	0.992	0.857	1	0.992	0.857	1	CLONAL	1	TRUE	1	0.290807214384422	2		489	409	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658877	3658877	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	72	659	0	ENST00000294008.3:c.89C>G	p.Ser30Cys	p.S30C	ENST00000294008	NM_032444.2	30	tCc/tGc	2/15	0.191065314846318	1	FACETS	0.706	0.617	0.802	0.706	0.617	0.802	SUBCLONAL	1	TRUE	0	0.290807214384422	1		659	599	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574025	7574026	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0029179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	77	702	1	ENST00000269305.4:c.1001_1002delinsTT	p.Gly334Val	p.G334V	ENST00000269305	NM_001126112.2	334	gGG/gTT	10/11	1	2	FACETS	0.766	0.673	0.867	0.766	0.673	0.867	SUBCLONAL	1	TRUE	1	0.290807214384422	2		703	691	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108632	8108632	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1037161645	NA	P-0029179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	70	793	0	ENST00000585124.1:c.763G>C	p.Asp255His	p.D255H	ENST00000585124	NM_004217.3	255	Gat/Cat	8/9	1	2	FACETS	0.644	0.561	0.735	0.644	0.561	0.735	SUBCLONAL	1	TRUE	1	0.290807214384422	2		793	747	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049823	16049823	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	58	399	0	ENST00000268712.3:c.949G>T	p.Ala317Ser	p.A317S	ENST00000268712	NM_006311.3	317	Gca/Tca	10/46	1	2	FACETS	0.995	0.858	1	0.995	0.858	1	CLONAL	1	TRUE	1	0.290807214384422	2		399	401	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127188	22127188	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	59	545	0	ENST00000215832.6:c.940G>C	p.Glu314Gln	p.E314Q	ENST00000215832	NM_002745.4	314	Gag/Cag	7/9	1	2	FACETS	0.743	0.64	0.856	0.743	0.64	0.856	SUBCLONAL	1	TRUE	1	0.290807214384422	2		545	546	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189881	66189881	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	30	476	0	ENST00000273854.3:c.3065G>T	p.Ser1022Ile	p.S1022I	ENST00000273854	NM_004439.5	1022	aGc/aTc	18/18	1	2	FACETS	0.473	0.381	0.578	0.473	0.381	0.578	SUBCLONAL	1	TRUE	1	0.290807214384422	2		476	436	SUCCESS
APC	324	MSKCC	GRCh37	5	112177748	112177748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	27	484	1	ENST00000257430.4:c.6457G>A	p.Asp2153Asn	p.D2153N	ENST00000257430	NM_000038.5	2153	Gat/Aat	16/16	1	2	FACETS	0.428	0.34	0.529	0.428	0.34	0.529	SUBCLONAL	1	TRUE	1	0.290807214384422	2		485	434	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412073	63412073	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1286062627	NA	P-0029179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	64	895	0	ENST00000330258.3:c.1094A>G	p.Tyr365Cys	p.Y365C	ENST00000330258	NM_152424.3	365	tAc/tGc	2/2	0.176034951724631	0	FACETS	0.444	0.384	0.509			1	SUBCLONAL	1	TRUE	0	0.290807214384422	0		895	703	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0029180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	173	498	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.231520748727523	1	FACETS	0.922	0.852	0.995	0.922	0.852	0.995	INDETERMINATE	1	TRUE	0	0.446349760897876	1		498	653	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46124999	46124999	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0029180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	38	266	0	ENST00000334344.6:c.187-1G>T		p.X63_splice	ENST00000334344	NM_152641.2	63			0.231520748727523	1	FACETS	0.345	0.286	0.412	0.345	0.286	0.412	INDETERMINATE	1	TRUE	0	0.446349760897876	1		266	383	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944971	31944971	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	110	700	0	ENST00000340398.3:c.130G>A	p.Gly44Arg	p.G44R	ENST00000340398	NM_001013699.2	44	Ggg/Agg	1/1	0.231520748727523	1	FACETS	0.433	0.389	0.48	0.433	0.389	0.48	INDETERMINATE	1	TRUE	0	0.446349760897876	1		700	884	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170556	7170556	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	69	434	0	ENST00000302850.5:c.1475A>T	p.Gln492Leu	p.Q492L	ENST00000302850	NM_000208.2	492	cAg/cTg	6/22	0.231520748727523	1	FACETS	0.408	0.356	0.465	0.408	0.356	0.465	INDETERMINATE	1	TRUE	0	0.446349760897876	1		434	588	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468275	50468275	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	214	566	2	ENST00000331340.3:c.1510G>T	p.Glu504Ter	p.E504*	ENST00000331340	NM_006060.4	504	Gag/Tag	8/8	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.446349760897876	2		568	921	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436603	8436603	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	208	515	0	ENST00000356435.5:c.4075C>T	p.Gln1359Ter	p.Q1359*	ENST00000356435		1359	Cag/Tag	24/35	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.446349760897876	2		515	775	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916458	39916458	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs750459436	NA	P-0029180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	228	755	0	ENST00000378444.4:c.4545C>A	p.His1515Gln	p.H1515Q	ENST00000378444	NM_001123385.1	1515	caC/caA	11/15	1	2	FACETS	0.9	0.838	0.964	0.9	0.838	0.964	CLONAL	1	TRUE	1	0.446349760897876	2		755	1135	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411513	63411513	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1436928166	NA	P-0029180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	311	843	0	ENST00000330258.3:c.1654G>T	p.Gly552Trp	p.G552W	ENST00000330258	NM_152424.3	552	Ggg/Tgg	2/2	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.446349760897876	2		843	1248	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0029183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	37	831	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	0.499378179086308	1	FACETS	0.116	0.095	0.14	0.116	0.095	0.14	SUBCLONAL	1	TRUE	0	0.539406560400887	1		831	860	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984021	2984021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766268425	NA	P-0029183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	30	636	0	ENST00000396946.4:c.509G>A	p.Arg170His	p.R170H	ENST00000396946	NM_032415.4	170	cGc/cAc	5/25	1	2	FACETS	0.141	0.113	0.173	0.141	0.113	0.173	SUBCLONAL	1	TRUE	1	0.539406560400887	2		636	789	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578456	7578464	+	inframe_deletion	In_Frame_Del	DEL	GCGGACGCG	GCGGACGCG	-	novel	NA	P-0029183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	297	786	0	ENST00000269305.4:c.466_474del	p.Arg156_Arg158del	p.R156_R158del	ENST00000269305	NM_001126112.2	156	CGCGTCCGC/-	5/11	0.539406560400887	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.539406560400887	1		786	793	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0029184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	393	683	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.749227861822549	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.749227861822549	1		685	650	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109744	115109744	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	522	794	0	ENST00000257566.3:c.2134G>A	p.Ala712Thr	p.A712T	ENST00000257566	NM_016569.3	712	Gcg/Acg	8/8	0.708709895278302	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.749227861822549	1		794	803	SUCCESS
APC	324	MSKCC	GRCh37	5	112162834	112162834	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	182	419	0	ENST00000257430.4:c.1438C>T	p.Gln480Ter	p.Q480*	ENST00000257430	NM_000038.5	480	Caa/Taa	12/16	0.749227861822549	1	FACETS	0.91	0.855	0.963	0.91	0.855	0.963	CLONAL	1	TRUE	0	0.749227861822549	1		419	334	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621011	1621011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs963433488	NA	P-0029184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	545	882	2	ENST00000344749.5:c.1049C>T	p.Ser350Leu	p.S350L	ENST00000344749	NM_001136139.2	350	tCg/tTg	13/19	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.749227861822549	2		884	1435	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215975	36215975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	432	728	1	ENST00000222270.7:c.3515G>A	p.Arg1172His	p.R1172H	ENST00000222270	NM_014727.1	1172	cGt/cAt	10/37	1	2	FACETS	0.948	0.905	0.992	0.948	0.905	0.992	CLONAL	1	TRUE	1	0.749227861822549	2		729	1216	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0029185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	297	554	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.844351800340245	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.844351800340245	1		554	312	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508499	106508499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752602335	NA	P-0029185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	132	335	0	ENST00000359195.3:c.493G>A	p.Val165Ile	p.V165I	ENST00000359195	NM_002649.2	165	Gtc/Atc	2/11	0.485953147454472	4	FACETS	1	0.97	1	1	0.97	1	INDETERMINATE	2	TRUE	2	0.844351800340245	4		335	264	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951053	48951053	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs587778831	NA	P-0029185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4	65	314	0	ENST00000267163.4:c.1216-1G>A		p.X406_splice	ENST00000267163	NM_000321.2	406			0.844351800340245	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.844351800340245	2		314	69	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330507	65330507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	114	523	1	ENST00000342505.4:c.1139C>T	p.Ser380Phe	p.S380F	ENST00000342505	NM_002227.2	380	tCt/tTt	8/25	0.53291029572052	3	FACETS	0.889	0.821	0.957	0.889	0.821	0.957	CLONAL	2	TRUE	1	0.844351800340245	3		524	216	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80040392	80040392	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776668872	NA	P-0029185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	119	703	0	ENST00000265081.6:c.1721G>A	p.Arg574Gln	p.R574Q	ENST00000265081	NM_002439.4	574	cGg/cAg	12/24	0.844351800340245	2	FACETS	0.881	0.831	0.928	0.881	0.831	0.928	CLONAL	2	TRUE	0	0.844351800340245	2		703	160	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786740	3786740	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	247	691	0	ENST00000262367.5:c.4471C>G	p.Gln1491Glu	p.Q1491E	ENST00000262367	NM_004380.2	1491	Caa/Gaa	27/31	0.844351800340245	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.844351800340245	2		691	278	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099881	27099881	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	273	636	0	ENST00000324856.7:c.3760G>T	p.Gly1254Cys	p.G1254C	ENST00000324856	NM_006015.4	1254	Ggc/Tgc	15/20	0.53291029572052	3	FACETS	0.964	0.918	1	0.964	0.918	1	CLONAL	2	TRUE	1	0.844351800340245	3		636	477	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130379	2130379	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs45517299	NA	P-0029185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	385	743	0	ENST00000219476.3:c.3610+1G>A		p.X1204_splice	ENST00000219476	NM_000548.3	1204			0.844351800340245	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.844351800340245	2		743	411	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573435	48573435	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	65	291	0	ENST00000342988.3:c.19A>T	p.Thr7Ser	p.T7S	ENST00000342988	NM_005359.5	7	Acg/Tcg	2/12	0.844351800340245	4	FACETS	1	0.972	1	0.466	0.411	0.524	CLONAL	1	TRUE	1	0.844351800340245	4		291	203	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481472	20481472	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	90	379	0	ENST00000346618.3:c.541A>T	p.Thr181Ser	p.T181S	ENST00000346618	NM_001949.4	181	Acg/Tcg	3/7	0.53291029572052	3	FACETS	1	0.974	1	0.624	0.563	0.687	CLONAL	1	TRUE	1	0.844351800340245	3		379	243	SUCCESS
BTK	695	MSKCC	GRCh37	X	100614299	100614299	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	89	506	1	ENST00000308731.7:c.876G>T	p.Glu292Asp	p.E292D	ENST00000308731	NM_000061.2	292	gaG/gaT	10/19	0.274496814530588	2	FACETS	0.696	0.624	0.771	0.348	0.312	0.386	INDETERMINATE	1	TRUE	0	0.844351800340245	2		507	303	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197755	123197755	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	55	647	0	ENST00000218089.9:c.1879G>T	p.Asp627Tyr	p.D627Y	ENST00000218089	NM_001042749.1	627	Gat/Tat	20/35	0.274496814530588	2	FACETS	0.651	0.565	0.742	0.326	0.282	0.371	INDETERMINATE	1	TRUE	0	0.844351800340245	2		647	200	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215315	123215315	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	73	596	0	ENST00000218089.9:c.2861G>C	p.Arg954Pro	p.R954P	ENST00000218089	NM_001042749.1	954	cGt/cCt	28/35	0.274496814530588	2	FACETS	0.655	0.58	0.734	0.327	0.29	0.367	INDETERMINATE	1	TRUE	0	0.844351800340245	2		596	264	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	284	404	0				ENST00000310581	NM_198253.2	-/1132			0.540228235188238	3	FACETS	0.998	0.946	1	0.998	0.946	1	CLONAL	2	TRUE	1	0.576110872614493	3		404	636	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591125	67591125	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	259	451	0	ENST00000274335.5:c.1718T>C	p.Leu573Pro	p.L573P	ENST00000274335		573	cTg/cCg	12/15	0.540228235188238	3	FACETS	0.905	0.854	0.957	0.905	0.854	0.957	CLONAL	2	TRUE	1	0.576110872614493	3		451	640	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932793	39932794	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0029186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	56	481	1	ENST00000378444.4:c.1805dup	p.Ala603GlyfsTer8	p.A603Gfs*8	ENST00000378444	NM_001123385.1	602	ccg/ccCg	4/15	1	1	FACETS	0.253	0.217	0.293	0.253	0.217	0.293	SUBCLONAL	1	TRUE	0	0.576110872614493	1		482	546	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999445	100999445	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	338	1063	0	ENST00000325455.5:c.357G>T	p.Leu119Phe	p.L119F	ENST00000325455	NM_001202474.3	119	ttG/ttT	1/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.576110872614493	2		1063	1030	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591086	67591086	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	279	457	0	ENST00000274335.5:c.1679A>T	p.Asp560Val	p.D560V	ENST00000274335		560	gAc/gTc	12/15	0.540228235188238	3	FACETS	0.992	0.939	1	0.992	0.939	1	CLONAL	2	TRUE	1	0.576110872614493	3		457	629	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238321	98238321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	140	515	0	ENST00000331920.6:c.1723C>T	p.Leu575Phe	p.L575F	ENST00000331920	NM_000264.3	575	Ctc/Ttc	12/24	1	2	FACETS	0.895	0.819	0.974	0.895	0.819	0.974	CLONAL	1	TRUE	1	0.576110872614493	2		515	543	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0029215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	835	747	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.52318634885196	3	FACETS	0.938	0.915	0.962	0.938	0.915	0.962	CLONAL	3	TRUE	0	0.58938874495909	3		750	1303	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0029215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	159	253	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.510494332796884	2	FACETS	1	0.99	1	0.737	0.685	0.79	CLONAL	1	TRUE	0	0.58938874495909	2		253	366	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762430	41762430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781426924	NA	P-0029215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	440	663	0	ENST00000301178.4:c.2110C>T	p.Arg704Cys	p.R704C	ENST00000301178	NM_021913.4	704	Cgc/Tgc	18/20	0.298893631239857	5	FACETS	0.912	0.869	0.956	0.608	0.579	0.638	INDETERMINATE	2	TRUE	2	0.58938874495909	5		663	1542	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184052	56184052	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0029215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	83	308	0	ENST00000399503.3:c.4258-1G>C		p.X1420_splice	ENST00000399503	NM_005921.1	1420			1	2	FACETS	0.722	0.641	0.808	0.722	0.641	0.808	SUBCLONAL	1	TRUE	1	0.58938874495909	2		308	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0029222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	522	737	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.645578439146807	1	FACETS	0.649	0.623	0.674	0.649	0.623	0.674	SUBCLONAL	1	TRUE	0	0.802052472594205	1		737	1202	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289247	33289247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1455644209	NA	P-0029222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	459	510	0	ENST00000374542.5:c.305C>T	p.Ser102Leu	p.S102L	ENST00000374542	NM_001141970.1	102	tCg/tTg	3/8	0.802052472594205	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.802052472594205	1		510	666	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105554	30105554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757417278	NA	P-0029222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	635	683	0	ENST00000331968.5:c.1132G>A	p.Asp378Asn	p.D378N	ENST00000331968	NM_002742.2	378	Gac/Aac	7/18	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.802052472594205	2		683	1333	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630539	47630539	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs587782481	NA	P-0029222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	316	460	0	ENST00000233146.2:c.209C>T	p.Ala70Val	p.A70V	ENST00000233146	NM_000251.2	70	gCa/gTa	1/16	0.802052472594205	1	FACETS	0.76	0.724	0.796	0.76	0.724	0.796	SUBCLONAL	1	TRUE	0	0.802052472594205	1		460	621	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106519989	106519989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	63	321	0	ENST00000359195.3:c.2417C>T	p.Ser806Phe	p.S806F	ENST00000359195	NM_002649.2	806	tCc/tTc	6/11	0.34499587324443	1	FACETS	0.155	0.133	0.178	0.155	0.133	0.178	INDETERMINATE	1	TRUE	0	0.802052472594205	1		321	609	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144859	11144859	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	66	661	0	ENST00000358026.2:c.3934G>T	p.Glu1312Ter	p.E1312*	ENST00000358026	NM_001128849.1	1312	Gag/Tag	28/36	1	2	FACETS	0.593	0.513	0.681	0.593	0.513	0.681	SUBCLONAL	1	TRUE	1	0.22	2		661	1011	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600429	10600429	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1184	104	767	0	ENST00000171111.5:c.1426G>T	p.Gly476Trp	p.G476W	ENST00000171111	NM_203500.1	476	Ggg/Tgg	4/6	1	2	FACETS	0.734	0.655	0.819	0.734	0.655	0.819	SUBCLONAL	1	TRUE	1	0.22	2		767	1288	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971423	15971423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	55	603	0	ENST00000268712.3:c.4526C>T	p.Ser1509Phe	p.S1509F	ENST00000268712	NM_006311.3	1509	tCt/tTt	32/46	1	2	FACETS	0.574	0.49	0.667	0.574	0.49	0.667	SUBCLONAL	1	TRUE	1	0.22	2		603	871	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226283	2226284	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0029224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	90	754	0	ENST00000398665.3:c.3763_3764del	p.Lys1255ValfsTer49	p.K1255Vfs*49	ENST00000398665	NM_032482.2	1255	AAg/g	27/28	1	2	FACETS	0.702	0.621	0.79	0.702	0.621	0.79	SUBCLONAL	1	TRUE	1	0.22	2		754	1165	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266516	41266516	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	52	424	0	ENST00000349496.5:c.313G>A	p.Glu105Lys	p.E105K	ENST00000349496	NM_001904.3	105	Gag/Aag	4/15	1	2	FACETS	0.566	0.481	0.661	0.566	0.481	0.661	SUBCLONAL	1	TRUE	1	0.22	2		424	835	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200075	123200076	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0029224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	46	243	0	ENST00000218089.9:c.2148dup	p.Lys717GlufsTer11	p.K717Efs*11	ENST00000218089	NM_001042749.1	716	ttg/ttGg	22/35	1	1	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	0	0.22	1		243	358	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144859	11144859	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	85	661	0	ENST00000358026.2:c.3934G>T	p.Glu1312Ter	p.E1312*	ENST00000358026	NM_001128849.1	1312	Gag/Tag	28/36	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.246141056868179	2		661	561	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600429	10600429	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	140	767	0	ENST00000171111.5:c.1426G>T	p.Gly476Trp	p.G476W	ENST00000171111	NM_203500.1	476	Ggg/Tgg	4/6	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.246141056868179	2		767	823	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971423	15971423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	80	603	0	ENST00000268712.3:c.4526C>T	p.Ser1509Phe	p.S1509F	ENST00000268712	NM_006311.3	1509	tCt/tTt	32/46	1	2	FACETS	0.923	0.813	1	0.923	0.813	1	CLONAL	1	TRUE	1	0.246141056868179	2		603	704	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226283	2226284	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0029224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	98	754	0	ENST00000398665.3:c.3763_3764del	p.Lys1255ValfsTer49	p.K1255Vfs*49	ENST00000398665	NM_032482.2	1255	AAg/g	27/28	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.246141056868179	2		754	724	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266516	41266516	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	77	424	0	ENST00000349496.5:c.313G>A	p.Glu105Lys	p.E105K	ENST00000349496	NM_001904.3	105	Gag/Aag	4/15	0.191586441545678	2	FACETS	1	0.944	1	0.565	0.496	0.638	CLONAL	1	TRUE	0	0.246141056868179	2		424	554	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200075	123200076	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0029224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	74	243	0	ENST00000218089.9:c.2148dup	p.Lys717GlufsTer11	p.K717Efs*11	ENST00000218089	NM_001042749.1	716	ttg/ttGg	22/35	1	1	FACETS	0.919	0.813	1	1	0.982	1	CLONAL	2	TRUE	0	0.246141056868179	1		243	287	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858738	9858738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149698593	NA	P-0029224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	31	336	1	ENST00000330684.3:c.2663C>T	p.Thr888Met	p.T888M	ENST00000330684	NM_001134407.1	888	aCg/aTg	13/13	1	2	FACETS	0.73	0.591	0.887	0.73	0.591	0.887	SUBCLONAL	1	TRUE	1	0.246141056868179	2		337	345	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131773	2131773	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	40	676	0	ENST00000219476.3:c.3788C>G	p.Pro1263Arg	p.P1263R	ENST00000219476	NM_000548.3	1263	cCc/cGc	31/42	1	2	FACETS	0.461	0.382	0.55	0.461	0.382	0.55	SUBCLONAL	1	TRUE	1	0.246141056868179	2		676	705	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216377	7216377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	57	636	0	ENST00000380728.2:c.871C>T	p.Leu291Phe	p.L291F	ENST00000380728		291	Ctc/Ttc	10/11	1	2	FACETS	0.68	0.583	0.787	0.68	0.583	0.787	SUBCLONAL	1	TRUE	1	0.246141056868179	2		636	681	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275717	41275717	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	43	583	0	ENST00000349496.5:c.1612C>G	p.Gln538Glu	p.Q538E	ENST00000349496	NM_001904.3	538	Cag/Gag	10/15	0.191586441545678	2	FACETS	0.618	0.517	0.731	0.309	0.258	0.366	SUBCLONAL	1	TRUE	0	0.246141056868179	2		583	565	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1955170	1955170	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	59	662	0	ENST00000382891.5:c.2257G>C	p.Glu753Gln	p.E753Q	ENST00000382891	NM_133335.3	753	Gag/Cag	12/22	1	2	FACETS	0.663	0.57	0.765	0.663	0.57	0.765	SUBCLONAL	1	TRUE	1	0.246141056868179	2		662	723	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778088	27778088	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1249317229	NA	P-0029224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	31	482	0	ENST00000369163.2:c.237C>A	p.Phe79Leu	p.F79L	ENST00000369163	NM_003536.2	79	ttC/ttA	1/1	0.246141056868179	2	FACETS	0.52	0.42	0.634	0.26	0.21	0.317	SUBCLONAL	1	TRUE	0	0.246141056868179	2		482	484	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163861	47163868	+	frameshift_variant	Frame_Shift_Del	DEL	TGGTGACA	TGGTGACA	-	novel	NA	P-0029224-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	91	376	1	ENST00000409792.3:c.2258_2265del	p.Val753AlafsTer4	p.V753Afs*4	ENST00000409792	NM_014159.6	753	gTGTCACCA/g	3/21	0.388905586331258	1	FACETS	0.802	0.715	0.894	0.802	0.715	0.894	CLONAL	1	TRUE	0	0.388905586331258	1		377	470	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440923	52440923	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029224-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	116	405	0	ENST00000460680.1:c.581G>A	p.Gly194Glu	p.G194E	ENST00000460680	NM_004656.3	194	gGg/gAg	8/17	0.388905586331258	1	FACETS	0.959	0.869	1	0.959	0.869	1	CLONAL	1	TRUE	0	0.388905586331258	1		405	501	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	999	483	2	ENST00000269305.4:c.542G>C	p.Arg181Pro	p.R181P	ENST00000269305	NM_001126112.2	181	cGc/cCc	5/11	0.696343278891442	4	FACETS	1	0.997	1	1	0.997	1	CLONAL	4	FALSE	0	0.696343278891442	4		485	1160	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121438954	121438954	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1316999782	NA	P-0029227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	760	769	2	ENST00000257555.6:c.1855G>A	p.Glu619Lys	p.E619K	ENST00000257555		619	Gag/Aag	10/10	0.565404808977581	4	FACETS	1	0.991	1			1	CLONAL	2	FALSE	NA	0.696343278891442	4		771	1741	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440957	56440957	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	243	511	0	ENST00000407977.2:c.380G>C	p.Arg127Pro	p.R127P	ENST00000407977		127	cGg/cCg	4/10	0.696343278891442	4	FACETS	0.856	0.798	0.916	0.428	0.399	0.458	CLONAL	1	FALSE	2	0.696343278891442	4		511	1383	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575383	64575386	+	frameshift_variant	Frame_Shift_Del	DEL	TGAC	TGAC	-	novel	NA	P-0029227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	481	641	0	ENST00000312049.6:c.631_634del	p.Val211MetfsTer12	p.V211Mfs*12	ENST00000312049	NM_130799.2	211	GTCAat/at	3/10	0.696343278891442	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	FALSE	0	0.696343278891442	2		641	687	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929439	81929439	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	472	490	0	ENST00000359376.3:c.1100A>C	p.Lys367Thr	p.K367T	ENST00000359376	NM_002661.3	367	aAg/aCg	13/33	0.332060584367302	6	FACETS	0.958	0.918	0.998	0.958	0.918	0.998	INDETERMINATE	3	FALSE	3	0.696343278891442	6		490	1129	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872198	45872198	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	572	548	0	ENST00000391945.4:c.236A>G	p.Glu79Gly	p.E79G	ENST00000391945	NM_000400.3	79	gAg/gGg	4/23	0.696343278891442	3	FACETS	0.968	0.934	1	0.968	0.934	1	CLONAL	2	FALSE	1	0.696343278891442	3		548	1144	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416454	29416454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751170666	NA	P-0029227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1973	126	681	1	ENST00000389048.3:c.4499C>T	p.Thr1500Ile	p.T1500I	ENST00000389048	NM_004304.4	1500	aCc/aTc	29/29	0.696343278891442	6	FACETS	0.413	0.371	0.456	0.103	0.092	0.114	SUBCLONAL	1	FALSE	2	0.696343278891442	6		682	2099	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873410	136873410	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	144	437	0	ENST00000241393.3:c.88C>A	p.Arg30Ser	p.R30S	ENST00000241393	NM_003467.2	30	Cgt/Agt	2/2	0.668166276411665	3	FACETS	0.78	0.712	0.85	0.39	0.356	0.425	SUBCLONAL	1	FALSE	1	0.696343278891442	3		437	715	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306793	41306793	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	213	276	0	ENST00000373198.4:c.866C>A	p.Pro289His	p.P289H	ENST00000373198	NM_133170.3	289	cCc/cAc	7/32	0.565404808977581	4	FACETS	0.998	0.936	1			1	CLONAL	2	FALSE	NA	0.696343278891442	4		276	520	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121103	29121103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	381	553	0	ENST00000328354.6:c.454C>T	p.Pro152Ser	p.P152S	ENST00000328354	NM_007194.3	152	Cct/Tct	4/15	0.656301553148879	4	FACETS	1	0.982	1			1	CLONAL	2	FALSE	NA	0.696343278891442	4		553	879	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440367	52440367	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	606	497	0	ENST00000460680.1:c.685A>C	p.Asn229His	p.N229H	ENST00000460680	NM_004656.3	229	Aac/Cac	9/17	0.696343278891442	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	FALSE	2	0.696343278891442	4		497	1336	SUCCESS
APC	324	MSKCC	GRCh37	5	112154682	112154682	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0029227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	243	344	0	ENST00000257430.4:c.953T>A	p.Leu318Ter	p.L318*	ENST00000257430	NM_000038.5	318	tTg/tAg	10/16	0.271881714981514	2	FACETS	1	0.994	1	0.727	0.688	0.766	INDETERMINATE	1	FALSE	0	0.696343278891442	2		344	480	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250776	26250776	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	35	279	0	ENST00000446824.2:c.58C>G	p.Gln20Glu	p.Q20E	ENST00000446824	NM_021018.2	20	Cag/Gag	1/1	0.425686163374083	4	FACETS	0.306	0.25	0.369	0.153	0.125	0.185	SUBCLONAL	1	FALSE	2	0.696343278891442	4		279	558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0029229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	194	747	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.253070615786417	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.253070615786417	1		750	969	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0029229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	94	532	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.239569161997644	2	FACETS	1	0.975	1	0.667	0.595	0.743	CLONAL	1	TRUE	0	0.253070615786417	2		532	557	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050677	30050677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867595517	NA	P-0029229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	121	516	2	ENST00000338641.4:c.479G>A	p.Arg160Gln	p.R160Q	ENST00000338641	NM_000268.3	160	cGg/cAg	5/16	0.253070615786417	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.253070615786417	1		518	754	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231437	46231437	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	135	488	1	ENST00000334344.6:c.1277C>T	p.Thr426Met	p.T426M	ENST00000334344	NM_152641.2	426	aCg/aTg	10/21	0.239569161997644	2	FACETS	0.903	0.823	0.985	0.903	0.823	0.985	CLONAL	2	TRUE	0	0.253070615786417	2		489	591	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670753	134670753	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780843040	NA	P-0029229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	129	434	0	ENST00000398015.3:c.664C>T	p.Arg222Trp	p.R222W	ENST00000398015	NM_004441.4	222	Cgg/Tgg	3/16	0.253070615786417	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.253070615786417	1		434	692	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732996	30732996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893809	NA	P-0029229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	120	434	0	ENST00000295754.5:c.1609C>T	p.Arg537Cys	p.R537C	ENST00000295754	NM_003242.5	537	Cgc/Tgc	7/7	0.253070615786417	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.253070615786417	1		434	643	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481599	56481599	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1481957883	NA	P-0029229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	67	646	0	ENST00000267101.3:c.634C>T	p.Pro212Ser	p.P212S	ENST00000267101	NM_001982.3	212	Cct/Tct	6/28	0.239569161997644	2	FACETS	0.611	0.53	0.7	0.306	0.265	0.35	SUBCLONAL	1	TRUE	0	0.253070615786417	2		646	866	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609581	46609581	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	189	780	0	ENST00000263734.3:c.2305C>A	p.Pro769Thr	p.P769T	ENST00000263734	NM_001430.4	769	Ccc/Acc	15/16	0.253070615786417	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.253070615786417	1		780	1145	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657076	45657076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770959767	NA	P-0029229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	30	353	1	ENST00000407780.3:c.80C>T	p.Ala27Val	p.A27V	ENST00000407780	NM_001283052.1	27	gCg/gTg	3/7	0.253070615786417	1	FACETS	0.361	0.29	0.443	0.361	0.29	0.443	SUBCLONAL	1	TRUE	0	0.253070615786417	1		354	573	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739725	145739725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs570331496	NA	P-0029229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	185	606	0	ENST00000428558.2:c.1726G>A	p.Val576Met	p.V576M	ENST00000428558	NM_004260.3	576	Gtg/Atg	11/22	0.253070615786417	1	FACETS	0.77	0.712	0.831	1	0.99	1	SUBCLONAL	2	TRUE	0	0.253070615786417	1		606	829	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485266	8485266	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	44	587	1	ENST00000356435.5:c.3114G>A	p.Trp1038Ter	p.W1038*	ENST00000356435		1038	tgG/tgA	18/35	0.253070615786417	1	FACETS	0.383	0.32	0.454	0.383	0.32	0.454	SUBCLONAL	1	TRUE	0	0.253070615786417	1		588	792	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127920582	127920582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140793926	NA	P-0029237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	66	662	1	ENST00000373547.4:c.317G>A	p.Arg106His	p.R106H	ENST00000373547	NM_002721.4	106	cGt/cAt	4/7	1	2	FACETS	0.735	0.635	0.843	0.735	0.635	0.843	SUBCLONAL	1	TRUE	1	0.16	2		663	1123	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0029237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	68	549	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.16	2		549	760	SUCCESS
APC	324	MSKCC	GRCh37	5	112175530	112175530	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	41	362	0	ENST00000257430.4:c.4240del	p.Val1414Ter	p.V1414*	ENST00000257430	NM_000038.5	1413	atG/at	16/16	1	2	FACETS	0.896	0.745	1	0.896	0.745	1	CLONAL	1	TRUE	1	0.16	2		362	572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs28934577	NA	P-0029237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	54	699	1	ENST00000269305.4:c.770T>A	p.Leu257Gln	p.L257Q	ENST00000269305	NM_001126112.2	257	cTg/cAg	7/11	1	2	FACETS	0.665	0.566	0.774	0.665	0.566	0.774	SUBCLONAL	1	TRUE	1	0.16	2		700	1015	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747087	40747087	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	82	601	0	ENST00000373198.4:c.2995T>A	p.Ser999Thr	p.S999T	ENST00000373198	NM_133170.3	999	Tcc/Acc	22/32	0.101055843768925	3	FACETS	1	0.943	1	0.561	0.493	0.634	CLONAL	1	TRUE	1	0.16	3		601	987	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910401	32910401	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs1566225769	NA	P-0029237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	40	331	0	ENST00000380152.3:c.1910-1G>T		p.X637_splice	ENST00000380152		637			0.101055843768925	3	FACETS	1	0.847	1	0.51	0.424	0.607	CLONAL	1	TRUE	1	0.16	3		331	529	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988359	41988360	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	85	596	0	ENST00000219905.7:c.1151_1152insT	p.Glu384AspfsTer5	p.E384Dfs*5	ENST00000219905	NM_001164273.1	384	gaa/gaTa	3/24	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.16	2		596	1005	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0029238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	61	181	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.984	0.849	1	0.984	0.849	1	CLONAL	1	TRUE	1	0.210552770865758	2		181	589	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215633979	215633979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	70	449	0	ENST00000260947.4:c.1372G>A	p.Asp458Asn	p.D458N	ENST00000260947	NM_000465.2	458	Gac/Aac	5/11	1	2	FACETS	0.762	0.663	0.869	0.762	0.663	0.869	SUBCLONAL	1	TRUE	1	0.210552770865758	2		449	873	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863668	68863702	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	AATCCCGATGAAATTGGAAATTTTATTGATGAAGT	AATCCCGATGAAATTGGAAATTTTATTGATGAAGT	-	novel	NA	P-0029238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	64	373	0	ENST00000261769.5:c.2409_2439+4del		p.X803_splice	ENST00000261769	NM_004360.3	803		15/16	0.210552770865758	1	FACETS	0.71	0.614	0.815	0.71	0.614	0.815	SUBCLONAL	1	TRUE	0	0.210552770865758	1		373	766	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0029240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	119	440	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.904	0.817	0.995	0.904	0.817	0.995	CLONAL	1	TRUE	1	0.387874486135527	2		440	679	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671746	67671746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	195	772	0	ENST00000264010.4:c.2155G>A	p.Glu719Lys	p.E719K	ENST00000264010	NM_006565.3	719	Gag/Aag	12/12	0.387874486135527	4	FACETS	1	0.971	1			1	CLONAL	1	TRUE	NA	0.387874486135527	4		772	1264	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599944	28599944	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779918408	NA	P-0029240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	208	741	1	ENST00000253063.3:c.826G>A	p.Glu276Lys	p.E276K	ENST00000253063	NM_031459.4	276	Gag/Aag	6/10	0.387874486135527	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.387874486135527	1		742	790	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212898	94212898	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	120	558	0	ENST00000323929.3:c.344A>G	p.Asn115Ser	p.N115S	ENST00000323929	NM_005591.3	115	aAc/aGc	5/20	1	2	FACETS	0.928	0.839	1	0.928	0.839	1	CLONAL	1	TRUE	1	0.387874486135527	2		558	667	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577497	7577497	+	splice_donor_variant	Splice_Site	SNP	A	A	C	rs876659076	NA	P-0029240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	213	717	0	ENST00000269305.4:c.782+2T>G		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.387874486135527	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.387874486135527	1		717	808	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0029242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	202	591	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.578634798838223	2		591	659	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0029242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	542	512	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.578634798838223	2	FACETS	0.97	0.937	1	0.97	0.937	1	CLONAL	2	TRUE	0	0.578634798838223	2		512	966	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245823	46245823	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	248	412	0	ENST00000334344.6:c.3917C>A	p.Pro1306His	p.P1306H	ENST00000334344	NM_152641.2	1306	cCt/cAt	15/21	1	2	FACETS	0.932	0.873	0.993	0.932	0.873	0.993	CLONAL	1	TRUE	1	0.578634798838223	2		412	920	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729877	30729877	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	328	277	0	ENST00000295754.5:c.1398A>C	p.Glu466Asp	p.E466D	ENST00000295754	NM_003242.5	466	gaA/gaC	6/7	0.565385701202824	3	FACETS	0.993	0.945	1	0.993	0.945	1	CLONAL	2	TRUE	1	0.578634798838223	3		277	736	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499071	149499072	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0029242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	280	585	2	ENST00000261799.4:c.2756_2757delinsAA	p.Arg919Gln	p.R919Q	ENST00000261799	NM_002609.3	919	cGG/cAA	20/23	0.578634798838223	1	FACETS	0.953	0.9	1	0.953	0.9	1	CLONAL	1	TRUE	0	0.578634798838223	1		587	722	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69050701	69050701	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	201	384	0	ENST00000288368.4:c.4036G>A	p.Glu1346Lys	p.E1346K	ENST00000288368	NM_024870.2	1346	Gaa/Aaa	33/40	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.578634798838223	2		384	690	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058741	47058741	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	214	277	0	ENST00000409792.3:c.7537A>G	p.Thr2513Ala	p.T2513A	ENST00000409792	NM_014159.6	2513	Act/Gct	21/21	0.865317162496498	1	FACETS	0.946	0.906	0.986	0.946	0.906	0.986	CLONAL	1	TRUE	0	0.871122742409636	1		277	293	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038865	47038865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556777933	NA	P-0029244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	377	558	1	ENST00000377604.3:c.872C>T	p.Ser291Leu	p.S291L	ENST00000377604	NM_001204468.1	291	tCg/tTg	9/24	1	2	FACETS	0.929	0.885	0.973	0.929	0.885	0.973	CLONAL	1	TRUE	1	0.871122742409636	2		559	932	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0029245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	16	483	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.266	0.196	0.351	0.266	0.196	0.351	SUBCLONAL	1	TRUE	1	0.28	2		483	429	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	65	404	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.28	2		404	396	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0029245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	43	631	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.55	0.46	0.651	0.55	0.46	0.651	SUBCLONAL	1	TRUE	1	0.28	2		632	558	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762959	40762959	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs387906659	NA	P-0029245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	36	523	0	ENST00000392038.2:c.49G>A	p.Glu17Lys	p.E17K	ENST00000392038	NM_001626.4	17	Gaa/Aaa	3/14	1	2	FACETS	0.359	0.294	0.432	0.359	0.294	0.432	SUBCLONAL	1	TRUE	1	0.28	2		523	716	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0029245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	78	483	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.805	0.709	0.906	0.805	0.709	0.906	CLONAL	1	TRUE	1	0.418773028066371	2		483	463	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	95	404	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.418773028066371	2		404	387	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0029245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	117	631	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.985	0.892	1	0.985	0.892	1	CLONAL	1	TRUE	1	0.418773028066371	2		632	567	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39567803	39567803	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs368043076	NA	P-0029245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	34	373	0	ENST00000262039.4:c.559A>G	p.Met187Val	p.M187V	ENST00000262039	NM_002647.2	187	Atg/Gtg	5/25	1	2	FACETS	0.346	0.282	0.418	0.346	0.282	0.418	SUBCLONAL	1	TRUE	1	0.418773028066371	2		373	469	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933353	39933353	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	40	336	1	ENST00000378444.4:c.1246C>T	p.Gln416Ter	p.Q416*	ENST00000378444	NM_001123385.1	416	Caa/Taa	4/15	1	1	FACETS	0.36	0.299	0.427	0.36	0.299	0.427	SUBCLONAL	1	TRUE	0	0.418773028066371	1		337	420	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	138	394	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.232337378470565	3	FACETS	1	0.982	1	0.658	0.599	0.719	CLONAL	1	TRUE	1	0.318866079711348	3		394	763	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605102	46605102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540130771	NA	P-0029247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	89	707	0	ENST00000263734.3:c.1319C>T	p.Thr440Met	p.T440M	ENST00000263734	NM_001430.4	440	aCg/aTg	10/16	0.232337378470565	3	FACETS	0.664	0.587	0.746	0.332	0.293	0.373	SUBCLONAL	1	TRUE	1	0.318866079711348	3		707	975	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	227	404	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.938	0.882	0.995	0.938	0.882	0.995	CLONAL	1	TRUE	1	0.901222353398167	2		404	537	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287446	46287446	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs774801990	NA	P-0029256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	223	409	2	ENST00000334344.6:c.5305C>T	p.Arg1769Ter	p.R1769*	ENST00000334344	NM_152641.2	1769	Cga/Tga	20/21	1	2	FACETS	0.611	0.57	0.653	0.611	0.57	0.653	SUBCLONAL	1	TRUE	1	0.901222353398167	2		411	810	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0029256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17208	7087	734	0	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.901222353398167	20	FACETS	0.983	0.971	0.995			1	CLONAL	6	TRUE	NA	0.901222353398167	20		734	24295	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372388	55372388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437921769	NA	P-0029256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	459	728	5	ENST00000297316.4:c.1078C>T	p.Arg360Cys	p.R360C	ENST00000297316	NM_022454.3	360	Cgc/Tgc	2/2	0.221540644853124	1	FACETS	0.504	0.482	0.525	0.504	0.482	0.525	INDETERMINATE	1	TRUE	0	0.901222353398167	1		733	1111	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740376	58740376	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1064797099	NA	P-0029256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	272	531	0	ENST00000305921.3:c.1281G>A	p.Trp427Ter	p.W427*	ENST00000305921	NM_003620.3	427	tgG/tgA	6/6	1	2	FACETS	0.792	0.747	0.838	0.792	0.747	0.838	SUBCLONAL	1	TRUE	1	0.901222353398167	2		531	762	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685267	89685269	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	AAG	AAG	-	novel	NA	P-0029256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	188	266	1	ENST00000371953.3:c.165-3_165-1del		p.X55_splice	ENST00000371953	NM_000314.4	55			0.901222353398167	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.901222353398167	1		267	221	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954961	2954961	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1473	216	659	0	ENST00000396946.4:c.2749G>T	p.Glu917Ter	p.E917*	ENST00000396946	NM_032415.4	917	Gag/Tag	21/25	0.901222353398167	3	FACETS	0.412	0.381	0.444	0.206	0.19	0.222	SUBCLONAL	1	TRUE	1	0.901222353398167	3		659	1689	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0029273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	63	591	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.250687716426159	2		591	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757274881	NA	P-0029273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	167	811	1	ENST00000269305.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	144	Cag/Tag	5/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.250687716426159	2		812	1068	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11206818	11206818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	96	498	0	ENST00000361445.4:c.4601G>A	p.Cys1534Tyr	p.C1534Y	ENST00000361445	NM_004958.3	1534	tGt/tAt	32/58	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.250687716426159	2		498	667	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525554	187525554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	25	375	0	ENST00000441802.2:c.10525G>A	p.Asp3509Asn	p.D3509N	ENST00000441802	NM_005245.3	3509	Gat/Aat	18/27	1	2	FACETS	0.41	0.322	0.511	0.41	0.322	0.511	SUBCLONAL	1	TRUE	1	0.250687716426159	2		375	487	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750820	57750820	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs771239107	NA	P-0029273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	38	386	0	ENST00000274289.3:c.1784T>C	p.Ile595Thr	p.I595T	ENST00000274289	NM_006622.3	595	aTt/aCt	13/14	1	2	FACETS	0.504	0.416	0.604	0.504	0.416	0.604	SUBCLONAL	1	TRUE	1	0.250687716426159	2		386	601	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0029274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	53	428	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.8	0.682	0.928	0.8	0.682	0.928	CLONAL	1	TRUE	1	0.265092429708428	2		428	500	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0029274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	51	401	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	0.824	0.701	0.958	0.824	0.701	0.958	CLONAL	1	TRUE	1	0.265092429708428	2		401	467	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916933	178916933	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	41	321	0	ENST00000263967.3:c.320A>T	p.Asn107Ile	p.N107I	ENST00000263967	NM_006218.2	107	aAc/aTc	2/21	1	2	FACETS	0.609	0.507	0.723	0.609	0.507	0.723	SUBCLONAL	1	TRUE	1	0.265092429708428	2		321	508	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256495	115256495	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	52	574	1	ENST00000369535.4:c.216G>A	p.Met72Ile	p.M72I	ENST00000369535	NM_002524.4	72	atG/atA	3/7	1	2	FACETS	0.647	0.551	0.754	0.647	0.551	0.754	SUBCLONAL	1	TRUE	1	0.265092429708428	2		575	606	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692889	89692889	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1554898127	NA	P-0029274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	35	301	0	ENST00000371953.3:c.373A>T	p.Lys125Ter	p.K125*	ENST00000371953	NM_000314.4	125	Aaa/Taa	5/9	0.232357194741529	3	FACETS	0.656	0.537	0.789	0.328	0.268	0.395	SUBCLONAL	1	TRUE	1	0.265092429708428	3		301	456	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645409	67645415	+	frameshift_variant	Frame_Shift_Del	DEL	TCTACGA	TCTACGA	-	novel	NA	P-0029274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	44	408	0	ENST00000264010.4:c.675_681del	p.Tyr226LeufsTer22	p.Y226Lfs*22	ENST00000264010	NM_006565.3	225	gTCTACGAt/gt	3/12	1	2	FACETS	0.646	0.541	0.762	0.646	0.541	0.762	SUBCLONAL	1	TRUE	1	0.265092429708428	2		408	514	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387400	17387400	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	75	827	0	ENST00000359435.4:c.666C>G	p.Cys222Trp	p.C222W	ENST00000359435	NM_001033549.1	222	tgC/tgG	7/9	1	2	FACETS	0.705	0.616	0.8	0.705	0.616	0.8	SUBCLONAL	1	TRUE	1	0.265092429708428	2		827	803	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098803	178098803	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	69	578	0	ENST00000397062.3:c.242G>T	p.Gly81Val	p.G81V	ENST00000397062	NM_006164.4	81	gGt/gTt	2/5	1	2	FACETS	0.767	0.667	0.874	0.767	0.667	0.874	SUBCLONAL	1	TRUE	1	0.265092429708428	2		578	679	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	116	404	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.769909833519301	2		404	280	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0029275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	141	489	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.92	0.847	0.995	0.92	0.847	0.995	CLONAL	1	TRUE	1	0.769909833519301	2		489	398	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039340	49039341	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0029275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	145	614	0	ENST00000267163.4:c.2330dup	p.Thr778TyrfsTer17	p.T778Yfs*17	ENST00000267163	NM_000321.2	775	-/C		0.769909833519301	1	FACETS	0.898	0.839	0.956	0.898	0.839	0.956	CLONAL	1	TRUE	0	0.769909833519301	1		614	258	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0029276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	64	424	2	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.19	2		426	664	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932068	39932068	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140780988	NA	P-0029276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	97	604	0	ENST00000378444.4:c.2531C>T	p.Pro844Leu	p.P844L	ENST00000378444	NM_001123385.1	844	cCg/cTg	4/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.19	2		604	841	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278100	18278100	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	101	661	0	ENST00000222254.8:c.1720C>T	p.Arg574Ter	p.R574*	ENST00000222254	NM_005027.3	574	Cga/Tga	13/16	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.19	2		661	1057	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068412	26068413	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	71	395	0	ENST00000435504.4:c.77dup	p.Asn26LysfsTer7	p.N26Kfs*7	ENST00000435504		26	aat/aaAt	2/13	0.167702183384679	2	FACETS	1	0.963	1	0.643	0.562	0.731	CLONAL	1	TRUE	0	0.19	2		395	581	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524447	44524447	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	31	309	0	ENST00000291552.4:c.110A>G	p.His37Arg	p.H37R	ENST00000291552	NM_006758.2	37	cAc/cGc	2/8	1	2	FACETS	0.67	0.541	0.816	0.67	0.541	0.816	SUBCLONAL	1	TRUE	1	0.19	2		309	487	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138857	64138857	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779234584	NA	P-0029277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	141	563	0	ENST00000334205.4:c.2224C>T	p.Arg742Cys	p.R742C	ENST00000334205	NM_003942.2	742	Cgc/Tgc	17/17	0.30344616444082	3	FACETS	1	0.951	1	0.534	0.486	0.585	CLONAL	1	TRUE	1	0.30344616444082	3		563	1002	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579491	7579500	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTGGGAGC	TTCTGGGAGC	-	novel	NA	P-0029277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	296	741	0	ENST00000269305.4:c.187_196del	p.Ala63CysfsTer57	p.A63Cfs*57	ENST00000269305	NM_001126112.2	63	GCTCCCAGAAtg/tg	4/11	0.30344616444082	2	FACETS	0.981	0.925	1	0.981	0.925	1	CLONAL	2	TRUE	0	0.30344616444082	2		741	994	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654848	29654848	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	24	292	0	ENST00000356175.3:c.5537C>T	p.Pro1846Leu	p.P1846L	ENST00000356175	NM_000267.3	1846	cCg/cTg	37/57	0.30344616444082	2	FACETS	0.412	0.322	0.515	0.206	0.161	0.258	SUBCLONAL	1	TRUE	0	0.30344616444082	2		292	384	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224379	36224379	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1253	159	888	0	ENST00000222270.7:c.6932del	p.Pro2311LeufsTer14	p.P2311Lfs*14	ENST00000222270	NM_014727.1	2310	aCc/ac	28/37	0.30344616444082	3	FACETS	0.855	0.781	0.932	0.427	0.39	0.466	CLONAL	1	TRUE	1	0.30344616444082	3		888	1412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	422	655	0	ENST00000269305.4:c.880del	p.Glu294SerfsTer51	p.E294Sfs*51	ENST00000269305	NM_001126112.2	294	Gag/ag	8/11	0.445966186853335	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.445966186853335	2		655	867	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17386609	17386609	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0029278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	55	714	0	ENST00000359435.4:c.545-1G>T		p.X182_splice	ENST00000359435	NM_001033549.1	182			1	2	FACETS	0.252	0.215	0.293	0.252	0.215	0.293	SUBCLONAL	1	TRUE	1	0.445966186853335	2		714	978	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098968	178098969	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCC	novel	NA	P-0029278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	86	301	0	ENST00000397062.3:c.74_76dup	p.Arg25dup	p.R25dup	ENST00000397062	NM_006164.4	25	caa/cGGCaa	2/5	1	2	FACETS	0.999	0.89	1	0.999	0.89	1	CLONAL	1	TRUE	1	0.445966186853335	2		301	386	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52685808	52685809	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	163	418	0	ENST00000394830.3:c.663dup	p.Ala222CysfsTer4	p.A222Cfs*4	ENST00000394830	NM_018313.4	221	-/T	7/30	0.445966186853335	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.445966186853335	1		418	555	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149465947	149465947	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	257	812	0	ENST00000286301.3:c.44G>T	p.Trp15Leu	p.W15L	ENST00000286301	NM_005211.3	15	tGg/tTg	2/22	0.445966186853335	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.445966186853335	1		812	803	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124438	94124438	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	120	417	0	ENST00000369303.4:c.145T>C	p.Ser49Pro	p.S49P	ENST00000369303	NM_004440.3	49	Tcc/Ccc	2/17	0.445966186853335	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.445966186853335	1		417	415	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	22	394	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.703	0.545	0.888	0.703	0.545	0.888	SUBCLONAL	1	TRUE	1	0.17	2		394	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577526	7577526	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121912653	NA	P-0029282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	53	646	0	ENST00000269305.4:c.755T>C	p.Leu252Pro	p.L252P	ENST00000269305	NM_001126112.2	252	cTc/cCc	7/11	1	2	FACETS	0.778	0.662	0.907	0.778	0.662	0.907	CLONAL	1	TRUE	1	0.17	2		646	801	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	127	404	0				ENST00000310581	NM_198253.2	-/1132			0.143957599738368	3	FACETS	0.907	0.826	0.99	0.907	0.826	0.99	INDETERMINATE	2	TRUE	1	0.328894167328428	3		404	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0029283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	97	649	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	0.278576853610646	4	FACETS	0.796	0.708	0.89	0.265	0.236	0.297	SUBCLONAL	1	TRUE	1	0.328894167328428	4		649	985	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0029283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	414	616	0	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.278576853610646	4	FACETS	0.974	0.929	1	0.974	0.929	1	CLONAL	3	TRUE	1	0.328894167328428	4		616	1145	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577151	7577517	+	splice_donor_variant,splice_acceptor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	TACCACTACTCAGGATAGGAAAAGAGAAGCAAGAGGCAGTAAGGAAATCAGGTCCTACCTGTCCCATTTAAAAAACCAGGCTCCATCTACTCCCAACCACCCTTGTCCTTTCTGGAGCCTAAGCTCCAGCTCCAGGTAGGTGGAGGAGAAGCCACAGGTTAAGAGGTCCCAAAGCCAGAGAAAAGAAAACTGAGTGGGAGCAGTAAGGAGATTCCCCGCCGGGGATGTGATGAGAGGTGGATGGGTAGTAGTATGGAAGAAATCGGTAAGAGGTGGGCCCAGGGGTCAGAGGCAAGCAGAGGCTGGGGCACAGCAGGCCAGTGTGCAGGGTGGCAAGTGGCTCCTGACCTGGAGTCTTCCAGTGTGA	TACCACTACTCAGGATAGGAAAAGAGAAGCAAGAGGCAGTAAGGAAATCAGGTCCTACCTGTCCCATTTAAAAAACCAGGCTCCATCTACTCCCAACCACCCTTGTCCTTTCTGGAGCCTAAGCTCCAGCTCCAGGTAGGTGGAGGAGAAGCCACAGGTTAAGAGGTCCCAAAGCCAGAGAAAAGAAAACTGAGTGGGAGCAGTAAGGAGATTCCCCGCCGGGGATGTGATGAGAGGTGGATGGGTAGTAGTATGGAAGAAATCGGTAAGAGGTGGGCCCAGGGGTCAGAGGCAAGCAGAGGCTGGGGCACAGCAGGCCAGTGTGCAGGGTGGCAAGTGGCTCCTGACCTGGAGTCTTCCAGTGTGA	-	novel	NA	P-0029284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	182	525	0	ENST00000269305.4:c.764_787del		p.X255_splice	ENST00000269305	NM_001126112.2	255	aTCACACTGGAAGACTCCAGGTCAGGAGCCACTTGCCACCCTGCACACTGGCCTGCTGTGCCCCAGCCTCTGCTTGCCTCTGACCCCTGGGCCCACCTCTTACCGATTTCTTCCATACTACTACCCATCCACCTCTCATCACATCCCCGGCGGGGAATCTCCTTACTGCTCCCACTCAGTTTTCTTTTCTCTGGCTTTGGGACCTCTTAACCTGTGGCTTCTCCTCCACCTACCTGGAGCTGGAGCTTAGGCTCCAGAAAGGACAAGGGTGGTTGGGAGTAGATGGAGCCTGGTTTTTTAAATGGGACAGGTAGGACCTGATTTCCTTACTGCCTCTTGCTTCTCTTTTCCTATCCTGAGTAGTGGTAat/aat	7-8/11	NA	2	FACETS	0.69	0.639	0.743			1	INDETERMINATE	1	TRUE	NA	0.761053220535356	2		525	693	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804168	46804168	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	341	666	0	ENST00000290295.7:c.839del	p.Asn280ThrfsTer102	p.N280Tfs*102	ENST00000290295	NM_006361.5	280	aAc/ac	2/2	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.761053220535356	2		666	831	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068349	26068349	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0029284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	39	374	0	ENST00000435504.4:c.140+1del		p.X47_splice	ENST00000435504		47			1	2	FACETS	0.172	0.142	0.206	0.172	0.142	0.206	SUBCLONAL	1	TRUE	1	0.761053220535356	2		374	596	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068434	26068434	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs867470858	NA	P-0029284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	168	382	0	ENST00000435504.4:c.58-2A>G		p.X20_splice	ENST00000435504		20			1	2	FACETS	0.769	0.711	0.829	0.769	0.711	0.829	SUBCLONAL	1	TRUE	1	0.761053220535356	2		382	574	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101090	26101090	+	start_lost	Translation_Start_Site	SNP	A	A	C	novel	NA	P-0029284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	128	408	0	ENST00000435504.4:c.2T>G	p.Met1?	p.M1?	ENST00000435504		1	aTg/aGg	1/13	1	2	FACETS	0.583	0.53	0.638	0.583	0.53	0.638	SUBCLONAL	1	TRUE	1	0.761053220535356	2		408	577	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490581	20490581	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	49	556	0	ENST00000346618.3:c.1318G>T	p.Glu440Ter	p.E440*	ENST00000346618	NM_001949.4	440	Gag/Tag	7/7	1	2	FACETS	0.191	0.161	0.224	0.191	0.161	0.224	SUBCLONAL	1	TRUE	1	0.761053220535356	2		556	674	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	52	394	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.789	0.671	0.919	0.789	0.671	0.919	CLONAL	1	TRUE	1	0.204578595594477	2		394	644	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004242	29004242	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766441216	NA	P-0029285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	68	421	0	ENST00000282397.4:c.1051C>T	p.Arg351Trp	p.R351W	ENST00000282397	NM_002019.4	351	Cgg/Tgg	8/30	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.204578595594477	2		421	633	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983059	201983060	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0029285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	332	736	0	ENST00000359651.3:c.909dup	p.Lys304GlnfsTer167	p.K304Qfs*167	ENST00000359651		303	ttc/ttCc	7/8	0.19233968575808	4	FACETS	0.89	0.839	0.941	0.89	0.839	0.941	CLONAL	3	TRUE	1	0.204578595594477	4		736	1465	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639884	3639884	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	80	621	0	ENST00000294008.3:c.3755A>G	p.Asp1252Gly	p.D1252G	ENST00000294008	NM_032444.2	1252	gAc/gGc	12/15	1	2	FACETS	0.82	0.72	0.928	0.82	0.72	0.928	CLONAL	1	TRUE	1	0.204578595594477	2		621	954	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993068	90993695	+	splice_donor_variant,splice_acceptor_variant,stop_lost,protein_altering_variant,intron_variant	Splice_Site	DEL	TTCCCAGAGACATCTAAACAAGAAGAGCATGCAACCAAAGGCTCATACTCTATTCTGTAAATGAGAATAAGTTAAATAAAGTCATAGTATCAGAGTTGCAGAGATGGCAATTTTTAGTACTTTAAAACTTTAAGCTCACATCATATACTGTTATTGTAACTTTTATTTATTGTTACCCTTTGTAACCTATGAAATTATCAGTTCCTCATCATTAAGCTTTGTAACCTAGAAAATTATCAAATCCTAAGTCTTGAGTCCAAATGAAGAAAAAACAATGACCAAAAGTTAACATTATACCTTCACCAATGAGGAATCGAAGAAATGTAACTTCCCATGAAGTCCCTCAGGGCCCACTCAAACTCTCATCACCGTGATGTACAAAATGCACTCACCACCCATGGCACAGAGTCCAATACTGTGCTAAGCAGGAACTAAATTATACTGTTTTAAATTCATTAATCAGAAATATCATTTTCCTTTAGGATTTGGCTGAAACAAAGCTGTCCATTTTAAAATCAATTTTAAAATGTCTTACCTGAATTTACTTCCAAACACTCCAAAAGTAATACCATCCCCCGACTTCAAAGTTCGGGAAAAGCCATTCTGCATTTTTTCCTCATTAACAAAG	TTCCCAGAGACATCTAAACAAGAAGAGCATGCAACCAAAGGCTCATACTCTATTCTGTAAATGAGAATAAGTTAAATAAAGTCATAGTATCAGAGTTGCAGAGATGGCAATTTTTAGTACTTTAAAACTTTAAGCTCACATCATATACTGTTATTGTAACTTTTATTTATTGTTACCCTTTGTAACCTATGAAATTATCAGTTCCTCATCATTAAGCTTTGTAACCTAGAAAATTATCAAATCCTAAGTCTTGAGTCCAAATGAAGAAAAAACAATGACCAAAAGTTAACATTATACCTTCACCAATGAGGAATCGAAGAAATGTAACTTCCCATGAAGTCCCTCAGGGCCCACTCAAACTCTCATCACCGTGATGTACAAAATGCACTCACCACCCATGGCACAGAGTCCAATACTGTGCTAAGCAGGAACTAAATTATACTGTTTTAAATTCATTAATCAGAAATATCATTTTCCTTTAGGATTTGGCTGAAACAAAGCTGTCCATTTTAAAATCAATTTTAAAATGTCTTACCTGAATTTACTTCCAAACACTCCAAAAGTAATACCATCCCCCGACTTCAAAGTTCGGGAAAAGCCATTCTGCATTTTTTCCTCATTAACAAAG	-	novel	NA	P-0029285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	32	402	0	ENST00000265433.3:c.228_374del		p.X76_splice	ENST00000265433	NM_002485.4	76	acCTTTGTTAATGAGGAAAAAATGCAGAATGGCTTTTCCCGAACTTTGAAGTCGGGGGATGGTATTACTTTTGGAGTGTTTGGAAGTAAATTCAGGTAAGACATTTTAAAATTGATTTTAAAATGGACAGCTTTGTTTCAGCCAAATCCTAAAGGAAAATGATATTTCTGATTAATGAATTTAAAACAGTATAATTTAGTTCCTGCTTAGCACAGTATTGGACTCTGTGCCATGGGTGGTGAGTGCATTTTGTACATCACGGTGATGAGAGTTTGAGTGGGCCCTGAGGGACTTCATGGGAAGTTACATTTCTTCGATTCCTCATTGGTGAAGGTATAATGTTAACTTTTGGTCATTGTTTTTTCTTCATTTGGACTCAAGACTTAGGATTTGATAATTTTCTAGGTTACAAAGCTTAATGATGAGGAACTGATAATTTCATAGGTTACAAAGGGTAACAATAAATAAAAGTTACAATAACAGTATATGATGTGAGCTTAAAGTTTTAAAGTACTAAAAATTGCCATCTCTGCAACTCTGATACTATGACTTTATTTAACTTATTCTCATTTACAGAATAGAGTATGAGCCTTTGGTTGCATGCTCTTCTTGTTTAGATGTCTCTGGGAAa/aca	3-4/16	1	2	FACETS	0.871	0.708	1	0.871	0.708	1	CLONAL	1	TRUE	1	0.204578595594477	2		402	359	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035987	47035987	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0029285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	106	658	0	ENST00000377604.3:c.663+2T>C		p.X221_splice	ENST00000377604	NM_001204468.1	221			1	2	FACETS	0.986	0.882	1	0.986	0.882	1	CLONAL	1	TRUE	1	0.204578595594477	2		658	1051	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0029287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	94	445	1	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	0.829310190711422	1	FACETS	0.745	0.683	0.808	0.745	0.683	0.808	SUBCLONAL	1	TRUE	0	0.829310190711422	1		446	178	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217872	7217875	+	frameshift_variant	Frame_Shift_Del	DEL	CTTC	CTTC	-	novel	NA	P-0029287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	134	549	1	ENST00000380728.2:c.136_139del	p.Glu46AsnfsTer16	p.E46Nfs*16	ENST00000380728		46	GAAGaa/aa	3/11	0.782649605032514	1	FACETS	0.73	0.678	0.782	0.73	0.678	0.782	SUBCLONAL	1	TRUE	0	0.829310190711422	1		550	259	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16203082	16203082	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0029287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	173	467	0	ENST00000375759.3:c.790A>T	p.Arg264Ter	p.R264*	ENST00000375759	NM_015001.2	264	Aga/Tga	3/15	0.793830871879002	1	FACETS	0.806	0.758	0.853	0.806	0.758	0.853	CLONAL	1	TRUE	0	0.829310190711422	1		467	303	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220343	98220343	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	162	430	0	ENST00000331920.6:c.3120C>G	p.Phe1040Leu	p.F1040L	ENST00000331920	NM_000264.3	1040	ttC/ttG	18/24	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.829310190711422	2		430	381	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0029288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	83	498	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.471292613564434	3	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	1	0.471292613564434	3		498	202	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934573	NA	P-0029288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	340	479	1	ENST00000269305.4:c.722C>A	p.Ser241Tyr	p.S241Y	ENST00000269305	NM_001126112.2	241	tCc/tAc	7/11	0.334099626218398	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.471292613564434	2		480	667	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0029288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	137	404	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.471292613564434	2		404	463	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106484	27106484	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	316	605	0	ENST00000324856.7:c.6098del	p.Lys2033ArgfsTer9	p.K2033Rfs*9	ENST00000324856	NM_006015.4	2032	gAa/ga	20/20	0.334099626218398	2	FACETS	0.986	0.938	1	0.986	0.938	1	CLONAL	2	TRUE	0	0.471292613564434	2		605	680	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828147	72828147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	94	560	0	ENST00000268489.5:c.8434G>A	p.Asp2812Asn	p.D2812N	ENST00000268489	NM_006885.3	2812	Gac/Aac	9/10	1	2	FACETS	0.883	0.789	0.981	0.883	0.789	0.981	CLONAL	1	TRUE	1	0.471292613564434	2		560	452	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584540	48584541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0029288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	135	374	0	ENST00000342988.3:c.714dup	p.Gln239AlafsTer25	p.Q239Afs*25	ENST00000342988	NM_005359.5	238	ttg/ttGg	6/12	0.471292613564434	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.471292613564434	1		374	368	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041358	47041359	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0029288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	352	665	0	ENST00000377604.3:c.1703_1704dup	p.Val569ThrfsTer136	p.V569Tfs*136	ENST00000377604	NM_001204468.1	568	gac/gACac	16/24	0.471292613564434	2	FACETS	0.988	0.942	1	0.988	0.942	1	CLONAL	2	TRUE	0	0.471292613564434	2		665	756	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	60	394	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		394	337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0029289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	55	557	1	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		558	877	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595810	52595810	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	107	443	0	ENST00000394830.3:c.4105G>C	p.Glu1369Gln	p.E1369Q	ENST00000394830	NM_018313.4	1369	Gag/Cag	26/30	0.53798571304592	1	FACETS	0.505	0.454	0.559	0.505	0.454	0.559	SUBCLONAL	1	TRUE	0	0.53798571304592	1		443	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579355	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519997	NA	P-0029291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	337	650	1	ENST00000269305.4:c.332T>A	p.Leu111Gln	p.L111Q	ENST00000269305	NM_001126112.2	111	cTg/cAg	4/11	0.53798571304592	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.53798571304592	1		651	810	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17355174	17355174	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200973284	NA	P-0029291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	325	477	0	ENST00000375499.3:c.344G>A	p.Arg115Gln	p.R115Q	ENST00000375499	NM_003000.2	115	cGa/cAa	4/8	0.53798571304592	3	FACETS	0.866	0.821	0.912	0.866	0.821	0.912	CLONAL	2	TRUE	1	0.53798571304592	3		477	885	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595786	52595786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	85	377	0	ENST00000394830.3:c.4129G>A	p.Glu1377Lys	p.E1377K	ENST00000394830	NM_018313.4	1377	Gaa/Aaa	26/30	0.53798571304592	1	FACETS	0.48	0.426	0.538	0.48	0.426	0.538	SUBCLONAL	1	TRUE	0	0.53798571304592	1		377	481	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805979	32805979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293561966	NA	P-0029291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	132	609	0	ENST00000374899.4:c.32C>T	p.Ser11Phe	p.S11F	ENST00000374899	NM_018833.2	11	tCc/tTc	2/12	0.172346986654896	2	FACETS	0.492	0.446	0.54	0.246	0.223	0.27	INDETERMINATE	1	TRUE	0	0.53798571304592	2		609	998	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881027	37881027	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8159	4436	662	0	ENST00000269571.5:c.2356C>G	p.Leu786Val	p.L786V	ENST00000269571		786	Ctg/Gtg	20/27	0.53798571304592	25	FACETS	1	0.997	1			1	CLONAL	9	TRUE	NA	0.53798571304592	25		662	12595	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883793	37884641	+	splice_acceptor_variant,splice_donor_variant,stop_lost,3_prime_UTR_variant,intron_variant	Splice_Site	DEL	CCAGCCTGGTATGGAGTCCAGTCTAAGCAGAGAGACTGATGGGCAGGGGAGGTGGGACCTTCAGCCCAGGGTCCACTGTGGGGGCAGAGGGAGTGGCAGAGACACCGGGGTTCCTTCCCCTAATGGGTCACCTTCTCTTGACCTTTCAGAATATGTGAACCAGCCAGATGTTCGGCCCCAGCCCCCTTCGCCCCGAGAGGGCCCTCTGCCTGCTGCCCGACCTGCTGGTGCCACTCTGGAAAGGCCCAAGACTCTCTCCCCAGGGAAGAATGGGGTCGTCAAAGACGTTTTTGCCTTTGGGGGTGCCGTGGAGAACCCCGAGTACTTGACACCCCAGGGAGGAGCTGCCCCTCAGCCCCACCCTCCTCCTGCCTTCAGCCCAGCCTTCGACAACCTCTATTACTGGGACCAGGACCCACCAGAGCGGGGGGCTCCACCCAGCACCTTCAAAGGGACACCTACGGCAGAGAACCCAGAGTACCTGGGTCTGGACGTGCCAGTGTGAACCAGAAGGCCAAGTCCGCAGAAGCCCTGATGTGTCCTCAGGGAGCAGGGAAGGCCTGACTTCTGCTGGCATCAAGAGGTGGGAGGGCCCTCCGACCACTTCCAGGGGAACCTGCCATGCCAGGAACCTGTCCTAAGGAACCTTCCTTCCTGCTTGAGTTCCCAGATGGCTGGAAGGGGTCCAGCCTCGTTGGAAGAGGAACAGCACTGGGGAGTCTTTGTGGATTCTGAGGCCCTGCCCAATGAGACTCTAGGGTCCAGTGGATGCCACAGCCCAGCTTGGCCCTTTCCTTCCAGATCCTGGGTACTGAAAGCCTTAGGGAAGCTGGCCTGAGAGGGGAAGCG	CCAGCCTGGTATGGAGTCCAGTCTAAGCAGAGAGACTGATGGGCAGGGGAGGTGGGACCTTCAGCCCAGGGTCCACTGTGGGGGCAGAGGGAGTGGCAGAGACACCGGGGTTCCTTCCCCTAATGGGTCACCTTCTCTTGACCTTTCAGAATATGTGAACCAGCCAGATGTTCGGCCCCAGCCCCCTTCGCCCCGAGAGGGCCCTCTGCCTGCTGCCCGACCTGCTGGTGCCACTCTGGAAAGGCCCAAGACTCTCTCCCCAGGGAAGAATGGGGTCGTCAAAGACGTTTTTGCCTTTGGGGGTGCCGTGGAGAACCCCGAGTACTTGACACCCCAGGGAGGAGCTGCCCCTCAGCCCCACCCTCCTCCTGCCTTCAGCCCAGCCTTCGACAACCTCTATTACTGGGACCAGGACCCACCAGAGCGGGGGGCTCCACCCAGCACCTTCAAAGGGACACCTACGGCAGAGAACCCAGAGTACCTGGGTCTGGACGTGCCAGTGTGAACCAGAAGGCCAAGTCCGCAGAAGCCCTGATGTGTCCTCAGGGAGCAGGGAAGGCCTGACTTCTGCTGGCATCAAGAGGTGGGAGGGCCCTCCGACCACTTCCAGGGGAACCTGCCATGCCAGGAACCTGTCCTAAGGAACCTTCCTTCCTGCTTGAGTTCCCAGATGGCTGGAAGGGGTCCAGCCTCGTTGGAAGAGGAACAGCACTGGGGAGTCTTTGTGGATTCTGAGGCCCTGCCCAATGAGACTCTAGGGTCCAGTGGATGCCACAGCCCAGCTTGGCCCTTTCCTTCCAGATCCTGGGTACTGAAAGCCTTAGGGAAGCTGGCCTGAGAGGGGAAGCG	-	novel	NA	P-0029291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8361	3604	688	1	ENST00000269571.5:c.3405_*344del		p.X1135_splice	ENST00000269571		1135		26-27/27	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.53798571304592	NA		689	11965	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46603835	46603835	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1283870670	NA	P-0029291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	111	511	0	ENST00000263734.3:c.1192G>A	p.Glu398Lys	p.E398K	ENST00000263734	NM_001430.4	398	Gag/Aag	9/16	1	2	FACETS	0.474	0.425	0.525	0.474	0.425	0.525	SUBCLONAL	1	TRUE	1	0.53798571304592	2		511	871	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719181	61719181	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	46	326	0	ENST00000401558.2:c.1876C>T	p.Gln626Ter	p.Q626*	ENST00000401558	NM_003400.3	626	Cag/Tag	16/25	1	2	FACETS	0.462	0.39	0.541	0.462	0.39	0.541	SUBCLONAL	1	TRUE	1	0.53798571304592	2		326	370	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723585	49723585	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	17	49	0	ENST00000449682.2:c.1057G>A	p.Glu353Lys	p.E353K	ENST00000449682	NM_020998.3	353	Gag/Aag	9/18	0.53798571304592	1	FACETS	0.84	0.65	1	0.84	0.65	1	CLONAL	1	TRUE	0	0.53798571304592	1		49	55	SUCCESS
ATR	545	MSKCC	GRCh37	3	142168426	142168426	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1227410272	NA	P-0029291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	45	332	0	ENST00000350721.4:c.7780G>C	p.Asp2594His	p.D2594H	ENST00000350721	NM_001184.3	2594	Gac/Cac	47/47	0.39218634626803	3	FACETS	0.503	0.423	0.591	0.252	0.211	0.296	SUBCLONAL	1	TRUE	1	0.53798571304592	3		332	422	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045953	26045953	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	111	397	0	ENST00000540144.1:c.315C>A	p.Phe105Leu	p.F105L	ENST00000540144	NM_003531.2	105	ttC/ttA	1/1	0.172346986654896	2	FACETS	0.696	0.627	0.768	0.348	0.313	0.384	INDETERMINATE	1	TRUE	0	0.53798571304592	2		397	593	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0029294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	231	747	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.544935077090901	2		750	827	SUCCESS
APC	324	MSKCC	GRCh37	5	112174580	112174580	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	34	509	0	ENST00000257430.4:c.3289G>T	p.Glu1097Ter	p.E1097*	ENST00000257430	NM_000038.5	1097	Gaa/Taa	16/16	0.544935077090901	1	FACETS	0.301	0.246	0.361	0.301	0.246	0.361	SUBCLONAL	1	TRUE	0	0.544935077090901	1		509	302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579440	7579440	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs867725248	NA	P-0029294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	246	892	0	ENST00000269305.4:c.247del	p.Ala83ArgfsTer40	p.A83Rfs*40	ENST00000269305	NM_001126112.2	83	Gcg/cg	4/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.544935077090901	2		892	835	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523645	176523645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	223	913	0	ENST00000292408.4:c.2056G>A	p.Gly686Arg	p.G686R	ENST00000292408	NM_213647.1	686	Ggg/Agg	16/18	0.544935077090901	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.544935077090901	1		913	545	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267710	198267710	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	70	446	0	ENST00000335508.6:c.1769G>T	p.Arg590Ile	p.R590I	ENST00000335508	NM_012433.2	590	aGa/aTa	13/25	1	2	FACETS	0.862	0.759	0.972	0.862	0.759	0.972	CLONAL	1	TRUE	1	0.544935077090901	2		446	298	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039888	47039888	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	249	476	0	ENST00000377604.3:c.1231C>T	p.Gln411Ter	p.Q411*	ENST00000377604	NM_001204468.1	411	Cag/Tag	12/24	1	1	FACETS	0.78	0.742	0.818	1	0.995	1	SUBCLONAL	2	TRUE	0	0.544935077090901	1		476	426	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657369	29657369	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	129	684	0	ENST00000356175.3:c.5602G>T	p.Glu1868Ter	p.E1868*	ENST00000356175	NM_000267.3	1868	Gag/Tag	38/57	1	2	FACETS	0.916	0.835	1	0.916	0.835	1	CLONAL	1	TRUE	1	0.544935077090901	2		684	517	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983018	201983018	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	66	947	0	ENST00000359651.3:c.867C>G	p.Asn289Lys	p.N289K	ENST00000359651		289	aaC/aaG	7/8	0.544935077090901	3	FACETS	0.294	0.254	0.337	0.147	0.127	0.169	SUBCLONAL	1	TRUE	1	0.544935077090901	3		947	1050	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809238	243809238	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	75	517	0	ENST00000263826.5:c.386G>T	p.Gly129Val	p.G129V	ENST00000263826	NM_005465.4	129	gGa/gTa	4/13	0.544935077090901	3	FACETS	0.939	0.828	1	0.47	0.414	0.529	CLONAL	1	TRUE	1	0.544935077090901	3		517	373	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344803	118344803	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	112	473	1	ENST00000534358.1:c.2929G>T	p.Gly977Cys	p.G977C	ENST00000534358	NM_005933.3	977	Ggc/Tgc	3/36	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.544935077090901	2		474	411	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281653	49281653	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	230	855	0	ENST00000282018.3:c.700C>A	p.Pro234Thr	p.P234T	ENST00000282018	NM_020377.2	234	Cca/Aca	1/1	0.133374325807104	3	FACETS	1	0.979	1	0.373	0.347	0.399	INDETERMINATE	1	TRUE	0	0.544935077090901	3		855	961	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436516	110436516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1204315518	NA	P-0029294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	231	868	0	ENST00000375856.3:c.1885C>T	p.Pro629Ser	p.P629S	ENST00000375856	NM_003749.2	629	Cca/Tca	1/2	0.133374325807104	3	FACETS	1	0.943	1	0.338	0.314	0.362	INDETERMINATE	1	TRUE	0	0.544935077090901	3		868	1065	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050268	128050268	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1211945316	NA	P-0029294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	168	597	0	ENST00000285398.2:c.389G>T	p.Gly130Val	p.G130V	ENST00000285398	NM_000122.1	130	gGg/gTg	3/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.544935077090901	2		597	563	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713470	40713470	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1318044562	NA	P-0029294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	165	668	0	ENST00000373198.4:c.4045C>G	p.Arg1349Gly	p.R1349G	ENST00000373198	NM_133170.3	1349	Cgt/Ggt	30/32	1	2	FACETS	0.999	0.922	1	0.999	0.922	1	CLONAL	1	TRUE	1	0.544935077090901	2		668	606	SUCCESS
APC	324	MSKCC	GRCh37	5	112174494	112174494	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1554084848	NA	P-0029294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	60	431	0	ENST00000257430.4:c.3203C>G	p.Ser1068Ter	p.S1068*	ENST00000257430	NM_000038.5	1068	tCa/tGa	16/16	0.544935077090901	1	FACETS	0.774	0.677	0.876	0.774	0.677	0.876	SUBCLONAL	1	TRUE	0	0.544935077090901	1		431	207	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514331	149514331	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	135	542	0	ENST00000261799.4:c.613T>G	p.Tyr205Asp	p.Y205D	ENST00000261799	NM_002609.3	205	Tat/Gat	4/23	0.544935077090901	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.544935077090901	1		542	315	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522717	176522717	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	169	810	0	ENST00000292408.4:c.1814C>A	p.Ser605Tyr	p.S605Y	ENST00000292408	NM_213647.1	605	tCc/tAc	13/18	0.544935077090901	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.544935077090901	1		810	447	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518430	8518430	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0029294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	49	229	0	ENST00000356435.5:c.962-1G>T		p.X321_splice	ENST00000356435		321			1	2	FACETS	0.967	0.831	1	0.967	0.831	1	CLONAL	1	TRUE	1	0.544935077090901	2		229	186	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97869526	97869526	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	141	568	0	ENST00000289081.3:c.1355A>T	p.His452Leu	p.H452L	ENST00000289081	NM_000136.2	452	cAc/cTc	14/15	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.544935077090901	2		568	512	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409106	139409106	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	200	957	0	ENST00000277541.6:c.2063A>G	p.His688Arg	p.H688R	ENST00000277541	NM_017617.3	688	cAc/cGc	13/34	1	2	FACETS	0.897	0.833	0.964	0.897	0.833	0.964	CLONAL	1	TRUE	1	0.544935077090901	2		957	818	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0029295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1294	50	793	2	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	1	2	FACETS	0.392	0.33	0.459	0.392	0.33	0.459	SUBCLONAL	1	TRUE	1	0.19	2		795	1344	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226550857	226550857	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	67	315	0	ENST00000366794.5:c.2791G>T	p.Glu931Ter	p.E931*	ENST00000366794	NM_001618.3	931	Gaa/Taa	21/23	0.369364491917998	2	FACETS	0.335	0.291	0.382	0.167	0.145	0.192	INDETERMINATE	1	TRUE	0	0.703028921608978	2		315	569	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625386	69625386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782272422	NA	P-0029296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3303	331	778	0	ENST00000334134.2:c.407C>T	p.Thr136Met	p.T136M	ENST00000334134	NM_005247.2	136	aCg/aTg	3/3	0.703028921608978	8	FACETS	0.806	0.756	0.857	0.115	0.108	0.123	CLONAL	1	TRUE	1	0.703028921608978	8		778	3634	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103541	77103541	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	71	265	0	ENST00000356341.3:c.25C>G	p.Gln9Glu	p.Q9E	ENST00000356341	NM_002576.4	9	Caa/Gaa	2/15	0.371710565195471	6	FACETS	0.542	0.472	0.618			1	INDETERMINATE	1	TRUE	NA	0.703028921608978	6		265	897	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78831634	78831634	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	109	630	0	ENST00000306801.3:c.1443G>C	p.Gln481His	p.Q481H	ENST00000306801	NM_020761.2	481	caG/caC	13/34	0.397854854103736	3	FACETS	0.441	0.395	0.489	0.22	0.197	0.245	INDETERMINATE	1	TRUE	1	0.703028921608978	3		630	951	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919021	50919021	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501811	NA	P-0029296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	48	827	0	ENST00000440232.2:c.2758G>A	p.Asp920Asn	p.D920N	ENST00000440232	NM_002691.3	920	Gac/Aac	22/27	0.703028921608978	1	FACETS	0.128	0.107	0.15	0.128	0.107	0.15	SUBCLONAL	1	TRUE	0	0.703028921608978	1		827	693	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961532	54961532	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	121	424	1	ENST00000312783.6:c.100C>T	p.Gln34Ter	p.Q34*	ENST00000312783	NM_198436.1	34	Cag/Tag	4/10	1	2	FACETS	0.478	0.432	0.526	0.478	0.432	0.526	SUBCLONAL	1	TRUE	1	0.703028921608978	2		425	720	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584549	187584549	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753470701	NA	P-0029296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	91	244	0	ENST00000441802.2:c.3484G>A	p.Glu1162Lys	p.E1162K	ENST00000441802	NM_005245.3	1162	Gag/Aag	3/27	1	2	FACETS	0.532	0.474	0.593	0.532	0.474	0.593	SUBCLONAL	1	TRUE	1	0.703028921608978	2		244	487	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163813	32163814	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0029296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	90	532	1	ENST00000375023.3:c.5412_5413delinsAA	p.Asp1805Asn	p.D1805N	ENST00000375023	NM_004557.3	1804	gcGGac/gcAAac	30/30	1	2	FACETS	0.411	0.365	0.46	0.411	0.365	0.46	SUBCLONAL	1	TRUE	1	0.703028921608978	2		533	623	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927649	131927650	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587782543	NA	P-0029296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	14	102	0	ENST00000265335.6:c.1722dup	p.Gln575ThrfsTer3	p.Q575Tfs*3	ENST00000265335		572	-/A	11/25	0.252024198105271	2	FACETS	0.166	0.12	0.222	0.083	0.06	0.111	INDETERMINATE	1	TRUE	0	0.703028921608978	2		102	240	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0029297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	294	512	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.79629467970679	2	FACETS	1	0.987	1	0.557	0.528	0.586	CLONAL	1	TRUE	0	0.811943175018319	2		512	650	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175492	108175492	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	177	393	0	ENST00000278616.4:c.5587T>C	p.Ser1863Pro	p.S1863P	ENST00000278616	NM_000051.3	1863	Tct/Cct	37/63	0.801382156881294	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.811943175018319	1		393	256	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272320	38272320	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751038400	NA	P-0029297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	263	541	0	ENST00000425967.3:c.2047G>A	p.Asp683Asn	p.D683N	ENST00000425967	NM_001174067.1	683	Gac/Aac	15/19	0.79629467970679	2	FACETS	0.992	0.936	1	0.496	0.468	0.525	CLONAL	1	TRUE	0	0.811943175018319	2		541	653	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40864896	40864896	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	517	368	0	ENST00000373198.4:c.2372G>T	p.Arg791Ile	p.R791I	ENST00000373198	NM_133170.3	791	aGa/aTa	16/32	0.778216790229261	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.786823751498326	2		368	630	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822645	72822645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149133285	NA	P-0029298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	366	609	0	ENST00000268489.5:c.9530C>T	p.Ser3177Leu	p.S3177L	ENST00000268489	NM_006885.3	3177	tCg/tTg	10/10	1	2	FACETS	0.951	0.905	0.998	0.951	0.905	0.998	CLONAL	1	TRUE	1	0.786823751498326	2		609	978	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944410	40944410	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs777227473	NA	P-0029298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	668	507	0	ENST00000373198.4:c.2092C>A	p.Leu698Met	p.L698M	ENST00000373198	NM_133170.3	698	Ctg/Atg	12/32	0.778216790229261	2	FACETS	0.978	0.956	1	0.978	0.956	1	CLONAL	2	TRUE	0	0.786823751498326	2		507	868	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600330	10600330	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	399	573	0	ENST00000171111.5:c.1525G>T	p.Gly509Trp	p.G509W	ENST00000171111	NM_203500.1	509	Ggg/Tgg	4/6	0.784187697937137	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.786823751498326	1		573	574	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513299	106513299	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	184	323	0	ENST00000359195.3:c.2203C>A	p.Gln735Lys	p.Q735K	ENST00000359195	NM_002649.2	735	Caa/Aaa	4/11	1	2	FACETS	0.826	0.768	0.886	0.826	0.768	0.886	CLONAL	1	TRUE	1	0.786823751498326	2		323	566	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987076	36987076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	428	560	0	ENST00000354822.5:c.613G>A	p.Glu205Lys	p.E205K	ENST00000354822	NM_001079668.2	205	Gag/Aag	3/3	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.786823751498326	2		560	1079	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69050700	69050700	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	30	435	0	ENST00000288368.4:c.4035G>T	p.Leu1345Phe	p.L1345F	ENST00000288368	NM_024870.2	1345	ttG/ttT	33/40	0.784187697937137	1	FACETS	0.141	0.113	0.172	0.141	0.113	0.172	SUBCLONAL	1	TRUE	0	0.786823751498326	1		435	328	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625457	69625457	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	335	566	1	ENST00000334134.2:c.336C>A	p.Ser112Arg	p.S112R	ENST00000334134	NM_005247.2	112	agC/agA	3/3	1	2	FACETS	0.907	0.86	0.954	0.907	0.86	0.954	CLONAL	1	TRUE	1	0.786823751498326	2		567	939	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955572	48955572	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	177	359	0	ENST00000267163.4:c.1688G>T	p.Trp563Leu	p.W563L	ENST00000267163	NM_000321.2	563	tGg/tTg	17/27	0.784187697937137	1	FACETS	0.964	0.911	1	0.964	0.911	1	CLONAL	1	TRUE	0	0.786823751498326	1		359	283	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436350	110436350	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	273	415	0	ENST00000375856.3:c.2051C>T	p.Ser684Phe	p.S684F	ENST00000375856	NM_003749.2	684	tCc/tTc	1/2	0.784187697937137	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.786823751498326	1		415	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579505	7579517	+	frameshift_variant	Frame_Shift_Del	DEL	TCTGGACCTGGGT	TCTGGACCTGGGT	-	novel	NA	P-0029298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	423	698	0	ENST00000269305.4:c.170_182del	p.Asp57ValfsTer62	p.D57Vfs*62	ENST00000269305	NM_001126112.2	57	gACCCAGGTCCAGAt/gt	4/11	0.784187697937137	1	FACETS	0.945	0.911	0.979	0.945	0.911	0.979	CLONAL	1	TRUE	0	0.786823751498326	1		698	690	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489465	40489465	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	312	410	1	ENST00000264657.5:c.785G>T	p.Arg262Leu	p.R262L	ENST00000264657	NM_139276.2	262	cGg/cTg	8/24	1	2	FACETS	0.991	0.94	1	0.991	0.94	1	CLONAL	1	TRUE	1	0.786823751498326	2		411	800	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643334	52643334	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	224	324	0	ENST00000394830.3:c.2562G>A	p.Met854Ile	p.M854I	ENST00000394830	NM_018313.4	854	atG/atA	17/30	0.784187697937137	1	FACETS	0.949	0.902	0.995	0.949	0.902	0.995	CLONAL	1	TRUE	0	0.786823751498326	1		324	364	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643624	52643624	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	317	451	0	ENST00000394830.3:c.2272G>T	p.Glu758Ter	p.E758*	ENST00000394830	NM_018313.4	758	Gaa/Taa	17/30	0.784187697937137	1	FACETS	0.964	0.924	1	0.964	0.924	1	CLONAL	1	TRUE	0	0.786823751498326	1		451	507	SUCCESS
APC	324	MSKCC	GRCh37	5	112174862	112174862	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	177	294	0	ENST00000257430.4:c.3571C>G	p.Gln1191Glu	p.Q1191E	ENST00000257430	NM_000038.5	1191	Cag/Gag	16/16	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.786823751498326	NA		294	275	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020990	26020990	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780000708	NA	P-0029298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	490	375	0	ENST00000357647.3:c.273G>A	p.Met91Ile	p.M91I	ENST00000357647	NM_003529.2	91	atG/atA	1/1	0.778216790229261	2	FACETS	0.976	0.95	1	0.976	0.95	1	CLONAL	2	TRUE	0	0.786823751498326	2		375	638	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672866	30672866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	506	733	0	ENST00000376406.3:c.4094C>T	p.Ser1365Leu	p.S1365L	ENST00000376406	NM_014641.2	1365	tCa/tTa	10/15	0.778216790229261	2	FACETS	1	0.969	1	0.506	0.485	0.527	CLONAL	1	TRUE	0	0.786823751498326	2		733	1271	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393352	139393352	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	54	579	0	ENST00000277541.6:c.6179G>T	p.Arg2060Met	p.R2060M	ENST00000277541	NM_017617.3	2060	aGg/aTg	33/34	0.784187697937137	1	FACETS	0.125	0.107	0.146	0.125	0.107	0.146	SUBCLONAL	1	TRUE	0	0.786823751498326	1		579	664	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039470	49039473	+	frameshift_variant	Frame_Shift_Del	DEL	CTGC	CTGC	-	novel	NA	P-0029299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	159	558	1	ENST00000267163.4:c.2456_2459del	p.Leu819GlnfsTer6	p.L819Qfs*6	ENST00000267163	NM_000321.2	819	CTGCca/ca	23/27	0.481312174090544	1	FACETS	0.784	0.721	0.849	0.784	0.721	0.849	SUBCLONAL	1	TRUE	0	0.481312174090544	1		559	640	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807343	3807343	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	94	431	0	ENST00000262367.5:c.3644G>A	p.Gly1215Glu	p.G1215E	ENST00000262367	NM_004380.2	1215	gGg/gAg	19/31	0.404338279003202	3	FACETS	0.563	0.5	0.63	0.281	0.25	0.315	SUBCLONAL	1	TRUE	1	0.481312174090544	3		431	861	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0029299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	142	499	0	ENST00000269305.4:c.783-1G>C		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.481312174090544	1	FACETS	0.966	0.887	1	0.966	0.887	1	CLONAL	1	TRUE	0	0.481312174090544	1		499	464	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138275	2138275	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	228	747	0	ENST00000219476.3:c.5211del	p.Ser1738ProfsTer88	p.S1738Pfs*88	ENST00000219476	NM_000548.3	1736	taC/ta	41/42	0.51831319639321	1	FACETS	0.949	0.888	1	0.949	0.888	1	CLONAL	1	TRUE	0	0.51831319639321	1		747	687	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0029302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	298	423	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.548988110847115	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.574139052391456	2		423	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577505	7577505	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs745425759	NA	P-0029302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	339	533	0	ENST00000269305.4:c.776A>T	p.Asp259Val	p.D259V	ENST00000269305	NM_001126112.2	259	gAc/gTc	7/11	0.538052459299504	2	FACETS	0.915	0.875	0.956	0.915	0.875	0.956	CLONAL	2	TRUE	0	0.574139052391456	2		533	645	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123685	11123685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	405	565	1	ENST00000358026.2:c.2335G>A	p.Asp779Asn	p.D779N	ENST00000358026	NM_001128849.1	779	Gac/Aac	16/36	0.574139052391456	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.574139052391456	2		566	703	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555240	106555240	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	140	450	0	ENST00000369096.4:c.2357C>T	p.Ser786Phe	p.S786F	ENST00000369096	NM_001198.3	786	tCc/tTc	7/7	0.525595522044422	3	FACETS	0.893	0.815	0.975	0.446	0.407	0.488	CLONAL	1	TRUE	1	0.574139052391456	3		450	703	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	67	494	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.431	0.376	0.49	0.431	0.376	0.49	SUBCLONAL	1	TRUE	1	0.817915901174985	2		494	380	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	31	768	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.172	0.139	0.21	0.172	0.139	0.21	SUBCLONAL	1	TRUE	1	0.817915901174985	2		768	440	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2492096	2492097	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs772088410	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	53	638	1	ENST00000355716.4:c.500dup	p.Thr169AspfsTer65	p.T169Dfs*65	ENST00000355716	NM_003820.2	165	tgc/tgCc	5/8	1	2	FACETS	0.267	0.227	0.31	0.267	0.227	0.31	SUBCLONAL	1	TRUE	1	0.817915901174985	2		639	486	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263973	104263974	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776579	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	35	220	0	ENST00000369902.3:c.71dup	p.Ala25GlyfsTer23	p.A25Gfs*23	ENST00000369902	NM_016169.3	22	gcc/gCcc	1/12	1	2	FACETS	0.484	0.401	0.574	0.484	0.401	0.574	SUBCLONAL	1	TRUE	1	0.817915901174985	2		220	177	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	89	648	4	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	0.533	0.476	0.594	0.533	0.476	0.594	SUBCLONAL	1	TRUE	1	0.817915901174985	2		652	408	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735466	40735466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182388300	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	96	536	2	ENST00000373198.4:c.3407G>A	p.Arg1136His	p.R1136H	ENST00000373198	NM_133170.3	1136	cGt/cAt	25/32	1	2	FACETS	0.558	0.5	0.618	0.558	0.5	0.618	SUBCLONAL	1	TRUE	1	0.817915901174985	2		538	421	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	83	422	7	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.54	0.479	0.603	0.54	0.479	0.603	SUBCLONAL	1	TRUE	1	0.817915901174985	2		429	376	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395737	45395737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	57	308	0	ENST00000262160.6:c.397C>T	p.Arg133Cys	p.R133C	ENST00000262160	NM_005901.5	133	Cgc/Tgc	4/11	1	2	FACETS	0.451	0.389	0.517	0.451	0.389	0.517	SUBCLONAL	1	TRUE	1	0.817915901174985	2		308	309	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424734	47424734	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	23	564	0	ENST00000377045.4:c.547del	p.Gln183ArgfsTer109	p.Q183Rfs*109	ENST00000377045	NM_001654.4	181	aCc/ac	6/16	1	2	FACETS	0.13	0.101	0.165	0.13	0.101	0.165	SUBCLONAL	1	TRUE	1	0.817915901174985	2		564	431	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390736	139390736	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	107	809	8	ENST00000277541.6:c.7455del	p.Ser2486ArgfsTer103	p.S2486Rfs*103	ENST00000277541	NM_017617.3	2485	ccC/cc	34/34	1	2	FACETS	0.518	0.467	0.572	0.518	0.467	0.572	SUBCLONAL	1	TRUE	1	0.817915901174985	2		817	505	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591105	67591107	+	inframe_deletion	In_Frame_Del	DEL	TAA	TAA	-	novel	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	66	324	0	ENST00000274335.5:c.1698_1700del	p.Lys567del	p.K567del	ENST00000274335		566	atTAAa/ata	12/15	1	2	FACETS	0.614	0.538	0.693	0.614	0.538	0.693	SUBCLONAL	1	TRUE	1	0.817915901174985	2		324	263	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405954	157405954	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	36	368	0	ENST00000346085.5:c.2201del	p.Gly734AlafsTer11	p.G734Afs*11	ENST00000346085	NM_020732.3	732	ccG/cc	6/20	1	2	FACETS	0.241	0.198	0.289	0.241	0.198	0.289	SUBCLONAL	1	TRUE	1	0.817915901174985	2		368	365	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991757	72991758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760959844	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	48	335	1	ENST00000268489.5:c.2287dup	p.Glu763GlyfsTer26	p.E763Gfs*26	ENST00000268489	NM_006885.3	763	gag/gGag	2/10	1	2	FACETS	0.435	0.37	0.505	0.435	0.37	0.505	SUBCLONAL	1	TRUE	1	0.817915901174985	2		336	270	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900329	101900329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	58	302	0	ENST00000374994.4:c.763C>T	p.Arg255Cys	p.R255C	ENST00000374994	NM_004612.2	255	Cgt/Tgt	4/9	1	2	FACETS	0.561	0.486	0.639	0.561	0.486	0.639	SUBCLONAL	1	TRUE	1	0.817915901174985	2		302	253	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828579	72828579	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	74	517	3	ENST00000268489.5:c.8002C>T	p.Arg2668Ter	p.R2668*	ENST00000268489	NM_006885.3	2668	Cga/Tga	9/10	1	2	FACETS	0.433	0.38	0.489	0.433	0.38	0.489	SUBCLONAL	1	TRUE	1	0.817915901174985	2		520	418	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	130	874	7	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.592	0.539	0.647	0.592	0.539	0.647	SUBCLONAL	1	TRUE	1	0.817915901174985	2		881	537	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107175	27107175	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	71	408	1	ENST00000324856.7:c.6787del	p.Val2263TyrfsTer4	p.V2263Yfs*4	ENST00000324856	NM_006015.4	2262	tcG/tc	20/20	1	2	FACETS	0.451	0.395	0.51	0.451	0.395	0.51	SUBCLONAL	1	TRUE	1	0.817915901174985	2		409	385	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518493	69518493	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	65	325	1	ENST00000294312.3:c.152G>C	p.Gly51Ala	p.G51A	ENST00000294312	NM_005117.2	51	gGc/gCc	1/3	1	2	FACETS	0.631	0.553	0.713	0.631	0.553	0.713	SUBCLONAL	1	TRUE	1	0.817915901174985	2		326	252	SUCCESS
APC	324	MSKCC	GRCh37	5	112174213	112174214	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554084587	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	33	341	0	ENST00000257430.4:c.2926dup	p.Arg976LysfsTer9	p.R976Kfs*9	ENST00000257430	NM_000038.5	974	-/A	16/16	1	2	FACETS	0.242	0.197	0.292	0.242	0.197	0.292	SUBCLONAL	1	TRUE	1	0.817915901174985	2		341	334	SUCCESS
APC	324	MSKCC	GRCh37	5	112154804	112154805	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	22	498	0	ENST00000257430.4:c.1079dup	p.Leu360PhefsTer5	p.L360Ffs*5	ENST00000257430	NM_000038.5	359	ctt/cTtt	10/16	1	2	FACETS	0.134	0.103	0.169	0.134	0.103	0.169	SUBCLONAL	1	TRUE	1	0.817915901174985	2		498	402	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178257	56178258	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	50	322	1	ENST00000399503.3:c.3236dup	p.Asn1079LysfsTer2	p.N1079Kfs*2	ENST00000399503	NM_005921.1	1077	tca/tcAa	14/20	1	2	FACETS	0.47	0.402	0.544	0.47	0.402	0.544	SUBCLONAL	1	TRUE	1	0.817915901174985	2		323	260	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023752	27023753	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	41	311	2	ENST00000324856.7:c.862dup	p.Gln288ProfsTer112	p.Q288Pfs*112	ENST00000324856	NM_006015.4	286	-/C	1/20	1	2	FACETS	0.477	0.402	0.56	0.477	0.402	0.56	SUBCLONAL	1	TRUE	1	0.817915901174985	2		313	210	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28601396	28601396	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1426669113	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	79	541	1	ENST00000253063.3:c.1081C>T	p.Gln361Ter	p.Q361*	ENST00000253063	NM_031459.4	361	Cag/Tag	8/10	1	2	FACETS	0.459	0.405	0.516	0.459	0.405	0.516	SUBCLONAL	1	TRUE	1	0.817915901174985	2		542	421	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310541	65310541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	77	432	0	ENST00000342505.4:c.2147G>A	p.Cys716Tyr	p.C716Y	ENST00000342505	NM_002227.2	716	tGt/tAt	16/25	1	2	FACETS	0.544	0.481	0.611	0.544	0.481	0.611	SUBCLONAL	1	TRUE	1	0.817915901174985	2		432	346	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65311269	65311269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1204670695	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	59	401	2	ENST00000342505.4:c.2042G>A	p.Arg681Gln	p.R681Q	ENST00000342505	NM_002227.2	681	cGg/cAg	15/25	1	2	FACETS	0.445	0.385	0.51	0.445	0.385	0.51	SUBCLONAL	1	TRUE	1	0.817915901174985	2		403	324	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690848	89690848	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	57	268	0	ENST00000371953.3:c.253+2T>G		p.X85_splice	ENST00000371953	NM_000314.4	85			1	2	FACETS	0.518	0.448	0.593	0.518	0.448	0.593	SUBCLONAL	1	TRUE	1	0.817915901174985	2		268	269	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466019	69466019	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	93	685	0	ENST00000227507.2:c.857C>G	p.Thr286Arg	p.T286R	ENST00000227507	NM_053056.2	286	aCa/aGa	5/5	1	2	FACETS	0.509	0.454	0.566	0.509	0.454	0.566	SUBCLONAL	1	TRUE	1	0.817915901174985	2		685	447	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942152	71942152	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	65	772	0	ENST00000298229.2:c.1416G>T	p.Gln472His	p.Q472H	ENST00000298229	NM_001567.3	472	caG/caT	12/28	1	2	FACETS	0.306	0.266	0.35	0.306	0.266	0.35	SUBCLONAL	1	TRUE	1	0.817915901174985	2		772	519	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71947005	71947005	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	97	791	2	ENST00000298229.2:c.2857del	p.Arg953GlyfsTer5	p.R953Gfs*5	ENST00000298229	NM_001567.3	952	Ccc/cc	25/28	1	2	FACETS	0.481	0.43	0.535	0.481	0.43	0.535	SUBCLONAL	1	TRUE	1	0.817915901174985	2		793	493	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343553	118343553	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	59	347	0	ENST00000534358.1:c.1679C>A	p.Ser560Tyr	p.S560Y	ENST00000534358	NM_005933.3	560	tCt/tAt	3/36	1	2	FACETS	0.462	0.4	0.529	0.462	0.4	0.529	SUBCLONAL	1	TRUE	1	0.817915901174985	2		347	312	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431679	49431680	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	88	673	1	ENST00000301067.7:c.9459dup	p.Leu3154AlafsTer22	p.L3154Afs*22	ENST00000301067	NM_003482.3	3153	-/G	34/54	1	2	FACETS	0.499	0.444	0.557	0.499	0.444	0.557	SUBCLONAL	1	TRUE	1	0.817915901174985	2		674	431	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433998	49433999	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	71	706	1	ENST00000301067.7:c.7554dup	p.Val2519CysfsTer136	p.V2519Cfs*136	ENST00000301067	NM_003482.3	2518	-/T	31/54	1	2	FACETS	0.361	0.316	0.41	0.361	0.316	0.41	SUBCLONAL	1	TRUE	1	0.817915901174985	2		707	481	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438318	110438318	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	31	171	0	ENST00000375856.3:c.83A>G	p.Asn28Ser	p.N28S	ENST00000375856	NM_003749.2	28	aAc/aGc	1/2	1	2	FACETS	0.538	0.441	0.643	0.538	0.441	0.643	SUBCLONAL	1	TRUE	1	0.817915901174985	2		171	141	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543339	65543339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	28	507	0	ENST00000358664.4:c.338C>T	p.Thr113Ile	p.T113I	ENST00000358664	NM_002382.4	113	aCc/aTc	5/5	1	2	FACETS	0.184	0.147	0.227	0.184	0.147	0.227	SUBCLONAL	1	TRUE	1	0.817915901174985	2		507	372	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136269	2136269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777592623	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	81	655	4	ENST00000219476.3:c.4738C>T	p.Arg1580Trp	p.R1580W	ENST00000219476	NM_000548.3	1580	Cgg/Tgg	37/42	NA	2	FACETS	0.474	0.419	0.532			1	INDETERMINATE	1	TRUE	NA	0.817915901174985	2		659	418	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779331	3779331	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	93	543	2	ENST00000262367.5:c.5717del	p.Pro1906LeufsTer9	p.P1906Lfs*9	ENST00000262367	NM_004380.2	1906	cCt/ct	31/31	1	2	FACETS	0.533	0.476	0.592	0.533	0.476	0.592	SUBCLONAL	1	TRUE	1	0.817915901174985	2		545	427	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532559	63532559	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	113	625	2	ENST00000307078.5:c.2020C>A	p.Pro674Thr	p.P674T	ENST00000307078	NM_004655.3	674	Ccc/Acc	8/11	1	2	FACETS	0.579	0.524	0.637	0.579	0.524	0.637	SUBCLONAL	1	TRUE	1	0.817915901174985	2		627	477	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216968	2216970	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs777625749	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	91	689	2	ENST00000398665.3:c.2425_2427del	p.Glu809del	p.E809del	ENST00000398665	NM_032482.2	808	aAGGag/aag	21/28	1	2	FACETS	0.461	0.41	0.514	0.461	0.41	0.514	SUBCLONAL	1	TRUE	1	0.817915901174985	2		691	483	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302381	15302381	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	101	795	2	ENST00000263388.2:c.890G>A	p.Gly297Asp	p.G297D	ENST00000263388	NM_000435.2	297	gGc/gAc	6/33	1	2	FACETS	0.488	0.438	0.541	0.488	0.438	0.541	SUBCLONAL	1	TRUE	1	0.817915901174985	2		797	506	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224340	36224340	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1568382485	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	68	739	0	ENST00000222270.7:c.6895del	p.Arg2299GlyfsTer26	p.R2299Gfs*26	ENST00000222270	NM_014727.1	2297	gCc/gc	28/37	1	2	FACETS	0.316	0.275	0.36	0.316	0.275	0.36	SUBCLONAL	1	TRUE	1	0.817915901174985	2		739	527	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967012	25967012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	73	558	2	ENST00000435504.4:c.2194G>A	p.Ala732Thr	p.A732T	ENST00000435504		732	Gca/Aca	13/13	1	2	FACETS	0.407	0.357	0.46	0.407	0.357	0.46	SUBCLONAL	1	TRUE	1	0.817915901174985	2		560	439	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73113287	73113287	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	21	171	0	ENST00000356692.5:c.632del	p.Asn211IlefsTer15	p.N211Ifs*15	ENST00000356692		210	Aaa/aa	7/9	1	2	FACETS	0.284	0.219	0.357	0.284	0.219	0.357	SUBCLONAL	1	TRUE	1	0.817915901174985	2		171	181	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950823	38950823	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	34	157	1	ENST00000357387.3:c.3128-1G>T		p.X1043_splice	ENST00000357387	NM_152756.3	1043			1	2	FACETS	0.52	0.43	0.617	0.52	0.43	0.617	SUBCLONAL	1	TRUE	1	0.817915901174985	2		158	160	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843224	128843224	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	50	483	0	ENST00000249373.3:c.332-1G>T		p.X111_splice	ENST00000249373	NM_005631.4	111			1	2	FACETS	0.327	0.278	0.38	0.327	0.278	0.38	SUBCLONAL	1	TRUE	1	0.817915901174985	2		483	374	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852163	128852163	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	59	763	0	ENST00000249373.3:c.2235G>T	p.Gln745His	p.Q745H	ENST00000249373	NM_005631.4	745	caG/caT	12/12	1	2	FACETS	0.306	0.263	0.352	0.306	0.263	0.352	SUBCLONAL	1	TRUE	1	0.817915901174985	2		763	472	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191805	123191805	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	61	347	0	ENST00000218089.9:c.1400del	p.Phe467SerfsTer3	p.F467Sfs*3	ENST00000218089	NM_001042749.1	465	gTt/gt	15/35	1	2	FACETS	0.455	0.395	0.519	0.455	0.395	0.519	SUBCLONAL	1	TRUE	1	0.817915901174985	2		347	328	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0029304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	49	538	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.586195843110382	3	FACETS	0.663	0.564	0.771	0.332	0.282	0.386	SUBCLONAL	1	TRUE	1	0.586195843110382	3		538	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579321	7579322	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs587780067	NA	P-0029304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	487	551	0	ENST00000269305.4:c.365_366del	p.Val122AspfsTer26	p.V122Dfs*26	ENST00000269305	NM_001126112.2	122	gTG/g	4/11	0.586195843110382	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.586195843110382	2		551	763	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175217	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	133	215	0	ENST00000257430.4:c.3929dup	p.Ile1311AspfsTer4	p.I1311Dfs*4	ENST00000257430	NM_000038.5	1309	gaa/gAaa	16/16	0.586195843110382	3	FACETS	0.981	0.907	1	0.981	0.907	1	CLONAL	2	TRUE	1	0.586195843110382	3		215	299	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223252	5223252	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763535247	NA	P-0029304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	260	645	2	ENST00000357368.4:c.2551C>T	p.Arg851Cys	p.R851C	ENST00000357368	NM_002850.3	851	Cgc/Tgc	18/38	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.586195843110382	2		647	860	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	140	404	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.99	0.916	1	0.99	0.916	1	CLONAL	1	TRUE	1	0.867211833030344	2		404	326	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913250	NA	P-0029306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	204	291	1	ENST00000369535.4:c.34G>A	p.Gly12Ser	p.G12S	ENST00000369535	NM_002524.4	12	Ggt/Agt	2/7	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.867211833030344	2		292	444	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220274	55220274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	344	615	0	ENST00000275493.2:c.664C>T	p.Arg222Cys	p.R222C	ENST00000275493	NM_005228.3	222	Cgc/Tgc	6/28	1	2	FACETS	0.776	0.736	0.817	0.776	0.736	0.817	SUBCLONAL	1	TRUE	1	0.867211833030344	2		615	1022	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413214	139413214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	69	706	0	ENST00000277541.6:c.928G>A	p.Gly310Arg	p.G310R	ENST00000277541	NM_017617.3	310	Ggg/Agg	6/34	1	2	FACETS	0.136	0.117	0.156	0.136	0.117	0.156	SUBCLONAL	1	TRUE	1	0.867211833030344	2		706	1172	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141492	11141492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	46	544	0	ENST00000358026.2:c.3469C>T	p.Arg1157Trp	p.R1157W	ENST00000358026	NM_001128849.1	1157	Cgg/Tgg	25/36	1	2	FACETS	0.121	0.101	0.143	0.121	0.101	0.143	SUBCLONAL	1	TRUE	1	0.867211833030344	2		544	874	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156719	20156719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	225	159	0	ENST00000379607.5:c.38G>A	p.Arg13His	p.R13H	ENST00000379607	NM_001412.3	13	cGc/cAc	2/7	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.867211833030344	1		159	265	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030387	49030387	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373601944	NA	P-0029306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	133	353	0	ENST00000267163.4:c.1862G>A	p.Arg621His	p.R621H	ENST00000267163	NM_000321.2	621	cGt/cAt	19/27	1	2	FACETS	0.673	0.615	0.732	0.673	0.615	0.732	SUBCLONAL	1	TRUE	1	0.867211833030344	2		353	456	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341329	89341329	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	36	318	0	ENST00000301030.4:c.7606C>T	p.Arg2536Trp	p.R2536W	ENST00000301030	NM_001256183.1	2536	Cgg/Tgg	11/13	1	2	FACETS	0.158	0.13	0.191	0.158	0.13	0.191	SUBCLONAL	1	TRUE	1	0.867211833030344	2		318	524	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650753	67650753	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	368	497	0	ENST00000264010.4:c.1058G>T	p.Cys353Phe	p.C353F	ENST00000264010	NM_006565.3	353	tGt/tTt	5/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.867211833030344	2		497	803	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350537	89350538	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	474	609	0	ENST00000301030.4:c.2412dup	p.Glu805ArgfsTer5	p.E805Rfs*5	ENST00000301030	NM_001256183.1	804	-/A	9/13	0.667581741126698	2	FACETS	1	0.996	1	0.643	0.619	0.667	CLONAL	1	TRUE	0	0.867211833030344	2		609	850	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923040	39923041	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0029306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	342	243	0	ENST00000378444.4:c.3666_3667dup	p.Ser1223CysfsTer16	p.S1223Cfs*16	ENST00000378444	NM_001123385.1	1223	tcg/tGTcg	8/15	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.867211833030344	1		243	414	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040937	47040938	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0029306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	437	390	0	ENST00000377604.3:c.1469_1470del	p.Ser490CysfsTer27	p.S490Cfs*27	ENST00000377604	NM_001204468.1	489	gaCTct/gact	14/24	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.867211833030344	1		390	536	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0029309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	129	344	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.964	1	1	0.993	1	CLONAL	3	TRUE	1	0.237586396246273	2		345	333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0029309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	343	489	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.916	0.872	0.96	1	0.997	1	CLONAL	4	TRUE	1	0.237586396246273	2		489	788	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1555525367	NA	P-0029309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	251	488	0	ENST00000269305.4:c.783-1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	1	0.941	1	1	0.996	1	CLONAL	3	TRUE	1	0.237586396246273	2		488	704	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36265225	36265225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	71	171	0	ENST00000300305.3:c.94C>T	p.His32Tyr	p.H32Y	ENST00000300305		32	Cac/Tac	2/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.237586396246273	2		171	433	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940087	76940087	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0029309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	237	413	0	ENST00000373344.5:c.663-2A>C		p.X221_splice	ENST00000373344	NM_000489.3	221			1	2	FACETS	0.892	0.84	0.945	1	0.996	1	CLONAL	4	TRUE	1	0.237586396246273	2		413	559	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854890	76854890	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	87	417	0	ENST00000373344.5:c.5946del	p.Lys1982AsnfsTer33	p.K1982Nfs*33	ENST00000373344	NM_000489.3	1982	aaA/aa	25/35	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.21261470157708	2		417	683	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30326011	30326011	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	34	307	0	ENST00000322652.5:c.2209del	p.Gln737LysfsTer7	p.Q737Kfs*7	ENST00000322652	NM_015355.2	737	Caa/aa	16/16	1	2	FACETS	0.65	0.53	0.785	0.65	0.53	0.785	SUBCLONAL	1	TRUE	1	0.21261470157708	2		307	492	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279347	38279347	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	58	669	0	ENST00000425967.3:c.1142C>G	p.Ser381Cys	p.S381C	ENST00000425967	NM_001174067.1	381	tCc/tGc	9/19	1	2	FACETS	0.534	0.457	0.618	0.534	0.457	0.618	SUBCLONAL	1	TRUE	1	0.21261470157708	2		669	1022	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	270	906	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.394916352739916	2	FACETS	1	0.989	1	0.619	0.58	0.658	CLONAL	1	TRUE	0	0.399391410416247	2		906	1093	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	72	768	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.38505337232468	2	FACETS	0.416	0.363	0.474	0.208	0.181	0.237	SUBCLONAL	1	TRUE	0	0.399391410416247	2		768	866	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	44	409	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	0.336634026288657	2	FACETS	0.299	0.249	0.353	0.149	0.124	0.177	SUBCLONAL	1	TRUE	0	0.399391410416247	2		411	738	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1023835002	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	152	339	0	ENST00000558401.1:c.1A>G	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Gtg	1/4	0.347130290629102	2	FACETS	1	0.988	1	0.722	0.664	0.782	CLONAL	1	TRUE	0	0.399391410416247	2		339	527	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198272771	198272771	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	34	537	1	ENST00000335508.6:c.1190G>A	p.Arg397His	p.R397H	ENST00000335508	NM_012433.2	397	cGc/cAc	9/25	0.394916352739916	2	FACETS	0.352	0.287	0.425	0.176	0.143	0.213	SUBCLONAL	1	TRUE	0	0.399391410416247	2		538	484	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119562107	119562107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139402886	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	75	272	1	ENST00000316626.5:c.1229C>T	p.Ala410Val	p.A410V	ENST00000316626		410	gCg/gTg	11/12	0.336634026288657	2	FACETS	0.909	0.801	1	0.455	0.4	0.513	CLONAL	1	TRUE	0	0.399391410416247	2		273	413	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796955	42796955	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149948572	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	606	856	0	ENST00000575354.2:c.3413C>T	p.Pro1138Leu	p.P1138L	ENST00000575354	NM_015125.3	1138	cCg/cTg	14/20	0.394916352739916	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.399391410416247	2		856	1428	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	365	677	0	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	0.394916352739916	2	FACETS	0.941	0.895	0.988	0.941	0.895	0.988	CLONAL	2	TRUE	0	0.399391410416247	2		677	971	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191507	10191507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs5030821	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	348	432	0	ENST00000256474.2:c.500G>A	p.Arg167Gln	p.R167Q	ENST00000256474	NM_000551.3	167	cGg/cAg	3/3	0.353354780104078	3	FACETS	0.879	0.837	0.921	0.879	0.837	0.921	CLONAL	3	TRUE	0	0.399391410416247	3		432	793	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259173	89259173	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	40	336	2	ENST00000336596.2:c.317G>A	p.Cys106Tyr	p.C106Y	ENST00000336596	NM_005233.5	106	tGc/tAc	3/17	0.336634026288657	2	FACETS	0.415	0.344	0.493	0.207	0.172	0.247	SUBCLONAL	1	TRUE	0	0.399391410416247	2		338	483	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796882	42796883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761345552	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	222	809	0	ENST00000575354.2:c.3347dup	p.Ser1117LysfsTer34	p.S1117Kfs*34	ENST00000575354	NM_015125.3	1114	gcc/gCcc	14/20	0.394916352739916	2	FACETS	0.859	0.798	0.923	0.43	0.399	0.462	CLONAL	1	TRUE	0	0.399391410416247	2		809	1294	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385113	41385113	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	223	586	0	ENST00000373198.4:c.848T>A	p.Leu283Gln	p.L283Q	ENST00000373198	NM_133170.3	283	cTg/cAg	6/32	0.353354780104078	3	FACETS	1	0.989	1	0.437	0.407	0.469	CLONAL	1	TRUE	0	0.399391410416247	3		586	1021	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222978	5222978	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293966082	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	210	442	0	ENST00000357368.4:c.2825C>T	p.Ser942Leu	p.S942L	ENST00000357368	NM_002850.3	942	tCg/tTg	18/38	0.347130290629102	2	FACETS	1	0.991	1	0.728	0.679	0.779	CLONAL	1	TRUE	0	0.399391410416247	2		442	722	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214581	5214581	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	182	615	0	ENST00000357368.4:c.4485G>C	p.Glu1495Asp	p.E1495D	ENST00000357368	NM_002850.3	1495	gaG/gaC	29/38	0.347130290629102	2	FACETS	1	0.98	1	0.583	0.539	0.629	CLONAL	1	TRUE	0	0.399391410416247	2		615	781	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871728	35871728	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528542318	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	108	444	1	ENST00000216797.5:c.778C>T	p.Arg260Cys	p.R260C	ENST00000216797	NM_020529.2	260	Cgc/Tgc	5/6	0.394916352739916	2	FACETS	0.639	0.573	0.709	0.32	0.286	0.355	SUBCLONAL	1	TRUE	0	0.399391410416247	2		445	846	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325170	123325170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371358242	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	80	424	0	ENST00000358487.5:c.158C>T	p.Ala53Val	p.A53V	ENST00000358487	NM_000141.4	53	gCg/gTg	3/18	0.394916352739916	2	FACETS	0.536	0.471	0.605	0.268	0.235	0.303	SUBCLONAL	1	TRUE	0	0.399391410416247	2		424	748	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638915	176638915	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	178	569	0	ENST00000439151.2:c.3515A>C	p.Lys1172Thr	p.K1172T	ENST00000439151	NM_022455.4	1172	aAg/aCg	5/23	0.347130290629102	2	FACETS	0.885	0.815	0.958	0.443	0.407	0.479	CLONAL	1	TRUE	0	0.399391410416247	2		569	1007	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950303	38950303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561445386	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	49	333	0	ENST00000357387.3:c.3647G>A	p.Arg1216His	p.R1216H	ENST00000357387	NM_152756.3	1216	cGt/cAt	31/38	0.294920868868004	3	FACETS	0.452	0.382	0.529			1	SUBCLONAL	1	TRUE	NA	0.399391410416247	3		333	651	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392144	81392145	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	13	246	0	ENST00000222390.5:c.132dup	p.Ser45IlefsTer28	p.S45Ifs*28	ENST00000222390	NM_000601.4	44	-/A	2/18	1	2	FACETS	0.693	0.5	0.92	0.693	0.5	0.92	SUBCLONAL	1	TRUE	1	0.399391410416247	2		246	94	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38184259	38184259	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	185	432	0	ENST00000317025.8:c.1697C>G	p.Ser566Cys	p.S566C	ENST00000317025	NM_023034.1	566	tCt/tGt	7/24	0.353354780104078	3	FACETS	0.924	0.865	0.983	0.924	0.865	0.983	CLONAL	3	TRUE	0	0.399391410416247	3		432	401	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561289	9561289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985722631	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	86	386	0	ENST00000353224.5:c.493G>A	p.Ala165Thr	p.A165T	ENST00000353224	NM_177990.2	165	Gca/Aca	4/10	0.353354780104078	3	FACETS	0.799	0.707	0.897	0.266	0.235	0.299	SUBCLONAL	1	TRUE	0	0.399391410416247	3		386	647	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258521	19258521	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	139	745	1	ENST00000162023.5:c.379C>T	p.Arg127Ter	p.R127*	ENST00000162023		127	Cga/Tga	8/13	0.394916352739916	2	FACETS	0.625	0.568	0.686	0.313	0.284	0.343	SUBCLONAL	1	TRUE	0	0.399391410416247	2		746	1113	SUCCESS
APC	324	MSKCC	GRCh37	5	112154771	112154771	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1314843920	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	116	440	0	ENST00000257430.4:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000257430	NM_000038.5	348	Cga/Tga	10/16	0.347130290629102	2	FACETS	0.85	0.768	0.938	0.425	0.384	0.469	CLONAL	1	TRUE	0	0.399391410416247	2		440	683	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645919	67645919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	216	531	2	ENST00000264010.4:c.847C>T	p.Arg283Cys	p.R283C	ENST00000264010	NM_006565.3	283	Cgt/Tgt	4/12	0.394916352739916	2	FACETS	1	0.99	1	0.67	0.624	0.717	CLONAL	1	TRUE	0	0.399391410416247	2		533	807	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944842	31944842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	167	963	0	ENST00000340398.3:c.259G>A	p.Ala87Thr	p.A87T	ENST00000340398	NM_001013699.2	87	Gca/Aca	1/1	0.38505337232468	2	FACETS	0.673	0.617	0.732	0.337	0.308	0.366	SUBCLONAL	1	TRUE	0	0.399391410416247	2		963	1242	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120572	2120572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934872	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	458	695	1	ENST00000219476.3:c.1832G>A	p.Arg611Gln	p.R611Q	ENST00000219476	NM_000548.3	611	cGg/cAg	17/42	0.394916352739916	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.399391410416247	2		696	1122	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212575	36212575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769208559	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	408	836	2	ENST00000222270.7:c.2326C>T	p.Arg776Trp	p.R776W	ENST00000222270	NM_014727.1	776	Cgg/Tgg	3/37	0.394916352739916	2	FACETS	1	0.994	1	0.674	0.641	0.709	CLONAL	1	TRUE	0	0.399391410416247	2		838	1515	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256174	123256174	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1564875549	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	232	460	0	ENST00000358487.5:c.1735C>T	p.Arg579Trp	p.R579W	ENST00000358487	NM_000141.4	579	Cgg/Tgg	13/18	0.394916352739916	2	FACETS	1	0.991	1	0.682	0.637	0.728	CLONAL	1	TRUE	0	0.399391410416247	2		460	852	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446261	187446261	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs535108808	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	125	529	1	ENST00000232014.4:c.1427C>T	p.Thr476Met	p.T476M	ENST00000232014	NM_001130845.1	476	aCg/aTg	6/10	0.336634026288657	2	FACETS	0.72	0.652	0.793	0.36	0.326	0.397	SUBCLONAL	1	TRUE	0	0.399391410416247	2		530	869	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394129	31394129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1330224703	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	148	358	2	ENST00000328111.2:c.2416G>A	p.Glu806Lys	p.E806K	ENST00000328111	NM_006892.3	806	Gaa/Aaa	22/23	0.353354780104078	3	FACETS	1	0.962	1	0.365	0.333	0.398	CLONAL	1	TRUE	0	0.399391410416247	3		360	813	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627217	37627217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370304179	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	71	475	0	ENST00000447079.4:c.1132C>T	p.Arg378Cys	p.R378C	ENST00000447079	NM_015083.1	378	Cgc/Tgc	2/14	0.38505337232468	2	FACETS	0.527	0.459	0.6	0.263	0.229	0.3	SUBCLONAL	1	TRUE	0	0.399391410416247	2		475	675	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194635	29194635	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147027609	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	277	846	0	ENST00000240100.2:c.1093G>A	p.Val365Ile	p.V365I	ENST00000240100	NM_001394.6	365	Gtc/Atc	4/4	0.353354780104078	3	FACETS	1	0.988	1	0.405	0.379	0.432	CLONAL	1	TRUE	0	0.399391410416247	3		846	1369	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640200	3640200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs974413437	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	144	871	0	ENST00000294008.3:c.3439G>A	p.Glu1147Lys	p.E1147K	ENST00000294008	NM_032444.2	1147	Gaa/Aaa	12/15	0.394916352739916	2	FACETS	0.539	0.49	0.591	0.27	0.245	0.296	SUBCLONAL	1	TRUE	0	0.399391410416247	2		871	1337	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422455	47422455	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398289359	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	145	293	0	ENST00000377045.4:c.89G>A	p.Arg30His	p.R30H	ENST00000377045	NM_001654.4	30	cGc/cAc	2/16	0.399391410416247	2	FACETS	0.862	0.787	0.941			1	CLONAL	1	TRUE	NA	0.399391410416247	2		293	842	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260969	16260969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs529018913	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	33	414	1	ENST00000375759.3:c.8234C>T	p.Ala2745Val	p.A2745V	ENST00000375759	NM_015001.2	2745	gCg/gTg	11/15	0.336634026288657	2	FACETS	0.288	0.234	0.349	0.144	0.117	0.175	SUBCLONAL	1	TRUE	0	0.399391410416247	2		415	574	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563278	21563278	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs750461080	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	159	745	0	ENST00000382592.4:c.641A>G	p.Tyr214Cys	p.Y214C	ENST00000382592	NM_014572.2	214	tAc/tGc	4/8	0.399391410416247	1	FACETS	0.548	0.501	0.597	0.548	0.501	0.597	SUBCLONAL	1	TRUE	0	0.399391410416247	1		745	1163	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099382	27099382	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	127	541	0	ENST00000324856.7:c.3619C>A	p.Pro1207Thr	p.P1207T	ENST00000324856	NM_006015.4	1207	Cca/Aca	14/20	0.336634026288657	2	FACETS	0.772	0.699	0.848	0.386	0.349	0.424	SUBCLONAL	1	TRUE	0	0.399391410416247	2		541	824	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903697	114903697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465566182	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	205	558	0	ENST00000543371.1:c.701C>T	p.Pro234Leu	p.P234L	ENST00000543371	NM_001198531.1	234	cCg/cTg	7/14	0.394916352739916	2	FACETS	1	0.973	1	0.548	0.509	0.589	CLONAL	1	TRUE	0	0.399391410416247	2		558	936	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572041	64572041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	269	630	1	ENST00000312049.6:c.1598G>A	p.Ser533Asn	p.S533N	ENST00000312049	NM_130799.2	533	aGc/aAc	10/10	0.353354780104078	3	FACETS	0.777	0.729	0.826	0.518	0.486	0.551	SUBCLONAL	2	TRUE	0	0.399391410416247	3		631	1040	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948527	71948527	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749369759	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	175	716	4	ENST00000298229.2:c.3239G>A	p.Arg1080His	p.R1080H	ENST00000298229	NM_001567.3	1080	cGt/cAt	26/28	0.353354780104078	3	FACETS	0.846	0.777	0.918	0.282	0.259	0.306	CLONAL	1	TRUE	0	0.399391410416247	3		720	1243	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285561	46285561	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	74	215	0	ENST00000334344.6:c.4923-2A>G		p.X1641_splice	ENST00000334344	NM_152641.2	1641			0.399391410416247	3	FACETS	1	0.976	1			1	CLONAL	1	TRUE	NA	0.399391410416247	3		215	301	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447841	49447841	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748834953	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	648	542	0	ENST00000301067.7:c.593C>T	p.Ala198Val	p.A198V	ENST00000301067	NM_003482.3	198	gCg/gTg	5/54	0.399391410416247	3	FACETS	1	0.988	1			1	CLONAL	3	TRUE	NA	0.399391410416247	3		542	1242	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549433	21549433	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	185	357	0	ENST00000382592.4:c.2843del	p.Ile948ThrfsTer20	p.I948Tfs*20	ENST00000382592	NM_014572.2	948	aTc/ac	8/8	0.399391410416247	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.399391410416247	1		357	513	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712824	43712824	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1201648831	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	299	673	0	ENST00000382044.4:c.4360C>T	p.Arg1454Ter	p.R1454*	ENST00000382044	NM_001141980.1	1454	Cga/Tga	21/28	0.347130290629102	2	FACETS	0.79	0.745	0.835	0.79	0.745	0.835	SUBCLONAL	2	TRUE	0	0.399391410416247	2		673	948	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654714	67654714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	41	432	0	ENST00000264010.4:c.1201C>T	p.His401Tyr	p.H401Y	ENST00000264010	NM_006565.3	401	Cat/Tat	6/12	0.394916352739916	2	FACETS	0.302	0.251	0.36	0.151	0.125	0.18	SUBCLONAL	1	TRUE	0	0.399391410416247	2		432	679	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652968	29652968	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	70	401	0	ENST00000356175.3:c.4903A>G	p.Thr1635Ala	p.T1635A	ENST00000356175	NM_000267.3	1635	Aca/Gca	36/57	0.38505337232468	2	FACETS	0.585	0.51	0.666	0.293	0.255	0.333	SUBCLONAL	1	TRUE	0	0.399391410416247	2		401	599	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685497	29685497	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs1417908560	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	22	260	0	ENST00000356175.3:c.7908-1G>T		p.X2636_splice	ENST00000356175	NM_000267.3	2636			0.38505337232468	2	FACETS	0.505	0.393	0.635	0.253	0.196	0.318	SUBCLONAL	1	TRUE	0	0.399391410416247	2		260	218	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4123850	4123850	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	70	333	0	ENST00000262948.5:c.23T>C	p.Val8Ala	p.V8A	ENST00000262948	NM_030662.3	8	gTg/gCg	1/11	0.347130290629102	2	FACETS	0.673	0.587	0.765	0.336	0.293	0.383	SUBCLONAL	1	TRUE	0	0.399391410416247	2		333	521	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245898	5245898	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376695892	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	270	822	0	ENST00000357368.4:c.877G>A	p.Val293Met	p.V293M	ENST00000357368	NM_002850.3	293	Gtg/Atg	10/38	0.347130290629102	2	FACETS	1	0.99	1	0.632	0.593	0.672	CLONAL	1	TRUE	0	0.399391410416247	2		822	1070	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024650	11024650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	272	449	1	ENST00000327064.4:c.767C>T	p.Ser256Leu	p.S256L	ENST00000327064	NM_199141.1	256	tCg/tTg	6/16	0.347130290629102	2	FACETS	0.862	0.812	0.913	0.862	0.812	0.913	CLONAL	2	TRUE	0	0.399391410416247	2		450	790	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966781	18966781	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	346	757	3	ENST00000262803.5:c.1592C>T	p.Thr531Met	p.T531M	ENST00000262803	NM_002911.3	531	aCg/aTg	12/24	0.347130290629102	2	FACETS	1	0.994	1	0.717	0.679	0.756	CLONAL	1	TRUE	0	0.399391410416247	2		760	1208	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229069	36229069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	208	656	2	ENST00000222270.7:c.7849C>T	p.Arg2617Trp	p.R2617W	ENST00000222270	NM_014727.1	2617	Cgg/Tgg	36/37	0.394916352739916	2	FACETS	0.892	0.827	0.96	0.446	0.413	0.48	CLONAL	1	TRUE	0	0.399391410416247	2		658	1168	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791224	42791224	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	71	752	0	ENST00000575354.2:c.284A>C	p.Glu95Ala	p.E95A	ENST00000575354	NM_015125.3	95	gAg/gCg	3/20	0.394916352739916	2	FACETS	0.335	0.292	0.383	0.168	0.146	0.192	SUBCLONAL	1	TRUE	0	0.399391410416247	2		752	1060	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920475	50920475	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772397517	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	176	483	1	ENST00000440232.2:c.3167C>T	p.Thr1056Met	p.T1056M	ENST00000440232	NM_002691.3	1056	aCg/aTg	26/27	0.394916352739916	2	FACETS	1	0.946	1	0.516	0.476	0.558	CLONAL	1	TRUE	0	0.399391410416247	2		484	854	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469632	25469632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1036696061	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	265	535	1	ENST00000264709.3:c.1136G>A	p.Arg379His	p.R379H	ENST00000264709	NM_175629.2	379	cGc/cAc	10/23	0.336634026288657	2	FACETS	0.797	0.75	0.846	0.797	0.75	0.846	SUBCLONAL	2	TRUE	0	0.399391410416247	2		536	832	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99162524	99162524	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1024484850	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	68	287	0	ENST00000074304.5:c.1042G>A	p.Asp348Asn	p.D348N	ENST00000074304	NM_001134224.1	348	Gat/Aat	12/26	0.394916352739916	2	FACETS	0.824	0.72	0.936	0.412	0.36	0.468	CLONAL	1	TRUE	0	0.399391410416247	2		287	413	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561523	9561523	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs201196548	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	80	442	0	ENST00000353224.5:c.259G>C	p.Glu87Gln	p.E87Q	ENST00000353224	NM_177990.2	87	Gag/Cag	4/10	0.353354780104078	3	FACETS	0.605	0.532	0.684	0.202	0.177	0.228	SUBCLONAL	1	TRUE	0	0.399391410416247	3		442	794	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39690075	39690075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1319354641	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	64	317	0	ENST00000361337.2:c.100C>T	p.Arg34Trp	p.R34W	ENST00000361337	NM_003286.2	34	Cgg/Tgg	3/21	0.353354780104078	3	FACETS	0.653	0.565	0.748	0.218	0.188	0.25	SUBCLONAL	1	TRUE	0	0.399391410416247	3		317	589	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057255	30057255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	120	549	0	ENST00000338641.4:c.737C>A	p.Pro246His	p.P246H	ENST00000338641	NM_000268.3	246	cCt/cAt	8/16	0.38505337232468	2	FACETS	0.643	0.58	0.71	0.322	0.29	0.355	SUBCLONAL	1	TRUE	0	0.399391410416247	2		549	934	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114680	73114680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778876392	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	51	426	1	ENST00000356692.5:c.1061C>T	p.Ala354Val	p.A354V	ENST00000356692		354	gCt/gTt	9/9	0.336634026288657	2	FACETS	0.694	0.592	0.805	0.347	0.296	0.403	SUBCLONAL	1	TRUE	0	0.399391410416247	2		427	368	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665096	138665096	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs758370933	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	23	259	0	ENST00000330315.3:c.469C>G	p.Pro157Ala	p.P157A	ENST00000330315	NM_023067.3	157	Ccc/Gcc	1/1	0.336634026288657	2	FACETS	0.304	0.236	0.382	0.152	0.118	0.191	SUBCLONAL	1	TRUE	0	0.399391410416247	2		259	379	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549374	187549374	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs754134821	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	114	535	0	ENST00000441802.2:c.4744T>G	p.Leu1582Val	p.L1582V	ENST00000441802	NM_005245.3	1582	Ttg/Gtg	9/27	0.399391410416247	1	FACETS	0.698	0.629	0.77	0.698	0.629	0.77	SUBCLONAL	1	TRUE	0	0.399391410416247	1		535	655	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549445	187549445	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	110	483	0	ENST00000441802.2:c.4673A>G	p.His1558Arg	p.H1558R	ENST00000441802	NM_005245.3	1558	cAc/cGc	9/27	0.399391410416247	1	FACETS	0.812	0.732	0.896	0.812	0.732	0.896	CLONAL	1	TRUE	0	0.399391410416247	1		483	543	SUCCESS
APC	324	MSKCC	GRCh37	5	112128213	112128213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	51	345	0	ENST00000257430.4:c.716C>T	p.Ala239Val	p.A239V	ENST00000257430	NM_000038.5	239	gCa/gTa	7/16	0.347130290629102	2	FACETS	0.786	0.671	0.91	0.393	0.335	0.455	CLONAL	1	TRUE	0	0.399391410416247	2		345	325	SUCCESS
APC	324	MSKCC	GRCh37	5	112170683	112170683	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	66	360	0	ENST00000257430.4:c.1779G>T	p.Trp593Cys	p.W593C	ENST00000257430	NM_000038.5	593	tgG/tgT	15/16	0.347130290629102	2	FACETS	0.778	0.677	0.885	0.389	0.338	0.443	SUBCLONAL	1	TRUE	0	0.399391410416247	2		360	425	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056104	26056104	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375520468	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	120	298	0	ENST00000343677.2:c.553G>A	p.Ala185Thr	p.A185T	ENST00000343677	NM_005319.3	185	Gct/Act	1/1	0.317348580036029	3	FACETS	1	0.978	1	0.427	0.387	0.469	CLONAL	1	TRUE	0	0.399391410416247	3		298	563	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225435	26225435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	75	223	1	ENST00000360408.1:c.53G>A	p.Arg18His	p.R18H	ENST00000360408	NM_003532.2	18	cGc/cAc	1/1	0.317348580036029	3	FACETS	1	0.947	1	0.379	0.334	0.428	CLONAL	1	TRUE	0	0.399391410416247	3		224	396	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004441	150004442	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	126	425	0	ENST00000253339.5:c.1783_1784del	p.Lys595GlufsTer3	p.K595Efs*3	ENST00000253339		595	AAg/g	3/7	0.336634026288657	2	FACETS	1	0.985	1	0.707	0.645	0.772	CLONAL	1	TRUE	0	0.399391410416247	2		425	446	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68984741	68984741	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	44	271	0	ENST00000288368.4:c.1505A>T	p.Tyr502Phe	p.Y502F	ENST00000288368	NM_024870.2	502	tAc/tTc	14/40	0.353354780104078	3	FACETS	1	0.954	1	0.454	0.385	0.528	CLONAL	1	TRUE	0	0.399391410416247	3		271	194	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141545613	141545613	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	218	754	0	ENST00000220592.5:c.2225A>G	p.His742Arg	p.H742R	ENST00000220592	NM_012154.3	742	cAc/cGc	17/19	0.38505337232468	2	FACETS	0.923	0.857	0.991	0.461	0.428	0.496	CLONAL	1	TRUE	0	0.399391410416247	2		754	1183	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841243	15841243	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	90	155	0	ENST00000307771.7:c.1327A>G	p.Ser443Gly	p.S443G	ENST00000307771	NM_005089.3	443	Agc/Ggc	11/11	0.399391410416247	2	FACETS	0.766	0.688	0.848			1	SUBCLONAL	2	TRUE	NA	0.399391410416247	2		155	294	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196821	123196821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	18	226	0	ENST00000218089.9:c.1708G>A	p.Ala570Thr	p.A570T	ENST00000218089	NM_001042749.1	570	Gcc/Acc	18/35	1	1	FACETS	0.515	0.391	0.659	0.515	0.391	0.659	SUBCLONAL	1	TRUE	0	0.399391410416247	1		226	140	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988238	36988240	+	missense_variant	Missense_Mutation	TNP	AGG	AGG	GGA	novel	NA	P-0029311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	169	428	2	ENST00000354822.5:c.413_415delinsTCC	p.Ala138_Ser139delinsValPro	p.A138_S139delinsVP	ENST00000354822	NM_001079668.2	138	gCCTct/gTCCct	2/3	0.394916352739916	2	FACETS	1	0.967	1	0.546	0.503	0.591	CLONAL	1	TRUE	0	0.399391410416247	2		430	775	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0029314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	614	1069	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.443004415458727	3	FACETS	0.984	0.952	1	0.984	0.952	1	CLONAL	3	TRUE	0	0.443004415458727	3		1071	1147	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424138	49424138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200638996	NA	P-0029314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	323	624	2	ENST00000301067.7:c.13924G>A	p.Val4642Ile	p.V4642I	ENST00000301067	NM_003482.3	4642	Gtc/Atc	42/54	0.357986913077911	2	FACETS	0.791	0.749	0.833	0.791	0.749	0.833	SUBCLONAL	2	TRUE	0	0.443004415458727	2		626	922	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076766	102076766	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	112	563	0	ENST00000282441.5:c.946del	p.Glu316ArgfsTer5	p.E316Rfs*5	ENST00000282441	NM_001130145.2	315	aaG/aa	5/9	0.372145495312511	3	FACETS	0.658	0.591	0.729	0.329	0.295	0.365	SUBCLONAL	1	TRUE	1	0.443004415458727	3		563	939	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732433	74732456	+	inframe_deletion	In_Frame_Del	DEL	GACCGAGATCGAGAACGAGTGCGG	GACCGAGATCGAGAACGAGTGCGG	-	rs760875189	NA	P-0029314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	100	296	0	ENST00000359995.5:c.453_476del	p.Arg152_Ser159del	p.R152_S159del	ENST00000359995	NM_001195427.1	151	tcCCGCACTCGTTCTCGATCTCGGTCg/tcg	2/3	0.357986913077911	2	FACETS	1	0.961	1	0.57	0.513	0.63	CLONAL	1	TRUE	0	0.443004415458727	2		296	396	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100934	41100934	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	164	474	1	ENST00000373198.4:c.1422G>T	p.Glu474Asp	p.E474D	ENST00000373198	NM_133170.3	474	gaG/gaT	8/32	0.310547514360029	4	FACETS	0.758	0.697	0.82	0.758	0.697	0.82	SUBCLONAL	2	TRUE	2	0.443004415458727	4		475	705	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0029315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	91	558	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	1	2	FACETS	0.772	0.685	0.866	0.772	0.685	0.866	SUBCLONAL	1	TRUE	1	0.289528015768135	2		558	814	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740284	162740284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1291790073	NA	P-0029315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	57	325	0	ENST00000367921.3:c.1486C>T	p.Pro496Ser	p.P496S	ENST00000367921	NM_006182.2	496	Cca/Tca	12/18	1	2	FACETS	0.865	0.744	0.997	0.865	0.744	0.997	CLONAL	1	TRUE	1	0.289528015768135	2		325	455	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850894	63850894	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	103	444	0	ENST00000279873.7:c.1672G>A	p.Gly558Arg	p.G558R	ENST00000279873	NM_032199.2	558	Ggg/Agg	10/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.289528015768135	2		444	598	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135091	11135091	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	137	851	0	ENST00000358026.2:c.3058G>C	p.Asp1020His	p.D1020H	ENST00000358026	NM_001128849.1	1020	Gat/Cat	21/36	1	2	FACETS	0.889	0.808	0.976	0.889	0.808	0.976	CLONAL	1	TRUE	1	0.289528015768135	2		851	1064	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142976	47142976	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	102	302	0	ENST00000409792.3:c.4987del	p.Thr1663ArgfsTer42	p.T1663Rfs*42	ENST00000409792	NM_014159.6	1663	Acg/cg	8/21	0.289528015768135	1	FACETS	0.993	0.89	1	0.993	0.89	1	CLONAL	1	TRUE	0	0.289528015768135	1		302	607	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950699	38950699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	44	353	0	ENST00000357387.3:c.3251C>T	p.Ser1084Leu	p.S1084L	ENST00000357387	NM_152756.3	1084	tCa/tTa	31/38	0.187552570009197	2	FACETS	0.811	0.681	0.953	0.405	0.34	0.477	CLONAL	1	TRUE	0	0.289528015768135	2		353	375	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225196	53225196	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	123	659	3	ENST00000375401.3:c.3022G>T	p.Glu1008Ter	p.E1008*	ENST00000375401	NM_004187.3	1008	Gaa/Taa	20/26	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.289528015768135	2		662	781	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142976	47142976	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029315-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	106	302	0	ENST00000409792.3:c.4987del	p.Thr1663ArgfsTer42	p.T1663Rfs*42	ENST00000409792	NM_014159.6	1663	Acg/cg	8/21	0.287605469520555	1	FACETS	0.935	0.839	1	0.935	0.839	1	CLONAL	1	TRUE	0	0.287605469520555	1		302	675	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105886	27105887	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0029315-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	38	245	0	ENST00000324856.7:c.5501_5502dup	p.Gln1835CysfsTer49	p.Q1835Cfs*49	ENST00000324856	NM_006015.4	1833	cgt/cGTgt	20/20	1	2	FACETS	0.379	0.312	0.454	0.379	0.312	0.454	SUBCLONAL	1	TRUE	1	0.287605469520555	2		245	698	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064427	30064430	+	frameshift_variant	Frame_Shift_Del	DEL	AGAA	AGAA	-	novel	NA	P-0029318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	108	406	0	ENST00000338641.4:c.993_996del	p.Arg331SerfsTer14	p.R331Sfs*14	ENST00000338641	NM_000268.3	331	AGAAag/ag	10/16	0.3	1	FACETS	0.988	0.893	1	0.988	0.893	1	CLONAL	1	TRUE	0	0.41	1		406	424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0029319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	218	1069	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.349421466500128	2	FACETS	0.989	0.927	1	0.989	0.927	1	CLONAL	2	TRUE	0	0.381228465040133	2		1071	578	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127487	55127487	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759729258	NA	P-0029319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	115	445	1	ENST00000257290.5:c.275C>T	p.Ala92Val	p.A92V	ENST00000257290	NM_006206.4	92	gCg/gTg	3/23	0.293216146107078	3	FACETS	1	0.972	1	0.401	0.362	0.442	CLONAL	1	TRUE	0	0.381228465040133	3		446	597	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874594	155874614	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCTACAGGAGGGAAGAAAGG	TTCTACAGGAGGGAAGAAAGG	-	novel	NA	P-0029319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	51	428	0	ENST00000368323.3:c.164-19_165del		p.X55_splice	ENST00000368323	NM_006912.5	55		4/6	0.298349474438599	3	FACETS	1	0.945	1	0.61	0.523	0.704	CLONAL	1	TRUE	1	0.381228465040133	3		428	261	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476327	88476327	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	78	598	0	ENST00000360948.2:c.1805A>G	p.Lys602Arg	p.K602R	ENST00000360948	NM_001012338.2	602	aAg/aGg	15/19	0.366707251802721	3	FACETS	0.924	0.814	1	0.462	0.407	0.522	CLONAL	1	TRUE	1	0.381228465040133	3		598	527	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552876	106552876	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	41	704	0	ENST00000369096.4:c.841G>T	p.Asp281Tyr	p.D281Y	ENST00000369096	NM_001198.3	281	Gat/Tat	5/7	0.307806499828006	2	FACETS	0.427	0.355	0.507	0.213	0.177	0.254	SUBCLONAL	1	TRUE	0	0.381228465040133	2		704	504	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509672	106509672	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	35	523	0	ENST00000359195.3:c.1666G>T	p.Glu556Ter	p.E556*	ENST00000359195	NM_002649.2	556	Gag/Tag	2/11	0.381228465040133	4	FACETS	0.562	0.461	0.677	0.187	0.153	0.226	SUBCLONAL	1	TRUE	1	0.381228465040133	4		523	451	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0029321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	272	532	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.122499818841402	5	FACETS	0.897	0.847	0.949			1	INDETERMINATE	3	TRUE	NA	0.489500043785505	5		532	716	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519998	NA	P-0029321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	417	507	0	ENST00000269305.4:c.581T>C	p.Leu194Pro	p.L194P	ENST00000269305	NM_001126112.2	194	cTt/cCt	6/11	0.489500043785505	2	FACETS	0.998	0.956	1	0.998	0.956	1	CLONAL	2	TRUE	0	0.489500043785505	2		507	854	SUCCESS
APC	324	MSKCC	GRCh37	5	112175531	112175532	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1554085654	NA	P-0029321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	197	285	0	ENST00000257430.4:c.4241dup	p.Ser1415LysfsTer8	p.S1415Kfs*8	ENST00000257430	NM_000038.5	1414	gta/gTta	16/16	0.489500043785505	2	FACETS	0.963	0.904	1	0.963	0.904	1	CLONAL	2	TRUE	0	0.489500043785505	2		285	418	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603006	48603006	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0029321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	184	231	0	ENST00000342988.3:c.1309-2A>G		p.X437_splice	ENST00000342988	NM_005359.5	437			0.489500043785505	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.489500043785505	2		231	369	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714418	40714418	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	116	431	0	ENST00000373198.4:c.3979A>T	p.Ile1327Phe	p.I1327F	ENST00000373198	NM_133170.3	1327	Atc/Ttc	29/32	0.325104225928528	2	FACETS	0.646	0.582	0.713	0.323	0.291	0.357	SUBCLONAL	1	TRUE	0	0.489500043785505	2		431	734	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	39	470	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.274	0.227	0.327	0.274	0.227	0.327	SUBCLONAL	1	TRUE	1	0.6	2		470	474	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	125	768	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.842	0.766	0.92	0.842	0.766	0.92	CLONAL	1	TRUE	1	0.6	2		768	495	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	143	681	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.85	0.778	0.924	0.85	0.778	0.924	CLONAL	1	TRUE	1	0.6	2		681	561	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	181	790	0	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.975	0.904	1	0.975	0.904	1	CLONAL	1	TRUE	1	0.6	2		790	619	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	110	254	2	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	1	FACETS	0.961	0.879	1	0.961	0.879	1	CLONAL	1	TRUE	0	0.6	1		256	267	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533904	63533904	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201460658	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	107	388	0	ENST00000307078.5:c.1250C>T	p.Ala417Val	p.A417V	ENST00000307078	NM_004655.3	417	gCg/gTg	6/11	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.6	2		388	348	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258927	16258928	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	189	759	0	ENST00000375759.3:c.6198dup	p.Pro2067ThrfsTer4	p.P2067Tfs*4	ENST00000375759	NM_015001.2	2064	-/A	11/15	1	2	FACETS	0.854	0.791	0.918	0.854	0.791	0.918	CLONAL	1	TRUE	1	0.6	2		759	738	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	84	331	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	NA	3	FACETS	0.91	0.809	1	0.455	0.404	0.509	INDETERMINATE	1	TRUE	1	0.6	3		332	400	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	107	331	0	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	1	2	FACETS	0.851	0.769	0.937	0.851	0.769	0.937	CLONAL	1	TRUE	1	0.6	2		331	419	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971195	13971195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777866452	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	109	350	2	ENST00000405192.2:c.734C>T	p.Ala245Val	p.A245V	ENST00000405192	NM_001163147.1	245	gCg/gTg	8/12	1	2	FACETS	0.939	0.85	1	0.939	0.85	1	CLONAL	1	TRUE	1	0.6	2		352	387	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	47	556	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	0.391	0.33	0.457	0.391	0.33	0.457	SUBCLONAL	1	TRUE	1	0.6	2		556	401	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799060	42799060	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	170	751	0	ENST00000575354.2:c.4544G>A	p.Arg1515His	p.R1515H	ENST00000575354	NM_015125.3	1515	cGc/cAc	20/20	1	2	FACETS	0.952	0.88	1	0.952	0.88	1	CLONAL	1	TRUE	1	0.6	2		751	595	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123836	46123836	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	150	243	1	ENST00000334344.6:c.102T>A	p.Phe34Leu	p.F34L	ENST00000334344	NM_152641.2	34	ttT/ttA	2/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.6	2		244	444	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	41	493	0	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	1	2	FACETS	0.241	0.2	0.286	0.241	0.2	0.286	SUBCLONAL	1	TRUE	1	0.6	2		493	568	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615691	1615691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141432924	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	153	699	2	ENST00000344749.5:c.1580G>A	p.Arg527Gln	p.R527Q	ENST00000344749	NM_001136139.2	527	cGg/cAg	17/19	1	2	FACETS	0.948	0.872	1	0.948	0.872	1	CLONAL	1	TRUE	1	0.6	2		701	538	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760024	133760024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	131	704	0	ENST00000318560.5:c.2352del	p.Arg785GlyfsTer3	p.R785Gfs*3	ENST00000318560	NM_005157.4	783	Ccc/cc	11/11	1	2	FACETS	0.771	0.703	0.843	0.771	0.703	0.843	SUBCLONAL	1	TRUE	1	0.6	2		704	566	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989345	7989345	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745541957	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	138	566	1	ENST00000319144.4:c.341G>A	p.Arg114Gln	p.R114Q	ENST00000319144	NM_001139.2	114	cGg/cAg	2/15	1	2	FACETS	0.9	0.824	0.979	0.9	0.824	0.979	CLONAL	1	TRUE	1	0.6	2		567	511	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058747	180058748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755445139	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	102	572	3	ENST00000261937.6:c.89dup	p.Thr31AspfsTer15	p.T31Dfs*15	ENST00000261937	NM_182925.4	30	ccg/ccCg	2/30	1	2	FACETS	0.8	0.72	0.884	0.8	0.72	0.884	SUBCLONAL	1	TRUE	1	0.6	2		575	425	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654856	29654856	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1049849034	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	62	277	1	ENST00000356175.3:c.5545C>T	p.Arg1849Trp	p.R1849W	ENST00000356175	NM_000267.3	1849	Cgg/Tgg	37/57	1	2	FACETS	0.78	0.681	0.885	0.78	0.681	0.885	SUBCLONAL	1	TRUE	1	0.6	2		278	265	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480396	89480396	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs369276620	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	49	261	0	ENST00000336596.2:c.2233C>T	p.Arg745Ter	p.R745*	ENST00000336596	NM_005233.5	745	Cga/Tga	13/17	1	2	FACETS	0.415	0.352	0.483	0.415	0.352	0.483	SUBCLONAL	1	TRUE	1	0.6	2		261	394	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398625	116398625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45587940	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	116	445	0	ENST00000397752.3:c.2215C>T	p.Arg739Cys	p.R739C	ENST00000397752	NM_000245.2	739	Cgt/Tgt	9/21	1	2	FACETS	0.923	0.838	1	0.923	0.838	1	CLONAL	1	TRUE	1	0.6	2		445	419	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825519	50825519	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	107	517	0	ENST00000398568.2:c.2156del	p.Asn719MetfsTer13	p.N719Mfs*13	ENST00000398568	NM_001042412.1	717	gAa/ga	14/18	1	2	FACETS	0.828	0.747	0.911	0.828	0.747	0.911	CLONAL	1	TRUE	1	0.6	2		517	431	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347553	118347553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555037629	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	111	386	1	ENST00000534358.1:c.3190C>T	p.Arg1064Ter	p.R1064*	ENST00000534358	NM_005933.3	1064	Cga/Tga	4/36	1	2	FACETS	0.782	0.707	0.861	0.782	0.707	0.861	SUBCLONAL	1	TRUE	1	0.6	2		387	473	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286255	66286255	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	79	340	0	ENST00000273854.3:c.1431del	p.Ile480LeufsTer21	p.I480Lfs*21	ENST00000273854	NM_004439.5	477	aaA/aa	6/18	1	2	FACETS	0.82	0.728	0.918	0.82	0.728	0.918	CLONAL	1	TRUE	1	0.6	2		340	321	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830807	72830807	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	144	551	3	ENST00000268489.5:c.5774del	p.Gly1925ValfsTer72	p.G1925Vfs*72	ENST00000268489	NM_006885.3	1925	gGt/gt	9/10	1	2	FACETS	0.95	0.873	1	0.95	0.873	1	CLONAL	1	TRUE	1	0.6	2		554	505	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771563	112771563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1185910534	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	30	397	1	ENST00000369452.4:c.1736G>A	p.Arg579His	p.R579H	ENST00000369452	NM_007373.3	579	cGt/cAt	9/9	1	2	FACETS	0.256	0.206	0.313	0.256	0.206	0.313	SUBCLONAL	1	TRUE	1	0.6	2		398	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574030	7574030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769934890	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	148	463	1	ENST00000269305.4:c.997C>T	p.Arg333Cys	p.R333C	ENST00000269305	NM_001126112.2	333	Cgt/Tgt	10/11	1	2	FACETS	0.879	0.807	0.954	0.879	0.807	0.954	CLONAL	1	TRUE	1	0.6	2		464	561	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478548	99478548	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	70	276	1	ENST00000268035.6:c.3190C>T	p.Arg1064Ter	p.R1064*	ENST00000268035	NM_000875.3	1064	Cga/Tga	17/21	1	2	FACETS	0.852	0.751	0.958	0.852	0.751	0.958	CLONAL	1	TRUE	1	0.6	2		277	274	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656525	3656525	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138615800	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	169	635	0	ENST00000294008.3:c.710G>A	p.Arg237Gln	p.R237Q	ENST00000294008	NM_032444.2	237	cGg/cAg	3/15	1	2	FACETS	0.93	0.859	1	0.93	0.859	1	CLONAL	1	TRUE	1	0.6	2		635	606	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794869	42794869	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	82	585	0	ENST00000575354.2:c.1953del	p.Ala652ProfsTer76	p.A652Pfs*76	ENST00000575354	NM_015125.3	650	gCc/gc	10/20	1	2	FACETS	0.708	0.628	0.793	0.708	0.628	0.793	SUBCLONAL	1	TRUE	1	0.6	2		585	386	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122996	7122996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377722635	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	139	583	0	ENST00000302850.5:c.3263G>A	p.Arg1088His	p.R1088H	ENST00000302850	NM_000208.2	1088	cGc/cAc	18/22	1	2	FACETS	0.889	0.814	0.967	0.889	0.814	0.967	CLONAL	1	TRUE	1	0.6	2		583	521	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28600661	28600661	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	160	503	0	ENST00000253063.3:c.1012C>T	p.Arg338Trp	p.R338W	ENST00000253063	NM_031459.4	338	Cgg/Tgg	7/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.6	2		503	477	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305357	65305357	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	119	531	2	ENST00000342505.4:c.2771del	p.Lys924ArgfsTer6	p.K924Rfs*6	ENST00000342505	NM_002227.2	924	aAg/ag	20/25	1	2	FACETS	0.732	0.663	0.804	0.732	0.663	0.804	SUBCLONAL	1	TRUE	1	0.6	2		533	542	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946379	71946379	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768017851	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	182	667	1	ENST00000298229.2:c.2543C>T	p.Thr848Met	p.T848M	ENST00000298229	NM_001567.3	848	aCg/aTg	23/28	1	2	FACETS	0.963	0.893	1	0.963	0.893	1	CLONAL	1	TRUE	1	0.6	2		668	630	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343804	118343804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868981857	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	139	475	1	ENST00000534358.1:c.1930C>T	p.Arg644Cys	p.R644C	ENST00000534358	NM_005933.3	644	Cgc/Tgc	3/36	1	2	FACETS	0.916	0.839	0.995	0.916	0.839	0.995	CLONAL	1	TRUE	1	0.6	2		476	506	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343849	118343849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374545538	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	63	480	0	ENST00000534358.1:c.1975G>A	p.Glu659Lys	p.E659K	ENST00000534358	NM_005933.3	659	Gag/Aag	3/36	1	2	FACETS	0.404	0.349	0.463	0.404	0.349	0.463	SUBCLONAL	1	TRUE	1	0.6	2		480	520	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422892	49422892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751383638	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	144	598	0	ENST00000301067.7:c.14203C>T	p.Arg4735Trp	p.R4735W	ENST00000301067	NM_003482.3	4735	Cgg/Tgg	44/54	1	2	FACETS	0.921	0.845	1	0.921	0.845	1	CLONAL	1	TRUE	1	0.6	2		598	521	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438655	49438655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1268188754	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	144	593	0	ENST00000301067.7:c.4835G>A	p.Arg1612His	p.R1612H	ENST00000301067	NM_003482.3	1612	cGc/cAc	19/54	1	2	FACETS	0.894	0.82	0.971	0.894	0.82	0.971	CLONAL	1	TRUE	1	0.6	2		593	537	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440420	49440420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1474346582	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	169	641	0	ENST00000301067.7:c.4390G>A	p.Val1464Ile	p.V1464I	ENST00000301067	NM_003482.3	1464	Gtc/Atc	15/54	1	2	FACETS	0.968	0.895	1	0.968	0.895	1	CLONAL	1	TRUE	1	0.6	2		641	582	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794763	120794763	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	199	674	0	ENST00000257552.2:c.594del	p.Arg199GlyfsTer50	p.R199Gfs*50	ENST00000257552	NM_002442.3	198	ggG/gg	9/15	1	2	FACETS	0.973	0.905	1	0.973	0.905	1	CLONAL	1	TRUE	1	0.6	2		674	682	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73342975	73342975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757306363	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	170	398	0	ENST00000377767.4:c.1831C>T	p.Arg611Cys	p.R611C	ENST00000377767	NM_014953.3	611	Cgt/Tgt	14/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.6	2		398	514	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435832	110435832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	101	342	0	ENST00000375856.3:c.2569G>A	p.Gly857Ser	p.G857S	ENST00000375856	NM_003749.2	857	Ggc/Agc	1/2	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.6	2		342	324	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68301899	68301899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749856572	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	142	414	0	ENST00000487270.1:c.301G>A	p.Gly101Arg	p.G101R	ENST00000487270	NM_133509.3	101	Gga/Aga	4/11	1	2	FACETS	0.919	0.843	0.998	0.919	0.843	0.998	CLONAL	1	TRUE	1	0.6	2		414	515	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784245	43784245	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754219111	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	53	648	0	ENST00000382044.4:c.241G>A	p.Gly81Ser	p.G81S	ENST00000382044	NM_001141980.1	81	Ggt/Agt	3/28	1	2	FACETS	0.231	0.196	0.269	0.231	0.196	0.269	SUBCLONAL	1	TRUE	1	0.6	2		648	765	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134569	2134569	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs397514939	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	120	730	0	ENST00000219476.3:c.4351del	p.Arg1451AlafsTer25	p.R1451Afs*25	ENST00000219476	NM_000548.3	1449	tCc/tc	34/42	1	2	FACETS	0.853	0.775	0.934	0.853	0.775	0.934	CLONAL	1	TRUE	1	0.6	2		730	469	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640370	3640370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780143733	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	36	761	1	ENST00000294008.3:c.3269C>T	p.Thr1090Met	p.T1090M	ENST00000294008	NM_032444.2	1090	aCg/aTg	12/15	1	2	FACETS	0.189	0.155	0.228	0.189	0.155	0.228	SUBCLONAL	1	TRUE	1	0.6	2		762	634	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827463	72827463	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750717662	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	153	584	0	ENST00000268489.5:c.9118C>T	p.Arg3040Cys	p.R3040C	ENST00000268489	NM_006885.3	3040	Cgt/Tgt	9/10	1	2	FACETS	0.951	0.876	1	0.951	0.876	1	CLONAL	1	TRUE	1	0.6	2		584	536	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829115	72829115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	30	490	0	ENST00000268489.5:c.7466del	p.Pro2489LeufsTer39	p.P2489Lfs*39	ENST00000268489	NM_006885.3	2489	cCt/ct	9/10	1	2	FACETS	0.253	0.203	0.309	0.253	0.203	0.309	SUBCLONAL	1	TRUE	1	0.6	2		490	396	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004570	16004571	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	29	318	0	ENST00000268712.3:c.2683_2684del	p.Arg895AlafsTer52	p.R895Afs*52	ENST00000268712	NM_006311.3	895	AGg/g	20/46	1	2	FACETS	0.31	0.249	0.379	0.31	0.249	0.379	SUBCLONAL	1	TRUE	1	0.6	2		318	312	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17125885	17125885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257705335	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	127	555	0	ENST00000285071.4:c.709G>A	p.Ala237Thr	p.A237T	ENST00000285071	NM_144997.5	237	Gcc/Acc	7/14	1	2	FACETS	0.753	0.685	0.824	0.753	0.685	0.824	SUBCLONAL	1	TRUE	1	0.6	2		555	562	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677260	29677262	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs786203184	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	23	377	0	ENST00000356175.3:c.7324_7326del	p.Leu2442del	p.L2442del	ENST00000356175	NM_000267.3	2440	CTT/-	49/57	1	2	FACETS	0.169	0.131	0.213	0.169	0.131	0.213	SUBCLONAL	1	TRUE	1	0.6	2		377	453	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879706	37879706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	89	458	2	ENST00000269571.5:c.2081C>T	p.Thr694Met	p.T694M	ENST00000269571		694	aCg/aTg	17/27	1	2	FACETS	0.852	0.762	0.947	0.852	0.762	0.947	CLONAL	1	TRUE	1	0.6	2		460	348	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436035	56436035	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568220750	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	88	408	1	ENST00000407977.2:c.1102C>T	p.Arg368Trp	p.R368W	ENST00000407977		368	Cgg/Tgg	9/10	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.6	2		409	287	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438199	56438199	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	139	662	0	ENST00000407977.2:c.794G>A	p.Ser265Asn	p.S265N	ENST00000407977		265	aGc/aAc	7/10	1	2	FACETS	0.949	0.87	1	0.949	0.87	1	CLONAL	1	TRUE	1	0.6	2		662	488	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097092	11097092	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1322190597	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	102	637	2	ENST00000358026.2:c.583C>T	p.Pro195Ser	p.P195S	ENST00000358026	NM_001128849.1	195	Ccc/Tcc	4/36	1	2	FACETS	0.774	0.697	0.856	0.774	0.697	0.856	SUBCLONAL	1	TRUE	1	0.6	2		639	439	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308365	15308365	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1362111590	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	65	649	2	ENST00000263388.2:c.143C>T	p.Pro48Leu	p.P48L	ENST00000263388	NM_000435.2	48	cCg/cTg	2/33	1	2	FACETS	0.341	0.295	0.39	0.341	0.295	0.39	SUBCLONAL	1	TRUE	1	0.6	2		651	636	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223892	36223892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1362756558	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	145	758	0	ENST00000222270.7:c.6442C>T	p.Pro2148Ser	p.P2148S	ENST00000222270	NM_014727.1	2148	Ccc/Tcc	28/37	1	2	FACETS	0.935	0.858	1	0.935	0.858	1	CLONAL	1	TRUE	1	0.6	2		758	517	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753717	42753717	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587777006	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	158	738	0	ENST00000222329.4:c.547C>T	p.Arg183Ter	p.R183*	ENST00000222329	NM_006494.2	183	Cga/Tga	4/4	1	2	FACETS	0.819	0.753	0.887	0.819	0.753	0.887	CLONAL	1	TRUE	1	0.6	2		738	643	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906845	50906845	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	83	487	0	ENST00000440232.2:c.1233G>T	p.Gln411His	p.Q411H	ENST00000440232	NM_002691.3	411	caG/caT	10/27	1	2	FACETS	0.8	0.711	0.892	0.8	0.711	0.892	SUBCLONAL	1	TRUE	1	0.6	2		487	346	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015227	128015227	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771245959	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	130	439	0	ENST00000285398.2:c.2294G>A	p.Arg765Gln	p.R765Q	ENST00000285398	NM_000122.1	765	cGg/cAg	15/15	1	2	FACETS	0.901	0.822	0.982	0.901	0.822	0.982	CLONAL	1	TRUE	1	0.6	2		439	481	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324311	62324311	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749800565	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	138	604	5	ENST00000360203.5:c.2806G>A	p.Gly936Ser	p.G936S	ENST00000360203	NM_001283009.1	936	Ggc/Agc	29/35	1	2	FACETS	0.96	0.88	1	0.96	0.88	1	CLONAL	1	TRUE	1	0.6	2		609	479	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421274	12421274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149324518	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	150	565	0	ENST00000287820.6:c.154G>A	p.Val52Ile	p.V52I	ENST00000287820	NM_015869.4	52	Gta/Ata	2/7	NA	2	FACETS	0.873	0.801	0.946			1	INDETERMINATE	1	TRUE	NA	0.6	2		565	573	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164507	47164507	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371758386	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	93	345	0	ENST00000409792.3:c.1619G>A	p.Arg540Gln	p.R540Q	ENST00000409792	NM_014159.6	540	cGa/cAa	3/21	NA	3	FACETS	1	0.96	1	0.572	0.513	0.634	INDETERMINATE	1	TRUE	1	0.6	3		345	352	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71064782	71064782	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	130	403	0	ENST00000318789.4:c.892del	p.His298IlefsTer27	p.H298Ifs*27	ENST00000318789	NM_032682.5	298	Cat/at	12/21	1	2	FACETS	0.886	0.809	0.966	0.886	0.809	0.966	CLONAL	1	TRUE	1	0.6	2		403	489	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73047240	73047240	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	122	381	1	ENST00000356692.5:c.51del	p.Lys19ArgfsTer14	p.K19Rfs*14	ENST00000356692		16	aGg/ag	2/9	1	2	FACETS	0.776	0.705	0.851	0.776	0.705	0.851	SUBCLONAL	1	TRUE	1	0.6	2		382	524	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391207	89391207	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	139	374	0	ENST00000336596.2:c.1273T>A	p.Phe425Ile	p.F425I	ENST00000336596	NM_005233.5	425	Ttt/Att	5/17	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.6	2		374	447	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801031	1801031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370940011	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	157	717	2	ENST00000260795.2:c.160G>A	p.Gly54Arg	p.G54R	ENST00000260795		54	Ggg/Agg	2/17	NA	2	FACETS	0.926	0.853	1			1	INDETERMINATE	1	TRUE	NA	0.6	2		719	565	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356347	66356347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	117	448	0	ENST00000273854.3:c.1150G>A	p.Gly384Ser	p.G384S	ENST00000273854	NM_004439.5	384	Ggt/Agt	5/18	1	2	FACETS	0.869	0.788	0.952	0.869	0.788	0.952	CLONAL	1	TRUE	1	0.6	2		448	449	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157927	106157929	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs772364798	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	89	309	0	ENST00000380013.4:c.2830_2832del	p.Lys944del	p.K944del	ENST00000380013	NM_001127208.2	943	cAGAag/cag	3/11	1	2	FACETS	0.883	0.79	0.98	0.883	0.79	0.98	CLONAL	1	TRUE	1	0.6	2		309	336	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247369	153247369	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	96	304	0	ENST00000281708.4:c.1433C>A	p.Ser478Tyr	p.S478Y	ENST00000281708	NM_033632.3	478	tCt/tAt	10/12	1	2	FACETS	0.788	0.707	0.873	0.788	0.707	0.873	SUBCLONAL	1	TRUE	1	0.6	2		304	406	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538953	187538956	+	frameshift_variant	Frame_Shift_Del	DEL	CTCA	CTCA	-	novel	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	106	398	0	ENST00000441802.2:c.8784_8787del	p.Ser2928ArgfsTer8	p.S2928Rfs*8	ENST00000441802	NM_005245.3	2928	agTGAG/ag	10/27	1	2	FACETS	0.805	0.726	0.887	0.805	0.726	0.887	CLONAL	1	TRUE	1	0.6	2		398	439	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79966006	79966006	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748207601	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	142	520	2	ENST00000265081.6:c.670C>T	p.Arg224Trp	p.R224W	ENST00000265081	NM_002439.4	224	Cgg/Tgg	4/24	1	2	FACETS	0.83	0.76	0.903	0.83	0.76	0.903	CLONAL	1	TRUE	1	0.6	2		522	570	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89791150	89791151	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	48	116	0	ENST00000336032.3:c.539_540del	p.Glu180GlyfsTer27	p.E180Gfs*27	ENST00000336032	NM_006813.2	179	aaAGag/aaag	1/2	1	2	FACETS	0.773	0.661	0.892	0.773	0.661	0.892	SUBCLONAL	1	TRUE	1	0.6	2		116	207	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956549	93956549	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	32	318	0	ENST00000369303.4:c.2687A>G	p.Asn896Ser	p.N896S	ENST00000369303	NM_004440.3	896	aAc/aGc	15/17	1	2	FACETS	0.268	0.217	0.325	0.268	0.217	0.325	SUBCLONAL	1	TRUE	1	0.6	2		318	398	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38139035	38139035	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	129	542	2	ENST00000317025.8:c.3568C>T	p.Arg1190Ter	p.R1190*	ENST00000317025	NM_023034.1	1190	Cga/Tga	20/24	1	2	FACETS	0.765	0.697	0.837	0.765	0.697	0.837	SUBCLONAL	1	TRUE	1	0.6	2		544	562	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595345	141595345	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777295689	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	148	618	2	ENST00000220592.5:c.88G>A	p.Asp30Asn	p.D30N	ENST00000220592	NM_012154.3	30	Gac/Aac	2/19	1	2	FACETS	0.803	0.737	0.873	0.803	0.737	0.873	CLONAL	1	TRUE	1	0.6	2		620	614	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460468	8460468	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	41	499	1	ENST00000356435.5:c.3818C>A	p.Pro1273His	p.P1273H	ENST00000356435		1273	cCt/cAt	22/35	1	2	FACETS	0.267	0.222	0.318	0.267	0.222	0.318	SUBCLONAL	1	TRUE	1	0.6	2		500	511	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730436	133730436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757951694	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	116	373	1	ENST00000318560.5:c.502G>A	p.Glu168Lys	p.E168K	ENST00000318560	NM_005157.4	168	Gaa/Aaa	3/11	1	2	FACETS	0.927	0.842	1	0.927	0.842	1	CLONAL	1	TRUE	1	0.6	2		374	417	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855027	76855027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782222942	NA	P-0029323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	94	194	0	ENST00000373344.5:c.5809G>A	p.Gly1937Arg	p.G1937R	ENST00000373344	NM_000489.3	1937	Ggg/Agg	25/35	1	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.6	1		194	198	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248998	55248999	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCCAGCG	rs727504263	NA	P-0029324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	189	448	0	ENST00000275493.2:c.2300_2308dup	p.Ala767_Val769dup	p.A767_V769dup	ENST00000275493	NM_005228.3	767	atg/aTGGCCAGCGtg	20/28	0.325047466523937	3	FACETS	1	0.99	1	0.725	0.671	0.781	CLONAL	1	TRUE	1	0.363838251719347	3		448	847	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0029325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	482	850	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.714161872546072	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.714161872546072	1		850	809	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197811	66197811	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	25	295	0	ENST00000273854.3:c.2888G>T	p.Gly963Val	p.G963V	ENST00000273854	NM_004439.5	963	gGa/gTa	17/18	0.714161872546072	1	FACETS	0.126	0.099	0.157	0.126	0.099	0.157	SUBCLONAL	1	TRUE	0	0.714161872546072	1		295	357	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362446	40362447	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1202978138	NA	P-0029327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	66	636	1	ENST00000293328.3:c.1749dup	p.His584ThrfsTer8	p.H584Tfs*8	ENST00000293328	NM_012448.3	583	-/A	14/19	1	2	FACETS	0.925	0.808	1	0.925	0.808	1	CLONAL	1	TRUE	1	0.400879314190393	2		637	356	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274734	123274734	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	94	479	0	ENST00000358487.5:c.1184T>A	p.Val395Asp	p.V395D	ENST00000358487	NM_000141.4	395	gTc/gAc	9/18	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.400879314190393	2		479	322	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43771677	43771677	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	32	555	0	ENST00000382044.4:c.706C>T	p.Gln236Ter	p.Q236*	ENST00000382044	NM_001141980.1	236	Cag/Tag	7/28	0.308901104469527	1	FACETS	0.421	0.343	0.509	0.421	0.343	0.509	SUBCLONAL	1	TRUE	0	0.400879314190393	1		555	303	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245350	41245350	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	36	636	0	ENST00000357654.3:c.2198A>G	p.Glu733Gly	p.E733G	ENST00000357654	NM_007294.3	733	gAg/gGg	10/23	1	2	FACETS	0.587	0.484	0.701	0.587	0.484	0.701	SUBCLONAL	1	TRUE	1	0.400879314190393	2		636	306	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163641	32163641	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	47	384	0	ENST00000375023.3:c.5585G>T	p.Arg1862Leu	p.R1862L	ENST00000375023	NM_004557.3	1862	cGg/cTg	30/30	0.264484614899361	1	FACETS	0.942	0.805	1	0.942	0.805	1	CLONAL	1	TRUE	0	0.400879314190393	1		384	199	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390280	139390774	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	CAGAATAGATAAAAGTTTCTACCTGGGGCCAGATAAAACAGTACATATAAATAAAAAGGCAGTGTTTCTGTGTAAAATAAAAGTACATAAATAAATACTAAAAAAAATTAAAATCCTCGTTCTTATTTTGTATAAAAACATGTGTTTTAAAAAGGCTCCTCTGGTCGGCCCTGGCATCCACAGAGCGCACACAGACGCCCGAAGGCTTGGGAAAGGAAGCCGGGGTCTCGTGGGGCGCGCCGTTTACTTGAAGGCCTCCGGAATGCGGGCGATCTGGGACTGCATGCTGGTGGGAGGGCTGGAGACGCCCTCGGACCAGTCGGAGACGTTGGAATGCGGGGACGAGCTGGACCACTGGTCAGGGGACTCAGGGGACGGGGTGAGGAAGGGGTGCTCAGGCACCTGTAGCTGGTGGCTGGGGGTGTTGTCCACAGGCGAGGAGTAGCTGTGCTGCGAGGGGGGCGTCAGGAACTGGGCTGCGGTCACGGGTGGGAC	CAGAATAGATAAAAGTTTCTACCTGGGGCCAGATAAAACAGTACATATAAATAAAAAGGCAGTGTTTCTGTGTAAAATAAAAGTACATAAATAAATACTAAAAAAAATTAAAATCCTCGTTCTTATTTTGTATAAAAACATGTGTTTTAAAAAGGCTCCTCTGGTCGGCCCTGGCATCCACAGAGCGCACACAGACGCCCGAAGGCTTGGGAAAGGAAGCCGGGGTCTCGTGGGGCGCGCCGTTTACTTGAAGGCCTCCGGAATGCGGGCGATCTGGGACTGCATGCTGGTGGGAGGGCTGGAGACGCCCTCGGACCAGTCGGAGACGTTGGAATGCGGGGACGAGCTGGACCACTGGTCAGGGGACTCAGGGGACGGGGTGAGGAAGGGGTGCTCAGGCACCTGTAGCTGGTGGCTGGGGGTGTTGTCCACAGGCGAGGAGTAGCTGTGCTGCGAGGGGGGCGTCAGGAACTGGGCTGCGGTCACGGGTGGGAC	-	novel	NA	P-0029327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	171	35	0	ENST00000277541.6:c.7417_*243del		p.*2473*	ENST00000277541	NM_017617.3	2473		34/34	0.311849281210464	4	FACETS		NA	1	1	0.995	1	NA	7	TRUE	0	0.400879314190393	4		35	181	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397717	139397717	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	201	632	1	ENST00000277541.6:c.5084G>T	p.Ser1695Ile	p.S1695I	ENST00000277541	NM_017617.3	1695	aGt/aTt	27/34	0.311849281210464	4	FACETS	0.982	0.92	1	0.736	0.69	0.784	CLONAL	3	TRUE	0	0.400879314190393	4		633	477	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399125	139399125	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	41	583	0	ENST00000277541.6:c.5018G>T	p.Gly1673Val	p.G1673V	ENST00000277541	NM_017617.3	1673	gGc/gTc	26/34	0.311849281210464	4	FACETS	0.663	0.553	0.786	0.166	0.138	0.197	SUBCLONAL	1	TRUE	0	0.400879314190393	4		583	432	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505637	186505652	+	frameshift_variant	Frame_Shift_Del	DEL	GATCTACCTACCAATC	GATCTACCTACCAATC	-	novel	NA	P-0029327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	22	285	0	ENST00000323963.5:c.1046_1061del	p.Asp349ValfsTer21	p.D349Vfs*21	ENST00000323963		349	GATCTACCTACCAATCgt/gt	10/11	0.166248264793088	3	FACETS	0.359	0.278	0.454	0.18	0.139	0.227	INDETERMINATE	1	TRUE	1	0.400879314190393	3		285	367	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0029328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	276	440	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.434911172099711	4	FACETS	0.907	0.863	0.95	0.907	0.863	0.95	CLONAL	4	TRUE	0	0.434911172099711	4		440	502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0029328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	428	477	0	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	0.434911172099711	4	FACETS	0.955	0.919	0.991	0.955	0.919	0.991	CLONAL	4	TRUE	0	0.434911172099711	4		477	739	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54948538	54948538	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	65	385	0	ENST00000312783.6:c.780G>T	p.Glu260Asp	p.E260D	ENST00000312783	NM_198436.1	260	gaG/gaT	8/10	0.434911172099711	4	FACETS	0.71	0.616	0.813	0.237	0.205	0.271	SUBCLONAL	1	TRUE	1	0.434911172099711	4		385	604	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0029329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	178	499	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	0.480093855645624	3	FACETS	0.966	0.899	1	0.966	0.899	1	CLONAL	2	TRUE	1	0.480031022562135	3		499	476	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856113	68856113	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782750	NA	P-0029329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	95	458	0	ENST00000261769.5:c.1921C>T	p.Gln641Ter	p.Q641*	ENST00000261769	NM_004360.3	641	Cag/Tag	12/16	0.480093855645624	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.480031022562135	1		458	265	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061461	38061461	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	56	330	0	ENST00000250448.2:c.528C>G	p.Ile176Met	p.I176M	ENST00000250448	NM_004496.3	176	atC/atG	2/2	1	2	FACETS	0.807	0.697	0.926	0.807	0.697	0.926	CLONAL	1	TRUE	1	0.480031022562135	2		330	289	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264401	46264401	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	79	357	0	ENST00000371998.3:c.1448C>T	p.Ser483Phe	p.S483F	ENST00000371998		483	tCt/tTt	11/23	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.480031022562135	2		357	306	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512162	120512162	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	42	338	0	ENST00000256646.2:c.1080C>A	p.Phe360Leu	p.F360L	ENST00000256646	NM_024408.3	360	ttC/ttA	6/34	0.17666726426899	1	FACETS	0.446	0.374	0.525	0.446	0.374	0.525	INDETERMINATE	1	TRUE	0	0.480031022562135	1		338	298	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192044	108192044	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	71	346	1	ENST00000278616.4:c.6469G>T	p.Glu2157Ter	p.E2157*	ENST00000278616	NM_000051.3	2157	Gag/Tag	45/63	0.476698632584263	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.480031022562135	1		347	215	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447881	49447881	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	92	450	0	ENST00000301067.7:c.553C>G	p.Arg185Gly	p.R185G	ENST00000301067	NM_003482.3	185	Cgc/Ggc	5/54	0.480093855645624	3	FACETS	1	0.909	1	0.51	0.455	0.568	CLONAL	1	TRUE	1	0.480031022562135	3		450	466	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111855984	111855984	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	72	376	0	ENST00000341259.2:c.35C>G	p.Ser12Cys	p.S12C	ENST00000341259	NM_005475.2	12	tCt/tGt	2/8	0.480093855645624	3	FACETS	0.916	0.804	1	0.458	0.402	0.518	CLONAL	1	TRUE	1	0.480031022562135	3		376	406	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068354	16068360	+	frameshift_variant	Frame_Shift_Del	DEL	TCCATAC	TCCATAC	-	novel	NA	P-0029329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	13	27	0	ENST00000268712.3:c.551_557del	p.Ser184IlefsTer3	p.S184Ifs*3	ENST00000268712	NM_006311.3	184	aGTATGGAt/at	5/46	1	2	FACETS	0.797	0.6	1	1	0.902	1	CLONAL	2	TRUE	1	0.480031022562135	2		27	34	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627841	37627841	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1462649581	NA	P-0029329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	94	520	0	ENST00000447079.4:c.1756C>T	p.Pro586Ser	p.P586S	ENST00000447079	NM_015083.1	586	Cct/Tct	2/14	1	2	FACETS	0.997	0.893	1	0.997	0.893	1	CLONAL	1	TRUE	1	0.480031022562135	2		520	393	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155372	99155372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	21	325	0	ENST00000074304.5:c.598G>A	p.Glu200Lys	p.E200K	ENST00000074304	NM_001134224.1	200	Gag/Aag	9/26	0.480093855645624	3	FACETS	0.274	0.21	0.348	0.137	0.105	0.174	SUBCLONAL	1	TRUE	1	0.480031022562135	3		325	396	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147564	47147564	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	68	346	0	ENST00000409792.3:c.4762G>C	p.Glu1588Gln	p.E1588Q	ENST00000409792	NM_014159.6	1588	Gag/Cag	6/21	0.480031022562135	2	FACETS	0.894	0.784	1	0.447	0.392	0.506	CLONAL	1	TRUE	0	0.480031022562135	2		346	317	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620496	52620496	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	24	381	0	ENST00000394830.3:c.3257A>C	p.Lys1086Thr	p.K1086T	ENST00000394830	NM_018313.4	1086	aAg/aCg	21/30	0.480031022562135	2	FACETS	0.306	0.24	0.382	0.153	0.12	0.191	SUBCLONAL	1	TRUE	0	0.480031022562135	2		381	327	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056609	26056609	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	36	133	0	ENST00000343677.2:c.48G>C	p.Glu16Asp	p.E16D	ENST00000343677	NM_005319.3	16	gaG/gaC	1/1	0.480093855645624	3	FACETS	0.899	0.745	1	0.449	0.372	0.534	CLONAL	1	TRUE	1	0.480031022562135	3		133	207	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146958	38146958	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1389385638	NA	P-0029329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	70	563	0	ENST00000317025.8:c.3184G>C	p.Glu1062Gln	p.E1062Q	ENST00000317025	NM_023034.1	1062	Gag/Cag	18/24	0.353170033196927	6	FACETS	0.747	0.651	0.852			1	SUBCLONAL	1	TRUE	NA	0.480031022562135	6		563	765	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	262	404	0				ENST00000310581	NM_198253.2	-/1132			0.798772573002403	3	FACETS	0.909	0.863	0.955	0.909	0.863	0.955	CLONAL	2	TRUE	1	0.798772573002403	3		404	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0029330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	693	434	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.782544892873524	3	FACETS	0.976	0.958	0.994	0.976	0.958	0.994	CLONAL	3	TRUE	0	0.798772573002403	3		434	829	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0029330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	423	631	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.798772573002403	5	FACETS	0.981	0.942	1	0.981	0.942	1	CLONAL	3	TRUE	2	0.798772573002403	5		632	791	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562870	21562870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1047262994	NA	P-0029330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	375	390	0	ENST00000382592.4:c.1049C>T	p.Pro350Leu	p.P350L	ENST00000382592	NM_014572.2	350	cCc/cTc	4/8	0.37111083540651	4	FACETS	0.941	0.897	0.986	0.941	0.897	0.986	INDETERMINATE	2	TRUE	2	0.798772573002403	4		390	897	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190742022	190742022	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	105	341	0	ENST00000441310.2:c.2659C>T	p.Gln887Ter	p.Q887*	ENST00000441310	NM_000534.4	887	Caa/Taa	13/13	0.798772573002403	3	FACETS	0.768	0.692	0.848	0.384	0.346	0.424	SUBCLONAL	1	TRUE	1	0.798772573002403	3		341	479	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55143560	55143560	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	35	213	0	ENST00000257290.5:c.1792G>A	p.Val598Ile	p.V598I	ENST00000257290	NM_006206.4	598	Gtc/Atc	13/23	0.78985988493567	3	FACETS	0.328	0.269	0.394	0.109	0.089	0.132	SUBCLONAL	1	TRUE	0	0.798772573002403	3		213	374	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983862	2983862	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1399673665	NA	P-0029330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	458	365	1	ENST00000396946.4:c.668G>A	p.Arg223Gln	p.R223Q	ENST00000396946	NM_032415.4	223	cGa/cAa	5/25	0.798772573002403	5	FACETS	0.964	0.921	1	0.643	0.614	0.672	CLONAL	2	TRUE	2	0.798772573002403	5		366	1307	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517301	157517302	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CC	CC	T	novel	NA	P-0029330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	88	267	0	ENST00000346085.5:c.3865_3866delinsT	p.Pro1289LeufsTer8	p.P1289Lfs*8	ENST00000346085	NM_020732.3	1289	CCt/Tt	16/20	0.440645796854898	3	FACETS	0.684	0.608	0.763	0.228	0.202	0.255	INDETERMINATE	1	TRUE	0	0.798772573002403	3		267	451	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912060	32912060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80358604	NA	P-0029331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	140	547	1	ENST00000380152.3:c.3568C>T	p.Arg1190Trp	p.R1190W	ENST00000380152		1190	Cgg/Tgg	11/27	0.154891257818878	3	FACETS	0.616	0.56	0.675	0.308	0.28	0.338	INDETERMINATE	1	TRUE	1	0.591965191675778	3		548	995	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579316	7579317	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	376	489	0	ENST00000269305.4:c.370dup	p.Cys124LeufsTer25	p.C124Lfs*25	ENST00000269305	NM_001126112.2	124	tgc/tTgc	4/11	0.529192920711261	2	FACETS	0.93	0.892	0.968	0.93	0.892	0.968	CLONAL	2	TRUE	0	0.591965191675778	2		489	683	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292679	62292679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1044603913	NA	P-0029331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1306	151	554	2	ENST00000360203.5:c.131C>T	p.Thr44Met	p.T44M	ENST00000360203	NM_001283009.1	44	aCg/aTg	3/35	0.474928393815872	5	FACETS	0.661	0.602	0.723	0.22	0.2	0.241	SUBCLONAL	1	TRUE	2	0.591965191675778	5		556	1457	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622258	162622258	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	83	334	1	ENST00000366898.1:c.439T>A	p.Tyr147Asn	p.Y147N	ENST00000366898	NM_004562.2	147	Tat/Aat	4/12	0.396143181001967	1	FACETS	0.465	0.412	0.52	0.465	0.412	0.52	SUBCLONAL	1	TRUE	0	0.591965191675778	1		335	425	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0029332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	81	591	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.672	0.594	0.755	0.672	0.594	0.755	SUBCLONAL	1	TRUE	1	0.528535767831909	2		591	456	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0029332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	184	512	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	0.528535767831909	2		512	786	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0029332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	83	227	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.84	0.746	0.939	0.84	0.746	0.939	CLONAL	1	TRUE	1	0.528535767831909	2		227	374	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306689	41306689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868376470	NA	P-0029332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	190	485	0	ENST00000373198.4:c.970G>A	p.Glu324Lys	p.E324K	ENST00000373198	NM_133170.3	324	Gaa/Aaa	7/32	0.381688180042565	3	FACETS	1	0.968	1	0.54	0.5	0.582	CLONAL	1	TRUE	1	0.528535767831909	3		485	841	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041527	14041527	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs756155469	NA	P-0029332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	128	352	0	ENST00000311895.7:c.2074C>T	p.Arg692Ter	p.R692*	ENST00000311895	NM_005236.2	692	Cga/Tga	11/11	1	2	FACETS	0.897	0.817	0.981	0.897	0.817	0.981	CLONAL	1	TRUE	1	0.528535767831909	2		352	540	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859571	57859571	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	167	452	0	ENST00000228682.2:c.625G>A	p.Asp209Asn	p.D209N	ENST00000228682	NM_005269.2	209	Gat/Aat	7/12	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.528535767831909	2		452	576	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675118	40675118	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	281	608	0	ENST00000249776.8:c.82C>T	p.Pro28Ser	p.P28S	ENST00000249776	NM_033286.3	28	Ccg/Tcg	1/9	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.528535767831909	2		608	1010	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42049996	42049996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	142	331	0	ENST00000219905.7:c.7150C>T	p.His2384Tyr	p.H2384Y	ENST00000219905	NM_001164273.1	2384	Cac/Tac	19/24	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.528535767831909	2		331	508	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639987	3639988	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0029332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	191	605	0	ENST00000294008.3:c.3651_3652delinsAA	p.Asp1218Asn	p.D1218N	ENST00000294008	NM_032444.2	1217	gaGGat/gaAAat	12/15	1	2	FACETS	0.86	0.797	0.926	0.86	0.797	0.926	CLONAL	1	TRUE	1	0.528535767831909	2		605	840	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56401556	56401556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781294249	NA	P-0029332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	104	332	0	ENST00000348428.3:c.1418C>T	p.Thr473Ile	p.T473I	ENST00000348428	NM_006785.3	473	aCc/aTc	12/17	1	2	FACETS	0.776	0.698	0.859	0.776	0.698	0.859	SUBCLONAL	1	TRUE	1	0.528535767831909	2		332	507	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797804	42797804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141205881	NA	P-0029332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	231	565	0	ENST00000575354.2:c.3856C>T	p.Arg1286Cys	p.R1286C	ENST00000575354	NM_015125.3	1286	Cgt/Tgt	16/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.528535767831909	2		565	815	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683695	162683695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	56	379	0	ENST00000366898.1:c.274G>A	p.Ala92Thr	p.A92T	ENST00000366898	NM_004562.2	92	Gcg/Acg	3/12	0.322879298494745	1	FACETS	0.321	0.275	0.372	0.321	0.275	0.372	SUBCLONAL	1	TRUE	0	0.528535767831909	1		379	485	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422659	47422659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11551157	NA	P-0029332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	215	498	0	ENST00000377045.4:c.131C>T	p.Ser44Phe	p.S44F	ENST00000377045	NM_001654.4	44	tCt/tTt	3/16	0.528535767831909	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.528535767831909	1		498	588	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812338	212812338	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	66	189	0	ENST00000342788.4:c.238G>T	p.Val80Phe	p.V80F	ENST00000342788	NM_005235.2	80	Gtt/Ttt	3/28	1	2	FACETS	0.919	0.801	1	0.919	0.801	1	CLONAL	1	TRUE	1	0.373126635322518	2		189	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0029334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	162	489	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.3	1	FACETS	1	0.986	1	1	0.994	1	CLONAL	2	TRUE	0	0.34	1		489	325	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0029334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	232	412	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.3	3	FACETS	0.937	0.881	0.994	1	0.992	1	CLONAL	3	TRUE	1	0.34	3		412	568	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214591	5214591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770889503	NA	P-0029334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	101	427	0	ENST00000357368.4:c.4475G>A	p.Arg1492Gln	p.R1492Q	ENST00000357368	NM_002850.3	1492	cGg/cAg	29/38	0.3	0	FACETS	1	0.922	1			1	CLONAL	1	TRUE	0	0.34	0		427	382	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389324	8389324	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	238	407	0	ENST00000356435.5:c.4294C>G	p.Leu1432Val	p.L1432V	ENST00000356435		1432	Ctc/Gtc	26/35	0.3	1	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	0	0.34	1		407	522	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242737	98242737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	165	301	0	ENST00000331920.6:c.880C>T	p.Arg294Cys	p.R294C	ENST00000331920	NM_000264.3	294	Cgc/Tgc	6/24	0.0222367621928092	3	FACETS	1	0.975	1	1	0.975	1	INDETERMINATE	2	TRUE	1	0.34	3		301	505	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682318	37682318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	57	409	0	ENST00000447079.4:c.3509C>T	p.Ser1170Leu	p.S1170L	ENST00000447079	NM_015083.1	1170	tCa/tTa	13/14	0.0765769091861179	3	FACETS	0.642	0.55	0.742	0.321	0.275	0.371	INDETERMINATE	1	TRUE	1	0.34	3		409	611	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974697	21974697	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	183	217	0	ENST00000304494.5:c.130del	p.Tyr44ThrfsTer9	p.Y44Tfs*9	ENST00000304494	NM_000077.4	44	Tac/ac	1/3	0.3	1	FACETS	0.892	0.839	0.944	1	0.995	1	CLONAL	3	TRUE	0	0.34	1		217	334	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	93	394	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.162044983877733	3	FACETS	1	0.975	1	0.667	0.594	0.744	INDETERMINATE	1	TRUE	1	0.284997963473751	3		394	559	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	52	440	5	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.593	0.505	0.691	0.593	0.505	0.691	SUBCLONAL	1	TRUE	1	0.284997963473751	2		445	615	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0029337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	53	255	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	0.162044983877733	3	FACETS	1	0.876	1	0.513	0.439	0.595	INDETERMINATE	1	TRUE	1	0.284997963473751	3		255	414	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0029337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	46	443	1	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.588	0.495	0.691	0.588	0.495	0.691	SUBCLONAL	1	TRUE	1	0.284997963473751	2		444	549	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0029337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	17	181	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.162044983877733	3	FACETS	0.528	0.394	0.687	0.264	0.197	0.344	INDETERMINATE	1	TRUE	1	0.284997963473751	3		181	258	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216477	108216477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587782558	NA	P-0029337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	15	182	2	ENST00000278616.4:c.8432del	p.Lys2811SerfsTer46	p.K2811Sfs*46	ENST00000278616	NM_000051.3	2809	cAa/ca	58/63	1	2	FACETS	0.397	0.29	0.526	0.397	0.29	0.526	SUBCLONAL	1	TRUE	1	0.284997963473751	2		184	265	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	44	351	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.564	0.473	0.666	0.564	0.473	0.666	SUBCLONAL	1	TRUE	1	0.284997963473751	2		351	547	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475061	40475063	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0029337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	52	434	0	ENST00000264657.5:c.1847_1849del	p.Glu616del	p.E616del	ENST00000264657	NM_139276.2	616	gAAGga/gga	20/24	1	2	FACETS	0.541	0.459	0.63	0.541	0.459	0.63	SUBCLONAL	1	TRUE	1	0.284997963473751	2		434	675	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921555	178921555	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	44	288	0	ENST00000263967.3:c.1037T>A	p.Val346Glu	p.V346E	ENST00000263967	NM_006218.2	346	gTa/gAa	5/21	1	2	FACETS	0.759	0.637	0.893	0.759	0.637	0.893	SUBCLONAL	1	TRUE	1	0.284997963473751	2		288	407	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100934	27100934	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	58	424	1	ENST00000324856.7:c.4220del	p.Pro1407GlnfsTer74	p.P1407Qfs*74	ENST00000324856	NM_006015.4	1406	Ccc/cc	18/20	1	2	FACETS	0.606	0.52	0.7	0.606	0.52	0.7	SUBCLONAL	1	TRUE	1	0.284997963473751	2		425	672	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060912	38060912	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	45	339	0	ENST00000250448.2:c.1077del	p.Ile360Ter	p.I360*	ENST00000250448	NM_004496.3	359	ccC/cc	2/2	1	2	FACETS	0.603	0.506	0.709	0.603	0.506	0.709	SUBCLONAL	1	TRUE	1	0.284997963473751	2		339	524	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220895	36220895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	70	191	0	ENST00000222270.7:c.4945G>A	p.Ala1649Thr	p.A1649T	ENST00000222270	NM_014727.1	1649	Gcc/Acc	23/37	0.284997963473751	3	FACETS	0.861	0.756	0.972	0.861	0.756	0.972	CLONAL	2	TRUE	1	0.284997963473751	3		191	326	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422524	225422524	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	33	339	0	ENST00000264414.4:c.116del	p.Asn39MetfsTer39	p.N39Mfs*39	ENST00000264414	NM_003590.4	39	aAt/at	2/16	1	2	FACETS	0.569	0.463	0.688	0.569	0.463	0.688	SUBCLONAL	1	TRUE	1	0.284997963473751	2		339	407	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175759	176175760	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1373807885	NA	P-0029337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	47	525	0	ENST00000367669.3:c.355dup	p.Leu119ProfsTer23	p.L119Pfs*23	ENST00000367669	NM_022457.5	119	ctc/cCtc	1/20	0.284997963473751	3	FACETS	0.452	0.38	0.532	0.226	0.19	0.266	SUBCLONAL	1	TRUE	1	0.284997963473751	3		525	834	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190636	11190636	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	47	436	0	ENST00000361445.4:c.5563A>C	p.Ser1855Arg	p.S1855R	ENST00000361445	NM_004958.3	1855	Agc/Cgc	39/58	1	2	FACETS	0.481	0.405	0.565	0.481	0.405	0.565	SUBCLONAL	1	TRUE	1	0.284997963473751	2		436	686	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298641	11298641	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1180068151	NA	P-0029337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	58	482	0	ENST00000361445.4:c.1820C>T	p.Ala607Val	p.A607V	ENST00000361445	NM_004958.3	607	gCg/gTg	12/58	1	2	FACETS	0.636	0.546	0.734	0.636	0.546	0.734	SUBCLONAL	1	TRUE	1	0.284997963473751	2		482	640	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88651911	88651913	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs876659086	NA	P-0029337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	40	335	0	ENST00000372037.3:c.264_266del	p.Glu88del	p.E88del	ENST00000372037	NM_004329.2	86	atAGAa/ata	5/13	0.162044983877733	3	FACETS	0.571	0.473	0.679	0.285	0.236	0.34	INDETERMINATE	1	TRUE	1	0.284997963473751	3		335	562	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88651957	88651957	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0029337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	33	317	0	ENST00000372037.3:c.304A>T	p.Lys102Ter	p.K102*	ENST00000372037	NM_004329.2	102	Aaa/Taa	5/13	0.162044983877733	3	FACETS	0.452	0.367	0.548	0.226	0.183	0.274	INDETERMINATE	1	TRUE	1	0.284997963473751	3		317	586	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1022570	1022570	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	54	430	0	ENST00000358495.3:c.1244A>G	p.Tyr415Cys	p.Y415C	ENST00000358495	NM_134424.2	415	tAt/tGt	12/12	0.162044983877733	3	FACETS	0.607	0.518	0.706	0.304	0.259	0.353	INDETERMINATE	1	TRUE	1	0.284997963473751	3		430	713	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984925	9984925	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	58	430	0	ENST00000330684.3:c.1040A>G	p.Asp347Gly	p.D347G	ENST00000330684	NM_001134407.1	347	gAc/gGc	4/13	1	2	FACETS	0.616	0.528	0.711	0.616	0.528	0.711	SUBCLONAL	1	TRUE	1	0.284997963473751	2		430	661	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217266	7217266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	63	460	1	ENST00000380728.2:c.439G>A	p.Ala147Thr	p.A147T	ENST00000380728		147	Gct/Act	6/11	1	2	FACETS	0.604	0.521	0.694	0.604	0.521	0.694	SUBCLONAL	1	TRUE	1	0.284997963473751	2		461	732	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554273	63554273	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	62	531	0	ENST00000307078.5:c.466T>C	p.Tyr156His	p.Y156H	ENST00000307078	NM_004655.3	156	Tac/Cac	2/11	1	2	FACETS	0.536	0.462	0.617	0.536	0.462	0.617	SUBCLONAL	1	TRUE	1	0.284997963473751	2		531	811	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224698	36224698	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	75	598	0	ENST00000222270.7:c.7085del	p.Pro2362ArgfsTer77	p.P2362Rfs*77	ENST00000222270	NM_014727.1	2362	Ccg/cg	30/37	0.284997963473751	3	FACETS	0.512	0.447	0.582	0.256	0.223	0.291	SUBCLONAL	1	TRUE	1	0.284997963473751	3		598	1175	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306775	41306775	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	29	299	0	ENST00000373198.4:c.884del	p.Pro295GlnfsTer28	p.P295Qfs*28	ENST00000373198	NM_133170.3	295	cCa/ca	7/32	1	2	FACETS	0.485	0.388	0.594	0.485	0.388	0.594	SUBCLONAL	1	TRUE	1	0.284997963473751	2		299	420	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627983	37627983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375471633	NA	P-0029337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	59	513	1	ENST00000249071.6:c.277G>A	p.Val93Ile	p.V93I	ENST00000249071	NM_002872.4	93	Gtc/Atc	4/7	1	2	FACETS	0.472	0.405	0.546	0.472	0.405	0.546	SUBCLONAL	1	TRUE	1	0.284997963473751	2		514	877	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456582	138456583	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0029337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	47	425	0	ENST00000289153.2:c.767_768del	p.Tyr256CysfsTer4	p.Y256Cfs*4	ENST00000289153	NM_006219.2	256	tAT/t	4/22	1	2	FACETS	0.571	0.481	0.67	0.571	0.481	0.67	SUBCLONAL	1	TRUE	1	0.284997963473751	2		425	578	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178941909	178941909	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	43	349	0	ENST00000263967.3:c.2228A>T	p.Asp743Val	p.D743V	ENST00000263967	NM_006218.2	743	gAt/gTt	15/21	1	2	FACETS	0.598	0.5	0.706	0.598	0.5	0.706	SUBCLONAL	1	TRUE	1	0.284997963473751	2		349	505	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410437	63410437	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	54	600	0	ENST00000330258.3:c.2730C>A	p.His910Gln	p.H910Q	ENST00000330258	NM_152424.3	910	caC/caA	2/2	1	2	FACETS	0.503	0.428	0.584	0.503	0.428	0.584	SUBCLONAL	1	TRUE	1	0.284997963473751	2		600	754	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034505	123034505	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1449553232	NA	P-0029337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	30	353	0	ENST00000355640.3:c.1262G>A	p.Ser421Asn	p.S421N	ENST00000355640		421	aGt/aAt	6/7	1	2	FACETS	0.405	0.325	0.495	0.405	0.325	0.495	SUBCLONAL	1	TRUE	1	0.284997963473751	2		353	520	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29197671	29197671	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs557956425	NA	P-0029337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	69	516	0	ENST00000240100.2:c.523G>A	p.Ala175Thr	p.A175T	ENST00000240100	NM_001394.6	175	Gcc/Acc	2/4	0.162044983877733	3	FACETS	0.647	0.562	0.739	0.324	0.281	0.37	INDETERMINATE	1	TRUE	1	0.284997963473751	3		516	855	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923732	72923741	+	frameshift_variant	Frame_Shift_Del	DEL	CGCTTCGCTG	CGCTTCGCTG	-	novel	NA	P-0029339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	526	422	0	ENST00000268489.5:c.3337_3346del	p.Gln1113ArgfsTer71	p.Q1113Rfs*71	ENST00000268489	NM_006885.3	1113	CAGCGAAGCGag/ag	4/10	0.728181722583926	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	FALSE	1	0.751419877903078	3		422	902	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696425	47696425	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519967	NA	P-0029339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	334	449	0	ENST00000347630.2:c.398T>C	p.Phe133Ser	p.F133S	ENST00000347630	NM_001007230.1	133	tTc/tCc	6/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.751419877903078	2		449	772	SUCCESS
APC	324	MSKCC	GRCh37	5	112175906	112175912	+	frameshift_variant	Frame_Shift_Del	DEL	TCAGAGC	TCAGAGC	-	novel	NA	P-0029339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	156	245	0	ENST00000257430.4:c.4615_4621del	p.Glu1540LeufsTer23	p.E1540Lfs*23	ENST00000257430	NM_000038.5	1539	TCAGAGCag/ag	16/16	0.751419877903078	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	0	0.751419877903078	1		245	219	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0029340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	134	227	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.318975318897226	3	FACETS	0.86	0.793	0.928	0.86	0.793	0.928	INDETERMINATE	2	TRUE	1	0.628423323116251	3		227	326	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599107	28599108	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0029340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	274	584	0	ENST00000253063.3:c.555_556dup	p.Glu186AlafsTer62	p.E186Afs*62	ENST00000253063	NM_031459.4	185	ggc/gGCgc	5/10	0.628423323116251	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.628423323116251	1		584	594	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252845	10252845	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	262	443	0	ENST00000340748.4:c.3120C>A	p.Asn1040Lys	p.N1040K	ENST00000340748		1040	aaC/aaA	29/40	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.628423323116251	2		443	770	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0029341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	48	458	0	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	1	2	FACETS	0.814	0.687	0.956	0.814	0.687	0.956	CLONAL	1	TRUE	1	0.155927248458121	2		458	756	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578452	7578457	+	missense_variant	Missense_Mutation	ONP	TGGCGC	TGGCGC	CGCGGG	novel	NA	P-0029341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	111	545	0	ENST00000269305.4:c.473_478delinsCCCGCG	p.Arg158_Met160delinsProArgVal	p.R158_M160delinsPRV	ENST00000269305	NM_001126112.2	158	cGCGCCAtg/cCCCGCGtg	5/11	0.155927248458121	3	FACETS	0.855	0.768	0.948	0.855	0.768	0.948	CLONAL	2	TRUE	1	0.155927248458121	3		545	897	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	175	404	0				ENST00000310581	NM_198253.2	-/1132			0.191978727463739	4	FACETS	0.79	0.734	0.848	0.79	0.734	0.848	INDETERMINATE	2	TRUE	2	0.791760560713385	4		404	501	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459076	120459076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	286	526	0	ENST00000256646.2:c.6269C>T	p.Ser2090Phe	p.S2090F	ENST00000256646	NM_024408.3	2090	tCt/tTt	34/34	0.191978727463739	4	FACETS	0.921	0.871	0.971	0.921	0.871	0.971	INDETERMINATE	2	TRUE	2	0.791760560713385	4		526	703	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432348	49432348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	346	745	0	ENST00000301067.7:c.8791C>T	p.Pro2931Ser	p.P2931S	ENST00000301067	NM_003482.3	2931	Cca/Tca	34/54	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.791760560713385	2		745	741	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120796848	120796848	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	358	680	0	ENST00000257552.2:c.411C>A	p.Asp137Glu	p.D137E	ENST00000257552	NM_002442.3	137	gaC/gaA	7/15	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.791760560713385	2		680	786	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727441	66727441	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519728	NA	P-0029351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	230	436	0	ENST00000307102.5:c.157T>C	p.Phe53Leu	p.F53L	ENST00000307102	NM_002755.3	53	Ttt/Ctt	2/11	0.188257005854918	3	FACETS	1	0.992	1	0.708	0.665	0.751	INDETERMINATE	1	TRUE	1	0.791760560713385	3		436	573	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857940	9857940	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1412461359	NA	P-0029351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	288	534	0	ENST00000330684.3:c.3461C>T	p.Pro1154Leu	p.P1154L	ENST00000330684	NM_001134407.1	1154	cCc/cTc	13/13	0.191978727463739	4	FACETS	0.961	0.91	1	0.961	0.91	1	INDETERMINATE	2	TRUE	2	0.791760560713385	4		534	678	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222245	2222245	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	432	801	0	ENST00000398665.3:c.3077G>T	p.Gly1026Val	p.G1026V	ENST00000398665	NM_032482.2	1026	gGa/gTa	24/28	0.191978727463739	4	FACETS	1	0.969	1	1	0.969	1	INDETERMINATE	2	TRUE	2	0.791760560713385	4		801	963	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051607	30051607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	265	320	0	ENST00000338641.4:c.541C>T	p.Pro181Ser	p.P181S	ENST00000338641	NM_000268.3	181	Ccg/Tcg	6/16	0.191978727463739	4	FACETS	1	0.98	1	1	0.98	1	INDETERMINATE	2	TRUE	2	0.791760560713385	4		320	560	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162186	47162186	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377488968	NA	P-0029351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	226	386	1	ENST00000409792.3:c.3940C>T	p.Pro1314Ser	p.P1314S	ENST00000409792	NM_014159.6	1314	Cct/Tct	3/21	0.191978727463739	4	FACETS	0.972	0.915	1	0.972	0.915	1	INDETERMINATE	2	TRUE	2	0.791760560713385	4		387	526	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0029351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	497	465	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.791760560713385	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.791760560713385	3		465	563	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111499	8111500	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0029353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	364	427	0	ENST00000346208.3:c.987dup	p.Arg330GlufsTer22	p.R330Efs*22	ENST00000346208		329	agg/aGgg	5/6	0.463376654105872	5	FACETS	0.839	0.794	0.884			1	CLONAL	2	TRUE	NA	0.597621029071173	5		427	1377	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068863	30068866	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TGAG	TGAG	-	novel	NA	P-0029353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	109	358	0	ENST00000331968.5:c.2063_2066del	p.Thr688ArgfsTer26	p.T688Rfs*26	ENST00000331968	NM_002742.2	688	aCTCAg/ag	14/18	0.597621029071173	6	FACETS	0.838	0.756	0.923			1	CLONAL	2	TRUE	NA	0.597621029071173	6		358	478	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47684692	47684692	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	261	366	0	ENST00000347630.2:c.757G>T	p.Glu253Ter	p.E253*	ENST00000347630	NM_001007230.1	253	Gaa/Taa	9/11	0.595583948871794	3	FACETS	0.873	0.832	0.914	0.873	0.832	0.914	CLONAL	3	TRUE	0	0.597621029071173	3		366	433	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62311237	62311237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760939207	NA	P-0029353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	118	276	1	ENST00000360203.5:c.1073C>T	p.Thr358Met	p.T358M	ENST00000360203	NM_001283009.1	358	aCg/aTg	13/35	0.597621029071173	14	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.597621029071173	14		277	1294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0029354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	225	950	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.528975588789995	3	FACETS	0.838	0.796	0.881	0.838	0.796	0.881	CLONAL	3	FALSE	0	0.615738822378963	3		950	380	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118602	11118602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	73	322	0	ENST00000358026.2:c.2026G>A	p.Ala676Thr	p.A676T	ENST00000358026	NM_001128849.1	676	Gca/Aca	14/36	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.615738822378963	NA		322	358	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912834	50912834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747628342	NA	P-0029354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	97	375	0	ENST00000440232.2:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000440232	NM_002691.3	689	Cgg/Tgg	17/27	0.435600143563068	5	FACETS	1	0.977	1			1	CLONAL	1	FALSE	NA	0.615738822378963	5		375	453	SUCCESS
APC	324	MSKCC	GRCh37	5	112175935	112175935	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	31	184	0	ENST00000257430.4:c.4644C>A	p.Asn1548Lys	p.N1548K	ENST00000257430	NM_000038.5	1548	aaC/aaA	16/16	0.627715242857981	4	FACETS	0.935	0.764	1	0.468	0.382	0.562	CLONAL	1	FALSE	2	0.615738822378963	4		184	174	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554345	141554345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748399150	NA	P-0029355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	11	519	2	ENST00000220592.5:c.1806del	p.Ala603ProfsTer92	p.A603Pfs*92	ENST00000220592	NM_012154.3	602	ccC/cc	14/19	0.160062411470237	3	FACETS	0.533	0.368	0.739	0.267	0.184	0.37	SUBCLONAL	1	TRUE	1	0.214417270427107	3		521	213	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0029355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	23	722	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	0.214417270427107	2		722	167	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61729435	61729435	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	11	249	0	ENST00000401558.2:c.312del	p.Lys104AsnfsTer17	p.K104Nfs*17	ENST00000401558	NM_003400.3	104	aaA/aa	5/25	1	2	FACETS	0.841	0.585	1	0.841	0.585	1	CLONAL	1	TRUE	1	0.214417270427107	2		249	122	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485747	57485747	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	88	216	0	ENST00000371085.3:c.1048A>G	p.Thr350Ala	p.T350A	ENST00000371085	NM_000516.4	350	Act/Gct	13/13	0.262483297523008	4	FACETS	1	0.975	1	0.686	0.609	0.768	CLONAL	1	TRUE	2	0.31	4		216	542	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411411	63411411	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	228	326	10	ENST00000330258.3:c.1756C>T	p.Arg586Ter	p.R586*	ENST00000330258	NM_152424.3	586	Cga/Tga	2/2	1	1	FACETS		NA	1			1	NA	NA	TRUE	0	NA	1		336	286	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0029357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	180	532	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		532	593	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411411	63411411	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	259	326	10	ENST00000330258.3:c.1756C>T	p.Arg586Ter	p.R586*	ENST00000330258	NM_152424.3	586	Cga/Tga	2/2	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		336	424	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163461	47163461	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	88	312	0	ENST00000409792.3:c.2665G>T	p.Gly889Ter	p.G889*	ENST00000409792	NM_014159.6	889	Gga/Tga	3/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		312	407	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876533	35876533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1329173277	NA	P-0029357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	384	547	0	ENST00000303115.3:c.1325G>A	p.Gly442Glu	p.G442E	ENST00000303115	NM_002185.3	442	gGa/gAa	8/8	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		547	915	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678335	88678335	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	109	572	0	ENST00000360948.2:c.1201C>A	p.Pro401Thr	p.P401T	ENST00000360948	NM_001012338.2	401	Cca/Aca	9/19	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		572	691	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993348	72993348	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	288	758	0	ENST00000268489.5:c.697G>T	p.Val233Leu	p.V233L	ENST00000268489	NM_006885.3	233	Gtg/Ttg	2/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		758	1038	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984968	55984968	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0029357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	154	340	0	ENST00000263923.4:c.162-1G>T		p.X54_splice	ENST00000263923	NM_002253.2	54			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		340	488	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242767	66242767	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	132	364	0	ENST00000273854.3:c.1805G>C	p.Gly602Ala	p.G602A	ENST00000273854	NM_004439.5	602	gGc/gCc	9/18	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		364	527	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0029358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	72	440	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.615596330141239	3	FACETS	0.947	0.834	1	0.474	0.417	0.534	CLONAL	1	TRUE	1	0.615596330141239	3		440	323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0029358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	300	411	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.615596330141239	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.615596330141239	2		411	449	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782238	56782238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	326	316	0	ENST00000308159.5:c.79C>T	p.Pro27Ser	p.P27S	ENST00000308159	NM_014669.4	27	Ccc/Tcc	2/22	0.437538888444747	5	FACETS	1	0.992	1			1	CLONAL	4	TRUE	NA	0.615596330141239	5		316	459	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131250	17131250	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587778365	NA	P-0029358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	106	498	0	ENST00000285071.4:c.202A>G	p.Ser68Gly	p.S68G	ENST00000285071	NM_144997.5	68	Agc/Ggc	4/14	0.615596330141239	2	FACETS	0.544	0.488	0.603	0.272	0.244	0.302	SUBCLONAL	1	TRUE	0	0.615596330141239	2		498	633	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619332	1619332	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2277754	NA	P-0029358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	65	457	0	ENST00000344749.5:c.1309G>A	p.Gly437Arg	p.G437R	ENST00000344749	NM_001136139.2	437	Ggg/Agg	15/19	NA	2	FACETS	0.443	0.384	0.506			1	INDETERMINATE	1	TRUE	NA	0.615596330141239	2		457	477	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891187	151891187	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	149	329	0	ENST00000262189.6:c.4567T>G	p.Leu1523Val	p.L1523V	ENST00000262189	NM_170606.2	1523	Tta/Gta	31/59	0.615596330141239	2	FACETS	1	0.958	1	0.531	0.489	0.574	CLONAL	1	TRUE	0	0.615596330141239	2		329	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0029362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	98	402	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.296916942106993	1	FACETS	0.835	0.746	0.93	0.835	0.746	0.93	CLONAL	1	TRUE	0	0.306266731305831	1		402	649	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271447	26271447	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	47	301	0	ENST00000305910.3:c.166C>G	p.Gln56Glu	p.Q56E	ENST00000305910	NM_003534.2	56	Cag/Gag	1/1	0.306266731305831	3	FACETS	0.575	0.484	0.675	0.287	0.242	0.338	SUBCLONAL	1	TRUE	1	0.306266731305831	3		301	616	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210377	36210377	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	98	424	1	ENST00000222270.7:c.370C>T	p.Gln124Ter	p.Q124*	ENST00000222270	NM_014727.1	124	Cag/Tag	2/37	1	2	FACETS	0.806	0.719	0.899	0.806	0.719	0.899	CLONAL	1	TRUE	1	0.306266731305831	2		425	794	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720681	89720681	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	35	178	0	ENST00000371953.3:c.833del	p.Phe278SerfsTer13	p.F278Sfs*13	ENST00000371953	NM_000314.4	278	Ttc/tc	8/9	0.306266731305831	1	FACETS	0.756	0.623	0.904	0.756	0.623	0.904	CLONAL	1	TRUE	0	0.306266731305831	1		178	256	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842603	68842603	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	77	379	0	ENST00000261769.5:c.539C>G	p.Ser180Cys	p.S180C	ENST00000261769	NM_004360.3	180	tCc/tGc	5/16	0.296916942106993	1	FACETS	0.751	0.66	0.848	0.751	0.66	0.848	SUBCLONAL	1	TRUE	0	0.306266731305831	1		379	567	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670631	134670631	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	127	449	0	ENST00000398015.3:c.542G>C	p.Gly181Ala	p.G181A	ENST00000398015	NM_004441.4	181	gGa/gCa	3/16	0.306266731305831	3	FACETS	0.925	0.836	1	0.462	0.418	0.509	CLONAL	1	TRUE	1	0.306266731305831	3		449	1034	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591136	67591144	+	inframe_deletion	In_Frame_Del	DEL	AGAGACCAA	AGAGACCAA	-	novel	NA	P-0029362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	57	236	0	ENST00000274335.5:c.1729_1737del	p.Arg577_Gln579del	p.R577_Q579del	ENST00000274335		577	AGAGACCAA/-	12/15	1	2	FACETS	0.818	0.703	0.943	0.818	0.703	0.943	CLONAL	1	TRUE	1	0.306266731305831	2		236	455	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523660	176523660	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	126	605	0	ENST00000292408.4:c.2071C>G	p.Pro691Ala	p.P691A	ENST00000292408	NM_213647.1	691	Cct/Gct	16/18	1	2	FACETS	0.912	0.825	1	0.912	0.825	1	CLONAL	1	TRUE	1	0.306266731305831	2		605	902	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525471	137525471	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	84	343	2	ENST00000367739.4:c.544G>A	p.Glu182Lys	p.E182K	ENST00000367739	NM_000416.2	182	Gag/Aag	4/7	0.306266731305831	3	FACETS	0.948	0.838	1	0.474	0.419	0.534	CLONAL	1	TRUE	1	0.306266731305831	3		345	667	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38173545	38173545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	88	260	0	ENST00000317025.8:c.1871C>T	p.Ser624Leu	p.S624L	ENST00000317025	NM_023034.1	624	tCa/tTa	10/24	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.306266731305831	2		260	524	SUCCESS
AR	367	MSKCC	GRCh37	X	66942821	66942821	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	102	326	1	ENST00000374690.3:c.2602C>T	p.Gln868Ter	p.Q868*	ENST00000374690	NM_000044.3	868	Cag/Tag	7/8	1	2	FACETS	0.939	0.841	1	0.939	0.841	1	CLONAL	1	TRUE	1	0.306266731305831	2		327	709	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441252	52441252	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	136	438	0	ENST00000460680.1:c.518A>G	p.Tyr173Cys	p.Y173C	ENST00000460680	NM_004656.3	173	tAt/tGt	7/17	0.364779011181751	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.369597145356683	1		438	598	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0029363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	65	231	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.369597145356683	2		231	347	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663033	227663033	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	137	394	0	ENST00000305123.5:c.422G>C	p.Gly141Ala	p.G141A	ENST00000305123	NM_005544.2	141	gGc/gCc	1/2	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.369597145356683	2		394	658	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0029364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	46	440	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.779	0.657	0.915	0.779	0.657	0.915	CLONAL	1	TRUE	1	0.247965911516167	2		440	476	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0029364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	45	532	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.787	0.662	0.926	0.787	0.662	0.926	CLONAL	1	TRUE	1	0.247965911516167	2		532	461	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247168	153247168	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1560758208	NA	P-0029364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	31	225	0	ENST00000281708.4:c.1634A>G	p.Tyr545Cys	p.Y545C	ENST00000281708	NM_033632.3	545	tAt/tGt	10/12	1	2	FACETS	0.687	0.556	0.835	0.687	0.556	0.835	SUBCLONAL	1	TRUE	1	0.247965911516167	2		225	364	SUCCESS
APC	324	MSKCC	GRCh37	5	112175760	112175761	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs398123122	NA	P-0029364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	32	241	0	ENST00000257430.4:c.4473dup	p.Ala1492CysfsTer22	p.A1492Cfs*22	ENST00000257430	NM_000038.5	1490	cat/caTt	16/16	1	2	FACETS	0.63	0.511	0.763	0.63	0.511	0.763	SUBCLONAL	1	TRUE	1	0.247965911516167	2		241	410	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457388	67457388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	172	487	1	ENST00000327367.4:c.362G>A	p.Cys121Tyr	p.C121Y	ENST00000327367	NM_005902.3	121	tGc/tAc	2/9	0.177648507868919	2	FACETS	0.795	0.732	0.861	0.795	0.732	0.861	SUBCLONAL	2	TRUE	0	0.247965911516167	2		488	872	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395647	45395647	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	31	416	0	ENST00000262160.6:c.487A>G	p.Asn163Asp	p.N163D	ENST00000262160	NM_005901.5	163	Aac/Gac	4/11	1	2	FACETS	0.495	0.4	0.604	0.495	0.4	0.604	SUBCLONAL	1	TRUE	1	0.247965911516167	2		416	505	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958075	54958075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	48	229	0	ENST00000312783.6:c.532C>T	p.Leu178Phe	p.L178F	ENST00000312783	NM_198436.1	178	Ctc/Ttc	6/10	1	2	FACETS	0.973	0.824	1	0.973	0.824	1	CLONAL	1	TRUE	1	0.247965911516167	2		229	398	SUCCESS
APC	324	MSKCC	GRCh37	5	112174303	112174303	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	36	253	0	ENST00000257430.4:c.3012del	p.Ala1005ProfsTer17	p.A1005Pfs*17	ENST00000257430	NM_000038.5	1004	ctA/ct	16/16	1	2	FACETS	0.811	0.668	0.971	0.811	0.668	0.971	CLONAL	1	TRUE	1	0.247965911516167	2		253	358	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971177	21971177	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913382	NA	P-0029366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	844	349	0	ENST00000304494.5:c.181G>T	p.Glu61Ter	p.E61*	ENST00000304494	NM_000077.4	61	Gag/Tag	2/3	0.950899217363002	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.959513449488028	2		349	857	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258611	16258611	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	834	383	0	ENST00000375759.3:c.5876G>T	p.Arg1959Leu	p.R1959L	ENST00000375759	NM_015001.2	1959	cGa/cTa	11/15	0.82783354856738	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.959513449488028	4		383	1666	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0029366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	1007	476	0	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	0.82783354856738	4	FACETS	0.923	0.898	0.949	0.923	0.898	0.949	CLONAL	2	TRUE	2	0.959513449488028	4		476	2227	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431982	49431983	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	789	578	0	ENST00000301067.7:c.9156dup	p.Thr3053TyrfsTer2	p.T3053Yfs*2	ENST00000301067	NM_003482.3	3052	-/T	34/54	0.948804870575383	3	FACETS	0.989	0.964	1	0.989	0.964	1	CLONAL	2	TRUE	1	0.959513449488028	3		578	1230	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440208	49440208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0029366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	314	391	1	ENST00000301067.7:c.4419-1G>T		p.X1473_splice	ENST00000301067	NM_003482.3	1473			0.948804870575383	3	FACETS	0.915	0.864	0.967	0.457	0.432	0.484	CLONAL	1	TRUE	1	0.959513449488028	3		392	1059	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988440	41988440	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	127	424	0	ENST00000219905.7:c.1232C>G	p.Thr411Arg	p.T411R	ENST00000219905	NM_001164273.1	411	aCg/aGg	3/24	0.950899217363002	2	FACETS	0.922	0.85	0.995	0.461	0.425	0.498	CLONAL	1	TRUE	0	0.959513449488028	2		424	287	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251093	99251093	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	253	439	0	ENST00000268035.6:c.397C>G	p.Leu133Val	p.L133V	ENST00000268035	NM_000875.3	133	Ctg/Gtg	2/21	0.95563578279491	4	FACETS	0.903	0.845	0.964	0.226	0.211	0.241	CLONAL	1	TRUE	0	0.959513449488028	4		439	1144	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969801	81969801	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	354	398	0	ENST00000359376.3:c.2870C>G	p.Ser957Cys	p.S957C	ENST00000359376	NM_002661.3	957	tCc/tGc	27/33	0.959513449488028	2	FACETS	0.992	0.946	1	0.496	0.473	0.519	CLONAL	1	TRUE	0	0.959513449488028	2		398	744	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs863224683	NA	P-0029366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	1035	692	0	ENST00000269305.4:c.388C>G	p.Leu130Val	p.L130V	ENST00000269305	NM_001126112.2	130	Ctc/Gtc	5/11	0.950899217363002	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.959513449488028	2		692	1062	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309568	30309568	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1845	659	502	0	ENST00000307677.4:c.454G>C	p.Val152Leu	p.V152L	ENST00000307677	NM_138578.1	152	Gtg/Ctg	2/3	0.959513449488028	5	FACETS	1	0.996	1			1	CLONAL	1	TRUE	NA	0.959513449488028	5		502	2504	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138375094	138375094	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	288	460	0	ENST00000289153.2:c.2965G>T	p.Ala989Ser	p.A989S	ENST00000289153	NM_006219.2	989	Gca/Tca	21/22	0.952724815343784	2	FACETS	1	0.961	1	0.507	0.481	0.533	CLONAL	1	TRUE	0	0.959513449488028	2		460	592	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149453012	149453012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	542	307	0	ENST00000286301.3:c.934G>T	p.Glu312Ter	p.E312*	ENST00000286301	NM_005211.3	312	Gag/Tag	7/22	0.954455091596277	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.959513449488028	2		307	560	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031997	26031997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	429	281	0	ENST00000244661.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000244661	NM_003537.3	98	Gag/Aag	1/1	0.89647902561893	3	FACETS	0.949	0.915	0.983	0.949	0.915	0.983	CLONAL	2	TRUE	1	0.959513449488028	3		281	697	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977611	2977611	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	1126	612	0	ENST00000396946.4:c.1073G>T	p.Cys358Phe	p.C358F	ENST00000396946	NM_032415.4	358	tGt/tTt	8/25	0.959513449488028	3	FACETS	1	0.998	1	1	0.998	1	CLONAL	3	TRUE	0	0.959513449488028	3		612	1145	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227978	55227978	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	219	357	0	ENST00000275493.2:c.1445G>T	p.Gly482Val	p.G482V	ENST00000275493	NM_005228.3	482	gGg/gTg	12/28	0.959513449488028	3	FACETS	0.992	0.975	1	0.992	0.975	1	CLONAL	3	TRUE	0	0.959513449488028	3		357	227	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868497	117868497	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	342	262	4	ENST00000297338.2:c.845A>T	p.Asp282Val	p.D282V	ENST00000297338	NM_006265.2	282	gAt/gTt	8/14	0.959513449488028	5	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	2	0.959513449488028	5		266	565	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215820	98215820	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	540	418	0	ENST00000331920.6:c.3389C>T	p.Ala1130Val	p.A1130V	ENST00000331920	NM_000264.3	1130	gCc/gTc	20/24	0.950899217363002	2	FACETS	1	0.97	1	0.504	0.485	0.523	CLONAL	1	TRUE	0	0.959513449488028	2		418	1117	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216529	7216532	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ACTG	ACTG	-	novel	NA	P-0029367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	409	453	0	ENST00000380728.2:c.803_804+2del		p.X268_splice	ENST00000380728		268		9/11	0.785162335426031	1	FACETS	0.982	0.95	1	0.982	0.95	1	CLONAL	1	TRUE	0	0.826712356775865	1		453	591	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499377	89499377	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	223	358	0	ENST00000336596.2:c.2547C>G	p.Cys849Trp	p.C849W	ENST00000336596	NM_005233.5	849	tgC/tgG	15/17	0.785162335426031	1	FACETS	0.831	0.788	0.873	0.831	0.788	0.873	CLONAL	1	TRUE	0	0.826712356775865	1		358	381	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939029	48939029	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0029368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	126	206	0	ENST00000267163.4:c.862-1G>A		p.X288_splice	ENST00000267163	NM_000321.2	288			0.520905260195312	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.520905260195312	1		206	286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578188	7578199	+	inframe_deletion	In_Frame_Del	DEL	CATAGGGCACCA	CATAGGGCACCA	-	novel	NA	P-0029368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	457	575	0	ENST00000269305.4:c.650_661del	p.Val217_Tyr220del	p.V217_Y220del	ENST00000269305	NM_001126112.2	217	gTGGTGCCCTATGag/gag	6/11	0.519462962735752	2	FACETS	0.968	0.93	1	0.968	0.93	1	CLONAL	2	TRUE	0	0.520905260195312	2		575	906	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0029370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	203	465	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.786	0.731	0.843	1	0.992	1	SUBCLONAL	2	TRUE	1	0.333218244523053	2		465	775	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448592	89448592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543425684	NA	P-0029370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	124	478	2	ENST00000336596.2:c.1556C>T	p.Thr519Met	p.T519M	ENST00000336596	NM_005233.5	519	aCg/aTg	7/17	1	2	FACETS	0.823	0.744	0.907	0.823	0.744	0.907	CLONAL	1	TRUE	1	0.333218244523053	2		480	904	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0029370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	31	312	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	0.290107470920169	1	FACETS	0.414	0.334	0.503	0.414	0.334	0.503	SUBCLONAL	1	TRUE	0	0.333218244523053	1		312	375	SUCCESS
APC	324	MSKCC	GRCh37	5	112175621	112175621	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	70	360	0	ENST00000257430.4:c.4330C>T	p.Gln1444Ter	p.Q1444*	ENST00000257430	NM_000038.5	1444	Caa/Taa	16/16	0.290107470920169	1	FACETS	0.695	0.607	0.789	0.695	0.607	0.789	SUBCLONAL	1	TRUE	0	0.333218244523053	1		360	504	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201082	108201082	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs773516672	NA	P-0029370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	23	359	0	ENST00000278616.4:c.7449G>A	p.Trp2483Ter	p.W2483*	ENST00000278616	NM_000051.3	2483	tgG/tgA	50/63	0.290107470920169	1	FACETS	0.256	0.199	0.322	0.256	0.199	0.322	SUBCLONAL	1	TRUE	0	0.333218244523053	1		359	450	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478795	56478795	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	119	538	0	ENST00000267101.3:c.251C>A	p.Thr84Lys	p.T84K	ENST00000267101	NM_001982.3	84	aCa/aAa	3/28	1	2	FACETS	0.87	0.785	0.96	0.87	0.785	0.96	CLONAL	1	TRUE	1	0.333218244523053	2		538	821	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124310	2124310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs936484229	NA	P-0029373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	269	636	2	ENST00000219476.3:c.2465C>T	p.Ala822Val	p.A822V	ENST00000219476	NM_000548.3	822	gCg/gTg	22/42	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.6	2		638	762	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49941020	49941020	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375375932	NA	P-0029373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	176	497	1	ENST00000296474.3:c.23C>T	p.Pro8Leu	p.P8L	ENST00000296474	NM_002447.2	8	cCt/cTt	1/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.6	2		498	516	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125636	47125636	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0121600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	244	311	0	ENST00000409792.3:c.5634del	p.Arg1879AlafsTer3	p.R1879Afs*3	ENST00000409792	NM_014159.6	1878	ttT/tt	12/21	0.783977430375079	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	NA	0	0.783977430375079	1		311	369	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692896	89692896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123322	NA	P-0029380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	133	418	0	ENST00000371953.3:c.380G>A	p.Gly127Glu	p.G127E	ENST00000371953	NM_000314.4	127	gGa/gAa	5/9	0.201821556452364	2	FACETS	0.971	0.883	1	0.971	0.883	1	CLONAL	2	TRUE	0	0.2	2		418	685	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0029380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	129	554	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.2	2		554	941	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956964	2956964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1395288944	NA	P-0029380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	76	584	3	ENST00000396946.4:c.2663G>A	p.Arg888His	p.R888H	ENST00000396946	NM_032415.4	888	cGt/cAt	20/25	1	2	FACETS	0.727	0.635	0.825	0.727	0.635	0.825	SUBCLONAL	1	TRUE	1	0.2	2		587	1046	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990389	81990389	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	121	553	0	ENST00000359376.3:c.3660C>G	p.His1220Gln	p.H1220Q	ENST00000359376	NM_002661.3	1220	caC/caG	32/33	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.2	2		553	964	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391980	139391980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	172	690	0	ENST00000277541.6:c.6211G>A	p.Glu2071Lys	p.E2071K	ENST00000277541	NM_017617.3	2071	Gag/Aag	34/34	1	2	FACETS	0.88	0.81	0.954	1	0.991	1	CLONAL	2	TRUE	1	0.2	2		690	977	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014192	14014192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	183	315	4	ENST00000311895.7:c.170G>A	p.Cys57Tyr	p.C57Y	ENST00000311895	NM_005236.2	57	tGc/tAc	1/11	0.863322187936749	4	FACETS	1	0.982	1	0.395	0.366	0.425	CLONAL	1	TRUE	1	0.897281321618255	4		319	653	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	175	394	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.854	0.789	0.922	0.854	0.789	0.922	CLONAL	1	TRUE	1	0.558256476321709	2		394	734	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0029382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	189	347	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.95	0.881	1	0.95	0.881	1	CLONAL	1	TRUE	1	0.558256476321709	2		347	713	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0029382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	171	393	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.921	0.85	0.994	0.921	0.85	0.994	CLONAL	1	TRUE	1	0.558256476321709	2		393	665	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66522006	66522007	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGAAAT	novel	NA	P-0029382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	169	319	1	ENST00000358598.2:c.664_669dup	p.Lys222_Leu223dup	p.K222_L223dup	ENST00000358598	NM_212471.2	222	gtg/gTGAAATtg	7/11	1	2	FACETS	0.888	0.819	0.959	0.888	0.819	0.959	CLONAL	1	TRUE	1	0.558256476321709	2		320	682	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410676	63410676	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	134	708	0	ENST00000330258.3:c.2491G>T	p.Asp831Tyr	p.D831Y	ENST00000330258	NM_152424.3	831	Gat/Tat	2/2	0.463029701297704	3	FACETS	0.503	0.456	0.553			1	SUBCLONAL	1	TRUE	NA	0.558256476321709	3		708	1221	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	571	404	0				ENST00000310581	NM_198253.2	-/1132			0.676168370784105	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	0	0.710444212280277	3		404	725	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257722	16257722	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	164	505	0	ENST00000375759.3:c.4987G>A	p.Val1663Ile	p.V1663I	ENST00000375759	NM_015001.2	1663	Gta/Ata	11/15	0.306952413894813	3	FACETS	1	0.97	1	0.551	0.508	0.595	INDETERMINATE	1	TRUE	1	0.710444212280277	3		505	568	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056302	27056302	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768302696	NA	P-0029387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	84	376	0	ENST00000324856.7:c.1298C>T	p.Thr433Ile	p.T433I	ENST00000324856	NM_006015.4	433	aCc/aTc	2/20	0.306952413894813	3	FACETS	0.714	0.633	0.799	0.357	0.316	0.4	INDETERMINATE	1	TRUE	1	0.710444212280277	3		376	449	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480015	120480015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	178	469	1	ENST00000256646.2:c.3412C>T	p.Pro1138Ser	p.P1138S	ENST00000256646	NM_024408.3	1138	Ccc/Tcc	21/34	NA	2	FACETS	0.984	0.915	1			1	INDETERMINATE	1	TRUE	NA	0.710444212280277	2		470	509	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690846	89690847	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0029387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	192	333	1	ENST00000371953.3:c.253_253+1delinsAA		p.X85_splice	ENST00000371953	NM_000314.4	85		4/9	0.710444212280277	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.710444212280277	1		334	314	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129113	64129113	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0029387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	350	479	0	ENST00000334205.4:c.652-1G>A		p.X218_splice	ENST00000334205	NM_003942.2	218			0.710444212280277	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.710444212280277	2		479	492	SUCCESS
CBL	867	MSKCC	GRCh37	11	119167632	119167632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	181	375	0	ENST00000264033.4:c.2041C>T	p.Leu681Phe	p.L681F	ENST00000264033	NM_005188.3	681	Ctt/Ttt	13/16	0.710444212280277	2	FACETS	0.891	0.843	0.938	0.891	0.843	0.938	CLONAL	2	TRUE	0	0.710444212280277	2		375	286	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143044	58143044	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	529	654	0	ENST00000257904.6:c.740G>T	p.Gly247Val	p.G247V	ENST00000257904	NM_000075.3	247	gGa/gTa	7/8	0.318509566412373	4	FACETS	1	0.996	1			1	INDETERMINATE	2	TRUE	NA	0.710444212280277	4		654	1026	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636143	28636143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371663652	NA	P-0029387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	291	555	1	ENST00000241453.7:c.229G>A	p.Glu77Lys	p.E77K	ENST00000241453	NM_004119.2	77	Gaa/Aaa	3/24	0.646768141644348	2	FACETS	0.896	0.858	0.934	0.896	0.858	0.934	CLONAL	2	TRUE	0	0.710444212280277	2		556	457	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907155	32907155	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	239	391	2	ENST00000380152.3:c.1540G>A	p.Glu514Lys	p.E514K	ENST00000380152		514	Gag/Aag	10/27	0.646768141644348	2	FACETS	0.929	0.887	0.97	0.929	0.887	0.97	CLONAL	2	TRUE	0	0.710444212280277	2		393	362	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873841	35873841	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	126	219	0	ENST00000216797.5:c.10G>A	p.Ala4Thr	p.A4T	ENST00000216797	NM_020529.2	4	Gcg/Acg	1/6	0.710444212280277	3	FACETS	1	0.982	1	0.646	0.591	0.702	CLONAL	1	TRUE	1	0.710444212280277	3		219	372	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857529	9857529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1325032512	NA	P-0029387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	67	290	0	ENST00000330684.3:c.3872C>T	p.Ser1291Phe	p.S1291F	ENST00000330684	NM_001134407.1	1291	tCc/tTc	13/13	0.338235659720824	2	FACETS	0.518	0.453	0.588	0.259	0.226	0.294	INDETERMINATE	1	TRUE	0	0.710444212280277	2		290	364	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647308	23647308	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	236	496	0	ENST00000261584.4:c.559C>T	p.Pro187Ser	p.P187S	ENST00000261584	NM_024675.3	187	Cct/Tct	4/13	0.338235659720824	2	FACETS	0.78	0.739	0.82	0.78	0.739	0.82	INDETERMINATE	2	TRUE	0	0.710444212280277	2		496	426	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783733	50783734	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0029387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	107	625	2	ENST00000398568.2:c.124_125delinsTT	p.Pro42Leu	p.P42L	ENST00000398568	NM_001042412.1	42	CCg/TTg	3/18	0.338235659720824	2	FACETS	0.498	0.447	0.551	0.249	0.223	0.276	INDETERMINATE	1	TRUE	0	0.710444212280277	2		627	605	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992885	72992885	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	117	508	0	ENST00000268489.5:c.1160C>T	p.Pro387Leu	p.P387L	ENST00000268489	NM_006885.3	387	cCc/cTc	2/10	0.338235659720824	2	FACETS	0.552	0.499	0.607	0.276	0.249	0.304	INDETERMINATE	1	TRUE	0	0.710444212280277	2		508	597	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663770	29663776	+	frameshift_variant	Frame_Shift_Del	DEL	TCCTTCA	TCCTTCA	-	novel	NA	P-0029387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	90	504	0	ENST00000356175.3:c.6202_6208del	p.Ser2068ThrfsTer20	p.S2068Tfs*20	ENST00000356175	NM_000267.3	2068	TCCTTCAac/ac	41/57	0.710444212280277	1	FACETS	0.636	0.573	0.701	0.636	0.573	0.701	SUBCLONAL	1	TRUE	0	0.710444212280277	1		504	257	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78811757	78811757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs929584625	NA	P-0029387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	158	526	0	ENST00000306801.3:c.1172C>T	p.Ser391Phe	p.S391F	ENST00000306801	NM_020761.2	391	tCt/tTt	10/34	0.710444212280277	2	FACETS	0.622	0.571	0.675	0.311	0.285	0.338	SUBCLONAL	1	TRUE	0	0.710444212280277	2		526	715	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246810	10246810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	364	612	0	ENST00000340748.4:c.4595C>T	p.Pro1532Leu	p.P1532L	ENST00000340748		1532	cCc/cTc	37/40	0.589718656379392	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.710444212280277	1		612	529	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209103954	209103954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	55	347	0	ENST00000345146.2:c.995C>T	p.Ser332Phe	p.S332F	ENST00000345146	NM_005896.2	332	tCc/tTc	9/10	1	2	FACETS	0.485	0.417	0.559	0.485	0.417	0.559	SUBCLONAL	1	TRUE	1	0.710444212280277	2		347	319	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663190	227663190	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1349427791	NA	P-0029387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	140	506	0	ENST00000305123.5:c.265C>T	p.Arg89Trp	p.R89W	ENST00000305123	NM_005544.2	89	Cgg/Tgg	1/2	1	2	FACETS	0.542	0.494	0.592	0.542	0.494	0.592	SUBCLONAL	1	TRUE	1	0.710444212280277	2		506	727	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023474	31023474	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376074119	NA	P-0029387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	199	418	0	ENST00000375687.4:c.2959G>A	p.Gly987Arg	p.G987R	ENST00000375687	NM_015338.5	987	Gga/Aga	13/13	0.380815513896953	3	FACETS	1	0.982	1	0.578	0.538	0.619	INDETERMINATE	1	TRUE	1	0.710444212280277	3		418	657	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739007	40739007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	205	463	0	ENST00000373198.4:c.3277C>T	p.Pro1093Ser	p.P1093S	ENST00000373198	NM_133170.3	1093	Ccc/Tcc	24/32	0.184659776142278	2	FACETS	1	0.988	1	0.617	0.578	0.655	INDETERMINATE	1	TRUE	0	0.710444212280277	2		463	468	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100905	41100905	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0029387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	70	385	0	ENST00000373198.4:c.1450+1G>A		p.X484_splice	ENST00000373198	NM_133170.3	484			0.184659776142278	2	FACETS	0.517	0.453	0.586	0.259	0.226	0.293	INDETERMINATE	1	TRUE	0	0.710444212280277	2		385	381	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306506	41306506	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	44	269	2	ENST00000373198.4:c.1153G>A	p.Asp385Asn	p.D385N	ENST00000373198	NM_133170.3	385	Gat/Aat	7/32	0.184659776142278	2	FACETS	0.418	0.353	0.491	0.209	0.176	0.246	INDETERMINATE	1	TRUE	0	0.710444212280277	2		271	296	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400190	41400190	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	103	400	0	ENST00000373198.4:c.569G>A	p.Arg190Lys	p.R190K	ENST00000373198	NM_133170.3	190	aGa/aAa	5/32	0.184659776142278	2	FACETS	0.734	0.662	0.809	0.367	0.331	0.405	INDETERMINATE	1	TRUE	0	0.710444212280277	2		400	395	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46276049	46276049	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	100	555	0	ENST00000371998.3:c.3485C>G	p.Pro1162Arg	p.P1162R	ENST00000371998		1162	cCc/cGc	18/23	0.184659776142278	2	FACETS	0.49	0.439	0.545	0.245	0.219	0.273	INDETERMINATE	1	TRUE	0	0.710444212280277	2		555	574	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185169095	185169095	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1245142546	NA	P-0029387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	69	407	0	ENST00000265026.3:c.1190G>A	p.Arg397Gln	p.R397Q	ENST00000265026	NM_004721.4	397	cGa/cAa	7/14	0.306952413894813	3	FACETS	0.504	0.44	0.574	0.252	0.22	0.287	INDETERMINATE	1	TRUE	1	0.710444212280277	3		407	522	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156102	106156102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	234	338	1	ENST00000380013.4:c.1003C>T	p.Pro335Ser	p.P335S	ENST00000380013	NM_001127208.2	335	Cct/Tct	3/11	0.593505629712563	3	FACETS	0.927	0.889	0.964	0.927	0.889	0.964	CLONAL	3	TRUE	0	0.710444212280277	3		339	321	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681829	30681829	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs774216207	NA	P-0029387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	218	579	1	ENST00000376406.3:c.268C>T	p.Arg90Ter	p.R90*	ENST00000376406	NM_014641.2	90	Cga/Tga	3/15	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.710444212280277	2		580	609	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729316	41729316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	193	430	0	ENST00000242208.4:c.1213G>A	p.Asp405Asn	p.D405N	ENST00000242208	NM_002192.2	405	Gat/Aat	3/3	0.380815513896953	3	FACETS	0.835	0.782	0.889	0.835	0.782	0.889	INDETERMINATE	2	TRUE	1	0.710444212280277	3		430	441	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268921	55268921	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs762795214	NA	P-0029387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	210	702	0	ENST00000275493.2:c.2987A>G	p.Asn996Ser	p.N996S	ENST00000275493	NM_005228.3	996	aAc/aGc	25/28	0.380815513896953	3	FACETS	1	0.976	1	0.551	0.513	0.59	INDETERMINATE	1	TRUE	1	0.710444212280277	3		702	727	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524340	148524340	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	215	352	0	ENST00000320356.2:c.644C>T	p.Pro215Leu	p.P215L	ENST00000320356	NM_004456.4	215	cCt/cTt	7/20	0.327538334913737	5	FACETS	0.874	0.821	0.926			1	INDETERMINATE	3	TRUE	NA	0.710444212280277	5		352	477	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271147	38271148	+	stop_lost	Nonstop_Mutation	DNP	CA	CA	AG	novel	NA	P-0029387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	358	426	0	ENST00000425967.3:c.2560_2561delinsCT	p.Ter854LeuextTer105	p.*854Lext*105	ENST00000425967	NM_001174067.1	854	TGa/CTa	19/19	0.345444233447899	5	FACETS	0.871	0.83	0.911	0.871	0.83	0.911	INDETERMINATE	3	TRUE	2	0.710444212280277	5		426	797	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101895007	101895007	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	50	207	0	ENST00000374994.4:c.560C>A	p.Ser187Ter	p.S187*	ENST00000374994	NM_004612.2	187	tCa/tAa	3/9	0.539270221853541	1	FACETS	0.378	0.324	0.437	0.378	0.324	0.437	SUBCLONAL	1	TRUE	0	0.710444212280277	1		207	240	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0029389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	118	498	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		498	760	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048780	180048780	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs780273008	NA	P-0029392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1197	91	563	2	ENST00000261937.6:c.1782C>A	p.Asn594Lys	p.N594K	ENST00000261937	NM_182925.4	594	aaC/aaA	13/30	1	2	FACETS	0.605	0.535	0.681	0.605	0.535	0.681	SUBCLONAL	1	TRUE	1	0.233410065068241	2		565	1288	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748543	43748543	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	78	408	0	ENST00000523873.1:c.497A>G	p.Tyr166Cys	p.Y166C	ENST00000523873		166	tAc/tGc	6/8	1	2	FACETS	0.797	0.699	0.902	0.797	0.699	0.902	CLONAL	1	TRUE	1	0.233410065068241	2		408	839	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814194	76814194	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	56	351	1	ENST00000373344.5:c.6450A>C	p.Arg2150Ser	p.R2150S	ENST00000373344	NM_000489.3	2150	agA/agC	29/35	0.183659047084341	1	FACETS	0.696	0.596	0.805	0.696	0.596	0.805	SUBCLONAL	1	TRUE	0	0.233410065068241	1		352	609	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0029393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	375	611	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	2	FALSE	NA	0.847419055082281	2		611	440	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439958	49439958	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0029393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	375	569	1	ENST00000301067.7:c.4584-1G>A		p.X1528_splice	ENST00000301067	NM_003482.3	1528			0.835399652287207	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	FALSE	0	0.847419055082281	2		570	442	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41228566	41228566	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	344	665	0	ENST00000357654.3:c.4423del	p.Asp1475ThrfsTer30	p.D1475Tfs*30	ENST00000357654	NM_007294.3	1475	Gac/ac	13/23	0.848098255649342	3	FACETS	0.975	0.952	0.997	0.975	0.952	0.997	CLONAL	3	FALSE	0	0.847419055082281	3		665	395	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280066	18280084	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGCCCCGGGCCCCGGCC	CGCGCCCCGGGCCCCGGCC	-	novel	NA	P-0029393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	73	169	0	ENST00000222254.8:c.2152_2170del	p.Ala718ArgfsTer150	p.A718Rfs*150	ENST00000222254	NM_005027.3	717	CGCGCCCCGGGCCCCGGCCcg/cg	16/16	0.848098255649342	4	FACETS	1	0.972	1	0.671	0.596	0.75	CLONAL	1	FALSE	2	0.847419055082281	4		169	237	SUCCESS
APC	324	MSKCC	GRCh37	5	112173791	112173791	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	119	360	0	ENST00000257430.4:c.2500T>A	p.Ser834Thr	p.S834T	ENST00000257430	NM_000038.5	834	Tcc/Acc	16/16	0.847419055082281	6	FACETS	1	0.918	1	0.17	0.153	0.188	CLONAL	1	FALSE	0	0.847419055082281	6		360	743	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055910	180055910	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1269	176	659	0	ENST00000261937.6:c.1075G>C	p.Ala359Pro	p.A359P	ENST00000261937	NM_182925.4	359	Gca/Cca	8/30	0.847419055082281	8	FACETS	1	0.933	1	0.17	0.155	0.185	CLONAL	1	FALSE	2	0.847419055082281	8		659	1445	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370717	55370717	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	100	545	1	ENST00000297316.4:c.19G>T	p.Gly7Ter	p.G7*	ENST00000297316	NM_022454.3	7	Gga/Tga	1/2	0.848098255649342	4	FACETS	0.877	0.787	0.972	0.439	0.393	0.486	CLONAL	1	FALSE	2	0.847419055082281	4		546	497	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438153	110438153	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1314168066	NA	P-0029394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	159	321	0	ENST00000375856.3:c.248G>A	p.Arg83Gln	p.R83Q	ENST00000375856	NM_003749.2	83	cGg/cAg	1/2	0.620094209989966	3	FACETS	1	0.923	1	0.502	0.461	0.544	CLONAL	1	TRUE	1	0.620094209989966	3		321	669	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332436	70332436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772124361	NA	P-0029394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	244	520	1	ENST00000373644.4:c.341G>A	p.Arg114Gln	p.R114Q	ENST00000373644	NM_030625.2	114	cGa/cAa	2/12	1	2	FACETS	0.954	0.894	1	0.954	0.894	1	CLONAL	1	TRUE	1	0.620094209989966	2		521	825	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778894	3778894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1421133831	NA	P-0029394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	152	456	0	ENST00000262367.5:c.6154C>T	p.Arg2052Trp	p.R2052W	ENST00000262367	NM_004380.2	2052	Cgg/Tgg	31/31	1	2	FACETS	0.99	0.912	1	0.99	0.912	1	CLONAL	1	TRUE	1	0.620094209989966	2		456	495	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560486	65560486	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	79	391	0	ENST00000358664.4:c.111C>G	p.Asp37Glu	p.D37E	ENST00000358664	NM_002382.4	37	gaC/gaG	3/5	0.620094209989966	1	FACETS	0.342	0.301	0.386	0.342	0.301	0.386	SUBCLONAL	1	TRUE	0	0.620094209989966	1		391	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578283	7578283	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	178	500	0	ENST00000269305.4:c.566C>A	p.Ala189Asp	p.A189D	ENST00000269305	NM_001126112.2	189	gCc/gAc	6/11	0.598370508474009	1	FACETS	0.861	0.802	0.922	0.861	0.802	0.922	CLONAL	1	TRUE	0	0.620094209989966	1		500	460	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575175	48575175	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0029394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	50	280	0	ENST00000342988.3:c.369T>A	p.Cys123Ter	p.C123*	ENST00000342988	NM_005359.5	123	tgT/tgA	3/12	0.618645079976032	1	FACETS	0.38	0.324	0.44	0.38	0.324	0.44	SUBCLONAL	1	TRUE	0	0.620094209989966	1		280	293	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323193	31323193	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	33	536	0	ENST00000412585.2:c.796C>T	p.Gln266Ter	p.Q266*	ENST00000412585	NM_005514.6	266	Cag/Tag	4/8	0.167943653781481	2	FACETS	0.161	0.131	0.196	0.081	0.065	0.098	INDETERMINATE	1	TRUE	0	0.620094209989966	2		536	660	SUCCESS
AR	367	MSKCC	GRCh37	X	66765070	66765070	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	48	623	2	ENST00000374690.3:c.82C>T	p.Gln28Ter	p.Q28*	ENST00000374690	NM_000044.3	28	Cag/Tag	1/8	0.620094209989966	2	FACETS	0.176	0.148	0.207	0.088	0.074	0.104	SUBCLONAL	1	TRUE	0	0.620094209989966	2		625	878	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0029395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	254	593	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.95	0.894	1	0.95	0.894	1	CLONAL	1	TRUE	1	0.746466940107366	2		593	716	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113361	209113361	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765848107	NA	P-0029395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	134	307	0	ENST00000345146.2:c.146G>A	p.Arg49His	p.R49H	ENST00000345146	NM_005896.2	49	cGt/cAt	4/10	1	2	FACETS	0.921	0.845	0.998	0.921	0.845	0.998	CLONAL	1	TRUE	1	0.746466940107366	2		307	390	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156734	20156734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	188	428	0	ENST00000379607.5:c.23G>A	p.Gly8Glu	p.G8E	ENST00000379607	NM_001412.3	8	gGa/gAa	2/7	1	2	FACETS	0.967	0.901	1	0.967	0.901	1	CLONAL	1	TRUE	1	0.746466940107366	2		428	521	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0029396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	152	532	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.267057050266226	1	FACETS	1	0.96	1	1	0.992	1	CLONAL	2	TRUE	0	0.267454993073233	1		532	463	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913399	NA	P-0029396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	36	265	0	ENST00000349496.5:c.100G>C	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Cga	3/15	1	2	FACETS	0.678	0.558	0.813	0.678	0.558	0.813	SUBCLONAL	1	TRUE	1	0.267454993073233	2		265	397	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338645	70338645	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	149	299	0	ENST00000374080.3:c.41T>C	p.Leu14Pro	p.L14P	ENST00000374080		14	cTg/cCg	1/45	1	1	FACETS	1	0.983	1	1	0.993	1	CLONAL	2	TRUE	0	0.267454993073233	1		299	394	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339327	70339327	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	42	191	0	ENST00000374080.3:c.204G>C	p.Lys68Asn	p.K68N	ENST00000374080		68	aaG/aaC	2/45	1	1	FACETS	0.919	0.771	1	0.919	0.771	1	CLONAL	1	TRUE	0	0.267454993073233	1		191	296	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413742	138413742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769082299	NA	P-0029396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	134	276	1	ENST00000289153.2:c.1778C>T	p.Ala593Val	p.A593V	ENST00000289153	NM_006219.2	593	gCg/gTg	12/22	1	2	FACETS	1	0.979	1	1	0.992	1	CLONAL	2	TRUE	1	0.267454993073233	2		277	414	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798111	45798111	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	51	516	0	ENST00000450313.1:c.740G>T	p.Arg247Leu	p.R247L	ENST00000450313	NM_012222.2	247	cGa/cTa	9/16	1	2	FACETS	0.482	0.409	0.563	0.482	0.409	0.563	SUBCLONAL	1	TRUE	1	0.267454993073233	2		516	791	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206942060	206942060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	79	295	0	ENST00000423557.1:c.458G>A	p.Gly153Asp	p.G153D	ENST00000423557	NM_000572.2	153	gGc/gAc	5/5	0.267454993073233	7	FACETS	1	0.973	1	0.352	0.309	0.398	CLONAL	1	TRUE	3	0.267454993073233	7		295	700	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793385	18793385	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	69	382	0	ENST00000266497.5:c.4082C>T	p.Pro1361Leu	p.P1361L	ENST00000266497		1361	cCc/cTc	30/31	0.267057050266226	1	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	0	0.267454993073233	1		382	440	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047907	180047907	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	461	633	1	ENST00000261937.6:c.2268C>A	p.Cys756Ter	p.C756*	ENST00000261937	NM_182925.4	756	tgC/tgA	15/30	0.197356008486552	4	FACETS	0.944	0.904	0.985	1	0.997	1	CLONAL	4	TRUE	2	0.267454993073233	4		634	1157	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431404	121431404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780357	NA	P-0029397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	235	493	0	ENST00000257555.6:c.608G>A	p.Arg203His	p.R203H	ENST00000257555		203	cGt/cAt	3/10	0.142989645768386	5	FACETS	1	0.934	1	0.668	0.622	0.715	INDETERMINATE	2	TRUE	2	0.29	5		493	1161	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465976	69465976	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775723921	NA	P-0029397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	306	586	0	ENST00000227507.2:c.814G>A	p.Glu272Lys	p.E272K	ENST00000227507	NM_053056.2	272	Gag/Aag	5/5	0.290028351605097	4	FACETS	1	0.983	1			1	CLONAL	2	TRUE	NA	0.29	4		586	1225	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443763	49443763	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	367	588	0	ENST00000301067.7:c.3608A>G	p.Asp1203Gly	p.D1203G	ENST00000301067	NM_003482.3	1203	gAc/gGc	11/54	0.295302319147779	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.29	3		588	1407	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842337	68842337	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	126	329	0	ENST00000261769.5:c.398C>G	p.Ser133Cys	p.S133C	ENST00000261769	NM_004360.3	133	tCt/tGt	4/16	0.200630066112549	3	FACETS	1	0.974	1	0.605	0.548	0.666	CLONAL	1	TRUE	1	0.29	3		329	822	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265291	10265291	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	165	357	0	ENST00000340748.4:c.1755C>G	p.Ile585Met	p.I585M	ENST00000340748		585	atC/atG	20/40	0.282226846919893	3	FACETS	0.879	0.809	0.952	0.879	0.809	0.952	CLONAL	2	TRUE	1	0.29	3		357	741	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044389	128044389	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	210	461	0	ENST00000285398.2:c.1232C>G	p.Ser411Cys	p.S411C	ENST00000285398	NM_000122.1	411	tCc/tGc	8/15	0.200630066112549	3	FACETS	0.888	0.825	0.953	0.888	0.825	0.953	CLONAL	2	TRUE	1	0.29	3		461	934	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62317187	62317187	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1366	78	575	0	ENST00000360203.5:c.1310G>T	p.Arg437Leu	p.R437L	ENST00000360203	NM_001283009.1	437	cGg/cTg	16/35	0.20714530037575	4	FACETS	0.481	0.42	0.546			1	SUBCLONAL	1	TRUE	NA	0.29	4		575	1444	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239871	53239871	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	50	188	1	ENST00000375401.3:c.1570A>T	p.Asn524Tyr	p.N524Y	ENST00000375401	NM_004187.3	524	Aac/Tac	11/26	0.295302319147779	2	FACETS	0.683	0.579	0.796			1	SUBCLONAL	1	TRUE	NA	0.29	2		189	505	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	173	483	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	0.54050505816769	2		483	621	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	173	440	5	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.973	0.899	1	0.973	0.899	1	CLONAL	1	TRUE	1	0.54050505816769	2		445	658	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	453	768	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.54050505816769	2	FACETS	0.977	0.939	1	0.977	0.939	1	CLONAL	2	TRUE	0	0.54050505816769	2		768	858	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	267	663	3	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	0.54050505816769	2		666	961	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007619	45007619	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs111482205	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	80	222	0	ENST00000558401.1:c.68-2A>G		p.X23_splice	ENST00000558401	NM_004048.2	23			1	2	FACETS	0.993	0.884	1	0.993	0.884	1	CLONAL	1	TRUE	1	0.54050505816769	2		222	298	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	536	698	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.949	0.915	0.983	1	0.998	1	CLONAL	2	TRUE	1	0.54050505816769	2		704	1045	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	130	631	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.814	0.741	0.89	0.814	0.741	0.89	CLONAL	1	TRUE	1	0.54050505816769	2		632	591	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	213	643	10	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.954	0.888	1	0.954	0.888	1	CLONAL	1	TRUE	1	0.54050505816769	2		653	826	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	209	648	4	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	0.888	0.825	0.952	0.888	0.825	0.952	CLONAL	1	TRUE	1	0.54050505816769	2		652	871	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	278	874	7	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.93	0.874	0.988	0.93	0.874	0.988	CLONAL	1	TRUE	1	0.54050505816769	2		881	1106	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	145	431	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.885	0.811	0.963	0.885	0.811	0.963	CLONAL	1	TRUE	1	0.54050505816769	2		431	606	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151289	202151290	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	168	500	0	ENST00000358485.4:c.1596dup	p.Leu533ThrfsTer6	p.L533Tfs*6	ENST00000358485	NM_001080125.1	530	aga/agAa	9/9	1	2	FACETS	0.823	0.758	0.891	0.823	0.758	0.891	CLONAL	1	TRUE	1	0.54050505816769	2		500	755	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	135	388	0	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.927	0.847	1	0.927	0.847	1	CLONAL	1	TRUE	1	0.54050505816769	2		388	539	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	221	692	10	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	0.931	0.868	0.997	0.931	0.868	0.997	CLONAL	1	TRUE	1	0.54050505816769	2		702	878	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141632	202141632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764461240	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	196	535	0	ENST00000358485.4:c.920G>A	p.Arg307Gln	p.R307Q	ENST00000358485	NM_001080125.1	307	cGg/cAg	7/9	1	2	FACETS	0.958	0.889	1	0.958	0.889	1	CLONAL	1	TRUE	1	0.54050505816769	2		535	757	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723126	49723128	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs751306787	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	238	585	0	ENST00000449682.2:c.1288_1290del	p.Glu430del	p.E430del	ENST00000449682	NM_020998.3	430	GAG/-	11/18	1	2	FACETS	0.983	0.919	1	0.983	0.919	1	CLONAL	1	TRUE	1	0.54050505816769	2		585	896	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336294	80336294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	141	369	0	ENST00000286548.4:c.1025C>T	p.Ala342Val	p.A342V	ENST00000286548	NM_002072.3	342	gCt/gTt	7/7	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.54050505816769	2		369	515	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778455	3778455	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	354	776	1	ENST00000262367.5:c.6593T>A	p.Leu2198Gln	p.L2198Q	ENST00000262367	NM_004380.2	2198	cTg/cAg	31/31	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.54050505816769	2		777	1094	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676268	37676268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	240	708	0	ENST00000447079.4:c.3023G>A	p.Arg1008Gln	p.R1008Q	ENST00000447079	NM_015083.1	1008	cGg/cAg	11/14	1	2	FACETS	0.996	0.931	1	0.996	0.931	1	CLONAL	1	TRUE	1	0.54050505816769	2		708	892	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319442	11319442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769877976	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	72	495	1	ENST00000361445.4:c.25G>A	p.Ala9Thr	p.A9T	ENST00000361445	NM_004958.3	9	Gcc/Acc	2/58	1	2	FACETS	0.356	0.31	0.405	0.356	0.31	0.405	SUBCLONAL	1	TRUE	1	0.54050505816769	2		496	749	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405806	157405806	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	101	304	0	ENST00000346085.5:c.2048G>A	p.Gly683Asp	p.G683D	ENST00000346085	NM_020732.3	683	gGc/gAc	6/20	1	2	FACETS	0.894	0.805	0.988	0.894	0.805	0.988	CLONAL	1	TRUE	1	0.54050505816769	2		304	418	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859006	57859006	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	277	685	0	ENST00000228682.2:c.502C>T	p.Pro168Ser	p.P168S	ENST00000228682	NM_005269.2	168	Cct/Tct	5/12	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.54050505816769	2		685	938	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986865	36986865	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748087644	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	118	175	0	ENST00000354822.5:c.824C>T	p.Pro275Leu	p.P275L	ENST00000354822	NM_001079668.2	275	cCg/cTg	3/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.54050505816769	2		175	343	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231345	5231345	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765642813	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	203	610	3	ENST00000357368.4:c.2131G>A	p.Val711Met	p.V711M	ENST00000357368	NM_002850.3	711	Gtg/Atg	14/38	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.54050505816769	2		613	727	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401492	401492	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752393433	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	134	311	0	ENST00000380956.4:c.814G>A	p.Glu272Lys	p.E272K	ENST00000380956	NM_001195286.1	272	Gag/Aag	7/9	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.54050505816769	2		311	469	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190752	11190754	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	rs767860672	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	231	593	0	ENST00000361445.4:c.5445_5447del	p.Lys1816del	p.K1816del	ENST00000361445	NM_004958.3	1815	aaGAAa/aaa	39/58	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.54050505816769	2		593	834	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16248819	16248819	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	51	535	0	ENST00000375759.3:c.1828del	p.Tyr610MetfsTer4	p.Y610Mfs*4	ENST00000375759	NM_015001.2	609	Ttt/tt	10/15	1	2	FACETS	0.255	0.216	0.298	0.255	0.216	0.298	SUBCLONAL	1	TRUE	1	0.54050505816769	2		535	739	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795027	45795027	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	254	552	0	ENST00000450313.1:c.1601G>T	p.Arg534Leu	p.R534L	ENST00000450313	NM_012222.2	534	cGg/cTg	16/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.54050505816769	2		552	851	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797856	45797856	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	208	545	0	ENST00000450313.1:c.915del	p.Cys306AlafsTer13	p.C306Afs*13	ENST00000450313	NM_012222.2	305	ctG/ct	10/16	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.54050505816769	2		545	769	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247929	59247929	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	266	708	7	ENST00000371222.2:c.814del	p.Arg272GlyfsTer13	p.R272Gfs*13	ENST00000371222	NM_002228.3	272	Agg/gg	1/1	1	2	FACETS	0.885	0.83	0.942	0.885	0.83	0.942	CLONAL	1	TRUE	1	0.54050505816769	2		715	1112	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204512038	204512038	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	31	385	1	ENST00000367182.3:c.638G>T	p.Arg213Ile	p.R213I	ENST00000367182	NM_001278516.1	213	aGa/aTa	8/11	1	2	FACETS	0.213	0.172	0.26	0.213	0.172	0.26	SUBCLONAL	1	TRUE	1	0.54050505816769	2		386	538	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263914	104263914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	25	69	0	ENST00000369902.3:c.5C>T	p.Ala2Val	p.A2V	ENST00000369902	NM_016169.3	2	gCg/gTg	1/12	1	2	FACETS	1	0.845	1	1	0.845	1	CLONAL	1	TRUE	1	0.54050505816769	2		69	88	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999297	100999297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368109236	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	243	794	1	ENST00000325455.5:c.505G>A	p.Gly169Arg	p.G169R	ENST00000325455	NM_001202474.3	169	Ggg/Agg	1/8	1	2	FACETS	0.933	0.872	0.995	0.933	0.872	0.995	CLONAL	1	TRUE	1	0.54050505816769	2		795	964	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21643235	21643235	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	72	722	1	ENST00000421138.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000421138		98	Gaa/Aaa	5/16	1	2	FACETS	0.287	0.25	0.328	0.287	0.25	0.328	SUBCLONAL	1	TRUE	1	0.54050505816769	2		723	927	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445166	49445166	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	317	821	0	ENST00000301067.7:c.2300A>T	p.Glu767Val	p.E767V	ENST00000301067	NM_003482.3	767	gAg/gTg	10/54	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.54050505816769	2		821	1078	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988192	36988192	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	54	461	0	ENST00000354822.5:c.461C>A	p.Ala154Asp	p.A154D	ENST00000354822	NM_001079668.2	154	gCc/gAc	2/3	1	2	FACETS	0.298	0.254	0.346	0.298	0.254	0.346	SUBCLONAL	1	TRUE	1	0.54050505816769	2		461	671	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007645	45007645	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	102	283	0	ENST00000558401.1:c.92del	p.Ser31TyrfsTer13	p.S31Yfs*13	ENST00000558401	NM_004048.2	31	tCa/ta	2/4	1	2	FACETS	0.993	0.896	1	0.993	0.896	1	CLONAL	1	TRUE	1	0.54050505816769	2		283	380	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678514	88678514	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1337303639	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	148	372	0	ENST00000360948.2:c.1022C>A	p.Pro341His	p.P341H	ENST00000360948	NM_001012338.2	341	cCt/cAt	9/19	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.54050505816769	2		372	523	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249237	10249239	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	175	564	0	ENST00000340748.4:c.3943_3945del	p.Ile1315del	p.I1315del	ENST00000340748		1315	ATC/-	34/40	1	2	FACETS	0.915	0.845	0.987	0.915	0.845	0.987	CLONAL	1	TRUE	1	0.54050505816769	2		564	708	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288780	15288780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	64	109	0	ENST00000263388.2:c.3959C>T	p.Ser1320Leu	p.S1320L	ENST00000263388	NM_000435.2	1320	tCg/tTg	24/33	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.54050505816769	2		109	178	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952246	17952246	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	244	671	1	ENST00000458235.1:c.1094C>T	p.Pro365Leu	p.P365L	ENST00000458235	NM_000215.3	365	cCg/cTg	8/24	1	2	FACETS	0.978	0.915	1	0.978	0.915	1	CLONAL	1	TRUE	1	0.54050505816769	2		672	923	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260136	19260136	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142232568	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	280	741	0	ENST00000162023.5:c.157C>T	p.Arg53Cys	p.R53C	ENST00000162023		53	Cgc/Tgc	7/13	1	2	FACETS	0.962	0.904	1	0.962	0.904	1	CLONAL	1	TRUE	1	0.54050505816769	2		741	1077	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213588	36213589	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	331	934	0	ENST00000222270.7:c.2693_2694del	p.Leu898ProfsTer18	p.L898Pfs*18	ENST00000222270	NM_014727.1	897	cCT/c	5/37	1	2	FACETS	0.962	0.909	1	0.962	0.909	1	CLONAL	1	TRUE	1	0.54050505816769	2		934	1273	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919073	50919073	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	190	667	0	ENST00000440232.2:c.2810T>C	p.Met937Thr	p.M937T	ENST00000440232	NM_002691.3	937	aTg/aCg	22/27	1	2	FACETS	0.936	0.868	1	0.936	0.868	1	CLONAL	1	TRUE	1	0.54050505816769	2		667	751	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457216	25457216	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	191	632	2	ENST00000264709.3:c.2671C>T	p.Arg891Trp	p.R891W	ENST00000264709	NM_175629.2	891	Cgg/Tgg	23/23	1	2	FACETS	0.876	0.811	0.943	0.876	0.811	0.943	CLONAL	1	TRUE	1	0.54050505816769	2		634	807	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39283898	39283898	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	190	570	1	ENST00000402219.2:c.455T>A	p.Ile152Lys	p.I152K	ENST00000402219	NM_005633.3	152	aTa/aAa	4/23	1	2	FACETS	0.982	0.911	1	0.982	0.911	1	CLONAL	1	TRUE	1	0.54050505816769	2		571	716	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627293	12627293	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	140	375	0	ENST00000251849.4:c.1423T>G	p.Phe475Val	p.F475V	ENST00000251849	NM_002880.3	475	Ttt/Gtt	14/17	1	2	FACETS	0.987	0.904	1	0.987	0.904	1	CLONAL	1	TRUE	1	0.54050505816769	2		375	525	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37038129	37038129	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs771649701	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	114	278	0	ENST00000231790.2:c.136A>G	p.Ser46Gly	p.S46G	ENST00000231790	NM_000249.3	46	Agt/Ggt	2/19	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.54050505816769	2		278	397	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096155	71096155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1450448594	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	122	356	0	ENST00000318789.4:c.602G>A	p.Arg201His	p.R201H	ENST00000318789	NM_032682.5	201	cGc/cAc	10/21	1	2	FACETS	0.923	0.839	1	0.923	0.839	1	CLONAL	1	TRUE	1	0.54050505816769	2		356	489	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998164	169998165	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	260	711	0	ENST00000295797.4:c.861dup	p.Glu288ArgfsTer4	p.E288Rfs*4	ENST00000295797	NM_002740.5	285	-/A	9/18	1	2	FACETS	0.981	0.92	1	0.981	0.92	1	CLONAL	1	TRUE	1	0.54050505816769	2		711	981	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575693	55575693	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	140	406	0	ENST00000288135.5:c.1219G>T	p.Val407Phe	p.V407F	ENST00000288135	NM_000222.2	407	Gtt/Ttt	7/21	1	2	FACETS	0.956	0.875	1	0.956	0.875	1	CLONAL	1	TRUE	1	0.54050505816769	2		406	542	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	231111	231111	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	193	279	0	ENST00000264932.6:c.891del	p.Thr298GlnfsTer50	p.T298Qfs*50	ENST00000264932	NM_004168.2	297	ccT/cc	7/15	1	2	FACETS	0.755	0.706	0.805	1	0.992	1	SUBCLONAL	2	TRUE	1	0.54050505816769	2		279	473	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177585	56177585	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768180463	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	152	364	1	ENST00000399503.3:c.2558G>A	p.Arg853His	p.R853H	ENST00000399503	NM_005921.1	853	cGt/cAt	14/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.54050505816769	2		365	472	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497231	149497231	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	219	631	0	ENST00000261799.4:c.3087A>C	p.Lys1029Asn	p.K1029N	ENST00000261799	NM_002609.3	1029	aaA/aaC	22/23	1	2	FACETS	0.89	0.828	0.953	0.89	0.828	0.953	CLONAL	1	TRUE	1	0.54050505816769	2		631	911	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180948	32180948	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776195186	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	166	609	1	ENST00000375023.3:c.2402G>A	p.Arg801His	p.R801H	ENST00000375023	NM_004557.3	801	cGc/cAc	15/30	1	2	FACETS	0.799	0.735	0.865	0.799	0.735	0.865	SUBCLONAL	1	TRUE	1	0.54050505816769	2		610	769	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821146	32821146	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	275	820	0	ENST00000354258.4:c.448C>A	p.Gln150Lys	p.Q150K	ENST00000354258	NM_000593.5	150	Cag/Aag	1/11	1	2	FACETS	0.999	0.938	1	0.999	0.938	1	CLONAL	1	TRUE	1	0.54050505816769	2		820	1019	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272418	38272418	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	109	370	0	ENST00000425967.3:c.1949G>C	p.Cys650Ser	p.C650S	ENST00000425967	NM_001174067.1	650	tGc/tCc	15/19	1	2	FACETS	0.797	0.719	0.879	0.797	0.719	0.879	SUBCLONAL	1	TRUE	1	0.54050505816769	2		370	506	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56879436	56879436	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	225	581	0	ENST00000519728.1:c.953T>C	p.Ile318Thr	p.I318T	ENST00000519728	NM_002350.3	318	aTc/aCc	9/13	1	2	FACETS	0.966	0.901	1	0.966	0.901	1	CLONAL	1	TRUE	1	0.54050505816769	2		581	862	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981921	70981921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	480	718	2	ENST00000276594.2:c.175G>A	p.Ala59Thr	p.A59T	ENST00000276594	NM_024504.3	59	Gca/Aca	2/8	0.54050505816769	3	FACETS	0.997	0.956	1	0.997	0.956	1	CLONAL	2	TRUE	1	0.54050505816769	3		720	1132	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128322000	128322000	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	244	732	0	ENST00000265960.3:c.760A>G	p.Ile254Val	p.I254V	ENST00000265960	NM_001006617.1	254	Att/Gtt	6/12	1	2	FACETS	0.868	0.811	0.927	0.868	0.811	0.927	CLONAL	1	TRUE	1	0.54050505816769	2		732	1040	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932321	39932321	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	331	870	1	ENST00000378444.4:c.2278C>A	p.Leu760Ile	p.L760I	ENST00000378444	NM_001123385.1	760	Ctc/Atc	4/15	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.54050505816769	2		871	1212	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428208	47428208	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	89	631	0	ENST00000377045.4:c.1168C>A	p.Leu390Ile	p.L390I	ENST00000377045	NM_001654.4	390	Ctc/Atc	11/16	1	2	FACETS	0.35	0.309	0.393	0.35	0.309	0.393	SUBCLONAL	1	TRUE	1	0.54050505816769	2		631	942	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226130	53226130	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	167	585	0	ENST00000375401.3:c.2719del	p.Arg907GlyfsTer28	p.R907Gfs*28	ENST00000375401	NM_004187.3	907	Agg/gg	19/26	1	2	FACETS	0.862	0.794	0.932	0.862	0.794	0.932	CLONAL	1	TRUE	1	0.54050505816769	2		585	717	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230751	53230751	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	245	633	3	ENST00000375401.3:c.2042G>A	p.Arg681Gln	p.R681Q	ENST00000375401	NM_004187.3	681	cGa/cAa	14/26	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.54050505816769	2		636	855	SUCCESS
AR	367	MSKCC	GRCh37	X	66941783	66941783	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	58	516	0	ENST00000374690.3:c.2427A>C	p.Lys809Asn	p.K809N	ENST00000374690	NM_000044.3	809	aaA/aaC	6/8	1	2	FACETS	0.317	0.271	0.366	0.317	0.271	0.366	SUBCLONAL	1	TRUE	1	0.54050505816769	2		516	678	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939832	76939832	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	187	459	0	ENST00000373344.5:c.916A>T	p.Asn306Tyr	p.N306Y	ENST00000373344	NM_000489.3	306	Aat/Tat	9/35	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.54050505816769	2		459	656	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939999	76939999	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	186	621	1	ENST00000373344.5:c.749G>A	p.Arg250Gln	p.R250Q	ENST00000373344	NM_000489.3	250	cGa/cAa	9/35	1	2	FACETS	0.868	0.803	0.935	0.868	0.803	0.935	CLONAL	1	TRUE	1	0.54050505816769	2		622	793	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0029401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	198	683	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.153150846902628	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	3	FALSE	0	0.153150846902628	3		685	863	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0029401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	134	671	1	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.153150846902628	6	FACETS	0.927	0.842	1	0.927	0.842	1	CLONAL	3	FALSE	3	0.153150846902628	6		672	822	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798968	45798968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781444	NA	P-0029401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	90	828	1	ENST00000450313.1:c.377G>A	p.Arg126Gln	p.R126Q	ENST00000450313	NM_012222.2	126	cGg/cAg	4/16	0.153150846902628	5	FACETS	0.814	0.721	0.913	0.814	0.721	0.913	CLONAL	2	FALSE	3	0.153150846902628	5		829	888	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0029402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	125	516	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	TRUE	1	0.28	2		516	793	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941195	36941196	+	missense_variant	Missense_Mutation	DNP	GA	GA	CC	novel	NA	P-0029402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	62	545	1	ENST00000361632.4:c.143_144delinsGG	p.Ile48Arg	p.I48R	ENST00000361632		48	aTC/aGG	3/16	0.301251361403572	3	FACETS	0.623	0.537	0.717	0.312	0.268	0.359	SUBCLONAL	1	TRUE	1	0.28	3		546	810	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941205	36941205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	64	573	0	ENST00000361632.4:c.134C>T	p.Ser45Phe	p.S45F	ENST00000361632		45	tCc/tTc	3/16	0.301251361403572	3	FACETS	0.629	0.544	0.723	0.315	0.272	0.362	SUBCLONAL	1	TRUE	1	0.28	3		573	828	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941230	36941230	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	62	579	0	ENST00000361632.4:c.109C>T	p.His37Tyr	p.H37Y	ENST00000361632		37	Cac/Tac	3/16	0.301251361403572	3	FACETS	0.627	0.541	0.722	0.314	0.27	0.361	SUBCLONAL	1	TRUE	1	0.28	3		579	805	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99486176	99486176	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs769891354	NA	P-0029402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	44	413	1	ENST00000268035.6:c.3482A>G	p.Tyr1161Cys	p.Y1161C	ENST00000268035	NM_000875.3	1161	tAt/tGt	19/21	0.142182598762346	0	FACETS	0.434	0.364	0.512			1	INDETERMINATE	1	TRUE	0	0.28	0		414	521	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137325974	137325974	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	96	662	2	ENST00000481739.1:c.1162G>T	p.Glu388Ter	p.E388*	ENST00000481739	NM_002957.4	388	Gag/Tag	9/10	1	2	FACETS	0.865	0.77	0.966	0.865	0.77	0.966	CLONAL	1	TRUE	1	0.28	2		664	793	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	330	540	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	0.352990192570389	1	FACETS	0.908	0.862	0.955	1	0.996	1	CLONAL	2	TRUE	0	0.352990192570389	1		540	848	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533838	533839	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATGTACTGGT	novel	NA	P-0029403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	369	599	0	ENST00000451590.1:c.206_217dup	p.Met72_Arg73insHisGlnTyrMet	p.M72_R73insHQYM	ENST00000451590	NM_001130442.1	73	cgc/cACCAGTACATGCgc	3/5	1	2	FACETS	0.858	0.814	0.902	1	0.996	1	CLONAL	2	TRUE	1	0.352990192570389	2		599	1219	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964901	55964902	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGAAGAACATGGCAATCACCGCCGTGCCTA	novel	NA	P-0029403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	271	356	0	ENST00000263923.4:c.2306_2335dup	p.Phe778_Trp779insLeuGlyThrAlaValIleAlaMetPhePhe	p.F778_W779insLGTAVIAMFF	ENST00000263923	NM_002253.2	779	tgg/tTAGGCACGGCGGTGATTGCCATGTTCTTCTgg	16/30	0.352990192570389	1	FACETS	0.784	0.739	0.831	1	0.994	1	SUBCLONAL	2	TRUE	0	0.352990192570389	1		356	806	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012244	152012244	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748254163	NA	P-0029403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	43	286	0	ENST00000262189.6:c.569G>A	p.Arg190Gln	p.R190Q	ENST00000262189	NM_170606.2	190	cGa/cAa	4/59	1	2	FACETS	0.376	0.314	0.445	0.376	0.314	0.445	SUBCLONAL	1	TRUE	1	0.352990192570389	2		286	648	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707683	176707683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587784154	NA	P-0029404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	241	359	0	ENST00000439151.2:c.5740C>T	p.Arg1914Cys	p.R1914C	ENST00000439151	NM_022455.4	1914	Cgc/Tgc	18/23	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		359	575	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495657	72495657	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	104	243	0	ENST00000477973.2:c.415A>G	p.Thr139Ala	p.T139A	ENST00000477973	NM_012234.5	139	Acc/Gcc	1/4	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.443110153024723	2		243	444	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720805	89720806	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	52	268	0	ENST00000371953.3:c.959dup	p.Leu320PhefsTer5	p.L320Ffs*5	ENST00000371953	NM_000314.4	319	act/acTt	8/9	0.443110153024723	1	FACETS	0.764	0.658	0.879	0.764	0.658	0.879	SUBCLONAL	1	TRUE	0	0.443110153024723	1		268	239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0029406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	122	650	1	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.2	2		651	937	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0029406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	78	389	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	1	2	FACETS	0.837	0.734	0.948	0.837	0.734	0.948	CLONAL	1	TRUE	1	0.2	2		389	932	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016628	12016628	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	71	383	0	ENST00000353533.5:c.764T>C	p.Val255Ala	p.V255A	ENST00000353533	NM_003010.3	255	gTg/gCg	7/11	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.2	2		383	671	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905602	50905602	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	107	708	0	ENST00000440232.2:c.730T>G	p.Tyr244Asp	p.Y244D	ENST00000440232	NM_002691.3	244	Tac/Gac	6/27	1	2	FACETS	0.864	0.772	0.961	0.864	0.772	0.961	CLONAL	1	TRUE	1	0.2	2		708	1239	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410489	63410489	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	96	649	1	ENST00000330258.3:c.2678G>T	p.Ser893Ile	p.S893I	ENST00000330258	NM_152424.3	893	aGc/aTc	2/2	0.261510280166802	1	FACETS	0.874	0.778	0.978	0.874	0.778	0.978	CLONAL	1	TRUE	0	0.2	1		650	988	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	383	394	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.571709031163084	6	FACETS	1	0.967	1	1	0.967	1	CLONAL	4	TRUE	2	0.571709031163084	6		394	711	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0029410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	103	747	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.695	0.622	0.773	0.695	0.622	0.773	SUBCLONAL	1	TRUE	1	0.368030889136916	2		750	805	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0029410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	56	549	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.412	0.352	0.478	0.412	0.352	0.478	SUBCLONAL	1	TRUE	1	0.368030889136916	2		549	738	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0029410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	66	387	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.499	0.432	0.571	0.499	0.432	0.571	SUBCLONAL	1	TRUE	1	0.368030889136916	2		387	719	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248150	110248150	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	74	344	0	ENST00000374672.4:c.1322A>G	p.Asp441Gly	p.D441G	ENST00000374672	NM_004235.4	441	gAt/gGt	5/5	1	2	FACETS	0.602	0.527	0.683	0.602	0.527	0.683	SUBCLONAL	1	TRUE	1	0.368030889136916	2		344	668	SUCCESS
APC	324	MSKCC	GRCh37	5	112173346	112173346	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	44	266	0	ENST00000257430.4:c.2055G>A	p.Trp685Ter	p.W685*	ENST00000257430	NM_000038.5	685	tgG/tgA	16/16	1	2	FACETS	0.504	0.423	0.595	0.504	0.423	0.595	SUBCLONAL	1	TRUE	1	0.368030889136916	2		266	474	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115928	8115929	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	91	372	0	ENST00000346208.3:c.1275dup	p.Ser426IlefsTer81	p.S426Ifs*81	ENST00000346208		425	cca/ccAa	6/6	1	2	FACETS	0.95	0.844	1	0.95	0.844	1	CLONAL	1	TRUE	1	0.28	2		372	684	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	59	564	0	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	0.266185304434074	2	FACETS	0.44	0.377	0.509	0.22	0.188	0.255	SUBCLONAL	1	TRUE	0	0.28	2		564	958	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542102	187542102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	68	321	0	ENST00000441802.2:c.5638G>A	p.Ala1880Thr	p.A1880T	ENST00000441802	NM_005245.3	1880	Gcc/Acc	10/27	1	2	FACETS	0.895	0.779	1	0.895	0.779	1	CLONAL	1	TRUE	1	0.28	2		321	543	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332904	152332904	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	29	315	0	ENST00000206249.3:c.1210T>A	p.Phe404Ile	p.F404I	ENST00000206249	NM_000125.3	404	Ttt/Att	5/8	0.266185304434074	2	FACETS	0.363	0.291	0.447	0.182	0.145	0.224	SUBCLONAL	1	TRUE	0	0.28	2		315	570	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155725	56155726	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0029415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	41	388	0	ENST00000399503.3:c.819_820del	p.Arg273SerfsTer27	p.R273Sfs*27	ENST00000399503	NM_005921.1	273	AGa/a	3/20	1	2	FACETS	0.487	0.405	0.578	0.487	0.405	0.578	SUBCLONAL	1	TRUE	1	0.283660903110313	2		388	594	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063718	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0029415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	31	266	0	ENST00000412916.2:c.165+2dup		p.X55_splice	ENST00000412916		55			0.202286401136283	1	FACETS	0.579	0.469	0.703	0.579	0.469	0.703	SUBCLONAL	1	TRUE	0	0.283660903110313	1		266	324	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589594	67589596	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	novel	NA	P-0029415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	65	291	0	ENST00000274335.5:c.1358_1360del	p.Asn453del	p.N453del	ENST00000274335		453	AAC/-	10/15	1	2	FACETS	0.814	0.706	0.931	0.814	0.706	0.931	CLONAL	1	TRUE	1	0.283660903110313	2		291	563	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075100	16075122	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGAGAACAAATATTTACCTTCTT	AGAGAACAAATATTTACCTTCTT	-	novel	NA	P-0029415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	52	204	0	ENST00000268712.3:c.430_435+17del		p.X144_splice	ENST00000268712	NM_006311.3	144		4/46	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.283660903110313	2		204	304	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273250	18273250	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	66	567	0	ENST00000222254.8:c.1043C>G	p.Pro348Arg	p.P348R	ENST00000222254	NM_005027.3	348	cCc/cGc	9/16	1	2	FACETS	0.551	0.477	0.631	0.551	0.477	0.631	SUBCLONAL	1	TRUE	1	0.283660903110313	2		567	845	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176481	123176483	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0029415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	48	414	0	ENST00000218089.9:c.451_453del	p.Glu151del	p.E151del	ENST00000218089	NM_001042749.1	150	GAA/-	7/35	1	2	FACETS	0.467	0.394	0.549	0.467	0.394	0.549	SUBCLONAL	1	TRUE	1	0.283660903110313	2		414	724	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435750	110435750	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1219457876	NA	P-0029430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	67	325	1	ENST00000375856.3:c.2651G>A	p.Arg884His	p.R884H	ENST00000375856	NM_003749.2	884	cGc/cAc	1/2	1	2	FACETS	0.75	0.652	0.854	0.75	0.652	0.854	SUBCLONAL	1	TRUE	1	0.352628019747109	2		326	507	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56412919	56412919	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	69	318	0	ENST00000348428.3:c.1933G>T	p.Asp645Tyr	p.D645Y	ENST00000348428	NM_006785.3	645	Gat/Tat	16/17	0.16609548687813	3	FACETS	0.752	0.661	0.849	0.752	0.661	0.849	INDETERMINATE	2	TRUE	1	0.352628019747109	3		318	306	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47601061	47601061	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	177	636	0	ENST00000263735.4:c.299A>C	p.Asp100Ala	p.D100A	ENST00000263735	NM_002354.2	100	gAt/gCt	3/9	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.352628019747109	2		636	997	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530146	212530146	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	34	435	0	ENST00000342788.4:c.1773A>T	p.Glu591Asp	p.E591D	ENST00000342788	NM_005235.2	591	gaA/gaT	15/28	1	2	FACETS	0.342	0.279	0.413	0.342	0.279	0.413	SUBCLONAL	1	TRUE	1	0.352628019747109	2		435	564	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	145	404	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		404	449	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0029432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	118	516	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.3	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	0	0.186279465462307	1		516	941	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913396	NA	P-0029432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	39	254	0	ENST00000349496.5:c.95A>T	p.Asp32Val	p.D32V	ENST00000349496	NM_001904.3	32	gAc/gTc	3/15	1	2	FACETS	0.701	0.58	0.837	0.701	0.58	0.837	SUBCLONAL	1	FALSE	1	0.186279465462307	2		254	597	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0029432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	25	423	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.3	1	FACETS	0.302	0.236	0.377	0.302	0.236	0.377	SUBCLONAL	1	FALSE	0	0.186279465462307	1		423	807	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285805	46285805	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	40	344	0	ENST00000334344.6:c.5073T>G	p.Cys1691Trp	p.C1691W	ENST00000334344	NM_152641.2	1691	tgT/tgG	18/21	1	2	FACETS	0.596	0.493	0.71	0.596	0.493	0.71	SUBCLONAL	1	FALSE	1	0.186279465462307	2		344	721	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604786	48604787	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0029432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	52	395	0	ENST00000342988.3:c.1609_1610del	p.Asp537ArgfsTer39	p.D537Rfs*39	ENST00000342988	NM_005359.5	536	ctAGac/ctac	12/12	1	2	FACETS	0.734	0.623	0.855	0.734	0.623	0.855	SUBCLONAL	1	FALSE	1	0.186279465462307	2		395	761	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0029433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	211	453	1	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.204299523639467	6	FACETS	0.986	0.919	1	0.986	0.919	1	CLONAL	4	TRUE	2	0.204299523639467	6		454	738	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942068	71942069	+	missense_variant	Missense_Mutation	DNP	CT	CT	AA	novel	NA	P-0029433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	140	763	1	ENST00000298229.2:c.1332_1333delinsAA	p.Trp445Arg	p.W445R	ENST00000298229	NM_001567.3	444	tcCTgg/tcAAgg	12/28	0.196947080106694	3	FACETS	0.864	0.787	0.945	0.864	0.787	0.945	CLONAL	2	TRUE	1	0.204299523639467	3		764	874	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590765	95590765	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs886037667	NA	P-0029433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	55	345	0	ENST00000393063.1:c.1144G>T	p.Glu382Ter	p.E382*	ENST00000393063	NM_030621.3	382	Gaa/Taa	9/28	0.184917030412778	3	FACETS	0.982	0.84	1	0.327	0.28	0.38	CLONAL	1	TRUE	0	0.204299523639467	3		345	604	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191298	185191298	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	56	500	0	ENST00000265026.3:c.2179G>T	p.Asp727Tyr	p.D727Y	ENST00000265026	NM_004721.4	727	Gac/Tac	11/14	0.204299523639467	2	FACETS	0.944	0.808	1	0.472	0.404	0.546	CLONAL	1	TRUE	0	0.204299523639467	2		500	581	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241706	55241707	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0029433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	238	554	0	ENST00000275493.2:c.2154_2155delinsTT	p.Gly719Cys	p.G719C	ENST00000275493	NM_005228.3	718	ctGGgc/ctTTgc	18/28	0.204299523639467	6	FACETS	1	0.974	1	0.813	0.759	0.869	CLONAL	3	TRUE	2	0.204299523639467	6		554	1009	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0029435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	166	664	1	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.300277424340234	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.31	1		665	765	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098962	178098962	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	128	323	0	ENST00000397062.3:c.83T>C	p.Ile28Thr	p.I28T	ENST00000397062	NM_006164.4	28	aTa/aCa	2/5	0.300277424340234	3	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	1	0.31	3		323	455	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850704	63850705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	44	394	0	ENST00000279873.7:c.1489dup	p.Ile497AsnfsTer31	p.I497Nfs*31	ENST00000279873	NM_032199.2	494	-/A	10/10	0.1462192092426	3	FACETS	0.508	0.425	0.6	0.254	0.212	0.3	INDETERMINATE	1	TRUE	1	0.31	3		394	646	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602767	10602767	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	189	659	0	ENST00000171111.5:c.811G>T	p.Val271Leu	p.V271L	ENST00000171111	NM_203500.1	271	Gtg/Ttg	3/6	0.300277424340234	2	FACETS	1	0.987	1	0.663	0.613	0.715	CLONAL	1	TRUE	0	0.31	2		659	919	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978461	2978461	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	94	571	0	ENST00000396946.4:c.869G>T	p.Gly290Val	p.G290V	ENST00000396946	NM_032415.4	290	gGg/gTg	7/25	0.300277424340234	5	FACETS	0.851	0.755	0.954	0.213	0.188	0.239	CLONAL	1	TRUE	1	0.31	5		571	1044	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971142	21971142	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	66	433	0	ENST00000304494.5:c.216C>A	p.Cys72Ter	p.C72*	ENST00000304494	NM_000077.4	72	tgC/tgA	2/3	0.300277424340234	1	FACETS	0.859	0.748	0.978	0.859	0.748	0.978	CLONAL	1	TRUE	0	0.31	1		433	419	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880543	155880543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	241	556	1	ENST00000368323.3:c.10G>A	p.Gly4Arg	p.G4R	ENST00000368323	NM_006912.5	4	Gga/Aga	2/6	0.133016698614401	4	FACETS	1	0.986	1	1	0.986	1	INDETERMINATE	2	TRUE	2	0.31	4		557	855	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172041	99172041	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1173362000	NA	P-0029435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	78	500	0	ENST00000074304.5:c.1607A>G	p.Lys536Arg	p.K536R	ENST00000074304	NM_001134224.1	536	aAg/aGg	17/26	0.300277424340234	3	FACETS	0.804	0.706	0.909	0.402	0.353	0.455	CLONAL	1	TRUE	1	0.31	3		500	723	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095650	178095650	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	70	469	0	ENST00000397062.3:c.1681T>C	p.Tyr561His	p.Y561H	ENST00000397062	NM_006164.4	561	Tat/Cat	5/5	0.300277424340234	3	FACETS	0.698	0.608	0.796	0.349	0.304	0.398	SUBCLONAL	1	TRUE	1	0.31	3		469	747	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356368	66356368	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	169	479	0	ENST00000273854.3:c.1129T>A	p.Trp377Arg	p.W377R	ENST00000273854	NM_004439.5	377	Tgg/Agg	5/18	0.224358358257543	2	FACETS	0.812	0.749	0.878	0.812	0.749	0.878	CLONAL	2	TRUE	0	0.31	2		479	671	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289665	33289665	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	100	441	0	ENST00000374542.5:c.38A>T	p.Asp13Val	p.D13V	ENST00000374542	NM_001141970.1	13	gAt/gTt	2/8	0.300277424340234	3	FACETS	1	0.946	1	0.546	0.488	0.608	CLONAL	1	TRUE	1	0.31	3		441	682	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43745247	43745247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	53	601	0	ENST00000523873.1:c.160C>T	p.Pro54Ser	p.P54S	ENST00000523873		54	Cca/Tca	3/8	0.300277424340234	3	FACETS	0.428	0.364	0.499	0.214	0.182	0.25	SUBCLONAL	1	TRUE	1	0.31	3		601	922	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403524	139403524	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0029435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	99	498	1	ENST00000277541.6:c.2970-1G>T		p.X990_splice	ENST00000277541	NM_017617.3	990			0.1462192092426	3	FACETS	1	0.938	1	0.536	0.479	0.597	INDETERMINATE	1	TRUE	1	0.31	3		499	688	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0029436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	283	747	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.194556397868883	1	FACETS	0.772	0.727	0.818	0.772	0.727	0.818	INDETERMINATE	1	TRUE	0	0.577959211603239	1		750	902	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	206	605	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.577959211603239	1	FACETS	0.832	0.777	0.889	0.832	0.777	0.889	CLONAL	1	TRUE	0	0.577959211603239	1		605	609	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152567	56152567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375239979	NA	P-0029436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	168	361	0	ENST00000399503.3:c.623G>A	p.Arg208Gln	p.R208Q	ENST00000399503	NM_005921.1	208	cGa/cAa	2/20	1	2	FACETS	0.958	0.884	1	0.958	0.884	1	CLONAL	1	TRUE	1	0.577959211603239	2		361	607	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637717	52637717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	242	468	0	ENST00000394830.3:c.2599G>A	p.Glu867Lys	p.E867K	ENST00000394830	NM_018313.4	867	Gaa/Aaa	18/30	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.577959211603239	2		468	812	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259921	16259921	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	273	580	0	ENST00000375759.3:c.7186C>T	p.Gln2396Ter	p.Q2396*	ENST00000375759	NM_015001.2	2396	Cag/Tag	11/15	0.545001847617194	1	FACETS	0.995	0.94	1	0.995	0.94	1	CLONAL	1	TRUE	0	0.577959211603239	1		580	675	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272363	15272363	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	298	845	0	ENST00000263388.2:c.6076C>T	p.Gln2026Ter	p.Q2026*	ENST00000263388	NM_000435.2	2026	Caa/Taa	33/33	1	2	FACETS	0.999	0.942	1	0.999	0.942	1	CLONAL	1	TRUE	1	0.577959211603239	2		845	1032	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638621	176638621	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766901249	NA	P-0029436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	319	698	0	ENST00000439151.2:c.3221G>A	p.Arg1074His	p.R1074H	ENST00000439151	NM_022455.4	1074	cGt/cAt	5/23	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.577959211603239	2		698	1085	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135804190	135804190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs984306144	NA	P-0029436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	197	467	0	ENST00000298552.3:c.70G>A	p.Asp24Asn	p.D24N	ENST00000298552	NM_001162426.1	24	Gac/Aac	3/23	1	2	FACETS	0.886	0.823	0.952	0.886	0.823	0.952	CLONAL	1	TRUE	1	0.577959211603239	2		467	769	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857507	68857518	+	frameshift_variant	Frame_Shift_Del	DEL	TGGAGGAATTCT	TGGAGGAATTCT	A	novel	NA	P-0029436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	177	410	0	ENST00000261769.5:c.2142_2153delinsA	p.Gly715CysfsTer29	p.G715Cfs*29	ENST00000261769	NM_004360.3	714	ctTGGAGGAATTCTt/ctAt	13/16	0.577959211603239	1	FACETS	0.931	0.866	0.997	0.931	0.866	0.997	CLONAL	1	TRUE	0	0.577959211603239	1		410	468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0029438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	121	1069	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.280693821402475	1	FACETS	0.854	0.771	0.941	0.854	0.771	0.941	CLONAL	1	TRUE	0	0.280693821402475	1		1071	868	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604750	48604750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	122	482	1	ENST00000342988.3:c.1572G>T	p.Trp524Cys	p.W524C	ENST00000342988	NM_005359.5	524	tgG/tgT	12/12	0.280693821402475	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.280693821402475	1		483	644	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878787	151878787	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	127	423	0	ENST00000262189.6:c.6158C>G	p.Ser2053Cys	p.S2053C	ENST00000262189	NM_170606.2	2053	tCt/tGt	36/59	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.280693821402475	2		423	761	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687599	29687599	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	108	531	0	ENST00000356175.3:c.8192A>C	p.Glu2731Ala	p.E2731A	ENST00000356175	NM_000267.3	2731	gAa/gCa	56/57	1	2	FACETS	0.889	0.797	0.986	0.889	0.797	0.986	CLONAL	1	TRUE	1	0.280693821402475	2		531	866	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945202	44945224	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GTTCTGAATGACTTCTGTGAAAA	GTTCTGAATGACTTCTGTGAAAA	-	novel	NA	P-0029438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	101	245	1	ENST00000377967.4:c.3528_3548+2del		p.VLNDFCEK1176fs	ENST00000377967	NM_021140.2	1176	GTTCTGAATGACTTCTGTGAAAAa/a	24/29	1	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.280693821402475	1		246	420	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0029439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	143	671	1	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.411980409873687	3	FACETS	1	0.963	1	0.552	0.503	0.602	CLONAL	1	TRUE	1	0.411980409873687	3		672	759	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578507	7578507	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519977	NA	P-0029439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	315	702	0	ENST00000269305.4:c.423C>G	p.Cys141Trp	p.C141W	ENST00000269305	NM_001126112.2	141	tgC/tgG	5/11	0.359370384113206	2	FACETS	0.985	0.935	1	0.985	0.935	1	CLONAL	2	TRUE	0	0.411980409873687	2		702	776	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133883	55133883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	81	368	0	ENST00000257290.5:c.1096G>A	p.Asp366Asn	p.D366N	ENST00000257290	NM_006206.4	366	Gat/Aat	7/23	1	2	FACETS	0.86	0.761	0.966	0.86	0.761	0.966	CLONAL	1	TRUE	1	0.411980409873687	2		368	457	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577220	64577220	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	341	670	0	ENST00000312049.6:c.362T>G	p.Val121Gly	p.V121G	ENST00000312049	NM_130799.2	121	gTc/gGc	2/10	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.411980409873687	2		670	738	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67132621	67132623	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	rs761606770	NA	P-0029439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	242	502	2	ENST00000412916.2:c.508_510del	p.Gln170del	p.Q170del	ENST00000412916		168	agACAa/aga	6/6	0.411980409873687	2	FACETS	0.927	0.871	0.983	0.927	0.871	0.983	CLONAL	2	TRUE	0	0.411980409873687	2		504	634	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862181	68862181	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	122	557	3	ENST00000261769.5:c.2269G>T	p.Glu757Ter	p.E757*	ENST00000261769	NM_004360.3	757	Gaa/Taa	14/16	0.411980409873687	2	FACETS	0.807	0.73	0.888	0.403	0.365	0.444	CLONAL	1	TRUE	0	0.411980409873687	2		560	734	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56367802	56367802	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775236927	NA	P-0029439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	267	412	0	ENST00000348428.3:c.628G>A	p.Asp210Asn	p.D210N	ENST00000348428	NM_006785.3	210	Gac/Aac	4/17	0.411980409873687	3	FACETS	0.88	0.833	0.928	0.88	0.833	0.928	CLONAL	3	TRUE	0	0.411980409873687	3		412	592	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051204	128051204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1251238422	NA	P-0029439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	112	535	0	ENST00000285398.2:c.119C>T	p.Ser40Leu	p.S40L	ENST00000285398	NM_000122.1	40	tCg/tTg	2/15	0.23104076086829	4	FACETS	1	0.938	1	0.529	0.476	0.585	INDETERMINATE	1	TRUE	2	0.411980409873687	4		535	726	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024689	31024689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368624471	NA	P-0029439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	145	463	0	ENST00000375687.4:c.4174C>T	p.Pro1392Ser	p.P1392S	ENST00000375687	NM_015338.5	1392	Ccc/Tcc	13/13	0.411980409873687	3	FACETS	1	0.965	1	0.369	0.337	0.403	CLONAL	1	TRUE	0	0.411980409873687	3		463	767	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522621	67522621	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	70	321	0	ENST00000274335.5:c.118C>G	p.Leu40Val	p.L40V	ENST00000274335		40	Ctt/Gtt	1/15	0.411980409873687	2	FACETS	0.742	0.649	0.842	0.371	0.324	0.421	SUBCLONAL	1	TRUE	0	0.411980409873687	2		321	458	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569301	67569301	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	105	360	0	ENST00000274335.5:c.418G>T	p.Glu140Ter	p.E140*	ENST00000274335		140	Gaa/Taa	2/15	0.411980409873687	2	FACETS	1	0.952	1	0.548	0.494	0.605	CLONAL	1	TRUE	0	0.411980409873687	2		360	465	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510159	149510159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	287	577	1	ENST00000261799.4:c.1310G>A	p.Arg437His	p.R437H	ENST00000261799	NM_002609.3	437	cGt/cAt	9/23	0.411980409873687	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.411980409873687	2		578	690	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041117	180041117	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1653	149	770	0	ENST00000261937.6:c.3282G>C	p.Gln1094His	p.Q1094H	ENST00000261937	NM_182925.4	1094	caG/caC	24/30	0.411980409873687	8	FACETS	0.898	0.816	0.983	0.15	0.136	0.164	CLONAL	1	TRUE	2	0.411980409873687	8		770	1802	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0029440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	14	532	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.316	0.227	0.425	0.316	0.227	0.425	SUBCLONAL	1	TRUE	1	0.13	2		532	681	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239889	53239889	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	38	517	0	ENST00000375401.3:c.1552C>T	p.His518Tyr	p.H518Y	ENST00000375401	NM_004187.3	518	Cac/Tac	11/26	0.3	1	FACETS	0.742	0.611	0.888	0.742	0.611	0.888	SUBCLONAL	1	TRUE	0	0.13	1		517	737	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198072	185198072	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	33	397	0	ENST00000265026.3:c.2554A>T	p.Asn852Tyr	p.N852Y	ENST00000265026	NM_004721.4	852	Aat/Tat	13/14	1	2	FACETS	0.859	0.698	1	0.859	0.698	1	CLONAL	1	TRUE	1	0.13	2		397	591	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041725	47041725	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	39	512	0	ENST00000377604.3:c.1950G>T	p.Gln650His	p.Q650H	ENST00000377604	NM_001204468.1	650	caG/caT	17/24	0.3	1	FACETS	0.821	0.679	0.981	0.821	0.679	0.981	CLONAL	1	TRUE	0	0.13	1		512	683	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0029443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	20	431	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.411	0.313	0.527	0.411	0.313	0.527	SUBCLONAL	1	TRUE	1	0.17	2		431	572	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457295	67457295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886038803	NA	P-0029443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	56	726	0	ENST00000327367.4:c.269G>A	p.Arg90His	p.R90H	ENST00000327367	NM_005902.3	90	cGc/cAc	2/9	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.17	2		726	617	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46240689	46240689	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	28	498	1	ENST00000334344.6:c.1549G>T	p.Glu517Ter	p.E517*	ENST00000334344	NM_152641.2	517	Gaa/Taa	12/21	1	2	FACETS	0.656	0.523	0.808	0.656	0.523	0.808	SUBCLONAL	1	TRUE	1	0.17	2		499	502	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371743	45371744	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	38	628	0	ENST00000262160.6:c.1247dup	p.Met416IlefsTer24	p.M416Ifs*24	ENST00000262160	NM_005901.5	416	atg/atTg	10/11	1	2	FACETS	0.811	0.67	0.97	0.811	0.67	0.97	CLONAL	1	TRUE	1	0.17	2		628	551	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428320	49428369	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCAGTGGCATAAGACACAAGTTCCTACTCCCACCTGACCACTTACCTGGC	CCAGTGGCATAAGACACAAGTTCCTACTCCCACCTGACCACTTACCTGGC	T	novel	NA	P-0029443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	65	709	0	ENST00000301067.7:c.10436_10440+45delinsA		p.X3479_splice	ENST00000301067	NM_003482.3	3479		36/54	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.17	2		709	688	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0029445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	589	494	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.656754754466531	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.656754754466531	3		494	761	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0029445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	704	591	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	2	TRUE	NA	0.656754754466531	2		592	1070	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0029445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	889	644	0	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	0.656754754466531	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.656754754466531	3		644	1175	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057874	27057874	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	355	717	0	ENST00000324856.7:c.1582C>T	p.Gln528Ter	p.Q528*	ENST00000324856	NM_006015.4	528	Cag/Tag	3/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.656754754466531	2		717	1031	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746131	162746131	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121964863	NA	P-0029445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	178	372	1	ENST00000367921.3:c.2254C>T	p.Arg752Cys	p.R752C	ENST00000367921	NM_006182.2	752	Cgc/Tgc	16/18	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.656754754466531	2		373	491	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870996	12870996	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	195	504	0	ENST00000228872.4:c.223G>T	p.Glu75Ter	p.E75*	ENST00000228872	NM_004064.3	75	Gag/Tag	1/3	1	2	FACETS	0.863	0.802	0.926	0.863	0.802	0.926	CLONAL	1	TRUE	1	0.656754754466531	2		504	688	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	285	408	0	ENST00000397062.3:c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	NM_006164.4	34	Cga/Gga	2/5	0.648301534995976	3	FACETS	0.999	0.949	1	0.999	0.949	1	CLONAL	2	TRUE	1	0.656754754466531	3		408	577	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898731	134898731	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	206	457	0	ENST00000398015.3:c.1789C>A	p.Pro597Thr	p.P597T	ENST00000398015	NM_004441.4	597	Ccc/Acc	10/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.656754754466531	2		457	593	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589153	67589155	+	inframe_deletion	In_Frame_Del	DEL	ATC	ATC	-	novel	NA	P-0029445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	97	337	0	ENST00000274335.5:c.1142_1144del	p.Ile381del	p.I381del	ENST00000274335		381	ATC/-	9/15	0.656754754466531	1	FACETS	0.977	0.893	1	0.977	0.893	1	CLONAL	1	TRUE	0	0.656754754466531	1		337	203	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112025222	112025222	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866100904	NA	P-0029445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	264	556	2	ENST00000368678.4:c.527G>A	p.Arg176His	p.R176H	ENST00000368678		176	cGc/cAc	6/13	0.648301534995976	3	FACETS	0.955	0.895	1	0.478	0.447	0.509	CLONAL	1	TRUE	1	0.656754754466531	3		558	1118	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370923	55370923	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	417	676	0	ENST00000297316.4:c.225C>A	p.Phe75Leu	p.F75L	ENST00000297316	NM_022454.3	75	ttC/ttA	1/2	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.656754754466531	2		676	1103	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101539	27101540	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	A	novel	NA	P-0029445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	362	757	1	ENST00000324856.7:c.4821_4822delinsA	p.His1608ThrfsTer4	p.H1608Tfs*4	ENST00000324856	NM_006015.4	1607	ctGCac/ctAac	18/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.656754754466531	2		758	1086	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	160	404	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.828927521020724	2		404	348	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913322	28913322	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765475765	NA	P-0029447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	336	686	0	ENST00000282397.4:c.2471G>A	p.Arg824Gln	p.R824Q	ENST00000282397	NM_002019.4	824	cGg/cAg	17/30	1	2	FACETS	0.964	0.916	1	0.964	0.916	1	CLONAL	1	TRUE	1	0.828927521020724	2		686	841	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0029447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27325	3830	592	3	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.828927521020724	34	FACETS	1	0.997	1	0.124	0.122	0.127	CLONAL	4	TRUE	0	0.828927521020724	34		595	31155	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865230	57865230	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	8658	716	0	ENST00000228682.2:c.2707C>G	p.Gln903Glu	p.Q903E	ENST00000228682	NM_005269.2	903	Caa/Gaa	12/12	0.828927521020724	18	FACETS	0.976	0.973	0.98			1	CLONAL	18	TRUE	NA	0.828927521020724	18		716	9070	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526292	31526292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751019044	NA	P-0029447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	165	854	3	ENST00000344624.3:c.748C>T	p.Arg250Trp	p.R250W	ENST00000344624		250	Cgg/Tgg	2/33	1	2	FACETS	0.384	0.352	0.417	0.384	0.352	0.417	SUBCLONAL	1	TRUE	1	0.828927521020724	2		857	1038	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0029449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	743	516	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.219187734959091	5	FACETS	1	0.994	1	0.651	0.632	0.67	INDETERMINATE	3	TRUE	0	0.727231840384493	5		516	1312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs11575997	NA	P-0029449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	369	624	0	ENST00000269305.4:c.993+1G>T		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.727231840384493	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.727231840384493	1		624	581	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948695	71948695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	444	674	2	ENST00000298229.2:c.3407C>T	p.Ala1136Val	p.A1136V	ENST00000298229	NM_001567.3	1136	gCc/gTc	26/28	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.727231840384493	2		676	1205	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937034	48937034	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	877	571	2	ENST00000267163.4:c.802G>T	p.Glu268Ter	p.E268*	ENST00000267163	NM_000321.2	268	Gaa/Taa	8/27	0.723421585609957	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.727231840384493	3		573	1075	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082718	16082718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1232039982	NA	P-0029449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	28	60	0	ENST00000281043.3:c.532G>A	p.Glu178Lys	p.E178K	ENST00000281043	NM_005378.4	178	Gag/Aag	2/3	0.485117835491559	1	FACETS	0.5	0.409	0.598	0.5	0.409	0.598	SUBCLONAL	1	TRUE	0	0.727231840384493	1		60	98	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193871	106193871	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	157	497	0	ENST00000380013.4:c.4333C>G	p.Gln1445Glu	p.Q1445E	ENST00000380013	NM_001127208.2	1445	Cag/Gag	10/11	0.184903242533897	1	FACETS	0.386	0.355	0.42	0.386	0.355	0.42	INDETERMINATE	1	TRUE	0	0.727231840384493	1		497	711	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288972	11288972	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	163	522	0	ENST00000361445.4:c.2783A>T	p.Asp928Val	p.D928V	ENST00000361445	NM_004958.3	928	gAc/gTc	19/58	0.455830369206486	3	FACETS	1	0.971	1			1	CLONAL	1	TRUE	NA	0.597319911396792	3		522	638	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430151	181430151	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs1340243791	NA	P-0029450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	56	76	0	ENST00000325404.1:c.3G>A	p.Met1?	p.M1?	ENST00000325404	NM_003106.3	1	atG/atA	1/1	0.597319911396792	3	FACETS	1	0.912	1	0.534	0.463	0.61	CLONAL	1	TRUE	1	0.597319911396792	3		76	228	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0029451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	50	568	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	1	2	FACETS	0.538	0.455	0.628	0.538	0.455	0.628	SUBCLONAL	1	TRUE	1	0.290165987248495	2		568	641	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0029452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	95	307	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.98	0.874	1	0.98	0.874	1	CLONAL	1	TRUE	1	0.282895469101031	2		307	685	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790031	40790031	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	58	567	0	ENST00000373198.4:c.2700G>A	p.Met900Ile	p.M900I	ENST00000373198	NM_133170.3	900	atG/atA	18/32	1	2	FACETS	0.483	0.414	0.559	0.483	0.414	0.559	SUBCLONAL	1	TRUE	1	0.282895469101031	2		567	849	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913413	32913413	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	59	459	0	ENST00000380152.3:c.4921G>A	p.Glu1641Lys	p.E1641K	ENST00000380152		1641	Gaa/Aaa	11/27	0.282895469101031	3	FACETS	0.448	0.384	0.519	0.224	0.192	0.26	SUBCLONAL	1	TRUE	1	0.282895469101031	3		459	1062	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41023345	41023345	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	79	576	0	ENST00000267868.3:c.989A>G	p.Asn330Ser	p.N330S	ENST00000267868	NM_002875.4	330	aAt/aGt	10/10	1	2	FACETS	0.595	0.522	0.674	0.595	0.522	0.674	SUBCLONAL	1	TRUE	1	0.282895469101031	2		576	938	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604733	48604733	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	113	529	0	ENST00000342988.3:c.1557del	p.Glu520LysfsTer17	p.E520Kfs*17	ENST00000342988	NM_005359.5	519	Aaa/aa	12/12	0.282895469101031	1	FACETS	0.957	0.862	1	0.957	0.862	1	CLONAL	1	TRUE	0	0.282895469101031	1		529	717	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379384	225379384	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780690634	NA	P-0029452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	133	666	0	ENST00000264414.4:c.484C>T	p.Arg162Trp	p.R162W	ENST00000264414	NM_003590.4	162	Cgg/Tgg	4/16	1	2	FACETS	0.83	0.752	0.912	0.83	0.752	0.912	CLONAL	1	TRUE	1	0.282895469101031	2		666	1133	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849834	151849834	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	40	403	0	ENST00000262189.6:c.12482del	p.Tyr4161SerfsTer3	p.Y4161Sfs*3	ENST00000262189	NM_170606.2	4161	tAc/tc	49/59	1	2	FACETS	0.427	0.354	0.509	0.427	0.354	0.509	SUBCLONAL	1	TRUE	1	0.282895469101031	2		403	662	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0029453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	11	290	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.867099236071856	1	FACETS	0.1	0.069	0.138	0.1	0.069	0.138	SUBCLONAL	1	TRUE	0	0.867099236071856	1		290	144	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878073	48878233	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACGGCCGCCACCGCCGCCGCTGCCGCCGCGGAACCCCCGGCACCGCCGCCGCCGCCCCCTCCTGAGGAGGACCCAGAGCAGGACAGCGGCCCGGAGGACCTGCCTCTCGTCAGGTGAGCGAGCAGAGCCGCCGTCGCCTCACGCGGGAAGGGCGCCCCGGG	ACGGCCGCCACCGCCGCCGCTGCCGCCGCGGAACCCCCGGCACCGCCGCCGCCGCCCCCTCCTGAGGAGGACCCAGAGCAGGACAGCGGCCCGGAGGACCTGCCTCTCGTCAGGTGAGCGAGCAGAGCCGCCGTCGCCTCACGCGGGAAGGGCGCCCCGGG	-	novel	NA	P-0029453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	153	221	0	ENST00000267163.4:c.25_137+48del		p.X9_splice	ENST00000267163	NM_000321.2	9		1/27	0.867099236071856	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.867099236071856	1		221	198	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578485	7578486	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATCAACCC	novel	NA	P-0029453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	469	758	0	ENST00000269305.4:c.437_444dup	p.Ser149GlyfsTer24	p.S149Gfs*24	ENST00000269305	NM_001126112.2	148	-/GGGTTGAT	5/11	0.852451944943903	1	FACETS	0.829	0.801	0.857	0.829	0.801	0.857	CLONAL	1	TRUE	0	0.867099236071856	1		758	739	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71064705	71064705	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	119	533	0	ENST00000318789.4:c.969T>A	p.Phe323Leu	p.F323L	ENST00000318789	NM_032682.5	323	ttT/ttA	12/21	1	2	FACETS	0.444	0.402	0.489	0.444	0.402	0.489	SUBCLONAL	1	TRUE	1	0.867099236071856	2		533	618	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106058	8106058	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	460	439	0	ENST00000346208.3:c.878T>G	p.Met293Arg	p.M293R	ENST00000346208		293	aTg/aGg	4/6	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.861056480747225	2		439	979	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089777	27089777	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0029459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	230	353	1	ENST00000324856.7:c.2732+1G>A		p.X911_splice	ENST00000324856	NM_006015.4	911			0.853818066391722	1	FACETS	0.948	0.907	0.987	0.948	0.907	0.987	CLONAL	1	TRUE	0	0.861056480747225	1		354	321	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741926	145741926	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs754986197	NA	P-0029459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	292	580	2	ENST00000428558.2:c.577C>T	p.Arg193Ter	p.R193*	ENST00000428558	NM_004260.3	193	Cga/Tga	5/22	1	2	FACETS	0.973	0.922	1	0.973	0.922	1	CLONAL	1	TRUE	1	0.861056480747225	2		582	697	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106058	8106058	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029459-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	296	439	0	ENST00000346208.3:c.878T>G	p.Met293Arg	p.M293R	ENST00000346208		293	aTg/aGg	4/6	0.127125290322503	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.855106622101458	0		439	688	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089777	27089777	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0029459-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	219	353	1	ENST00000324856.7:c.2732+1G>A		p.X911_splice	ENST00000324856	NM_006015.4	911			0.855106622101458	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	0	0.855106622101458	1		354	290	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741926	145741926	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs754986197	NA	P-0029459-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	226	580	2	ENST00000428558.2:c.577C>T	p.Arg193Ter	p.R193*	ENST00000428558	NM_004260.3	193	Cga/Tga	5/22	1	2	FACETS	0.995	0.936	1	0.995	0.936	1	CLONAL	1	FALSE	1	0.855106622101458	2		582	531	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0029460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	102	483	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.379887057745301	2	FACETS	0.979	0.879	1	0.49	0.439	0.543	CLONAL	1	TRUE	0	0.392354870593056	2		483	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0029460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	253	906	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.308302721891109	2	FACETS	0.907	0.853	0.962	0.907	0.853	0.962	CLONAL	2	TRUE	0	0.392354870593056	2		906	711	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0029460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	105	353	2	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	0.379887057745301	2	FACETS	1	0.982	1	0.716	0.647	0.787	CLONAL	1	TRUE	0	0.392354870593056	2		355	374	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912188	114912188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	143	739	0	ENST00000543371.1:c.1258C>T	p.Arg420Trp	p.R420W	ENST00000543371	NM_001198531.1	420	Cgg/Tgg	11/14	1	2	FACETS	0.976	0.891	1	0.976	0.891	1	CLONAL	1	TRUE	1	0.392354870593056	2		739	747	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557569	21557569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750816560	NA	P-0029460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	123	745	3	ENST00000382592.4:c.2276G>A	p.Arg759Gln	p.R759Q	ENST00000382592	NM_014572.2	759	cGg/cAg	5/8	0.392354870593056	3	FACETS	0.931	0.842	1	0.465	0.421	0.512	CLONAL	1	TRUE	1	0.392354870593056	3		748	806	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028790	47028790	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	328	461	2	ENST00000377604.3:c.94C>T	p.Arg32Ter	p.R32*	ENST00000377604	NM_001204468.1	32	Cga/Tga	3/24	0.391827458097337	2	FACETS	0.918	0.877	0.959			1	CLONAL	3	TRUE	NA	0.392354870593056	2		463	607	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249007	55249007	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147149347	NA	P-0029460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	278	610	0	ENST00000275493.2:c.2305G>A	p.Val769Met	p.V769M	ENST00000275493	NM_005228.3	769	Gtg/Atg	20/28	0.351152559890098	3	FACETS	0.953	0.903	1			1	CLONAL	3	TRUE	NA	0.392354870593056	3		610	593	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945409	71945411	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	novel	NA	P-0029460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	146	845	0	ENST00000298229.2:c.2299_2301del	p.Ile767del	p.I767del	ENST00000298229	NM_001567.3	766	tTCAtc/ttc	20/28	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.392354870593056	2		845	691	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500519	99500519	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138696883	NA	P-0029460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	198	724	4	ENST00000268035.6:c.3952G>A	p.Asp1318Asn	p.D1318N	ENST00000268035	NM_000875.3	1318	Gac/Aac	21/21	0.374041425171079	3	FACETS	0.894	0.832	0.959	0.596	0.554	0.639	CLONAL	2	TRUE	0	0.392354870593056	3		728	675	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967244	134967244	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs151302345	NA	P-0029460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	106	648	0	ENST00000398015.3:c.2583G>A	p.Trp861Ter	p.W861*	ENST00000398015	NM_004441.4	861	tgG/tgA	14/16	0.379887057745301	2	FACETS	1	0.911	1	0.507	0.456	0.561	CLONAL	1	TRUE	0	0.392354870593056	2		648	533	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638411	176638411	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	41	721	1	ENST00000439151.2:c.3011A>G	p.Asp1004Gly	p.D1004G	ENST00000439151	NM_022455.4	1004	gAc/gGc	5/23	0.379887057745301	2	FACETS	0.261	0.216	0.311	0.13	0.108	0.156	SUBCLONAL	1	TRUE	0	0.392354870593056	2		722	801	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468215	50468215	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	360	754	1	ENST00000331340.3:c.1450C>A	p.His484Asn	p.H484N	ENST00000331340	NM_006060.4	484	Cac/Aac	8/8	0.351152559890098	3	FACETS	0.97	0.926	1			1	CLONAL	3	TRUE	NA	0.392354870593056	3		755	754	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0029462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	190	385	1	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	0.845810605269879	3	FACETS	0.912	0.846	0.98	0.456	0.423	0.49	CLONAL	1	TRUE	1	0.845810605269879	3		386	701	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589619	67589620	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0029462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	302	422	0	ENST00000274335.5:c.1384_1385del	p.Glu462IlefsTer2	p.E462Ifs*2	ENST00000274335		461	cGA/c	10/15	0.784825698877372	3	FACETS	0.899	0.857	0.941	0.899	0.857	0.941	CLONAL	2	TRUE	1	0.845810605269879	3		422	565	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699360	47699360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	266	591	1	ENST00000347630.2:c.148G>A	p.Glu50Lys	p.E50K	ENST00000347630	NM_001007230.1	50	Gaa/Aaa	4/11	1	2	FACETS	0.918	0.866	0.971	0.918	0.866	0.971	CLONAL	1	TRUE	1	0.845810605269879	2		592	685	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592163	67592164	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTAG	novel	NA	P-0029462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	124	280	0	ENST00000274335.5:c.1984_1985+3dup		p.S660fs	ENST00000274335		660	tct/tcTGTAGt	14/15	0.784825698877372	3	FACETS	0.742	0.674	0.814	0.371	0.337	0.407	SUBCLONAL	1	TRUE	1	0.845810605269879	3		280	562	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094441	27094441	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	739	815	0	ENST00000324856.7:c.3149A>G	p.Asp1050Gly	p.D1050G	ENST00000324856	NM_006015.4	1050	gAc/gGc	11/20	0.824136007750079	2	FACETS	0.988	0.97	1	0.988	0.97	1	CLONAL	2	TRUE	0	0.845810605269879	2		815	884	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692926	89692926	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	251	698	0	ENST00000371953.3:c.410C>A	p.Ala137Glu	p.A137E	ENST00000371953	NM_000314.4	137	gCa/gAa	5/9	1	2	FACETS	0.873	0.821	0.925	0.873	0.821	0.925	CLONAL	1	TRUE	1	0.845810605269879	2		698	680	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720675	89720675	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	60	208	0	ENST00000371953.3:c.826A>C	p.Asn276His	p.N276H	ENST00000371953	NM_000314.4	276	Aat/Cat	8/9	1	2	FACETS	0.85	0.748	0.955	0.85	0.748	0.955	CLONAL	1	TRUE	1	0.845810605269879	2		208	167	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0029463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	298	649	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	0.681160800963801	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.697846373976059	1		649	554	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874147	151874148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs747256476	NA	P-0029463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	176	569	9	ENST00000262189.6:c.8390dup	p.Glu2798GlyfsTer11	p.E2798Gfs*11	ENST00000262189	NM_170606.2	2797	aag/aaAg	38/59	0.192144067325585	1	FACETS	0.479	0.443	0.517	0.479	0.443	0.517	INDETERMINATE	1	TRUE	0	0.697846373976059	1		578	685	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023324	27023327	+	frameshift_variant	Frame_Shift_Del	DEL	CCGC	CCGC	-	novel	NA	P-0029463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	73	134	0	ENST00000324856.7:c.432_435del	p.Pro145GlnfsTer86	p.P145Qfs*86	ENST00000324856	NM_006015.4	144	CCGCcc/cc	1/20	0.697846373976059	1	FACETS	0.668	0.595	0.743	0.668	0.595	0.743	SUBCLONAL	1	TRUE	0	0.697846373976059	1		134	204	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023622	27023634	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCGGCGGCTGC	CGGCGGCGGCTGC	-	novel	NA	P-0029463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	228	345	0	ENST00000324856.7:c.732_744del	p.Ala245ProfsTer114	p.A245Pfs*114	ENST00000324856	NM_006015.4	243	gCGGCGGCGGCTGCc/gc	1/20	0.697846373976059	1	FACETS	0.969	0.916	1	0.969	0.916	1	CLONAL	1	TRUE	0	0.697846373976059	1		345	439	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600450	43600511	+	frameshift_variant	Frame_Shift_Del	DEL	CGCTGGGCCCTGGACCGCGAGCAGCGGGAGAAGTACGAGCTGGTGGCCGTGTGCACCGTGCA	CGCTGGGCCCTGGACCGCGAGCAGCGGGAGAAGTACGAGCTGGTGGCCGTGTGCACCGTGCA	-	novel	NA	P-0029463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	249	486	0	ENST00000355710.3:c.679_740del	p.Trp227ArgfsTer106	p.W227Rfs*106	ENST00000355710	NM_020975.4	226	CGCTGGGCCCTGGACCGCGAGCAGCGGGAGAAGTACGAGCTGGTGGCCGTGTGCACCGTGCAc/c	4/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.697846373976059	2		486	643	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481347	56481378	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCTTCCCAACCAGGTCCCCCCTGTCATGAGG	TCCTTCCCAACCAGGTCCCCCCTGTCATGAGG	-	novel	NA	P-0029463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	191	561	0	ENST00000267101.3:c.548-13_566del		p.X183_splice	ENST00000267101	NM_001982.3	183		5/28	1	2	FACETS	0.747	0.692	0.803	0.747	0.692	0.803	SUBCLONAL	1	TRUE	1	0.697846373976059	2		561	733	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860035	152860035	+	synonymous_variant	Silent	SNP	G	G	A	novel	NA	P-0029463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	182	683	0	ENST00000406277.2:c.393C>T	p.Arg131=	p.R131=	ENST00000406277	NM_152274.4	131	cgC/cgT	5/7	NA		FACETS		0.749	0.87				INDETERMINATE	1	TRUE	NA	0.697846373976059	2		683	645	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0029464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	492	737	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.565740583979033	2	FACETS	0.985	0.95	1	0.985	0.95	1	CLONAL	2	TRUE	0	0.578271745891531	2		737	864	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496924	29496927	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs786201874	NA	P-0029464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	175	402	0	ENST00000356175.3:c.499_502del	p.Cys167GlnfsTer10	p.C167Qfs*10	ENST00000356175	NM_000267.3	165	acTGTT/ac	5/57	0.565740583979033	2	FACETS	0.903	0.847	0.959	0.903	0.847	0.959	CLONAL	2	TRUE	0	0.578271745891531	2		402	335	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105631	30105631	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	206	830	0	ENST00000331968.5:c.1055G>T	p.Arg352Met	p.R352M	ENST00000331968	NM_002742.2	352	aGg/aTg	7/18	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.578271745891531	2		830	683	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486060	29486060	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs752208826	NA	P-0029464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	237	461	1	ENST00000356175.3:c.237A>T	p.Leu79Phe	p.L79F	ENST00000356175	NM_000267.3	79	ttA/ttT	3/57	0.565740583979033	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.578271745891531	2		462	370	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94067974	94067974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	78	334	0	ENST00000369303.4:c.988A>T	p.Arg330Trp	p.R330W	ENST00000369303	NM_004440.3	330	Agg/Tgg	4/17	0.578271745891531	2	FACETS	1	0.905	1	0.509	0.453	0.568	CLONAL	1	TRUE	0	0.578271745891531	2		334	265	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566285	141566285	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	146	485	0	ENST00000220592.5:c.1127A>T	p.Gln376Leu	p.Q376L	ENST00000220592	NM_012154.3	376	cAa/cTa	9/19	0.578271745891531	4	FACETS	0.988	0.902	1	0.329	0.3	0.359	CLONAL	1	TRUE	1	0.578271745891531	4		485	807	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769886672	NA	P-0029465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	74	351	3	ENST00000405192.2:c.414dup	p.Thr139HisfsTer24	p.T139Hfs*24	ENST00000405192	NM_001163147.1	138	-/C	7/12	0.664998451321911	3	FACETS	0.583	0.511	0.66	0.291	0.255	0.33	SUBCLONAL	1	TRUE	1	0.673280689467689	3		354	504	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0029465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	388	497	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	0.599934488789634	2	FACETS	0.888	0.854	0.922	0.888	0.854	0.922	CLONAL	2	TRUE	0	0.673280689467689	2		497	649	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106182928	106182928	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	161	495	0	ENST00000380013.4:c.3967G>T	p.Glu1323Ter	p.E1323*	ENST00000380013	NM_001127208.2	1323	Gag/Tag	8/11	0.599934488789634	2	FACETS	0.789	0.738	0.84	0.789	0.738	0.84	SUBCLONAL	2	TRUE	0	0.673280689467689	2		495	303	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0029465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	458	615	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.627983912010882	2	FACETS	0.946	0.914	0.978	0.946	0.914	0.978	CLONAL	2	TRUE	0	0.673280689467689	2		615	719	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097782	27097782	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	400	560	1	ENST00000324856.7:c.3371A>T	p.Lys1124Met	p.K1124M	ENST00000324856	NM_006015.4	1124	aAg/aTg	12/20	0.614176723005191	2	FACETS	0.874	0.84	0.907	0.874	0.84	0.907	CLONAL	2	TRUE	0	0.673280689467689	2		561	680	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604233	189604233	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1694	284	798	0	ENST00000264731.3:c.1400A>C	p.Asn467Thr	p.N467T	ENST00000264731	NM_003722.4	467	aAc/aCc	11/14	0.673280689467689	6	FACETS	1	0.937	1	0.334	0.312	0.356	CLONAL	1	TRUE	3	0.673280689467689	6		798	1978	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1906005	1906005	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	208	870	0	ENST00000382891.5:c.660C>A	p.Tyr220Ter	p.Y220*	ENST00000382891	NM_133335.3	220	taC/taA	3/22	0.599934488789634	2	FACETS	0.637	0.591	0.684	0.318	0.295	0.342	SUBCLONAL	1	TRUE	0	0.673280689467689	2		870	970	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84384055	84384645	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTAAACAAAATAGAATAACAGTTCAACATATAACATTTCTTCTACAAAGCTTTTATAATTAACTATTTGTAAGTAAAATTAAGTCAAAAAGATTTTAACAGTTGTATTATCTAAAGTGAGGATAACATACATAATTCTGAATTCTAATTTATATGCCACAGTATTCTAAGACAAAATTAAAGTTGTGTTCTTTCATGTCAGCAATATAGCTACCATAGTATTATGTTCTTTAAAAGCACAGAAAGGGCCGAGCGCAGTGGCTCACACCTATAATCCCAGCACTTTGGGAGGCTGAGGCGGGTGGATCACTTGAGGTCAGAAGTTCAAGACCAGCCTGGCCAACATGGTGAAACCCTGTCTCTATTAAAAATACAAAAAAAATTAGCCAGGCATGGTGGCAGGCACCTGGAATCCCAGCGTTTCAGGAGGCTGAGGCAGGAGAATCGCTTGACCCCAGGAGGCAGAGGTTGCAGTAAGCTGAGATCACACCTTTGCACTCCAACCTAGGCGACAGAGCGAGACTCCGTCTCAAAAATAAATAAATAAATAAAAATTTTTAGCACAGAAAGTAGAGATGTGTTGTTTACTTA	CCTAAACAAAATAGAATAACAGTTCAACATATAACATTTCTTCTACAAAGCTTTTATAATTAACTATTTGTAAGTAAAATTAAGTCAAAAAGATTTTAACAGTTGTATTATCTAAAGTGAGGATAACATACATAATTCTGAATTCTAATTTATATGCCACAGTATTCTAAGACAAAATTAAAGTTGTGTTCTTTCATGTCAGCAATATAGCTACCATAGTATTATGTTCTTTAAAAGCACAGAAAGGGCCGAGCGCAGTGGCTCACACCTATAATCCCAGCACTTTGGGAGGCTGAGGCGGGTGGATCACTTGAGGTCAGAAGTTCAAGACCAGCCTGGCCAACATGGTGAAACCCTGTCTCTATTAAAAATACAAAAAAAATTAGCCAGGCATGGTGGCAGGCACCTGGAATCCCAGCGTTTCAGGAGGCTGAGGCAGGAGAATCGCTTGACCCCAGGAGGCAGAGGTTGCAGTAAGCTGAGATCACACCTTTGCACTCCAACCTAGGCGACAGAGCGAGACTCCGTCTCAAAAATAAATAAATAAATAAAAATTTTTAGCACAGAAAGTAGAGATGTGTTGTTTACTTA	-	novel	NA	P-0029465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	28	569	0	ENST00000321945.7:c.796+2_797del		p.X266_splice	ENST00000321945	NM_139076.2	266		9/9	0.599934488789634	2	FACETS	0.157	0.125	0.193	0.078	0.062	0.097	SUBCLONAL	1	TRUE	0	0.673280689467689	2		569	531	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876167	35876167	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	608	596	1	ENST00000303115.3:c.959T>A	p.Val320Glu	p.V320E	ENST00000303115	NM_002185.3	320	gTg/gAg	8/8	0.464510710636808	6	FACETS	1	0.993	1	0.827	0.798	0.856	CLONAL	3	TRUE	2	0.673280689467689	6		597	1281	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494266	140494266	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	68	863	1	ENST00000288602.6:c.982C>T	p.Pro328Ser	p.P328S	ENST00000288602	NM_004333.4	328	Ccc/Tcc	8/18	0.456240228443706	2	FACETS	0.196	0.17	0.225	0.098	0.085	0.113	SUBCLONAL	1	TRUE	0	0.673280689467689	2		864	1030	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424299	47424383	+	splice_acceptor_variant,splice_donor_variant,intron_variant	Splice_Site	DEL	GTGAGTGCAGGGTGGACGGTGGGGGTGGACCATGGTTGGGGGTGTCCTTGACCAGGTCTCAAACTTCCCTGCTCTGTGGCATCAG	GTGAGTGCAGGGTGGACGGTGGGGGTGGACCATGGTTGGGGGTGTCCTTGACCAGGTCTCAAACTTCCCTGCTCTGTGGCATCAG	-	novel	NA	P-0029465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	57	611	0	ENST00000377045.4:c.303+3_305del		p.X101_splice	ENST00000377045	NM_001654.4	101			0.599934488789634	2	FACETS	0.223	0.191	0.259	0.112	0.095	0.13	SUBCLONAL	1	TRUE	0	0.673280689467689	2		611	758	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424539	47424650	+	splice_acceptor_variant,splice_donor_variant,intron_variant	Splice_Site	DEL	GTGAGCCCAGCCTGGGGTGGGTGGGGGGATGGGGAGCACAGAGGCCCAGCCACGAGGCCCTTACAGACAGCTGACCCGTGTCCCCTTGCTTTATACCCTTCATGCCCTCAAG	GTGAGCCCAGCCTGGGGTGGGTGGGGGGATGGGGAGCACAGAGGCCCAGCCACGAGGCCCTTACAGACAGCTGACCCGTGTCCCCTTGCTTTATACCCTTCATGCCCTCAAG	-	novel	NA	P-0029465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	103	467	0	ENST00000377045.4:c.458+3_460del		p.X153_splice	ENST00000377045	NM_001654.4	153			0.599934488789634	2	FACETS	0.514	0.461	0.57	0.257	0.23	0.285	SUBCLONAL	1	TRUE	0	0.673280689467689	2		467	595	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722761	49722761	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs62262682	NA	P-0029466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	16	45	2	ENST00000449682.2:c.1478G>T	p.Arg493Leu	p.R493L	ENST00000449682	NM_020998.3	493	cGt/cTt	13/18	0.14095257321753	5	FACETS	0.908	0.69	1	0.908	0.69	1	INDETERMINATE	3	FALSE	2	0.247875355353188	5		47	65	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618715	37618716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	524	594	3	ENST00000447079.4:c.397dup	p.Ser133LysfsTer24	p.S133Kfs*24	ENST00000447079	NM_015083.1	131	gaa/gAaa	1/14	0.247875355353188	5	FACETS	0.943	0.909	0.977			1	CLONAL	6	FALSE	NA	0.247875355353188	5		597	1025	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389278	8389278	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752508898	NA	P-0029466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	76	700	1	ENST00000356435.5:c.4340G>A	p.Arg1447Gln	p.R1447Q	ENST00000356435		1447	cGg/cAg	26/35	0.151764952126073	4	FACETS	0.85	0.744	0.965	0.283	0.248	0.322	CLONAL	1	FALSE	1	0.247875355353188	4		701	900	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86668002	86668002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769775990	NA	P-0029466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	32	408	1	ENST00000274376.6:c.1766G>A	p.Arg589His	p.R589H	ENST00000274376	NM_002890.2	589	cGc/cAc	13/25	0.247875355353188	3	FACETS	0.797	0.648	0.966	0.399	0.324	0.483	CLONAL	1	FALSE	1	0.247875355353188	3		409	364	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206728	102206728	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	63	493	0	ENST00000263464.3:c.1356G>C	p.Met452Ile	p.M452I	ENST00000263464	NM_001165.4	452	atG/atC	7/9	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	FALSE	1	0.247875355353188	2		493	477	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550566	29550585	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AATTTCTTCTTAAAAATAAG	AATTTCTTCTTAAAAATAAG	-	novel	NA	P-0029466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	78	398	0	ENST00000356175.3:c.1826_1845del	p.Lys609ThrfsTer4	p.K609Tfs*4	ENST00000356175	NM_000267.3	609	aAATTTCTTCTTAAAAATAAG/a	16/57	0.247875355353188	1	FACETS	0.992	0.882	1	1	0.984	1	CLONAL	2	FALSE	0	0.247875355353188	1		398	278	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1976630	1976630	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	81	771	1	ENST00000382891.5:c.3413G>T	p.Arg1138Leu	p.R1138L	ENST00000382891	NM_133335.3	1138	cGa/cTa	19/22	0.247875355353188	2	FACETS	0.918	0.808	1	0.459	0.404	0.518	CLONAL	1	FALSE	0	0.247875355353188	2		772	712	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223802	53223802	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	141	514	0	ENST00000375401.3:c.3557C>G	p.Ser1186Cys	p.S1186C	ENST00000375401	NM_004187.3	1186	tCt/tGt	23/26	0.197615451116004	2	FACETS	1	0.927	1			1	CLONAL	2	FALSE	NA	0.247875355353188	2		514	561	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593603	55593603	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913235	NA	P-0029467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	253	534	0	ENST00000288135.5:c.1669T>C	p.Trp557Arg	p.W557R	ENST00000288135	NM_000222.2	557	Tgg/Cgg	11/21	0.54239529034954	3	FACETS	0.884	0.845	0.923	0.884	0.845	0.923	CLONAL	3	TRUE	0	0.651671679464697	3		534	388	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106497	27106498	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0029467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	236	722	0	ENST00000324856.7:c.6109dup	p.Gln2037ProfsTer62	p.Q2037Pfs*62	ENST00000324856	NM_006015.4	2036	-/C	20/20	0.620584008868664	2	FACETS	0.905	0.847	0.965	0.453	0.423	0.483	CLONAL	1	TRUE	0	0.651671679464697	2		722	800	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871242	12871242	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	102	258	1	ENST00000228872.4:c.469A>T	p.Thr157Ser	p.T157S	ENST00000228872	NM_004064.3	157	Acc/Tcc	1/3	0.651671679464697	3	FACETS	1	0.952	1	0.546	0.492	0.602	CLONAL	1	TRUE	1	0.651671679464697	3		259	380	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460516	149460516	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	331	704	1	ENST00000286301.3:c.121C>T	p.Arg41Ter	p.R41*	ENST00000286301	NM_005211.3	41	Cga/Tga	3/22	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.491562522688408	2		705	1111	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579412	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCAGGAG	GGCCAGGAG	A	novel	NA	P-0029468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	430	701	0	ENST00000269305.4:c.267_275delinsT	p.Ser90ProfsTer56	p.S90Pfs*56	ENST00000269305	NM_001126112.2	89	ccCTCCTGGCCc/ccTc	4/11	NA	2	FACETS	0.949	0.909	0.989			1	INDETERMINATE	2	TRUE	NA	0.491562522688408	2		701	922	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453145	140453145	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913366	NA	P-0029469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	38	649	0	ENST00000288602.6:c.1790T>A	p.Leu597Gln	p.L597Q	ENST00000288602	NM_004333.4	597	cTa/cAa	15/18	1	2	FACETS	0.63	0.52	0.754	0.63	0.52	0.754	SUBCLONAL	1	TRUE	1	0.18	2		649	670	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519913	29519913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	44	513	0	ENST00000389048.3:c.1658C>T	p.Ser553Phe	p.S553F	ENST00000389048	NM_004304.4	553	tCc/tTc	9/29	0.15897081278868	0	FACETS	0.901	0.756	1			1	CLONAL	1	TRUE	0	0.18	0		513	445	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061116	38061199	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGCCGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTT	AGGGCCGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTT	GGGG	novel	NA	P-0029469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	35	493	2	ENST00000250448.2:c.790_873delinsCCCC	p.Lys264ProfsTer12	p.K264Pfs*12	ENST00000250448	NM_004496.3	264	AAGCGCTTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGCGGCGCCAAGGGCGGCCCT/CCCC	2/2	1	2	FACETS	0.727	0.595	0.876	0.727	0.595	0.876	SUBCLONAL	1	TRUE	1	0.18	2		495	535	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434507	140434507	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	30	501	0	ENST00000288602.6:c.2191C>G	p.Pro731Ala	p.P731A	ENST00000288602	NM_004333.4	731	Ccc/Gcc	18/18	1	2	FACETS	0.581	0.467	0.711	0.581	0.467	0.711	SUBCLONAL	1	TRUE	1	0.18	2		501	574	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563452	87563452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	44	788	0	ENST00000277120.3:c.1840G>A	p.Glu614Lys	p.E614K	ENST00000277120		614	Gag/Aag	16/19	0.3	1	FACETS	0.719	0.602	0.849	0.719	0.602	0.849	SUBCLONAL	1	TRUE	0	0.18	1		788	619	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0029470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	305	628	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	0.180137786137805	3	FACETS	0.865	0.816	0.914	0.865	0.816	0.914	INDETERMINATE	2	TRUE	1	0.43023913785767	3		628	996	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958879	38958879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	100	391	0	ENST00000357387.3:c.2233G>A	p.Glu745Lys	p.E745K	ENST00000357387	NM_152756.3	745	Gaa/Aaa	23/38	0.180137786137805	3	FACETS	0.956	0.856	1	0.478	0.428	0.531	INDETERMINATE	1	TRUE	1	0.43023913785767	3		391	591	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547265	106547265	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587778623	NA	P-0029470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	214	505	0	ENST00000369096.4:c.502C>G	p.Pro168Ala	p.P168A	ENST00000369096	NM_001198.3	168	Ccc/Gcc	4/7	0.181560701589481	4	FACETS	0.833	0.775	0.892	0.833	0.775	0.892	INDETERMINATE	2	TRUE	2	0.43023913785767	4		505	854	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	264	779	2	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.420553506957809	1	FACETS	0.965	0.906	1	0.965	0.906	1	CLONAL	1	TRUE	0	0.450366381848139	1		781	941	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971159	18971159	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	252	668	0	ENST00000262803.5:c.2212C>A	p.Gln738Lys	p.Q738K	ENST00000262803	NM_002911.3	738	Cag/Aag	16/24	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.450366381848139	2		668	1078	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467433	66467434	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0029473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	94	279	0	ENST00000273854.3:c.835_836delinsTT	p.Glu279Leu	p.E279L	ENST00000273854	NM_004439.5	279	GAa/TTa	3/18	1	2	FACETS	0.852	0.761	0.948	0.852	0.761	0.948	CLONAL	1	TRUE	1	0.450366381848139	2		279	490	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725043	89725043	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1057517809	NA	P-0029474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	91	261	0	ENST00000371953.3:c.1027-1G>A		p.X343_splice	ENST00000371953	NM_000314.4	343			0.625201763915654	2	FACETS	0.758	0.69	0.827	0.758	0.69	0.827	SUBCLONAL	2	TRUE	0	0.625201763915654	2		261	192	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944505	40944505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	94	672	1	ENST00000373198.4:c.1997C>T	p.Ala666Val	p.A666V	ENST00000373198	NM_133170.3	666	gCt/gTt	12/32	0.435412616148769	1	FACETS	0.45	0.402	0.501	0.45	0.402	0.501	SUBCLONAL	1	TRUE	0	0.625201763915654	1		673	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578429	7578429	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1567553148	NA	P-0029474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	712	814	0	ENST00000269305.4:c.501del	p.Gln167HisfsTer3	p.Q167Hfs*3	ENST00000269305	NM_001126112.2	167	caG/ca	5/11	0.625201763915654	3	FACETS	0.877	0.861	0.893	1	0.998	1	CLONAL	4	TRUE	0	0.625201763915654	3		814	852	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29195903	29195903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180215862	NA	P-0029474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	143	779	1	ENST00000240100.2:c.695G>A	p.Cys232Tyr	p.C232Y	ENST00000240100	NM_001394.6	232	tGc/tAc	3/4	0.625201763915654	1	FACETS	0.866	0.8	0.934	0.866	0.8	0.934	CLONAL	1	TRUE	0	0.625201763915654	1		780	363	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322754	39322754	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	112	548	0	ENST00000373001.3:c.238G>A	p.Val80Met	p.V80M	ENST00000373001	NM_022157.3	80	Gtg/Atg	2/7	0.625201763915654	5	FACETS	1	0.974	1	0.41	0.37	0.453	CLONAL	1	TRUE	2	0.625201763915654	5		548	564	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176132118	176132118	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	147	620	0	ENST00000367669.3:c.649C>T	p.His217Tyr	p.H217Y	ENST00000367669	NM_022457.5	217	Cac/Tac	5/20	0.522583495725642	4	FACETS	1	0.987	1	0.476	0.437	0.517	CLONAL	1	TRUE	1	0.625201763915654	4		620	535	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619972	21619972	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	238	767	0	ENST00000382592.4:c.194G>C	p.Arg65Thr	p.R65T	ENST00000382592	NM_014572.2	65	aGa/aCa	2/8	0.295144860913736	3	FACETS	0.775	0.728	0.823	0.775	0.728	0.823	INDETERMINATE	2	TRUE	1	0.625201763915654	3		767	645	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56867254	56867254	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1364576973	NA	P-0029474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	24	520	0	ENST00000308159.5:c.1473T>G	p.His491Gln	p.H491Q	ENST00000308159	NM_014669.4	491	caT/caG	13/22	0.503888534015899	1	FACETS	0.168	0.131	0.21	0.168	0.131	0.21	SUBCLONAL	1	TRUE	0	0.625201763915654	1		520	314	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81968080	81968080	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	171	771	0	ENST00000359376.3:c.2786A>G	p.Glu929Gly	p.E929G	ENST00000359376	NM_002661.3	929	gAg/gGg	26/33	0.625201763915654	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.625201763915654	1		771	357	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955201	17955201	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1686	268	934	0	ENST00000458235.1:c.26C>G	p.Pro9Arg	p.P9R	ENST00000458235	NM_000215.3	9	cCc/cGc	2/24	0.625201763915654	5	FACETS	0.85	0.794	0.909	0.283	0.264	0.303	CLONAL	1	TRUE	2	0.625201763915654	5		934	1954	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	151	404	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.949	0.874	1	0.949	0.874	1	CLONAL	1	TRUE	1	0.67	2		404	475	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0029479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	158	631	1	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	0.67	2		632	469	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710578	117710578	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142303126	NA	P-0029479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	166	423	2	ENST00000368508.3:c.1694C>T	p.Ser565Leu	p.S565L	ENST00000368508	NM_002944.2	565	tCg/tTg	12/43	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.67	2		425	490	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783622	50783622	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	21	361	0	ENST00000398568.2:c.13T>G	p.Leu5Val	p.L5V	ENST00000398568	NM_001042412.1	5	Tta/Gta	3/18	0.576150061744568	3	FACETS	0.256	0.197	0.325	0.128	0.098	0.163	SUBCLONAL	1	TRUE	1	0.60944678746773	3		361	351	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945994	17945994	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	132	548	0	ENST00000458235.1:c.1945T>C	p.Ser649Pro	p.S649P	ENST00000458235	NM_000215.3	649	Tct/Cct	15/24	0.555697462564301	4	FACETS	1	0.94	1	0.522	0.475	0.571	CLONAL	1	TRUE	2	0.60944678746773	4		548	668	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643450	38643450	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	187	531	0	ENST00000299084.4:c.920A>T	p.Asp307Val	p.D307V	ENST00000299084	NM_152594.2	307	gAc/gTc	7/7	0.639466798830538	3	FACETS	0.9	0.832	0.97	0.45	0.416	0.485	CLONAL	1	TRUE	1	0.639466798830538	3		531	858	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0029507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	80	440	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.336280327652267	2		440	468	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99452114	99452114	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	36	334	0	ENST00000268035.6:c.1448G>T	p.Gly483Val	p.G483V	ENST00000268035	NM_000875.3	483	gGg/gTg	6/21	1	2	FACETS	0.533	0.438	0.638	0.533	0.438	0.638	SUBCLONAL	1	TRUE	1	0.336280327652267	2		334	402	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983028	149983028	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	106	481	0	ENST00000253339.5:c.3230A>T	p.Glu1077Val	p.E1077V	ENST00000253339		1077	gAa/gTa	7/7	1	2	FACETS	0.919	0.825	1	0.919	0.825	1	CLONAL	1	TRUE	1	0.336280327652267	2		481	686	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0029508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	57	437	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.571	0.492	0.655	0.571	0.492	0.655	SUBCLONAL	1	TRUE	1	0.577423920640883	2		437	346	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420090	49420090	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	66	444	0	ENST00000301067.7:c.15659G>C	p.Arg5220Pro	p.R5220P	ENST00000301067	NM_003482.3	5220	cGc/cCc	48/54	1	2	FACETS	0.529	0.461	0.603	0.529	0.461	0.603	SUBCLONAL	1	TRUE	1	0.577423920640883	2		444	432	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061211	+	inframe_deletion	In_Frame_Del	DEL	GAAGCGCTTCTGGCGGCGCAA	GAAGCGCTTCTGGCGGCGCAA	-	novel	NA	P-0029508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	87	359	0	ENST00000250448.2:c.778_798del	p.Leu260_Phe266del	p.L260_F266del	ENST00000250448	NM_004496.3	260	TTGCGCCGCCAGAAGCGCTTC/-	2/2	1	2	FACETS	0.706	0.628	0.788	0.706	0.628	0.788	SUBCLONAL	1	TRUE	1	0.577423920640883	2		359	427	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627544	37627545	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0029508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	73	553	0	ENST00000447079.4:c.1461dup	p.Glu488ArgfsTer6	p.E488Rfs*6	ENST00000447079	NM_015083.1	487	tcc/tCcc	2/14	1	2	FACETS	0.461	0.403	0.522	0.461	0.403	0.522	SUBCLONAL	1	TRUE	1	0.577423920640883	2		553	549	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0029511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	21	549	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.364	0.28	0.461	0.364	0.28	0.461	SUBCLONAL	1	TRUE	1	0.386074151206059	2		549	299	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106465	27106465	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	25	539	0	ENST00000324856.7:c.6076C>T	p.Gln2026Ter	p.Q2026*	ENST00000324856	NM_006015.4	2026	Cag/Tag	20/20	0.386074151206059	5	FACETS	0.593	0.467	0.737	0.296	0.233	0.369	SUBCLONAL	1	TRUE	3	0.386074151206059	5		539	345	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981260	201981261	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	72	585	0	ENST00000359651.3:c.342dup	p.Gly115TrpfsTer20	p.G115Wfs*20	ENST00000359651		113	-/T	2/8	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.386074151206059	2		585	370	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670709	86670711	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0029511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	10	210	0	ENST00000274376.6:c.1989_1991del	p.Lys664del	p.K664del	ENST00000274376	NM_002890.2	663	AAG/-	15/25	0.254004753120891	4	FACETS	0.482	0.327	0.675	0.241	0.163	0.338	SUBCLONAL	1	TRUE	2	0.386074151206059	4		210	149	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174395	11174395	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	56	521	0	ENST00000361445.4:c.7280T>G	p.Leu2427Arg	p.L2427R	ENST00000361445	NM_004958.3	2427	cTg/cGg	53/58	0.281258030850373	1	FACETS	0.59	0.509	0.676	0.59	0.509	0.676	INDETERMINATE	1	FALSE	0	0.514731026229631	1		521	274	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714188	43714188	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	30	741	0	ENST00000382044.4:c.3965G>T	p.Ser1322Ile	p.S1322I	ENST00000382044	NM_001141980.1	1322	aGt/aTt	19/28	0.173513033856098	0	FACETS	0.175	0.141	0.214			1	INDETERMINATE	1	FALSE	0	0.514731026229631	0		741	323	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191470	10191470	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs5030817	NA	P-0029512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	44	327	0	ENST00000256474.2:c.464-1G>T		p.X155_splice	ENST00000256474	NM_000551.3	155			0.46165367475548	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	FALSE	0	0.514731026229631	1		327	114	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161334	185161334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	20	563	0	ENST00000265026.3:c.761G>T	p.Arg254Leu	p.R254L	ENST00000265026	NM_004721.4	254	cGa/cTa	4/14	0.281258030850373	1	FACETS	0.337	0.26	0.427	0.337	0.26	0.427	INDETERMINATE	1	FALSE	0	0.514731026229631	1		563	171	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	109	404	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.94	0.858	1	0.94	0.858	1	CLONAL	1	TRUE	1	0.821971643537754	2		404	282	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0029513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	112	344	1	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	0.821971643537754	2		345	270	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900329	101900329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	22	302	0	ENST00000374994.4:c.763C>T	p.Arg255Cys	p.R255C	ENST00000374994	NM_004612.2	255	Cgt/Tgt	4/9	1	2	FACETS	0.153	0.118	0.193	0.153	0.118	0.193	SUBCLONAL	1	TRUE	1	0.821971643537754	2		302	350	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74859031	74859031	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	123	312	0	ENST00000284811.8:c.173A>G	p.Asn58Ser	p.N58S	ENST00000284811		58	aAt/aGt	4/4	1	2	FACETS	0.805	0.735	0.876	0.805	0.735	0.876	CLONAL	1	TRUE	1	0.821971643537754	2		312	372	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266921	18266921	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	150	413	0	ENST00000222254.8:c.232C>G	p.Leu78Val	p.L78V	ENST00000222254	NM_005027.3	78	Ctg/Gtg	2/16	0.166852798863108	4	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.821971643537754	4		413	567	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799051	42799051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	220	637	0	ENST00000575354.2:c.4535G>A	p.Arg1512His	p.R1512H	ENST00000575354	NM_015125.3	1512	cGt/cAt	20/20	0.821971643537754	1	FACETS	0.941	0.896	0.985	0.941	0.896	0.985	CLONAL	1	TRUE	0	0.821971643537754	1		637	335	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0029515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	87	440	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.99	0.88	1	0.99	0.88	1	CLONAL	1	TRUE	1	0.363984874399055	2		440	483	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	30	368	0	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	1	2	FACETS	0.392	0.315	0.478	0.392	0.315	0.478	SUBCLONAL	1	TRUE	1	0.363984874399055	2		368	421	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56878430	56878430	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771046738	NA	P-0029515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	73	395	0	ENST00000308159.5:c.2369G>A	p.Arg790His	p.R790H	ENST00000308159	NM_014669.4	790	cGc/cAc	22/22	1	2	FACETS	0.764	0.669	0.866	0.764	0.669	0.866	SUBCLONAL	1	TRUE	1	0.363984874399055	2		395	525	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27190644	27190644	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	101	562	0	ENST00000380036.4:c.1445T>C	p.Leu482Pro	p.L482P	ENST00000380036	NM_000459.3	482	cTa/cCa	10/23	1	2	FACETS	0.838	0.75	0.932	0.838	0.75	0.932	CLONAL	1	TRUE	1	0.363984874399055	2		562	662	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	134	394	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.188532130144689	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	0	0.237063081691314	3		394	371	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0029516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	38	538	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.911	0.755	1	0.911	0.755	1	CLONAL	1	TRUE	1	0.237063081691314	2		538	352	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0029516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	23	262	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.237063081691314	2		262	151	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188287	10188287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs869025650	NA	P-0029516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	98	539	0	ENST00000256474.2:c.430G>A	p.Gly144Arg	p.G144R	ENST00000256474	NM_000551.3	144	Gga/Aga	2/3	0.228727961250559	3	FACETS	0.881	0.788	0.978	0.881	0.788	0.978	CLONAL	2	TRUE	1	0.237063081691314	3		539	525	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114799869	114799869	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0029516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	34	536	0	ENST00000543371.1:c.536C>G	p.Ser179Ter	p.S179*	ENST00000543371	NM_001198531.1	179	tCa/tGa	5/14	1	2	FACETS	0.795	0.65	0.957	0.795	0.65	0.957	CLONAL	1	TRUE	1	0.237063081691314	2		536	361	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882334	89882334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	38	461	0	ENST00000389301.3:c.140C>T	p.Ala47Val	p.A47V	ENST00000389301	NM_000135.2	47	gCt/gTt	2/43	0.221913198827574	3	FACETS	0.89	0.736	1	0.445	0.368	0.531	CLONAL	1	TRUE	1	0.237063081691314	3		461	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577084	7577111	+	frameshift_variant	Frame_Shift_Del	DEL	TCTGTGCGCCGGTCTCTCCCAGGACAGG	TCTGTGCGCCGGTCTCTCCCAGGACAGG	-	novel	NA	P-0029516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	87	607	0	ENST00000269305.4:c.827_854del	p.Ala276GlyfsTer60	p.A276Gfs*60	ENST00000269305	NM_001126112.2	276	gCCTGTCCTGGGAGAGACCGGCGCACAGAg/gg	8/11	0.237063081691314	2	FACETS	0.941	0.839	1	0.941	0.839	1	CLONAL	2	TRUE	0	0.237063081691314	2		607	390	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584575	48584575	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	18	411	0	ENST00000342988.3:c.748C>T	p.Gln250Ter	p.Q250*	ENST00000342988	NM_005359.5	250	Cag/Tag	6/12	0.237063081691314	2	FACETS	0.475	0.357	0.614	0.237	0.178	0.307	SUBCLONAL	1	TRUE	0	0.237063081691314	2		411	320	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0029520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	161	434	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.374098794182034	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.374098794182034	1		434	688	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0029520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	150	423	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.374098794182034	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.374098794182034	1		423	538	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0029520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	64	341	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	1	2	FACETS	0.597	0.517	0.684	0.597	0.517	0.684	SUBCLONAL	1	TRUE	1	0.374098794182034	2		341	573	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127164	22127164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057519911	NA	P-0029520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	94	344	0	ENST00000215832.6:c.964G>A	p.Glu322Lys	p.E322K	ENST00000215832	NM_002745.4	322	Gag/Aag	7/9	0.374098794182034	2	FACETS	0.858	0.765	0.956	0.429	0.382	0.478	CLONAL	1	TRUE	0	0.374098794182034	2		344	586	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0029520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	103	267	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	0.374098794182034	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.374098794182034	1		267	367	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088785	27088794	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGGGGGGT	CCAGGGGGGT	-	novel	NA	P-0029520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	222	470	0	ENST00000324856.7:c.2395_2404del	p.Gln799SerfsTer31	p.Q799Sfs*31	ENST00000324856	NM_006015.4	798	ccCCAGGGGGGT/cc	7/20	0.331763665482957	2	FACETS	0.896	0.839	0.955	0.896	0.839	0.955	CLONAL	2	TRUE	0	0.374098794182034	2		470	662	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515455	103515455	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0029520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	78	234	0	ENST00000355739.4:c.1954+2T>C		p.X652_splice	ENST00000355739	NM_000123.3	652			0.374098794182034	2	FACETS	1	0.963	1	0.608	0.538	0.682	CLONAL	1	TRUE	0	0.374098794182034	2		234	343	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645075	67645075	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	89	565	1	ENST00000264010.4:c.340C>T	p.Gln114Ter	p.Q114*	ENST00000264010	NM_006565.3	114	Cag/Tag	3/12	1	2	FACETS	0.5	0.442	0.562	0.5	0.442	0.562	SUBCLONAL	1	TRUE	1	0.374098794182034	2		566	951	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114603	73114603	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	51	380	0	ENST00000356692.5:c.984A>T	p.Glu328Asp	p.E328D	ENST00000356692		328	gaA/gaT	9/9	1	2	FACETS	0.441	0.374	0.515	0.441	0.374	0.515	SUBCLONAL	1	TRUE	1	0.374098794182034	2		380	618	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0029522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	44	428	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.154691321909638	3	FACETS	0.574	0.481	0.678	0.287	0.24	0.339	INDETERMINATE	1	TRUE	1	0.31	3		428	571	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0029522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	78	375	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	0.922	0.811	1	0.922	0.811	1	CLONAL	1	TRUE	1	0.31	2		375	546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0029522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	106	438	0	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.31	2		438	670	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56171040	56171040	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	55	211	0	ENST00000399503.3:c.1870del	p.Gln624ArgfsTer32	p.Q624Rfs*32	ENST00000399503	NM_005921.1	623	tCc/tc	10/20	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.31	2		211	324	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0029523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	16	343	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.234	0.172	0.308	0.234	0.172	0.308	SUBCLONAL	1	FALSE	1	0.416938983350333	2		343	328	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650368	48650368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782208453	NA	P-0029523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	273	233	0	ENST00000376670.3:c.338G>A	p.Arg113His	p.R113H	ENST00000376670	NM_002049.3	113	cGc/cAc	3/6	1	1	FACETS	1	0.991	1	1	0.997	1	CLONAL	3	FALSE	0	0.416938983350333	1		233	326	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0029524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	241	502	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	1	2	FACETS	0.896	0.841	0.952	0.896	0.841	0.952	CLONAL	1	TRUE	1	0.780884192917664	2		502	689	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704487	117704487	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	127	275	0	ENST00000368508.3:c.2489G>T	p.Gly830Val	p.G830V	ENST00000368508	NM_002944.2	830	gGg/gTg	16/43	1	2	FACETS	0.921	0.845	1	0.921	0.845	1	CLONAL	1	TRUE	1	0.780884192917664	2		275	353	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099079	157099079	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	111	231	0	ENST00000346085.5:c.16G>A	p.Gly6Ser	p.G6S	ENST00000346085	NM_020732.3	6	Ggc/Agc	1/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.780884192917664	2		231	257	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0029525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	84	906	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.233595734787459	1	FACETS	0.964	0.852	1	0.964	0.852	1	CLONAL	1	TRUE	0	0.233595734787459	1		906	659	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0029527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	64	532	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.438191594838319	1	FACETS	0.955	0.837	1	0.955	0.837	1	CLONAL	1	TRUE	0	0.441025751478936	1		532	237	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0029529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	153	591	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.811462697965229	NA		591	372	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115397	115115397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866796237	NA	P-0029529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	215	456	1	ENST00000257566.3:c.929G>A	p.Arg310Gln	p.R310Q	ENST00000257566	NM_016569.3	310	cGa/cAa	5/8	0.165414521887437	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.811462697965229	0		457	560	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28886202	28886202	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	193	409	0	ENST00000282397.4:c.3420C>A	p.Asp1140Glu	p.D1140E	ENST00000282397	NM_002019.4	1140	gaC/gaA	26/30	0.165414521887437	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.811462697965229	0		409	513	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051273	128051273	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	196	416	0	ENST00000285398.2:c.50G>A	p.Arg17Gln	p.R17Q	ENST00000285398	NM_000122.1	17	cGg/cAg	2/15	1	2	FACETS	0.942	0.879	1	0.942	0.879	1	CLONAL	1	TRUE	1	0.811462697965229	2		416	513	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026861	6026861	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	166	350	0	ENST00000265849.7:c.1535G>C	p.Gly512Ala	p.G512A	ENST00000265849	NM_000535.5	512	gGc/gCc	11/15	0.811462697965229	3	FACETS	0.948	0.874	1	0.474	0.437	0.512	CLONAL	1	TRUE	1	0.811462697965229	3		350	607	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195166	123195166	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	241	380	0	ENST00000218089.9:c.1510del	p.Glu504LysfsTer10	p.E504Kfs*10	ENST00000218089	NM_001042749.1	503	ctG/ct	16/35	0.293207117106278	1	FACETS	0.637	0.601	0.674	0.637	0.601	0.674	INDETERMINATE	1	TRUE	0	0.811462697965229	1		380	554	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	155	404	0				ENST00000310581	NM_198253.2	-/1132			0.363503201278772	6	FACETS	0.975	0.897	1	0.488	0.448	0.528	CLONAL	2	TRUE	2	0.595078021267621	6		404	585	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589623	67589634	+	inframe_deletion	In_Frame_Del	DEL	ATATGATAGATT	ATATGATAGATT	-	novel	NA	P-0029531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	85	315	0	ENST00000274335.5:c.1392_1403del	p.Asp464_Tyr467del	p.D464_Y467del	ENST00000274335		462	gaATATGATAGATTa/gaa	10/15	0.363503201278772	6	FACETS	1	0.979	1	0.374	0.332	0.419	CLONAL	1	TRUE	2	0.595078021267621	6		315	418	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226579954	226579954	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	30	453	0	ENST00000366794.5:c.348G>T	p.Glu116Asp	p.E116D	ENST00000366794	NM_001618.3	116	gaG/gaT	3/23	1	2	FACETS	0.174	0.14	0.214	0.174	0.14	0.214	SUBCLONAL	1	TRUE	1	0.595078021267621	2		453	579	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0029532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	8	272	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.626	0.408	0.899	0.626	0.408	0.899	SUBCLONAL	1	TRUE	1	0.36	2		272	71	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0029532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	18	671	1	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	1	0.839	1	1	0.839	1	CLONAL	1	TRUE	1	0.36	2		672	89	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165688	47165688	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	12	400	1	ENST00000409792.3:c.438A>T	p.Lys146Asn	p.K146N	ENST00000409792	NM_014159.6	146	aaA/aaT	3/21	1	2	FACETS	0.901	0.644	1	0.901	0.644	1	CLONAL	1	TRUE	1	0.36	2		401	74	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0029533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	182	399	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	1	2	FACETS	0.89	0.831	0.951	0.89	0.831	0.951	CLONAL	1	TRUE	1	0.929002658616779	2		399	440	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0029533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	766	593	1	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.925964687881149	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.929002658616779	2		594	814	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363896	118363896	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	192	324	0	ENST00000534358.1:c.5129A>T	p.Asp1710Val	p.D1710V	ENST00000534358	NM_005933.3	1710	gAt/gTt	16/36	1	2	FACETS	0.952	0.892	1	0.952	0.892	1	CLONAL	1	TRUE	1	0.929002658616779	2		324	434	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89851282	89851282	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	436	407	0	ENST00000389301.3:c.1450G>C	p.Glu484Gln	p.E484Q	ENST00000389301	NM_000135.2	484	Gag/Cag	15/43	0.523584931567804	4	FACETS	0.888	0.857	0.918	0.888	0.857	0.918	INDETERMINATE	3	TRUE	1	0.929002658616779	4		407	680	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376227	15376227	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs767133260	NA	P-0029533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	188	392	0	ENST00000263377.2:c.787C>G	p.Pro263Ala	p.P263A	ENST00000263377	NM_058243.2	263	Cca/Gca	5/20	0.463250238038152	4	FACETS	1	0.989	1	0.459	0.427	0.492	INDETERMINATE	1	TRUE	1	0.929002658616779	4		392	567	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961655	18961655	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1288491879	NA	P-0029534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	256	509	0	ENST00000262803.5:c.788A>G	p.Asn263Ser	p.N263S	ENST00000262803	NM_002911.3	263	aAc/aGc	5/24	0.656597849418763	3	FACETS	0.959	0.898	1	0.479	0.449	0.511	CLONAL	1	TRUE	1	0.697334226445974	3		509	1033	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs863224499	NA	P-0029535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	213	513	0	ENST00000269305.4:c.672+1G>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.363638381158906	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.363638381158906	2		513	563	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69230517	69230517	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	63	324	0	ENST00000462284.1:c.906A>T	p.Glu302Asp	p.E302D	ENST00000462284	NM_002392.5	302	gaA/gaT	10/11	0.363638381158906	3	FACETS	0.824	0.714	0.943	0.412	0.357	0.472	CLONAL	1	TRUE	1	0.363638381158906	3		324	497	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838180	89838180	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772737454	NA	P-0029535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	31	386	0	ENST00000389301.3:c.2057C>T	p.Ala686Val	p.A686V	ENST00000389301	NM_000135.2	686	gCt/gTt	23/43	0.212805301191092	3	FACETS	0.39	0.314	0.475	0.195	0.157	0.238	INDETERMINATE	1	TRUE	1	0.363638381158906	3		386	517	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780598	56780598	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	56	433	0	ENST00000337432.4:c.613C>G	p.Leu205Val	p.L205V	ENST00000337432	NM_058216.2	205	Ctt/Gtt	4/9	0.204875812651099	4	FACETS	0.576	0.493	0.668	0.288	0.246	0.334	INDETERMINATE	1	TRUE	2	0.363638381158906	4		433	729	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211121	36211121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	102	692	0	ENST00000222270.7:c.872G>A	p.Gly291Glu	p.G291E	ENST00000222270	NM_014727.1	291	gGa/gAa	3/37	0.315380860341856	3	FACETS	0.942	0.843	1	0.471	0.421	0.524	CLONAL	1	TRUE	1	0.363638381158906	3		692	704	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439878	220439878	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	57	520	0	ENST00000243786.2:c.731C>G	p.Ser244Cys	p.S244C	ENST00000243786	NM_002191.3	244	tCt/tGt	2/2	0.315380860341856	3	FACETS	0.762	0.655	0.879	0.381	0.327	0.44	SUBCLONAL	1	TRUE	1	0.363638381158906	3		520	486	SUCCESS
APC	324	MSKCC	GRCh37	5	112175447	112175447	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0029535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	63	226	0	ENST00000257430.4:c.4156A>T	p.Arg1386Ter	p.R1386*	ENST00000257430	NM_000038.5	1386	Aga/Tga	16/16	0.363638381158906	2	FACETS	0.777	0.681	0.877	0.777	0.681	0.877	SUBCLONAL	2	TRUE	0	0.363638381158906	2		226	223	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5064896	5064896	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	23	299	0	ENST00000381652.3:c.1070G>C	p.Ser357Thr	p.S357T	ENST00000381652	NM_004972.3	357	aGc/aCc	9/25	1	2	FACETS	0.382	0.298	0.48	0.382	0.298	0.48	SUBCLONAL	1	TRUE	1	0.363638381158906	2		299	331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577595	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0029538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	406	414	0	ENST00000269305.4:c.686_687del	p.Cys229TyrfsTer10	p.C229Yfs*10	ENST00000269305	NM_001126112.2	229	tGT/t	7/11	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	2	TRUE	NA	0.739856073348927	2		414	548	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426665	212426665	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	159	413	0	ENST00000342788.4:c.2450C>T	p.Ser817Leu	p.S817L	ENST00000342788	NM_005235.2	817	tCa/tTa	20/28	0.739856073348927	1	FACETS	0.548	0.506	0.591	0.548	0.506	0.591	SUBCLONAL	1	TRUE	0	0.739856073348927	1		413	494	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426738	212426739	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0029538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	135	429	0	ENST00000342788.4:c.2376_2377delinsTT	p.Gln793Ter	p.Q793*	ENST00000342788	NM_005235.2	792	atCCag/atTTag	20/28	0.739856073348927	1	FACETS	0.478	0.437	0.52	0.478	0.437	0.52	SUBCLONAL	1	TRUE	0	0.739856073348927	1		429	481	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426786	212426786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866491191	NA	P-0029538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	75	376	0	ENST00000342788.4:c.2329C>T	p.His777Tyr	p.H777Y	ENST00000342788	NM_005235.2	777	Cat/Tat	20/28	0.739856073348927	1	FACETS	0.347	0.306	0.391	0.347	0.306	0.391	SUBCLONAL	1	TRUE	0	0.739856073348927	1		376	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0029540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	207	1069	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.467636323011447	2	FACETS	0.981	0.922	1	0.981	0.922	1	CLONAL	2	TRUE	0	0.467636323011447	2		1071	451	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913250	NA	P-0029540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	47	340	0	ENST00000369535.4:c.34G>T	p.Gly12Cys	p.G12C	ENST00000369535	NM_002524.4	12	Ggt/Tgt	2/7	1	2	FACETS	0.926	0.79	1	0.926	0.79	1	CLONAL	1	TRUE	1	0.467636323011447	2		340	217	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033946	49033946	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	56	386	2	ENST00000267163.4:c.2083A>T	p.Met695Leu	p.M695L	ENST00000267163	NM_000321.2	695	Atg/Ttg	20/27	0.173798571757881	3	FACETS	1	0.955	1	0.419	0.363	0.479	INDETERMINATE	1	TRUE	0	0.467636323011447	3		388	235	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964917	25964917	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	64	379	0	ENST00000435504.4:c.4289C>T	p.Ser1430Phe	p.S1430F	ENST00000435504		1430	tCc/tTc	13/13	0.459393013693576	3	FACETS	1	0.94	1	0.567	0.495	0.643	CLONAL	1	TRUE	1	0.467636323011447	3		379	298	SUCCESS
APC	324	MSKCC	GRCh37	5	112175759	112175759	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1554085898	NA	P-0029540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	37	309	0	ENST00000257430.4:c.4468del	p.His1490IlefsTer17	p.H1490Ifs*17	ENST00000257430	NM_000038.5	1490	Cat/at	16/16	1	2	FACETS	0.791	0.672	0.915	1	0.962	1	CLONAL	2	TRUE	1	0.467636323011447	2		309	100	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0029542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	441	768	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.904	0.864	0.945	0.904	0.864	0.945	CLONAL	1	TRUE	1	0.840730226950237	2		768	1160	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0029542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	480	950	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.840730226950237	2		950	1124	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149251	119149251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267606708	NA	P-0029542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	367	488	0	ENST00000264033.4:c.1259G>A	p.Arg420Gln	p.R420Q	ENST00000264033	NM_005188.3	420	cGa/cAa	9/16	1	2	FACETS	0.939	0.894	0.984	0.939	0.894	0.984	CLONAL	1	TRUE	1	0.840730226950237	2		488	930	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599332	55599332	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519710	NA	P-0029542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2157	641	392	0	ENST00000288135.5:c.2458G>T	p.Asp820Tyr	p.D820Y	ENST00000288135	NM_000222.2	820	Gat/Tat	17/21	0.840730226950237	8	FACETS	0.96	0.92	1	0.274	0.263	0.286	CLONAL	2	TRUE	1	0.840730226950237	8		392	2798	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	334	266	0	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.840730226950237	1		266	408	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007871	45007872	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0029542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	323	353	0	ENST00000558401.1:c.319_320del	p.Leu107ValfsTer7	p.L107Vfs*7	ENST00000558401	NM_004048.2	106	acTTtg/actg	2/4	0.840730226950237	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.840730226950237	1		353	425	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813014	76813014	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	361	260	1	ENST00000373344.5:c.6607G>T	p.Glu2203Ter	p.E2203*	ENST00000373344	NM_000489.3	2203	Gag/Tag	30/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.840730226950237	1		261	416	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194110	94194110	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773469981	NA	P-0029542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	273	421	3	ENST00000323929.3:c.1318G>A	p.Ala440Thr	p.A440T	ENST00000323929	NM_005591.3	440	Gca/Aca	12/20	1	2	FACETS	0.906	0.855	0.957	0.906	0.855	0.957	CLONAL	1	TRUE	1	0.840730226950237	2		424	717	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980558	1980559	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs752037034	NA	P-0029542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	401	563	14	ENST00000382891.5:c.4028dup	p.Glu1344ArgfsTer91	p.E1344Rfs*91	ENST00000382891	NM_133335.3	1340	-/C	22/22	0.840730226950237	1	FACETS	0.849	0.818	0.881	0.849	0.818	0.881	CLONAL	1	TRUE	0	0.840730226950237	1		577	651	SUCCESS
APC	324	MSKCC	GRCh37	5	112176350	112176350	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554086415	NA	P-0029542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	222	338	0	ENST00000257430.4:c.5059C>T	p.Arg1687Ter	p.R1687*	ENST00000257430	NM_000038.5	1687	Cga/Tga	16/16	0.840730226950237	1	FACETS	0.966	0.923	1	0.966	0.923	1	CLONAL	1	TRUE	0	0.840730226950237	1		338	317	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505652	186505652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	204	278	0	ENST00000323963.5:c.1060C>T	p.Arg354Cys	p.R354C	ENST00000323963		354	Cgt/Tgt	10/11	0.840730226950237	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.840730226950237	1		278	274	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737073	162737093	+	inframe_deletion	In_Frame_Del	DEL	TGGCCATCATCTTTATCCTCC	TGGCCATCATCTTTATCCTCC	-	novel	NA	P-0029542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	277	427	0	ENST00000367921.3:c.1227_1247del	p.Phe410_Ile416del	p.F410_I416del	ENST00000367921	NM_006182.2	406	gTGGCCATCATCTTTATCCTCCtg/gtg	11/18	1	2	FACETS	0.814	0.767	0.861	0.814	0.767	0.861	CLONAL	1	TRUE	1	0.840730226950237	2		427	810	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998489	100998489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762341135	NA	P-0029542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	357	398	0	ENST00000325455.5:c.1313C>T	p.Ala438Val	p.A438V	ENST00000325455	NM_001202474.3	438	gCg/gTg	1/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.840730226950237	2		398	825	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123892041	123892041	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	296	414	0	ENST00000330479.4:c.850G>A	p.Val284Met	p.V284M	ENST00000330479	NM_020382.3	284	Gtg/Atg	8/9	NA	2	FACETS	0.873	0.825	0.921			1	INDETERMINATE	1	TRUE	NA	0.840730226950237	2		414	807	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046581	30046581	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	349	433	0	ENST00000331968.5:c.2602A>G	p.Arg868Gly	p.R868G	ENST00000331968	NM_002742.2	868	Agg/Ggg	18/18	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.840730226950237	2		433	811	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280034	18280034	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs202137312	NA	P-0029542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	270	339	0	ENST00000222254.8:c.2117A>G	p.Asp706Gly	p.D706G	ENST00000222254	NM_005027.3	706	gAc/gGc	16/16	1	2	FACETS	0.996	0.941	1	0.996	0.941	1	CLONAL	1	TRUE	1	0.840730226950237	2		339	645	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593606	55593606	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520031	NA	P-0029542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1981	608	440	0	ENST00000288135.5:c.1672A>G	p.Lys558Glu	p.K558E	ENST00000288135	NM_000222.2	558	Aag/Gag	11/21	0.840730226950237	8	FACETS	0.984	0.943	1	0.281	0.269	0.293	CLONAL	2	TRUE	1	0.840730226950237	8		440	2589	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187560874	187560874	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0029542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	169	333	0	ENST00000441802.2:c.3642+2T>C		p.X1214_splice	ENST00000441802	NM_005245.3	1214			1	2	FACETS	0.872	0.809	0.936	0.872	0.809	0.936	CLONAL	1	TRUE	1	0.840730226950237	2		333	461	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953633	38953633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202045287	NA	P-0029542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	282	223	0	ENST00000357387.3:c.2720G>A	p.Arg907His	p.R907H	ENST00000357387	NM_152756.3	907	cGt/cAt	28/38	0.838288370685581	2	FACETS	0.992	0.962	1	0.992	0.962	1	CLONAL	2	TRUE	0	0.840730226950237	2		223	338	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519224	137519224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55924399	NA	P-0029542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	254	321	1	ENST00000367739.4:c.1414G>A	p.Gly472Ser	p.G472S	ENST00000367739	NM_000416.2	472	Ggt/Agt	7/7	0.83989228615028	2	FACETS	1	0.979	1	0.536	0.506	0.566	CLONAL	1	TRUE	0	0.840730226950237	2		322	564	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753909	133753909	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746156716	NA	P-0029542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	351	466	1	ENST00000318560.5:c.1378C>T	p.Arg460Cys	p.R460C	ENST00000318560	NM_005157.4	460	Cgc/Tgc	8/11	0.31530878840059	1	FACETS	0.648	0.618	0.678	0.648	0.618	0.678	INDETERMINATE	1	TRUE	0	0.840730226950237	1		467	747	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930276	39930276	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	405	290	0	ENST00000378444.4:c.3188A>C	p.Lys1063Thr	p.K1063T	ENST00000378444	NM_001123385.1	1063	aAg/aCg	6/15	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.840730226950237	1		290	490	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0029543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	304	483	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.809474122880029	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.810768182804386	3		483	503	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784041	9784041	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	130	504	0	ENST00000377346.4:c.2609G>T	p.Arg870Leu	p.R870L	ENST00000377346	NM_005026.3	870	cGa/cTa	21/24	0.809474122880029	3	FACETS	0.971	0.887	1	0.486	0.443	0.529	CLONAL	1	TRUE	1	0.810768182804386	3		504	464	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456263	32456263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	138	565	0	ENST00000332351.3:c.629C>T	p.Pro210Leu	p.P210L	ENST00000332351	NM_024426.4	210	cCc/cTc	1/10	0.374257540707535	5	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.810768182804386	5		565	658	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0029545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	11	207	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	1	2	FACETS	0.331	0.228	0.459	0.331	0.228	0.459	SUBCLONAL	1	TRUE	1	0.253037305232094	2		207	263	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204506572	204506572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	36	409	0	ENST00000367182.3:c.358C>T	p.Leu120Phe	p.L120F	ENST00000367182	NM_001278516.1	120	Ctc/Ttc	6/11	0.227392253333429	3	FACETS	0.553	0.453	0.664	0.276	0.226	0.332	SUBCLONAL	1	TRUE	1	0.253037305232094	3		409	580	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218414	1218414	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs876658584	NA	P-0029545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	50	450	0	ENST00000326873.7:c.291-2A>G		p.X97_splice	ENST00000326873	NM_000455.4	97			NA	2	FACETS	0.761	0.646	0.888			1	INDETERMINATE	1	TRUE	NA	0.253037305232094	2		450	519	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841926	151841926	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	18	276	0	ENST00000262189.6:c.14215C>T	p.Gln4739Ter	p.Q4739*	ENST00000262189	NM_170606.2	4739	Cag/Tag	55/59	1	2	FACETS	0.409	0.307	0.529	0.409	0.307	0.529	SUBCLONAL	1	TRUE	1	0.253037305232094	2		276	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0029546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	367	504	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.567276418990932	3	FACETS	0.979	0.943	1	0.979	0.943	1	CLONAL	3	TRUE	0	0.587986204599202	3		504	550	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0029546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	119	146	0	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	0.479115125249223	3	FACETS	1	0.968	1	0.731	0.674	0.787	CLONAL	2	TRUE	0	0.587986204599202	3		146	239	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78435678	78435678	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	88	269	0	ENST00000370768.2:c.142G>T	p.Asp48Tyr	p.D48Y	ENST00000370768	NM_003902.3	48	Gat/Tat	2/20	0.567276418990932	3	FACETS	0.833	0.741	0.93	0.278	0.247	0.31	CLONAL	1	TRUE	0	0.587986204599202	3		269	465	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94908739	94908739	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	331	440	1	ENST00000536441.1:c.1315A>T	p.Thr439Ser	p.T439S	ENST00000536441	NM_144665.3	439	Aca/Tca	9/10	0.57662522887081	2	FACETS	0.949	0.908	0.99	0.949	0.908	0.99	CLONAL	2	TRUE	0	0.587986204599202	2		441	593	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245478	153245478	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	138	386	0	ENST00000281708.4:c.1713del	p.Asn572IlefsTer6	p.N572Ifs*6	ENST00000281708	NM_033632.3	571	ggG/gg	11/12	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.587986204599202	2		386	455	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990400	81990400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370547009	NA	P-0029550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	156	709	2	ENST00000359376.3:c.3671G>A	p.Arg1224His	p.R1224H	ENST00000359376	NM_002661.3	1224	cGc/cAc	32/33	0.318039553524902	1	FACETS	0.66	0.604	0.719	0.66	0.604	0.719	SUBCLONAL	1	TRUE	0	0.395786435356817	1		711	958	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772809	135772809	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0029550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	138	654	1	ENST00000298552.3:c.2813+1G>A		p.X938_splice	ENST00000298552	NM_001162426.1	938			0.318039553524902	1	FACETS	0.66	0.601	0.723	0.66	0.601	0.723	SUBCLONAL	1	TRUE	0	0.395786435356817	1		655	847	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0029554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	236	498	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.974	0.91	1	0.974	0.91	1	CLONAL	1	TRUE	1	0.517700123378519	2		498	936	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715619	30715619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730880224	NA	P-0029554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	37	246	0	ENST00000295754.5:c.1277C>T	p.Ala426Val	p.A426V	ENST00000295754	NM_003242.5	426	gCt/gTt	5/7	1	2	FACETS	0.275	0.226	0.33	0.275	0.226	0.33	SUBCLONAL	1	TRUE	1	0.517700123378519	2		246	520	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0029556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	448	532	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.403480239053342	5	FACETS	0.908	0.876	0.939	0.908	0.876	0.939	CLONAL	5	TRUE	0	0.469013536986657	5		532	717	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230523	46230523	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0029556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	66	345	0	ENST00000334344.6:c.773-1G>C		p.X258_splice	ENST00000334344	NM_152641.2	258			0.403480239053342	5	FACETS	0.856	0.744	0.978	0.171	0.148	0.196	CLONAL	1	TRUE	0	0.469013536986657	5		345	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	284	680	0	ENST00000269305.4:c.472C>G	p.Arg158Gly	p.R158G	ENST00000269305	NM_001126112.2	158	Cgc/Ggc	5/11	0.315369159565955	3	FACETS	0.985	0.93	1	0.657	0.62	0.694	CLONAL	2	TRUE	0	0.469013536986657	3		680	759	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106003	8106003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	48	477	0	ENST00000346208.3:c.823C>T	p.Arg275Trp	p.R275W	ENST00000346208		275	Cgg/Tgg	4/6	0.241556993768799	4	FACETS	0.495	0.417	0.58			1	INDETERMINATE	1	TRUE	NA	0.469013536986657	4		477	608	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938121	76938121	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	112	587	0	ENST00000373344.5:c.2627C>G	p.Ser876Cys	p.S876C	ENST00000373344	NM_000489.3	876	tCt/tGt	9/35	0.342566792918505	3	FACETS	0.884	0.796	0.977	0.295	0.265	0.326	CLONAL	1	TRUE	0	0.469013536986657	3		587	667	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2493255	2493256	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0029556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	44	375	0	ENST00000355716.4:c.694+2dup		p.X232_splice	ENST00000355716	NM_003820.2	232			0.335270598609137	3	FACETS	0.491	0.411	0.578	0.245	0.205	0.289	SUBCLONAL	1	TRUE	1	0.469013536986657	3		375	472	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154832	2154832	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	392	819	0	ENST00000434045.2:c.389G>T	p.Ser130Ile	p.S130I	ENST00000434045	NM_001127598.1	130	aGc/aTc	4/5	0.404044384835843	5	FACETS	0.962	0.917	1			1	CLONAL	3	TRUE	NA	0.469013536986657	5		819	987	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913531	32913531	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555284041	NA	P-0029556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	106	492	1	ENST00000380152.3:c.5039C>A	p.Ser1680Tyr	p.S1680Y	ENST00000380152		1680	tCt/tAt	11/27	1	2	FACETS	0.868	0.781	0.959	0.868	0.781	0.959	CLONAL	1	TRUE	1	0.469013536986657	2		493	521	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506107	103506107	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	53	277	1	ENST00000355739.4:c.265G>T	p.Val89Leu	p.V89L	ENST00000355739	NM_000123.3	89	Gtg/Ttg	3/15	1	2	FACETS	0.84	0.722	0.967	0.84	0.722	0.967	CLONAL	1	TRUE	1	0.469013536986657	2		278	269	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993899	72993899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	68	484	0	ENST00000268489.5:c.146C>T	p.Pro49Leu	p.P49L	ENST00000268489	NM_006885.3	49	cCc/cTc	2/10	0.404319462671084	4	FACETS	0.656	0.571	0.749	0.164	0.142	0.188	SUBCLONAL	1	TRUE	0	0.469013536986657	4		484	649	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983993	7983993	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	89	350	2	ENST00000319144.4:c.633C>A	p.Phe211Leu	p.F211L	ENST00000319144	NM_001139.2	211	ttC/ttA	5/15	0.315369159565955	3	FACETS	1	0.976	1	0.446	0.399	0.496	CLONAL	1	TRUE	0	0.469013536986657	3		352	350	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119875	70119875	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	293	659	0	ENST00000245479.2:c.877G>T	p.Glu293Ter	p.E293*	ENST00000245479	NM_000346.3	293	Gag/Tag	3/3	0.469013536986657	4	FACETS	0.993	0.937	1	0.993	0.937	1	CLONAL	2	TRUE	2	0.469013536986657	4		659	924	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439661	220439661	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	179	649	0	ENST00000243786.2:c.514G>T	p.Ala172Ser	p.A172S	ENST00000243786	NM_002191.3	172	Gct/Tct	2/2	0.325758567818831	4	FACETS	0.792	0.732	0.854	0.792	0.732	0.854	SUBCLONAL	2	TRUE	2	0.469013536986657	4		649	708	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927421	178927421	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	131	404	0	ENST00000263967.3:c.1184A>G	p.Asp395Gly	p.D395G	ENST00000263967	NM_006218.2	395	gAt/gGt	7/21	0.325758567818831	4	FACETS	0.853	0.779	0.93	0.853	0.779	0.93	CLONAL	2	TRUE	2	0.469013536986657	4		404	481	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250656	26250656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	78	500	0	ENST00000446824.2:c.178G>A	p.Glu60Lys	p.E60K	ENST00000446824	NM_021018.2	60	Gag/Aag	1/1	0.469013536986657	6	FACETS	0.777	0.681	0.879			1	SUBCLONAL	1	TRUE	NA	0.469013536986657	6		500	830	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681100	30681100	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	154	327	0	ENST00000376406.3:c.619G>T	p.Gly207Cys	p.G207C	ENST00000376406	NM_014641.2	207	Ggc/Tgc	5/15	0.469013536986657	4	FACETS	0.796	0.731	0.863	0.796	0.731	0.863	SUBCLONAL	2	TRUE	2	0.469013536986657	4		327	606	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938397	76938397	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	118	662	0	ENST00000373344.5:c.2351C>A	p.Ser784Tyr	p.S784Y	ENST00000373344	NM_000489.3	784	tCt/tAt	9/35	0.342566792918505	3	FACETS	0.794	0.717	0.876	0.265	0.239	0.292	SUBCLONAL	1	TRUE	0	0.469013536986657	3		662	782	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0029559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	209	532	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.203292712957042	3	FACETS	0.902	0.839	0.967	0.902	0.839	0.967	CLONAL	3	TRUE	0	0.203292712957042	3		532	837	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857686	59857686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781321	NA	P-0029559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	84	457	0	ENST00000259008.2:c.1871C>T	p.Ser624Leu	p.S624L	ENST00000259008	NM_032043.2	624	tCg/tTg	13/20	0.203292712957042	4	FACETS	1	0.91	1	0.52	0.458	0.586	CLONAL	1	TRUE	2	0.203292712957042	4		457	957	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199925	108199925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555122245	NA	P-0029559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	135	322	0	ENST00000278616.4:c.7267G>A	p.Glu2423Lys	p.E2423K	ENST00000278616	NM_000051.3	2423	Gaa/Aaa	49/63	0.203292712957042	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.203292712957042	2		322	565	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95579559	95579559	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	51	308	0	ENST00000393063.1:c.1910A>T	p.Tyr637Phe	p.Y637F	ENST00000393063	NM_030621.3	637	tAc/tTc	13/28	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.203292712957042	2		308	448	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465526	99465526	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	100	652	0	ENST00000268035.6:c.2351A>T	p.Asn784Ile	p.N784I	ENST00000268035	NM_000875.3	784	aAc/aTc	11/21	0.203292712957042	3	FACETS	1	0.952	1	0.562	0.501	0.627	CLONAL	1	TRUE	1	0.203292712957042	3		652	965	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619170	1619170	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs566431636	NA	P-0029559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	115	805	0	ENST00000344749.5:c.1390G>T	p.Ala464Ser	p.A464S	ENST00000344749	NM_001136139.2	464	Gcc/Tcc	16/19	0.203292712957042	3	FACETS	1	0.932	1	0.524	0.471	0.581	CLONAL	1	TRUE	1	0.203292712957042	3		805	1189	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247785	10247785	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	265	852	1	ENST00000340748.4:c.4417C>T	p.Arg1473Cys	p.R1473C	ENST00000340748		1473	Cgt/Tgt	36/40	0.203292712957042	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.203292712957042	3		853	1220	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032513	47032529	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATCTCCCCGTATAGATC	ATCTCCCCGTATAGATC	-	novel	NA	P-0029559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	61	458	0	ENST00000377604.3:c.433-14_435del		p.X145_splice	ENST00000377604	NM_001204468.1	145		5/24	0.161764605598417	1	FACETS	0.853	0.736	0.981	0.853	0.736	0.981	CLONAL	1	TRUE	0	0.203292712957042	1		458	632	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	68	404	0				ENST00000310581	NM_198253.2	-/1132			0.262279622056128	1	FACETS	0.812	0.707	0.925	0.812	0.707	0.925	CLONAL	1	TRUE	0	0.262279622056128	1		404	555	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0029560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	149	489	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.999	0.911	1	0.999	0.911	1	CLONAL	1	TRUE	1	0.262279622056128	2		489	1137	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056560	26056560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766992808	NA	P-0029560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	54	212	0	ENST00000343677.2:c.97C>T	p.Arg33Cys	p.R33C	ENST00000343677	NM_005319.3	33	Cgt/Tgt	1/1	1	2	FACETS	0.944	0.808	1	0.944	0.808	1	CLONAL	1	TRUE	1	0.262279622056128	2		212	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0029560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	178	713	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.262279622056128	2		713	1295	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223707	53223707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1288544172	NA	P-0029560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	73	428	1	ENST00000375401.3:c.3652C>T	p.Arg1218Cys	p.R1218C	ENST00000375401	NM_004187.3	1218	Cgc/Tgc	23/26	1	1	FACETS	0.676	0.591	0.769	0.676	0.591	0.769	SUBCLONAL	1	TRUE	0	0.262279622056128	1		429	715	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724469	162724469	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	63	523	0	ENST00000367921.3:c.241G>C	p.Asp81His	p.D81H	ENST00000367921	NM_006182.2	81	Gat/Cat	5/18	1	2	FACETS	0.492	0.424	0.566	0.492	0.424	0.566	SUBCLONAL	1	TRUE	1	0.262279622056128	2		523	977	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210453	2210453	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	152	686	0	ENST00000398665.3:c.1060G>A	p.Ala354Thr	p.A354T	ENST00000398665	NM_032482.2	354	Gcc/Acc	13/28	1	2	FACETS	0.868	0.792	0.949	0.868	0.792	0.949	CLONAL	1	TRUE	1	0.262279622056128	2		686	1335	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276307	15276307	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	136	681	0	ENST00000263388.2:c.5687C>G	p.Ser1896Cys	p.S1896C	ENST00000263388	NM_000435.2	1896	tCt/tGt	31/33	1	2	FACETS	0.851	0.772	0.935	0.851	0.772	0.935	CLONAL	1	TRUE	1	0.262279622056128	2		681	1218	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249002	55249003	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCGTGGA	rs397517109	NA	P-0029561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	85	578	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		578	440	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	191	394	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.2068605080385	3	FACETS	0.851	0.789	0.915			1	CLONAL	3	TRUE	NA	0.215860855309698	3		394	768	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432799	432799	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	57	457	0	ENST00000399788.2:c.2117T>G	p.Leu706Arg	p.L706R	ENST00000399788	NM_001042603.1	706	cTg/cGg	15/28	1	2	FACETS	0.731	0.626	0.846	0.731	0.626	0.846	SUBCLONAL	1	TRUE	1	0.215860855309698	2		457	722	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579440	7579441	+	frameshift_variant	Frame_Shift_Ins	INS	CC	CC	AAG	novel	NA	P-0029562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	138	593	0	ENST00000269305.4:c.246_247delinsCTT	p.Ala83PhefsTer66	p.A83Ffs*66	ENST00000269305	NM_001126112.2	82	ccGGcg/ccCTTcg	4/11	0.215860855309698	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.215860855309698	1		593	874	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554409	63554410	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	70	471	0	ENST00000307078.5:c.329dup	p.Trp111LeufsTer30	p.W111Lfs*30	ENST00000307078	NM_004655.3	110	ttc/ttTc	2/11	0.215860855309698	1	FACETS	0.692	0.602	0.79	0.692	0.602	0.79	SUBCLONAL	1	TRUE	0	0.215860855309698	1		471	836	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974769	21974769	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs760065045	NA	P-0029562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	44	177	0	ENST00000304494.5:c.58G>C	p.Ala20Pro	p.A20P	ENST00000304494	NM_000077.4	20	Gcg/Ccg	1/3	0.215860855309698	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.215860855309698	1		177	250	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029562-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	29	394	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.166718407490794	3	FACETS	0.821	0.658	1	0.411	0.329	0.504	CLONAL	1	TRUE	1	0.15	3		394	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579440	7579441	+	frameshift_variant	Frame_Shift_Ins	INS	CC	CC	AAG	novel	NA	P-0029562-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	29	593	0	ENST00000269305.4:c.246_247delinsCTT	p.Ala83PhefsTer66	p.A83Ffs*66	ENST00000269305	NM_001126112.2	82	ccGGcg/ccCTTcg	4/11	1	2	FACETS	0.83	0.665	1	0.83	0.665	1	CLONAL	1	TRUE	1	0.15	2		593	466	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554409	63554410	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029562-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	32	471	0	ENST00000307078.5:c.329dup	p.Trp111LeufsTer30	p.W111Lfs*30	ENST00000307078	NM_004655.3	110	ttc/ttTc	2/11	1	2	FACETS	0.99	0.803	1	0.99	0.803	1	CLONAL	1	TRUE	1	0.15	2		471	431	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696450	47696450	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	189	468	0	ENST00000347630.2:c.373T>G	p.Phe125Val	p.F125V	ENST00000347630	NM_001007230.1	125	Ttt/Gtt	6/11	1	2	FACETS	0.946	0.878	1	0.946	0.878	1	CLONAL	1	TRUE	1	0.602780748388716	2		468	663	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663356	67663356	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	212	481	2	ENST00000264010.4:c.1757A>G	p.Glu586Gly	p.E586G	ENST00000264010	NM_006565.3	586	gAa/gGa	10/12	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.602780748388716	2		483	673	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120554424	120554425	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	A	novel	NA	P-0029563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	50	174	0	ENST00000229340.5:c.30_31delinsT	p.Lys10AsnfsTer48	p.K10Nfs*48	ENST00000229340	NM_006861.6	10	aaGCtg/aaTtg	1/6	1	2	FACETS	0.758	0.65	0.872	0.758	0.65	0.872	SUBCLONAL	1	TRUE	1	0.602780748388716	2		174	219	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0029564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	203	344	1	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	0.994	1	CLONAL	2	TRUE	1	0.365126465460603	2		345	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0029564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	1103	906	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.365126465460603	2	FACETS	1	0.991	1			1	CLONAL	5	TRUE	0	0.365126465460603	2		906	1206	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855014	76855017	+	frameshift_variant	Frame_Shift_Del	DEL	CTAT	CTAT	-	novel	NA	P-0029564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	147	237	0	ENST00000373344.5:c.5819_5822del	p.Asp1940ValfsTer14	p.D1940Vfs*14	ENST00000373344	NM_000489.3	1940	gATAGt/gt	25/35	0.350892141365454	0	FACETS	0.888	0.844	0.928			1	CLONAL	3	TRUE	NA	0.365126465460603	0		237	192	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0029567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	152	181	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.799	0.737	0.864	0.799	0.737	0.864	SUBCLONAL	1	TRUE	1	0.810792840661841	2		181	469	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591246	67591246	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0029567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	235	398	0	ENST00000274335.5:c.1746-2A>G		p.X582_splice	ENST00000274335		582			1	2	FACETS	0.846	0.794	0.9	0.846	0.794	0.9	CLONAL	1	TRUE	1	0.810792840661841	2		398	685	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0029567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	161	300	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.74	0.683	0.798	0.74	0.683	0.798	SUBCLONAL	1	TRUE	1	0.810792840661841	2		300	537	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692891	89692891	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	245	328	0	ENST00000371953.3:c.375A>C	p.Lys125Asn	p.K125N	ENST00000371953	NM_000314.4	125	aaA/aaC	5/9	1	2	FACETS	0.863	0.811	0.917	0.863	0.811	0.917	CLONAL	1	TRUE	1	0.810792840661841	2		328	700	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692800	89692800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204856	NA	P-0029567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	150	193	0	ENST00000371953.3:c.284C>T	p.Pro95Leu	p.P95L	ENST00000371953	NM_000314.4	95	cCa/cTa	5/9	1	2	FACETS	0.782	0.721	0.846	0.782	0.721	0.846	SUBCLONAL	1	TRUE	1	0.810792840661841	2		193	473	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088795	27088795	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	262	503	0	ENST00000324856.7:c.2404C>T	p.Gln802Ter	p.Q802*	ENST00000324856	NM_006015.4	802	Cag/Tag	7/20	0.699318226685467	1	FACETS	0.712	0.674	0.749	0.712	0.674	0.749	SUBCLONAL	1	TRUE	0	0.810792840661841	1		503	540	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	244006467	244006472	+	start_lost,inframe_deletion	Translation_Start_Site	DEL	GCTCAT	GCTCAT	-	novel	NA	P-0029567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1500	240	409	0	ENST00000263826.5:c.1_6del	p.MetSer1_?2	p.MS1_?2	ENST00000263826	NM_005465.4	1	ATGAGC/-	1/13	0.810792840661841	5	FACETS	0.754	0.701	0.809	0.189	0.175	0.203	SUBCLONAL	1	TRUE	1	0.810792840661841	5		409	1740	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3634794	3634794	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs182432298	NA	P-0029567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	390	640	0	ENST00000294008.3:c.4715C>T	p.Pro1572Leu	p.P1572L	ENST00000294008	NM_032444.2	1572	cCg/cTg	13/15	1	2	FACETS	0.845	0.804	0.886	0.845	0.804	0.886	CLONAL	1	TRUE	1	0.810792840661841	2		640	1139	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063632	67063633	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	194	343	0	ENST00000412916.2:c.83dup	p.Tyr29ValfsTer54	p.Y29Vfs*54	ENST00000412916		27	-/A	2/6	0.699318226685467	1	FACETS	0.751	0.706	0.796	0.751	0.706	0.796	SUBCLONAL	1	TRUE	0	0.810792840661841	1		343	379	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349904	15349904	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	257	499	0	ENST00000263377.2:c.3748A>G	p.Lys1250Glu	p.K1250E	ENST00000263377	NM_058243.2	1250	Aag/Gag	18/20	0.810792840661841	3	FACETS	0.825	0.772	0.879	0.412	0.386	0.44	CLONAL	1	TRUE	1	0.810792840661841	3		499	1080	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625281	69625281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35983315	NA	P-0029568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3408	281	759	1	ENST00000334134.2:c.512G>A	p.Arg171His	p.R171H	ENST00000334134	NM_005247.2	171	cGc/cAc	3/3	0.633819324716723	13	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.633819324716723	13		760	3689	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741817	162741817	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	103	399	0	ENST00000367921.3:c.1508G>T	p.Cys503Phe	p.C503F	ENST00000367921	NM_006182.2	503	tGc/tTc	13/18	1	2	FACETS	0.821	0.74	0.905	0.821	0.74	0.905	CLONAL	1	TRUE	1	0.633819324716723	2		399	396	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351820	89351820	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	114	882	0	ENST00000301030.4:c.1130C>G	p.Ser377Cys	p.S377C	ENST00000301030	NM_001256183.1	377	tCc/tGc	9/13	0.433138997174854	1	FACETS	0.31	0.279	0.343	0.31	0.279	0.343	SUBCLONAL	1	TRUE	0	0.633819324716723	1		882	792	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565885	55565885	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	175	528	0	ENST00000288135.5:c.709G>T	p.Asp237Tyr	p.D237Y	ENST00000288135	NM_000222.2	237	Gat/Tat	4/21	1	2	FACETS	0.917	0.849	0.988	0.917	0.849	0.988	CLONAL	1	TRUE	1	0.633819324716723	2		528	602	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741711	145741711	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554902811	NA	P-0029568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	107	693	0	ENST00000428558.2:c.792G>A	p.Trp264Ter	p.W264*	ENST00000428558	NM_004260.3	264	tgG/tgA	5/22	0.633819324716723	3	FACETS	0.401	0.358	0.446			1	SUBCLONAL	1	TRUE	NA	0.633819324716723	3		693	1110	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20152079	20152079	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	14	244	0	ENST00000379607.5:c.251A>G	p.Tyr84Cys	p.Y84C	ENST00000379607	NM_001412.3	84	tAc/tGc	4/7	1	1	FACETS	0.109	0.078	0.146	0.109	0.078	0.146	SUBCLONAL	1	TRUE	0	0.633819324716723	1		244	277	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0029569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	185	591	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	0.926	0.858	0.995	0.926	0.858	0.995	CLONAL	1	TRUE	1	0.598318742587869	2		591	668	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865216	57865216	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	264	893	0	ENST00000228682.2:c.2693T>C	p.Val898Ala	p.V898A	ENST00000228682	NM_005269.2	898	gTg/gCg	12/12	1	2	FACETS	0.973	0.914	1	0.973	0.914	1	CLONAL	1	TRUE	1	0.598318742587869	2		893	907	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574339	95574339	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	155	402	0	ENST00000393063.1:c.2528T>G	p.Leu843Arg	p.L843R	ENST00000393063	NM_030621.3	843	cTt/cGt	17/28	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.598318742587869	2		402	486	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442561	52442574	+	frameshift_variant	Frame_Shift_Del	DEL	CCTTTCGCCGGGAC	CCTTTCGCCGGGAC	-	novel	NA	P-0029569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	292	689	0	ENST00000460680.1:c.171_184del	p.Ser58LeufsTer6	p.S58Lfs*6	ENST00000460680	NM_004656.3	57	cgGTCCCGGCGAAAGGtc/cgtc	4/17	0.560497572025869	2	FACETS	0.855	0.813	0.896	0.855	0.813	0.896	CLONAL	2	TRUE	0	0.598318742587869	2		689	571	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	104	404	0				ENST00000310581	NM_198253.2	-/1132			0.160546915975817	3	FACETS	0.822	0.741	0.906			1	INDETERMINATE	2	TRUE	NA	0.361937725246228	3		404	413	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954248	17954248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776850935	NA	P-0029575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	368	623	1	ENST00000458235.1:c.361C>T	p.Arg121Cys	p.R121C	ENST00000458235	NM_000215.3	121	Cgc/Tgc	4/24	0.229826565985379	3	FACETS	0.889	0.847	0.932	0.889	0.847	0.932	CLONAL	3	TRUE	0	0.361937725246228	3		624	900	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578261	7578265	+	frameshift_variant	Frame_Shift_Del	DEL	TCGGA	TCGGA	-	novel	NA	P-0029575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	388	558	1	ENST00000269305.4:c.584_588del	p.Ile195SerfsTer12	p.I195Sfs*12	ENST00000269305	NM_001126112.2	195	aTCCGA/a	6/11	0.278849928214128	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	0	0.361937725246228	3		559	812	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339155	87339155	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	158	382	0	ENST00000277120.3:c.737C>T	p.Thr246Ile	p.T246I	ENST00000277120		246	aCa/aTa	8/19	0.358131059203298	3	FACETS	0.883	0.813	0.955	0.883	0.813	0.955	CLONAL	2	TRUE	1	0.361937725246228	3		382	584	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0029577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	106	591	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.878	0.793	0.968	0.878	0.793	0.968	CLONAL	1	TRUE	1	0.565395332773534	2		591	427	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224307	55224307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1164954595	NA	P-0029577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	11789	592	1	ENST00000275493.2:c.1088C>T	p.Thr363Ile	p.T363I	ENST00000275493	NM_005228.3	363	aCc/aTc	9/28	0.565395332773534	64	FACETS	1	0.997	1	0.969	0.966	0.972	CLONAL	62	TRUE	0	0.565395332773534	64		593	12455	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495391	149495391	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	217	729	0	ENST00000261799.4:c.3256C>G	p.Leu1086Val	p.L1086V	ENST00000261799	NM_002609.3	1086	Ctg/Gtg	23/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.565395332773534	2		729	699	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0029578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	303	617	1	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.354943670191107	2	FACETS	0.982	0.929	1	0.982	0.929	1	CLONAL	2	TRUE	0	0.354943670191107	2		618	869	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105748	27105748	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	116	345	1	ENST00000324856.7:c.5359G>T	p.Glu1787Ter	p.E1787*	ENST00000324856	NM_006015.4	1787	Gag/Tag	20/20	0.354943670191107	3	FACETS	0.822	0.745	0.902	0.822	0.745	0.902	CLONAL	2	TRUE	1	0.354943670191107	3		346	468	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098975	178098975	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1328994103	NA	P-0029578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	78	188	0	ENST00000397062.3:c.70T>C	p.Trp24Arg	p.W24R	ENST00000397062	NM_006164.4	24	Tgg/Cgg	2/5	0.349360291698195	3	FACETS	0.837	0.743	0.937	0.837	0.743	0.937	CLONAL	2	TRUE	1	0.354943670191107	3		188	309	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212611	36212611	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	373	953	1	ENST00000222270.7:c.2362G>T	p.Val788Leu	p.V788L	ENST00000222270	NM_014727.1	788	Gta/Tta	3/37	0.319947062836934	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.354943670191107	4		954	1374	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735354	204735354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	42	203	0	ENST00000302823.3:c.155G>A	p.Gly52Asp	p.G52D	ENST00000302823	NM_005214.4	52	gGc/gAc	2/4	0.349360291698195	3	FACETS	0.902	0.756	1	0.451	0.378	0.531	CLONAL	1	TRUE	1	0.354943670191107	3		203	309	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107293	193107293	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	49	247	0	ENST00000367435.3:c.502G>T	p.Glu168Ter	p.E168*	ENST00000367435	NM_024529.4	168	Gaa/Taa	6/17	0.349360291698195	3	FACETS	0.829	0.704	0.966	0.415	0.352	0.483	CLONAL	1	TRUE	1	0.354943670191107	3		247	392	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201868	102201868	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	74	401	0	ENST00000263464.3:c.1220G>C	p.Gly407Ala	p.G407A	ENST00000263464	NM_001165.4	407	gGa/gCa	6/9	0.349360291698195	3	FACETS	0.99	0.869	1	0.495	0.434	0.56	CLONAL	1	TRUE	1	0.354943670191107	3		401	496	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436578	49436578	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	290	647	0	ENST00000301067.7:c.5728G>T	p.Gly1910Ter	p.G1910*	ENST00000301067	NM_003482.3	1910	Gga/Tga	26/54	0.354943670191107	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.354943670191107	2		647	777	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900414	32900414	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	87	333	0	ENST00000380152.3:c.511G>T	p.Val171Leu	p.V171L	ENST00000380152		171	Gtg/Ttg	6/27	0.286120695147015	3	FACETS	1	0.979	1	0.742	0.661	0.827	CLONAL	1	TRUE	1	0.354943670191107	3		333	389	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821874	59821875	+	missense_variant	Missense_Mutation	DNP	CT	CT	TA	novel	NA	P-0029578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	50	454	1	ENST00000259008.2:c.2175_2176delinsTA	p.Glu726Lys	p.E726K	ENST00000259008	NM_032043.2	725	gtAGaa/gtTAaa	15/20	0.349360291698195	3	FACETS	0.557	0.472	0.65	0.278	0.236	0.325	SUBCLONAL	1	TRUE	1	0.354943670191107	3		455	596	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793197	33793197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1382321984	NA	P-0029578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	84	183	1	ENST00000498907.2:c.124C>T	p.Pro42Ser	p.P42S	ENST00000498907	NM_004364.3	42	Cct/Tct	1/1	0.319947062836934	4	FACETS	0.902	0.81	0.997	1	0.977	1	CLONAL	3	TRUE	2	0.354943670191107	4		184	237	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182580	99182580	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	98	414	1	ENST00000074304.5:c.2383C>A	p.Gln795Lys	p.Q795K	ENST00000074304	NM_001134224.1	795	Cag/Aag	22/26	0.349360291698195	3	FACETS	1	0.953	1	0.559	0.499	0.621	CLONAL	1	TRUE	1	0.354943670191107	3		415	582	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204612	128204612	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	160	664	0	ENST00000341105.2:c.829A>T	p.Ser277Cys	p.S277C	ENST00000341105	NM_032638.4	277	Agc/Tgc	3/6	0.354943670191107	6	FACETS	1	0.982	1	0.317	0.289	0.345	CLONAL	1	TRUE	2	0.354943670191107	6		664	1217	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157044	106157044	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	185	468	0	ENST00000380013.4:c.1945C>T	p.Gln649Ter	p.Q649*	ENST00000380013	NM_001127208.2	649	Caa/Taa	3/11	0.349360291698195	3	FACETS	0.941	0.873	1	0.941	0.873	1	CLONAL	2	TRUE	1	0.354943670191107	3		468	652	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128849189	128849189	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	220	586	1	ENST00000249373.3:c.1417G>T	p.Asp473Tyr	p.D473Y	ENST00000249373	NM_005631.4	473	Gac/Tac	8/12	0.319947062836934	4	FACETS	0.985	0.918	1	0.985	0.918	1	CLONAL	2	TRUE	2	0.354943670191107	4		587	853	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879018	151879018	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	222	469	0	ENST00000262189.6:c.5927A>C	p.Asp1976Ala	p.D1976A	ENST00000262189	NM_170606.2	1976	gAt/gCt	36/59	0.319947062836934	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.354943670191107	4		469	786	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0029578-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	231	617	1	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.267137847482395	2	FACETS	0.968	0.904	1	0.968	0.904	1	CLONAL	2	TRUE	0	0.267137847482395	2		618	893	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105748	27105748	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029578-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	95	345	1	ENST00000324856.7:c.5359G>T	p.Glu1787Ter	p.E1787*	ENST00000324856	NM_006015.4	1787	Gag/Tag	20/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.267137847482395	2		346	523	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098975	178098975	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1328994103	NA	P-0029578-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	87	188	0	ENST00000397062.3:c.70T>C	p.Trp24Arg	p.W24R	ENST00000397062	NM_006164.4	24	Tgg/Cgg	2/5	0.17161698087697	2	FACETS	0.859	0.766	0.957	0.859	0.766	0.957	CLONAL	2	TRUE	0	0.267137847482395	2		188	379	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212611	36212611	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029578-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	273	953	1	ENST00000222270.7:c.2362G>T	p.Val788Leu	p.V788L	ENST00000222270	NM_014727.1	788	Gta/Tta	3/37	0.14134261128079	4	FACETS	1	0.946	1	1	0.946	1	INDETERMINATE	2	TRUE	2	0.267137847482395	4		954	1282	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735354	204735354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029578-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	19	203	0	ENST00000302823.3:c.155G>A	p.Gly52Asp	p.G52D	ENST00000302823	NM_005214.4	52	gGc/gAc	2/4	0.17161698087697	2	FACETS	0.494	0.375	0.634	0.247	0.187	0.317	SUBCLONAL	1	TRUE	0	0.267137847482395	2		203	288	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107293	193107293	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029578-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	32	247	0	ENST00000367435.3:c.502G>T	p.Glu168Ter	p.E168*	ENST00000367435	NM_024529.4	168	Gaa/Taa	6/17	0.246181341852612	3	FACETS	0.752	0.611	0.911	0.376	0.305	0.456	CLONAL	1	TRUE	1	0.267137847482395	3		247	361	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201868	102201868	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029578-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	55	401	0	ENST00000263464.3:c.1220G>C	p.Gly407Ala	p.G407A	ENST00000263464	NM_001165.4	407	gGa/gCa	6/9	0.246181341852612	3	FACETS	0.847	0.725	0.981	0.424	0.362	0.491	CLONAL	1	TRUE	1	0.267137847482395	3		401	551	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436578	49436578	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029578-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	216	647	0	ENST00000301067.7:c.5728G>T	p.Gly1910Ter	p.G1910*	ENST00000301067	NM_003482.3	1910	Gga/Tga	26/54	0.267137847482395	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.267137847482395	2		647	714	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900414	32900414	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029578-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	77	333	0	ENST00000380152.3:c.511G>T	p.Val171Leu	p.V171L	ENST00000380152		171	Gtg/Ttg	6/27	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.267137847482395	2		333	525	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793197	33793197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1382321984	NA	P-0029578-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	36	183	1	ENST00000498907.2:c.124C>T	p.Pro42Ser	p.P42S	ENST00000498907	NM_004364.3	42	Cct/Tct	1/1	0.14134261128079	4	FACETS	0.759	0.629	0.902	0.759	0.629	0.902	INDETERMINATE	2	TRUE	2	0.267137847482395	4		184	225	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182580	99182580	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029578-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	43	414	1	ENST00000074304.5:c.2383C>A	p.Gln795Lys	p.Q795K	ENST00000074304	NM_001134224.1	795	Cag/Aag	22/26	0.17161698087697	2	FACETS	0.545	0.455	0.644	0.272	0.227	0.322	SUBCLONAL	1	TRUE	0	0.267137847482395	2		415	591	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204612	128204612	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029578-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	187	664	0	ENST00000341105.2:c.829A>T	p.Ser277Cys	p.S277C	ENST00000341105	NM_032638.4	277	Agc/Tgc	3/6	0.267137847482395	5	FACETS	0.85	0.784	0.919			1	CLONAL	2	TRUE	NA	0.267137847482395	5		664	1153	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157044	106157044	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029578-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	136	468	0	ENST00000380013.4:c.1945C>T	p.Gln649Ter	p.Q649*	ENST00000380013	NM_001127208.2	649	Caa/Taa	3/11	1	2	FACETS	0.781	0.712	0.853	1	0.987	1	SUBCLONAL	2	TRUE	1	0.267137847482395	2		468	652	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128849189	128849189	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029578-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	127	586	1	ENST00000249373.3:c.1417G>T	p.Asp473Tyr	p.D473Y	ENST00000249373	NM_005631.4	473	Gac/Tac	8/12	0.214003831190368	4	FACETS	0.76	0.688	0.835	0.76	0.688	0.835	SUBCLONAL	2	TRUE	2	0.267137847482395	4		587	793	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879018	151879018	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029578-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	161	469	0	ENST00000262189.6:c.5927A>C	p.Asp1976Ala	p.D1976A	ENST00000262189	NM_170606.2	1976	gAt/gCt	36/59	0.214003831190368	4	FACETS	0.973	0.894	1	0.973	0.894	1	CLONAL	2	TRUE	2	0.267137847482395	4		469	785	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	140	394	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.209053943983026	2	FACETS	0.802	0.731	0.877	0.802	0.731	0.877	CLONAL	2	TRUE	0	0.222264804441391	2		394	785	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0029579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	96	591	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.222264804441391	2		592	836	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974693	21974693	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	51	396	0	ENST00000304494.5:c.134del	p.Gly45ValfsTer8	p.G45Vfs*8	ENST00000304494	NM_000077.4	45	gGt/gt	1/3	0.222264804441391	1	FACETS	0.742	0.63	0.864	0.742	0.63	0.864	SUBCLONAL	1	TRUE	0	0.222264804441391	1		396	550	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924891	49924892	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0029579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	118	696	0	ENST00000296474.3:c.4051dup	p.Asp1351GlyfsTer20	p.D1351Gfs*20	ENST00000296474	NM_002447.2	1351	gac/gGac	20/20	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.222264804441391	2		696	1007	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	116	404	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.901	0.822	0.981	0.901	0.822	0.981	CLONAL	1	TRUE	1	0.797589165966285	2		404	323	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200046	123200046	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	149	176	0	ENST00000218089.9:c.2118G>A	p.Trp706Ter	p.W706*	ENST00000218089	NM_001042749.1	706	tgG/tgA	22/35	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.797589165966285	1		176	192	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	82	404	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.805	0.71	0.908	0.805	0.71	0.908	CLONAL	1	TRUE	1	0.284458768840267	2		404	716	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588751	29588751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760703505	NA	P-0029581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	43	297	0	ENST00000356175.3:c.4537C>T	p.Arg1513Ter	p.R1513*	ENST00000356175	NM_000267.3	1513	Cga/Tga	34/57	1	2	FACETS	0.822	0.689	0.967	0.822	0.689	0.967	CLONAL	1	TRUE	1	0.284458768840267	2		297	368	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106439	27106439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	185	546	0	ENST00000324856.7:c.6050del	p.Leu2017ArgfsTer13	p.L2017Rfs*13	ENST00000324856	NM_006015.4	2017	cTg/cg	20/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.284458768840267	2		546	980	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117855	70117855	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	114	470	0	ENST00000245479.2:c.323C>A	p.Pro108His	p.P108H	ENST00000245479	NM_000346.3	108	cCc/cAc	1/3	1	2	FACETS	0.936	0.843	1	0.936	0.843	1	CLONAL	1	TRUE	1	0.284458768840267	2		470	856	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0029582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	53	482	2	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.829	0.708	0.961	0.829	0.708	0.961	CLONAL	1	TRUE	1	0.29	2		484	441	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0029582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	40	412	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.533	0.442	0.633	0.533	0.442	0.633	SUBCLONAL	1	TRUE	1	0.29	2		412	518	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374293	138374293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	72	592	1	ENST00000289153.2:c.3151G>A	p.Glu1051Lys	p.E1051K	ENST00000289153	NM_006219.2	1051	Gaa/Aaa	22/22	1	2	FACETS	0.758	0.662	0.862	0.758	0.662	0.862	SUBCLONAL	1	TRUE	1	0.29	2		593	655	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106364	27106364	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	128	521	1	ENST00000324856.7:c.5975C>A	p.Ser1992Ter	p.S1992*	ENST00000324856	NM_006015.4	1992	tCa/tAa	20/20	1	2	FACETS	0.807	0.735	0.882	1	0.988	1	CLONAL	2	TRUE	1	0.29	2		522	547	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222659	69222659	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	79	622	1	ENST00000462284.1:c.632T>A	p.Ile211Lys	p.I211K	ENST00000462284	NM_002392.5	211	aTa/aAa	8/11	1	2	FACETS	0.755	0.663	0.853	0.755	0.663	0.853	SUBCLONAL	1	TRUE	1	0.29	2		623	722	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479774	67479774	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs387906856	NA	P-0029582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	50	566	0	ENST00000327367.4:c.1081G>C	p.Glu361Gln	p.E361Q	ENST00000327367	NM_005902.3	361	Gag/Cag	8/9	1	2	FACETS	0.572	0.485	0.668	0.572	0.485	0.668	SUBCLONAL	1	TRUE	1	0.29	2		566	603	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0029583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	215	516	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.224752658581363	5	FACETS	0.964	0.897	1	0.964	0.897	1	CLONAL	3	TRUE	2	0.224752658581363	5		516	885	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	255	763	0	ENST00000269305.4:c.404G>C	p.Cys135Ser	p.C135S	ENST00000269305	NM_001126112.2	135	tGc/tCc	5/11	NA	3	FACETS	1	0.982	1			1	INDETERMINATE	2	TRUE	NA	0.224752658581363	3		763	1112	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257640	19257640	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	88	716	0	ENST00000162023.5:c.586A>G	p.Thr196Ala	p.T196A	ENST00000162023		196	Aca/Gca	10/13	0.224752658581363	2	FACETS	0.807	0.714	0.908	0.404	0.357	0.454	CLONAL	1	TRUE	0	0.224752658581363	2		716	970	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0029584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	57	440	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.196976966481958	2		440	540	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0029584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	69	549	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.196976966481958	2		549	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0029584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	81	1069	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.927	0.815	1	0.927	0.815	1	CLONAL	1	TRUE	1	0.196976966481958	2		1071	887	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0029584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	57	387	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.897	0.769	1	0.897	0.769	1	CLONAL	1	TRUE	1	0.196976966481958	2		387	645	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501260	140501260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730880413	NA	P-0029584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	53	515	0	ENST00000288602.6:c.812G>A	p.Arg271His	p.R271H	ENST00000288602	NM_004333.4	271	cGt/cAt	6/18	0.196976966481958	3	FACETS	0.733	0.623	0.853	0.366	0.311	0.427	SUBCLONAL	1	TRUE	1	0.196976966481958	3		515	807	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395746	45395746	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	79	373	1	ENST00000262160.6:c.388C>T	p.Arg130Ter	p.R130*	ENST00000262160	NM_005901.5	130	Cga/Tga	4/11	0.196976966481958	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.196976966481958	1		374	605	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912189	114912189	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	68	487	0	ENST00000543371.1:c.1259G>T	p.Arg420Leu	p.R420L	ENST00000543371	NM_001198531.1	420	cGg/cTg	11/14	1	2	FACETS	0.862	0.749	0.985	0.862	0.749	0.985	CLONAL	1	TRUE	1	0.196976966481958	2		487	801	SUCCESS
APC	324	MSKCC	GRCh37	5	112175350	112175354	+	frameshift_variant	Frame_Shift_Del	DEL	ATTTT	ATTTT	-	novel	NA	P-0029584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	43	222	0	ENST00000257430.4:c.4059_4063del	p.Glu1353AspfsTer20	p.E1353Dfs*20	ENST00000257430	NM_000038.5	1353	gaATTTTct/gact	16/16	0.16544253045373	2	FACETS	1	0.958	1	0.743	0.625	0.872	CLONAL	1	TRUE	0	0.196976966481958	2		222	294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0029586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	271	598	1	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	0.319503360861834	2	FACETS	0.945	0.888	1	0.945	0.888	1	CLONAL	2	TRUE	0	0.319503360861834	2		599	898	SUCCESS
APC	324	MSKCC	GRCh37	5	112175770	112175771	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0029586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	86	273	0	ENST00000257430.4:c.4479_4480del	p.Glu1494LysfsTer19	p.E1494Kfs*19	ENST00000257430	NM_000038.5	1493	acGGaa/acaa	16/16	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.319503360861834	2		273	447	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727441	66727441	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519728	NA	P-0029586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	197	436	0	ENST00000307102.5:c.157T>C	p.Phe53Leu	p.F53L	ENST00000307102	NM_002755.3	53	Ttt/Ctt	2/11	0.306451447845004	3	FACETS	0.993	0.923	1	0.993	0.923	1	CLONAL	2	TRUE	1	0.319503360861834	3		436	720	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268762	41268762	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1245266458	NA	P-0029586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	98	429	0	ENST00000349496.5:c.1000G>A	p.Glu334Lys	p.E334K	ENST00000349496	NM_001904.3	334	Gaa/Aaa	7/15	1	2	FACETS	0.938	0.838	1	0.938	0.838	1	CLONAL	1	TRUE	1	0.319503360861834	2		429	654	SUCCESS
APC	324	MSKCC	GRCh37	5	112157613	112157613	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658802	NA	P-0029586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	95	403	1	ENST00000257430.4:c.1333C>T	p.Gln445Ter	p.Q445*	ENST00000257430	NM_000038.5	445	Cag/Tag	11/16	1	2	FACETS	0.878	0.783	0.98	0.878	0.783	0.98	CLONAL	1	TRUE	1	0.319503360861834	2		404	677	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506443	148506443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554481435	NA	P-0029586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	51	347	0	ENST00000320356.2:c.2069G>A	p.Arg690His	p.R690H	ENST00000320356	NM_004456.4	690	cGt/cAt	18/20	0.263052535647019	4	FACETS	0.548	0.464	0.64	0.274	0.232	0.32	SUBCLONAL	1	TRUE	2	0.319503360861834	4		347	769	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249925	39249925	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	136	597	0	ENST00000402219.2:c.1644T>G	p.Ser548Arg	p.S548R	ENST00000402219	NM_005633.3	548	agT/agG	10/23	0.306451447845004	3	FACETS	1	0.911	1	0.502	0.455	0.55	CLONAL	1	TRUE	1	0.319503360861834	3		597	984	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405995	157405995	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	86	456	0	ENST00000346085.5:c.2237G>C	p.Ser746Thr	p.S746T	ENST00000346085	NM_020732.3	746	aGc/aCc	6/20	0.306451447845004	3	FACETS	0.868	0.768	0.976	0.434	0.384	0.488	CLONAL	1	TRUE	1	0.319503360861834	3		456	719	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1188	75	877	0	ENST00000269305.4:c.380C>A	p.Ser127Tyr	p.S127Y	ENST00000269305	NM_001126112.2	127	tCc/tAc	5/11	1	2	FACETS	0.132	0.115	0.15	0.132	0.115	0.15	SUBCLONAL	1	TRUE	1	0.90124618666614	2		877	1263	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514221	69514221	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	86	706	0	ENST00000294312.3:c.460T>A	p.Tyr154Asn	p.Y154N	ENST00000294312	NM_005117.2	154	Tac/Aac	3/3	1	2	FACETS	0.177	0.156	0.2	0.177	0.156	0.2	SUBCLONAL	1	TRUE	1	0.90124618666614	2		706	1078	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128268652	128268652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145885264	NA	P-0029587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	81	787	0	ENST00000265960.3:c.1003G>A	p.Val335Ile	p.V335I	ENST00000265960	NM_001006617.1	335	Gtt/Att	8/12	1	2	FACETS	0.168	0.147	0.191	0.168	0.147	0.191	SUBCLONAL	1	TRUE	1	0.90124618666614	2		787	1069	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0029588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	26	737	0	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		737	602	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0029588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	36	498	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		498	557	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	118	394	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	0.24683097151014	2		394	764	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0029589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	125	722	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.24683097151014	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.24683097151014	1		722	834	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0029589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	24	431	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.335	0.262	0.421	0.335	0.262	0.421	SUBCLONAL	1	TRUE	1	0.24683097151014	2		431	580	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473722	67473722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs794727798	NA	P-0029589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	101	681	1	ENST00000327367.4:c.802C>T	p.Arg268Cys	p.R268C	ENST00000327367	NM_005902.3	268	Cgc/Tgc	6/9	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.24683097151014	2		682	702	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942739	44942739	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	27	306	0	ENST00000377967.4:c.3320del	p.Pro1107LeufsTer13	p.P1107Lfs*13	ENST00000377967	NM_021140.2	1107	Cct/ct	23/29	1	1	FACETS	0.435	0.345	0.537	0.435	0.345	0.537	SUBCLONAL	1	TRUE	0	0.24683097151014	1		306	441	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016559	12016559	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	58	309	0	ENST00000353533.5:c.695C>T	p.Pro232Leu	p.P232L	ENST00000353533	NM_003010.3	232	cCt/cTt	7/11	0.24683097151014	1	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	0	0.24683097151014	1		309	391	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176133021	176133021	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	84	382	0	ENST00000367669.3:c.572A>T	p.Glu191Val	p.E191V	ENST00000367669	NM_022457.5	191	gAa/gTa	4/20	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.24683097151014	2		382	671	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337228	89337228	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	122	589	0	ENST00000301030.4:c.7803G>C	p.Met2601Ile	p.M2601I	ENST00000301030	NM_001256183.1	2601	atG/atC	12/13	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.24683097151014	2		589	782	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581197	48581197	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	92	420	0	ENST00000342988.3:c.503del	p.Gly168AspfsTer34	p.G168Dfs*34	ENST00000342988	NM_005359.5	167	gaG/ga	5/12	0.24683097151014	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.24683097151014	1		420	553	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390211	89390211	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	55	307	0	ENST00000336596.2:c.960G>T	p.Met320Ile	p.M320I	ENST00000336596	NM_005233.5	320	atG/atT	4/17	1	2	FACETS	0.909	0.779	1	0.909	0.779	1	CLONAL	1	TRUE	1	0.24683097151014	2		307	490	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415654	152415654	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	105	556	0	ENST00000206249.3:c.1504C>T	p.Gln502Ter	p.Q502*	ENST00000206249	NM_000125.3	502	Cag/Tag	7/8	0.24683097151014	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.24683097151014	1		556	634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0029590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	737	500	4	ENST00000269305.4:c.559+1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.865642490411658	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.865642490411658	2		504	781	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878166	48878166	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	454	170	0	ENST00000267163.4:c.118G>T	p.Glu40Ter	p.E40*	ENST00000267163	NM_000321.2	40	Gag/Tag	1/27	0.584533849833047	4	FACETS	1	0.997	1			1	CLONAL	4	TRUE	NA	0.865642490411658	4		170	470	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934603	9934603	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	221	453	1	ENST00000330684.3:c.1552C>A	p.Arg518Ser	p.R518S	ENST00000330684	NM_001134407.1	518	Cgt/Agt	7/13	1	2	FACETS	0.978	0.919	1	0.978	0.919	1	CLONAL	1	TRUE	1	0.865642490411658	2		454	522	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246027182	246027182	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	180	461	0	ENST00000388985.4:c.820G>A	p.Asp274Asn	p.D274N	ENST00000388985		274	Gat/Aat	9/12	0.865642490411658	3	FACETS	0.998	0.925	1	0.499	0.462	0.537	CLONAL	1	TRUE	1	0.865642490411658	3		461	597	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424489	49424489	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	861	594	2	ENST00000301067.7:c.13734del	p.Phe4579LeufsTer13	p.F4579Lfs*13	ENST00000301067	NM_003482.3	4578	ccC/cc	41/54	0.865642490411658	4	FACETS	1	0.986	1	0.683	0.663	0.703	CLONAL	2	TRUE	1	0.865642490411658	4		596	1811	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427562	49427562	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	983	475	3	ENST00000301067.7:c.10926G>C	p.Gln3642His	p.Q3642H	ENST00000301067	NM_003482.3	3642	caG/caC	39/54	0.865642490411658	4	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	1	0.865642490411658	4		478	1303	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346816	91346816	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	136	520	3	ENST00000355112.3:c.3424G>T	p.Ala1142Ser	p.A1142S	ENST00000355112	NM_000057.2	1142	Gcc/Tcc	18/22	1	2	FACETS	0.927	0.855	1	0.927	0.855	1	CLONAL	1	TRUE	1	0.865642490411658	2		523	339	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014213	14014213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	214	264	0	ENST00000311895.7:c.191C>T	p.Thr64Met	p.T64M	ENST00000311895	NM_005236.2	64	aCg/aTg	1/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.865642490411658	2		264	424	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993687	72993687	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	338	483	1	ENST00000268489.5:c.358G>T	p.Gly120Trp	p.G120W	ENST00000268489	NM_006885.3	120	Ggg/Tgg	2/10	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.865642490411658	2		484	778	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30302650	30302658	+	inframe_deletion	In_Frame_Del	DEL	TTACTCGTT	TTACTCGTT	-	novel	NA	P-0029590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	207	273	1	ENST00000322652.5:c.741_749del	p.Tyr248_Leu250del	p.Y248_L250del	ENST00000322652	NM_015355.2	247	tcTTACTCGTTg/tcg	7/16	0.742007335106655	4	FACETS	0.981	0.921	1	0.981	0.921	1	CLONAL	2	TRUE	2	0.865642490411658	4		274	455	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858356	59858356	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	203	373	4	ENST00000259008.2:c.1639G>T	p.Asp547Tyr	p.D547Y	ENST00000259008	NM_032043.2	547	Gat/Tat	12/20	0.742007335106655	4	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	2	0.865642490411658	4		377	434	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621043	1621043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	1048	832	0	ENST00000344749.5:c.1017C>G	p.Ile339Met	p.I339M	ENST00000344749	NM_001136139.2	339	atC/atG	13/19	0.865642490411658	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.865642490411658	3		832	1681	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584538	52584538	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	353	546	0	ENST00000394830.3:c.4475C>T	p.Pro1492Leu	p.P1492L	ENST00000394830	NM_018313.4	1492	cCa/cTa	29/30	0.865642490411658	2	FACETS	1	0.97	1	0.512	0.488	0.537	CLONAL	1	TRUE	0	0.865642490411658	2		546	796	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920315	134920315	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0029590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	365	280	1	ENST00000398015.3:c.2131-1G>T		p.X711_splice	ENST00000398015	NM_004441.4	711			0.742007335106655	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.865642490411658	4		281	748	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549769	187549769	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	176	388	0	ENST00000441802.2:c.4472A>G	p.Tyr1491Cys	p.Y1491C	ENST00000441802	NM_005245.3	1491	tAc/tGc	8/27	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.865642490411658	2		388	353	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504276	8504276	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	936	429	6	ENST00000356435.5:c.1807A>G	p.Arg603Gly	p.R603G	ENST00000356435		603	Aga/Gga	12/35	0.865642490411658	4	FACETS	1	0.998	1	1	0.998	1	CLONAL	4	TRUE	0	0.865642490411658	4		435	975	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	270	404	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.848020305736141	2		404	628	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0029592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	29632	734	0	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.848020305736141	20	FACETS	0.983	0.981	0.985	0.983	0.981	0.985	CLONAL	20	TRUE	0	0.848020305736141	20		734	30678	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941094	36941094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760367363	NA	P-0029592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	372	576	0	ENST00000361632.4:c.245C>T	p.Thr82Ile	p.T82I	ENST00000361632		82	aCc/aTc	3/16	1	2	FACETS	0.964	0.919	1	0.964	0.919	1	CLONAL	1	TRUE	1	0.848020305736141	2		576	910	SUCCESS
APC	324	MSKCC	GRCh37	5	112179541	112179541	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	68	346	0	ENST00000257430.4:c.8250G>T	p.Glu2750Asp	p.E2750D	ENST00000257430	NM_000038.5	2750	gaG/gaT	16/16	1	2	FACETS	0.271	0.236	0.31	0.271	0.236	0.31	SUBCLONAL	1	TRUE	1	0.848020305736141	2		346	591	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0029593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	58	301	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	0.311329223341529	3	FACETS	0.629	0.541	0.725	0.315	0.27	0.363	SUBCLONAL	1	TRUE	1	0.481544298238614	3		301	475	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0029593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	147	498	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	0.481544298238614	2		498	597	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031973	26031973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	124	341	0	ENST00000244661.2:c.316G>C	p.Glu106Gln	p.E106Q	ENST00000244661	NM_003537.3	106	Gag/Cag	1/1	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.481544298238614	2		341	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0029593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	202	771	1	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.481544298238614	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.481544298238614	1		772	572	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397219	397219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143144957	NA	P-0029593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	133	318	0	ENST00000380956.4:c.604G>A	p.Gly202Ser	p.G202S	ENST00000380956	NM_001195286.1	202	Ggc/Agc	5/9	NA	2	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.481544298238614	2		318	488	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637631	23637631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45476495	NA	P-0029593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	93	519	0	ENST00000261584.4:c.2674G>A	p.Glu892Lys	p.E892K	ENST00000261584	NM_024675.3	892	Gaa/Aaa	7/13	1	2	FACETS	0.469	0.416	0.525	0.469	0.416	0.525	SUBCLONAL	1	TRUE	1	0.481544298238614	2		519	824	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013720	170013720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	147	365	0	ENST00000295797.4:c.1439G>A	p.Arg480His	p.R480H	ENST00000295797	NM_002740.5	480	cGc/cAc	15/18	0.311329223341529	3	FACETS	1	0.963	1	0.547	0.5	0.595	CLONAL	1	TRUE	1	0.481544298238614	3		365	693	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351211	89351211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs558841201	NA	P-0029593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	233	528	0	ENST00000301030.4:c.1739C>T	p.Ser580Phe	p.S580F	ENST00000301030	NM_001256183.1	580	tCc/tTc	9/13	0.271604178293274	1	FACETS	1	0.98	1	1	0.98	1	INDETERMINATE	1	TRUE	0	0.481544298238614	1		528	664	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073773	8073773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	108	261	0	ENST00000377482.5:c.886C>T	p.Pro296Ser	p.P296S	ENST00000377482	NM_018948.3	296	Cca/Tca	4/4	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.481544298238614	2		261	398	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561462	9561462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1176133163	NA	P-0029593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	133	406	0	ENST00000353224.5:c.320C>T	p.Thr107Ile	p.T107I	ENST00000353224	NM_177990.2	107	aCc/aTc	4/10	1	2	FACETS	0.997	0.91	1	0.997	0.91	1	CLONAL	1	TRUE	1	0.481544298238614	2		406	554	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188950	32188950	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	216	651	0	ENST00000375023.3:c.604C>T	p.Pro202Ser	p.P202S	ENST00000375023	NM_004557.3	202	Cca/Tca	4/30	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.481544298238614	2		651	887	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128201190	128201190	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	112	469	0	ENST00000265960.3:c.1545G>T	p.Lys515Asn	p.K515N	ENST00000265960	NM_001006617.1	515	aaG/aaT	12/12	0.271604178293274	1	FACETS	0.583	0.525	0.643	0.583	0.525	0.643	INDETERMINATE	1	TRUE	0	0.481544298238614	1		469	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0029594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	325	649	1	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.484458746371791	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.484458746371791	1		650	912	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0029594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	212	564	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	1	2	FACETS	0.747	0.693	0.803	0.747	0.693	0.803	SUBCLONAL	1	TRUE	1	0.484458746371791	2		564	1172	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638795	176638795	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1195	262	645	0	ENST00000439151.2:c.3395G>A	p.Gly1132Glu	p.G1132E	ENST00000439151	NM_022455.4	1132	gGa/gAa	5/23	0.484458746371791	3	FACETS	0.922	0.862	0.984	0.461	0.431	0.492	CLONAL	1	TRUE	1	0.484458746371791	3		645	1457	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356266	70356301	+	inframe_deletion	In_Frame_Del	DEL	CAGCGGTTGCTGCTCTACCACACACACCTGAGGCCC	CAGCGGTTGCTGCTCTACCACACACACCTGAGGCCC	-	novel	NA	P-0029594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	239	629	0	ENST00000374080.3:c.5162_5197del	p.Gln1721_Pro1732del	p.Q1721_P1732del	ENST00000374080		1721	CAGCGGTTGCTGCTCTACCACACACACCTGAGGCCC/-	37/45	1	2	FACETS	0.908	0.847	0.97	0.908	0.847	0.97	CLONAL	1	TRUE	1	0.484458746371791	2		629	1087	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0029595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	107	591	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.567206915201751	NA		591	495	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131142	55131142	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	3422	491	0	ENST00000257290.5:c.685G>A	p.Glu229Lys	p.E229K	ENST00000257290	NM_006206.4	229	Gaa/Aaa	5/23	0.567206915201751	20	FACETS	1	0.993	1			1	CLONAL	17	TRUE	NA	0.567206915201751	20		491	4320	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271668	15271668	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	268	888	0	ENST00000263388.2:c.6771C>A	p.Ser2257Arg	p.S2257R	ENST00000263388	NM_000435.2	2257	agC/agA	33/33	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.40252284953152	2		888	1227	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001128	150001128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	128	478	0	ENST00000253339.5:c.2476C>T	p.His826Tyr	p.H826Y	ENST00000253339		826	Cat/Tat	4/7	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.40252284953152	2		478	550	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405167	139405167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	189	712	0	ENST00000277541.6:c.2678G>A	p.Cys893Tyr	p.C893Y	ENST00000277541	NM_017617.3	893	tGc/tAc	17/34	1	2	FACETS	0.961	0.888	1	0.961	0.888	1	CLONAL	1	TRUE	1	0.40252284953152	2		712	977	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	132	394	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.93	0.847	1	0.93	0.847	1	CLONAL	1	TRUE	1	0.457944431532369	2		394	620	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0029597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	247	950	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.457944431532369	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.457944431532369	1		950	823	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650717	67650717	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	108	552	1	ENST00000264010.4:c.1022G>T	p.Arg341Leu	p.R341L	ENST00000264010	NM_006565.3	341	cGt/cTt	5/12	1	2	FACETS	0.6	0.538	0.666	0.6	0.538	0.666	SUBCLONAL	1	TRUE	1	0.457944431532369	2		553	786	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581256	48581265	+	frameshift_variant	Frame_Shift_Del	DEL	GTAATCGTGC	GTAATCGTGC	-	novel	NA	P-0029597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	63	518	0	ENST00000342988.3:c.560_569del	p.Ser187AsnfsTer12	p.S187Nfs*12	ENST00000342988	NM_005359.5	187	aGTAATCGTGCa/aa	5/12	0.457944431532369	1	FACETS	0.389	0.336	0.445	0.389	0.336	0.445	SUBCLONAL	1	TRUE	0	0.457944431532369	1		518	546	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218417	1218418	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	164	586	0	ENST00000326873.7:c.295dup	p.Ile99AsnfsTer64	p.I99Nfs*64	ENST00000326873	NM_000455.4	98	gaa/gAaa	2/10	0.457944431532369	1	FACETS	0.835	0.77	0.904	0.835	0.77	0.904	CLONAL	1	TRUE	0	0.457944431532369	1		586	661	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0029598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	53	532	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.15071078959468	2		532	530	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717777	89717777	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0029598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	94	271	0	ENST00000371953.3:c.801+1G>T		p.X267_splice	ENST00000371953	NM_000314.4	267			0.141969081207306	3	FACETS	0.972	0.869	1	0.972	0.869	1	CLONAL	3	TRUE	0	0.15071078959468	3		271	460	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	127	404	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.904	0.822	0.99	0.904	0.822	0.99	CLONAL	1	TRUE	1	0.485168664705567	2		404	579	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653796	89653798	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs1554893765	NA	P-0029600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	120	405	0	ENST00000371953.3:c.97_99del	p.Ile33del	p.I33del	ENST00000371953	NM_000314.4	32	ATT/-	2/9	0.485168664705567	1	FACETS	0.914	0.832	0.998	0.914	0.832	0.998	CLONAL	1	TRUE	0	0.485168664705567	1		405	410	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793186	42793186	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	238	794	1	ENST00000575354.2:c.1078G>A	p.Val360Ile	p.V360I	ENST00000575354	NM_015125.3	360	Gta/Ata	7/20	1	2	FACETS	0.831	0.775	0.889	0.831	0.775	0.889	CLONAL	1	TRUE	1	0.485168664705567	2		795	1181	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182249	38182251	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TGC	TGC	CA	novel	NA	P-0029600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	109	395	0	ENST00000396334.3:c.685_687delinsCA	p.Cys229HisfsTer37	p.C229Hfs*37	ENST00000396334	NM_002468.4	229	TGC/CA	4/5	1	2	FACETS	0.731	0.657	0.808	0.731	0.657	0.808	SUBCLONAL	1	TRUE	1	0.485168664705567	2		395	615	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259043	16259043	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	250	584	1	ENST00000375759.3:c.6313del	p.Ala2105LeufsTer33	p.A2105Lfs*33	ENST00000375759	NM_015001.2	2103	aGg/ag	11/15	0.493012923720004	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.493012923720004	1		585	581	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039374	49039374	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853293	NA	P-0029601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	141	659	0	ENST00000267163.4:c.2359C>T	p.Arg787Ter	p.R787*	ENST00000267163	NM_000321.2	787	Cga/Tga	23/27	0.493012923720004	1	FACETS	0.655	0.598	0.714	0.655	0.598	0.714	SUBCLONAL	1	TRUE	0	0.493012923720004	1		659	658	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579585	7579585	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	266	538	0	ENST00000269305.4:c.102del	p.Leu35CysfsTer9	p.L35Cfs*9	ENST00000269305	NM_001126112.2	34	ccC/cc	4/11	0.493012923720004	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.493012923720004	1		538	638	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266486	41266486	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775104326	NA	P-0029601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	125	393	1	ENST00000349496.5:c.283C>T	p.Arg95Ter	p.R95*	ENST00000349496	NM_001904.3	95	Cga/Tga	4/15	0.493012923720004	1	FACETS	0.914	0.834	0.996	0.914	0.834	0.996	CLONAL	1	TRUE	0	0.493012923720004	1		394	418	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933617	39933617	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	235	253	0	ENST00000378444.4:c.982del	p.Asp328ThrfsTer50	p.D328Tfs*50	ENST00000378444	NM_001123385.1	328	Gac/ac	4/15	1	1	FACETS	0.822	0.778	0.865	1	0.994	1	CLONAL	2	TRUE	0	0.493012923720004	1		253	437	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321242	65321242	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761801070	NA	P-0029601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	236	483	1	ENST00000342505.4:c.1598C>T	p.Thr533Met	p.T533M	ENST00000342505	NM_002227.2	533	aCg/aTg	11/25	0.493012923720004	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.493012923720004	1		484	647	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185545	27185545	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1564083506	NA	P-0029601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	276	595	0	ENST00000380036.4:c.1250del	p.Pro417LeufsTer10	p.P417Lfs*10	ENST00000380036	NM_000459.3	415	ctC/ct	9/23	0.493012923720004	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.493012923720004	1		595	737	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231105	98231105	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	291	479	0	ENST00000331920.6:c.2178del	p.Cys727ValfsTer19	p.C727Vfs*19	ENST00000331920	NM_000264.3	726	ccC/cc	14/24	0.493012923720004	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.493012923720004	1		479	665	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77060289	77060289	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	126	317	0	ENST00000356341.3:c.880C>T	p.Gln294Ter	p.Q294*	ENST00000356341	NM_002576.4	294	Cag/Tag	9/15	0.493012923720004	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.493012923720004	1		317	369	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343550	118343550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	245	391	0	ENST00000534358.1:c.1676C>T	p.Ser559Leu	p.S559L	ENST00000534358	NM_005933.3	559	tCg/tTg	3/36	0.493012923720004	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.493012923720004	1		391	514	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435070	110435070	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	377	693	0	ENST00000375856.3:c.3331A>G	p.Met1111Val	p.M1111V	ENST00000375856	NM_003749.2	1111	Atg/Gtg	1/2	0.493012923720004	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.493012923720004	1		693	867	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826571	50826571	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1489875475	NA	P-0029601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	123	305	0	ENST00000398568.2:c.2296A>T	p.Ile766Phe	p.I766F	ENST00000398568	NM_001042412.1	766	Att/Ttt	15/18	0.493012923720004	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.493012923720004	1		305	368	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2189756	2189756	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	458	780	0	ENST00000398665.3:c.226G>A	p.Asp76Asn	p.D76N	ENST00000398665	NM_032482.2	76	Gac/Aac	4/28	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.493012923720004	2		780	1371	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18943143	18943143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	196	232	0	ENST00000262803.5:c.125G>A	p.Ser42Asn	p.S42N	ENST00000262803	NM_002911.3	42	aGc/aAc	1/24	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.493012923720004	2		232	591	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47607059	47607059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	89	559	0	ENST00000263735.4:c.809C>T	p.Ala270Val	p.A270V	ENST00000263735	NM_002354.2	270	gCt/gTt	7/9	0.493012923720004	1	FACETS	0.43	0.381	0.482	0.43	0.381	0.482	SUBCLONAL	1	TRUE	0	0.493012923720004	1		559	633	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225600	225600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777600956	NA	P-0029601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	128	243	0	ENST00000264932.6:c.379G>A	p.Val127Met	p.V127M	ENST00000264932	NM_004168.2	127	Gtg/Atg	4/15	0.493012923720004	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.493012923720004	1		243	334	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399489	139399489	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1438164851	NA	P-0029601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	432	712	1	ENST00000277541.6:c.4654G>A	p.Ala1552Thr	p.A1552T	ENST00000277541	NM_017617.3	1552	Gcg/Acg	26/34	0.493012923720004	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.493012923720004	1		713	1061	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	287	404	0				ENST00000310581	NM_198253.2	-/1132			0.184520075214735	3	FACETS	0.814	0.77	0.858	0.814	0.77	0.858	INDETERMINATE	2	TRUE	1	0.651286376811731	3		404	718	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099874	157099898	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGCCGCCGCCGGGGCCCCCGGCA	GCCGCCGCCGCCGGGGCCCCCGGCA	-	novel	NA	P-0029602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	305	633	0	ENST00000346085.5:c.813_837del	p.Ala272TrpfsTer89	p.A272Wfs*89	ENST00000346085	NM_020732.3	271	GCCGCCGCCGCCGGGGCCCCCGGCAgc/gc	1/20	1	2	FACETS	0.88	0.83	0.931	0.88	0.83	0.931	CLONAL	1	TRUE	1	0.651286376811731	2		633	1064	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166057	118166057	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	57	341	0	ENST00000369448.3:c.567T>G	p.Asp189Glu	p.D189E	ENST00000369448	NM_017709.3	189	gaT/gaG	2/2	1	2	FACETS	0.394	0.338	0.455	0.394	0.338	0.455	SUBCLONAL	1	TRUE	1	0.519481918729889	2		341	557	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32918753	32918753	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	52	306	0	ENST00000380152.3:c.6900A>C	p.Gln2300His	p.Q2300H	ENST00000380152		2300	caA/caC	12/27	0.519481918729889	1	FACETS	0.456	0.39	0.527	0.456	0.39	0.527	SUBCLONAL	1	TRUE	0	0.519481918729889	1		306	325	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041633	14041633	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs977543746	NA	P-0029603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	44	357	0	ENST00000311895.7:c.2180A>G	p.Lys727Arg	p.K727R	ENST00000311895	NM_005236.2	727	aAg/aGg	11/11	1	2	FACETS	0.272	0.227	0.321	0.272	0.227	0.321	SUBCLONAL	1	TRUE	1	0.519481918729889	2		357	623	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0029604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	79	437	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.18	2		437	822	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696432	47696432	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519968	NA	P-0029604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	38	401	0	ENST00000347630.2:c.391T>G	p.Trp131Gly	p.W131G	ENST00000347630	NM_001007230.1	131	Tgg/Ggg	6/11	1	2	FACETS	0.475	0.391	0.57	0.475	0.391	0.57	SUBCLONAL	1	TRUE	1	0.18	2		401	888	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	rs886039483	NA	P-0029604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1267	122	679	0	ENST00000269305.4:c.376T>A	p.Tyr126Asn	p.Y126N	ENST00000269305	NM_001126112.2	126	Tac/Aac	5/11	1	2	FACETS	0.976	0.879	1	0.976	0.879	1	CLONAL	1	TRUE	1	0.18	2		679	1389	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629212	187629213	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0029605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	102	578	0	ENST00000441802.2:c.1769_1770del	p.Thr590SerfsTer5	p.T590Sfs*5	ENST00000441802	NM_005245.3	590	aCT/a	2/27	0.203774774922251	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.203774774922251	1		578	732	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904853	101904853	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	53	382	0	ENST00000374994.4:c.841G>C	p.Asp281His	p.D281H	ENST00000374994	NM_004612.2	281	Gat/Cat	5/9	1	2	FACETS	0.944	0.805	1	0.944	0.805	1	CLONAL	1	TRUE	1	0.203774774922251	2		382	551	SUCCESS
BLM	641	MSKCC	GRCh37	15	91295073	91295073	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs758301305	NA	P-0029606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	136	423	0	ENST00000355112.3:c.856G>T	p.Val286Phe	p.V286F	ENST00000355112	NM_000057.2	286	Gtt/Ttt	4/22	0.543342230238443	5	FACETS	1	0.97	1	0.385	0.35	0.422	CLONAL	1	TRUE	2	0.543342230238443	5		423	787	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15280905	15280905	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	239	703	0	ENST00000263388.2:c.5191C>T	p.Arg1731Trp	p.R1731W	ENST00000263388	NM_000435.2	1731	Cgg/Tgg	28/33	1	2	FACETS	0.969	0.906	1	0.969	0.906	1	CLONAL	1	TRUE	1	0.543342230238443	2		703	908	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692851	89692851	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121909230	NA	P-0029608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	26	194	0	ENST00000371953.3:c.335T>C	p.Leu112Pro	p.L112P	ENST00000371953	NM_000314.4	112	cTa/cCa	5/9	0.233019805287084	3	FACETS	1	0.906	1	0.629	0.502	0.772	CLONAL	1	TRUE	1	0.248558210236991	3		194	187	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182641	38182641	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs387907272	NA	P-0029608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	9	335	0	ENST00000396334.3:c.794T>C	p.Leu265Pro	p.L265P	ENST00000396334	NM_002468.4	265	cTg/cCg	5/5	1	2	FACETS	0.175	0.115	0.253	0.175	0.115	0.253	SUBCLONAL	1	TRUE	1	0.248558210236991	2		335	413	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148875	119148875	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs397517076	NA	P-0029608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	83	260	0	ENST00000264033.4:c.1096-1G>T		p.X366_splice	ENST00000264033	NM_005188.3	366			0.245620491362653	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.248558210236991	2		260	304	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913495	NA	P-0029608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	147	356	0	ENST00000371085.3:c.602G>T	p.Arg201Leu	p.R201L	ENST00000371085	NM_000516.4	201	cGt/cTt	8/13	0.248558210236991	6	FACETS	1	0.978	1	0.805	0.736	0.877	CLONAL	2	TRUE	3	0.248558210236991	6		356	733	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967047	18967047	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	85	642	0	ENST00000262803.5:c.1762T>C	p.Ser588Pro	p.S588P	ENST00000262803	NM_002911.3	588	Tcg/Ccg	13/24	1	2	FACETS	0.855	0.755	0.962	0.855	0.755	0.962	CLONAL	1	TRUE	1	0.248558210236991	2		642	800	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518446	69518446	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	740	326	0	ENST00000294312.3:c.199G>T	p.Val67Phe	p.V67F	ENST00000294312	NM_005117.2	67	Gtc/Ttc	1/3	0.248558210236991	16	FACETS	1	0.982	1			1	CLONAL	15	TRUE	NA	0.248558210236991	16		326	1078	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117853	108117853	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	96	372	0	ENST00000278616.4:c.1064A>T	p.Gln355Leu	p.Q355L	ENST00000278616	NM_000051.3	355	cAg/cTg	8/63	0.245620491362653	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	0	0.248558210236991	2		372	362	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431486	49431486	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	163	756	0	ENST00000301067.7:c.9653G>T	p.Gly3218Val	p.G3218V	ENST00000301067	NM_003482.3	3218	gGg/gTg	34/54	0.172532497282342	4	FACETS	1	0.987	1	0.723	0.662	0.786	CLONAL	1	TRUE	2	0.248558210236991	4		756	1133	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493446	56493446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	56	412	0	ENST00000267101.3:c.2854G>A	p.Glu952Lys	p.E952K	ENST00000267101	NM_001982.3	952	Gag/Aag	24/28	0.172532497282342	4	FACETS	0.785	0.671	0.909	0.392	0.335	0.455	CLONAL	1	TRUE	2	0.248558210236991	4		412	717	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654826	29654826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	50	327	0	ENST00000356175.3:c.5515C>T	p.Leu1839Phe	p.L1839F	ENST00000356175	NM_000267.3	1839	Ctt/Ttt	37/57	0.172532497282342	4	FACETS	1	0.909	1	0.55	0.467	0.64	CLONAL	1	TRUE	2	0.248558210236991	4		327	457	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129911	55129911	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	182	590	1	ENST00000257290.5:c.445C>A	p.Pro149Thr	p.P149T	ENST00000257290	NM_006206.4	149	Cct/Act	4/23	0.245620491362653	2	FACETS	0.948	0.877	1	0.948	0.877	1	CLONAL	2	TRUE	0	0.248558210236991	2		591	772	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222513	157222513	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	83	489	1	ENST00000346085.5:c.1780C>T	p.Pro594Ser	p.P594S	ENST00000346085	NM_020732.3	594	Cca/Tca	4/20	0.248558210236991	4	FACETS	1	0.954	1	0.388	0.342	0.438	CLONAL	1	TRUE	1	0.248558210236991	4		490	716	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522253	157522253	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1340183572	NA	P-0029608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	232	644	1	ENST00000346085.5:c.4525G>T	p.Glu1509Ter	p.E1509*	ENST00000346085	NM_020732.3	1509	Gag/Tag	18/20	0.248558210236991	4	FACETS	1	0.986	1	0.808	0.754	0.864	CLONAL	2	TRUE	1	0.248558210236991	4		645	961	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946436	2946436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761965340	NA	P-0029608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	155	783	2	ENST00000396946.4:c.3301C>T	p.Arg1101Cys	p.R1101C	ENST00000396946	NM_032415.4	1101	Cgc/Tgc	25/25	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.248558210236991	2		785	1044	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0029609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	12	373	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		373	530	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	180	404	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.905	0.834	0.98	0.905	0.834	0.98	CLONAL	1	TRUE	1	0.36929027451961	2		404	1077	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929428	44929429	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0029610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	190	364	0	ENST00000377967.4:c.2530dup	p.Leu844ProfsTer2	p.L844Pfs*2	ENST00000377967	NM_021140.2	843	agc/agCc	17/29	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.36929027451961	1		364	571	SUCCESS
AR	367	MSKCC	GRCh37	X	66905872	66905872	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137852569	NA	P-0029611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	333	321	0	ENST00000374690.3:c.1789G>A	p.Ala597Thr	p.A597T	ENST00000374690	NM_000044.3	597	Gcc/Acc	3/8	0.650502692861146	3	FACETS	0.973	0.928	1	0.973	0.928	1	CLONAL	2	TRUE	1	0.650502692861146	3		321	697	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692791	89692791	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	118	289	0	ENST00000371953.3:c.275A>T	p.Asp92Val	p.D92V	ENST00000371953	NM_000314.4	92	gAc/gTc	5/9	0.650502692861146	1	FACETS	0.868	0.796	0.941	0.868	0.796	0.941	CLONAL	1	TRUE	0	0.650502692861146	1		289	282	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0029612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	75	440	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.783	0.688	0.883	0.783	0.688	0.883	SUBCLONAL	1	TRUE	1	0.42404621432899	2		440	452	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217251	7217251	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	101	690	2	ENST00000380728.2:c.454C>T	p.Gln152Ter	p.Q152*	ENST00000380728		152	Caa/Taa	6/11	0.271636881385501	1	FACETS	0.569	0.509	0.632	0.569	0.509	0.632	SUBCLONAL	1	TRUE	0	0.42404621432899	1		692	660	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100603	67100603	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	77	514	0	ENST00000412916.2:c.301A>G	p.Met101Val	p.M101V	ENST00000412916		101	Atg/Gtg	4/6	0.271636881385501	1	FACETS	0.567	0.499	0.64	0.567	0.499	0.64	SUBCLONAL	1	TRUE	0	0.42404621432899	1		514	505	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032525	12032526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	51	430	0	ENST00000353533.5:c.962dup	p.Lys322GlufsTer9	p.K322Efs*9	ENST00000353533	NM_003010.3	321	gtg/gTtg	9/11	0.271636881385501	1	FACETS	0.556	0.474	0.644	0.556	0.474	0.644	SUBCLONAL	1	TRUE	0	0.42404621432899	1		430	341	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0029613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	217	532	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.310334330184553	3	FACETS	0.997	0.931	1	0.665	0.621	0.71	CLONAL	2	TRUE	0	0.361272087407601	3		532	711	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0029613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	201	734	2	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	0.361272087407601	1	FACETS	0.993	0.921	1	0.993	0.921	1	CLONAL	1	TRUE	0	0.361272087407601	1		736	918	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117669	70117669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	167	684	0	ENST00000245479.2:c.137C>T	p.Thr46Met	p.T46M	ENST00000245479	NM_000346.3	46	aCg/aTg	1/3	0.341039352754478	2	FACETS	0.79	0.724	0.858	0.395	0.362	0.429	SUBCLONAL	1	TRUE	0	0.361272087407601	2		684	1171	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793058	33793058	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	233	368	0	ENST00000498907.2:c.263A>T	p.Gln88Leu	p.Q88L	ENST00000498907	NM_004364.3	88	cAg/cTg	1/1	0.361272087407601	3	FACETS	0.97	0.908	1			1	CLONAL	2	TRUE	NA	0.361272087407601	3		368	785	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087395	27087396	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	146	632	0	ENST00000324856.7:c.1970dup	p.Ser658GlufsTer18	p.S658Efs*18	ENST00000324856	NM_006015.4	657	ctg/cTtg	5/20	1	2	FACETS	0.826	0.754	0.903	0.826	0.754	0.903	CLONAL	1	TRUE	1	0.361272087407601	2		632	978	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777756	3777756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772690401	NA	P-0029613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1482	95	990	2	ENST00000262367.5:c.7292C>T	p.Thr2431Met	p.T2431M	ENST00000262367	NM_004380.2	2431	aCg/aTg	31/31	1	2	FACETS	0.333	0.295	0.374	0.333	0.295	0.374	SUBCLONAL	1	TRUE	1	0.361272087407601	2		992	1577	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745588	162745588	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs754868982	NA	P-0029613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	96	452	2	ENST00000367921.3:c.2003G>T	p.Arg668Leu	p.R668L	ENST00000367921	NM_006182.2	668	cGc/cTc	15/18	0.361272087407601	3	FACETS	0.804	0.716	0.898	0.402	0.358	0.449	CLONAL	1	TRUE	1	0.361272087407601	3		454	780	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243778454	243778454	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	136	346	0	ENST00000263826.5:c.571G>A	p.Ala191Thr	p.A191T	ENST00000263826	NM_005465.4	191	Gca/Aca	6/13	0.361272087407601	3	FACETS	0.853	0.78	0.929	0.853	0.78	0.929	CLONAL	2	TRUE	1	0.361272087407601	3		346	521	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856196	111856196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	59	340	3	ENST00000341259.2:c.247C>T	p.Arg83Trp	p.R83W	ENST00000341259	NM_005475.2	83	Cgg/Tgg	2/8	0.216750734408556	2	FACETS	0.524	0.451	0.605	0.262	0.225	0.303	INDETERMINATE	1	TRUE	0	0.361272087407601	2		343	623	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420205	88420205	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	50	507	0	ENST00000360948.2:c.2481G>C	p.Leu827Phe	p.L827F	ENST00000360948	NM_001012338.2	827	ttG/ttC	19/19	0.322020327334852	1	FACETS	0.394	0.334	0.461	0.394	0.334	0.461	SUBCLONAL	1	TRUE	0	0.361272087407601	1		507	575	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085890	16085890	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	191	485	0	ENST00000281043.3:c.1066C>A	p.Pro356Thr	p.P356T	ENST00000281043	NM_005378.4	356	Cca/Aca	3/3	0.341039352754478	2	FACETS	1	0.987	1	0.643	0.596	0.692	CLONAL	1	TRUE	0	0.361272087407601	2		485	822	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470462	25470462	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	231	648	0	ENST00000264709.3:c.1012G>A	p.Val338Met	p.V338M	ENST00000264709	NM_175629.2	338	Gtg/Atg	8/23	0.341039352754478	2	FACETS	1	0.984	1	0.587	0.546	0.628	CLONAL	1	TRUE	0	0.361272087407601	2		648	1090	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456524	29456524	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	363	625	0	ENST00000389048.3:c.2394C>A	p.Asn798Lys	p.N798K	ENST00000389048	NM_004304.4	798	aaC/aaA	14/29	0.341039352754478	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.361272087407601	2		625	979	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715319	61715319	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	222	736	0	ENST00000401558.2:c.2294G>T	p.Arg765Leu	p.R765L	ENST00000401558	NM_003400.3	765	cGa/cTa	19/25	0.341039352754478	2	FACETS	1	0.984	1	0.594	0.552	0.636	CLONAL	1	TRUE	0	0.361272087407601	2		736	1035	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99180036	99180036	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	388	611	0	ENST00000074304.5:c.1979G>C	p.Ser660Thr	p.S660T	ENST00000074304	NM_001134224.1	660	aGc/aCc	19/26	0.341039352754478	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.361272087407601	2		611	1029	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215215	142215215	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1306647370	NA	P-0029613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	78	245	1	ENST00000350721.4:c.5886G>T	p.Trp1962Cys	p.W1962C	ENST00000350721	NM_001184.3	1962	tgG/tgT	34/47	0.361272087407601	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.361272087407601	1		246	320	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509760	187509761	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0029613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	36	200	0	ENST00000441802.2:c.13752_13753delinsTT	p.Gln4584_His4585delinsHisTyr	p.Q4584_H4585delinsHY	ENST00000441802	NM_005245.3	4584	caGCac/caTTac	27/27	0.216750734408556	2	FACETS	0.595	0.49	0.712	0.297	0.245	0.356	INDETERMINATE	1	TRUE	0	0.361272087407601	2		200	335	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233619	233619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457666982	NA	P-0029613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	43	334	0	ENST00000264932.6:c.923C>T	p.Thr308Met	p.T308M	ENST00000264932	NM_004168.2	308	aCg/aTg	8/15	NA	2	FACETS	0.397	0.331	0.47			1	INDETERMINATE	1	TRUE	NA	0.361272087407601	2		334	600	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449511	31449511	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	56	297	0	ENST00000344624.3:c.2698C>T	p.Pro900Ser	p.P900S	ENST00000344624		900	Cca/Tca	19/33	0.361272087407601	4	FACETS	0.808	0.693	0.934			1	CLONAL	1	TRUE	NA	0.361272087407601	4		297	522	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645169	86645169	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	60	294	0	ENST00000274376.6:c.1241G>T	p.Arg414Leu	p.R414L	ENST00000274376	NM_002890.2	414	cGg/cTg	8/25	0.361272087407601	1	FACETS	0.935	0.812	1	0.935	0.812	1	CLONAL	1	TRUE	0	0.361272087407601	1		294	291	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151893097	151893097	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0029613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	58	298	1	ENST00000262189.6:c.4274-1G>T		p.X1425_splice	ENST00000262189	NM_170606.2	1425			1	2	FACETS	0.811	0.699	0.932	0.811	0.699	0.932	CLONAL	1	TRUE	1	0.361272087407601	2		299	396	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104759	69104759	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs139672596	NA	P-0029613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	50	414	1	ENST00000288368.4:c.4603C>T	p.Arg1535Trp	p.R1535W	ENST00000288368	NM_024870.2	1535	Cgg/Tgg	37/40	0.341039352754478	2	FACETS	0.49	0.415	0.572	0.245	0.207	0.286	SUBCLONAL	1	TRUE	0	0.361272087407601	2		415	565	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069098	5069099	+	missense_variant	Missense_Mutation	DNP	AG	AG	TT	novel	NA	P-0029613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	80	448	1	ENST00000381652.3:c.1403_1404delinsTT	p.Lys468Ile	p.K468I	ENST00000381652	NM_004972.3	468	aAG/aTT	11/25	1	2	FACETS	0.717	0.631	0.808	0.717	0.631	0.808	SUBCLONAL	1	TRUE	1	0.361272087407601	2		449	618	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499763	8499763	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	153	514	0	ENST00000356435.5:c.2206G>T	p.Val736Leu	p.V736L	ENST00000356435		736	Gtg/Ttg	14/35	1	2	FACETS	0.985	0.901	1	0.985	0.901	1	CLONAL	1	TRUE	1	0.361272087407601	2		514	860	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27190611	27190611	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	65	654	1	ENST00000380036.4:c.1412T>A	p.Phe471Tyr	p.F471Y	ENST00000380036	NM_000459.3	471	tTt/tAt	10/23	0.139136959542823	4	FACETS	0.493	0.426	0.566	0.247	0.213	0.283	INDETERMINATE	1	TRUE	2	0.361272087407601	4		655	993	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209627	98209627	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	142	450	1	ENST00000331920.6:c.3911G>T	p.Arg1304Met	p.R1304M	ENST00000331920	NM_000264.3	1304	aGg/aTg	23/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.361272087407601	2		451	700	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820343	139820343	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	66	544	0	ENST00000247668.2:c.1496C>A	p.Thr499Lys	p.T499K	ENST00000247668	NM_021138.3	499	aCa/aAa	11/11	1	2	FACETS	0.422	0.365	0.484	0.422	0.365	0.484	SUBCLONAL	1	TRUE	1	0.361272087407601	2		544	866	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412756	63412756	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	103	529	0	ENST00000330258.3:c.411G>T	p.Leu137Phe	p.L137F	ENST00000330258	NM_152424.3	137	ttG/ttT	2/2	0.361272087407601	1	FACETS	0.73	0.654	0.81	0.73	0.654	0.81	SUBCLONAL	1	TRUE	0	0.361272087407601	1		529	640	SUCCESS
AR	367	MSKCC	GRCh37	X	66766414	66766414	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	15	146	0	ENST00000374690.3:c.1426G>A	p.Gly476Arg	p.G476R	ENST00000374690	NM_000044.3	476	Gga/Aga	1/8	0.361272087407601	1	FACETS	0.33	0.242	0.436	0.33	0.242	0.436	SUBCLONAL	1	TRUE	0	0.361272087407601	1		146	206	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0029614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	93	591	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.375209371407814	2		591	430	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624275	89624275	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204910	NA	P-0029614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	85	469	0	ENST00000371953.3:c.49C>T	p.Gln17Ter	p.Q17*	ENST00000371953	NM_000314.4	17	Caa/Taa	1/9	0.375209371407814	1	FACETS	0.969	0.862	1	0.969	0.862	1	CLONAL	1	TRUE	0	0.375209371407814	1		469	380	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984935	9984935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	110	546	0	ENST00000330684.3:c.1030G>A	p.Asp344Asn	p.D344N	ENST00000330684	NM_001134407.1	344	Gat/Aat	4/13	1	2	FACETS	0.985	0.888	1	0.985	0.888	1	CLONAL	1	TRUE	1	0.375209371407814	2		546	595	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261382	16261382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	119	554	0	ENST00000375759.3:c.8647C>T	p.His2883Tyr	p.H2883Y	ENST00000375759	NM_015001.2	2883	Cat/Tat	11/15	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.375209371407814	2		554	614	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818343	43818343	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	126	654	0	ENST00000372470.3:c.1808C>T	p.Pro603Leu	p.P603L	ENST00000372470	NM_005373.2	603	cCc/cTc	12/12	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.375209371407814	2		654	648	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913926	32913926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358767	NA	P-0029614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	79	603	0	ENST00000380152.3:c.5434G>A	p.Glu1812Lys	p.E1812K	ENST00000380152		1812	Gaa/Aaa	11/27	1	2	FACETS	0.818	0.721	0.921	0.818	0.721	0.921	CLONAL	1	TRUE	1	0.375209371407814	2		603	515	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38641648	38641648	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	88	520	0	ENST00000299084.4:c.608A>G	p.Asp203Gly	p.D203G	ENST00000299084	NM_152594.2	203	gAc/gGc	6/7	0.375209371407814	3	FACETS	0.901	0.8	1	0.451	0.4	0.505	CLONAL	1	TRUE	1	0.375209371407814	3		520	618	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032237	10032237	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	124	655	1	ENST00000330684.3:c.586G>A	p.Val196Met	p.V196M	ENST00000330684	NM_001134407.1	196	Gtg/Atg	3/13	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.375209371407814	2		656	594	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582040	189582040	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	162	424	0	ENST00000264731.3:c.599A>T	p.Lys200Ile	p.K200I	ENST00000264731	NM_003722.4	200	aAa/aTa	5/14	0.337024511639162	3	FACETS	0.906	0.836	0.978	0.906	0.836	0.978	CLONAL	2	TRUE	1	0.375209371407814	3		424	566	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294054	1294054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	147	1036	2	ENST00000310581.5:c.947C>T	p.Pro316Leu	p.P316L	ENST00000310581	NM_198253.2	316	cCc/cTc	2/16	1	2	FACETS	0.928	0.848	1	0.928	0.848	1	CLONAL	1	TRUE	1	0.375209371407814	2		1038	844	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751585	57751585	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	61	237	0	ENST00000274289.3:c.1406G>A	p.Gly469Glu	p.G469E	ENST00000274289	NM_006622.3	469	gGa/gAa	11/14	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.375209371407814	2		237	276	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453137	140453138	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGT	novel	NA	P-0029614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	246	426	0	ENST00000288602.6:c.1795_1797dup	p.Thr599dup	p.T599dup	ENST00000288602	NM_004333.4	599	-/ACA	15/18	0.375209371407814	3	FACETS	0.944	0.891	0.997			1	CLONAL	3	TRUE	NA	0.375209371407814	3		426	550	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635148	87635148	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1324578301	NA	P-0029614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	99	414	0	ENST00000277120.3:c.2200C>T	p.Arg734Cys	p.R734C	ENST00000277120		734	Cgc/Tgc	18/19	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.375209371407814	2		414	495	SUCCESS
AR	367	MSKCC	GRCh37	X	66905968	66905968	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1421832550	NA	P-0029614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	59	192	0	ENST00000374690.3:c.1885G>A	p.Ala629Thr	p.A629T	ENST00000374690	NM_000044.3	629	Gcc/Acc	3/8	1	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.375209371407814	1		192	183	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	97	394	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.248216390407017	2		394	775	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0029615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	139	756	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.248216390407017	1	FACETS	0.973	0.885	1	0.973	0.885	1	CLONAL	1	TRUE	0	0.248216390407017	1		756	1008	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089574	27089574	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	127	647	0	ENST00000324856.7:c.2530C>T	p.Gln844Ter	p.Q844*	ENST00000324856	NM_006015.4	844	Cag/Tag	8/20	0.248216390407017	1	FACETS	0.905	0.819	0.997	0.905	0.819	0.997	CLONAL	1	TRUE	0	0.248216390407017	1		647	990	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032479	12032480	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0029615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	40	349	0	ENST00000353533.5:c.915_916delinsAA	p.Phe305_Pro306delinsLeuThr	p.F305_P306delinsLT	ENST00000353533	NM_003010.3	305	ttTCct/ttAAct	9/11	0.248216390407017	1	FACETS	0.677	0.563	0.804	0.677	0.563	0.804	SUBCLONAL	1	TRUE	0	0.248216390407017	1		349	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0029617-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	180	1069	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.266349301250817	2		1071	1290	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0029617-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	9	300	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.266349301250817	1	FACETS	0.134	0.088	0.194	0.134	0.088	0.194	SUBCLONAL	1	TRUE	0	0.266349301250817	1		300	436	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323150	31323150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029617-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	134	693	0	ENST00000412585.2:c.839G>A	p.Arg280Lys	p.R280K	ENST00000412585	NM_005514.6	280	aGa/aAa	4/8	0.266349301250817	1	FACETS	0.87	0.79	0.956	0.87	0.79	0.956	CLONAL	1	TRUE	0	0.266349301250817	1		693	1002	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0029622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	456	571	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.810248191279897	1	FACETS	0.943	0.911	0.974	0.943	0.911	0.974	CLONAL	1	TRUE	0	0.813639186718087	1		571	705	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661387	227661387	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	371	403	0	ENST00000305123.5:c.2068C>G	p.Pro690Ala	p.P690A	ENST00000305123	NM_005544.2	690	Cct/Gct	1/2	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.813639186718087	2		403	881	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578467	7578467	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	496	844	0	ENST00000269305.4:c.463A>C	p.Thr155Pro	p.T155P	ENST00000269305	NM_001126112.2	155	Acc/Ccc	5/11	0.255250476316681	3	FACETS	1	0.991	1	0.746	0.715	0.778	CLONAL	2	TRUE	0	0.405892402587155	3		844	1313	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480133	20480133	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	177	531	2	ENST00000346618.3:c.454del	p.Thr152ProfsTer43	p.T152Pfs*43	ENST00000346618	NM_001949.4	150	ttA/tt	2/7	0.287292234726525	3	FACETS	1	0.987	1	0.448	0.413	0.484	CLONAL	1	TRUE	0	0.405892402587155	3		533	781	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188513	11188513	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	201	404	0	ENST00000361445.4:c.5908C>G	p.Gln1970Glu	p.Q1970E	ENST00000361445	NM_004958.3	1970	Cag/Gag	42/58	0.264153977114297	3	FACETS	0.819	0.762	0.879	0.819	0.762	0.879	CLONAL	2	TRUE	1	0.405892402587155	3		404	727	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245025	133245025	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs36120395	NA	P-0029623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	216	708	0	ENST00000320574.5:c.2090C>A	p.Pro697His	p.P697H	ENST00000320574	NM_006231.2	697	cCc/cAc	19/49	0.136385184981293	4	FACETS	1	0.986	1	0.628	0.583	0.674	INDETERMINATE	1	TRUE	2	0.405892402587155	4		708	1192	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339033	225339033	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	148	566	0	ENST00000264414.4:c.2236G>T	p.Glu746Ter	p.E746*	ENST00000264414	NM_003590.4	746	Gaa/Taa	16/16	0.136385184981293	4	FACETS	0.791	0.725	0.86	0.791	0.725	0.86	INDETERMINATE	2	TRUE	2	0.405892402587155	4		566	648	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560922	9560922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	38	430	1	ENST00000353224.5:c.860G>A	p.Arg287Lys	p.R287K	ENST00000353224	NM_177990.2	287	aGg/aAg	4/10	0.231825239886193	4	FACETS	0.353	0.291	0.423	0.177	0.145	0.212	INDETERMINATE	1	TRUE	2	0.405892402587155	4		431	745	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403529	138403529	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	283	704	0	ENST00000289153.2:c.2253C>A	p.Tyr751Ter	p.Y751*	ENST00000289153	NM_006219.2	751	taC/taA	15/22	0.305423711732745	5	FACETS	0.801	0.751	0.853	0.534	0.501	0.569	CLONAL	2	TRUE	2	0.405892402587155	5		704	1400	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80088551	80088551	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0029623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	137	352	0	ENST00000265081.6:c.2544-1G>A		p.X848_splice	ENST00000265081	NM_002439.4	848			0.157564149543223	3	FACETS	1	0.963	1			1	INDETERMINATE	2	TRUE	NA	0.405892402587155	3		352	376	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418278	139418278	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	876	936	2	ENST00000277541.6:c.294C>A	p.Cys98Ter	p.C98*	ENST00000277541	NM_017617.3	98	tgC/tgA	3/34	0.405892402587155	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	0	0.405892402587155	3		938	1696	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409831	63409831	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	100	239	0	ENST00000330258.3:c.3336G>C	p.Glu1112Asp	p.E1112D	ENST00000330258	NM_152424.3	1112	gaG/gaC	2/2	0.222537135686031	2	FACETS	1	0.975	1			1	INDETERMINATE	1	TRUE	NA	0.405892402587155	2		239	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0029624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	150	523	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.17895163915655	2	FACETS	0.977	0.893	1	0.977	0.893	1	CLONAL	2	FALSE	0	0.17895163915655	2		523	858	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0029624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	120	412	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.174397948618557	4	FACETS	1	0.926	1			1	CLONAL	2	FALSE	NA	0.17895163915655	4		412	768	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0029624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	115	443	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.17724134234668	3	FACETS	0.88	0.792	0.972	0.88	0.792	0.972	CLONAL	2	FALSE	1	0.17895163915655	3		443	796	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971069	21971069	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	51	391	0	ENST00000304494.5:c.289C>G	p.Leu97Val	p.L97V	ENST00000304494	NM_000077.4	97	Ctg/Gtg	2/3	0.17895163915655	1	FACETS	0.828	0.703	0.965	0.828	0.703	0.965	CLONAL	1	FALSE	0	0.17895163915655	1		391	627	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891687	28891687	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1441660026	NA	P-0029624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	67	596	0	ENST00000282397.4:c.3334C>A	p.Arg1112Ser	p.R1112S	ENST00000282397	NM_002019.4	1112	Cgc/Agc	25/30	1	2	FACETS	0.852	0.739	0.975	0.852	0.739	0.975	CLONAL	1	FALSE	1	0.17895163915655	2		596	879	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828630	72828630	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	84	599	0	ENST00000268489.5:c.7951G>C	p.Glu2651Gln	p.E2651Q	ENST00000268489	NM_006885.3	2651	Gaa/Caa	9/10	1	2	FACETS	0.918	0.808	1	0.918	0.808	1	CLONAL	1	FALSE	1	0.17895163915655	2		599	1023	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37863276	37863324	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCCAGTCCCGAGACCCACCTGGACATGCTCCGCCACCTCTACCAGGG	CTGCCAGTCCCGAGACCCACCTGGACATGCTCCGCCACCTCTACCAGGG	-	novel	NA	P-0029624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	124	642	0	ENST00000269571.5:c.114_162del	p.Ser38ArgfsTer38	p.S38Rfs*38	ENST00000269571		36	cCTGCCAGTCCCGAGACCCACCTGGACATGCTCCGCCACCTCTACCAGGGc/cc	2/27	0.17724134234668	3	FACETS	0.795	0.718	0.876	0.795	0.718	0.876	SUBCLONAL	2	FALSE	1	0.17895163915655	3		642	950	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909736	50909736	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0029624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1185	96	797	1	ENST00000440232.2:c.1456A>T	p.Lys486Ter	p.K486*	ENST00000440232	NM_002691.3	486	Aag/Tag	12/27	0.17724134234668	3	FACETS	0.913	0.81	1	0.456	0.405	0.511	CLONAL	1	FALSE	1	0.17895163915655	3		798	1281	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724289	52724289	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	72	536	0	ENST00000322088.6:c.1421G>T	p.Gly474Val	p.G474V	ENST00000322088	NM_014225.5	474	gGg/gTg	12/15	0.17724134234668	3	FACETS	0.875	0.762	0.997	0.437	0.381	0.499	CLONAL	1	FALSE	1	0.17895163915655	3		536	1002	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733244	40733244	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	65	590	1	ENST00000373198.4:c.3562del	p.Gln1188ArgfsTer17	p.Q1188Rfs*17	ENST00000373198	NM_133170.3	1188	Cag/ag	26/32	1	2	FACETS	0.747	0.645	0.857	0.747	0.645	0.857	SUBCLONAL	1	FALSE	1	0.17895163915655	2		591	973	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86682652	86682652	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	25	293	0	ENST00000274376.6:c.2857A>G	p.Met953Val	p.M953V	ENST00000274376	NM_002890.2	953	Atg/Gtg	23/25	1	2	FACETS	0.632	0.497	0.788	0.632	0.497	0.788	SUBCLONAL	1	FALSE	1	0.17895163915655	2		293	442	SUCCESS
MET	4233	MSKCC	GRCh37	7	116409820	116409820	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	49	305	0	ENST00000397752.3:c.2705A>T	p.Lys902Ile	p.K902I	ENST00000397752	NM_000245.2	902	aAa/aTa	12/21	0.17724134234668	3	FACETS	1	0.894	1	0.536	0.453	0.626	CLONAL	1	FALSE	1	0.17895163915655	3		305	557	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391149	139391149	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	80	683	1	ENST00000277541.6:c.7042G>T	p.Gly2348Cys	p.G2348C	ENST00000277541	NM_017617.3	2348	Ggc/Tgc	34/34	1	2	FACETS	0.951	0.835	1	0.951	0.835	1	CLONAL	1	FALSE	1	0.17895163915655	2		684	940	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0029625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	488	771	1	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.490253639995917	2	FACETS	0.97	0.933	1	0.97	0.933	1	CLONAL	2	TRUE	0	0.500892122355707	2		772	1004	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731167	162731167	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs769041297	NA	P-0029625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	563	440	0	ENST00000367921.3:c.1022G>T	p.Arg341Leu	p.R341L	ENST00000367921	NM_006182.2	341	cGa/cTa	9/18	0.492706806382745	4	FACETS	0.98	0.95	1	0.98	0.95	1	CLONAL	4	TRUE	0	0.500892122355707	4		440	861	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32905132	32905132	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	402	509	1	ENST00000380152.3:c.758G>T	p.Ser253Ile	p.S253I	ENST00000380152		253	aGt/aTt	9/27	0.48306222795067	2	FACETS	0.906	0.866	0.946	0.906	0.866	0.946	CLONAL	2	TRUE	0	0.500892122355707	2		510	886	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955568	48955568	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	332	378	0	ENST00000267163.4:c.1684G>C	p.Ala562Pro	p.A562P	ENST00000267163	NM_000321.2	562	Gca/Cca	17/27	0.500892122355707	3	FACETS	0.893	0.853	0.932	0.893	0.853	0.932	CLONAL	3	TRUE	0	0.500892122355707	3		378	619	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218809	5218809	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	543	657	0	ENST00000357368.4:c.3924C>A	p.Asn1308Lys	p.N1308K	ENST00000357368	NM_002850.3	1308	aaC/aaA	24/38	0.48070056812007	3	FACETS	0.878	0.847	0.909	0.878	0.847	0.909	CLONAL	3	TRUE	0	0.500892122355707	3		657	1029	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260135	19260135	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	516	714	0	ENST00000162023.5:c.158G>T	p.Arg53Leu	p.R53L	ENST00000162023		53	cGc/cTc	7/13	0.490253639995917	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.500892122355707	2		714	984	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564503	55564503	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	153	463	0	ENST00000288135.5:c.391G>T	p.Asp131Tyr	p.D131Y	ENST00000288135	NM_000222.2	131	Gac/Tac	3/21	0.498709037303222	4	FACETS	1	0.919	1	0.335	0.306	0.365	CLONAL	1	TRUE	1	0.500892122355707	4		463	913	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526981	31526981	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2310	580	675	0	ENST00000344624.3:c.59G>T	p.Arg20Leu	p.R20L	ENST00000344624		20	cGa/cTa	2/33	0.500892122355707	11	FACETS	0.869	0.831	0.908	0.326	0.311	0.341	CLONAL	3	TRUE	3	0.500892122355707	11		675	2890	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152461	56152461	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	237	251	0	ENST00000399503.3:c.517T>A	p.Leu173Met	p.L173M	ENST00000399503	NM_005921.1	173	Ttg/Atg	2/20	0.500892122355707	3	FACETS	0.896	0.849	0.943	0.896	0.849	0.943	CLONAL	3	TRUE	0	0.500892122355707	3		251	440	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412749	63412749	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	330	288	0	ENST00000330258.3:c.418G>T	p.Gly140Cys	p.G140C	ENST00000330258	NM_152424.3	140	Ggc/Tgc	2/2	0.480114899315826	2	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.500892122355707	2		288	529	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947596	48947596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1566196458	NA	P-0029628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	115	540	0	ENST00000267163.4:c.1183C>T	p.Gln395Ter	p.Q395*	ENST00000267163	NM_000321.2	395	Caa/Taa	12/27	0.516275519245964	5	FACETS	0.82	0.738	0.908	0.273	0.246	0.303	CLONAL	1	TRUE	2	0.516275519245964	5		540	964	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28600635	28600635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1383227659	NA	P-0029628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	81	764	0	ENST00000253063.3:c.986G>A	p.Arg329Lys	p.R329K	ENST00000253063	NM_031459.4	329	aGa/aAa	7/10	0.487592144859854	3	FACETS	0.321	0.282	0.364	0.161	0.141	0.182	SUBCLONAL	1	TRUE	1	0.516275519245964	3		764	1229	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251911	153251911	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	497	600	2	ENST00000281708.4:c.1095G>A	p.Trp365Ter	p.W365*	ENST00000281708	NM_033632.3	365	tgG/tgA	7/12	0.516275519245964	3	FACETS	0.968	0.935	1	0.968	0.935	1	CLONAL	3	TRUE	0	0.516275519245964	3		602	834	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0029630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	147	489	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.210605218066577	2		489	1034	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	181	578	1	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	NA	2	FACETS	0.779	0.718	0.843			1	INDETERMINATE	2	TRUE	NA	0.210605218066577	2		579	1103	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10283806	10283806	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	87	652	3	ENST00000340748.4:c.680C>T	p.Ser227Leu	p.S227L	ENST00000340748		227	tCa/tTa	8/40	1	2	FACETS	0.638	0.563	0.72	0.638	0.563	0.72	SUBCLONAL	1	TRUE	1	0.210605218066577	2		655	1294	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	171	404	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.97	0.898	1	0.97	0.898	1	CLONAL	1	TRUE	1	0.635473199582819	2		404	555	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149260	119149260	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs868103494	NA	P-0029632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	113	601	0	ENST00000264033.4:c.1268T>A	p.Ile423Asn	p.I423N	ENST00000264033	NM_005188.3	423	aTt/aAt	9/16	0.635473199582819	1	FACETS	0.355	0.319	0.392	0.355	0.319	0.392	SUBCLONAL	1	TRUE	0	0.635473199582819	1		601	684	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720670	89720670	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786204875	NA	P-0029632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	202	245	0	ENST00000371953.3:c.821G>T	p.Trp274Leu	p.W274L	ENST00000371953	NM_000314.4	274	tGg/tTg	8/9	0.635473199582819	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.635473199582819	1		245	379	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585418	29585418	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	312	666	0	ENST00000356175.3:c.4168del	p.Leu1390SerfsTer17	p.L1390Sfs*17	ENST00000356175	NM_000267.3	1389	ttC/tt	31/57	0.635473199582819	1	FACETS	0.979	0.931	1	0.979	0.931	1	CLONAL	1	TRUE	0	0.635473199582819	1		666	684	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302812	15302812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	361	859	0	ENST00000263388.2:c.638G>A	p.Arg213Lys	p.R213K	ENST00000263388	NM_000435.2	213	aGg/aAg	4/33	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.635473199582819	2		859	1106	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161733	47161733	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0029632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	180	313	0	ENST00000409792.3:c.4393A>T	p.Lys1465Ter	p.K1465*	ENST00000409792	NM_014159.6	1465	Aag/Tag	3/21	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.635473199582819	2		313	560	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0029635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	457	591	0				ENST00000310581	NM_198253.2	-/1132			0.500181574046084	3	FACETS	0.961	0.92	1	0.961	0.92	1	CLONAL	2	TRUE	1	0.570799775923739	3		591	1071	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414967	78414967	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	311	471	3	ENST00000370768.2:c.1799C>A	p.Pro600Gln	p.P600Q	ENST00000370768	NM_003902.3	600	cCg/cAg	19/20	0.16821258858183	3	FACETS	0.966	0.917	1	0.644	0.611	0.677	INDETERMINATE	2	TRUE	0	0.570799775923739	3		474	725	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724607	112724607	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	100	621	0	ENST00000369452.4:c.491C>G	p.Ser164Cys	p.S164C	ENST00000369452	NM_007373.3	164	tCt/tGt	2/9	0.197514570051273	2	FACETS	0.506	0.452	0.564	0.253	0.226	0.282	INDETERMINATE	1	TRUE	0	0.570799775923739	2		621	692	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	464379	464379	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0029635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	118	680	0	ENST00000399788.2:c.815C>G	p.Ser272Ter	p.S272*	ENST00000399788	NM_001042603.1	272	tCa/tGa	7/28	0.248781952694138	3	FACETS	0.611	0.551	0.675	0.204	0.183	0.225	INDETERMINATE	1	TRUE	0	0.570799775923739	3		680	870	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866632	37866632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773759626	NA	P-0029635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	134	688	1	ENST00000269571.5:c.799C>T	p.His267Tyr	p.H267Y	ENST00000269571		267	Cac/Tac	7/27	0.185934489285774	2	FACETS	0.492	0.446	0.54	0.246	0.223	0.27	INDETERMINATE	1	TRUE	0	0.570799775923739	2		689	955	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991722	25991722	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	93	440	0	ENST00000435504.4:c.520C>T	p.Gln174Ter	p.Q174*	ENST00000435504		174	Cag/Tag	7/13	0.185934489285774	2	FACETS	0.445	0.395	0.497	0.222	0.197	0.249	INDETERMINATE	1	TRUE	0	0.570799775923739	2		440	733	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096539	178096539	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	62	367	0	ENST00000397062.3:c.792C>G	p.Asn264Lys	p.N264K	ENST00000397062	NM_006164.4	264	aaC/aaG	5/5	0.185934489285774	2	FACETS	0.495	0.428	0.567	0.247	0.214	0.284	INDETERMINATE	1	TRUE	0	0.570799775923739	2		367	439	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180171	38180171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	83	440	0	ENST00000396334.3:c.19G>A	p.Glu7Lys	p.E7K	ENST00000396334	NM_002468.4	7	Gag/Aag	1/5	1	2	FACETS	0.62	0.549	0.695	0.62	0.549	0.695	SUBCLONAL	1	TRUE	1	0.570799775923739	2		440	469	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629328	187629328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772458580	NA	P-0029635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	150	680	2	ENST00000441802.2:c.1654G>A	p.Glu552Lys	p.E552K	ENST00000441802	NM_005245.3	552	Gaa/Aaa	2/27	0.534024099910273	1	FACETS	0.409	0.373	0.446	0.409	0.373	0.446	SUBCLONAL	1	TRUE	0	0.570799775923739	1		682	919	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045882	26045882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	194	573	1	ENST00000540144.1:c.244G>A	p.Asp82Asn	p.D82N	ENST00000540144	NM_003531.2	82	Gac/Aac	1/1	0.570799775923739	2	FACETS	0.929	0.862	0.997	0.464	0.431	0.499	CLONAL	1	TRUE	0	0.570799775923739	2		574	732	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331669	8331669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	96	526	0	ENST00000356435.5:c.5447C>A	p.Ser1816Tyr	p.S1816Y	ENST00000356435		1816	tCc/tAc	33/35	0.570799775923739	3	FACETS	0.544	0.484	0.608	0.272	0.242	0.304	SUBCLONAL	1	TRUE	1	0.570799775923739	3		526	795	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44920576	44920576	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	63	469	0	ENST00000377967.4:c.1337C>G	p.Ser446Cys	p.S446C	ENST00000377967	NM_021140.2	446	tCt/tGt	14/29	0.570799775923739	4	FACETS	0.383	0.33	0.44	0.191	0.165	0.22	SUBCLONAL	1	TRUE	2	0.570799775923739	4		469	906	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045482	47045482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1758	161	847	1	ENST00000377604.3:c.2449C>T	p.Arg817Cys	p.R817C	ENST00000377604	NM_001204468.1	817	Cgt/Tgt	22/24	0.570799775923739	4	FACETS	0.462	0.421	0.504	0.231	0.21	0.252	SUBCLONAL	1	TRUE	2	0.570799775923739	4		848	1919	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651663	48651663	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1978	183	924	0	ENST00000376670.3:c.829C>G	p.Pro277Ala	p.P277A	ENST00000376670	NM_002049.3	277	Ccc/Gcc	5/6	0.570799775923739	4	FACETS	0.466	0.428	0.506	0.233	0.214	0.253	SUBCLONAL	1	TRUE	2	0.570799775923739	4		924	2161	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652236	48652236	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1696	142	753	1	ENST00000376670.3:c.907C>T	p.Gln303Ter	p.Q303*	ENST00000376670	NM_002049.3	303	Cag/Tag	6/6	0.570799775923739	4	FACETS	0.425	0.386	0.467	0.213	0.193	0.234	SUBCLONAL	1	TRUE	2	0.570799775923739	4		754	1838	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0029637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	133	532	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.63	0.572	0.692	0.63	0.572	0.692	SUBCLONAL	1	TRUE	1	0.468884553091686	2		532	900	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481530	20481530	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	53	340	1	ENST00000346618.3:c.599G>T	p.Gly200Val	p.G200V	ENST00000346618	NM_001949.4	200	gGg/gTg	3/7	1	2	FACETS	0.397	0.338	0.461	0.397	0.338	0.461	SUBCLONAL	1	TRUE	1	0.468884553091686	2		341	570	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0029637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	42	348	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.25	0.207	0.296	0.25	0.207	0.296	SUBCLONAL	1	TRUE	1	0.468884553091686	2		348	718	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028898	47028898	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0029637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	41	489	0	ENST00000377604.3:c.201+1G>T		p.X67_splice	ENST00000377604	NM_001204468.1	67			1	2	FACETS	0.282	0.234	0.335	0.282	0.234	0.335	SUBCLONAL	1	TRUE	1	0.468884553091686	2		489	621	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714396	40714396	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1176843344	NA	P-0029637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	60	528	1	ENST00000373198.4:c.4001G>T	p.Arg1334Ile	p.R1334I	ENST00000373198	NM_133170.3	1334	aGa/aTa	29/32	1	2	FACETS	0.342	0.294	0.394	0.342	0.294	0.394	SUBCLONAL	1	TRUE	1	0.468884553091686	2		529	749	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35857096	35857096	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	28	334	0	ENST00000303115.3:c.17C>G	p.Thr6Arg	p.T6R	ENST00000303115	NM_002185.3	6	aCa/aGa	1/8	1	2	FACETS	0.217	0.172	0.267	0.217	0.172	0.267	SUBCLONAL	1	TRUE	1	0.468884553091686	2		334	551	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944842	31944842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1239	310	963	0	ENST00000340398.3:c.259G>A	p.Ala87Thr	p.A87T	ENST00000340398	NM_001013699.2	87	Gca/Aca	1/1	0.129778163934311	4	FACETS	0.788	0.741	0.837	0.526	0.494	0.558	INDETERMINATE	2	TRUE	1	0.340185061048821	4		963	1549	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670843	134670843	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	113	470	0	ENST00000398015.3:c.754C>T	p.Arg252Ter	p.R252*	ENST00000398015	NM_004441.4	252	Cga/Tga	3/16	0.340185061048821	2	FACETS	1	0.971	1	0.599	0.54	0.66	CLONAL	1	TRUE	0	0.340185061048821	2		470	555	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576853	7576853	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs11575996	NA	P-0029638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	327	745	0	ENST00000269305.4:c.993G>T	p.Gln331His	p.Q331H	ENST00000269305	NM_001126112.2	331	caG/caT	9/11	0.340185061048821	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.340185061048821	2		745	875	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127424	17127424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372918705	NA	P-0029638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	414	892	3	ENST00000285071.4:c.430G>A	p.Gly144Arg	p.G144R	ENST00000285071	NM_144997.5	144	Gga/Aga	6/14	0.340185061048821	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.340185061048821	2		895	1051	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037402	12037402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765031845	NA	P-0029638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	312	887	0	ENST00000396373.4:c.1033G>A	p.Val345Ile	p.V345I	ENST00000396373	NM_001987.4	345	Gtc/Atc	6/8	0.129778163934311	4	FACETS	0.998	0.941	1	0.666	0.627	0.705	INDETERMINATE	2	TRUE	1	0.340185061048821	4		887	1231	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15280904	15280904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1251693132	NA	P-0029638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	382	900	1	ENST00000263388.2:c.5192G>A	p.Arg1731Gln	p.R1731Q	ENST00000263388	NM_000435.2	1731	cGg/cAg	28/33	0.340185061048821	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.340185061048821	2		901	985	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240768	55240768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1266662784	NA	P-0029638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	462	1149	3	ENST00000275493.2:c.2012G>A	p.Arg671His	p.R671H	ENST00000275493	NM_005228.3	671	cGc/cAc	17/28	0.340185061048821	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.340185061048821	2		1152	1273	SUCCESS
ATM	472	MSKCC	GRCh37	11	108168092	108168092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	126	465	0	ENST00000278616.4:c.4988G>A	p.Gly1663Asp	p.G1663D	ENST00000278616	NM_000051.3	1663	gGt/gAt	33/63	0.340185061048821	2	FACETS	0.803	0.732	0.877	0.803	0.732	0.877	CLONAL	2	TRUE	0	0.340185061048821	2		465	461	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3645686	3645686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769084265	NA	P-0029638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1480	223	927	0	ENST00000294008.3:c.1933G>A	p.Val645Met	p.V645M	ENST00000294008	NM_032444.2	645	Gtg/Atg	9/15	0.126131568683203	5	FACETS	1	0.981	1	0.388	0.359	0.417	INDETERMINATE	1	TRUE	2	0.340185061048821	5		927	1703	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647972	3647972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138799572	NA	P-0029638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1395	488	1204	2	ENST00000294008.3:c.1192C>T	p.Arg398Trp	p.R398W	ENST00000294008	NM_032444.2	398	Cgg/Tgg	6/15	0.126131568683203	5	FACETS	1	0.991	1	0.767	0.732	0.803	INDETERMINATE	2	TRUE	2	0.340185061048821	5		1206	1883	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352533	89352533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771447879	NA	P-0029638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	254	691	2	ENST00000301030.4:c.806C>T	p.Thr269Met	p.T269M	ENST00000301030	NM_001256183.1	269	aCg/aTg	8/13	0.126131568683203	5	FACETS	0.942	0.881	1	0.628	0.587	0.67	INDETERMINATE	2	TRUE	2	0.340185061048821	5		693	1197	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032080	48032082	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	rs587779265	NA	P-0029638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	177	417	0	ENST00000234420.5:c.3473_3475del	p.Cys1158del	p.C1158del	ENST00000234420	NM_000179.2	1157	gGTTgt/ggt	6/10	0.340185061048821	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	0	0.340185061048821	2		417	512	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62309632	62309632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771452777	NA	P-0029638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	160	832	2	ENST00000360203.5:c.970C>T	p.Arg324Cys	p.R324C	ENST00000360203	NM_001283009.1	324	Cgc/Tgc	12/35	0.126131568683203	5	FACETS	1	0.97	1	0.377	0.344	0.411	INDETERMINATE	1	TRUE	2	0.340185061048821	5		834	1257	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80074561	80074561	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1006511779	NA	P-0029638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	318	607	1	ENST00000265081.6:c.2341C>T	p.His781Tyr	p.H781Y	ENST00000265081	NM_002439.4	781	Cac/Tac	17/24	0.340185061048821	4	FACETS	0.913	0.864	0.962	0.913	0.864	0.962	CLONAL	3	TRUE	1	0.340185061048821	4		608	915	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527903	157527910	+	frameshift_variant	Frame_Shift_Del	DEL	CATCGATG	CATCGATG	-	novel	NA	P-0029638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	307	677	0	ENST00000346085.5:c.5628_5635del	p.Ile1877ArgfsTer11	p.I1877Rfs*11	ENST00000346085	NM_020732.3	1876	acCATCGATGac/acac	20/20	0.340185061048821	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.340185061048821	2		677	889	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50358670	50358670	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	27	389	1	ENST00000331340.3:c.13G>T	p.Glu5Ter	p.E5*	ENST00000331340	NM_006060.4	5	Gag/Tag	2/8	0.340185061048821	2	FACETS	0.354	0.281	0.437	0.177	0.14	0.219	SUBCLONAL	1	TRUE	0	0.340185061048821	2		390	449	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0029639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	130	483	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.802826536483589	2		483	324	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856623	111856623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	172	238	0	ENST00000341259.2:c.674G>A	p.Arg225His	p.R225H	ENST00000341259	NM_005475.2	225	cGc/cAc	2/8	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.802826536483589	2		238	316	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951166	48951166	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1060503079	NA	P-0029639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	132	421	0	ENST00000267163.4:c.1328C>A	p.Ser443Ter	p.S443*	ENST00000267163	NM_000321.2	443	tCa/tAa	13/27	0.802826536483589	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.802826536483589	1		421	182	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663350	29663350	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0029639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	154	432	2	ENST00000356175.3:c.5944-1G>T		p.X1982_splice	ENST00000356175	NM_000267.3	1982			0.765737125211273	1	FACETS	0.986	0.93	1	0.986	0.93	1	CLONAL	1	TRUE	0	0.802826536483589	1		434	233	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952142	178952142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253171657	NA	P-0029639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	107	324	0	ENST00000263967.3:c.3197C>T	p.Ala1066Val	p.A1066V	ENST00000263967	NM_006218.2	1066	gCa/gTa	21/21	1	2	FACETS	0.828	0.752	0.906	0.828	0.752	0.906	CLONAL	1	TRUE	1	0.802826536483589	2		324	322	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426893	6426893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519948	NA	P-0029639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	197	536	0	ENST00000356142.4:c.86C>T	p.Pro29Leu	p.P29L	ENST00000356142	NM_018890.3	29	cCt/cTt	2/7	1	2	FACETS	0.983	0.919	1	0.983	0.919	1	CLONAL	1	TRUE	1	0.802826536483589	2		536	499	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	52	394	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.13	2		394	786	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0029641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	28	431	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.627	0.499	0.774	0.627	0.499	0.774	SUBCLONAL	1	TRUE	1	0.13	2		431	687	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473722	67473722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs794727798	NA	P-0029641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	90	681	1	ENST00000327367.4:c.802C>T	p.Arg268Cys	p.R268C	ENST00000327367	NM_005902.3	268	Cgc/Tgc	6/9	1	2	FACETS	0.912	0.809	1	1	0.984	1	CLONAL	2	TRUE	1	0.13	2		682	759	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0029641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	23	440	0	ENST00000262160.6:c.1391C>G	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tGa	11/11	1	2	FACETS	0.774	0.602	0.974	0.774	0.602	0.974	CLONAL	1	TRUE	1	0.13	2		440	457	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982095	93982095	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779416238	NA	P-0029641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	46	557	0	ENST00000369303.4:c.1370G>A	p.Arg457Gln	p.R457Q	ENST00000369303	NM_004440.3	457	cGg/cAg	6/17	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.13	2		557	637	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445629	49445629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1369	77	1262	1	ENST00000301067.7:c.1837G>A	p.Glu613Lys	p.E613K	ENST00000301067	NM_003482.3	613	Gag/Aag	10/54	1	2	FACETS	0.819	0.716	0.931	0.819	0.716	0.931	CLONAL	1	TRUE	1	0.13	2		1263	1446	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813324	102813324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377124814	NA	P-0029641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	35	595	0	ENST00000307046.8:c.365G>A	p.Arg122His	p.R122H	ENST00000307046	NM_001111285.1	122	cGt/cAt	3/4	1	2	FACETS	0.784	0.641	0.946	0.784	0.641	0.946	CLONAL	1	TRUE	1	0.13	2		595	687	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0029643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	505	421	0	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	0.663612436481308	3	FACETS	0.946	0.919	0.973	0.946	0.919	0.973	CLONAL	3	TRUE	0	0.663612436481308	3		421	714	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0029643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	434	683	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.663612436481308	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.663612436481308	1		685	747	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	497	578	1	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.663612436481308	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.663612436481308	1		579	761	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092966	29092966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	93	519	0	ENST00000328354.6:c.1018G>A	p.Glu340Lys	p.E340K	ENST00000328354	NM_007194.3	340	Gaa/Aaa	10/15	0.346775587768046	1	FACETS	0.271	0.241	0.304	0.271	0.241	0.304	INDETERMINATE	1	TRUE	0	0.663612436481308	1		519	690	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916957	178916957	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200018596	NA	P-0029643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	651	425	0	ENST00000263967.3:c.344G>T	p.Arg115Leu	p.R115L	ENST00000263967	NM_006218.2	115	cGa/cTa	2/21	0.663612436481308	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.663612436481308	3		425	856	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515049	148515049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	76	526	0	ENST00000320356.2:c.1160G>A	p.Arg387Lys	p.R387K	ENST00000320356	NM_004456.4	387	aGg/aAg	10/20	0.663612436481308	1	FACETS	0.289	0.254	0.327	0.289	0.254	0.327	SUBCLONAL	1	TRUE	0	0.663612436481308	1		526	529	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574431	95574431	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0029643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	29	217	0	ENST00000393063.1:c.2437-1G>C		p.X813_splice	ENST00000393063	NM_030621.3	813			1	2	FACETS	0.311	0.25	0.38	0.311	0.25	0.38	SUBCLONAL	1	TRUE	1	0.663612436481308	2		217	281	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110723	2110723	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1225	170	956	0	ENST00000219476.3:c.1028C>G	p.Thr343Ser	p.T343S	ENST00000219476	NM_000548.3	343	aCc/aGc	11/42	0.165914819856859	3	FACETS	0.489	0.448	0.532	0.245	0.224	0.266	INDETERMINATE	1	TRUE	1	0.663612436481308	3		956	1395	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130294	2130294	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	130	861	1	ENST00000219476.3:c.3526C>A	p.Pro1176Thr	p.P1176T	ENST00000219476	NM_000548.3	1176	Cct/Act	30/42	0.165914819856859	3	FACETS	0.411	0.371	0.452	0.205	0.185	0.226	INDETERMINATE	1	TRUE	1	0.663612436481308	3		862	1271	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050932	13050961	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GTGCTGATCAACAAGGACATCCGTTGCAAG	GTGCTGATCAACAAGGACATCCGTTGCAAG	-	novel	NA	P-0029643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	48	486	0	ENST00000316448.5:c.466_492+3del		p.VLINKDIRCKdel	ENST00000316448	NM_004343.3	155	GTGCTGATCAACAAGGACATCCGTTGCAAG/-	4/9	0.411350135284226	2	FACETS	0.218	0.184	0.256	0.109	0.092	0.128	SUBCLONAL	1	TRUE	0	0.663612436481308	2		486	663	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182662914	182662914	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1403059883	NA	P-0029643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	92	592	0	ENST00000292782.4:c.748C>G	p.Gln250Glu	p.Q250E	ENST00000292782	NM_020640.2	250	Caa/Gaa	7/7	0.663612436481308	3	FACETS	0.289	0.255	0.325	0.096	0.085	0.109	SUBCLONAL	1	TRUE	0	0.663612436481308	3		592	1279	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099098	157099098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	18	233	0	ENST00000346085.5:c.35G>A	p.Gly12Asp	p.G12D	ENST00000346085	NM_020732.3	12	gGc/gAc	1/20	0.470066186173846	1	FACETS	0.129	0.096	0.166	0.129	0.096	0.166	SUBCLONAL	1	TRUE	0	0.663612436481308	1		233	282	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0029645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	59	370	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.52282763962602	1	FACETS	0.453	0.391	0.519	0.453	0.391	0.519	SUBCLONAL	1	TRUE	0	0.536059492611739	1		370	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0029645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	200	906	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.52282763962602	1	FACETS	0.813	0.756	0.871	0.813	0.756	0.871	CLONAL	1	TRUE	0	0.536059492611739	1		906	672	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0029645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	20	393	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.52282763962602	1	FACETS	0.153	0.117	0.196	0.153	0.117	0.196	SUBCLONAL	1	TRUE	0	0.536059492611739	1		393	356	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798968	45798968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781444	NA	P-0029645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	80	828	1	ENST00000450313.1:c.377G>A	p.Arg126Gln	p.R126Q	ENST00000450313	NM_012222.2	126	cGg/cAg	4/16	1	2	FACETS	0.323	0.284	0.366	0.323	0.284	0.366	SUBCLONAL	1	TRUE	1	0.536059492611739	2		829	923	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0029645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	37	674	1	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	1	2	FACETS	0.191	0.157	0.23	0.191	0.157	0.23	SUBCLONAL	1	TRUE	1	0.536059492611739	2		675	723	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775467	39775467	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1048054600	NA	P-0029645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	191	656	3	ENST00000288319.7:c.553G>A	p.Ala185Thr	p.A185T	ENST00000288319	NM_182918.3	185	Gcc/Acc	4/10	1	2	FACETS	0.923	0.855	0.993	0.923	0.855	0.993	CLONAL	1	TRUE	1	0.536059492611739	2		659	772	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279516	1279516	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773813809	NA	P-0029645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	220	1013	3	ENST00000310581.5:c.2020G>A	p.Gly674Ser	p.G674S	ENST00000310581	NM_198253.2	674	Ggc/Agc	5/16	1	2	FACETS	0.899	0.837	0.963	0.899	0.837	0.963	CLONAL	1	TRUE	1	0.536059492611739	2		1016	913	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0029645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	243	610	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.536059492611739	2		610	846	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779253	3779253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867074201	NA	P-0029645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	47	496	0	ENST00000262367.5:c.5795C>T	p.Thr1932Met	p.T1932M	ENST00000262367	NM_004380.2	1932	aCg/aTg	31/31	1	2	FACETS	0.382	0.322	0.448	0.382	0.322	0.448	SUBCLONAL	1	TRUE	1	0.536059492611739	2		496	459	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828024	72828024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200701402	NA	P-0029645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	64	930	2	ENST00000268489.5:c.8557G>A	p.Ala2853Thr	p.A2853T	ENST00000268489	NM_006885.3	2853	Gca/Aca	9/10	1	2	FACETS	0.225	0.194	0.26	0.225	0.194	0.26	SUBCLONAL	1	TRUE	1	0.536059492611739	2		932	1059	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754484	42754484	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777008	NA	P-0029645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	68	721	3	ENST00000222329.4:c.256C>T	p.Arg86Cys	p.R86C	ENST00000222329	NM_006494.2	86	Cgc/Tgc	2/4	1	2	FACETS	0.3	0.26	0.343	0.3	0.26	0.343	SUBCLONAL	1	TRUE	1	0.536059492611739	2		724	847	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863054	56863054	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1266824391	NA	P-0029645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	146	764	2	ENST00000519728.1:c.327del	p.Glu110LysfsTer15	p.E110Kfs*15	ENST00000519728	NM_002350.3	107	acA/ac	5/13	0.515160222052715	4	FACETS	0.789	0.719	0.863	0.263	0.239	0.288	SUBCLONAL	1	TRUE	1	0.536059492611739	4		766	1060	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827474	72827474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749152788	NA	P-0029645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	94	682	0	ENST00000268489.5:c.9107G>A	p.Arg3036Gln	p.R3036Q	ENST00000268489	NM_006885.3	3036	cGg/cAg	9/10	1	2	FACETS	0.424	0.377	0.475	0.424	0.377	0.475	SUBCLONAL	1	TRUE	1	0.536059492611739	2		682	827	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16097786	16097786	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201037902	NA	P-0029645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	32	708	2	ENST00000268712.3:c.98G>A	p.Arg33His	p.R33H	ENST00000268712	NM_006311.3	33	cGc/cAc	2/46	0.52282763962602	1	FACETS	0.161	0.13	0.196	0.161	0.13	0.196	SUBCLONAL	1	TRUE	0	0.536059492611739	1		710	544	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933540	36933540	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3917997	NA	P-0029645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	243	972	0	ENST00000361632.4:c.1747C>T	p.Arg583Cys	p.R583C	ENST00000361632		583	Cgt/Tgt	13/16	1	2	FACETS	0.916	0.856	0.977	0.916	0.856	0.977	CLONAL	1	TRUE	1	0.536059492611739	2		972	990	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699223	117699224	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0029645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	158	490	0	ENST00000369458.3:c.417dup	p.Asn140GlufsTer3	p.N140Efs*3	ENST00000369458	NM_024626.3	139	-/G	3/6	1	2	FACETS	0.96	0.883	1	0.96	0.883	1	CLONAL	1	TRUE	1	0.536059492611739	2		490	614	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226576422	226576430	+	inframe_deletion	In_Frame_Del	DEL	CATCCACTC	CATCCACTC	-	rs767944519	NA	P-0029645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	44	625	0	ENST00000366794.5:c.644_652del	p.Gly215_Asp217del	p.G215_D217del	ENST00000366794	NM_001618.3	215	gGAGTGGATGaa/gaa	5/23	1	2	FACETS	0.232	0.193	0.274	0.232	0.193	0.274	SUBCLONAL	1	TRUE	1	0.536059492611739	2		625	709	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155685	119155685	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	44	464	2	ENST00000264033.4:c.1438C>T	p.Arg480Trp	p.R480W	ENST00000264033	NM_005188.3	480	Cgg/Tgg	10/16	1	2	FACETS	0.319	0.267	0.377	0.319	0.267	0.377	SUBCLONAL	1	TRUE	1	0.536059492611739	2		466	514	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427612	49427612	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	135	550	0	ENST00000301067.7:c.10876del	p.Arg3626GlyfsTer32	p.R3626Gfs*32	ENST00000301067	NM_003482.3	3626	Cgg/gg	39/54	1	2	FACETS	0.867	0.791	0.946	0.867	0.791	0.946	CLONAL	1	TRUE	1	0.536059492611739	2		550	581	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041756	29041756	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0029645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	126	343	0	ENST00000282397.4:c.65-2A>G		p.X22_splice	ENST00000282397	NM_002019.4	22			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.536059492611739	2		343	391	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060611	38060611	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	251	1168	0	ENST00000250448.2:c.1378T>C	p.Tyr460His	p.Y460H	ENST00000250448	NM_004496.3	460	Tac/Cac	2/2	1	2	FACETS	0.837	0.782	0.893	0.837	0.782	0.893	CLONAL	1	TRUE	1	0.536059492611739	2		1168	1119	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647433	23647433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	202	572	1	ENST00000261584.4:c.434G>A	p.Ser145Asn	p.S145N	ENST00000261584	NM_024675.3	145	aGc/aAc	4/13	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.536059492611739	2		573	675	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627769	14627769	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs756719881	NA	P-0029645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	41	698	0	ENST00000254322.2:c.301A>G	p.Met101Val	p.M101V	ENST00000254322	NM_006145.1	101	Atg/Gtg	2/3	1	2	FACETS	0.188	0.156	0.224	0.188	0.156	0.224	SUBCLONAL	1	TRUE	1	0.536059492611739	2		698	813	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024605	31024605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	60	567	0	ENST00000375687.4:c.4090G>A	p.Val1364Ile	p.V1364I	ENST00000375687	NM_015338.5	1364	Gtt/Att	13/13	1	2	FACETS	0.321	0.276	0.37	0.321	0.276	0.37	SUBCLONAL	1	TRUE	1	0.536059492611739	2		567	697	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026859	71026859	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	120	326	0	ENST00000318789.4:c.1363A>G	p.Asn455Asp	p.N455D	ENST00000318789	NM_032682.5	455	Aac/Gac	16/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.536059492611739	2		326	396	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526816	31526816	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs546365755	NA	P-0029645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	74	875	1	ENST00000344624.3:c.224G>A	p.Arg75Gln	p.R75Q	ENST00000344624		75	cGa/cAa	2/33	1	2	FACETS	0.265	0.231	0.302	0.265	0.231	0.302	SUBCLONAL	1	TRUE	1	0.536059492611739	2		876	1040	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293517	137293517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747209166	NA	P-0029645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	125	1184	0	ENST00000481739.1:c.68C>T	p.Thr23Met	p.T23M	ENST00000481739	NM_002957.4	23	aCg/aTg	2/10	1	2	FACETS	0.418	0.377	0.461	0.418	0.377	0.461	SUBCLONAL	1	TRUE	1	0.536059492611739	2		1184	1116	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	201	768	0	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	0.375921570116746	2		768	881	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	169	441	9	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	NA	2	FACETS	0.931	0.863	1			1	INDETERMINATE	2	TRUE	NA	0.375921570116746	2		450	483	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	78	601	0	ENST00000311936.3:c.180_181delinsAA	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggAAaa	3/5	1	2	FACETS	0.635	0.558	0.718	0.635	0.558	0.718	SUBCLONAL	1	TRUE	1	0.375921570116746	2		601	653	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825519	50825519	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	73	517	0	ENST00000398568.2:c.2156del	p.Asn719MetfsTer13	p.N719Mfs*13	ENST00000398568	NM_001042412.1	717	gAa/ga	14/18	1	2	FACETS	0.738	0.647	0.837	0.738	0.647	0.837	SUBCLONAL	1	TRUE	1	0.375921570116746	2		517	526	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	88	443	1	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.89	0.791	0.996	0.89	0.791	0.996	CLONAL	1	TRUE	1	0.375921570116746	2		444	526	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262097	16262097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1481024603	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	91	333	1	ENST00000375759.3:c.9362G>A	p.Arg3121Gln	p.R3121Q	ENST00000375759	NM_015001.2	3121	cGg/cAg	11/15	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.375921570116746	2		334	439	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101472	27101472	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	208	863	0	ENST00000324856.7:c.4754T>C	p.Val1585Ala	p.V1585A	ENST00000324856	NM_006015.4	1585	gTa/gCa	18/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.375921570116746	2		863	989	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939219	36939219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762191036	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	190	751	1	ENST00000361632.4:c.490C>T	p.Arg164Trp	p.R164W	ENST00000361632		164	Cgg/Tgg	5/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.375921570116746	2		752	864	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804304	43804304	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763568293	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	164	638	2	ENST00000372470.3:c.304C>T	p.Arg102Cys	p.R102C	ENST00000372470	NM_005373.2	102	Cgt/Tgt	3/12	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.375921570116746	2		640	801	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743758	46743760	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	205	771	0	ENST00000371975.4:c.2050_2052del	p.Cys684del	p.C684del	ENST00000371975	NM_003579.3	683	cGTTgt/cgt	18/18	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.375921570116746	2		771	947	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458436	120458436	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs771237928	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	144	594	2	ENST00000256646.2:c.6909del	p.Ile2304LeufsTer2	p.I2304Lfs*2	ENST00000256646	NM_024408.3	2303	ccC/cc	34/34	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.375921570116746	2		596	745	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468424	120468424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1395799589	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	153	635	0	ENST00000256646.2:c.4015G>A	p.Gly1339Arg	p.G1339R	ENST00000256646	NM_024408.3	1339	Ggg/Agg	25/34	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.375921570116746	2		635	733	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150549868	150549868	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	100	448	0	ENST00000369026.2:c.1036G>A	p.Ala346Thr	p.A346T	ENST00000369026	NM_021960.4	346	Gca/Aca	3/3	1	2	FACETS	0.953	0.854	1	0.953	0.854	1	CLONAL	1	TRUE	1	0.375921570116746	2		448	558	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956113	175956113	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	61	573	0	ENST00000367669.3:c.2099T>C	p.Val700Ala	p.V700A	ENST00000367669	NM_022457.5	700	gTt/gCt	18/20	1	2	FACETS	0.634	0.547	0.728	0.634	0.547	0.728	SUBCLONAL	1	TRUE	1	0.375921570116746	2		573	512	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612921	228612921	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779185305	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	169	538	0	ENST00000366696.1:c.106G>A	p.Val36Met	p.V36M	ENST00000366696	NM_003493.2	36	Gtg/Atg	1/1	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.375921570116746	2		538	777	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097781	8097781	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763176056	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	236	899	0	ENST00000346208.3:c.163G>A	p.Gly55Ser	p.G55S	ENST00000346208		55	Ggt/Agt	2/6	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.375921570116746	2		899	1081	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63662003	63662003	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	99	426	0	ENST00000279873.7:c.107T>C	p.Leu36Ser	p.L36S	ENST00000279873	NM_032199.2	36	tTg/tCg	2/10	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.375921570116746	2		426	511	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446284	70446284	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	167	660	2	ENST00000373644.4:c.5230del	p.Arg1744GlufsTer18	p.R1744Efs*18	ENST00000373644	NM_030625.2	1742	Aaa/aa	11/12	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.375921570116746	2		662	860	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690802	89690802	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1114167621	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	23	353	0	ENST00000371953.3:c.210-1G>A		p.X70_splice	ENST00000371953	NM_000314.4	70			1	2	FACETS	0.332	0.258	0.417	0.332	0.258	0.417	SUBCLONAL	1	TRUE	1	0.375921570116746	2		353	369	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690814	89690814	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	30	373	0	ENST00000371953.3:c.221G>C	p.Arg74Thr	p.R74T	ENST00000371953	NM_000314.4	74	aGa/aCa	4/9	1	2	FACETS	0.401	0.323	0.49	0.401	0.323	0.49	SUBCLONAL	1	TRUE	1	0.375921570116746	2		373	398	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692979	89692979	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs398123325	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	94	550	0	ENST00000371953.3:c.463T>A	p.Tyr155Asn	p.Y155N	ENST00000371953	NM_000314.4	155	Tat/Aat	5/9	1	2	FACETS	0.891	0.795	0.994	0.891	0.795	0.994	CLONAL	1	TRUE	1	0.375921570116746	2		550	561	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200491	67200491	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	207	690	0	ENST00000312629.5:c.685T>G	p.Phe229Val	p.F229V	ENST00000312629	NM_003952.2	229	Ttc/Gtc	8/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.375921570116746	2		690	960	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518084	69518084	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	248	875	0	ENST00000294312.3:c.281G>A	p.Gly94Asp	p.G94D	ENST00000294312	NM_005117.2	94	gGc/gAc	2/3	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.375921570116746	2		875	1102	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588088	69588088	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	146	558	0	ENST00000168712.1:c.610C>A	p.Pro204Thr	p.P204T	ENST00000168712	NM_002007.2	204	Ccc/Acc	3/3	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.375921570116746	2		558	702	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18649053	18649053	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	53	498	0	ENST00000266497.5:c.2728A>G	p.Asn910Asp	p.N910D	ENST00000266497		910	Aat/Gat	19/31	1	2	FACETS	0.618	0.528	0.717	0.618	0.528	0.717	SUBCLONAL	1	TRUE	1	0.375921570116746	2		498	456	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242662	46242662	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	37	447	1	ENST00000334344.6:c.1624C>T	p.Arg542Ter	p.R542*	ENST00000334344	NM_152641.2	542	Cga/Tga	13/21	1	2	FACETS	0.531	0.438	0.634	0.531	0.438	0.634	SUBCLONAL	1	TRUE	1	0.375921570116746	2		448	371	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432206	49432206	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	276	892	0	ENST00000301067.7:c.8933C>A	p.Pro2978His	p.P2978H	ENST00000301067	NM_003482.3	2978	cCt/cAt	34/54	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.375921570116746	2		892	1128	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439750	49439750	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs200119692	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	146	642	0	ENST00000301067.7:c.4694C>T	p.Ala1565Val	p.A1565V	ENST00000301067	NM_003482.3	1565	gCg/gTg	18/54	1	2	FACETS	0.977	0.893	1	0.977	0.893	1	CLONAL	1	TRUE	1	0.375921570116746	2		642	795	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578215	28578216	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	146	602	0	ENST00000241453.7:c.2955_2956del	p.Pro986AlafsTer27	p.P986Afs*27	ENST00000241453	NM_004119.2	985	tcTCcg/tccg	24/24	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.375921570116746	2		602	719	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915054	32915054	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507373	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	73	611	1	ENST00000380152.3:c.6566del	p.Asn2189ThrfsTer2	p.N2189Tfs*2	ENST00000380152		2188	Aaa/aa	11/27	1	2	FACETS	0.675	0.591	0.766	0.675	0.591	0.766	SUBCLONAL	1	TRUE	1	0.375921570116746	2		612	575	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135384	30135384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373748041	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	91	477	0	ENST00000331968.5:c.434G>A	p.Arg145His	p.R145H	ENST00000331968	NM_002742.2	145	cGt/cAt	3/18	1	2	FACETS	0.858	0.764	0.959	0.858	0.764	0.959	CLONAL	1	TRUE	1	0.375921570116746	2		477	564	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987024	36987024	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	166	699	0	ENST00000354822.5:c.665A>G	p.Glu222Gly	p.E222G	ENST00000354822	NM_001079668.2	222	gAg/gGg	3/3	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.375921570116746	2		699	774	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246533	105246533	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	159	697	1	ENST00000349310.3:c.67C>T	p.Arg23Trp	p.R23W	ENST00000349310	NM_001014432.1	23	Cgg/Tgg	4/15	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.375921570116746	2		698	823	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643392	38643392	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	45	612	0	ENST00000299084.4:c.867del	p.Lys289AsnfsTer14	p.K289Nfs*14	ENST00000299084	NM_152594.2	288	Aaa/aa	7/7	0.375921570116746	3	FACETS	0.372	0.312	0.44	0.186	0.156	0.22	SUBCLONAL	1	TRUE	1	0.375921570116746	3		612	764	SUCCESS
BLM	641	MSKCC	GRCh37	15	91333913	91333913	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587778102	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	131	523	1	ENST00000355112.3:c.2858T>C	p.Ile953Thr	p.I953T	ENST00000355112	NM_000057.2	953	aTt/aCt	15/22	0.375921570116746	3	FACETS	0.966	0.877	1	0.483	0.438	0.53	CLONAL	1	TRUE	1	0.375921570116746	3		524	857	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442809	99442809	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	163	663	0	ENST00000268035.6:c.1211del	p.Asn404ThrfsTer6	p.N404Tfs*6	ENST00000268035	NM_000875.3	402	ctA/ct	5/21	0.375921570116746	3	FACETS	1	0.973	1	0.57	0.523	0.619	CLONAL	1	TRUE	1	0.375921570116746	3		663	904	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343595	343595	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	238	861	1	ENST00000262320.3:c.2079del	p.Thr694ProfsTer11	p.T694Pfs*11	ENST00000262320	NM_003502.3	693	ccC/cc	8/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.375921570116746	2		862	1041	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396234	396234	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	181	680	3	ENST00000262320.3:c.792del	p.Gly265GlufsTer149	p.G265Efs*149	ENST00000262320	NM_003502.3	264	ccC/cc	2/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.375921570116746	2		683	880	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136333	2136333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	242	954	1	ENST00000219476.3:c.4802G>A	p.Gly1601Asp	p.G1601D	ENST00000219476	NM_000548.3	1601	gGt/gAt	37/42	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.375921570116746	2		955	1062	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2137913	2137913	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150558493	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	231	876	0	ENST00000219476.3:c.5039G>A	p.Cys1680Tyr	p.C1680Y	ENST00000219476	NM_000548.3	1680	tGc/tAc	39/42	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.375921570116746	2		876	1060	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644532	3644532	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	282	1009	0	ENST00000294008.3:c.2082G>C	p.Gln694His	p.Q694H	ENST00000294008	NM_032444.2	694	caG/caC	10/15	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.375921570116746	2		1009	1193	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808876	3808876	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	139	550	0	ENST00000262367.5:c.3348T>A	p.Asp1116Glu	p.D1116E	ENST00000262367	NM_004380.2	1116	gaT/gaA	17/31	1	2	FACETS	0.967	0.881	1	0.967	0.881	1	CLONAL	1	TRUE	1	0.375921570116746	2		550	765	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274042	10274042	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184494228	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	234	848	0	ENST00000330684.3:c.227G>A	p.Arg76His	p.R76H	ENST00000330684	NM_001134407.1	76	cGc/cAc	2/13	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.375921570116746	2		848	1041	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349160	11349160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	110	332	0	ENST00000332029.2:c.176G>A	p.Arg59His	p.R59H	ENST00000332029	NM_003745.1	59	cGt/cAt	2/2	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.375921570116746	2		332	429	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660536	67660536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	142	566	1	ENST00000264010.4:c.1436G>A	p.Arg479His	p.R479H	ENST00000264010	NM_006565.3	479	cGc/cAc	8/12	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.375921570116746	2		567	742	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671655	67671655	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1400980130	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	144	614	1	ENST00000264010.4:c.2070del	p.Glu691SerfsTer30	p.E691Sfs*30	ENST00000264010	NM_006565.3	688	gtA/gt	12/12	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.375921570116746	2		615	705	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829578	72829578	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	142	578	1	ENST00000268489.5:c.7003C>A	p.Leu2335Met	p.L2335M	ENST00000268489	NM_006885.3	2335	Ctg/Atg	9/10	1	2	FACETS	0.988	0.901	1	0.988	0.901	1	CLONAL	1	TRUE	1	0.375921570116746	2		579	765	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993776	72993776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200056605	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	191	540	0	ENST00000268489.5:c.269G>A	p.Ser90Asn	p.S90N	ENST00000268489	NM_006885.3	90	aGc/aAc	2/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.375921570116746	2		540	747	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81927400	81927400	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	198	665	0	ENST00000359376.3:c.1072+1G>A		p.X358_splice	ENST00000359376	NM_002661.3	358			1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.375921570116746	2		665	832	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347474	89347474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	149	660	2	ENST00000301030.4:c.5476C>T	p.Pro1826Ser	p.P1826S	ENST00000301030	NM_001256183.1	1826	Cca/Tca	9/13	1	2	FACETS	0.988	0.904	1	0.988	0.904	1	CLONAL	1	TRUE	1	0.375921570116746	2		662	802	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89874775	89874775	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	116	535	0	ENST00000389301.3:c.523A>G	p.Ser175Gly	p.S175G	ENST00000389301	NM_000135.2	175	Agt/Ggt	6/43	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.375921570116746	2		535	565	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216536	7216536	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	122	579	0	ENST00000380728.2:c.799G>A	p.Asp267Asn	p.D267N	ENST00000380728		267	Gac/Aac	9/11	1	2	FACETS	0.925	0.837	1	0.925	0.837	1	CLONAL	1	TRUE	1	0.375921570116746	2		579	702	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882019	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	273	1011	0	ENST00000269305.4:c.455del	p.Pro152ArgfsTer18	p.P152Rfs*18	ENST00000269305	NM_001126112.2	152	cCg/cg	5/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.375921570116746	2		1011	1157	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979014	7979014	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751283247	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	153	637	1	ENST00000319144.4:c.1553C>T	p.Thr518Ile	p.T518I	ENST00000319144	NM_001139.2	518	aCc/aTc	12/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.375921570116746	2		638	761	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016635	12016636	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	97	375	0	ENST00000353533.5:c.772_773del	p.Ile258CysfsTer9	p.I258Cfs*9	ENST00000353533	NM_003010.3	257	tcTAtt/tctt	7/11	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.375921570116746	2		375	499	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	131	792	7	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	0.715	0.648	0.786	0.715	0.648	0.786	SUBCLONAL	1	TRUE	1	0.375921570116746	2		799	975	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40376873	40376873	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1475711023	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	151	627	0	ENST00000293328.3:c.299G>A	p.Arg100His	p.R100H	ENST00000293328	NM_012448.3	100	cGc/cAc	4/19	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.375921570116746	2		627	734	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804235	46804235	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	171	739	0	ENST00000290295.7:c.772C>A	p.Arg258Ser	p.R258S	ENST00000290295	NM_006361.5	258	Cgc/Agc	2/2	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.375921570116746	2		739	884	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926603	59926603	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	53	501	0	ENST00000259008.2:c.394del	p.Thr132ProfsTer25	p.T132Pfs*25	ENST00000259008	NM_032043.2	132	Acc/cc	5/20	1	2	FACETS	0.606	0.518	0.703	0.606	0.518	0.703	SUBCLONAL	1	TRUE	1	0.375921570116746	2		501	465	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78935279	78935279	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	206	807	0	ENST00000306801.3:c.3691A>G	p.Ser1231Gly	p.S1231G	ENST00000306801	NM_020761.2	1231	Agc/Ggc	31/34	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.375921570116746	2		807	930	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231449	5231449	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	224	922	2	ENST00000357368.4:c.2027del	p.Pro676ArgfsTer134	p.P676Rfs*134	ENST00000357368	NM_002850.3	676	cCg/cg	14/38	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.375921570116746	2		924	1038	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629036	14629036	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	175	579	1	ENST00000254322.2:c.126G>T	p.Glu42Asp	p.E42D	ENST00000254322	NM_006145.1	42	gaG/gaT	1/3	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.375921570116746	2		580	776	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794551	42794551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	236	993	0	ENST00000575354.2:c.1631C>T	p.Ala544Val	p.A544V	ENST00000575354	NM_015125.3	544	gCc/gTc	10/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.375921570116746	2		993	1150	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	120	421	1	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.375921570116746	2		422	620	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725018	47725019	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs762488821	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	220	955	0	ENST00000449228.1:c.725dup	p.Arg243GlnfsTer7	p.R243Qfs*7	ENST00000449228	NM_001127240.2	242	ggc/ggGc	4/4	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.375921570116746	2		955	1159	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912806	50912806	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1419624611	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	194	821	0	ENST00000440232.2:c.2041del	p.Leu681SerfsTer13	p.L681Sfs*13	ENST00000440232	NM_002691.3	679	gaC/ga	17/27	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.375921570116746	2		821	970	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46611684	46611684	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	222	871	0	ENST00000263734.3:c.2498C>T	p.Ser833Phe	p.S833F	ENST00000263734	NM_001430.4	833	tCc/tTc	16/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.375921570116746	2		871	1088	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99136555	99136555	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	207	814	0	ENST00000074304.5:c.44del	p.Arg15LeufsTer32	p.R15Lfs*32	ENST00000074304	NM_001134224.1	15	cGt/ct	3/26	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.375921570116746	2		814	941	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046263	128046263	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1308398082	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	160	594	0	ENST00000285398.2:c.1000C>T	p.Arg334Cys	p.R334C	ENST00000285398	NM_000122.1	334	Cgt/Tgt	7/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.375921570116746	2		594	735	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561521	9561521	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	125	582	0	ENST00000353224.5:c.261G>T	p.Glu87Asp	p.E87D	ENST00000353224	NM_177990.2	87	gaG/gaT	4/10	1	2	FACETS	0.999	0.906	1	0.999	0.906	1	CLONAL	1	TRUE	1	0.375921570116746	2		582	666	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022374	31022374	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	88	342	0	ENST00000375687.4:c.1859del	p.Arg620LeufsTer83	p.R620Lfs*83	ENST00000375687	NM_015338.5	620	cGt/ct	13/13	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.375921570116746	2		342	453	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40789999	40789999	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	51	530	0	ENST00000373198.4:c.2732A>G	p.Glu911Gly	p.E911G	ENST00000373198	NM_133170.3	911	gAa/gGa	18/32	1	2	FACETS	0.406	0.344	0.474	0.406	0.344	0.474	SUBCLONAL	1	TRUE	1	0.375921570116746	2		530	668	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281743	46281743	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	154	715	0	ENST00000371998.3:c.4190G>A	p.Gly1397Asp	p.G1397D	ENST00000371998		1397	gGc/gAc	22/23	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.375921570116746	2		715	805	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074295	30074295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	95	527	0	ENST00000338641.4:c.1557G>A	p.Met519Ile	p.M519I	ENST00000338641	NM_000268.3	519	atG/atA	14/16	1	2	FACETS	0.851	0.759	0.948	0.851	0.759	0.948	CLONAL	1	TRUE	1	0.375921570116746	2		527	594	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573318	41573318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781609478	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	209	821	2	ENST00000263253.7:c.5603C>T	p.Thr1868Met	p.T1868M	ENST00000263253	NM_001429.3	1868	aCg/aTg	31/31	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.375921570116746	2		823	992	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664989	138664989	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	90	375	0	ENST00000330315.3:c.576del	p.Lys193SerfsTer78	p.K193Sfs*78	ENST00000330315	NM_023067.3	192	ccC/cc	1/1	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.375921570116746	2		375	452	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665170	138665170	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	251	885	2	ENST00000330315.3:c.395C>T	p.Pro132Leu	p.P132L	ENST00000330315	NM_023067.3	132	cCg/cTg	1/1	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.375921570116746	2		887	1032	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928078	178928080	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs587776933	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	79	568	0	ENST00000263967.3:c.1359_1361del	p.Glu453del	p.E453del	ENST00000263967	NM_006218.2	452	ttAGAa/tta	8/21	1	2	FACETS	0.671	0.591	0.758	0.671	0.591	0.758	SUBCLONAL	1	TRUE	1	0.375921570116746	2		568	626	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182681667	182681667	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	60	378	0	ENST00000292782.4:c.389+2T>C		p.X130_splice	ENST00000292782	NM_020640.2	130			1	2	FACETS	0.725	0.627	0.832	0.725	0.627	0.832	SUBCLONAL	1	TRUE	1	0.375921570116746	2		378	440	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38954898	38954898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	35	357	0	ENST00000357387.3:c.2675G>A	p.Gly892Asp	p.G892D	ENST00000357387	NM_152756.3	892	gGc/gAc	27/38	1	2	FACETS	0.64	0.526	0.766	0.64	0.526	0.766	SUBCLONAL	1	TRUE	1	0.375921570116746	2		357	291	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177683	56177683	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	106	366	0	ENST00000399503.3:c.2656C>T	p.Gln886Ter	p.Q886*	ENST00000399503	NM_005921.1	886	Cag/Tag	14/20	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.375921570116746	2		366	526	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754554	57754554	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	55	396	0	ENST00000274289.3:c.493del	p.Arg165GlyfsTer7	p.R165Gfs*7	ENST00000274289	NM_006622.3	165	Agg/gg	3/14	1	2	FACETS	0.611	0.523	0.707	0.611	0.523	0.707	SUBCLONAL	1	TRUE	1	0.375921570116746	2		396	479	SUCCESS
APC	324	MSKCC	GRCh37	5	112175392	112175392	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	48	303	0	ENST00000257430.4:c.4101G>T	p.Gln1367His	p.Q1367H	ENST00000257430	NM_000038.5	1367	caG/caT	16/16	1	2	FACETS	0.791	0.672	0.92	0.791	0.672	0.92	CLONAL	1	TRUE	1	0.375921570116746	2		303	323	SUCCESS
APC	324	MSKCC	GRCh37	5	112175525	112175525	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	95	397	0	ENST00000257430.4:c.4234G>A	p.Gly1412Arg	p.G1412R	ENST00000257430	NM_000038.5	1412	Gga/Aga	16/16	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.375921570116746	2		397	470	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401582	401582	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	184	520	0	ENST00000380956.4:c.908del	p.Asn303ThrfsTer6	p.N303Tfs*6	ENST00000380956	NM_001195286.1	302	Aaa/aa	7/9	0.163947210510948	3	FACETS	0.767	0.71	0.827	0.767	0.71	0.827	INDETERMINATE	2	TRUE	1	0.375921570116746	3		520	758	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20486919	20486919	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs376318599	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	55	368	0	ENST00000346618.3:c.885-1C>T		p.X295_splice	ENST00000346618	NM_001949.4	295			0.163947210510948	3	FACETS	0.934	0.803	1	0.467	0.401	0.539	INDETERMINATE	1	TRUE	1	0.375921570116746	3		368	372	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032218	26032218	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	71	279	0	ENST00000244661.2:c.71A>T	p.Lys24Met	p.K24M	ENST00000244661	NM_003537.3	24	aAg/aTg	1/1	0.163947210510948	3	FACETS	1	0.963	1	0.628	0.552	0.71	INDETERMINATE	1	TRUE	1	0.375921570116746	3		279	357	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911045	29911045	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	225	999	0	ENST00000376809.5:c.344G>A	p.Gly115Asp	p.G115D	ENST00000376809	NM_002116.7	115	gGt/gAt	3/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.375921570116746	2		999	1106	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903836	41903836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540997482	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	149	539	0	ENST00000372991.4:c.721C>T	p.Arg241Trp	p.R241W	ENST00000372991	NM_001760.3	241	Cgg/Tgg	5/5	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.375921570116746	2		539	666	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120889	94120889	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	61	401	0	ENST00000369303.4:c.163-1G>C		p.X55_splice	ENST00000369303	NM_004440.3	55			1	2	FACETS	0.805	0.697	0.922	0.805	0.697	0.922	CLONAL	1	TRUE	1	0.375921570116746	2		401	403	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109308826	109308826	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	56	318	0	ENST00000436639.2:c.1577T>C	p.Val526Ala	p.V526A	ENST00000436639	NM_014454.2	526	gTt/gCt	10/10	1	2	FACETS	0.908	0.783	1	0.908	0.783	1	CLONAL	1	TRUE	1	0.375921570116746	2		318	328	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109322606	109322606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762972224	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	108	726	2	ENST00000436639.2:c.431C>T	p.Thr144Met	p.T144M	ENST00000436639	NM_014454.2	144	aCg/aTg	3/10	1	2	FACETS	0.748	0.671	0.83	0.748	0.671	0.83	SUBCLONAL	1	TRUE	1	0.375921570116746	2		728	768	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138195980	138195980	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	61	154	0	ENST00000237289.4:c.296-2A>G		p.X99_splice	ENST00000237289	NM_001270507.1	99			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.375921570116746	2		154	228	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505503	157505503	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	89	405	0	ENST00000346085.5:c.3488del	p.Pro1163ArgfsTer48	p.P1163Rfs*48	ENST00000346085	NM_020732.3	1162	Ccc/cc	13/20	1	2	FACETS	0.96	0.855	1	0.96	0.855	1	CLONAL	1	TRUE	1	0.375921570116746	2		405	493	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035204	6035207	+	frameshift_variant	Frame_Shift_Del	DEL	CTGT	CTGT	-	rs267608154	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	53	557	1	ENST00000265849.7:c.861_864del	p.Arg287SerfsTer19	p.R287Sfs*19	ENST00000265849	NM_000535.5	287	agACAG/ag	8/15	1	2	FACETS	0.486	0.414	0.565	0.486	0.414	0.565	SUBCLONAL	1	TRUE	1	0.375921570116746	2		558	580	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946143	13946143	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	95	720	0	ENST00000405192.2:c.953del	p.Leu318TrpfsTer2	p.L318Wfs*2	ENST00000405192	NM_001163147.1	318	tTg/tg	10/12	1	2	FACETS	0.748	0.666	0.834	0.748	0.666	0.834	SUBCLONAL	1	TRUE	1	0.375921570116746	2		720	676	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739962	41739962	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	126	565	0	ENST00000242208.4:c.11T>C	p.Leu4Pro	p.L4P	ENST00000242208	NM_002192.2	4	cTt/cCt	2/3	1	2	FACETS	0.955	0.866	1	0.955	0.866	1	CLONAL	1	TRUE	1	0.375921570116746	2		565	702	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277182	38277182	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	200	732	0	ENST00000425967.3:c.1246T>G	p.Phe416Val	p.F416V	ENST00000425967	NM_001174067.1	416	Ttc/Gtc	10/19	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.375921570116746	2		732	895	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967527	90967527	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554559015	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	41	365	0	ENST00000265433.3:c.1381C>T	p.Pro461Ser	p.P461S	ENST00000265433	NM_002485.4	461	Ccg/Tcg	10/16	1	2	FACETS	0.567	0.473	0.671	0.567	0.473	0.671	SUBCLONAL	1	TRUE	1	0.375921570116746	2		365	385	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971104	21971104	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	168	496	0	ENST00000304494.5:c.254C>T	p.Ala85Val	p.A85V	ENST00000304494	NM_000077.4	85	gCt/gTt	2/3	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.375921570116746	2		496	639	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250127	110250127	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	187	818	1	ENST00000374672.4:c.548C>T	p.Ala183Val	p.A183V	ENST00000374672	NM_004235.4	183	gCt/gTt	3/5	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.375921570116746	2		819	975	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110251245	110251245	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	210	729	2	ENST00000374672.4:c.92A>T	p.Glu31Val	p.E31V	ENST00000374672	NM_004235.4	31	gAg/gTg	2/5	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.375921570116746	2		731	978	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912079	127912079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	25	422	0	ENST00000373547.4:c.791G>A	p.Arg264His	p.R264H	ENST00000373547	NM_002721.4	264	cGt/cAt	7/7	1	2	FACETS	0.273	0.214	0.341	0.273	0.214	0.341	SUBCLONAL	1	TRUE	1	0.375921570116746	2		422	487	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915960	127915960	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	115	522	0	ENST00000373547.4:c.521A>T	p.Asp174Val	p.D174V	ENST00000373547	NM_002721.4	174	gAt/gTt	6/7	1	2	FACETS	0.985	0.89	1	0.985	0.89	1	CLONAL	1	TRUE	1	0.375921570116746	2		522	621	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772614	135772615	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	135	561	0	ENST00000298552.3:c.2931dup	p.Leu978ThrfsTer2	p.L978Tfs*2	ENST00000298552	NM_001162426.1	977	-/A	22/23	1	2	FACETS	0.992	0.903	1	0.992	0.903	1	CLONAL	1	TRUE	1	0.375921570116746	2		561	724	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782722	135782722	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	71	571	0	ENST00000298552.3:c.1299del	p.His433GlnfsTer7	p.H433Qfs*7	ENST00000298552	NM_001162426.1	433	caC/ca	13/23	1	2	FACETS	0.602	0.526	0.685	0.602	0.526	0.685	SUBCLONAL	1	TRUE	1	0.375921570116746	2		571	627	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391338	139391338	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61751489	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	255	1055	0	ENST00000277541.6:c.6853G>A	p.Val2285Ile	p.V2285I	ENST00000277541	NM_017617.3	2285	Gtc/Atc	34/34	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.375921570116746	2		1055	1138	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20153947	20153947	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	61	571	1	ENST00000379607.5:c.113T>C	p.Val38Ala	p.V38A	ENST00000379607	NM_001412.3	38	gTa/gCa	3/7	1	2	FACETS	0.691	0.597	0.792	0.691	0.597	0.792	SUBCLONAL	1	TRUE	1	0.375921570116746	2		572	470	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921553	39921553	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	214	848	0	ENST00000378444.4:c.4267C>T	p.Gln1423Ter	p.Q1423*	ENST00000378444	NM_001123385.1	1423	Cag/Tag	10/15	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.375921570116746	2		848	894	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932474	39932474	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	228	860	0	ENST00000378444.4:c.2125G>T	p.Gly709Cys	p.G709C	ENST00000378444	NM_001123385.1	709	Ggc/Tgc	4/15	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.375921570116746	2		860	938	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426301	47426301	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	191	827	0	ENST00000377045.4:c.718A>C	p.Ser240Arg	p.S240R	ENST00000377045	NM_001654.4	240	Agc/Cgc	8/16	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.375921570116746	2		827	986	SUCCESS
AR	367	MSKCC	GRCh37	X	66943553	66943554	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	103	491	0	ENST00000374690.3:c.2637dup	p.Asp880Ter	p.D880*	ENST00000374690	NM_000044.3	878	act/acTt	8/8	1	2	FACETS	0.943	0.846	1	0.943	0.846	1	CLONAL	1	TRUE	1	0.375921570116746	2		491	581	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938089	76938090	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	82	598	1	ENST00000373344.5:c.2658_2659del	p.Glu886AspfsTer10	p.E886Dfs*10	ENST00000373344	NM_000489.3	886	gaGAct/gact	9/35	1	2	FACETS	0.721	0.636	0.812	0.721	0.636	0.812	SUBCLONAL	1	TRUE	1	0.375921570116746	2		599	605	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224762	123224763	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	112	642	0	ENST00000218089.9:c.3531_3532del	p.Arg1177SerfsTer7	p.R1177Sfs*7	ENST00000218089	NM_001042749.1	1176	GAg/g	32/35	1	2	FACETS	0.901	0.812	0.996	0.901	0.812	0.996	CLONAL	1	TRUE	1	0.375921570116746	2		642	661	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950775	38950775	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	32	283	0	ENST00000357387.3:c.3175A>T	p.Thr1059Ser	p.T1059S	ENST00000357387	NM_152756.3	1059	Aca/Tca	31/38	1	2	FACETS	0.66	0.538	0.796	0.66	0.538	0.796	SUBCLONAL	1	TRUE	1	0.375921570116746	2		283	258	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188298	32188298	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	232	848	0	ENST00000375023.3:c.1043G>T	p.Gly348Val	p.G348V	ENST00000375023	NM_004557.3	348	gGc/gTc	6/30	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.375921570116746	2		848	1008	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	213	704	7	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.375921570116746	2		711	877	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0029649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	34	498	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.777	0.633	0.941	0.777	0.633	0.941	CLONAL	1	TRUE	1	0.12	2		498	729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0029649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	62	850	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.957	0.824	1	0.957	0.824	1	CLONAL	1	TRUE	1	0.12	2		850	1080	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713750	30713750	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	30	474	0	ENST00000295754.5:c.1075G>C	p.Ala359Pro	p.A359P	ENST00000295754	NM_003242.5	359	Gct/Cct	4/7	1	2	FACETS	0.969	0.779	1	0.969	0.779	1	CLONAL	1	TRUE	1	0.12	2		474	516	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727136	41727136	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	46	697	0	ENST00000301178.4:c.394T>C	p.Tyr132His	p.Y132H	ENST00000301178	NM_021913.4	132	Tat/Cat	3/20	1	2	FACETS	0.887	0.745	1	0.887	0.745	1	CLONAL	1	TRUE	1	0.12	2		697	864	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921598	39921598	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	47	343	0	ENST00000378444.4:c.4222G>A	p.Asp1408Asn	p.D1408N	ENST00000378444	NM_001123385.1	1408	Gat/Aat	10/15	1	1	FACETS	0.902	0.763	1	1	0.97	1	CLONAL	2	TRUE	0	0.12	1		343	408	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	60	394	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.548792607276038	4	FACETS	0.396	0.34	0.457	0.198	0.17	0.229	SUBCLONAL	1	TRUE	2	0.548792607276038	4		394	856	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0029654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1202	112	737	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.196711482546187	6	FACETS	0.652	0.584	0.724			1	INDETERMINATE	1	TRUE	NA	0.548792607276038	6		737	1314	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971035	21971035	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	61	384	0	ENST00000304494.5:c.323A>G	p.Asp108Gly	p.D108G	ENST00000304494	NM_000077.4	108	gAt/gGt	2/3	0.136327394200052	5	FACETS	0.669	0.577	0.769	0.223	0.192	0.257	INDETERMINATE	1	TRUE	2	0.548792607276038	5		384	606	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189861	66189861	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	63	413	1	ENST00000273854.3:c.3085C>T	p.Gln1029Ter	p.Q1029*	ENST00000273854	NM_004439.5	1029	Cag/Tag	18/18	0.541393617061108	4	FACETS	0.413	0.357	0.476	0.207	0.178	0.238	SUBCLONAL	1	TRUE	2	0.548792607276038	4		414	860	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336606	81336606	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	52	400	0	ENST00000222390.5:c.1616G>A	p.Arg539Gln	p.R539Q	ENST00000222390	NM_000601.4	539	cGa/cAa	14/18	0.196711482546187	6	FACETS	0.594	0.505	0.692			1	INDETERMINATE	1	TRUE	NA	0.548792607276038	6		400	669	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	168	404	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.908	0.842	0.976	1	0.992	1	CLONAL	2	TRUE	1	0.384481839862597	2		404	481	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0029656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	290	593	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.384481839862597	1	FACETS	0.98	0.93	1	1	0.996	1	CLONAL	2	TRUE	0	0.384481839862597	1		593	622	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943304	71943304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376117918	NA	P-0029656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	140	573	0	ENST00000298229.2:c.1636G>A	p.Val546Ile	p.V546I	ENST00000298229	NM_001567.3	546	Gtc/Atc	14/28	0.384481839862597	1	FACETS	0.883	0.806	0.964	0.883	0.806	0.964	CLONAL	1	TRUE	0	0.384481839862597	1		573	666	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383185	42383185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782563209	NA	P-0029660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	183	569	1	ENST00000221972.3:c.205G>A	p.Val69Ile	p.V69I	ENST00000221972	NM_021601.3	69	Gtc/Atc	2/5	0.356662117551577	2	FACETS	1	0.943	1	0.513	0.473	0.555	CLONAL	1	TRUE	0	0.374126271759696	2		570	953	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436297	110436305	+	inframe_deletion	In_Frame_Del	DEL	CGGCGGCGG	CGGCGGCGG	-	rs34412495	NA	P-0029660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	51	135	0	ENST00000375856.3:c.2096_2104del	p.Ala699_Ala701del	p.A699_A701del	ENST00000375856	NM_003749.2	699	gCCGCCGCCGtg/gtg	1/2	0.164300097882284	3	FACETS	1	0.959	1	0.677	0.581	0.78	INDETERMINATE	1	TRUE	1	0.374126271759696	3		135	239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579378	7579378	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	389	693	1	ENST00000269305.4:c.309C>A	p.Tyr103Ter	p.Y103*	ENST00000269305	NM_001126112.2	103	taC/taA	4/11	0.313868079276128	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.374126271759696	2		694	965	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143966	11143966	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	103	375	0	ENST00000358026.2:c.3547G>A	p.Asp1183Asn	p.D1183N	ENST00000358026	NM_001128849.1	1183	Gac/Aac	26/36	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.374126271759696	2		375	528	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736346	243736346	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	70	319	0	ENST00000263826.5:c.701T>C	p.Phe234Ser	p.F234S	ENST00000263826	NM_005465.4	234	tTt/tCt	8/13	0.295454366208277	3	FACETS	0.814	0.71	0.925			1	CLONAL	1	TRUE	NA	0.374126271759696	3		319	546	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748318	41748318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	129	659	0	ENST00000226382.2:c.451G>A	p.Ala151Thr	p.A151T	ENST00000226382	NM_003924.3	151	Gcc/Acc	3/3	1	2	FACETS	0.738	0.668	0.811	0.738	0.668	0.811	SUBCLONAL	1	TRUE	1	0.374126271759696	2		659	935	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180568	94180568	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	695	783	0	ENST00000323929.3:c.1600G>T	p.Glu534Ter	p.E534*	ENST00000323929	NM_005591.3	534	Gag/Tag	15/20	0.521922188964834	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.521922188964834	2		783	1219	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348821	118348821	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0029663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	556	556	0	ENST00000534358.1:c.3474T>A	p.Cys1158Ter	p.C1158*	ENST00000534358	NM_005933.3	1158	tgT/tgA	5/36	0.521922188964834	2	FACETS	0.961	0.927	0.996	0.961	0.927	0.996	CLONAL	2	TRUE	0	0.521922188964834	2		556	1108	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398283	25398284	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	novel	NA	P-0029663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	278	806	2	ENST00000311936.3:c.35_36delinsAA	p.Gly12Glu	p.G12E	ENST00000311936	NM_004985.3	12	gGT/gAA	2/5	1	2	FACETS	0.847	0.795	0.902	0.847	0.795	0.902	CLONAL	1	TRUE	1	0.521922188964834	2		808	1257	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45396851	45396851	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	304	665	0	ENST00000262160.6:c.321A>T	p.Gln107His	p.Q107H	ENST00000262160	NM_005901.5	107	caA/caT	3/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.521922188964834	2		665	1026	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267359	198267359	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs377023736	NA	P-0029663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1216	418	853	2	ENST00000335508.6:c.1998G>T	p.Lys666Asn	p.K666N	ENST00000335508	NM_012433.2	666	aaG/aaT	14/25	1	2	FACETS	0.98	0.932	1	0.98	0.932	1	CLONAL	1	TRUE	1	0.521922188964834	2		855	1634	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046728	180046728	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1510	572	1483	0	ENST00000261937.6:c.2584G>T	p.Ala862Ser	p.A862S	ENST00000261937	NM_182925.4	862	Gcc/Tcc	18/30	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.521922188964834	2		1483	2082	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120318	94120318	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	173	395	0	ENST00000369303.4:c.733G>C	p.Ala245Pro	p.A245P	ENST00000369303	NM_004440.3	245	Gcc/Ccc	3/17	0.521922188964834	1	FACETS	0.939	0.87	1	0.939	0.87	1	CLONAL	1	TRUE	0	0.521922188964834	1		395	522	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626618	100626618	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	A	novel	NA	P-0029663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	319	753	0	ENST00000308731.7:c.309+3G>T		p.X103_splice	ENST00000308731	NM_000061.2	103			0.281873457385524	1	FACETS	0.888	0.84	0.938	0.888	0.84	0.938	INDETERMINATE	1	TRUE	0	0.521922188964834	1		753	1017	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448146	49448146	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	131	527	0	ENST00000301067.7:c.454C>A	p.Gln152Lys	p.Q152K	ENST00000301067	NM_003482.3	152	Cag/Aag	4/54	1	2	FACETS	0.963	0.877	1	0.963	0.877	1	CLONAL	1	TRUE	1	0.462593297665092	2		527	588	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912243	32912243	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	24	495	0	ENST00000380152.3:c.3751A>G	p.Thr1251Ala	p.T1251A	ENST00000380152		1251	Act/Gct	11/27	1	2	FACETS	0.324	0.254	0.405	0.324	0.254	0.405	SUBCLONAL	1	TRUE	1	0.462593297665092	2		495	320	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976449	25976450	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	49	469	0	ENST00000435504.4:c.1095dup	p.Val366SerfsTer10	p.V366Sfs*10	ENST00000435504		365	-/A	11/13	0.462593297665092	1	FACETS	0.608	0.518	0.704	0.608	0.518	0.704	SUBCLONAL	1	TRUE	0	0.462593297665092	1		469	268	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991729	25991730	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	17	268	0	ENST00000435504.4:c.512dup	p.Gln172AlafsTer33	p.Q172Afs*33	ENST00000435504		171	aag/aaAg	7/13	0.462593297665092	1	FACETS	0.183	0.136	0.239	0.183	0.136	0.239	SUBCLONAL	1	TRUE	0	0.462593297665092	1		268	308	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564512	86564512	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs767017718	NA	P-0029664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	137	395	0	ENST00000274376.6:c.244G>C	p.Gly82Arg	p.G82R	ENST00000274376	NM_002890.2	82	Ggg/Cgg	1/25	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.462593297665092	2		395	466	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129249	152129249	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771540162	NA	P-0029664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	152	578	5	ENST00000206249.3:c.202G>A	p.Ala68Thr	p.A68T	ENST00000206249	NM_000125.3	68	Gcc/Acc	1/8	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.462593297665092	2		583	629	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874412	151874416	+	frameshift_variant	Frame_Shift_Del	DEL	ACTTC	ACTTC	-	novel	NA	P-0029664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	34	327	0	ENST00000262189.6:c.8122_8126del	p.Glu2708GlnfsTer5	p.E2708Qfs*5	ENST00000262189	NM_170606.2	2708	GAAGTc/c	38/59	1	2	FACETS	0.527	0.432	0.632	0.527	0.432	0.632	SUBCLONAL	1	TRUE	1	0.462593297665092	2		327	279	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0029665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	59	670	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.14	2		670	817	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0029665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	59	1069	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.708	0.607	0.82	0.708	0.607	0.82	SUBCLONAL	1	TRUE	1	0.14	2		1071	1190	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48586286	48586286	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	rs1555686086	NA	P-0029665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	34	674	0	ENST00000342988.3:c.955+1del		p.A319fs	ENST00000342988	NM_005359.5	319	Gct/ct	8/12	1	2	FACETS	0.766	0.624	0.926	0.766	0.624	0.926	CLONAL	1	TRUE	1	0.14	2		674	634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0029666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	371	747	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.542193126932314	2	FACETS	0.94	0.901	0.979	0.94	0.901	0.979	CLONAL	2	TRUE	0	0.586543662187166	2		750	673	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913476	NA	P-0029666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	473	702	0	ENST00000358487.5:c.1647T>G	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaG	12/18	0.528563644263233	3	FACETS	0.903	0.872	0.934	0.903	0.872	0.934	CLONAL	3	TRUE	0	0.586543662187166	3		702	770	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685314	89685315	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TG	TG	-	rs1564826836	NA	P-0029666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	234	385	1	ENST00000371953.3:c.209+1_209+2del		p.X70_splice	ENST00000371953	NM_000314.4	70		3/9	0.528563644263233	3	FACETS	1	0.985	1	0.745	0.704	0.785	CLONAL	2	TRUE	0	0.586543662187166	3		386	462	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922328	178922328	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	263	617	0	ENST00000263967.3:c.1097C>G	p.Pro366Arg	p.P366R	ENST00000263967	NM_006218.2	366	cCc/cGc	6/21	0.15535384918395	6	FACETS	1	0.94	1	0.668	0.626	0.71	INDETERMINATE	2	TRUE	3	0.586543662187166	6		617	973	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938935	178938935	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519928	NA	P-0029666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	265	553	0	ENST00000263967.3:c.2177A>C	p.Glu726Ala	p.E726A	ENST00000263967	NM_006218.2	726	gAa/gCa	14/21	0.15535384918395	6	FACETS	1	0.985	1	0.758	0.713	0.805	INDETERMINATE	2	TRUE	3	0.586543662187166	6		553	863	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970971	21970971	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0029666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	803	787	0	ENST00000304494.5:c.387C>G	p.Tyr129Ter	p.Y129*	ENST00000304494	NM_000077.4	129	taC/taG	2/3	0.586543662187166	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.586543662187166	3		787	1119	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665015	138665015	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	46	224	0	ENST00000330315.3:c.550G>A	p.Asp184Asn	p.D184N	ENST00000330315	NM_023067.3	184	Gac/Aac	1/1	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.24	2		224	303	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	120	404	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	0.854	0.781	0.928	0.854	0.781	0.928	INDETERMINATE	1	TRUE	0	0.6	1		404	328	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0029668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	142	869	2	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	0.518	0.472	0.567	0.518	0.472	0.567	SUBCLONAL	1	TRUE	1	0.6	2		871	913	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652890	29652890	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	78	439	0	ENST00000356175.3:c.4825A>C	p.Thr1609Pro	p.T1609P	ENST00000356175	NM_000267.3	1609	Act/Cct	36/57	1	2	FACETS	0.67	0.592	0.753	0.67	0.592	0.753	SUBCLONAL	1	TRUE	1	0.6	2		439	388	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55754355	55754355	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	129	889	0	ENST00000284073.2:c.953T>G	p.Leu318Trp	p.L318W	ENST00000284073	NM_138962.2	318	tTg/tGg	13/14	1	2	FACETS	0.625	0.568	0.685	0.625	0.568	0.685	SUBCLONAL	1	TRUE	1	0.6	2		889	688	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418436	49418436	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	117	776	0	ENST00000301067.7:c.15977T>G	p.Leu5326Arg	p.L5326R	ENST00000301067	NM_003482.3	5326	cTt/cGt	50/54	0.106005702796271	5	FACETS	1	0.951	1	0.362	0.326	0.399	INDETERMINATE	1	TRUE	2	0.6	5		776	683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0029670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	239	747	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.414892880037696	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.414892880037696	1		750	759	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0029670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	133	498	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.902	0.82	0.987	0.902	0.82	0.987	CLONAL	1	TRUE	1	0.414892880037696	2		498	711	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0029670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	144	482	2	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.414892880037696	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.414892880037696	1		484	514	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004247	150004247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	108	474	0	ENST00000253339.5:c.1978C>T	p.Arg660Cys	p.R660C	ENST00000253339		660	Cgt/Tgt	3/7	0.414892880037696	1	FACETS	0.969	0.875	1	0.969	0.875	1	CLONAL	1	TRUE	0	0.414892880037696	1		474	426	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608309	28608309	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767430269	NA	P-0029670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	65	781	0	ENST00000241453.7:c.1747G>A	p.Gly583Ser	p.G583S	ENST00000241453	NM_004119.2	583	Ggc/Agc	14/24	0.341407449334536	1	FACETS	0.346	0.3	0.397	0.346	0.3	0.397	SUBCLONAL	1	TRUE	0	0.414892880037696	1		781	717	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212935	36213957	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTCTCACTTTGTCCAGGCTGGAGTGCAGTGGCGTGATCTCGGCTCACTGCAGCCTTTGCCTCCCGGGTTCAAGAGATTCTCCTGCCTCAGTCTCTCGAGTAGCTGGGACTACAGGTGCCCATCACCACGCCTGGCTAATTTTTGTATTTTTAGTAGAGACAGGGTTTCACCACATTGGCTAGGCTGGTCTTGAACTCCTGACCTCGTGATCTGCCCGTCTCGGCCTCCCAAAGTGCTGGGATTACAGGCATCAGCCACCACACCCAGCTCCCTGTCCCTATCTTTCCTCACTGTCCAGCCCCTGACCCTGTTTATTCCCTGCCAGCTGAGCCCTGGAGGGCAGATGGAGGAGGTGGCCGGGGCTGTCAAGCAGATCTCCGACAGAGGCCCTGTCCGGTCTGAAGATGAGTCGGTGGAAGCTAAGAGAGAGCGGCCCTCAGTATGCATCGGGAGGAGGGCCCTGAAGAAGACTGGCGGGAGGAGTGGGGCTGCGGGAGCGCAAGCTGCCCACACACACTCCGATTTCTCCCCCAGGGTCCCGAGTCCCCTGTGCAAGGTCCCCGCATCAAACATGTCTGCCGTCATGCTGCTGTGGCCCTGGGTCAGGCCCGGGCCATGGTGCCTGAAGATGTCCCTCGCCTCAGTGCCCTCCCTCTCCGGGATCGGCAGGACCTCGCCACAGAGGGTAGGTGGGGAGACTGGACAGCCATGTCAGGTTTGGGGATGACCCCACACTTGGGTGACATGCACCAAGAGCCTAGGAGAGAGGGAGCCAAGTCAGGTGCTCAGGGGTTAGGTGGCAAGTGGGCTGGAGTGCTAGGTCCTAGAGCAACTTCATTTGGGGGCACCAGGAACCTGGCGCTGTGAGAAAGCGAGAGCCAGGTTGTGGGAAAGCAGGGAAGTGAGGTAGAAGCCTGGTGGCTTTGTGGCTCCATCCCCTCCTCCCTGCCTGCTGCAATAGATACATCATCGGCGTCCGAGACTGAGAGTGTCCCGTCACGGTCCCGGCGGGGAAAGGTGGA	AGTCTCACTTTGTCCAGGCTGGAGTGCAGTGGCGTGATCTCGGCTCACTGCAGCCTTTGCCTCCCGGGTTCAAGAGATTCTCCTGCCTCAGTCTCTCGAGTAGCTGGGACTACAGGTGCCCATCACCACGCCTGGCTAATTTTTGTATTTTTAGTAGAGACAGGGTTTCACCACATTGGCTAGGCTGGTCTTGAACTCCTGACCTCGTGATCTGCCCGTCTCGGCCTCCCAAAGTGCTGGGATTACAGGCATCAGCCACCACACCCAGCTCCCTGTCCCTATCTTTCCTCACTGTCCAGCCCCTGACCCTGTTTATTCCCTGCCAGCTGAGCCCTGGAGGGCAGATGGAGGAGGTGGCCGGGGCTGTCAAGCAGATCTCCGACAGAGGCCCTGTCCGGTCTGAAGATGAGTCGGTGGAAGCTAAGAGAGAGCGGCCCTCAGTATGCATCGGGAGGAGGGCCCTGAAGAAGACTGGCGGGAGGAGTGGGGCTGCGGGAGCGCAAGCTGCCCACACACACTCCGATTTCTCCCCCAGGGTCCCGAGTCCCCTGTGCAAGGTCCCCGCATCAAACATGTCTGCCGTCATGCTGCTGTGGCCCTGGGTCAGGCCCGGGCCATGGTGCCTGAAGATGTCCCTCGCCTCAGTGCCCTCCCTCTCCGGGATCGGCAGGACCTCGCCACAGAGGGTAGGTGGGGAGACTGGACAGCCATGTCAGGTTTGGGGATGACCCCACACTTGGGTGACATGCACCAAGAGCCTAGGAGAGAGGGAGCCAAGTCAGGTGCTCAGGGGTTAGGTGGCAAGTGGGCTGGAGTGCTAGGTCCTAGAGCAACTTCATTTGGGGGCACCAGGAACCTGGCGCTGTGAGAAAGCGAGAGCCAGGTTGTGGGAAAGCAGGGAAGTGAGGTAGAAGCCTGGTGGCTTTGTGGCTCCATCCCCTCCTCCCTGCCTGCTGCAATAGATACATCATCGGCGTCCGAGACTGAGAGTGTCCCGTCACGGTCCCGGCGGGGAAAGGTGGA	-	novel	NA	P-0029670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	104	36	0	ENST00000222270.7:c.2457+229_2783del		p.X819_splice	ENST00000222270	NM_014727.1	819		4-6/37	1	2	FACETS	0.957	0.904	1	1	0.992	1	CLONAL	4	TRUE	1	0.414892880037696	2		36	131	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	125	483	2	ENST00000269305.4:c.542G>C	p.Arg181Pro	p.R181P	ENST00000269305	NM_001126112.2	181	cGc/cCc	5/11	NA	2	FACETS	0.826	0.748	0.909			1	INDETERMINATE	2	TRUE	NA	0.185020186831079	2		485	818	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602329	28602329	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	68	503	0	ENST00000241453.7:c.2039C>A	p.Ala680Glu	p.A680E	ENST00000241453	NM_004119.2	680	gCg/gAg	16/24	NA	2	FACETS	0.984	0.855	1			1	INDETERMINATE	1	TRUE	NA	0.185020186831079	2		503	747	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596053	43596053	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	106	570	1	ENST00000355710.3:c.220G>T	p.Gly74Cys	p.G74C	ENST00000355710	NM_020975.4	74	Ggc/Tgc	2/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.185020186831079	2		571	1006	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524158	18524158	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	29	441	0	ENST00000266497.5:c.1670T>G	p.Met557Arg	p.M557R	ENST00000266497		557	aTg/aGg	11/31	NA	2	FACETS	1	0.922	1			1	INDETERMINATE	1	TRUE	NA	0.185020186831079	2		441	238	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448140	49448140	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	84	563	0	ENST00000301067.7:c.460G>T	p.Gly154Cys	p.G154C	ENST00000301067	NM_003482.3	154	Ggc/Tgc	4/54	1	2	FACETS	0.924	0.814	1	0.924	0.814	1	CLONAL	1	TRUE	1	0.185020186831079	2		563	983	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155211	55155211	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	115	482	0	ENST00000257290.5:c.2810C>A	p.Pro937Gln	p.P937Q	ENST00000257290	NM_006206.4	937	cCg/cAg	21/23	0.154127292377626	2	FACETS	1	0.981	1	0.701	0.631	0.775	CLONAL	1	TRUE	0	0.185020186831079	2		482	887	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156606	106156606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1188062738	NA	P-0029684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	83	376	0	ENST00000380013.4:c.1507G>A	p.Glu503Lys	p.E503K	ENST00000380013	NM_001127208.2	503	Gag/Aag	3/11	0.154127292377626	2	FACETS	0.777	0.687	0.874	0.777	0.687	0.874	SUBCLONAL	2	TRUE	0	0.185020186831079	2		376	577	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0029685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	357	483	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.859243892660733	7	FACETS	1	0.988	1	0.721	0.691	0.75	CLONAL	4	TRUE	1	0.859243892660733	7		483	605	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519922	NA	P-0029685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	97	585	0	ENST00000397062.3:c.235G>A	p.Glu79Lys	p.E79K	ENST00000397062	NM_006164.4	79	Gag/Aag	2/5	1	2	FACETS	0.945	0.858	1	0.945	0.858	1	CLONAL	1	TRUE	1	0.859243892660733	2		585	239	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258619	16258619	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	80	480	0	ENST00000375759.3:c.5884G>A	p.Glu1962Lys	p.E1962K	ENST00000375759	NM_015001.2	1962	Gaa/Aaa	11/15	1	2	FACETS	0.913	0.82	1	0.913	0.82	1	CLONAL	1	TRUE	1	0.859243892660733	2		480	204	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115267844	115267844	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	87	498	0	ENST00000438362.2:c.1889C>T	p.Ser630Leu	p.S630L	ENST00000438362	NM_001242891.1	630	tCa/tTa	15/20	1	2	FACETS	0.892	0.804	0.982	0.892	0.804	0.982	CLONAL	1	TRUE	1	0.859243892660733	2		498	227	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457304	67457304	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	100	520	0	ENST00000327367.4:c.278G>C	p.Arg93Pro	p.R93P	ENST00000327367	NM_005902.3	93	cGa/cCa	2/9	1	2	FACETS	0.916	0.833	1	0.916	0.833	1	CLONAL	1	TRUE	1	0.859243892660733	2		520	254	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785636	50785636	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	107	520	0	ENST00000398568.2:c.626A>G	p.Asp209Gly	p.D209G	ENST00000398568	NM_001042412.1	209	gAc/gGc	4/18	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.859243892660733	2		520	232	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752972	42752972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	95	618	0	ENST00000222329.4:c.1292C>T	p.Ser431Leu	p.S431L	ENST00000222329	NM_006494.2	431	tCg/tTg	4/4	1	2	FACETS	0.921	0.835	1	0.921	0.835	1	CLONAL	1	TRUE	1	0.859243892660733	2		618	240	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097218	178097218	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	107	497	0	ENST00000397062.3:c.496G>A	p.Glu166Lys	p.E166K	ENST00000397062	NM_006164.4	166	Gaa/Aaa	4/5	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.859243892660733	2		497	248	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566709	212566709	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	63	275	0	ENST00000342788.4:c.1472G>C	p.Arg491Thr	p.R491T	ENST00000342788	NM_005235.2	491	aGa/aCa	12/28	1	2	FACETS	0.934	0.828	1	0.934	0.828	1	CLONAL	1	TRUE	1	0.859243892660733	2		275	157	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775433	39775433	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1168532464	NA	P-0029685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	94	373	0	ENST00000288319.7:c.587G>A	p.Arg196Lys	p.R196K	ENST00000288319	NM_182918.3	196	aGa/aAa	4/10	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.859243892660733	2		373	202	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933409	39933409	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776961342	NA	P-0029685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	300	222	1	ENST00000378444.4:c.1190C>T	p.Pro397Leu	p.P397L	ENST00000378444	NM_001123385.1	397	cCg/cTg	4/15	0.721481323382874	3	FACETS	1	0.996	1			1	CLONAL	3	TRUE	NA	0.859243892660733	3		223	311	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259525	16259531	+	stop_gained	Nonsense_Mutation	ONP	GAGACAG	GAGACAG	TAGACAA	novel	NA	P-0029685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	90	414	1	ENST00000375759.3:c.6790_6796delinsTAGACAA	p.Glu2264_Asp2266delinsTer	p.E2264_D2266delins*	ENST00000375759	NM_015001.2	2264	GAGACAGat/TAGACAAat	11/15	1	2	FACETS	0.895	0.809	0.984	0.895	0.809	0.984	CLONAL	1	TRUE	1	0.859243892660733	2		415	234	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522669	176522669	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	200	698	0	ENST00000292408.4:c.1766T>G	p.Leu589Arg	p.L589R	ENST00000292408	NM_213647.1	589	cTg/cGg	13/18	1	2	FACETS	0.949	0.881	1	0.949	0.881	1	CLONAL	1	TRUE	1	0.503053303691222	2		698	838	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351460	70351460	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	62	483	0	ENST00000374080.3:c.4108A>G	p.Thr1370Ala	p.T1370A	ENST00000374080		1370	Acc/Gcc	29/45	0.440046208362756	1	FACETS	0.304	0.263	0.35	0.304	0.263	0.35	SUBCLONAL	1	TRUE	0	0.503053303691222	1		483	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0029688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	234	477	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.345579942258029	2	FACETS	0.927	0.871	0.983	0.927	0.871	0.983	CLONAL	2	TRUE	0	0.430897173947899	2		477	586	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59770829	59770829	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	248	485	0	ENST00000259008.2:c.2537A>G	p.Asp846Gly	p.D846G	ENST00000259008	NM_032043.2	846	gAt/gGt	18/20	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	2	TRUE	NA	0.430897173947899	2		485	548	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	65	476	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.788	0.683	0.901	0.788	0.683	0.901	CLONAL	1	TRUE	1	0.29	2		476	569	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	108	445	1	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.29	2		446	630	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	34	227	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.79	0.647	0.948	0.79	0.647	0.948	CLONAL	1	TRUE	1	0.29	2		227	297	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11264672	11264672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	55	548	1	ENST00000361445.4:c.3890C>T	p.Ser1297Leu	p.S1297L	ENST00000361445	NM_004958.3	1297	tCg/tTg	26/58	1	2	FACETS	0.589	0.503	0.683	0.589	0.503	0.683	SUBCLONAL	1	TRUE	1	0.29	2		549	644	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237635	16237635	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	104	447	0	ENST00000375759.3:c.1082A>C	p.Lys361Thr	p.K361T	ENST00000375759	NM_015001.2	361	aAa/aCa	5/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.29	2		447	588	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242692	16242692	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	85	575	0	ENST00000375759.3:c.1313G>T	p.Arg438Ile	p.R438I	ENST00000375759	NM_015001.2	438	aGa/aTa	6/15	1	2	FACETS	0.687	0.606	0.774	0.687	0.606	0.774	SUBCLONAL	1	TRUE	1	0.29	2		575	853	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256435	16256435	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199763346	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	89	537	0	ENST00000375759.3:c.3700G>A	p.Asp1234Asn	p.D1234N	ENST00000375759	NM_015001.2	1234	Gat/Aat	11/15	1	2	FACETS	0.897	0.796	1	0.897	0.796	1	CLONAL	1	TRUE	1	0.29	2		537	684	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521540	46521540	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	104	539	0	ENST00000262741.5:c.868G>T	p.Glu290Ter	p.E290*	ENST00000262741	NM_003629.3	290	Gaa/Taa	7/10	1	2	FACETS	0.865	0.774	0.962	0.865	0.774	0.962	CLONAL	1	TRUE	1	0.29	2		539	829	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46527650	46527650	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1287980956	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	92	421	0	ENST00000262741.5:c.715G>T	p.Glu239Ter	p.E239*	ENST00000262741	NM_003629.3	239	Gaa/Taa	6/10	1	2	FACETS	0.826	0.734	0.925	0.826	0.734	0.925	CLONAL	1	TRUE	1	0.29	2		421	768	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301842	65301842	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	44	303	1	ENST00000342505.4:c.3197C>A	p.Ser1066Tyr	p.S1066Y	ENST00000342505	NM_002227.2	1066	tCt/tAt	23/25	1	2	FACETS	0.702	0.59	0.827	0.702	0.59	0.827	SUBCLONAL	1	TRUE	1	0.29	2		304	432	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335121	65335121	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	128	538	0	ENST00000342505.4:c.520C>T	p.Arg174Ter	p.R174*	ENST00000342505	NM_002227.2	174	Cga/Tga	6/25	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.29	2		538	685	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913255	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	94	536	0	ENST00000369535.4:c.183A>C	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caC	3/7	1	2	FACETS	0.894	0.796	0.999	0.894	0.796	0.999	CLONAL	1	TRUE	1	0.29	2		536	725	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115284182	115284182	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	68	515	0	ENST00000438362.2:c.104A>G	p.Lys35Arg	p.K35R	ENST00000438362	NM_001242891.1	35	aAa/aGa	2/20	1	2	FACETS	0.735	0.639	0.839	0.735	0.639	0.839	SUBCLONAL	1	TRUE	1	0.29	2		515	638	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120508124	120508124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	65	460	0	ENST00000256646.2:c.1633G>A	p.Ala545Thr	p.A545T	ENST00000256646	NM_024408.3	545	Gca/Aca	10/34	1	2	FACETS	0.805	0.698	0.92	0.805	0.698	0.92	CLONAL	1	TRUE	1	0.29	2		460	557	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510194	120510194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199565938	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	60	360	0	ENST00000256646.2:c.1315G>A	p.Ala439Thr	p.A439T	ENST00000256646	NM_024408.3	439	Gcc/Acc	8/34	1	2	FACETS	0.762	0.657	0.876	0.762	0.657	0.876	SUBCLONAL	1	TRUE	1	0.29	2		360	543	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725511	162725511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	98	471	0	ENST00000367921.3:c.623C>T	p.Ser208Phe	p.S208F	ENST00000367921	NM_006182.2	208	tCc/tTc	7/18	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.29	2		471	663	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746018	162746018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	61	364	0	ENST00000367921.3:c.2141G>A	p.Arg714Gln	p.R714Q	ENST00000367921	NM_006182.2	714	cGa/cAa	16/18	1	2	FACETS	0.786	0.679	0.903	0.786	0.679	0.903	CLONAL	1	TRUE	1	0.29	2		364	535	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748503	162748503	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201041695	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	70	322	0	ENST00000367921.3:c.2417G>A	p.Arg806Gln	p.R806Q	ENST00000367921	NM_006182.2	806	cGa/cAa	17/18	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.29	2		322	441	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175914300	175914300	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	71	426	0	ENST00000367669.3:c.2185G>T	p.Glu729Ter	p.E729*	ENST00000367669	NM_022457.5	729	Gaa/Taa	20/20	1	2	FACETS	0.987	0.864	1	0.987	0.864	1	CLONAL	1	TRUE	1	0.29	2		426	496	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226579905	226579905	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	87	522	0	ENST00000366794.5:c.397G>T	p.Glu133Ter	p.E133*	ENST00000366794	NM_001618.3	133	Gaa/Taa	3/23	1	2	FACETS	0.849	0.751	0.953	0.849	0.751	0.953	CLONAL	1	TRUE	1	0.29	2		522	707	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716179	243716179	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	34	550	0	ENST00000263826.5:c.1015A>G	p.Met339Val	p.M339V	ENST00000263826	NM_005465.4	339	Atg/Gtg	10/13	1	2	FACETS	0.352	0.287	0.426	0.352	0.287	0.426	SUBCLONAL	1	TRUE	1	0.29	2		550	666	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63661997	63661997	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	53	371	0	ENST00000279873.7:c.101G>T	p.Arg34Ile	p.R34I	ENST00000279873	NM_032199.2	34	aGa/aTa	2/10	1	2	FACETS	0.665	0.567	0.772	0.665	0.567	0.772	SUBCLONAL	1	TRUE	1	0.29	2		371	550	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332415	70332415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1419371452	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	91	534	0	ENST00000373644.4:c.320G>A	p.Arg107Gln	p.R107Q	ENST00000373644	NM_030625.2	107	cGa/cAa	2/12	1	2	FACETS	0.808	0.717	0.905	0.808	0.717	0.905	CLONAL	1	TRUE	1	0.29	2		534	777	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333555	70333555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150689919	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	85	418	0	ENST00000373644.4:c.1460C>T	p.Ser487Leu	p.S487L	ENST00000373644	NM_030625.2	487	tCa/tTa	2/12	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.29	2		418	515	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692940	89692940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746152219	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	104	544	1	ENST00000371953.3:c.424C>T	p.Arg142Trp	p.R142W	ENST00000371953	NM_000314.4	142	Cgg/Tgg	5/9	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.29	2		545	566	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94201025	94201025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780133	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	70	376	0	ENST00000323929.3:c.1052G>A	p.Arg351His	p.R351H	ENST00000323929	NM_005591.3	351	cGt/cAt	10/20	1	2	FACETS	0.934	0.816	1	0.934	0.816	1	CLONAL	1	TRUE	1	0.29	2		376	517	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122662	108122662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	91	507	0	ENST00000278616.4:c.1706G>A	p.Ser569Asn	p.S569N	ENST00000278616	NM_000051.3	569	aGc/aAc	11/63	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.29	2		507	600	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344108	118344108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	77	387	1	ENST00000534358.1:c.2234G>A	p.Arg745Gln	p.R745Q	ENST00000534358	NM_005933.3	745	cGa/cAa	3/36	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.29	2		388	513	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374901	118374901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	67	392	0	ENST00000534358.1:c.8294G>A	p.Gly2765Glu	p.G2765E	ENST00000534358	NM_005933.3	2765	gGg/gAg	27/36	1	2	FACETS	0.88	0.766	1	0.88	0.766	1	CLONAL	1	TRUE	1	0.29	2		392	525	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435490	18435490	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs760928254	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	30	260	0	ENST00000266497.5:c.475G>T	p.Glu159Ter	p.E159*	ENST00000266497		159	Gaa/Taa	1/31	1	2	FACETS	0.625	0.504	0.762	0.625	0.504	0.762	SUBCLONAL	1	TRUE	1	0.29	2		260	331	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230538	46230538	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	62	336	2	ENST00000334344.6:c.787G>T	p.Glu263Ter	p.E263*	ENST00000334344	NM_152641.2	263	Gaa/Taa	8/21	1	2	FACETS	0.963	0.834	1	0.963	0.834	1	CLONAL	1	TRUE	1	0.29	2		338	444	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242710	46242710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777576250	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	80	409	0	ENST00000334344.6:c.1672C>T	p.Arg558Cys	p.R558C	ENST00000334344	NM_152641.2	558	Cgt/Tgt	13/21	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.29	2		409	479	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435183	49435183	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	61	343	0	ENST00000301067.7:c.6370A>T	p.Ile2124Phe	p.I2124F	ENST00000301067	NM_003482.3	2124	Att/Ttt	31/54	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.29	2		343	406	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443806	49443806	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556879323	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	104	579	0	ENST00000301067.7:c.3565C>T	p.Arg1189Cys	p.R1189C	ENST00000301067	NM_003482.3	1189	Cgt/Tgt	11/54	1	2	FACETS	0.856	0.766	0.952	0.856	0.766	0.952	CLONAL	1	TRUE	1	0.29	2		579	838	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482336	56482336	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	85	478	0	ENST00000267101.3:c.884T>C	p.Val295Ala	p.V295A	ENST00000267101	NM_001982.3	295	gTg/gCg	8/28	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.29	2		478	573	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861997	57861997	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	51	368	0	ENST00000228682.2:c.1298A>G	p.Glu433Gly	p.E433G	ENST00000228682	NM_005269.2	433	gAg/gGg	10/12	1	2	FACETS	0.79	0.673	0.919	0.79	0.673	0.919	CLONAL	1	TRUE	1	0.29	2		368	445	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112893859	112893859	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	75	446	0	ENST00000351677.2:c.748G>T	p.Glu250Ter	p.E250*	ENST00000351677	NM_002834.3	250	Gaa/Taa	6/16	1	2	FACETS	0.732	0.641	0.83	0.732	0.641	0.83	SUBCLONAL	1	TRUE	1	0.29	2		446	707	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112910820	112910820	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	120	467	0	ENST00000351677.2:c.829A>C	p.Asn277His	p.N277H	ENST00000351677	NM_002834.3	277	Aat/Cat	7/16	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.29	2		467	751	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117340	115117340	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	67	438	0	ENST00000257566.3:c.834C>A	p.Phe278Leu	p.F278L	ENST00000257566	NM_016569.3	278	ttC/ttA	4/8	1	2	FACETS	0.917	0.798	1	0.917	0.798	1	CLONAL	1	TRUE	1	0.29	2		438	504	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212572	133212572	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	73	515	0	ENST00000320574.5:c.5717C>A	p.Ser1906Tyr	p.S1906Y	ENST00000320574	NM_006231.2	1906	tCt/tAt	42/49	1	2	FACETS	0.75	0.656	0.852	0.75	0.656	0.852	SUBCLONAL	1	TRUE	1	0.29	2		515	671	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250213	133250213	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs864622766	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	79	520	0	ENST00000320574.5:c.1307C>G	p.Pro436Arg	p.P436R	ENST00000320574	NM_006231.2	436	cCc/cGc	13/49	1	2	FACETS	0.846	0.744	0.955	0.846	0.744	0.955	CLONAL	1	TRUE	1	0.29	2		520	644	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253197	133253197	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	127	543	0	ENST00000320574.5:c.844C>A	p.Pro282Thr	p.P282T	ENST00000320574	NM_006231.2	282	Ccc/Acc	9/49	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.29	2		543	761	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623637	28623637	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	68	494	0	ENST00000241453.7:c.920G>T	p.Arg307Ile	p.R307I	ENST00000241453	NM_004119.2	307	aGa/aTa	8/24	1	2	FACETS	0.729	0.634	0.832	0.729	0.634	0.832	SUBCLONAL	1	TRUE	1	0.29	2		494	643	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910943	32910943	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs767686668	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	95	408	0	ENST00000380152.3:c.2451G>T	p.Lys817Asn	p.K817N	ENST00000380152		817	aaG/aaT	11/27	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.29	2		408	593	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337650	73337650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	48	282	0	ENST00000377767.4:c.2066G>A	p.Arg689Gln	p.R689Q	ENST00000377767	NM_014953.3	689	cGa/cAa	16/21	1	2	FACETS	0.744	0.63	0.869	0.744	0.63	0.869	SUBCLONAL	1	TRUE	1	0.29	2		282	445	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527907	103527907	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	53	384	0	ENST00000355739.4:c.3215G>T	p.Arg1072Ile	p.R1072I	ENST00000355739	NM_000123.3	1072	aGa/aTa	15/15	1	2	FACETS	0.778	0.664	0.902	0.778	0.664	0.902	CLONAL	1	TRUE	1	0.29	2		384	470	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609899	81609899	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	37	277	0	ENST00000298171.2:c.1497C>A	p.Phe499Leu	p.F499L	ENST00000298171	NM_000369.2	499	ttC/ttA	10/10	1	2	FACETS	0.648	0.534	0.774	0.648	0.534	0.774	SUBCLONAL	1	TRUE	1	0.29	2		277	394	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95599700	95599700	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	47	378	0	ENST00000393063.1:c.96G>A	p.Trp32Ter	p.W32*	ENST00000393063	NM_030621.3	32	tgG/tgA	3/28	1	2	FACETS	0.681	0.575	0.798	0.681	0.575	0.798	SUBCLONAL	1	TRUE	1	0.29	2		378	476	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105240310	105240310	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	67	569	0	ENST00000349310.3:c.641A>G	p.Lys214Arg	p.K214R	ENST00000349310	NM_001014432.1	214	aAg/aGg	9/15	1	2	FACETS	0.613	0.532	0.701	0.613	0.532	0.701	SUBCLONAL	1	TRUE	1	0.29	2		569	754	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000058	42000058	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	42	463	0	ENST00000219905.7:c.2320+1G>A		p.X774_splice	ENST00000219905	NM_001164273.1	774			1	2	FACETS	0.413	0.344	0.491	0.413	0.344	0.491	SUBCLONAL	1	TRUE	1	0.29	2		463	701	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749297	43749297	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs748115671	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	115	556	0	ENST00000382044.4:c.1509G>T	p.Lys503Asn	p.K503N	ENST00000382044	NM_001141980.1	503	aaG/aaT	12/28	1	2	FACETS	0.929	0.836	1	0.929	0.836	1	CLONAL	1	TRUE	1	0.29	2		556	854	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784496	43784496	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	74	448	0	ENST00000382044.4:c.178G>T	p.Glu60Ter	p.E60*	ENST00000382044	NM_001141980.1	60	Gaa/Taa	2/28	1	2	FACETS	0.765	0.67	0.868	0.765	0.67	0.868	SUBCLONAL	1	TRUE	1	0.29	2		448	667	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727483	66727483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504317	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	83	434	2	ENST00000307102.5:c.199G>A	p.Asp67Asn	p.D67N	ENST00000307102	NM_002755.3	67	Gac/Aac	2/11	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.29	2		436	569	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670452	88670452	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143617169	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	38	302	1	ENST00000360948.2:c.1234G>A	p.Glu412Lys	p.E412K	ENST00000360948	NM_001012338.2	412	Gaa/Aaa	11/19	1	2	FACETS	0.665	0.55	0.793	0.665	0.55	0.793	SUBCLONAL	1	TRUE	1	0.29	2		303	394	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358483	91358483	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	73	546	0	ENST00000355112.3:c.4228C>A	p.Leu1410Ile	p.L1410I	ENST00000355112	NM_000057.2	1410	Ctt/Att	22/22	1	2	FACETS	0.75	0.656	0.852	0.75	0.656	0.852	SUBCLONAL	1	TRUE	1	0.29	2		546	671	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801803	3801803	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	74	426	0	ENST00000262367.5:c.3703C>A	p.His1235Asn	p.H1235N	ENST00000262367	NM_004380.2	1235	Cat/Aat	20/31	1	2	FACETS	0.859	0.753	0.974	0.859	0.753	0.974	CLONAL	1	TRUE	1	0.29	2		426	594	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116170	67116170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761036715	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	105	516	1	ENST00000412916.2:c.454G>A	p.Glu152Lys	p.E152K	ENST00000412916		152	Gaa/Aaa	5/6	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.29	2		517	711	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858343	59858343	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375246789	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	41	409	0	ENST00000259008.2:c.1652C>T	p.Ala551Val	p.A551V	ENST00000259008	NM_032043.2	551	gCg/gTg	12/20	1	2	FACETS	0.473	0.393	0.562	0.473	0.393	0.562	SUBCLONAL	1	TRUE	1	0.29	2		409	598	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45377669	45377669	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	94	353	0	ENST00000262160.6:c.760C>T	p.Leu254Phe	p.L254F	ENST00000262160	NM_005901.5	254	Ctt/Ttt	7/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.29	2		353	546	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627677	14627677	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	99	466	0	ENST00000254322.2:c.393C>A	p.Phe131Leu	p.F131L	ENST00000254322	NM_006145.1	131	ttC/ttA	2/3	1	2	FACETS	0.987	0.881	1	0.987	0.881	1	CLONAL	1	TRUE	1	0.29	2		466	692	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029172	26029172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	76	419	0	ENST00000435504.4:c.178C>T	p.Leu60Phe	p.L60F	ENST00000435504		60	Ctt/Ttt	4/13	1	2	FACETS	0.902	0.792	1	0.902	0.792	1	CLONAL	1	TRUE	1	0.29	2		419	581	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015651	27015651	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1392372965	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	83	523	1	ENST00000335756.4:c.238C>T	p.Arg80Cys	p.R80C	ENST00000335756	NM_001809.3	80	Cgt/Tgt	3/5	1	2	FACETS	0.858	0.758	0.966	0.858	0.758	0.966	CLONAL	1	TRUE	1	0.29	2		524	667	SUCCESS
ALK	238	MSKCC	GRCh37	2	29541235	29541235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758494304	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	127	505	0	ENST00000389048.3:c.1582G>A	p.Ala528Thr	p.A528T	ENST00000389048	NM_004304.4	528	Gct/Act	8/29	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.29	2		505	685	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222281	39222281	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572955351	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	41	464	0	ENST00000402219.2:c.3329C>T	p.Ser1110Leu	p.S1110L	ENST00000402219	NM_005633.3	1110	tCg/tTg	20/23	1	2	FACETS	0.406	0.337	0.483	0.406	0.337	0.483	SUBCLONAL	1	TRUE	1	0.29	2		464	696	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033753	48033753	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1553333707	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	77	344	0	ENST00000234420.5:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000234420	NM_000179.2	1322	Gaa/Taa	9/10	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.29	2		344	486	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630699	158630699	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	23	276	0	ENST00000263640.3:c.544G>A	p.Asp182Asn	p.D182N	ENST00000263640	NM_001105.4	182	Gat/Aat	6/11	1	2	FACETS	0.389	0.302	0.489	0.389	0.302	0.489	SUBCLONAL	1	TRUE	1	0.29	2		276	408	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095644	178095644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763240080	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	71	456	0	ENST00000397062.3:c.1687G>A	p.Glu563Lys	p.E563K	ENST00000397062	NM_006164.4	563	Gaa/Aaa	5/5	1	2	FACETS	0.884	0.772	1	0.884	0.772	1	CLONAL	1	TRUE	1	0.29	2		456	554	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660526	190660526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1376121914	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	26	286	0	ENST00000441310.2:c.164G>A	p.Arg55Gln	p.R55Q	ENST00000441310	NM_000534.4	55	cGa/cAa	3/13	1	2	FACETS	0.466	0.369	0.577	0.466	0.369	0.577	SUBCLONAL	1	TRUE	1	0.29	2		286	385	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270162	198270162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	95	363	0	ENST00000335508.6:c.1274G>A	p.Arg425Gln	p.R425Q	ENST00000335508	NM_012433.2	425	cGa/cAa	10/25	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.29	2		363	521	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495220	212495220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	59	454	2	ENST00000342788.4:c.2046G>T	p.Lys682Asn	p.K682N	ENST00000342788	NM_005235.2	682	aaG/aaT	17/28	1	2	FACETS	0.691	0.594	0.796	0.691	0.594	0.796	SUBCLONAL	1	TRUE	1	0.29	2		456	589	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400170	41400170	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	91	462	1	ENST00000373198.4:c.589C>T	p.Arg197Ter	p.R197*	ENST00000373198	NM_133170.3	197	Cga/Tga	5/32	1	2	FACETS	0.963	0.855	1	0.963	0.855	1	CLONAL	1	TRUE	1	0.29	2		463	652	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523642	41523642	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1386169409	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	102	580	2	ENST00000263253.7:c.1058G>A	p.Arg353His	p.R353H	ENST00000263253	NM_001429.3	353	cGc/cAc	4/31	1	2	FACETS	0.923	0.826	1	0.923	0.826	1	CLONAL	1	TRUE	1	0.29	2		582	762	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537115	41537115	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853039	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	82	472	0	ENST00000263253.7:c.1942C>T	p.Arg648Ter	p.R648*	ENST00000263253	NM_001429.3	648	Cga/Tga	10/31	1	2	FACETS	0.938	0.828	1	0.938	0.828	1	CLONAL	1	TRUE	1	0.29	2		472	603	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050355	37050355	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	83	501	0	ENST00000231790.2:c.504T>G	p.Asn168Lys	p.N168K	ENST00000231790	NM_000249.3	168	aaT/aaG	6/19	1	2	FACETS	0.881	0.778	0.991	0.881	0.778	0.991	CLONAL	1	TRUE	1	0.29	2		501	650	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277233	41277233	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	40	299	0	ENST00000349496.5:c.1702G>T	p.Glu568Ter	p.E568*	ENST00000349496	NM_001904.3	568	Gaa/Taa	11/15	1	2	FACETS	0.6	0.498	0.713	0.6	0.498	0.713	SUBCLONAL	1	TRUE	1	0.29	2		299	460	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164885	47164885	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	17	252	0	ENST00000409792.3:c.1241G>T	p.Arg414Ile	p.R414I	ENST00000409792	NM_014159.6	414	aGa/aTa	3/21	1	2	FACETS	0.406	0.302	0.528	0.406	0.302	0.528	SUBCLONAL	1	TRUE	1	0.29	2		252	289	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933243	49933243	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	41	608	0	ENST00000296474.3:c.2867G>T	p.Ser956Ile	p.S956I	ENST00000296474	NM_002447.2	956	aGc/aTc	12/20	1	2	FACETS	0.347	0.288	0.414	0.347	0.288	0.414	SUBCLONAL	1	TRUE	1	0.29	2		608	814	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643768	52643768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	80	504	1	ENST00000394830.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000394830	NM_018313.4	710	Cga/Tga	17/30	1	2	FACETS	0.833	0.734	0.94	0.833	0.734	0.94	CLONAL	1	TRUE	1	0.29	2		505	662	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014163	70014163	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868519483	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	116	550	0	ENST00000394351.3:c.1024G>A	p.Asp342Asn	p.D342N	ENST00000394351	NM_000248.3	342	Gat/Aat	9/9	1	2	FACETS	0.978	0.881	1	0.978	0.881	1	CLONAL	1	TRUE	1	0.29	2		550	818	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114551	73114551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs910462101	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	37	271	0	ENST00000356692.5:c.932C>A	p.Ser311Tyr	p.S311Y	ENST00000356692		311	tCt/tAt	9/9	1	2	FACETS	0.778	0.643	0.928	0.778	0.643	0.928	CLONAL	1	TRUE	1	0.29	2		271	328	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457258	89457258	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779282250	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	59	486	0	ENST00000336596.2:c.1739G>T	p.Arg580Ile	p.R580I	ENST00000336596	NM_005233.5	580	aGa/aTa	9/17	1	2	FACETS	0.725	0.624	0.835	0.725	0.624	0.835	SUBCLONAL	1	TRUE	1	0.29	2		486	561	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119666143	119666143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769576748	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	95	451	0	ENST00000316626.5:c.338G>A	p.Arg113His	p.R113H	ENST00000316626		113	cGt/cAt	3/12	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.29	2		451	598	SUCCESS
ATR	545	MSKCC	GRCh37	3	142180887	142180887	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs868378229	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	68	373	1	ENST00000350721.4:c.7087C>T	p.Arg2363Ter	p.R2363*	ENST00000350721	NM_001184.3	2363	Cga/Tga	42/47	1	2	FACETS	0.907	0.79	1	0.907	0.79	1	CLONAL	1	TRUE	1	0.29	2		374	517	SUCCESS
ATR	545	MSKCC	GRCh37	3	142243002	142243002	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	53	370	0	ENST00000350721.4:c.3985G>T	p.Glu1329Ter	p.E1329*	ENST00000350721	NM_001184.3	1329	Gaa/Taa	22/47	1	2	FACETS	0.735	0.628	0.853	0.735	0.628	0.853	SUBCLONAL	1	TRUE	1	0.29	2		370	497	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749415085	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	51	337	1	ENST00000263967.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000263967	NM_006218.2	38	Cgt/Tgt	2/21	1	2	FACETS	0.809	0.688	0.94	0.809	0.688	0.94	CLONAL	1	TRUE	1	0.29	2		338	435	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	16	384	0	ENST00000263967.3:c.333G>T	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaT	2/21	1	2	FACETS	0.209	0.154	0.276	0.209	0.154	0.276	SUBCLONAL	1	TRUE	1	0.29	2		384	527	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921533	178921533	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1428379257	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	56	394	0	ENST00000263967.3:c.1015C>A	p.Leu339Ile	p.L339I	ENST00000263967	NM_006218.2	339	Ctt/Att	5/21	1	2	FACETS	0.82	0.704	0.947	0.82	0.704	0.947	CLONAL	1	TRUE	1	0.29	2		394	471	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	73	377	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.29	2		377	498	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902403	1902403	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	111	580	0	ENST00000382891.5:c.22A>G	p.Ser8Gly	p.S8G	ENST00000382891	NM_133335.3	8	Agt/Ggt	2/22	1	2	FACETS	0.942	0.846	1	0.942	0.846	1	CLONAL	1	TRUE	1	0.29	2		580	813	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155583	106155583	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	74	367	0	ENST00000380013.4:c.484G>T	p.Asp162Tyr	p.D162Y	ENST00000380013	NM_001127208.2	162	Gat/Tat	3/11	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.29	2		367	510	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	18	464	1	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	0.192	0.143	0.249	0.192	0.143	0.249	SUBCLONAL	1	TRUE	1	0.29	2		465	648	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	81	460	1	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.29	2		461	536	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532612	187532612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	39	341	0	ENST00000441802.2:c.9781G>A	p.Ala3261Thr	p.A3261T	ENST00000441802	NM_005245.3	3261	Gca/Aca	14/27	1	2	FACETS	0.617	0.511	0.734	0.617	0.511	0.734	SUBCLONAL	1	TRUE	1	0.29	2		341	436	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293525	1293525	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	118	624	0	ENST00000310581.5:c.1476G>T	p.Lys492Asn	p.K492N	ENST00000310581	NM_198253.2	492	aaG/aaT	2/16	1	2	FACETS	0.938	0.845	1	0.938	0.845	1	CLONAL	1	TRUE	1	0.29	2		624	868	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449464	31449464	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	107	401	0	ENST00000344624.3:c.2745T>G	p.Asn915Lys	p.N915K	ENST00000344624		915	aaT/aaG	19/33	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.29	2		401	637	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945790	38945790	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1316909708	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	38	250	0	ENST00000357387.3:c.4436C>A	p.Ser1479Tyr	p.S1479Y	ENST00000357387	NM_152756.3	1479	tCt/tAt	34/38	1	2	FACETS	0.797	0.66	0.948	0.797	0.66	0.948	CLONAL	1	TRUE	1	0.29	2		250	329	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950648	38950648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776074870	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	57	333	0	ENST00000357387.3:c.3302C>T	p.Ser1101Leu	p.S1101L	ENST00000357387	NM_152756.3	1101	tCg/tTg	31/38	1	2	FACETS	0.897	0.772	1	0.897	0.772	1	CLONAL	1	TRUE	1	0.29	2		333	438	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184142	56184142	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	74	396	0	ENST00000399503.3:c.4347G>A	p.Trp1449Ter	p.W1449*	ENST00000399503	NM_005921.1	1449	tgG/tgA	19/20	1	2	FACETS	0.865	0.758	0.98	0.865	0.758	0.98	CLONAL	1	TRUE	1	0.29	2		396	590	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184161	56184161	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	89	337	0	ENST00000399503.3:c.4366A>G	p.Asn1456Asp	p.N1456D	ENST00000399503	NM_005921.1	1456	Aat/Gat	19/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.29	2		337	501	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79960969	79960969	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1472947441	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	43	322	0	ENST00000265081.6:c.366G>T	p.Lys122Asn	p.K122N	ENST00000265081	NM_002439.4	122	aaG/aaT	3/24	1	2	FACETS	0.69	0.578	0.814	0.69	0.578	0.814	SUBCLONAL	1	TRUE	1	0.29	2		322	430	SUCCESS
APC	324	MSKCC	GRCh37	5	112173582	112173582	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	43	299	0	ENST00000257430.4:c.2291T>G	p.Leu764Ter	p.L764*	ENST00000257430	NM_000038.5	764	tTa/tGa	16/16	1	2	FACETS	0.768	0.644	0.905	0.768	0.644	0.905	CLONAL	1	TRUE	1	0.29	2		299	386	SUCCESS
APC	324	MSKCC	GRCh37	5	112175925	112175925	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs863225356	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	51	264	0	ENST00000257430.4:c.4634C>A	p.Ser1545Ter	p.S1545*	ENST00000257430	NM_000038.5	1545	tCa/tAa	16/16	1	2	FACETS	0.873	0.744	1	0.873	0.744	1	CLONAL	1	TRUE	1	0.29	2		264	403	SUCCESS
APC	324	MSKCC	GRCh37	5	112176873	112176873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	74	382	0	ENST00000257430.4:c.5582C>A	p.Ser1861Tyr	p.S1861Y	ENST00000257430	NM_000038.5	1861	tCt/tAt	16/16	1	2	FACETS	0.95	0.833	1	0.95	0.833	1	CLONAL	1	TRUE	1	0.29	2		382	537	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638491	176638491	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784096	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	78	597	1	ENST00000439151.2:c.3091C>T	p.Arg1031Ter	p.R1031*	ENST00000439151	NM_022455.4	1031	Cga/Tga	5/23	1	2	FACETS	0.67	0.588	0.758	0.67	0.588	0.758	SUBCLONAL	1	TRUE	1	0.29	2		598	803	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057021	180057021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752512978	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	117	724	0	ENST00000261937.6:c.598G>A	p.Asp200Asn	p.D200N	ENST00000261937	NM_182925.4	200	Gat/Aat	5/30	1	2	FACETS	0.975	0.878	1	0.975	0.878	1	CLONAL	1	TRUE	1	0.29	2		724	828	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858171	27858171	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	37	347	0	ENST00000359303.2:c.400G>A	p.Glu134Lys	p.E134K	ENST00000359303	NM_003535.2	134	Gag/Aag	1/1	1	2	FACETS	0.513	0.423	0.615	0.513	0.423	0.615	SUBCLONAL	1	TRUE	1	0.29	2		347	497	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681925	30681925	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1347359920	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	67	421	2	ENST00000376406.3:c.172C>T	p.Arg58Ter	p.R58*	ENST00000376406	NM_014641.2	58	Cga/Tga	3/15	1	2	FACETS	0.917	0.798	1	0.917	0.798	1	CLONAL	1	TRUE	1	0.29	2		423	504	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169953	32169953	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202197092	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	105	629	2	ENST00000375023.3:c.3655C>T	p.Arg1219Trp	p.R1219W	ENST00000375023	NM_004557.3	1219	Cgg/Tgg	21/30	1	2	FACETS	0.925	0.828	1	0.925	0.828	1	CLONAL	1	TRUE	1	0.29	2		631	783	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798510	32798510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746574637	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	111	622	1	ENST00000374899.4:c.1346G>A	p.Arg449Gln	p.R449Q	ENST00000374899	NM_018833.2	449	cGa/cAa	8/12	1	2	FACETS	0.955	0.858	1	0.955	0.858	1	CLONAL	1	TRUE	1	0.29	2		623	802	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956553	93956553	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1035177735	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	75	399	0	ENST00000369303.4:c.2683C>T	p.Arg895Ter	p.R895*	ENST00000369303	NM_004440.3	895	Cga/Tga	15/17	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.29	2		399	500	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622269	117622269	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	85	466	0	ENST00000368508.3:c.6601G>T	p.Glu2201Ter	p.E2201*	ENST00000368508	NM_002944.2	2201	Gaa/Taa	42/43	1	2	FACETS	0.876	0.775	0.985	0.876	0.775	0.985	CLONAL	1	TRUE	1	0.29	2		466	669	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665270	117665270	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	34	306	0	ENST00000368508.3:c.4477G>T	p.Glu1493Ter	p.E1493*	ENST00000368508	NM_002944.2	1493	Gaa/Taa	27/43	1	2	FACETS	0.56	0.457	0.675	0.56	0.457	0.675	SUBCLONAL	1	TRUE	1	0.29	2		306	419	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687405	117687405	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	47	353	0	ENST00000368508.3:c.2646A>C	p.Glu882Asp	p.E882D	ENST00000368508	NM_002944.2	882	gaA/gaC	18/43	1	2	FACETS	0.785	0.663	0.918	0.785	0.663	0.918	CLONAL	1	TRUE	1	0.29	2		353	413	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016267	150016267	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	87	468	2	ENST00000253339.5:c.439C>T	p.Arg147Ter	p.R147*	ENST00000253339		147	Cga/Tga	2/7	1	2	FACETS	0.987	0.875	1	0.987	0.875	1	CLONAL	1	TRUE	1	0.29	2		470	608	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206903	162206903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756064095	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	75	423	0	ENST00000366898.1:c.772G>A	p.Val258Met	p.V258M	ENST00000366898	NM_004562.2	258	Gtg/Atg	7/12	1	2	FACETS	0.94	0.825	1	0.94	0.825	1	CLONAL	1	TRUE	1	0.29	2		423	550	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026643	6026643	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs63750947	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	211	797	0	ENST00000265849.7:c.1753C>A	p.Leu585Ile	p.L585I	ENST00000265849	NM_000535.5	585	Ctt/Att	11/15	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.29	2		797	1207	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509660	106509660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757849968	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	72	450	1	ENST00000359195.3:c.1654C>T	p.Arg552Cys	p.R552C	ENST00000359195	NM_002649.2	552	Cgc/Tgc	2/11	1	2	FACETS	0.801	0.7	0.91	0.801	0.7	0.91	CLONAL	1	TRUE	1	0.29	2		451	620	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515182	106515182	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	99	485	1	ENST00000359195.3:c.2325G>T	p.Gln775His	p.Q775H	ENST00000359195	NM_002649.2	775	caG/caT	5/11	1	2	FACETS	0.955	0.853	1	0.955	0.853	1	CLONAL	1	TRUE	1	0.29	2		486	715	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5466775	5466775	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1487811405	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	49	231	0	ENST00000381577.3:c.796A>G	p.Met266Val	p.M266V	ENST00000381577	NM_014143.3	266	Atg/Gtg	6/7	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.29	2		231	313	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486004	8486004	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	28	449	0	ENST00000356435.5:c.2813C>A	p.Ser938Tyr	p.S938Y	ENST00000356435		938	tCt/tAt	17/35	1	2	FACETS	0.366	0.291	0.451	0.366	0.291	0.451	SUBCLONAL	1	TRUE	1	0.29	2		449	528	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971037	21971037	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs772527888	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	70	411	0	ENST00000579755.1:c.364C>T	p.Arg122Ter	p.R122*	ENST00000579755		122	Cga/Tga	2/3	1	2	FACETS	0.939	0.82	1	0.939	0.82	1	CLONAL	1	TRUE	1	0.29	2		411	514	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864023	97864023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881729	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	73	470	0	ENST00000289081.3:c.1643G>A	p.Arg548Gln	p.R548Q	ENST00000289081	NM_000136.2	548	cGa/cAa	15/15	1	2	FACETS	0.8	0.7	0.908	0.8	0.7	0.908	CLONAL	1	TRUE	1	0.29	2		470	629	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787834	135787834	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	67	320	0	ENST00000298552.3:c.748T>A	p.Leu250Ile	p.L250I	ENST00000298552	NM_001162426.1	250	Tta/Ata	9/23	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.29	2		320	417	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916551	39916551	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	128	506	1	ENST00000378444.4:c.4452G>T	p.Glu1484Asp	p.E1484D	ENST00000378444	NM_001123385.1	1484	gaG/gaT	11/15	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.29	2		507	729	SUCCESS
AR	367	MSKCC	GRCh37	X	66942671	66942671	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	25	366	0	ENST00000374690.3:c.2452C>T	p.Pro818Ser	p.P818S	ENST00000374690	NM_000044.3	818	Cca/Tca	7/8	1	2	FACETS	0.355	0.279	0.443	0.355	0.279	0.443	SUBCLONAL	1	TRUE	1	0.29	2		366	486	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938995	76938995	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs886044898	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	94	548	0	ENST00000373344.5:c.1753G>T	p.Glu585Ter	p.E585*	ENST00000373344	NM_000489.3	585	Gaa/Taa	9/35	1	2	FACETS	0.85	0.756	0.95	0.85	0.756	0.95	CLONAL	1	TRUE	1	0.29	2		548	763	SUCCESS
BTK	695	MSKCC	GRCh37	X	100612528	100612528	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	75	482	0	ENST00000308731.7:c.1146G>T	p.Lys382Asn	p.K382N	ENST00000308731	NM_000061.2	382	aaG/aaT	13/19	1	2	FACETS	0.811	0.711	0.919	0.811	0.711	0.919	CLONAL	1	TRUE	1	0.29	2		482	638	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123022564	123022564	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1193388815	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	72	453	0	ENST00000355640.3:c.973C>A	p.Pro325Thr	p.P325T	ENST00000355640		325	Cca/Aca	3/7	1	2	FACETS	0.979	0.858	1	0.979	0.858	1	CLONAL	1	TRUE	1	0.29	2		453	507	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229252	123229252	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	31	396	0	ENST00000218089.9:c.3736G>T	p.Glu1246Ter	p.E1246*	ENST00000218089	NM_001042749.1	1246	Gaa/Taa	34/35	1	2	FACETS	0.352	0.283	0.429	0.352	0.283	0.429	SUBCLONAL	1	TRUE	1	0.29	2		396	608	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716326	52716326	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	162	466	0	ENST00000322088.6:c.770G>T	p.Trp257Leu	p.W257L	ENST00000322088	NM_014225.5	257	tGg/tTg	6/15	0.282592782359636	5	FACETS	0.774	0.713	0.837			1	INDETERMINATE	2	TRUE	NA	0.647790420117124	5		466	637	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0029692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	341	411	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	0.577387793127632	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	2	0.647790420117124	4		411	710	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576861	7576870	+	frameshift_variant	Frame_Shift_Del	DEL	TGAAATATTC	TGAAATATTC	-	novel	NA	P-0029692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	424	550	0	ENST00000269305.4:c.976_985del	p.Glu326ProfsTer16	p.E326Pfs*16	ENST00000269305	NM_001126112.2	326	GAATATTTCAcc/cc	9/11	0.647790420117124	3	FACETS	0.963	0.932	0.993			1	CLONAL	3	TRUE	NA	0.647790420117124	3		550	600	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560952	9560952	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	215	394	0	ENST00000353224.5:c.830G>T	p.Ser277Ile	p.S277I	ENST00000353224	NM_177990.2	277	aGc/aTc	4/10	0.529158866398217	4	FACETS	0.965	0.904	1	0.965	0.904	1	CLONAL	2	TRUE	2	0.647790420117124	4		394	567	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89791098	89791098	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	121	159	0	ENST00000336032.3:c.485C>T	p.Pro162Leu	p.P162L	ENST00000336032	NM_006813.2	162	cCc/cTc	1/2	0.577387793127632	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.647790420117124	4		159	273	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0029693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	15	282	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.719	0.533	0.937	0.719	0.533	0.937	CLONAL	1	FALSE	1	0.408934017545216	2		282	102	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0029693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	43	428	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.301855577984658	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	FALSE	0	0.408934017545216	1		428	149	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0029693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	52	440	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.408934017545216	2	FACETS	0.986	0.863	1	0.986	0.863	1	CLONAL	2	FALSE	0	0.408934017545216	2		440	129	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	76	394	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.311645740989241	3	FACETS	1	0.928	1	1	0.928	1	CLONAL	3	FALSE	0	0.408934017545216	3		394	145	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762846821	NA	P-0029693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	8	630	1	ENST00000269305.4:c.461G>A	p.Gly154Asp	p.G154D	ENST00000269305	NM_001126112.2	154	gGc/gAc	5/11	1	2	FACETS	0.115	0.074	0.17	0.115	0.074	0.17	SUBCLONAL	1	FALSE	1	0.408934017545216	2		631	339	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1485978447	NA	P-0029693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	45	398	0	ENST00000324856.7:c.5164C>T	p.Arg1722Ter	p.R1722*	ENST00000324856	NM_006015.4	1722	Cga/Tga	20/20	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	FALSE	1	0.408934017545216	2		398	214	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	31	632	0	ENST00000227507.2:c.859C>T	p.Pro287Ser	p.P287S	ENST00000227507	NM_053056.2	287	Ccc/Tcc	5/5	1	2	FACETS	0.59	0.479	0.714	0.59	0.479	0.714	SUBCLONAL	1	FALSE	1	0.408934017545216	2		632	257	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058047	27058048	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	TT	novel	NA	P-0029693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	34	399	0	ENST00000324856.7:c.1755_1756delinsTT	p.Gln585_Gln586delinsHisTer	p.Q585_Q586delinsH*	ENST00000324856	NM_006015.4	585	caGCag/caTTag	3/20	1	2	FACETS	0.819	0.675	0.978	0.819	0.675	0.978	CLONAL	1	FALSE	1	0.408934017545216	2		399	203	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578393	7578393	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876660821	NA	P-0029704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	441	698	0	ENST00000269305.4:c.537T>A	p.His179Gln	p.H179Q	ENST00000269305	NM_001126112.2	179	caT/caA	5/11	0.568594142850149	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.568594142850149	1		698	910	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623658	28623658	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	228	529	0	ENST00000241453.7:c.899T>A	p.Met300Lys	p.M300K	ENST00000241453	NM_004119.2	300	aTg/aAg	8/24	NA	2	FACETS	0.809	0.754	0.866			1	INDETERMINATE	1	TRUE	NA	0.568594142850149	2		529	991	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399435	139399435	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	1283	988	0	ENST00000277541.6:c.4708G>C	p.Ala1570Pro	p.A1570P	ENST00000277541	NM_017617.3	1570	Gcg/Ccg	26/34	0.568594142850149	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.568594142850149	2		988	1930	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0029705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	566	498	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.547441155334554	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	TRUE	0	0.552355669428649	3		498	872	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993057	72993057	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1171562821	NA	P-0029705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	286	818	2	ENST00000268489.5:c.988G>A	p.Gly330Ser	p.G330S	ENST00000268489	NM_006885.3	330	Ggc/Agc	2/10	0.492641420522058	2	FACETS	0.899	0.845	0.954	0.449	0.422	0.477	CLONAL	1	TRUE	0	0.552355669428649	2		820	1152	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0029706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	50	440	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.576	0.488	0.673	0.576	0.488	0.673	SUBCLONAL	1	FALSE	1	0.266750002882728	2		440	651	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0029706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	98	740	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.602	0.535	0.674	0.602	0.535	0.674	SUBCLONAL	1	FALSE	1	0.266750002882728	2		741	1220	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922364	178922364	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397514565	NA	P-0029706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	97	510	1	ENST00000263967.3:c.1133G>A	p.Cys378Tyr	p.C378Y	ENST00000263967	NM_006218.2	378	tGt/tAt	6/21	1	2	FACETS	0.732	0.652	0.819	0.732	0.652	0.819	SUBCLONAL	1	FALSE	1	0.266750002882728	2		511	993	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554613	29554613	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	62	527	0	ENST00000356175.3:c.2398G>T	p.Glu800Ter	p.E800*	ENST00000356175	NM_000267.3	800	Gaa/Taa	20/57	1	2	FACETS	0.549	0.473	0.632	0.549	0.473	0.632	SUBCLONAL	1	FALSE	1	0.266750002882728	2		527	847	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692889	89692889	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	242	455	0	ENST00000371953.3:c.373A>G	p.Lys125Glu	p.K125E	ENST00000371953	NM_000314.4	125	Aaa/Gaa	5/9	0.68705635698365	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.68705635698365	1		455	416	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707849	43707849	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	494	845	0	ENST00000382044.4:c.5032T>A	p.Ser1678Thr	p.S1678T	ENST00000382044	NM_001141980.1	1678	Tct/Act	23/28	0.68705635698365	1	FACETS	0.901	0.866	0.936	0.901	0.866	0.936	CLONAL	1	TRUE	0	0.68705635698365	1		845	1048	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882005	NA	P-0029712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	335	616	0	ENST00000269305.4:c.713G>C	p.Cys238Ser	p.C238S	ENST00000269305	NM_001126112.2	238	tGt/tCt	7/11	0.319457225639215	3	FACETS	0.91	0.864	0.957	0.91	0.864	0.957	CLONAL	3	TRUE	0	0.319457225639215	3		616	891	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926888	112926888	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397507546	NA	P-0029712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	148	643	0	ENST00000351677.2:c.1508G>T	p.Gly503Val	p.G503V	ENST00000351677	NM_002834.3	503	gGg/gTg	13/16	0.319457225639215	3	FACETS	1	0.987	1	0.729	0.667	0.794	CLONAL	1	TRUE	1	0.319457225639215	3		643	737	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	43	650	1	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.328559961670478	4	FACETS	0.344	0.287	0.408	0.086	0.071	0.102	SUBCLONAL	1	TRUE	0	0.54435318773013	4		651	709	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	497	771	1	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.328559961670478	4	FACETS	0.878	0.849	0.907	0.878	0.849	0.907	CLONAL	4	TRUE	0	0.54435318773013	4		772	803	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241726	55241726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767505234	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	163	579	0	ENST00000275493.2:c.2174C>T	p.Thr725Met	p.T725M	ENST00000275493	NM_005228.3	725	aCg/aTg	18/28	0.54435318773013	3	FACETS	1	0.98	1	0.599	0.552	0.648	CLONAL	1	TRUE	1	0.54435318773013	3		579	636	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730802	40730802	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	243	770	0	ENST00000373198.4:c.3733G>T	p.Gly1245Ter	p.G1245*	ENST00000373198	NM_133170.3	1245	Gga/Tga	27/32	0.481329147632976	3	FACETS	1	0.993	1	0.741	0.695	0.789	CLONAL	1	TRUE	1	0.54435318773013	3		770	766	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202552	67202552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373972783	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	433	904	0	ENST00000312629.5:c.1361C>T	p.Pro454Leu	p.P454L	ENST00000312629	NM_003952.2	454	cCg/cTg	15/15	0.54435318773013	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.54435318773013	3		904	932	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398863	398863	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1321465734	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1265	792	588	0	ENST00000380956.4:c.673C>A	p.Pro225Thr	p.P225T	ENST00000380956	NM_001195286.1	225	Cca/Aca	6/9	0.54435318773013	10	FACETS	1	0.994	1	0.562	0.543	0.581	CLONAL	4	TRUE	2	0.54435318773013	10		588	2057	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031947	26031947	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	168	383	0	ENST00000244661.2:c.342T>A	p.His114Gln	p.H114Q	ENST00000244661	NM_003537.3	114	caT/caA	1/1	0.54435318773013	10	FACETS	0.979	0.899	1	0.245	0.224	0.266	CLONAL	2	TRUE	2	0.54435318773013	10		383	1002	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557699	21557699	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	447	733	0	ENST00000382592.4:c.2146G>T	p.Glu716Ter	p.E716*	ENST00000382592	NM_014572.2	716	Gag/Tag	5/8	0.509566034053891	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	0	0.54435318773013	3		733	683	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106939	27106939	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	278	485	1	ENST00000324856.7:c.6550G>T	p.Ala2184Ser	p.A2184S	ENST00000324856	NM_006015.4	2184	Gcc/Tcc	20/20	0.531726919170502	3	FACETS	0.998	0.955	1	0.998	0.955	1	CLONAL	3	TRUE	0	0.54435318773013	3		486	434	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468310	120468310	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1368507640	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	844	624	0	ENST00000256646.2:c.4129G>T	p.Gly1377Cys	p.G1377C	ENST00000256646	NM_024408.3	1377	Ggc/Tgc	25/34	0.54435318773013	7	FACETS	0.984	0.965	1	1	0.998	1	CLONAL	7	TRUE	1	0.54435318773013	7		624	1063	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317684	163317684	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	32	545	0	ENST00000271452.3:c.1080T>A	p.Asn360Lys	p.N360K	ENST00000271452	NM_145697.2	360	aaT/aaA	12/14	0.531726919170502	3	FACETS	0.273	0.221	0.332	0.091	0.073	0.111	SUBCLONAL	1	TRUE	0	0.54435318773013	3		545	548	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555271	226555271	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	55	571	1	ENST00000366794.5:c.2316G>T	p.Glu772Asp	p.E772D	ENST00000366794	NM_001618.3	772	gaG/gaT	17/23	0.531726919170502	3	FACETS	0.415	0.355	0.482	0.138	0.118	0.161	SUBCLONAL	1	TRUE	0	0.54435318773013	3		572	619	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309769	104309769	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	317	759	0	ENST00000369902.3:c.360del	p.Thr121ProfsTer4	p.T121Pfs*4	ENST00000369902	NM_016169.3	120	ttG/tt	3/12	0.288422807718267	4	FACETS	1	0.991	1	1	0.991	1	INDETERMINATE	2	TRUE	2	0.54435318773013	4		759	744	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999633	100999633	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs3740754	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	188	1168	0	ENST00000325455.5:c.169G>T	p.Gly57Trp	p.G57W	ENST00000325455	NM_001202474.3	57	Ggg/Tgg	1/8	0.259246102249315	4	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.54435318773013	4		1168	989	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245244	46245244	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	422	481	0	ENST00000334344.6:c.3338G>T	p.Gly1113Val	p.G1113V	ENST00000334344	NM_152641.2	1113	gGg/gTg	15/21	0.54435318773013	4	FACETS	0.994	0.962	1	0.994	0.962	1	CLONAL	4	TRUE	0	0.54435318773013	4		481	602	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287501	46287501	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	477	488	1	ENST00000334344.6:c.5360G>T	p.Arg1787Leu	p.R1787L	ENST00000334344	NM_152641.2	1787	cGc/cTc	20/21	0.54435318773013	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	4	TRUE	0	0.54435318773013	4		489	667	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562918	21562918	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	528	795	1	ENST00000382592.4:c.1001G>T	p.Arg334Leu	p.R334L	ENST00000382592	NM_014572.2	334	cGc/cTc	4/8	0.509566034053891	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.54435318773013	3		796	776	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588670	28588670	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	314	540	0	ENST00000241453.7:c.2778G>C	p.Trp926Cys	p.W926C	ENST00000241453	NM_004119.2	926	tgG/tgC	23/24	0.509566034053891	3	FACETS	0.965	0.925	1	0.965	0.925	1	CLONAL	3	TRUE	0	0.54435318773013	3		540	507	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435867	110435867	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	455	664	0	ENST00000375856.3:c.2534C>A	p.Pro845Gln	p.P845Q	ENST00000375856	NM_003749.2	845	cCa/cAa	1/2	0.509566034053891	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.54435318773013	3		664	654	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30047509	30047509	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	239	550	0	ENST00000331968.5:c.2492A>T	p.Asp831Val	p.D831V	ENST00000331968	NM_002742.2	831	gAt/gTt	17/18	0.54435318773013	3	FACETS	0.94	0.885	0.997	0.94	0.885	0.997	CLONAL	2	TRUE	1	0.54435318773013	3		550	594	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132970	30132970	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	183	665	0	ENST00000331968.5:c.631G>T	p.Gly211Trp	p.G211W	ENST00000331968	NM_002742.2	211	Ggg/Tgg	4/18	0.54435318773013	3	FACETS	1	0.979	1	0.58	0.536	0.624	CLONAL	1	TRUE	1	0.54435318773013	3		665	738	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988424	36988424	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs758796327	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	117	462	0	ENST00000354822.5:c.229G>T	p.Ala77Ser	p.A77S	ENST00000354822	NM_001079668.2	77	Gca/Tca	2/3	0.54435318773013	3	FACETS	1	0.971	1	0.589	0.535	0.646	CLONAL	1	TRUE	1	0.54435318773013	3		462	464	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003384	42003384	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	243	519	0	ENST00000219905.7:c.2921A>T	p.Gln974Leu	p.Q974L	ENST00000219905	NM_001164273.1	974	cAg/cTg	8/24	0.481329147632976	3	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	1	0.54435318773013	3		519	565	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712790	43712790	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	282	812	0	ENST00000382044.4:c.4394G>T	p.Ser1465Ile	p.S1465I	ENST00000382044	NM_001141980.1	1465	aGt/aTt	21/28	0.481329147632976	3	FACETS	0.897	0.847	0.947	0.897	0.847	0.947	CLONAL	2	TRUE	1	0.54435318773013	3		812	735	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221961	1221961	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	398	904	0	ENST00000326873.7:c.876C>G	p.Tyr292Ter	p.Y292*	ENST00000326873	NM_000455.4	292	taC/taG	7/10	0.54435318773013	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.54435318773013	2		904	722	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466766	25466766	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1238786275	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	221	566	0	ENST00000264709.3:c.1936+1G>A		p.X646_splice	ENST00000264709	NM_175629.2	646			0.54435318773013	6	FACETS	0.873	0.813	0.936	0.437	0.406	0.468	CLONAL	2	TRUE	2	0.54435318773013	6		566	971	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248702	212248702	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	157	430	2	ENST00000342788.4:c.3565C>A	p.His1189Asn	p.H1189N	ENST00000342788	NM_005235.2	1189	Cac/Aac	28/28	0.522365322503661	4	FACETS	0.839	0.773	0.906	0.839	0.773	0.906	CLONAL	2	TRUE	2	0.54435318773013	4		432	531	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663452	227663452	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	142	225	0	ENST00000305123.5:c.3G>A	p.Met1?	p.M1?	ENST00000305123	NM_005544.2	1	atG/atA	1/2	0.54435318773013	5	FACETS	0.852	0.786	0.919			1	CLONAL	3	TRUE	NA	0.54435318773013	5		225	371	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368135	31368135	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	247	766	2	ENST00000328111.2:c.6G>T	p.Lys2Asn	p.K2N	ENST00000328111	NM_006892.3	2	aaG/aaT	2/23	0.304605051756645	5	FACETS	1	0.985	1	0.764	0.718	0.812	INDETERMINATE	2	TRUE	2	0.54435318773013	5		768	719	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827935	40827935	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs145661499	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	191	509	0	ENST00000373198.4:c.2493C>G	p.Ser831Arg	p.S831R	ENST00000373198	NM_133170.3	831	agC/agG	17/32	0.481329147632976	3	FACETS	1	0.991	1	0.739	0.687	0.792	CLONAL	1	TRUE	1	0.54435318773013	3		509	604	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292742	62292742	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs767133792	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	248	635	1	ENST00000360203.5:c.194A>G	p.Asp65Gly	p.D65G	ENST00000360203	NM_001283009.1	65	gAc/gGc	3/35	0.522365322503661	4	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	2	0.54435318773013	4		636	695	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035172	30035172	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	221	591	1	ENST00000338641.4:c.334G>T	p.Glu112Ter	p.E112*	ENST00000338641	NM_000268.3	112	Gag/Tag	3/16	0.522365322503661	4	FACETS	0.805	0.751	0.86	0.805	0.751	0.86	CLONAL	2	TRUE	2	0.54435318773013	4		592	779	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670601	134670601	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	336	810	0	ENST00000398015.3:c.512A>T	p.Asn171Ile	p.N171I	ENST00000398015	NM_004441.4	171	aAt/aTt	3/16	0.509926437821006	5	FACETS	1	0.969	1	0.688	0.651	0.726	CLONAL	2	TRUE	2	0.54435318773013	5		810	1086	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270185	66270185	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	70	329	0	ENST00000273854.3:c.1697C>G	p.Ser566Cys	p.S566C	ENST00000273854	NM_004439.5	566	tCc/tGc	8/18	0.481329147632976	3	FACETS	1	0.906	1	0.518	0.455	0.584	CLONAL	1	TRUE	1	0.54435318773013	3		329	316	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398836	398836	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	1339	503	1	ENST00000380956.4:c.646G>T	p.Val216Leu	p.V216L	ENST00000380956	NM_001195286.1	216	Gtg/Ttg	6/9	0.54435318773013	10	FACETS	0.981	0.964	0.997	1	0.998	1	CLONAL	9	TRUE	2	0.54435318773013	10		504	1771	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023085	150023085	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	250	710	0	ENST00000253339.5:c.178G>T	p.Glu60Ter	p.E60*	ENST00000253339		60	Gaa/Taa	1/7	0.54435318773013	2	FACETS	0.99	0.939	1	0.99	0.939	1	CLONAL	2	TRUE	0	0.54435318773013	2		710	464	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334988	81334988	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	348	532	0	ENST00000222390.5:c.1839T>G	p.Ser613Arg	p.S613R	ENST00000222390	NM_000601.4	613	agT/agG	16/18	0.517230995106972	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	3	TRUE	1	0.54435318773013	4		532	651	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845140	128845140	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	522	965	2	ENST00000249373.3:c.634G>T	p.Gly212Cys	p.G212C	ENST00000249373	NM_005631.4	212	Ggc/Tgc	3/12	0.517230995106972	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	1	0.54435318773013	4		967	982	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030838	69030838	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	329	416	1	ENST00000288368.4:c.3380G>T	p.Ser1127Ile	p.S1127I	ENST00000288368	NM_024870.2	1127	aGc/aTc	27/40	0.524534910017965	5	FACETS	1	0.99	1	0.852	0.813	0.892	CLONAL	3	TRUE	1	0.54435318773013	5		417	644	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089819	5089819	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	12	382	0	ENST00000381652.3:c.2717A>T	p.Gln906Leu	p.Q906L	ENST00000381652	NM_004972.3	906	cAg/cTg	20/25	0.522207591268027	1	FACETS	0.199	0.14	0.272	0.199	0.14	0.272	SUBCLONAL	1	TRUE	0	0.54435318773013	1		382	161	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460565	8460565	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	105	451	0	ENST00000356435.5:c.3721T>A	p.Tyr1241Asn	p.Y1241N	ENST00000356435		1241	Tat/Aat	22/35	0.522207591268027	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.54435318773013	1		451	267	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250476	110250476	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	153	560	0	ENST00000374672.4:c.199del	p.Ala67ArgfsTer47	p.A67Rfs*47	ENST00000374672	NM_004235.4	67	Gcg/cg	3/5	0.109955079098587	4	FACETS	0.969	0.895	1	0.969	0.895	1	INDETERMINATE	2	TRUE	2	0.54435318773013	4		560	448	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402487	139402487	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	238	921	0	ENST00000277541.6:c.3430G>T	p.Asp1144Tyr	p.D1144Y	ENST00000277541	NM_017617.3	1144	Gac/Tac	21/34	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.54435318773013	2		921	769	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932954	39932954	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	258	286	0	ENST00000378444.4:c.1645G>T	p.Gly549Cys	p.G549C	ENST00000378444	NM_001123385.1	549	Ggc/Tgc	4/15	0.510976313475131	2	FACETS	0.88	0.845	0.914			1	CLONAL	3	TRUE	NA	0.54435318773013	2		286	359	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69032497	69032499	+	frameshift_variant	Frame_Shift_Ins	INS	CTC	CTC	TTCA	novel	NA	P-0029713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	478	826	0	ENST00000288368.4:c.3571_3573delinsTTCA	p.Leu1191PhefsTer51	p.L1191Ffs*51	ENST00000288368	NM_024870.2	1191	CTC/TTCA	29/40	0.524534910017965	5	FACETS	1	0.991	1	0.823	0.791	0.855	CLONAL	3	TRUE	1	0.54435318773013	5		826	969	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0029714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	679	677	0	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	0.610285008717439	2	FACETS	0.982	0.954	1	0.982	0.954	1	CLONAL	2	TRUE	0	0.611133166953329	2		677	1131	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188177	11188177	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	191	515	0	ENST00000361445.4:c.5917A>T	p.Ile1973Phe	p.I1973F	ENST00000361445	NM_004958.3	1973	Atc/Ttc	43/58	1	2	FACETS	0.771	0.714	0.83	0.771	0.714	0.83	SUBCLONAL	1	TRUE	1	0.611133166953329	2		515	811	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16062188	16062188	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0029715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	49	513	0	ENST00000268712.3:c.619-1G>A		p.X207_splice	ENST00000268712	NM_006311.3	207			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		513	642	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786952	135786952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752290177	NA	P-0029716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	74	346	0	ENST00000298552.3:c.917G>A	p.Cys306Tyr	p.C306Y	ENST00000298552	NM_001162426.1	306	tGt/tAt	10/23	0.496706415394454	3	FACETS	0.503	0.44	0.572	0.252	0.22	0.286	SUBCLONAL	1	TRUE	1	0.496706415394454	3		346	739	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	217	404	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.934	0.876	0.992	0.934	0.876	0.992	CLONAL	1	TRUE	1	0.862380234696422	2		404	539	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0029718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	166	344	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.939	0.873	1	0.939	0.873	1	CLONAL	1	TRUE	1	0.862380234696422	2		345	410	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794440	42794441	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0029718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	46	1154	0	ENST00000575354.2:c.1526dup	p.Leu510ThrfsTer4	p.L510Tfs*4	ENST00000575354	NM_015125.3	507	cgc/cgCc	10/20	0.862380234696422	1	FACETS	0.082	0.069	0.097	0.082	0.069	0.097	SUBCLONAL	1	TRUE	0	0.862380234696422	1		1154	737	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413085	139413085	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1300110216	NA	P-0029718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	166	739	0	ENST00000277541.6:c.1057C>T	p.Arg353Cys	p.R353C	ENST00000277541	NM_017617.3	353	Cgt/Tgt	6/34	1	2	FACETS	0.389	0.357	0.423	0.389	0.357	0.423	SUBCLONAL	1	TRUE	1	0.862380234696422	2		739	989	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414842	78414842	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	44	348	0	ENST00000370768.2:c.1924C>T	p.Gln642Ter	p.Q642*	ENST00000370768	NM_003902.3	642	Cag/Tag	19/20	0.862380234696422	1	FACETS	0.21	0.177	0.247	0.21	0.177	0.247	SUBCLONAL	1	TRUE	0	0.862380234696422	1		348	276	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78435655	78436167	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGAATTCAGTGATGTCCCTGCATCACCTCCAATTTTTGCTGCAATCTAAAAAAAAAAAAGAAAAATACCATCATAAACTATTATATACTATTCATTACTAAATTACCCCCATTTACTTCCTGATACATGTATATGTGAAATATTTAGTATCACATAAGAAAATTTACTTGAAAAATTAAAATTATAGTTCAATTTATTGCTACCATTAATACTTCAGGCAGTTAACATAATAATCATAAGATTATTAAACTTCTGATACATCCCTATAAGAAGCAACAAAGAAGTAATCAACTAGGAATCCGGAAGAGAGACCAGATTTAAAGAAAATCTGGATCCTATCTGGCTCTGTCATGACACTTCAAAAGATGTGTGTAAACACATAGAATGTGAACACTTTGTGGGACTCAAAGGCTATGCTATCTAGTAAGGTAGCCACTAGCCATATGTGGTTATTGAGTACTCAAAATGTGACTAGTCTGAAATGATACTTGCTCTAAGTGTAAAATTACTCAC	TGAATTCAGTGATGTCCCTGCATCACCTCCAATTTTTGCTGCAATCTAAAAAAAAAAAAGAAAAATACCATCATAAACTATTATATACTATTCATTACTAAATTACCCCCATTTACTTCCTGATACATGTATATGTGAAATATTTAGTATCACATAAGAAAATTTACTTGAAAAATTAAAATTATAGTTCAATTTATTGCTACCATTAATACTTCAGGCAGTTAACATAATAATCATAAGATTATTAAACTTCTGATACATCCCTATAAGAAGCAACAAAGAAGTAATCAACTAGGAATCCGGAAGAGAGACCAGATTTAAAGAAAATCTGGATCCTATCTGGCTCTGTCATGACACTTCAAAAGATGTGTGTAAACACATAGAATGTGAACACTTTGTGGGACTCAAAGGCTATGCTATCTAGTAAGGTAGCCACTAGCCATATGTGGTTATTGAGTACTCAAAATGTGACTAGTCTGAAATGATACTTGCTCTAAGTGTAAAATTACTCAC	-	novel	NA	P-0029718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	94	546	1	ENST00000370768.2:c.121-468_165del		p.X41_splice	ENST00000370768	NM_003902.3	41		2/20	0.862380234696422	1	FACETS	0.248	0.221	0.276	0.248	0.221	0.276	SUBCLONAL	1	TRUE	0	0.862380234696422	1		547	501	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795709	42795709	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0029718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	152	985	0	ENST00000575354.2:c.2699-1G>A		p.X900_splice	ENST00000575354	NM_015125.3	900			0.862380234696422	1	FACETS	0.309	0.284	0.336	0.309	0.284	0.336	SUBCLONAL	1	TRUE	0	0.862380234696422	1		985	648	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796618	42796618	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	127	600	0	ENST00000575354.2:c.3175G>A	p.Ala1059Thr	p.A1059T	ENST00000575354	NM_015125.3	1059	Gca/Aca	13/20	0.862380234696422	1	FACETS	0.423	0.387	0.461	0.423	0.387	0.461	SUBCLONAL	1	TRUE	0	0.862380234696422	1		600	396	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418385	139418385	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	68	996	0	ENST00000277541.6:c.187T>C	p.Cys63Arg	p.C63R	ENST00000277541	NM_017617.3	63	Tgc/Cgc	3/34	1	2	FACETS	0.135	0.117	0.155	0.135	0.117	0.155	SUBCLONAL	1	TRUE	1	0.862380234696422	2		996	1166	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0029720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	95	343	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.45	2		343	412	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570063	212570063	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746784831	NA	P-0029720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	144	513	0	ENST00000342788.4:c.1178G>A	p.Arg393Gln	p.R393Q	ENST00000342788	NM_005235.2	393	cGg/cAg	10/28	1	2	FACETS	0.994	0.909	1	0.994	0.909	1	CLONAL	1	TRUE	1	0.45	2		513	644	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653148	29653148	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	85	372	0	ENST00000356175.3:c.5083G>T	p.Ala1695Ser	p.A1695S	ENST00000356175	NM_000267.3	1695	Gct/Tct	36/57	1	2	FACETS	0.823	0.731	0.921	0.823	0.731	0.921	CLONAL	1	TRUE	1	0.45	2		372	459	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88651937	88651937	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	145	568	0	ENST00000372037.3:c.284C>T	p.Thr95Ile	p.T95I	ENST00000372037	NM_004329.2	95	aCa/aTa	5/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.508843637588316	2		568	536	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680890	30680890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1431411009	NA	P-0029722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	172	761	0	ENST00000376406.3:c.829G>A	p.Gly277Ser	p.G277S	ENST00000376406	NM_014641.2	277	Ggt/Agt	5/15	1	2	FACETS	0.92	0.848	0.994	0.92	0.848	0.994	CLONAL	1	FALSE	1	0.508843637588316	2		761	735	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579533	7579533	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	837	745	0	ENST00000269305.4:c.154C>T	p.Gln52Ter	p.Q52*	ENST00000269305	NM_001126112.2	52	Caa/Taa	4/11	0.0654791590451529	3	FACETS	1	0.981	1			1	INDETERMINATE	3	TRUE	NA	0.679592293199323	3		745	1098	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120872	94120872	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	125	404	0	ENST00000369303.4:c.179G>T	p.Gly60Val	p.G60V	ENST00000369303	NM_004440.3	60	gGt/gTt	3/17	0.653597529877163	5	FACETS	0.984	0.891	1	0.246	0.222	0.271	CLONAL	1	TRUE	1	0.679592293199323	5		404	755	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0029724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	506	549	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.527872182722901	3	FACETS	0.869	0.84	0.899	0.869	0.84	0.899	CLONAL	3	TRUE	0	0.58610022600044	3		549	856	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	362	785	1	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.58610022600044	2		786	1148	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0029724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	293	399	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.579649560866178	2	FACETS	0.907	0.864	0.95	0.907	0.864	0.95	CLONAL	2	TRUE	0	0.58610022600044	2		399	551	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0029724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	138	538	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.537293303195902	2	FACETS	0.717	0.654	0.782	0.358	0.327	0.391	SUBCLONAL	1	TRUE	0	0.58610022600044	2		538	657	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0029724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	391	950	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	0.97	0.921	1	0.97	0.921	1	CLONAL	1	TRUE	1	0.58610022600044	2		950	1375	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617517	158617517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	246	611	0	ENST00000263640.3:c.1139G>A	p.Arg380His	p.R380H	ENST00000263640	NM_001105.4	380	cGc/cAc	9/11	1	2	FACETS	0.989	0.926	1	0.989	0.926	1	CLONAL	1	TRUE	1	0.58610022600044	2		611	849	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1036329	1036329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	94	762	0	ENST00000358495.3:c.449G>A	p.Gly150Glu	p.G150E	ENST00000358495	NM_134424.2	150	gGg/gAg	6/12	0.527872182722901	3	FACETS	0.358	0.318	0.402	0.119	0.106	0.134	SUBCLONAL	1	TRUE	0	0.58610022600044	3		762	1157	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169878	32169878	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	518	924	1	ENST00000375023.3:c.3730G>T	p.Asp1244Tyr	p.D1244Y	ENST00000375023	NM_004557.3	1244	Gac/Tac	21/30	0.281851802460991	3	FACETS	0.774	0.742	0.807	0.774	0.742	0.807	INDETERMINATE	2	TRUE	1	0.58610022600044	3		925	1476	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0029725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	170	344	1	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	0.811176200503912	2		345	407	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782664	NA	P-0029725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	858	750	0	ENST00000269305.4:c.711G>C	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atC	7/11	0.786866546478047	2	FACETS	0.948	0.929	0.966	0.948	0.929	0.966	CLONAL	2	TRUE	0	0.811176200503912	2		750	1116	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938573	76938574	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0029725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	378	317	0	ENST00000373344.5:c.2174_2175del	p.Val725GlyfsTer7	p.V725Gfs*7	ENST00000373344	NM_000489.3	725	gTG/g	9/35	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.811176200503912	1		317	428	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798178	42798179	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0029725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	480	996	0	ENST00000575354.2:c.4135_4136del	p.Leu1379GlyfsTer61	p.L1379Gfs*61	ENST00000575354	NM_015125.3	1378	TCt/t	17/20	0.382466929473639	2	FACETS	0.936	0.896	0.976	0.468	0.448	0.488	INDETERMINATE	1	TRUE	0	0.811176200503912	2		996	1265	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0029726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	276	291	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.299051119566036	8	FACETS	0.931	0.881	0.981			1	CLONAL	6	TRUE	NA	0.299051119566036	8		291	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577138	7577138	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587780075	NA	P-0029726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	276	665	0	ENST00000269305.4:c.800G>C	p.Arg267Pro	p.R267P	ENST00000269305	NM_001126112.2	267	cGg/cCg	8/11	0.269323740581657	2	FACETS	0.977	0.919	1	0.977	0.919	1	CLONAL	2	TRUE	0	0.299051119566036	2		665	945	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560085	29560085	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	170	343	1	ENST00000356175.3:c.3562C>T	p.Gln1188Ter	p.Q1188*	ENST00000356175	NM_000267.3	1188	Caa/Taa	27/57	0.269323740581657	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.299051119566036	2		344	525	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16005060	16005060	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0029726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	122	482	0	ENST00000268712.3:c.2194A>T	p.Lys732Ter	p.K732*	ENST00000268712	NM_006311.3	732	Aag/Tag	20/46	0.269323740581657	2	FACETS	1	0.964	1	0.567	0.512	0.624	CLONAL	1	TRUE	0	0.299051119566036	2		482	720	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890321	72890321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	209	496	2	ENST00000325599.8:c.361G>A	p.Asp121Asn	p.D121N	ENST00000325599	NM_018130.2	121	Gac/Aac	4/11	0.298309542165139	3	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	1	0.299051119566036	3		498	797	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410535	139410535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572103199	NA	P-0029726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	140	591	0	ENST00000277541.6:c.1567C>T	p.His523Tyr	p.H523Y	ENST00000277541	NM_017617.3	523	Cat/Tat	10/34	0.299051119566036	2	FACETS	0.995	0.905	1	0.498	0.452	0.545	CLONAL	1	TRUE	0	0.299051119566036	2		591	941	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	270	404	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.67751706575423	2		404	628	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201015	108201015	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs768461085	NA	P-0029727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	179	390	0	ENST00000278616.4:c.7382G>C	p.Arg2461Pro	p.R2461P	ENST00000278616	NM_000051.3	2461	cGc/cCc	50/63	1	2	FACETS	0.95	0.882	1	0.95	0.882	1	CLONAL	1	TRUE	1	0.67751706575423	2		390	556	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224493	108224493	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs748192003	NA	P-0029727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	99	253	0	ENST00000278616.4:c.8672G>T	p.Gly2891Val	p.G2891V	ENST00000278616	NM_000051.3	2891	gGt/gTt	60/63	1	2	FACETS	0.828	0.746	0.913	0.828	0.746	0.913	CLONAL	1	TRUE	1	0.67751706575423	2		253	353	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525086	9525086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	262	549	1	ENST00000353224.5:c.1799G>A	p.Arg600Lys	p.R600K	ENST00000353224	NM_177990.2	600	aGg/aAg	8/10	1	2	FACETS	0.961	0.903	1	0.961	0.903	1	CLONAL	1	TRUE	1	0.67751706575423	2		550	805	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs985033810	NA	P-0029728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	117	660	0	ENST00000269305.4:c.731G>T	p.Gly244Val	p.G244V	ENST00000269305	NM_001126112.2	244	gGc/gTc	7/11	NA	2	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.263652624637517	2		660	815	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417865	138417865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	118	577	0	ENST00000289153.2:c.1654G>A	p.Glu552Lys	p.E552K	ENST00000289153	NM_006219.2	552	Gaa/Aaa	11/22	0.173136552029848	4	FACETS	1	0.981	1	0.689	0.621	0.76	CLONAL	1	TRUE	2	0.263652624637517	4		577	821	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692930	89692930	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1554898163	NA	P-0029728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	149	653	0	ENST00000371953.3:c.416del	p.Leu139TyrfsTer8	p.L139Yfs*8	ENST00000371953	NM_000314.4	138	taT/ta	5/9	1	2	FACETS	0.818	0.749	0.89	1	0.989	1	CLONAL	2	TRUE	1	0.263652624637517	2		653	691	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224169	36224169	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	67	624	0	ENST00000222270.7:c.6719T>A	p.Leu2240His	p.L2240H	ENST00000222270	NM_014727.1	2240	cTc/cAc	28/37	1	2	FACETS	0.621	0.538	0.71	0.621	0.538	0.71	SUBCLONAL	1	TRUE	1	0.263652624637517	2		624	819	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430921	181430921	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	89	812	0	ENST00000325404.1:c.773C>A	p.Ser258Tyr	p.S258Y	ENST00000325404	NM_003106.3	258	tCc/tAc	1/1	0.173136552029848	4	FACETS	0.716	0.632	0.805	0.358	0.316	0.403	SUBCLONAL	1	TRUE	2	0.263652624637517	4		812	1192	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937067	36937067	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767670169	NA	P-0029729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	25	485	1	ENST00000361632.4:c.1252C>T	p.Arg418Cys	p.R418C	ENST00000361632		418	Cgt/Tgt	9/16	1	2	FACETS	0.188	0.148	0.235	0.188	0.148	0.235	SUBCLONAL	1	TRUE	1	0.607535778450878	2		486	437	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650598	18650598	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	19	478	0	ENST00000266497.5:c.2809C>G	p.Gln937Glu	p.Q937E	ENST00000266497		937	Caa/Gaa	20/31	1	2	FACETS	0.17	0.129	0.22	0.17	0.129	0.22	SUBCLONAL	1	TRUE	1	0.607535778450878	2		478	367	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477063	67477063	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0029729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	89	380	0	ENST00000327367.4:c.872-2A>T		p.X291_splice	ENST00000327367	NM_005902.3	291			1	2	FACETS	0.891	0.797	0.988	0.891	0.797	0.988	CLONAL	1	TRUE	1	0.607535778450878	2		380	329	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572510	41572510	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	297	618	0	ENST00000263253.7:c.5039G>C	p.Arg1680Pro	p.R1680P	ENST00000263253	NM_001429.3	1680	cGc/cCc	30/31	0.607535778450878	3	FACETS	0.999	0.949	1	0.999	0.949	1	CLONAL	2	TRUE	1	0.607535778450878	3		618	638	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165131	47165131	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0029729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	23	232	0	ENST00000409792.3:c.995C>G	p.Ser332Ter	p.S332*	ENST00000409792	NM_014159.6	332	tCa/tGa	3/21	1	2	FACETS	0.549	0.433	0.679	0.549	0.433	0.679	SUBCLONAL	1	TRUE	1	0.607535778450878	2		232	138	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117630033	117630033	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780713592	NA	P-0029729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	18	478	0	ENST00000368508.3:c.6493C>T	p.His2165Tyr	p.H2165Y	ENST00000368508	NM_002944.2	2165	Cat/Tat	41/43	0.405710233577876	1	FACETS	0.161	0.121	0.208	0.161	0.121	0.208	SUBCLONAL	1	TRUE	0	0.607535778450878	1		478	257	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211019	55211019	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	100	406	0	ENST00000275493.2:c.262T>A	p.Tyr88Asn	p.Y88N	ENST00000275493	NM_005228.3	88	Tat/Aat	3/28	1	2	FACETS	0.946	0.853	1	0.946	0.853	1	CLONAL	1	TRUE	1	0.607535778450878	2		406	348	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928225	178928225	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	28	315	0	ENST00000263967.3:c.1411C>G	p.Pro471Ala	p.P471A	ENST00000263967	NM_006218.2	471	Cca/Gca	9/21	1	2	FACETS	0.472	0.376	0.581	0.472	0.376	0.581	SUBCLONAL	1	TRUE	1	0.253159675696449	2		315	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578505	7578506	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0029730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1315	214	898	1	ENST00000269305.4:c.424_425del	p.Pro142CysfsTer6	p.P142Cfs*6	ENST00000269305	NM_001126112.2	142	CCt/t	5/11	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.253159675696449	2		899	1529	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851566	63851566	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	52	498	0	ENST00000279873.7:c.2344G>C	p.Asp782His	p.D782H	ENST00000279873	NM_032199.2	782	Gat/Cat	10/10	1	2	FACETS	0.447	0.379	0.521	0.447	0.379	0.521	SUBCLONAL	1	TRUE	1	0.253159675696449	2		498	920	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627657	37627657	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1382306405	NA	P-0029730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2724	373	664	0	ENST00000447079.4:c.1572G>C	p.Glu524Asp	p.E524D	ENST00000447079	NM_015083.1	524	gaG/gaC	2/14	0.253159675696449	28	FACETS	1	0.959	1			1	CLONAL	4	TRUE	NA	0.253159675696449	28		664	3097	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	37	404	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	TRUE	1	0.13	2		404	552	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0029733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	58	762	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	1	2	FACETS	0.826	0.707	0.957	0.826	0.707	0.957	CLONAL	1	TRUE	1	0.13	2		762	1080	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894230	NA	P-0029733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	36	600	0	ENST00000451590.1:c.35G>A	p.Gly12Asp	p.G12D	ENST00000451590	NM_001130442.1	12	gGc/gAc	2/5	1	2	FACETS	0.662	0.542	0.797	0.662	0.542	0.797	SUBCLONAL	1	TRUE	1	0.13	2		600	837	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652097	36652098	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0029733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	57	816	0	ENST00000244741.5:c.222dup	p.Lys75GlnfsTer14	p.K75Qfs*14	ENST00000244741	NM_000389.4	73	-/C	2/3	1	2	FACETS	0.784	0.67	0.909	0.784	0.67	0.909	CLONAL	1	TRUE	1	0.13	2		816	1119	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251273	99251273	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1394608159	NA	P-0029733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	62	652	0	ENST00000268035.6:c.577G>A	p.Glu193Lys	p.E193K	ENST00000268035	NM_000875.3	193	Gag/Aag	2/21	1	2	FACETS	0.867	0.746	0.999	0.867	0.746	0.999	CLONAL	1	TRUE	1	0.13	2		652	1100	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0029734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	163	956	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.315024311635863	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	FALSE	0	0.381081977707457	2		956	417	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670670	67670670	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	107	794	0	ENST00000264010.4:c.1915C>A	p.Gln639Lys	p.Q639K	ENST00000264010	NM_006565.3	639	Cag/Aag	11/12	0.169121644233334	4	FACETS	1	0.974	1	0.633	0.568	0.7	INDETERMINATE	1	FALSE	2	0.381081977707457	4		794	613	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117750	115117750	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	67	589	0	ENST00000257566.3:c.685A>T	p.Thr229Ser	p.T229S	ENST00000257566	NM_016569.3	229	Acg/Tcg	3/8	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.381081977707457	2		589	278	SUCCESS
APC	324	MSKCC	GRCh37	5	112136985	112136985	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	42	515	0	ENST00000257430.4:c.739C>T	p.Gln247Ter	p.Q247*	ENST00000257430	NM_000038.5	247	Cag/Tag	8/16	0.315024311635863	2	FACETS	1	0.931	1	0.596	0.504	0.695	CLONAL	1	FALSE	0	0.381081977707457	2		515	185	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115928	8115929	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	259	372	0	ENST00000346208.3:c.1275dup	p.Ser426IlefsTer81	p.S426Ifs*81	ENST00000346208		425	cca/ccAa	6/6	1	2	FACETS	0.972	0.916	1	0.972	0.916	1	CLONAL	1	FALSE	1	0.795424122335816	2		372	670	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0029737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	395	573	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.388164738185643	1	FACETS	0.75	0.718	0.782	0.75	0.718	0.782	INDETERMINATE	1	FALSE	0	0.795424122335816	1		573	798	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829598	72829598	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	166	575	0	ENST00000268489.5:c.6983A>G	p.Tyr2328Cys	p.Y2328C	ENST00000268489	NM_006885.3	2328	tAc/tGc	9/10	0.795424122335816	1	FACETS	0.492	0.455	0.53	0.492	0.455	0.53	SUBCLONAL	1	FALSE	0	0.795424122335816	1		575	511	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953126	81953126	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	179	276	0	ENST00000359376.3:c.2092G>A	p.Asp698Asn	p.D698N	ENST00000359376	NM_002661.3	698	Gac/Aac	20/33	0.795424122335816	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	0	0.795424122335816	1		276	264	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0029738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	124	671	1	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.123665577344399	3	FACETS	0.85	0.768	0.938	0.425	0.384	0.469	INDETERMINATE	1	FALSE	1	0.3	3		672	1118	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303184	11303184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	50	620	0	ENST00000361445.4:c.1399G>A	p.Asp467Asn	p.D467N	ENST00000361445	NM_004958.3	467	Gac/Aac	9/58	1	2	FACETS	0.389	0.328	0.455	0.389	0.328	0.455	SUBCLONAL	1	FALSE	1	0.3	2		620	858	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034888	42034888	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	62	566	0	ENST00000219905.7:c.4730T>C	p.Val1577Ala	p.V1577A	ENST00000219905	NM_001164273.1	1577	gTc/gCc	15/24	0.294286360401591	1	FACETS	0.456	0.393	0.524	0.456	0.393	0.524	SUBCLONAL	1	FALSE	0	0.3	1		566	771	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579395	7579398	+	frameshift_variant	Frame_Shift_Del	DEL	GGAC	GGAC	-	novel	NA	P-0029738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	153	902	2	ENST00000269305.4:c.289_292del	p.Val97LeufsTer25	p.V97Lfs*25	ENST00000269305	NM_001126112.2	97	GTCCct/ct	4/11	1	2	FACETS	0.849	0.775	0.926	0.849	0.775	0.926	CLONAL	1	FALSE	1	0.3	2		904	1202	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149290747	149290747	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	63	625	0	ENST00000360632.3:c.472G>T	p.Ala158Ser	p.A158S	ENST00000360632	NM_015472.4	158	Gcg/Tcg	3/7	0.173920561447394	3	FACETS	0.476	0.41	0.548	0.159	0.136	0.183	INDETERMINATE	1	FALSE	0	0.3	3		625	1014	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106648	27106648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553153748	NA	P-0029740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	14	646	3	ENST00000324856.7:c.6259G>A	p.Gly2087Arg	p.G2087R	ENST00000324856	NM_006015.4	2087	Gga/Aga	20/20	1	2	FACETS	0.075	0.053	0.101	0.075	0.053	0.101	SUBCLONAL	1	TRUE	1	0.672627468350346	2		649	558	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105800	27105809	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTGATCAG	AGCTGATCAG	-	novel	NA	P-0029740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	77	453	0	ENST00000324856.7:c.5411_5420del	p.Lys1804IlefsTer8	p.K1804Ifs*8	ENST00000324856	NM_006015.4	1804	aAGCTGATCAGt/at	20/20	1	2	FACETS	0.443	0.389	0.5	0.443	0.389	0.5	SUBCLONAL	1	TRUE	1	0.672627468350346	2		453	517	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0029741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	185	581	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.801	0.74	0.864	0.801	0.74	0.864	CLONAL	1	TRUE	1	0.545605164618691	2		581	847	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0029741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	155	276	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.968	0.89	1	0.968	0.89	1	CLONAL	1	TRUE	1	0.545605164618691	2		276	587	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473723	67473723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223740	NA	P-0029741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	529	648	0	ENST00000327367.4:c.803G>A	p.Arg268His	p.R268H	ENST00000327367	NM_005902.3	268	cGc/cAc	6/9	0.545605164618691	2	FACETS	0.962	0.927	0.996	0.962	0.927	0.996	CLONAL	2	TRUE	0	0.545605164618691	2		648	1008	SUCCESS
APC	324	MSKCC	GRCh37	5	112173893	112173893	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	206	434	0	ENST00000257430.4:c.2602G>T	p.Glu868Ter	p.E868*	ENST00000257430	NM_000038.5	868	Gaa/Taa	16/16	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.545605164618691	2		434	744	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347196	70347196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	302	291	1	ENST00000374080.3:c.2860G>A	p.Val954Ile	p.V954I	ENST00000374080		954	Gtc/Atc	21/45	1	1	FACETS	0.797	0.762	0.832	1	0.996	1	SUBCLONAL	2	TRUE	0	0.545605164618691	1		292	505	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211118	36211118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200835025	NA	P-0029741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1275	471	1029	1	ENST00000222270.7:c.869G>A	p.Arg290His	p.R290H	ENST00000222270	NM_014727.1	290	cGt/cAt	3/37	1	2	FACETS	0.989	0.943	1	0.989	0.943	1	CLONAL	1	TRUE	1	0.545605164618691	2		1030	1746	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851930	128851930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779777438	NA	P-0029741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	337	724	0	ENST00000249373.3:c.2002C>T	p.Arg668Cys	p.R668C	ENST00000249373	NM_005631.4	668	Cgc/Tgc	12/12	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.545605164618691	2		724	1225	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439714	51439714	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	154	373	0	ENST00000262662.1:c.279A>C	p.Gln93His	p.Q93H	ENST00000262662		93	caA/caC	4/4	1	2	FACETS	0.919	0.845	0.997	0.919	0.845	0.997	CLONAL	1	TRUE	1	0.545605164618691	2		373	614	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518356	204518356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758146762	NA	P-0029741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	231	468	0	ENST00000367182.3:c.1019C>T	p.Ser340Phe	p.S340F	ENST00000367182	NM_001278516.1	340	tCt/tTt	11/11	1	2	FACETS	0.983	0.919	1	0.983	0.919	1	CLONAL	1	TRUE	1	0.545605164618691	2		468	861	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354364	40354365	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0029741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1306	421	1214	1	ENST00000293328.3:c.2230_2231del	p.Pro744ThrfsTer4	p.P744Tfs*4	ENST00000293328	NM_012448.3	744	CCa/a	18/19	1	2	FACETS	0.894	0.849	0.939	0.894	0.849	0.939	CLONAL	1	TRUE	1	0.545605164618691	2		1215	1727	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132548	11132548	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	331	774	0	ENST00000358026.2:c.2764T>G	p.Trp922Gly	p.W922G	ENST00000358026	NM_001128849.1	922	Tgg/Ggg	19/36	1	2	FACETS	0.943	0.89	0.996	0.943	0.89	0.996	CLONAL	1	TRUE	1	0.545605164618691	2		774	1287	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919738	96919752	+	inframe_deletion	In_Frame_Del	DEL	AACGGCGAAGGTGAC	AACGGCGAAGGTGAC	-	novel	NA	P-0029741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	209	547	0	ENST00000258439.3:c.511_525del	p.Val171_Val175del	p.V171_V175del	ENST00000258439	NM_001193304.2	171	GTCACCTTCGCCGTT/-	4/4	1	2	FACETS	0.77	0.715	0.827	0.77	0.715	0.827	SUBCLONAL	1	TRUE	1	0.545605164618691	2		547	995	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249519	153249519	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	261	565	0	ENST00000281708.4:c.1259A>T	p.His420Leu	p.H420L	ENST00000281708	NM_033632.3	420	cAt/cTt	9/12	1	2	FACETS	0.992	0.931	1	0.992	0.931	1	CLONAL	1	TRUE	1	0.545605164618691	2		565	964	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151919099	151919099	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	144	430	0	ENST00000262189.6:c.3486A>C	p.Lys1162Asn	p.K1162N	ENST00000262189	NM_170606.2	1162	aaA/aaC	22/59	1	2	FACETS	0.893	0.818	0.971	0.893	0.818	0.971	CLONAL	1	TRUE	1	0.545605164618691	2		430	591	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412012	63412012	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	247	329	0	ENST00000330258.3:c.1155del	p.Glu386LysfsTer5	p.E386Kfs*5	ENST00000330258	NM_152424.3	385	gaA/ga	2/2	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.545605164618691	1		329	461	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	63	404	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.534	0.461	0.613	0.534	0.461	0.613	SUBCLONAL	1	TRUE	1	0.362412229417126	2		404	651	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0029742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	214	529	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.362412229417126	2	FACETS	0.883	0.824	0.942	0.883	0.824	0.942	CLONAL	2	TRUE	0	0.362412229417126	2		529	669	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441986	6441986	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	252	578	2	ENST00000356142.4:c.545G>A	p.Arg182Gln	p.R182Q	ENST00000356142	NM_018890.3	182	cGa/cAa	7/7	0.214414049676065	2	FACETS	0.773	0.725	0.823	0.773	0.725	0.823	INDETERMINATE	2	TRUE	0	0.362412229417126	2		580	899	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959350	26959350	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	95	289	0	ENST00000381527.3:c.517G>C	p.Asp173His	p.D173H	ENST00000381527	NM_001260.1	173	Gac/Cac	6/13	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.362412229417126	2		289	417	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094386	27094386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	142	556	1	ENST00000324856.7:c.3094G>A	p.Glu1032Lys	p.E1032K	ENST00000324856	NM_006015.4	1032	Gag/Aag	11/20	1	2	FACETS	0.849	0.773	0.929	0.849	0.773	0.929	CLONAL	1	TRUE	1	0.362412229417126	2		557	923	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151947033	151947033	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	62	445	0	ENST00000262189.6:c.1741C>T	p.Gln581Ter	p.Q581*	ENST00000262189	NM_170606.2	581	Caa/Taa	13/59	1	2	FACETS	0.817	0.708	0.934	0.817	0.708	0.934	CLONAL	1	TRUE	1	0.362412229417126	2		445	419	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40865395	40865395	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	72	696	0	ENST00000428826.2:c.1036G>C	p.Glu346Gln	p.E346Q	ENST00000428826		346	Gag/Cag	11/21	1	2	FACETS	0.372	0.323	0.424	0.372	0.323	0.424	SUBCLONAL	1	TRUE	1	0.362412229417126	2		696	1069	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753155	42753155	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	151	675	0	ENST00000222329.4:c.1109C>T	p.Ser370Phe	p.S370F	ENST00000222329	NM_006494.2	370	tCt/tTt	4/4	1	2	FACETS	0.815	0.745	0.89	0.815	0.745	0.89	CLONAL	1	TRUE	1	0.362412229417126	2		675	1022	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795414	39795414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	109	686	0	ENST00000288319.7:c.306G>A	p.Met102Ile	p.M102I	ENST00000288319	NM_182918.3	102	atG/atA	3/10	1	2	FACETS	0.582	0.522	0.647	0.582	0.522	0.647	SUBCLONAL	1	TRUE	1	0.362412229417126	2		686	1033	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221643	22221643	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	133	356	0	ENST00000215832.6:c.88T>A	p.Tyr30Asn	p.Y30N	ENST00000215832	NM_002745.4	30	Tac/Aac	1/9	0.264316519143907	3	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.362412229417126	3		356	691	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652060	36652060	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	244	828	1	ENST00000244741.5:c.182G>T	p.Gly61Val	p.G61V	ENST00000244741	NM_000389.4	61	gGt/gTt	2/3	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.362412229417126	2		829	1166	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0029745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	80	448	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.989	0.872	1	0.989	0.872	1	CLONAL	1	TRUE	1	0.29	2		448	558	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448337	49448337	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	69	876	3	ENST00000301067.7:c.374C>A	p.Thr125Lys	p.T125K	ENST00000301067	NM_003482.3	125	aCa/aAa	3/54	1	2	FACETS	0.647	0.562	0.738	0.647	0.562	0.738	SUBCLONAL	1	TRUE	1	0.29	2		879	736	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577330	64577333	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	rs587776841	NA	P-0029749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	390	563	0	ENST00000312049.6:c.249_252del	p.Ile85SerfsTer33	p.I85Sfs*33	ENST00000312049	NM_130799.2	83	ctGTCT/ct	2/10	0.638346816945905	2	FACETS	0.862	0.827	0.897	0.862	0.827	0.897	CLONAL	2	TRUE	0	0.638346816945905	2		563	709	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135297	2135297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1332979299	NA	P-0029749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	473	622	1	ENST00000219476.3:c.4636G>A	p.Ala1546Thr	p.A1546T	ENST00000219476	NM_000548.3	1546	Gcc/Acc	36/42	0.638346816945905	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.638346816945905	2		623	729	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286525	33286526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0029749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	254	316	0	ENST00000374542.5:c.2217_2218insTT	p.Asp740LeufsTer27	p.D740Lfs*27	ENST00000374542	NM_001141970.1	739	-/TT	8/8	0.638346816945905	2	FACETS	0.892	0.848	0.936	0.892	0.848	0.936	CLONAL	2	TRUE	0	0.638346816945905	2		316	446	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0029750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	9	489	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.295594694098486	2	FACETS	0.128	0.084	0.184	0.064	0.042	0.092	SUBCLONAL	1	TRUE	0	0.35136147060544	2		489	401	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760929	59760929	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	61	388	0	ENST00000259008.2:c.3478A>G	p.Asn1160Asp	p.N1160D	ENST00000259008	NM_032043.2	1160	Aac/Gac	20/20	0.35136147060544	3	FACETS	0.943	0.816	1	0.471	0.408	0.54	CLONAL	1	TRUE	1	0.35136147060544	3		388	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0000080-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	515	537	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.710649354581136	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.710649354581136	2		540	655	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636984	176636984	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000080-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	186	301	0	ENST00000439151.2:c.1584G>C	p.Lys528Asn	p.K528N	ENST00000439151	NM_022455.4	528	aaG/aaC	5/23	NA	2	FACETS	0.931	0.866	0.998			1	INDETERMINATE	1	TRUE	NA	0.710649354581136	2		301	562	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954210	48954210	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1354030520	NA	P-0000080-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1194	438	357	1	ENST00000267163.4:c.1411C>T	p.Gln471Ter	p.Q471*	ENST00000267163	NM_000321.2	471	Caa/Taa	15/27	0.214489431812689	5	FACETS	0.78	0.743	0.819	0.52	0.495	0.546	INDETERMINATE	2	TRUE	2	0.710649354581136	5		358	1632	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039374	49039374	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853293	NA	P-0000080-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	640	539	4	ENST00000267163.4:c.2359C>T	p.Arg787Ter	p.R787*	ENST00000267163	NM_000321.2	787	Cga/Tga	23/27	0.214489431812689	5	FACETS	1	0.995	1	0.797	0.768	0.826	INDETERMINATE	2	TRUE	2	0.710649354581136	5		543	1557	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720805	89720808	+	frameshift_variant	Frame_Shift_Del	DEL	CTTT	CTTT	-	rs398123330	NA	P-0000131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	129	288	0	ENST00000371953.3:c.956_959del	p.Thr319LysfsTer24	p.T319Kfs*24	ENST00000371953	NM_000314.4	319	aCTTTa/aa	8/9	0.372466441850149	3	FACETS	0.889	0.818	0.96	0.889	0.818	0.96	CLONAL	3	TRUE	0	0.372826488833809	3		288	308	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs786202525	NA	P-0000131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	504	636	0	ENST00000269305.4:c.532del	p.His178ThrfsTer69	p.H178Tfs*69	ENST00000269305	NM_001126112.2	178	Cac/ac	5/11	0.334063631894753	4	FACETS	0.921	0.886	0.955	0.921	0.886	0.955	CLONAL	4	TRUE	0	0.372826488833809	4		636	1008	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521707	89521707	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000257-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	102	365	0	ENST00000336596.2:c.2784C>G	p.Cys928Trp	p.C928W	ENST00000336596	NM_005233.5	928	tgC/tgG	16/17	0.383532246908503	3	FACETS	0.357	0.318	0.398	0.178	0.159	0.199	INDETERMINATE	1	TRUE	1	0.765886753568539	3		365	1032	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686363	117686363	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000257-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	127	298	0	ENST00000368508.3:c.2978T>C	p.Leu993Ser	p.L993S	ENST00000368508	NM_002944.2	993	tTg/tCg	20/43	0.765886753568539	1	FACETS	0.583	0.534	0.633	0.583	0.534	0.633	SUBCLONAL	1	TRUE	0	0.765886753568539	1		298	351	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656911	45656911	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000257-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1317	450	386	0	ENST00000407780.3:c.245A>G	p.Asn82Ser	p.N82S	ENST00000407780	NM_001283052.1	82	aAc/aGc	3/7	0.646367163783508	4	FACETS	1	0.992	1	0.391	0.372	0.411	CLONAL	1	TRUE	1	0.765886753568539	4		386	1767	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061208	38061208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000847-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	192	484	0	ENST00000250448.2:c.781C>T	p.Arg261Cys	p.R261C	ENST00000250448	NM_004496.3	261	Cgc/Tgc	2/2	0.335717098049497	5	FACETS	0.965	0.893	1			1	CLONAL	2	TRUE	NA	0.335717098049497	5		484	891	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578505	7578506	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0000847-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	251	751	0	ENST00000269305.4:c.424_425del	p.Pro142CysfsTer6	p.P142Cfs*6	ENST00000269305	NM_001126112.2	142	CCt/t	5/11	0.255824368955237	2	FACETS	0.889	0.834	0.945	0.889	0.834	0.945	CLONAL	2	TRUE	0	0.335717098049497	2		751	841	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0001554-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	106	436	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.125990551734175	4	FACETS	0.882	0.794	0.974	0.882	0.794	0.974	INDETERMINATE	2	FALSE	2	0.313911688340031	4		437	503	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0001554-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	43	387	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.958	0.806	1	0.958	0.806	1	CLONAL	1	FALSE	1	0.313911688340031	2		387	286	SUCCESS
APC	324	MSKCC	GRCh37	5	112175006	112175006	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0001554-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	48	344	0	ENST00000257430.4:c.3715A>T	p.Arg1239Ter	p.R1239*	ENST00000257430	NM_000038.5	1239	Aga/Tga	16/16	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	FALSE	1	0.313911688340031	2		344	268	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240338	5240338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001554-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	58	309	0	ENST00000357368.4:c.1576G>A	p.Gly526Ser	p.G526S	ENST00000357368	NM_002850.3	526	Ggc/Agc	12/38	0.313911688340031	0	FACETS	1	0.883	1			1	CLONAL	1	FALSE	0	0.313911688340031	0		309	249	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577571	+	frameshift_variant	Frame_Shift_Del	DEL	GAACTGTTACACA	GAACTGTTACACA	TG	novel	NA	P-0001554-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	54	303	0	ENST00000269305.4:c.710_722delinsCA	p.Met237ThrfsTer23	p.M237Tfs*23	ENST00000269305	NM_001126112.2	237	aTGTGTAACAGTTCc/aCAc	7/11	0.268951516964093	0	FACETS	1	0.878	1			1	CLONAL	1	FALSE	0	0.313911688340031	0		303	232	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	87	376	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.97	0.876	1	0.97	0.876	1	CLONAL	1	TRUE	1	0.830444613296915	2		376	216	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0002224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	226	599	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.830444613296915	2		599	504	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0002224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	214	615	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.995	0.934	1	0.995	0.934	1	CLONAL	1	TRUE	1	0.830444613296915	2		615	518	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591246	67591246	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0002224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	84	475	0	ENST00000274335.5:c.1746-2A>T		p.X582_splice	ENST00000274335		582			1	2	FACETS	0.524	0.466	0.586	0.524	0.466	0.586	SUBCLONAL	1	TRUE	1	0.830444613296915	2		475	386	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506284	120506284	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	163	589	0	ENST00000256646.2:c.1828G>T	p.Glu610Ter	p.E610*	ENST00000256646	NM_024408.3	610	Gaa/Taa	11/34	0.830444613296915	1	FACETS	0.755	0.707	0.803	0.755	0.707	0.803	SUBCLONAL	1	TRUE	0	0.830444613296915	1		589	304	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035002	42035002	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	45	727	0	ENST00000219905.7:c.4844T>C	p.Met1615Thr	p.M1615T	ENST00000219905	NM_001164273.1	1615	aTg/aCg	15/24	1	2	FACETS	0.233	0.196	0.274	0.233	0.196	0.274	SUBCLONAL	1	TRUE	1	0.830444613296915	2		727	465	SUCCESS
APC	324	MSKCC	GRCh37	5	112176159	112176159	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	130	588	1	ENST00000257430.4:c.4868G>T	p.Arg1623Met	p.R1623M	ENST00000257430	NM_000038.5	1623	aGg/aTg	16/16	1	2	FACETS	0.529	0.481	0.579	0.529	0.481	0.579	SUBCLONAL	1	TRUE	1	0.830444613296915	2		589	592	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402454	139402454	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	389	884	1	ENST00000277541.6:c.3463C>T	p.Gln1155Ter	p.Q1155*	ENST00000277541	NM_017617.3	1155	Cag/Tag	21/34	0.749557917485973	2	FACETS	0.76	0.732	0.788	0.76	0.732	0.788	SUBCLONAL	2	TRUE	0	0.830444613296915	2		885	616	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410528	139410529	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0002224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	47	752	0	ENST00000277541.6:c.1573_1574del	p.Cys525ProfsTer44	p.C525Pfs*44	ENST00000277541	NM_017617.3	525	TGc/c	10/34	0.749557917485973	2	FACETS	0.232	0.195	0.272	0.116	0.097	0.136	SUBCLONAL	1	TRUE	0	0.830444613296915	2		752	488	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0002768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	51	1141	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	1	2	FACETS	0.367	0.311	0.429	0.367	0.311	0.429	SUBCLONAL	1	TRUE	1	0.370677515629156	2		1142	749	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954198	48954198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123331	NA	P-0002768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	36	235	0	ENST00000267163.4:c.1399C>T	p.Arg467Ter	p.R467*	ENST00000267163	NM_000321.2	467	Cga/Tga	15/27	0.249720620341564	1	FACETS	0.41	0.337	0.491	0.41	0.337	0.491	SUBCLONAL	1	TRUE	0	0.370677515629156	1		235	386	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374244	138374244	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	40	389	0	ENST00000289153.2:c.3200A>T	p.Asp1067Val	p.D1067V	ENST00000289153	NM_006219.2	1067	gAc/gTc	22/22	1	2	FACETS	0.383	0.317	0.456	0.383	0.317	0.456	SUBCLONAL	1	TRUE	1	0.370677515629156	2		389	564	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231127	46231131	+	frameshift_variant	Frame_Shift_Del	DEL	CAAAA	CAAAA	-	novel	NA	P-0002768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	28	331	0	ENST00000334344.6:c.1048_1052del	p.Lys350TyrfsTer17	p.K350Yfs*17	ENST00000334344	NM_152641.2	349	ttCAAAAct/ttct	9/21	1	2	FACETS	0.297	0.237	0.367	0.297	0.237	0.367	SUBCLONAL	1	TRUE	1	0.370677515629156	2		331	508	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0002768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	48	424	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	1	2	FACETS	0.368	0.311	0.432	0.368	0.311	0.432	SUBCLONAL	1	TRUE	1	0.370677515629156	2		424	703	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249091	55249091	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519861	NA	P-0002768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	61	550	0	ENST00000275493.2:c.2389T>A	p.Cys797Ser	p.C797S	ENST00000275493	NM_005228.3	797	Tgc/Agc	20/28	1	2	FACETS	0.41	0.353	0.472	0.41	0.353	0.472	SUBCLONAL	1	TRUE	1	0.370677515629156	2		550	803	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003052-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	144	598	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.321904793677538	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.321904793677538	1		598	639	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711927	89711928	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554900593	NA	P-0003052-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	188	529	1	ENST00000371953.3:c.548dup	p.Asn184GlufsTer6	p.N184Efs*6	ENST00000371953	NM_000314.4	182	tta/ttAa	6/9	0.321904793677538	2	FACETS	0.908	0.843	0.975	0.908	0.843	0.975	CLONAL	2	TRUE	0	0.321904793677538	2		530	643	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942605	71942605	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003052-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	257	684	0	ENST00000298229.2:c.1561C>G	p.Arg521Gly	p.R521G	ENST00000298229	NM_001567.3	521	Cgt/Ggt	13/28	0.321904793677538	3	FACETS	0.949	0.889	1	0.949	0.889	1	CLONAL	2	TRUE	1	0.321904793677538	3		684	977	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934578	NA	P-0003132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	69	159	0	ENST00000269305.4:c.524G>T	p.Arg175Leu	p.R175L	ENST00000269305	NM_001126112.2	175	cGc/cTc	5/11	0.420684225630675	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	0	0.420684225630675	1		159	250	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131505	202131505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	77	147	0	ENST00000358485.4:c.473C>T	p.Ser158Phe	p.S158F	ENST00000358485	NM_001080125.1	158	tCt/tTt	2/9	1	2	FACETS	0.948	0.838	1	0.948	0.838	1	CLONAL	1	TRUE	1	0.420684225630675	2		147	386	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439886	51439886	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	55	99	0	ENST00000262662.1:c.451G>C	p.Glu151Gln	p.E151Q	ENST00000262662		151	Gag/Cag	4/4	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.420684225630675	2		99	235	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097986	178097986	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	143	212	0	ENST00000397062.3:c.394G>C	p.Asp132His	p.D132H	ENST00000397062	NM_006164.4	132	Gac/Cac	3/5	1	2	FACETS	0.971	0.887	1	0.971	0.887	1	CLONAL	1	TRUE	1	0.420684225630675	2		212	700	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098816	178098816	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	173	305	0	ENST00000397062.3:c.229G>C	p.Asp77His	p.D77H	ENST00000397062	NM_006164.4	77	Gat/Cat	2/5	1	2	FACETS	0.974	0.898	1	0.974	0.898	1	CLONAL	1	TRUE	1	0.420684225630675	2		305	844	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151270	202151270	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	193	900	1	ENST00000358485.4:c.1570C>T	p.Gln524Ter	p.Q524*	ENST00000358485	NM_001080125.1	524	Cag/Tag	9/9	1	2	FACETS	0.919	0.85	0.991	0.919	0.85	0.991	CLONAL	1	TRUE	1	0.420684225630675	2		901	998	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098545	47098545	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	137	216	0	ENST00000409792.3:c.6729G>C	p.Gln2243His	p.Q2243H	ENST00000409792	NM_014159.6	2243	caG/caC	15/21	0.420684225630675	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.420684225630675	1		216	432	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506999	186506999	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	187	306	0	ENST00000323963.5:c.1165G>C	p.Glu389Gln	p.E389Q	ENST00000323963		389	Gag/Cag	11/11	0.420684225630675	4	FACETS	0.95	0.875	1	0.317	0.291	0.343	CLONAL	1	TRUE	1	0.420684225630675	4		306	1330	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754898	57754898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	121	210	0	ENST00000274289.3:c.292G>A	p.Glu98Lys	p.E98K	ENST00000274289	NM_006622.3	98	Gag/Aag	2/14	1	2	FACETS	0.952	0.863	1	0.952	0.863	1	CLONAL	1	TRUE	1	0.420684225630675	2		210	604	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26021093	26021093	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs746389934	NA	P-0003132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	173	348	0	ENST00000357647.3:c.376C>G	p.Gln126Glu	p.Q126E	ENST00000357647	NM_003529.2	126	Cag/Gag	1/1	1	2	FACETS	0.978	0.901	1	0.978	0.901	1	CLONAL	1	TRUE	1	0.420684225630675	2		348	841	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148507491	148507491	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	138	242	0	ENST00000320356.2:c.1963G>C	p.Glu655Gln	p.E655Q	ENST00000320356	NM_004456.4	655	Gaa/Caa	17/20	1	2	FACETS	0.966	0.881	1	0.966	0.881	1	CLONAL	1	TRUE	1	0.420684225630675	2		242	679	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750684	128750684	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	128	253	0	ENST00000377970.2:c.221C>G	p.Pro74Arg	p.P74R	ENST00000377970	NM_002467.4	74	cCg/cGg	2/3	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.420684225630675	2		253	502	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037473	12037473	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	162	183	0	ENST00000396373.4:c.1104C>A	p.Phe368Leu	p.F368L	ENST00000396373	NM_001987.4	368	ttC/ttA	6/8	0.230052263570961	6	FACETS	0.958	0.881	1			1	INDETERMINATE	2	TRUE	NA	0.420684225630675	6		183	740	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038958	12038958	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	143	182	0	ENST00000396373.4:c.1251C>A	p.Phe417Leu	p.F417L	ENST00000396373	NM_001987.4	417	ttC/ttA	7/8	0.230052263570961	6	FACETS	0.787	0.718	0.86			1	INDETERMINATE	2	TRUE	NA	0.420684225630675	6		182	795	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988358	41988358	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	187	429	0	ENST00000219905.7:c.1150G>A	p.Glu384Lys	p.E384K	ENST00000219905	NM_001164273.1	384	Gaa/Aaa	3/24	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.420684225630675	2		429	873	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988433	41988433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	188	361	0	ENST00000219905.7:c.1225G>A	p.Glu409Lys	p.E409K	ENST00000219905	NM_001164273.1	409	Gaa/Aaa	3/24	1	2	FACETS	0.965	0.892	1	0.965	0.892	1	CLONAL	1	TRUE	1	0.420684225630675	2		361	926	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988442	41988442	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	208	359	0	ENST00000219905.7:c.1234G>T	p.Asp412Tyr	p.D412Y	ENST00000219905	NM_001164273.1	412	Gat/Tat	3/24	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.420684225630675	2		359	931	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988745	41988745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	232	410	2	ENST00000219905.7:c.1537G>A	p.Glu513Lys	p.E513K	ENST00000219905	NM_001164273.1	513	Gaa/Aaa	3/24	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.420684225630675	2		412	959	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989055	41989055	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	250	424	0	ENST00000219905.7:c.1847G>A	p.Arg616Lys	p.R616K	ENST00000219905	NM_001164273.1	616	aGg/aAg	3/24	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.420684225630675	2		424	975	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989061	41989061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769469171	NA	P-0003132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	254	417	1	ENST00000219905.7:c.1853G>A	p.Arg618Gln	p.R618Q	ENST00000219905	NM_001164273.1	618	cGa/cAa	3/24	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.420684225630675	2		418	972	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989147	41989147	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	190	362	0	ENST00000219905.7:c.1939G>A	p.Gly647Arg	p.G647R	ENST00000219905	NM_001164273.1	647	Ggg/Agg	3/24	1	2	FACETS	0.884	0.817	0.954	0.884	0.817	0.954	CLONAL	1	TRUE	1	0.420684225630675	2		362	1022	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989174	41989174	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	189	356	0	ENST00000219905.7:c.1966G>C	p.Asp656His	p.D656H	ENST00000219905	NM_001164273.1	656	Gat/Cat	3/24	1	2	FACETS	0.898	0.829	0.969	0.898	0.829	0.969	CLONAL	1	TRUE	1	0.420684225630675	2		356	1001	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991303	41991303	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	264	331	0	ENST00000219905.7:c.2134G>A	p.Glu712Lys	p.E712K	ENST00000219905	NM_001164273.1	712	Gaa/Aaa	5/24	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.420684225630675	2		331	1034	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035074	42035074	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	272	377	0	ENST00000219905.7:c.4916A>T	p.Glu1639Val	p.E1639V	ENST00000219905	NM_001164273.1	1639	gAg/gTg	15/24	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.420684225630675	2		377	1032	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354521	91354521	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs7167216	NA	P-0003132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	140	214	0	ENST00000355112.3:c.3961G>C	p.Val1321Leu	p.V1321L	ENST00000355112	NM_000057.2	1321	Gta/Cta	21/22	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.420684225630675	2		214	626	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972490	81972490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	230	361	0	ENST00000359376.3:c.3283G>A	p.Asp1095Asn	p.D1095N	ENST00000359376	NM_002661.3	1095	Gac/Aac	29/33	0.420684225630675	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.420684225630675	1		361	714	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732535	74732535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	88	183	0	ENST00000359995.5:c.374G>A	p.Arg125His	p.R125H	ENST00000359995	NM_001195427.1	125	cGt/cAt	2/3	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.420684225630675	2		183	389	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099375	4099375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761669626	NA	P-0003132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	105	258	1	ENST00000262948.5:c.743C>T	p.Ser248Leu	p.S248L	ENST00000262948	NM_030662.3	248	tCg/tTg	7/11	0.420684225630675	4	FACETS	0.862	0.772	0.957			1	CLONAL	1	TRUE	NA	0.420684225630675	4		259	823	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051236	13051236	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	176	338	0	ENST00000316448.5:c.672G>C	p.Lys224Asn	p.K224N	ENST00000316448	NM_004343.3	224	aaG/aaC	5/9	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.420684225630675	2		338	751	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098623	47098871	+	inframe_deletion	In_Frame_Del	DEL	AAGGGGTTCTGTAGAATGTCCCACCAAGGGCTGAGCATGATCATAAGGAGCAGGAGAACACACTGGGTCCATGCTGGGTGTGGGCAGGAGCACCTTTCCAGCATTAGGGTTGCTGGGATCCACATAGGCCTGCATGGGATAACCTGGTGGGTAACCAGCAAAGGGATGATGCGGGGCATTATAACCAAGAGAGTCATAGGGCAGTGGTGATGTCATTCCCAGGTTCTGCATCTGTTGCTGTTGTTTCTG	AAGGGGTTCTGTAGAATGTCCCACCAAGGGCTGAGCATGATCATAAGGAGCAGGAGAACACACTGGGTCCATGCTGGGTGTGGGCAGGAGCACCTTTCCAGCATTAGGGTTGCTGGGATCCACATAGGCCTGCATGGGATAACCTGGTGGGTAACCAGCAAAGGGATGATGCGGGGCATTATAACCAAGAGAGTCATAGGGCAGTGGTGATGTCATTCCCAGGTTCTGCATCTGTTGCTGTTGTTTCTG	-	novel	NA	P-0003132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	66	210	0	ENST00000409792.3:c.6403_6651del	p.Gln2135_Leu2217del	p.Q2135_L2217del	ENST00000409792	NM_014159.6	2135	CAGAAACAACAGCAACAGATGCAGAACCTGGGAATGACATCACCACTGCCCTATGACTCTCTTGGTTATAATGCCCCGCATCATCCCTTTGCTGGTTACCCACCAGGTTATCCCATGCAGGCCTATGTGGATCCCAGCAACCCTAATGCTGGAAAGGTGCTCCTGCCCACACCCAGCATGGACCCAGTGTGTTCTCCTGCTCCTTATGATCATGCTCAGCCCTTGGTGGGACATTCTACAGAACCCCTT/-	15/21	0.420684225630675	1	FACETS	0.662	0.578	0.753	0.662	0.578	0.753	SUBCLONAL	1	TRUE	0	0.420684225630675	1		210	374	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989042	41989042	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	255	429	0	ENST00000219905.7:c.1835del	p.Gly612GlufsTer9	p.G612Efs*9	ENST00000219905	NM_001164273.1	612	Gga/ga	3/24	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.420684225630675	2		429	985	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026961	71026984	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAAAGGTGGAGTATCTACCTGACG	AAAAGGTGGAGTATCTACCTGACG	-	novel	NA	P-0003132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	79	111	0	ENST00000318789.4:c.1343_1348+18del		p.X448_splice	ENST00000318789	NM_032682.5	448		15/21	0.420684225630675	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.420684225630675	1		111	262	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57569947	57569947	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	245	201	0	ENST00000316660.6:c.127del	p.Leu43Ter	p.L43*	ENST00000316660	NM_021127.2	43	Ctg/tg	2/2	NA	2	FACETS	0.966	0.91	1			1	INDETERMINATE	2	TRUE	NA	0.420684225630675	2		201	603	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988895	41988899	+	missense_variant	Missense_Mutation	ONP	GAAAG	GAAAG	AAAAA	novel	NA	P-0003132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	245	366	0	ENST00000219905.7:c.1687_1691delinsAAAAA	p.Glu563_Arg564delinsLysLys	p.E563_R564delinsKK	ENST00000219905	NM_001164273.1	563	GAAAGa/AAAAAa	3/24	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.420684225630675	2		366	1076	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003233-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	106	615	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	0.355279714805632	2		615	575	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458525	120458525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369659944	NA	P-0003233-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	107	515	0	ENST00000256646.2:c.6820C>T	p.Pro2274Ser	p.P2274S	ENST00000256646	NM_024408.3	2274	Cca/Tca	34/34	0.355279714805632	6	FACETS	1	0.963	1			1	CLONAL	1	TRUE	NA	0.355279714805632	6		515	887	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940138	71940138	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003233-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	118	588	0	ENST00000298229.2:c.523C>T	p.Pro175Ser	p.P175S	ENST00000298229	NM_001567.3	175	Ccc/Tcc	5/28	NA	2	FACETS	0.798	0.72	0.881			1	INDETERMINATE	1	TRUE	NA	0.355279714805632	2		588	832	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12043924	12043924	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003233-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	56	441	0	ENST00000396373.4:c.1303G>C	p.Glu435Gln	p.E435Q	ENST00000396373	NM_001987.4	435	Gag/Cag	8/8	0.24800190934927	4	FACETS	0.558	0.477	0.648	0.279	0.238	0.324	SUBCLONAL	1	TRUE	2	0.355279714805632	4		441	765	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43700158	43700158	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003233-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	33	381	1	ENST00000382044.4:c.5729C>A	p.Ser1910Ter	p.S1910*	ENST00000382044	NM_001141980.1	1910	tCa/tAa	27/28	1	2	FACETS	0.402	0.327	0.487	0.402	0.327	0.487	SUBCLONAL	1	TRUE	1	0.355279714805632	2		382	462	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867343	68867343	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142927667	NA	P-0003233-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	121	508	0	ENST00000261769.5:c.2590G>A	p.Glu864Lys	p.E864K	ENST00000261769	NM_004360.3	864	Gaa/Aaa	16/16	0.355279714805632	0	FACETS	0.873	0.793	0.957			1	CLONAL	1	TRUE	0	0.355279714805632	0		508	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203436	NA	P-0003233-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	169	677	0	ENST00000269305.4:c.487T>C	p.Tyr163His	p.Y163H	ENST00000269305	NM_001126112.2	163	Tac/Cac	5/11	0.355279714805632	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.355279714805632	1		677	626	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207627	2207627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003233-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	165	615	1	ENST00000398665.3:c.911C>T	p.Ser304Leu	p.S304L	ENST00000398665	NM_032482.2	304	tCg/tTg	11/28	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.355279714805632	2		616	750	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10267166	10267166	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003233-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	50	468	0	ENST00000340748.4:c.1252C>A	p.His418Asn	p.H418N	ENST00000340748		418	Cac/Aac	17/40	1	2	FACETS	0.403	0.341	0.471	0.403	0.341	0.471	SUBCLONAL	1	TRUE	1	0.355279714805632	2		468	699	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170513	11170513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003233-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	170	669	0	ENST00000358026.2:c.4816G>T	p.Glu1606Ter	p.E1606*	ENST00000358026	NM_001128849.1	1606	Gag/Tag	34/36	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.355279714805632	2		669	765	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170519	11170519	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1235280916	NA	P-0003233-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	169	649	0	ENST00000358026.2:c.4822G>A	p.Glu1608Lys	p.E1608K	ENST00000358026	NM_001128849.1	1608	Gag/Aag	34/36	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.355279714805632	2		649	757	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170531	11170531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003233-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	161	644	0	ENST00000358026.2:c.4834G>A	p.Glu1612Lys	p.E1612K	ENST00000358026	NM_001128849.1	1612	Gag/Aag	34/36	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.355279714805632	2		644	720	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082580	16082580	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775268500	NA	P-0003233-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	55	292	1	ENST00000281043.3:c.394G>A	p.Glu132Lys	p.E132K	ENST00000281043	NM_005378.4	132	Gag/Aag	2/3	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.355279714805632	2		293	288	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047037	128047037	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003233-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	113	491	0	ENST00000285398.2:c.698C>A	p.Ser233Tyr	p.S233Y	ENST00000285398	NM_000122.1	233	tCc/tAc	6/15	0.280632466214675	1	FACETS	0.865	0.78	0.954	0.865	0.78	0.954	CLONAL	1	TRUE	0	0.355279714805632	1		491	605	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41489079	41489079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373061594	NA	P-0003233-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	117	366	0	ENST00000263253.7:c.71C>T	p.Ser24Leu	p.S24L	ENST00000263253	NM_001429.3	24	tCg/tTg	1/31	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.355279714805632	2		366	639	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271460	26271460	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003233-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	122	453	0	ENST00000305910.3:c.153G>C	p.Glu51Asp	p.E51D	ENST00000305910	NM_003534.2	51	gaG/gaC	1/1	0.355279714805632	7	FACETS	0.777	0.702	0.856			1	SUBCLONAL	2	TRUE	NA	0.355279714805632	7		453	835	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673794	30673794	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003233-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	52	449	0	ENST00000376406.3:c.3166C>G	p.Gln1056Glu	p.Q1056E	ENST00000376406	NM_014641.2	1056	Cag/Gag	10/15	0.262960569332642	5	FACETS	0.557	0.473	0.649	0.186	0.157	0.217	SUBCLONAL	1	TRUE	2	0.355279714805632	5		449	806	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874425	151874425	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003233-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	82	396	0	ENST00000262189.6:c.8113G>C	p.Glu2705Gln	p.E2705Q	ENST00000262189	NM_170606.2	2705	Gag/Cag	38/59	0.226125027934253	1	FACETS	0.978	0.868	1	0.978	0.868	1	CLONAL	1	TRUE	0	0.355279714805632	1		396	388	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849304	76849304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003233-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	96	457	0	ENST00000373344.5:c.5972C>T	p.Ser1991Phe	p.S1991F	ENST00000373344	NM_000489.3	1991	tCt/tTt	26/35	0.355279714805632	1	FACETS	0.972	0.871	1	0.972	0.871	1	CLONAL	1	TRUE	0	0.355279714805632	1		457	457	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623167	52623167	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	143	354	0	ENST00000394830.3:c.2884G>T	p.Asp962Tyr	p.D962Y	ENST00000394830	NM_018313.4	962	Gat/Tat	19/30	0.35827821135047	1	FACETS	0.938	0.859	1	0.938	0.859	1	CLONAL	1	TRUE	0	0.417324741985238	1		354	578	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143040	47143042	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0003366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	103	315	0	ENST00000409792.3:c.4921_4923del	p.Thr1641del	p.T1641del	ENST00000409792	NM_014159.6	1641	ACT/-	8/21	0.390682395090552	1	FACETS	0.882	0.794	0.974	0.882	0.794	0.974	CLONAL	1	TRUE	0	0.417324741985238	1		315	443	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191645	10191646	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0003366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	84	204	0	ENST00000256474.2:c.640dup	p.Ter214LeufsTer42	p.*214Lfs*42	ENST00000256474	NM_000551.3	213	gat/gaTt	3/3	0.390682395090552	1	FACETS	0.913	0.813	1	0.913	0.813	1	CLONAL	1	TRUE	0	0.417324741985238	1		204	349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0003513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	114	551	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.19511197808223	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.28	2		551	334	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0003513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	109	317	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.22254271382777	3	FACETS	0.993	0.897	1	0.993	0.897	1	CLONAL	2	TRUE	1	0.28	3		317	447	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0003513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	61	358	1	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	NA	2	FACETS	1	0.95	1			1	INDETERMINATE	1	TRUE	NA	0.28	2		359	361	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0003513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	36	320	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	0.299446859341159	3	FACETS	0.79	0.65	0.946	0.395	0.325	0.473	CLONAL	1	TRUE	1	0.28	3		320	371	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0003513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	39	319	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	NA	2	FACETS	1	0.879	1			1	INDETERMINATE	1	TRUE	NA	0.28	2		319	261	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0003513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	94	429	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	NA	2	FACETS	1	0.941	1			1	INDETERMINATE	1	TRUE	NA	0.28	2		429	619	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754890	29754890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370848188	NA	P-0003513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	26	317	0	ENST00000389048.3:c.1045G>A	p.Val349Ile	p.V349I	ENST00000389048	NM_004304.4	349	Gtc/Atc	4/29	0.299446859341159	0	FACETS	0.686	0.547	0.842			1	SUBCLONAL	1	TRUE	0	0.28	0		317	195	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275099	41275099	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	42	391	0	ENST00000349496.5:c.1265G>T	p.Gly422Val	p.G422V	ENST00000349496	NM_001904.3	422	gGa/gTa	9/15	0.299446859341159	3	FACETS	0.792	0.662	0.936	0.396	0.331	0.468	CLONAL	1	TRUE	1	0.28	3		391	432	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037144	71037144	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	59	260	0	ENST00000318789.4:c.1146+1G>A		p.X382_splice	ENST00000318789	NM_032682.5	382			0.299446859341159	3	FACETS	1	0.958	1	0.647	0.559	0.742	CLONAL	1	TRUE	1	0.28	3		260	371	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952086	178952086	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519932	NA	P-0003513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	51	317	0	ENST00000263967.3:c.3141T>G	p.His1047Gln	p.H1047Q	ENST00000263967	NM_006218.2	1047	caT/caG	21/21	0.299446859341159	3	FACETS	1	0.872	1	0.513	0.437	0.596	CLONAL	1	TRUE	1	0.28	3		317	405	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355010	73355010	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	91	258	0	ENST00000377767.4:c.360C>G	p.Phe120Leu	p.F120L	ENST00000377767	NM_014953.3	120	ttC/ttG	2/21	0.299446859341159	3	FACETS	1	0.979	1	0.726	0.647	0.811	CLONAL	1	TRUE	1	0.28	3		258	510	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52725412	52725412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770194852	NA	P-0003513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	31	390	0	ENST00000322088.6:c.1579C>T	p.Arg527Cys	p.R527C	ENST00000322088	NM_014225.5	527	Cgc/Tgc	13/15	0.299446859341159	1	FACETS	0.7	0.568	0.848	0.7	0.568	0.848	SUBCLONAL	1	TRUE	0	0.28	1		390	272	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119829	70119832	+	frameshift_variant	Frame_Shift_Del	DEL	GCTG	GCTG	CCT	novel	NA	P-0003513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	180	424	0	ENST00000245479.2:c.831_834delinsCCT	p.Glu277AspfsTer106	p.E277Dfs*106	ENST00000245479	NM_000346.3	277	gaGCTG/gaCCT	3/3	0.299446859341159	5	FACETS	1	0.949	1	1	0.989	1	CLONAL	4	TRUE	2	0.28	5		424	447	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0003595-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	29	454	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.0973585517802205	0	FACETS	0.625	0.5	0.768			1	SUBCLONAL	1	TRUE	0	0.14	0		454	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0003595-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	52	595	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	1	2	FACETS	0.965	0.82	1	0.965	0.82	1	CLONAL	1	TRUE	1	0.14	2		595	770	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517959	187517959	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003595-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	43	409	0	ENST00000441802.2:c.12735A>G	p.Ile4245Met	p.I4245M	ENST00000441802	NM_005245.3	4245	atA/atG	25/27	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.14	2		409	597	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508689	106508689	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003595-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	44	441	0	ENST00000359195.3:c.683C>A	p.Thr228Asn	p.T228N	ENST00000359195	NM_002649.2	228	aCc/aAc	2/11	1	2	FACETS	0.919	0.769	1	0.919	0.769	1	CLONAL	1	TRUE	1	0.14	2		441	684	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450747	70450747	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003595-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	41	384	0	ENST00000373644.4:c.5587A>C	p.Lys1863Gln	p.K1863Q	ENST00000373644	NM_030625.2	1863	Aag/Cag	12/12	1	2	FACETS	0.976	0.812	1	0.976	0.812	1	CLONAL	1	TRUE	1	0.14	2		384	600	SUCCESS
AR	367	MSKCC	GRCh37	X	66937401	66937401	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003595-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	78	533	0	ENST00000374690.3:c.2255G>A	p.Trp752Ter	p.W752*	ENST00000374690	NM_000044.3	752	tGg/tAg	5/8	0.3	3	FACETS	1	0.968	1			1	CLONAL	1	TRUE	NA	0.14	3		533	894	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971037	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0003595-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	37	411	0	ENST00000304494.5:c.321_322del	p.Asp108CysfsTer11	p.D108Cfs*11	ENST00000304494	NM_000077.4	107	cgCGat/cgat	2/3	1	2	FACETS	0.961	0.791	1	0.961	0.791	1	CLONAL	1	TRUE	1	0.14	2		411	550	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003866-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	207	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.941	0.876	1	0.941	0.876	1	CLONAL	1	TRUE	1	0.575057231370832	2		511	765	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351374	89351374	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318137276	NA	P-0003866-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	52	756	0	ENST00000301030.4:c.1576C>T	p.His526Tyr	p.H526Y	ENST00000301030	NM_001256183.1	526	Cac/Tac	9/13	0.575057231370832	1	FACETS	0.168	0.142	0.196	0.168	0.142	0.196	SUBCLONAL	1	TRUE	0	0.575057231370832	1		756	768	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190708802	190708802	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003866-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	136	527	0	ENST00000441310.2:c.695C>G	p.Ser232Cys	p.S232C	ENST00000441310	NM_000534.4	232	tCt/tGt	6/13	NA	2	FACETS	0.625	0.569	0.684			1	INDETERMINATE	1	TRUE	NA	0.575057231370832	2		527	757	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057727	27057727	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004094-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	173	854	0	ENST00000324856.7:c.1435C>T	p.Gln479Ter	p.Q479*	ENST00000324856	NM_006015.4	479	Cag/Tag	3/20	1	2	FACETS	0.955	0.88	1	0.955	0.88	1	CLONAL	1	TRUE	1	0.425277899733216	2		854	852	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779766	3779766	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0004094-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	138	602	0	ENST00000262367.5:c.5282C>G	p.Ser1761Ter	p.S1761*	ENST00000262367	NM_004380.2	1761	tCa/tGa	31/31	NA	2	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.425277899733216	2		602	583	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243494	41243494	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80357202	NA	P-0004094-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	166	653	0	ENST00000357654.3:c.4054G>A	p.Glu1352Lys	p.E1352K	ENST00000357654	NM_007294.3	1352	Gaa/Aaa	10/23	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.425277899733216	2		653	724	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245110	41245110	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004094-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	184	794	0	ENST00000357654.3:c.2438G>A	p.Gly813Glu	p.G813E	ENST00000357654	NM_007294.3	813	gGa/gAa	10/23	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.425277899733216	2		794	858	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058739	47058741	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0004094-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	195	378	0	ENST00000409792.3:c.7537_7539del	p.Thr2513del	p.T2513del	ENST00000409792	NM_014159.6	2513	ACT/-	21/21	0.425277899733216	2	FACETS	0.924	0.864	0.986	0.924	0.864	0.986	CLONAL	2	TRUE	0	0.425277899733216	2		378	496	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79974807	79974807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004094-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	137	605	0	ENST00000265081.6:c.1235C>T	p.Ser412Leu	p.S412L	ENST00000265081	NM_002439.4	412	tCa/tTa	8/24	0.425277899733216	3	FACETS	0.966	0.879	1	0.483	0.439	0.529	CLONAL	1	TRUE	1	0.425277899733216	3		605	809	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140487374	140487374	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004094-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	188	651	0	ENST00000288602.6:c.1151G>C	p.Arg384Thr	p.R384T	ENST00000288602	NM_004333.4	384	aGa/aCa	9/18	0.425277899733216	3	FACETS	0.984	0.908	1	0.492	0.454	0.532	CLONAL	1	TRUE	1	0.425277899733216	3		651	1090	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0004264-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	161	387	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.461019911605241	4	FACETS	0.914	0.862	0.964	0.914	0.862	0.964	CLONAL	4	TRUE	0	0.540921909528119	4		387	251	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0004264-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	106	535	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.474747388446472	2	FACETS	0.859	0.787	0.932	0.859	0.787	0.932	CLONAL	2	TRUE	0	0.540921909528119	2		535	228	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413566	32413566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121907900	NA	P-0004264-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	11	368	0	ENST00000332351.3:c.1384C>T	p.Arg462Trp	p.R462W	ENST00000332351	NM_024426.4	462	Cgg/Tgg	9/10	0.420557631966832	3	FACETS	0.169	0.116	0.235	0.084	0.058	0.118	SUBCLONAL	1	TRUE	1	0.540921909528119	3		368	306	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096187	178096187	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004264-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	14	398	0	ENST00000397062.3:c.1144G>C	p.Asp382His	p.D382H	ENST00000397062	NM_006164.4	382	Gat/Cat	5/5	0.420557631966832	3	FACETS	0.355	0.257	0.473	0.178	0.128	0.237	SUBCLONAL	1	TRUE	1	0.540921909528119	3		398	185	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	173	475	0	ENST00000347630.2:c.397T>C	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	Ttc/Ctc	6/11	1	2	FACETS	0.89	0.823	0.959	0.89	0.823	0.959	CLONAL	1	TRUE	1	0.626111941215578	2		475	621	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857794	57857794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1392573638	NA	P-0004756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	440	557	1	ENST00000228682.2:c.113C>T	p.Pro38Leu	p.P38L	ENST00000228682	NM_005269.2	38	cCg/cTg	3/12	0.626111941215578	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.626111941215578	3		558	913	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627524	14627531	+	frameshift_variant	Frame_Shift_Del	DEL	CTTCTTGG	CTTCTTGG	-	novel	NA	P-0004756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	150	414	0	ENST00000254322.2:c.539_546del	p.Thr180AsnfsTer52	p.T180Nfs*52	ENST00000254322	NM_006145.1	180	aCCAAGAAG/a	2/3	1	2	FACETS	0.807	0.74	0.875	0.807	0.74	0.875	CLONAL	1	TRUE	1	0.626111941215578	2		414	594	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569224	67569224	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	135	389	0	ENST00000274335.5:c.341C>T	p.Thr114Ile	p.T114I	ENST00000274335		114	aCt/aTt	2/15	1	2	FACETS	0.963	0.882	1	0.963	0.882	1	CLONAL	1	TRUE	1	0.626111941215578	2		389	448	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0004937-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	553	429	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	0.97016983226959	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.97016983226959	1		429	574	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271201	153271202	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004937-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	273	248	0	ENST00000281708.4:c.576dup	p.Tyr193IlefsTer63	p.Y193Ifs*63	ENST00000281708	NM_033632.3	192	-/A	3/12	0.97016983226959	1	FACETS	0.929	0.904	0.952	0.929	0.904	0.952	CLONAL	1	TRUE	0	0.97016983226959	1		248	312	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0004937-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	402	429	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	0.958389865077205	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.958389865077205	1		429	427	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271201	153271202	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004937-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	177	248	0	ENST00000281708.4:c.576dup	p.Tyr193IlefsTer63	p.Y193Ifs*63	ENST00000281708	NM_033632.3	192	-/A	3/12	0.958389865077205	1	FACETS	0.987	0.957	1	0.987	0.957	1	CLONAL	1	TRUE	0	0.958389865077205	1		248	195	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324613	62324613	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs370171864	NA	P-0005297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	219	449	0	ENST00000360203.5:c.2969C>A	p.Ala990Glu	p.A990E	ENST00000360203	NM_001283009.1	990	gCa/gAa	30/35	0.910296313001142	3	FACETS	0.619	0.575	0.664	0.309	0.287	0.332	SUBCLONAL	1	TRUE	1	0.910296313001142	3		449	1132	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0005502-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	872	857	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.219807270960335	4	FACETS	1	0.991	1			1	INDETERMINATE	4	TRUE	NA	0.828242002518445	4		858	957	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939103	36939103	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005502-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	393	843	3	ENST00000361632.4:c.606G>A	p.Trp202Ter	p.W202*	ENST00000361632		202	tgG/tgA	5/16	0.828242002518445	2	FACETS	0.952	0.908	0.997	0.476	0.454	0.499	CLONAL	1	TRUE	0	0.828242002518445	2		846	997	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718114	117718114	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs759261834	NA	P-0005502-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	436	643	1	ENST00000368508.3:c.743T>A	p.Phe248Tyr	p.F248Y	ENST00000368508	NM_002944.2	248	tTc/tAc	7/43	0.779975189995137	4	FACETS	0.951	0.91	0.992	0.951	0.91	0.992	CLONAL	2	TRUE	2	0.828242002518445	4		644	1012	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024570	14024570	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005502-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	257	359	0	ENST00000311895.7:c.796A>G	p.Ile266Val	p.I266V	ENST00000311895	NM_005236.2	266	Atc/Gtc	5/11	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.828242002518445	2		359	291	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044474	12044474	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005502-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	453	349	0	ENST00000353533.5:c.1097T>C	p.Phe366Ser	p.F366S	ENST00000353533	NM_003010.3	366	tTt/tCt	11/11	0.219807270960335	4	FACETS	1	0.991	1			1	INDETERMINATE	4	TRUE	NA	0.828242002518445	4		349	493	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324219	31324463	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTGGCCCCGGCCCCGCGGTCAGCCCAGTCCCCCGAGCCCCGCCCCGCCCCGACCAACCCGCGGGGATTTTGGCCTCAACTGAAAATGAAACCGGGTAAACGCGCCTGGGGCTCTCGCCGGTCGAGGGTCTGGGCGGGTCCCGCGGCCTCAGGGAGGCGGATCTCGGACCCGGAGACTCGGGGCGACCCGGGCCGTACGTGGGGGATGGGGAGTCGTGACCTGCGCCCCGGGCCGGGGTCACTCA	CCTGGCCCCGGCCCCGCGGTCAGCCCAGTCCCCCGAGCCCCGCCCCGCCCCGACCAACCCGCGGGGATTTTGGCCTCAACTGAAAATGAAACCGGGTAAACGCGCCTGGGGCTCTCGCCGGTCGAGGGTCTGGGCGGGTCCCGCGGCCTCAGGGAGGCGGATCTCGGACCCGGAGACTCGGGGCGACCCGGGCCGTACGTGGGGGATGGGGAGTCGTGACCTGCGCCCCGGGCCGGGGTCACTCA	-	novel	NA	P-0005502-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	125	492	0	ENST00000412585.2:c.343+2_344del		p.X115_splice	ENST00000412585	NM_005514.6	115		3/8	0.779975189995137	4	FACETS	0.436	0.393	0.481	0.218	0.196	0.241	SUBCLONAL	1	TRUE	2	0.828242002518445	4		492	1266	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323001	31323093	+	splice_acceptor_variant,splice_donor_variant,intron_variant	Splice_Site	DEL	CTGGGAAAGGAGGGGAAGATGAGGGGCCCTGACCCTGCTGAAGGGCTCCTGCTTTCCCTGAGAAGAGATATGACCCCTCATCCCCCTCCTTAC	CTGGGAAAGGAGGGGAAGATGAGGGGCCCTGACCCTGCTGAAGGGCTCCTGCTTTCCCTGAGAAGAGATATGACCCCTCATCCCCCTCCTTAC	-	novel	NA	P-0005502-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1673	352	887	0	ENST00000412585.2:c.895+1_896-1del		p.X299_splice	ENST00000412585	NM_005514.6	299			0.779975189995137	4	FACETS	0.767	0.724	0.812	0.384	0.362	0.406	SUBCLONAL	1	TRUE	2	0.828242002518445	4		887	2025	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0005763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	232	1141	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.301455587176577	5	FACETS	1	0.99	1	0.277	0.257	0.297	CLONAL	1	TRUE	0	0.386751743943178	5		1142	1369	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947564	48947567	+	frameshift_variant	Frame_Shift_Del	DEL	AATT	AATT	-	novel	NA	P-0005763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	121	591	0	ENST00000267163.4:c.1154_1157del	p.Leu385Ter	p.L385*	ENST00000267163	NM_000321.2	384	cAATTa/ca	12/27	0.197123853168877	2	FACETS	0.89	0.805	0.979	0.445	0.402	0.49	INDETERMINATE	1	TRUE	0	0.386751743943178	2		591	703	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357724	70357727	+	frameshift_variant	Frame_Shift_Del	DEL	AACA	AACA	-	novel	NA	P-0005763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	299	558	0	ENST00000374080.3:c.5975_5978del	p.Gln1992ArgfsTer18	p.Q1992Rfs*18	ENST00000374080		1992	cAACAg/cg	41/45	0.386751743943178	2	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.386751743943178	2		558	641	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242478	55242507	+	protein_altering_variant	In_Frame_Del	DEL	GCAACATCTCCGAAAGCCAACAAGGAAATC	GCAACATCTCCGAAAGCCAACAAGGAAATC	CCAACA	novel	NA	P-0005763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	321	674	0	ENST00000275493.2:c.2248_2277delinsCCAACA	p.Ala750_Ile759delinsProThr	p.A750_I759delinsPT	ENST00000275493	NM_005228.3	750	GCAACATCTCCGAAAGCCAACAAGGAAATC/CCAACA	19/28	0.301455587176577	5	FACETS	0.878	0.83	0.926	0.527	0.498	0.556	CLONAL	3	TRUE	0	0.386751743943178	5		674	996	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0006418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	290	474	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	NA	2	FACETS	0.955	0.899	1			1	INDETERMINATE	1	TRUE	NA	0.608671293776179	2		474	998	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0006418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	128	326	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.864	0.787	0.943	0.864	0.787	0.943	CLONAL	1	TRUE	1	0.608671293776179	2		326	487	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692793	89692793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	60	217	0	ENST00000371953.3:c.277C>T	p.His93Tyr	p.H93Y	ENST00000371953	NM_000314.4	93	Cat/Tat	5/9	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.608671293776179	2		217	197	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745587	162745587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751660319	NA	P-0006418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	138	450	1	ENST00000367921.3:c.2002C>T	p.Arg668Cys	p.R668C	ENST00000367921	NM_006182.2	668	Cgc/Tgc	15/18	0.608671293776179	4	FACETS	0.982	0.895	1	0.327	0.298	0.358	CLONAL	1	TRUE	1	0.608671293776179	4		451	743	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1268664	1268664	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	256	684	0	ENST00000310581.5:c.2553C>A	p.Asn851Lys	p.N851K	ENST00000310581	NM_198253.2	851	aaC/aaA	9/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.608671293776179	2		684	812	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591116	67591116	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	149	362	1	ENST00000274335.5:c.1709T>C	p.Leu570Pro	p.L570P	ENST00000274335		570	cTt/cCt	12/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.608671293776179	2		363	433	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023360	27023361	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	350	268	1	ENST00000324856.7:c.466_467insA	p.Arg156GlnfsTer244	p.R156Qfs*244	ENST00000324856	NM_006015.4	156	cgg/cAgg	1/20	0.608671293776179	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.608671293776179	2		269	482	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692988	89693009	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	GTAAGGACCAGAGACAAAAAGG	GTAAGGACCAGAGACAAAAAGG	AGT	novel	NA	P-0006418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	46	288	0	ENST00000371953.3:c.472_492+1delinsAGT		p.X158_splice	ENST00000371953	NM_000314.4	158		5/9	1	2	FACETS	0.579	0.491	0.675	0.579	0.491	0.675	SUBCLONAL	1	TRUE	1	0.608671293776179	2		288	261	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	197	525	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.839	0.778	0.902	0.839	0.778	0.902	CLONAL	1	TRUE	1	0.558833890785794	2		525	840	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0006531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	132	352	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.872	0.795	0.951	0.872	0.795	0.951	CLONAL	1	TRUE	1	0.558833890785794	2		352	542	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692791	89692791	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1114167623	NA	P-0006531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	153	125	0	ENST00000371953.3:c.275A>G	p.Asp92Gly	p.D92G	ENST00000371953	NM_000314.4	92	gAc/gGc	5/9	NA	2	FACETS	0.904	0.843	0.965			1	INDETERMINATE	2	TRUE	NA	0.558833890785794	2		125	303	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589535	67589535	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1403833564	NA	P-0006531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	87	150	0	ENST00000274335.5:c.1300-2A>G		p.X434_splice	ENST00000274335		434			NA	2	FACETS	0.905	0.808	1			1	INDETERMINATE	1	TRUE	NA	0.558833890785794	2		150	344	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524387	176524387	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143758924	NA	P-0006531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	295	419	0	ENST00000292408.4:c.2248G>A	p.Val750Ile	p.V750I	ENST00000292408	NM_213647.1	750	Gtc/Atc	17/18	1	2	FACETS	0.852	0.801	0.904	0.852	0.801	0.904	CLONAL	1	TRUE	1	0.558833890785794	2		419	1239	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106811	27106840	+	inframe_deletion	In_Frame_Del	DEL	TCAGCCGCCTGGAGAAGTTGTATAGCACTA	TCAGCCGCCTGGAGAAGTTGTATAGCACTA	-	novel	NA	P-0006531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	477	286	0	ENST00000324856.7:c.6423_6452del	p.Phe2141_Met2151delinsLeu	p.F2141_M2151delinsL	ENST00000324856	NM_006015.4	2141	tTCAGCCGCCTGGAGAAGTTGTATAGCACTAtg/ttg	20/20	1	2	FACETS	0.901	0.867	0.936	1	0.997	1	CLONAL	2	TRUE	1	0.558833890785794	2		286	947	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0006546-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	622	599	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.930032685080182	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.930032685080182	2		599	660	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0006546-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	86	226	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.505215465212341	1	FACETS	0.462	0.417	0.509	0.462	0.417	0.509	INDETERMINATE	1	TRUE	0	0.930032685080182	1		227	214	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951087	48951088	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs1131690889	NA	P-0006546-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	237	298	0	ENST00000267163.4:c.1251_1252del	p.Arg418SerfsTer9	p.R418Sfs*9	ENST00000267163	NM_000321.2	417	AAa/a	13/27	0.930032685080182	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.930032685080182	1		298	267	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230432	46230432	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006546-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	145	334	0	ENST00000334344.6:c.766T>G	p.Ser256Ala	p.S256A	ENST00000334344	NM_152641.2	256	Tct/Gct	7/21	0.465611126552205	1	FACETS	0.351	0.323	0.381	0.351	0.323	0.381	INDETERMINATE	1	TRUE	0	0.930032685080182	1		334	475	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857663	78857663	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006546-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	293	570	0	ENST00000306801.3:c.1733C>G	p.Ala578Gly	p.A578G	ENST00000306801	NM_020761.2	578	gCc/gGc	16/34	1	2	FACETS	0.947	0.898	0.997	0.947	0.898	0.997	CLONAL	1	TRUE	1	0.930032685080182	2		570	665	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778806	76778807	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0006546-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	296	213	1	ENST00000373344.5:c.6772_6773del	p.Leu2258GlyfsTer10	p.L2258Gfs*10	ENST00000373344	NM_000489.3	2258	TTg/g	31/35	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.930032685080182	1		214	334	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041678	29041678	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006546-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	99	353	0	ENST00000282397.4:c.141G>C	p.Gln47His	p.Q47H	ENST00000282397	NM_002019.4	47	caG/caC	2/30	1	2	FACETS	0.431	0.386	0.478	0.431	0.386	0.478	SUBCLONAL	1	TRUE	1	0.930032685080182	2		353	494	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421380	12421380	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs773848402	NA	P-0006546-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	348	532	0	ENST00000287820.6:c.260A>G	p.Asp87Gly	p.D87G	ENST00000287820	NM_015869.4	87	gAt/gGt	2/7	0.930032685080182	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.930032685080182	1		532	382	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532837	187532843	+	frameshift_variant	Frame_Shift_Del	DEL	GTTTTTC	GTTTTTC	-	novel	NA	P-0006546-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	126	405	0	ENST00000441802.2:c.9550_9556del	p.Glu3184LeufsTer14	p.E3184Lfs*14	ENST00000441802	NM_005245.3	3184	GAAAAACct/ct	14/27	0.930032685080182	1	FACETS	0.404	0.37	0.439	0.404	0.37	0.439	SUBCLONAL	1	TRUE	0	0.930032685080182	1		405	359	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738348	133738348	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006546-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	282	466	0	ENST00000318560.5:c.752del	p.Gly251AlafsTer16	p.G251Afs*16	ENST00000318560	NM_005157.4	250	Ggg/gg	4/11	0.396358783694465	5	FACETS	0.806	0.759	0.854			1	INDETERMINATE	2	TRUE	NA	0.930032685080182	5		466	901	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426052	47426052	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006546-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	132	271	0	ENST00000377045.4:c.572A>T	p.His191Leu	p.H191L	ENST00000377045	NM_001654.4	191	cAc/cTc	7/16	0.904380571422289	2	FACETS	0.558	0.509	0.608			1	SUBCLONAL	1	TRUE	NA	0.930032685080182	2		271	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0006546-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	477	599	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.37211975282073	4	FACETS	1	0.994	1	0.872	0.839	0.904	CLONAL	3	TRUE	0	0.429358597193456	4		599	911	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0006546-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	52	226	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.871	0.747	1	0.871	0.747	1	CLONAL	1	TRUE	1	0.429358597193456	2		227	278	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951087	48951088	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs1131690889	NA	P-0006546-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	163	298	0	ENST00000267163.4:c.1251_1252del	p.Arg418SerfsTer9	p.R418Sfs*9	ENST00000267163	NM_000321.2	417	AAa/a	13/27	0.429358597193456	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.429358597193456	2		298	355	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230432	46230432	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006546-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	96	334	0	ENST00000334344.6:c.766T>G	p.Ser256Ala	p.S256A	ENST00000334344	NM_152641.2	256	Tct/Gct	7/21	0.417012689915031	3	FACETS	1	0.949	1	0.551	0.493	0.612	CLONAL	1	TRUE	1	0.429358597193456	3		334	493	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857663	78857663	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006546-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	260	570	0	ENST00000306801.3:c.1733C>G	p.Ala578Gly	p.A578G	ENST00000306801	NM_020761.2	578	gCc/gGc	16/34	0.386747981203094	4	FACETS	0.943	0.885	1	0.943	0.885	1	CLONAL	2	TRUE	2	0.429358597193456	4		570	918	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778806	76778807	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0006546-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	198	213	1	ENST00000373344.5:c.6772_6773del	p.Leu2258GlyfsTer10	p.L2258Gfs*10	ENST00000373344	NM_000489.3	2258	TTg/g	31/35	0.373932783480568	2	FACETS	0.883	0.834	0.932			1	CLONAL	3	TRUE	NA	0.429358597193456	2		214	348	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041678	29041678	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006546-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	70	353	0	ENST00000282397.4:c.141G>C	p.Gln47His	p.Q47H	ENST00000282397	NM_002019.4	47	caG/caC	2/30	0.21757230142236	5	FACETS	0.834	0.727	0.949	0.278	0.242	0.317	INDETERMINATE	1	TRUE	2	0.429358597193456	5		353	643	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421380	12421380	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs773848402	NA	P-0006546-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	254	532	0	ENST00000287820.6:c.260A>G	p.Asp87Gly	p.D87G	ENST00000287820	NM_015869.4	87	gAt/gGt	2/7	0.429358597193456	2	FACETS	0.909	0.856	0.962	0.909	0.856	0.962	CLONAL	2	TRUE	0	0.429358597193456	2		532	651	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532837	187532843	+	frameshift_variant	Frame_Shift_Del	DEL	GTTTTTC	GTTTTTC	-	novel	NA	P-0006546-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	77	405	0	ENST00000441802.2:c.9550_9556del	p.Glu3184LeufsTer14	p.E3184Lfs*14	ENST00000441802	NM_005245.3	3184	GAAAAACct/ct	14/27	NA	2	FACETS	0.757	0.666	0.853			1	INDETERMINATE	1	TRUE	NA	0.429358597193456	2		405	474	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738348	133738348	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006546-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	209	466	0	ENST00000318560.5:c.752del	p.Gly251AlafsTer16	p.G251Afs*16	ENST00000318560	NM_005157.4	250	Ggg/gg	4/11	0.429358597193456	5	FACETS	0.89	0.827	0.955			1	CLONAL	2	TRUE	NA	0.429358597193456	5		466	899	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410892	63410892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369264970	NA	P-0006546-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	131	262	0	ENST00000330258.3:c.2275G>A	p.Val759Ile	p.V759I	ENST00000330258	NM_152424.3	759	Gtt/Att	2/2	0.373932783480568	2	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.429358597193456	2		262	475	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006075	22006075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762253433	NA	P-0006546-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	157	442	0	ENST00000276925.6:c.328G>A	p.Asp110Asn	p.D110N	ENST00000276925	NM_004936.3	110	Gat/Aat	2/2	0.387814811502321	5	FACETS	1	0.982	1	0.421	0.385	0.458	CLONAL	1	TRUE	2	0.429358597193456	5		442	953	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247519	123247519	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520027	NA	P-0006546-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	105	430	0	ENST00000358487.5:c.1972A>G	p.Lys658Glu	p.K658E	ENST00000358487	NM_000141.4	658	Aaa/Gaa	14/18	0.412901949299832	3	FACETS	0.897	0.805	0.995	0.299	0.268	0.332	CLONAL	1	TRUE	0	0.429358597193456	3		430	662	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373245	118373245	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006546-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	86	367	0	ENST00000534358.1:c.6638T>G	p.Met2213Arg	p.M2213R	ENST00000534358	NM_005933.3	2213	aTg/aGg	27/36	0.395458602523358	4	FACETS	0.913	0.809	1	0.304	0.269	0.342	CLONAL	1	TRUE	1	0.429358597193456	4		367	627	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222288	2222288	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006546-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	125	514	0	ENST00000326181.6:c.572G>A	p.Gly191Asp	p.G191D	ENST00000326181	NM_032271.2	191	gGc/gAc	8/21	0.429358597193456	3	FACETS	0.849	0.768	0.934	0.425	0.384	0.467	CLONAL	1	TRUE	1	0.429358597193456	3		514	833	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845677	68845677	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006546-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	152	579	0	ENST00000261769.5:c.923A>G	p.Asp308Gly	p.D308G	ENST00000261769	NM_004360.3	308	gAt/gGt	7/16	0.429358597193456	3	FACETS	1	0.955	1	0.533	0.488	0.58	CLONAL	1	TRUE	1	0.429358597193456	3		579	807	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89818613	89818613	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1166883043	NA	P-0006546-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	125	416	1	ENST00000389301.3:c.2999A>G	p.His1000Arg	p.H1000R	ENST00000389301	NM_000135.2	1000	cAc/cGc	31/43	0.429358597193456	3	FACETS	1	0.958	1	0.549	0.498	0.603	CLONAL	1	TRUE	1	0.429358597193456	3		417	644	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617162	100617162	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006546-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	19	202	0	ENST00000308731.7:c.587A>G	p.Gln196Arg	p.Q196R	ENST00000308731	NM_000061.2	196	cAg/cGg	7/19	0.373932783480568	2	FACETS	0.25	0.189	0.322			1	SUBCLONAL	1	TRUE	NA	0.429358597193456	2		202	354	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593653	55593654	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACACAACTTCCTTATGATCAT	novel	NA	P-0006664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	204	506	0	ENST00000288135.5:c.1739_1740insTACACAACTTCCTTATGATCA	p.Thr574_His580dup	p.T574_H580dup	ENST00000288135	NM_000222.2	574	-/ACACAACTTCCTTATGATCAT	11/21	1	2	FACETS	0.544	0.504	0.585	0.544	0.504	0.585	SUBCLONAL	1	TRUE	1	0.746753821514541	2		506	1005	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622565	28622565	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	240	315	0	ENST00000241453.7:c.1052del	p.Asn351MetfsTer83	p.N351Mfs*83	ENST00000241453	NM_004119.2	351	aAt/at	9/24	1	2	FACETS	0.99	0.931	1	0.99	0.931	1	CLONAL	1	TRUE	1	0.746753821514541	2		315	649	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599334	55599334	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519711	NA	P-0006664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	336	484	1	ENST00000288135.5:c.2460T>A	p.Asp820Glu	p.D820E	ENST00000288135	NM_000222.2	820	gaT/gaA	17/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.746753821514541	2		485	876	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0006995-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	23	758	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	1	2	FACETS	0.625	0.487	0.783	0.625	0.487	0.783	SUBCLONAL	1	FALSE	1	0.243809309141992	2		758	302	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242483	55242506	+	inframe_deletion	In_Frame_Del	DEL	ATCTCCGAAAGCCAACAAGGAAAT	ATCTCCGAAAGCCAACAAGGAAAT	-	rs727504232	NA	P-0006995-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	135	492	0	ENST00000275493.2:c.2253_2276del	p.Ser752_Ile759del	p.S752_I759del	ENST00000275493	NM_005228.3	751	acATCTCCGAAAGCCAACAAGGAAATc/acc	19/28	0.243809309141992	9	FACETS	1	0.966	1	0.684	0.629	0.741	CLONAL	5	FALSE	1	0.243809309141992	9		492	375	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0007121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	189	441	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.222749455497325	6	FACETS	1	0.957	1			1	CLONAL	4	TRUE	NA	0.222749455497325	6		441	590	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508064	106508064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	23	186	0	ENST00000359195.3:c.58C>T	p.Arg20Cys	p.R20C	ENST00000359195	NM_002649.2	20	Cgc/Tgc	2/11	0.222749455497325	7	FACETS	1	0.849	1	0.223	0.174	0.28	CLONAL	1	TRUE	2	0.222749455497325	7		186	288	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782177	NA	P-0007121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	168	689	0	ENST00000269305.4:c.644G>T	p.Ser215Ile	p.S215I	ENST00000269305	NM_001126112.2	215	aGt/aTt	6/11	0.222915375522058	3	FACETS	0.962	0.889	1	0.962	0.889	1	CLONAL	3	TRUE	0	0.222749455497325	3		689	581	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158594123	158594123	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	22	346	0	ENST00000263640.3:c.1450G>T	p.Ala484Ser	p.A484S	ENST00000263640	NM_001105.4	484	Gca/Tca	11/11	0.222749455497325	5	FACETS	0.89	0.691	1	0.223	0.172	0.281	CLONAL	1	TRUE	1	0.222749455497325	5		346	296	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522532	157522532	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1273529067	NA	P-0007121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	159	720	0	ENST00000346085.5:c.4804A>G	p.Ile1602Val	p.I1602V	ENST00000346085	NM_020732.3	1602	Atc/Gtc	18/20	0.222915375522058	4	FACETS	0.867	0.797	0.94	1	0.985	1	CLONAL	3	TRUE	2	0.222749455497325	4		720	671	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467821	50467821	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	155	399	1	ENST00000331340.3:c.1056G>T	p.Lys352Asn	p.K352N	ENST00000331340	NM_006060.4	352	aaG/aaT	8/8	0.222749455497325	6	FACETS	0.962	0.886	1	0.962	0.886	1	CLONAL	4	TRUE	2	0.222749455497325	6		400	523	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526687	106526687	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	36	448	0	ENST00000359195.3:c.2980G>T	p.Val994Leu	p.V994L	ENST00000359195	NM_002649.2	994	Gtg/Ttg	10/11	0.222749455497325	7	FACETS	1	0.915	1	0.24	0.197	0.288	CLONAL	1	TRUE	2	0.222749455497325	7		448	419	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602715	10602715	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	288	764	3	ENST00000171111.5:c.863G>T	p.Cys288Phe	p.C288F	ENST00000171111	NM_203500.1	288	tGc/tTc	3/6	0.222915375522058	4	FACETS	1	0.972	1			1	CLONAL	4	TRUE	NA	0.222749455497325	4		767	757	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152006	11152018	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGATCGAAGAG	GGAGATCGAAGAG	-	novel	NA	P-0007121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	150	476	0	ENST00000358026.2:c.4291_4303del	p.Glu1431ArgfsTer60	p.E1431Rfs*60	ENST00000358026	NM_001128849.1	1430	gaGGAGATCGAAGAG/ga	31/36	0.222915375522058	3	FACETS	1	0.943	1			1	CLONAL	3	TRUE	NA	0.222749455497325	3		476	485	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218475	1218497	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TATACAACGAAGAGAAGCAGAAA	TATACAACGAAGAGAAGCAGAAA	-	novel	NA	P-0007121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	170	553	0	ENST00000326873.7:c.350_372del	p.Leu117TyrfsTer38	p.L117Yfs*38	ENST00000326873	NM_000455.4	117	tTATACAACGAAGAGAAGCAGAAA/t	2/10	0.222915375522058	4	FACETS	1	0.977	1	0.853	0.789	0.918	CLONAL	3	TRUE	0	0.222749455497325	4		553	547	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312724	30312724	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	123	429	0	ENST00000262643.3:c.705G>T	p.Lys235Asn	p.K235N	ENST00000262643	NM_001238.2	235	aaG/aaT	8/12	0.222749455497325	7	FACETS	1	0.938	1			1	CLONAL	3	TRUE	NA	0.222749455497325	7		429	550	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022367	26022367	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	36	449	0	ENST00000435504.4:c.290G>T	p.Gly97Val	p.G97V	ENST00000435504		97	gGt/gTt	5/13	0.222749455497325	6	FACETS	1	0.847	1	0.258	0.212	0.31	CLONAL	1	TRUE	2	0.222749455497325	6		449	452	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359888	87359888	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	78	327	0	ENST00000277120.3:c.1196A>G	p.Asp399Gly	p.D399G	ENST00000277120		399	gAt/gGt	11/19	0.222915375522058	1	FACETS	1	0.949	1	1	0.986	1	CLONAL	2	TRUE	0	0.222749455497325	1		327	278	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932811	39932811	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	78	702	0	ENST00000378444.4:c.1788G>T	p.Gln596His	p.Q596H	ENST00000378444	NM_001123385.1	596	caG/caT	4/15	0.191732935356348	4	FACETS	0.814	0.717	0.918			1	CLONAL	2	TRUE	NA	0.222749455497325	4		702	526	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933730	39933730	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	69	534	0	ENST00000378444.4:c.869A>T	p.Lys290Met	p.K290M	ENST00000378444	NM_001123385.1	290	aAg/aTg	4/15	0.191732935356348	4	FACETS	0.928	0.812	1			1	CLONAL	2	TRUE	NA	0.222749455497325	4		534	408	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	83	525	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.453880551854154	10	FACETS	0.955	0.845	1			1	CLONAL	2	FALSE	NA	0.453880551854154	10		525	539	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434070	121434070	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766770471	NA	P-0008082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	39	373	5	ENST00000257555.6:c.961C>T	p.Arg321Cys	p.R321C	ENST00000257555		321	Cgc/Tgc	5/10	0.456716588792639	4	FACETS	1	0.924	1			1	CLONAL	1	FALSE	NA	0.453880551854154	4		378	210	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660665	190660665	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0008082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	44	229	1	ENST00000441310.2:c.303T>A	p.Cys101Ter	p.C101*	ENST00000441310	NM_000534.4	101	tgT/tgA	3/13	0.303622511289332	5	FACETS	1	0.939	1	0.413	0.349	0.483	CLONAL	1	FALSE	2	0.453880551854154	5		230	263	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645564	215645564	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	19	267	0	ENST00000260947.4:c.1034G>A	p.Gly345Glu	p.G345E	ENST00000260947	NM_000465.2	345	gGa/gAa	4/11	0.303622511289332	5	FACETS	0.643	0.489	0.822	0.214	0.163	0.274	SUBCLONAL	1	FALSE	2	0.453880551854154	5		267	219	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281231	142281231	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	36	295	0	ENST00000350721.4:c.1013A>C	p.Lys338Thr	p.K338T	ENST00000350721	NM_001184.3	338	aAg/aCg	4/47	NA	2	FACETS	1	0.858	1			1	INDETERMINATE	1	FALSE	NA	0.453880551854154	2		295	154	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554900	187554900	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	17	399	0	ENST00000441802.2:c.4261C>A	p.Gln1421Lys	p.Q1421K	ENST00000441802	NM_005245.3	1421	Cag/Aag	7/27	0.432156003485547	0	FACETS	0.401	0.303	0.513			1	SUBCLONAL	1	FALSE	0	0.453880551854154	0		399	102	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527875	157527875	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1435112076	NA	P-0008082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	62	295	0	ENST00000346085.5:c.5600A>G	p.Glu1867Gly	p.E1867G	ENST00000346085	NM_020732.3	1867	gAg/gGg	20/20	0.453880551854154	10	FACETS	0.945	0.819	1			1	CLONAL	2	FALSE	NA	0.453880551854154	10		295	407	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8501060	8501060	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0008082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	18	191	0	ENST00000356435.5:c.1823-1G>C		p.X608_splice	ENST00000356435		608			0.346987892999513	0	FACETS	0.747	0.582	0.926			1	CLONAL	1	FALSE	0	0.453880551854154	0		191	58	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245315	46245315	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	34	296	0	ENST00000334344.6:c.3409T>C	p.Ser1137Pro	p.S1137P	ENST00000334344	NM_152641.2	1137	Tca/Cca	15/21	0.421510343827219	5	FACETS	0.965	0.792	1	0.322	0.264	0.386	CLONAL	1	FALSE	2	0.453880551854154	5		296	261	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864655	57864655	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	48	638	0	ENST00000228682.2:c.2132C>A	p.Thr711Asn	p.T711N	ENST00000228682	NM_005269.2	711	aCc/aAc	12/12	0.43914381215932	1	FACETS	0.87	0.746	1	0.87	0.746	1	CLONAL	1	FALSE	0	0.453880551854154	1		638	188	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954172	32954172	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs200924727	NA	P-0008082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	45	366	0	ENST00000380152.3:c.9146A>G	p.Tyr3049Cys	p.Y3049C	ENST00000380152		3049	tAc/tGc	24/27	0.34222954907359	4	FACETS	1	0.938	1			1	CLONAL	1	FALSE	NA	0.453880551854154	4		366	236	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650795	37650795	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	54	365	0	ENST00000447079.4:c.2267A>C	p.Lys756Thr	p.K756T	ENST00000447079	NM_015083.1	756	aAg/aCg	5/14	0.34222954907359	4	FACETS	0.874	0.757	0.997			1	CLONAL	2	FALSE	NA	0.453880551854154	4		365	198	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59861688	59861688	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	41	384	0	ENST00000259008.2:c.1571A>T	p.Gln524Leu	p.Q524L	ENST00000259008	NM_032043.2	524	cAa/cTa	11/20	0.453880551854154	6	FACETS	0.732	0.61	0.868			1	SUBCLONAL	1	FALSE	NA	0.453880551854154	6		384	471	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240259	5240259	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	34	395	0	ENST00000357368.4:c.1655G>T	p.Ser552Ile	p.S552I	ENST00000357368	NM_002850.3	552	aGt/aTt	12/38	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.453880551854154	2		395	104	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47679313	47679345	+	inframe_deletion	In_Frame_Del	DEL	GGACAGGTTACTGCAGAGGGCATCCTCACACAT	GGACAGGTTACTGCAGAGGGCATCCTCACACAT	-	novel	NA	P-0008082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	170	325	0	ENST00000347630.2:c.862_894del	p.Met288_Ser298del	p.M288_S298del	ENST00000347630	NM_001007230.1	288	ATGTGTGAGGATGCCCTCTGCAGTAACCTGTCC/-	10/11	0.453880551854154	6	FACETS	1	0.979	1			1	CLONAL	5	FALSE	NA	0.453880551854154	6		325	265	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104320	2104342	+	frameshift_variant	Frame_Shift_Del	DEL	AGCCCTCTTCTTTAAGGTCATCA	AGCCCTCTTCTTTAAGGTCATCA	-	novel	NA	P-0008082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	53	370	1	ENST00000219476.3:c.362_384del	p.Ala121GlyfsTer34	p.A121Gfs*34	ENST00000219476	NM_000548.3	120	agAGCCCTCTTCTTTAAGGTCATCAag/agag	5/42	0.434523147304496	5	FACETS	1	0.959	1			1	CLONAL	1	FALSE	NA	0.453880551854154	5		371	291	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158749	26158760	+	inframe_deletion	In_Frame_Del	DEL	GCCGTCACCAAG	GCCGTCACCAAG	-	novel	NA	P-0008082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	115	136	0	ENST00000289316.2:c.352_363del	p.Ala118_Lys121del	p.A118_K121del	ENST00000289316	NM_138720.2	118	GCCGTCACCAAG/-	1/2	0.453880551854154	16	FACETS	0.959	0.867	1			1	CLONAL	4	FALSE	NA	0.453880551854154	16		136	552	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226093	2226093	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008525-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	60	663	0	ENST00000326181.6:c.1790G>T	p.Gly597Val	p.G597V	ENST00000326181	NM_032271.2	597	gGc/gTc	19/21	1	2	FACETS	0.227	0.194	0.262	0.227	0.194	0.262	SUBCLONAL	1	TRUE	1	0.604712372233252	2		663	876	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579355	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519997	NA	P-0008525-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	232	610	0	ENST00000269305.4:c.332T>A	p.Leu111Gln	p.L111Q	ENST00000269305	NM_001126112.2	111	cTg/cAg	4/11	0.604712372233252	1	FACETS	0.958	0.901	1	0.958	0.901	1	CLONAL	1	TRUE	0	0.604712372233252	1		610	559	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	70	811	0	ENST00000397752.3:c.3028G>C	p.Asp1010His	p.D1010H	ENST00000397752	NM_000245.2	1010	Gat/Cat	14/21	1	2	FACETS	1	0.949	1	1	0.983	1	CLONAL	2	TRUE	1	0.057	2		811	1032	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0008678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	38	639	0	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	1	2	FACETS	0.838	0.69	1	1	0.958	1	CLONAL	2	TRUE	1	0.057	2		639	796	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911477	134911477	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1341771878	NA	P-0008678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	36	668	1	ENST00000398015.3:c.1942G>T	p.Val648Leu	p.V648L	ENST00000398015	NM_004441.4	648	Gtg/Ttg	11/16	0.132578135735098	1	FACETS	0.897	0.735	1	1	0.959	1	CLONAL	2	TRUE	0	0.057	1		669	684	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707743	176707743	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	35	572	0	ENST00000439151.2:c.5800C>G	p.Gln1934Glu	p.Q1934E	ENST00000439151	NM_022455.4	1934	Cag/Gag	18/23	0.132578135735098	3	FACETS	0.925	0.756	1	0.925	0.756	1	CLONAL	2	TRUE	1	0.057	3		572	683	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045157	47045157	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	49	804	1	ENST00000377604.3:c.2398G>T	p.Glu800Ter	p.E800*	ENST00000377604	NM_001204468.1	800	Gag/Tag	21/24	1	2	FACETS	0.985	0.831	1	1	0.972	1	CLONAL	2	TRUE	1	0.057	2		805	873	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008712-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	210	525	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.390846324074638	2	FACETS	1	0.962	1	0.527	0.489	0.567	CLONAL	1	TRUE	0	0.390846324074638	2		525	1019	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207627	2207627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008712-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	220	615	1	ENST00000398665.3:c.911C>T	p.Ser304Leu	p.S304L	ENST00000398665	NM_032482.2	304	tCg/tTg	11/28	0.390846324074638	2	FACETS	1	0.942	1	0.507	0.471	0.544	CLONAL	1	TRUE	0	0.390846324074638	2		616	1110	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0008712-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	168	479	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	0.384944500835664	3	FACETS	0.984	0.904	1	0.492	0.452	0.535	CLONAL	1	TRUE	1	0.390846324074638	3		479	1044	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0008712-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	8	100	2	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	2	FACETS	0.129	0.082	0.19	0.129	0.082	0.19	SUBCLONAL	1	TRUE	1	0.390846324074638	2		102	317	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40879676	40879676	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008712-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	192	498	0	ENST00000428826.2:c.223A>T	p.Ser75Cys	p.S75C	ENST00000428826		75	Agt/Tgt	4/21	0.318606527193118	3	FACETS	0.994	0.918	1			1	CLONAL	1	TRUE	NA	0.390846324074638	3		498	1181	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193510	99193510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008712-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	194	577	0	ENST00000074304.5:c.2705C>T	p.Thr902Ile	p.T902I	ENST00000074304	NM_001134224.1	902	aCa/aTa	25/26	0.384944500835664	3	FACETS	1	0.928	1	0.502	0.464	0.543	CLONAL	1	TRUE	1	0.390846324074638	3		577	1181	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510349	187510349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008712-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	68	239	0	ENST00000441802.2:c.13164G>T	p.Trp4388Cys	p.W4388C	ENST00000441802	NM_005245.3	4388	tgG/tgT	27/27	1	2	FACETS	0.845	0.738	0.959	0.845	0.738	0.959	CLONAL	1	TRUE	1	0.390846324074638	2		239	412	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32438072	32438072	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	196	557	0	ENST00000332351.3:c.965G>T	p.Ser322Ile	p.S322I	ENST00000332351	NM_024426.4	322	aGc/aTc	5/10	0.33771756568308	3	FACETS	0.836	0.777	0.897	0.836	0.777	0.897	CLONAL	2	TRUE	1	0.396764757908401	3		557	708	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114135	115114135	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	117	611	0	ENST00000257566.3:c.1082G>C	p.Gly361Ala	p.G361A	ENST00000257566	NM_016569.3	361	gGg/gCg	6/8	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.396764757908401	2		611	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0008925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	175	690	1	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.321854712168207	2	FACETS	1	0.99	1	0.745	0.69	0.802	CLONAL	1	TRUE	0	0.396764757908401	2		691	592	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867301	45867301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1269826858	NA	P-0008925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	55	592	1	ENST00000391945.4:c.892G>A	p.Ala298Thr	p.A298T	ENST00000391945	NM_000400.3	298	Gcc/Acc	10/23	0.270747490316825	2	FACETS	0.531	0.454	0.615	0.266	0.227	0.308	SUBCLONAL	1	TRUE	0	0.396764757908401	2		593	522	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0008925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	966	587	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.396764757908401	15	FACETS	0.967	0.943	0.991			1	CLONAL	11	TRUE	NA	0.396764757908401	15		587	1639	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933871	39933871	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	222	697	0	ENST00000378444.4:c.728G>T	p.Arg243Leu	p.R243L	ENST00000378444	NM_001123385.1	243	cGc/cTc	4/15	0.234032592819828	5	FACETS	1	0.983	1	0.768	0.717	0.82	INDETERMINATE	2	TRUE	2	0.396764757908401	5		697	775	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931463	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622007	NA	P-0008960-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1428	433	435	0	ENST00000374690.3:c.2105T>A	p.Leu702His	p.L702H	ENST00000374690	NM_000044.3	702	cTc/cAc	4/8	0.519217459839055	12	FACETS	1	0.983	1			1	CLONAL	3	TRUE	NA	0.519217459839055	12		435	1861	SUCCESS
AR	367	MSKCC	GRCh37	X	66766357	66766374	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGCGGCGGCGGC	GGCGGCGGCGGCGGCGGC	-	rs746853821	NA	P-0009014-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	11	77	0	ENST00000374690.3:c.1403_1420del	p.Gly468_Gly473del	p.G468_G473del	ENST00000374690	NM_000044.3	457	GGCGGCGGCGGCGGCGGC/-	1/8	0.30581467336449	3	FACETS	0.564	0.391	0.778	0.188	0.13	0.26	SUBCLONAL	1	TRUE	0	0.305810855221941	3		77	147	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509060	106509060	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009014-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	152	375	0	ENST00000359195.3:c.1054G>A	p.Val352Met	p.V352M	ENST00000359195	NM_002649.2	352	Gtg/Atg	2/11	1	2	FACETS	0.83	0.762	0.9	1	0.99	1	CLONAL	2	TRUE	1	0.305810855221941	2		375	599	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608531	28608531	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1220647027	NA	P-0009014-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	85	552	0	ENST00000241453.7:c.1611C>A	p.Phe537Leu	p.F537L	ENST00000241453	NM_004119.2	537	ttC/ttA	13/24	0.305810855221941	5	FACETS	0.644	0.567	0.726			1	SUBCLONAL	1	TRUE	NA	0.305810855221941	5		552	1260	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533668	63533668	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773033390	NA	P-0009014-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	91	483	0	ENST00000307078.5:c.1486G>A	p.Ala496Thr	p.A496T	ENST00000307078	NM_004655.3	496	Gcc/Acc	6/11	0.291897956044408	5	FACETS	1	0.922	1			1	CLONAL	1	TRUE	NA	0.305810855221941	5		483	827	SUCCESS
AR	367	MSKCC	GRCh37	X	66766357	66766374	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGCGGCGGCGGC	GGCGGCGGCGGCGGCGGC	-	rs746853821	NA	P-0009014-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	7	77	0	ENST00000374690.3:c.1403_1420del	p.Gly468_Gly473del	p.G468_G473del	ENST00000374690	NM_000044.3	457	GGCGGCGGCGGCGGCGGC/-	1/8	0.392608126431335	3	FACETS	0.52	0.327	0.77	0.26	0.163	0.385	SUBCLONAL	1	TRUE	1	0.392608126431335	3		77	82	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509060	106509060	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009014-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	98	375	0	ENST00000359195.3:c.1054G>A	p.Val352Met	p.V352M	ENST00000359195	NM_002649.2	352	Gtg/Atg	2/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.392608126431335	2		375	425	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490331	29490331	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1262333812	NA	P-0009014-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	34	352	0	ENST00000356175.3:c.416C>T	p.Ser139Phe	p.S139F	ENST00000356175	NM_000267.3	139	tCt/tTt	4/57	1	2	FACETS	0.391	0.319	0.472	0.391	0.319	0.472	SUBCLONAL	1	TRUE	1	0.392608126431335	2		352	443	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0009275-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	182	441	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.138777522306782	6	FACETS	1	0.973	1	0.737	0.682	0.794	INDETERMINATE	2	TRUE	3	0.448897310694205	6		441	696	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815712	32815712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1374606443	NA	P-0009275-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	136	724	0	ENST00000354258.4:c.1904G>A	p.Arg635His	p.R635H	ENST00000354258	NM_000593.5	635	cGc/cAc	8/11	0.346774079957124	3	FACETS	0.734	0.666	0.805	0.367	0.333	0.403	SUBCLONAL	1	TRUE	1	0.448897310694205	3		724	1011	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100929	27100929	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009275-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	244	611	0	ENST00000324856.7:c.4211A>T	p.Gln1404Leu	p.Q1404L	ENST00000324856	NM_006015.4	1404	cAg/cTg	18/20	0.37925570832979	2	FACETS	0.875	0.824	0.928	0.875	0.824	0.928	CLONAL	2	TRUE	0	0.448897310694205	2		611	621	SUCCESS
ATM	472	MSKCC	GRCh37	11	108214050	108214050	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1010206130	NA	P-0009275-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	133	350	0	ENST00000278616.4:c.8370A>C	p.Arg2790Ser	p.R2790S	ENST00000278616	NM_000051.3	2790	agA/agC	57/63	0.37925570832979	2	FACETS	1	0.986	1	0.702	0.643	0.763	CLONAL	1	TRUE	0	0.448897310694205	2		350	422	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220578	1220582	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGGCA	AGGCA	-	novel	NA	P-0009275-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	289	721	0	ENST00000326873.7:c.598-2_600del		p.X200_splice	ENST00000326873	NM_000455.4	200		5/10	0.383882554701479	2	FACETS	0.945	0.895	0.996	0.945	0.895	0.996	CLONAL	2	TRUE	0	0.448897310694205	2		721	681	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555167	106555167	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009275-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	299	664	0	ENST00000369096.4:c.2284G>T	p.Val762Leu	p.V762L	ENST00000369096	NM_001198.3	762	Gtg/Ttg	7/7	0.346774079957124	3	FACETS	0.859	0.81	0.908	0.859	0.81	0.908	CLONAL	2	TRUE	1	0.448897310694205	3		664	950	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912259	97912259	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140781259	NA	P-0009275-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	113	542	2	ENST00000289081.3:c.632C>T	p.Pro211Leu	p.P211L	ENST00000289081	NM_000136.2	211	cCt/cTt	7/15	0.448897310694205	1	FACETS	0.526	0.473	0.581	0.526	0.473	0.581	SUBCLONAL	1	TRUE	0	0.448897310694205	1		544	743	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0009404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	42	434	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	NA	2	FACETS	0.458	0.381	0.543			1	INDETERMINATE	1	TRUE	NA	0.294574404017038	2		434	623	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0009404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	31	359	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.294574404017038	1	FACETS	0.594	0.482	0.721	0.594	0.482	0.721	SUBCLONAL	1	TRUE	0	0.294574404017038	1		359	302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0009404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	78	509	3	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	1	2	FACETS	0.831	0.731	0.939	0.831	0.731	0.939	CLONAL	1	TRUE	1	0.294574404017038	2		512	637	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346185	152346185	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	74	887	0	ENST00000359321.1:c.385A>G	p.Thr129Ala	p.T129A	ENST00000359321	NM_005431.1	129	Aca/Gca	3/3	1	2	FACETS	0.706	0.617	0.801	0.706	0.617	0.801	SUBCLONAL	1	TRUE	1	0.294574404017038	2		887	712	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604764	48604765	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs377767376	NA	P-0009404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	56	470	0	ENST00000342988.3:c.1587dup	p.His530ThrfsTer47	p.H530Tfs*47	ENST00000342988	NM_005359.5	529	tta/ttAa	12/12	1	2	FACETS	0.807	0.693	0.932	0.807	0.693	0.932	CLONAL	1	TRUE	1	0.294574404017038	2		470	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0009621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	53	543	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	1	2	FACETS	0.904	0.769	1	0.904	0.769	1	CLONAL	1	TRUE	1	0.16	2		543	733	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0009621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	118	974	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.99	0.894	1	1	0.989	1	CLONAL	2	TRUE	1	0.16	2		974	745	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913384	NA	P-0009621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	36	138	0	ENST00000304494.5:c.262G>T	p.Glu88Ter	p.E88*	ENST00000304494	NM_000077.4	88	Gag/Tag	2/3	1	2	FACETS	1	0.924	1	1	0.97	1	CLONAL	2	TRUE	1	0.16	2		138	185	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732298	74732298	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	79	771	0	ENST00000359995.5:c.611C>T	p.Ser204Leu	p.S204L	ENST00000359995	NM_001195427.1	204	tCg/tTg	2/3	1	2	FACETS	0.961	0.843	1	0.961	0.843	1	CLONAL	1	TRUE	1	0.16	2		771	1028	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028025	69028025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200550325	NA	P-0009687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	94	490	2	ENST00000288368.4:c.3184C>T	p.Arg1062Cys	p.R1062C	ENST00000288368	NM_024870.2	1062	Cgt/Tgt	26/40	0.505875227605141	3	FACETS	0.504	0.448	0.565	0.252	0.224	0.283	SUBCLONAL	1	TRUE	1	0.505875227605141	3		492	923	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0009691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	477	619	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.662814687632184	3	FACETS	0.98	0.951	1			1	CLONAL	3	TRUE	NA	0.662814687632184	3		619	652	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937109	39937109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757971608	NA	P-0009691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	130	576	0	ENST00000378444.4:c.74C>T	p.Ala25Val	p.A25V	ENST00000378444	NM_001123385.1	25	gCg/gTg	2/15	1	2	FACETS	0.881	0.806	0.96	0.881	0.806	0.96	CLONAL	1	TRUE	1	0.662814687632184	2		576	445	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073323	8073323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	454	515	0	ENST00000377482.5:c.1336G>T	p.Asp446Tyr	p.D446Y	ENST00000377482	NM_018948.3	446	Gat/Tat	4/4	0.639436284973109	5	FACETS	0.848	0.812	0.884	0.848	0.812	0.884	CLONAL	3	TRUE	2	0.662814687632184	5		515	1074	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153657	55153657	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	287	551	0	ENST00000257290.5:c.2623C>A	p.Leu875Met	p.L875M	ENST00000257290	NM_006206.4	875	Ctg/Atg	19/23	0.662814687632184	5	FACETS	0.907	0.854	0.961			1	CLONAL	2	TRUE	NA	0.662814687632184	5		551	952	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593669	55593669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	555	572	1	ENST00000288135.5:c.1735G>T	p.Asp579Tyr	p.D579Y	ENST00000288135	NM_000222.2	579	Gat/Tat	11/21	0.662814687632184	5	FACETS	1	0.989	1			1	CLONAL	3	TRUE	NA	0.662814687632184	5		573	1052	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946329	55946329	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	64	238	0	ENST00000263923.4:c.3850G>C	p.Gly1284Arg	p.G1284R	ENST00000263923	NM_002253.2	1284	Gga/Cga	30/30	NA	2	FACETS	1	0.956	1			1	INDETERMINATE	1	TRUE	NA	0.662814687632184	2		238	165	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242776	66242776	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	176	353	1	ENST00000273854.3:c.1796G>T	p.Cys599Phe	p.C599F	ENST00000273854	NM_004439.5	599	tGc/tTc	9/18	0.662814687632184	3	FACETS	1	0.99	1			1	CLONAL	1	TRUE	NA	0.662814687632184	3		354	485	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729968	41729968	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	299	581	1	ENST00000242208.4:c.561C>A	p.Asp187Glu	p.D187E	ENST00000242208	NM_002192.2	187	gaC/gaA	3/3	0.662814687632184	4	FACETS	0.994	0.941	1	0.994	0.941	1	CLONAL	2	TRUE	2	0.662814687632184	4		582	755	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459467	50459467	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	184	371	0	ENST00000331340.3:c.756C>G	p.Asp252Glu	p.D252E	ENST00000331340	NM_006060.4	252	gaC/gaG	7/8	0.662814687632184	4	FACETS	0.788	0.731	0.846	0.788	0.731	0.846	SUBCLONAL	2	TRUE	2	0.662814687632184	4		371	586	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492867	8492867	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	386	456	0	ENST00000356435.5:c.2462G>T	p.Gly821Val	p.G821V	ENST00000356435		821	gGg/gTg	16/35	0.639436284973109	5	FACETS	0.97	0.928	1	0.97	0.928	1	CLONAL	3	TRUE	2	0.662814687632184	5		456	798	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518363	8518363	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	267	313	0	ENST00000356435.5:c.1028G>T	p.Trp343Leu	p.W343L	ENST00000356435		343	tGg/tTg	10/35	0.639436284973109	5	FACETS	0.915	0.867	0.965	0.915	0.867	0.965	CLONAL	3	TRUE	2	0.662814687632184	5		313	585	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451003	70451003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	105	517	0	ENST00000373644.4:c.5843C>T	p.Ser1948Phe	p.S1948F	ENST00000373644	NM_030625.2	1948	tCt/tTt	12/12	1	2	FACETS	0.771	0.696	0.849	0.771	0.696	0.849	SUBCLONAL	1	TRUE	1	0.662814687632184	2		517	411	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416218	416218	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs368037236	NA	P-0009691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	317	478	1	ENST00000399788.2:c.3968G>T	p.Arg1323Leu	p.R1323L	ENST00000399788	NM_001042603.1	1323	cGg/cTg	24/28	0.662814687632184	6	FACETS	1	0.97	1			1	CLONAL	2	TRUE	NA	0.662814687632184	6		479	1070	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117759	115117759	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	245	479	0	ENST00000257566.3:c.676G>T	p.Asp226Tyr	p.D226Y	ENST00000257566	NM_016569.3	226	Gat/Tat	3/8	0.602048480840637	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	2	0.662814687632184	4		479	590	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36989288	36989288	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	204	510	0	ENST00000354822.5:c.47C>A	p.Ala16Glu	p.A16E	ENST00000354822	NM_001079668.2	16	gCg/gAg	1/3	0.662814687632184	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.662814687632184	4		510	486	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023013	33023013	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	90	419	0	ENST00000300177.4:c.122A>C	p.His41Pro	p.H41P	ENST00000300177	NM_001191322.1	41	cAc/cCc	2/2	0.659945945863878	1	FACETS	0.873	0.792	0.955	0.873	0.792	0.955	CLONAL	1	TRUE	0	0.662814687632184	1		419	208	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273974	10273974	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	285	683	0	ENST00000330684.3:c.295G>C	p.Val99Leu	p.V99L	ENST00000330684	NM_001134407.1	99	Gtg/Ctg	2/13	0.633932850368864	2	FACETS	0.975	0.934	1	0.975	0.934	1	CLONAL	2	TRUE	0	0.662814687632184	2		683	441	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645032	67645032	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	136	600	0	ENST00000264010.4:c.297G>T	p.Gln99His	p.Q99H	ENST00000264010	NM_006565.3	99	caG/caT	3/12	0.590452954287814	3	FACETS	0.957	0.874	1	0.478	0.437	0.522	CLONAL	1	TRUE	1	0.662814687632184	3		600	571	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923738	72923738	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	124	530	0	ENST00000268489.5:c.3340C>G	p.Arg1114Gly	p.R1114G	ENST00000268489	NM_006885.3	1114	Cga/Gga	4/10	0.590452954287814	3	FACETS	1	0.947	1	0.529	0.481	0.578	CLONAL	1	TRUE	1	0.662814687632184	3		530	471	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220488	1220488	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913316	NA	P-0009691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	257	575	0	ENST00000326873.7:c.581A>T	p.Asp194Val	p.D194V	ENST00000326873	NM_000455.4	194	gAc/gTc	4/10	0.633932850368864	2	FACETS	0.948	0.905	0.99	0.948	0.905	0.99	CLONAL	2	TRUE	0	0.662814687632184	2		575	409	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523275	9523275	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	410	631	0	ENST00000353224.5:c.1962G>T	p.Arg654Ser	p.R654S	ENST00000353224	NM_177990.2	654	agG/agT	9/10	0.662814687632184	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	2	0.662814687632184	4		631	883	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714387	40714387	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	109	502	0	ENST00000373198.4:c.4010G>T	p.Arg1337Leu	p.R1337L	ENST00000373198	NM_133170.3	1337	cGc/cTc	29/32	0.501473072420515	3	FACETS	0.952	0.86	1			1	CLONAL	1	TRUE	NA	0.662814687632184	3		502	460	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796865	45796865	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782263	NA	P-0009691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	344	558	0	ENST00000450313.1:c.1465G>T	p.Ala489Ser	p.A489S	ENST00000450313	NM_012222.2	489	Gcc/Tcc	14/16	0.662814687632184	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	1	0.662814687632184	3		558	688	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798613	45798613	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	319	614	0	ENST00000450313.1:c.481G>T	p.Asp161Tyr	p.D161Y	ENST00000450313	NM_012222.2	161	Gac/Tac	6/16	0.662814687632184	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.662814687632184	3		614	629	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166215	118166215	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	102	381	0	ENST00000369448.3:c.725G>T	p.Gly242Val	p.G242V	ENST00000369448	NM_017709.3	242	gGg/gTg	2/2	1	2	FACETS	0.9	0.813	0.99	0.9	0.813	0.99	CLONAL	1	TRUE	1	0.662814687632184	2		381	342	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239360	105239360	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	147	614	2	ENST00000349310.3:c.1027A>T	p.Met343Leu	p.M343L	ENST00000349310	NM_001014432.1	343	Atg/Ttg	12/15	0.662814687632184	3	FACETS	0.911	0.835	0.991			1	CLONAL	1	TRUE	NA	0.662814687632184	3		616	648	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139907	50139907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	124	624	0	ENST00000246792.3:c.422G>A	p.Gly141Glu	p.G141E	ENST00000246792	NM_006270.3	141	gGg/gAg	4/6	0.557902358794382	4	FACETS	0.802	0.726	0.882	0.401	0.363	0.441	CLONAL	1	TRUE	2	0.662814687632184	4		624	776	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987123	69987123	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1416	263	577	0	ENST00000394351.3:c.184A>T	p.Met62Leu	p.M62L	ENST00000394351	NM_000248.3	62	Atg/Ttg	2/9	0.662814687632184	11	FACETS	0.941	0.879	1			1	CLONAL	2	TRUE	NA	0.662814687632184	11		577	1679	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467598	66467598	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	132	434	0	ENST00000273854.3:c.671T>G	p.Val224Gly	p.V224G	ENST00000273854	NM_004439.5	224	gTt/gGt	3/18	0.662814687632184	3	FACETS	0.529	0.48	0.582			1	SUBCLONAL	1	TRUE	NA	0.662814687632184	3		434	1002	SUCCESS
MET	4233	MSKCC	GRCh37	7	116413264	116413264	+	intron_variant	Intron	SNP	G	G	A	rs1004574017	NA	P-0009691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	231	836	0	ENST00000397752.3:c.3028+1221G>A		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.662814687632184	2		836	638	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411016	63411016	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	352	559	0	ENST00000330258.3:c.2151C>A	p.Cys717Ter	p.C717*	ENST00000330258	NM_152424.3	717	tgC/tgA	2/2	0.400241090279511	6	FACETS	0.959	0.912	1	0.959	0.912	1	CLONAL	3	TRUE	3	0.662814687632184	6		559	859	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0010053-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	411	855	1	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	0.478416678461477	4	FACETS	1	0.987	1	0.803	0.77	0.836	CLONAL	3	TRUE	0	0.476374253898509	4		856	793	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0010053-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	3393	845	1	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.476374253898509	26	FACETS	1	0.997	1			1	CLONAL	26	TRUE	NA	0.476374253898509	26		846	3661	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559089	29559089	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1131691089	NA	P-0010053-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	71	130	0	ENST00000356175.3:c.3198-2A>G		p.X1066_splice	ENST00000356175	NM_000267.3	1066			0.478416678461477	3	FACETS	0.954	0.863	1			1	CLONAL	3	TRUE	NA	0.476374253898509	3		130	129	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0010082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	1201	634	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.923142916512819	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.931173616045685	3		634	1250	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192386	138192386	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	177	241	0	ENST00000237289.4:c.22C>T	p.Gln8Ter	p.Q8*	ENST00000237289	NM_001270507.1	8	Cag/Tag	2/9	0.921646346386352	3	FACETS	1	0.97	1	0.541	0.502	0.581	CLONAL	1	TRUE	1	0.931173616045685	3		241	515	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625252	69625252	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782761826	NA	P-0010082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1542	170	707	0	ENST00000334134.2:c.541C>T	p.Arg181Cys	p.R181C	ENST00000334134	NM_005247.2	181	Cgc/Tgc	3/3	0.860499155516033	4	FACETS	0.412	0.377	0.449	0.206	0.188	0.225	SUBCLONAL	1	TRUE	2	0.931173616045685	4		707	1712	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167784	185167793	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCCACCTT	CCTCCACCTT	-	novel	NA	P-0010082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	365	564	0	ENST00000265026.3:c.1109_1118del	p.Leu370GlnfsTer14	p.L370Qfs*14	ENST00000265026	NM_004721.4	369	agCCTCCACCTT/ag	6/14	0.931173616045685	3	FACETS	0.991	0.941	1			1	CLONAL	1	TRUE	NA	0.931173616045685	3		564	1159	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681705	78681705	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1452445269	NA	P-0010468-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	80	645	0	ENST00000306801.3:c.413G>A	p.Arg138His	p.R138H	ENST00000306801	NM_020761.2	138	cGt/cAt	4/34	0.263168206902835	5	FACETS	1	0.901	1			1	CLONAL	1	TRUE	NA	0.263168206902835	5		645	825	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204512003	204512003	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	176	610	0	ENST00000367182.3:c.603G>T	p.Trp201Cys	p.W201C	ENST00000367182	NM_001278516.1	201	tgG/tgT	8/11	0.299853778906667	5	FACETS	0.854	0.787	0.925	0.427	0.393	0.463	CLONAL	2	TRUE	1	0.299853778906667	5		610	996	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379429	225379429	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	57	544	0	ENST00000264414.4:c.439T>C	p.Phe147Leu	p.F147L	ENST00000264414	NM_003590.4	147	Ttt/Ctt	4/16	0.299853778906667	3	FACETS	0.615	0.527	0.712	0.307	0.263	0.356	SUBCLONAL	1	TRUE	1	0.299853778906667	3		544	711	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4097336	4097336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377755503	NA	P-0010511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	64	373	0	ENST00000262948.5:c.925G>A	p.Gly309Arg	p.G309R	ENST00000262948	NM_030662.3	309	Ggg/Agg	8/11	0.278923182323826	3	FACETS	0.832	0.721	0.953	0.416	0.36	0.477	CLONAL	1	TRUE	1	0.299853778906667	3		373	590	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107164	27107196	+	inframe_deletion	In_Frame_Del	DEL	TTGGACATCTCGGTATCACCGTTGATGAACTCA	TTGGACATCTCGGTATCACCGTTGATGAACTCA	-	novel	NA	P-0010511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	34	276	0	ENST00000324856.7:c.6779_6811del	p.Asp2260_Leu2270del	p.D2260_L2270del	ENST00000324856	NM_006015.4	2259	TTGGACATCTCGGTATCACCGTTGATGAACTCA/-	20/20	0.217520064883053	4	FACETS	0.596	0.486	0.719	0.298	0.243	0.36	SUBCLONAL	1	TRUE	2	0.299853778906667	4		276	495	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141790	108141790	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0010511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	95	654	0	ENST00000278616.4:c.2839-1del		p.X947_splice	ENST00000278616	NM_000051.3	947			0.285608947519653	2	FACETS	0.925	0.824	1	0.463	0.412	0.516	CLONAL	1	TRUE	0	0.299853778906667	2		654	685	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0010563-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	765	424	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	0.52278483374887	6	FACETS	1	0.994	1			1	CLONAL	4	TRUE	NA	0.52278483374887	6		424	1377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579559	7579559	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010563-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	246	493	0	ENST00000269305.4:c.128del	p.Leu43Ter	p.L43*	ENST00000269305	NM_001126112.2	43	tTg/tg	4/11	0.52278483374887	1	FACETS	0.961	0.903	1	0.961	0.903	1	CLONAL	1	TRUE	0	0.52278483374887	1		493	723	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56367749	56367749	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010563-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	82	323	0	ENST00000348428.3:c.575T>G	p.Val192Gly	p.V192G	ENST00000348428	NM_006785.3	192	gTt/gGt	4/17	0.255511699245783	1	FACETS	0.434	0.383	0.488	0.434	0.383	0.488	INDETERMINATE	1	TRUE	0	0.52278483374887	1		323	534	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89176389	89176389	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010563-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	90	245	0	ENST00000336596.2:c.119G>T	p.Gly40Val	p.G40V	ENST00000336596	NM_005233.5	40	gGg/gTg	2/17	1	2	FACETS	0.97	0.868	1	0.97	0.868	1	CLONAL	1	TRUE	1	0.52278483374887	2		245	355	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010837-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	33	974	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.369706490176267	3	FACETS	0.575	0.468	0.694	0.287	0.234	0.347	SUBCLONAL	1	FALSE	1	0.369706490176267	3		974	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0010837-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	35	862	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.318228129082963	3	FACETS	0.471	0.386	0.567	0.236	0.193	0.284	SUBCLONAL	1	FALSE	1	0.369706490176267	3		862	476	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921430	39921430	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010837-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	28	725	2	ENST00000378444.4:c.4390G>A	p.Glu1464Lys	p.E1464K	ENST00000378444	NM_001123385.1	1464	Gag/Aag	10/15	1	2	FACETS	0.371	0.296	0.457	0.371	0.296	0.457	SUBCLONAL	1	FALSE	1	0.369706490176267	2		727	408	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971145	21971146	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010837-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	22	253	0	ENST00000304494.5:c.212dup	p.Asn71LysfsTer49	p.N71Kfs*49	ENST00000304494	NM_000077.4	71	aac/aaAc	2/3	0.318228129082963	3	FACETS	0.754	0.588	0.944	0.377	0.294	0.472	CLONAL	1	FALSE	1	0.369706490176267	3		253	187	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476376	88476376	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010977-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	108	481	0	ENST00000360948.2:c.1756C>A	p.Gln586Lys	p.Q586K	ENST00000360948	NM_001012338.2	586	Cag/Aag	15/19	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.330978573707998	2		481	635	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426127	47426127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010977-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	68	320	0	ENST00000377045.4:c.647C>T	p.Pro216Leu	p.P216L	ENST00000377045	NM_001654.4	216	cCc/cTc	7/16	0.330978573707998	3	FACETS	0.527	0.458	0.603	0.264	0.229	0.302	SUBCLONAL	1	TRUE	1	0.330978573707998	3		320	908	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041235	29041235	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010977-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	57	382	0	ENST00000282397.4:c.193G>T	p.Glu65Ter	p.E65*	ENST00000282397	NM_002019.4	65	Gaa/Taa	3/30	1	2	FACETS	0.639	0.548	0.738	0.639	0.548	0.738	SUBCLONAL	1	TRUE	1	0.330978573707998	2		382	539	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47596678	47596678	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs746990000	NA	P-0010977-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	54	417	0	ENST00000263735.4:c.34C>A	p.Leu12Met	p.L12M	ENST00000263735	NM_002354.2	12	Ctg/Atg	1/9	1	2	FACETS	0.875	0.75	1	0.875	0.75	1	CLONAL	1	TRUE	1	0.330978573707998	2		417	373	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282707	1282707	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1049929004	NA	P-0010977-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	68	541	0	ENST00000310581.5:c.1606C>A	p.Leu536Met	p.L536M	ENST00000310581	NM_198253.2	536	Ctg/Atg	3/16	1	2	FACETS	0.66	0.574	0.752	0.66	0.574	0.752	SUBCLONAL	1	TRUE	1	0.330978573707998	2		541	623	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	119	376	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.82	0.745	0.898	0.82	0.745	0.898	CLONAL	1	FALSE	1	0.644980430432472	2		376	450	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339223	87339223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	213	413	0	ENST00000277120.3:c.805G>A	p.Glu269Lys	p.E269K	ENST00000277120		269	Gaa/Aaa	8/19	0.181282371866981	0	FACETS	0.273	0.253	0.293			1	INDETERMINATE	1	FALSE	0	0.644980430432472	0		413	860	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967960	93967960	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	315	547	0	ENST00000369303.4:c.1967G>A	p.Gly656Glu	p.G656E	ENST00000369303	NM_004440.3	656	gGg/gAg	11/17	0.644980430432472	1	FACETS	0.873	0.829	0.918	0.873	0.829	0.918	CLONAL	1	FALSE	0	0.644980430432472	1		547	758	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84403342	84403342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	276	416	0	ENST00000321945.7:c.143C>T	p.Ser48Phe	p.S48F	ENST00000321945	NM_139076.2	48	tCc/tTc	2/9	1	2	FACETS	0.979	0.922	1	0.979	0.922	1	CLONAL	1	FALSE	1	0.644980430432472	2		416	874	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710603	40710603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	229	324	0	ENST00000373198.4:c.4248G>A	p.Met1416Ile	p.M1416I	ENST00000373198	NM_133170.3	1416	atG/atA	31/32	1	2	FACETS	0.958	0.897	1	0.958	0.897	1	CLONAL	1	FALSE	1	0.644980430432472	2		324	741	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843533	156843533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	586	473	0	ENST00000524377.1:c.959C>T	p.Ser320Phe	p.S320F	ENST00000524377	NM_002529.3	320	tCc/tTc	8/17	0.580227858587613	3	FACETS	0.995	0.96	1	0.995	0.96	1	CLONAL	2	FALSE	1	0.644980430432472	3		473	1207	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101072	27101072	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	300	481	0	ENST00000324856.7:c.4354C>T	p.Gln1452Ter	p.Q1452*	ENST00000324856	NM_006015.4	1452	Cag/Tag	18/20	1	2	FACETS	0.796	0.75	0.844	0.796	0.75	0.844	SUBCLONAL	1	FALSE	1	0.644980430432472	2		481	1168	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43806063	43806063	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	325	514	1	ENST00000372470.3:c.859C>T	p.Leu287Phe	p.L287F	ENST00000372470	NM_005373.2	287	Ctt/Ttt	6/12	1	2	FACETS	0.873	0.825	0.923	0.873	0.825	0.923	CLONAL	1	FALSE	1	0.644980430432472	2		515	1154	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120493422	120493422	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	248	435	0	ENST00000256646.2:c.2404A>T	p.Asn802Tyr	p.N802Y	ENST00000256646	NM_024408.3	802	Aat/Tat	15/34	1	2	FACETS	0.885	0.829	0.942	0.885	0.829	0.942	CLONAL	1	FALSE	1	0.644980430432472	2		435	869	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576880	212576880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	109	258	0	ENST00000342788.4:c.1019G>A	p.Gly340Glu	p.G340E	ENST00000342788	NM_005235.2	340	gGa/gAa	9/28	1	2	FACETS	0.744	0.672	0.82	0.744	0.672	0.82	SUBCLONAL	1	FALSE	1	0.644980430432472	2		258	454	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713775	30713775	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1226482581	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	205	280	0	ENST00000295754.5:c.1100C>T	p.Pro367Leu	p.P367L	ENST00000295754	NM_003242.5	367	cCa/cTa	4/7	0.5722216265597	4	FACETS	0.913	0.846	0.983	0.304	0.282	0.328	CLONAL	1	FALSE	1	0.644980430432472	4		280	1145	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127759	47127759	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1225	262	334	0	ENST00000409792.3:c.5323G>T	p.Gly1775Trp	p.G1775W	ENST00000409792	NM_014159.6	1775	Ggg/Tgg	11/21	0.5722216265597	4	FACETS	0.899	0.84	0.96	0.3	0.28	0.32	CLONAL	1	FALSE	1	0.644980430432472	4		334	1487	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598087	52598087	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	255	517	1	ENST00000394830.3:c.3779A>T	p.Asp1260Val	p.D1260V	ENST00000394830	NM_018313.4	1260	gAt/gTt	24/30	0.5722216265597	4	FACETS	0.875	0.817	0.935	0.292	0.272	0.312	CLONAL	1	FALSE	1	0.644980430432472	4		518	1487	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294421	1294421	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1478353801	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	163	304	0	ENST00000310581.5:c.580C>T	p.Arg194Ter	p.R194*	ENST00000310581	NM_198253.2	194	Cga/Tga	2/16	1	2	FACETS	0.844	0.778	0.912	0.844	0.778	0.912	CLONAL	1	FALSE	1	0.644980430432472	2		304	599	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519768	176519768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	256	393	0	ENST00000292408.4:c.1040G>A	p.Trp347Ter	p.W347*	ENST00000292408	NM_213647.1	347	tGg/tAg	8/18	1	2	FACETS	0.985	0.925	1	0.985	0.925	1	CLONAL	1	FALSE	1	0.644980430432472	2		393	806	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066617	94066617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	376	664	0	ENST00000369303.4:c.1142C>T	p.Pro381Leu	p.P381L	ENST00000369303	NM_004440.3	381	cCc/cTc	5/17	0.644980430432472	1	FACETS	0.866	0.826	0.907	0.866	0.826	0.907	CLONAL	1	FALSE	0	0.644980430432472	1		664	912	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527974	157527974	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	156	187	0	ENST00000346085.5:c.5699G>A	p.Ser1900Asn	p.S1900N	ENST00000346085	NM_020732.3	1900	aGc/aAc	20/20	0.644980430432472	1	FACETS	0.934	0.868	1	0.934	0.868	1	CLONAL	1	FALSE	0	0.644980430432472	1		187	351	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968326	2968326	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	252	324	1	ENST00000396946.4:c.1660C>T	p.Pro554Ser	p.P554S	ENST00000396946	NM_032415.4	554	Ccc/Tcc	13/25	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.644980430432472	2		325	762	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132847	152132847	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	257	386	0	ENST00000262189.6:c.25G>C	p.Val9Leu	p.V9L	ENST00000262189	NM_170606.2	9	Gtg/Ctg	1/59	1	2	FACETS	0.985	0.925	1	0.985	0.925	1	CLONAL	1	FALSE	1	0.644980430432472	2		386	809	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624580	93624580	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	286	429	0	ENST00000375746.1:c.671G>A	p.Gly224Glu	p.G224E	ENST00000375746	NM_001174167.1	224	gGg/gAg	4/14	0.181282371866981	0	FACETS	0.357	0.336	0.378			1	INDETERMINATE	1	FALSE	0	0.644980430432472	0		429	883	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900146	101900146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1403864711	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	129	311	0	ENST00000374994.4:c.580C>T	p.Pro194Ser	p.P194S	ENST00000374994	NM_004612.2	194	Cca/Tca	4/9	0.181282371866981	0	FACETS	0.298	0.272	0.326			1	INDETERMINATE	1	FALSE	0	0.644980430432472	0		311	476	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738160	133738160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	224	360	0	ENST00000318560.5:c.560C>T	p.Ser187Phe	p.S187F	ENST00000318560	NM_005157.4	187	tCc/tTc	4/11	0.181282371866981	0	FACETS	0.287	0.268	0.308			1	INDETERMINATE	1	FALSE	0	0.644980430432472	0		360	858	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202485	67202485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1256430551	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	351	526	0	ENST00000312629.5:c.1294G>A	p.Gly432Arg	p.G432R	ENST00000312629	NM_003952.2	432	Ggg/Agg	15/15	1	2	FACETS	0.956	0.906	1	0.956	0.906	1	CLONAL	1	FALSE	1	0.644980430432472	2		526	1138	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148876	119148876	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	117	234	0	ENST00000264033.4:c.1096G>T	p.Glu366Ter	p.E366*	ENST00000264033	NM_005188.3	366	Gaa/Taa	8/16	NA	2	FACETS	0.905	0.823	0.99			1	INDETERMINATE	1	FALSE	NA	0.644980430432472	2		234	401	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170450	119170450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	268	345	0	ENST00000264033.4:c.2680G>A	p.Glu894Lys	p.E894K	ENST00000264033	NM_005188.3	894	Gaa/Aaa	16/16	NA	2	FACETS	0.867	0.814	0.921			1	INDETERMINATE	1	FALSE	NA	0.644980430432472	2		345	959	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432338	49432338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	383	505	2	ENST00000301067.7:c.8801C>T	p.Pro2934Leu	p.P2934L	ENST00000301067	NM_003482.3	2934	cCc/cTc	34/54	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.644980430432472	2		507	1117	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201495	133201495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	286	456	0	ENST00000320574.5:c.6743C>T	p.Thr2248Ile	p.T2248I	ENST00000320574	NM_006231.2	2248	aCc/aTc	48/49	1	2	FACETS	0.977	0.921	1	0.977	0.921	1	CLONAL	1	FALSE	1	0.644980430432472	2		456	908	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622575	28622575	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	180	231	0	ENST00000241453.7:c.1042G>C	p.Gly348Arg	p.G348R	ENST00000241453	NM_004119.2	348	Gga/Cga	9/24	0.612385237740825	2	FACETS	0.875	0.823	0.926	0.875	0.823	0.926	CLONAL	2	FALSE	0	0.644980430432472	2		231	319	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459355	99459355	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	190	318	0	ENST00000268035.6:c.1991C>G	p.Ser664Cys	p.S664C	ENST00000268035	NM_000875.3	664	tCc/tGc	9/21	NA	2	FACETS	0.623	0.576	0.672			1	INDETERMINATE	1	FALSE	NA	0.644980430432472	2		318	945	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858751	9858751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777684328	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	214	332	0	ENST00000330684.3:c.2650G>A	p.Asp884Asn	p.D884N	ENST00000330684	NM_001134407.1	884	Gac/Aac	13/13	NA	2	FACETS	0.929	0.867	0.993			1	INDETERMINATE	1	FALSE	NA	0.644980430432472	2		332	714	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847319	68847319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755571454	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	395	511	0	ENST00000261769.5:c.1241C>T	p.Thr414Ile	p.T414I	ENST00000261769	NM_004360.3	414	aCc/aTc	9/16	0.644980430432472	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	0	0.644980430432472	1		511	787	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487555	38487555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	429	559	0	ENST00000254066.5:c.85C>T	p.Pro29Ser	p.P29S	ENST00000254066	NM_000964.3	29	Ccc/Tcc	2/9	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.644980430432472	2		559	1327	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222945	5222945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	227	372	0	ENST00000357368.4:c.2858C>T	p.Pro953Leu	p.P953L	ENST00000357368	NM_002850.3	953	cCc/cTc	18/38	0.381257119420412	1	FACETS	0.701	0.657	0.747	0.701	0.657	0.747	INDETERMINATE	1	FALSE	0	0.644980430432472	1		372	680	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902705	50902705	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	428	615	0	ENST00000440232.2:c.280C>T	p.Leu94Phe	p.L94F	ENST00000440232	NM_002691.3	94	Ctc/Ttc	3/27	0.301551257776862	3	FACETS	1	0.99	1	0.572	0.545	0.601	INDETERMINATE	1	FALSE	1	0.644980430432472	3		615	1533	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713470	40713470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318044562	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	229	316	3	ENST00000373198.4:c.4045C>T	p.Arg1349Cys	p.R1349C	ENST00000373198	NM_133170.3	1349	Cgt/Tgt	30/32	1	2	FACETS	0.946	0.884	1	0.946	0.884	1	CLONAL	1	FALSE	1	0.644980430432472	2		319	751	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593660	55593662	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	460	382	0	ENST00000288135.5:c.1727_1729del	p.Leu576del	p.L576del	ENST00000288135	NM_000222.2	576	CTT/-	11/21	0.644980430432472	3	FACETS	0.956	0.917	0.995	0.956	0.917	0.995	CLONAL	2	FALSE	1	0.644980430432472	3		382	987	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655402	45655403	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0011047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	206	392	0	ENST00000407780.3:c.449_450delinsTT	p.Ser150Phe	p.S150F	ENST00000407780	NM_001283052.1	150	tCC/tTT	4/7	0.264833000393762	1	FACETS	0.537	0.499	0.576	0.537	0.499	0.576	INDETERMINATE	1	FALSE	0	0.644980430432472	1		392	806	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857087	9857087	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1262244793	NA	P-0011067-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	164	247	0	ENST00000330684.3:c.4314G>A	p.Met1438Ile	p.M1438I	ENST00000330684	NM_001134407.1	1438	atG/atA	13/13	0.857677117188975	3	FACETS	0.949	0.876	1	0.474	0.438	0.512	CLONAL	1	TRUE	1	0.857677117188975	3		247	576	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0011389-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	122	1128	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.313294886257492	3	FACETS	0.958	0.865	1	0.479	0.432	0.528	CLONAL	1	TRUE	1	0.320850932611799	3		1128	921	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0011389-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	63	1141	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.313294886257492	3	FACETS	0.491	0.423	0.564	0.245	0.211	0.282	SUBCLONAL	1	TRUE	1	0.320850932611799	3		1142	929	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0011389-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	176	563	0	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.313294886257492	3	FACETS	1	0.967	1	0.548	0.504	0.595	CLONAL	1	TRUE	1	0.320850932611799	3		563	1161	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577084	7577084	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121912667	NA	P-0011389-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	244	506	0	ENST00000269305.4:c.854A>T	p.Glu285Val	p.E285V	ENST00000269305	NM_001126112.2	285	gAg/gTg	8/11	NA	2	FACETS	0.814	0.762	0.868			1	INDETERMINATE	2	TRUE	NA	0.320850932611799	2		506	934	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248666	212248666	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770116535	NA	P-0011389-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	94	349	0	ENST00000342788.4:c.3601G>A	p.Glu1201Lys	p.E1201K	ENST00000342788	NM_005235.2	1201	Gag/Aag	28/28	0.128006111378104	3	FACETS	1	0.924	1	0.349	0.311	0.39	INDETERMINATE	1	TRUE	0	0.320850932611799	3		349	649	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450876	70450876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757931991	NA	P-0011389-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	94	369	0	ENST00000373644.4:c.5716G>A	p.Glu1906Lys	p.E1906K	ENST00000373644	NM_030625.2	1906	Gaa/Aaa	12/12	1	2	FACETS	0.895	0.797	0.999	0.895	0.797	0.999	CLONAL	1	TRUE	1	0.320850932611799	2		369	655	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0011420-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	245	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.568820637463807	3	FACETS	0.999	0.942	1	0.999	0.942	1	CLONAL	2	TRUE	1	0.568820637463807	3		511	554	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952142	178952142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253171657	NA	P-0011420-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	211	360	0	ENST00000263967.3:c.3197C>T	p.Ala1066Val	p.A1066V	ENST00000263967	NM_006218.2	1066	gCa/gTa	21/21	0.568820637463807	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.568820637463807	3		360	451	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016625	12016625	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011420-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	228	319	0	ENST00000353533.5:c.761T>G	p.Leu254Arg	p.L254R	ENST00000353533	NM_003010.3	254	cTt/cGt	7/11	0.568820637463807	2	FACETS	0.954	0.903	1	0.954	0.903	1	CLONAL	2	TRUE	0	0.568820637463807	2		319	420	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651630	206651630	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011420-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1634	120	771	0	ENST00000367120.3:c.940T>G	p.Phe314Val	p.F314V	ENST00000367120	NM_014002.3	314	Ttc/Gtc	9/22	0.553376922367297	5	FACETS	0.446	0.401	0.494	0.149	0.133	0.165	SUBCLONAL	1	TRUE	2	0.568820637463807	5		771	1754	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156714	2156714	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011420-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	50	630	0	ENST00000434045.2:c.208A>C	p.Thr70Pro	p.T70P	ENST00000434045	NM_001127598.1	70	Acc/Ccc	3/5	0.568820637463807	2	FACETS	0.226	0.191	0.264	0.113	0.095	0.132	SUBCLONAL	1	TRUE	0	0.568820637463807	2		630	779	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061412	38061412	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011420-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	256	433	0	ENST00000250448.2:c.577C>A	p.Leu193Met	p.L193M	ENST00000250448	NM_004496.3	193	Ctg/Atg	2/2	0.38736786350619	4	FACETS	0.862	0.81	0.916			1	CLONAL	2	TRUE	NA	0.568820637463807	4		433	819	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469997	25469997	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011420-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	34	448	0	ENST00000264709.3:c.1045T>C	p.Ser349Pro	p.S349P	ENST00000264709	NM_175629.2	349	Tcg/Ccg	9/23	0.568820637463807	2	FACETS	0.191	0.156	0.232	0.096	0.078	0.116	SUBCLONAL	1	TRUE	0	0.568820637463807	2		448	625	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665391	182665391	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011420-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	64	340	0	ENST00000292782.4:c.550T>G	p.Leu184Val	p.L184V	ENST00000292782	NM_020640.2	184	Tta/Gta	5/7	0.568820637463807	3	FACETS	0.463	0.401	0.531	0.232	0.2	0.266	SUBCLONAL	1	TRUE	1	0.568820637463807	3		340	624	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519211	187519211	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011420-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	36	565	0	ENST00000441802.2:c.12172T>G	p.Ser4058Ala	p.S4058A	ENST00000441802	NM_005245.3	4058	Tcc/Gcc	23/27	0.568820637463807	2	FACETS	0.182	0.148	0.219	0.091	0.074	0.11	SUBCLONAL	1	TRUE	0	0.568820637463807	2		565	697	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629003	187629003	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011420-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	37	498	0	ENST00000441802.2:c.1979A>C	p.Asn660Thr	p.N660T	ENST00000441802	NM_005245.3	660	aAc/aCc	2/27	0.568820637463807	2	FACETS	0.209	0.172	0.251	0.105	0.086	0.126	SUBCLONAL	1	TRUE	0	0.568820637463807	2		498	622	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915167	131915167	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011420-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	96	485	0	ENST00000265335.6:c.524A>T	p.Lys175Met	p.K175M	ENST00000265335		175	aAg/aTg	4/25	0.568820637463807	4	FACETS	0.623	0.554	0.696	0.311	0.277	0.348	SUBCLONAL	1	TRUE	2	0.568820637463807	4		485	850	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041071	180041071	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011420-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1154	172	709	0	ENST00000261937.6:c.3328C>G	p.Leu1110Val	p.L1110V	ENST00000261937	NM_182925.4	1110	Ctg/Gtg	24/30	0.51526947760406	4	FACETS	0.716	0.657	0.777	0.358	0.328	0.389	SUBCLONAL	1	TRUE	2	0.568820637463807	4		709	1326	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041133	180041133	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011420-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1179	216	791	0	ENST00000261937.6:c.3266A>C	p.Lys1089Thr	p.K1089T	ENST00000261937	NM_182925.4	1089	aAg/aCg	24/30	0.51526947760406	4	FACETS	0.854	0.792	0.919	0.427	0.396	0.46	CLONAL	1	TRUE	2	0.568820637463807	4		791	1395	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405634	139405634	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011420-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	149	780	0	ENST00000277541.6:c.2557T>G	p.Phe853Val	p.F853V	ENST00000277541	NM_017617.3	853	Ttc/Gtc	16/34	1	2	FACETS	0.564	0.515	0.615	0.564	0.515	0.615	SUBCLONAL	1	TRUE	1	0.568820637463807	2		780	929	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0011544-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	147	218	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.988	0.91	1	0.988	0.91	1	CLONAL	1	TRUE	1	0.687374620252987	2		218	433	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0011544-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	156	266	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	0.687374620252987	1	FACETS	0.955	0.891	1	0.955	0.891	1	CLONAL	1	TRUE	0	0.687374620252987	1		266	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577102	7577102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793881	NA	P-0011544-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	320	680	0	ENST00000269305.4:c.836G>A	p.Gly279Glu	p.G279E	ENST00000269305	NM_001126112.2	279	gGg/gAg	8/11	1	2	FACETS	0.984	0.932	1	0.984	0.932	1	CLONAL	1	TRUE	1	0.687374620252987	2		680	946	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61729428	61729428	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011544-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	206	359	0	ENST00000401558.2:c.319G>T	p.Val107Phe	p.V107F	ENST00000401558	NM_003400.3	107	Gtt/Ttt	5/25	1	2	FACETS	0.904	0.843	0.967	0.904	0.843	0.967	CLONAL	1	TRUE	1	0.687374620252987	2		359	663	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633831	86633831	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011544-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	120	226	0	ENST00000274376.6:c.940G>C	p.Glu314Gln	p.E314Q	ENST00000274376	NM_002890.2	314	Gaa/Caa	5/25	1	2	FACETS	0.852	0.776	0.93	0.852	0.776	0.93	CLONAL	1	TRUE	1	0.687374620252987	2		226	410	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216521	36216521	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011544-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	279	704	0	ENST00000222270.7:c.3784T>C	p.Ser1262Pro	p.S1262P	ENST00000222270	NM_014727.1	1262	Tcc/Ccc	12/37	0.687374620252987	3	FACETS	0.961	0.903	1	0.481	0.451	0.511	CLONAL	1	TRUE	1	0.687374620252987	3		704	1135	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0012045-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	98	354	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.808	0.72	0.901	0.808	0.72	0.901	CLONAL	1	TRUE	1	0.294147046587687	2		354	825	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981851	201981852	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0012045-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	188	770	2	ENST00000359651.3:c.567dup	p.Ser190LeufsTer6	p.S190Lfs*6	ENST00000359651		188	gcc/gCcc	4/8	1	2	FACETS	0.958	0.882	1	0.958	0.882	1	CLONAL	1	TRUE	1	0.294147046587687	2		772	1335	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982433	25982433	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012045-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	188	475	0	ENST00000435504.4:c.857T>C	p.Leu286Pro	p.L286P	ENST00000435504		286	cTg/cCg	9/13	0.261486399548491	2	FACETS	0.826	0.765	0.889	0.826	0.765	0.889	CLONAL	2	TRUE	0	0.294147046587687	2		475	774	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678766	52678767	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0012045-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	100	514	1	ENST00000394830.3:c.852_853delinsTT	p.Lys284_Ala285delinsAsnSer	p.K284_A285delinsNS	ENST00000394830	NM_018313.4	284	aaGGct/aaTTct	9/30	1	2	FACETS	0.838	0.748	0.934	0.838	0.748	0.934	CLONAL	1	TRUE	1	0.294147046587687	2		515	811	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0012095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	18	349	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.102018479678145	0	FACETS	0.633	0.477	0.817			1	INDETERMINATE	1	TRUE	0	0.18	0		349	259	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0012095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	12	456	3	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	NA	2	FACETS	0.447	0.313	0.613			1	INDETERMINATE	1	TRUE	NA	0.18	2		459	298	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	CT	rs121913227	NA	P-0012095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	23	298	0	ENST00000288602.6:c.1798_1799delinsAG	p.Val600Arg	p.V600R	ENST00000288602	NM_004333.4	600	GTg/AGg	15/18	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.18	2		298	224	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971201	21971204	+	frameshift_variant	Frame_Shift_Del	DEL	TCAT	TCAT	-	novel	NA	P-0012095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	12	144	0	ENST00000304494.5:c.154_157del	p.Met52Ter	p.M52*	ENST00000304494	NM_000077.4	52	ATGAtg/tg	2/3	1	2	FACETS	0.966	0.683	1	0.966	0.683	1	CLONAL	1	TRUE	1	0.18	2		144	138	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579315	7579316	+	missense_variant	Missense_Mutation	DNP	GC	GC	TA	novel	NA	P-0012095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	13	306	1	ENST00000269305.4:c.371_372delinsTA	p.Cys124Leu	p.C124L	ENST00000269305	NM_001126112.2	124	tGC/tTA	4/11	1	2	FACETS	0.607	0.433	0.819	0.607	0.433	0.819	SUBCLONAL	1	TRUE	1	0.18	2		307	238	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012393-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	55	436	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.420318653123234	5	FACETS	1	0.885	1	1	0.885	1	CLONAL	3	TRUE	2	0.420318653123234	5		437	141	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0012393-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	18	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.420318653123234	3	FACETS	1	0.858	1	0.589	0.452	0.744	CLONAL	1	TRUE	1	0.420318653123234	3		511	88	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0012393-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	139	565	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.420318653123234	8	FACETS	0.971	0.911	1	0.971	0.911	1	CLONAL	7	TRUE	1	0.420318653123234	8		565	220	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465979	69465979	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012393-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	16	716	1	ENST00000227507.2:c.817G>T	p.Glu273Ter	p.E273*	ENST00000227507	NM_053056.2	273	Gag/Tag	5/5	0.420318653123234	3	FACETS	0.627	0.466	0.815	0.313	0.233	0.408	SUBCLONAL	1	TRUE	1	0.420318653123234	3		717	147	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967580	26967580	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012393-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	28	587	0	ENST00000381527.3:c.723C>G	p.Ile241Met	p.I241M	ENST00000381527	NM_001260.1	241	atC/atG	7/13	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.420318653123234	2		587	99	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24135752	24135752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012393-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	14	441	0	ENST00000263121.7:c.239G>A	p.Gly80Glu	p.G80E	ENST00000263121	NM_003073.3	80	gGa/gAa	3/9	0.420318653123234	3	FACETS	0.768	0.561	1	0.384	0.28	0.506	CLONAL	1	TRUE	1	0.420318653123234	3		441	105	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864597	56864597	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012393-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	17	637	0	ENST00000519728.1:c.560G>T	p.Ser187Ile	p.S187I	ENST00000519728	NM_002350.3	187	aGt/aTt	7/13	0.38347968699678	3	FACETS	0.837	0.632	1	0.418	0.316	0.537	CLONAL	1	TRUE	1	0.420318653123234	3		637	117	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0012635-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	90	387	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.81	0.721	0.905	0.81	0.721	0.905	CLONAL	1	TRUE	1	0.406853058919263	2		387	546	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0012635-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	124	398	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.406853058919263	2		398	607	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063718	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0012635-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	80	346	0	ENST00000412916.2:c.165+2dup		p.X55_splice	ENST00000412916		55			0.406853058919263	1	FACETS	0.994	0.884	1	0.994	0.884	1	CLONAL	1	TRUE	0	0.406853058919263	1		346	315	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0012635-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	118	375	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.965	0.873	1	0.965	0.873	1	CLONAL	1	TRUE	1	0.406853058919263	2		375	601	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252075	226252075	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012635-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	92	264	0	ENST00000366813.1:c.23C>A	p.Ala8Asp	p.A8D	ENST00000366813		8	gCc/gAc	1/3	0.406853058919263	5	FACETS	1	0.98	1	0.498	0.444	0.556	CLONAL	1	TRUE	2	0.406853058919263	5		264	487	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	51	974	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.809	0.685	0.945	0.809	0.685	0.945	CLONAL	1	TRUE	1	0.15	2		974	841	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0012661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	77	496	2	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.15	2		498	996	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971170	21971170	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	25	197	0	ENST00000304494.5:c.188T>A	p.Leu63Gln	p.L63Q	ENST00000304494	NM_000077.4	63	cTg/cAg	2/3	1	2	FACETS	0.697	0.548	0.869	0.697	0.548	0.869	SUBCLONAL	1	TRUE	1	0.15	2		197	478	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219390	1219391	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCCCA	novel	NA	P-0012661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	51	528	0	ENST00000326873.7:c.443_447dup	p.Val150SerfsTer13	p.V150Sfs*13	ENST00000326873	NM_000455.4	148	ttc/tTCCCAtc	3/10	1	2	FACETS	0.679	0.575	0.794	0.679	0.575	0.794	SUBCLONAL	1	TRUE	1	0.15	2		528	1002	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971066	21971068	+	inframe_deletion	In_Frame_Del	DEL	GCA	GCA	-	novel	NA	P-0012661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	40	333	0	ENST00000304494.5:c.290_292del	p.Leu97del	p.L97del	ENST00000304494	NM_000077.4	97	cTGCac/cac	2/3	1				0.621	0.893				SUBCLONAL	1	TRUE	1	0.15	2		333	712	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0012695-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	273	691	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.431275596536759	1	FACETS	0.922	0.866	0.98	0.922	0.866	0.98	CLONAL	1	TRUE	0	0.431275596536759	1		691	1077	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916929	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519931	NA	P-0012695-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	270	593	0	ENST00000263967.3:c.316G>C	p.Gly106Arg	p.G106R	ENST00000263967	NM_006218.2	106	Ggc/Cgc	2/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.431275596536759	2		593	1084	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244115	133244115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200825008	NA	P-0012695-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	214	362	1	ENST00000320574.5:c.2293C>T	p.Arg765Cys	p.R765C	ENST00000320574	NM_006231.2	765	Cgt/Tgt	20/49	1	2	FACETS	0.877	0.814	0.942	0.877	0.814	0.942	CLONAL	1	TRUE	1	0.431275596536759	2		363	1132	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645905	67645905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779012125	NA	P-0012695-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	284	425	1	ENST00000264010.4:c.833G>A	p.Arg278His	p.R278H	ENST00000264010	NM_006565.3	278	cGt/cAt	4/12	0.32679824069174	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.431275596536759	1		426	940	SUCCESS
APC	324	MSKCC	GRCh37	5	112175271	112175272	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012695-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	325	341	0	ENST00000257430.4:c.3981dup	p.Gln1328ThrfsTer4	p.Q1328Tfs*4	ENST00000257430	NM_000038.5	1327	tca/tcAa	16/16	0.428065731901863	2	FACETS	0.988	0.939	1	0.988	0.939	1	CLONAL	2	TRUE	0	0.431275596536759	2		341	763	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77043899	77043900	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGAGG	novel	NA	P-0012695-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1184	272	503	0	ENST00000356341.3:c.1422_1426dup	p.Ile476ThrfsTer25	p.I476Tfs*25	ENST00000356341	NM_002576.4	476	att/aCCTCAtt	14/15	1	2	FACETS	0.866	0.811	0.924	0.866	0.811	0.924	CLONAL	1	TRUE	1	0.431275596536759	2		503	1456	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443610	29443610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759845895	NA	P-0012778-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	98	700	0	ENST00000389048.3:c.3607G>A	p.Asp1203Asn	p.D1203N	ENST00000389048	NM_004304.4	1203	Gac/Aac	23/29	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.194404813539505	2		700	893	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445213	29445213	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519698	NA	P-0012778-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	83	674	0	ENST00000389048.3:c.3512T>A	p.Ile1171Asn	p.I1171N	ENST00000389048	NM_004304.4	1171	aTc/aAc	22/29	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.194404813539505	2		674	841	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012778-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	95	836	0	ENST00000375333.2:c.265G>C	p.Asp89His	p.D89H	ENST00000375333	NM_032454.1	89	Gac/Cac	2/8	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.194404813539505	2		836	879	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013276-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	309	376	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.895	0.849	0.94	0.895	0.849	0.94	CLONAL	1	TRUE	1	0.964906528915874	2		376	716	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0013276-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	201	226	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.892	0.836	0.949	0.892	0.836	0.949	CLONAL	1	TRUE	1	0.964906528915874	2		227	467	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409016	139409016	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013276-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1347	99	809	0	ENST00000277541.6:c.2153A>G	p.Asn718Ser	p.N718S	ENST00000277541	NM_017617.3	718	aAt/aGt	13/34	1	2	FACETS	0.142	0.126	0.159	0.142	0.126	0.159	SUBCLONAL	1	TRUE	1	0.964906528915874	2		809	1446	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413085	139413085	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1300110216	NA	P-0013276-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	620	644	1	ENST00000277541.6:c.1057C>T	p.Arg353Cys	p.R353C	ENST00000277541	NM_017617.3	353	Cgt/Tgt	6/34	1	2	FACETS	0.988	0.954	1	0.988	0.954	1	CLONAL	1	TRUE	1	0.964906528915874	2		645	1301	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926872	112926872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507541	NA	P-0013276-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	400	584	0	ENST00000351677.2:c.1492C>T	p.Arg498Trp	p.R498W	ENST00000351677	NM_002834.3	498	Cgg/Tgg	13/16	1	2	FACETS	0.803	0.765	0.84	0.803	0.765	0.84	CLONAL	1	TRUE	1	0.964906528915874	2		584	1033	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794721	42794722	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0013276-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	569	686	0	ENST00000575354.2:c.1801_1802del	p.Lys601GlufsTer88	p.K601Efs*88	ENST00000575354	NM_015125.3	601	AAg/g	10/20	0.964906528915874	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.964906528915874	1		686	604	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395069	139395069	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013276-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	146	573	1	ENST00000277541.6:c.5869C>T	p.Gln1957Ter	p.Q1957*	ENST00000277541	NM_017617.3	1957	Cag/Tag	31/34	1	2	FACETS	0.242	0.22	0.265	0.242	0.22	0.265	SUBCLONAL	1	TRUE	1	0.964906528915874	2		574	1252	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0013328-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	32	491	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	0.718	0.586	0.867	0.718	0.586	0.867	SUBCLONAL	1	TRUE	1	0.34	2		491	262	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013328-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	34	974	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.251	0.204	0.304	0.251	0.204	0.304	SUBCLONAL	1	TRUE	1	0.34	2		974	797	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732969	30732969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893810	NA	P-0013328-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	46	506	1	ENST00000295754.5:c.1582C>T	p.Arg528Cys	p.R528C	ENST00000295754	NM_003242.5	528	Cgt/Tgt	7/7	1	2	FACETS	0.444	0.373	0.523	0.444	0.373	0.523	SUBCLONAL	1	TRUE	1	0.34	2		507	609	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0013411-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	54	279	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.16	2		279	639	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063347	67063347	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013411-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	57	366	1	ENST00000412916.2:c.37G>T	p.Glu13Ter	p.E13*	ENST00000412916		13	Gag/Tag	1/6	0.3	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.16	1		367	540	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847167	68847249	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGCTAGCAGTCTTGGTACTTTGTAAATGACACATCTCTTTGCTCTGCAGTACAAGGGTCAGGTGCCTGAGAACGAGGCTAACG	TGCTAGCAGTCTTGGTACTTTGTAAATGACACATCTCTTTGCTCTGCAGTACAAGGGTCAGGTGCCTGAGAACGAGGCTAACG	-	novel	NA	P-0013411-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	50	324	0	ENST00000261769.5:c.1138-48_1172del		p.X380_splice	ENST00000261769	NM_004360.3	380		9/16	0.3	1	FACETS	0.946	0.807	1	1	0.973	1	CLONAL	2	TRUE	0	0.16	1		324	304	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864652	57864652	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141789719	NA	P-0013411-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	69	953	0	ENST00000228682.2:c.2129G>A	p.Gly710Glu	p.G710E	ENST00000228682	NM_005269.2	710	gGg/gAg	12/12	0.0515472944266322	3	FACETS	1	0.933	1	0.558	0.485	0.638	INDETERMINATE	1	TRUE	1	0.16	3		953	834	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510612	38510612	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013411-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	59	773	0	ENST00000254066.5:c.866G>C	p.Gly289Ala	p.G289A	ENST00000254066	NM_000964.3	289	gGg/gCg	7/9	1	2	FACETS	0.812	0.697	0.939	0.812	0.697	0.939	CLONAL	1	TRUE	1	0.16	2		773	908	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577152	7577154	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	ACC	ACC	-	rs1567548347	NA	P-0013650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	193	566	0	ENST00000269305.4:c.784_786del	p.Gly262del	p.G262del	ENST00000269305	NM_001126112.2	262	GGT/-	8/11	0.372629541922165	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.372629541922165	1		566	832	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710585	114710585	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	155	901	0	ENST00000543371.1:c.70G>T	p.Glu24Ter	p.E24*	ENST00000543371	NM_001198531.1	24	Gag/Tag	1/14	0.372629541922165	1	FACETS	0.541	0.494	0.59	0.541	0.494	0.59	SUBCLONAL	1	TRUE	0	0.372629541922165	1		901	1252	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206696	36206760	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGGTACTTACCCTGCATCTGACTCTGAGGCTGAGGGTTAAAGGCAGTGGAGTGGTTCAGGGAGG	CTGGTACTTACCCTGCATCTGACTCTGAGGCTGAGGGTTAAAGGCAGTGGAGTGGTTCAGGGAGG	-	novel	NA	P-0013650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	66	385	0	ENST00000300305.3:c.752_805+11del		p.X251_splice	ENST00000300305		251		6/8	1	2	FACETS	0.485	0.42	0.556	0.485	0.42	0.556	SUBCLONAL	1	TRUE	1	0.372629541922165	2		385	730	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430660	181430660	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	49	327	0	ENST00000325404.1:c.512A>C	p.Tyr171Ser	p.Y171S	ENST00000325404	NM_003106.3	171	tAc/tCc	1/1	0.292664144961351	3	FACETS	0.564	0.477	0.66	0.282	0.238	0.33	SUBCLONAL	1	TRUE	1	0.372629541922165	3		327	553	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589577	67589609	+	inframe_deletion	In_Frame_Del	DEL	AAAAATTACATGAATATAACACTCAGTTTCAAG	AAAAATTACATGAATATAACACTCAGTTTCAAG	-	novel	NA	P-0013650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	101	315	0	ENST00000274335.5:c.1345_1377del	p.Leu449_Lys459del	p.L449_K459del	ENST00000274335		447	aAAAAATTACATGAATATAACACTCAGTTTCAAGaa/aaa	10/15	0.372629541922165	1	FACETS	0.879	0.789	0.974	0.879	0.789	0.974	CLONAL	1	TRUE	0	0.372629541922165	1		315	502	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222591	157222591	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	153	565	0	ENST00000346085.5:c.1862del	p.Pro621ArgfsTer47	p.P621Rfs*47	ENST00000346085	NM_020732.3	620	Ccc/cc	4/20	0.372629541922165	1	FACETS	0.902	0.826	0.98	0.902	0.826	0.98	CLONAL	1	TRUE	0	0.372629541922165	1		565	741	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0013719-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	721	1128	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.470155913626312	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	2	0.686578355892296	4		1128	1683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0013719-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	495	637	0	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	0.686578355892296	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.686578355892296	1		637	874	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858183	27858183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1561947224	NA	P-0013719-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	112	453	0	ENST00000359303.2:c.388C>T	p.Arg130Cys	p.R130C	ENST00000359303	NM_003535.2	130	Cgt/Tgt	1/1	0.653426440063695	2	FACETS	0.446	0.401	0.494	0.223	0.2	0.247	SUBCLONAL	1	TRUE	0	0.686578355892296	2		453	731	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944813	31944813	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013755-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	218	649	0	ENST00000340398.3:c.288C>A	p.Ser96Arg	p.S96R	ENST00000340398	NM_001013699.2	96	agC/agA	1/1	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.388043484265491	2		649	1015	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231391	46231391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1317781343	NA	P-0013755-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	126	435	0	ENST00000334344.6:c.1231G>A	p.Asp411Asn	p.D411N	ENST00000334344	NM_152641.2	411	Gat/Aat	10/21	1	2	FACETS	0.904	0.82	0.993	0.904	0.82	0.993	CLONAL	1	TRUE	1	0.388043484265491	2		435	718	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433066	49433066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772742966	NA	P-0013755-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	127	740	0	ENST00000301067.7:c.8305G>A	p.Asp2769Asn	p.D2769N	ENST00000301067	NM_003482.3	2769	Gat/Aat	33/54	1	2	FACETS	0.549	0.496	0.605	0.549	0.496	0.605	SUBCLONAL	1	TRUE	1	0.388043484265491	2		740	1193	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910545	32910545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013755-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	77	352	0	ENST00000380152.3:c.2053G>A	p.Asp685Asn	p.D685N	ENST00000380152		685	Gat/Aat	11/27	1	2	FACETS	0.614	0.539	0.695	0.614	0.539	0.695	SUBCLONAL	1	TRUE	1	0.388043484265491	2		352	646	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0013755-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	342	659	1	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.315244491924806	2	FACETS	0.82	0.777	0.864	0.82	0.777	0.864	CLONAL	2	TRUE	0	0.388043484265491	2		660	1075	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40856680	40856680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013755-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	76	365	0	ENST00000428826.2:c.1957G>A	p.Asp653Asn	p.D653N	ENST00000428826		653	Gat/Aat	18/21	1	2	FACETS	0.59	0.517	0.668	0.59	0.517	0.668	SUBCLONAL	1	TRUE	1	0.388043484265491	2		365	664	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604656	48604656	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013755-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	156	293	0	ENST00000342988.3:c.1478A>T	p.Asp493Val	p.D493V	ENST00000342988	NM_005359.5	493	gAt/gTt	12/12	0.315244491924806	2	FACETS	0.854	0.788	0.921	0.854	0.788	0.921	CLONAL	2	TRUE	0	0.388043484265491	2		293	471	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221318	1221319	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	T	novel	NA	P-0013755-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	311	629	2	ENST00000326873.7:c.841_842delinsT	p.Pro281CysfsTer6	p.P281Cfs*6	ENST00000326873	NM_000455.4	281	CCg/Tg	6/10	0.312213828273938	2	FACETS	0.831	0.786	0.878	0.831	0.786	0.878	CLONAL	2	TRUE	0	0.388043484265491	2		631	964	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216497	36216497	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013755-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	519	809	0	ENST00000222270.7:c.3760G>T	p.Val1254Phe	p.V1254F	ENST00000222270	NM_014727.1	1254	Gtc/Ttc	12/37	0.368614382498574	2	FACETS	0.986	0.945	1	0.986	0.945	1	CLONAL	2	TRUE	0	0.388043484265491	2		809	1357	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741972	40741972	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013755-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	449	743	0	ENST00000392038.2:c.1000T>G	p.Trp334Gly	p.W334G	ENST00000392038	NM_001626.4	334	Tgg/Ggg	11/14	0.368614382498574	2	FACETS	0.933	0.891	0.975	0.933	0.891	0.975	CLONAL	2	TRUE	0	0.388043484265491	2		743	1240	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61711165	61711165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770962905	NA	P-0013755-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	53	647	0	ENST00000401558.2:c.2584G>A	p.Ala862Thr	p.A862T	ENST00000401558	NM_003400.3	862	Gca/Aca	21/25	1	2	FACETS	0.261	0.222	0.305	0.261	0.222	0.305	SUBCLONAL	1	TRUE	1	0.388043484265491	2		647	1045	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098815	178098815	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013755-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	144	705	1	ENST00000397062.3:c.230A>T	p.Asp77Val	p.D77V	ENST00000397062	NM_006164.4	77	gAt/gTt	2/5	0.388043484265491	3	FACETS	0.723	0.657	0.792	0.361	0.328	0.396	SUBCLONAL	1	TRUE	1	0.388043484265491	3		706	1226	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024668	31024668	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013755-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	273	549	0	ENST00000375687.4:c.4153A>T	p.Arg1385Trp	p.R1385W	ENST00000375687	NM_015338.5	1385	Agg/Tgg	13/13	0.312213828273938	2	FACETS	0.843	0.793	0.893	0.843	0.793	0.893	CLONAL	2	TRUE	0	0.388043484265491	2		549	835	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143269	24143269	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0013755-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	243	711	0	ENST00000263121.7:c.500+1G>A		p.X167_splice	ENST00000263121	NM_003073.3	167			0.366687829017734	3	FACETS	1	0.983	1	0.582	0.543	0.623	CLONAL	1	TRUE	1	0.388043484265491	3		711	1284	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131217	55131217	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0013755-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	170	321	0	ENST00000257290.5:c.759+1G>T		p.X253_splice	ENST00000257290	NM_006206.4	253			0.197655660828229	2	FACETS	1	0.989	1	0.722	0.667	0.778	INDETERMINATE	1	TRUE	0	0.388043484265491	2		321	607	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467609	66467609	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013755-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	27	336	0	ENST00000273854.3:c.660C>A	p.Cys220Ter	p.C220*	ENST00000273854	NM_004439.5	220	tgC/tgA	3/18	0.254488922912878	1	FACETS	0.219	0.174	0.272	0.219	0.174	0.272	SUBCLONAL	1	TRUE	0	0.388043484265491	1		336	511	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553631	106553631	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013755-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	122	337	0	ENST00000369096.4:c.1596A>T	p.Lys532Asn	p.K532N	ENST00000369096	NM_001198.3	532	aaA/aaT	5/7	0.388043484265491	1	FACETS	0.988	0.897	1	0.988	0.897	1	CLONAL	1	TRUE	0	0.388043484265491	1		337	513	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515161	106515161	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013755-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	160	453	0	ENST00000359195.3:c.2304A>T	p.Lys768Asn	p.K768N	ENST00000359195	NM_002649.2	768	aaA/aaT	5/11	0.366687829017734	3	FACETS	1	0.936	1	0.513	0.47	0.558	CLONAL	1	TRUE	1	0.388043484265491	3		453	960	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545602	106545602	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013755-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	163	492	0	ENST00000359195.3:c.3079C>A	p.Leu1027Met	p.L1027M	ENST00000359195	NM_002649.2	1027	Ctg/Atg	11/11	0.366687829017734	3	FACETS	1	0.973	1	0.571	0.524	0.62	CLONAL	1	TRUE	1	0.388043484265491	3		492	879	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439656	140439656	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013755-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	147	395	0	ENST00000288602.6:c.2083G>C	p.Glu695Gln	p.E695Q	ENST00000288602	NM_004333.4	695	Gag/Cag	17/18	0.366687829017734	3	FACETS	1	0.984	1	0.667	0.611	0.726	CLONAL	1	TRUE	1	0.388043484265491	3		395	678	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579359	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587780066	NA	P-0013798-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	508	723	0	ENST00000269305.4:c.328del	p.Arg110ValfsTer13	p.R110Vfs*13	ENST00000269305	NM_001126112.2	110	Cgt/gt	4/11	0.441735379219218	4	FACETS	0.93	0.898	0.963	0.93	0.898	0.963	CLONAL	4	TRUE	0	0.441735379219218	4		723	891	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143032	58143032	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs143670820	NA	P-0013798-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	146	733	0	ENST00000257904.6:c.752C>G	p.Pro251Arg	p.P251R	ENST00000257904	NM_000075.3	251	cCc/cGc	7/8	0.256945384967306	5	FACETS	1	0.979	1	0.413	0.377	0.452	INDETERMINATE	1	TRUE	2	0.441735379219218	5		733	886	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163618	32163618	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013798-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	149	408	0	ENST00000375023.3:c.5608C>A	p.Pro1870Thr	p.P1870T	ENST00000375023	NM_004557.3	1870	Cct/Act	30/30	0.441735379219218	6	FACETS	0.919	0.842	1	0.46	0.421	0.5	CLONAL	2	TRUE	2	0.441735379219218	6		408	691	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81979826	81979826	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013798-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	55	571	0	ENST00000359376.3:c.3528G>C	p.Glu1176Asp	p.E1176D	ENST00000359376	NM_002661.3	1176	gaG/gaC	31/33	0.441735379219218	4	FACETS	0.547	0.467	0.635	0.274	0.233	0.318	SUBCLONAL	1	TRUE	2	0.441735379219218	4		571	656	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774910	73774910	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013798-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	81	536	1	ENST00000254810.4:c.263C>A	p.Ala88Glu	p.A88E	ENST00000254810	NM_005324.3	88	gCa/gAa	3/4	0.441735379219218	4	FACETS	0.595	0.523	0.672	0.149	0.13	0.168	SUBCLONAL	1	TRUE	0	0.441735379219218	4		537	889	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923160	48923160	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587776789	NA	P-0013934-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	45	250	0	ENST00000267163.4:c.607+1G>T		p.X203_splice	ENST00000267163	NM_000321.2	203			0.363581314489626	3	FACETS	1	0.925	1	0.574	0.488	0.666	CLONAL	1	TRUE	1	0.487955618172586	3		250	200	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0013934-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	405	798	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	0.313780145240524	3	FACETS	1	0.994	1	0.821	0.786	0.856	CLONAL	2	TRUE	0	0.487955618172586	3		798	838	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462772	69462772	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013934-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	85	524	0	ENST00000227507.2:c.585C>A	p.Phe195Leu	p.F195L	ENST00000227507	NM_053056.2	195	ttC/ttA	4/5	0.363581314489626	3	FACETS	0.842	0.746	0.943	0.421	0.373	0.472	CLONAL	1	TRUE	1	0.487955618172586	3		524	515	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870915	12870916	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0013934-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	131	363	0	ENST00000228872.4:c.143_144del	p.His48LeufsTer76	p.H48Lfs*76	ENST00000228872	NM_004064.3	48	CAc/c	1/3	0.14289054922077	4	FACETS	0.942	0.862	1			1	INDETERMINATE	2	TRUE	NA	0.487955618172586	4		363	424	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198264998	198264998	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013934-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	74	418	0	ENST00000335508.6:c.2879T>C	p.Val960Ala	p.V960A	ENST00000335508	NM_012433.2	960	gTt/gCt	19/25	0.349890734394283	3	FACETS	0.985	0.867	1	0.493	0.433	0.555	CLONAL	1	TRUE	1	0.487955618172586	3		418	383	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468480	89468480	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013934-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	112	484	0	ENST00000336596.2:c.2014A>T	p.Ser672Cys	p.S672C	ENST00000336596	NM_005233.5	672	Agc/Tgc	11/17	0.487955618172586	3	FACETS	1	0.974	1	0.61	0.552	0.671	CLONAL	1	TRUE	1	0.487955618172586	3		484	468	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032278	26032278	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013934-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	32	274	0	ENST00000244661.2:c.11C>G	p.Thr4Ser	p.T4S	ENST00000244661	NM_003537.3	4	aCt/aGt	1/1	0.347165280444372	5	FACETS	0.697	0.567	0.843	0.232	0.189	0.281	SUBCLONAL	1	TRUE	2	0.487955618172586	5		274	326	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62293892	62293892	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0013934-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	69	772	0	ENST00000360203.5:c.396-7C>T		p.X132_splice	ENST00000360203	NM_001283009.1	132			0.312156662712014	5	FACETS	0.426	0.369	0.487	0.142	0.123	0.163	SUBCLONAL	1	TRUE	2	0.487955618172586	5		772	1151	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961832	15961832	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013934-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	36	549	0	ENST00000268712.3:c.5963A>C	p.Lys1988Thr	p.K1988T	ENST00000268712	NM_006311.3	1988	aAa/aCa	38/46	0.313780145240524	3	FACETS	0.27	0.221	0.326	0.09	0.073	0.109	SUBCLONAL	1	TRUE	0	0.487955618172586	3		549	679	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982478	10982478	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013934-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	34	72	0	ENST00000327064.4:c.101del	p.Gly34AlafsTer91	p.G34Afs*91	ENST00000327064	NM_199141.1	34	Ggc/gc	1/16	0.349890734394283	3	FACETS	1	0.952	1	0.735	0.613	0.864	CLONAL	1	TRUE	1	0.487955618172586	3		72	118	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577563	7577563	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1567549584	NA	P-0014061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	167	696	0	ENST00000269305.4:c.718A>G	p.Ser240Gly	p.S240G	ENST00000269305	NM_001126112.2	240	Agt/Ggt	7/11	0.398315570018838	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.398315570018838	1		696	491	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105709	27105709	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	112	444	0	ENST00000324856.7:c.5320G>T	p.Glu1774Ter	p.E1774*	ENST00000324856	NM_006015.4	1774	Gaa/Taa	20/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.398315570018838	2		444	388	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608255	28608255	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	92	729	1	ENST00000241453.7:c.1801C>A	p.Leu601Ile	p.L601I	ENST00000241453	NM_004119.2	601	Ctc/Atc	14/24	0.197252741519575	1	FACETS	0.631	0.562	0.705	0.631	0.562	0.705	INDETERMINATE	1	TRUE	0	0.398315570018838	1		730	586	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001320	29001320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	91	385	0	ENST00000282397.4:c.1412G>T	p.Cys471Phe	p.C471F	ENST00000282397	NM_002019.4	471	tGt/tTt	10/30	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.398315570018838	2		385	422	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476242	88476243	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0014061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	142	644	0	ENST00000360948.2:c.1889_1889+1delinsTT		p.X630_splice	ENST00000360948	NM_001012338.2	630		15/19	0.376779329266499	2	FACETS	0.825	0.759	0.893	0.825	0.759	0.893	CLONAL	2	TRUE	0	0.398315570018838	2		644	432	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041474	14041474	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	95	354	0	ENST00000311895.7:c.2021G>T	p.Gly674Val	p.G674V	ENST00000311895	NM_005236.2	674	gGc/gTc	11/11	0.265519869547808	3	FACETS	1	0.972	1	0.63	0.564	0.7	CLONAL	1	TRUE	1	0.398315570018838	3		354	454	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028622	12028622	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	139	402	0	ENST00000353533.5:c.825A>G	p.Ile275Met	p.I275M	ENST00000353533	NM_003010.3	275	atA/atG	8/11	0.398315570018838	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.398315570018838	1		402	503	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679336	29679336	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	146	548	0	ENST00000356175.3:c.7456A>T	p.Thr2486Ser	p.T2486S	ENST00000356175	NM_000267.3	2486	Acc/Tcc	50/57	0.266818939830637	4	FACETS	0.816	0.747	0.888	0.816	0.747	0.888	CLONAL	2	TRUE	2	0.398315570018838	4		548	628	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207031	1207031	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	151	769	1	ENST00000326873.7:c.119G>T	p.Arg40Leu	p.R40L	ENST00000326873	NM_000455.4	40	cGc/cTc	1/10	0.282985958074349	4	FACETS	1	0.974	1	0.388	0.355	0.424	CLONAL	1	TRUE	1	0.398315570018838	4		770	910	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946770	17946770	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	166	869	1	ENST00000458235.1:c.1877A>T	p.Gln626Leu	p.Q626L	ENST00000458235	NM_000215.3	626	cAg/cTg	14/24	0.349259625901719	4	FACETS	1	0.982	1	0.62	0.569	0.673	CLONAL	1	TRUE	2	0.398315570018838	4		870	940	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143164	30143164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779147984	NA	P-0014061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	247	723	1	ENST00000389048.3:c.362G>A	p.Arg121Gln	p.R121Q	ENST00000389048	NM_004304.4	121	cGg/cAg	1/29	0.398315570018838	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.398315570018838	3		724	653	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273179	198273179	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1242817545	NA	P-0014061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	76	685	0	ENST00000335508.6:c.1031G>T	p.Ser344Ile	p.S344I	ENST00000335508	NM_012433.2	344	aGt/aTt	8/25	0.398315570018838	3	FACETS	0.584	0.511	0.662	0.292	0.255	0.331	SUBCLONAL	1	TRUE	1	0.398315570018838	3		685	784	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955946	55955946	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	75	669	0	ENST00000263923.4:c.3216G>T	p.Met1072Ile	p.M1072I	ENST00000263923	NM_002253.2	1072	atG/atT	24/30	0.398315570018838	3	FACETS	0.64	0.56	0.725	0.32	0.28	0.363	SUBCLONAL	1	TRUE	1	0.398315570018838	3		669	706	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282703	1282703	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1272053273	NA	P-0014061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	340	724	0	ENST00000310581.5:c.1610G>A	p.Arg537His	p.R537H	ENST00000310581	NM_198253.2	537	cGt/cAt	3/16	0.398315570018838	7	FACETS	1	0.962	1	0.51	0.482	0.538	CLONAL	3	TRUE	1	0.398315570018838	7		724	1114	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294669	1294669	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	258	554	0	ENST00000310581.5:c.332C>T	p.Pro111Leu	p.P111L	ENST00000310581	NM_198253.2	111	cCc/cTc	2/16	0.398315570018838	7	FACETS	0.948	0.89	1	0.474	0.445	0.504	CLONAL	3	TRUE	1	0.398315570018838	7		554	909	SUCCESS
APC	324	MSKCC	GRCh37	5	112174995	112174995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554085244	NA	P-0014061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	45	312	0	ENST00000257430.4:c.3704C>T	p.Ser1235Phe	p.S1235F	ENST00000257430	NM_000038.5	1235	tCt/tTt	16/16	0.265519869547808	3	FACETS	0.757	0.638	0.887	0.378	0.319	0.444	SUBCLONAL	1	TRUE	1	0.398315570018838	3		312	358	SUCCESS
BTK	695	MSKCC	GRCh37	X	100624986	100624987	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	76	558	0	ENST00000308731.7:c.390_391insA	p.Val131SerfsTer7	p.V131Sfs*7	ENST00000308731	NM_000061.2	130	-/A	5/19	1	2	FACETS	0.63	0.553	0.713	0.63	0.553	0.713	SUBCLONAL	1	TRUE	1	0.398315570018838	2		558	606	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932902	39932902	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	56	650	0	ENST00000378444.4:c.1697G>T	p.Arg566Leu	p.R566L	ENST00000378444	NM_001123385.1	566	cGc/cTc	4/15	1	2	FACETS	0.618	0.53	0.713	0.618	0.53	0.713	SUBCLONAL	1	TRUE	1	0.398315570018838	2		650	455	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163325235	163325235	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	64	445	1	ENST00000271452.3:c.1371G>T	p.Arg457Ser	p.R457S	ENST00000271452	NM_145697.2	457	agG/agT	14/14	0.398315570018838	4	FACETS	0.702	0.608	0.805	0.234	0.202	0.269	SUBCLONAL	1	TRUE	1	0.398315570018838	4		446	640	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70432785	70432785	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	133	577	0	ENST00000373644.4:c.4807C>G	p.Pro1603Ala	p.P1603A	ENST00000373644	NM_030625.2	1603	Cca/Gca	8/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.398315570018838	2		577	524	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431363	49431386	+	inframe_deletion	In_Frame_Del	DEL	TCCTTCTTCTCATGCTCCAACAGG	TCCTTCTTCTCATGCTCCAACAGG	-	novel	NA	P-0014061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	106	574	0	ENST00000301067.7:c.9753_9776del	p.Asp3251_Lys3258del	p.D3251_K3258del	ENST00000301067	NM_003482.3	3251	gaCCTGTTGGAGCATGAGAAGAAGGAg/gag	34/54	0.180230058154718	3	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.398315570018838	3		574	435	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245014	133245014	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	93	877	0	ENST00000320574.5:c.2101G>C	p.Glu701Gln	p.E701Q	ENST00000320574	NM_006231.2	701	Gag/Cag	19/49	0.353783934285563	3	FACETS	0.733	0.651	0.82	0.244	0.217	0.274	SUBCLONAL	1	TRUE	0	0.398315570018838	3		877	764	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245044	133245044	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	85	837	0	ENST00000320574.5:c.2071G>C	p.Glu691Gln	p.E691Q	ENST00000320574	NM_006231.2	691	Gag/Cag	19/49	0.353783934285563	3	FACETS	0.648	0.572	0.729	0.216	0.19	0.243	SUBCLONAL	1	TRUE	0	0.398315570018838	3		837	790	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753557	42753557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	208	941	1	ENST00000222329.4:c.707C>T	p.Pro236Leu	p.P236L	ENST00000222329	NM_006494.2	236	cCc/cTc	4/4	0.398315570018838	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.398315570018838	1		942	619	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50143240	50143240	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	149	504	1	ENST00000246792.3:c.116G>T	p.Gly39Val	p.G39V	ENST00000246792	NM_006270.3	39	gGc/gTc	1/6	0.398315570018838	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.398315570018838	1		505	442	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449693	187449693	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	67	512	0	ENST00000232014.4:c.187G>T	p.Asp63Tyr	p.D63Y	ENST00000232014	NM_001130845.1	63	Gac/Tac	4/10	0.398315570018838	3	FACETS	0.657	0.571	0.75	0.329	0.285	0.375	SUBCLONAL	1	TRUE	1	0.398315570018838	3		512	614	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808916	1808916	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	82	905	1	ENST00000260795.2:c.2348C>T	p.Ser783Leu	p.S783L	ENST00000260795		783	tCa/tTa	17/17	0.398315570018838	3	FACETS	0.755	0.666	0.85	0.377	0.333	0.425	SUBCLONAL	1	TRUE	1	0.398315570018838	3		906	654	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968065	68968065	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	130	508	0	ENST00000288368.4:c.1094G>T	p.Gly365Val	p.G365V	ENST00000288368	NM_024870.2	365	gGt/gTt	10/40	0.265519869547808	3	FACETS	1	0.985	1	0.713	0.649	0.779	CLONAL	1	TRUE	1	0.398315570018838	3		508	549	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020242	123020242	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	70	713	0	ENST00000355640.3:c.730G>T	p.Val244Leu	p.V244L	ENST00000355640		244	Gtg/Ttg	2/7	1	2	FACETS	0.528	0.46	0.601	0.528	0.46	0.601	SUBCLONAL	1	TRUE	1	0.398315570018838	2		713	666	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599333	55599333	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913682	NA	P-0014399-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	587	306	0	ENST00000288135.5:c.2459A>G	p.Asp820Gly	p.D820G	ENST00000288135	NM_000222.2	820	gAt/gGt	17/21	0.782372990227346	2	FACETS	0.954	0.932	0.976	0.954	0.932	0.976	CLONAL	2	TRUE	0	0.825634716965291	2		306	745	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593657	55593679	+	protein_altering_variant	In_Frame_Del	DEL	CAACTTCCTTATGATCACAAATG	CAACTTCCTTATGATCACAAATG	TT	novel	NA	P-0014399-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	481	419	1	ENST00000288135.5:c.1723_1745delinsTT	p.Gln575_Trp582delinsLeu	p.Q575_W582delinsL	ENST00000288135	NM_000222.2	575	CAACTTCCTTATGATCACAAATGg/TTg	11/21	0.782372990227346	2	FACETS	0.88	0.854	0.905	0.88	0.854	0.905	CLONAL	2	TRUE	0	0.825634716965291	2		420	662	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778122	135778123	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0014399-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	523	410	0	ENST00000298552.3:c.2260dup	p.Leu754ProfsTer7	p.L754Pfs*7	ENST00000298552	NM_001162426.1	754	ctg/cCtg	18/23	0.825634716965291	1	FACETS	0.989	0.96	1	0.989	0.96	1	CLONAL	1	TRUE	0	0.825634716965291	1		410	752	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599333	55599333	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913682	NA	P-0014399-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	547	306	0	ENST00000288135.5:c.2459A>G	p.Asp820Gly	p.D820G	ENST00000288135	NM_000222.2	820	gAt/gGt	17/21	0.899717818740105	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.899717818740105	1		306	643	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593657	55593679	+	protein_altering_variant	In_Frame_Del	DEL	CAACTTCCTTATGATCACAAATG	CAACTTCCTTATGATCACAAATG	TT	novel	NA	P-0014399-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	471	419	1	ENST00000288135.5:c.1723_1745delinsTT	p.Gln575_Trp582delinsLeu	p.Q575_W582delinsL	ENST00000288135	NM_000222.2	575	CAACTTCCTTATGATCACAAATGg/TTg	11/21	0.899717818740105	1	FACETS	0.976	0.951	1	0.976	0.951	1	CLONAL	1	TRUE	0	0.899717818740105	1		420	590	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778122	135778123	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0014399-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	538	410	0	ENST00000298552.3:c.2260dup	p.Leu754ProfsTer7	p.L754Pfs*7	ENST00000298552	NM_001162426.1	754	ctg/cCtg	18/23	0.89785969649723	1	FACETS	0.954	0.93	0.976	0.954	0.93	0.976	CLONAL	1	TRUE	0	0.899717818740105	1		410	690	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599333	55599333	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913682	NA	P-0014399-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	290	306	0	ENST00000288135.5:c.2459A>G	p.Asp820Gly	p.D820G	ENST00000288135	NM_000222.2	820	gAt/gGt	17/21	0.553597210665665	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.553597210665665	1		306	651	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593657	55593679	+	protein_altering_variant	In_Frame_Del	DEL	CAACTTCCTTATGATCACAAATG	CAACTTCCTTATGATCACAAATG	TT	novel	NA	P-0014399-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	238	419	1	ENST00000288135.5:c.1723_1745delinsTT	p.Gln575_Trp582delinsLeu	p.Q575_W582delinsL	ENST00000288135	NM_000222.2	575	CAACTTCCTTATGATCACAAATGg/TTg	11/21	0.553597210665665	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.553597210665665	1		420	599	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778122	135778123	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0014399-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	231	410	0	ENST00000298552.3:c.2260dup	p.Leu754ProfsTer7	p.L754Pfs*7	ENST00000298552	NM_001162426.1	754	ctg/cCtg	18/23	0.553597210665665	1	FACETS	0.969	0.909	1	0.969	0.909	1	CLONAL	1	TRUE	0	0.553597210665665	1		410	623	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599333	55599333	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913682	NA	P-0014399-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	400	306	0	ENST00000288135.5:c.2459A>G	p.Asp820Gly	p.D820G	ENST00000288135	NM_000222.2	820	gAt/gGt	17/21	0.714943775410405	2	FACETS	0.986	0.956	1	0.986	0.956	1	CLONAL	2	TRUE	0	0.777457152211931	2		306	522	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593657	55593679	+	protein_altering_variant	In_Frame_Del	DEL	CAACTTCCTTATGATCACAAATG	CAACTTCCTTATGATCACAAATG	TT	novel	NA	P-0014399-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	299	419	1	ENST00000288135.5:c.1723_1745delinsTT	p.Gln575_Trp582delinsLeu	p.Q575_W582delinsL	ENST00000288135	NM_000222.2	575	CAACTTCCTTATGATCACAAATGg/TTg	11/21	0.714943775410405	2	FACETS	0.818	0.784	0.852	0.818	0.784	0.852	CLONAL	2	TRUE	0	0.777457152211931	2		420	470	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778122	135778123	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0014399-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	272	410	0	ENST00000298552.3:c.2260dup	p.Leu754ProfsTer7	p.L754Pfs*7	ENST00000298552	NM_001162426.1	754	ctg/cCtg	18/23	0.777457152211931	1	FACETS	0.948	0.905	0.991	0.948	0.905	0.991	CLONAL	1	TRUE	0	0.777457152211931	1		410	451	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014434-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	54	387	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	0.18	2		387	510	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106592	27106592	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014434-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	75	786	0	ENST00000324856.7:c.6203C>G	p.Ser2068Trp	p.S2068W	ENST00000324856	NM_006015.4	2068	tCg/tGg	20/20	1	2	FACETS	0.761	0.665	0.865	0.761	0.665	0.865	SUBCLONAL	1	TRUE	1	0.18	2		786	1095	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189395	56189396	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014434-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	84	579	0	ENST00000399503.3:c.4430dup	p.Leu1477PhefsTer46	p.L1477Ffs*46	ENST00000399503	NM_005921.1	1476	cat/caTt	20/20	0.21069877039877	3	FACETS	0.966	0.851	1	0.483	0.425	0.545	CLONAL	1	TRUE	1	0.18	3		579	1053	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563281	21563281	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014493-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	75	748	0	ENST00000382592.4:c.638A>C	p.Asp213Ala	p.D213A	ENST00000382592	NM_014572.2	213	gAc/gCc	4/8	1	2	FACETS	0.791	0.693	0.897	0.791	0.693	0.897	SUBCLONAL	1	TRUE	1	0.291132250500846	2		748	651	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99192848	99192848	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014493-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	65	409	0	ENST00000268035.6:c.38T>C	p.Leu13Pro	p.L13P	ENST00000268035	NM_000875.3	13	cTg/cCg	1/21	0.191091014496503	3	FACETS	0.857	0.743	0.98	0.428	0.371	0.49	CLONAL	1	TRUE	1	0.291132250500846	3		409	597	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952149	178952159	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	CTGAAAAGATA	CTGAAAAGATA	GAT	novel	NA	P-0014493-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	26	274	1	ENST00000263967.3:c.3204_*7delinsGAT		p.*1068*	ENST00000263967	NM_006218.2	1068		21/21	1	2	FACETS	0.572	0.454	0.708	0.572	0.454	0.708	SUBCLONAL	1	TRUE	1	0.291132250500846	2		275	312	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161227	56161230	+	frameshift_variant	Frame_Shift_Del	DEL	TTTC	TTTC	-	novel	NA	P-0014493-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	95	466	0	ENST00000399503.3:c.1096_1099del	p.Phe366AsnfsTer2	p.F366Nfs*2	ENST00000399503	NM_005921.1	366	TTTCaa/aa	5/20	0.191091014496503	3	FACETS	1	0.926	1	0.526	0.468	0.587	CLONAL	1	TRUE	1	0.291132250500846	3		466	711	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184090	56184090	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014493-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	114	428	1	ENST00000399503.3:c.4295T>C	p.Val1432Ala	p.V1432A	ENST00000399503	NM_005921.1	1432	gTa/gCa	19/20	0.191091014496503	3	FACETS	0.816	0.737	0.898	0.816	0.737	0.898	CLONAL	2	TRUE	1	0.291132250500846	3		429	550	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442569	52442569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1298276806	NA	P-0014576-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	79	493	0	ENST00000460680.1:c.176G>A	p.Arg59Gln	p.R59Q	ENST00000460680	NM_004656.3	59	cGg/cAg	4/17	0.637592053833256	3	FACETS	0.34	0.298	0.385	0.17	0.149	0.193	SUBCLONAL	1	TRUE	1	0.637592053833256	3		493	962	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40367558	40367561	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	CATG	CATG	-	novel	NA	P-0014576-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	14	5	0	ENST00000397332.2:c.-1_3del		p.*1*	ENST00000397332	NM_001033082.2	?-1/394		1/3	0.637592053833256	3	FACETS	1	0.85	1	1	0.85	1	CLONAL	2	TRUE	1	0.637592053833256	3		5	26	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577137	7577138	+	missense_variant	Missense_Mutation	DNP	CC	CC	GG	novel	NA	P-0014576-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	475	639	1	ENST00000269305.4:c.800_801inv	p.Arg267Pro	p.R267P	ENST00000269305	NM_001126112.2	267	cGG/cCC	8/11	NA	2	FACETS	0.942	0.909	0.974			1	INDETERMINATE	2	TRUE	NA	0.637592053833256	2		640	791	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638900	176638900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763399938	NA	P-0014576-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	205	643	1	ENST00000439151.2:c.3500G>A	p.Arg1167His	p.R1167H	ENST00000439151	NM_022455.4	1167	cGc/cAc	5/23	0.533017487469724	4	FACETS	0.829	0.768	0.893			1	CLONAL	1	TRUE	NA	0.637592053833256	4		644	1270	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880531	155880531	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014685-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	382	565	0	ENST00000368323.3:c.22G>C	p.Val8Leu	p.V8L	ENST00000368323	NM_006912.5	8	Gtt/Ctt	2/6	0.172666125899957	5	FACETS	1	0.992	1	0.788	0.75	0.826	INDETERMINATE	2	TRUE	2	0.608177120079216	5		565	1016	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717709	89717713	+	frameshift_variant	Frame_Shift_Del	DEL	AGCCG	AGCCG	-	novel	NA	P-0014685-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	229	477	0	ENST00000371953.3:c.734_738del	p.Gln245LeufsTer6	p.Q245Lfs*6	ENST00000371953	NM_000314.4	245	cAGCCG/c	7/9	0.608177120079216	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.608177120079216	1		477	471	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251067	99251067	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs748252733	NA	P-0014685-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	213	519	0	ENST00000268035.6:c.371A>G	p.Asn124Ser	p.N124S	ENST00000268035	NM_000875.3	124	aAt/aGt	2/21	1	2	FACETS	0.992	0.926	1	0.992	0.926	1	CLONAL	1	TRUE	1	0.608177120079216	2		519	706	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943375	71943393	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCTCGGTGAGGGGGCGCC	GGCTCGGTGAGGGGGCGCC	A	novel	NA	P-0014685-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	156	449	0	ENST00000298229.2:c.1707_1712+13delinsA		p.X569_splice	ENST00000298229	NM_001567.3	569		14/28	0.608177120079216	1	FACETS	0.826	0.764	0.89	0.826	0.764	0.89	CLONAL	1	TRUE	0	0.608177120079216	1		449	432	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143044	30143044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014851-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	149	614	0	ENST00000389048.3:c.482C>T	p.Ala161Val	p.A161V	ENST00000389048	NM_004304.4	161	gCg/gTg	1/29	1	2	FACETS	0.484	0.441	0.529	0.484	0.441	0.529	SUBCLONAL	1	TRUE	1	0.551479814505484	2		614	1116	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862206	68862217	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTGGGTTTTG	AGGTGGGTTTTG	-	novel	NA	P-0014851-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	183	493	0	ENST00000261769.5:c.2295_2295+11del		p.X765_splice	ENST00000261769	NM_004360.3	765		14/16	0.551479814505484	1	FACETS	0.93	0.865	0.996	0.93	0.865	0.996	CLONAL	1	TRUE	0	0.551479814505484	1		493	517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587781702	NA	P-0014851-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	259	499	0	ENST00000269305.4:c.920-1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.551479814505484	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.551479814505484	1		499	664	SUCCESS
ALK	238	MSKCC	GRCh37	2	29473986	29473986	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014851-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	150	552	0	ENST00000389048.3:c.2189C>T	p.Ala730Val	p.A730V	ENST00000389048	NM_004304.4	730	gCc/gTc	12/29	1	2	FACETS	0.556	0.508	0.607	0.556	0.508	0.607	SUBCLONAL	1	TRUE	1	0.551479814505484	2		552	978	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143044542	143044542	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014851-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	80	361	0	ENST00000262992.4:c.1920C>G	p.Ile640Met	p.I640M	ENST00000262992	NM_001101669.1	640	atC/atG	18/24	0.29866857361668	1	FACETS	0.351	0.309	0.396	0.351	0.309	0.396	INDETERMINATE	1	TRUE	0	0.551479814505484	1		361	598	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0014883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	899	691	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.768878720800757	2	FACETS	0.983	0.963	1	0.983	0.963	1	CLONAL	2	TRUE	0	0.768878720800757	2		691	1190	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913499	NA	P-0014883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	63	295	0	ENST00000345146.2:c.394C>A	p.Arg132Ser	p.R132S	ENST00000345146	NM_005896.2	132	Cgt/Agt	4/10	1	2	FACETS	0.97	0.857	1	0.97	0.857	1	CLONAL	1	TRUE	1	0.768878720800757	2		295	169	SUCCESS
BTK	695	MSKCC	GRCh37	X	100614333	100614333	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	93	208	0	ENST00000308731.7:c.842G>A	p.Trp281Ter	p.W281*	ENST00000308731	NM_000061.2	281	tGg/tAg	10/19	1	1	FACETS	0.415	0.372	0.46	0.415	0.372	0.46	SUBCLONAL	1	TRUE	0	0.768878720800757	1		208	359	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417574	139417574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1281	316	839	0	ENST00000277541.6:c.470C>T	p.Pro157Leu	p.P157L	ENST00000277541	NM_017617.3	157	cCc/cTc	4/34	0.196656556775705	3	FACETS	0.713	0.67	0.756	0.356	0.335	0.378	INDETERMINATE	1	TRUE	1	0.768878720800757	3		839	1597	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735593	204735593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	83	479	0	ENST00000302823.3:c.394G>A	p.Glu132Lys	p.E132K	ENST00000302823	NM_005214.4	132	Gag/Aag	2/4	1	2	FACETS	0.309	0.273	0.349	0.309	0.273	0.349	SUBCLONAL	1	TRUE	1	0.768878720800757	2		479	698	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872107	76872108	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0014883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4	57	104	0	ENST00000373344.5:c.5539dup	p.Tyr1847LeufsTer14	p.Y1847Lfs*14	ENST00000373344	NM_000489.3	1847	tat/tTat	22/35	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.768878720800757	1		104	61	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609942	43609942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767407	NA	P-0014883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	470	817	2	ENST00000355710.3:c.1894G>A	p.Glu632Lys	p.E632K	ENST00000355710	NM_020975.4	632	Gag/Aag	11/20	1	2	FACETS	0.821	0.783	0.858	0.821	0.783	0.858	CLONAL	1	TRUE	1	0.768878720800757	2		819	1490	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546985	9546985	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	172	343	0	ENST00000353224.5:c.1037G>A	p.Gly346Glu	p.G346E	ENST00000353224	NM_177990.2	346	gGg/gAg	5/10	0.196656556775705	3	FACETS	1	0.983	1	0.599	0.555	0.644	INDETERMINATE	1	TRUE	1	0.768878720800757	3		343	517	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981876	201981876	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	499	794	0	ENST00000359651.3:c.587T>C	p.Val196Ala	p.V196A	ENST00000359651		196	gTc/gCc	4/8	0.196656556775705	3	FACETS	1	0.992	1	0.574	0.549	0.6	INDETERMINATE	1	TRUE	1	0.768878720800757	3		794	1564	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729097	66729097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs797044593	NA	P-0014883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	295	563	0	ENST00000307102.5:c.305A>G	p.Glu102Gly	p.E102G	ENST00000307102	NM_002755.3	102	gAg/gGg	3/11	0.109055105579664	3	FACETS	1	0.993	1	0.689	0.652	0.727	INDETERMINATE	1	TRUE	1	0.768878720800757	3		563	771	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347162	347162	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	69	819	0	ENST00000262320.3:c.1849A>G	p.Thr617Ala	p.T617A	ENST00000262320	NM_003502.3	617	Acc/Gcc	7/11	0.607137059503343	1	FACETS	0.123	0.106	0.141	0.123	0.106	0.141	SUBCLONAL	1	TRUE	0	0.768878720800757	1		819	898	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222296	2222296	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	396	795	0	ENST00000326181.6:c.580G>A	p.Val194Ile	p.V194I	ENST00000326181	NM_032271.2	194	Gta/Ata	8/21	NA	2	FACETS	0.864	0.822	0.907			1	INDETERMINATE	1	TRUE	NA	0.768878720800757	2		795	1192	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639090	3639090	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	326	728	0	ENST00000294008.3:c.4549G>A	p.Glu1517Lys	p.E1517K	ENST00000294008	NM_032444.2	1517	Gaa/Aaa	12/15	0.768878720800757	1	FACETS	0.641	0.609	0.674	0.641	0.609	0.674	SUBCLONAL	1	TRUE	0	0.768878720800757	1		728	814	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992901	72992901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754027540	NA	P-0014883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	43	699	0	ENST00000268489.5:c.1144G>A	p.Gly382Ser	p.G382S	ENST00000268489	NM_006885.3	382	Ggc/Agc	2/10	0.662912376001512	1	FACETS	0.086	0.072	0.103	0.086	0.072	0.103	SUBCLONAL	1	TRUE	0	0.768878720800757	1		699	798	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573571	48573571	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	42	184	0	ENST00000342988.3:c.155A>G	p.Asp52Gly	p.D52G	ENST00000342988	NM_005359.5	52	gAt/gGt	2/12	0.109055105579664	3	FACETS	1	0.957	1	0.675	0.58	0.774	INDETERMINATE	1	TRUE	1	0.768878720800757	3		184	112	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257634	19257634	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	463	850	1	ENST00000162023.5:c.592C>T	p.Pro198Ser	p.P198S	ENST00000162023		198	Ccc/Tcc	10/13	0.196656556775705	3	FACETS	1	0.993	1	0.593	0.566	0.62	INDETERMINATE	1	TRUE	1	0.768878720800757	3		851	1407	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797231	42797231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	379	780	2	ENST00000575354.2:c.3593G>A	p.Gly1198Glu	p.G1198E	ENST00000575354	NM_015125.3	1198	gGg/gAg	15/20	0.196656556775705	3	FACETS	1	0.991	1	0.595	0.565	0.625	INDETERMINATE	1	TRUE	1	0.768878720800757	3		782	1147	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37061950	37061950	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750980386	NA	P-0014883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	172	427	0	ENST00000231790.2:c.1034C>T	p.Thr345Ile	p.T345I	ENST00000231790	NM_000249.3	345	aCc/aTc	11/19	0.196656556775705	3	FACETS	1	0.94	1	0.509	0.471	0.549	INDETERMINATE	1	TRUE	1	0.768878720800757	3		427	608	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190949	185190954	+	inframe_deletion	In_Frame_Del	DEL	AGCCCA	AGCCCA	-	novel	NA	P-0014883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	475	935	0	ENST00000265026.3:c.1830_1835del	p.Ala611_Gln612del	p.A611_Q612del	ENST00000265026	NM_004721.4	610	ccAGCCCAg/ccg	11/14	0.681004667084709	1	FACETS	0.859	0.827	0.891	0.859	0.827	0.891	CLONAL	1	TRUE	0	0.768878720800757	1		935	885	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273285	55273285	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	255	532	0	ENST00000275493.2:c.3608A>G	p.Gln1203Arg	p.Q1203R	ENST00000275493	NM_005228.3	1203	cAa/cGa	28/28	0.121085799894504	4	FACETS	0.806	0.758	0.855	0.806	0.758	0.855	INDETERMINATE	2	TRUE	2	0.768878720800757	4		532	728	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055761	152055761	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0014883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	54	304	2	ENST00000262189.6:c.162-1G>A		p.X54_splice	ENST00000262189	NM_170606.2	54			0.513291580267039	4	FACETS	1	0.966	1	0.463	0.402	0.527	CLONAL	1	TRUE	1	0.768878720800757	4		306	179	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641096	93641096	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	99	493	0	ENST00000375746.1:c.1442G>C	p.Gly481Ala	p.G481A	ENST00000375746	NM_001174167.1	481	gGc/gCc	11/14	0.196656556775705	3	FACETS	1	0.95	1	0.542	0.489	0.597	INDETERMINATE	1	TRUE	1	0.768878720800757	3		493	329	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014929-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	168	387	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.559142228701175	4	FACETS	1	0.988	1	0.717	0.662	0.775	CLONAL	1	FALSE	2	0.551395358073787	4		387	659	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965472	68965472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200682883	NA	P-0014929-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	166	837	0	ENST00000288368.4:c.1084C>T	p.Arg362Trp	p.R362W	ENST00000288368	NM_024870.2	362	Cgg/Tgg	9/40	1	2	FACETS	0.901	0.831	0.974	0.901	0.831	0.974	CLONAL	1	FALSE	1	0.551395358073787	2		837	668	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014929-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	163	387	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.459479994715282	5	FACETS	1	0.975	1	0.748	0.693	0.805	CLONAL	2	FALSE	2	0.60970021936976	5		387	456	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965472	68965472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200682883	NA	P-0014929-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	220	837	0	ENST00000288368.4:c.1084C>T	p.Arg362Trp	p.R362W	ENST00000288368	NM_024870.2	362	Cgg/Tgg	9/40	0.41730346218235	3	FACETS	0.942	0.886	0.998			1	CLONAL	2	FALSE	NA	0.60970021936976	3		837	500	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063312	67063313	+	frameshift_variant,start_lost	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0014929-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	77	217	0	ENST00000412916.2:c.3dup	p.Pro2_?1	p.P2_?1	ENST00000412916		1	atg/atGg	1/6	0.41730346218235	3	FACETS	0.999	0.901	1			1	CLONAL	2	FALSE	NA	0.60970021936976	3		217	165	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847342	68847342	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014929-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	247	773	0	ENST00000261769.5:c.1264C>T	p.Gln422Ter	p.Q422*	ENST00000261769	NM_004360.3	422	Caa/Taa	9/16	0.41730346218235	3	FACETS	0.868	0.826	0.909			1	CLONAL	3	FALSE	NA	0.60970021936976	3		773	406	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123875192	123875192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745678227	NA	P-0014929-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	58	551	0	ENST00000330479.4:c.148G>A	p.Gly50Arg	p.G50R	ENST00000330479	NM_020382.3	50	Ggg/Agg	3/9	0.453053031363688	4	FACETS	0.586	0.503	0.675			1	SUBCLONAL	1	FALSE	NA	0.60970021936976	4		551	523	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675468	30675468	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014929-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	39	770	0	ENST00000376406.3:c.2888C>T	p.Ser963Phe	p.S963F	ENST00000376406	NM_014641.2	963	tCc/tTc	8/15	0.60970021936976	7	FACETS	0.545	0.451	0.651			1	SUBCLONAL	1	FALSE	NA	0.60970021936976	7		770	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0015059-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	45	575	0	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.173305865940072	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		575	677	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496913	29496913	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555607073	NA	P-0015059-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	32	330	0	ENST00000356175.3:c.484C>T	p.Gln162Ter	p.Q162*	ENST00000356175	NM_000267.3	162	Cag/Tag	5/57	0.173305865940072	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		330	348	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965664	93965664	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015059-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	54	524	0	ENST00000369303.4:c.2264T>C	p.Val755Ala	p.V755A	ENST00000369303	NM_004440.3	755	gTt/gCt	13/17	0.284002320237561	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		524	582	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015116-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	399	487	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	0.808259563762598	3	FACETS	0.871	0.834	0.907	0.871	0.834	0.907	CLONAL	2	TRUE	1	0.831804284446768	3		487	780	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100189	27100189	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015116-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	210	447	0	ENST00000324856.7:c.3985C>T	p.Gln1329Ter	p.Q1329*	ENST00000324856	NM_006015.4	1329	Cag/Tag	16/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.831804284446768	2		447	484	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239876	41239876	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015116-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	151	325	0	ENST00000379561.5:c.474C>G	p.Asn158Lys	p.N158K	ENST00000379561	NM_002015.3	158	aaC/aaG	1/3	0.81593114326154	2	FACETS	1	0.954	1	0.519	0.481	0.557	CLONAL	1	TRUE	0	0.831804284446768	2		325	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0015116-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	595	399	0	ENST00000269305.4:c.673-2A>C		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.831804284446768	3	FACETS	0.973	0.954	0.991	0.973	0.954	0.991	CLONAL	3	TRUE	0	0.831804284446768	3		399	694	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876518	59876518	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs779237423	NA	P-0015116-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1833	198	234	0	ENST00000259008.2:c.1283A>C	p.Asn428Thr	p.N428T	ENST00000259008	NM_032043.2	428	aAt/aCt	9/20	0.831804284446768	9	FACETS	0.917	0.845	0.992	0.183	0.169	0.199	CLONAL	1	TRUE	4	0.831804284446768	9		234	2031	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551727	150551727	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015116-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	125	171	0	ENST00000369026.2:c.280G>T	p.Ala94Ser	p.A94S	ENST00000369026	NM_021960.4	94	Gcg/Tcg	1/3	0.831804284446768	8	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.831804284446768	8		171	821	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0015206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	49	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.113584915383078	7	FACETS	1	0.89	1	0.354	0.3	0.414	CLONAL	2	TRUE	1	0.113584915383078	7		511	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555526097	NA	P-0015206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	71	589	0	ENST00000269305.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000269305	NM_001126112.2	167	Cag/Tag	5/11	1	2	FACETS	1	0.954	1	1	0.984	1	CLONAL	2	TRUE	1	0.113584915383078	2		589	520	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696689	47696689	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519972	NA	P-0015206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	46	399	0	ENST00000347630.2:c.259T>A	p.Tyr87Asn	p.Y87N	ENST00000347630	NM_001007230.1	87	Tac/Aac	5/11	1	2	FACETS	0.948	0.8	1	1	0.97	1	CLONAL	2	TRUE	1	0.113584915383078	2		399	427	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533099	63533099	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	72	441	0	ENST00000307078.5:c.1795G>T	p.Ala599Ser	p.A599S	ENST00000307078	NM_004655.3	599	Gcc/Tcc	7/11	1	2	FACETS	0.852	0.746	0.966	1	0.985	1	CLONAL	3	TRUE	1	0.113584915383078	2		441	496	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325622	87325622	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	57	352	2	ENST00000277120.3:c.499T>C	p.Ser167Pro	p.S167P	ENST00000277120		167	Tcc/Ccc	6/19	1	2	FACETS	1	0.941	1	1	0.98	1	CLONAL	2	TRUE	1	0.113584915383078	2		354	425	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929401	44929407	+	frameshift_variant	Frame_Shift_Del	DEL	AGCAGAC	AGCAGAC	-	novel	NA	P-0015206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	61	294	0	ENST00000377967.4:c.2502_2508del	p.Gln835ProfsTer30	p.Q835Pfs*30	ENST00000377967	NM_021140.2	834	gAGCAGACa/ga	17/29	0.113584915383078	0	FACETS	0.826	0.719	0.941			1	CLONAL	4	TRUE	NA	0.113584915383078	0		294	288	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579510	7580293	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	ACCTGGGTCTTCAGTGAACCATTGTTCAATATCGTCCGGGGACAGCATCAAATCATCCATTGCTTGGGACGGCAAGGGGGACTGTAGATGGGTGAAAAGAGCAGTCAGAGGACCAGGTCCTCAGCCCCCCAGCCCCCCAGCCCTCCAGGTCCCCAGCCCTCCAGGTCCCCAGCCCAACCCTTGTCCTTACCAGAACGTTGTTTTCAGGAAGTCTGAAAGACAAGAGCAGAAAGTCAGTCCCATGGAATTTTCGCTTCCCACAGGTCTCTGCTAGGGGGCTGGGGTTGGGGTGGGGGTGGTGGGCCTGCCCTTCCAATGGATCCACTCACAGTTTCCATAGGTCTGAAAATGTTTCCTGACTCAGAGGGGGCTCGACGCTAGGATCTGACTGCGGCTCCTCCATGGCAGTGACCCGGAAGGCAGTCTGGCTGCTGCAAGAGGAAAAGTGGGGATCCAGCATGAGACACTTCCAACCCTGGGTCACCTGGGCCTGCAGAGAAGGAACCCCCTCCCCCAACACCATGCCAGTGTCTGAGACAGCTCGGCTTCCTGTGGAGCAGGAAAAGAATGGCTGCTTCACATTCTCTCTTCCAATGTTTCACCACAACCCAAGCACTCCTGCCCCACCCCTCACCAGCCATGCACTTCTTTGAGGAAAAGACAATCAGAGAGGGACTTCCAACCTTCCCACCACTAAATCCCCAAGACTTCCTAAATGTGCACCCTATTCCCAACTCCCTTCCTGTATTTTTTTTTTTTTTTTGAGATGGAGTCTCTCTCTGTC	ACCTGGGTCTTCAGTGAACCATTGTTCAATATCGTCCGGGGACAGCATCAAATCATCCATTGCTTGGGACGGCAAGGGGGACTGTAGATGGGTGAAAAGAGCAGTCAGAGGACCAGGTCCTCAGCCCCCCAGCCCCCCAGCCCTCCAGGTCCCCAGCCCTCCAGGTCCCCAGCCCAACCCTTGTCCTTACCAGAACGTTGTTTTCAGGAAGTCTGAAAGACAAGAGCAGAAAGTCAGTCCCATGGAATTTTCGCTTCCCACAGGTCTCTGCTAGGGGGCTGGGGTTGGGGTGGGGGTGGTGGGCCTGCCCTTCCAATGGATCCACTCACAGTTTCCATAGGTCTGAAAATGTTTCCTGACTCAGAGGGGGCTCGACGCTAGGATCTGACTGCGGCTCCTCCATGGCAGTGACCCGGAAGGCAGTCTGGCTGCTGCAAGAGGAAAAGTGGGGATCCAGCATGAGACACTTCCAACCCTGGGTCACCTGGGCCTGCAGAGAAGGAACCCCCTCCCCCAACACCATGCCAGTGTCTGAGACAGCTCGGCTTCCTGTGGAGCAGGAAAAGAATGGCTGCTTCACATTCTCTCTTCCAATGTTTCACCACAACCCAAGCACTCCTGCCCCACCCCTCACCAGCCATGCACTTCTTTGAGGAAAAGACAATCAGAGAGGGACTTCCAACCTTCCCACCACTAAATCCCCAAGACTTCCTAAATGTGCACCCTATTCCCAACTCCCTTCCTGTATTTTTTTTTTTTTTTTGAGATGGAGTCTCTCTCTGTC	-	novel	NA	P-0015206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	61	591	0	ENST00000269305.4:c.-28-353_177del		p.X10_splice	ENST00000269305	NM_001126112.2	10		2-4/11	1	2	FACETS	0.945	0.816	1	1	0.977	1	CLONAL	2	TRUE	1	0.113584915383078	2		591	568	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288475	15288475	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	25	268	0	ENST00000263388.2:c.4264G>C	p.Gly1422Arg	p.G1422R	ENST00000263388	NM_000435.2	1422	Ggc/Cgc	24/33	1	2	FACETS	0.87	0.688	1	1	0.942	1	CLONAL	2	TRUE	1	0.113584915383078	2		268	253	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411915	116411915	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	83	600	0	ENST00000397752.3:c.2900A>G	p.Glu967Gly	p.E967G	ENST00000397752	NM_000245.2	967	gAa/gGa	14/21	0.0718450643785116	0	FACETS	1	0.947	1			1	CLONAL	2	TRUE	0	0.113584915383078	0		600	576	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356152	70356152	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	45	297	0	ENST00000374080.3:c.5047C>A	p.Gln1683Lys	p.Q1683K	ENST00000374080		1683	Cag/Aag	37/45	0.0996962136244544	0	FACETS	1	0.858	1			1	CLONAL	2	TRUE	NA	0.113584915383078	0		297	345	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015238-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	171	376	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.890287077140086	2		376	358	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0015238-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	174	226	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.915	0.853	0.979	0.915	0.853	0.979	CLONAL	1	TRUE	1	0.890287077140086	2		227	427	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971029	21971029	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519852	NA	P-0015238-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	24	191	0	ENST00000304494.5:c.329G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tGg/tAg	2/3	0.885684123508177	2	FACETS	0.113	0.088	0.142	0.056	0.044	0.071	SUBCLONAL	1	TRUE	0	0.890287077140086	2		191	478	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780815	9780815	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015238-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	182	513	0	ENST00000377346.4:c.1537G>A	p.Glu513Lys	p.E513K	ENST00000377346	NM_005026.3	513	Gaa/Aaa	13/24	0.890287077140086	1	FACETS	0.438	0.407	0.47	0.438	0.407	0.47	SUBCLONAL	1	TRUE	0	0.890287077140086	1		513	518	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912309	29912309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015238-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	323	901	0	ENST00000376809.5:c.928G>A	p.Gly310Ser	p.G310S	ENST00000376809	NM_002116.7	310	Ggc/Agc	5/8	1	2	FACETS	0.67	0.633	0.708	0.67	0.633	0.708	SUBCLONAL	1	TRUE	1	0.890287077140086	2		901	1083	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026348	48026348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015238-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	37	421	2	ENST00000234420.5:c.1226G>A	p.Gly409Glu	p.G409E	ENST00000234420	NM_000179.2	409	gGg/gAg	4/10	1	2	FACETS	0.116	0.095	0.14	0.116	0.095	0.14	SUBCLONAL	1	TRUE	1	0.890287077140086	2		423	717	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374348	31374348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015238-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	54	606	1	ENST00000328111.2:c.347G>A	p.Arg116Lys	p.R116K	ENST00000328111	NM_006892.3	116	aGg/aAg	5/23	1	2	FACETS	0.135	0.115	0.158	0.135	0.115	0.158	SUBCLONAL	1	TRUE	1	0.890287077140086	2		607	897	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256177	133256177	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015238-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	253	670	2	ENST00000320574.5:c.484G>A	p.Asp162Asn	p.D162N	ENST00000320574	NM_006231.2	162	Gat/Aat	6/49	1	2	FACETS	0.629	0.589	0.669	0.629	0.589	0.669	SUBCLONAL	1	TRUE	1	0.890287077140086	2		672	904	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120509086	120509086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015238-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	258	514	0	ENST00000256646.2:c.1480G>A	p.Glu494Lys	p.E494K	ENST00000256646	NM_024408.3	494	Gaa/Aaa	9/34	0.890287077140086	1	FACETS	0.652	0.619	0.686	0.652	0.619	0.686	SUBCLONAL	1	TRUE	0	0.890287077140086	1		514	493	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263436	123263436	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015238-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	119	507	0	ENST00000358487.5:c.1307C>T	p.Ser436Phe	p.S436F	ENST00000358487	NM_000141.4	436	tCc/tTc	10/18	1	2	FACETS	0.42	0.38	0.463	0.42	0.38	0.463	SUBCLONAL	1	TRUE	1	0.890287077140086	2		507	636	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310844	123310844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1409994363	NA	P-0015238-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	258	659	0	ENST00000358487.5:c.584G>A	p.Gly195Glu	p.G195E	ENST00000358487	NM_000141.4	195	gGg/gAg	5/18	1	2	FACETS	0.609	0.571	0.649	0.609	0.571	0.649	SUBCLONAL	1	TRUE	1	0.890287077140086	2		659	951	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352607	118352607	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015238-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1229	183	598	1	ENST00000534358.1:c.3812G>A	p.Ser1271Asn	p.S1271N	ENST00000534358	NM_005933.3	1271	aGt/aAt	7/36	0.558031518924529	4	FACETS	0.55	0.506	0.597	0.183	0.168	0.199	SUBCLONAL	1	TRUE	1	0.890287077140086	4		599	1412	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500516	99500516	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1218278245	NA	P-0015238-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	234	601	0	ENST00000268035.6:c.3949C>T	p.Pro1317Ser	p.P1317S	ENST00000268035	NM_000875.3	1317	Ccc/Tcc	21/21	1	2	FACETS	0.64	0.599	0.683	0.64	0.599	0.683	SUBCLONAL	1	TRUE	1	0.890287077140086	2		601	821	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644959	67644959	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015238-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	175	578	1	ENST00000264010.4:c.224C>T	p.Thr75Ile	p.T75I	ENST00000264010	NM_006565.3	75	aCt/aTt	3/12	1	2	FACETS	0.475	0.438	0.514	0.475	0.438	0.514	SUBCLONAL	1	TRUE	1	0.890287077140086	2		579	827	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976555	7976555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015238-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	55	740	1	ENST00000319144.4:c.1837G>A	p.Glu613Lys	p.E613K	ENST00000319144	NM_001139.2	613	Gag/Aag	14/15	1	2	FACETS	0.12	0.102	0.14	0.12	0.102	0.14	SUBCLONAL	1	TRUE	1	0.890287077140086	2		741	1031	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881639	111881639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773443902	NA	P-0015238-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	290	665	0	ENST00000393256.3:c.317C>T	p.Ala106Val	p.A106V	ENST00000393256	NM_006538.4	106	gCa/gTa	2/4	1	2	FACETS	0.619	0.582	0.656	0.619	0.582	0.656	SUBCLONAL	1	TRUE	1	0.890287077140086	2		665	1053	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119562191	119562191	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015238-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	180	402	0	ENST00000316626.5:c.1145G>A	p.Ser382Asn	p.S382N	ENST00000316626		382	aGt/aAt	11/12	1	2	FACETS	0.57	0.527	0.615	0.57	0.527	0.615	SUBCLONAL	1	TRUE	1	0.890287077140086	2		402	709	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542591	187542591	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015238-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	253	501	0	ENST00000441802.2:c.5149G>A	p.Gly1717Arg	p.G1717R	ENST00000441802	NM_005245.3	1717	Gga/Aga	10/27	0.890287077140086	1	FACETS	0.645	0.611	0.678	0.645	0.611	0.678	SUBCLONAL	1	TRUE	0	0.890287077140086	1		501	489	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41904413	41904413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775205121	NA	P-0015238-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	174	700	1	ENST00000372991.4:c.595C>T	p.Pro199Ser	p.P199S	ENST00000372991	NM_001760.3	199	Ccg/Tcg	4/5	1	2	FACETS	0.366	0.336	0.397	0.366	0.336	0.397	SUBCLONAL	1	TRUE	1	0.890287077140086	2		701	1069	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853289	151853289	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0015238-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	38	458	0	ENST00000262189.6:c.11812+1G>A		p.X3938_splice	ENST00000262189	NM_170606.2	3938			1	2	FACETS	0.123	0.101	0.147	0.123	0.101	0.147	SUBCLONAL	1	TRUE	1	0.890287077140086	2		458	696	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020732	37020732	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015238-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	172	581	1	ENST00000358127.4:c.113G>A	p.Arg38His	p.R38H	ENST00000358127	NM_001280556.1	38	cGc/cAc	2/10	1	2	FACETS	0.427	0.393	0.463	0.427	0.393	0.463	SUBCLONAL	1	TRUE	1	0.890287077140086	2		582	904	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128322039	128322039	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015238-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	261	700	1	ENST00000265960.3:c.721G>A	p.Val241Met	p.V241M	ENST00000265960	NM_001006617.1	241	Gtg/Atg	6/12	1	2	FACETS	0.553	0.518	0.589	0.553	0.518	0.589	SUBCLONAL	1	TRUE	1	0.890287077140086	2		701	1060	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796885	42796886	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	T	novel	NA	P-0015238-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	438	750	0	ENST00000575354.2:c.3343_3344delinsT	p.Pro1115SerfsTer46	p.P1115Sfs*46	ENST00000575354	NM_015125.3	1115	CCc/Tc	14/20	0.890287077140086	1	FACETS	0.965	0.938	0.99	0.965	0.938	0.99	CLONAL	1	TRUE	0	0.890287077140086	1		750	566	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111478	8111479	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0015351-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	247	709	0	ENST00000346208.3:c.966dup	p.Thr323HisfsTer29	p.T323Hfs*29	ENST00000346208		322	acc/aCcc	5/6	NA	2	FACETS	0.73	0.683	0.778			1	INDETERMINATE	1	TRUE	NA	0.733946492181766	2		709	922	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	27	974	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.642	0.509	0.795	0.642	0.509	0.795	SUBCLONAL	1	TRUE	1	0.13	2		974	647	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882019	NA	P-0015390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	51	779	0	ENST00000269305.4:c.455dup	p.Pro153AlafsTer28	p.P153Afs*28	ENST00000269305	NM_001126112.2	152	ccg/ccCg	5/11	1	2	FACETS	0.814	0.689	0.952	0.814	0.689	0.952	CLONAL	1	TRUE	1	0.13	2		779	964	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971209	21971209	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1554654224	NA	P-0015390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	27	315	0	ENST00000304494.5:c.151-2A>G		p.X51_splice	ENST00000304494	NM_000077.4	51			1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.13	2		315	363	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	158	974	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.175193895314323	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	FALSE	2	0.208316892012842	4		974	846	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574011	7574012	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CG	novel	NA	P-0015567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	189	707	0	ENST00000269305.4:c.1014_1015dup	p.Glu339AlafsTer7	p.E339Afs*7	ENST00000269305	NM_001126112.2	339	gag/gCGag	10/11	0.208316892012842	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	FALSE	1	0.208316892012842	3		707	954	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172269	99172269	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	114	526	0	ENST00000074304.5:c.1835C>T	p.Thr612Ile	p.T612I	ENST00000074304	NM_001134224.1	612	aCa/aTa	17/26	0.159724033054821	3	FACETS	0.778	0.7	0.86	0.778	0.7	0.86	SUBCLONAL	2	FALSE	1	0.208316892012842	3		526	777	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680815	30680815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	140	555	0	ENST00000376406.3:c.904G>A	p.Asp302Asn	p.D302N	ENST00000376406	NM_014641.2	302	Gat/Aat	5/15	0.159724033054821	3	FACETS	0.969	0.883	1	0.969	0.883	1	CLONAL	2	FALSE	1	0.208316892012842	3		555	766	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs869320707	NA	P-0015601-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	116	705	1	ENST00000397752.3:c.3028+1G>T		p.X1010_splice	ENST00000397752	NM_000245.2	1010			1	2	FACETS	0.761	0.685	0.841	1	0.984	1	SUBCLONAL	2	TRUE	1	0.16	2		706	953	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485091	57485091	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015601-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	41	346	0	ENST00000371085.3:c.925G>C	p.Glu309Gln	p.E309Q	ENST00000371085	NM_000516.4	309	Gag/Cag	11/13	1	2	FACETS	0.976	0.813	1	0.976	0.813	1	CLONAL	1	TRUE	1	0.16	2		346	525	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458444	120458457	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGCTCCCGAGGG	AGGGCTCCCGAGGG	-	novel	NA	P-0015634-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	47	438	0	ENST00000256646.2:c.6888_6901del	p.Pro2297AlafsTer11	p.P2297Afs*11	ENST00000256646	NM_024408.3	2296	acCCCTCGGGAGCCCTtg/actg	34/34	1	2	FACETS	0.398	0.336	0.466	0.398	0.336	0.466	SUBCLONAL	1	TRUE	1	0.511289159522499	2		438	462	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844190	68844190	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015634-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	106	524	1	ENST00000261769.5:c.778C>A	p.Pro260Thr	p.P260T	ENST00000261769	NM_004360.3	260	Ccc/Acc	6/16	0.328225648953584	1	FACETS	0.41	0.367	0.455	0.41	0.367	0.455	SUBCLONAL	1	TRUE	0	0.511289159522499	1		525	753	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44935946	44935953	+	frameshift_variant	Frame_Shift_Del	DEL	CTAGGTAA	CTAGGTAA	-	novel	NA	P-0015634-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	22	193	0	ENST00000377967.4:c.2707_2714del	p.Leu903LysfsTer5	p.L903Kfs*5	ENST00000377967	NM_021140.2	903	CTAGGTAAa/a	18/29	1	2	FACETS	0.297	0.23	0.374	0.297	0.23	0.374	SUBCLONAL	1	TRUE	1	0.511289159522499	2		193	290	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	272	436	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.4183992529953	3	FACETS	0.995	0.938	1	0.995	0.938	1	CLONAL	2	TRUE	1	0.4183992529953	3		437	790	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0015746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	161	255	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.4183992529953	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.4183992529953	1		255	559	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220649	1220649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060499964	NA	P-0015746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	256	725	2	ENST00000326873.7:c.667G>A	p.Glu223Lys	p.E223K	ENST00000326873	NM_000455.4	223	Gag/Aag	5/10	0.4183992529953	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.4183992529953	1		727	844	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141992	108141998	+	frameshift_variant	Frame_Shift_Del	DEL	TGTATCG	TGTATCG	-	novel	NA	P-0015746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	77	420	0	ENST00000278616.4:c.2937_2943del	p.Leu979PhefsTer11	p.L979Ffs*11	ENST00000278616	NM_000051.3	979	tTGTATCGt/tt	20/63	0.4183992529953	1	FACETS	0.703	0.62	0.791	0.703	0.62	0.791	SUBCLONAL	1	TRUE	0	0.4183992529953	1		420	414	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289167	33289167	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371678103	NA	P-0015746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	58	432	1	ENST00000374542.5:c.385G>A	p.Glu129Lys	p.E129K	ENST00000374542	NM_001141970.1	129	Gag/Aag	3/8	0.190591539316338	1	FACETS	0.373	0.32	0.43	0.373	0.32	0.43	INDETERMINATE	1	TRUE	0	0.4183992529953	1		433	588	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904946	101904946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760079636	NA	P-0015746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	85	271	0	ENST00000374994.4:c.934G>A	p.Gly312Ser	p.G312S	ENST00000374994	NM_004612.2	312	Ggt/Agt	5/9	0.4183992529953	1	FACETS	0.871	0.775	0.971	0.871	0.775	0.971	CLONAL	1	TRUE	0	0.4183992529953	1		271	369	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0015824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	91	615	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.228047812231247	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.228047812231247	1		615	671	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0015824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	47	359	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.228047812231247	1	FACETS	0.982	0.831	1	0.982	0.831	1	CLONAL	1	TRUE	0	0.228047812231247	1		359	372	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579361	7579361	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1064796722	NA	P-0015824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	94	769	0	ENST00000269305.4:c.326T>C	p.Phe109Ser	p.F109S	ENST00000269305	NM_001126112.2	109	tTc/tCc	4/11	0.228047812231247	1	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	0	0.228047812231247	1		769	725	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0015871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	116	387	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.290674320329591	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		387	598	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0015871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	48	778	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		778	849	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015931-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	150	674	4	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.401013278970567	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.401013278970567	1		678	483	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259141	36259141	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015931-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	70	464	0	ENST00000300305.3:c.350del	p.Lys117ArgfsTer5	p.K117Rfs*5	ENST00000300305		117	aAg/ag	3/8	1	2	FACETS	0.648	0.565	0.736	0.648	0.565	0.736	SUBCLONAL	1	TRUE	1	0.401013278970567	2		464	539	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44910951	44910951	+	splice_region_variant,intron_variant	Splice_Region	SNP	T	T	C	rs1024351607	NA	P-0015931-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	101	212	0	ENST00000377967.4:c.655-3T>C		p.X219_splice	ENST00000377967	NM_021140.2	219			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.401013278970567	2		212	407	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022844	31022844	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015931-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	35	306	1	ENST00000375687.4:c.2329G>T	p.Glu777Ter	p.E777*	ENST00000375687	NM_015338.5	777	Gag/Tag	13/13	0.279810259282812	3	FACETS	0.429	0.351	0.516	0.214	0.175	0.258	SUBCLONAL	1	TRUE	1	0.401013278970567	3		307	489	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106138	27106138	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	82	330	0	ENST00000324856.7:c.5749A>G	p.Thr1917Ala	p.T1917A	ENST00000324856	NM_006015.4	1917	Act/Gct	20/20	1	2	FACETS	0.92	0.811	1	0.92	0.811	1	CLONAL	1	TRUE	1	0.256560217504181	2		330	695	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692780	89692780	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1554898056	NA	P-0015981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	67	228	1	ENST00000371953.3:c.264T>A	p.Tyr88Ter	p.Y88*	ENST00000371953	NM_000314.4	88	taT/taA	5/9	0.220247551381258	1	FACETS	0.854	0.743	0.974	0.854	0.743	0.974	CLONAL	1	TRUE	0	0.256560217504181	1		229	533	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835622	68835622	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	89	370	0	ENST00000261769.5:c.213del	p.Asp72ThrfsTer11	p.D72Tfs*11	ENST00000261769	NM_004360.3	71	ctC/ct	3/16	0.230625068422044	1	FACETS	0.877	0.777	0.982	0.877	0.777	0.982	CLONAL	1	TRUE	0	0.256560217504181	1		370	690	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332914	152332914	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	50	217	0	ENST00000206249.3:c.1220A>T	p.Asn407Ile	p.N407I	ENST00000206249	NM_000125.3	407	aAc/aTc	5/8	1	2	FACETS	0.999	0.85	1	0.999	0.85	1	CLONAL	1	TRUE	1	0.256560217504181	2		217	390	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023118	27023124	+	frameshift_variant	Frame_Shift_Del	DEL	ACGGGGC	ACGGGGC	CCGGGT	novel	NA	P-0015981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	21	71	0	ENST00000324856.7:c.224_230delinsCCGGGT	p.Asp75AlafsTer26	p.D75Afs*26	ENST00000324856	NM_006015.4	75	gACGGGGCc/gCCGGGTc	1/20	1	2	FACETS	0.895	0.693	1	0.895	0.693	1	CLONAL	1	TRUE	1	0.256560217504181	2		71	183	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0016041-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	44	318	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.520489083611103	2		318	160	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0016041-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	57	375	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.961	0.834	1	0.961	0.834	1	CLONAL	1	TRUE	1	0.520489083611103	2		375	228	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0016041-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	73	481	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.882	0.778	0.992	0.882	0.778	0.992	CLONAL	1	TRUE	1	0.520489083611103	2		481	318	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063717	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0016041-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	30	252	0	ENST00000412916.2:c.165+1G>T		p.X55_splice	ENST00000412916		55			0.520489083611103	1	FACETS	0.898	0.743	1	0.898	0.743	1	CLONAL	1	TRUE	0	0.520489083611103	1		252	95	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177451	56177452	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0016041-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	29	280	0	ENST00000399503.3:c.2426_2427dup	p.Ser810ThrfsTer13	p.S810Tfs*13	ENST00000399503	NM_005921.1	808	-/CA	14/20	1	2	FACETS	0.796	0.648	0.959	0.796	0.648	0.959	CLONAL	1	TRUE	1	0.520489083611103	2		280	140	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543650	148543650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768812143	NA	P-0016178-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	317	367	1	ENST00000320356.2:c.158C>T	p.Thr53Met	p.T53M	ENST00000320356	NM_004456.4	53	aCg/aTg	3/20	1	2	FACETS	0.971	0.922	1	0.971	0.922	1	CLONAL	1	TRUE	1	0.864652650913832	2		368	755	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864627	37864627	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016178-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	42	569	0	ENST00000269571.5:c.279G>T	p.Gln93His	p.Q93H	ENST00000269571		93	caG/caT	3/27	1	2	FACETS	0.127	0.105	0.151	0.127	0.105	0.151	SUBCLONAL	1	TRUE	1	0.864652650913832	2		569	766	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0016407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	22	491	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.119984676463891	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		491	195	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	28	974	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		974	756	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242511	55242511	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs121913418	NA	P-0016407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	8	751	0	ENST00000275493.2:c.2281G>A	p.Asp761Asn	p.D761N	ENST00000275493	NM_005228.3	761	Gat/Aat	19/28	0.259298371260611	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		751	299	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591889	48591889	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	17	663	0	ENST00000342988.3:c.1052A>G	p.Asp351Gly	p.D351G	ENST00000342988	NM_005359.5	351	gAt/gGt	9/12	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		663	300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0016476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	498	754	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.837869139336003	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.857036068864752	1		754	596	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739068	145739068	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1026729951	NA	P-0016476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	344	347	0	ENST00000428558.2:c.2087G>A	p.Arg696His	p.R696H	ENST00000428558	NM_004260.3	696	cGt/cAt	13/22	1	2	FACETS	0.936	0.889	0.982	0.936	0.889	0.982	CLONAL	1	TRUE	1	0.857036068864752	2		347	858	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440453	49440453	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	576	539	0	ENST00000301067.7:c.4357C>T	p.His1453Tyr	p.H1453Y	ENST00000301067	NM_003482.3	1453	Cac/Tac	15/54	1	2	FACETS	0.962	0.926	0.999	0.962	0.926	0.999	CLONAL	1	TRUE	1	0.857036068864752	2		539	1397	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434491	121434491	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	544	589	0	ENST00000257555.6:c.1255C>A	p.Pro419Thr	p.P419T	ENST00000257555		419	Cct/Act	6/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.857036068864752	2		589	1245	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954215	48954249	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTAGGTAAATTTTTTACTTTTAGTAAAAAATTT	TTTTAGGTAAATTTTTTACTTTTAGTAAAAAATTT	-	novel	NA	P-0016476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	49	310	0	ENST00000267163.4:c.1420_1421+33del		p.X474_splice	ENST00000267163	NM_000321.2	474		15/27	0.837869139336003	1	FACETS	0.207	0.176	0.241	0.207	0.176	0.241	SUBCLONAL	1	TRUE	0	0.857036068864752	1		310	316	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830807	72830807	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	480	455	0	ENST00000268489.5:c.5774G>T	p.Gly1925Val	p.G1925V	ENST00000268489	NM_006885.3	1925	gGt/gTt	9/10	1	2	FACETS	0.984	0.944	1	0.984	0.944	1	CLONAL	1	TRUE	1	0.857036068864752	2		455	1138	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882340	89882340	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	491	580	0	ENST00000389301.3:c.134A>T	p.Glu45Val	p.E45V	ENST00000389301	NM_000135.2	45	gAa/gTa	2/43	1	2	FACETS	0.948	0.909	0.987	0.948	0.909	0.987	CLONAL	1	TRUE	1	0.857036068864752	2		580	1209	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518143	187518143	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	414	525	0	ENST00000441802.2:c.12551del	p.Gly4184GlufsTer22	p.G4184Efs*22	ENST00000441802	NM_005245.3	4184	gGa/ga	25/27	0.857036068864752	1	FACETS	0.929	0.899	0.959	0.929	0.899	0.959	CLONAL	1	TRUE	0	0.857036068864752	1		525	594	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20153912	20153912	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	467	263	0	ENST00000379607.5:c.148A>G	p.Met50Val	p.M50V	ENST00000379607	NM_001412.3	50	Atg/Gtg	3/7	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.857036068864752	1		263	544	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0016537-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	404	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.865876497780835	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.871237635054907	1		511	505	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338671	70338671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016537-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	363	523	0	ENST00000374080.3:c.67G>T	p.Asp23Tyr	p.D23Y	ENST00000374080		23	Gat/Tat	1/45	1	2	FACETS	0.987	0.941	1	0.987	0.941	1	CLONAL	1	TRUE	1	0.871237635054907	2		523	844	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913396	NA	P-0016537-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	172	266	0	ENST00000349496.5:c.95A>T	p.Asp32Val	p.D32V	ENST00000349496	NM_001904.3	32	gAc/gTc	3/15	1	2	FACETS	0.916	0.852	0.981	0.916	0.852	0.981	CLONAL	1	TRUE	1	0.871237635054907	2		266	431	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016537-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	329	526	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	0.884	0.839	0.93	0.884	0.839	0.93	CLONAL	1	TRUE	1	0.871237635054907	2		526	854	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624274	89624274	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs587782187	NA	P-0016537-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	599	298	0	ENST00000371953.3:c.48T>A	p.Tyr16Ter	p.Y16*	ENST00000371953	NM_000314.4	16	taT/taA	1/9	NA	2	FACETS	0.974	0.955	0.992			1	INDETERMINATE	2	TRUE	NA	0.871237635054907	2		298	706	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132542	11132542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016537-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	372	556	0	ENST00000358026.2:c.2758G>A	p.Glu920Lys	p.E920K	ENST00000358026	NM_001128849.1	920	Gag/Aag	19/36	1	2	FACETS	0.961	0.916	1	0.961	0.916	1	CLONAL	1	TRUE	1	0.871237635054907	2		556	889	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617533	158617533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751000395	NA	P-0016537-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	299	396	0	ENST00000263640.3:c.1123C>T	p.Arg375Cys	p.R375C	ENST00000263640	NM_001105.4	375	Cgt/Tgt	9/11	1	2	FACETS	0.938	0.888	0.988	0.938	0.888	0.988	CLONAL	1	TRUE	1	0.871237635054907	2		396	732	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753615	42753615	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016537-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	418	691	0	ENST00000222329.4:c.649T>G	p.Phe217Val	p.F217V	ENST00000222329	NM_006494.2	217	Ttc/Gtc	4/4	1	2	FACETS	0.968	0.926	1	0.968	0.926	1	CLONAL	1	TRUE	1	0.871237635054907	2		691	991	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521425	187521425	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs929790232	NA	P-0016537-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	252	420	0	ENST00000441802.2:c.11730G>T	p.Gln3910His	p.Q3910H	ENST00000441802	NM_005245.3	3910	caG/caT	22/27	1	2	FACETS	0.95	0.896	1	0.95	0.896	1	CLONAL	1	TRUE	1	0.871237635054907	2		420	609	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0016584-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	177	487	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	0.346888451538657	3	FACETS	0.76	0.702	0.821	0.76	0.702	0.821	SUBCLONAL	2	TRUE	1	0.358465270121534	3		487	766	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0016584-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	147	604	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.169597467006656	2	FACETS	1	0.985	1	0.683	0.626	0.743	INDETERMINATE	1	TRUE	0	0.358465270121534	2		604	600	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0016786-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	25	398	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	0.200665802843328	4	FACETS	0.855	0.674	1	0.427	0.337	0.532	CLONAL	1	TRUE	2	0.21	4		398	337	SUCCESS
AR	367	MSKCC	GRCh37	X	66943543	66943543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852581	NA	P-0016786-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	31	349	0	ENST00000374690.3:c.2623C>T	p.His875Tyr	p.H875Y	ENST00000374690	NM_000044.3	875	Cat/Tat	8/8	0.200665802843328	0	FACETS	1	0.896	1			1	CLONAL	1	TRUE	0	0.21	0		349	202	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431460	121431460	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016786-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	23	671	0	ENST00000257555.6:c.664A>C	p.Lys222Gln	p.K222Q	ENST00000257555		222	Aag/Cag	3/10	0.111012145005176	0	FACETS	0.801	0.627	1			1	INDETERMINATE	1	TRUE	0	0.21	0		671	216	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842405	68842409	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGT	TGGGT	-	novel	NA	P-0016786-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	28	630	0	ENST00000261769.5:c.467_471del	p.Trp156TyrfsTer10	p.W156Yfs*10	ENST00000261769	NM_004360.3	156	TGGGTt/t	4/16	0.3	2	FACETS	1	0.865	1			1	CLONAL	1	TRUE	NA	0.21	2		630	242	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444737	49444737	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016811-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	347	675	0	ENST00000301067.7:c.2729C>G	p.Pro910Arg	p.P910R	ENST00000301067	NM_003482.3	910	cCt/cGt	10/54	0.640442031618436	2	FACETS	0.996	0.96	1	0.996	0.96	1	CLONAL	2	TRUE	0	0.685495545351379	2		675	508	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954343	48954344	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCGCTCT	novel	NA	P-0016811-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	128	269	0	ENST00000267163.4:c.1467_1474dup	p.Glu492AlafsTer6	p.E492Afs*6	ENST00000267163	NM_000321.2	488	-/TGCGCTCT	16/27	0.685495545351379	3	FACETS	0.796	0.732	0.861	0.531	0.488	0.574	SUBCLONAL	2	TRUE	0	0.685495545351379	3		269	315	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823802	3823802	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016811-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	281	395	0	ENST00000262367.5:c.2413del	p.Ala805ArgfsTer2	p.A805Rfs*2	ENST00000262367	NM_004380.2	805	Gcg/cg	13/31	0.630443469140172	3	FACETS	0.943	0.907	0.978	0.943	0.907	0.978	CLONAL	3	TRUE	0	0.685495545351379	3		395	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576858	7576858	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016811-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	378	415	0	ENST00000269305.4:c.988del	p.Leu330PhefsTer15	p.L330Ffs*15	ENST00000269305	NM_001126112.2	330	Ctt/tt	9/11	0.685495545351379	3	FACETS	0.944	0.913	0.974	0.944	0.913	0.974	CLONAL	3	TRUE	0	0.685495545351379	3		415	523	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375163	31375163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774622592	NA	P-0016811-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	144	546	2	ENST00000328111.2:c.560C>T	p.Pro187Leu	p.P187L	ENST00000328111	NM_006892.3	187	cCc/cTc	6/23	0.601931538506676	4	FACETS	0.938	0.857	1	0.469	0.428	0.512	CLONAL	1	TRUE	2	0.685495545351379	4		548	755	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114546	73114547	+	splice_acceptor_variant	Splice_Site	DEL	AG	AG	-	novel	NA	P-0016811-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	72	182	0	ENST00000356692.5:c.929_930del		p.X310_splice	ENST00000356692		310			0.640442031618436	2	FACETS	0.913	0.834	0.99	0.913	0.834	0.99	CLONAL	2	TRUE	0	0.685495545351379	2		182	115	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	241	436	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.51931009755117	3	FACETS	0.89	0.836	0.944	0.89	0.836	0.944	CLONAL	2	TRUE	1	0.51931009755117	3		437	657	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0016847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	128	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.97	0.884	1	0.97	0.884	1	CLONAL	1	TRUE	1	0.51931009755117	2		511	508	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943641	9943641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	171	569	0	ENST00000330684.3:c.1300G>A	p.Val434Met	p.V434M	ENST00000330684	NM_001134407.1	434	Gtg/Atg	5/13	1	2	FACETS	0.938	0.865	1	0.938	0.865	1	CLONAL	1	TRUE	1	0.51931009755117	2		569	702	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577137	7577137	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	389	357	1	ENST00000269305.4:c.801del	p.Asn268ThrfsTer77	p.N268Tfs*77	ENST00000269305	NM_001126112.2	267	cgG/cg	8/11	0.512023359759365	2	FACETS	0.997	0.956	1	0.997	0.956	1	CLONAL	2	TRUE	0	0.51931009755117	2		358	751	SUCCESS
APC	324	MSKCC	GRCh37	5	112137081	112137081	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0016847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	96	380	0	ENST00000257430.4:c.834+1G>C		p.X278_splice	ENST00000257430	NM_000038.5	278			0.51931009755117	3	FACETS	0.937	0.838	1	0.469	0.419	0.521	CLONAL	1	TRUE	1	0.51931009755117	3		380	497	SUCCESS
APC	324	MSKCC	GRCh37	5	112174759	112174762	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs786203020	NA	P-0016847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	191	353	0	ENST00000257430.4:c.3471_3474del	p.Glu1157AspfsTer7	p.E1157Dfs*7	ENST00000257430	NM_000038.5	1156	gaAGAG/ga	16/16	0.51931009755117	3	FACETS	0.877	0.818	0.938	0.877	0.818	0.938	CLONAL	2	TRUE	1	0.51931009755117	3		353	528	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584512	48584555	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGGGGGCAGCCATAGTGAAGGACTGTTGCAGATAGCATCAGG	CTGGGGGGCAGCCATAGTGAAGGACTGTTGCAGATAGCATCAGG	-	novel	NA	P-0016847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	91	391	0	ENST00000342988.3:c.685_728del	p.Leu229AlafsTer20	p.L229Afs*20	ENST00000342988	NM_005359.5	229	CTGGGGGGCAGCCATAGTGAAGGACTGTTGCAGATAGCATCAGGg/g	6/12	0.51931009755117	1	FACETS	0.777	0.696	0.861	0.777	0.696	0.861	SUBCLONAL	1	TRUE	0	0.51931009755117	1		391	334	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937152	76937152	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	27	281	0	ENST00000373344.5:c.3596A>G	p.Asp1199Gly	p.D1199G	ENST00000373344	NM_000489.3	1199	gAc/gGc	9/35	1	1	FACETS	0.277	0.221	0.341	0.277	0.221	0.341	SUBCLONAL	1	TRUE	0	0.51931009755117	1		281	278	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0016926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	21	411	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		411	479	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	42	974	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		974	785	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971209	21971209	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1554654224	NA	P-0016926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	25	315	0	ENST00000304494.5:c.151-2A>G		p.X51_splice	ENST00000304494	NM_000077.4	51			1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		315	286	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0016926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	14	384	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.139307066195585	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		384	413	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532603	63532603	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881400	NA	P-0016926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	32	584	0	ENST00000307078.5:c.1976G>A	p.Arg659Gln	p.R659Q	ENST00000307078	NM_004655.3	659	cGg/cAg	8/11	0.139307066195585	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		584	468	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120085	70120085	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017062-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	16	55	0	ENST00000245479.2:c.1087C>T	p.Gln363Ter	p.Q363*	ENST00000245479	NM_000346.3	363	Cag/Tag	3/3	0.479938442520703	2	FACETS	0.944	0.745	1	0.944	0.745	1	CLONAL	2	TRUE	0	0.498257454352005	2		55	34	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064794618	NA	P-0017062-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	380	878	0	ENST00000269305.4:c.159G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgG/tgA	4/11	0.316242725376777	3	FACETS	1	0.993	1	0.795	0.76	0.83	CLONAL	2	TRUE	0	0.498257454352005	3		878	799	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944715	31944715	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147097287	NA	P-0017062-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	29	40	0	ENST00000340398.3:c.386G>A	p.Arg129Gln	p.R129Q	ENST00000340398	NM_001013699.2	129	cGg/cAg	1/1	0.26735364668999	4	FACETS	1	0.876	1	1	0.957	1	INDETERMINATE	3	TRUE	2	0.498257454352005	4		40	56	SUCCESS
APC	324	MSKCC	GRCh37	5	112175253	112175255	+	stop_gained	Nonsense_Mutation	TNP	GCG	GCG	ACT	novel	NA	P-0017062-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	131	300	0	ENST00000257430.4:c.3962_3964delinsACT	p.Ser1321_Glu1322delinsAsnTer	p.S1321_E1322delinsN*	ENST00000257430	NM_000038.5	1321	aGCGaa/aACTaa	16/16	0.430312692246189	3	FACETS	1	0.972	1	0.742	0.685	0.8	CLONAL	2	TRUE	0	0.498257454352005	3		300	295	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	144	674	4	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.280102718061833	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.280102718061833	1		678	726	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442788	187442788	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	176	564	0	ENST00000232014.4:c.1918C>T	p.Arg640Trp	p.R640W	ENST00000232014	NM_001130845.1	640	Cgg/Tgg	9/10	1	2	FACETS	0.751	0.692	0.812	1	0.99	1	SUBCLONAL	2	TRUE	1	0.280102718061833	2		564	837	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871182	12871182	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1328655695	NA	P-0017261-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	55	283	0	ENST00000228872.4:c.410del	p.Pro137ArgfsTer8	p.P137Rfs*8	ENST00000228872	NM_004064.3	137	Ccg/cg	1/3	1	2	FACETS	0.984	0.847	1	0.984	0.847	1	CLONAL	1	TRUE	1	0.345064873910177	2		283	324	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871249	12871249	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1174921391	NA	P-0017261-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	20	191	0	ENST00000228872.4:c.475+1G>T		p.X159_splice	ENST00000228872	NM_004064.3	159			1	2	FACETS	0.449	0.344	0.572	0.449	0.344	0.572	SUBCLONAL	1	TRUE	1	0.345064873910177	2		191	258	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0017322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	36	974	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.831	0.681	0.999	0.831	0.681	0.999	CLONAL	1	TRUE	1	0.14	2		974	619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0017322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	58	785	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	1	2	FACETS	0.917	0.785	1	0.917	0.785	1	CLONAL	1	TRUE	1	0.14	2		785	904	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0017322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	96	398	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	0.230715374106417	3	FACETS	0.965	0.863	1	1	0.98	1	CLONAL	3	TRUE	1	0.14	3		398	507	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629768	187629768	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	52	618	0	ENST00000441802.2:c.1214C>A	p.Thr405Lys	p.T405K	ENST00000441802	NM_005245.3	405	aCa/aAa	2/27	1	2	FACETS	0.799	0.678	0.932	0.799	0.678	0.932	CLONAL	1	TRUE	1	0.14	2		618	930	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520088	106520088	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	25	273	0	ENST00000359195.3:c.2516G>C	p.Arg839Pro	p.R839P	ENST00000359195	NM_002649.2	839	cGc/cCc	6/11	1	2	FACETS	0.852	0.671	1	0.852	0.671	1	CLONAL	1	TRUE	1	0.14	2		273	419	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349924	70349924	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	69	564	0	ENST00000374080.3:c.3907G>T	p.Asp1303Tyr	p.D1303Y	ENST00000374080		1303	Gac/Tac	28/45	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.14	2		564	940	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	327	376	0				ENST00000310581	NM_198253.2	-/1132			0.334535109262469	6	FACETS	1	0.988	1	1	0.988	1	CLONAL	5	TRUE	1	0.334535109262469	6		376	598	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0017472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	179	535	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.334535109262469	2		535	1062	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952142	178952142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253171657	NA	P-0017472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	77	360	0	ENST00000263967.3:c.3197C>T	p.Ala1066Val	p.A1066V	ENST00000263967	NM_006218.2	1066	gCa/gTa	21/21	1	2	FACETS	0.884	0.777	0.997	0.884	0.777	0.997	CLONAL	1	TRUE	1	0.334535109262469	2		360	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0017472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	179	674	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.334535109262469	2		674	1041	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434943	56434943	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775335997	NA	P-0017472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	178	716	1	ENST00000407977.2:c.2194C>T	p.Arg732Cys	p.R732C	ENST00000407977		732	Cgc/Tgc	9/10	1	2	FACETS	0.921	0.848	0.998	0.921	0.848	0.998	CLONAL	1	TRUE	1	0.334535109262469	2		717	1155	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178002	56178002	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs775205606	NA	P-0017472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	123	486	0	ENST00000399503.3:c.2975C>G	p.Ser992Cys	p.S992C	ENST00000399503	NM_005921.1	992	tCt/tGt	14/20	0.198559338922804	1	FACETS	0.875	0.792	0.962	0.875	0.792	0.962	INDETERMINATE	1	TRUE	0	0.334535109262469	1		486	700	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111855996	111855996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779622961	NA	P-0017472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	141	335	0	ENST00000341259.2:c.47C>T	p.Ser16Leu	p.S16L	ENST00000341259	NM_005475.2	16	tCa/tTa	2/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.334535109262469	2		335	637	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625349	69625349	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	184	652	2	ENST00000334134.2:c.444C>A	p.Ser148Arg	p.S148R	ENST00000334134	NM_005247.2	148	agC/agA	3/3	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.334535109262469	2		654	1020	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037873	49037874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0017472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	185	442	0	ENST00000267163.4:c.2117_2118dup	p.Ser707ValfsTer9	p.S707Vfs*9	ENST00000267163	NM_000321.2	705	atg/aTGtg	21/27	0.294532130660235	2	FACETS	0.814	0.755	0.876	0.814	0.755	0.876	CLONAL	2	TRUE	0	0.334535109262469	2		442	679	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792449	33792449	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	131	629	0	ENST00000498907.2:c.872G>C	p.Arg291Pro	p.R291P	ENST00000498907	NM_004364.3	291	cGc/cCc	1/1	1	2	FACETS	0.752	0.681	0.826	0.752	0.681	0.826	SUBCLONAL	1	TRUE	1	0.334535109262469	2		629	1042	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41526001	41526001	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	231	522	0	ENST00000263253.7:c.1276C>G	p.Gln426Glu	p.Q426E	ENST00000263253	NM_001429.3	426	Caa/Gaa	5/31	0.294532130660235	2	FACETS	0.814	0.761	0.869	0.814	0.761	0.869	CLONAL	2	TRUE	0	0.334535109262469	2		522	848	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531867	41531867	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	306	642	0	ENST00000263253.7:c.1579C>G	p.Leu527Val	p.L527V	ENST00000263253	NM_001429.3	527	Ctt/Gtt	7/31	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.334535109262469	NA		642	1061	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556674	41556674	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	200	604	0	ENST00000263253.7:c.3619G>A	p.Glu1207Lys	p.E1207K	ENST00000263253	NM_001429.3	1207	Gag/Aag	20/31	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.334535109262469	NA		604	877	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499444	89499444	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	137	607	0	ENST00000336596.2:c.2614G>C	p.Glu872Gln	p.E872Q	ENST00000336596	NM_005233.5	872	Gag/Cag	15/17	1	2	FACETS	0.881	0.8	0.965	0.881	0.8	0.965	CLONAL	1	TRUE	1	0.334535109262469	2		607	930	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652324	36652324	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0017472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	110	543	0	ENST00000244741.5:c.445+1G>T		p.X149_splice	ENST00000244741	NM_000389.4	149			1	2	FACETS	0.744	0.668	0.825	0.744	0.668	0.825	SUBCLONAL	1	TRUE	1	0.334535109262469	2		543	884	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135804167	135804167	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	136	464	0	ENST00000298552.3:c.93G>C	p.Glu31Asp	p.E31D	ENST00000298552	NM_001162426.1	31	gaG/gaC	3/23	1	2	FACETS	0.982	0.893	1	0.982	0.893	1	CLONAL	1	TRUE	1	0.334535109262469	2		464	828	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184635	185184635	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	112	501	0	ENST00000265026.3:c.1527G>C	p.Lys509Asn	p.K509N	ENST00000265026	NM_004721.4	509	aaG/aaC	10/14	1	2	FACETS	0.864	0.777	0.956	0.864	0.777	0.956	CLONAL	1	TRUE	1	0.334535109262469	2		501	775	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609656	28609656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	232	662	0	ENST00000241453.7:c.1573G>A	p.Glu525Lys	p.E525K	ENST00000241453	NM_004119.2	525	Gag/Aag	12/24	0.249679171979829	3	FACETS	0.794	0.741	0.85	0.794	0.741	0.85	SUBCLONAL	2	TRUE	1	0.334535109262469	3		662	1019	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18649003	18649003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	79	492	0	ENST00000266497.5:c.2678C>T	p.Ser893Leu	p.S893L	ENST00000266497		893	tCa/tTa	19/31	1	2	FACETS	0.75	0.66	0.846	0.75	0.66	0.846	SUBCLONAL	1	TRUE	1	0.334535109262469	2		492	630	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112884087	112884087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	102	484	0	ENST00000351677.2:c.22C>T	p.His8Tyr	p.H8Y	ENST00000351677	NM_002834.3	8	Cac/Tac	2/16	1	2	FACETS	0.785	0.702	0.873	0.785	0.702	0.873	SUBCLONAL	1	TRUE	1	0.334535109262469	2		484	777	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891015	112891015	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	87	341	0	ENST00000351677.2:c.349C>G	p.Leu117Val	p.L117V	ENST00000351677	NM_002834.3	117	Ctc/Gtc	4/16	1	2	FACETS	0.985	0.874	1	0.985	0.874	1	CLONAL	1	TRUE	1	0.334535109262469	2		341	528	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569715	95569715	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	66	250	0	ENST00000393063.1:c.4018G>A	p.Glu1340Lys	p.E1340K	ENST00000393063	NM_030621.3	1340	Gag/Aag	22/28	1	2	FACETS	0.974	0.849	1	0.974	0.849	1	CLONAL	1	TRUE	1	0.334535109262469	2		250	405	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268968	55268968	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	187	768	1	ENST00000275493.2:c.3034G>T	p.Asp1012Tyr	p.D1012Y	ENST00000275493	NM_005228.3	1012	Gat/Tat	25/28	1	2	FACETS	0.91	0.839	0.985	0.91	0.839	0.985	CLONAL	1	TRUE	1	0.334535109262469	2		769	1228	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268975	55268975	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	180	760	0	ENST00000275493.2:c.3041A>C	p.Asp1014Ala	p.D1014A	ENST00000275493	NM_005228.3	1014	gAc/gCc	25/28	1	2	FACETS	0.891	0.82	0.965	0.891	0.82	0.965	CLONAL	1	TRUE	1	0.334535109262469	2		760	1208	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98241284	98241284	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	146	542	0	ENST00000331920.6:c.1213G>T	p.Glu405Ter	p.E405*	ENST00000331920	NM_000264.3	405	Gag/Tag	8/24	1	2	FACETS	0.96	0.876	1	0.96	0.876	1	CLONAL	1	TRUE	1	0.334535109262469	2		542	909	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305399	65305399	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017698-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	188	486	0	ENST00000342505.4:c.2729T>C	p.Leu910Pro	p.L910P	ENST00000342505	NM_002227.2	910	cTg/cCg	20/25	1	2	FACETS	0.879	0.82	0.939	0.879	0.82	0.939	CLONAL	1	TRUE	1	0.86963982619576	2		486	492	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274911	41274911	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017698-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	142	346	0	ENST00000349496.5:c.1161T>G	p.Asn387Lys	p.N387K	ENST00000349496	NM_001904.3	387	aaT/aaG	8/15	1	2	FACETS	0.848	0.782	0.916	0.848	0.782	0.916	CLONAL	1	TRUE	1	0.86963982619576	2		346	385	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106426	27106426	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017698-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	193	445	0	ENST00000324856.7:c.6038del	p.Lys2013SerfsTer2	p.K2013Sfs*2	ENST00000324856	NM_006015.4	2013	Aag/ag	20/20	1	2	FACETS	0.8	0.745	0.856	0.8	0.745	0.856	SUBCLONAL	1	TRUE	1	0.86963982619576	2		445	555	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266107	41266107	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017698-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	114	295	0	ENST00000349496.5:c.104T>A	p.Ile35Asn	p.I35N	ENST00000349496	NM_001904.3	35	aTc/aAc	3/15	1	2	FACETS	0.799	0.729	0.872	0.799	0.729	0.872	SUBCLONAL	1	TRUE	1	0.86963982619576	2		295	328	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989651	68989651	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017698-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	261	432	0	ENST00000288368.4:c.1589A>G	p.Glu530Gly	p.E530G	ENST00000288368	NM_024870.2	530	gAa/gGa	15/40	0.86963982619576	6	FACETS	1	0.99	1	0.257	0.24	0.274	CLONAL	1	TRUE	1	0.86963982619576	6		432	1280	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0017892-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	267	627	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	0.411092796603235	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.411092796603235	1		627	791	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711887	89711887	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776673	NA	P-0017892-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	139	395	0	ENST00000371953.3:c.507del	p.Ser170ValfsTer13	p.S170Vfs*13	ENST00000371953	NM_000314.4	169	Ccc/cc	6/9	0.411092796603235	1	FACETS	0.92	0.841	1	0.92	0.841	1	CLONAL	1	TRUE	0	0.411092796603235	1		395	584	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0017892-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	135	457	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	0.255694612541862	3	FACETS	0.883	0.802	0.968	0.441	0.401	0.484	CLONAL	1	TRUE	1	0.411092796603235	3		457	897	SUCCESS
ATM	472	MSKCC	GRCh37	11	108159786	108159786	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0017892-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	43	260	0	ENST00000278616.4:c.4192A>T	p.Lys1398Ter	p.K1398*	ENST00000278616	NM_000051.3	1398	Aaa/Taa	28/63	0.201053794812746	1	FACETS	0.388	0.325	0.458	0.388	0.325	0.458	INDETERMINATE	1	TRUE	0	0.411092796603235	1		260	428	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555721	21555721	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017892-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	250	621	0	ENST00000382592.4:c.2549G>T	p.Cys850Phe	p.C850F	ENST00000382592	NM_014572.2	850	tGt/tTt	6/8	0.411092796603235	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.411092796603235	1		621	822	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44911044	44911045	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TAGGTATGTACACAATTATGTG	novel	NA	P-0017892-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	39	202	0	ENST00000377967.4:c.748+7_748+8insCACAATTATGTGTAGGTATGTA		p.L249fs	ENST00000377967	NM_021140.2	249	tta/tTAGGTATGTACACAATTATGTGta	9/29	1	1	FACETS	0.431	0.358	0.512	0.431	0.358	0.512	SUBCLONAL	1	TRUE	0	0.411092796603235	1		202	350	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115873	8115874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0018046-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	290	489	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	0.524372049253069	2		489	1047	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115873	8115874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0018046-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	87	489	0	ENST00000346208.3:c.1220dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tCcg	6/6	1	2	FACETS	0.904	0.801	1	0.904	0.801	1	CLONAL	1	TRUE	1	0.327978444945283	2		489	587	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0018052-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	189	279	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.451803853099182	2		279	663	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115719	8115720	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0018052-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	245	372	0	ENST00000346208.3:c.1066_1067del	p.Met356GlufsTer14	p.M356Efs*14	ENST00000346208		355	acTAtg/actg	6/6	NA	2	FACETS	0.759	0.713	0.807			1	INDETERMINATE	2	TRUE	NA	0.451803853099182	2		372	714	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070644	67070645	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018052-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	150	227	0	ENST00000412916.2:c.268_269insT	p.Arg90MetfsTer26	p.R90Mfs*26	ENST00000412916		90	aga/aTga	3/6	0.32992998111581	0	FACETS	0.535	0.497	0.574			1	SUBCLONAL	2	TRUE	0	0.451803853099182	0		227	340	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	233	436	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.69715023264809	2	FACETS	0.944	0.902	0.986	0.944	0.902	0.986	CLONAL	2	TRUE	0	0.713179835045107	2		437	346	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0018064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	113	439	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.943	0.859	1	0.943	0.859	1	CLONAL	1	TRUE	1	0.713179835045107	2		439	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0018064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	548	640	0	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	0.704178309256567	2	FACETS	0.99	0.962	1	0.99	0.962	1	CLONAL	2	TRUE	0	0.713179835045107	2		640	776	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293262	91293262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	130	489	1	ENST00000355112.3:c.764G>A	p.Ser255Asn	p.S255N	ENST00000355112	NM_000057.2	255	aGt/aAt	3/22	0.569307101864015	3	FACETS	1	0.982	1	0.641	0.587	0.696	CLONAL	1	TRUE	1	0.713179835045107	3		490	386	SUCCESS
APC	324	MSKCC	GRCh37	5	112175770	112175771	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0018064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	83	348	0	ENST00000257430.4:c.4479_4480del	p.Glu1494LysfsTer19	p.E1494Kfs*19	ENST00000257430	NM_000038.5	1493	acGGaa/acaa	16/16	1	2	FACETS	0.902	0.808	1	0.902	0.808	1	CLONAL	1	TRUE	1	0.713179835045107	2		348	258	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038209	30038209	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	46	560	0	ENST00000338641.4:c.382G>T	p.Asp128Tyr	p.D128Y	ENST00000338641	NM_000268.3	128	Gat/Tat	4/16	1	2	FACETS	0.194	0.163	0.229	0.194	0.163	0.229	SUBCLONAL	1	TRUE	1	0.713179835045107	2		560	664	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066641	94066641	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs772199348	NA	P-0018064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	118	564	0	ENST00000369303.4:c.1118G>T	p.Ser373Ile	p.S373I	ENST00000369303	NM_004440.3	373	aGt/aTt	5/17	0.713179835045107	3	FACETS	0.747	0.676	0.822	0.373	0.338	0.411	SUBCLONAL	1	TRUE	1	0.713179835045107	3		564	601	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444245	50444245	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	19	299	0	ENST00000331340.3:c.175G>C	p.Val59Leu	p.V59L	ENST00000331340	NM_006060.4	59	Gta/Cta	4/8	0.314159271724768	4	FACETS	0.291	0.22	0.374	0.073	0.055	0.094	INDETERMINATE	1	TRUE	0	0.713179835045107	4		299	314	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0018106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	86	974	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.856	0.758	0.96	0.856	0.758	0.96	CLONAL	1	TRUE	1	0.326809237364876	2		974	615	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429978	78429978	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	73	482	2	ENST00000370768.2:c.901del	p.Ile301TyrfsTer22	p.I301Yfs*22	ENST00000370768	NM_003902.3	301	Ata/ta	11/20	1	2	FACETS	0.853	0.747	0.966	0.853	0.747	0.966	CLONAL	1	TRUE	1	0.326809237364876	2		484	524	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	137	371	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.832	0.761	0.905	1	0.989	1	CLONAL	2	TRUE	1	0.326809237364876	2		371	504	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0018106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	113	429	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.982	0.885	1	0.982	0.885	1	CLONAL	1	TRUE	1	0.326809237364876	2		429	704	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0018106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	133	854	0	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	1	2	FACETS	0.964	0.876	1	0.964	0.876	1	CLONAL	1	TRUE	1	0.326809237364876	2		854	844	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696802	176696802	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	59	208	2	ENST00000439151.2:c.5508del	p.Ala1837LeufsTer12	p.A1837Lfs*12	ENST00000439151	NM_022455.4	1835	Aaa/aa	16/23	1	2	FACETS	0.923	0.798	1	0.923	0.798	1	CLONAL	1	TRUE	1	0.326809237364876	2		210	391	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0018106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	51	294	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.575	0.488	0.67	0.575	0.488	0.67	SUBCLONAL	1	TRUE	1	0.326809237364876	2		294	543	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	76	267	0	ENST00000397062.3:c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	NM_006164.4	34	Cga/Gga	2/5	1	2	FACETS	0.955	0.84	1	0.955	0.84	1	CLONAL	1	TRUE	1	0.326809237364876	2		267	487	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796883	42796883	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	188	773	2	ENST00000575354.2:c.3347del	p.Pro1116GlnfsTer45	p.P1116Qfs*45	ENST00000575354	NM_015125.3	1114	gCc/gc	14/20	1	2	FACETS	0.95	0.876	1	0.95	0.876	1	CLONAL	1	TRUE	1	0.326809237364876	2		775	1211	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830902	72830903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0018106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	95	474	0	ENST00000268489.5:c.5677_5678dup	p.Asp1894GlyfsTer21	p.D1894Gfs*21	ENST00000268489	NM_006885.3	1893	agg/agAGg	9/10	1	2	FACETS	0.855	0.762	0.954	0.855	0.762	0.954	CLONAL	1	TRUE	1	0.326809237364876	2		474	680	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0018106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	91	439	0	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	0.987	0.879	1	0.987	0.879	1	CLONAL	1	TRUE	1	0.326809237364876	2		439	564	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572404	41572404	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs139310551	NA	P-0018106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	143	597	0	ENST00000263253.7:c.4933C>T	p.Arg1645Ter	p.R1645*	ENST00000263253	NM_001429.3	1645	Cga/Tga	30/31	1	2	FACETS	0.942	0.858	1	0.942	0.858	1	CLONAL	1	TRUE	1	0.326809237364876	2		597	929	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998483	100998483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	57	422	1	ENST00000325455.5:c.1319C>T	p.Thr440Met	p.T440M	ENST00000325455	NM_001202474.3	440	aCg/aTg	1/8	1	2	FACETS	0.55	0.472	0.636	0.55	0.472	0.636	SUBCLONAL	1	TRUE	1	0.326809237364876	2		423	634	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043349	6043349	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781716	NA	P-0018106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	72	196	0	ENST00000265849.7:c.325del	p.Glu109LysfsTer3	p.E109Kfs*3	ENST00000265849	NM_000535.5	109	Gaa/aa	4/15	0.326809237364876	1	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	0	0.326809237364876	1		196	365	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566524	41566525	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	102	461	3	ENST00000263253.7:c.4408dup	p.Met1470AsnfsTer3	p.M1470Nfs*3	ENST00000263253	NM_001429.3	1467	-/A	27/31	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.326809237364876	2		464	594	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	134	627	1	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	0.933	0.847	1	0.933	0.847	1	CLONAL	1	TRUE	1	0.326809237364876	2		628	879	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521525	46521525	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	104	420	1	ENST00000262741.5:c.883del	p.Met295Ter	p.M295*	ENST00000262741	NM_003629.3	295	Atg/tg	7/10	1	2	FACETS	0.886	0.794	0.984	0.886	0.794	0.984	CLONAL	1	TRUE	1	0.326809237364876	2		421	718	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780921	9780921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1297091785	NA	P-0018106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	142	618	1	ENST00000377346.4:c.1643G>A	p.Arg548Gln	p.R548Q	ENST00000377346	NM_005026.3	548	cGg/cAg	13/24	1	2	FACETS	0.952	0.867	1	0.952	0.867	1	CLONAL	1	TRUE	1	0.326809237364876	2		619	913	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845638	63845638	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	51	242	0	ENST00000279873.7:c.1379del	p.Lys460SerfsTer19	p.K460Sfs*19	ENST00000279873	NM_032199.2	459	ccA/cc	9/10	1	2	FACETS	0.857	0.732	0.995	0.857	0.732	0.995	CLONAL	1	TRUE	1	0.326809237364876	2		242	364	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456497	32456497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	68	179	0	ENST00000332351.3:c.395C>T	p.Pro132Leu	p.P132L	ENST00000332351	NM_024426.4	132	cCg/cTg	1/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.326809237364876	2		179	313	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418618	49418618	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	110	469	0	ENST00000301067.7:c.15896A>G	p.His5299Arg	p.H5299R	ENST00000301067	NM_003482.3	5299	cAt/cGt	49/54	1	2	FACETS	0.907	0.815	1	0.907	0.815	1	CLONAL	1	TRUE	1	0.326809237364876	2		469	742	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644826	67644826	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	114	419	0	ENST00000264010.4:c.95del	p.Gly32AlafsTer30	p.G32Afs*30	ENST00000264010	NM_006565.3	31	Ggg/gg	3/12	1	2	FACETS	0.872	0.785	0.964	0.872	0.785	0.964	CLONAL	1	TRUE	1	0.326809237364876	2		419	800	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936093	178936093	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913275	NA	P-0018106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	121	544	0	ENST00000263967.3:c.1635G>C	p.Glu545Asp	p.E545D	ENST00000263967	NM_006218.2	545	gaG/gaC	10/21	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.326809237364876	2		544	700	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590693	189590693	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	108	462	0	ENST00000264731.3:c.1258T>C	p.Ser420Pro	p.S420P	ENST00000264731	NM_003722.4	420	Tcc/Ccc	10/14	1	2	FACETS	0.899	0.807	0.997	0.899	0.807	0.997	CLONAL	1	TRUE	1	0.326809237364876	2		462	735	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38966741	38966741	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0018106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	54	188	0	ENST00000357387.3:c.1299+2T>C		p.X433_splice	ENST00000357387	NM_152756.3	433			1	2	FACETS	0.918	0.787	1	0.918	0.787	1	CLONAL	1	TRUE	1	0.326809237364876	2		188	360	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286921	33286921	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	125	524	0	ENST00000374542.5:c.2016del	p.Leu673TrpfsTer22	p.L673Wfs*22	ENST00000374542	NM_001141970.1	672	ccC/cc	7/8	1	2	FACETS	0.784	0.708	0.863	0.784	0.708	0.863	SUBCLONAL	1	TRUE	1	0.326809237364876	2		524	976	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223787	53223788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0018106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	178	875	0	ENST00000375401.3:c.3570_3571dup	p.Gly1191ValfsTer74	p.G1191Vfs*74	ENST00000375401	NM_004187.3	1191	ggg/gTGgg	23/26	1	2	FACETS	0.864	0.794	0.937	0.864	0.794	0.937	CLONAL	1	TRUE	1	0.326809237364876	2		875	1261	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431874	49431874	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	87	640	3	ENST00000301067.7:c.9265del	p.Val3089TrpfsTer30	p.V3089Wfs*30	ENST00000301067	NM_003482.3	3089	Gtg/tg	34/54	1	2	FACETS	0.545	0.481	0.613	0.545	0.481	0.613	SUBCLONAL	1	TRUE	1	0.326809237364876	2		643	977	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984846	55984846	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371800274	NA	P-0018106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	112	394	0	ENST00000263923.4:c.283G>A	p.Gly95Arg	p.G95R	ENST00000263923	NM_002253.2	95	Gga/Aga	3/30	1	2	FACETS	0.981	0.883	1	0.981	0.883	1	CLONAL	1	TRUE	1	0.326809237364876	2		394	699	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258894	16258894	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	163	675	4	ENST00000375759.3:c.6164del	p.Pro2055LeufsTer9	p.P2055Lfs*9	ENST00000375759	NM_015001.2	2053	aaC/aa	11/15	1	2	FACETS	0.941	0.863	1	0.941	0.863	1	CLONAL	1	TRUE	1	0.326809237364876	2		679	1060	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29662009	29662009	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	94	383	0	ENST00000356175.3:c.5903A>G	p.Tyr1968Cys	p.Y1968C	ENST00000356175	NM_000267.3	1968	tAc/tGc	39/57	1	2	FACETS	0.841	0.749	0.939	0.841	0.749	0.939	CLONAL	1	TRUE	1	0.326809237364876	2		383	684	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541144	187541144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374542025	NA	P-0018106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	84	297	0	ENST00000441802.2:c.6596G>A	p.Ser2199Asn	p.S2199N	ENST00000441802	NM_005245.3	2199	aGc/aAc	10/27	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.326809237364876	2		297	493	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549413	21549413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764574613	NA	P-0018287-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	268	358	0	ENST00000382592.4:c.2863G>A	p.Ala955Thr	p.A955T	ENST00000382592	NM_014572.2	955	Gca/Aca	8/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.816228781121995	2		358	627	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549413	21549413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764574613	NA	P-0018287-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	149	358	0	ENST00000382592.4:c.2863G>A	p.Ala955Thr	p.A955T	ENST00000382592	NM_014572.2	955	Gca/Aca	8/8	1	2	FACETS	0.971	0.896	1	0.971	0.896	1	CLONAL	1	TRUE	1	0.732698839377017	2		358	419	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987301	2987301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018287-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	227	427	1	ENST00000396946.4:c.128C>T	p.Thr43Met	p.T43M	ENST00000396946	NM_032415.4	43	aCg/aTg	3/25	0.536561412405005	3	FACETS	1	0.977	1	0.549	0.513	0.586	CLONAL	1	TRUE	1	0.732698839377017	3		428	771	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0018317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	76	226	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.245072344382607	2	FACETS	0.87	0.772	0.971	0.87	0.772	0.971	CLONAL	2	TRUE	0	0.330993018929968	2		227	264	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	155	292	0	ENST00000304494.5:c.322G>C	p.Asp108His	p.D108H	ENST00000304494	NM_000077.4	108	Gat/Cat	2/3	0.330993018929968	1	FACETS	1	0.975	1	1	0.994	1	CLONAL	3	TRUE	0	0.330993018929968	1		292	244	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578528	7578528	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	508	911	0	ENST00000269305.4:c.402T>G	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	ttT/ttG	5/11	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	3	TRUE	NA	0.330993018929968	2		911	969	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs863224451	NA	P-0018317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	177	675	0	ENST00000269305.4:c.824G>C	p.Cys275Ser	p.C275S	ENST00000269305	NM_001126112.2	275	tGt/tCt	8/11	NA	2	FACETS	0.796	0.736	0.858			1	INDETERMINATE	2	TRUE	NA	0.330993018929968	2		675	672	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938358	76938358	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	394	297	0	ENST00000373344.5:c.2390del	p.Ser797Ter	p.S797*	ENST00000373344	NM_000489.3	797	tCa/ta	9/35	0.283831893195938	2	FACETS	1	0.974	1			1	CLONAL	5	TRUE	NA	0.330993018929968	2		297	476	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100066	11100066	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	70	733	0	ENST00000358026.2:c.1192A>C	p.Thr398Pro	p.T398P	ENST00000358026	NM_001128849.1	398	Acc/Ccc	7/36	0.330993018929968	5	FACETS	0.679	0.591	0.775	0.226	0.197	0.259	SUBCLONAL	1	TRUE	2	0.330993018929968	5		733	932	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858913	243858913	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs866698621	NA	P-0018317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	199	451	0	ENST00000263826.5:c.152T>G	p.Leu51Arg	p.L51R	ENST00000263826	NM_005465.4	51	cTc/cGc	2/13	0.265059629212713	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.330993018929968	4		451	666	SUCCESS
ATM	472	MSKCC	GRCh37	11	108159819	108159819	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	90	128	0	ENST00000278616.4:c.4225T>C	p.Ser1409Pro	p.S1409P	ENST00000278616	NM_000051.3	1409	Tcc/Ccc	28/63	0.330993018929968	4	FACETS	1	0.93	1	1	0.984	1	CLONAL	3	TRUE	2	0.330993018929968	4		128	233	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307621	118307621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	47	484	0	ENST00000534358.1:c.394G>A	p.Val132Met	p.V132M	ENST00000534358	NM_005933.3	132	Gtg/Atg	1/36	0.330993018929968	4	FACETS	0.592	0.498	0.695	0.296	0.249	0.348	SUBCLONAL	1	TRUE	2	0.330993018929968	4		484	639	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444370	49444370	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	59	667	1	ENST00000301067.7:c.3001del	p.Leu1001PhefsTer16	p.L1001Ffs*16	ENST00000301067	NM_003482.3	1001	Ctt/tt	11/54	0.265059629212713	4	FACETS	0.649	0.557	0.749	0.325	0.278	0.375	SUBCLONAL	1	TRUE	2	0.330993018929968	4		668	731	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467218	99467218	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	44	354	0	ENST00000268035.6:c.2599A>C	p.Ile867Leu	p.I867L	ENST00000268035	NM_000875.3	867	Ata/Cta	12/21	0.277177323571043	3	FACETS	0.699	0.587	0.824	0.35	0.293	0.412	SUBCLONAL	1	TRUE	1	0.330993018929968	3		354	443	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341202	341202	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	58	784	0	ENST00000262320.3:c.2282T>C	p.Leu761Pro	p.L761P	ENST00000262320	NM_003502.3	761	cTc/cCc	9/11	0.256106571412861	3	FACETS	0.571	0.49	0.66			1	SUBCLONAL	1	TRUE	NA	0.330993018929968	3		784	715	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842444	68842444	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	51	605	0	ENST00000261769.5:c.506del	p.Gly169AlafsTer46	p.G169Afs*46	ENST00000261769	NM_004360.3	169	Ggc/gc	4/16	0.277177323571043	3	FACETS	0.478	0.405	0.559	0.239	0.202	0.28	SUBCLONAL	1	TRUE	1	0.330993018929968	3		605	751	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226581	1226581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1386678110	NA	P-0018317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	41	530	0	ENST00000326873.7:c.1237C>T	p.Pro413Ser	p.P413S	ENST00000326873	NM_000455.4	413	Cct/Tct	9/10	0.330993018929968	3	FACETS	0.522	0.434	0.62	0.261	0.217	0.31	SUBCLONAL	1	TRUE	1	0.330993018929968	3		530	553	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791349	42791349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771287929	NA	P-0018317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	56	749	0	ENST00000575354.2:c.409G>A	p.Glu137Lys	p.E137K	ENST00000575354	NM_015125.3	137	Gag/Aag	3/20	0.323909234039947	0	FACETS	0.625	0.538	0.72			1	SUBCLONAL	1	TRUE	0	0.330993018929968	0		749	362	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902883	1902883	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	61	649	0	ENST00000382891.5:c.502A>G	p.Asn168Asp	p.N168D	ENST00000382891	NM_133335.3	168	Aac/Gac	2/22	0.283831893195938	4	FACETS	0.562	0.483	0.648			1	SUBCLONAL	1	TRUE	NA	0.330993018929968	4		649	873	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630686	187630686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	75	609	1	ENST00000441802.2:c.296G>A	p.Arg99Lys	p.R99K	ENST00000441802	NM_005245.3	99	aGg/aAg	2/27	0.330993018929968	0	FACETS	0.652	0.573	0.736			1	SUBCLONAL	1	TRUE	0	0.330993018929968	0		610	465	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109319784	109319785	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0018317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	50	544	0	ENST00000436639.2:c.903dup	p.Ile302HisfsTer3	p.I302Hfs*3	ENST00000436639	NM_014454.2	301	-/C	5/10	0.330993018929968	3	FACETS	0.504	0.426	0.589	0.252	0.213	0.295	SUBCLONAL	1	TRUE	1	0.330993018929968	3		544	699	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109414990	109414996	+	splice_donor_variant,intron_variant	Splice_Site	DEL	TTCCTTA	TTCCTTA	GG	novel	NA	P-0018317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	37	405	0	ENST00000436639.2:c.279+2_279+8delinsCC		p.X93_splice	ENST00000436639	NM_014454.2	93			0.330993018929968	3	FACETS	0.454	0.373	0.544	0.227	0.186	0.272	SUBCLONAL	1	TRUE	1	0.330993018929968	3		405	574	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879471	151879471	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	44	357	0	ENST00000262189.6:c.5474T>C	p.Phe1825Ser	p.F1825S	ENST00000262189	NM_170606.2	1825	tTc/tCc	36/59	0.330993018929968	5	FACETS	0.685	0.574	0.808	0.171	0.143	0.202	SUBCLONAL	1	TRUE	1	0.330993018929968	5		357	581	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739710	145739710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776147492	NA	P-0018317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	58	633	0	ENST00000428558.2:c.1741C>T	p.Pro581Ser	p.P581S	ENST00000428558	NM_004260.3	581	Cct/Tct	11/22	0.23027892515818	4	FACETS	0.636	0.546	0.736	0.318	0.273	0.368	SUBCLONAL	1	TRUE	2	0.330993018929968	4		633	733	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295195	15295195	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	71	878	0	ENST00000263388.2:c.2477del	p.Cys826SerfsTer34	p.C826Sfs*34	ENST00000263388	NM_000435.2	826	tGc/tc	16/33	0.283831893195938	4	FACETS	0.56	0.487	0.64			1	SUBCLONAL	1	TRUE	NA	0.330993018929968	4		878	1019	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	45	436	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.767	0.643	0.904	0.767	0.643	0.904	CLONAL	1	TRUE	1	0.18	2		437	652	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0018417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	45	479	0	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	1	2	FACETS	0.799	0.67	0.941	0.799	0.67	0.941	CLONAL	1	TRUE	1	0.18	2		479	626	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039638	47039638	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1556778349	NA	P-0018417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	55	538	0	ENST00000377604.3:c.1090C>T	p.Gln364Ter	p.Q364*	ENST00000377604	NM_001204468.1	364	Cag/Tag	11/24	1	2	FACETS	0.959	0.82	1	0.959	0.82	1	CLONAL	1	TRUE	1	0.18	2		538	637	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971114	21971115	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0018417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	66	410	0	ENST00000304494.5:c.243dup	p.Val82ArgfsTer38	p.V82Rfs*38	ENST00000304494	NM_000077.4	81	-/C	2/3	1	2	FACETS	0.772	0.672	0.88	1	0.973	1	SUBCLONAL	2	TRUE	1	0.18	2		410	475	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0018583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	438	640	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	1	2	FACETS	0.885	0.846	0.925	0.885	0.846	0.925	CLONAL	1	TRUE	1	0.867622686145653	2		640	1141	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0018888-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	76	710	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	1	2	FACETS	0.837	0.734	0.949	0.837	0.734	0.949	CLONAL	1	FALSE	1	0.250741759843188	2		710	724	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0019124-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	133	615	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.166365934257628	3	FACETS	1	0.939	1	0.52	0.473	0.569	INDETERMINATE	1	TRUE	1	0.46	3		615	684	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0019124-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	193	580	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.150050188969981	4	FACETS	1	0.99	1	0.744	0.69	0.801	INDETERMINATE	1	TRUE	2	0.46	4		580	823	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436825	110436825	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019124-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	95	678	0	ENST00000375856.3:c.1576G>A	p.Glu526Lys	p.E526K	ENST00000375856	NM_003749.2	526	Gag/Aag	1/2	0.152159786700143	0	FACETS	0.348	0.31	0.388			1	INDETERMINATE	1	TRUE	0	0.46	0		678	641	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231817	36231817	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019124-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	280	640	0	ENST00000300305.3:c.567C>A	p.Tyr189Ter	p.Y189*	ENST00000300305		189	taC/taA	5/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.46	2		640	1096	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265312	16265313	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0019124-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	46	530	0	ENST00000375759.3:c.10805dup	p.Tyr3602Ter	p.Y3602*	ENST00000375759	NM_015001.2	3602	tac/tAac	14/15	0.3	3	FACETS	0.345	0.29	0.406	0.115	0.096	0.136	SUBCLONAL	1	TRUE	0	0.46	3		530	713	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835608	68835609	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0019124-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	144	477	0	ENST00000261769.5:c.201dup	p.Tyr68LeufsTer26	p.Y68Lfs*26	ENST00000261769	NM_004360.3	67	gcc/gCcc	3/16	0.23863106942117	0	FACETS	0.748	0.688	0.81			1	INDETERMINATE	1	TRUE	0	0.46	0		477	452	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272222	142272222	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019124-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	110	335	0	ENST00000350721.4:c.2652G>T	p.Leu884Phe	p.L884F	ENST00000350721	NM_001184.3	884	ttG/ttT	13/47	1	2	FACETS	0.854	0.77	0.943	0.854	0.77	0.943	CLONAL	1	TRUE	1	0.46	2		335	560	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0019179-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	122	558	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	0.367882601995787	2		558	613	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0019179-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	80	375	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.731	0.644	0.824	0.731	0.644	0.824	SUBCLONAL	1	TRUE	1	0.367882601995787	2		375	595	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469995	25470003	+	inframe_deletion	In_Frame_Del	DEL	CGAGCTCAG	CGAGCTCAG	-	novel	NA	P-0019179-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	181	957	0	ENST00000264709.3:c.1039_1047del	p.Leu347_Ser349del	p.L347_S349del	ENST00000264709	NM_175629.2	347	CTGAGCTCG/-	9/23	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.367882601995787	2		957	721	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231782	36231783	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0019179-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	239	1223	0	ENST00000300305.3:c.601dup	p.Arg201ProfsTer12	p.R201Pfs*12	ENST00000300305		201	cga/cCga	5/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.367882601995787	2		1223	1149	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508814	148508814	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0019179-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	209	578	0	ENST00000320356.2:c.1852-2A>G		p.X618_splice	ENST00000320356	NM_004456.4	618			NA	2	FACETS	0.913	0.853	0.975			1	INDETERMINATE	2	TRUE	NA	0.367882601995787	2		578	622	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	15	387	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.149	0.108	0.198	0.149	0.108	0.198	SUBCLONAL	1	TRUE	1	0.340615483400799	2		387	593	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001524	150001524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	152	557	0	ENST00000253339.5:c.2080C>T	p.Arg694Cys	p.R694C	ENST00000253339		694	Cgt/Tgt	4/7	0.340615483400799	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.340615483400799	1		557	669	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984774	11984774	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	122	482	0	ENST00000353533.5:c.322del	p.Ile108LeufsTer20	p.I108Lfs*20	ENST00000353533	NM_003010.3	107	gAa/ga	3/11	0.338498832733236	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.340615483400799	1		482	539	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039236	49039236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019246-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	232	588	1	ENST00000267163.4:c.2314G>A	p.Ala772Thr	p.A772T	ENST00000267163	NM_000321.2	772	Gct/Act	22/27	1	2	FACETS	0.917	0.86	0.975	0.917	0.86	0.975	CLONAL	1	TRUE	1	0.751982620123604	2		589	673	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610306	10610306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019246-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	327	964	1	ENST00000171111.5:c.404G>A	p.Arg135His	p.R135H	ENST00000171111	NM_203500.1	135	cGc/cAc	2/6	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.751982620123604	2		965	862	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442545	52442545	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019246-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	218	734	0	ENST00000460680.1:c.200del	p.Asp67ValfsTer5	p.D67Vfs*5	ENST00000460680	NM_004656.3	67	gAt/gt	4/17	0.751982620123604	1	FACETS	0.882	0.834	0.931	0.882	0.834	0.931	CLONAL	1	TRUE	0	0.751982620123604	1		734	410	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0019488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	103	470	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	0.83	0.746	0.919	0.83	0.746	0.919	CLONAL	1	TRUE	1	0.483795808901032	2		470	513	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061227	38061227	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	117	470	0	ENST00000250448.2:c.762C>G	p.Phe254Leu	p.F254L	ENST00000250448	NM_004496.3	254	ttC/ttG	2/2	1	2	FACETS	0.759	0.686	0.836	0.759	0.686	0.836	SUBCLONAL	1	TRUE	1	0.483795808901032	2		470	637	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115710	8115711	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0019488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	105	474	0	ENST00000346208.3:c.1060dup	p.Leu354ProfsTer17	p.L354Pfs*17	ENST00000346208		352	-/C	6/6	NA	2	FACETS	0.927	0.835	1			1	INDETERMINATE	1	TRUE	NA	0.483795808901032	2		474	468	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063389	67063389	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0019488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	122	403	0	ENST00000412916.2:c.78+1G>A		p.X26_splice	ENST00000412916		26			0.483795808901032	1	FACETS	0.991	0.904	1	0.991	0.904	1	CLONAL	1	TRUE	0	0.483795808901032	1		403	386	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650368	48650368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782208453	NA	P-0019488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	53	637	1	ENST00000376670.3:c.338G>A	p.Arg113His	p.R113H	ENST00000376670	NM_002049.3	113	cGc/cAc	3/6	0.44224755609776	3	FACETS	0.306	0.26	0.357	0.153	0.13	0.179	SUBCLONAL	1	TRUE	1	0.483795808901032	3		638	888	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913255	NA	P-0019543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	197	708	0	ENST00000369535.4:c.183A>C	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caC	3/7	0.220733964942511	4	FACETS	0.839	0.78	0.9	1	0.987	1	CLONAL	3	FALSE	2	0.296727919405858	4		708	684	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626694	28626694	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	84	598	0	ENST00000241453.7:c.602C>T	p.Ser201Leu	p.S201L	ENST00000241453	NM_004119.2	201	tCa/tTa	5/24	0.296727919405858	4	FACETS	1	0.959	1	0.397	0.351	0.447	CLONAL	1	FALSE	1	0.296727919405858	4		598	616	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652870	29652870	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	60	303	0	ENST00000356175.3:c.4805T>G	p.Leu1602Arg	p.L1602R	ENST00000356175	NM_000267.3	1602	cTg/cGg	36/57	0.220733964942511	4	FACETS	0.874	0.759	0.997	0.874	0.759	0.997	CLONAL	2	FALSE	2	0.296727919405858	4		303	300	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021577	31021581	+	frameshift_variant	Frame_Shift_Del	DEL	TCCTT	TCCTT	-	novel	NA	P-0019543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	137	610	0	ENST00000375687.4:c.1577_1581del	p.Ser526Ter	p.S526*	ENST00000375687	NM_015338.5	526	TCCTTt/t	12/13	0.220733964942511	4	FACETS	0.991	0.905	1	0.991	0.905	1	CLONAL	2	FALSE	2	0.296727919405858	4		610	604	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591083	67591084	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGACAAACGTATGAACAGCATTAAACCAGACCTTATCCA	novel	NA	P-0019543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	36	475	0	ENST00000274335.5:c.1677_1715dup	p.Ile571_Gln572insHisAspLysArgMetAsnSerIleLysProAspLeuIle	p.I571_Q572insHDKRMNSIKPDLI	ENST00000274335		559	att/atTGACAAACGTATGAACAGCATTAAACCAGACCTTATCCAt	12/15	0.220733964942511	4	FACETS	0.596	0.489	0.716	0.298	0.244	0.358	SUBCLONAL	1	FALSE	2	0.296727919405858	4		475	528	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023909	27023923	+	inframe_deletion	In_Frame_Del	DEL	GCTGCGGCGGCGGCA	GCTGCGGCGGCGGCA	-	rs751352361	NA	P-0019709-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	81	124	0	ENST00000324856.7:c.1029_1043del	p.Ala345_Ala349del	p.A345_A349del	ENST00000324856	NM_006015.4	339	GCTGCGGCGGCGGCA/-	1/20	0.898892034403726	3	FACETS	1	0.913	1	0.341	0.305	0.38	CLONAL	1	TRUE	0	0.898892034403726	3		124	255	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578217	7578217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019709-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	903	644	0	ENST00000269305.4:c.632C>T	p.Thr211Ile	p.T211I	ENST00000269305	NM_001126112.2	211	aCt/aTt	6/11	0.898892034403726	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.898892034403726	2		644	953	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106928	11106928	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0019709-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	869	713	1	ENST00000358026.2:c.1633A>T	p.Lys545Ter	p.K545*	ENST00000358026	NM_001128849.1	545	Aag/Tag	10/36	0.898892034403726	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.898892034403726	2		714	904	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790791	89790791	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019709-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	467	731	0	ENST00000336032.3:c.178T>G	p.Phe60Val	p.F60V	ENST00000336032	NM_006813.2	60	Ttc/Gtc	1/2	0.898892034403726	3	FACETS	0.975	0.93	1	0.487	0.465	0.51	CLONAL	1	TRUE	1	0.898892034403726	3		731	1545	SUCCESS
APC	324	MSKCC	GRCh37	5	112179360	112179360	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019709-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	271	359	0	ENST00000257430.4:c.8069C>A	p.Ala2690Glu	p.A2690E	ENST00000257430	NM_000038.5	2690	gCa/gAa	16/16	0.898892034403726	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.898892034403726	1		359	301	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	33	974	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.562	0.456	0.683	0.562	0.456	0.683	SUBCLONAL	1	TRUE	1	0.13	2		974	903	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0019728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	42	255	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	0.856	0.713	1	0.856	0.713	1	CLONAL	1	TRUE	1	0.13	2		255	755	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0019728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	68	758	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	1	2	FACETS	0.942	0.817	1	0.942	0.817	1	CLONAL	1	TRUE	1	0.13	2		758	1110	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0019736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	28	255	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.163314661433888	1	FACETS	0.89	0.71	1	0.89	0.71	1	CLONAL	1	TRUE	0	0.12	1		255	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs760043106	NA	P-0019736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	55	814	0	ENST00000269305.4:c.584T>G	p.Ile195Ser	p.I195S	ENST00000269305	NM_001126112.2	195	aTc/aGc	6/11	0.3	2	FACETS	1	0.945	1			1	CLONAL	1	TRUE	NA	0.12	2		814	741	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206595	108206595	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1431188311	NA	P-0019736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	27	525	0	ENST00000278616.4:c.8175T>A	p.Asp2725Glu	p.D2725E	ENST00000278616	NM_000051.3	2725	gaT/gaA	56/63	1	2	FACETS	0.84	0.666	1	0.84	0.666	1	CLONAL	1	TRUE	1	0.12	2		525	536	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380269	25380270	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCCTCTTGACCTGCTGTGTCG	novel	NA	P-0019736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	35	688	0	ENST00000311936.3:c.168_188dup	p.Glu62_Glu63insAspAspThrAlaGlyGlnGlu	p.E62_E63insDDTAGQE	ENST00000311936	NM_004985.3	63	gag/gaCGACACAGCAGGTCAAGAGGAg	3/5	1	2	FACETS	0.911	0.745	1	0.911	0.745	1	CLONAL	1	TRUE	1	0.12	2		688	640	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420660	49420660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	30	647	2	ENST00000301067.7:c.15089G>A	p.Arg5030His	p.R5030H	ENST00000301067	NM_003482.3	5030	cGt/cAt	48/54	1	2	FACETS	0.879	0.706	1	0.879	0.706	1	CLONAL	1	TRUE	1	0.12	2		649	569	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155088	108155090	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	novel	NA	P-0019854-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	668	451	0	ENST00000278616.4:c.3884_3886del	p.Leu1295del	p.L1295del	ENST00000278616	NM_000051.3	1294	aTTCtt/att	26/63	0.934362938596174	2	FACETS	0.977	0.962	0.99	0.977	0.962	0.99	CLONAL	2	TRUE	0	0.934362938596174	2		451	732	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	113	387	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.399817810251965	2		387	446	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0019945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	158	384	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	0.399817810251965	2		384	633	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182028	38182028	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	113	469	0	ENST00000396334.3:c.652T>G	p.Trp218Gly	p.W218G	ENST00000396334	NM_002468.4	218	Tgg/Ggg	3/5	0.399817810251965	1	FACETS	0.931	0.842	1	0.931	0.842	1	CLONAL	1	TRUE	0	0.399817810251965	1		469	486	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	19	553	0	ENST00000206249.3:c.1610A>G	p.Tyr537Cys	p.Y537C	ENST00000206249	NM_000125.3	537	tAt/tGt	8/8	1	2	FACETS	0.099	0.074	0.128	0.099	0.074	0.128	SUBCLONAL	1	TRUE	1	0.434741114153564	2		553	883	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879794	37879794	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	76	347	0	ENST00000269571.5:c.2089G>T	p.Val697Leu	p.V697L	ENST00000269571		697	Gtg/Ttg	18/27	1	2	FACETS	0.644	0.566	0.728	0.644	0.566	0.728	SUBCLONAL	1	TRUE	1	0.434741114153564	2		347	543	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099412	157099426	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAA	CAGCAGCAGCAGCAA	-	rs774668010	NA	P-0020030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	17	248	0	ENST00000346085.5:c.363_377del	p.Gln127_Gln131del	p.Q127_Q131del	ENST00000346085	NM_020732.3	117	CAGCAGCAGCAGCAA/-	1/20	1	2	FACETS	0.282	0.21	0.368	0.282	0.21	0.368	SUBCLONAL	1	TRUE	1	0.434741114153564	2		248	277	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070599	67070599	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	56	328	0	ENST00000412916.2:c.223G>T	p.Gly75Ter	p.G75*	ENST00000412916		75	Gga/Tga	3/6	0.380862687787339	1	FACETS	0.443	0.38	0.512	0.443	0.38	0.512	SUBCLONAL	1	TRUE	0	0.434741114153564	1		328	455	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874908	151874908	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	84	373	0	ENST00000262189.6:c.7630C>T	p.Gln2544Ter	p.Q2544*	ENST00000262189	NM_170606.2	2544	Cag/Tag	38/59	1	2	FACETS	0.658	0.582	0.74	0.658	0.582	0.74	SUBCLONAL	1	TRUE	1	0.434741114153564	2		373	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0020038-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	153	754	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.250417011939179	2		754	972	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213912	36213912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020038-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	130	754	1	ENST00000222270.7:c.2738C>T	p.Ser913Phe	p.S913F	ENST00000222270	NM_014727.1	913	tCc/tTc	6/37	0.129059928741079	3	FACETS	1	0.938	1	0.524	0.474	0.577	INDETERMINATE	1	FALSE	1	0.250417011939179	3		755	1115	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0020076-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	92	1128	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.3	3	FACETS	0.939	0.832	1	0.469	0.416	0.527	CLONAL	1	TRUE	1	0.22	3		1128	989	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636057	28636057	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020076-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	87	776	0	ENST00000241453.7:c.315G>C	p.Trp105Cys	p.W105C	ENST00000241453	NM_004119.2	105	tgG/tgC	3/24	1	2	FACETS	0.963	0.852	1	0.963	0.852	1	CLONAL	1	TRUE	1	0.22	2		776	821	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519988	NA	P-0020076-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	78	853	0	ENST00000269305.4:c.808T>A	p.Phe270Ile	p.F270I	ENST00000269305	NM_001126112.2	270	Ttt/Att	8/11	NA	2	FACETS	0.829	0.727	0.939			1	INDETERMINATE	1	TRUE	NA	0.22	2		853	855	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209457	98209457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753535745	NA	P-0020080-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	185	537	0	ENST00000331920.6:c.4081G>A	p.Val1361Met	p.V1361M	ENST00000331920	NM_000264.3	1361	Gtg/Atg	23/24	0.316865527546153	3	FACETS	0.885	0.825	0.946	0.885	0.825	0.946	INDETERMINATE	2	TRUE	1	0.562400492312877	3		537	476	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115701	8115704	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GATT	GATT	-	novel	NA	P-0020091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	72	244	0	ENST00000346208.3:c.1048-1_1050del		p.X350_splice	ENST00000346208		350		6/6	1	2	FACETS	0.722	0.634	0.815	0.722	0.634	0.815	SUBCLONAL	1	TRUE	1	0.533341559311264	2		244	374	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171657	36171657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	114	309	1	ENST00000300305.3:c.908C>A	p.Ser303Ter	p.S303*	ENST00000300305		303	tCa/tAa	7/8	1	2	FACETS	0.671	0.605	0.74	0.671	0.605	0.74	SUBCLONAL	1	TRUE	1	0.533341559311264	2		310	637	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0020138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	20	609	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.22014997711209	1	FACETS	0.223	0.169	0.286	0.223	0.169	0.286	SUBCLONAL	1	TRUE	0	0.22014997711209	1		610	725	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0020138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	75	398	0	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.22014997711209	2		398	549	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691003	NA	P-0020138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	38	828	0	ENST00000269305.4:c.96+1G>T		p.X32_splice	ENST00000269305	NM_001126112.2	32			0.22014997711209	1	FACETS	0.511	0.422	0.612	0.511	0.422	0.612	SUBCLONAL	1	TRUE	0	0.22014997711209	1		828	601	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14015940	14015940	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	36	679	3	ENST00000311895.7:c.260G>T	p.Arg87Leu	p.R87L	ENST00000311895	NM_005236.2	87	cGt/cTt	2/11	1	2	FACETS	0.705	0.579	0.846	0.705	0.579	0.846	SUBCLONAL	1	TRUE	1	0.22014997711209	2		682	464	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504915	186504915	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0020138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	44	517	0	ENST00000323963.5:c.772del		p.X258_splice	ENST00000323963		258			1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.22014997711209	2		517	391	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971006	21971006	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	60	811	0	ENST00000304494.5:c.352G>C	p.Ala118Pro	p.A118P	ENST00000304494	NM_000077.4	118	Gct/Cct	2/3	1				0.745	0.996				CLONAL	1	TRUE	1	0.22014997711209	2		811	630	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020223-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	224	524	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	0.197025605651037	3	FACETS	0.759	0.708	0.811	0.759	0.708	0.811	INDETERMINATE	2	TRUE	1	0.428758808135085	3		524	836	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740713	58740713	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs751126916	NA	P-0020223-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	214	501	0	ENST00000305921.3:c.1618G>T	p.Glu540Ter	p.E540*	ENST00000305921	NM_003620.3	540	Gag/Tag	6/6	0.428758808135085	6	FACETS	0.813	0.754	0.873			1	CLONAL	2	TRUE	NA	0.428758808135085	6		501	1141	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789627	3789627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201186078	NA	P-0020223-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	139	463	0	ENST00000262367.5:c.4232G>A	p.Gly1411Glu	p.G1411E	ENST00000262367	NM_004380.2	1411	gGa/gAa	25/31	0.429387299122368	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.428758808135085	1		463	412	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179385	56179386	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020241-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	100	325	0	ENST00000399503.3:c.3702dup	p.Gln1235ThrfsTer4	p.Q1235Tfs*4	ENST00000399503	NM_005921.1	1233	gca/gcAa	15/20	0.125416522096836	4	FACETS	1	0.973	1	0.631	0.566	0.699	INDETERMINATE	1	TRUE	2	0.499338799125689	4		325	476	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179459	56179460	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0020241-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	176	459	0	ENST00000399503.3:c.3773dup	p.Tyr1258Ter	p.Y1258*	ENST00000399503	NM_005921.1	1258	tat/tAat	15/20	0.125416522096836	4	FACETS	0.773	0.714	0.833	0.773	0.714	0.833	INDETERMINATE	2	TRUE	2	0.499338799125689	4		459	684	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0020290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	73	565	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.148883852305051	2	FACETS	0.914	0.797	1	0.457	0.398	0.521	CLONAL	1	TRUE	0	0.166038776722579	2		565	962	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602493	10602493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	89	716	0	ENST00000171111.5:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000171111	NM_203500.1	362	cGg/cAg	3/6	0.166038776722579	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.166038776722579	1		716	866	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578448	7578448	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1064795691	NA	P-0020290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	187	847	1	ENST00000269305.4:c.482C>A	p.Ala161Asp	p.A161D	ENST00000269305	NM_001126112.2	161	gCc/gAc	5/11	0.166038776722579	2	FACETS	0.985	0.909	1	0.985	0.909	1	CLONAL	2	TRUE	0	0.166038776722579	2		848	1143	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30061031	30061031	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0020290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	112	820	0	ENST00000338641.4:c.863C>G	p.Ser288Ter	p.S288*	ENST00000338641	NM_000268.3	288	tCa/tGa	9/16	0.166038776722579	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.166038776722579	1		820	1074	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141534	11141534	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	119	814	0	ENST00000358026.2:c.3511G>A	p.Val1171Met	p.V1171M	ENST00000358026	NM_001128849.1	1171	Gtg/Atg	25/36	0.166038776722579	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.166038776722579	1		814	1052	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040945	47040945	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1447493714	NA	P-0020290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	134	990	1	ENST00000377604.3:c.1475C>T	p.Ser492Leu	p.S492L	ENST00000377604	NM_001204468.1	492	tCg/tTg	14/24	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.166038776722579	2		991	1232	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77070038	77070038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777870573	NA	P-0020290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	48	746	0	ENST00000356341.3:c.502C>T	p.Pro168Ser	p.P168S	ENST00000356341	NM_002576.4	168	Cct/Tct	6/15	1	2	FACETS	0.676	0.57	0.794	0.676	0.57	0.794	SUBCLONAL	1	TRUE	1	0.166038776722579	2		746	855	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973622	15973622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	90	649	1	ENST00000268712.3:c.4370C>T	p.Ser1457Phe	p.S1457F	ENST00000268712	NM_006311.3	1457	tCc/tTc	31/46	0.166038776722579	2	FACETS	1	0.972	1	0.658	0.583	0.738	CLONAL	1	TRUE	0	0.166038776722579	2		650	824	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597494	10597494	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	107	637	0	ENST00000171111.5:c.1709G>C	p.Gly570Ala	p.G570A	ENST00000171111	NM_203500.1	570	gGa/gCa	6/6	0.166038776722579	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.166038776722579	1		637	896	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600000	10600000	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	115	904	0	ENST00000171111.5:c.1576G>C	p.Asp526His	p.D526H	ENST00000171111	NM_203500.1	526	Gat/Cat	5/6	0.166038776722579	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.166038776722579	1		904	1133	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663064	227663064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	52	644	1	ENST00000305123.5:c.391G>A	p.Gly131Ser	p.G131S	ENST00000305123	NM_005544.2	131	Ggt/Agt	1/2	1	2	FACETS	0.733	0.622	0.855	0.733	0.622	0.855	SUBCLONAL	1	TRUE	1	0.166038776722579	2		645	855	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589569	67589610	+	inframe_deletion	In_Frame_Del	DEL	TGTAGGGAAAAAATTACATGAATATAACACTCAGTTTCAAGA	TGTAGGGAAAAAATTACATGAATATAACACTCAGTTTCAAGA	-	novel	NA	P-0020290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	89	495	0	ENST00000274335.5:c.1332_1373del	p.Val445_Glu458del	p.V445_E458del	ENST00000274335		444	gcTGTAGGGAAAAAATTACATGAATATAACACTCAGTTTCAAGAa/gca	10/15	0.166038776722579	2	FACETS	0.873	0.775	0.977	0.873	0.775	0.977	CLONAL	2	TRUE	0	0.166038776722579	2		495	614	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518025	8518025	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	122	639	0	ENST00000356435.5:c.1366A>G	p.Thr456Ala	p.T456A	ENST00000356435		456	Aca/Gca	10/35	0.148883852305051	2	FACETS	0.82	0.741	0.904	0.82	0.741	0.904	CLONAL	2	TRUE	0	0.166038776722579	2		639	896	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759875	133759875	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	180	826	1	ENST00000318560.5:c.2198C>T	p.Ser733Leu	p.S733L	ENST00000318560	NM_005157.4	733	tCa/tTa	11/11	0.148883852305051	2	FACETS	0.931	0.857	1	0.931	0.857	1	CLONAL	2	TRUE	0	0.166038776722579	2		827	1165	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858152	40858152	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020324-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	237	574	0	ENST00000428826.2:c.1712A>G	p.Gln571Arg	p.Q571R	ENST00000428826		571	cAa/cGa	16/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		574	1062	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020344-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	70	307	0	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	1	2	FACETS	0.536	0.466	0.612	0.536	0.466	0.612	SUBCLONAL	1	TRUE	1	0.324011372356994	2		307	806	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855991	68855992	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATTCTTCTGTGAGAGGA	novel	NA	P-0020344-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	103	691	0	ENST00000261769.5:c.1802_1818dup	p.Pro607SerfsTer12	p.P607Sfs*12	ENST00000261769	NM_004360.3	600	ata/atATTCTTCTGTGAGAGGAa	12/16	0.324011372356994	1	FACETS	0.843	0.756	0.935	0.843	0.756	0.935	CLONAL	1	TRUE	0	0.324011372356994	1		691	632	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0020428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	114	669	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.26096589769531	1	FACETS	0.938	0.844	1	0.938	0.844	1	CLONAL	1	TRUE	0	0.267013936041475	1		669	789	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840564	36840564	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771002648	NA	P-0020428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	133	828	1	ENST00000358127.4:c.1169G>A	p.Arg390His	p.R390H	ENST00000358127	NM_001280556.1	390	cGt/cAt	10/10	1	2	FACETS	0.992	0.9	1	0.992	0.9	1	CLONAL	1	TRUE	1	0.267013936041475	2		829	1004	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416304	29416304	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	112	729	0	ENST00000389048.3:c.4649T>A	p.Leu1550His	p.L1550H	ENST00000389048	NM_004304.4	1550	cTt/cAt	29/29	NA	2	FACETS	0.907	0.815	1			1	INDETERMINATE	1	TRUE	NA	0.267013936041475	2		729	925	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	280	770	0	ENST00000397752.3:c.3028G>T	p.Asp1010Tyr	p.D1010Y	ENST00000397752	NM_000245.2	1010	Gat/Tat	14/21	0.312175020755895	3	FACETS	0.793	0.744	0.844	0.793	0.744	0.844	SUBCLONAL	2	TRUE	1	0.312175020755895	3		770	1307	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155548	106155549	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	90	457	0	ENST00000380013.4:c.450dup	p.Val151CysfsTer11	p.V151Cfs*11	ENST00000380013	NM_001127208.2	150	tct/tcTt	3/11	0.312175020755895	6	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.312175020755895	6		457	662	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675414	30675414	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	37	501	0	ENST00000376406.3:c.2942C>T	p.Ser981Leu	p.S981L	ENST00000376406	NM_014641.2	981	tCa/tTa	8/15	0.312175020755895	3	FACETS	0.753	0.622	0.899	0.376	0.311	0.45	SUBCLONAL	1	TRUE	1	0.312175020755895	3		501	364	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040962	47040963	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0020513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	40	644	0	ENST00000377604.3:c.1495_1496del	p.Ala499ProfsTer18	p.A499Pfs*18	ENST00000377604	NM_001204468.1	498	CGc/c	14/24	1	2	FACETS	0.588	0.489	0.698	0.588	0.489	0.698	SUBCLONAL	1	TRUE	1	0.312175020755895	2		644	436	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907692	111907693	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0020513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	63	433	0	ENST00000393256.3:c.466_467delinsTT	p.Gly156Leu	p.G156L	ENST00000393256	NM_006538.4	156	GGa/TTa	3/4	0.163032860917231	3	FACETS	0.982	0.851	1	0.491	0.425	0.562	INDETERMINATE	1	TRUE	1	0.312175020755895	3		433	475	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100436	8100436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1220437638	NA	P-0020545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	72	530	1	ENST00000346208.3:c.410C>T	p.Ser137Leu	p.S137L	ENST00000346208		137	tCg/tTg	3/6	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.31327184032193	2		531	419	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115416	115115416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	87	446	0	ENST00000257566.3:c.910C>T	p.Arg304Trp	p.R304W	ENST00000257566	NM_016569.3	304	Cgg/Tgg	5/8	1	2	FACETS	0.978	0.867	1	0.978	0.867	1	CLONAL	1	TRUE	1	0.31327184032193	2		446	568	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627748	37627748	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	94	513	0	ENST00000447079.4:c.1663C>T	p.Pro555Ser	p.P555S	ENST00000447079	NM_015083.1	555	Cct/Tct	2/14	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.31327184032193	2		513	575	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176494	123176494	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	35	376	0	ENST00000218089.9:c.461A>T	p.Glu154Val	p.E154V	ENST00000218089	NM_001042749.1	154	gAg/gTg	7/35	1	2	FACETS	0.681	0.56	0.817	0.681	0.56	0.817	SUBCLONAL	1	TRUE	1	0.31327184032193	2		376	328	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253850	30253850	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751979681	NA	P-0020545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	29	353	0	ENST00000307677.4:c.604G>A	p.Glu202Lys	p.E202K	ENST00000307677	NM_138578.1	202	Gag/Aag	3/3	1	2	FACETS	0.422	0.338	0.517	0.422	0.338	0.517	SUBCLONAL	1	TRUE	1	0.31327184032193	2		353	439	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176494	123176494	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020545-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	85	376	0	ENST00000218089.9:c.461A>T	p.Glu154Val	p.E154V	ENST00000218089	NM_001042749.1	154	gAg/gTg	7/35	1	2	FACETS	0.866	0.77	0.968	0.866	0.77	0.968	CLONAL	1	TRUE	1	0.467276868992288	2		376	420	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111543	8111545	+	inframe_deletion	In_Frame_Del	DEL	CTA	CTA	-	novel	NA	P-0020545-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	126	531	0	ENST00000346208.3:c.1033_1035del	p.Tyr345del	p.Y345del	ENST00000346208		343	ctCTAc/ctc	5/6	1	2	FACETS	0.888	0.807	0.974	0.888	0.807	0.974	CLONAL	1	TRUE	1	0.467276868992288	2		531	607	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115865	8115866	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020545-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	125	564	0	ENST00000346208.3:c.1213dup	p.His405ProfsTer102	p.H405Pfs*102	ENST00000346208		404	agc/agCc	6/6	1	2	FACETS	0.864	0.784	0.948	0.864	0.784	0.948	CLONAL	1	TRUE	1	0.467276868992288	2		564	619	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285249	212285249	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	372	668	1	ENST00000342788.4:c.3052G>T	p.Asp1018Tyr	p.D1018Y	ENST00000342788	NM_005235.2	1018	Gat/Tat	25/28	0.305761147939045	4	FACETS	0.976	0.928	1	0.976	0.928	1	CLONAL	3	TRUE	1	0.305761147939045	4		669	1085	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602473	10602473	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	119	671	0	ENST00000171111.5:c.1105G>T	p.Val369Leu	p.V369L	ENST00000171111	NM_203500.1	369	Gtg/Ttg	3/6	0.305761147939045	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.305761147939045	1		671	594	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81891885	81891885	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	87	560	0	ENST00000359376.3:c.355G>T	p.Ala119Ser	p.A119S	ENST00000359376	NM_002661.3	119	Gca/Tca	4/33	1	2	FACETS	0.889	0.788	0.997	0.889	0.788	0.997	CLONAL	1	TRUE	1	0.305761147939045	2		560	640	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41219712	41219712	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	rs80357117	NA	P-0020766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	81	427	0	ENST00000357654.3:c.4987A>T	p.Met1663Leu	p.M1663L	ENST00000357654	NM_007294.3	1663	Atg/Ttg	16/23	1	2	FACETS	0.976	0.861	1	0.976	0.861	1	CLONAL	1	TRUE	1	0.305761147939045	2		427	543	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207181	1207196	+	frameshift_variant	Frame_Shift_Del	DEL	ACGGGGAGGCCAACGT	ACGGGGAGGCCAACGT	-	novel	NA	P-0020766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	121	864	0	ENST00000326873.7:c.269_284del	p.Asn90ArgfsTer8	p.N90Rfs*8	ENST00000326873	NM_000455.4	90	aACGGGGAGGCCAACGTg/ag	1/10	0.226682943219452	1	FACETS	0.842	0.761	0.928	0.842	0.761	0.928	CLONAL	1	TRUE	0	0.305761147939045	1		864	796	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922307	178922307	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	110	532	0	ENST00000263967.3:c.1076G>C	p.Gly359Ala	p.G359A	ENST00000263967	NM_006218.2	359	gGt/gCt	6/21	1	2	FACETS	0.832	0.747	0.922	0.832	0.747	0.922	CLONAL	1	TRUE	1	0.305761147939045	2		532	865	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155046	55155046	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	105	490	2	ENST00000257290.5:c.2755G>T	p.Asp919Tyr	p.D919Y	ENST00000257290	NM_006206.4	919	Gac/Tac	20/23	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.305761147939045	2		492	575	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332822	65332828	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCATC	CCGCATC	-	novel	NA	P-0020868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	160	357	0	ENST00000342505.4:c.711_717del	p.Met238Ter	p.M238*	ENST00000342505	NM_002227.2	237	agGATGCGG/ag	7/25	0.828773561524475	1	FACETS	0.927	0.875	0.977	0.927	0.875	0.977	CLONAL	1	TRUE	0	0.828773561524475	1		357	244	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281660	49281660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61735175	NA	P-0020868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	381	886	4	ENST00000282018.3:c.707C>T	p.Ser236Leu	p.S236L	ENST00000282018	NM_020377.2	236	tCg/tTg	1/1	0.828773561524475	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.828773561524475	1		890	538	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226494	1226494	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752015385	NA	P-0020868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	382	790	0	ENST00000326873.7:c.1150C>T	p.Arg384Trp	p.R384W	ENST00000326873	NM_000455.4	384	Cgg/Tgg	9/10	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.828773561524475	2		790	828	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056057	26056072	+	protein_altering_variant	In_Frame_Del	DEL	GGGCTTAGCGGCCTTG	GGGCTTAGCGGCCTTG	CTTA	novel	NA	P-0020868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1572	143	334	0	ENST00000343677.2:c.585_600delinsTAAG	p.Ala197_Pro200del	p.A197_P200del	ENST00000343677	NM_005319.3	195	ccCAAGGCCGCTAAGCCC/ccTAAG	1/1	0.828773561524475	10	FACETS	0.868	0.788	0.953			1	CLONAL	1	TRUE	NA	0.828773561524475	10		334	1715	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323264	31323274	+	frameshift_variant	Frame_Shift_Del	DEL	TGCCAGGTCAG	TGCCAGGTCAG	-	novel	NA	P-0020868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	132	321	0	ENST00000412585.2:c.715_725del	p.Leu239AlafsTer11	p.L239Afs*11	ENST00000412585	NM_005514.6	239	CTGACCTGGCAg/g	4/8	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.828773561524475	2		321	315	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419939	152419939	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	51	654	0	ENST00000206249.3:c.1626G>C	p.Glu542Asp	p.E542D	ENST00000206249	NM_000125.3	542	gaG/gaC	8/8	0.828773561524475	2	FACETS	0.178	0.15	0.208	0.089	0.075	0.104	SUBCLONAL	1	TRUE	0	0.828773561524475	2		654	693	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0020900-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	50	387	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.640666441854786	4	FACETS	0.235	0.199	0.276	0.078	0.066	0.092	SUBCLONAL	1	TRUE	1	0.830596982187019	4		387	937	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020900-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	216	481	0	ENST00000425967.3:c.1731C>G	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaG	13/19	0.830596982187019	1	FACETS	0.939	0.894	0.982	0.939	0.894	0.982	CLONAL	1	TRUE	0	0.830596982187019	1		481	324	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849261	76849261	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020900-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	357	313	0	ENST00000373344.5:c.6015del	p.Phe2005LeufsTer10	p.F2005Lfs*10	ENST00000373344	NM_000489.3	2005	ttT/tt	26/35	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.830596982187019	1		313	436	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0021089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	24	255	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		255	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0021112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	628	518	3	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	2	TRUE	NA	0.68109304294638	2		521	910	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195988	102195988	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs755783862	NA	P-0021112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	218	480	0	ENST00000263464.3:c.748C>G	p.Leu250Val	p.L250V	ENST00000263464	NM_001165.4	250	Ctg/Gtg	2/9	0.536515413103502	4	FACETS	0.759	0.709	0.81	0.506	0.472	0.54	SUBCLONAL	2	TRUE	1	0.68109304294638	4		480	709	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43730603	43730603	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	233	700	0	ENST00000382044.4:c.3110C>G	p.Thr1037Ser	p.T1037S	ENST00000382044	NM_001141980.1	1037	aCc/aGc	16/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.68109304294638	2		700	614	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732542	74732542	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	23	147	0	ENST00000359995.5:c.367A>T	p.Arg123Trp	p.R123W	ENST00000359995	NM_001195427.1	123	Agg/Tgg	2/3	0.415861199497362	3	FACETS	0.592	0.466	0.734	0.197	0.155	0.245	SUBCLONAL	1	TRUE	0	0.68109304294638	3		147	153	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445112	89445112	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0021112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	63	401	0	ENST00000336596.2:c.1431+1G>T		p.X477_splice	ENST00000336596	NM_005233.5	477			0.458794887802645	3	FACETS	0.551	0.478	0.63	0.276	0.239	0.315	SUBCLONAL	1	TRUE	1	0.68109304294638	3		401	450	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469829	157469829	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	777	975	4	ENST00000346085.5:c.2623G>T	p.Gly875Cys	p.G875C	ENST00000346085	NM_020732.3	875	Ggt/Tgt	9/20	0.683721663678464	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.68109304294638	2		979	1026	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984002	2984023	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGGTTAGCAGCTCCACGCGC	GAAGGTTAGCAGCTCCACGCGC	-	novel	NA	P-0021112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	888	991	0	ENST00000396946.4:c.507_528del	p.Val171SerfsTer6	p.V171Sfs*6	ENST00000396946	NM_032415.4	169	acGCGCGTGGAGCTGCTAACCTTC/ac	5/25	0.68109304294638	5	FACETS	0.967	0.939	0.994	0.725	0.704	0.746	CLONAL	3	TRUE	1	0.68109304294638	5		991	1818	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411861	116411889	+	intron_variant	Intron	DEL	ATAGCCGTCTTTAACAAGCTCTTTCTTTC	ATAGCCGTCTTTAACAAGCTCTTTCTTTC	-	novel	NA	P-0021112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	915	1490	0	ENST00000397752.3:c.2888-42_2888-14del		p.*963*	ENST00000397752	NM_000245.2	-/1390			0.284122622813739	4	FACETS	1	0.975	1	0.75	0.731	0.769	INDETERMINATE	3	TRUE	0	0.68109304294638	4		1490	1505	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117861199	117861199	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	228	803	1	ENST00000297338.2:c.1690C>A	p.Leu564Ile	p.L564I	ENST00000297338	NM_006265.2	564	Ctt/Att	13/14	0.67246693419458	4	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.68109304294638	4		804	1030	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5081802	5081802	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	132	528	0	ENST00000381652.3:c.2512G>C	p.Asp838His	p.D838H	ENST00000381652	NM_004972.3	838	Gac/Cac	19/25	0.612984918738659	5	FACETS	0.769	0.697	0.845	0.256	0.232	0.282	SUBCLONAL	1	TRUE	2	0.68109304294638	5		528	1019	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0021113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	193	845	1	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.282890644944097	2		846	1038	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0021113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	170	837	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.282890644944097	2		837	1029	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247157	153247157	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0021167-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	164	295	0	ENST00000281708.4:c.1644+1G>A		p.X548_splice	ENST00000281708	NM_033632.3	548			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.79	2		295	395	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842339	151842339	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0021167-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	189	373	0	ENST00000262189.6:c.14073C>G	p.Tyr4691Ter	p.Y4691*	ENST00000262189	NM_170606.2	4691	taC/taG	54/59	1	2	FACETS	0.961	0.896	1	0.961	0.896	1	CLONAL	1	TRUE	1	0.79	2		373	498	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945447	151945448	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021167-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	345	724	0	ENST00000262189.6:c.2071dup	p.Ser691PhefsTer14	p.S691Ffs*14	ENST00000262189	NM_170606.2	691	tct/tTct	14/59	1	2	FACETS	0.855	0.81	0.9	0.855	0.81	0.9	CLONAL	1	TRUE	1	0.79	2		724	1022	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0021202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1327	62	785	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	1	2	FACETS	0.812	0.698	0.936	0.812	0.698	0.936	CLONAL	1	TRUE	1	0.11	2		785	1389	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	13	387	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.223490654239692	4	FACETS	0.219	0.155	0.297	0.109	0.077	0.149	SUBCLONAL	1	TRUE	2	0.333862032079978	4		387	475	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115947	8115951	+	frameshift_variant	Frame_Shift_Del	DEL	ACCAC	ACCAC	-	novel	NA	P-0021242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	51	360	0	ENST00000346208.3:c.1298_1302del	p.His433ProfsTer72	p.H433Pfs*72	ENST00000346208		431	ggACCACac/ggac	6/6	1	2	FACETS	0.83	0.708	0.963	0.83	0.708	0.963	CLONAL	1	TRUE	1	0.333862032079978	2		360	368	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984779	11984783	+	frameshift_variant	Frame_Shift_Del	DEL	GGACG	GGACG	-	novel	NA	P-0021242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	49	484	0	ENST00000353533.5:c.325_329del	p.Gly109ArgfsTer21	p.G109Rfs*21	ENST00000353533	NM_003010.3	109	GGACGa/a	3/11	0.202106055513221	2	FACETS	0.836	0.711	0.973	0.418	0.355	0.487	CLONAL	1	TRUE	0	0.333862032079978	2		484	351	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933889	39933889	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	153	772	1	ENST00000378444.4:c.710T>A	p.Val237Asp	p.V237D	ENST00000378444	NM_001123385.1	237	gTc/gAc	4/15	0.271872488840647	3	FACETS	1	0.954	1			1	CLONAL	2	TRUE	NA	0.333862032079978	3		773	509	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641392	23641392	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1567218141	NA	P-0021242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	53	900	0	ENST00000261584.4:c.2083A>G	p.Lys695Glu	p.K695E	ENST00000261584	NM_024675.3	695	Aag/Gag	5/13	0.313643789656497	4	FACETS	0.46	0.391	0.537			1	SUBCLONAL	1	TRUE	NA	0.333862032079978	4		900	920	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115947	8115951	+	frameshift_variant	Frame_Shift_Del	DEL	ACCAC	ACCAC	-	novel	NA	P-0021242-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	103	360	0	ENST00000346208.3:c.1298_1302del	p.His433ProfsTer72	p.H433Pfs*72	ENST00000346208		431	ggACCACac/ggac	6/6	0.197827070389543	0	FACETS	0.311	0.28	0.343			1	INDETERMINATE	1	FALSE	0	0.627592108912574	0		360	393	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984779	11984783	+	frameshift_variant	Frame_Shift_Del	DEL	GGACG	GGACG	-	novel	NA	P-0021242-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	110	484	0	ENST00000353533.5:c.325_329del	p.Gly109ArgfsTer21	p.G109Rfs*21	ENST00000353533	NM_003010.3	109	GGACGa/a	3/11	0.627592108912574	1	FACETS	0.745	0.677	0.814	0.745	0.677	0.814	SUBCLONAL	1	FALSE	0	0.627592108912574	1		484	323	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933889	39933889	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021242-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	288	772	1	ENST00000378444.4:c.710T>A	p.Val237Asp	p.V237D	ENST00000378444	NM_001123385.1	237	gTc/gAc	4/15	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	1	FALSE	NA	0.627592108912574	2		773	664	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0021295-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	35	1141	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.236159077166013	4	FACETS	0.396	0.323	0.478	0.198	0.161	0.239	SUBCLONAL	1	TRUE	2	0.3253310164319	4		1142	720	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0021295-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	84	565	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.236159077166013	4	FACETS	1	0.955	1	0.583	0.515	0.655	CLONAL	1	TRUE	2	0.3253310164319	4		565	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576853	7576853	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs11575996	NA	P-0021295-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	134	414	0	ENST00000269305.4:c.993G>T	p.Gln331His	p.Q331H	ENST00000269305	NM_001126112.2	331	caG/caT	9/11	0.249565303372109	2	FACETS	1	0.985	1	0.697	0.635	0.761	CLONAL	1	TRUE	0	0.3253310164319	2		414	591	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120460296	120460296	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021295-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	43	348	0	ENST00000256646.2:c.6019G>A	p.Asp2007Asn	p.D2007N	ENST00000256646	NM_024408.3	2007	Gac/Aac	33/34	0.3253310164319	3	FACETS	0.626	0.524	0.739	0.313	0.262	0.37	SUBCLONAL	1	TRUE	1	0.3253310164319	3		348	491	SUCCESS
APC	324	MSKCC	GRCh37	5	112175437	112175438	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	37	426	0	ENST00000257430.4:c.4147dup	p.Met1383AsnfsTer3	p.M1383Nfs*3	ENST00000257430	NM_000038.5	1382	-/A	16/16	0.20721732041483	2	FACETS	0.817	0.677	0.973	0.409	0.338	0.487	CLONAL	1	TRUE	0	0.31	2		426	292	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579476	7579484	+	frameshift_variant	Frame_Shift_Del	DEL	GAGCAGCCT	GAGCAGCCT	CCTC	novel	NA	P-0021312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	159	920	0	ENST00000269305.4:c.203_211delinsGAGG	p.Glu68GlyfsTer79	p.E68Gfs*79	ENST00000269305	NM_001126112.2	68	gAGGCTGCTCcc/gGAGGcc	4/11	0.20721732041483	2	FACETS	0.875	0.806	0.947	0.875	0.806	0.947	CLONAL	2	TRUE	0	0.31	2		920	586	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0021322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	47	279	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	FALSE	1	0.210903324073459	2		279	405	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690805	89690805	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1554897856	NA	P-0021322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	57	293	0	ENST00000371953.3:c.212G>T	p.Cys71Phe	p.C71F	ENST00000371953	NM_000314.4	71	tGt/tTt	4/9	0.194183376584029	2	FACETS	1	0.943	1	0.599	0.515	0.691	CLONAL	1	FALSE	0	0.210903324073459	2		293	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0021330-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	345	515	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.469148911095925	3	FACETS	0.936	0.896	0.976	0.936	0.896	0.976	CLONAL	3	TRUE	0	0.494139071156628	3		515	620	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489788	2489788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs527252361	NA	P-0021330-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	89	655	0	ENST00000355716.4:c.185G>A	p.Arg62His	p.R62H	ENST00000355716	NM_003820.2	62	cGt/cAt	3/8	0.462546186304122	4	FACETS	1	0.91	1	0.514	0.456	0.574	CLONAL	1	TRUE	2	0.494139071156628	4		655	524	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321199	65321199	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021330-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	63	400	0	ENST00000342505.4:c.1641G>C	p.Lys547Asn	p.K547N	ENST00000342505	NM_002227.2	547	aaG/aaC	11/25	0.462546186304122	4	FACETS	0.874	0.758	0.999	0.437	0.379	0.5	CLONAL	1	TRUE	2	0.494139071156628	4		400	436	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968326	134968326	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021330-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	65	543	0	ENST00000398015.3:c.2839A>G	p.Thr947Ala	p.T947A	ENST00000398015	NM_004441.4	947	Aca/Gca	15/16	0.426380843568332	3	FACETS	0.679	0.59	0.776	0.34	0.295	0.388	SUBCLONAL	1	TRUE	1	0.494139071156628	3		543	483	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86676345	86676345	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021330-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	42	372	1	ENST00000274376.6:c.2623G>T	p.Gly875Trp	p.G875W	ENST00000274376	NM_002890.2	875	Ggg/Tgg	20/25	0.45055656296548	4	FACETS	0.767	0.643	0.904	0.192	0.16	0.226	CLONAL	1	TRUE	0	0.494139071156628	4		373	331	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772901	135772901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748845915	NA	P-0021330-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	102	717	0	ENST00000298552.3:c.2722C>T	p.Arg908Trp	p.R908W	ENST00000298552	NM_001162426.1	908	Cgg/Tgg	21/23	0.466859792507084	2	FACETS	0.701	0.628	0.778	0.35	0.314	0.389	SUBCLONAL	1	TRUE	0	0.494139071156628	2		717	589	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0021379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	93	436	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.207065771773722	2	FACETS	1	0.965	1	0.603	0.537	0.672	CLONAL	1	TRUE	0	0.271711779958216	2		437	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578541	7578541	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	158	1322	0	ENST00000269305.4:c.389T>G	p.Leu130Arg	p.L130R	ENST00000269305	NM_001126112.2	130	cTc/cGc	5/11	1	2	FACETS	0.871	0.8	0.944	1	0.991	1	CLONAL	2	TRUE	1	0.271711779958216	2		1322	668	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165686	185165686	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	52	694	0	ENST00000265026.3:c.961G>T	p.Ala321Ser	p.A321S	ENST00000265026	NM_004721.4	321	Gcg/Tcg	5/14	1	2	FACETS	0.821	0.7	0.954	0.821	0.7	0.954	CLONAL	1	TRUE	1	0.271711779958216	2		694	466	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012261	152012261	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	100	806	0	ENST00000262189.6:c.552del	p.Met184IlefsTer22	p.M184Ifs*22	ENST00000262189	NM_170606.2	184	atG/at	4/59	0.174029540801524	4	FACETS	0.821	0.735	0.912	0.821	0.735	0.912	CLONAL	2	TRUE	2	0.271711779958216	4		806	570	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971082	21971089	+	frameshift_variant	Frame_Shift_Del	DEL	GTCCAGGA	GTCCAGGA	-	novel	NA	P-0021379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	83	442	0	ENST00000304494.5:c.269_276del	p.Phe90TyrfsTer27	p.F90Yfs*27	ENST00000304494	NM_000077.4	90	tTCCTGGAC/t	2/3	1	2	FACETS	1	0.917	1	1	0.986	1	CLONAL	2	TRUE	1	0.271711779958216	2		442	296	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0021394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	21	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.703250475585929	3	FACETS	0.157	0.12	0.201	0.079	0.06	0.101	SUBCLONAL	1	TRUE	1	0.703250475585929	3		511	513	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913237	NA	P-0021394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	475	574	1	ENST00000369535.4:c.35G>T	p.Gly12Val	p.G12V	ENST00000369535	NM_002524.4	12	gGt/gTt	2/7	0.703250475585929	3	FACETS	0.997	0.959	1			1	CLONAL	2	TRUE	NA	0.703250475585929	3		575	916	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0021394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	33	215	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.703250475585929	3	FACETS	0.268	0.217	0.324	0.134	0.108	0.162	SUBCLONAL	1	TRUE	1	0.703250475585929	3		215	474	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156711	20156711	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	255	718	0	ENST00000379607.5:c.46A>G	p.Lys16Glu	p.K16E	ENST00000379607	NM_001412.3	16	Aag/Gag	2/7	0.703250475585929	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.703250475585929	1		718	459	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432330	49432330	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	371	860	0	ENST00000301067.7:c.8809C>G	p.Pro2937Ala	p.P2937A	ENST00000301067	NM_003482.3	2937	Cca/Gca	34/54	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.703250475585929	2		860	1030	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487295	56487295	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1488014391	NA	P-0021394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	221	559	3	ENST00000267101.3:c.1441C>T	p.Arg481Ter	p.R481*	ENST00000267101	NM_001982.3	481	Cga/Tga	12/28	1	2	FACETS	0.973	0.911	1	0.973	0.911	1	CLONAL	1	TRUE	1	0.703250475585929	2		562	646	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021467-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	89	376	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.397074185956403	2		376	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0021467-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	149	535	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.397074185956403	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.397074185956403	1		535	567	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165942	118165942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749332682	NA	P-0021467-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	85	294	0	ENST00000369448.3:c.452G>A	p.Arg151His	p.R151H	ENST00000369448	NM_017709.3	151	cGc/cAc	2/2	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.397074185956403	2		294	427	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879680	151879680	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0021467-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	47	113	0	ENST00000262189.6:c.5266-1G>A		p.X1756_splice	ENST00000262189	NM_170606.2	1756			0.259140810036287	4	FACETS	1	0.937	1	0.402	0.342	0.468	CLONAL	1	TRUE	1	0.397074185956403	4		113	274	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0021693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	78	379	0	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	0.402767766093721	1	FACETS	0.749	0.661	0.842	0.749	0.661	0.842	SUBCLONAL	1	TRUE	0	0.402767766093721	1		379	413	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233751	233751	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199844384	NA	P-0021693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	107	660	3	ENST00000264932.6:c.1055G>A	p.Arg352Gln	p.R352Q	ENST00000264932	NM_004168.2	352	cGa/cAa	8/15	0.147146806425467	5	FACETS	0.974	0.873	1			1	INDETERMINATE	1	TRUE	NA	0.402767766093721	5		663	875	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	50	387	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.3457155003473	3	FACETS	1	0.962	1	0.713	0.611	0.822	CLONAL	1	TRUE	1	0.3457155003473	3		387	238	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0021735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	83	686	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.262953871552287	5	FACETS	1	0.934	1	0.713	0.634	0.795	CLONAL	2	TRUE	2	0.3457155003473	5		686	341	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599949	10599950	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0021735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	41	796	0	ENST00000171111.5:c.1626_1627del	p.Glu542AspfsTer31	p.E542Dfs*31	ENST00000171111	NM_203500.1	542	gaGAcg/gacg	5/6	0.159168870534949	2	FACETS	0.841	0.704	0.991	0.421	0.352	0.496	INDETERMINATE	1	TRUE	0	0.3457155003473	2		796	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577129	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519986	NA	P-0021735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	42	656	1	ENST00000269305.4:c.809T>C	p.Phe270Ser	p.F270S	ENST00000269305	NM_001126112.2	270	tTt/tCt	8/11	0.3457155003473	3	FACETS	1	0.84	1	0.5	0.42	0.588	CLONAL	1	TRUE	1	0.3457155003473	3		657	285	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710911	117710911	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	34	508	1	ENST00000368508.3:c.1361C>G	p.Thr454Arg	p.T454R	ENST00000368508	NM_002944.2	454	aCg/aGg	12/43	0.3457155003473	1	FACETS	0.6	0.493	0.72	0.6	0.493	0.72	SUBCLONAL	1	TRUE	0	0.3457155003473	1		509	271	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	104	713	0	ENST00000269571.5:c.829G>T	p.Asp277Tyr	p.D277Y	ENST00000269571		277	Gac/Tac	7/27	0.262953871552287	5	FACETS	1	0.952	1	0.729	0.657	0.804	CLONAL	2	TRUE	2	0.3457155003473	5		713	418	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482926	140482927	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs777474487	NA	P-0021735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	13	654	3	ENST00000288602.6:c.1208dup	p.Ala404CysfsTer9	p.A404Cfs*9	ENST00000288602	NM_004333.4	403	cct/ccCt	10/18	NA	2	FACETS	0.294	0.209	0.397			1	INDETERMINATE	1	TRUE	NA	0.3457155003473	2		657	256	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103391	2103391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1325855418	NA	P-0021735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	19	740	2	ENST00000219476.3:c.274G>A	p.Glu92Lys	p.E92K	ENST00000219476	NM_000548.3	92	Gag/Aag	4/42	0.262459371103993	4	FACETS	0.406	0.308	0.523			1	SUBCLONAL	1	TRUE	NA	0.3457155003473	4		742	364	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612247	189612247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	30	453	1	ENST00000264731.3:c.1999G>A	p.Ala667Thr	p.A667T	ENST00000264731	NM_003722.4	667	Gct/Act	14/14	0.3457155003473	4	FACETS	1	0.94	1	0.725	0.591	0.873	CLONAL	1	TRUE	2	0.3457155003473	4		454	161	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188940	11188940	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	34	707	0	ENST00000361445.4:c.5783A>G	p.Lys1928Arg	p.K1928R	ENST00000361445	NM_004958.3	1928	aAa/aGa	41/58	NA	2	FACETS	0.906	0.746	1			1	INDETERMINATE	1	TRUE	NA	0.3457155003473	2		707	217	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451555	70451555	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	13	668	0	ENST00000373644.4:c.6395A>G	p.Tyr2132Cys	p.Y2132C	ENST00000373644	NM_030625.2	2132	tAt/tGt	12/12	0.192195165925625	1	FACETS	0.321	0.229	0.432	0.321	0.229	0.432	INDETERMINATE	1	TRUE	0	0.3457155003473	1		668	194	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21626494	21626494	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0021735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	25	697	0	ENST00000421138.2:c.1438A>T	p.Lys480Ter	p.K480*	ENST00000421138		480	Aaa/Taa	13/16	0.212163649228629	5	FACETS	0.735	0.58	0.912	0.245	0.193	0.304	CLONAL	1	TRUE	2	0.3457155003473	5		697	299	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515307	103515307	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	19	427	1	ENST00000355739.4:c.1808T>A	p.Val603Glu	p.V603E	ENST00000355739	NM_000123.3	603	gTg/gAg	8/15	0.330514513115358	3	FACETS	0.594	0.452	0.76	0.297	0.226	0.38	SUBCLONAL	1	TRUE	1	0.3457155003473	3		428	217	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105656	30105656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	13	732	0	ENST00000331968.5:c.1030G>A	p.Gly344Arg	p.G344R	ENST00000331968	NM_002742.2	344	Ggg/Agg	7/18	NA	2	FACETS	0.356	0.254	0.481			1	INDETERMINATE	1	TRUE	NA	0.3457155003473	2		732	211	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096184	2096184	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	19	804	0	ENST00000219066.1:c.323C>A	p.Ala108Glu	p.A108E	ENST00000219066	NM_002528.5	108	gCa/gAa	2/6	0.262459371103993	4	FACETS	0.424	0.321	0.545			1	SUBCLONAL	1	TRUE	NA	0.3457155003473	4		804	349	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600032	10600032	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	51	705	0	ENST00000171111.5:c.1544T>C	p.Leu515Pro	p.L515P	ENST00000171111	NM_203500.1	515	cTg/cCg	5/6	0.159168870534949	2	FACETS	1	0.904	1	0.536	0.459	0.62	INDETERMINATE	1	TRUE	0	0.3457155003473	2		705	275	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	8	344	1	ENST00000263967.3:c.353G>T	p.Gly118Val	p.G118V	ENST00000263967	NM_006218.2	118	gGt/gTt	3/21	0.3457155003473	3	FACETS	0.292	0.188	0.427	0.146	0.094	0.214	SUBCLONAL	1	TRUE	1	0.3457155003473	3		345	186	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526520	31526520	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886155627	NA	P-0021735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	21	903	0	ENST00000344624.3:c.520C>T	p.His174Tyr	p.H174Y	ENST00000344624		174	Cac/Tac	2/33	0.159168870534949	2	FACETS	0.473	0.365	0.598	0.236	0.182	0.299	INDETERMINATE	1	TRUE	0	0.3457155003473	2		903	257	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222789	53222790	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	43	810	0	ENST00000375401.3:c.4146dup	p.Gln1383ThrfsTer11	p.Q1383Tfs*11	ENST00000375401	NM_004187.3	1382	-/A	25/26	0.235330466088002	1	FACETS	0.948	0.802	1	0.948	0.802	1	CLONAL	1	TRUE	0	0.3457155003473	1		810	217	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912060	76912060	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	11	624	0	ENST00000373344.5:c.4204C>A	p.Pro1402Thr	p.P1402T	ENST00000373344	NM_000489.3	1402	Ccc/Acc	13/35	0.235330466088002	1	FACETS	0.249	0.172	0.346	0.249	0.172	0.346	SUBCLONAL	1	TRUE	0	0.3457155003473	1		624	211	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021738-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	67	387	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	0.271209375864062	2		387	428	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216702	36216702	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748120825	NA	P-0021738-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	66	464	1	ENST00000222270.7:c.3868C>T	p.Arg1290Cys	p.R1290C	ENST00000222270	NM_014727.1	1290	Cgc/Tgc	13/37	1	2	FACETS	0.842	0.731	0.962	0.842	0.731	0.962	CLONAL	1	TRUE	1	0.271209375864062	2		465	578	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351055	89351055	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs751008206	NA	P-0021738-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	97	717	0	ENST00000301030.4:c.1895A>G	p.His632Arg	p.H632R	ENST00000301030	NM_001256183.1	632	cAt/cGt	9/13	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.271209375864062	2		717	696	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021738-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	225	387	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.457240876181349	2		387	852	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216702	36216702	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748120825	NA	P-0021738-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	133	464	1	ENST00000222270.7:c.3868C>T	p.Arg1290Cys	p.R1290C	ENST00000222270	NM_014727.1	1290	Cgc/Tgc	13/37	0.324059091747207	1	FACETS	0.834	0.761	0.91	0.834	0.761	0.91	CLONAL	1	FALSE	0	0.457240876181349	1		465	538	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0021866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	62	493	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.164913895654108	1	FACETS	1	0.974	1	1	0.974	1	INDETERMINATE	1	TRUE	0	0.552257736334593	1		493	120	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207065	1207065	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	312	726	1	ENST00000326873.7:c.157del	p.Asp53ThrfsTer11	p.D53Tfs*11	ENST00000326873	NM_000455.4	51	atG/at	1/10	0.552257736334593	2	FACETS	0.91	0.866	0.953	0.91	0.866	0.953	CLONAL	2	TRUE	0	0.552257736334593	2		727	621	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969845	81969845	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	134	594	3	ENST00000359376.3:c.2914G>T	p.Val972Phe	p.V972F	ENST00000359376	NM_002661.3	972	Gtc/Ttc	27/33	0.398391825156061	3	FACETS	1	0.98	1	0.776	0.72	0.832	CLONAL	2	TRUE	0	0.552257736334593	3		597	266	SUCCESS
ATM	472	MSKCC	GRCh37	11	108127056	108127056	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	14	495	0	ENST00000278616.4:c.2239C>T	p.Gln747Ter	p.Q747*	ENST00000278616	NM_000051.3	747	Cag/Tag	14/63	0.552851362088846	3	FACETS	0.84	0.619	1	0.42	0.309	0.549	CLONAL	1	TRUE	1	0.552257736334593	3		495	77	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216543	108216543	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	51	611	0	ENST00000278616.4:c.8492T>C	p.Phe2831Ser	p.F2831S	ENST00000278616	NM_000051.3	2831	tTc/tCc	58/63	0.552851362088846	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.552257736334593	3		611	96	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522595	106522595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1430500907	NA	P-0021866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	33	730	0	ENST00000359195.3:c.2572G>A	p.Glu858Lys	p.E858K	ENST00000359195	NM_002649.2	858	Gaa/Aaa	7/11	0.552851362088846	3	FACETS	1	0.951	1	0.733	0.613	0.861	CLONAL	1	TRUE	1	0.552257736334593	3		730	104	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937117	39937117	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs947946150	NA	P-0021866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	150	814	0	ENST00000378444.4:c.66G>T	p.Met22Ile	p.M22I	ENST00000378444	NM_001123385.1	22	atG/atT	2/15	0.151204475271373	0	FACETS	0.668	0.619	0.718			1	INDETERMINATE	1	TRUE	0	0.552257736334593	0		814	364	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	162	376	0				ENST00000310581	NM_198253.2	-/1132			0.337065577217398	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	3	TRUE	0	0.337065577217398	3		376	357	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0022011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	253	854	0	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.337065577217398	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.337065577217398	2		854	716	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054615	13054615	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs143880510	NA	P-0022011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	71	643	2	ENST00000316448.5:c.1142A>C	p.Glu381Ala	p.E381A	ENST00000316448	NM_004343.3	381	gAg/gCg	9/9	1	2	FACETS	0.891	0.78	1	0.891	0.78	1	CLONAL	1	TRUE	1	0.337065577217398	2		645	473	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665360	138665360	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906920	NA	P-0022011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	105	889	0	ENST00000330315.3:c.205G>A	p.Glu69Lys	p.E69K	ENST00000330315	NM_023067.3	69	Gag/Aag	1/1	1	2	FACETS	0.986	0.885	1	0.986	0.885	1	CLONAL	1	TRUE	1	0.337065577217398	2		889	632	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421575	32421575	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	82	898	0	ENST00000332351.3:c.1017C>A	p.Tyr339Ter	p.Y339*	ENST00000332351	NM_024426.4	339	taC/taA	6/10	1	2	FACETS	0.807	0.712	0.908	0.807	0.712	0.908	CLONAL	1	TRUE	1	0.337065577217398	2		898	603	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559787	29559787	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1567851054	NA	P-0022011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	148	585	0	ENST00000356175.3:c.3384del	p.Gly1129AlafsTer13	p.G1129Afs*13	ENST00000356175	NM_000267.3	1128	ggT/gg	26/57	0.337065577217398	3	FACETS	0.981	0.902	1	0.981	0.902	1	CLONAL	2	TRUE	1	0.337065577217398	3		585	523	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663932	29663932	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	62	395	0	ENST00000356175.3:c.6364G>T	p.Glu2122Ter	p.E2122*	ENST00000356175	NM_000267.3	2122	Gaa/Taa	41/57	0.337065577217398	3	FACETS	0.935	0.809	1	0.467	0.404	0.535	CLONAL	1	TRUE	1	0.337065577217398	3		395	460	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965575	25965575	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	232	912	0	ENST00000435504.4:c.3631A>T	p.Ser1211Cys	p.S1211C	ENST00000435504		1211	Agt/Tgt	13/13	0.337065577217398	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.337065577217398	2		912	678	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504965	186504965	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	79	566	0	ENST00000323963.5:c.821C>A	p.Thr274Lys	p.T274K	ENST00000323963		274	aCa/aAa	8/11	1	2	FACETS	0.898	0.792	1	0.898	0.792	1	CLONAL	1	TRUE	1	0.337065577217398	2		566	522	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127447	55127447	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	98	938	0	ENST00000257290.5:c.235G>T	p.Gly79Cys	p.G79C	ENST00000257290	NM_006206.4	79	Ggc/Tgc	3/23	1	2	FACETS	0.873	0.78	0.972	0.873	0.78	0.972	CLONAL	1	TRUE	1	0.337065577217398	2		938	666	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081516	143081516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	69	568	0	ENST00000262992.4:c.1558G>A	p.Glu520Lys	p.E520K	ENST00000262992	NM_001101669.1	520	Gag/Aag	15/24	1	2	FACETS	0.957	0.836	1	0.957	0.836	1	CLONAL	1	TRUE	1	0.337065577217398	2		568	428	SUCCESS
APC	324	MSKCC	GRCh37	5	112178876	112178877	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0022011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	67	559	1	ENST00000257430.4:c.7585_7586delinsTT	p.Ala2529Leu	p.A2529L	ENST00000257430	NM_000038.5	2529	GCa/TTa	16/16	1	2	FACETS	0.933	0.814	1	0.933	0.814	1	CLONAL	1	TRUE	1	0.337065577217398	2		560	426	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271555	26271555	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	37	525	0	ENST00000305910.3:c.58C>T	p.Gln20Ter	p.Q20*	ENST00000305910	NM_003534.2	20	Cag/Tag	1/1	1	2	FACETS	0.606	0.501	0.724	0.606	0.501	0.724	SUBCLONAL	1	TRUE	1	0.337065577217398	2		525	362	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675520	30675520	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	130	1051	2	ENST00000376406.3:c.2836A>T	p.Thr946Ser	p.T946S	ENST00000376406	NM_014641.2	946	Aca/Tca	8/15	1	2	FACETS	0.967	0.877	1	0.967	0.877	1	CLONAL	1	TRUE	1	0.337065577217398	2		1053	798	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	316	387	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.559125370407304	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.559125370407304	3		387	677	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0022069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	130	778	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.448483040437912	1	FACETS	0.397	0.36	0.437	0.397	0.36	0.437	SUBCLONAL	1	TRUE	0	0.559125370407304	1		778	843	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916947	178916947	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022080-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	305	289	0	ENST00000263967.3:c.334A>T	p.Ile112Phe	p.I112F	ENST00000263967	NM_006218.2	112	Atc/Ttc	2/21	0.201672160828562	5	FACETS	1	0.98	1	1	0.98	1	CLONAL	5	FALSE	0	0.201672160828562	5		289	740	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754717	41754717	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749923407	NA	P-0022080-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	74	665	0	ENST00000301178.4:c.1703C>T	p.Thr568Met	p.T568M	ENST00000301178	NM_021913.4	568	aCg/aTg	14/20	0.201672160828562	3	FACETS	1	0.912	1	0.527	0.461	0.599	CLONAL	1	FALSE	1	0.201672160828562	3		665	766	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286237	66286238	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022080-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	46	402	0	ENST00000273854.3:c.1448dup	p.Asn483LysfsTer21	p.N483Kfs*21	ENST00000273854	NM_004439.5	483	aac/aaAc	6/18	0.201672160828562	3	FACETS	0.975	0.821	1	0.488	0.41	0.573	CLONAL	1	FALSE	1	0.201672160828562	3		402	515	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980413	1980413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022080-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	120	1089	1	ENST00000382891.5:c.3875C>T	p.Ser1292Leu	p.S1292L	ENST00000382891	NM_133335.3	1292	tCg/tTg	22/22	0.201672160828562	3	FACETS	0.763	0.689	0.842	0.763	0.689	0.842	SUBCLONAL	2	FALSE	1	0.201672160828562	3		1090	858	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500612	99500612	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs774314535	NA	P-0022080-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	54	518	0	ENST00000268035.6:c.4045A>G	p.Met1349Val	p.M1349V	ENST00000268035	NM_000875.3	1349	Atg/Gtg	21/21	0.111054583862781	4	FACETS	1	0.944	1	0.612	0.523	0.709	INDETERMINATE	1	FALSE	2	0.201672160828562	4		518	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0022100-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	229	559	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.699323559220867	1	FACETS	0.979	0.927	1	0.979	0.927	1	CLONAL	1	TRUE	0	0.715590058909466	1		559	420	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277892	41277892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022100-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	267	279	0	ENST00000349496.5:c.1856G>A	p.Cys619Tyr	p.C619Y	ENST00000349496	NM_001904.3	619	tGt/tAt	12/15	0.715590058909466	2	FACETS	0.969	0.929	1	0.969	0.929	1	CLONAL	2	TRUE	0	0.715590058909466	2		279	385	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28601391	28601391	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022100-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	45	389	1	ENST00000253063.3:c.1076G>T	p.Gly359Val	p.G359V	ENST00000253063	NM_031459.4	359	gGt/gTt	8/10	1	2	FACETS	0.18	0.151	0.213	0.18	0.151	0.213	SUBCLONAL	1	TRUE	1	0.715590058909466	2		390	698	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28605731	28605731	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022100-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	173	446	0	ENST00000253063.3:c.1335G>T	p.Arg445Ser	p.R445S	ENST00000253063	NM_031459.4	445	agG/agT	9/10	1	2	FACETS	0.754	0.697	0.813	0.754	0.697	0.813	SUBCLONAL	1	TRUE	1	0.715590058909466	2		446	641	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916160	9916160	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022100-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	34	363	0	ENST00000330684.3:c.2129A>G	p.Gln710Arg	p.Q710R	ENST00000330684	NM_001134407.1	710	cAg/cGg	10/13	1	2	FACETS	0.182	0.148	0.22	0.182	0.148	0.22	SUBCLONAL	1	TRUE	1	0.715590058909466	2		363	522	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678783	52678783	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022100-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	218	256	0	ENST00000394830.3:c.836del	p.Ile279AsnfsTer4	p.I279Nfs*4	ENST00000394830	NM_018313.4	279	aTa/aa	9/30	0.715590058909466	2	FACETS	0.878	0.834	0.921	0.878	0.834	0.921	CLONAL	2	TRUE	0	0.715590058909466	2		256	347	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880191	151880191	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022100-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	354	367	0	ENST00000262189.6:c.5133G>A	p.Met1711Ile	p.M1711I	ENST00000262189	NM_170606.2	1711	atG/atA	35/59	0.611251106388907	3	FACETS	0.916	0.875	0.958	0.916	0.875	0.958	CLONAL	2	TRUE	1	0.715590058909466	3		367	733	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0022119-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	79	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.19	2		511	830	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945474	151945474	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0022119-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	60	1012	1	ENST00000262189.6:c.2045C>G	p.Ser682Ter	p.S682*	ENST00000262189	NM_170606.2	682	tCa/tGa	14/59	0.151351080081323	3	FACETS	0.609	0.523	0.704	0.305	0.261	0.352	SUBCLONAL	1	TRUE	1	0.19	3		1013	1135	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858366	27858366	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022119-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	41	530	0	ENST00000359303.2:c.205C>A	p.Gln69Lys	p.Q69K	ENST00000359303	NM_003535.2	69	Cag/Aag	1/1	1	2	FACETS	0.788	0.655	0.935	0.788	0.655	0.935	CLONAL	1	TRUE	1	0.19	2		530	548	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0022119-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	54	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.202311850565275	2		511	444	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106923	27106940	+	inframe_deletion	In_Frame_Del	DEL	CAGCCTGGCAGCTCGTGC	CAGCCTGGCAGCTCGTGC	-	novel	NA	P-0022119-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	22	246	0	ENST00000324856.7:c.6536_6553del	p.Ser2179_Ala2184del	p.S2179_A2184del	ENST00000324856	NM_006015.4	2178	gaCAGCCTGGCAGCTCGTGCc/gac	20/20	1	2	FACETS	0.651	0.504	0.822	0.651	0.504	0.822	SUBCLONAL	1	TRUE	1	0.202311850565275	2		246	334	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949753	151949753	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022119-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	44	323	0	ENST00000262189.6:c.1347G>A	p.Trp449Ter	p.W449*	ENST00000262189	NM_170606.2	449	tgG/tgA	10/59	1	2	FACETS	0.927	0.778	1	0.927	0.778	1	CLONAL	1	TRUE	1	0.202311850565275	2		323	469	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30303600	30303600	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	14	10	0	ENST00000322652.5:c.884T>C	p.Phe295Ser	p.F295S	ENST00000322652	NM_015355.2	295	tTt/tCt	8/16	1	2	FACETS	0.89	0.668	1	0.89	0.668	1	CLONAL	1	TRUE	1	0.669146655540085	2		10	47	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874261	155874261	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs483352822	NA	P-0022304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	139	621	0	ENST00000368323.3:c.270G>T	p.Met90Ile	p.M90I	ENST00000368323	NM_006912.5	90	atG/atT	5/6	1	2	FACETS	0.865	0.787	0.948	1	0.989	1	CLONAL	2	TRUE	1	0.16	2		621	1004	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0022320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	152	1128	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	NA	2	FACETS	0.495	0.454	0.539			1	INDETERMINATE	1	TRUE	NA	0.841818541506315	2		1128	729	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047507	49047507	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0022320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	331	215	0	ENST00000267163.4:c.2501C>G	p.Ser834Ter	p.S834*	ENST00000267163	NM_000321.2	834	tCa/tGa	24/27	NA	2	FACETS	0.849	0.819	0.879			1	INDETERMINATE	2	TRUE	NA	0.841818541506315	2		215	463	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578273	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0022320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	505	329	2	ENST00000269305.4:c.576_577delinsTT	p.Gln192_His193delinsHisTyr	p.Q192_H193delinsHY	ENST00000269305	NM_001126112.2	192	caGCat/caTTat	6/11	0.834778781854672	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.841818541506315	2		331	581	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16248742	16248742	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0022320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	199	200	0	ENST00000375759.3:c.1750-2A>G		p.X584_splice	ENST00000375759	NM_015001.2	584			0.634522789625479	1	FACETS	0.736	0.694	0.778	0.736	0.694	0.778	SUBCLONAL	1	TRUE	0	0.841818541506315	1		200	372	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939782	71939782	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	145	363	0	ENST00000298229.2:c.409G>A	p.Glu137Lys	p.E137K	ENST00000298229	NM_001567.3	137	Gag/Aag	4/28	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.841818541506315	NA		363	602	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426745	49426745	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555188518	NA	P-0022320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	130	120	0	ENST00000301067.7:c.11743C>T	p.Gln3915Ter	p.Q3915*	ENST00000301067	NM_003482.3	3915	Cag/Tag	39/54	0.822967298315282	2	FACETS	0.83	0.782	0.877	0.83	0.782	0.877	CLONAL	2	TRUE	0	0.841818541506315	2		120	186	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640899	3640899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763209133	NA	P-0022320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	160	425	0	ENST00000294008.3:c.2740G>A	p.Asp914Asn	p.D914N	ENST00000294008	NM_032444.2	914	Gat/Aat	12/15	0.725570341693201	1	FACETS	0.346	0.318	0.375	0.346	0.318	0.375	SUBCLONAL	1	TRUE	0	0.841818541506315	1		425	636	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555347	106555347	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	106	278	0	ENST00000369096.4:c.2464C>G	p.Pro822Ala	p.P822A	ENST00000369096	NM_001198.3	822	Cca/Gca	7/7	1	2	FACETS	0.454	0.408	0.502	0.454	0.408	0.502	SUBCLONAL	1	TRUE	1	0.841818541506315	2		278	555	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089692	5089692	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	211	154	0	ENST00000381652.3:c.2590G>C	p.Glu864Gln	p.E864Q	ENST00000381652	NM_004972.3	864	Gag/Cag	20/25	0.841818541506315	2	FACETS	1	0.962	1	0.517	0.485	0.549	CLONAL	1	TRUE	0	0.841818541506315	2		154	485	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0022320-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	167	1128	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.454372898076687	2	FACETS	0.519	0.478	0.562	0.26	0.239	0.281	INDETERMINATE	1	TRUE	0	0.901956106706292	2		1128	713	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047507	49047507	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0022320-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	133	215	0	ENST00000267163.4:c.2501C>G	p.Ser834Ter	p.S834*	ENST00000267163	NM_000321.2	834	tCa/tGa	24/27	0.858385064524003	1	FACETS	0.981	0.935	1	0.981	0.935	1	CLONAL	1	TRUE	0	0.901956106706292	1		215	165	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578273	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0022320-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	476	329	2	ENST00000269305.4:c.576_577delinsTT	p.Gln192_His193delinsHisTyr	p.Q192_H193delinsHY	ENST00000269305	NM_001126112.2	192	caGCat/caTTat	6/11	0.901956106706292	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.901956106706292	2		331	522	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16248742	16248742	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0022320-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	31	200	0	ENST00000375759.3:c.1750-2A>G		p.X584_splice	ENST00000375759	NM_015001.2	584			0.420900574071514	1	FACETS	0.143	0.116	0.173	0.143	0.116	0.173	INDETERMINATE	1	TRUE	0	0.901956106706292	1		200	264	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939782	71939782	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022320-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	251	363	0	ENST00000298229.2:c.409G>A	p.Glu137Lys	p.E137K	ENST00000298229	NM_001567.3	137	Gag/Aag	4/28	0.65123979116826	1	FACETS	0.605	0.573	0.637	0.605	0.573	0.637	SUBCLONAL	1	TRUE	0	0.901956106706292	1		363	505	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426745	49426745	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555188518	NA	P-0022320-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	67	120	0	ENST00000301067.7:c.11743C>T	p.Gln3915Ter	p.Q3915*	ENST00000301067	NM_003482.3	3915	Cag/Tag	39/54	0.898305497416621	2	FACETS	0.895	0.796	0.996	0.447	0.398	0.498	CLONAL	1	TRUE	0	0.901956106706292	2		120	166	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640899	3640899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763209133	NA	P-0022320-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	317	425	0	ENST00000294008.3:c.2740G>A	p.Asp914Asn	p.D914N	ENST00000294008	NM_032444.2	914	Gat/Aat	12/15	0.502641166038266	1	FACETS	0.723	0.692	0.753	0.723	0.692	0.753	INDETERMINATE	1	TRUE	0	0.901956106706292	1		425	534	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555347	106555347	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022320-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	22	278	0	ENST00000369096.4:c.2464C>G	p.Pro822Ala	p.P822A	ENST00000369096	NM_001198.3	822	Cca/Gca	7/7	0.350575961697474	1	FACETS	0.067	0.051	0.085	0.067	0.051	0.085	INDETERMINATE	1	TRUE	0	0.901956106706292	1		278	400	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089692	5089692	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022320-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	182	154	0	ENST00000381652.3:c.2590G>C	p.Glu864Gln	p.E864Q	ENST00000381652	NM_004972.3	864	Gag/Cag	20/25	0.901956106706292	1	FACETS	0.901	0.859	0.94	0.901	0.859	0.94	CLONAL	1	TRUE	0	0.901956106706292	1		154	246	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555347	106555347	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs75859409	NA	P-0022320-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	88	277	1	ENST00000369096.4:c.2464C>A	p.Pro822Thr	p.P822T	ENST00000369096	NM_001198.3	822	Cca/Aca	7/7	0.350575961697474	1	FACETS	0.268	0.238	0.299	0.268	0.238	0.299	INDETERMINATE	1	TRUE	0	0.901956106706292	1		278	400	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182681670	182681670	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022320-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	24	240	0	ENST00000292782.4:c.388G>T	p.Gly130Ter	p.G130*	ENST00000292782	NM_020640.2	130	Gga/Tga	3/7	0.858385064524003	1	FACETS	0.109	0.085	0.136	0.109	0.085	0.136	SUBCLONAL	1	TRUE	0	0.901956106706292	1		240	269	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665029	138665029	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs7432551	NA	P-0022332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	30	264	0	ENST00000330315.3:c.536C>G	p.Ala179Gly	p.A179G	ENST00000330315	NM_023067.3	179	gCg/gGg	1/1	0.602249127437872	3	FACETS	0.581	0.471	0.704			1	SUBCLONAL	1	TRUE	NA	0.609421117377328	3		264	221	SUCCESS
APC	324	MSKCC	GRCh37	5	112174840	112174840	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0022332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	64	443	0	ENST00000257430.4:c.3549T>A	p.Tyr1183Ter	p.Y1183*	ENST00000257430	NM_000038.5	1183	taT/taA	16/16	0.445698212075809	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.609421117377328	1		443	136	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220295	55220295	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	600	1019	0	ENST00000275493.2:c.685A>T	p.Ser229Cys	p.S229C	ENST00000275493	NM_005228.3	229	Agt/Tgt	6/28	0.609421117377328	7	FACETS	1	0.98	1	0.771	0.741	0.801	CLONAL	3	TRUE	3	0.609421117377328	7		1019	1611	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556992	29556992	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1555614462	NA	P-0022332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	32	230	0	ENST00000356175.3:c.2990G>T	p.Arg997Met	p.R997M	ENST00000356175	NM_000267.3	997	aGg/aTg	22/57	0.614438621150884	3	FACETS	0.841	0.691	1	0.42	0.345	0.503	CLONAL	1	TRUE	1	0.609421117377328	3		230	163	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567556006	NA	P-0022332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	371	747	1	ENST00000269305.4:c.298del	p.Gln100ArgfsTer23	p.Q100Rfs*23	ENST00000269305	NM_001126112.2	100	Cag/ag	4/11	0.614438621150884	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.609421117377328	2		748	598	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494641	2494641	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1260	244	943	1	ENST00000355716.4:c.781C>A	p.Pro261Thr	p.P261T	ENST00000355716	NM_003820.2	261	Cct/Act	8/8	0.609421117377328	6	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.609421117377328	6		944	1504	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246021850	246021850	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145115256	NA	P-0022332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	188	994	1	ENST00000388985.4:c.1024G>A	p.Gly342Ser	p.G342S	ENST00000388985		342	Ggc/Agc	10/12	0.609421117377328	7	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.609421117377328	7		995	1217	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18747483	18747483	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	248	700	0	ENST00000266497.5:c.3944A>G	p.Glu1315Gly	p.E1315G	ENST00000266497		1315	gAa/gGa	28/31	0.614438621150884	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.609421117377328	3		700	497	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425819	49425819	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	373	804	0	ENST00000301067.7:c.12669G>T	p.Gln4223His	p.Q4223H	ENST00000301067	NM_003482.3	4223	caG/caT	39/54	0.349142374408353	5	FACETS	0.957	0.914	1			1	INDETERMINATE	3	TRUE	NA	0.609421117377328	5		804	816	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28886131	28886131	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs777732747	NA	P-0022332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	188	798	2	ENST00000282397.4:c.3491A>G	p.Gln1164Arg	p.Q1164R	ENST00000282397	NM_002019.4	1164	cAg/cGg	26/30	0.332510506834355	1	FACETS	0.758	0.719	0.795	1	0.993	1	INDETERMINATE	2	TRUE	0	0.609421117377328	1		800	283	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646259	3646259	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	226	1145	0	ENST00000294008.3:c.1819A>T	p.Arg607Trp	p.R607W	ENST00000294008	NM_032444.2	607	Agg/Tgg	8/15	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	1	TRUE	NA	0.609421117377328	2		1145	687	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351902	89351902	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	219	1293	0	ENST00000301030.4:c.1048G>C	p.Asp350His	p.D350H	ENST00000301030	NM_001256183.1	350	Gat/Cat	9/13	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.609421117377328	2		1293	705	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29563039	29563039	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs863224447	NA	P-0022332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	163	508	0	ENST00000356175.3:c.3974G>T	p.Arg1325Met	p.R1325M	ENST00000356175	NM_000267.3	1325	aGg/aTg	29/57	0.614438621150884	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.609421117377328	3		508	317	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268479	46268479	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	264	573	0	ENST00000371998.3:c.2866G>T	p.Gly956Cys	p.G956C	ENST00000371998		956	Ggc/Tgc	15/23	0.614438621150884	5	FACETS	1	0.958	1	1	0.958	1	CLONAL	3	TRUE	2	0.609421117377328	5		573	546	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016342	150016342	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	249	765	0	ENST00000253339.5:c.364del	p.Ala122LeufsTer10	p.A122Lfs*10	ENST00000253339		122	Gct/ct	2/7	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	2	TRUE	NA	0.609421117377328	2		765	381	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455070	50455070	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	360	573	0	ENST00000331340.3:c.617G>C	p.Cys206Ser	p.C206S	ENST00000331340	NM_006060.4	206	tGt/tCt	6/8	0.609421117377328	7	FACETS	0.912	0.87	0.955	0.912	0.87	0.955	CLONAL	4	TRUE	3	0.609421117377328	7		573	817	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0022429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	310	785	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.264143363784702	2	FACETS	0.983	0.93	1	0.983	0.93	1	CLONAL	2	TRUE	0	0.335694456172259	2		785	939	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485807	8485807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	55	391	1	ENST00000356435.5:c.3010C>A	p.Pro1004Thr	p.P1004T	ENST00000356435		1004	Cca/Aca	17/35	0.335694456172259	4	FACETS	0.711	0.607	0.824	0.237	0.202	0.275	SUBCLONAL	1	TRUE	1	0.335694456172259	4		392	616	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11264642	11264642	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1288973496	NA	P-0022429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	100	621	0	ENST00000361445.4:c.3920C>G	p.Ala1307Gly	p.A1307G	ENST00000361445	NM_004958.3	1307	gCa/gGa	26/58	0.335694456172259	5	FACETS	1	0.96	1	0.386	0.345	0.431	CLONAL	1	TRUE	2	0.335694456172259	5		621	773	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456356	32456356	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1452803548	NA	P-0022429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	121	751	0	ENST00000332351.3:c.536C>T	p.Pro179Leu	p.P179L	ENST00000332351	NM_024426.4	179	cCc/cTc	1/10	0.2993374739669	3	FACETS	0.86	0.776	0.949	0.43	0.388	0.475	CLONAL	1	TRUE	1	0.335694456172259	3		751	979	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012412	29012412	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	149	708	0	ENST00000282397.4:c.459G>T	p.Glu153Asp	p.E153D	ENST00000282397	NM_002019.4	153	gaG/gaT	4/30	0.326421528322307	2	FACETS	0.976	0.899	1	0.976	0.899	1	CLONAL	2	TRUE	0	0.335694456172259	2		708	455	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778522	3778522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773651163	NA	P-0022429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	347	934	1	ENST00000262367.5:c.6526C>T	p.Pro2176Ser	p.P2176S	ENST00000262367	NM_004380.2	2176	Cca/Tca	31/31	0.2993374739669	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.335694456172259	3		935	1140	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585516	29585516	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0022429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	24	151	0	ENST00000356175.3:c.4265C>G	p.Ser1422Ter	p.S1422*	ENST00000356175	NM_000267.3	1422	tCa/tGa	31/57	0.264143363784702	2	FACETS	1	0.899	1	0.616	0.491	0.755	CLONAL	1	TRUE	0	0.335694456172259	2		151	116	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281319	142281319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1301199562	NA	P-0022429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	87	718	0	ENST00000350721.4:c.925G>A	p.Ala309Thr	p.A309T	ENST00000350721	NM_001184.3	309	Gct/Act	4/47	0.2993374739669	3	FACETS	1	0.92	1	0.524	0.464	0.587	CLONAL	1	TRUE	1	0.335694456172259	3		718	578	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231686	66231686	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs36050417	NA	P-0022429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	20	658	0	ENST00000273854.3:c.2014G>T	p.Ala672Ser	p.A672S	ENST00000273854	NM_004439.5	672	Gca/Tca	11/18	1	2	FACETS	0.63	0.485	0.799	0.63	0.485	0.799	SUBCLONAL	1	TRUE	1	0.335694456172259	2		658	189	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235377	235377	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs748683825	NA	P-0022429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	431	654	0	ENST00000264932.6:c.1183G>T	p.Val395Phe	p.V395F	ENST00000264932	NM_004168.2	395	Gtc/Ttc	9/15	0.26399966880777	4	FACETS	0.961	0.917	1	1	0.996	1	CLONAL	3	TRUE	2	0.335694456172259	4		654	1190	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908251	41908251	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	290	821	0	ENST00000372991.4:c.271T>A	p.Cys91Ser	p.C91S	ENST00000372991	NM_001760.3	91	Tgc/Agc	2/5	0.2993374739669	3	FACETS	0.855	0.804	0.908	0.855	0.804	0.908	CLONAL	2	TRUE	1	0.335694456172259	3		821	1180	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508932	106508932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	71	418	0	ENST00000359195.3:c.926C>T	p.Thr309Met	p.T309M	ENST00000359195	NM_002649.2	309	aCg/aTg	2/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.233498423319322	2		418	440	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847224	68847232	+	inframe_deletion	In_Frame_Del	DEL	TCAGGTGCC	TCAGGTGCC	-	novel	NA	P-0022521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	128	489	0	ENST00000261769.5:c.1147_1155del	p.Gln383_Pro385del	p.Q383_P385del	ENST00000261769	NM_004360.3	382	ggTCAGGTGCCt/ggt	9/16	0.233678174197802	0	FACETS	0.772	0.707	0.838			1	SUBCLONAL	3	FALSE	0	0.233498423319322	0		489	363	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881002	37881003	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCTCCCCC	novel	NA	P-0022521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	181	779	0	ENST00000269571.5:c.2339_2340insCGGCTCCCC	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	-/GGCTCCCCC	20/27	0.233678174197802	3	FACETS	1	0.98	1			1	CLONAL	2	FALSE	NA	0.233498423319322	3		779	740	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171628	36171628	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	123	281	0	ENST00000300305.3:c.937del	p.Leu313SerfsTer15	p.L313Sfs*15	ENST00000300305		313	Ctc/tc	7/8	1	2	FACETS	0.838	0.764	0.915	1	0.991	1	CLONAL	3	FALSE	1	0.233498423319322	2		281	419	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022530-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	308	307	0	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	0.170241293724028	10	FACETS	0.975	0.926	1			1	CLONAL	9	TRUE	NA	0.170241293724028	10		307	693	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252994	36252995	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0022530-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	190	401	0	ENST00000300305.3:c.367dup	p.Asp123GlyfsTer15	p.D123Gfs*15	ENST00000300305		123	gat/gGat	4/8	0.170241293724028	5	FACETS	0.956	0.89	1	1	0.992	1	CLONAL	5	TRUE	2	0.170241293724028	5		401	586	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564734	139564735	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0022530-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	41	426	0	ENST00000308874.7:c.525_526del	p.Val177AlafsTer106	p.V177Afs*106	ENST00000308874		175	CTc/c	7/10	0.170241293724028	2	FACETS	1	0.843	1	0.506	0.421	0.6	CLONAL	1	TRUE	0	0.170241293724028	2		426	476	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022530-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	350	371	0	ENST00000267101.3:c.850G>C	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Cga	7/28	0.170241293724028	10	FACETS	1	0.953	1			1	CLONAL	8	TRUE	NA	0.170241293724028	10		371	862	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577148	7577148	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1060501194	NA	P-0022530-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	72	312	0	ENST00000269305.4:c.790del	p.Leu264TyrfsTer81	p.L264Yfs*81	ENST00000269305	NM_001126112.2	264	Cta/ta	8/11	0.170241293724028	3	FACETS	0.966	0.847	1	0.966	0.847	1	CLONAL	2	TRUE	1	0.170241293724028	3		312	475	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948172	55948172	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022530-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	22	327	0	ENST00000263923.4:c.3799G>A	p.Glu1267Lys	p.E1267K	ENST00000263923	NM_002253.2	1267	Gaa/Aaa	29/30	0.170241293724028	2	FACETS	0.67	0.518	0.846	0.335	0.259	0.423	SUBCLONAL	1	TRUE	0	0.170241293724028	2		327	386	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38135877	38135877	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs780032475	NA	P-0022530-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	65	342	0	ENST00000317025.8:c.3814G>C	p.Glu1272Gln	p.E1272Q	ENST00000317025	NM_023034.1	1272	Gag/Cag	22/24	0.170241293724028	2	FACETS	1	0.96	1	0.645	0.559	0.738	CLONAL	1	TRUE	0	0.170241293724028	2		342	592	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950030	44950031	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022530-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	64	390	0	ENST00000377967.4:c.3800dup	p.Val1268SerfsTer23	p.V1268Sfs*23	ENST00000377967	NM_021140.2	1267	ata/aTta	26/29	0.170241293724028	1	FACETS	0.819	0.712	0.934	1	0.975	1	CLONAL	2	TRUE	0	0.170241293724028	1		390	420	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9787016	9787016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750587940	NA	P-0022530-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	37	352	1	ENST00000377346.4:c.3047G>A	p.Arg1016Gln	p.R1016Q	ENST00000377346	NM_005026.3	1016	cGa/cAa	24/24	0.170241293724028	3	FACETS	1	0.864	1	0.529	0.436	0.633	CLONAL	1	TRUE	1	0.170241293724028	3		353	446	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417117	417117	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0022530-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	28	233	0	ENST00000399788.2:c.3433A>T	p.Arg1145Ter	p.R1145*	ENST00000399788	NM_001042603.1	1145	Aga/Tga	23/28	0.170241293724028	6	FACETS	1	0.868	1	0.279	0.223	0.343	CLONAL	1	TRUE	2	0.170241293724028	6		233	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0022571-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	310	627	0	ENST00000269305.4:c.838A>T	p.Arg280Ter	p.R280*	ENST00000269305	NM_001126112.2	280	Aga/Tga	8/11	0.614743787418883	1	FACETS	0.88	0.834	0.926	0.88	0.834	0.926	CLONAL	1	TRUE	0	0.620279975037096	1		627	784	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950869	32950869	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397507411	NA	P-0022571-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	269	546	1	ENST00000380152.3:c.8695C>T	p.Gln2899Ter	p.Q2899*	ENST00000380152		2899	Caa/Taa	21/27	0.614743787418883	1	FACETS	0.901	0.851	0.952	0.901	0.851	0.952	CLONAL	1	TRUE	0	0.620279975037096	1		547	664	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934295	68934295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022571-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	255	559	0	ENST00000288368.4:c.361G>A	p.Glu121Lys	p.E121K	ENST00000288368	NM_024870.2	121	Gaa/Aaa	4/40	NA	2	FACETS	0.938	0.88	0.997			1	INDETERMINATE	1	TRUE	NA	0.620279975037096	2		559	877	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739583	145739583	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201734382	NA	P-0022571-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1525	324	777	0	ENST00000428558.2:c.1868G>A	p.Arg623His	p.R623H	ENST00000428558	NM_004260.3	623	cGc/cAc	11/22	0.572670095925387	4	FACETS	0.915	0.861	0.971	0.458	0.43	0.486	CLONAL	1	TRUE	2	0.620279975037096	4		777	1849	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0022843-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	214	615	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.973	0.908	1	0.973	0.908	1	CLONAL	1	TRUE	1	0.635885832848671	2		615	692	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858119	152858119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370810560	NA	P-0022843-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	295	654	0	ENST00000406277.2:c.496G>A	p.Val166Ile	p.V166I	ENST00000406277	NM_152274.4	166	Gtc/Atc	6/7	0.142565762852759	1	FACETS	0.673	0.634	0.712	0.673	0.634	0.712	INDETERMINATE	1	TRUE	0	0.635885832848671	1		654	941	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0022922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	170	509	3	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.161358017979927	2	FACETS	0.803	0.739	0.871	0.803	0.739	0.871	CLONAL	2	TRUE	0	0.226603691601443	2		512	934	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729626	162729626	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	54	691	0	ENST00000367921.3:c.712G>T	p.Gly238Cys	p.G238C	ENST00000367921	NM_006182.2	238	Ggc/Tgc	8/18	0.170297179953555	4	FACETS	0.664	0.565	0.772	0.221	0.188	0.258	SUBCLONAL	1	TRUE	1	0.226603691601443	4		691	881	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022747	12022747	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	39	657	0	ENST00000396373.4:c.853G>T	p.Val285Leu	p.V285L	ENST00000396373	NM_001987.4	285	Gtg/Ttg	5/8	1	2	FACETS	0.607	0.502	0.724	0.607	0.502	0.724	SUBCLONAL	1	TRUE	1	0.226603691601443	2		657	567	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73995383	73995383	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	77	591	0	ENST00000318443.5:c.689A>T	p.Asp230Val	p.D230V	ENST00000318443	NM_001024736.1	230	gAt/gTt	4/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.226603691601443	2		591	524	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813729	50813729	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	136	905	0	ENST00000398568.2:c.1283G>T	p.Gly428Val	p.G428V	ENST00000398568	NM_001042412.1	428	gGa/gTa	8/18	0.17484620823041	2	FACETS	1	0.983	1	0.677	0.616	0.742	CLONAL	1	TRUE	0	0.226603691601443	2		905	886	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123688	11123688	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	150	895	0	ENST00000358026.2:c.2338G>T	p.Glu780Ter	p.E780*	ENST00000358026	NM_001128849.1	780	Gag/Tag	16/36	0.17484620823041	2	FACETS	0.763	0.697	0.831	0.763	0.697	0.831	SUBCLONAL	2	TRUE	0	0.226603691601443	2		895	868	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795045	42795045	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	351	1087	0	ENST00000575354.2:c.2125A>T	p.Thr709Ser	p.T709S	ENST00000575354	NM_015125.3	709	Act/Tct	10/20	0.226597835797941	3	FACETS	0.972	0.921	1	0.972	0.921	1	CLONAL	3	TRUE	0	0.226603691601443	3		1087	1183	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730817	40730817	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	82	963	0	ENST00000373198.4:c.3718C>G	p.Leu1240Val	p.L1240V	ENST00000373198	NM_133170.3	1240	Ctt/Gtt	27/32	0.031874594654937	3	FACETS	0.735	0.646	0.831	0.368	0.323	0.416	INDETERMINATE	1	TRUE	1	0.226603691601443	3		963	1096	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748612	40748612	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0022922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	48	514	0	ENST00000373198.4:c.2905-1G>T		p.X969_splice	ENST00000373198	NM_133170.3	969			0.031874594654937	3	FACETS	0.756	0.638	0.886	0.378	0.319	0.443	INDETERMINATE	1	TRUE	1	0.226603691601443	3		514	624	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058615	47058615	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	182	796	0	ENST00000409792.3:c.7663T>C	p.Tyr2555His	p.Y2555H	ENST00000409792	NM_014159.6	2555	Tac/Cac	21/21	0.161358017979927	2	FACETS	0.865	0.799	0.935	0.865	0.799	0.935	CLONAL	2	TRUE	0	0.226603691601443	2		796	928	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136903	55136903	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	52	625	0	ENST00000257290.5:c.1225C>A	p.Leu409Met	p.L409M	ENST00000257290	NM_006206.4	409	Ctg/Atg	8/23	1	2	FACETS	0.682	0.58	0.795	0.682	0.58	0.795	SUBCLONAL	1	TRUE	1	0.226603691601443	2		625	673	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976735	55976735	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0022922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	50	624	1	ENST00000263923.4:c.1092-2A>T		p.X364_splice	ENST00000263923	NM_002253.2	364			1	2	FACETS	0.739	0.627	0.863	0.739	0.627	0.863	SUBCLONAL	1	TRUE	1	0.226603691601443	2		625	597	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176715876	176715876	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	61	837	0	ENST00000439151.2:c.6208T>C	p.Cys2070Arg	p.C2070R	ENST00000439151	NM_022455.4	2070	Tgc/Cgc	21/23	1	2	FACETS	0.676	0.582	0.779	0.676	0.582	0.779	SUBCLONAL	1	TRUE	1	0.226603691601443	2		837	796	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631369	117631369	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	69	645	0	ENST00000368508.3:c.6309T>A	p.Phe2103Leu	p.F2103L	ENST00000368508	NM_002944.2	2103	ttT/ttA	40/43	1	2	FACETS	0.811	0.705	0.925	0.811	0.705	0.925	CLONAL	1	TRUE	1	0.226603691601443	2		645	751	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001244	150001244	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	57	751	0	ENST00000253339.5:c.2360G>T	p.Gly787Val	p.G787V	ENST00000253339		787	gGg/gTg	4/7	1	2	FACETS	0.701	0.6	0.811	0.701	0.6	0.811	SUBCLONAL	1	TRUE	1	0.226603691601443	2		751	718	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771151	161771151	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	127	805	2	ENST00000366898.1:c.1378del	p.Asp460ThrfsTer181	p.D460Tfs*181	ENST00000366898	NM_004562.2	460	Gac/ac	12/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.226603691601443	2		807	864	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467722	50467722	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	253	777	0	ENST00000331340.3:c.957C>G	p.Ile319Met	p.I319M	ENST00000331340	NM_006060.4	319	atC/atG	8/8	0.202901497342622	4	FACETS	0.93	0.871	0.99	0.93	0.871	0.99	CLONAL	3	TRUE	1	0.226603691601443	4		777	982	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436018	116436018	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0022922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	61	883	0	ENST00000397752.3:c.4013C>G	p.Ser1338Ter	p.S1338*	ENST00000397752	NM_000245.2	1338	tCa/tGa	21/21	0.226603691601443	2	FACETS	0.601	0.517	0.693	0.3	0.258	0.347	SUBCLONAL	1	TRUE	0	0.226603691601443	2		883	896	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424239	47424239	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	131	886	1	ENST00000377045.4:c.244G>T	p.Asp82Tyr	p.D82Y	ENST00000377045	NM_001654.4	82	Gat/Tat	4/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.226603691601443	2		887	873	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937617	76937617	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	39	568	0	ENST00000373344.5:c.3131A>G	p.Lys1044Arg	p.K1044R	ENST00000373344	NM_000489.3	1044	aAg/aGg	9/35	1	2	FACETS	0.566	0.468	0.676	0.566	0.468	0.676	SUBCLONAL	1	TRUE	1	0.226603691601443	2		568	608	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	46	436	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.051468295164141	3	FACETS	0.828	0.696	0.974	0.414	0.348	0.487	INDETERMINATE	1	TRUE	1	0.18	3		437	673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0023018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	47	537	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	1	0.18	2		540	519	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	36	615	0	ENST00000304494.5:c.247C>A	p.His83Asn	p.H83N	ENST00000304494	NM_000077.4	83	Cac/Aac	2/3	1	2	FACETS	0.993	0.817	1	0.993	0.817	1	CLONAL	1	TRUE	1	0.18	2		615	403	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121912580	NA	P-0023018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	23	465	0	ENST00000342988.3:c.1157G>T	p.Gly386Val	p.G386V	ENST00000342988	NM_005359.5	386	gGt/gTt	10/12	0.3	1	FACETS	0.661	0.515	0.83	0.661	0.515	0.83	SUBCLONAL	1	TRUE	0	0.18	1		465	352	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906451	32906451	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs431825364	NA	P-0023018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	46	569	0	ENST00000380152.3:c.836G>T	p.Cys279Phe	p.C279F	ENST00000380152		279	tGc/tTc	10/27	0.263925204385003	3	FACETS	1	0.938	1	0.62	0.523	0.728	CLONAL	1	TRUE	1	0.18	3		569	449	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151270	202151270	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	191	900	1	ENST00000358485.4:c.1570C>T	p.Gln524Ter	p.Q524*	ENST00000358485	NM_001080125.1	524	Cag/Tag	9/9	1	2	FACETS	0.875	0.811	0.941	0.875	0.811	0.941	CLONAL	1	TRUE	1	0.583828774863061	2		901	748	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141546	11141546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1298515852	NA	P-0023156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	196	953	0	ENST00000358026.2:c.3523G>A	p.Asp1175Asn	p.D1175N	ENST00000358026	NM_001128849.1	1175	Gac/Aac	25/36	0.583828774863061	1	FACETS	0.86	0.802	0.919	0.86	0.802	0.919	CLONAL	1	TRUE	0	0.583828774863061	1		953	553	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220394	1220394	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs730881972	NA	P-0023156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	249	1011	0	ENST00000326873.7:c.487G>C	p.Gly163Arg	p.G163R	ENST00000326873	NM_000455.4	163	Ggc/Cgc	4/10	0.583828774863061	1	FACETS	0.977	0.921	1	0.977	0.921	1	CLONAL	1	TRUE	0	0.583828774863061	1		1011	618	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770065	56770065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752608224	NA	P-0023156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	180	778	2	ENST00000337432.4:c.61C>T	p.Pro21Ser	p.P21S	ENST00000337432	NM_058216.2	21	Cca/Tca	1/9	1	2	FACETS	0.977	0.905	1	0.977	0.905	1	CLONAL	1	TRUE	1	0.583828774863061	2		780	631	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661663	227661664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761880048	NA	P-0023156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	125	682	13	ENST00000305123.5:c.1791dup	p.His598AlafsTer13	p.H598Afs*13	ENST00000305123	NM_005544.2	597	-/G	1/2	1	2	FACETS	0.78	0.709	0.854	0.78	0.709	0.854	SUBCLONAL	1	TRUE	1	0.583828774863061	2		695	549	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37876038	37876038	+	splice_acceptor_variant	In_Frame_Del	SNP	A	A	G	novel	NA	P-0023156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	217	1064	0	ENST00000269571.5:c.1899-2A>G		p.C634_S649del	ENST00000269571		634			1	2	FACETS	0.912	0.85	0.976	0.912	0.85	0.976	CLONAL	1	TRUE	1	0.583828774863061	2		1064	815	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602939	10602939	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0023156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	239	1068	0	ENST00000171111.5:c.640-1G>T		p.X214_splice	ENST00000171111	NM_203500.1	214			0.583828774863061	1	FACETS	0.957	0.9	1	0.957	0.9	1	CLONAL	1	TRUE	0	0.583828774863061	1		1068	606	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947596	48947596	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	110	756	0	ENST00000267163.4:c.1183C>G	p.Gln395Glu	p.Q395E	ENST00000267163	NM_000321.2	395	Caa/Gaa	12/27	1	2	FACETS	0.669	0.603	0.739	0.669	0.603	0.739	SUBCLONAL	1	TRUE	1	0.583828774863061	2		756	563	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654796	29654796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	147	581	0	ENST00000356175.3:c.5485G>A	p.Val1829Ile	p.V1829I	ENST00000356175	NM_000267.3	1829	Gtc/Atc	37/57	1	2	FACETS	0.904	0.83	0.981	0.904	0.83	0.981	CLONAL	1	TRUE	1	0.583828774863061	2		581	557	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211749	2211749	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0023156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	219	1142	0	ENST00000398665.3:c.1466-1G>A		p.X489_splice	ENST00000398665	NM_032482.2	489			0.583828774863061	1	FACETS	0.788	0.737	0.841	0.788	0.737	0.841	SUBCLONAL	1	TRUE	0	0.583828774863061	1		1142	674	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791157	42791157	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0023156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	192	909	0	ENST00000575354.2:c.218-1G>C		p.X73_splice	ENST00000575354	NM_015125.3	73			0.133348745916731	6	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.583828774863061	6		909	997	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799167	42799167	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	200	1051	0	ENST00000575354.2:c.4651C>G	p.Pro1551Ala	p.P1551A	ENST00000575354	NM_015125.3	1551	Ccc/Gcc	20/20	0.133348745916731	6	FACETS	0.767	0.711	0.826			1	INDETERMINATE	2	TRUE	NA	0.583828774863061	6		1051	968	SUCCESS
REL	5966	MSKCC	GRCh37	2	61144151	61144151	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	157	762	0	ENST00000295025.8:c.534C>G	p.Asn178Lys	p.N178K	ENST00000295025	NM_002908.2	178	aaC/aaG	5/11	1	2	FACETS	0.901	0.829	0.975	0.901	0.829	0.975	CLONAL	1	TRUE	1	0.583828774863061	2		762	597	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495239	212495239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	155	920	0	ENST00000342788.4:c.2027G>A	p.Arg676Lys	p.R676K	ENST00000342788	NM_005235.2	676	aGa/aAa	17/28	1	2	FACETS	0.744	0.682	0.808	0.744	0.682	0.808	SUBCLONAL	1	TRUE	1	0.583828774863061	2		920	714	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069270	30069270	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	371	829	1	ENST00000338641.4:c.1135G>T	p.Glu379Ter	p.E379*	ENST00000338641	NM_000268.3	379	Gag/Tag	12/16	0.540957104371302	2	FACETS	0.975	0.935	1	0.975	0.935	1	CLONAL	2	TRUE	0	0.583828774863061	2		830	652	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155359	185155359	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	158	651	0	ENST00000265026.3:c.600G>C	p.Gln200His	p.Q200H	ENST00000265026	NM_004721.4	200	caG/caC	3/14	1	2	FACETS	0.948	0.873	1	0.948	0.873	1	CLONAL	1	TRUE	1	0.583828774863061	2		651	571	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153668	55153669	+	missense_variant	Missense_Mutation	DNP	CT	CT	AC	novel	NA	P-0023156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	200	933	2	ENST00000257290.5:c.2634_2635delinsAC	p.Trp879Arg	p.W879R	ENST00000257290	NM_006206.4	878	gtCTgg/gtACgg	19/23	1	2	FACETS	0.836	0.776	0.897	0.836	0.776	0.897	CLONAL	1	TRUE	1	0.583828774863061	2		935	820	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007146	152007146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	141	731	0	ENST00000262189.6:c.754C>T	p.His252Tyr	p.H252Y	ENST00000262189	NM_170606.2	252	Cat/Tat	6/59	1	2	FACETS	0.761	0.695	0.829	0.761	0.695	0.829	SUBCLONAL	1	TRUE	1	0.583828774863061	2		731	635	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344020	70344025	+	inframe_deletion	In_Frame_Del	DEL	AGTGAG	AGTGAG	-	novel	NA	P-0023156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	222	614	0	ENST00000374080.3:c.1762_1767del	p.Ser588_Glu589del	p.S588_E589del	ENST00000374080		586	AGTGAG/-	13/45	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.583828774863061	1		614	445	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0023160-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	45	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.102716550540236	4	FACETS	0.473	0.396	0.558	0.237	0.198	0.279	INDETERMINATE	1	TRUE	2	0.327601886812612	4		511	771	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115697	8115703	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTAGAT	TTTAGAT	-	novel	NA	P-0023160-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	68	390	0	ENST00000346208.3:c.1048-4_1050del		p.X350_splice	ENST00000346208		350		6/6	1	2	FACETS	0.918	0.801	1	0.918	0.801	1	CLONAL	1	TRUE	1	0.327601886812612	2		390	452	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063676	67063676	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023160-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	99	467	0	ENST00000412916.2:c.125del	p.Ala42AspfsTer47	p.A42Dfs*47	ENST00000412916		42	gCa/ga	2/6	0.327601886812612	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.327601886812612	1		467	403	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112447	115112448	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCTTTGTCCAGCCG	novel	NA	P-0023192-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	497	574	0	ENST00000257566.3:c.1279_1292dup	p.Ser432GlyfsTer205	p.S432Gfs*205	ENST00000257566	NM_016569.3	431	gcg/gcCGGCTGGACAAAGCg	7/8	0.689932677825155	3	FACETS	1	0.996	1	0.749	0.718	0.781	CLONAL	1	TRUE	1	0.689932677825155	3		574	1293	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134246	11134246	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023192-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	356	470	0	ENST00000358026.2:c.2912T>C	p.Val971Ala	p.V971A	ENST00000358026	NM_001128849.1	971	gTg/gCg	20/36	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.689932677825155	2		470	921	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045806	180045806	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1051985552	NA	P-0023192-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	208	670	0	ENST00000261937.6:c.2965G>C	p.Glu989Gln	p.E989Q	ENST00000261937	NM_182925.4	989	Gag/Cag	21/30	1	2	FACETS	0.605	0.562	0.651	0.605	0.562	0.651	SUBCLONAL	1	TRUE	1	0.689932677825155	2		670	996	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501461	149501461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751904503	NA	P-0023264-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	144	626	1	ENST00000261799.4:c.2326G>A	p.Asp776Asn	p.D776N	ENST00000261799	NM_002609.3	776	Gat/Aat	16/23	0.360799738688032	1	FACETS	0.663	0.604	0.725	0.663	0.604	0.725	SUBCLONAL	1	TRUE	0	0.360799738688032	1		627	987	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856050	68856050	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023264-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	175	580	0	ENST00000261769.5:c.1859del	p.Pro620LeufsTer11	p.P620Lfs*11	ENST00000261769	NM_004360.3	620	Cct/ct	12/16	0.360799738688032	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.360799738688032	1		580	733	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984980	101984981	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0023264-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	73	260	0	ENST00000282441.5:c.432dup	p.Thr145HisfsTer22	p.T145Hfs*22	ENST00000282441	NM_001130145.2	143	acc/aCcc	2/9	0.360799738688032	1	FACETS	0.88	0.774	0.992	0.88	0.774	0.992	CLONAL	1	TRUE	0	0.360799738688032	1		260	377	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0023306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	204	587	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.662161786739905	6	FACETS	0.916	0.857	0.976	0.916	0.857	0.976	CLONAL	3	TRUE	3	0.662161786739905	6		587	521	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004331	150004331	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	27	547	0	ENST00000253339.5:c.1894C>G	p.Gln632Glu	p.Q632E	ENST00000253339		632	Caa/Gaa	3/7	0.624435939764817	3	FACETS	0.733	0.591	0.892	0.244	0.197	0.298	SUBCLONAL	1	TRUE	0	0.662161786739905	3		547	148	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437308	121437308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	62	776	1	ENST00000257555.6:c.1646C>T	p.Ala549Val	p.A549V	ENST00000257555		549	gCc/gTc	9/10	0.565058876990991	4	FACETS	0.486	0.419	0.558	0.243	0.209	0.279	SUBCLONAL	1	TRUE	2	0.662161786739905	4		777	641	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100227	30100227	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	19	411	0	ENST00000331968.5:c.1393G>C	p.Glu465Gln	p.E465Q	ENST00000331968	NM_002742.2	465	Gaa/Caa	10/18	0.662161786739905	3	FACETS	0.311	0.236	0.398	0.155	0.118	0.199	SUBCLONAL	1	TRUE	1	0.662161786739905	3		411	246	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265563	198265563	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	38	802	0	ENST00000335508.6:c.2594G>A	p.Arg865Lys	p.R865K	ENST00000335508	NM_012433.2	865	aGa/aAa	18/25	0.634057339453642	4	FACETS	0.292	0.241	0.35	0.146	0.12	0.175	SUBCLONAL	1	TRUE	2	0.662161786739905	4		802	653	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015117	71015117	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	34	578	0	ENST00000318789.4:c.1813G>C	p.Glu605Gln	p.E605Q	ENST00000318789	NM_032682.5	605	Gag/Cag	20/21	0.662161786739905	3	FACETS	0.278	0.226	0.336	0.139	0.113	0.168	SUBCLONAL	1	TRUE	1	0.662161786739905	3		578	492	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628749	187628749	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	67	733	0	ENST00000441802.2:c.2233G>C	p.Asp745His	p.D745H	ENST00000441802	NM_005245.3	745	Gac/Cac	2/27	0.662161786739905	3	FACETS	0.589	0.514	0.671	0.295	0.257	0.336	SUBCLONAL	1	TRUE	1	0.662161786739905	3		733	457	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979559	2979559	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	43	489	0	ENST00000396946.4:c.688G>C	p.Asp230His	p.D230H	ENST00000396946	NM_032415.4	230	Gat/Cat	6/25	0.662161786739905	6	FACETS	0.598	0.5	0.706	0.149	0.125	0.177	SUBCLONAL	1	TRUE	2	0.662161786739905	6		489	505	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983440	90983440	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	27	504	0	ENST00000265433.3:c.663C>G	p.Ile221Met	p.I221M	ENST00000265433	NM_002485.4	221	atC/atG	6/16	0.662161786739905	5	FACETS	0.326	0.258	0.403	0.081	0.064	0.101	SUBCLONAL	1	TRUE	1	0.662161786739905	5		504	499	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788651	3788651	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023320-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	84	544	1	ENST00000262367.5:c.4303G>T	p.Asp1435Tyr	p.D1435Y	ENST00000262367	NM_004380.2	1435	Gat/Tat	26/31	0.203905877731428	2	FACETS	1	0.95	1	0.561	0.499	0.626	INDETERMINATE	1	TRUE	0	0.417085156629231	2		545	359	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391330	139391331	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCA	novel	NA	P-0023320-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	213	937	0	ENST00000277541.6:c.6857_6860dup	p.Ser2288GlyfsTer67	p.S2288Gfs*67	ENST00000277541	NM_017617.3	2287	ggc/ggTGGGc	34/34	0.421482332454477	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	TRUE	1	0.417085156629231	4		937	462	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942703	44942703	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0023320-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	63	402	1	ENST00000377967.4:c.3285-2A>G		p.X1095_splice	ENST00000377967	NM_021140.2	1095			NA	2	FACETS	1	0.896	1			1	INDETERMINATE	1	TRUE	NA	0.417085156629231	2		403	293	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864736	68864736	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375306652	NA	P-0023320-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	31	524	1	ENST00000288368.4:c.107G>A	p.Arg36Gln	p.R36Q	ENST00000288368	NM_024870.2	36	cGg/cAg	1/40	0.417085156629231	6	FACETS	0.605	0.488	0.736	0.151	0.122	0.184	SUBCLONAL	1	TRUE	2	0.417085156629231	6		525	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0023342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	204	509	3	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.30282678205208	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.388613245789052	2		512	513	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	155	538	0	ENST00000206249.3:c.1607T>C	p.Leu536Pro	p.L536P	ENST00000206249	NM_000125.3	536	cTc/cCc	8/8	0.388613245789052	3	FACETS	0.816	0.75	0.883	0.816	0.75	0.883	CLONAL	2	TRUE	1	0.388613245789052	3		538	584	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240430	98240430	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1227338966	NA	P-0023342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	88	407	0	ENST00000331920.6:c.1254G>T	p.Lys418Asn	p.K418N	ENST00000331920	NM_000264.3	418	aaG/aaT	9/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.388613245789052	2		407	367	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149323	119149323	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	73	362	0	ENST00000264033.4:c.1331G>T	p.Arg444Met	p.R444M	ENST00000264033	NM_005188.3	444	aGg/aTg	9/16	1	2	FACETS	0.837	0.734	0.946	0.837	0.734	0.946	CLONAL	1	TRUE	1	0.388613245789052	2		362	449	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385183	4385183	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	56	343	0	ENST00000261254.3:c.208C>G	p.Gln70Glu	p.Q70E	ENST00000261254	NM_001759.3	70	Cag/Gag	2/5	NA	2	FACETS	0.745	0.64	0.858			1	INDETERMINATE	1	TRUE	NA	0.388613245789052	2		343	387	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112097	115112098	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0023342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	63	611	1	ENST00000257566.3:c.1642_1643delinsTT	p.Gly548Leu	p.G548L	ENST00000257566	NM_016569.3	548	GGg/TTg	7/8	1	2	FACETS	0.663	0.574	0.759	0.663	0.574	0.759	SUBCLONAL	1	TRUE	1	0.388613245789052	2		612	489	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047507	49047507	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1131690906	NA	P-0023342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	52	312	0	ENST00000267163.4:c.2501C>A	p.Ser834Ter	p.S834*	ENST00000267163	NM_000321.2	834	tCa/tAa	24/27	0.388613245789052	1	FACETS	0.88	0.757	1	0.88	0.757	1	CLONAL	1	TRUE	0	0.388613245789052	1		312	245	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81914531	81914531	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	64	331	0	ENST00000359376.3:c.665A>C	p.Lys222Thr	p.K222T	ENST00000359376	NM_002661.3	222	aAa/aCa	8/33	0.255916035531743	2	FACETS	1	0.921	1	0.538	0.47	0.611	CLONAL	1	TRUE	0	0.388613245789052	2		331	306	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39708796	39708796	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	65	310	0	ENST00000361337.2:c.407T>C	p.Leu136Ser	p.L136S	ENST00000361337	NM_003286.2	136	tTa/tCa	6/21	1	2	FACETS	0.967	0.843	1	0.967	0.843	1	CLONAL	1	TRUE	1	0.388613245789052	2		310	346	SUCCESS
ATR	545	MSKCC	GRCh37	3	142180857	142180857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	70	359	0	ENST00000350721.4:c.7117G>A	p.Glu2373Lys	p.E2373K	ENST00000350721	NM_001184.3	2373	Gaa/Aaa	42/47	0.388613245789052	3	FACETS	0.921	0.806	1	0.461	0.403	0.523	CLONAL	1	TRUE	1	0.388613245789052	3		359	467	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169985715	169985715	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs567380681	NA	P-0023342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	69	369	0	ENST00000295797.4:c.377G>T	p.Arg126Leu	p.R126L	ENST00000295797	NM_002740.5	126	cGt/cTt	5/18	0.388613245789052	3	FACETS	0.871	0.76	0.99	0.435	0.38	0.495	CLONAL	1	TRUE	1	0.388613245789052	3		369	487	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139725	55139725	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	66	367	0	ENST00000257290.5:c.1386G>A	p.Trp462Ter	p.W462*	ENST00000257290	NM_006206.4	462	tgG/tgA	10/23	1	2	FACETS	0.839	0.731	0.954	0.839	0.731	0.954	CLONAL	1	TRUE	1	0.388613245789052	2		367	405	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972957	68972957	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	72	398	0	ENST00000288368.4:c.1282C>A	p.Pro428Thr	p.P428T	ENST00000288368	NM_024870.2	428	Cct/Act	11/40	1	2	FACETS	0.917	0.805	1	0.917	0.805	1	CLONAL	1	TRUE	1	0.388613245789052	2		398	404	SUCCESS
AR	367	MSKCC	GRCh37	X	66765773	66765773	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	232	359	0	ENST00000374690.3:c.785A>G	p.Gln262Arg	p.Q262R	ENST00000374690	NM_000044.3	262	cAg/cGg	1/8	0.385507440550724	2	FACETS	0.877	0.829	0.924			1	CLONAL	3	TRUE	NA	0.388613245789052	2		359	454	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019990	123019990	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	188	290	0	ENST00000355640.3:c.478A>G	p.Met160Val	p.M160V	ENST00000355640		160	Atg/Gtg	2/7	0.385507440550724	2	FACETS	0.898	0.845	0.952			1	CLONAL	3	TRUE	NA	0.388613245789052	2		290	359	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112098	115112098	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	63	612	0	ENST00000257566.3:c.1642G>T	p.Gly548Trp	p.G548W	ENST00000257566	NM_016569.3	548	Ggg/Tgg	7/8	1	2	FACETS	0.663	0.574	0.759	0.663	0.574	0.759	SUBCLONAL	1	TRUE	1	0.388613245789052	2		612	489	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426061	49426061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	96	513	0	ENST00000301067.7:c.12427G>A	p.Asp4143Asn	p.D4143N	ENST00000301067	NM_003482.3	4143	Gat/Aat	39/54	1	2	FACETS	0.945	0.845	1	0.945	0.845	1	CLONAL	1	TRUE	1	0.388613245789052	2		513	523	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266731	198266731	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	63	410	0	ENST00000335508.6:c.2201G>T	p.Gly734Val	p.G734V	ENST00000335508	NM_012433.2	734	gGt/gTt	15/25	1	2	FACETS	0.787	0.683	0.899	0.787	0.683	0.899	SUBCLONAL	1	TRUE	1	0.388613245789052	2		410	412	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435186	49435186	+	frameshift_variant	Frame_Shift_Ins	INS	T	T	AG	novel	NA	P-0023342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	89	395	0	ENST00000301067.7:c.6367delinsCT	p.Thr2123LeufsTer32	p.T2123Lfs*32	ENST00000301067	NM_003482.3	2123	Acc/CTcc	31/54	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.388613245789052	2		395	436	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0023357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	47	215	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.27302960644506	2		215	330	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226174	2226174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	97	603	0	ENST00000326181.6:c.1871C>T	p.Ser624Phe	p.S624F	ENST00000326181	NM_032271.2	624	tCc/tTc	19/21	1	2	FACETS	0.789	0.703	0.882	0.789	0.703	0.882	SUBCLONAL	1	TRUE	1	0.27302960644506	2		603	900	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270593	98270595	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	rs756897237	NA	P-0023357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	10	74	0	ENST00000331920.6:c.49_51del	p.Gly17del	p.G17del	ENST00000331920	NM_000264.3	17	GGC/-	1/24	1	2	FACETS	0.555	0.377	0.776	0.555	0.377	0.776	SUBCLONAL	1	TRUE	1	0.27302960644506	2		74	132	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252880	36252880	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	100	375	0	ENST00000300305.3:c.482T>A	p.Leu161His	p.L161H	ENST00000300305		161	cTc/cAc	4/8	0.27302960644506	1	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	0	0.27302960644506	1		375	627	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217458	7217458	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	112	428	0	ENST00000380728.2:c.338C>A	p.Ser113Ter	p.S113*	ENST00000380728		113	tCa/tAa	5/11	0.27302960644506	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.27302960644506	1		428	669	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849652	68849652	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	112	420	0	ENST00000261769.5:c.1555C>T	p.Gln519Ter	p.Q519*	ENST00000261769	NM_004360.3	519	Cag/Tag	10/16	0.27302960644506	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.27302960644506	1		420	666	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016559	12016559	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	52	305	0	ENST00000353533.5:c.695C>T	p.Pro232Leu	p.P232L	ENST00000353533	NM_003010.3	232	cCt/cTt	7/11	0.27302960644506	1	FACETS	0.839	0.716	0.973	0.839	0.716	0.973	CLONAL	1	TRUE	0	0.27302960644506	1		305	392	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729435	41729435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	95	642	1	ENST00000242208.4:c.1094C>T	p.Ser365Leu	p.S365L	ENST00000242208	NM_002192.2	365	tCa/tTa	3/3	0.427734402626719	8	FACETS	1	0.899	1	0.202	0.179	0.227	CLONAL	1	TRUE	3	0.427734402626719	8		643	1002	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143293	30143293	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748978993	NA	P-0023534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	172	778	1	ENST00000389048.3:c.233C>T	p.Ser78Leu	p.S78L	ENST00000389048	NM_004304.4	78	tCg/tTg	1/29	0.427734402626719	3	FACETS	1	0.988	1	0.696	0.642	0.752	CLONAL	1	TRUE	1	0.427734402626719	3		779	701	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412046	116412046	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	G	novel	NA	P-0023534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	374	989	2	ENST00000397752.3:c.3028+3A>G		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.427734402626719	3	FACETS	0.984	0.942	1	0.984	0.942	1	CLONAL	3	TRUE	0	0.427734402626719	3		991	719	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237786	16237786	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	47	470	0	ENST00000375759.3:c.1233G>C	p.Trp411Cys	p.W411C	ENST00000375759	NM_015001.2	411	tgG/tgC	5/15	1	2	FACETS	0.624	0.529	0.729	0.624	0.529	0.729	SUBCLONAL	1	TRUE	1	0.427734402626719	2		470	352	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257520	16257520	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	84	538	0	ENST00000375759.3:c.4785G>C	p.Gln1595His	p.Q1595H	ENST00000375759	NM_015001.2	1595	caG/caC	11/15	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.427734402626719	2		538	363	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818205	43818205	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0023534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	93	549	0	ENST00000372470.3:c.1670C>G	p.Ser557Ter	p.S557*	ENST00000372470	NM_005373.2	557	tCa/tGa	12/12	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.427734402626719	2		549	399	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818270	43818270	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	113	730	0	ENST00000372470.3:c.1735C>G	p.Pro579Ala	p.P579A	ENST00000372470	NM_005373.2	579	Cct/Gct	12/12	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.427734402626719	2		730	519	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729659	162729659	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	80	596	0	ENST00000367921.3:c.745C>G	p.His249Asp	p.H249D	ENST00000367921	NM_006182.2	249	Cac/Gac	8/18	0.427734402626719	4	FACETS	0.853	0.751	0.962	0.284	0.25	0.321	CLONAL	1	TRUE	1	0.427734402626719	4		596	626	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343663	343663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	121	1016	3	ENST00000262320.3:c.2011G>A	p.Glu671Lys	p.E671K	ENST00000262320	NM_003502.3	671	Gag/Aag	8/11	0.40242264293432	4	FACETS	0.901	0.813	0.993	0.45	0.406	0.497	CLONAL	1	TRUE	2	0.427734402626719	4		1019	897	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444299	50444299	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	41	348	0	ENST00000331340.3:c.229G>C	p.Glu77Gln	p.E77Q	ENST00000331340	NM_006060.4	77	Gaa/Caa	4/8	0.427734402626719	8	FACETS	0.738	0.614	0.877	0.148	0.122	0.176	SUBCLONAL	1	TRUE	3	0.427734402626719	8		348	593	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424493	47424493	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	76	631	0	ENST00000377045.4:c.413C>G	p.Ser138Cys	p.S138C	ENST00000377045	NM_001654.4	138	tCc/tGc	5/16	NA	2	FACETS	0.728	0.64	0.822			1	INDETERMINATE	1	TRUE	NA	0.427734402626719	2		631	488	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352234	70352234	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	88	595	0	ENST00000374080.3:c.4261G>A	p.Glu1421Lys	p.E1421K	ENST00000374080		1421	Gag/Aag	31/45	0.261458367539509	3	FACETS	1	0.92	1	0.348	0.309	0.389	CLONAL	1	TRUE	0	0.427734402626719	3		595	479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577126	7577126	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	216	664	0	ENST00000269305.4:c.812A>T	p.Glu271Val	p.E271V	ENST00000269305	NM_001126112.2	271	gAg/gTg	8/11	0.281458588611363	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.281458588611363	2		664	747	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805142	43805142	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	87	663	0	ENST00000372470.3:c.592C>T	p.Gln198Ter	p.Q198*	ENST00000372470	NM_005373.2	198	Cag/Tag	4/12	0.238855417494736	3	FACETS	1	0.955	1	0.579	0.513	0.649	CLONAL	1	TRUE	1	0.281458588611363	3		663	609	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111118	193111118	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	70	455	0	ENST00000367435.3:c.651G>T	p.Glu217Asp	p.E217D	ENST00000367435	NM_024529.4	217	gaG/gaT	7/17	0.281458588611363	7	FACETS	1	0.889	1			1	CLONAL	1	TRUE	NA	0.281458588611363	7		455	828	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741558	17741558	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	70	408	0	ENST00000250003.3:c.229G>C	p.Glu77Gln	p.E77Q	ENST00000250003	NM_002478.4	77	Gag/Cag	1/3	0.117364403728601	3	FACETS	1	0.948	1	0.584	0.51	0.663	INDETERMINATE	1	TRUE	1	0.281458588611363	3		408	486	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170484	108170484	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	71	510	0	ENST00000278616.4:c.5049C>G	p.Phe1683Leu	p.F1683L	ENST00000278616	NM_000051.3	1683	ttC/ttG	34/63	0.117364403728601	3	FACETS	0.846	0.738	0.963	0.423	0.369	0.482	INDETERMINATE	1	TRUE	1	0.281458588611363	3		510	680	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231179	46231179	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	163	466	0	ENST00000334344.6:c.1099G>T	p.Asp367Tyr	p.D367Y	ENST00000334344	NM_152641.2	367	Gat/Tat	9/21	0.219541711791946	5	FACETS	1	0.968	1	0.734	0.675	0.796	CLONAL	2	TRUE	2	0.281458588611363	5		466	748	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563399	21563399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769467425	NA	P-0023598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	256	929	2	ENST00000382592.4:c.520G>A	p.Glu174Lys	p.E174K	ENST00000382592	NM_014572.2	174	Gaa/Aaa	4/8	0.234012002907784	2	FACETS	0.98	0.919	1	0.98	0.919	1	CLONAL	2	TRUE	0	0.281458588611363	2		931	928	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38064133	38064133	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	100	596	0	ENST00000250448.2:c.45G>A	p.Trp15Ter	p.W15*	ENST00000250448	NM_004496.3	15	tgG/tgA	1/2	0.238855417494736	3	FACETS	1	0.955	1	0.565	0.505	0.629	CLONAL	1	TRUE	1	0.281458588611363	3		596	717	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170756	11170756	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0023598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	171	758	0	ENST00000358026.2:c.4900A>T	p.Lys1634Ter	p.K1634*	ENST00000358026	NM_001128849.1	1634	Aag/Tag	35/36	0.227582197980796	2	FACETS	0.935	0.863	1	0.935	0.863	1	CLONAL	2	TRUE	0	0.281458588611363	2		758	650	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912435	50912435	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	245	898	0	ENST00000440232.2:c.1949C>T	p.Ser650Leu	p.S650L	ENST00000440232	NM_002691.3	650	tCa/tTa	16/27	0.250559812200685	3	FACETS	0.85	0.797	0.904	0.85	0.797	0.904	CLONAL	3	TRUE	0	0.281458588611363	3		898	779	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143522	30143522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	35	384	0	ENST00000389048.3:c.4G>A	p.Gly2Arg	p.G2R	ENST00000389048	NM_004304.4	2	Gga/Aga	1/29	0.238855417494736	3	FACETS	1	0.847	1	0.516	0.425	0.617	CLONAL	1	TRUE	1	0.281458588611363	3		384	275	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702579	52702579	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	198	754	0	ENST00000394830.3:c.319G>C	p.Asp107His	p.D107H	ENST00000394830	NM_018313.4	107	Gat/Cat	4/30	0.219541711791946	5	FACETS	0.812	0.751	0.876	0.541	0.5	0.584	CLONAL	2	TRUE	2	0.281458588611363	5		754	1232	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876458	35876458	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	177	717	0	ENST00000303115.3:c.1250C>A	p.Pro417His	p.P417H	ENST00000303115	NM_002185.3	417	cCt/cAt	8/8	0.281458588611363	5	FACETS	0.909	0.837	0.984	0.606	0.558	0.656	CLONAL	2	TRUE	2	0.281458588611363	5		717	984	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662382	117662383	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	81	629	0	ENST00000368508.3:c.4994dup	p.Leu1665PhefsTer7	p.L1665Ffs*7	ENST00000368508	NM_002944.2	1665	ttg/ttTg	30/43	0.238855417494736	3	FACETS	0.824	0.725	0.93	0.412	0.362	0.465	CLONAL	1	TRUE	1	0.281458588611363	3		629	797	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917721	151917721	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0023598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	40	192	0	ENST00000262189.6:c.3599C>G	p.Ser1200Ter	p.S1200*	ENST00000262189	NM_170606.2	1200	tCa/tGa	23/59	0.281458588611363	4	FACETS	1	0.926	1			1	CLONAL	1	TRUE	NA	0.281458588611363	4		192	301	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217369	123217369	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs752542119	NA	P-0023598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	48	603	0	ENST00000218089.9:c.3023C>G	p.Ser1008Cys	p.S1008C	ENST00000218089	NM_001042749.1	1008	tCt/tGt	29/35	0.238855417494736	3	FACETS	0.431	0.363	0.507	0.216	0.181	0.254	SUBCLONAL	1	TRUE	1	0.281458588611363	3		603	902	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152864441	152864441	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	62	263	0	ENST00000406277.2:c.85G>T	p.Ala29Ser	p.A29S	ENST00000406277	NM_152274.4	29	Gcg/Tcg	3/7	0.238855417494736		FACETS		0.768	1				CLONAL	2	TRUE	1	0.281458588611363	3		263	285	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954196	48954198	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	novel	NA	P-0023771-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	72	260	0	ENST00000267163.4:c.1397_1399del	p.Glu466_Arg467delinsGly	p.E466_R467delinsG	ENST00000267163	NM_000321.2	466	gAACga/gga	15/27	0.452336453246536	2	FACETS	0.977	0.86	1	0.488	0.43	0.55	CLONAL	1	FALSE	0	0.452336453246536	2		260	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577052	7577053	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0023771-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	705	578	0	ENST00000269305.4:c.885_886del	p.His296ProfsTer9	p.H296Pfs*9	ENST00000269305	NM_001126112.2	295	ccTCac/ccac	8/11	0.452336453246536	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	FALSE	0	0.452336453246536	3		578	1239	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372094	55372094	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1041891434	NA	P-0023771-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	573	409	1	ENST00000297316.4:c.784C>T	p.Pro262Ser	p.P262S	ENST00000297316	NM_022454.3	262	Ccc/Tcc	2/2	0.452336453246536	5	FACETS	0.887	0.855	0.919	0.887	0.855	0.919	CLONAL	4	FALSE	1	0.452336453246536	5		410	1199	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0023904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	176	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.780217372148675	6	FACETS	0.84	0.777	0.905	0.42	0.388	0.453	CLONAL	2	TRUE	2	0.88426977114643	6		511	656	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0023904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	300	551	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.821247763904419	2	FACETS	0.958	0.931	0.983	0.958	0.931	0.983	CLONAL	2	TRUE	0	0.88426977114643	2		551	354	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0023904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	45	565	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.847717894807633	4	FACETS	0.562	0.474	0.659	0.187	0.158	0.22	SUBCLONAL	1	TRUE	1	0.88426977114643	4		565	341	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809308	243809308	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	325	374	2	ENST00000263826.5:c.316G>T	p.Ala106Ser	p.A106S	ENST00000263826	NM_005465.4	106	Gca/Tca	4/13	0.88426977114643	4	FACETS	1	0.987	1	0.785	0.758	0.811	CLONAL	3	TRUE	0	0.88426977114643	4		376	441	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941665	48941665	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0023904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	167	297	0	ENST00000267163.4:c.975T>G	p.Tyr325Ter	p.Y325*	ENST00000267163	NM_000321.2	325	taT/taG	10/27	0.74947574982398	4	FACETS	0.927	0.894	0.956	0.927	0.894	0.956	CLONAL	4	TRUE	0	0.88426977114643	4		297	192	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434526	110434526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	126	527	0	ENST00000375856.3:c.3875G>A	p.Gly1292Asp	p.G1292D	ENST00000375856	NM_003749.2	1292	gGt/gAt	1/2	0.830692471238085	3	FACETS	1	0.968	1	0.373	0.342	0.406	CLONAL	1	TRUE	0	0.88426977114643	3		527	367	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032005	10032005	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	182	562	2	ENST00000330684.3:c.818C>A	p.Pro273Gln	p.P273Q	ENST00000330684	NM_001134407.1	273	cCa/cAa	3/13	0.724925410408604	4	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	2	0.88426977114643	4		564	372	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955083	93955083	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	147	356	1	ENST00000369303.4:c.2815A>G	p.Arg939Gly	p.R939G	ENST00000369303	NM_004440.3	939	Aga/Gga	16/17	0.823441157203682	3	FACETS	1	0.98	1	0.73	0.688	0.77	CLONAL	2	TRUE	0	0.88426977114643	3		357	219	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434503	140434503	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758134174	NA	P-0023904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	83	313	2	ENST00000288602.6:c.2195C>T	p.Ser732Phe	p.S732F	ENST00000288602	NM_004333.4	732	tCc/tTc	18/18	1	2	FACETS	0.925	0.833	1	0.925	0.833	1	CLONAL	1	TRUE	1	0.88426977114643	2		315	203	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0023984-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	195	615	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.4409517451613	2		615	805	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063347	67063347	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023984-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	100	366	1	ENST00000412916.2:c.37G>T	p.Glu13Ter	p.E13*	ENST00000412916		13	Gag/Tag	1/6	0.4409517451613	1	FACETS	0.735	0.66	0.815	0.735	0.66	0.815	SUBCLONAL	1	FALSE	0	0.4409517451613	1		367	481	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252855	36252856	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0023984-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	124	307	0	ENST00000300305.3:c.506dup	p.Gly170ArgfsTer43	p.G170Rfs*43	ENST00000300305		169	aga/agGa	4/8	0.186652494185239	0	FACETS	0.617	0.561	0.675			1	INDETERMINATE	1	FALSE	0	0.4409517451613	0		307	510	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120528	70120528	+	stop_lost	Nonstop_Mutation	SNP	A	A	T	novel	NA	P-0023984-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	398	825	0	ENST00000245479.2:c.1530A>T	p.Ter510CysextTer49	p.*510Cext*49	ENST00000245479	NM_000346.3	510	tgA/tgT	3/3	0.386242864243784	2	FACETS	0.807	0.769	0.846	0.807	0.769	0.846	CLONAL	2	FALSE	0	0.4409517451613	2		825	1118	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845971	151845972	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0023984-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	34	439	0	ENST00000262189.6:c.13040dup	p.Leu4348AlafsTer3	p.L4348Afs*3	ENST00000262189	NM_170606.2	4347	ccg/ccCg	52/59	1	2	FACETS	0.228	0.185	0.276	0.228	0.185	0.276	SUBCLONAL	1	FALSE	1	0.4409517451613	2		439	676	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0024200-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	128	441	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.108152383790671	5	FACETS	1	0.962	1	0.551	0.502	0.603	INDETERMINATE	2	TRUE	1	0.31466184709305	5		441	543	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610113	10610113	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024200-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	247	719	0	ENST00000171111.5:c.597G>T	p.Leu199Phe	p.L199F	ENST00000171111	NM_203500.1	199	ttG/ttT	2/6	0.31466184709305	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.31466184709305	2		719	670	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857426	9857426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024200-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	83	472	0	ENST00000330684.3:c.3975C>A	p.Tyr1325Ter	p.Y1325*	ENST00000330684	NM_001134407.1	1325	taC/taA	13/13	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.31466184709305	2		472	464	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120508998	120508998	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0024200-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	71	453	0	ENST00000256646.2:c.1567+1del		p.X523_splice	ENST00000256646	NM_024408.3	523			1	2	FACETS	0.831	0.726	0.944	0.831	0.726	0.944	CLONAL	1	TRUE	1	0.31466184709305	2		453	543	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753837	42753842	+	inframe_deletion	In_Frame_Del	DEL	GGAAGT	GGAAGT	-	novel	NA	P-0024200-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	232	906	0	ENST00000222329.4:c.422_427del	p.His141_Phe142del	p.H141_F142del	ENST00000222329	NM_006494.2	141	cACTTCCgc/cgc	4/4	NA	2	FACETS	1	0.942	1			1	INDETERMINATE	2	TRUE	NA	0.31466184709305	2		906	733	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532770	187532770	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024200-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	81	612	0	ENST00000441802.2:c.9623G>T	p.Arg3208Met	p.R3208M	ENST00000441802	NM_005245.3	3208	aGg/aTg	14/27	1	2	FACETS	0.734	0.647	0.828	0.734	0.647	0.828	SUBCLONAL	1	TRUE	1	0.31466184709305	2		612	701	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0024229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	200	851	2	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.22313772150475	3	FACETS	0.919	0.854	0.985	0.919	0.854	0.985	CLONAL	3	TRUE	0	0.22313772150475	3		853	723	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683659	162683659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769099303	NA	P-0024229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	50	607	0	ENST00000366898.1:c.310C>T	p.Arg104Trp	p.R104W	ENST00000366898	NM_004562.2	104	Cgg/Tgg	3/12	0.193729433534305	4	FACETS	0.95	0.806	1	0.475	0.403	0.555	CLONAL	1	TRUE	2	0.22313772150475	4		607	577	SUCCESS
APC	324	MSKCC	GRCh37	5	112154933	112154933	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660612	NA	P-0024229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	55	739	1	ENST00000257430.4:c.1204C>T	p.Arg402Cys	p.R402C	ENST00000257430	NM_000038.5	402	Cgt/Tgt	10/16	0.178717459326818	2	FACETS	0.854	0.731	0.99	0.427	0.365	0.495	CLONAL	1	TRUE	0	0.22313772150475	2		740	577	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546394	46546394	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	42	648	0	ENST00000262741.5:c.135G>C	p.Met45Ile	p.M45I	ENST00000262741	NM_003629.3	45	atG/atC	2/10	0.197012538500935	3	FACETS	0.808	0.674	0.956	0.404	0.337	0.478	CLONAL	1	TRUE	1	0.22313772150475	3		648	518	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430582	78430582	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	45	720	0	ENST00000370768.2:c.708G>C	p.Arg236Ser	p.R236S	ENST00000370768	NM_003902.3	236	agG/agC	9/20	0.197012538500935	3	FACETS	0.958	0.806	1	0.479	0.403	0.563	CLONAL	1	TRUE	1	0.22313772150475	3		720	468	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138858	64138858	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs111697527	NA	P-0024229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	111	438	1	ENST00000334205.4:c.2225G>T	p.Arg742Leu	p.R742L	ENST00000334205	NM_003942.2	742	cGc/cTc	17/17	0.201021488987988	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.22313772150475	3		439	482	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442811	442811	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	60	424	0	ENST00000399788.2:c.1495G>C	p.Glu499Gln	p.E499Q	ENST00000399788	NM_001042603.1	499	Gag/Cag	12/28	0.183880300124594	5	FACETS	0.918	0.794	1	0.612	0.529	0.701	CLONAL	2	TRUE	2	0.22313772150475	5		424	391	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222604	69222604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	43	787	0	ENST00000462284.1:c.577G>A	p.Asp193Asn	p.D193N	ENST00000462284	NM_002392.5	193	Gat/Aat	8/11	0.22313772150475	4	FACETS	0.688	0.575	0.815			1	SUBCLONAL	1	TRUE	NA	0.22313772150475	4		787	685	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724477	43724477	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	48	1012	0	ENST00000382044.4:c.3590A>T	p.Gln1197Leu	p.Q1197L	ENST00000382044	NM_001141980.1	1197	cAa/cTa	17/28	0.22313772150475	3	FACETS	0.558	0.47	0.655	0.186	0.156	0.219	SUBCLONAL	1	TRUE	0	0.22313772150475	3		1012	857	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718779	190718779	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	75	471	0	ENST00000441310.2:c.937G>T	p.Asp313Tyr	p.D313Y	ENST00000441310	NM_000534.4	313	Gat/Tat	8/13	0.22313772150475	4	FACETS	0.981	0.864	1			1	CLONAL	2	TRUE	NA	0.22313772150475	4		471	419	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719766	190719766	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	24	424	0	ENST00000441310.2:c.1768C>G	p.Leu590Val	p.L590V	ENST00000441310	NM_000534.4	590	Ctc/Gtc	9/13	0.22313772150475	4	FACETS	0.997	0.783	1			1	CLONAL	1	TRUE	NA	0.22313772150475	4		424	264	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125825	47125825	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	67	377	1	ENST00000409792.3:c.5445G>T	p.Leu1815Phe	p.L1815F	ENST00000409792	NM_014159.6	1815	ttG/ttT	12/21	0.22313772150475	3	FACETS	0.993	0.869	1	0.993	0.869	1	CLONAL	2	TRUE	1	0.22313772150475	3		378	336	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164061	106164061	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	25	442	0	ENST00000380013.4:c.3571C>G	p.Gln1191Glu	p.Q1191E	ENST00000380013	NM_001127208.2	1191	Cag/Gag	5/11	0.22313772150475	3	FACETS	0.825	0.651	1	0.412	0.325	0.512	CLONAL	1	TRUE	1	0.22313772150475	3		442	302	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322916	31322916	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	184	1016	0	ENST00000412585.2:c.980T>C	p.Val327Ala	p.V327A	ENST00000412585	NM_005514.6	327	gTc/gCc	5/8	0.183880300124594	5	FACETS	0.952	0.88	1	0.952	0.88	1	CLONAL	3	TRUE	2	0.22313772150475	5		1016	771	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027747	152027747	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	62	918	1	ENST00000262189.6:c.328C>T	p.Arg110Ter	p.R110*	ENST00000262189	NM_170606.2	110	Cga/Tga	3/59	1	2	FACETS	0.917	0.792	1	0.917	0.792	1	CLONAL	1	TRUE	1	0.22313772150475	2		919	606	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205115	38205115	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	66	885	3	ENST00000317025.8:c.575G>T	p.Ser192Ile	p.S192I	ENST00000317025	NM_023034.1	192	aGc/aTc	2/24	0.22313772150475	7	FACETS	0.924	0.8	1	0.185	0.16	0.212	CLONAL	1	TRUE	2	0.22313772150475	7		888	997	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995534	68995534	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	39	883	1	ENST00000288368.4:c.1938G>A	p.Met646Ile	p.M646I	ENST00000288368	NM_024870.2	646	atG/atA	18/40	0.201322641167166	4	FACETS	0.732	0.606	0.874	0.244	0.202	0.292	SUBCLONAL	1	TRUE	1	0.22313772150475	4		884	584	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009337	69009337	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	46	584	0	ENST00000288368.4:c.2454A>T	p.Glu818Asp	p.E818D	ENST00000288368	NM_024870.2	818	gaA/gaT	22/40	0.201322641167166	4	FACETS	0.934	0.786	1	0.311	0.262	0.366	CLONAL	1	TRUE	1	0.22313772150475	4		584	540	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69050741	69050741	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	35	453	0	ENST00000288368.4:c.4076C>A	p.Pro1359His	p.P1359H	ENST00000288368	NM_024870.2	1359	cCt/cAt	33/40	0.201322641167166	4	FACETS	1	0.872	1	0.359	0.295	0.431	CLONAL	1	TRUE	1	0.22313772150475	4		453	356	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967543	90967543	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	33	592	0	ENST00000265433.3:c.1365C>G	p.Ile455Met	p.I455M	ENST00000265433	NM_002485.4	455	atC/atG	10/16	0.201322641167166	4	FACETS	0.855	0.697	1	0.285	0.232	0.345	CLONAL	1	TRUE	1	0.22313772150475	4		592	423	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2114342	2114342	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45517179	NA	P-0024309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	609	734	2	ENST00000219476.3:c.1513C>T	p.Arg505Ter	p.R505*	ENST00000219476	NM_000548.3	505	Cga/Tga	15/42	0.917597526695713	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.918033658108902	2		736	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577571	7577586	+	frameshift_variant	Frame_Shift_Del	DEL	ATGTAGTTGTAGTGGA	ATGTAGTTGTAGTGGA	-	novel	NA	P-0024309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	492	655	0	ENST00000269305.4:c.695_710del	p.Ile232SerfsTer10	p.I232Sfs*10	ENST00000269305	NM_001126112.2	232	aTCCACTACAACTACATg/ag	7/11	0.911405349539637	2	FACETS	0.964	0.945	0.981	0.964	0.945	0.981	CLONAL	2	TRUE	0	0.918033658108902	2		655	556	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0024356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	561	816	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.368651975401778	8	FACETS	0.94	0.906	0.973	0.805	0.776	0.834	CLONAL	6	TRUE	1	0.368651975401778	8		816	1137	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834552	156834552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540521894	NA	P-0024356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1255	225	1063	0	ENST00000524377.1:c.320C>T	p.Ala107Val	p.A107V	ENST00000524377	NM_002529.3	107	gCg/gTg	3/17	0.368651975401778	6	FACETS	1	0.991	1	0.358	0.332	0.385	CLONAL	1	TRUE	2	0.368651975401778	6		1063	1480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578204	7578204	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	438	943	1	ENST00000269305.4:c.645T>A	p.Ser215Arg	p.S215R	ENST00000269305	NM_001126112.2	215	agT/agA	6/11	0.368651975401778	3	FACETS	0.896	0.857	0.935	0.896	0.857	0.935	CLONAL	3	TRUE	0	0.368651975401778	3		944	1047	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743310	162743310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	71	654	1	ENST00000367921.3:c.1780G>A	p.Ala594Thr	p.A594T	ENST00000367921	NM_006182.2	594	Gcc/Acc	14/18	0.368651975401778	6	FACETS	0.693	0.604	0.791	0.173	0.151	0.198	SUBCLONAL	1	TRUE	2	0.368651975401778	6		655	965	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48921921	48921961	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACGAAAAAATGTTAAAAAGTCATAATGTTTTTCTTTTCAGG	ACGAAAAAATGTTAAAAAGTCATAATGTTTTTCTTTTCAGG	-	novel	NA	P-0024356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	48	577	1	ENST00000267163.4:c.501-38_503del		p.X167_splice	ENST00000267163	NM_000321.2	167		5/27	0.256627555783802	2	FACETS	0.819	0.696	0.953	0.409	0.348	0.477	CLONAL	1	TRUE	0	0.368651975401778	2		578	318	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0024397-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	251	496	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.711405120594276	2		496	683	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355129	73355129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024397-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	234	425	0	ENST00000377767.4:c.241G>A	p.Glu81Lys	p.E81K	ENST00000377767	NM_014953.3	81	Gag/Aag	2/21	0.711405120594276	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.711405120594276	1		425	401	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150547	157150547	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554256749	NA	P-0024397-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	256	459	1	ENST00000346085.5:c.1729C>T	p.Gln577Ter	p.Q577*	ENST00000346085	NM_020732.3	577	Cag/Tag	2/20	0.661482891816878	3	FACETS	1	0.993	1	0.467	0.44	0.495	CLONAL	1	TRUE	0	0.711405120594276	3		460	696	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106037	8106050	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGCGGGCTCTAT	CCTGCGGGCTCTAT	-	novel	NA	P-0024397-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	298	552	0	ENST00000346208.3:c.858_871del	p.Cys287GlnfsTer11	p.C287Qfs*11	ENST00000346208		286	gCCTGCGGGCTCTAT/g	4/6	1	2	FACETS	0.982	0.928	1	0.982	0.928	1	CLONAL	1	TRUE	1	0.711405120594276	2		552	853	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827919	40827919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024397-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	279	525	0	ENST00000373198.4:c.2509G>A	p.Glu837Lys	p.E837K	ENST00000373198	NM_133170.3	837	Gaa/Aaa	17/32	1	2	FACETS	0.877	0.826	0.93	0.877	0.826	0.93	CLONAL	1	TRUE	1	0.711405120594276	2		525	894	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148907	119148907	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024397-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	32	397	0	ENST00000264033.4:c.1127C>G	p.Ser376Cys	p.S376C	ENST00000264033	NM_005188.3	376	tCc/tGc	8/16	0.711405120594276	1	FACETS	0.123	0.1	0.15	0.123	0.1	0.15	SUBCLONAL	1	TRUE	0	0.711405120594276	1		397	470	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222595	2222595	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024397-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	311	531	0	ENST00000326181.6:c.789G>T	p.Lys263Asn	p.K263N	ENST00000326181	NM_032271.2	263	aaG/aaT	9/21	0.711405120594276	3	FACETS	1	0.981	1	0.542	0.511	0.574	CLONAL	1	TRUE	1	0.711405120594276	3		531	1093	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89818569	89818569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024397-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	255	601	0	ENST00000389301.3:c.3043G>A	p.Glu1015Lys	p.E1015K	ENST00000389301	NM_000135.2	1015	Gag/Aag	31/43	0.711405120594276	3	FACETS	0.761	0.711	0.813	0.381	0.355	0.407	SUBCLONAL	1	TRUE	1	0.711405120594276	3		601	1277	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119682	70119683	+	splice_acceptor_variant	Splice_Site	INS	-	-	G	novel	NA	P-0024397-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	564	527	0	ENST00000245479.2:c.687dup		p.X229_splice	ENST00000245479	NM_000346.3	229			0.711405120594276	3	FACETS	0.925	0.892	0.958	0.925	0.892	0.958	CLONAL	2	TRUE	1	0.711405120594276	3		527	1162	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745607	41745607	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024397-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	290	673	0	ENST00000301178.4:c.1294C>T	p.Gln432Ter	p.Q432*	ENST00000301178	NM_021913.4	432	Cag/Tag	10/20	1	2	FACETS	0.799	0.753	0.847	0.799	0.753	0.847	SUBCLONAL	1	TRUE	1	0.711405120594276	2		673	1020	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144549	55144549	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024397-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	203	465	0	ENST00000257290.5:c.2023G>A	p.Glu675Lys	p.E675K	ENST00000257290	NM_006206.4	675	Gag/Aag	15/23	NA	2	FACETS	0.762	0.709	0.817			1	INDETERMINATE	1	TRUE	NA	0.711405120594276	2		465	749	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462998	120462998	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024498-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	227	428	0	ENST00000256646.2:c.5333C>T	p.Ser1778Leu	p.S1778L	ENST00000256646	NM_024408.3	1778	tCa/tTa	30/34	0.698449083535005	3	FACETS	1	0.982	1	0.566	0.529	0.603	CLONAL	1	TRUE	1	0.794015402496626	3		428	706	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189447	94189447	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024498-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	96	489	0	ENST00000323929.3:c.1558C>G	p.Arg520Gly	p.R520G	ENST00000323929	NM_005591.3	520	Cgt/Ggt	14/20	1	2	FACETS	0.902	0.816	0.991	0.902	0.816	0.991	CLONAL	1	TRUE	1	0.794015402496626	2		489	268	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396232	396232	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024498-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	398	616	3	ENST00000262320.3:c.794del	p.Gly265GlufsTer149	p.G265Efs*149	ENST00000262320	NM_003502.3	265	gGa/ga	2/11	0.689836550388573	1	FACETS	0.811	0.778	0.845	0.811	0.778	0.845	CLONAL	1	TRUE	0	0.794015402496626	1		619	745	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857629	9857629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1159089801	NA	P-0024498-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	121	333	0	ENST00000330684.3:c.3772G>A	p.Gly1258Ser	p.G1258S	ENST00000330684	NM_001134407.1	1258	Ggt/Agt	13/13	0.137385308461922	4	FACETS	0.896	0.812	0.985	0.448	0.406	0.493	INDETERMINATE	1	TRUE	2	0.794015402496626	4		333	610	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508735	29508735	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1131691126	NA	P-0024498-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	107	590	0	ENST00000356175.3:c.662G>A	p.Trp221Ter	p.W221*	ENST00000356175	NM_000267.3	221	tGg/tAg	7/57	0.794015402496626	3	FACETS	0.848	0.795	0.898	0.848	0.795	0.898	CLONAL	3	TRUE	0	0.794015402496626	3		590	148	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513276	44513276	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024498-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	596	679	0	ENST00000291552.4:c.659G>T	p.Gly220Val	p.G220V	ENST00000291552	NM_006758.2	220	gGt/gTt	8/8	0.187545433372989	3	FACETS	1	0.996	1	0.645	0.62	0.67	INDETERMINATE	1	TRUE	1	0.794015402496626	3		679	1626	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0024498-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	111	252	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.876	0.798	0.957	0.876	0.798	0.957	CLONAL	1	TRUE	1	0.794015402496626	2		252	319	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495388	149495388	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024498-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	532	749	0	ENST00000261799.4:c.3259del	p.Glu1087AsnfsTer45	p.E1087Nfs*45	ENST00000261799	NM_002609.3	1087	Gaa/aa	23/23	1	2	FACETS	0.896	0.859	0.933	0.896	0.859	0.933	CLONAL	1	TRUE	1	0.794015402496626	2		749	1496	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045559	47045560	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	T	novel	NA	P-0024498-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	391	302	0	ENST00000377604.3:c.2526_2527delinsT	p.Thr843GlnfsTer4	p.T843Qfs*4	ENST00000377604	NM_001204468.1	842	tcCAca/tcTca	22/24	0.375246869001479	2	FACETS	0.843	0.814	0.872			1	INDETERMINATE	2	TRUE	NA	0.794015402496626	2		302	584	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352756	70352756	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024498-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	393	411	0	ENST00000374080.3:c.4477G>T	p.Asp1493Tyr	p.D1493Y	ENST00000374080		1493	Gat/Tat	32/45	0.375246869001479	2	FACETS	0.817	0.787	0.846			1	INDETERMINATE	2	TRUE	NA	0.794015402496626	2		411	606	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909590	76909590	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0024498-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	60	282	0	ENST00000373344.5:c.4315A>T	p.Lys1439Ter	p.K1439*	ENST00000373344	NM_000489.3	1439	Aag/Tag	14/35	1	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.794015402496626	1		282	79	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0024500-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	111	387	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.781	0.703	0.864	0.781	0.703	0.864	SUBCLONAL	1	TRUE	1	0.431137502270841	2		387	659	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0024500-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	81	728	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.315	0.276	0.357	0.315	0.276	0.357	SUBCLONAL	1	TRUE	1	0.431137502270841	2		728	1193	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178342	56178343	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0024500-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	170	356	0	ENST00000399503.3:c.3316dup	p.Ile1106AsnfsTer4	p.I1106Nfs*4	ENST00000399503	NM_005921.1	1105	-/A	14/20	0.309262536585531	3	FACETS	0.888	0.822	0.955	0.888	0.822	0.955	CLONAL	2	TRUE	1	0.431137502270841	3		356	540	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179455	56179457	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	novel	NA	P-0024500-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	83	437	0	ENST00000399503.3:c.3770_3772del	p.Cys1257del	p.C1257del	ENST00000399503	NM_005921.1	1256	tcTTGt/tct	15/20	0.309262536585531	3	FACETS	0.695	0.614	0.783	0.348	0.307	0.392	SUBCLONAL	1	TRUE	1	0.431137502270841	3		437	673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs11575997	NA	P-0024510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	284	486	0	ENST00000269305.4:c.993+1G>T		p.X331_splice	ENST00000269305	NM_001126112.2	331			NA	3	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.527206648044819	3		486	600	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71947022	71947022	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	403	781	1	ENST00000298229.2:c.2871G>C	p.Leu957Phe	p.L957F	ENST00000298229	NM_001567.3	957	ttG/ttC	25/28	0.479912680720036	2	FACETS	0.939	0.899	0.979	0.939	0.899	0.979	CLONAL	2	TRUE	0	0.527206648044819	2		782	814	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28901614	28901614	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	55	428	0	ENST00000282397.4:c.2781A>T	p.Leu927Phe	p.L927F	ENST00000282397	NM_002019.4	927	ttA/ttT	20/30	0.479912680720036	2	FACETS	0.389	0.332	0.45	0.194	0.166	0.225	SUBCLONAL	1	TRUE	0	0.527206648044819	2		428	537	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881039	37881039	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024589-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	181	671	0	ENST00000269571.5:c.2368C>G	p.Leu790Val	p.L790V	ENST00000269571		790	Ctg/Gtg	20/27	0.620781060358974	1	FACETS	0.843	0.785	0.902	0.843	0.785	0.902	CLONAL	1	TRUE	0	0.620781060358974	1		671	477	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443695	29443695	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs863225281	NA	P-0121495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	529	478	1	ENST00000389048.3:c.3522C>A	p.Phe1174Leu	p.F1174L	ENST00000389048	NM_004304.4	1174	ttC/ttA	23/29	0.508193506215566	4	FACETS	0.842	0.814	0.868	0.842	0.814	0.868	INDETERMINATE	3	NA	1	0.970191192307961	4		479	851	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867376	68867378	+	frameshift_variant	Frame_Shift_Del	DEL	ATG	ATG	T	novel	NA	P-0024631-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	100	431	0	ENST00000261769.5:c.2623_2625delinsT	p.Met875LeufsTer39	p.M875Lfs*39	ENST00000261769	NM_004360.3	875	ATG/T	16/16	0.358218246196291	1	FACETS	0.846	0.758	0.938	0.846	0.758	0.938	CLONAL	1	TRUE	0	0.358218246196291	1		431	542	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867376	68867378	+	frameshift_variant	Frame_Shift_Del	DEL	ATG	ATG	T	novel	NA	P-0024631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	70	431	0	ENST00000261769.5:c.2623_2625delinsT	p.Met875LeufsTer39	p.M875Lfs*39	ENST00000261769	NM_004360.3	875	ATG/T	16/16	0.295990347989111	1	FACETS	0.757	0.661	0.859	0.757	0.661	0.859	SUBCLONAL	1	TRUE	0	0.318685188869184	1		431	488	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0024631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	59	419	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.295990347989111	1	FACETS	0.547	0.471	0.63	0.547	0.471	0.63	SUBCLONAL	1	TRUE	0	0.318685188869184	1		419	569	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0024653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	47	434	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.787	0.663	0.924	0.787	0.663	0.924	CLONAL	1	TRUE	1	0.19	2		434	629	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0024653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	78	255	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	0.19	2		255	662	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0024653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	74	738	1	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.19	2		739	758	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604778	48604778	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767383	NA	P-0024653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	31	498	1	ENST00000342988.3:c.1600C>T	p.Gln534Ter	p.Q534*	ENST00000342988	NM_005359.5	534	Cag/Tag	12/12	1	2	FACETS	0.663	0.536	0.808	0.663	0.536	0.808	SUBCLONAL	1	TRUE	1	0.19	2		499	492	SUCCESS
YES1	7525	MSKCC	GRCh37	18	751726	751726	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1010928891	NA	P-0024653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	40	614	0	ENST00000314574.4:c.350G>T	p.Arg117Ile	p.R117I	ENST00000314574	NM_005433.3	117	aGa/aTa	3/12	1	2	FACETS	0.672	0.557	0.8	0.672	0.557	0.8	SUBCLONAL	1	TRUE	1	0.19	2		614	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0024677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	227	535	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.252914404678273	2	FACETS	0.944	0.88	1	0.944	0.88	1	CLONAL	2	TRUE	0	0.252914404678273	2		535	951	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0024677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	152	418	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	0.252914404678273	5	FACETS	0.962	0.88	1	0.641	0.586	0.698	CLONAL	2	TRUE	2	0.252914404678273	5		418	862	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281360	49281360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201503697	NA	P-0024677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	266	712	0	ENST00000282018.3:c.407G>A	p.Arg136His	p.R136H	ENST00000282018	NM_020377.2	136	cGt/cAt	1/1	0.245327218393104	2	FACETS	0.958	0.898	1	0.958	0.898	1	CLONAL	2	TRUE	0	0.252914404678273	2		712	1098	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0024690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	100	387	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.956	0.857	1	0.956	0.857	1	CLONAL	1	TRUE	1	0.390167215364269	2		387	536	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0024690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	36	255	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	0.503	0.414	0.602	0.503	0.414	0.602	SUBCLONAL	1	TRUE	1	0.390167215364269	2		255	367	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259199	36259199	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1569084170	NA	P-0024690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	117	416	0	ENST00000300305.3:c.292del	p.Leu98SerfsTer24	p.L98Sfs*24	ENST00000300305		98	Ctc/tc	3/8	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.390167215364269	2		416	514	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1273199332	NA	P-0024690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	162	564	0	ENST00000534358.1:c.2312C>T	p.Thr771Ile	p.T771I	ENST00000534358	NM_005933.3	771	aCc/aTc	3/36	1	2	FACETS	0.953	0.875	1	0.953	0.875	1	CLONAL	1	TRUE	1	0.390167215364269	2		564	871	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0024761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	128	565	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.305046243162953	3	FACETS	1	0.984	1	0.705	0.64	0.773	CLONAL	1	TRUE	1	0.305046243162953	3		565	686	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0024761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	283	688	0	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	0.264162223206871	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.305046243162953	2		688	913	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211506	46211506	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	55	341	0	ENST00000334344.6:c.472T>A	p.Tyr158Asn	p.Y158N	ENST00000334344	NM_152641.2	158	Tat/Aat	5/21	1	2	FACETS	0.882	0.756	1	0.882	0.756	1	CLONAL	1	TRUE	1	0.305046243162953	2		341	409	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633610	69633610	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	78	103	0	ENST00000334134.2:c.92G>T	p.Gly31Val	p.G31V	ENST00000334134	NM_005247.2	31	gGc/gTc	1/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.746237451840594	2		103	168	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712692	43712692	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	323	632	0	ENST00000382044.4:c.4492G>T	p.Ala1498Ser	p.A1498S	ENST00000382044	NM_001141980.1	1498	Gcc/Tcc	21/28	NA	2	FACETS	0.834	0.789	0.88			1	INDETERMINATE	1	TRUE	NA	0.746237451840594	2		632	1038	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892220	9892220	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	268	562	1	ENST00000330684.3:c.2270C>A	p.Ala757Asp	p.A757D	ENST00000330684	NM_001134407.1	757	gCc/gAc	11/13	1	2	FACETS	0.939	0.884	0.994	0.939	0.884	0.994	CLONAL	1	TRUE	1	0.746237451840594	2		563	765	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783988	50783988	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	318	613	0	ENST00000398568.2:c.379G>T	p.Val127Leu	p.V127L	ENST00000398568	NM_001042412.1	127	Gtg/Ttg	3/18	1	2	FACETS	0.916	0.867	0.966	0.916	0.867	0.966	CLONAL	1	TRUE	1	0.746237451840594	2		613	930	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208399	5208399	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	258	473	2	ENST00000357368.4:c.5491G>T	p.Gly1831Cys	p.G1831C	ENST00000357368	NM_002850.3	1831	Ggc/Tgc	36/38	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.746237451840594	2		475	663	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568577	41568577	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	318	612	0	ENST00000263253.7:c.4527G>T	p.Trp1509Cys	p.W1509C	ENST00000263253	NM_001429.3	1509	tgG/tgT	28/31	1	2	FACETS	0.958	0.907	1	0.958	0.907	1	CLONAL	1	TRUE	1	0.746237451840594	2		612	890	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713761	30713761	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	188	375	0	ENST00000295754.5:c.1086C>A	p.His362Gln	p.H362Q	ENST00000295754	NM_003242.5	362	caC/caA	4/7	0.746237451840594	1	FACETS	0.921	0.867	0.974	0.921	0.867	0.974	CLONAL	1	TRUE	0	0.746237451840594	1		375	343	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031919	26031919	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1270004025	NA	P-0024869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	186	387	0	ENST00000244661.2:c.370G>C	p.Asp124His	p.D124H	ENST00000244661	NM_003537.3	124	Gac/Cac	1/1	0.746237451840594	3	FACETS	0.915	0.847	0.985	0.458	0.423	0.493	CLONAL	1	TRUE	1	0.746237451840594	3		387	748	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593603	55593603	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913235	NA	P-0024909-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	477	489	0	ENST00000288135.5:c.1669T>C	p.Trp557Arg	p.W557R	ENST00000288135	NM_000222.2	557	Tgg/Cgg	11/21	0.833678422447977	4	FACETS	0.939	0.901	0.977	0.939	0.901	0.977	CLONAL	2	TRUE	2	0.939208390328007	4		489	1049	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0024943-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	519	649	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.608744639689854	2	FACETS	0.917	0.897	0.936	1	0.998	1	CLONAL	3	TRUE	0	0.608327527755165	2		649	620	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518262	8518262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024943-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	120	339	0	ENST00000356435.5:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000356435		377	Cgc/Tgc	10/35	0.608744639689854	3	FACETS	1	0.948	1	0.532	0.483	0.583	CLONAL	1	TRUE	1	0.608327527755165	3		339	484	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639540	3639540	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs17136464	NA	P-0024943-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	271	622	0	ENST00000294008.3:c.4099G>A	p.Ala1367Thr	p.A1367T	ENST00000294008	NM_032444.2	1367	Gcc/Acc	12/15	0.608744639689854	3	FACETS	1	0.993	1	0.723	0.68	0.766	CLONAL	1	TRUE	1	0.608327527755165	3		622	804	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718213	117718213	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024943-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	243	463	2	ENST00000368508.3:c.644G>A	p.Trp215Ter	p.W215*	ENST00000368508	NM_002944.2	215	tGg/tAg	7/43	0.608744639689854	4	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.608327527755165	4		465	1191	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567556006	NA	P-0025069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	239	747	1	ENST00000269305.4:c.298del	p.Gln100ArgfsTer23	p.Q100Rfs*23	ENST00000269305	NM_001126112.2	100	Cag/ag	4/11	0.291984777632586	2	FACETS	0.934	0.876	0.993	0.934	0.876	0.993	CLONAL	2	TRUE	0	0.350537636789572	2		748	730	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	159	391	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	0.350537636789572	3	FACETS	1	0.988	1	0.742	0.682	0.805	CLONAL	1	TRUE	1	0.350537636789572	3		391	718	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612073	189612073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142762485	NA	P-0025069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	184	571	0	ENST00000264731.3:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000264731	NM_003722.4	609	Gaa/Aaa	14/14	0.350537636789572	6	FACETS	0.905	0.835	0.977	0.452	0.417	0.489	CLONAL	2	TRUE	2	0.350537636789572	6		571	987	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411420	63411420	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	91	565	0	ENST00000330258.3:c.1747G>T	p.Ala583Ser	p.A583S	ENST00000330258	NM_152424.3	583	Gca/Tca	2/2	0.350537636789572	1	FACETS	0.872	0.777	0.972	0.872	0.777	0.972	CLONAL	1	TRUE	0	0.350537636789572	1		565	491	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076937	41076937	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	104	575	0	ENST00000373198.4:c.1483G>T	p.Gly495Trp	p.G495W	ENST00000373198	NM_133170.3	495	Ggg/Tgg	9/32	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.350537636789572	2		575	581	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486175	8486175	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	150	405	0	ENST00000356435.5:c.2642C>A	p.Thr881Lys	p.T881K	ENST00000356435		881	aCa/aAa	17/35	0.263644363441549	4	FACETS	0.909	0.833	0.987	0.909	0.833	0.987	CLONAL	2	TRUE	2	0.350537636789572	4		405	636	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716403	18716403	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	104	476	0	ENST00000266497.5:c.3750G>T	p.Gln1250His	p.Q1250H	ENST00000266497		1250	caG/caT	26/31	0.350537636789572	3	FACETS	0.926	0.829	1	0.463	0.414	0.515	CLONAL	1	TRUE	1	0.350537636789572	3		476	753	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252687	133252687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	69	552	0	ENST00000320574.5:c.1013C>T	p.Pro338Leu	p.P338L	ENST00000320574	NM_006231.2	338	cCc/cTc	10/49	0.322831716829977	3	FACETS	0.61	0.531	0.697	0.305	0.265	0.349	SUBCLONAL	1	TRUE	1	0.350537636789572	3		552	758	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799210	88799210	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	205	605	1	ENST00000360948.2:c.175G>T	p.Gly59Trp	p.G59W	ENST00000360948	NM_001012338.2	59	Ggg/Tgg	2/19	0.291984777632586	2	FACETS	0.839	0.781	0.898	0.839	0.781	0.898	CLONAL	2	TRUE	0	0.350537636789572	2		606	697	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654637	67654637	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	234	580	1	ENST00000264010.4:c.1124G>T	p.Gly375Val	p.G375V	ENST00000264010	NM_006565.3	375	gGa/gTa	6/12	0.284493110102973	3	FACETS	0.942	0.881	1	0.942	0.881	1	CLONAL	2	TRUE	1	0.350537636789572	3		581	833	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41209088	41209088	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs397509246	NA	P-0025069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	228	621	0	ENST00000357654.3:c.5258G>C	p.Arg1753Thr	p.R1753T	ENST00000357654	NM_007294.3	1753	aGa/aCa	19/23	0.297581985219324	4	FACETS	0.862	0.803	0.923	0.862	0.803	0.923	CLONAL	2	TRUE	2	0.350537636789572	4		621	1019	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440688	56440688	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs752845745	NA	P-0025069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	83	671	1	ENST00000407977.2:c.530A>T	p.Tyr177Phe	p.Y177F	ENST00000407977		177	tAc/tTc	5/10	0.297581985219324	4	FACETS	0.697	0.614	0.787	0.349	0.307	0.394	SUBCLONAL	1	TRUE	2	0.350537636789572	4		672	917	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66525117	66525117	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	70	287	0	ENST00000358598.2:c.876C>G	p.Phe292Leu	p.F292L	ENST00000358598	NM_212471.2	292	ttC/ttG	9/11	0.297581985219324	4	FACETS	0.851	0.742	0.969	0.425	0.371	0.485	CLONAL	1	TRUE	2	0.350537636789572	4		287	634	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971792	18971792	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0025069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	161	481	1	ENST00000262803.5:c.2457+1G>T		p.X819_splice	ENST00000262803	NM_002911.3	819			0.263644363441549	4	FACETS	1	0.922	1	1	0.922	1	CLONAL	2	TRUE	2	0.350537636789572	4		482	620	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980757	40980757	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	46	487	0	ENST00000373198.4:c.1729C>G	p.Pro577Ala	p.P577A	ENST00000373198	NM_133170.3	577	Cct/Gct	10/32	1	2	FACETS	0.55	0.463	0.646	0.55	0.463	0.646	SUBCLONAL	1	TRUE	1	0.350537636789572	2		487	477	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101008	41101008	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	87	541	1	ENST00000373198.4:c.1348C>G	p.Arg450Gly	p.R450G	ENST00000373198	NM_133170.3	450	Cga/Gga	8/32	1	2	FACETS	0.904	0.802	1	0.904	0.802	1	CLONAL	1	TRUE	1	0.350537636789572	2		542	549	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164763	47164764	+	missense_variant	Missense_Mutation	DNP	CT	CT	AA	novel	NA	P-0025069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	55	435	0	ENST00000409792.3:c.1362_1363delinsTT	p.Arg454_Ala455delinsSerSer	p.R454_A455delinsSS	ENST00000409792	NM_014159.6	454	agAGca/agTTca	3/21	0.350537636789572	3	FACETS	0.625	0.534	0.724	0.313	0.267	0.362	SUBCLONAL	1	TRUE	1	0.350537636789572	3		435	590	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521614	89521614	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	156	397	0	ENST00000336596.2:c.2691G>T	p.Arg897Ser	p.R897S	ENST00000336596	NM_005233.5	897	agG/agT	16/17	0.297581985219324	4	FACETS	0.839	0.77	0.911	0.839	0.77	0.911	CLONAL	2	TRUE	2	0.350537636789572	4		397	716	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1918750	1918750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	134	415	0	ENST00000382891.5:c.913G>T	p.Ala305Ser	p.A305S	ENST00000382891	NM_133335.3	305	Gct/Tct	4/22	0.284493110102973	3	FACETS	0.83	0.758	0.906	0.83	0.758	0.906	CLONAL	2	TRUE	1	0.350537636789572	3		415	541	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968139	55968139	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	109	515	3	ENST00000263923.4:c.2191G>A	p.Asp731Asn	p.D731N	ENST00000263923	NM_002253.2	731	Gac/Aac	15/30	0.284493110102973	3	FACETS	1	0.927	1	0.519	0.466	0.575	CLONAL	1	TRUE	1	0.350537636789572	3		518	704	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356347	66356347	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	85	524	0	ENST00000273854.3:c.1150G>T	p.Gly384Cys	p.G384C	ENST00000273854	NM_004439.5	384	Ggt/Tgt	5/18	0.284493110102973	3	FACETS	0.759	0.67	0.854	0.379	0.335	0.427	SUBCLONAL	1	TRUE	1	0.350537636789572	3		524	751	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522458	187522458	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	116	586	0	ENST00000441802.2:c.11605A>G	p.Met3869Val	p.M3869V	ENST00000441802	NM_005245.3	3869	Atg/Gtg	21/27	0.297581985219324	4	FACETS	0.891	0.802	0.986	0.446	0.401	0.493	CLONAL	1	TRUE	2	0.350537636789572	4		586	1003	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525586	187525586	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	226	597	0	ENST00000441802.2:c.10493T>A	p.Leu3498Gln	p.L3498Q	ENST00000441802	NM_005245.3	3498	cTg/cAg	18/27	0.297581985219324	4	FACETS	0.942	0.879	1	0.942	0.879	1	CLONAL	2	TRUE	2	0.350537636789572	4		597	924	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531164	187531164	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	128	386	2	ENST00000441802.2:c.9859G>T	p.Val3287Leu	p.V3287L	ENST00000441802	NM_005245.3	3287	Gta/Tta	15/27	0.297581985219324	4	FACETS	0.794	0.722	0.87	0.794	0.722	0.87	SUBCLONAL	2	TRUE	2	0.350537636789572	4		388	621	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250476	26250476	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	148	560	0	ENST00000446824.2:c.358A>T	p.Ile120Phe	p.I120F	ENST00000446824	NM_021018.2	120	Atc/Ttc	1/1	0.258497650968969	5	FACETS	0.759	0.693	0.828	0.506	0.462	0.552	SUBCLONAL	2	TRUE	2	0.350537636789572	5		560	849	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001138	150001138	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	249	516	0	ENST00000253339.5:c.2466G>T	p.Met822Ile	p.M822I	ENST00000253339		822	atG/atT	4/7	0.304310649461823	2	FACETS	0.912	0.856	0.969	0.912	0.856	0.969	CLONAL	2	TRUE	0	0.350537636789572	2		516	779	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520076	106520076	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	147	368	0	ENST00000359195.3:c.2504G>T	p.Gly835Val	p.G835V	ENST00000359195	NM_002649.2	835	gGt/gTt	6/11	0.350537636789572	3	FACETS	0.754	0.69	0.82	0.754	0.69	0.82	SUBCLONAL	2	TRUE	1	0.350537636789572	3		368	654	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423362	116423362	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	85	299	0	ENST00000397752.3:c.3637G>C	p.Asp1213His	p.D1213H	ENST00000397752	NM_000245.2	1213	Gat/Cat	19/21	0.350537636789572	3	FACETS	1	0.908	1	0.514	0.455	0.577	CLONAL	1	TRUE	1	0.350537636789572	3		299	554	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650898	93650898	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	75	520	0	ENST00000375746.1:c.1824C>A	p.Cys608Ter	p.C608*	ENST00000375746	NM_001174167.1	608	tgC/tgA	13/14	0.326030016085181	3	FACETS	0.759	0.665	0.86	0.253	0.221	0.287	SUBCLONAL	1	TRUE	0	0.350537636789572	3		520	663	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426121	47426122	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	1066	792	2	ENST00000377045.4:c.641_642delinsTT	p.Ser214Phe	p.S214F	ENST00000377045	NM_001654.4	214	tCC/tTT	7/16	0.350537636789572	9	FACETS	1	0.995	1			1	CLONAL	8	TRUE	NA	0.350537636789572	9		794	1613	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410712	63410712	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	110	663	0	ENST00000330258.3:c.2455G>C	p.Glu819Gln	p.E819Q	ENST00000330258	NM_152424.3	819	Gaa/Caa	2/2	0.350537636789572	1	FACETS	0.811	0.73	0.897	0.811	0.73	0.897	CLONAL	1	TRUE	0	0.350537636789572	1		663	638	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985571	60985571	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	45	337	1	ENST00000333681.4:c.329G>A	p.Arg110His	p.R110H	ENST00000333681		110	cGc/cAc	2/3	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.192900466298933	2		338	441	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227784	53227784	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	93	601	0	ENST00000375401.3:c.2404del	p.Arg802ValfsTer14	p.R802Vfs*14	ENST00000375401	NM_004187.3	802	Cgt/gt	17/26	0.192900466298933	1	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	0	0.192900466298933	1		601	869	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023501	27023501	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1251950978	NA	P-0025100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	89	477	0	ENST00000324856.7:c.607C>T	p.His203Tyr	p.H203Y	ENST00000324856	NM_006015.4	203	Cac/Tac	1/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.192900466298933	2		477	666	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913878	32913878	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	69	484	0	ENST00000380152.3:c.5386G>C	p.Asp1796His	p.D1796H	ENST00000380152		1796	Gat/Cat	11/27	0.192900466298933	1	FACETS	0.948	0.825	1	0.948	0.825	1	CLONAL	1	TRUE	0	0.192900466298933	1		484	682	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841123	15841124	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0025100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	81	522	0	ENST00000307771.7:c.1212dup	p.Lys405GlufsTer23	p.K405Efs*23	ENST00000307771	NM_005089.3	403	agg/aGgg	11/11	0.192900466298933	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.192900466298933	1		522	693	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0025349-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	45	387	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.29	0.243	0.342	0.29	0.243	0.342	SUBCLONAL	1	TRUE	1	0.530117315230388	2		387	586	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115695	8115708	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTTTAGATTAACA	TGTTTAGATTAACA	GT	novel	NA	P-0025349-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	40	405	3	ENST00000346208.3:c.1048-7_1054delinsGT		p.X350_splice	ENST00000346208		350		6/6	1	2	FACETS	0.349	0.289	0.414	0.349	0.289	0.414	SUBCLONAL	1	TRUE	1	0.530117315230388	2		408	433	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070564	67070564	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025349-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	119	319	0	ENST00000412916.2:c.188A>T	p.Asn63Ile	p.N63I	ENST00000412916		63	aAt/aTt	3/6	0.530117315230388	1	FACETS	0.922	0.841	1	0.922	0.841	1	CLONAL	1	TRUE	0	0.530117315230388	1		319	358	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644799	67644802	+	frameshift_variant	Frame_Shift_Del	DEL	AGAA	AGAA	-	novel	NA	P-0025349-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	60	557	0	ENST00000264010.4:c.67_70del	p.Lys23LeufsTer38	p.K23Lfs*38	ENST00000264010	NM_006565.3	22	AGAAag/ag	3/12	0.530117315230388	1	FACETS	0.304	0.262	0.35	0.304	0.262	0.35	SUBCLONAL	1	TRUE	0	0.530117315230388	1		557	547	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853287	68853308	+	frameshift_variant	Frame_Shift_Del	DEL	AGAACAGCACGTACACAGCCCT	AGAACAGCACGTACACAGCCCT	-	novel	NA	P-0025349-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	149	646	0	ENST00000261769.5:c.1671_1692del	p.Asn558SerfsTer2	p.N558Sfs*2	ENST00000261769	NM_004360.3	557	aAGAACAGCACGTACACAGCCCTa/aa	11/16	0.530117315230388	1	FACETS	0.79	0.726	0.856	0.79	0.726	0.856	SUBCLONAL	1	TRUE	0	0.530117315230388	1		646	523	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171636	36171637	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025349-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	47	424	0	ENST00000300305.3:c.928dup	p.Met310AsnfsTer290	p.M310Nfs*290	ENST00000300305		310	atg/aAtg	7/8	1	2	FACETS	0.304	0.256	0.357	0.304	0.256	0.357	SUBCLONAL	1	TRUE	1	0.530117315230388	2		424	583	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853312	68853312	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025349-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	150	575	0	ENST00000261769.5:c.1695C>G	p.Ile565Met	p.I565M	ENST00000261769	NM_004360.3	565	atC/atG	11/16	0.530117315230388	1	FACETS	0.827	0.761	0.895	0.827	0.761	0.895	CLONAL	1	TRUE	0	0.530117315230388	1		575	503	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111506	8111507	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCCAATGGGGACCCTGTCTGCAATGCCTGTGGGCTCTAC	novel	NA	P-0025483-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	113	518	0	ENST00000346208.3:c.994_1033dup	p.Tyr345CysfsTer20	p.Y345Cfs*20	ENST00000346208		331	aat/aaTGCCAATGGGGACCCTGTCTGCAATGCCTGTGGGCTCTACt	5/6	0.173820884717627	5	FACETS	0.707	0.635	0.783			1	INDETERMINATE	1	TRUE	NA	0.650663137293951	5		518	971	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578384	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	GAG	GAG	-	novel	NA	P-0025483-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	152	494	0	ENST00000269305.4:c.546_548del	p.Cys182_Ser183delinsTer	p.C182_S183delins*	ENST00000269305	NM_001126112.2	182	tgCTCa/tga	5/11	0.636443353319609	1	FACETS	0.958	0.891	1	0.958	0.891	1	CLONAL	1	TRUE	0	0.650663137293951	1		494	329	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125697	47125697	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750379129	NA	P-0025483-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	145	327	0	ENST00000409792.3:c.5573C>T	p.Pro1858Leu	p.P1858L	ENST00000409792	NM_014159.6	1858	cCt/cTt	12/21	0.636443353319609	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.650663137293951	1		327	294	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111506	8111507	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCCAATGGGGACCCTGTCTGCAATGCCTGTGGGCTCTAC	novel	NA	P-0025483-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	47	518	0	ENST00000346208.3:c.994_1033dup	p.Tyr345CysfsTer20	p.Y345Cfs*20	ENST00000346208		331	aat/aaTGCCAATGGGGACCCTGTCTGCAATGCCTGTGGGCTCTACt	5/6	1	2	FACETS	0.474	0.399	0.557	0.474	0.399	0.557	SUBCLONAL	1	FALSE	1	0.31324188225041	2		518	633	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578384	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	GAG	GAG	-	novel	NA	P-0025483-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	69	494	0	ENST00000269305.4:c.546_548del	p.Cys182_Ser183delinsTer	p.C182_S183delins*	ENST00000269305	NM_001126112.2	182	tgCTCa/tga	5/11	0.269388208167516	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	0	0.31324188225041	1		494	321	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248072	59248073	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0025483-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	23	250	0	ENST00000371222.2:c.670dup	p.Ala224GlyfsTer86	p.A224Gfs*86	ENST00000371222	NM_002228.3	224	gcc/gGcc	1/1	0.31324188225041	5	FACETS	0.771	0.602	0.966			1	CLONAL	1	FALSE	NA	0.31324188225041	5		250	280	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755531	39755531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025561-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	53	430	0	ENST00000288319.7:c.1234C>T	p.Pro412Ser	p.P412S	ENST00000288319	NM_182918.3	412	Ccc/Tcc	10/10	0.27980889261135	3	FACETS	0.923	0.788	1	0.461	0.394	0.535	CLONAL	1	TRUE	1	0.27980889261135	3		430	468	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588210	69588210	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025561-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	157	571	0	ENST00000168712.1:c.488C>T	p.Pro163Leu	p.P163L	ENST00000168712	NM_002007.2	163	cCc/cTc	3/3	0.27980889261135	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.27980889261135	2		571	522	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233757	133233759	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs1555225139	NA	P-0025561-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	120	397	0	ENST00000320574.5:c.3545_3547del	p.Lys1182del	p.K1182del	ENST00000320574	NM_006231.2	1182	aAGAtc/atc	29/49	0.27980889261135	2	FACETS	0.849	0.771	0.931	0.849	0.771	0.931	CLONAL	2	TRUE	0	0.27980889261135	2		397	505	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106162523	106162523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025561-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	45	300	0	ENST00000380013.4:c.3437C>T	p.Pro1146Leu	p.P1146L	ENST00000380013	NM_001127208.2	1146	cCt/cTt	4/11	0.27980889261135	3	FACETS	0.822	0.692	0.966	0.411	0.346	0.483	CLONAL	1	TRUE	1	0.27980889261135	3		300	446	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148526831	148526831	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025561-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	123	285	0	ENST00000320356.2:c.473A>T	p.His158Leu	p.H158L	ENST00000320356	NM_004456.4	158	cAc/cTc	5/20	0.27980889261135	4	FACETS	1	0.919	1	1	0.919	1	CLONAL	2	TRUE	2	0.27980889261135	4		285	555	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0025636-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	181	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.86	0.793	0.929	0.86	0.793	0.929	CLONAL	1	TRUE	1	0.468858397456887	2		511	898	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106058	8106058	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025636-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	143	444	0	ENST00000346208.3:c.878T>A	p.Met293Lys	p.M293K	ENST00000346208		293	aTg/aAg	4/6	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.468858397456887	2		444	602	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855984	68855984	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121964877	NA	P-0025636-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	180	447	0	ENST00000261769.5:c.1792C>T	p.Arg598Ter	p.R598*	ENST00000261769	NM_004360.3	598	Cga/Tga	12/16	0.468858397456887	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.468858397456887	1		447	520	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089676	27089676	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025636-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	163	499	0	ENST00000324856.7:c.2632C>T	p.Gln878Ter	p.Q878*	ENST00000324856	NM_006015.4	878	Cag/Tag	8/20	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.468858397456887	2		499	679	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	22	436	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.249	0.192	0.316	0.249	0.192	0.316	SUBCLONAL	1	TRUE	1	0.276288835819539	2		437	640	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039610	47039610	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0026003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	36	277	0	ENST00000377604.3:c.1063-1G>A		p.X355_splice	ENST00000377604	NM_001204468.1	355			1	2	FACETS	0.376	0.308	0.453	0.376	0.308	0.453	SUBCLONAL	1	TRUE	1	0.276288835819539	2		277	693	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602698	10602698	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	102	469	0	ENST00000171111.5:c.880G>T	p.Asp294Tyr	p.D294Y	ENST00000171111	NM_203500.1	294	Gac/Tac	3/6	1	2	FACETS	0.655	0.584	0.731	0.655	0.584	0.731	SUBCLONAL	1	TRUE	1	0.276288835819539	2		469	1127	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221962	1221962	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	70	367	2	ENST00000326873.7:c.877del	p.Glu293AsnfsTer43	p.E293Nfs*43	ENST00000326873	NM_000455.4	293	Gaa/aa	7/10	1	2	FACETS	0.508	0.441	0.58	0.508	0.441	0.58	SUBCLONAL	1	TRUE	1	0.276288835819539	2		369	998	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538775	23538775	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	35	232	0	ENST00000380871.4:c.664T>A	p.Tyr222Asn	p.Y222N	ENST00000380871	NM_006167.3	222	Tac/Aac	2/2	1	2	FACETS	0.464	0.379	0.559	0.464	0.379	0.559	SUBCLONAL	1	TRUE	1	0.276288835819539	2		232	546	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0026165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	118	974	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.331427064050005	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.331427064050005	1		974	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0026165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	211	561	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.305844125476092	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.331427064050005	1		561	872	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971209	21971209	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1554654224	NA	P-0026165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	169	315	0	ENST00000304494.5:c.151-2A>G		p.X51_splice	ENST00000304494	NM_000077.4	51			0.31565690958023	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.331427064050005	2		315	478	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088658	27088659	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0026165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	119	574	0	ENST00000324856.7:c.2272dup	p.Gln758ProfsTer59	p.Q758Pfs*59	ENST00000324856	NM_006015.4	756	aac/aaCc	7/20	1	2	FACETS	0.839	0.757	0.926	0.839	0.757	0.926	CLONAL	1	TRUE	1	0.331427064050005	2		574	856	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603080	48603080	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	144	426	1	ENST00000342988.3:c.1381C>T	p.Gln461Ter	p.Q461*	ENST00000342988	NM_005359.5	461	Cag/Tag	11/12	0.305844125476092	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.331427064050005	1		427	685	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97869512	97869512	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	133	459	0	ENST00000289081.3:c.1369T>C	p.Ser457Pro	p.S457P	ENST00000289081	NM_000136.2	457	Tcc/Ccc	14/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.331427064050005	2		459	658	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0026261-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	98	615	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.809	0.722	0.9	1	0.983	1	CLONAL	2	TRUE	1	0.192988644071191	2		615	628	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139157	108139157	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026261-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	93	593	0	ENST00000278616.4:c.2659G>A	p.Glu887Lys	p.E887K	ENST00000278616	NM_000051.3	887	Gaa/Aaa	18/63	1	2	FACETS	0.757	0.673	0.845	1	0.98	1	SUBCLONAL	2	TRUE	1	0.192988644071191	2		593	637	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271447	26271447	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026261-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	54	697	0	ENST00000305910.3:c.166C>G	p.Gln56Glu	p.Q56E	ENST00000305910	NM_003534.2	56	Cag/Gag	1/1	1	2	FACETS	0.913	0.779	1	0.913	0.779	1	CLONAL	1	TRUE	1	0.192988644071191	2		697	613	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847399	68847399	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0026261-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	82	638	0	ENST00000261769.5:c.1320+1G>A		p.X440_splice	ENST00000261769	NM_004360.3	440			0.192988644071191	1	FACETS	0.777	0.687	0.873	1	0.979	1	SUBCLONAL	2	TRUE	0	0.192988644071191	1		638	494	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652272	36652272	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026261-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	99	730	0	ENST00000244741.5:c.394G>A	p.Gly132Ser	p.G132S	ENST00000244741	NM_000389.4	132	Ggt/Agt	2/3	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.192988644071191	2		730	723	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831915	72831915	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026261-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	88	998	0	ENST00000268489.5:c.4666C>T	p.Gln1556Ter	p.Q1556*	ENST00000268489	NM_006885.3	1556	Caa/Taa	9/10	0.192988644071191	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	0	0.192988644071191	1		998	801	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	104	481	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	1	0.686708534322026	2		481	286	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	92	419	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	FALSE	1	0.686708534322026	2		419	216	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491347	2491347	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	208	621	0	ENST00000355716.4:c.390G>T	p.Gln130His	p.Q130H	ENST00000355716	NM_003820.2	130	caG/caT	4/8	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.686708534322026	2		621	581	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775933	9775933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754053878	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	49	473	0	ENST00000377346.4:c.397G>A	p.Asp133Asn	p.D133N	ENST00000377346	NM_005026.3	133	Gac/Aac	5/24	1	2	FACETS	0.264	0.223	0.309	0.264	0.223	0.309	SUBCLONAL	1	FALSE	1	0.686708534322026	2		473	541	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11269446	11269446	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	23	448	0	ENST00000361445.4:c.3724G>T	p.Gly1242Trp	p.G1242W	ENST00000361445	NM_004958.3	1242	Ggg/Tgg	25/58	1	2	FACETS	0.196	0.152	0.246	0.196	0.152	0.246	SUBCLONAL	1	FALSE	1	0.686708534322026	2		448	342	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199369	16199369	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	82	328	1	ENST00000375759.3:c.142G>A	p.Ala48Thr	p.A48T	ENST00000375759	NM_015001.2	48	Gct/Act	2/15	1	2	FACETS	0.915	0.818	1	0.915	0.818	1	CLONAL	1	FALSE	1	0.686708534322026	2		329	261	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245539	16245539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1471081719	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	72	303	0	ENST00000375759.3:c.1514G>A	p.Arg505His	p.R505H	ENST00000375759	NM_015001.2	505	cGc/cAc	7/15	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	FALSE	1	0.686708534322026	2		303	201	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254764	16254764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	134	511	1	ENST00000375759.3:c.2029C>T	p.Pro677Ser	p.P677S	ENST00000375759	NM_015001.2	677	Cct/Tct	11/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.686708534322026	2		512	335	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254929	16254929	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs751475729	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	139	404	0	ENST00000375759.3:c.2194C>T	p.Arg732Ter	p.R732*	ENST00000375759	NM_015001.2	732	Cga/Tga	11/15	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	FALSE	1	0.686708534322026	2		404	398	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255402	16255402	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	18	465	1	ENST00000375759.3:c.2667G>T	p.Lys889Asn	p.K889N	ENST00000375759	NM_015001.2	889	aaG/aaT	11/15	1	2	FACETS	0.148	0.111	0.192	0.148	0.111	0.192	SUBCLONAL	1	FALSE	1	0.686708534322026	2		466	355	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265301	16265301	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	191	450	0	ENST00000375759.3:c.10793C>A	p.Ala3598Asp	p.A3598D	ENST00000375759	NM_015001.2	3598	gCc/gAc	14/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.686708534322026	2		450	513	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023522	27023522	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	241	379	2	ENST00000324856.7:c.628C>A	p.His210Asn	p.H210N	ENST00000324856	NM_006015.4	210	Cac/Aac	1/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.686708534322026	2		381	614	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105815	27105815	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	131	382	0	ENST00000324856.7:c.5426T>G	p.Phe1809Cys	p.F1809C	ENST00000324856	NM_006015.4	1809	tTt/tGt	20/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.686708534322026	2		382	336	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106047	27106047	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	141	354	0	ENST00000324856.7:c.5658G>T	p.Glu1886Asp	p.E1886D	ENST00000324856	NM_006015.4	1886	gaG/gaT	20/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.686708534322026	2		354	377	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106133	27106133	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	164	454	0	ENST00000324856.7:c.5744T>C	p.Leu1915Ser	p.L1915S	ENST00000324856	NM_006015.4	1915	tTg/tCg	20/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.686708534322026	2		454	398	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106327	27106327	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780084398	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	174	483	0	ENST00000324856.7:c.5938C>T	p.Arg1980Cys	p.R1980C	ENST00000324856	NM_006015.4	1980	Cgc/Tgc	20/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.686708534322026	2		483	488	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932085	36932085	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	161	484	0	ENST00000361632.4:c.2384G>T	p.Ser795Ile	p.S795I	ENST00000361632		795	aGc/aTc	16/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.686708534322026	2		484	406	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932327	36932327	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	193	547	0	ENST00000361632.4:c.2142C>A	p.Ser714Arg	p.S714R	ENST00000361632		714	agC/agA	16/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	1	0.686708534322026	2		547	538	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935334	36935334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	225	559	0	ENST00000361632.4:c.1393C>A	p.Leu465Met	p.L465M	ENST00000361632		465	Ctg/Atg	10/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.686708534322026	2		559	573	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939179	36939179	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	33	540	0	ENST00000361632.4:c.530G>A	p.Cys177Tyr	p.C177Y	ENST00000361632		177	tGc/tAc	5/16	1	2	FACETS	0.152	0.123	0.185	0.152	0.123	0.185	SUBCLONAL	1	FALSE	1	0.686708534322026	2		540	633	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939205	36939205	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	219	531	0	ENST00000361632.4:c.504G>T	p.Gln168His	p.Q168H	ENST00000361632		168	caG/caT	5/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.686708534322026	2		531	573	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805223	43805223	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	159	554	0	ENST00000372470.3:c.673A>G	p.Thr225Ala	p.T225A	ENST00000372470	NM_005373.2	225	Acc/Gcc	4/12	1	2	FACETS	0.998	0.923	1	0.998	0.923	1	CLONAL	1	FALSE	1	0.686708534322026	2		554	464	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46512241	46512241	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	91	388	0	ENST00000262741.5:c.998A>G	p.Lys333Arg	p.K333R	ENST00000262741	NM_003629.3	333	aAg/aGg	8/10	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.686708534322026	2		388	239	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521574	46521574	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	87	417	0	ENST00000262741.5:c.834G>T	p.Glu278Asp	p.E278D	ENST00000262741	NM_003629.3	278	gaG/gaT	7/10	1	2	FACETS	0.734	0.656	0.817	0.734	0.656	0.817	SUBCLONAL	1	FALSE	1	0.686708534322026	2		417	345	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531852	46531852	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	43	112	0	ENST00000262741.5:c.496-1G>T		p.X166_splice	ENST00000262741	NM_003629.3	166			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.686708534322026	2		112	98	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739108	46739108	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1355367346	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	76	470	0	ENST00000371975.4:c.1457G>A	p.Ser486Asn	p.S486N	ENST00000371975	NM_003579.3	486	aGc/aAc	13/18	1	2	FACETS	0.611	0.54	0.687	0.611	0.54	0.687	SUBCLONAL	1	FALSE	1	0.686708534322026	2		470	362	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301888	65301888	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	55	289	0	ENST00000342505.4:c.3151G>T	p.Glu1051Ter	p.E1051*	ENST00000342505	NM_002227.2	1051	Gaa/Taa	23/25	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	1	0.686708534322026	2		289	140	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306960	65306960	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	8	336	0	ENST00000342505.4:c.2617C>T	p.Arg873Cys	p.R873C	ENST00000342505	NM_002227.2	873	Cgc/Tgc	19/25	1	2	FACETS	0.061	0.039	0.09	0.061	0.039	0.09	SUBCLONAL	1	FALSE	1	0.686708534322026	2		336	382	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65311282	65311282	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	79	357	0	ENST00000342505.4:c.2029C>A	p.Leu677Ile	p.L677I	ENST00000342505	NM_002227.2	677	Ctc/Atc	15/25	1	2	FACETS	0.767	0.681	0.857	0.767	0.681	0.857	SUBCLONAL	1	FALSE	1	0.686708534322026	2		357	300	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339110	65339111	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	118	457	1	ENST00000342505.4:c.425dup	p.Ile143AspfsTer9	p.I143Dfs*9	ENST00000342505	NM_002227.2	142	aag/aaAg	5/25	1	2	FACETS	0.909	0.828	0.993	0.909	0.828	0.993	CLONAL	1	FALSE	1	0.686708534322026	2		458	378	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115272983	115272983	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	100	566	0	ENST00000438362.2:c.1390G>T	p.Val464Phe	p.V464F	ENST00000438362	NM_001242891.1	464	Gtt/Ttt	12/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	1	0.686708534322026	2		566	277	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276614	115276614	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	97	402	0	ENST00000438362.2:c.845G>T	p.Arg282Ile	p.R282I	ENST00000438362	NM_001242891.1	282	aGa/aTa	8/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.686708534322026	2		402	231	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166370	118166370	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	18	301	0	ENST00000369448.3:c.880A>C	p.Asn294His	p.N294H	ENST00000369448	NM_017709.3	294	Aac/Cac	2/2	1	2	FACETS	0.183	0.137	0.236	0.183	0.137	0.236	SUBCLONAL	1	FALSE	1	0.686708534322026	2		301	287	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458982	120458982	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	160	547	0	ENST00000256646.2:c.6363G>T	p.Lys2121Asn	p.K2121N	ENST00000256646	NM_024408.3	2121	aaG/aaT	34/34	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.686708534322026	2		547	375	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843599	156843599	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770090356	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	264	589	2	ENST00000524377.1:c.1025G>A	p.Arg342Gln	p.R342Q	ENST00000524377	NM_002529.3	342	cGg/cAg	8/17	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.686708534322026	2		591	650	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851379	156851379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	219	565	0	ENST00000524377.1:c.2336C>T	p.Ala779Val	p.A779V	ENST00000524377	NM_002529.3	779	gCc/gTc	17/17	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.686708534322026	2		565	523	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743329	162743329	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1266317724	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	121	295	0	ENST00000367921.3:c.1799A>G	p.Asn600Ser	p.N600S	ENST00000367921	NM_006182.2	600	aAc/aGc	14/18	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.686708534322026	2		295	288	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746072	162746072	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757948884	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	85	275	0	ENST00000367921.3:c.2195G>A	p.Ser732Asn	p.S732N	ENST00000367921	NM_006182.2	732	aGc/aAc	16/18	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.686708534322026	2		275	221	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749905	162749905	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	95	342	0	ENST00000367921.3:c.2437T>C	p.Tyr813His	p.Y813H	ENST00000367921	NM_006182.2	813	Tac/Cac	18/18	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.686708534322026	2		342	246	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162750032	162750032	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	119	277	0	ENST00000367921.3:c.2564A>G	p.Glu855Gly	p.E855G	ENST00000367921	NM_006182.2	855	gAg/gGg	18/18	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.686708534322026	2		277	286	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176145075	176145075	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	47	293	0	ENST00000367669.3:c.536A>C	p.Asn179Thr	p.N179T	ENST00000367669	NM_022457.5	179	aAt/aCt	3/20	1	2	FACETS	0.825	0.708	0.948	0.825	0.708	0.948	CLONAL	1	FALSE	1	0.686708534322026	2		293	166	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104562	193104562	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	78	368	0	ENST00000367435.3:c.349G>T	p.Gly117Cys	p.G117C	ENST00000367435	NM_024529.4	117	Ggt/Tgt	4/17	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.686708534322026	2		368	187	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649665	206649665	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	218	438	2	ENST00000367120.3:c.500A>G	p.Asp167Gly	p.D167G	ENST00000367120	NM_014002.3	167	gAt/gGt	6/22	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.686708534322026	2		440	557	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650023	206650023	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	177	336	0	ENST00000367120.3:c.543T>A	p.His181Gln	p.H181Q	ENST00000367120	NM_014002.3	181	caT/caA	7/22	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.686708534322026	2		336	412	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612893	228612893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1358711210	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	200	452	0	ENST00000366696.1:c.134G>A	p.Gly45Asp	p.G45D	ENST00000366696	NM_003493.2	45	gGc/gAc	1/1	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.686708534322026	2		452	450	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663773	241663773	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	81	323	0	ENST00000366560.3:c.1354T>C	p.Ser452Pro	p.S452P	ENST00000366560	NM_000143.3	452	Tct/Cct	9/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.686708534322026	2		323	207	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828129	243828129	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	77	275	0	ENST00000263826.5:c.229C>A	p.Leu77Ile	p.L77I	ENST00000263826	NM_005465.4	77	Ctc/Atc	3/13	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	FALSE	1	0.686708534322026	2		275	218	SUCCESS
RET	5979	MSKCC	GRCh37	10	43602002	43602002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754859905	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	228	545	0	ENST00000355710.3:c.1046C>T	p.Ala349Val	p.A349V	ENST00000355710	NM_020975.4	349	gCg/gTg	5/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.686708534322026	2		545	611	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619222	43619222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	176	411	0	ENST00000355710.3:c.2905C>T	p.Arg969Trp	p.R969W	ENST00000355710	NM_020975.4	969	Cgg/Tgg	17/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.686708534322026	2		411	420	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851550	63851550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	36	501	0	ENST00000279873.7:c.2328G>T	p.Glu776Asp	p.E776D	ENST00000279873	NM_032199.2	776	gaG/gaT	10/10	1	2	FACETS	0.229	0.188	0.275	0.229	0.188	0.275	SUBCLONAL	1	FALSE	1	0.686708534322026	2		501	458	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852461	63852461	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	111	417	0	ENST00000279873.7:c.3239G>A	p.Gly1080Asp	p.G1080D	ENST00000279873	NM_032199.2	1080	gGt/gAt	10/10	1	2	FACETS	0.754	0.682	0.828	0.754	0.682	0.828	SUBCLONAL	1	FALSE	1	0.686708534322026	2		417	429	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333132	70333132	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	192	513	0	ENST00000373644.4:c.1037A>G	p.Gln346Arg	p.Q346R	ENST00000373644	NM_030625.2	346	cAa/cGa	2/12	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	1	0.686708534322026	2		513	400	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70441190	70441190	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	87	345	0	ENST00000373644.4:c.4859C>T	p.Ala1620Val	p.A1620V	ENST00000373644	NM_030625.2	1620	gCt/gTt	9/12	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	FALSE	1	0.686708534322026	2		345	244	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450771	70450771	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196438709	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	42	385	0	ENST00000373644.4:c.5611G>A	p.Gly1871Arg	p.G1871R	ENST00000373644	NM_030625.2	1871	Ggg/Agg	12/12	1	2	FACETS	0.287	0.24	0.34	0.287	0.24	0.34	SUBCLONAL	1	FALSE	1	0.686708534322026	2		385	426	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451407	70451407	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	140	495	0	ENST00000373644.4:c.6247C>T	p.Gln2083Ter	p.Q2083*	ENST00000373644	NM_030625.2	2083	Caa/Taa	12/12	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.686708534322026	2		495	350	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720857	89720857	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	85	239	0	ENST00000371953.3:c.1008C>A	p.Tyr336Ter	p.Y336*	ENST00000371953	NM_000314.4	336	taC/taA	8/9	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.686708534322026	2		239	200	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114905804	114905804	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	51	431	0	ENST00000543371.1:c.823G>T	p.Gly275Ter	p.G275*	ENST00000543371	NM_001198531.1	275	Gga/Tga	8/14	1	2	FACETS	0.333	0.283	0.388	0.333	0.283	0.388	SUBCLONAL	1	FALSE	1	0.686708534322026	2		431	446	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123246939	123246939	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	103	367	0	ENST00000358487.5:c.1987-1G>T		p.X663_splice	ENST00000358487	NM_000141.4	663			1	2	FACETS	0.984	0.892	1	0.984	0.892	1	CLONAL	1	FALSE	1	0.686708534322026	2		367	305	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247618	123247618	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1466101220	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	117	326	0	ENST00000358487.5:c.1873C>T	p.Arg625Ter	p.R625*	ENST00000358487	NM_000141.4	625	Cga/Tga	14/18	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.686708534322026	2		326	265	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310916	123310916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	234	325	0	ENST00000358487.5:c.512C>T	p.Ala171Val	p.A171V	ENST00000358487	NM_000141.4	171	gCg/gTg	5/18	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	1	0.686708534322026	2		325	498	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741928	17741928	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	90	194	0	ENST00000250003.3:c.599C>A	p.Ser200Tyr	p.S200Y	ENST00000250003	NM_002478.4	200	tCc/tAc	1/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.686708534322026	2		194	215	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456365	32456365	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	230	509	0	ENST00000332351.3:c.527G>A	p.Arg176His	p.R176H	ENST00000332351	NM_024426.4	176	cGc/cAc	1/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.686708534322026	2		509	561	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138145	64138145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757839757	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	302	538	0	ENST00000334205.4:c.2068G>A	p.Val690Met	p.V690M	ENST00000334205	NM_003942.2	690	Gtg/Atg	16/17	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	1	0.686708534322026	2		538	708	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138835	64138835	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	256	535	0	ENST00000334205.4:c.2202G>T	p.Lys734Asn	p.K734N	ENST00000334205	NM_003942.2	734	aaG/aaT	17/17	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.686708534322026	2		535	627	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138840	64138840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761347218	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	256	530	1	ENST00000334205.4:c.2207G>A	p.Arg736Gln	p.R736Q	ENST00000334205	NM_003942.2	736	cGg/cAg	17/17	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.686708534322026	2		531	618	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572181	64572181	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	149	373	0	ENST00000312049.6:c.1458G>T	p.Glu486Asp	p.E486D	ENST00000312049	NM_130799.2	486	gaG/gaT	10/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.686708534322026	2		373	392	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575491	64575491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376872829	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	210	478	0	ENST00000312049.6:c.526G>A	p.Ala176Thr	p.A176T	ENST00000312049	NM_130799.2	176	Gcc/Acc	3/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.686708534322026	2		478	562	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462845	69462845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1404273153	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	201	574	0	ENST00000227507.2:c.658C>T	p.Pro220Ser	p.P220S	ENST00000227507	NM_053056.2	220	Ccc/Tcc	4/5	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	FALSE	1	0.686708534322026	2		574	576	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462909	69462909	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	175	452	0	ENST00000227507.2:c.722C>A	p.Pro241Gln	p.P241Q	ENST00000227507	NM_053056.2	241	cCg/cAg	4/5	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.686708534322026	2		452	470	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625236	69625236	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	192	579	0	ENST00000334134.2:c.557G>T	p.Arg186Met	p.R186M	ENST00000334134	NM_005247.2	186	aGg/aTg	3/3	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.686708534322026	2		579	521	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940537	71940537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	203	458	0	ENST00000298229.2:c.688G>A	p.Glu230Lys	p.E230K	ENST00000298229	NM_001567.3	230	Gag/Aag	6/28	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.686708534322026	2		458	516	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940993	71940993	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	346	632	1	ENST00000298229.2:c.869G>T	p.Ser290Ile	p.S290I	ENST00000298229	NM_001567.3	290	aGc/aTc	8/28	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	FALSE	1	0.686708534322026	2		633	771	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942084	71942084	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	240	634	0	ENST00000298229.2:c.1348G>T	p.Gly450Cys	p.G450C	ENST00000298229	NM_001567.3	450	Ggt/Tgt	12/28	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.686708534322026	2		634	592	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942624	71942624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	220	469	0	ENST00000298229.2:c.1580C>T	p.Thr527Met	p.T527M	ENST00000298229	NM_001567.3	527	aCg/aTg	13/28	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.686708534322026	2		469	563	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948508	71948508	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	259	632	0	ENST00000298229.2:c.3220G>T	p.Gly1074Trp	p.G1074W	ENST00000298229	NM_001567.3	1074	Ggg/Tgg	26/28	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.686708534322026	2		632	616	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047283	77047283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs972319037	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	117	367	0	ENST00000356341.3:c.1261C>T	p.Arg421Trp	p.R421W	ENST00000356341	NM_002576.4	421	Cgg/Tgg	13/15	1	2	FACETS	0.976	0.891	1	0.976	0.891	1	CLONAL	1	FALSE	1	0.686708534322026	2		367	349	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194193	94194193	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	48	220	0	ENST00000323929.3:c.1235T>C	p.Ile412Thr	p.I412T	ENST00000323929	NM_005591.3	412	aTc/aCc	12/20	1	2	FACETS	0.842	0.725	0.967	0.842	0.725	0.967	CLONAL	1	FALSE	1	0.686708534322026	2		220	166	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204870	94204870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	69	332	0	ENST00000323929.3:c.715G>A	p.Asp239Asn	p.D239N	ENST00000323929	NM_005591.3	239	Gat/Aat	8/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.686708534322026	2		332	164	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911965	94911965	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	77	438	0	ENST00000536441.1:c.965C>A	p.Ser322Tyr	p.S322Y	ENST00000536441	NM_144665.3	322	tCt/tAt	7/10	1	2	FACETS	0.798	0.709	0.892	0.798	0.709	0.892	SUBCLONAL	1	FALSE	1	0.686708534322026	2		438	281	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94923009	94923009	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	99	437	0	ENST00000536441.1:c.459A>C	p.Lys153Asn	p.K153N	ENST00000536441	NM_144665.3	153	aaA/aaC	4/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.686708534322026	2		437	230	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998565	100998565	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	215	474	0	ENST00000325455.5:c.1237G>T	p.Ala413Ser	p.A413S	ENST00000325455	NM_001202474.3	413	Gcc/Tcc	1/8	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.686708534322026	2		474	496	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153601	108153601	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	23	102	0	ENST00000278616.4:c.3741C>A	p.Phe1247Leu	p.F1247L	ENST00000278616	NM_000051.3	1247	ttC/ttA	25/63	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	FALSE	1	0.686708534322026	2		102	59	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190748	108190748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	70	266	0	ENST00000278616.4:c.6415G>A	p.Glu2139Lys	p.E2139K	ENST00000278616	NM_000051.3	2139	Gaa/Aaa	44/63	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	FALSE	1	0.686708534322026	2		266	203	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235896	108235896	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786203721	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	60	407	0	ENST00000278616.4:c.8938C>A	p.Leu2980Ile	p.L2980I	ENST00000278616	NM_000051.3	2980	Ctt/Att	62/63	1	2	FACETS	0.832	0.728	0.942	0.832	0.728	0.942	CLONAL	1	FALSE	1	0.686708534322026	2		407	210	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347553	118347553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555037629	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	113	365	0	ENST00000534358.1:c.3190C>T	p.Arg1064Ter	p.R1064*	ENST00000534358	NM_005933.3	1064	Cga/Tga	4/36	1	2	FACETS	0.959	0.873	1	0.959	0.873	1	CLONAL	1	FALSE	1	0.686708534322026	2		365	343	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348681	118348681	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	81	173	0	ENST00000534358.1:c.3335-1G>T		p.X1112_splice	ENST00000534358	NM_005933.3	1112			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.686708534322026	2		173	212	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514435	125514435	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	64	281	0	ENST00000428830.2:c.1130T>C	p.Met377Thr	p.M377T	ENST00000428830	NM_001114121.2	377	aTg/aCg	11/14	1	2	FACETS	0.84	0.738	0.947	0.84	0.738	0.947	CLONAL	1	FALSE	1	0.686708534322026	2		281	222	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416751	416751	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	99	267	0	ENST00000399788.2:c.3799G>T	p.Asp1267Tyr	p.D1267Y	ENST00000399788	NM_001042603.1	1267	Gat/Tat	23/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.686708534322026	2		267	229	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1036330	1036333	+	missense_variant	Missense_Mutation	ONP	CGTC	CGTC	TGTA	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	250	425	1	ENST00000358495.3:c.445_448delinsTACA	p.Asp149_Gly150delinsTyrArg	p.D149_G150delinsYR	ENST00000358495	NM_134424.2	149	GACGgg/TACAgg	6/12	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.686708534322026	2		426	656	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006463	12006463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	134	568	0	ENST00000396373.4:c.431C>T	p.Pro144Leu	p.P144L	ENST00000396373	NM_001987.4	144	cCg/cTg	4/8	1	2	FACETS	0.996	0.914	1	0.996	0.914	1	CLONAL	1	FALSE	1	0.686708534322026	2		568	392	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022652	12022652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200525003	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	197	374	0	ENST00000396373.4:c.758C>T	p.Pro253Leu	p.P253L	ENST00000396373	NM_001987.4	253	cCg/cTg	5/8	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.686708534322026	2		374	494	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435295	18435295	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752140066	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	24	323	1	ENST00000266497.5:c.280C>T	p.Arg94Cys	p.R94C	ENST00000266497		94	Cgt/Tgt	1/31	1	2	FACETS	0.353	0.278	0.438	0.353	0.278	0.438	SUBCLONAL	1	FALSE	1	0.686708534322026	2		324	198	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446852	18446852	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs766981923	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	49	212	0	ENST00000266497.5:c.937G>T	p.Asp313Tyr	p.D313Y	ENST00000266497		313	Gat/Tat	4/31	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	1	0.686708534322026	2		212	122	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21643203	21643203	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	114	539	0	ENST00000421138.2:c.324G>T	p.Glu108Asp	p.E108D	ENST00000421138		108	gaG/gaT	5/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.686708534322026	2		539	298	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944961	31944961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1441610501	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	197	400	1	ENST00000340398.3:c.140C>T	p.Ala47Val	p.A47V	ENST00000340398	NM_001013699.2	47	gCg/gTg	1/1	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	FALSE	1	0.686708534322026	2		401	571	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231286	46231286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	12	243	0	ENST00000334344.6:c.1126G>A	p.Glu376Lys	p.E376K	ENST00000334344	NM_152641.2	376	Gaa/Aaa	10/21	1	2	FACETS	0.259	0.183	0.352	0.259	0.183	0.352	SUBCLONAL	1	FALSE	1	0.686708534322026	2		243	135	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49430997	49430997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	192	392	0	ENST00000301067.7:c.10142C>T	p.Pro3381Leu	p.P3381L	ENST00000301067	NM_003482.3	3381	cCc/cTc	34/54	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.686708534322026	2		392	482	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433620	49433620	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555191740	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	294	747	1	ENST00000301067.7:c.7933C>T	p.Arg2645Ter	p.R2645*	ENST00000301067	NM_003482.3	2645	Cga/Tga	31/54	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.686708534322026	2		748	773	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434402	49434402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	70	623	0	ENST00000301067.7:c.7151C>T	p.Thr2384Ile	p.T2384I	ENST00000301067	NM_003482.3	2384	aCt/aTt	31/54	1	2	FACETS	0.328	0.286	0.374	0.328	0.286	0.374	SUBCLONAL	1	FALSE	1	0.686708534322026	2		623	621	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438643	49438643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370897971	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	265	568	0	ENST00000301067.7:c.4847G>A	p.Gly1616Glu	p.G1616E	ENST00000301067	NM_003482.3	1616	gGa/gAa	19/54	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.686708534322026	2		568	653	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493772	56493772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370221639	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	163	445	2	ENST00000267101.3:c.3088G>A	p.Ala1030Thr	p.A1030T	ENST00000267101	NM_001982.3	1030	Gcc/Acc	25/28	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	1	0.686708534322026	2		447	467	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495736	56495736	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747453114	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	121	368	0	ENST00000267101.3:c.3926G>A	p.Arg1309His	p.R1309H	ENST00000267101	NM_001982.3	1309	cGc/cAc	28/28	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.686708534322026	2		368	321	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861822	57861822	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	195	463	0	ENST00000228682.2:c.1123G>T	p.Asp375Tyr	p.D375Y	ENST00000228682	NM_005269.2	375	Gat/Tat	10/12	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.686708534322026	2		463	504	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69203052	69203052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	85	346	0	ENST00000462284.1:c.79G>A	p.Ala27Thr	p.A27T	ENST00000462284	NM_002392.5	27	Gct/Act	2/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	1	0.686708534322026	2		346	218	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856283	111856283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1420086510	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	22	24	0	ENST00000341259.2:c.334G>A	p.Ala112Thr	p.A112T	ENST00000341259	NM_005475.2	112	Gcc/Acc	2/8	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	FALSE	1	0.686708534322026	2		24	44	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885260	111885260	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	42	460	0	ENST00000341259.2:c.1148C>A	p.Pro383His	p.P383H	ENST00000341259	NM_005475.2	383	cCt/cAt	6/8	1	2	FACETS	0.229	0.191	0.272	0.229	0.191	0.272	SUBCLONAL	1	FALSE	1	0.686708534322026	2		460	534	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111886089	111886089	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs766652046	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	151	414	2	ENST00000341259.2:c.1711C>T	p.Gln571Ter	p.Q571*	ENST00000341259	NM_005475.2	571	Cag/Tag	8/8	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.686708534322026	2		416	417	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112884204	112884204	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	31	527	0	ENST00000351677.2:c.137+2T>C		p.X46_splice	ENST00000351677	NM_002834.3	46			1	2	FACETS	0.29	0.235	0.353	0.29	0.235	0.353	SUBCLONAL	1	FALSE	1	0.686708534322026	2		527	311	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110046	115110046	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867049310	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	77	592	0	ENST00000257566.3:c.1832C>T	p.Ala611Val	p.A611V	ENST00000257566	NM_016569.3	611	gCg/gTg	8/8	1	2	FACETS	0.345	0.303	0.391	0.345	0.303	0.391	SUBCLONAL	1	FALSE	1	0.686708534322026	2		592	650	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120785294	120785294	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767743668	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	216	444	0	ENST00000257552.2:c.814C>T	p.Pro272Ser	p.P272S	ENST00000257552	NM_002442.3	272	Cca/Tca	12/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.686708534322026	2		444	605	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120806843	120806843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	13	63	1	ENST00000257552.2:c.52G>A	p.Asp18Asn	p.D18N	ENST00000257552	NM_002442.3	18	Gac/Aac	1/15	1	2	FACETS	0.308	0.221	0.412	0.308	0.221	0.412	SUBCLONAL	1	FALSE	1	0.686708534322026	2		64	123	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201565	133201565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765125852	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	173	468	1	ENST00000320574.5:c.6673C>T	p.Arg2225Cys	p.R2225C	ENST00000320574	NM_006231.2	2225	Cgc/Tgc	48/49	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.686708534322026	2		469	471	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244184	133244184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768004570	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	27	416	0	ENST00000320574.5:c.2224C>T	p.Arg742Cys	p.R742C	ENST00000320574	NM_006231.2	742	Cgt/Tgt	20/49	1	2	FACETS	0.146	0.116	0.181	0.146	0.116	0.181	SUBCLONAL	1	FALSE	1	0.686708534322026	2		416	538	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252328	133252328	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	155	377	0	ENST00000320574.5:c.1099T>G	p.Phe367Val	p.F367V	ENST00000320574	NM_006231.2	367	Ttt/Gtt	11/49	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.686708534322026	2		377	363	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562141	21562141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373012826	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	76	760	1	ENST00000382592.4:c.1778G>A	p.Arg593His	p.R593H	ENST00000382592	NM_014572.2	593	cGc/cAc	4/8	0.216857847536743	1	FACETS	0.191	0.167	0.217	0.191	0.167	0.217	INDETERMINATE	1	FALSE	0	0.686708534322026	1		761	762	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597589	28597589	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	93	434	0	ENST00000241453.7:c.2316A>C	p.Lys772Asn	p.K772N	ENST00000241453	NM_004119.2	772	aaA/aaC	19/24	0.216857847536743	1	FACETS	0.717	0.648	0.788	0.717	0.648	0.788	INDETERMINATE	1	FALSE	0	0.686708534322026	1		434	248	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29002001	29002001	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	42	358	0	ENST00000282397.4:c.1164C>A	p.Tyr388Ter	p.Y388*	ENST00000282397	NM_002019.4	388	taC/taA	9/30	0.216857847536743	1	FACETS	0.427	0.361	0.499	0.427	0.361	0.499	INDETERMINATE	1	FALSE	0	0.686708534322026	1		358	188	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900240	32900240	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	44	165	0	ENST00000380152.3:c.428C>A	p.Pro143His	p.P143H	ENST00000380152		143	cCt/cAt	5/27	0.216857847536743	1	FACETS	0.601	0.515	0.692	0.601	0.515	0.692	INDETERMINATE	1	FALSE	0	0.686708534322026	1		165	140	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913665	32913665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786204275	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	47	245	0	ENST00000380152.3:c.5173G>A	p.Ala1725Thr	p.A1725T	ENST00000380152		1725	Gct/Act	11/27	0.216857847536743	1	FACETS	0.603	0.519	0.691	0.603	0.519	0.691	INDETERMINATE	1	FALSE	0	0.686708534322026	1		245	149	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914815	32914815	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35029074	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	61	347	0	ENST00000380152.3:c.6323G>A	p.Arg2108His	p.R2108H	ENST00000380152		2108	cGt/cAt	11/27	0.216857847536743	1	FACETS	0.711	0.627	0.798	0.711	0.627	0.798	INDETERMINATE	1	FALSE	0	0.686708534322026	1		347	164	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936799	32936799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	55	346	0	ENST00000380152.3:c.7945C>A	p.Pro2649Thr	p.P2649T	ENST00000380152		2649	Cca/Aca	17/27	0.216857847536743	1	FACETS	0.666	0.582	0.753	0.666	0.582	0.753	INDETERMINATE	1	FALSE	0	0.686708534322026	1		346	158	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950810	32950810	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	68	259	0	ENST00000380152.3:c.8636A>G	p.Asn2879Ser	p.N2879S	ENST00000380152		2879	aAc/aGc	21/27	0.216857847536743	1	FACETS	0.699	0.621	0.78	0.699	0.621	0.78	INDETERMINATE	1	FALSE	0	0.686708534322026	1		259	186	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954015	32954015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	21	349	0	ENST00000380152.3:c.9082G>A	p.Ala3028Thr	p.A3028T	ENST00000380152		3028	Gca/Aca	23/27	0.216857847536743	1	FACETS	0.183	0.141	0.231	0.183	0.141	0.231	INDETERMINATE	1	FALSE	0	0.686708534322026	1		349	220	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972571	32972571	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	144	440	0	ENST00000380152.3:c.9921A>C	p.Lys3307Asn	p.K3307N	ENST00000380152		3307	aaA/aaC	27/27	0.216857847536743	1	FACETS	0.894	0.83	0.959	0.894	0.83	0.959	INDETERMINATE	1	FALSE	0	0.686708534322026	1		440	308	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934264	48934264	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	51	264	0	ENST00000267163.4:c.718+1G>T		p.X240_splice	ENST00000267163	NM_000321.2	240			0.216857847536743	1	FACETS	0.57	0.493	0.652	0.57	0.493	0.652	INDETERMINATE	1	FALSE	0	0.686708534322026	1		264	171	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953730	48953730	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs3092891	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	81	167	1	ENST00000267163.4:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000267163	NM_000321.2	445	Cga/Tga	14/27	0.216857847536743	1	FACETS	0.771	0.693	0.85	0.771	0.693	0.85	INDETERMINATE	1	FALSE	0	0.686708534322026	1		168	201	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037934	49037934	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	73	247	0	ENST00000267163.4:c.2174T>C	p.Val725Ala	p.V725A	ENST00000267163	NM_000321.2	725	gTa/gCa	21/27	0.216857847536743	1	FACETS	0.759	0.678	0.841	0.759	0.678	0.841	INDETERMINATE	1	FALSE	0	0.686708534322026	1		247	184	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281699	49281699	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	193	607	1	ENST00000282018.3:c.746T>C	p.Ile249Thr	p.I249T	ENST00000282018	NM_020377.2	249	aTc/aCc	1/1	0.216857847536743	1	FACETS	0.692	0.646	0.74	0.692	0.646	0.74	INDETERMINATE	1	FALSE	0	0.686708534322026	1		608	533	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435303	110435303	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1260159870	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	78	127	0	ENST00000375856.3:c.3098C>T	p.Pro1033Leu	p.P1033L	ENST00000375856	NM_003749.2	1033	cCa/cTa	1/2	0.216857847536743	1	FACETS	0.681	0.609	0.756	0.681	0.609	0.756	INDETERMINATE	1	FALSE	0	0.686708534322026	1		127	219	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435436	110435436	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	208	381	0	ENST00000375856.3:c.2965C>A	p.Pro989Thr	p.P989T	ENST00000375856	NM_003749.2	989	Cct/Act	1/2	0.216857847536743	1	FACETS	0.687	0.642	0.733	0.687	0.642	0.733	INDETERMINATE	1	FALSE	0	0.686708534322026	1		381	579	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436654	110436654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1200592095	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	212	542	0	ENST00000375856.3:c.1747C>T	p.Arg583Trp	p.R583W	ENST00000375856	NM_003749.2	583	Cgg/Tgg	1/2	0.216857847536743	1	FACETS	0.694	0.649	0.74	0.694	0.649	0.74	INDETERMINATE	1	FALSE	0	0.686708534322026	1		542	584	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436946	110436947	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	99	201	1	ENST00000375856.3:c.1454_1455delinsTT	p.Ser485Ile	p.S485I	ENST00000375856	NM_003749.2	485	aGC/aTT	1/2	0.216857847536743	1	FACETS	0.889	0.812	0.967	0.889	0.812	0.967	INDETERMINATE	1	FALSE	0	0.686708534322026	1		202	213	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436947	110436947	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	99	195	0	ENST00000375856.3:c.1454G>T	p.Ser485Ile	p.S485I	ENST00000375856	NM_003749.2	485	aGc/aTc	1/2	0.216857847536743	1	FACETS	0.906	0.828	0.984	0.906	0.828	0.984	INDETERMINATE	1	FALSE	0	0.686708534322026	1		195	209	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105574	30105574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	133	455	2	ENST00000331968.5:c.1112C>T	p.Ala371Val	p.A371V	ENST00000331968	NM_002742.2	371	gCa/gTa	7/18	1	2	FACETS	0.711	0.648	0.776	0.711	0.648	0.776	SUBCLONAL	1	FALSE	1	0.686708534322026	2		457	545	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132946	30132946	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	171	422	1	ENST00000331968.5:c.655T>G	p.Ser219Ala	p.S219A	ENST00000331968	NM_002742.2	219	Tct/Gct	4/18	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.686708534322026	2		423	452	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988463	36988463	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs201631950	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	179	355	0	ENST00000354822.5:c.190C>A	p.Leu64Ile	p.L64I	ENST00000354822	NM_001079668.2	64	Ctc/Atc	2/3	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.686708534322026	2		355	400	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606120	81606120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1279981655	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	158	485	0	ENST00000298171.2:c.790C>A	p.Pro264Thr	p.P264T	ENST00000298171	NM_000369.2	264	Cca/Aca	9/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.686708534322026	2		485	396	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239596	105239596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	58	461	1	ENST00000349310.3:c.949G>A	p.Ala317Thr	p.A317T	ENST00000349310	NM_001014432.1	317	Gcc/Acc	11/15	1	2	FACETS	0.388	0.334	0.447	0.388	0.334	0.447	SUBCLONAL	1	FALSE	1	0.686708534322026	2		462	435	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022974	33022974	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	154	340	0	ENST00000300177.4:c.83G>A	p.Gly28Glu	p.G28E	ENST00000300177	NM_001191322.1	28	gGg/gAg	2/2	0.686708534322026	2	FACETS	1	0.953	1	0.522	0.482	0.562	CLONAL	1	FALSE	0	0.686708534322026	2		340	430	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961688	41961688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	93	366	0	ENST00000219905.7:c.596G>A	p.Arg199His	p.R199H	ENST00000219905	NM_001164273.1	199	cGt/cAt	2/24	0.686708534322026	2	FACETS	0.974	0.878	1	0.487	0.439	0.537	CLONAL	1	FALSE	0	0.686708534322026	2		366	278	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43766946	43766946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	59	225	0	ENST00000382044.4:c.1105G>A	p.Ala369Thr	p.A369T	ENST00000382044	NM_001141980.1	369	Gct/Act	10/28	0.686708534322026	2	FACETS	0.993	0.872	1	0.497	0.436	0.56	CLONAL	1	FALSE	0	0.686708534322026	2		225	173	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477188	67477188	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	169	334	0	ENST00000327367.4:c.995G>A	p.Cys332Tyr	p.C332Y	ENST00000327367	NM_005902.3	332	tGc/tAc	7/9	0.686708534322026	2	FACETS	1	0.978	1	0.567	0.527	0.608	CLONAL	1	FALSE	0	0.686708534322026	2		334	434	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994790	73994790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs562558740	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	165	459	0	ENST00000318443.5:c.274C>T	p.Arg92Cys	p.R92C	ENST00000318443	NM_001024736.1	92	Cgc/Tgc	3/10	0.686708534322026	2	FACETS	1	0.952	1	0.518	0.48	0.557	CLONAL	1	FALSE	0	0.686708534322026	2		459	464	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358400	91358400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	19	481	0	ENST00000355112.3:c.4145C>T	p.Ala1382Val	p.A1382V	ENST00000355112	NM_000057.2	1382	gCc/gTc	22/22	0.686708534322026	2	FACETS	0.16	0.121	0.207	0.08	0.06	0.104	SUBCLONAL	1	FALSE	0	0.686708534322026	2		481	345	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434761	99434761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	30	441	0	ENST00000268035.6:c.848C>T	p.Ala283Val	p.A283V	ENST00000268035	NM_000875.3	283	gCc/gTc	3/21	0.686708534322026	2	FACETS	0.17	0.137	0.209	0.085	0.068	0.105	SUBCLONAL	1	FALSE	0	0.686708534322026	2		441	513	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347941	347941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	183	623	0	ENST00000262320.3:c.1565C>T	p.Ala522Val	p.A522V	ENST00000262320	NM_003502.3	522	gCg/gTg	6/11	1	2	FACETS	0.857	0.795	0.921	0.857	0.795	0.921	CLONAL	1	FALSE	1	0.686708534322026	2		623	622	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348077	348077	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1185544639	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	158	525	2	ENST00000262320.3:c.1429C>T	p.Arg477Cys	p.R477C	ENST00000262320	NM_003502.3	477	Cgt/Tgt	6/11	1	2	FACETS	0.804	0.741	0.87	0.804	0.741	0.87	CLONAL	1	FALSE	1	0.686708534322026	2		527	572	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354413	354413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150141520	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	265	464	1	ENST00000262320.3:c.1145G>A	p.Arg382His	p.R382H	ENST00000262320	NM_003502.3	382	cGc/cAc	5/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.686708534322026	2		465	756	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100438	2100438	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	26	487	0	ENST00000219476.3:c.176G>T	p.Arg59Leu	p.R59L	ENST00000219476	NM_000548.3	59	cGg/cTg	3/42	1	2	FACETS	0.156	0.123	0.194	0.156	0.123	0.194	SUBCLONAL	1	FALSE	1	0.686708534322026	2		487	485	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126499	2126499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397515046	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	218	453	0	ENST00000219476.3:c.2750G>A	p.Arg917Gln	p.R917Q	ENST00000219476	NM_000548.3	917	cGg/cAg	25/42	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.686708534322026	2		453	551	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138115	2138115	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45517394	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	261	569	0	ENST00000219476.3:c.5135C>T	p.Ala1712Val	p.A1712V	ENST00000219476	NM_000548.3	1712	gCc/gTc	40/42	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.686708534322026	2		569	685	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213991	2213991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758738357	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	219	486	0	ENST00000326181.6:c.70G>A	p.Val24Ile	p.V24I	ENST00000326181	NM_032271.2	24	Gtc/Atc	2/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.686708534322026	2		486	556	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2221338	2221338	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	36	528	0	ENST00000326181.6:c.422C>A	p.Pro141His	p.P141H	ENST00000326181	NM_032271.2	141	cCc/cAc	6/21	1	2	FACETS	0.187	0.153	0.225	0.187	0.153	0.225	SUBCLONAL	1	FALSE	1	0.686708534322026	2		528	560	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223810	2223810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	264	587	0	ENST00000326181.6:c.1108G>A	p.Ala370Thr	p.A370T	ENST00000326181	NM_032271.2	370	Gcg/Acg	12/21	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.686708534322026	2		587	650	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225338	2225338	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	266	547	0	ENST00000326181.6:c.1423A>G	p.Ile475Val	p.I475V	ENST00000326181	NM_032271.2	475	Atc/Gtc	16/21	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.686708534322026	2		547	656	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636771	2636771	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	235	514	1	ENST00000342085.4:c.1220G>T	p.Arg407Met	p.R407M	ENST00000342085	NM_002613.4	407	aGg/aTg	11/14	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.686708534322026	2		515	584	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633258	3633258	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	283	728	1	ENST00000294008.3:c.4993C>T	p.Pro1665Ser	p.P1665S	ENST00000294008	NM_032444.2	1665	Ccc/Tcc	14/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.686708534322026	2		729	773	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779578	3779578	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	328	725	1	ENST00000262367.5:c.5470G>A	p.Ala1824Thr	p.A1824T	ENST00000262367	NM_004380.2	1824	Gcc/Acc	31/31	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	1	0.686708534322026	2		726	772	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788617	3788617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519884	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	140	426	0	ENST00000262367.5:c.4337G>A	p.Arg1446His	p.R1446H	ENST00000262367	NM_004380.2	1446	cGc/cAc	26/31	1	2	FACETS	0.953	0.876	1	0.953	0.876	1	CLONAL	1	FALSE	1	0.686708534322026	2		426	428	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808010	3808010	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	122	362	0	ENST00000262367.5:c.3409A>G	p.Thr1137Ala	p.T1137A	ENST00000262367	NM_004380.2	1137	Acc/Gcc	18/31	1	2	FACETS	0.995	0.91	1	0.995	0.91	1	CLONAL	1	FALSE	1	0.686708534322026	2		362	357	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820836	3820836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747877878	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	324	641	1	ENST00000262367.5:c.2615C>T	p.Thr872Met	p.T872M	ENST00000262367	NM_004380.2	872	aCg/aTg	14/31	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.686708534322026	2		642	842	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923363	9923363	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1555492766	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	31	471	0	ENST00000330684.3:c.1924C>A	p.Leu642Met	p.L642M	ENST00000330684	NM_001134407.1	642	Ctg/Atg	9/13	1	2	FACETS	0.315	0.255	0.382	0.315	0.255	0.382	SUBCLONAL	1	FALSE	1	0.686708534322026	2		471	287	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923431	9923431	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	107	478	0	ENST00000330684.3:c.1856T>C	p.Val619Ala	p.V619A	ENST00000330684	NM_001134407.1	619	gTc/gCc	9/13	1	2	FACETS	0.992	0.902	1	0.992	0.902	1	CLONAL	1	FALSE	1	0.686708534322026	2		478	314	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349302	11349302	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	181	322	2	ENST00000332029.2:c.34G>A	p.Ala12Thr	p.A12T	ENST00000332029	NM_003745.1	12	Gca/Aca	2/2	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	1	0.686708534322026	2		324	511	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14028108	14028108	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs199505105	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	81	364	0	ENST00000311895.7:c.1162T>G	p.Leu388Val	p.L388V	ENST00000311895	NM_005236.2	388	Tta/Gta	7/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.686708534322026	2		364	204	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614985	23614985	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs515726116	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	15	310	0	ENST00000261584.4:c.3356T>C	p.Leu1119Pro	p.L1119P	ENST00000261584	NM_024675.3	1119	cTg/cCg	13/13	1	2	FACETS	0.202	0.148	0.267	0.202	0.148	0.267	SUBCLONAL	1	FALSE	1	0.686708534322026	2		310	216	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133308	30133308	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	192	396	1	ENST00000263025.4:c.190C>T	p.Arg64Cys	p.R64C	ENST00000263025	NM_002746.2	64	Cgc/Tgc	2/9	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.686708534322026	2		397	512	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785726	50785726	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	106	389	0	ENST00000398568.2:c.716A>C	p.Lys239Thr	p.K239T	ENST00000398568	NM_001042412.1	239	aAg/aCg	4/18	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.686708534322026	2		389	266	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56832443	56832443	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371252223	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	22	315	4	ENST00000308159.5:c.353G>A	p.Arg118Gln	p.R118Q	ENST00000308159	NM_014669.4	118	cGg/cAg	4/22	1	2	FACETS	0.22	0.17	0.278	0.22	0.17	0.278	SUBCLONAL	1	FALSE	1	0.686708534322026	2		319	291	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56867177	56867177	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	211	469	0	ENST00000308159.5:c.1396C>A	p.Leu466Met	p.L466M	ENST00000308159	NM_014669.4	466	Ctg/Atg	13/22	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.686708534322026	2		469	555	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849630	68849630	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876658342	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	51	468	2	ENST00000261769.5:c.1533G>T	p.Gln511His	p.Q511H	ENST00000261769	NM_004360.3	511	caG/caT	10/16	1	2	FACETS	0.316	0.269	0.368	0.316	0.269	0.368	SUBCLONAL	1	FALSE	1	0.686708534322026	2		470	470	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822199	72822199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781682309	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	223	546	0	ENST00000268489.5:c.9976G>A	p.Ala3326Thr	p.A3326T	ENST00000268489	NM_006885.3	3326	Gcc/Acc	10/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.686708534322026	2		546	560	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991395	72991395	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148618101	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	256	557	1	ENST00000268489.5:c.2650G>A	p.Ala884Thr	p.A884T	ENST00000268489	NM_006885.3	884	Gcc/Acc	2/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.686708534322026	2		558	698	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341503	89341503	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	158	509	2	ENST00000301030.4:c.7567C>T	p.Arg2523Trp	p.R2523W	ENST00000301030	NM_001256183.1	2523	Cgg/Tgg	10/13	1	2	FACETS	0.987	0.913	1	0.987	0.913	1	CLONAL	1	FALSE	1	0.686708534322026	2		511	466	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346177	89346177	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	67	203	0	ENST00000301030.4:c.6773C>T	p.Ala2258Val	p.A2258V	ENST00000301030	NM_001256183.1	2258	gCt/gTt	9/13	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	FALSE	1	0.686708534322026	2		203	185	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346291	89346291	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758225743	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	113	268	1	ENST00000301030.4:c.6659C>T	p.Ala2220Val	p.A2220V	ENST00000301030	NM_001256183.1	2220	gCg/gTg	9/13	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.686708534322026	2		269	284	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348341	89348341	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1347006212	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	192	649	2	ENST00000301030.4:c.4609G>A	p.Gly1537Ser	p.G1537S	ENST00000301030	NM_001256183.1	1537	Ggt/Agt	9/13	1	2	FACETS	0.816	0.758	0.877	0.816	0.758	0.877	CLONAL	1	FALSE	1	0.686708534322026	2		651	685	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348595	89348595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	173	622	0	ENST00000301030.4:c.4355C>T	p.Ala1452Val	p.A1452V	ENST00000301030	NM_001256183.1	1452	gCc/gTc	9/13	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.686708534322026	2		622	482	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351763	89351763	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145699896	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	288	684	0	ENST00000301030.4:c.1187C>T	p.Thr396Met	p.T396M	ENST00000301030	NM_001256183.1	396	aCg/aTg	9/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.686708534322026	2		684	763	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912664	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	259	511	0	ENST00000269305.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000269305	NM_001126112.2	337	cGc/cAc	10/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.686708534322026	2		511	654	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	270	552	1	ENST00000269305.4:c.859G>T	p.Glu287Ter	p.E287*	ENST00000269305	NM_001126112.2	287	Gag/Tag	8/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.686708534322026	2		553	704	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578277	7578277	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587778718	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	151	533	0	ENST00000269305.4:c.572C>A	p.Pro191His	p.P191H	ENST00000269305	NM_001126112.2	191	cCt/cAt	6/11	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	FALSE	1	0.686708534322026	2		533	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578421	7578421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779000871	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	236	545	0	ENST00000269305.4:c.509C>T	p.Thr170Met	p.T170M	ENST00000269305	NM_001126112.2	170	aCg/aTg	5/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.686708534322026	2		545	626	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976980	7976980	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	202	459	0	ENST00000319144.4:c.1750G>T	p.Gly584Cys	p.G584C	ENST00000319144	NM_001139.2	584	Ggc/Tgc	13/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.686708534322026	2		459	559	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990615	7990615	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs143526675	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	116	304	0	ENST00000319144.4:c.146C>T	p.Ala49Val	p.A49V	ENST00000319144	NM_001139.2	49	gCg/gTg	1/15	1	2	FACETS	0.871	0.792	0.952	0.871	0.792	0.952	CLONAL	1	FALSE	1	0.686708534322026	2		304	388	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108559	8108559	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	244	535	0	ENST00000585124.1:c.836A>C	p.Asn279Thr	p.N279T	ENST00000585124	NM_004217.3	279	aAc/aCc	8/9	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.686708534322026	2		535	639	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17124919	17124919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775085512	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	188	463	0	ENST00000285071.4:c.803G>A	p.Arg268Gln	p.R268Q	ENST00000285071	NM_144997.5	268	cGg/cAg	8/14	1	2	FACETS	0.987	0.918	1	0.987	0.918	1	CLONAL	1	FALSE	1	0.686708534322026	2		463	555	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546096	29546096	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	157	438	0	ENST00000356175.3:c.1601C>A	p.Pro534His	p.P534H	ENST00000356175	NM_000267.3	534	cCt/cAt	14/57	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.686708534322026	2		438	391	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428252	33428252	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372038369	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	191	341	0	ENST00000345365.6:c.871C>T	p.Arg291Cys	p.R291C	ENST00000345365	NM_002878.3	291	Cgc/Tgc	9/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.686708534322026	2		341	439	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33446632	33446632	+	start_lost	Translation_Start_Site	SNP	T	T	C	rs561425038	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	159	433	0	ENST00000345365.6:c.1A>G	p.Met1?	p.M1?	ENST00000345365	NM_002878.3	1	Atg/Gtg	1/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.686708534322026	2		433	422	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627163	37627163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	28	306	0	ENST00000447079.4:c.1078C>T	p.Pro360Ser	p.P360S	ENST00000447079	NM_015083.1	360	Cct/Tct	2/14	1	2	FACETS	0.358	0.287	0.437	0.358	0.287	0.437	SUBCLONAL	1	FALSE	1	0.686708534322026	2		306	228	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883983	37883983	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	224	588	0	ENST00000269571.5:c.3454C>T	p.Pro1152Ser	p.P1152S	ENST00000269571		1152	Ccc/Tcc	27/27	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.686708534322026	2		588	641	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441486	40441486	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	37	462	0	ENST00000345506.4:c.57G>T	p.Gln19His	p.Q19H	ENST00000345506	NM_003152.3	19	caG/caT	3/20	1	2	FACETS	0.196	0.161	0.236	0.196	0.161	0.236	SUBCLONAL	1	FALSE	1	0.686708534322026	2		462	549	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780639	56780639	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	77	444	0	ENST00000337432.4:c.654G>T	p.Glu218Asp	p.E218D	ENST00000337432	NM_058216.2	218	gaG/gaT	4/9	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	FALSE	1	0.686708534322026	2		444	210	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58711261	58711261	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571290585	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	117	456	2	ENST00000305921.3:c.749G>A	p.Arg250Gln	p.R250Q	ENST00000305921	NM_003620.3	250	cGa/cAa	3/6	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.686708534322026	2		458	308	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58725369	58725369	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	93	437	0	ENST00000305921.3:c.943G>A	p.Gly315Arg	p.G315R	ENST00000305921	NM_003620.3	315	Gga/Aga	4/6	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.686708534322026	2		437	233	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526105	63526105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs527766429	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	199	447	0	ENST00000307078.5:c.2521C>T	p.Arg841Trp	p.R841W	ENST00000307078	NM_004655.3	841	Cgg/Tgg	11/11	1	2	FACETS	0.984	0.917	1	0.984	0.917	1	CLONAL	1	FALSE	1	0.686708534322026	2		447	589	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526219	63526219	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	149	322	0	ENST00000307078.5:c.2407T>C	p.Tyr803His	p.Y803H	ENST00000307078	NM_004655.3	803	Tat/Cat	11/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.686708534322026	2		322	354	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511581	66511581	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757185291	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	136	297	0	ENST00000358598.2:c.41G>A	p.Ser14Asn	p.S14N	ENST00000358598	NM_212471.2	14	aGc/aAc	2/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.686708534322026	2		297	336	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526082	66526082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	68	306	0	ENST00000358598.2:c.913C>T	p.Arg305Cys	p.R305C	ENST00000358598	NM_212471.2	305	Cgt/Tgt	10/11	1	2	FACETS	0.904	0.799	1	0.904	0.799	1	CLONAL	1	FALSE	1	0.686708534322026	2		306	219	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117684	70117684	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs969167599	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	219	521	0	ENST00000245479.2:c.152A>G	p.Asn51Ser	p.N51S	ENST00000245479	NM_000346.3	51	aAc/aGc	1/3	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.686708534322026	2		521	540	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120208	70120208	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	28	474	0	ENST00000245479.2:c.1210C>A	p.Pro404Thr	p.P404T	ENST00000245479	NM_000346.3	404	Ccc/Acc	3/3	1	2	FACETS	0.148	0.118	0.183	0.148	0.118	0.183	SUBCLONAL	1	FALSE	1	0.686708534322026	2		474	551	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120271	70120271	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	44	656	0	ENST00000245479.2:c.1273C>A	p.Leu425Ile	p.L425I	ENST00000245479	NM_000346.3	425	Ctc/Atc	3/3	1	2	FACETS	0.163	0.136	0.193	0.163	0.136	0.193	SUBCLONAL	1	FALSE	1	0.686708534322026	2		656	786	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897382	78897382	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	225	520	0	ENST00000306801.3:c.2717C>A	p.Pro906Gln	p.P906Q	ENST00000306801	NM_020761.2	906	cCg/cAg	23/34	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.686708534322026	2		520	542	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919548	78919548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769436510	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	164	368	0	ENST00000306801.3:c.3107C>T	p.Pro1036Leu	p.P1036L	ENST00000306801	NM_020761.2	1036	cCg/cTg	26/34	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.686708534322026	2		368	463	SUCCESS
YES1	7525	MSKCC	GRCh37	18	751704	751704	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs368508541	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	89	244	0	ENST00000314574.4:c.371+1G>A		p.X124_splice	ENST00000314574	NM_005433.3	124			NA	2	FACETS	1	0.978	1			1	INDETERMINATE	1	FALSE	NA	0.686708534322026	2		244	200	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39550371	39550371	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	65	312	0	ENST00000262039.4:c.482G>A	p.Gly161Asp	p.G161D	ENST00000262039	NM_002647.2	161	gGc/gAc	4/25	1	2	FACETS	0.915	0.806	1	0.915	0.806	1	CLONAL	1	FALSE	1	0.686708534322026	2		312	207	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56411684	56411684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1004957123	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	54	280	0	ENST00000348428.3:c.1868C>T	p.Pro623Leu	p.P623L	ENST00000348428	NM_006785.3	623	cCg/cTg	15/17	1	2	FACETS	0.983	0.857	1	0.983	0.857	1	CLONAL	1	FALSE	1	0.686708534322026	2		280	160	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612244	1612244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1325068914	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	165	331	0	ENST00000344749.5:c.1775C>T	p.Ala592Val	p.A592V	ENST00000344749	NM_001136139.2	592	gCc/gTc	18/19	NA	2	FACETS	1	0.931	1			1	INDETERMINATE	1	FALSE	NA	0.686708534322026	2		331	478	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2199928	2199928	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372248188	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	221	484	1	ENST00000398665.3:c.697G>A	p.Ala233Thr	p.A233T	ENST00000398665	NM_032482.2	233	Gcc/Acc	8/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.686708534322026	2		485	577	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207668	2207668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	216	473	1	ENST00000398665.3:c.952G>A	p.Asp318Asn	p.D318N	ENST00000398665	NM_032482.2	318	Gac/Aac	11/28	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.686708534322026	2		474	572	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099303	4099303	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	291	591	1	ENST00000262948.5:c.815C>T	p.Ala272Val	p.A272V	ENST00000262948	NM_030662.3	272	gCc/gTc	7/11	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	FALSE	1	0.686708534322026	2		592	651	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208051	5208051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1477222866	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	159	421	0	ENST00000357368.4:c.5660C>T	p.Thr1887Met	p.T1887M	ENST00000357368	NM_002850.3	1887	aCg/aTg	37/38	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.686708534322026	2		421	394	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212088	5212088	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	283	522	0	ENST00000357368.4:c.4943C>T	p.Ala1648Val	p.A1648V	ENST00000357368	NM_002850.3	1648	gCc/gTc	32/38	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	1	0.686708534322026	2		522	643	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214574	5214574	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1205787412	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	196	505	0	ENST00000357368.4:c.4492C>T	p.Arg1498Trp	p.R1498W	ENST00000357368	NM_002850.3	1498	Cgg/Tgg	29/38	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.686708534322026	2		505	550	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244223	5244223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199851847	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	210	480	1	ENST00000357368.4:c.1259G>A	p.Arg420His	p.R420H	ENST00000357368	NM_002850.3	420	cGc/cAc	11/38	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.686708534322026	2		481	543	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246438	10246438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	273	517	0	ENST00000340748.4:c.4699G>A	p.Gly1567Ser	p.G1567S	ENST00000340748		1567	Ggc/Agc	38/40	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.686708534322026	2		517	659	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248654	10248654	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	197	372	0	ENST00000340748.4:c.4099G>T	p.Val1367Leu	p.V1367L	ENST00000340748		1367	Gtg/Ttg	35/40	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.686708534322026	2		372	476	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10274006	10274006	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	35	469	0	ENST00000340748.4:c.874G>T	p.Asp292Tyr	p.D292Y	ENST00000340748		292	Gat/Tat	11/40	1	2	FACETS	0.276	0.226	0.332	0.276	0.226	0.332	SUBCLONAL	1	FALSE	1	0.686708534322026	2		469	369	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599948	10599948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs111830952	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	287	536	0	ENST00000171111.5:c.1628C>T	p.Thr543Met	p.T543M	ENST00000171111	NM_203500.1	543	aCg/aTg	5/6	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.686708534322026	2		536	735	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097158	11097158	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	200	552	0	ENST00000358026.2:c.649A>G	p.Met217Val	p.M217V	ENST00000358026	NM_001128849.1	217	Atg/Gtg	4/36	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.686708534322026	2		552	546	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101977	11101977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1374559246	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	260	532	2	ENST00000358026.2:c.1397G>A	p.Arg466His	p.R466H	ENST00000358026	NM_001128849.1	466	cGc/cAc	8/36	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.686708534322026	2		534	674	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121076	11121076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1131691371	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	224	455	0	ENST00000358026.2:c.2143G>A	p.Asp715Asn	p.D715N	ENST00000358026	NM_001128849.1	715	Gat/Aat	15/36	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.686708534322026	2		455	592	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135066	11135066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	59	559	0	ENST00000358026.2:c.3033G>A	p.Met1011Ile	p.M1011I	ENST00000358026	NM_001128849.1	1011	atG/atA	21/36	1	2	FACETS	0.255	0.219	0.295	0.255	0.219	0.295	SUBCLONAL	1	FALSE	1	0.686708534322026	2		559	673	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141422	11141422	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	218	499	0	ENST00000358026.2:c.3399G>T	p.Glu1133Asp	p.E1133D	ENST00000358026	NM_001128849.1	1133	gaG/gaT	25/36	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.686708534322026	2		499	562	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144113	11144113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	311	533	1	ENST00000358026.2:c.3694G>A	p.Gly1232Ser	p.G1232S	ENST00000358026	NM_001128849.1	1232	Ggc/Agc	26/36	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	1	0.686708534322026	2		534	732	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144150	11144150	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502060	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	257	473	0	ENST00000358026.2:c.3731G>A	p.Arg1244His	p.R1244H	ENST00000358026	NM_001128849.1	1244	cGc/cAc	26/36	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.686708534322026	2		473	655	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145645	11145645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	269	590	0	ENST00000358026.2:c.4007G>A	p.Arg1336His	p.R1336H	ENST00000358026	NM_001128849.1	1336	cGc/cAc	29/36	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.686708534322026	2		590	650	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276310	15276310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369768722	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	214	498	0	ENST00000263388.2:c.5684G>A	p.Arg1895His	p.R1895H	ENST00000263388	NM_000435.2	1895	cGc/cAc	31/33	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.686708534322026	2		498	598	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285167	15285167	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs940480447	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	290	552	2	ENST00000263388.2:c.4448G>A	p.Arg1483His	p.R1483H	ENST00000263388	NM_000435.2	1483	cGc/cAc	25/33	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.686708534322026	2		554	753	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302865	15302865	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	217	583	0	ENST00000263388.2:c.585G>T	p.Glu195Asp	p.E195D	ENST00000263388	NM_000435.2	195	gaG/gaT	4/33	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.686708534322026	2		583	606	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349769	15349769	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	50	537	0	ENST00000263377.2:c.3805C>A	p.Leu1269Met	p.L1269M	ENST00000263377	NM_058243.2	1269	Ctg/Atg	19/20	1	2	FACETS	0.297	0.251	0.346	0.297	0.251	0.346	SUBCLONAL	1	FALSE	1	0.686708534322026	2		537	491	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366389	15366389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs577973488	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	108	252	0	ENST00000263377.2:c.1766C>T	p.Ala589Val	p.A589V	ENST00000263377	NM_058243.2	589	gCg/gTg	10/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.686708534322026	2		252	276	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945726	17945726	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	213	578	1	ENST00000458235.1:c.2134G>T	p.Gly712Cys	p.G712C	ENST00000458235	NM_000215.3	712	Ggc/Tgc	16/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.686708534322026	2		579	583	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954613	17954613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	248	627	0	ENST00000458235.1:c.281G>A	p.Ser94Asn	p.S94N	ENST00000458235	NM_000215.3	94	aGc/aAc	3/24	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.686708534322026	2		627	669	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976943	18976943	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	195	440	0	ENST00000262803.5:c.3328G>A	p.Gly1110Ser	p.G1110S	ENST00000262803	NM_002911.3	1110	Ggc/Agc	23/24	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	1	0.686708534322026	2		440	560	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256641	19256641	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	159	454	0	ENST00000162023.5:c.1072C>T	p.Arg358Cys	p.R358C	ENST00000162023		358	Cgc/Tgc	13/13	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	FALSE	1	0.686708534322026	2		454	463	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256769	19256769	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	132	561	3	ENST00000162023.5:c.944del	p.Pro315GlnfsTer?	p.P315Qfs*?	ENST00000162023		315	cCa/ca	13/13	1	2	FACETS	0.746	0.681	0.814	0.746	0.681	0.814	SUBCLONAL	1	FALSE	1	0.686708534322026	2		564	515	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258529	19258529	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	38	567	0	ENST00000162023.5:c.371C>T	p.Ala124Val	p.A124V	ENST00000162023		124	gCc/gTc	8/13	1	2	FACETS	0.161	0.132	0.193	0.161	0.132	0.193	SUBCLONAL	1	FALSE	1	0.686708534322026	2		567	689	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212371	36212371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753909605	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	269	536	0	ENST00000222270.7:c.2122G>A	p.Ala708Thr	p.A708T	ENST00000222270	NM_014727.1	708	Gcc/Acc	3/37	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.686708534322026	2		536	667	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216454	36216454	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	42	678	0	ENST00000222270.7:c.3717G>T	p.Gln1239His	p.Q1239H	ENST00000222270	NM_014727.1	1239	caG/caT	12/37	1	2	FACETS	0.16	0.133	0.19	0.16	0.133	0.19	SUBCLONAL	1	FALSE	1	0.686708534322026	2		678	765	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223009	36223009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	239	679	3	ENST00000222270.7:c.5638G>A	p.Val1880Ile	p.V1880I	ENST00000222270	NM_014727.1	1880	Gtc/Atc	27/37	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.686708534322026	2		682	593	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224588	36224588	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	260	627	0	ENST00000222270.7:c.7049+1G>A		p.X2350_splice	ENST00000222270	NM_014727.1	2350			1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.686708534322026	2		627	640	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228979	36228979	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555734923	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	244	483	2	ENST00000222270.7:c.7759C>T	p.Arg2587Ter	p.R2587*	ENST00000222270	NM_014727.1	2587	Cga/Tga	36/37	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.686708534322026	2		485	621	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40743884	40743884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	240	394	0	ENST00000392038.2:c.823G>A	p.Asp275Asn	p.D275N	ENST00000392038	NM_001626.4	275	Gac/Aac	9/14	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.686708534322026	2		394	572	SUCCESS
AXL	558	MSKCC	GRCh37	19	41737105	41737105	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140448864	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	56	559	0	ENST00000301178.4:c.685C>T	p.Arg229Cys	p.R229C	ENST00000301178	NM_021913.4	229	Cgt/Tgt	6/20	1	2	FACETS	0.276	0.236	0.32	0.276	0.236	0.32	SUBCLONAL	1	FALSE	1	0.686708534322026	2		559	591	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765712	41765712	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	103	428	1	ENST00000301178.4:c.2588C>A	p.Ala863Asp	p.A863D	ENST00000301178	NM_021913.4	863	gCt/gAt	20/20	1	2	FACETS	0.798	0.72	0.879	0.798	0.72	0.879	SUBCLONAL	1	FALSE	1	0.686708534322026	2		429	376	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383069	42383069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1263805787	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	98	296	0	ENST00000221972.3:c.89G>A	p.Cys30Tyr	p.C30Y	ENST00000221972	NM_021601.3	30	tGc/tAc	2/5	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.686708534322026	2		296	246	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752786	42752786	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762382429	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	274	621	0	ENST00000222329.4:c.1478G>A	p.Arg493His	p.R493H	ENST00000222329	NM_006494.2	493	cGc/cAc	4/4	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.686708534322026	2		621	708	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860600	45860600	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	62	632	0	ENST00000391945.4:c.1407G>T	p.Lys469Asn	p.K469N	ENST00000391945	NM_000400.3	469	aaG/aaT	15/23	1	2	FACETS	0.222	0.191	0.255	0.222	0.191	0.255	SUBCLONAL	1	FALSE	1	0.686708534322026	2		632	815	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868157	45868157	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	259	617	0	ENST00000391945.4:c.533A>C	p.Asp178Ala	p.D178A	ENST00000391945	NM_000400.3	178	gAt/gCt	7/23	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.686708534322026	2		617	684	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872377	45872377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	185	504	1	ENST00000391945.4:c.134G>A	p.Gly45Asp	p.G45D	ENST00000391945	NM_000400.3	45	gGc/gAc	3/23	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.686708534322026	2		505	508	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905041	50905041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs577686721	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	176	357	0	ENST00000440232.2:c.323C>T	p.Ala108Val	p.A108V	ENST00000440232	NM_002691.3	108	gCg/gTg	4/27	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.686708534322026	2		357	379	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50916693	50916693	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	181	413	0	ENST00000440232.2:c.2165G>A	p.Gly722Glu	p.G722E	ENST00000440232	NM_002691.3	722	gGg/gAg	18/27	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.686708534322026	2		413	504	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52693428	52693428	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	262	525	0	ENST00000322088.6:c.78+1G>A		p.X26_splice	ENST00000322088	NM_014225.5	26			1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.686708534322026	2		525	641	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52705233	52705233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs949208712	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	141	354	0	ENST00000322088.6:c.115G>A	p.Ala39Thr	p.A39T	ENST00000322088	NM_014225.5	39	Gcc/Acc	2/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.686708534322026	2		354	383	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716036	52716036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749905469	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	232	530	0	ENST00000322088.6:c.601G>A	p.Val201Ile	p.V201I	ENST00000322088	NM_014225.5	201	Gtc/Atc	5/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.686708534322026	2		530	591	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716069	52716069	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	237	572	1	ENST00000322088.6:c.634C>A	p.Leu212Met	p.L212M	ENST00000322088	NM_014225.5	212	Ctg/Atg	5/15	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.686708534322026	2		573	572	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52725363	52725363	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	141	380	0	ENST00000322088.6:c.1530G>T	p.Glu510Asp	p.E510D	ENST00000322088	NM_014225.5	510	gaG/gaT	13/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.686708534322026	2		380	349	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52725461	52725461	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	156	433	0	ENST00000322088.6:c.1628C>A	p.Ser543Tyr	p.S543Y	ENST00000322088	NM_014225.5	543	tCt/tAt	13/15	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	FALSE	1	0.686708534322026	2		433	449	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467124	25467124	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	37	497	0	ENST00000264709.3:c.1751A>G	p.Tyr584Cys	p.Y584C	ENST00000264709	NM_175629.2	584	tAc/tGc	15/23	1	2	FACETS	0.184	0.151	0.221	0.184	0.151	0.221	SUBCLONAL	1	FALSE	1	0.686708534322026	2		497	586	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469141	25469141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1004570713	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	32	541	0	ENST00000264709.3:c.1317G>A	p.Met439Ile	p.M439I	ENST00000264709	NM_175629.2	439	atG/atA	11/23	1	2	FACETS	0.169	0.136	0.206	0.169	0.136	0.206	SUBCLONAL	1	FALSE	1	0.686708534322026	2		541	552	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469587	25469587	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	239	508	0	ENST00000264709.3:c.1181A>G	p.Asp394Gly	p.D394G	ENST00000264709	NM_175629.2	394	gAc/gGc	10/23	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.686708534322026	2		508	598	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964989	25964989	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746010291	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	170	393	0	ENST00000435504.4:c.4217C>T	p.Ala1406Val	p.A1406V	ENST00000435504		1406	gCc/gTc	13/13	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.686708534322026	2		393	451	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973187	25973187	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	82	277	0	ENST00000435504.4:c.1238C>A	p.Pro413His	p.P413H	ENST00000435504		413	cCt/cAt	12/13	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	FALSE	1	0.686708534322026	2		277	233	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443646	29443646	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	192	515	1	ENST00000389048.3:c.3571C>T	p.Pro1191Ser	p.P1191S	ENST00000389048	NM_004304.4	1191	Ccc/Tcc	23/29	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.686708534322026	2		516	530	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519846	29519846	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	165	473	0	ENST00000389048.3:c.1725G>T	p.Lys575Asn	p.K575N	ENST00000389048	NM_004304.4	575	aaG/aaT	9/29	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.686708534322026	2		473	444	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143248	30143248	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	50	432	0	ENST00000389048.3:c.278T>C	p.Leu93Pro	p.L93P	ENST00000389048	NM_004304.4	93	cTg/cCg	1/29	1	2	FACETS	0.329	0.279	0.383	0.329	0.279	0.383	SUBCLONAL	1	FALSE	1	0.686708534322026	2		432	443	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39294807	39294807	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1442738935	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	91	411	0	ENST00000402219.2:c.175C>A	p.Leu59Ile	p.L59I	ENST00000402219	NM_005633.3	59	Cta/Ata	2/23	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.686708534322026	2		411	244	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574157	46574157	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	197	515	2	ENST00000263734.3:c.172C>T	p.Arg58Ter	p.R58*	ENST00000263734	NM_001430.4	58	Cga/Tga	2/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.686708534322026	2		517	495	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47672741	47672741	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs557339938	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	74	361	0	ENST00000233146.2:c.1331G>A	p.Arg444His	p.R444H	ENST00000233146	NM_000251.2	444	cGt/cAt	8/16	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	FALSE	1	0.686708534322026	2		361	210	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026414	48026414	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	103	374	0	ENST00000234420.5:c.1292A>C	p.Lys431Thr	p.K431T	ENST00000234420	NM_000179.2	431	aAa/aCa	4/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.686708534322026	2		374	263	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026572	48026572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782706	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	75	387	1	ENST00000234420.5:c.1450G>A	p.Glu484Lys	p.E484K	ENST00000234420	NM_000179.2	484	Gaa/Aaa	4/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.686708534322026	2		388	201	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027661	48027661	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	41	291	0	ENST00000234420.5:c.2539G>T	p.Glu847Ter	p.E847*	ENST00000234420	NM_000179.2	847	Gaa/Taa	4/10	1	2	FACETS	0.878	0.747	1	0.878	0.747	1	CLONAL	1	FALSE	1	0.686708534322026	2		291	136	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189332	99189332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	232	449	0	ENST00000074304.5:c.2588G>A	p.Gly863Asp	p.G863D	ENST00000074304	NM_001134224.1	863	gGt/gAt	24/26	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.686708534322026	2		449	533	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015293	128015293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770995913	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	166	332	0	ENST00000285398.2:c.2228G>A	p.Arg743His	p.R743H	ENST00000285398	NM_000122.1	743	cGc/cAc	15/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.686708534322026	2		332	422	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038135	128038135	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753633161	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	163	357	0	ENST00000285398.2:c.1415G>A	p.Arg472His	p.R472H	ENST00000285398	NM_000122.1	472	cGc/cAc	9/15	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.686708534322026	2		357	459	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050215	128050215	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	25	399	0	ENST00000285398.2:c.442G>A	p.Val148Ile	p.V148I	ENST00000285398	NM_000122.1	148	Gtc/Atc	3/15	1	2	FACETS	0.234	0.184	0.291	0.234	0.184	0.291	SUBCLONAL	1	FALSE	1	0.686708534322026	2		399	311	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872714	136872714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1275022868	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	139	331	0	ENST00000241393.3:c.784G>A	p.Asp262Asn	p.D262N	ENST00000241393	NM_003467.2	262	Gac/Aac	2/2	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.686708534322026	2		331	325	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095539	178095539	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	38	231	0	ENST00000397062.3:c.1792A>G	p.Lys598Glu	p.K598E	ENST00000397062	NM_006164.4	598	Aag/Gag	5/5	1	2	FACETS	0.988	0.839	1	0.988	0.839	1	CLONAL	1	FALSE	1	0.686708534322026	2		231	112	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190656635	190656635	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	55	222	0	ENST00000441310.2:c.100G>T	p.Asp34Tyr	p.D34Y	ENST00000441310	NM_000534.4	34	Gat/Tat	2/13	1	2	FACETS	0.931	0.812	1	0.931	0.812	1	CLONAL	1	FALSE	1	0.686708534322026	2		222	172	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660559	190660559	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	66	281	0	ENST00000441310.2:c.197C>T	p.Ala66Val	p.A66V	ENST00000441310	NM_000534.4	66	gCa/gTa	3/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.686708534322026	2		281	166	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660669	190660669	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	88	295	0	ENST00000441310.2:c.307A>G	p.Ile103Val	p.I103V	ENST00000441310	NM_000534.4	103	Ata/Gta	3/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.686708534322026	2		295	206	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732536	190732536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	46	282	0	ENST00000441310.2:c.2354G>A	p.Gly785Glu	p.G785E	ENST00000441310	NM_000534.4	785	gGa/gAa	11/13	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	FALSE	1	0.686708534322026	2		282	125	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149587	202149587	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	73	384	0	ENST00000358485.4:c.1028A>G	p.His343Arg	p.H343R	ENST00000358485	NM_001080125.1	343	cAc/cGc	8/9	1	2	FACETS	0.958	0.851	1	0.958	0.851	1	CLONAL	1	FALSE	1	0.686708534322026	2		384	222	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735456	204735456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376038796	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	119	307	0	ENST00000302823.3:c.257C>T	p.Ala86Val	p.A86V	ENST00000302823	NM_005214.4	86	gCg/gTg	2/4	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	FALSE	1	0.686708534322026	2		307	345	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113210	209113210	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs142883642	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	23	379	0	ENST00000345146.2:c.297A>G	p.Ile99Met	p.I99M	ENST00000345146	NM_005896.2	99	atA/atG	4/10	1	2	FACETS	0.291	0.228	0.364	0.291	0.228	0.364	SUBCLONAL	1	FALSE	1	0.686708534322026	2		379	230	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989579	212989579	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	80	236	0	ENST00000342788.4:c.132G>T	p.Gln44His	p.Q44H	ENST00000342788	NM_005235.2	44	caG/caT	2/28	1	2	FACETS	0.939	0.839	1	0.939	0.839	1	CLONAL	1	FALSE	1	0.686708534322026	2		236	248	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645387	215645387	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1559423578	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	23	522	0	ENST00000260947.4:c.1211A>G	p.Tyr404Cys	p.Y404C	ENST00000260947	NM_000465.2	404	tAc/tGc	4/11	1	2	FACETS	0.278	0.217	0.348	0.278	0.217	0.348	SUBCLONAL	1	FALSE	1	0.686708534322026	2		522	241	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346651	225346651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	81	273	0	ENST00000264414.4:c.1987G>A	p.Asp663Asn	p.D663N	ENST00000264414	NM_003590.4	663	Gat/Aat	14/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.686708534322026	2		273	202	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378351	225378351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	49	200	2	ENST00000264414.4:c.544G>A	p.Ala182Thr	p.A182T	ENST00000264414	NM_003590.4	182	Gca/Aca	5/16	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	FALSE	1	0.686708534322026	2		202	129	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793286	242793286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757334336	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	282	588	1	ENST00000334409.5:c.791G>A	p.Arg264His	p.R264H	ENST00000334409	NM_005018.2	264	cGc/cAc	5/5	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.686708534322026	2		589	722	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242800974	242800974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769034572	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	203	499	2	ENST00000334409.5:c.17C>T	p.Ala6Val	p.A6V	ENST00000334409	NM_005018.2	6	gCg/gTg	1/5	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.686708534322026	2		501	526	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31020692	31020692	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	61	261	0	ENST00000375687.4:c.989C>A	p.Thr330Asn	p.T330N	ENST00000375687	NM_015338.5	330	aCt/aAt	11/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.686708534322026	2		261	128	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021181	31021181	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs534065676	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	208	445	0	ENST00000375687.4:c.1180C>T	p.Arg394Cys	p.R394C	ENST00000375687	NM_015338.5	394	Cgt/Tgt	12/13	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.686708534322026	2		445	539	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024768	31024768	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	141	460	0	ENST00000375687.4:c.4253G>T	p.Gly1418Val	p.G1418V	ENST00000375687	NM_015338.5	1418	gGg/gTg	13/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.686708534322026	2		460	363	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368254	31368254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751741367	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	250	436	1	ENST00000328111.2:c.125G>A	p.Arg42His	p.R42H	ENST00000328111	NM_006892.3	42	cGc/cAc	2/23	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.686708534322026	2		437	591	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376760	31376760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754201724	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	156	414	2	ENST00000328111.2:c.755G>A	p.Arg252Gln	p.R252Q	ENST00000328111	NM_006892.3	252	cGa/cAa	7/23	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	1	0.686708534322026	2		416	446	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012603	36012603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	199	300	0	ENST00000358208.4:c.47G>A	p.Arg16His	p.R16H	ENST00000358208		16	cGc/cAc	2/12	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	1	0.686708534322026	2		300	410	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36024634	36024634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867236697	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	276	609	1	ENST00000358208.4:c.623G>A	p.Arg208His	p.R208H	ENST00000358208		208	cGc/cAc	6/12	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.686708534322026	2		610	668	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39721152	39721152	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	109	450	0	ENST00000361337.2:c.655T>G	p.Phe219Val	p.F219V	ENST00000361337	NM_003286.2	219	Ttc/Gtc	9/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.686708534322026	2		450	270	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39729934	39729934	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1287698565	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	104	419	1	ENST00000361337.2:c.1249A>G	p.Thr417Ala	p.T417A	ENST00000361337	NM_003286.2	417	Aca/Gca	13/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.686708534322026	2		420	237	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790066	40790066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1357627666	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	195	433	0	ENST00000373198.4:c.2665C>T	p.Arg889Trp	p.R889W	ENST00000373198	NM_133170.3	889	Cgg/Tgg	18/32	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.686708534322026	2		433	477	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790071	40790071	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	158	444	2	ENST00000373198.4:c.2660C>T	p.Ala887Val	p.A887V	ENST00000373198	NM_133170.3	887	gCc/gTc	18/32	1	2	FACETS	0.939	0.867	1	0.939	0.867	1	CLONAL	1	FALSE	1	0.686708534322026	2		446	490	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62294213	62294213	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750794827	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	197	561	0	ENST00000360203.5:c.509G>A	p.Arg170His	p.R170H	ENST00000360203	NM_001283009.1	170	cGc/cAc	6/35	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	1	0.686708534322026	2		561	559	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62317222	62317222	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	181	484	0	ENST00000360203.5:c.1345C>T	p.Arg449Ter	p.R449*	ENST00000360203	NM_001283009.1	449	Cga/Tga	16/35	1	2	FACETS	0.987	0.917	1	0.987	0.917	1	CLONAL	1	FALSE	1	0.686708534322026	2		484	534	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231774	36231774	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1569061768	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	221	511	0	ENST00000300305.3:c.610C>T	p.Arg204Ter	p.R204*	ENST00000300305		204	Cga/Tga	5/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.686708534322026	2		511	587	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755623	39755623	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	193	485	0	ENST00000288319.7:c.1142T>G	p.Val381Gly	p.V381G	ENST00000288319	NM_182918.3	381	gTc/gGc	10/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.686708534322026	2		485	485	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514810	44514810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	55	395	0	ENST00000291552.4:c.437C>T	p.Pro146Leu	p.P146L	ENST00000291552	NM_006758.2	146	cCc/cTc	6/8	1	2	FACETS	0.264	0.226	0.307	0.264	0.226	0.307	SUBCLONAL	1	FALSE	1	0.686708534322026	2		395	606	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655419	45655419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1181740577	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	259	556	0	ENST00000407780.3:c.433G>A	p.Ala145Thr	p.A145T	ENST00000407780	NM_001283052.1	145	Gcc/Acc	4/7	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.686708534322026	2		556	669	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288246	21288246	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200712124	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	180	520	0	ENST00000354336.3:c.491G>A	p.Arg164Gln	p.R164Q	ENST00000354336	NM_005207.3	164	cGg/cAg	2/3	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.686708534322026	2		520	447	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288474	21288474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749456958	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	126	484	1	ENST00000354336.3:c.719C>T	p.Ala240Val	p.A240V	ENST00000354336	NM_005207.3	240	gCg/gTg	2/3	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	1	0.686708534322026	2		485	353	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145483	24145483	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	43	369	0	ENST00000263121.7:c.502T>G	p.Phe168Val	p.F168V	ENST00000263121	NM_003073.3	168	Ttt/Gtt	5/9	1	2	FACETS	0.31	0.26	0.366	0.31	0.26	0.366	SUBCLONAL	1	FALSE	1	0.686708534322026	2		369	404	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035186	30035186	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	104	362	0	ENST00000338641.4:c.348T>G	p.His116Gln	p.H116Q	ENST00000338641	NM_000268.3	116	caT/caG	3/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.686708534322026	2		362	262	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574545	41574545	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	248	576	1	ENST00000263253.7:c.6830C>A	p.Pro2277His	p.P2277H	ENST00000263253	NM_001429.3	2277	cCc/cAc	31/31	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.686708534322026	2		577	615	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475528	12475528	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	162	475	1	ENST00000287820.6:c.1402A>G	p.Thr468Ala	p.T468A	ENST00000287820	NM_015869.4	468	Aca/Gca	7/7	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.686708534322026	2		476	407	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650419	12650419	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	16	330	0	ENST00000251849.4:c.427C>T	p.Arg143Trp	p.R143W	ENST00000251849	NM_002880.3	143	Cgg/Tgg	5/17	1	2	FACETS	0.21	0.155	0.275	0.21	0.155	0.275	SUBCLONAL	1	FALSE	1	0.686708534322026	2		330	222	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686388	30686388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	78	294	0	ENST00000295754.5:c.244G>A	p.Glu82Lys	p.E82K	ENST00000295754	NM_003242.5	82	Gaa/Aaa	2/7	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	FALSE	1	0.686708534322026	2		294	213	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713298	30713298	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	163	322	0	ENST00000295754.5:c.623A>C	p.Lys208Thr	p.K208T	ENST00000295754	NM_003242.5	208	aAg/aCg	4/7	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.686708534322026	2		322	414	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713616	30713616	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	62	383	0	ENST00000295754.5:c.941A>G	p.Lys314Arg	p.K314R	ENST00000295754	NM_003242.5	314	aAg/aGg	4/7	1	2	FACETS	0.492	0.427	0.562	0.492	0.427	0.562	SUBCLONAL	1	FALSE	1	0.686708534322026	2		383	367	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713801	30713801	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755967723	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	175	407	0	ENST00000295754.5:c.1126G>A	p.Val376Met	p.V376M	ENST00000295754	NM_003242.5	376	Gtg/Atg	4/7	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.686708534322026	2		407	469	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729968	30729968	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs863223852	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	38	297	0	ENST00000295754.5:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000295754	NM_003242.5	497	Cga/Tga	6/7	1	2	FACETS	0.294	0.243	0.351	0.294	0.243	0.351	SUBCLONAL	1	FALSE	1	0.686708534322026	2		297	376	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275751	41275751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	157	398	0	ENST00000349496.5:c.1646G>A	p.Arg549His	p.R549H	ENST00000349496	NM_001904.3	549	cGc/cAc	10/15	1	2	FACETS	0.998	0.923	1	0.998	0.923	1	CLONAL	1	FALSE	1	0.686708534322026	2		398	458	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277225	41277225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760837728	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	74	257	1	ENST00000349496.5:c.1694G>A	p.Arg565His	p.R565H	ENST00000349496	NM_001904.3	565	cGc/cAc	11/15	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	FALSE	1	0.686708534322026	2		258	200	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277885	41277885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1168206875	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	90	308	0	ENST00000349496.5:c.1849G>A	p.Val617Ile	p.V617I	ENST00000349496	NM_001904.3	617	Gtc/Atc	12/15	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.686708534322026	2		308	239	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280637	41280637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753246841	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	160	402	0	ENST00000349496.5:c.2150G>A	p.Arg717His	p.R717H	ENST00000349496	NM_001904.3	717	cGt/cAt	15/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.686708534322026	2		402	401	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125328	47125328	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs189529024	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	93	333	0	ENST00000409792.3:c.5942A>G	p.Gln1981Arg	p.Q1981R	ENST00000409792	NM_014159.6	1981	cAa/cGa	12/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.686708534322026	2		333	206	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163098	47163098	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	53	319	0	ENST00000409792.3:c.3028G>T	p.Glu1010Ter	p.E1010*	ENST00000409792	NM_014159.6	1010	Gaa/Taa	3/21	1	2	FACETS	0.989	0.862	1	0.989	0.862	1	CLONAL	1	FALSE	1	0.686708534322026	2		319	156	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725078	49725078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	250	519	0	ENST00000449682.2:c.266G>A	p.Ser89Asn	p.S89N	ENST00000449682	NM_020998.3	89	aGc/aAc	3/18	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.686708534322026	2		519	612	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936050	49936050	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs747000944	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	260	587	1	ENST00000296474.3:c.1620G>T	p.Trp540Cys	p.W540C	ENST00000296474	NM_002447.2	540	tgG/tgT	4/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.686708534322026	2		588	717	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440346	52440346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1559589762	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	229	438	0	ENST00000460680.1:c.706G>A	p.Asp236Asn	p.D236N	ENST00000460680	NM_004656.3	236	Gac/Aac	9/17	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.686708534322026	2		438	549	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443582	52443582	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	135	321	0	ENST00000460680.1:c.110G>T	p.Ser37Ile	p.S37I	ENST00000460680	NM_004656.3	37	aGc/aTc	3/17	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.686708534322026	2		321	373	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651348	52651348	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	137	469	0	ENST00000394830.3:c.1748A>C	p.Glu583Ala	p.E583A	ENST00000394830	NM_018313.4	583	gAa/gCa	15/30	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.686708534322026	2		469	332	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72866465	72866465	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	16	320	0	ENST00000325599.8:c.798A>C	p.Arg266Ser	p.R266S	ENST00000325599	NM_018130.2	266	agA/agC	7/11	1	2	FACETS	0.235	0.174	0.308	0.235	0.174	0.308	SUBCLONAL	1	FALSE	1	0.686708534322026	2		320	198	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448555	89448555	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	111	414	0	ENST00000336596.2:c.1519T>C	p.Phe507Leu	p.F507L	ENST00000336596	NM_005233.5	507	Ttc/Ctc	7/17	1	2	FACETS	0.736	0.666	0.81	0.736	0.666	0.81	SUBCLONAL	1	FALSE	1	0.686708534322026	2		414	439	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498444	89498444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	68	330	0	ENST00000336596.2:c.2416G>A	p.Asp806Asn	p.D806N	ENST00000336596	NM_005233.5	806	Gat/Aat	14/17	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	FALSE	1	0.686708534322026	2		330	195	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498508	89498508	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	59	260	0	ENST00000336596.2:c.2480A>T	p.Glu827Val	p.E827V	ENST00000336596	NM_005233.5	827	gAg/gTg	14/17	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.686708534322026	2		260	149	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670437	134670437	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	106	440	0	ENST00000398015.3:c.348G>T	p.Glu116Asp	p.E116D	ENST00000398015	NM_004441.4	116	gaG/gaT	3/16	1	2	FACETS	0.986	0.896	1	0.986	0.896	1	CLONAL	1	FALSE	1	0.686708534322026	2		440	313	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880912	134880912	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	34	405	0	ENST00000398015.3:c.1475G>T	p.Arg492Met	p.R492M	ENST00000398015	NM_004441.4	492	aGg/aTg	7/16	1	2	FACETS	0.258	0.211	0.311	0.258	0.211	0.311	SUBCLONAL	1	FALSE	1	0.686708534322026	2		405	384	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898780	134898780	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	79	295	0	ENST00000398015.3:c.1838A>G	p.Glu613Gly	p.E613G	ENST00000398015	NM_004441.4	613	gAg/gGg	10/16	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	1	0.686708534322026	2		295	214	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911432	134911432	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	110	393	0	ENST00000398015.3:c.1897G>A	p.Val633Met	p.V633M	ENST00000398015	NM_004441.4	633	Gtg/Atg	11/16	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.686708534322026	2		393	301	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413742	138413742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769082299	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	107	263	0	ENST00000289153.2:c.1778C>T	p.Ala593Val	p.A593V	ENST00000289153	NM_006219.2	593	gCg/gTg	12/22	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	1	0.686708534322026	2		263	298	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138423310	138423310	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	92	363	0	ENST00000289153.2:c.1556C>A	p.Ala519Glu	p.A519E	ENST00000289153	NM_006219.2	519	gCa/gAa	10/22	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.686708534322026	2		363	236	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665353	138665353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	165	509	0	ENST00000330315.3:c.212C>T	p.Ala71Val	p.A71V	ENST00000330315	NM_023067.3	71	gCg/gTg	1/1	1	2	FACETS	0.779	0.718	0.841	0.779	0.718	0.841	SUBCLONAL	1	FALSE	1	0.686708534322026	2		509	617	SUCCESS
ATR	545	MSKCC	GRCh37	3	142171992	142171992	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	100	466	0	ENST00000350721.4:c.7739C>A	p.Thr2580Asn	p.T2580N	ENST00000350721	NM_001184.3	2580	aCt/aAt	46/47	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	1	0.686708534322026	2		466	274	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278201	142278201	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs200491706	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	27	414	0	ENST00000350721.4:c.1624A>G	p.Lys542Glu	p.K542E	ENST00000350721	NM_001184.3	542	Aaa/Gaa	7/47	1	2	FACETS	0.348	0.278	0.427	0.348	0.278	0.427	SUBCLONAL	1	FALSE	1	0.686708534322026	2		414	226	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279152	142279152	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	93	359	0	ENST00000350721.4:c.1494A>C	p.Gln498His	p.Q498H	ENST00000350721	NM_001184.3	498	caA/caC	6/47	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.686708534322026	2		359	239	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281651	142281651	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759878676	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	93	397	0	ENST00000350721.4:c.593G>A	p.Ser198Asn	p.S198N	ENST00000350721	NM_001184.3	198	aGt/aAt	4/47	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.686708534322026	2		397	238	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170011280	170011280	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	15	399	0	ENST00000295797.4:c.1401G>T	p.Glu467Asp	p.E467D	ENST00000295797	NM_002740.5	467	gaG/gaT	14/18	1	2	FACETS	0.152	0.111	0.202	0.152	0.111	0.202	SUBCLONAL	1	FALSE	1	0.686708534322026	2		399	287	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919203	178919203	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	58	206	0	ENST00000263967.3:c.688C>T	p.Arg230Ter	p.R230*	ENST00000263967	NM_006218.2	230	Cga/Tga	4/21	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.686708534322026	2		206	145	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921567	178921567	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553821144	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	50	219	0	ENST00000263967.3:c.1049A>G	p.Asp350Gly	p.D350G	ENST00000263967	NM_006218.2	350	gAc/gGc	5/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.686708534322026	2		219	126	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927439	178927439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	12	335	0	ENST00000263967.3:c.1202G>A	p.Arg401Gln	p.R401Q	ENST00000263967	NM_006218.2	401	cGa/cAa	7/21	1	2	FACETS	0.163	0.114	0.222	0.163	0.114	0.222	SUBCLONAL	1	FALSE	1	0.686708534322026	2		335	215	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430522	181430522	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	40	471	0	ENST00000325404.1:c.374A>G	p.Tyr125Cys	p.Y125C	ENST00000325404	NM_003106.3	125	tAc/tGc	1/1	1	2	FACETS	0.212	0.176	0.253	0.212	0.176	0.253	SUBCLONAL	1	FALSE	1	0.686708534322026	2		471	549	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430591	181430591	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754275280	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	201	398	0	ENST00000325404.1:c.443G>A	p.Gly148Asp	p.G148D	ENST00000325404	NM_003106.3	148	gGc/gAc	1/1	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	1	0.686708534322026	2		398	435	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430869	181430869	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	287	596	1	ENST00000325404.1:c.721G>T	p.Gly241Cys	p.G241C	ENST00000325404	NM_003106.3	241	Ggt/Tgt	1/1	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.686708534322026	2		597	721	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146718	185146718	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	208	496	0	ENST00000265026.3:c.349A>G	p.Lys117Glu	p.K117E	ENST00000265026	NM_004721.4	117	Aag/Gag	2/14	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.686708534322026	2		496	497	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198255	185198255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759993681	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	50	433	0	ENST00000265026.3:c.2737G>A	p.Val913Met	p.V913M	ENST00000265026	NM_004721.4	913	Gtg/Atg	13/14	1	2	FACETS	0.321	0.273	0.375	0.321	0.273	0.375	SUBCLONAL	1	FALSE	1	0.686708534322026	2		433	453	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447384	187447384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780987785	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	167	463	0	ENST00000232014.4:c.809G>A	p.Arg270Gln	p.R270Q	ENST00000232014	NM_001130845.1	270	cGa/cAa	5/10	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.686708534322026	2		463	465	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607140	189607140	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1394017323	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	42	487	0	ENST00000264731.3:c.1519G>A	p.Gly507Ser	p.G507S	ENST00000264731	NM_003722.4	507	Ggc/Agc	12/14	1	2	FACETS	0.274	0.229	0.325	0.274	0.229	0.325	SUBCLONAL	1	FALSE	1	0.686708534322026	2		487	446	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607189	189607189	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1362748295	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	250	554	0	ENST00000264731.3:c.1568A>C	p.Gln523Pro	p.Q523P	ENST00000264731	NM_003722.4	523	cAg/cCg	12/14	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.686708534322026	2		554	637	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612208	189612208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	48	371	0	ENST00000264731.3:c.1960C>T	p.Pro654Ser	p.P654S	ENST00000264731	NM_003722.4	654	Ccc/Tcc	14/14	1	2	FACETS	0.357	0.302	0.416	0.357	0.302	0.416	SUBCLONAL	1	FALSE	1	0.686708534322026	2		371	392	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808381	1808381	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	67	749	0	ENST00000260795.2:c.2139G>T	p.Met713Ile	p.M713I	ENST00000260795		713	atG/atT	15/17	1	2	FACETS	0.278	0.241	0.318	0.278	0.241	0.318	SUBCLONAL	1	FALSE	1	0.686708534322026	2		749	701	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920295	1920295	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	183	610	0	ENST00000382891.5:c.1355G>T	p.Arg452Met	p.R452M	ENST00000382891	NM_133335.3	452	aGg/aTg	5/22	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.686708534322026	2		610	483	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957835	1957835	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388626156	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	233	529	1	ENST00000382891.5:c.2801C>T	p.Ala934Val	p.A934V	ENST00000382891	NM_133335.3	934	gCg/gTg	15/22	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.686708534322026	2		530	624	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749500	41749500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	186	355	1	ENST00000226382.2:c.295C>T	p.Arg99Trp	p.R99W	ENST00000226382	NM_003924.3	99	Cgg/Tgg	2/3	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.686708534322026	2		356	511	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138639	55138639	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	202	404	1	ENST00000257290.5:c.1316G>A	p.Gly439Asp	p.G439D	ENST00000257290	NM_006206.4	439	gGc/gAc	9/23	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.686708534322026	2		405	491	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144627	55144627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	102	348	0	ENST00000257290.5:c.2101C>T	p.Pro701Ser	p.P701S	ENST00000257290	NM_006206.4	701	Cca/Tca	15/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.686708534322026	2		348	250	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561755	55561755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759250095	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	90	256	0	ENST00000288135.5:c.145C>T	p.Arg49Cys	p.R49C	ENST00000288135	NM_000222.2	49	Cgc/Tgc	2/21	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	1	0.686708534322026	2		256	252	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594075	55594075	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1560418178	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	92	299	1	ENST00000288135.5:c.1861G>A	p.Ala621Thr	p.A621T	ENST00000288135	NM_000222.2	621	Gct/Act	12/21	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	FALSE	1	0.686708534322026	2		300	265	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602770	55602770	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	64	293	0	ENST00000288135.5:c.2591C>A	p.Ser864Tyr	p.S864Y	ENST00000288135	NM_000222.2	864	tCt/tAt	18/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.686708534322026	2		293	164	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970876	55970876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	17	421	0	ENST00000263923.4:c.1921G>A	p.Val641Ile	p.V641I	ENST00000263923	NM_002253.2	641	Gtc/Atc	13/30	1	2	FACETS	0.189	0.141	0.246	0.189	0.141	0.246	SUBCLONAL	1	FALSE	1	0.686708534322026	2		421	262	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972013	55972013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	109	342	0	ENST00000263923.4:c.1631C>T	p.Ser544Phe	p.S544F	ENST00000263923	NM_002253.2	544	tCc/tTc	12/30	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.686708534322026	2		342	284	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197721	66197721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs74487329	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	72	368	0	ENST00000273854.3:c.2978C>T	p.Ser993Leu	p.S993L	ENST00000273854	NM_004439.5	993	tCa/tTa	17/18	1	2	FACETS	0.962	0.854	1	0.962	0.854	1	CLONAL	1	FALSE	1	0.686708534322026	2		368	218	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217258	66217258	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	13	328	0	ENST00000273854.3:c.2357C>T	p.Ala786Val	p.A786V	ENST00000273854	NM_004439.5	786	gCa/gTa	14/18	1	2	FACETS	0.221	0.158	0.298	0.221	0.158	0.298	SUBCLONAL	1	FALSE	1	0.686708534322026	2		328	171	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230797	66230797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	53	346	0	ENST00000273854.3:c.2174C>T	p.Ala725Val	p.A725V	ENST00000273854	NM_004439.5	725	gCa/gTa	12/18	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	FALSE	1	0.686708534322026	2		346	137	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280125	66280125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	42	252	0	ENST00000273854.3:c.1564G>A	p.Glu522Lys	p.E522K	ENST00000273854	NM_004439.5	522	Gag/Aag	7/18	1	2	FACETS	0.799	0.679	0.927	0.799	0.679	0.927	CLONAL	1	FALSE	1	0.686708534322026	2		252	153	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535333	66535333	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	185	482	0	ENST00000273854.3:c.128G>A	p.Cys43Tyr	p.C43Y	ENST00000273854	NM_004439.5	43	tGc/tAc	1/18	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	FALSE	1	0.686708534322026	2		482	538	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99809104	99809104	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	49	182	0	ENST00000280892.6:c.282-1G>A		p.X94_splice	ENST00000280892	NM_001130678.1	94			1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	FALSE	1	0.686708534322026	2		182	132	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164848	106164848	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	178	340	0	ENST00000380013.4:c.3716C>A	p.Ser1239Tyr	p.S1239Y	ENST00000380013	NM_001127208.2	1239	tCt/tAt	6/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.686708534322026	2		340	439	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180813	106180813	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	13	227	0	ENST00000380013.4:c.3841T>G	p.Cys1281Gly	p.C1281G	ENST00000380013	NM_001127208.2	1281	Tgt/Ggt	7/11	1	2	FACETS	0.166	0.118	0.224	0.166	0.118	0.224	SUBCLONAL	1	FALSE	1	0.686708534322026	2		227	228	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197216	106197216	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	88	264	0	ENST00000380013.4:c.5549G>T	p.Ser1850Ile	p.S1850I	ENST00000380013	NM_001127208.2	1850	aGc/aTc	11/11	1	2	FACETS	0.89	0.798	0.985	0.89	0.798	0.985	CLONAL	1	FALSE	1	0.686708534322026	2		264	288	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007331	143007332	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs772784869	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	74	274	0	ENST00000262992.4:c.2452dup	p.Arg818LysfsTer26	p.R818Kfs*26	ENST00000262992	NM_001101669.1	818	aga/aAga	22/24	1	2	FACETS	0.945	0.841	1	0.945	0.841	1	CLONAL	1	FALSE	1	0.686708534322026	2		274	228	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081657	143081657	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	88	298	0	ENST00000262992.4:c.1417C>A	p.Leu473Ile	p.L473I	ENST00000262992	NM_001101669.1	473	Ctc/Atc	15/24	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.686708534322026	2		298	229	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538232	187538232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1310860834	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	109	488	0	ENST00000441802.2:c.9002G>A	p.Gly3001Asp	p.G3001D	ENST00000441802	NM_005245.3	3001	gGc/gAc	11/27	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.686708534322026	2		488	243	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542357	187542357	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs769432838	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	53	309	0	ENST00000441802.2:c.5383C>T	p.Arg1795Ter	p.R1795*	ENST00000441802	NM_005245.3	1795	Cga/Tga	10/27	1	2	FACETS	0.947	0.824	1	0.947	0.824	1	CLONAL	1	FALSE	1	0.686708534322026	2		309	163	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557908	187557908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113970444	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	157	352	0	ENST00000441802.2:c.3803G>A	p.Arg1268Gln	p.R1268Q	ENST00000441802	NM_005245.3	1268	cGg/cAg	5/27	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.686708534322026	2		352	391	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584619	187584619	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	98	423	0	ENST00000441802.2:c.3414G>T	p.Gln1138His	p.Q1138H	ENST00000441802	NM_005245.3	1138	caG/caT	3/27	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.686708534322026	2		423	270	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628551	187628551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765982067	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	164	613	0	ENST00000441802.2:c.2431G>A	p.Val811Met	p.V811M	ENST00000441802	NM_005245.3	811	Gtg/Atg	2/27	1	2	FACETS	0.935	0.864	1	0.935	0.864	1	CLONAL	1	FALSE	1	0.686708534322026	2		613	511	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628574	187628574	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	184	624	0	ENST00000441802.2:c.2408C>A	p.Ala803Asp	p.A803D	ENST00000441802	NM_005245.3	803	gCt/gAt	2/27	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.686708534322026	2		624	517	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628841	187628841	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200579335	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	98	487	1	ENST00000441802.2:c.2141C>T	p.Pro714Leu	p.P714L	ENST00000441802	NM_005245.3	714	cCg/cTg	2/27	1	2	FACETS	0.977	0.884	1	0.977	0.884	1	CLONAL	1	FALSE	1	0.686708534322026	2		488	292	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629942	187629942	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	36	541	0	ENST00000441802.2:c.1040T>G	p.Phe347Cys	p.F347C	ENST00000441802	NM_005245.3	347	tTc/tGc	2/27	1	2	FACETS	0.285	0.234	0.341	0.285	0.234	0.341	SUBCLONAL	1	FALSE	1	0.686708534322026	2		541	368	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251560	251560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1042170	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	169	451	0	ENST00000264932.6:c.1771G>A	p.Ala591Thr	p.A591T	ENST00000264932	NM_004168.2	591	Gcg/Acg	13/15	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	FALSE	1	0.686708534322026	2		451	488	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282710	1282710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	177	484	0	ENST00000310581.5:c.1603C>T	p.Arg535Cys	p.R535C	ENST00000310581	NM_198253.2	535	Cgt/Tgt	3/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.686708534322026	2		484	448	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293767	1293767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34094720	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	211	626	0	ENST00000310581.5:c.1234C>T	p.His412Tyr	p.H412Y	ENST00000310581	NM_198253.2	412	Cac/Tac	2/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.686708534322026	2		626	578	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294123	1294123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1309920442	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	244	643	2	ENST00000310581.5:c.878G>A	p.Arg293His	p.R293H	ENST00000310581	NM_198253.2	293	cGc/cAc	2/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.686708534322026	2		645	635	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31464386	31464386	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	152	625	0	ENST00000344624.3:c.2531G>A	p.Ser844Asn	p.S844N	ENST00000344624		844	aGc/aAc	17/33	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.686708534322026	2		625	418	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31466354	31466354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376262500	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	129	547	2	ENST00000344624.3:c.2401C>T	p.Arg801Cys	p.R801C	ENST00000344624		801	Cgc/Tgc	16/33	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.686708534322026	2		549	310	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515115	31515115	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	154	496	0	ENST00000344624.3:c.1270A>G	p.Ser424Gly	p.S424G	ENST00000344624		424	Agt/Ggt	5/33	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.686708534322026	2		496	350	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515239	31515239	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1478716580	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	165	583	0	ENST00000344624.3:c.1146G>T	p.Lys382Asn	p.K382N	ENST00000344624		382	aaG/aaT	5/33	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.686708534322026	2		583	377	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515324	31515324	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs187981384	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	57	400	0	ENST00000344624.3:c.1061G>A	p.Arg354His	p.R354H	ENST00000344624		354	cGc/cAc	5/33	1	2	FACETS	0.712	0.618	0.812	0.712	0.618	0.812	SUBCLONAL	1	FALSE	1	0.686708534322026	2		400	233	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871205	35871205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372676633	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	82	309	0	ENST00000303115.3:c.427G>A	p.Ala143Thr	p.A143T	ENST00000303115	NM_002185.3	143	Gcc/Acc	4/8	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.686708534322026	2		309	207	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875634	35875634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	87	326	0	ENST00000303115.3:c.821C>T	p.Pro274Leu	p.P274L	ENST00000303115	NM_002185.3	274	cCc/cTc	7/8	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.686708534322026	2		326	229	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876343	35876343	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200570812	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	132	384	2	ENST00000303115.3:c.1135G>A	p.Ala379Thr	p.A379T	ENST00000303115	NM_002185.3	379	Gcc/Acc	8/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.686708534322026	2		386	331	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38949907	38949907	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	18	305	0	ENST00000357387.3:c.4043C>A	p.Ser1348Tyr	p.S1348Y	ENST00000357387	NM_152756.3	1348	tCt/tAt	31/38	1	2	FACETS	0.322	0.243	0.413	0.322	0.243	0.413	SUBCLONAL	1	FALSE	1	0.686708534322026	2		305	163	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177771	56177771	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	69	282	0	ENST00000399503.3:c.2744T>G	p.Leu915Ter	p.L915*	ENST00000399503	NM_005921.1	915	tTa/tGa	14/20	1	2	FACETS	0.971	0.86	1	0.971	0.86	1	CLONAL	1	FALSE	1	0.686708534322026	2		282	207	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591109	67591109	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	61	354	0	ENST00000274335.5:c.1702C>T	p.Pro568Ser	p.P568S	ENST00000274335		568	Cca/Tca	12/15	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	FALSE	1	0.686708534322026	2		354	173	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79952342	79952342	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1456712758	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	88	418	0	ENST00000265081.6:c.350G>A	p.Gly117Asp	p.G117D	ENST00000265081	NM_002439.4	117	gGc/gAc	2/24	1	2	FACETS	0.978	0.879	1	0.978	0.879	1	CLONAL	1	FALSE	1	0.686708534322026	2		418	262	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970948	79970948	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	103	431	1	ENST00000265081.6:c.1173+1G>T		p.X391_splice	ENST00000265081	NM_002439.4	391			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.686708534322026	2		432	261	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86682664	86682664	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	52	173	0	ENST00000274376.6:c.2869A>G	p.Asn957Asp	p.N957D	ENST00000274376	NM_002890.2	957	Aat/Gat	23/25	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.686708534322026	2		173	123	SUCCESS
APC	324	MSKCC	GRCh37	5	112176302	112176302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781600	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	18	288	0	ENST00000257430.4:c.5011G>A	p.Ala1671Thr	p.A1671T	ENST00000257430	NM_000038.5	1671	Gct/Act	16/16	1	2	FACETS	0.247	0.186	0.319	0.247	0.186	0.319	SUBCLONAL	1	FALSE	1	0.686708534322026	2		288	212	SUCCESS
APC	324	MSKCC	GRCh37	5	112176873	112176873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	69	341	0	ENST00000257430.4:c.5582C>T	p.Ser1861Phe	p.S1861F	ENST00000257430	NM_000038.5	1861	tCt/tTt	16/16	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	FALSE	1	0.686708534322026	2		341	185	SUCCESS
APC	324	MSKCC	GRCh37	5	112177591	112177591	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	63	328	0	ENST00000257430.4:c.6300T>G	p.Asp2100Glu	p.D2100E	ENST00000257430	NM_000038.5	2100	gaT/gaG	16/16	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	1	0.686708534322026	2		328	166	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441342	149441342	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	193	537	1	ENST00000286301.3:c.1697C>A	p.Pro566His	p.P566H	ENST00000286301	NM_005211.3	566	cCc/cAc	12/22	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.686708534322026	2		538	543	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512332	149512332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200684708	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	166	403	0	ENST00000261799.4:c.1108C>T	p.Arg370Cys	p.R370C	ENST00000261799	NM_002609.3	370	Cgc/Tgc	7/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.686708534322026	2		403	445	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149516600	149516600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144923639	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	261	517	2	ENST00000261799.4:c.11C>T	p.Pro4Leu	p.P4L	ENST00000261799	NM_002609.3	4	cCg/cTg	2/23	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.686708534322026	2		519	674	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170814993	170814993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	145	312	0	ENST00000296930.5:c.41C>T	p.Pro14Leu	p.P14L	ENST00000296930	NM_002520.6	14	cCc/cTc	1/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.686708534322026	2		312	384	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522584	176522584	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	212	561	0	ENST00000292408.4:c.1681T>G	p.Phe561Val	p.F561V	ENST00000292408	NM_213647.1	561	Ttc/Gtc	13/18	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.686708534322026	2		561	544	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562861	176562861	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	98	546	0	ENST00000439151.2:c.757C>T	p.Leu253Phe	p.L253F	ENST00000439151	NM_022455.4	253	Ctt/Ttt	2/23	1	2	FACETS	0.734	0.66	0.811	0.734	0.66	0.811	SUBCLONAL	1	FALSE	1	0.686708534322026	2		546	389	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030390	180030390	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	209	455	0	ENST00000261937.6:c.3894C>A	p.Ser1298Arg	p.S1298R	ENST00000261937	NM_182925.4	1298	agC/agA	30/30	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.686708534322026	2		455	556	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481629	20481629	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	102	275	0	ENST00000346618.3:c.698A>G	p.Lys233Arg	p.K233R	ENST00000346618	NM_001949.4	233	aAg/aGg	3/7	0.186529253785963	3	FACETS	0.811	0.739	0.884	0.811	0.739	0.884	INDETERMINATE	2	FALSE	1	0.686708534322026	3		275	246	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20488362	20488362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	43	435	0	ENST00000346618.3:c.1018G>A	p.Ala340Thr	p.A340T	ENST00000346618	NM_001949.4	340	Gca/Aca	6/7	0.186529253785963	3	FACETS	0.89	0.755	1	0.445	0.377	0.518	INDETERMINATE	1	FALSE	1	0.686708534322026	3		435	189	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778262	27778262	+	stop_lost	Nonstop_Mutation	SNP	A	A	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	151	338	0	ENST00000369163.2:c.411A>T	p.Ter137CysextTer6	p.*137Cext*6	ENST00000369163	NM_003536.2	137	tgA/tgT	1/1	0.186529253785963	3	FACETS	0.812	0.752	0.872	0.812	0.752	0.872	INDETERMINATE	2	FALSE	1	0.686708534322026	3		338	364	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910691	29910691	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	286	784	0	ENST00000376809.5:c.231G>T	p.Glu77Asp	p.E77D	ENST00000376809	NM_002116.7	77	gaG/gaT	2/8	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	FALSE	NA	0.686708534322026	2		784	761	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30668274	30668274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	45	394	0	ENST00000376406.3:c.6238G>A	p.Val2080Ile	p.V2080I	ENST00000376406	NM_014641.2	2080	Gtc/Atc	15/15	1	2	FACETS	0.32	0.269	0.377	0.32	0.269	0.377	SUBCLONAL	1	FALSE	1	0.686708534322026	2		394	409	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670441	30670441	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	129	393	0	ENST00000376406.3:c.5992-1G>T		p.X1998_splice	ENST00000376406	NM_014641.2	1998			1	2	FACETS	0.994	0.911	1	0.994	0.911	1	CLONAL	1	FALSE	1	0.686708534322026	2		393	378	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672050	30672050	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	177	596	0	ENST00000376406.3:c.4910C>T	p.Ala1637Val	p.A1637V	ENST00000376406	NM_014641.2	1637	gCc/gTc	10/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.686708534322026	2		596	477	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681702	30681702	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1045903416	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	154	452	1	ENST00000376406.3:c.395G>A	p.Arg132His	p.R132H	ENST00000376406	NM_014641.2	132	cGc/cAc	3/15	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	1	0.686708534322026	2		453	439	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940432	31940432	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	215	496	0	ENST00000375333.2:c.465G>T	p.Gln155His	p.Q155H	ENST00000375333	NM_032454.1	155	caG/caT	3/8	1	2	FACETS	0.939	0.877	1	0.939	0.877	1	CLONAL	1	FALSE	1	0.686708534322026	2		496	667	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940482	31940482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1179080235	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	277	555	0	ENST00000375333.2:c.515G>A	p.Arg172Lys	p.R172K	ENST00000375333	NM_032454.1	172	aGg/aAg	3/8	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	1	0.686708534322026	2		555	630	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165092	32165092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1463590184	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	178	543	0	ENST00000375023.3:c.5036C>T	p.Ala1679Val	p.A1679V	ENST00000375023	NM_004557.3	1679	gCt/gTt	27/30	1	2	FACETS	0.995	0.924	1	0.995	0.924	1	CLONAL	1	FALSE	1	0.686708534322026	2		543	521	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185808	32185808	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	207	444	0	ENST00000375023.3:c.1588G>A	p.Asp530Asn	p.D530N	ENST00000375023	NM_004557.3	530	Gac/Aac	9/30	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.686708534322026	2		444	562	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800133	32800133	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	100	336	0	ENST00000374899.4:c.1249G>T	p.Glu417Ter	p.E417*	ENST00000374899	NM_018833.2	417	Gag/Tag	7/12	1	2	FACETS	0.842	0.759	0.927	0.842	0.759	0.927	CLONAL	1	FALSE	1	0.686708534322026	2		336	346	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816896	32816896	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1159721335	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	100	382	0	ENST00000354258.4:c.1429-1G>T		p.X477_splice	ENST00000354258	NM_000593.5	477			1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	FALSE	1	0.686708534322026	2		382	280	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818162	32818162	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	164	517	1	ENST00000354258.4:c.1363C>T	p.Gln455Ter	p.Q455*	ENST00000354258	NM_000593.5	455	Caa/Taa	5/11	1	2	FACETS	0.92	0.851	0.992	0.92	0.851	0.992	CLONAL	1	FALSE	1	0.686708534322026	2		518	519	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288785	33288785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765273333	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	146	319	0	ENST00000374542.5:c.767G>A	p.Arg256His	p.R256H	ENST00000374542	NM_001141970.1	256	cGc/cAc	3/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.686708534322026	2		319	364	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140787	37140787	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1183187519	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	166	323	3	ENST00000373509.5:c.623G>T	p.Ser208Ile	p.S208I	ENST00000373509	NM_002648.3	208	aGc/aTc	5/6	1	2	FACETS	0.995	0.921	1	0.995	0.921	1	CLONAL	1	FALSE	1	0.686708534322026	2		326	486	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066669	94066669	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	116	330	0	ENST00000369303.4:c.1090A>G	p.Thr364Ala	p.T364A	ENST00000369303	NM_004440.3	364	Acc/Gcc	5/17	NA	2	FACETS	1	0.946	1			1	INDETERMINATE	1	FALSE	NA	0.686708534322026	2		330	322	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120297	94120297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	86	236	0	ENST00000369303.4:c.754G>A	p.Ala252Thr	p.A252T	ENST00000369303	NM_004440.3	252	Gca/Aca	3/17	NA	2	FACETS	1	0.974	1			1	INDETERMINATE	1	FALSE	NA	0.686708534322026	2		236	201	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109311950	109311950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1261981726	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	77	471	0	ENST00000436639.2:c.1322C>T	p.Ala441Val	p.A441V	ENST00000436639	NM_014454.2	441	gCt/gTt	8/10	NA	2	FACETS	1	0.955	1			1	INDETERMINATE	1	FALSE	NA	0.686708534322026	2		471	199	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109319765	109319765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	14	359	1	ENST00000436639.2:c.923G>A	p.Gly308Asp	p.G308D	ENST00000436639	NM_014454.2	308	gGc/gAc	5/10	NA	2	FACETS	0.146	0.105	0.195			1	INDETERMINATE	1	FALSE	NA	0.686708534322026	2		360	280	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631362	117631362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150262256	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	100	362	0	ENST00000368508.3:c.6316G>A	p.Ala2106Thr	p.A2106T	ENST00000368508	NM_002944.2	2106	Gcc/Acc	40/43	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	1	FALSE	NA	0.686708534322026	2		362	258	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709026	117709026	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	113	419	0	ENST00000368508.3:c.1931A>C	p.Lys644Thr	p.K644T	ENST00000368508	NM_002944.2	644	aAa/aCa	13/43	NA	2	FACETS	1	0.911	1			1	INDETERMINATE	1	FALSE	NA	0.686708534322026	2		419	329	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983373	149983373	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	92	305	0	ENST00000253339.5:c.2885T>C	p.Val962Ala	p.V962A	ENST00000253339		962	gTt/gCt	7/7	0.186529253785963	3	FACETS	0.861	0.782	0.941	0.861	0.782	0.941	INDETERMINATE	2	FALSE	1	0.686708534322026	3		305	209	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001335	150001335	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	92	497	0	ENST00000253339.5:c.2269C>A	p.Leu757Met	p.L757M	ENST00000253339		757	Ctg/Atg	4/7	0.186529253785963	3	FACETS	0.8	0.725	0.876	0.8	0.725	0.876	INDETERMINATE	2	FALSE	1	0.686708534322026	3		497	225	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004595	150004595	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	148	515	1	ENST00000253339.5:c.1630C>A	p.Pro544Thr	p.P544T	ENST00000253339		544	Cca/Aca	3/7	0.186529253785963	3	FACETS	0.776	0.718	0.835	0.776	0.718	0.835	INDETERMINATE	2	FALSE	1	0.686708534322026	3		516	373	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099610	157099610	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	51	46	0	ENST00000346085.5:c.547G>T	p.Gly183Cys	p.G183C	ENST00000346085	NM_020732.3	183	Ggc/Tgc	1/20	0.186529253785963	3	FACETS	0.773	0.675	0.874	0.773	0.675	0.874	INDETERMINATE	2	FALSE	1	0.686708534322026	3		46	129	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527565	157527565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1280712992	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	34	485	0	ENST00000346085.5:c.5290G>A	p.Ala1764Thr	p.A1764T	ENST00000346085	NM_020732.3	1764	Gct/Act	20/20	0.186529253785963	3	FACETS	0.216	0.176	0.261	0.108	0.088	0.131	INDETERMINATE	1	FALSE	1	0.686708534322026	3		485	616	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042116	6042116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881916	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	74	142	0	ENST00000265849.7:c.505C>T	p.Arg169Cys	p.R169C	ENST00000265849	NM_000535.5	169	Cgc/Tgc	5/15	1	2	FACETS	0.998	0.889	1	0.998	0.889	1	CLONAL	1	FALSE	1	0.686708534322026	2		142	216	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441629	6441629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	145	513	0	ENST00000356142.4:c.476C>T	p.Pro159Leu	p.P159L	ENST00000356142	NM_018890.3	159	cCg/cTg	6/7	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.686708534322026	2		513	333	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975457	13975457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	111	282	0	ENST00000405192.2:c.430C>T	p.Pro144Ser	p.P144S	ENST00000405192	NM_001163147.1	144	Cca/Tca	7/12	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	FALSE	1	0.686708534322026	2		282	317	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730125	41730125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142519810	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	75	269	0	ENST00000242208.4:c.404C>T	p.Thr135Met	p.T135M	ENST00000242208	NM_002192.2	135	aCg/aTg	3/3	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.686708534322026	2		269	191	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221761	55221761	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	177	438	0	ENST00000275493.2:c.805C>A	p.Leu269Ile	p.L269I	ENST00000275493	NM_005228.3	269	Ctc/Atc	7/28	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	1	0.686708534322026	2		438	506	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268030	55268030	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	32	491	0	ENST00000275493.2:c.2870G>C	p.Ser957Thr	p.S957T	ENST00000275493	NM_005228.3	957	aGt/aCt	24/28	1	2	FACETS	0.195	0.158	0.238	0.195	0.158	0.238	SUBCLONAL	1	FALSE	1	0.686708534322026	2		491	477	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508409	106508409	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	73	188	0	ENST00000359195.3:c.403A>G	p.Ile135Val	p.I135V	ENST00000359195	NM_002649.2	135	Atc/Gtc	2/11	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	FALSE	1	0.686708534322026	2		188	208	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509138	106509138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753981231	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	152	431	0	ENST00000359195.3:c.1132G>A	p.Asp378Asn	p.D378N	ENST00000359195	NM_002649.2	378	Gac/Aac	2/11	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	FALSE	1	0.686708534322026	2		431	428	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509484	106509484	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	118	502	0	ENST00000359195.3:c.1478A>G	p.Asp493Gly	p.D493G	ENST00000359195	NM_002649.2	493	gAc/gGc	2/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.686708534322026	2		502	318	SUCCESS
MET	4233	MSKCC	GRCh37	7	116413350	116413350	+	intron_variant	Intron	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	151	734	0	ENST00000397752.3:c.3028+1307G>A		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.686708534322026	2		734	397	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843243	128843243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173715127	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	223	475	0	ENST00000249373.3:c.350G>A	p.Arg117His	p.R117H	ENST00000249373	NM_005631.4	117	cGc/cAc	2/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.686708534322026	2		475	592	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128849189	128849189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17710891	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	151	468	1	ENST00000249373.3:c.1417G>A	p.Asp473Asn	p.D473N	ENST00000249373	NM_005631.4	473	Gac/Aac	8/12	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	FALSE	1	0.686708534322026	2		469	437	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851955	128851955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	224	533	1	ENST00000249373.3:c.2027G>A	p.Arg676Lys	p.R676K	ENST00000249373	NM_005631.4	676	aGg/aAg	12/12	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.686708534322026	2		534	548	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846039	151846039	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	133	415	0	ENST00000262189.6:c.12973C>A	p.Leu4325Met	p.L4325M	ENST00000262189	NM_170606.2	4325	Ctg/Atg	52/59	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	1	0.686708534322026	2		415	371	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860837	151860837	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	136	359	0	ENST00000262189.6:c.9825G>A	p.Met3275Ile	p.M3275I	ENST00000262189	NM_170606.2	3275	atG/atA	43/59	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.686708534322026	2		359	294	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133352	38133352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1271164016	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	163	347	0	ENST00000317025.8:c.4121C>T	p.Ala1374Val	p.A1374V	ENST00000317025	NM_023034.1	1374	gCt/gTt	24/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.686708534322026	2		347	395	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970924	70970924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1277239045	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	127	467	0	ENST00000276594.2:c.1337G>A	p.Arg446Gln	p.R446Q	ENST00000276594	NM_024504.3	446	cGg/cAg	6/8	1	2	FACETS	0.956	0.875	1	0.956	0.875	1	CLONAL	1	FALSE	1	0.686708534322026	2		467	387	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978600	70978600	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	152	534	0	ENST00000276594.2:c.1053G>T	p.Glu351Asp	p.E351D	ENST00000276594	NM_024504.3	351	gaG/gaT	5/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.686708534322026	2		534	352	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868966	117868966	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	89	305	0	ENST00000297338.2:c.733C>A	p.Pro245Thr	p.P245T	ENST00000297338	NM_006265.2	245	Ccc/Acc	7/14	1	2	FACETS	0.885	0.794	0.979	0.885	0.794	0.979	CLONAL	1	FALSE	1	0.686708534322026	2		305	293	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595218	141595218	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	146	417	0	ENST00000220592.5:c.215G>A	p.Arg72Lys	p.R72K	ENST00000220592	NM_012154.3	72	aGg/aAg	2/19	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.686708534322026	2		417	369	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738094	145738094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561220929	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	257	652	0	ENST00000428558.2:c.2816C>T	p.Ala939Val	p.A939V	ENST00000428558	NM_004260.3	939	gCg/gTg	17/22	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.686708534322026	2		652	682	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739584	145739584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772515188	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	254	540	0	ENST00000428558.2:c.1867C>T	p.Arg623Cys	p.R623C	ENST00000428558	NM_004260.3	623	Cgc/Tgc	11/22	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.686708534322026	2		540	655	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080541	5080541	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs199661171	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	52	259	0	ENST00000381652.3:c.2292A>C	p.Gln764His	p.Q764H	ENST00000381652	NM_004972.3	764	caA/caC	18/25	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.686708534322026	2		259	110	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8338930	8338930	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1380382010	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	75	315	0	ENST00000356435.5:c.5371G>T	p.Asp1791Tyr	p.D1791Y	ENST00000356435		1791	Gat/Tat	32/35	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.686708534322026	2		315	191	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518120	8518120	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	151	319	0	ENST00000356435.5:c.1271T>C	p.Val424Ala	p.V424A	ENST00000356435		424	gTc/gCc	10/35	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.686708534322026	2		319	396	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180244	27180244	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1564080006	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	103	416	0	ENST00000380036.4:c.908A>G	p.His303Arg	p.H303R	ENST00000380036	NM_000459.3	303	cAc/cGc	7/23	0.292774541385251	1	FACETS	0.706	0.641	0.772	0.706	0.641	0.772	INDETERMINATE	1	FALSE	0	0.686708534322026	1		416	279	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002653	37002653	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	141	324	0	ENST00000358127.4:c.596G>T	p.Arg199Ile	p.R199I	ENST00000358127	NM_001280556.1	199	aGa/aTa	5/10	0.292774541385251	1	FACETS	0.683	0.629	0.738	0.683	0.629	0.738	INDETERMINATE	1	FALSE	0	0.686708534322026	1		324	395	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37006526	37006526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	82	273	1	ENST00000358127.4:c.419G>A	p.Arg140Gln	p.R140Q	ENST00000358127	NM_001280556.1	140	cGg/cAg	4/10	0.292774541385251	1	FACETS	0.648	0.58	0.718	0.648	0.58	0.718	INDETERMINATE	1	FALSE	0	0.686708534322026	1		274	242	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020790	37020790	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	151	381	0	ENST00000358127.4:c.55G>T	p.Gly19Ter	p.G19*	ENST00000358127	NM_001280556.1	19	Gga/Tga	2/10	0.292774541385251	1	FACETS	0.748	0.692	0.805	0.748	0.692	0.805	INDETERMINATE	1	FALSE	0	0.686708534322026	1		381	386	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342722	87342722	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	100	471	0	ENST00000277120.3:c.1007T>G	p.Val336Gly	p.V336G	ENST00000277120		336	gTt/gGt	9/19	0.292774541385251	1	FACETS	0.59	0.533	0.65	0.59	0.533	0.65	INDETERMINATE	1	FALSE	0	0.686708534322026	1		471	324	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209585	98209585	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536440590	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	157	458	0	ENST00000331920.6:c.3953C>T	p.Pro1318Leu	p.P1318L	ENST00000331920	NM_000264.3	1318	cCg/cTg	23/24	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	1	0.686708534322026	2		458	448	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220348	98220348	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	176	392	0	ENST00000331920.6:c.3115A>C	p.Thr1039Pro	p.T1039P	ENST00000331920	NM_000264.3	1039	Aca/Cca	18/24	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.686708534322026	2		392	443	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231238	98231238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1366288601	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	306	438	2	ENST00000331920.6:c.2045G>A	p.Arg682His	p.R682H	ENST00000331920	NM_000264.3	682	cGc/cAc	14/24	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	FALSE	1	0.686708534322026	2		440	673	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242737	98242737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	217	385	0	ENST00000331920.6:c.880C>T	p.Arg294Cys	p.R294C	ENST00000331920	NM_000264.3	294	Cgc/Tgc	6/24	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.686708534322026	2		385	555	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891254	101891254	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	73	373	0	ENST00000374994.4:c.215T>C	p.Ile72Thr	p.I72T	ENST00000374994	NM_004612.2	72	aTa/aCa	2/9	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	FALSE	1	0.686708534322026	2		373	208	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891287	101891287	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757374917	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	91	459	0	ENST00000374994.4:c.248C>T	p.Pro83Leu	p.P83L	ENST00000374994	NM_004612.2	83	cCg/cTg	2/9	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	FALSE	1	0.686708534322026	2		459	251	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894964	101894964	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	90	265	0	ENST00000374994.4:c.517G>T	p.Glu173Ter	p.E173*	ENST00000374994	NM_004612.2	173	Gag/Tag	3/9	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.686708534322026	2		265	220	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907023	101907023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	47	237	0	ENST00000374994.4:c.983C>T	p.Ala328Val	p.A328V	ENST00000374994	NM_004612.2	328	gCc/gTc	6/9	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	1	0.686708534322026	2		237	118	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911535	101911535	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs113605875	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	19	337	0	ENST00000374994.4:c.1460G>T	p.Arg487Leu	p.R487L	ENST00000374994	NM_004612.2	487	cGg/cTg	9/9	1	2	FACETS	0.226	0.171	0.29	0.226	0.171	0.29	SUBCLONAL	1	FALSE	1	0.686708534322026	2		337	245	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250311	110250311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753267332	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	221	587	1	ENST00000374672.4:c.364G>A	p.Ala122Thr	p.A122T	ENST00000374672	NM_004235.4	122	Gcc/Acc	3/5	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.686708534322026	2		588	524	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128230383	128230383	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	13	383	0	ENST00000265960.3:c.1213T>G	p.Ser405Ala	p.S405A	ENST00000265960	NM_001006617.1	405	Tct/Gct	10/12	1	2	FACETS	0.146	0.103	0.197	0.146	0.103	0.197	SUBCLONAL	1	FALSE	1	0.686708534322026	2		383	260	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781287	135781287	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746304922	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	29	486	0	ENST00000298552.3:c.1678G>A	p.Gly560Ser	p.G560S	ENST00000298552	NM_001162426.1	560	Ggc/Agc	15/23	1	2	FACETS	0.18	0.144	0.221	0.18	0.144	0.221	SUBCLONAL	1	FALSE	1	0.686708534322026	2		486	469	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797271	135797271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs118203410	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	18	295	1	ENST00000298552.3:c.598G>A	p.Val200Ile	p.V200I	ENST00000298552	NM_001162426.1	200	Gtc/Atc	7/23	1	2	FACETS	0.253	0.191	0.326	0.253	0.191	0.326	SUBCLONAL	1	FALSE	1	0.686708534322026	2		296	207	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137321022	137321022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	220	582	0	ENST00000481739.1:c.979G>A	p.Ala327Thr	p.A327T	ENST00000481739	NM_002957.4	327	Gcc/Acc	7/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.686708534322026	2		582	597	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390606	139390606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1052013977	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	293	680	0	ENST00000277541.6:c.7585G>A	p.Val2529Ile	p.V2529I	ENST00000277541	NM_017617.3	2529	Gtc/Atc	34/34	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.686708534322026	2		680	754	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391608	139391608	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376422513	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	273	652	0	ENST00000277541.6:c.6583G>A	p.Gly2195Ser	p.G2195S	ENST00000277541	NM_017617.3	2195	Ggc/Agc	34/34	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.686708534322026	2		652	685	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391992	139391992	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	195	484	1	ENST00000277541.6:c.6199C>A	p.Leu2067Met	p.L2067M	ENST00000277541	NM_017617.3	2067	Ctg/Atg	34/34	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.686708534322026	2		485	516	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399216	139399216	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs566680728	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	204	526	1	ENST00000277541.6:c.4927G>A	p.Ala1643Thr	p.A1643T	ENST00000277541	NM_017617.3	1643	Gcc/Acc	26/34	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.686708534322026	2		527	523	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400206	139400206	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752551426	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	266	572	0	ENST00000277541.6:c.4142C>T	p.Pro1381Leu	p.P1381L	ENST00000277541	NM_017617.3	1381	cCc/cTc	25/34	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	1	0.686708534322026	2		572	618	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400299	139400299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150343794	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	230	490	0	ENST00000277541.6:c.4049G>A	p.Arg1350His	p.R1350H	ENST00000277541	NM_017617.3	1350	cGt/cAt	25/34	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.686708534322026	2		490	565	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139563116	139563116	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	153	386	0	ENST00000308874.7:c.188G>A	p.Ser63Asn	p.S63N	ENST00000308874		63	aGc/aAc	4/10	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	FALSE	1	0.686708534322026	2		386	441	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916542	39916542	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	149	528	0	ENST00000378444.4:c.4461T>G	p.Ile1487Met	p.I1487M	ENST00000378444	NM_001123385.1	1487	atT/atG	11/15	0.292774541385251	1	FACETS	0.683	0.631	0.737	0.683	0.631	0.737	INDETERMINATE	1	FALSE	0	0.686708534322026	1		528	417	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921574	39921574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	280	456	0	ENST00000378444.4:c.4246C>T	p.Pro1416Ser	p.P1416S	ENST00000378444	NM_001123385.1	1416	Cca/Tca	10/15	0.292774541385251	1	FACETS	0.948	0.9	0.996	0.948	0.9	0.996	INDETERMINATE	1	FALSE	0	0.686708534322026	1		456	565	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933872	39933872	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1274186244	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	272	581	0	ENST00000378444.4:c.727C>T	p.Arg243Cys	p.R243C	ENST00000378444	NM_001123385.1	243	Cgc/Tgc	4/15	0.292774541385251	1	FACETS	0.936	0.887	0.984	0.936	0.887	0.984	INDETERMINATE	1	FALSE	0	0.686708534322026	1		581	556	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430729	47430729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	148	482	0	ENST00000377045.4:c.1694C>T	p.Ala565Val	p.A565V	ENST00000377045	NM_001654.4	565	gCc/gTc	16/16	0.292774541385251	1	FACETS	0.552	0.507	0.598	0.552	0.507	0.598	INDETERMINATE	1	FALSE	0	0.686708534322026	1		482	513	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430798	47430798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776912006	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	303	513	2	ENST00000377045.4:c.1763G>A	p.Arg588His	p.R588H	ENST00000377045	NM_001654.4	588	cGc/cAc	16/16	0.292774541385251	1	FACETS	0.901	0.856	0.946	0.901	0.856	0.946	INDETERMINATE	1	FALSE	0	0.686708534322026	1		515	643	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650778	48650778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104894809	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	245	564	0	ENST00000376670.3:c.647G>A	p.Arg216Gln	p.R216Q	ENST00000376670	NM_002049.3	216	cGg/cAg	4/6	0.292774541385251	1	FACETS	0.879	0.83	0.928	0.879	0.83	0.928	INDETERMINATE	1	FALSE	0	0.686708534322026	1		564	533	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224571	53224571	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	222	555	1	ENST00000375401.3:c.3142C>A	p.Leu1048Met	p.L1048M	ENST00000375401	NM_004187.3	1048	Ctg/Atg	21/26	0.292774541385251	1	FACETS	0.812	0.763	0.861	0.812	0.763	0.861	INDETERMINATE	1	FALSE	0	0.686708534322026	1		556	523	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239882	53239882	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	160	520	0	ENST00000375401.3:c.1559G>T	p.Ser520Ile	p.S520I	ENST00000375401	NM_004187.3	520	aGt/aTt	11/26	0.292774541385251	1	FACETS	0.729	0.675	0.783	0.729	0.675	0.783	INDETERMINATE	1	FALSE	0	0.686708534322026	1		520	420	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240770	53240770	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	115	532	0	ENST00000375401.3:c.1310C>A	p.Thr437Asn	p.T437N	ENST00000375401	NM_004187.3	437	aCt/aAt	10/26	0.292774541385251	1	FACETS	0.723	0.661	0.787	0.723	0.661	0.787	INDETERMINATE	1	FALSE	0	0.686708534322026	1		532	304	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411914	63411914	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758890390	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	30	751	0	ENST00000330258.3:c.1253G>A	p.Arg418Gln	p.R418Q	ENST00000330258	NM_152424.3	418	cGg/cAg	2/2	0.292774541385251	1	FACETS	0.108	0.086	0.132	0.108	0.086	0.132	INDETERMINATE	1	FALSE	0	0.686708534322026	1		751	533	SUCCESS
AR	367	MSKCC	GRCh37	X	66765382	66765382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770661499	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	194	521	1	ENST00000374690.3:c.394G>A	p.Val132Ile	p.V132I	ENST00000374690	NM_000044.3	132	Gtc/Atc	1/8	0.292774541385251	1	FACETS	0.781	0.73	0.833	0.781	0.73	0.833	INDETERMINATE	1	FALSE	0	0.686708534322026	1		522	475	SUCCESS
AR	367	MSKCC	GRCh37	X	66766027	66766027	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	253	682	0	ENST00000374690.3:c.1039C>A	p.Leu347Ile	p.L347I	ENST00000374690	NM_000044.3	347	Ctc/Atc	1/8	0.292774541385251	1	FACETS	0.766	0.721	0.81	0.766	0.721	0.81	INDETERMINATE	1	FALSE	0	0.686708534322026	1		682	632	SUCCESS
AR	367	MSKCC	GRCh37	X	66863187	66863187	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	90	444	0	ENST00000374690.3:c.1706G>T	p.Gly569Val	p.G569V	ENST00000374690	NM_000044.3	569	gGg/gTg	2/8	0.292774541385251	1	FACETS	0.594	0.533	0.656	0.594	0.533	0.656	INDETERMINATE	1	FALSE	0	0.686708534322026	1		444	290	SUCCESS
AR	367	MSKCC	GRCh37	X	66863211	66863211	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	76	427	0	ENST00000374690.3:c.1730G>A	p.Cys577Tyr	p.C577Y	ENST00000374690	NM_000044.3	577	tGt/tAt	2/8	0.292774541385251	1	FACETS	0.51	0.452	0.571	0.51	0.452	0.571	INDETERMINATE	1	FALSE	0	0.686708534322026	1		427	285	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338681	70338681	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	169	493	0	ENST00000374080.3:c.77C>A	p.Pro26His	p.P26H	ENST00000374080		26	cCt/cAt	1/45	0.292774541385251	1	FACETS	0.64	0.593	0.688	0.64	0.593	0.688	INDETERMINATE	1	FALSE	0	0.686708534322026	1		493	505	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340917	70340917	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	186	450	0	ENST00000374080.3:c.650C>A	p.Ser217Tyr	p.S217Y	ENST00000374080		217	tCc/tAc	5/45	0.292774541385251	1	FACETS	0.634	0.589	0.68	0.634	0.589	0.68	INDETERMINATE	1	FALSE	0	0.686708534322026	1		450	561	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342197	70342197	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	110	374	1	ENST00000374080.3:c.1248+1G>A		p.X416_splice	ENST00000374080		416			0.292774541385251	1	FACETS	0.649	0.59	0.71	0.649	0.59	0.71	INDETERMINATE	1	FALSE	0	0.686708534322026	1		375	324	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342400	70342400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	194	445	3	ENST00000374080.3:c.1291C>T	p.Arg431Trp	p.R431W	ENST00000374080		431	Cgg/Tgg	9/45	0.292774541385251	1	FACETS	0.75	0.7	0.8	0.75	0.7	0.8	INDETERMINATE	1	FALSE	0	0.686708534322026	1		448	495	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348505	70348505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	30	401	1	ENST00000374080.3:c.3412C>T	p.Arg1138Trp	p.R1138W	ENST00000374080		1138	Cgg/Tgg	24/45	0.292774541385251	1	FACETS	0.173	0.139	0.212	0.173	0.139	0.212	INDETERMINATE	1	FALSE	0	0.686708534322026	1		402	331	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76777797	76777797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	21	503	0	ENST00000373344.5:c.6919C>T	p.Pro2307Ser	p.P2307S	ENST00000373344	NM_000489.3	2307	Cct/Tct	32/35	0.292774541385251	1	FACETS	0.157	0.121	0.2	0.157	0.121	0.2	INDETERMINATE	1	FALSE	0	0.686708534322026	1		503	255	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76931785	76931785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	95	317	0	ENST00000373344.5:c.3745G>A	p.Ala1249Thr	p.A1249T	ENST00000373344	NM_000489.3	1249	Gcc/Acc	10/35	0.292774541385251	1	FACETS	0.913	0.833	0.993	0.913	0.833	0.993	INDETERMINATE	1	FALSE	0	0.686708534322026	1		317	199	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939957	76939957	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	63	482	0	ENST00000373344.5:c.791A>G	p.Tyr264Cys	p.Y264C	ENST00000373344	NM_000489.3	264	tAt/tGt	9/35	0.292774541385251	1	FACETS	0.56	0.492	0.632	0.56	0.492	0.632	INDETERMINATE	1	FALSE	0	0.686708534322026	1		482	215	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613644	100613644	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	92	439	0	ENST00000308731.7:c.935C>T	p.Ala312Val	p.A312V	ENST00000308731	NM_000061.2	312	gCt/gTt	11/19	0.292774541385251	1	FACETS	0.687	0.62	0.756	0.687	0.62	0.756	INDETERMINATE	1	FALSE	0	0.686708534322026	1		439	256	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630236	100630236	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs128620187	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	58	310	0	ENST00000308731.7:c.37C>T	p.Arg13Ter	p.R13*	ENST00000308731	NM_000061.2	13	Cga/Tga	2/19	0.292774541385251	1	FACETS	0.523	0.456	0.594	0.523	0.456	0.594	INDETERMINATE	1	FALSE	0	0.686708534322026	1		310	212	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020144	123020144	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	179	565	0	ENST00000355640.3:c.632A>G	p.Glu211Gly	p.E211G	ENST00000355640		211	gAa/gGa	2/7	0.292774541385251	1	FACETS	0.951	0.891	1	0.951	0.891	1	INDETERMINATE	1	FALSE	0	0.686708534322026	1		565	360	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200235	123200235	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	56	393	0	ENST00000218089.9:c.2214C>A	p.His738Gln	p.H738Q	ENST00000218089	NM_001042749.1	738	caC/caA	23/35	0.292774541385251	1	FACETS	0.546	0.475	0.621	0.546	0.475	0.621	INDETERMINATE	1	FALSE	0	0.686708534322026	1		393	196	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480557	123480557	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	34	451	0	ENST00000371139.4:c.65C>T	p.Ala22Val	p.A22V	ENST00000371139	NM_001114937.2	22	gCc/gTc	1/4	0.292774541385251	1	FACETS	0.124	0.101	0.15	0.124	0.101	0.15	INDETERMINATE	1	FALSE	0	0.686708534322026	1		451	524	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123505215	123505215	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	45	227	0	ENST00000371139.4:c.361C>A	p.Pro121Thr	p.P121T	ENST00000371139	NM_001114937.2	121	Cct/Act	4/4	0.292774541385251	1	FACETS	0.509	0.435	0.589	0.509	0.435	0.589	INDETERMINATE	1	FALSE	0	0.686708534322026	1		227	169	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860040	152860040	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	136	471	0	ENST00000406277.2:c.388C>A	p.Leu130Met	p.L130M	ENST00000406277	NM_152274.4	130	Ctg/Atg	5/7	0.292774541385251		FACETS		0.553	0.655				INDETERMINATE	1	FALSE	0	0.686708534322026	1		471	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0026498-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	235	559	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.449491898991792	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.449491898991792	1		559	750	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147577	47147579	+	inframe_deletion	In_Frame_Del	DEL	TAC	TAC	-	novel	NA	P-0026498-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	132	431	0	ENST00000409792.3:c.4747_4749del	p.Val1583del	p.V1583del	ENST00000409792	NM_014159.6	1583	GTA/-	6/21	0.449491898991792	1	FACETS	0.842	0.768	0.919	0.842	0.768	0.919	CLONAL	1	TRUE	0	0.449491898991792	1		431	541	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440835	52440855	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGCCCTTACCCTGCAGTGGC	GGGCCCTTACCCTGCAGTGGC	-	novel	NA	P-0026498-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	143	604	0	ENST00000460680.1:c.649_659+10del		p.X217_splice	ENST00000460680	NM_004656.3	217		8/17	0.449491898991792	1	FACETS	0.853	0.781	0.928	0.853	0.781	0.928	CLONAL	1	TRUE	0	0.449491898991792	1		604	578	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0026530-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	194	411	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.4192675953031	2		411	803	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0026530-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	205	493	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.23244322702215	1	FACETS	1	0.936	1	1	0.936	1	INDETERMINATE	1	TRUE	0	0.4192675953031	1		493	768	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17371376	17371376	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026530-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	134	418	0	ENST00000375499.3:c.80G>T	p.Arg27Leu	p.R27L	ENST00000375499	NM_003000.2	27	cGa/cTa	2/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.4192675953031	2		418	571	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593588	55593605	+	inframe_deletion	In_Frame_Del	DEL	ATGTATGAAGTACAGTGG	ATGTATGAAGTACAGTGG	-	novel	NA	P-0026664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	274	490	0	ENST00000288135.5:c.1655_1672del	p.Met552_Trp557del	p.M552_W557del	ENST00000288135	NM_000222.2	552	ATGTATGAAGTACAGTGG/-	11/21	1	2	FACETS	0.83	0.783	0.877	0.83	0.783	0.877	CLONAL	1	TRUE	1	0.90593060357122	2		490	729	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636701	176636701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026684-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	165	435	0	ENST00000439151.2:c.1301C>T	p.Pro434Leu	p.P434L	ENST00000439151	NM_022455.4	434	cCc/cTc	5/23	1	2	FACETS	0.982	0.908	1	0.982	0.908	1	CLONAL	1	TRUE	1	0.669750606848329	2		435	502	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624611	93624611	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026684-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	81	549	1	ENST00000375746.1:c.702C>A	p.Phe234Leu	p.F234L	ENST00000375746	NM_001174167.1	234	ttC/ttA	4/14	1	2	FACETS	0.463	0.409	0.521	0.463	0.409	0.521	SUBCLONAL	1	TRUE	1	0.669750606848329	2		550	522	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636701	176636701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026684-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	158	435	0	ENST00000439151.2:c.1301C>T	p.Pro434Leu	p.P434L	ENST00000439151	NM_022455.4	434	cCc/cTc	5/23	1	2	FACETS	0.987	0.907	1	0.987	0.907	1	CLONAL	1	TRUE	1	0.456608986377735	2		435	701	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223555	55223555	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749132706	NA	P-0026684-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	116	648	1	ENST00000275493.2:c.922G>A	p.Val308Ile	p.V308I	ENST00000275493	NM_005228.3	308	Gtc/Atc	8/28	1	2	FACETS	0.63	0.567	0.696	0.63	0.567	0.696	SUBCLONAL	1	TRUE	1	0.456608986377735	2		649	807	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272266	15272266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1363323415	NA	P-0026838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	75	607	0	ENST00000263388.2:c.6173C>T	p.Ser2058Leu	p.S2058L	ENST00000263388	NM_000435.2	2058	tCg/tTg	33/33	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.23	2		607	635	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624295	89624298	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	novel	NA	P-0026838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	54	454	0	ENST00000371953.3:c.69_72del	p.Leu23PhefsTer2	p.L23Ffs*2	ENST00000371953	NM_000314.4	23	ttAGAC/tt	1/9	1	2	FACETS	0.93	0.795	1	0.93	0.795	1	CLONAL	1	TRUE	1	0.23	2		454	505	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0026929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	209	493	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.924	0.864	0.985	1	0.994	1	CLONAL	2	TRUE	1	0.391927097900576	2		493	577	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353740	15353740	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768856782	NA	P-0026929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	222	976	0	ENST00000263377.2:c.3140G>A	p.Arg1047Gln	p.R1047Q	ENST00000263377	NM_058243.2	1047	cGg/cAg	14/20	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.391927097900576	2		976	1128	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106870	27106877	+	frameshift_variant	Frame_Shift_Del	DEL	CCGGTGTG	CCGGTGTG	-	novel	NA	P-0026929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	158	478	0	ENST00000324856.7:c.6485_6492del	p.Val2162GlyfsTer60	p.V2162Gfs*60	ENST00000324856	NM_006015.4	2161	CCGGTGTGc/c	20/20	0.272025651668874	2	FACETS	0.771	0.711	0.832	0.771	0.711	0.832	SUBCLONAL	2	TRUE	0	0.391927097900576	2		478	523	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115400	115115400	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	101	594	0	ENST00000257566.3:c.926G>T	p.Gly309Val	p.G309V	ENST00000257566	NM_016569.3	309	gGc/gTc	5/8	1	2	FACETS	0.803	0.719	0.892	0.803	0.719	0.892	CLONAL	1	TRUE	1	0.391927097900576	2		594	642	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31495412	31495412	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	99	540	0	ENST00000344624.3:c.1736C>T	p.Ser579Phe	p.S579F	ENST00000344624		579	tCc/tTc	9/33	1	2	FACETS	0.736	0.658	0.82	0.736	0.658	0.82	SUBCLONAL	1	TRUE	1	0.391927097900576	2		540	686	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476283	88476283	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027006-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	283	667	0	ENST00000360948.2:c.1849T>A	p.Phe617Ile	p.F617I	ENST00000360948	NM_001012338.2	617	Ttt/Att	15/19	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.81387336187715	2		667	658	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634812	158634812	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027006-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	165	414	0	ENST00000263640.3:c.374G>C	p.Gly125Ala	p.G125A	ENST00000263640	NM_001105.4	125	gGc/gCc	5/11	0.810264711296111	2	FACETS	0.848	0.786	0.912	0.424	0.393	0.456	CLONAL	1	TRUE	0	0.81387336187715	2		414	478	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191316	185191316	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027006-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	216	443	0	ENST00000265026.3:c.2197C>G	p.Leu733Val	p.L733V	ENST00000265026	NM_004721.4	733	Ctt/Gtt	11/14	1	2	FACETS	0.981	0.92	1	0.981	0.92	1	CLONAL	1	TRUE	1	0.81387336187715	2		443	541	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971169	21971176	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCAGCT	CAGCAGCT	-	novel	NA	P-0027006-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	346	426	0	ENST00000304494.5:c.182_189del	p.Glu61AlafsTer56	p.E61Afs*56	ENST00000304494	NM_000077.4	61	gAGCTGCTG/g	2/3	0.81387336187715	2	FACETS	0.962	0.932	0.99	0.962	0.932	0.99	CLONAL	2	TRUE	0	0.81387336187715	2		426	442	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191316	185191316	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027006-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	230	443	0	ENST00000265026.3:c.2197C>G	p.Leu733Val	p.L733V	ENST00000265026	NM_004721.4	733	Ctt/Gtt	11/14	1	2	FACETS	0.962	0.904	1	0.962	0.904	1	CLONAL	1	TRUE	1	0.817162461860158	2		443	585	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971169	21971176	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCAGCT	CAGCAGCT	-	novel	NA	P-0027006-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	376	426	0	ENST00000304494.5:c.182_189del	p.Glu61AlafsTer56	p.E61Afs*56	ENST00000304494	NM_000077.4	61	gAGCTGCTG/g	2/3	0.801816177640563	2	FACETS	0.975	0.947	1	0.975	0.947	1	CLONAL	2	TRUE	0	0.817162461860158	2		426	472	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733230	40733230	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027006-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	256	486	0	ENST00000373198.4:c.3576C>G	p.Ser1192Arg	p.S1192R	ENST00000373198	NM_133170.3	1192	agC/agG	26/32	0.686812921120364	3	FACETS	0.928	0.87	0.988	0.464	0.435	0.494	CLONAL	1	TRUE	1	0.817162461860158	3		486	951	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981889	70981889	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027006-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	250	661	0	ENST00000276594.2:c.207C>A	p.Phe69Leu	p.F69L	ENST00000276594	NM_024504.3	69	ttC/ttA	2/8	0.807684072880761	3	FACETS	0.918	0.86	0.978	0.306	0.286	0.326	CLONAL	1	TRUE	0	0.817162461860158	3		661	939	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0027197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	89	635	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	0.998	0.886	1	0.998	0.886	1	CLONAL	1	FALSE	1	0.28626040873	2		635	623	SUCCESS
AR	367	MSKCC	GRCh37	X	66931247	66931247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868669253	NA	P-0027197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	25	215	0	ENST00000374690.3:c.1889G>A	p.Arg630Gln	p.R630Q	ENST00000374690	NM_000044.3	630	cGg/cAg	4/8	1	1	FACETS	0.73	0.579	0.902	0.73	0.579	0.902	CLONAL	1	FALSE	0	0.28626040873	1		215	205	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39567798	39567798	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	40	434	0	ENST00000262039.4:c.554G>C	p.Gly185Ala	p.G185A	ENST00000262039	NM_002647.2	185	gGa/gCa	5/25	1	2	FACETS	1	0.84	1	1	0.84	1	CLONAL	1	FALSE	1	0.28626040873	2		434	278	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952088	+	missense_variant	Missense_Mutation	ONP	ATCA	ATCA	GTCG	novel	NA	P-0027550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	87	307	0	ENST00000263967.3:c.3140_3143delinsGTCG	p.His1047_His1048delinsArgArg	p.H1047_H1048delinsRR	ENST00000263967	NM_006218.2	1047	cATCAt/cGTCGt	21/21	1	2	FACETS	0.848	0.753	0.949	0.848	0.753	0.949	CLONAL	1	TRUE	1	0.409462163080443	2		307	501	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0027721-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	144	609	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.317456754593596	3	FACETS	0.761	0.695	0.829	0.761	0.695	0.829	SUBCLONAL	2	FALSE	1	0.317456754593596	3		610	691	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513219	44513219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1288331595	NA	P-0027721-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	69	287	0	ENST00000291552.4:c.716G>A	p.Arg239Gln	p.R239Q	ENST00000291552	NM_006758.2	239	cGa/cAa	8/8	0.317456754593596	3	FACETS	0.909	0.8	1	0.909	0.8	1	CLONAL	2	FALSE	1	0.317456754593596	3		287	277	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216548	108216549	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0027721-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	51	491	1	ENST00000278616.4:c.8498dup	p.Tyr2833Ter	p.Y2833*	ENST00000278616	NM_000051.3	2833	tac/tAac	58/63	0.317456754593596	3	FACETS	0.899	0.766	1	0.45	0.383	0.523	CLONAL	1	FALSE	1	0.317456754593596	3		492	414	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372427	55372427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	324	662	0	ENST00000297316.4:c.1117C>T	p.Pro373Ser	p.P373S	ENST00000297316	NM_022454.3	373	Cct/Tct	2/2	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.5	2		662	1042	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660421	227660441	+	inframe_deletion	In_Frame_Del	DEL	AGCTTACAGGGGCAGCTGGCG	AGCTTACAGGGGCAGCTGGCG	-	novel	NA	P-0027938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	154	384	0	ENST00000305123.5:c.3014_3034del	p.Ser1005_Ser1011del	p.S1005_S1011del	ENST00000305123	NM_005544.2	1005	tCGCCAGCTGCCCCTGTAAGCTat/tat	1/2	0.3	2	FACETS	1	0.976	1			1	CLONAL	1	TRUE	NA	0.5	2		384	534	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0027992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	19	974	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		974	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0027992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	41	1233	2	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1235	825	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579429	7579429	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028094-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	845	1333	0	ENST00000269305.4:c.258del	p.Pro87GlnfsTer36	p.P87Qfs*36	ENST00000269305	NM_001126112.2	86	gcA/gc	4/11	0.646495827652995	2	FACETS	0.936	0.913	0.958	0.936	0.913	0.958	CLONAL	2	TRUE	0	0.696767050190403	2		1333	1296	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853807	59853807	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028094-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	229	853	0	ENST00000259008.2:c.2052C>A	p.Cys684Ter	p.C684*	ENST00000259008	NM_032043.2	684	tgC/tgA	14/20	0.696767050190403	2	FACETS	0.598	0.557	0.641	0.299	0.278	0.321	SUBCLONAL	1	TRUE	0	0.696767050190403	2		853	1099	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554186	63554186	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028094-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1226	443	1143	0	ENST00000307078.5:c.553A>T	p.Asn185Tyr	p.N185Y	ENST00000307078	NM_004655.3	185	Aat/Tat	2/11	0.696767050190403	2	FACETS	0.762	0.725	0.799	0.381	0.362	0.4	SUBCLONAL	1	TRUE	0	0.696767050190403	2		1143	1669	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211680	36211680	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028094-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1285	242	984	0	ENST00000222270.7:c.1431C>A	p.Ser477Arg	p.S477R	ENST00000222270	NM_014727.1	477	agC/agA	3/37	0.687582025182719	4	FACETS	0.772	0.719	0.827	0.257	0.239	0.276	SUBCLONAL	1	TRUE	1	0.696767050190403	4		984	1527	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076954	41076954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028094-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	133	836	1	ENST00000373198.4:c.1466C>T	p.Pro489Leu	p.P489L	ENST00000373198	NM_133170.3	489	cCt/cTt	9/32	0.696767050190403	3	FACETS	0.466	0.422	0.513	0.233	0.211	0.257	SUBCLONAL	1	TRUE	1	0.696767050190403	3		837	1104	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225666	225666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs575617625	NA	P-0028094-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2204	245	1529	1	ENST00000264932.6:c.445G>A	p.Ala149Thr	p.A149T	ENST00000264932	NM_004168.2	149	Gcc/Acc	4/15	0.340538252967387	4	FACETS	0.487	0.453	0.523	0.244	0.226	0.262	INDETERMINATE	1	TRUE	2	0.696767050190403	4		1530	2449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0028108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	87	559	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.779	0.689	0.876	0.779	0.689	0.876	SUBCLONAL	1	TRUE	1	0.259118023890101	2		559	862	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0028108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	31	281	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	0.454	0.366	0.554	0.454	0.366	0.554	SUBCLONAL	1	TRUE	1	0.259118023890101	2		281	527	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279368	38279368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	90	661	2	ENST00000425967.3:c.1121C>T	p.Ala374Val	p.A374V	ENST00000425967	NM_001174067.1	374	gCg/gTg	9/19	1	2	FACETS	0.704	0.623	0.791	0.704	0.623	0.791	SUBCLONAL	1	TRUE	1	0.259118023890101	2		663	987	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604673	48604673	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060500738	NA	P-0028108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	36	373	0	ENST00000342988.3:c.1495T>C	p.Cys499Arg	p.C499R	ENST00000342988	NM_005359.5	499	Tgc/Cgc	12/12	0.259118023890101	1	FACETS	0.451	0.37	0.542	0.451	0.37	0.542	SUBCLONAL	1	TRUE	0	0.259118023890101	1		373	536	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453987	140453987	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs180177040	NA	P-0028108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	33	293	0	ENST00000288602.6:c.1741A>C	p.Asn581His	p.N581H	ENST00000288602	NM_004333.4	581	Aat/Cat	14/18	1	2	FACETS	0.47	0.382	0.57	0.47	0.382	0.57	SUBCLONAL	1	TRUE	1	0.259118023890101	2		293	542	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407903	139407903	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	58	599	0	ENST00000277541.6:c.2294G>T	p.Gly765Val	p.G765V	ENST00000277541	NM_017617.3	765	gGc/gTc	14/34	1	2	FACETS	0.445	0.381	0.516	0.445	0.381	0.516	SUBCLONAL	1	TRUE	1	0.259118023890101	2		599	1005	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0028114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	353	436	1	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	0.996	1	CLONAL	2	TRUE	1	0.415738365388928	2		437	831	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0028114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	172	638	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	0.415738365388928	1	FACETS	0.998	0.921	1	0.998	0.921	1	CLONAL	1	TRUE	0	0.415738365388928	1		638	657	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478902	56478902	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	181	812	0	ENST00000267101.3:c.358A>G	p.Met120Val	p.M120V	ENST00000267101	NM_001982.3	120	Atg/Gtg	3/28	1	2	FACETS	0.892	0.823	0.965	0.892	0.823	0.965	CLONAL	1	TRUE	1	0.415738365388928	2		812	976	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028139-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	2281	770	0	ENST00000397752.3:c.3028G>T	p.Asp1010Tyr	p.D1010Y	ENST00000397752	NM_000245.2	1010	Gat/Tat	14/21	0.625716288576126	11	FACETS	0.968	0.959	0.977	0.968	0.959	0.977	CLONAL	11	TRUE	0	0.625716288576126	11		770	2613	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268978	115268978	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs947495575	NA	P-0028139-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	132	483	0	ENST00000438362.2:c.1632G>C	p.Arg544Ser	p.R544S	ENST00000438362	NM_001242891.1	544	agG/agC	14/20	0.523447139530929	3	FACETS	0.83	0.756	0.909	0.415	0.378	0.455	CLONAL	1	TRUE	1	0.625716288576126	3		483	667	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41489052	41489095	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCTAAACTCTCATCTCCGGCCCTCTCGGCGTCCGCCAGCGAT	GGCCTAAACTCTCATCTCCGGCCCTCTCGGCGTCCGCCAGCGAT	-	novel	NA	P-0028139-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	65	485	0	ENST00000263253.7:c.47_90del	p.Pro16HisfsTer8	p.P16Hfs*8	ENST00000263253	NM_001429.3	15	cGGCCTAAACTCTCATCTCCGGCCCTCTCGGCGTCCGCCAGCGAT/c	1/31	1	2	FACETS	0.423	0.367	0.483	0.423	0.367	0.483	SUBCLONAL	1	TRUE	1	0.625716288576126	2		485	491	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170814962	170814962	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028139-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	105	244	0	ENST00000296930.5:c.10T>G	p.Ser4Ala	p.S4A	ENST00000296930	NM_002520.6	4	Tcg/Gcg	1/11	0.523447139530929	3	FACETS	0.765	0.695	0.836	0.765	0.695	0.836	SUBCLONAL	2	TRUE	1	0.625716288576126	3		244	288	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	194	474	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	0.500679865083911	2		474	710	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	209	835	0	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.899	0.835	0.965	0.899	0.835	0.965	CLONAL	1	TRUE	1	0.500679865083911	2		835	929	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	137	326	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.500679865083911	2		326	543	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	121	371	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.81	0.734	0.889	0.81	0.734	0.889	CLONAL	1	TRUE	1	0.500679865083911	2		371	597	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	220	457	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.995	0.927	1	0.995	0.927	1	CLONAL	1	TRUE	1	0.500679865083911	2		457	883	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	138	473	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	1	2	FACETS	0.928	0.848	1	0.928	0.848	1	CLONAL	1	TRUE	1	0.500679865083911	2		473	594	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	227	530	6	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.500679865083911	2		536	842	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101268	27101268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	191	627	3	ENST00000324856.7:c.4555del	p.Gln1519ArgfsTer8	p.Q1519Rfs*8	ENST00000324856	NM_006015.4	1517	gCc/gc	18/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.500679865083911	2		630	725	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793442	42793442	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748865223	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	191	541	0	ENST00000575354.2:c.1244G>A	p.Arg415Gln	p.R415Q	ENST00000575354	NM_015125.3	415	cGg/cAg	8/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.500679865083911	2		541	675	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692893	89692893	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	255	396	0	ENST00000371953.3:c.377C>A	p.Ala126Asp	p.A126D	ENST00000371953	NM_000314.4	126	gCt/gAt	5/9	0.500679865083911	2	FACETS	0.965	0.913	1	0.965	0.913	1	CLONAL	2	TRUE	0	0.500679865083911	2		396	528	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	217	490	1	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.500679865083911	2		491	795	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	161	525	2	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	0.748	0.686	0.812	0.748	0.686	0.812	SUBCLONAL	1	TRUE	1	0.500679865083911	2		527	860	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	144	437	1	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.968	0.887	1	0.968	0.887	1	CLONAL	1	TRUE	1	0.500679865083911	2		438	594	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551952	150551952	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	170	552	2	ENST00000369026.2:c.55del	p.Ala19ProfsTer30	p.A19Pfs*30	ENST00000369026	NM_021960.4	19	Gcc/cc	1/3	0.500679865083911	4	FACETS	0.916	0.841	0.994	0.305	0.28	0.332	CLONAL	1	TRUE	1	0.500679865083911	4		554	1113	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	295	789	2	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.500679865083911	2		791	1082	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	203	554	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.983	0.913	1	0.983	0.913	1	CLONAL	1	TRUE	1	0.500679865083911	2		557	825	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	291	788	2	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.500679865083911	2		790	1047	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	202	644	3	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.965	0.896	1	0.965	0.896	1	CLONAL	1	TRUE	1	0.500679865083911	2		647	836	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732825	44732825	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1332106985	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	191	626	0	ENST00000377967.4:c.28A>G	p.Thr10Ala	p.T10A	ENST00000377967	NM_021140.2	10	Acc/Gcc	1/29	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.500679865083911	2		626	754	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527354	187527354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373193128	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	192	492	1	ENST00000441802.2:c.10220C>T	p.Thr3407Met	p.T3407M	ENST00000441802	NM_005245.3	3407	aCg/aTg	17/27	0.202397017318161	4	FACETS	1	0.989	1	0.707	0.655	0.761	INDETERMINATE	1	TRUE	2	0.500679865083911	4		493	814	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621912	1621914	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs748560717	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	259	757	0	ENST00000344749.5:c.878_880del	p.Phe293del	p.F293del	ENST00000344749	NM_001136139.2	293	tTCTcc/tcc	11/19	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.500679865083911	2		757	944	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598909	28598909	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765112783	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	261	614	1	ENST00000253063.3:c.469C>T	p.Arg157Cys	p.R157C	ENST00000253063	NM_031459.4	157	Cgc/Tgc	4/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.500679865083911	2		615	947	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306933	65306933	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	162	438	0	ENST00000342505.4:c.2644G>A	p.Gly882Arg	p.G882R	ENST00000342505	NM_002227.2	882	Gga/Aga	19/25	1	2	FACETS	0.994	0.915	1	0.994	0.915	1	CLONAL	1	TRUE	1	0.500679865083911	2		438	651	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115269618	115269620	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs745372505	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	175	774	0	ENST00000438362.2:c.1586_1588del	p.Pro529del	p.P529del	ENST00000438362	NM_001242891.1	529	cCTCaa/caa	13/20	1	2	FACETS	0.832	0.767	0.9	0.832	0.767	0.9	CLONAL	1	TRUE	1	0.500679865083911	2		774	840	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176118198	176118198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	84	322	0	ENST00000367669.3:c.775G>A	p.Ala259Thr	p.A259T	ENST00000367669	NM_022457.5	259	Gcc/Acc	6/20	0.500679865083911	4	FACETS	0.852	0.754	0.957	0.284	0.251	0.319	CLONAL	1	TRUE	1	0.500679865083911	4		322	591	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612647	228612647	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	261	505	0	ENST00000366696.1:c.380T>C	p.Leu127Pro	p.L127P	ENST00000366696	NM_003493.2	127	cTg/cCg	1/1	0.500679865083911	4	FACETS	1	0.983	1	0.382	0.357	0.408	CLONAL	1	TRUE	1	0.500679865083911	4		505	1365	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644494	21644494	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	132	466	1	ENST00000421138.2:c.173G>T	p.Ser58Ile	p.S58I	ENST00000421138		58	aGc/aTc	4/16	1	2	FACETS	0.817	0.744	0.894	0.817	0.744	0.894	CLONAL	1	TRUE	1	0.500679865083911	2		467	645	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444909	49444909	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	231	611	0	ENST00000301067.7:c.2557C>A	p.Pro853Thr	p.P853T	ENST00000301067	NM_003482.3	853	Cct/Act	10/54	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.500679865083911	2		611	898	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563278	21563278	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs750461080	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	224	750	0	ENST00000382592.4:c.641A>G	p.Tyr214Cys	p.Y214C	ENST00000382592	NM_014572.2	214	tAc/tGc	4/8	1	2	FACETS	0.973	0.907	1	0.973	0.907	1	CLONAL	1	TRUE	1	0.500679865083911	2		750	920	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438206	110438206	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	73	192	0	ENST00000375856.3:c.195del	p.Ser66ArgfsTer27	p.S66Rfs*27	ENST00000375856	NM_003749.2	65	ggG/gg	1/2	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.500679865083911	2		192	260	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105653	30105653	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	192	702	0	ENST00000331968.5:c.1033A>G	p.Ser345Gly	p.S345G	ENST00000331968	NM_002742.2	345	Agt/Ggt	7/18	1	2	FACETS	0.896	0.83	0.965	0.896	0.83	0.965	CLONAL	1	TRUE	1	0.500679865083911	2		702	856	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678610	88678610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766271262	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	118	316	0	ENST00000360948.2:c.926G>A	p.Ser309Asn	p.S309N	ENST00000360948	NM_001012338.2	309	aGc/aAc	9/19	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.500679865083911	2		316	421	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872590	37872590	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759579850	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	240	580	0	ENST00000269571.5:c.1550G>A	p.Arg517Gln	p.R517Q	ENST00000269571		517	cGa/cAa	13/27	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.500679865083911	2		580	769	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097057	11097057	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	68	745	0	ENST00000358026.2:c.548A>T	p.Gln183Leu	p.Q183L	ENST00000358026	NM_001128849.1	183	cAg/cTg	4/36	1	2	FACETS	0.285	0.247	0.326	0.285	0.247	0.326	SUBCLONAL	1	TRUE	1	0.500679865083911	2		745	953	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123710	11123710	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	243	626	0	ENST00000358026.2:c.2360T>C	p.Ile787Thr	p.I787T	ENST00000358026	NM_001128849.1	787	aTc/aCc	16/36	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.500679865083911	2		626	927	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297972	15297972	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1433631796	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	261	731	0	ENST00000263388.2:c.1784G>A	p.Gly595Asp	p.G595D	ENST00000263388	NM_000435.2	595	gGc/gAc	11/33	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.500679865083911	2		731	1008	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044299	128044299	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	150	467	0	ENST00000285398.2:c.1322A>T	p.Asp441Val	p.D441V	ENST00000285398	NM_000122.1	441	gAt/gTt	8/15	1	2	FACETS	0.96	0.881	1	0.96	0.881	1	CLONAL	1	TRUE	1	0.500679865083911	2		467	624	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098674	178098802	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTTGCTCAGTGTTTCCTTAAACCTGCCATAACTTTCCCAAGAACTGAGTACTCTGTACCTGGGAGTAGTTGGCAGATCCACTGGTTTCTGACTGGATGTGCTGGGCTGGCTGAATTGGGAGAAATTCA	CCTTGCTCAGTGTTTCCTTAAACCTGCCATAACTTTCCCAAGAACTGAGTACTCTGTACCTGGGAGTAGTTGGCAGATCCACTGGTTTCTGACTGGATGTGCTGGGCTGGCTGAATTGGGAGAAATTCA	-	novel	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	87	203	0	ENST00000397062.3:c.243_312+59del		p.X81_splice	ENST00000397062	NM_006164.4	81		2/5	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.500679865083911	2		203	288	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47108579	47108579	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	152	429	0	ENST00000409792.3:c.6090A>C	p.Gln2030His	p.Q2030H	ENST00000409792	NM_014159.6	2030	caA/caC	13/21	1	2	FACETS	0.842	0.772	0.916	0.842	0.772	0.916	CLONAL	1	TRUE	1	0.500679865083911	2		429	721	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205687	128205687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	207	538	1	ENST00000341105.2:c.188C>T	p.Pro63Leu	p.P63L	ENST00000341105	NM_032638.4	63	cCc/cTc	2/6	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.500679865083911	2		539	786	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164835	106164835	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	185	473	0	ENST00000380013.4:c.3703G>T	p.Gly1235Ter	p.G1235*	ENST00000380013	NM_001127208.2	1235	Gga/Tga	6/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.500679865083911	2		473	704	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251948	153251948	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	116	572	0	ENST00000281708.4:c.1058G>A	p.Ser353Asn	p.S353N	ENST00000281708	NM_033632.3	353	aGt/aAt	7/12	0.202397017318161	4	FACETS	1	0.953	1	0.545	0.492	0.601	INDETERMINATE	1	TRUE	2	0.500679865083911	4		572	638	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642452	117642452	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	199	632	0	ENST00000368508.3:c.5747T>C	p.Val1916Ala	p.V1916A	ENST00000368508	NM_002944.2	1916	gTa/gCa	35/43	1	2	FACETS	0.945	0.877	1	0.945	0.877	1	CLONAL	1	TRUE	1	0.500679865083911	2		632	841	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222547	157222547	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	195	584	0	ENST00000346085.5:c.1814A>G	p.Tyr605Cys	p.Y605C	ENST00000346085	NM_020732.3	605	tAc/tGc	4/20	1	2	FACETS	0.902	0.835	0.97	0.902	0.835	0.97	CLONAL	1	TRUE	1	0.500679865083911	2		584	864	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848534	151848534	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	111	445	0	ENST00000262189.6:c.12659del	p.Leu4220Ter	p.L4220*	ENST00000262189	NM_170606.2	4220	tTg/tg	50/59	1	2	FACETS	0.781	0.704	0.861	0.781	0.704	0.861	SUBCLONAL	1	TRUE	1	0.500679865083911	2		445	568	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243893	53243893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1284574780	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	298	719	2	ENST00000375401.3:c.1100G>A	p.Arg367Gln	p.R367Q	ENST00000375401	NM_004187.3	367	cGg/cAg	8/26	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.500679865083911	2		721	993	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540061	187540061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530048131	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	144	367	0	ENST00000441802.2:c.7679C>T	p.Ala2560Val	p.A2560V	ENST00000441802	NM_005245.3	2560	gCg/gTg	10/27	0.202397017318161	4	FACETS	1	0.987	1	0.717	0.656	0.78	INDETERMINATE	1	TRUE	2	0.500679865083911	4		367	602	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542351	187542351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	99	352	0	ENST00000441802.2:c.5389G>A	p.Ala1797Thr	p.A1797T	ENST00000441802	NM_005245.3	1797	Gct/Act	10/27	0.202397017318161	4	FACETS	1	0.975	1	0.645	0.579	0.715	INDETERMINATE	1	TRUE	2	0.500679865083911	4		352	460	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829005	128829005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	28	77	0	ENST00000249373.3:c.13C>T	p.Arg5Cys	p.R5C	ENST00000249373	NM_005631.4	5	Cgc/Tgc	1/12	1	2	FACETS	0.94	0.765	1	0.94	0.765	1	CLONAL	1	TRUE	1	0.500679865083911	2		77	119	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650611	48650611	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	66	593	6	ENST00000376670.3:c.581T>C	p.Leu194Pro	p.L194P	ENST00000376670	NM_002049.3	194	cTc/cCc	3/6	1	2	FACETS	0.311	0.269	0.356	0.311	0.269	0.356	SUBCLONAL	1	TRUE	1	0.500679865083911	2		599	849	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356450	70356450	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	209	719	2	ENST00000374080.3:c.5345G>T	p.Arg1782Leu	p.R1782L	ENST00000374080		1782	cGc/cTc	37/45	1	2	FACETS	0.844	0.784	0.907	0.844	0.784	0.907	CLONAL	1	TRUE	1	0.500679865083911	2		721	989	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954299	48954299	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs1395304450	NA	P-0028269-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	384	390	0	ENST00000267163.4:c.1422-2A>T		p.X474_splice	ENST00000267163	NM_000321.2	474			0.574205512665911	3	FACETS	0.923	0.888	0.957	0.923	0.888	0.957	CLONAL	3	TRUE	0	0.574205512665911	3		390	622	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649921	88649922	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028269-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	113	606	1	ENST00000372037.3:c.176dup	p.Leu59PhefsTer12	p.L59Ffs*12	ENST00000372037	NM_004329.2	57	cct/ccTt	4/13	0.487191962778217	2	FACETS	0.77	0.696	0.848	0.385	0.348	0.424	SUBCLONAL	1	TRUE	0	0.574205512665911	2		607	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577108	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCCAGGAC	CTCCCAGGAC	-	novel	NA	P-0028269-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	511	917	0	ENST00000269305.4:c.830_839del	p.Cys277Ter	p.C277*	ENST00000269305	NM_001126112.2	277	tGTCCTGGGAGa/ta	8/11	0.415247541741834	4	FACETS	1	0.991	1	0.805	0.778	0.832	CLONAL	3	TRUE	0	0.574205512665911	4		917	870	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110593	8110593	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028269-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	390	850	0	ENST00000585124.1:c.299A>G	p.His100Arg	p.H100R	ENST00000585124	NM_004217.3	100	cAt/cGt	5/9	0.415247541741834	4	FACETS	1	0.985	1	0.788	0.757	0.819	CLONAL	3	TRUE	0	0.574205512665911	4		850	678	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082788	16082788	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028269-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	60	144	0	ENST00000281043.3:c.602A>T	p.Glu201Val	p.E201V	ENST00000281043	NM_005378.4	201	gAg/gTg	2/3	0.530777533800973	3	FACETS	0.868	0.766	0.973	0.868	0.766	0.973	CLONAL	2	TRUE	1	0.574205512665911	3		144	155	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387123	31387123	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028269-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	297	748	0	ENST00000328111.2:c.1748G>T	p.Gly583Val	p.G583V	ENST00000328111	NM_006892.3	583	gGc/gTc	16/23	0.13392987765901	5	FACETS	1	0.989	1	0.783	0.74	0.826	INDETERMINATE	2	TRUE	2	0.574205512665911	5		748	820	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012711	36012711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028269-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	111	144	0	ENST00000358208.4:c.155C>T	p.Ala52Val	p.A52V	ENST00000358208		52	gCg/gTg	2/12	0.13392987765901	5	FACETS	1	0.966	1	1	0.966	1	INDETERMINATE	3	TRUE	2	0.574205512665911	5		144	220	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262307	46262307	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028269-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	182	830	0	ENST00000371998.3:c.891C>G	p.Ile297Met	p.I297M	ENST00000371998		297	atC/atG	9/23	0.13392987765901	5	FACETS	1	0.982	1	0.407	0.375	0.44	INDETERMINATE	1	TRUE	2	0.574205512665911	5		830	967	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200963	108200963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	44	404	0	ENST00000278616.4:c.7330G>A	p.Glu2444Lys	p.E2444K	ENST00000278616	NM_000051.3	2444	Gag/Aag	50/63	1	2	FACETS	0.15	0.125	0.178	0.15	0.125	0.178	SUBCLONAL	1	TRUE	1	0.92	2		404	637	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437565	49437565	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	1847	549	0	ENST00000301067.7:c.5320G>C	p.Glu1774Gln	p.E1774Q	ENST00000301067	NM_003482.3	1774	Gaa/Caa	23/54	0.3	20	FACETS	1	0.995	1			1	INDETERMINATE	13	TRUE	NA	0.92	20		549	2780	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437706	49437723	+	inframe_deletion	In_Frame_Del	DEL	TGTTGCTTCTTCTTCTCA	TGTTGCTTCTTCTTCTCA	-	novel	NA	P-0028361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1348	2041	694	0	ENST00000301067.7:c.5247_5264del	p.Asp1749_Gln1755delinsGlu	p.D1749_Q1755delinsE	ENST00000301067	NM_003482.3	1749	gaTGAGAAGAAGAAGCAACAg/gag	22/54	0.3	20	FACETS	1	0.991	1			1	INDETERMINATE	12	TRUE	NA	0.92	20		694	3389	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81941304	81941304	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	86	647	0	ENST00000359376.3:c.1482C>G	p.His494Gln	p.H494Q	ENST00000359376	NM_002661.3	494	caC/caG	16/33	1	2	FACETS	0.179	0.158	0.202	0.179	0.158	0.202	SUBCLONAL	1	TRUE	1	0.92	2		647	1043	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0028419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	306	436	1	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	0.708542536360849	2		437	853	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520006	NA	P-0028419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	470	729	0	ENST00000269305.4:c.821T>G	p.Val274Gly	p.V274G	ENST00000269305	NM_001126112.2	274	gTt/gGt	8/11	0.708542536360849	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.708542536360849	1		729	815	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908797	101908827	+	frameshift_variant	Frame_Shift_Del	DEL	CATAAATATGAAACATTTTGAATCCTTCAAA	CATAAATATGAAACATTTTGAATCCTTCAAA	-	novel	NA	P-0028419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	230	400	0	ENST00000374994.4:c.1162_1192del	p.Ile388ValfsTer9	p.I388Vfs*9	ENST00000374994	NM_004612.2	387	tcCATAAATATGAAACATTTTGAATCCTTCAAA/tc	7/9	0.708542536360849	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.708542536360849	1		400	411	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15943741	15944309	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTTTCAATCTTACCTGACGTAGTAACTGCTGGCAGATTAAAGATCTCAGTTCCTGGCTGAGCAGCTGCTATATTTAAGCAAACATTCAAGTTAATTAAGATGTGATAATCATATATACCAAACTAAAGTCTCAAAAAATTCCTATAATAAAATTAATCTTTTTATTTTTCATGATCTCAACCTTTATTTCTCACCCATTAAGTGAAGATAAAATGGAAGTATTTTTTTTTTTTGAGACAGGGTCTCACTCTGTTGCCCAGGCTATTTTTAAAGGGAAATCAGGAAATAGGTAAGGTAGGAACATCAAAAGAAGAGCAATAAGCTGTGTGCAGTGGTGCACTCCTAGTCCCCCAGCTACTCAGCAGGCTGAGGCGGTAGGACTGCTTGAGCATAGGAATTTGAGGCCAGCCTGGGCAACACAGTGAGACTCTCCCATCTGTTTACCAAAAATAAATAAATAAATAAAAAAAGAAGCAGTGTAACCCAGAAAAGGGAAAGGAACTTTGCACTGCTGGAGAAAAACAAATAGGAAAATGCTGTTCTCAGAACAGGAACCAAGGCTTTCTGA	CTTTTCAATCTTACCTGACGTAGTAACTGCTGGCAGATTAAAGATCTCAGTTCCTGGCTGAGCAGCTGCTATATTTAAGCAAACATTCAAGTTAATTAAGATGTGATAATCATATATACCAAACTAAAGTCTCAAAAAATTCCTATAATAAAATTAATCTTTTTATTTTTCATGATCTCAACCTTTATTTCTCACCCATTAAGTGAAGATAAAATGGAAGTATTTTTTTTTTTTGAGACAGGGTCTCACTCTGTTGCCCAGGCTATTTTTAAAGGGAAATCAGGAAATAGGTAAGGTAGGAACATCAAAAGAAGAGCAATAAGCTGTGTGCAGTGGTGCACTCCTAGTCCCCCAGCTACTCAGCAGGCTGAGGCGGTAGGACTGCTTGAGCATAGGAATTTGAGGCCAGCCTGGGCAACACAGTGAGACTCTCCCATCTGTTTACCAAAAATAAATAAATAAATAAAAAAAGAAGCAGTGTAACCCAGAAAAGGGAAAGGAACTTTGCACTGCTGGAGAAAAACAAATAGGAAAATGCTGTTCTCAGAACAGGAACCAAGGCTTTCTGA	-	novel	NA	P-0028420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	28	403	0	ENST00000268712.3:c.6680-501_6733+14del		p.X2227_splice	ENST00000268712	NM_006311.3	2227		43/46	1	2	FACETS	0.324	0.258	0.399	0.324	0.258	0.399	SUBCLONAL	1	TRUE	1	0.374198153034092	2		403	462	SUCCESS
APC	324	MSKCC	GRCh37	5	112177398	112177734	+	frameshift_variant	Frame_Shift_Del	DEL	ATGACCTGTTGCAGGAATGTATAAGCTCCGCAATGCCAAAAAAGAAAAAGCCTTCAAGACTCAAGGGTGATAATGAAAAACATAGTCCCAGAAATATGGGTGGCATATTAGGTGAAGATCTGACACTTGATTTGAAAGATATACAGAGACCAGATTCAGAACATGGTCTATCCCCTGATTCAGAAAATTTTGATTGGAAAGCTATTCAGGAAGGTGCAAATTCCATAGTAAGTAGTTTACATCAAGCTGCTGCTGCTGCATGTTTATCTAGACAAGCTTCGTCTGATTCAGATTCCATCCTTTCCCTGAAATCAGGAATCTCTCTGGGATCACCATT	ATGACCTGTTGCAGGAATGTATAAGCTCCGCAATGCCAAAAAAGAAAAAGCCTTCAAGACTCAAGGGTGATAATGAAAAACATAGTCCCAGAAATATGGGTGGCATATTAGGTGAAGATCTGACACTTGATTTGAAAGATATACAGAGACCAGATTCAGAACATGGTCTATCCCCTGATTCAGAAAATTTTGATTGGAAAGCTATTCAGGAAGGTGCAAATTCCATAGTAAGTAGTTTACATCAAGCTGCTGCTGCTGCATGTTTATCTAGACAAGCTTCGTCTGATTCAGATTCCATCCTTTCCCTGAAATCAGGAATCTCTCTGGGATCACCATT	-	novel	NA	P-0028420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	113	337	0	ENST00000257430.4:c.6107_6443del	p.Asp2036ValfsTer21	p.D2036Vfs*21	ENST00000257430	NM_000038.5	2036	gATGACCTGTTGCAGGAATGTATAAGCTCCGCAATGCCAAAAAAGAAAAAGCCTTCAAGACTCAAGGGTGATAATGAAAAACATAGTCCCAGAAATATGGGTGGCATATTAGGTGAAGATCTGACACTTGATTTGAAAGATATACAGAGACCAGATTCAGAACATGGTCTATCCCCTGATTCAGAAAATTTTGATTGGAAAGCTATTCAGGAAGGTGCAAATTCCATAGTAAGTAGTTTACATCAAGCTGCTGCTGCTGCATGTTTATCTAGACAAGCTTCGTCTGATTCAGATTCCATCCTTTCCCTGAAATCAGGAATCTCTCTGGGATCACCATTt/gt	16/16	0.375386974432402	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.374198153034092	1		337	389	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0028421-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	589	558	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.620524692372116	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.620524692372116	2		558	898	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416526	49416526	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028421-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	324	670	0	ENST00000301067.7:c.16185G>A	p.Trp5395Ter	p.W5395*	ENST00000301067	NM_003482.3	5395	tgG/tgA	51/54	0.620524692372116	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.620524692372116	1		670	664	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885939	111885939	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028421-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	267	600	2	ENST00000341259.2:c.1561C>A	p.Pro521Thr	p.P521T	ENST00000341259	NM_005475.2	521	Ccc/Acc	8/8	1	2	FACETS	0.962	0.904	1	0.962	0.904	1	CLONAL	1	TRUE	1	0.620524692372116	2		602	895	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553441	106553441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746535819	NA	P-0028421-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	174	355	0	ENST00000369096.4:c.1406C>T	p.Ser469Leu	p.S469L	ENST00000369096	NM_001198.3	469	tCg/tTg	5/7	1	2	FACETS	0.991	0.918	1	0.991	0.918	1	CLONAL	1	TRUE	1	0.620524692372116	2		355	566	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	110	376	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.687	0.621	0.755			1	INDETERMINATE	1	FALSE	NA	0.753768775105718	2		376	425	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0028454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	104	354	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.421	0.377	0.467	0.421	0.377	0.467	SUBCLONAL	1	FALSE	1	0.753768775105718	2		354	656	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652198	36652199	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0028454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	164	534	0	ENST00000244741.5:c.322dup	p.Glu108GlyfsTer21	p.E108Gfs*21	ENST00000244741	NM_000389.4	107	gag/gaGg	2/3	NA	2	FACETS	0.427	0.391	0.464			1	INDETERMINATE	1	FALSE	NA	0.753768775105718	2		534	1020	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333335	70333335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	228	608	2	ENST00000373644.4:c.1240G>A	p.Asp414Asn	p.D414N	ENST00000373644	NM_030625.2	414	Gac/Aac	2/12	1	2	FACETS	0.56	0.522	0.6	0.56	0.522	0.6	SUBCLONAL	1	FALSE	1	0.753768775105718	2		610	1080	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254211	133254211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1166189035	NA	P-0028454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	164	503	3	ENST00000320574.5:c.673G>A	p.Asp225Asn	p.D225N	ENST00000320574	NM_006231.2	225	Gat/Aat	7/49	1	2	FACETS	0.485	0.445	0.527	0.485	0.445	0.527	SUBCLONAL	1	FALSE	1	0.753768775105718	2		506	897	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212565	36212566	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0028454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	240	651	2	ENST00000222270.7:c.2316_2317delinsTT	p.Glu773Ter	p.E773*	ENST00000222270	NM_014727.1	772	ctGGaa/ctTTaa	3/37	1	2	FACETS	0.525	0.489	0.562	0.525	0.489	0.562	SUBCLONAL	1	FALSE	1	0.753768775105718	2		653	1213	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779810	135779810	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	139	477	0	ENST00000298552.3:c.2029A>G	p.Thr677Ala	p.T677A	ENST00000298552	NM_001162426.1	677	Acc/Gcc	16/23	1	2	FACETS	0.521	0.475	0.569	0.521	0.475	0.569	SUBCLONAL	1	FALSE	1	0.753768775105718	2		477	708	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0028456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	40	387	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.955	0.797	1	0.955	0.797	1	CLONAL	1	TRUE	1	0.272735775626165	2		387	307	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0028456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	104	798	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	1	2	FACETS	0.773	0.691	0.86	0.773	0.691	0.86	SUBCLONAL	1	TRUE	1	0.272735775626165	2		798	987	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799108	45799108	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765123255	NA	P-0028456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	55	955	1	ENST00000450313.1:c.325C>T	p.Arg109Trp	p.R109W	ENST00000450313	NM_012222.2	109	Cgg/Tgg	3/16	1	2	FACETS	0.444	0.379	0.516	0.444	0.379	0.516	SUBCLONAL	1	TRUE	1	0.272735775626165	2		956	908	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162016	22162016	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	38	589	0	ENST00000215832.6:c.239A>T	p.His80Leu	p.H80L	ENST00000215832	NM_002745.4	80	cAt/cTt	2/9	1	2	FACETS	0.585	0.484	0.699	0.585	0.484	0.699	SUBCLONAL	1	TRUE	1	0.272735775626165	2		589	476	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569689	41569689	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	32	489	3	ENST00000263253.7:c.4680G>T	p.Lys1560Asn	p.K1560N	ENST00000263253	NM_001429.3	1560	aaG/aaT	29/31	1	2	FACETS	0.458	0.371	0.557	0.458	0.371	0.557	SUBCLONAL	1	TRUE	1	0.272735775626165	2		492	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0028479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	308	635	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.824670916877681	2	FACETS	0.996	0.967	1	0.996	0.967	1	CLONAL	2	TRUE	0	0.826463060380888	2		635	374	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0028479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	117	322	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	0.826463060380888	2	FACETS	0.963	0.913	1	0.963	0.913	1	CLONAL	2	TRUE	0	0.826463060380888	2		322	147	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974744	21974775	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTCCTCTACCCGACCCCGGGCCGCGGCCGT	ACCTCCTCTACCCGACCCCGGGCCGCGGCCGT	-	novel	NA	P-0028479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	127	297	0	ENST00000304494.5:c.52_83del	p.Thr18AlafsTer15	p.T18Afs*15	ENST00000304494	NM_000077.4	18	ACGGCCGCGGCCCGGGGTCGGGTAGAGGAGGTg/g	1/3	0.656110317055198	3	FACETS	0.905	0.86	0.946	1	0.991	1	CLONAL	3	TRUE	1	0.826463060380888	3		297	160	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611131	100611131	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782338603	NA	P-0028479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	130	261	0	ENST00000308731.7:c.1475G>A	p.Arg492His	p.R492H	ENST00000308731	NM_000061.2	492	cGc/cAc	15/19	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.826463060380888	1		261	156	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88676928	88676928	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	18	336	0	ENST00000372037.3:c.713G>C	p.Arg238Pro	p.R238P	ENST00000372037	NM_004329.2	238	cGg/cCg	9/13	0.433983797929887	3	FACETS	0.293	0.221	0.378	0.098	0.073	0.126	INDETERMINATE	1	TRUE	0	0.826463060380888	3		336	210	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671952	30671952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200530869	NA	P-0028479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	130	647	1	ENST00000376406.3:c.5008G>A	p.Val1670Ile	p.V1670I	ENST00000376406	NM_014641.2	1670	Gtc/Atc	10/15	0.826757676662218	3	FACETS	0.944	0.862	1	0.472	0.431	0.515	CLONAL	1	TRUE	1	0.826463060380888	3		648	471	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552789	106552789	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	59	606	0	ENST00000369096.4:c.754G>A	p.Glu252Lys	p.E252K	ENST00000369096	NM_001198.3	252	Gaa/Aaa	5/7	0.266293662383128	5	FACETS	0.941	0.814	1	0.188	0.162	0.216	INDETERMINATE	1	TRUE	0	0.826463060380888	5		606	340	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0028486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	149	1128	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.305474137793161	2		1128	803	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0028486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	139	547	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.228269884503953	1	FACETS	0.981	0.894	1	0.981	0.894	1	CLONAL	1	TRUE	0	0.305474137793161	1		547	786	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578281	7578281	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	136	536	0	ENST00000269305.4:c.568C>G	p.Pro190Ala	p.P190A	ENST00000269305	NM_001126112.2	190	Cct/Gct	6/11	0.228269884503953	1	FACETS	0.971	0.884	1	0.971	0.884	1	CLONAL	1	TRUE	0	0.305474137793161	1		536	777	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017604	112017604	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	79	590	0	ENST00000368678.4:c.909G>T	p.Met303Ile	p.M303I	ENST00000368678		303	atG/atT	9/13	1	2	FACETS	0.693	0.609	0.784	0.693	0.609	0.784	SUBCLONAL	1	TRUE	1	0.305474137793161	2		590	746	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0028511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	398	595	0	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	0.669297294983286	2	FACETS	0.985	0.95	1	0.985	0.95	1	CLONAL	2	TRUE	0	0.669297294983286	2		595	604	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665237	117665237	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0028511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	97	279	0	ENST00000368508.3:c.4510A>T	p.Lys1504Ter	p.K1504*	ENST00000368508	NM_002944.2	1504	Aaa/Taa	27/43	0.66792361988012	3	FACETS	0.879	0.788	0.975	0.44	0.394	0.488	CLONAL	1	TRUE	1	0.669297294983286	3		279	440	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0028512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	45	535	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.388896437252708	3	FACETS	1	0.932	1	0.584	0.498	0.676	CLONAL	1	TRUE	1	0.551916990498142	3		535	178	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0028512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	46	436	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.551916990498142	4	FACETS	1	0.896	1	1	0.896	1	CLONAL	2	TRUE	2	0.551916990498142	4		437	124	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0028512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	17	317	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.78	0.595	0.989	0.78	0.595	0.989	CLONAL	1	TRUE	1	0.551916990498142	2		317	79	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542810	187542810	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	22	511	0	ENST00000441802.2:c.4930A>G	p.Ser1644Gly	p.S1644G	ENST00000441802	NM_005245.3	1644	Agt/Ggt	10/27	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.551916990498142	2		511	67	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175857	24175859	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs875989800	NA	P-0028512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	63	585	0	ENST00000263121.7:c.1091_1093del	p.Lys364del	p.K364del	ENST00000263121	NM_003073.3	362	gAGAag/gag	8/9	0.469341079848389	3	FACETS	1	0.955	1	0.759	0.678	0.839	CLONAL	2	TRUE	0	0.551916990498142	3		585	128	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400905	72400905	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	13	490	0	ENST00000357731.5:c.266C>A	p.Pro89His	p.P89H	ENST00000357731	NM_173808.2	89	cCt/cAt	2/7	0.155102996867057	2	FACETS	0.841	0.617	1	0.421	0.308	0.549	INDETERMINATE	1	TRUE	0	0.551916990498142	2		490	56	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	27	786	0	ENST00000269305.4:c.377A>C	p.Tyr126Ser	p.Y126S	ENST00000269305	NM_001126112.2	126	tAc/tCc	5/11	0.388896437252708	3	FACETS	1	0.931	1	0.678	0.554	0.813	CLONAL	1	TRUE	1	0.551916990498142	3		786	92	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796215	45796215	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	rs1064793198	NA	P-0028512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	23	624	0	ENST00000450313.1:c.1491T>G	p.Tyr497Ter	p.Y497*	ENST00000450313	NM_012222.2	497	taT/taG	15/16	0.155102996867057	2	FACETS	1	0.896	1	0.595	0.48	0.719	INDETERMINATE	1	TRUE	0	0.551916990498142	2		624	70	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994738	73994738	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	33	830	0	ENST00000318443.5:c.222G>C	p.Gln74His	p.Q74H	ENST00000318443	NM_001024736.1	74	caG/caC	3/10	0.548432405183153	2	FACETS	0.913	0.757	1	0.456	0.378	0.541	CLONAL	1	TRUE	0	0.551916990498142	2		830	131	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827504	72827504	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	41	665	0	ENST00000268489.5:c.9077G>T	p.Cys3026Phe	p.C3026F	ENST00000268489	NM_006885.3	3026	tGc/tTc	9/10	0.548432405183153	2	FACETS	0.99	0.867	1	0.99	0.867	1	CLONAL	2	TRUE	0	0.551916990498142	2		665	75	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218440	36218440	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	29	495	0	ENST00000222270.7:c.4219G>C	p.Gly1407Arg	p.G1407R	ENST00000222270	NM_014727.1	1407	Ggg/Cgg	16/37	0.551916990498142	9	FACETS	0.718	0.576	0.88	0.103	0.082	0.126	SUBCLONAL	1	TRUE	2	0.551916990498142	9		495	429	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096153	71096153	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	72	426	0	ENST00000318789.4:c.604C>G	p.Gln202Glu	p.Q202E	ENST00000318789	NM_032682.5	202	Caa/Gaa	10/21	0.469341079848389	3	FACETS	0.895	0.813	0.975	0.895	0.813	0.975	CLONAL	3	TRUE	0	0.551916990498142	3		426	124	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0028513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	610	710	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.357789840633057	3	FACETS	0.95	0.917	0.982	0.95	0.917	0.982	CLONAL	3	TRUE	0	0.433559755507275	3		710	1202	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0028515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	819	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.718659819885499	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	4	TRUE	0	0.718659819885499	4		511	960	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857692	9857692	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1389208302	NA	P-0028515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	153	401	0	ENST00000330684.3:c.3709G>A	p.Asp1237Asn	p.D1237N	ENST00000330684	NM_001134407.1	1237	Gat/Aat	13/13	0.718659819885499	6	FACETS	0.823	0.751	0.899	0.206	0.187	0.225	CLONAL	1	TRUE	2	0.718659819885499	6		401	1261	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060782	38060784	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0028515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1399	369	980	0	ENST00000250448.2:c.1205_1207del	p.Ile402del	p.I402del	ENST00000250448	NM_004496.3	402	aTCAac/aac	2/2	0.718659819885499	4	FACETS	0.998	0.944	1	0.499	0.472	0.527	CLONAL	1	TRUE	2	0.718659819885499	4		980	1768	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692892	89692892	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	472	403	0	ENST00000371953.3:c.376G>C	p.Ala126Pro	p.A126P	ENST00000371953	NM_000314.4	126	Gct/Cct	5/9	0.718659819885499	3	FACETS	0.994	0.968	1	0.994	0.968	1	CLONAL	3	TRUE	0	0.718659819885499	3		403	599	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80024744	80024744	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	217	597	0	ENST00000265081.6:c.1528C>T	p.Leu510Phe	p.L510F	ENST00000265081	NM_002439.4	510	Ctc/Ttc	10/24	0.718659819885499	4	FACETS	0.935	0.869	1	0.468	0.434	0.502	CLONAL	1	TRUE	2	0.718659819885499	4		597	1110	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931682	39931682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1275	259	713	1	ENST00000378444.4:c.2917G>A	p.Val973Met	p.V973M	ENST00000378444	NM_001123385.1	973	Gtg/Atg	4/15	0.712777967281929	5	FACETS	0.976	0.912	1			1	CLONAL	1	TRUE	NA	0.718659819885499	5		714	1534	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0028516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	315	609	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.424426623281759	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.424426623281759	2		610	600	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220333	98220333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138458710	NA	P-0028516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	111	424	0	ENST00000331920.6:c.3130G>A	p.Ala1044Thr	p.A1044T	ENST00000331920	NM_000264.3	1044	Gct/Act	18/24	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.424426623281759	2		424	437	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195838	102195838	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	55	403	0	ENST00000263464.3:c.598G>A	p.Gly200Arg	p.G200R	ENST00000263464	NM_001165.4	200	Gga/Aga	2/9	0.424426623281759	4	FACETS	0.669	0.572	0.775	0.334	0.286	0.388	SUBCLONAL	1	TRUE	2	0.424426623281759	4		403	552	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27220088	27220088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760667841	NA	P-0028516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	115	699	0	ENST00000380036.4:c.3145G>A	p.Glu1049Lys	p.E1049K	ENST00000380036	NM_000459.3	1049	Gag/Aag	21/23	0.424426623281759	4	FACETS	0.871	0.784	0.964			1	CLONAL	1	TRUE	NA	0.424426623281759	4		699	886	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846398	128846398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879255280	NA	P-0028517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	200	698	0	ENST00000249373.3:c.1234C>T	p.Leu412Phe	p.L412F	ENST00000249373	NM_005631.4	412	Ctc/Ttc	6/12	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.54	2		698	695	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0028520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	103	493	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.247695163835359	2		493	679	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1131691023	NA	P-0028520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	73	620	0	ENST00000269305.4:c.470T>A	p.Val157Asp	p.V157D	ENST00000269305	NM_001126112.2	157	gTc/gAc	5/11	1	2	FACETS	0.776	0.677	0.882	0.776	0.677	0.882	SUBCLONAL	1	TRUE	1	0.247695163835359	2		620	760	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054986	176054986	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	63	623	0	ENST00000367669.3:c.1067G>T	p.Arg356Ile	p.R356I	ENST00000367669	NM_022457.5	356	aGa/aTa	10/20	1	2	FACETS	0.728	0.629	0.836	0.728	0.629	0.836	SUBCLONAL	1	TRUE	1	0.247695163835359	2		623	699	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42002898	42002898	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	25	334	0	ENST00000219905.7:c.2435C>A	p.Ser812Ter	p.S812*	ENST00000219905	NM_001164273.1	812	tCa/tAa	8/24	0.247695163835359	1	FACETS	0.413	0.325	0.515	0.413	0.325	0.515	SUBCLONAL	1	TRUE	0	0.247695163835359	1		334	428	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625652	1625652	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs533848977	NA	P-0028520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	42	657	0	ENST00000344749.5:c.422C>T	p.Ser141Leu	p.S141L	ENST00000344749	NM_001136139.2	141	tCg/tTg	7/19	1	2	FACETS	0.461	0.383	0.547	0.461	0.383	0.547	SUBCLONAL	1	TRUE	1	0.247695163835359	2		657	736	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290061	15290061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1376652903	NA	P-0028520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	60	690	0	ENST00000263388.2:c.3493G>A	p.Gly1165Ser	p.G1165S	ENST00000263388	NM_000435.2	1165	Ggc/Agc	22/33	1	2	FACETS	0.63	0.542	0.727	0.63	0.542	0.727	SUBCLONAL	1	TRUE	1	0.247695163835359	2		690	769	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483976	212483976	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	38	480	0	ENST00000342788.4:c.2227A>T	p.Thr743Ser	p.T743S	ENST00000342788	NM_005235.2	743	Act/Tct	19/28	1	2	FACETS	0.536	0.443	0.642	0.536	0.443	0.642	SUBCLONAL	1	TRUE	1	0.247695163835359	2		480	572	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968311	134968311	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs772031329	NA	P-0028520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	94	537	1	ENST00000398015.3:c.2824C>A	p.Leu942Met	p.L942M	ENST00000398015	NM_004441.4	942	Ctg/Atg	15/16	0.247695163835359	3	FACETS	1	0.976	1	0.68	0.606	0.759	CLONAL	1	TRUE	1	0.247695163835359	3		538	627	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196847	138196847	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs373331557	NA	P-0028520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	47	352	0	ENST00000237289.4:c.509A>G	p.Asn170Ser	p.N170S	ENST00000237289	NM_001270507.1	170	aAt/aGt	4/9	1	2	FACETS	0.75	0.633	0.879	0.75	0.633	0.879	SUBCLONAL	1	TRUE	1	0.247695163835359	2		352	506	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039709	47039709	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1556778444	NA	P-0028520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	23	250	1	ENST00000377604.3:c.1160+1G>T		p.X387_splice	ENST00000377604	NM_001204468.1	387			1	1	FACETS	0.486	0.378	0.61	0.486	0.378	0.61	SUBCLONAL	1	TRUE	0	0.247695163835359	1		251	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0028523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	205	635	1	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.3	1	FACETS	0.861	0.799	0.926	1	0.992	1	CLONAL	2	TRUE	0	0.22	1		636	963	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252066	226252066	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	83	206	0	ENST00000366813.1:c.14A>T	p.Lys5Met	p.K5M	ENST00000366813		5	aAg/aTg	1/3	0.159929492920574	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	0	0.22	2		206	347	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488649	212488652	+	frameshift_variant	Frame_Shift_Del	DEL	TATA	TATA	ATT	novel	NA	P-0028523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	70	416	0	ENST00000342788.4:c.2197_2200delinsAAT	p.Tyr733AsnfsTer12	p.Y733Nfs*12	ENST00000342788	NM_005235.2	733	TATAaa/AATaa	18/28	1	2	FACETS	0.831	0.723	0.947	0.831	0.723	0.947	CLONAL	1	TRUE	1	0.22	2		416	766	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524351	187524351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	81	413	1	ENST00000441802.2:c.11329G>A	p.Ala3777Thr	p.A3777T	ENST00000441802	NM_005245.3	3777	Gca/Aca	19/27	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.22	2		414	698	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0028525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	61	429	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.988	0.852	1	0.988	0.852	1	CLONAL	1	TRUE	1	0.19	2		429	650	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0028525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	15	456	3	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.227	0.164	0.302	0.227	0.164	0.302	SUBCLONAL	1	TRUE	1	0.19	2		459	697	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0028525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	42	384	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.638	0.531	0.757	0.638	0.531	0.757	SUBCLONAL	1	TRUE	1	0.19	2		384	693	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0028525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	14	239	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.366	0.263	0.491	0.366	0.263	0.491	SUBCLONAL	1	TRUE	1	0.19	2		239	403	SUCCESS
APC	324	MSKCC	GRCh37	5	112175358	112175358	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	69	242	0	ENST00000257430.4:c.4067C>A	p.Ser1356Ter	p.S1356*	ENST00000257430	NM_000038.5	1356	tCa/tAa	16/16	0.149017903997337	3	FACETS	0.97	0.848	1	0.647	0.565	0.734	CLONAL	2	TRUE	0	0.19	3		242	410	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953040	2953040	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141751925	NA	P-0028525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	63	521	2	ENST00000396946.4:c.2900G>A	p.Arg967His	p.R967H	ENST00000396946	NM_032415.4	967	cGc/cAc	22/25	1	2	FACETS	0.847	0.731	0.973	0.847	0.731	0.973	CLONAL	1	TRUE	1	0.19	2		523	783	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244163	5244163	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373884789	NA	P-0028525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	39	466	2	ENST00000357368.4:c.1319C>T	p.Ala440Val	p.A440V	ENST00000357368	NM_002850.3	440	gCg/gTg	11/38	1	2	FACETS	0.612	0.506	0.731	0.612	0.506	0.731	SUBCLONAL	1	TRUE	1	0.19	2		468	671	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462971	120462971	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1317975644	NA	P-0028525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	55	407	0	ENST00000256646.2:c.5360G>A	p.Arg1787Gln	p.R1787Q	ENST00000256646	NM_024408.3	1787	cGg/cAg	30/34	1	2	FACETS	0.983	0.841	1	0.983	0.841	1	CLONAL	1	TRUE	1	0.19	2		407	589	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0028528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	218	531	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.485857656103875	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.485857656103875	1		531	667	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441246	52441246	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	367	486	0	ENST00000460680.1:c.524C>G	p.Pro175Arg	p.P175R	ENST00000460680	NM_004656.3	175	cCt/cGt	7/17	0.485857656103875	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.485857656103875	2		486	747	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0028531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	90	538	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.328094831701497	1	FACETS	0.859	0.764	0.959	0.859	0.764	0.959	CLONAL	1	TRUE	0	0.328094831701497	1		538	534	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243777010	243777010	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200428825	NA	P-0028531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	90	496	0	ENST00000263826.5:c.659G>A	p.Arg220His	p.R220H	ENST00000263826	NM_005465.4	220	cGt/cAt	7/13	0.27471965439165	3	FACETS	0.946	0.84	1	0.473	0.42	0.53	CLONAL	1	TRUE	1	0.328094831701497	3		496	675	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0028531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	91	478	0	ENST00000269305.4:c.97-1G>A		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.328094831701497	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	0	0.328094831701497	1		478	454	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075564	8075564	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	93	450	0	ENST00000377482.5:c.116A>T	p.Glu39Val	p.E39V	ENST00000377482	NM_018948.3	39	gAg/gTg	2/4	1	2	FACETS	0.958	0.853	1	0.958	0.853	1	CLONAL	1	TRUE	1	0.328094831701497	2		450	592	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603041	48603041	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	71	369	0	ENST00000342988.3:c.1342del	p.Gln448SerfsTer28	p.Q448Sfs*28	ENST00000342988	NM_005359.5	448	Cag/ag	11/12	0.328094831701497	1	FACETS	0.859	0.753	0.973	0.859	0.753	0.973	CLONAL	1	TRUE	0	0.328094831701497	1		369	421	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459741	149459743	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0028531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	82	568	0	ENST00000286301.3:c.464_466del	p.Ser155del	p.S155del	ENST00000286301	NM_005211.3	155	tCCTtc/ttc	4/22	0.328094831701497	1	FACETS	0.65	0.573	0.732	0.65	0.573	0.732	SUBCLONAL	1	TRUE	0	0.328094831701497	1		568	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0028537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	16	535	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.115	0.084	0.152	0.115	0.084	0.152	SUBCLONAL	1	TRUE	1	0.36	2		535	776	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252994	36252995	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0028537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	75	401	0	ENST00000300305.3:c.367dup	p.Asp123GlyfsTer15	p.D123Gfs*15	ENST00000300305		123	gat/gGat	4/8	1	2	FACETS	0.671	0.588	0.76	0.671	0.588	0.76	SUBCLONAL	1	TRUE	1	0.36	2		401	621	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168811	56168811	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	89	306	0	ENST00000399503.3:c.1667del	p.Leu556Ter	p.L556*	ENST00000399503	NM_005921.1	555	gaT/ga	9/20	1	2	FACETS	0.872	0.775	0.976	0.872	0.775	0.976	CLONAL	1	TRUE	1	0.36	2		306	567	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259258	36259259	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	122	582	0	ENST00000300305.3:c.232dup	p.Met78AsnfsTer60	p.M78Nfs*60	ENST00000300305		78	atg/aAtg	3/8	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.36	2		582	631	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168490	56168491	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0028537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	68	124	0	ENST00000399503.3:c.1447dup	p.Arg483LysfsTer10	p.R483Kfs*10	ENST00000399503	NM_005921.1	482	-/A	8/20	1	2	FACETS	0.989	0.865	1	0.989	0.865	1	CLONAL	1	TRUE	1	0.36	2		124	382	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0028539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	415	441	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.631094723537294	5	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	2	0.631094723537294	5		441	822	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145549	24145549	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	41	600	0	ENST00000263121.7:c.568C>T	p.Arg190Trp	p.R190W	ENST00000263121	NM_003073.3	190	Cgg/Tgg	5/9	0.631094723537294	2	FACETS	0.187	0.155	0.222	0.093	0.077	0.111	SUBCLONAL	1	TRUE	0	0.631094723537294	2		600	696	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147532	61147532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543671237	NA	P-0028539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	14	44	0	ENST00000295025.8:c.937C>T	p.Arg313Cys	p.R313C	ENST00000295025	NM_002908.2	313	Cgc/Tgc	9/11	0.631094723537294	3	FACETS	0.941	0.698	1	0.471	0.349	0.609	CLONAL	1	TRUE	1	0.631094723537294	3		44	62	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298672	11298672	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	177	483	0	ENST00000361445.4:c.1789C>T	p.His597Tyr	p.H597Y	ENST00000361445	NM_004958.3	597	Cac/Tac	12/58	0.631094723537294	3	FACETS	1	0.955	1	0.523	0.483	0.565	CLONAL	1	TRUE	1	0.631094723537294	3		483	705	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122643	108122644	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	213	380	0	ENST00000278616.4:c.1688dup	p.Met563IlefsTer3	p.M563Ifs*3	ENST00000278616	NM_000051.3	563	atg/aTtg	11/63	0.631094723537294	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.631094723537294	2		380	335	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983229	7983229	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	160	519	0	ENST00000319144.4:c.785C>A	p.Thr262Asn	p.T262N	ENST00000319144	NM_001139.2	262	aCc/aAc	7/15	1	2	FACETS	0.964	0.89	1	0.964	0.89	1	CLONAL	1	TRUE	1	0.631094723537294	2		519	526	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39567819	39567819	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	131	282	0	ENST00000262039.4:c.575G>T	p.Trp192Leu	p.W192L	ENST00000262039	NM_002647.2	192	tGg/tTg	5/25	0.631094723537294	4	FACETS	0.786	0.719	0.855	0.786	0.719	0.855	SUBCLONAL	2	TRUE	2	0.631094723537294	4		282	431	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281421	142281421	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	321	530	0	ENST00000350721.4:c.823del	p.Glu275AsnfsTer3	p.E275Nfs*3	ENST00000350721	NM_001184.3	275	Gaa/aa	4/47	0.631094723537294	3	FACETS	0.908	0.863	0.953	0.908	0.863	0.953	CLONAL	2	TRUE	1	0.631094723537294	3		530	737	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0028540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	108	525	2	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.279877189911724	4	FACETS	0.908	0.831	0.986	0.908	0.831	0.986	CLONAL	4	TRUE	0	0.317254796463726	4		527	247	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030479	49030479	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	77	318	0	ENST00000267163.4:c.1959del	p.Val654CysfsTer4	p.V654Cfs*4	ENST00000267163	NM_000321.2	652	Aaa/aa	19/27	0.317254796463726	2	FACETS	0.904	0.813	0.997	1	0.977	1	CLONAL	3	TRUE	0	0.317254796463726	2		318	179	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534753	18534753	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	47	400	0	ENST00000266497.5:c.1811C>G	p.Pro604Arg	p.P604R	ENST00000266497		604	cCc/cGc	12/31	0.317254796463726	4	FACETS	0.92	0.786	1	0.92	0.786	1	CLONAL	2	TRUE	2	0.317254796463726	4		400	212	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472666	88472666	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0028540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	30	273	0	ENST00000360948.2:c.1890-1G>T		p.X630_splice	ENST00000360948	NM_001012338.2	630			0.311161413802133	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	2	TRUE	0	0.317254796463726	2		273	88	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912062	50912062	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	50	708	0	ENST00000440232.2:c.1796C>T	p.Ala599Val	p.A599V	ENST00000440232	NM_002691.3	599	gCc/gTc	15/27	0.089944998959371	4	FACETS	0.984	0.845	1	0.984	0.845	1	INDETERMINATE	2	TRUE	2	0.317254796463726	4		708	211	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190717454	190717454	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	27	348	0	ENST00000441310.2:c.773G>A	p.Ser258Asn	p.S258N	ENST00000441310	NM_000534.4	258	aGt/aAt	7/13	0.256057743045152	3	FACETS	1	0.847	1	0.355	0.285	0.434	CLONAL	1	TRUE	0	0.317254796463726	3		348	185	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528823	157528823	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	43	514	0	ENST00000346085.5:c.6548A>G	p.Gln2183Arg	p.Q2183R	ENST00000346085	NM_020732.3	2183	cAg/cGg	20/20	0.317254796463726	3	FACETS	0.827	0.701	0.962	0.827	0.701	0.962	CLONAL	2	TRUE	1	0.317254796463726	3		514	190	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239843	98239843	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	64	582	0	ENST00000331920.6:c.1489G>T	p.Ala497Ser	p.A497S	ENST00000331920	NM_000264.3	497	Gct/Tct	10/24	0.126509021944734	6	FACETS	0.986	0.866	1	0.986	0.866	1	INDETERMINATE	3	TRUE	3	0.317254796463726	6		582	223	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937697	44937697	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	73	277	0	ENST00000377967.4:c.2885A>T	p.Asn962Ile	p.N962I	ENST00000377967	NM_021140.2	962	aAt/aTt	19/29	0.317254796463726	2	FACETS	1	0.94	1			1	CLONAL	3	TRUE	NA	0.317254796463726	2		277	145	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771545	112771545	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	115	467	1	ENST00000369452.4:c.1718A>T	p.Lys573Met	p.K573M	ENST00000369452	NM_007373.3	573	aAg/aTg	9/9	0.599916660810952	3	FACETS	0.824	0.746	0.907	0.412	0.373	0.454	CLONAL	1	TRUE	1	0.718104996556118	3		468	528	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443679	29443679	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	149	619	0	ENST00000389048.3:c.3538G>C	p.Val1180Leu	p.V1180L	ENST00000389048	NM_004304.4	1180	Gtt/Ctt	23/29	0.623950481667372	4	FACETS	0.893	0.817	0.973	0.223	0.204	0.244	CLONAL	1	TRUE	0	0.718104996556118	4		619	798	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0028543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	39	467	0	ENST00000311936.3:c.180_181delinsAA	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggAAaa	3/5	1	2	FACETS	1	0.834	1	1	0.834	1	CLONAL	1	TRUE	1	0.14	2		467	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0028544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	237	537	3	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	0.61200350331044	2		540	768	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0028544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	132	441	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.983	0.899	1	0.983	0.899	1	CLONAL	1	TRUE	1	0.61200350331044	2		441	439	SUCCESS
APC	324	MSKCC	GRCh37	5	112175153	112175153	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	186	228	0	ENST00000257430.4:c.3862G>T	p.Gly1288Ter	p.G1288*	ENST00000257430	NM_000038.5	1288	Gga/Tga	16/16	0.61200350331044	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.61200350331044	2		228	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs878854073	NA	P-0028544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	164	468	0	ENST00000269305.4:c.673-1G>A		p.X225_splice	ENST00000269305	NM_001126112.2	225			1	2	FACETS	0.78	0.718	0.844	0.78	0.718	0.844	SUBCLONAL	1	TRUE	1	0.61200350331044	2		468	687	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984085	2984085	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	145	407	0	ENST00000396946.4:c.445C>T	p.Arg149Cys	p.R149C	ENST00000396946	NM_032415.4	149	Cgc/Tgc	5/25	0.345499159403334	3	FACETS	1	0.945	1	0.521	0.477	0.567	INDETERMINATE	1	TRUE	1	0.61200350331044	3		407	594	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71050193	71050195	+	frameshift_variant	Frame_Shift_Del	DEL	TGC	TGC	GA	novel	NA	P-0028544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	127	299	0	ENST00000318789.4:c.990_992delinsTC	p.Glu330AspfsTer22	p.E330Dfs*22	ENST00000318789	NM_032682.5	330	gaGCAt/gaTCt	13/21	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.61200350331044	2		299	394	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526886	31526886	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	267	741	0	ENST00000344624.3:c.154C>T	p.Gln52Ter	p.Q52*	ENST00000344624		52	Caa/Taa	2/33	1	2	FACETS	0.971	0.912	1	0.971	0.912	1	CLONAL	1	TRUE	1	0.61200350331044	2		741	899	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864459	162864459	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	180	464	0	ENST00000366898.1:c.54T>A	p.Asp18Glu	p.D18E	ENST00000366898	NM_004562.2	18	gaT/gaA	2/12	1	2	FACETS	0.967	0.897	1	0.967	0.897	1	CLONAL	1	TRUE	1	0.61200350331044	2		464	608	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380238	25380238	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs770020203	NA	P-0028548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	142	606	0	ENST00000311936.3:c.220A>G	p.Thr74Ala	p.T74A	ENST00000311936	NM_004985.3	74	Act/Gct	3/5	0.41624670580101	4	FACETS	1	0.926	1	0.509	0.464	0.557	CLONAL	1	TRUE	2	0.472874037051215	4		606	869	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363842	118363846	+	frameshift_variant	Frame_Shift_Del	DEL	CTGAT	CTGAT	-	novel	NA	P-0028548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	283	609	0	ENST00000534358.1:c.5076_5080del	p.Asp1693ThrfsTer5	p.D1693Tfs*5	ENST00000534358	NM_005933.3	1692	cCTGAT/c	16/36	0.472874037051215	2	FACETS	0.922	0.873	0.971	0.922	0.873	0.971	CLONAL	2	TRUE	0	0.472874037051215	2		609	649	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80071555	80071555	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	226	250	0	ENST00000265081.6:c.2296A>G	p.Thr766Ala	p.T766A	ENST00000265081	NM_002439.4	766	Act/Gct	16/24	0.472874037051215	6	FACETS	1	0.979	1	0.557	0.52	0.595	CLONAL	2	TRUE	2	0.472874037051215	6		250	835	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508685	106508685	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	272	594	0	ENST00000359195.3:c.679A>T	p.Ser227Cys	p.S227C	ENST00000359195	NM_002649.2	227	Agc/Tgc	2/11	0.472874037051215	4	FACETS	0.897	0.844	0.953	0.897	0.844	0.953	CLONAL	2	TRUE	2	0.472874037051215	4		594	944	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146049	38146049	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	172	818	0	ENST00000317025.8:c.3457G>C	p.Glu1153Gln	p.E1153Q	ENST00000317025	NM_023034.1	1153	Gag/Cag	19/24	0.430557029229072	3	FACETS	0.965	0.888	1	0.483	0.444	0.523	CLONAL	1	TRUE	1	0.472874037051215	3		818	932	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272308	38272308	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs869320694	NA	P-0028550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	515	529	1	ENST00000425967.3:c.2059A>G	p.Lys687Glu	p.K687E	ENST00000425967	NM_001174067.1	687	Aag/Gag	15/19	0.315429268676239	0	FACETS	0.828	0.807	0.847			1	CLONAL	3	TRUE	0	0.387792698643137	0		530	655	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148991	119148991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs192712314	NA	P-0028550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	20	535	1	ENST00000264033.4:c.1211G>A	p.Cys404Tyr	p.C404Y	ENST00000264033	NM_005188.3	404	tGt/tAt	8/16	0.393751007298859	1	FACETS	0.088	0.066	0.113	0.088	0.066	0.113	SUBCLONAL	1	TRUE	0	0.387792698643137	1		536	946	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683508	29683508	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	548	443	1	ENST00000356175.3:c.7583C>A	p.Ser2528Ter	p.S2528*	ENST00000356175	NM_000267.3	2528	tCa/tAa	51/57	0.393751007298859	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	3	TRUE	0	0.387792698643137	2		444	877	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105559	27105624	+	inframe_deletion	In_Frame_Del	DEL	CTGATTGAGATCTTTGGCATTTTAAAGGAGTATGAGGTGGGTGACCCAGGACAGAGAACGCTACTG	CTGATTGAGATCTTTGGCATTTTAAAGGAGTATGAGGTGGGTGACCCAGGACAGAGAACGCTACTG	-	novel	NA	P-0028550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	175	483	0	ENST00000324856.7:c.5170_5235del	p.Leu1724_Leu1745del	p.L1724_L1745del	ENST00000324856	NM_006015.4	1724	CTGATTGAGATCTTTGGCATTTTAAAGGAGTATGAGGTGGGTGACCCAGGACAGAGAACGCTACTG/-	20/20	0.230891859634944	4	FACETS	1	0.954	1			1	INDETERMINATE	1	TRUE	NA	0.387792698643137	4		483	1189	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578445	7578445	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587780069	NA	P-0028551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	306	879	1	ENST00000269305.4:c.485T>G	p.Ile162Ser	p.I162S	ENST00000269305	NM_001126112.2	162	aTc/aGc	5/11	0.303253624935259	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	FALSE	0	0.303253624935259	2		880	943	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913492	NA	P-0028552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	343	511	0	ENST00000286548.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000286548	NM_002072.3	209	cAa/cTa	5/7	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.708239256936285	2		511	884	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437773	52437776	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	novel	NA	P-0028552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	333	538	0	ENST00000460680.1:c.1385_1388del	p.Pro462ArgfsTer108	p.P462Rfs*108	ENST00000460680	NM_004656.3	462	cCTCTg/cg	13/17	0.708239256936285	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.708239256936285	1		538	566	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593594	55593608	+	inframe_deletion	In_Frame_Del	DEL	GAAGTACAGTGGAAG	GAAGTACAGTGGAAG	-	novel	NA	P-0028553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	303	471	1	ENST00000288135.5:c.1661_1675del	p.Glu554_Lys558del	p.E554_K558del	ENST00000288135	NM_000222.2	554	GAAGTACAGTGGAAG/-	11/21	0.923883583556813	3	FACETS	0.84	0.801	0.879			1	CLONAL	2	TRUE	NA	0.930179349618436	3		472	568	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593594	55593608	+	inframe_deletion	In_Frame_Del	DEL	GAAGTACAGTGGAAG	GAAGTACAGTGGAAG	-	novel	NA	P-0028553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	473	471	1	ENST00000288135.5:c.1661_1675del	p.Glu554_Lys558del	p.E554_K558del	ENST00000288135	NM_000222.2	554	GAAGTACAGTGGAAG/-	11/21	0.97838438918267	3	FACETS		NA	1			1	NA	NA	TRUE	NA	NA	3		472	860	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0028554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	1061	441	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.351903293830463	10	FACETS	0.977	0.957	0.996	0.977	0.957	0.996	CLONAL	10	TRUE	0	0.351903293830463	10		441	1486	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937184	36937184	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	173	349	1	ENST00000361632.4:c.1135G>T	p.Gly379Cys	p.G379C	ENST00000361632		379	Ggc/Tgc	9/16	0.351903293830463	3	FACETS	1	0.978	1	0.585	0.538	0.634	CLONAL	1	TRUE	1	0.351903293830463	3		350	989	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439842	51439842	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	97	309	0	ENST00000262662.1:c.407A>G	p.Lys136Arg	p.K136R	ENST00000262662		136	aAg/aGg	4/4	0.351903293830463	3	FACETS	0.987	0.881	1	0.493	0.44	0.55	CLONAL	1	TRUE	1	0.351903293830463	3		309	657	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317568	163317568	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	150	347	0	ENST00000271452.3:c.964G>T	p.Asp322Tyr	p.D322Y	ENST00000271452	NM_145697.2	322	Gac/Tac	12/14	0.297546514741907	4	FACETS	0.85	0.779	0.924	0.85	0.779	0.924	CLONAL	2	TRUE	2	0.351903293830463	4		347	678	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40451799	40451799	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	304	385	0	ENST00000345506.4:c.581C>G	p.Pro194Arg	p.P194R	ENST00000345506	NM_003152.3	194	cCc/cGc	7/20	0.351903293830463	5	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	3	0.351903293830463	5		385	1056	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439799	220439799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	301	274	1	ENST00000243786.2:c.652C>A	p.His218Asn	p.H218N	ENST00000243786	NM_002191.3	218	Cac/Aac	2/2	0.321871374064809	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	2	0.351903293830463	4		275	1118	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747862	41747862	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	125	312	1	ENST00000226382.2:c.907G>A	p.Gly303Ser	p.G303S	ENST00000226382	NM_003924.3	303	Ggt/Agt	3/3	NA	2	FACETS	1	0.913	1			1	INDETERMINATE	1	TRUE	NA	0.351903293830463	2		313	705	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937732	44937732	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	243	454	0	ENST00000377967.4:c.2920G>T	p.Ala974Ser	p.A974S	ENST00000377967	NM_021140.2	974	Gct/Tct	19/29	0.351903293830463	2	FACETS	0.979	0.92	1	0.979	0.92	1	CLONAL	2	TRUE	0	0.351903293830463	2		454	705	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520006	NA	P-0028558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	56	610	0	ENST00000269305.4:c.821T>C	p.Val274Ala	p.V274A	ENST00000269305	NM_001126112.2	274	gTt/gCt	8/11	1	2	FACETS	0.956	0.819	1	0.956	0.819	1	CLONAL	1	TRUE	1	0.2	2		610	586	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054600	5054600	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	25	346	0	ENST00000381652.3:c.652A>T	p.Ile218Phe	p.I218F	ENST00000381652	NM_004972.3	218	Atc/Ttc	7/25	1	2	FACETS	1	0.824	1	1	0.824	1	CLONAL	1	TRUE	1	0.2	2		346	239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0028568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	364	537	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.506165080654156	5	FACETS	0.975	0.927	1	0.65	0.618	0.683	CLONAL	2	FALSE	2	0.775393821834325	5		540	1041	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817720	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	283	457	1	ENST00000262367.5:c.3250dup	p.Ile1084AsnfsTer3	p.I1084Nfs*3	ENST00000262367	NM_004380.2	1084	atc/aAtc		0.775393821834325	6	FACETS	0.882	0.829	0.936	0.588	0.552	0.624	CLONAL	2	FALSE	3	0.775393821834325	6		458	1056	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992187	72992187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1413049341	NA	P-0028568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	245	672	0	ENST00000268489.5:c.1858C>T	p.His620Tyr	p.H620Y	ENST00000268489	NM_006885.3	620	Cac/Tac	2/10	1	2	FACETS	0.928	0.872	0.985	0.928	0.872	0.985	CLONAL	1	FALSE	1	0.775393821834325	2		672	681	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528454	29528454	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	363	524	0	ENST00000356175.3:c.1211C>G	p.Ser404Cys	p.S404C	ENST00000356175	NM_000267.3	404	tCt/tGt	11/57	0.775393821834325	6	FACETS	0.982	0.931	1	0.655	0.621	0.689	CLONAL	2	FALSE	3	0.775393821834325	6		524	1216	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653263	29653263	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	49	328	0	ENST00000356175.3:c.5198C>G	p.Ser1733Cys	p.S1733C	ENST00000356175	NM_000267.3	1733	tCt/tGt	36/57	0.775393821834325	6	FACETS	0.34	0.287	0.4	0.113	0.095	0.134	SUBCLONAL	1	FALSE	3	0.775393821834325	6		328	947	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907661	111907662	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0028568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	412	462	0	ENST00000393256.3:c.438_439dup	p.Trp147TyrfsTer24	p.W147Yfs*24	ENST00000393256	NM_006538.4	145	-/AT	3/4	0.791837067361467	4	FACETS	0.808	0.77	0.846			1	CLONAL	2	FALSE	NA	0.775393821834325	4		462	1168	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164910	47164910	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	284	299	0	ENST00000409792.3:c.1216C>G	p.His406Asp	p.H406D	ENST00000409792	NM_014159.6	406	Cac/Gac	3/21	0.530108880821016	4	FACETS	1	0.976	1	0.769	0.737	0.799	CLONAL	3	FALSE	0	0.775393821834325	4		299	423	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396203	139396218	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCGCGGACATTGAC	GCCCGCGGACATTGAC	-	novel	NA	P-0028568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	440	628	0	ENST00000277541.6:c.5620_5635del	p.Val1874LeufsTer8	p.V1874Lfs*8	ENST00000277541	NM_017617.3	1874	GTCAATGTCCGCGGGCct/ct	30/34	0.791837067361467	4	FACETS	0.863	0.825	0.902	0.863	0.825	0.902	CLONAL	2	FALSE	2	0.775393821834325	4		628	1167	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578226	7578226	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1464727668	NA	P-0028569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	273	598	1	ENST00000269305.4:c.623A>T	p.Asp208Val	p.D208V	ENST00000269305	NM_001126112.2	208	gAc/gTc	6/11	0.564099081883893	1	FACETS	0.933	0.88	0.987	0.933	0.88	0.987	CLONAL	1	TRUE	0	0.564099081883893	1		599	745	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	115	387	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.985	0.89	1	0.985	0.89	1	CLONAL	1	TRUE	1	0.397731303915177	2		387	587	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	250	436	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.327059748874692	3	FACETS	0.84	0.787	0.894	0.84	0.787	0.894	CLONAL	2	TRUE	1	0.397731303915177	3		437	897	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251907	153251907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	111	488	0	ENST00000281708.4:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000281708	NM_033632.3	367	Cga/Tga	7/12	1	2	FACETS	0.885	0.797	0.977	0.885	0.797	0.977	CLONAL	1	TRUE	1	0.397731303915177	2		488	631	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	348	539	5	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	0.327059748874692	3	FACETS	0.856	0.81	0.902	0.856	0.81	0.902	CLONAL	2	TRUE	1	0.397731303915177	3		544	1226	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608923	100608923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	107	325	4	ENST00000308731.7:c.1685G>A	p.Arg562Gln	p.R562Q	ENST00000308731	NM_000061.2	562	cGg/cAg	17/19	0.297473292128102	2	FACETS	0.841	0.755	0.931			1	CLONAL	1	TRUE	NA	0.397731303915177	2		329	640	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	58	221	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.733	0.632	0.842	0.733	0.632	0.842	SUBCLONAL	1	TRUE	1	0.397731303915177	2		221	398	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713427	40713427	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752787425	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	53	611	4	ENST00000373198.4:c.4088G>A	p.Arg1363Gln	p.R1363Q	ENST00000373198	NM_133170.3	1363	cGg/cAg	30/32	NA	2	FACETS	0.293	0.248	0.341			1	INDETERMINATE	1	TRUE	NA	0.397731303915177	2		615	911	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752960	128752960	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	149	515	0	ENST00000377970.2:c.1121A>G	p.His374Arg	p.H374R	ENST00000377970	NM_002467.4	374	cAc/cGc	3/3	1	2	FACETS	0.951	0.87	1	0.951	0.87	1	CLONAL	1	TRUE	1	0.397731303915177	2		515	788	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	127	473	8	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.377428950637728	2	FACETS	0.932	0.846	1	0.466	0.423	0.512	CLONAL	1	TRUE	0	0.397731303915177	2		481	685	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123833	46123833	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	91	292	1	ENST00000334344.6:c.102del	p.Phe34LeufsTer24	p.F34Lfs*24	ENST00000334344	NM_152641.2	33	ccT/cc	2/21	0.327059748874692	3	FACETS	1	0.926	1	0.525	0.468	0.587	CLONAL	1	TRUE	1	0.397731303915177	3		293	522	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021232	31021232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148964601	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	146	555	2	ENST00000375687.4:c.1231C>T	p.Arg411Cys	p.R411C	ENST00000375687	NM_015338.5	411	Cgc/Tgc	12/13	0.327059748874692	3	FACETS	0.858	0.782	0.938	0.429	0.391	0.469	CLONAL	1	TRUE	1	0.397731303915177	3		557	1026	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649544	206649544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370426628	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	121	530	0	ENST00000367120.3:c.379C>T	p.Arg127Trp	p.R127W	ENST00000367120	NM_014002.3	127	Cgg/Tgg	6/22	1	2	FACETS	0.77	0.696	0.849	0.77	0.696	0.849	SUBCLONAL	1	TRUE	1	0.397731303915177	2		530	790	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982386	25982386	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	165	379	0	ENST00000435504.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000435504		302	Cga/Tga	9/13	0.377428950637728	2	FACETS	0.799	0.739	0.861	0.799	0.739	0.861	SUBCLONAL	2	TRUE	0	0.397731303915177	2		379	519	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	302	687	4	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	0.377428950637728	2	FACETS	0.842	0.795	0.889	0.842	0.795	0.889	CLONAL	2	TRUE	0	0.397731303915177	2		691	902	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948208	71948209	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs749079348	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	57	774	1	ENST00000298229.2:c.2927dup	p.Pro977ThrfsTer7	p.P977Tfs*7	ENST00000298229	NM_001567.3	974	gcc/gCcc	26/28	1	2	FACETS	0.252	0.215	0.293	0.252	0.215	0.293	SUBCLONAL	1	TRUE	1	0.397731303915177	2		775	1137	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242899	142242899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750252420	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	180	601	0	ENST00000350721.4:c.4088C>T	p.Ala1363Val	p.A1363V	ENST00000350721	NM_001184.3	1363	gCg/gTg	22/47	1	2	FACETS	0.921	0.849	0.996	0.921	0.849	0.996	CLONAL	1	TRUE	1	0.397731303915177	2		601	983	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180050958	180050958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781305649	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	181	742	0	ENST00000261937.6:c.1525G>A	p.Glu509Lys	p.E509K	ENST00000261937	NM_182925.4	509	Gag/Aag	11/30	0.191959146342118	0	FACETS	0.531	0.489	0.575			1	INDETERMINATE	1	TRUE	0	0.397731303915177	0		742	1032	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281344	49281344	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202077345	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	409	799	2	ENST00000282018.3:c.391G>A	p.Val131Met	p.V131M	ENST00000282018	NM_020377.2	131	Gtg/Atg	1/1	0.327059748874692	3	FACETS	0.899	0.855	0.944	0.899	0.855	0.944	CLONAL	2	TRUE	1	0.397731303915177	3		801	1371	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631343	117631343	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	104	429	0	ENST00000368508.3:c.6335del	p.Asn2112MetfsTer22	p.N2112Mfs*22	ENST00000368508	NM_002944.2	2112	aAt/at	40/43	0.377428950637728	2	FACETS	0.796	0.714	0.883	0.398	0.357	0.442	SUBCLONAL	1	TRUE	0	0.397731303915177	2		429	657	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653803	89653803	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554893773	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	279	489	0	ENST00000371953.3:c.101C>T	p.Ala34Val	p.A34V	ENST00000371953	NM_000314.4	34	gCt/gTt	2/9	0.377428950637728	2	FACETS	0.94	0.888	0.994	0.94	0.888	0.994	CLONAL	2	TRUE	0	0.397731303915177	2		489	746	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255919	16255919	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	162	516	0	ENST00000375759.3:c.3184A>C	p.Ser1062Arg	p.S1062R	ENST00000375759	NM_015001.2	1062	Agc/Cgc	11/15	1	2	FACETS	0.948	0.871	1	0.948	0.871	1	CLONAL	1	TRUE	1	0.397731303915177	2		516	859	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256591	16256591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	76	586	1	ENST00000375759.3:c.3856G>A	p.Gly1286Arg	p.G1286R	ENST00000375759	NM_015001.2	1286	Ggg/Agg	11/15	1	2	FACETS	0.463	0.405	0.526	0.463	0.405	0.526	SUBCLONAL	1	TRUE	1	0.397731303915177	2		587	825	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870250	155870251	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs746629883	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	149	659	0	ENST00000368323.3:c.588dup	p.Ser197IlefsTer2	p.S197Ifs*2	ENST00000368323	NM_006912.5	196	-/A	6/6	1	2	FACETS	0.743	0.678	0.812	0.743	0.678	0.812	SUBCLONAL	1	TRUE	1	0.397731303915177	2		659	1008	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193219001	193219001	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	77	337	0	ENST00000367435.3:c.1559G>C	p.Arg520Thr	p.R520T	ENST00000367435	NM_024529.4	520	aGg/aCg	16/17	1	2	FACETS	0.903	0.796	1	0.903	0.796	1	CLONAL	1	TRUE	1	0.397731303915177	2		337	429	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982141	201982142	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	175	717	1	ENST00000359651.3:c.666_667dup	p.Asp223ValfsTer32	p.D223Vfs*32	ENST00000359651		222	act/acTGt	5/8	1	2	FACETS	0.862	0.793	0.934	0.862	0.793	0.934	CLONAL	1	TRUE	1	0.397731303915177	2		718	1021	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111855951	111855951	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	128	406	1	ENST00000341259.2:c.2T>C	p.Met1?	p.M1?	ENST00000341259	NM_005475.2	1	aTg/aCg	2/8	0.327059748874692	3	FACETS	0.93	0.843	1	0.465	0.421	0.511	CLONAL	1	TRUE	1	0.397731303915177	3		407	830	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437289	121437289	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	162	726	0	ENST00000257555.6:c.1627T>C	p.Phe543Leu	p.F543L	ENST00000257555		543	Ttc/Ctc	9/10	0.327059748874692	3	FACETS	0.821	0.751	0.893	0.41	0.375	0.447	CLONAL	1	TRUE	1	0.397731303915177	3		726	1190	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913305	28913305	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	129	565	0	ENST00000282397.4:c.2488G>T	p.Gly830Cys	p.G830C	ENST00000282397	NM_002019.4	830	Ggc/Tgc	17/30	0.327059748874692	3	FACETS	0.781	0.707	0.859	0.39	0.353	0.43	SUBCLONAL	1	TRUE	1	0.397731303915177	3		565	996	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001372	29001372	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	104	456	0	ENST00000282397.4:c.1360T>C	p.Cys454Arg	p.C454R	ENST00000282397	NM_002019.4	454	Tgt/Cgt	10/30	0.327059748874692	3	FACETS	0.815	0.73	0.906	0.408	0.365	0.453	CLONAL	1	TRUE	1	0.397731303915177	3		456	769	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226539	41226539	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs80358189	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	109	458	0	ENST00000357654.3:c.4485-1G>T		p.X1495_splice	ENST00000357654	NM_007294.3	1495			1	2	FACETS	0.962	0.866	1	0.962	0.866	1	CLONAL	1	TRUE	1	0.397731303915177	2		458	570	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266704	18266704	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	156	538	1	ENST00000222254.8:c.15G>T	p.Glu5Asp	p.E5D	ENST00000222254	NM_005027.3	5	gaG/gaT	2/16	0.338081431963524	3	FACETS	0.906	0.829	0.987	0.453	0.414	0.494	CLONAL	1	TRUE	1	0.397731303915177	3		539	1038	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211568	36211568	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	75	498	0	ENST00000222270.7:c.1319C>A	p.Pro440His	p.P440H	ENST00000222270	NM_014727.1	440	cCt/cAt	3/37	0.338081431963524	3	FACETS	0.532	0.465	0.604	0.266	0.232	0.302	SUBCLONAL	1	TRUE	1	0.397731303915177	3		498	850	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212249	36212251	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs768916658	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	241	620	1	ENST00000222270.7:c.2009_2011del	p.Pro670del	p.P670del	ENST00000222270	NM_014727.1	667	aCTCct/act	3/37	0.338081431963524	3	FACETS	1	0.992	1	0.719	0.671	0.767	CLONAL	1	TRUE	1	0.397731303915177	3		621	1011	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224532	36224532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759167832	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	242	865	0	ENST00000222270.7:c.6994C>T	p.Arg2332Cys	p.R2332C	ENST00000222270	NM_014727.1	2332	Cgt/Tgt	29/37	0.338081431963524	3	FACETS	1	0.979	1	0.56	0.522	0.599	CLONAL	1	TRUE	1	0.397731303915177	3		865	1303	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248729	212248729	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs764925334	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	44	386	0	ENST00000342788.4:c.3538C>A	p.Leu1180Ile	p.L1180I	ENST00000342788	NM_005235.2	1180	Ctt/Att	28/28	0.354121402057344	2	FACETS	0.424	0.355	0.5	0.212	0.177	0.25	SUBCLONAL	1	TRUE	0	0.397731303915177	2		386	522	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30733069	30733069	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	110	470	0	ENST00000295754.5:c.1682G>T	p.Gly561Val	p.G561V	ENST00000295754	NM_003242.5	561	gGc/gTc	7/7	1	2	FACETS	0.803	0.722	0.888	0.803	0.722	0.888	CLONAL	1	TRUE	1	0.397731303915177	2		470	689	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890204	72890204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764950055	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	109	464	0	ENST00000325599.8:c.478C>T	p.Arg160Trp	p.R160W	ENST00000325599	NM_018130.2	160	Cgg/Tgg	4/11	1	2	FACETS	0.696	0.625	0.772	0.696	0.625	0.772	SUBCLONAL	1	TRUE	1	0.397731303915177	2		464	787	SUCCESS
APC	324	MSKCC	GRCh37	5	112151233	112151240	+	frameshift_variant	Frame_Shift_Del	DEL	GAGTTCTA	GAGTTCTA	-	novel	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	131	477	0	ENST00000257430.4:c.877_884del	p.Ser293Ter	p.S293*	ENST00000257430	NM_000038.5	292	ttGAGTTCTAgt/ttgt	9/16	1	2	FACETS	0.81	0.735	0.889	0.81	0.735	0.889	CLONAL	1	TRUE	1	0.397731303915177	2		477	813	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931411	131931411	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772468452	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	131	436	0	ENST00000265335.6:c.2116C>T	p.Arg706Ter	p.R706*	ENST00000265335		706	Cga/Tga	13/25	1	2	FACETS	0.911	0.828	0.998	0.911	0.828	0.998	CLONAL	1	TRUE	1	0.397731303915177	2		436	723	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515273	149515273	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	120	567	0	ENST00000261799.4:c.209del	p.Pro70HisfsTer18	p.P70Hfs*18	ENST00000261799	NM_002609.3	70	cCa/ca	3/23	1	2	FACETS	0.794	0.717	0.875	0.794	0.717	0.875	SUBCLONAL	1	TRUE	1	0.397731303915177	2		567	760	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859884	151859884	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs544987067	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	84	342	0	ENST00000262189.6:c.10778A>G	p.Tyr3593Cys	p.Y3593C	ENST00000262189	NM_170606.2	3593	tAt/tGt	43/59	0.293240835791902	3	FACETS	0.827	0.732	0.93	0.276	0.244	0.31	CLONAL	1	TRUE	0	0.397731303915177	3		342	612	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371677	55371677	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	120	609	1	ENST00000297316.4:c.367C>T	p.Arg123Trp	p.R123W	ENST00000297316	NM_022454.3	123	Cgg/Tgg	2/2	1	2	FACETS	0.772	0.697	0.85	0.772	0.697	0.85	SUBCLONAL	1	TRUE	1	0.397731303915177	2		610	782	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971109	21971109	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs34968276	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	80	303	0	ENST00000579755.1:c.292C>T	p.Arg98Ter	p.R98*	ENST00000579755		98	Cga/Tga	2/3	1	2	FACETS	0.916	0.81	1	0.916	0.81	1	CLONAL	1	TRUE	1	0.397731303915177	2		303	439	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760706	133760706	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	167	783	0	ENST00000318560.5:c.3029T>C	p.Val1010Ala	p.V1010A	ENST00000318560	NM_005157.4	1010	gTg/gCg	11/11	1	2	FACETS	0.833	0.765	0.904	0.833	0.765	0.904	CLONAL	1	TRUE	1	0.397731303915177	2		783	1008	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911007	94911007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	195	597	0	ENST00000536441.1:c.1123C>T	p.Leu375Phe	p.L375F	ENST00000536441	NM_144665.3	375	Ctt/Ttt	8/10	0.425427910752729	7	FACETS	0.909	0.841	0.98			1	CLONAL	2	FALSE	NA	0.425427910752729	7		597	1040	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579309	7579310	+	splice_donor_variant,intron_variant	Splice_Site	DEL	GA	GA	-	novel	NA	P-0028572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	93	473	0	ENST00000269305.4:c.375+2_375+3del		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.291798367447042	3	FACETS	1	0.977	1			1	CLONAL	1	FALSE	NA	0.425427910752729	3		473	388	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176571	56176571	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	97	382	0	ENST00000399503.3:c.2122del	p.Glu708AsnfsTer17	p.E708Nfs*17	ENST00000399503	NM_005921.1	707	ttG/tt	12/20	0.389289947204285	3	FACETS	1	0.906	1	0.507	0.453	0.564	CLONAL	1	FALSE	1	0.425427910752729	3		382	545	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94910975	94910977	+	missense_variant	Missense_Mutation	TNP	GAG	GAG	AAA	novel	NA	P-0028572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	174	570	0	ENST00000536441.1:c.1153_1155delinsTTT	p.Leu385Phe	p.L385F	ENST00000536441	NM_144665.3	385	CTC/TTT	8/10	0.425427910752729	7	FACETS	0.905	0.833	0.979			1	CLONAL	2	FALSE	NA	0.425427910752729	7		570	933	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0028574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	133	218	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.826	0.757	0.896	0.826	0.757	0.896	CLONAL	1	TRUE	1	0.78582669637787	2		218	410	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0028574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6627	6470	602	1	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.78582669637787	22	FACETS	1	0.996	1	0.53	0.524	0.536	CLONAL	11	TRUE	1	0.78582669637787	22		603	13097	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711973	89711975	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	rs1064793244	NA	P-0028574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	170	386	0	ENST00000371953.3:c.595_597del	p.Met199del	p.M199del	ENST00000371953	NM_000314.4	197	aaGATg/aag	6/9	0.78582669637787	1	FACETS	0.906	0.852	0.958	0.906	0.852	0.958	CLONAL	1	TRUE	0	0.78582669637787	1		386	290	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048602	180048602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778453271	NA	P-0028574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	419	782	0	ENST00000261937.6:c.1960G>A	p.Glu654Lys	p.E654K	ENST00000261937	NM_182925.4	654	Gaa/Aaa	13/30	NA	2	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.78582669637787	2		782	1027	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220329	55220329	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12517	2453	777	0	ENST00000275493.2:c.719G>C	p.Cys240Ser	p.C240S	ENST00000275493	NM_005228.3	240	tGc/tCc	6/28	0.78582669637787	22	FACETS	0.924	0.903	0.944	0.176	0.172	0.18	CLONAL	4	TRUE	1	0.78582669637787	22		777	14970	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242741	66242741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777294375	NA	P-0028574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	62	482	0	ENST00000273854.3:c.1831G>A	p.Ala611Thr	p.A611T	ENST00000273854	NM_004439.5	611	Gct/Act	9/18	1	2	FACETS	0.267	0.23	0.307	0.267	0.23	0.307	SUBCLONAL	1	TRUE	1	0.78582669637787	2		482	591	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719992	18719992	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs376472161	NA	P-0028574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	118	291	0	ENST00000266497.5:c.3888+1G>A		p.X1296_splice	ENST00000266497		1296			1	2	FACETS	0.902	0.824	0.982	0.902	0.824	0.982	CLONAL	1	TRUE	1	0.78582669637787	2		291	333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0028576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	147	535	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.54	0.492	0.59	0.54	0.492	0.59	SUBCLONAL	1	TRUE	1	0.52290741936409	2		535	1041	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0028576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	89	221	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.52290741936409	1	FACETS	0.924	0.831	1	0.924	0.831	1	CLONAL	1	TRUE	0	0.52290741936409	1		221	272	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061213	38061213	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	148	453	0	ENST00000250448.2:c.776A>G	p.Tyr259Cys	p.Y259C	ENST00000250448	NM_004496.3	259	tAc/tGc	2/2	1	2	FACETS	0.864	0.792	0.94	0.864	0.792	0.94	CLONAL	1	TRUE	1	0.52290741936409	2		453	655	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696430	47696430	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519970	NA	P-0028576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	203	443	0	ENST00000347630.2:c.393G>T	p.Trp131Cys	p.W131C	ENST00000347630	NM_001007230.1	131	tgG/tgT	6/11	1	2	FACETS	0.864	0.801	0.928	0.864	0.801	0.928	CLONAL	1	TRUE	1	0.52290741936409	2		443	899	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162820	38162820	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	447	517	0	ENST00000317025.8:c.2386C>G	p.Gln796Glu	p.Q796E	ENST00000317025	NM_023034.1	796	Cag/Gag	13/24	0.52290741936409	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.52290741936409	1		517	1189	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162848	38162848	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs757817622	NA	P-0028576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	507	590	0	ENST00000317025.8:c.2358C>G	p.Ile786Met	p.I786M	ENST00000317025	NM_023034.1	786	atC/atG	13/24	0.52290741936409	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.52290741936409	1		590	1315	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915940	127915940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	266	446	0	ENST00000373547.4:c.541C>T	p.Arg181Trp	p.R181W	ENST00000373547	NM_002721.4	181	Cgg/Tgg	6/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.52290741936409	2		446	942	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0028576-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	51	535	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.351	0.297	0.41	0.351	0.297	0.41	SUBCLONAL	1	TRUE	1	0.340162088140342	2		535	855	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0028576-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	35	221	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.339913778400209	1	FACETS	0.564	0.463	0.675	0.564	0.463	0.675	SUBCLONAL	1	TRUE	0	0.340162088140342	1		221	303	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061213	38061213	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028576-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	109	453	0	ENST00000250448.2:c.776A>G	p.Tyr259Cys	p.Y259C	ENST00000250448	NM_004496.3	259	tAc/tGc	2/2	1	2	FACETS	0.987	0.888	1	0.987	0.888	1	CLONAL	1	TRUE	1	0.340162088140342	2		453	649	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696430	47696430	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519970	NA	P-0028576-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	130	443	0	ENST00000347630.2:c.393G>T	p.Trp131Cys	p.W131C	ENST00000347630	NM_001007230.1	131	tgG/tgT	6/11	1	2	FACETS	0.937	0.85	1	0.937	0.85	1	CLONAL	1	TRUE	1	0.340162088140342	2		443	816	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162820	38162820	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028576-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	128	517	0	ENST00000317025.8:c.2386C>G	p.Gln796Glu	p.Q796E	ENST00000317025	NM_023034.1	796	Cag/Gag	13/24	0.340162088140342	3	FACETS	0.913	0.826	1	0.456	0.413	0.502	CLONAL	1	TRUE	1	0.340162088140342	3		517	965	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162848	38162848	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs757817622	NA	P-0028576-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	159	590	0	ENST00000317025.8:c.2358C>G	p.Ile786Met	p.I786M	ENST00000317025	NM_023034.1	786	atC/atG	13/24	0.340162088140342	3	FACETS	0.983	0.899	1	0.491	0.449	0.535	CLONAL	1	TRUE	1	0.340162088140342	3		590	1113	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915940	127915940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028576-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	120	446	0	ENST00000373547.4:c.541C>T	p.Arg181Trp	p.R181W	ENST00000373547	NM_002721.4	181	Cgg/Tgg	6/7	1	2	FACETS	0.928	0.839	1	0.928	0.839	1	CLONAL	1	TRUE	1	0.340162088140342	2		446	760	SUCCESS
APC	324	MSKCC	GRCh37	5	112174782	112174783	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0028576-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	26	266	0	ENST00000257430.4:c.3495dup	p.Tyr1166IlefsTer2	p.Y1166Ifs*2	ENST00000257430	NM_000038.5	1164	ata/atAa	16/16	0.339913778400209	1	FACETS	0.304	0.24	0.377	0.304	0.24	0.377	SUBCLONAL	1	TRUE	0	0.340162088140342	1		266	418	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350741	89350741	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028576-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	73	656	0	ENST00000301030.4:c.2209G>C	p.Asp737His	p.D737H	ENST00000301030	NM_001256183.1	737	Gac/Cac	9/13	1	2	FACETS	0.359	0.313	0.41	0.359	0.313	0.41	SUBCLONAL	1	TRUE	1	0.340162088140342	2		656	1195	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0028577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	126	434	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.939	0.853	1	1	0.989	1	CLONAL	2	TRUE	1	0.208592984321334	2		434	643	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920469	134920469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	41	696	0	ENST00000398015.3:c.2284G>A	p.Asp762Asn	p.D762N	ENST00000398015	NM_004441.4	762	Gac/Aac	12/16	1	2	FACETS	0.537	0.446	0.639	0.537	0.446	0.639	SUBCLONAL	1	TRUE	1	0.208592984321334	2		696	732	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0028577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	10	442	1	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.208592984321334	1	FACETS	0.209	0.141	0.296	0.209	0.141	0.296	SUBCLONAL	1	TRUE	0	0.208592984321334	1		443	411	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264932	46264932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1228109191	NA	P-0028577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	56	577	0	ENST00000371998.3:c.1802G>A	p.Ser601Asn	p.S601N	ENST00000371998		601	aGc/aAc	12/23	1	2	FACETS	0.905	0.775	1	0.905	0.775	1	CLONAL	1	TRUE	1	0.208592984321334	2		577	593	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253911	NA	P-0028578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	211	666	1	ENST00000269305.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000269305	NM_001126112.2	180	Gag/Aag	5/11	0.078927794599707	5	FACETS	1	0.985	1			1	INDETERMINATE	3	FALSE	NA	0.572258822589671	5		667	406	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117680985	117680985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771443531	NA	P-0028578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	68	474	2	ENST00000368508.3:c.3635G>A	p.Arg1212His	p.R1212H	ENST00000368508	NM_002944.2	1212	cGc/cAc	23/43	NA	2	FACETS	0.867	0.763	0.978			1	INDETERMINATE	1	FALSE	NA	0.572258822589671	2		476	274	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578380	7578380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs72661117	NA	P-0028578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	177	612	0	ENST00000269305.4:c.550G>A	p.Asp184Asn	p.D184N	ENST00000269305	NM_001126112.2	184	Gat/Aat	5/11	0.078927794599707	5	FACETS	1	0.976	1			1	INDETERMINATE	3	FALSE	NA	0.572258822589671	5		612	353	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609962	43609962	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	66	884	0	ENST00000355710.3:c.1914C>G	p.Ile638Met	p.I638M	ENST00000355710	NM_020975.4	638	atC/atG	11/20	0.152193800972535	0	FACETS	0.344	0.301	0.389			1	INDETERMINATE	1	FALSE	0	0.572258822589671	0		884	287	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355041	73355041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs976754238	NA	P-0028578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	79	506	0	ENST00000377767.4:c.329G>A	p.Arg110Gln	p.R110Q	ENST00000377767	NM_014953.3	110	cGa/cAa	2/21	0.578553579143747	4	FACETS	0.613	0.539	0.693	0.204	0.179	0.231	SUBCLONAL	1	FALSE	1	0.572258822589671	4		506	708	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727405	66727405	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	71	472	0	ENST00000307102.5:c.121G>C	p.Glu41Gln	p.E41Q	ENST00000307102	NM_002755.3	41	Gag/Cag	2/11	0.578553579143747	4	FACETS	0.686	0.599	0.779			1	SUBCLONAL	1	FALSE	NA	0.572258822589671	4		472	569	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313035	30313035	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	127	514	0	ENST00000262643.3:c.838G>C	p.Glu280Gln	p.E280Q	ENST00000262643	NM_001238.2	280	Gag/Cag	9/12	0.535642333881186	3	FACETS	0.83	0.761	0.9	0.83	0.761	0.9	CLONAL	2	FALSE	1	0.572258822589671	3		514	344	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227816	36227816	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190286476	NA	P-0028578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	119	801	1	ENST00000222270.7:c.7301C>T	p.Ala2434Val	p.A2434V	ENST00000222270	NM_014727.1	2434	gCg/gTg	32/37	0.535642333881186	3	FACETS	0.964	0.873	1	0.482	0.436	0.53	CLONAL	1	FALSE	1	0.572258822589671	3		802	555	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97879642	97879642	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	131	747	1	ENST00000289081.3:c.1027T>A	p.Tyr343Asn	p.Y343N	ENST00000289081	NM_000136.2	343	Tac/Aac	11/15	0.535642333881186	3	FACETS	0.959	0.873	1	0.48	0.436	0.525	CLONAL	1	FALSE	1	0.572258822589671	3		748	614	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572261	64572261	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs104894267	NA	P-0028579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	61	461	2	ENST00000312049.6:c.1378C>T	p.Arg460Ter	p.R460*	ENST00000312049	NM_130799.2	460	Cga/Tga	10/10	0.275362033745849	1	FACETS	0.766	0.663	0.878	0.766	0.663	0.878	SUBCLONAL	1	TRUE	0	0.31	1		463	434	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218428	36218428	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs971655293	NA	P-0028579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	93	664	2	ENST00000222270.7:c.4207G>A	p.Glu1403Lys	p.E1403K	ENST00000222270	NM_014727.1	1403	Gag/Aag	16/37	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.31	2		666	591	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849823	151849823	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	82	369	0	ENST00000262189.6:c.12493C>T	p.Gln4165Ter	p.Q4165*	ENST00000262189	NM_170606.2	4165	Cag/Tag	49/59	0.285750817624708	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.31	1		369	407	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	167	485	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.42189670970495	4	FACETS	0.887	0.825	0.95	0.887	0.825	0.95	CLONAL	3	TRUE	1	0.433588043327405	4		485	415	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	12	100	2	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	1	FACETS	1	0.798	1	1	0.798	1	CLONAL	1	TRUE	0	0.433588043327405	1		102	39	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	74	456	3	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.433588043327405	2		459	318	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429978	78429978	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	118	482	2	ENST00000370768.2:c.901del	p.Ile301TyrfsTer22	p.I301Yfs*22	ENST00000370768	NM_003902.3	301	Ata/ta	11/20	1	2	FACETS	0.78	0.712	0.85	1	0.987	1	SUBCLONAL	2	TRUE	1	0.433588043327405	2		484	349	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566524	41566525	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	93	461	3	ENST00000263253.7:c.4408dup	p.Met1470AsnfsTer3	p.M1470Nfs*3	ENST00000263253	NM_001429.3	1467	-/A	27/31	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.433588043327405	2		464	293	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	90	627	1	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.433588043327405	2		628	328	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	90	473	8	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.783	0.705	0.864	1	0.983	1	SUBCLONAL	2	TRUE	1	0.433588043327405	2		481	265	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242743	16242743	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756096700	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	123	639	1	ENST00000375759.3:c.1364G>A	p.Arg455His	p.R455H	ENST00000375759	NM_015001.2	455	cGc/cAc	6/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.433588043327405	2		640	404	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259751	16259751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	125	610	2	ENST00000375759.3:c.7016G>A	p.Arg2339His	p.R2339H	ENST00000375759	NM_015001.2	2339	cGc/cAc	11/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.433588043327405	2		612	390	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023285	27023285	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs797045263	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	65	137	1	ENST00000324856.7:c.394del	p.Val132TrpfsTer100	p.V132Wfs*100	ENST00000324856	NM_006015.4	131	Ggg/gg	1/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.433588043327405	2		138	250	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226564855	226564855	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138228205	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	86	520	1	ENST00000366794.5:c.1895C>T	p.Thr632Met	p.T632M	ENST00000366794	NM_001618.3	632	aCg/aTg	13/23	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.433588043327405	2		521	297	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680490	241680490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139642944	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	113	487	0	ENST00000366560.3:c.259C>T	p.Arg87Cys	p.R87C	ENST00000366560	NM_000143.3	87	Cgc/Tgc	2/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.433588043327405	2		487	422	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246091255	246091255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs549272016	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	98	560	0	ENST00000388985.4:c.680G>A	p.Arg227Gln	p.R227Q	ENST00000388985		227	cGa/cAa	7/12	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.433588043327405	2		560	303	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332841	70332841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	78	714	1	ENST00000373644.4:c.746G>A	p.Cys249Tyr	p.C249Y	ENST00000373644	NM_030625.2	249	tGt/tAt	2/12	1	2	FACETS	0.759	0.677	0.844	1	0.98	1	SUBCLONAL	2	TRUE	1	0.433588043327405	2		715	237	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406360	70406360	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	84	685	0	ENST00000373644.4:c.3874G>A	p.Ala1292Thr	p.A1292T	ENST00000373644	NM_030625.2	1292	Gcc/Acc	4/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.433588043327405	2		685	312	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939260	71939260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	153	720	0	ENST00000298229.2:c.209G>A	p.Arg70His	p.R70H	ENST00000298229	NM_001567.3	70	cGc/cAc	2/28	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.433588043327405	2		720	488	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949102	71949102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	114	539	0	ENST00000298229.2:c.3569G>A	p.Gly1190Asp	p.G1190D	ENST00000298229	NM_001567.3	1190	gGc/gAc	27/28	1	2	FACETS	0.848	0.774	0.924	1	0.988	1	CLONAL	2	TRUE	1	0.433588043327405	2		539	310	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998882	100998882	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	111	563	0	ENST00000325455.5:c.920C>A	p.Pro307His	p.P307H	ENST00000325455	NM_001202474.3	307	cCt/cAt	1/8	1	2	FACETS	0.785	0.715	0.858	1	0.986	1	SUBCLONAL	2	TRUE	1	0.433588043327405	2		563	326	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	86	488	5	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.433588043327405	2		493	271	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	108	426	5	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.433588043327405	2		431	420	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524203	18524203	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	156	650	0	ENST00000266497.5:c.1715C>T	p.Ala572Val	p.A572V	ENST00000266497		572	gCa/gTa	11/31	0.0904530960956511	3	FACETS	1	0.979	1			1	INDETERMINATE	2	TRUE	NA	0.433588043327405	3		650	381	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441815	49441816	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs756471180	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	258	612	4	ENST00000301067.7:c.4168dup	p.Ala1390GlyfsTer42	p.A1390Gfs*42	ENST00000301067	NM_003482.3	1390	gca/gGca	14/54	0.42189670970495	4	FACETS	0.894	0.843	0.945	0.894	0.843	0.945	CLONAL	3	TRUE	1	0.433588043327405	4		616	636	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480445	50480445	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	153	560	0	ENST00000394963.4:c.407G>T	p.Arg136Met	p.R136M	ENST00000394963	NM_003076.4	136	aGg/aTg	3/13	0.42189670970495	4	FACETS	1	0.984	1	0.436	0.399	0.474	CLONAL	1	TRUE	1	0.433588043327405	4		560	774	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	88	600	4	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	0.282543962209262	2	FACETS	0.983	0.876	1	0.491	0.438	0.548	CLONAL	1	TRUE	0	0.433588043327405	2		604	413	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240613	133240613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201115064	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	153	557	1	ENST00000320574.5:c.2683G>A	p.Ala895Thr	p.A895T	ENST00000320574	NM_006231.2	895	Gcc/Acc	23/49	0.282543962209262	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.433588043327405	2		558	324	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248878	133248878	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373000452	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	254	656	0	ENST00000320574.5:c.1717C>T	p.Arg573Trp	p.R573W	ENST00000320574	NM_006231.2	573	Cgg/Tgg	16/49	0.282543962209262	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.433588043327405	2		656	492	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929041	32929041	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358930	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	76	574	0	ENST00000380152.3:c.7051G>A	p.Ala2351Thr	p.A2351T	ENST00000380152		2351	Gca/Aca	14/27	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.433588043327405	2		574	282	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	76	478	3	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	0.433588043327405	2		481	318	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524568	103524568	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	74	275	0	ENST00000355739.4:c.2705del	p.Asn902IlefsTer4	p.N902Ifs*4	ENST00000355739	NM_000123.3	900	cAa/ca	13/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.433588043327405	2		275	231	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242099	105242099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768800433	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	112	674	0	ENST00000349310.3:c.325G>A	p.Gly109Ser	p.G109S	ENST00000349310	NM_001014432.1	109	Ggc/Agc	6/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.433588043327405	2		674	371	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	95	738	4	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	1	2	FACETS	0.753	0.679	0.829	1	0.983	1	SUBCLONAL	2	TRUE	1	0.433588043327405	2		742	291	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	120	572	6	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.433588043327405	2		578	401	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	112	454	1	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.929	0.85	1	1	0.989	1	CLONAL	2	TRUE	1	0.433588043327405	2		455	278	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830776	3830776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424319951	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	101	554	0	ENST00000262367.5:c.1780G>A	p.Glu594Lys	p.E594K	ENST00000262367	NM_004380.2	594	Gaa/Aaa	8/31	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.433588043327405	2		554	315	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670755	67670755	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	89	520	0	ENST00000264010.4:c.1999+1G>A		p.X667_splice	ENST00000264010	NM_006565.3	667			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.433588043327405	2		520	275	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830319	72830319	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	58	342	0	ENST00000268489.5:c.6262C>T	p.Leu2088Phe	p.L2088F	ENST00000268489	NM_006885.3	2088	Ctc/Ttc	9/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.433588043327405	2		342	197	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830431	72830432	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	29	292	1	ENST00000268489.5:c.6149dup	p.Leu2051ThrfsTer105	p.L2051Tfs*105	ENST00000268489	NM_006885.3	2050	cca/ccCa	9/10	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.433588043327405	2		293	97	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993679	72993679	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	76	541	0	ENST00000268489.5:c.366G>T	p.Glu122Asp	p.E122D	ENST00000268489	NM_006885.3	122	gaG/gaT	2/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.433588043327405	2		541	289	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89874763	89874763	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	107	640	1	ENST00000389301.3:c.535C>T	p.Leu179Phe	p.L179F	ENST00000389301	NM_000135.2	179	Ctt/Ttt	6/43	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.433588043327405	2		641	339	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979987	7979987	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746723399	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	192	681	0	ENST00000319144.4:c.1350del	p.Leu451SerfsTer16	p.L451Sfs*16	ENST00000319144	NM_001139.2	450	ggG/gg	10/15	1	2	FACETS	0.893	0.833	0.953	1	0.993	1	CLONAL	2	TRUE	1	0.433588043327405	2		681	496	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508464	29508464	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	75	482	0	ENST00000356175.3:c.611T>C	p.Leu204Pro	p.L204P	ENST00000356175	NM_000267.3	204	cTa/cCa	6/57	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.433588043327405	2		482	258	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29579995	29579996	+	intron_variant	Intron	INS	-	-	A	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	84	423	2	ENST00000356175.3:c.4110+3865dup		p.*1370*	ENST00000356175	NM_000267.3	1384/2839			1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.433588043327405	2		425	347	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512401	38512402	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs745553450	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	82	520	0	ENST00000254066.5:c.1319dup	p.Pro441AlafsTer5	p.P441Afs*5	ENST00000254066	NM_000964.3	438	gcc/gCcc	9/9	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.433588043327405	2		520	338	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40483548	40483548	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	67	434	0	ENST00000264657.5:c.1051T>G	p.Leu351Val	p.L351V	ENST00000264657	NM_139276.2	351	Ttg/Gtg	11/24	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.433588043327405	2		434	251	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	126	691	4	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.801	0.733	0.87	1	0.988	1	CLONAL	2	TRUE	1	0.433588043327405	2		695	363	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78617569	78617569	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	97	500	0	ENST00000306801.3:c.307G>A	p.Gly103Ser	p.G103S	ENST00000306801	NM_020761.2	103	Ggt/Agt	3/34	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.433588043327405	2		500	316	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78831665	78831665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1000105279	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	134	697	1	ENST00000306801.3:c.1474G>A	p.Val492Ile	p.V492I	ENST00000306801	NM_020761.2	492	Gtt/Att	13/34	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.433588043327405	2		698	517	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223115	1223115	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	175	672	0	ENST00000326873.7:c.1052A>G	p.Glu351Gly	p.E351G	ENST00000326873	NM_000455.4	351	gAg/gGg	8/10	0.384831984150785	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.433588043327405	1		672	626	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226304	2226304	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	128	730	1	ENST00000398665.3:c.3784C>T	p.Gln1262Ter	p.Q1262*	ENST00000398665	NM_032482.2	1262	Cag/Tag	27/28	0.384831984150785	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.433588043327405	1		731	405	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218538	5218538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767763908	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	97	681	1	ENST00000357368.4:c.3941G>A	p.Arg1314His	p.R1314H	ENST00000357368	NM_002850.3	1314	cGc/cAc	25/38	0.384831984150785	1	FACETS	0.987	0.888	1	0.987	0.888	1	CLONAL	1	TRUE	0	0.433588043327405	1		682	355	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	110	824	4	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	0.433588043327405	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.433588043327405	1		828	336	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765754	41765754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	91	507	0	ENST00000301178.4:c.2630C>T	p.Ala877Val	p.A877V	ENST00000301178	NM_021913.4	877	gCt/gTt	20/20	0.116070869469764	4	FACETS	1	0.935	1	1	0.935	1	INDETERMINATE	2	TRUE	2	0.433588043327405	4		507	286	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	337	637	0	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	0.116070869469764	4	FACETS	1	0.984	1	1	0.996	1	INDETERMINATE	3	TRUE	2	0.433588043327405	4		637	694	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795483	42795483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751769419	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	82	517	0	ENST00000575354.2:c.2563G>A	p.Gly855Ser	p.G855S	ENST00000575354	NM_015125.3	855	Ggc/Agc	10/20	0.116070869469764	4	FACETS	0.948	0.846	1	0.948	0.846	1	INDETERMINATE	2	TRUE	2	0.433588043327405	4		517	286	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797435	42797435	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	98	600	0	ENST00000575354.2:c.3795+2T>C		p.X1265_splice	ENST00000575354	NM_015125.3	1265			0.116070869469764	4	FACETS	0.79	0.71	0.875	0.79	0.71	0.875	INDETERMINATE	2	TRUE	2	0.433588043327405	4		600	410	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910264	50910264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878854523	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	111	697	1	ENST00000440232.2:c.1519C>T	p.Arg507Cys	p.R507C	ENST00000440232	NM_002691.3	507	Cgc/Tgc	13/27	0.261235113032811	0	FACETS	0.808	0.734	0.885			1	CLONAL	1	TRUE	0	0.433588043327405	0		698	359	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991736	25991736	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs530632623	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	75	407	0	ENST00000435504.4:c.506C>T	p.Ala169Val	p.A169V	ENST00000435504		169	gCg/gTg	7/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.433588043327405	2		407	279	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	104	392	0	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.433588043327405	2		392	367	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033352	48033352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750949	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	100	452	0	ENST00000234420.5:c.3656C>T	p.Thr1219Ile	p.T1219I	ENST00000234420	NM_000179.2	1219	aCt/aTt	8/10	1	2	FACETS	0.761	0.689	0.836	1	0.984	1	SUBCLONAL	2	TRUE	1	0.433588043327405	2		452	303	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39713151	39713151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	111	365	0	ENST00000361337.2:c.557C>T	p.Pro186Leu	p.P186L	ENST00000361337	NM_003286.2	186	cCt/cTt	8/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.433588043327405	2		365	388	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	193	355	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.433588043327405	2	FACETS	0.951	0.9	1	1	0.993	1	CLONAL	3	TRUE	0	0.433588043327405	2		355	312	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412922	49412922	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	132	795	0	ENST00000418115.1:c.101A>G	p.Tyr34Cys	p.Y34C	ENST00000418115	NM_001664.2	34	tAt/tGt	2/5	0.433588043327405	2	FACETS	1	0.964	1	0.554	0.505	0.604	CLONAL	1	TRUE	0	0.433588043327405	2		795	550	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935972	49935972	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	133	693	0	ENST00000296474.3:c.1698C>A	p.His566Gln	p.H566Q	ENST00000296474	NM_002447.2	566	caC/caA	4/20	0.433588043327405	2	FACETS	1	0.987	1	0.743	0.681	0.807	CLONAL	1	TRUE	0	0.433588043327405	2		693	413	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	128	359	1	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.433588043327405	2		360	406	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474616	138474617	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	86	506	0	ENST00000289153.2:c.376dup	p.Ile126AsnfsTer11	p.I126Nfs*11	ENST00000289153	NM_006219.2	126	att/aAtt	2/22	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.433588043327405	2		506	306	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998127	169998128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs753143066	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	121	728	2	ENST00000295797.4:c.826dup	p.Thr276AsnfsTer16	p.T276Nfs*16	ENST00000295797	NM_002740.5	273	tta/ttAa	9/18	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.433588043327405	2		730	422	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510239	187510239	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	113	501	0	ENST00000441802.2:c.13274A>G	p.Tyr4425Cys	p.Y4425C	ENST00000441802	NM_005245.3	4425	tAc/tGc	27/27	1	2	FACETS	0.914	0.836	0.994	1	0.989	1	CLONAL	2	TRUE	1	0.433588043327405	2		501	285	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294163	1294163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199701877	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	129	796	0	ENST00000310581.5:c.838G>A	p.Glu280Lys	p.E280K	ENST00000310581	NM_198253.2	280	Gaa/Aaa	2/16	0.208081250026496	0	FACETS	1	0.919	1			1	INDETERMINATE	1	TRUE	0	0.433588043327405	0		796	337	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575459	67575459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751832841	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	90	410	0	ENST00000274335.5:c.532G>A	p.Asp178Asn	p.D178N	ENST00000274335		178	Gat/Aat	4/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.433588043327405	2		410	350	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515235	149515235	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	127	626	0	ENST00000261799.4:c.247A>G	p.Ser83Gly	p.S83G	ENST00000261799	NM_002609.3	83	Agc/Ggc	3/23	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.433588043327405	2		626	415	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519423	176519423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	112	790	2	ENST00000292408.4:c.829G>A	p.Ala277Thr	p.A277T	ENST00000292408	NM_213647.1	277	Gcc/Acc	7/18	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.433588043327405	2		792	368	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058747	180058748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755445139	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	75	626	1	ENST00000261937.6:c.89dup	p.Thr31AspfsTer15	p.T31Dfs*15	ENST00000261937	NM_182925.4	30	ccg/ccCg	2/30	0.336735059137562	0	FACETS	0.778	0.691	0.869			1	SUBCLONAL	1	TRUE	0	0.433588043327405	0		627	252	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138798	37138798	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	138	431	0	ENST00000373509.5:c.231G>T	p.Trp77Cys	p.W77C	ENST00000373509	NM_002648.3	77	tgG/tgT	3/6	0.243179978729506	6	FACETS	1	0.965	1	0.738	0.675	0.803	INDETERMINATE	2	TRUE	3	0.433588043327405	6		431	537	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192384	138192384	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	70	225	0	ENST00000237289.4:c.20C>A	p.Pro7His	p.P7H	ENST00000237289	NM_001270507.1	7	cCt/cAt	2/9	0.433588043327405	6	FACETS	0.828	0.726	0.937			1	CLONAL	2	TRUE	NA	0.433588043327405	6		225	364	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851988	128851988	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55722779	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	97	686	1	ENST00000249373.3:c.2060C>T	p.Pro687Leu	p.P687L	ENST00000249373	NM_005631.4	687	cCg/cTg	12/12	1	2	FACETS	0.819	0.742	0.9	1	0.985	1	CLONAL	2	TRUE	1	0.433588043327405	2		687	273	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	86	691	2	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.433588043327405	2		693	291	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860073	151860074	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	67	427	0	ENST00000262189.6:c.10588dup	p.Ser3530PhefsTer36	p.S3530Ffs*36	ENST00000262189	NM_170606.2	3530	tct/tTct	43/59	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.433588043327405	2		427	221	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860448	151860448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs962041154	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	98	597	0	ENST00000262189.6:c.10214G>A	p.Arg3405Gln	p.R3405Q	ENST00000262189	NM_170606.2	3405	cGa/cAa	43/59	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.433588043327405	2		597	316	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012326	152012326	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	118	460	0	ENST00000262189.6:c.487T>C	p.Trp163Arg	p.W163R	ENST00000262189	NM_170606.2	163	Tgg/Cgg	4/59	1	2	FACETS	0.758	0.691	0.827	1	0.986	1	SUBCLONAL	2	TRUE	1	0.433588043327405	2		460	359	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740324	145740324	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	325	637	0	ENST00000428558.2:c.1616A>C	p.Asp539Ala	p.D539A	ENST00000428558	NM_004260.3	539	gAc/gCc	9/22	0.433588043327405	5	FACETS	0.934	0.89	0.978	1	0.993	1	CLONAL	4	TRUE	2	0.433588043327405	5		637	662	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340442	8340442	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	84	399	0	ENST00000356435.5:c.5154G>T	p.Gln1718His	p.Q1718H	ENST00000356435		1718	caG/caT	31/35	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.433588043327405	2		399	289	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882049	36882050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs780753361	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	105	764	0	ENST00000358127.4:c.963dup	p.Ala322ArgfsTer19	p.A322Rfs*19	ENST00000358127	NM_001280556.1	321	-/C	8/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.433588043327405	2		764	366	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211539	98211539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772537644	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	99	554	0	ENST00000331920.6:c.3616C>T	p.Arg1206Cys	p.R1206C	ENST00000331920	NM_000264.3	1206	Cgc/Tgc	22/24	1	2	FACETS	0.818	0.741	0.898	1	0.986	1	CLONAL	2	TRUE	1	0.433588043327405	2		554	279	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918253	44918253	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	86	207	0	ENST00000377967.4:c.878G>A	p.Cys293Tyr	p.C293Y	ENST00000377967	NM_021140.2	293	tGc/tAc	11/29	1	1	FACETS	1	0.973	1	1	0.989	1	CLONAL	2	TRUE	0	0.433588043327405	1		207	136	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413109	63413109	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	126	358	0	ENST00000330258.3:c.58A>G	p.Thr20Ala	p.T20A	ENST00000330258	NM_152424.3	20	Acc/Gcc	2/2	1	1	FACETS	1	0.986	1	1	0.993	1	CLONAL	2	TRUE	0	0.433588043327405	1		358	188	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348996	70348996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1389138246	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	138	323	1	ENST00000374080.3:c.3508C>T	p.Arg1170Trp	p.R1170W	ENST00000374080		1170	Cgg/Tgg	25/45	1	1	FACETS	0.97	0.903	1	1	0.992	1	CLONAL	2	TRUE	0	0.433588043327405	1		324	257	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855252	76855252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	81	236	0	ENST00000373344.5:c.5735C>T	p.Ala1912Val	p.A1912V	ENST00000373344	NM_000489.3	1912	gCc/gTc	24/35	1	1	FACETS	1	0.959	1	1	0.988	1	CLONAL	2	TRUE	0	0.433588043327405	1		236	135	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0028581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	102	707	2	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	1	2	FACETS	0.771	0.688	0.86	0.771	0.688	0.86	SUBCLONAL	1	TRUE	1	0.226708161379345	2		709	1167	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754051	42754051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769239795	NA	P-0028581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	203	757	1	ENST00000222329.4:c.301C>T	p.Arg101Trp	p.R101W	ENST00000222329	NM_006494.2	101	Cgg/Tgg	3/4	0.150509610990423	2	FACETS	1	0.988	1	0.673	0.622	0.725	CLONAL	1	TRUE	0	0.226708161379345	2		758	1331	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0028582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	474	387	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.668288863834385	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.668288863834385	3		387	939	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	386	770	0	ENST00000269305.4:c.503A>C	p.His168Pro	p.H168P	ENST00000269305	NM_001126112.2	168	cAc/cCc	5/11	0.668288863834385	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.668288863834385	1		770	758	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0028583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	373	778	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.92	0.874	0.967	0.92	0.874	0.967	CLONAL	1	TRUE	1	0.703802482442919	2		778	1152	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972509	81972509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755617580	NA	P-0028583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	296	683	0	ENST00000359376.3:c.3302C>T	p.Thr1101Met	p.T1101M	ENST00000359376	NM_002661.3	1101	aCg/aTg	29/33	1	2	FACETS	0.899	0.848	0.951	0.899	0.848	0.951	CLONAL	1	TRUE	1	0.703802482442919	2		683	936	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898755	134898755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs546798910	NA	P-0028583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	260	543	0	ENST00000398015.3:c.1813G>A	p.Glu605Lys	p.E605K	ENST00000398015	NM_004441.4	605	Gaa/Aaa	10/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.703802482442919	2		543	732	SUCCESS
YES1	7525	MSKCC	GRCh37	18	732914	732914	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1384930568	NA	P-0028583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	416	832	2	ENST00000314574.4:c.1343G>A	p.Arg448Gln	p.R448Q	ENST00000314574	NM_005433.3	448	cGg/cAg	11/12	1	2	FACETS	0.967	0.922	1	0.967	0.922	1	CLONAL	1	TRUE	1	0.703802482442919	2		834	1222	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	88	376	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.454661675108141	2		376	375	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0028584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	445	436	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.451950959251613	3	FACETS	0.994	0.95	1	0.994	0.95	1	CLONAL	2	TRUE	1	0.454661675108141	3		437	1208	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0028584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	216	558	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.992	0.923	1	0.992	0.923	1	CLONAL	1	TRUE	1	0.454661675108141	2		558	958	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189847	11189847	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	281	709	0	ENST00000361445.4:c.5662T>C	p.Phe1888Leu	p.F1888L	ENST00000361445	NM_004958.3	1888	Ttc/Ctc	40/58	1	2	FACETS	0.997	0.936	1	0.997	0.936	1	CLONAL	1	TRUE	1	0.454661675108141	2		709	1240	SUCCESS
APC	324	MSKCC	GRCh37	5	112174213	112174214	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554084587	NA	P-0028584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	186	499	0	ENST00000257430.4:c.2926dup	p.Arg976LysfsTer9	p.R976Kfs*9	ENST00000257430	NM_000038.5	974	-/A	16/16	1	2	FACETS	0.951	0.88	1	0.951	0.88	1	CLONAL	1	TRUE	1	0.454661675108141	2		499	860	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980403	201980404	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCAGATG	novel	NA	P-0028584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1291	279	729	0	ENST00000359651.3:c.140_147dup	p.Ser50ProfsTer108	p.S50Pfs*108	ENST00000359651		47	ccc/cCCCAGATGcc	1/8	0.19248764359244	4	FACETS	1	0.983	1	0.569	0.532	0.606	INDETERMINATE	1	TRUE	2	0.454661675108141	4		729	1570	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457409	67457410	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs863223757	NA	P-0028584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	61	687	0	ENST00000327367.4:c.387_388del	p.Arg129SerfsTer36	p.R129Sfs*36	ENST00000327367	NM_005902.3	128	cAG/c	2/9	1	2	FACETS	0.259	0.223	0.299	0.259	0.223	0.299	SUBCLONAL	1	TRUE	1	0.454661675108141	2		687	1035	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394778	45394778	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	64	511	0	ENST00000262160.6:c.571C>T	p.Pro191Ser	p.P191S	ENST00000262160	NM_005901.5	191	Ccg/Tcg	5/11	1	2	FACETS	0.335	0.289	0.385	0.335	0.289	0.385	SUBCLONAL	1	TRUE	1	0.454661675108141	2		511	840	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281281	15281281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776163983	NA	P-0028584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	308	695	2	ENST00000263388.2:c.4975G>A	p.Val1659Ile	p.V1659I	ENST00000263388	NM_000435.2	1659	Gtc/Atc	27/33	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.454661675108141	2		697	1239	SUCCESS
APC	324	MSKCC	GRCh37	5	112175729	112175729	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	158	358	0	ENST00000257430.4:c.4438C>T	p.Gln1480Ter	p.Q1480*	ENST00000257430	NM_000038.5	1480	Cag/Tag	16/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.454661675108141	2		358	633	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0028585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	90	436	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.909	0.805	1	0.909	0.805	1	CLONAL	1	TRUE	1	0.227876503140923	2		437	869	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577129	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519986	NA	P-0028585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	87	656	1	ENST00000269305.4:c.809T>C	p.Phe270Ser	p.F270S	ENST00000269305	NM_001126112.2	270	tTt/tCt	8/11	0.227876503140923	1	FACETS	0.839	0.742	0.943	0.839	0.742	0.943	CLONAL	1	TRUE	0	0.227876503140923	1		657	806	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519934	NA	P-0028587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	87	502	0	ENST00000263967.3:c.333G>C	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaC	2/21	1	2	FACETS	0.805	0.716	0.898	1	0.982	1	CLONAL	2	FALSE	1	0.25554593570128	2		502	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs879253911	NA	P-0028587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	34	680	0	ENST00000269305.4:c.538G>T	p.Glu180Ter	p.E180*	ENST00000269305	NM_001126112.2	180	Gag/Tag	5/11	1	2	FACETS	0.811	0.664	0.976	0.811	0.664	0.976	CLONAL	1	FALSE	1	0.25554593570128	2		680	328	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421790	49421790	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0028587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	58	795	1	ENST00000301067.7:c.14515+2T>C		p.X4839_splice	ENST00000301067	NM_003482.3	4839			0.1800993611642	3	FACETS	1	0.923	1	0.555	0.478	0.639	CLONAL	1	FALSE	1	0.25554593570128	3		796	461	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907268	32907269	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	67	663	0	ENST00000380152.3:c.1654dup	p.Ser552PhefsTer8	p.S552Ffs*8	ENST00000380152		551	-/T	10/27	0.25554593570128	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	0	0.25554593570128	1		663	338	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56852645	56852645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs189324020	NA	P-0028587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	50	593	0	ENST00000308159.5:c.559C>T	p.Arg187Trp	p.R187W	ENST00000308159	NM_014669.4	187	Cgg/Tgg	6/22	NA	2	FACETS	0.921	0.783	1			1	INDETERMINATE	1	FALSE	NA	0.25554593570128	2		593	425	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395683	45395683	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	39	511	0	ENST00000262160.6:c.451T>G	p.Tyr151Asp	p.Y151D	ENST00000262160	NM_005901.5	151	Tat/Gat	4/11	0.1800993611642	3	FACETS	0.774	0.641	0.921	0.387	0.32	0.461	CLONAL	1	FALSE	1	0.25554593570128	3		511	445	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793241	42793241	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	43	724	0	ENST00000575354.2:c.1133A>C	p.Gln378Pro	p.Q378P	ENST00000575354	NM_015125.3	378	cAg/cCg	7/20	NA	2	FACETS	0.825	0.691	0.972			1	INDETERMINATE	1	FALSE	NA	0.25554593570128	2		724	408	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082441	16082441	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs747547602	NA	P-0028587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	26	771	0	ENST00000281043.3:c.255C>A	p.Asn85Lys	p.N85K	ENST00000281043	NM_005378.4	85	aaC/aaA	2/3	1	2	FACETS	0.804	0.639	0.992	0.804	0.639	0.992	CLONAL	1	FALSE	1	0.25554593570128	2		771	253	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628769	187628769	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	45	760	0	ENST00000441802.2:c.2213T>A	p.Phe738Tyr	p.F738Y	ENST00000441802	NM_005245.3	738	tTc/tAc	2/27	0.245537772232249	0	FACETS	0.659	0.555	0.773			1	SUBCLONAL	1	FALSE	0	0.25554593570128	0		760	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0028600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	325	710	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.313637695105911	5	FACETS	1	0.983	1	0.731	0.69	0.773	CLONAL	2	TRUE	2	0.383413418876011	5		710	1218	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913315	NA	P-0028600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	274	617	0	ENST00000326873.7:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000326873	NM_000455.4	194	Gac/Tac	4/10	0.375550446063852	2	FACETS	0.837	0.788	0.887	0.837	0.788	0.887	CLONAL	2	TRUE	0	0.383413418876011	2		617	854	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584438	39584438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	221	559	0	ENST00000262039.4:c.1103C>T	p.Ser368Phe	p.S368F	ENST00000262039	NM_002647.2	368	tCc/tTc	10/25	0.375550446063852	2	FACETS	0.876	0.82	0.934	0.876	0.82	0.934	CLONAL	2	TRUE	0	0.383413418876011	2		559	658	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	416	849	1	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.313637695105911	5	FACETS	1	0.978	1	0.7	0.665	0.736	CLONAL	2	TRUE	2	0.383413418876011	5		850	1627	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974799	21974799	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	96	166	0	ENST00000304494.5:c.28G>T	p.Glu10Ter	p.E10*	ENST00000304494	NM_000077.4	10	Gag/Tag	1/3	0.37551225823043	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	0	0.383413418876011	2		166	243	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649856	88649856	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	67	411	0	ENST00000372037.3:c.105G>A	p.Met35Ile	p.M35I	ENST00000372037	NM_004329.2	35	atG/atA	4/13	0.383413418876011	3	FACETS	0.879	0.765	1	0.439	0.382	0.501	CLONAL	1	TRUE	1	0.383413418876011	3		411	474	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117545	70117545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	209	600	0	ENST00000245479.2:c.13G>A	p.Asp5Asn	p.D5N	ENST00000245479	NM_000346.3	5	Gac/Aac	1/3	0.272349241336447	4	FACETS	0.835	0.776	0.896	0.835	0.776	0.896	CLONAL	2	TRUE	2	0.383413418876011	4		600	903	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257226	16257226	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	268	686	0	ENST00000375759.3:c.4491G>C	p.Lys1497Asn	p.K1497N	ENST00000375759	NM_015001.2	1497	aaG/aaC	11/15	0.347183525555946	2	FACETS	0.93	0.876	0.984	0.93	0.876	0.984	CLONAL	2	TRUE	0	0.383413418876011	2		686	752	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927422	245927422	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1345998603	NA	P-0028600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	126	656	0	ENST00000388985.4:c.1106G>C	p.Arg369Thr	p.R369T	ENST00000388985		369	aGa/aCa	11/12	0.383413418876011	3	FACETS	0.814	0.736	0.896	0.271	0.245	0.299	CLONAL	1	TRUE	0	0.383413418876011	3		656	962	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443859	18443859	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	157	604	0	ENST00000266497.5:c.832T>A	p.Phe278Ile	p.F278I	ENST00000266497		278	Ttt/Att	3/31	0.272349241336447	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	2	0.383413418876011	4		604	536	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445703	49445703	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780108221	NA	P-0028600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1507	183	1076	1	ENST00000301067.7:c.1763C>T	p.Ser588Leu	p.S588L	ENST00000301067	NM_003482.3	588	tCa/tTa	10/54	0.383413418876011	4	FACETS	0.781	0.718	0.848			1	SUBCLONAL	1	TRUE	NA	0.383413418876011	4		1077	1690	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673804	37673804	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	61	643	0	ENST00000447079.4:c.2958C>G	p.Phe986Leu	p.F986L	ENST00000447079	NM_015083.1	986	ttC/ttG	10/14	0.272349241336447	4	FACETS	0.444	0.382	0.513	0.222	0.191	0.257	SUBCLONAL	1	TRUE	2	0.383413418876011	4		643	991	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374945	45374945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	245	641	0	ENST00000262160.6:c.898G>A	p.Asp300Asn	p.D300N	ENST00000262160	NM_005901.5	300	Gat/Aat	8/11	0.375550446063852	2	FACETS	0.949	0.893	1	0.949	0.893	1	CLONAL	2	TRUE	0	0.383413418876011	2		641	673	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602863	10602871	+	inframe_deletion	In_Frame_Del	DEL	CGTTCAGGT	CGTTCAGGT	-	novel	NA	P-0028600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	368	856	0	ENST00000171111.5:c.707_715del	p.Asp236_Asn238del	p.D236_N238del	ENST00000171111	NM_203500.1	236	gACCTGAACGtg/gtg	3/6	0.21003416279604	3	FACETS	0.981	0.931	1			1	INDETERMINATE	2	TRUE	NA	0.383413418876011	3		856	1166	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118590	11118590	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	99	409	0	ENST00000358026.2:c.2014G>C	p.Glu672Gln	p.E672Q	ENST00000358026	NM_001128849.1	672	Gag/Cag	14/36	0.383413418876011	5	FACETS	0.95	0.847	1			1	CLONAL	1	TRUE	NA	0.383413418876011	5		409	856	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62293947	62293949	+	missense_variant	Missense_Mutation	TNP	TGA	TGA	CCT	novel	NA	P-0028600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	134	732	2	ENST00000360203.5:c.444_446delinsCCT	p.Glu149Leu	p.E149L	ENST00000360203	NM_001283009.1	148	ccTGAg/ccCCTg	5/35	0.313637695105911	5	FACETS	0.83	0.751	0.912	0.277	0.25	0.304	CLONAL	1	TRUE	2	0.383413418876011	5		734	1327	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71008508	71008508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	199	410	0	ENST00000318789.4:c.1924C>T	p.Pro642Ser	p.P642S	ENST00000318789	NM_032682.5	642	Cca/Tca	21/21	0.383413418876011	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.383413418876011	3		410	582	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119545642	119545642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	100	500	1	ENST00000316626.5:c.1295C>T	p.Ser432Phe	p.S432F	ENST00000316626		432	tCc/tTc	12/12	0.383413418876011	3	FACETS	0.877	0.784	0.976	0.438	0.392	0.488	CLONAL	1	TRUE	1	0.383413418876011	3		501	709	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964346	55964346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	98	620	1	ENST00000263923.4:c.2467G>A	p.Asp823Asn	p.D823N	ENST00000263923	NM_002253.2	823	Gat/Aat	17/30	0.383413418876011	3	FACETS	0.813	0.726	0.907	0.407	0.363	0.454	CLONAL	1	TRUE	1	0.383413418876011	3		621	749	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542903	187542903	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	79	370	0	ENST00000441802.2:c.4837G>C	p.Asp1613His	p.D1613H	ENST00000441802	NM_005245.3	1613	Gat/Cat	10/27	0.383413418876011	3	FACETS	0.95	0.837	1	0.475	0.418	0.535	CLONAL	1	TRUE	1	0.383413418876011	3		370	517	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631156	176631156	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	256	583	0	ENST00000439151.2:c.1099G>C	p.Glu367Gln	p.E367Q	ENST00000439151	NM_022455.4	367	Gag/Cag	4/23	0.383413418876011	4	FACETS	0.853	0.798	0.909	0.853	0.798	0.909	CLONAL	2	TRUE	2	0.383413418876011	4		583	1083	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287875	33287875	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	277	605	0	ENST00000374542.5:c.1378G>C	p.Asp460His	p.D460H	ENST00000374542	NM_001141970.1	460	Gat/Cat	5/8	0.383413418876011	4	FACETS	0.977	0.918	1	0.977	0.918	1	CLONAL	2	TRUE	2	0.383413418876011	4		605	1023	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045491	47045491	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	272	373	0	ENST00000377604.3:c.2458G>T	p.Glu820Ter	p.E820*	ENST00000377604	NM_001204468.1	820	Gaa/Taa	22/24	0.383413418876011	2	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.383413418876011	2		373	602	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426126	47426126	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	373	436	0	ENST00000377045.4:c.646C>A	p.Pro216Thr	p.P216T	ENST00000377045	NM_001654.4	216	Ccc/Acc	7/16	0.383413418876011	2	FACETS	0.856	0.818	0.893			1	CLONAL	3	TRUE	NA	0.383413418876011	2		436	758	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578188	7578194	+	frameshift_variant	Frame_Shift_Del	DEL	CATAGGG	CATAGGG	-	novel	NA	P-0028601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	209	777	0	ENST00000269305.4:c.655_661del	p.Pro219SerfsTer26	p.P219Sfs*26	ENST00000269305	NM_001126112.2	219	CCCTATGag/ag	6/11	0.412642652146167	1	FACETS	0.952	0.886	1	0.952	0.886	1	CLONAL	1	TRUE	0	0.428112074904403	1		777	806	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291897	15291897	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	254	862	2	ENST00000263388.2:c.2869G>A	p.Ala957Thr	p.A957T	ENST00000263388	NM_000435.2	957	Gcc/Acc	18/33	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.428112074904403	2		864	1007	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317078	87317078	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	100	535	0	ENST00000277120.3:c.217A>G	p.Ile73Val	p.I73V	ENST00000277120		73	Atc/Gtc	3/19	1	2	FACETS	0.737	0.659	0.819	0.737	0.659	0.819	SUBCLONAL	1	TRUE	1	0.428112074904403	2		535	634	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576112	29576112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540108477	NA	P-0028606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	464	607	0	ENST00000356175.3:c.4085G>A	p.Arg1362Gln	p.R1362Q	ENST00000356175	NM_000267.3	1362	cGa/cAa	30/57	0.73980299006336	4	FACETS	0.874	0.836	0.911	0.874	0.836	0.911	CLONAL	2	TRUE	2	0.816066439728317	4		607	1182	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747075	40747075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199637632	NA	P-0028606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	504	682	3	ENST00000373198.4:c.3007G>A	p.Val1003Ile	p.V1003I	ENST00000373198	NM_133170.3	1003	Gtc/Atc	22/32	0.766101971539996	5	FACETS	0.844	0.807	0.881	0.562	0.538	0.588	CLONAL	2	TRUE	2	0.816066439728317	5		685	1628	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38314894	38314894	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	468	536	0	ENST00000425967.3:c.170C>A	p.Ser57Tyr	p.S57Y	ENST00000425967	NM_001174067.1	57	tCc/tAc	3/19	0.676150443567605	4	FACETS	0.989	0.949	1	0.989	0.949	1	CLONAL	2	TRUE	2	0.816066439728317	4		536	1053	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711873	89711873	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs587781784	NA	P-0028606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	335	445	0	ENST00000371953.3:c.493-2A>T		p.X165_splice	ENST00000371953	NM_000314.4	165			0.676150443567605	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	2	0.816066439728317	4		445	733	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417803	32417803	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	335	406	0	ENST00000332351.3:c.1249G>A	p.Gly417Ser	p.G417S	ENST00000332351	NM_024426.4	417	Ggt/Agt	7/10	0.73980299006336	4	FACETS	0.872	0.828	0.916	0.872	0.828	0.916	CLONAL	2	TRUE	2	0.816066439728317	4		406	855	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218763	133218763	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	682	521	0	ENST00000320574.5:c.5173G>T	p.Val1725Leu	p.V1725L	ENST00000320574	NM_006231.2	1725	Gtg/Ttg	38/49	0.816066439728317	3	FACETS	0.959	0.94	0.977			1	CLONAL	3	TRUE	NA	0.816066439728317	3		521	818	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562852	21562852	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	660	728	1	ENST00000382592.4:c.1067A>G	p.Asn356Ser	p.N356S	ENST00000382592	NM_014572.2	356	aAc/aGc	4/8	0.767117551094211	2	FACETS	1	0.997	1	0.662	0.641	0.683	CLONAL	1	TRUE	0	0.816066439728317	2		729	1222	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514535	103514535	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	562	342	0	ENST00000355739.4:c.1036C>G	p.Leu346Val	p.L346V	ENST00000355739	NM_000123.3	346	Cta/Gta	8/15	0.816066439728317	6	FACETS	1	0.974	1	1	0.974	1	CLONAL	4	TRUE	2	0.816066439728317	6		342	901	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293193	91293193	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	436	587	0	ENST00000355112.3:c.695G>T	p.Ser232Ile	p.S232I	ENST00000355112	NM_000057.2	232	aGc/aTc	3/22	0.676150443567605	4	FACETS	0.86	0.822	0.899	0.86	0.822	0.899	CLONAL	2	TRUE	2	0.816066439728317	4		587	1128	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578254	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0028606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	624	718	1	ENST00000269305.4:c.595_596delinsAT	p.Gly199Ile	p.G199I	ENST00000269305	NM_001126112.2	199	GGa/ATa	6/11	0.739412743547198	2	FACETS	0.928	0.906	0.95	0.928	0.906	0.95	CLONAL	2	TRUE	0	0.816066439728317	2		719	824	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653064	29653064	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1135402869	NA	P-0028606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	373	418	0	ENST00000356175.3:c.4999G>T	p.Glu1667Ter	p.E1667*	ENST00000356175	NM_000267.3	1667	Gag/Tag	36/57	0.73980299006336	4	FACETS	0.92	0.877	0.964	0.92	0.877	0.964	CLONAL	2	TRUE	2	0.816066439728317	4		418	902	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207143	1207143	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	813	911	3	ENST00000326873.7:c.231del	p.Lys78ArgfsTer18	p.K78Rfs*18	ENST00000326873	NM_000455.4	77	gtC/gt	1/10	0.767117551094211	2	FACETS	0.942	0.922	0.961	0.942	0.922	0.961	CLONAL	2	TRUE	0	0.816066439728317	2		914	1058	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132428	11132428	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	674	753	0	ENST00000358026.2:c.2644G>C	p.Glu882Gln	p.E882Q	ENST00000358026	NM_001128849.1	882	Gaa/Caa	19/36	0.767117551094211	2	FACETS	0.972	0.951	0.992	0.972	0.951	0.992	CLONAL	2	TRUE	0	0.816066439728317	2		753	850	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455302	29455302	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	418	494	0	ENST00000389048.3:c.2500G>T	p.Val834Leu	p.V834L	ENST00000389048	NM_004304.4	834	Gtg/Ttg	15/29	0.676150443567605	4	FACETS	0.961	0.919	1	0.961	0.919	1	CLONAL	2	TRUE	2	0.816066439728317	4		494	968	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170804	99170804	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	521	562	0	ENST00000074304.5:c.1433G>T	p.Arg478Leu	p.R478L	ENST00000074304	NM_001134224.1	478	cGg/cTg	16/26	0.676150443567605	4	FACETS	0.969	0.931	1	0.969	0.931	1	CLONAL	2	TRUE	2	0.816066439728317	4		562	1197	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189350	99189350	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	578	698	0	ENST00000074304.5:c.2606G>T	p.Arg869Leu	p.R869L	ENST00000074304	NM_001134224.1	869	cGg/cTg	24/26	0.676150443567605	4	FACETS	0.912	0.878	0.947	0.912	0.878	0.947	CLONAL	2	TRUE	2	0.816066439728317	4		698	1410	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546901	9546901	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	433	553	0	ENST00000353224.5:c.1121C>G	p.Pro374Arg	p.P374R	ENST00000353224	NM_177990.2	374	cCg/cGg	5/10	0.451401118657555	4	FACETS	1	0.995	1	1	0.995	1	INDETERMINATE	2	TRUE	2	0.816066439728317	4		553	787	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561251	9561251	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	385	540	0	ENST00000353224.5:c.531C>A	p.His177Gln	p.H177Q	ENST00000353224	NM_177990.2	177	caC/caA	4/10	0.451401118657555	4	FACETS	1	0.994	1	1	0.994	1	INDETERMINATE	2	TRUE	2	0.816066439728317	4		540	705	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023564	31023564	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	720	567	1	ENST00000375687.4:c.3049G>T	p.Asp1017Tyr	p.D1017Y	ENST00000375687	NM_015338.5	1017	Gac/Tac	13/13	0.766101971539996	5	FACETS	0.885	0.857	0.913	0.885	0.857	0.913	CLONAL	3	TRUE	2	0.816066439728317	5		568	1478	SUCCESS
ATR	545	MSKCC	GRCh37	3	142168299	142168299	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1259374276	NA	P-0028606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	352	488	0	ENST00000350721.4:c.7907T>G	p.Met2636Arg	p.M2636R	ENST00000350721	NM_001184.3	2636	aTg/aGg	47/47	0.73980299006336	4	FACETS	0.885	0.842	0.929	0.885	0.842	0.929	CLONAL	2	TRUE	2	0.816066439728317	4		488	885	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526314	189526314	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	382	382	0	ENST00000264731.3:c.578C>A	p.Thr193Lys	p.T193K	ENST00000264731	NM_003722.4	193	aCg/aAg	4/14	0.73980299006336	4	FACETS	0.95	0.906	0.994	0.95	0.906	0.994	CLONAL	2	TRUE	2	0.816066439728317	4		382	895	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1955114	1955114	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	737	756	0	ENST00000382891.5:c.2201A>T	p.Gln734Leu	p.Q734L	ENST00000382891	NM_133335.3	734	cAg/cTg	12/22	NA	2	FACETS	0.949	0.928	0.968			1	INDETERMINATE	2	TRUE	NA	0.816066439728317	2		756	952	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964872	55964872	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	193	451	0	ENST00000263923.4:c.2365G>C	p.Val789Leu	p.V789L	ENST00000263923	NM_002253.2	789	Gtt/Ctt	16/30	0.80587070152845	3	FACETS	0.845	0.783	0.909	0.423	0.391	0.455	CLONAL	1	TRUE	1	0.816066439728317	3		451	788	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944305	131944305	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0028606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	121	307	0	ENST00000265335.6:c.2719-2A>C		p.X907_splice	ENST00000265335		907			1	2	FACETS	0.793	0.724	0.864	0.793	0.724	0.864	SUBCLONAL	1	TRUE	1	0.816066439728317	2		307	374	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047245	180047245	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs796052104	NA	P-0028606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	341	816	2	ENST00000261937.6:c.2470C>A	p.Leu824Met	p.L824M	ENST00000261937	NM_182925.4	824	Ctg/Atg	17/30	1	2	FACETS	0.963	0.915	1	0.963	0.915	1	CLONAL	1	TRUE	1	0.816066439728317	2		818	868	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490522	20490522	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	809	688	1	ENST00000346618.3:c.1259G>T	p.Gly420Val	p.G420V	ENST00000346618	NM_001949.4	420	gGa/gTa	7/7	0.742004427380823	5	FACETS	0.92	0.893	0.947	0.552	0.535	0.568	CLONAL	3	TRUE	0	0.816066439728317	5		689	1598	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181947	32181947	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	1524	717	0	ENST00000375023.3:c.2107G>T	p.Gly703Trp	p.G703W	ENST00000375023	NM_004557.3	703	Ggg/Tgg	13/30	0.742004427380823	5	FACETS	0.972	0.961	0.982	0.972	0.961	0.982	CLONAL	5	TRUE	0	0.816066439728317	5		717	1710	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536190	106536190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	431	519	0	ENST00000369096.4:c.157G>A	p.Glu53Lys	p.E53K	ENST00000369096	NM_001198.3	53	Gag/Aag	2/7	0.767117551094211	2	FACETS	0.914	0.887	0.94	0.914	0.887	0.94	CLONAL	2	TRUE	0	0.816066439728317	2		519	578	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359944	87359944	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	464	508	0	ENST00000277120.3:c.1252C>A	p.Pro418Thr	p.P418T	ENST00000277120		418	Cct/Act	11/19	0.767117551094211	2	FACETS	0.935	0.909	0.96	0.935	0.909	0.96	CLONAL	2	TRUE	0	0.816066439728317	2		508	608	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030485	47030485	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	658	424	0	ENST00000377604.3:c.261del	p.Arg87SerfsTer47	p.R87Sfs*47	ENST00000377604	NM_001204468.1	87	aGg/ag	4/24	0.729539757063614	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.816066439728317	2		424	764	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974812	21974813	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	T	novel	NA	P-0028606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	123	126	0	ENST00000304494.5:c.14_15delinsA	p.Ala5GlufsTer21	p.A5Efs*21	ENST00000304494	NM_000077.4	5	gCG/gA	1/3	0.767117551094211	2	FACETS	0.913	0.862	0.961	0.913	0.862	0.961	CLONAL	2	TRUE	0	0.816066439728317	2		126	165	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0028608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	186	439	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	FALSE	1	0.491671436255188	2		439	646	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0028608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	476	429	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.24045777283572	4	FACETS	1	0.977	1			1	INDETERMINATE	3	FALSE	NA	0.491671436255188	4		429	941	SUCCESS
APC	324	MSKCC	GRCh37	5	112175651	112175651	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	136	420	0	ENST00000257430.4:c.4364del	p.Asn1455IlefsTer18	p.N1455Ifs*18	ENST00000257430	NM_000038.5	1454	Aaa/aa	16/16	1	2	FACETS	0.88	0.802	0.96	0.88	0.802	0.96	CLONAL	1	FALSE	1	0.491671436255188	2		420	629	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519980	NA	P-0028608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	281	623	0	ENST00000269305.4:c.528C>G	p.Cys176Trp	p.C176W	ENST00000269305	NM_001126112.2	176	tgC/tgG	5/11	0.491671436255188	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	0	0.491671436255188	1		623	757	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661726	227661726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760281604	NA	P-0028608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	242	477	0	ENST00000305123.5:c.1729G>A	p.Val577Met	p.V577M	ENST00000305123	NM_005544.2	577	Gtg/Atg	1/2	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.491671436255188	2		477	813	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219317	1219321	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CCCCA	CCCCA	-	novel	NA	P-0028608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	250	623	0	ENST00000326873.7:c.375-5_375-1del		p.X125_splice	ENST00000326873	NM_000455.4	125			0.261325495018851	3	FACETS	1	0.99	1	0.428	0.401	0.457	INDETERMINATE	1	FALSE	0	0.491671436255188	3		623	986	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277009	18277009	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	90	621	0	ENST00000222254.8:c.1456G>T	p.Glu486Ter	p.E486*	ENST00000222254	NM_005027.3	486	Gag/Tag	12/16	0.261325495018851	3	FACETS	0.434	0.384	0.488	0.145	0.128	0.163	INDETERMINATE	1	FALSE	0	0.491671436255188	3		621	1050	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0028609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	123	436	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.206922544687478	4	FACETS	0.92	0.836	1	0.92	0.836	1	CLONAL	3	TRUE	1	0.206863003221863	4		437	520	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044713	47044713	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	62	831	0	ENST00000377604.3:c.2113G>T	p.Glu705Ter	p.E705*	ENST00000377604	NM_001204468.1	705	Gag/Tag	19/24	0.206922544687478	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	0	0.206863003221863	1		831	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0028609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	74	739	0	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.206863003221863	2		739	526	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514079	69514079	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	47	706	1	ENST00000294312.3:c.602G>T	p.Gly201Val	p.G201V	ENST00000294312	NM_005117.2	201	gGg/gTg	3/3	1	2	FACETS	0.933	0.788	1	0.933	0.788	1	CLONAL	1	TRUE	1	0.206863003221863	2		707	487	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0028610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	203	493	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.931	0.867	0.995	0.931	0.867	0.995	CLONAL	1	TRUE	1	0.687076639160282	2		493	635	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0028610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	309	412	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.663446037275847	5	FACETS	1	0.95	1	0.67	0.633	0.707	CLONAL	2	TRUE	2	0.687076639160282	5		412	909	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423601	88423601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	173	607	1	ENST00000360948.2:c.2234G>A	p.Arg745Gln	p.R745Q	ENST00000360948	NM_001012338.2	745	cGg/cAg	18/19	1	2	FACETS	0.882	0.816	0.949	0.882	0.816	0.949	CLONAL	1	TRUE	1	0.687076639160282	2		608	571	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225060	NA	P-0028610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	456	652	0	ENST00000263967.3:c.311C>T	p.Pro104Leu	p.P104L	ENST00000263967	NM_006218.2	104	cCa/cTa	2/21	0.663446037275847	5	FACETS	1	0.959	1	0.669	0.639	0.7	CLONAL	2	TRUE	2	0.687076639160282	5		652	1342	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578566	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CTGTAGGAAGAG	CTGTAGGAAGAG	-	novel	NA	P-0028610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	450	801	0	ENST00000269305.4:c.376-12_376-1del		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.687076639160282	2	FACETS	0.948	0.916	0.979	0.948	0.916	0.979	CLONAL	2	TRUE	0	0.687076639160282	2		801	691	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353966	15353966	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	108	218	1	ENST00000263377.2:c.2914C>T	p.Gln972Ter	p.Q972*	ENST00000263377	NM_058243.2	972	Cag/Tag	14/20	0.546550046096681	4	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	2	0.687076639160282	4		219	262	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0028613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	23	387	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.526	0.409	0.662	0.526	0.409	0.662	SUBCLONAL	1	TRUE	1	0.197712787066464	2		387	442	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0028613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	46	319	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.197712787066464	2	FACETS	1	0.941	1	0.625	0.528	0.732	CLONAL	1	TRUE	0	0.197712787066464	2		319	372	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0028613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	22	429	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.53	0.41	0.67	0.53	0.41	0.67	SUBCLONAL	1	TRUE	1	0.197712787066464	2		429	420	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120178	70120178	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057518216	NA	P-0028613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	70	400	0	ENST00000245479.2:c.1180C>T	p.Arg394Ter	p.R394*	ENST00000245479	NM_000346.3	394	Cga/Tga	3/3	1	2	FACETS	0.778	0.68	0.883	1	0.975	1	SUBCLONAL	2	TRUE	1	0.197712787066464	2		400	455	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438641	49438641	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759226682	NA	P-0028613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	42	562	0	ENST00000301067.7:c.4849C>T	p.Arg1617Trp	p.R1617W	ENST00000301067	NM_003482.3	1617	Cgg/Tgg	19/54	1	2	FACETS	0.605	0.504	0.718	0.605	0.504	0.718	SUBCLONAL	1	TRUE	1	0.197712787066464	2		562	702	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300434	11300434	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	223	437	0	ENST00000361445.4:c.1712C>G	p.Thr571Arg	p.T571R	ENST00000361445	NM_004958.3	571	aCg/aGg	11/58	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.6	2		437	723	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	231115	231115	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	262	468	1	ENST00000264932.6:c.895G>A	p.Gly299Ser	p.G299S	ENST00000264932	NM_004168.2	299	Ggc/Agc	7/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.6	2		469	752	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0028615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	1449	565	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.293543750820821	18	FACETS	0.984	0.966	1			1	CLONAL	15	TRUE	NA	0.293543750820821	18		565	2239	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536921	120536921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	243	640	0	ENST00000229340.5:c.265G>A	p.Asp89Asn	p.D89N	ENST00000229340	NM_006861.6	89	Gac/Aac	4/6	0.234035062482339	2	FACETS	0.825	0.771	0.881	0.825	0.771	0.881	CLONAL	2	TRUE	0	0.293543750820821	2		640	1003	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579408	7579408	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	235	732	0	ENST00000269305.4:c.279del	p.Ser94HisfsTer29	p.S94Hfs*29	ENST00000269305	NM_001126112.2	93	ctG/ct	4/11	NA	2	FACETS	0.775	0.723	0.829			1	INDETERMINATE	2	TRUE	NA	0.293543750820821	2		732	1033	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136260	202136262	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs763516126	NA	P-0028615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	57	496	0	ENST00000358485.4:c.509_511del	p.Glu170del	p.E170del	ENST00000358485	NM_001080125.1	168	tcAGAa/tca	3/9	0.271023859748236	2	FACETS	0.414	0.354	0.48	0.207	0.177	0.24	SUBCLONAL	1	TRUE	0	0.293543750820821	2		496	939	SUCCESS
APC	324	MSKCC	GRCh37	5	112154820	112154820	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	82	524	0	ENST00000257430.4:c.1091A>T	p.Asp364Val	p.D364V	ENST00000257430	NM_000038.5	364	gAc/gTc	10/16	0.234035062482339	2	FACETS	0.69	0.607	0.778	0.345	0.303	0.389	SUBCLONAL	1	TRUE	0	0.293543750820821	2		524	810	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275463	38275463	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	143	698	0	ENST00000425967.3:c.1570G>T	p.Val524Leu	p.V524L	ENST00000425967	NM_001174067.1	524	Gtg/Ttg	12/19	0.178861502500715	2	FACETS	0.895	0.815	0.98	0.448	0.407	0.49	CLONAL	1	TRUE	0	0.293543750820821	2		698	1088	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs985033810	NA	P-0028616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	730	501	5	ENST00000269305.4:c.731G>T	p.Gly244Val	p.G244V	ENST00000269305	NM_001126112.2	244	gGc/gTc	7/11	0.815275155515551	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.821297019254333	3		506	834	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309758	65309758	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	157	409	0	ENST00000342505.4:c.2392A>G	p.Thr798Ala	p.T798A	ENST00000342505	NM_002227.2	798	Acg/Gcg	17/25	0.821297019254333	3	FACETS	0.826	0.759	0.895	0.413	0.379	0.448	CLONAL	1	TRUE	1	0.821297019254333	3		409	653	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624258	89624284	+	inframe_deletion	In_Frame_Del	DEL	GAAACAAAAGGAGATATCAAGAGGATG	GAAACAAAAGGAGATATCAAGAGGATG	-	novel	NA	P-0028616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	291	300	0	ENST00000371953.3:c.34_60del	p.Asn12_Gly20del	p.N12_G20del	ENST00000371953	NM_000314.4	11	aGAAACAAAAGGAGATATCAAGAGGATGga/aga	1/9	0.821297019254333	2	FACETS	0.984	0.953	1	0.984	0.953	1	CLONAL	2	TRUE	0	0.821297019254333	2		300	360	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947539	48947539	+	splice_acceptor_variant	Splice_Site	DEL	A	A	-	novel	NA	P-0028616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	228	422	1	ENST00000267163.4:c.1128-2del		p.X376_splice	ENST00000267163	NM_000321.2	376			0.815275155515551	3	FACETS	0.985	0.955	1	0.985	0.955	1	CLONAL	3	TRUE	0	0.821297019254333	3		423	265	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849326	89849326	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs757157897	NA	P-0028616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	209	515	0	ENST00000389301.3:c.1567G>T	p.Val523Phe	p.V523F	ENST00000389301	NM_000135.2	523	Gtt/Ttt	17/43	0.821297019254333	3	FACETS	0.871	0.81	0.934	0.436	0.405	0.467	CLONAL	1	TRUE	1	0.821297019254333	3		515	824	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552188	29552188	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs769154907	NA	P-0028616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	491	365	0	ENST00000356175.3:c.1921A>T	p.Ser641Cys	p.S641C	ENST00000356175	NM_000267.3	641	Agt/Tgt	17/57	0.821297019254333	3	FACETS	1	0.988	1			1	CLONAL	3	TRUE	NA	0.821297019254333	3		365	556	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443620	29443620	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	537	626	2	ENST00000389048.3:c.3597G>T	p.Met1199Ile	p.M1199I	ENST00000389048	NM_004304.4	1199	atG/atT	23/29	0.821297019254333	3	FACETS	0.975	0.942	1	0.975	0.942	1	CLONAL	2	TRUE	1	0.821297019254333	3		628	946	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403451	139403457	+	frameshift_variant	Frame_Shift_Del	DEL	CGTGAAG	CGTGAAG	-	novel	NA	P-0028616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	278	787	0	ENST00000277541.6:c.3036_3042del	p.Phe1013AlafsTer164	p.F1013Afs*164	ENST00000277541	NM_017617.3	1012	ggCTTCACG/gg	19/34	1	2	FACETS	0.841	0.793	0.89	0.841	0.793	0.89	CLONAL	1	TRUE	1	0.821297019254333	2		787	805	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941998	44941998	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	109	219	0	ENST00000377967.4:c.3248A>T	p.Lys1083Met	p.K1083M	ENST00000377967	NM_021140.2	1083	aAg/aTg	22/29	0.735086806673806	2	FACETS	0.891	0.811	0.972			1	CLONAL	1	TRUE	NA	0.821297019254333	2		219	298	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs967461896	NA	P-0028617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	323	601	0	ENST00000269305.4:c.526T>A	p.Cys176Ser	p.C176S	ENST00000269305	NM_001126112.2	176	Tgc/Agc	5/11	0.629409010731425	2	FACETS	0.901	0.863	0.938	0.901	0.863	0.938	CLONAL	2	TRUE	0	0.671349829334683	2		601	534	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883554	37883554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs574436396	NA	P-0028617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	91	509	0	ENST00000269571.5:c.3166G>A	p.Gly1056Ser	p.G1056S	ENST00000269571		1056	Ggt/Agt	26/27	0.629409010731425	2	FACETS	0.46	0.409	0.515	0.23	0.204	0.258	SUBCLONAL	1	TRUE	0	0.671349829334683	2		509	589	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618928	37618928	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1389471686	NA	P-0028617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	290	567	0	ENST00000447079.4:c.604C>T	p.Arg202Ter	p.R202*	ENST00000447079	NM_015083.1	202	Cga/Tga	1/14	0.629409010731425	2	FACETS	1	0.994	1	0.7	0.664	0.736	CLONAL	1	TRUE	0	0.671349829334683	2		567	617	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671277	30671280	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	novel	NA	P-0028617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	336	459	0	ENST00000376406.3:c.5597_5600del	p.Arg1866ThrfsTer104	p.R1866Tfs*104	ENST00000376406	NM_014641.2	1866	aGAGAc/ac	11/15	0.143093983083684	6	FACETS	0.903	0.862	0.944			1	INDETERMINATE	4	TRUE	NA	0.671349829334683	6		459	649	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0028618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	271	535	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.544298514445746	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.544298514445746	1		535	626	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0028618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	148	974	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.299277398901116	1	FACETS	0.956	0.882	1	0.956	0.882	1	INDETERMINATE	1	TRUE	0	0.544298514445746	1		974	414	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0028619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	122	599	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.26	2		599	732	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168999	11168999	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	116	739	0	ENST00000358026.2:c.4589A>G	p.Tyr1530Cys	p.Y1530C	ENST00000358026	NM_001128849.1	1530	tAc/tGc	32/36	1	2	FACETS	0.906	0.815	1	0.906	0.815	1	CLONAL	1	TRUE	1	0.26	2		739	985	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441414	52441414	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1553645838	NA	P-0028619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	89	595	0	ENST00000460680.1:c.437+1G>T		p.X146_splice	ENST00000460680	NM_004656.3	146			0.300373157883809	1	FACETS	0.97	0.861	1	0.97	0.861	1	CLONAL	1	TRUE	0	0.26	1		595	614	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0028622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	150	594	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.265681248193955	3	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	1	0.19	3		594	855	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436854	110436854	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	68	646	0	ENST00000375856.3:c.1547A>G	p.His516Arg	p.H516R	ENST00000375856	NM_003749.2	516	cAc/cGc	1/2	1	2	FACETS	0.963	0.837	1	0.963	0.837	1	CLONAL	1	TRUE	1	0.19	2		646	743	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992825	72992825	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	41	507	0	ENST00000268489.5:c.1220C>T	p.Thr407Ile	p.T407I	ENST00000268489	NM_006885.3	407	aCc/aTc	2/10	1	2	FACETS	0.652	0.542	0.775	0.652	0.542	0.775	SUBCLONAL	1	TRUE	1	0.19	2		507	662	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730882	40730882	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	69	637	1	ENST00000373198.4:c.3653T>A	p.Leu1218Gln	p.L1218Q	ENST00000373198	NM_133170.3	1218	cTg/cAg	27/32	1	2	FACETS	0.994	0.864	1	0.994	0.864	1	CLONAL	1	TRUE	1	0.19	2		638	731	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552120	29552120	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	28	195	0	ENST00000356175.3:c.1853A>G	p.Asp618Gly	p.D618G	ENST00000356175	NM_000267.3	618	gAt/gGt	17/57	0.265681248193955	3	FACETS	1	0.892	1	0.591	0.474	0.724	CLONAL	1	TRUE	1	0.19	3		195	273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0028623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	125	599	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.26734720541929	1	FACETS	0.974	0.881	1	0.974	0.881	1	CLONAL	1	TRUE	0	0.26734720541929	1		599	832	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0028623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	163	1128	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.3	3	FACETS	1	0.978	1	0.598	0.548	0.651	CLONAL	1	TRUE	1	0.26734720541929	3		1128	1156	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449800	29449800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs76742576	NA	P-0028623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	216	851	2	ENST00000389048.3:c.3055G>A	p.Val1019Ile	p.V1019I	ENST00000389048	NM_004304.4	1019	Gtc/Atc	18/29	0.26734720541929	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.26734720541929	1		853	1235	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65323451	65323451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	51	421	0	ENST00000342505.4:c.1346C>T	p.Ala449Val	p.A449V	ENST00000342505	NM_002227.2	449	gCc/gTc	10/25	1	2	FACETS	0.563	0.477	0.657	0.563	0.477	0.657	SUBCLONAL	1	TRUE	1	0.26734720541929	2		421	678	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045184	47045198	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATGGAGGTGAGGTGT	ATGGAGGTGAGGTGT	-	novel	NA	P-0028623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	115	558	2	ENST00000377604.3:c.2425_2430+9del		p.X809_splice	ENST00000377604	NM_001204468.1	809		21/24	1	2	FACETS	0.923	0.83	1	0.923	0.83	1	CLONAL	1	TRUE	1	0.26734720541929	2		560	932	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	70	373	0	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.822	0.729	0.92	1	0.98	1	CLONAL	2	TRUE	1	0.392266890547801	2		373	217	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578195	7578197	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0028624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	119	621	0	ENST00000269305.4:c.652_654del	p.Val218del	p.V218del	ENST00000269305	NM_001126112.2	218	GTG/-	6/11	0.392266890547801	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.392266890547801	1		621	334	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421078	49421078	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	65	387	0	ENST00000301067.7:c.14671C>T	p.Gln4891Ter	p.Q4891*	ENST00000301067	NM_003482.3	4891	Cag/Tag	48/54	0.201000952133974	4	FACETS	0.815	0.713	0.923	0.815	0.713	0.923	INDETERMINATE	2	TRUE	2	0.392266890547801	4		387	283	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023258	27023258	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	44	205	0	ENST00000324856.7:c.364G>T	p.Gly122Cys	p.G122C	ENST00000324856	NM_006015.4	122	Ggc/Tgc	1/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.392266890547801	2		205	171	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984387	201984406	+	frameshift_variant	Frame_Shift_Del	DEL	TCTACAAGTTTGGCAAAAAC	TCTACAAGTTTGGCAAAAAC	-	novel	NA	P-0028624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	160	582	0	ENST00000359651.3:c.1054_1073del	p.Tyr352LysfsTer112	p.Y352Kfs*112	ENST00000359651		351	gTCTACAAGTTTGGCAAAAAC/g	8/8	0.245774621457871	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.392266890547801	4		582	536	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440551	49440554	+	frameshift_variant	Frame_Shift_Ins	INS	TTGA	TTGA	ATAGG	novel	NA	P-0028624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	113	696	2	ENST00000301067.7:c.4256_4259delinsCCTAT	p.Leu1419ProfsTer13	p.L1419Pfs*13	ENST00000301067	NM_003482.3	1419	cTCAAg/cCCTATg	15/54	0.201000952133974	4	FACETS	0.814	0.736	0.895	0.814	0.736	0.895	INDETERMINATE	2	TRUE	2	0.392266890547801	4		698	493	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727514	88727514	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	133	377	0	ENST00000360948.2:c.265C>A	p.Arg89Ser	p.R89S	ENST00000360948	NM_001012338.2	89	Cgc/Agc	3/19	0.385556268283426	3	FACETS	1	0.979	1	0.795	0.732	0.86	CLONAL	2	TRUE	0	0.392266890547801	3		377	340	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169510	11169511	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0028624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	35	607	0	ENST00000358026.2:c.4678dup	p.Asp1560GlyfsTer21	p.D1560Gfs*21	ENST00000358026	NM_001128849.1	1559	aag/aaGg	33/36	1	2	FACETS	0.472	0.387	0.567	0.472	0.387	0.567	SUBCLONAL	1	TRUE	1	0.392266890547801	2		607	378	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290231	15290231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	91	807	0	ENST00000263388.2:c.3404G>A	p.Gly1135Asp	p.G1135D	ENST00000263388	NM_000435.2	1135	gGt/gAt	21/33	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.392266890547801	2		807	418	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840090	27840090	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	37	214	0	ENST00000328488.2:c.4G>A	p.Ala2Thr	p.A2T	ENST00000328488	NM_003533.2	2	Gca/Aca	1/1	0.322833527475973	2	FACETS	1	0.952	1	0.709	0.596	0.83	CLONAL	1	TRUE	0	0.392266890547801	2		214	133	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993339	72993339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368995910	NA	P-0028625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	402	714	0	ENST00000268489.5:c.706G>A	p.Val236Met	p.V236M	ENST00000268489	NM_006885.3	236	Gtg/Atg	2/10	1	2	FACETS	0.994	0.947	1	0.994	0.947	1	CLONAL	1	TRUE	1	0.725549451437352	2		714	1115	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579536	7579537	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AATA	novel	NA	P-0028625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	751	680	1	ENST00000269305.4:c.147_150dup	p.Glu51TyrfsTer2	p.E51Yfs*2	ENST00000269305	NM_001126112.2	50	-/TATT	4/11	0.725549451437352	2	FACETS	0.909	0.885	0.932	0.909	0.885	0.932	CLONAL	2	TRUE	0	0.725549451437352	2		681	1139	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670040	86670040	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	84	451	0	ENST00000274376.6:c.1837A>G	p.Asn613Asp	p.N613D	ENST00000274376	NM_002890.2	613	Aat/Gat	14/25	0.687226292176005	2	FACETS	0.525	0.466	0.588	0.263	0.233	0.294	SUBCLONAL	1	TRUE	0	0.725549451437352	2		451	441	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374326	81374326	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	110	316	0	ENST00000222390.5:c.736T>A	p.Leu246Met	p.L246M	ENST00000222390	NM_000601.4	246	Ttg/Atg	6/18	0.391711959878681	3	FACETS	0.664	0.598	0.734	0.332	0.299	0.367	INDETERMINATE	1	TRUE	1	0.725549451437352	3		316	622	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0028626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	42	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.18242861832584	3	FACETS	0.756	0.63	0.897	0.378	0.315	0.449	SUBCLONAL	1	TRUE	1	0.17	3		511	709	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271321	26271321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	35	454	0	ENST00000305910.3:c.292G>A	p.Glu98Lys	p.E98K	ENST00000305910	NM_003534.2	98	Gag/Aag	1/1	1	2	FACETS	0.773	0.632	0.931	0.773	0.632	0.931	CLONAL	1	TRUE	1	0.17	2		454	533	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155491	106155491	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	29	334	0	ENST00000380013.4:c.392G>T	p.Arg131Ile	p.R131I	ENST00000380013	NM_001127208.2	131	aGa/aTa	3/11	1	2	FACETS	0.629	0.504	0.773	0.629	0.504	0.773	SUBCLONAL	1	TRUE	1	0.17	2		334	542	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40874888	40874888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	51	476	1	ENST00000428826.2:c.412G>A	p.Glu138Lys	p.E138K	ENST00000428826		138	Gaa/Aaa	6/21	1	2	FACETS	0.736	0.624	0.86	0.736	0.624	0.86	SUBCLONAL	1	TRUE	1	0.17	2		477	815	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710987	114710987	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	37	363	0	ENST00000543371.1:c.211C>G	p.Arg71Gly	p.R71G	ENST00000543371	NM_001198531.1	71	Cgc/Ggc	2/14	1	2	FACETS	0.751	0.618	0.9	0.751	0.618	0.9	SUBCLONAL	1	TRUE	1	0.17	2		363	580	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099423	27099423	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1384822065	NA	P-0028626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	60	512	0	ENST00000324856.7:c.3660G>A	p.Met1220Ile	p.M1220I	ENST00000324856	NM_006015.4	1220	atG/atA	14/20	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.17	2		512	699	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945760	206945761	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0028626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	112	422	0	ENST00000423557.1:c.20_21delinsAT	p.Leu7His	p.L7H	ENST00000423557	NM_000572.2	7	cTC/cAT	1/5	1	2	FACETS	1	0.902	1	1	0.988	1	CLONAL	2	TRUE	1	0.17	2		422	658	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940151	71940151	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs145769072	NA	P-0028626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	60	713	0	ENST00000298229.2:c.536G>C	p.Ser179Thr	p.S179T	ENST00000298229	NM_001567.3	179	aGc/aCc	5/28	1	2	FACETS	0.862	0.741	0.994	0.862	0.741	0.994	CLONAL	1	TRUE	1	0.17	2		713	819	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940566	71940566	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	71	603	0	ENST00000298229.2:c.717G>C	p.Gln239His	p.Q239H	ENST00000298229	NM_001567.3	239	caG/caC	6/28	1	2	FACETS	0.941	0.819	1	0.941	0.819	1	CLONAL	1	TRUE	1	0.17	2		603	888	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56787283	56787283	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs750551012	NA	P-0028626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	43	441	0	ENST00000337432.4:c.769C>G	p.Leu257Val	p.L257V	ENST00000337432	NM_058216.2	257	Ctt/Gtt	5/9	1	2	FACETS	0.752	0.628	0.89	0.752	0.628	0.89	SUBCLONAL	1	TRUE	1	0.17	2		441	673	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910632	50910632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1354117345	NA	P-0028626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	68	677	0	ENST00000440232.2:c.1735G>A	p.Glu579Lys	p.E579K	ENST00000440232	NM_002691.3	579	Gag/Aag	14/27	1	2	FACETS	0.746	0.646	0.854	0.746	0.646	0.854	SUBCLONAL	1	TRUE	1	0.17	2		677	1073	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205192	128205192	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	52	476	0	ENST00000341105.2:c.249G>C	p.Gln83His	p.Q83H	ENST00000341105	NM_032638.4	83	caG/caC	3/6	0.18242861832584	3	FACETS	0.931	0.791	1	0.465	0.395	0.543	CLONAL	1	TRUE	1	0.17	3		476	713	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201794	66201794	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	43	462	0	ENST00000273854.3:c.2708G>T	p.Cys903Phe	p.C903F	ENST00000273854	NM_004439.5	903	tGt/tTt	16/18	1	2	FACETS	0.798	0.666	0.944	0.798	0.666	0.944	CLONAL	1	TRUE	1	0.17	2		462	634	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741458	145741458	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1045634487	NA	P-0028626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	83	776	0	ENST00000428558.2:c.1045G>A	p.Asp349Asn	p.D349N	ENST00000428558	NM_004260.3	349	Gac/Aac	5/22	0.18242861832584	3	FACETS	1	0.884	1	0.502	0.442	0.567	CLONAL	1	TRUE	1	0.17	3		776	1055	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741857	145741857	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201301365	NA	P-0028626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	54	673	0	ENST00000428558.2:c.646G>A	p.Glu216Lys	p.E216K	ENST00000428558	NM_004260.3	216	Gaa/Aaa	5/22	0.18242861832584	3	FACETS	0.711	0.605	0.828	0.356	0.302	0.414	SUBCLONAL	1	TRUE	1	0.17	3		673	969	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742108	145742108	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	76	566	0	ENST00000428558.2:c.395G>A	p.Arg132Lys	p.R132K	ENST00000428558	NM_004260.3	132	aGa/aAa	5/22	0.18242861832584	3	FACETS	1	0.946	1	0.575	0.503	0.652	CLONAL	1	TRUE	1	0.17	3		566	844	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100950	41100950	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	35	455	0	ENST00000373198.4:c.1406G>T	p.Gly469Val	p.G469V	ENST00000373198	NM_133170.3	469	gGc/gTc	8/32	1	2	FACETS	0.374	0.305	0.451	0.374	0.305	0.451	SUBCLONAL	1	TRUE	1	0.326326300578748	2		455	574	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42053934	42053941	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAGGCCTT	TAGGCCTT	-	novel	NA	P-0028627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	77	283	0	ENST00000219905.7:c.7399-3_7403del		p.X2467_splice	ENST00000219905	NM_001164273.1	2467		21/24	0.326326300578748	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.326326300578748	1		283	342	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39233616	39233616	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	98	449	0	ENST00000402219.2:c.2728G>T	p.Asp910Tyr	p.D910Y	ENST00000402219	NM_005633.3	910	Gat/Tat	17/23	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.326326300578748	2		449	554	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391202	89391202	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	33	373	0	ENST00000336596.2:c.1268G>T	p.Arg423Ile	p.R423I	ENST00000336596	NM_005233.5	423	aGa/aTa	5/17	1	2	FACETS	0.364	0.295	0.441	0.364	0.295	0.441	SUBCLONAL	1	TRUE	1	0.326326300578748	2		373	556	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564686	55564686	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	42	475	0	ENST00000288135.5:c.574G>A	p.Gly192Ser	p.G192S	ENST00000288135	NM_000222.2	192	Ggc/Agc	3/21	1	2	FACETS	0.417	0.347	0.495	0.417	0.347	0.495	SUBCLONAL	1	TRUE	1	0.326326300578748	2		475	617	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197762	66197762	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	47	419	0	ENST00000273854.3:c.2937G>C	p.Met979Ile	p.M979I	ENST00000273854	NM_004439.5	979	atG/atC	17/18	1	2	FACETS	0.471	0.396	0.553	0.471	0.396	0.553	SUBCLONAL	1	TRUE	1	0.326326300578748	2		419	612	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412042	116412047	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTAT	AGGTAT	-	novel	NA	P-0028627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	172	642	0	ENST00000397752.3:c.3028_3028+5del		p.X1010_splice	ENST00000397752	NM_000245.2	1010		14/21	0.326326300578748	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.326326300578748	1		642	626	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8525018	8525018	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	25	356	0	ENST00000356435.5:c.586C>A	p.Gln196Lys	p.Q196K	ENST00000356435		196	Cag/Aag	7/35	1	2	FACETS	0.331	0.26	0.413	0.331	0.26	0.413	SUBCLONAL	1	TRUE	1	0.326326300578748	2		356	463	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340847	70340847	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	46	585	0	ENST00000374080.3:c.580T>G	p.Leu194Val	p.L194V	ENST00000374080		194	Tta/Gta	5/45	1	2	FACETS	0.407	0.342	0.479	0.407	0.342	0.479	SUBCLONAL	1	TRUE	1	0.326326300578748	2		585	693	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0028628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	58	387	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.722	0.618	0.835	0.722	0.618	0.835	SUBCLONAL	1	TRUE	1	0.19	2		387	846	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0028628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	149	638	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	0.180239177222233	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	0	0.19	2		638	774	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741564	39742586	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTGAGAGCATCTTCCCATCGGCATTGTCTAGTGTTGAGCTTAACAAAGGGAGTTTCTGCTCTGCCCCAGGCCCTGTGCCACATACTGTATATCACAACTCAACATACATATATTTGTATGTAAAACTGAATCAAAAGTTGCACAAAACAATGCTTAGCCTTACTGTGAGCAGTAGATTCTGATCTTTTTTTAACTCTATTTCATTCCTTTAGAAAGTTGGTTATAACTTATAAAATTGTTTAAATAAACCATGCAGGTATCACCATTATATAGTTTTAAAGACCACGCTCTAGAGGAGATCAATTTCTTGGTACTCACGAGAAGAAAAAAAAGTTCATGTTTTTCCCCCAGTCTTGTATTTTAACATAAGTTCTGAATTGTCTCAAAATTCACACTAGCTTTTTGAGTTTGATTGCCCAGAGTAGCAGCACTCCCTCATTTGCTGCCTTATTTAATTTTTTTTTTCCTTTTCTCCATCCCTATTTCAGAGGACAGAATAGAAAGAAAAGGAGCATGAATATTTAACATCCCTATAGATTTCATAGTGAGTGGGGGAGGAAGTAACACTGCAGAATCCAGAGTTCCCAGGCCATGCTGACTGATGCTGTGGCTTCAAACAGAATTGGGAGGCTTCTGTTTTGGATGCCTAGAAATTGCATAAGGGTCAAAAGGCTGGGCGCAGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGTGGAACACGAGGTCAAGAGACCATCCTGGCCAATGTGGTGAAACCCCATCTCTACTAAAAATACAAAAAAAAAAAAAAAAATAAAAATTGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTTCGGAGGCTGAGGCAGGAGAATGGCATGAACCCGGGAGACGGAGCTTGCAGTGAGCCAAAATTGCGCCATTGCACTCTAGCCTGGCGACAGAGCGAGACTGTCTCAAAAAAAAAAAAAAAAAAAACACAGAACGAAATTGTGTAAGGATCATGTCTCTTCCATTCATGCTCA	AGGTGAGAGCATCTTCCCATCGGCATTGTCTAGTGTTGAGCTTAACAAAGGGAGTTTCTGCTCTGCCCCAGGCCCTGTGCCACATACTGTATATCACAACTCAACATACATATATTTGTATGTAAAACTGAATCAAAAGTTGCACAAAACAATGCTTAGCCTTACTGTGAGCAGTAGATTCTGATCTTTTTTTAACTCTATTTCATTCCTTTAGAAAGTTGGTTATAACTTATAAAATTGTTTAAATAAACCATGCAGGTATCACCATTATATAGTTTTAAAGACCACGCTCTAGAGGAGATCAATTTCTTGGTACTCACGAGAAGAAAAAAAAGTTCATGTTTTTCCCCCAGTCTTGTATTTTAACATAAGTTCTGAATTGTCTCAAAATTCACACTAGCTTTTTGAGTTTGATTGCCCAGAGTAGCAGCACTCCCTCATTTGCTGCCTTATTTAATTTTTTTTTTCCTTTTCTCCATCCCTATTTCAGAGGACAGAATAGAAAGAAAAGGAGCATGAATATTTAACATCCCTATAGATTTCATAGTGAGTGGGGGAGGAAGTAACACTGCAGAATCCAGAGTTCCCAGGCCATGCTGACTGATGCTGTGGCTTCAAACAGAATTGGGAGGCTTCTGTTTTGGATGCCTAGAAATTGCATAAGGGTCAAAAGGCTGGGCGCAGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGTGGAACACGAGGTCAAGAGACCATCCTGGCCAATGTGGTGAAACCCCATCTCTACTAAAAATACAAAAAAAAAAAAAAAAATAAAAATTGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTTCGGAGGCTGAGGCAGGAGAATGGCATGAACCCGGGAGACGGAGCTTGCAGTGAGCCAAAATTGCGCCATTGCACTCTAGCCTGGCGACAGAGCGAGACTGTCTCAAAAAAAAAAAAAAAAAAAACACAGAACGAAATTGTGTAAGGATCATGTCTCTTCCATTCATGCTCA	-	novel	NA	P-0028628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	41	367	0	ENST00000361337.2:c.1451_1453-24del		p.X484_splice	ENST00000361337	NM_003286.2	484		14/21	0.200025687917166	3	FACETS	0.58	0.481	0.69	0.29	0.24	0.345	SUBCLONAL	1	TRUE	1	0.19	3		367	815	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099394	27099395	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0028628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	129	680	0	ENST00000324856.7:c.3632_3633del	p.Tyr1211SerfsTer8	p.Y1211Sfs*8	ENST00000324856	NM_006015.4	1211	TAt/t	14/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.19	2		680	1009	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559209	29559209	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0028628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	117	331	0	ENST00000356175.3:c.3314+2T>C		p.X1105_splice	ENST00000356175	NM_000267.3	1105			0.180239177222233	2	FACETS	0.964	0.871	1	0.964	0.871	1	CLONAL	2	TRUE	0	0.19	2		331	639	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728884	39729848	+	splice_donor_variant,splice_acceptor_variant,intron_variant	Splice_Site	DEL	GTGAGCTCGCACTTCATCCTATGGGCCAAAAAGGGGGTGGAGGGCGTCCTTTATTGTACTTGGGAATATTTCCCAGGTTACACAGGACTGTTTGGGAAGGGAGATACTTAAGAGCAGGACAGTATTTCATGCGTAGGTCTCCAGATGTTTTTGAGGTACAGTTGTCTCCCCTCATCCACAGGGGATATGTTCCAAGACCCCCAGTGGATGCCTGCAACTTCGACCCAATTGCTGTCACTTGGAACACATTTCTGTTGATGTCTTCCACCCCCAAATTTAATGTCTTTTCCATGTTTATTAAGTACTTATCACATAGAGTGGCTATAACTTTTGCAGTCTGAGGCACAACAGCAAAACTAGCACGACTTTCTTTTTCCTTCTTCACAATTTCACAGATGGAAGGTTAATTCTTACCTTAGATCTTAGCAACTTCACCATACAGTTTTTTTTATTAAGTCGATAATTTCCACCTTTTCATTTAAAGCACTCTGTGCAGCTTCTGTATGGCATATCCAAATTGCCAACATCACCACTTTCACACTTTGGGGCCTTTATTAAGTAAAAGAAGGATTACTTGAACACAAGCAATGTAAAACCATTAAAGTCAACCTGATAAATAAGGCAGCTACTAGGTTACCCATGGGCAAGTGACATATACAGCATGGTATGTTGTATATATGGTTCACGCATCCCAGGTGGGACTACAAGAGATTTCATCATGCTCCTCAGAATGATGTGCAATTTAAAACTTACAAAATGTTTATTTCTGGAATTTTGTATTGAATATTTTCGGATGACAGTTGGCTGAGGGTAAGTAAAACCATGCATAAGGTGGGACTACTGTATTGACTGTTAAGAAGGAAACTTGGAAAATTATGCTCAGCAGATAGGTCCACTTGGGGTCATGAAAGGTGAAATTATTCCTCACATCTTATTTCACTATCCTCGTGCTCTGTTATTTCCAG	GTGAGCTCGCACTTCATCCTATGGGCCAAAAAGGGGGTGGAGGGCGTCCTTTATTGTACTTGGGAATATTTCCCAGGTTACACAGGACTGTTTGGGAAGGGAGATACTTAAGAGCAGGACAGTATTTCATGCGTAGGTCTCCAGATGTTTTTGAGGTACAGTTGTCTCCCCTCATCCACAGGGGATATGTTCCAAGACCCCCAGTGGATGCCTGCAACTTCGACCCAATTGCTGTCACTTGGAACACATTTCTGTTGATGTCTTCCACCCCCAAATTTAATGTCTTTTCCATGTTTATTAAGTACTTATCACATAGAGTGGCTATAACTTTTGCAGTCTGAGGCACAACAGCAAAACTAGCACGACTTTCTTTTTCCTTCTTCACAATTTCACAGATGGAAGGTTAATTCTTACCTTAGATCTTAGCAACTTCACCATACAGTTTTTTTTATTAAGTCGATAATTTCCACCTTTTCATTTAAAGCACTCTGTGCAGCTTCTGTATGGCATATCCAAATTGCCAACATCACCACTTTCACACTTTGGGGCCTTTATTAAGTAAAAGAAGGATTACTTGAACACAAGCAATGTAAAACCATTAAAGTCAACCTGATAAATAAGGCAGCTACTAGGTTACCCATGGGCAAGTGACATATACAGCATGGTATGTTGTATATATGGTTCACGCATCCCAGGTGGGACTACAAGAGATTTCATCATGCTCCTCAGAATGATGTGCAATTTAAAACTTACAAAATGTTTATTTCTGGAATTTTGTATTGAATATTTTCGGATGACAGTTGGCTGAGGGTAAGTAAAACCATGCATAAGGTGGGACTACTGTATTGACTGTTAAGAAGGAAACTTGGAAAATTATGCTCAGCAGATAGGTCCACTTGGGGTCATGAAAGGTGAAATTATTCCTCACATCTTATTTCACTATCCTCGTGCTCTGTTATTTCCAG	-	novel	NA	P-0028628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	41	332	0	ENST00000361337.2:c.1163+1_1164-1del		p.X388_splice	ENST00000361337	NM_003286.2	388			0.200025687917166	3	FACETS	0.654	0.543	0.777	0.327	0.271	0.389	SUBCLONAL	1	TRUE	1	0.19	3		332	723	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665706	86665706	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	60	321	0	ENST00000274376.6:c.1687G>T	p.Glu563Ter	p.E563*	ENST00000274376	NM_002890.2	563	Gaa/Taa	12/25	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.19	2		321	486	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	47	376	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.966	0.819	1	0.966	0.819	1	CLONAL	1	TRUE	1	0.307963265003654	2		376	316	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	51	398	0	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	1	2	FACETS	0.779	0.664	0.906	0.779	0.664	0.906	CLONAL	1	TRUE	1	0.307963265003654	2		398	425	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090327	77090327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196615739	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	85	556	0	ENST00000356341.3:c.398C>T	p.Ser133Leu	p.S133L	ENST00000356341	NM_002576.4	133	tCg/tTg	4/15	1	2	FACETS	0.861	0.762	0.968	0.861	0.762	0.968	CLONAL	1	TRUE	1	0.307963265003654	2		556	641	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913255	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	276	629	0	ENST00000369535.4:c.183A>T	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caT	3/7	0.288911722324108	4	FACETS	0.928	0.874	0.983	0.928	0.874	0.983	CLONAL	3	TRUE	1	0.307963265003654	4		629	842	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606679	29606679	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs865931787	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	81	599	0	ENST00000389048.3:c.1201C>T	p.Arg401Ter	p.R401*	ENST00000389048	NM_004304.4	401	Cga/Tga	5/29	1	2	FACETS	0.881	0.777	0.992	0.881	0.777	0.992	CLONAL	1	TRUE	1	0.307963265003654	2		599	597	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922294	100922294	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1315135533	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	35	412	0	ENST00000325455.5:c.2218C>T	p.Arg740Ter	p.R740*	ENST00000325455	NM_001202474.3	740	Cga/Tga	5/8	1	2	FACETS	0.715	0.587	0.857	0.715	0.587	0.857	SUBCLONAL	1	TRUE	1	0.307963265003654	2		412	318	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876163	35876163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	88	592	0	ENST00000303115.3:c.955G>A	p.Glu319Lys	p.E319K	ENST00000303115	NM_002185.3	319	Gaa/Aaa	8/8	1	2	FACETS	0.885	0.784	0.992	0.885	0.784	0.992	CLONAL	1	TRUE	1	0.307963265003654	2		592	646	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643672	52643672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	72	618	0	ENST00000394830.3:c.2224G>A	p.Glu742Lys	p.E742K	ENST00000394830	NM_018313.4	742	Gag/Aag	17/30	1	2	FACETS	0.809	0.707	0.918	0.809	0.707	0.918	CLONAL	1	TRUE	1	0.307963265003654	2		618	578	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524726	187524726	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	127	712	0	ENST00000441802.2:c.10954C>T	p.Pro3652Ser	p.P3652S	ENST00000441802	NM_005245.3	3652	Ccg/Tcg	19/27	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.307963265003654	2		712	724	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934225	49934225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868140197	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	96	660	0	ENST00000296474.3:c.2282C>T	p.Ser761Phe	p.S761F	ENST00000296474	NM_002447.2	761	tCc/tTc	8/20	1	2	FACETS	0.784	0.698	0.876	0.784	0.698	0.876	SUBCLONAL	1	TRUE	1	0.307963265003654	2		660	795	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450394	50450394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	62	472	0	ENST00000331340.3:c.578G>A	p.Arg193Lys	p.R193K	ENST00000331340	NM_006060.4	193	aGg/aAg	5/8	1	2	FACETS	0.764	0.661	0.876	0.764	0.661	0.876	SUBCLONAL	1	TRUE	1	0.307963265003654	2		472	527	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622236	117622236	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866580908	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	69	474	0	ENST00000368508.3:c.6634C>T	p.Gln2212Ter	p.Q2212*	ENST00000368508	NM_002944.2	2212	Cag/Tag	42/43	1	2	FACETS	0.88	0.768	1	0.88	0.768	1	CLONAL	1	TRUE	1	0.307963265003654	2		474	509	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69143593	69143593	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	116	422	0	ENST00000288368.4:c.4801C>T	p.Pro1601Ser	p.P1601S	ENST00000288368	NM_024870.2	1601	Ccc/Tcc	40/40	0.307963265003654	3	FACETS	1	0.982	1	0.706	0.637	0.777	CLONAL	1	TRUE	1	0.307963265003654	3		422	616	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41521995	41521995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764980716	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	92	575	0	ENST00000263253.7:c.857C>T	p.Pro286Leu	p.P286L	ENST00000263253	NM_001429.3	286	cCa/cTa	3/31	0.307963265003654	3	FACETS	0.886	0.787	0.992	0.443	0.393	0.496	CLONAL	1	TRUE	1	0.307963265003654	3		575	778	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226995	2226995	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	86	499	0	ENST00000398665.3:c.4475C>T	p.Ser1492Phe	p.S1492F	ENST00000398665	NM_032482.2	1492	tCc/tTc	27/28	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.307963265003654	2		499	516	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699447	117699447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	60	517	0	ENST00000369458.3:c.194C>T	p.Ser65Phe	p.S65F	ENST00000369458	NM_024626.3	65	tCt/tTt	3/6	0.251739574691247	3	FACETS	0.677	0.583	0.78	0.339	0.291	0.39	SUBCLONAL	1	TRUE	1	0.307963265003654	3		517	664	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950469	68950469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	74	492	0	ENST00000288368.4:c.781C>T	p.Gln261Ter	p.Q261*	ENST00000288368	NM_024870.2	261	Caa/Taa	7/40	0.307963265003654	3	FACETS	0.912	0.799	1	0.456	0.399	0.517	CLONAL	1	TRUE	1	0.307963265003654	3		492	608	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757459	40757459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303277916	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	90	634	0	ENST00000373198.4:c.2839C>T	p.Arg947Trp	p.R947W	ENST00000373198	NM_133170.3	947	Cgg/Tgg	20/32	1	2	FACETS	0.81	0.718	0.907	0.81	0.718	0.907	CLONAL	1	TRUE	1	0.307963265003654	2		634	722	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087929	27087929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	82	685	0	ENST00000324856.7:c.2216C>T	p.Pro739Leu	p.P739L	ENST00000324856	NM_006015.4	739	cCt/cTt	6/20	0.288911722324108	4	FACETS	0.714	0.628	0.807	0.238	0.209	0.269	SUBCLONAL	1	TRUE	1	0.307963265003654	4		685	975	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956141	175956141	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	28	571	1	ENST00000367669.3:c.2071C>T	p.Arg691Ter	p.R691*	ENST00000367669	NM_022457.5	691	Cga/Tga	18/20	1	2	FACETS	0.426	0.34	0.524	0.426	0.34	0.524	SUBCLONAL	1	TRUE	1	0.307963265003654	2		572	427	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944372	206944372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	50	477	0	ENST00000423557.1:c.258G>A	p.Met86Ile	p.M86I	ENST00000423557	NM_000572.2	86	atG/atA	3/5	1	2	FACETS	0.523	0.443	0.611	0.523	0.443	0.611	SUBCLONAL	1	TRUE	1	0.307963265003654	2		477	621	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212923	94212923	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	51	405	0	ENST00000323929.3:c.319C>G	p.Pro107Ala	p.P107A	ENST00000323929	NM_005591.3	107	Cca/Gca	5/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.307963265003654	2		405	277	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933387	100933387	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	63	517	1	ENST00000325455.5:c.2003C>T	p.Ala668Val	p.A668V	ENST00000325455	NM_001202474.3	668	gCc/gTc	4/8	1	2	FACETS	0.684	0.592	0.785	0.684	0.592	0.785	SUBCLONAL	1	TRUE	1	0.307963265003654	2		518	598	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205805	108205805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	84	537	0	ENST00000278616.4:c.8120C>T	p.Ser2707Phe	p.S2707F	ENST00000278616	NM_000051.3	2707	tCc/tTc	55/63	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.307963265003654	2		537	488	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348802	118348802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	74	439	0	ENST00000534358.1:c.3455C>T	p.Ser1152Leu	p.S1152L	ENST00000534358	NM_005933.3	1152	tCg/tTg	5/36	1	2	FACETS	0.864	0.758	0.979	0.864	0.758	0.979	CLONAL	1	TRUE	1	0.307963265003654	2		439	556	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641559	18641559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	46	439	0	ENST00000266497.5:c.2558G>A	p.Arg853Lys	p.R853K	ENST00000266497		853	aGa/aAa	17/31	1	2	FACETS	0.782	0.66	0.916	0.782	0.66	0.916	CLONAL	1	TRUE	1	0.307963265003654	2		439	382	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691095	18691095	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1368705250	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	35	441	0	ENST00000266497.5:c.3206G>A	p.Arg1069Gln	p.R1069Q	ENST00000266497		1069	cGa/cAa	23/31	1	2	FACETS	0.601	0.493	0.722	0.601	0.493	0.722	SUBCLONAL	1	TRUE	1	0.307963265003654	2		441	378	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246111	46246111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	64	446	0	ENST00000334344.6:c.4205C>T	p.Thr1402Ile	p.T1402I	ENST00000334344	NM_152641.2	1402	aCt/aTt	15/21	1	2	FACETS	0.807	0.7	0.923	0.807	0.7	0.923	CLONAL	1	TRUE	1	0.307963265003654	2		446	515	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424207	49424207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	40	207	0	ENST00000301067.7:c.13855C>T	p.Pro4619Ser	p.P4619S	ENST00000301067	NM_003482.3	4619	Ccg/Tcg	42/54	1	2	FACETS	0.86	0.718	1	0.86	0.718	1	CLONAL	1	TRUE	1	0.307963265003654	2		207	302	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432237	49432237	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1238123508	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	110	694	0	ENST00000301067.7:c.8902C>T	p.Pro2968Ser	p.P2968S	ENST00000301067	NM_003482.3	2968	Ccg/Tcg	34/54	1	2	FACETS	0.785	0.704	0.871	0.785	0.704	0.871	SUBCLONAL	1	TRUE	1	0.307963265003654	2		694	910	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549225	21549226	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	118	675	0	ENST00000382592.4:c.3049_3050dup	p.Ser1018ValfsTer55	p.S1018Vfs*55	ENST00000382592	NM_014572.2	1017	ggt/ggGGt	8/8	1	2	FACETS	0.958	0.864	1	0.958	0.864	1	CLONAL	1	TRUE	1	0.307963265003654	2		675	800	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28963972	28963972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	56	450	0	ENST00000282397.4:c.1930G>A	p.Gly644Arg	p.G644R	ENST00000282397	NM_002019.4	644	Ggg/Agg	13/30	1	2	FACETS	0.806	0.692	0.931	0.806	0.692	0.931	CLONAL	1	TRUE	1	0.307963265003654	2		450	451	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28971168	28971168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	65	393	0	ENST00000282397.4:c.1589C>T	p.Ser530Phe	p.S530F	ENST00000282397	NM_002019.4	530	tCt/tTt	12/30	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.307963265003654	2		393	422	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483892	88483892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	94	609	0	ENST00000360948.2:c.1678C>T	p.Leu560Phe	p.L560F	ENST00000360948	NM_001012338.2	560	Ctc/Ttc	14/19	1	2	FACETS	0.924	0.822	1	0.924	0.822	1	CLONAL	1	TRUE	1	0.307963265003654	2		609	661	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292979	91292979	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	100	586	0	ENST00000355112.3:c.481G>T	p.Asp161Tyr	p.D161Y	ENST00000355112	NM_000057.2	161	Gat/Tat	3/22	1	2	FACETS	0.968	0.865	1	0.968	0.865	1	CLONAL	1	TRUE	1	0.307963265003654	2		586	671	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251264	99251264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144739747	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	90	606	0	ENST00000268035.6:c.568C>T	p.Pro190Ser	p.P190S	ENST00000268035	NM_000875.3	190	Ccg/Tcg	2/21	1	2	FACETS	0.908	0.806	1	0.908	0.806	1	CLONAL	1	TRUE	1	0.307963265003654	2		606	644	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786152	3786152	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	100	706	2	ENST00000262367.5:c.4613C>T	p.Pro1538Leu	p.P1538L	ENST00000262367	NM_004380.2	1538	cCc/cTc	28/31	1	2	FACETS	0.864	0.771	0.962	0.864	0.771	0.962	CLONAL	1	TRUE	1	0.307963265003654	2		708	752	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965195	81965195	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	102	637	0	ENST00000359376.3:c.2675G>A	p.Arg892Lys	p.R892K	ENST00000359376	NM_002661.3	892	aGg/aAg	25/33	1	2	FACETS	0.873	0.78	0.971	0.873	0.78	0.971	CLONAL	1	TRUE	1	0.307963265003654	2		637	759	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509638	29509639	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	47	589	0	ENST00000356175.3:c.843_844delinsTT	p.Gln282Ter	p.Q282*	ENST00000356175	NM_000267.3	281	atCCag/atTTag	8/57	1	2	FACETS	0.613	0.517	0.718	0.613	0.517	0.718	SUBCLONAL	1	TRUE	1	0.307963265003654	2		589	498	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627689	37627689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866863743	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	92	660	1	ENST00000447079.4:c.1604C>T	p.Pro535Leu	p.P535L	ENST00000447079	NM_015083.1	535	cCc/cTc	2/14	1	2	FACETS	0.728	0.646	0.815	0.728	0.646	0.815	SUBCLONAL	1	TRUE	1	0.307963265003654	2		661	821	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245007	41245007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80357195	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	82	649	0	ENST00000357654.3:c.2541G>A	p.Met847Ile	p.M847I	ENST00000357654	NM_007294.3	847	atG/atA	10/23	1	2	FACETS	0.728	0.641	0.82	0.728	0.641	0.82	SUBCLONAL	1	TRUE	1	0.307963265003654	2		649	732	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604662	48604662	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	61	358	1	ENST00000342988.3:c.1484T>A	p.Leu495His	p.L495H	ENST00000342988	NM_005359.5	495	cTt/cAt	12/12	0.261093599354047	1	FACETS	0.789	0.682	0.903	0.789	0.682	0.903	CLONAL	1	TRUE	0	0.307963265003654	1		359	425	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943508	17943508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	86	567	0	ENST00000458235.1:c.2500G>A	p.Gly834Ser	p.G834S	ENST00000458235	NM_000215.3	834	Ggc/Agc	19/24	0.292617421263479	4	FACETS	0.817	0.722	0.92			1	CLONAL	1	TRUE	NA	0.307963265003654	4		567	894	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443589	29443589	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	113	638	1	ENST00000389048.3:c.3628G>A	p.Glu1210Lys	p.E1210K	ENST00000389048	NM_004304.4	1210	Gag/Aag	23/29	1	2	FACETS	0.928	0.835	1	0.928	0.835	1	CLONAL	1	TRUE	1	0.307963265003654	2		639	791	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62325761	62325761	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs750539539	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	106	567	0	ENST00000360203.5:c.3029C>A	p.Thr1010Lys	p.T1010K	ENST00000360203	NM_001283009.1	1010	aCg/aAg	31/35	1	2	FACETS	0.988	0.886	1	0.988	0.886	1	CLONAL	1	TRUE	1	0.307963265003654	2		567	697	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462370	89462371	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	77	574	2	ENST00000336596.2:c.1842_1843delinsAA	p.Glu615Lys	p.E615K	ENST00000336596	NM_005233.5	614	aaGGaa/aaAAaa	10/17	1	2	FACETS	0.808	0.71	0.913	0.808	0.71	0.913	CLONAL	1	TRUE	1	0.307963265003654	2		576	619	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898747	134898747	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	84	417	0	ENST00000398015.3:c.1805A>T	p.Asp602Val	p.D602V	ENST00000398015	NM_004441.4	602	gAt/gTt	10/16	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.307963265003654	2		417	493	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281301	142281301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	90	564	0	ENST00000350721.4:c.943C>T	p.Pro315Ser	p.P315S	ENST00000350721	NM_001184.3	315	Cct/Tct	4/47	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.307963265003654	2		564	573	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612086	189612086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1191791499	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	92	593	0	ENST00000264731.3:c.1838C>T	p.Pro613Leu	p.P613L	ENST00000264731	NM_003722.4	613	cCt/cTt	14/14	1	2	FACETS	0.829	0.736	0.927	0.829	0.736	0.927	CLONAL	1	TRUE	1	0.307963265003654	2		593	721	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157359	106157359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210417590	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	72	516	2	ENST00000380013.4:c.2260G>A	p.Glu754Lys	p.E754K	ENST00000380013	NM_001127208.2	754	Gag/Aag	3/11	1	2	FACETS	0.868	0.759	0.984	0.868	0.759	0.984	CLONAL	1	TRUE	1	0.307963265003654	2		518	539	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197072	106197072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	60	337	0	ENST00000380013.4:c.5405C>T	p.Pro1802Leu	p.P1802L	ENST00000380013	NM_001127208.2	1802	cCa/cTa	11/11	1	2	FACETS	0.838	0.723	0.962	0.838	0.723	0.962	CLONAL	1	TRUE	1	0.307963265003654	2		337	465	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167812	56167812	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	88	462	0	ENST00000399503.3:c.1377T>G	p.Cys459Trp	p.C459W	ENST00000399503	NM_005921.1	459	tgT/tgG	7/20	1	2	FACETS	0.975	0.866	1	0.975	0.866	1	CLONAL	1	TRUE	1	0.307963265003654	2		462	586	SUCCESS
APC	324	MSKCC	GRCh37	5	112102990	112102990	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1414406816	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	58	512	0	ENST00000257430.4:c.325G>A	p.Glu109Lys	p.E109K	ENST00000257430	NM_000038.5	109	Gag/Aag	4/16	0.292320164803375	1	FACETS	0.661	0.569	0.761	0.661	0.569	0.761	SUBCLONAL	1	TRUE	0	0.307963265003654	1		512	482	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032137	26032137	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	58	371	0	ENST00000244661.2:c.152A>G	p.Glu51Gly	p.E51G	ENST00000244661	NM_003537.3	51	gAg/gGg	1/1	0.307963265003654	3	FACETS	0.689	0.591	0.795	0.344	0.295	0.398	SUBCLONAL	1	TRUE	1	0.307963265003654	3		371	631	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771213	161771214	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	78	547	1	ENST00000366898.1:c.1315_1316delinsTT	p.Pro439Phe	p.P439F	ENST00000366898	NM_004562.2	439	CCc/TTc	12/12	1	2	FACETS	0.828	0.728	0.935	0.828	0.728	0.935	CLONAL	1	TRUE	1	0.307963265003654	2		548	612	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622244	162622244	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	60	410	0	ENST00000366898.1:c.453A>C	p.Lys151Asn	p.K151N	ENST00000366898	NM_004562.2	151	aaA/aaC	4/12	1	2	FACETS	0.824	0.711	0.946	0.824	0.711	0.946	CLONAL	1	TRUE	1	0.307963265003654	2		410	473	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729835	41729835	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	68	344	0	ENST00000242208.4:c.694G>A	p.Asp232Asn	p.D232N	ENST00000242208	NM_002192.2	232	Gac/Aac	3/3	0.307963265003654	3	FACETS	0.849	0.739	0.968	0.425	0.369	0.484	CLONAL	1	TRUE	1	0.307963265003654	3		344	600	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739950	41739950	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1164410355	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	83	471	0	ENST00000242208.4:c.23G>A	p.Gly8Glu	p.G8E	ENST00000242208	NM_002192.2	8	gGa/gAa	2/3	0.307963265003654	3	FACETS	0.834	0.735	0.939	0.417	0.367	0.47	CLONAL	1	TRUE	1	0.307963265003654	3		471	746	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956759	68956759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777080876	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	83	663	1	ENST00000288368.4:c.877C>T	p.Arg293Trp	p.R293W	ENST00000288368	NM_024870.2	293	Cgg/Tgg	8/40	0.307963265003654	3	FACETS	0.864	0.762	0.973	0.432	0.381	0.487	CLONAL	1	TRUE	1	0.307963265003654	3		664	720	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518124	8518124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	93	468	0	ENST00000356435.5:c.1267G>A	p.Asp423Asn	p.D423N	ENST00000356435		423	Gat/Aat	10/35	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.307963265003654	2		468	556	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180337	27180337	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	89	448	0	ENST00000380036.4:c.1001G>A	p.Gly334Glu	p.G334E	ENST00000380036	NM_000459.3	334	gGa/gAa	7/23	1	2	FACETS	0.967	0.858	1	0.967	0.858	1	CLONAL	1	TRUE	1	0.307963265003654	2		448	598	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27190614	27190614	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	89	651	1	ENST00000380036.4:c.1415G>A	p.Gly472Glu	p.G472E	ENST00000380036	NM_000459.3	472	gGg/gAg	10/23	1	2	FACETS	0.869	0.771	0.974	0.869	0.771	0.974	CLONAL	1	TRUE	1	0.307963265003654	2		652	665	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27203051	27203051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	93	643	0	ENST00000380036.4:c.2143G>A	p.Glu715Lys	p.E715K	ENST00000380036	NM_000459.3	715	Gag/Aag	13/23	1	2	FACETS	0.897	0.798	1	0.897	0.798	1	CLONAL	1	TRUE	1	0.307963265003654	2		643	673	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240386	98240386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	70	469	0	ENST00000331920.6:c.1298C>T	p.Ser433Phe	p.S433F	ENST00000331920	NM_000264.3	433	tCc/tTc	9/24	0.292320164803375	1	FACETS	0.801	0.7	0.91	0.801	0.7	0.91	CLONAL	1	TRUE	0	0.307963265003654	1		469	480	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750254	133750254	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	72	459	0	ENST00000318560.5:c.1086-1G>A		p.X362_splice	ENST00000318560	NM_005157.4	362			0.292320164803375	1	FACETS	0.836	0.733	0.947	0.836	0.733	0.947	CLONAL	1	TRUE	0	0.307963265003654	1		459	473	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652965	29652969	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAC	AAAAC	-	novel	NA	P-0028629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	88	533	0	ENST00000356175.3:c.4901_4905del	p.Lys1634ArgfsTer5	p.K1634Rfs*5	ENST00000356175	NM_000267.3	1634	AAAACa/a	36/57	1	2	FACETS	0.935	0.83	1	0.935	0.83	1	CLONAL	1	TRUE	1	0.307963265003654	2		533	611	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	456	704	2	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.50846544761855	4	FACETS	0.968	0.935	0.999			1	CLONAL	4	TRUE	NA	0.50846544761855	4		706	699	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727111	40727111	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779663880	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	126	574	2	ENST00000373198.4:c.3853G>A	p.Asp1285Asn	p.D1285N	ENST00000373198	NM_133170.3	1285	Gat/Aat	28/32	NA	2	FACETS	1	0.948	1			1	INDETERMINATE	1	TRUE	NA	0.50846544761855	2		576	469	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849818	156849818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761967383	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	237	494	0	ENST00000524377.1:c.2074C>T	p.Arg692Cys	p.R692C	ENST00000524377	NM_002529.3	692	Cgc/Tgc	16/17	0.489235163058264	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.50846544761855	2		494	423	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32439161	32439161	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	77	535	1	ENST00000332351.3:c.912G>A	p.Met304Ile	p.M304I	ENST00000332351	NM_024426.4	304	atG/atA	4/10	1	2	FACETS	0.941	0.833	1	0.941	0.833	1	CLONAL	1	TRUE	1	0.50846544761855	2		536	322	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814253	76814253	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	35	435	2	ENST00000373344.5:c.6391C>T	p.Arg2131Ter	p.R2131*	ENST00000373344	NM_000489.3	2131	Cga/Tga	29/35	0.258802602019988	1	FACETS	0.446	0.368	0.533	0.446	0.368	0.533	INDETERMINATE	1	TRUE	0	0.50846544761855	1		437	230	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940000	76940000	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1311466929	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	63	626	2	ENST00000373344.5:c.748C>T	p.Arg250Ter	p.R250*	ENST00000373344	NM_000489.3	250	Cga/Tga	9/35	0.258802602019988	1	FACETS	0.562	0.489	0.64	0.562	0.489	0.64	INDETERMINATE	1	TRUE	0	0.50846544761855	1		628	329	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376071	8376071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	97	329	1	ENST00000356435.5:c.4526G>A	p.Arg1509Lys	p.R1509K	ENST00000356435		1509	aGa/aAa	28/35	0.385355728193632	2	FACETS	1	0.982	1	0.709	0.642	0.778	CLONAL	1	TRUE	0	0.50846544761855	2		330	269	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932047	36932047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146617729	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	114	611	0	ENST00000361632.4:c.2422G>A	p.Glu808Lys	p.E808K	ENST00000361632		808	Gag/Aag	16/16	1	2	FACETS	0.899	0.813	0.988	0.899	0.813	0.988	CLONAL	1	TRUE	1	0.50846544761855	2		611	499	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562641	29562641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854562	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	86	425	0	ENST00000356175.3:c.3721C>T	p.Arg1241Ter	p.R1241*	ENST00000356175	NM_000267.3	1241	Cga/Tga	28/57	0.385355728193632	2	FACETS	1	0.974	1	0.641	0.575	0.709	CLONAL	1	TRUE	0	0.50846544761855	2		425	264	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802558	139802558	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773154383	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	158	649	0	ENST00000247668.2:c.403G>A	p.Glu135Lys	p.E135K	ENST00000247668	NM_021138.3	135	Gaa/Aaa	5/11	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.50846544761855	2		649	482	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255076	16255076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1283954838	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	128	494	0	ENST00000375759.3:c.2341C>T	p.Arg781Cys	p.R781C	ENST00000375759	NM_015001.2	781	Cgt/Tgt	11/15	0.246947337250396	5	FACETS	1	0.976	1	0.785	0.719	0.852	INDETERMINATE	2	TRUE	2	0.50846544761855	5		494	377	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992737	68992737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200411060	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	74	577	1	ENST00000288368.4:c.1702G>A	p.Glu568Lys	p.E568K	ENST00000288368	NM_024870.2	568	Gaa/Aaa	16/40	0.239313849880599	3	FACETS	1	0.915	1	0.523	0.461	0.589	INDETERMINATE	1	TRUE	1	0.50846544761855	3		578	349	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523279	9523279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763590647	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	113	588	1	ENST00000353224.5:c.1958G>A	p.Arg653Gln	p.R653Q	ENST00000353224	NM_177990.2	653	cGg/cAg	9/10	0.50252349180869	3	FACETS	1	0.982	1	0.688	0.624	0.755	CLONAL	1	TRUE	1	0.50846544761855	3		589	405	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262225	16262225	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1340812093	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	67	278	0	ENST00000375759.3:c.9490C>T	p.Leu3164Phe	p.L3164F	ENST00000375759	NM_015001.2	3164	Ctt/Ttt	11/15	0.246947337250396	5	FACETS	0.86	0.756	0.971	0.574	0.504	0.647	INDETERMINATE	2	TRUE	2	0.50846544761855	5		278	270	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933540	36933540	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3917997	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	174	682	0	ENST00000361632.4:c.1747C>T	p.Arg583Cys	p.R583C	ENST00000361632		583	Cgt/Tgt	13/16	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.50846544761855	2		682	505	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371780	45371780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	79	498	0	ENST00000262160.6:c.1211C>T	p.Ala404Val	p.A404V	ENST00000262160	NM_005901.5	404	gCc/gTc	10/11	0.206330206786158	4	FACETS	1	0.975	1	0.698	0.618	0.781	INDETERMINATE	1	TRUE	2	0.50846544761855	4		498	336	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927368	245927368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	151	517	2	ENST00000388985.4:c.1160C>T	p.Pro387Leu	p.P387L	ENST00000388985		387	cCc/cTc	11/12	0.4704714988821	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.50846544761855	2		519	281	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615585	43615585	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	112	585	0	ENST00000355710.3:c.2664G>A	p.Met888Ile	p.M888I	ENST00000355710	NM_020975.4	888	atG/atA	15/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.50846544761855	2		585	413	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18649031	18649031	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	42	355	0	ENST00000266497.5:c.2706G>T	p.Leu902Phe	p.L902F	ENST00000266497		902	ttG/ttT	19/31	0.50252349180869	3	FACETS	0.816	0.686	0.958	0.408	0.343	0.479	CLONAL	1	TRUE	1	0.50846544761855	3		355	254	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28624268	28624268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	111	563	0	ENST00000241453.7:c.706G>A	p.Glu236Lys	p.E236K	ENST00000241453	NM_004119.2	236	Gaa/Aaa	6/24	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.50846544761855	2		563	401	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256143	41256143	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502358	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	134	517	0	ENST00000357654.3:c.437C>T	p.Ser146Phe	p.S146F	ENST00000357654	NM_007294.3	146	tCc/tTc	6/23	0.385355728193632	2	FACETS	0.899	0.832	0.968	0.899	0.832	0.968	CLONAL	2	TRUE	0	0.50846544761855	2		517	293	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208321	5208321	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	176	691	0	ENST00000357368.4:c.5569A>G	p.Ile1857Val	p.I1857V	ENST00000357368	NM_002850.3	1857	Atc/Gtc	36/38	0.50846544761855	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.50846544761855	1		691	404	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193476	99193476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	136	564	0	ENST00000074304.5:c.2671C>T	p.Arg891Trp	p.R891W	ENST00000074304	NM_001134224.1	891	Cgg/Tgg	25/26	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.50846544761855	2		564	414	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044360	128044360	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	125	638	0	ENST00000285398.2:c.1261T>C	p.Trp421Arg	p.W421R	ENST00000285398	NM_000122.1	421	Tgg/Cgg	8/15	0.239313849880599	3	FACETS	1	0.985	1	0.702	0.64	0.766	INDETERMINATE	1	TRUE	1	0.50846544761855	3		638	439	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288680	198288680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	24	474	0	ENST00000335508.6:c.47G>A	p.Arg16Gln	p.R16Q	ENST00000335508	NM_012433.2	16	cGa/cAa	2/25	1	2	FACETS	0.379	0.298	0.472	0.379	0.298	0.472	SUBCLONAL	1	TRUE	1	0.50846544761855	2		474	249	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019413	31019413	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs146637943	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	121	482	1	ENST00000375687.4:c.910A>T	p.Ser304Cys	p.S304C	ENST00000375687	NM_015338.5	304	Agc/Tgc	10/13	0.50252349180869	3	FACETS	1	0.983	1	0.683	0.622	0.747	CLONAL	1	TRUE	1	0.50846544761855	3		483	437	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730801	40730801	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	102	596	0	ENST00000373198.4:c.3734G>A	p.Gly1245Glu	p.G1245E	ENST00000373198	NM_133170.3	1245	gGa/gAa	27/32	NA	2	FACETS	1	0.904	1			1	INDETERMINATE	1	TRUE	NA	0.50846544761855	2		596	400	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743883	40743883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	82	524	0	ENST00000373198.4:c.3112G>A	p.Glu1038Lys	p.E1038K	ENST00000373198	NM_133170.3	1038	Gag/Aag	23/32	NA	2	FACETS	0.853	0.757	0.955			1	INDETERMINATE	1	TRUE	NA	0.50846544761855	2		524	378	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920319	1920319	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1270483441	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	207	672	0	ENST00000382891.5:c.1379T>A	p.Phe460Tyr	p.F460Y	ENST00000382891	NM_133335.3	460	tTt/tAt	5/22	0.258802602019988	1	FACETS	0.81	0.765	0.854	1	0.994	1	INDETERMINATE	2	TRUE	0	0.50846544761855	1		672	375	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967526	38967526	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	57	342	0	ENST00000357387.3:c.1064C>A	p.Pro355Gln	p.P355Q	ENST00000357387	NM_152756.3	355	cCa/cAa	13/38	0.206330206786158	4	FACETS	1	0.95	1	0.61	0.528	0.699	INDETERMINATE	1	TRUE	2	0.50846544761855	4		342	277	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26046032	26046032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749656611	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	107	293	0	ENST00000540144.1:c.394C>T	p.Arg132Cys	p.R132C	ENST00000540144	NM_003531.2	132	Cgt/Tgt	1/1	0.50846544761855	5	FACETS	0.989	0.895	1	0.659	0.597	0.725	CLONAL	2	TRUE	2	0.50846544761855	5		293	375	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289110	33289110	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	348	599	0	ENST00000374542.5:c.442G>T	p.Ala148Ser	p.A148S	ENST00000374542	NM_001141970.1	148	Gcc/Tcc	3/8	0.50846544761855	6	FACETS	0.945	0.902	0.989	0.945	0.902	0.989	CLONAL	4	TRUE	2	0.50846544761855	6		599	730	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708124	117708124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758924871	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	56	510	0	ENST00000368508.3:c.2053G>A	p.Gly685Arg	p.G685R	ENST00000368508	NM_002944.2	685	Ggg/Agg	14/43	1	2	FACETS	0.798	0.689	0.914	0.798	0.689	0.914	CLONAL	1	TRUE	1	0.50846544761855	2		510	276	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196106	138196106	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	21	385	0	ENST00000237289.4:c.420C>A	p.Phe140Leu	p.F140L	ENST00000237289	NM_001270507.1	140	ttC/ttA	3/9	1	2	FACETS	0.256	0.197	0.325	0.256	0.197	0.325	SUBCLONAL	1	TRUE	1	0.50846544761855	2		385	323	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509861	106509861	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	149	663	2	ENST00000359195.3:c.1855C>T	p.Gln619Ter	p.Q619*	ENST00000359195	NM_002649.2	619	Caa/Taa	2/11	0.220676859744386	5	FACETS	1	0.956	1	0.704	0.648	0.762	INDETERMINATE	2	TRUE	2	0.50846544761855	5		665	489	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738319	133738319	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	108	483	0	ENST00000318560.5:c.719C>G	p.Thr240Arg	p.T240R	ENST00000318560	NM_005157.4	240	aCg/aGg	4/11	0.319507414161786	3	FACETS	1	0.977	1	0.639	0.577	0.703	CLONAL	1	TRUE	1	0.50846544761855	3		483	417	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226141	53226141	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	53	606	0	ENST00000375401.3:c.2708C>T	p.Ser903Phe	p.S903F	ENST00000375401	NM_004187.3	903	tCc/tTc	19/26	0.50846544761855	1	FACETS	0.682	0.588	0.782	0.682	0.588	0.782	SUBCLONAL	1	TRUE	0	0.50846544761855	1		606	228	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354285	70354285	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	110	704	1	ENST00000374080.3:c.4696A>G	p.Ile1566Val	p.I1566V	ENST00000374080		1566	Atc/Gtc	34/45	0.258802602019988	1	FACETS	0.756	0.684	0.831	0.756	0.684	0.831	INDETERMINATE	1	TRUE	0	0.50846544761855	1		705	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0028632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	218	450	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.345939231391204	1	FACETS	0.821	0.768	0.875	1	0.993	1	CLONAL	2	TRUE	0	0.345939231391204	1		451	635	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0028632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	8	317	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.318807401928701	1	FACETS	0.114	0.073	0.168	0.114	0.073	0.168	SUBCLONAL	1	TRUE	0	0.345939231391204	1		317	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577137	7577137	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	98	357	1	ENST00000269305.4:c.801del	p.Asn268ThrfsTer77	p.N268Tfs*77	ENST00000269305	NM_001126112.2	267	cgG/cg	8/11	0.345939231391204	1	FACETS	0.881	0.788	0.978	0.881	0.788	0.978	CLONAL	1	TRUE	0	0.345939231391204	1		358	532	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916947	178916947	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	93	289	0	ENST00000263967.3:c.334A>T	p.Ile112Phe	p.I112F	ENST00000263967	NM_006218.2	112	Atc/Ttc	2/21	1	2	FACETS	0.781	0.701	0.865	1	0.983	1	SUBCLONAL	2	TRUE	1	0.345939231391204	2		289	344	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735503	40735503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763584414	NA	P-0028632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	70	387	1	ENST00000373198.4:c.3370G>A	p.Glu1124Lys	p.E1124K	ENST00000373198	NM_133170.3	1124	Gag/Aag	25/32	1	2	FACETS	0.621	0.541	0.707	0.621	0.541	0.707	SUBCLONAL	1	TRUE	1	0.345939231391204	2		388	652	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873587	151873588	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0028632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	142	343	0	ENST00000262189.6:c.8950dup	p.Ser2984PhefsTer18	p.S2984Ffs*18	ENST00000262189	NM_170606.2	2984	tct/tTct	38/59	0.108874777381592	3	FACETS	0.784	0.717	0.854	0.784	0.717	0.854	INDETERMINATE	2	TRUE	1	0.345939231391204	3		343	614	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797706	32797706	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0028632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	146	352	0	ENST00000374899.4:c.1795+1del		p.X599_splice	ENST00000374899	NM_018833.2	599			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.345939231391204	2		352	657	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925523	114925523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780741000	NA	P-0028634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	332	450	0	ENST00000543371.1:c.1601C>T	p.Pro534Leu	p.P534L	ENST00000543371	NM_001198531.1	534	cCg/cTg	14/14	0.328547818157268	3	FACETS	0.851	0.807	0.895	0.851	0.807	0.895	CLONAL	3	TRUE	0	0.328547818157268	3		450	922	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938390	44938390	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0028634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	211	399	0	ENST00000377967.4:c.2939-1G>A		p.X980_splice	ENST00000377967	NM_021140.2	980			0.328547818157268	2	FACETS	0.982	0.917	1	0.982	0.917	1	CLONAL	2	TRUE	0	0.328547818157268	2		399	654	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873483	151873483	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	514	478	0	ENST00000262189.6:c.9055C>T	p.Gln3019Ter	p.Q3019*	ENST00000262189	NM_170606.2	3019	Cag/Tag	38/59	0.328547818157268	4	FACETS	0.911	0.875	0.946	1	0.995	1	CLONAL	4	TRUE	1	0.328547818157268	4		478	1141	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998645	100998645	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	91	431	0	ENST00000325455.5:c.1157A>C	p.Lys386Thr	p.K386T	ENST00000325455	NM_001202474.3	386	aAg/aCg	1/8	0.328547818157268	3	FACETS	0.718	0.637	0.806	0.359	0.318	0.403	SUBCLONAL	1	TRUE	1	0.328547818157268	3		431	898	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076717	102076717	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs112417656	NA	P-0028634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	146	448	0	ENST00000282441.5:c.896A>G	p.Asn299Ser	p.N299S	ENST00000282441	NM_001130145.2	299	aAc/aGc	5/9	0.328547818157268	3	FACETS	1	0.946	1	0.525	0.479	0.574	CLONAL	1	TRUE	1	0.328547818157268	3		448	985	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857433	68857433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	179	548	0	ENST00000261769.5:c.2068G>A	p.Gly690Arg	p.G690R	ENST00000261769	NM_004360.3	690	Ggg/Agg	13/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.328547818157268	2		548	970	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414829	56414829	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	196	519	0	ENST00000348428.3:c.2230T>C	p.Ser744Pro	p.S744P	ENST00000348428	NM_006785.3	744	Tca/Cca	17/17	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.328547818157268	2		519	1000	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937710	17937710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200580168	NA	P-0028634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	146	407	0	ENST00000458235.1:c.3217C>T	p.Leu1073Phe	p.L1073F	ENST00000458235	NM_000215.3	1073	Ctc/Ttc	24/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.328547818157268	2		407	791	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693810	47693813	+	frameshift_variant	Frame_Shift_Del	DEL	CAAA	CAAA	-	novel	NA	P-0028634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	98	315	0	ENST00000233146.2:c.1526_1529del	p.Lys509ArgfsTer16	p.K509Rfs*16	ENST00000233146	NM_000251.2	508	ggCAAA/gg	10/16	0.328547818157268	3	FACETS	0.902	0.804	1	0.451	0.402	0.503	CLONAL	1	TRUE	1	0.328547818157268	3		315	770	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279802	46279802	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	102	363	0	ENST00000371998.3:c.3728T>A	p.Val1243Glu	p.V1243E	ENST00000371998		1243	gTg/gAg	20/23	0.288498278647008	4	FACETS	0.879	0.785	0.98	0.293	0.261	0.327	CLONAL	1	TRUE	1	0.328547818157268	4		363	938	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267311	41267311	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	102	323	0	ENST00000349496.5:c.895G>C	p.Asp299His	p.D299H	ENST00000349496	NM_001904.3	299	Gac/Cac	6/15	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.328547818157268	2		323	555	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156252	106156252	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	106	337	0	ENST00000380013.4:c.1153T>G	p.Ser385Ala	p.S385A	ENST00000380013	NM_001127208.2	385	Tca/Gca	3/11	0.328547818157268	2	FACETS	1	0.924	1	0.517	0.464	0.573	CLONAL	1	TRUE	0	0.328547818157268	2		337	624	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6029442	6029442	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	101	426	0	ENST00000265849.7:c.1133T>C	p.Leu378Pro	p.L378P	ENST00000265849	NM_000535.5	378	cTg/cCg	10/15	0.328547818157268	4	FACETS	0.929	0.83	1	0.31	0.276	0.345	CLONAL	1	TRUE	1	0.328547818157268	4		426	879	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346255	152346255	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	293	510	0	ENST00000359321.1:c.315A>C	p.Glu105Asp	p.E105D	ENST00000359321	NM_005431.1	105	gaA/gaC	3/3	0.328547818157268	4	FACETS	0.903	0.849	0.959	0.602	0.566	0.64	CLONAL	2	TRUE	1	0.328547818157268	4		510	1312	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341196	8341196	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	108	393	0	ENST00000356435.5:c.5020del	p.Arg1674AlafsTer21	p.R1674Afs*21	ENST00000356435		1674	Cgc/gc	30/35	1	2	FACETS	0.953	0.856	1	0.953	0.856	1	CLONAL	1	TRUE	1	0.328547818157268	2		393	690	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554345	141554345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748399150	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	282	757	8	ENST00000220592.5:c.1806del	p.Ala603ProfsTer92	p.A603Pfs*92	ENST00000220592	NM_012154.3	602	ccC/cc	14/19	1	2	FACETS	0.882	0.829	0.937	0.882	0.829	0.937	CLONAL	1	TRUE	1	0.59082421462931	2		765	1082	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	254	576	2	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	0.947	0.888	1	0.947	0.888	1	CLONAL	1	TRUE	1	0.59082421462931	2		578	908	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	226	490	1	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.59082421462931	2		491	755	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259751	16259751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	302	610	2	ENST00000375759.3:c.7016G>A	p.Arg2339His	p.R2339H	ENST00000375759	NM_015001.2	2339	cGc/cAc	11/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.59082421462931	2		612	973	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	83	478	3	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	1	2	FACETS	0.401	0.354	0.452	0.401	0.354	0.452	SUBCLONAL	1	TRUE	1	0.59082421462931	2		481	700	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	298	637	0	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.959	0.904	1	0.959	0.904	1	CLONAL	1	TRUE	1	0.59082421462931	2		637	1052	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	126	359	1	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	1	2	FACETS	0.504	0.456	0.555	0.504	0.456	0.555	SUBCLONAL	1	TRUE	1	0.59082421462931	2		360	846	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023861	27023861	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1336228861	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	100	145	0	ENST00000324856.7:c.971del	p.Gly324AlafsTer39	p.G324Afs*39	ENST00000324856	NM_006015.4	323	Ggg/gg	1/20	1	2	FACETS	0.967	0.872	1	0.967	0.872	1	CLONAL	1	TRUE	1	0.59082421462931	2		145	350	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	222	490	4	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.935	0.872	0.999	0.935	0.872	0.999	CLONAL	1	TRUE	1	0.59082421462931	2		494	804	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599939	28599939	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757342510	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	267	550	0	ENST00000253063.3:c.821G>A	p.Arg274Gln	p.R274Q	ENST00000253063	NM_031459.4	274	cGg/cAg	6/10	1	2	FACETS	0.973	0.914	1	0.973	0.914	1	CLONAL	1	TRUE	1	0.59082421462931	2		550	929	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	305	630	6	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.59082421462931	2		636	902	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436044	51436044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	164	360	0	ENST00000262662.1:c.4G>A	p.Ala2Thr	p.A2T	ENST00000262662		2	Gcc/Acc	3/4	1	2	FACETS	0.941	0.868	1	0.941	0.868	1	CLONAL	1	TRUE	1	0.59082421462931	2		360	590	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339175	65339175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180823763	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	215	411	1	ENST00000342505.4:c.361G>A	p.Asp121Asn	p.D121N	ENST00000342505	NM_002227.2	121	Gac/Aac	5/25	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.59082421462931	2		412	695	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551928	150551928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	180	381	1	ENST00000369026.2:c.79G>A	p.Gly27Ser	p.G27S	ENST00000369026	NM_021960.4	27	Ggc/Agc	1/3	1	2	FACETS	0.94	0.871	1	0.94	0.871	1	CLONAL	1	TRUE	1	0.59082421462931	2		382	648	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729614	162729614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773580613	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	230	518	0	ENST00000367921.3:c.700G>A	p.Asp234Asn	p.D234N	ENST00000367921	NM_006182.2	234	Gat/Aat	8/18	1	2	FACETS	0.913	0.853	0.975	0.913	0.853	0.975	CLONAL	1	TRUE	1	0.59082421462931	2		518	853	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944344	206944344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	272	490	1	ENST00000423557.1:c.286C>T	p.Pro96Ser	p.P96S	ENST00000423557	NM_000572.2	96	Ccc/Tcc	3/5	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.59082421462931	2		491	882	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852118	63852118	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	164	523	0	ENST00000279873.7:c.2901del	p.Lys967AsnfsTer15	p.K967Nfs*15	ENST00000279873	NM_032199.2	966	Aaa/aa	10/10	1	2	FACETS	0.602	0.553	0.654	0.602	0.553	0.654	SUBCLONAL	1	TRUE	1	0.59082421462931	2		523	922	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263302	123263302	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	159	389	0	ENST00000358487.5:c.1439+2T>C		p.X480_splice	ENST00000358487	NM_000141.4	480			1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.59082421462931	2		389	532	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251892	8251892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	71	571	0	ENST00000335790.3:c.185G>A	p.Gly62Asp	p.G62D	ENST00000335790	NM_002315.2	62	gGc/gAc	2/4	1	2	FACETS	0.276	0.24	0.315	0.276	0.24	0.315	SUBCLONAL	1	TRUE	1	0.59082421462931	2		571	871	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456619	32456621	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	rs770519620	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	125	122	1	ENST00000332351.3:c.271_273del	p.Gly91del	p.G91del	ENST00000332351	NM_024426.4	91	GGC/-	1/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.59082421462931	2		123	321	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61213502	61213502	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778585796	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	282	512	0	ENST00000301761.2:c.460C>T	p.Arg154Cys	p.R154C	ENST00000301761	NM_017841.2	154	Cgt/Tgt	4/4	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.59082421462931	2		512	881	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180441	94180441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139461096	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	258	493	1	ENST00000323929.3:c.1727G>A	p.Arg576Gln	p.R576Q	ENST00000323929	NM_005591.3	576	cGa/cAa	15/20	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.59082421462931	2		494	869	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376556	118376556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	140	439	0	ENST00000534358.1:c.9949G>A	p.Ala3317Thr	p.A3317T	ENST00000534358	NM_005933.3	3317	Gca/Aca	27/36	1	2	FACETS	0.719	0.657	0.784	0.719	0.657	0.784	SUBCLONAL	1	TRUE	1	0.59082421462931	2		439	659	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446875	18446875	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	42	373	0	ENST00000266497.5:c.964del	p.Cys322AlafsTer13	p.C322Afs*13	ENST00000266497		320	caT/ca	4/31	0.505513097654467	1	FACETS	0.211	0.176	0.25	0.211	0.176	0.25	SUBCLONAL	1	TRUE	0	0.59082421462931	1		373	474	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425667	49425667	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	39	589	0	ENST00000301067.7:c.12821T>C	p.Leu4274Pro	p.L4274P	ENST00000301067	NM_003482.3	4274	cTc/cCc	39/54	1	2	FACETS	0.172	0.141	0.206	0.172	0.141	0.206	SUBCLONAL	1	TRUE	1	0.59082421462931	2		589	769	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426973	49426973	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1565778024	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	213	511	1	ENST00000301067.7:c.11515del	p.Gln3839SerfsTer42	p.Q3839Sfs*42	ENST00000301067	NM_003482.3	3839	Cag/ag	39/54	1	2	FACETS	0.924	0.861	0.989	0.924	0.861	0.989	CLONAL	1	TRUE	1	0.59082421462931	2		512	780	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	277	632	1	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.939	0.882	0.996	0.939	0.882	0.996	CLONAL	1	TRUE	1	0.59082421462931	2		633	999	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857566	57857566	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	213	463	0	ENST00000228682.2:c.92G>T	p.Gly31Val	p.G31V	ENST00000228682	NM_005269.2	31	gGg/gTg	2/12	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.59082421462931	2		463	651	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861998	57861998	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	74	446	0	ENST00000228682.2:c.1299G>T	p.Glu433Asp	p.E433D	ENST00000228682	NM_005269.2	433	gaG/gaT	10/12	1	2	FACETS	0.354	0.309	0.402	0.354	0.309	0.402	SUBCLONAL	1	TRUE	1	0.59082421462931	2		446	708	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811690	102811690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	78	686	1	ENST00000307046.8:c.494C>T	p.Thr165Ile	p.T165I	ENST00000307046	NM_001111285.1	165	aCa/aTa	4/4	1	2	FACETS	0.271	0.237	0.308	0.271	0.237	0.308	SUBCLONAL	1	TRUE	1	0.59082421462931	2		687	974	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856193	111856193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1424493907	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	54	228	0	ENST00000341259.2:c.244G>A	p.Gly82Arg	p.G82R	ENST00000341259	NM_005475.2	82	Gga/Aga	2/8	1	2	FACETS	0.344	0.293	0.399	0.344	0.293	0.399	SUBCLONAL	1	TRUE	1	0.59082421462931	2		228	532	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112064	115112064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757023811	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	243	635	3	ENST00000257566.3:c.1676C>T	p.Thr559Met	p.T559M	ENST00000257566	NM_016569.3	559	aCg/aTg	7/8	1	2	FACETS	0.983	0.921	1	0.983	0.921	1	CLONAL	1	TRUE	1	0.59082421462931	2		638	837	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117749	115117749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs554364556	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	168	522	1	ENST00000257566.3:c.686C>T	p.Thr229Met	p.T229M	ENST00000257566	NM_016569.3	229	aCg/aTg	3/8	1	2	FACETS	0.798	0.735	0.863	0.798	0.735	0.863	SUBCLONAL	1	TRUE	1	0.59082421462931	2		523	713	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437383	121437383	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773895173	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	239	583	1	ENST00000257555.6:c.1721G>A	p.Ser574Asn	p.S574N	ENST00000257555		574	aGc/aAc	9/10	1	2	FACETS	0.994	0.931	1	0.994	0.931	1	CLONAL	1	TRUE	1	0.59082421462931	2		584	814	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218864	133218864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1235110857	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	324	552	0	ENST00000320574.5:c.5072G>A	p.Arg1691His	p.R1691H	ENST00000320574	NM_006231.2	1691	cGc/cAc	38/49	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.59082421462931	2		552	974	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28674623	28674623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	26	36	0	ENST00000241453.7:c.25G>A	p.Gly9Ser	p.G9S	ENST00000241453	NM_004119.2	9	Ggc/Agc	1/24	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.59082421462931	2		36	82	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105683	30105683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	55	495	0	ENST00000331968.5:c.1003G>A	p.Ala335Thr	p.A335T	ENST00000331968	NM_002742.2	335	Gca/Aca	7/18	1	2	FACETS	0.31	0.265	0.36	0.31	0.265	0.36	SUBCLONAL	1	TRUE	1	0.59082421462931	2		495	600	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562189	95562189	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	35	390	0	ENST00000393063.1:c.5068G>A	p.Ala1690Thr	p.A1690T	ENST00000393063	NM_030621.3	1690	Gcc/Acc	24/28	1	2	FACETS	0.195	0.159	0.235	0.195	0.159	0.235	SUBCLONAL	1	TRUE	1	0.59082421462931	2		390	609	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467177	99467177	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149217017	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	219	496	1	ENST00000268035.6:c.2558C>T	p.Pro853Leu	p.P853L	ENST00000268035	NM_000875.3	853	cCg/cTg	12/21	1	2	FACETS	0.981	0.915	1	0.981	0.915	1	CLONAL	1	TRUE	1	0.59082421462931	2		497	756	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339524	339524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	304	667	2	ENST00000262320.3:c.2378C>T	p.Pro793Leu	p.P793L	ENST00000262320	NM_003502.3	793	cCc/cTc	10/11	1	2	FACETS	0.955	0.901	1	0.955	0.901	1	CLONAL	1	TRUE	1	0.59082421462931	2		669	1077	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134248	2134250	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs878854100	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	227	518	0	ENST00000219476.3:c.4030_4032del	p.Glu1344del	p.E1344del	ENST00000219476	NM_000548.3	1342	cAGGag/cag	34/42	1	2	FACETS	0.935	0.873	0.998	0.935	0.873	0.998	CLONAL	1	TRUE	1	0.59082421462931	2		518	822	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136829	2136829	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	328	662	0	ENST00000219476.3:c.4946T>G	p.Val1649Gly	p.V1649G	ENST00000219476	NM_000548.3	1649	gTc/gGc	38/42	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.59082421462931	2		662	1101	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644599	3644599	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	152	589	0	ENST00000294008.3:c.2015T>G	p.Leu672Arg	p.L672R	ENST00000294008	NM_032444.2	672	cTc/cGc	10/15	1	2	FACETS	0.571	0.522	0.622	0.571	0.522	0.622	SUBCLONAL	1	TRUE	1	0.59082421462931	2		589	901	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779322	3779322	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	231	514	0	ENST00000262367.5:c.5726C>T	p.Pro1909Leu	p.P1909L	ENST00000262367	NM_004380.2	1909	cCc/cTc	31/31	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.59082421462931	2		514	772	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822586	72822586	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	138	428	7	ENST00000268489.5:c.9589del	p.Gln3197SerfsTer44	p.Q3197Sfs*44	ENST00000268489	NM_006885.3	3197	Cag/ag	10/10	1	2	FACETS	0.803	0.733	0.875	0.803	0.733	0.875	CLONAL	1	TRUE	1	0.59082421462931	2		435	582	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992051	72992051	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs562347029	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	134	545	0	ENST00000268489.5:c.1994G>A	p.Arg665His	p.R665H	ENST00000268489	NM_006885.3	665	cGt/cAt	2/10	1	2	FACETS	0.581	0.528	0.636	0.581	0.528	0.636	SUBCLONAL	1	TRUE	1	0.59082421462931	2		545	781	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217628	7217628	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	76	462	0	ENST00000380728.2:c.299G>A	p.Arg100Gln	p.R100Q	ENST00000380728		100	cGg/cAg	4/11	1	2	FACETS	0.333	0.291	0.378	0.333	0.291	0.378	SUBCLONAL	1	TRUE	1	0.59082421462931	2		462	773	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998958	11998958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567657403	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	116	371	0	ENST00000353533.5:c.460C>T	p.Arg154Trp	p.R154W	ENST00000353533	NM_003010.3	154	Cgg/Tgg	4/11	1	2	FACETS	0.761	0.689	0.836	0.761	0.689	0.836	SUBCLONAL	1	TRUE	1	0.59082421462931	2		371	516	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16040642	16040642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	131	412	1	ENST00000268712.3:c.1492C>T	p.Arg498Cys	p.R498C	ENST00000268712	NM_006311.3	498	Cgc/Tgc	14/46	1	2	FACETS	0.718	0.653	0.785	0.718	0.653	0.785	SUBCLONAL	1	TRUE	1	0.59082421462931	2		413	618	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131273	17131273	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779900587	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	307	628	0	ENST00000285071.4:c.179C>T	p.Ala60Val	p.A60V	ENST00000285071	NM_144997.5	60	gCg/gTg	4/14	1	2	FACETS	0.93	0.877	0.985	0.93	0.877	0.985	CLONAL	1	TRUE	1	0.59082421462931	2		628	1117	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486050	29486050	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1438566555	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	251	319	1	ENST00000356175.3:c.233del	p.Asn78IlefsTer7	p.N78Ifs*7	ENST00000356175	NM_000267.3	76	gAa/ga	3/57	1	2	FACETS	0.95	0.903	0.997	1	0.995	1	CLONAL	2	TRUE	1	0.59082421462931	2		320	447	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686901	37686901	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	233	457	2	ENST00000447079.4:c.3810del	p.Gly1271AspfsTer23	p.G1271Dfs*23	ENST00000447079	NM_015083.1	1269	Ccc/cc	14/14	1	2	FACETS	0.947	0.885	1	0.947	0.885	1	CLONAL	1	TRUE	1	0.59082421462931	2		459	833	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687472	37687472	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	215	316	3	ENST00000447079.4:c.4382del	p.Gly1461AlafsTer38	p.G1461Afs*38	ENST00000447079	NM_015083.1	1459	tGg/tg	14/14	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.59082421462931	2		319	581	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866710	37866710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1258412021	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	347	657	2	ENST00000269571.5:c.877G>A	p.Ala293Thr	p.A293T	ENST00000269571		293	Gcc/Acc	7/27	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.59082421462931	2		659	1169	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489837	40489837	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	278	590	0	ENST00000264657.5:c.589A>G	p.Arg197Gly	p.R197G	ENST00000264657	NM_139276.2	197	Agg/Ggg	7/24	1	2	FACETS	0.958	0.901	1	0.958	0.901	1	CLONAL	1	TRUE	1	0.59082421462931	2		590	982	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244618	41244618	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	205	634	0	ENST00000357654.3:c.2930del	p.Pro977HisfsTer23	p.P977Hfs*23	ENST00000357654	NM_007294.3	977	cCa/ca	10/23	1	2	FACETS	0.901	0.838	0.966	0.901	0.838	0.966	CLONAL	1	TRUE	1	0.59082421462931	2		634	770	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435162	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	266	592	0	ENST00000407977.2:c.1975_1976del	p.Gly659SerfsTer87	p.G659Sfs*87	ENST00000407977		659	GGt/t	9/10	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.59082421462931	2		592	890	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	323	602	1	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.59082421462931	2		603	958	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533905	63533905	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	44	403	0	ENST00000307078.5:c.1249del	p.Ala417ArgfsTer41	p.A417Rfs*41	ENST00000307078	NM_004655.3	417	Gcg/cg	6/11	1	2	FACETS	0.217	0.181	0.257	0.217	0.181	0.257	SUBCLONAL	1	TRUE	1	0.59082421462931	2		403	687	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120031	70120031	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	25	71	0	ENST00000245479.2:c.1037del	p.Pro346ArgfsTer37	p.P346Rfs*37	ENST00000245479	NM_000346.3	345	Ccc/cc	3/3	1	2	FACETS	0.749	0.601	0.912	0.749	0.601	0.912	CLONAL	1	TRUE	1	0.59082421462931	2		71	113	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39644789	39644789	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	114	322	0	ENST00000262039.4:c.2522del	p.Lys841ArgfsTer8	p.K841Rfs*8	ENST00000262039	NM_002647.2	840	Aaa/aa	23/25	1	2	FACETS	0.748	0.676	0.823	0.748	0.676	0.823	SUBCLONAL	1	TRUE	1	0.59082421462931	2		322	516	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612344	1612344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1320707074	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	330	722	0	ENST00000344749.5:c.1675G>A	p.Val559Met	p.V559M	ENST00000344749	NM_001136139.2	559	Gtg/Atg	18/19	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.59082421462931	2		722	1104	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223104	5223104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773778652	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	259	564	0	ENST00000357368.4:c.2699C>T	p.Thr900Met	p.T900M	ENST00000357368	NM_002850.3	900	aCg/aTg	18/38	1	2	FACETS	0.954	0.895	1	0.954	0.895	1	CLONAL	1	TRUE	1	0.59082421462931	2		564	919	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249244	10249244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	255	505	0	ENST00000340748.4:c.3938C>T	p.Ala1313Val	p.A1313V	ENST00000340748		1313	gCc/gTc	34/40	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.59082421462931	2		505	800	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272337	15272337	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs771517374	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	240	626	5	ENST00000263388.2:c.6102del	p.Gly2035ValfsTer50	p.G2035Vfs*50	ENST00000263388	NM_000435.2	2034	ccC/cc	33/33	1	2	FACETS	0.88	0.823	0.939	0.88	0.823	0.939	CLONAL	1	TRUE	1	0.59082421462931	2		631	923	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276285	15276285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	83	645	0	ENST00000263388.2:c.5709G>A	p.Met1903Ile	p.M1903I	ENST00000263388	NM_000435.2	1903	atG/atA	31/33	1	2	FACETS	0.284	0.25	0.321	0.284	0.25	0.321	SUBCLONAL	1	TRUE	1	0.59082421462931	2		645	988	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211082	36211082	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	283	726	0	ENST00000222270.7:c.837del	p.Arg280GlyfsTer25	p.R280Gfs*25	ENST00000222270	NM_014727.1	278	aCc/ac	3/37	1	2	FACETS	0.849	0.797	0.901	0.849	0.797	0.901	CLONAL	1	TRUE	1	0.59082421462931	2		726	1129	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213999	36213999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774513604	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	301	671	0	ENST00000222270.7:c.2825G>A	p.Gly942Glu	p.G942E	ENST00000222270	NM_014727.1	942	gGa/gAa	6/37	1	2	FACETS	0.962	0.907	1	0.962	0.907	1	CLONAL	1	TRUE	1	0.59082421462931	2		671	1059	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905543	50905543	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373001984	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	285	683	2	ENST00000440232.2:c.671G>A	p.Arg224His	p.R224H	ENST00000440232	NM_002691.3	224	cGc/cAc	6/27	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.59082421462931	2		685	864	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022303	26022304	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTG	rs750598660	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	176	545	0	ENST00000435504.4:c.351_353dup	p.Ser118dup	p.S118dup	ENST00000435504		118	agt/agCAGt	5/13	1	2	FACETS	0.695	0.641	0.752	0.695	0.641	0.752	SUBCLONAL	1	TRUE	1	0.59082421462931	2		545	857	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026570	48026570	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	67	446	0	ENST00000234420.5:c.1448T>C	p.Val483Ala	p.V483A	ENST00000234420	NM_000179.2	483	gTg/gCg	4/10	1	2	FACETS	0.329	0.285	0.376	0.329	0.285	0.376	SUBCLONAL	1	TRUE	1	0.59082421462931	2		446	690	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026881	48026881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868575342	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	160	516	1	ENST00000234420.5:c.1759G>A	p.Ala587Thr	p.A587T	ENST00000234420	NM_000179.2	587	Gca/Aca	4/10	1	2	FACETS	0.871	0.802	0.942	0.871	0.802	0.942	CLONAL	1	TRUE	1	0.59082421462931	2		517	622	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198262763	198262763	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	42	521	4	ENST00000335508.6:c.3212del	p.Lys1071ArgfsTer28	p.K1071Rfs*28	ENST00000335508	NM_012433.2	1071	aAg/ag	22/25	1	2	FACETS	0.188	0.156	0.224	0.188	0.156	0.224	SUBCLONAL	1	TRUE	1	0.59082421462931	2		525	756	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989529	212989529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	180	397	0	ENST00000342788.4:c.182G>A	p.Gly61Asp	p.G61D	ENST00000342788	NM_005235.2	61	gGc/gAc	2/28	1	2	FACETS	0.903	0.835	0.972	0.903	0.835	0.972	CLONAL	1	TRUE	1	0.59082421462931	2		397	675	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376297	225376297	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	27	236	0	ENST00000264414.4:c.657G>T	p.Met219Ile	p.M219I	ENST00000264414	NM_003590.4	219	atG/atT	6/16	NA	2	FACETS	0.394	0.315	0.483			1	INDETERMINATE	1	TRUE	NA	0.59082421462931	2		236	232	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659793	227659793	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766758551	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	66	400	2	ENST00000305123.5:c.3662G>A	p.Arg1221His	p.R1221H	ENST00000305123	NM_005544.2	1221	cGc/cAc	1/2	NA	2	FACETS	0.36	0.312	0.412			1	INDETERMINATE	1	TRUE	NA	0.59082421462931	2		402	620	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661381	227661381	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367626263	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	201	574	0	ENST00000305123.5:c.2074G>A	p.Gly692Arg	p.G692R	ENST00000305123	NM_005544.2	692	Ggg/Agg	1/2	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.59082421462931	2		574	635	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735533	40735533	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs777602624	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	182	470	0	ENST00000373198.4:c.3340A>G	p.Ile1114Val	p.I1114V	ENST00000373198	NM_133170.3	1114	Att/Gtt	25/32	1	2	FACETS	0.79	0.73	0.852	0.79	0.73	0.852	SUBCLONAL	1	TRUE	1	0.59082421462931	2		470	780	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42861463	42861463	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201949634	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	270	546	0	ENST00000398585.3:c.407C>T	p.Ala136Val	p.A136V	ENST00000398585	NM_001135099.1	136	gCg/gTg	4/14	1	2	FACETS	0.969	0.911	1	0.969	0.911	1	CLONAL	1	TRUE	1	0.59082421462931	2		546	943	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37038192	37038192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750206	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	209	319	0	ENST00000231790.2:c.199G>A	p.Gly67Arg	p.G67R	ENST00000231790	NM_000249.3	67	Ggg/Agg	2/19	0.556779350145227	2	FACETS	0.795	0.747	0.843	0.795	0.747	0.843	SUBCLONAL	2	TRUE	0	0.59082421462931	2		319	445	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070349	37070349	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs63750855	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	202	480	0	ENST00000231790.2:c.1489del	p.Arg497GlyfsTer11	p.R497Gfs*11	ENST00000231790	NM_000249.3	495	aCc/ac	13/19	0.556779350145227	2	FACETS	0.887	0.824	0.951	0.443	0.412	0.476	CLONAL	1	TRUE	0	0.59082421462931	2		480	771	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651496	52651496	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	252	508	1	ENST00000394830.3:c.1600C>T	p.Arg534Ter	p.R534*	ENST00000394830	NM_018313.4	534	Cga/Tga	15/30	0.556779350145227	2	FACETS	1	0.973	1	0.532	0.5	0.566	CLONAL	1	TRUE	0	0.59082421462931	2		509	801	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014097	70014097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757354709	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	217	603	0	ENST00000394351.3:c.958G>A	p.Val320Ile	p.V320I	ENST00000394351	NM_000248.3	320	Gtt/Att	9/9	1	2	FACETS	0.856	0.797	0.917	0.856	0.797	0.917	CLONAL	1	TRUE	1	0.59082421462931	2		603	858	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670324	134670324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775406650	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	184	508	0	ENST00000398015.3:c.235C>T	p.Arg79Trp	p.R79W	ENST00000398015	NM_004441.4	79	Cgg/Tgg	3/16	1	2	FACETS	0.982	0.911	1	0.982	0.911	1	CLONAL	1	TRUE	1	0.59082421462931	2		508	634	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664761	138664761	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs797044528	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	152	208	0	ENST00000330315.3:c.804del	p.Gly269AlafsTer2	p.G269Afs*2	ENST00000330315	NM_023067.3	268	ccC/cc	1/1	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.59082421462931	2		208	459	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664989	138664989	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	93	180	0	ENST00000330315.3:c.576del	p.Lys193SerfsTer78	p.K193Sfs*78	ENST00000330315	NM_023067.3	192	ccC/cc	1/1	1	2	FACETS	0.846	0.758	0.938	0.846	0.758	0.938	CLONAL	1	TRUE	1	0.59082421462931	2		180	372	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665498	138665498	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	43	398	0	ENST00000330315.3:c.67A>G	p.Thr23Ala	p.T23A	ENST00000330315	NM_023067.3	23	Aca/Gca	1/1	1	2	FACETS	0.257	0.215	0.304	0.257	0.215	0.304	SUBCLONAL	1	TRUE	1	0.59082421462931	2		398	566	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916935	178916935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	145	490	0	ENST00000263967.3:c.322C>T	p.Arg108Cys	p.R108C	ENST00000263967	NM_006218.2	108	Cgt/Tgt	2/21	1	2	FACETS	0.851	0.78	0.924	0.851	0.78	0.924	CLONAL	1	TRUE	1	0.59082421462931	2		490	577	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961213	1961213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	227	459	0	ENST00000382891.5:c.3001G>A	p.Gly1001Arg	p.G1001R	ENST00000382891	NM_133335.3	1001	Ggg/Agg	17/22	1	2	FACETS	0.952	0.889	1	0.952	0.889	1	CLONAL	1	TRUE	1	0.59082421462931	2		459	807	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517817	187517817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	153	360	0	ENST00000441802.2:c.12877C>T	p.His4293Tyr	p.H4293Y	ENST00000441802	NM_005245.3	4293	Cac/Tac	25/27	1	2	FACETS	0.952	0.876	1	0.952	0.876	1	CLONAL	1	TRUE	1	0.59082421462931	2		360	544	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518260	187518260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	138	336	0	ENST00000441802.2:c.12434C>T	p.Thr4145Met	p.T4145M	ENST00000441802	NM_005245.3	4145	aCg/aTg	25/27	1	2	FACETS	0.936	0.857	1	0.936	0.857	1	CLONAL	1	TRUE	1	0.59082421462931	2		336	499	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531029	187531029	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	61	488	0	ENST00000441802.2:c.9994A>G	p.Thr3332Ala	p.T3332A	ENST00000441802	NM_005245.3	3332	Acc/Gcc	15/27	1	2	FACETS	0.22	0.189	0.254	0.22	0.189	0.254	SUBCLONAL	1	TRUE	1	0.59082421462931	2		488	939	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	248	535	3	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	0.954	1	CLONAL	1	TRUE	1	0.59082421462931	2		538	823	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931452	131931453	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	94	422	0	ENST00000265335.6:c.2164_2165del	p.Lys722GlyfsTer5	p.K722Gfs*5	ENST00000265335		719	ctAAaa/ctaa	13/25	1	2	FACETS	0.519	0.462	0.579	0.519	0.462	0.579	SUBCLONAL	1	TRUE	1	0.59082421462931	2		422	613	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523340	176523341	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	115	607	0	ENST00000292408.4:c.2003_2004del	p.His668ProfsTer3	p.H668Pfs*3	ENST00000292408	NM_213647.1	666	tAC/t	15/18	1	2	FACETS	0.389	0.349	0.43	0.389	0.349	0.43	SUBCLONAL	1	TRUE	1	0.59082421462931	2		607	1002	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	166	403	2	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.802	0.738	0.867	0.802	0.738	0.867	CLONAL	1	TRUE	1	0.59082421462931	2		405	701	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045918	180045920	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CTC	CTC	-	rs746341092	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	116	332	0	ENST00000261937.6:c.2851_2853del	p.Glu951del	p.E951del	ENST00000261937	NM_182925.4	951	GAG/-	21/30	1	2	FACETS	0.726	0.657	0.798	0.726	0.657	0.798	SUBCLONAL	1	TRUE	1	0.59082421462931	2		332	541	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180050994	180050994	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	164	645	0	ENST00000261937.6:c.1489G>A	p.Ala497Thr	p.A497T	ENST00000261937	NM_182925.4	497	Gcc/Acc	11/30	1	2	FACETS	0.603	0.553	0.655	0.603	0.553	0.655	SUBCLONAL	1	TRUE	1	0.59082421462931	2		645	921	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397126	397126	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1236233284	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	81	378	0	ENST00000380956.4:c.511A>G	p.Met171Val	p.M171V	ENST00000380956	NM_001195286.1	171	Atg/Gtg	5/9	1	2	FACETS	0.428	0.377	0.483	0.428	0.377	0.483	SUBCLONAL	1	TRUE	1	0.59082421462931	2		378	640	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056425	26056427	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	rs774779034	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	108	346	0	ENST00000343677.2:c.230_232del	p.Asn77del	p.N77del	ENST00000343677	NM_005319.3	77	aACAgc/agc	1/1	1	2	FACETS	0.762	0.687	0.84	0.762	0.687	0.84	SUBCLONAL	1	TRUE	1	0.59082421462931	2		346	480	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681462	30681463	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1185288475	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	155	532	0	ENST00000376406.3:c.549dup	p.Ser184IlefsTer14	p.S184Ifs*14	ENST00000376406	NM_014641.2	183	-/A	4/15	1	2	FACETS	0.714	0.655	0.776	0.714	0.655	0.776	SUBCLONAL	1	TRUE	1	0.59082421462931	2		532	735	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324221	31324221	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	228	520	0	ENST00000412585.2:c.344-2A>G		p.X115_splice	ENST00000412585	NM_005514.6	115			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.59082421462931	2		520	689	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805571	32805571	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779856379	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	352	679	1	ENST00000374899.4:c.440C>T	p.Pro147Leu	p.P147L	ENST00000374899	NM_018833.2	147	cCg/cTg	2/12	1	2	FACETS	0.995	0.942	1	0.995	0.942	1	CLONAL	1	TRUE	1	0.59082421462931	2		680	1198	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149982867	149982867	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	120	370	0	ENST00000253339.5:c.3391T>C	p.Ter1131GlnextTer5	p.*1131Qext*5	ENST00000253339		1131	Taa/Caa	7/7	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.59082421462931	2		370	397	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367244	50367244	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	165	354	0	ENST00000331340.3:c.56del	p.Pro19LeufsTer2	p.P19Lfs*2	ENST00000331340	NM_006060.4	17	agC/ag	3/8	1	2	FACETS	0.98	0.905	1	0.98	0.905	1	CLONAL	1	TRUE	1	0.59082421462931	2		354	570	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249073	55249073	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	51	579	1	ENST00000275493.2:c.2371C>T	p.Gln791Ter	p.Q791*	ENST00000275493	NM_005228.3	791	Cag/Tag	20/28	1	2	FACETS	0.235	0.199	0.275	0.235	0.199	0.275	SUBCLONAL	1	TRUE	1	0.59082421462931	2		580	735	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268059	55268059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	293	630	1	ENST00000275493.2:c.2899G>A	p.Glu967Lys	p.E967K	ENST00000275493	NM_005228.3	967	Gaa/Aaa	24/28	1	2	FACETS	0.965	0.909	1	0.965	0.909	1	CLONAL	1	TRUE	1	0.59082421462931	2		631	1028	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845086	128845086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761395599	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	317	665	0	ENST00000249373.3:c.580G>A	p.Glu194Lys	p.E194K	ENST00000249373	NM_005631.4	194	Gaa/Aaa	3/12	1	2	FACETS	0.905	0.854	0.957	0.905	0.854	0.957	CLONAL	1	TRUE	1	0.59082421462931	2		665	1186	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851352	151851352	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	183	465	0	ENST00000262189.6:c.12139del	p.Ser4047ValfsTer36	p.S4047Vfs*36	ENST00000262189	NM_170606.2	4047	Agt/gt	47/59	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.59082421462931	2		465	614	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879375	151879377	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	196	524	0	ENST00000262189.6:c.5568_5570del	p.Pro1857del	p.P1857del	ENST00000262189	NM_170606.2	1856	ccTCCa/cca	36/59	1	2	FACETS	0.845	0.784	0.908	0.845	0.784	0.908	CLONAL	1	TRUE	1	0.59082421462931	2		524	785	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38147995	38147995	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	216	524	1	ENST00000317025.8:c.3116del	p.Lys1039ArgfsTer13	p.K1039Rfs*13	ENST00000317025	NM_023034.1	1039	aAg/ag	17/24	1	2	FACETS	0.879	0.819	0.941	0.879	0.819	0.941	CLONAL	1	TRUE	1	0.59082421462931	2		525	832	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285440	38285440	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	60	564	0	ENST00000425967.3:c.713A>G	p.Lys238Arg	p.K238R	ENST00000425967	NM_001174067.1	238	aAg/aGg	6/19	1	2	FACETS	0.206	0.177	0.239	0.206	0.177	0.239	SUBCLONAL	1	TRUE	1	0.59082421462931	2		564	984	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372313	55372313	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	53	475	0	ENST00000297316.4:c.1007del	p.Pro336LeufsTer51	p.P336Lfs*51	ENST00000297316	NM_022454.3	335	Ccc/cc	2/2	1	2	FACETS	0.251	0.213	0.292	0.251	0.213	0.292	SUBCLONAL	1	TRUE	1	0.59082421462931	2		475	715	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751254	128751254	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	45	345	0	ENST00000377970.2:c.791G>A	p.Ser264Asn	p.S264N	ENST00000377970	NM_002467.4	264	aGc/aAc	2/3	1	2	FACETS	0.233	0.195	0.275	0.233	0.195	0.275	SUBCLONAL	1	TRUE	1	0.59082421462931	2		345	655	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561511	141561511	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	103	481	2	ENST00000220592.5:c.1294C>T	p.Gln432Ter	p.Q432*	ENST00000220592	NM_012154.3	432	Cag/Tag	11/19	1	2	FACETS	0.486	0.435	0.54	0.486	0.435	0.54	SUBCLONAL	1	TRUE	1	0.59082421462931	2		483	718	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141570600	141570600	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	185	433	0	ENST00000220592.5:c.528del	p.Val177TrpfsTer37	p.V177Wfs*37	ENST00000220592	NM_012154.3	176	ccC/cc	5/19	1	2	FACETS	0.85	0.787	0.915	0.85	0.787	0.915	CLONAL	1	TRUE	1	0.59082421462931	2		433	737	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5456142	5456142	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	62	302	0	ENST00000381577.3:c.29T>C	p.Met10Thr	p.M10T	ENST00000381577	NM_014143.3	10	aTg/aCg	2/7	1	2	FACETS	0.521	0.451	0.596	0.521	0.451	0.596	SUBCLONAL	1	TRUE	1	0.59082421462931	2		302	403	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389407	8389407	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	44	337	0	ENST00000356435.5:c.4211G>T	p.Gly1404Val	p.G1404V	ENST00000356435		1404	gGg/gTg	26/35	1	2	FACETS	0.366	0.307	0.431	0.366	0.307	0.431	SUBCLONAL	1	TRUE	1	0.59082421462931	2		337	407	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27213538	27213538	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	201	602	0	ENST00000380036.4:c.2938del	p.Ile980Ter	p.I980*	ENST00000380036	NM_000459.3	978	gcA/gc	18/23	1	2	FACETS	0.836	0.776	0.898	0.836	0.776	0.898	CLONAL	1	TRUE	1	0.59082421462931	2		602	814	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391799	139391799	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1455334351	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	227	582	3	ENST00000277541.6:c.6392del	p.Gly2131AlafsTer117	p.G2131Afs*117	ENST00000277541	NM_017617.3	2131	gGc/gc	34/34	1	2	FACETS	0.93	0.869	0.994	0.93	0.869	0.994	CLONAL	1	TRUE	1	0.59082421462931	2		585	826	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399488	139399488	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748862853	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	303	585	0	ENST00000277541.6:c.4655C>T	p.Ala1552Val	p.A1552V	ENST00000277541	NM_017617.3	1552	gCg/gTg	26/34	1	2	FACETS	0.944	0.89	1	0.944	0.89	1	CLONAL	1	TRUE	1	0.59082421462931	2		585	1086	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399937	139399937	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1414066424	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	361	670	0	ENST00000277541.6:c.4411G>A	p.Ala1471Thr	p.A1471T	ENST00000277541	NM_017617.3	1471	Gcg/Acg	25/34	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.59082421462931	2		670	1200	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417607	139417607	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1372084604	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	261	690	0	ENST00000277541.6:c.437C>A	p.Ser146Tyr	p.S146Y	ENST00000277541	NM_017617.3	146	tCc/tAc	4/34	1	2	FACETS	0.958	0.899	1	0.958	0.899	1	CLONAL	1	TRUE	1	0.59082421462931	2		690	922	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139794066	139794066	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	128	642	1	ENST00000247668.2:c.209C>A	p.Ala70Asp	p.A70D	ENST00000247668	NM_021138.3	70	gCt/gAt	3/11	1	2	FACETS	0.375	0.339	0.413	0.375	0.339	0.413	SUBCLONAL	1	TRUE	1	0.59082421462931	2		643	1156	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814962	139814962	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	224	444	0	ENST00000247668.2:c.955A>G	p.Ser319Gly	p.S319G	ENST00000247668	NM_021138.3	319	Agc/Ggc	8/11	1	2	FACETS	0.991	0.926	1	0.991	0.926	1	CLONAL	1	TRUE	1	0.59082421462931	2		444	765	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47004894	47004894	+	intron_variant	Intron	SNP	G	G	A	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	223	430	0	ENST00000377604.3:c.-126+10G>A		p.*42*	ENST00000377604	NM_001204468.1	-/163			1	2	FACETS	0.984	0.919	1	0.984	0.919	1	CLONAL	1	TRUE	1	0.59082421462931	2		430	767	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357642	70357642	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	245	720	1	ENST00000374080.3:c.5898del	p.Ser1967AlafsTer19	p.S1967Afs*19	ENST00000374080		1965	Ccc/cc	41/45	1	2	FACETS	0.801	0.749	0.855	0.801	0.749	0.855	CLONAL	1	TRUE	1	0.59082421462931	2		721	1035	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0028914-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	257	537	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.589389323958846	4	FACETS	0.855	0.803	0.907	0.855	0.803	0.907	CLONAL	2	TRUE	2	0.644923563552739	4		540	767	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0028914-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	300	581	0	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	0.589389323958846	4	FACETS	0.853	0.806	0.901	0.853	0.806	0.901	CLONAL	2	TRUE	2	0.644923563552739	4		581	897	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718995	190718995	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028914-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	51	217	0	ENST00000441310.2:c.997A>T	p.Met333Leu	p.M333L	ENST00000441310	NM_000534.4	333	Atg/Ttg	9/13	0.639929903024191	4	FACETS	0.913	0.781	1	0.304	0.26	0.352	CLONAL	1	TRUE	1	0.644923563552739	4		217	285	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739096	40739096	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028914-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	273	462	0	ENST00000373198.4:c.3188T>A	p.Leu1063His	p.L1063H	ENST00000373198	NM_133170.3	1063	cTc/cAc	24/32	0.630113917426201	2	FACETS	0.953	0.91	0.996	0.953	0.91	0.996	CLONAL	2	TRUE	0	0.644923563552739	2		462	444	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163405	32163405	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028914-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	188	676	0	ENST00000375023.3:c.5821G>C	p.Gly1941Arg	p.G1941R	ENST00000375023	NM_004557.3	1941	Gga/Cga	30/30	0.542188826661388	2	FACETS	0.954	0.886	1	0.477	0.443	0.512	CLONAL	1	TRUE	0	0.644923563552739	2		676	611	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099598	157099598	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028914-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	47	54	0	ENST00000346085.5:c.535C>G	p.Leu179Val	p.L179V	ENST00000346085	NM_020732.3	179	Ctg/Gtg	1/20	0.575335949632337	3	FACETS	0.964	0.844	1	0.964	0.844	1	CLONAL	2	TRUE	1	0.644923563552739	3		54	100	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0029751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	532	515	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.767554875582307	2	FACETS	0.962	0.937	0.986	0.962	0.937	0.986	CLONAL	2	TRUE	0	0.791254126477584	2		515	699	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	102	376	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.883	0.801	0.968			1	INDETERMINATE	1	TRUE	NA	0.791254126477584	2		376	292	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589587	67589588	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTA	novel	NA	P-0029751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	100	229	0	ENST00000274335.5:c.1351_1352insTAG	p.His450_Glu451insVal	p.H450_E451insV	ENST00000274335		450	-/GTA	10/15	1	2	FACETS	0.84	0.76	0.922	0.84	0.76	0.922	CLONAL	1	TRUE	1	0.791254126477584	2		229	301	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	352	598	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.718693649826197	1	FACETS	0.974	0.936	1	0.974	0.936	1	CLONAL	1	TRUE	0	0.785487979942971	1		598	559	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113191	209113191	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	209	277	0	ENST00000345146.2:c.316A>G	p.Thr106Ala	p.T106A	ENST00000345146	NM_005896.2	106	Acg/Gcg	4/10	1	2	FACETS	0.95	0.889	1	0.95	0.889	1	CLONAL	1	TRUE	1	0.785487979942971	2		277	560	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	76	376	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		376	262	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023909	27023923	+	inframe_deletion	In_Frame_Del	DEL	GCTGCGGCGGCGGCA	GCTGCGGCGGCGGCA	-	rs751352361	NA	P-0029756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	25	124	0	ENST00000324856.7:c.1029_1043del	p.Ala345_Ala349del	p.A345_A349del	ENST00000324856	NM_006015.4	339	GCTGCGGCGGCGGCA/-	1/20	1	2	FACETS	0.792	0.632	0.969	0.792	0.632	0.969	CLONAL	1	TRUE	1	0.471336682093715	2		124	134	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578191	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs530941076	NA	P-0029756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	405	598	0	ENST00000269305.4:c.658T>G	p.Tyr220Asp	p.Y220D	ENST00000269305	NM_001126112.2	220	Tat/Gat	6/11	0.471336682093715	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.471336682093715	1		598	910	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620566	52620566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746373271	NA	P-0029756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	170	419	0	ENST00000394830.3:c.3187C>T	p.Arg1063Trp	p.R1063W	ENST00000394830	NM_018313.4	1063	Cgg/Tgg	21/30	0.471336682093715	1	FACETS	0.928	0.858	1	0.928	0.858	1	CLONAL	1	TRUE	0	0.471336682093715	1		419	594	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150240	108150240	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555090114	NA	P-0029756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	67	254	0	ENST00000278616.4:c.3307G>A	p.Asp1103Asn	p.D1103N	ENST00000278616	NM_000051.3	1103	Gat/Aat	23/63	NA	2	FACETS	0.576	0.501	0.656			1	INDETERMINATE	1	TRUE	NA	0.471336682093715	2		254	494	SUCCESS
APC	324	MSKCC	GRCh37	5	112174080	112174080	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	99	274	0	ENST00000257430.4:c.2789del	p.Thr930AsnfsTer25	p.T930Nfs*25	ENST00000257430	NM_000038.5	930	aCa/aa	16/16	0.471336682093715	1	FACETS	0.947	0.854	1	0.947	0.854	1	CLONAL	1	TRUE	0	0.471336682093715	1		274	339	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0029757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	252	342	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.730575854838043	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.730575854838043	1		342	428	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591132	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	rs1057519842	NA	P-0029757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	147	240	0	ENST00000274335.5:c.1727_1729del	p.Thr576del	p.T576del	ENST00000274335		575	aaGACg/aag	12/15	0.730575854838043	1	FACETS	0.957	0.894	1	0.957	0.894	1	CLONAL	1	TRUE	0	0.730575854838043	1		240	267	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0029757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	452	516	0	ENST00000269305.4:c.376-1G>T		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.730575854838043	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.730575854838043	1		516	737	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460576	149460576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757795589	NA	P-0029757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	58	393	0	ENST00000286301.3:c.61C>T	p.Pro21Ser	p.P21S	ENST00000286301	NM_005211.3	21	Cca/Tca	3/22	NA	2	FACETS	0.27	0.232	0.312			1	INDETERMINATE	1	TRUE	NA	0.730575854838043	2		393	588	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101260	27101260	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	260	430	0	ENST00000324856.7:c.4544del	p.Gly1515AlafsTer12	p.G1515Afs*12	ENST00000324856	NM_006015.4	1514	acG/ac	18/20	0.52045915315915	1	FACETS	0.864	0.819	0.909	0.864	0.819	0.909	CLONAL	1	TRUE	0	0.730575854838043	1		430	523	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481622	56481622	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	236	390	0	ENST00000267101.3:c.657T>G	p.Phe219Leu	p.F219L	ENST00000267101	NM_001982.3	219	ttT/ttG	6/28	0.206747514802804	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.730575854838043	0		390	719	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250181	133250181	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs376095661	NA	P-0029757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	161	354	0	ENST00000320574.5:c.1339A>G	p.Met447Val	p.M447V	ENST00000320574	NM_006231.2	447	Atg/Gtg	13/49	0.206747514802804	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.730575854838043	0		354	476	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653018	29653018	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	232	259	0	ENST00000356175.3:c.4953del	p.Asp1651GlufsTer26	p.D1651Efs*26	ENST00000356175	NM_000267.3	1651	gaC/ga	36/57	0.730575854838043	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.730575854838043	1		259	388	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30293169	30293169	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1224353866	NA	P-0029757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	59	186	0	ENST00000322652.5:c.459G>T	p.Leu153Phe	p.L153F	ENST00000322652	NM_015355.2	153	ttG/ttT	5/16	0.730575854838043	1	FACETS	0.308	0.266	0.353	0.308	0.266	0.353	SUBCLONAL	1	TRUE	0	0.730575854838043	1		186	333	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962959	2962959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780894425	NA	P-0029757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	244	503	0	ENST00000396946.4:c.1949G>A	p.Arg650Gln	p.R650Q	ENST00000396946	NM_032415.4	650	cGg/cAg	16/25	1	2	FACETS	0.79	0.74	0.842	0.79	0.74	0.842	SUBCLONAL	1	TRUE	1	0.730575854838043	2		503	845	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0029758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	72	387	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.823	0.722	0.93	0.823	0.722	0.93	CLONAL	1	TRUE	1	0.43	2		387	407	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011150	12011150	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	72	273	0	ENST00000353533.5:c.557A>G	p.Asp186Gly	p.D186G	ENST00000353533	NM_003010.3	186	gAt/gGt	5/11	0.3	1	FACETS	0.854	0.752	0.961	0.854	0.752	0.961	CLONAL	1	TRUE	0	0.43	1		273	308	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578439	7578439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	359	494	0	ENST00000269305.4:c.491del	p.Lys164SerfsTer6	p.K164Sfs*6	ENST00000269305	NM_001126112.2	164	aAg/ag	5/11	0.524467603548014	3	FACETS	0.851	0.814	0.887	0.851	0.814	0.887	CLONAL	3	TRUE	0	0.524467603548014	3		494	677	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940753	49940753	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	62	391	0	ENST00000296474.3:c.290G>T	p.Gly97Val	p.G97V	ENST00000296474	NM_002447.2	97	gGa/gTa	1/20	0.270671696300656	4	FACETS	0.941	0.817	1	0.471	0.408	0.538	INDETERMINATE	1	TRUE	2	0.524467603548014	4		391	383	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527740	157527740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	301	369	2	ENST00000346085.5:c.5465G>A	p.Gly1822Asp	p.G1822D	ENST00000346085	NM_020732.3	1822	gGc/gAc	20/20	0.524467603548014	4	FACETS	0.967	0.92	1	0.967	0.92	1	CLONAL	3	TRUE	1	0.524467603548014	4		371	603	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0029760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	363	389	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.487094900612284	5	FACETS	0.976	0.929	1	0.976	0.929	1	CLONAL	3	TRUE	2	0.487094900612284	5		389	881	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0029760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	306	521	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.487094900612284	2	FACETS	0.985	0.936	1	0.985	0.936	1	CLONAL	2	TRUE	0	0.487094900612284	2		522	638	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524486	44524486	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	66	249	0	ENST00000291552.4:c.71T>C	p.Ile24Thr	p.I24T	ENST00000291552	NM_006758.2	24	aTt/aCt	2/8	0.487094900612284	3	FACETS	0.818	0.713	0.931	0.409	0.356	0.466	CLONAL	1	TRUE	1	0.487094900612284	3		249	412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0029761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	96	618	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.230689409280058	1	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	0	0.230689409280058	1		618	732	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0029762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	399	535	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.678499290776198	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.681544690732425	2		535	552	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133305	38133305	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	290	587	0	ENST00000317025.8:c.4168G>C	p.Glu1390Gln	p.E1390Q	ENST00000317025	NM_023034.1	1390	Gaa/Caa	24/24	0.482200208843686	4	FACETS	0.908	0.858	0.959			1	CLONAL	2	TRUE	NA	0.681544690732425	4		587	788	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100129	27100129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	749	631	0	ENST00000324856.7:c.3925C>T	p.Leu1309Phe	p.L1309F	ENST00000324856	NM_006015.4	1309	Ctc/Ttc	16/20	0.345899507907533	2	FACETS	0.8	0.775	0.824	0.8	0.775	0.824	INDETERMINATE	2	TRUE	0	0.662485904912824	2		631	1414	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838343	156838344	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1397	441	750	2	ENST00000524377.1:c.621_622delinsAA	p.Gly208Arg	p.G208R	ENST00000524377	NM_002529.3	207	gtGGgg/gtAAgg	6/17	1	2	FACETS	0.724	0.689	0.761	0.724	0.689	0.761	SUBCLONAL	1	TRUE	1	0.662485904912824	2		752	1838	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333437	70333437	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	354	577	0	ENST00000373644.4:c.1342A>G	p.Lys448Glu	p.K448E	ENST00000373644	NM_030625.2	448	Aaa/Gaa	2/12	1	2	FACETS	0.891	0.844	0.939	0.891	0.844	0.939	CLONAL	1	TRUE	1	0.662485904912824	2		577	1199	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344269	118344269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	143	399	0	ENST00000534358.1:c.2395C>T	p.Pro799Ser	p.P799S	ENST00000534358	NM_005933.3	799	Cct/Tct	3/36	0.662485904912824	1	FACETS	0.503	0.46	0.547	0.503	0.46	0.547	SUBCLONAL	1	TRUE	0	0.662485904912824	1		399	574	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230543	46230543	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	91	329	0	ENST00000334344.6:c.792G>A	p.Trp264Ter	p.W264*	ENST00000334344	NM_152641.2	264	tgG/tgA	8/21	0.261765398315031	1	FACETS	0.297	0.264	0.332	0.297	0.264	0.332	INDETERMINATE	1	TRUE	0	0.662485904912824	1		329	619	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233128	46233194	+	frameshift_variant	Frame_Shift_Del	DEL	GGTTTCTATGGATATTCAGATGTTTGGCCCTGATGCACTAGCTGCGGTAAAACTCATTGAACACCCA	GGTTTCTATGGATATTCAGATGTTTGGCCCTGATGCACTAGCTGCGGTAAAACTCATTGAACACCCA	-	novel	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	111	221	0	ENST00000334344.6:c.1347_1413del	p.Ser451ProfsTer14	p.S451Pfs*14	ENST00000334344	NM_152641.2	449	ctGGTTTCTATGGATATTCAGATGTTTGGCCCTGATGCACTAGCTGCGGTAAAACTCATTGAACACCCA/ct	11/21	0.261765398315031	1	FACETS	0.614	0.557	0.673	0.614	0.557	0.673	INDETERMINATE	1	TRUE	0	0.662485904912824	1		221	365	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926270	112926270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918457	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	347	429	1	ENST00000351677.2:c.1403C>T	p.Thr468Met	p.T468M	ENST00000351677	NM_002834.3	468	aCg/aTg	12/16	0.662485904912824	1	FACETS	0.945	0.901	0.99	0.945	0.901	0.99	CLONAL	1	TRUE	0	0.662485904912824	1		430	741	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060679	38060679	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	384	784	0	ENST00000250448.2:c.1310T>G	p.Leu437Arg	p.L437R	ENST00000250448	NM_004496.3	437	cTg/cGg	2/2	0.261765398315031	1	FACETS	0.541	0.513	0.57	0.541	0.513	0.57	INDETERMINATE	1	TRUE	0	0.662485904912824	1		784	1433	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66735628	66735628	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	161	300	0	ENST00000307102.5:c.449C>T	p.Ser150Phe	p.S150F	ENST00000307102	NM_002755.3	150	tCt/tTt	4/11	0.381286327389359	1	FACETS	0.396	0.364	0.431	0.396	0.364	0.431	INDETERMINATE	1	TRUE	0	0.662485904912824	1		300	820	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396310	396310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768412292	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	239	701	0	ENST00000262320.3:c.716C>T	p.Pro239Leu	p.P239L	ENST00000262320	NM_003502.3	239	cCg/cTg	2/11	0.344793325834953	0	FACETS	0.24	0.223	0.256			1	INDETERMINATE	1	TRUE	0	0.662485904912824	0		701	1016	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857365	9857365	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	365	455	0	ENST00000330684.3:c.4036C>A	p.Gln1346Lys	p.Q1346K	ENST00000330684	NM_001134407.1	1346	Caa/Aaa	13/13	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.662485904912824	2		455	861	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349280	11349280	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	344	372	0	ENST00000332029.2:c.56C>T	p.Pro19Leu	p.P19L	ENST00000332029	NM_003745.1	19	cCc/cTc	2/2	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.662485904912824	2		372	824	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81973508	81973508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	262	429	1	ENST00000359376.3:c.3325C>T	p.Leu1109Phe	p.L1109F	ENST00000359376	NM_002661.3	1109	Ctc/Ttc	30/33	0.381286327389359	1	FACETS	0.799	0.754	0.845	0.799	0.754	0.845	INDETERMINATE	1	TRUE	0	0.662485904912824	1		430	662	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	511	543	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.662485904912824	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.662485904912824	1		543	1028	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971304	15971304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752564662	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	376	480	0	ENST00000268712.3:c.4645C>T	p.Pro1549Ser	p.P1549S	ENST00000268712	NM_006311.3	1549	Ccc/Tcc	32/46	0.662485904912824	1	FACETS	0.962	0.919	1	0.962	0.919	1	CLONAL	1	TRUE	0	0.662485904912824	1		480	789	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560226	29560226	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555615109	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	329	246	0	ENST00000356175.3:c.3703C>T	p.Gln1235Ter	p.Q1235*	ENST00000356175	NM_000267.3	1235	Cag/Tag	27/57	NA	2	FACETS	0.964	0.926	1			1	INDETERMINATE	2	TRUE	NA	0.662485904912824	2		246	515	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786205228	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	373	554	0	ENST00000322088.6:c.536C>T	p.Pro179Leu	p.P179L	ENST00000322088	NM_014225.5	179	cCc/cTc	5/15	0.662485904912824	1	FACETS	0.996	0.952	1	0.996	0.952	1	CLONAL	1	TRUE	0	0.662485904912824	1		554	756	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149561	61149562	+	missense_variant	Missense_Mutation	DNP	CT	CT	TC	novel	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	294	364	0	ENST00000295025.8:c.1751_1752delinsTC	p.Thr584Ile	p.T584I	ENST00000295025	NM_002908.2	584	aCT/aTC	11/11	0.435205316375334	1	FACETS	0.751	0.71	0.793	0.751	0.71	0.793	SUBCLONAL	1	TRUE	0	0.662485904912824	1		364	790	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248486	212248486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1178525913	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	271	330	0	ENST00000342788.4:c.3781G>A	p.Glu1261Lys	p.E1261K	ENST00000342788	NM_005235.2	1261	Gag/Aag	28/28	NA	2	FACETS	1	0.958	1			1	INDETERMINATE	1	TRUE	NA	0.662485904912824	2		330	802	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530082	212530082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	214	292	0	ENST00000342788.4:c.1837G>A	p.Glu613Lys	p.E613K	ENST00000342788	NM_005235.2	613	Gag/Aag	15/28	NA	2	FACETS	0.988	0.923	1			1	INDETERMINATE	1	TRUE	NA	0.662485904912824	2		292	654	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561555	9561555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	119	407	0	ENST00000353224.5:c.227C>T	p.Pro76Leu	p.P76L	ENST00000353224	NM_177990.2	76	cCc/cTc	4/10	1	2	FACETS	0.426	0.384	0.47	0.426	0.384	0.47	SUBCLONAL	1	TRUE	1	0.662485904912824	2		407	843	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727078	40727078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs896375033	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	315	427	0	ENST00000373198.4:c.3886G>A	p.Glu1296Lys	p.E1296K	ENST00000373198	NM_133170.3	1296	Gag/Aag	28/32	1	2	FACETS	0.865	0.817	0.915	0.865	0.817	0.915	CLONAL	1	TRUE	1	0.662485904912824	2		427	1099	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400190	41400190	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	274	430	0	ENST00000373198.4:c.569G>A	p.Arg190Lys	p.R190K	ENST00000373198	NM_133170.3	190	aGa/aAa	5/32	1	2	FACETS	0.882	0.829	0.936	0.882	0.829	0.936	CLONAL	1	TRUE	1	0.662485904912824	2		430	938	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42842633	42842633	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	496	635	0	ENST00000398585.3:c.1224G>A	p.Met408Ile	p.M408I	ENST00000398585	NM_001135099.1	408	atG/atA	11/14	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.662485904912824	2		635	1448	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604259	189604259	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	371	504	2	ENST00000264731.3:c.1426C>T	p.Pro476Ser	p.P476S	ENST00000264731	NM_003722.4	476	Cct/Tct	11/14	1	2	FACETS	0.961	0.912	1	0.961	0.912	1	CLONAL	1	TRUE	1	0.662485904912824	2		506	1166	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233645	233645	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	137	172	0	ENST00000264932.6:c.949A>T	p.Ile317Phe	p.I317F	ENST00000264932	NM_004168.2	317	Att/Ttt	8/15	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.662485904912824	2		172	399	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294376	1294376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	440	565	1	ENST00000310581.5:c.625G>A	p.Glu209Lys	p.E209K	ENST00000310581	NM_198253.2	209	Gag/Aag	2/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.662485904912824	2		566	1300	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	334	218	0				ENST00000310581	NM_198253.2	-/1132			1				0.93	1				CLONAL	1	TRUE	1	0.662485904912824	2		218	1027	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168680	56168680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1450545724	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	280	385	0	ENST00000399503.3:c.1534C>T	p.Pro512Ser	p.P512S	ENST00000399503	NM_005921.1	512	Cct/Tct	9/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.662485904912824	2		385	808	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662625	117662625	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	172	385	0	ENST00000368508.3:c.4840C>T	p.Pro1614Ser	p.P1614S	ENST00000368508	NM_002944.2	1614	Cca/Tca	29/43	0.662485904912824	1	FACETS	0.692	0.642	0.743	0.692	0.642	0.743	SUBCLONAL	1	TRUE	0	0.662485904912824	1		385	502	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968280	2968280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	203	700	1	ENST00000396946.4:c.1706G>A	p.Gly569Glu	p.G569E	ENST00000396946	NM_032415.4	569	gGa/gAa	13/25	0.542532947717108	1	FACETS	0.303	0.28	0.327	0.303	0.28	0.327	SUBCLONAL	1	TRUE	0	0.662485904912824	1		701	1354	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346631	81346631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	184	315	0	ENST00000222390.5:c.1322G>A	p.Arg441Gln	p.R441Q	ENST00000222390	NM_000601.4	441	cGa/cAa	11/18	1	2	FACETS	0.825	0.765	0.888	0.825	0.765	0.888	CLONAL	1	TRUE	1	0.662485904912824	2		315	673	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381505	81381505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745308839	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	202	334	0	ENST00000222390.5:c.556G>A	p.Gly186Arg	p.G186R	ENST00000222390	NM_000601.4	186	Gga/Aga	5/18	1	2	FACETS	0.855	0.796	0.917	0.855	0.796	0.917	CLONAL	1	TRUE	1	0.662485904912824	2		334	713	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401389	139401389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754998450	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	459	649	1	ENST00000277541.6:c.3680C>T	p.Pro1227Leu	p.P1227L	ENST00000277541	NM_017617.3	1227	cCc/cTc	23/34	0.662485904912824	1	FACETS	0.873	0.836	0.909	0.873	0.836	0.909	CLONAL	1	TRUE	0	0.662485904912824	1		650	1062	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932639	39932639	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1277864433	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	617	442	1	ENST00000378444.4:c.1960C>T	p.Pro654Ser	p.P654S	ENST00000378444	NM_001123385.1	654	Ccc/Tcc	4/15	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.662485904912824	1		443	933	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939801	76939801	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	397	248	0	ENST00000373344.5:c.947C>T	p.Ser316Phe	p.S316F	ENST00000373344	NM_000489.3	316	tCt/tTt	9/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.662485904912824	1		248	579	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0029766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	141	597	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		597	872	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0029767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	94	436	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.812	0.724	0.905	0.812	0.724	0.905	CLONAL	1	TRUE	1	0.414051529883566	2		437	559	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0029767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	146	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.285797121258706	1	FACETS	0.845	0.773	0.919	0.845	0.773	0.919	CLONAL	1	TRUE	0	0.414051529883566	1		511	662	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0029767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	90	318	1	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.414051529883566	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.414051529883566	1		319	321	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727143	40727143	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	62	554	1	ENST00000373198.4:c.3821A>T	p.Asn1274Ile	p.N1274I	ENST00000373198	NM_133170.3	1274	aAc/aTc	28/32	0.379173864679641	1	FACETS	0.391	0.338	0.449	0.391	0.338	0.449	SUBCLONAL	1	TRUE	0	0.414051529883566	1		555	607	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	124	376	0				ENST00000310581	NM_198253.2	-/1132			0.140140039243722	6	FACETS	1	0.979	1	0.83	0.757	0.905	INDETERMINATE	2	TRUE	3	0.459534437250012	6		376	416	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692823	89692829	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTTTT	CCCTTTT	-	novel	NA	P-0029769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	67	215	0	ENST00000371953.3:c.307_313del	p.Pro103ValfsTer8	p.P103Vfs*8	ENST00000371953	NM_000314.4	103	CCCTTTTgt/gt	5/9	0.459534437250012	2	FACETS	0.9	0.802	1	0.9	0.802	1	CLONAL	2	TRUE	0	0.459534437250012	2		215	162	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0029771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	32	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.104	0.084	0.127	0.104	0.084	0.127	SUBCLONAL	1	TRUE	1	0.640650101296176	2		511	961	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	303	525	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.269266580340568	1	FACETS	0.669	0.631	0.707	0.669	0.631	0.707	INDETERMINATE	1	TRUE	0	0.640650101296176	1		525	961	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115916	8115917	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0029771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	183	383	0	ENST00000346208.3:c.1263dup	p.Met422AspfsTer85	p.M422Dfs*85	ENST00000346208		421	ccg/ccGg	6/6	1	2	FACETS	0.767	0.709	0.826	0.767	0.709	0.826	SUBCLONAL	1	TRUE	1	0.640650101296176	2		383	745	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	135	376	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.71	2		376	378	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0029772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	114	454	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.918	0.835	1	0.918	0.835	1	CLONAL	1	TRUE	1	0.71	2		454	350	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0029772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	124	411	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.878	0.801	0.956	0.878	0.801	0.956	CLONAL	1	TRUE	1	0.71	2		411	398	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014128	14014128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	223	502	0	ENST00000311895.7:c.106G>A	p.Ala36Thr	p.A36T	ENST00000311895	NM_005236.2	36	Gcc/Acc	1/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.71	2		502	559	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518155	187518155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747017523	NA	P-0029774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	61	359	0	ENST00000441802.2:c.12539C>T	p.Ala4180Val	p.A4180V	ENST00000441802	NM_005245.3	4180	gCg/gTg	25/27	1	2	FACETS	0.433	0.373	0.498	0.433	0.373	0.498	SUBCLONAL	1	TRUE	1	0.451317747782732	2		359	625	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0029775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	235	489	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.448902134736759	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.448902134736759	1		489	652	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70441169	70441169	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	63	329	0	ENST00000373644.4:c.4838A>G	p.Glu1613Gly	p.E1613G	ENST00000373644	NM_030625.2	1613	gAa/gGa	9/12	0.353071656969581	1	FACETS	0.424	0.367	0.485	0.424	0.367	0.485	SUBCLONAL	1	TRUE	0	0.448902134736759	1		329	514	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871772	35871772	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	38	403	0	ENST00000216797.5:c.734G>A	p.Arg245Lys	p.R245K	ENST00000216797	NM_020529.2	245	aGa/aAa	5/6	0.448902134736759	1	FACETS	0.24	0.197	0.287	0.24	0.197	0.287	SUBCLONAL	1	TRUE	0	0.448902134736759	1		403	548	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526299	189526304	+	inframe_deletion	In_Frame_Del	DEL	AGTCGG	AGTCGG	-	novel	NA	P-0029775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	327	332	0	ENST00000264731.3:c.563_568del	p.Lys188_Ala190delinsThr	p.K188_A190delinsT	ENST00000264731	NM_003722.4	188	aAGTCGGcc/acc	4/14	0.448902134736759	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.448902134736759	3		332	717	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681880	30681880	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0029775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	84	359	0	ENST00000376406.3:c.217A>T	p.Lys73Ter	p.K73*	ENST00000376406	NM_014641.2	73	Aaa/Taa	3/15	1	2	FACETS	0.608	0.537	0.683	0.608	0.537	0.683	SUBCLONAL	1	TRUE	1	0.448902134736759	2		359	616	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974705	21974706	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0029775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	104	309	0	ENST00000304494.5:c.121_122insTT	p.Pro41LeufsTer13	p.P41Lfs*13	ENST00000304494	NM_000077.4	41	ccg/cTTcg	1/3	0.448902134736759	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.448902134736759	1		309	318	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111496	8111512	+	frameshift_variant	Frame_Shift_Del	DEL	TGGAGGAGGAATGCCAA	TGGAGGAGGAATGCCAA	-	novel	NA	P-0029777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	123	464	0	ENST00000346208.3:c.985_1001del	p.Arg329GlyfsTer17	p.R329Gfs*17	ENST00000346208		328	TGGAGGAGGAATGCCAAt/t	5/6	1	2	FACETS	0.863	0.782	0.948	0.863	0.782	0.948	CLONAL	1	TRUE	1	0.427391062268122	2		464	667	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246445	105246445	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	45	465	0	ENST00000349310.3:c.155T>G	p.Leu52Arg	p.L52R	ENST00000349310	NM_001014432.1	52	cTc/cGc	4/15	1	2	FACETS	0.3	0.252	0.355	0.3	0.252	0.355	SUBCLONAL	1	TRUE	1	0.427391062268122	2		465	701	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	14	436	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.14	0.1	0.188	0.14	0.1	0.188	SUBCLONAL	1	TRUE	1	0.38	2		437	528	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	151	474	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	0.38	2		474	548	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	151	242	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.38	2		242	671	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	59	266	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	0.38	2		266	294	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	45	473	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	1	2	FACETS	0.355	0.297	0.418	0.355	0.297	0.418	SUBCLONAL	1	TRUE	1	0.38	2		473	668	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	117	167	0	ENST00000263967.3:c.3012G>A	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atA	21/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.38	2		167	486	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	63	158	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	0.2337365092789	3	FACETS	1	0.903	1	0.523	0.455	0.597	CLONAL	1	TRUE	1	0.38	3		158	377	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	53	835	0	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	0.107873989425955	3	FACETS	0.424	0.36	0.494	0.212	0.18	0.247	INDETERMINATE	1	TRUE	1	0.38	3		835	783	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446269	187446270	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770320988	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	55	565	0	ENST00000232014.4:c.1418dup	p.Lys474GlufsTer26	p.K474Efs*26	ENST00000232014	NM_001130845.1	473	ccg/ccCg	6/10	1	2	FACETS	0.417	0.355	0.483	0.417	0.355	0.483	SUBCLONAL	1	TRUE	1	0.38	2		565	695	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203691	94203691	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	27	107	0	ENST00000323929.3:c.963del	p.Phe321LeufsTer8	p.F321Lfs*8	ENST00000323929	NM_005591.3	321	ttT/tt	9/20	1	2	FACETS	0.429	0.342	0.529	0.429	0.342	0.529	SUBCLONAL	1	TRUE	1	0.38	2		107	331	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346157	89346158	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs878855327	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	20	215	1	ENST00000301030.4:c.6792dup	p.Ala2265ArgfsTer8	p.A2265Rfs*8	ENST00000301030	NM_001256183.1	2264	-/C	9/13	1	2	FACETS	0.504	0.386	0.64	0.504	0.386	0.64	SUBCLONAL	1	TRUE	1	0.38	2		216	209	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338671	70338671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	210	523	0	ENST00000374080.3:c.67G>T	p.Asp23Tyr	p.D23Y	ENST00000374080		23	Gat/Tat	1/45	1	2	FACETS	0.766	0.714	0.82	1	0.992	1	SUBCLONAL	2	TRUE	1	0.38	2		523	721	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107257	193107257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	44	207	0	ENST00000367435.3:c.466C>T	p.Arg156Cys	p.R156C	ENST00000367435	NM_024529.4	156	Cgt/Tgt	6/17	1	2	FACETS	0.652	0.549	0.766	0.652	0.549	0.766	SUBCLONAL	1	TRUE	1	0.38	2		207	355	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752695	42752695	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1366176199	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	33	657	6	ENST00000222329.4:c.1569del	p.Leu525SerfsTer6	p.L525Sfs*6	ENST00000222329	NM_006494.2	523	ggG/gg	4/4	1	2	FACETS	0.292	0.237	0.354	0.292	0.237	0.354	SUBCLONAL	1	TRUE	1	0.38	2		663	595	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614463	38614463	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	38	117	0	ENST00000299084.4:c.234del	p.Asp79ThrfsTer42	p.D79Tfs*42	ENST00000299084	NM_152594.2	77	Aaa/aa	3/7	1	2	FACETS	0.536	0.444	0.639	0.536	0.444	0.639	SUBCLONAL	1	TRUE	1	0.38	2		117	373	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692900	89692900	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	19	180	0	ENST00000371953.3:c.384G>T	p.Lys128Asn	p.K128N	ENST00000371953	NM_000314.4	128	aaG/aaT	5/9	1	2	FACETS	0.22	0.166	0.284	0.22	0.166	0.284	SUBCLONAL	1	TRUE	1	0.38	2		180	454	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554345	141554345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748399150	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	163	757	8	ENST00000220592.5:c.1806del	p.Ala603ProfsTer92	p.A603Pfs*92	ENST00000220592	NM_012154.3	602	ccC/cc	14/19	1	2	FACETS	0.953	0.875	1	0.953	0.875	1	CLONAL	1	TRUE	1	0.38	2		765	900	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799248	42799248	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	107	585	0	ENST00000575354.2:c.4736del	p.Pro1579GlnfsTer41	p.P1579Qfs*41	ENST00000575354	NM_015125.3	1578	Ccc/cc	20/20	1	2	FACETS	0.986	0.887	1	0.986	0.887	1	CLONAL	1	TRUE	1	0.38	2		585	571	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020771	112020771	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374907658	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	33	362	1	ENST00000368678.4:c.800C>T	p.Ser267Leu	p.S267L	ENST00000368678		267	tCg/tTg	8/13	1	2	FACETS	0.29	0.236	0.352	0.29	0.236	0.352	SUBCLONAL	1	TRUE	1	0.38	2		363	598	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948755	71948755	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1565399032	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	50	659	0	ENST00000298229.2:c.3470del	p.Gly1157AspfsTer45	p.G1157Dfs*45	ENST00000298229	NM_001567.3	1156	cGg/cg	26/28	1	2	FACETS	0.363	0.307	0.425	0.363	0.307	0.425	SUBCLONAL	1	TRUE	1	0.38	2		659	724	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023338	27023338	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	54	118	0	ENST00000324856.7:c.444C>G	p.Tyr148Ter	p.Y148*	ENST00000324856	NM_006015.4	148	taC/taG	1/20	1	2	FACETS	0.98	0.858	1	1	0.979	1	CLONAL	2	TRUE	1	0.38	2		118	145	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699404	117699404	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	59	485	0	ENST00000369458.3:c.237G>T	p.Leu79Phe	p.L79F	ENST00000369458	NM_024626.3	79	ttG/ttT	3/6	1	2	FACETS	0.427	0.367	0.493	0.427	0.367	0.493	SUBCLONAL	1	TRUE	1	0.38	2		485	727	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111146	193111147	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	97	207	1	ENST00000367435.3:c.687_688del	p.Arg229SerfsTer37	p.R229Sfs*37	ENST00000367435	NM_024529.4	227	AGa/a	7/17	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.38	2		208	416	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852552	63852553	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	26	393	0	ENST00000279873.7:c.3332_3333del	p.Val1111AlafsTer49	p.V1111Afs*49	ENST00000279873	NM_032199.2	1110	acTGtg/actg	10/10	1	2	FACETS	0.274	0.216	0.341	0.274	0.216	0.341	SUBCLONAL	1	TRUE	1	0.38	2		393	499	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405477	70405477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	141	245	0	ENST00000373644.4:c.2994del	p.Val999SerfsTer27	p.V999Sfs*27	ENST00000373644	NM_030625.2	997	tcA/tc	4/12	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.38	2		245	696	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720693	89720693	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554825519	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	35	28	0	ENST00000371953.3:c.844G>T	p.Gly282Ter	p.G282*	ENST00000371953	NM_000314.4	282	Gga/Tga	8/9	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.38	2		28	177	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29068966	29068966	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	16	227	0	ENST00000282397.4:c.15G>T	p.Trp5Cys	p.W5C	ENST00000282397	NM_002019.4	5	tgG/tgT	1/30	1	2	FACETS	0.275	0.203	0.362	0.275	0.203	0.362	SUBCLONAL	1	TRUE	1	0.38	2		227	306	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346981	89346981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	123	413	0	ENST00000301030.4:c.5969C>T	p.Ser1990Phe	p.S1990F	ENST00000301030	NM_001256183.1	1990	tCc/tTc	9/13	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.38	2		413	435	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295219	15295219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751712914	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	46	836	0	ENST00000263388.2:c.2453C>T	p.Ala818Val	p.A818V	ENST00000263388	NM_000435.2	818	gCa/gTa	16/33	1	2	FACETS	0.279	0.234	0.329	0.279	0.234	0.329	SUBCLONAL	1	TRUE	1	0.38	2		836	868	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375215	15375215	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	46	352	0	ENST00000263377.2:c.1212G>T	p.Lys404Asn	p.K404N	ENST00000263377	NM_058243.2	404	aaG/aaT	6/20	1	2	FACETS	0.527	0.444	0.619	0.527	0.444	0.619	SUBCLONAL	1	TRUE	1	0.38	2		352	459	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639649	47639649	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63749832	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	47	245	0	ENST00000233146.2:c.746del	p.Lys249ArgfsTer5	p.K249Rfs*5	ENST00000233146	NM_000251.2	248	Aaa/aa	4/16	1	2	FACETS	0.426	0.359	0.5	0.426	0.359	0.5	SUBCLONAL	1	TRUE	1	0.38	2		245	581	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437222	220437223	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1286117855	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	53	686	0	ENST00000243786.2:c.132dup	p.Ala45ArgfsTer29	p.A45Rfs*29	ENST00000243786	NM_002191.3	42	-/C	1/2	0.107873989425955	3	FACETS	0.36	0.306	0.42	0.18	0.153	0.21	INDETERMINATE	1	TRUE	1	0.38	3		686	922	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32189036	32189036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	40	599	1	ENST00000375023.3:c.518C>T	p.Ala173Val	p.A173V	ENST00000375023	NM_004557.3	173	gCc/gTc	4/30	1	2	FACETS	0.31	0.257	0.37	0.31	0.257	0.37	SUBCLONAL	1	TRUE	1	0.38	2		600	679	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090759	5090759	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	21	85	0	ENST00000381652.3:c.2911del	p.Arg971GlyfsTer27	p.R971Gfs*27	ENST00000381652	NM_004972.3	969	acA/ac	22/25	1	2	FACETS	0.385	0.297	0.488	0.385	0.297	0.488	SUBCLONAL	1	TRUE	1	0.38	2		85	287	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912223	97912223	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs751410815	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	138	490	0	ENST00000289081.3:c.668T>C	p.Val223Ala	p.V223A	ENST00000289081	NM_000136.2	223	gTa/gCa	7/15	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.38	2		490	682	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867518	101867518	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	11	32	0	ENST00000374994.4:c.31C>G	p.Arg11Gly	p.R11G	ENST00000374994	NM_004612.2	11	Cgg/Ggg	1/9	1	2	FACETS	0.998	0.706	1	0.998	0.706	1	CLONAL	1	TRUE	1	0.38	2		32	58	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156731	20156731	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	116	167	0	ENST00000379607.5:c.26G>T	p.Gly9Val	p.G9V	ENST00000379607	NM_001412.3	9	gGt/gTt	2/7	0.795406655087937	1	FACETS	0.993	0.927	1	0.993	0.927	1	CLONAL	1	TRUE	0	0.795406655087937	1		167	177	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426812	121426812	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377110124	NA	P-0029779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	305	469	0	ENST00000257555.6:c.503G>A	p.Arg168His	p.R168H	ENST00000257555		168	cGc/cAc	2/10	1	2	FACETS	0.966	0.915	1	0.966	0.915	1	CLONAL	1	TRUE	1	0.795406655087937	2		469	794	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0029780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	131	436	1	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		437	624	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0029780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	48	609	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		610	611	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0029780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	63	491	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.169583846363409	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		491	400	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969369	44969369	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1318649487	NA	P-0029781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	67	179	0	ENST00000377967.4:c.4051C>T	p.Arg1351Ter	p.R1351*	ENST00000377967	NM_021140.2	1351	Cga/Tga	28/29	0.687142047168119	2	FACETS	1	0.914	1			1	CLONAL	1	TRUE	NA	0.687142047168119	2		179	188	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325170	39325170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	350	401	0	ENST00000373001.3:c.149G>A	p.Gly50Asp	p.G50D	ENST00000373001	NM_022157.3	50	gGt/gAt	1/7	0.687142047168119	2	FACETS	0.891	0.845	0.939	0.446	0.422	0.47	CLONAL	1	TRUE	0	0.687142047168119	2		401	1143	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577441	64577441	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	847	467	1	ENST00000312049.6:c.141del	p.Leu48TrpfsTer71	p.L48Wfs*71	ENST00000312049	NM_130799.2	47	ttT/tt	2/10	0.686949068256553	2	FACETS	0.975	0.952	0.998	0.975	0.952	0.998	CLONAL	2	TRUE	0	0.687142047168119	2		468	1264	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434527	110434527	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1408	313	342	0	ENST00000375856.3:c.3874G>A	p.Gly1292Ser	p.G1292S	ENST00000375856	NM_003749.2	1292	Ggt/Agt	1/2	0.472104479721853	4	FACETS	0.893	0.84	0.948	0.447	0.42	0.474	CLONAL	1	TRUE	2	0.687142047168119	4		342	1721	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80646131	80646131	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	50	48	0	ENST00000286548.4:c.21G>T	p.Met7Ile	p.M7I	ENST00000286548	NM_002072.3	7	atG/atT	1/7	0.687142047168119	3	FACETS	0.978	0.841	1	0.489	0.42	0.562	CLONAL	1	TRUE	1	0.687142047168119	3		48	200	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0029784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	23	318	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.668	0.52	0.84	0.668	0.52	0.84	SUBCLONAL	1	TRUE	1	0.17	2		318	405	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	78	552	0	ENST00000418115.1:c.50G>T	p.Gly17Val	p.G17V	ENST00000418115	NM_001664.2	17	gGa/gTa	2/5	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.17	2		552	808	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032573	12032594	+	frameshift_variant	Frame_Shift_Del	DEL	TCCCCGAGTTTCATCAACTTTG	TCCCCGAGTTTCATCAACTTTG	-	novel	NA	P-0029784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	55	386	0	ENST00000353533.5:c.1011_1032del	p.Pro338ThrfsTer18	p.P338Tfs*18	ENST00000353533	NM_003010.3	337	TCCCCGAGTTTCATCAACTTTGtc/tc	9/11	0.197503929296616	2	FACETS	1	0.953	1	0.644	0.552	0.746	CLONAL	1	TRUE	0	0.17	2		386	502	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089879	16089921	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGTGAAATTCTGAAAGCAAGGAAGGTCGCCTTCGAAGCTGT	TGGGTGAAATTCTGAAAGCAAGGAAGGTCGCCTTCGAAGCTGT	-	novel	NA	P-0029784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	56	275	0	ENST00000268712.3:c.189_231del	p.Gln64ValfsTer52	p.Q64Vfs*52	ENST00000268712	NM_006311.3	63	caACAGCTTCGAAGGCGACCTTCCTTGCTTTCAGAATTTCACCCA/ca	3/46	0.170821814597467	3	FACETS	0.88	0.757	1	0.88	0.757	1	CLONAL	2	TRUE	1	0.17	3		275	406	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240039	53240039	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	55	543	0	ENST00000375401.3:c.1402G>T	p.Glu468Ter	p.E468*	ENST00000375401	NM_004187.3	468	Gag/Tag	11/26	0.383323106386096	1	FACETS	0.389	0.332	0.451	0.389	0.332	0.451	SUBCLONAL	1	TRUE	0	0.386228607523929	1		543	591	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798440	45798440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761101420	NA	P-0029785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	96	529	0	ENST00000450313.1:c.571C>T	p.Arg191Trp	p.R191W	ENST00000450313	NM_012222.2	191	Cgg/Tgg	7/16	1	2	FACETS	0.938	0.838	1	0.938	0.838	1	CLONAL	1	TRUE	1	0.386228607523929	2		529	530	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130612	29130612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	78	399	0	ENST00000328354.6:c.98C>T	p.Ser33Leu	p.S33L	ENST00000328354	NM_007194.3	33	tCa/tTa	2/15	1	2	FACETS	0.935	0.825	1	0.935	0.825	1	CLONAL	1	TRUE	1	0.386228607523929	2		399	432	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0029786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	194	387	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.647838413609434	5	FACETS	0.986	0.927	1	0.986	0.927	1	CLONAL	3	TRUE	2	0.736617552929357	5		387	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573988	7573988	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	575	622	0	ENST00000269305.4:c.1039G>A	p.Ala347Thr	p.A347T	ENST00000269305	NM_001126112.2	347	Gcc/Acc	10/11	0.727499393462014	2	FACETS	0.916	0.89	0.942	0.916	0.89	0.942	CLONAL	2	TRUE	0	0.736617552929357	2		622	852	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0029789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	131	535	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.361238858348009	1	FACETS	0.917	0.834	1	0.917	0.834	1	CLONAL	1	TRUE	0	0.361238858348009	1		535	648	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	74	376	0				ENST00000310581	NM_198253.2	-/1132			0.105435961360592	4	FACETS	1	0.887	1	1	0.887	1	INDETERMINATE	2	TRUE	2	0.270827315360093	4		376	345	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0029790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	34	450	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.389	0.317	0.471	0.389	0.317	0.471	SUBCLONAL	1	TRUE	1	0.270827315360093	2		451	645	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0029790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	115	691	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	0.270827315360093	2		691	597	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0029790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	61	511	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	1	2	FACETS	0.728	0.628	0.837	0.728	0.628	0.837	SUBCLONAL	1	TRUE	1	0.270827315360093	2		511	619	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468297	50468297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343071492	NA	P-0029790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	30	385	0	ENST00000331340.3:c.1532G>A	p.Arg511Gln	p.R511Q	ENST00000331340	NM_006060.4	511	cGa/cAa	8/8	1	2	FACETS	0.47	0.378	0.575	0.47	0.378	0.575	SUBCLONAL	1	TRUE	1	0.270827315360093	2		385	471	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214899	36214899	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	73	494	0	ENST00000222270.7:c.3325C>T	p.Arg1109Ter	p.R1109*	ENST00000222270	NM_014727.1	1109	Cga/Tga	8/37	1	2	FACETS	0.856	0.748	0.971	0.856	0.748	0.971	CLONAL	1	TRUE	1	0.270827315360093	2		494	630	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211622	36211643	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCTGTGGTCCCAGCTACGTG	CTCCTGTGGTCCCAGCTACGTG	-	novel	NA	P-0029790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	19	440	0	ENST00000222270.7:c.1377_1398del	p.Val460GlyfsTer8	p.V460Gfs*8	ENST00000222270	NM_014727.1	458	cCTCCTGTGGTCCCAGCTACGTGc/cc	3/37	1	2	FACETS	0.406	0.307	0.521	0.406	0.307	0.521	SUBCLONAL	1	TRUE	1	0.270827315360093	2		440	346	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	99	376	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.897	0.814	0.983	0.897	0.814	0.983	CLONAL	1	TRUE	1	0.823404295929568	2		376	268	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0029791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	166	535	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.944	0.877	1	0.944	0.877	1	CLONAL	1	TRUE	1	0.823404295929568	2		535	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0029791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	252	543	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	1	2	FACETS	0.93	0.876	0.985	0.93	0.876	0.985	CLONAL	1	TRUE	1	0.823404295929568	2		543	658	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0029791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	259	551	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	0.953	0.899	1	0.953	0.899	1	CLONAL	1	TRUE	1	0.823404295929568	2		551	660	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0029791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	162	346	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	1	2	FACETS	0.935	0.867	1	0.935	0.867	1	CLONAL	1	TRUE	1	0.823404295929568	2		346	421	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685281	89685281	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1060500116	NA	P-0029791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	85	106	0	ENST00000371953.3:c.176C>G	p.Ser59Ter	p.S59*	ENST00000371953	NM_000314.4	59	tCa/tGa	3/9	1	2	FACETS	0.914	0.822	1	0.914	0.822	1	CLONAL	1	TRUE	1	0.823404295929568	2		106	226	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677876	47677876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	131	418	1	ENST00000347630.2:c.989C>T	p.Ser330Leu	p.S330L	ENST00000347630	NM_001007230.1	330	tCg/tTg	11/11	1	2	FACETS	0.862	0.792	0.935	0.862	0.792	0.935	CLONAL	1	TRUE	1	0.823404295929568	2		419	369	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253817	153253817	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	110	276	0	ENST00000281708.4:c.916C>T	p.Gln306Ter	p.Q306*	ENST00000281708	NM_033632.3	306	Cag/Tag	6/12	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.823404295929568	2		276	188	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954326	48954326	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	125	230	0	ENST00000267163.4:c.1447C>T	p.His483Tyr	p.H483Y	ENST00000267163	NM_000321.2	483	Cat/Tat	16/27	0.823649066457298	1	FACETS	0.889	0.83	0.946	0.889	0.83	0.946	CLONAL	1	TRUE	0	0.823404295929568	1		230	201	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056349	27056349	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	116	280	0	ENST00000324856.7:c.1345C>T	p.Gln449Ter	p.Q449*	ENST00000324856	NM_006015.4	449	Cag/Tag	2/20	1	2	FACETS	0.962	0.88	1	0.962	0.88	1	CLONAL	1	TRUE	1	0.823404295929568	2		280	293	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435971	49435971	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	191	561	0	ENST00000301067.7:c.6010C>T	p.Gln2004Ter	p.Q2004*	ENST00000301067	NM_003482.3	2004	Cag/Tag	28/54	1	2	FACETS	0.854	0.796	0.914	0.854	0.796	0.914	CLONAL	1	TRUE	1	0.823404295929568	2		561	543	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929171	32929171	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	133	421	0	ENST00000380152.3:c.7181G>C	p.Arg2394Thr	p.R2394T	ENST00000380152		2394	aGa/aCa	14/27	NA	2	FACETS	0.804	0.737	0.872			1	INDETERMINATE	1	TRUE	NA	0.823404295929568	2		421	402	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78914317	78914317	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	253	478	0	ENST00000306801.3:c.2941G>C	p.Glu981Gln	p.E981Q	ENST00000306801	NM_020761.2	981	Gag/Cag	25/34	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.823404295929568	2		478	591	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56376765	56376765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1489009237	NA	P-0029791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	124	344	0	ENST00000348428.3:c.805C>T	p.His269Tyr	p.H269Y	ENST00000348428	NM_006785.3	269	Cat/Tat	5/17	1	2	FACETS	0.883	0.809	0.959	0.883	0.809	0.959	CLONAL	1	TRUE	1	0.823404295929568	2		344	341	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467472	25467472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	244	498	0	ENST00000264709.3:c.1604C>T	p.Ser535Phe	p.S535F	ENST00000264709	NM_175629.2	535	tCc/tTc	14/23	1	2	FACETS	0.986	0.929	1	0.986	0.929	1	CLONAL	1	TRUE	1	0.823404295929568	2		498	601	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61724140	61724140	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	111	203	0	ENST00000401558.2:c.762C>G	p.Phe254Leu	p.F254L	ENST00000401558	NM_003400.3	254	ttC/ttG	10/25	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.823404295929568	2		203	237	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626364	12626364	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	147	427	0	ENST00000251849.4:c.1785G>C	p.Glu595Asp	p.E595D	ENST00000251849	NM_002880.3	595	gaG/gaC	16/17	1	2	FACETS	0.858	0.792	0.927	0.858	0.792	0.927	CLONAL	1	TRUE	1	0.823404295929568	2		427	416	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851865	134851865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	175	426	0	ENST00000398015.3:c.1271C>T	p.Ser424Phe	p.S424F	ENST00000398015	NM_004441.4	424	tCt/tTt	5/16	1	2	FACETS	0.871	0.809	0.934	0.871	0.809	0.934	CLONAL	1	TRUE	1	0.823404295929568	2		426	488	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170011194	170011194	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	168	345	0	ENST00000295797.4:c.1315C>G	p.Leu439Val	p.L439V	ENST00000295797	NM_002740.5	439	Ctt/Gtt	14/18	0.823404295929568	7	FACETS	1	0.98	1	0.202	0.185	0.22	CLONAL	1	TRUE	1	0.823404295929568	7		345	1029	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170011231	170011231	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	222	427	1	ENST00000295797.4:c.1352C>A	p.Ser451Tyr	p.S451Y	ENST00000295797	NM_002740.5	451	tCt/tAt	14/18	0.823404295929568	7	FACETS	1	0.989	1	0.22	0.204	0.236	CLONAL	1	TRUE	1	0.823404295929568	7		428	1252	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389336	8389336	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1285563381	NA	P-0029791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	150	455	0	ENST00000356435.5:c.4282A>G	p.Thr1428Ala	p.T1428A	ENST00000356435		1428	Aca/Gca	26/35	1	2	FACETS	0.929	0.859	1	0.929	0.859	1	CLONAL	1	TRUE	1	0.823404295929568	2		455	392	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123199738	123199738	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	144	84	0	ENST00000218089.9:c.2038G>A	p.Asp680Asn	p.D680N	ENST00000218089	NM_001042749.1	680	Gat/Aat	21/35	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.823404295929568	1		84	170	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0029792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	70	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.807	0.705	0.916	0.807	0.705	0.916	CLONAL	1	TRUE	1	0.360721087977703	2		511	481	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	136	974	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.257841502856499	3	FACETS	0.859	0.786	0.935			1	CLONAL	2	TRUE	NA	0.360721087977703	3		974	518	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991076	41991076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	83	327	0	ENST00000219905.7:c.2029C>T	p.His677Tyr	p.H677Y	ENST00000219905	NM_001164273.1	677	Cat/Tat	4/24	1	2	FACETS	0.913	0.808	1	0.913	0.808	1	CLONAL	1	TRUE	1	0.360721087977703	2		327	504	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992138	72992138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764598603	NA	P-0029792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	85	455	0	ENST00000268489.5:c.1907C>T	p.Ser636Leu	p.S636L	ENST00000268489	NM_006885.3	636	tCg/tTg	2/10	1	2	FACETS	0.968	0.858	1	0.968	0.858	1	CLONAL	1	TRUE	1	0.360721087977703	2		455	487	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044713	47044713	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	145	831	0	ENST00000377604.3:c.2113G>T	p.Glu705Ter	p.E705*	ENST00000377604	NM_001204468.1	705	Gag/Tag	19/24	1	1	FACETS	0.961	0.889	1	1	0.992	1	CLONAL	2	TRUE	0	0.360721087977703	1		831	343	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864852	57864852	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	98	533	0	ENST00000228682.2:c.2329C>G	p.Gln777Glu	p.Q777E	ENST00000228682	NM_005269.2	777	Caa/Gaa	12/12	0.332253062407645	3	FACETS	0.851	0.759	0.948	0.425	0.379	0.474	CLONAL	1	TRUE	1	0.360721087977703	3		533	754	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941652	48941652	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1566194338	NA	P-0029792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	31	281	0	ENST00000267163.4:c.962A>G	p.Tyr321Cys	p.Y321C	ENST00000267163	NM_000321.2	321	tAc/tGc	10/27	1	2	FACETS	0.994	0.812	1	0.994	0.812	1	CLONAL	1	TRUE	1	0.360721087977703	2		281	173	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194799	30194799	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	130	529	0	ENST00000331968.5:c.346C>G	p.Leu116Val	p.L116V	ENST00000331968	NM_002742.2	116	Ctg/Gtg	2/18	1	2	FACETS	0.932	0.846	1	0.932	0.846	1	CLONAL	1	TRUE	1	0.360721087977703	2		529	773	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273574	5273574	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	89	497	0	ENST00000357368.4:c.258T>G	p.Ser86Arg	p.S86R	ENST00000357368	NM_002850.3	86	agT/agG	4/38	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.360721087977703	2		497	435	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291932	15291932	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	148	673	0	ENST00000263388.2:c.2834C>G	p.Ser945Trp	p.S945W	ENST00000263388	NM_000435.2	945	tCg/tGg	18/33	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.360721087977703	2		673	744	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469594	25469594	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1472367159	NA	P-0029792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	112	558	1	ENST00000264709.3:c.1174G>T	p.Glu392Ter	p.E392*	ENST00000264709	NM_175629.2	392	Gag/Tag	10/23	1	2	FACETS	0.957	0.862	1	0.957	0.862	1	CLONAL	1	TRUE	1	0.360721087977703	2		559	649	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606597	29606597	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0029792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	82	396	0	ENST00000389048.3:c.1282+1G>T		p.X428_splice	ENST00000389048	NM_004304.4	428			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.360721087977703	2		396	369	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714479	40714479	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	88	451	0	ENST00000373198.4:c.3918C>A	p.Tyr1306Ter	p.Y1306*	ENST00000373198	NM_133170.3	1306	taC/taA	29/32	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.360721087977703	2		451	465	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411009	63411010	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0029792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	77	253	0	ENST00000330258.3:c.2157_2158delinsAA	p.Met719_Gln720delinsIleLys	p.M719_Q720delinsIK	ENST00000330258	NM_152424.3	719	atGCag/atAAag	2/2	1	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.360721087977703	1		253	252	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029792-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	89	974	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	0.273162694851605	2		974	627	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044713	47044713	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029792-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	147	831	0	ENST00000377604.3:c.2113G>T	p.Glu705Ter	p.E705*	ENST00000377604	NM_001204468.1	705	Gag/Tag	19/24	1	1	FACETS	1	0.975	1	1	0.992	1	CLONAL	2	TRUE	0	0.273162694851605	1		831	408	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941652	48941652	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1566194338	NA	P-0029792-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	74	281	0	ENST00000267163.4:c.962A>G	p.Tyr321Cys	p.Y321C	ENST00000267163	NM_000321.2	321	tAc/tGc	10/27	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.273162694851605	2		281	400	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273574	5273574	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029792-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	96	497	0	ENST00000357368.4:c.258T>G	p.Ser86Arg	p.S86R	ENST00000357368	NM_002850.3	86	agT/agG	4/38	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.273162694851605	2		497	478	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606597	29606597	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0029792-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	97	396	0	ENST00000389048.3:c.1282+1G>T		p.X428_splice	ENST00000389048	NM_004304.4	428			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.273162694851605	2		396	555	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714479	40714479	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029792-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	87	451	0	ENST00000373198.4:c.3918C>A	p.Tyr1306Ter	p.Y1306*	ENST00000373198	NM_133170.3	1306	taC/taA	29/32	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.273162694851605	2		451	539	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0029793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	80	691	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.84	0.739	0.949	0.84	0.739	0.949	CLONAL	1	FALSE	1	0.261953013546887	2		691	727	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643942	52643943	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	41	343	0	ENST00000394830.3:c.1953dup	p.Ser652IlefsTer13	p.S652Ifs*13	ENST00000394830	NM_018313.4	651	-/A	17/30	1	2	FACETS	0.64	0.533	0.759	0.64	0.533	0.759	SUBCLONAL	1	FALSE	1	0.261953013546887	2		343	489	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0029794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	178	733	1	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	0.185487479064905	3	FACETS	1	0.99	1	0.745	0.687	0.804	INDETERMINATE	1	TRUE	1	0.348200596722694	3		734	806	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057705	27057705	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	61	621	1	ENST00000324856.7:c.1413C>A	p.Tyr471Ter	p.Y471*	ENST00000324856	NM_006015.4	471	taC/taA	3/20	1	2	FACETS	0.556	0.479	0.64	0.556	0.479	0.64	SUBCLONAL	1	TRUE	1	0.348200596722694	2		622	630	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988287	41988287	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	70	398	0	ENST00000219905.7:c.1079G>A	p.Ser360Asn	p.S360N	ENST00000219905	NM_001164273.1	360	aGt/aAt	3/24	1	2	FACETS	0.788	0.689	0.896	0.788	0.689	0.896	SUBCLONAL	1	TRUE	1	0.348200596722694	2		398	510	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099403	157099426	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAGCAGCAA	CAGCAGCAGCAGCAGCAGCAGCAA	-	rs770869529	NA	P-0029795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	70	216	0	ENST00000346085.5:c.369_392del	p.Gln124_Gln131del	p.Q124_Q131del	ENST00000346085	NM_020732.3	114	CAGCAGCAGCAGCAGCAGCAGCAA/-	1/20	1	2	FACETS	0.596	0.525	0.671	0.596	0.525	0.671	SUBCLONAL	1	TRUE	1	0.824011888093954	2		216	285	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343304	118343304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	130	270	0	ENST00000534358.1:c.1430C>T	p.Ser477Phe	p.S477F	ENST00000534358	NM_005933.3	477	tCt/tTt	3/36	1	2	FACETS	0.986	0.908	1	0.986	0.908	1	CLONAL	1	TRUE	1	0.824011888093954	2		270	320	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589663	67589663	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587777709	NA	P-0029796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	38	217	0	ENST00000274335.5:c.1425+1G>A		p.X475_splice	ENST00000274335		475			1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.22	2		217	254	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941034	71941034	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	56	663	0	ENST00000298229.2:c.910G>T	p.Ala304Ser	p.A304S	ENST00000298229	NM_001567.3	304	Gcc/Tcc	8/28	1	2	FACETS	0.666	0.57	0.772	0.666	0.57	0.772	SUBCLONAL	1	TRUE	1	0.22	2		663	764	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617643	100617644	+	stop_gained	Nonsense_Mutation	INS	-	-	TATTTC	novel	NA	P-0029796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	67	278	0	ENST00000308731.7:c.420_425dup	p.Lys141_Tyr142insTer	p.K141_Y142ins*	ENST00000308731	NM_000061.2	142	tat/taGAAATAt	6/19	1	1	FACETS	0.779	0.681	0.883	1	0.975	1	SUBCLONAL	2	TRUE	0	0.22	1		278	348	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16247449	16247449	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	51	277	0	ENST00000375759.3:c.1720G>C	p.Gly574Arg	p.G574R	ENST00000375759	NM_015001.2	574	Ggg/Cgg	9/15	1	2	FACETS	0.884	0.752	1	0.884	0.752	1	CLONAL	1	TRUE	1	0.26	2		277	444	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677780	58677780	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	87	431	0	ENST00000305921.3:c.5C>A	p.Ala2Glu	p.A2E	ENST00000305921	NM_003620.3	2	gCg/gAg	1/6	1	2	FACETS	0.919	0.814	1	0.919	0.814	1	CLONAL	1	TRUE	1	0.26	2		431	728	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221327	1221343	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GACCTGCTGAAAGGTGG	GACCTGCTGAAAGGTGG	-	novel	NA	P-0029798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	155	455	0	ENST00000326873.7:c.852_862+6del		p.X284_splice	ENST00000326873	NM_000455.4	284		6/10	1	2	FACETS	0.775	0.711	0.843	1	0.989	1	SUBCLONAL	2	TRUE	1	0.26	2		455	769	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197814	66197814	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	46	296	0	ENST00000273854.3:c.2885T>A	p.Leu962Gln	p.L962Q	ENST00000273854	NM_004439.5	962	cTa/cAa	17/18	1	2	FACETS	0.813	0.686	0.954	0.813	0.686	0.954	CLONAL	1	TRUE	1	0.26	2		296	435	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499667	149499667	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	54	489	0	ENST00000261799.4:c.2606G>A	p.Trp869Ter	p.W869*	ENST00000261799	NM_002609.3	869	tGg/tAg	19/23	1	2	FACETS	0.591	0.504	0.687	0.591	0.504	0.687	SUBCLONAL	1	TRUE	1	0.26	2		489	703	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731631	47731631	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	26	148	0	ENST00000449228.1:c.161G>C	p.Arg54Pro	p.R54P	ENST00000449228	NM_001127240.2	54	cGa/cCa	2/4	1	2	FACETS	0.781	0.621	0.964	0.781	0.621	0.964	CLONAL	1	TRUE	1	0.26	2		148	256	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597493	52597493	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	53	286	1	ENST00000394830.3:c.3817C>T	p.Gln1273Ter	p.Q1273*	ENST00000394830	NM_018313.4	1273	Cag/Tag	25/30	0.324795269584162	1	FACETS	0.987	0.848	1	0.987	0.848	1	CLONAL	1	TRUE	0	0.324795269584162	1		287	277	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81558892	81558892	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	54	332	0	ENST00000298171.2:c.485C>A	p.Pro162His	p.P162H	ENST00000298171	NM_000369.2	162	cCt/cAt	6/10	1	2	FACETS	0.929	0.797	1	0.929	0.797	1	CLONAL	1	TRUE	1	0.324795269584162	2		332	358	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039505	49039505	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs764754259	NA	P-0029799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	97	419	0	ENST00000267163.4:c.2489+1G>A		p.X830_splice	ENST00000267163	NM_000321.2	830			0.324795269584162	1	FACETS	0.903	0.807	1	0.903	0.807	1	CLONAL	1	TRUE	0	0.324795269584162	1		419	554	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562632	29562632	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1060500346	NA	P-0029799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	83	288	0	ENST00000356175.3:c.3712G>T	p.Glu1238Ter	p.E1238*	ENST00000356175	NM_000267.3	1238	Gaa/Taa	28/57	0.185646676463637	3	FACETS	0.77	0.683	0.861	0.77	0.683	0.861	INDETERMINATE	2	TRUE	1	0.324795269584162	3		288	386	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585506	29585506	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0029799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	40	129	0	ENST00000356175.3:c.4255A>T	p.Lys1419Ter	p.K1419*	ENST00000356175	NM_000267.3	1419	Aag/Tag	31/57	0.185646676463637	3	FACETS	1	0.944	1	0.657	0.551	0.772	INDETERMINATE	1	TRUE	1	0.324795269584162	3		129	218	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3114940	3114940	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0029799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	96	450	1	ENST00000078429.4:c.477-2A>T		p.X159_splice	ENST00000078429	NM_002067.2	159			1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.324795269584162	2		451	554	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335071	81335071	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0029799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	51	264	0	ENST00000222390.5:c.1758-2A>T		p.X586_splice	ENST00000222390	NM_000601.4	586			1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.324795269584162	2		264	312	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38283763	38283763	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	100	439	0	ENST00000425967.3:c.715G>T	p.Val239Phe	p.V239F	ENST00000425967	NM_001174067.1	239	Gtc/Ttc	7/19	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.324795269584162	2		439	538	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579472	7579474	+	frameshift_variant	Frame_Shift_Del	DEL	GGG	GGG	C	novel	NA	P-0029799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	145	556	0	ENST00000269305.4:c.213_215delinsG	p.Pro72ArgfsTer76	p.P72Rfs*76	ENST00000269305	NM_001126112.2	71	ccCCCc/ccGc	4/11	1	2	FACETS	0.754	0.691	0.82	1	0.988	1	SUBCLONAL	2	TRUE	1	0.324795269584162	2		556	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0029800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	129	573	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.287241980286389	3	FACETS	1	0.984	1	0.718	0.65	0.789	CLONAL	1	TRUE	1	0.21	3		573	946	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857648	59857648	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs541203428	NA	P-0029800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	27	315	0	ENST00000259008.2:c.1909G>T	p.Ala637Ser	p.A637S	ENST00000259008	NM_032043.2	637	Gct/Tct	13/20	0.287241980286389	3	FACETS	0.941	0.75	1	0.47	0.375	0.579	CLONAL	1	TRUE	1	0.21	3		315	302	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741187	145741187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs117670586	NA	P-0029800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1191	66	609	1	ENST00000428558.2:c.1219G>A	p.Glu407Lys	p.E407K	ENST00000428558	NM_004260.3	407	Gag/Aag	6/22	1	2	FACETS	0.5	0.432	0.574	0.5	0.432	0.574	SUBCLONAL	1	TRUE	1	0.21	2		610	1257	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058446	69058446	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	17	361	0	ENST00000288368.4:c.4090G>T	p.Val1364Phe	p.V1364F	ENST00000288368	NM_024870.2	1364	Gtt/Ttt	34/40	1	2	FACETS	0.692	0.517	0.899	0.692	0.517	0.899	SUBCLONAL	1	TRUE	1	0.21	2		361	234	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602583	10602583	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	95	624	0	ENST00000171111.5:c.995G>A	p.Gly332Asp	p.G332D	ENST00000171111	NM_203500.1	332	gGc/gAc	3/6	1	2	FACETS	0.806	0.715	0.903	0.806	0.715	0.903	CLONAL	1	TRUE	1	0.21	2		624	1123	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113768	11113768	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0029800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	100	653	0	ENST00000358026.2:c.1876A>T	p.Lys626Ter	p.K626*	ENST00000358026	NM_001128849.1	626	Aag/Tag	12/36	1	2	FACETS	0.84	0.748	0.938	0.84	0.748	0.938	CLONAL	1	TRUE	1	0.21	2		653	1134	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102909	71102909	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	77	262	0	ENST00000318789.4:c.298G>C	p.Ala100Pro	p.A100P	ENST00000318789	NM_032682.5	100	Gct/Cct	8/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.21	2		262	534	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449535	149449535	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	158	572	0	ENST00000286301.3:c.1411C>A	p.Leu471Met	p.L471M	ENST00000286301	NM_005211.3	471	Ctg/Atg	10/22	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.21	2		572	1167	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974721	21974721	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	65	304	0	ENST00000304494.5:c.106G>C	p.Ala36Pro	p.A36P	ENST00000304494	NM_000077.4	36	Gcg/Ccg	1/3	1	2	FACETS	0.838	0.725	0.96	0.838	0.725	0.96	CLONAL	1	TRUE	1	0.21	2		304	739	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28963931	28963931	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0029800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	21	331	1	ENST00000282397.4:c.1969+2T>A		p.X657_splice	ENST00000282397	NM_002019.4	657			1	2	FACETS	0.613	0.472	0.778	0.613	0.472	0.778	SUBCLONAL	1	TRUE	1	0.21	2		332	326	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641896	12641896	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	17	302	0	ENST00000251849.4:c.853A>T	p.Ser285Cys	p.S285C	ENST00000251849	NM_002880.3	285	Agc/Tgc	8/17	0.2578508869613	3	FACETS	0.531	0.395	0.692			1	SUBCLONAL	1	TRUE	NA	0.21	3		302	337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0029801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	381	515	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.550413261936067	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.550413261936067	2		515	665	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0029801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	159	295	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	0.550413261936067	3	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	1	0.550413261936067	3		295	364	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939078	48939078	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	122	253	0	ENST00000267163.4:c.910G>T	p.Gly304Ter	p.G304*	ENST00000267163	NM_000321.2	304	Gga/Tga	9/27	0.550413261936067	2	FACETS	0.955	0.885	1	0.955	0.885	1	CLONAL	2	TRUE	0	0.550413261936067	2		253	232	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0029802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	240	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.745513972647715	2		511	635	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0029802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	207	615	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.999	0.934	1	0.999	0.934	1	CLONAL	1	TRUE	1	0.745513972647715	2		615	556	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	342	674	4	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.745513972647715	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.745513972647715	1		678	522	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088788	27088788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	221	482	1	ENST00000324856.7:c.2402del	p.Gly801ValfsTer32	p.G801Vfs*32	ENST00000324856	NM_006015.4	799	caG/ca	7/20	1	2	FACETS	0.941	0.881	1	0.941	0.881	1	CLONAL	1	TRUE	1	0.745513972647715	2		483	630	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574023	7574023	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	261	494	0	ENST00000269305.4:c.1004del	p.Arg335LeufsTer10	p.R335Lfs*10	ENST00000269305	NM_001126112.2	335	cGt/ct	10/11	0.745513972647715	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.745513972647715	1		494	439	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522416	176522416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519792	NA	P-0029802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	284	593	4	ENST00000292408.4:c.1605C>A	p.Asn535Lys	p.N535K	ENST00000292408	NM_213647.1	535	aaC/aaA	12/18	1	2	FACETS	0.926	0.873	0.979	0.926	0.873	0.979	CLONAL	1	TRUE	1	0.745513972647715	2		597	823	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951053	48951053	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0029802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	79	203	2	ENST00000267163.4:c.1216-1G>C		p.X406_splice	ENST00000267163	NM_000321.2	406			0.745513972647715	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.745513972647715	1		205	131	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518851	187518851	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	204	372	1	ENST00000441802.2:c.12353G>T	p.Gly4118Val	p.G4118V	ENST00000441802	NM_005245.3	4118	gGt/gTt	24/27	0.745513972647715	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.745513972647715	1		373	331	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913499	NA	P-0029803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	35	164	0	ENST00000345146.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000345146	NM_005896.2	132	Cgt/Ggt	4/10	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.413702425176552	2		164	155	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107162	27107162	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	73	312	0	ENST00000324856.7:c.6773T>A	p.Leu2258Gln	p.L2258Q	ENST00000324856	NM_006015.4	2258	cTg/cAg	20/20	0.402877507558827	1	FACETS	0.838	0.739	0.944	0.838	0.739	0.944	CLONAL	1	TRUE	0	0.413702425176552	1		312	334	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279563	123279563	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	153	371	0	ENST00000358487.5:c.869G>T	p.Trp290Leu	p.W290L	ENST00000358487	NM_000141.4	290	tGg/tTg	7/18	NA	2	FACETS	1	0.929	1			1	INDETERMINATE	2	TRUE	NA	0.413702425176552	2		371	369	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	92	376	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.807	0.72	0.898	0.807	0.72	0.898	CLONAL	1	FALSE	1	0.512615942658537	2		376	445	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0029804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	223	454	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.496827050849489	4	FACETS	0.864	0.807	0.922	0.864	0.807	0.922	CLONAL	2	FALSE	2	0.512615942658537	4		454	762	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933480	100933480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766277966	NA	P-0029804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	79	160	0	ENST00000325455.5:c.1910G>A	p.Arg637Gln	p.R637Q	ENST00000325455	NM_001202474.3	637	cGa/cAa	4/8	0.496827050849489	4	FACETS	0.851	0.757	0.948	0.851	0.757	0.948	CLONAL	2	FALSE	2	0.512615942658537	4		160	274	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576926	7576956	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTAGGAAAGAGGCAAGGAAAGGTGATAAAA	GCTAGGAAAGAGGCAAGGAAAGGTGATAAAA	-	novel	NA	P-0029804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	390	612	0	ENST00000269305.4:c.920-30_920del		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	0.512615942658537	3	FACETS	1	0.994	1	0.832	0.797	0.867	CLONAL	2	FALSE	0	0.512615942658537	3		612	766	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285191	212285191	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	165	404	0	ENST00000342788.4:c.3110C>T	p.Ser1037Phe	p.S1037F	ENST00000342788	NM_005235.2	1037	tCc/tTc	25/28	0.155548609540688	5	FACETS	0.995	0.919	1			1	INDETERMINATE	2	FALSE	NA	0.512615942658537	5		404	572	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321666	62321666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759789479	NA	P-0029804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	307	597	0	ENST00000360203.5:c.2285G>A	p.Arg762Gln	p.R762Q	ENST00000360203	NM_001283009.1	762	cGg/cAg	26/35	0.496827050849489	4	FACETS	0.951	0.898	1	0.951	0.898	1	CLONAL	2	FALSE	2	0.512615942658537	4		597	953	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671036	30671036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747584377	NA	P-0029804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	373	610	0	ENST00000376406.3:c.5710C>T	p.Arg1904Trp	p.R1904W	ENST00000376406	NM_014641.2	1904	Cgg/Tgg	12/15	0.496827050849489	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	FALSE	2	0.512615942658537	4		610	1034	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0029805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	91	537	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.948	0.84	1	0.948	0.84	1	CLONAL	1	TRUE	1	0.19	2		540	1010	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528621	89528621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780470195	NA	P-0029805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	31	227	0	ENST00000336596.2:c.2921C>T	p.Thr974Met	p.T974M	ENST00000336596	NM_005233.5	974	aCg/aTg	17/17	1	2	FACETS	0.694	0.561	0.846	0.694	0.561	0.846	SUBCLONAL	1	TRUE	1	0.19	2		227	470	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847399	68847399	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0029805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	80	230	0	ENST00000261769.5:c.1320+1G>T		p.X440_splice	ENST00000261769	NM_004360.3	440			1	2	FACETS	0.946	0.836	1	1	0.983	1	CLONAL	2	TRUE	1	0.19	2		230	445	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300569	11300569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1363405074	NA	P-0029805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	82	687	0	ENST00000361445.4:c.1577G>A	p.Arg526His	p.R526H	ENST00000361445	NM_004958.3	526	cGt/cAt	11/58	1	2	FACETS	0.782	0.687	0.884	0.782	0.687	0.884	SUBCLONAL	1	TRUE	1	0.19	2		687	1104	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443676	29443676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56315533	NA	P-0029805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	59	572	0	ENST00000389048.3:c.3541C>T	p.Arg1181Cys	p.R1181C	ENST00000389048	NM_004304.4	1181	Cgc/Tgc	23/29	1	2	FACETS	0.594	0.509	0.687	0.594	0.509	0.687	SUBCLONAL	1	TRUE	1	0.19	2		572	1046	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5286082	5286082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200430287	NA	P-0029805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1317	88	784	0	ENST00000357368.4:c.70G>A	p.Val24Ile	p.V24I	ENST00000357368	NM_002850.3	24	Gtt/Att	2/38	1	2	FACETS	0.659	0.582	0.743	0.659	0.582	0.743	SUBCLONAL	1	TRUE	1	0.19	2		784	1405	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032526	12032526	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	32	310	1	ENST00000353533.5:c.962T>A	p.Val321Glu	p.V321E	ENST00000353533	NM_003010.3	321	gTg/gAg	9/11	1	2	FACETS	0.571	0.462	0.694	0.571	0.462	0.694	SUBCLONAL	1	TRUE	1	0.19	2		311	590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0029806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	204	798	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	1	2	FACETS	0.964	0.894	1	0.964	0.894	1	CLONAL	1	TRUE	1	0.439245871779949	2		798	964	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663862	241663862	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	134	330	0	ENST00000366560.3:c.1265T>C	p.Leu422Pro	p.L422P	ENST00000366560	NM_000143.3	422	cTg/cCg	9/10	0.439245871779949	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.439245871779949	1		330	377	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245084	133245090	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	TGGCACT	TGGCACT	-	novel	NA	P-0029806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	107	583	0	ENST00000320574.5:c.2027-2_2031del		p.X676_splice	ENST00000320574	NM_006231.2	676		19/49	1	2	FACETS	0.679	0.61	0.753	0.679	0.61	0.753	SUBCLONAL	1	TRUE	1	0.439245871779949	2		583	717	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52685802	52685802	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	117	412	0	ENST00000394830.3:c.670A>T	p.Ile224Phe	p.I224F	ENST00000394830	NM_018313.4	224	Att/Ttt	7/30	0.439245871779949	1	FACETS	0.987	0.897	1	0.987	0.897	1	CLONAL	1	TRUE	0	0.439245871779949	1		412	421	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651904	36651904	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143419412	NA	P-0029806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	122	444	0	ENST00000244741.5:c.26G>A	p.Arg9His	p.R9H	ENST00000244741	NM_000389.4	9	cGt/cAt	2/3	1	2	FACETS	0.827	0.748	0.909	0.827	0.748	0.909	CLONAL	1	TRUE	1	0.439245871779949	2		444	672	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0029808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	79	218	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.2	2		218	716	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0029808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	89	454	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	0.2	2		454	693	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058361	42058361	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	51	269	0	ENST00000219905.7:c.8081C>T	p.Ser2694Phe	p.S2694F	ENST00000219905	NM_001164273.1	2694	tCc/tTc	24/24	1	2	FACETS	0.981	0.834	1	0.981	0.834	1	CLONAL	1	TRUE	1	0.2	2		269	520	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367317	50367317	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	73	349	0	ENST00000331340.3:c.124G>A	p.Gly42Arg	p.G42R	ENST00000331340	NM_006060.4	42	Gga/Aga	3/8	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.2	2		349	646	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259967	16259967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	67	550	1	ENST00000375759.3:c.7232C>T	p.Ser2411Leu	p.S2411L	ENST00000375759	NM_015001.2	2411	tCg/tTg	11/15	1	2	FACETS	0.731	0.633	0.837	0.731	0.633	0.837	SUBCLONAL	1	TRUE	1	0.2	2		551	917	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295789	212295789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1240072004	NA	P-0029808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	68	424	2	ENST00000342788.4:c.2524C>T	p.Arg842Trp	p.R842W	ENST00000342788	NM_005235.2	842	Cgg/Tgg	21/28	1	2	FACETS	0.842	0.731	0.962	0.842	0.731	0.962	CLONAL	1	TRUE	1	0.2	2		426	808	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851651	134851651	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1486100057	NA	P-0029808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	57	400	2	ENST00000398015.3:c.1057G>A	p.Asp353Asn	p.D353N	ENST00000398015	NM_004441.4	353	Gat/Aat	5/16	1	2	FACETS	0.912	0.782	1	0.912	0.782	1	CLONAL	1	TRUE	1	0.2	2		402	625	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976903	55976903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	72	432	0	ENST00000263923.4:c.1009G>A	p.Glu337Lys	p.E337K	ENST00000263923	NM_002253.2	337	Gaa/Aaa	8/30	1	2	FACETS	0.961	0.839	1	0.961	0.839	1	CLONAL	1	TRUE	1	0.2	2		432	749	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032246	26032246	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	22	198	0	ENST00000244661.2:c.43A>G	p.Lys15Glu	p.K15E	ENST00000244661	NM_003537.3	15	Aaa/Gaa	1/1	1	2	FACETS	0.751	0.582	0.946	0.751	0.582	0.946	CLONAL	1	TRUE	1	0.2	2		198	293	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137271	64137271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	152	670	0	ENST00000334205.4:c.1703C>T	p.Thr568Met	p.T568M	ENST00000334205	NM_003942.2	568	aCg/aTg	14/17	1	2	FACETS	0.702	0.643	0.764	0.702	0.643	0.764	SUBCLONAL	1	TRUE	1	0.533221106361135	2		670	812	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448295	56448295	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	147	577	0	ENST00000407977.2:c.352C>A	p.Pro118Thr	p.P118T	ENST00000407977		118	Ccc/Acc	3/10	1	2	FACETS	0.682	0.623	0.744	0.682	0.623	0.744	SUBCLONAL	1	TRUE	1	0.533221106361135	2		577	808	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939307	76939307	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0121564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	276	641	0	ENST00000373344.5:c.1441G>T	p.Glu481Ter	p.E481*	ENST00000373344	NM_000489.3	481	Gag/Tag	9/35	1	2	FACETS	0.938	0.884	0.993	0.938	0.884	0.993	CLONAL	1	NA	1	0.730858885436545	2		641	805	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0029813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	65	691	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.769	0.665	0.882	0.769	0.665	0.882	SUBCLONAL	1	TRUE	1	0.2	2		691	845	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0029813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	80	514	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.2	2		514	799	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405969	49405969	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	64	457	0	ENST00000418115.1:c.169T>G	p.Leu57Val	p.L57V	ENST00000418115	NM_001664.2	57	Ttg/Gtg	3/5	1	2	FACETS	0.813	0.703	0.933	0.813	0.703	0.933	CLONAL	1	TRUE	1	0.2	2		457	787	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845496	151845496	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	96	409	0	ENST00000262189.6:c.13516C>T	p.His4506Tyr	p.H4506Y	ENST00000262189	NM_170606.2	4506	Cac/Tac	52/59	0.189021913330893	3	FACETS	0.752	0.67	0.839	0.752	0.67	0.839	SUBCLONAL	2	TRUE	1	0.2	3		409	702	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0029814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	63	387	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.203845883591396	3	FACETS	1	0.97	1	0.736	0.638	0.841	CLONAL	1	TRUE	1	0.203845883591396	3		387	463	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0029814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	199	634	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.19360059710917	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.203845883591396	2		634	876	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663669	29663669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	39	341	1	ENST00000356175.3:c.6101G>T	p.Cys2034Phe	p.C2034F	ENST00000356175	NM_000267.3	2034	tGc/tTc	41/57	0.176560556386777	4	FACETS	0.918	0.76	1	0.306	0.253	0.365	CLONAL	1	TRUE	1	0.203845883591396	4		342	502	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181757	56181757	+	splice_acceptor_variant	Splice_Site	DEL	A	A	-	novel	NA	P-0029814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	87	248	0	ENST00000399503.3:c.3983-2del		p.X1328_splice	ENST00000399503	NM_005921.1	1328			0.201344519356345	3	FACETS	1	0.967	1	0.816	0.728	0.91	CLONAL	2	TRUE	0	0.203845883591396	3		248	384	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975459	13975459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80157564	NA	P-0029814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	53	283	1	ENST00000405192.2:c.428C>T	p.Thr143Met	p.T143M	ENST00000405192	NM_001163147.1	143	aCg/aTg	7/12	0.203845883591396	5	FACETS	0.82	0.701	0.95			1	CLONAL	2	TRUE	NA	0.203845883591396	5		284	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0029816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	43	535	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.809	0.676	0.958	0.809	0.676	0.958	CLONAL	1	TRUE	1	0.17	2		535	625	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	37	974	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.675	0.555	0.81	0.675	0.555	0.81	SUBCLONAL	1	TRUE	1	0.17	2		974	645	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857275	9857275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426934537	NA	P-0029816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	33	409	0	ENST00000330684.3:c.4126C>T	p.Arg1376Cys	p.R1376C	ENST00000330684	NM_001134407.1	1376	Cgc/Tgc	13/13	1	2	FACETS	0.676	0.55	0.82	0.676	0.55	0.82	SUBCLONAL	1	TRUE	1	0.17	2		409	574	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0029818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	45	492	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.856	0.718	1	0.856	0.718	1	CLONAL	1	TRUE	1	0.16	2		492	657	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082254	16082254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	63	857	0	ENST00000281043.3:c.68C>T	p.Ser23Leu	p.S23L	ENST00000281043	NM_005378.4	23	tCg/tTg	2/3	1	2	FACETS	0.74	0.638	0.852	0.74	0.638	0.852	SUBCLONAL	1	TRUE	1	0.16	2		857	1064	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828812	72828812	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	41	523	1	ENST00000268489.5:c.7769C>G	p.Ser2590Cys	p.S2590C	ENST00000268489	NM_006885.3	2590	tCt/tGt	9/10	1	2	FACETS	0.742	0.616	0.882	0.742	0.616	0.882	SUBCLONAL	1	TRUE	1	0.16	2		524	691	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545622	106545622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	36	443	0	ENST00000359195.3:c.3099G>A	p.Met1033Ile	p.M1033I	ENST00000359195	NM_002649.2	1033	atG/atA	11/11	1	2	FACETS	0.632	0.518	0.761	0.632	0.518	0.761	SUBCLONAL	1	TRUE	1	0.16	2		443	712	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89791019	89791019	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226649883	NA	P-0029818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	11	135	0	ENST00000336032.3:c.406G>A	p.Gly136Arg	p.G136R	ENST00000336032	NM_006813.2	136	Gga/Aga	1/2	1	2	FACETS	0.735	0.508	1	0.735	0.508	1	CLONAL	1	TRUE	1	0.16	2		135	187	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520524	176520524	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763461529	NA	P-0029818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	57	737	1	ENST00000292408.4:c.1369G>A	p.Asp457Asn	p.D457N	ENST00000292408	NM_213647.1	457	Gac/Aac	10/18	1	2	FACETS	0.748	0.64	0.867	0.748	0.64	0.867	SUBCLONAL	1	TRUE	1	0.16	2		738	952	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170486	108170486	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1565473651	NA	P-0029818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	33	352	0	ENST00000278616.4:c.5051C>G	p.Ser1684Cys	p.S1684C	ENST00000278616	NM_000051.3	1684	tCt/tGt	34/63	1	2	FACETS	0.828	0.674	1	0.828	0.674	1	CLONAL	1	TRUE	1	0.16	2		352	498	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2488131	2488131	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	45	531	0	ENST00000355716.4:c.28C>T	p.Pro10Ser	p.P10S	ENST00000355716	NM_003820.2	10	Cct/Tct	1/8	0.3	2	FACETS	0.836	0.701	0.985			1	CLONAL	1	TRUE	NA	0.16	2		531	673	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14022075	14022075	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	34	429	0	ENST00000311895.7:c.775G>T	p.Gly259Ter	p.G259*	ENST00000311895	NM_005236.2	259	Gga/Tga	4/11	1	2	FACETS	0.835	0.681	1	0.835	0.681	1	CLONAL	1	TRUE	1	0.16	2		429	509	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670646	67670646	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35257000	NA	P-0029818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	53	466	0	ENST00000264010.4:c.1891G>A	p.Glu631Lys	p.E631K	ENST00000264010	NM_006565.3	631	Gaa/Aaa	11/12	1	2	FACETS	0.937	0.798	1	0.937	0.798	1	CLONAL	1	TRUE	1	0.16	2		466	707	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741040	40741040	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	40	617	0	ENST00000392038.2:c.1278C>G	p.Phe426Leu	p.F426L	ENST00000392038	NM_001626.4	426	ttC/ttG	13/14	1	2	FACETS	0.714	0.592	0.851	0.714	0.592	0.851	SUBCLONAL	1	TRUE	1	0.16	2		617	700	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204737436	204737436	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	39	399	0	ENST00000302823.3:c.573G>T	p.Lys191Asn	p.K191N	ENST00000302823	NM_005214.4	191	aaG/aaT	4/4	1	2	FACETS	0.81	0.67	0.966	0.81	0.67	0.966	CLONAL	1	TRUE	1	0.16	2		399	602	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42848536	42848536	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs547544037	NA	P-0029818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	52	499	0	ENST00000398585.3:c.806C>T	p.Ser269Phe	p.S269F	ENST00000398585	NM_001135099.1	269	tCt/tTt	8/14	1	2	FACETS	0.892	0.758	1	0.892	0.758	1	CLONAL	1	TRUE	1	0.16	2		499	729	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221645	22221645	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	30	257	0	ENST00000215832.6:c.86C>G	p.Ser29Trp	p.S29W	ENST00000215832	NM_002745.4	29	tCg/tGg	1/9	1	2	FACETS	0.945	0.761	1	0.945	0.761	1	CLONAL	1	TRUE	1	0.16	2		257	397	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158056	106158056	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	31	321	0	ENST00000380013.4:c.2957G>C	p.Gly986Ala	p.G986A	ENST00000380013	NM_001127208.2	986	gGa/gCa	3/11	1	2	FACETS	0.881	0.712	1	0.881	0.712	1	CLONAL	1	TRUE	1	0.16	2		321	440	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751523	57751523	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	36	309	0	ENST00000274289.3:c.1468G>C	p.Asp490His	p.D490H	ENST00000274289	NM_006622.3	490	Gat/Cat	11/14	1	2	FACETS	0.879	0.722	1	0.879	0.722	1	CLONAL	1	TRUE	1	0.16	2		309	512	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517414	176517414	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1217937501	NA	P-0029818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	43	450	0	ENST00000292408.4:c.115G>C	p.Glu39Gln	p.E39Q	ENST00000292408	NM_213647.1	39	Gag/Cag	3/18	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.16	2		450	514	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0029820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	170	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.357238142863739	2		511	914	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0029820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	164	609	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.357238142863739	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.357238142863739	1		610	725	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	98	974	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.357238142863739	1	FACETS	0.718	0.641	0.799	0.718	0.641	0.799	SUBCLONAL	1	TRUE	0	0.357238142863739	1		974	628	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167577	NA	P-0029820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	168	274	0	ENST00000257430.4:c.4463del	p.Leu1488TyrfsTer19	p.L1488Yfs*19	ENST00000257430	NM_000038.5	1487	acT/ac	16/16	0.357238142863739	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	0	0.357238142863739	2		274	466	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0029820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	124	317	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.933	0.845	1	0.933	0.845	1	CLONAL	1	TRUE	1	0.357238142863739	2		317	744	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045136	47045136	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	173	295	0	ENST00000377604.3:c.2377C>T	p.Arg793Ter	p.R793*	ENST00000377604	NM_001204468.1	793	Cga/Tga	21/24	1	1	FACETS	0.759	0.704	0.816	1	0.99	1	SUBCLONAL	2	TRUE	0	0.357238142863739	1		295	524	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464368	120464368	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1034013158	NA	P-0029820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	183	500	1	ENST00000256646.2:c.5278G>A	p.Asp1760Asn	p.D1760N	ENST00000256646	NM_024408.3	1760	Gat/Aat	29/34	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.357238142863739	2		501	940	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989060	41989060	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	168	580	0	ENST00000219905.7:c.1852C>T	p.Arg618Ter	p.R618*	ENST00000219905	NM_001164273.1	618	Cga/Tga	3/24	1	2	FACETS	0.972	0.893	1	0.972	0.893	1	CLONAL	1	TRUE	1	0.357238142863739	2		580	968	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749074	43749074	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	235	645	0	ENST00000382044.4:c.1732C>T	p.Gln578Ter	p.Q578*	ENST00000382044	NM_001141980.1	578	Cag/Tag	12/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.357238142863739	2		645	1218	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120223	70120223	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	180	617	0	ENST00000245479.2:c.1225G>T	p.Glu409Ter	p.E409*	ENST00000245479	NM_000346.3	409	Gag/Tag	3/3	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.357238142863739	2		617	963	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814684	139814684	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0029820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	116	376	0	ENST00000247668.2:c.679-2A>C		p.X227_splice	ENST00000247668	NM_021138.3	227			1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.357238142863739	2		376	614	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44935993	44935993	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0029820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	31	229	0	ENST00000377967.4:c.2754T>A	p.Cys918Ter	p.C918*	ENST00000377967	NM_021140.2	918	tgT/tgA	18/29	1	1	FACETS	0.291	0.235	0.355	0.291	0.235	0.355	SUBCLONAL	1	TRUE	0	0.357238142863739	1		229	490	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0029821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	348	493	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.611405319458322	3	FACETS	0.873	0.831	0.916	0.873	0.831	0.916	CLONAL	2	TRUE	1	0.620045630110708	3		493	842	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	131	248	1	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	0.303874978905826	2	FACETS	1	0.987	1	0.69	0.637	0.745	INDETERMINATE	1	TRUE	0	0.620045630110708	2		249	306	SUCCESS
APC	324	MSKCC	GRCh37	5	112175246	112175246	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1057517558	NA	P-0029821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	215	263	0	ENST00000257430.4:c.3956del	p.Pro1319LeufsTer2	p.P1319Lfs*2	ENST00000257430	NM_000038.5	1319	Cct/ct	16/16	0.620045630110708	2	FACETS	0.996	0.946	1	0.996	0.946	1	CLONAL	2	TRUE	0	0.620045630110708	2		263	348	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247168	153247168	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1560758208	NA	P-0029821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	34	239	0	ENST00000281708.4:c.1634A>G	p.Tyr545Cys	p.Y545C	ENST00000281708	NM_033632.3	545	tAt/tGt	10/12	0.303874978905826	2	FACETS	0.263	0.215	0.317	0.131	0.107	0.159	INDETERMINATE	1	TRUE	0	0.620045630110708	2		239	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs967461896	NA	P-0029821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	135	601	0	ENST00000269305.4:c.526T>A	p.Cys176Ser	p.C176S	ENST00000269305	NM_001126112.2	176	Tgc/Agc	5/11	0.33075733424181	1	FACETS	0.395	0.359	0.433	0.395	0.359	0.433	INDETERMINATE	1	TRUE	0	0.620045630110708	1		601	760	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17125941	17125941	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367843558	NA	P-0029821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	149	503	0	ENST00000285071.4:c.653G>A	p.Arg218His	p.R218H	ENST00000285071	NM_144997.5	218	cGt/cAt	7/14	0.33075733424181	1	FACETS	0.483	0.443	0.526	0.483	0.443	0.526	INDETERMINATE	1	TRUE	0	0.620045630110708	1		503	686	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154868	2154868	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768105151	NA	P-0029821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	142	641	0	ENST00000434045.2:c.353G>A	p.Arg118His	p.R118H	ENST00000434045	NM_001127598.1	118	cGc/cAc	4/5	1	2	FACETS	0.42	0.382	0.46	0.42	0.382	0.46	SUBCLONAL	1	TRUE	1	0.620045630110708	2		641	1090	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554363	63555385	+	splice_acceptor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	TGGTATCCTTCAGGTTCATCTGCCTGAATCCATTGCAGGCAAACCAGAAGTCTAAGGTATCCACGCATTTCTCCCTCTCCAGGAAAGTTCGGAACAGGTAAGCACCGTCTTGATCGCCCAATAAGGAGTGTAAGGACTTGGTCCACCGGGTCAGAGGGGAATCCGGAGATGCCCGCCCCTCCGGCTCCCCCAACCCATCTTCGTTCCGCCTGGTGTTGGAAGAGACAGGCATGGGTTTGGTGACCTGGCCCTTGCCCACCCCTGGCTGACACGGTGGGGTCTCCCCTTCTTCCCCTGGCACTGGGGGCCGCGGGGCATCCTCACGGAAGCTGCTGCTGGGGTCCGGGAGGCAAGTCACCAACATAGCGCTACTCATGGTGAGGGAGCTCTTCCCACTGAGTCTGGGAATTTTTCTTCTTCCAGTTCCTCTCAGCAATCGGCGTGGTCTCTCTGTCTCTCTCAAGTCAGCAGGGGCTCATCTGAACCTCCTCTCTGGAAAGAAAAGGAAGGGGGGAGGTGGGGAGAGAGAAAAGGGTATTGATCTAATCAAAACCAGATCTACCCAACATCAAAGCAAGAAAGTAAACAGGCTTTTCAACTCCTCAAATTCAAATCAAGCAACCCAGCTATCTGCGAGGTGCTCATCTAAAGTATCAGGCGCTGCTTTTCAAAAGCGAAATCTGAGCTCCCTGCACACTTTTCGGGGTTGGGGGTGGGAGGGAGCTGTTGGGAAAGAGGCGGGGAAGGTGAGAGGAAGGCAAGAGCTGGGGACGGCAGGGGGACACTGGAGGTGTAAGACACAACCTTCCAAAAACCCACTCGGCCAGGGCGCACGCAGGGCAGCTCAGCCCGCGCCTCGCCTTCCCTCCCTTCCCCTCCCCCGATACCATCAACTCCAAAAAGGCGCACTCCCAGCCGCTAGGCTGTGTGCAGGTGAAACCAATTTCGGTATATTTCCCCACTCGGCCCTGCACAGATAACTCGAGCTCCAAACGTGCCCTTCCCCGGCATCTGGTTCCCATT	TGGTATCCTTCAGGTTCATCTGCCTGAATCCATTGCAGGCAAACCAGAAGTCTAAGGTATCCACGCATTTCTCCCTCTCCAGGAAAGTTCGGAACAGGTAAGCACCGTCTTGATCGCCCAATAAGGAGTGTAAGGACTTGGTCCACCGGGTCAGAGGGGAATCCGGAGATGCCCGCCCCTCCGGCTCCCCCAACCCATCTTCGTTCCGCCTGGTGTTGGAAGAGACAGGCATGGGTTTGGTGACCTGGCCCTTGCCCACCCCTGGCTGACACGGTGGGGTCTCCCCTTCTTCCCCTGGCACTGGGGGCCGCGGGGCATCCTCACGGAAGCTGCTGCTGGGGTCCGGGAGGCAAGTCACCAACATAGCGCTACTCATGGTGAGGGAGCTCTTCCCACTGAGTCTGGGAATTTTTCTTCTTCCAGTTCCTCTCAGCAATCGGCGTGGTCTCTCTGTCTCTCTCAAGTCAGCAGGGGCTCATCTGAACCTCCTCTCTGGAAAGAAAAGGAAGGGGGGAGGTGGGGAGAGAGAAAAGGGTATTGATCTAATCAAAACCAGATCTACCCAACATCAAAGCAAGAAAGTAAACAGGCTTTTCAACTCCTCAAATTCAAATCAAGCAACCCAGCTATCTGCGAGGTGCTCATCTAAAGTATCAGGCGCTGCTTTTCAAAAGCGAAATCTGAGCTCCCTGCACACTTTTCGGGGTTGGGGGTGGGAGGGAGCTGTTGGGAAAGAGGCGGGGAAGGTGAGAGGAAGGCAAGAGCTGGGGACGGCAGGGGGACACTGGAGGTGTAAGACACAACCTTCCAAAAACCCACTCGGCCAGGGCGCACGCAGGGCAGCTCAGCCCGCGCCTCGCCTTCCCTCCCTTCCCCTCCCCCGATACCATCAACTCCAAAAAGGCGCACTCCCAGCCGCTAGGCTGTGTGCAGGTGAAACCAATTTCGGTATATTTCCCCACTCGGCCCTGCACAGATAACTCGAGCTCCAAACGTGCCCTTCCCCGGCATCTGGTTCCCATT	-	novel	NA	P-0029821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	114	579	0	ENST00000307078.5:c.-116-529_378del		p.X39_splice	ENST00000307078	NM_004655.3	39		2/11	0.269274711135728	3	FACETS	0.562	0.506	0.622	0.281	0.253	0.311	INDETERMINATE	1	TRUE	1	0.620045630110708	3		579	857	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564451	41564451	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0029821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	145	246	0	ENST00000263253.7:c.3875-2A>T		p.X1292_splice	ENST00000263253	NM_001429.3	1292			1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.620045630110708	2		246	446	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103652	47103652	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0029821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	49	267	0	ENST00000409792.3:c.6293+1G>A		p.X2098_splice	ENST00000409792	NM_014159.6	2098			0.303874978905826	2	FACETS	0.405	0.344	0.472	0.203	0.172	0.236	INDETERMINATE	1	TRUE	0	0.620045630110708	2		267	390	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542205	187542205	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	76	363	0	ENST00000441802.2:c.5535del	p.Phe1845LeufsTer21	p.F1845Lfs*21	ENST00000441802	NM_005245.3	1845	ttT/tt	10/27	0.303874978905826	2	FACETS	0.407	0.357	0.46	0.203	0.178	0.23	INDETERMINATE	1	TRUE	0	0.620045630110708	2		363	603	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0029822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	124	436	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.229300219139905	1	FACETS	0.702	0.638	0.77	0.702	0.638	0.77	INDETERMINATE	1	TRUE	0	0.476825043314864	1		437	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0029822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	257	609	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.476825043314864	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.476825043314864	1		610	789	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0029822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	143	387	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.476825043314864	2		387	563	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222886	5222886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372440262	NA	P-0029822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	168	509	3	ENST00000357368.4:c.2917G>A	p.Gly973Ser	p.G973S	ENST00000357368	NM_002850.3	973	Ggt/Agt	18/38	1	2	FACETS	0.817	0.751	0.885	0.817	0.751	0.885	CLONAL	1	TRUE	1	0.476825043314864	2		512	863	SUCCESS
APC	324	MSKCC	GRCh37	5	112174973	112174973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085227	NA	P-0029822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	102	217	1	ENST00000257430.4:c.3682C>T	p.Gln1228Ter	p.Q1228*	ENST00000257430	NM_000038.5	1228	Cag/Tag	16/16	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.476825043314864	2		218	415	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916922	178916924	+	inframe_deletion	In_Frame_Del	DEL	ACC	ACC	-	novel	NA	P-0029822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	187	475	3	ENST00000263967.3:c.310_312del	p.Pro104del	p.P104del	ENST00000263967	NM_006218.2	103	gaACCa/gaa	2/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.476825043314864	2		478	701	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411798	63411798	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	295	394	0	ENST00000330258.3:c.1369C>T	p.Gln457Ter	p.Q457*	ENST00000330258	NM_152424.3	457	Cag/Tag	2/2	1	1	FACETS	0.76	0.722	0.798	1	0.995	1	SUBCLONAL	2	TRUE	0	0.476825043314864	1		394	620	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0029823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	104	436	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.996	0.894	1	0.996	0.894	1	CLONAL	1	TRUE	1	0.342182338782517	2		437	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0029823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	168	537	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.342182338782517	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.342182338782517	1		540	766	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928226	178928226	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519872	NA	P-0029823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	42	334	0	ENST00000263967.3:c.1412C>T	p.Pro471Leu	p.P471L	ENST00000263967	NM_006218.2	471	cCa/cTa	9/21	0.342182338782517	3	FACETS	0.423	0.352	0.502	0.212	0.176	0.251	SUBCLONAL	1	TRUE	1	0.342182338782517	3		334	679	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038349	180038349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373742042	NA	P-0029823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	283	513	1	ENST00000261937.6:c.3668G>A	p.Arg1223His	p.R1223H	ENST00000261937	NM_182925.4	1223	cGc/cAc	27/30	0.32273137453032	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.342182338782517	3		514	937	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220718	1220718	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0029823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	146	563	0	ENST00000326873.7:c.734+2T>A		p.X245_splice	ENST00000326873	NM_000455.4	245			0.342182338782517	1	FACETS	0.961	0.879	1	0.961	0.879	1	CLONAL	1	TRUE	0	0.342182338782517	1		563	736	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741472	17741472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1428517652	NA	P-0029823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	189	658	0	ENST00000250003.3:c.143C>T	p.Pro48Leu	p.P48L	ENST00000250003	NM_002478.4	48	cCg/cTg	1/3	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.342182338782517	2		658	1102	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129867	69129867	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	56	206	0	ENST00000288368.4:c.4621A>G	p.Thr1541Ala	p.T1541A	ENST00000288368	NM_024870.2	1541	Acg/Gcg	38/40	0.342182338782517	3	FACETS	0.883	0.758	1	0.442	0.379	0.51	CLONAL	1	TRUE	1	0.342182338782517	3		206	434	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	144	974	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.133583146130997	4	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	2	0.21478160293888	4		974	780	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0029824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	100	599	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.21478160293888	1	FACETS	0.83	0.74	0.927	0.83	0.74	0.927	CLONAL	1	TRUE	0	0.21478160293888	1		599	1001	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0029826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	113	785	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.220255345166039	4	FACETS	0.894	0.814	0.978	1	0.974	1	CLONAL	4	TRUE	1	0.220255345166039	4		785	350	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0029826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	105	409	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.220255345166039	3	FACETS	1	0.948	1	1	0.986	1	CLONAL	3	TRUE	1	0.220255345166039	3		409	330	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130342	11130342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	35	555	1	ENST00000358026.2:c.2581G>A	p.Glu861Lys	p.E861K	ENST00000358026	NM_001128849.1	861	Gag/Aag	18/36	0.220255345166039	2	FACETS	0.89	0.731	1	0.445	0.365	0.534	CLONAL	1	TRUE	0	0.220255345166039	2		556	357	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611089	100611089	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	30	606	0	ENST00000308731.7:c.1517G>T	p.Cys506Phe	p.C506F	ENST00000308731	NM_000061.2	506	tGt/tTt	15/19	1	2	FACETS	0.851	0.687	1	0.851	0.687	1	CLONAL	1	TRUE	1	0.220255345166039	2		606	320	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589843	69589843	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1367222161	NA	P-0029826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	18	53	0	ENST00000168712.1:c.10C>A	p.Pro4Thr	p.P4T	ENST00000168712	NM_002007.2	4	Ccc/Acc	1/3	0.220255345166039	5	FACETS	1	0.835	1	0.824	0.639	1	CLONAL	3	TRUE	1	0.220255345166039	5		53	66	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738808	145738808	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367570292	NA	P-0029826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	36	739	1	ENST00000428558.2:c.2257C>T	p.Arg753Trp	p.R753W	ENST00000428558	NM_004260.3	753	Cgg/Tgg	14/22	0.220255345166039	8	FACETS	1	0.827	1	0.201	0.165	0.242	CLONAL	1	TRUE	3	0.220255345166039	8		740	539	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980488	70980488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267601982	NA	P-0029826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	33	611	0	ENST00000276594.2:c.889G>A	p.Gly297Arg	p.G297R	ENST00000276594	NM_024504.3	297	Gga/Aga	4/8	0.220255345166039	3	FACETS	0.796	0.648	0.962			1	CLONAL	1	TRUE	NA	0.220255345166039	3		611	418	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748369	162748369	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0029826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	52	264	2	ENST00000367921.3:c.2284-1G>T		p.X762_splice	ENST00000367921	NM_006182.2	762			0.220255345166039	3	FACETS	0.861	0.743	0.986	1	0.956	1	CLONAL	3	TRUE	1	0.220255345166039	3		266	203	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111520	8111520	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	30	488	0	ENST00000346208.3:c.1006C>A	p.Pro336Thr	p.P336T	ENST00000346208		336	Cct/Act	5/6	1	2	FACETS	0.887	0.717	1	0.887	0.717	1	CLONAL	1	TRUE	1	0.220255345166039	2		488	307	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154780	2154780	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	31	750	0	ENST00000434045.2:c.441G>C	p.Glu147Asp	p.E147D	ENST00000434045	NM_001127598.1	147	gaG/gaC	4/5	1	2	FACETS	0.894	0.724	1	0.894	0.724	1	CLONAL	1	TRUE	1	0.220255345166039	2		750	315	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633518	69633518	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	16	259	1	ENST00000334134.2:c.184G>A	p.Gly62Ser	p.G62S	ENST00000334134	NM_005247.2	62	Ggc/Agc	1/3	0.220255345166039	5	FACETS	1	0.772	1	0.261	0.193	0.341	CLONAL	1	TRUE	1	0.220255345166039	5		260	185	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948572	71948572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	87	606	0	ENST00000298229.2:c.3284C>T	p.Pro1095Leu	p.P1095L	ENST00000298229	NM_001567.3	1095	cCa/cTa	26/28	0.220255345166039	5	FACETS	0.88	0.784	0.982	0.66	0.588	0.736	CLONAL	3	TRUE	1	0.220255345166039	5		606	398	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912717	100912717	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	27	355	0	ENST00000325455.5:c.2605C>G	p.Arg869Gly	p.R869G	ENST00000325455	NM_001202474.3	869	Cgt/Ggt	7/8	0.220255345166039	5	FACETS	0.901	0.717	1	0.225	0.179	0.278	CLONAL	1	TRUE	1	0.220255345166039	5		355	362	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115409	115115409	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	16	486	0	ENST00000257566.3:c.917C>G	p.Thr306Ser	p.T306S	ENST00000257566	NM_016569.3	306	aCt/aGt	5/8	0.220255345166039	2	FACETS	0.498	0.367	0.653	0.249	0.183	0.327	SUBCLONAL	1	TRUE	0	0.220255345166039	2		486	292	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43738717	43738717	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	23	458	0	ENST00000382044.4:c.2908G>T	p.Asp970Tyr	p.D970Y	ENST00000382044	NM_001141980.1	970	Gat/Tat	14/28	NA	2	FACETS	0.703	0.549	0.881			1	INDETERMINATE	1	TRUE	NA	0.220255345166039	2		458	297	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945921	17945921	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	88	698	0	ENST00000458235.1:c.2018G>T	p.Gly673Val	p.G673V	ENST00000458235	NM_000215.3	673	gGg/gTg	15/24	0.220255345166039	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.220255345166039	2		698	349	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024891	31024891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	65	491	0	ENST00000375687.4:c.4376G>T	p.Ser1459Ile	p.S1459I	ENST00000375687	NM_015338.5	1459	aGc/aTc	13/13	0.220255345166039	4	FACETS	1	0.899	1	1	0.899	1	CLONAL	2	TRUE	2	0.220255345166039	4		491	348	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252854	36252875	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CTCTTCCACTTCGACCGACAAA	CTCTTCCACTTCGACCGACAAA	-	novel	NA	P-0029826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	21	307	0	ENST00000300305.3:c.487_508del	p.Phe163GlyfsTer6	p.F163Gfs*6	ENST00000300305		163	TTTGTCGGTCGAAGTGGAAGAGgg/gg	4/8	1	2	FACETS	0.805	0.621	1	0.805	0.621	1	CLONAL	1	TRUE	1	0.220255345166039	2		307	237	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817408	39817408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	18	405	0	ENST00000288319.7:c.155C>T	p.Pro52Leu	p.P52L	ENST00000288319	NM_182918.3	52	cCt/cTt	2/10	1	2	FACETS	0.79	0.596	1	0.79	0.596	1	CLONAL	1	TRUE	1	0.220255345166039	2		405	207	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670633	134670633	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	27	576	0	ENST00000398015.3:c.544G>T	p.Ala182Ser	p.A182S	ENST00000398015	NM_004441.4	182	Gcc/Tcc	3/16	1	2	FACETS	0.776	0.618	0.955	0.776	0.618	0.955	CLONAL	1	TRUE	1	0.220255345166039	2		576	316	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530998	187530998	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	41	417	0	ENST00000441802.2:c.10025C>T	p.Thr3342Ile	p.T3342I	ENST00000441802	NM_005245.3	3342	aCa/aTa	15/27	0.191423760618865	4	FACETS	1	0.948	1	0.69	0.577	0.815	CLONAL	1	TRUE	2	0.220255345166039	4		417	329	SUCCESS
APC	324	MSKCC	GRCh37	5	112177860	112177860	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	28	320	0	ENST00000257430.4:c.6569G>T	p.Gly2190Val	p.G2190V	ENST00000257430	NM_000038.5	2190	gGa/gTa	16/16	0.220255345166039	2	FACETS	1	0.854	1	0.539	0.432	0.658	CLONAL	1	TRUE	0	0.220255345166039	2		320	236	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739644	41739644	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	32	521	0	ENST00000242208.4:c.329G>T	p.Arg110Met	p.R110M	ENST00000242208	NM_002192.2	110	aGg/aTg	2/3	0.191423760618865	4	FACETS	1	0.816	1	0.502	0.408	0.608	CLONAL	1	TRUE	2	0.220255345166039	4		521	353	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104720	69104720	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	17	375	0	ENST00000288368.4:c.4564G>T	p.Gly1522Cys	p.G1522C	ENST00000288368	NM_024870.2	1522	Ggc/Tgc	37/40	0.220255345166039	3	FACETS	0.589	0.439	0.767			1	SUBCLONAL	1	TRUE	NA	0.220255345166039	3		375	291	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650523	48650523	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	28	733	0	ENST00000376670.3:c.493G>T	p.Gly165Cys	p.G165C	ENST00000376670	NM_002049.3	165	Ggc/Tgc	3/6	1	2	FACETS	0.689	0.551	0.847	0.689	0.551	0.847	SUBCLONAL	1	TRUE	1	0.220255345166039	2		733	369	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410193	63410193	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	27	552	0	ENST00000330258.3:c.2974G>C	p.Ala992Pro	p.A992P	ENST00000330258	NM_152424.3	992	Gca/Cca	2/2	1	2	FACETS	0.848	0.677	1	0.848	0.677	1	CLONAL	1	TRUE	1	0.220255345166039	2		552	289	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343504	70343504	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	45	450	0	ENST00000374080.3:c.1678G>C	p.Ala560Pro	p.A560P	ENST00000374080		560	Gct/Cct	12/45	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.220255345166039	2		450	319	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357627	70357627	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	63	716	0	ENST00000374080.3:c.5878G>C	p.Ala1960Pro	p.A1960P	ENST00000374080		1960	Gca/Cca	41/45	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.220255345166039	2		716	396	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858051	152858051	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	33	433	1	ENST00000406277.2:c.564C>A	p.His188Gln	p.H188Q	ENST00000406277	NM_152274.4	188	caC/caA	6/7	0.220255345166039	5	FACETS	1	0.93	1			1	CLONAL	1	TRUE	NA	0.220255345166039	5		434	302	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0029827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	119	436	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.223018130184517	3	FACETS	1	0.959	1	0.732	0.665	0.802	CLONAL	2	FALSE	0	0.259384119529952	3		437	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs864622237	NA	P-0029827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	193	417	0	ENST00000269305.4:c.700T>C	p.Tyr234His	p.Y234H	ENST00000269305	NM_001126112.2	234	Tac/Cac	7/11	0.226695987906884	3	FACETS	0.932	0.868	0.999	0.932	0.868	0.999	CLONAL	3	FALSE	0	0.259384119529952	3		417	601	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39708783	39708783	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	132	292	0	ENST00000361337.2:c.394G>T	p.Asp132Tyr	p.D132Y	ENST00000361337	NM_003286.2	132	Gat/Tat	6/21	0.259384119529952	4	FACETS	1	0.943	1	1	0.943	1	CLONAL	3	FALSE	1	0.259384119529952	4		292	412	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39744078	39744078	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs372925211	NA	P-0029827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	178	239	0	ENST00000361337.2:c.1706A>G	p.Asn569Ser	p.N569S	ENST00000361337	NM_003286.2	569	aAt/aGt	16/21	0.259384119529952	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	FALSE	1	0.259384119529952	4		239	522	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974702	21974702	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	69	284	0	ENST00000304494.5:c.125A>T	p.Asn42Ile	p.N42I	ENST00000304494	NM_000077.4	42	aAt/aTt	1/3	0.191076655357182	2	FACETS	0.799	0.701	0.903	0.799	0.701	0.903	CLONAL	2	FALSE	0	0.259384119529952	2		284	333	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524948	8524948	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	83	225	1	ENST00000356435.5:c.656C>A	p.Ala219Asp	p.A219D	ENST00000356435		219	gCt/gAt	7/35	0.191076655357182	2	FACETS	0.842	0.748	0.941	0.842	0.748	0.941	CLONAL	2	FALSE	0	0.259384119529952	2		226	380	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398262	25398262	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913538	NA	P-0029828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	120	339	0	ENST00000311936.3:c.57G>C	p.Leu19Phe	p.L19F	ENST00000311936	NM_004985.3	19	ttG/ttC	2/5	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.31375363287596	2		339	690	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0029828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	69	276	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	1	2	FACETS	0.816	0.712	0.929	0.816	0.712	0.929	CLONAL	1	TRUE	1	0.31375363287596	2		276	539	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0029828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	95	199	0	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	0.31375363287596	2	FACETS	0.952	0.857	1	0.952	0.857	1	CLONAL	2	TRUE	0	0.31375363287596	2		199	318	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457279	67457279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	70	484	0	ENST00000327367.4:c.253C>T	p.His85Tyr	p.H85Y	ENST00000327367	NM_005902.3	85	Cat/Tat	2/9	1	2	FACETS	0.572	0.498	0.652	0.572	0.498	0.652	SUBCLONAL	1	TRUE	1	0.31375363287596	2		484	780	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473654	67473654	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	116	411	0	ENST00000327367.4:c.734G>A	p.Gly245Glu	p.G245E	ENST00000327367	NM_005902.3	245	gGg/gAg	6/9	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.31375363287596	2		411	660	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479756	67479756	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	58	413	0	ENST00000327367.4:c.1063T>C	p.Ser355Pro	p.S355P	ENST00000327367	NM_005902.3	355	Tcg/Ccg	8/9	1	2	FACETS	0.545	0.468	0.63	0.545	0.468	0.63	SUBCLONAL	1	TRUE	1	0.31375363287596	2		413	678	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639657	3639657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1394177026	NA	P-0029828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	176	651	1	ENST00000294008.3:c.3982G>A	p.Val1328Ile	p.V1328I	ENST00000294008	NM_032444.2	1328	Gtc/Atc	12/15	1	2	FACETS	0.926	0.851	1	0.926	0.851	1	CLONAL	1	TRUE	1	0.31375363287596	2		652	1212	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368200	45368200	+	stop_lost	Nonstop_Mutation	SNP	A	A	T	novel	NA	P-0029828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	64	224	0	ENST00000262160.6:c.1402T>A	p.Ter468LysextTer8	p.*468Kext*8	ENST00000262160	NM_005901.5	468	Taa/Aaa	11/11	0.284177380468598	1	FACETS	0.94	0.818	1	0.94	0.818	1	CLONAL	1	TRUE	0	0.31375363287596	1		224	366	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115871	8115872	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0029831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	156	431	0	ENST00000346208.3:c.1219_1220del	p.Ser407AlafsTer99	p.S407Afs*99	ENST00000346208		406	aTC/a	6/6	0.514939161920784	3	FACETS	0.885	0.81	0.962	0.442	0.405	0.481	CLONAL	1	TRUE	1	0.512802820831322	3		431	864	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78435650	78435650	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1218224822	NA	P-0029831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	166	479	0	ENST00000370768.2:c.170A>G	p.Asp57Gly	p.D57G	ENST00000370768	NM_003902.3	57	gAc/gGc	2/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.512802820831322	2		479	626	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227707	36227707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1454808380	NA	P-0029831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	228	590	0	ENST00000222270.7:c.7276G>A	p.Val2426Ile	p.V2426I	ENST00000222270	NM_014727.1	2426	Gtt/Att	31/37	0.514939161920784	3	FACETS	1	0.984	1	0.587	0.548	0.628	CLONAL	1	TRUE	1	0.512802820831322	3		590	951	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909677	50909678	+	missense_variant	Missense_Mutation	DNP	AG	AG	TT	novel	NA	P-0029831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	226	663	1	ENST00000440232.2:c.1397_1398delinsTT	p.Glu466Val	p.E466V	ENST00000440232	NM_002691.3	466	gAG/gTT	12/27	0.514939161920784	3	FACETS	1	0.977	1	0.553	0.515	0.592	CLONAL	1	TRUE	1	0.512802820831322	3		664	1001	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011150	12011150	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	86	273	0	ENST00000353533.5:c.557A>G	p.Asp186Gly	p.D186G	ENST00000353533	NM_003010.3	186	gAt/gGt	5/11	NA	2	FACETS	0.988	0.906	1			1	INDETERMINATE	2	FALSE	NA	0.596426862832808	2		273	146	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0029833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	160	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.499991629073177	4	FACETS	0.989	0.916	1	0.989	0.916	1	CLONAL	2	FALSE	2	0.596426862832808	4		511	433	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50358670	50358670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	44	213	0	ENST00000331340.3:c.13G>A	p.Glu5Lys	p.E5K	ENST00000331340	NM_006060.4	5	Gag/Aag	2/8	0.596426862832808	3	FACETS	0.948	0.805	1	0.474	0.402	0.552	CLONAL	1	FALSE	1	0.596426862832808	3		213	202	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28880827	28880827	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368266056	NA	P-0029833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	114	454	0	ENST00000282397.4:c.3803C>T	p.Ser1268Leu	p.S1268L	ENST00000282397	NM_002019.4	1268	tCg/tTg	29/30	0.171946901174993	2	FACETS	0.659	0.595	0.726	0.33	0.297	0.363	INDETERMINATE	1	FALSE	0	0.596426862832808	2		454	580	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111496	8111497	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0029833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	350	548	0	ENST00000346208.3:c.984dup	p.Arg329GlufsTer23	p.R329Efs*23	ENST00000346208		328	tgg/tGgg	5/6	0.578884768103657	4	FACETS	0.82	0.777	0.863	0.546	0.518	0.576	CLONAL	2	FALSE	1	0.596426862832808	4		548	1143	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640691	3640694	+	frameshift_variant	Frame_Shift_Del	DEL	TAAT	TAAT	-	novel	NA	P-0029833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	339	576	0	ENST00000294008.3:c.2945_2948del	p.Asp982AlafsTer18	p.D982Afs*18	ENST00000294008	NM_032444.2	982	gATTAc/gc	12/15	0.596426862832808	5	FACETS	1	0.964	1	0.681	0.645	0.718	CLONAL	2	FALSE	2	0.596426862832808	5		576	1054	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40368072	40368072	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555548678	NA	P-0029833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	389	505	4	ENST00000293328.3:c.1433C>T	p.Ala478Val	p.A478V	ENST00000293328	NM_012448.3	478	gCg/gTg	12/19	0.596279882264435	3	FACETS	0.952	0.909	0.996	0.952	0.909	0.996	CLONAL	2	FALSE	1	0.596426862832808	3		509	889	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003260	143003260	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	65	447	0	ENST00000262992.4:c.2566G>A	p.Glu856Lys	p.E856K	ENST00000262992	NM_001101669.1	856	Gaa/Aaa	23/24	0.596279882264435	3	FACETS	0.922	0.806	1	0.461	0.403	0.523	CLONAL	1	FALSE	1	0.596426862832808	3		447	307	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0029834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	404	485	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.51333988496448	5	FACETS	0.893	0.856	0.93	0.893	0.856	0.93	CLONAL	4	TRUE	1	0.51333988496448	5		485	780	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0029834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	94	439	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.496415432000566	3	FACETS	0.983	0.879	1	0.492	0.439	0.547	CLONAL	1	TRUE	1	0.51333988496448	3		439	468	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384726	17384726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368554117	NA	P-0029834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	186	636	0	ENST00000359435.4:c.358G>A	p.Ala120Thr	p.A120T	ENST00000359435	NM_001033549.1	120	Gcc/Acc	4/9	0.496415432000566	3	FACETS	0.89	0.822	0.962	0.445	0.411	0.481	CLONAL	1	TRUE	1	0.51333988496448	3		636	1023	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578432	7578445	+	frameshift_variant	Frame_Shift_Del	DEL	TGACTGCTTGTAGA	TGACTGCTTGTAGA	-	novel	NA	P-0029834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	396	613	0	ENST00000269305.4:c.485_498del	p.Ile162ThrfsTer14	p.I162Tfs*14	ENST00000269305	NM_001126112.2	162	aTCTACAAGCAGTCA/a	5/11	0.51333988496448	2	FACETS	0.905	0.866	0.945	0.905	0.866	0.945	CLONAL	2	TRUE	0	0.51333988496448	2		613	852	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45422921	45422922	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	101	298	0	ENST00000262160.6:c.206dup	p.Asn69LysfsTer3	p.N69Kfs*3	ENST00000262160	NM_005901.5	69	aac/aaAc	2/11	0.51333988496448	1	FACETS	0.932	0.843	1	0.932	0.843	1	CLONAL	1	TRUE	0	0.51333988496448	1		298	314	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1650241	1650241	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	188	578	0	ENST00000344749.5:c.7C>T	p.Gln3Ter	p.Q3*	ENST00000344749	NM_001136139.2	3	Cag/Tag	2/19	0.496415432000566	3	FACETS	0.883	0.815	0.953	0.441	0.407	0.477	CLONAL	1	TRUE	1	0.51333988496448	3		578	1043	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5239014	5239015	+	missense_variant	Missense_Mutation	DNP	CC	CC	GG	novel	NA	P-0029834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	192	678	2	ENST00000357368.4:c.1764_1765inv	p.Glu589Gln	p.E589Q	ENST00000357368	NM_002850.3	588	acGGag/acCCag	13/38	0.496415432000566	3	FACETS	0.888	0.82	0.958	0.444	0.41	0.479	CLONAL	1	TRUE	1	0.51333988496448	3		680	1059	SUCCESS
APC	324	MSKCC	GRCh37	5	112175684	112175685	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0029834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	146	265	0	ENST00000257430.4:c.4394_4395insCG	p.Gly1466ValfsTer8	p.G1466Vfs*8	ENST00000257430	NM_000038.5	1465	agt/aGCgt	16/16	0.496415432000566	3	FACETS	0.843	0.777	0.911	0.843	0.777	0.911	CLONAL	2	TRUE	1	0.51333988496448	3		265	424	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121047	3121047	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	79	582	0	ENST00000078429.4:c.950A>G	p.Asn317Ser	p.N317S	ENST00000078429	NM_002067.2	317	aAc/aGc	7/7	1	2	FACETS	0.871	0.773	0.975	0.871	0.773	0.975	CLONAL	1	TRUE	1	0.552892251387057	2		582	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578179	7578182	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CAGG	CAGG	-	novel	NA	P-0029835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	224	610	2	ENST00000269305.4:c.667_670del	p.Pro223ArgfsTer23	p.P223Rfs*23	ENST00000269305	NM_001126112.2	223	CCTGag/ag	6/11	NA	2	FACETS	0.858	0.809	0.908			1	INDETERMINATE	2	TRUE	NA	0.552892251387057	2		612	472	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645666	12645666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	36	178	0	ENST00000251849.4:c.803C>T	p.Thr268Ile	p.T268I	ENST00000251849	NM_002880.3	268	aCc/aTc	7/17	0.485509518595991	4	FACETS	0.958	0.795	1	0.479	0.397	0.569	CLONAL	1	TRUE	2	0.552892251387057	4		178	211	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467812	50467812	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs937630364	NA	P-0029835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	40	398	0	ENST00000331340.3:c.1047G>C	p.Gln349His	p.Q349H	ENST00000331340	NM_006060.4	349	caG/caC	8/8	0.552892251387057	4	FACETS	0.633	0.527	0.75	0.316	0.263	0.375	SUBCLONAL	1	TRUE	2	0.552892251387057	4		398	355	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913237	NA	P-0029836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	141	574	1	ENST00000369535.4:c.35G>T	p.Gly12Val	p.G12V	ENST00000369535	NM_002524.4	12	gGt/gTt	2/7	0.773888235121722	1	FACETS	0.824	0.767	0.881	0.824	0.767	0.881	CLONAL	1	TRUE	0	0.773888235121722	1		575	271	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836786	151836787	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTTG	novel	NA	P-0029836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	160	385	0	ENST00000262189.6:c.14430_14433dup	p.Arg4812GlnfsTer8	p.R4812Qfs*8	ENST00000262189	NM_170606.2	4811	-/CAAC	56/59	1	2	FACETS	0.839	0.775	0.904	0.839	0.775	0.904	CLONAL	1	TRUE	1	0.773888235121722	2		385	493	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728619	190728619	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	209	502	0	ENST00000441310.2:c.2007A>T	p.Lys669Asn	p.K669N	ENST00000441310	NM_000534.4	669	aaA/aaT	10/13	0.12016124882825	5	FACETS	1	0.986	1	0.785	0.737	0.834	INDETERMINATE	2	TRUE	2	0.810631971749037	5		502	485	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204622	128204623	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1559986946	NA	P-0029838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	155	577	0	ENST00000341105.2:c.818dup	p.Pro274ThrfsTer8	p.P274Tfs*8	ENST00000341105	NM_032638.4	273	gga/ggGa	3/6	0.12016124882825	5	FACETS	0.954	0.882	1	0.636	0.588	0.686	INDETERMINATE	2	TRUE	2	0.810631971749037	5		577	444	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0029839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	116	615	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.748	0.679	0.82	0.748	0.679	0.82	SUBCLONAL	1	TRUE	1	0.692404936115897	2		615	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0029839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	181	507	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.568847550630518	1	FACETS	0.775	0.723	0.828	0.775	0.723	0.828	SUBCLONAL	1	TRUE	0	0.692404936115897	1		507	441	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411900	63411900	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	92	799	0	ENST00000330258.3:c.1267C>A	p.Leu423Met	p.L423M	ENST00000330258	NM_152424.3	423	Ctg/Atg	2/2	0.509215799004531	1	FACETS	0.256	0.227	0.287	0.256	0.227	0.287	SUBCLONAL	1	TRUE	0	0.692404936115897	1		799	679	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508264	38508285	+	frameshift_variant	Frame_Shift_Del	DEL	TGCGCAAAGCGCACCAGGAAAC	TGCGCAAAGCGCACCAGGAAAC	-	novel	NA	P-0029839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	69	488	0	ENST00000254066.5:c.572_593del	p.Val191AlafsTer72	p.V191Afs*72	ENST00000254066	NM_000964.3	191	gTGCGCAAAGCGCACCAGGAAACc/gc	5/9	0.622310167875913	1	FACETS	0.314	0.274	0.357	0.314	0.274	0.357	SUBCLONAL	1	TRUE	0	0.692404936115897	1		488	415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0029840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	349	535	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.545771366680093	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.545771366680093	2		535	617	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531031	187531031	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	144	390	0	ENST00000441802.2:c.9992del	p.Asn3331IlefsTer45	p.N3331Ifs*45	ENST00000441802	NM_005245.3	3331	aAt/at	15/27	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.545771366680093	2		390	507	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679486	30679486	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	143	443	0	ENST00000376406.3:c.2086C>G	p.Leu696Val	p.L696V	ENST00000376406	NM_014641.2	696	Cta/Gta	6/15	0.545771366680093	4	FACETS	0.941	0.858	1	0.47	0.429	0.514	CLONAL	1	TRUE	2	0.545771366680093	4		443	861	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061185	38061185	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1449268552	NA	P-0029842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	193	360	0	ENST00000250448.2:c.804C>A	p.Cys268Ter	p.C268*	ENST00000250448	NM_004496.3	268	tgC/tgA	2/2	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.718298828559157	2		360	430	SUCCESS
CBL	867	MSKCC	GRCh37	11	119145612	119145612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	13	287	0	ENST00000264033.4:c.818C>T	p.Thr273Met	p.T273M	ENST00000264033	NM_005188.3	273	aCg/aTg	5/16	0.718298828559157	1	FACETS	0.092	0.065	0.125	0.092	0.065	0.125	SUBCLONAL	1	TRUE	0	0.718298828559157	1		287	251	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627736	37627736	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	188	606	0	ENST00000447079.4:c.1651T>A	p.Leu551Met	p.L551M	ENST00000447079	NM_015083.1	551	Ttg/Atg	2/14	0.242670216326798	3	FACETS	1	0.979	1	0.571	0.53	0.613	INDETERMINATE	1	TRUE	1	0.718298828559157	3		606	623	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543906	212543906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	107	298	1	ENST00000342788.4:c.1493C>T	p.Ala498Val	p.A498V	ENST00000342788	NM_005235.2	498	gCt/gTt	13/28	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.718298828559157	2		299	270	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332801	70332801	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	143	454	0	ENST00000373644.4:c.706A>G	p.Thr236Ala	p.T236A	ENST00000373644	NM_030625.2	236	Acc/Gcc	2/12	0.564234387304526	4	FACETS	0.945	0.871	1			1	CLONAL	2	FALSE	NA	0.639768389631534	4		454	388	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720828	89720828	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	148	312	1	ENST00000371953.3:c.981del	p.Ala328GlnfsTer16	p.A328Qfs*16	ENST00000371953	NM_000314.4	327	Aaa/aa	8/9	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	2	FALSE	NA	0.639768389631534	2		313	221	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961228	1961228	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	54	378	0	ENST00000382891.5:c.3016T>G	p.Tyr1006Asp	p.Y1006D	ENST00000382891	NM_133335.3	1006	Tac/Gac	17/22	0.220745186520475	6	FACETS	1	0.934	1			1	INDETERMINATE	1	FALSE	NA	0.639768389631534	6		378	333	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540752	187540752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	41	267	1	ENST00000441802.2:c.6988C>T	p.His2330Tyr	p.H2330Y	ENST00000441802	NM_005245.3	2330	Cat/Tat	10/27	0.171925990962334	5	FACETS	1	0.873	1			1	INDETERMINATE	1	FALSE	NA	0.639768389631534	5		268	240	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540781	187541624	+	frameshift_variant	Frame_Shift_Del	DEL	TATGAGATTCCTCTATTTGGTTCTGAATCAGAATCGGTGGCTCTAACTTGAACAACAGACGTTCCAATTACAGATGCCTCAGACAGGGTCACCGCATAAGACTGCTGAGCAAACACAGGAGGGTTATCATTGATGTCGTCTACTATGATGTCCACAAATACTTCAGCATGAGCGCCCGTCAAGGAGTCAGTTGCGCGTATGCTCAGCTTATATGCCGGGTGGGCCTCAAAGTCCAGAGGAGCTATGACATTGATAACTCCAGTATTGAAGTTAATAGTGAACTGGCTGAAAGGGTCTCCGTCTGTGATGCTGTAGAACACTTTCAGGCCTTCCGGGCTGTTAGCCTGCACGTGGACCACAGGGCTGTGCACCTGGATGCTCTCTGCAATCTCTGCACTGTAGAAAGGTTTTTCAAACACAGGCATGGCTTTATTCATGACAGTGATCGGAACGATAACTTCCGCTGAAAAGGCCGGGTTCCCTCCATCTTTTGCAACCACTGTAACAAGATATTCTTTATTTAAGGTGTCAAGCTCAAATTGCTTTTTCAGTGAAATTTCACCCAAGGGTCCAATTTGAAAGTGTTCATGATGTTCCTTGAGGTAGTAATGCACTTCCCCGTTTCTGCCACTGTCTCTGTCTACAGCAGTGACATAGCGAATGACATGGCCCACCTCAGTGTCCACTTTAACAACGGCGTAGTAGGGAAGGTTGACAAACACCGGCGCATTATCATTTTGGTCTTCTACAATGACCTTCACGACAACGTGGGCCACTGCAGAAGGCTTATGTTCCTCTGTCACTTCTACAACCACATCAAACGCCTCCTGCTGCTCACGATCGA	TATGAGATTCCTCTATTTGGTTCTGAATCAGAATCGGTGGCTCTAACTTGAACAACAGACGTTCCAATTACAGATGCCTCAGACAGGGTCACCGCATAAGACTGCTGAGCAAACACAGGAGGGTTATCATTGATGTCGTCTACTATGATGTCCACAAATACTTCAGCATGAGCGCCCGTCAAGGAGTCAGTTGCGCGTATGCTCAGCTTATATGCCGGGTGGGCCTCAAAGTCCAGAGGAGCTATGACATTGATAACTCCAGTATTGAAGTTAATAGTGAACTGGCTGAAAGGGTCTCCGTCTGTGATGCTGTAGAACACTTTCAGGCCTTCCGGGCTGTTAGCCTGCACGTGGACCACAGGGCTGTGCACCTGGATGCTCTCTGCAATCTCTGCACTGTAGAAAGGTTTTTCAAACACAGGCATGGCTTTATTCATGACAGTGATCGGAACGATAACTTCCGCTGAAAAGGCCGGGTTCCCTCCATCTTTTGCAACCACTGTAACAAGATATTCTTTATTTAAGGTGTCAAGCTCAAATTGCTTTTTCAGTGAAATTTCACCCAAGGGTCCAATTTGAAAGTGTTCATGATGTTCCTTGAGGTAGTAATGCACTTCCCCGTTTCTGCCACTGTCTCTGTCTACAGCAGTGACATAGCGAATGACATGGCCCACCTCAGTGTCCACTTTAACAACGGCGTAGTAGGGAAGGTTGACAAACACCGGCGCATTATCATTTTGGTCTTCTACAATGACCTTCACGACAACGTGGGCCACTGCAGAAGGCTTATGTTCCTCTGTCACTTCTACAACCACATCAAACGCCTCCTGCTGCTCACGATCGA	-	novel	NA	P-0029843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	45	254	0	ENST00000441802.2:c.6116_6959del	p.Phe2039SerfsTer16	p.F2039Sfs*16	ENST00000441802	NM_005245.3	2039	tTCGATCGTGAGCAGCAGGAGGCGTTTGATGTGGTTGTAGAAGTGACAGAGGAACATAAGCCTTCTGCAGTGGCCCACGTTGTCGTGAAGGTCATTGTAGAAGACCAAAATGATAATGCGCCGGTGTTTGTCAACCTTCCCTACTACGCCGTTGTTAAAGTGGACACTGAGGTGGGCCATGTCATTCGCTATGTCACTGCTGTAGACAGAGACAGTGGCAGAAACGGGGAAGTGCATTACTACCTCAAGGAACATCATGAACACTTTCAAATTGGACCCTTGGGTGAAATTTCACTGAAAAAGCAATTTGAGCTTGACACCTTAAATAAAGAATATCTTGTTACAGTGGTTGCAAAAGATGGAGGGAACCCGGCCTTTTCAGCGGAAGTTATCGTTCCGATCACTGTCATGAATAAAGCCATGCCTGTGTTTGAAAAACCTTTCTACAGTGCAGAGATTGCAGAGAGCATCCAGGTGCACAGCCCTGTGGTCCACGTGCAGGCTAACAGCCCGGAAGGCCTGAAAGTGTTCTACAGCATCACAGACGGAGACCCTTTCAGCCAGTTCACTATTAACTTCAATACTGGAGTTATCAATGTCATAGCTCCTCTGGACTTTGAGGCCCACCCGGCATATAAGCTGAGCATACGCGCAACTGACTCCTTGACGGGCGCTCATGCTGAAGTATTTGTGGACATCATAGTAGACGACATCAATGATAACCCTCCTGTGTTTGCTCAGCAGTCTTATGCGGTGACCCTGTCTGAGGCATCTGTAATTGGAACGTCTGTTGTTCAAGTTAGAGCCACCGATTCTGATTCAGAACCAAATAGAGGAATCTCATAc/tc	10/27	0.171925990962334	5	FACETS	1	0.937	1			1	INDETERMINATE	1	FALSE	NA	0.639768389631534	5		254	227	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997439	149997440	+	missense_variant	Missense_Mutation	DNP	TG	TG	AT	novel	NA	P-0029843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	65	504	2	ENST00000253339.5:c.2839_2840delinsAT	p.Gln947Ile	p.Q947I	ENST00000253339		947	CAa/ATa	6/7	0.623083656052478	4	FACETS	0.666	0.579	0.761	0.222	0.193	0.254	SUBCLONAL	1	FALSE	1	0.639768389631534	4		506	500	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0029845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	230	558	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.247836843616004	3	FACETS	1	0.986	1			1	CLONAL	6	FALSE	NA	0.252136247435381	3		558	320	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0029845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	9	564	1	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	1	2	FACETS	0.159	0.104	0.229	0.159	0.104	0.229	SUBCLONAL	1	FALSE	1	0.252136247435381	2		565	450	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862204	68862205	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0029845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	107	515	0	ENST00000261769.5:c.2293_2294dup	p.Gln765HisfsTer6	p.Q765Hfs*6	ENST00000261769	NM_004360.3	764	-/CA	14/16	0.252136247435381	0	FACETS	0.818	0.755	0.88			1	CLONAL	4	FALSE	0	0.252136247435381	0		515	194	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244613	41244613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80356970	NA	P-0029845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	99	676	4	ENST00000357654.3:c.2935C>T	p.Arg979Cys	p.R979C	ENST00000357654	NM_007294.3	979	Cgt/Tgt	10/23	1	2	FACETS	0.973	0.882	1	1	0.99	1	CLONAL	3	FALSE	1	0.252136247435381	2		680	269	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178217	56178217	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0029845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	90	296	2	ENST00000399503.3:c.3190A>T	p.Arg1064Ter	p.R1064*	ENST00000399503	NM_005921.1	1064	Aga/Tga	14/20	0.218625151369031	0	FACETS	0.872	0.802	0.941			1	CLONAL	4	FALSE	0	0.252136247435381	0		298	153	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554840	187554840	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	139	282	0	ENST00000441802.2:c.4321C>T	p.Gln1441Ter	p.Q1441*	ENST00000441802	NM_005245.3	1441	Cag/Tag	7/27	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	2	TRUE	NA	0.373283318749876	2		282	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0029848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	285	536	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.370675721648358	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.373283318749876	2		536	647	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022277	31022277	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1486082302	NA	P-0029848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	75	325	0	ENST00000375687.4:c.1762C>T	p.Gln588Ter	p.Q588*	ENST00000375687	NM_015338.5	588	Cag/Tag	13/13	1	2	FACETS	0.825	0.725	0.932	0.825	0.725	0.932	CLONAL	1	TRUE	1	0.373283318749876	2		325	487	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0029848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	368	459	0				ENST00000310581	NM_198253.2	-/1132			0.373283318749876	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	1	0.373283318749876	4		459	839	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282512	115282512	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0029848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	164	278	0	ENST00000438362.2:c.139-1G>C		p.X47_splice	ENST00000438362	NM_001242891.1	47			0.370675721648358	2	FACETS	0.923	0.855	0.993	0.923	0.855	0.993	CLONAL	2	TRUE	0	0.373283318749876	2		278	476	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631144	69631144	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	548	655	1	ENST00000334134.2:c.268G>T	p.Gly90Cys	p.G90C	ENST00000334134	NM_005247.2	90	Ggt/Tgt	2/3	0.373283318749876	4	FACETS	1	0.993	1			1	CLONAL	3	TRUE	NA	0.373283318749876	4		656	1187	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900318	3900318	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	140	493	0	ENST00000262367.5:c.778C>T	p.Gln260Ter	p.Q260*	ENST00000262367	NM_004380.2	260	Cag/Tag	2/31	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.373283318749876	2		493	703	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274705	198274705	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	87	323	0	ENST00000335508.6:c.693A>C	p.Arg231Ser	p.R231S	ENST00000335508	NM_012433.2	231	agA/agC	7/25	1	2	FACETS	0.903	0.802	1	0.903	0.802	1	CLONAL	1	TRUE	1	0.373283318749876	2		323	516	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136256	202136256	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	116	440	0	ENST00000358485.4:c.500T>G	p.Ile167Ser	p.I167S	ENST00000358485	NM_001080125.1	167	aTt/aGt	3/9	1	2	FACETS	0.884	0.798	0.975	0.884	0.798	0.975	CLONAL	1	TRUE	1	0.373283318749876	2		440	703	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729879	30729880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	86	234	0	ENST00000295754.5:c.1404dup	p.Asp469ArgfsTer3	p.D469Rfs*3	ENST00000295754	NM_003242.5	467	gta/gtAa	6/7	0.373283318749876	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.373283318749876	1		234	345	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936067	49936067	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201544530	NA	P-0029848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	195	723	2	ENST00000296474.3:c.1603C>T	p.Arg535Cys	p.R535C	ENST00000296474	NM_002447.2	535	Cgt/Tgt	4/20	0.373283318749876	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.373283318749876	1		725	803	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240805	53240805	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	112	236	1	ENST00000375401.3:c.1275C>A	p.Phe425Leu	p.F425L	ENST00000375401	NM_004187.3	425	ttC/ttA	10/26	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.373283318749876	1		237	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0029849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	174	428	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.214407038432744	2	FACETS	0.778	0.718	0.84	0.778	0.718	0.84	SUBCLONAL	2	TRUE	0	0.311149096927745	2		428	719	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246457	46246457	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	39	242	0	ENST00000334344.6:c.4551G>C	p.Arg1517Ser	p.R1517S	ENST00000334344	NM_152641.2	1517	agG/agC	15/21	0.195564634550874	3	FACETS	0.685	0.568	0.815	0.342	0.284	0.408	SUBCLONAL	1	TRUE	1	0.311149096927745	3		242	423	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674212	86674212	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0029849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	128	202	0	ENST00000274376.6:c.2345-1G>C		p.X782_splice	ENST00000274376	NM_002890.2	782			0.227160114017025	3	FACETS	1	0.973	1	0.773	0.707	0.841	CLONAL	2	TRUE	0	0.311149096927745	3		202	410	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061240	38061240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	147	521	1	ENST00000250448.2:c.749C>T	p.Ser250Phe	p.S250F	ENST00000250448	NM_004496.3	250	tCc/tTc	2/2	0.338266985473404	1	FACETS	0.422	0.386	0.46	0.422	0.386	0.46	INDETERMINATE	1	TRUE	0	0.641135207354305	1		522	738	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856025	68856026	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	295	409	0	ENST00000261769.5:c.1834dup	p.Ile612AsnfsTer5	p.I612Nfs*5	ENST00000261769	NM_004360.3	611	-/A	12/16	0.641135207354305	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.641135207354305	1		409	575	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460410	8460410	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0029850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	45	177	0	ENST00000356435.5:c.3875+1G>T		p.X1292_splice	ENST00000356435		1292			1	2	FACETS	0.386	0.325	0.452	0.386	0.325	0.452	SUBCLONAL	1	TRUE	1	0.641135207354305	2		177	364	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0029851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	84	436	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.176304828624864	3	FACETS	0.978	0.863	1	0.489	0.431	0.551	CLONAL	1	TRUE	1	0.246995173772899	3		437	781	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1131691023	NA	P-0029851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	118	620	0	ENST00000269305.4:c.470T>A	p.Val157Asp	p.V157D	ENST00000269305	NM_001126112.2	157	gTc/gAc	5/11	0.246995173772899	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.246995173772899	1		620	782	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604656	48604656	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	48	237	0	ENST00000342988.3:c.1478A>G	p.Asp493Gly	p.D493G	ENST00000342988	NM_005359.5	493	gAt/gGt	12/12	1	2	FACETS	0.946	0.801	1	0.946	0.801	1	CLONAL	1	TRUE	1	0.246995173772899	2		237	411	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019604	42019605	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	TT	novel	NA	P-0029851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	64	317	1	ENST00000219905.7:c.3657_3657+1delinsTT		p.X1219_splice	ENST00000219905	NM_001164273.1	1219		10/24	1	2	FACETS	0.922	0.799	1	0.922	0.799	1	CLONAL	1	TRUE	1	0.246995173772899	2		318	562	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0029852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	78	172	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.536418295561562	2		172	284	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715621	30715621	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	107	193	0	ENST00000295754.5:c.1279C>G	p.Pro427Ala	p.P427A	ENST00000295754	NM_003242.5	427	Cca/Gca	5/7	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.536418295561562	2		193	333	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214613	5214613	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	226	615	0	ENST00000357368.4:c.4453G>T	p.Ala1485Ser	p.A1485S	ENST00000357368	NM_002850.3	1485	Gcg/Tcg	29/38	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.536418295561562	2		615	796	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0029853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	593	691	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.636937980269504	3	FACETS	0.963	0.936	0.989	0.963	0.936	0.989	CLONAL	3	TRUE	0	0.636937980269504	3		691	850	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0029853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	322	379	0	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	0.636937980269504	2	FACETS	0.98	0.939	1	0.98	0.939	1	CLONAL	2	TRUE	0	0.636937980269504	2		379	516	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115595	108115595	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs769166447	NA	P-0029853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	116	387	0	ENST00000278616.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000278616	NM_000051.3	248	cGa/cTa	7/63	0.636937980269504	2	FACETS	0.987	0.899	1	0.494	0.449	0.539	CLONAL	1	TRUE	0	0.636937980269504	2		387	369	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772422	56772422	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2448	460	464	0	ENST00000337432.4:c.276G>C	p.Glu92Asp	p.E92D	ENST00000337432	NM_058216.2	92	gaG/gaC	2/9	0.636937980269504	13	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.636937980269504	13		464	2908	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989515	212989515	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	116	309	0	ENST00000342788.4:c.196A>G	p.Thr66Ala	p.T66A	ENST00000342788	NM_005235.2	66	Acc/Gcc	2/28	0.201693203412746	3	FACETS	1	0.963	1	0.373	0.339	0.409	INDETERMINATE	1	TRUE	0	0.636937980269504	3		309	429	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524698	106524698	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	83	224	0	ENST00000359195.3:c.2859G>C	p.Met953Ile	p.M953I	ENST00000359195	NM_002649.2	953	atG/atC	9/11	0.633645613586383	3	FACETS	0.868	0.77	0.971	0.434	0.385	0.486	CLONAL	1	TRUE	1	0.636937980269504	3		224	396	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0029868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	138	778	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.400210416747353	2		778	631	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0029868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	138	493	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.400210416747353	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.400210416747353	1		493	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0029869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	200	561	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.479584647468588	1	FACETS	0.942	0.877	1	0.942	0.877	1	CLONAL	1	TRUE	0	0.479584647468588	1		561	673	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727575	66727575	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	20	231	0	ENST00000307102.5:c.291G>T	p.Lys97Asn	p.K97N	ENST00000307102	NM_002755.3	97	aaG/aaT	2/11	0.479584647468588	1	FACETS	0.255	0.195	0.324	0.255	0.195	0.324	SUBCLONAL	1	TRUE	0	0.479584647468588	1		231	249	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651461	52651462	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGGTC	novel	NA	P-0029869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	41	471	0	ENST00000394830.3:c.1630_1634dup	p.Phe546ThrfsTer25	p.F546Tfs*25	ENST00000394830	NM_018313.4	545	cta/ctGACCTa	15/30	1	2	FACETS	0.302	0.251	0.359	0.302	0.251	0.359	SUBCLONAL	1	TRUE	1	0.479584647468588	2		471	566	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	34	974	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.895	0.732	1	0.895	0.732	1	CLONAL	1	TRUE	1	0.20587217812603	2		974	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0029870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	39	559	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.761	0.63	0.907	0.761	0.63	0.907	CLONAL	1	TRUE	1	0.20587217812603	2		559	498	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543828	212543828	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371593463	NA	P-0029870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	35	329	1	ENST00000342788.4:c.1571G>A	p.Arg524His	p.R524H	ENST00000342788	NM_005235.2	524	cGc/cAc	13/28	1	2	FACETS	0.746	0.611	0.897	0.746	0.611	0.897	SUBCLONAL	1	TRUE	1	0.20587217812603	2		330	456	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482874	67482874	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	rs1555414506	NA	P-0029870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	31	336	0	ENST00000327367.4:c.1278G>C	p.Ter426TyrextTer6	p.*426Yext*6	ENST00000327367	NM_005902.3	426	taG/taC	9/9	0.20587217812603	1	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	0	0.20587217812603	1		336	248	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149778	202149778	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	52	449	0	ENST00000358485.4:c.1219C>G	p.Leu407Val	p.L407V	ENST00000358485	NM_001080125.1	407	Ctt/Gtt	8/9	1	2	FACETS	0.869	0.74	1	0.869	0.74	1	CLONAL	1	TRUE	1	0.20587217812603	2		449	581	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2105497	2105514	+	inframe_deletion	In_Frame_Del	DEL	CGAGTACATCGCAAGGAT	CGAGTACATCGCAAGGAT	-	novel	NA	P-0029871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	93	334	0	ENST00000219476.3:c.576_593del	p.Asp192_Met198delinsGlu	p.D192_M198delinsE	ENST00000219476	NM_000548.3	192	gaCGAGTACATCGCAAGGATg/gag	6/42	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		334	595	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135239	2135240	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs137854329	NA	P-0029871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	124	498	0	ENST00000219476.3:c.4581dup	p.Glu1528Ter	p.E1528*	ENST00000219476	NM_000548.3	1526	-/T	36/42	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		498	671	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0029873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	277	399	0	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.879672344249665	2		399	612	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0029874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	111	411	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.988	0.892	1	0.988	0.892	1	CLONAL	1	TRUE	1	0.451403850848276	2		411	498	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0029874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	146	288	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	0.451403850848276	2		288	546	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267710	198267710	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	134	303	0	ENST00000335508.6:c.1769G>T	p.Arg590Ile	p.R590I	ENST00000335508	NM_012433.2	590	aGa/aTa	13/25	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.451403850848276	2		303	568	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863241	57863241	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	107	384	0	ENST00000228682.2:c.1336T>A	p.Ser446Thr	p.S446T	ENST00000228682	NM_005269.2	446	Tca/Aca	11/12	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.451403850848276	2		384	474	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976651	55976651	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2034964	NA	P-0029874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	132	432	0	ENST00000263923.4:c.1174G>A	p.Asp392Asn	p.D392N	ENST00000263923	NM_002253.2	392	Gac/Aac	9/30	1	2	FACETS	0.946	0.862	1	0.946	0.862	1	CLONAL	1	TRUE	1	0.451403850848276	2		432	618	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924426	131924426	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1186633489	NA	P-0029874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	164	270	0	ENST00000265335.6:c.1099A>T	p.Arg367Ter	p.R367*	ENST00000265335		367	Aga/Tga	8/25	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.451403850848276	2		270	541	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459672	149459672	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	83	477	0	ENST00000286301.3:c.535G>T	p.Ala179Ser	p.A179S	ENST00000286301	NM_005211.3	179	Gcc/Tcc	4/22	0.208219211878957	0	FACETS	0.297	0.262	0.334			1	INDETERMINATE	1	TRUE	0	0.451403850848276	0		477	680	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430341	47430341	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	172	530	0	ENST00000377045.4:c.1616C>T	p.Pro539Leu	p.P539L	ENST00000377045	NM_001654.4	539	cCc/cTc	15/16	1	2	FACETS	0.965	0.889	1	0.965	0.889	1	CLONAL	1	TRUE	1	0.451403850848276	2		530	790	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627164	86627170	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GGTGGTA	GGTGGTA	-	novel	NA	P-0029874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	22	138	0	ENST00000274376.6:c.540-1_545del		p.X180_splice	ENST00000274376	NM_002890.2	180		2/25	1	2	FACETS	0.497	0.387	0.623	0.497	0.387	0.623	SUBCLONAL	1	TRUE	1	0.451403850848276	2		138	196	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0029874-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	82	441	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.401311108424645	2		441	396	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219357	1219357	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730881970	NA	P-0029874-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	100	553	0	ENST00000326873.7:c.409C>T	p.Gln137Ter	p.Q137*	ENST00000326873	NM_000455.4	137	Cag/Tag	3/10	0.401311108424645	1	FACETS	0.815	0.731	0.903	0.815	0.731	0.903	CLONAL	1	TRUE	0	0.401311108424645	1		553	489	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431580	49431580	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs760323567	NA	P-0029874-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	96	485	0	ENST00000301067.7:c.9559G>T	p.Ala3187Ser	p.A3187S	ENST00000301067	NM_003482.3	3187	Gcc/Tcc	34/54	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.401311108424645	2		485	438	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414814	56414814	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029874-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	92	432	0	ENST00000348428.3:c.2215A>T	p.Ser739Cys	p.S739C	ENST00000348428	NM_006785.3	739	Agt/Tgt	17/17	1	2	FACETS	0.963	0.86	1	0.963	0.86	1	CLONAL	1	TRUE	1	0.401311108424645	2		432	476	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513276	44513276	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029874-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	108	482	0	ENST00000291552.4:c.659G>A	p.Gly220Asp	p.G220D	ENST00000291552	NM_006758.2	220	gGt/gAt	8/8	0.392894620253727	1	FACETS	0.935	0.844	1	0.935	0.844	1	CLONAL	1	TRUE	0	0.401311108424645	1		482	460	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271497	26271497	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780883968	NA	P-0029874-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	62	299	0	ENST00000305910.3:c.116C>T	p.Pro39Leu	p.P39L	ENST00000305910	NM_003534.2	39	cCt/cTt	1/1	1	2	FACETS	0.981	0.853	1	0.981	0.853	1	CLONAL	1	TRUE	1	0.401311108424645	2		299	315	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188223	32188223	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029874-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	105	458	0	ENST00000375023.3:c.1118G>T	p.Arg373Leu	p.R373L	ENST00000375023	NM_004557.3	373	cGg/cTg	6/30	1	2	FACETS	0.991	0.891	1	0.991	0.891	1	CLONAL	1	TRUE	1	0.401311108424645	2		458	528	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120579	94120579	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029874-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	61	287	0	ENST00000369303.4:c.472G>T	p.Gly158Cys	p.G158C	ENST00000369303	NM_004440.3	158	Ggt/Tgt	3/17	1	2	FACETS	0.859	0.745	0.981	0.859	0.745	0.981	CLONAL	1	TRUE	1	0.401311108424645	2		287	354	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528640	8528640	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029874-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	58	297	0	ENST00000356435.5:c.492A>C	p.Leu164Phe	p.L164F	ENST00000356435		164	ttA/ttC	4/35	1	2	FACETS	0.898	0.776	1	0.898	0.776	1	CLONAL	1	TRUE	1	0.401311108424645	2		297	322	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849208	76849210	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0029874-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	79	300	0	ENST00000373344.5:c.6066_6068del	p.Leu2023del	p.L2023del	ENST00000373344	NM_000489.3	2022	ctTCTc/ctc	26/35	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.401311108424645	2		300	393	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907774	76907774	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029874-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	82	261	0	ENST00000373344.5:c.4387G>T	p.Glu1463Ter	p.E1463*	ENST00000373344	NM_000489.3	1463	Gag/Tag	15/35	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.401311108424645	2		261	351	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019972	123019972	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029874-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	67	510	0	ENST00000355640.3:c.460T>G	p.Tyr154Asp	p.Y154D	ENST00000355640		154	Tac/Gac	2/7	1	2	FACETS	0.71	0.619	0.809	0.71	0.619	0.809	SUBCLONAL	1	TRUE	1	0.401311108424645	2		510	470	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	70	376	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		376	278	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332816	70332816	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs752995764	NA	P-0029916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	230	814	0	ENST00000373644.4:c.721A>G	p.Lys241Glu	p.K241E	ENST00000373644	NM_030625.2	241	Aaa/Gaa	2/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.52343732055007	2		814	828	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577447	64577447	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs778670301	NA	P-0029916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	243	743	0	ENST00000312049.6:c.135G>C	p.Glu45Asp	p.E45D	ENST00000312049	NM_130799.2	45	gaG/gaC	2/10	0.52343732055007	1	FACETS	0.993	0.933	1	0.993	0.933	1	CLONAL	1	TRUE	0	0.52343732055007	1		743	690	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560535	65560535	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0029916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	120	409	1	ENST00000358664.4:c.64-2A>G		p.X22_splice	ENST00000358664	NM_002382.4	22			0.52343732055007	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.52343732055007	1		410	335	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577222	64577224	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs794728657	NA	P-0029917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	273	709	0	ENST00000312049.6:c.358_360del	p.Lys120del	p.K120del	ENST00000312049	NM_130799.2	120	AAG/-	2/10	0.426473780656617	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	0	0.469420833078689	1		709	828	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410486	63410486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779325879	NA	P-0029917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	205	632	0	ENST00000330258.3:c.2681G>A	p.Arg894His	p.R894H	ENST00000330258	NM_152424.3	894	cGc/cAc	2/2	1	2	FACETS	0.88	0.817	0.947	0.88	0.817	0.947	CLONAL	1	FALSE	1	0.469420833078689	2		632	992	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685268	89685268	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs1085308043	NA	P-0029917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	52	109	0	ENST00000371953.3:c.165-2A>T		p.X55_splice	ENST00000371953	NM_000314.4	55			1	2	FACETS	0.943	0.811	1	0.943	0.811	1	CLONAL	1	FALSE	1	0.469420833078689	2		109	235	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711892	89711892	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121909221	NA	P-0029917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	141	417	0	ENST00000371953.3:c.510T>A	p.Ser170Arg	p.S170R	ENST00000371953	NM_000314.4	170	agT/agA	6/9	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	1	0.469420833078689	2		417	590	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933460	100933464	+	frameshift_variant	Frame_Shift_Del	DEL	TATTG	TATTG	AATA	novel	NA	P-0029917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	115	280	0	ENST00000325455.5:c.1926_1930delinsTATT	p.Asn643IlefsTer6	p.N643Ifs*6	ENST00000325455	NM_001202474.3	642	ttCAATAaa/ttTATTaa	4/8	0.469420833078689	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	0	0.469420833078689	1		280	358	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085613	16085621	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGATGATGA	AGATGATGA	-	rs794727504	NA	P-0029917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	158	465	0	ENST00000281043.3:c.801_809del		p.X267_splice	ENST00000281043	NM_005378.4	267		3/3	1	2	FACETS	0.918	0.843	0.997	0.918	0.843	0.997	CLONAL	1	FALSE	1	0.469420833078689	2		465	733	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589615	67589616	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTC	novel	NA	P-0029917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	161	174	0	ENST00000274335.5:c.1380_1382dup	p.Arg461dup	p.R461dup	ENST00000274335		461	agt/aGTCgt	10/15	0.255329476300506	3	FACETS	1	0.956	1	0.694	0.644	0.745	INDETERMINATE	2	FALSE	0	0.469420833078689	3		174	407	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0029920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	110	591	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.358222459937496	1	FACETS	0.865	0.779	0.955	0.865	0.779	0.955	CLONAL	1	TRUE	0	0.358222459937496	1		591	583	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115903	8115904	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0029920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	104	590	0	ENST00000346208.3:c.1251dup	p.Thr418HisfsTer89	p.T418Hfs*89	ENST00000346208		417	acc/aCcc	6/6	1	2	FACETS	0.963	0.864	1	0.963	0.864	1	CLONAL	1	TRUE	1	0.358222459937496	2		590	603	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864215	117864215	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	85	461	0	ENST00000297338.2:c.1442G>A	p.Gly481Glu	p.G481E	ENST00000297338	NM_006265.2	481	gGa/gAa	11/14	1	2	FACETS	0.822	0.728	0.923	0.822	0.728	0.923	CLONAL	1	TRUE	1	0.358222459937496	2		461	577	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675343	241675343	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	79	487	0	ENST00000366560.3:c.479G>A	p.Arg160Lys	p.R160K	ENST00000366560	NM_000143.3	160	aGa/aAa	4/10	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.243613190812723	2		487	607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0029929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	246	521	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.280283927450073	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.285052096308534	2		522	820	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0029929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	138	454	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.213179365021415	3	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	1	0.285052096308534	3		454	540	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	46	371	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.781	0.659	0.916	0.781	0.659	0.916	CLONAL	1	TRUE	1	0.285052096308534	2		371	413	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	89	480	2	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	0.140919867533498	5	FACETS	1	0.975	1	0.347	0.308	0.389	INDETERMINATE	1	TRUE	1	0.285052096308534	5		482	642	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755554	39755554	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	93	432	2	ENST00000288319.7:c.1211del	p.Pro404ArgfsTer25	p.P404Rfs*25	ENST00000288319	NM_182918.3	404	cCg/cg	10/10	0.285052096308534	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.285052096308534	1		434	528	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968266	2968266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773909937	NA	P-0029929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	151	647	0	ENST00000396946.4:c.1720G>A	p.Val574Ile	p.V574I	ENST00000396946	NM_032415.4	574	Gtc/Atc	13/25	0.213179365021415	3	FACETS	1	0.945	1	0.524	0.478	0.572	CLONAL	1	TRUE	1	0.285052096308534	3		647	1155	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073804	8073804	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1557463619	NA	P-0029929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	32	296	1	ENST00000377482.5:c.855del	p.Arg286GlufsTer9	p.R286Efs*9	ENST00000377482	NM_018948.3	285	ccC/cc	4/4	0.0345415018790138	3	FACETS	0.598	0.485	0.726			1	INDETERMINATE	1	TRUE	NA	0.285052096308534	3		297	429	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739109	40739109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1166590993	NA	P-0029929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	43	501	0	ENST00000373198.4:c.3175C>T	p.Arg1059Trp	p.R1059W	ENST00000373198	NM_133170.3	1059	Cgg/Tgg	24/32	1	2	FACETS	0.384	0.32	0.455	0.384	0.32	0.455	SUBCLONAL	1	TRUE	1	0.285052096308534	2		501	786	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137360	202137360	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0029929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	53	354	0	ENST00000358485.4:c.589-1G>T		p.X197_splice	ENST00000358485	NM_001080125.1	197			0.140919867533498	5	FACETS	1	0.948	1	0.314	0.268	0.365	INDETERMINATE	1	TRUE	1	0.285052096308534	5		354	422	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17354304	17354306	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs1173714647	NA	P-0029929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	70	449	0	ENST00000375499.3:c.478_480del	p.Lys160del	p.K160del	ENST00000375499	NM_003000.2	160	AAG/-	5/8	1	2	FACETS	0.756	0.659	0.86	0.756	0.659	0.86	SUBCLONAL	1	TRUE	1	0.285052096308534	2		449	650	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213243	39213243	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	153	823	4	ENST00000402219.2:c.3724del	p.Ser1242ValfsTer37	p.S1242Vfs*37	ENST00000402219	NM_005633.3	1242	Agt/gt	23/23	0.140919867533498	5	FACETS	1	0.981	1	0.318	0.29	0.347	INDETERMINATE	1	TRUE	1	0.285052096308534	5		827	1205	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572597	141572597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376660302	NA	P-0029929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1928	123	541	0	ENST00000220592.5:c.473C>T	p.Thr158Met	p.T158M	ENST00000220592	NM_012154.3	158	aCg/aTg	4/19	0.285052096308534	18	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.285052096308534	18		541	2051	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88677064	88677064	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	98	526	0	ENST00000372037.3:c.849G>A	p.Met283Ile	p.M283I	ENST00000372037	NM_004329.2	283	atG/atA	9/13	1	2	FACETS	0.987	0.881	1	0.987	0.881	1	CLONAL	1	TRUE	1	0.285052096308534	2		526	697	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589791	69589791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	26	32	2	ENST00000168712.1:c.62C>T	p.Ala21Val	p.A21V	ENST00000168712	NM_002007.2	21	gCg/gTg	1/3	1	2	FACETS	1	0.919	1	1	0.962	1	CLONAL	2	TRUE	1	0.285052096308534	2		34	73	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142124	108142124	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	57	431	0	ENST00000278616.4:c.3068G>T	p.Gly1023Val	p.G1023V	ENST00000278616	NM_000051.3	1023	gGa/gTa	20/63	1	2	FACETS	0.921	0.793	1	0.921	0.793	1	CLONAL	1	TRUE	1	0.285052096308534	2		431	434	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500606	99500606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs909142461	NA	P-0029929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	50	394	0	ENST00000268035.6:c.4039G>A	p.Ala1347Thr	p.A1347T	ENST00000268035	NM_000875.3	1347	Gcc/Acc	21/21	1	2	FACETS	0.625	0.53	0.73	0.625	0.53	0.73	SUBCLONAL	1	TRUE	1	0.285052096308534	2		394	561	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832455	72832455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	25	378	0	ENST00000268489.5:c.4126G>A	p.Ala1376Thr	p.A1376T	ENST00000268489	NM_006885.3	1376	Gcc/Acc	9/10	1	2	FACETS	0.379	0.298	0.472	0.379	0.298	0.472	SUBCLONAL	1	TRUE	1	0.285052096308534	2		378	463	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991926	72991926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550330554	NA	P-0029929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	102	492	0	ENST00000268489.5:c.2119G>A	p.Gly707Arg	p.G707R	ENST00000268489	NM_006885.3	707	Ggg/Agg	2/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.285052096308534	2		492	577	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085821	16085821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	65	538	0	ENST00000281043.3:c.997G>A	p.Ala333Thr	p.A333T	ENST00000281043	NM_005378.4	333	Gcc/Acc	3/3	0.140919867533498	5	FACETS	0.841	0.728	0.964	0.21	0.182	0.241	INDETERMINATE	1	TRUE	1	0.285052096308534	5		538	774	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629406	187629406	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	132	713	1	ENST00000441802.2:c.1576G>T	p.Asp526Tyr	p.D526Y	ENST00000441802	NM_005245.3	526	Gac/Tac	2/27	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.285052096308534	2		714	842	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778195	27778195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	85	623	0	ENST00000369163.2:c.344C>T	p.Ala115Val	p.A115V	ENST00000369163	NM_003536.2	115	gCc/gTc	1/1	0.285052096308534	3	FACETS	0.865	0.764	0.973	0.288	0.254	0.325	CLONAL	1	TRUE	0	0.285052096308534	3		623	788	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041014	112041014	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	68	371	1	ENST00000368678.4:c.241G>A	p.Gly81Arg	p.G81R	ENST00000368678		81	Gga/Aga	3/13	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.285052096308534	2		372	432	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240773	55240773	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1199980775	NA	P-0029929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	72	757	0	ENST00000275493.2:c.2017A>G	p.Ile673Val	p.I673V	ENST00000275493	NM_005228.3	673	Atc/Gtc	17/28	0.213179365021415	3	FACETS	0.534	0.465	0.609	0.267	0.232	0.305	SUBCLONAL	1	TRUE	1	0.285052096308534	3		757	1081	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846323	128846323	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	79	587	0	ENST00000249373.3:c.1159A>G	p.Ser387Gly	p.S387G	ENST00000249373	NM_005631.4	387	Agt/Ggt	6/12	0.213179365021415	3	FACETS	0.763	0.67	0.863	0.381	0.335	0.432	SUBCLONAL	1	TRUE	1	0.285052096308534	3		587	830	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848067	151848067	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	44	315	0	ENST00000262189.6:c.12692T>C	p.Val4231Ala	p.V4231A	ENST00000262189	NM_170606.2	4231	gTa/gCa	51/59	0.213179365021415	3	FACETS	0.698	0.586	0.823	0.349	0.293	0.412	SUBCLONAL	1	TRUE	1	0.285052096308534	3		315	505	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759564	133759564	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	86	697	0	ENST00000318560.5:c.1887G>T	p.Glu629Asp	p.E629D	ENST00000318560	NM_005157.4	629	gaG/gaT	11/11	0.140919867533498	5	FACETS	0.843	0.744	0.95	0.211	0.186	0.238	INDETERMINATE	1	TRUE	1	0.285052096308534	5		697	1022	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0029935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	156	218	0				ENST00000310581	NM_198253.2	-/1132			0.248722882122942	4	FACETS	1	0.98	1	1	0.98	1	INDETERMINATE	2	TRUE	2	0.534868312545637	4		218	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0029935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	264	591	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.534868312545637	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.534868312545637	1		591	531	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099352	27099353	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0029935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	256	545	0	ENST00000324856.7:c.3591dup	p.Thr1198HisfsTer22	p.T1198Hfs*22	ENST00000324856	NM_006015.4	1197	tcc/tCcc	14/20	0.379784727800283	2	FACETS	0.804	0.759	0.85	0.804	0.759	0.85	CLONAL	2	TRUE	0	0.534868312545637	2		545	595	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667867	37667867	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	107	414	0	ENST00000447079.4:c.2752G>T	p.Asp918Tyr	p.D918Y	ENST00000447079	NM_015083.1	918	Gat/Tat	8/14	0.225723934615785	2	FACETS	0.788	0.709	0.87	0.394	0.354	0.435	INDETERMINATE	1	TRUE	0	0.534868312545637	2		414	508	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62322264	62322264	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	127	745	0	ENST00000360203.5:c.2520C>A	p.His840Gln	p.H840Q	ENST00000360203	NM_001283009.1	840	caC/caA	27/35	0.248722882122942	4	FACETS	0.695	0.628	0.765	0.347	0.314	0.383	INDETERMINATE	1	TRUE	2	0.534868312545637	4		745	1049	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617593	100617593	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	216	649	0	ENST00000308731.7:c.476C>G	p.Ala159Gly	p.A159G	ENST00000308731	NM_000061.2	159	gCc/gGc	6/19	0.130547111962122	3	FACETS	1	0.986	1	0.409	0.381	0.438	INDETERMINATE	1	TRUE	0	0.534868312545637	3		649	834	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864273	57864273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	39	468	0	ENST00000228682.2:c.1750G>A	p.Ala584Thr	p.A584T	ENST00000228682	NM_005269.2	584	Gcc/Acc	12/12	1	2	FACETS	0.813	0.675	0.967	0.813	0.675	0.967	CLONAL	1	TRUE	1	0.235052219858056	2		468	408	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867333	45867333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765839639	NA	P-0029937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	74	683	0	ENST00000391945.4:c.860G>A	p.Arg287His	p.R287H	ENST00000391945	NM_000400.3	287	cGt/cAt	10/23	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.235052219858056	2		683	574	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576091	29576091	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1131691087	NA	P-0029937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	100	529	0	ENST00000356175.3:c.4064C>G	p.Ser1355Ter	p.S1355*	ENST00000356175	NM_000267.3	1355	tCa/tGa	30/57	0.15755376490152	2	FACETS	0.789	0.707	0.876	0.789	0.707	0.876	SUBCLONAL	2	TRUE	0	0.235052219858056	2		529	539	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610154	10610154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	107	679	1	ENST00000171111.5:c.556G>A	p.Gly186Ser	p.G186S	ENST00000171111	NM_203500.1	186	Ggc/Agc	2/6	0.235052219858056	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.235052219858056	1		680	580	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432297	49432297	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	38	837	0	ENST00000301067.7:c.8842C>T	p.Pro2948Ser	p.P2948S	ENST00000301067	NM_003482.3	2948	Cca/Tca	34/54	1	2	FACETS	0.513	0.423	0.614	0.513	0.423	0.614	SUBCLONAL	1	TRUE	1	0.235052219858056	2		837	630	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577527	7577528	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAA	novel	NA	P-0029939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	234	630	0	ENST00000269305.4:c.753_754insTTC	p.Ile251_Leu252insPhe	p.I251_L252insF	ENST00000269305	NM_001126112.2	251	-/TTC	7/11	0.536771788363082	1	FACETS	0.898	0.844	0.953	0.898	0.844	0.953	CLONAL	1	TRUE	0	0.606839944285961	1		630	598	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953792	131953792	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	86	301	0	ENST00000265335.6:c.3195C>A	p.Asp1065Glu	p.D1065E	ENST00000265335		1065	gaC/gaA	21/25	1	2	FACETS	0.785	0.699	0.875	0.785	0.699	0.875	SUBCLONAL	1	TRUE	1	0.592418909557769	2		301	370	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251243	99251243	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	140	491	0	ENST00000268035.6:c.547C>T	p.Pro183Ser	p.P183S	ENST00000268035	NM_000875.3	183	Cca/Tca	2/21	0.199345271954817	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.258401099666798	1		491	786	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651316	45651316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756890702	NA	P-0029943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	51	457	0	ENST00000407780.3:c.709G>A	p.Gly237Arg	p.G237R	ENST00000407780	NM_001283052.1	237	Gga/Aga	5/7	0.228369323697281	3	FACETS	0.559	0.474	0.653	0.28	0.237	0.327	SUBCLONAL	1	TRUE	1	0.258401099666798	3		457	797	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs397516896	NA	P-0029943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	104	311	0	ENST00000288602.6:c.1780G>C	p.Asp594His	p.D594H	ENST00000288602	NM_004333.4	594	Gat/Cat	15/18	1	2	FACETS	0.791	0.711	0.875	1	0.984	1	SUBCLONAL	2	TRUE	1	0.258401099666798	2		311	509	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63819019	63819019	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	32	239	0	ENST00000279873.7:c.1066T>G	p.Phe356Val	p.F356V	ENST00000279873	NM_032199.2	356	Ttt/Gtt	7/10	0.258401099666798	3	FACETS	0.827	0.673	1	0.414	0.336	0.501	CLONAL	1	TRUE	1	0.258401099666798	3		239	338	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627731	37627731	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	324	577	0	ENST00000447079.4:c.1646C>G	p.Pro549Arg	p.P549R	ENST00000447079	NM_015083.1	549	cCc/cGc	2/14	0.258401099666798	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.258401099666798	3		577	1319	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793308	33793308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	38	103	0	ENST00000498907.2:c.13G>A	p.Asp5Asn	p.D5N	ENST00000498907	NM_004364.3	5	Gac/Aac	1/1	0.258401099666798	3	FACETS	0.692	0.572	0.826	0.231	0.19	0.276	SUBCLONAL	1	TRUE	0	0.258401099666798	3		103	480	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024264	31024271	+	frameshift_variant	Frame_Shift_Del	DEL	CACAGGAC	CACAGGAC	-	novel	NA	P-0029943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	60	486	0	ENST00000375687.4:c.3749_3756del	p.Ser1250Ter	p.S1250*	ENST00000375687	NM_015338.5	1250	tCACAGGAC/t	13/13	0.258401099666798	3	FACETS	0.768	0.661	0.885	0.384	0.33	0.443	SUBCLONAL	1	TRUE	1	0.258401099666798	3		486	683	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514570	41514570	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	160	301	0	ENST00000373198.4:c.91G>T	p.Gly31Cys	p.G31C	ENST00000373198	NM_133170.3	31	Ggc/Tgc	2/32	0.258401099666798	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.258401099666798	3		301	653	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874952	151874952	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0029943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	29	246	0	ENST00000262189.6:c.7586C>G	p.Ser2529Ter	p.S2529*	ENST00000262189	NM_170606.2	2529	tCa/tGa	38/59	1	2	FACETS	0.456	0.365	0.56	0.456	0.365	0.56	SUBCLONAL	1	TRUE	1	0.258401099666798	2		246	492	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0029944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	624	441	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.718112107732348	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.718112107732348	2		441	786	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675622	86675622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	82	313	0	ENST00000274376.6:c.2558C>T	p.Ser853Leu	p.S853L	ENST00000274376	NM_002890.2	853	tCa/tTa	19/25	1	2	FACETS	0.524	0.464	0.587	0.524	0.464	0.587	SUBCLONAL	1	TRUE	1	0.718112107732348	2		313	436	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61720134	61720134	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	93	388	0	ENST00000401558.2:c.1300G>C	p.Glu434Gln	p.E434Q	ENST00000401558	NM_003400.3	434	Gag/Cag	13/25	0.370895077852976	2	FACETS	0.499	0.445	0.556	0.25	0.222	0.278	INDETERMINATE	1	TRUE	0	0.718112107732348	2		388	519	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66735666	66735666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	94	346	0	ENST00000307102.5:c.487G>A	p.Glu163Lys	p.E163K	ENST00000307102	NM_002755.3	163	Gaa/Aaa	4/11	0.689810872139809	2	FACETS	0.533	0.476	0.594	0.267	0.238	0.297	SUBCLONAL	1	TRUE	0	0.718112107732348	2		346	491	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031997	26031997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	70	264	0	ENST00000244661.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000244661	NM_003537.3	98	Gag/Aag	1/1	0.672614639764714	2	FACETS	0.584	0.512	0.659	0.292	0.256	0.33	SUBCLONAL	1	TRUE	0	0.718112107732348	2		264	334	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777996	27777996	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	104	286	0	ENST00000369163.2:c.145C>G	p.Leu49Val	p.L49V	ENST00000369163	NM_003536.2	49	Ctc/Gtc	1/1	0.672614639764714	2	FACETS	0.691	0.623	0.762	0.346	0.311	0.381	SUBCLONAL	1	TRUE	0	0.718112107732348	2		286	419	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795017	45795017	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	116	431	0	ENST00000450313.1:c.1611C>G	p.Ile537Met	p.I537M	ENST00000450313	NM_012222.2	537	atC/atG	16/16	1	2	FACETS	0.499	0.45	0.55	0.499	0.45	0.55	SUBCLONAL	1	TRUE	1	0.718112107732348	2		431	648	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115284252	115284252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	93	398	1	ENST00000438362.2:c.34C>T	p.His12Tyr	p.H12Y	ENST00000438362	NM_001242891.1	12	Cat/Tat	2/20	1	2	FACETS	0.428	0.381	0.478	0.428	0.381	0.478	SUBCLONAL	1	TRUE	1	0.718112107732348	2		399	605	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251992	8251992	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	433	530	2	ENST00000335790.3:c.85C>A	p.Arg29Ser	p.R29S	ENST00000335790	NM_002315.2	29	Cgc/Agc	2/4	0.189762290749827	5	FACETS	0.852	0.816	0.889	0.852	0.816	0.889	INDETERMINATE	3	TRUE	2	0.718112107732348	5		532	980	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514302	69514302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	324	462	0	ENST00000294312.3:c.379C>A	p.Arg127Ser	p.R127S	ENST00000294312	NM_005117.2	127	Cgc/Agc	3/3	0.189762290749827	5	FACETS	1	0.983	1	0.724	0.686	0.762	INDETERMINATE	2	TRUE	2	0.718112107732348	5		462	863	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962529	100962529	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	314	373	0	ENST00000325455.5:c.1868G>T	p.Arg623Leu	p.R623L	ENST00000325455	NM_001202474.3	623	cGc/cTc	3/8	0.189762290749827	5	FACETS	1	0.989	1	0.765	0.725	0.805	INDETERMINATE	2	TRUE	2	0.718112107732348	5		373	792	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424087	49424087	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	684	641	0	ENST00000301067.7:c.13975C>G	p.Arg4659Gly	p.R4659G	ENST00000301067	NM_003482.3	4659	Cgg/Ggg	42/54	0.718112107732348	2	FACETS	0.989	0.964	1	0.989	0.964	1	CLONAL	2	TRUE	0	0.718112107732348	2		641	963	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435766	110435766	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs549588978	NA	P-0029944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	26	117	0	ENST00000375856.3:c.2635G>C	p.Gly879Arg	p.G879R	ENST00000375856	NM_003749.2	879	Ggc/Cgc	1/2	0.411961696896162	1	FACETS	0.283	0.226	0.347	0.283	0.226	0.347	INDETERMINATE	1	TRUE	0	0.718112107732348	1		117	164	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000362	42000363	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0029944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	275	342	0	ENST00000219905.7:c.2381_2382insTT	p.Trp795TyrfsTer23	p.W795Yfs*23	ENST00000219905	NM_001164273.1	794	gga/ggTTa	7/24	0.689810872139809	2	FACETS	0.882	0.844	0.92	0.882	0.844	0.92	CLONAL	2	TRUE	0	0.718112107732348	2		342	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577125	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0029944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	415	543	1	ENST00000269305.4:c.813_814delinsTT	p.Glu271_Val272delinsAspLeu	p.E271_V272delinsDL	ENST00000269305	NM_001126112.2	271	gaGGtg/gaTTtg	8/11	0.662445323379133	2	FACETS	0.872	0.84	0.903	0.872	0.84	0.903	CLONAL	2	TRUE	0	0.718112107732348	2		544	663	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15952254	15952254	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	441	451	0	ENST00000268712.3:c.6441C>A	p.Tyr2147Ter	p.Y2147*	ENST00000268712	NM_006311.3	2147	taC/taA	41/46	0.662445323379133	2	FACETS	0.984	0.953	1	0.984	0.953	1	CLONAL	2	TRUE	0	0.718112107732348	2		451	624	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288885	15288885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1193870306	NA	P-0029944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	54	208	0	ENST00000263388.2:c.3854G>A	p.Arg1285His	p.R1285H	ENST00000263388	NM_000435.2	1285	cGt/cAt	24/33	0.672614639764714	2	FACETS	0.568	0.489	0.652	0.284	0.244	0.326	SUBCLONAL	1	TRUE	0	0.718112107732348	2		208	265	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210796	36210796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	194	668	0	ENST00000222270.7:c.547G>A	p.Glu183Lys	p.E183K	ENST00000222270	NM_014727.1	183	Gag/Aag	3/37	0.672614639764714	2	FACETS	0.675	0.625	0.725	0.337	0.312	0.363	SUBCLONAL	1	TRUE	0	0.718112107732348	2		668	801	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376719	31376719	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	232	300	0	ENST00000328111.2:c.714G>T	p.Trp238Cys	p.W238C	ENST00000328111	NM_006892.3	238	tgG/tgT	7/23	0.484746193772342	3	FACETS	1	0.987	1	0.606	0.568	0.646	CLONAL	1	TRUE	1	0.718112107732348	3		300	724	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101188	41101188	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	185	420	0	ENST00000373198.4:c.1168C>A	p.Pro390Thr	p.P390T	ENST00000373198	NM_133170.3	390	Cca/Aca	8/32	1	2	FACETS	0.92	0.855	0.986	0.92	0.855	0.986	CLONAL	1	TRUE	1	0.718112107732348	2		420	560	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101197	41101197	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	205	406	0	ENST00000373198.4:c.1159G>T	p.Val387Leu	p.V387L	ENST00000373198	NM_133170.3	387	Gta/Tta	8/32	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.718112107732348	2		406	541	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405870	49405870	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	141	434	0	ENST00000418115.1:c.268G>C	p.Asp90His	p.D90H	ENST00000418115	NM_001664.2	90	Gat/Cat	3/5	1	2	FACETS	0.518	0.472	0.566	0.518	0.472	0.566	SUBCLONAL	1	TRUE	1	0.718112107732348	2		434	758	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119634978	119634978	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	65	264	0	ENST00000316626.5:c.521C>A	p.Ser174Tyr	p.S174Y	ENST00000316626		174	tCc/tAc	5/12	0.370999833479632	1	FACETS	0.43	0.376	0.486	0.43	0.376	0.486	INDETERMINATE	1	TRUE	0	0.718112107732348	1		264	270	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670721	134670721	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	213	422	0	ENST00000398015.3:c.632C>A	p.Thr211Lys	p.T211K	ENST00000398015	NM_004441.4	211	aCa/aAa	3/16	0.370999833479632	1	FACETS	0.789	0.741	0.837	0.789	0.741	0.837	INDETERMINATE	1	TRUE	0	0.718112107732348	1		422	482	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188406	142188406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910993590	NA	P-0029944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	61	298	0	ENST00000350721.4:c.6325C>T	p.Arg2109Cys	p.R2109C	ENST00000350721	NM_001184.3	2109	Cgc/Tgc	38/47	0.370999833479632	1	FACETS	0.377	0.328	0.429	0.377	0.328	0.429	INDETERMINATE	1	TRUE	0	0.718112107732348	1		298	289	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467698	66467698	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	155	291	0	ENST00000273854.3:c.571C>G	p.Arg191Gly	p.R191G	ENST00000273854	NM_004439.5	191	Cgt/Ggt	3/18	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.718112107732348	2		291	429	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253754	153253754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	142	251	0	ENST00000281708.4:c.979G>A	p.Glu327Lys	p.E327K	ENST00000281708	NM_033632.3	327	Gaa/Aaa	6/12	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.718112107732348	2		251	387	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517454	176517461	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTGCGT	CTGTGCGT	-	novel	NA	P-0029944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	284	507	0	ENST00000292408.4:c.161_168del	p.Arg54LeufsTer5	p.R54Lfs*5	ENST00000292408	NM_213647.1	52	cCTGTGCGT/c	3/18	1	2	FACETS	0.991	0.936	1	0.991	0.936	1	CLONAL	1	TRUE	1	0.718112107732348	2		507	798	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341782	8341782	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	234	470	0	ENST00000356435.5:c.4858G>C	p.Val1620Leu	p.V1620L	ENST00000356435		1620	Gtg/Ctg	29/35	1	2	FACETS	0.97	0.91	1	0.97	0.91	1	CLONAL	1	TRUE	1	0.718112107732348	2		470	672	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413103	63413103	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	265	484	1	ENST00000330258.3:c.64G>A	p.Glu22Lys	p.E22K	ENST00000330258	NM_152424.3	22	Gaa/Aaa	2/2	NA	2	FACETS	0.921	0.867	0.977			1	INDETERMINATE	1	TRUE	NA	0.718112107732348	2		485	801	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118857	115118860	+	frameshift_variant	Frame_Shift_Del	DEL	GACA	GACA	-	novel	NA	P-0029945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	39	391	0	ENST00000257566.3:c.481_484del	p.Cys161ValfsTer46	p.C161Vfs*46	ENST00000257566	NM_016569.3	161	TGTCgt/gt	2/8	0.469701105791759	1	FACETS	0.312	0.259	0.372	0.312	0.259	0.372	SUBCLONAL	1	TRUE	0	0.469701105791759	1		391	407	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138487	2138487	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	87	770	0	ENST00000219476.3:c.5300T>C	p.Leu1767Pro	p.L1767P	ENST00000219476	NM_000548.3	1767	cTg/cCg	42/42	1	2	FACETS	0.423	0.374	0.476	0.423	0.374	0.476	SUBCLONAL	1	TRUE	1	0.469701105791759	2		770	875	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578429	7578429	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1567553148	NA	P-0029946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	386	633	0	ENST00000269305.4:c.501del	p.Gln167HisfsTer3	p.Q167Hfs*3	ENST00000269305	NM_001126112.2	167	caG/ca	5/11	0.710546266821933	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.710546266821933	1		633	693	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50483719	50483719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746898820	NA	P-0029946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	250	401	0	ENST00000394963.4:c.824C>T	p.Pro275Leu	p.P275L	ENST00000394963	NM_003076.4	275	cCg/cTg	7/13	1	2	FACETS	0.928	0.872	0.986	0.928	0.872	0.986	CLONAL	1	TRUE	1	0.710546266821933	2		401	758	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864815	57864815	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	363	620	0	ENST00000228682.2:c.2292C>A	p.Asn764Lys	p.N764K	ENST00000228682	NM_005269.2	764	aaC/aaA	12/12	1	2	FACETS	0.967	0.918	1	0.967	0.918	1	CLONAL	1	TRUE	1	0.710546266821933	2		620	1057	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663336	67663336	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	213	383	0	ENST00000264010.4:c.1739del	p.Pro580GlnfsTer4	p.P580Qfs*4	ENST00000264010	NM_006565.3	579	ggC/gg	10/12	0.622101238770371	3	FACETS	0.979	0.911	1			1	CLONAL	1	TRUE	NA	0.710546266821933	3		383	830	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55704589	55704589	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0029946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	306	562	0	ENST00000284073.2:c.653-1G>A		p.X218_splice	ENST00000284073	NM_138962.2	218			0.710546266821933	3	FACETS	0.956	0.901	1	0.319	0.3	0.338	CLONAL	1	TRUE	0	0.710546266821933	3		562	1221	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449794	29449794	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	422	810	0	ENST00000389048.3:c.3061T>C	p.Cys1021Arg	p.C1021R	ENST00000389048	NM_004304.4	1021	Tgc/Cgc	18/29	1	2	FACETS	0.937	0.893	0.981	0.937	0.893	0.981	CLONAL	1	TRUE	1	0.710546266821933	2		810	1268	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189300	99189300	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	228	375	0	ENST00000074304.5:c.2556G>T	p.Gln852His	p.Q852H	ENST00000074304	NM_001134224.1	852	caG/caT	24/26	0.525976487072509	3	FACETS	0.989	0.924	1			1	CLONAL	1	TRUE	NA	0.710546266821933	3		375	879	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379395	225379395	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	253	567	0	ENST00000264414.4:c.473G>C	p.Arg158Thr	p.R158T	ENST00000264414	NM_003590.4	158	aGg/aCg	4/16	0.710546266821933	1	FACETS	0.935	0.886	0.984	0.935	0.886	0.984	CLONAL	1	TRUE	0	0.710546266821933	1		567	491	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37048483	37048483	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs63750866	NA	P-0029946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	168	310	0	ENST00000231790.2:c.382G>A	p.Ala128Thr	p.A128T	ENST00000231790	NM_000249.3	128	Gca/Aca	5/19	0.710546266821933	1	FACETS	0.921	0.862	0.98	0.921	0.862	0.98	CLONAL	1	TRUE	0	0.710546266821933	1		310	331	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486050	8486050	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	232	432	1	ENST00000356435.5:c.2767C>T	p.Gln923Ter	p.Q923*	ENST00000356435		923	Caa/Taa	17/35	0.621338777173033	3	FACETS	1	0.939	1	0.503	0.469	0.537	CLONAL	1	TRUE	1	0.710546266821933	3		433	880	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430384	47430384	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	337	569	0	ENST00000377045.4:c.1659G>T	p.Gln553His	p.Q553H	ENST00000377045	NM_001654.4	553	caG/caT	15/16	NA	2	FACETS	0.962	0.912	1			1	INDETERMINATE	1	TRUE	NA	0.710546266821933	2		569	986	SUCCESS
ATRX	546	MSKCC	GRCh37	X	77041466	77041466	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0029946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	206	396	0	ENST00000373344.5:c.20+2T>C		p.X7_splice	ENST00000373344	NM_000489.3	7			NA	2	FACETS	0.805	0.75	0.862			1	INDETERMINATE	1	TRUE	NA	0.710546266821933	2		396	720	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613671	100613671	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	222	460	0	ENST00000308731.7:c.908G>T	p.Gly303Val	p.G303V	ENST00000308731	NM_000061.2	303	gGt/gTt	11/19	NA	2	FACETS	0.995	0.932	1			1	INDETERMINATE	1	TRUE	NA	0.710546266821933	2		460	628	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0029948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	188	559	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.435088418862393	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.435088418862393	1		559	603	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098857	178098857	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	92	543	0	ENST00000397062.3:c.188A>G	p.Gln63Arg	p.Q63R	ENST00000397062	NM_006164.4	63	cAa/cGa	2/5	0.591616359696326	2	FACETS	0.497	0.442	0.555	0.248	0.221	0.278	SUBCLONAL	1	TRUE	0	0.591616359696326	2		543	626	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030050	36030050	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	226	578	1	ENST00000358208.4:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000358208		362	cGg/cAg	9/12	0.589723482327976	3	FACETS	1	0.952	1	0.513	0.478	0.55	CLONAL	1	TRUE	1	0.591616359696326	3		579	964	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807587	1807587	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	265	754	2	ENST00000260795.2:c.1756G>T	p.Glu586Ter	p.E586*	ENST00000260795		586	Gag/Tag	12/17	0.348723606258557	3	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.591616359696326	3		756	1067	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522612	176522615	+	frameshift_variant	Frame_Shift_Del	DEL	CCGA	CCGA	-	novel	NA	P-0029949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	115	712	0	ENST00000292408.4:c.1711_1714del	p.Asp571SerfsTer49	p.D571Sfs*49	ENST00000292408	NM_213647.1	570	cCCGAc/cc	13/18	0.589723482327976	3	FACETS	0.451	0.405	0.499	0.225	0.202	0.25	SUBCLONAL	1	TRUE	1	0.591616359696326	3		712	1118	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681138	117681138	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	121	380	0	ENST00000368508.3:c.3482G>A	p.Gly1161Asp	p.G1161D	ENST00000368508	NM_002944.2	1161	gGt/gAt	23/43	0.589723482327976	3	FACETS	0.908	0.823	0.997	0.454	0.411	0.499	CLONAL	1	TRUE	1	0.591616359696326	3		380	584	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0029951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	204	441	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.743388607570896	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.743388607570896	3		441	369	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207065	1207065	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	314	726	1	ENST00000326873.7:c.157del	p.Asp53ThrfsTer11	p.D53Tfs*11	ENST00000326873	NM_000455.4	51	atG/at	1/10	0.739016065908405	2	FACETS	0.969	0.934	1	0.969	0.934	1	CLONAL	2	TRUE	0	0.743388607570896	2		727	436	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245316	46245316	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	207	418	0	ENST00000334344.6:c.3410C>A	p.Ser1137Ter	p.S1137*	ENST00000334344	NM_152641.2	1137	tCa/tAa	15/21	0.743388607570896	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.743388607570896	3		418	356	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119075	70119075	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	178	410	0	ENST00000245479.2:c.647C>A	p.Ser216Tyr	p.S216Y	ENST00000245479	NM_000346.3	216	tCc/tAc	2/3	0.743388607570896	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.743388607570896	3		410	316	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020205	123020205	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	130	572	1	ENST00000355640.3:c.693G>T	p.Leu231Phe	p.L231F	ENST00000355640		231	ttG/ttT	2/7	NA	2	FACETS	0.874	0.801	0.95			1	INDETERMINATE	1	TRUE	NA	0.743388607570896	2		573	400	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430019	78430019	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	19	292	0	ENST00000370768.2:c.860T>G	p.Val287Gly	p.V287G	ENST00000370768	NM_003902.3	287	gTt/gGt	11/20	0.743388607570896	2	FACETS	0.2	0.152	0.257	0.1	0.076	0.129	SUBCLONAL	1	TRUE	0	0.743388607570896	2		292	255	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623712	43623712	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	180	420	0	ENST00000355710.3:c.3340A>C	p.Ser1114Arg	p.S1114R	ENST00000355710	NM_020975.4	1114	Agt/Cgt	20/20	0.639116988082083	4	FACETS	0.91	0.847	0.973			1	CLONAL	2	TRUE	NA	0.743388607570896	4		420	464	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141987	108141987	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	237	439	0	ENST00000278616.4:c.2931T>G	p.Cys977Trp	p.C977W	ENST00000278616	NM_000051.3	977	tgT/tgG	20/63	0.743388607570896	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.743388607570896	2		439	312	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871173	12871173	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0029951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	117	245	0	ENST00000228872.4:c.400A>T	p.Lys134Ter	p.K134*	ENST00000228872	NM_004064.3	134	Aag/Tag	1/3	0.743388607570896	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.743388607570896	3		245	195	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562533	95562534	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0029951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	324	343	0	ENST00000393063.1:c.4723_4724delinsTT	p.Gly1575Leu	p.G1575L	ENST00000393063	NM_030621.3	1575	GGg/TTg	24/28	0.743388607570896	5	FACETS	0.92	0.892	0.946			1	CLONAL	5	TRUE	NA	0.743388607570896	5		343	401	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213251	39213251	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	319	687	1	ENST00000402219.2:c.3716G>T	p.Gly1239Val	p.G1239V	ENST00000402219	NM_005633.3	1239	gGc/gTc	23/23	0.701478330072269	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.743388607570896	4		688	696	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278291	39278291	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	277	489	0	ENST00000402219.2:c.858A>T	p.Leu286Phe	p.L286F	ENST00000402219	NM_005633.3	286	ttA/ttT	6/23	0.701478330072269	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.743388607570896	4		489	634	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189287	99189287	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	183	356	0	ENST00000074304.5:c.2544del	p.Ser849LeufsTer58	p.S849Lfs*58	ENST00000074304	NM_001134224.1	848	cGg/cg	24/26	0.701478330072269	4	FACETS	0.941	0.878	1	0.941	0.878	1	CLONAL	2	TRUE	2	0.743388607570896	4		356	456	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840057	27840057	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1385431916	NA	P-0029951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	167	301	0	ENST00000328488.2:c.37G>A	p.Gly13Ser	p.G13S	ENST00000328488	NM_003533.2	13	Ggc/Agc	1/1	0.701478330072269	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.743388607570896	4		301	362	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525130	157525130	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	52	173	0	ENST00000346085.5:c.5025G>T	p.Gln1675His	p.Q1675H	ENST00000346085	NM_020732.3	1675	caG/caT	19/20	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.743388607570896	2		173	133	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0029954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	30	454	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.559	0.448	0.685	0.559	0.448	0.685	SUBCLONAL	1	TRUE	1	0.14	2		454	767	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197044	123197044	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	204	409	0	ENST00000218089.9:c.1810C>T	p.Arg604Ter	p.R604*	ENST00000218089	NM_001042749.1	604	Cga/Tga	19/35	0.465331253038768	1	FACETS	0.682	0.645	0.719	0.682	0.645	0.719	INDETERMINATE	1	TRUE	0	0.913068222859892	1		409	356	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143999	11143999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1171822727	NA	P-0029956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	219	505	1	ENST00000358026.2:c.3580G>A	p.Gly1194Arg	p.G1194R	ENST00000358026	NM_001128849.1	1194	Ggg/Agg	26/36	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.913068222859892	2		506	463	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247516	123247516	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519795	NA	P-0029956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	125	432	0	ENST00000358487.5:c.1975A>G	p.Lys659Glu	p.K659E	ENST00000358487	NM_000141.4	659	Aag/Gag	14/18	0.913068222859892	3	FACETS	0.504	0.456	0.555	0.252	0.228	0.278	SUBCLONAL	1	TRUE	1	0.913068222859892	3		432	791	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256219	123256219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519797	NA	P-0029956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	96	395	0	ENST00000358487.5:c.1690G>A	p.Val564Ile	p.V564I	ENST00000358487	NM_000141.4	564	Gtt/Att	13/18	0.913068222859892	3	FACETS	0.548	0.489	0.61	0.274	0.244	0.305	SUBCLONAL	1	TRUE	1	0.913068222859892	3		395	559	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41554496	41554496	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	94	421	1	ENST00000263253.7:c.3582C>A	p.Tyr1194Ter	p.Y1194*	ENST00000263253	NM_001429.3	1194	taC/taA	19/31	0.512042428878926	2	FACETS	0.453	0.404	0.503	0.226	0.202	0.252	INDETERMINATE	1	TRUE	0	0.913068222859892	2		422	455	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839897	27839897	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	143	630	0	ENST00000328488.2:c.197T>C	p.Leu66Pro	p.L66P	ENST00000328488	NM_003533.2	66	cTa/cCa	1/1	0.913068222859892	3	FACETS	0.603	0.551	0.659	0.302	0.275	0.33	SUBCLONAL	1	TRUE	1	0.913068222859892	3		630	756	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163360	32163360	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	302	758	0	ENST00000375023.3:c.5866C>G	p.Leu1956Val	p.L1956V	ENST00000375023	NM_004557.3	1956	Ctg/Gtg	30/30	0.913068222859892	3	FACETS	1	0.971	1	0.522	0.493	0.552	CLONAL	1	TRUE	1	0.913068222859892	3		758	923	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0029957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	204	493	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.39012194607645	2	FACETS	0.944	0.884	1	0.944	0.884	1	CLONAL	2	TRUE	0	0.427738546024876	2		493	505	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366981	118366981	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	91	375	0	ENST00000534358.1:c.5563G>C	p.Asp1855His	p.D1855H	ENST00000534358	NM_005933.3	1855	Gat/Cat	20/36	0.274470868124878	4	FACETS	0.799	0.709	0.895			1	SUBCLONAL	1	TRUE	NA	0.427738546024876	4		375	760	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230632	46230632	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	217	402	0	ENST00000334344.6:c.881G>T	p.Arg294Ile	p.R294I	ENST00000334344	NM_152641.2	294	aGa/aTa	8/21	0.389819560722262	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.427738546024876	3		402	572	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	181	307	0	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	1	2	FACETS	0.793	0.733	0.854	0.793	0.733	0.854	SUBCLONAL	1	TRUE	1	0.654258326640774	2		307	698	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853286	68853286	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0029958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	232	425	0	ENST00000261769.5:c.1669A>T	p.Lys557Ter	p.K557*	ENST00000261769	NM_004360.3	557	Aag/Tag	11/16	0.654258326640774	1	FACETS	0.986	0.931	1	0.986	0.931	1	CLONAL	1	TRUE	0	0.654258326640774	1		425	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0029960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	92	857	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.825	0.733	0.923	1	0.982	1	CLONAL	2	TRUE	1	0.16	2		858	697	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593613	55593614	+	missense_variant	Missense_Mutation	DNP	TT	TT	AG	novel	NA	P-0029963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	248	376	0	ENST00000288135.5:c.1679_1680delinsAG	p.Val560Glu	p.V560E	ENST00000288135	NM_000222.2	560	gTT/gAG	11/21	0.289957913628288	4	FACETS	0.908	0.856	0.96	0.908	0.856	0.96	INDETERMINATE	2	TRUE	2	0.884370086225271	4		376	582	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0029964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	218	532	0	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	0.508072387986699	1	FACETS	0.989	0.925	1	0.989	0.925	1	CLONAL	1	FALSE	0	0.508072387986699	1		532	647	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263351	123263355	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGA	GGAGA	-	novel	NA	P-0029964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	83	326	0	ENST00000358487.5:c.1388_1392del	p.Val463GlyfsTer3	p.V463Gfs*3	ENST00000358487	NM_000141.4	463	gTCTCC/g	10/18	0.277449840595819	0	FACETS	0.313	0.276	0.351			1	INDETERMINATE	1	FALSE	0	0.508072387986699	0		326	514	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865774	56865774	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	198	260	0	ENST00000308159.5:c.1106A>G	p.Asn369Ser	p.N369S	ENST00000308159	NM_014669.4	369	aAc/aGc	11/22	0.447474636447781	2	FACETS	0.836	0.783	0.89	0.836	0.783	0.89	CLONAL	2	FALSE	0	0.508072387986699	2		260	466	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441227	52441228	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0029964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	163	362	1	ENST00000460680.1:c.542_543del	p.Phe181Ter	p.F181*	ENST00000460680	NM_004656.3	181	tTT/t	7/17	0.508072387986699	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	0	0.508072387986699	1		363	470	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021734	71021734	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs794727215	NA	P-0029964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	179	318	0	ENST00000318789.4:c.1624C>T	p.Gln542Ter	p.Q542*	ENST00000318789	NM_032682.5	542	Caa/Taa	18/21	0.508072387986699	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	0	0.508072387986699	1		318	472	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670096	86670211	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGAAGGGCAAAACCCAGTATGGTCAGAAGAGTTTGTCTTTGAGTAAGTCTTATTTTATCATTACATTAATCATTTTCTTTTACCATATTGCATTTCTTTCTGTTTTTTTGGTCTCT	GGAAGGGCAAAACCCAGTATGGTCAGAAGAGTTTGTCTTTGAGTAAGTCTTATTTTATCATTACATTAATCATTTTCTTTTACCATATTGCATTTCTTTCTGTTTTTTTGGTCTCT	-	novel	NA	P-0029964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	65	412	0	ENST00000274376.6:c.1894_1934+75del		p.X632_splice	ENST00000274376	NM_002890.2	632		14/25	0.508072387986699	1	FACETS	0.541	0.471	0.615	0.541	0.471	0.615	SUBCLONAL	1	FALSE	0	0.508072387986699	1		412	353	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0029966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	111	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.189959036311746	2	FACETS	0.901	0.812	0.994	0.45	0.406	0.497	INDETERMINATE	1	TRUE	0	0.412885195004596	2		511	597	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984782	11984782	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1164096095	NA	P-0029966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	38	396	1	ENST00000353533.5:c.328C>T	p.Arg110Ter	p.R110*	ENST00000353533	NM_003010.3	110	Cga/Tga	3/11	0.412885195004596	1	FACETS	0.455	0.377	0.541	0.455	0.377	0.541	SUBCLONAL	1	TRUE	0	0.412885195004596	1		397	321	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612900	228612900	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	40	456	0	ENST00000366696.1:c.127C>T	p.Arg43Trp	p.R43W	ENST00000366696	NM_003493.2	43	Cgg/Tgg	1/1	0.254652111767836	3	FACETS	0.379	0.314	0.452	0.19	0.157	0.226	SUBCLONAL	1	TRUE	1	0.412885195004596	3		456	616	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	99	368	1	ENST00000263967.3:c.3132T>G	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaG	21/21	0.189959036311746	2	FACETS	1	0.964	1	0.579	0.52	0.641	INDETERMINATE	1	TRUE	0	0.412885195004596	2		369	414	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643510	52643510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	50	452	1	ENST00000394830.3:c.2386G>A	p.Glu796Lys	p.E796K	ENST00000394830	NM_018313.4	796	Gag/Aag	17/30	0.189959036311746	2	FACETS	0.506	0.429	0.589	0.253	0.214	0.295	INDETERMINATE	1	TRUE	0	0.412885195004596	2		453	479	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55143614	55143614	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	21	326	0	ENST00000257290.5:c.1846A>G	p.Ser616Gly	p.S616G	ENST00000257290	NM_006206.4	616	Agc/Ggc	13/23	0.412885195004596	1	FACETS	0.286	0.22	0.363	0.286	0.22	0.363	SUBCLONAL	1	TRUE	0	0.412885195004596	1		326	282	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0029969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	969	441	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.548221860233439	6	FACETS	0.957	0.938	0.975			1	CLONAL	6	TRUE	NA	0.548221860233439	6		441	1291	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0029969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	118	412	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.43304303339099	4	FACETS	0.919	0.83	1	0.46	0.415	0.507	CLONAL	1	TRUE	2	0.548221860233439	4		412	725	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259011	89259011	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	70	176	0	ENST00000336596.2:c.157del	p.Glu53LysfsTer30	p.E53Kfs*30	ENST00000336596	NM_005233.5	52	tGg/tg	3/17	0.43304303339099	4	FACETS	0.807	0.713	0.906	0.807	0.713	0.906	CLONAL	2	TRUE	2	0.548221860233439	4		176	245	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410853	63410853	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	145	557	0	ENST00000330258.3:c.2314G>T	p.Ala772Ser	p.A772S	ENST00000330258	NM_152424.3	772	Gcc/Tcc	2/2	1	2	FACETS	0.705	0.644	0.769	0.705	0.644	0.769	SUBCLONAL	1	TRUE	1	0.548221860233439	2		557	750	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533123	63533123	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs754833574	NA	P-0029969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	254	538	0	ENST00000307078.5:c.1771G>T	p.Ala591Ser	p.A591S	ENST00000307078	NM_004655.3	591	Gcc/Tcc	7/11	0.548221860233439	3	FACETS	0.973	0.918	1	0.973	0.918	1	CLONAL	2	TRUE	1	0.548221860233439	3		538	607	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800901	18800901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767127006	NA	P-0029969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	336	409	0	ENST00000266497.5:c.4277G>A	p.Arg1426Gln	p.R1426Q	ENST00000266497		1426	cGa/cAa	31/31	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.548221860233439	NA		409	610	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462005	120462005	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	261	414	0	ENST00000256646.2:c.5711A>G	p.Asn1904Ser	p.N1904S	ENST00000256646	NM_024408.3	1904	aAt/aGt	31/34	0.524875006864626	3	FACETS	0.961	0.907	1	0.961	0.907	1	CLONAL	2	TRUE	1	0.548221860233439	3		414	631	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809292	243809292	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	114	414	0	ENST00000263826.5:c.332G>T	p.Arg111Met	p.R111M	ENST00000263826	NM_005465.4	111	aGg/aTg	4/13	0.524875006864626	3	FACETS	0.953	0.861	1	0.477	0.43	0.525	CLONAL	1	TRUE	1	0.548221860233439	3		414	556	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577035	7577036	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	320	603	0	ENST00000269305.4:c.902_903insT	p.Gly302ArgfsTer4	p.G302Rfs*4	ENST00000269305	NM_001126112.2	301	cca/ccTa	8/11	0.548221860233439	2	FACETS	0.958	0.914	1	0.958	0.914	1	CLONAL	2	TRUE	0	0.548221860233439	2		603	609	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248588	10248588	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	295	586	0	ENST00000340748.4:c.4165A>T	p.Asn1389Tyr	p.N1389Y	ENST00000340748		1389	Aac/Tac	35/40	0.548221860233439	2	FACETS	0.936	0.891	0.981	0.936	0.891	0.981	CLONAL	2	TRUE	0	0.548221860233439	2		586	575	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906760	50906760	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201654210	NA	P-0029969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	297	595	0	ENST00000440232.2:c.1148C>T	p.Thr383Ile	p.T383I	ENST00000440232	NM_002691.3	383	aCc/aTc	10/27	0.548221860233439	2	FACETS	0.924	0.88	0.969	0.924	0.88	0.969	CLONAL	2	TRUE	0	0.548221860233439	2		595	586	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215674222	215674222	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	132	557	2	ENST00000260947.4:c.72del	p.Ala25ProfsTer33	p.A25Pfs*33	ENST00000260947	NM_000465.2	24	ccC/cc	1/11	0.548221860233439	3	FACETS	0.883	0.803	0.967	0.441	0.401	0.484	CLONAL	1	TRUE	1	0.548221860233439	3		559	695	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978364	2978364	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	344	556	0	ENST00000396946.4:c.966G>T	p.Arg322Ser	p.R322S	ENST00000396946	NM_032415.4	322	agG/agT	7/25	0.43304303339099	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.548221860233439	4		556	928	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980609	70980609	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	284	555	0	ENST00000276594.2:c.768G>T	p.Met256Ile	p.M256I	ENST00000276594	NM_024504.3	256	atG/atT	4/8	0.238505505875575	5	FACETS	1	0.987	1	0.765	0.721	0.809	INDETERMINATE	2	TRUE	2	0.548221860233439	5		555	823	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939766	76939766	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	140	566	0	ENST00000373344.5:c.982G>C	p.Glu328Gln	p.E328Q	ENST00000373344	NM_000489.3	328	Gaa/Caa	9/35	0.278840356961789	6	FACETS	0.881	0.8	0.966			1	INDETERMINATE	1	TRUE	NA	0.548221860233439	6		566	1216	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	26	391	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.146	0.115	0.182	0.146	0.115	0.182	SUBCLONAL	1	TRUE	1	0.46944109070919	2		391	760	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830902	72830903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	60	474	0	ENST00000268489.5:c.5677_5678dup	p.Asp1894GlyfsTer21	p.D1894Gfs*21	ENST00000268489	NM_006885.3	1893	agg/agAGg	9/10	1	2	FACETS	0.595	0.513	0.684	0.595	0.513	0.684	SUBCLONAL	1	TRUE	1	0.38	2		474	531	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	143	538	0	ENST00000206249.3:c.1607T>C	p.Leu536Pro	p.L536P	ENST00000206249	NM_000125.3	536	cTc/cCc	8/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.38	2		538	609	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339110	65339111	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	122	457	1	ENST00000342505.4:c.425dup	p.Ile143AspfsTer9	p.I143Dfs*9	ENST00000342505	NM_002227.2	142	aag/aaAg	5/25	1	2	FACETS	0.961	0.87	1	0.961	0.87	1	CLONAL	1	TRUE	1	0.38	2		458	668	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	145	253	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	0.992	1	CLONAL	2	TRUE	1	0.38	2		253	359	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435160	56435161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755128667	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	46	586	0	ENST00000407977.2:c.1976dup	p.Pro660SerfsTer87	p.P660Sfs*87	ENST00000407977		659	ggt/ggGt	9/10	1	2	FACETS	0.406	0.341	0.478	0.406	0.341	0.478	SUBCLONAL	1	TRUE	1	0.38	2		586	596	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265629	152265629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	95	318	3	ENST00000206249.3:c.1082C>T	p.Ala361Val	p.A361V	ENST00000206249	NM_000125.3	361	gCg/gTg	4/8	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.38	2		321	489	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021785	71021785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs112795301	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	97	284	0	ENST00000318789.4:c.1573C>T	p.Arg525Ter	p.R525*	ENST00000318789	NM_032682.5	525	Cga/Tga	18/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.38	2		284	416	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166353	118166353	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	24	352	0	ENST00000369448.3:c.863T>C	p.Leu288Ser	p.L288S	ENST00000369448	NM_017709.3	288	tTg/tCg	2/2	1	2	FACETS	0.281	0.219	0.352	0.281	0.219	0.352	SUBCLONAL	1	TRUE	1	0.38	2		352	450	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097733	27097733	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	46	532	0	ENST00000324856.7:c.3322G>T	p.Glu1108Ter	p.E1108*	ENST00000324856	NM_006015.4	1108	Gaa/Taa	12/20	1	2	FACETS	0.353	0.297	0.416	0.353	0.297	0.416	SUBCLONAL	1	TRUE	1	0.38	2		532	685	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281743	46281743	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	104	558	0	ENST00000371998.3:c.4190G>A	p.Gly1397Asp	p.G1397D	ENST00000371998		1397	gGc/gAc	22/23	1	2	FACETS	0.736	0.659	0.817	0.736	0.659	0.817	SUBCLONAL	1	TRUE	1	0.38	2		558	744	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453398	40453399	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs759027671	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	92	715	0	ENST00000345506.4:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000345506	NM_003152.3	365	-/C	10/20	1	2	FACETS	0.635	0.563	0.711	0.635	0.563	0.711	SUBCLONAL	1	TRUE	1	0.38	2		715	763	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993730	72993731	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769936196	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	32	429	1	ENST00000268489.5:c.314dup	p.Pro106AlafsTer13	p.P106Afs*13	ENST00000268489	NM_006885.3	105	ccg/ccCg	2/10	1	2	FACETS	0.413	0.335	0.501	0.413	0.335	0.501	SUBCLONAL	1	TRUE	1	0.38	2		430	408	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836659	89836659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	114	681	0	ENST00000389301.3:c.2231C>T	p.Pro744Leu	p.P744L	ENST00000389301	NM_000135.2	744	cCc/cTc	25/43	1	2	FACETS	0.862	0.777	0.952	0.862	0.777	0.952	CLONAL	1	TRUE	1	0.38	2		681	696	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732740	204732741	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	59	313	0	ENST00000302823.3:c.81dup	p.Leu28SerfsTer32	p.L28Sfs*32	ENST00000302823	NM_005214.4	25	-/T	1/4	1	2	FACETS	0.588	0.506	0.677	0.588	0.506	0.677	SUBCLONAL	1	TRUE	1	0.38	2		313	528	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330610	65330611	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	37	410	0	ENST00000342505.4:c.1035dup	p.Leu346ThrfsTer4	p.L346Tfs*4	ENST00000342505	NM_002227.2	345	-/A	8/25	1	2	FACETS	0.332	0.273	0.399	0.332	0.273	0.399	SUBCLONAL	1	TRUE	1	0.38	2		410	586	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989590	212989591	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	86	264	0	ENST00000342788.4:c.119_120dup	p.Asp41LeufsTer26	p.D41Lfs*26	ENST00000342788	NM_005235.2	40	-/CT	2/28	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.38	2		264	430	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154241	2154242	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755455183	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	112	560	5	ENST00000434045.2:c.686dup	p.Glu230ArgfsTer50	p.E230Rfs*50	ENST00000434045	NM_001127598.1	229	cca/ccCa	5/5	1	2	FACETS	0.97	0.874	1	0.97	0.874	1	CLONAL	1	TRUE	1	0.38	2		565	608	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806180	1806181	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760502257	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	83	632	2	ENST00000260795.2:c.1206dup	p.Lys403GlnfsTer93	p.K403Qfs*93	ENST00000260795		400	agc/agCc	8/17	1	2	FACETS	0.655	0.578	0.737	0.655	0.578	0.737	SUBCLONAL	1	TRUE	1	0.38	2		634	667	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355551	15355552	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	80	502	0	ENST00000263377.2:c.2180dup	p.Lys728GlufsTer91	p.K728Efs*91	ENST00000263377	NM_058243.2	727	aag/aaAg	12/20	1	2	FACETS	0.638	0.562	0.72	0.638	0.562	0.72	SUBCLONAL	1	TRUE	1	0.38	2		502	660	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671654	67671655	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	63	439	0	ENST00000264010.4:c.2070dup	p.Glu691ArgfsTer5	p.E691Rfs*5	ENST00000264010	NM_006565.3	688	gta/gtAa	12/12	1	2	FACETS	0.622	0.538	0.713	0.622	0.538	0.713	SUBCLONAL	1	TRUE	1	0.38	2		439	533	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59934482	59934482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780247	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	42	381	0	ENST00000259008.2:c.316C>T	p.Arg106Cys	p.R106C	ENST00000259008	NM_032043.2	106	Cgt/Tgt	4/20	1	2	FACETS	0.482	0.402	0.57	0.482	0.402	0.57	SUBCLONAL	1	TRUE	1	0.38	2		381	459	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472442	88472442	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1323245430	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	34	427	0	ENST00000360948.2:c.2113T>C	p.Tyr705His	p.Y705H	ENST00000360948	NM_001012338.2	705	Tac/Cac	16/19	1	2	FACETS	0.32	0.261	0.387	0.32	0.261	0.387	SUBCLONAL	1	TRUE	1	0.38	2		427	559	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032275	26032275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs780546148	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	18	175	0	ENST00000244661.2:c.14A>T	p.Lys5Ile	p.K5I	ENST00000244661	NM_003537.3	5	aAa/aTa	1/1	1	2	FACETS	0.377	0.284	0.487	0.377	0.284	0.487	SUBCLONAL	1	TRUE	1	0.38	2		175	251	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176614	56176614	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	73	302	0	ENST00000399503.3:c.2164G>T	p.Glu722Ter	p.E722*	ENST00000399503	NM_005921.1	722	Gaa/Taa	12/20	1	2	FACETS	0.682	0.597	0.774	0.682	0.597	0.774	SUBCLONAL	1	TRUE	1	0.38	2		302	563	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384650	31384651	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs756395138	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	142	587	3	ENST00000328111.2:c.1359dup	p.Leu454AlafsTer11	p.L454Afs*11	ENST00000328111	NM_006892.3	451	gag/gaGg	13/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.38	2		590	646	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156935	106156936	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs763386429	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	30	454	0	ENST00000380013.4:c.1842dup	p.Leu615AlafsTer23	p.L615Afs*23	ENST00000380013	NM_001127208.2	612	-/G	3/11	1	2	FACETS	0.297	0.239	0.364	0.297	0.239	0.364	SUBCLONAL	1	TRUE	1	0.38	2		454	531	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	190	579	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.38	2		579	735	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563545	87563545	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	99	390	0	ENST00000277120.3:c.1933C>T	p.Leu645Phe	p.L645F	ENST00000277120		645	Ctc/Ttc	16/19	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.38	2		390	491	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259119	89259119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1244334822	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	53	346	0	ENST00000336596.2:c.263C>T	p.Pro88Leu	p.P88L	ENST00000336596	NM_005233.5	88	cCc/cTc	3/17	1	2	FACETS	0.635	0.543	0.736	0.635	0.543	0.736	SUBCLONAL	1	TRUE	1	0.38	2		346	439	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437353	220437353	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1389002726	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	42	612	0	ENST00000243786.2:c.257T>C	p.Phe86Ser	p.F86S	ENST00000243786	NM_002191.3	86	tTc/tCc	1/2	1	2	FACETS	0.321	0.267	0.381	0.321	0.267	0.381	SUBCLONAL	1	TRUE	1	0.38	2		612	688	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444932	49444933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs767415197	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	91	544	0	ENST00000301067.7:c.2533dup	p.Arg845ProfsTer3	p.R845Pfs*3	ENST00000301067	NM_003482.3	845	cgg/cCgg	10/54	1	2	FACETS	0.871	0.775	0.972	0.871	0.775	0.972	CLONAL	1	TRUE	1	0.38	2		544	550	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81902829	81902829	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	73	403	0	ENST00000359376.3:c.490C>T	p.Arg164Ter	p.R164*	ENST00000359376	NM_002661.3	164	Cga/Tga	6/33	0.283525985680122	0	FACETS	0.391	0.342	0.444			1	SUBCLONAL	1	TRUE	0	0.38	0		403	609	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30326004	30326005	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs769517721	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	69	389	0	ENST00000322652.5:c.2208dup	p.Gln737ThrfsTer20	p.Q737Tfs*20	ENST00000322652	NM_015355.2	734	-/A	16/16	1	2	FACETS	0.665	0.58	0.757	0.665	0.58	0.757	SUBCLONAL	1	TRUE	1	0.38	2		389	546	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741688	17741688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	103	304	0	ENST00000250003.3:c.359G>A	p.Arg120His	p.R120H	ENST00000250003	NM_002478.4	120	cGc/cAc	1/3	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.38	2		304	428	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437531	56437531	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	58	537	0	ENST00000407977.2:c.931del	p.Leu311SerfsTer108	p.L311Sfs*108	ENST00000407977		311	Ctc/tc	8/10	1	2	FACETS	0.427	0.366	0.494	0.427	0.366	0.494	SUBCLONAL	1	TRUE	1	0.38	2		537	715	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438703	49438703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	105	579	1	ENST00000301067.7:c.4787G>A	p.Gly1596Asp	p.G1596D	ENST00000301067	NM_003482.3	1596	gGc/gAc	19/54	1	2	FACETS	0.721	0.645	0.8	0.721	0.645	0.8	SUBCLONAL	1	TRUE	1	0.38	2		580	767	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645976	67645976	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	57	469	1	ENST00000264010.4:c.904G>A	p.Ala302Thr	p.A302T	ENST00000264010	NM_006565.3	302	Gca/Aca	4/12	1	2	FACETS	0.41	0.351	0.475	0.41	0.351	0.475	SUBCLONAL	1	TRUE	1	0.38	2		470	731	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344212	70344212	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	27	303	0	ENST00000374080.3:c.1948G>T	p.Glu650Ter	p.E650*	ENST00000374080		650	Gaa/Taa	13/45	1	2	FACETS	0.495	0.395	0.609	0.495	0.395	0.609	SUBCLONAL	1	TRUE	1	0.38	2		303	287	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602745	10602745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1040740503	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	103	694	0	ENST00000171111.5:c.833C>T	p.Pro278Leu	p.P278L	ENST00000171111	NM_203500.1	278	cCg/cTg	3/6	1	2	FACETS	0.652	0.583	0.725	0.652	0.583	0.725	SUBCLONAL	1	TRUE	1	0.38	2		694	832	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553714	106553714	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	86	414	0	ENST00000369096.4:c.1679A>G	p.Lys560Arg	p.K560R	ENST00000369096	NM_001198.3	560	aAg/aGg	5/7	1	2	FACETS	0.707	0.626	0.794	0.707	0.626	0.794	SUBCLONAL	1	TRUE	1	0.38	2		414	640	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983295	15983295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1355823096	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	76	375	0	ENST00000268712.3:c.3484C>T	p.Arg1162Trp	p.R1162W	ENST00000268712	NM_006311.3	1162	Cgg/Tgg	26/46	1	2	FACETS	0.741	0.651	0.837	0.741	0.651	0.837	SUBCLONAL	1	TRUE	1	0.38	2		375	540	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868981	117868981	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	36	349	0	ENST00000297338.2:c.718G>T	p.Gly240Cys	p.G240C	ENST00000297338	NM_006265.2	240	Ggt/Tgt	7/14	1	2	FACETS	0.347	0.285	0.417	0.347	0.285	0.417	SUBCLONAL	1	TRUE	1	0.38	2		349	546	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918759	50918759	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	168	707	2	ENST00000440232.2:c.2629G>T	p.Asp877Tyr	p.D877Y	ENST00000440232	NM_002691.3	877	Gat/Tat	21/27	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.38	2		709	664	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851847	134851847	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	48	497	1	ENST00000398015.3:c.1253T>C	p.Phe418Ser	p.F418S	ENST00000398015	NM_004441.4	418	tTc/tCc	5/16	1	2	FACETS	0.403	0.34	0.473	0.403	0.34	0.473	SUBCLONAL	1	TRUE	1	0.38	2		498	627	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057282	30057282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	40	467	0	ENST00000338641.4:c.764C>T	p.Ser255Phe	p.S255F	ENST00000338641	NM_000268.3	255	tCc/tTc	8/16	1	2	FACETS	0.338	0.28	0.403	0.338	0.28	0.403	SUBCLONAL	1	TRUE	1	0.38	2		467	623	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481473	20481473	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138776759	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	90	286	0	ENST00000346618.3:c.542C>T	p.Thr181Met	p.T181M	ENST00000346618	NM_001949.4	181	aCg/aTg	3/7	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.38	2		286	457	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416717	121416717	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs780298807	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	146	654	0	ENST00000257555.6:c.146C>A	p.Ser49Tyr	p.S49Y	ENST00000257555		49	tCc/tAc	1/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.38	2		654	640	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103525619	103525619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs574826021	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	31	267	0	ENST00000355739.4:c.2890C>T	p.Arg964Trp	p.R964W	ENST00000355739	NM_000123.3	964	Cgg/Tgg	14/15	1	2	FACETS	0.347	0.28	0.423	0.347	0.28	0.423	SUBCLONAL	1	TRUE	1	0.38	2		267	470	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122581	108122581	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	38	383	0	ENST00000278616.4:c.1625T>C	p.Leu542Ser	p.L542S	ENST00000278616	NM_000051.3	542	tTg/tCg	11/63	1	2	FACETS	0.363	0.299	0.434	0.363	0.299	0.434	SUBCLONAL	1	TRUE	1	0.38	2		383	551	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2492119	2492119	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	35	633	0	ENST00000355716.4:c.517A>G	p.Asn173Asp	p.N173D	ENST00000355716	NM_003820.2	173	Aat/Gat	5/8	1	2	FACETS	0.295	0.241	0.356	0.295	0.241	0.356	SUBCLONAL	1	TRUE	1	0.38	2		633	624	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11314023	11314023	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	36	443	0	ENST00000361445.4:c.713T>C	p.Phe238Ser	p.F238S	ENST00000361445	NM_004958.3	238	tTt/tCt	6/58	1	2	FACETS	0.331	0.272	0.398	0.331	0.272	0.398	SUBCLONAL	1	TRUE	1	0.38	2		443	572	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255782	16255783	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	33	396	0	ENST00000375759.3:c.3053dup	p.Gln1019AlafsTer3	p.Q1019Afs*3	ENST00000375759	NM_015001.2	1016	tca/tcAa	11/15	1	2	FACETS	0.323	0.263	0.392	0.323	0.263	0.392	SUBCLONAL	1	TRUE	1	0.38	2		396	537	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17349135	17349135	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	32	500	0	ENST00000375499.3:c.733A>C	p.Thr245Pro	p.T245P	ENST00000375499	NM_003000.2	245	Acc/Ccc	7/8	1	2	FACETS	0.291	0.236	0.355	0.291	0.236	0.355	SUBCLONAL	1	TRUE	1	0.38	2		500	578	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17359570	17359570	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	78	414	0	ENST00000375499.3:c.271A>G	p.Arg91Gly	p.R91G	ENST00000375499	NM_003000.2	91	Aga/Gga	3/8	1	2	FACETS	0.597	0.524	0.675	0.597	0.524	0.675	SUBCLONAL	1	TRUE	1	0.38	2		414	688	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092946	27092946	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	48	343	0	ENST00000324856.7:c.2879-2A>G		p.X960_splice	ENST00000324856	NM_006015.4	960			1	2	FACETS	0.63	0.534	0.736	0.63	0.534	0.736	SUBCLONAL	1	TRUE	1	0.38	2		343	401	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099407	27099407	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs757460729	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	88	511	0	ENST00000324856.7:c.3644T>C	p.Met1215Thr	p.M1215T	ENST00000324856	NM_006015.4	1215	aTg/aCg	14/20	1	2	FACETS	0.72	0.639	0.808	0.72	0.639	0.808	SUBCLONAL	1	TRUE	1	0.38	2		511	643	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100175	27100176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	87	448	0	ENST00000324856.7:c.3976_3977dup	p.Gln1327ArgfsTer155	p.Q1327Rfs*155	ENST00000324856	NM_006015.4	1324	tac/taCCc	16/20	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.38	2		448	453	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101163	27101163	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1557616295	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	78	596	0	ENST00000324856.7:c.4445G>A	p.Gly1482Asp	p.G1482D	ENST00000324856	NM_006015.4	1482	gGc/gAc	18/20	1	2	FACETS	0.634	0.557	0.716	0.634	0.557	0.716	SUBCLONAL	1	TRUE	1	0.38	2		596	648	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36823947	36823947	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	105	613	0	ENST00000373129.3:c.235G>T	p.Glu79Ter	p.E79*	ENST00000373129	NM_032017.1	79	Gag/Tag	5/12	1	2	FACETS	0.789	0.708	0.876	0.789	0.708	0.876	SUBCLONAL	1	TRUE	1	0.38	2		613	700	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937233	36937233	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	83	519	0	ENST00000361632.4:c.1086G>T	p.Glu362Asp	p.E362D	ENST00000361632		362	gaG/gaT	9/16	1	2	FACETS	0.669	0.59	0.753	0.669	0.59	0.753	SUBCLONAL	1	TRUE	1	0.38	2		519	653	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739838	46739838	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	89	417	0	ENST00000371975.4:c.1639A>T	p.Met547Leu	p.M547L	ENST00000371975	NM_003579.3	547	Atg/Ttg	15/18	1	2	FACETS	0.829	0.737	0.927	0.829	0.737	0.927	CLONAL	1	TRUE	1	0.38	2		417	565	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310551	65310551	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	58	415	0	ENST00000342505.4:c.2137G>T	p.Gly713Ter	p.G713*	ENST00000342505	NM_002227.2	713	Gga/Tga	16/25	1	2	FACETS	0.619	0.533	0.713	0.619	0.533	0.713	SUBCLONAL	1	TRUE	1	0.38	2		415	493	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78422289	78422289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	133	313	0	ENST00000370768.2:c.1673G>A	p.Gly558Asp	p.G558D	ENST00000370768	NM_003902.3	558	gGt/gAt	17/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.38	2		313	542	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733593	85733593	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	72	405	0	ENST00000370580.1:c.419A>G	p.Glu140Gly	p.E140G	ENST00000370580	NM_003921.4	140	gAg/gGg	3/3	1	2	FACETS	0.679	0.594	0.771	0.679	0.594	0.771	SUBCLONAL	1	TRUE	1	0.38	2		405	558	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258765	115258765	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	32	294	0	ENST00000369535.4:c.17T>G	p.Leu6Arg	p.L6R	ENST00000369535	NM_002524.4	6	cTg/cGg	2/7	1	2	FACETS	0.323	0.261	0.392	0.323	0.261	0.392	SUBCLONAL	1	TRUE	1	0.38	2		294	522	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115277099	115277099	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	117	415	0	ENST00000438362.2:c.684A>C	p.Lys228Asn	p.K228N	ENST00000438362	NM_001242891.1	228	aaA/aaC	7/20	1	2	FACETS	0.753	0.679	0.831	0.753	0.679	0.831	SUBCLONAL	1	TRUE	1	0.38	2		415	818	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695865	117695865	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	188	555	0	ENST00000369458.3:c.572T>C	p.Phe191Ser	p.F191S	ENST00000369458	NM_024626.3	191	tTc/tCc	4/6	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.38	2		555	725	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699222	117699222	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	70	393	0	ENST00000369458.3:c.419A>G	p.Asn140Ser	p.N140S	ENST00000369458	NM_024626.3	140	aAt/aGt	3/6	1	2	FACETS	0.704	0.615	0.801	0.704	0.615	0.801	SUBCLONAL	1	TRUE	1	0.38	2		393	523	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458516	120458516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	107	480	1	ENST00000256646.2:c.6829G>A	p.Gly2277Ser	p.G2277S	ENST00000256646	NM_024408.3	2277	Ggc/Agc	34/34	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.38	2		481	496	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462183	120462183	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	35	435	0	ENST00000256646.2:c.5533A>G	p.Ser1845Gly	p.S1845G	ENST00000256646	NM_024408.3	1845	Agt/Ggt	31/34	1	2	FACETS	0.352	0.287	0.424	0.352	0.287	0.424	SUBCLONAL	1	TRUE	1	0.38	2		435	524	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510816	120510816	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	34	360	0	ENST00000256646.2:c.1148C>A	p.Pro383His	p.P383H	ENST00000256646	NM_024408.3	383	cCt/cAt	7/34	1	2	FACETS	0.346	0.282	0.418	0.346	0.282	0.418	SUBCLONAL	1	TRUE	1	0.38	2		360	517	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846213	156846213	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs753191749	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	28	531	0	ENST00000524377.1:c.1654A>G	p.Ser552Gly	p.S552G	ENST00000524377	NM_002529.3	552	Agt/Ggt	14/17	1	2	FACETS	0.273	0.218	0.337	0.273	0.218	0.337	SUBCLONAL	1	TRUE	1	0.38	2		531	539	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945625	206945625	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	116	387	0	ENST00000423557.1:c.156G>T	p.Lys52Asn	p.K52N	ENST00000423557	NM_000572.2	52	aaG/aaT	1/5	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.38	2		387	517	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945716	206945716	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	109	410	0	ENST00000423557.1:c.65A>G	p.Gln22Arg	p.Q22R	ENST00000423557	NM_000572.2	22	cAg/cGg	1/5	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.38	2		410	538	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226590025	226590025	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	64	523	0	ENST00000366794.5:c.176A>C	p.Lys59Thr	p.K59T	ENST00000366794	NM_001618.3	59	aAg/aCg	2/23	1	2	FACETS	0.512	0.443	0.587	0.512	0.443	0.587	SUBCLONAL	1	TRUE	1	0.38	2		523	658	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682928	241682928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	60	311	0	ENST00000366560.3:c.95C>T	p.Ala32Val	p.A32V	ENST00000366560	NM_000143.3	32	gCc/gTc	1/10	1	2	FACETS	0.851	0.737	0.975	0.851	0.737	0.975	CLONAL	1	TRUE	1	0.38	2		311	371	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243668572	243668572	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	56	363	0	ENST00000263826.5:c.1419C>A	p.Tyr473Ter	p.Y473*	ENST00000263826	NM_005465.4	473	taC/taA	13/13	1	2	FACETS	0.588	0.504	0.68	0.588	0.504	0.68	SUBCLONAL	1	TRUE	1	0.38	2		363	501	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727092	243727093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	144	432	0	ENST00000263826.5:c.877dup	p.Cys293LeufsTer29	p.C293Lfs*29	ENST00000263826	NM_005465.4	293	tgc/tTgc	9/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.38	2		432	578	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851041	63851041	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	90	490	0	ENST00000279873.7:c.1819A>G	p.Asn607Asp	p.N607D	ENST00000279873	NM_032199.2	607	Aac/Gac	10/10	1	2	FACETS	0.757	0.672	0.847	0.757	0.672	0.847	SUBCLONAL	1	TRUE	1	0.38	2		490	626	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851246	63851246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141236035	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	39	529	0	ENST00000279873.7:c.2024C>T	p.Thr675Met	p.T675M	ENST00000279873	NM_032199.2	675	aCg/aTg	10/10	1	2	FACETS	0.358	0.296	0.427	0.358	0.296	0.427	SUBCLONAL	1	TRUE	1	0.38	2		529	574	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333291	70333291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1417939173	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	49	549	0	ENST00000373644.4:c.1196C>T	p.Pro399Leu	p.P399L	ENST00000373644	NM_030625.2	399	cCt/cTt	2/12	1	2	FACETS	0.374	0.316	0.438	0.374	0.316	0.438	SUBCLONAL	1	TRUE	1	0.38	2		549	690	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333407	70333407	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	105	675	0	ENST00000373644.4:c.1312A>G	p.Asn438Asp	p.N438D	ENST00000373644	NM_030625.2	438	Aat/Gat	2/12	1	2	FACETS	0.739	0.662	0.82	0.739	0.662	0.82	SUBCLONAL	1	TRUE	1	0.38	2		675	748	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405124	70405124	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	52	545	0	ENST00000373644.4:c.2638T>G	p.Leu880Val	p.L880V	ENST00000373644	NM_030625.2	880	Tta/Gta	4/12	1	2	FACETS	0.452	0.385	0.527	0.452	0.385	0.527	SUBCLONAL	1	TRUE	1	0.38	2		545	605	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406347	70406347	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	70	659	1	ENST00000373644.4:c.3861G>T	p.Gln1287His	p.Q1287H	ENST00000373644	NM_030625.2	1287	caG/caT	4/12	1	2	FACETS	0.453	0.394	0.516	0.453	0.394	0.516	SUBCLONAL	1	TRUE	1	0.38	2		660	814	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683249	88683249	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs112883778	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	164	529	0	ENST00000372037.3:c.1459T>C	p.Trp487Arg	p.W487R	ENST00000372037	NM_004329.2	487	Tgg/Cgg	12/13	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.38	2		529	639	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104357050	104357050	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1385719041	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	67	343	0	ENST00000369902.3:c.910G>T	p.Asp304Tyr	p.D304Y	ENST00000369902	NM_016169.3	304	Gac/Tac	7/12	1	2	FACETS	0.738	0.643	0.84	0.738	0.643	0.84	SUBCLONAL	1	TRUE	1	0.38	2		343	478	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112767368	112767368	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	99	430	0	ENST00000369452.4:c.1241T>C	p.Leu414Pro	p.L414P	ENST00000369452	NM_007373.3	414	cTc/cCc	6/9	1	2	FACETS	0.87	0.778	0.967	0.87	0.778	0.967	CLONAL	1	TRUE	1	0.38	2		430	599	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925621	114925622	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	72	594	3	ENST00000543371.1:c.1704dup	p.Ser569LeufsTer40	p.S569Lfs*40	ENST00000543371	NM_001198531.1	567	gcc/gCcc	14/14	1	2	FACETS	0.578	0.504	0.657	0.578	0.504	0.657	SUBCLONAL	1	TRUE	1	0.38	2		597	656	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123260378	123260378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	126	475	0	ENST00000358487.5:c.1523C>T	p.Pro508Leu	p.P508L	ENST00000358487	NM_000141.4	508	cCc/cTc	11/18	1	2	FACETS	0.96	0.87	1	0.96	0.87	1	CLONAL	1	TRUE	1	0.38	2		475	691	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123260400	123260400	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	106	480	0	ENST00000358487.5:c.1501G>T	p.Val501Leu	p.V501L	ENST00000358487	NM_000141.4	501	Gtg/Ttg	11/18	1	2	FACETS	0.753	0.675	0.835	0.753	0.675	0.835	SUBCLONAL	1	TRUE	1	0.38	2		480	741	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161424	2161424	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs921491029	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	89	508	0	ENST00000434045.2:c.103T>C	p.Phe35Leu	p.F35L	ENST00000434045	NM_001127598.1	35	Ttt/Ctt	2/5	1	2	FACETS	0.764	0.678	0.856	0.764	0.678	0.856	SUBCLONAL	1	TRUE	1	0.38	2		508	613	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741720	17741720	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	47	395	0	ENST00000250003.3:c.391A>G	p.Thr131Ala	p.T131A	ENST00000250003	NM_002478.4	131	Aca/Gca	1/3	1	2	FACETS	0.488	0.412	0.572	0.488	0.412	0.572	SUBCLONAL	1	TRUE	1	0.38	2		395	507	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410623	32410623	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	57	387	0	ENST00000332351.3:c.1535A>G	p.Lys512Arg	p.K512R	ENST00000332351	NM_024426.4	512	aAa/aGa	10/10	1	2	FACETS	0.547	0.47	0.632	0.547	0.47	0.632	SUBCLONAL	1	TRUE	1	0.38	2		387	548	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413586	32413586	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs766697865	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	36	355	0	ENST00000332351.3:c.1364C>A	p.Thr455Asn	p.T455N	ENST00000332351	NM_024426.4	455	aCt/aAt	9/10	1	2	FACETS	0.317	0.26	0.381	0.317	0.26	0.381	SUBCLONAL	1	TRUE	1	0.38	2		355	598	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129350	64129350	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	90	557	1	ENST00000334205.4:c.782T>C	p.Phe261Ser	p.F261S	ENST00000334205	NM_003942.2	261	tTc/tCc	8/17	1	2	FACETS	0.76	0.675	0.851	0.76	0.675	0.851	SUBCLONAL	1	TRUE	1	0.38	2		558	623	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196626	67196626	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	34	468	0	ENST00000312629.5:c.155A>C	p.Glu52Ala	p.E52A	ENST00000312629	NM_003952.2	52	gAg/gCg	3/15	1	2	FACETS	0.302	0.246	0.365	0.302	0.246	0.365	SUBCLONAL	1	TRUE	1	0.38	2		468	593	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514323	69514323	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	56	377	0	ENST00000294312.3:c.358T>G	p.Cys120Gly	p.C120G	ENST00000294312	NM_005117.2	120	Tgt/Ggt	3/3	1	2	FACETS	0.67	0.575	0.773	0.67	0.575	0.773	SUBCLONAL	1	TRUE	1	0.38	2		377	440	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941408	71941408	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs762904903	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	41	626	0	ENST00000298229.2:c.1093C>T	p.Arg365Cys	p.R365C	ENST00000298229	NM_001567.3	365	Cgc/Tgc	10/28	1	2	FACETS	0.325	0.27	0.387	0.325	0.27	0.387	SUBCLONAL	1	TRUE	1	0.38	2		626	663	SUCCESS
EED	8726	MSKCC	GRCh37	11	85967433	85967433	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	59	292	0	ENST00000263360.6:c.431A>G	p.Asp144Gly	p.D144G	ENST00000263360	NM_003797.3	144	gAt/gGt	5/12	1	2	FACETS	0.679	0.586	0.781	0.679	0.586	0.781	SUBCLONAL	1	TRUE	1	0.38	2		292	457	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197307	94197308	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	118	405	0	ENST00000323929.3:c.1196dup	p.Arg400GlnfsTer3	p.R400Qfs*3	ENST00000323929	NM_005591.3	399	ttc/ttTc	11/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.38	2		405	565	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998496	100998496	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	27	303	0	ENST00000325455.5:c.1306del	p.Glu436LysfsTer4	p.E436Kfs*4	ENST00000325455	NM_001202474.3	436	Gaa/aa	1/8	1	2	FACETS	0.35	0.278	0.432	0.35	0.278	0.432	SUBCLONAL	1	TRUE	1	0.38	2		303	406	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106478	108106478	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	76	251	0	ENST00000278616.4:c.413G>A	p.Gly138Glu	p.G138E	ENST00000278616	NM_000051.3	138	gGa/gAa	5/63	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.38	2		251	367	SUCCESS
ATM	472	MSKCC	GRCh37	11	108128286	108128286	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	80	373	0	ENST00000278616.4:c.2329A>G	p.Arg777Gly	p.R777G	ENST00000278616	NM_000051.3	777	Aga/Gga	15/63	1	2	FACETS	0.763	0.673	0.859	0.763	0.673	0.859	SUBCLONAL	1	TRUE	1	0.38	2		373	552	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158413	108158413	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	82	418	0	ENST00000278616.4:c.4080T>A	p.Ser1360Arg	p.S1360R	ENST00000278616	NM_000051.3	1360	agT/agA	27/63	1	2	FACETS	0.651	0.574	0.733	0.651	0.574	0.733	SUBCLONAL	1	TRUE	1	0.38	2		418	663	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172509	108172510	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	92	288	0	ENST00000278616.4:c.5318dup	p.Phe1774ValfsTer8	p.F1774Vfs*8	ENST00000278616	NM_000051.3	1771	aga/agAa	35/63	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.38	2		288	387	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190743	108190743	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	125	448	0	ENST00000278616.4:c.6410A>T	p.Asp2137Val	p.D2137V	ENST00000278616	NM_000051.3	2137	gAc/gTc	44/63	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.38	2		448	581	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236109	108236109	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	35	498	0	ENST00000278616.4:c.9045G>T	p.Glu3015Asp	p.E3015D	ENST00000278616	NM_000051.3	3015	gaG/gaT	63/63	1	2	FACETS	0.265	0.217	0.321	0.265	0.217	0.321	SUBCLONAL	1	TRUE	1	0.38	2		498	694	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416852	416852	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	31	359	0	ENST00000399788.2:c.3698T>G	p.Leu1233Arg	p.L1233R	ENST00000399788	NM_001042603.1	1233	cTt/cGt	23/28	1	2	FACETS	0.358	0.289	0.436	0.358	0.289	0.436	SUBCLONAL	1	TRUE	1	0.38	2		359	456	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420199	420199	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	39	342	0	ENST00000399788.2:c.3068T>C	p.Leu1023Pro	p.L1023P	ENST00000399788	NM_001042603.1	1023	cTt/cCt	21/28	1	2	FACETS	0.371	0.307	0.443	0.371	0.307	0.443	SUBCLONAL	1	TRUE	1	0.38	2		342	553	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475143	475143	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	52	556	0	ENST00000399788.2:c.494T>G	p.Ile165Ser	p.I165S	ENST00000399788	NM_001042603.1	165	aTt/aGt	4/28	1	2	FACETS	0.373	0.317	0.435	0.373	0.317	0.435	SUBCLONAL	1	TRUE	1	0.38	2		556	734	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524150	18524150	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	67	361	1	ENST00000266497.5:c.1662G>T	p.Arg554Ser	p.R554S	ENST00000266497		554	agG/agT	11/31	1	2	FACETS	0.553	0.48	0.631	0.553	0.48	0.631	SUBCLONAL	1	TRUE	1	0.38	2		362	638	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644584	21644584	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	146	410	0	ENST00000421138.2:c.83T>G	p.Leu28Arg	p.L28R	ENST00000421138		28	cTt/cGt	4/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.38	2		410	679	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944810	31944810	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	74	591	0	ENST00000340398.3:c.291A>C	p.Glu97Asp	p.E97D	ENST00000340398	NM_001013699.2	97	gaA/gaC	1/1	1	2	FACETS	0.474	0.414	0.539	0.474	0.414	0.539	SUBCLONAL	1	TRUE	1	0.38	2		591	822	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425683	49425683	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	46	570	0	ENST00000301067.7:c.12805C>A	p.Pro4269Thr	p.P4269T	ENST00000301067	NM_003482.3	4269	Cca/Aca	39/54	1	2	FACETS	0.408	0.343	0.48	0.408	0.343	0.48	SUBCLONAL	1	TRUE	1	0.38	2		570	593	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427029	49427029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1259806161	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	38	463	0	ENST00000301067.7:c.11459C>T	p.Pro3820Leu	p.P3820L	ENST00000301067	NM_003482.3	3820	cCc/cTc	39/54	1	2	FACETS	0.528	0.437	0.629	0.528	0.437	0.629	SUBCLONAL	1	TRUE	1	0.38	2		463	379	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433298	49433298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201336660	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	79	533	0	ENST00000301067.7:c.8149C>T	p.Pro2717Ser	p.P2717S	ENST00000301067	NM_003482.3	2717	Cca/Tca	32/54	1	2	FACETS	0.71	0.625	0.8	0.71	0.625	0.8	SUBCLONAL	1	TRUE	1	0.38	2		533	586	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434049	49434049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	38	612	0	ENST00000301067.7:c.7504C>T	p.Pro2502Ser	p.P2502S	ENST00000301067	NM_003482.3	2502	Cca/Tca	31/54	1	2	FACETS	0.345	0.284	0.413	0.345	0.284	0.413	SUBCLONAL	1	TRUE	1	0.38	2		612	580	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434180	49434180	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	176	783	0	ENST00000301067.7:c.7373A>G	p.Gln2458Arg	p.Q2458R	ENST00000301067	NM_003482.3	2458	cAg/cGg	31/54	1	2	FACETS	0.98	0.903	1	0.98	0.903	1	CLONAL	1	TRUE	1	0.38	2		783	945	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50488327	50488327	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	70	434	0	ENST00000394963.4:c.1241A>G	p.Gln414Arg	p.Q414R	ENST00000394963	NM_003076.4	414	cAa/cGa	10/13	1	2	FACETS	0.593	0.517	0.675	0.593	0.517	0.675	SUBCLONAL	1	TRUE	1	0.38	2		434	621	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487280	56487280	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	50	458	0	ENST00000267101.3:c.1426G>A	p.Gly476Arg	p.G476R	ENST00000267101	NM_001982.3	476	Ggg/Agg	12/28	1	2	FACETS	0.424	0.359	0.496	0.424	0.359	0.496	SUBCLONAL	1	TRUE	1	0.38	2		458	620	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490866	56490866	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	68	439	0	ENST00000267101.3:c.2312T>A	p.Ile771Asn	p.I771N	ENST00000267101	NM_001982.3	771	aTt/aAt	20/28	1	2	FACETS	0.713	0.621	0.812	0.713	0.621	0.812	SUBCLONAL	1	TRUE	1	0.38	2		439	502	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602374	28602374	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	120	396	0	ENST00000241453.7:c.1994T>C	p.Met665Thr	p.M665T	ENST00000241453	NM_004119.2	665	aTg/aCg	16/24	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.38	2		396	595	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877388	28877388	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	42	384	1	ENST00000282397.4:c.3933C>A	p.His1311Gln	p.H1311Q	ENST00000282397	NM_002019.4	1311	caC/caA	30/30	1	2	FACETS	0.402	0.335	0.476	0.402	0.335	0.476	SUBCLONAL	1	TRUE	1	0.38	2		385	550	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28880833	28880833	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	70	571	0	ENST00000282397.4:c.3797A>G	p.Lys1266Arg	p.K1266R	ENST00000282397	NM_002019.4	1266	aAg/aGg	29/30	1	2	FACETS	0.546	0.475	0.622	0.546	0.475	0.622	SUBCLONAL	1	TRUE	1	0.38	2		571	675	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964076	28964077	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	38	390	0	ENST00000282397.4:c.1825dup	p.Met609AsnfsTer5	p.M609Nfs*5	ENST00000282397	NM_002019.4	609	atg/aAtg	13/30	1	2	FACETS	0.406	0.335	0.485	0.406	0.335	0.485	SUBCLONAL	1	TRUE	1	0.38	2		390	493	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28979976	28979976	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1198904737	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	37	506	0	ENST00000282397.4:c.1492A>G	p.Met498Val	p.M498V	ENST00000282397	NM_002019.4	498	Atg/Gtg	11/30	1	2	FACETS	0.279	0.229	0.336	0.279	0.229	0.336	SUBCLONAL	1	TRUE	1	0.38	2		506	697	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913684	32913684	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs765259371	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	26	374	0	ENST00000380152.3:c.5192A>G	p.His1731Arg	p.H1731R	ENST00000380152		1731	cAt/cGt	11/27	1	2	FACETS	0.273	0.216	0.339	0.273	0.216	0.339	SUBCLONAL	1	TRUE	1	0.38	2		374	501	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914013	32914013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	37	502	0	ENST00000380152.3:c.5521C>T	p.Pro1841Ser	p.P1841S	ENST00000380152		1841	Cca/Tca	11/27	1	2	FACETS	0.333	0.274	0.399	0.333	0.274	0.399	SUBCLONAL	1	TRUE	1	0.38	2		502	585	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32931916	32931916	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	52	317	0	ENST00000380152.3:c.7655T>A	p.Ile2552Asn	p.I2552N	ENST00000380152		2552	aTt/aAt	16/27	1	2	FACETS	0.581	0.495	0.675	0.581	0.495	0.675	SUBCLONAL	1	TRUE	1	0.38	2		317	471	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954022	32954023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	53	495	0	ENST00000380152.3:c.9096_9097dup	p.Thr3033LysfsTer30	p.T3033Kfs*30	ENST00000380152		3030	aca/acAAa	23/27	1	2	FACETS	0.374	0.318	0.436	0.374	0.318	0.436	SUBCLONAL	1	TRUE	1	0.38	2		495	746	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281864	49281864	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	57	585	0	ENST00000282018.3:c.911T>A	p.Leu304His	p.L304H	ENST00000282018	NM_020377.2	304	cTc/cAc	1/1	1	2	FACETS	0.462	0.395	0.534	0.462	0.395	0.534	SUBCLONAL	1	TRUE	1	0.38	2		585	650	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73342935	73342935	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	90	309	0	ENST00000377767.4:c.1871G>T	p.Arg624Met	p.R624M	ENST00000377767	NM_014953.3	624	aGg/aTg	14/21	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.38	2		309	446	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100088	30100088	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	88	606	0	ENST00000331968.5:c.1532C>A	p.Ser511Tyr	p.S511Y	ENST00000331968	NM_002742.2	511	tCc/tAc	10/18	1	2	FACETS	0.646	0.572	0.725	0.646	0.572	0.725	SUBCLONAL	1	TRUE	1	0.38	2		606	717	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061738	38061738	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	90	362	0	ENST00000250448.2:c.251G>T	p.Gly84Val	p.G84V	ENST00000250448	NM_004496.3	84	gGc/gTc	2/2	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.38	2		362	369	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061780	38061780	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs943056111	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	43	497	0	ENST00000250448.2:c.209A>T	p.Asn70Ile	p.N70I	ENST00000250448	NM_004496.3	70	aAc/aTc	2/2	1	2	FACETS	0.375	0.313	0.444	0.375	0.313	0.444	SUBCLONAL	1	TRUE	1	0.38	2		497	603	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609633	81609633	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1397760048	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	37	622	0	ENST00000298171.2:c.1231A>G	p.Ile411Val	p.I411V	ENST00000298171	NM_000369.2	411	Ata/Gta	10/10	1	2	FACETS	0.286	0.234	0.343	0.286	0.234	0.343	SUBCLONAL	1	TRUE	1	0.38	2		622	682	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570309	95570309	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1257619891	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	61	308	0	ENST00000393063.1:c.3424T>C	p.Ser1142Pro	p.S1142P	ENST00000393063	NM_030621.3	1142	Tct/Cct	22/28	1	2	FACETS	0.721	0.624	0.827	0.721	0.624	0.827	SUBCLONAL	1	TRUE	1	0.38	2		308	445	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643687	38643688	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	190	555	0	ENST00000299084.4:c.1162dup	p.Ser388PhefsTer2	p.S388Ffs*2	ENST00000299084	NM_152594.2	386	gat/gaTt	7/7	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.38	2		555	748	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961981	41961981	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs993448976	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	38	459	0	ENST00000219905.7:c.889G>T	p.Gly297Cys	p.G297C	ENST00000219905	NM_001164273.1	297	Ggt/Tgt	2/24	1	2	FACETS	0.314	0.259	0.376	0.314	0.259	0.376	SUBCLONAL	1	TRUE	1	0.38	2		459	637	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41962058	41962058	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1321628372	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	36	401	0	ENST00000219905.7:c.966G>T	p.Glu322Asp	p.E322D	ENST00000219905	NM_001164273.1	322	gaG/gaT	2/24	1	2	FACETS	0.313	0.257	0.377	0.313	0.257	0.377	SUBCLONAL	1	TRUE	1	0.38	2		401	605	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059461	42059461	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1016638503	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	63	324	0	ENST00000219905.7:c.9181A>G	p.Ser3061Gly	p.S3061G	ENST00000219905	NM_001164273.1	3061	Agt/Ggt	24/24	1	2	FACETS	0.752	0.652	0.86	0.752	0.652	0.86	SUBCLONAL	1	TRUE	1	0.38	2		324	441	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74000807	74000807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	43	383	0	ENST00000318443.5:c.1497G>T	p.Glu499Asp	p.E499D	ENST00000318443	NM_001024736.1	499	gaG/gaT	7/10	1	2	FACETS	0.449	0.375	0.531	0.449	0.375	0.531	SUBCLONAL	1	TRUE	1	0.38	2		383	504	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292971	91292971	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	207	516	0	ENST00000355112.3:c.473A>G	p.Asp158Gly	p.D158G	ENST00000355112	NM_000057.2	158	gAt/gGt	3/22	1	2	FACETS	0.788	0.735	0.844	1	0.992	1	SUBCLONAL	2	TRUE	1	0.38	2		516	691	SUCCESS
BLM	641	MSKCC	GRCh37	15	91298050	91298050	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	39	334	1	ENST00000355112.3:c.969G>T	p.Lys323Asn	p.K323N	ENST00000355112	NM_000057.2	323	aaG/aaT	5/22	1	2	FACETS	0.387	0.32	0.461	0.387	0.32	0.461	SUBCLONAL	1	TRUE	1	0.38	2		335	531	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2089996	2089996	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	87	691	0	ENST00000219066.1:c.868T>C	p.Cys290Arg	p.C290R	ENST00000219066	NM_002528.5	290	Tgt/Cgt	6/6	1	2	FACETS	0.652	0.577	0.732	0.652	0.577	0.732	SUBCLONAL	1	TRUE	1	0.38	2		691	702	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136198	2136198	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	28	362	0	ENST00000219476.3:c.4667A>T	p.Asn1556Ile	p.N1556I	ENST00000219476	NM_000548.3	1556	aAc/aTc	37/42	1	2	FACETS	0.355	0.283	0.437	0.355	0.283	0.437	SUBCLONAL	1	TRUE	1	0.38	2		362	415	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639794	3639794	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	34	621	0	ENST00000294008.3:c.3845T>C	p.Leu1282Pro	p.L1282P	ENST00000294008	NM_032444.2	1282	cTg/cCg	12/15	1	2	FACETS	0.264	0.215	0.32	0.264	0.215	0.32	SUBCLONAL	1	TRUE	1	0.38	2		621	677	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779694	3779694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1343303954	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	144	528	0	ENST00000262367.5:c.5354G>A	p.Cys1785Tyr	p.C1785Y	ENST00000262367	NM_004380.2	1785	tGc/tAc	31/31	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.38	2		528	542	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789585	3789585	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	71	343	1	ENST00000262367.5:c.4274A>G	p.Asn1425Ser	p.N1425S	ENST00000262367	NM_004380.2	1425	aAc/aGc	25/31	1	2	FACETS	0.792	0.693	0.898	0.792	0.693	0.898	SUBCLONAL	1	TRUE	1	0.38	2		344	472	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860634	3860634	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	59	569	0	ENST00000262367.5:c.945G>T	p.Lys315Asn	p.K315N	ENST00000262367	NM_004380.2	315	aaG/aaT	3/31	1	2	FACETS	0.421	0.361	0.486	0.421	0.361	0.486	SUBCLONAL	1	TRUE	1	0.38	2		569	738	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857574	9857574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	48	374	0	ENST00000330684.3:c.3827C>T	p.Ala1276Val	p.A1276V	ENST00000330684	NM_001134407.1	1276	gCc/gTc	13/13	1	2	FACETS	0.628	0.532	0.734	0.628	0.532	0.734	SUBCLONAL	1	TRUE	1	0.38	2		374	402	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14031664	14031664	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760922582	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	67	395	0	ENST00000311895.7:c.1853G>A	p.Arg618His	p.R618H	ENST00000311895	NM_005236.2	618	cGc/cAc	9/11	1	2	FACETS	0.63	0.548	0.718	0.63	0.548	0.718	SUBCLONAL	1	TRUE	1	0.38	2		395	560	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783694	50783694	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	86	534	0	ENST00000398568.2:c.85A>G	p.Ser29Gly	p.S29G	ENST00000398568	NM_001042412.1	29	Agc/Ggc	3/18	1	2	FACETS	0.567	0.501	0.638	0.567	0.501	0.638	SUBCLONAL	1	TRUE	1	0.38	2		534	798	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50788282	50788282	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	65	540	0	ENST00000398568.2:c.860G>T	p.Ser287Ile	p.S287I	ENST00000398568	NM_001042412.1	287	aGt/aTt	5/18	1	2	FACETS	0.432	0.374	0.495	0.432	0.374	0.495	SUBCLONAL	1	TRUE	1	0.38	2		540	792	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50811817	50811817	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	139	457	0	ENST00000398568.2:c.1094A>G	p.Gln365Arg	p.Q365R	ENST00000398568	NM_001042412.1	365	cAa/cGa	7/18	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.38	2		457	574	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56857730	56857730	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	64	329	0	ENST00000308159.5:c.766A>G	p.Arg256Gly	p.R256G	ENST00000308159	NM_014669.4	256	Agg/Ggg	8/22	1	2	FACETS	0.612	0.531	0.701	0.612	0.531	0.701	SUBCLONAL	1	TRUE	1	0.38	2		329	550	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645382	67645382	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	40	399	0	ENST00000264010.4:c.647A>G	p.Glu216Gly	p.E216G	ENST00000264010	NM_006565.3	216	gAg/gGg	3/12	1	2	FACETS	0.362	0.3	0.432	0.362	0.3	0.432	SUBCLONAL	1	TRUE	1	0.38	2		399	581	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831659	72831659	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	57	508	1	ENST00000268489.5:c.4922A>T	p.Asn1641Ile	p.N1641I	ENST00000268489	NM_006885.3	1641	aAc/aTc	9/10	1	2	FACETS	0.498	0.427	0.576	0.498	0.427	0.576	SUBCLONAL	1	TRUE	1	0.38	2		509	602	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819778	81819778	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	99	401	0	ENST00000359376.3:c.184G>A	p.Glu62Lys	p.E62K	ENST00000359376	NM_002661.3	62	Gag/Aag	2/33	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.38	NA		401	473	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972497	81972497	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	32	407	0	ENST00000359376.3:c.3290A>G	p.Asn1097Ser	p.N1097S	ENST00000359376	NM_002661.3	1097	aAc/aGc	29/33	0.283525985680122	0	FACETS	0.167	0.135	0.204			1	SUBCLONAL	1	TRUE	0	0.38	0		407	624	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352025	89352025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145678880	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	184	627	3	ENST00000301030.4:c.925G>A	p.Ala309Thr	p.A309T	ENST00000301030	NM_001256183.1	309	Gca/Aca	9/13	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.38	2		630	807	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217234	7217234	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	40	546	0	ENST00000380728.2:c.471A>C	p.Gln157His	p.Q157H	ENST00000380728		157	caA/caC	6/11	1	2	FACETS	0.318	0.263	0.379	0.318	0.263	0.379	SUBCLONAL	1	TRUE	1	0.38	2		546	663	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942809	15942809	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs774282901	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	129	487	0	ENST00000268712.3:c.6893A>G	p.Asn2298Ser	p.N2298S	ENST00000268712	NM_006311.3	2298	aAc/aGc	44/46	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.38	2		487	613	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004562	16004562	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	93	282	0	ENST00000268712.3:c.2690+2T>C		p.X897_splice	ENST00000268712	NM_006311.3	897			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.38	2		282	349	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089914	16089914	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	92	349	1	ENST00000268712.3:c.196C>T	p.Arg66Ter	p.R66*	ENST00000268712	NM_006311.3	66	Cga/Tga	3/46	1	2	FACETS	0.775	0.689	0.866	0.775	0.689	0.866	SUBCLONAL	1	TRUE	1	0.38	2		350	625	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17117165	17117165	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	67	374	0	ENST00000285071.4:c.1544T>C	p.Val515Ala	p.V515A	ENST00000285071	NM_144997.5	515	gTg/gCg	14/14	1	2	FACETS	0.8	0.697	0.91	0.8	0.697	0.91	CLONAL	1	TRUE	1	0.38	2		374	441	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127328	17127328	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	74	541	0	ENST00000285071.4:c.526A>G	p.Met176Val	p.M176V	ENST00000285071	NM_144997.5	176	Atg/Gtg	6/14	1	2	FACETS	0.599	0.524	0.68	0.599	0.524	0.68	SUBCLONAL	1	TRUE	1	0.38	2		541	650	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533294	29533294	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	44	224	0	ENST00000356175.3:c.1297T>C	p.Tyr433His	p.Y433H	ENST00000356175	NM_000267.3	433	Tat/Cat	12/57	1	2	FACETS	0.468	0.392	0.552	0.468	0.392	0.552	SUBCLONAL	1	TRUE	1	0.38	2		224	495	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556884	29556884	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	20	273	0	ENST00000356175.3:c.2882T>C	p.Val961Ala	p.V961A	ENST00000356175	NM_000267.3	961	gTa/gCa	22/57	1	2	FACETS	0.307	0.234	0.392	0.307	0.234	0.392	SUBCLONAL	1	TRUE	1	0.38	2		273	343	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559740	29559741	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	83	227	0	ENST00000356175.3:c.3341dup	p.Leu1114PhefsTer3	p.L1114Ffs*3	ENST00000356175	NM_000267.3	1113	ctt/cTtt	26/57	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.38	2		227	369	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592335	29592336	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs876658492	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	138	439	0	ENST00000356175.3:c.4756dup	p.Tyr1586LeufsTer15	p.Y1586Lfs*15	ENST00000356175	NM_000267.3	1584	att/aTtt	35/57	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.38	2		439	622	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687569	29687569	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	40	423	0	ENST00000356175.3:c.8162A>G	p.Tyr2721Cys	p.Y2721C	ENST00000356175	NM_000267.3	2721	tAc/tGc	56/57	1	2	FACETS	0.3	0.249	0.358	0.3	0.249	0.358	SUBCLONAL	1	TRUE	1	0.38	2		423	701	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881139	37881139	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	42	526	0	ENST00000269571.5:c.2468T>C	p.Leu823Pro	p.L823P	ENST00000269571		823	cTg/cCg	20/27	1	2	FACETS	0.346	0.288	0.41	0.346	0.288	0.41	SUBCLONAL	1	TRUE	1	0.38	2		526	639	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487511	38487511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567751373	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	42	441	1	ENST00000254066.5:c.41G>A	p.Gly14Glu	p.G14E	ENST00000254066	NM_000964.3	14	gGg/gAg	2/9	1	2	FACETS	0.54	0.452	0.639	0.54	0.452	0.639	SUBCLONAL	1	TRUE	1	0.38	2		442	409	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40871210	40871210	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	35	424	0	ENST00000428826.2:c.680C>A	p.Ser227Tyr	p.S227Y	ENST00000428826		227	tCc/tAc	8/21	1	2	FACETS	0.325	0.266	0.392	0.325	0.266	0.392	SUBCLONAL	1	TRUE	1	0.38	2		424	566	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244874	41244874	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	74	579	0	ENST00000357654.3:c.2674T>G	p.Leu892Val	p.L892V	ENST00000357654	NM_007294.3	892	Tta/Gta	10/23	1	2	FACETS	0.578	0.506	0.656	0.578	0.506	0.656	SUBCLONAL	1	TRUE	1	0.38	2		579	674	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256164	41256164	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	66	529	0	ENST00000357654.3:c.416A>C	p.Gln139Pro	p.Q139P	ENST00000357654	NM_007294.3	139	cAg/cCg	6/23	1	2	FACETS	0.424	0.367	0.486	0.424	0.367	0.486	SUBCLONAL	1	TRUE	1	0.38	2		529	819	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677873	47677873	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	63	472	0	ENST00000347630.2:c.992A>G	p.Asp331Gly	p.D331G	ENST00000347630	NM_001007230.1	331	gAt/gGt	11/11	1	2	FACETS	0.569	0.492	0.652	0.569	0.492	0.652	SUBCLONAL	1	TRUE	1	0.38	2		472	583	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492894	56492894	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	24	268	0	ENST00000407977.2:c.45G>T	p.Trp15Cys	p.W15C	ENST00000407977		15	tgG/tgT	2/10	1	2	FACETS	0.433	0.339	0.54	0.433	0.339	0.54	SUBCLONAL	1	TRUE	1	0.38	2		268	292	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761153	59761153	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	107	540	0	ENST00000259008.2:c.3254G>T	p.Arg1085Ile	p.R1085I	ENST00000259008	NM_032043.2	1085	aGa/aTa	20/20	1	2	FACETS	0.907	0.815	1	0.907	0.815	1	CLONAL	1	TRUE	1	0.38	2		540	621	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761378	59761378	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	89	421	0	ENST00000259008.2:c.3029A>C	p.Gln1010Pro	p.Q1010P	ENST00000259008	NM_032043.2	1010	cAg/cCg	20/20	1	2	FACETS	0.747	0.663	0.837	0.747	0.663	0.837	SUBCLONAL	1	TRUE	1	0.38	2		421	627	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763424	59763424	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	91	546	0	ENST00000259008.2:c.2678A>G	p.Asn893Ser	p.N893S	ENST00000259008	NM_032043.2	893	aAt/aGt	19/20	1	2	FACETS	0.666	0.591	0.746	0.666	0.591	0.746	SUBCLONAL	1	TRUE	1	0.38	2		546	719	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59924582	59924582	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	26	255	0	ENST00000259008.2:c.508-1G>T		p.X170_splice	ENST00000259008	NM_032043.2	170			1	2	FACETS	0.406	0.322	0.503	0.406	0.322	0.503	SUBCLONAL	1	TRUE	1	0.38	2		255	337	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62008712	62008712	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371573435	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	124	511	0	ENST00000392795.3:c.104G>C	p.Arg35Pro	p.R35P	ENST00000392795	NM_001039933.1	35	cGg/cCg	2/6	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.38	2		511	586	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519948	66519948	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	61	419	0	ENST00000358598.2:c.431A>T	p.Asn144Ile	p.N144I	ENST00000358598	NM_212471.2	144	aAt/aTt	4/11	1	2	FACETS	0.525	0.453	0.604	0.525	0.453	0.604	SUBCLONAL	1	TRUE	1	0.38	2		419	611	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120397	70120397	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1567911726	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	141	840	0	ENST00000245479.2:c.1399A>G	p.Thr467Ala	p.T467A	ENST00000245479	NM_000346.3	467	Acc/Gcc	3/3	1	2	FACETS	0.784	0.714	0.859	0.784	0.714	0.859	SUBCLONAL	1	TRUE	1	0.38	2		840	946	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774994	73774994	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	58	218	0	ENST00000254810.4:c.179A>G	p.Glu60Gly	p.E60G	ENST00000254810	NM_005324.3	60	gAg/gGg	3/4	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.38	2		218	274	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796020	78796020	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	96	567	0	ENST00000306801.3:c.910G>T	p.Asp304Tyr	p.D304Y	ENST00000306801	NM_020761.2	304	Gac/Tac	8/34	1	2	FACETS	0.774	0.69	0.863	0.774	0.69	0.863	SUBCLONAL	1	TRUE	1	0.38	2		567	653	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78931442	78931442	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	120	482	0	ENST00000306801.3:c.3389A>G	p.Asp1130Gly	p.D1130G	ENST00000306801	NM_020761.2	1130	gAc/gGc	29/34	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.38	2		482	577	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39550409	39550409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774626618	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	95	270	0	ENST00000262039.4:c.520C>T	p.Arg174Cys	p.R174C	ENST00000262039	NM_002647.2	174	Cgt/Tgt	4/25	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.38	2		270	436	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213557	2213557	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	62	563	0	ENST00000398665.3:c.1577T>C	p.Leu526Pro	p.L526P	ENST00000398665	NM_032482.2	526	cTg/cCg	17/28	1	2	FACETS	0.489	0.422	0.562	0.489	0.422	0.562	SUBCLONAL	1	TRUE	1	0.38	2		563	667	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214419	5214419	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	40	453	0	ENST00000357368.4:c.4567A>G	p.Thr1523Ala	p.T1523A	ENST00000357368	NM_002850.3	1523	Acc/Gcc	30/38	1	2	FACETS	0.354	0.294	0.422	0.354	0.294	0.422	SUBCLONAL	1	TRUE	1	0.38	2		453	594	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273488	5273488	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	113	627	0	ENST00000357368.4:c.344A>G	p.Glu115Gly	p.E115G	ENST00000357368	NM_002850.3	115	gAg/gGg	4/38	1	2	FACETS	0.743	0.669	0.822	0.743	0.669	0.822	SUBCLONAL	1	TRUE	1	0.38	2		627	800	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7119578	7119578	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	63	467	0	ENST00000302850.5:c.3676C>A	p.Leu1226Ile	p.L1226I	ENST00000302850	NM_000208.2	1226	Ctt/Att	21/22	1	2	FACETS	0.483	0.417	0.554	0.483	0.417	0.554	SUBCLONAL	1	TRUE	1	0.38	2		467	687	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7152859	7152859	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	82	629	0	ENST00000302850.5:c.2109G>T	p.Glu703Asp	p.E703D	ENST00000302850	NM_000208.2	703	gaG/gaT	10/22	1	2	FACETS	0.643	0.567	0.725	0.643	0.567	0.725	SUBCLONAL	1	TRUE	1	0.38	2		629	671	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170655	7170655	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	59	619	0	ENST00000302850.5:c.1376C>A	p.Pro459His	p.P459H	ENST00000302850	NM_000208.2	459	cCc/cAc	6/22	1	2	FACETS	0.376	0.323	0.435	0.376	0.323	0.435	SUBCLONAL	1	TRUE	1	0.38	2		619	825	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10284556	10284556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	49	475	0	ENST00000340748.4:c.626C>T	p.Ser209Phe	p.S209F	ENST00000340748		209	tCc/tTc	7/40	1	2	FACETS	0.362	0.305	0.424	0.362	0.305	0.424	SUBCLONAL	1	TRUE	1	0.38	2		475	713	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610644	10610644	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	114	505	0	ENST00000171111.5:c.66G>T	p.Gln22His	p.Q22H	ENST00000171111	NM_203500.1	22	caG/caT	2/6	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.38	2		505	523	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094852	11094852	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568416609	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	207	685	0	ENST00000358026.2:c.25G>A	p.Gly9Ser	p.G9S	ENST00000358026	NM_001128849.1	9	Ggc/Agc	2/36	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.38	2		685	747	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302259	15302259	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1376158768	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	162	586	0	ENST00000263388.2:c.1012T>C	p.Cys338Arg	p.C338R	ENST00000263388	NM_000435.2	338	Tgt/Cgt	6/33	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.38	2		586	736	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311598	15311598	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	14	89	0	ENST00000263388.2:c.118+1G>A		p.X40_splice	ENST00000263388	NM_000435.2	40			1	2	FACETS	0.676	0.494	0.891	0.676	0.494	0.891	SUBCLONAL	1	TRUE	1	0.38	2		89	109	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366971	15366971	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	43	508	0	ENST00000263377.2:c.1655A>T	p.Lys552Ile	p.K552I	ENST00000263377	NM_058243.2	552	aAa/aTa	9/20	1	2	FACETS	0.292	0.244	0.347	0.292	0.244	0.347	SUBCLONAL	1	TRUE	1	0.38	2		508	774	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221484	36221484	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	41	652	0	ENST00000222270.7:c.5243A>G	p.Asp1748Gly	p.D1748G	ENST00000222270	NM_014727.1	1748	gAc/gGc	25/37	1	2	FACETS	0.338	0.281	0.402	0.338	0.281	0.402	SUBCLONAL	1	TRUE	1	0.38	2		652	638	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223001	36223002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	169	783	1	ENST00000222270.7:c.5636dup	p.Val1880CysfsTer92	p.V1880Cfs*92	ENST00000222270	NM_014727.1	1877	ttg/ttGg	27/37	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.38	2		784	772	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223996	36223997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs747928028	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	170	653	0	ENST00000222270.7:c.6552dup	p.Lys2185GlnfsTer25	p.K2185Qfs*25	ENST00000222270	NM_014727.1	2182	-/C	28/37	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.38	2		653	845	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40744828	40744828	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	164	621	0	ENST00000392038.2:c.692A>G	p.Tyr231Cys	p.Y231C	ENST00000392038	NM_001626.4	231	tAt/tGt	8/14	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.38	2		621	736	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52705213	52705213	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	129	328	0	ENST00000322088.6:c.95T>C	p.Ile32Thr	p.I32T	ENST00000322088	NM_014225.5	32	aTc/aCc	2/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.38	2		328	528	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457289	25457289	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	36	406	0	ENST00000264709.3:c.2598G>T	p.Arg866Ser	p.R866S	ENST00000264709	NM_175629.2	866	agG/agT	23/23	1	2	FACETS	0.362	0.297	0.435	0.362	0.297	0.435	SUBCLONAL	1	TRUE	1	0.38	2		406	523	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463520	25463520	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	127	517	0	ENST00000264709.3:c.2162A>C	p.Lys721Thr	p.K721T	ENST00000264709	NM_175629.2	721	aAg/aCg	18/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.38	2		517	516	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068420	26068421	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	53	271	0	ENST00000435504.4:c.69dup	p.Tyr24IlefsTer9	p.Y24Ifs*9	ENST00000435504		23	-/A	2/13	1	2	FACETS	0.597	0.51	0.693	0.597	0.51	0.693	SUBCLONAL	1	TRUE	1	0.38	2		271	467	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449788	29449789	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	50	773	0	ENST00000389048.3:c.3066dup	p.Val1023CysfsTer55	p.V1023Cfs*55	ENST00000389048	NM_004304.4	1022	-/T	18/29	1	2	FACETS	0.317	0.268	0.372	0.317	0.268	0.372	SUBCLONAL	1	TRUE	1	0.38	2		773	829	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39234266	39234266	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	63	442	0	ENST00000402219.2:c.2579A>G	p.Gln860Arg	p.Q860R	ENST00000402219	NM_005633.3	860	cAa/cGa	16/23	1	2	FACETS	0.475	0.41	0.546	0.475	0.41	0.546	SUBCLONAL	1	TRUE	1	0.38	2		442	698	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39347515	39347515	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	112	250	0	ENST00000402219.2:c.49C>T	p.Pro17Ser	p.P17S	ENST00000402219	NM_005633.3	17	Ccc/Tcc	1/23	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.38	2		250	459	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46588097	46588097	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	44	563	0	ENST00000263734.3:c.647A>G	p.Glu216Gly	p.E216G	ENST00000263734	NM_001430.4	216	gAg/gGg	6/16	1	2	FACETS	0.354	0.296	0.418	0.354	0.296	0.418	SUBCLONAL	1	TRUE	1	0.38	2		563	655	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46602889	46602889	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	132	566	0	ENST00000263734.3:c.947A>G	p.Tyr316Cys	p.Y316C	ENST00000263734	NM_001430.4	316	tAc/tGc	8/16	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.38	2		566	672	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47643570	47643570	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	50	397	0	ENST00000233146.2:c.1076+2T>C		p.X359_splice	ENST00000233146	NM_000251.2	359			1	2	FACETS	0.543	0.461	0.633	0.543	0.461	0.633	SUBCLONAL	1	TRUE	1	0.38	2		397	485	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630663	158630663	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	90	332	0	ENST00000263640.3:c.580T>C	p.Ser194Pro	p.S194P	ENST00000263640	NM_001105.4	194	Tct/Cct	6/11	1	2	FACETS	0.918	0.817	1	0.918	0.817	1	CLONAL	1	TRUE	1	0.38	2		332	516	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158637023	158637023	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	97	485	0	ENST00000263640.3:c.157T>C	p.Cys53Arg	p.C53R	ENST00000263640	NM_001105.4	53	Tgc/Cgc	4/11	1	2	FACETS	0.756	0.675	0.843	0.756	0.675	0.843	SUBCLONAL	1	TRUE	1	0.38	2		485	675	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660585	190660585	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs902001045	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	74	302	0	ENST00000441310.2:c.223A>G	p.Thr75Ala	p.T75A	ENST00000441310	NM_000534.4	75	Acc/Gcc	3/13	1	2	FACETS	0.736	0.646	0.833	0.736	0.646	0.833	SUBCLONAL	1	TRUE	1	0.38	2		302	529	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190717499	190717499	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs750303019	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	86	221	0	ENST00000441310.2:c.818T>C	p.Leu273Ser	p.L273S	ENST00000441310	NM_000534.4	273	tTa/tCa	7/13	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.38	2		221	357	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131283	202131283	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	91	389	0	ENST00000358485.4:c.251T>C	p.Leu84Pro	p.L84P	ENST00000358485	NM_001080125.1	84	cTg/cCg	2/9	1	2	FACETS	0.804	0.715	0.898	0.804	0.715	0.898	CLONAL	1	TRUE	1	0.38	2		389	596	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104641	209104641	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	44	377	0	ENST00000345146.2:c.937A>C	p.Thr313Pro	p.T313P	ENST00000345146	NM_005896.2	313	Acc/Ccc	8/10	1	2	FACETS	0.394	0.33	0.465	0.394	0.33	0.465	SUBCLONAL	1	TRUE	1	0.38	2		377	588	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543903	212543903	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	117	324	0	ENST00000342788.4:c.1496A>G	p.Glu499Gly	p.E499G	ENST00000342788	NM_005235.2	499	gAa/gGa	13/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.38	2		324	473	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566696	212566697	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	26	231	0	ENST00000342788.4:c.1484dup	p.Asn495LysfsTer5	p.N495Kfs*5	ENST00000342788	NM_005235.2	495	aat/aaAt	12/28	1	2	FACETS	0.453	0.359	0.56	0.453	0.359	0.56	SUBCLONAL	1	TRUE	1	0.38	2		231	302	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439701	220439701	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	100	598	0	ENST00000243786.2:c.554C>A	p.Ala185Asp	p.A185D	ENST00000243786	NM_002191.3	185	gCt/gAt	2/2	1	2	FACETS	0.821	0.734	0.913	0.821	0.734	0.913	CLONAL	1	TRUE	1	0.38	2		598	641	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225365158	225365158	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	86	325	0	ENST00000264414.4:c.1532G>T	p.Gly511Val	p.G511V	ENST00000264414	NM_003590.4	511	gGa/gTa	11/16	1	2	FACETS	0.782	0.693	0.877	0.782	0.693	0.877	SUBCLONAL	1	TRUE	1	0.38	2		325	579	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660352	227660352	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	24	423	0	ENST00000305123.5:c.3103T>C	p.Ser1035Pro	p.S1035P	ENST00000305123	NM_005544.2	1035	Tcc/Ccc	1/2	1	2	FACETS	0.373	0.292	0.466	0.373	0.292	0.466	SUBCLONAL	1	TRUE	1	0.38	2		423	339	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794128	242794128	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	192	557	0	ENST00000334409.5:c.600A>G	p.Ile200Met	p.I200M	ENST00000334409	NM_005018.2	200	atA/atG	4/5	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.38	2		557	774	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546967	9546967	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	40	288	0	ENST00000353224.5:c.1055G>T	p.Arg352Met	p.R352M	ENST00000353224	NM_177990.2	352	aGg/aTg	5/10	1	2	FACETS	0.595	0.495	0.705	0.595	0.495	0.705	SUBCLONAL	1	TRUE	1	0.38	2		288	354	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561120	9561120	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	50	373	0	ENST00000353224.5:c.662G>T	p.Arg221Ile	p.R221I	ENST00000353224	NM_177990.2	221	aGa/aTa	4/10	1	2	FACETS	0.663	0.564	0.771	0.663	0.564	0.771	SUBCLONAL	1	TRUE	1	0.38	2		373	397	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386319	31386319	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	43	540	0	ENST00000328111.2:c.1544A>G	p.Glu515Gly	p.E515G	ENST00000328111	NM_006892.3	515	gAg/gGg	15/23	1	2	FACETS	0.364	0.304	0.431	0.364	0.304	0.431	SUBCLONAL	1	TRUE	1	0.38	2		540	622	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39706241	39706242	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	55	227	0	ENST00000361337.2:c.304dup	p.Ile102AsnfsTer11	p.I102Nfs*11	ENST00000361337	NM_003286.2	100	gca/gcAa	5/21	1	2	FACETS	0.888	0.764	1	0.888	0.764	1	CLONAL	1	TRUE	1	0.38	2		227	326	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750372	39750372	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	58	328	0	ENST00000361337.2:c.1987A>G	p.Arg663Gly	p.R663G	ENST00000361337	NM_003286.2	663	Aga/Gga	19/21	1	2	FACETS	0.619	0.533	0.713	0.619	0.533	0.713	SUBCLONAL	1	TRUE	1	0.38	2		328	493	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713328	40713328	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	50	467	0	ENST00000373198.4:c.4187A>G	p.His1396Arg	p.H1396R	ENST00000373198	NM_133170.3	1396	cAc/cGc	30/32	1	2	FACETS	0.478	0.406	0.559	0.478	0.406	0.559	SUBCLONAL	1	TRUE	1	0.38	2		467	550	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735518	40735518	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	46	495	0	ENST00000373198.4:c.3355A>G	p.Met1119Val	p.M1119V	ENST00000373198	NM_133170.3	1119	Atg/Gtg	25/32	1	2	FACETS	0.402	0.338	0.473	0.402	0.338	0.473	SUBCLONAL	1	TRUE	1	0.38	2		495	602	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877388	40877388	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs775272997	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	74	480	0	ENST00000373198.4:c.2308A>G	p.Ile770Val	p.I770V	ENST00000373198	NM_133170.3	770	Atc/Gtc	15/32	1	2	FACETS	0.663	0.581	0.752	0.663	0.581	0.752	SUBCLONAL	1	TRUE	1	0.38	2		480	587	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326797	62326797	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	142	678	0	ENST00000360203.5:c.3616T>G	p.Ser1206Ala	p.S1206A	ENST00000360203	NM_001283009.1	1206	Tca/Gca	34/35	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.38	2		678	695	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36265243	36265243	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	63	338	0	ENST00000300305.3:c.76A>G	p.Asn26Asp	p.N26D	ENST00000300305		26	Aat/Gat	2/8	1	2	FACETS	0.667	0.578	0.764	0.667	0.578	0.764	SUBCLONAL	1	TRUE	1	0.38	2		338	497	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21304055	21304055	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	108	514	0	ENST00000354336.3:c.834A>T	p.Glu278Asp	p.E278D	ENST00000354336	NM_005207.3	278	gaA/gaT	3/3	1	2	FACETS	0.706	0.633	0.783	0.706	0.633	0.783	SUBCLONAL	1	TRUE	1	0.38	2		514	805	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21304129	21304129	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	117	500	0	ENST00000354336.3:c.908A>T	p.Glu303Val	p.E303V	ENST00000354336	NM_005207.3	303	gAg/gTg	3/3	1	2	FACETS	0.836	0.754	0.922	0.836	0.754	0.922	CLONAL	1	TRUE	1	0.38	2		500	737	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000012	30000012	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1249717688	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	36	330	0	ENST00000338641.4:c.25A>G	p.Met9Val	p.M9V	ENST00000338641	NM_000268.3	9	Atg/Gtg	1/16	1	2	FACETS	0.544	0.448	0.652	0.544	0.448	0.652	SUBCLONAL	1	TRUE	1	0.38	2		330	348	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633225	12633225	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	57	490	0	ENST00000251849.4:c.1175A>C	p.Asn392Thr	p.N392T	ENST00000251849	NM_002880.3	392	aAt/aCt	11/17	1	2	FACETS	0.406	0.347	0.47	0.406	0.347	0.47	SUBCLONAL	1	TRUE	1	0.38	2		490	739	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691925	30691925	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	44	335	0	ENST00000295754.5:c.427T>C	p.Cys143Arg	p.C143R	ENST00000295754	NM_003242.5	143	Tgc/Cgc	3/7	1	2	FACETS	0.529	0.444	0.623	0.529	0.444	0.623	SUBCLONAL	1	TRUE	1	0.38	2		335	438	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161957	47161958	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	90	331	0	ENST00000409792.3:c.4168dup	p.Ser1390PhefsTer8	p.S1390Ffs*8	ENST00000409792	NM_014159.6	1390	tca/tTca	3/21	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.38	2		331	437	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163845	47163845	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	74	421	0	ENST00000409792.3:c.2281A>G	p.Met761Val	p.M761V	ENST00000409792	NM_014159.6	761	Atg/Gtg	3/21	1	2	FACETS	0.635	0.556	0.72	0.635	0.556	0.72	SUBCLONAL	1	TRUE	1	0.38	2		421	613	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015045	71015045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	86	252	0	ENST00000318789.4:c.1885G>A	p.Ala629Thr	p.A629T	ENST00000318789	NM_032682.5	629	Gcc/Acc	20/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.38	2		252	357	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73110192	73110192	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	35	373	0	ENST00000356692.5:c.400T>C	p.Cys134Arg	p.C134R	ENST00000356692		134	Tgt/Cgt	5/9	1	2	FACETS	0.307	0.25	0.37	0.307	0.25	0.37	SUBCLONAL	1	TRUE	1	0.38	2		373	601	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114187	73114187	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	73	395	0	ENST00000356692.5:c.823G>T	p.Glu275Ter	p.E275*	ENST00000356692		275	Gaa/Taa	8/9	1	2	FACETS	0.666	0.583	0.755	0.666	0.583	0.755	SUBCLONAL	1	TRUE	1	0.38	2		395	577	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670796	134670796	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747340696	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	112	364	0	ENST00000398015.3:c.707T>C	p.Ile236Thr	p.I236T	ENST00000398015	NM_004441.4	236	aTc/aCc	3/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.38	2		364	467	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138382768	138382768	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	84	404	0	ENST00000289153.2:c.2776A>T	p.Met926Leu	p.M926L	ENST00000289153	NM_006219.2	926	Atg/Ttg	19/22	1	2	FACETS	0.816	0.722	0.916	0.816	0.722	0.916	CLONAL	1	TRUE	1	0.38	2		404	542	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456693	138456693	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	129	387	0	ENST00000289153.2:c.657T>G	p.Asn219Lys	p.N219K	ENST00000289153	NM_006219.2	219	aaT/aaG	4/22	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.38	2		387	554	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215276	142215276	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	51	446	0	ENST00000350721.4:c.5825A>C	p.Asn1942Thr	p.N1942T	ENST00000350721	NM_001184.3	1942	aAt/aCt	34/47	1	2	FACETS	0.45	0.382	0.525	0.45	0.382	0.525	SUBCLONAL	1	TRUE	1	0.38	2		446	596	SUCCESS
ATR	545	MSKCC	GRCh37	3	142259823	142259823	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	59	475	0	ENST00000350721.4:c.3504T>G	p.Ser1168Arg	p.S1168R	ENST00000350721	NM_001184.3	1168	agT/agG	18/47	1	2	FACETS	0.406	0.348	0.469	0.406	0.348	0.469	SUBCLONAL	1	TRUE	1	0.38	2		475	765	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374901	149374901	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	125	396	0	ENST00000360632.3:c.193T>A	p.Ser65Thr	p.S65T	ENST00000360632	NM_015472.4	65	Tcc/Acc	2/7	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.38	2		396	493	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170002329	170002329	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1373137084	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	30	157	0	ENST00000295797.4:c.1148A>G	p.Asn383Ser	p.N383S	ENST00000295797	NM_002740.5	383	aAt/aGt	12/18	1	2	FACETS	0.759	0.616	0.919	0.759	0.616	0.919	CLONAL	1	TRUE	1	0.38	2		157	208	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952152	178952152	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	57	238	0	ENST00000263967.3:c.3207A>G	p.Ter1069TrpextTer4	p.*1069Wext*4	ENST00000263967	NM_006218.2	1069	tgA/tgG	21/21	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.38	2		238	295	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803467	1803467	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	48	377	0	ENST00000260795.2:c.736C>A	p.Leu246Met	p.L246M	ENST00000260795		246	Ctg/Atg	5/17	1	2	FACETS	0.556	0.471	0.651	0.556	0.471	0.651	SUBCLONAL	1	TRUE	1	0.38	2		377	454	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1932437	1932437	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	59	565	0	ENST00000382891.5:c.1495A>T	p.Arg499Ter	p.R499*	ENST00000382891	NM_133335.3	499	Aga/Tga	6/22	1	2	FACETS	0.393	0.337	0.454	0.393	0.337	0.454	SUBCLONAL	1	TRUE	1	0.38	2		565	790	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1952919	1952919	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	161	523	0	ENST00000382891.5:c.2002T>A	p.Tyr668Asn	p.Y668N	ENST00000382891	NM_133335.3	668	Tat/Aat	10/22	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.38	2		523	664	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146599	55146599	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	94	468	0	ENST00000257290.5:c.2273A>G	p.Gln758Arg	p.Q758R	ENST00000257290	NM_006206.4	758	cAg/cGg	16/23	1	2	FACETS	0.694	0.617	0.775	0.694	0.617	0.775	SUBCLONAL	1	TRUE	1	0.38	2		468	713	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156706	55156706	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	63	327	0	ENST00000257290.5:c.3107A>T	p.Lys1036Met	p.K1036M	ENST00000257290	NM_006206.4	1036	aAg/aTg	22/23	1	2	FACETS	0.831	0.722	0.949	0.831	0.722	0.949	CLONAL	1	TRUE	1	0.38	2		327	399	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592069	55592069	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	88	405	0	ENST00000288135.5:c.1393T>C	p.Ser465Pro	p.S465P	ENST00000288135	NM_000222.2	465	Tct/Cct	9/21	1	2	FACETS	0.785	0.697	0.879	0.785	0.697	0.879	SUBCLONAL	1	TRUE	1	0.38	2		405	590	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598057	55598057	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	76	332	0	ENST00000288135.5:c.2254G>T	p.Val752Leu	p.V752L	ENST00000288135	NM_000222.2	752	Gtg/Ttg	16/21	1	2	FACETS	0.857	0.754	0.966	0.857	0.754	0.966	CLONAL	1	TRUE	1	0.38	2		332	467	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984908	55984908	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs201868960	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	122	403	0	ENST00000263923.4:c.221T>C	p.Val74Ala	p.V74A	ENST00000263923	NM_002253.2	74	gTg/gCg	3/30	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.38	2		403	592	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197689	66197689	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	60	310	0	ENST00000273854.3:c.3008+2T>C		p.X1003_splice	ENST00000273854	NM_004439.5	1003			1	2	FACETS	0.718	0.62	0.824	0.718	0.62	0.824	SUBCLONAL	1	TRUE	1	0.38	2		310	440	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106162547	106162547	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756322110	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	32	378	0	ENST00000380013.4:c.3461G>A	p.Gly1154Asp	p.G1154D	ENST00000380013	NM_001127208.2	1154	gGt/gAt	4/11	1	2	FACETS	0.398	0.323	0.483	0.398	0.323	0.483	SUBCLONAL	1	TRUE	1	0.38	2		378	423	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519132	187519132	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	47	421	0	ENST00000441802.2:c.12251G>T	p.Gly4084Val	p.G4084V	ENST00000441802	NM_005245.3	4084	gGt/gTt	23/27	1	2	FACETS	0.361	0.303	0.424	0.361	0.303	0.424	SUBCLONAL	1	TRUE	1	0.38	2		421	686	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540282	187540282	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs567534936	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	65	420	0	ENST00000441802.2:c.7458T>A	p.Asn2486Lys	p.N2486K	ENST00000441802	NM_005245.3	2486	aaT/aaA	10/27	1	2	FACETS	0.652	0.566	0.745	0.652	0.566	0.745	SUBCLONAL	1	TRUE	1	0.38	2		420	525	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541217	187541217	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	34	314	0	ENST00000441802.2:c.6523A>G	p.Met2175Val	p.M2175V	ENST00000441802	NM_005245.3	2175	Atg/Gtg	10/27	1	2	FACETS	0.365	0.298	0.441	0.365	0.298	0.441	SUBCLONAL	1	TRUE	1	0.38	2		314	490	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542740	187542740	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	102	387	0	ENST00000441802.2:c.5000T>A	p.Phe1667Tyr	p.F1667Y	ENST00000441802	NM_005245.3	1667	tTt/tAt	10/27	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.38	2		387	477	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	223643	223643	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	41	443	0	ENST00000264932.6:c.110T>A	p.Val37Asp	p.V37D	ENST00000264932	NM_004168.2	37	gTt/gAt	2/15	1	2	FACETS	0.303	0.251	0.361	0.303	0.251	0.361	SUBCLONAL	1	TRUE	1	0.38	2		443	712	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1253925	1253925	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	40	484	0	ENST00000310581.5:c.3317A>G	p.Lys1106Arg	p.K1106R	ENST00000310581	NM_198253.2	1106	aAg/aGg	16/16	1	2	FACETS	0.397	0.33	0.473	0.397	0.33	0.473	SUBCLONAL	1	TRUE	1	0.38	2		484	530	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31483700	31483700	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	52	308	0	ENST00000344624.3:c.2032A>G	p.Arg678Gly	p.R678G	ENST00000344624		678	Aga/Gga	13/33	1	2	FACETS	0.568	0.484	0.66	0.568	0.484	0.66	SUBCLONAL	1	TRUE	1	0.38	2		308	482	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31504744	31504744	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	83	366	0	ENST00000344624.3:c.1588-2A>G		p.X530_splice	ENST00000344624		530			1	2	FACETS	0.76	0.671	0.854	0.76	0.671	0.854	SUBCLONAL	1	TRUE	1	0.38	2		366	575	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526493	31526493	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs767215647	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	71	793	0	ENST00000344624.3:c.547A>G	p.Asn183Asp	p.N183D	ENST00000344624		183	Aat/Gat	2/33	1	2	FACETS	0.374	0.325	0.427	0.374	0.325	0.427	SUBCLONAL	1	TRUE	1	0.38	2		793	1000	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526743	31526743	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	52	659	1	ENST00000344624.3:c.297G>T	p.Arg99Ser	p.R99S	ENST00000344624		99	agG/agT	2/33	1	2	FACETS	0.371	0.315	0.433	0.371	0.315	0.433	SUBCLONAL	1	TRUE	1	0.38	2		660	737	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959897	38959898	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	74	237	0	ENST00000357387.3:c.2034dup	p.Cys679MetfsTer9	p.C679Mfs*9	ENST00000357387	NM_152756.3	678	-/A	21/38	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.38	2		237	356	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589149	67589149	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	98	249	0	ENST00000274335.5:c.1137A>C	p.Lys379Asn	p.K379N	ENST00000274335		379	aaA/aaC	9/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.38	2		249	357	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591294	67591294	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	42	378	0	ENST00000274335.5:c.1792T>A	p.Leu598Met	p.L598M	ENST00000274335		598	Ttg/Atg	13/15	1	2	FACETS	0.41	0.342	0.486	0.41	0.342	0.486	SUBCLONAL	1	TRUE	1	0.38	2		378	539	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679534	86679534	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	29	295	0	ENST00000274376.6:c.2695T>C	p.Phe899Leu	p.F899L	ENST00000274376	NM_002890.2	899	Ttt/Ctt	21/25	1	2	FACETS	0.346	0.277	0.425	0.346	0.277	0.425	SUBCLONAL	1	TRUE	1	0.38	2		295	441	SUCCESS
APC	324	MSKCC	GRCh37	5	112162841	112162841	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	101	356	0	ENST00000257430.4:c.1445A>G	p.Asp482Gly	p.D482G	ENST00000257430	NM_000038.5	482	gAc/gGc	12/16	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.38	2		356	492	SUCCESS
APC	324	MSKCC	GRCh37	5	112174647	112174647	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	66	313	0	ENST00000257430.4:c.3356A>G	p.His1119Arg	p.H1119R	ENST00000257430	NM_000038.5	1119	cAt/cGt	16/16	1	2	FACETS	0.715	0.622	0.815	0.715	0.622	0.815	SUBCLONAL	1	TRUE	1	0.38	2		313	486	SUCCESS
APC	324	MSKCC	GRCh37	5	112175858	112175858	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1384213186	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	28	274	0	ENST00000257430.4:c.4567A>G	p.Arg1523Gly	p.R1523G	ENST00000257430	NM_000038.5	1523	Aga/Gga	16/16	1	2	FACETS	0.435	0.348	0.534	0.435	0.348	0.534	SUBCLONAL	1	TRUE	1	0.38	2		274	339	SUCCESS
APC	324	MSKCC	GRCh37	5	112176498	112176498	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs863224544	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	93	369	0	ENST00000257430.4:c.5207A>G	p.Lys1736Arg	p.K1736R	ENST00000257430	NM_000038.5	1736	aAa/aGa	16/16	1	2	FACETS	0.987	0.881	1	0.987	0.881	1	CLONAL	1	TRUE	1	0.38	2		369	496	SUCCESS
APC	324	MSKCC	GRCh37	5	112176739	112176740	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	38	270	0	ENST00000257430.4:c.5453dup	p.Asn1818LysfsTer2	p.N1818Kfs*2	ENST00000257430	NM_000038.5	1816	-/A	16/16	1	2	FACETS	0.559	0.463	0.665	0.559	0.463	0.665	SUBCLONAL	1	TRUE	1	0.38	2		270	358	SUCCESS
APC	324	MSKCC	GRCh37	5	112176955	112176955	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	57	465	1	ENST00000257430.4:c.5664G>T	p.Lys1888Asn	p.K1888N	ENST00000257430	NM_000038.5	1888	aaG/aaT	16/16	1	2	FACETS	0.57	0.489	0.658	0.57	0.489	0.658	SUBCLONAL	1	TRUE	1	0.38	2		466	526	SUCCESS
APC	324	MSKCC	GRCh37	5	112177025	112177025	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554086930	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	161	537	1	ENST00000257430.4:c.5734G>A	p.Ala1912Thr	p.A1912T	ENST00000257430	NM_000038.5	1912	Gct/Act	16/16	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.38	2		538	642	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636723	176636724	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	72	415	0	ENST00000439151.2:c.1324dup	p.Cys442LeufsTer11	p.C442Lfs*11	ENST00000439151	NM_022455.4	441	-/T	5/23	1	2	FACETS	0.596	0.52	0.677	0.596	0.52	0.677	SUBCLONAL	1	TRUE	1	0.38	2		415	636	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696711	176696711	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	90	328	0	ENST00000439151.2:c.5412T>G	p.Tyr1804Ter	p.Y1804*	ENST00000439151	NM_022455.4	1804	taT/taG	16/23	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.38	2		328	444	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176715855	176715855	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	118	453	0	ENST00000439151.2:c.6187C>A	p.Leu2063Ile	p.L2063I	ENST00000439151	NM_022455.4	2063	Ctt/Att	21/23	1	2	FACETS	0.857	0.773	0.944	0.857	0.773	0.944	CLONAL	1	TRUE	1	0.38	2		453	725	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720920	176720920	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	24	392	0	ENST00000439151.2:c.6551A>T	p.Lys2184Met	p.K2184M	ENST00000439151	NM_022455.4	2184	aAg/aTg	23/23	1	2	FACETS	0.266	0.208	0.334	0.266	0.208	0.334	SUBCLONAL	1	TRUE	1	0.38	2		392	474	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721148	176721148	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	40	384	0	ENST00000439151.2:c.6779A>G	p.Gln2260Arg	p.Q2260R	ENST00000439151	NM_022455.4	2260	cAg/cGg	23/23	1	2	FACETS	0.569	0.474	0.675	0.569	0.474	0.675	SUBCLONAL	1	TRUE	1	0.38	2		384	370	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271336	26271336	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	46	439	1	ENST00000305910.3:c.277C>A	p.Leu93Met	p.L93M	ENST00000305910	NM_003534.2	93	Ctg/Atg	1/1	1	2	FACETS	0.53	0.446	0.622	0.53	0.446	0.622	SUBCLONAL	1	TRUE	1	0.38	2		440	457	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672400	30672401	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs753948048	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	119	637	0	ENST00000376406.3:c.4559dup	p.Asn1520LysfsTer9	p.N1520Kfs*9	ENST00000376406	NM_014641.2	1520	aat/aaAt	10/15	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.38	2		637	592	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652096	36652096	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	59	616	0	ENST00000244741.5:c.218T>G	p.Leu73Arg	p.L73R	ENST00000244741	NM_000389.4	73	cTg/cGg	2/3	1	2	FACETS	0.485	0.417	0.56	0.485	0.417	0.56	SUBCLONAL	1	TRUE	1	0.38	2		616	640	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956574	93956574	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	68	366	0	ENST00000369303.4:c.2662G>T	p.Gly888Ter	p.G888*	ENST00000369303	NM_004440.3	888	Gga/Tga	15/17	1	2	FACETS	0.761	0.664	0.866	0.761	0.664	0.866	SUBCLONAL	1	TRUE	1	0.38	2		366	470	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109322501	109322501	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs151284724	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	64	450	0	ENST00000436639.2:c.536T>C	p.Ile179Thr	p.I179T	ENST00000436639	NM_014454.2	179	aTt/aCt	3/10	1	2	FACETS	0.488	0.422	0.56	0.488	0.422	0.56	SUBCLONAL	1	TRUE	1	0.38	2		450	690	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111995719	111995719	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	34	332	0	ENST00000368678.4:c.1379del	p.Gly460GlufsTer8	p.G460Efs*8	ENST00000368678		460	gGa/ga	12/13	1	2	FACETS	0.426	0.348	0.514	0.426	0.348	0.514	SUBCLONAL	1	TRUE	1	0.38	2		332	420	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662657	117662657	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	32	459	0	ENST00000368508.3:c.4808T>C	p.Ile1603Thr	p.I1603T	ENST00000368508	NM_002944.2	1603	aTt/aCt	29/43	1	2	FACETS	0.293	0.237	0.357	0.293	0.237	0.357	SUBCLONAL	1	TRUE	1	0.38	2		459	574	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679171	117679171	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	45	310	0	ENST00000368508.3:c.3650T>C	p.Leu1217Pro	p.L1217P	ENST00000368508	NM_002944.2	1217	cTt/cCt	24/43	1	2	FACETS	0.679	0.572	0.795	0.679	0.572	0.795	SUBCLONAL	1	TRUE	1	0.38	2		310	349	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710551	117710551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	22	236	0	ENST00000368508.3:c.1721T>C	p.Leu574Pro	p.L574P	ENST00000368508	NM_002944.2	574	cTt/cCt	12/43	1	2	FACETS	0.459	0.357	0.578	0.459	0.357	0.578	SUBCLONAL	1	TRUE	1	0.38	2		236	252	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715899	117715899	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	28	326	0	ENST00000368508.3:c.859C>T	p.Gln287Ter	p.Q287*	ENST00000368508	NM_002944.2	287	Caa/Taa	9/43	1	2	FACETS	0.389	0.311	0.478	0.389	0.311	0.478	SUBCLONAL	1	TRUE	1	0.38	2		326	379	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199574	138199574	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	35	234	1	ENST00000237289.4:c.992A>G	p.Asp331Gly	p.D331G	ENST00000237289	NM_001270507.1	331	gAt/gGt	7/9	1	2	FACETS	0.526	0.432	0.632	0.526	0.432	0.632	SUBCLONAL	1	TRUE	1	0.38	2		235	350	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527316	157527316	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1308269596	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	93	277	1	ENST00000346085.5:c.5041G>T	p.Glu1681Ter	p.E1681*	ENST00000346085	NM_020732.3	1681	Gaa/Taa	20/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.38	2		278	386	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864497	162864497	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	62	375	0	ENST00000366898.1:c.16A>G	p.Arg6Gly	p.R6G	ENST00000366898	NM_004562.2	6	Agg/Ggg	2/12	1	2	FACETS	0.703	0.609	0.805	0.703	0.609	0.805	SUBCLONAL	1	TRUE	1	0.38	2		375	464	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962840	2962840	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	142	577	0	ENST00000396946.4:c.2068A>G	p.Ser690Gly	p.S690G	ENST00000396946	NM_032415.4	690	Agc/Ggc	16/25	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.38	2		577	685	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983925	2983925	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	93	663	0	ENST00000396946.4:c.605A>G	p.Tyr202Cys	p.Y202C	ENST00000396946	NM_032415.4	202	tAc/tGc	5/25	1	2	FACETS	0.624	0.554	0.698	0.624	0.554	0.698	SUBCLONAL	1	TRUE	1	0.38	2		663	785	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729810	41729810	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	81	310	0	ENST00000242208.4:c.719T>C	p.Val240Ala	p.V240A	ENST00000242208	NM_002192.2	240	gTt/gCt	3/3	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.38	2		310	340	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450370	50450370	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	42	424	0	ENST00000331340.3:c.554G>T	p.Arg185Met	p.R185M	ENST00000331340	NM_006060.4	185	aGg/aTg	5/8	1	2	FACETS	0.469	0.392	0.555	0.469	0.392	0.555	SUBCLONAL	1	TRUE	1	0.38	2		424	471	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55269037	55269037	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	51	598	0	ENST00000275493.2:c.3103C>A	p.Leu1035Met	p.L1035M	ENST00000275493	NM_005228.3	1035	Ctg/Atg	25/28	1	2	FACETS	0.404	0.343	0.472	0.404	0.343	0.472	SUBCLONAL	1	TRUE	1	0.38	2		598	664	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386572	81386572	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	40	418	0	ENST00000222390.5:c.415A>G	p.Thr139Ala	p.T139A	ENST00000222390	NM_000601.4	139	Aca/Gca	4/18	1	2	FACETS	0.343	0.284	0.409	0.343	0.284	0.409	SUBCLONAL	1	TRUE	1	0.38	2		418	614	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509835	106509835	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	35	593	0	ENST00000359195.3:c.1829T>G	p.Leu610Trp	p.L610W	ENST00000359195	NM_002649.2	610	tTg/tGg	2/11	1	2	FACETS	0.279	0.228	0.337	0.279	0.228	0.337	SUBCLONAL	1	TRUE	1	0.38	2		593	660	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340137	116340137	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	62	246	0	ENST00000397752.3:c.999A>G	p.Ile333Met	p.I333M	ENST00000397752	NM_000245.2	333	atA/atG	2/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.38	2		246	270	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340238	116340238	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	81	292	1	ENST00000397752.3:c.1100T>A	p.Ile367Asn	p.I367N	ENST00000397752	NM_000245.2	367	aTc/aAc	2/21	1	2	FACETS	0.949	0.84	1	0.949	0.84	1	CLONAL	1	TRUE	1	0.38	2		293	449	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398662	116398662	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	39	329	0	ENST00000397752.3:c.2252A>G	p.Lys751Arg	p.K751R	ENST00000397752	NM_000245.2	751	aAa/aGa	9/21	1	2	FACETS	0.476	0.395	0.567	0.476	0.395	0.567	SUBCLONAL	1	TRUE	1	0.38	2		329	431	SUCCESS
MET	4233	MSKCC	GRCh37	7	116414995	116414995	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	72	587	0	ENST00000397752.3:c.3089A>G	p.Asp1030Gly	p.D1030G	ENST00000397752	NM_000245.2	1030	gAc/gGc	15/21	1	2	FACETS	0.497	0.434	0.566	0.497	0.434	0.566	SUBCLONAL	1	TRUE	1	0.38	2		587	762	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852099	128852099	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	42	751	0	ENST00000249373.3:c.2171C>A	p.Ser724Tyr	p.S724Y	ENST00000249373	NM_005631.4	724	tCt/tAt	12/12	1	2	FACETS	0.302	0.251	0.358	0.302	0.251	0.358	SUBCLONAL	1	TRUE	1	0.38	2		751	733	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501302	140501302	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs180177035	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	83	374	0	ENST00000288602.6:c.770A>G	p.Gln257Arg	p.Q257R	ENST00000288602	NM_004333.4	257	cAg/cGg	6/18	1	2	FACETS	0.643	0.568	0.724	0.643	0.568	0.724	SUBCLONAL	1	TRUE	1	0.38	2		374	679	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859701	151859701	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	91	261	0	ENST00000262189.6:c.10961A>G	p.Gln3654Arg	p.Q3654R	ENST00000262189	NM_170606.2	3654	cAa/cGa	43/59	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.38	2		261	391	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878613	151878613	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	137	505	0	ENST00000262189.6:c.6332A>G	p.His2111Arg	p.H2111R	ENST00000262189	NM_170606.2	2111	cAt/cGt	36/59	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.38	2		505	598	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152373136	152373136	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	69	440	1	ENST00000359321.1:c.29C>A	p.Ser10Tyr	p.S10Y	ENST00000359321	NM_005431.1	10	tCt/tAt	1/3	1	2	FACETS	0.718	0.626	0.816	0.718	0.626	0.816	SUBCLONAL	1	TRUE	1	0.38	2		441	506	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539020	23539020	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	74	493	0	ENST00000380871.4:c.419A>T	p.Glu140Val	p.E140V	ENST00000380871	NM_006167.3	140	gAg/gTg	2/2	1	2	FACETS	0.752	0.659	0.851	0.752	0.659	0.851	SUBCLONAL	1	TRUE	1	0.38	2		493	518	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133907	38133907	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	131	674	0	ENST00000317025.8:c.3979T>C	p.Cys1327Arg	p.C1327R	ENST00000317025	NM_023034.1	1327	Tgt/Cgt	23/24	1	2	FACETS	0.685	0.62	0.753	0.685	0.62	0.753	SUBCLONAL	1	TRUE	1	0.38	2		674	1007	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028169	69028169	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	76	476	0	ENST00000288368.4:c.3326+2T>C		p.X1109_splice	ENST00000288368	NM_024870.2	1109			1	2	FACETS	0.581	0.51	0.659	0.581	0.51	0.659	SUBCLONAL	1	TRUE	1	0.38	2		476	688	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5070003	5070003	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	57	349	0	ENST00000381652.3:c.1592A>G	p.His531Arg	p.H531R	ENST00000381652	NM_004972.3	531	cAt/cGt	12/25	1	2	FACETS	0.676	0.581	0.779	0.676	0.581	0.779	SUBCLONAL	1	TRUE	1	0.38	2		349	444	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341193	8341193	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	41	364	0	ENST00000356435.5:c.5023C>A	p.Leu1675Ile	p.L1675I	ENST00000356435		1675	Ctt/Att	30/35	1	2	FACETS	0.431	0.358	0.511	0.431	0.358	0.511	SUBCLONAL	1	TRUE	1	0.38	2		364	501	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492946	8492946	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1336605025	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	133	447	0	ENST00000356435.5:c.2383T>C	p.Ser795Pro	p.S795P	ENST00000356435		795	Tcc/Ccc	16/35	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.38	2		447	614	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8497255	8497255	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	84	357	0	ENST00000356435.5:c.2336A>T	p.Asp779Val	p.D779V	ENST00000356435		779	gAt/gTt	15/35	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.38	2		357	433	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93636523	93636523	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	72	447	0	ENST00000375746.1:c.953T>C	p.Val318Ala	p.V318A	ENST00000375746	NM_001174167.1	318	gTg/gCg	8/14	1	2	FACETS	0.583	0.509	0.663	0.583	0.509	0.663	SUBCLONAL	1	TRUE	1	0.38	2		447	650	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912278	97912278	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747249669	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	56	433	0	ENST00000289081.3:c.613A>G	p.Ile205Val	p.I205V	ENST00000289081	NM_000136.2	205	Atc/Gtc	7/15	1	2	FACETS	0.523	0.448	0.605	0.523	0.448	0.605	SUBCLONAL	1	TRUE	1	0.38	2		433	564	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133710873	133710873	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	45	247	2	ENST00000318560.5:c.40A>G	p.Lys14Glu	p.K14E	ENST00000318560	NM_005157.4	14	Aag/Gag	1/11	1	2	FACETS	0.504	0.424	0.593	0.504	0.424	0.593	SUBCLONAL	1	TRUE	1	0.38	2		249	470	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738397	133738397	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	37	402	0	ENST00000318560.5:c.797T>C	p.Leu266Pro	p.L266P	ENST00000318560	NM_005157.4	266	cTg/cCg	4/11	1	2	FACETS	0.389	0.321	0.467	0.389	0.321	0.467	SUBCLONAL	1	TRUE	1	0.38	2		402	500	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760915	133760915	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	65	712	0	ENST00000318560.5:c.3238A>G	p.Lys1080Glu	p.K1080E	ENST00000318560	NM_005157.4	1080	Aag/Gag	11/11	1	2	FACETS	0.441	0.381	0.506	0.441	0.381	0.506	SUBCLONAL	1	TRUE	1	0.38	2		712	776	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391443	139391443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1436539393	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	39	618	0	ENST00000277541.6:c.6748G>A	p.Ala2250Thr	p.A2250T	ENST00000277541	NM_017617.3	2250	Gcg/Acg	34/34	1	2	FACETS	0.321	0.265	0.384	0.321	0.265	0.384	SUBCLONAL	1	TRUE	1	0.38	2		618	639	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325431	1325431	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	41	439	0	ENST00000400841.2:c.244T>C	p.Ser82Pro	p.S82P	ENST00000400841		82	Tcg/Ccg	3/6	1	2	FACETS	0.373	0.31	0.444	0.373	0.31	0.444	SUBCLONAL	1	TRUE	1	0.38	2		439	578	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923040	44923040	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	193	532	0	ENST00000377967.4:c.1901A>C	p.Asn634Thr	p.N634T	ENST00000377967	NM_021140.2	634	aAc/aCc	16/29	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.38	2		532	800	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650828	48650828	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	168	669	0	ENST00000376670.3:c.697A>G	p.Lys233Glu	p.K233E	ENST00000376670	NM_002049.3	233	Aag/Gag	4/6	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.38	2		669	758	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652231	48652231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	59	589	0	ENST00000376670.3:c.902G>A	p.Gly301Asp	p.G301D	ENST00000376670	NM_002049.3	301	gGt/gAt	6/6	1	2	FACETS	0.521	0.448	0.601	0.521	0.448	0.601	SUBCLONAL	1	TRUE	1	0.38	2		589	596	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225949	53225949	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1354865830	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	38	728	0	ENST00000375401.3:c.2900A>G	p.Asp967Gly	p.D967G	ENST00000375401	NM_004187.3	967	gAt/gGt	19/26	1	2	FACETS	0.29	0.239	0.347	0.29	0.239	0.347	SUBCLONAL	1	TRUE	1	0.38	2		728	690	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225964	53225964	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	80	731	0	ENST00000375401.3:c.2885C>A	p.Pro962His	p.P962H	ENST00000375401	NM_004187.3	962	cCt/cAt	19/26	1	2	FACETS	0.612	0.538	0.691	0.612	0.538	0.691	SUBCLONAL	1	TRUE	1	0.38	2		731	688	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410955	63410955	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	96	534	1	ENST00000330258.3:c.2212G>T	p.Gly738Ter	p.G738*	ENST00000330258	NM_152424.3	738	Gga/Tga	2/2	1	2	FACETS	0.849	0.758	0.946	0.849	0.758	0.946	CLONAL	1	TRUE	1	0.38	2		535	595	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888773	76888773	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	33	437	0	ENST00000373344.5:c.5056T>C	p.Tyr1686His	p.Y1686H	ENST00000373344	NM_000489.3	1686	Tat/Cat	19/35	1	2	FACETS	0.284	0.23	0.344	0.284	0.23	0.344	SUBCLONAL	1	TRUE	1	0.38	2		437	612	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019624	123019624	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	165	478	0	ENST00000355640.3:c.112A>T	p.Ser38Cys	p.S38C	ENST00000355640		38	Agt/Tgt	2/7	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.38	2		478	729	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210263	123210263	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	66	509	0	ENST00000218089.9:c.2615T>C	p.Ile872Thr	p.I872T	ENST00000218089	NM_001042749.1	872	aTt/aCt	26/35	1	2	FACETS	0.586	0.508	0.669	0.586	0.508	0.669	SUBCLONAL	1	TRUE	1	0.38	2		509	593	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860007	152860007	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	87	334	0	ENST00000406277.2:c.421A>G	p.Lys141Glu	p.K141E	ENST00000406277	NM_152274.4	141	Aag/Gag	5/7	1		FACETS		0.971	1				CLONAL	1	TRUE	1	0.38	2		334	360	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	58	376	0				ENST00000310581	NM_198253.2	-/1132			0.212036852197962	3	FACETS	0.77	0.666	0.88	0.257	0.222	0.294	INDETERMINATE	1	TRUE	0	0.712294223927147	3		376	287	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579355	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519997	NA	P-0029973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	481	648	2	ENST00000269305.4:c.332T>C	p.Leu111Pro	p.L111P	ENST00000269305	NM_001126112.2	111	cTg/cCg	4/11	0.712294223927147	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.712294223927147	1		650	703	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164842	36164842	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1234144396	NA	P-0029973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	304	613	0	ENST00000300305.3:c.1033C>T	p.Pro345Ser	p.P345S	ENST00000300305		345	Ccc/Tcc	8/8	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.712294223927147	2		613	837	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564534	55564534	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	280	431	0	ENST00000288135.5:c.422C>A	p.Pro141Gln	p.P141Q	ENST00000288135	NM_000222.2	141	cCa/cAa	3/21	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.712294223927147	2		431	642	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249042	55249042	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26031	3271	427	0	ENST00000275493.2:c.2340C>G	p.Ile780Met	p.I780M	ENST00000275493	NM_005228.3	780	atC/atG	20/28	0.712294223927147	38	FACETS	1	0.997	1			1	CLONAL	4	TRUE	NA	0.712294223927147	38		427	29302	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0029974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	94	314	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	1	2	FACETS	0.818	0.728	0.914	0.818	0.728	0.914	CLONAL	1	TRUE	1	0.32	2		314	718	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904860	101904860	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1064796037	NA	P-0029974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	72	256	0	ENST00000374994.4:c.848A>G	p.His283Arg	p.H283R	ENST00000374994	NM_004612.2	283	cAt/cGt	5/9	0.299183491074511	1	FACETS	0.909	0.797	1	0.909	0.797	1	CLONAL	1	TRUE	0	0.32	1		256	416	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007461	62007461	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	81	355	0	ENST00000392795.3:c.406G>T	p.Gly136Cys	p.G136C	ENST00000392795	NM_001039933.1	136	Ggc/Tgc	3/6	1	2	FACETS	0.932	0.823	1	0.932	0.823	1	CLONAL	1	TRUE	1	0.32	2		355	543	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221983	1221991	+	inframe_deletion	In_Frame_Del	DEL	ATCCGGCAG	ATCCGGCAG	-	novel	NA	P-0029974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	67	379	0	ENST00000326873.7:c.907_915del	p.Ile303_Gln305del	p.I303_Q305del	ENST00000326873	NM_000455.4	300	ATCCGGCAG/-	7/10	0.299183491074511	1	FACETS	0.697	0.606	0.794	0.697	0.606	0.794	SUBCLONAL	1	TRUE	0	0.32	1		379	505	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610405	10610405	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	121	461	0	ENST00000171111.5:c.305C>A	p.Ser102Ter	p.S102*	ENST00000171111	NM_203500.1	102	tCa/tAa	2/6	0.299183491074511	1	FACETS	0.968	0.877	1	0.968	0.877	1	CLONAL	1	TRUE	0	0.32	1		461	656	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117630084	117630084	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	72	237	0	ENST00000368508.3:c.6442G>T	p.Gly2148Ter	p.G2148*	ENST00000368508	NM_002944.2	2148	Gga/Tga	41/43	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.32	2		237	426	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398675	116398675	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0029974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	61	231	0	ENST00000397752.3:c.2264+1G>T		p.X755_splice	ENST00000397752	NM_000245.2	755			1	2	FACETS	0.843	0.729	0.967	0.843	0.729	0.967	CLONAL	1	TRUE	1	0.32	2		231	452	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411762	63411762	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	118	265	1	ENST00000330258.3:c.1405G>T	p.Glu469Ter	p.E469*	ENST00000330258	NM_152424.3	469	Gaa/Taa	2/2	1	1	FACETS	0.798	0.727	0.872	1	0.987	1	SUBCLONAL	2	TRUE	0	0.32	1		266	388	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	154	974	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	0.61620597400776	2		974	499	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602532	10602532	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1237235830	NA	P-0029976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	193	539	0	ENST00000171111.5:c.1046A>G	p.Asp349Gly	p.D349G	ENST00000171111	NM_203500.1	349	gAc/gGc	3/6	0.61620597400776	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.61620597400776	1		539	383	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578183	7578210	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCTCATAGGGCACCACCACACTATGT	CGGCTCATAGGGCACCACCACACTATGT	-	novel	NA	P-0029976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	390	640	0	ENST00000269305.4:c.639_666del	p.His214LeufsTer24	p.H214Lfs*24	ENST00000269305	NM_001126112.2	213	cgACATAGTGTGGTGGTGCCCTATGAGCCG/cg	6/11	NA	2	FACETS	0.881	0.845	0.917			1	INDETERMINATE	2	TRUE	NA	0.61620597400776	2		640	718	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584651	187584651	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	75	514	0	ENST00000441802.2:c.3382G>C	p.Glu1128Gln	p.E1128Q	ENST00000441802	NM_005245.3	1128	Gag/Cag	3/27	0.276521904788463	2	FACETS	0.728	0.637	0.825	0.364	0.318	0.413	SUBCLONAL	1	TRUE	0	0.278943851816403	2		514	739	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057230	180057230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780661773	NA	P-0029977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	100	619	0	ENST00000261937.6:c.508C>T	p.Arg170Cys	p.R170C	ENST00000261937	NM_182925.4	170	Cgc/Tgc	4/30	0.232411957441564	3	FACETS	1	0.906	1	0.508	0.453	0.566	CLONAL	1	TRUE	1	0.278943851816403	3		619	804	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221313	1221314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs121913321	NA	P-0029977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	213	604	0	ENST00000326873.7:c.842dup	p.Leu282AlafsTer3	p.L282Afs*3	ENST00000326873	NM_000455.4	279	ggc/ggCc	6/10	0.276521904788463	2	FACETS	0.893	0.831	0.957	0.893	0.831	0.957	CLONAL	2	TRUE	0	0.278943851816403	2		604	855	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069931	5069931	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0029977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	32	256	0	ENST00000381652.3:c.1520C>G	p.Ser507Ter	p.S507*	ENST00000381652	NM_004972.3	507	tCa/tGa	12/25	0.278943851816403	0	FACETS	0.591	0.481	0.714			1	SUBCLONAL	1	TRUE	0	0.278943851816403	0		256	280	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0029977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	409	499	0	ENST00000269305.4:c.375+1del		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.266315052971388	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	4	TRUE	0	0.278943851816403	4		499	917	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187726	11187726	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	118	565	0	ENST00000361445.4:c.6171G>C	p.Met2057Ile	p.M2057I	ENST00000361445	NM_004958.3	2057	atG/atC	44/58	0.232411957441564	3	FACETS	0.898	0.809	0.994	0.449	0.404	0.497	CLONAL	1	TRUE	1	0.278943851816403	3		565	1073	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518564	69518564	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	60	339	0	ENST00000294312.3:c.81C>G	p.Phe27Leu	p.F27L	ENST00000294312	NM_005117.2	27	ttC/ttG	1/3	1	2	FACETS	0.682	0.587	0.785	0.682	0.587	0.785	SUBCLONAL	1	TRUE	1	0.278943851816403	2		339	631	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435131	49435131	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	180	504	1	ENST00000301067.7:c.6422G>T	p.Gly2141Val	p.G2141V	ENST00000301067	NM_003482.3	2141	gGg/gTg	31/54	0.278943851816403	3	FACETS	0.959	0.886	1	0.959	0.886	1	CLONAL	2	TRUE	1	0.278943851816403	3		505	767	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488249	56488249	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	92	514	0	ENST00000267101.3:c.1768C>G	p.Pro590Ala	p.P590A	ENST00000267101	NM_001982.3	590	Ccc/Gcc	15/28	0.278943851816403	3	FACETS	0.809	0.718	0.907	0.405	0.359	0.454	CLONAL	1	TRUE	1	0.278943851816403	3		514	929	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641276	3641276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs748659860	NA	P-0029977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	168	637	0	ENST00000294008.3:c.2363A>G	p.Gln788Arg	p.Q788R	ENST00000294008	NM_032444.2	788	cAg/cGg	12/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.278943851816403	2		637	1019	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509623	29509623	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	106	536	1	ENST00000356175.3:c.828G>T	p.Leu276Phe	p.L276F	ENST00000356175	NM_000267.3	276	ttG/ttT	8/57	0.232411957441564	3	FACETS	1	0.926	1	0.521	0.467	0.579	CLONAL	1	TRUE	1	0.278943851816403	3		537	831	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602480	10602505	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCAGGCCGCTCCGCGGCACCTGCA	GGCCAGGCCGCTCCGCGGCACCTGCA	-	novel	NA	P-0029977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	246	504	0	ENST00000171111.5:c.1073_1098del	p.Leu358ArgfsTer48	p.L358Rfs*48	ENST00000171111	NM_203500.1	358	cTGCAGGTGCCGCGGAGCGGCCTGGCC/c	3/6	0.276521904788463	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.278943851816403	2		504	738	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135095	11135095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	275	669	0	ENST00000358026.2:c.3062G>A	p.Gly1021Asp	p.G1021D	ENST00000358026	NM_001128849.1	1021	gGc/gAc	21/36	0.276521904788463	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.278943851816403	2		669	953	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096626	178096626	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	71	270	0	ENST00000397062.3:c.705G>T	p.Met235Ile	p.M235I	ENST00000397062	NM_006164.4	235	atG/atT	5/5	0.232411957441564	3	FACETS	1	0.966	1	0.661	0.579	0.749	CLONAL	1	TRUE	1	0.278943851816403	3		270	439	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384639	31384639	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	296	592	0	ENST00000328111.2:c.1343del	p.Pro448LeufsTer142	p.P448Lfs*142	ENST00000328111	NM_006892.3	447	caC/ca	13/23	0.278943851816403	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.278943851816403	2		592	930	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557193	187557193	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	100	356	0	ENST00000441802.2:c.4169G>C	p.Trp1390Ser	p.W1390S	ENST00000441802	NM_005245.3	1390	tGg/tCg	6/27	0.276521904788463	2	FACETS	1	0.914	1	0.513	0.458	0.571	CLONAL	1	TRUE	0	0.278943851816403	2		356	699	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722053	176722053	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778167470	NA	P-0029977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	68	361	0	ENST00000439151.2:c.7684G>A	p.Gly2562Arg	p.G2562R	ENST00000439151	NM_022455.4	2562	Ggg/Agg	23/23	0.232411957441564	3	FACETS	1	0.882	1	0.507	0.441	0.578	CLONAL	1	TRUE	1	0.278943851816403	3		361	548	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797305	32797305	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	96	550	0	ENST00000374899.4:c.1804G>C	p.Glu602Gln	p.E602Q	ENST00000374899	NM_018833.2	602	Gag/Cag	11/12	0.278943851816403	3	FACETS	0.874	0.778	0.977	0.437	0.389	0.489	CLONAL	1	TRUE	1	0.278943851816403	3		550	897	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202236	138202236	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779416381	NA	P-0029977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	102	455	0	ENST00000237289.4:c.2153G>A	p.Arg718Gln	p.R718Q	ENST00000237289	NM_001270507.1	718	cGg/cAg	9/9	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.278943851816403	2		455	687	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506483	148506483	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1229491969	NA	P-0029977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	93	192	0	ENST00000320356.2:c.2030-1G>T		p.X677_splice	ENST00000320356	NM_004456.4	677			0.232411957441564	3	FACETS	0.933	0.835	1	0.933	0.835	1	CLONAL	2	TRUE	1	0.278943851816403	3		192	407	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978602	70978602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	104	601	0	ENST00000276594.2:c.1051G>A	p.Glu351Lys	p.E351K	ENST00000276594	NM_024504.3	351	Gag/Aag	5/8	NA	2	FACETS	0.756	0.676	0.842			1	INDETERMINATE	1	TRUE	NA	0.278943851816403	2		601	986	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128348003	128348003	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	114	538	0	ENST00000265960.3:c.502C>A	p.His168Asn	p.H168N	ENST00000265960	NM_001006617.1	168	Cat/Aat	5/12	0.278943851816403	2	FACETS	1	0.917	1	0.51	0.459	0.564	CLONAL	1	TRUE	0	0.278943851816403	2		538	801	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912126	76912126	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	57	171	0	ENST00000373344.5:c.4138G>A	p.Glu1380Lys	p.E1380K	ENST00000373344	NM_000489.3	1380	Gaa/Aaa	13/35	1	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.278943851816403	1		171	244	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0029978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	89	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.703	0.623	0.789	0.703	0.623	0.789	SUBCLONAL	1	TRUE	1	0.32963872318029	2		511	768	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910350	29910350	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1562680966	NA	P-0029978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1228	79	825	0	ENST00000376809.5:c.20G>C	p.Arg7Pro	p.R7P	ENST00000376809	NM_002116.7	7	cGa/cCa	1/8	1	2	FACETS	0.367	0.321	0.416	0.367	0.321	0.416	SUBCLONAL	1	TRUE	1	0.32963872318029	2		825	1307	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576862	7576862	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	102	519	0	ENST00000269305.4:c.984del	p.Phe328LeufsTer17	p.F328Lfs*17	ENST00000269305	NM_001126112.2	328	ttC/tt	9/11	1	2	FACETS	0.664	0.593	0.74	0.664	0.593	0.74	SUBCLONAL	1	TRUE	1	0.32963872318029	2		519	932	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404821	404821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	50	450	0	ENST00000399788.2:c.4373C>T	p.Ser1458Phe	p.S1458F	ENST00000399788	NM_001042603.1	1458	tCt/tTt	26/28	1	2	FACETS	0.35	0.296	0.41	0.35	0.296	0.41	SUBCLONAL	1	TRUE	1	0.32963872318029	2		450	866	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960027	134960027	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	60	431	0	ENST00000398015.3:c.2384C>T	p.Ala795Val	p.A795V	ENST00000398015	NM_004441.4	795	gCc/gTc	13/16	1	2	FACETS	0.495	0.425	0.57	0.495	0.425	0.57	SUBCLONAL	1	TRUE	1	0.32963872318029	2		431	736	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0029979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	259	691	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.327464700893195	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.327464700893195	2		691	760	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0029979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	250	298	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	0.327464700893195	3	FACETS	0.987	0.931	1	0.987	0.931	1	CLONAL	3	TRUE	0	0.327464700893195	3		298	600	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928834	49928834	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs878910700	NA	P-0029979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	77	638	1	ENST00000296474.3:c.3532C>T	p.Arg1178Trp	p.R1178W	ENST00000296474	NM_002447.2	1178	Cgg/Tgg	16/20	0.156071103137557	2	FACETS	0.636	0.558	0.721	0.318	0.279	0.361	INDETERMINATE	1	TRUE	0	0.327464700893195	2		639	739	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911644	114911644	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0029979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	203	390	0	ENST00000543371.1:c.1161+1G>A		p.X387_splice	ENST00000543371	NM_001198531.1	387			0.310730262381734	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.327464700893195	3		390	647	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435071	18435071	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	80	325	0	ENST00000266497.5:c.56A>C	p.Tyr19Ser	p.Y19S	ENST00000266497		19	tAt/tCt	1/31	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.327464700893195	2		325	477	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437222	220437223	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1286117855	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	176	686	0	ENST00000243786.2:c.132dup	p.Ala45ArgfsTer29	p.A45Rfs*29	ENST00000243786	NM_002191.3	42	-/C	1/2	1	2	FACETS	0.851	0.784	0.92	0.851	0.784	0.92	CLONAL	1	TRUE	1	0.489097201906603	2		686	846	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	222	514	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.489097201906603	2		514	765	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	253	429	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.489097201906603	2	FACETS	0.969	0.916	1	0.969	0.916	1	CLONAL	2	TRUE	0	0.489097201906603	2		429	534	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	227	294	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	0.489097201906603	2	FACETS	0.858	0.807	0.91	0.858	0.807	0.91	CLONAL	2	TRUE	0	0.489097201906603	2		294	541	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	431	518	3	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	1	2	FACETS	1	0.989	1	1	0.997	1	CLONAL	2	TRUE	1	0.489097201906603	2		521	815	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	60	215	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.774	0.671	0.884	0.774	0.671	0.884	SUBCLONAL	1	TRUE	1	0.489097201906603	2		215	317	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	156	457	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.926	0.85	1	0.926	0.85	1	CLONAL	1	TRUE	1	0.489097201906603	2		457	689	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	132	490	1	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	0.731	0.665	0.801	0.731	0.665	0.801	SUBCLONAL	1	TRUE	1	0.489097201906603	2		491	738	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	150	554	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.848	0.777	0.923	0.848	0.777	0.923	CLONAL	1	TRUE	1	0.489097201906603	2		557	723	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	273	539	5	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.489097201906603	2		544	938	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	97	359	1	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	1	2	FACETS	0.603	0.538	0.672	0.603	0.538	0.672	SUBCLONAL	1	TRUE	1	0.489097201906603	2		360	658	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	128	592	2	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	1	2	FACETS	0.532	0.481	0.585	0.532	0.481	0.585	SUBCLONAL	1	TRUE	1	0.489097201906603	2		594	984	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105520	27105520	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	31	273	2	ENST00000324856.7:c.5131G>T	p.Gly1711Trp	p.G1711W	ENST00000324856	NM_006015.4	1711	Ggg/Tgg	20/20	1	2	FACETS	0.253	0.204	0.308	0.253	0.204	0.308	SUBCLONAL	1	TRUE	1	0.489097201906603	2		275	502	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28607257	28607257	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373820243	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	160	402	0	ENST00000253063.3:c.1387C>T	p.Arg463Cys	p.R463C	ENST00000253063	NM_031459.4	463	Cgc/Tgc	10/10	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.489097201906603	2		402	630	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933563	36933563	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	48	516	1	ENST00000361632.4:c.1724C>T	p.Ser575Phe	p.S575F	ENST00000361632		575	tCc/tTc	13/16	1	2	FACETS	0.265	0.223	0.312	0.265	0.223	0.312	SUBCLONAL	1	TRUE	1	0.489097201906603	2		517	740	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798458	45798458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750592289	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	191	552	2	ENST00000450313.1:c.553C>T	p.Arg185Trp	p.R185W	ENST00000450313	NM_012222.2	185	Cgg/Tgg	7/16	1	2	FACETS	0.975	0.903	1	0.975	0.903	1	CLONAL	1	TRUE	1	0.489097201906603	2		554	801	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058500	72058500	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	62	284	0	ENST00000357731.5:c.940C>A	p.Pro314Thr	p.P314T	ENST00000357731	NM_173808.2	314	Cct/Act	6/7	1	2	FACETS	0.447	0.386	0.513	0.447	0.386	0.513	SUBCLONAL	1	TRUE	1	0.489097201906603	2		284	567	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275252	115275252	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	46	401	2	ENST00000438362.2:c.1161del	p.Gln388SerfsTer11	p.Q388Sfs*11	ENST00000438362	NM_001242891.1	387	ttT/tt	10/20	1	2	FACETS	0.261	0.219	0.307	0.261	0.219	0.307	SUBCLONAL	1	TRUE	1	0.489097201906603	2		403	722	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466515	120466515	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	184	404	1	ENST00000256646.2:c.4604C>T	p.Ala1535Val	p.A1535V	ENST00000256646	NM_024408.3	1535	gCt/gTt	26/34	1	2	FACETS	0.927	0.857	0.999	0.927	0.857	0.999	CLONAL	1	TRUE	1	0.489097201906603	2		405	812	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957464	175957465	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	145	395	1	ENST00000367669.3:c.1931dup	p.Asn644LysfsTer17	p.N644Kfs*17	ENST00000367669	NM_022457.5	644	aac/aaAc	17/20	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.489097201906603	2		396	572	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680594	241680594	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	127	351	0	ENST00000366560.3:c.155T>C	p.Ile52Thr	p.I52T	ENST00000366560	NM_000143.3	52	aTa/aCa	2/10	1	2	FACETS	0.955	0.869	1	0.955	0.869	1	CLONAL	1	TRUE	1	0.489097201906603	2		351	544	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649922	88649922	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786201038	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	146	415	0	ENST00000372037.3:c.176del	p.Leu59Ter	p.L59*	ENST00000372037	NM_004329.2	57	ccT/cc	4/13	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.489097201906603	2		415	551	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	47	221	0	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	0.524	0.443	0.612	0.524	0.443	0.612	SUBCLONAL	1	TRUE	1	0.489097201906603	2		221	367	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572198	64572198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	85	241	2	ENST00000312049.6:c.1441C>T	p.Arg481Trp	p.R481W	ENST00000312049	NM_130799.2	481	Cgg/Tgg	10/10	1	2	FACETS	0.965	0.86	1	0.965	0.86	1	CLONAL	1	TRUE	1	0.489097201906603	2		243	360	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199881	108199881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881315	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	99	266	1	ENST00000278616.4:c.7223C>T	p.Ser2408Leu	p.S2408L	ENST00000278616	NM_000051.3	2408	tCg/tTg	49/63	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.489097201906603	2		267	387	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	180	500	1	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.919	0.849	0.992	0.919	0.849	0.992	CLONAL	1	TRUE	1	0.489097201906603	2		501	801	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442811	442811	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	212	322	0	ENST00000399788.2:c.1495del	p.Glu499SerfsTer19	p.E499Sfs*19	ENST00000399788	NM_001042603.1	499	Gag/ag	12/28	0.489097201906603	2	FACETS	0.909	0.854	0.964	0.909	0.854	0.964	CLONAL	2	TRUE	0	0.489097201906603	2		322	477	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420859	49420859	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759822794	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	179	464	0	ENST00000301067.7:c.14890C>T	p.Arg4964Cys	p.R4964C	ENST00000301067	NM_003482.3	4964	Cgt/Tgt	48/54	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.489097201906603	2		464	645	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435119	49435119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs574231443	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	143	419	0	ENST00000301067.7:c.6434C>T	p.Pro2145Leu	p.P2145L	ENST00000301067	NM_003482.3	2145	cCg/cTg	31/54	1	2	FACETS	0.984	0.901	1	0.984	0.901	1	CLONAL	1	TRUE	1	0.489097201906603	2		419	594	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209086	133209086	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	82	362	0	ENST00000320574.5:c.6145A>G	p.Thr2049Ala	p.T2049A	ENST00000320574	NM_006231.2	2049	Acc/Gcc	45/49	1	2	FACETS	0.618	0.545	0.694	0.618	0.545	0.694	SUBCLONAL	1	TRUE	1	0.489097201906603	2		362	543	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219113	133219113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771896231	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	179	540	0	ENST00000320574.5:c.4931C>T	p.Ser1644Leu	p.S1644L	ENST00000320574	NM_006231.2	1644	tCg/tTg	37/49	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.489097201906603	2		540	682	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26911760	26911760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	100	318	1	ENST00000381527.3:c.185C>T	p.Ser62Leu	p.S62L	ENST00000381527	NM_001260.1	62	tCg/tTg	2/13	1	2	FACETS	0.885	0.795	0.98	0.885	0.795	0.98	CLONAL	1	TRUE	1	0.489097201906603	2		319	462	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434683	110434683	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771644657	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	202	449	0	ENST00000375856.3:c.3718C>T	p.Arg1240Cys	p.R1240C	ENST00000375856	NM_003749.2	1240	Cgc/Tgc	1/2	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.489097201906603	2		449	731	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060686	38060686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780579934	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	138	610	0	ENST00000250448.2:c.1303G>A	p.Ala435Thr	p.A435T	ENST00000250448	NM_004496.3	435	Gcc/Acc	2/2	1	2	FACETS	0.556	0.505	0.61	0.556	0.505	0.61	SUBCLONAL	1	TRUE	1	0.489097201906603	2		610	1015	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	136	459	0	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	0.794	0.724	0.869	0.794	0.724	0.869	SUBCLONAL	1	TRUE	1	0.489097201906603	2		459	700	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647028	23647028	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1555461597	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	40	560	0	ENST00000261584.4:c.839del	p.Asn280ThrfsTer8	p.N280Tfs*8	ENST00000261584	NM_024675.3	280	aAc/ac	4/13	0.489097201906603	2	FACETS	0.207	0.171	0.248	0.104	0.085	0.124	SUBCLONAL	1	TRUE	0	0.489097201906603	2		560	789	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992483	72992483	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	129	631	1	ENST00000268489.5:c.1562del	p.Lys521ArgfsTer15	p.K521Rfs*15	ENST00000268489	NM_006885.3	521	aAg/ag	2/10	1	2	FACETS	0.578	0.524	0.636	0.578	0.524	0.636	SUBCLONAL	1	TRUE	1	0.489097201906603	2		632	912	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357135	89357135	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	182	453	0	ENST00000301030.4:c.499C>T	p.Arg167Cys	p.R167C	ENST00000301030	NM_001256183.1	167	Cgt/Tgt	6/13	1	2	FACETS	0.888	0.82	0.958	0.888	0.82	0.958	CLONAL	1	TRUE	1	0.489097201906603	2		453	838	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805041	89805041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772505725	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	205	509	1	ENST00000389301.3:c.4336G>A	p.Ala1446Thr	p.A1446T	ENST00000389301	NM_000135.2	1446	Gct/Act	43/43	1	2	FACETS	0.976	0.907	1	0.976	0.907	1	CLONAL	1	TRUE	1	0.489097201906603	2		510	859	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320963	30320963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371166327	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	186	492	1	ENST00000322652.5:c.1373G>A	p.Arg458His	p.R458H	ENST00000322652	NM_015355.2	458	cGc/cAc	12/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.489097201906603	2		493	727	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	194	646	4	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	0.831	0.769	0.895	0.831	0.769	0.895	CLONAL	1	TRUE	1	0.489097201906603	2		650	955	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804188	46804190	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	215	512	0	ENST00000290295.7:c.817_819del	p.Lys273del	p.K273del	ENST00000290295	NM_006361.5	273	AAG/-	2/2	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.489097201906603	2		512	807	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434861	56434861	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1450476536	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	48	436	0	ENST00000407977.2:c.2276A>G	p.Tyr759Cys	p.Y759C	ENST00000407977		759	tAt/tGt	9/10	1	2	FACETS	0.3	0.253	0.352	0.3	0.253	0.352	SUBCLONAL	1	TRUE	1	0.489097201906603	2		436	654	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435168	56435168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766439784	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	113	442	1	ENST00000407977.2:c.1969C>T	p.Arg657Trp	p.R657W	ENST00000407977		657	Cgg/Tgg	9/10	1	2	FACETS	0.666	0.6	0.736	0.666	0.6	0.736	SUBCLONAL	1	TRUE	1	0.489097201906603	2		443	694	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	179	506	0	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	1	2	FACETS	0.94	0.868	1	0.94	0.868	1	CLONAL	1	TRUE	1	0.489097201906603	2		506	779	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740809	58740809	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs765769406	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	180	405	0	ENST00000305921.3:c.1714C>T	p.Arg572Ter	p.R572*	ENST00000305921	NM_003620.3	572	Cga/Tga	6/6	1	2	FACETS	0.932	0.861	1	0.932	0.861	1	CLONAL	1	TRUE	1	0.489097201906603	2		405	790	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763508	59763508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781609846	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	101	371	0	ENST00000259008.2:c.2594G>A	p.Arg865Gln	p.R865Q	ENST00000259008	NM_032043.2	865	cGg/cAg	19/20	1	2	FACETS	0.99	0.891	1	0.99	0.891	1	CLONAL	1	TRUE	1	0.489097201906603	2		371	417	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876602	59876602	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	171	385	0	ENST00000259008.2:c.1199A>C	p.Asp400Ala	p.D400A	ENST00000259008	NM_032043.2	400	gAc/gCc	9/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.489097201906603	2		385	643	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39593518	39593518	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	48	306	0	ENST00000262039.4:c.1286del	p.Asn429MetfsTer7	p.N429Mfs*7	ENST00000262039	NM_002647.2	428	gAa/ga	11/25	1	2	FACETS	0.499	0.423	0.583	0.499	0.423	0.583	SUBCLONAL	1	TRUE	1	0.489097201906603	2		306	393	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1627411	1627411	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377688933	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	212	565	2	ENST00000344749.5:c.313C>T	p.Arg105Trp	p.R105W	ENST00000344749	NM_001136139.2	105	Cgg/Tgg	6/19	1	2	FACETS	0.998	0.928	1	0.998	0.928	1	CLONAL	1	TRUE	1	0.489097201906603	2		567	869	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222418	2222418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1195770308	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	146	385	1	ENST00000398665.3:c.3250C>T	p.Arg1084Cys	p.R1084C	ENST00000398665	NM_032482.2	1084	Cgc/Tgc	24/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.489097201906603	2		386	528	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210796	5210796	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758652323	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	172	460	0	ENST00000357368.4:c.5255C>T	p.Ala1752Val	p.A1752V	ENST00000357368	NM_002850.3	1752	gCg/gTg	34/38	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.489097201906603	2		460	649	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270519	10270519	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	174	488	0	ENST00000340748.4:c.1121C>T	p.Ala374Val	p.A374V	ENST00000340748		374	gCg/gTg	15/40	1	2	FACETS	0.972	0.897	1	0.972	0.897	1	CLONAL	1	TRUE	1	0.489097201906603	2		488	732	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302830	15302830	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs570703724	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	247	613	1	ENST00000263388.2:c.620G>A	p.Arg207His	p.R207H	ENST00000263388	NM_000435.2	207	cGt/cAt	4/33	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.489097201906603	2		614	965	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257890	19257890	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1386180499	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	246	641	1	ENST00000162023.5:c.496C>T	p.Arg166Cys	p.R166C	ENST00000162023		166	Cgc/Tgc	9/13	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.489097201906603	2		642	928	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	205	719	7	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	1	2	FACETS	0.933	0.867	1	0.933	0.867	1	CLONAL	1	TRUE	1	0.489097201906603	2		726	898	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218480	36218480	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	87	454	0	ENST00000222270.7:c.4259T>G	p.Leu1420Arg	p.L1420R	ENST00000222270	NM_014727.1	1420	cTg/cGg	16/37	1	2	FACETS	0.609	0.54	0.683	0.609	0.54	0.683	SUBCLONAL	1	TRUE	1	0.489097201906603	2		454	584	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40740959	40740960	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	211	617	0	ENST00000392038.2:c.1358dup	p.Asp454Ter	p.D454*	ENST00000392038	NM_001626.4	453	cct/ccCt	13/14	1	2	FACETS	0.976	0.908	1	0.976	0.908	1	CLONAL	1	TRUE	1	0.489097201906603	2		617	884	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139919	50139919	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	246	649	0	ENST00000246792.3:c.410T>C	p.Val137Ala	p.V137A	ENST00000246792	NM_006270.3	137	gTt/gCt	4/6	1	2	FACETS	0.994	0.93	1	0.994	0.93	1	CLONAL	1	TRUE	1	0.489097201906603	2		649	1012	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082761	16082761	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	28	73	0	ENST00000281043.3:c.575T>A	p.Val192Asp	p.V192D	ENST00000281043	NM_005378.4	192	gTc/gAc	2/3	1	2	FACETS	0.795	0.644	0.962	0.795	0.644	0.962	CLONAL	1	TRUE	1	0.489097201906603	2		73	144	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660879	227660879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756434990	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	168	371	0	ENST00000305123.5:c.2576C>T	p.Thr859Met	p.T859M	ENST00000305123	NM_005544.2	859	aCg/aTg	1/2	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.489097201906603	2		371	629	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661836	227661836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs577407654	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	221	580	0	ENST00000305123.5:c.1619C>T	p.Pro540Leu	p.P540L	ENST00000305123	NM_005544.2	540	cCg/cTg	1/2	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.489097201906603	2		580	864	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750723	39750723	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	105	291	0	ENST00000361337.2:c.2123G>A	p.Arg708Gln	p.R708Q	ENST00000361337	NM_003286.2	708	cGa/cAa	20/21	1	2	FACETS	0.927	0.835	1	0.927	0.835	1	CLONAL	1	TRUE	1	0.489097201906603	2		291	463	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743943	40743943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs763964405	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	30	332	2	ENST00000373198.4:c.3052C>T	p.Arg1018Ter	p.R1018*	ENST00000373198	NM_133170.3	1018	Cga/Tga	23/32	1	2	FACETS	0.212	0.17	0.259	0.212	0.17	0.259	SUBCLONAL	1	TRUE	1	0.489097201906603	2		334	580	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513282	44513287	+	inframe_deletion	In_Frame_Del	DEL	CCACCG	CCACCG	-	rs745888281	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	175	546	0	ENST00000291552.4:c.648_653del	p.Gly222_Gly223del	p.G222_G223del	ENST00000291552	NM_006758.2	216	ggCGGTGGt/ggt	8/8	0.465466498724325	1	FACETS	0.778	0.719	0.839	0.778	0.719	0.839	SUBCLONAL	1	TRUE	0	0.489097201906603	1		546	695	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288333	21288333	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	200	555	0	ENST00000354336.3:c.578G>T	p.Arg193Met	p.R193M	ENST00000354336	NM_005207.3	193	aGg/aTg	2/3	1	2	FACETS	0.936	0.868	1	0.936	0.868	1	CLONAL	1	TRUE	1	0.489097201906603	2		555	874	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221726	22221726	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	11	20	0	ENST00000215832.6:c.5C>T	p.Ala2Val	p.A2V	ENST00000215832	NM_002745.4	2	gCg/gTg	1/9	1	2	FACETS	1	0.823	1	1	0.823	1	CLONAL	1	TRUE	1	0.489097201906603	2		20	37	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24158966	24158966	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	155	452	0	ENST00000263121.7:c.638T>C	p.Met213Thr	p.M213T	ENST00000263121	NM_003073.3	213	aTg/aCg	6/9	1	2	FACETS	0.963	0.885	1	0.963	0.885	1	CLONAL	1	TRUE	1	0.489097201906603	2		452	658	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130561	29130561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	154	434	0	ENST00000328354.6:c.149G>A	p.Ser50Asn	p.S50N	ENST00000328354	NM_007194.3	50	aGc/aAc	2/15	1	2	FACETS	0.911	0.836	0.99	0.911	0.836	0.99	CLONAL	1	TRUE	1	0.489097201906603	2		434	691	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41279558	41279558	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748653573	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	136	361	0	ENST00000349496.5:c.2128C>T	p.Arg710Cys	p.R710C	ENST00000349496	NM_001904.3	710	Cgc/Tgc	14/15	0.489097201906603	2	FACETS	0.995	0.909	1	0.497	0.454	0.542	CLONAL	1	TRUE	0	0.489097201906603	2		361	559	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52661290	52661290	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	30	286	0	ENST00000394830.3:c.1540del	p.Ser514ValfsTer5	p.S514Vfs*5	ENST00000394830	NM_018313.4	514	Agt/gt	14/30	0.489097201906603	2	FACETS	0.233	0.187	0.286	0.117	0.093	0.143	SUBCLONAL	1	TRUE	0	0.489097201906603	2		286	526	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451328	187451328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	113	233	1	ENST00000232014.4:c.154G>A	p.Ala52Thr	p.A52T	ENST00000232014	NM_001130845.1	52	Gcc/Acc	3/10	1	2	FACETS	0.985	0.892	1	0.985	0.892	1	CLONAL	1	TRUE	1	0.489097201906603	2		234	469	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1941480	1941482	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	143	384	0	ENST00000382891.5:c.1858_1860del	p.Ser620del	p.S620del	ENST00000382891	NM_133335.3	619	cCTTct/cct	9/22	NA	2	FACETS	0.875	0.8	0.954			1	INDETERMINATE	1	TRUE	NA	0.489097201906603	2		384	668	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106182961	106182961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	32	315	1	ENST00000380013.4:c.4000G>A	p.Ala1334Thr	p.A1334T	ENST00000380013	NM_001127208.2	1334	Gca/Aca	8/11	1	2	FACETS	0.354	0.287	0.429	0.354	0.287	0.429	SUBCLONAL	1	TRUE	1	0.489097201906603	2		316	370	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197552	106197552	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	38	310	0	ENST00000380013.4:c.5885C>A	p.Pro1962His	p.P1962H	ENST00000380013	NM_001127208.2	1962	cCc/cAc	11/11	1	2	FACETS	0.294	0.243	0.352	0.294	0.243	0.352	SUBCLONAL	1	TRUE	1	0.489097201906603	2		310	528	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143181693	143181693	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	41	332	0	ENST00000262992.4:c.640G>A	p.Ala214Thr	p.A214T	ENST00000262992	NM_001101669.1	214	Gcc/Acc	9/24	1	2	FACETS	0.292	0.242	0.347	0.292	0.242	0.347	SUBCLONAL	1	TRUE	1	0.489097201906603	2		332	575	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80057492	80057492	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	18	239	0	ENST00000265081.6:c.1896del	p.Lys632AsnfsTer9	p.K632Nfs*9	ENST00000265081	NM_002439.4	631	Aaa/aa	13/24	1	2	FACETS	0.224	0.168	0.291	0.224	0.168	0.291	SUBCLONAL	1	TRUE	1	0.489097201906603	2		239	328	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460436	149460436	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	199	494	1	ENST00000286301.3:c.201C>A	p.Ser67Arg	p.S67R	ENST00000286301	NM_005211.3	67	agC/agA	3/22	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.489097201906603	2		495	769	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522651	176522651	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138800021	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	244	586	2	ENST00000292408.4:c.1748C>T	p.Pro583Leu	p.P583L	ENST00000292408	NM_213647.1	583	cCg/cTg	13/18	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.489097201906603	2		588	904	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562199	176562199	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	181	538	0	ENST00000439151.2:c.95T>G	p.Phe32Cys	p.F32C	ENST00000439151	NM_022455.4	32	tTc/tGc	2/23	1	2	FACETS	0.929	0.858	1	0.929	0.858	1	CLONAL	1	TRUE	1	0.489097201906603	2		538	797	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638803	176638803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	230	527	0	ENST00000439151.2:c.3403C>T	p.Pro1135Ser	p.P1135S	ENST00000439151	NM_022455.4	1135	Cca/Tca	5/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.489097201906603	2		527	839	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405044	405044	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768893830	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	28	316	0	ENST00000380956.4:c.1126C>T	p.Arg376Cys	p.R376C	ENST00000380956	NM_001195286.1	376	Cgc/Tgc	8/9	0.489097201906603	2	FACETS	0.221	0.176	0.272	0.11	0.088	0.136	SUBCLONAL	1	TRUE	0	0.489097201906603	2		316	519	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673000	30673000	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	116	665	0	ENST00000376406.3:c.3960G>T	p.Lys1320Asn	p.K1320N	ENST00000376406	NM_014641.2	1320	aaG/aaT	10/15	0.489097201906603	2	FACETS	0.507	0.456	0.561	0.254	0.228	0.281	SUBCLONAL	1	TRUE	0	0.489097201906603	2		665	935	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322882	31322882	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1476457470	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	283	450	1	ENST00000412585.2:c.1012+2T>C		p.X338_splice	ENST00000412585	NM_005514.6	338			0.489097201906603	2	FACETS	0.964	0.915	1	0.964	0.915	1	CLONAL	2	TRUE	0	0.489097201906603	2		451	600	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181463	32181463	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	32	471	0	ENST00000375023.3:c.2320+2T>C		p.X774_splice	ENST00000375023	NM_004557.3	774			0.489097201906603	2	FACETS	0.228	0.184	0.278	0.114	0.092	0.139	SUBCLONAL	1	TRUE	0	0.489097201906603	2		471	574	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112029219	112029219	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	128	287	0	ENST00000368678.4:c.349G>T	p.Gly117Ter	p.G117*	ENST00000368678		117	Gga/Tga	5/13	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.489097201906603	2		287	458	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681120	117681120	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs748436511	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	136	420	1	ENST00000368508.3:c.3500del	p.Leu1167Ter	p.L1167*	ENST00000368508	NM_002944.2	1167	tTa/ta	23/43	1	2	FACETS	0.861	0.785	0.94	0.861	0.785	0.94	CLONAL	1	TRUE	1	0.489097201906603	2		421	646	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710512	117710512	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	51	151	0	ENST00000368508.3:c.1759+1G>A		p.X587_splice	ENST00000368508	NM_002944.2	587			1	2	FACETS	0.887	0.762	1	0.887	0.762	1	CLONAL	1	TRUE	1	0.489097201906603	2		151	235	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200338	138200338	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753284576	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	179	331	0	ENST00000237289.4:c.1756G>A	p.Ala586Thr	p.A586T	ENST00000237289	NM_001270507.1	586	Gcc/Acc	7/9	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.489097201906603	2		331	634	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138201243	138201243	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	125	357	1	ENST00000237289.4:c.1942G>T	p.Ala648Ser	p.A648S	ENST00000237289	NM_001270507.1	648	Gcg/Tcg	8/9	1	2	FACETS	0.809	0.734	0.887	0.809	0.734	0.887	CLONAL	1	TRUE	1	0.489097201906603	2		358	632	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201808	152201808	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	45	340	0	ENST00000206249.3:c.662G>T	p.Cys221Phe	p.C221F	ENST00000206249	NM_000125.3	221	tGt/tTt	3/8	1	2	FACETS	0.356	0.299	0.419	0.356	0.299	0.419	SUBCLONAL	1	TRUE	1	0.489097201906603	2		340	517	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528284	157528284	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs749055122	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	185	523	0	ENST00000346085.5:c.6013del	p.Val2005TrpfsTer16	p.V2005Wfs*16	ENST00000346085	NM_020732.3	2003	aaG/aa	20/20	1	2	FACETS	0.812	0.75	0.876	0.812	0.75	0.876	CLONAL	1	TRUE	1	0.489097201906603	2		523	932	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683658	162683658	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748892763	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	163	384	0	ENST00000366898.1:c.311G>A	p.Arg104Gln	p.R104Q	ENST00000366898	NM_004562.2	104	cGg/cAg	3/12	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.489097201906603	2		384	664	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6027150	6027150	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	14	12	0	ENST00000265849.7:c.1246T>C	p.Ser416Pro	p.S416P	ENST00000265849	NM_000535.5	416	Tcc/Ccc	11/15	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.489097201906603	2		12	43	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934323	68934323	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs748748350	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	114	522	0	ENST00000288368.4:c.393del	p.Lys131AsnfsTer9	p.K131Nfs*9	ENST00000288368	NM_024870.2	130	cAa/ca	4/40	0.454172326264083	3	FACETS	0.504	0.453	0.559	0.252	0.226	0.28	SUBCLONAL	1	TRUE	1	0.489097201906603	3		522	1150	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980542	70980542	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	60	561	0	ENST00000276594.2:c.835A>G	p.Arg279Gly	p.R279G	ENST00000276594	NM_024504.3	279	Agg/Ggg	4/8	0.454172326264083	3	FACETS	0.256	0.219	0.296	0.128	0.109	0.148	SUBCLONAL	1	TRUE	1	0.489097201906603	3		561	1193	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981892	70981892	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	353	594	1	ENST00000276594.2:c.204del	p.Phe69SerfsTer10	p.F69Sfs*10	ENST00000276594	NM_024504.3	68	ccC/cc	2/8	0.454172326264083	3	FACETS	0.95	0.902	0.997	0.95	0.902	0.997	CLONAL	2	TRUE	1	0.489097201906603	3		595	946	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738411	145738416	+	inframe_deletion	In_Frame_Del	DEL	GGTGCA	GGTGCA	-	rs548804317	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	230	580	0	ENST00000428558.2:c.2569_2574del	p.Cys857_Thr858del	p.C857_T858del	ENST00000428558	NM_004260.3	857	TGCACC/-	16/22	0.454172326264083	3	FACETS	1	0.99	1	0.675	0.63	0.721	CLONAL	1	TRUE	1	0.489097201906603	3		580	867	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485971	8485971	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	114	383	0	ENST00000356435.5:c.2846G>A	p.Gly949Asp	p.G949D	ENST00000356435		949	gGc/gAc	17/35	1	2	FACETS	0.971	0.879	1	0.971	0.879	1	CLONAL	1	TRUE	1	0.489097201906603	2		383	480	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209504	98209504	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766315655	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	137	447	1	ENST00000331920.6:c.4034G>A	p.Arg1345His	p.R1345H	ENST00000331920	NM_000264.3	1345	cGt/cAt	23/24	1	2	FACETS	0.959	0.876	1	0.959	0.876	1	CLONAL	1	TRUE	1	0.489097201906603	2		448	584	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	41	445	1	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.283	0.235	0.336	0.283	0.235	0.336	SUBCLONAL	1	TRUE	1	0.489097201906603	2		446	593	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218572	98218572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748726158	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	131	336	2	ENST00000331920.6:c.3292G>A	p.Val1098Ile	p.V1098I	ENST00000331920	NM_000264.3	1098	Gtt/Att	19/24	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.489097201906603	2		338	521	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139811047	139811047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559816825	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	172	470	4	ENST00000247668.2:c.658G>A	p.Ala220Thr	p.A220T	ENST00000247668	NM_021138.3	220	Gcc/Acc	7/11	1	2	FACETS	0.919	0.848	0.994	0.919	0.848	0.994	CLONAL	1	TRUE	1	0.489097201906603	2		474	765	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412133	63412133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763438860	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	63	321	0	ENST00000330258.3:c.1034C>T	p.Ala345Val	p.A345V	ENST00000330258	NM_152424.3	345	gCc/gTc	2/2	0.489097201906603	2	FACETS	0.393	0.339	0.451			1	SUBCLONAL	1	TRUE	NA	0.489097201906603	2		321	656	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	227	238	0	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	0.489097201906603	2	FACETS	1	0.98	1			1	CLONAL	2	TRUE	NA	0.489097201906603	2		238	431	SUCCESS
BTK	695	MSKCC	GRCh37	X	100625048	100625048	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	26	207	0	ENST00000308731.7:c.329C>A	p.Pro110His	p.P110H	ENST00000308731	NM_000061.2	110	cCt/cAt	5/19	0.489097201906603	2	FACETS	0.242	0.191	0.3			1	SUBCLONAL	1	TRUE	NA	0.489097201906603	2		207	440	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220540	123220540	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	280	255	0	ENST00000218089.9:c.3197G>A	p.Arg1066Gln	p.R1066Q	ENST00000218089	NM_001042749.1	1066	cGg/cAg	30/35	0.489097201906603	2	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.489097201906603	2		255	464	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0029983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	218	474	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.534739718645899	2		474	789	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0029983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	156	392	0	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.825	0.757	0.896	0.825	0.757	0.896	CLONAL	1	TRUE	1	0.534739718645899	2		392	707	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	190	480	2	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	1	2	FACETS	0.982	0.91	1	0.982	0.91	1	CLONAL	1	TRUE	1	0.534739718645899	2		482	724	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0029983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	87	254	2	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.927	0.828	1	0.927	0.828	1	CLONAL	1	TRUE	1	0.534739718645899	2		256	351	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750363	39750363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	152	362	1	ENST00000361337.2:c.1978G>A	p.Asp660Asn	p.D660N	ENST00000361337	NM_003286.2	660	Gat/Aat	19/21	1	2	FACETS	0.965	0.887	1	0.965	0.887	1	CLONAL	1	TRUE	1	0.534739718645899	2		363	589	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0029983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	150	463	1	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.927	0.851	1	0.927	0.851	1	CLONAL	1	TRUE	1	0.534739718645899	2		464	605	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100727	8100728	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs771019738	NA	P-0029983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	220	586	2	ENST00000346208.3:c.708dup	p.Ser237GlnfsTer66	p.S237Qfs*66	ENST00000346208		234	ttc/ttCc	3/6	1	2	FACETS	0.877	0.817	0.94	0.877	0.817	0.94	CLONAL	1	TRUE	1	0.534739718645899	2		588	938	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412958	49412958	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	290	572	0	ENST00000418115.1:c.65T>G	p.Leu22Arg	p.L22R	ENST00000418115	NM_001664.2	22	cTc/cGc	2/5	1	2	FACETS	0.999	0.94	1	0.999	0.94	1	CLONAL	1	TRUE	1	0.534739718645899	2		572	1086	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710652	114710652	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	182	447	2	ENST00000543371.1:c.137C>A	p.Ser46Ter	p.S46*	ENST00000543371	NM_001198531.1	46	tCg/tAg	1/14	1	2	FACETS	0.985	0.912	1	0.985	0.912	1	CLONAL	1	TRUE	1	0.534739718645899	2		449	691	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99154399	99154399	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	196	489	3	ENST00000074304.5:c.545del	p.Pro182LeufsTer2	p.P182Lfs*2	ENST00000074304	NM_001134224.1	181	Ccc/cc	8/26	1	2	FACETS	0.924	0.858	0.993	0.924	0.858	0.993	CLONAL	1	TRUE	1	0.534739718645899	2		492	793	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109746	115109746	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	246	590	0	ENST00000257566.3:c.2132G>A	p.Cys711Tyr	p.C711Y	ENST00000257566	NM_016569.3	711	tGc/tAc	8/8	1	2	FACETS	0.952	0.891	1	0.952	0.891	1	CLONAL	1	TRUE	1	0.534739718645899	2		590	966	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448408	49448408	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs797045661	NA	P-0029983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	238	526	5	ENST00000301067.7:c.303del	p.Ser102AlafsTer28	p.S102Afs*28	ENST00000301067	NM_003482.3	101	ggG/gg	3/54	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.534739718645899	2		531	859	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188512	11188512	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	168	342	0	ENST00000361445.4:c.5909A>G	p.Gln1970Arg	p.Q1970R	ENST00000361445	NM_004958.3	1970	cAg/cGg	42/58	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.534739718645899	2		342	622	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692817	89692817	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	122	209	1	ENST00000371953.3:c.301del	p.Ile101SerfsTer12	p.I101Sfs*12	ENST00000371953	NM_000314.4	101	Atc/tc	5/9	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.534739718645899	2		210	415	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725041	89725052	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAGGTGAAGCTG	TAGGTGAAGCTG	-	novel	NA	P-0029983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	95	241	0	ENST00000371953.3:c.1027-1_1037del		p.X343_splice	ENST00000371953	NM_000314.4	343		9/9	1	2	FACETS	0.948	0.85	1	0.948	0.85	1	CLONAL	1	TRUE	1	0.534739718645899	2		241	375	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481857	56481857	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519817	NA	P-0029983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	296	545	0	ENST00000267101.3:c.785C>G	p.Pro262Arg	p.P262R	ENST00000267101	NM_001982.3	262	cCt/cGt	7/28	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.534739718645899	2		545	988	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209095	133209095	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0029983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	176	390	0	ENST00000320574.5:c.6137-1G>T		p.X2046_splice	ENST00000320574	NM_006231.2	2046			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.534739718645899	2		390	582	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591712	38591713	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	195	387	1	ENST00000299084.4:c.177dup	p.Ile60TyrfsTer18	p.I60Yfs*18	ENST00000299084	NM_152594.2	57	-/T	2/7	1	2	FACETS	0.97	0.9	1	0.97	0.9	1	CLONAL	1	TRUE	1	0.534739718645899	2		388	752	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118394	17118394	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	227	650	0	ENST00000285071.4:c.1443del	p.Ile482SerfsTer2	p.I482Sfs*2	ENST00000285071	NM_144997.5	481	acC/ac	13/14	1	2	FACETS	0.894	0.833	0.956	0.894	0.833	0.956	CLONAL	1	TRUE	1	0.534739718645899	2		650	950	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223887	36223887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1165351797	NA	P-0029983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	311	676	0	ENST00000222270.7:c.6437G>A	p.Ser2146Asn	p.S2146N	ENST00000222270	NM_014727.1	2146	aGc/aAc	28/37	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.534739718645899	2		676	1118	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637513	47637513	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs876658996	NA	P-0029983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	128	369	0	ENST00000233146.2:c.645+2T>C		p.X215_splice	ENST00000233146	NM_000251.2	215			1	2	FACETS	0.81	0.737	0.887	0.81	0.737	0.887	CLONAL	1	TRUE	1	0.534739718645899	2		369	591	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031943	26031943	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	147	299	0	ENST00000244661.2:c.346A>G	p.Lys116Glu	p.K116E	ENST00000244661	NM_003537.3	116	Aag/Gag	1/1	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.534739718645899	2		299	539	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412669	139412700	+	frameshift_variant	Frame_Shift_Del	DEL	ACAGGGTTGGTGTCGCAGTTGGAGCCCTCGTT	ACAGGGTTGGTGTCGCAGTTGGAGCCCTCGTT	-	novel	NA	P-0029983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	207	673	2	ENST00000277541.6:c.1144_1175del	p.Asn382GlnfsTer23	p.N382Qfs*23	ENST00000277541	NM_017617.3	382	AACGAGGGCTCCAACTGCGACACCAACCCTGTc/c	7/34	1	2	FACETS	0.752	0.697	0.808	0.752	0.697	0.808	SUBCLONAL	1	TRUE	1	0.534739718645899	2		675	1030	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317442	1317442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758461223	NA	P-0029983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	237	548	2	ENST00000400841.2:c.623G>A	p.Cys208Tyr	p.C208Y	ENST00000400841		208	tGc/tAc	5/6	1	2	FACETS	0.957	0.895	1	0.957	0.895	1	CLONAL	1	TRUE	1	0.534739718645899	2		550	926	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591122	67591134	+	protein_altering_variant	In_Frame_Del	DEL	AGCTGAGAAAGAC	AGCTGAGAAAGAC	T	novel	NA	P-0029983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	105	312	0	ENST00000274335.5:c.1715_1727delinsT	p.Gln572_Thr576delinsLeu	p.Q572_T576delinsL	ENST00000274335		572	cAGCTGAGAAAGACg/cTg	12/15	1	2	FACETS	0.792	0.713	0.875	0.792	0.713	0.875	SUBCLONAL	1	TRUE	1	0.534739718645899	2		312	496	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993831	72993831	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	CG	novel	NA	P-0029983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	105	396	0	ENST00000268489.5:c.214delinsCG	p.Ser72ArgfsTer47	p.S72Rfs*47	ENST00000268489	NM_006885.3	72	Tcc/CGcc	2/10	1	2	FACETS	0.683	0.613	0.756	0.683	0.613	0.756	SUBCLONAL	1	TRUE	1	0.534739718645899	2		396	575	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0029984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	113	252	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	0.339315403452019	2	FACETS	1	0.983	1	0.69	0.626	0.755	CLONAL	1	TRUE	0	0.440535562359482	2		252	372	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912580	NA	P-0029984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	113	263	0	ENST00000342988.3:c.1157G>A	p.Gly386Asp	p.G386D	ENST00000342988	NM_005359.5	386	gGt/gAt	10/12	0.36586257560786	2	FACETS	1	0.981	1	0.663	0.602	0.726	CLONAL	1	TRUE	0	0.440535562359482	2		263	387	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119795	108119795	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772529339	NA	P-0029984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	85	209	0	ENST00000278616.4:c.1201C>T	p.Gln401Ter	p.Q401*	ENST00000278616	NM_000051.3	401	Cag/Tag	9/63	0.183443431582416	3	FACETS	1	0.97	1	0.424	0.377	0.473	INDETERMINATE	1	TRUE	0	0.440535562359482	3		209	370	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940819	49940819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1489965247	NA	P-0029984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	42	476	2	ENST00000296474.3:c.224G>A	p.Arg75His	p.R75H	ENST00000296474	NM_002447.2	75	cGc/cAc	1/20	0.339315403452019	2	FACETS	0.336	0.28	0.398	0.168	0.14	0.199	SUBCLONAL	1	TRUE	0	0.440535562359482	2		478	568	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056207	27056207	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0029984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	78	422	1	ENST00000324856.7:c.1203C>G	p.Tyr401Ter	p.Y401*	ENST00000324856	NM_006015.4	401	taC/taG	2/20	0.34209046482605	2	FACETS	0.554	0.487	0.626	0.277	0.243	0.313	SUBCLONAL	1	TRUE	0	0.440535562359482	2		423	639	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989034	85989034	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0029984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	64	295	0	ENST00000263360.6:c.1199+1G>T		p.X400_splice	ENST00000263360	NM_003797.3	400			0.34209046482605	2	FACETS	0.612	0.531	0.699	0.306	0.265	0.35	SUBCLONAL	1	TRUE	0	0.440535562359482	2		295	475	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119700	108119700	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	85	168	0	ENST00000278616.4:c.1106C>G	p.Ser369Cys	p.S369C	ENST00000278616	NM_000051.3	369	tCt/tGt	9/63	0.183443431582416	3	FACETS	0.752	0.672	0.837	0.501	0.448	0.558	INDETERMINATE	2	TRUE	0	0.440535562359482	3		168	313	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216630	108216630	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1158350157	NA	P-0029984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	78	239	0	ENST00000278616.4:c.8579C>G	p.Ser2860Cys	p.S2860C	ENST00000278616	NM_000051.3	2860	tCt/tGt	58/63	0.183443431582416	3	FACETS	0.822	0.731	0.916	0.548	0.487	0.611	INDETERMINATE	2	TRUE	0	0.440535562359482	3		239	263	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266484	198266484	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	137	283	0	ENST00000335508.6:c.2352G>A	p.Met784Ile	p.M784I	ENST00000335508	NM_012433.2	784	atG/atA	16/25	0.205941603174082	4	FACETS	0.757	0.691	0.825	0.757	0.691	0.825	INDETERMINATE	2	TRUE	2	0.440535562359482	4		283	592	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273251	198273251	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	168	388	0	ENST00000335508.6:c.959G>A	p.Gly320Glu	p.G320E	ENST00000335508	NM_012433.2	320	gGa/gAa	8/25	0.205941603174082	4	FACETS	0.752	0.692	0.813	0.752	0.692	0.813	INDETERMINATE	2	TRUE	2	0.440535562359482	4		388	731	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385169	41385169	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	58	492	0	ENST00000373198.4:c.792G>T	p.Lys264Asn	p.K264N	ENST00000373198	NM_133170.3	264	aaG/aaT	6/32	0.440535562359482	1	FACETS	0.402	0.345	0.463	0.402	0.345	0.463	SUBCLONAL	1	TRUE	0	0.440535562359482	1		492	511	SUCCESS
APC	324	MSKCC	GRCh37	5	112179000	112179000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	28	265	0	ENST00000257430.4:c.7709C>A	p.Ser2570Ter	p.S2570*	ENST00000257430	NM_000038.5	2570	tCa/tAa	16/16	0.339315403452019	2	FACETS	0.33	0.264	0.406	0.165	0.132	0.203	SUBCLONAL	1	TRUE	0	0.440535562359482	2		265	385	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715354	117715354	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	41	304	0	ENST00000368508.3:c.1135C>T	p.Gln379Ter	p.Q379*	ENST00000368508	NM_002944.2	379	Caa/Taa	10/43	0.144031931921632	4	FACETS	0.549	0.457	0.652	0.275	0.228	0.326	INDETERMINATE	1	TRUE	2	0.440535562359482	4		304	488	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457255	5457255	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	128	286	0	ENST00000381577.3:c.229C>T	p.Gln77Ter	p.Q77*	ENST00000381577	NM_014143.3	77	Cag/Tag	3/7	0.34209046482605	2	FACETS	1	0.984	1	0.674	0.616	0.734	CLONAL	1	TRUE	0	0.440535562359482	2		286	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0029985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	614	644	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.671567098292123	2	FACETS	0.976	0.949	1	0.976	0.949	1	CLONAL	2	TRUE	0	0.695907442658105	2		644	904	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740479	58740479	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	366	565	1	ENST00000305921.3:c.1384C>T	p.Gln462Ter	p.Q462*	ENST00000305921	NM_003620.3	462	Caa/Taa	6/6	0.695907442658105	3	FACETS	0.992	0.948	1	0.992	0.948	1	CLONAL	2	TRUE	1	0.695907442658105	3		566	715	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945071	151945071	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs202184064	NA	P-0029985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	29	621	0	ENST00000262189.6:c.2448C>A	p.Tyr816Ter	p.Y816*	ENST00000262189	NM_170606.2	816	taC/taA	14/59	0.695907442658105	3	FACETS	0.237	0.189	0.29	0.118	0.094	0.145	SUBCLONAL	1	TRUE	1	0.695907442658105	3		621	475	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860126	57860126	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	507	619	0	ENST00000228682.2:c.866T>C	p.Val289Ala	p.V289A	ENST00000228682	NM_005269.2	289	gTg/gCg	8/12	0.695907442658105	3	FACETS	0.932	0.896	0.967	0.932	0.896	0.967	CLONAL	2	TRUE	1	0.695907442658105	3		619	1054	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027108	49027131	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTTCATCATGTTTCATATAGGAT	ATTTCATCATGTTTCATATAGGAT	-	novel	NA	P-0029985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	70	258	0	ENST00000267163.4:c.1696-21_1698del		p.X566_splice	ENST00000267163	NM_000321.2	566		18/27	0.665152613437505	2	FACETS	0.914	0.835	0.991	0.914	0.835	0.991	CLONAL	2	TRUE	0	0.695907442658105	2		258	110	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39647398	39647398	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs752123097	NA	P-0029985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	335	413	0	ENST00000262039.4:c.2570A>G	p.His857Arg	p.H857R	ENST00000262039	NM_002647.2	857	cAt/cGt	24/25	0.695907442658105	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.695907442658105	3		413	624	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517874	187517874	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	130	423	1	ENST00000441802.2:c.12820G>T	p.Glu4274Ter	p.E4274*	ENST00000441802	NM_005245.3	4274	Gaa/Taa	25/27	1	2	FACETS	0.807	0.737	0.879	0.807	0.737	0.879	CLONAL	1	TRUE	1	0.695907442658105	2		424	463	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557332	187557332	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	166	557	1	ENST00000441802.2:c.4030G>T	p.Glu1344Ter	p.E1344*	ENST00000441802	NM_005245.3	1344	Gaa/Taa	6/27	1	2	FACETS	0.982	0.909	1	0.982	0.909	1	CLONAL	1	TRUE	1	0.695907442658105	2		558	486	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346092	152346092	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144079294	NA	P-0029985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	131	460	0	ENST00000359321.1:c.478G>A	p.Val160Ile	p.V160I	ENST00000359321	NM_005431.1	160	Gtc/Atc	3/3	0.695907442658105	3	FACETS	0.94	0.857	1	0.47	0.428	0.513	CLONAL	1	TRUE	1	0.695907442658105	3		460	540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0029986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	46	515	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.731	0.614	0.861	0.731	0.614	0.861	SUBCLONAL	1	TRUE	1	0.15	2		515	839	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0029986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	70	429	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.755	0.658	0.86	1	0.973	1	SUBCLONAL	2	TRUE	1	0.15	2		429	618	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0029986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	35	294	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	1	2	FACETS	0.972	0.796	1	0.972	0.796	1	CLONAL	1	TRUE	1	0.15	2		294	480	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0029989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	239	218	0				ENST00000310581	NM_198253.2	-/1132			0.760998378499189	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.760998378499189	3		218	429	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0029989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	279	434	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.704612322476538	2	FACETS	0.933	0.896	0.968	0.933	0.896	0.968	CLONAL	2	TRUE	0	0.760998378499189	2		434	393	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426127	47426127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	515	320	0	ENST00000377045.4:c.647C>T	p.Pro216Leu	p.P216L	ENST00000377045	NM_001654.4	216	cCc/cTc	7/16	0.685851678857256	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.760998378499189	2		320	611	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190477	32190477	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	228	652	0	ENST00000375023.3:c.262C>A	p.Leu88Ile	p.L88I	ENST00000375023	NM_004557.3	88	Cta/Ata	3/30	0.760998378499189	5	FACETS	0.909	0.845	0.976	0.303	0.281	0.326	CLONAL	1	TRUE	2	0.760998378499189	5		652	1411	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662655	117662655	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408672277	NA	P-0029989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	330	387	0	ENST00000368508.3:c.4810C>T	p.Pro1604Ser	p.P1604S	ENST00000368508	NM_002944.2	1604	Cct/Tct	29/43	0.727565398632673	2	FACETS	0.997	0.964	1	0.997	0.964	1	CLONAL	2	TRUE	0	0.760998378499189	2		387	435	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517785	176517785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	432	565	0	ENST00000292408.4:c.395C>T	p.Ser132Phe	p.S132F	ENST00000292408	NM_213647.1	132	tCc/tTc	4/18	0.760998378499189	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.760998378499189	3		565	778	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156662	2156662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	238	567	0	ENST00000434045.2:c.260C>T	p.Thr87Ile	p.T87I	ENST00000434045	NM_001127598.1	87	aCc/aTc	3/5	1	2	FACETS	0.955	0.897	1	0.955	0.897	1	CLONAL	1	TRUE	1	0.760998378499189	2		567	655	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205275	46205282	+	frameshift_variant	Frame_Shift_Del	DEL	CACAGCTT	CACAGCTT	-	novel	NA	P-0029989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	294	395	0	ENST00000334344.6:c.360_367del	p.Gln121TyrfsTer30	p.Q121Yfs*30	ENST00000334344	NM_152641.2	120	cCACAGCTT/c	4/21	0.760998378499189	3	FACETS	0.959	0.913	1	0.959	0.913	1	CLONAL	2	TRUE	1	0.760998378499189	3		395	556	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987066	36987066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1325836054	NA	P-0029989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	464	457	5	ENST00000354822.5:c.623G>A	p.Arg208Gln	p.R208Q	ENST00000354822	NM_001079668.2	208	cGa/cAa	3/3	0.678742214675843	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.760998378499189	4		462	1010	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031925	10031925	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	175	467	0	ENST00000330684.3:c.898A>G	p.Thr300Ala	p.T300A	ENST00000330684	NM_001134407.1	300	Acc/Gcc	3/13	0.760998378499189	3	FACETS	0.819	0.756	0.885	0.41	0.378	0.443	CLONAL	1	TRUE	1	0.760998378499189	3		467	775	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42381385	42381385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	178	474	0	ENST00000221972.3:c.11G>A	p.Gly4Asp	p.G4D	ENST00000221972	NM_021601.3	4	gGt/gAt	1/5	0.656660107761938	3	FACETS	0.935	0.864	1	0.467	0.432	0.504	CLONAL	1	TRUE	1	0.760998378499189	3		474	691	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514780	44514781	+	missense_variant	Missense_Mutation	DNP	CG	CG	AA	novel	NA	P-0029989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	165	438	2	ENST00000291552.4:c.466_467delinsTT	p.Arg156Phe	p.R156F	ENST00000291552	NM_006758.2	156	CGt/TTt	6/8	0.601524731267403	3	FACETS	0.864	0.796	0.935	0.432	0.398	0.468	CLONAL	1	TRUE	1	0.760998378499189	3		440	693	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630710	187630710	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	183	531	0	ENST00000441802.2:c.272G>T	p.Gly91Val	p.G91V	ENST00000441802	NM_005245.3	91	gGa/gTa	2/27	0.760998378499189	3	FACETS	0.695	0.641	0.751	0.348	0.32	0.376	SUBCLONAL	1	TRUE	1	0.760998378499189	3		531	955	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850355	128850355	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	353	468	0	ENST00000249373.3:c.1618G>A	p.Ala540Thr	p.A540T	ENST00000249373	NM_005631.4	540	Gcc/Acc	9/12	0.760998378499189	5	FACETS	0.963	0.914	1	0.642	0.609	0.675	CLONAL	2	TRUE	2	0.760998378499189	5		468	1032	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	28	376	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.607	0.486	0.743	0.607	0.486	0.743	SUBCLONAL	1	TRUE	1	0.31834773484466	2		376	290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0029991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	153	618	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.307466449286654	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.31834773484466	1		618	728	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100592	157100592	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	21	236	0	ENST00000346085.5:c.1529T>C	p.Met510Thr	p.M510T	ENST00000346085	NM_020732.3	510	aTg/aCg	1/20	0.31834773484466	1	FACETS	0.389	0.3	0.493	0.389	0.3	0.493	SUBCLONAL	1	TRUE	0	0.31834773484466	1		236	285	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375209	118375209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	100	395	0	ENST00000534358.1:c.8602G>A	p.Glu2868Lys	p.E2868K	ENST00000534358	NM_005933.3	2868	Gag/Aag	27/36	1	2	FACETS	0.997	0.892	1	0.997	0.892	1	CLONAL	1	TRUE	1	0.31834773484466	2		395	630	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783844	50783844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	60	579	1	ENST00000398568.2:c.235C>T	p.His79Tyr	p.H79Y	ENST00000398568	NM_001042412.1	79	Cat/Tat	3/18	1	2	FACETS	0.458	0.393	0.529	0.458	0.393	0.529	SUBCLONAL	1	TRUE	1	0.31834773484466	2		580	823	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942554	17942554	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	145	640	0	ENST00000458235.1:c.2734G>T	p.Asp912Tyr	p.D912Y	ENST00000458235	NM_000215.3	912	Gac/Tac	20/24	0.307466449286654	1	FACETS	0.974	0.89	1	0.974	0.89	1	CLONAL	1	TRUE	0	0.31834773484466	1		640	786	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808928	1808928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	136	641	0	ENST00000260795.2:c.2360C>T	p.Ser787Phe	p.S787F	ENST00000260795		787	tCc/tTc	17/17	0.307466449286654	1	FACETS	0.975	0.888	1	0.975	0.888	1	CLONAL	1	TRUE	0	0.31834773484466	1		641	737	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028865	47028866	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0029991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	133	597	0	ENST00000377604.3:c.170dup	p.Tyr57Ter	p.Y57*	ENST00000377604	NM_001204468.1	57	tat/tAat	3/24	1	2	FACETS	0.972	0.882	1	0.972	0.882	1	CLONAL	1	TRUE	1	0.31834773484466	2		597	860	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776621	9776621	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	318	523	1	ENST00000377346.4:c.724C>A	p.Gln242Lys	p.Q242K	ENST00000377346	NM_005026.3	242	Cag/Aag	6/24	1	2	FACETS	0.987	0.938	1	0.987	0.938	1	CLONAL	1	TRUE	1	0.884853270727059	2		524	728	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058033	27058033	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	93	620	0	ENST00000324856.7:c.1741C>T	p.Gln581Ter	p.Q581*	ENST00000324856	NM_006015.4	581	Cag/Tag	3/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.427604648699361	2		620	405	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692794	89692794	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121909238	NA	P-0029997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	91	363	0	ENST00000371953.3:c.278A>G	p.His93Arg	p.H93R	ENST00000371953	NM_000314.4	93	cAt/cGt	5/9	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.427604648699361	2		363	284	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0029999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	185	386	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.165925732645251	4	FACETS	0.909	0.841	0.979	0.909	0.841	0.979	INDETERMINATE	2	TRUE	2	0.352537420374393	4		386	781	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764146326	NA	P-0029999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	280	681	0	ENST00000269305.4:c.841G>A	p.Asp281Asn	p.D281N	ENST00000269305	NM_001126112.2	281	Gac/Aac	8/11	0.352537420374393	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.352537420374393	2		681	698	SUCCESS
APC	324	MSKCC	GRCh37	5	112175162	112175162	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561588104	NA	P-0029999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	65	190	0	ENST00000257430.4:c.3871C>T	p.Gln1291Ter	p.Q1291*	ENST00000257430	NM_000038.5	1291	Cag/Tag	16/16	0.165925732645251	4	FACETS	0.777	0.678	0.882	0.777	0.678	0.882	INDETERMINATE	2	TRUE	2	0.352537420374393	4		190	321	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803144	1803144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219348193	NA	P-0029999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	47	715	1	ENST00000260795.2:c.496G>A	p.Val166Met	p.V166M	ENST00000260795		166	Gtg/Atg	4/17	0.352537420374393	3	FACETS	0.381	0.32	0.448	0.191	0.16	0.224	SUBCLONAL	1	TRUE	1	0.352537420374393	3		716	823	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609969	43609969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767411	NA	P-0029999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	93	791	1	ENST00000355710.3:c.1921G>A	p.Ala641Thr	p.A641T	ENST00000355710	NM_020975.4	641	Gct/Act	11/20	0.352537420374393	3	FACETS	0.697	0.619	0.781	0.349	0.309	0.391	SUBCLONAL	1	TRUE	1	0.352537420374393	3		792	890	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900942	114900942	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0029999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	52	422	0	ENST00000543371.1:c.553-1del		p.X185_splice	ENST00000543371	NM_001198531.1	185			0.352537420374393	3	FACETS	0.69	0.588	0.802	0.345	0.294	0.401	SUBCLONAL	1	TRUE	1	0.352537420374393	3		422	503	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326776	62326776	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1465	78	842	0	ENST00000360203.5:c.3595G>T	p.Asp1199Tyr	p.D1199Y	ENST00000360203	NM_001283009.1	1199	Gat/Tat	34/35	0.352537420374393	6	FACETS	0.489	0.428	0.556	0.122	0.107	0.139	SUBCLONAL	1	TRUE	2	0.352537420374393	6		842	1543	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245344	153245344	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	98	323	0	ENST00000281708.4:c.1847C>A	p.Thr616Lys	p.T616K	ENST00000281708	NM_033632.3	616	aCa/aAa	11/12	0.33173884897507	3	FACETS	1	0.901	1	0.505	0.45	0.562	CLONAL	1	TRUE	1	0.352537420374393	3		323	648	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	75	376	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.95	1	1	0.985	1	CLONAL	2	TRUE	1	0.14	2		376	463	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0030000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	326	441	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.276420026662399	3	FACETS	0.963	0.914	1			1	CLONAL	6	TRUE	NA	0.14	3		441	862	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098781	47098782	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	91	704	0	ENST00000409792.3:c.6492dup	p.Ala2165CysfsTer19	p.A2165Cfs*19	ENST00000409792	NM_014159.6	2164	-/T	15/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.14	2		704	882	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829764	76829764	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	80	617	0	ENST00000373344.5:c.6277C>T	p.Gln2093Ter	p.Q2093*	ENST00000373344	NM_000489.3	2093	Cag/Tag	28/35	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.14	2		617	813	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446106	49446106	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	118	856	0	ENST00000301067.7:c.1360G>C	p.Glu454Gln	p.E454Q	ENST00000301067	NM_003482.3	454	Gag/Cag	10/54	1	2	FACETS	0.789	0.71	0.873	1	0.985	1	SUBCLONAL	2	TRUE	1	0.14	2		856	1068	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555650	21555650	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	88	553	0	ENST00000382592.4:c.2620G>T	p.Val874Leu	p.V874L	ENST00000382592	NM_014572.2	874	Gtg/Ttg	6/8	1	2	FACETS	0.844	0.747	0.947	1	0.982	1	CLONAL	2	TRUE	1	0.14	2		553	745	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557745	21557746	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0030000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	101	668	1	ENST00000382592.4:c.2099_2100delinsTT	p.Arg700Ile	p.R700I	ENST00000382592	NM_014572.2	700	aGG/aTT	5/8	1	2	FACETS	0.846	0.755	0.942	1	0.984	1	CLONAL	2	TRUE	1	0.14	2		669	853	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778000	3778000	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	114	938	1	ENST00000262367.5:c.7048C>T	p.Gln2350Ter	p.Q2350*	ENST00000262367	NM_004380.2	2350	Cag/Tag	31/31	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.14	2		939	1102	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349314	89349315	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCTT	novel	NA	P-0030000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	111	960	0	ENST00000301030.4:c.3632_3635dup	p.Ser1213ArgfsTer21	p.S1213Rfs*21	ENST00000301030	NM_001256183.1	1212	gag/gaAAGAg	9/13	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.14	2		960	1194	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113720	11113720	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	88	564	0	ENST00000358026.2:c.1828A>T	p.Ser610Cys	p.S610C	ENST00000358026	NM_001128849.1	610	Agc/Tgc	12/36	1	2	FACETS	0.851	0.753	0.955	1	0.982	1	CLONAL	2	TRUE	1	0.14	2		564	739	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289895	15289895	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs370233852	NA	P-0030000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	126	794	0	ENST00000263388.2:c.3659G>C	p.Arg1220Pro	p.R1220P	ENST00000263388	NM_000435.2	1220	cGg/cCg	22/33	1	2	FACETS	0.865	0.781	0.952	1	0.988	1	CLONAL	2	TRUE	1	0.14	2		794	1041	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215961	142215961	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	60	426	0	ENST00000350721.4:c.5632G>C	p.Glu1878Gln	p.E1878Q	ENST00000350721	NM_001184.3	1878	Gaa/Caa	33/47	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.14	2		426	650	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136818	55136818	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	57	387	0	ENST00000257290.5:c.1140G>T	p.Lys380Asn	p.K380N	ENST00000257290	NM_006206.4	380	aaG/aaT	8/23	1	2	FACETS	0.819	0.704	0.945	1	0.971	1	CLONAL	2	TRUE	1	0.14	2		387	497	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146484	55146484	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	25	240	0	ENST00000257290.5:c.2158T>A	p.Tyr720Asn	p.Y720N	ENST00000257290	NM_006206.4	720	Tat/Aat	16/23	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.14	2		240	317	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293829	1293829	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	125	919	0	ENST00000310581.5:c.1172C>A	p.Pro391His	p.P391H	ENST00000310581	NM_198253.2	391	cCc/cAc	2/16	1	2	FACETS	0.856	0.773	0.944	1	0.987	1	CLONAL	2	TRUE	1	0.14	2		919	1043	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176542	56176542	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	71	425	0	ENST00000399503.3:c.2092A>T	p.Thr698Ser	p.T698S	ENST00000399503	NM_005921.1	698	Aca/Tca	12/20	1	2	FACETS	0.826	0.721	0.939	1	0.977	1	CLONAL	2	TRUE	1	0.14	2		425	614	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959214	2959214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773303917	NA	P-0030000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	95	622	0	ENST00000396946.4:c.2302G>A	p.Gly768Ser	p.G768S	ENST00000396946	NM_032415.4	768	Ggc/Agc	18/25	1	2	FACETS	0.798	0.71	0.893	1	0.982	1	SUBCLONAL	2	TRUE	1	0.14	2		622	850	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467756	50467756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781662160	NA	P-0030000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	80	576	0	ENST00000331340.3:c.991G>A	p.Val331Met	p.V331M	ENST00000331340	NM_006060.4	331	Gtg/Atg	8/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.14	2		576	768	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453117	140453117	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	86	440	0	ENST00000288602.6:c.1818del	p.Ser607ProfsTer43	p.S607Pfs*43	ENST00000288602	NM_004333.4	606	ggG/gg	15/18	1	2	FACETS	0.889	0.786	0.999	1	0.983	1	CLONAL	2	TRUE	1	0.14	2		440	691	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934420	39934420	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	64	477	0	ENST00000378444.4:c.179C>G	p.Thr60Arg	p.T60R	ENST00000378444	NM_001123385.1	60	aCg/aGg	4/15	1	2	FACETS	0.788	0.683	0.903	1	0.973	1	CLONAL	2	TRUE	1	0.14	2		477	580	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223412	53223412	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	90	749	0	ENST00000375401.3:c.3947A>T	p.Gln1316Leu	p.Q1316L	ENST00000375401	NM_004187.3	1316	cAg/cTg	23/26	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.14	2		749	997	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226078	53226078	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	62	739	0	ENST00000375401.3:c.2771A>T	p.Gln924Leu	p.Q924L	ENST00000375401	NM_004187.3	924	cAg/cTg	19/26	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.14	2		739	781	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412630	63412630	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	95	553	2	ENST00000330258.3:c.537C>A	p.His179Gln	p.H179Q	ENST00000330258	NM_152424.3	179	caC/caA	2/2	1	2	FACETS	0.833	0.741	0.931	1	0.983	1	CLONAL	2	TRUE	1	0.14	2		555	815	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909677	76909677	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	34	358	0	ENST00000373344.5:c.4228G>T	p.Ala1410Ser	p.A1410S	ENST00000373344	NM_000489.3	1410	Gca/Tca	14/35	1	2	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	TRUE	1	0.14	2		358	466	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0030001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	78	387	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.332955232536335	3	FACETS	0.96	0.845	1	0.48	0.422	0.542	CLONAL	1	TRUE	1	0.348772698385951	3		387	547	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0030001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	84	375	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			0.348772698385951	4	FACETS	0.807	0.712	0.909	0.269	0.237	0.303	CLONAL	1	TRUE	1	0.348772698385951	4		375	805	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405899	70405899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	142	609	0	ENST00000373644.4:c.3413C>T	p.Ser1138Leu	p.S1138L	ENST00000373644	NM_030625.2	1138	tCa/tTa	4/12	1	2	FACETS	0.896	0.816	0.98	0.896	0.816	0.98	CLONAL	1	TRUE	1	0.348772698385951	2		609	909	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164701	36164701	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	270	741	0	ENST00000300305.3:c.1174C>T	p.Gln392Ter	p.Q392*	ENST00000300305		392	Cag/Tag	8/8	1	2	FACETS	0.941	0.885	0.997	1	0.995	1	CLONAL	2	TRUE	1	0.348772698385951	2		741	823	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120806010	120806010	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	285	606	1	ENST00000257552.2:c.167T>A	p.Leu56Gln	p.L56Q	ENST00000257552	NM_002442.3	56	cTg/cAg	3/15	0.340069093513563	2	FACETS	0.937	0.884	0.992	0.937	0.884	0.992	CLONAL	2	TRUE	0	0.348772698385951	2		607	872	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838145	89838145	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	214	532	0	ENST00000389301.3:c.2092G>C	p.Glu698Gln	p.E698Q	ENST00000389301	NM_000135.2	698	Gag/Cag	23/43	0.340069093513563	2	FACETS	0.885	0.826	0.946	0.885	0.826	0.946	CLONAL	2	TRUE	0	0.348772698385951	2		532	693	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	86	376	0				ENST00000310581	NM_198253.2	-/1132			0.169623554335231	3	FACETS	0.875	0.778	0.977	1	0.972	1	CLONAL	3	TRUE	1	0.169623554335231	3		376	419	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741558	17741558	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	50	408	0	ENST00000250003.3:c.229G>C	p.Glu77Gln	p.E77Q	ENST00000250003	NM_002478.4	77	Gag/Cag	1/3	1	2	FACETS	0.782	0.665	0.909	1	0.966	1	CLONAL	2	TRUE	1	0.169623554335231	2		408	377	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641162	117641162	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	63	754	0	ENST00000368508.3:c.5809C>G	p.Leu1937Val	p.L1937V	ENST00000368508	NM_002944.2	1937	Ctt/Gtt	36/43	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.169623554335231	2		754	588	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950806	32950806	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0030002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	69	308	0	ENST00000380152.3:c.8633-1G>C		p.X2878_splice	ENST00000380152		2878			1	2	FACETS	0.864	0.758	0.975	1	0.985	1	CLONAL	3	TRUE	1	0.169623554335231	2		308	314	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443703	49443703	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0030002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	84	719	0	ENST00000301067.7:c.3668C>G	p.Ser1223Ter	p.S1223*	ENST00000301067	NM_003482.3	1223	tCa/tGa	11/54	0.168488455378815	1	FACETS	0.839	0.743	0.942	1	0.981	1	CLONAL	2	TRUE	0	0.169623554335231	1		719	540	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097818	8097818	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	91	695	1	ENST00000346208.3:c.200C>G	p.Ser67Trp	p.S67W	ENST00000346208		67	tCg/tGg	2/6	0.169623554335231	3	FACETS	0.997	0.887	1	0.997	0.887	1	CLONAL	2	TRUE	1	0.169623554335231	3		696	584	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295236	15295236	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	43	809	0	ENST00000263388.2:c.2436C>A	p.Asp812Glu	p.D812E	ENST00000263388	NM_000435.2	812	gaC/gaA	16/33	1	2	FACETS	0.768	0.641	0.909	0.768	0.641	0.909	CLONAL	1	TRUE	1	0.169623554335231	2		809	660	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573144	41573158	+	inframe_deletion	In_Frame_Del	DEL	AGCAGAAGCTCCGGC	AGCAGAAGCTCCGGC	-	novel	NA	P-0030002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	45	754	0	ENST00000263253.7:c.5433_5447del	p.Lys1812_Gln1816del	p.K1812_Q1816del	ENST00000263253	NM_001429.3	1810	aAGCAGAAGCTCCGGCag/aag	31/31	1	2	FACETS	0.884	0.742	1	0.884	0.742	1	CLONAL	1	TRUE	1	0.169623554335231	2		754	600	SUCCESS
ATR	545	MSKCC	GRCh37	3	142168318	142168318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	23	405	0	ENST00000350721.4:c.7888G>A	p.Glu2630Lys	p.E2630K	ENST00000350721	NM_001184.3	2630	Gaa/Aaa	47/47	0.112614399477325	4	FACETS	1	0.879	1	0.601	0.469	0.752	CLONAL	1	TRUE	2	0.169623554335231	4		405	264	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499105	149499105	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	28	544	0	ENST00000261799.4:c.2723C>A	p.Pro908His	p.P908H	ENST00000261799	NM_002609.3	908	cCc/cAc	20/23	1	2	FACETS	0.644	0.513	0.793	0.644	0.513	0.793	SUBCLONAL	1	TRUE	1	0.169623554335231	2		544	513	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992807	68992807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	30	532	0	ENST00000288368.4:c.1772C>T	p.Ala591Val	p.A591V	ENST00000288368	NM_024870.2	591	gCt/gTt	16/40	0.169623554335231	3	FACETS	1	0.927	1	0.671	0.542	0.816	CLONAL	1	TRUE	1	0.169623554335231	3		532	286	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639929	93639929	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	21	265	0	ENST00000375746.1:c.1258G>C	p.Glu420Gln	p.E420Q	ENST00000375746	NM_001174167.1	420	Gaa/Caa	10/14	0.169623554335231	2	FACETS	0.863	0.665	1	0.431	0.332	0.547	CLONAL	1	TRUE	0	0.169623554335231	2		265	287	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759956	133759956	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	43	788	1	ENST00000318560.5:c.2279C>A	p.Pro760Gln	p.P760Q	ENST00000318560	NM_005157.4	760	cCg/cAg	11/11	0.169623554335231	2	FACETS	0.746	0.622	0.883	0.373	0.311	0.442	SUBCLONAL	1	TRUE	0	0.169623554335231	2		789	680	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391860	139391861	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0030002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	35	724	1	ENST00000277541.6:c.6330_6331delinsTT	p.Arg2111Trp	p.R2111W	ENST00000277541	NM_017617.3	2110	gtGAgg/gtTTgg	34/34	0.169623554335231	2	FACETS	0.653	0.534	0.787	0.326	0.267	0.394	SUBCLONAL	1	TRUE	0	0.169623554335231	2		725	632	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044539	47044539	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	54	401	0	ENST00000377604.3:c.2036del	p.Leu679ArgfsTer25	p.L679Rfs*25	ENST00000377604	NM_001204468.1	679	cTg/cg	18/24	1	1	FACETS	0.994	0.855	1	1	0.977	1	CLONAL	2	TRUE	0	0.169623554335231	1		401	293	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692980	89692980	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1060500126	NA	P-0030004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	86	383	0	ENST00000371953.3:c.464A>G	p.Tyr155Cys	p.Y155C	ENST00000371953	NM_000314.4	155	tAt/tGt	5/9	0.668955721438029	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.668955721438029	1		383	156	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513280	106513280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752876335	NA	P-0030007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	177	281	0	ENST00000359195.3:c.2184G>A	p.Met728Ile	p.M728I	ENST00000359195	NM_002649.2	728	atG/atA	4/11	1	2	FACETS	1	0.986	1	1	0.994	1	CLONAL	2	TRUE	1	0.306353881539384	2		281	468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0030008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	188	635	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.257784287930251	3	FACETS	1	0.94	1	1	0.94	1	CLONAL	3	TRUE	0	0.389378958582212	3		635	384	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211823	36211823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1007147127	NA	P-0030008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	144	787	1	ENST00000222270.7:c.1574G>A	p.Arg525Gln	p.R525Q	ENST00000222270	NM_014727.1	525	cGg/cAg	3/37	0.2689889878149	5	FACETS	0.862	0.793	0.933	0.862	0.793	0.933	CLONAL	3	TRUE	2	0.389378958582212	5		788	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0030017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	221	450	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.562665853867323	1	FACETS	0.873	0.817	0.93	0.873	0.817	0.93	CLONAL	1	TRUE	0	0.562665853867323	1		451	647	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0030019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	267	436	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.395890178731677	3	FACETS	0.928	0.872	0.984	0.928	0.872	0.984	CLONAL	2	TRUE	1	0.395890178731677	3		437	871	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251907	153251907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	155	488	0	ENST00000281708.4:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000281708	NM_033632.3	367	Cga/Tga	7/12	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.395890178731677	2		488	751	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245393	153245393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	203	531	0	ENST00000281708.4:c.1798G>A	p.Asp600Asn	p.D600N	ENST00000281708	NM_033632.3	600	Gat/Aat	11/12	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.395890178731677	2		531	940	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0030019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	222	302	0	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	0.376795112272372	2	FACETS	0.974	0.913	1	0.974	0.913	1	CLONAL	2	TRUE	0	0.395890178731677	2		302	576	SUCCESS
APC	324	MSKCC	GRCh37	5	112176008	112176008	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	199	344	0	ENST00000257430.4:c.4717G>T	p.Glu1573Ter	p.E1573*	ENST00000257430	NM_000038.5	1573	Gaa/Taa	16/16	0.395890178731677	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.395890178731677	3		344	554	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231728	66231728	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	114	413	0	ENST00000273854.3:c.1972G>T	p.Asp658Tyr	p.D658Y	ENST00000273854	NM_004439.5	658	Gat/Tat	11/18	1	2	FACETS	0.92	0.83	1	0.92	0.83	1	CLONAL	1	TRUE	1	0.395890178731677	2		413	626	SUCCESS
APC	324	MSKCC	GRCh37	5	112174223	112174223	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	79	372	0	ENST00000257430.4:c.2932C>T	p.Gln978Ter	p.Q978*	ENST00000257430	NM_000038.5	978	Caa/Taa	16/16	0.395890178731677	3	FACETS	0.609	0.535	0.689	0.305	0.267	0.345	SUBCLONAL	1	TRUE	1	0.395890178731677	3		372	785	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243362	46243362	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0030019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	71	234	0	ENST00000334344.6:c.1716-1G>A		p.X572_splice	ENST00000334344	NM_152641.2	572			0.395890178731677	3	FACETS	0.863	0.755	0.979	0.431	0.377	0.49	CLONAL	1	TRUE	1	0.395890178731677	3		234	498	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120261	70120261	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	228	778	0	ENST00000245479.2:c.1266del	p.Phe423SerfsTer47	p.F423Sfs*47	ENST00000245479	NM_000346.3	421	agC/ag	3/3	1	2	FACETS	0.892	0.83	0.957	0.892	0.83	0.957	CLONAL	1	TRUE	1	0.395890178731677	2		778	1291	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467685	66467685	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	106	360	0	ENST00000273854.3:c.584T>G	p.Leu195Arg	p.L195R	ENST00000273854	NM_004439.5	195	cTg/cGg	3/18	1	2	FACETS	0.961	0.865	1	0.961	0.865	1	CLONAL	1	TRUE	1	0.395890178731677	2		360	557	SUCCESS
APC	324	MSKCC	GRCh37	5	112102931	112102931	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs876658846	NA	P-0030019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	252	356	0	ENST00000257430.4:c.266C>A	p.Ser89Ter	p.S89*	ENST00000257430	NM_000038.5	89	tCa/tAa	4/16	0.395890178731677	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.395890178731677	3		356	728	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247013	53247013	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	97	595	0	ENST00000375401.3:c.487C>A	p.Pro163Thr	p.P163T	ENST00000375401	NM_004187.3	163	Ccc/Acc	4/26	0.395890178731677	3	FACETS	0.475	0.422	0.532	0.237	0.211	0.266	SUBCLONAL	1	TRUE	1	0.395890178731677	3		595	1236	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	106	376	0				ENST00000310581	NM_198253.2	-/1132			0.399867483979655	3	FACETS	1	0.98	1	0.679	0.613	0.747	CLONAL	1	FALSE	1	0.48950819789122	3		376	397	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0030022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	65	454	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.891	0.779	1	0.891	0.779	1	CLONAL	1	FALSE	1	0.48950819789122	2		454	298	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443518	49443518	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	25	488	0	ENST00000301067.7:c.3853G>C	p.Glu1285Gln	p.E1285Q	ENST00000301067	NM_003482.3	1285	Gag/Cag	11/54	1	2	FACETS	0.252	0.198	0.314	0.252	0.198	0.314	SUBCLONAL	1	FALSE	1	0.48950819789122	2		488	406	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40456361	40456361	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs763602853	NA	P-0030022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	47	428	0	ENST00000345506.4:c.1171G>A	p.Glu391Lys	p.E391K	ENST00000345506	NM_003152.3	391	Gag/Aag	11/20	0.399867483979655	3	FACETS	0.657	0.556	0.767	0.328	0.278	0.384	SUBCLONAL	1	FALSE	1	0.48950819789122	3		428	364	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470606	25470606	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	101	651	0	ENST00000264709.3:c.868T>G	p.Phe290Val	p.F290V	ENST00000264709	NM_175629.2	290	Ttt/Gtt	8/23	1	2	FACETS	0.729	0.653	0.809	0.729	0.653	0.809	SUBCLONAL	1	FALSE	1	0.48950819789122	2		651	566	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068091	94068091	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	57	297	1	ENST00000369303.4:c.871C>A	p.Leu291Ile	p.L291I	ENST00000369303	NM_004440.3	291	Ctt/Att	4/17	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	FALSE	1	0.48950819789122	2		298	223	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539153	23539153	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0030022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	56	334	0	ENST00000380871.4:c.287-1G>A		p.X96_splice	ENST00000380871	NM_006167.3	96			1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	FALSE	1	0.48950819789122	2		334	222	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242323	98242323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	59	490	0	ENST00000331920.6:c.995G>A	p.Arg332Lys	p.R332K	ENST00000331920	NM_000264.3	332	aGa/aAa	7/24	0.48950819789122	1	FACETS	0.72	0.626	0.82	0.72	0.626	0.82	SUBCLONAL	1	FALSE	0	0.48950819789122	1		490	253	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0030024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	44	525	2	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	1	2	FACETS	0.833	0.696	0.984	0.833	0.696	0.984	CLONAL	1	TRUE	1	0.14	2		527	755	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0030024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	58	538	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.14	2		538	736	SUCCESS
APC	324	MSKCC	GRCh37	5	112154992	112154992	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554080106	NA	P-0030025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	98	429	1	ENST00000257430.4:c.1263G>A	p.Trp421Ter	p.W421*	ENST00000257430	NM_000038.5	421	tgG/tgA	10/16	0.323642249901415	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	3	TRUE	0	0.338399332206294	3		430	214	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578412	7578413	+	missense_variant	Missense_Mutation	DNP	AC	AC	CT	novel	NA	P-0030025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	53	469	0	ENST00000269305.4:c.517_518delinsAG	p.Val173Arg	p.V173R	ENST00000269305	NM_001126112.2	173	GTg/AGg	5/11	0.198953751863627	3	FACETS	0.911	0.788	1	0.607	0.525	0.695	INDETERMINATE	2	TRUE	0	0.338399332206294	3		469	201	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0030026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	431	703	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.650281605974355	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.650281605974355	1		703	761	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051652	30051652	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555993336	NA	P-0030026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	44	274	0	ENST00000338641.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000338641	NM_000268.3	196	Cga/Tga	6/16	0.650281605974355	1	FACETS	0.273	0.23	0.321	0.273	0.23	0.321	SUBCLONAL	1	TRUE	0	0.650281605974355	1		274	334	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981047	55981047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145458680	NA	P-0030026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	98	392	0	ENST00000263923.4:c.652G>A	p.Val218Ile	p.V218I	ENST00000263923	NM_002253.2	218	Gtt/Att	5/30	0.650281605974355	1	FACETS	0.77	0.698	0.844	0.77	0.698	0.844	SUBCLONAL	1	TRUE	0	0.650281605974355	1		392	264	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123324007	123324022	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTTACTTACTCTTGTT	GTTACTTACTCTTGTT	-	novel	NA	P-0030026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	221	458	0	ENST00000358487.5:c.448_454+9del		p.X150_splice	ENST00000358487	NM_000141.4	150		4/18	0.650281605974355	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.650281605974355	1		458	435	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945421	71945421	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	80	599	0	ENST00000298229.2:c.2309A>T	p.Tyr770Phe	p.Y770F	ENST00000298229	NM_001567.3	770	tAc/tTc	20/28	1	2	FACETS	0.261	0.229	0.296	0.261	0.229	0.296	SUBCLONAL	1	TRUE	1	0.650281605974355	2		599	942	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947565	48947787	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTAATGATGATTTTAAATTCAGCAAGTGATCAACCTTCAGAAAATCTGATTTCCTATTTTAACGTAAGCCATATATGAAACATTATTTATTGTAATATCTTGGCAAAGAAACTTGAAATTAAAAGTTAAAGTACTGAGTTCTTTTTAAAATACTAATCTCCTATCTAACATGTAGTTATCCATAATCTTTTCTTGCTTTTTTAATCTTACAAATTATATATT	ATTAATGATGATTTTAAATTCAGCAAGTGATCAACCTTCAGAAAATCTGATTTCCTATTTTAACGTAAGCCATATATGAAACATTATTTATTGTAATATCTTGGCAAAGAAACTTGAAATTAAAAGTTAAAGTACTGAGTTCTTTTTAAAATACTAATCTCCTATCTAACATGTAGTTATCCATAATCTTTTCTTGCTTTTTTAATCTTACAAATTATATATT	-	novel	NA	P-0030026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	89	385	0	ENST00000267163.4:c.1156_1215+163del		p.X386_splice	ENST00000267163	NM_000321.2	386		12/27	0.650281605974355	1	FACETS	0.553	0.495	0.614	0.553	0.495	0.614	SUBCLONAL	1	TRUE	0	0.650281605974355	1		385	334	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592266	29592266	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	96	225	1	ENST00000356175.3:c.4681del	p.Glu1561LysfsTer6	p.E1561Kfs*6	ENST00000356175	NM_000267.3	1561	Gaa/aa	35/57	0.650281605974355	1	FACETS	0.991	0.905	1	0.991	0.905	1	CLONAL	1	TRUE	0	0.650281605974355	1		226	201	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568668	41568668	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0030026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	155	306	1	ENST00000263253.7:c.4617+1G>T		p.X1539_splice	ENST00000263253	NM_001429.3	1539			0.650281605974355	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.650281605974355	1		307	307	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0030027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	106	474	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.531139307680325	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.529063031686227	1		474	269	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243778450	243778450	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	86	308	0	ENST00000263826.5:c.575A>G	p.His192Arg	p.H192R	ENST00000263826	NM_005465.4	192	cAc/cGc	6/13	NA	2	FACETS	1	0.948	1			1	INDETERMINATE	1	TRUE	NA	0.529063031686227	2		308	296	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451123	70451123	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	668	526	0	ENST00000373644.4:c.5963C>A	p.Pro1988His	p.P1988H	ENST00000373644	NM_030625.2	1988	cCc/cAc	12/12	0.529063031686227	6	FACETS	0.934	0.911	0.957			1	CLONAL	6	TRUE	NA	0.529063031686227	6		526	927	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428662	49428662	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	354	569	2	ENST00000301067.7:c.10288G>T	p.Val3430Leu	p.V3430L	ENST00000301067	NM_003482.3	3430	Gtg/Ttg	35/54	0.527319954125505	3	FACETS	0.932	0.894	0.97	0.932	0.894	0.97	CLONAL	3	TRUE	0	0.529063031686227	3		571	605	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878139	48878139	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	44	104	0	ENST00000267163.4:c.91G>T	p.Glu31Ter	p.E31*	ENST00000267163	NM_000321.2	31	Gag/Tag	1/27	0.524432073311724	2	FACETS	0.84	0.73	0.952	0.84	0.73	0.952	CLONAL	2	TRUE	0	0.529063031686227	2		104	99	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675512	40675512	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	88	395	0	ENST00000249776.8:c.293G>T	p.Gly98Val	p.G98V	ENST00000249776	NM_033286.3	98	gGc/gTc	2/9	0.524432073311724	2	FACETS	0.942	0.842	1	0.471	0.421	0.524	CLONAL	1	TRUE	0	0.529063031686227	2		395	353	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843618	3844079	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCATCTGAGACTAAAATAAAGCAAAATAATAAAAATACTTTAACCTCTCAGAGTTCCAAGTCATATTCATTAATTATTTCTCAAACAAAAGCAAAAGCTGATGGATAATACCGACCACAGAGAGAAGGCTGGTGTAGTTCTCTAACCCACTGATGACTTTAAGAAGATCCAGCAGCACAGAAATCAACCCAACTCAGCAGCAAGGCTGATTCAAGTTCACTTGTATACAATTATCATCCAAGCAAGACAATGGCTGGCTCTTCACTGTAGCAACCAAAATCCAACTCACTCTACAATATACACAACTACAGGAAAAGCTGTGTACTATACCAGCTGGACCATATGAAACTGCTGTTTCTGTAGGTCCCAAATGGCCAAACACTGGCAATTTCATAGGGTACAACCTAATTAAAAAGATTGCCAAGGCCTGGCCGAGCGCGTTGGCTCACGCCTGTAATCTCA	GCATCTGAGACTAAAATAAAGCAAAATAATAAAAATACTTTAACCTCTCAGAGTTCCAAGTCATATTCATTAATTATTTCTCAAACAAAAGCAAAAGCTGATGGATAATACCGACCACAGAGAGAAGGCTGGTGTAGTTCTCTAACCCACTGATGACTTTAAGAAGATCCAGCAGCACAGAAATCAACCCAACTCAGCAGCAAGGCTGATTCAAGTTCACTTGTATACAATTATCATCCAAGCAAGACAATGGCTGGCTCTTCACTGTAGCAACCAAAATCCAACTCACTCTACAATATACACAACTACAGGAAAAGCTGTGTACTATACCAGCTGGACCATATGAAACTGCTGTTTCTGTAGGTCCCAAATGGCCAAACACTGGCAATTTCATAGGGTACAACCTAATTAAAAAGATTGCCAAGGCCTGGCCGAGCGCGTTGGCTCACGCCTGTAATCTCA	-	novel	NA	P-0030027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	106	372	0	ENST00000262367.5:c.976-452_985del		p.X326_splice	ENST00000262367	NM_004380.2	326		4/31	0.524432073311724	2	FACETS	1	0.983	1	0.696	0.633	0.76	CLONAL	1	TRUE	0	0.529063031686227	2		372	288	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577533	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0030027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	298	520	1	ENST00000269305.4:c.748_749delinsTT	p.Pro250Phe	p.P250F	ENST00000269305	NM_001126112.2	250	CCc/TTc	7/11	0.527319954125505	3	FACETS	0.884	0.843	0.925	0.884	0.843	0.925	CLONAL	3	TRUE	0	0.529063031686227	3		521	537	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281100	142281159	+	inframe_deletion	In_Frame_Del	DEL	CATCCAAAAGAGCTTTACAAATATTTCTCACATAGACCTTCCTGACTTGTAAAGCAGATT	CATCCAAAAGAGCTTTACAAATATTTCTCACATAGACCTTCCTGACTTGTAAAGCAGATT	-	novel	NA	P-0030027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	132	348	0	ENST00000350721.4:c.1085_1144del	p.Glu362_Asp381del	p.E362_D381del	ENST00000350721	NM_001184.3	362	gAATCTGCTTTACAAGTCAGGAAGGTCTATGTGAGAAATATTTGTAAAGCTCTTTTGGATGtg/gtg	4/47	0.531139307680325	4	FACETS	1	0.98	1	0.317	0.289	0.347	CLONAL	1	TRUE	0	0.529063031686227	4		348	601	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	240508	240508	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554000360	NA	P-0030027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	16	59	0	ENST00000264932.6:c.1468G>T	p.Glu490Ter	p.E490*	ENST00000264932	NM_004168.2	490	Gaa/Taa	11/15	0.475366736892191	3	FACETS	0.921	0.694	1			1	CLONAL	1	TRUE	NA	0.529063031686227	3		59	83	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140454030	140454030	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	47	207	0	ENST00000288602.6:c.1698C>A	p.Tyr566Ter	p.Y566*	ENST00000288602	NM_004333.4	566	taC/taA	14/18	0.522772092751829	3	FACETS	0.854	0.726	0.993	0.285	0.242	0.331	CLONAL	1	TRUE	0	0.529063031686227	3		207	263	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413083	63413084	+	missense_variant	Missense_Mutation	DNP	TC	TC	GT	novel	NA	P-0030027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	162	677	1	ENST00000330258.3:c.83_84delinsAC	p.Gly28Asp	p.G28D	ENST00000330258	NM_152424.3	28	gGA/gAC	2/2	0.531139307680325	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.529063031686227	1		678	421	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0030028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	115	454	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		454	473	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350593	15350593	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	292	679	0	ENST00000263377.2:c.3322G>C	p.Val1108Leu	p.V1108L	ENST00000263377	NM_058243.2	1108	Gtg/Ctg	16/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.74514983103056	2		679	746	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119595341	119595342	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0030029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	86	211	0	ENST00000316626.5:c.827dup	p.Thr277AsnfsTer16	p.T277Nfs*16	ENST00000316626		276	cca/ccCa	8/12	1	2	FACETS	0.606	0.539	0.676	0.606	0.539	0.676	SUBCLONAL	1	FALSE	1	0.74514983103056	2		211	381	SUCCESS
AR	367	MSKCC	GRCh37	X	66765964	66765964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	82	431	1	ENST00000374690.3:c.976G>A	p.Gly326Ser	p.G326S	ENST00000374690	NM_000044.3	326	Ggc/Agc	1/8	0.422806203397136	4	FACETS	0.605	0.532	0.683			1	SUBCLONAL	1	TRUE	NA	0.422806203397136	4		432	912	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717699	89717699	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554825210	NA	P-0030032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	374	319	0	ENST00000371953.3:c.724G>T	p.Glu242Ter	p.E242*	ENST00000371953	NM_000314.4	242	Gag/Tag	7/9	0.740556671049077	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.740556671049077	1		319	540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0030032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	383	425	0	ENST00000269305.4:c.673-1G>C		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.740556671049077	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.740556671049077	1		425	603	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103660	47103660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	157	257	0	ENST00000409792.3:c.6286G>A	p.Asp2096Asn	p.D2096N	ENST00000409792	NM_014159.6	2096	Gat/Aat	14/21	0.685966064860388	1	FACETS	0.462	0.425	0.5	0.462	0.425	0.5	SUBCLONAL	1	TRUE	0	0.740556671049077	1		257	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0030033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	211	537	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.260587583159308	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	0	0.260587583159308	3		540	548	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434367	121434367	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	55	607	2	ENST00000257555.6:c.1136del	p.Pro379LeufsTer5	p.P379Lfs*5	ENST00000257555		377	ctC/ct	6/10	0.260587583159308	3	FACETS	0.918	0.785	1	0.459	0.392	0.531	CLONAL	1	TRUE	1	0.260587583159308	3		609	520	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429810	78429836	+	inframe_deletion	In_Frame_Del	DEL	TGTTATTTGTGCTATCCTTTCGGGTGT	TGTTATTTGTGCTATCCTTTCGGGTGT	-	novel	NA	P-0030033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	88	333	0	ENST00000370768.2:c.952_978del	p.Thr318_Thr326del	p.T318_T326del	ENST00000370768	NM_003902.3	318	ACACCCGAAAGGATAGCACAAATAACA/-	12/20	0.260587583159308	5	FACETS	0.995	0.885	1	0.663	0.59	0.741	CLONAL	2	TRUE	2	0.260587583159308	5		333	472	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244730	46244730	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	71	531	0	ENST00000334344.6:c.2824G>T	p.Ala942Ser	p.A942S	ENST00000334344	NM_152641.2	942	Gcc/Tcc	15/21	0.260587583159308	5	FACETS	1	0.94	1	0.378	0.33	0.431	CLONAL	1	TRUE	2	0.260587583159308	5		531	668	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987109	36987109	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	58	548	0	ENST00000354822.5:c.580C>T	p.Arg194Cys	p.R194C	ENST00000354822	NM_001079668.2	194	Cgc/Tgc	3/3	0.157143893736707	4	FACETS	1	0.947	1	0.405	0.348	0.466	CLONAL	1	TRUE	1	0.260587583159308	4		548	462	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331795	68331795	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	64	447	0	ENST00000487270.1:c.391A>T	p.Met131Leu	p.M131L	ENST00000487270	NM_133509.3	131	Atg/Ttg	5/11	0.157143893736707	4	FACETS	1	0.926	1	0.368	0.319	0.421	CLONAL	1	TRUE	1	0.260587583159308	4		447	561	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32182030	32182030	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1450662001	NA	P-0030033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	77	645	0	ENST00000375023.3:c.2024C>T	p.Ser675Phe	p.S675F	ENST00000375023	NM_004557.3	675	tCc/tTc	13/30	0.260587583159308	5	FACETS	1	0.946	1	0.381	0.334	0.431	CLONAL	1	TRUE	2	0.260587583159308	5		645	720	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412714	139412714	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	25	652	0	ENST00000277541.6:c.1130T>A	p.Ile377Asn	p.I377N	ENST00000277541	NM_017617.3	377	aTc/aAc	7/34	0.260587583159308	2	FACETS	0.387	0.304	0.483	0.193	0.152	0.242	SUBCLONAL	1	TRUE	0	0.260587583159308	2		652	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577544	7577544	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587780074	NA	P-0030049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	557	544	0	ENST00000269305.4:c.737T>C	p.Met246Thr	p.M246T	ENST00000269305	NM_001126112.2	246	aTg/aCg	7/11	0.849294416681296	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.861081517353556	2		544	645	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0030050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	41	441	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.918	0.765	1	0.918	0.765	1	CLONAL	1	TRUE	1	0.19	2		441	470	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220579	1220579	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0030050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	184	616	3	ENST00000326873.7:c.598-1G>T		p.X200_splice	ENST00000326873	NM_000455.4	200			1	2	FACETS	1	0.931	1	1	0.993	1	CLONAL	2	TRUE	1	0.19	2		619	960	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344369	118344369	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	26	217	0	ENST00000534358.1:c.2495C>G	p.Pro832Arg	p.P832R	ENST00000534358	NM_005933.3	832	cCt/cGt	3/36	1	2	FACETS	0.674	0.533	0.836	0.674	0.533	0.836	SUBCLONAL	1	TRUE	1	0.19	2		217	406	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63531780	63531780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	100	553	2	ENST00000307078.5:c.2201C>T	p.Ala734Val	p.A734V	ENST00000307078	NM_004655.3	734	gCc/gTc	9/11	0.24316340483127	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.19	1		555	900	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729699	41729699	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	82	482	0	ENST00000242208.4:c.830G>T	p.Gly277Val	p.G277V	ENST00000242208	NM_002192.2	277	gGt/gTt	3/3	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.19	2		482	842	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851432	151851432	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	71	491	0	ENST00000262189.6:c.12059A>G	p.Asp4020Gly	p.D4020G	ENST00000262189	NM_170606.2	4020	gAt/gGt	47/59	1	2	FACETS	0.918	0.8	1	0.918	0.8	1	CLONAL	1	TRUE	1	0.19	2		491	814	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426509	47426509	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	97	314	0	ENST00000377045.4:c.852G>T	p.Leu284Phe	p.L284F	ENST00000377045	NM_001654.4	284	ttG/ttT	9/16	1	1	FACETS	0.769	0.687	0.856	1	0.982	1	SUBCLONAL	2	TRUE	0	0.19	1		314	601	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0030051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	212	615	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	0.702455339744224	2		615	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0030051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	231	525	2	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.702455339744224	1	FACETS	0.867	0.818	0.917	0.867	0.818	0.917	CLONAL	1	TRUE	0	0.702455339744224	1		527	492	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0030051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	31	434	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.171	0.138	0.209	0.171	0.138	0.209	SUBCLONAL	1	TRUE	1	0.702455339744224	2		434	515	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0030051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	299	349	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.333047702024546	3	FACETS	1	0.986	1	0.722	0.689	0.755	INDETERMINATE	2	TRUE	0	0.702455339744224	3		349	531	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59793346	59793346	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	373	357	0	ENST00000259008.2:c.2458C>G	p.Gln820Glu	p.Q820E	ENST00000259008	NM_032043.2	820	Caa/Gaa	17/20	0.698599086248682	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.702455339744224	2		357	502	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861885	57861885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374429707	NA	P-0030051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	146	656	0	ENST00000228682.2:c.1186C>T	p.Arg396Trp	p.R396W	ENST00000228682	NM_005269.2	396	Cgg/Tgg	10/12	0.170521520563115	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.702455339744224	0		656	463	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564680	86564680	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	198	735	0	ENST00000274376.6:c.416del	p.Pro139LeufsTer35	p.P139Lfs*35	ENST00000274376	NM_002890.2	138	Ccc/cc	1/25	0.169609778636072	3	FACETS	1	0.989	1	0.65	0.606	0.695	INDETERMINATE	1	TRUE	1	0.702455339744224	3		735	586	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294297	11294297	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	189	576	0	ENST00000361445.4:c.2234G>T	p.Gly745Val	p.G745V	ENST00000361445	NM_004958.3	745	gGg/gTg	14/58	1	2	FACETS	0.964	0.897	1	0.964	0.897	1	CLONAL	1	TRUE	1	0.702455339744224	2		576	558	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294291	11294291	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	188	607	0	ENST00000361445.4:c.2240G>T	p.Gly747Val	p.G747V	ENST00000361445	NM_004958.3	747	gGa/gTa	14/58	1	2	FACETS	0.97	0.902	1	0.97	0.902	1	CLONAL	1	TRUE	1	0.702455339744224	2		607	552	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69456216	69456216	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	192	664	0	ENST00000227507.2:c.135C>G	p.Phe45Leu	p.F45L	ENST00000227507	NM_053056.2	45	ttC/ttG	1/5	0.702455339744224	1	FACETS	0.921	0.865	0.977	0.921	0.865	0.977	CLONAL	1	TRUE	0	0.702455339744224	1		664	385	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572337	41572337	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	294	755	0	ENST00000263253.7:c.4866T>G	p.Asp1622Glu	p.D1622E	ENST00000263253	NM_001429.3	1622	gaT/gaG	30/31	0.702455339744224	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.702455339744224	1		755	509	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103819	47103819	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	184	407	0	ENST00000409792.3:c.6127G>C	p.Asp2043His	p.D2043H	ENST00000409792	NM_014159.6	2043	Gat/Cat	14/21	0.702455339744224	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.702455339744224	1		407	336	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155410	106155410	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	188	368	0	ENST00000380013.4:c.311C>G	p.Ser104Cys	p.S104C	ENST00000380013	NM_001127208.2	104	tCt/tGt	3/11	0.702455339744224	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.702455339744224	1		368	329	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80074579	80074579	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	212	420	0	ENST00000265081.6:c.2359G>A	p.Glu787Lys	p.E787K	ENST00000265081	NM_002439.4	787	Gaa/Aaa	17/24	0.169609778636072	3	FACETS	0.934	0.869	1	0.467	0.434	0.501	INDETERMINATE	1	TRUE	1	0.702455339744224	3		420	873	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131976391	131976391	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	68	540	0	ENST00000265335.6:c.3646G>A	p.Ala1216Thr	p.A1216T	ENST00000265335		1216	Gcc/Acc	24/25	0.169609778636072	3	FACETS	0.438	0.381	0.5	0.219	0.19	0.25	INDETERMINATE	1	TRUE	1	0.702455339744224	3		540	597	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858351	27858351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	231	662	0	ENST00000359303.2:c.220G>A	p.Glu74Lys	p.E74K	ENST00000359303	NM_003535.2	74	Gaa/Aaa	1/1	0.702455339744224	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.702455339744224	1		662	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0030052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	229	537	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.434354582947801	2	FACETS	0.978	0.92	1	0.978	0.92	1	CLONAL	2	TRUE	0	0.439478318234864	2		540	533	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915083	32915084	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs80359605	NA	P-0030052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	108	471	0	ENST00000380152.3:c.6591_6592del	p.Glu2198AsnfsTer4	p.E2198Nfs*4	ENST00000380152		2197	acTGaa/acaa	11/27	0.434354582947801	2	FACETS	0.8	0.728	0.875	0.8	0.728	0.875	SUBCLONAL	2	TRUE	0	0.439478318234864	2		471	307	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402120	402120	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	172	472	0	ENST00000399788.2:c.4671del	p.Glu1558LysfsTer19	p.E1558Kfs*19	ENST00000399788	NM_001042603.1	1557	aaA/aa	27/28	0.439478318234864	6	FACETS	0.773	0.711	0.838			1	SUBCLONAL	2	TRUE	NA	0.439478318234864	6		472	951	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610587	81610587	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs750689462	NA	P-0030052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	127	396	0	ENST00000298171.2:c.2185A>T	p.Arg729Trp	p.R729W	ENST00000298171	NM_000369.2	729	Agg/Tgg	10/10	0.439478318234864	6	FACETS	0.842	0.769	0.917	0.421	0.384	0.459	CLONAL	3	TRUE	0	0.439478318234864	6		396	430	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523636	176523636	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	180	742	1	ENST00000292408.4:c.2047T>C	p.Phe683Leu	p.F683L	ENST00000292408	NM_213647.1	683	Ttc/Ctc	16/18	0.385563081912801	4	FACETS	0.767	0.708	0.827	0.767	0.708	0.827	SUBCLONAL	2	TRUE	2	0.439478318234864	4		743	769	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523638	176523638	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	186	740	2	ENST00000292408.4:c.2049C>A	p.Phe683Leu	p.F683L	ENST00000292408	NM_213647.1	683	ttC/ttA	16/18	0.385563081912801	4	FACETS	0.8	0.74	0.861	0.8	0.74	0.861	SUBCLONAL	2	TRUE	2	0.439478318234864	4		742	762	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662654	117662654	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	22	417	0	ENST00000368508.3:c.4811C>A	p.Pro1604His	p.P1604H	ENST00000368508	NM_002944.2	1604	cCt/cAt	29/43	0.439478318234864	4	FACETS	0.34	0.263	0.43	0.085	0.065	0.108	SUBCLONAL	1	TRUE	0	0.439478318234864	4		417	424	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523634	176523638	+	missense_variant	Missense_Mutation	ONP	TCTTC	TCTTC	CCCTA	novel	NA	P-0030052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	192	725	0	ENST00000292408.4:c.2045_2049delinsCCCTA	p.Ile682_Phe683delinsThrLeu	p.I682_F683delinsTL	ENST00000292408	NM_213647.1	682	aTCTTC/aCCCTA	16/18	0.385563081912801	4	FACETS	0.813	0.753	0.874	0.813	0.753	0.874	CLONAL	2	TRUE	2	0.439478318234864	4		725	774	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0030053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	348	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.923825463391017	4	FACETS	1	0.993	1	0.327	0.309	0.344	CLONAL	1	TRUE	0	0.923825463391017	4		511	1109	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0030053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	359	1128	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.627227139051704	3	FACETS	1	0.988	1	0.559	0.53	0.587	CLONAL	1	TRUE	1	0.923825463391017	3		1128	1017	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998756	100998756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749674024	NA	P-0030053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	201	497	1	ENST00000325455.5:c.1046C>T	p.Ser349Leu	p.S349L	ENST00000325455	NM_001202474.3	349	tCg/tTg	1/8	0.468183424460768	1	FACETS	0.368	0.342	0.394	0.368	0.342	0.394	INDETERMINATE	1	TRUE	0	0.923825463391017	1		498	637	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259442	55259442	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397517127	NA	P-0030053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	297	345	0	ENST00000275493.2:c.2500G>T	p.Val834Leu	p.V834L	ENST00000275493	NM_005228.3	834	Gtg/Ttg	21/28	0.627227139051704	3	FACETS	1	0.988	1	0.58	0.548	0.613	CLONAL	1	TRUE	1	0.923825463391017	3		345	810	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0030053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	508	520	0	ENST00000269305.4:c.559+1G>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.923825463391017	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.923825463391017	2		520	549	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246498703	246498703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	185	509	0	ENST00000388985.4:c.302C>T	p.Ser101Phe	p.S101F	ENST00000388985		101	tCc/tTc	3/12	0.613704710264038	3	FACETS	0.629	0.581	0.679			1	SUBCLONAL	1	TRUE	NA	0.923825463391017	3		509	931	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120467977	120467977	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1131691315	NA	P-0030053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	219	612	0	ENST00000256646.2:c.4462G>A	p.Glu1488Lys	p.E1488K	ENST00000256646	NM_024408.3	1488	Gag/Aag	25/34	0.923825463391017	2	FACETS	0.755	0.706	0.804	0.377	0.353	0.402	SUBCLONAL	1	TRUE	0	0.923825463391017	2		612	628	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550938	150550938	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	207	350	1	ENST00000369026.2:c.718G>A	p.Glu240Lys	p.E240K	ENST00000369026	NM_021960.4	240	Gaa/Aaa	2/3	0.916058983119613	5	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.923825463391017	5		351	942	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942698	48942701	+	frameshift_variant	Frame_Shift_Del	DEL	TTGA	TTGA	-	novel	NA	P-0030053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	389	314	0	ENST00000267163.4:c.1086_1089del	p.Asp363LysfsTer3	p.D363Kfs*3	ENST00000267163	NM_000321.2	362	cTTGAt/ct	11/27	0.923825463391017	2	FACETS	0.993	0.975	1	0.993	0.975	1	CLONAL	2	TRUE	0	0.923825463391017	2		314	424	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640430	3640430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1863	216	756	1	ENST00000294008.3:c.3209C>T	p.Ser1070Phe	p.S1070F	ENST00000294008	NM_032444.2	1070	tCc/tTc	12/15	0.923825463391017	4	FACETS	0.433	0.4	0.467			1	SUBCLONAL	1	TRUE	NA	0.923825463391017	4		757	2079	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857332	9857332	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs763809945	NA	P-0030053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	135	468	0	ENST00000330684.3:c.4069C>G	p.Leu1357Val	p.L1357V	ENST00000330684	NM_001134407.1	1357	Ctc/Gtc	13/13	0.865409736820071	6	FACETS	0.62	0.561	0.681	0.155	0.14	0.171	SUBCLONAL	1	TRUE	2	0.923825463391017	6		468	1343	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17117161	17117161	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	158	369	0	ENST00000285071.4:c.1548G>C	p.Lys516Asn	p.K516N	ENST00000285071	NM_144997.5	516	aaG/aaC	14/14	0.923825463391017	2	FACETS	0.794	0.735	0.854	0.397	0.367	0.427	SUBCLONAL	1	TRUE	0	0.923825463391017	2		369	431	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883071	37883071	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	160	601	0	ENST00000269571.5:c.2974G>A	p.Glu992Lys	p.E992K	ENST00000269571		992	Gag/Aag	25/27	NA	2	FACETS	0.404	0.37	0.439			1	INDETERMINATE	1	TRUE	NA	0.923825463391017	2		601	857	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219785	36219785	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0030053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1941	229	739	0	ENST00000222270.7:c.4682C>G	p.Ser1561Ter	p.S1561*	ENST00000222270	NM_014727.1	1561	tCa/tGa	20/37	0.868688468666788	6	FACETS	0.651	0.603	0.7	0.163	0.15	0.175	SUBCLONAL	1	TRUE	2	0.923825463391017	6		739	2170	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753376	57753376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	156	405	0	ENST00000274289.3:c.748G>A	p.Glu250Lys	p.E250K	ENST00000274289	NM_006622.3	250	Gaa/Aaa	6/14	0.923825463391017	4	FACETS	0.506	0.462	0.553	0.169	0.154	0.185	SUBCLONAL	1	TRUE	1	0.923825463391017	4		405	1283	SUCCESS
APC	324	MSKCC	GRCh37	5	112174884	112174884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	93	343	0	ENST00000257430.4:c.3593C>T	p.Ser1198Leu	p.S1198L	ENST00000257430	NM_000038.5	1198	tCa/tTa	16/16	0.923825463391017	4	FACETS	0.455	0.404	0.51	0.114	0.101	0.128	SUBCLONAL	1	TRUE	0	0.923825463391017	4		343	851	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500777	149500777	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	325	446	0	ENST00000261799.4:c.2453C>A	p.Ala818Asp	p.A818D	ENST00000261799	NM_002609.3	818	gCc/gAc	17/23	0.923825463391017	4	FACETS	1	0.986	1	0.283	0.267	0.299	CLONAL	1	TRUE	0	0.923825463391017	4		446	1196	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520432	176520432	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	420	620	0	ENST00000292408.4:c.1277G>T	p.Gly426Val	p.G426V	ENST00000292408	NM_213647.1	426	gGc/gTc	10/18	NA	2	FACETS	0.962	0.921	1			1	INDETERMINATE	1	TRUE	NA	0.923825463391017	2		620	945	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6442022	6442022	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	332	152	0	ENST00000356142.4:c.581C>G	p.Ala194Gly	p.A194G	ENST00000356142	NM_018890.3	194	gCa/gGa	7/7	0.627227139051704	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	1	0.923825463391017	3		152	441	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	201	376	0				ENST00000310581	NM_198253.2	-/1132			0.760508312708692	4	FACETS	0.967	0.907	1	0.967	0.907	1	CLONAL	2	TRUE	2	0.857867476570758	4		376	450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0030056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	286	635	1	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	1	2	FACETS	0.973	0.921	1	0.973	0.921	1	CLONAL	1	TRUE	1	0.857867476570758	2		636	685	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0030056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	196	507	0	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	1	2	FACETS	0.933	0.872	0.994	0.933	0.872	0.994	CLONAL	1	TRUE	1	0.857867476570758	2		507	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0030058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	356	700	1	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.748088270312603	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.748088270312603	1		701	559	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047527	49047527	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0030058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	82	181	0	ENST00000267163.4:c.2520+1G>C		p.X840_splice	ENST00000267163	NM_000321.2	840			0.748088270312603	1	FACETS	0.966	0.884	1	0.966	0.884	1	CLONAL	1	TRUE	0	0.748088270312603	1		181	142	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61709564	61709564	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	175	330	0	ENST00000401558.2:c.2923del	p.Gln975ArgfsTer20	p.Q975Rfs*20	ENST00000401558	NM_003400.3	975	Cag/ag	23/25	1	2	FACETS	0.878	0.814	0.943	0.878	0.814	0.943	CLONAL	1	TRUE	1	0.748088270312603	2		330	533	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0030111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	77	441	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.329399498209836	1	FACETS	0.91	0.803	1	0.91	0.803	1	CLONAL	1	TRUE	0	0.329399498209836	1		441	429	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857679	9857679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886042648	NA	P-0030111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	68	332	0	ENST00000330684.3:c.3722G>A	p.Arg1241Gln	p.R1241Q	ENST00000330684	NM_001134407.1	1241	cGg/cAg	13/13	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.329399498209836	2		332	374	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600429	10600429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	139	616	0	ENST00000171111.5:c.1426G>A	p.Gly476Arg	p.G476R	ENST00000171111	NM_203500.1	476	Ggg/Agg	4/6	0.329399498209836	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.329399498209836	1		616	637	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207065	1207074	+	protein_altering_variant	In_Frame_Del	DEL	GGGGGACCTG	GGGGGACCTG	CCCC	novel	NA	P-0030111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	104	617	3	ENST00000326873.7:c.153_162delinsCCCC	p.Met51_Leu54delinsIlePro	p.M51_L54delinsIP	ENST00000326873	NM_000455.4	51	atGGGGGACCTG/atCCCC	1/10	0.329399498209836	1	FACETS	0.922	0.828	1	0.922	0.828	1	CLONAL	1	TRUE	0	0.329399498209836	1		620	572	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123623	11123623	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0030111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	83	419	0	ENST00000358026.2:c.2275-2A>T		p.X759_splice	ENST00000358026	NM_001128849.1	759			0.329399498209836	1	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	0	0.329399498209836	1		419	412	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031951	26031955	+	stop_gained	Nonsense_Mutation	INS	ATGGC	ATGGC	TTTGTGTCCTCAAAGAGCCTTAGCAAAGGTTTGTGTCCTTA	novel	NA	P-0030111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	24	345	0	ENST00000244661.2:c.334_338delinsTAAGGACACAAACCTTTGCTAAGGCTCTTTGAGGACACAAA	p.Ala112_Ile113delinsTer	p.A112_I113delins*	ENST00000244661	NM_003537.3	112	GCCATc/TAAGGACACAAACCTTTGCTAAGGCTCTTTGAGGACACAAAc	1/1	1	2	FACETS	0.443	0.347	0.553	0.443	0.347	0.553	SUBCLONAL	1	TRUE	1	0.329399498209836	2		345	329	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775698	9775698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000095-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	87	341	0	ENST00000377346.4:c.241G>A	p.Glu81Lys	p.E81K	ENST00000377346	NM_005026.3	81	Gag/Aag	4/24	0.131603472150527	3	FACETS	1	0.971	1			1	INDETERMINATE	2	TRUE	NA	0.333030988640022	3		341	248	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378648	25378648	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000095-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	495	514	0	ENST00000311936.3:c.350A>G	p.Lys117Arg	p.K117R	ENST00000311936	NM_004985.3	117	aAa/aGa	4/5	0.333030988640022	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	1	0.333030988640022	4		514	1245	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634289	23634289	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs886039626	NA	P-0000095-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	55	635	0	ENST00000261584.4:c.2996+1G>T		p.X999_splice	ENST00000261584	NM_024675.3	999			0.300763295736527	2	FACETS	0.506	0.432	0.587	0.253	0.216	0.294	SUBCLONAL	1	TRUE	0	0.333030988640022	2		635	653	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0000095-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	110	534	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			NA	2	FACETS	1	0.959	1			1	INDETERMINATE	2	TRUE	NA	0.333030988640022	2		534	303	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874945	151874945	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267601428	NA	P-0000170-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	268	401	0	ENST00000262189.6:c.7593G>A	p.Met2531Ile	p.M2531I	ENST00000262189	NM_170606.2	2531	atG/atA	38/59	0.466325700399163	4	FACETS	1	0.98	1			1	CLONAL	2	TRUE	NA	0.546232226406381	4		401	699	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239387	123239387	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000181-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	74	291	0	ENST00000358487.5:c.2450G>A	p.Gly817Asp	p.G817D	ENST00000358487	NM_000141.4	817	gGc/gAc	18/18	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.168540652613765	2		291	661	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988540	36988540	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs765587544	NA	P-0000181-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1564	84	637	0	ENST00000354822.5:c.113C>G	p.Thr38Arg	p.T38R	ENST00000354822	NM_001079668.2	38	aCg/aGg	2/3	NA	2	FACETS	0.605	0.532	0.684			1	INDETERMINATE	1	TRUE	NA	0.168540652613765	2		637	1648	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16056663	16056663	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000181-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1571	105	654	0	ENST00000268712.3:c.779A>T	p.Lys260Ile	p.K260I	ENST00000268712	NM_006311.3	260	aAa/aTa	7/46	0.168540652613765	2	FACETS	0.743	0.663	0.83	0.372	0.331	0.415	SUBCLONAL	1	TRUE	0	0.168540652613765	2		654	1676	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278176	15278176	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000287-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	15	451	0	ENST00000263388.2:c.5246A>T	p.Gln1749Leu	p.Q1749L	ENST00000263388	NM_000435.2	1749	cAg/cTg	29/33	0.138821283446938	4	FACETS	0.407	0.299	0.535	0.203	0.149	0.268	INDETERMINATE	1	FALSE	2	0.876132966483678	4		451	158	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075191	16075192	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0000287-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	50	244	0	ENST00000268712.3:c.360_361delinsTT	p.Gln120_Arg121delinsHisCys	p.Q120_R121delinsHC	ENST00000268712	NM_006311.3	120	caGCgt/caTTgt	4/46	0.756513759158088	3	FACETS	0.995	0.86	1			1	CLONAL	1	FALSE	NA	0.876132966483678	3		244	165	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65323365	65323365	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000443-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	154	354	0	ENST00000342505.4:c.1432A>G	p.Thr478Ala	p.T478A	ENST00000342505	NM_002227.2	478	Acc/Gcc	10/25	0.54527254068425	3	FACETS	0.992	0.909	1	0.496	0.454	0.539	CLONAL	1	TRUE	1	0.54527254068425	3		354	725	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666409	206666409	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000443-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	147	406	1	ENST00000367120.3:c.1889C>A	p.Ala630Asp	p.A630D	ENST00000367120	NM_014002.3	630	gCc/gAc	19/22	0.54527254068425		FACETS		0.873	1				CLONAL	1	TRUE	1	0.54527254068425	3		407	719	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520413	176520413	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000443-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	137	434	0	ENST00000292408.4:c.1258C>A	p.Leu420Met	p.L420M	ENST00000292408	NM_213647.1	420	Ctg/Atg	10/18	NA	2	FACETS	0.814	0.743	0.889			1	INDETERMINATE	1	TRUE	NA	0.54527254068425	2		434	617	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164654	36164654	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000443-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	201	489	1	ENST00000300305.3:c.1221C>A	p.Tyr407Ter	p.Y407*	ENST00000300305		407	taC/taA	8/8	0.422932858471561	5	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.54527254068425	5		490	1096	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347814	347814	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000450-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	86	442	0	ENST00000262320.3:c.1692G>A	p.Trp564Ter	p.W564*	ENST00000262320	NM_003502.3	564	tgG/tgA	6/11	0.457019238436117	1	FACETS	0.76	0.677	0.848	0.76	0.677	0.848	SUBCLONAL	1	TRUE	0	0.457019238436117	1		442	382	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105612	11105612	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000450-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	39	332	0	ENST00000358026.2:c.1528A>G	p.Asn510Asp	p.N510D	ENST00000358026	NM_001128849.1	510	Aac/Gac	9/36	0.331638616115499	1	FACETS	0.362	0.3	0.43	0.362	0.3	0.43	SUBCLONAL	1	TRUE	0	0.457019238436117	1		332	364	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9770548	9770548	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000456-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	71	493	0	ENST00000377346.4:c.35G>A	p.Trp12Ter	p.W12*	ENST00000377346	NM_005026.3	12	tGg/tAg	3/24	0.204773958601114	1	FACETS	0.747	0.651	0.852	0.747	0.651	0.852	SUBCLONAL	1	TRUE	0	0.204773958601114	1		493	833	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794784	242794784	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000456-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	35	207	0	ENST00000334409.5:c.425T>C	p.Leu142Pro	p.L142P	ENST00000334409	NM_005018.2	142	cTc/cCc	2/5	0.204773958601114	3	FACETS	1	0.909	1	0.589	0.484	0.706	CLONAL	1	TRUE	1	0.204773958601114	3		207	320	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602333	28602333	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000456-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	75	431	0	ENST00000241453.7:c.2035G>A	p.Gly679Arg	p.G679R	ENST00000241453	NM_004119.2	679	Ggg/Agg	16/24	0.204773958601114	1	FACETS	0.735	0.643	0.835	0.735	0.643	0.835	SUBCLONAL	1	TRUE	0	0.204773958601114	1		431	894	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179194	123179194	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000456-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	65	213	0	ENST00000218089.9:c.643T>G	p.Phe215Val	p.F215V	ENST00000218089	NM_001042749.1	215	Ttt/Gtt	8/35	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.204773958601114	NA		213	499	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514159	69514160	+	missense_variant	Missense_Mutation	DNP	CT	CT	AC	novel	NA	P-0000456-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	51	429	0	ENST00000294312.3:c.521_522delinsGT	p.Glu174Gly	p.E174G	ENST00000294312	NM_005117.2	174	gAG/gGT	3/3	1	2	FACETS	0.684	0.58	0.799	0.684	0.58	0.799	SUBCLONAL	1	TRUE	1	0.204773958601114	2		429	728	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0000461-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	270	578	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.511921130672469	1	FACETS	1	0.985	1	1	0.985	1	INDETERMINATE	1	TRUE	0	0.882114251107665	1		578	331	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593603	55593603	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913235	NA	P-0000461-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	84	501	0	ENST00000288135.5:c.1669T>G	p.Trp557Gly	p.W557G	ENST00000288135	NM_000222.2	557	Tgg/Ggg	11/21	0.717552295558664	1	FACETS	0.305	0.271	0.341	0.305	0.271	0.341	SUBCLONAL	1	TRUE	0	0.882114251107665	1		501	349	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714421	117714421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745334216	NA	P-0000461-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	109	458	0	ENST00000368508.3:c.1228G>A	p.Ala410Thr	p.A410T	ENST00000368508	NM_002944.2	410	Gca/Aca	11/43	0.662283679036114	1	FACETS	0.315	0.284	0.347	0.315	0.284	0.347	SUBCLONAL	1	TRUE	0	0.882114251107665	1		458	439	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8338979	8338979	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000461-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	95	520	0	ENST00000356435.5:c.5322G>T	p.Met1774Ile	p.M1774I	ENST00000356435		1774	atG/atT	32/35	1	2	FACETS	0.326	0.29	0.364	0.326	0.29	0.364	SUBCLONAL	1	TRUE	1	0.882114251107665	2		520	661	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279964	18279964	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000461-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	208	437	0	ENST00000222254.8:c.2047T>G	p.Tyr683Asp	p.Y683D	ENST00000222254	NM_005027.3	683	Tac/Gac	16/16	0.882114251107665	1	FACETS	0.915	0.875	0.954	0.915	0.875	0.954	CLONAL	1	TRUE	0	0.882114251107665	1		437	288	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0000598-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	312	830	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	2	TRUE	NA	0.689861117822436	2		830	439	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250022	53250022	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000598-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	320	333	0	ENST00000375401.3:c.227A>T	p.Glu76Val	p.E76V	ENST00000375401	NM_004187.3	76	gAg/gTg	2/26	0.241919470705253	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.689861117822436	2		333	804	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0000650-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	60	298	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.455454648003338	3	FACETS	0.699	0.604	0.801	0.233	0.201	0.267	SUBCLONAL	1	TRUE	0	0.502023779815789	3		298	428	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0000650-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	292	606	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.502023779815789	2		608	515	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024674	14024674	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000650-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	256	562	0	ENST00000311895.7:c.900G>C	p.Gln300His	p.Q300H	ENST00000311895	NM_005236.2	300	caG/caC	5/11	0.256111068112669	3	FACETS	0.89	0.832	0.951			1	INDETERMINATE	1	TRUE	NA	0.502023779815789	3		562	1433	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938923	178938925	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs1560145921	NA	P-0000650-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	28	92	0	ENST00000263967.3:c.2170_2172del	p.Lys724del	p.K724del	ENST00000263967	NM_006218.2	722	gAGAag/gag	14/21	0.455454648003338	3	FACETS	0.429	0.343	0.527	0.143	0.114	0.176	SUBCLONAL	1	TRUE	0	0.502023779815789	3		92	325	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505122	149505122	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1460983846	NA	P-0000663-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	198	400	0	ENST00000261799.4:c.1693C>T	p.Arg565Ter	p.R565*	ENST00000261799	NM_002609.3	565	Cga/Tga	12/23	0.241796848625325	4	FACETS	1	0.987	1	0.443	0.409	0.479	CLONAL	1	TRUE	1	0.29	4		400	1324	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877347	28877347	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs760994884	NA	P-0000664-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	83	175	0	ENST00000282397.4:c.3974C>G	p.Pro1325Arg	p.P1325R	ENST00000282397	NM_002019.4	1325	cCa/cGa	30/30	1	2	FACETS	0.392	0.346	0.442	0.392	0.346	0.442	SUBCLONAL	1	TRUE	1	0.542570460505093	2		175	780	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21304024	21304024	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000664-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1641	134	335	0	ENST00000354336.3:c.803G>C	p.Arg268Thr	p.R268T	ENST00000354336	NM_005207.3	268	aGg/aCg	3/3	0.268975701288038	3	FACETS	0.354	0.32	0.39			1	INDETERMINATE	1	TRUE	NA	0.542570460505093	3		335	1775	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539120	187539120	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs760240050	NA	P-0000685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	32	320	0	ENST00000441802.2:c.8620G>T	p.Glu2874Ter	p.E2874*	ENST00000441802	NM_005245.3	2874	Gaa/Taa	10/27	0.935637706915261	1	FACETS	0.082	0.066	0.1	0.082	0.066	0.1	SUBCLONAL	1	TRUE	0	0.935637706915261	1		320	443	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540249	23540249	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	68	102	0	ENST00000380871.4:c.154C>A	p.Arg52Ser	p.R52S	ENST00000380871	NM_006167.3	52	Cgc/Agc	1/2	0.435767407938957	2	FACETS	0.682	0.603	0.765	0.341	0.301	0.383	INDETERMINATE	1	TRUE	0	0.935637706915261	2		102	213	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745479	162745479	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000747-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	49	366	0	ENST00000367921.3:c.1894C>A	p.Leu632Ile	p.L632I	ENST00000367921	NM_006182.2	632	Ctc/Atc	15/18	0.606635470816919	3	FACETS	0.402	0.341	0.469	0.134	0.113	0.157	SUBCLONAL	1	FALSE	0	0.720863542979563	3		366	460	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675945	30675945	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000747-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	90	590	0	ENST00000376406.3:c.2411G>T	p.Gly804Val	p.G804V	ENST00000376406	NM_014641.2	804	gGc/gTc	8/15	0.495824677027491	4	FACETS	0.659	0.585	0.738	0.22	0.195	0.246	SUBCLONAL	1	FALSE	1	0.720863542979563	4		590	652	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0000782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	541	656	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.630863918045891	3	FACETS	0.856	0.831	0.882	0.856	0.831	0.882	CLONAL	3	TRUE	0	0.703656127597805	3		656	809	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150521	157150521	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	166	158	0	ENST00000346085.5:c.1703G>A	p.Gly568Glu	p.G568E	ENST00000346085	NM_020732.3	568	gGg/gAg	2/20	1	2	FACETS	0.904	0.836	0.973	0.904	0.836	0.973	CLONAL	1	TRUE	1	0.703656127597805	2		158	522	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0000784-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	171	230	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.568181093927333	2		230	534	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032805	48032805	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587779273	NA	P-0000784-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	59	323	0	ENST00000234420.5:c.3605T>C	p.Met1202Thr	p.M1202T	ENST00000234420	NM_000179.2	1202	aTg/aCg	7/10	1	2	FACETS	0.267	0.229	0.309	0.267	0.229	0.309	SUBCLONAL	1	TRUE	1	0.568181093927333	2		323	777	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686252	117686252	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000784-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	44	208	0	ENST00000368508.3:c.3089C>G	p.Thr1030Arg	p.T1030R	ENST00000368508	NM_002944.2	1030	aCa/aGa	20/43	0.272845371297588	2	FACETS	0.376	0.315	0.443	0.188	0.157	0.222	INDETERMINATE	1	TRUE	0	0.568181093927333	2		208	412	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968329	2968329	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs778162676	NA	P-0000784-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	82	200	0	ENST00000396946.4:c.1657C>A	p.Pro553Thr	p.P553T	ENST00000396946	NM_032415.4	553	Ccc/Acc	13/25	0.395695425151934	3	FACETS	0.507	0.447	0.572	0.254	0.223	0.286	SUBCLONAL	1	TRUE	1	0.568181093927333	3		200	731	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13949304	13949304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000784-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	107	291	0	ENST00000405192.2:c.824C>T	p.Pro275Leu	p.P275L	ENST00000405192	NM_001163147.1	275	cCc/cTc	9/12	0.395695425151934	3	FACETS	0.503	0.45	0.559	0.252	0.225	0.28	SUBCLONAL	1	TRUE	1	0.568181093927333	3		291	961	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593389	48593389	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000992-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	56	149	0	ENST00000342988.3:c.1140G>T	p.Arg380Ser	p.R380S	ENST00000342988	NM_005359.5	380	agG/agT	10/12	0.526301177626902	2	FACETS	0.791	0.686	0.904	0.396	0.343	0.452	CLONAL	1	TRUE	0	0.604805458702926	2		149	234	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431628	6431628	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001004-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	81	337	0	ENST00000356142.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000356142	NM_018890.3	61	Caa/Aaa	3/7	0.288407127759406	5	FACETS	0.963	0.852	1	0.481	0.426	0.54	CLONAL	2	TRUE	1	0.288407127759406	5		337	418	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843461	3843461	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001009-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	80	366	0	ENST00000262367.5:c.1142C>A	p.Ser381Ter	p.S381*	ENST00000262367	NM_004380.2	381	tCg/tAg	4/31	0.268777345371736	1	FACETS	0.357	0.314	0.404	0.357	0.314	0.404	SUBCLONAL	1	TRUE	0	0.416422456708914	1		366	852	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973548	15973548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1000518180	NA	P-0001009-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	52	273	0	ENST00000268712.3:c.4444C>T	p.Arg1482Trp	p.R1482W	ENST00000268712	NM_006311.3	1482	Cgg/Tgg	31/46	0.394970191966087	1	FACETS	0.313	0.266	0.365	0.313	0.266	0.365	SUBCLONAL	1	TRUE	0	0.416422456708914	1		273	632	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546022	29546022	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0001009-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	43	200	0	ENST00000356175.3:c.1528-1G>C		p.X510_splice	ENST00000356175	NM_000267.3	510			0.394970191966087	1	FACETS	0.265	0.221	0.314	0.265	0.221	0.314	SUBCLONAL	1	TRUE	0	0.416422456708914	1		200	617	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527496	157527504	+	inframe_deletion	In_Frame_Del	DEL	GACGAGGAA	GACGAGGAA	-	rs1562351526	NA	P-0001009-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	38	256	0	ENST00000346085.5:c.5229_5237del	p.Asp1747_Glu1749del	p.D1747_E1749del	ENST00000346085	NM_020732.3	1741	GACGAGGAA/-	20/20	1	2	FACETS	0.342	0.282	0.409	0.342	0.282	0.409	SUBCLONAL	1	TRUE	1	0.416422456708914	2		256	534	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934874	NA	P-0001058-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	75	291	0	ENST00000269305.4:c.451C>A	p.Pro151Thr	p.P151T	ENST00000269305	NM_001126112.2	151	Ccc/Acc	5/11	0.385057558370785	1	FACETS	0.381	0.334	0.431	0.381	0.334	0.431	SUBCLONAL	1	TRUE	0	0.550536560888289	1		291	518	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685315	89685315	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1554897280	NA	P-0001058-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	165	267	0	ENST00000371953.3:c.209+1G>A		p.X70_splice	ENST00000371953	NM_000314.4	70			0.550536560888289	1	FACETS	0.634	0.584	0.686	0.634	0.584	0.686	SUBCLONAL	1	TRUE	0	0.550536560888289	1		267	685	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47613722	47613722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758824634	NA	P-0001058-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	72	324	0	ENST00000263735.4:c.915G>A	p.Met305Ile	p.M305I	ENST00000263735	NM_002354.2	305	atG/atA	9/9	0.34338812092981	1	FACETS	0.279	0.243	0.317	0.279	0.243	0.317	SUBCLONAL	1	TRUE	0	0.550536560888289	1		324	680	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969983	161969983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774445597	NA	P-0001058-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	168	523	0	ENST00000366898.1:c.986G>A	p.Gly329Asp	p.G329D	ENST00000366898	NM_004562.2	329	gGc/gAc	9/12	NA	2	FACETS	0.677	0.623	0.735			1	INDETERMINATE	1	TRUE	NA	0.550536560888289	2		523	901	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846073	128846073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001058-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	112	654	0	ENST00000249373.3:c.1003C>T	p.Leu335Phe	p.L335F	ENST00000249373	NM_005631.4	335	Ctc/Ttc	5/12	0.243031520666193	3	FACETS	0.588	0.528	0.651	0.196	0.176	0.217	INDETERMINATE	1	TRUE	0	0.550536560888289	3		654	883	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609788	28609788	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001058-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	78	410	0	ENST00000241453.7:c.1441G>A	p.Gly481Arg	p.G481R	ENST00000241453	NM_004119.2	481	Gga/Aga	12/24	0.550536560888289	1	FACETS	0.32	0.281	0.362	0.32	0.281	0.362	SUBCLONAL	1	TRUE	0	0.550536560888289	1		410	642	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347107	347107	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001058-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	106	724	0	ENST00000262320.3:c.1904G>A	p.Trp635Ter	p.W635*	ENST00000262320	NM_003502.3	635	tGg/tAg	7/11	0.550536560888289	1	FACETS	0.38	0.341	0.422	0.38	0.341	0.422	SUBCLONAL	1	TRUE	0	0.550536560888289	1		724	734	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779266	3779266	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001058-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	68	190	0	ENST00000262367.5:c.5782C>T	p.Gln1928Ter	p.Q1928*	ENST00000262367	NM_004380.2	1928	Cag/Tag	31/31	0.550536560888289	1	FACETS	0.829	0.733	0.929	0.829	0.733	0.929	CLONAL	1	TRUE	0	0.550536560888289	1		190	216	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574005	7574005	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001058-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	241	465	0	ENST00000269305.4:c.1022T>C	p.Phe341Ser	p.F341S	ENST00000269305	NM_001126112.2	341	tTc/tCc	10/11	0.385057558370785	1	FACETS	0.813	0.762	0.866	0.813	0.762	0.866	CLONAL	1	TRUE	0	0.550536560888289	1		465	780	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309672	30309672	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774178481	NA	P-0001058-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	86	378	0	ENST00000307677.4:c.350G>A	p.Gly117Glu	p.G117E	ENST00000307677	NM_138578.1	117	gGg/gAg	2/3	0.385057558370785	1	FACETS	0.301	0.266	0.338	0.301	0.266	0.338	SUBCLONAL	1	TRUE	0	0.550536560888289	1		378	753	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924351	112924351	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001058-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	62	422	0	ENST00000351677.2:c.1301del	p.Gly434AlafsTer38	p.G434Afs*38	ENST00000351677	NM_002834.3	433	Ggg/gg	11/16	1	2	FACETS	0.292	0.252	0.336	0.292	0.252	0.336	SUBCLONAL	1	TRUE	1	0.550536560888289	2		422	771	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001058-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	56	243	0	ENST00000269305.4:c.528C>A	p.Cys176Ter	p.C176*	ENST00000269305	NM_001126112.2	176	tgC/tgA	5/11	0.385057558370785	1	FACETS	0.421	0.362	0.485	0.421	0.362	0.485	SUBCLONAL	1	TRUE	0	0.550536560888289	1		243	350	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586454	189586454	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001106-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	30	203	0	ENST00000264731.3:c.1078A>G	p.Arg360Gly	p.R360G	ENST00000264731	NM_003722.4	360	Aga/Gga	8/14	0.449556385935613	2	FACETS	0.258	0.208	0.316	0.129	0.104	0.158	SUBCLONAL	1	TRUE	0	0.514887549778186	2		203	451	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549797	187549797	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001106-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	56	521	0	ENST00000441802.2:c.4444G>T	p.Asp1482Tyr	p.D1482Y	ENST00000441802	NM_005245.3	1482	Gat/Tat	8/27	0.162253098614181	1	FACETS	0.218	0.186	0.253	0.218	0.186	0.253	INDETERMINATE	1	TRUE	0	0.514887549778186	1		521	742	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853311	151853311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762439579	NA	P-0001106-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1469	104	327	0	ENST00000262189.6:c.11791G>A	p.Gly3931Arg	p.G3931R	ENST00000262189	NM_170606.2	3931	Gga/Aga	45/59	0.514887549778186	9	FACETS	0.72	0.642	0.803			1	SUBCLONAL	1	TRUE	NA	0.514887549778186	9		327	1573	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220506	133220506	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001106-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	130	354	0	ENST00000320574.5:c.4207C>A	p.Pro1403Thr	p.P1403T	ENST00000320574	NM_006231.2	1403	Cca/Aca	33/49	0.184222325013084	3	FACETS	1	0.97	1	0.383	0.349	0.419	INDETERMINATE	1	TRUE	0	0.514887549778186	3		354	552	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38506167	38506167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001106-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	113	253	0	ENST00000254066.5:c.459G>A	p.Met153Ile	p.M153I	ENST00000254066	NM_000964.3	153	atG/atA	4/9	0.405902198341385	3	FACETS	1	0.949	1			1	CLONAL	1	TRUE	NA	0.514887549778186	3		253	512	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222736	5222736	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752821383	NA	P-0001106-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	56	138	0	ENST00000357368.4:c.3067C>T	p.Pro1023Ser	p.P1023S	ENST00000357368	NM_002850.3	1023	Ccc/Tcc	18/38	0.216541054841721	2	FACETS	0.827	0.715	0.947	0.414	0.357	0.474	INDETERMINATE	1	TRUE	0	0.514887549778186	2		138	263	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	395	298	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.873328144738881	2		298	865	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203436	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	618	765	0	ENST00000269305.4:c.487T>C	p.Tyr163His	p.Y163H	ENST00000269305	NM_001126112.2	163	Tac/Cac	5/11	0.873328144738881	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.873328144738881	1		765	768	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394992	394992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	64	562	0	ENST00000380956.4:c.388G>A	p.Glu130Lys	p.E130K	ENST00000380956	NM_001195286.1	130	Gag/Aag	3/9	0.14700444979286	5	FACETS	0.335	0.288	0.385	0.112	0.096	0.129	INDETERMINATE	1	TRUE	2	0.873328144738881	5		562	1012	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271460	26271460	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	380	483	0	ENST00000305910.3:c.153G>C	p.Glu51Asp	p.E51D	ENST00000305910	NM_003534.2	51	gaG/gaC	1/1	0.14700444979286	5	FACETS	1	0.991	1	0.764	0.729	0.799	INDETERMINATE	2	TRUE	2	0.873328144738881	5		483	877	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41489079	41489079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373061594	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	953	520	0	ENST00000263253.7:c.71C>T	p.Ser24Leu	p.S24L	ENST00000263253	NM_001429.3	24	tCg/tTg	1/31	0.604083613672713	4	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.873328144738881	4		520	1748	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849304	76849304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	458	558	0	ENST00000373344.5:c.5972C>T	p.Ser1991Phe	p.S1991F	ENST00000373344	NM_000489.3	1991	tCt/tTt	26/35	0.873328144738881	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.873328144738881	1		558	580	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060925	38060925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1388855660	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	242	480	0	ENST00000250448.2:c.1064C>T	p.Ser355Leu	p.S355L	ENST00000250448	NM_004496.3	355	tCa/tTa	2/2	1	2	FACETS	0.59	0.552	0.63	0.59	0.552	0.63	SUBCLONAL	1	TRUE	1	0.873328144738881	2		480	939	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709028	117709028	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	280	548	1	ENST00000368508.3:c.1929G>A	p.Met643Ile	p.M643I	ENST00000368508	NM_002944.2	643	atG/atA	13/43	0.873328144738881	1	FACETS	0.557	0.527	0.587	0.557	0.527	0.587	SUBCLONAL	1	TRUE	0	0.873328144738881	1		549	649	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437669	52437669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	572	643	0	ENST00000460680.1:c.1492G>A	p.Glu498Lys	p.E498K	ENST00000460680	NM_004656.3	498	Gag/Aag	13/17	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.873328144738881	2		643	1256	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522416	176522416	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519792	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1278	671	789	0	ENST00000292408.4:c.1605C>G	p.Asn535Lys	p.N535K	ENST00000292408	NM_213647.1	535	aaC/aaG	12/18	0.8150407294028	3	FACETS	1	0.994	1	0.566	0.545	0.588	CLONAL	1	TRUE	1	0.873328144738881	3		789	1949	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955394	48955394	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886043247	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	384	271	0	ENST00000267163.4:c.1510C>T	p.Gln504Ter	p.Q504*	ENST00000267163	NM_000321.2	504	Cag/Tag	17/27	0.873328144738881	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.873328144738881	1		271	455	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350061	15350061	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1249	78	735	0	ENST00000263377.2:c.3591G>C	p.Lys1197Asn	p.K1197N	ENST00000263377	NM_058243.2	1197	aaG/aaC	18/20	0.220059504466649	1	FACETS	0.076	0.066	0.087	0.076	0.066	0.087	INDETERMINATE	1	TRUE	0	0.873328144738881	1		735	1327	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940138	71940138	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1350	457	672	0	ENST00000298229.2:c.523C>T	p.Pro175Ser	p.P175S	ENST00000298229	NM_001567.3	175	Ccc/Tcc	5/28	0.676595543631597	3	FACETS	0.832	0.792	0.873			1	CLONAL	1	TRUE	NA	0.873328144738881	3		672	1807	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170513	11170513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	572	750	1	ENST00000358026.2:c.4816G>T	p.Glu1606Ter	p.E1606*	ENST00000358026	NM_001128849.1	1606	Gag/Tag	34/36	0.220059504466649	1	FACETS	0.579	0.557	0.6	0.579	0.557	0.6	INDETERMINATE	1	TRUE	0	0.873328144738881	1		751	1275	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170519	11170519	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1235280916	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	560	736	1	ENST00000358026.2:c.4822G>A	p.Glu1608Lys	p.E1608K	ENST00000358026	NM_001128849.1	1608	Gag/Aag	34/36	0.220059504466649	1	FACETS	0.572	0.551	0.594	0.572	0.551	0.594	INDETERMINATE	1	TRUE	0	0.873328144738881	1		737	1262	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170531	11170531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	557	715	0	ENST00000358026.2:c.4834G>A	p.Glu1612Lys	p.E1612K	ENST00000358026	NM_001128849.1	1612	Gag/Aag	34/36	0.220059504466649	1	FACETS	0.591	0.569	0.614	0.591	0.569	0.614	INDETERMINATE	1	TRUE	0	0.873328144738881	1		715	1215	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275140	41275140	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	325	405	0	ENST00000349496.5:c.1306A>T	p.Met436Leu	p.M436L	ENST00000349496	NM_001904.3	436	Atg/Ttg	9/15	1	2	FACETS	0.981	0.932	1	0.981	0.932	1	CLONAL	1	TRUE	1	0.873328144738881	2		405	759	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032111	26032111	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	384	466	0	ENST00000244661.2:c.178G>C	p.Glu60Gln	p.E60Q	ENST00000244661	NM_003537.3	60	Gag/Cag	1/1	0.14700444979286	5	FACETS	1	0.994	1	0.828	0.791	0.865	INDETERMINATE	2	TRUE	2	0.873328144738881	5		466	818	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960160	151960160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	517	487	0	ENST00000262189.6:c.1240C>T	p.His414Tyr	p.H414Y	ENST00000262189	NM_170606.2	414	Cat/Tat	9/59	0.398200384401284	3	FACETS	1	0.995	1	0.645	0.619	0.672	INDETERMINATE	1	TRUE	1	0.873328144738881	3		487	1318	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932114	39932114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	1182	745	1	ENST00000378444.4:c.2485G>A	p.Glu829Lys	p.E829K	ENST00000378444	NM_001123385.1	829	Gag/Aag	4/15	0.873328144738881	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.873328144738881	3		746	1886	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143094	7143094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752552480	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	423	557	0	ENST00000302850.5:c.2275C>T	p.Arg759Trp	p.R759W	ENST00000302850	NM_000208.2	759	Cgg/Tgg	12/22	0.220059504466649	1	FACETS	0.553	0.529	0.577	0.553	0.529	0.577	INDETERMINATE	1	TRUE	0	0.873328144738881	1		557	987	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133950	38133950	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	60	779	0	ENST00000317025.8:c.3936C>G	p.Ile1312Met	p.I1312M	ENST00000317025	NM_023034.1	1312	atC/atG	23/24	0.873328144738881	1	FACETS	0.087	0.074	0.101	0.087	0.074	0.101	SUBCLONAL	1	TRUE	0	0.873328144738881	1		779	890	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725071	89725071	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	125	206	0	ENST00000371953.3:c.1054G>A	p.Glu352Lys	p.E352K	ENST00000371953	NM_000314.4	352	Gag/Aag	9/9	0.460297954355855	1	FACETS	0.45	0.412	0.49	0.45	0.412	0.49	INDETERMINATE	1	TRUE	0	0.873328144738881	1		206	358	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196032	67196032	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	455	588	0	ENST00000312629.5:c.16G>C	p.Asp6His	p.D6H	ENST00000312629	NM_003952.2	6	Gat/Cat	1/15	0.676595543631597	3	FACETS	1	0.96	1			1	CLONAL	1	TRUE	NA	0.873328144738881	3		588	1486	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69210621	69210621	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	194	381	0	ENST00000462284.1:c.204G>C	p.Met68Ile	p.M68I	ENST00000462284	NM_002392.5	68	atG/atC	4/11	0.34033732248978	4	FACETS	0.826	0.764	0.891	0.413	0.382	0.446	INDETERMINATE	1	TRUE	2	0.873328144738881	4		381	1007	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28880875	28880875	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415091072	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	258	625	1	ENST00000282397.4:c.3755C>T	p.Ser1252Phe	p.S1252F	ENST00000282397	NM_002019.4	1252	tCt/tTt	29/30	0.873328144738881	1	FACETS	0.508	0.479	0.538	0.508	0.479	0.538	SUBCLONAL	1	TRUE	0	0.873328144738881	1		626	655	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041709	42041709	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	203	460	1	ENST00000219905.7:c.5904G>A	p.Met1968Ile	p.M1968I	ENST00000219905	NM_001164273.1	1968	atG/atA	17/24	1	2	FACETS	0.519	0.481	0.558	0.519	0.481	0.558	SUBCLONAL	1	TRUE	1	0.873328144738881	2		461	896	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50788263	50788263	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1433	113	653	0	ENST00000398568.2:c.841G>C	p.Asp281His	p.D281H	ENST00000398568	NM_001042412.1	281	Gat/Cat	5/18	NA	2	FACETS	0.167	0.15	0.186			1	INDETERMINATE	1	TRUE	NA	0.873328144738881	2		653	1546	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37680952	37680952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	132	488	1	ENST00000447079.4:c.3121G>A	p.Glu1041Lys	p.E1041K	ENST00000447079	NM_015083.1	1041	Gag/Aag	12/14	0.873328144738881	1	FACETS	0.323	0.294	0.352	0.323	0.294	0.352	SUBCLONAL	1	TRUE	0	0.873328144738881	1		489	528	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271474	15271474	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	novel	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	685	933	0	ENST00000263388.2:c.6965G>C	p.Ter2322SerextTer106	p.*2322Sext*106	ENST00000263388	NM_000435.2	2322	tGa/tCa	33/33	0.220059504466649	1	FACETS	0.564	0.544	0.583	0.564	0.544	0.583	INDETERMINATE	1	TRUE	0	0.873328144738881	1		933	1568	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798426	42798426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1296	99	776	1	ENST00000575354.2:c.4297G>A	p.Glu1433Lys	p.E1433K	ENST00000575354	NM_015125.3	1433	Gag/Aag	18/20	1	2	FACETS	0.163	0.144	0.182	0.163	0.144	0.182	SUBCLONAL	1	TRUE	1	0.873328144738881	2		777	1395	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380530	31380530	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	96	575	0	ENST00000328111.2:c.1020C>G	p.Phe340Leu	p.F340L	ENST00000328111	NM_006892.3	340	ttC/ttG	9/23	1	2	FACETS	0.178	0.157	0.199	0.178	0.157	0.199	SUBCLONAL	1	TRUE	1	0.873328144738881	2		575	1238	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852500	42852500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	564	787	0	ENST00000398585.3:c.586C>T	p.Gln196Ter	p.Q196*	ENST00000398585	NM_001135099.1	196	Cag/Tag	6/14	1	2	FACETS	0.841	0.807	0.875	0.841	0.807	0.875	CLONAL	1	TRUE	1	0.873328144738881	2		787	1536	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092969	29092969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371207635	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	457	504	1	ENST00000328354.6:c.1015C>T	p.His339Tyr	p.H339Y	ENST00000328354	NM_007194.3	339	Cat/Tat	10/15	1	2	FACETS	0.967	0.926	1	0.967	0.926	1	CLONAL	1	TRUE	1	0.873328144738881	2		505	1082	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752903	57752903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	57	487	0	ENST00000274289.3:c.1025G>A	p.Arg342Lys	p.R342K	ENST00000274289	NM_006622.3	342	aGa/aAa	8/14	1	2	FACETS	0.117	0.1	0.137	0.117	0.1	0.137	SUBCLONAL	1	TRUE	1	0.873328144738881	2		487	1112	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517769	176517769	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142240686	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1855	463	682	0	ENST00000292408.4:c.379G>A	p.Asp127Asn	p.D127N	ENST00000292408	NM_213647.1	127	Gat/Aat	4/18	0.8150407294028	3	FACETS	0.657	0.625	0.69	0.329	0.312	0.345	SUBCLONAL	1	TRUE	1	0.873328144738881	3		682	2318	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534666	140534666	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753354016	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	502	383	0	ENST00000288602.6:c.247G>A	p.Glu83Lys	p.E83K	ENST00000288602	NM_004333.4	83	Gaa/Aaa	3/18	0.398200384401284	3	FACETS	0.888	0.856	0.92	0.888	0.856	0.92	INDETERMINATE	2	TRUE	1	0.873328144738881	3		383	930	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110251297	110251297	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003233-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	90	627	1	ENST00000374672.4:c.40G>T	p.Asp14Tyr	p.D14Y	ENST00000374672	NM_004235.4	14	Gac/Tac	2/5	0.481182629653714	1	FACETS	0.137	0.121	0.155	0.137	0.121	0.155	INDETERMINATE	1	TRUE	0	0.873328144738881	1		628	845	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003833-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	185	210	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.821	0.764	0.879	0.821	0.764	0.879	CLONAL	1	TRUE	1	0.871726340682134	2		210	517	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0003833-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	171	253	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	0.871726340682134	2		253	369	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978823	13978824	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003833-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	393	596	0	ENST00000405192.2:c.283_284insT	p.Pro95LeufsTer16	p.P95Lfs*16	ENST00000405192	NM_001163147.1	95	cca/cTca	6/12	1	2	FACETS	0.976	0.932	1	0.976	0.932	1	CLONAL	1	TRUE	1	0.871726340682134	2		596	924	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795826	42795827	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCA	novel	NA	P-0003833-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	361	700	0	ENST00000575354.2:c.2820_2823dup	p.Leu942AlafsTer210	p.L942Afs*210	ENST00000575354	NM_015125.3	939	ggc/gGCCAgc	11/20	0.871726340682134	1	FACETS	0.931	0.899	0.961	0.931	0.899	0.961	CLONAL	1	TRUE	0	0.871726340682134	1		700	502	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528791	157528791	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003833-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	119	532	0	ENST00000346085.5:c.6517del	p.Gln2173SerfsTer20	p.Q2173Sfs*20	ENST00000346085	NM_020732.3	2172	taC/ta	20/20	1	2	FACETS	0.396	0.357	0.436	0.396	0.357	0.436	SUBCLONAL	1	TRUE	1	0.871726340682134	2		532	690	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0004918-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	552	445	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.653699292602779	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.653699292602779	3		445	1120	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100304	8100304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004918-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	373	815	2	ENST00000346208.3:c.278C>T	p.Ser93Phe	p.S93F	ENST00000346208		93	tCc/tTc	3/6	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.653699292602779	2		817	1098	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17359566	17359566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004918-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	327	741	0	ENST00000375499.3:c.275C>T	p.Ser92Leu	p.S92L	ENST00000375499	NM_003000.2	92	tCa/tTa	3/8	1	2	FACETS	0.914	0.864	0.964	0.914	0.864	0.964	CLONAL	1	TRUE	1	0.653699292602779	2		741	1095	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117443	115117444	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	AGTTCATATAT	novel	NA	P-0004918-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	255	561	0	ENST00000257566.3:c.730_731insATATATGAACT	p.Ser244TyrfsTer3	p.S244Yfs*3	ENST00000257566	NM_016569.3	244	tcc/tATATATGAACTcc	4/8	1	2	FACETS	0.886	0.831	0.942	0.886	0.831	0.942	CLONAL	1	TRUE	1	0.653699292602779	2		561	881	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579348	7579350	+	missense_variant	Missense_Mutation	TNP	GAA	GAA	AGG	novel	NA	P-0004918-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	330	828	1	ENST00000269305.4:c.337_339delinsCCT	p.Phe113Pro	p.F113P	ENST00000269305	NM_001126112.2	113	TTC/CCT	4/11	0.653699292602779	1	FACETS	0.88	0.837	0.924	0.88	0.837	0.924	CLONAL	1	TRUE	0	0.653699292602779	1		829	772	SUCCESS
BLM	641	MSKCC	GRCh37	15	91308592	91308592	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004918-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	312	718	0	ENST00000355112.3:c.2141C>T	p.Ser714Phe	p.S714F	ENST00000355112	NM_000057.2	714	tCt/tTt	9/22	1	2	FACETS	0.883	0.833	0.934	0.883	0.833	0.934	CLONAL	1	TRUE	1	0.653699292602779	2		718	1081	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79952253	79952253	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004918-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	272	613	0	ENST00000265081.6:c.261G>C	p.Lys87Asn	p.K87N	ENST00000265081	NM_002439.4	87	aaG/aaC	2/24	1	2	FACETS	0.953	0.897	1	0.953	0.897	1	CLONAL	1	TRUE	1	0.653699292602779	2		613	873	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047674	180047674	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004918-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	408	787	0	ENST00000261937.6:c.2341G>A	p.Gly781Ser	p.G781S	ENST00000261937	NM_182925.4	781	Ggt/Agt	16/30	NA	2	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.653699292602779	2		787	1221	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0005063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	87	518	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.326425464871774	2	FACETS	0.802	0.713	0.897	0.401	0.356	0.449	CLONAL	1	TRUE	0	0.443614072489156	2		518	489	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0005063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	112	586	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.443614072489156	5	FACETS	0.738	0.662	0.819	0.246	0.22	0.273	SUBCLONAL	1	TRUE	2	0.443614072489156	5		586	1140	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0005063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	220	643	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	0.443614072489156	5	FACETS	0.926	0.863	0.991	0.617	0.575	0.661	CLONAL	2	TRUE	2	0.443614072489156	5		643	892	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574022	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	160	721	0	ENST00000269305.4:c.1005dup	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	335	-/T	10/11	0.31259531593997	1	FACETS	0.799	0.734	0.866	0.799	0.734	0.866	SUBCLONAL	1	TRUE	0	0.443614072489156	1		721	703	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776888	76776888	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	104	470	1	ENST00000373344.5:c.7064C>T	p.Ser2355Leu	p.S2355L	ENST00000373344	NM_000489.3	2355	tCa/tTa	33/35	0.379098677755061	1	FACETS	0.775	0.697	0.856	0.775	0.697	0.856	SUBCLONAL	1	TRUE	0	0.443614072489156	1		471	471	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349235	11349235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1019392987	NA	P-0005063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	26	118	0	ENST00000332029.2:c.101C>T	p.Ala34Val	p.A34V	ENST00000332029	NM_003745.1	34	gCg/gTg	2/2	0.324346178996688	2	FACETS	0.797	0.639	0.974	0.399	0.319	0.487	CLONAL	1	TRUE	0	0.443614072489156	2		118	147	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016048	31016048	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771925643	NA	P-0006682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	51	613	2	ENST00000375687.4:c.370G>A	p.Asp124Asn	p.D124N	ENST00000375687	NM_015338.5	124	Gat/Aat	5/13	0.34137129229067	3	FACETS	0.166	0.14	0.194	0.083	0.07	0.097	INDETERMINATE	1	TRUE	1	0.870023153163557	3		615	1016	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0006682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	243	529	1	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	0.441775564032037	4	FACETS	1	0.987	1	0.3	0.281	0.32	INDETERMINATE	1	TRUE	0	0.870023153163557	4		530	870	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0006682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	584	518	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.441775564032037	4	FACETS	0.888	0.861	0.915	0.666	0.646	0.687	INDETERMINATE	3	TRUE	0	0.870023153163557	4		518	942	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294284	11294284	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs757090752	NA	P-0006682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	307	627	0	ENST00000361445.4:c.2247C>G	p.Ile749Met	p.I749M	ENST00000361445	NM_004958.3	749	atC/atG	14/58	1	2	FACETS	0.965	0.916	1	0.965	0.916	1	CLONAL	1	TRUE	1	0.870023153163557	2		627	731	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506320	120506320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	270	512	1	ENST00000256646.2:c.1792G>A	p.Gly598Arg	p.G598R	ENST00000256646	NM_024408.3	598	Ggg/Agg	11/34	0.870023153163557	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.870023153163557	1		513	346	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746102	162746102	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs550210469	NA	P-0006682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	213	372	1	ENST00000367921.3:c.2225G>A	p.Arg742Gln	p.R742Q	ENST00000367921	NM_006182.2	742	cGg/cAg	16/18	0.769796250817638	3	FACETS	0.946	0.882	1	0.473	0.441	0.506	CLONAL	1	TRUE	1	0.870023153163557	3		373	743	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202152	67202152	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773369786	NA	P-0006682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	227	648	1	ENST00000312629.5:c.1255C>T	p.Arg419Trp	p.R419W	ENST00000312629	NM_003952.2	419	Cgg/Tgg	14/15	0.378682343400087	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.870023153163557	0		649	699	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748815	41748815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774958319	NA	P-0006682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	396	867	2	ENST00000301178.4:c.1340C>T	p.Ser447Leu	p.S447L	ENST00000301178	NM_021913.4	447	tCg/tTg	11/20	0.352800579684976	3	FACETS	1	0.989	1	0.566	0.539	0.594	INDETERMINATE	1	TRUE	1	0.870023153163557	3		869	1154	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855588	45855588	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	455	696	2	ENST00000391945.4:c.2069G>T	p.Arg690Leu	p.R690L	ENST00000391945	NM_000400.3	690	cGg/cTg	22/23	0.352800579684976	3	FACETS	1	0.995	1	0.675	0.646	0.704	INDETERMINATE	1	TRUE	1	0.870023153163557	3		698	1112	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40761077	40761077	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764512283	NA	P-0006682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	73	615	0	ENST00000392038.2:c.275C>T	p.Ser92Phe	p.S92F	ENST00000392038	NM_001626.4	92	tCt/tTt	4/14	0.352800579684976	3	FACETS	0.21	0.183	0.24	0.105	0.091	0.12	INDETERMINATE	1	TRUE	1	0.870023153163557	3		615	1145	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396541	30396541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746045993	NA	P-0006682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	411	570	0	ENST00000331968.5:c.178G>A	p.Glu60Lys	p.E60K	ENST00000331968	NM_002742.2	60	Gag/Aag	1/18	0.870023153163557	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.870023153163557	1		570	472	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105937	27105937	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	75	528	0	ENST00000324856.7:c.5548G>T	p.Asp1850Tyr	p.D1850Y	ENST00000324856	NM_006015.4	1850	Gac/Tac	20/20	1	2	FACETS	0.264	0.231	0.3	0.264	0.231	0.3	SUBCLONAL	1	TRUE	1	0.870023153163557	2		528	653	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465282	120465282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	23	424	0	ENST00000256646.2:c.4979C>T	p.Ser1660Leu	p.S1660L	ENST00000256646	NM_024408.3	1660	tCa/tTa	27/34	0.870023153163557	1	FACETS	0.082	0.063	0.104	0.082	0.063	0.104	SUBCLONAL	1	TRUE	0	0.870023153163557	1		424	364	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549260	21549260	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	56	817	0	ENST00000382592.4:c.3016G>A	p.Asp1006Asn	p.D1006N	ENST00000382592	NM_014572.2	1006	Gat/Aat	8/8	0.848446939601436	2	FACETS	0.179	0.152	0.207	0.089	0.076	0.104	SUBCLONAL	1	TRUE	0	0.870023153163557	2		817	721	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348771	11348771	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	122	488	0	ENST00000332029.2:c.565G>C	p.Glu189Gln	p.E189Q	ENST00000332029	NM_003745.1	189	Gag/Cag	2/2	1	2	FACETS	0.474	0.429	0.52	0.474	0.429	0.52	SUBCLONAL	1	TRUE	1	0.870023153163557	2		488	592	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038581	14038581	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	134	472	0	ENST00000311895.7:c.1906G>T	p.Glu636Ter	p.E636*	ENST00000311895	NM_005236.2	636	Gaa/Taa	10/11	1	2	FACETS	0.488	0.445	0.534	0.488	0.445	0.534	SUBCLONAL	1	TRUE	1	0.870023153163557	2		472	631	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41201157	41201157	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357055	NA	P-0006682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	194	825	0	ENST00000357654.3:c.5387C>T	p.Ser1796Leu	p.S1796L	ENST00000357654	NM_007294.3	1796	tCa/tTa	21/23	0.385023901299804	1	FACETS	0.34	0.315	0.365	0.34	0.315	0.365	INDETERMINATE	1	TRUE	0	0.870023153163557	1		825	742	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470018	25470018	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	32	472	0	ENST00000264709.3:c.1024G>C	p.Glu342Gln	p.E342Q	ENST00000264709	NM_175629.2	342	Gag/Cag	9/23	1	2	FACETS	0.118	0.095	0.144	0.118	0.095	0.144	SUBCLONAL	1	TRUE	1	0.870023153163557	2		472	623	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458223	12458223	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	45	521	2	ENST00000287820.6:c.840G>T	p.Met280Ile	p.M280I	ENST00000287820	NM_015869.4	280	atG/atT	6/7	0.438984343675534	1	FACETS	0.109	0.091	0.128	0.109	0.091	0.128	INDETERMINATE	1	TRUE	0	0.870023153163557	1		523	538	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190870	106190870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1357011805	NA	P-0006682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	38	455	0	ENST00000380013.4:c.4148G>A	p.Arg1383Lys	p.R1383K	ENST00000380013	NM_001127208.2	1383	aGa/aAa	9/11	0.492182300615811	1	FACETS	0.091	0.075	0.109	0.091	0.075	0.109	INDETERMINATE	1	TRUE	0	0.870023153163557	1		455	541	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674215	86674215	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	24	342	0	ENST00000274376.6:c.2347G>A	p.Glu783Lys	p.E783K	ENST00000274376	NM_002890.2	783	Gaa/Aaa	18/25	0.152770946572608	2	FACETS	0.125	0.097	0.157	0.062	0.048	0.079	INDETERMINATE	1	TRUE	0	0.870023153163557	2		342	442	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864854	117864854	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750846442	NA	P-0006682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	73	626	1	ENST00000297338.2:c.1255G>A	p.Glu419Lys	p.E419K	ENST00000297338	NM_006265.2	419	Gaa/Aaa	10/14	1	2	FACETS	0.228	0.199	0.259	0.228	0.199	0.259	SUBCLONAL	1	TRUE	1	0.870023153163557	2		627	737	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399817	139399817	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	257	840	0	ENST00000277541.6:c.4531T>A	p.Ser1511Thr	p.S1511T	ENST00000277541	NM_017617.3	1511	Tca/Aca	25/34	0.492182300615811	1	FACETS	0.338	0.317	0.36	0.338	0.317	0.36	INDETERMINATE	1	TRUE	0	0.870023153163557	1		840	987	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0006768-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	670	717	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.633339353071918	2	FACETS	0.97	0.943	0.998	0.97	0.943	0.998	CLONAL	2	TRUE	0	0.642803591418624	2		718	1074	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531749	46531749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006768-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	436	404	0	ENST00000262741.5:c.598G>A	p.Glu200Lys	p.E200K	ENST00000262741	NM_003629.3	200	Gaa/Aaa	5/10	0.574887913082929	4	FACETS	0.891	0.85	0.932	0.594	0.566	0.622	CLONAL	2	TRUE	1	0.642803591418624	4		404	1251	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420318	88420318	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006768-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	253	453	0	ENST00000360948.2:c.2368G>C	p.Glu790Gln	p.E790Q	ENST00000360948	NM_001012338.2	790	Gag/Cag	19/19	0.368875618194745	1	FACETS	0.812	0.765	0.86	0.812	0.765	0.86	INDETERMINATE	1	TRUE	0	0.642803591418624	1		453	658	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819237	3819237	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006768-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	311	580	0	ENST00000262367.5:c.2998G>A	p.Glu1000Lys	p.E1000K	ENST00000262367	NM_004380.2	1000	Gag/Aag	15/31	0.642803591418624	3	FACETS	0.99	0.932	1	0.495	0.466	0.524	CLONAL	1	TRUE	1	0.642803591418624	3		580	1292	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923647	72923647	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006768-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	230	568	0	ENST00000268489.5:c.3431G>T	p.Cys1144Phe	p.C1144F	ENST00000268489	NM_006885.3	1144	tGc/tTc	4/10	0.544699384010965	3	FACETS	0.876	0.816	0.937			1	CLONAL	1	TRUE	NA	0.642803591418624	3		568	1080	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853923	59853923	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006768-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	201	396	0	ENST00000259008.2:c.1936G>T	p.Val646Phe	p.V646F	ENST00000259008	NM_032043.2	646	Gtt/Ttt	14/20	0.607988662208114	3	FACETS	0.936	0.868	1	0.468	0.434	0.503	CLONAL	1	TRUE	1	0.642803591418624	3		396	883	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226627	1226627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781537	NA	P-0006768-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	190	363	0	ENST00000326873.7:c.1283C>T	p.Ser428Leu	p.S428L	ENST00000326873	NM_000455.4	428	tCg/tTg	9/10	0.642803591418624	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.642803591418624	1		363	387	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561234	9561234	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006768-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	203	453	0	ENST00000353224.5:c.548C>G	p.Ser183Cys	p.S183C	ENST00000353224	NM_177990.2	183	tCt/tGt	4/10	0.607988662208114	3	FACETS	0.897	0.833	0.965	0.449	0.416	0.483	CLONAL	1	TRUE	1	0.642803591418624	3		453	930	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37871576	37871576	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006768-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	355	614	1	ENST00000269571.5:c.1186C>A	p.Gln396Lys	p.Q396K	ENST00000269571		396	Cag/Aag	10/27	0.607988662208114	3	FACETS	0.989	0.935	1	0.494	0.467	0.522	CLONAL	1	TRUE	1	0.642803591418624	3		615	1476	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42861455	42861455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006768-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	269	545	0	ENST00000398585.3:c.415G>A	p.Ala139Thr	p.A139T	ENST00000398585	NM_001135099.1	139	Gct/Act	4/14	0.532874254889857	4	FACETS	1	0.944	1			1	CLONAL	1	TRUE	NA	0.642803591418624	4		545	1363	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143352394	143352394	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006768-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	272	505	0	ENST00000262992.4:c.19G>T	p.Gly7Trp	p.G7W	ENST00000262992	NM_001101669.1	7	Ggg/Tgg	2/24	1	2	FACETS	0.982	0.924	1	0.982	0.924	1	CLONAL	1	TRUE	1	0.642803591418624	2		505	862	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741429	145741429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006768-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1238	523	746	1	ENST00000428558.2:c.1074G>A	p.Met358Ile	p.M358I	ENST00000428558	NM_004260.3	358	atG/atA	5/22	0.304977534188635	5	FACETS	0.908	0.868	0.948	0.363	0.347	0.379	INDETERMINATE	2	TRUE	0	0.642803591418624	5		747	1761	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807959	3807959	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006768-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1191	149	508	0	ENST00000262367.5:c.3460G>A	p.Val1154Met	p.V1154M	ENST00000262367	NM_004380.2	1154	Gtg/Atg	18/31	0.642803591418624	3	FACETS	0.457	0.416	0.5	0.229	0.208	0.25	SUBCLONAL	1	TRUE	1	0.642803591418624	3		508	1340	SUCCESS
APC	324	MSKCC	GRCh37	5	112157650	112157650	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1060503333	NA	P-0007110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	334	525	0	ENST00000257430.4:c.1370C>A	p.Ser457Ter	p.S457*	ENST00000257430	NM_000038.5	457	tCa/tAa	11/16	0.432884148333862	2	FACETS	0.837	0.796	0.879	0.837	0.796	0.879	CLONAL	2	TRUE	0	0.504503249321341	2		525	791	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17380487	17380487	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	49	548	0	ENST00000375499.3:c.28A>T	p.Arg10Trp	p.R10W	ENST00000375499	NM_003000.2	10	Agg/Tgg	1/8	NA	2	FACETS	0.289	0.244	0.339			1	INDETERMINATE	1	TRUE	NA	0.504503249321341	2		548	671	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288549	15288549	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	10	42	0	ENST00000263388.2:c.4190G>A	p.Gly1397Glu	p.G1397E	ENST00000263388	NM_000435.2	1397	gGg/gAg	24/33	1	2	FACETS	0.924	0.628	1	0.924	0.628	1	CLONAL	1	TRUE	1	0.159200647148681	2		42	136	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430454	181430454	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	223	748	2	ENST00000325404.1:c.306G>A	p.Met102Ile	p.M102I	ENST00000325404	NM_003106.3	102	atG/atA	1/1	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.537627490020379	2		750	823	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864883	57864883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	197	713	0	ENST00000228682.2:c.2360C>T	p.Ser787Phe	p.S787F	ENST00000228682	NM_005269.2	787	tCt/tTt	12/12	1	2	FACETS	0.958	0.889	1	0.958	0.889	1	CLONAL	1	TRUE	1	0.537627490020379	2		713	765	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426645	47426645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	171	317	3	ENST00000377045.4:c.890G>A	p.Arg297Gln	p.R297Q	ENST00000377045	NM_001654.4	297	cGg/cAg	10/16	0.51029042654454	2	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.537627490020379	2		320	553	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248709	59248709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1363866933	NA	P-0008665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	280	771	1	ENST00000371222.2:c.34G>A	p.Asp12Asn	p.D12N	ENST00000371222	NM_002228.3	12	Gat/Aat	1/1	0.537627490020379	2	FACETS	1	0.982	1	0.554	0.521	0.588	CLONAL	1	TRUE	0	0.537627490020379	2		772	940	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390368	118390368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	111	705	2	ENST00000534358.1:c.11182G>A	p.Asp3728Asn	p.D3728N	ENST00000534358	NM_005933.3	3728	Gat/Aat	32/36	0.537627490020379	3	FACETS	0.519	0.466	0.576	0.26	0.233	0.288	SUBCLONAL	1	TRUE	1	0.537627490020379	3		707	1009	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233144	46233144	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs994352749	NA	P-0008665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	117	447	1	ENST00000334344.6:c.1363C>T	p.Gln455Ter	p.Q455*	ENST00000334344	NM_152641.2	455	Cag/Tag	11/21	1	2	FACETS	0.869	0.787	0.954	0.869	0.787	0.954	CLONAL	1	TRUE	1	0.537627490020379	2		448	501	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885224	111885224	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	53	688	1	ENST00000341259.2:c.1112G>A	p.Arg371Lys	p.R371K	ENST00000341259	NM_005475.2	371	aGa/aAa	6/8	1	2	FACETS	0.252	0.214	0.294	0.252	0.214	0.294	SUBCLONAL	1	TRUE	1	0.537627490020379	2		689	783	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677989	58677989	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	94	344	0	ENST00000305921.3:c.214G>T	p.Ala72Ser	p.A72S	ENST00000305921	NM_003620.3	72	Gcc/Tcc	1/6	0.537627490020379	3	FACETS	1	0.952	1	0.555	0.497	0.615	CLONAL	1	TRUE	1	0.537627490020379	3		344	400	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885931	59885931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	196	701	0	ENST00000259008.2:c.815C>T	p.Pro272Leu	p.P272L	ENST00000259008	NM_032043.2	272	cCa/cTa	7/20	0.537627490020379	3	FACETS	0.964	0.892	1	0.482	0.446	0.519	CLONAL	1	TRUE	1	0.537627490020379	3		701	960	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554240	63554240	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	219	803	0	ENST00000307078.5:c.499G>C	p.Asp167His	p.D167H	ENST00000307078	NM_004655.3	167	Gat/Cat	2/11	0.537627490020379	3	FACETS	1	0.965	1	0.528	0.492	0.567	CLONAL	1	TRUE	1	0.537627490020379	3		803	978	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743012	743012	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4426	8981	691	9	ENST00000314574.4:c.966G>T	p.Gln322His	p.Q322H	ENST00000314574	NM_005433.3	322	caG/caT	8/12	0.537627490020379	38	FACETS	0.985	0.978	0.993			1	CLONAL	27	TRUE	NA	0.537627490020379	38		700	13407	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604655	48604655	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	128	364	1	ENST00000342988.3:c.1477G>T	p.Asp493Tyr	p.D493Y	ENST00000342988	NM_005359.5	493	Gat/Tat	12/12	0.537627490020379	1	FACETS	0.946	0.867	1	0.946	0.867	1	CLONAL	1	TRUE	0	0.537627490020379	1		365	368	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47735850	47735850	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs982515440	NA	P-0008665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	76	707	1	ENST00000449228.1:c.10G>T	p.Gly4Cys	p.G4C	ENST00000449228	NM_001127240.2	4	Ggc/Tgc	1/4	0.537627490020379	1	FACETS	0.313	0.274	0.355	0.313	0.274	0.355	SUBCLONAL	1	TRUE	0	0.537627490020379	1		708	660	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032759	48032759	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs1553332616	NA	P-0008665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	85	299	0	ENST00000234420.5:c.3559G>C	p.Glu1187Gln	p.E1187Q	ENST00000234420	NM_000179.2	1187	Gaa/Caa	7/10	0.537627490020379	2	FACETS	0.839	0.747	0.936	0.419	0.373	0.468	CLONAL	1	TRUE	0	0.537627490020379	2		299	377	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478613	57478613	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	187	569	0	ENST00000371085.3:c.285C>G	p.Ile95Met	p.I95M	ENST00000371085	NM_000516.4	95	atC/atG	4/13	0.513841920723129	3	FACETS	0.905	0.836	0.977			1	CLONAL	1	TRUE	NA	0.537627490020379	3		569	975	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613112	52613113	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0008665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	65	557	0	ENST00000394830.3:c.3415_3416del	p.Val1139LeufsTer16	p.V1139Lfs*16	ENST00000394830	NM_018313.4	1139	GTc/c	22/30	1	2	FACETS	0.322	0.278	0.369	0.322	0.278	0.369	SUBCLONAL	1	TRUE	1	0.537627490020379	2		557	752	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467383	66467383	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	68	251	0	ENST00000273854.3:c.886G>A	p.Glu296Lys	p.E296K	ENST00000273854	NM_004439.5	296	Gaa/Aaa	3/18	0.537627490020379	3	FACETS	0.8	0.699	0.909	0.4	0.349	0.455	CLONAL	1	TRUE	1	0.537627490020379	3		251	401	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158713	26158713	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	81	266	0	ENST00000289316.2:c.316G>T	p.Glu106Ter	p.E106*	ENST00000289316	NM_138720.2	106	Gag/Tag	1/2	1	2	FACETS	0.897	0.797	1	0.897	0.797	1	CLONAL	1	TRUE	1	0.537627490020379	2		266	336	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242483	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACA	AATTAAGAGAAGCAACA	TTGCT	novel	NA	P-0008665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	446	704	6	ENST00000275493.2:c.2237_2253delinsTTGCT	p.Glu746_Thr751delinsValAla	p.E746_T751delinsVA	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACA/gTTGCT	19/28	0.533369085555539	4	FACETS	1	0.994	1	0.809	0.775	0.844	CLONAL	2	TRUE	1	0.537627490020379	4		710	1051	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853017	151853017	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	134	445	0	ENST00000262189.6:c.11938C>G	p.His3980Asp	p.H3980D	ENST00000262189	NM_170606.2	3980	Cat/Gat	46/59	0.533369085555539	4	FACETS	0.833	0.756	0.914	0.278	0.252	0.305	CLONAL	1	TRUE	1	0.537627490020379	4		445	920	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873941	151873941	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	68	639	2	ENST00000262189.6:c.8597A>G	p.Glu2866Gly	p.E2866G	ENST00000262189	NM_170606.2	2866	gAa/gGa	38/59	0.533369085555539	4	FACETS	0.358	0.31	0.41	0.119	0.103	0.137	SUBCLONAL	1	TRUE	1	0.537627490020379	4		641	1087	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5534882	5534882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	234	649	1	ENST00000397747.3:c.193G>A	p.Asp65Asn	p.D65N	ENST00000397747	NM_025239.3	65	Gat/Aat	3/7	0.47675357048467	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.537627490020379	1		650	599	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27190569	27190569	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	276	773	0	ENST00000380036.4:c.1370G>C	p.Gly457Ala	p.G457A	ENST00000380036	NM_000459.3	457	gGa/gCa	10/23	0.537627490020379	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.537627490020379	1		773	707	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636686	2636694	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCTGAGC	CTCCTGAGC	G	novel	NA	P-0008665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	34	517	0	ENST00000342085.4:c.1135_1143delinsG	p.Leu379AlafsTer44	p.L379Afs*44	ENST00000342085	NM_002613.4	379	CTCCTGAGC/G	11/14	0.537627490020379	2	FACETS	0.2	0.163	0.243	0.1	0.081	0.122	SUBCLONAL	1	TRUE	0	0.537627490020379	2		517	631	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0008885-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	402	630	2	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.609931224620781	2	FACETS	0.971	0.934	1	0.971	0.934	1	CLONAL	2	TRUE	0	0.609931224620781	2		632	679	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775907	9775907	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008885-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	305	897	3	ENST00000377346.4:c.371G>A	p.Gly124Asp	p.G124D	ENST00000377346	NM_005026.3	124	gGc/gAc	5/24	0.555711049027257	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	2	0.609931224620781	4		900	797	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133748326	133748326	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs753103329	NA	P-0008885-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	482	563	1	ENST00000318560.5:c.987G>T	p.Glu329Asp	p.E329D	ENST00000318560	NM_005157.4	329	gaG/gaT	6/11	0.609931224620781	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	0	0.609931224620781	3		564	679	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133208900	133208900	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0008885-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	243	422	0	ENST00000320574.5:c.6330+1G>T		p.X2110_splice	ENST00000320574	NM_006231.2	2110			0.609931224620781	4	FACETS	0.953	0.896	1	0.953	0.896	1	CLONAL	2	TRUE	2	0.609931224620781	4		422	673	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104377049	104377049	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008996-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	59	303	0	ENST00000369902.3:c.1160G>C	p.Gly387Ala	p.G387A	ENST00000369902	NM_016169.3	387	gGc/gCc	10/12	0.429661622045123	4	FACETS	0.928	0.801	1	0.464	0.4	0.533	CLONAL	1	TRUE	2	0.432954436417488	4		303	421	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443613	29443613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519783	NA	P-0009301-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	174	748	0	ENST00000389048.3:c.3604G>A	p.Gly1202Arg	p.G1202R	ENST00000389048	NM_004304.4	1202	Gga/Aga	23/29	0.392636956083012	3	FACETS	0.957	0.88	1			1	CLONAL	1	TRUE	NA	0.392636956083012	3		748	1108	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445273	29445273	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs113994091	NA	P-0009301-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	133	616	1	ENST00000389048.3:c.3452C>T	p.Thr1151Met	p.T1151M	ENST00000389048	NM_004304.4	1151	aCg/aTg	22/29	0.392636956083012	3	FACETS	0.932	0.846	1			1	CLONAL	1	TRUE	NA	0.392636956083012	3		617	870	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902729	50902729	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766784938	NA	P-0009301-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	174	907	0	ENST00000440232.2:c.304G>A	p.Asp102Asn	p.D102N	ENST00000440232	NM_002691.3	102	Gac/Aac	3/27	1	2	FACETS	0.768	0.706	0.833	0.768	0.706	0.833	SUBCLONAL	1	TRUE	1	0.392636956083012	2		907	1154	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112764487	112764487	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009301-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	129	526	1	ENST00000369452.4:c.1096C>T	p.Arg366Ter	p.R366*	ENST00000369452	NM_007373.3	366	Cga/Tga	5/9	0.388754913745638	3	FACETS	0.836	0.757	0.919	0.418	0.378	0.46	CLONAL	1	TRUE	1	0.392636956083012	3		527	940	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562861	95562862	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0009301-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	76	333	0	ENST00000393063.1:c.4395_4396del	p.Lys1466AsnfsTer10	p.K1466Nfs*10	ENST00000393063	NM_030621.3	1465	aaGAaa/aaaa	24/28	0.388754913745638	3	FACETS	0.834	0.733	0.943	0.417	0.366	0.472	CLONAL	1	TRUE	1	0.392636956083012	3		333	555	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0009346-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2123	353	586	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.758810657257558	5	FACETS	0.803	0.757	0.851	0.268	0.252	0.284	CLONAL	1	TRUE	2	0.758810657257558	5		586	2476	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937070	48937093	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GAACATGAATGTAATATAGATGAG	GAACATGAATGTAATATAGATGAG	-	novel	NA	P-0009346-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	221	367	0	ENST00000267163.4:c.839_861+1del		p.EHECNIDEdel	ENST00000267163	NM_000321.2	280	GAACATGAATGTAATATAGATGAG/-	8/27	0.758810657257558	1	FACETS	0.934	0.885	0.983	0.934	0.885	0.983	CLONAL	1	TRUE	0	0.758810657257558	1		367	387	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073546	8073547	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0009346-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	231	346	0	ENST00000377482.5:c.1112dup	p.Ser372IlefsTer4	p.S372Ifs*4	ENST00000377482	NM_018948.3	371	gga/ggGa	4/4	0.738488390660107	1	FACETS	0.969	0.92	1	0.969	0.92	1	CLONAL	1	TRUE	0	0.758810657257558	1		346	390	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249092	55249092	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009346-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2155	336	724	0	ENST00000275493.2:c.2390G>C	p.Cys797Ser	p.C797S	ENST00000275493	NM_005228.3	797	tGc/tCc	20/28	0.758810657257558	5	FACETS	0.76	0.715	0.807	0.253	0.238	0.269	SUBCLONAL	1	TRUE	2	0.758810657257558	5		724	2491	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211810	36211810	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009346-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	543	826	0	ENST00000222270.7:c.1561C>G	p.Leu521Val	p.L521V	ENST00000222270	NM_014727.1	521	Ctg/Gtg	3/37	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.758810657257558	2		826	1325	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242481	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAA	AATTAAGAGAAGCAA	TCC	novel	NA	P-0009346-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	755	615	2	ENST00000275493.2:c.2237_2251delinsTCC	p.Glu746_Thr751delinsValPro	p.E746_T751delinsVP	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAAca/gTCCca	19/28	0.758810657257558	5	FACETS	1	0.996	1	0.802	0.776	0.829	CLONAL	2	TRUE	2	0.758810657257558	5		617	1768	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242481	+	inframe_deletion	In_Frame_Del	DEL	AATTAAGAGAAGCAA	AATTAAGAGAAGCAA	-	rs121913425	NA	P-0009535-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	166	580	0	ENST00000275493.2:c.2237_2251del	p.Glu746_Thr751delinsAla	p.E746_T751delinsA	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAAca/gca	19/28	0.285693903503542	3	FACETS	0.798	0.734	0.865	0.798	0.734	0.865	SUBCLONAL	2	TRUE	1	0.285693903503542	3		580	832	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313315	65313315	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	62	425	0	ENST00000342505.4:c.1799G>A	p.Gly600Glu	p.G600E	ENST00000342505	NM_002227.2	600	gGg/gAg	13/25	0.23302782179709	4	FACETS	0.522	0.45	0.601	0.261	0.225	0.301	INDETERMINATE	1	TRUE	2	0.4023676705394	4		425	828	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6038877	6038877	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	69	385	0	ENST00000265849.7:c.567T>A	p.His189Gln	p.H189Q	ENST00000265849	NM_000535.5	189	caT/caA	6/15	NA	2	FACETS	0.542	0.472	0.618			1	INDETERMINATE	1	TRUE	NA	0.4023676705394	2		385	633	SUCCESS
CBL	867	MSKCC	GRCh37	11	119167737	119167737	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	32	235	0	ENST00000264033.4:c.2146A>G	p.Ser716Gly	p.S716G	ENST00000264033	NM_005188.3	716	Agt/Ggt	13/16	0.322926826590167	2	FACETS	0.426	0.346	0.517	0.213	0.173	0.259	SUBCLONAL	1	TRUE	0	0.4023676705394	2		235	373	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	33	273	0	ENST00000349310.3:c.49G>T	p.Glu17Ter	p.E17*	ENST00000349310	NM_001014432.1	17	Gag/Tag	4/15	0.353647030392423	3	FACETS	0.301	0.244	0.365	0.15	0.122	0.183	SUBCLONAL	1	TRUE	1	0.4023676705394	3		273	655	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973512	15973520	+	inframe_deletion	In_Frame_Del	DEL	TGGACATGG	TGGACATGG	-	novel	NA	P-0010455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	31	234	0	ENST00000268712.3:c.4472_4480del	p.Thr1491_Ser1493del	p.T1491_S1493del	ENST00000268712	NM_006311.3	1491	aCCATGTCCAga/aga	31/46	0.23302782179709	4	FACETS	0.539	0.436	0.656	0.269	0.218	0.328	INDETERMINATE	1	TRUE	2	0.4023676705394	4		234	401	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161293408	161293408	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs774768866	NA	P-0010646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	178	530	2	ENST00000367975.2:c.25G>T	p.Val9Phe	p.V9F	ENST00000367975	NM_003001.3	9	Gtt/Ttt	2/6	0.374563217084252	3	FACETS	0.863	0.793	0.936	0.431	0.396	0.468	CLONAL	1	TRUE	1	0.374563217084252	3		532	1308	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473653	67473653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223737	NA	P-0010955-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	120	531	2	ENST00000327367.4:c.733G>A	p.Gly245Arg	p.G245R	ENST00000327367	NM_005902.3	245	Ggg/Agg	6/9	0.153833271527855	2	FACETS	0.701	0.634	0.772	0.351	0.317	0.386	INDETERMINATE	1	TRUE	0	0.510094577057935	2		533	671	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18747438	18747438	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010955-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	69	250	0	ENST00000266497.5:c.3899T>A	p.Val1300Glu	p.V1300E	ENST00000266497		1300	gTa/gAa	28/31	0.510094577057935	5	FACETS	1	0.966	1	0.263	0.23	0.298	CLONAL	1	TRUE	0	0.510094577057935	5		250	363	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844713	156844713	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	110	769	0	ENST00000524377.1:c.1267G>T	p.Gly423Cys	p.G423C	ENST00000524377	NM_002529.3	423	Ggc/Tgc	11/17	0.22299396069023	3	FACETS	1	0.981	1	0.713	0.641	0.79	CLONAL	1	TRUE	1	0.22299396069023	3		769	769	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195965	102195966	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTCAATATACACAG	novel	NA	P-0010965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	21	333	0	ENST00000263464.3:c.730_731insTATACACAGTTCAA	p.Arg244IlefsTer12	p.R244Ifs*12	ENST00000263464	NM_001165.4	242	act/acTTCAATATACACAGt	2/9	0.154296899124789	2	FACETS	0.523	0.402	0.664	0.262	0.201	0.332	SUBCLONAL	1	TRUE	0	0.22299396069023	2		333	360	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942725	48942726	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0010965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	93	339	0	ENST00000267163.4:c.1117_1118del	p.Thr373SerfsTer3	p.T373Sfs*3	ENST00000267163	NM_000321.2	371	cCA/c	11/27	0.207766188351139	2	FACETS	0.913	0.815	1	0.913	0.815	1	CLONAL	2	TRUE	0	0.22299396069023	2		339	457	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335926	73335926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	95	392	0	ENST00000377767.4:c.2369T>C	p.Leu790Pro	p.L790P	ENST00000377767	NM_014953.3	790	cTt/cCt	18/21	0.207766188351139	2	FACETS	0.92	0.823	1	0.92	0.823	1	CLONAL	2	TRUE	0	0.22299396069023	2		392	463	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0010965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	66	594	2	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.22299396069023	2		596	579	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995341	15995341	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	30	370	0	ENST00000268712.3:c.2852del	p.Gly951GlufsTer4	p.G951Efs*4	ENST00000268712	NM_006311.3	951	gGa/ga	22/46	1	2	FACETS	0.674	0.543	0.823	0.674	0.543	0.823	SUBCLONAL	1	TRUE	1	0.22299396069023	2		370	399	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395613	45395613	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0010965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	46	399	0	ENST00000262160.6:c.520+1G>T		p.X174_splice	ENST00000262160	NM_005901.5	174			1	2	FACETS	0.975	0.823	1	0.975	0.823	1	CLONAL	1	TRUE	1	0.22299396069023	2		399	423	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944537	40944538	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0010965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	271	463	1	ENST00000373198.4:c.1964_1965delinsAA	p.Ala655Glu	p.A655E	ENST00000373198	NM_133170.3	655	gCC/gAA	12/32	0.22299396069023	4	FACETS	1	0.97	1	1	0.993	1	CLONAL	4	TRUE	1	0.22299396069023	4		464	713	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521616	89521616	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	26	381	0	ENST00000336596.2:c.2693C>A	p.Pro898Gln	p.P898Q	ENST00000336596	NM_005233.5	898	cCa/cAa	16/17	1	2	FACETS	0.641	0.507	0.793	0.641	0.507	0.793	SUBCLONAL	1	TRUE	1	0.22299396069023	2		381	364	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178202	142178202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	26	274	0	ENST00000350721.4:c.7216C>T	p.Leu2406Phe	p.L2406F	ENST00000350721	NM_001184.3	2406	Ctt/Ttt	43/47	0.22299396069023	3	FACETS	0.734	0.582	0.909	0.367	0.291	0.455	CLONAL	1	TRUE	1	0.22299396069023	3		274	353	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778240	27778240	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	51	459	0	ENST00000369163.2:c.389G>T	p.Arg130Leu	p.R130L	ENST00000369163	NM_003536.2	130	cGt/cTt	1/1	1	2	FACETS	0.963	0.819	1	0.963	0.819	1	CLONAL	1	TRUE	1	0.22299396069023	2		459	475	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289543	33289543	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	62	668	0	ENST00000374542.5:c.160G>T	p.Gly54Cys	p.G54C	ENST00000374542	NM_001141970.1	54	Ggc/Tgc	2/8	1	2	FACETS	0.804	0.693	0.924	0.804	0.693	0.924	CLONAL	1	TRUE	1	0.22299396069023	2		668	692	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662585	117662585	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	49	422	2	ENST00000368508.3:c.4880G>A	p.Gly1627Asp	p.G1627D	ENST00000368508	NM_002944.2	1627	gGt/gAt	29/43	NA	2	FACETS	1	0.897	1			1	INDETERMINATE	1	TRUE	NA	0.22299396069023	2		424	409	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55260529	55260529	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	49	511	0	ENST00000275493.2:c.2696G>A	p.Ser899Asn	p.S899N	ENST00000275493	NM_005228.3	899	aGc/aAc	22/28	0.22299396069023	3	FACETS	0.782	0.661	0.914	0.391	0.33	0.457	CLONAL	1	TRUE	1	0.22299396069023	3		511	625	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852282	128852282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1425442829	NA	P-0010965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	43	571	0	ENST00000249373.3:c.2354C>T	p.Ser785Leu	p.S785L	ENST00000249373	NM_005631.4	785	tCg/tTg	12/12	1	2	FACETS	0.759	0.635	0.897	0.759	0.635	0.897	SUBCLONAL	1	TRUE	1	0.22299396069023	2		571	508	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0011137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	942	297	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.762010511087911	5	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	2	0.762010511087911	5		297	1694	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0011137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	171	242	0	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	0.703604608363267	3	FACETS	1	0.97	1	0.546	0.505	0.588	CLONAL	1	TRUE	1	0.762010511087911	3		242	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578191	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs530941076	NA	P-0011137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	521	477	0	ENST00000269305.4:c.658T>A	p.Tyr220Asn	p.Y220N	ENST00000269305	NM_001126112.2	220	Tat/Aat	6/11	0.703604608363267	3	FACETS	0.805	0.774	0.836	0.805	0.774	0.836	CLONAL	2	TRUE	1	0.762010511087911	3		477	1173	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	426	534	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.627236656155412	2	FACETS	0.927	0.894	0.96	0.927	0.894	0.96	CLONAL	2	TRUE	0	0.662892813753836	2		534	693	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412950	49412950	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	489	769	0	ENST00000418115.1:c.73T>G	p.Phe25Val	p.F25V	ENST00000418115	NM_001664.2	25	Ttc/Gtc	2/5	0.327916137750801	3	FACETS	0.789	0.756	0.822	0.789	0.756	0.822	INDETERMINATE	2	TRUE	1	0.662892813753836	3		769	1245	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611809	1611809	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779908158	NA	P-0012206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1192	197	691	2	ENST00000344749.5:c.1853G>A	p.Arg618Gln	p.R618Q	ENST00000344749	NM_001136139.2	618	cGa/cAa	19/19	0.530016243460929	3	FACETS	0.57	0.526	0.615	0.285	0.263	0.308	SUBCLONAL	1	TRUE	1	0.662892813753836	3		693	1389	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212023	5212023	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	297	583	0	ENST00000357368.4:c.5008C>G	p.Gln1670Glu	p.Q1670E	ENST00000357368	NM_002850.3	1670	Cag/Gag	32/38	0.530016243460929	3	FACETS	1	0.989	1	0.591	0.557	0.626	CLONAL	1	TRUE	1	0.662892813753836	3		583	1009	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44515577	44515577	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	271	625	0	ENST00000291552.4:c.319G>C	p.Asp107His	p.D107H	ENST00000291552	NM_006758.2	107	Gac/Cac	5/8	0.662892813753836	3	FACETS	0.823	0.771	0.877	0.411	0.385	0.439	CLONAL	1	TRUE	1	0.662892813753836	3		625	1323	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650400	48650400	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	256	779	0	ENST00000376670.3:c.370C>A	p.Leu124Met	p.L124M	ENST00000376670	NM_002049.3	124	Ctg/Atg	3/6	1	2	FACETS	0.767	0.718	0.817	0.767	0.718	0.817	SUBCLONAL	1	TRUE	1	0.662892813753836	2		779	1007	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494608	2494608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	63	675	0	ENST00000355716.4:c.748G>A	p.Gly250Ser	p.G250S	ENST00000355716	NM_003820.2	250	Ggt/Agt	8/8	1	2	FACETS	0.239	0.206	0.275	0.239	0.206	0.275	SUBCLONAL	1	TRUE	1	0.662892813753836	2		675	795	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263339	115263339	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0012206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	195	664	0	ENST00000438362.2:c.2012-1G>T		p.X671_splice	ENST00000438362	NM_001242891.1	671			1	2	FACETS	0.835	0.775	0.896	0.835	0.775	0.896	CLONAL	1	TRUE	1	0.662892813753836	2		664	705	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92247396	92247396	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	109	237	0	ENST00000265734.4:c.824A>G	p.Asp275Gly	p.D275G	ENST00000265734	NM_001259.6	275	gAc/gGc	7/8	0.530016243460929	3	FACETS	1	0.962	1	0.56	0.507	0.615	CLONAL	1	TRUE	1	0.662892813753836	3		237	391	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836278	151836278	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	435	561	0	ENST00000262189.6:c.14527C>A	p.Pro4843Thr	p.P4843T	ENST00000262189	NM_170606.2	4843	Ccc/Acc	57/59	0.530016243460929	3	FACETS	0.869	0.832	0.907	0.869	0.832	0.907	CLONAL	2	TRUE	1	0.662892813753836	3		561	1005	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224411	53224411	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0012206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	115	587	0	ENST00000375401.3:c.3300+2T>C		p.X1100_splice	ENST00000375401	NM_004187.3	1100			1	2	FACETS	0.401	0.36	0.443	0.401	0.36	0.443	SUBCLONAL	1	TRUE	1	0.662892813753836	2		587	866	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012689-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	137	210	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.949	0.87	1			1	INDETERMINATE	1	TRUE	NA	0.664071353383895	2		210	435	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711973	89711975	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	rs1064793244	NA	P-0012689-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	229	352	0	ENST00000371953.3:c.595_597del	p.Met199del	p.M199del	ENST00000371953	NM_000314.4	197	aaGATg/aag	6/9	0.664071353383895	1	FACETS	0.958	0.903	1	0.958	0.903	1	CLONAL	1	TRUE	0	0.664071353383895	1		352	481	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061532	38061532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781269308	NA	P-0012689-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	131	268	0	ENST00000250448.2:c.457G>A	p.Ala153Thr	p.A153T	ENST00000250448	NM_004496.3	153	Gcg/Acg	2/2	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.664071353383895	2		268	360	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196093	138196093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1405321250	NA	P-0012689-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	182	303	0	ENST00000237289.4:c.407G>A	p.Arg136His	p.R136H	ENST00000237289	NM_001270507.1	136	cGc/cAc	3/9	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.664071353383895	2		303	519	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012893-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	823	497	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.578702022492112	9	FACETS	0.979	0.952	1	0.839	0.816	0.862	CLONAL	6	TRUE	2	0.578702022492112	9		497	1465	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913514	NA	P-0013114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	251	553	0	ENST00000288135.5:c.2466T>G	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaG	17/21	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.905389467725584	2		553	511	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913517	NA	P-0013114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	218	486	0	ENST00000288135.5:c.1676T>A	p.Val559Asp	p.V559D	ENST00000288135	NM_000222.2	559	gTt/gAt	11/21	1	2	FACETS	0.91	0.855	0.967	0.91	0.855	0.967	CLONAL	1	TRUE	1	0.905389467725584	2		486	529	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870896	12870896	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	317	290	0	ENST00000228872.4:c.124del	p.Thr42ProfsTer29	p.T42Pfs*29	ENST00000228872	NM_004064.3	41	ttA/tt	1/3	0.905389467725584	2	FACETS	0.973	0.949	0.994	0.973	0.949	0.994	CLONAL	2	TRUE	0	0.905389467725584	2		290	360	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913514	NA	P-0013114-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	258	553	0	ENST00000288135.5:c.2466T>G	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaG	17/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.809965445180475	2		553	620	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913517	NA	P-0013114-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	280	486	0	ENST00000288135.5:c.1676T>A	p.Val559Asp	p.V559D	ENST00000288135	NM_000222.2	559	gTt/gAt	11/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.809965445180475	2		486	688	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870896	12870896	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013114-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	338	290	0	ENST00000228872.4:c.124del	p.Thr42ProfsTer29	p.T42Pfs*29	ENST00000228872	NM_004064.3	41	ttA/tt	1/3	0.809965445180475	2	FACETS	0.931	0.901	0.961	0.931	0.901	0.961	CLONAL	2	TRUE	0	0.809965445180475	2		290	448	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096156	178096156	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013841-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	277	620	0	ENST00000397062.3:c.1175G>T	p.Gly392Val	p.G392V	ENST00000397062	NM_006164.4	392	gGt/gTt	5/5	1	2	FACETS	0.949	0.898	1	0.949	0.898	1	CLONAL	1	TRUE	1	0.872299749659617	2		620	669	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971093	21971093	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013841-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	181	321	0	ENST00000304494.5:c.265G>C	p.Gly89Arg	p.G89R	ENST00000304494	NM_000077.4	89	Ggc/Cgc	2/3	1	2	FACETS	0.995	0.93	1	0.995	0.93	1	CLONAL	1	TRUE	1	0.872299749659617	2		321	417	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038524	47038524	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556777452	NA	P-0013841-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	402	405	0	ENST00000377604.3:c.686G>A	p.Arg229His	p.R229H	ENST00000377604	NM_001204468.1	229	cGc/cAc	8/24	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.872299749659617	1		405	443	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	236	497	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.240337424726079	1	FACETS	0.6	0.565	0.636	0.6	0.565	0.636	INDETERMINATE	1	TRUE	0	0.816353816085159	1		497	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555525857	NA	P-0014154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	489	795	1	ENST00000269305.4:c.596G>A	p.Gly199Glu	p.G199E	ENST00000269305	NM_001126112.2	199	gGa/gAa	6/11	0.527508237875712	1	FACETS	0.87	0.84	0.9	0.87	0.84	0.9	CLONAL	1	TRUE	0	0.816353816085159	1		796	815	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9779982	9779982	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587777390	NA	P-0014154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	388	743	0	ENST00000377346.4:c.1246T>C	p.Cys416Arg	p.C416R	ENST00000377346	NM_005026.3	416	Tgc/Cgc	10/24	0.787990102198064	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.816353816085159	1		743	547	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514662	44514662	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	619	600	0	ENST00000291552.4:c.494G>A	p.Arg165Gln	p.R165Q	ENST00000291552	NM_006758.2	165	cGa/cAa	7/8	0.744363380138582	3	FACETS	0.927	0.896	0.957	0.927	0.896	0.957	CLONAL	2	TRUE	1	0.816353816085159	3		600	1152	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594261	55594261	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	180	468	0	ENST00000288135.5:c.1964A>C	p.Asn655Thr	p.N655T	ENST00000288135	NM_000222.2	655	aAt/aCt	13/21	NA	2	FACETS	0.821	0.763	0.881			1	INDETERMINATE	1	TRUE	NA	0.816353816085159	2		468	537	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265064	10265064	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	130	573	0	ENST00000340748.4:c.1876C>T	p.Gln626Ter	p.Q626*	ENST00000340748		626	Cag/Tag	21/40	0.23688244918654	3	FACETS	1	0.946	1	0.533	0.482	0.587	CLONAL	1	TRUE	1	0.23688244918654	3		573	1152	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272308	38272308	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs869320694	NA	P-0014433-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	330	659	0	ENST00000425967.3:c.2059A>G	p.Lys687Glu	p.K687E	ENST00000425967	NM_001174067.1	687	Aag/Gag	15/19	0.958763442576527	1	FACETS	0.985	0.963	1	0.985	0.963	1	CLONAL	1	TRUE	0	0.958763442576527	1		659	364	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543174	65543196	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	GCTGGCCTGCCCCGAGTGGCTTA	GCTGGCCTGCCCCGAGTGGCTTA	-	novel	NA	P-0014433-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	128	268	0	ENST00000358664.4:c.481_*20del		p.*161*	ENST00000358664	NM_002382.4	161		5/5	0.951974757330162	1	FACETS	0.993	0.959	1	0.993	0.959	1	CLONAL	1	TRUE	0	0.958763442576527	1		268	140	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147578	47147578	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014433-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	209	429	0	ENST00000409792.3:c.4748T>C	p.Val1583Ala	p.V1583A	ENST00000409792	NM_014159.6	1583	gTa/gCa	6/21	0.951974757330162	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.958763442576527	1		429	219	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814930	139814930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371121908	NA	P-0014689-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	26	640	0	ENST00000247668.2:c.923G>A	p.Arg308Gln	p.R308Q	ENST00000247668	NM_021138.3	308	cGg/cAg	8/11	0.469060117275543	5	FACETS	0.591	0.468	0.73	0.118	0.093	0.146	SUBCLONAL	1	TRUE	0	0.484045008300011	5		640	314	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	60	210	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.830690809819364	2		210	129	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934874	NA	P-0014791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	663	799	0	ENST00000269305.4:c.451C>G	p.Pro151Ala	p.P151A	ENST00000269305	NM_001126112.2	151	Ccc/Gcc	5/11	0.754269276335088	4	FACETS	0.91	0.883	0.936	0.91	0.883	0.936	CLONAL	3	TRUE	1	0.830690809819364	4		799	1071	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0014791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	623	661	3	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.830690809819364	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.830690809819364	2		664	734	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93627350	93627350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756047567	NA	P-0014791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	90	615	0	ENST00000375746.1:c.817C>T	p.Arg273Cys	p.R273C	ENST00000375746	NM_001174167.1	273	Cgt/Tgt	6/14	1	2	FACETS	0.32	0.284	0.359	0.32	0.284	0.359	SUBCLONAL	1	TRUE	1	0.830690809819364	2		615	677	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941488	71941488	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	144	762	0	ENST00000298229.2:c.1173G>C	p.Lys391Asn	p.K391N	ENST00000298229	NM_001567.3	391	aaG/aaC	10/28	0.828185325651468	1	FACETS	0.494	0.455	0.534	0.494	0.455	0.534	SUBCLONAL	1	TRUE	0	0.830690809819364	1		762	410	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100043	157100043	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1455234951	NA	P-0014947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	11	93	0	ENST00000346085.5:c.980G>C	p.Gly327Ala	p.G327A	ENST00000346085	NM_020732.3	327	gGa/gCa	1/20	0.893507973817881	3	FACETS	0.184	0.127	0.255			1	SUBCLONAL	1	TRUE	NA	0.94475275946205	3		93	186	SUCCESS
APC	324	MSKCC	GRCh37	5	112178331	112178331	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	141	554	0	ENST00000257430.4:c.7040G>A	p.Arg2347Lys	p.R2347K	ENST00000257430	NM_000038.5	2347	aGg/aAg	16/16	1	2	FACETS	0.545	0.499	0.593	0.545	0.499	0.593	SUBCLONAL	1	TRUE	1	0.94475275946205	2		554	548	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250256	133250256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745356467	NA	P-0014947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	179	648	0	ENST00000320574.5:c.1264C>T	p.His422Tyr	p.H422Y	ENST00000320574	NM_006231.2	422	Cat/Tat	13/49	0.486029352362531	1	FACETS	0.337	0.312	0.362	0.337	0.312	0.362	INDETERMINATE	1	TRUE	0	0.94475275946205	1		648	594	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534355	63534355	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060502142	NA	P-0014947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	516	721	0	ENST00000307078.5:c.1166A>G	p.His389Arg	p.H389R	ENST00000307078	NM_004655.3	389	cAc/cGc	5/11	0.94475275946205	2	FACETS	1	0.988	1	0.53	0.51	0.55	CLONAL	1	TRUE	0	0.94475275946205	2		721	1030	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051238	128051238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	482	714	0	ENST00000285398.2:c.85G>A	p.Ala29Thr	p.A29T	ENST00000285398	NM_000122.1	29	Gcc/Acc	2/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.94475275946205	2		714	1010	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953932	131953932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	197	475	0	ENST00000265335.6:c.3335G>A	p.Arg1112Lys	p.R1112K	ENST00000265335		1112	aGg/aAg	21/25	1	2	FACETS	0.979	0.918	1	0.979	0.918	1	CLONAL	1	TRUE	1	0.94475275946205	2		475	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0015027-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	278	671	2	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.637649718850936	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.637649718850936	1		673	578	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0015027-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	315	654	1	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.637649718850936	2		655	980	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739843	41739843	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015027-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	339	371	0	ENST00000242208.4:c.130C>A	p.Pro44Thr	p.P44T	ENST00000242208	NM_002192.2	44	Cca/Aca	2/3	0.624305105196808	3	FACETS	0.87	0.827	0.913	0.87	0.827	0.913	CLONAL	2	TRUE	1	0.637649718850936	3		371	806	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248145	59248145	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015027-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	30	40	0	ENST00000371222.2:c.598C>T	p.Gln200Ter	p.Q200*	ENST00000371222	NM_002228.3	200	Caa/Taa	1/1	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.637649718850936	2		40	81	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32449541	32449541	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015027-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	277	574	0	ENST00000332351.3:c.833C>A	p.Thr278Asn	p.T278N	ENST00000332351	NM_024426.4	278	aCc/aAc	3/10	1	2	FACETS	0.95	0.894	1	0.95	0.894	1	CLONAL	1	TRUE	1	0.637649718850936	2		574	915	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962530	100962530	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015027-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	274	639	0	ENST00000325455.5:c.1867C>G	p.Arg623Gly	p.R623G	ENST00000325455	NM_001202474.3	623	Cgc/Ggc	3/8	0.624305105196808	3	FACETS	1	0.963	1	0.518	0.486	0.551	CLONAL	1	TRUE	1	0.637649718850936	3		639	1094	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216485	108216485	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015027-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	68	300	0	ENST00000278616.4:c.8434T>A	p.Ser2812Thr	p.S2812T	ENST00000278616	NM_000051.3	2812	Tct/Act	58/63	0.624305105196808	3	FACETS	0.425	0.369	0.485	0.212	0.184	0.243	SUBCLONAL	1	TRUE	1	0.637649718850936	3		300	662	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134966	41134966	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015027-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	169	328	1	ENST00000379561.5:c.662G>T	p.Ser221Ile	p.S221I	ENST00000379561	NM_002015.3	221	aGc/aTc	2/3	0.637649718850936	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.637649718850936	1		329	360	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120127	70120127	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015027-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	80	86	0	ENST00000245479.2:c.1129C>A	p.Pro377Thr	p.P377T	ENST00000245479	NM_000346.3	377	Cca/Aca	3/3	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.637649718850936	2		86	182	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7168103	7168103	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015027-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	87	498	0	ENST00000302850.5:c.1486G>A	p.Glu496Lys	p.E496K	ENST00000302850	NM_000208.2	496	Gaa/Aaa	7/22	0.386306701552115	1	FACETS	0.396	0.352	0.443	0.396	0.352	0.443	SUBCLONAL	1	TRUE	0	0.637649718850936	1		498	469	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543668	29543668	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015027-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	298	686	0	ENST00000389048.3:c.1495C>A	p.Pro499Thr	p.P499T	ENST00000389048	NM_004304.4	499	Cct/Act	7/29	0.386306701552115	1	FACETS	0.8	0.757	0.844	0.8	0.757	0.844	SUBCLONAL	1	TRUE	0	0.637649718850936	1		686	796	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607816	46607816	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015027-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	288	616	0	ENST00000263734.3:c.2009del	p.Pro670LeufsTer26	p.P670Lfs*26	ENST00000263734	NM_001430.4	669	Ccc/cc	12/16	0.386306701552115	1	FACETS	0.777	0.734	0.821	0.777	0.734	0.821	SUBCLONAL	1	TRUE	0	0.637649718850936	1		616	792	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911166	40911166	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0015027-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	226	628	0	ENST00000373198.4:c.2140-1G>A		p.X714_splice	ENST00000373198	NM_133170.3	714			0.181651575967689	1	FACETS	0.63	0.589	0.673	0.63	0.589	0.673	INDETERMINATE	1	TRUE	0	0.637649718850936	1		628	766	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164507	47164507	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015027-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	278	432	0	ENST00000409792.3:c.1619G>T	p.Arg540Leu	p.R540L	ENST00000409792	NM_014159.6	540	cGa/cTa	3/21	0.6006247706931	2	FACETS	0.87	0.829	0.912	0.87	0.829	0.912	CLONAL	2	TRUE	0	0.637649718850936	2		432	501	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89478259	89478259	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015027-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	89	548	0	ENST00000336596.2:c.2078A>C	p.Lys693Thr	p.K693T	ENST00000336596	NM_005233.5	693	aAg/aCg	12/17	NA	2	FACETS	0.392	0.347	0.44			1	INDETERMINATE	1	TRUE	NA	0.637649718850936	2		548	712	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217206	66217207	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0015027-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	88	534	0	ENST00000273854.3:c.2408_2409delinsAA	p.Ala803Glu	p.A803E	ENST00000273854	NM_004439.5	803	gCC/gAA	14/18	0.315256595661717	1	FACETS	0.289	0.256	0.325	0.289	0.256	0.325	INDETERMINATE	1	TRUE	0	0.637649718850936	1		534	650	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064719	80064719	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015027-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	289	681	0	ENST00000265081.6:c.2150A>T	p.Asp717Val	p.D717V	ENST00000265081	NM_002439.4	717	gAt/gTt	15/24	0.181651575967689	1	FACETS	0.702	0.662	0.742	0.702	0.662	0.742	INDETERMINATE	1	TRUE	0	0.637649718850936	1		681	880	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829102	128829102	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015027-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	14	31	0	ENST00000249373.3:c.110C>A	p.Thr37Asn	p.T37N	ENST00000249373	NM_005631.4	37	aCc/aAc	1/12	0.353764756775295	1	FACETS	0.554	0.413	0.712	0.554	0.413	0.712	INDETERMINATE	1	TRUE	0	0.637649718850936	1		31	54	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829138	128829138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015027-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	10	32	0	ENST00000249373.3:c.146G>A	p.Arg49Lys	p.R49K	ENST00000249373	NM_005631.4	49	aGg/aAg	1/12	0.353764756775295	1	FACETS	0.791	0.569	1	0.791	0.569	1	INDETERMINATE	1	TRUE	0	0.637649718850936	1		32	27	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399282	139399282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs867637156	NA	P-0015027-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	407	609	1	ENST00000277541.6:c.4861G>T	p.Gly1621Cys	p.G1621C	ENST00000277541	NM_017617.3	1621	Ggc/Tgc	26/34	0.637649718850936	2	FACETS	0.787	0.754	0.82	0.787	0.754	0.82	SUBCLONAL	2	TRUE	0	0.637649718850936	2		610	811	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732959	44732959	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015027-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	152	211	0	ENST00000377967.4:c.161+1G>A		p.X54_splice	ENST00000377967	NM_021140.2	54			0.455673798071985	1	FACETS	0.928	0.861	0.995	0.928	0.861	0.995	CLONAL	1	TRUE	0	0.637649718850936	1		211	350	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160489	108160489	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs749770110	NA	P-0015027-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	127	673	1	ENST00000278616.4:c.4397G>T	p.Arg1466Leu	p.R1466L	ENST00000278616	NM_000051.3	1466	cGa/cTa	29/63	0.624305105196808	3	FACETS	0.438	0.395	0.483	0.219	0.197	0.242	SUBCLONAL	1	TRUE	1	0.637649718850936	3		674	1200	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392772	118392772	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015027-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	240	588	0	ENST00000534358.1:c.11804G>T	p.Arg3935Leu	p.R3935L	ENST00000534358	NM_005933.3	3935	cGt/cTt	36/36	0.624305105196808	3	FACETS	0.99	0.925	1	0.495	0.462	0.529	CLONAL	1	TRUE	1	0.637649718850936	3		588	1003	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841865	151841865	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015027-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	101	387	1	ENST00000262189.6:c.14276C>A	p.Ser4759Ter	p.S4759*	ENST00000262189	NM_170606.2	4759	tCa/tAa	55/59	0.353764756775295	1	FACETS	0.438	0.393	0.485	0.438	0.393	0.485	INDETERMINATE	1	TRUE	0	0.637649718850936	1		388	493	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873552	151873552	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015027-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	141	519	0	ENST00000262189.6:c.8986G>C	p.Gly2996Arg	p.G2996R	ENST00000262189	NM_170606.2	2996	Ggt/Cgt	38/59	0.353764756775295	1	FACETS	0.414	0.378	0.453	0.414	0.378	0.453	INDETERMINATE	1	TRUE	0	0.637649718850936	1		519	727	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0015129-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	432	581	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.226034267284897	5	FACETS	0.857	0.817	0.899	0.857	0.817	0.899	INDETERMINATE	3	TRUE	2	0.384638643889248	5		581	1377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0015129-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	291	539	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.203354250240003	1	FACETS	1	0.965	1	1	0.965	1	INDETERMINATE	1	TRUE	0	0.384638643889248	1		539	1178	SUCCESS
AR	367	MSKCC	GRCh37	X	66765170	66765170	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs62636528	NA	P-0015129-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	12	98	1	ENST00000374690.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000374690	NM_000044.3	61	cAg/cTg	1/8	0.384638643889248	0	FACETS	0.323	0.228	0.437			1	SUBCLONAL	1	TRUE	NA	0.384638643889248	0		99	119	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0015434-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	333	828	4	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.413017523934543	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.413017523934543	1		832	1275	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971168	21971178	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGCAGCTCC	GCAGCAGCTCC	CCA	novel	NA	P-0015434-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	245	447	1	ENST00000304494.5:c.180_190delinsTGG	p.Glu61GlyfsTer56	p.E61Gfs*56	ENST00000304494	NM_000077.4	60	gcGGAGCTGCTGCtg/gcTGGtg	2/3	0.413017523934543	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.413017523934543	1		448	725	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0015989-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	494	586	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.435174526581208	6	FACETS	1	0.974	1	1	0.974	1	CLONAL	5	TRUE	1	0.435174526581208	6		587	840	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859397	57859397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015989-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	229	461	0	ENST00000228682.2:c.542C>T	p.Ser181Phe	p.S181F	ENST00000228682	NM_005269.2	181	tCt/tTt	6/12	0.435174526581208	6	FACETS	1	0.992	1			1	CLONAL	1	TRUE	NA	0.435174526581208	6		461	1316	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859638	57859638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777659251	NA	P-0015989-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1343	346	537	2	ENST00000228682.2:c.692C>T	p.Ser231Phe	p.S231F	ENST00000228682	NM_005269.2	231	tCt/tTt	7/12	0.435174526581208	6	FACETS	0.88	0.831	0.931			1	CLONAL	2	TRUE	NA	0.435174526581208	6		539	1689	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652882	212652882	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015989-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	51	333	0	ENST00000342788.4:c.424A>G	p.Ile142Val	p.I142V	ENST00000342788	NM_005235.2	142	Atc/Gtc	4/28	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.435174526581208	2		333	230	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0016008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	121	364	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.415465596565595	5	FACETS	1	0.984	1	0.493	0.446	0.542	CLONAL	1	TRUE	2	0.4266421285526	5		364	629	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330628	65330628	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0016008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	176	320	0	ENST00000342505.4:c.1018A>T	p.Lys340Ter	p.K340*	ENST00000342505	NM_002227.2	340	Aaa/Taa	8/25	NA	2	FACETS	0.806	0.748	0.865			1	INDETERMINATE	2	TRUE	NA	0.4266421285526	2		320	512	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29120968	29120968	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	218	447	0	ENST00000328354.6:c.589A>G	p.Lys197Glu	p.K197E	ENST00000328354	NM_007194.3	197	Aaa/Gaa	4/15	0.269009019039555	2	FACETS	0.859	0.804	0.914	0.859	0.804	0.914	CLONAL	2	TRUE	0	0.4266421285526	2		447	595	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940079	49940079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778931500	NA	P-0016008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	323	578	1	ENST00000296474.3:c.964C>T	p.Arg322Trp	p.R322W	ENST00000296474	NM_002447.2	322	Cgg/Tgg	1/20	0.353071675970839	2	FACETS	0.994	0.944	1	0.994	0.944	1	CLONAL	2	TRUE	0	0.4266421285526	2		579	762	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295382	1295382	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0016008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	106	240	1				ENST00000310581	NM_198253.2	-/1132			0.315120943709239	4	FACETS	0.985	0.891	1	0.985	0.891	1	CLONAL	2	TRUE	2	0.4266421285526	4		241	360	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662622	117662622	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1456345928	NA	P-0016008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	213	469	0	ENST00000368508.3:c.4843A>G	p.Asn1615Asp	p.N1615D	ENST00000368508	NM_002944.2	1615	Aat/Gat	29/43	0.315120943709239	4	FACETS	0.895	0.833	0.958	0.895	0.833	0.958	CLONAL	2	TRUE	2	0.4266421285526	4		469	796	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092811	27092811	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	218	534	0	ENST00000324856.7:c.2832G>T	p.Gln944His	p.Q944H	ENST00000324856	NM_006015.4	944	caG/caT	9/20	0.269009019039555	2	FACETS	1	0.992	1	0.726	0.678	0.775	CLONAL	1	TRUE	0	0.4266421285526	2		534	704	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593602	55593613	+	inframe_deletion	In_Frame_Del	DEL	GTGGAAGGTTGT	GTGGAAGGTTGT	-	novel	NA	P-0016532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	127	371	0	ENST00000288135.5:c.1668_1679del	p.Gln556_Val560delinsHis	p.Q556_V560delinsH	ENST00000288135	NM_000222.2	556	caGTGGAAGGTTGTt/cat	11/21	1	2	FACETS	0.845	0.776	0.915	0.845	0.776	0.915	CLONAL	1	TRUE	1	0.919418567892884	2		371	327	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22412959	22412959	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	53	108	0	ENST00000344548.3:c.206C>G	p.Pro69Arg	p.P69R	ENST00000344548	NM_001039802.1	69	cCg/cGg	5/7	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.919418567892884	2		108	115	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339211	87339211	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	87	569	0	ENST00000277120.3:c.793T>C	p.Ser265Pro	p.S265P	ENST00000277120		265	Tct/Cct	8/19	0.42416470102027	3	FACETS	0.345	0.304	0.389			1	SUBCLONAL	1	TRUE	NA	0.610581805605735	3		569	1079	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923045	44923048	+	frameshift_variant	Frame_Shift_Del	DEL	CTAT	CTAT	-	rs398122969	NA	P-0016833-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	372	665	0	ENST00000377967.4:c.1909_1912del	p.Ser637ThrfsTer53	p.S637Tfs*53	ENST00000377967	NM_021140.2	636	CTATct/ct	16/29	1	2	FACETS	0.905	0.862	0.95	0.905	0.862	0.95	CLONAL	1	TRUE	1	0.83	2		665	990	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86686635	86686635	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016833-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	233	384	0	ENST00000274376.6:c.3079del	p.Leu1027TrpfsTer3	p.L1027Wfs*3	ENST00000274376	NM_002890.2	1027	Ctg/tg	25/25	1	2	FACETS	0.91	0.855	0.966	0.91	0.855	0.966	CLONAL	1	TRUE	1	0.83	2		384	617	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	217	297	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.325872285036978	4	FACETS	0.83	0.773	0.888	0.83	0.773	0.888	CLONAL	2	TRUE	2	0.452854708420793	4		297	839	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0016873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	365	606	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.350333935805336	2	FACETS	0.784	0.745	0.824	0.784	0.745	0.824	SUBCLONAL	2	TRUE	0	0.452854708420793	2		608	1028	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867546	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGC	GGCGGCGGC	-	rs11466445	NA	P-0016873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	25	27	0	ENST00000374994.4:c.70_78del	p.Ala24_Ala26del	p.A24_A26del	ENST00000374994	NM_004612.2	17	ctGGCGGCGGCg/ctg	1/9	0.34010497653655	3	FACETS	1	0.931	1	0.713	0.575	0.863	CLONAL	1	TRUE	1	0.452854708420793	3		27	95	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347546	89347546	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	134	618	1	ENST00000301030.4:c.5404G>A	p.Glu1802Lys	p.E1802K	ENST00000301030	NM_001256183.1	1802	Gaa/Aaa	9/13	0.391872591686464	3	FACETS	0.813	0.738	0.891	0.406	0.369	0.446	CLONAL	1	TRUE	1	0.452854708420793	3		619	893	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414297	32414297	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	197	502	0	ENST00000332351.3:c.1254G>C	p.Glu418Asp	p.E418D	ENST00000332351	NM_024426.4	418	gaG/gaC	8/10	0.169244063011236	3	FACETS	1	0.989	1	0.457	0.424	0.491	INDETERMINATE	1	TRUE	0	0.452854708420793	3		502	778	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907119	32907120	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs886038066	NA	P-0016873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	300	482	0	ENST00000380152.3:c.1507_1508del	p.Lys503ValfsTer10	p.K503Vfs*10	ENST00000380152		502	AAa/a	10/27	0.327963218997946	3	FACETS	1	0.99	1	0.779	0.739	0.82	CLONAL	2	TRUE	0	0.452854708420793	3		482	695	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46603751	46603751	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1233737038	NA	P-0016873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	323	744	0	ENST00000263734.3:c.1108A>G	p.Met370Val	p.M370V	ENST00000263734	NM_001430.4	370	Atg/Gtg	9/16	0.34010497653655	3	FACETS	0.759	0.717	0.803	0.759	0.717	0.803	SUBCLONAL	2	TRUE	1	0.452854708420793	3		744	1152	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0017214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	75	716	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.86	0.752	0.977	0.86	0.752	0.977	CLONAL	1	TRUE	1	0.180399483840597	2		716	967	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017254-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	168	410	0	ENST00000304494.5:c.247C>A	p.His83Asn	p.H83N	ENST00000304494	NM_000077.4	83	Cac/Aac	2/3	0.414112330418657	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.41875171021548	2		410	356	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741859	162741859	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017254-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	55	347	0	ENST00000367921.3:c.1550G>A	p.Gly517Glu	p.G517E	ENST00000367921	NM_006182.2	517	gGg/gAg	13/18	0.41875171021548	3	FACETS	0.966	0.831	1	0.483	0.415	0.556	CLONAL	1	TRUE	1	0.41875171021548	3		347	329	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0017278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	406	559	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.41450993920878	8	FACETS	0.885	0.843	0.929	0.708	0.674	0.743	CLONAL	4	TRUE	3	0.41450993920878	8		559	1241	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0017326-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	95	738	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.182073614152389	2		738	822	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032594	47032594	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017326-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	81	730	2	ENST00000377604.3:c.500del	p.Ser167Ter	p.S167*	ENST00000377604	NM_001204468.1	167	tCa/ta	5/24	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	FALSE	1	0.182073614152389	2		732	829	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114817	108114817	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786204543	NA	P-0017565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	240	333	1	ENST00000278616.4:c.640del	p.Ser214ProfsTer16	p.S214Pfs*16	ENST00000278616	NM_000051.3	212	Ttt/tt	6/63	0.767572388916007	2	FACETS	0.926	0.888	0.963	0.926	0.888	0.963	CLONAL	2	TRUE	0	0.77565106499008	2		334	334	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976198	7976198	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1274525093	NA	P-0017565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	339	375	0	ENST00000319144.4:c.1997G>A	p.Arg666His	p.R666H	ENST00000319144	NM_001139.2	666	cGc/cAc	15/15	0.765449392786623	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.77565106499008	2		375	411	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713463	30713536	+	frameshift_variant	Frame_Shift_Del	DEL	TGAAGCAGAACACTTCAGAGCAGTTTGAGACAGTGGCAGTCAAGATCTTTCCCTATGAGGAGTATGCCTCTTGG	TGAAGCAGAACACTTCAGAGCAGTTTGAGACAGTGGCAGTCAAGATCTTTCCCTATGAGGAGTATGCCTCTTGG	-	novel	NA	P-0017565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	222	373	1	ENST00000295754.5:c.788_861del	p.Leu263GlnfsTer15	p.L263Qfs*15	ENST00000295754	NM_003242.5	263	cTGAAGCAGAACACTTCAGAGCAGTTTGAGACAGTGGCAGTCAAGATCTTTCCCTATGAGGAGTATGCCTCTTGG/c	4/7	0.765449392786623	2	FACETS	0.92	0.88	0.959	0.92	0.88	0.959	CLONAL	2	TRUE	0	0.77565106499008	2		374	311	SUCCESS
APC	324	MSKCC	GRCh37	5	112162945	112162945	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1114167599	NA	P-0017565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	166	267	0	ENST00000257430.4:c.1548+1G>A		p.X516_splice	ENST00000257430	NM_000038.5	516			0.767572388916007	2	FACETS	0.986	0.941	1	0.986	0.941	1	CLONAL	2	TRUE	0	0.77565106499008	2		267	217	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783720	50783720	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1627	350	457	0	ENST00000398568.2:c.111G>C	p.Lys37Asn	p.K37N	ENST00000398568	NM_001042412.1	37	aaG/aaC	3/18	0.77565106499008	9	FACETS	0.848	0.8	0.897			1	CLONAL	2	TRUE	NA	0.77565106499008	9		457	1977	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0017752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	82	518	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.769	0.677	0.867	0.769	0.677	0.867	SUBCLONAL	1	TRUE	1	0.28	2		518	762	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727402	66727443	+	inframe_deletion	In_Frame_Del	DEL	CTAGAGCTTGATGAGCAGCAGCGAAAGCGCCTTGAGGCCTTT	CTAGAGCTTGATGAGCAGCAGCGAAAGCGCCTTGAGGCCTTT	-	novel	NA	P-0017752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	38	381	0	ENST00000307102.5:c.120_161del	p.Glu41_Leu54del	p.E41_L54del	ENST00000307102	NM_002755.3	40	CTAGAGCTTGATGAGCAGCAGCGAAAGCGCCTTGAGGCCTTT/-	2/11	1	2	FACETS	0.544	0.449	0.65	0.544	0.449	0.65	SUBCLONAL	1	TRUE	1	0.28	2		381	499	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100523	157100527	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCG	GCCCG	-	novel	NA	P-0017752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	25	239	0	ENST00000346085.5:c.1463_1467del	p.Pro488LeufsTer45	p.P488Lfs*45	ENST00000346085	NM_020732.3	487	aGCCCG/a	1/20	1	2	FACETS	0.589	0.465	0.732	0.589	0.465	0.732	SUBCLONAL	1	TRUE	1	0.28	2		239	303	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-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	22	232	0	ENST00000218089.9:c.377_385+68del		p.X126_splice	ENST00000218089	NM_001042749.1	126		6/35	0.198144781477058	2	FACETS	0.459	0.356	0.58			1	SUBCLONAL	1	TRUE	NA	0.28	2		232	342	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	193	210	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.998	0.934	1	0.998	0.934	1	CLONAL	1	TRUE	1	0.849644534432457	2		210	455	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240690	55240690	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs772046081	NA	P-0018572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	9228	606	0	ENST00000275493.2:c.1934C>G	p.Ser645Cys	p.S645C	ENST00000275493	NM_005228.3	645	tCc/tGc	17/28	0.849644534432457	20	FACETS	1	0.998	1			1	CLONAL	18	TRUE	NA	0.849644534432457	20		606	10384	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544756	65544756	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0018572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	84	327	0	ENST00000358664.4:c.172-2A>G		p.X58_splice	ENST00000358664	NM_002382.4	58			1	2	FACETS	0.382	0.338	0.429	0.382	0.338	0.429	SUBCLONAL	1	TRUE	1	0.849644534432457	2		327	518	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228644	36228652	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTATGGAG	GGTATGGAG	-	novel	NA	P-0018572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	268	540	0	ENST00000222270.7:c.7658_7658+8del		p.X2553_splice	ENST00000222270	NM_014727.1	2553		34/37	0.849644534432457	3	FACETS	0.681	0.638	0.726	0.341	0.319	0.363	SUBCLONAL	1	TRUE	1	0.849644534432457	3		540	1319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578517	7578517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750600586	NA	P-0018995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	271	817	0	ENST00000269305.4:c.413C>T	p.Ala138Val	p.A138V	ENST00000269305	NM_001126112.2	138	gCc/gTc	5/11	0.717576878150688	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.830164986326554	1		817	375	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128305406	128305406	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	99	823	0	ENST00000265960.3:c.890C>G	p.Thr297Arg	p.T297R	ENST00000265960	NM_001006617.1	297	aCa/aGa	7/12	1	2	FACETS	0.453	0.406	0.504	0.453	0.406	0.504	SUBCLONAL	1	TRUE	1	0.830164986326554	2		823	526	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875964	76875964	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	148	681	0	ENST00000373344.5:c.5171del	p.Leu1724GlnfsTer12	p.L1724Qfs*12	ENST00000373344	NM_000489.3	1724	cTa/ca	20/35	0.754463634743898	4	FACETS	0.817	0.746	0.89	0.408	0.373	0.445	CLONAL	1	TRUE	2	0.830164986326554	4		681	799	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0019042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	153	634	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	1	2	FACETS	0.832	0.765	0.901	0.832	0.765	0.901	CLONAL	1	TRUE	1	0.652158365164141	2		634	564	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125222	47125222	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	135	432	1	ENST00000409792.3:c.6048G>A	p.Trp2016Ter	p.W2016*	ENST00000409792	NM_014159.6	2016	tgG/tgA	12/21	1	2	FACETS	0.993	0.911	1	0.993	0.911	1	CLONAL	1	TRUE	1	0.652158365164141	2		433	417	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0019042-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	233	634	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	1	2	FACETS	0.811	0.76	0.864	0.811	0.76	0.864	CLONAL	1	TRUE	1	0.795848009340744	2		634	722	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125222	47125222	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019042-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	153	432	1	ENST00000409792.3:c.6048G>A	p.Trp2016Ter	p.W2016*	ENST00000409792	NM_014159.6	2016	tgG/tgA	12/21	1	2	FACETS	0.803	0.74	0.867	0.803	0.74	0.867	CLONAL	1	TRUE	1	0.795848009340744	2		433	479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587781525	NA	P-0019424-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	644	782	0	ENST00000269305.4:c.842A>T	p.Asp281Val	p.D281V	ENST00000269305	NM_001126112.2	281	gAc/gTc	8/11	NA	2	FACETS	1	0.998	1			1	INDETERMINATE	2	TRUE	NA	0.89519424053252	2		782	678	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43769902	43769902	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019424-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	360	511	0	ENST00000382044.4:c.844G>T	p.Glu282Ter	p.E282*	ENST00000382044	NM_001141980.1	282	Gaa/Taa	8/28	0.89519424053252	4	FACETS	0.975	0.93	1	0.65	0.62	0.68	CLONAL	2	TRUE	1	0.89519424053252	4		511	782	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81954842	81954842	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019424-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	490	657	1	ENST00000359376.3:c.2275T>A	p.Tyr759Asn	p.Y759N	ENST00000359376	NM_002661.3	759	Tat/Aat	21/33	0.89519424053252	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.89519424053252	2		658	522	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983258	7983258	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019424-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	300	372	0	ENST00000319144.4:c.756G>C	p.Glu252Asp	p.E252D	ENST00000319144	NM_001139.2	252	gaG/gaC	7/15	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.89519424053252	2		372	327	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78882646	78882646	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019424-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	108	641	1	ENST00000306801.3:c.2437A>G	p.Arg813Gly	p.R813G	ENST00000306801	NM_020761.2	813	Aga/Gga	21/34	0.89519424053252	2	FACETS	0.466	0.42	0.514	0.233	0.21	0.257	SUBCLONAL	1	TRUE	0	0.89519424053252	2		642	518	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215323	5215323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019424-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	200	561	0	ENST00000357368.4:c.4295G>T	p.Arg1432Leu	p.R1432L	ENST00000357368	NM_002850.3	1432	cGt/cTt	28/38	0.785284937216968	4	FACETS	0.999	0.927	1	0.499	0.463	0.537	CLONAL	1	TRUE	2	0.89519424053252	4		561	848	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	167	445	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.451394451555252	3	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	1	0.451394451555252	3		445	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0019711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	432	581	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.451394451555252	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.451394451555252	2		583	846	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0019711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	205	245	1	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	0.451394451555252	3	FACETS	1	0.945	1	1	0.945	1	CLONAL	3	TRUE	0	0.451394451555252	3		246	371	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385221	41385221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375454640	NA	P-0019711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	151	456	2	ENST00000373198.4:c.740G>A	p.Arg247His	p.R247H	ENST00000373198	NM_133170.3	247	cGc/cAc	6/32	0.317402036796435	5	FACETS	1	0.948	1	0.351	0.32	0.384	CLONAL	1	TRUE	2	0.451394451555252	5		458	1065	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943806	9943806	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	115	339	0	ENST00000330684.3:c.1135G>A	p.Glu379Lys	p.E379K	ENST00000330684	NM_001134407.1	379	Gag/Aag	5/13	0.451394451555252	3	FACETS	1	0.945	1	0.533	0.481	0.587	CLONAL	1	TRUE	1	0.451394451555252	3		339	586	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0019711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	322	519	0	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	0.451394451555252	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.451394451555252	2		519	682	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953214	81953214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369516453	NA	P-0019711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	89	290	0	ENST00000359376.3:c.2180G>A	p.Arg727Gln	p.R727Q	ENST00000359376	NM_002661.3	727	cGa/cAa	20/33	0.451394451555252	3	FACETS	0.812	0.721	0.909	0.406	0.36	0.455	CLONAL	1	TRUE	1	0.451394451555252	3		290	595	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016634	12016634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	162	304	1	ENST00000353533.5:c.770C>T	p.Ser257Phe	p.S257F	ENST00000353533	NM_003010.3	257	tCt/tTt	7/11	0.451394451555252	2	FACETS	0.952	0.885	1	0.952	0.885	1	CLONAL	2	TRUE	0	0.451394451555252	2		305	377	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650377	48650377	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1557020191	NA	P-0019711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	232	631	0	ENST00000376670.3:c.347C>G	p.Ser116Cys	p.S116C	ENST00000376670	NM_002049.3	116	tCt/tGt	3/6	0.336362141637299	3	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.451394451555252	3		631	1063	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864618	37864618	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	200	576	0	ENST00000269571.5:c.270A>T	p.Gln90His	p.Q90H	ENST00000269571		90	caA/caT	3/27	0.451394451555252	3	FACETS	1	0.977	1	0.565	0.523	0.608	CLONAL	1	TRUE	1	0.451394451555252	3		576	962	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44515621	44515621	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	161	585	0	ENST00000291552.4:c.275A>C	p.Lys92Thr	p.K92T	ENST00000291552	NM_006758.2	92	aAg/aCg	5/8	0.451394451555252	3	FACETS	1	0.944	1	0.518	0.475	0.563	CLONAL	1	TRUE	1	0.451394451555252	3		585	844	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933824	49933824	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	180	552	0	ENST00000296474.3:c.2453T>C	p.Leu818Pro	p.L818P	ENST00000296474	NM_002447.2	818	cTt/cCt	10/20	0.451394451555252	3	FACETS	1	0.956	1	0.526	0.485	0.569	CLONAL	1	TRUE	1	0.451394451555252	3		552	929	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931335	131931335	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	117	407	0	ENST00000265335.6:c.2040T>G	p.Cys680Trp	p.C680W	ENST00000265335		680	tgT/tgG	13/25	0.451394451555252	3	FACETS	0.838	0.756	0.925	0.279	0.252	0.309	CLONAL	1	TRUE	0	0.451394451555252	3		407	758	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642513	117642513	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	112	579	0	ENST00000368508.3:c.5686G>T	p.Val1896Leu	p.V1896L	ENST00000368508	NM_002944.2	1896	Gtg/Ttg	35/43	0.330295845227057	3	FACETS	0.606	0.544	0.672	0.202	0.181	0.224	SUBCLONAL	1	TRUE	0	0.451394451555252	3		579	1003	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987307	2987307	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	155	478	0	ENST00000396946.4:c.122A>C	p.Lys41Thr	p.K41T	ENST00000396946	NM_032415.4	41	aAg/aCg	3/25	0.451394451555252	4	FACETS	1	0.95	1	0.351	0.321	0.383	CLONAL	1	TRUE	1	0.451394451555252	4		478	946	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227918	55227918	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	352	466	0	ENST00000275493.2:c.1385T>G	p.Ile462Arg	p.I462R	ENST00000275493	NM_005228.3	462	aTa/aGa	12/28	0.451394451555252	8	FACETS	0.992	0.943	1	0.567	0.539	0.596	CLONAL	4	TRUE	1	0.451394451555252	8		466	925	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090898	5090898	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	23	195	0	ENST00000381652.3:c.3046A>C	p.Ser1016Arg	p.S1016R	ENST00000381652	NM_004972.3	1016	Agt/Cgt	22/25	0.451394451555252	3	FACETS	0.781	0.614	0.969	0.39	0.307	0.485	CLONAL	1	TRUE	1	0.451394451555252	3		195	160	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217345	123217345	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	99	519	0	ENST00000218089.9:c.2999T>G	p.Leu1000Arg	p.L1000R	ENST00000218089	NM_001042749.1	1000	cTt/cGt	29/35	0.336362141637299	3	FACETS	0.962	0.861	1			1	CLONAL	1	TRUE	NA	0.451394451555252	3		519	559	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775907	9775907	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	151	897	3	ENST00000377346.4:c.371G>A	p.Gly124Asp	p.G124D	ENST00000377346	NM_005026.3	124	gGc/gAc	5/24	0.650290624808095	3	FACETS	0.833	0.763	0.906	0.416	0.381	0.453	CLONAL	1	TRUE	1	0.650278964371343	3		900	739	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223032	5223032	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370088739	NA	P-0019928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	168	945	0	ENST00000357368.4:c.2771C>T	p.Pro924Leu	p.P924L	ENST00000357368	NM_002850.3	924	cCg/cTg	18/38	0.128054531412824	4	FACETS	0.831	0.77	0.894	0.831	0.77	0.894	INDETERMINATE	2	TRUE	2	0.650278964371343	4		945	513	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0019948-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	292	509	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	NA	2	FACETS	0.895	0.847	0.943			1	INDETERMINATE	1	TRUE	NA	0.921775898167042	2		509	708	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052601	42052601	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0019948-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	377	474	0	ENST00000219905.7:c.7272T>G	p.Tyr2424Ter	p.Y2424*	ENST00000219905	NM_001164273.1	2424	taT/taG	20/24	0.807682920494708	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.921775898167042	1		474	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0020597-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	526	907	1	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	0.719864750119453	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.719864750119453	2		908	701	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599332	55599332	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519710	NA	P-0020597-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	479	611	3	ENST00000288135.5:c.2458G>T	p.Asp820Tyr	p.D820Y	ENST00000288135	NM_000222.2	820	Gat/Tat	17/21	0.590629380076341	5	FACETS	1	0.977	1			1	CLONAL	4	TRUE	NA	0.719864750119453	5		614	686	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70442713	70442713	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020597-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	108	418	0	ENST00000373644.4:c.5035A>T	p.Asn1679Tyr	p.N1679Y	ENST00000373644	NM_030625.2	1679	Aat/Tat	10/12	0.719864750119453	4	FACETS	0.86	0.774	0.951	0.215	0.193	0.238	CLONAL	1	TRUE	0	0.719864750119453	4		418	600	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	364555	364555	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs534120185	NA	P-0020597-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	276	970	2	ENST00000262320.3:c.1007C>T	p.Thr336Met	p.T336M	ENST00000262320	NM_003502.3	336	aCg/aTg	3/11	0.719864750119453	3	FACETS	0.923	0.866	0.981	0.461	0.433	0.491	CLONAL	1	TRUE	1	0.719864750119453	3		972	1130	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55569930	55569930	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020597-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	290	442	0	ENST00000288135.5:c.797A>C	p.Asp266Ala	p.D266A	ENST00000288135	NM_000222.2	266	gAc/gCc	5/21	0.590629380076341	5	FACETS	0.917	0.878	0.955			1	CLONAL	4	TRUE	NA	0.719864750119453	5		442	457	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23640966	23640966	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778587	NA	P-0020985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	33	488	0	ENST00000261584.4:c.2509G>A	p.Glu837Lys	p.E837K	ENST00000261584	NM_024675.3	837	Gaa/Aaa	5/13	0.133604507977355	3	FACETS	0.594	0.482	0.72	0.297	0.241	0.36	SUBCLONAL	1	FALSE	1	0.222174684581725	3		488	556	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905505	11905505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774396176	NA	P-0020985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	26	312	1	ENST00000396373.4:c.155C>T	p.Ala52Val	p.A52V	ENST00000396373	NM_001987.4	52	gCg/gTg	2/8	0.222174684581725	6	FACETS	0.655	0.518	0.814	0.164	0.129	0.204	SUBCLONAL	1	FALSE	2	0.222174684581725	6		313	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0020994-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	312	570	0	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	0.71036969400227	1	FACETS	0.973	0.928	1	0.973	0.928	1	CLONAL	1	TRUE	0	0.71036969400227	1		570	582	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935319	36935319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748675453	NA	P-0020994-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	274	628	0	ENST00000361632.4:c.1408G>A	p.Ala470Thr	p.A470T	ENST00000361632		470	Gcg/Acg	10/16	1	2	FACETS	0.808	0.759	0.857	0.808	0.759	0.857	CLONAL	1	TRUE	1	0.71036969400227	2		628	955	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379426	225379427	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020994-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	306	573	0	ENST00000264414.4:c.441dup	p.Arg148SerfsTer11	p.R148Sfs*11	ENST00000264414	NM_003590.4	147	-/T	4/16	0.216529620481523	3	FACETS	1	0.991	1	0.613	0.579	0.648	INDETERMINATE	1	TRUE	1	0.71036969400227	3		573	952	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5077570	5077570	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020994-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	142	370	0	ENST00000381652.3:c.1982T>C	p.Met661Thr	p.M661T	ENST00000381652	NM_004972.3	661	aTg/aCg	15/25	0.71036969400227	1	FACETS	0.868	0.806	0.93	0.868	0.806	0.93	CLONAL	1	TRUE	0	0.71036969400227	1		370	297	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675419	241675419	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020994-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	39	260	0	ENST00000366560.3:c.403C>A	p.His135Asn	p.H135N	ENST00000366560	NM_000143.3	135	Cat/Aat	4/10	0.71036969400227	3	FACETS	0.259	0.214	0.309	0.129	0.107	0.155	SUBCLONAL	1	TRUE	1	0.71036969400227	3		260	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1131691023	NA	P-0021045-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	340	700	0	ENST00000269305.4:c.470T>A	p.Val157Asp	p.V157D	ENST00000269305	NM_001126112.2	157	gTc/gAc	5/11	0.854132539184922	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.854132539184922	1		700	419	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450156	32450156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779451877	NA	P-0021045-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	230	499	0	ENST00000332351.3:c.656C>T	p.Thr219Met	p.T219M	ENST00000332351	NM_024426.4	219	aCg/aTg	2/10	0.854132539184922	2	FACETS	1	0.978	1	0.539	0.507	0.57	CLONAL	1	TRUE	0	0.854132539184922	2		499	500	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434732	49434732	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767236217	NA	P-0021045-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	245	711	1	ENST00000301067.7:c.6821C>T	p.Ser2274Leu	p.S2274L	ENST00000301067	NM_003482.3	2274	tCg/tTg	31/54	0.794477973988608	4	FACETS	0.96	0.897	1	0.48	0.448	0.513	CLONAL	1	TRUE	2	0.854132539184922	4		712	1108	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278167	142278167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs952177176	NA	P-0021045-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	482	555	0	ENST00000350721.4:c.1658C>T	p.Ser553Phe	p.S553F	ENST00000350721	NM_001184.3	553	tCt/tTt	7/47	0.786371366736308	5	FACETS	0.928	0.893	0.963	0.928	0.893	0.963	CLONAL	3	TRUE	2	0.854132539184922	5		555	925	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442492	49442492	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021045-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	221	645	1	ENST00000301067.7:c.4081C>A	p.Gln1361Lys	p.Q1361K	ENST00000301067	NM_003482.3	1361	Cag/Aag	13/54	0.794477973988608	4	FACETS	1	0.972	1	0.539	0.502	0.577	CLONAL	1	TRUE	2	0.854132539184922	4		646	890	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3929859	3929859	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021045-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	247	539	0	ENST00000262367.5:c.59C>G	p.Pro20Arg	p.P20R	ENST00000262367	NM_004380.2	20	cCc/cGc	1/31	0.718461853918406	3	FACETS	1	0.974	1			1	CLONAL	1	TRUE	NA	0.854132539184922	3		539	772	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62311285	62311285	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021045-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	27	350	0	ENST00000360203.5:c.1121A>G	p.Gln374Arg	p.Q374R	ENST00000360203	NM_001283009.1	374	cAg/cGg	13/35	0.718461853918406	3	FACETS	0.168	0.133	0.209			1	SUBCLONAL	1	TRUE	NA	0.854132539184922	3		350	536	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710768	117710768	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021045-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	160	448	0	ENST00000368508.3:c.1504T>G	p.Phe502Val	p.F502V	ENST00000368508	NM_002944.2	502	Ttt/Gtt	12/43	0.854132539184922	3	FACETS	0.933	0.86	1	0.467	0.43	0.504	CLONAL	1	TRUE	1	0.854132539184922	3		448	573	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0021177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	145	267	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	0.475510039948765	4	FACETS	0.856	0.793	0.92	0.856	0.793	0.92	CLONAL	3	TRUE	1	0.504106960048488	4		267	337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578266	7578266	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs942158624	NA	P-0021177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	310	634	0	ENST00000269305.4:c.583A>T	p.Ile195Phe	p.I195F	ENST00000269305	NM_001126112.2	195	Atc/Ttc	6/11	0.504106960048488	3	FACETS	1	0.991	1	0.793	0.755	0.832	CLONAL	2	TRUE	0	0.504106960048488	3		634	647	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045875	26045875	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	140	417	0	ENST00000540144.1:c.237C>G	p.Phe79Leu	p.F79L	ENST00000540144	NM_003531.2	79	ttC/ttG	1/1	0.499323683813361	4	FACETS	1	0.987	1	0.738	0.675	0.803	CLONAL	1	TRUE	2	0.504106960048488	4		417	566	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199310	16199310	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0021177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	151	214	0	ENST00000375759.3:c.84-1G>T		p.X28_splice	ENST00000375759	NM_015001.2	28			0.504106960048488	3	FACETS	1	0.986	1	0.831	0.774	0.887	CLONAL	2	TRUE	0	0.504106960048488	3		214	301	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233496	69233496	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	119	350	0	ENST00000462284.1:c.1361G>A	p.Gly454Asp	p.G454D	ENST00000462284	NM_002392.5	454	gGt/gAt	11/11	0.499323683813361	4	FACETS	0.777	0.706	0.851	0.777	0.706	0.851	SUBCLONAL	2	TRUE	2	0.504106960048488	4		350	457	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068451	16068451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	20	105	0	ENST00000268712.3:c.460G>A	p.Glu154Lys	p.E154K	ENST00000268712	NM_006311.3	154	Gaa/Aaa	5/46	0.504106960048488	3	FACETS	0.835	0.647	1	0.278	0.215	0.35	CLONAL	1	TRUE	0	0.504106960048488	3		105	119	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748601	40748601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200545231	NA	P-0021177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	102	348	0	ENST00000373198.4:c.2915G>A	p.Arg972Gln	p.R972Q	ENST00000373198	NM_133170.3	972	cGa/cAa	21/32	0.405869424753667	3	FACETS	0.831	0.752	0.911	0.554	0.501	0.608	CLONAL	2	TRUE	0	0.504106960048488	3		348	305	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186501409	186501409	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	143	241	0	ENST00000323963.5:c.10G>T	p.Gly4Cys	p.G4C	ENST00000323963		4	Ggc/Tgc	1/11	0.504106960048488	5	FACETS	0.879	0.811	0.948	0.659	0.608	0.711	CLONAL	3	TRUE	1	0.504106960048488	5		241	378	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992752	68992752	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	156	591	0	ENST00000288368.4:c.1717A>G	p.Asn573Asp	p.N573D	ENST00000288368	NM_024870.2	573	Aat/Gat	16/40	0.451922647134591	5	FACETS	0.832	0.765	0.902	0.555	0.51	0.602	CLONAL	2	TRUE	2	0.504106960048488	5		591	653	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971152	21971164	+	frameshift_variant	Frame_Shift_Del	DEL	TCCGCGCCGTGGA	TCCGCGCCGTGGA	CG	novel	NA	P-0021177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	193	467	2	ENST00000304494.5:c.194_206delinsCG	p.Leu65ProfsTer51	p.L65Pfs*51	ENST00000304494	NM_000077.4	65	cTCCACGGCGCGGAg/cCGg	2/3	0.504106960048488	3	FACETS	0.982	0.918	1	0.655	0.612	0.699	CLONAL	2	TRUE	0	0.504106960048488	3		469	488	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251908	8251908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763199508	NA	P-0021177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	215	556	0	ENST00000335790.3:c.169C>T	p.Arg57Cys	p.R57C	ENST00000335790	NM_002315.2	57	Cgc/Tgc	2/4	0.489589769695437	4	FACETS	0.916	0.855	0.979	0.458	0.427	0.49	CLONAL	2	TRUE	0	0.504106960048488	4		556	700	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42050033	42050033	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	34	330	0	ENST00000219905.7:c.7187del	p.Arg2396GlnfsTer8	p.R2396Qfs*8	ENST00000219905	NM_001164273.1	2396	cGa/ca	19/24	0.382650768828344	2	FACETS	0.6	0.493	0.717	0.3	0.246	0.359	SUBCLONAL	1	TRUE	0	0.504106960048488	2		330	225	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038612	14038612	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	65	329	0	ENST00000311895.7:c.1937G>T	p.Arg646Ile	p.R646I	ENST00000311895	NM_005236.2	646	aGa/aTa	10/11	0.474392479457528	4	FACETS	0.892	0.776	1	0.446	0.388	0.509	CLONAL	1	TRUE	2	0.504106960048488	4		329	435	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56855471	56855471	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	48	310	1	ENST00000308159.5:c.620A>T	p.Asp207Val	p.D207V	ENST00000308159	NM_014669.4	207	gAc/gTc	7/22	0.474392479457528	4	FACETS	0.665	0.563	0.776	0.332	0.281	0.388	SUBCLONAL	1	TRUE	2	0.504106960048488	4		311	431	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448310	56448310	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	113	595	0	ENST00000407977.2:c.337C>G	p.Arg113Gly	p.R113G	ENST00000407977		113	Cga/Gga	3/10	0.471300094106365	5	FACETS	0.982	0.883	1	0.327	0.294	0.362	CLONAL	1	TRUE	2	0.504106960048488	5		595	802	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15378278	15378278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	38	950	2	ENST00000263377.2:c.508G>A	p.Glu170Lys	p.E170K	ENST00000263377	NM_058243.2	170	Gag/Aag	4/20	0.20491713452635	2	FACETS	0.373	0.308	0.447	0.187	0.154	0.224	SUBCLONAL	1	TRUE	0	0.305164809896147	2		952	667	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349620	15349620	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	48	1043	1	ENST00000263377.2:c.3954G>T	p.Gln1318His	p.Q1318H	ENST00000263377	NM_058243.2	1318	caG/caT	19/20	0.20491713452635	2	FACETS	0.379	0.319	0.445	0.19	0.159	0.223	SUBCLONAL	1	TRUE	0	0.305164809896147	2		1044	830	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15378253	15378253	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	33	877	1	ENST00000263377.2:c.533G>A	p.Gly178Glu	p.G178E	ENST00000263377	NM_058243.2	178	gGa/gAa	4/20	0.20491713452635	2	FACETS	0.363	0.295	0.44	0.181	0.147	0.22	SUBCLONAL	1	TRUE	0	0.305164809896147	2		878	596	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266924	18266924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	184	747	0	ENST00000222254.8:c.235G>A	p.Gly79Arg	p.G79R	ENST00000222254	NM_005027.3	79	Ggg/Agg	2/16	0.20491713452635	2	FACETS	0.918	0.851	0.987	0.918	0.851	0.987	CLONAL	2	TRUE	0	0.305164809896147	2		747	657	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974706	21974707	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	29	622	0	ENST00000304494.5:c.120dup	p.Pro41ThrfsTer3	p.P41Tfs*3	ENST00000304494	NM_000077.4	40	-/A	1/3	1	2	FACETS	0.355	0.284	0.436	0.355	0.284	0.436	SUBCLONAL	1	TRUE	1	0.305164809896147	2		622	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0021377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	449	606	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.777996509920008	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.777996509920008	1		608	700	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0021377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	283	688	1	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	1	2	FACETS	0.983	0.929	1	0.983	0.929	1	CLONAL	1	TRUE	1	0.777996509920008	2		689	740	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217299	11217299	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519779	NA	P-0021377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	483	1114	1	ENST00000361445.4:c.4379T>C	p.Leu1460Pro	p.L1460P	ENST00000361445	NM_004958.3	1460	cTt/cCt	30/58	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.777996509920008	2		1115	1203	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348156	89348164	+	inframe_deletion	In_Frame_Del	DEL	GTGGCGCTC	GTGGCGCTC	-	novel	NA	P-0021447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	267	689	1	ENST00000301030.4:c.4786_4794del	p.Glu1596_His1598del	p.E1596_H1598del	ENST00000301030	NM_001256183.1	1596	GAGCGCCAC/-	9/13	0.758220819519361	2	FACETS	0.641	0.601	0.682	0.32	0.3	0.341	SUBCLONAL	1	TRUE	0	0.767319761537957	2		690	1086	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280676	41280676	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	199	705	0	ENST00000349496.5:c.2189G>C	p.Gly730Ala	p.G730A	ENST00000349496	NM_001904.3	730	gGt/gCt	15/15	0.598999870444974	3	FACETS	0.596	0.551	0.643	0.298	0.275	0.322	SUBCLONAL	1	TRUE	1	0.767319761537957	3		705	1204	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662634	227662634	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	61	750	0	ENST00000305123.5:c.821C>G	p.Ser274Cys	p.S274C	ENST00000305123	NM_005544.2	274	tCc/tGc	1/2	0.267107196501293	3	FACETS	0.95	0.82	1	0.475	0.41	0.546	CLONAL	1	TRUE	1	0.267107196501293	3		750	545	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0021626-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	318	688	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.298515038841202	5	FACETS	0.9	0.849	0.952	0.6	0.566	0.635	INDETERMINATE	2	TRUE	2	0.534376374863824	5		688	1191	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72842185	72842185	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	63	467	0	ENST00000325599.8:c.1063A>G	p.Lys355Glu	p.K355E	ENST00000325599	NM_018130.2	355	Aaa/Gaa	10/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.560510984310205	2		467	186	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278049	18278049	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs372272045	NA	P-0021699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	116	940	2	ENST00000222254.8:c.1669G>T	p.Asp557Tyr	p.D557Y	ENST00000222254	NM_005027.3	557	Gac/Tac	13/16	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.560510984310205	2		942	372	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481418	140481418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913349	NA	P-0021699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	55	783	3	ENST00000288602.6:c.1390G>A	p.Gly464Arg	p.G464R	ENST00000288602	NM_004333.4	464	Gga/Aga	11/18	0.336830107588154	3	FACETS	1	0.872	1	0.336	0.29	0.386	CLONAL	1	TRUE	0	0.560510984310205	3		786	249	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	143	565	3	ENST00000256196.4:c.68G>T	p.Gly23Val	p.G23V	ENST00000256196		23	gGc/gTc	1/6	0.560510984310205	2	FACETS	0.911	0.848	0.974	0.911	0.848	0.974	CLONAL	2	TRUE	0	0.560510984310205	2		568	280	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501249	140501249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	68	747	0	ENST00000288602.6:c.823G>A	p.Glu275Lys	p.E275K	ENST00000288602	NM_004333.4	275	Gaa/Aaa	6/18	0.336830107588154	3	FACETS	1	0.935	1	0.367	0.322	0.415	CLONAL	1	TRUE	0	0.560510984310205	3		747	282	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931830	39931831	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0021699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	22	456	0	ENST00000378444.4:c.2768dup	p.Phe924IlefsTer22	p.F924Ifs*22	ENST00000378444	NM_001123385.1	923	cca/ccCa	4/15	0.560510984310205	2	FACETS	0.314	0.244	0.395			1	SUBCLONAL	1	TRUE	NA	0.560510984310205	2		456	250	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0021770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	312	398	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.718065538096439	4	FACETS	1	0.979	1	0.361	0.339	0.383	CLONAL	1	FALSE	1	0.718065538096439	4		398	1380	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380350	14380350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	179	217	0	ENST00000256196.4:c.67G>A	p.Gly23Ser	p.G23S	ENST00000256196		23	Ggc/Agc	1/6	0.162391267010632	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.718065538096439	0		217	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578373	7578409	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TCGCTATCTGAGCAGCGCTCATGGTGGGGGCAGCGCC	TCGCTATCTGAGCAGCGCTCATGGTGGGGGCAGCGCC	-	novel	NA	P-0021770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	348	392	0	ENST00000269305.4:c.521_557del	p.Arg174MetfsTer61	p.R174Mfs*61	ENST00000269305	NM_001126112.2	174	aGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCGAt/at	5/11	1	2	FACETS	0.963	0.929	0.997	1	0.997	1	CLONAL	2	FALSE	1	0.718065538096439	2		392	503	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0021770-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	1959	398	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.575763299909063	10	FACETS	1	0.996	1	1	0.999	1	CLONAL	8	TRUE	3	0.575763299909063	10		398	2723	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380350	14380350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021770-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	128	217	0	ENST00000256196.4:c.67G>A	p.Gly23Ser	p.G23S	ENST00000256196		23	Ggc/Agc	1/6	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.575763299909063	2		217	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578373	7578409	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TCGCTATCTGAGCAGCGCTCATGGTGGGGGCAGCGCC	TCGCTATCTGAGCAGCGCTCATGGTGGGGGCAGCGCC	-	novel	NA	P-0021770-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	349	392	0	ENST00000269305.4:c.521_557del	p.Arg174MetfsTer61	p.R174Mfs*61	ENST00000269305	NM_001126112.2	174	aGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCGAt/at	5/11	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.575763299909063	2		392	559	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528094	157528094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	191	475	0	ENST00000346085.5:c.5819C>T	p.Ser1940Leu	p.S1940L	ENST00000346085	NM_020732.3	1940	tCg/tTg	20/20	0.495119572673837	6	FACETS	1	0.96	1	0.526	0.487	0.565	CLONAL	2	TRUE	2	0.495119572673837	6		475	730	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685283	89685283	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1554897262	NA	P-0021983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	84	268	0	ENST00000371953.3:c.178A>T	p.Lys60Ter	p.K60*	ENST00000371953	NM_000314.4	60	Aag/Tag	3/9	0.49685085058134	2	FACETS	0.87	0.786	0.955	0.87	0.786	0.955	CLONAL	2	TRUE	0	0.495119572673837	2		268	195	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046701	42046701	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	303	592	0	ENST00000219905.7:c.7075T>A	p.Ser2359Thr	p.S2359T	ENST00000219905	NM_001164273.1	2359	Tca/Aca	18/24	0.49685085058134	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.495119572673837	2		592	578	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72863707	72863707	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1313136028	NA	P-0021983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	185	544	0	ENST00000268489.5:c.3500A>C	p.Glu1167Ala	p.E1167A	ENST00000268489	NM_006885.3	1167	gAg/gCg	5/10	0.242364330033526	5	FACETS	0.928	0.859	0.998	0.618	0.573	0.666	INDETERMINATE	2	TRUE	2	0.495119572673837	5		544	702	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579359	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGAAA	novel	NA	P-0021983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	570	697	0	ENST00000269305.4:c.324_328dup	p.Arg110LeufsTer15	p.R110Lfs*15	ENST00000269305	NM_001126112.2	110	cgt/cTTTCCgt	4/11	0.48555563507282	4	FACETS	0.915	0.886	0.943	0.915	0.886	0.943	CLONAL	4	TRUE	0	0.495119572673837	4		697	941	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248569	10248569	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	261	674	0	ENST00000340748.4:c.4184G>T	p.Trp1395Leu	p.W1395L	ENST00000340748		1395	tGg/tTg	35/40	0.495119572673837	6	FACETS	1	0.943	1	0.503	0.471	0.536	CLONAL	2	TRUE	2	0.495119572673837	6		674	1043	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451758	29451758	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1340992656	NA	P-0021983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	216	586	0	ENST00000389048.3:c.2807G>T	p.Gly936Val	p.G936V	ENST00000389048	NM_004304.4	936	gGa/gTa	16/29	0.495119572673837	6	FACETS	0.984	0.916	1	0.492	0.458	0.528	CLONAL	2	TRUE	2	0.495119572673837	6		586	882	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916661	178916661	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	162	390	0	ENST00000263967.3:c.48G>A	p.Met16Ile	p.M16I	ENST00000263967	NM_006218.2	16	atG/atA	2/21	0.495119572673837	9	FACETS	1	0.953	1			1	CLONAL	2	TRUE	NA	0.495119572673837	9		390	848	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163276	32163276	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	343	868	1	ENST00000375023.3:c.5950G>T	p.Asp1984Tyr	p.D1984Y	ENST00000375023	NM_004557.3	1984	Gac/Tac	30/30	0.495119572673837	6	FACETS	1	0.953	1	0.504	0.476	0.533	CLONAL	2	TRUE	2	0.495119572673837	6		869	1367	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115923	8115924	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0021983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	125	402	0	ENST00000346208.3:c.1270_1271del	p.Pro424AlafsTer82	p.P424Afs*82	ENST00000346208		423	caCCcg/cacg	6/6	0.495119572673837	7	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.495119572673837	7		402	792	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571997	64571997	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	297	745	0	ENST00000312049.6:c.1642G>T	p.Gly548Cys	p.G548C	ENST00000312049	NM_130799.2	548	Ggt/Tgt	10/10	0.495119572673837	5	FACETS	0.904	0.85	0.958			1	CLONAL	2	TRUE	NA	0.495119572673837	5		745	1157	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712914	43712914	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs200611664	NA	P-0021983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	207	606	0	ENST00000382044.4:c.4270C>G	p.Pro1424Ala	p.P1424A	ENST00000382044	NM_001141980.1	1424	Ccc/Gcc	21/28	0.49685085058134	2	FACETS	0.991	0.932	1	0.991	0.932	1	CLONAL	2	TRUE	0	0.495119572673837	2		606	422	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47079200	47079200	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	220	512	0	ENST00000409792.3:c.7306G>C	p.Glu2436Gln	p.E2436Q	ENST00000409792	NM_014159.6	2436	Gag/Cag	18/21	0.492808494327426	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.495119572673837	2		512	432	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64289965	64289965	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	45	431	0	ENST00000370651.3:c.408G>C	p.Lys136Asn	p.K136N	ENST00000370651	NM_003463.4	136	aaG/aaC	6/6	0.215317295762228	2	FACETS	0.794	0.672	0.926	0.397	0.336	0.463	INDETERMINATE	1	TRUE	0	0.427870051463066	2		431	265	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6442018	6442018	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	63	189	0	ENST00000356142.4:c.577C>T	p.Arg193Ter	p.R193*	ENST00000356142	NM_018890.3	193	Cga/Tga	7/7	0.428375985825655	4	FACETS	1	0.946	1	0.39	0.339	0.445	CLONAL	1	TRUE	1	0.427870051463066	4		189	359	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220539	133220539	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	112	588	0	ENST00000320574.5:c.4174A>G	p.Asn1392Asp	p.N1392D	ENST00000320574	NM_006231.2	1392	Aac/Gac	33/49	0.465255663982906	5	FACETS	0.957	0.862	1			1	CLONAL	1	TRUE	NA	0.602893905628649	5		588	739	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285806	87285806	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	324	695	0	ENST00000277120.3:c.143C>A	p.Pro48His	p.P48H	ENST00000277120		48	cCt/cAt	2/19	0.582369288208438	4	FACETS	0.885	0.843	0.926	0.885	0.843	0.926	CLONAL	3	TRUE	1	0.602893905628649	4		695	649	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922313	39922330	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACACAGGCAAGCCTAAAT	ACACAGGCAAGCCTAAAT	-	novel	NA	P-0022056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	65	198	0	ENST00000378444.4:c.3848-6_3859del		p.X1283_splice	ENST00000378444	NM_001123385.1	1283		9/15	0.300456677071505	2	FACETS	0.781	0.698	0.865			1	INDETERMINATE	2	TRUE	NA	0.602893905628649	2		198	138	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0022072-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	390	692	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	1	2	FACETS	0.974	0.927	1	0.974	0.927	1	CLONAL	1	TRUE	1	0.720326543059236	2		692	1112	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121913370	NA	P-0022072-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	194	286	0	ENST00000288602.6:c.1742A>G	p.Asn581Ser	p.N581S	ENST00000288602	NM_004333.4	581	aAt/aGt	15/18	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.720326543059236	2		286	503	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338671	70338671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022072-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	323	469	1	ENST00000374080.3:c.67G>T	p.Asp23Tyr	p.D23Y	ENST00000374080		23	Gat/Tat	1/45	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.720326543059236	2		470	815	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007499	62007499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022072-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	281	493	0	ENST00000392795.3:c.368G>A	p.Cys123Tyr	p.C123Y	ENST00000392795	NM_001039933.1	123	tGt/tAt	3/6	1	2	FACETS	0.996	0.94	1	0.996	0.94	1	CLONAL	1	TRUE	1	0.720326543059236	2		493	783	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0022072-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	536	509	1	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	0.720326543059236	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.720326543059236	2		510	737	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18975056	18975056	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022072-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	147	217	0	ENST00000262803.5:c.2853C>A	p.Ser951Arg	p.S951R	ENST00000262803	NM_002911.3	951	agC/agA	20/24	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.720326543059236	2		217	398	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305252	39305252	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	93	735	0	ENST00000373001.3:c.1173C>G	p.His391Gln	p.H391Q	ENST00000373001	NM_022157.3	391	caC/caG	7/7	0.271459224103654	3	FACETS	0.991	0.88	1	0.496	0.44	0.555	CLONAL	1	TRUE	1	0.254585990438837	3		735	831	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627584	37627584	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	43	720	0	ENST00000447079.4:c.1499C>G	p.Thr500Arg	p.T500R	ENST00000447079	NM_015083.1	500	aCa/aGa	2/14	0.21228442049028	4	FACETS	1	0.935	1	0.618	0.519	0.727	CLONAL	1	TRUE	2	0.254585990438837	4		720	343	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0022291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	292	385	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.418112994065041	2	FACETS	0.975	0.923	1	0.975	0.923	1	CLONAL	2	TRUE	0	0.418112994065041	2		385	716	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220578	1220578	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0022291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	269	488	0	ENST00000326873.7:c.598-2A>T		p.X200_splice	ENST00000326873	NM_000455.4	200			0.343924038268711	2	FACETS	0.811	0.764	0.86	0.811	0.764	0.86	CLONAL	2	TRUE	0	0.418112994065041	2		488	793	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781380	135781380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751125011	NA	P-0022291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	190	581	2	ENST00000298552.3:c.1585G>A	p.Ala529Thr	p.A529T	ENST00000298552	NM_001162426.1	529	Gcc/Acc	15/23	0.29619749351557	2	FACETS	1	0.95	1	0.518	0.479	0.558	CLONAL	1	TRUE	0	0.418112994065041	2		583	878	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36826887	36826887	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	272	594	0	ENST00000373129.3:c.47G>T	p.Arg16Met	p.R16M	ENST00000373129	NM_032017.1	16	aGg/aTg	3/12	0.418154856763067	3	FACETS	1	0.993	1	0.746	0.7	0.792	CLONAL	1	TRUE	1	0.418112994065041	3		594	1055	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651643	206651643	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1236	178	770	0	ENST00000367120.3:c.953A>T	p.Gln318Leu	p.Q318L	ENST00000367120	NM_014002.3	318	cAg/cTg	9/22	0.164171363281407	4	FACETS	0.854	0.785	0.927	0.427	0.392	0.464	INDETERMINATE	1	TRUE	2	0.418112994065041	4		770	1414	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186757	108186757	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs864622251	NA	P-0022291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	56	496	0	ENST00000278616.4:c.6115G>T	p.Glu2039Ter	p.E2039*	ENST00000278616	NM_000051.3	2039	Gaa/Taa	42/63	0.418154856763067	4	FACETS	0.352	0.3	0.409	0.117	0.1	0.137	SUBCLONAL	1	TRUE	1	0.418112994065041	4		496	1078	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218027	108218027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555139531	NA	P-0022291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	249	391	0	ENST00000278616.4:c.8606G>A	p.Gly2869Asp	p.G2869D	ENST00000278616	NM_000051.3	2869	gGt/gAt	59/63	0.418154856763067	4	FACETS	1	0.987	1	0.782	0.735	0.83	CLONAL	2	TRUE	1	0.418112994065041	4		391	720	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302935	15302936	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0022291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	366	623	2	ENST00000263388.2:c.514_515delinsTT	p.Gly172Phe	p.G172F	ENST00000263388	NM_000435.2	172	GGc/TTc	4/33	0.343924038268711	2	FACETS	0.822	0.781	0.864	0.822	0.781	0.864	CLONAL	2	TRUE	0	0.418112994065041	2		625	1065	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388732	31388732	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0022291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	85	460	0	ENST00000328111.2:c.1996+1G>A		p.X666_splice	ENST00000328111	NM_006892.3	666			0.418154856763067	3	FACETS	0.538	0.474	0.606	0.269	0.237	0.303	SUBCLONAL	1	TRUE	1	0.418112994065041	3		460	914	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577095	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519984	NA	P-0022380-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	284	677	0	ENST00000269305.4:c.843C>A	p.Asp281Glu	p.D281E	ENST00000269305	NM_001126112.2	281	gaC/gaA	8/11	0.221924070981492	2	FACETS	1	0.992	1	0.69	0.649	0.733	INDETERMINATE	1	TRUE	0	0.373371830009625	2		677	1102	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272105	15272105	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372833545	NA	P-0022380-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	117	669	1	ENST00000263388.2:c.6334G>A	p.Gly2112Ser	p.G2112S	ENST00000263388	NM_000435.2	2112	Ggt/Agt	33/33	1	2	FACETS	0.581	0.523	0.643	0.581	0.523	0.643	SUBCLONAL	1	TRUE	1	0.373371830009625	2		670	1078	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729399	41729399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022380-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	140	484	2	ENST00000242208.4:c.1130G>A	p.Arg377His	p.R377H	ENST00000242208	NM_002192.2	377	cGc/cAc	3/3	1	2	FACETS	0.754	0.686	0.826	0.754	0.686	0.826	SUBCLONAL	1	TRUE	1	0.373371830009625	2		486	994	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933337	100933337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767006543	NA	P-0022380-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	231	494	0	ENST00000325455.5:c.2053C>T	p.Pro685Ser	p.P685S	ENST00000325455	NM_001202474.3	685	Cca/Tca	4/8	0.373371830009625	4	FACETS	1	0.992	1	0.49	0.457	0.526	CLONAL	1	TRUE	1	0.373371830009625	4		494	1155	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40872362	40872362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022380-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	236	632	1	ENST00000428826.2:c.593C>T	p.Ser198Leu	p.S198L	ENST00000428826		198	tCa/tTa	7/21	0.202267292545575	3	FACETS	1	0.984	1	0.587	0.547	0.629	INDETERMINATE	1	TRUE	1	0.373371830009625	3		633	1277	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998189	169998189	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022380-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	110	608	0	ENST00000295797.4:c.880G>C	p.Glu294Gln	p.E294Q	ENST00000295797	NM_002740.5	294	Gag/Cag	9/18	1	2	FACETS	0.565	0.506	0.627	0.565	0.506	0.627	SUBCLONAL	1	TRUE	1	0.373371830009625	2		608	1043	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934144	39934144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375342424	NA	P-0022380-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	103	468	0	ENST00000378444.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000378444	NM_001123385.1	152	cCg/cTg	4/15	1	2	FACETS	0.613	0.548	0.683	0.613	0.548	0.683	SUBCLONAL	1	TRUE	1	0.373371830009625	2		468	900	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123324067	123324067	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022380-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	83	490	0	ENST00000358487.5:c.403G>T	p.Asp135Tyr	p.D135Y	ENST00000358487	NM_000141.4	135	Gat/Tat	4/18	0.299030507155325	3	FACETS	0.584	0.514	0.659	0.292	0.257	0.33	SUBCLONAL	1	TRUE	1	0.373371830009625	3		490	903	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370674	225370674	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022380-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	54	302	0	ENST00000264414.4:c.1205G>A	p.Gly402Glu	p.G402E	ENST00000264414	NM_003590.4	402	gGg/gAg	8/16	1	2	FACETS	0.462	0.394	0.537	0.462	0.394	0.537	SUBCLONAL	1	TRUE	1	0.373371830009625	2		302	626	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024096	112024096	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022380-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	83	411	0	ENST00000368678.4:c.689A>T	p.His230Leu	p.H230L	ENST00000368678		230	cAt/cTt	7/13	0.326805111478335	2	FACETS	0.567	0.5	0.639	0.284	0.25	0.32	SUBCLONAL	1	TRUE	0	0.373371830009625	2		411	784	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517878	8517878	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022380-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	24	314	0	ENST00000356435.5:c.1513A>T	p.Ser505Cys	p.S505C	ENST00000356435		505	Agt/Tgt	10/35	0.373371830009625	1	FACETS	0.24	0.187	0.3	0.24	0.187	0.3	SUBCLONAL	1	TRUE	0	0.373371830009625	1		314	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	661	925	1	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	2	TRUE	NA	0.612195541373971	2		926	1061	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101031	4101031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375843855	NA	P-0022593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	427	624	2	ENST00000262948.5:c.691C>T	p.Arg231Cys	p.R231C	ENST00000262948	NM_030662.3	231	Cgc/Tgc	6/11	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	2	TRUE	NA	0.612195541373971	2		626	692	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226550815	226550815	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0022593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1404	256	690	1	ENST00000366794.5:c.2833A>T	p.Lys945Ter	p.K945*	ENST00000366794	NM_001618.3	945	Aag/Tag	21/23	0.316946042484613	6	FACETS	1	0.98	1	0.374	0.348	0.4	INDETERMINATE	1	TRUE	3	0.612195541373971	6		691	1660	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28624345	28624348	+	frameshift_variant	Frame_Shift_Del	DEL	CTTT	CTTT	-	novel	NA	P-0022593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	162	653	0	ENST00000241453.7:c.626_629del	p.Glu209ValfsTer20	p.E209Vfs*20	ENST00000241453	NM_004119.2	209	gAAAGt/gt	6/24	0.516287193687429	3	FACETS	0.784	0.719	0.851	0.392	0.359	0.426	SUBCLONAL	1	TRUE	1	0.612195541373971	3		653	882	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243482	41243482	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886040193	NA	P-0022593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	336	820	0	ENST00000357654.3:c.4066C>T	p.Gln1356Ter	p.Q1356*	ENST00000357654	NM_007294.3	1356	Caa/Taa	10/23	0.612195541373971	2	FACETS	1	0.959	1	0.507	0.48	0.535	CLONAL	1	TRUE	0	0.612195541373971	2		820	1082	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27209173	27209173	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	228	791	0	ENST00000380036.4:c.2630G>A	p.Cys877Tyr	p.C877Y	ENST00000380036	NM_000459.3	877	tGt/tAt	16/23	0.612195541373971	2	FACETS	0.856	0.799	0.915	0.428	0.399	0.458	CLONAL	1	TRUE	0	0.612195541373971	2		791	870	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129208	152129208	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1997	299	942	1	ENST00000206249.3:c.161A>T	p.Tyr54Phe	p.Y54F	ENST00000206249	NM_000125.3	54	tAc/tTc	1/8	0.612195541373971	6	FACETS	0.946	0.887	1	0.237	0.221	0.252	CLONAL	1	TRUE	2	0.612195541373971	6		943	2296	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	155	433	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	0.44	2		433	678	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	168	795	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.909	0.836	0.985	0.909	0.836	0.985	CLONAL	1	TRUE	1	0.44	2		801	840	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	22	318	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.185	0.142	0.234	0.185	0.142	0.234	SUBCLONAL	1	TRUE	1	0.44	2		318	542	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954198	48954198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123331	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	79	283	0	ENST00000267163.4:c.1399C>T	p.Arg467Ter	p.R467*	ENST00000267163	NM_000321.2	467	Cga/Tga	15/27	1	2	FACETS	0.839	0.741	0.943	0.839	0.741	0.943	CLONAL	1	TRUE	1	0.44	2		283	428	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	218	508	0	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.44	2		508	864	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771932	135771932	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755396992	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	110	365	0	ENST00000298552.3:c.3185G>A	p.Arg1062Gln	p.R1062Q	ENST00000298552	NM_001162426.1	1062	cGg/cAg	23/23	1	2	FACETS	0.982	0.887	1	0.982	0.887	1	CLONAL	1	TRUE	1	0.44	2		365	509	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856093	68856093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121964878	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	172	504	0	ENST00000261769.5:c.1901C>T	p.Ala634Val	p.A634V	ENST00000261769	NM_004360.3	634	gCg/gTg	12/16	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.44	2		504	751	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821594	72821596	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	rs374416547	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	13	67	1	ENST00000268489.5:c.10579_10581del	p.Gly3527del	p.G3527del	ENST00000268489	NM_006885.3	3527	GGC/-	10/10	1	2	FACETS	0.497	0.357	0.664	0.497	0.357	0.664	SUBCLONAL	1	TRUE	1	0.44	2		68	119	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747889	41747889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772358257	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	218	412	1	ENST00000226382.2:c.880G>A	p.Val294Ile	p.V294I	ENST00000226382	NM_003924.3	294	Gtc/Atc	3/3	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.44	2		413	816	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919007	50919007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1483458869	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	223	526	0	ENST00000440232.2:c.2744C>T	p.Ala915Val	p.A915V	ENST00000440232	NM_002691.3	915	gCg/gTg	22/27	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.44	2		526	833	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217705	7217707	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs757139280	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	107	381	0	ENST00000380728.2:c.220_222del	p.Glu74del	p.E74del	ENST00000380728		74	GAG/-	4/11	1	2	FACETS	0.83	0.746	0.918	0.83	0.746	0.918	CLONAL	1	TRUE	1	0.44	2		381	586	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930730	32930730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs74047012	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	186	462	0	ENST00000380152.3:c.7601C>T	p.Ala2534Val	p.A2534V	ENST00000380152		2534	gCg/gTg	15/27	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.44	2		462	673	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324132	31324132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41561215	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	84	413	0	ENST00000412585.2:c.431G>A	p.Gly144Asp	p.G144D	ENST00000412585	NM_005514.6	144	gGc/gAc	3/8	1	2	FACETS	0.784	0.695	0.879	0.784	0.695	0.879	SUBCLONAL	1	TRUE	1	0.44	2		413	487	SUCCESS
RET	5979	MSKCC	GRCh37	10	43572750	43572755	+	inframe_deletion	In_Frame_Del	DEL	TGCTGC	TGCTGC	-	novel	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	60	172	0	ENST00000355710.3:c.53_58del	p.Leu18_Leu19del	p.L18_L19del	ENST00000355710	NM_020975.4	15	tTGCTGCtg/ttg	1/20	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.44	2		172	242	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246643	46246643	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	62	170	0	ENST00000334344.6:c.4737G>T	p.Gln1579His	p.Q1579H	ENST00000334344	NM_152641.2	1579	caG/caT	15/21	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.44	2		170	245	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285628	46285629	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	154	387	0	ENST00000334344.6:c.4989dup	p.Pro1664SerfsTer10	p.P1664Sfs*10	ENST00000334344	NM_152641.2	1663	tat/taTt	17/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.44	2		387	580	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109746	115109746	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	174	594	0	ENST00000257566.3:c.2132G>A	p.Cys711Tyr	p.C711Y	ENST00000257566	NM_016569.3	711	tGc/tAc	8/8	1	2	FACETS	0.821	0.756	0.89	0.821	0.756	0.89	CLONAL	1	TRUE	1	0.44	2		594	963	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434360	121434360	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	151	491	0	ENST00000257555.6:c.1124G>C	p.Gly375Ala	p.G375A	ENST00000257555		375	gGc/gCc	6/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.44	2		491	581	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032405	10032405	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	89	210	0	ENST00000330684.3:c.418C>A	p.Pro140Thr	p.P140T	ENST00000330684	NM_001134407.1	140	Ccg/Acg	3/13	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.44	2		210	336	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829497	72829497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761486040	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	103	415	1	ENST00000268489.5:c.7084G>A	p.Asp2362Asn	p.D2362N	ENST00000268489	NM_006885.3	2362	Gac/Aac	9/10	1	2	FACETS	0.763	0.684	0.846	0.763	0.684	0.846	SUBCLONAL	1	TRUE	1	0.44	2		416	614	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118881	70118882	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	144	453	0	ENST00000245479.2:c.454dup	p.Arg152ProfsTer100	p.R152Pfs*100	ENST00000245479	NM_000346.3	151	-/C	2/3	1	2	FACETS	0.963	0.88	1	0.963	0.88	1	CLONAL	1	TRUE	1	0.44	2		453	680	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40739787	40739787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769806554	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	270	600	0	ENST00000392038.2:c.1438C>T	p.Arg480Cys	p.R480C	ENST00000392038	NM_001626.4	480	Cgc/Tgc	14/14	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.44	2		600	1003	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716301	52716301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	188	385	1	ENST00000322088.6:c.745C>T	p.Arg249Cys	p.R249C	ENST00000322088	NM_014225.5	249	Cgc/Tgc	6/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.44	2		386	682	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920652	96920652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767739392	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	167	451	0	ENST00000258439.3:c.328G>A	p.Ala110Thr	p.A110T	ENST00000258439	NM_001193304.2	110	Gct/Act	3/4	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.44	2		451	733	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172161	99172161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs571358585	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	171	432	0	ENST00000074304.5:c.1727C>T	p.Pro576Leu	p.P576L	ENST00000074304	NM_001134224.1	576	cCg/cTg	17/26	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.44	2		432	631	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215674206	215674206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	102	504	0	ENST00000260947.4:c.88G>A	p.Gly30Ser	p.G30S	ENST00000260947	NM_000465.2	30	Ggt/Agt	1/11	1	2	FACETS	0.681	0.609	0.757	0.681	0.609	0.757	SUBCLONAL	1	TRUE	1	0.44	2		504	681	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39721125	39721125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	136	358	0	ENST00000361337.2:c.628C>T	p.Arg210Cys	p.R210C	ENST00000361337	NM_003286.2	210	Cgc/Tgc	9/21	1	2	FACETS	0.997	0.91	1	0.997	0.91	1	CLONAL	1	TRUE	1	0.44	2		358	620	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755786	39755786	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	95	292	0	ENST00000288319.7:c.979T>C	p.Ser327Pro	p.S327P	ENST00000288319	NM_182918.3	327	Tcc/Ccc	10/10	0.3	2	FACETS	1	0.927	1	0.522	0.467	0.579	CLONAL	1	TRUE	0	0.44	2		292	414	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521384	187521384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375087606	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	128	376	1	ENST00000441802.2:c.11771G>A	p.Arg3924His	p.R3924H	ENST00000441802	NM_005245.3	3924	cGc/cAc	22/27	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.44	2		377	532	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629114	187629114	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	83	395	0	ENST00000441802.2:c.1868T>C	p.Val623Ala	p.V623A	ENST00000441802	NM_005245.3	623	gTa/gCa	2/27	1	2	FACETS	0.562	0.496	0.633	0.562	0.496	0.633	SUBCLONAL	1	TRUE	1	0.44	2		395	671	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226016	226016	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	25	95	0	ENST00000264932.6:c.475C>T	p.Pro159Ser	p.P159S	ENST00000264932	NM_004168.2	159	Ccg/Tcg	5/15	1	2	FACETS	0.947	0.759	1	0.947	0.759	1	CLONAL	1	TRUE	1	0.44	2		95	120	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268940	55268940	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	204	574	0	ENST00000275493.2:c.3006G>T	p.Met1002Ile	p.M1002I	ENST00000275493	NM_005228.3	1002	atG/atT	25/28	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.44	2		574	860	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513348	106513348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528601604	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	101	293	1	ENST00000359195.3:c.2252C>T	p.Ser751Leu	p.S751L	ENST00000359195	NM_002649.2	751	tCg/tTg	4/11	1	2	FACETS	0.881	0.79	0.977	0.881	0.79	0.977	CLONAL	1	TRUE	1	0.44	2		294	521	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169575	27169575	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	181	567	0	ENST00000380036.4:c.576G>T	p.Arg192Ser	p.R192S	ENST00000380036	NM_000459.3	192	agG/agT	4/23	1	2	FACETS	0.978	0.903	1	0.978	0.903	1	CLONAL	1	TRUE	1	0.44	2		567	841	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76812935	76812935	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	137	431	1	ENST00000373344.5:c.6686C>A	p.Pro2229His	p.P2229H	ENST00000373344	NM_000489.3	2229	cCc/cAc	30/35	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.44	2		432	610	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019795	123019795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745844064	NA	P-0022648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	136	432	0	ENST00000355640.3:c.283G>A	p.Gly95Ser	p.G95S	ENST00000355640		95	Ggc/Agc	2/7	1	2	FACETS	0.927	0.845	1	0.927	0.845	1	CLONAL	1	TRUE	1	0.44	2		432	667	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223860	36223860	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	146	947	0	ENST00000222270.7:c.6410C>T	p.Pro2137Leu	p.P2137L	ENST00000222270	NM_014727.1	2137	cCc/cTc	28/37	0.664603563768498	3	FACETS	0.987	0.905	1	0.494	0.452	0.537	CLONAL	1	TRUE	1	0.664603563768498	3		947	593	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs786201057	NA	P-0022884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	324	849	3	ENST00000269305.4:c.374C>A	p.Thr125Lys	p.T125K	ENST00000269305	NM_001126112.2	125	aCg/aAg	4/11	0.660658649093935	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.678500578105409	2		852	472	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78426041	78426041	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	221	851	1	ENST00000370768.2:c.1484G>T	p.Gly495Val	p.G495V	ENST00000370768	NM_003902.3	495	gGc/gTc	15/20	0.125887913691624	4	FACETS	0.866	0.811	0.923	0.866	0.811	0.923	INDETERMINATE	2	TRUE	2	0.678500578105409	4		852	631	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0023085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	31	298	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.356353999885804	3	FACETS	0.372	0.301	0.452	0.186	0.15	0.226	SUBCLONAL	1	TRUE	1	0.579787948334669	3		298	371	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0023085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	8	525	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.554103358267845	0	FACETS	0.045	0.029	0.067			1	SUBCLONAL	1	TRUE	0	0.579787948334669	0		525	255	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199619	16199619	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1425005992	NA	P-0023085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	140	607	0	ENST00000375759.3:c.392G>A	p.Arg131Gln	p.R131Q	ENST00000375759	NM_015001.2	131	cGg/cAg	2/15	0.543462528216781	3	FACETS	1	0.933	1	0.512	0.468	0.558	CLONAL	1	TRUE	1	0.579787948334669	3		607	608	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466824	57466826	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0023085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	57	410	0	ENST00000371085.3:c.46_48del	p.Glu16del	p.E16del	ENST00000371085	NM_000516.4	15	GAG/-	1/13	0.498201317754408	4	FACETS	0.51	0.437	0.59	0.17	0.145	0.197	SUBCLONAL	1	TRUE	1	0.579787948334669	4		410	609	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606487	93606487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	230	898	0	ENST00000375746.1:c.307C>T	p.Leu103Phe	p.L103F	ENST00000375746	NM_001174167.1	103	Ctc/Ttc	2/14	0.700620995475759	3	FACETS	1	0.949	1	0.34	0.317	0.363	CLONAL	1	TRUE	0	0.700620995475759	3		898	870	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398280	25398281	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCA	novel	NA	P-0023106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	48	799	0	ENST00000311936.3:c.36_38dup	p.Gly13dup	p.G13dup	ENST00000311936	NM_004985.3	13	ggc/ggTGGc	2/5	0.297984333335427	7	FACETS	0.892	0.752	1	0.178	0.15	0.21	CLONAL	1	TRUE	2	0.23	7		799	737	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503785	186503787	+	inframe_deletion	In_Frame_Del	DEL	TAT	TAT	-	rs767682413	NA	P-0023106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	20	778	0	ENST00000323963.5:c.463_465del	p.Ile155del	p.I155del	ENST00000323963		154	caTATt/cat	5/11	1	2	FACETS	0.466	0.356	0.596	0.466	0.356	0.596	SUBCLONAL	1	TRUE	1	0.23	2		778	373	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797265	135797265	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	21	445	0	ENST00000298552.3:c.604T>G	p.Phe202Val	p.F202V	ENST00000298552	NM_001162426.1	202	Ttt/Gtt	7/23	1	2	FACETS	0.607	0.467	0.769	0.607	0.467	0.769	SUBCLONAL	1	TRUE	1	0.23	2		445	301	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0023275-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	252	298	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.42507627038927	3	FACETS	1	0.993	1	0.735	0.688	0.783	CLONAL	1	TRUE	1	0.433727636477964	3		298	962	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0023446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	44	586	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.3	3	FACETS	0.55	0.46	0.651	0.275	0.23	0.326	SUBCLONAL	1	TRUE	1	0.24	3		587	746	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599320	55599320	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913506	NA	P-0023446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	14	672	0	ENST00000288135.5:c.2446G>C	p.Asp816His	p.D816H	ENST00000288135	NM_000222.2	816	Gac/Cac	17/21	0.3	1	FACETS	0.221	0.159	0.297	0.221	0.159	0.297	SUBCLONAL	1	TRUE	0	0.24	1		672	465	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356134	66356134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756357402	NA	P-0023854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	29	381	0	ENST00000273854.3:c.1363C>T	p.Arg455Trp	p.R455W	ENST00000273854	NM_004439.5	455	Cgg/Tgg	5/18	0.244382505399304	3	FACETS	0.6	0.482	0.734	0.3	0.241	0.367	SUBCLONAL	1	TRUE	1	0.317162822200317	3		381	353	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352680	118352680	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	58	658	1	ENST00000534358.1:c.3885C>A	p.Ser1295Arg	p.S1295R	ENST00000534358	NM_005933.3	1295	agC/agA	7/36	1	2	FACETS	0.429	0.367	0.496	0.429	0.367	0.496	SUBCLONAL	1	TRUE	1	0.343489262693655	2		659	788	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948288	71948288	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	86	1100	0	ENST00000298229.2:c.3000G>T	p.Glu1000Asp	p.E1000D	ENST00000298229	NM_001567.3	1000	gaG/gaT	26/28	0.48301125843786	2	FACETS	0.628	0.556	0.704	0.314	0.278	0.352	SUBCLONAL	1	TRUE	0	0.48301125843786	2		1100	567	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40745953	40745953	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	125	739	1	ENST00000392038.2:c.638C>T	p.Thr213Ile	p.T213I	ENST00000392038	NM_001626.4	213	aCt/aTt	7/14	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.48301125843786	2		740	509	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	239	297	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.978	0.918	1	0.978	0.918	1	CLONAL	1	TRUE	1	0.699123448806919	2		297	699	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0024553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	255	485	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	1	2	FACETS	0.999	0.94	1	0.999	0.94	1	CLONAL	1	TRUE	1	0.699123448806919	2		485	730	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690406	117690406	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs762367712	NA	P-0024553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	556	451	0	ENST00000369458.3:c.725-2A>G		p.X242_splice	ENST00000369458	NM_024626.3	242			NA	2	FACETS	1	0.977	1			1	INDETERMINATE	2	TRUE	NA	0.699123448806919	2		451	791	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150290	108150291	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0024553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	217	434	0	ENST00000278616.4:c.3359_3360del	p.Phe1120Ter	p.F1120*	ENST00000278616	NM_000051.3	1119	gcTTtt/gctt	23/63	0.699123448806919	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.699123448806919	1		434	380	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740458	58740458	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	337	629	0	ENST00000305921.3:c.1363del	p.Glu455ArgfsTer2	p.E455Rfs*2	ENST00000305921	NM_003620.3	455	Gag/ag	6/6	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.699123448806919	2		629	912	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132422	11132422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	426	703	1	ENST00000358026.2:c.2638G>A	p.Val880Met	p.V880M	ENST00000358026	NM_001128849.1	880	Gtg/Atg	19/36	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.699123448806919	2		704	1107	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525131	157525131	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0024553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	106	201	0	ENST00000346085.5:c.5025+1G>T		p.X1675_splice	ENST00000346085	NM_020732.3	1675			1	2	FACETS	0.975	0.885	1	0.975	0.885	1	CLONAL	1	TRUE	1	0.699123448806919	2		201	311	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482181	87482181	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	114	730	1	ENST00000277120.3:c.1468G>T	p.Asp490Tyr	p.D490Y	ENST00000277120		490	Gat/Tat	14/19	0.699123448806919	1	FACETS	0.358	0.323	0.395	0.358	0.323	0.395	SUBCLONAL	1	TRUE	0	0.699123448806919	1		731	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579448	7579448	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	215	585	0	ENST00000269305.4:c.239del	p.Pro80LeufsTer43	p.P80Lfs*43	ENST00000269305	NM_001126112.2	80	cCt/ct	4/11	0.622640341718182	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.622640341718182	1		585	424	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591147	67591298	+	splice_donor_variant,splice_acceptor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	CTTGATGTAAGTATTTGAAATGGAATCCTATACATGAATAATTGGTGATTGCTACAATTCAGGATGAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGGTTGACTCAAAAAGGTGTTCGGCAAAAGAAGTTGAACGAGTGGTTGGG	CTTGATGTAAGTATTTGAAATGGAATCCTATACATGAATAATTGGTGATTGCTACAATTCAGGATGAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGGTTGACTCAAAAAGGTGTTCGGCAAAAGAAGTTGAACGAGTGGTTGGG	-	novel	NA	P-0024872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	117	465	0	ENST00000274335.5:c.1741_1797del		p.X581_splice	ENST00000274335		581	taCTTGATGTAAGTATTTGAAATGGAATCCTATACATGAATAATTGGTGATTGCTACAATTCAGGATGAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGGTTGACTCAAAAAGGTGTTCGGCAAAAGAAGTTGAACGAGTGGTTGGGc/tac	12-13/15	1	2	FACETS	0.845	0.767	0.925	0.845	0.767	0.925	CLONAL	1	TRUE	1	0.622640341718182	2		465	445	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0024931-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	20	559	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.19563250205875	4	FACETS	0.438	0.335	0.56	0.219	0.167	0.28	INDETERMINATE	1	FALSE	2	0.361324628163941	4		559	344	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480611	120480611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146014987	NA	P-0024931-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	29	468	0	ENST00000256646.2:c.3206G>A	p.Arg1069Gln	p.R1069Q	ENST00000256646	NM_024408.3	1069	cGg/cAg	20/34	1	2	FACETS	0.435	0.349	0.533	0.435	0.349	0.533	SUBCLONAL	1	FALSE	1	0.361324628163941	2		468	369	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624263	89624263	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	60	419	1	ENST00000371953.3:c.40del	p.Arg14GlyfsTer10	p.R14Gfs*10	ENST00000371953	NM_000314.4	13	Aaa/aa	1/9	0.782374920154251	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.81082478670659	2		420	69	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380282	25380282	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	108	711	0	ENST00000311936.3:c.176C>G	p.Ala59Gly	p.A59G	ENST00000311936	NM_004985.3	59	gCa/gGa	3/5	0.760681229648882	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.81082478670659	2		711	132	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559864	29559864	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs371544233	NA	P-0025114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	142	356	0	ENST00000356175.3:c.3461A>T	p.Asn1154Ile	p.N1154I	ENST00000356175	NM_000267.3	1154	aAt/aTt	26/57	0.785776266782767	3	FACETS	0.96	0.918	0.997	0.96	0.918	0.997	CLONAL	3	TRUE	0	0.81082478670659	3		356	171	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923236	26923236	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	43	509	0	ENST00000381527.3:c.232G>C	p.Val78Leu	p.V78L	ENST00000381527	NM_001260.1	78	Gtc/Ctc	3/13	0.750132150745063	4	FACETS	1	0.943	1	0.31	0.264	0.359	CLONAL	1	TRUE	0	0.81082478670659	4		509	155	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7132255	7132255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1041809996	NA	P-0025114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	135	754	0	ENST00000302850.5:c.2756G>A	p.Gly919Glu	p.G919E	ENST00000302850	NM_000208.2	919	gGg/gAg	14/22	0.123152601099838	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.81082478670659	0		754	395	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0025206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	369	519	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.474678937357347	3	FACETS	1	0.976	1	1	0.996	1	CLONAL	3	FALSE	1	0.474678937357347	3		519	627	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309776	104309776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202247756	NA	P-0025206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	210	823	0	ENST00000369902.3:c.367C>T	p.Arg123Cys	p.R123C	ENST00000369902	NM_016169.3	123	Cgt/Tgt	3/12	0.145693071901817	4	FACETS	0.764	0.71	0.819	0.764	0.71	0.819	INDETERMINATE	2	FALSE	2	0.474678937357347	4		823	854	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118708	115118708	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	150	596	2	ENST00000257566.3:c.633C>A	p.Asn211Lys	p.N211K	ENST00000257566	NM_016569.3	211	aaC/aaA	2/8	1	2	FACETS	0.923	0.845	1	0.923	0.845	1	CLONAL	1	FALSE	1	0.474678937357347	2		598	685	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28880885	28880885	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	56	587	0	ENST00000282397.4:c.3745C>G	p.Leu1249Val	p.L1249V	ENST00000282397	NM_002019.4	1249	Ctg/Gtg	29/30	0.145693071901817	4	FACETS	0.577	0.494	0.668	0.289	0.247	0.334	INDETERMINATE	1	FALSE	2	0.474678937357347	4		587	603	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959097	28959097	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	136	507	0	ENST00000282397.4:c.2041G>C	p.Asp681His	p.D681H	ENST00000282397	NM_002019.4	681	Gac/Cac	14/30	0.145693071901817	4	FACETS	1	0.983	1	0.675	0.615	0.737	INDETERMINATE	1	FALSE	2	0.474678937357347	4		507	626	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893389	32893389	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	176	605	0	ENST00000380152.3:c.243C>G	p.Phe81Leu	p.F81L	ENST00000380152		81	ttC/ttG	3/27	0.145693071901817	4	FACETS	1	0.983	1	0.614	0.566	0.665	INDETERMINATE	1	FALSE	2	0.474678937357347	4		605	890	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842716	68842716	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	156	740	1	ENST00000261769.5:c.652G>T	p.Glu218Ter	p.E218*	ENST00000261769	NM_004360.3	218	Gag/Tag	5/16	0.466017302541205	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	FALSE	0	0.474678937357347	1		741	496	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984731	11984731	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	69	346	0	ENST00000353533.5:c.277C>T	p.Gln93Ter	p.Q93*	ENST00000353533	NM_003010.3	93	Caa/Taa	3/11	0.474678937357347	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	FALSE	0	0.474678937357347	1		346	203	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029511	16029511	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	25	536	0	ENST00000268712.3:c.1519C>T	p.Arg507Ter	p.R507*	ENST00000268712	NM_006311.3	507	Cga/Tga	15/46	0.474678937357347	1	FACETS	0.168	0.132	0.21	0.168	0.132	0.21	SUBCLONAL	1	FALSE	0	0.474678937357347	1		536	478	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225360568	225360568	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	66	258	0	ENST00000264414.4:c.1823G>C	p.Arg608Thr	p.R608T	ENST00000264414	NM_003590.4	608	aGa/aCa	13/16	0.474678937357347	1	FACETS	0.968	0.853	1	0.968	0.853	1	CLONAL	1	FALSE	0	0.474678937357347	1		258	219	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164748	106164748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	98	466	0	ENST00000380013.4:c.3616G>A	p.Glu1206Lys	p.E1206K	ENST00000380013	NM_001127208.2	1206	Gaa/Aaa	6/11	1	2	FACETS	0.846	0.758	0.939	0.846	0.758	0.939	CLONAL	1	FALSE	1	0.474678937357347	2		466	488	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157837	27157837	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	30	521	0	ENST00000380036.4:c.61G>C	p.Glu21Gln	p.E21Q	ENST00000380036	NM_000459.3	21	Gaa/Caa	2/23	1	2	FACETS	0.285	0.229	0.349	0.285	0.229	0.349	SUBCLONAL	1	FALSE	1	0.474678937357347	2		521	443	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400002	139400002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	104	853	2	ENST00000277541.6:c.4346G>A	p.Cys1449Tyr	p.C1449Y	ENST00000277541	NM_017617.3	1449	tGc/tAc	25/34	1	2	FACETS	0.787	0.707	0.871	0.787	0.707	0.871	SUBCLONAL	1	FALSE	1	0.474678937357347	2		855	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0025360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	999	689	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.647581732302386	2	FACETS	0.882	0.869	0.895	1	0.998	1	CLONAL	3	TRUE	0	0.647581732302386	2		689	1166	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73995302	73995302	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs752504093	NA	P-0025360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	12	113	0	ENST00000318443.5:c.608A>T	p.Asp203Val	p.D203V	ENST00000318443	NM_001024736.1	203	gAt/gTt	4/10	0.33961333920317	3	FACETS	0.296	0.208	0.403	0.099	0.069	0.135	INDETERMINATE	1	TRUE	0	0.647581732302386	3		113	166	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218414	36218414	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	128	664	0	ENST00000222270.7:c.4193A>C	p.Gln1398Pro	p.Q1398P	ENST00000222270	NM_014727.1	1398	cAg/cCg	16/37	0.647581732302386	3	FACETS	0.437	0.395	0.482	0.218	0.197	0.241	SUBCLONAL	1	TRUE	1	0.647581732302386	3		664	1198	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051645	128051645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	69	608	0	ENST00000285398.2:c.13G>A	p.Asp5Asn	p.D5N	ENST00000285398	NM_000122.1	5	Gac/Aac	1/15	0.329043461088927	3	FACETS	0.288	0.25	0.33	0.096	0.083	0.11	INDETERMINATE	1	TRUE	0	0.647581732302386	3		608	979	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80083466	80083466	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1561478663	NA	P-0025360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	53	749	0	ENST00000265081.6:c.2518G>T	p.Val840Phe	p.V840F	ENST00000265081	NM_002439.4	840	Gtc/Ttc	18/24	1	2	FACETS	0.227	0.193	0.265	0.227	0.193	0.265	SUBCLONAL	1	TRUE	1	0.647581732302386	2		749	721	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948289	71948289	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	119	644	0	ENST00000298229.2:c.3001C>G	p.Pro1001Ala	p.P1001A	ENST00000298229	NM_001567.3	1001	Cca/Gca	26/28	1	2	FACETS	0.939	0.847	1	0.939	0.847	1	CLONAL	1	FALSE	1	0.270190184493256	2		644	938	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426908	6426908	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	240	453	1	ENST00000356142.4:c.101C>G	p.Pro34Arg	p.P34R	ENST00000356142	NM_018890.3	34	cCt/cGt	2/7	0.394480115558907	5	FACETS	0.898	0.839	0.96	0.599	0.559	0.64	CLONAL	2	TRUE	2	0.394480115558907	5		454	1078	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026082-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	189	210	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.802224701343388	2		210	460	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0026082-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	218	374	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.942	0.883	1	0.942	0.883	1	CLONAL	1	TRUE	1	0.802224701343388	2		374	577	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148507438	148507438	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026082-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	500	477	0	ENST00000320356.2:c.2016C>G	p.Phe672Leu	p.F672L	ENST00000320356	NM_004456.4	672	ttC/ttG	17/20	0.802224701343388	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.802224701343388	3		477	844	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787747	135787747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1467020958	NA	P-0026082-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	266	506	0	ENST00000298552.3:c.835C>T	p.His279Tyr	p.H279Y	ENST00000298552	NM_001162426.1	279	Cac/Tac	9/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.802224701343388	2		506	613	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588196	69588196	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026082-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	41	558	0	ENST00000168712.1:c.502G>C	p.Ala168Pro	p.A168P	ENST00000168712	NM_002007.2	168	Gcc/Ccc	3/3	1	2	FACETS	0.14	0.116	0.167	0.14	0.116	0.167	SUBCLONAL	1	TRUE	1	0.802224701343388	2		558	729	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432396	49432396	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783729	NA	P-0026082-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	361	664	0	ENST00000301067.7:c.8743C>T	p.Arg2915Ter	p.R2915*	ENST00000301067	NM_003482.3	2915	Cga/Tga	34/54	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.802224701343388	2		664	879	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720282	43720282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026082-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	286	566	0	ENST00000382044.4:c.3760C>T	p.Leu1254Phe	p.L1254F	ENST00000382044	NM_001141980.1	1254	Ctt/Ttt	18/28	0.273291110846945	3	FACETS	1	0.991	1	0.627	0.592	0.662	INDETERMINATE	1	TRUE	1	0.802224701343388	3		566	797	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788675	3788675	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0026082-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	449	422	0	ENST00000262367.5:c.4281-2A>G		p.X1427_splice	ENST00000262367	NM_004380.2	1427			0.802224701343388	3	FACETS	0.965	0.928	1	0.965	0.928	1	CLONAL	2	TRUE	1	0.802224701343388	3		422	813	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849994	151849994	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026082-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	377	367	0	ENST00000262189.6:c.12322C>T	p.Arg4108Ter	p.R4108*	ENST00000262189	NM_170606.2	4108	Cga/Tga	49/59	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.802224701343388	2		367	457	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224595	123224595	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026082-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	287	251	0	ENST00000218089.9:c.3448C>T	p.Gln1150Ter	p.Q1150*	ENST00000218089	NM_001042749.1	1150	Caa/Taa	31/35	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.802224701343388	1		251	346	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026082-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	67	210	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.818	0.717	0.924	1	0.977	1	CLONAL	2	TRUE	1	0.283483013135795	2		210	289	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0026082-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	20	518	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.228	0.173	0.292	0.228	0.173	0.292	SUBCLONAL	1	TRUE	1	0.283483013135795	2		518	620	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806119	1806119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931614	NA	P-0026082-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	105	661	1	ENST00000260795.2:c.1138G>A	p.Gly380Arg	p.G380R	ENST00000260795		380	Ggg/Agg	8/17	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.283483013135795	2		662	640	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0026082-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	108	666	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.283483013135795	2		666	613	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983059	201983060	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0026082-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	115	693	0	ENST00000359651.3:c.909dup	p.Lys304GlnfsTer167	p.K304Qfs*167	ENST00000359651		303	ttc/ttCc	7/8	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.283483013135795	2		693	703	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416439	29416439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026082-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	121	583	0	ENST00000389048.3:c.4514C>T	p.Pro1505Leu	p.P1505L	ENST00000389048	NM_004304.4	1505	cCa/cTa	29/29	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.283483013135795	2		583	687	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833939	44833939	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026082-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	128	256	0	ENST00000377967.4:c.365del	p.Leu122TyrfsTer58	p.L122Yfs*58	ENST00000377967	NM_021140.2	121	agT/ag	4/29	0.234585705216906	2	FACETS	0.926	0.851	1			1	CLONAL	3	TRUE	NA	0.283483013135795	2		256	325	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184035	123184035	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0026082-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	74	162	0	ENST00000218089.9:c.894-1G>A		p.X298_splice	ENST00000218089	NM_001042749.1	298			1	1	FACETS	0.844	0.756	0.933	1	0.987	1	CLONAL	3	TRUE	0	0.283483013135795	1		162	177	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0026258-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	180	518	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	0.461053785431427	2		518	769	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041621	14041621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026258-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	151	557	0	ENST00000311895.7:c.2168G>A	p.Cys723Tyr	p.C723Y	ENST00000311895	NM_005236.2	723	tGc/tAc	11/11	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.461053785431427	2		557	645	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626468	12626468	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026258-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	129	455	0	ENST00000251849.4:c.1681G>A	p.Val561Met	p.V561M	ENST00000251849	NM_002880.3	561	Gtg/Atg	16/17	1	2	FACETS	0.928	0.844	1	0.928	0.844	1	CLONAL	1	TRUE	1	0.461053785431427	2		455	603	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0026319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	124	518	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	0.552891774902407	2		518	425	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111475	8111476	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	228	596	1	ENST00000346208.3:c.962dup	p.Thr322AspfsTer30	p.T322Dfs*30	ENST00000346208		321	cag/cAag	5/6	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.552891774902407	2		597	782	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226564916	226564916	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	90	449	0	ENST00000366794.5:c.1834G>C	p.Glu612Gln	p.E612Q	ENST00000366794	NM_001618.3	612	Gag/Cag	13/23	0.552891774902407	4	FACETS	0.567	0.502	0.636	0.189	0.167	0.212	SUBCLONAL	1	TRUE	1	0.552891774902407	4		449	892	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061125	38061194	+	frameshift_variant	Frame_Shift_Del	DEL	CTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAG	CTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAG	-	novel	NA	P-0026319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	234	189	0	ENST00000250448.2:c.795_864del	p.Phe266AlafsTer32	p.F266Afs*32	ENST00000250448	NM_004496.3	265	cgCTTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGCGGCGCCAAG/cg	2/2	1	2	FACETS	1	0.991	1	1	0.996	1	CLONAL	2	TRUE	1	0.552891774902407	2		189	361	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0026445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	375	380	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.511163563835264	5	FACETS	1	0.989	1	0.833	0.796	0.87	CLONAL	3	TRUE	1	0.511163563835264	5		380	778	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577548	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0026445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	186	394	2	ENST00000269305.4:c.733_734delinsTT	p.Gly245Phe	p.G245F	ENST00000269305	NM_001126112.2	245	GGc/TTc	7/11	0.324541824026794	2	FACETS	1	0.991	1	0.731	0.681	0.782	CLONAL	1	TRUE	0	0.511163563835264	2		396	498	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458606	120458606	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	180	393	0	ENST00000256646.2:c.6739G>T	p.Val2247Phe	p.V2247F	ENST00000256646	NM_024408.3	2247	Gtc/Ttc	34/34	0.420226118567875	3	FACETS	0.791	0.734	0.849	0.791	0.734	0.849	SUBCLONAL	2	TRUE	1	0.511163563835264	3		393	559	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352439	118352444	+	inframe_deletion	In_Frame_Del	DEL	AGAAAG	AGAAAG	-	rs1245434285	NA	P-0026445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	66	241	0	ENST00000534358.1:c.3649_3654del	p.Glu1217_Lys1218del	p.E1217_K1218del	ENST00000534358	NM_005933.3	1215	aAGAAAGag/aag	7/36	0.420226118567875	3	FACETS	0.862	0.752	0.98	0.431	0.376	0.49	CLONAL	1	TRUE	1	0.511163563835264	3		241	376	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032042	26032042	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1464188573	NA	P-0026445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	99	296	0	ENST00000244661.2:c.247C>T	p.Leu83Phe	p.L83F	ENST00000244661	NM_003537.3	83	Ctt/Ttt	1/1	0.400795513162955	4	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.511163563835264	4		296	455	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40476729	40476729	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	102	390	0	ENST00000264657.5:c.1600G>T	p.Gly534Ter	p.G534*	ENST00000264657	NM_139276.2	534	Gga/Tga	17/24	1	2	FACETS	0.951	0.852	1	0.951	0.852	1	CLONAL	1	TRUE	1	0.329532941439767	2		390	651	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098944	178098944	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	69	383	0	ENST00000397062.3:c.101G>C	p.Arg34Pro	p.R34P	ENST00000397062	NM_006164.4	34	cGa/cCa	2/5	0.231874336207865	3	FACETS	0.867	0.759	0.982	0.867	0.759	0.982	CLONAL	2	TRUE	1	0.231874336207865	3		383	383	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344869	70344869	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	95	362	0	ENST00000374080.3:c.2099C>T	p.Ser700Phe	p.S700F	ENST00000374080		700	tCc/tTc	15/45	0.231874336207865	2	FACETS	1	0.925	1			1	CLONAL	3	TRUE	NA	0.231874336207865	2		362	266	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs11575997	NA	P-0026574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	95	623	0	ENST00000269305.4:c.993+1G>T		p.X331_splice	ENST00000269305	NM_001126112.2	331			NA	2	FACETS	0.969	0.868	1			1	INDETERMINATE	2	TRUE	NA	0.231874336207865	2		623	423	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344973	70344973	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756039521	NA	P-0026574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	92	369	0	ENST00000374080.3:c.2203G>A	p.Ala735Thr	p.A735T	ENST00000374080		735	Gcc/Acc	15/45	0.231874336207865	2	FACETS	0.976	0.88	1			1	CLONAL	3	TRUE	NA	0.231874336207865	2		369	271	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490319	29490319	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	27	506	0	ENST00000356175.3:c.404G>T	p.Arg135Leu	p.R135L	ENST00000356175	NM_000267.3	135	cGg/cTg	4/57	1	2	FACETS	0.528	0.42	0.652	0.528	0.42	0.652	SUBCLONAL	1	TRUE	1	0.231874336207865	2		506	441	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792100	42792100	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	67	601	0	ENST00000575354.2:c.904G>T	p.Glu302Ter	p.E302*	ENST00000575354	NM_015125.3	302	Gag/Tag	6/20	0.231874336207865	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.231874336207865	1		601	348	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165725	118165725	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	52	416	0	ENST00000369448.3:c.235G>T	p.Val79Phe	p.V79F	ENST00000369448	NM_017709.3	79	Gtt/Ttt	2/2	0.231874336207865	2	FACETS	1	0.962	1	0.712	0.61	0.823	CLONAL	1	TRUE	0	0.231874336207865	2		416	315	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731044	162731044	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	80	546	0	ENST00000367921.3:c.899A>T	p.Lys300Met	p.K300M	ENST00000367921	NM_006182.2	300	aAg/aTg	9/18	0.231874336207865	3	FACETS	0.77	0.68	0.866	0.77	0.68	0.866	SUBCLONAL	2	TRUE	1	0.231874336207865	3		546	500	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212844	94212844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	52	508	0	ENST00000323929.3:c.398C>T	p.Thr133Ile	p.T133I	ENST00000323929	NM_005591.3	133	aCa/aTa	5/20	0.199830345331946	2	FACETS	1	0.94	1	0.6	0.512	0.695	CLONAL	1	TRUE	0	0.231874336207865	2		508	374	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475121	475121	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	37	618	2	ENST00000399788.2:c.516C>A	p.Phe172Leu	p.F172L	ENST00000399788	NM_001042603.1	172	ttC/ttA	4/28	1	2	FACETS	0.753	0.621	0.9	0.753	0.621	0.9	SUBCLONAL	1	TRUE	1	0.231874336207865	2		620	424	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439883	49439883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	91	743	0	ENST00000301067.7:c.4658G>A	p.Cys1553Tyr	p.C1553Y	ENST00000301067	NM_003482.3	1553	tGt/tAt	17/54	1	2	FACETS	0.791	0.705	0.882	1	0.982	1	SUBCLONAL	2	TRUE	1	0.231874336207865	2		743	496	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783959	50783959	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1379681515	NA	P-0026574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	96	747	0	ENST00000398568.2:c.350A>G	p.Asn117Ser	p.N117S	ENST00000398568	NM_001042412.1	117	aAc/aGc	3/18	0.231874336207865	3	FACETS	1	0.98	1	0.733	0.654	0.817	CLONAL	1	TRUE	1	0.231874336207865	3		747	630	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89345511	89345511	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	51	424	0	ENST00000301030.4:c.7439G>C	p.Gly2480Ala	p.G2480A	ENST00000301030	NM_001256183.1	2480	gGc/gCc	9/13	0.231874336207865	3	FACETS	0.873	0.748	1	0.873	0.748	1	CLONAL	2	TRUE	1	0.231874336207865	3		424	281	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057685	180057685	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	130	781	0	ENST00000261937.6:c.270G>T	p.Arg90Ser	p.R90S	ENST00000261937	NM_182925.4	90	agG/agT	3/30	0.231874336207865	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.231874336207865	2		781	449	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109319831	109319831	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	45	591	0	ENST00000436639.2:c.857G>C	p.Cys286Ser	p.C286S	ENST00000436639	NM_014454.2	286	tGt/tCt	5/10	1	2	FACETS	0.81	0.681	0.953	0.81	0.681	0.953	CLONAL	1	TRUE	1	0.231874336207865	2		591	479	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981846	70981846	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	47	795	1	ENST00000276594.2:c.250C>A	p.Leu84Ile	p.L84I	ENST00000276594	NM_024504.3	84	Cta/Ata	2/8	1	2	FACETS	0.876	0.739	1	0.876	0.739	1	CLONAL	1	TRUE	1	0.231874336207865	2		796	463	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139408961	139408961	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0026574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	27	623	0	ENST00000277541.6:c.2207+1G>T		p.X736_splice	ENST00000277541	NM_017617.3	736			NA	2	FACETS	0.624	0.497	0.77			1	INDETERMINATE	1	TRUE	NA	0.231874336207865	2		623	373	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0026631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	423	529	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.695378899204795	4	FACETS	1	0.994	1	0.805	0.772	0.838	CLONAL	2	TRUE	1	0.695378899204795	4		529	854	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653796	89653798	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs1554893765	NA	P-0026631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	174	309	0	ENST00000371953.3:c.97_99del	p.Ile33del	p.I33del	ENST00000371953	NM_000314.4	32	ATT/-	2/9	0.695378899204795	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.695378899204795	2		309	239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0026631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	959	702	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.694258041190969	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.695378899204795	2		702	1353	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434182	12434182	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776687	NA	P-0026631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	80	395	2	ENST00000287820.6:c.556del	p.Ser186ValfsTer47	p.S186Vfs*47	ENST00000287820	NM_015869.4	184	Aaa/aa	4/7	0.221241014550246	2	FACETS	0.4	0.352	0.451	0.2	0.176	0.226	INDETERMINATE	1	TRUE	0	0.695378899204795	2		397	575	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349709	89349709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1384052546	NA	P-0026631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	120	601	0	ENST00000301030.4:c.3241G>A	p.Asp1081Asn	p.D1081N	ENST00000301030	NM_001256183.1	1081	Gac/Aac	9/13	0.307280678525298	2	FACETS	0.407	0.368	0.45	0.204	0.184	0.225	INDETERMINATE	1	TRUE	0	0.695378899204795	2		601	847	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40879652	40879652	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0026631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	47	461	0	ENST00000428826.2:c.246+1G>T		p.X82_splice	ENST00000428826		82			0.355140531311089	2	FACETS	0.205	0.172	0.241	0.102	0.086	0.121	INDETERMINATE	1	TRUE	0	0.695378899204795	2		461	661	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965926	25965926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	125	539	1	ENST00000435504.4:c.3280G>A	p.Gly1094Ser	p.G1094S	ENST00000435504		1094	Ggt/Agt	13/13	0.355140531311089	2	FACETS	0.4	0.361	0.441	0.2	0.18	0.221	INDETERMINATE	1	TRUE	0	0.695378899204795	2		540	899	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401634	401634	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	98	443	0	ENST00000380956.4:c.956T>A	p.Met319Lys	p.M319K	ENST00000380956	NM_001195286.1	319	aTg/aAg	7/9	0.307280678525298	2	FACETS	0.432	0.385	0.481	0.216	0.192	0.241	INDETERMINATE	1	TRUE	0	0.695378899204795	2		443	653	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636836	8636836	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	85	360	0	ENST00000356435.5:c.73A>T	p.Arg25Trp	p.R25W	ENST00000356435		25	Agg/Tgg	2/35	1	2	FACETS	0.411	0.363	0.462	0.411	0.363	0.462	SUBCLONAL	1	TRUE	1	0.695378899204795	2		360	595	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929066	44929067	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0026631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	94	204	0	ENST00000377967.4:c.2167_2168del	p.Asn723HisfsTer6	p.N723Hfs*6	ENST00000377967	NM_021140.2	722	ggAAac/ggac	17/29	0.534837018679388	2	FACETS	0.663	0.593	0.735			1	SUBCLONAL	1	TRUE	NA	0.695378899204795	2		204	408	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0026766-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	12	445	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.909	0.647	1	0.909	0.647	1	CLONAL	1	FALSE	1	0.3	2		445	88	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177874	56177875	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0026766-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	12	382	0	ENST00000399503.3:c.2849_2850del	p.Glu950AlafsTer53	p.E950Afs*53	ENST00000399503	NM_005921.1	949	acAGag/acag	14/20	0.206737983084576	3	FACETS	1	0.795	1	0.575	0.41	0.771	CLONAL	1	FALSE	1	0.3	3		382	80	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180586	56180588	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	rs1357146419	NA	P-0026766-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	27	435	0	ENST00000399503.3:c.3918_3920del	p.Ile1307del	p.I1307del	ENST00000399503	NM_005921.1	1305	aaCATc/aac	16/20	0.206737983084576	3	FACETS	0.863	0.698	1	0.863	0.698	1	CLONAL	2	FALSE	1	0.3	3		435	120	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879598	151879598	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026766-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	10	274	0	ENST00000262189.6:c.5347C>T	p.Gln1783Ter	p.Q1783*	ENST00000262189	NM_170606.2	1783	Cag/Tag	36/59	1	2	FACETS	0.823	0.565	1	0.823	0.565	1	CLONAL	1	FALSE	1	0.3	2		274	81	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69998232	69998232	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026777-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	162	545	0	ENST00000394351.3:c.472T>G	p.Tyr158Asp	p.Y158D	ENST00000394351	NM_000248.3	158	Tat/Gat	5/9	0.55160152935175	1	FACETS	0.561	0.516	0.608	0.561	0.516	0.608	SUBCLONAL	1	TRUE	0	0.581161146860849	1		545	705	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21629860	21629860	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs757070119	NA	P-0026865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	65	644	0	ENST00000421138.2:c.934T>C	p.Tyr312His	p.Y312H	ENST00000421138		312	Tac/Cac	9/16	0.415602291967534	5	FACETS	0.576	0.498	0.661	0.192	0.166	0.221	SUBCLONAL	1	TRUE	2	0.415602291967534	5		644	881	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971213	13971213	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs773736818	NA	P-0026865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	223	468	0	ENST00000405192.2:c.716A>G	p.Asn239Ser	p.N239S	ENST00000405192	NM_001163147.1	239	aAc/aGc	8/12	0.415602291967534	5	FACETS	0.959	0.894	1	0.64	0.596	0.685	CLONAL	2	TRUE	2	0.415602291967534	5		468	908	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0027045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	49	445	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.736	0.625	0.857	0.736	0.625	0.857	SUBCLONAL	1	TRUE	1	0.35513246948785	2		445	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577527	7577531	+	frameshift_variant	Frame_Shift_Del	DEL	GGATG	GGATG	-	novel	NA	P-0027045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	196	865	0	ENST00000269305.4:c.750_754del	p.Ile251HisfsTer11	p.I251Hfs*11	ENST00000269305	NM_001126112.2	250	ccCATCCtc/cctc	7/11	0.334001536232358	2	FACETS	0.905	0.842	0.969	0.905	0.842	0.969	CLONAL	2	TRUE	0	0.35513246948785	2		865	610	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677209	29677210	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0027045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	95	462	1	ENST00000356175.3:c.7268_7269del	p.Thr2423SerfsTer3	p.T2423Sfs*3	ENST00000356175	NM_000267.3	2423	ACa/a	49/57	0.334001536232358	2	FACETS	0.871	0.785	0.961	0.871	0.785	0.961	CLONAL	2	TRUE	0	0.35513246948785	2		463	307	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509665	106509665	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	69	805	2	ENST00000359195.3:c.1659G>T	p.Lys553Asn	p.K553N	ENST00000359195	NM_002649.2	553	aaG/aaT	2/11	1	2	FACETS	0.709	0.618	0.807	0.709	0.618	0.807	SUBCLONAL	1	TRUE	1	0.35513246948785	2		807	548	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431669	49431669	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	194	587	0	ENST00000301067.7:c.9470G>C	p.Gly3157Ala	p.G3157A	ENST00000301067	NM_003482.3	3157	gGa/gCa	34/54	0.238979572307349	6	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.664899093859982	6		587	928	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004945	16004945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	176	541	0	ENST00000268712.3:c.2309C>T	p.Pro770Leu	p.P770L	ENST00000268712	NM_006311.3	770	cCa/cTa	20/46	1	2	FACETS	0.884	0.818	0.951	0.884	0.818	0.951	CLONAL	1	TRUE	1	0.664899093859982	2		541	599	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0027119-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	282	250	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		250	476	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	151	297	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.205289565908942	3	FACETS	0.965	0.887	1	0.965	0.887	1	CLONAL	3	TRUE	0	0.205302274749569	3		297	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0027144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	126	717	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.192025792784066	2	FACETS	0.842	0.763	0.925	0.842	0.763	0.925	CLONAL	2	TRUE	0	0.205302274749569	2		718	729	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600398	10600398	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	82	715	0	ENST00000171111.5:c.1457C>T	p.Ser486Leu	p.S486L	ENST00000171111	NM_203500.1	486	tCa/tTa	4/6	0.205302274749569	2	FACETS	0.944	0.831	1	0.472	0.415	0.533	CLONAL	1	TRUE	0	0.205302274749569	2		715	846	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755653	57755653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752655180	NA	P-0027144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	69	665	0	ENST00000274289.3:c.134C>T	p.Pro45Leu	p.P45L	ENST00000274289	NM_006622.3	45	cCt/cTt	1/14	0.205302274749569	3	FACETS	0.984	0.856	1	0.492	0.428	0.562	CLONAL	1	TRUE	1	0.205302274749569	3		665	753	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577460	64577460	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027159-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	251	459	0	ENST00000312049.6:c.122T>G	p.Leu41Arg	p.L41R	ENST00000312049	NM_130799.2	41	cTg/cGg	2/10	0.3	3	FACETS	1	0.99	1	0.822	0.776	0.87	CLONAL	2	TRUE	0	0.41	3		459	598	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0027192-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	89	559	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.979	0.868	1	0.979	0.868	1	CLONAL	1	TRUE	1	0.260805441442744	2		559	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587782272	NA	P-0027192-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	82	516	0	ENST00000269305.4:c.994-1G>C		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.216131173384235	1	FACETS	0.732	0.645	0.826	0.732	0.645	0.826	SUBCLONAL	1	TRUE	0	0.260805441442744	1		516	747	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456366	32456366	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027192-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	56	578	0	ENST00000332351.3:c.526C>T	p.Arg176Cys	p.R176C	ENST00000332351	NM_024426.4	176	Cgc/Tgc	1/10	1	2	FACETS	0.487	0.416	0.566	0.487	0.416	0.566	SUBCLONAL	1	TRUE	1	0.260805441442744	2		578	881	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534781	18534781	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027192-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	92	416	0	ENST00000266497.5:c.1839G>A	p.Trp613Ter	p.W613*	ENST00000266497		613	tgG/tgA	12/31	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.260805441442744	2		416	698	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612346	1612346	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs769011342	NA	P-0027192-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	137	598	1	ENST00000344749.5:c.1673G>T	p.Arg558Leu	p.R558L	ENST00000344749	NM_001136139.2	558	cGc/cTc	18/19	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.260805441442744	2		599	991	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713432	40713432	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027192-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	102	553	0	ENST00000373198.4:c.4083del	p.Tyr1362ThrfsTer37	p.Y1362Tfs*37	ENST00000373198	NM_133170.3	1361	gcC/gc	30/32	0.185119056195532	3	FACETS	0.989	0.883	1	0.495	0.441	0.551	CLONAL	1	TRUE	1	0.260805441442744	3		553	894	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527581	41527581	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027192-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	97	451	0	ENST00000263253.7:c.1472A>C	p.Gln491Pro	p.Q491P	ENST00000263253	NM_001429.3	491	cAg/cCg	6/31	1	2	FACETS	0.91	0.811	1	0.91	0.811	1	CLONAL	1	TRUE	1	0.260805441442744	2		451	817	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713566	30713566	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027192-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	86	378	0	ENST00000295754.5:c.891del	p.Asn298IlefsTer2	p.N298Ifs*2	ENST00000295754	NM_003242.5	297	atC/at	4/7	0.260805441442744	1	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	0	0.260805441442744	1		378	568	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141557566	141557566	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0027192-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	82	545	0	ENST00000220592.5:c.1748+1G>T		p.X583_splice	ENST00000220592	NM_012154.3	583			1	2	FACETS	0.75	0.661	0.847	0.75	0.661	0.847	SUBCLONAL	1	TRUE	1	0.260805441442744	2		545	838	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760801	133760801	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027192-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	83	507	1	ENST00000318560.5:c.3124G>T	p.Ala1042Ser	p.A1042S	ENST00000318560	NM_005157.4	1042	Gcc/Tcc	11/11	1	2	FACETS	0.904	0.798	1	0.904	0.798	1	CLONAL	1	TRUE	1	0.260805441442744	2		508	704	SUCCESS
BTK	695	MSKCC	GRCh37	X	100612547	100612547	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027192-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	50	404	0	ENST00000308731.7:c.1127C>A	p.Pro376Gln	p.P376Q	ENST00000308731	NM_000061.2	376	cCa/cAa	13/19	1	2	FACETS	0.674	0.571	0.787	0.674	0.571	0.787	SUBCLONAL	1	TRUE	1	0.260805441442744	2		404	569	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861611	152861611	+	synonymous_variant	Silent	SNP	G	G	T	novel	NA	P-0027192-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	101	590	0	ENST00000406277.2:c.141C>A	p.Ala47=	p.A47=	ENST00000406277	NM_152274.4	47	gcC/gcA	4/7	1		FACETS		0.794	0.991				CLONAL	1	TRUE	1	0.260805441442744	2		590	871	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410673	63410673	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027275-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	162	701	0	ENST00000330258.3:c.2494G>A	p.Glu832Lys	p.E832K	ENST00000330258	NM_152424.3	832	Gaa/Aaa	2/2	0.271171588783351	1	FACETS	0.242	0.222	0.263	0.242	0.222	0.263	INDETERMINATE	1	TRUE	0	0.894846047694081	1		701	826	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174386	11174386	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027275-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	330	524	0	ENST00000361445.4:c.7289G>T	p.Arg2430Met	p.R2430M	ENST00000361445	NM_004958.3	2430	aGg/aTg	53/58	0.894846047694081	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.894846047694081	1		524	381	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131976376	131976376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027275-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	310	458	0	ENST00000265335.6:c.3631C>T	p.Leu1211Phe	p.L1211F	ENST00000265335		1211	Ctc/Ttc	24/25	0.894846047694081	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.894846047694081	1		458	375	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504319	149504319	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1250625415	NA	P-0027275-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	324	611	1	ENST00000261799.4:c.1883C>T	p.Thr628Met	p.T628M	ENST00000261799	NM_002609.3	628	aCg/aTg	13/23	0.894846047694081	1	FACETS	0.998	0.968	1	0.998	0.968	1	CLONAL	1	TRUE	0	0.894846047694081	1		612	401	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922956	39922956	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027275-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	305	562	0	ENST00000378444.4:c.3752A>G	p.Asn1251Ser	p.N1251S	ENST00000378444	NM_001123385.1	1251	aAc/aGc	8/15	1	2	FACETS	0.972	0.923	1	0.972	0.923	1	CLONAL	1	TRUE	1	0.894846047694081	2		562	701	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410661	63410661	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027275-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	163	701	0	ENST00000330258.3:c.2506G>A	p.Ala836Thr	p.A836T	ENST00000330258	NM_152424.3	836	Gcc/Acc	2/2	0.271171588783351	1	FACETS	0.248	0.227	0.269	0.248	0.227	0.269	INDETERMINATE	1	TRUE	0	0.894846047694081	1		701	813	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410695	63410695	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027275-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	157	666	0	ENST00000330258.3:c.2472G>C	p.Glu824Asp	p.E824D	ENST00000330258	NM_152424.3	824	gaG/gaC	2/2	0.271171588783351	1	FACETS	0.243	0.223	0.265	0.243	0.223	0.265	INDETERMINATE	1	TRUE	0	0.894846047694081	1		666	797	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410718	63410718	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1220943330	NA	P-0027275-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	169	650	0	ENST00000330258.3:c.2449G>C	p.Asp817His	p.D817H	ENST00000330258	NM_152424.3	817	Gat/Cat	2/2	0.271171588783351	1	FACETS	0.27	0.248	0.293	0.27	0.248	0.293	INDETERMINATE	1	TRUE	0	0.894846047694081	1		650	773	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411030	63411030	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027275-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	165	558	0	ENST00000330258.3:c.2137G>C	p.Asp713His	p.D713H	ENST00000330258	NM_152424.3	713	Gat/Cat	2/2	0.271171588783351	1	FACETS	0.302	0.278	0.327	0.302	0.278	0.327	INDETERMINATE	1	TRUE	0	0.894846047694081	1		558	674	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411334	63411335	+	missense_variant	Missense_Mutation	DNP	CC	CC	TG	novel	NA	P-0027275-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	179	711	1	ENST00000330258.3:c.1832_1833delinsCA	p.Arg611Thr	p.R611T	ENST00000330258	NM_152424.3	611	aGG/aCA	2/2	0.271171588783351	1	FACETS	0.289	0.266	0.312	0.289	0.266	0.312	INDETERMINATE	1	TRUE	0	0.894846047694081	1		712	766	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578266	7578266	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs942158624	NA	P-0027307-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	201	634	0	ENST00000269305.4:c.583A>T	p.Ile195Phe	p.I195F	ENST00000269305	NM_001126112.2	195	Atc/Ttc	6/11	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.494482367935044	2		634	638	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027307-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1780	358	570	0	ENST00000263967.3:c.278G>T	p.Arg93Leu	p.R93L	ENST00000263967	NM_006218.2	93	cGg/cTg	2/21	0.494482367935044	8	FACETS	0.841	0.793	0.89			1	CLONAL	2	TRUE	NA	0.494482367935044	8		570	2138	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148507443	148507443	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027307-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	154	450	0	ENST00000320356.2:c.2011C>G	p.Leu671Val	p.L671V	ENST00000320356	NM_004456.4	671	Ctg/Gtg	17/20	1	2	FACETS	0.92	0.844	0.999	0.92	0.844	0.999	CLONAL	1	TRUE	1	0.494482367935044	2		450	677	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415856	49415858	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	rs587783704	NA	P-0027307-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	85	402	0	ENST00000301067.7:c.16489_16491del	p.Ile5497del	p.I5497del	ENST00000301067	NM_003482.3	5497	ATC/-	53/54	1	2	FACETS	0.638	0.565	0.715	0.638	0.565	0.715	SUBCLONAL	1	TRUE	1	0.494482367935044	2		402	539	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582990	95582990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027307-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	83	325	0	ENST00000393063.1:c.1552G>A	p.Ala518Thr	p.A518T	ENST00000393063	NM_030621.3	518	Gca/Aca	11/28	0.494482367935044	3	FACETS	0.889	0.787	0.997	0.444	0.393	0.499	CLONAL	1	TRUE	1	0.494482367935044	3		325	471	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304069	91304069	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027307-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	220	610	0	ENST00000355112.3:c.1467del	p.Arg489SerfsTer13	p.R489Sfs*13	ENST00000355112	NM_000057.2	489	aGg/ag	7/22	0.444564122087952	3	FACETS	1	0.978	1	0.373	0.346	0.4	CLONAL	1	TRUE	0	0.494482367935044	3		610	993	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855832	45855832	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs761085729	NA	P-0027307-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	94	805	0	ENST00000391945.4:c.1978G>T	p.Ala660Ser	p.A660S	ENST00000391945	NM_000400.3	660	Gcg/Tcg	21/23	0.371178817705269	1	FACETS	0.373	0.332	0.417	0.373	0.332	0.417	SUBCLONAL	1	TRUE	0	0.494482367935044	1		805	767	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141680	202141680	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027307-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	144	410	0	ENST00000358485.4:c.968A>T	p.His323Leu	p.H323L	ENST00000358485	NM_001080125.1	323	cAc/cTc	7/9	0.494482367935044	1	FACETS	0.882	0.81	0.957	0.882	0.81	0.957	CLONAL	1	TRUE	0	0.494482367935044	1		410	497	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790179	40790179	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs762081981	NA	P-0027307-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	120	337	0	ENST00000373198.4:c.2552A>T	p.Asp851Val	p.D851V	ENST00000373198	NM_133170.3	851	gAt/gTt	18/32	1	2	FACETS	0.989	0.898	1	0.989	0.898	1	CLONAL	1	TRUE	1	0.494482367935044	2		337	491	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24135779	24135779	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027307-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	174	560	0	ENST00000263121.7:c.266C>G	p.Thr89Ser	p.T89S	ENST00000263121	NM_003073.3	89	aCc/aGc	3/9	1	2	FACETS	0.87	0.802	0.941	0.87	0.802	0.941	CLONAL	1	TRUE	1	0.494482367935044	2		560	809	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968096	68968096	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027307-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	254	493	0	ENST00000288368.4:c.1125G>C	p.Trp375Cys	p.W375C	ENST00000288368	NM_024870.2	375	tgG/tgC	10/40	0.382426697703643	3	FACETS	0.845	0.794	0.897	0.845	0.794	0.897	CLONAL	2	TRUE	1	0.494482367935044	3		493	758	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045134	47045134	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027307-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	232	310	0	ENST00000377604.3:c.2375G>T	p.Arg792Leu	p.R792L	ENST00000377604	NM_001204468.1	792	cGg/cTg	21/24	1	1	FACETS	0.841	0.797	0.885	1	0.995	1	CLONAL	2	TRUE	0	0.494482367935044	1		310	420	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596162	43596162	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764421264	NA	P-0027307-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	144	450	0	ENST00000355710.3:c.329G>A	p.Ser110Asn	p.S110N	ENST00000355710	NM_020975.4	110	aGt/aAt	2/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.494482367935044	2		450	546	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361244	66361244	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027307-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	51	300	0	ENST00000273854.3:c.928T>C	p.Phe310Leu	p.F310L	ENST00000273854	NM_004439.5	310	Ttc/Ctc	4/18	1	2	FACETS	0.449	0.382	0.523	0.449	0.382	0.523	SUBCLONAL	1	TRUE	1	0.494482367935044	2		300	459	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77054959	77054959	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	151	465	0	ENST00000356341.3:c.903G>A	p.Met301Ile	p.M301I	ENST00000356341	NM_002576.4	301	atG/atA	10/15	1	2	FACETS	0.968	0.896	1	0.968	0.896	1	CLONAL	1	TRUE	1	0.797696457207104	2		465	391	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064431	30064431	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	61	496	0	ENST00000338641.4:c.995A>G	p.Lys332Arg	p.K332R	ENST00000338641	NM_000268.3	332	aAg/aGg	10/16	1	2	FACETS	0.272	0.234	0.312	0.272	0.234	0.312	SUBCLONAL	1	TRUE	1	0.797696457207104	2		496	563	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498302	29498302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	26	575	1	ENST00000389048.3:c.1878C>A	p.Asp626Glu	p.D626E	ENST00000389048	NM_004304.4	626	gaC/gaA	10/29	1	2	FACETS	0.152	0.12	0.189	0.152	0.12	0.189	SUBCLONAL	1	TRUE	1	0.797696457207104	2		576	428	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0027422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	308	576	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.873199386085718	2		576	685	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0027422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	308	581	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.873199386085718	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.873199386085718	1		583	395	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0027422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	348	518	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.873199386085718	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.873199386085718	2		518	384	SUCCESS
APC	324	MSKCC	GRCh37	5	112175675	112175676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0027422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	176	423	0	ENST00000257430.4:c.4393_4394dup	p.Ser1465ArgfsTer9	p.S1465Rfs*9	ENST00000257430	NM_000038.5	1462	aag/aAGag	16/16	1	2	FACETS	0.797	0.74	0.855	0.797	0.74	0.855	SUBCLONAL	1	TRUE	1	0.873199386085718	2		423	506	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0027422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	200	438	1	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.873199386085718	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.873199386085718	1		439	251	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0027422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	219	424	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.954	0.896	1	0.954	0.896	1	CLONAL	1	TRUE	1	0.873199386085718	2		425	526	SUCCESS
AR	367	MSKCC	GRCh37	X	66765159	66765188	+	inframe_deletion	In_Frame_Del	DEL	GCAGCAGCAGCAGCAGCAGCAGCAGCAGCA	GCAGCAGCAGCAGCAGCAGCAGCAGCAGCA	-	rs3032358	NA	P-0027422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	43	270	0	ENST00000374690.3:c.210_239del	p.Gln71_Gln80del	p.Q71_Q80del	ENST00000374690	NM_000044.3	57	ctGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAg/ctg	1/8	1	2	FACETS	0.324	0.272	0.381	0.324	0.272	0.381	SUBCLONAL	1	TRUE	1	0.873199386085718	2		270	304	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468357	89468357	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs867931903	NA	P-0027422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	150	197	0	ENST00000336596.2:c.1891G>A	p.Glu631Lys	p.E631K	ENST00000336596	NM_005233.5	631	Gaa/Aaa	11/17	0.281475721949165	5	FACETS	0.84	0.781	0.899			1	INDETERMINATE	3	TRUE	NA	0.873199386085718	5		197	315	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980416	201980417	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGAGG	novel	NA	P-0027422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	294	680	3	ENST00000359651.3:c.154_158dup	p.Thr54ArgfsTer103	p.T54Rfs*103	ENST00000359651		51	ttg/ttGGAGGg	1/8	1	2	FACETS	0.867	0.82	0.914	0.867	0.82	0.914	CLONAL	1	TRUE	1	0.873199386085718	2		683	777	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578228	226578228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	312	552	0	ENST00000366794.5:c.500G>A	p.Arg167Lys	p.R167K	ENST00000366794	NM_001618.3	167	aGg/aAg	4/23	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.873199386085718	2		552	699	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55524201	55524201	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	269	489	1	ENST00000288135.5:c.20C>A	p.Ala7Asp	p.A7D	ENST00000288135	NM_000222.2	7	gCc/gAc	1/21	0.24103900657473	1	FACETS	0.575	0.544	0.606	0.575	0.544	0.606	INDETERMINATE	1	TRUE	0	0.873199386085718	1		490	604	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593598	55593598	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	170	471	0	ENST00000288135.5:c.1664T>A	p.Val555Glu	p.V555E	ENST00000288135	NM_000222.2	555	gTa/gAa	11/21	0.24103900657473	1	FACETS	0.494	0.459	0.53	0.494	0.459	0.53	INDETERMINATE	1	TRUE	0	0.873199386085718	1		471	444	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528267	157528267	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	274	586	2	ENST00000346085.5:c.5992G>C	p.Glu1998Gln	p.E1998Q	ENST00000346085	NM_020732.3	1998	Gag/Cag	20/20	1	2	FACETS	0.799	0.754	0.846	0.799	0.754	0.846	SUBCLONAL	1	TRUE	1	0.873199386085718	2		588	785	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411119	63411119	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	229	518	1	ENST00000330258.3:c.2048C>A	p.Ser683Ter	p.S683*	ENST00000330258	NM_152424.3	683	tCa/tAa	2/2	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.873199386085718	2		519	524	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0027431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	50	281	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.964	0.82	1	0.964	0.82	1	CLONAL	1	TRUE	1	0.26	2		281	399	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0027431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	132	544	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	TRUE	1	0.26	2		544	803	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777894	NA	P-0027431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	99	713	0	ENST00000361445.4:c.6644C>T	p.Ser2215Phe	p.S2215F	ENST00000361445	NM_004958.3	2215	tCt/tTt	47/58	1	2	FACETS	0.802	0.715	0.896	0.802	0.715	0.896	CLONAL	1	TRUE	1	0.26	2		713	949	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216624	108216626	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs786203976	NA	P-0027431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	60	354	0	ENST00000278616.4:c.8578_8580del	p.Ser2860del	p.S2860del	ENST00000278616	NM_000051.3	2858	aCTTct/act	58/63	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.26	2		354	416	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692794	89692794	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121909238	NA	P-0027431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	65	377	0	ENST00000371953.3:c.278A>G	p.His93Arg	p.H93R	ENST00000371953	NM_000314.4	93	cAt/cGt	5/9	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.26	2		377	497	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268150	153268150	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	41	446	1	ENST00000281708.4:c.658C>T	p.Gln220Ter	p.Q220*	ENST00000281708	NM_033632.3	220	Caa/Taa	4/12	1	2	FACETS	0.419	0.348	0.499	0.419	0.348	0.499	SUBCLONAL	1	TRUE	1	0.26	2		447	752	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952064	178952064	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	76	481	0	ENST00000263967.3:c.3119T>A	p.Met1040Lys	p.M1040K	ENST00000263967	NM_006218.2	1040	aTg/aAg	21/21	1	2	FACETS	0.943	0.827	1	0.943	0.827	1	CLONAL	1	TRUE	1	0.26	2		481	620	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105551	27105551	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	77	555	0	ENST00000324856.7:c.5162G>C	p.Arg1721Pro	p.R1721P	ENST00000324856	NM_006015.4	1721	cGa/cCa	20/20	1	2	FACETS	0.779	0.683	0.883	0.779	0.683	0.883	SUBCLONAL	1	TRUE	1	0.26	2		555	760	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105651	27105652	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	85	531	0	ENST00000324856.7:c.5263dup	p.Ser1755LysfsTer18	p.S1755Kfs*18	ENST00000324856	NM_006015.4	1754	-/A	20/20	1	2	FACETS	0.953	0.843	1	0.953	0.843	1	CLONAL	1	TRUE	1	0.26	2		531	686	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432638	49432638	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0027431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	169	733	0	ENST00000301067.7:c.8501C>G	p.Ser2834Ter	p.S2834*	ENST00000301067	NM_003482.3	2834	tCa/tGa	34/54	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.26	2		733	1128	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645252	67645252	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	113	715	0	ENST00000264010.4:c.517G>T	p.Gly173Ter	p.G173*	ENST00000264010	NM_006565.3	173	Gga/Tga	3/12	1	2	FACETS	0.832	0.747	0.922	0.832	0.747	0.922	CLONAL	1	TRUE	1	0.26	2		715	1045	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880988	134880988	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	93	572	0	ENST00000398015.3:c.1551C>A	p.Phe517Leu	p.F517L	ENST00000398015	NM_004441.4	517	ttC/ttA	7/16	1	2	FACETS	0.908	0.807	1	0.908	0.807	1	CLONAL	1	TRUE	1	0.26	2		572	788	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181850	56181850	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	83	524	0	ENST00000399503.3:c.4074del	p.Tyr1359IlefsTer18	p.Y1359Ifs*18	ENST00000399503	NM_005921.1	1358	tcG/tc	17/20	1	2	FACETS	0.869	0.766	0.979	0.869	0.766	0.979	CLONAL	1	TRUE	1	0.26	2		524	735	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568656	41568656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027469-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	64	517	0	ENST00000263253.7:c.4606G>A	p.Glu1536Lys	p.E1536K	ENST00000263253	NM_001429.3	1536	Gaa/Aaa	28/31	1	2	FACETS	0.846	0.735	0.964	0.846	0.735	0.964	CLONAL	1	FALSE	1	0.385210348593733	2		517	393	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541660	187541660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745765579	NA	P-0027469-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	34	469	0	ENST00000441802.2:c.6080G>A	p.Arg2027His	p.R2027H	ENST00000441802	NM_005245.3	2027	cGc/cAc	10/27	NA	2	FACETS	0.59	0.484	0.709			1	INDETERMINATE	1	FALSE	NA	0.385210348593733	2		469	299	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285014	15285014	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027469-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	61	911	0	ENST00000263388.2:c.4601G>A	p.Arg1534Gln	p.R1534Q	ENST00000263388	NM_000435.2	1534	cGg/cAg	25/33	0.246099742448927	0	FACETS	0.525	0.455	0.6			1	SUBCLONAL	1	FALSE	0	0.385210348593733	0		911	371	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568662	41568662	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027469-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	55	492	0	ENST00000263253.7:c.4612A>T	p.Thr1538Ser	p.T1538S	ENST00000263253	NM_001429.3	1538	Aca/Tca	28/31	1	2	FACETS	0.78	0.67	0.899	0.78	0.67	0.899	SUBCLONAL	1	FALSE	1	0.385210348593733	2		492	366	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444413	50444413	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027469-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	59	506	0	ENST00000331340.3:c.343G>T	p.Gly115Ter	p.G115*	ENST00000331340	NM_006060.4	115	Gga/Tga	4/8	1	2	FACETS	0.646	0.557	0.743	0.646	0.557	0.743	SUBCLONAL	1	FALSE	1	0.385210348593733	2		506	474	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444481	50444481	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027469-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	49	402	0	ENST00000331340.3:c.411A>C	p.Arg137Ser	p.R137S	ENST00000331340	NM_006060.4	137	agA/agC	4/8	1	2	FACETS	0.697	0.592	0.811	0.697	0.592	0.811	SUBCLONAL	1	FALSE	1	0.385210348593733	2		402	365	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0027470-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	102	298	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.547	0.49	0.606	0.547	0.49	0.606	SUBCLONAL	1	TRUE	1	0.688330697148671	2		298	542	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351980	89351980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027470-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	616	1171	1	ENST00000301030.4:c.970G>A	p.Glu324Lys	p.E324K	ENST00000301030	NM_001256183.1	324	Gaa/Aaa	9/13	0.642994590494593	2	FACETS	0.909	0.882	0.935	0.909	0.882	0.935	CLONAL	2	TRUE	0	0.688330697148671	2		1172	985	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497530	125497530	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027470-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	68	358	0	ENST00000428830.2:c.94G>A	p.Glu32Lys	p.E32K	ENST00000428830	NM_001114121.2	32	Gaa/Aaa	3/14	NA	2	FACETS	0.489	0.427	0.555			1	INDETERMINATE	1	TRUE	NA	0.688330697148671	2		358	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578512	7578532	+	inframe_deletion	In_Frame_Del	DEL	TCTTGGCCAGTTGGCAAAACA	TCTTGGCCAGTTGGCAAAACA	-	novel	NA	P-0027470-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	821	1045	0	ENST00000269305.4:c.398_418del	p.Met133_Lys139del	p.M133_K139del	ENST00000269305	NM_001126112.2	133	aTGTTTTGCCAACTGGCCAAGAcc/acc	5/11	1	2	FACETS	0.959	0.935	0.982	1	0.998	1	CLONAL	2	TRUE	1	0.688330697148671	2		1045	1244	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488681	212488681	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027470-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	94	553	0	ENST00000342788.4:c.2168T>C	p.Val723Ala	p.V723A	ENST00000342788	NM_005235.2	723	gTc/gCc	18/28	0.33994196986566	1	FACETS	0.331	0.295	0.369	0.331	0.295	0.369	INDETERMINATE	1	TRUE	0	0.688330697148671	1		553	541	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530118	212530118	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027470-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	111	441	0	ENST00000342788.4:c.1801A>C	p.Asn601His	p.N601H	ENST00000342788	NM_005235.2	601	Aac/Cac	15/28	0.33994196986566	1	FACETS	0.465	0.42	0.512	0.465	0.42	0.512	INDETERMINATE	1	TRUE	0	0.688330697148671	1		441	455	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0027519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	159	433	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		433	948	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0027540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	189	398	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.372617260375795	3	FACETS	0.899	0.835	0.966	0.899	0.835	0.966	CLONAL	2	TRUE	1	0.372617260375795	3		398	669	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112769553	112769553	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	158	561	0	ENST00000369452.4:c.1505G>T	p.Gly502Val	p.G502V	ENST00000369452	NM_007373.3	502	gGa/gTa	8/9	1	2	FACETS	0.908	0.832	0.988	0.908	0.832	0.988	CLONAL	1	TRUE	1	0.372617260375795	2		561	934	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0027540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	102	456	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	0.372617260375795	3	FACETS	0.773	0.691	0.861	0.387	0.345	0.431	SUBCLONAL	1	TRUE	1	0.372617260375795	3		456	840	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220718	1220718	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0027540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	127	464	0	ENST00000326873.7:c.734+2T>A		p.X245_splice	ENST00000326873	NM_000455.4	245			0.372617260375795	1	FACETS	0.909	0.826	0.996	0.909	0.826	0.996	CLONAL	1	TRUE	0	0.372617260375795	1		464	610	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223012	5223012	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	155	530	0	ENST00000357368.4:c.2791C>T	p.His931Tyr	p.H931Y	ENST00000357368	NM_002850.3	931	Cac/Tac	18/38	0.372617260375795	1	FACETS	0.953	0.875	1	0.953	0.875	1	CLONAL	1	TRUE	0	0.372617260375795	1		530	710	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602907	10602907	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	206	679	1	ENST00000171111.5:c.671C>T	p.Ser224Phe	p.S224F	ENST00000171111	NM_203500.1	224	tCc/tTc	3/6	0.372617260375795	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.372617260375795	1		680	897	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121082	11121082	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	146	505	0	ENST00000358026.2:c.2149G>T	p.Glu717Ter	p.E717*	ENST00000358026	NM_001128849.1	717	Gaa/Taa	15/36	0.372617260375795	1	FACETS	0.881	0.805	0.96	0.881	0.805	0.96	CLONAL	1	TRUE	0	0.372617260375795	1		505	724	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795049	242795049	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	208	746	0	ENST00000334409.5:c.160T>A	p.Cys54Ser	p.C54S	ENST00000334409	NM_005018.2	54	Tgc/Agc	2/5	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.372617260375795	2		746	1115	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755492	39755492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	105	360	0	ENST00000288319.7:c.1273C>T	p.Pro425Ser	p.P425S	ENST00000288319	NM_182918.3	425	Cca/Tca	10/10	1	2	FACETS	0.775	0.695	0.861	0.775	0.695	0.861	SUBCLONAL	1	TRUE	1	0.372617260375795	2		360	727	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039611	47039611	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	115	190	0	ENST00000377604.3:c.1063G>T	p.Glu355Ter	p.E355*	ENST00000377604	NM_001204468.1	355	Gag/Tag	11/24	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.372617260375795	1		190	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0027572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	650	567	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.332210991423519	2	FACETS	1	0.995	1	1	0.998	1	CLONAL	4	FALSE	0	0.332210991423519	2		568	904	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0027572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	124	267	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.995	0.91	1	1	0.99	1	CLONAL	2	FALSE	1	0.332210991423519	2		267	375	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959220	2959220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	295	673	2	ENST00000396946.4:c.2296G>A	p.Glu766Lys	p.E766K	ENST00000396946	NM_032415.4	766	Gag/Aag	18/25	0.332210991423519	4	FACETS	0.977	0.919	1	0.651	0.612	0.691	CLONAL	2	FALSE	1	0.332210991423519	4		675	1211	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193859	106193859	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	187	436	0	ENST00000380013.4:c.4321del	p.Ser1441ValfsTer7	p.S1441Vfs*7	ENST00000380013	NM_001127208.2	1441	Agt/gt	10/11	1	2	FACETS	1	0.964	1	1	0.994	1	CLONAL	2	FALSE	1	0.332210991423519	2		436	534	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914349	32914349	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027575-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	200	472	0	ENST00000380152.3:c.5857G>C	p.Glu1953Gln	p.E1953Q	ENST00000380152		1953	Gaa/Caa	11/27	NA	2	FACETS	0.871	0.81	0.933			1	INDETERMINATE	1	TRUE	NA	0.688670198293344	2		472	667	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827915	40827915	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs749979947	NA	P-0027575-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	223	446	0	ENST00000373198.4:c.2513G>T	p.Gly838Val	p.G838V	ENST00000373198	NM_133170.3	838	gGc/gTc	17/32	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.688670198293344	2		446	641	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0027576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	14	586	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.487	0.35	0.654	0.487	0.35	0.654	SUBCLONAL	1	TRUE	1	0.1	2		587	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0027576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	28	903	1	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	1	2	FACETS	0.744	0.592	0.918	0.744	0.592	0.918	CLONAL	1	TRUE	1	0.1	2		904	753	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760711	59760711	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	23	822	0	ENST00000259008.2:c.3696G>C	p.Lys1232Asn	p.K1232N	ENST00000259008	NM_032043.2	1232	aaG/aaC	20/20	1	2	FACETS	1	0.803	1	1	0.803	1	CLONAL	1	TRUE	1	0.1	2		822	445	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213917	66213917	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	21	453	0	ENST00000273854.3:c.2513del	p.Gly838GlufsTer13	p.G838Efs*13	ENST00000273854	NM_004439.5	838	gGa/ga	15/18	1	2	FACETS	1	0.808	1	1	0.808	1	CLONAL	1	TRUE	1	0.1	2		453	397	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413040	63413040	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	33	474	0	ENST00000330258.3:c.127G>T	p.Glu43Ter	p.E43*	ENST00000330258	NM_152424.3	43	Gag/Tag	2/2	1	1	FACETS	0.857	0.698	1	1	0.954	1	CLONAL	2	TRUE	0	0.1	1		474	366	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0027615-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	171	581	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.190311225023214	3	FACETS	0.799	0.736	0.864	0.799	0.736	0.864	INDETERMINATE	2	TRUE	1	0.331469685735049	3		581	753	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075211	16075217	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTGTT	ACCTGTT	-	novel	NA	P-0027615-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	97	384	0	ENST00000268712.3:c.335_341del	p.Glu112ValfsTer16	p.E112Vfs*16	ENST00000268712	NM_006311.3	112	gAACAGGTt/gt	4/46	0.331469685735049	3	FACETS	1	0.965	1	0.595	0.532	0.663	CLONAL	1	TRUE	1	0.331469685735049	3		384	573	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246527	41246527	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027615-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	154	567	0	ENST00000357654.3:c.1021G>C	p.Asp341His	p.D341H	ENST00000357654	NM_007294.3	341	Gat/Cat	10/23	0.331469685735049	3	FACETS	1	0.986	1	0.687	0.63	0.748	CLONAL	1	TRUE	1	0.331469685735049	3		567	788	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573560	48573560	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027615-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	45	297	0	ENST00000342988.3:c.144G>T	p.Lys48Asn	p.K48N	ENST00000342988	NM_005359.5	48	aaG/aaT	2/12	1	2	FACETS	0.707	0.596	0.83	0.707	0.596	0.83	SUBCLONAL	1	TRUE	1	0.331469685735049	2		297	384	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568876	212568876	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027615-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	87	444	0	ENST00000342788.4:c.1242C>A	p.Phe414Leu	p.F414L	ENST00000342788	NM_005235.2	414	ttC/ttA	11/28	0.113477118431219	3	FACETS	1	0.931	1	0.356	0.315	0.399	INDETERMINATE	1	TRUE	0	0.331469685735049	3		444	573	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264625	1264625	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027615-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	100	663	0	ENST00000310581.5:c.2737G>T	p.Ala913Ser	p.A913S	ENST00000310581	NM_198253.2	913	Gcc/Tcc	11/16	0.297085267137196	3	FACETS	0.96	0.857	1	0.48	0.428	0.534	CLONAL	1	TRUE	1	0.331469685735049	3		663	733	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797767	32797767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758318646	NA	P-0027615-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	47	501	1	ENST00000374899.4:c.1735G>A	p.Ala579Thr	p.A579T	ENST00000374899	NM_018833.2	579	Gct/Act	10/12	0.297085267137196	3	FACETS	0.498	0.419	0.585	0.249	0.209	0.293	SUBCLONAL	1	TRUE	1	0.331469685735049	3		502	664	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0027643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	627	518	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.89384856966159	6	FACETS	0.974	0.952	0.996	0.812	0.793	0.83	CLONAL	5	TRUE	0	0.89384856966159	6		518	803	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0027643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	225	350	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.89384856966159	2		350	462	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	309	454	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.89384856966159	2		454	666	SUCCESS
APC	324	MSKCC	GRCh37	5	112176386	112176386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	138	285	0	ENST00000257430.4:c.5095G>A	p.Glu1699Lys	p.E1699K	ENST00000257430	NM_000038.5	1699	Gag/Aag	16/16	0.579643226562886	3	FACETS	1	0.979	1	0.594	0.547	0.642	CLONAL	1	TRUE	1	0.89384856966159	3		285	376	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566158	95566158	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	459	476	0	ENST00000393063.1:c.4165C>G	p.Gln1389Glu	p.Q1389E	ENST00000393063	NM_030621.3	1389	Caa/Gaa	23/28	0.876775898441473	3	FACETS	0.911	0.877	0.944	0.911	0.877	0.944	CLONAL	2	TRUE	1	0.89384856966159	3		476	816	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944012	71944012	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs777831045	NA	P-0027643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	281	612	0	ENST00000298229.2:c.1945C>T	p.Arg649Ter	p.R649*	ENST00000298229	NM_001567.3	649	Cga/Tga	16/28	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.89384856966159	2		612	621	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982057	38982057	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	514	559	0	ENST00000357387.3:c.665G>A	p.Arg222Gln	p.R222Q	ENST00000357387	NM_152756.3	222	cGa/cAa	8/38	0.490868639252909	4	FACETS	0.878	0.849	0.906	0.878	0.849	0.906	INDETERMINATE	3	TRUE	1	0.89384856966159	4		559	827	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340820	70340820	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0027643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	191	455	0	ENST00000374080.3:c.554-1G>A		p.X185_splice	ENST00000374080		185			1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.89384856966159	2		455	362	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984705	11984705	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	169	261	1	ENST00000353533.5:c.251C>T	p.Ser84Leu	p.S84L	ENST00000353533	NM_003010.3	84	tCa/tTa	3/11	0.89384856966159	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.89384856966159	2		262	188	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121074	3121074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	419	737	0	ENST00000078429.4:c.977C>T	p.Ser326Leu	p.S326L	ENST00000078429	NM_002067.2	326	tCa/tTa	7/7	1	2	FACETS	0.985	0.942	1	0.985	0.942	1	CLONAL	1	TRUE	1	0.89384856966159	2		737	952	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791744	42791744	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	432	559	1	ENST00000575354.2:c.630C>A	p.Phe210Leu	p.F210L	ENST00000575354	NM_015125.3	210	ttC/ttA	5/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.89384856966159	2		560	896	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45864501	45864886	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTGAGCTGACCCCATAGAATTTCTCTGGCCTCCTCCCTTACCACTGCCCATGCCATCCTTCTCCACTCTGCAGCCCGAGGAAGTCTGTGAAAATGTAAATCTGAGCACAAGGCTTACTCAAGAACTATGTATGGCTCCCCACTGCCTTCAAAATAGGGCCCACACTTCCAAGCCAAACCCCACAAAGCCCTGTGTGTCCTGCCAACAACCCTCTAGACCCTGCTGGGACCCTGATTCCAGCTGCTAGGAGGCCCAGCAGGGACAGAAAAAGGTGAGCTTACCTTTGGCGTAGGTGCTGACAAGGGTGGCAAAGTTAGCAAGGAGGGTGAGCGGGGAGAAGTCAGCAAGGTCGGTGATCTCCAGAGTATGCAGCAGGGACCGGAGGC	GTGAGCTGACCCCATAGAATTTCTCTGGCCTCCTCCCTTACCACTGCCCATGCCATCCTTCTCCACTCTGCAGCCCGAGGAAGTCTGTGAAAATGTAAATCTGAGCACAAGGCTTACTCAAGAACTATGTATGGCTCCCCACTGCCTTCAAAATAGGGCCCACACTTCCAAGCCAAACCCCACAAAGCCCTGTGTGTCCTGCCAACAACCCTCTAGACCCTGCTGGGACCCTGATTCCAGCTGCTAGGAGGCCCAGCAGGGACAGAAAAAGGTGAGCTTACCTTTGGCGTAGGTGCTGACAAGGGTGGCAAAGTTAGCAAGGAGGGTGAGCGGGGAGAAGTCAGCAAGGTCGGTGATCTCCAGAGTATGCAGCAGGGACCGGAGGC	-	novel	NA	P-0027643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	90	3	0	ENST00000391945.4:c.1133_1237+281del		p.X378_splice	ENST00000391945	NM_000400.3	378		12/23	1	2	FACETS	1	0.976	1	1	0.991	1	CLONAL	2	TRUE	1	0.89384856966159	2		3	98	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281284	46281284	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	379	380	1	ENST00000371998.3:c.4081G>A	p.Glu1361Lys	p.E1361K	ENST00000371998		1361	Gaa/Aaa	21/23	0.89384856966159	4	FACETS	0.965	0.922	1	0.643	0.614	0.673	CLONAL	2	TRUE	1	0.89384856966159	4		381	832	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37092097	37092097	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778992	NA	P-0027643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	135	473	0	ENST00000231790.2:c.2224C>T	p.Gln742Ter	p.Q742*	ENST00000231790	NM_000249.3	742	Cag/Tag	19/19	1	2	FACETS	0.888	0.819	0.959	0.888	0.819	0.959	CLONAL	1	TRUE	1	0.89384856966159	2		473	340	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323333	31323333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1258632613	NA	P-0027643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	124	269	0	ENST00000412585.2:c.656C>T	p.Ser219Phe	p.S219F	ENST00000412585	NM_005514.6	219	tCt/tTt	4/8	0.581184658913986	4	FACETS	1	0.986	1	0.484	0.442	0.526	CLONAL	1	TRUE	1	0.89384856966159	4		269	362	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93973611	93973611	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	97	457	1	ENST00000369303.4:c.1765G>A	p.Asp589Asn	p.D589N	ENST00000369303	NM_004440.3	589	Gac/Aac	9/17	0.581184658913986	4	FACETS	0.954	0.855	1	0.318	0.285	0.353	CLONAL	1	TRUE	1	0.89384856966159	4		458	431	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334756	81334756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	213	508	0	ENST00000222390.5:c.1960G>A	p.Glu654Lys	p.E654K	ENST00000222390	NM_000601.4	654	Gag/Aag	17/18	1	2	FACETS	0.903	0.846	0.96	0.903	0.846	0.96	CLONAL	1	TRUE	1	0.89384856966159	2		508	528	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868972	117868972	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	389	421	0	ENST00000297338.2:c.727G>C	p.Asp243His	p.D243H	ENST00000297338	NM_006265.2	243	Gat/Cat	7/14	0.149831726219326	4	FACETS	1	0.993	1	0.579	0.555	0.602	INDETERMINATE	2	TRUE	0	0.89384856966159	4		421	712	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006071	22006071	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	404	560	0	ENST00000276925.6:c.332C>T	p.Ala111Val	p.A111V	ENST00000276925	NM_004936.3	111	gCc/gTc	2/2	0.150594963072885	3	FACETS	1	0.996	1	0.72	0.688	0.752	INDETERMINATE	1	TRUE	1	0.89384856966159	3		560	908	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0027647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	99	529	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.304196493604149	2	FACETS	1	0.981	1	0.711	0.639	0.787	CLONAL	1	TRUE	0	0.342015826353172	2		529	407	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0027647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	74	518	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.27600009537941	3	FACETS	0.997	0.875	1	0.499	0.437	0.565	CLONAL	1	TRUE	1	0.342015826353172	3		518	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579536	7579536	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567556930	NA	P-0027647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	190	551	1	ENST00000269305.4:c.151G>T	p.Glu51Ter	p.E51*	ENST00000269305	NM_001126112.2	51	Gaa/Taa	4/11	0.304196493604149	2	FACETS	0.88	0.818	0.945	0.88	0.818	0.945	CLONAL	2	TRUE	0	0.342015826353172	2		552	631	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28897070	28897070	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	109	294	0	ENST00000282397.4:c.2810A>T	p.His937Leu	p.H937L	ENST00000282397	NM_002019.4	937	cAc/cTc	21/30	0.342015826353172	3	FACETS	0.824	0.744	0.907	0.549	0.496	0.605	CLONAL	2	TRUE	0	0.342015826353172	3		294	453	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488754	212488754	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs774321172	NA	P-0027647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	63	372	0	ENST00000342788.4:c.2095A>C	p.Thr699Pro	p.T699P	ENST00000342788	NM_005235.2	699	Act/Cct	18/28	0.27600009537941	3	FACETS	0.808	0.699	0.925	0.404	0.349	0.463	CLONAL	1	TRUE	1	0.342015826353172	3		372	534	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502388	186502389	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	101	351	0	ENST00000323963.5:c.112dup	p.Met38AsnfsTer17	p.M38Nfs*17	ENST00000323963		37	-/A	3/11	0.27600009537941	3	FACETS	1	0.981	1	0.731	0.657	0.809	CLONAL	1	TRUE	1	0.342015826353172	3		351	473	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858054	152858054	+	synonymous_variant	Silent	SNP	C	C	T	novel	NA	P-0027647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	28	361	0	ENST00000406277.2:c.561G>A	p.Gln187=	p.Q187=	ENST00000406277	NM_152274.4	187	caG/caA	6/7	0.202677574941447	4	FACETS	0.413	0.329	0.509	0.207	0.164	0.255	INDETERMINATE	1	TRUE	2	0.342015826353172	4		361	532	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81557479	81557479	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	31	355	1	ENST00000298171.2:c.459C>A	p.Phe153Leu	p.F153L	ENST00000298171	NM_000369.2	153	ttC/ttA	5/10	1	2	FACETS	0.944	0.763	1	0.944	0.763	1	CLONAL	1	TRUE	1	0.15	2		356	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	51	717	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.848	0.719	0.99	0.848	0.719	0.99	CLONAL	1	TRUE	1	0.15	2		718	802	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665230	117665230	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1258207555	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	19	254	0	ENST00000368508.3:c.4517G>T	p.Arg1506Ile	p.R1506I	ENST00000368508	NM_002944.2	1506	aGa/aTa	27/43	1	2	FACETS	0.925	0.702	1	0.925	0.702	1	CLONAL	1	TRUE	1	0.15	2		254	274	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141631	202141631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs17860424	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	37	457	3	ENST00000358485.4:c.919C>T	p.Arg307Trp	p.R307W	ENST00000358485	NM_001080125.1	307	Cgg/Tgg	7/9	1	2	FACETS	0.72	0.592	0.864	0.72	0.592	0.864	SUBCLONAL	1	TRUE	1	0.15	2		460	685	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911630	39911630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754470140	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	52	469	0	ENST00000378444.4:c.5000C>T	p.Ser1667Leu	p.S1667L	ENST00000378444	NM_001123385.1	1667	tCg/tTg	15/15	1	2	FACETS	0.936	0.795	1	0.936	0.795	1	CLONAL	1	TRUE	1	0.15	2		469	741	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584530	187584530	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200633985	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	31	411	0	ENST00000441802.2:c.3503C>T	p.Ser1168Leu	p.S1168L	ENST00000441802	NM_005245.3	1168	tCg/tTg	3/27	1	2	FACETS	0.955	0.772	1	0.955	0.772	1	CLONAL	1	TRUE	1	0.15	2		411	433	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434839	99434839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1353303081	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	27	390	1	ENST00000268035.6:c.926C>T	p.Ser309Leu	p.S309L	ENST00000268035	NM_000875.3	309	tCg/tTg	3/21	1	2	FACETS	0.724	0.575	0.896	0.724	0.575	0.896	SUBCLONAL	1	TRUE	1	0.15	2		391	497	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103513972	103513972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61749896	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	33	448	0	ENST00000355739.4:c.788G>A	p.Arg263Gln	p.R263Q	ENST00000355739	NM_000123.3	263	cGa/cAa	7/15	1	2	FACETS	0.924	0.752	1	0.924	0.752	1	CLONAL	1	TRUE	1	0.15	2		448	476	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501449	149501449	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	29	529	0	ENST00000261799.4:c.2338C>T	p.Pro780Ser	p.P780S	ENST00000261799	NM_002609.3	780	Ccc/Tcc	16/23	1	2	FACETS	0.712	0.57	0.874	0.712	0.57	0.874	SUBCLONAL	1	TRUE	1	0.15	2		529	543	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267385	7267385	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1189720431	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	40	398	0	ENST00000302850.5:c.623G>A	p.Arg208Gln	p.R208Q	ENST00000302850	NM_000208.2	208	cGa/cAa	2/22	1	2	FACETS	0.86	0.713	1	0.86	0.713	1	CLONAL	1	TRUE	1	0.15	2		398	620	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982356	25982356	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	18	204	0	ENST00000435504.4:c.934C>T	p.Arg312Ter	p.R312*	ENST00000435504		312	Cga/Tga	9/13	1	2	FACETS	1	0.779	1	1	0.779	1	CLONAL	1	TRUE	1	0.15	2		204	232	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	35	577	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	0.703	0.574	0.848	0.703	0.574	0.848	SUBCLONAL	1	TRUE	1	0.15	2		577	664	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171607	36171607	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1569008655	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	26	276	0	ENST00000300305.3:c.958C>T	p.Arg320Ter	p.R320*	ENST00000300305		320	Cga/Tga	7/8	1	2	FACETS	0.915	0.724	1	0.915	0.724	1	CLONAL	1	TRUE	1	0.15	2		276	379	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045676	47045676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	29	547	1	ENST00000377604.3:c.2557C>T	p.Arg853Trp	p.R853W	ENST00000377604	NM_001204468.1	853	Cgg/Tgg	23/24	1	2	FACETS	0.67	0.536	0.823	0.67	0.536	0.823	SUBCLONAL	1	TRUE	1	0.15	2		548	577	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58142357	58142357	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761577371	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	40	397	1	ENST00000257904.6:c.863G>A	p.Arg288Gln	p.R288Q	ENST00000257904	NM_000075.3	288	cGa/cAa	8/8	1	2	FACETS	0.819	0.679	0.976	0.819	0.679	0.976	CLONAL	1	TRUE	1	0.15	2		398	651	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938029	76938029	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	36	495	0	ENST00000373344.5:c.2719C>T	p.Arg907Ter	p.R907*	ENST00000373344	NM_000489.3	907	Cga/Tga	9/35	1	2	FACETS	0.778	0.638	0.935	0.778	0.638	0.935	CLONAL	1	TRUE	1	0.15	2		495	617	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509723	106509723	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	38	491	1	ENST00000359195.3:c.1717G>T	p.Glu573Ter	p.E573*	ENST00000359195	NM_002649.2	573	Gaa/Taa	2/11	1	2	FACETS	0.898	0.742	1	0.898	0.742	1	CLONAL	1	TRUE	1	0.15	2		492	564	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050770	5050770	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	33	413	0	ENST00000381652.3:c.553G>T	p.Asp185Tyr	p.D185Y	ENST00000381652	NM_004972.3	185	Gat/Tat	6/25	1	2	FACETS	0.853	0.693	1	0.853	0.693	1	CLONAL	1	TRUE	1	0.15	2		413	516	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63661997	63661997	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	38	327	0	ENST00000279873.7:c.101G>T	p.Arg34Ile	p.R34I	ENST00000279873	NM_032199.2	34	aGa/aTa	2/10	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.15	2		327	486	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337650	73337650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	23	317	0	ENST00000377767.4:c.2066G>A	p.Arg689Gln	p.R689Q	ENST00000377767	NM_014953.3	689	cGa/cAa	16/21	1	2	FACETS	0.79	0.616	0.993	0.79	0.616	0.993	CLONAL	1	TRUE	1	0.15	2		317	388	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	29	502	1	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.711	0.569	0.873	0.711	0.569	0.873	SUBCLONAL	1	TRUE	1	0.15	2		503	544	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468516	89468516	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1453560937	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	27	339	0	ENST00000336596.2:c.2050C>T	p.Arg684Ter	p.R684*	ENST00000336596	NM_005233.5	684	Cga/Tga	11/17	1	2	FACETS	0.889	0.707	1	0.889	0.707	1	CLONAL	1	TRUE	1	0.15	2		339	405	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912815	100912815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1000609240	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	31	390	0	ENST00000325455.5:c.2507G>A	p.Arg836Gln	p.R836Q	ENST00000325455	NM_001202474.3	836	cGa/cAa	7/8	1	2	FACETS	0.946	0.765	1	0.946	0.765	1	CLONAL	1	TRUE	1	0.15	2		390	437	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965260	81965260	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	18	391	0	ENST00000359376.3:c.2739+1G>A		p.X913_splice	ENST00000359376	NM_002661.3	913			1	2	FACETS	0.67	0.504	0.868	0.67	0.504	0.868	SUBCLONAL	1	TRUE	1	0.15	2		391	358	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936083	178936083	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519927	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	37	436	0	ENST00000263967.3:c.1625A>C	p.Glu542Ala	p.E542A	ENST00000263967	NM_006218.2	542	gAa/gCa	10/21	1	2	FACETS	0.933	0.768	1	0.933	0.768	1	CLONAL	1	TRUE	1	0.15	2		436	529	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350146	89350146	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs575811373	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	37	565	0	ENST00000301030.4:c.2804C>T	p.Ser935Leu	p.S935L	ENST00000301030	NM_001256183.1	935	tCg/tTg	9/13	1	2	FACETS	0.724	0.596	0.869	0.724	0.596	0.869	SUBCLONAL	1	TRUE	1	0.15	2		565	681	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948183	55948183	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	50	463	0	ENST00000263923.4:c.3788T>C	p.Val1263Ala	p.V1263A	ENST00000263923	NM_002253.2	1263	gTt/gCt	29/30	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.15	2		463	571	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622269	117622269	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	38	458	0	ENST00000368508.3:c.6601G>T	p.Glu2201Ter	p.E2201*	ENST00000368508	NM_002944.2	2201	Gaa/Taa	42/43	1	2	FACETS	0.784	0.647	0.939	0.784	0.647	0.939	CLONAL	1	TRUE	1	0.15	2		458	646	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120360	94120360	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs749418654	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	18	250	0	ENST00000369303.4:c.691C>T	p.Arg231Ter	p.R231*	ENST00000369303	NM_004440.3	231	Cga/Tga	3/17	1	2	FACETS	0.848	0.639	1	0.848	0.639	1	CLONAL	1	TRUE	1	0.15	2		250	283	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453185	140453185	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	22	312	0	ENST00000288602.6:c.1750C>T	p.Leu584Phe	p.L584F	ENST00000288602	NM_004333.4	584	Ctt/Ttt	15/18	1	2	FACETS	0.797	0.617	1	0.797	0.617	1	CLONAL	1	TRUE	1	0.15	2		312	368	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77048448	77048448	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	34	507	0	ENST00000356341.3:c.1137C>A	p.Phe379Leu	p.F379L	ENST00000356341	NM_002576.4	379	ttC/ttA	12/15	1	2	FACETS	0.889	0.725	1	0.889	0.725	1	CLONAL	1	TRUE	1	0.15	2		507	510	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6027082	6027082	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	19	196	0	ENST00000265849.7:c.1314G>T	p.Lys438Asn	p.K438N	ENST00000265849	NM_000535.5	438	aaG/aaT	11/15	1	2	FACETS	1	0.801	1	1	0.801	1	CLONAL	1	TRUE	1	0.15	2		196	239	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950648	38950648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776074870	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	22	325	0	ENST00000357387.3:c.3302C>T	p.Ser1101Leu	p.S1101L	ENST00000357387	NM_152756.3	1101	tCg/tTg	31/38	1	2	FACETS	0.746	0.578	0.943	0.746	0.578	0.943	CLONAL	1	TRUE	1	0.15	2		325	393	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215787	133215787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762000608	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	38	618	1	ENST00000320574.5:c.5476C>T	p.Arg1826Trp	p.R1826W	ENST00000320574	NM_006231.2	1826	Cgg/Tgg	40/49	1	2	FACETS	0.714	0.588	0.855	0.714	0.588	0.855	SUBCLONAL	1	TRUE	1	0.15	2		619	710	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858202	9858202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	26	385	0	ENST00000330684.3:c.3199C>T	p.Arg1067Trp	p.R1067W	ENST00000330684	NM_001134407.1	1067	Cgg/Tgg	13/13	1	2	FACETS	0.767	0.606	0.952	0.767	0.606	0.952	CLONAL	1	TRUE	1	0.15	2		385	452	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793716	89793716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754149624	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	26	339	0	ENST00000336032.3:c.785C>T	p.Ser262Leu	p.S262L	ENST00000336032	NM_006813.2	262	tCg/tTg	2/2	1	2	FACETS	0.696	0.55	0.864	0.696	0.55	0.864	SUBCLONAL	1	TRUE	1	0.15	2		339	498	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861149	57861149	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774058977	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	27	446	0	ENST00000228682.2:c.946G>A	p.Glu316Lys	p.E316K	ENST00000228682	NM_005269.2	316	Gaa/Aaa	9/12	1	2	FACETS	0.668	0.53	0.826	0.668	0.53	0.826	SUBCLONAL	1	TRUE	1	0.15	2		446	539	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99203950	99203950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755469992	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	31	296	0	ENST00000074304.5:c.2813G>A	p.Arg938Gln	p.R938Q	ENST00000074304	NM_001134224.1	938	cGa/cAa	26/26	1	2	FACETS	0.977	0.79	1	0.977	0.79	1	CLONAL	1	TRUE	1	0.15	2		296	423	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157539	106157539	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs192553789	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	29	309	1	ENST00000380013.4:c.2440C>T	p.Arg814Cys	p.R814C	ENST00000380013	NM_001127208.2	814	Cgt/Tgt	3/11	1	2	FACETS	0.889	0.713	1	0.889	0.713	1	CLONAL	1	TRUE	1	0.15	2		310	435	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642470	117642470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765146445	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	32	512	0	ENST00000368508.3:c.5729G>A	p.Arg1910Gln	p.R1910Q	ENST00000368508	NM_002944.2	1910	cGa/cAa	35/43	1	2	FACETS	0.68	0.551	0.828	0.68	0.551	0.828	SUBCLONAL	1	TRUE	1	0.15	2		512	627	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984839	11984839	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	26	370	1	ENST00000353533.5:c.385G>A	p.Ala129Thr	p.A129T	ENST00000353533	NM_003010.3	129	Gca/Aca	3/11	1	2	FACETS	0.827	0.655	1	0.827	0.655	1	CLONAL	1	TRUE	1	0.15	2		371	419	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294283	1294283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	32	540	2	ENST00000310581.5:c.718C>T	p.Arg240Cys	p.R240C	ENST00000310581	NM_198253.2	240	Cgt/Tgt	2/16	1	2	FACETS	0.821	0.665	0.997	0.821	0.665	0.997	CLONAL	1	TRUE	1	0.15	2		542	520	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332605	70332605	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs781424040	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	30	485	1	ENST00000373644.4:c.510G>T	p.Glu170Asp	p.E170D	ENST00000373644	NM_030625.2	170	gaG/gaT	2/12	1	2	FACETS	0.787	0.633	0.963	0.787	0.633	0.963	CLONAL	1	TRUE	1	0.15	2		486	508	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662140	227662140	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760127800	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	31	549	0	ENST00000305123.5:c.1315C>T	p.Arg439Trp	p.R439W	ENST00000305123	NM_005544.2	439	Cgg/Tgg	1/2	1	2	FACETS	0.767	0.619	0.935	0.767	0.619	0.935	CLONAL	1	TRUE	1	0.15	2		549	539	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692811	89692811	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	24	235	1	ENST00000371953.3:c.295G>T	p.Glu99Ter	p.E99*	ENST00000371953	NM_000314.4	99	Gaa/Taa	5/9	1	2	FACETS	1	0.79	1	1	0.79	1	CLONAL	1	TRUE	1	0.15	2		236	318	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578238	7578238	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1260903787	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	37	567	0	ENST00000269305.4:c.611A>G	p.Glu204Gly	p.E204G	ENST00000269305	NM_001126112.2	204	gAg/gGg	6/11	1	2	FACETS	0.678	0.557	0.814	0.678	0.557	0.814	SUBCLONAL	1	TRUE	1	0.15	2		567	728	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913224	39913224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769982436	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	31	446	0	ENST00000378444.4:c.4891G>A	p.Asp1631Asn	p.D1631N	ENST00000378444	NM_001123385.1	1631	Gat/Aat	14/15	1	2	FACETS	0.682	0.55	0.832	0.682	0.55	0.832	SUBCLONAL	1	TRUE	1	0.15	2		446	606	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14303198	14303198	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	31	482	0	ENST00000256196.4:c.477G>T	p.Lys159Asn	p.K159N	ENST00000256196		159	aaG/aaT	5/6	1	2	FACETS	0.726	0.586	0.886	0.726	0.586	0.886	SUBCLONAL	1	TRUE	1	0.15	2		482	569	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184142	56184142	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	27	443	0	ENST00000399503.3:c.4347G>A	p.Trp1449Ter	p.W1449*	ENST00000399503	NM_005921.1	1449	tgG/tgA	19/20	1	2	FACETS	0.716	0.568	0.885	0.716	0.568	0.885	SUBCLONAL	1	TRUE	1	0.15	2		443	503	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602334	10602334	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1379198956	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	39	634	1	ENST00000171111.5:c.1244G>A	p.Arg415His	p.R415H	ENST00000171111	NM_203500.1	415	cGc/cAc	3/6	1	2	FACETS	0.698	0.577	0.834	0.698	0.577	0.834	SUBCLONAL	1	TRUE	1	0.15	2		635	745	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926960	112926960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770363146	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	30	417	0	ENST00000351677.2:c.1580G>A	p.Arg527His	p.R527H	ENST00000351677	NM_002834.3	527	cGc/cAc	13/16	1	2	FACETS	0.786	0.632	0.961	0.786	0.632	0.961	CLONAL	1	TRUE	1	0.15	2		417	509	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617503	158617503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1034717563	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	35	443	0	ENST00000263640.3:c.1153G>A	p.Glu385Lys	p.E385K	ENST00000263640	NM_001105.4	385	Gaa/Aaa	9/11	1	2	FACETS	0.836	0.684	1	0.836	0.684	1	CLONAL	1	TRUE	1	0.15	2		443	558	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624296	89624296	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786201995	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	37	453	1	ENST00000371953.3:c.70G>T	p.Asp24Tyr	p.D24Y	ENST00000371953	NM_000314.4	24	Gac/Tac	1/9	1	2	FACETS	0.81	0.666	0.971	0.81	0.666	0.971	CLONAL	1	TRUE	1	0.15	2		454	609	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101118	4101118	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769471250	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	29	356	0	ENST00000262948.5:c.604G>A	p.Val202Met	p.V202M	ENST00000262948	NM_030662.3	202	Gtg/Atg	6/11	1	2	FACETS	0.962	0.772	1	0.962	0.772	1	CLONAL	1	TRUE	1	0.15	2		356	402	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144632	55144632	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	27	403	0	ENST00000257290.5:c.2106G>T	p.Lys702Asn	p.K702N	ENST00000257290	NM_006206.4	702	aaG/aaT	15/23	1	2	FACETS	0.752	0.597	0.929	0.752	0.597	0.929	CLONAL	1	TRUE	1	0.15	2		403	479	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527931	103527931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs4150388	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	23	320	2	ENST00000355739.4:c.3239G>A	p.Gly1080Glu	p.G1080E	ENST00000355739	NM_000123.3	1080	gGa/gAa	15/15	1	2	FACETS	0.735	0.572	0.925	0.735	0.572	0.925	CLONAL	1	TRUE	1	0.15	2		322	417	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625110	69625110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782454437	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	27	528	0	ENST00000334134.2:c.683C>T	p.Ser228Leu	p.S228L	ENST00000334134	NM_005247.2	228	tCg/tTg	3/3	1	2	FACETS	0.768	0.61	0.949	0.768	0.61	0.949	CLONAL	1	TRUE	1	0.15	2		528	469	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374726	118374726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437799270	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	24	350	1	ENST00000534358.1:c.8119C>T	p.Arg2707Trp	p.R2707W	ENST00000534358	NM_005933.3	2707	Cgg/Tgg	27/36	1	2	FACETS	0.688	0.538	0.862	0.688	0.538	0.862	SUBCLONAL	1	TRUE	1	0.15	2		351	465	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967567	26967567	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	33	482	0	ENST00000381527.3:c.710G>A	p.Arg237Gln	p.R237Q	ENST00000381527	NM_001260.1	237	cGa/cAa	7/13	1	2	FACETS	0.685	0.557	0.831	0.685	0.557	0.831	SUBCLONAL	1	TRUE	1	0.15	2		482	642	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188271	142188271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202193482	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	45	409	0	ENST00000350721.4:c.6460G>A	p.Asp2154Asn	p.D2154N	ENST00000350721	NM_001184.3	2154	Gat/Aat	38/47	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.15	2		409	589	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609759	117609759	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs771164515	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	35	447	1	ENST00000368508.3:c.6940G>T	p.Asp2314Tyr	p.D2314Y	ENST00000368508	NM_002944.2	2314	Gat/Tat	43/43	1	2	FACETS	0.943	0.772	1	0.943	0.772	1	CLONAL	1	TRUE	1	0.15	2		448	495	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796753	135796753	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755859330	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	18	325	1	ENST00000298552.3:c.734G>A	p.Arg245Gln	p.R245Q	ENST00000298552	NM_001162426.1	245	cGa/cAa	8/23	1	2	FACETS	0.757	0.57	0.979	0.757	0.57	0.979	CLONAL	1	TRUE	1	0.15	2		326	317	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818837	32818837	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1336232266	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	35	514	0	ENST00000354258.4:c.1114C>T	p.Arg372Ter	p.R372*	ENST00000354258	NM_000593.5	372	Cga/Tga	4/11	1	2	FACETS	0.698	0.57	0.841	0.698	0.57	0.841	SUBCLONAL	1	TRUE	1	0.15	2		514	669	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251876	212251876	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1553519044	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	25	214	0	ENST00000342788.4:c.3184-1G>T		p.X1062_splice	ENST00000342788	NM_005235.2	1062			1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.15	2		214	269	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874295	76874295	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	33	505	0	ENST00000373344.5:c.5427G>T	p.Glu1809Asp	p.E1809D	ENST00000373344	NM_000489.3	1809	gaG/gaT	21/35	1	2	FACETS	0.876	0.713	1	0.876	0.713	1	CLONAL	1	TRUE	1	0.15	2		505	502	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374921	149374921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	36	549	1	ENST00000360632.3:c.173C>T	p.Ser58Leu	p.S58L	ENST00000360632	NM_015472.4	58	tCg/tTg	2/7	1	2	FACETS	0.743	0.609	0.894	0.743	0.609	0.894	SUBCLONAL	1	TRUE	1	0.15	2		550	646	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780619	56780619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137947462	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	49	464	0	ENST00000337432.4:c.634C>T	p.Arg212Cys	p.R212C	ENST00000337432	NM_058216.2	212	Cgc/Tgc	4/9	1	2	FACETS	0.905	0.765	1	0.905	0.765	1	CLONAL	1	TRUE	1	0.15	2		464	722	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188404	32188404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763926116	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	28	397	0	ENST00000375023.3:c.937G>A	p.Glu313Lys	p.E313K	ENST00000375023	NM_004557.3	313	Gaa/Aaa	6/30	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.15	2		397	344	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40871210	40871210	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	28	369	0	ENST00000428826.2:c.680C>T	p.Ser227Phe	p.S227F	ENST00000428826		227	tCc/tTc	8/21	1	2	FACETS	0.806	0.644	0.992	0.806	0.644	0.992	CLONAL	1	TRUE	1	0.15	2		369	463	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163297332	163297332	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1292835761	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	36	467	1	ENST00000271452.3:c.178C>T	p.Arg60Ter	p.R60*	ENST00000271452	NM_145697.2	60	Cga/Tga	3/14	1	2	FACETS	0.783	0.642	0.942	0.783	0.642	0.942	CLONAL	1	TRUE	1	0.15	2		468	613	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467723	66467723	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	32	336	0	ENST00000273854.3:c.546C>A	p.Ser182Arg	p.S182R	ENST00000273854	NM_004439.5	182	agC/agA	3/18	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.15	2		336	364	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305238	39305238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs890472037	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	48	415	0	ENST00000373001.3:c.1187G>A	p.Arg396Gln	p.R396Q	ENST00000373001	NM_022157.3	396	cGa/cAa	7/7	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.15	2		415	545	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741894	40741894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs930976777	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	40	573	1	ENST00000392038.2:c.1078G>A	p.Glu360Lys	p.E360K	ENST00000392038	NM_001626.4	360	Gag/Aag	11/14	1	2	FACETS	0.796	0.66	0.948	0.796	0.66	0.948	CLONAL	1	TRUE	1	0.15	2		574	670	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31451654	31451654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600599	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	34	404	0	ENST00000344624.3:c.2668C>T	p.Arg890Cys	p.R890C	ENST00000344624		890	Cgt/Tgt	18/33	1	2	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	TRUE	1	0.15	2		404	436	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705445	47705445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63751477	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	17	275	0	ENST00000233146.2:c.2245G>A	p.Glu749Lys	p.E749K	ENST00000233146	NM_000251.2	749	Gaa/Aaa	14/16	1	2	FACETS	0.812	0.606	1	0.812	0.606	1	CLONAL	1	TRUE	1	0.15	2		275	279	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056157	27056157	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	32	386	1	ENST00000324856.7:c.1153G>A	p.Asp385Asn	p.D385N	ENST00000324856	NM_006015.4	385	Gat/Aat	2/20	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.15	2		387	401	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932848	36932848	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	35	646	0	ENST00000361632.4:c.2023C>T	p.Pro675Ser	p.P675S	ENST00000361632		675	Ccc/Tcc	15/16	1	2	FACETS	0.827	0.677	0.997	0.827	0.677	0.997	CLONAL	1	TRUE	1	0.15	2		646	564	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363354	40363354	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	37	551	0	ENST00000397332.2:c.875G>T	p.Ser292Ile	p.S292I	ENST00000397332	NM_001033082.2	292	aGt/aTt	3/3	1	2	FACETS	0.835	0.687	1	0.835	0.687	1	CLONAL	1	TRUE	1	0.15	2		551	591	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739132	46739132	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	22	422	0	ENST00000371975.4:c.1481T>C	p.Leu494Pro	p.L494P	ENST00000371975	NM_003579.3	494	cTg/cCg	13/18	1	2	FACETS	0.7	0.542	0.885	0.7	0.542	0.885	SUBCLONAL	1	TRUE	1	0.15	2		422	419	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736485	85736485	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	39	327	0	ENST00000370580.1:c.162A>C	p.Glu54Asp	p.E54D	ENST00000370580	NM_003921.4	54	gaA/gaC	2/3	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.15	2		327	487	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275269	115275269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1259671915	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	45	512	0	ENST00000438362.2:c.1144G>A	p.Val382Ile	p.V382I	ENST00000438362	NM_001242891.1	382	Gtt/Att	10/20	1	2	FACETS	0.851	0.714	1	0.851	0.714	1	CLONAL	1	TRUE	1	0.15	2		512	705	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729744	162729744	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750450749	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	34	576	0	ENST00000367921.3:c.830G>A	p.Arg277His	p.R277H	ENST00000367921	NM_006182.2	277	cGc/cAc	8/18	1	2	FACETS	0.827	0.675	0.999	0.827	0.675	0.999	CLONAL	1	TRUE	1	0.15	2		576	548	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306627	163306627	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	26	266	0	ENST00000271452.3:c.424C>A	p.Leu142Ile	p.L142I	ENST00000271452	NM_145697.2	142	Ctt/Att	6/14	1	2	FACETS	0.898	0.711	1	0.898	0.711	1	CLONAL	1	TRUE	1	0.15	2		266	386	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957481	175957481	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	37	442	0	ENST00000367669.3:c.1915C>A	p.His639Asn	p.H639N	ENST00000367669	NM_022457.5	639	Cat/Aat	17/20	1	2	FACETS	0.842	0.693	1	0.842	0.693	1	CLONAL	1	TRUE	1	0.15	2		442	586	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175810	176175810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	24	458	2	ENST00000367669.3:c.305G>A	p.Ser102Asn	p.S102N	ENST00000367669	NM_022457.5	102	aGc/aAc	1/20	1	2	FACETS	0.838	0.656	1	0.838	0.656	1	CLONAL	1	TRUE	1	0.15	2		460	382	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622080	43622080	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	27	383	0	ENST00000355710.3:c.3097C>A	p.Leu1033Ile	p.L1033I	ENST00000355710	NM_020975.4	1033	Ctc/Atc	19/20	1	2	FACETS	0.855	0.68	1	0.855	0.68	1	CLONAL	1	TRUE	1	0.15	2		383	421	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850731	63850731	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	27	448	0	ENST00000279873.7:c.1509T>G	p.Phe503Leu	p.F503L	ENST00000279873	NM_032199.2	503	ttT/ttG	10/10	1	2	FACETS	0.727	0.578	0.899	0.727	0.578	0.899	SUBCLONAL	1	TRUE	1	0.15	2		448	495	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332922	70332922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753994987	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	33	523	0	ENST00000373644.4:c.827G>A	p.Arg276Gln	p.R276Q	ENST00000373644	NM_030625.2	276	cGa/cAa	2/12	1	2	FACETS	0.667	0.541	0.809	0.667	0.541	0.809	SUBCLONAL	1	TRUE	1	0.15	2		523	660	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77051735	77051735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	45	495	1	ENST00000356341.3:c.1072G>A	p.Glu358Lys	p.E358K	ENST00000356341	NM_002576.4	358	Gaa/Aaa	11/15	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.15	2		496	591	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94153295	94153295	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	43	397	0	ENST00000323929.3:c.2123G>T	p.Arg708Ile	p.R708I	ENST00000323929	NM_005591.3	708	aGa/aTa	20/20	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.15	2		397	535	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912728	100912728	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs2020880	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	43	433	0	ENST00000325455.5:c.2594C>T	p.Ser865Leu	p.S865L	ENST00000325455	NM_001202474.3	865	tCg/tTg	7/8	1	2	FACETS	0.913	0.763	1	0.913	0.763	1	CLONAL	1	TRUE	1	0.15	2		433	628	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102056830	102056830	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	55	574	0	ENST00000282441.5:c.770C>A	p.Ser257Tyr	p.S257Y	ENST00000282441	NM_001130145.2	257	tCt/tAt	4/9	1	2	FACETS	0.982	0.838	1	0.982	0.838	1	CLONAL	1	TRUE	1	0.15	2		574	747	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342687	118342687	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	20	318	0	ENST00000534358.1:c.813A>C	p.Lys271Asn	p.K271N	ENST00000534358	NM_005933.3	271	aaA/aaC	3/36	1	2	FACETS	0.677	0.517	0.865	0.677	0.517	0.865	SUBCLONAL	1	TRUE	1	0.15	2		318	394	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719961	18719961	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	36	476	1	ENST00000266497.5:c.3858G>T	p.Gln1286His	p.Q1286H	ENST00000266497		1286	caG/caT	27/31	1	2	FACETS	0.847	0.695	1	0.847	0.695	1	CLONAL	1	TRUE	1	0.15	2		477	567	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864405	57864405	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	28	520	0	ENST00000228682.2:c.1882G>T	p.Gly628Ter	p.G628*	ENST00000228682	NM_005269.2	628	Gga/Tga	12/12	1	2	FACETS	0.719	0.574	0.886	0.719	0.574	0.886	SUBCLONAL	1	TRUE	1	0.15	2		520	519	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865639	57865639	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	38	681	2	ENST00000228682.2:c.3116C>A	p.Ser1039Tyr	p.S1039Y	ENST00000228682	NM_005269.2	1039	tCt/tAt	12/12	1	2	FACETS	0.711	0.586	0.851	0.711	0.586	0.851	SUBCLONAL	1	TRUE	1	0.15	2		683	713	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885978	111885978	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	31	472	1	ENST00000341259.2:c.1600G>T	p.Glu534Ter	p.E534*	ENST00000341259	NM_005475.2	534	Gaa/Taa	8/8	1	2	FACETS	0.895	0.723	1	0.895	0.723	1	CLONAL	1	TRUE	1	0.15	2		473	462	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426774	121426774	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	42	580	1	ENST00000257555.6:c.465G>T	p.Lys155Asn	p.K155N	ENST00000257555		155	aaG/aaT	2/10	1	2	FACETS	0.951	0.793	1	0.951	0.793	1	CLONAL	1	TRUE	1	0.15	2		581	589	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123892065	123892065	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	32	333	0	ENST00000330479.4:c.874C>T	p.Arg292Cys	p.R292C	ENST00000330479	NM_020382.3	292	Cgc/Tgc	8/9	1	2	FACETS	0.99	0.803	1	0.99	0.803	1	CLONAL	1	TRUE	1	0.15	2		333	431	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959449	26959449	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	32	394	0	ENST00000381527.3:c.616C>A	p.Leu206Ile	p.L206I	ENST00000381527	NM_001260.1	206	Ctt/Att	6/13	1	2	FACETS	0.811	0.657	0.986	0.811	0.657	0.986	CLONAL	1	TRUE	1	0.15	2		394	526	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28883029	28883029	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs370986273	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	34	426	1	ENST00000282397.4:c.3671G>T	p.Arg1224Ile	p.R1224I	ENST00000282397	NM_002019.4	1224	aGa/aTa	28/30	1	2	FACETS	0.829	0.676	1	0.829	0.676	1	CLONAL	1	TRUE	1	0.15	2		427	547	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349471	73349471	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777245855	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	29	418	0	ENST00000377767.4:c.865G>A	p.Glu289Lys	p.E289K	ENST00000377767	NM_014953.3	289	Gaa/Aaa	6/21	1	2	FACETS	0.748	0.599	0.918	0.748	0.599	0.918	CLONAL	1	TRUE	1	0.15	2		418	517	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30102097	30102097	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs754526309	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	37	504	0	ENST00000331968.5:c.1370A>G	p.Asp457Gly	p.D457G	ENST00000331968	NM_002742.2	457	gAc/gGc	9/18	1	2	FACETS	0.833	0.686	0.999	0.833	0.686	0.999	CLONAL	1	TRUE	1	0.15	2		504	592	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570317	95570317	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	19	325	0	ENST00000393063.1:c.3416G>T	p.Arg1139Ile	p.R1139I	ENST00000393063	NM_030621.3	1139	aGa/aTa	22/28	1	2	FACETS	0.667	0.505	0.857	0.667	0.505	0.857	SUBCLONAL	1	TRUE	1	0.15	2		325	380	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582911	95582911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143533680	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	26	336	1	ENST00000393063.1:c.1631G>A	p.Arg544Gln	p.R544Q	ENST00000393063	NM_030621.3	544	cGa/cAa	11/28	1	2	FACETS	0.749	0.592	0.929	0.749	0.592	0.929	CLONAL	1	TRUE	1	0.15	2		337	463	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988899	41988899	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	43	498	0	ENST00000219905.7:c.1691G>T	p.Arg564Ile	p.R564I	ENST00000219905	NM_001164273.1	564	aGa/aTa	3/24	1	2	FACETS	0.886	0.74	1	0.886	0.74	1	CLONAL	1	TRUE	1	0.15	2		498	647	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035003	42035003	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	43	483	0	ENST00000219905.7:c.4845G>T	p.Met1615Ile	p.M1615I	ENST00000219905	NM_001164273.1	1615	atG/atT	15/24	1	2	FACETS	0.851	0.71	1	0.851	0.71	1	CLONAL	1	TRUE	1	0.15	2		483	674	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726694	88726694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766899479	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	28	388	0	ENST00000360948.2:c.350G>A	p.Ser117Asn	p.S117N	ENST00000360948	NM_001012338.2	117	aGc/aAc	4/19	1	2	FACETS	0.771	0.615	0.95	0.771	0.615	0.95	CLONAL	1	TRUE	1	0.15	2		388	484	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121536	2121536	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45517206	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	31	559	0	ENST00000219476.3:c.1865G>A	p.Arg622Gln	p.R622Q	ENST00000219476	NM_000548.3	622	cGg/cAg	18/42	1	2	FACETS	0.739	0.597	0.902	0.739	0.597	0.902	CLONAL	1	TRUE	1	0.15	2		559	559	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640689	3640689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750906921	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	34	544	0	ENST00000294008.3:c.2950G>A	p.Glu984Lys	p.E984K	ENST00000294008	NM_032444.2	984	Gaa/Aaa	12/15	1	2	FACETS	0.749	0.611	0.906	0.749	0.611	0.906	CLONAL	1	TRUE	1	0.15	2		544	605	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640733	3640733	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	29	422	0	ENST00000294008.3:c.2906G>T	p.Arg969Ile	p.R969I	ENST00000294008	NM_032444.2	969	aGa/aTa	12/15	1	2	FACETS	0.869	0.697	1	0.869	0.697	1	CLONAL	1	TRUE	1	0.15	2		422	445	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644491	3644491	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	52	673	0	ENST00000294008.3:c.2123T>C	p.Phe708Ser	p.F708S	ENST00000294008	NM_032444.2	708	tTc/tCc	10/15	1	2	FACETS	0.855	0.726	0.997	0.855	0.726	0.997	CLONAL	1	TRUE	1	0.15	2		673	811	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646333	3646333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755044096	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	45	594	1	ENST00000294008.3:c.1745G>A	p.Arg582Gln	p.R582Q	ENST00000294008	NM_032444.2	582	cGa/cAa	8/15	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.15	2		595	582	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860642	3860642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	37	543	0	ENST00000262367.5:c.937G>A	p.Asp313Asn	p.D313N	ENST00000262367	NM_004380.2	313	Gat/Aat	3/31	1	2	FACETS	0.692	0.569	0.831	0.692	0.569	0.831	SUBCLONAL	1	TRUE	1	0.15	2		543	713	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827388	72827388	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	54	559	1	ENST00000268489.5:c.9193G>T	p.Glu3065Ter	p.E3065*	ENST00000268489	NM_006885.3	3065	Gaa/Taa	9/10	1	2	FACETS	0.997	0.85	1	0.997	0.85	1	CLONAL	1	TRUE	1	0.15	2		560	722	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350687	89350687	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	68	774	1	ENST00000301030.4:c.2263G>T	p.Glu755Ter	p.E755*	ENST00000301030	NM_001256183.1	755	Gaa/Taa	9/13	1	2	FACETS	0.888	0.77	1	0.888	0.77	1	CLONAL	1	TRUE	1	0.15	2		775	1021	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37863269	37863269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149937802	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	39	543	1	ENST00000269571.5:c.100C>T	p.Arg34Trp	p.R34W	ENST00000269571		34	Cgg/Tgg	2/27	1	2	FACETS	0.967	0.8	1	0.967	0.8	1	CLONAL	1	TRUE	1	0.15	2		544	538	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772321	56772321	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	24	340	0	ENST00000337432.4:c.175G>T	p.Glu59Ter	p.E59*	ENST00000337432	NM_058216.2	59	Gaa/Taa	2/9	1	2	FACETS	0.668	0.523	0.837	0.668	0.523	0.837	SUBCLONAL	1	TRUE	1	0.15	2		340	479	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756761	756761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	34	414	0	ENST00000314574.4:c.67G>A	p.Glu23Lys	p.E23K	ENST00000314574	NM_005433.3	23	Gag/Aag	2/12	1	2	FACETS	0.798	0.651	0.964	0.798	0.651	0.964	CLONAL	1	TRUE	1	0.15	2		414	568	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39570468	39570468	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs267605182	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	23	220	0	ENST00000262039.4:c.664C>T	p.Arg222Ter	p.R222*	ENST00000262039	NM_002647.2	222	Cga/Tga	6/25	1	2	FACETS	0.913	0.712	1	0.913	0.712	1	CLONAL	1	TRUE	1	0.15	2		220	336	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56363605	56363605	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs771527830	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	14	190	0	ENST00000348428.3:c.384G>T	p.Lys128Asn	p.K128N	ENST00000348428	NM_006785.3	128	aaG/aaT	3/17	1	2	FACETS	0.686	0.495	0.918	0.686	0.495	0.918	SUBCLONAL	1	TRUE	1	0.15	2		190	272	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122781	7122781	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	24	412	0	ENST00000302850.5:c.3373A>C	p.Asn1125His	p.N1125H	ENST00000302850	NM_000208.2	1125	Aat/Cat	19/22	1	2	FACETS	0.737	0.577	0.923	0.737	0.577	0.923	CLONAL	1	TRUE	1	0.15	2		412	434	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265391	10265391	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748821501	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	46	551	0	ENST00000340748.4:c.1655G>A	p.Arg552Gln	p.R552Q	ENST00000340748		552	cGa/cAa	20/40	1	2	FACETS	0.907	0.763	1	0.907	0.763	1	CLONAL	1	TRUE	1	0.15	2		551	676	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602848	10602848	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	56	693	2	ENST00000171111.5:c.730G>A	p.Glu244Lys	p.E244K	ENST00000171111	NM_203500.1	244	Gag/Aag	3/6	1	2	FACETS	0.847	0.723	0.982	0.847	0.723	0.982	CLONAL	1	TRUE	1	0.15	2		695	882	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271550	15271550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	47	707	3	ENST00000263388.2:c.6889C>A	p.Pro2297Thr	p.P2297T	ENST00000263388	NM_000435.2	2297	Ccc/Acc	33/33	1	2	FACETS	0.919	0.774	1	0.919	0.774	1	CLONAL	1	TRUE	1	0.15	2		710	682	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257373	19257373	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	30	545	0	ENST00000162023.5:c.760G>T	p.Gly254Cys	p.G254C	ENST00000162023		254	Ggc/Tgc	11/13	1	2	FACETS	0.721	0.579	0.882	0.721	0.579	0.882	SUBCLONAL	1	TRUE	1	0.15	2		545	555	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905959	50905959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201010746	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	37	606	3	ENST00000440232.2:c.931C>T	p.Arg311Cys	p.R311C	ENST00000440232	NM_002691.3	311	Cgc/Tgc	8/27	1	2	FACETS	0.801	0.659	0.96	0.801	0.659	0.96	CLONAL	1	TRUE	1	0.15	2		609	616	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467155	25467155	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	27	442	0	ENST00000264709.3:c.1720G>A	p.Ala574Thr	p.A574T	ENST00000264709	NM_175629.2	574	Gca/Aca	15/23	1	2	FACETS	0.709	0.563	0.876	0.709	0.563	0.876	SUBCLONAL	1	TRUE	1	0.15	2		442	508	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213369	39213369	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	57	636	0	ENST00000402219.2:c.3598G>T	p.Asp1200Tyr	p.D1200Y	ENST00000402219	NM_005633.3	1200	Gac/Tac	23/23	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.15	2		636	740	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250080	39250080	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	38	442	0	ENST00000402219.2:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000402219	NM_005633.3	497	Cga/Tga	10/23	1	2	FACETS	0.804	0.663	0.962	0.804	0.663	0.962	CLONAL	1	TRUE	1	0.15	2		442	630	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46602873	46602873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749317556	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	45	566	0	ENST00000263734.3:c.931G>A	p.Ala311Thr	p.A311T	ENST00000263734	NM_001430.4	311	Gca/Aca	8/16	1	2	FACETS	0.844	0.708	0.995	0.844	0.708	0.995	CLONAL	1	TRUE	1	0.15	2		566	711	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61710198	61710198	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	45	326	0	ENST00000401558.2:c.2706A>C	p.Gln902His	p.Q902H	ENST00000401558	NM_003400.3	902	caA/caC	22/25	1	2	FACETS	0.962	0.807	1	0.962	0.807	1	CLONAL	1	TRUE	1	0.15	2		326	624	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719835	61719835	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	32	490	0	ENST00000401558.2:c.1433A>G	p.Glu478Gly	p.E478G	ENST00000401558	NM_003400.3	478	gAg/gGg	14/25	1	2	FACETS	0.678	0.549	0.825	0.678	0.549	0.825	SUBCLONAL	1	TRUE	1	0.15	2		490	629	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61725926	61725926	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	26	400	0	ENST00000401558.2:c.641A>C	p.Glu214Ala	p.E214A	ENST00000401558	NM_003400.3	214	gAa/gCa	9/25	1	2	FACETS	0.707	0.559	0.878	0.707	0.559	0.878	SUBCLONAL	1	TRUE	1	0.15	2		400	490	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920658	96920658	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	30	440	0	ENST00000258439.3:c.322C>A	p.Leu108Ile	p.L108I	ENST00000258439	NM_001193304.2	108	Ctc/Atc	3/4	1	2	FACETS	0.677	0.544	0.828	0.677	0.544	0.828	SUBCLONAL	1	TRUE	1	0.15	2		440	591	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136254	202136254	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	56	448	1	ENST00000358485.4:c.498G>T	p.Gln166His	p.Q166H	ENST00000358485	NM_001080125.1	166	caG/caT	3/9	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.15	2		449	627	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632309	215632309	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1559409974	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	32	458	0	ENST00000260947.4:c.1465A>G	p.Thr489Ala	p.T489A	ENST00000260947	NM_000465.2	489	Acc/Gcc	6/11	1	2	FACETS	0.776	0.628	0.943	0.776	0.628	0.943	CLONAL	1	TRUE	1	0.15	2		458	550	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525053	9525053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	31	440	0	ENST00000353224.5:c.1832C>T	p.Ala611Val	p.A611V	ENST00000353224	NM_177990.2	611	gCc/gTc	8/10	1	2	FACETS	0.878	0.709	1	0.878	0.709	1	CLONAL	1	TRUE	1	0.15	2		440	471	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546695	9546695	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	15	266	0	ENST00000353224.5:c.1327G>T	p.Gly443Ter	p.G443*	ENST00000353224	NM_177990.2	443	Gga/Tga	5/10	1	2	FACETS	0.667	0.487	0.883	0.667	0.487	0.883	SUBCLONAL	1	TRUE	1	0.15	2		266	300	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624953	9624953	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764122690	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	21	224	0	ENST00000353224.5:c.24G>T	p.Lys8Asn	p.K8N	ENST00000353224	NM_177990.2	8	aaG/aaT	3/10	1	2	FACETS	0.943	0.726	1	0.943	0.726	1	CLONAL	1	TRUE	1	0.15	2		224	297	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394020	31394020	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	29	345	3	ENST00000328111.2:c.2307G>T	p.Lys769Asn	p.K769N	ENST00000328111	NM_006892.3	769	aaG/aaT	22/23	1	2	FACETS	0.893	0.716	1	0.893	0.716	1	CLONAL	1	TRUE	1	0.15	2		348	433	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262828	46262828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148666287	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	32	415	0	ENST00000371998.3:c.1001G>A	p.Arg334Gln	p.R334Q	ENST00000371998		334	cGa/cAa	10/23	1	2	FACETS	0.835	0.677	1	0.835	0.677	1	CLONAL	1	TRUE	1	0.15	2		415	511	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62290789	62290789	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	18	197	0	ENST00000360203.5:c.34G>T	p.Asp12Tyr	p.D12Y	ENST00000360203	NM_001283009.1	12	Gac/Tac	2/35	1	2	FACETS	0.96	0.724	1	0.96	0.724	1	CLONAL	1	TRUE	1	0.15	2		197	250	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62316900	62316900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1417269541	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	28	538	1	ENST00000360203.5:c.1216G>A	p.Glu406Lys	p.E406K	ENST00000360203	NM_001283009.1	406	Gag/Aag	15/35	1	2	FACETS	0.686	0.547	0.846	0.686	0.547	0.846	SUBCLONAL	1	TRUE	1	0.15	2		539	544	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21272445	21272445	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	46	619	1	ENST00000354336.3:c.223G>T	p.Asp75Tyr	p.D75Y	ENST00000354336	NM_005207.3	75	Gac/Tac	1/3	1	2	FACETS	0.688	0.577	0.811	0.688	0.577	0.811	SUBCLONAL	1	TRUE	1	0.15	2		620	892	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064325	30064325	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	19	257	0	ENST00000338641.4:c.889C>A	p.Leu297Ile	p.L297I	ENST00000338641	NM_000268.3	297	Ctc/Atc	10/16	1	2	FACETS	0.931	0.708	1	0.931	0.708	1	CLONAL	1	TRUE	1	0.15	2		257	272	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41521967	41521967	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	36	538	0	ENST00000263253.7:c.829A>C	p.Lys277Gln	p.K277Q	ENST00000263253	NM_001429.3	277	Aaa/Caa	3/31	1	2	FACETS	0.803	0.658	0.965	0.803	0.658	0.965	CLONAL	1	TRUE	1	0.15	2		538	598	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47108588	47108588	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	30	393	0	ENST00000409792.3:c.6081G>T	p.Lys2027Asn	p.K2027N	ENST00000409792	NM_014159.6	2027	aaG/aaT	13/21	1	2	FACETS	0.73	0.587	0.893	0.73	0.587	0.893	SUBCLONAL	1	TRUE	1	0.15	2		393	548	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725045	49725045	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	41	545	0	ENST00000449682.2:c.299A>G	p.His100Arg	p.H100R	ENST00000449682	NM_020998.3	100	cAc/cGc	3/18	1	2	FACETS	0.766	0.636	0.91	0.766	0.636	0.91	CLONAL	1	TRUE	1	0.15	2		545	714	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582227	52582227	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1307117980	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	23	248	0	ENST00000394830.3:c.4601C>T	p.Ser1534Leu	p.S1534L	ENST00000394830	NM_018313.4	1534	tCg/tTg	30/30	1	2	FACETS	0.84	0.655	1	0.84	0.655	1	CLONAL	1	TRUE	1	0.15	2		248	365	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096156	71096156	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	28	298	0	ENST00000318789.4:c.601C>T	p.Arg201Cys	p.R201C	ENST00000318789	NM_032682.5	201	Cgc/Tgc	10/21	1	2	FACETS	0.776	0.619	0.956	0.776	0.619	0.956	CLONAL	1	TRUE	1	0.15	2		298	481	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799478	72799478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	40	567	0	ENST00000325599.8:c.1691G>A	p.Ser564Asn	p.S564N	ENST00000325599	NM_018130.2	564	aGc/aAc	11/11	1	2	FACETS	0.682	0.565	0.813	0.682	0.565	0.813	SUBCLONAL	1	TRUE	1	0.15	2		567	782	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528631	89528631	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	20	221	0	ENST00000336596.2:c.2931G>T	p.Lys977Asn	p.K977N	ENST00000336596	NM_005233.5	977	aaG/aaT	17/17	1	2	FACETS	0.803	0.614	1	0.803	0.614	1	CLONAL	1	TRUE	1	0.15	2		221	332	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453494	138453494	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1291010707	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	24	374	0	ENST00000289153.2:c.954G>T	p.Lys318Asn	p.K318N	ENST00000289153	NM_006219.2	318	aaG/aaT	5/22	1	2	FACETS	0.677	0.529	0.847	0.677	0.529	0.847	SUBCLONAL	1	TRUE	1	0.15	2		374	473	SUCCESS
ATR	545	MSKCC	GRCh37	3	142183952	142183952	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	29	410	0	ENST00000350721.4:c.7028C>A	p.Ser2343Tyr	p.S2343Y	ENST00000350721	NM_001184.3	2343	tCc/tAc	41/47	1	2	FACETS	0.769	0.616	0.943	0.769	0.616	0.943	CLONAL	1	TRUE	1	0.15	2		410	503	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226778	142226778	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	23	288	0	ENST00000350721.4:c.5026T>G	p.Leu1676Val	p.L1676V	ENST00000350721	NM_001184.3	1676	Tta/Gta	28/47	1	2	FACETS	0.881	0.687	1	0.881	0.687	1	CLONAL	1	TRUE	1	0.15	2		288	348	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261513	142261513	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	43	397	0	ENST00000350721.4:c.3444G>T	p.Lys1148Asn	p.K1148N	ENST00000350721	NM_001184.3	1148	aaG/aaT	17/47	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.15	2		397	518	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281400	142281400	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	45	491	1	ENST00000350721.4:c.844G>T	p.Glu282Ter	p.E282*	ENST00000350721	NM_001184.3	282	Gaa/Taa	4/47	1	2	FACETS	0.992	0.832	1	0.992	0.832	1	CLONAL	1	TRUE	1	0.15	2		492	605	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178941913	178941913	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	35	409	0	ENST00000263967.3:c.2232C>A	p.Phe744Leu	p.F744L	ENST00000263967	NM_006218.2	744	ttC/ttA	15/21	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.15	2		409	440	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430292	181430292	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	21	288	0	ENST00000325404.1:c.144C>A	p.Phe48Leu	p.F48L	ENST00000325404	NM_003106.3	48	ttC/ttA	1/1	1	2	FACETS	0.776	0.597	0.985	0.776	0.597	0.985	CLONAL	1	TRUE	1	0.15	2		288	361	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191157	185191157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs903937665	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	27	335	0	ENST00000265026.3:c.2038C>T	p.Arg680Trp	p.R680W	ENST00000265026	NM_004721.4	680	Cgg/Tgg	11/14	1	2	FACETS	0.921	0.732	1	0.921	0.732	1	CLONAL	1	TRUE	1	0.15	2		335	391	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590657	189590657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1282887680	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	30	364	1	ENST00000264731.3:c.1222C>T	p.Arg408Cys	p.R408C	ENST00000264731	NM_003722.4	408	Cgt/Tgt	10/14	1	2	FACETS	0.995	0.802	1	0.995	0.802	1	CLONAL	1	TRUE	1	0.15	2		365	402	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801220	1801220	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs554790290	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	46	601	1	ENST00000260795.2:c.349G>A	p.Val117Ile	p.V117I	ENST00000260795		117	Gta/Ata	2/17	1	2	FACETS	0.936	0.787	1	0.936	0.787	1	CLONAL	1	TRUE	1	0.15	2		602	655	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902934	1902934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	56	506	0	ENST00000382891.5:c.553G>A	p.Glu185Lys	p.E185K	ENST00000382891	NM_133335.3	185	Gaa/Aaa	2/22	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.15	2		506	669	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127484	55127484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs538480165	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	39	529	0	ENST00000257290.5:c.272C>T	p.Ser91Leu	p.S91L	ENST00000257290	NM_006206.4	91	tCg/tTg	3/23	1	2	FACETS	0.715	0.591	0.855	0.715	0.591	0.855	SUBCLONAL	1	TRUE	1	0.15	2		529	727	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230807	66230807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	29	368	0	ENST00000273854.3:c.2164C>A	p.Leu722Ile	p.L722I	ENST00000273854	NM_004439.5	722	Cta/Ata	12/18	1	2	FACETS	0.796	0.638	0.976	0.796	0.638	0.976	CLONAL	1	TRUE	1	0.15	2		368	486	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233089	66233089	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	31	296	0	ENST00000273854.3:c.1910T>C	p.Phe637Ser	p.F637S	ENST00000273854	NM_004439.5	637	tTt/tCt	10/18	1	2	FACETS	0.81	0.654	0.988	0.81	0.654	0.988	CLONAL	1	TRUE	1	0.15	2		296	510	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391522	84391522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779497289	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	31	389	0	ENST00000321945.7:c.310C>T	p.Arg104Cys	p.R104C	ENST00000321945	NM_139076.2	104	Cgt/Tgt	5/9	1	2	FACETS	0.887	0.717	1	0.887	0.717	1	CLONAL	1	TRUE	1	0.15	2		389	466	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007331	143007331	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	37	382	0	ENST00000262992.4:c.2453G>T	p.Arg818Ile	p.R818I	ENST00000262992	NM_001101669.1	818	aGa/aTa	22/24	1	2	FACETS	0.887	0.73	1	0.887	0.73	1	CLONAL	1	TRUE	1	0.15	2		382	556	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542600	187542600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760161934	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	23	346	1	ENST00000441802.2:c.5140C>T	p.Pro1714Ser	p.P1714S	ENST00000441802	NM_005245.3	1714	Cca/Tca	10/27	1	2	FACETS	0.683	0.531	0.859	0.683	0.531	0.859	SUBCLONAL	1	TRUE	1	0.15	2		347	449	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950735	38950735	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	24	247	0	ENST00000357387.3:c.3215T>G	p.Phe1072Cys	p.F1072C	ENST00000357387	NM_152756.3	1072	tTt/tGt	31/38	1	2	FACETS	1	0.845	1	1	0.845	1	CLONAL	1	TRUE	1	0.15	2		247	292	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590492	67590492	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	31	268	0	ENST00000274335.5:c.1554G>T	p.Glu518Asp	p.E518D	ENST00000274335		518	gaG/gaT	11/15	1	2	FACETS	0.809	0.653	0.986	0.809	0.653	0.986	CLONAL	1	TRUE	1	0.15	2		268	511	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649005	86649005	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	33	375	0	ENST00000274376.6:c.1285G>A	p.Glu429Lys	p.E429K	ENST00000274376	NM_002890.2	429	Gaa/Aaa	9/25	1	2	FACETS	0.849	0.691	1	0.849	0.691	1	CLONAL	1	TRUE	1	0.15	2		375	518	SUCCESS
APC	324	MSKCC	GRCh37	5	112177230	112177230	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs180727920	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	16	297	0	ENST00000257430.4:c.5939A>G	p.Asn1980Ser	p.N1980S	ENST00000257430	NM_000038.5	1980	aAc/aGc	16/16	1	2	FACETS	0.695	0.513	0.913	0.695	0.513	0.913	SUBCLONAL	1	TRUE	1	0.15	2		297	307	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925341	131925341	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	12	166	0	ENST00000265335.6:c.1264G>T	p.Glu422Ter	p.E422*	ENST00000265335		422	Gag/Tag	9/25	1	2	FACETS	0.821	0.577	1	0.821	0.577	1	CLONAL	1	TRUE	1	0.15	2		166	195	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670921	30670921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	49	544	1	ENST00000376406.3:c.5825G>A	p.Gly1942Glu	p.G1942E	ENST00000376406	NM_014641.2	1942	gGg/gAg	12/15	1	2	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	TRUE	1	0.15	2		545	648	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800592	32800592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771425114	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	43	540	0	ENST00000374899.4:c.955C>T	p.Arg319Trp	p.R319W	ENST00000374899	NM_018833.2	319	Cgg/Tgg	6/12	1	2	FACETS	0.82	0.685	0.971	0.82	0.685	0.971	CLONAL	1	TRUE	1	0.15	2		540	699	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818213	32818213	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs143800384	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	51	506	2	ENST00000354258.4:c.1312C>T	p.Arg438Ter	p.R438*	ENST00000354258	NM_000593.5	438	Cga/Tga	5/11	1	2	FACETS	0.875	0.742	1	0.875	0.742	1	CLONAL	1	TRUE	1	0.15	2		508	777	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547182	106547182	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	18	196	0	ENST00000369096.4:c.419C>T	p.Ser140Phe	p.S140F	ENST00000369096	NM_001198.3	140	tCc/tTc	4/7	1	2	FACETS	0.822	0.619	1	0.822	0.619	1	CLONAL	1	TRUE	1	0.15	2		196	292	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109323533	109323533	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	37	503	0	ENST00000436639.2:c.293G>T	p.Arg98Ile	p.R98I	ENST00000436639	NM_014454.2	98	aGa/aTa	2/10	1	2	FACETS	0.772	0.635	0.926	0.772	0.635	0.926	CLONAL	1	TRUE	1	0.15	2		503	639	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715853	117715853	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	26	368	0	ENST00000368508.3:c.905G>T	p.Arg302Ile	p.R302I	ENST00000368508	NM_002944.2	302	aGa/aTa	9/43	1	2	FACETS	0.686	0.542	0.852	0.686	0.542	0.852	SUBCLONAL	1	TRUE	1	0.15	2		368	505	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129446	152129446	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	20	382	1	ENST00000206249.3:c.399G>T	p.Glu133Asp	p.E133D	ENST00000206249	NM_000125.3	133	gaG/gaT	1/8	1	2	FACETS	0.686	0.523	0.876	0.686	0.523	0.876	SUBCLONAL	1	TRUE	1	0.15	2		383	389	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265359	152265359	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	27	453	0	ENST00000206249.3:c.812G>T	p.Arg271Ile	p.R271I	ENST00000206249	NM_000125.3	271	aGa/aTa	4/8	1	2	FACETS	0.72	0.572	0.89	0.72	0.572	0.89	SUBCLONAL	1	TRUE	1	0.15	2		453	500	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026895	6026895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540287433	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	15	240	0	ENST00000265849.7:c.1501G>A	p.Val501Met	p.V501M	ENST00000265849	NM_000535.5	501	Gtg/Atg	11/15	1	2	FACETS	0.889	0.651	1	0.889	0.651	1	CLONAL	1	TRUE	1	0.15	2		240	225	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513165	106513165	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs778461029	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	20	244	0	ENST00000359195.3:c.2069G>T	p.Arg690Ile	p.R690I	ENST00000359195	NM_002649.2	690	aGa/aTa	4/11	1	2	FACETS	0.798	0.61	1	0.798	0.61	1	CLONAL	1	TRUE	1	0.15	2		244	334	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836798	151836798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1179701584	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	33	461	0	ENST00000262189.6:c.14422G>A	p.Glu4808Lys	p.E4808K	ENST00000262189	NM_170606.2	4808	Gaa/Aaa	56/59	1	2	FACETS	0.703	0.571	0.852	0.703	0.571	0.852	SUBCLONAL	1	TRUE	1	0.15	2		461	626	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055755	152055755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1403418496	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	33	352	0	ENST00000262189.6:c.167G>A	p.Arg56Gln	p.R56Q	ENST00000262189	NM_170606.2	56	cGa/cAa	2/59	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.15	2		352	361	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38315030	38315030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs548408836	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	51	571	1	ENST00000425967.3:c.34G>A	p.Glu12Lys	p.E12K	ENST00000425967	NM_001174067.1	12	Gag/Aag	3/19	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.15	2		572	600	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992765	68992765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs900217349	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	35	518	2	ENST00000288368.4:c.1730G>A	p.Arg577Gln	p.R577Q	ENST00000288368	NM_024870.2	577	cGa/cAa	16/40	1	2	FACETS	0.679	0.555	0.82	0.679	0.555	0.82	SUBCLONAL	1	TRUE	1	0.15	2		520	687	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054652	5054652	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	28	352	1	ENST00000381652.3:c.704G>T	p.Arg235Ile	p.R235I	ENST00000381652	NM_004972.3	235	aGa/aTa	7/25	1	2	FACETS	0.847	0.676	1	0.847	0.676	1	CLONAL	1	TRUE	1	0.15	2		353	441	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080532	5080532	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	14	239	0	ENST00000381652.3:c.2284-1G>T		p.X762_splice	ENST00000381652	NM_004972.3	762			1	2	FACETS	0.699	0.505	0.935	0.699	0.505	0.935	SUBCLONAL	1	TRUE	1	0.15	2		239	267	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8339020	8339020	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	25	424	0	ENST00000356435.5:c.5281G>T	p.Glu1761Ter	p.E1761*	ENST00000356435		1761	Gaa/Taa	32/35	1	2	FACETS	0.799	0.629	0.995	0.799	0.629	0.995	CLONAL	1	TRUE	1	0.15	2		424	417	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971088	21971088	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	27	421	0	ENST00000304494.5:c.270C>A	p.Phe90Leu	p.F90L	ENST00000304494	NM_000077.4	90	ttC/ttA	2/3	1	2	FACETS	0.843	0.67	1	0.843	0.67	1	CLONAL	1	TRUE	1	0.15	2		421	427	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933985	39933985	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	47	605	3	ENST00000378444.4:c.614C>A	p.Pro205His	p.P205H	ENST00000378444	NM_001123385.1	205	cCt/cAt	4/15	1	2	FACETS	0.839	0.706	0.986	0.839	0.706	0.986	CLONAL	1	TRUE	1	0.15	2		608	747	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650370	48650370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1317593957	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	31	564	2	ENST00000376670.3:c.340G>A	p.Glu114Lys	p.E114K	ENST00000376670	NM_002049.3	114	Gag/Aag	3/6	1	2	FACETS	0.698	0.563	0.852	0.698	0.563	0.852	SUBCLONAL	1	TRUE	1	0.15	2		566	592	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410499	63410499	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	39	533	0	ENST00000330258.3:c.2668A>C	p.Asn890His	p.N890H	ENST00000330258	NM_152424.3	890	Aac/Cac	2/2	1	2	FACETS	0.911	0.754	1	0.911	0.754	1	CLONAL	1	TRUE	1	0.15	2		533	571	SUCCESS
AR	367	MSKCC	GRCh37	X	66765677	66765677	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1315081227	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	51	636	0	ENST00000374690.3:c.689C>T	p.Ser230Leu	p.S230L	ENST00000374690	NM_000044.3	230	tCg/tTg	1/8	1	2	FACETS	0.823	0.698	0.962	0.823	0.698	0.962	CLONAL	1	TRUE	1	0.15	2		636	826	SUCCESS
AR	367	MSKCC	GRCh37	X	66766198	66766198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	23	342	0	ENST00000374690.3:c.1210G>A	p.Ala404Thr	p.A404T	ENST00000374690	NM_000044.3	404	Gcg/Acg	1/8	1	2	FACETS	1	0.811	1	1	0.811	1	CLONAL	1	TRUE	1	0.15	2		342	294	SUCCESS
AR	367	MSKCC	GRCh37	X	66931446	66931446	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	37	545	0	ENST00000374690.3:c.2088C>A	p.Asp696Glu	p.D696E	ENST00000374690	NM_000044.3	696	gaC/gaA	4/8	1	2	FACETS	0.745	0.613	0.894	0.745	0.613	0.894	SUBCLONAL	1	TRUE	1	0.15	2		545	662	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352321	70352321	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	39	556	0	ENST00000374080.3:c.4348G>T	p.Glu1450Ter	p.E1450*	ENST00000374080		1450	Gaa/Taa	31/45	1	2	FACETS	0.799	0.661	0.954	0.799	0.661	0.954	CLONAL	1	TRUE	1	0.15	2		556	651	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814139	76814139	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	18	260	0	ENST00000373344.5:c.6504+1G>T		p.X2168_splice	ENST00000373344	NM_000489.3	2168			1	2	FACETS	0.87	0.655	1	0.87	0.655	1	CLONAL	1	TRUE	1	0.15	2		260	276	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888725	76888725	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	31	368	1	ENST00000373344.5:c.5104G>T	p.Glu1702Ter	p.E1702*	ENST00000373344	NM_000489.3	1702	Gaa/Taa	19/35	1	2	FACETS	0.709	0.572	0.865	0.709	0.572	0.865	SUBCLONAL	1	TRUE	1	0.15	2		369	583	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890143	76890143	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	52	492	0	ENST00000373344.5:c.4751A>C	p.Lys1584Thr	p.K1584T	ENST00000373344	NM_000489.3	1584	aAa/aCa	17/35	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.15	2		492	674	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912098	76912098	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	38	461	0	ENST00000373344.5:c.4166T>G	p.Val1389Gly	p.V1389G	ENST00000373344	NM_000489.3	1389	gTt/gGt	13/35	1	2	FACETS	0.843	0.696	1	0.843	0.696	1	CLONAL	1	TRUE	1	0.15	2		461	601	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939604	76939604	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	33	468	0	ENST00000373344.5:c.1144G>T	p.Glu382Ter	p.E382*	ENST00000373344	NM_000489.3	382	Gaa/Taa	9/35	1	2	FACETS	0.741	0.602	0.898	0.741	0.602	0.898	SUBCLONAL	1	TRUE	1	0.15	2		468	594	SUCCESS
BTK	695	MSKCC	GRCh37	X	100604881	100604881	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	34	416	0	ENST00000308731.7:c.1972G>T	p.Glu658Ter	p.E658*	ENST00000308731	NM_000061.2	658	Gaa/Taa	19/19	1	2	FACETS	0.999	0.816	1	0.999	0.816	1	CLONAL	1	TRUE	1	0.15	2		416	454	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019817	123019817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	50	427	0	ENST00000355640.3:c.305C>T	p.Ala102Val	p.A102V	ENST00000355640		102	gCc/gTc	2/7	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.15	2		427	549	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0027655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	182	335	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.238799747754382	3	FACETS	0.777	0.721	0.835	0.777	0.721	0.835	INDETERMINATE	2	TRUE	1	0.472240536879573	3		335	613	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0027655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	98	298	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.967	0.868	1	0.967	0.868	1	CLONAL	1	TRUE	1	0.472240536879573	2		298	429	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0027655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	246	529	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.472240536879573	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.472240536879573	3		529	620	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553591	106553591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376600972	NA	P-0027655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	127	310	0	ENST00000369096.4:c.1556C>T	p.Ala519Val	p.A519V	ENST00000369096	NM_001198.3	519	gCg/gTg	5/7	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.472240536879573	2		310	459	SUCCESS
APC	324	MSKCC	GRCh37	5	112137036	112137036	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	172	468	0	ENST00000257430.4:c.790C>T	p.Gln264Ter	p.Q264*	ENST00000257430	NM_000038.5	264	Caa/Taa	8/16	0.238799747754382	3	FACETS	1	0.976	1	0.573	0.528	0.62	INDETERMINATE	1	TRUE	1	0.472240536879573	3		468	786	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907037	101907037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	175	288	0	ENST00000374994.4:c.997G>A	p.Asp333Asn	p.D333N	ENST00000374994	NM_004612.2	333	Gat/Aat	6/9	0.472240536879573	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.472240536879573	2		288	348	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926828	112926828	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	204	550	0	ENST00000351677.2:c.1448G>C	p.Gly483Ala	p.G483A	ENST00000351677	NM_002834.3	483	gGt/gCt	13/16	0.472240536879573	3	FACETS	0.889	0.823	0.958	0.445	0.411	0.479	CLONAL	1	TRUE	1	0.472240536879573	3		550	1201	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293198	91293198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878853555	NA	P-0027655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	155	378	0	ENST00000355112.3:c.700G>A	p.Asp234Asn	p.D234N	ENST00000355112	NM_000057.2	234	Gat/Aat	3/22	1	2	FACETS	0.96	0.881	1	0.96	0.881	1	CLONAL	1	TRUE	1	0.472240536879573	2		378	684	SUCCESS
APC	324	MSKCC	GRCh37	5	112116602	112116602	+	splice_donor_variant	Splice_Site	SNP	T	T	G	rs786202351	NA	P-0027655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	140	342	0	ENST00000257430.4:c.645+2T>G		p.X215_splice	ENST00000257430	NM_000038.5	215			0.238799747754382	3	FACETS	0.879	0.808	0.951	0.879	0.808	0.951	INDETERMINATE	2	TRUE	1	0.472240536879573	3		342	417	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979319	40979319	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1217327426	NA	P-0027658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	75	540	0	ENST00000373198.4:c.1814C>T	p.Thr605Met	p.T605M	ENST00000373198	NM_133170.3	605	aCg/aTg	11/32	1	2	FACETS	0.89	0.781	1	0.89	0.781	1	CLONAL	1	TRUE	1	0.29	2		540	581	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0027658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	85	277	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.298047161106759	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.29	1		277	410	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0027658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	29	531	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.464	0.372	0.569	0.464	0.372	0.569	SUBCLONAL	1	TRUE	1	0.29	2		531	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572986	7572986	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555524156	NA	P-0027658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	65	443	0	ENST00000269305.4:c.1123C>T	p.Gln375Ter	p.Q375*	ENST00000269305	NM_001126112.2	375	Cag/Tag	11/11	0.22513744798541	3	FACETS	1	0.894	1			1	CLONAL	1	TRUE	NA	0.29	3		443	497	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099989	27099989	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0027658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	132	535	0	ENST00000324856.7:c.3866+2T>C		p.X1289_splice	ENST00000324856	NM_006015.4	1289			0.244016269357903	2	FACETS	0.849	0.775	0.927	0.849	0.775	0.927	CLONAL	2	TRUE	0	0.29	2		535	536	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046750	42046750	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1205582948	NA	P-0027658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	85	527	1	ENST00000219905.7:c.7124A>G	p.Gln2375Arg	p.Q2375R	ENST00000219905	NM_001164273.1	2375	cAg/cGg	18/24	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.29	2		528	540	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116172	67116173	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	91	481	0	ENST00000412916.2:c.459dup	p.Glu154Ter	p.E154*	ENST00000412916		152	-/T	5/6	0.298047161106759	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.29	1		481	493	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683788	117683788	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	54	387	0	ENST00000368508.3:c.3359C>G	p.Pro1120Arg	p.P1120R	ENST00000368508	NM_002944.2	1120	cCc/cGc	21/43	0.244016269357903	2	FACETS	1	0.945	1	0.607	0.521	0.699	CLONAL	1	TRUE	0	0.29	2		387	307	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs760043106	NA	P-0027663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	513	535	0	ENST00000269305.4:c.584T>A	p.Ile195Asn	p.I195N	ENST00000269305	NM_001126112.2	195	aTc/aAc	6/11	0.525114387286012	3	FACETS	0.9	0.87	0.929	0.9	0.87	0.929	CLONAL	3	TRUE	0	0.599593268131837	3		535	824	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162216	47162216	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	78	342	0	ENST00000409792.3:c.3910G>T	p.Gly1304Cys	p.G1304C	ENST00000409792	NM_014159.6	1304	Ggt/Tgt	3/21	0.575322675828524	1	FACETS	0.462	0.408	0.52	0.462	0.408	0.52	SUBCLONAL	1	TRUE	0	0.599593268131837	1		342	394	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0027667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	138	581	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.554763936211515	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.657336165034315	3		581	251	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0027667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	51	285	0	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	0.657336165034315	2		285	146	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252075	226252075	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	22	132	0	ENST00000366813.1:c.23C>G	p.Ala8Gly	p.A8G	ENST00000366813		8	gCc/gGc	1/3	0.442341560883074	4	FACETS	0.88	0.692	1	0.22	0.173	0.274	CLONAL	1	TRUE	0	0.657336165034315	4		132	126	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874013	123874013	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1160486006	NA	P-0027667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	33	49	0	ENST00000330479.4:c.44C>T	p.Ala15Val	p.A15V	ENST00000330479	NM_020382.3	15	gCg/gTg	2/9	0.657336165034315	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.657336165034315	1		49	52	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147545	47147709	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCACTCGAGCTTTAAACTCTTTATGATCGAGTACCTCTCCACAATATTCTAGGACAAAGGTGTTCCTGCAAACCAAAAGGAAAAAAATAGCACTTCCTACCTAGGAGCAGTAGGGAAAACATATATGCTCAGGCAAAAATAAGGAATTTAAATAAATACTGCAA	TTCACTCGAGCTTTAAACTCTTTATGATCGAGTACCTCTCCACAATATTCTAGGACAAAGGTGTTCCTGCAAACCAAAAGGAAAAAAATAGCACTTCCTACCTAGGAGCAGTAGGGAAAACATATATGCTCAGGCAAAAATAAGGAATTTAAATAAATACTGCAA	-	novel	NA	P-0027667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	44	434	0	ENST00000409792.3:c.4716-99_4781del		p.X1572_splice	ENST00000409792	NM_014159.6	1572		6/21	1	2	FACETS	0.93	0.796	1	0.93	0.796	1	CLONAL	1	TRUE	1	0.657336165034315	2		434	144	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242462	55242462	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	132	490	0	ENST00000275493.2:c.2232C>G	p.Ile744Met	p.I744M	ENST00000275493	NM_005228.3	744	atC/atG	19/28	0.554763936211515	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.657336165034315	3		490	245	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899088	40899088	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs534320934	NA	P-0027693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	254	530	0	ENST00000373198.4:c.2182A>G	p.Met728Val	p.M728V	ENST00000373198	NM_133170.3	728	Atg/Gtg	14/32	0.51366252295072	5	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.531389271779416	5		530	1381	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750513	57750514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0027693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	107	508	0	ENST00000274289.3:c.1953_1954dup	p.Ser652TyrfsTer7	p.S652Yfs*7	ENST00000274289	NM_006622.3	652	tct/tATct	14/14	0.464770555604468	4	FACETS	0.634	0.567	0.705	0.317	0.283	0.353	SUBCLONAL	1	TRUE	2	0.531389271779416	4		508	973	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864771	68864771	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0027693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	148	458	1	ENST00000288368.4:c.141+1G>A		p.X47_splice	ENST00000288368	NM_024870.2	47			0.531389271779416	3	FACETS	0.867	0.793	0.945	0.434	0.396	0.473	CLONAL	1	TRUE	1	0.531389271779416	3		459	813	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0027694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	84	497	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	0.313414791328367	NA		497	498	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0027694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	104	657	1	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.273340193703961	3	FACETS	1	0.968	1	0.773	0.7	0.849	CLONAL	2	TRUE	0	0.313414791328367	3		658	331	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440637	56440637	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	80	843	2	ENST00000407977.2:c.581G>A	p.Trp194Ter	p.W194*	ENST00000407977		194	tGg/tAg	5/10	0.313414791328367	1	FACETS	0.95	0.84	1	0.95	0.84	1	CLONAL	1	TRUE	0	0.313414791328367	1		845	453	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214831	36214831	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	78	1025	0	ENST00000222270.7:c.3257A>G	p.Tyr1086Cys	p.Y1086C	ENST00000222270	NM_014727.1	1086	tAt/tGt	8/37	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.313414791328367	2		1025	492	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056196	26056219	+	inframe_deletion	In_Frame_Del	DEL	GTTTTCTTAGCGCTCTTCTTCGGA	GTTTTCTTAGCGCTCTTCTTCGGA	-	novel	NA	P-0027694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	85	568	0	ENST00000343677.2:c.438_461del	p.Ser150_Lys157del	p.S150_K157del	ENST00000343677	NM_005319.3	146	acTCCGAAGAAGAGCGCTAAGAAAACa/aca	1/1	0.313414791328367	7	FACETS	1	0.976	1	0.357	0.316	0.402	CLONAL	1	TRUE	3	0.313414791328367	7		568	677	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974723	21974738	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGCCTCCAGCAGCG	CCCGCCTCCAGCAGCG	-	novel	NA	P-0027694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	42	505	0	ENST00000304494.5:c.89_104del	p.Ala30GlyfsTer18	p.A30Gfs*18	ENST00000304494	NM_000077.4	30	gCGCTGCTGGAGGCGGGg/gg	1/3	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.313414791328367	2		505	235	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750272	133750272	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	52	697	1	ENST00000318560.5:c.1103A>G	p.Asn368Ser	p.N368S	ENST00000318560	NM_005157.4	368	aAc/aGc	7/11	1	2	FACETS	0.866	0.74	1	0.866	0.74	1	CLONAL	1	TRUE	1	0.313414791328367	2		698	383	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	56	297	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.737	0.63	0.853	0.737	0.63	0.853	SUBCLONAL	1	TRUE	1	0.223604179825102	2		297	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514495	NA	P-0027695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	132	525	0	ENST00000269305.4:c.542G>A	p.Arg181His	p.R181H	ENST00000269305	NM_001126112.2	181	cGc/cAc	5/11	0.191560392585362	2	FACETS	0.9	0.819	0.985	0.9	0.819	0.985	CLONAL	2	TRUE	0	0.223604179825102	2		525	656	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0027695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	54	202	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	0.223604179825102	2		202	333	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604750	48604750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	62	519	0	ENST00000342988.3:c.1572G>T	p.Trp524Cys	p.W524C	ENST00000342988	NM_005359.5	524	tgG/tgT	12/12	1	2	FACETS	0.886	0.765	1	0.886	0.765	1	CLONAL	1	TRUE	1	0.223604179825102	2		519	626	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875919	76875919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	75	591	0	ENST00000373344.5:c.5216G>A	p.Arg1739Gln	p.R1739Q	ENST00000373344	NM_000489.3	1739	cGa/cAa	20/35	1	2	FACETS	0.884	0.774	1	0.884	0.774	1	CLONAL	1	TRUE	1	0.223604179825102	2		591	759	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088768	27088768	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs372272181	NA	P-0027695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	63	611	0	ENST00000324856.7:c.2377A>G	p.Met793Val	p.M793V	ENST00000324856	NM_006015.4	793	Atg/Gtg	7/20	0.223604179825102	1	FACETS	0.798	0.69	0.916	0.798	0.69	0.916	CLONAL	1	TRUE	0	0.223604179825102	1		611	627	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720702	89720702	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	28	130	0	ENST00000371953.3:c.853G>T	p.Glu285Ter	p.E285*	ENST00000371953	NM_000314.4	285	Gaa/Taa	8/9	0.223604179825102	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.223604179825102	1		130	164	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920404	114920404	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	69	496	0	ENST00000543371.1:c.1345G>C	p.Ala449Pro	p.A449P	ENST00000543371	NM_001198531.1	449	Gca/Cca	13/14	0.223604179825102	1	FACETS	0.755	0.657	0.861	0.755	0.657	0.861	SUBCLONAL	1	TRUE	0	0.223604179825102	1		496	726	SUCCESS
APC	324	MSKCC	GRCh37	5	112175147	112175147	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	90	219	0	ENST00000257430.4:c.3856G>T	p.Glu1286Ter	p.E1286*	ENST00000257430	NM_000038.5	1286	Gaa/Taa	16/16	1	2	FACETS	0.988	0.887	1	0.988	0.887	1	CLONAL	1	TRUE	1	0.617802993035323	2		219	295	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0027697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	168	439	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.617802993035323	2		439	534	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0027697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	181	390	1	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.953	0.883	1	0.953	0.883	1	CLONAL	1	TRUE	1	0.617802993035323	2		391	615	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480483	57480483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	147	332	3	ENST00000371085.3:c.478C>T	p.Arg160Cys	p.R160C	ENST00000371085	NM_000516.4	160	Cgt/Tgt	6/13	0.289527385483348	3	FACETS	1	0.948	1	0.523	0.479	0.568	INDETERMINATE	1	TRUE	1	0.617802993035323	3		335	596	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976744	2976744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs577877958	NA	P-0027697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	531	657	0	ENST00000396946.4:c.1268G>A	p.Arg423Gln	p.R423Q	ENST00000396946	NM_032415.4	423	cGg/cAg	9/25	0.614616288849343	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.617802993035323	3		657	1098	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114799872	114799872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753187602	NA	P-0027697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	270	509	0	ENST00000543371.1:c.539C>T	p.Pro180Leu	p.P180L	ENST00000543371	NM_001198531.1	180	cCg/cTg	5/14	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.617802993035323	2		509	833	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356239	66356239	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370503988	NA	P-0027697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	232	571	0	ENST00000273854.3:c.1258G>A	p.Gly420Ser	p.G420S	ENST00000273854	NM_004439.5	420	Ggc/Agc	5/18	0.322865448213893	1	FACETS	0.732	0.686	0.779	0.732	0.686	0.779	INDETERMINATE	1	TRUE	0	0.617802993035323	1		571	709	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480408	89480408	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	145	313	1	ENST00000336596.2:c.2245G>T	p.Ala749Ser	p.A749S	ENST00000336596	NM_005233.5	749	Gct/Tct	13/17	1	2	FACETS	0.937	0.861	1	0.937	0.861	1	CLONAL	1	TRUE	1	0.617802993035323	2		314	501	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243482	46243484	+	stop_gained	Nonsense_Mutation	TNP	ATC	ATC	TTT	novel	NA	P-0027697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	97	469	0	ENST00000334344.6:c.1835_1837delinsTTT	p.Tyr612_Gln613delinsPheTer	p.Y612_Q613delinsF*	ENST00000334344	NM_152641.2	612	tATCag/tTTTag	14/21	0.322865448213893	1	FACETS	0.463	0.414	0.514	0.463	0.414	0.514	INDETERMINATE	1	TRUE	0	0.617802993035323	1		469	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0027699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	257	792	1	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.743236462147213	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.743236462147213	2		793	326	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288222	33288226	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTT	CTCTT	-	novel	NA	P-0027699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	199	480	0	ENST00000374542.5:c.1182_1186del	p.Arg394SerfsTer22	p.R394Sfs*22	ENST00000374542	NM_001141970.1	394	agAAGAGct/agct	4/8	0.743236462147213	2	FACETS	0.884	0.839	0.927	0.884	0.839	0.927	CLONAL	2	TRUE	0	0.743236462147213	2		480	303	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779037	135779037	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0027699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	94	419	1	ENST00000298552.3:c.2208+1G>A		p.X736_splice	ENST00000298552	NM_001162426.1	736			0.743236462147213	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.743236462147213	2		420	121	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0027705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	217	497	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	0.994	1	CLONAL	2	TRUE	1	0.21	2		497	967	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	rs886039483	NA	P-0027705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1212	81	807	0	ENST00000269305.4:c.376T>A	p.Tyr126Asn	p.Y126N	ENST00000269305	NM_001126112.2	126	Tac/Aac	5/11	1	2	FACETS	0.597	0.524	0.676	0.597	0.524	0.676	SUBCLONAL	1	TRUE	1	0.21	2		807	1293	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50811826	50811826	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs886040872	NA	P-0027708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	91	742	0	ENST00000398568.2:c.1103C>A	p.Ser368Ter	p.S368*	ENST00000398568	NM_001042412.1	368	tCa/tAa	7/18	0.297985980177867	1	FACETS	0.959	0.853	1	0.959	0.853	1	CLONAL	1	TRUE	0	0.27	1		742	608	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0027708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	13	574	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	1	2	FACETS	0.158	0.112	0.216	0.158	0.112	0.216	SUBCLONAL	1	TRUE	1	0.27	2		574	608	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610608	52610609	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	94	667	0	ENST00000394830.3:c.3564dup	p.Glu1189ArgfsTer6	p.E1189Rfs*6	ENST00000394830	NM_018313.4	1188	-/A	23/30	0.297985980177867	1	FACETS	0.906	0.807	1	0.906	0.807	1	CLONAL	1	TRUE	0	0.27	1		667	665	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566521	41566521	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	108	618	0	ENST00000263253.7:c.4398G>C	p.Trp1466Cys	p.W1466C	ENST00000263253	NM_001429.3	1466	tgG/tgC	27/31	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.27	2		618	768	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931815	68931815	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	34	762	1	ENST00000288368.4:c.245C>A	p.Ala82Glu	p.A82E	ENST00000288368	NM_024870.2	82	gCa/gAa	3/40	0.297985980177867	1	FACETS	0.343	0.279	0.415	0.343	0.279	0.415	SUBCLONAL	1	TRUE	0	0.27	1		763	636	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0027710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	309	573	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	0.30579899247481	3	FACETS	0.867	0.82	0.915	0.867	0.82	0.915	CLONAL	3	TRUE	0	0.30579899247481	3		573	896	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	63	723	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	NA	2	FACETS	0.392	0.338	0.451			1	INDETERMINATE	1	TRUE	NA	0.30579899247481	2		723	1051	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0027710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	285	520	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	0.30579899247481	3	FACETS	0.973	0.92	1	0.973	0.92	1	CLONAL	3	TRUE	0	0.30579899247481	3		520	736	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953748	48953748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759079385	NA	P-0027710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	27	342	2	ENST00000267163.4:c.1351C>T	p.Arg451Cys	p.R451C	ENST00000267163	NM_000321.2	451	Cgc/Tgc	14/27	1	2	FACETS	0.389	0.309	0.481	0.389	0.309	0.481	SUBCLONAL	1	TRUE	1	0.30579899247481	2		344	454	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906528	32906528	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80359169	NA	P-0027710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	107	501	1	ENST00000380152.3:c.913G>A	p.Glu305Lys	p.E305K	ENST00000380152		305	Gaa/Aaa	10/27	1	2	FACETS	0.848	0.76	0.942	0.848	0.76	0.942	CLONAL	1	TRUE	1	0.30579899247481	2		502	825	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847397	68847398	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0027710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	295	653	0	ENST00000261769.5:c.1320_1320+1dup		p.K440fs	ENST00000261769	NM_004360.3	440	aag/aaGGg	9/16	0.30579899247481	2	FACETS	0.991	0.935	1	0.991	0.935	1	CLONAL	2	TRUE	0	0.30579899247481	2		653	973	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696642	47696642	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519965	NA	P-0027711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	225	624	0	ENST00000347630.2:c.306C>G	p.Phe102Leu	p.F102L	ENST00000347630	NM_001007230.1	102	ttC/ttG	5/11	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.733501917972399	2		624	613	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041845	42041846	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0027711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	38	680	0	ENST00000219905.7:c.6041dup	p.Ala2015CysfsTer9	p.A2015Cfs*9	ENST00000219905	NM_001164273.1	2014	gct/gCct	17/24	1	2	FACETS	0.159	0.131	0.191	0.159	0.131	0.191	SUBCLONAL	1	TRUE	1	0.733501917972399	2		680	651	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864230	151864230	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0027711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	108	326	0	ENST00000262189.6:c.9750+1G>C		p.X3250_splice	ENST00000262189	NM_170606.2	3250			1	2	FACETS	0.882	0.8	0.966	0.882	0.8	0.966	CLONAL	1	TRUE	1	0.733501917972399	2		326	334	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0027712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	405	654	1	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.51959706567038	2		655	1110	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0027712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	328	837	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.51959706567038	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.51959706567038	1		837	914	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604750	48604750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	169	519	0	ENST00000342988.3:c.1572G>T	p.Trp524Cys	p.W524C	ENST00000342988	NM_005359.5	524	tgG/tgT	12/12	0.51959706567038	1	FACETS	0.9	0.833	0.969	0.9	0.833	0.969	CLONAL	1	TRUE	0	0.51959706567038	1		519	535	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0027712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	138	287	1	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.492011203381667	2	FACETS	0.877	0.812	0.942	0.877	0.812	0.942	CLONAL	2	TRUE	0	0.51959706567038	2		288	303	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0027712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	172	498	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	0.49644255847597	1	FACETS	0.963	0.893	1	0.963	0.893	1	CLONAL	1	TRUE	0	0.51959706567038	1		498	509	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41562637	41562637	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555910814	NA	P-0027712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	164	464	0	ENST00000263253.7:c.3841C>T	p.Arg1281Ter	p.R1281*	ENST00000263253	NM_001429.3	1281	Cga/Tga	23/31	1	2	FACETS	0.798	0.734	0.865	0.798	0.734	0.865	SUBCLONAL	1	TRUE	1	0.51959706567038	2		464	791	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489788	2489788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs527252361	NA	P-0027712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	417	680	0	ENST00000355716.4:c.185G>A	p.Arg62His	p.R62H	ENST00000355716	NM_003820.2	62	cGt/cAt	3/8	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.51959706567038	2		680	1094	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036938	180036938	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	281	832	0	ENST00000261937.6:c.3774C>A	p.Phe1258Leu	p.F1258L	ENST00000261937	NM_182925.4	1258	ttC/ttA	28/30	0.492011203381667	2	FACETS	1	0.952	1	0.507	0.477	0.539	CLONAL	1	TRUE	0	0.51959706567038	2		832	1066	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786705	3786705	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1282	262	880	0	ENST00000262367.5:c.4506G>C	p.Trp1502Cys	p.W1502C	ENST00000262367	NM_004380.2	1502	tgG/tgC	27/31	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.326445769653721	2		880	1544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578385	7578386	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	321	686	1	ENST00000269305.4:c.544dup	p.Cys182LeufsTer4	p.C182Lfs*4	ENST00000269305	NM_001126112.2	182	tgc/tTgc	5/11	0.273060845216118	2	FACETS	0.908	0.858	0.959	0.908	0.858	0.959	CLONAL	2	TRUE	0	0.326445769653721	2		687	1083	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86681205	86681205	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	127	383	0	ENST00000274376.6:c.2846A>C	p.Lys949Thr	p.K949T	ENST00000274376	NM_002890.2	949	aAg/aCg	22/25	0.326445769653721	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.326445769653721	1		383	606	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	177	346	4	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.823	0.765	0.882	0.823	0.765	0.882	CLONAL	1	TRUE	1	0.885418061198257	2		350	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0027722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	311	573	7	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.789018481910022	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.885418061198257	1		580	378	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030367	49030368	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	177	291	5	ENST00000267163.4:c.1848dup	p.Gly617ArgfsTer36	p.G617Rfs*36	ENST00000267163	NM_000321.2	614	-/A	19/27	0.885418061198257	1	FACETS	0.936	0.893	0.977	0.936	0.893	0.977	CLONAL	1	TRUE	0	0.885418061198257	1		296	238	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404576	8404576	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146844299	NA	P-0027722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	110	225	4	ENST00000356435.5:c.4171G>A	p.Ala1391Thr	p.A1391T	ENST00000356435		1391	Gca/Aca	25/35	1	2	FACETS	0.857	0.781	0.934	0.857	0.781	0.934	CLONAL	1	TRUE	1	0.885418061198257	2		229	290	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729390	41729390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866652548	NA	P-0027722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	266	424	4	ENST00000242208.4:c.1139G>A	p.Gly380Asp	p.G380D	ENST00000242208	NM_002192.2	380	gGc/gAc	3/3	0.844241053587966	3	FACETS	1	0.981	1	0.549	0.516	0.582	CLONAL	1	TRUE	1	0.885418061198257	3		428	790	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870961	12870961	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	145	299	1	ENST00000228872.4:c.188A>T	p.Asp63Val	p.D63V	ENST00000228872	NM_004064.3	63	gAt/gTt	1/3	0.885418061198257	1	FACETS	0.981	0.934	1	0.981	0.934	1	CLONAL	1	TRUE	0	0.885418061198257	1		300	186	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976111	7976111	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs776908057	NA	P-0027722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	296	513	9	ENST00000319144.4:c.2084T>C	p.Ile695Thr	p.I695T	ENST00000319144	NM_001139.2	695	aTt/aCt	15/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.885418061198257	2		522	629	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754493	42754493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766762597	NA	P-0027722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	312	545	10	ENST00000222329.4:c.247C>T	p.Arg83Trp	p.R83W	ENST00000222329	NM_006494.2	83	Cgg/Tgg	2/4	0.882595970667008	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.885418061198257	1		555	373	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778103	27778104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	255	440	4	ENST00000369163.2:c.254dup	p.Gln86ProfsTer21	p.Q86Pfs*21	ENST00000369163	NM_003536.2	84	-/T	1/1	1	2	FACETS	0.973	0.919	1	0.973	0.919	1	CLONAL	1	TRUE	1	0.885418061198257	2		444	592	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476301	88476301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	78	490	0	ENST00000360948.2:c.1831G>A	p.Asp611Asn	p.D611N	ENST00000360948	NM_001012338.2	611	Gac/Aac	15/19	1	2	FACETS	0.62	0.544	0.702	0.62	0.544	0.702	SUBCLONAL	1	TRUE	1	0.33	2		490	762	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980872	40980872	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	122	337	0	ENST00000373198.4:c.1614G>C	p.Gln538His	p.Q538H	ENST00000373198	NM_133170.3	538	caG/caC	10/32	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.33	2		337	581	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670438	246670438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	60	348	0	ENST00000388985.4:c.82G>A	p.Glu28Lys	p.E28K	ENST00000388985		28	Gag/Aag	1/12	1	2	FACETS	0.664	0.572	0.763	0.664	0.572	0.763	SUBCLONAL	1	TRUE	1	0.33	2		348	548	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953930	131953930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	32	294	0	ENST00000265335.6:c.3333G>A	p.Met1111Ile	p.M1111I	ENST00000265335		1111	atG/atA	21/25	0.298874621078761	3	FACETS	0.385	0.311	0.468	0.192	0.155	0.234	SUBCLONAL	1	TRUE	1	0.33	3		294	587	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	170	297	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.380195148434786	1	FACETS	0.766	0.711	0.822	0.766	0.711	0.822	INDETERMINATE	1	TRUE	0	0.649094668826089	1		297	462	SUCCESS
APC	324	MSKCC	GRCh37	5	112175921	112175921	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	96	194	0	ENST00000257430.4:c.4630G>T	p.Glu1544Ter	p.E1544*	ENST00000257430	NM_000038.5	1544	Gaa/Taa	16/16	0.649094668826089	1	FACETS	0.961	0.876	1	0.961	0.876	1	CLONAL	1	TRUE	0	0.649094668826089	1		194	208	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1485978447	NA	P-0027724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	174	280	2	ENST00000324856.7:c.5164C>T	p.Arg1722Ter	p.R1722*	ENST00000324856	NM_006015.4	1722	Cga/Tga	20/20	0.649094668826089	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.649094668826089	1		282	341	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979611	7979611	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	107	399	0	ENST00000319144.4:c.1414T>C	p.Ser472Pro	p.S472P	ENST00000319144	NM_001139.2	472	Tcg/Ccg	11/15	0.380195148434786	1	FACETS	0.437	0.393	0.482	0.437	0.393	0.482	INDETERMINATE	1	TRUE	0	0.649094668826089	1		399	510	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607376	46607376	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs755032969	NA	P-0027724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	110	408	0	ENST00000263734.3:c.1565A>G	p.Asn522Ser	p.N522S	ENST00000263734	NM_001430.4	522	aAt/aGt	12/16	0.394537667591143	1	FACETS	0.381	0.343	0.421	0.381	0.343	0.421	SUBCLONAL	1	TRUE	0	0.649094668826089	1		408	601	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168830	56168830	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	20	253	0	ENST00000399503.3:c.1684C>T	p.Gln562Ter	p.Q562*	ENST00000399503	NM_005921.1	562	Cag/Tag	9/20	1	2	FACETS	0.237	0.181	0.303	0.237	0.181	0.303	SUBCLONAL	1	TRUE	1	0.582868341976059	2		253	289	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0027726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	115	586	1	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	0.291805453823456	2		587	771	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587778720	NA	P-0027726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	141	813	0	ENST00000269305.4:c.638G>C	p.Arg213Pro	p.R213P	ENST00000269305	NM_001126112.2	213	cGa/cCa	6/11	0.164403161617727	2	FACETS	1	0.94	1	0.521	0.474	0.571	INDETERMINATE	1	TRUE	0	0.291805453823456	2		813	927	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922297	39922297	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	26	392	0	ENST00000378444.4:c.3875C>T	p.Pro1292Leu	p.P1292L	ENST00000378444	NM_001123385.1	1292	cCc/cTc	9/15	1	2	FACETS	0.374	0.295	0.464	0.374	0.295	0.464	SUBCLONAL	1	TRUE	1	0.291805453823456	2		392	477	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028127	69028127	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	102	825	0	ENST00000288368.4:c.3286G>T	p.Asp1096Tyr	p.D1096Y	ENST00000288368	NM_024870.2	1096	Gat/Tat	26/40	0.219681464058185	1	FACETS	0.646	0.577	0.72	0.646	0.577	0.72	SUBCLONAL	1	TRUE	0	0.291805453823456	1		825	924	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435523	18435523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	68	373	0	ENST00000266497.5:c.508G>A	p.Gly170Arg	p.G170R	ENST00000266497		170	Gga/Aga	1/31	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.291805453823456	2		373	436	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431673	49431673	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	162	816	0	ENST00000301067.7:c.9466C>G	p.Pro3156Ala	p.P3156A	ENST00000301067	NM_003482.3	3156	Cca/Gca	34/54	0.164403161617727	2	FACETS	1	0.976	1	0.583	0.535	0.634	INDETERMINATE	1	TRUE	0	0.291805453823456	2		816	952	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210810	133210811	+	missense_variant	Missense_Mutation	DNP	GC	GC	CT	novel	NA	P-0027726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	61	721	1	ENST00000320574.5:c.5965_5966delinsAG	p.Ala1989Arg	p.A1989R	ENST00000320574	NM_006231.2	1989	GCa/AGa	43/49	0.164403161617727	2	FACETS	0.539	0.464	0.621	0.269	0.232	0.311	INDETERMINATE	1	TRUE	0	0.291805453823456	2		722	776	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39595442	39595442	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	36	391	0	ENST00000262039.4:c.1330del	p.Gln444LysfsTer3	p.Q444Kfs*3	ENST00000262039	NM_002647.2	443	tCc/tc	12/25	0.178069842459255	2	FACETS	0.424	0.348	0.51	0.212	0.174	0.255	SUBCLONAL	1	TRUE	0	0.291805453823456	2		391	582	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222550	2222550	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	97	663	0	ENST00000398665.3:c.3382A>C	p.Asn1128His	p.N1128H	ENST00000398665	NM_032482.2	1128	Aac/Cac	24/28	0.164403161617727	2	FACETS	0.971	0.866	1	0.485	0.433	0.541	INDETERMINATE	1	TRUE	0	0.291805453823456	2		663	685	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292520	15292520	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1333872267	NA	P-0027726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	146	860	2	ENST00000263388.2:c.2659G>T	p.Asp887Tyr	p.D887Y	ENST00000263388	NM_000435.2	887	Gat/Tat	17/33	0.164403161617727	2	FACETS	1	0.972	1	0.577	0.527	0.63	INDETERMINATE	1	TRUE	0	0.291805453823456	2		862	867	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101005	41101005	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	114	665	0	ENST00000373198.4:c.1351G>T	p.Gly451Cys	p.G451C	ENST00000373198	NM_133170.3	451	Ggc/Tgc	8/32	0.164403161617727	2	FACETS	1	0.951	1	0.546	0.491	0.603	INDETERMINATE	1	TRUE	0	0.291805453823456	2		665	716	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747945	41747945	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	30	273	0	ENST00000226382.2:c.824C>A	p.Pro275His	p.P275H	ENST00000226382	NM_003924.3	275	cCc/cAc	3/3	1	2	FACETS	0.533	0.429	0.65	0.533	0.429	0.65	SUBCLONAL	1	TRUE	1	0.291805453823456	2		273	386	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144642	55144642	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	54	486	0	ENST00000257290.5:c.2116G>T	p.Asp706Tyr	p.D706Y	ENST00000257290	NM_006206.4	706	Gat/Tat	15/23	1	2	FACETS	0.578	0.493	0.672	0.578	0.493	0.672	SUBCLONAL	1	TRUE	1	0.291805453823456	2		486	640	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961763	55961763	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	59	569	0	ENST00000263923.4:c.2798A>T	p.Asn933Ile	p.N933I	ENST00000263923	NM_002253.2	933	aAt/aTt	20/30	1	2	FACETS	0.556	0.478	0.642	0.556	0.478	0.642	SUBCLONAL	1	TRUE	1	0.291805453823456	2		569	727	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518061	187518061	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	79	708	0	ENST00000441802.2:c.12633del	p.Lys4211AsnfsTer27	p.K4211Nfs*27	ENST00000441802	NM_005245.3	4211	aaG/aa	25/27	1	2	FACETS	0.659	0.578	0.745	0.659	0.578	0.745	SUBCLONAL	1	TRUE	1	0.291805453823456	2		708	822	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524498	187524498	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	97	727	0	ENST00000441802.2:c.11182G>T	p.Val3728Phe	p.V3728F	ENST00000441802	NM_005245.3	3728	Gtt/Ttt	19/27	1	2	FACETS	0.8	0.713	0.893	0.8	0.713	0.893	SUBCLONAL	1	TRUE	1	0.291805453823456	2		727	831	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30676052	30676052	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	56	560	0	ENST00000376406.3:c.2304T>A	p.Phe768Leu	p.F768L	ENST00000376406	NM_014641.2	768	ttT/ttA	8/15	0.164403161617727	2	FACETS	0.654	0.56	0.757	0.327	0.28	0.379	INDETERMINATE	1	TRUE	0	0.291805453823456	2		560	587	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554887	106554887	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	112	633	2	ENST00000369096.4:c.2004C>A	p.Phe668Leu	p.F668L	ENST00000369096	NM_001198.3	668	ttC/ttA	7/7	0.164403161617727	2	FACETS	1	0.961	1	0.567	0.51	0.627	INDETERMINATE	1	TRUE	0	0.291805453823456	2		635	677	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194643	29194643	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	93	920	0	ENST00000240100.2:c.1085C>A	p.Ser362Ter	p.S362*	ENST00000240100	NM_001394.6	362	tCg/tAg	4/4	0.164403161617727	2	FACETS	0.613	0.544	0.688	0.307	0.272	0.344	INDETERMINATE	1	TRUE	0	0.291805453823456	2		920	1039	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249415	110249416	+	missense_variant	Missense_Mutation	DNP	TC	TC	CA	novel	NA	P-0027726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	190	1134	1	ENST00000374672.4:c.1157_1158delinsTG	p.Arg386Leu	p.R386L	ENST00000374672	NM_004235.4	386	cGA/cTG	4/5	0.198384397117551	3	FACETS	1	0.985	1	0.632	0.583	0.683	CLONAL	1	TRUE	1	0.291805453823456	3		1135	1180	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778754	76778754	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	92	589	1	ENST00000373344.5:c.6825G>T	p.Trp2275Cys	p.W2275C	ENST00000373344	NM_000489.3	2275	tgG/tgT	31/35	1	2	FACETS	0.863	0.766	0.965	0.863	0.766	0.965	CLONAL	1	TRUE	1	0.291805453823456	2		590	731	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71161722	71161722	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	26	364	1	ENST00000318789.4:c.247T>A	p.Ser83Thr	p.S83T	ENST00000318789	NM_032682.5	83	Tct/Act	7/21	0.164403161617727	2	FACETS	0.343	0.27	0.426	0.171	0.135	0.213	INDETERMINATE	1	TRUE	0	0.291805453823456	2		365	520	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933533	39933533	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	48	751	0	ENST00000378444.4:c.1066G>T	p.Glu356Ter	p.E356*	ENST00000378444	NM_001123385.1	356	Gag/Tag	4/15	1	2	FACETS	0.39	0.328	0.458	0.39	0.328	0.458	SUBCLONAL	1	TRUE	1	0.291805453823456	2		751	844	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	144	210	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.991	0.917	1	0.991	0.917	1	CLONAL	1	TRUE	1	0.859753125236413	2		210	338	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0027727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	306	374	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.769368524469024	2	FACETS	0.97	0.942	0.996	0.97	0.942	0.996	CLONAL	2	TRUE	0	0.859753125236413	2		374	367	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781324	3781326	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs587783502	NA	P-0027727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	294	545	0	ENST00000262367.5:c.5039_5041del	p.Ser1680del	p.S1680del	ENST00000262367	NM_004380.2	1680	tCCTtg/ttg	30/31	1	2	FACETS	0.951	0.901	1	0.951	0.901	1	CLONAL	1	TRUE	1	0.859753125236413	2		545	719	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436440	110436440	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	304	433	0	ENST00000375856.3:c.1961del	p.Met654SerfsTer3	p.M654Sfs*3	ENST00000375856	NM_003749.2	654	aTg/ag	1/2	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.859753125236413	2		433	686	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437840	52437840	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1559587104	NA	P-0027727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	308	474	0	ENST00000460680.1:c.1321C>T	p.Gln441Ter	p.Q441*	ENST00000460680	NM_004656.3	441	Cag/Tag	13/17	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.859753125236413	2		474	714	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443864	52443864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	268	409	1	ENST00000460680.1:c.31G>A	p.Asp11Asn	p.D11N	ENST00000460680	NM_004656.3	11	Gac/Aac	1/17	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.859753125236413	2		410	592	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938404	44938404	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	265	178	0	ENST00000377967.4:c.2952C>G	p.Phe984Leu	p.F984L	ENST00000377967	NM_021140.2	984	ttC/ttG	20/29	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.859753125236413	1		178	304	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0027728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	100	298	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.417309945505225	2	FACETS	1	0.967	1	0.589	0.53	0.651	CLONAL	1	TRUE	0	0.423530365195978	2		298	401	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0027728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	132	654	1	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	0.949	0.863	1	0.949	0.863	1	CLONAL	1	TRUE	1	0.423530365195978	2		655	657	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457303	67457303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768713596	NA	P-0027728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	154	373	1	ENST00000327367.4:c.277C>T	p.Arg93Ter	p.R93*	ENST00000327367	NM_005902.3	93	Cga/Tga	2/9	0.423530365195978	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.423530365195978	1		374	517	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143306	108143306	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	106	294	0	ENST00000278616.4:c.3125T>C	p.Leu1042Pro	p.L1042P	ENST00000278616	NM_000051.3	1042	cTa/cCa	21/63	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.423530365195978	2		294	479	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265982	41266276	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAA	AATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAA	-	novel	NA	P-0027728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	20	68	0	ENST00000349496.5:c.14-34_241+33del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.417309945505225	2	FACETS	0.787	0.61	0.988	0.394	0.305	0.494	CLONAL	1	TRUE	0	0.423530365195978	2		68	120	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153537	108153537	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555092445	NA	P-0027729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	20	290	0	ENST00000278616.4:c.3677A>G	p.Asp1226Gly	p.D1226G	ENST00000278616	NM_000051.3	1226	gAt/gGt	25/63	1	2	FACETS	0.581	0.444	0.742	0.581	0.444	0.742	SUBCLONAL	1	TRUE	1	0.2	2		290	344	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533564	63533566	+	missense_variant	Missense_Mutation	TNP	CTC	CTC	TTT	novel	NA	P-0027729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	182	561	0	ENST00000307078.5:c.1588_1590delinsAAA	p.Glu530Lys	p.E530K	ENST00000307078	NM_004655.3	530	GAG/AAA	6/11	0.3	5	FACETS	0.946	0.874	1			1	CLONAL	3	TRUE	NA	0.2	5		561	834	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153537	108153537	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555092445	NA	P-0027729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	374	290	0	ENST00000278616.4:c.3677A>G	p.Asp1226Gly	p.D1226G	ENST00000278616	NM_000051.3	1226	gAt/gGt	25/63	0.767071156221652	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.767071156221652	1		290	594	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716357	18716357	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	145	525	0	ENST00000266497.5:c.3704C>A	p.Thr1235Lys	p.T1235K	ENST00000266497		1235	aCa/aAa	26/31	1	2	FACETS	0.402	0.366	0.44	0.402	0.366	0.44	SUBCLONAL	1	TRUE	1	0.767071156221652	2		525	940	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533566	63533567	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0027729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	4639	611	1	ENST00000307078.5:c.1587_1588delinsAA	p.Glu530Lys	p.E530K	ENST00000307078	NM_004655.3	529	gaGGag/gaAAag	6/11	0.767071156221652	11	FACETS	1	0.998	1			1	CLONAL	10	TRUE	NA	0.767071156221652	11		612	5276	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152095	55152106	+	inframe_deletion	In_Frame_Del	DEL	ATCATGCATGAT	ATCATGCATGAT	-	rs121913267	NA	P-0027730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	310	437	0	ENST00000257290.5:c.2527_2538del	p.Ile843_Asp846del	p.I843_D846del	ENST00000257290	NM_006206.4	843	ATCATGCATGAT/-	18/23	1	2	FACETS	0.965	0.916	1	0.965	0.916	1	CLONAL	1	TRUE	1	0.875138185635022	2		437	734	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266564	115266564	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	255	403	0	ENST00000438362.2:c.1951del	p.Leu651Ter	p.L651*	ENST00000438362	NM_001242891.1	651	Ctg/tg	16/20	0.875138185635022	1	FACETS	0.947	0.91	0.983	0.947	0.91	0.983	CLONAL	1	TRUE	0	0.875138185635022	1		403	346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	214	511	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.245205613386576	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.357114234629752	2		511	579	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499520	89499520	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	49	235	0	ENST00000336596.2:c.2690G>T	p.Arg897Met	p.R897M	ENST00000336596	NM_005233.5	897	aGg/aTg	15/17	0.138221669058096	5	FACETS	1	0.88	1	0.348	0.295	0.405	INDETERMINATE	1	TRUE	2	0.357114234629752	5		235	404	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226046	133226046	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	102	474	0	ENST00000320574.5:c.3851G>T	p.Arg1284Leu	p.R1284L	ENST00000320574	NM_006231.2	1284	cGg/cTg	31/49	0.357114234629752	3	FACETS	1	0.935	1	0.53	0.475	0.589	CLONAL	1	TRUE	1	0.357114234629752	3		474	635	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023916	27023916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs974979838	NA	P-0027731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	27	59	1	ENST00000324856.7:c.1022C>T	p.Ala341Val	p.A341V	ENST00000324856	NM_006015.4	341	gCg/gTg	1/20	0.232661273809387	3	FACETS	1	0.868	1	0.716	0.587	0.853	CLONAL	2	TRUE	0	0.357114234629752	3		60	83	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935320	36935321	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0027731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	175	411	0	ENST00000361632.4:c.1406dup	p.Ser469ArgfsTer5	p.S469Rfs*5	ENST00000361632		469	agc/agGc	10/16	0.232661273809387	3	FACETS	0.966	0.894	1	0.644	0.596	0.693	CLONAL	2	TRUE	0	0.357114234629752	3		411	598	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724481	162724481	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	164	376	0	ENST00000367921.3:c.253G>T	p.Glu85Ter	p.E85*	ENST00000367921	NM_006182.2	85	Gag/Tag	5/18	0.357114234629752	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.357114234629752	3		376	471	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724337	112724337	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	175	471	1	ENST00000369452.4:c.221G>T	p.Arg74Leu	p.R74L	ENST00000369452	NM_007373.3	74	cGg/cTg	2/9	0.357114234629752	2	FACETS	0.875	0.811	0.941	0.875	0.811	0.941	CLONAL	2	TRUE	0	0.357114234629752	2		472	560	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588865	69588865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	290	397	0	ENST00000168712.1:c.371G>A	p.Gly124Asp	p.G124D	ENST00000168712	NM_002007.2	124	gGc/gAc	2/3	0.355468175418214	4	FACETS	0.982	0.935	1	0.982	0.935	1	CLONAL	4	TRUE	0	0.357114234629752	4		397	561	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188146	108188146	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	179	309	0	ENST00000278616.4:c.6245A>T	p.Lys2082Ile	p.K2082I	ENST00000278616	NM_000051.3	2082	aAa/aTa	43/63	0.355468175418214	4	FACETS	1	0.983	1	0.865	0.809	0.922	CLONAL	3	TRUE	0	0.357114234629752	4		309	393	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68878140	68878140	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0027731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	77	223	0	ENST00000487270.1:c.854-1G>T		p.X285_splice	ENST00000487270	NM_133509.3	285			0.0683687090243035	3	FACETS	0.938	0.833	1	0.938	0.833	1	INDETERMINATE	2	TRUE	1	0.357114234629752	3		223	271	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026167	36026168	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0027731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	416	514	1	ENST00000358208.4:c.769_770delinsTT	p.Gly257Phe	p.G257F	ENST00000358208		257	GGc/TTc	7/12	0.355468175418214	4	FACETS	0.979	0.94	1	0.979	0.94	1	CLONAL	4	TRUE	0	0.357114234629752	4		515	807	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739104	40739104	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	265	365	0	ENST00000373198.4:c.3180G>T	p.Glu1060Asp	p.E1060D	ENST00000373198	NM_133170.3	1060	gaG/gaT	24/32	0.355468175418214	4	FACETS	0.952	0.903	1	0.952	0.903	1	CLONAL	4	TRUE	0	0.357114234629752	4		365	529	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944539	40944539	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	72	368	0	ENST00000373198.4:c.1963G>T	p.Ala655Ser	p.A655S	ENST00000373198	NM_133170.3	655	Gcc/Tcc	12/32	0.355468175418214	4	FACETS	0.979	0.856	1	0.245	0.214	0.278	CLONAL	1	TRUE	0	0.357114234629752	4		368	559	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448571	89448571	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	121	388	0	ENST00000336596.2:c.1535G>T	p.Arg512Leu	p.R512L	ENST00000336596	NM_005233.5	512	cGa/cTa	7/17	0.138221669058096	5	FACETS	0.809	0.733	0.89	0.539	0.488	0.593	INDETERMINATE	2	TRUE	2	0.357114234629752	5		388	643	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920418	134920418	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	121	408	0	ENST00000398015.3:c.2233C>G	p.Leu745Val	p.L745V	ENST00000398015	NM_004441.4	745	Ctg/Gtg	12/16	0.138221669058096	5	FACETS	0.978	0.888	1	0.652	0.592	0.715	INDETERMINATE	2	TRUE	2	0.357114234629752	5		408	532	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138400848	138400848	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0027731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	58	390	0	ENST00000289153.2:c.2465T>A	p.Leu822Ter	p.L822*	ENST00000289153	NM_006219.2	822	tTg/tAg	17/22	0.138221669058096	5	FACETS	0.902	0.775	1	0.301	0.258	0.347	INDETERMINATE	1	TRUE	2	0.357114234629752	5		390	553	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612122	189612122	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	151	406	0	ENST00000264731.3:c.1874C>T	p.Thr625Ile	p.T625I	ENST00000264731	NM_003722.4	625	aCa/aTa	14/14	0.22443738126771	2	FACETS	0.968	0.893	1	0.968	0.893	1	CLONAL	2	TRUE	0	0.357114234629752	2		406	437	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225612	225612	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	80	220	0	ENST00000264932.6:c.391G>T	p.Asp131Tyr	p.D131Y	ENST00000264932	NM_004168.2	131	Gac/Tac	4/15	0.333768508045423	4	FACETS	1	0.964	1	0.415	0.366	0.467	CLONAL	1	TRUE	1	0.357114234629752	4		220	488	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513239	149513239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	87	464	0	ENST00000261799.4:c.844G>T	p.Glu282Ter	p.E282*	ENST00000261799	NM_002609.3	282	Gag/Tag	6/23	0.357114234629752	2	FACETS	1	0.922	1	0.523	0.465	0.585	CLONAL	1	TRUE	0	0.357114234629752	2		464	466	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515139	149515139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776224834	NA	P-0027731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	209	388	0	ENST00000261799.4:c.343C>T	p.Arg115Trp	p.R115W	ENST00000261799	NM_002609.3	115	Cgg/Tgg	3/23	0.357114234629752	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.357114234629752	2		388	540	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710528	117710528	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	58	153	0	ENST00000368508.3:c.1744C>G	p.Leu582Val	p.L582V	ENST00000368508	NM_002944.2	582	Ctt/Gtt	12/43	0.357114234629752	3	FACETS	0.829	0.721	0.943	0.829	0.721	0.943	CLONAL	2	TRUE	1	0.357114234629752	3		153	231	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38315002	38315002	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	117	441	0	ENST00000425967.3:c.62G>T	p.Cys21Phe	p.C21F	ENST00000425967	NM_001174067.1	21	tGt/tTt	3/19	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.357114234629752	2		441	540	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878162	48878162	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	59	95	0	ENST00000267163.4:c.116del	p.Pro39ArgfsTer26	p.P39Rfs*26	ENST00000267163	NM_000321.2	38	ggC/gg	1/27	0.494041527469995	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.494041527469995	1		95	165	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577109	7578131	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGCACAAACACGCACCTCAAAGCTGTTCCGTCCCAGTAGATTACCACTACTCAGGATAGGAAAAGAGAAGCAAGAGGCAGTAAGGAAATCAGGTCCTACCTGTCCCATTTAAAAAACCAGGCTCCATCTACTCCCAACCACCCTTGTCCTTTCTGGAGCCTAAGCTCCAGCTCCAGGTAGGTGGAGGAGAAGCCACAGGTTAAGAGGTCCCAAAGCCAGAGAAAAGAAAACTGAGTGGGAGCAGTAAGGAGATTCCCCGCCGGGGATGTGATGAGAGGTGGATGGGTAGTAGTATGGAAGAAATCGGTAAGAGGTGGGCCCAGGGGTCAGAGGCAAGCAGAGGCTGGGGCACAGCAGGCCAGTGTGCAGGGTGGCAAGTGGCTCCTGACCTGGAGTCTTCCAGTGTGATGATGGTGAGGATGGGCCTCCGGTTCATGCCGCCCATGCAGGAACTGTTACACATGTAGTTGTAGTGGATGGTGGTACAGTCAGAGCCAACCTAGGAGATAACACAGGCCCAAGATGAGGCCAGTGCGCCTTGGGGAGACCTGTGGCAAGCAGGGGAGGCCTTTTTTTTTTTTTTTTGAGATGGAATCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGTGATCTCAGCTCACTGCAAGCTCCACCGCCCAGGTTCACGCCATTCTCCTTCCTCAGCCTCCCGAGTAGCTGGGACTACAGGTGCCCAGCACCACGCCCGGCTAATTTTTTTTTGTATTTTTCAGTAGAGACGGGGTTTCACCGTTAGCCAGGATGGTCTCGATCTCCCAACCTCGTGATCCGCCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACTGCGCCCAGCCAAGCAGGGGAGGCCCTTAGCCTCTGTAAGCTTCAGTTTTTTCAACTGTGCAATAGTTAAACCCATTTACTTTGCACATCTCATGGGGTTATAGGGAGGTCAAATAAGCAGCAGGAGAAAGCCCCCCTACTGCTCACCTGGAGGGCCACTGACAA	AGGCACAAACACGCACCTCAAAGCTGTTCCGTCCCAGTAGATTACCACTACTCAGGATAGGAAAAGAGAAGCAAGAGGCAGTAAGGAAATCAGGTCCTACCTGTCCCATTTAAAAAACCAGGCTCCATCTACTCCCAACCACCCTTGTCCTTTCTGGAGCCTAAGCTCCAGCTCCAGGTAGGTGGAGGAGAAGCCACAGGTTAAGAGGTCCCAAAGCCAGAGAAAAGAAAACTGAGTGGGAGCAGTAAGGAGATTCCCCGCCGGGGATGTGATGAGAGGTGGATGGGTAGTAGTATGGAAGAAATCGGTAAGAGGTGGGCCCAGGGGTCAGAGGCAAGCAGAGGCTGGGGCACAGCAGGCCAGTGTGCAGGGTGGCAAGTGGCTCCTGACCTGGAGTCTTCCAGTGTGATGATGGTGAGGATGGGCCTCCGGTTCATGCCGCCCATGCAGGAACTGTTACACATGTAGTTGTAGTGGATGGTGGTACAGTCAGAGCCAACCTAGGAGATAACACAGGCCCAAGATGAGGCCAGTGCGCCTTGGGGAGACCTGTGGCAAGCAGGGGAGGCCTTTTTTTTTTTTTTTTGAGATGGAATCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGTGATCTCAGCTCACTGCAAGCTCCACCGCCCAGGTTCACGCCATTCTCCTTCCTCAGCCTCCCGAGTAGCTGGGACTACAGGTGCCCAGCACCACGCCCGGCTAATTTTTTTTTGTATTTTTCAGTAGAGACGGGGTTTCACCGTTAGCCAGGATGGTCTCGATCTCCCAACCTCGTGATCCGCCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACTGCGCCCAGCCAAGCAGGGGAGGCCCTTAGCCTCTGTAAGCTTCAGTTTTTTCAACTGTGCAATAGTTAAACCCATTTACTTTGCACATCTCATGGGGTTATAGGGAGGTCAAATAAGCAGCAGGAGAAAGCCCCCCTACTGCTCACCTGGAGGGCCACTGACAA	-	novel	NA	P-0027732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	195	441	0	ENST00000269305.4:c.672+46_829del		p.X224_splice	ENST00000269305	NM_001126112.2	224		7-8/11	0.494041527469995	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.494041527469995	1		441	584	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486112	29486112	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1567816131	NA	P-0027732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	190	226	0	ENST00000356175.3:c.288+1G>T		p.X96_splice	ENST00000356175	NM_000267.3	96			0.347887321056975	3	FACETS	0.967	0.902	1	0.967	0.902	1	CLONAL	2	TRUE	1	0.494041527469995	3		226	496	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664851	29664852	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGAA	novel	NA	P-0027732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	89	238	0	ENST00000356175.3:c.6594_6595insGGAA	p.Ile2199GlyfsTer23	p.I2199Gfs*23	ENST00000356175	NM_000267.3	2198	-/GGAA	43/57	0.347887321056975	3	FACETS	0.773	0.687	0.865	0.387	0.343	0.433	SUBCLONAL	1	TRUE	1	0.494041527469995	3		238	581	SUCCESS
APC	324	MSKCC	GRCh37	5	112176530	112176530	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	44	301	0	ENST00000257430.4:c.5239A>G	p.Met1747Val	p.M1747V	ENST00000257430	NM_000038.5	1747	Atg/Gtg	16/16	0.226967164500965	1	FACETS	0.322	0.27	0.38	0.322	0.27	0.38	INDETERMINATE	1	TRUE	0	0.494041527469995	1		301	416	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341090	8341090	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	111	315	0	ENST00000356435.5:c.5126G>T	p.Arg1709Ile	p.R1709I	ENST00000356435		1709	aGa/aTa	30/35	1	2	FACETS	0.968	0.876	1	0.968	0.876	1	CLONAL	1	TRUE	1	0.494041527469995	2		315	464	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	144	210	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.982	0.907	1	0.982	0.907	1	CLONAL	1	TRUE	1	0.798908878250366	2		210	367	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692901	89692901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786204929	NA	P-0027747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	180	413	0	ENST00000371953.3:c.385G>A	p.Gly129Arg	p.G129R	ENST00000371953	NM_000314.4	129	Gga/Aga	5/9	0.798908878250366	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.798908878250366	1		413	268	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0027750-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	261	497	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.439275055412074	3	FACETS	0.865	0.813	0.918	0.865	0.813	0.918	CLONAL	2	TRUE	1	0.439275055412074	3		497	838	SUCCESS
APC	324	MSKCC	GRCh37	5	112173837	112173838	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0027750-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	179	364	0	ENST00000257430.4:c.2547_2548del	p.Asp849GlufsTer62	p.D849Efs*62	ENST00000257430	NM_000038.5	849	gAT/g	16/16	0.439275055412074	2	FACETS	0.804	0.747	0.862	0.804	0.747	0.862	CLONAL	2	TRUE	0	0.439275055412074	2		364	507	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813438	102813438	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027750-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	120	481	0	ENST00000307046.8:c.251G>T	p.Arg84Leu	p.R84L	ENST00000307046	NM_001111285.1	84	cGg/cTg	3/4	0.439275055412074	3	FACETS	0.799	0.721	0.881	0.399	0.36	0.441	SUBCLONAL	1	TRUE	1	0.439275055412074	3		481	834	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133989	41133989	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027750-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	171	437	1	ENST00000379561.5:c.1639C>T	p.Pro547Ser	p.P547S	ENST00000379561	NM_002015.3	547	Ccc/Tcc	2/3	0.439275055412074	3	FACETS	1	0.977	1	0.577	0.531	0.625	CLONAL	1	TRUE	1	0.439275055412074	3		438	823	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727463	88727463	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027750-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	156	472	2	ENST00000360948.2:c.316C>A	p.Gln106Lys	p.Q106K	ENST00000360948	NM_001012338.2	106	Caa/Aaa	3/19	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.439275055412074	2		474	710	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341572	89341572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754093852	NA	P-0027750-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	150	462	0	ENST00000301030.4:c.7498C>T	p.Pro2500Ser	p.P2500S	ENST00000301030	NM_001256183.1	2500	Ccc/Tcc	10/13	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.439275055412074	2		462	606	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026112	71026112	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027750-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	359	379	0	ENST00000318789.4:c.1510del	p.Arg504AlafsTer23	p.R504Afs*23	ENST00000318789	NM_032682.5	504	Cgc/gc	17/21	0.439275055412074	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.439275055412074	2		379	753	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410934	63410934	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027750-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	180	658	4	ENST00000330258.3:c.2233T>A	p.Tyr745Asn	p.Y745N	ENST00000330258	NM_152424.3	745	Tac/Aac	2/2	0.428297169291082	3	FACETS	0.997	0.918	1	0.498	0.459	0.539	CLONAL	1	TRUE	1	0.439275055412074	3		662	1003	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411748	63411748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027750-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	490	776	0	ENST00000330258.3:c.1419del	p.Ser474ProfsTer67	p.S474Pfs*67	ENST00000330258	NM_152424.3	473	gaC/ga	2/2	0.428297169291082	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.439275055412074	3		776	1281	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611162	100611162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027750-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	152	496	0	ENST00000308731.7:c.1444C>T	p.Leu482Phe	p.L482F	ENST00000308731	NM_000061.2	482	Ctc/Ttc	15/19	0.428297169291082	3	FACETS	0.947	0.866	1	0.474	0.433	0.516	CLONAL	1	TRUE	1	0.439275055412074	3		496	891	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270085	198270085	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	266	481	0	ENST00000335508.6:c.1351C>T	p.Arg451Ter	p.R451*	ENST00000335508	NM_012433.2	451	Cga/Tga	10/25	1	2	FACETS	0.92	0.867	0.974	0.92	0.867	0.974	CLONAL	1	TRUE	1	0.78879340571929	2		481	733	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439617	140439617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	308	544	0	ENST00000288602.6:c.2122C>T	p.Pro708Ser	p.P708S	ENST00000288602	NM_004333.4	708	Ccc/Tcc	17/18	0.740064325879997	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.78879340571929	1		544	436	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546761	9546761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768724288	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	92	275	0	ENST00000353224.5:c.1261G>A	p.Asp421Asn	p.D421N	ENST00000353224	NM_177990.2	421	Gac/Aac	5/10	0.351230078587063	1	FACETS	0.604	0.546	0.663	0.604	0.546	0.663	INDETERMINATE	1	TRUE	0	0.78879340571929	1		275	234	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836659	89836659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	357	690	0	ENST00000389301.3:c.2231C>T	p.Pro744Leu	p.P744L	ENST00000389301	NM_000135.2	744	cCc/cTc	25/43	1	2	FACETS	0.982	0.934	1	0.982	0.934	1	CLONAL	1	TRUE	1	0.78879340571929	2		690	922	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556367	29556367	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	311	495	1	ENST00000356175.3:c.2734C>T	p.Gln912Ter	p.Q912*	ENST00000356175	NM_000267.3	912	Caa/Taa	21/57	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.78879340571929	2		496	697	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790129	40790129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	285	527	1	ENST00000373198.4:c.2602C>T	p.Pro868Ser	p.P868S	ENST00000373198	NM_133170.3	868	Ccc/Tcc	18/32	0.688485875338652	3	FACETS	1	0.99	1	0.606	0.571	0.641	CLONAL	1	TRUE	1	0.78879340571929	3		528	832	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944983	31944983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1175067252	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	330	645	0	ENST00000340398.3:c.118C>T	p.Arg40Cys	p.R40C	ENST00000340398	NM_001013699.2	40	Cgc/Tgc	1/1	NA	2	FACETS	0.976	0.927	1			1	INDETERMINATE	1	TRUE	NA	0.78879340571929	2		645	857	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157926	106157926	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1048995426	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	155	320	0	ENST00000380013.4:c.2827C>T	p.Gln943Ter	p.Q943*	ENST00000380013	NM_001127208.2	943	Cag/Tag	3/11	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.78879340571929	2		320	383	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265308	152265308	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	182	299	0	ENST00000206249.3:c.761G>A	p.Gly254Glu	p.G254E	ENST00000206249	NM_000125.3	254	gGg/gAg	4/8	0.78879340571929	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.78879340571929	1		299	260	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577540	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	rs1555525498	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	358	547	2	ENST00000269305.4:c.741_742delinsTT	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	247	aaCCgg/aaTTgg	7/11	0.78879340571929	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.78879340571929	1		549	453	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226549706	226549706	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	299	545	0	ENST00000366794.5:c.2927C>T	p.Ser976Leu	p.S976L	ENST00000366794	NM_001618.3	976	tCa/tTa	22/23	1	2	FACETS	0.991	0.938	1	0.991	0.938	1	CLONAL	1	TRUE	1	0.78879340571929	2		545	765	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112745473	112745473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	332	658	0	ENST00000369452.4:c.791C>T	p.Thr264Ile	p.T264I	ENST00000369452	NM_007373.3	264	aCc/aTc	3/9	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.78879340571929	2		658	800	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123324081	123324081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	243	468	0	ENST00000358487.5:c.389C>T	p.Ser130Phe	p.S130F	ENST00000358487	NM_000141.4	130	tCc/tTc	4/18	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.78879340571929	2		468	573	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123353291	123353291	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753987054	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	327	641	0	ENST00000358487.5:c.41C>T	p.Thr14Ile	p.T14I	ENST00000358487	NM_000141.4	14	aCc/aTc	2/18	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.78879340571929	2		641	822	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	441059	441059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	53	512	0	ENST00000399788.2:c.1699C>T	p.Pro567Ser	p.P567S	ENST00000399788	NM_001042603.1	567	Cct/Tct	13/28	0.753213024439013	1	FACETS	0.163	0.139	0.19	0.163	0.139	0.19	SUBCLONAL	1	TRUE	0	0.78879340571929	1		512	499	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025562	1025563	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	278	573	3	ENST00000358495.3:c.812_813delinsAA	p.Arg271Gln	p.R271Q	ENST00000358495	NM_134424.2	271	cGG/cAA	9/12	0.753213024439013	1	FACETS	0.901	0.859	0.942	0.901	0.859	0.942	CLONAL	1	TRUE	0	0.78879340571929	1		576	474	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433989	49433989	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210845628	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	304	673	0	ENST00000301067.7:c.7564C>T	p.Pro2522Ser	p.P2522S	ENST00000301067	NM_003482.3	2522	Cct/Tct	31/54	NA	2	FACETS	0.94	0.89	0.991			1	INDETERMINATE	1	TRUE	NA	0.78879340571929	2		673	820	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251250	99251250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371283551	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	407	556	0	ENST00000268035.6:c.554C>T	p.Thr185Ile	p.T185I	ENST00000268035	NM_000875.3	185	aCc/aTc	2/21	0.20928118174274	5	FACETS	1	0.993	1	0.795	0.759	0.83	INDETERMINATE	2	TRUE	2	0.78879340571929	5		556	945	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348281	89348281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	390	771	1	ENST00000301030.4:c.4669C>T	p.Pro1557Ser	p.P1557S	ENST00000301030	NM_001256183.1	1557	Cca/Tca	9/13	1	2	FACETS	0.936	0.892	0.982	0.936	0.892	0.982	CLONAL	1	TRUE	1	0.78879340571929	2		772	1056	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592312	29592312	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	277	487	0	ENST00000356175.3:c.4727G>A	p.Gly1576Glu	p.G1576E	ENST00000356175	NM_000267.3	1576	gGg/gAg	35/57	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.78879340571929	2		487	664	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599892	10599892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199953210	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	473	725	0	ENST00000171111.5:c.1684C>T	p.His562Tyr	p.H562Y	ENST00000171111	NM_203500.1	562	Cac/Tac	5/6	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.78879340571929	2		725	1110	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054581	13054581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	244	441	0	ENST00000316448.5:c.1108G>A	p.Glu370Lys	p.E370K	ENST00000316448	NM_004343.3	370	Gag/Aag	9/9	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.78879340571929	2		441	576	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276302	15276302	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	435	654	0	ENST00000263388.2:c.5692G>A	p.Asp1898Asn	p.D1898N	ENST00000263388	NM_000435.2	1898	Gac/Aac	31/33	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.78879340571929	2		654	989	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966774	18966774	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	475	806	0	ENST00000262803.5:c.1585C>A	p.Gln529Lys	p.Q529K	ENST00000262803	NM_002911.3	529	Cag/Aag	12/24	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.78879340571929	2		806	1099	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214067	36214067	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	781	695	2	ENST00000222270.7:c.2893C>T	p.Arg965Ter	p.R965*	ENST00000222270	NM_014727.1	965	Cga/Tga	6/37	0.536287465041778	3	FACETS	0.955	0.927	0.983			1	CLONAL	2	TRUE	NA	0.78879340571929	3		697	1446	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467473	25467474	+	missense_variant	Missense_Mutation	DNP	AC	AC	TA	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	305	652	0	ENST00000264709.3:c.1602_1603delinsTA	p.Gln534_Ser535delinsHisThr	p.Q534_S535delinsHT	ENST00000264709	NM_175629.2	534	caGTcc/caTAcc	14/23	1	2	FACETS	0.923	0.873	0.973	0.923	0.873	0.973	CLONAL	1	TRUE	1	0.78879340571929	2		652	838	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416377	29416377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	357	719	1	ENST00000389048.3:c.4576G>A	p.Glu1526Lys	p.E1526K	ENST00000389048	NM_004304.4	1526	Gag/Aag	29/29	1	2	FACETS	0.923	0.877	0.969	0.923	0.877	0.969	CLONAL	1	TRUE	1	0.78879340571929	2		720	981	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39234320	39234320	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	182	348	1	ENST00000402219.2:c.2525C>T	p.Thr842Ile	p.T842I	ENST00000402219	NM_005633.3	842	aCt/aTt	16/23	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.78879340571929	2		349	453	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248623	212248623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	236	461	0	ENST00000342788.4:c.3644C>T	p.Thr1215Ile	p.T1215I	ENST00000342788	NM_005235.2	1215	aCc/aTc	28/28	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.78879340571929	2		461	584	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37628012	37628012	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	394	725	0	ENST00000249071.6:c.248C>T	p.Ser83Phe	p.S83F	ENST00000249071	NM_002872.4	83	tCc/tTc	4/7	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.78879340571929	2		725	894	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437446	52437446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553644798	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	265	417	2	ENST00000460680.1:c.1715C>T	p.Pro572Leu	p.P572L	ENST00000460680	NM_004656.3	572	cCc/cTc	13/17	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.78879340571929	2		419	573	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670547	134670547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	352	645	0	ENST00000398015.3:c.458G>A	p.Gly153Glu	p.G153E	ENST00000398015	NM_004441.4	153	gGa/gAa	3/16	0.78879340571929	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.78879340571929	1		645	528	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973952	55973952	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	211	483	1	ENST00000263923.4:c.1364A>G	p.His455Arg	p.H455R	ENST00000263923	NM_002253.2	455	cAc/cGc	10/30	1	2	FACETS	0.828	0.773	0.884	0.828	0.773	0.884	CLONAL	1	TRUE	1	0.78879340571929	2		484	646	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927644	131927644	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	336	521	0	ENST00000265335.6:c.1711C>T	p.Pro571Ser	p.P571S	ENST00000265335		571	Ccc/Tcc	11/25	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.78879340571929	2		521	735	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149436929	149436929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	301	640	0	ENST00000286301.3:c.2240G>A	p.Gly747Glu	p.G747E	ENST00000286301	NM_005211.3	747	gGa/gAa	17/22	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.78879340571929	2		640	685	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055898	180055898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	214	442	0	ENST00000261937.6:c.1087C>T	p.Pro363Ser	p.P363S	ENST00000261937	NM_182925.4	363	Ccg/Tcg	8/30	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.78879340571929	2		442	542	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163446	32163446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	344	572	0	ENST00000375023.3:c.5780C>T	p.Pro1927Leu	p.P1927L	ENST00000375023	NM_004557.3	1927	cCt/cTt	30/30	0.659528436356798	3	FACETS	1	0.99	1	0.589	0.558	0.621	CLONAL	1	TRUE	1	0.78879340571929	3		572	1032	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117684026	117684026	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1185167609	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	160	321	0	ENST00000368508.3:c.3121C>T	p.Pro1041Ser	p.P1041S	ENST00000368508	NM_002944.2	1041	Cca/Tca	21/43	0.78879340571929	1	FACETS	0.983	0.927	1	0.983	0.927	1	CLONAL	1	TRUE	0	0.78879340571929	1		321	250	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511303	157511303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759771283	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	250	459	0	ENST00000346085.5:c.3821C>T	p.Pro1274Leu	p.P1274L	ENST00000346085	NM_020732.3	1274	cCc/cTc	15/20	0.78879340571929	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.78879340571929	1		459	377	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528741	8528741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1277243866	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	208	403	0	ENST00000356435.5:c.391G>A	p.Gly131Ser	p.G131S	ENST00000356435		131	Ggc/Agc	4/35	0.78879340571929	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.78879340571929	1		403	279	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849194	76849194	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	277	246	2	ENST00000373344.5:c.6082C>T	p.Arg2028Ter	p.R2028*	ENST00000373344	NM_000489.3	2028	Cga/Tga	26/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.78879340571929	1		248	319	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230641	46230641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	56	477	0	ENST00000334344.6:c.890C>T	p.Ser297Phe	p.S297F	ENST00000334344	NM_152641.2	297	tCc/tTc	8/21	NA	2	FACETS	0.235	0.201	0.272			1	INDETERMINATE	1	TRUE	NA	0.78879340571929	2		477	605	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435061	18435061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267603400	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	24	431	0	ENST00000266497.5:c.46G>A	p.Glu16Lys	p.E16K	ENST00000266497		16	Gaa/Aaa	1/31	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.78879340571929	NA		431	380	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885295	111885295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148636776	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	35	447	0	ENST00000341259.2:c.1183G>A	p.Glu395Lys	p.E395K	ENST00000341259	NM_005475.2	395	Gag/Aag	6/8	1	2	FACETS	0.148	0.121	0.179	0.148	0.121	0.179	SUBCLONAL	1	TRUE	1	0.78879340571929	2		447	599	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410516	63410516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201092215	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	34	347	0	ENST00000330258.3:c.2651C>T	p.Pro884Leu	p.P884L	ENST00000330258	NM_152424.3	884	cCt/cTt	2/2	1	1	FACETS	0.13	0.106	0.157	0.13	0.106	0.157	SUBCLONAL	1	TRUE	0	0.78879340571929	1		347	401	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398246	25398246	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	32	534	0	ENST00000311936.3:c.73C>T	p.Gln25Ter	p.Q25*	ENST00000311936	NM_004985.3	25	Cag/Tag	2/5	0.77192917576002	1	FACETS	0.126	0.102	0.154	0.126	0.102	0.154	SUBCLONAL	1	TRUE	0	0.78879340571929	1		534	389	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805540	46805540	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	44	794	0	ENST00000290295.7:c.416C>T	p.Pro139Leu	p.P139L	ENST00000290295	NM_006361.5	139	cCt/cTt	1/2	0.753213024439013	1	FACETS	0.097	0.081	0.116	0.097	0.081	0.116	SUBCLONAL	1	TRUE	0	0.78879340571929	1		794	693	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488728	212488728	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	308	483	0	ENST00000342788.4:c.2121A>C	p.Gln707His	p.Q707H	ENST00000342788	NM_005235.2	707	caA/caC	18/28	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.78879340571929	2		483	722	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177968	56177968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	41	449	0	ENST00000399503.3:c.2941C>T	p.Pro981Ser	p.P981S	ENST00000399503	NM_005921.1	981	Cca/Tca	14/20	1	2	FACETS	0.172	0.143	0.205	0.172	0.143	0.205	SUBCLONAL	1	TRUE	1	0.78879340571929	2		449	603	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638428	117638428	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	15	382	0	ENST00000368508.3:c.6013A>C	p.Asn2005His	p.N2005H	ENST00000368508	NM_002944.2	2005	Aat/Cat	38/43	0.78879340571929	1	FACETS	0.079	0.058	0.106	0.079	0.058	0.106	SUBCLONAL	1	TRUE	0	0.78879340571929	1		382	290	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658454	117658454	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	35	600	0	ENST00000368508.3:c.5129C>T	p.Pro1710Leu	p.P1710L	ENST00000368508	NM_002944.2	1710	cCt/cTt	31/43	0.78879340571929	1	FACETS	0.129	0.105	0.155	0.129	0.105	0.155	SUBCLONAL	1	TRUE	0	0.78879340571929	1		600	417	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953056	2953056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	352	646	0	ENST00000396946.4:c.2884C>T	p.Pro962Ser	p.P962S	ENST00000396946	NM_032415.4	962	Ccc/Tcc	22/25	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.78879340571929	2		646	848	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820632	44820632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	29	193	0	ENST00000377967.4:c.329C>T	p.Pro110Leu	p.P110L	ENST00000377967	NM_021140.2	110	cCa/cTa	3/29	1	1	FACETS	0.158	0.127	0.193	0.158	0.127	0.193	SUBCLONAL	1	TRUE	0	0.78879340571929	1		193	282	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338639	70338639	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	50	292	0	ENST00000374080.3:c.35G>A	p.Arg12Gln	p.R12Q	ENST00000374080		12	cGg/cAg	1/45	1	1	FACETS	0.2	0.17	0.233	0.2	0.17	0.233	SUBCLONAL	1	TRUE	0	0.78879340571929	1		292	384	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270085	198270085	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	253	481	0	ENST00000335508.6:c.1351C>T	p.Arg451Ter	p.R451*	ENST00000335508	NM_012433.2	451	Cga/Tga	10/25	1	2	FACETS	0.936	0.88	0.993	0.936	0.88	0.993	CLONAL	1	TRUE	1	0.740356867074977	2		481	730	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439617	140439617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	216	544	0	ENST00000288602.6:c.2122C>T	p.Pro708Ser	p.P708S	ENST00000288602	NM_004333.4	708	Ccc/Tcc	17/18	NA	2	FACETS	0.891	0.833	0.95			1	INDETERMINATE	1	TRUE	NA	0.740356867074977	2		544	655	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546761	9546761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768724288	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	121	275	0	ENST00000353224.5:c.1261G>A	p.Asp421Asn	p.D421N	ENST00000353224	NM_177990.2	421	Gac/Aac	5/10	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.740356867074977	2		275	325	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836659	89836659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	199	690	0	ENST00000389301.3:c.2231C>T	p.Pro744Leu	p.P744L	ENST00000389301	NM_000135.2	744	cCc/cTc	25/43	0.152067431164062	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.740356867074977	0		690	670	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663425	67663425	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	35	392	0	ENST00000264010.4:c.1826C>T	p.Ser609Phe	p.S609F	ENST00000264010	NM_006565.3	609	tCc/tTc	10/12	1	2	FACETS	0.17	0.139	0.206	0.17	0.139	0.206	SUBCLONAL	1	TRUE	1	0.740356867074977	2		392	555	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556367	29556367	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	260	495	1	ENST00000356175.3:c.2734C>T	p.Gln912Ter	p.Q912*	ENST00000356175	NM_000267.3	912	Caa/Taa	21/57	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.740356867074977	2		496	670	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295253	1295253	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1232074117	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	126	290	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.915	0.838	0.995	0.915	0.838	0.995	CLONAL	1	TRUE	1	0.740356867074977	2		290	372	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790129	40790129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	222	527	1	ENST00000373198.4:c.2602C>T	p.Pro868Ser	p.P868S	ENST00000373198	NM_133170.3	868	Ccc/Tcc	18/32	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.740356867074977	2		528	552	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601228	28601228	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772146579	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	45	393	0	ENST00000241453.7:c.2204C>T	p.Ser735Phe	p.S735F	ENST00000241453	NM_004119.2	735	tCc/tTc	17/24	0.628270570215581	1	FACETS	0.183	0.153	0.215	0.183	0.153	0.215	SUBCLONAL	1	TRUE	0	0.740356867074977	1		393	419	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944983	31944983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1175067252	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	270	645	0	ENST00000340398.3:c.118C>T	p.Arg40Cys	p.R40C	ENST00000340398	NM_001013699.2	40	Cgc/Tgc	1/1	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.740356867074977	2		645	676	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157926	106157926	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1048995426	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	172	320	0	ENST00000380013.4:c.2827C>T	p.Gln943Ter	p.Q943*	ENST00000380013	NM_001127208.2	943	Cag/Tag	3/11	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.740356867074977	2		320	464	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265308	152265308	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	152	299	0	ENST00000206249.3:c.761G>A	p.Gly254Glu	p.G254E	ENST00000206249	NM_000125.3	254	gGg/gAg	4/8	0.740356867074977	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.740356867074977	1		299	250	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577540	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	rs1555525498	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	326	547	2	ENST00000269305.4:c.741_742delinsTT	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	247	aaCCgg/aaTTgg	7/11	0.686222185777823	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.740356867074977	1		549	539	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850885	128850885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61740964	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	251	582	1	ENST00000249373.3:c.1732G>A	p.Glu578Lys	p.E578K	ENST00000249373	NM_005631.4	578	Gag/Aag	10/12	NA	2	FACETS	0.94	0.884	0.998			1	INDETERMINATE	1	TRUE	NA	0.740356867074977	2		583	721	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950465	38950465	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	45	364	0	ENST00000357387.3:c.3485C>T	p.Ser1162Leu	p.S1162L	ENST00000357387	NM_152756.3	1162	tCa/tTa	31/38	1	2	FACETS	0.229	0.192	0.27	0.229	0.192	0.27	SUBCLONAL	1	TRUE	1	0.740356867074977	2		364	531	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226549706	226549706	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	249	545	0	ENST00000366794.5:c.2927C>T	p.Ser976Leu	p.S976L	ENST00000366794	NM_001618.3	976	tCa/tTa	22/23	1	2	FACETS	0.986	0.928	1	0.986	0.928	1	CLONAL	1	TRUE	1	0.740356867074977	2		545	682	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112745473	112745473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	244	658	0	ENST00000369452.4:c.791C>T	p.Thr264Ile	p.T264I	ENST00000369452	NM_007373.3	264	aCc/aTc	3/9	1	2	FACETS	0.903	0.847	0.96	0.903	0.847	0.96	CLONAL	1	TRUE	1	0.740356867074977	2		658	730	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123324081	123324081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	220	468	0	ENST00000358487.5:c.389C>T	p.Ser130Phe	p.S130F	ENST00000358487	NM_000141.4	130	tCc/tTc	4/18	1	2	FACETS	0.995	0.933	1	0.995	0.933	1	CLONAL	1	TRUE	1	0.740356867074977	2		468	597	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123353291	123353291	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753987054	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	289	641	0	ENST00000358487.5:c.41C>T	p.Thr14Ile	p.T14I	ENST00000358487	NM_000141.4	14	aCc/aTc	2/18	1	2	FACETS	0.98	0.925	1	0.98	0.925	1	CLONAL	1	TRUE	1	0.740356867074977	2		641	797	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	441059	441059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	255	512	0	ENST00000399788.2:c.1699C>T	p.Pro567Ser	p.P567S	ENST00000399788	NM_001042603.1	567	Cct/Tct	13/28	1	2	FACETS	0.954	0.898	1	0.954	0.898	1	CLONAL	1	TRUE	1	0.740356867074977	2		512	722	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025562	1025563	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	230	573	3	ENST00000358495.3:c.812_813delinsAA	p.Arg271Gln	p.R271Q	ENST00000358495	NM_134424.2	271	cGG/cAA	9/12	1	2	FACETS	0.96	0.901	1	0.96	0.901	1	CLONAL	1	TRUE	1	0.740356867074977	2		576	647	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433989	49433989	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210845628	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	253	673	0	ENST00000301067.7:c.7564C>T	p.Pro2522Ser	p.P2522S	ENST00000301067	NM_003482.3	2522	Cct/Tct	31/54	1	2	FACETS	0.915	0.86	0.971	0.915	0.86	0.971	CLONAL	1	TRUE	1	0.740356867074977	2		673	747	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251250	99251250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371283551	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	254	556	0	ENST00000268035.6:c.554C>T	p.Thr185Ile	p.T185I	ENST00000268035	NM_000875.3	185	aCc/aTc	2/21	1	2	FACETS	0.977	0.92	1	0.977	0.92	1	CLONAL	1	TRUE	1	0.740356867074977	2		556	702	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348281	89348281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	288	771	1	ENST00000301030.4:c.4669C>T	p.Pro1557Ser	p.P1557S	ENST00000301030	NM_001256183.1	1557	Cca/Tca	9/13	0.152067431164062	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.740356867074977	0		772	747	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592312	29592312	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	212	487	0	ENST00000356175.3:c.4727G>A	p.Gly1576Glu	p.G1576E	ENST00000356175	NM_000267.3	1576	gGg/gAg	35/57	1	2	FACETS	0.984	0.921	1	0.984	0.921	1	CLONAL	1	TRUE	1	0.740356867074977	2		487	582	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599892	10599892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199953210	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	270	725	0	ENST00000171111.5:c.1684C>T	p.His562Tyr	p.H562Y	ENST00000171111	NM_203500.1	562	Cac/Tac	5/6	1	2	FACETS	0.877	0.825	0.929	0.877	0.825	0.929	CLONAL	1	TRUE	1	0.740356867074977	2		725	832	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054581	13054581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	184	441	0	ENST00000316448.5:c.1108G>A	p.Glu370Lys	p.E370K	ENST00000316448	NM_004343.3	370	Gag/Aag	9/9	1	2	FACETS	0.88	0.817	0.944	0.88	0.817	0.944	CLONAL	1	TRUE	1	0.740356867074977	2		441	565	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276302	15276302	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	283	654	0	ENST00000263388.2:c.5692G>A	p.Asp1898Asn	p.D1898N	ENST00000263388	NM_000435.2	1898	Gac/Aac	31/33	1	2	FACETS	0.969	0.915	1	0.969	0.915	1	CLONAL	1	TRUE	1	0.740356867074977	2		654	789	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966774	18966774	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	273	806	0	ENST00000262803.5:c.1585C>A	p.Gln529Lys	p.Q529K	ENST00000262803	NM_002911.3	529	Cag/Aag	12/24	1	2	FACETS	0.891	0.839	0.944	0.891	0.839	0.944	CLONAL	1	TRUE	1	0.740356867074977	2		806	828	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214067	36214067	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	277	695	2	ENST00000222270.7:c.2893C>T	p.Arg965Ter	p.R965*	ENST00000222270	NM_014727.1	965	Cga/Tga	6/37	1	2	FACETS	0.979	0.924	1	0.979	0.924	1	CLONAL	1	TRUE	1	0.740356867074977	2		697	764	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467473	25467474	+	missense_variant	Missense_Mutation	DNP	AC	AC	TA	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	197	652	0	ENST00000264709.3:c.1602_1603delinsTA	p.Gln534_Ser535delinsHisThr	p.Q534_S535delinsHT	ENST00000264709	NM_175629.2	534	caGTcc/caTAcc	14/23	1	2	FACETS	0.77	0.716	0.826	0.77	0.716	0.826	SUBCLONAL	1	TRUE	1	0.740356867074977	2		652	691	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416377	29416377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	337	719	1	ENST00000389048.3:c.4576G>A	p.Glu1526Lys	p.E1526K	ENST00000389048	NM_004304.4	1526	Gag/Aag	29/29	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.740356867074977	2		720	847	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39234320	39234320	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	142	348	1	ENST00000402219.2:c.2525C>T	p.Thr842Ile	p.T842I	ENST00000402219	NM_005633.3	842	aCt/aTt	16/23	1	2	FACETS	0.888	0.817	0.961	0.888	0.817	0.961	CLONAL	1	TRUE	1	0.740356867074977	2		349	432	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248623	212248623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	221	461	0	ENST00000342788.4:c.3644C>T	p.Thr1215Ile	p.T1215I	ENST00000342788	NM_005235.2	1215	aCc/aTc	28/28	1	2	FACETS	0.984	0.922	1	0.984	0.922	1	CLONAL	1	TRUE	1	0.740356867074977	2		461	607	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37628012	37628012	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	239	725	0	ENST00000249071.6:c.248C>T	p.Ser83Phe	p.S83F	ENST00000249071	NM_002872.4	83	tCc/tTc	4/7	1	2	FACETS	0.876	0.821	0.932	0.876	0.821	0.932	CLONAL	1	TRUE	1	0.740356867074977	2		725	737	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437446	52437446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553644798	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	166	417	2	ENST00000460680.1:c.1715C>T	p.Pro572Leu	p.P572L	ENST00000460680	NM_004656.3	572	cCc/cTc	13/17	NA	2	FACETS	0.817	0.755	0.881			1	INDETERMINATE	1	TRUE	NA	0.740356867074977	2		419	549	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670547	134670547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	242	645	0	ENST00000398015.3:c.458G>A	p.Gly153Glu	p.G153E	ENST00000398015	NM_004441.4	153	gGa/gAa	3/16	1	2	FACETS	0.942	0.885	1	0.942	0.885	1	CLONAL	1	TRUE	1	0.740356867074977	2		645	694	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973952	55973952	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	250	483	1	ENST00000263923.4:c.1364A>G	p.His455Arg	p.H455R	ENST00000263923	NM_002253.2	455	cAc/cGc	10/30	1	2	FACETS	0.993	0.934	1	0.993	0.934	1	CLONAL	1	TRUE	1	0.740356867074977	2		484	680	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927644	131927644	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	254	521	0	ENST00000265335.6:c.1711C>T	p.Pro571Ser	p.P571S	ENST00000265335		571	Ccc/Tcc	11/25	1	2	FACETS	0.979	0.921	1	0.979	0.921	1	CLONAL	1	TRUE	1	0.740356867074977	2		521	701	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149436929	149436929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	262	640	0	ENST00000286301.3:c.2240G>A	p.Gly747Glu	p.G747E	ENST00000286301	NM_005211.3	747	gGa/gAa	17/22	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.740356867074977	2		640	670	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055898	180055898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	185	442	0	ENST00000261937.6:c.1087C>T	p.Pro363Ser	p.P363S	ENST00000261937	NM_182925.4	363	Ccg/Tcg	8/30	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.740356867074977	2		442	496	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163446	32163446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	222	572	0	ENST00000375023.3:c.5780C>T	p.Pro1927Leu	p.P1927L	ENST00000375023	NM_004557.3	1927	cCt/cTt	30/30	0.679851608839301	3	FACETS	1	0.943	1	0.506	0.472	0.541	CLONAL	1	TRUE	1	0.740356867074977	3		572	812	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117684026	117684026	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1185167609	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	170	321	0	ENST00000368508.3:c.3121C>T	p.Pro1041Ser	p.P1041S	ENST00000368508	NM_002944.2	1041	Cca/Tca	21/43	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.740356867074977	NA		321	292	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511303	157511303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759771283	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	200	459	0	ENST00000346085.5:c.3821C>T	p.Pro1274Leu	p.P1274L	ENST00000346085	NM_020732.3	1274	cCc/cTc	15/20	0.740356867074977	1	FACETS	0.866	0.815	0.917	0.866	0.815	0.917	CLONAL	1	TRUE	0	0.740356867074977	1		459	393	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528741	8528741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1277243866	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	176	403	0	ENST00000356435.5:c.391G>A	p.Gly131Ser	p.G131S	ENST00000356435		131	Ggc/Agc	4/35	0.740356867074977	1	FACETS	0.913	0.857	0.968	0.913	0.857	0.968	CLONAL	1	TRUE	0	0.740356867074977	1		403	328	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849194	76849194	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	228	246	2	ENST00000373344.5:c.6082C>T	p.Arg2028Ter	p.R2028*	ENST00000373344	NM_000489.3	2028	Cga/Tga	26/35	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.740356867074977	1		248	323	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	472250	472250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1316241491	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	61	352	0	ENST00000399788.2:c.551C>T	p.Pro184Leu	p.P184L	ENST00000399788	NM_001042603.1	184	cCt/cTt	5/28	1	2	FACETS	0.372	0.321	0.427	0.372	0.321	0.427	SUBCLONAL	1	TRUE	1	0.740356867074977	2		352	443	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906881	32906881	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	203	488	0	ENST00000380152.3:c.1266T>A	p.Asn422Lys	p.N422K	ENST00000380152		422	aaT/aaA	10/27	0.628270570215581	1	FACETS	0.751	0.704	0.798	0.751	0.704	0.798	SUBCLONAL	1	TRUE	0	0.740356867074977	1		488	460	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913981	32913981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	211	459	2	ENST00000380152.3:c.5489C>T	p.Ser1830Phe	p.S1830F	ENST00000380152		1830	tCc/tTc	11/27	0.628270570215581	1	FACETS	0.737	0.692	0.783	0.737	0.692	0.783	SUBCLONAL	1	TRUE	0	0.740356867074977	1		461	487	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857872	9857872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	24	511	0	ENST00000330684.3:c.3529G>A	p.Gly1177Arg	p.G1177R	ENST00000330684	NM_001134407.1	1177	Ggg/Agg	13/13	0.740356867074977	1	FACETS	0.093	0.072	0.117	0.093	0.072	0.117	SUBCLONAL	1	TRUE	0	0.740356867074977	1		511	440	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346775	89346775	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1482843507	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	45	448	0	ENST00000301030.4:c.6175C>T	p.Pro2059Ser	p.P2059S	ENST00000301030	NM_001256183.1	2059	Ccc/Tcc	9/13	0.152067431164062	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.740356867074977	0		448	411	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7119578	7119578	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	55	538	0	ENST00000302850.5:c.3676C>T	p.Leu1226Phe	p.L1226F	ENST00000302850	NM_000208.2	1226	Ctt/Ttt	21/22	1	2	FACETS	0.203	0.173	0.236	0.203	0.173	0.236	SUBCLONAL	1	TRUE	1	0.740356867074977	2		538	732	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211675	36211675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	28	471	0	ENST00000222270.7:c.1426C>T	p.Pro476Ser	p.P476S	ENST00000222270	NM_014727.1	476	Ccc/Tcc	3/37	1	2	FACETS	0.149	0.118	0.183	0.149	0.118	0.183	SUBCLONAL	1	TRUE	1	0.740356867074977	2		471	509	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543689	29543689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	37	616	0	ENST00000389048.3:c.1474G>A	p.Gly492Ser	p.G492S	ENST00000389048	NM_004304.4	492	Ggc/Agc	7/29	1	2	FACETS	0.144	0.118	0.173	0.144	0.118	0.173	SUBCLONAL	1	TRUE	1	0.740356867074977	2		616	696	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449521	187449521	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	130	315	0	ENST00000232014.4:c.359C>T	p.Thr120Ile	p.T120I	ENST00000232014	NM_001130845.1	120	aCt/aTt	4/10	1	2	FACETS	0.907	0.832	0.985	0.907	0.832	0.985	CLONAL	1	TRUE	1	0.740356867074977	2		315	387	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146501	55146501	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	146	297	0	ENST00000257290.5:c.2175T>G	p.Phe725Leu	p.F725L	ENST00000257290	NM_006206.4	725	ttT/ttG	16/23	1	2	FACETS	0.825	0.759	0.894	0.825	0.759	0.894	CLONAL	1	TRUE	1	0.740356867074977	2		297	478	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185023	32185023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762392289	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	223	606	0	ENST00000375023.3:c.1645G>A	p.Glu549Lys	p.E549K	ENST00000375023	NM_004557.3	549	Gag/Aag	10/30	0.679851608839301	3	FACETS	0.934	0.871	0.999	0.467	0.435	0.5	CLONAL	1	TRUE	1	0.740356867074977	3		606	884	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704511	117704512	+	stop_gained	Nonsense_Mutation	DNP	AG	AG	TA	novel	NA	P-0027752-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	52	383	0	ENST00000368508.3:c.2464_2465delinsTA	p.Leu822Ter	p.L822*	ENST00000368508	NM_002944.2	822	CTa/TAa	16/43	0.740356867074977	1	FACETS	0.234	0.2	0.272	0.234	0.2	0.272	SUBCLONAL	1	TRUE	0	0.740356867074977	1		383	378	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913514	NA	P-0027753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	289	553	0	ENST00000288135.5:c.2466T>G	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaG	17/21	0.408162423105099	24	FACETS	0.983	0.954	1			1	CLONAL	23	TRUE	NA	0.408162423105099	24		553	344	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211093	36211093	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	10	879	1	ENST00000222270.7:c.844G>A	p.Gly282Arg	p.G282R	ENST00000222270	NM_014727.1	282	Gga/Aga	3/37	0.408162423105099	3	FACETS	0.756	0.519	1	0.252	0.173	0.349	CLONAL	1	TRUE	0	0.408162423105099	3		880	78	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252962	36252962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	11	446	0	ENST00000300305.3:c.400G>A	p.Ala134Thr	p.A134T	ENST00000300305		134	Gct/Act	4/8	1	2	FACETS	0.829	0.584	1	0.829	0.584	1	CLONAL	1	TRUE	1	0.408162423105099	2		446	65	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567546196	NA	P-0027754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	169	625	0	ENST00000269305.4:c.949del	p.Gln317SerfsTer28	p.Q317Sfs*28	ENST00000269305	NM_001126112.2	317	Cag/ag	9/11	0.23177178248926	3	FACETS	1	0.92	1	1	0.92	1	CLONAL	2	TRUE	1	0.23177178248926	3		625	814	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869691	117869691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772999578	NA	P-0027754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	25	401	0	ENST00000297338.2:c.503G>A	p.Arg168His	p.R168H	ENST00000297338	NM_006265.2	168	cGt/cAt	6/14	1	2	FACETS	0.562	0.442	0.699	0.562	0.442	0.699	SUBCLONAL	1	TRUE	1	0.23177178248926	2		401	384	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984937	9984937	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1231057100	NA	P-0027754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	51	549	0	ENST00000330684.3:c.1028G>A	p.Trp343Ter	p.W343*	ENST00000330684	NM_001134407.1	343	tGg/tAg	4/13	1	2	FACETS	0.702	0.596	0.819	0.702	0.596	0.819	SUBCLONAL	1	TRUE	1	0.23177178248926	2		549	627	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155106	108155106	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs183263185	NA	P-0027754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	49	524	0	ENST00000278616.4:c.3899A>G	p.Tyr1300Cys	p.Y1300C	ENST00000278616	NM_000051.3	1300	tAt/tGt	26/63	1	2	FACETS	0.779	0.659	0.91	0.779	0.659	0.91	CLONAL	1	TRUE	1	0.23177178248926	2		524	543	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0027755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	203	681	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.453439210151621	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.453439210151621	1		681	642	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217230	11217230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786205165	NA	P-0027755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	171	489	2	ENST00000361445.4:c.4448G>A	p.Cys1483Tyr	p.C1483Y	ENST00000361445	NM_004958.3	1483	tGc/tAc	30/58	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.453439210151621	2		491	683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0027755-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	227	681	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.417966519875339	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.417966519875339	1		681	823	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217230	11217230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786205165	NA	P-0027755-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	184	489	2	ENST00000361445.4:c.4448G>A	p.Cys1483Tyr	p.C1483Y	ENST00000361445	NM_004958.3	1483	tGc/tAc	30/58	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.417966519875339	2		491	841	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39317369	39317369	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027755-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	129	551	0	ENST00000373001.3:c.817G>C	p.Asp273His	p.D273H	ENST00000373001	NM_022157.3	273	Gac/Cac	5/7	1	2	FACETS	0.56	0.506	0.616	0.56	0.506	0.616	SUBCLONAL	1	TRUE	1	0.417966519875339	2		551	1103	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0027756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	127	611	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	0.969	1	CLONAL	1	TRUE	1	0.495039240797152	2		611	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0027756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	219	545	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	0.495039240797152	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.495039240797152	1		545	651	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554234	29554234	+	splice_acceptor_variant	Splice_Site	DEL	A	A	-	novel	NA	P-0027756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	96	266	0	ENST00000356175.3:c.2252-2del		p.X751_splice	ENST00000356175	NM_000267.3	751			0.495039240797152	1	FACETS	0.954	0.86	1	0.954	0.86	1	CLONAL	1	TRUE	0	0.495039240797152	1		266	306	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511587	66511587	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	125	372	0	ENST00000358598.2:c.47G>C	p.Arg16Pro	p.R16P	ENST00000358598	NM_212471.2	16	cGa/cCa	2/11	0.495039240797152	3	FACETS	0.903	0.818	0.991	0.451	0.409	0.496	CLONAL	1	TRUE	1	0.495039240797152	3		372	698	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117123	7117123	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	193	630	1	ENST00000302850.5:c.4093A>C	p.Asn1365His	p.N1365H	ENST00000302850	NM_000208.2	1365	Aac/Cac	22/22	0.495039240797152	1	FACETS	0.867	0.805	0.93	0.867	0.805	0.93	CLONAL	1	TRUE	0	0.495039240797152	1		631	677	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0027758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	146	529	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.566449769993858	3	FACETS	0.713	0.651	0.779			1	SUBCLONAL	1	TRUE	NA	0.593779483007954	3		529	894	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007475	62007475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1389559363	NA	P-0027758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	123	458	0	ENST00000392795.3:c.392C>T	p.Ser131Leu	p.S131L	ENST00000392795	NM_001039933.1	131	tCg/tTg	3/6	0.537498302285051	1	FACETS	0.55	0.499	0.602	0.55	0.499	0.602	SUBCLONAL	1	TRUE	0	0.593779483007954	1		458	530	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740225	162740225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	128	442	0	ENST00000367921.3:c.1427C>T	p.Pro476Leu	p.P476L	ENST00000367921	NM_006182.2	476	cCc/cTc	12/18	0.356152364257966	3	FACETS	0.607	0.55	0.668	0.304	0.275	0.334	INDETERMINATE	1	TRUE	1	0.593779483007954	3		442	921	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106141	27106142	+	stop_gained	Nonsense_Mutation	DNP	CG	CG	TA	novel	NA	P-0027758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	83	443	2	ENST00000324856.7:c.5752_5753delinsTA	p.Arg1918Ter	p.R1918*	ENST00000324856	NM_006015.4	1918	CGg/TAg	20/20	0.537498302285051	1	FACETS	0.363	0.321	0.408	0.363	0.321	0.408	SUBCLONAL	1	TRUE	0	0.593779483007954	1		445	541	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114705	108114706	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	168	351	0	ENST00000278616.4:c.523dup	p.Tyr175LeufsTer10	p.Y175Lfs*10	ENST00000278616	NM_000051.3	174	-/T	6/63	0.396109432547275	1	FACETS	0.93	0.864	0.996	0.93	0.864	0.996	CLONAL	1	TRUE	0	0.593779483007954	1		351	428	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0027759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	116	445	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.327654923399502	3	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	1	0.327654923399502	3		445	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0027759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	318	580	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.322889009283722	2	FACETS	0.984	0.931	1	0.984	0.931	1	CLONAL	2	TRUE	0	0.327654923399502	2		580	986	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120674	115120675	+	protein_altering_variant	In_Frame_Ins	INS	-	-	TAA	novel	NA	P-0027759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	377	783	0	ENST00000257566.3:c.331_332insTTA	p.Glu111delinsValLys	p.E111delinsVK	ENST00000257566	NM_016569.3	111	gaa/gTTAaa	1/8	0.322889009283722	2	FACETS	0.963	0.914	1	0.963	0.914	1	CLONAL	2	TRUE	0	0.327654923399502	2		783	1195	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0027760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	198	586	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.505349720864474	2		587	695	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0027760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	195	518	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.972	0.901	1	0.972	0.901	1	CLONAL	1	TRUE	1	0.505349720864474	2		518	794	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395776	45395776	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	125	314	0	ENST00000262160.6:c.358C>T	p.Arg120Ter	p.R120*	ENST00000262160	NM_005901.5	120	Cga/Tga	4/11	0.505349720864474	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.505349720864474	1		314	349	SUCCESS
APC	324	MSKCC	GRCh37	5	112175784	112175799	+	frameshift_variant	Frame_Shift_Del	DEL	ATGGATTTTCTTGTTC	ATGGATTTTCTTGTTC	-	novel	NA	P-0027760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	189	283	0	ENST00000257430.4:c.4495_4510del	p.Gly1499ProfsTer3	p.G1499Pfs*3	ENST00000257430	NM_000038.5	1498	gATGGATTTTCTTGTTCa/ga	16/16	NA	2	FACETS	0.912	0.855	0.97			1	INDETERMINATE	2	TRUE	NA	0.505349720864474	2		283	410	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911512	114911512	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	137	278	0	ENST00000543371.1:c.1030G>T	p.Glu344Ter	p.E344*	ENST00000543371	NM_001198531.1	344	Gaa/Taa	10/14	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.505349720864474	2		278	464	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962788	2962788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201948130	NA	P-0027760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	184	490	1	ENST00000396946.4:c.2120G>A	p.Arg707His	p.R707H	ENST00000396946	NM_032415.4	707	cGt/cAt	16/25	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.505349720864474	2		491	695	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114337	143114337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747045725	NA	P-0027761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	91	461	1	ENST00000262992.4:c.1084G>A	p.Asp362Asn	p.D362N	ENST00000262992	NM_001101669.1	362	Gat/Aat	13/24	0.332161466985025	2	FACETS	1	0.933	1	0.532	0.474	0.594	CLONAL	1	TRUE	0	0.33651159053366	2		462	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0027761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	290	581	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.328033114528358	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.33651159053366	2		583	729	SUCCESS
APC	324	MSKCC	GRCh37	5	112154942	112154942	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779780	NA	P-0027761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	74	581	2	ENST00000257430.4:c.1213C>T	p.Arg405Ter	p.R405*	ENST00000257430	NM_000038.5	405	Cga/Tga	10/16	0.33651159053366	1	FACETS	0.622	0.545	0.705	0.622	0.545	0.705	SUBCLONAL	1	TRUE	0	0.33651159053366	1		583	588	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443675	29443675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1034835558	NA	P-0027761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	286	580	1	ENST00000389048.3:c.3542G>A	p.Arg1181His	p.R1181H	ENST00000389048	NM_004304.4	1181	cGc/cAc	23/29	0.335909134103948	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.33651159053366	2		581	735	SUCCESS
APC	324	MSKCC	GRCh37	5	112175902	112175903	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906236	NA	P-0027761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	27	276	0	ENST00000257430.4:c.4612_4613del	p.Glu1538IlefsTer5	p.E1538Ifs*5	ENST00000257430	NM_000038.5	1537	acAGaa/acaa	16/16	0.33651159053366	1	FACETS	0.515	0.411	0.633	0.515	0.411	0.633	SUBCLONAL	1	TRUE	0	0.33651159053366	1		276	259	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600621	43600621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	87	505	2	ENST00000355710.3:c.847G>A	p.Val283Met	p.V283M	ENST00000355710	NM_020975.4	283	Gtg/Atg	4/20	1	2	FACETS	0.876	0.777	0.982	0.876	0.777	0.982	CLONAL	1	TRUE	1	0.33651159053366	2		507	590	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907071	32907071	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs80358434	NA	P-0027761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	95	446	0	ENST00000380152.3:c.1456C>T	p.Gln486Ter	p.Q486*	ENST00000380152		486	Cag/Tag	10/27	0.33651159053366	5	FACETS	0.993	0.883	1	0.248	0.22	0.278	CLONAL	1	TRUE	1	0.33651159053366	5		446	856	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89345482	89345482	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	67	405	0	ENST00000301030.4:c.7468G>A	p.Val2490Met	p.V2490M	ENST00000301030	NM_001256183.1	2490	Gtg/Atg	9/13	1	2	FACETS	0.793	0.691	0.904	0.793	0.691	0.904	CLONAL	1	TRUE	1	0.33651159053366	2		405	502	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264450	30264450	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	93	569	0	ENST00000322652.5:c.185C>G	p.Ala62Gly	p.A62G	ENST00000322652	NM_015355.2	62	gCa/gGa	1/16	0.328033114528358	2	FACETS	0.751	0.668	0.84	0.375	0.334	0.42	SUBCLONAL	1	TRUE	0	0.33651159053366	2		569	736	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0027762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	164	581	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.288104158379609	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.17	3		581	957	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578551	7578553	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0027762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	129	593	0	ENST00000269305.4:c.377_379del	p.Tyr126del	p.Y126del	ENST00000269305	NM_001126112.2	126	tACTcc/tcc	5/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.17	2		593	1104	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928231	178928232	+	inframe_insertion	In_Frame_Ins	INS	-	-	TAG	novel	NA	P-0027762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	72	325	0	ENST00000263967.3:c.1418_1420dup	p.Leu473_Glu474insVal	p.L473_E474insV	ENST00000263967	NM_006218.2	473	tta/tTAGta	9/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.17	2		325	595	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056057	26056057	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	55	223	0	ENST00000343677.2:c.600del	p.Lys201ArgfsTer?	p.K201Rfs*?	ENST00000343677	NM_005319.3	200	ccC/cc	1/1	0.3	3	FACETS	1	0.96	1			1	CLONAL	1	TRUE	NA	0.17	3		223	508	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0027762-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	145	581	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.175714178231029	3	FACETS	0.83	0.756	0.909	0.83	0.756	0.909	CLONAL	2	TRUE	1	0.16	3		581	1179	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578551	7578553	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0027762-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1209	94	593	0	ENST00000269305.4:c.377_379del	p.Tyr126del	p.Y126del	ENST00000269305	NM_001126112.2	126	tACTcc/tcc	5/11	1	2	FACETS	0.902	0.8	1	0.902	0.8	1	CLONAL	1	TRUE	1	0.16	2		593	1303	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928231	178928232	+	inframe_insertion	In_Frame_Ins	INS	-	-	TAG	novel	NA	P-0027762-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	46	325	0	ENST00000263967.3:c.1418_1420dup	p.Leu473_Glu474insVal	p.L473_E474insV	ENST00000263967	NM_006218.2	473	tta/tTAGta	9/21	1	2	FACETS	0.792	0.665	0.933	0.792	0.665	0.933	CLONAL	1	TRUE	1	0.16	2		325	726	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056057	26056057	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027762-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	68	223	0	ENST00000343677.2:c.600del	p.Lys201ArgfsTer?	p.K201Rfs*?	ENST00000343677	NM_005319.3	200	ccC/cc	1/1	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.16	2		223	654	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0027763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	208	702	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.485999162594445	1	FACETS	0.988	0.922	1	0.988	0.922	1	CLONAL	1	TRUE	0	0.488801258059586	1		702	651	SUCCESS
APC	324	MSKCC	GRCh37	5	112175198	112175198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	58	199	0	ENST00000257430.4:c.3907C>T	p.Gln1303Ter	p.Q1303*	ENST00000257430	NM_000038.5	1303	Caa/Taa	16/16	1	2	FACETS	0.845	0.732	0.965	0.845	0.732	0.965	CLONAL	1	TRUE	1	0.488801258059586	2		199	281	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564081	139564081	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200217167	NA	P-0027763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	151	549	2	ENST00000308874.7:c.221G>A	p.Arg74His	p.R74H	ENST00000308874		74	cGc/cAc	5/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.488801258059586	2		551	569	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218078	108218083	+	inframe_deletion	In_Frame_Del	DEL	TACATA	TACATA	-	novel	NA	P-0027763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	139	355	0	ENST00000278616.4:c.8659_8664del	p.His2887_Ile2888del	p.H2887_I2888del	ENST00000278616	NM_000051.3	2886	gTACATAta/gta	59/63	1	2	FACETS	0.87	0.794	0.949	0.87	0.794	0.949	CLONAL	1	TRUE	1	0.488801258059586	2		355	654	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220326	5220326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1034131598	NA	P-0027763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	160	529	0	ENST00000357368.4:c.3494G>A	p.Arg1165His	p.R1165H	ENST00000357368	NM_002850.3	1165	cGt/cAt	21/38	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.488801258059586	2		529	603	SUCCESS
APC	324	MSKCC	GRCh37	5	112174724	112174724	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	113	296	0	ENST00000257430.4:c.3433G>T	p.Glu1145Ter	p.E1145*	ENST00000257430	NM_000038.5	1145	Gaa/Taa	16/16	1	2	FACETS	0.859	0.776	0.946	0.859	0.776	0.946	CLONAL	1	TRUE	1	0.488801258059586	2		296	538	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845260	151845261	+	missense_variant	Missense_Mutation	DNP	CC	CC	GG	novel	NA	P-0027763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	78	333	0	ENST00000262189.6:c.13751_13752inv	p.Arg4584Pro	p.R4584P	ENST00000262189	NM_170606.2	4584	cGG/cCC	52/59	0.479335198893537	2	FACETS	0.802	0.708	0.901	0.401	0.354	0.451	CLONAL	1	TRUE	0	0.488801258059586	2		333	398	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026535	6026535	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	64	667	0	ENST00000265849.7:c.1861del	p.Ser621LeufsTer2	p.S621Lfs*2	ENST00000265849	NM_000535.5	621	Tct/ct	11/15	0.301558888929814	3	FACETS	0.48	0.414	0.552	0.24	0.207	0.276	SUBCLONAL	1	TRUE	1	0.311502625039767	3		667	989	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148504767	148504767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	95	412	1	ENST00000320356.2:c.2227G>A	p.Gly743Ser	p.G743S	ENST00000320356	NM_004456.4	743	Ggc/Agc	20/20	0.301558888929814	3	FACETS	1	0.945	1	0.549	0.489	0.613	CLONAL	1	TRUE	1	0.311502625039767	3		413	642	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0027766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	157	433	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA	2	FACETS	0.989	0.909	1			1	INDETERMINATE	1	TRUE	NA	0.478965782204143	2		433	663	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0027766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	203	535	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.478965782204143	1	FACETS	0.936	0.871	1	0.936	0.871	1	CLONAL	1	TRUE	0	0.478965782204143	1		535	689	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280142	66280142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1327931544	NA	P-0027766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	84	262	2	ENST00000273854.3:c.1547C>T	p.Thr516Met	p.T516M	ENST00000273854	NM_004439.5	516	aCg/aTg	7/18	1	2	FACETS	0.935	0.832	1	0.935	0.832	1	CLONAL	1	TRUE	1	0.478965782204143	2		264	375	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973061	25973061	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	103	380	2	ENST00000435504.4:c.1364C>T	p.Pro455Leu	p.P455L	ENST00000435504		455	cCg/cTg	12/13	0.478965782204143	1	FACETS	0.982	0.889	1	0.982	0.889	1	CLONAL	1	TRUE	0	0.478965782204143	1		382	333	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2114414	2114414	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	189	659	0	ENST00000219476.3:c.1585G>A	p.Asp529Asn	p.D529N	ENST00000219476	NM_000548.3	529	Gac/Aac	15/42	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.478965782204143	2		659	743	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778389	3778394	+	inframe_deletion	In_Frame_Del	DEL	CCGGCA	CCGGCA	-	novel	NA	P-0027766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	160	515	0	ENST00000262367.5:c.6654_6659del	p.Ala2219_Gly2220del	p.A2219_G2220del	ENST00000262367	NM_004380.2	2218	agTGCCGGc/agc	31/31	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.478965782204143	2		515	533	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14021925	14021925	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	164	424	0	ENST00000311895.7:c.625C>A	p.Pro209Thr	p.P209T	ENST00000311895	NM_005236.2	209	Cct/Act	4/11	1	2	FACETS	0.947	0.872	1	0.947	0.872	1	CLONAL	1	TRUE	1	0.478965782204143	2		424	723	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574579	41574579	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	186	651	0	ENST00000263253.7:c.6864G>C	p.Gln2288His	p.Q2288H	ENST00000263253	NM_001429.3	2288	caG/caC	31/31	NA	2	FACETS	0.996	0.922	1			1	INDETERMINATE	1	TRUE	NA	0.478965782204143	2		651	780	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200021	128200021	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	160	573	0	ENST00000341105.2:c.1284C>G	p.Phe428Leu	p.F428L	ENST00000341105	NM_032638.4	428	ttC/ttG	6/6	1	2	FACETS	0.996	0.916	1	0.996	0.916	1	CLONAL	1	TRUE	1	0.478965782204143	2		573	671	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043967	180043967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	139	522	0	ENST00000261937.6:c.3029C>T	p.Thr1010Ile	p.T1010I	ENST00000261937	NM_182925.4	1010	aCc/aTc	22/30	1	2	FACETS	0.966	0.882	1	0.966	0.882	1	CLONAL	1	TRUE	1	0.478965782204143	2		522	601	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023301	27023304	+	frameshift_variant	Frame_Shift_Del	DEL	CTCA	CTCA	-	novel	NA	P-0027767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	47	198	0	ENST00000324856.7:c.411_414del	p.His137GlnfsTer94	p.H137Qfs*94	ENST00000324856	NM_006015.4	136	cCTCAc/cc	1/20	1	2	FACETS	0.405	0.344	0.471	0.405	0.344	0.471	SUBCLONAL	1	TRUE	1	0.910590167441123	2		198	255	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058743	47058743	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	194	331	0	ENST00000409792.3:c.7535T>C	p.Leu2512Pro	p.L2512P	ENST00000409792	NM_014159.6	2512	cTg/cCg	21/21	0.910590167441123	1	FACETS	0.975	0.938	1	0.975	0.938	1	CLONAL	1	TRUE	0	0.910590167441123	1		331	238	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	133	210	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		210	381	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244872	46244872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766470086	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	244	673	0	ENST00000334344.6:c.2966C>T	p.Ser989Leu	p.S989L	ENST00000334344	NM_152641.2	989	tCg/tTg	15/21	0.375179131794245	3	FACETS	1	0.991	1	0.689	0.645	0.735	CLONAL	1	TRUE	1	0.480382772984189	3		673	914	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716098	243716098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	360	629	1	ENST00000263826.5:c.1096C>T	p.Pro366Ser	p.P366S	ENST00000263826	NM_005465.4	366	Cct/Tct	10/13	NA	2	FACETS	0.936	0.892	0.979			1	INDETERMINATE	2	TRUE	NA	0.480382772984189	2		630	801	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32918761	32918761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1239798218	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	77	466	2	ENST00000380152.3:c.6908C>T	p.Ser2303Phe	p.S2303F	ENST00000380152		2303	tCc/tTc	12/27	0.219581195479907	2	FACETS	0.489	0.429	0.553	0.244	0.214	0.277	INDETERMINATE	1	TRUE	0	0.480382772984189	2		468	656	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968251	2968251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377769236	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	545	704	2	ENST00000396946.4:c.1735G>A	p.Glu579Lys	p.E579K	ENST00000396946	NM_032415.4	579	Gag/Aag	13/25	0.480382772984189	3	FACETS	0.983	0.95	1	0.983	0.95	1	CLONAL	3	TRUE	0	0.480382772984189	3		706	954	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760169	133760169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768153649	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	141	654	1	ENST00000318560.5:c.2492C>T	p.Pro831Leu	p.P831L	ENST00000318560	NM_005157.4	831	cCc/cTc	11/11	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.480382772984189	2		655	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576857	7576857	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	230	594	0	ENST00000269305.4:c.989T>C	p.Leu330Pro	p.L330P	ENST00000269305	NM_001126112.2	330	cTt/cCt	9/11	0.480382772984189	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.480382772984189	1		594	642	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508783	106508783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	112	521	1	ENST00000359195.3:c.777G>A	p.Met259Ile	p.M259I	ENST00000359195	NM_002649.2	259	atG/atA	2/11	0.480382772984189	4	FACETS	0.724	0.65	0.802	0.241	0.216	0.268	SUBCLONAL	1	TRUE	1	0.480382772984189	4		522	954	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249501	153249501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1316840275	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	85	617	1	ENST00000281708.4:c.1277C>T	p.Ser426Leu	p.S426L	ENST00000281708	NM_033632.3	426	tCa/tTa	9/12	1	2	FACETS	0.446	0.394	0.503	0.446	0.394	0.503	SUBCLONAL	1	TRUE	1	0.480382772984189	2		618	793	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470474	25470474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024296111	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	67	758	0	ENST00000264709.3:c.1000G>A	p.Gly334Ser	p.G334S	ENST00000264709	NM_175629.2	334	Ggc/Agc	8/23	0.304782856957926	3	FACETS	0.345	0.298	0.395	0.115	0.099	0.132	SUBCLONAL	1	TRUE	0	0.480382772984189	3		758	1004	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588868	69588868	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	147	605	0	ENST00000168712.1:c.368G>A	p.Arg123Gln	p.R123Q	ENST00000168712	NM_002007.2	123	cGg/cAg	2/3	0.35906839284831	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.480382772984189	1		605	429	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015732	112015732	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	92	473	0	ENST00000368678.4:c.1111-1G>A		p.X371_splice	ENST00000368678		371			0.219581195479907	2	FACETS	0.606	0.539	0.677	0.303	0.269	0.339	INDETERMINATE	1	TRUE	0	0.480382772984189	2		473	632	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31429602	31429602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370990538	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	200	652	0	ENST00000344624.3:c.3196C>T	p.Arg1066Cys	p.R1066C	ENST00000344624		1066	Cgc/Tgc	24/33	0.480382772984189	3	FACETS	0.977	0.905	1	0.488	0.452	0.526	CLONAL	1	TRUE	1	0.480382772984189	3		652	1057	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101274	27101274	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	42	594	0	ENST00000324856.7:c.4556A>G	p.Gln1519Arg	p.Q1519R	ENST00000324856	NM_006015.4	1519	cAg/cGg	18/20	0.219581195479907	2	FACETS	0.273	0.227	0.324	0.136	0.113	0.162	INDETERMINATE	1	TRUE	0	0.480382772984189	2		594	641	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903757	114903757	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	85	653	0	ENST00000543371.1:c.761C>T	p.Pro254Leu	p.P254L	ENST00000543371	NM_001198531.1	254	cCc/cTc	7/14	0.35906839284831	1	FACETS	0.401	0.354	0.451	0.401	0.354	0.451	SUBCLONAL	1	TRUE	0	0.480382772984189	1		653	671	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180390	94180390	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	61	406	0	ENST00000323929.3:c.1778G>A	p.Gly593Glu	p.G593E	ENST00000323929	NM_005591.3	593	gGa/gAa	15/20	0.35906839284831	1	FACETS	0.343	0.296	0.395	0.343	0.296	0.395	SUBCLONAL	1	TRUE	0	0.480382772984189	1		406	562	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006496	12006496	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	592	817	0	ENST00000396373.4:c.463+1G>A		p.X155_splice	ENST00000396373	NM_001987.4	155			0.480382772984189	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.480382772984189	3		817	1396	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420939	49420940	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	182	584	2	ENST00000301067.7:c.14809_14810delinsTT	p.Pro4937Phe	p.P4937F	ENST00000301067	NM_003482.3	4937	CCc/TTc	48/54	0.375179131794245	3	FACETS	1	0.988	1	0.669	0.619	0.721	CLONAL	1	TRUE	1	0.480382772984189	3		586	702	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421833	49421833	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	251	801	0	ENST00000301067.7:c.14474G>T	p.Arg4825Leu	p.R4825L	ENST00000301067	NM_003482.3	4825	cGg/cTg	46/54	0.375179131794245	3	FACETS	1	0.987	1	0.608	0.568	0.648	CLONAL	1	TRUE	1	0.480382772984189	3		801	1066	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436429	49436429	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	127	462	0	ENST00000301067.7:c.5783-1G>A		p.X1928_splice	ENST00000301067	NM_003482.3	1928			0.375179131794245	3	FACETS	1	0.95	1	0.534	0.485	0.585	CLONAL	1	TRUE	1	0.480382772984189	3		462	614	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445343	49445343	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	306	909	1	ENST00000301067.7:c.2123C>T	p.Ser708Phe	p.S708F	ENST00000301067	NM_003482.3	708	tCc/tTc	10/54	0.375179131794245	3	FACETS	0.761	0.718	0.805	0.761	0.718	0.805	SUBCLONAL	2	TRUE	1	0.480382772984189	3		910	1038	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913380	28913380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	133	662	1	ENST00000282397.4:c.2413C>T	p.Pro805Ser	p.P805S	ENST00000282397	NM_002019.4	805	Cct/Tct	17/30	0.219581195479907	2	FACETS	0.634	0.575	0.695	0.317	0.287	0.348	INDETERMINATE	1	TRUE	0	0.480382772984189	2		663	874	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32932058	32932058	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	24	345	0	ENST00000380152.3:c.7797A>T	p.Glu2599Asp	p.E2599D	ENST00000380152		2599	gaA/gaT	16/27	0.219581195479907	2	FACETS	0.247	0.193	0.309	0.123	0.096	0.155	INDETERMINATE	1	TRUE	0	0.480382772984189	2		345	405	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046616	30046616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	138	638	2	ENST00000331968.5:c.2567G>A	p.Gly856Glu	p.G856E	ENST00000331968	NM_002742.2	856	gGg/gAg	18/18	0.375179131794245	3	FACETS	0.805	0.732	0.882	0.403	0.366	0.441	CLONAL	1	TRUE	1	0.480382772984189	3		640	885	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066913	30066914	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	111	580	2	ENST00000331968.5:c.2217_2218delinsTT	p.Arg740Trp	p.R740W	ENST00000331968	NM_002742.2	739	ttCCgg/ttTTgg	16/18	0.375179131794245	3	FACETS	0.701	0.629	0.776	0.35	0.314	0.388	SUBCLONAL	1	TRUE	1	0.480382772984189	3		582	818	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609817	81609817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	178	293	0	ENST00000298171.2:c.1415C>T	p.Ser472Phe	p.S472F	ENST00000298171	NM_000369.2	472	tCt/tTt	10/10	0.375179131794245	3	FACETS	0.982	0.914	1	0.982	0.914	1	CLONAL	2	TRUE	1	0.480382772984189	3		293	468	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574239	95574239	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	97	404	0	ENST00000393063.1:c.2628C>A	p.Tyr876Ter	p.Y876*	ENST00000393063	NM_030621.3	876	taC/taA	17/28	0.375179131794245	3	FACETS	0.794	0.709	0.884	0.397	0.354	0.442	SUBCLONAL	1	TRUE	1	0.480382772984189	3		404	631	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714275	43714275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	119	696	1	ENST00000382044.4:c.3878C>T	p.Ser1293Phe	p.S1293F	ENST00000382044	NM_001141980.1	1293	tCc/tTc	19/28	0.35906839284831	1	FACETS	0.491	0.444	0.542	0.491	0.444	0.542	SUBCLONAL	1	TRUE	0	0.480382772984189	1		697	766	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43767787	43767787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	82	565	0	ENST00000382044.4:c.1061C>T	p.Ser354Phe	p.S354F	ENST00000382044	NM_001141980.1	354	tCc/tTc	9/28	0.35906839284831	1	FACETS	0.372	0.328	0.42	0.372	0.328	0.42	SUBCLONAL	1	TRUE	0	0.480382772984189	1		565	697	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245953	41245953	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	166	700	0	ENST00000357654.3:c.1595T>G	p.Ile532Arg	p.I532R	ENST00000357654	NM_007294.3	532	aTa/aGa	10/23	1	2	FACETS	0.828	0.761	0.897	0.828	0.761	0.897	CLONAL	1	TRUE	1	0.480382772984189	2		700	835	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285131	15285131	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	190	700	0	ENST00000263388.2:c.4484G>A	p.Trp1495Ter	p.W1495*	ENST00000263388	NM_000435.2	1495	tGg/tAg	25/33	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.480382772984189	2		700	760	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505337	25505337	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	343	606	1	ENST00000264709.3:c.421G>A	p.Glu141Lys	p.E141K	ENST00000264709	NM_175629.2	141	Gag/Aag	4/23	0.304782856957926	3	FACETS	1	0.993	1	0.813	0.775	0.851	CLONAL	2	TRUE	0	0.480382772984189	3		607	726	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018095	48018095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	447	623	0	ENST00000234420.5:c.290G>A	p.Trp97Ter	p.W97*	ENST00000234420	NM_000179.2	97	tGg/tAg	2/10	0.304782856957926	3	FACETS	1	0.992	1	0.766	0.734	0.799	CLONAL	2	TRUE	0	0.480382772984189	3		623	1004	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015228	128015228	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774571443	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	94	578	0	ENST00000285398.2:c.2293C>T	p.Arg765Trp	p.R765W	ENST00000285398	NM_000122.1	765	Cgg/Tgg	15/15	0.237577440783312	3	FACETS	0.551	0.489	0.617	0.184	0.163	0.206	INDETERMINATE	1	TRUE	0	0.480382772984189	3		578	881	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046242	128046242	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	68	463	0	ENST00000285398.2:c.1021C>T	p.Pro341Ser	p.P341S	ENST00000285398	NM_000122.1	341	Ccc/Tcc	7/15	0.237577440783312	3	FACETS	0.446	0.387	0.51	0.149	0.129	0.17	INDETERMINATE	1	TRUE	0	0.480382772984189	3		463	787	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812204	212812204	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	71	419	0	ENST00000342788.4:c.372A>C	p.Arg124Ser	p.R124S	ENST00000342788	NM_005235.2	124	agA/agC	3/28	0.304782856957926	3	FACETS	0.53	0.462	0.603	0.177	0.154	0.201	SUBCLONAL	1	TRUE	0	0.480382772984189	3		419	692	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031762	36031762	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913314	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	79	619	0	ENST00000358208.4:c.1591C>T	p.Gln531Ter	p.Q531*	ENST00000358208		531	Cag/Tag	12/12	0.219581195479907	2	FACETS	0.471	0.413	0.532	0.235	0.206	0.266	INDETERMINATE	1	TRUE	0	0.480382772984189	2		619	699	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755594	39755594	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780042015	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	175	495	1	ENST00000288319.7:c.1171G>A	p.Asp391Asn	p.D391N	ENST00000288319	NM_182918.3	391	Gac/Aac	10/10	0.35906839284831	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.480382772984189	1		496	494	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648469	30648470	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	161	454	1	ENST00000295754.5:c.94_94+1delinsAA		p.X32_splice	ENST00000295754	NM_003242.5	32		1/7	0.480382772984189	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.480382772984189	1		455	424	SUCCESS
ATR	545	MSKCC	GRCh37	3	142286973	142286973	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs578209052	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	123	568	0	ENST00000350721.4:c.83C>T	p.Thr28Ile	p.T28I	ENST00000350721	NM_001184.3	28	aCa/aTa	2/47	0.288373896298154	5	FACETS	0.88	0.795	0.971	0.293	0.265	0.324	CLONAL	1	TRUE	2	0.480382772984189	5		568	1001	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526301	189526301	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	137	429	0	ENST00000264731.3:c.565T>C	p.Ser189Pro	p.S189P	ENST00000264731	NM_003722.4	189	Tcg/Ccg	4/14	0.288373896298154	5	FACETS	1	0.976	1	0.403	0.366	0.441	CLONAL	1	TRUE	2	0.480382772984189	5		429	812	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607239	189607239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	181	747	1	ENST00000264731.3:c.1618C>T	p.Pro540Ser	p.P540S	ENST00000264731	NM_003722.4	540	Cca/Tca	12/14	0.288373896298154	5	FACETS	1	0.974	1	0.376	0.346	0.408	CLONAL	1	TRUE	2	0.480382772984189	5		748	1149	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976617	55976617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759869837	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	185	607	2	ENST00000263923.4:c.1208C>T	p.Pro403Leu	p.P403L	ENST00000263923	NM_002253.2	403	cCc/cTc	9/30	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.480382772984189	2		609	704	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213898	66213899	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	84	463	0	ENST00000273854.3:c.2531_2532delinsAA	p.Trp844Ter	p.W844*	ENST00000273854	NM_004439.5	844	tGG/tAA	15/18	1	2	FACETS	0.621	0.549	0.698	0.621	0.549	0.698	SUBCLONAL	1	TRUE	1	0.480382772984189	2		463	563	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534307	187534307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375308616	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	42	599	0	ENST00000441802.2:c.9419C>T	p.Pro3140Leu	p.P3140L	ENST00000441802	NM_005245.3	3140	cCg/cTg	13/27	1	2	FACETS	0.247	0.205	0.293	0.247	0.205	0.293	SUBCLONAL	1	TRUE	1	0.480382772984189	2		599	708	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180496	56180497	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	27	411	0	ENST00000399503.3:c.3825_3826del	p.Tyr1276CysfsTer7	p.Y1276Cfs*7	ENST00000399503	NM_005921.1	1275	acTTat/acat	16/20	0.480382772984189	1	FACETS	0.211	0.168	0.261	0.211	0.168	0.261	SUBCLONAL	1	TRUE	0	0.480382772984189	1		411	404	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459615	149459615	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	196	494	0	ENST00000286301.3:c.592G>A	p.Val198Ile	p.V198I	ENST00000286301	NM_005211.3	198	Gtc/Atc	4/22	0.480382772984189	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.480382772984189	1		494	490	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26021061	26021061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	125	480	1	ENST00000357647.3:c.344C>T	p.Ala115Val	p.A115V	ENST00000357647	NM_003529.2	115	gCc/gTc	1/1	0.219581195479907	2	FACETS	1	0.934	1	0.516	0.47	0.565	INDETERMINATE	1	TRUE	0	0.480382772984189	2		481	504	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30668357	30668357	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	286	608	0	ENST00000376406.3:c.6155C>T	p.Pro2052Leu	p.P2052L	ENST00000376406	NM_014641.2	2052	cCa/cTa	15/15	0.219581195479907	2	FACETS	0.755	0.712	0.797	0.755	0.712	0.797	INDETERMINATE	2	TRUE	0	0.480382772984189	2		608	789	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670912	30670912	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	195	698	0	ENST00000376406.3:c.5834T>C	p.Ile1945Thr	p.I1945T	ENST00000376406	NM_014641.2	1945	aTc/aCc	12/15	0.219581195479907	2	FACETS	0.94	0.871	1	0.47	0.435	0.506	INDETERMINATE	1	TRUE	0	0.480382772984189	2		698	864	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940288	31940288	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	57	573	0	ENST00000375333.2:c.430G>A	p.Gly144Arg	p.G144R	ENST00000375333	NM_032454.1	144	Ggg/Agg	2/8	0.219581195479907	2	FACETS	0.431	0.369	0.498	0.215	0.184	0.249	INDETERMINATE	1	TRUE	0	0.480382772984189	2		573	551	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185017	32185017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	100	712	0	ENST00000375023.3:c.1651G>A	p.Asp551Asn	p.D551N	ENST00000375023	NM_004557.3	551	Gat/Aat	10/30	0.219581195479907	2	FACETS	0.491	0.438	0.547	0.245	0.219	0.274	INDETERMINATE	1	TRUE	0	0.480382772984189	2		712	848	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709176	117709176	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	61	452	1	ENST00000368508.3:c.1781T>A	p.Ile594Asn	p.I594N	ENST00000368508	NM_002944.2	594	aTt/aAt	13/43	0.219581195479907	2	FACETS	0.551	0.476	0.632	0.275	0.238	0.316	INDETERMINATE	1	TRUE	0	0.480382772984189	2		453	461	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873694	151873695	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	340	627	3	ENST00000262189.6:c.8843_8844delinsTT	p.Ser2948Phe	p.S2948F	ENST00000262189	NM_170606.2	2948	tCC/tTT	38/59	0.480382772984189	4	FACETS	1	0.992	1	0.824	0.783	0.865	CLONAL	2	TRUE	1	0.480382772984189	4		630	848	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486016	8486016	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	156	573	0	ENST00000356435.5:c.2801C>T	p.Ser934Phe	p.S934F	ENST00000356435		934	tCc/tTc	17/35	0.480382772984189	1	FACETS	0.995	0.918	1	0.995	0.918	1	CLONAL	1	TRUE	0	0.480382772984189	1		573	496	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971147	21971161	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGCTCCGCGCCGT	TGGGCTCCGCGCCGT	GGTC	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	118	397	2	ENST00000304494.5:c.197_211delinsGACC	p.His66ArgfsTer50	p.H66Rfs*50	ENST00000304494	NM_000077.4	66	cACGGCGCGGAGCCCAac/cGACCac	2/3	0.480382772984189	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.480382772984189	1		399	322	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399276	139399276	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	426	617	0	ENST00000277541.6:c.4867G>T	p.Glu1623Ter	p.E1623*	ENST00000277541	NM_017617.3	1623	Gag/Tag	26/34	0.480382772984189	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.480382772984189	2		617	802	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357501	89357501	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779404022	NA	P-0027807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	154	691	2	ENST00000301030.4:c.317G>A	p.Arg106Gln	p.R106Q	ENST00000301030	NM_001256183.1	106	cGa/cAa	5/13	1	2	FACETS	0.956	0.88	1	0.956	0.88	1	CLONAL	1	TRUE	1	0.565966233804933	2		693	569	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057221	30057221	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	157	505	0	ENST00000338641.4:c.703G>T	p.Gly235Ter	p.G235*	ENST00000338641	NM_000268.3	235	Gga/Tga	8/16	0.565966233804933	1	FACETS	0.925	0.856	0.996	0.925	0.856	0.996	CLONAL	1	TRUE	0	0.565966233804933	1		505	430	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0027808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	14	250	0				ENST00000310581	NM_198253.2	-/1132			0.223009042851069	0	FACETS	0.717	0.53	0.932			1	CLONAL	2	FALSE	0	0.223009042851069	0		250	68	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0027808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	28	656	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.223009042851069	3	FACETS	0.976	0.791	1	0.976	0.791	1	CLONAL	2	FALSE	1	0.223009042851069	3		656	143	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230691	46230691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424958105	NA	P-0027808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	23	462	0	ENST00000334344.6:c.940C>T	p.Arg314Cys	p.R314C	ENST00000334344	NM_152641.2	314	Cgt/Tgt	8/21	0.223009042851069	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	0	0.223009042851069	1		462	127	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0027808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	80	575	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.184152040494494	4	FACETS	1	0.944	1	1	0.982	1	CLONAL	3	FALSE	2	0.223009042851069	4		575	267	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735525	204735525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144988077	NA	P-0027808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	22	480	0	ENST00000302823.3:c.326G>A	p.Gly109Glu	p.G109E	ENST00000302823	NM_005214.4	109	gGa/gAa	2/4	1	2	FACETS	0.958	0.746	1	0.958	0.746	1	CLONAL	1	FALSE	1	0.223009042851069	2		480	206	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528644	89528644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147992008	NA	P-0027808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	12	260	0	ENST00000336596.2:c.2944C>T	p.Pro982Ser	p.P982S	ENST00000336596	NM_005233.5	982	Ccc/Tcc	17/17	0.223009042851069	0	FACETS	1	0.767	1			1	CLONAL	1	FALSE	0	0.223009042851069	0		260	77	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892177	9892177	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555488097	NA	P-0027808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	27	630	0	ENST00000330684.3:c.2313G>A	p.Trp771Ter	p.W771*	ENST00000330684	NM_001134407.1	771	tgG/tgA	11/13	1	2	FACETS	1	0.906	1	1	0.962	1	CLONAL	2	FALSE	1	0.223009042851069	2		630	101	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139408984	139408984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	115	581	1	ENST00000277541.6:c.2185G>A	p.Ala729Thr	p.A729T	ENST00000277541	NM_017617.3	729	Gcc/Acc	13/34	1	2	FACETS	1	0.972	1	1	0.99	1	CLONAL	2	FALSE	1	0.223009042851069	2		582	436	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331729	68331729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	23	188	0	ENST00000487270.1:c.325C>T	p.Pro109Ser	p.P109S	ENST00000487270	NM_133509.3	109	Cca/Tca	5/11	1	2	FACETS	0.838	0.663	1	1	0.938	1	CLONAL	2	FALSE	1	0.223009042851069	2		188	123	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0027808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	80	687	1	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	0.223009042851069	3	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	FALSE	1	0.223009042851069	3		688	361	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78938099	78938099	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	60	621	1	ENST00000306801.3:c.3977C>T	p.Ser1326Phe	p.S1326F	ENST00000306801	NM_020761.2	1326	tCc/tTc	34/34	1	2	FACETS	0.871	0.762	0.985	1	0.983	1	CLONAL	3	FALSE	1	0.223009042851069	2		622	206	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100912	41100912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866253502	NA	P-0027808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	13	535	0	ENST00000373198.4:c.1444G>A	p.Glu482Lys	p.E482K	ENST00000373198	NM_133170.3	482	Gaa/Aaa	8/32	0.223009042851069	0	FACETS	1	0.811	1			1	CLONAL	1	FALSE	0	0.223009042851069	0		535	78	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658353	18658353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868506094	NA	P-0027808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	23	508	0	ENST00000266497.5:c.3158G>A	p.Gly1053Glu	p.G1053E	ENST00000266497		1053	gGa/gAa	22/31	0.223009042851069	1	FACETS	0.945	0.752	1	1	0.946	1	CLONAL	2	FALSE	0	0.223009042851069	1		508	97	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11227555	11227555	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	80	523	0	ENST00000361445.4:c.4273C>A	p.Gln1425Lys	p.Q1425K	ENST00000361445	NM_004958.3	1425	Cag/Aag	29/58	0.223009042851069	3	FACETS	1	0.913	1	1	0.98	1	CLONAL	3	FALSE	1	0.223009042851069	3		523	259	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112884196	112884196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	27	603	0	ENST00000351677.2:c.131C>T	p.Ser44Phe	p.S44F	ENST00000351677	NM_002834.3	44	tCc/tTc	2/16	0.168141848426978	0	FACETS	1	0.912	1			1	CLONAL	1	FALSE	0	0.223009042851069	0		603	149	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134637	2134637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs558737770	NA	P-0027808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	74	729	0	ENST00000219476.3:c.4414G>A	p.Gly1472Ser	p.G1472S	ENST00000219476	NM_000548.3	1472	Ggc/Agc	34/42	1	2	FACETS	1	0.958	1	1	0.985	1	CLONAL	2	FALSE	1	0.223009042851069	2		729	281	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831587	72831587	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	17	608	1	ENST00000268489.5:c.4994C>G	p.Thr1665Ser	p.T1665S	ENST00000268489	NM_006885.3	1665	aCc/aGc	9/10	0.223009042851069	0	FACETS	1	0.847	1			1	CLONAL	1	FALSE	0	0.223009042851069	0		609	101	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845289	42845289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	15	659	0	ENST00000398585.3:c.973C>T	p.Pro325Ser	p.P325S	ENST00000398585	NM_001135099.1	325	Ccc/Tcc	9/14	0.210252651457262	0	FACETS	0.352	0.257	0.467			1	SUBCLONAL	1	FALSE	0	0.223009042851069	0		659	297	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30733072	30733072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	37	443	0	ENST00000295754.5:c.1685C>T	p.Ser562Phe	p.S562F	ENST00000295754	NM_003242.5	562	tCc/tTc	7/7	0.184152040494494	4	FACETS	0.98	0.816	1	0.98	0.816	1	CLONAL	2	FALSE	2	0.223009042851069	4		443	207	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0027811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	382	380	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.233944920483515	7	FACETS	0.936	0.89	0.982	0.78	0.742	0.819	CLONAL	5	TRUE	1	0.233944920483515	7		380	1106	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0027811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	47	586	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.233944920483515	7	FACETS	0.593	0.498	0.698	0.099	0.083	0.117	SUBCLONAL	1	TRUE	1	0.233944920483515	7		586	1074	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0027811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	109	657	1	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.233944920483515	NA		658	519	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508266	38508266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	103	543	2	ENST00000254066.5:c.574C>T	p.Arg192Cys	p.R192C	ENST00000254066	NM_000964.3	192	Cgc/Tgc	5/9	0.231578946090751	3	FACETS	1	0.98	1	0.476	0.426	0.529	CLONAL	1	TRUE	0	0.233944920483515	3		545	689	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0027812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	165	586	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.190670171546224	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	0	0.190670171546224	2		587	839	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579485	7579485	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs869312782	NA	P-0027812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	302	601	0	ENST00000269305.4:c.202G>T	p.Glu68Ter	p.E68*	ENST00000269305	NM_001126112.2	68	Gag/Tag	4/11	0.190670171546224	3	FACETS	0.951	0.898	1	1	0.992	1	CLONAL	4	TRUE	0	0.190670171546224	3		601	912	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691209	18691209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	144	409	1	ENST00000266497.5:c.3320G>A	p.Arg1107Lys	p.R1107K	ENST00000266497		1107	aGa/aAa	23/31	0.190670171546224	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.190670171546224	2		410	669	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246227	46246227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	137	426	1	ENST00000334344.6:c.4321C>T	p.Gln1441Ter	p.Q1441*	ENST00000334344	NM_152641.2	1441	Caa/Taa	15/21	0.190670171546224	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.190670171546224	2		427	648	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416717	121416717	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs780298807	NA	P-0027812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	175	675	0	ENST00000257555.6:c.146C>A	p.Ser49Tyr	p.S49Y	ENST00000257555		49	tCc/tAc	1/10	0.190670171546224	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.190670171546224	2		675	793	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560459	65560459	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	137	452	0	ENST00000358664.4:c.138G>C	p.Leu46Phe	p.L46F	ENST00000358664	NM_002382.4	46	ttG/ttC	3/5	0.190670171546224	2	FACETS	0.98	0.893	1	0.98	0.893	1	CLONAL	2	TRUE	0	0.190670171546224	2		452	733	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991922	72991922	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	131	495	0	ENST00000268489.5:c.2123A>C	p.Gln708Pro	p.Q708P	ENST00000268489	NM_006885.3	708	cAg/cCg	2/10	0.138265571856211	4	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	2	0.190670171546224	4		495	770	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346236	89346236	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	57	300	0	ENST00000301030.4:c.6714C>G	p.Ser2238Arg	p.S2238R	ENST00000301030	NM_001256183.1	2238	agC/agG	9/13	0.138265571856211	4	FACETS	1	0.889	1	1	0.889	1	CLONAL	2	TRUE	2	0.190670171546224	4		300	344	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512341	38512341	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	116	546	0	ENST00000254066.5:c.1252G>C	p.Glu418Gln	p.E418Q	ENST00000254066	NM_000964.3	418	Gag/Cag	9/9	0.138265571856211	4	FACETS	1	0.907	1	1	0.907	1	CLONAL	2	TRUE	2	0.190670171546224	4		546	720	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339416	116339416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1306740707	NA	P-0027812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	49	421	0	ENST00000397752.3:c.278C>T	p.Pro93Leu	p.P93L	ENST00000397752	NM_000245.2	93	cCa/cTa	2/21	0.190670171546224	3	FACETS	0.891	0.753	1	0.445	0.376	0.521	CLONAL	1	TRUE	1	0.190670171546224	3		421	632	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	248	574	0	ENST00000269305.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	336	Gag/Tag	10/11	0.305042186810343	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.38120727200203	1		574	868	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155365	47155365	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0027813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	136	436	0	ENST00000409792.3:c.4715+1G>T		p.X1572_splice	ENST00000409792	NM_014159.6	1572			0.38120727200203	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.38120727200203	1		436	534	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089776	27089777	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	TT	novel	NA	P-0027813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	149	450	1	ENST00000324856.7:c.2732_2732+1delinsTT		p.X911_splice	ENST00000324856	NM_006015.4	911		8/20	0.38120727200203	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.38120727200203	1		451	629	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109730	115109731	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0027813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	281	652	0	ENST00000257566.3:c.2147dup	p.Ala717GlyfsTer13	p.A717Gfs*13	ENST00000257566	NM_016569.3	716	gcg/gcCg	8/8	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.38120727200203	2		652	1109	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609769	28609769	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	145	565	1	ENST00000241453.7:c.1460C>A	p.Ala487Asp	p.A487D	ENST00000241453	NM_004119.2	487	gCt/gAt	12/24	1	2	FACETS	0.905	0.826	0.987	0.905	0.826	0.987	CLONAL	1	TRUE	1	0.38120727200203	2		566	841	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032207	10032207	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	134	647	0	ENST00000330684.3:c.616C>A	p.Leu206Met	p.L206M	ENST00000330684	NM_001134407.1	206	Ctg/Atg	3/13	1	2	FACETS	0.717	0.65	0.787	0.717	0.65	0.787	SUBCLONAL	1	TRUE	1	0.38120727200203	2		647	981	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129968	55129968	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	159	595	0	ENST00000257290.5:c.502G>T	p.Val168Leu	p.V168L	ENST00000257290	NM_006206.4	168	Gta/Tta	4/23	1	2	FACETS	0.842	0.771	0.916	0.842	0.771	0.916	CLONAL	1	TRUE	1	0.38120727200203	2		595	991	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31939814	31939814	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	61	681	0	ENST00000375333.2:c.41A>G	p.Gln14Arg	p.Q14R	ENST00000375333	NM_032454.1	14	cAg/cGg	1/8	1	2	FACETS	0.306	0.263	0.354	0.306	0.263	0.354	SUBCLONAL	1	TRUE	1	0.38120727200203	2		681	1045	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864536	56864536	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	40	581	0	ENST00000519728.1:c.499C>G	p.Leu167Val	p.L167V	ENST00000519728	NM_002350.3	167	Ctg/Gtg	7/13	0.38120727200203	1	FACETS	0.284	0.235	0.338	0.284	0.235	0.338	SUBCLONAL	1	TRUE	0	0.38120727200203	1		581	599	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0027814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	95	658	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.239039765571579	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.248518936099537	1		658	628	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0027814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	156	497	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	1	0.978	1			1	INDETERMINATE	2	TRUE	NA	0.248518936099537	2		497	539	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	159	210	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.978	0.91	1	0.978	0.91	1	CLONAL	1	TRUE	1	0.94	2		210	346	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0027815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	477	648	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	TRUE	1	0.94	2		648	960	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045016	47045016	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0027815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	241	349	0	ENST00000377604.3:c.2342C>G	p.Ser781Ter	p.S781*	ENST00000377604	NM_001204468.1	781	tCa/tGa	20/24	1	1	FACETS	0.416	0.391	0.442	0.416	0.391	0.442	SUBCLONAL	1	TRUE	0	0.94	1		349	653	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148727	20148727	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0027815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	148	194	0	ENST00000379607.5:c.338-2A>C		p.X113_splice	ENST00000379607	NM_001412.3	113			1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.94	1		194	161	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034489	47034489	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	112	330	0	ENST00000377604.3:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000377604	NM_001204468.1	192	Cag/Tag	6/24	1	1	FACETS	0.221	0.199	0.244	0.221	0.199	0.244	SUBCLONAL	1	TRUE	0	0.94	1		330	572	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398255	25398255	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913236	NA	P-0027817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	83	867	0	ENST00000311936.3:c.64C>A	p.Gln22Lys	p.Q22K	ENST00000311936	NM_004985.3	22	Cag/Aag	2/5	1	2	FACETS	0.802	0.707	0.905	0.802	0.707	0.905	CLONAL	1	TRUE	1	0.245725922693976	2		867	842	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602341	10602341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1178941219	NA	P-0027817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	89	987	1	ENST00000171111.5:c.1237C>T	p.Arg413Cys	p.R413C	ENST00000171111	NM_203500.1	413	Cgt/Tgt	3/6	0.245725922693976	1	FACETS	0.846	0.75	0.949	0.846	0.75	0.949	CLONAL	1	TRUE	0	0.245725922693976	1		988	751	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982968	201982968	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	61	903	1	ENST00000359651.3:c.817A>T	p.Thr273Ser	p.T273S	ENST00000359651		273	Acc/Tcc	7/8	0.218419849664185	3	FACETS	0.655	0.564	0.755	0.328	0.282	0.378	SUBCLONAL	1	TRUE	1	0.245725922693976	3		904	851	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435644	18435644	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	55	564	0	ENST00000266497.5:c.629G>T	p.Gly210Val	p.G210V	ENST00000266497		210	gGc/gTc	1/31	1	2	FACETS	0.801	0.685	0.927	0.801	0.685	0.927	CLONAL	1	TRUE	1	0.245725922693976	2		564	559	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481792	40481793	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0027817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	69	607	0	ENST00000264657.5:c.1111dup	p.Asp371GlyfsTer15	p.D371Gfs*15	ENST00000264657	NM_139276.2	371	gac/gGac	12/24	1	2	FACETS	0.785	0.683	0.896	0.785	0.683	0.896	SUBCLONAL	1	TRUE	1	0.245725922693976	2		607	715	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207042	1207042	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	84	888	0	ENST00000326873.7:c.131del	p.Lys44SerfsTer7	p.K44Sfs*7	ENST00000326873	NM_000455.4	44	Aag/ag	1/10	0.245725922693976	1	FACETS	0.909	0.803	1	0.909	0.803	1	CLONAL	1	TRUE	0	0.245725922693976	1		888	660	SUCCESS
AR	367	MSKCC	GRCh37	X	66766348	66766348	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	18	202	0	ENST00000374690.3:c.1360G>T	p.Gly454Trp	p.G454W	ENST00000374690	NM_000044.3	454	Ggg/Tgg	1/8	1	2	FACETS	0.837	0.634	1	0.837	0.634	1	CLONAL	1	TRUE	1	0.245725922693976	2		202	175	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344883	70344883	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	64	986	1	ENST00000374080.3:c.2113G>T	p.Asp705Tyr	p.D705Y	ENST00000374080		705	Gat/Tat	15/45	1	2	FACETS	0.644	0.556	0.739	0.644	0.556	0.739	SUBCLONAL	1	TRUE	1	0.245725922693976	2		987	809	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0027817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	105	401	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.855	0.769	0.945	0.855	0.769	0.945	CLONAL	1	TRUE	1	0.481798182959125	2		401	510	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602878	10602878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	193	638	1	ENST00000171111.5:c.700C>T	p.Arg234Trp	p.R234W	ENST00000171111	NM_203500.1	234	Cgg/Tgg	3/6	0.481798182959125	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.481798182959125	1		639	543	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604590	43604590	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	141	634	0	ENST00000355710.3:c.1175A>T	p.His392Leu	p.H392L	ENST00000355710	NM_020975.4	392	cAc/cTc	6/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.481798182959125	2		634	511	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32969016	32969016	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	92	429	0	ENST00000380152.3:c.9447T>A	p.Ser3149Arg	p.S3149R	ENST00000380152		3149	agT/agA	25/27	1	2	FACETS	0.743	0.662	0.828	0.743	0.662	0.828	SUBCLONAL	1	TRUE	1	0.481798182959125	2		429	514	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001238	150001238	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	129	592	1	ENST00000253339.5:c.2366A>T	p.Asp789Val	p.D789V	ENST00000253339		789	gAt/gTt	4/7	1	2	FACETS	0.931	0.848	1	0.931	0.848	1	CLONAL	1	TRUE	1	0.481798182959125	2		593	575	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341977	8341977	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	81	345	0	ENST00000356435.5:c.4663G>A	p.Ala1555Thr	p.A1555T	ENST00000356435		1555	Gcg/Acg	29/35	1	2	FACETS	0.871	0.772	0.976	0.871	0.772	0.976	CLONAL	1	TRUE	1	0.481798182959125	2		345	386	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727819	78727819	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs202162615	NA	P-0027817-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	86	695	0	ENST00000306801.3:c.664A>G	p.Ile222Val	p.I222V	ENST00000306801	NM_020761.2	222	Atc/Gtc	6/34	1	2	FACETS	0.613	0.543	0.687	0.613	0.543	0.687	SUBCLONAL	1	TRUE	1	0.52	2		695	540	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045667	47045667	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1556782537	NA	P-0027817-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	51	576	1	ENST00000377604.3:c.2548C>T	p.Gln850Ter	p.Q850*	ENST00000377604	NM_001204468.1	850	Cag/Tag	23/24	0.128834561437781	1	FACETS	0.388	0.331	0.451	0.388	0.331	0.451	INDETERMINATE	1	TRUE	0	0.52	1		577	374	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913351	NA	P-0027817-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	64	401	0	ENST00000288602.6:c.1397G>T	p.Gly466Val	p.G466V	ENST00000288602	NM_004333.4	466	gGa/gTa	11/18	1	2	FACETS	0.748	0.652	0.851	0.748	0.652	0.851	SUBCLONAL	1	TRUE	1	0.52	2		401	329	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613209	52613210	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027817-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	59	540	0	ENST00000394830.3:c.3318dup	p.Glu1107ArgfsTer11	p.E1107Rfs*11	ENST00000394830	NM_018313.4	1106	-/A	22/30	1	2	FACETS	0.424	0.365	0.489	0.424	0.365	0.489	SUBCLONAL	1	TRUE	1	0.52	2		540	535	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220384	1220389	+	inframe_deletion	In_Frame_Del	DEL	GCTGAT	GCTGAT	-	novel	NA	P-0027817-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	49	522	0	ENST00000326873.7:c.477_482del	p.Gln159_Ile161delinsHis	p.Q159_I161delinsH	ENST00000326873	NM_000455.4	159	caGCTGATt/cat	4/10	0.278765190111036	1	FACETS	0.37	0.314	0.431	0.37	0.314	0.431	INDETERMINATE	1	TRUE	0	0.52	1		522	377	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597406	10597413	+	frameshift_variant	Frame_Shift_Del	DEL	CGATGTCA	CGATGTCA	GAAGGCC	novel	NA	P-0027817-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	50	721	2	ENST00000171111.5:c.1790_1797delinsGGCCTTC	p.Met597ArgfsTer75	p.M597Rfs*75	ENST00000171111	NM_203500.1	597	aTGACATCG/aGGCCTTC	6/6	0.292043686411435	1	FACETS	0.337	0.286	0.393	0.337	0.286	0.393	INDETERMINATE	1	TRUE	0	0.52	1		723	422	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242716	66242716	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027817-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	51	471	0	ENST00000273854.3:c.1856G>T	p.Trp619Leu	p.W619L	ENST00000273854	NM_004439.5	619	tGg/tTg	9/18	1	2	FACETS	0.562	0.48	0.652	0.562	0.48	0.652	SUBCLONAL	1	TRUE	1	0.52	2		471	349	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468144	50468144	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027817-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	50	504	0	ENST00000331340.3:c.1379A>T	p.Lys460Met	p.K460M	ENST00000331340	NM_006060.4	460	aAg/aTg	8/8	1	2	FACETS	0.502	0.427	0.584	0.502	0.427	0.584	SUBCLONAL	1	TRUE	1	0.52	2		504	383	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0027819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	31	245	1	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	0.44354548237572	1	FACETS	0.716	0.598	0.841	0.716	0.598	0.841	SUBCLONAL	1	TRUE	0	0.664451323360121	1		246	87	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123026603	123026603	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	50	798	0	ENST00000355640.3:c.1079C>A	p.Pro360Gln	p.P360Q	ENST00000355640		360	cCa/cAa	5/7	0.293118841523348	2	FACETS	0.453	0.386	0.526	0.227	0.193	0.263	INDETERMINATE	1	TRUE	0	0.664451323360121	2		798	332	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578378	7578379	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	215	692	0	ENST00000269305.4:c.551dup	p.Asp184GlufsTer2	p.D184Efs*2	ENST00000269305	NM_001126112.2	184	gat/gaAt	5/11	0.555508809564468	2	FACETS	0.828	0.782	0.872	0.828	0.782	0.872	CLONAL	2	TRUE	0	0.664451323360121	2		692	391	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739325	145739325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	291	770	0	ENST00000428558.2:c.2045G>A	p.Arg682Lys	p.R682K	ENST00000428558	NM_004260.3	682	aGg/aAg	12/22	0.391464885949532	3	FACETS	0.913	0.866	0.96	0.913	0.866	0.96	INDETERMINATE	2	TRUE	1	0.664451323360121	3		770	639	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0027822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	91	586	1	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	0.218679565698533	2		587	693	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220370	1220370	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0027822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	108	657	0	ENST00000326873.7:c.465-2A>T		p.X155_splice	ENST00000326873	NM_000455.4	155			0.218679565698533	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.218679565698533	1		657	692	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226092	226092	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	67	434	0	ENST00000264932.6:c.551G>T	p.Gly184Val	p.G184V	ENST00000264932	NM_004168.2	184	gGg/gTg	5/15	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.218679565698533	2		434	513	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395569	116395569	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs375951814	NA	P-0027822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	81	578	0	ENST00000397752.3:c.1862C>T	p.Thr621Ile	p.T621I	ENST00000397752	NM_000245.2	621	aCa/aTa	6/21	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.218679565698533	2		578	731	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446282	70446282	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs371499355	NA	P-0027822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	89	769	2	ENST00000373644.4:c.5222G>T	p.Arg1741Leu	p.R1741L	ENST00000373644	NM_030625.2	1741	cGc/cTc	11/12	1	2	FACETS	0.955	0.846	1	0.955	0.846	1	CLONAL	1	TRUE	1	0.218679565698533	2		771	852	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625180	69625180	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	61	795	0	ENST00000334134.2:c.613G>T	p.Gly205Trp	p.G205W	ENST00000334134	NM_005247.2	205	Ggg/Tgg	3/3	1	2	FACETS	0.64	0.55	0.737	0.64	0.55	0.737	SUBCLONAL	1	TRUE	1	0.218679565698533	2		795	872	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349130	11349130	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	42	291	0	ENST00000332029.2:c.206G>T	p.Arg69Leu	p.R69L	ENST00000332029	NM_003745.1	69	cGc/cTc	2/2	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.218679565698533	2		291	334	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550532	29550532	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	40	711	0	ENST00000356175.3:c.1792A>G	p.Lys598Glu	p.K598E	ENST00000356175	NM_000267.3	598	Aag/Gag	16/57	1	2	FACETS	0.521	0.432	0.621	0.521	0.432	0.621	SUBCLONAL	1	TRUE	1	0.218679565698533	2		711	702	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790018	40790018	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	42	634	0	ENST00000373198.4:c.2713G>C	p.Gly905Arg	p.G905R	ENST00000373198	NM_133170.3	905	Ggc/Cgc	18/32	1	2	FACETS	0.477	0.396	0.566	0.477	0.396	0.566	SUBCLONAL	1	TRUE	1	0.218679565698533	2		634	806	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626158	12626183	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TGAAACAAAGCCCAAGAATGCTCTCA	TGAAACAAAGCCCAAGAATGCTCTCA	-	novel	NA	P-0027822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	26	331	0	ENST00000251849.4:c.1804-27_1804-2del		p.X602_splice	ENST00000251849	NM_002880.3	602			0.218679565698533	1	FACETS	0.593	0.47	0.735	0.593	0.47	0.735	SUBCLONAL	1	TRUE	0	0.218679565698533	1		331	357	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866422	56866422	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	86	766	0	ENST00000519728.1:c.669G>T	p.Glu223Asp	p.E223D	ENST00000519728	NM_002350.3	223	gaG/gaT	8/13	1	2	FACETS	0.951	0.84	1	0.951	0.84	1	CLONAL	1	TRUE	1	0.218679565698533	2		766	827	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030834	69030834	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	131	603	0	ENST00000288368.4:c.3376A>T	p.Ser1126Cys	p.S1126C	ENST00000288368	NM_024870.2	1126	Agc/Tgc	27/40	0.218679565698533	3	FACETS	0.904	0.821	0.991	0.904	0.821	0.991	CLONAL	2	TRUE	1	0.218679565698533	3		603	735	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224128	53224129	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0027822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	127	456	0	ENST00000375401.3:c.3422_3423delinsTT	p.Arg1141Ile	p.R1141I	ENST00000375401	NM_004187.3	1141	aGG/aTT	22/26	1	1	FACETS	0.868	0.789	0.951	1	0.988	1	CLONAL	2	TRUE	0	0.218679565698533	1		456	596	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577571	7577571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	224	687	0	ENST00000269305.4:c.710del	p.Met237SerfsTer10	p.M237Sfs*10	ENST00000269305	NM_001126112.2	237	aTg/ag	7/11	0.383350201620023	1	FACETS	0.831	0.775	0.89	0.831	0.775	0.89	CLONAL	1	TRUE	0	0.45188554855772	1		687	923	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579383	7579383	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	168	743	0	ENST00000269305.4:c.304A>G	p.Thr102Ala	p.T102A	ENST00000269305	NM_001126112.2	102	Acc/Gcc	4/11	0.383350201620023	1	FACETS	0.506	0.464	0.55	0.506	0.464	0.55	SUBCLONAL	1	TRUE	0	0.45188554855772	1		743	1137	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164348	47164348	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1317109866	NA	P-0027823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	187	395	0	ENST00000409792.3:c.1778C>G	p.Pro593Arg	p.P593R	ENST00000409792	NM_014159.6	593	cCt/cGt	3/21	0.203407107324192	1	FACETS	0.804	0.744	0.866	0.804	0.744	0.866	INDETERMINATE	1	TRUE	0	0.45188554855772	1		395	797	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0027824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	363	581	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.701352326543563	2	FACETS	0.982	0.947	1	0.982	0.947	1	CLONAL	2	TRUE	0	0.701352326543563	2		583	527	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843634	156843634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201035170	NA	P-0027824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	241	820	4	ENST00000524377.1:c.1060G>A	p.Val354Ile	p.V354I	ENST00000524377	NM_002529.3	354	Gtc/Atc	8/17	0.696779273391398	4	FACETS	1	0.963	1	0.349	0.325	0.373	CLONAL	1	TRUE	1	0.701352326543563	4		824	1118	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318754	163318755	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	279	561	1	ENST00000271452.3:c.1150dup	p.Arg384LysfsTer6	p.R384Kfs*6	ENST00000271452	NM_145697.2	382	gaa/gAaa	13/14	0.696779273391398	4	FACETS	0.986	0.924	1	0.329	0.308	0.35	CLONAL	1	TRUE	1	0.701352326543563	4		562	1373	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562493	21562493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1417916199	NA	P-0027824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	10	37	0	ENST00000382592.4:c.1426G>A	p.Ala476Thr	p.A476T	ENST00000382592	NM_014572.2	476	Gcc/Acc	4/8	0.701352326543563	6	FACETS	0.761	0.521	1	0.152	0.104	0.212	CLONAL	1	TRUE	1	0.701352326543563	6		37	90	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643503	38643503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057518683	NA	P-0027824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	1124	674	4	ENST00000299084.4:c.973C>T	p.Arg325Ter	p.R325*	ENST00000299084	NM_152594.2	325	Cga/Tga	7/7	0.667435286688154	4	FACETS	0.986	0.97	1	0.986	0.97	1	CLONAL	4	TRUE	0	0.701352326543563	4		678	1383	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828336	50828336	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	182	475	0	ENST00000398568.2:c.2674G>T	p.Asp892Tyr	p.D892Y	ENST00000398568	NM_001042412.1	892	Gat/Tat	17/18	0.638849779906713	4	FACETS	0.929	0.858	1	0.31	0.286	0.335	CLONAL	1	TRUE	1	0.701352326543563	4		475	950	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029445	16029446	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	250	508	11	ENST00000268712.3:c.1584dup	p.Glu529ArgfsTer7	p.E529Rfs*7	ENST00000268712	NM_006311.3	528	-/A	15/46	0.701352326543563	2	FACETS	0.829	0.777	0.882	0.414	0.388	0.441	CLONAL	1	TRUE	0	0.701352326543563	2		519	860	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59770808	59770808	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501775	NA	P-0027824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	195	562	1	ENST00000259008.2:c.2558C>T	p.Pro853Leu	p.P853L	ENST00000259008	NM_032043.2	853	cCa/cTa	18/20	0.701352326543563	3	FACETS	0.862	0.799	0.928	0.431	0.399	0.464	CLONAL	1	TRUE	1	0.701352326543563	3		563	871	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79974804	79974804	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764885728	NA	P-0027824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	528	632	1	ENST00000265081.6:c.1232G>A	p.Arg411His	p.R411H	ENST00000265081	NM_002439.4	411	cGt/cAt	8/24	0.701352326543563	3	FACETS	0.963	0.928	0.998	0.963	0.928	0.998	CLONAL	2	TRUE	1	0.701352326543563	3		633	1056	SUCCESS
APC	324	MSKCC	GRCh37	5	112173278	112173278	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730881240	NA	P-0027824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	101	295	0	ENST00000257430.4:c.1987C>T	p.Gln663Ter	p.Q663*	ENST00000257430	NM_000038.5	663	Caa/Taa	16/16	0.701352326543563	3	FACETS	0.898	0.808	0.993	0.449	0.404	0.497	CLONAL	1	TRUE	1	0.701352326543563	3		295	433	SUCCESS
APC	324	MSKCC	GRCh37	5	112175171	112175171	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085373	NA	P-0027824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	177	311	0	ENST00000257430.4:c.3880C>T	p.Gln1294Ter	p.Q1294*	ENST00000257430	NM_000038.5	1294	Cag/Tag	16/16	0.701352326543563	3	FACETS	0.919	0.86	0.978	0.919	0.86	0.978	CLONAL	2	TRUE	1	0.701352326543563	3		311	371	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0027825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	196	567	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.867	0.809	0.926	0.867	0.809	0.926	CLONAL	1	TRUE	1	0.851217429771157	2		568	531	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0027825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	71	253	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.999	0.894	1	0.999	0.894	1	CLONAL	1	TRUE	1	0.851217429771157	2		253	167	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0027825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	199	578	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.851217429771157	2		578	447	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909923	100909923	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	64	605	0	ENST00000325455.5:c.2726T>A	p.Met909Lys	p.M909K	ENST00000325455	NM_001202474.3	909	aTg/aAg	8/8	0.851217429771157	3	FACETS	0.882	0.773	0.997	0.441	0.386	0.499	CLONAL	1	TRUE	1	0.851217429771157	3		605	243	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939864	76939864	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	91	296	0	ENST00000373344.5:c.884del	p.Lys295ArgfsTer4	p.K295Rfs*4	ENST00000373344	NM_000489.3	295	aAg/ag	9/35	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.851217429771157	1		296	100	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0027828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	4051	380	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.435999678118923	34	FACETS	1	0.997	1	0.978	0.971	0.985	CLONAL	32	TRUE	1	0.435999678118923	34		380	4592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0027828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	198	667	0	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	0.435999678118923	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.435999678118923	1		667	703	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4387998	4387998	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	165	445	0	ENST00000261254.3:c.484C>T	p.His162Tyr	p.H162Y	ENST00000261254	NM_001759.3	162	Cac/Tac	3/5	0.435999678118923	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.435999678118923	1		445	541	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0027832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	101	442	0	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	0.32722647135606	3	FACETS	0.789	0.705	0.878	0.394	0.352	0.439	SUBCLONAL	1	TRUE	1	0.417792858167901	3		442	741	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602878	10602878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	304	638	1	ENST00000171111.5:c.700C>T	p.Arg234Trp	p.R234W	ENST00000171111	NM_203500.1	234	Cgg/Tgg	3/6	0.326761999670077	2	FACETS	0.776	0.733	0.82	0.776	0.733	0.82	SUBCLONAL	2	TRUE	0	0.417792858167901	2		639	938	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882019	NA	P-0027832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	279	579	0	ENST00000269305.4:c.455del	p.Pro152ArgfsTer18	p.P152Rfs*18	ENST00000269305	NM_001126112.2	152	cCg/cg	5/11	0.32722647135606	3	FACETS	0.877	0.826	0.93	0.877	0.826	0.93	CLONAL	2	TRUE	1	0.417792858167901	3		579	920	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220717	1220717	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0027832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	178	441	0	ENST00000326873.7:c.734+1G>A		p.X245_splice	ENST00000326873	NM_000455.4	245			0.326761999670077	2	FACETS	0.826	0.767	0.886	0.826	0.767	0.886	CLONAL	2	TRUE	0	0.417792858167901	2		441	516	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233073	69233073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	60	240	0	ENST00000462284.1:c.938C>T	p.Ser313Leu	p.S313L	ENST00000462284	NM_002392.5	313	tCa/tTa	11/11	0.283783221335299	3	FACETS	0.804	0.694	0.922			1	CLONAL	1	TRUE	NA	0.417792858167901	3		240	432	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900314	3900314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567361652	NA	P-0027832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	98	394	0	ENST00000262367.5:c.782C>T	p.Ala261Val	p.A261V	ENST00000262367	NM_004380.2	261	gCa/gTa	2/31	1	2	FACETS	0.768	0.686	0.854	0.768	0.686	0.854	SUBCLONAL	1	TRUE	1	0.417792858167901	2		394	611	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277045	18277045	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	101	487	0	ENST00000222254.8:c.1492C>G	p.Gln498Glu	p.Q498E	ENST00000222254	NM_005027.3	498	Caa/Gaa	12/16	0.326761999670077	2	FACETS	0.734	0.656	0.816	0.367	0.328	0.408	SUBCLONAL	1	TRUE	0	0.417792858167901	2		487	659	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31472312	31472312	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	79	415	0	ENST00000344624.3:c.2099A>G	p.His700Arg	p.H700R	ENST00000344624		700	cAc/cGc	14/33	0.322625796652844	3	FACETS	0.689	0.605	0.778	0.23	0.201	0.26	SUBCLONAL	1	TRUE	0	0.417792858167901	3		415	664	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685294	86685294	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	63	160	0	ENST00000274376.6:c.3010G>T	p.Ala1004Ser	p.A1004S	ENST00000274376	NM_002890.2	1004	Gct/Tct	24/25	0.326761999670077	2	FACETS	1	0.968	1	0.679	0.596	0.767	CLONAL	1	TRUE	0	0.417792858167901	2		160	222	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92462508	92462508	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	337	400	0	ENST00000265734.4:c.130C>A	p.Arg44Ser	p.R44S	ENST00000265734	NM_001259.6	44	Cgc/Agc	2/8	0.417792858167901	8	FACETS	1	0.961	1	0.611	0.578	0.646	CLONAL	3	TRUE	3	0.417792858167901	8		400	1189	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528742	8528742	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	123	290	0	ENST00000356435.5:c.390G>T	p.Met130Ile	p.M130I	ENST00000356435		130	atG/atT	4/35	0.333334836849954	2	FACETS	0.809	0.739	0.88	0.809	0.739	0.88	CLONAL	2	TRUE	0	0.417792858167901	2		290	364	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	53	210	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.493	0.422	0.57	0.493	0.422	0.57	SUBCLONAL	1	TRUE	1	0.595602698363895	2		210	361	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0027834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	238	683	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	0.30263612613205	2	FACETS	0.909	0.85	0.97	0.455	0.425	0.485	INDETERMINATE	1	TRUE	0	0.595602698363895	2		683	879	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717695	89717696	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1060500115	NA	P-0027834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	54	450	0	ENST00000371953.3:c.723dup	p.Glu242Ter	p.E242*	ENST00000371953	NM_000314.4	240	-/T	7/9	1	2	FACETS	0.27	0.23	0.314	0.27	0.23	0.314	SUBCLONAL	1	TRUE	1	0.595602698363895	2		450	671	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913409	NA	P-0027834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	67	319	0	ENST00000349496.5:c.134C>A	p.Ser45Tyr	p.S45Y	ENST00000349496	NM_001904.3	45	tCt/tAt	3/15	0.324830618808997	3	FACETS	0.527	0.458	0.601	0.264	0.229	0.301	INDETERMINATE	1	TRUE	1	0.595602698363895	3		319	554	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506467	148506467	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519833	NA	P-0027834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	50	321	0	ENST00000320356.2:c.2045C>G	p.Ala682Gly	p.A682G	ENST00000320356	NM_004456.4	682	gCa/gGa	18/20	1	2	FACETS	0.354	0.301	0.413	0.354	0.301	0.413	SUBCLONAL	1	TRUE	1	0.595602698363895	2		321	474	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0027834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	95	669	1	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	0.368	0.327	0.412	0.368	0.327	0.412	SUBCLONAL	1	TRUE	1	0.595602698363895	2		670	866	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711895	89711895	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	91	451	0	ENST00000371953.3:c.513G>C	p.Gln171His	p.Q171H	ENST00000371953	NM_000314.4	171	caG/caC	6/9	1	2	FACETS	0.44	0.39	0.492	0.44	0.39	0.492	SUBCLONAL	1	TRUE	1	0.595602698363895	2		451	695	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099387	27099393	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTGGG	CCCTGGG	-	novel	NA	P-0027834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	100	624	0	ENST00000324856.7:c.3624_3630del	p.Pro1209IlefsTer5	p.P1209Ifs*5	ENST00000324856	NM_006015.4	1208	aaCCCTGGG/aa	14/20	1	2	FACETS	0.409	0.364	0.456	0.409	0.364	0.456	SUBCLONAL	1	TRUE	1	0.595602698363895	2		624	822	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828161	3828161	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	63	308	0	ENST00000262367.5:c.1964del	p.Ala655GlufsTer11	p.A655Efs*11	ENST00000262367	NM_004380.2	655	gCa/ga	10/31	1	2	FACETS	0.434	0.376	0.497	0.434	0.376	0.497	SUBCLONAL	1	TRUE	1	0.595602698363895	2		308	487	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0027837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	102	277	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.197416995952229	1	FACETS	1	0.974	1	1	0.99	1	CLONAL	2	TRUE	0	0.225195877050411	1		277	328	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0027837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	50	412	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.157403493010833	0	FACETS	0.791	0.672	0.921			1	CLONAL	1	TRUE	0	0.225195877050411	0		412	435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0027837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	47	540	0	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	0.197416995952229	1	FACETS	0.811	0.685	0.949	0.811	0.685	0.949	CLONAL	1	TRUE	0	0.225195877050411	1		540	457	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041459	42041459	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	38	509	1	ENST00000219905.7:c.5654C>A	p.Ser1885Ter	p.S1885*	ENST00000219905	NM_001164273.1	1885	tCa/tAa	17/24	0.197416995952229	1	FACETS	0.803	0.665	0.956	0.803	0.665	0.956	CLONAL	1	TRUE	0	0.225195877050411	1		510	373	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591825	48591825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767342	NA	P-0027839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	32	339	0	ENST00000342988.3:c.988G>A	p.Glu330Lys	p.E330K	ENST00000342988	NM_005359.5	330	Gaa/Aaa	9/12	0.156576443462323	1	FACETS	0.572	0.463	0.694	0.572	0.463	0.694	SUBCLONAL	1	TRUE	0	0.22	1		339	453	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879043	151879043	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	57	508	0	ENST00000262189.6:c.5902G>A	p.Asp1968Asn	p.D1968N	ENST00000262189	NM_170606.2	1968	Gac/Aac	36/59	1	2	FACETS	0.855	0.733	0.988	0.855	0.733	0.988	CLONAL	1	TRUE	1	0.22	2		508	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0027841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	463	717	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.453361995768302	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.477665095588886	2		718	948	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76856030	76856030	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	71	480	0	ENST00000373344.5:c.5570T>C	p.Val1857Ala	p.V1857A	ENST00000373344	NM_000489.3	1857	gTg/gCg	23/35	0.254558695897136	1	FACETS	0.504	0.441	0.571	0.504	0.441	0.571	INDETERMINATE	1	TRUE	0	0.477665095588886	1		480	449	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453145	140453145	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913366	NA	P-0027847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	14	489	0	ENST00000288602.6:c.1790T>G	p.Leu597Arg	p.L597R	ENST00000288602	NM_004333.4	597	cTa/cGa	15/18	1	2	FACETS	0.061	0.043	0.082	0.061	0.043	0.082	SUBCLONAL	1	TRUE	1	0.73800736847796	2		489	626	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680827	30680827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	281	613	0	ENST00000376406.3:c.892G>A	p.Asp298Asn	p.D298N	ENST00000376406	NM_014641.2	298	Gac/Aac	5/15	1	2	FACETS	0.989	0.934	1	0.989	0.934	1	CLONAL	1	TRUE	1	0.73800736847796	2		613	770	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0027848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	130	587	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.268529139502852	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.292982858184318	2		587	426	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420272	88420272	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	107	515	1	ENST00000360948.2:c.2414G>T	p.Gly805Val	p.G805V	ENST00000360948	NM_001012338.2	805	gGg/gTg	19/19	0.292982858184318	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	2	TRUE	0	0.292982858184318	2		516	363	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846267	156846267	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	126	589	0	ENST00000524377.1:c.1708C>A	p.Gln570Lys	p.Q570K	ENST00000524377	NM_002529.3	570	Cag/Aag	14/17	0.292982858184318	4	FACETS	0.986	0.896	1	0.986	0.896	1	CLONAL	2	TRUE	2	0.292982858184318	4		589	564	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175795	176175795	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	32	380	0	ENST00000367669.3:c.320G>T	p.Gly107Val	p.G107V	ENST00000367669	NM_022457.5	107	gGc/gTc	1/20	0.292982858184318	4	FACETS	0.995	0.81	1	0.497	0.405	0.601	CLONAL	1	TRUE	2	0.292982858184318	4		380	284	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518341	204518341	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0027848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	30	500	0	ENST00000367182.3:c.1004C>G	p.Ser335Ter	p.S335*	ENST00000367182	NM_001278516.1	335	tCa/tGa	11/11	0.292982858184318	4	FACETS	0.48	0.385	0.587	0.24	0.192	0.294	SUBCLONAL	1	TRUE	2	0.292982858184318	4		500	552	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936170	71936170	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	17	291	0	ENST00000298229.2:c.142G>C	p.Asp48His	p.D48H	ENST00000298229	NM_001567.3	48	Gac/Cac	1/28	0.292982858184318	4	FACETS	0.956	0.718	1	0.478	0.359	0.617	CLONAL	1	TRUE	2	0.292982858184318	4		291	157	SUCCESS
EED	8726	MSKCC	GRCh37	11	85979551	85979551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	124	552	0	ENST00000263360.6:c.914A>G	p.His305Arg	p.H305R	ENST00000263360	NM_003797.3	305	cAt/cGt	9/12	0.292982858184318	4	FACETS	0.87	0.789	0.955	0.87	0.789	0.955	CLONAL	2	TRUE	2	0.292982858184318	4		552	629	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201517	133201517	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	21	634	0	ENST00000320574.5:c.6721G>C	p.Asp2241His	p.D2241H	ENST00000320574	NM_006231.2	2241	Gac/Cac	48/49	0.292982858184318	2	FACETS	0.361	0.277	0.459	0.181	0.138	0.23	SUBCLONAL	1	TRUE	0	0.292982858184318	2		634	397	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42053967	42053967	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	90	450	0	ENST00000219905.7:c.7429C>T	p.Gln2477Ter	p.Q2477*	ENST00000219905	NM_001164273.1	2477	Cag/Tag	21/24	0.292982858184318	2	FACETS	0.89	0.797	0.988	0.89	0.797	0.988	CLONAL	2	TRUE	0	0.292982858184318	2		450	345	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900860	3900860	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	174	513	0	ENST00000262367.5:c.236G>T	p.Gly79Val	p.G79V	ENST00000262367	NM_004380.2	79	gGc/gTc	2/31	0.292982858184318	3	FACETS	0.868	0.805	0.932	0.868	0.805	0.932	CLONAL	3	TRUE	0	0.292982858184318	3		513	523	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641722	23641722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878855102	NA	P-0027848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	166	508	1	ENST00000261584.4:c.1753G>A	p.Asp585Asn	p.D585N	ENST00000261584	NM_024675.3	585	Gat/Aat	5/13	0.292982858184318	3	FACETS	1	0.984	1	0.828	0.766	0.892	CLONAL	2	TRUE	0	0.292982858184318	3		509	523	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67132656	67132656	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	182	607	0	ENST00000412916.2:c.539G>T	p.Gly180Val	p.G180V	ENST00000412916		180	gGt/gTt	6/6	0.292982858184318	5	FACETS	0.882	0.817	0.949	0.882	0.817	0.949	CLONAL	3	TRUE	2	0.292982858184318	5		607	676	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59878810	59878810	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	73	328	0	ENST00000259008.2:c.944G>C	p.Gly315Ala	p.G315A	ENST00000259008	NM_032043.2	315	gGa/gCa	8/20	0.292982858184318	4	FACETS	0.883	0.777	0.995	0.883	0.777	0.995	CLONAL	2	TRUE	2	0.292982858184318	4		328	365	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2194536	2194536	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	54	482	0	ENST00000398665.3:c.611A>T	p.Lys204Met	p.K204M	ENST00000398665	NM_032482.2	204	aAg/aTg	7/28	0.292982858184318	2	FACETS	1	0.885	1	0.518	0.444	0.598	CLONAL	1	TRUE	0	0.292982858184318	2		482	356	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17949122	17949122	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	140	691	0	ENST00000458235.1:c.1519C>A	p.Gln507Lys	p.Q507K	ENST00000458235	NM_000215.3	507	Cag/Aag	11/24	0.292982858184318	2	FACETS	0.967	0.887	1	0.967	0.887	1	CLONAL	2	TRUE	0	0.292982858184318	2		691	494	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21272281	21272281	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	78	380	0	ENST00000354336.3:c.59C>G	p.Ser20Cys	p.S20C	ENST00000354336	NM_005207.3	20	tCt/tGt	1/3	0.292982858184318	4	FACETS	0.964	0.853	1	0.964	0.853	1	CLONAL	2	TRUE	2	0.292982858184318	4		380	357	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73110172	73110172	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0027848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	84	591	0	ENST00000356692.5:c.382-2A>C		p.X128_splice	ENST00000356692		128			0.21540034534546	2	FACETS	1	0.967	1	0.627	0.556	0.703	CLONAL	1	TRUE	0	0.292982858184318	2		591	457	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250661	26250661	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	106	500	0	ENST00000446824.2:c.173C>A	p.Ser58Ter	p.S58*	ENST00000446824	NM_021018.2	58	tCg/tAg	1/1	0.292982858184318	3	FACETS	0.888	0.801	0.98	0.888	0.801	0.98	CLONAL	2	TRUE	1	0.292982858184318	3		500	467	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0027849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	12	401	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.137	0.096	0.189	0.137	0.096	0.189	SUBCLONAL	1	TRUE	1	0.364063193582263	2		401	480	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28929495	NA	P-0027849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	142	621	0	ENST00000275493.2:c.2155G>A	p.Gly719Ser	p.G719S	ENST00000275493	NM_005228.3	719	Ggc/Agc	18/28	0.364063193582263	3	FACETS	1	0.986	1	0.71	0.649	0.774	CLONAL	1	TRUE	1	0.364063193582263	3		621	649	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0027849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	125	530	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.364063193582263	3	FACETS	0.761	0.692	0.834	0.761	0.692	0.834	SUBCLONAL	2	TRUE	1	0.364063193582263	3		530	533	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0027850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	177	298	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.890227996508562	3	FACETS	1	0.984	1	0.402	0.373	0.431	CLONAL	1	TRUE	0	0.890227996508562	3		298	477	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782177	NA	P-0027850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	694	681	3	ENST00000269305.4:c.644G>A	p.Ser215Asn	p.S215N	ENST00000269305	NM_001126112.2	215	aGt/aAt	6/11	0.890227996508562	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.890227996508562	2		684	763	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465606	99465606	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	266	520	1	ENST00000268035.6:c.2431G>A	p.Glu811Lys	p.E811K	ENST00000268035	NM_000875.3	811	Gag/Aag	11/21	0.885177178422232	4	FACETS	1	0.972	1	0.532	0.499	0.566	CLONAL	1	TRUE	2	0.890227996508562	4		521	1062	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133282	30133282	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	264	661	1	ENST00000263025.4:c.216G>T	p.Lys72Asn	p.K72N	ENST00000263025	NM_002746.2	72	aaG/aaT	2/9	0.890227996508562	4	FACETS	1	0.959	1	0.343	0.321	0.366	CLONAL	1	TRUE	1	0.890227996508562	4		662	1089	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099026	27099026	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	264	634	1	ENST00000324856.7:c.3442C>T	p.Gln1148Ter	p.Q1148*	ENST00000324856	NM_006015.4	1148	Cag/Tag	13/20	0.890227996508562	3	FACETS	0.987	0.928	1	0.494	0.464	0.524	CLONAL	1	TRUE	1	0.890227996508562	3		635	868	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945543	54945543	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs774552788	NA	P-0027850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2378	340	766	1	ENST00000312783.6:c.1027C>T	p.Arg343Trp	p.R343W	ENST00000312783	NM_198436.1	343	Cgg/Tgg	9/10	0.890227996508562	7	FACETS	0.906	0.853	0.962			1	CLONAL	1	TRUE	NA	0.890227996508562	7		767	2718	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59934430	59934430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1238	178	339	0	ENST00000259008.2:c.368C>T	p.Ser123Leu	p.S123L	ENST00000259008	NM_032043.2	123	tCa/tTa	4/20	0.890227996508562	7	FACETS	0.911	0.837	0.988	0.182	0.167	0.198	CLONAL	1	TRUE	2	0.890227996508562	7		339	1416	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099345	193099345	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	194	492	0	ENST00000367435.3:c.279T>A	p.Asp93Glu	p.D93E	ENST00000367435	NM_024529.4	93	gaT/gaA	3/17	0.890227996508562	4	FACETS	1	0.928	1	0.501	0.464	0.539	CLONAL	1	TRUE	2	0.890227996508562	4		492	823	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604551	43604551	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0027850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	262	645	0	ENST00000355710.3:c.1136C>G	p.Ser379Ter	p.S379*	ENST00000355710	NM_020975.4	379	tCa/tGa	6/20	0.890227996508562	3	FACETS	0.921	0.864	0.978	0.46	0.432	0.489	CLONAL	1	TRUE	1	0.890227996508562	3		645	924	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597579	28597579	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	253	631	0	ENST00000241453.7:c.2326G>C	p.Glu776Gln	p.E776Q	ENST00000241453	NM_004119.2	776	Gaa/Caa	19/24	0.890227996508562	3	FACETS	0.923	0.865	0.982	0.461	0.432	0.491	CLONAL	1	TRUE	1	0.890227996508562	3		631	890	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724843	43724843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	216	575	0	ENST00000382044.4:c.3224G>A	p.Gly1075Glu	p.G1075E	ENST00000382044	NM_001141980.1	1075	gGa/gAa	17/28	0.885177178422232	4	FACETS	0.941	0.875	1	0.47	0.437	0.505	CLONAL	1	TRUE	2	0.890227996508562	4		575	975	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690576	88690576	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	245	581	0	ENST00000360948.2:c.454C>G	p.Leu152Val	p.L152V	ENST00000360948	NM_001012338.2	152	Ctt/Gtt	5/19	0.885177178422232	4	FACETS	0.924	0.863	0.987	0.462	0.431	0.494	CLONAL	1	TRUE	2	0.890227996508562	4		581	1126	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778106	3778106	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	308	803	1	ENST00000262367.5:c.6942G>A	p.Met2314Ile	p.M2314I	ENST00000262367	NM_004380.2	2314	atG/atA	31/31	0.890227996508562	4	FACETS	0.954	0.898	1	0.318	0.299	0.338	CLONAL	1	TRUE	1	0.890227996508562	4		804	1371	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670664	67670664	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	490	661	0	ENST00000264010.4:c.1909G>A	p.Glu637Lys	p.E637K	ENST00000264010	NM_006565.3	637	Gag/Aag	11/12	0.890227996508562	4	FACETS	0.955	0.916	0.993	0.636	0.611	0.662	CLONAL	2	TRUE	1	0.890227996508562	4		661	1090	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81957186	81957186	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	186	560	0	ENST00000359376.3:c.2404G>C	p.Glu802Gln	p.E802Q	ENST00000359376	NM_002661.3	802	Gag/Cag	22/33	0.890227996508562	4	FACETS	0.794	0.733	0.857	0.265	0.244	0.286	SUBCLONAL	1	TRUE	1	0.890227996508562	4		560	995	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290186	15290186	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1401733240	NA	P-0027850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	283	649	0	ENST00000263388.2:c.3449C>T	p.Pro1150Leu	p.P1150L	ENST00000263388	NM_000435.2	1150	cCa/cTa	21/33	1	2	FACETS	0.965	0.914	1	0.965	0.914	1	CLONAL	1	TRUE	1	0.890227996508562	2		649	659	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139013	50139013	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	306	786	0	ENST00000246792.3:c.550G>C	p.Glu184Gln	p.E184Q	ENST00000246792	NM_006270.3	184	Gag/Cag	5/6	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.890227996508562	2		786	676	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241081	39241081	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs138555160	NA	P-0027850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	224	632	0	ENST00000402219.2:c.1990G>C	p.Glu664Gln	p.E664Q	ENST00000402219	NM_005633.3	664	Gag/Cag	12/23	0.890227996508562	3	FACETS	0.949	0.887	1	0.475	0.443	0.507	CLONAL	1	TRUE	1	0.890227996508562	3		632	766	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403179	213403179	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	191	508	1	ENST00000342788.4:c.76C>T	p.Gln26Ter	p.Q26*	ENST00000342788	NM_005235.2	26	Cag/Tag	1/28	0.890227996508562	3	FACETS	0.978	0.909	1	0.489	0.454	0.525	CLONAL	1	TRUE	1	0.890227996508562	3		509	634	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019283	31019283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	188	385	1	ENST00000375687.4:c.878G>A	p.Arg293Lys	p.R293K	ENST00000375687	NM_015338.5	293	aGa/aAa	9/13	0.890227996508562	4	FACETS	0.983	0.91	1	0.492	0.455	0.53	CLONAL	1	TRUE	2	0.890227996508562	4		386	812	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961410	1961410	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	268	659	0	ENST00000382891.5:c.3198G>T	p.Lys1066Asn	p.K1066N	ENST00000382891	NM_133335.3	1066	aaG/aaT	17/22	0.890227996508562	4	FACETS	0.931	0.873	0.992	0.31	0.291	0.331	CLONAL	1	TRUE	1	0.890227996508562	4		659	1222	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595596	55595596	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	154	372	0	ENST00000288135.5:c.2086G>C	p.Asp696His	p.D696H	ENST00000288135	NM_000222.2	696	Gat/Cat	14/21	0.890227996508562	4	FACETS	0.986	0.906	1	0.329	0.302	0.357	CLONAL	1	TRUE	1	0.890227996508562	4		372	663	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629120	187629120	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370787232	NA	P-0027850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	271	557	1	ENST00000441802.2:c.1862C>T	p.Ser621Leu	p.S621L	ENST00000441802	NM_005245.3	621	tCg/tTg	2/27	0.890227996508562	4	FACETS	0.969	0.908	1	0.323	0.302	0.344	CLONAL	1	TRUE	1	0.890227996508562	4		558	1188	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31401599	31401599	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	268	686	1	ENST00000344624.3:c.4065G>C	p.Met1355Ile	p.M1355I	ENST00000344624		1355	atG/atC	33/33	1	2	FACETS	0.91	0.859	0.961	0.91	0.859	0.961	CLONAL	1	TRUE	1	0.890227996508562	2		687	662	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79968621	79968621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs887040509	NA	P-0027850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	210	709	0	ENST00000265081.6:c.971C>T	p.Ser324Leu	p.S324L	ENST00000265081	NM_002439.4	324	tCa/tTa	6/24	0.853164897430178	3	FACETS	0.763	0.709	0.818	0.381	0.354	0.409	SUBCLONAL	1	TRUE	1	0.890227996508562	3		709	894	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86667950	86667950	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	120	338	2	ENST00000274376.6:c.1714C>G	p.Leu572Val	p.L572V	ENST00000274376	NM_002890.2	572	Ctg/Gtg	13/25	0.853164897430178	3	FACETS	0.845	0.768	0.925	0.423	0.384	0.463	CLONAL	1	TRUE	1	0.890227996508562	3		340	461	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979461	2979461	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	235	582	0	ENST00000396946.4:c.786G>C	p.Lys262Asn	p.K262N	ENST00000396946	NM_032415.4	262	aaG/aaC	6/25	0.86774916711862	4	FACETS	0.857	0.798	0.917	0.286	0.266	0.306	CLONAL	1	TRUE	1	0.890227996508562	4		582	1165	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372128	55372128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	115	345	0	ENST00000297316.4:c.818G>A	p.Arg273Gln	p.R273Q	ENST00000297316	NM_022454.3	273	cGa/cAa	2/2	0.890227996508562	4	FACETS	1	0.943	1	0.352	0.319	0.387	CLONAL	1	TRUE	1	0.890227996508562	4		345	462	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98011567	98011567	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1046396741	NA	P-0027850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	184	552	0	ENST00000289081.3:c.7C>G	p.Gln3Glu	p.Q3E	ENST00000289081	NM_000136.2	3	Caa/Gaa	2/15	1	2	FACETS	0.887	0.827	0.948	0.887	0.827	0.948	CLONAL	1	TRUE	1	0.890227996508562	2		552	466	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961608	18961608	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	AGCAG	novel	NA	P-0027850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	221	658	0	ENST00000262803.5:c.741delinsAGCAG	p.Glu248AlafsTer82	p.E248Afs*82	ENST00000262803	NM_002911.3	247	tcC/tcAGCAG	5/24	1	2	FACETS	0.966	0.908	1	0.966	0.908	1	CLONAL	1	TRUE	1	0.890227996508562	2		658	514	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	180	210	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.835768688718919	2		210	319	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0027851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	4406	641	4	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.835768688718919	10	FACETS	1	0.999	1			1	CLONAL	8	TRUE	NA	0.835768688718919	10		645	5509	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs149840192	NA	P-0027851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5378	142	648	0	ENST00000275493.2:c.866C>A	p.Ala289Asp	p.A289D	ENST00000275493	NM_005228.3	289	gCc/gAc	7/28	0.835768688718919	10	FACETS	0.267	0.242	0.295			1	SUBCLONAL	1	TRUE	NA	0.835768688718919	10		648	5520	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118928	70118929	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0027851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	389	644	0	ENST00000245479.2:c.502dup	p.Asp168GlyfsTer84	p.D168Gfs*84	ENST00000245479	NM_000346.3	167	aag/aaGg	2/3	1	2	FACETS	0.969	0.924	1	0.969	0.924	1	CLONAL	1	TRUE	1	0.835768688718919	2		644	961	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0027852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	98	705	1	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	1	2	FACETS	0.455	0.405	0.51	0.455	0.405	0.51	SUBCLONAL	1	TRUE	1	0.343240031428615	2		706	1254	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098944	178098944	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	56	383	0	ENST00000397062.3:c.101G>C	p.Arg34Pro	p.R34P	ENST00000397062	NM_006164.4	34	cGa/cCa	2/5	1	2	FACETS	0.531	0.454	0.614	0.531	0.454	0.614	SUBCLONAL	1	TRUE	1	0.343240031428615	2		383	615	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191385	185191385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	200	683	0	ENST00000265026.3:c.2266G>A	p.Asp756Asn	p.D756N	ENST00000265026	NM_004721.4	756	Gac/Aac	11/14	0.343240031428615	3	FACETS	1	0.928	1	0.502	0.464	0.542	CLONAL	1	TRUE	1	0.343240031428615	3		683	1360	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933432	100933432	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	81	346	0	ENST00000325455.5:c.1958C>A	p.Ala653Asp	p.A653D	ENST00000325455	NM_001202474.3	653	gCt/gAt	4/8	1	2	FACETS	0.678	0.597	0.765	0.678	0.597	0.765	SUBCLONAL	1	TRUE	1	0.343240031428615	2		346	696	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574035	7574035	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0027852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	101	630	1	ENST00000269305.4:c.994-2A>T		p.X332_splice	ENST00000269305	NM_001126112.2	332			1	2	FACETS	0.535	0.476	0.597	0.535	0.476	0.597	SUBCLONAL	1	TRUE	1	0.343240031428615	2		631	1101	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120535178	120535178	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0027852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	36	301	0	ENST00000229340.5:c.478-1G>C		p.X160_splice	ENST00000229340	NM_006861.6	160			1	2	FACETS	0.333	0.273	0.401	0.333	0.273	0.401	SUBCLONAL	1	TRUE	1	0.343240031428615	2		301	630	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437359	110437359	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	12	45	0	ENST00000375856.3:c.1042G>T	p.Ala348Ser	p.A348S	ENST00000375856	NM_003749.2	348	Gcc/Tcc	1/2	1	2	FACETS	0.51	0.36	0.693	0.51	0.36	0.693	SUBCLONAL	1	TRUE	1	0.343240031428615	2		45	137	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16097873	16097873	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	26	194	0	ENST00000268712.3:c.11C>T	p.Ser4Leu	p.S4L	ENST00000268712	NM_006311.3	4	tCa/tTa	2/46	1	2	FACETS	0.411	0.325	0.509	0.411	0.325	0.509	SUBCLONAL	1	TRUE	1	0.343240031428615	2		194	369	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553499	29553499	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	69	578	0	ENST00000356175.3:c.2048C>G	p.Ala683Gly	p.A683G	ENST00000356175	NM_000267.3	683	gCc/gGc	18/57	1	2	FACETS	0.337	0.292	0.386	0.337	0.292	0.386	SUBCLONAL	1	TRUE	1	0.343240031428615	2		578	1192	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657360	29657360	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	79	698	0	ENST00000356175.3:c.5593T>G	p.Leu1865Val	p.L1865V	ENST00000356175	NM_000267.3	1865	Tta/Gta	38/57	1	2	FACETS	0.534	0.469	0.604	0.534	0.469	0.604	SUBCLONAL	1	TRUE	1	0.343240031428615	2		698	862	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272495	15272495	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	67	699	1	ENST00000263388.2:c.5944G>A	p.Glu1982Lys	p.E1982K	ENST00000263388	NM_000435.2	1982	Gag/Aag	33/33	1	2	FACETS	0.351	0.304	0.403	0.351	0.304	0.403	SUBCLONAL	1	TRUE	1	0.343240031428615	2		700	1111	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376350	15376350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201267392	NA	P-0027852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1260	191	853	1	ENST00000263377.2:c.664C>T	p.Pro222Ser	p.P222S	ENST00000263377	NM_058243.2	222	Cct/Tct	5/20	1	2	FACETS	0.767	0.707	0.83	0.767	0.707	0.83	SUBCLONAL	1	TRUE	1	0.343240031428615	2		854	1451	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374336	31374336	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs769854649	NA	P-0027852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	148	599	0	ENST00000328111.2:c.335C>G	p.Ser112Cys	p.S112C	ENST00000328111	NM_006892.3	112	tCc/tGc	5/23	NA	2	FACETS	0.77	0.702	0.842			1	INDETERMINATE	1	TRUE	NA	0.343240031428615	2		599	1120	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590490	67590490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	56	362	1	ENST00000274335.5:c.1552G>A	p.Glu518Lys	p.E518K	ENST00000274335		518	Gag/Aag	11/15	1	2	FACETS	0.585	0.501	0.676	0.585	0.501	0.676	SUBCLONAL	1	TRUE	1	0.343240031428615	2		363	558	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658367	117658367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1200612813	NA	P-0027852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	53	759	0	ENST00000368508.3:c.5216G>A	p.Ser1739Asn	p.S1739N	ENST00000368508	NM_002944.2	1739	aGc/aAc	31/43	1	2	FACETS	0.386	0.328	0.45	0.386	0.328	0.45	SUBCLONAL	1	TRUE	1	0.343240031428615	2		759	800	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274189	10274189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367543129	NA	P-0027853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	158	387	1	ENST00000330684.3:c.80C>T	p.Ala27Val	p.A27V	ENST00000330684	NM_001134407.1	27	gCg/gTg	2/13	0.682490204741848	4	FACETS	1	0.965	1	0.545	0.5	0.591	CLONAL	1	TRUE	2	0.695017191061723	4		388	707	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843749	156843749	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	586	722	1	ENST00000524377.1:c.1175C>T	p.Pro392Leu	p.P392L	ENST00000524377	NM_002529.3	392	cCt/cTt	8/17	0.663164697316134	4	FACETS	1	0.993	1	0.563	0.543	0.584	CLONAL	2	TRUE	0	0.695017191061723	4		723	1269	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144121	11144121	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	245	627	1	ENST00000358026.2:c.3702C>A	p.Phe1234Leu	p.F1234L	ENST00000358026	NM_001128849.1	1234	ttC/ttA	26/36	0.695017191061723	3	FACETS	0.977	0.914	1	0.489	0.457	0.521	CLONAL	1	TRUE	1	0.695017191061723	3		628	972	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47205366	47205366	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	165	361	0	ENST00000409792.3:c.49G>C	p.Asp17His	p.D17H	ENST00000409792	NM_014159.6	17	Gac/Cac	1/21	0.695017191061723	2	FACETS	1	0.972	1	0.548	0.509	0.589	CLONAL	1	TRUE	0	0.695017191061723	2		361	433	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0027854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	204	529	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.185265134850404	2	FACETS	1	0.991	1	0.73	0.679	0.783	INDETERMINATE	1	TRUE	0	0.358729477598008	2		529	779	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0027854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	180	603	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.358729477598008	1	FACETS	0.985	0.909	1	0.985	0.909	1	CLONAL	1	TRUE	0	0.358729477598008	1		604	836	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034427	47034427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	319	289	1	ENST00000377604.3:c.512G>A	p.Arg171Gln	p.R171Q	ENST00000377604	NM_001204468.1	171	cGg/cAg	6/24	0.350511035465528	2	FACETS	0.912	0.869	0.955			1	CLONAL	3	TRUE	NA	0.358729477598008	2		290	650	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0027854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	100	511	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.358729477598008	1	FACETS	0.843	0.755	0.935	0.843	0.755	0.935	CLONAL	1	TRUE	0	0.358729477598008	1		511	543	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0027854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	65	536	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.185443375890565	1	FACETS	0.38	0.328	0.436	0.38	0.328	0.436	INDETERMINATE	1	TRUE	0	0.358729477598008	1		536	783	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247168	153247168	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1560758208	NA	P-0027854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	91	298	0	ENST00000281708.4:c.1634A>G	p.Tyr545Cys	p.Y545C	ENST00000281708	NM_033632.3	545	tAt/tGt	10/12	0.185443375890565	1	FACETS	0.884	0.788	0.985	0.884	0.788	0.985	INDETERMINATE	1	TRUE	0	0.358729477598008	1		298	471	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468282	50468282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	84	528	0	ENST00000331340.3:c.1517C>T	p.Ser506Leu	p.S506L	ENST00000331340	NM_006060.4	506	tCg/tTg	8/8	0.185443375890565	1	FACETS	0.494	0.436	0.557	0.494	0.436	0.557	INDETERMINATE	1	TRUE	0	0.358729477598008	1		528	778	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687289	117687289	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	91	406	0	ENST00000368508.3:c.2762C>A	p.Ala921Asp	p.A921D	ENST00000368508	NM_002944.2	921	gCc/gAc	18/43	1	2	FACETS	0.821	0.73	0.918	0.821	0.73	0.918	CLONAL	1	TRUE	1	0.358729477598008	2		406	618	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739470	145739470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747895651	NA	P-0027854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	92	559	0	ENST00000428558.2:c.1900G>A	p.Val634Met	p.V634M	ENST00000428558	NM_004260.3	634	Gtg/Atg	12/22	0.185265134850404	2	FACETS	0.524	0.465	0.588	0.262	0.232	0.294	INDETERMINATE	1	TRUE	0	0.358729477598008	2		559	978	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0027855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	189	564	2	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.45817673414835	1	FACETS	0.838	0.776	0.902	0.838	0.776	0.902	CLONAL	1	TRUE	0	0.45817673414835	1		566	759	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584352	39584352	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	104	338	2	ENST00000262039.4:c.1017G>T	p.Trp339Cys	p.W339C	ENST00000262039	NM_002647.2	339	tgG/tgT	10/25	1	2	FACETS	0.932	0.839	1	0.932	0.839	1	CLONAL	1	TRUE	1	0.45817673414835	2		340	487	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281778	39281778	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519963	NA	P-0027855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	151	394	0	ENST00000402219.2:c.697A>T	p.Asn233Tyr	p.N233Y	ENST00000402219	NM_005633.3	233	Aat/Tat	5/23	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.45817673414835	2		394	602	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610162	10610162	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	219	654	0	ENST00000171111.5:c.548A>G	p.Asn183Ser	p.N183S	ENST00000171111	NM_203500.1	183	aAt/aGt	2/6	0.45817673414835	1	FACETS	0.919	0.857	0.983	0.919	0.857	0.983	CLONAL	1	TRUE	0	0.45817673414835	1		654	802	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597433	52597433	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	134	543	0	ENST00000394830.3:c.3877G>T	p.Glu1293Ter	p.E1293*	ENST00000394830	NM_018313.4	1293	Gag/Tag	25/30	1	2	FACETS	0.728	0.662	0.798	0.728	0.662	0.798	SUBCLONAL	1	TRUE	1	0.45817673414835	2		543	803	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538867	187538867	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	98	220	0	ENST00000441802.2:c.8873T>C	p.Ile2958Thr	p.I2958T	ENST00000441802	NM_005245.3	2958	aTa/aCa	10/27	0.45817673414835	1	FACETS	0.984	0.887	1	0.984	0.887	1	CLONAL	1	TRUE	0	0.45817673414835	1		220	335	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528776	8528776	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	87	310	0	ENST00000356435.5:c.356A>T	p.Asp119Val	p.D119V	ENST00000356435		119	gAt/gTt	4/35	1	2	FACETS	0.842	0.749	0.941	0.842	0.749	0.941	CLONAL	1	TRUE	1	0.45817673414835	2		310	451	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955563	48955600	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCTTGCATGGCTCTCAGTAAGTAGCTAAATAATTGAA	CCCTTGCATGGCTCTCAGTAAGTAGCTAAATAATTGAA	-	novel	NA	P-0027855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	98	472	0	ENST00000267163.4:c.1679_1695+21del		p.X560_splice	ENST00000267163	NM_000321.2	560		17/27	0.45817673414835	1	FACETS	0.65	0.582	0.722	0.65	0.582	0.722	SUBCLONAL	1	TRUE	0	0.45817673414835	1		472	507	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056308	27056308	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	70	440	0	ENST00000324856.7:c.1304del	p.Gln435ArgfsTer184	p.Q435Rfs*184	ENST00000324856	NM_006015.4	435	cAg/cg	2/20	0.128460585104405	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.19	1		440	583	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550345	29550467	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAAAACTAAGCTTCTCTAAACTTGTATTCATTATGGGAGAATGCCATTCTTATGTCTGGTTATATCTGCATTAGGTTATTGATGATGCTAGTAACAATGAACTTTATGTTACTGCAGCTCACA	AAAAACTAAGCTTCTCTAAACTTGTATTCATTATGGGAGAATGCCATTCTTATGTCTGGTTATATCTGCATTAGGTTATTGATGATGCTAGTAACAATGAACTTTATGTTACTGCAGCTCACA	-	novel	NA	P-0027856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	25	35	0	ENST00000356175.3:c.1722-115_1729del		p.X574_splice	ENST00000356175	NM_000267.3	574		16/57	1	2	FACETS	1	0.883	1	1	0.965	1	CLONAL	3	TRUE	1	0.19	2		35	78	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589586	67589595	+	protein_altering_variant	In_Frame_Del	DEL	ATGAATATAA	ATGAATATAA	C	novel	NA	P-0027856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	35	327	0	ENST00000274335.5:c.1349_1358delinsC	p.His450_Asn453delinsPro	p.H450_N453delinsP	ENST00000274335		450	cATGAATATAAc/cCc	10/15	1	2	FACETS	0.975	0.8	1	0.975	0.8	1	CLONAL	1	TRUE	1	0.19	2		327	378	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	179	600	6	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	0.74415147913301	2		606	437	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	192	795	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.92	0.857	0.984	0.92	0.857	0.984	CLONAL	1	TRUE	1	0.74415147913301	2		801	561	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	282	846	1	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	0.74415147913301	3	FACETS	1	0.993	1	0.696	0.657	0.735	CLONAL	1	TRUE	1	0.74415147913301	3		847	747	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	88	661	2	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.497	0.442	0.555	0.497	0.442	0.555	SUBCLONAL	1	TRUE	1	0.74415147913301	2		663	476	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905061	50905061	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	207	565	0	ENST00000440232.2:c.347del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	115	Ccc/cc	4/27	0.74415147913301	3	FACETS	0.79	0.741	0.84	0.79	0.741	0.84	SUBCLONAL	2	TRUE	1	0.74415147913301	3		565	483	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346220	152346220	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	96	701	7	ENST00000359321.1:c.350del	p.Leu117TrpfsTer17	p.L117Wfs*17	ENST00000359321	NM_005431.1	117	tTg/tg	3/3	1	2	FACETS	0.505	0.451	0.562	0.505	0.451	0.562	SUBCLONAL	1	TRUE	1	0.74415147913301	2		708	511	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	55	609	1	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.407	0.35	0.47	0.407	0.35	0.47	SUBCLONAL	1	TRUE	1	0.74415147913301	2		610	363	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	84	611	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.512	0.454	0.573	0.512	0.454	0.573	SUBCLONAL	1	TRUE	1	0.74415147913301	2		611	441	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	68	496	3	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.593	0.52	0.671	0.593	0.52	0.671	SUBCLONAL	1	TRUE	1	0.74415147913301	2		499	308	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966873	25966873	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1271466699	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	80	512	2	ENST00000435504.4:c.2333del	p.Pro778GlnfsTer21	p.P778Qfs*21	ENST00000435504		778	cCa/ca	13/13	1	2	FACETS	0.591	0.523	0.662	0.591	0.523	0.662	SUBCLONAL	1	TRUE	1	0.74415147913301	2		514	364	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	56	463	2	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	0.413	0.356	0.476	0.413	0.356	0.476	SUBCLONAL	1	TRUE	1	0.74415147913301	2		465	364	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776535	9776535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	108	815	0	ENST00000377346.4:c.638C>T	p.Pro213Leu	p.P213L	ENST00000377346	NM_005026.3	213	cCg/cTg	6/24	1	2	FACETS	0.606	0.547	0.668	0.606	0.547	0.668	SUBCLONAL	1	TRUE	1	0.74415147913301	2		815	479	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257572	16257572	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs750074484	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	102	702	0	ENST00000375759.3:c.4837A>G	p.Thr1613Ala	p.T1613A	ENST00000375759	NM_015001.2	1613	Aca/Gca	11/15	1	2	FACETS	0.592	0.532	0.655	0.592	0.532	0.655	SUBCLONAL	1	TRUE	1	0.74415147913301	2		702	463	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023904	27023904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1232964733	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	15	86	0	ENST00000324856.7:c.1015del	p.Ala339LeufsTer24	p.A339Lfs*24	ENST00000324856	NM_006015.4	337	tGg/tg	1/20	1	2	FACETS	0.51	0.38	0.66	0.51	0.38	0.66	SUBCLONAL	1	TRUE	1	0.74415147913301	2		86	79	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099480	27099480	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	70	384	0	ENST00000324856.7:c.3715+2T>C		p.X1239_splice	ENST00000324856	NM_006015.4	1239			1	2	FACETS	0.633	0.557	0.714	0.633	0.557	0.714	SUBCLONAL	1	TRUE	1	0.74415147913301	2		384	297	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43817931	43817931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3820551	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	96	670	1	ENST00000372470.3:c.1610G>A	p.Arg537Gln	p.R537Q	ENST00000372470	NM_005373.2	537	cGg/cAg	11/12	1	2	FACETS	0.545	0.488	0.606	0.545	0.488	0.606	SUBCLONAL	1	TRUE	1	0.74415147913301	2		671	473	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797230	45797230	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs587781628	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	71	571	0	ENST00000450313.1:c.1187-2A>G		p.X396_splice	ENST00000450313	NM_012222.2	396			1	2	FACETS	0.591	0.52	0.666	0.591	0.52	0.666	SUBCLONAL	1	TRUE	1	0.74415147913301	2		571	323	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797710	45797710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	99	736	2	ENST00000450313.1:c.982G>A	p.Asp328Asn	p.D328N	ENST00000450313	NM_012222.2	328	Gac/Aac	11/16	1	2	FACETS	0.557	0.499	0.617	0.557	0.499	0.617	SUBCLONAL	1	TRUE	1	0.74415147913301	2		738	478	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743505	46743507	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs768106067	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	58	551	0	ENST00000371975.4:c.1889_1891del	p.Lys630del	p.K630del	ENST00000371975	NM_003579.3	629	gAGAag/gag	17/18	1	2	FACETS	0.405	0.349	0.465	0.405	0.349	0.465	SUBCLONAL	1	TRUE	1	0.74415147913301	2		551	385	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161326487	161326487	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	81	569	0	ENST00000367975.2:c.262T>C	p.Ser88Pro	p.S88P	ENST00000367975	NM_003001.3	88	Tcg/Ccg	5/6	1	2	FACETS	0.535	0.474	0.6	0.535	0.474	0.6	SUBCLONAL	1	TRUE	1	0.74415147913301	2		569	407	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659789	88659789	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs762900005	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	174	566	2	ENST00000372037.3:c.441del	p.Phe147LeufsTer18	p.F147Lfs*18	ENST00000372037	NM_004329.2	146	Ttt/tt	7/13	0.38261049448631	2	FACETS	1	0.975	1	0.549	0.511	0.587	INDETERMINATE	1	TRUE	0	0.74415147913301	2		568	426	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742865	17742865	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	73	625	3	ENST00000250003.3:c.773G>A	p.Arg258His	p.R258H	ENST00000250003	NM_002478.4	258	cGc/cAc	3/3	1	2	FACETS	0.535	0.47	0.603	0.535	0.47	0.603	SUBCLONAL	1	TRUE	1	0.74415147913301	2		628	367	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577137	64577137	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	118	741	1	ENST00000312049.6:c.445G>A	p.Gly149Ser	p.G149S	ENST00000312049	NM_130799.2	149	Ggc/Agc	2/10	1	2	FACETS	0.63	0.572	0.692	0.63	0.572	0.692	SUBCLONAL	1	TRUE	1	0.74415147913301	2		742	503	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999479	100999479	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1324015244	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	70	810	0	ENST00000325455.5:c.323G>T	p.Ser108Ile	p.S108I	ENST00000325455	NM_001202474.3	108	aGc/aTc	1/8	1	2	FACETS	0.361	0.315	0.411	0.361	0.315	0.411	SUBCLONAL	1	TRUE	1	0.74415147913301	2		810	521	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204662	108204664	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	30	455	0	ENST00000278616.4:c.7980_7982del	p.Glu2660del	p.E2660del	ENST00000278616	NM_000051.3	2659	ttAGAa/tta	54/63	1	2	FACETS	0.263	0.212	0.32	0.263	0.212	0.32	SUBCLONAL	1	TRUE	1	0.74415147913301	2		455	307	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	430192	430192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745469846	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	47	503	2	ENST00000399788.2:c.2510C>T	p.Pro837Leu	p.P837L	ENST00000399788	NM_001042603.1	837	cCg/cTg	18/28	1	2	FACETS	0.314	0.265	0.368	0.314	0.265	0.368	SUBCLONAL	1	TRUE	1	0.74415147913301	2		505	402	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244454	46244454	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs751704736	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	84	551	0	ENST00000334344.6:c.2552del	p.Pro851HisfsTer4	p.P851Hfs*4	ENST00000334344	NM_152641.2	850	Ccc/cc	15/21	1	2	FACETS	0.569	0.505	0.636	0.569	0.505	0.636	SUBCLONAL	1	TRUE	1	0.74415147913301	2		551	397	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416545	49416545	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	89	604	0	ENST00000301067.7:c.16166G>T	p.Arg5389Leu	p.R5389L	ENST00000301067	NM_003482.3	5389	cGg/cTg	51/54	1	2	FACETS	0.525	0.467	0.585	0.525	0.467	0.585	SUBCLONAL	1	TRUE	1	0.74415147913301	2		604	456	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	111	821	5	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.556	0.501	0.613	0.556	0.501	0.613	SUBCLONAL	1	TRUE	1	0.74415147913301	2		826	537	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856064	111856064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs933970612	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	54	337	0	ENST00000341259.2:c.115C>T	p.Arg39Trp	p.R39W	ENST00000341259	NM_005475.2	39	Cgg/Tgg	2/8	1	2	FACETS	0.607	0.524	0.696	0.607	0.524	0.696	SUBCLONAL	1	TRUE	1	0.74415147913301	2		337	239	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	78	675	9	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.485	0.428	0.546	0.485	0.428	0.546	SUBCLONAL	1	TRUE	1	0.74415147913301	2		684	432	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219860	133219860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758114596	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	92	661	0	ENST00000320574.5:c.4501G>A	p.Gly1501Arg	p.G1501R	ENST00000320574	NM_006231.2	1501	Ggg/Agg	35/49	1	2	FACETS	0.552	0.493	0.614	0.552	0.493	0.614	SUBCLONAL	1	TRUE	1	0.74415147913301	2		661	448	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235942	133235942	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555225652	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	85	567	0	ENST00000320574.5:c.3214G>A	p.Ala1072Thr	p.A1072T	ENST00000320574	NM_006231.2	1072	Gca/Aca	26/49	1	2	FACETS	0.533	0.473	0.596	0.533	0.473	0.596	SUBCLONAL	1	TRUE	1	0.74415147913301	2		567	429	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914860	32914860	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	83	508	0	ENST00000380152.3:c.6368A>G	p.Glu2123Gly	p.E2123G	ENST00000380152		2123	gAa/gGa	11/27	1	2	FACETS	0.554	0.491	0.62	0.554	0.491	0.62	SUBCLONAL	1	TRUE	1	0.74415147913301	2		508	403	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066895	30066895	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	49	611	0	ENST00000331968.5:c.2236A>G	p.Thr746Ala	p.T746A	ENST00000331968	NM_002742.2	746	Acc/Gcc	16/18	1	2	FACETS	0.289	0.245	0.337	0.289	0.245	0.337	SUBCLONAL	1	TRUE	1	0.74415147913301	2		611	456	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591743	38591743	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	66	411	0	ENST00000299084.4:c.205del	p.Met69TrpfsTer52	p.M69Wfs*52	ENST00000299084	NM_152594.2	68	Aaa/aa	2/7	1	2	FACETS	0.561	0.491	0.636	0.561	0.491	0.636	SUBCLONAL	1	TRUE	1	0.74415147913301	2		411	316	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989087	41989087	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	92	771	0	ENST00000219905.7:c.1879C>T	p.Arg627Ter	p.R627*	ENST00000219905	NM_001164273.1	627	Cga/Tga	3/24	1	2	FACETS	0.561	0.501	0.624	0.561	0.501	0.624	SUBCLONAL	1	TRUE	1	0.74415147913301	2		771	441	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007675	45007675	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	67	474	0	ENST00000558401.1:c.122A>T	p.Asn41Ile	p.N41I	ENST00000558401	NM_004048.2	41	aAt/aTt	2/4	1	2	FACETS	0.496	0.433	0.563	0.496	0.433	0.563	SUBCLONAL	1	TRUE	1	0.74415147913301	2		474	363	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007824	45007825	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	89	563	0	ENST00000558401.1:c.276dup	p.Thr93HisfsTer2	p.T93Hfs*2	ENST00000558401	NM_004048.2	91	acc/aCcc	2/4	1	2	FACETS	0.476	0.423	0.531	0.476	0.423	0.531	SUBCLONAL	1	TRUE	1	0.74415147913301	2		563	503	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434566	99434566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773552392	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	74	500	0	ENST00000268035.6:c.653C>T	p.Thr218Met	p.T218M	ENST00000268035	NM_000875.3	218	aCg/aTg	3/21	1	2	FACETS	0.467	0.41	0.527	0.467	0.41	0.527	SUBCLONAL	1	TRUE	1	0.74415147913301	2		500	426	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348211	348211	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1458136153	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	112	687	1	ENST00000262320.3:c.1295del	p.Pro432GlnfsTer48	p.P432Qfs*48	ENST00000262320	NM_003502.3	432	cCa/ca	6/11	1	2	FACETS	0.654	0.592	0.72	0.654	0.592	0.72	SUBCLONAL	1	TRUE	1	0.74415147913301	2		688	460	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640044	3640044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	132	878	0	ENST00000294008.3:c.3595G>A	p.Ala1199Thr	p.A1199T	ENST00000294008	NM_032444.2	1199	Gca/Aca	12/15	1	2	FACETS	0.609	0.554	0.665	0.609	0.554	0.665	SUBCLONAL	1	TRUE	1	0.74415147913301	2		878	583	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786767	3786767	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	65	583	0	ENST00000262367.5:c.4444T>C	p.Tyr1482His	p.Y1482H	ENST00000262367	NM_004380.2	1482	Tac/Cac	27/31	1	2	FACETS	0.421	0.366	0.48	0.421	0.366	0.48	SUBCLONAL	1	TRUE	1	0.74415147913301	2		583	415	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934825	9934825	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	95	707	0	ENST00000330684.3:c.1465G>T	p.Val489Phe	p.V489F	ENST00000330684	NM_001134407.1	489	Gtt/Ttt	6/13	1	2	FACETS	0.532	0.475	0.592	0.532	0.475	0.592	SUBCLONAL	1	TRUE	1	0.74415147913301	2		707	480	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020559	14020559	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1567243770	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	80	638	0	ENST00000311895.7:c.530A>G	p.His177Arg	p.H177R	ENST00000311895	NM_005236.2	177	cAt/cGt	3/11	1	2	FACETS	0.502	0.444	0.564	0.502	0.444	0.564	SUBCLONAL	1	TRUE	1	0.74415147913301	2		638	428	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831936	72831936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs181722888	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	108	868	3	ENST00000268489.5:c.4645G>A	p.Val1549Ile	p.V1549I	ENST00000268489	NM_006885.3	1549	Gtc/Atc	9/10	1	2	FACETS	0.508	0.457	0.562	0.508	0.457	0.562	SUBCLONAL	1	TRUE	1	0.74415147913301	2		871	571	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	33	307	0	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.441	0.362	0.528	0.441	0.362	0.528	SUBCLONAL	1	TRUE	1	0.74415147913301	2		307	201	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81914559	81914559	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	61	488	0	ENST00000359376.3:c.692+1G>A		p.X231_splice	ENST00000359376	NM_002661.3	231			1	2	FACETS	0.462	0.4	0.528	0.462	0.4	0.528	SUBCLONAL	1	TRUE	1	0.74415147913301	2		488	355	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346433	89346433	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764262189	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	71	709	0	ENST00000301030.4:c.6517G>A	p.Val2173Ile	p.V2173I	ENST00000301030	NM_001256183.1	2173	Gtc/Atc	9/13	1	2	FACETS	0.422	0.369	0.479	0.422	0.369	0.479	SUBCLONAL	1	TRUE	1	0.74415147913301	2		709	452	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346961	89346961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775491352	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	52	377	1	ENST00000301030.4:c.5989G>A	p.Ala1997Thr	p.A1997T	ENST00000301030	NM_001256183.1	1997	Gcg/Acg	9/13	1	2	FACETS	0.57	0.49	0.656	0.57	0.49	0.656	SUBCLONAL	1	TRUE	1	0.74415147913301	2		378	245	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964937	15964937	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	103	649	0	ENST00000268712.3:c.5659T>G	p.Phe1887Val	p.F1887V	ENST00000268712	NM_006311.3	1887	Ttt/Gtt	37/46	1	2	FACETS	0.633	0.57	0.7	0.633	0.57	0.7	SUBCLONAL	1	TRUE	1	0.74415147913301	2		649	437	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687472	37687472	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	49	362	0	ENST00000447079.4:c.4382del	p.Gly1461AlafsTer38	p.G1461Afs*38	ENST00000447079	NM_015083.1	1459	tGg/tg	14/14	1	2	FACETS	0.565	0.483	0.653	0.565	0.483	0.653	SUBCLONAL	1	TRUE	1	0.74415147913301	2		362	233	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41219706	41219706	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80357169	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	85	471	0	ENST00000357654.3:c.4993G>A	p.Val1665Met	p.V1665M	ENST00000357654	NM_007294.3	1665	Gtg/Atg	16/23	1	2	FACETS	0.629	0.56	0.702	0.629	0.56	0.702	SUBCLONAL	1	TRUE	1	0.74415147913301	2		471	363	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007580	62007580	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778771873	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	113	701	3	ENST00000392795.3:c.287G>A	p.Arg96His	p.R96H	ENST00000392795	NM_001039933.1	96	cGc/cAc	3/6	1	2	FACETS	0.587	0.531	0.647	0.587	0.531	0.647	SUBCLONAL	1	TRUE	1	0.74415147913301	2		704	517	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368208	45368208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	64	413	0	ENST00000262160.6:c.1394G>A	p.Ser465Asn	p.S465N	ENST00000262160	NM_005901.5	465	aGc/aAc	11/11	1	2	FACETS	0.485	0.422	0.552	0.485	0.422	0.552	SUBCLONAL	1	TRUE	1	0.74415147913301	2		413	355	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573505	48573506	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	44	421	0	ENST00000342988.3:c.94_95del	p.Ser32Ter	p.S32*	ENST00000342988	NM_005359.5	30	gGA/g	2/12	1	2	FACETS	0.383	0.322	0.449	0.383	0.322	0.449	SUBCLONAL	1	TRUE	1	0.74415147913301	2		421	309	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604668	48604668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	52	457	1	ENST00000342988.3:c.1490G>A	p.Arg497His	p.R497H	ENST00000342988	NM_005359.5	497	cGc/cAc	12/12	1	2	FACETS	0.427	0.366	0.494	0.427	0.366	0.494	SUBCLONAL	1	TRUE	1	0.74415147913301	2		458	327	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985439	60985439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	100	741	1	ENST00000333681.4:c.461G>A	p.Gly154Asp	p.G154D	ENST00000333681		154	gGt/gAt	2/3	1	2	FACETS	0.471	0.421	0.523	0.471	0.421	0.523	SUBCLONAL	1	TRUE	1	0.74415147913301	2		742	571	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1627410	1627410	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs535762587	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	107	769	0	ENST00000344749.5:c.314G>A	p.Arg105Gln	p.R105Q	ENST00000344749	NM_001136139.2	105	cGg/cAg	6/19	1	2	FACETS	0.612	0.552	0.675	0.612	0.552	0.675	SUBCLONAL	1	TRUE	1	0.74415147913301	2		769	470	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610153	10610153	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	123	753	1	ENST00000171111.5:c.557G>A	p.Gly186Asp	p.G186D	ENST00000171111	NM_203500.1	186	gGc/gAc	2/6	1	2	FACETS	0.644	0.586	0.706	0.644	0.586	0.706	SUBCLONAL	1	TRUE	1	0.74415147913301	2		754	513	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145789	11145789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	85	636	0	ENST00000358026.2:c.4151C>T	p.Thr1384Met	p.T1384M	ENST00000358026	NM_001128849.1	1384	aCg/aTg	29/36	1	2	FACETS	0.518	0.46	0.58	0.518	0.46	0.58	SUBCLONAL	1	TRUE	1	0.74415147913301	2		636	441	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272513	15272513	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	70	576	0	ENST00000263388.2:c.5926del	p.Leu1976TyrfsTer36	p.L1976Yfs*36	ENST00000263388	NM_000435.2	1976	Cta/ta	33/33	1	2	FACETS	0.53	0.465	0.599	0.53	0.465	0.599	SUBCLONAL	1	TRUE	1	0.74415147913301	2		576	355	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966819	18966819	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	108	796	0	ENST00000262803.5:c.1630C>T	p.Leu544Phe	p.L544F	ENST00000262803	NM_002911.3	544	Ctc/Ttc	12/24	1	2	FACETS	0.539	0.485	0.595	0.539	0.485	0.595	SUBCLONAL	1	TRUE	1	0.74415147913301	2		796	539	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976541	18976541	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	25	735	1	ENST00000262803.5:c.3191C>A	p.Pro1064His	p.P1064H	ENST00000262803	NM_002911.3	1064	cCt/cAt	22/24	1	2	FACETS	0.135	0.106	0.169	0.135	0.106	0.169	SUBCLONAL	1	TRUE	1	0.74415147913301	2		736	497	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224135	36224135	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	68	570	0	ENST00000222270.7:c.6685C>A	p.Pro2229Thr	p.P2229T	ENST00000222270	NM_014727.1	2229	Ccc/Acc	28/37	0.74415147913301	3	FACETS	0.452	0.393	0.515	0.226	0.196	0.258	SUBCLONAL	1	TRUE	1	0.74415147913301	3		570	555	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752873	42752873	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	88	816	0	ENST00000222329.4:c.1391del	p.Pro464LeufsTer67	p.P464Lfs*67	ENST00000222329	NM_006494.2	464	cCt/ct	4/4	0.74415147913301	3	FACETS	0.419	0.371	0.471	0.21	0.185	0.236	SUBCLONAL	1	TRUE	1	0.74415147913301	3		816	774	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731488	47731488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	12	60	0	ENST00000449228.1:c.304C>T	p.Arg102Cys	p.R102C	ENST00000449228	NM_001127240.2	102	Cgt/Tgt	2/4	0.74415147913301	3	FACETS	0.738	0.531	0.978	0.369	0.265	0.489	CLONAL	1	TRUE	1	0.74415147913301	3		60	60	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47735818	47735818	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	111	718	0	ENST00000449228.1:c.42G>T	p.Gln14His	p.Q14H	ENST00000449228	NM_001127240.2	14	caG/caT	1/4	0.74415147913301	3	FACETS	0.491	0.441	0.544	0.245	0.22	0.272	SUBCLONAL	1	TRUE	1	0.74415147913301	3		718	834	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906475	50906475	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	83	683	0	ENST00000440232.2:c.1136A>C	p.Gln379Pro	p.Q379P	ENST00000440232	NM_002691.3	379	cAg/cCg	9/27	0.74415147913301	3	FACETS	0.504	0.445	0.567	0.252	0.222	0.284	SUBCLONAL	1	TRUE	1	0.74415147913301	3		683	607	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	80	868	3	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	1	2	FACETS	0.435	0.384	0.49	0.435	0.384	0.49	SUBCLONAL	1	TRUE	1	0.74415147913301	2		871	494	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682742	190682742	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	42	340	0	ENST00000441310.2:c.419-1G>T		p.X140_splice	ENST00000441310	NM_000534.4	140			1	2	FACETS	0.47	0.396	0.552	0.47	0.396	0.552	SUBCLONAL	1	TRUE	1	0.74415147913301	2		340	240	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150030	202150030	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs931648756	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	97	673	3	ENST00000358485.4:c.1471C>T	p.Arg491Ter	p.R491*	ENST00000358485	NM_001080125.1	491	Cga/Tga	8/9	1	2	FACETS	0.564	0.505	0.626	0.564	0.505	0.626	SUBCLONAL	1	TRUE	1	0.74415147913301	2		676	462	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251685	212251685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781181705	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	53	392	0	ENST00000342788.4:c.3374C>T	p.Thr1125Ile	p.T1125I	ENST00000342788	NM_005235.2	1125	aCc/aTc	27/28	1	2	FACETS	0.452	0.388	0.522	0.452	0.388	0.522	SUBCLONAL	1	TRUE	1	0.74415147913301	2		392	315	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645527	215645527	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786202366	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	88	657	0	ENST00000260947.4:c.1071A>G	p.Ile357Met	p.I357M	ENST00000260947	NM_000465.2	357	atA/atG	4/11	1	2	FACETS	0.501	0.446	0.56	0.501	0.446	0.56	SUBCLONAL	1	TRUE	1	0.74415147913301	2		657	472	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439569	220439569	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	88	603	1	ENST00000243786.2:c.422G>A	p.Gly141Asp	p.G141D	ENST00000243786	NM_002191.3	141	gGc/gAc	2/2	1	2	FACETS	0.56	0.499	0.625	0.56	0.499	0.625	SUBCLONAL	1	TRUE	1	0.74415147913301	2		604	422	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538380	9538380	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	69	372	0	ENST00000353224.5:c.1618A>C	p.Met540Leu	p.M540L	ENST00000353224	NM_177990.2	540	Atg/Ctg	7/10	1	2	FACETS	0.562	0.493	0.635	0.562	0.493	0.635	SUBCLONAL	1	TRUE	1	0.74415147913301	2		372	330	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958198	54958198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756121188	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	59	589	0	ENST00000312783.6:c.409C>T	p.Arg137Cys	p.R137C	ENST00000312783	NM_198436.1	137	Cgc/Tgc	6/10	1	2	FACETS	0.37	0.319	0.425	0.37	0.319	0.425	SUBCLONAL	1	TRUE	1	0.74415147913301	2		589	429	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564765	41564765	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	94	683	2	ENST00000263253.7:c.4066C>T	p.Arg1356Ter	p.R1356*	ENST00000263253	NM_001429.3	1356	Cga/Tga	25/31	1	2	FACETS	0.493	0.44	0.55	0.493	0.44	0.55	SUBCLONAL	1	TRUE	1	0.74415147913301	2		685	512	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566478	41566478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	98	620	0	ENST00000263253.7:c.4355C>T	p.Pro1452Leu	p.P1452L	ENST00000263253	NM_001429.3	1452	cCt/cTt	27/31	1	2	FACETS	0.55	0.493	0.61	0.55	0.493	0.61	SUBCLONAL	1	TRUE	1	0.74415147913301	2		620	479	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574679	41574679	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	208	743	2	ENST00000263253.7:c.6970del	p.His2324ThrfsTer29	p.H2324Tfs*29	ENST00000263253	NM_001429.3	2322	Ccc/cc	31/31	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.74415147913301	2		745	524	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713565	30713565	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	80	542	0	ENST00000295754.5:c.890T>C	p.Ile297Thr	p.I297T	ENST00000295754	NM_003242.5	297	aTc/aCc	4/7	1	2	FACETS	0.526	0.465	0.59	0.526	0.465	0.59	SUBCLONAL	1	TRUE	1	0.74415147913301	2		542	409	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070349	37070349	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs63750855	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	72	644	1	ENST00000231790.2:c.1489del	p.Arg497GlyfsTer11	p.R497Gfs*11	ENST00000231790	NM_000249.3	495	aCc/ac	13/19	1	2	FACETS	0.47	0.412	0.531	0.47	0.412	0.531	SUBCLONAL	1	TRUE	1	0.74415147913301	2		645	412	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436841	52436841	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1377099523	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	70	718	0	ENST00000460680.1:c.1937A>G	p.Tyr646Cys	p.Y646C	ENST00000460680	NM_004656.3	646	tAt/tGt	15/17	1	2	FACETS	0.463	0.406	0.525	0.463	0.406	0.525	SUBCLONAL	1	TRUE	1	0.74415147913301	2		718	406	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613121	52613121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	85	664	2	ENST00000394830.3:c.3407G>A	p.Gly1136Asp	p.G1136D	ENST00000394830	NM_018313.4	1136	gGc/gAc	22/30	1	2	FACETS	0.533	0.473	0.596	0.533	0.473	0.596	SUBCLONAL	1	TRUE	1	0.74415147913301	2		666	429	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027093	71027093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200629338	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	81	547	1	ENST00000318789.4:c.1234G>A	p.Ala412Thr	p.A412T	ENST00000318789	NM_032682.5	412	Gcc/Acc	15/21	1	2	FACETS	0.494	0.437	0.554	0.494	0.437	0.554	SUBCLONAL	1	TRUE	1	0.74415147913301	2		548	441	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149290678	149290678	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	105	705	0	ENST00000360632.3:c.541T>C	p.Ser181Pro	p.S181P	ENST00000360632	NM_015472.4	181	Tcc/Ccc	3/7	1	2	FACETS	0.522	0.469	0.577	0.522	0.469	0.577	SUBCLONAL	1	TRUE	1	0.74415147913301	2		705	541	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440319	187440319	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	99	609	3	ENST00000232014.4:c.2048C>T	p.Ala683Val	p.A683V	ENST00000232014	NM_001130845.1	683	gCc/gTc	10/10	1	2	FACETS	0.614	0.552	0.68	0.614	0.552	0.68	SUBCLONAL	1	TRUE	1	0.74415147913301	2		612	433	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808398	1808398	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	88	946	0	ENST00000260795.2:c.2156G>A	p.Cys719Tyr	p.C719Y	ENST00000260795		719	tGc/tAc	15/17	1	2	FACETS	0.451	0.401	0.505	0.451	0.401	0.505	SUBCLONAL	1	TRUE	1	0.74415147913301	2		946	524	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1932444	1932444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	111	663	1	ENST00000382891.5:c.1502G>A	p.Arg501His	p.R501H	ENST00000382891	NM_133335.3	501	cGc/cAc	6/22	1	2	FACETS	0.577	0.521	0.636	0.577	0.521	0.636	SUBCLONAL	1	TRUE	1	0.74415147913301	2		664	517	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361115	66361115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	48	367	0	ENST00000273854.3:c.1057G>A	p.Ala353Thr	p.A353T	ENST00000273854	NM_004439.5	353	Gca/Aca	4/18	1	2	FACETS	0.466	0.396	0.541	0.466	0.396	0.541	SUBCLONAL	1	TRUE	1	0.74415147913301	2		367	277	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99823066	99823066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	86	448	0	ENST00000280892.6:c.146C>T	p.Ala49Val	p.A49V	ENST00000280892	NM_001130678.1	49	gCt/gTt	2/7	1	2	FACETS	0.664	0.592	0.74	0.664	0.592	0.74	SUBCLONAL	1	TRUE	1	0.74415147913301	2		448	348	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871206	35871206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	78	506	0	ENST00000303115.3:c.428C>T	p.Ala143Val	p.A143V	ENST00000303115	NM_002185.3	143	gCc/gTc	4/8	0.74415147913301	3	FACETS	0.533	0.469	0.601	0.266	0.234	0.301	SUBCLONAL	1	TRUE	1	0.74415147913301	3		506	540	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522741	67522741	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	38	360	0	ENST00000274335.5:c.244del	p.Ile82SerfsTer32	p.I82Sfs*32	ENST00000274335		80	Aaa/aa	1/15	1	2	FACETS	0.462	0.385	0.547	0.462	0.385	0.547	SUBCLONAL	1	TRUE	1	0.74415147913301	2		360	221	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	48	332	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	1	2	FACETS	0.529	0.451	0.613	0.529	0.451	0.613	SUBCLONAL	1	TRUE	1	0.74415147913301	2		332	244	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672839	86672840	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	59	399	0	ENST00000274376.6:c.2329_2330del	p.Glu777AsnfsTer6	p.E777Nfs*6	ENST00000274376	NM_002890.2	776	AGa/a	17/25	1	2	FACETS	0.575	0.499	0.656	0.575	0.499	0.656	SUBCLONAL	1	TRUE	1	0.74415147913301	2		399	276	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460583	149460583	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	67	627	0	ENST00000286301.3:c.54G>T	p.Gln18His	p.Q18H	ENST00000286301	NM_005211.3	18	caG/caT	3/22	1	2	FACETS	0.44	0.384	0.501	0.44	0.384	0.501	SUBCLONAL	1	TRUE	1	0.74415147913301	2		627	409	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500480	149500480	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778844346	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	91	745	1	ENST00000261799.4:c.2557C>T	p.Arg853Trp	p.R853W	ENST00000261799	NM_002609.3	853	Cgg/Tgg	18/23	1	2	FACETS	0.536	0.478	0.598	0.536	0.478	0.598	SUBCLONAL	1	TRUE	1	0.74415147913301	2		746	456	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052992	180052992	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	89	811	0	ENST00000261937.6:c.1298G>T	p.Ser433Ile	p.S433I	ENST00000261937	NM_182925.4	433	aGc/aTc	10/30	0.116405921266717	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.74415147913301	0		811	495	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323240	31323240	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	81	563	0	ENST00000412585.2:c.749A>G	p.Gln250Arg	p.Q250R	ENST00000412585	NM_005514.6	250	cAg/cGg	4/8	1	2	FACETS	0.5	0.443	0.562	0.5	0.443	0.562	SUBCLONAL	1	TRUE	1	0.74415147913301	2		563	435	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181563	32181563	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	92	812	0	ENST00000375023.3:c.2222G>T	p.Gly741Val	p.G741V	ENST00000375023	NM_004557.3	741	gGc/gTc	14/30	1	2	FACETS	0.515	0.459	0.574	0.515	0.459	0.574	SUBCLONAL	1	TRUE	1	0.74415147913301	2		812	480	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803446	32803446	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	129	719	0	ENST00000374899.4:c.713T>G	p.Leu238Arg	p.L238R	ENST00000374899	NM_018833.2	238	cTc/cGc	4/12	1	2	FACETS	0.609	0.554	0.667	0.609	0.554	0.667	SUBCLONAL	1	TRUE	1	0.74415147913301	2		719	569	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805537	32805539	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	109	794	0	ENST00000374899.4:c.472_474del	p.Phe158del	p.F158del	ENST00000374899	NM_018833.2	158	TTC/-	2/12	1	2	FACETS	0.456	0.41	0.505	0.456	0.41	0.505	SUBCLONAL	1	TRUE	1	0.74415147913301	2		794	642	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	183	692	0	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.74415147913301	2		692	489	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289197	33289197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773142629	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	84	534	0	ENST00000374542.5:c.355C>T	p.Arg119Trp	p.R119W	ENST00000374542	NM_001141970.1	119	Cgg/Tgg	3/8	1	2	FACETS	0.594	0.528	0.664	0.594	0.528	0.664	SUBCLONAL	1	TRUE	1	0.74415147913301	2		534	380	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415703	152415703	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	61	518	0	ENST00000206249.3:c.1553G>T	p.Ser518Ile	p.S518I	ENST00000206249	NM_000125.3	518	aGt/aTt	7/8	1	2	FACETS	0.475	0.412	0.543	0.475	0.412	0.543	SUBCLONAL	1	TRUE	1	0.74415147913301	2		518	345	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468306	50468306	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	89	541	0	ENST00000331340.3:c.1541A>G	p.His514Arg	p.H514R	ENST00000331340	NM_006060.4	514	cAc/cGc	8/8	1	2	FACETS	0.621	0.555	0.691	0.621	0.555	0.691	SUBCLONAL	1	TRUE	1	0.74415147913301	2		541	385	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	54	413	0	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	0.474	0.407	0.546	0.474	0.407	0.546	SUBCLONAL	1	TRUE	1	0.74415147913301	2		413	306	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992721	68992721	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs764112302	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	73	757	6	ENST00000288368.4:c.1693del	p.Ser565ArgfsTer10	p.S565Rfs*10	ENST00000288368	NM_024870.2	562	cgT/cg	16/40	1	2	FACETS	0.464	0.407	0.524	0.464	0.407	0.524	SUBCLONAL	1	TRUE	1	0.74415147913301	2		763	423	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242284	98242284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1288810300	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	81	702	0	ENST00000331920.6:c.1034G>A	p.Gly345Asp	p.G345D	ENST00000331920	NM_000264.3	345	gGc/gAc	7/24	1	2	FACETS	0.449	0.396	0.505	0.449	0.396	0.505	SUBCLONAL	1	TRUE	1	0.74415147913301	2		702	485	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900238	101900238	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs201021249	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	56	498	0	ENST00000374994.4:c.672G>A	p.Trp224Ter	p.W224*	ENST00000374994	NM_004612.2	224	tgG/tgA	4/9	1	2	FACETS	0.475	0.409	0.546	0.475	0.409	0.546	SUBCLONAL	1	TRUE	1	0.74415147913301	2		498	317	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418325	139418325	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377532588	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	83	841	2	ENST00000277541.6:c.247G>A	p.Ala83Thr	p.A83T	ENST00000277541	NM_017617.3	83	Gca/Aca	3/34	1	2	FACETS	0.458	0.405	0.514	0.458	0.405	0.514	SUBCLONAL	1	TRUE	1	0.74415147913301	2		843	487	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932953	39932953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	59	581	0	ENST00000378444.4:c.1646G>A	p.Gly549Asp	p.G549D	ENST00000378444	NM_001123385.1	549	gGc/gAc	4/15	1	2	FACETS	0.429	0.37	0.492	0.429	0.37	0.492	SUBCLONAL	1	TRUE	1	0.74415147913301	2		581	370	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030503	47030503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs933666676	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	90	726	1	ENST00000377604.3:c.278C>T	p.Pro93Leu	p.P93L	ENST00000377604	NM_001204468.1	93	cCg/cTg	4/24	1	2	FACETS	0.488	0.434	0.545	0.488	0.434	0.545	SUBCLONAL	1	TRUE	1	0.74415147913301	2		727	496	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038535	47038535	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	62	759	1	ENST00000377604.3:c.697T>C	p.Cys233Arg	p.C233R	ENST00000377604	NM_001204468.1	233	Tgc/Cgc	8/24	1	2	FACETS	0.351	0.303	0.402	0.351	0.303	0.402	SUBCLONAL	1	TRUE	1	0.74415147913301	2		760	475	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	75	675	2	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	2	FACETS	0.494	0.435	0.557	0.494	0.435	0.557	SUBCLONAL	1	TRUE	1	0.74415147913301	2		677	408	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222308	53222309	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	100	793	0	ENST00000375401.3:c.4523dup	p.Ala1509CysfsTer75	p.A1509Cfs*75	ENST00000375401	NM_004187.3	1508	cct/ccCt	26/26	1	2	FACETS	0.554	0.497	0.614	0.554	0.497	0.614	SUBCLONAL	1	TRUE	1	0.74415147913301	2		793	485	SUCCESS
AR	367	MSKCC	GRCh37	X	66766454	66766454	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	59	373	0	ENST00000374690.3:c.1466G>A	p.Gly489Glu	p.G489E	ENST00000374690	NM_000044.3	489	gGg/gAg	1/8	1	2	FACETS	0.585	0.508	0.667	0.585	0.508	0.667	SUBCLONAL	1	TRUE	1	0.74415147913301	2		373	271	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356450	70356450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502167	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	88	829	1	ENST00000374080.3:c.5345G>A	p.Arg1782His	p.R1782H	ENST00000374080		1782	cGc/cAc	37/45	1	2	FACETS	0.45	0.399	0.503	0.45	0.399	0.503	SUBCLONAL	1	TRUE	1	0.74415147913301	2		830	526	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380260	25380265	+	protein_altering_variant	In_Frame_Ins	INS	TGCACT	TGCACT	GTACTGGTCAAG	novel	NA	P-0027858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	79	618	0	ENST00000311936.3:c.193_198delinsCTTGACCAGTAC	p.Ser65_Ala66delinsLeuAspGlnTyr	p.S65_A66delinsLDQY	ENST00000311936	NM_004985.3	65	AGTGCA/CTTGACCAGTAC	3/5	1	2	FACETS	0.45	0.397	0.506	0.45	0.397	0.506	SUBCLONAL	1	TRUE	1	0.74415147913301	2		618	472	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	125	297	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.166237468612577	3	FACETS	1	0.984	1	0.703	0.641	0.768	INDETERMINATE	1	TRUE	1	0.485551938312698	3		297	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579485	7579485	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs869312782	NA	P-0027864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	218	601	0	ENST00000269305.4:c.202G>T	p.Glu68Ter	p.E68*	ENST00000269305	NM_001126112.2	68	Gag/Tag	4/11	0.485551938312698	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.485551938312698	1		601	663	SUCCESS
APC	324	MSKCC	GRCh37	5	112175600	112175600	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	148	385	0	ENST00000257430.4:c.4312del	p.Thr1438HisfsTer35	p.T1438Hfs*35	ENST00000257430	NM_000038.5	1437	Aaa/aa	16/16	0.485551938312698	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.485551938312698	1		385	416	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9770578	9770578	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	125	660	0	ENST00000377346.4:c.66del	p.Asp23ThrfsTer10	p.D23Tfs*10	ENST00000377346	NM_005026.3	22	gTt/gt	3/24	1	2	FACETS	0.495	0.447	0.545	0.495	0.447	0.545	SUBCLONAL	1	TRUE	1	0.485551938312698	2		660	1041	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577111	7577111	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs786202082	NA	P-0027865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	436	719	2	ENST00000269305.4:c.827C>G	p.Ala276Gly	p.A276G	ENST00000269305	NM_001126112.2	276	gCc/gGc	8/11	0.695040195267112	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.695040195267112	1		721	816	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0027865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	190	358	0	ENST00000267163.4:c.1215+1G>T		p.X405_splice	ENST00000267163	NM_000321.2	405			0.695040195267112	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.695040195267112	1		358	354	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816229	89816229	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	430	760	5	ENST00000389301.3:c.3148G>C	p.Glu1050Gln	p.E1050Q	ENST00000389301	NM_000135.2	1050	Gag/Cag	32/43	0.695040195267112	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.695040195267112	1		765	775	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218521	36218521	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	1284	536	2	ENST00000222270.7:c.4300C>T	p.Gln1434Ter	p.Q1434*	ENST00000222270	NM_014727.1	1434	Cag/Tag	16/37	0.551876633749541	5	FACETS	0.946	0.927	0.965			1	CLONAL	4	TRUE	NA	0.695040195267112	5		538	1995	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124444	94124444	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	75	518	0	ENST00000369303.4:c.139T>A	p.Trp47Arg	p.W47R	ENST00000369303	NM_004440.3	47	Tgg/Agg	2/17	1	2	FACETS	0.31	0.271	0.351	0.31	0.271	0.351	SUBCLONAL	1	TRUE	1	0.695040195267112	2		518	697	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	43	210	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.210953489500267	2		210	290	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913233	NA	P-0027867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	117	756	0	ENST00000451590.1:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000451590	NM_001130442.1	61	cAg/cTg	3/5	0.210953489500267	4	FACETS	1	0.974	1	0.416	0.374	0.46	CLONAL	1	TRUE	1	0.210953489500267	4		756	1077	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566709	212566709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	56	396	0	ENST00000342788.4:c.1472G>A	p.Arg491Lys	p.R491K	ENST00000342788	NM_005235.2	491	aGa/aAa	12/28	1	2	FACETS	0.851	0.728	0.985	0.851	0.728	0.985	CLONAL	1	TRUE	1	0.210953489500267	2		396	624	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169209	119169209	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778158	NA	P-0027867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	71	618	0	ENST00000264033.4:c.2393C>T	p.Ser798Phe	p.S798F	ENST00000264033	NM_005188.3	798	tCc/tTc	15/16	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.210953489500267	2		618	669	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046378	69046378	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375506738	NA	P-0027867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	85	650	0	ENST00000288368.4:c.3851C>T	p.Ala1284Val	p.A1284V	ENST00000288368	NM_024870.2	1284	gCg/gTg	32/40	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.210953489500267	2		650	692	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004206	29004206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	60	484	0	ENST00000282397.4:c.1087C>T	p.Pro363Ser	p.P363S	ENST00000282397	NM_002019.4	363	Ccc/Tcc	8/30	1	2	FACETS	0.861	0.741	0.991	0.861	0.741	0.991	CLONAL	1	TRUE	1	0.210953489500267	2		484	661	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486154	8486154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	76	528	0	ENST00000356435.5:c.2663G>A	p.Gly888Glu	p.G888E	ENST00000356435		888	gGa/gAa	17/35	0.210953489500267	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.210953489500267	1		528	596	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420327	88420327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs548727485	NA	P-0027867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	77	544	0	ENST00000360948.2:c.2359C>T	p.Arg787Cys	p.R787C	ENST00000360948	NM_001012338.2	787	Cgt/Tgt	19/19	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.210953489500267	2		544	636	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262589	16262589	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	76	506	0	ENST00000375759.3:c.9854C>T	p.Pro3285Leu	p.P3285L	ENST00000375759	NM_015001.2	3285	cCt/cTt	11/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.210953489500267	2		506	534	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22412940	22412940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	24	204	1	ENST00000344548.3:c.187G>A	p.Asp63Asn	p.D63N	ENST00000344548	NM_001039802.1	63	Gat/Aat	5/7	1	2	FACETS	0.709	0.556	0.885	0.709	0.556	0.885	SUBCLONAL	1	TRUE	1	0.210953489500267	2		205	321	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235997	133235998	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0027867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	94	668	1	ENST00000320574.5:c.3158_3159delinsTT	p.Ser1053Phe	p.S1053F	ENST00000320574	NM_006231.2	1053	tCC/tTT	26/49	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.210953489500267	2		669	752	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913101	32913101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753244927	NA	P-0027867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	112	646	0	ENST00000380152.3:c.4609G>A	p.Glu1537Lys	p.E1537K	ENST00000380152		1537	Gaa/Aaa	11/27	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.210953489500267	2		646	929	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701895	43701895	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1296419356	NA	P-0027867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	79	429	1	ENST00000382044.4:c.5350C>T	p.Gln1784Ter	p.Q1784*	ENST00000382044	NM_001141980.1	1784	Cag/Tag	25/28	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.210953489500267	2		430	637	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857515	9857515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	52	474	1	ENST00000330684.3:c.3886G>A	p.Val1296Ile	p.V1296I	ENST00000330684	NM_001134407.1	1296	Gtc/Atc	13/13	1	2	FACETS	0.952	0.811	1	0.952	0.811	1	CLONAL	1	TRUE	1	0.210953489500267	2		475	518	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678237	58678237	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	116	749	2	ENST00000305921.3:c.462G>A	p.Trp154Ter	p.W154*	ENST00000305921	NM_003620.3	154	tgG/tgA	1/6	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.210953489500267	2		751	870	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533512	63533512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367624903	NA	P-0027867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	86	722	1	ENST00000307078.5:c.1642G>A	p.Glu548Lys	p.E548K	ENST00000307078	NM_004655.3	548	Gag/Aag	6/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.210953489500267	2		723	695	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593478	48593479	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs730881952	NA	P-0027867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	165	480	0	ENST00000342988.3:c.1231_1232del	p.Ser411LeufsTer17	p.S411Lfs*17	ENST00000342988	NM_005359.5	410	cAG/c	10/12	0.210953489500267	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.210953489500267	2		480	726	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955042	17955042	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0027867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	97	817	0	ENST00000458235.1:c.184+1G>A		p.X62_splice	ENST00000458235	NM_000215.3	62			1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.210953489500267	2		817	788	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966852	18966853	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0027867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	94	817	2	ENST00000262803.5:c.1663_1664delinsTT	p.Pro555Leu	p.P555L	ENST00000262803	NM_002911.3	555	CCg/TTg	12/24	1	2	FACETS	0.998	0.887	1	0.998	0.887	1	CLONAL	1	TRUE	1	0.210953489500267	2		819	893	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73110202	73110202	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	140	597	0	ENST00000356692.5:c.410C>T	p.Pro137Leu	p.P137L	ENST00000356692		137	cCt/cTt	5/9	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.210953489500267	2		597	1020	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205662	128205663	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0027867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	71	496	2	ENST00000341105.2:c.212_213delinsTT	p.Ser71Phe	p.S71F	ENST00000341105	NM_032638.4	71	tCC/tTT	2/6	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.210953489500267	2		498	524	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720825	89720825	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	265	278	0	ENST00000371953.3:c.976G>C	p.Asp326His	p.D326H	ENST00000371953	NM_000314.4	326	Gac/Cac	8/9	0.765746407372057	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.792316041801226	1		278	382	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587781702	NA	P-0027868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	295	645	0	ENST00000269305.4:c.920-1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.792316041801226	1	FACETS	0.955	0.914	0.995	0.955	0.914	0.995	CLONAL	1	TRUE	0	0.792316041801226	1		645	471	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555287	226555287	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	400	573	0	ENST00000366794.5:c.2300A>C	p.Asn767Thr	p.N767T	ENST00000366794	NM_001618.3	767	aAc/aCc	17/23	0.382265411080554	2	FACETS	1	0.996	1	0.695	0.667	0.723	INDETERMINATE	1	TRUE	0	0.792316041801226	2		573	726	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431019	49431019	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	386	680	0	ENST00000301067.7:c.10120C>T	p.Gln3374Ter	p.Q3374*	ENST00000301067	NM_003482.3	3374	Cag/Tag	34/54	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	1	TRUE	NA	0.792316041801226	2		680	651	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433280	49433280	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	436	593	0	ENST00000301067.7:c.8167G>C	p.Glu2723Gln	p.E2723Q	ENST00000301067	NM_003482.3	2723	Gag/Cag	32/54	NA	2	FACETS	0.787	0.759	0.815			1	INDETERMINATE	2	TRUE	NA	0.792316041801226	2		593	699	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26970455	26970455	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	83	488	0	ENST00000381527.3:c.824A>T	p.Glu275Val	p.E275V	ENST00000381527	NM_001260.1	275	gAa/gTa	8/13	0.792316041801226	1	FACETS	0.217	0.191	0.244	0.217	0.191	0.244	SUBCLONAL	1	TRUE	0	0.792316041801226	1		488	584	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943800	9943800	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757464009	NA	P-0027868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	108	385	0	ENST00000330684.3:c.1141C>T	p.His381Tyr	p.H381Y	ENST00000330684	NM_001134407.1	381	Cat/Tat	5/13	0.461416001223238	1	FACETS	0.367	0.331	0.404	0.367	0.331	0.404	INDETERMINATE	1	TRUE	0	0.792316041801226	1		385	449	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865902	56865902	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	200	440	0	ENST00000308159.5:c.1234G>A	p.Asp412Asn	p.D412N	ENST00000308159	NM_014669.4	412	Gat/Aat	11/22	0.461416001223238	1	FACETS	0.661	0.62	0.703	0.661	0.62	0.703	INDETERMINATE	1	TRUE	0	0.792316041801226	1		440	461	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560051	29560051	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	230	367	0	ENST00000356175.3:c.3528del	p.Ala1177LeufsTer7	p.A1177Lfs*7	ENST00000356175	NM_000267.3	1176	agA/ag	27/57	0.765746407372057	1	FACETS	0.979	0.933	1	0.979	0.933	1	CLONAL	1	TRUE	0	0.792316041801226	1		367	358	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393377	139393377	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	699	691	1	ENST00000277541.6:c.6154del	p.Ala2052LeufsTer59	p.A2052Lfs*59	ENST00000277541	NM_017617.3	2052	Gct/ct	33/34	0.792316041801226	2	FACETS	0.988	0.967	1	0.988	0.967	1	CLONAL	2	TRUE	0	0.792316041801226	2		692	893	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938316	76938316	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	169	569	0	ENST00000373344.5:c.2432A>T	p.Gln811Leu	p.Q811L	ENST00000373344	NM_000489.3	811	cAg/cTg	9/35	0.413019075525863	1	FACETS	0.343	0.316	0.371	0.343	0.316	0.371	INDETERMINATE	1	TRUE	0	0.792316041801226	1		569	751	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0027869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	471	983	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.531452104761876	2	FACETS	0.969	0.932	1	0.969	0.932	1	CLONAL	2	TRUE	0	0.535519903234082	2		983	908	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921487	39921487	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	139	452	1	ENST00000378444.4:c.4333C>T	p.Gln1445Ter	p.Q1445*	ENST00000378444	NM_001123385.1	1445	Cag/Tag	10/15	0.450098141190738	0	FACETS	0.652	0.6	0.704			1	SUBCLONAL	1	TRUE	NA	0.535519903234082	0		453	370	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873713	35873713	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	479	643	0	ENST00000303115.3:c.669T>G	p.Ser223Arg	p.S223R	ENST00000303115	NM_002185.3	223	agT/agG	5/8	0.532362317740217	3	FACETS	0.924	0.892	0.957	0.924	0.892	0.957	CLONAL	3	TRUE	0	0.535519903234082	3		643	818	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492862	8492862	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	159	684	1	ENST00000356435.5:c.2467G>A	p.Val823Ile	p.V823I	ENST00000356435		823	Gtt/Att	16/35	0.531452104761876	2	FACETS	0.827	0.76	0.897	0.414	0.38	0.449	CLONAL	1	TRUE	0	0.535519903234082	2		685	718	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247094	53247094	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	409	434	0	ENST00000375401.3:c.406C>G	p.Arg136Gly	p.R136G	ENST00000375401	NM_004187.3	136	Cgg/Ggg	4/26	0.185259258152822	3	FACETS	1	0.991	1			1	INDETERMINATE	3	TRUE	NA	0.535519903234082	3		434	602	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923148	48923148	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0027871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	40	398	0	ENST00000267163.4:c.596T>G	p.Leu199Ter	p.L199*	ENST00000267163	NM_000321.2	199	tTa/tGa	6/27	0.462328584451957	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		398	701	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579392	7579392	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1555526593	NA	P-0027871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	28	737	0	ENST00000269305.4:c.295del	p.Ser99ProfsTer24	p.S99Pfs*24	ENST00000269305	NM_001126112.2	99	Tcc/cc	4/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		737	546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138729528	NA	P-0027874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	338	742	0	ENST00000269305.4:c.523C>G	p.Arg175Gly	p.R175G	ENST00000269305	NM_001126112.2	175	Cgc/Ggc	5/11	0.710566128098254	1	FACETS	0.999	0.955	1	0.999	0.955	1	CLONAL	1	TRUE	0	0.710566128098254	1		742	614	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685304	89685310	+	frameshift_variant	Frame_Shift_Del	DEL	ATATACA	ATATACA	-	novel	NA	P-0027874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	223	479	4	ENST00000371953.3:c.201_207del	p.Tyr68PhefsTer29	p.Y68Ffs*29	ENST00000371953	NM_000314.4	67	ATATACAat/at	3/9	0.710566128098254	1	FACETS	0.989	0.936	1	0.989	0.936	1	CLONAL	1	TRUE	0	0.710566128098254	1		483	409	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743858	40743858	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374930365	NA	P-0027874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	184	584	5	ENST00000373198.4:c.3137G>A	p.Arg1046His	p.R1046H	ENST00000373198	NM_133170.3	1046	cGc/cAc	23/32	NA	2	FACETS	0.676	0.625	0.729			1	INDETERMINATE	1	TRUE	NA	0.710566128098254	2		589	766	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0027875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	388	654	1	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.716971561910116	2		655	978	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711876	89711876	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	213	450	0	ENST00000371953.3:c.494G>A	p.Gly165Glu	p.G165E	ENST00000371953	NM_000314.4	165	gGa/gAa	6/9	0.716971561910116	1	FACETS	0.985	0.931	1	0.985	0.931	1	CLONAL	1	TRUE	0	0.716971561910116	1		450	387	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7141705	7141705	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs76077021	NA	P-0027875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	434	705	0	ENST00000302850.5:c.2665C>T	p.Arg889Trp	p.R889W	ENST00000302850	NM_000208.2	889	Cgg/Tgg	13/22	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.716971561910116	2		705	1032	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937187	36937187	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	419	715	0	ENST00000361632.4:c.1132T>C	p.Ser378Pro	p.S378P	ENST00000361632		378	Tca/Cca	9/16	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.716971561910116	2		715	1048	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115982	8115982	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	137	352	0	ENST00000346208.3:c.1328G>T	p.Gly443Val	p.G443V	ENST00000346208		443	gGt/gTt	6/6	0.716971561910116	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.716971561910116	1		352	234	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941013	71941028	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCAGCCATCCACAC	CCGCAGCCATCCACAC	-	novel	NA	P-0027875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	336	729	2	ENST00000298229.2:c.889_904del	p.Pro297ValfsTer13	p.P297Vfs*13	ENST00000298229	NM_001567.3	297	CCGCAGCCATCCACACgt/gt	8/28	0.716971561910116	1	FACETS	0.857	0.816	0.897	0.857	0.816	0.897	CLONAL	1	TRUE	0	0.716971561910116	1		731	702	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235900	133235901	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0027875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	249	491	1	ENST00000320574.5:c.3255_3256delinsAA	p.Gly1086Ser	p.G1086S	ENST00000320574	NM_006231.2	1085	gaGGgc/gaAAgc	26/49	0.416654433971365	1	FACETS	0.755	0.712	0.799	0.755	0.712	0.799	INDETERMINATE	1	TRUE	0	0.716971561910116	1		492	590	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098025	178098025	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	346	480	0	ENST00000397062.3:c.355T>C	p.Cys119Arg	p.C119R	ENST00000397062	NM_006164.4	119	Tgc/Cgc	3/5	0.428742068581639	1	FACETS	0.934	0.892	0.975	0.934	0.892	0.975	INDETERMINATE	1	TRUE	0	0.716971561910116	1		480	663	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794935	242794936	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0027875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	175	670	0	ENST00000334409.5:c.273_274delinsAA	p.Asp92Asn	p.D92N	ENST00000334409	NM_005018.2	91	caGGac/caAAac	2/5	0.716971561910116	1	FACETS	0.495	0.457	0.533	0.495	0.457	0.533	SUBCLONAL	1	TRUE	0	0.716971561910116	1		670	633	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274932	38274932	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	421	711	0	ENST00000425967.3:c.1648G>A	p.Asp550Asn	p.D550N	ENST00000425967	NM_001174067.1	550	Gac/Aac	13/19	0.716971561910116	1	FACETS	0.99	0.951	1	0.99	0.951	1	CLONAL	1	TRUE	0	0.716971561910116	1		711	761	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0027877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	48	364	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.862	0.727	1	0.862	0.727	1	CLONAL	1	TRUE	1	0.18	2		364	619	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256528	16256528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	97	622	1	ENST00000375759.3:c.3793C>T	p.Arg1265Ter	p.R1265*	ENST00000375759	NM_015001.2	1265	Cga/Tga	11/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.18	2		623	824	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645884	67645884	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	65	552	0	ENST00000264010.4:c.812G>C	p.Cys271Ser	p.C271S	ENST00000264010	NM_006565.3	271	tGc/tCc	4/12	1	2	FACETS	0.95	0.823	1	0.95	0.823	1	CLONAL	1	TRUE	1	0.18	2		552	760	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268419	198268419	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	49	518	0	ENST00000335508.6:c.1609C>T	p.Pro537Ser	p.P537S	ENST00000335508	NM_012433.2	537	Cct/Tct	12/25	1	2	FACETS	0.701	0.592	0.821	0.701	0.592	0.821	SUBCLONAL	1	TRUE	1	0.18	2		518	777	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275654	41275666	+	frameshift_variant	Frame_Shift_Del	DEL	CTTGCCCTTTGTC	CTTGCCCTTTGTC	-	novel	NA	P-0027877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	35	446	0	ENST00000349496.5:c.1550_1562del	p.Leu517ProfsTer16	p.L517Pfs*16	ENST00000349496	NM_001904.3	517	CTTGCCCTTTGTCcc/cc	10/15	1	2	FACETS	0.641	0.524	0.772	0.641	0.524	0.772	SUBCLONAL	1	TRUE	1	0.18	2		446	607	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168721	56168728	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGCCTT	GCAGCCTT	-	novel	NA	P-0027877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	52	468	0	ENST00000399503.3:c.1575_1582del	p.Gln525HisfsTer13	p.Q525Hfs*13	ENST00000399503	NM_005921.1	525	caGCAGCCTTtg/catg	9/20	1	2	FACETS	0.841	0.715	0.98	0.841	0.715	0.98	CLONAL	1	TRUE	1	0.18	2		468	687	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178338	56178338	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	47	346	0	ENST00000399503.3:c.3311del	p.Ala1104ValfsTer13	p.A1104Vfs*13	ENST00000399503	NM_005921.1	1104	gCt/gt	14/20	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.18	2		346	516	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0027879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	288	610	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	1	2	FACETS	0.911	0.857	0.966	0.911	0.857	0.966	CLONAL	1	TRUE	1	0.586465219290676	2		610	1078	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151946975	151946978	+	frameshift_variant	Frame_Shift_Del	DEL	CTAT	CTAT	-	novel	NA	P-0027879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	208	534	0	ENST00000262189.6:c.1796_1799del	p.Asp599ValfsTer12	p.D599Vfs*12	ENST00000262189	NM_170606.2	599	gATAGt/gt	13/59	1	2	FACETS	0.962	0.896	1	0.962	0.896	1	CLONAL	1	TRUE	1	0.586465219290676	2		534	737	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0027883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	194	497	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.397576232519479	2		497	806	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0027883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	229	789	1	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.397576232519479	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	0	0.397576232519479	1		790	807	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043381	180043381	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760077499	NA	P-0027883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	99	650	3	ENST00000261937.6:c.3205G>A	p.Val1069Ile	p.V1069I	ENST00000261937	NM_182925.4	1069	Gtc/Atc	23/30	1	2	FACETS	0.627	0.559	0.699	0.627	0.559	0.699	SUBCLONAL	1	FALSE	1	0.397576232519479	2		653	794	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121909229	NA	P-0027884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	213	548	0	ENST00000371953.3:c.389G>C	p.Arg130Pro	p.R130P	ENST00000371953	NM_000314.4	130	cGa/cCa	5/9	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.46156081867752	2		548	742	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589589	67589591	+	inframe_deletion	In_Frame_Del	DEL	AAT	AAT	-	novel	NA	P-0027884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	188	436	0	ENST00000274335.5:c.1353_1355del	p.Glu451_Tyr452delinsAsp	p.E451_Y452delinsD	ENST00000274335		451	gAATat/gat	10/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.46156081867752	2		436	741	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114169	115114169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773465537	NA	P-0027884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	348	709	2	ENST00000257566.3:c.1048G>A	p.Ala350Thr	p.A350T	ENST00000257566	NM_016569.3	350	Gcc/Acc	6/8	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.46156081867752	2		711	1237	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46271042	46271042	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	348	684	1	ENST00000371998.3:c.3166C>T	p.Gln1056Ter	p.Q1056*	ENST00000371998		1056	Cag/Tag	17/23	0.814554955845624	2	FACETS	0.88	0.855	0.903	0.88	0.855	0.903	CLONAL	2	FALSE	0	0.928457480372163	2		685	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs17849781	NA	P-0027886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	1235	704	0	ENST00000269305.4:c.832C>G	p.Pro278Ala	p.P278A	ENST00000269305	NM_001126112.2	278	Cct/Gct	8/11	0.707997869944576	4	FACETS	0.996	0.982	1	0.996	0.982	1	CLONAL	4	TRUE	0	0.728583795213071	4		704	1471	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818268	43818268	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	573	644	0	ENST00000372470.3:c.1733C>G	p.Thr578Ser	p.T578S	ENST00000372470	NM_005373.2	578	aCt/aGt	12/12	0.728583795213071	4	FACETS	0.997	0.96	1			1	CLONAL	2	TRUE	NA	0.728583795213071	4		644	1363	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619952	21619952	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	247	631	0	ENST00000382592.4:c.214C>A	p.Pro72Thr	p.P72T	ENST00000382592	NM_014572.2	72	Cct/Act	2/8	1	2	FACETS	0.887	0.833	0.943	0.887	0.833	0.943	CLONAL	1	TRUE	1	0.728583795213071	2		631	764	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592117	55592117	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	235	576	0	ENST00000288135.5:c.1441A>T	p.Ser481Cys	p.S481C	ENST00000288135	NM_000222.2	481	Agt/Tgt	9/21	0.718719933004738	3	FACETS	0.958	0.895	1	0.479	0.447	0.512	CLONAL	1	TRUE	1	0.728583795213071	3		576	919	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397617	139397646	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GATGGGGCCACACTTACTCTGCACGGCCTC	GATGGGGCCACACTTACTCTGCACGGCCTC	-	novel	NA	P-0027886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	206	588	0	ENST00000277541.6:c.5155_5167+17del		p.X1719_splice	ENST00000277541	NM_017617.3	1719		27/34	0.718719933004738	3	FACETS	0.868	0.806	0.932	0.434	0.403	0.466	CLONAL	1	TRUE	1	0.728583795213071	3		588	889	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413079	139413079	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	229	611	0	ENST00000277541.6:c.1063G>C	p.Ala355Pro	p.A355P	ENST00000277541	NM_017617.3	355	Gcc/Ccc	6/34	0.718719933004738	3	FACETS	0.963	0.898	1	0.481	0.449	0.515	CLONAL	1	TRUE	1	0.728583795213071	3		611	891	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0027887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	28	497	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.317037569598535	5	FACETS	1	0.861	1	0.709	0.58	0.849	CLONAL	2	TRUE	2	0.427769947346134	5		497	101	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395523	116395523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	12	601	1	ENST00000397752.3:c.1816G>A	p.Gly606Arg	p.G606R	ENST00000397752	NM_000245.2	606	Gga/Aga	6/21	0.228003679384172	6	FACETS	1	0.831	1	0.317	0.226	0.426	INDETERMINATE	1	TRUE	2	0.427769947346134	6		602	82	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954222	48954222	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0027888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	178	408	1	ENST00000267163.4:c.1421+2T>A		p.X474_splice	ENST00000267163	NM_000321.2	474			1	2	FACETS	0.832	0.772	0.894	0.832	0.772	0.894	CLONAL	1	TRUE	1	0.759655466610559	2		409	563	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130342	11130342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	389	772	3	ENST00000358026.2:c.2581G>A	p.Glu861Lys	p.E861K	ENST00000358026	NM_001128849.1	861	Gag/Aag	18/36	0.759655466610559	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.759655466610559	1		775	559	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911143	40911143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370795038	NA	P-0027888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	212	682	2	ENST00000373198.4:c.2162G>A	p.Arg721His	p.R721H	ENST00000373198	NM_133170.3	721	cGt/cAt	13/32	0.759655466610559	3	FACETS	0.884	0.823	0.948	0.442	0.411	0.474	CLONAL	1	TRUE	1	0.759655466610559	3		684	871	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665015	138665015	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	90	162	1	ENST00000330315.3:c.550G>A	p.Asp184Asn	p.D184N	ENST00000330315	NM_023067.3	184	Gac/Aac	1/1	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.759655466610559	2		163	201	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151893008	151893008	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	235	615	0	ENST00000262189.6:c.4362del	p.Lys1454AsnfsTer30	p.K1454Nfs*30	ENST00000262189	NM_170606.2	1454	aaA/aa	28/59	NA	2	FACETS	0.894	0.838	0.951			1	INDETERMINATE	1	TRUE	NA	0.759655466610559	2		615	692	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0027889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	21	298	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.3	3	FACETS	0.466	0.357	0.593			1	SUBCLONAL	1	TRUE	NA	0.18	3		298	546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0027889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	51	545	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	1	2	FACETS	0.583	0.494	0.682	0.583	0.494	0.682	SUBCLONAL	1	TRUE	1	0.18	2		545	972	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208380	5208380	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs368767528	NA	P-0027889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	47	676	0	ENST00000357368.4:c.5510G>T	p.Arg1837Leu	p.R1837L	ENST00000357368	NM_002850.3	1837	cGg/cTg	36/38	1	2	FACETS	0.591	0.497	0.696	0.591	0.497	0.696	SUBCLONAL	1	TRUE	1	0.18	2		676	883	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610155	10610155	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	65	811	0	ENST00000171111.5:c.555C>G	p.Ile185Met	p.I185M	ENST00000171111	NM_203500.1	185	atC/atG	2/6	1	2	FACETS	0.708	0.612	0.813	0.708	0.612	0.813	SUBCLONAL	1	TRUE	1	0.18	2		811	1020	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224523	36224523	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	106	973	1	ENST00000222270.7:c.6985C>A	p.Pro2329Thr	p.P2329T	ENST00000222270	NM_014727.1	2329	Ccc/Acc	29/37	1	2	FACETS	0.95	0.849	1	0.95	0.849	1	CLONAL	1	TRUE	1	0.18	2		974	1240	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1936926	1936926	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	54	806	0	ENST00000382891.5:c.1611A>C	p.Glu537Asp	p.E537D	ENST00000382891	NM_133335.3	537	gaA/gaC	7/22	1	2	FACETS	0.628	0.534	0.731	0.628	0.534	0.731	SUBCLONAL	1	TRUE	1	0.18	2		806	956	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979207	93979207	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	19	416	0	ENST00000369303.4:c.1621A>C	p.Lys541Gln	p.K541Q	ENST00000369303	NM_004440.3	541	Aaa/Caa	7/17	1	2	FACETS	0.569	0.431	0.732	0.569	0.431	0.732	SUBCLONAL	1	TRUE	1	0.18	2		416	371	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465632	8465632	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs144936979	NA	P-0027889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	49	664	1	ENST00000356435.5:c.3548G>T	p.Gly1183Val	p.G1183V	ENST00000356435		1183	gGg/gTg	21/35	1	2	FACETS	0.779	0.658	0.912	0.779	0.658	0.912	CLONAL	1	TRUE	1	0.18	2		665	699	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249503	153249503	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	208	634	0	ENST00000281708.4:c.1275G>C	p.Trp425Cys	p.W425C	ENST00000281708	NM_033632.3	425	tgG/tgC	9/12	0.682399382225649	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.740403602276929	1		634	320	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578441	7578441	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1567553246	NA	P-0027892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	289	737	0	ENST00000269305.4:c.489C>G	p.Tyr163Ter	p.Y163*	ENST00000269305	NM_001126112.2	163	taC/taG	5/11	0.740403602276929	1	FACETS	0.955	0.91	0.999	0.955	0.91	0.999	CLONAL	1	TRUE	0	0.740403602276929	1		737	515	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952075	178952075	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	349	492	0	ENST00000263967.3:c.3130A>C	p.Asn1044His	p.N1044H	ENST00000263967	NM_006218.2	1044	Aat/Cat	21/21	0.595818256130293	4	FACETS	1	0.989	1	0.803	0.773	0.831	CLONAL	3	TRUE	0	0.740403602276929	4		492	511	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39214691	39214691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs727505383	NA	P-0027892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	186	583	0	ENST00000402219.2:c.3433G>A	p.Asp1145Asn	p.D1145N	ENST00000402219	NM_005633.3	1145	Gat/Aat	22/23	1	2	FACETS	0.991	0.923	1	0.991	0.923	1	CLONAL	1	TRUE	1	0.740403602276929	2		583	507	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099341	157099341	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587779741	NA	P-0027917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	14	314	0	ENST00000346085.5:c.278A>T	p.His93Leu	p.H93L	ENST00000346085	NM_020732.3	93	cAc/cTc	1/20	0.225414750498309	3	FACETS	0.369	0.267	0.494	0.185	0.133	0.247	SUBCLONAL	1	FALSE	1	0.341351015429011	3		314	260	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528697	8528697	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	20	328	0	ENST00000356435.5:c.435G>A	p.Met145Ile	p.M145I	ENST00000356435		145	atG/atA	4/35	1	2	FACETS	0.337	0.257	0.43	0.337	0.257	0.43	SUBCLONAL	1	FALSE	1	0.341351015429011	2		328	348	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593603	55593620	+	protein_altering_variant	In_Frame_Del	DEL	TGGAAGGTTGTTGAGGAG	TGGAAGGTTGTTGAGGAG	AGGGAA	novel	NA	P-0027918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	108	437	2	ENST00000288135.5:c.1669_1686delinsAGGGAA	p.Trp557_Glu561delinsArg	p.W557_E561delinsR	ENST00000288135	NM_000222.2	557	TGGAAGGTTGTTGAGGAG/AGGGAA	11/21	1	2	FACETS	0.63	0.566	0.698	0.63	0.566	0.698	SUBCLONAL	1	TRUE	1	0.512245915433032	2		439	669	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0027919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	23	497	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.459	0.357	0.578	0.459	0.357	0.578	SUBCLONAL	1	TRUE	1	0.2	2		497	501	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0027919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	92	581	2	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	0.2	2		583	678	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0027921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	69	315	1	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	0.994	0.872	1	0.994	0.872	1	CLONAL	1	TRUE	1	0.424682320875503	2		316	327	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696430	47696430	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	132	624	0	ENST00000347630.2:c.393G>C	p.Trp131Cys	p.W131C	ENST00000347630	NM_001007230.1	131	tgG/tgC	6/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.424682320875503	2		624	570	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0027925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	86	430	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.811	0.718	0.911	0.811	0.718	0.911	CLONAL	1	TRUE	1	0.333318423001646	2		430	636	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375370	15375370	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	107	598	0	ENST00000263377.2:c.1057C>A	p.Gln353Lys	p.Q353K	ENST00000263377	NM_058243.2	353	Cag/Aag	6/20	1	2	FACETS	0.814	0.73	0.903	0.814	0.73	0.903	CLONAL	1	TRUE	1	0.333318423001646	2		598	789	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106868	27106881	+	frameshift_variant	Frame_Shift_Del	DEL	ACCCGGTGTGCCGG	ACCCGGTGTGCCGG	-	novel	NA	P-0027925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	55	470	0	ENST00000324856.7:c.6479_6492del	p.Asn2160ArgfsTer60	p.N2160Rfs*60	ENST00000324856	NM_006015.4	2160	aACCCGGTGTGCCGG/a	20/20	0.333318423001646	1	FACETS	0.469	0.4	0.543	0.469	0.4	0.543	SUBCLONAL	1	TRUE	0	0.333318423001646	1		470	587	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410807	63410807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	185	520	0	ENST00000330258.3:c.2360C>A	p.Ser787Tyr	p.S787Y	ENST00000330258	NM_152424.3	787	tCc/tAc	2/2	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.405632448499061	2		520	904	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103717	47103717	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1205330893	NA	P-0027928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	292	446	1	ENST00000409792.3:c.6229C>T	p.Arg2077Ter	p.R2077*	ENST00000409792	NM_014159.6	2077	Cga/Tga	14/21	1	2	FACETS	0.939	0.89	0.988	0.939	0.89	0.988	CLONAL	1	TRUE	1	0.931384558748565	2		447	668	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593589	55593608	+	protein_altering_variant	In_Frame_Del	DEL	TGTATGAAGTACAGTGGAAG	TGTATGAAGTACAGTGGAAG	GA	novel	NA	P-0027928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	192	450	1	ENST00000288135.5:c.1655_1674delinsGA	p.Met552_Lys558delinsArg	p.M552_K558delinsR	ENST00000288135	NM_000222.2	552	aTGTATGAAGTACAGTGGAAG/aGA	11/21	1	2	FACETS	0.742	0.691	0.794	0.742	0.691	0.794	SUBCLONAL	1	TRUE	1	0.931384558748565	2		451	556	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575446	64575446	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	224	505	0	ENST00000312049.6:c.571G>T	p.Glu191Ter	p.E191*	ENST00000312049	NM_130799.2	191	Gag/Tag	3/10	0.910018316852543	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.910018316852543	1		505	257	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0027939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	76	568	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.15	2		568	951	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597964	43597964	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	64	671	0	ENST00000355710.3:c.512G>T	p.Arg171Met	p.R171M	ENST00000355710	NM_020975.4	171	aGg/aTg	3/20	1	2	FACETS	0.804	0.693	0.924	0.804	0.693	0.924	CLONAL	1	TRUE	1	0.15	2		671	1062	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	70	297	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.33318085950836	2		297	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574004	7574005	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	149	774	0	ENST00000269305.4:c.1022dup	p.Arg342ProfsTer5	p.R342Pfs*5	ENST00000269305	NM_001126112.2	341	ttc/ttTc	10/11	0.246731926554713	2	FACETS	1	0.982	1	0.636	0.582	0.692	CLONAL	1	TRUE	0	0.33318085950836	2		774	703	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112431	115112431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	289	516	1	ENST00000257566.3:c.1309C>T	p.His437Tyr	p.H437Y	ENST00000257566	NM_016569.3	437	Cat/Tat	7/8	1	2	FACETS	0.971	0.915	1	0.971	0.915	1	CLONAL	1	TRUE	1	0.65	2		517	916	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502663	149502663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	185	471	3	ENST00000261799.4:c.2125C>T	p.Arg709Cys	p.R709C	ENST00000261799	NM_002609.3	709	Cgc/Tgc	15/23	1	2	FACETS	0.876	0.812	0.941	0.876	0.812	0.941	CLONAL	1	TRUE	1	0.65	2		474	650	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492554	50492554	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	205	645	1	ENST00000394963.4:c.1450C>T	p.Gln484Ter	p.Q484*	ENST00000394963	NM_003076.4	484	Cag/Tag	12/13	0.209889036564883	4	FACETS	0.906	0.847	0.966	0.906	0.847	0.966	INDETERMINATE	2	TRUE	2	0.712103744153676	4		646	544	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443893	52443893	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1467015377	NA	P-0027951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	211	582	0	ENST00000460680.1:c.2T>C	p.Met1?	p.M1?	ENST00000460680	NM_004656.3	1	aTg/aCg	1/17	0.712103744153676	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.712103744153676	1		582	357	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287361	33287361	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	193	482	0	ENST00000374542.5:c.1736del	p.Pro579LeufsTer23	p.P579Lfs*23	ENST00000374542	NM_001141970.1	579	cCt/ct	6/8	0.19737062554214	5	FACETS	1	0.952	1	0.684	0.638	0.732	INDETERMINATE	2	TRUE	2	0.712103744153676	5		482	546	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0027952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	80	433	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		433	488	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119459	193119459	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	73	357	0	ENST00000367435.3:c.854C>G	p.Pro285Arg	p.P285R	ENST00000367435	NM_024529.4	285	cCt/cGt	9/17	0.132123849311459	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		357	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	113	534	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.309277154241792	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.309277154241792	1		534	596	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125222	47125222	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	58	309	0	ENST00000409792.3:c.6048G>T	p.Trp2016Cys	p.W2016C	ENST00000409792	NM_014159.6	2016	tgG/tgT	12/21	1	2	FACETS	0.826	0.711	0.951	0.826	0.711	0.951	CLONAL	1	TRUE	1	0.309277154241792	2		309	454	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057733	27057733	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	167	718	1	ENST00000324856.7:c.1441C>T	p.Gln481Ter	p.Q481*	ENST00000324856	NM_006015.4	481	Cag/Tag	3/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.309277154241792	2		719	852	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111494	8111494	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	156	546	0	ENST00000346208.3:c.980T>C	p.Leu327Pro	p.L327P	ENST00000346208		327	cTc/cCc	5/6	0.222255279784949	3	FACETS	0.823	0.755	0.893	0.823	0.755	0.893	CLONAL	2	TRUE	1	0.309277154241792	3		546	708	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143026	47143027	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTTGTCC	novel	NA	P-0027953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	60	524	0	ENST00000409792.3:c.4930_4936dup	p.Leu1646ArgfsTer22	p.L1646Rfs*22	ENST00000409792	NM_014159.6	1646	ctg/cGGACAACtg	8/21	1	2	FACETS	0.492	0.423	0.568	0.492	0.423	0.568	SUBCLONAL	1	TRUE	1	0.309277154241792	2		524	788	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184634	185184713	+	frameshift_variant	Frame_Shift_Del	DEL	AGAAGTATCCTGGGACCTACAAACGACACCCTGTTCGTCCTATCATCCATCCCAATGCCATGGAGAAACTCATGAAAAGG	AGAAGTATCCTGGGACCTACAAACGACACCCTGTTCGTCCTATCATCCATCCCAATGCCATGGAGAAACTCATGAAAAGG	-	novel	NA	P-0027953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	60	356	0	ENST00000265026.3:c.1527_1606del	p.Lys510ArgfsTer43	p.K510Rfs*43	ENST00000265026	NM_004721.4	509	aAGAAGTATCCTGGGACCTACAAACGACACCCTGTTCGTCCTATCATCCATCCCAATGCCATGGAGAAACTCATGAAAAGG/a	10/14	0.222255279784949	3	FACETS	0.966	0.834	1	0.483	0.417	0.554	CLONAL	1	TRUE	1	0.309277154241792	3		356	464	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0027956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	146	298	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.654442501699728	3	FACETS	1	0.976	1	0.584	0.536	0.633	CLONAL	1	TRUE	1	0.654442501699728	3		298	507	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0027956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	29	150	0	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	0.654442501699728	3	FACETS	0.764	0.621	0.922			1	CLONAL	1	TRUE	NA	0.654442501699728	3		150	154	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0027956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	417	789	1	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	2	TRUE	NA	0.654442501699728	2		790	624	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367937	15367937	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	173	750	0	ENST00000263377.2:c.1389del	p.Glu463AspfsTer121	p.E463Dfs*121	ENST00000263377	NM_058243.2	463	gaG/ga	8/20	0.647650052704493	4	FACETS	0.902	0.83	0.977			1	CLONAL	1	TRUE	NA	0.654442501699728	4		750	970	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899060	40899060	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	122	515	0	ENST00000373198.4:c.2210C>A	p.Thr737Asn	p.T737N	ENST00000373198	NM_133170.3	737	aCt/aAt	14/32	0.654442501699728	3	FACETS	0.895	0.812	0.981	0.447	0.406	0.491	CLONAL	1	TRUE	1	0.654442501699728	3		515	553	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0027956-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	23	150	0	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	0.641000832118145	2	FACETS	0.834	0.667	1			1	CLONAL	1	TRUE	NA	0.641000832118145	2		150	86	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0027956-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	363	789	1	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.641000832118145	2		790	526	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899060	40899060	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027956-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	103	515	0	ENST00000373198.4:c.2210C>A	p.Thr737Asn	p.T737N	ENST00000373198	NM_133170.3	737	aCt/aAt	14/32	0.641000832118145	3	FACETS	1	0.902	1	0.5	0.451	0.553	CLONAL	1	TRUE	1	0.641000832118145	3		515	424	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274007	10274007	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027956-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	70	823	0	ENST00000330684.3:c.262G>A	p.Asp88Asn	p.D88N	ENST00000330684	NM_001134407.1	88	Gac/Aac	2/13	0.641000832118145	2	FACETS	0.563	0.493	0.637	0.281	0.246	0.319	SUBCLONAL	1	TRUE	0	0.641000832118145	2		823	388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577070	7577070	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	549	623	0	ENST00000269305.4:c.868del	p.Arg290AlafsTer55	p.R290Afs*55	ENST00000269305	NM_001126112.2	290	Cgc/gc	8/11	0.57368626884913	3	FACETS	0.909	0.88	0.938	0.909	0.88	0.938	CLONAL	3	TRUE	0	0.57368626884913	3		623	903	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495296	212495296	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	99	473	0	ENST00000342788.4:c.1970T>A	p.Val657Glu	p.V657E	ENST00000342788	NM_005235.2	657	gTa/gAa	17/28	0.539150220315013	4	FACETS	0.973	0.871	1	0.324	0.29	0.361	CLONAL	1	TRUE	1	0.57368626884913	4		473	558	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376455	118376455	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781886946	NA	P-0027978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	127	388	0	ENST00000534358.1:c.9848G>A	p.Arg3283Gln	p.R3283Q	ENST00000534358	NM_005933.3	3283	cGa/cAa	27/36	0.57368626884913	3	FACETS	1	0.96	1	0.548	0.499	0.599	CLONAL	1	TRUE	1	0.57368626884913	3		388	520	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371914	55371914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	97	361	0	ENST00000297316.4:c.604C>T	p.His202Tyr	p.H202Y	ENST00000297316	NM_022454.3	202	Cac/Tac	2/2	0.537468666528021	4	FACETS	1	0.927	1	0.349	0.312	0.387	CLONAL	1	TRUE	1	0.57368626884913	4		361	509	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255058	16255058	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1414658127	NA	P-0027979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	96	374	0	ENST00000375759.3:c.2323G>A	p.Glu775Lys	p.E775K	ENST00000375759	NM_015001.2	775	Gag/Aag	11/15	0.494960326452396	3	FACETS	0.885	0.79	0.984	0.295	0.263	0.328	CLONAL	1	TRUE	0	0.494960326452396	3		374	547	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486805	56486805	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	176	509	1	ENST00000267101.3:c.1219C>A	p.His407Asn	p.H407N	ENST00000267101	NM_001982.3	407	Cac/Aac	11/28	0.494960326452396	3	FACETS	0.937	0.863	1	0.468	0.431	0.507	CLONAL	1	TRUE	1	0.494960326452396	3		510	947	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481426	40481454	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ACATCACAATTGGCTCGGCCCCCATTCCC	ACATCACAATTGGCTCGGCCCCCATTCCC	-	novel	NA	P-0027979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	106	499	0	ENST00000264657.5:c.1255_1281+2del		p.X419_splice	ENST00000264657	NM_139276.2	419		14/24	0.101110036401819	4	FACETS	0.758	0.679	0.842	0.379	0.339	0.421	INDETERMINATE	1	TRUE	2	0.494960326452396	4		499	845	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194904	29194904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372203752	NA	P-0027979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	377	680	3	ENST00000240100.2:c.824G>A	p.Arg275His	p.R275H	ENST00000240100	NM_001394.6	275	cGc/cAc	4/4	0.327041674994192	5	FACETS	1	0.986	1	0.735	0.698	0.773	CLONAL	2	TRUE	2	0.494960326452396	5		683	1204	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942889	68942889	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	131	519	0	ENST00000288368.4:c.701G>T	p.Trp234Leu	p.W234L	ENST00000288368	NM_024870.2	234	tGg/tTg	6/40	0.494960326452396	3	FACETS	0.753	0.683	0.827	0.376	0.341	0.414	SUBCLONAL	1	TRUE	1	0.494960326452396	3		519	877	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630490	47630490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749212640	NA	P-0027980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	113	571	0	ENST00000233146.2:c.160G>A	p.Ala54Thr	p.A54T	ENST00000233146	NM_000251.2	54	Gcc/Acc	1/16	1	2	FACETS	0.706	0.634	0.783	0.706	0.634	0.783	SUBCLONAL	1	TRUE	1	0.282662823635569	2		571	1132	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509551	29509554	+	frameshift_variant	Frame_Shift_Del	DEL	GGTG	GGTG	-	novel	NA	P-0027980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	19	428	0	ENST00000356175.3:c.757_760del	p.Val253MetfsTer27	p.V253Mfs*27	ENST00000356175	NM_000267.3	252	ttGGTG/tt	8/57	1	2	FACETS	0.711	0.542	0.908	0.711	0.542	0.908	CLONAL	1	TRUE	1	0.282662823635569	2		428	189	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985543	2985543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	95	426	1	ENST00000396946.4:c.268G>A	p.Val90Ile	p.V90I	ENST00000396946	NM_032415.4	90	Gtc/Atc	4/25	0.282662823635569	3	FACETS	1	0.939	1	0.54	0.481	0.603	CLONAL	1	TRUE	1	0.282662823635569	3		427	710	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030616	47030616	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293292014	NA	P-0027980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	132	678	0	ENST00000377604.3:c.391G>A	p.Val131Ile	p.V131I	ENST00000377604	NM_001204468.1	131	Gtc/Atc	4/24	1	2	FACETS	0.832	0.754	0.915	0.832	0.754	0.915	CLONAL	1	TRUE	1	0.282662823635569	2		678	1122	SUCCESS
APC	324	MSKCC	GRCh37	5	112179218	112179239	+	frameshift_variant	Frame_Shift_Del	DEL	CTAATTTATCAAATGGCACCTG	CTAATTTATCAAATGGCACCTG	-	novel	NA	P-0027981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	18	327	0	ENST00000257430.4:c.7929_7950del	p.Ile2644PhefsTer9	p.I2644Ffs*9	ENST00000257430	NM_000038.5	2643	CTAATTTATCAAATGGCACCTGct/ct	16/16	0.482963374158876	1	FACETS	0.287	0.217	0.369	0.287	0.217	0.369	SUBCLONAL	1	FALSE	0	0.482963374158876	1		327	197	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882104	36882104	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0027981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	163	535	0	ENST00000358127.4:c.911-2A>G		p.X304_splice	ENST00000358127	NM_001280556.1	304			0.482963374158876	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	0	0.482963374158876	1		535	486	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0027982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	150	497	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.198990229071726	3	FACETS	0.844	0.774	0.917	0.844	0.774	0.917	CLONAL	2	TRUE	1	0.322874175092554	3		497	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0027982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	98	557	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.322874175092554	1	FACETS	0.951	0.852	1	0.951	0.852	1	CLONAL	1	TRUE	0	0.322874175092554	1		557	535	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175869	24175869	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555881572	NA	P-0027982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	70	400	0	ENST00000263121.7:c.1097G>A	p.Arg366His	p.R366H	ENST00000263121	NM_003073.3	366	cGc/cAc	8/9	1	2	FACETS	0.955	0.835	1	0.955	0.835	1	CLONAL	1	TRUE	1	0.322874175092554	2		400	454	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0027984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	84	529	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.245996907318927	6	FACETS	1	0.966	1	0.615	0.546	0.688	CLONAL	2	TRUE	2	0.245996907318927	6		529	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0027984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	174	606	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.245996907318927	2	FACETS	0.907	0.852	0.961	1	0.994	1	CLONAL	5	TRUE	0	0.245996907318927	2		608	312	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221987	1221987	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370222210	NA	P-0027984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	207	642	3	ENST00000326873.7:c.902G>A	p.Arg301Gln	p.R301Q	ENST00000326873	NM_000455.4	301	cGg/cAg	7/10	0.245996907318927	4	FACETS	1	0.959	1	1	0.994	1	CLONAL	5	TRUE	1	0.245996907318927	4		645	410	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446317	29446317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768123237	NA	P-0027984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	86	703	1	ENST00000389048.3:c.3250C>T	p.Arg1084Cys	p.R1084C	ENST00000389048	NM_004304.4	1084	Cgc/Tgc	20/29	0.245996907318927	4	FACETS	1	0.954	1	0.756	0.673	0.844	CLONAL	2	TRUE	1	0.245996907318927	4		704	384	SUCCESS
APC	324	MSKCC	GRCh37	5	112154858	112154859	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0027984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	93	547	0	ENST00000257430.4:c.1130_1131del	p.Lys377ArgfsTer19	p.K377Rfs*19	ENST00000257430	NM_000038.5	377	AAa/a	10/16	0.245996907318927	5	FACETS	1	0.967	1	0.602	0.538	0.669	CLONAL	2	TRUE	1	0.245996907318927	5		547	430	SUCCESS
APC	324	MSKCC	GRCh37	5	112174096	112174096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs137854575	NA	P-0027984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	157	367	0	ENST00000257430.4:c.2805C>A	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	taC/taA	16/16	0.245996907318927	5	FACETS	0.974	0.905	1	1	0.984	1	CLONAL	5	TRUE	1	0.245996907318927	5		367	359	SUCCESS
APC	324	MSKCC	GRCh37	5	112175621	112175621	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	83	355	0	ENST00000257430.4:c.4330del	p.Gln1444LysfsTer29	p.Q1444Kfs*29	ENST00000257430	NM_000038.5	1444	Caa/aa	16/16	0.245996907318927	5	FACETS	1	0.966	1	0.618	0.549	0.69	CLONAL	2	TRUE	1	0.245996907318927	5		355	374	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168752	32168752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444374238	NA	P-0027984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	68	778	2	ENST00000375023.3:c.4171C>T	p.Arg1391Cys	p.R1391C	ENST00000375023	NM_004557.3	1391	Cgc/Tgc	23/30	0.245996907318927	4	FACETS	1	0.887	1	0.675	0.591	0.765	CLONAL	2	TRUE	1	0.245996907318927	4		780	340	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0027985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	72	439	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	0.29	2		439	460	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842414	68842414	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	96	579	0	ENST00000261769.5:c.476del	p.Pro159LeufsTer56	p.P159Lfs*56	ENST00000261769	NM_004360.3	159	Cct/ct	4/16	0.300596485495335	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.29	1		579	513	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0027987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	29	600	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.12	2		606	416	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0027987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	36	564	2	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.12	2		566	480	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	13	346	4	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.697	0.496	0.943	0.697	0.496	0.943	SUBCLONAL	1	TRUE	1	0.12	2		350	311	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518190	8518190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	19	323	0	ENST00000356435.5:c.1201C>T	p.Arg401Trp	p.R401W	ENST00000356435		401	Cgg/Tgg	10/35	1	2	FACETS	0.926	0.702	1	0.926	0.702	1	CLONAL	1	TRUE	1	0.12	2		323	342	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226574031	226574031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201975538	NA	P-0027987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	14	327	0	ENST00000366794.5:c.830C>T	p.Ser277Leu	p.S277L	ENST00000366794	NM_001618.3	277	tCg/tTg	6/23	1	2	FACETS	0.93	0.672	1	0.93	0.672	1	CLONAL	1	TRUE	1	0.12	2		327	251	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094384	27094384	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	23	470	0	ENST00000324856.7:c.3092C>G	p.Thr1031Ser	p.T1031S	ENST00000324856	NM_006015.4	1031	aCt/aGt	11/20	1	2	FACETS	0.97	0.756	1	0.97	0.756	1	CLONAL	1	TRUE	1	0.12	2		470	395	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434545	110434545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	21	580	0	ENST00000375856.3:c.3856C>T	p.Arg1286Trp	p.R1286W	ENST00000375856	NM_003749.2	1286	Cgg/Tgg	1/2	1	2	FACETS	0.931	0.716	1	0.931	0.716	1	CLONAL	1	TRUE	1	0.12	2		580	376	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243987	5243987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1425401879	NA	P-0027987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	24	593	0	ENST00000357368.4:c.1495G>A	p.Val499Met	p.V499M	ENST00000357368	NM_002850.3	499	Gtg/Atg	11/38	1	2	FACETS	0.922	0.722	1	0.922	0.722	1	CLONAL	1	TRUE	1	0.12	2		593	434	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971667	18971667	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	26	645	0	ENST00000262803.5:c.2333C>T	p.Thr778Met	p.T778M	ENST00000262803	NM_002911.3	778	aCg/aTg	17/24	1	2	FACETS	0.846	0.669	1	0.846	0.669	1	CLONAL	1	TRUE	1	0.12	2		645	512	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846425	128846425	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	22	402	2	ENST00000249373.3:c.1261C>T	p.Arg421Ter	p.R421*	ENST00000249373	NM_005631.4	421	Cga/Tga	6/12	1	2	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	TRUE	1	0.12	2		404	330	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0027990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	36	298	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.582	0.477	0.699	0.582	0.477	0.699	SUBCLONAL	1	TRUE	1	0.2	2		298	619	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117377	115117378	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0027990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	52	414	0	ENST00000257566.3:c.796_797insAA	p.Ser266LysfsTer17	p.S266Kfs*17	ENST00000257566	NM_016569.3	266	agt/aAAgt	4/8	1	2	FACETS	0.889	0.756	1	0.889	0.756	1	CLONAL	1	TRUE	1	0.2	2		414	585	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070557	67070557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	24	223	0	ENST00000412916.2:c.181G>A	p.Gly61Arg	p.G61R	ENST00000412916		61	Gga/Aga	3/6	1	2	FACETS	0.736	0.577	0.919	0.736	0.577	0.919	CLONAL	1	TRUE	1	0.2	2		223	326	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844182	68844182	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	87	598	0	ENST00000261769.5:c.770A>C	p.Asp257Ala	p.D257A	ENST00000261769	NM_004360.3	257	gAc/gCc	6/16	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.2	2		598	808	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138729528	NA	P-0027991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	82	742	0	ENST00000269305.4:c.523C>G	p.Arg175Gly	p.R175G	ENST00000269305	NM_001126112.2	175	Cgc/Ggc	5/11	1	2	FACETS	0.768	0.675	0.868	0.768	0.675	0.868	SUBCLONAL	1	TRUE	1	0.209624041664593	2		742	1019	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38949877	38949877	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	72	411	0	ENST00000357387.3:c.4073T>A	p.Val1358Glu	p.V1358E	ENST00000357387	NM_152756.3	1358	gTg/gAg	31/38	0.179875083330161	4	FACETS	1	0.968	1			1	CLONAL	1	TRUE	NA	0.209624041664593	4		411	613	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286824	33286824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555856847	NA	P-0027991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	48	564	0	ENST00000374542.5:c.2113C>T	p.Arg705Trp	p.R705W	ENST00000374542	NM_001141970.1	705	Cgg/Tgg	7/8	1	2	FACETS	0.482	0.405	0.566	0.482	0.405	0.566	SUBCLONAL	1	TRUE	1	0.209624041664593	2		564	951	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0027994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	100	518	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.893	0.805	0.986	0.893	0.805	0.986	CLONAL	1	TRUE	1	0.600285681611721	2		518	373	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399937	139399937	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1414066424	NA	P-0027994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	231	872	0	ENST00000277541.6:c.4411G>A	p.Ala1471Thr	p.A1471T	ENST00000277541	NM_017617.3	1471	Gcg/Acg	25/34	1	2	FACETS	0.966	0.903	1	0.966	0.903	1	CLONAL	1	TRUE	1	0.600285681611721	2		872	797	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111446	8111447	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0027994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	163	508	0	ENST00000346208.3:c.936_937dup	p.Ala313GlufsTer43	p.A313Efs*43	ENST00000346208		311	agg/agGAg	5/6	1	2	FACETS	0.982	0.907	1	0.982	0.907	1	CLONAL	1	TRUE	1	0.600285681611721	2		508	553	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100693	67100693	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	144	470	1	ENST00000412916.2:c.391C>T	p.Arg131Ter	p.R131*	ENST00000412916		131	Cga/Tga	4/6	0.591343574614792	1	FACETS	0.781	0.719	0.845	0.781	0.719	0.845	SUBCLONAL	1	TRUE	0	0.600285681611721	1		471	430	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0027995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	182	545	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.291489678342828	2	FACETS	0.934	0.866	1	0.934	0.866	1	CLONAL	2	TRUE	0	0.310900311444443	2		545	627	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0027995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	139	573	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	0.230431256151119	4	FACETS	0.777	0.708	0.85	0.777	0.708	0.85	SUBCLONAL	2	TRUE	2	0.310900311444443	4		573	754	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998739	100998739	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	82	604	0	ENST00000325455.5:c.1063G>T	p.Val355Leu	p.V355L	ENST00000325455	NM_001202474.3	355	Gta/Tta	1/8	0.302419352620858	3	FACETS	0.915	0.807	1	0.458	0.403	0.516	CLONAL	1	TRUE	1	0.310900311444443	3		604	666	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95595913	95595913	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	98	499	0	ENST00000393063.1:c.630A>T	p.Leu210Phe	p.L210F	ENST00000393063	NM_030621.3	210	ttA/ttT	7/28	0.291489678342828	2	FACETS	1	0.963	1	0.584	0.522	0.649	CLONAL	1	TRUE	0	0.310900311444443	2		499	540	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259570	89259570	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs769787086	NA	P-0027995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	62	327	1	ENST00000336596.2:c.714T>A	p.Asp238Glu	p.D238E	ENST00000336596	NM_005233.5	238	gaT/gaA	3/17	0.230431256151119	4	FACETS	1	0.922	1	0.548	0.474	0.628	CLONAL	1	TRUE	2	0.310900311444443	4		328	477	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0027996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	128	380	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.160122472788193	3	FACETS	0.972	0.882	1	0.648	0.588	0.71	CLONAL	2	TRUE	0	0.21593851367397	3		380	676	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852243	128852243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149170801	NA	P-0027996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	44	691	0	ENST00000249373.3:c.2315G>A	p.Arg772His	p.R772H	ENST00000249373	NM_005631.4	772	cGc/cAc	12/12	0.212811434312917	4	FACETS	0.593	0.496	0.702	0.198	0.165	0.234	SUBCLONAL	1	TRUE	1	0.21593851367397	4		691	835	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95593018	95593018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1251925935	NA	P-0027996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	101	498	0	ENST00000393063.1:c.802G>A	p.Glu268Lys	p.E268K	ENST00000393063	NM_030621.3	268	Gaa/Aaa	8/28	0.21593851367397	2	FACETS	1	0.979	1	0.704	0.63	0.783	CLONAL	1	TRUE	0	0.21593851367397	2		498	664	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0027997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	88	567	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.601	0.531	0.676	0.601	0.531	0.676	SUBCLONAL	1	TRUE	1	0.285833099228144	2		568	1025	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100175	27100176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0027997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	98	397	0	ENST00000324856.7:c.3977dup	p.Gln1327AlafsTer11	p.Q1327Afs*11	ENST00000324856	NM_006015.4	1324	tac/taCc	16/20	1	2	FACETS	0.872	0.778	0.973	0.872	0.778	0.973	CLONAL	1	TRUE	1	0.285833099228144	2		397	786	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591077	67591077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	51	308	1	ENST00000274335.5:c.1670G>A	p.Arg557Gln	p.R557Q	ENST00000274335		557	cGa/cAa	12/15	1	2	FACETS	0.67	0.569	0.78	0.67	0.569	0.78	SUBCLONAL	1	TRUE	1	0.285833099228144	2		309	533	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019392	31019392	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	80	288	0	ENST00000375687.4:c.889A>G	p.Thr297Ala	p.T297A	ENST00000375687	NM_015338.5	297	Acg/Gcg	10/13	1	2	FACETS	0.761	0.669	0.859	0.761	0.669	0.859	SUBCLONAL	1	TRUE	1	0.285833099228144	2		288	736	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197836	66197836	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	22	225	0	ENST00000273854.3:c.2863T>G	p.Leu955Val	p.L955V	ENST00000273854	NM_004439.5	955	Tta/Gta	17/18	1	2	FACETS	0.379	0.293	0.479	0.379	0.293	0.479	SUBCLONAL	1	TRUE	1	0.285833099228144	2		225	406	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484231	8484231	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1405369086	NA	P-0027997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	66	386	0	ENST00000356435.5:c.3301G>T	p.Ala1101Ser	p.A1101S	ENST00000356435		1101	Gca/Tca	19/35	1	2	FACETS	0.608	0.527	0.696	0.608	0.527	0.696	SUBCLONAL	1	TRUE	1	0.285833099228144	2		386	760	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355839	73355839	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	107	529	0	ENST00000377767.4:c.132G>T	p.Glu44Asp	p.E44D	ENST00000377767	NM_014953.3	44	gaG/gaT	1/21	0.424613169696962	2	FACETS	0.538	0.481	0.597	0.269	0.24	0.299	SUBCLONAL	1	TRUE	0	0.448788046370999	2		529	887	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578440	7578440	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs879254249	NA	P-0027998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	363	659	0	ENST00000269305.4:c.490A>G	p.Lys164Glu	p.K164E	ENST00000269305	NM_001126112.2	164	Aag/Gag	5/11	0.339768823992061	2	FACETS	0.818	0.777	0.859	0.818	0.777	0.859	CLONAL	2	TRUE	0	0.448788046370999	2		659	989	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983728	15983728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	232	431	0	ENST00000268712.3:c.3394G>A	p.Val1132Ile	p.V1132I	ENST00000268712	NM_006311.3	1132	Gtc/Atc	25/46	0.339768823992061	2	FACETS	0.959	0.903	1	0.959	0.903	1	CLONAL	2	TRUE	0	0.448788046370999	2		431	539	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949102	71949114	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGGCGGGCCAG	GCGGGCGGGCCAG	AA	novel	NA	P-0027998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	126	593	4	ENST00000298229.2:c.3569_3581delinsAA	p.Gly1190GlufsTer21	p.G1190Efs*21	ENST00000298229	NM_001567.3	1190	gGCGGGCGGGCCAGc/gAAc	27/28	0.13421314798593	4	FACETS	0.788	0.713	0.868	0.197	0.178	0.217	INDETERMINATE	1	TRUE	0	0.448788046370999	4		597	1032	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81971495	81971495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767605816	NA	P-0027998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	183	526	0	ENST00000359376.3:c.3185C>T	p.Thr1062Met	p.T1062M	ENST00000359376	NM_002661.3	1062	aCg/aTg	28/33	0.448788046370999	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.448788046370999	1		526	589	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576810	67576863	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGAATGAACGACAGCCTGCACCAGGTAATGCTTTTTGAGCATTTAACATTCTC	TGGAATGAACGACAGCCTGCACCAGGTAATGCTTTTTGAGCATTTAACATTCTC	-	novel	NA	P-0027998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	54	369	0	ENST00000274335.5:c.893_916+30del		p.X298_splice	ENST00000274335		298		6/15	0.448788046370999	1	FACETS	0.566	0.486	0.652	0.566	0.486	0.652	SUBCLONAL	1	TRUE	0	0.448788046370999	1		369	330	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397803	116397803	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	81	514	0	ENST00000397752.3:c.2077G>C	p.Gly693Arg	p.G693R	ENST00000397752	NM_000245.2	693	Ggt/Cgt	8/21	0.224771697348355	6	FACETS	0.731	0.643	0.826			1	INDETERMINATE	1	TRUE	NA	0.448788046370999	6		514	937	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs967461896	NA	P-0027999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	577	532	1	ENST00000269305.4:c.526T>A	p.Cys176Ser	p.C176S	ENST00000269305	NM_001126112.2	176	Tgc/Agc	5/11	0.827075854364796	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.840462846172341	3		533	649	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450898	70450898	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	169	435	0	ENST00000373644.4:c.5738T>A	p.Leu1913Gln	p.L1913Q	ENST00000373644	NM_030625.2	1913	cTg/cAg	12/12	0.827075854364796	3	FACETS	1	0.974	1	0.371	0.343	0.399	CLONAL	1	TRUE	0	0.840462846172341	3		435	513	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120845	115120845	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	130	439	0	ENST00000257566.3:c.161T>A	p.Leu54His	p.L54H	ENST00000257566	NM_016569.3	54	cTc/cAc	1/8	0.131004987267686	5	FACETS	0.863	0.791	0.938			1	INDETERMINATE	2	TRUE	NA	0.840462846172341	5		439	405	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965755	18965755	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	166	694	0	ENST00000262803.5:c.1333C>G	p.Leu445Val	p.L445V	ENST00000262803	NM_002911.3	445	Ctg/Gtg	10/24	0.369536365911711	5	FACETS	0.842	0.772	0.914	0.168	0.154	0.183	INDETERMINATE	1	TRUE	0	0.840462846172341	5		694	1061	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636701	8636701	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	57	169	0	ENST00000356435.5:c.208G>A	p.Glu70Lys	p.E70K	ENST00000356435		70	Gag/Aag	2/35	0.667353354894307	3	FACETS	0.926	0.806	1			1	CLONAL	1	TRUE	NA	0.840462846172341	3		169	208	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0028006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	123	654	1	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.254047558015333	2		655	904	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934578	NA	P-0028006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	124	635	1	ENST00000269305.4:c.524G>T	p.Arg175Leu	p.R175L	ENST00000269305	NM_001126112.2	175	cGc/cTc	5/11	0.254047558015333	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.254047558015333	1		636	821	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040911	47040911	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs782684857	NA	P-0028006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	113	373	0	ENST00000377604.3:c.1441G>T	p.Glu481Ter	p.E481*	ENST00000377604	NM_001204468.1	481	Gag/Tag	14/24	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.254047558015333	1		373	560	SUCCESS
RET	5979	MSKCC	GRCh37	10	43602016	43602016	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	80	645	0	ENST00000355710.3:c.1060T>A	p.Tyr354Asn	p.Y354N	ENST00000355710	NM_020975.4	354	Tat/Aat	5/20	0.254047558015333	1	FACETS	0.635	0.558	0.718	0.635	0.558	0.718	SUBCLONAL	1	TRUE	0	0.254047558015333	1		645	866	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027228	49027231	+	frameshift_variant	Frame_Shift_Del	DEL	AATC	AATC	-	novel	NA	P-0028006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	58	462	0	ENST00000267163.4:c.1796_1799del	p.Asn599ThrfsTer11	p.N599Tfs*11	ENST00000267163	NM_000321.2	599	AATCac/ac	18/27	0.254047558015333	1	FACETS	0.892	0.768	1	0.892	0.768	1	CLONAL	1	TRUE	0	0.254047558015333	1		462	447	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021361	42021361	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0028006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	51	287	0	ENST00000219905.7:c.3658-1G>T		p.X1220_splice	ENST00000219905	NM_001164273.1	1220			0.254047558015333	1	FACETS	0.974	0.831	1	0.974	0.831	1	CLONAL	1	TRUE	0	0.254047558015333	1		287	360	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416551	29416551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	120	566	1	ENST00000389048.3:c.4402G>A	p.Gly1468Arg	p.G1468R	ENST00000389048	NM_004304.4	1468	Ggg/Agg	29/29	0.254047558015333	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.254047558015333	1		567	794	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499681	8499681	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs781164830	NA	P-0028006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	33	438	0	ENST00000356435.5:c.2288C>G	p.Pro763Arg	p.P763R	ENST00000356435		763	cCc/cGc	14/35	0.254047558015333	1	FACETS	0.366	0.297	0.444	0.366	0.297	0.444	SUBCLONAL	1	TRUE	0	0.254047558015333	1		438	620	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs760043106	NA	P-0028009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	469	535	0	ENST00000269305.4:c.584T>A	p.Ile195Asn	p.I195N	ENST00000269305	NM_001126112.2	195	aTc/aAc	6/11	0.55255343924585	4	FACETS	0.982	0.952	1	0.982	0.952	1	CLONAL	4	FALSE	0	0.55255343924585	4		535	671	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135691	64135691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151034403	NA	P-0028009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	139	661	1	ENST00000334205.4:c.1159C>T	p.Arg387Trp	p.R387W	ENST00000334205	NM_003942.2	387	Cgg/Tgg	10/17	0.55255343924585	3	FACETS	0.824	0.751	0.901	0.412	0.375	0.451	CLONAL	1	FALSE	1	0.55255343924585	3		662	779	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022526	12022526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs111871763	NA	P-0028009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	47	597	2	ENST00000396373.4:c.632G>A	p.Arg211His	p.R211H	ENST00000396373	NM_001987.4	211	cGc/cAc	5/8	0.55255343924585	4	FACETS	0.391	0.329	0.459	0.13	0.109	0.153	SUBCLONAL	1	FALSE	1	0.55255343924585	4		599	676	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595547	55595547	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	80	435	0	ENST00000288135.5:c.2037G>T	p.Leu679Phe	p.L679F	ENST00000288135	NM_000222.2	679	ttG/ttT	14/21	0.55255343924585	3	FACETS	0.915	0.81	1	0.305	0.27	0.342	CLONAL	1	FALSE	0	0.55255343924585	3		435	404	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334993	81334993	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	86	524	0	ENST00000222390.5:c.1834T>A	p.Cys612Ser	p.C612S	ENST00000222390	NM_000601.4	612	Tgc/Agc	16/18	0.330219440691847	5	FACETS	0.944	0.836	1	0.315	0.278	0.353	INDETERMINATE	1	FALSE	2	0.55255343924585	5		524	603	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392077	81392077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	82	348	3	ENST00000222390.5:c.200C>T	p.Ala67Val	p.A67V	ENST00000222390	NM_000601.4	67	gCa/gTa	2/18	0.330219440691847	5	FACETS	0.991	0.875	1	0.33	0.291	0.372	INDETERMINATE	1	FALSE	2	0.55255343924585	5		351	548	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781391	135781391	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	179	544	0	ENST00000298552.3:c.1574G>T	p.Ser525Ile	p.S525I	ENST00000298552	NM_001162426.1	525	aGt/aTt	15/23	0.106985544325479	3	FACETS	0.903	0.841	0.966	0.602	0.56	0.644	INDETERMINATE	2	FALSE	0	0.55255343924585	3		544	458	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	107	210	0				ENST00000310581	NM_198253.2	-/1132			0.722734341232824	3	FACETS	0.833	0.751	0.919	0.416	0.375	0.46	CLONAL	1	FALSE	1	0.722734341232824	3		210	484	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281668	49281668	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201815757	NA	P-0028011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	299	664	0	ENST00000282018.3:c.715C>T	p.Arg239Trp	p.R239W	ENST00000282018	NM_020377.2	239	Cgg/Tgg	1/1	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.722734341232824	2		664	749	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653217	29653217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	143	277	0	ENST00000356175.3:c.5152G>A	p.Val1718Ile	p.V1718I	ENST00000356175	NM_000267.3	1718	Gta/Ata	36/57	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.722734341232824	2		277	360	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0028012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	241	497	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.246457217438868	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.246457217438868	3		497	893	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0028012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	62	318	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.781	0.674	0.898	0.781	0.674	0.898	SUBCLONAL	1	TRUE	1	0.246457217438868	2		318	644	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620336	43620336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368550200	NA	P-0028012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	69	359	0	ENST00000355710.3:c.2945G>A	p.Arg982His	p.R982H	ENST00000355710	NM_020975.4	982	cGc/cAc	18/20	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.246457217438868	2		359	468	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	142	210	0				ENST00000310581	NM_198253.2	-/1132			0.206926458794465	4	FACETS	0.917	0.844	0.992	0.611	0.562	0.661	INDETERMINATE	2	TRUE	1	0.6	4		210	413	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0028013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	21	606	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.094	0.072	0.12	0.094	0.072	0.12	SUBCLONAL	1	TRUE	1	0.6	2		608	744	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	335	571	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.968	0.922	1	1	0.996	1	CLONAL	2	TRUE	1	0.479218419994727	2		571	722	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438316	110438317	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	rs532810290	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	47	196	1	ENST00000375856.3:c.82_84dup	p.Asn28dup	p.N28dup	ENST00000375856	NM_003749.2	28	-/AAC	1/2	0.247922063002316	5	FACETS	0.826	0.699	0.967	0.275	0.233	0.323	INDETERMINATE	1	TRUE	2	0.479218419994727	5		197	408	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141631	202141631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs17860424	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	96	457	3	ENST00000358485.4:c.919C>T	p.Arg307Trp	p.R307W	ENST00000358485	NM_001080125.1	307	Cgg/Tgg	7/9	0.479218419994727	2	FACETS	0.619	0.552	0.69	0.31	0.276	0.345	SUBCLONAL	1	TRUE	0	0.479218419994727	2		460	647	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	229	742	3	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.479218419994727	2		745	915	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	49	281	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.629	0.535	0.731	0.629	0.535	0.731	SUBCLONAL	1	TRUE	1	0.479218419994727	2		281	325	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614463	38614463	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	45	425	1	ENST00000299084.4:c.234del	p.Asp79ThrfsTer42	p.D79Tfs*42	ENST00000299084	NM_152594.2	77	Aaa/aa	3/7	1	2	FACETS	0.441	0.371	0.518	0.441	0.371	0.518	SUBCLONAL	1	TRUE	1	0.479218419994727	2		426	426	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444659	78444659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs908264837	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	37	385	1	ENST00000370768.2:c.30del	p.Ser11LeufsTer43	p.S11Lfs*43	ENST00000370768	NM_003902.3	10	ccC/cc	1/20	1	2	FACETS	0.259	0.213	0.311	0.259	0.213	0.311	SUBCLONAL	1	TRUE	1	0.479218419994727	2		386	596	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	128	469	6	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.945	0.86	1	0.945	0.86	1	CLONAL	1	TRUE	1	0.479218419994727	2		475	565	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	41	401	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	1	2	FACETS	0.369	0.307	0.437	0.369	0.307	0.437	SUBCLONAL	1	TRUE	1	0.479218419994727	2		401	464	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	112	438	0	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	0.114731072440708	5	FACETS	1	0.979	1	0.336	0.303	0.371	INDETERMINATE	1	TRUE	1	0.479218419994727	5		438	598	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	80	253	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	1	2	FACETS	0.869	0.77	0.975	0.869	0.77	0.975	CLONAL	1	TRUE	1	0.479218419994727	2		253	384	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251907	153251907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	19	389	0	ENST00000281708.4:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000281708	NM_033632.3	367	Cga/Tga	7/12	1	2	FACETS	0.209	0.158	0.269	0.209	0.158	0.269	SUBCLONAL	1	TRUE	1	0.479218419994727	2		389	380	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430396	181430396	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	238	682	1	ENST00000325404.1:c.248C>T	p.Ser83Leu	p.S83L	ENST00000325404	NM_003106.3	83	tCg/tTg	1/1	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.479218419994727	2		683	860	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120196	70120196	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	215	529	0	ENST00000245479.2:c.1198G>T	p.Glu400Ter	p.E400*	ENST00000245479	NM_000346.3	400	Gag/Tag	3/3	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.479218419994727	2		529	684	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383999	84383999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150371881	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	42	547	0	ENST00000321945.7:c.853C>T	p.Arg285Trp	p.R285W	ENST00000321945	NM_139076.2	285	Cgg/Tgg	9/9	1	2	FACETS	0.256	0.213	0.304	0.256	0.213	0.304	SUBCLONAL	1	TRUE	1	0.479218419994727	2		547	684	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482927	140482927	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	113	588	6	ENST00000288602.6:c.1208del	p.Pro403LeufsTer8	p.P403Lfs*8	ENST00000288602	NM_004333.4	403	cCt/ct	10/18	0.156188357583351	3	FACETS	0.805	0.725	0.89	0.403	0.362	0.445	INDETERMINATE	1	TRUE	1	0.479218419994727	3		594	726	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	29	463	2	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	0.244	0.195	0.3	0.244	0.195	0.3	SUBCLONAL	1	TRUE	1	0.479218419994727	2		465	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138729528	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	201	604	1	ENST00000269305.4:c.523C>T	p.Arg175Cys	p.R175C	ENST00000269305	NM_001126112.2	175	Cgc/Tgc	5/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.479218419994727	2		605	704	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195701	123195701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777363856	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	54	270	1	ENST00000218089.9:c.1615G>A	p.Val539Met	p.V539M	ENST00000218089	NM_001042749.1	539	Gtg/Atg	17/35	1	1	FACETS	0.471	0.404	0.544	0.471	0.404	0.544	SUBCLONAL	1	TRUE	0	0.479218419994727	1		271	364	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1255443	1255443	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763381198	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	184	582	1	ENST00000310581.5:c.3116C>T	p.Thr1039Met	p.T1039M	ENST00000310581	NM_198253.2	1039	aCg/aTg	14/16	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.479218419994727	2		583	754	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321300	65321300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757281554	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	88	515	1	ENST00000342505.4:c.1540C>T	p.Arg514Cys	p.R514C	ENST00000342505	NM_002227.2	514	Cgc/Tgc	11/25	1	2	FACETS	0.486	0.431	0.546	0.486	0.431	0.546	SUBCLONAL	1	TRUE	1	0.479218419994727	2		516	755	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988452	41988455	+	frameshift_variant	Frame_Shift_Del	DEL	CAAA	CAAA	-	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	51	510	0	ENST00000219905.7:c.1246_1249del	p.Asn416ValfsTer7	p.N416Vfs*7	ENST00000219905	NM_001164273.1	415	tCAAAc/tc	3/24	1	2	FACETS	0.384	0.326	0.447	0.384	0.326	0.447	SUBCLONAL	1	TRUE	1	0.479218419994727	2		510	555	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007689	45007690	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	32	349	0	ENST00000558401.1:c.137_138del	p.Tyr46CysfsTer10	p.Y46Cfs*10	ENST00000558401	NM_004048.2	46	TAt/t	2/4	1	2	FACETS	0.341	0.276	0.413	0.341	0.276	0.413	SUBCLONAL	1	TRUE	1	0.479218419994727	2		349	392	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447317	187447317	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	175	543	0	ENST00000232014.4:c.876del	p.Tyr293ThrfsTer31	p.Y293Tfs*31	ENST00000232014	NM_001130845.1	292	ccC/cc	5/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.479218419994727	2		543	647	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285669	46285669	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1368075571	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	97	381	0	ENST00000334344.6:c.5029C>T	p.Arg1677Ter	p.R1677*	ENST00000334344	NM_152641.2	1677	Cga/Tga	17/21	1	2	FACETS	0.792	0.709	0.88	0.792	0.709	0.88	SUBCLONAL	1	TRUE	1	0.479218419994727	2		381	511	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919548	78919548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769436510	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	63	411	0	ENST00000306801.3:c.3107C>T	p.Pro1036Leu	p.P1036L	ENST00000306801	NM_020761.2	1036	cCg/cTg	26/34	1	2	FACETS	0.464	0.401	0.532	0.464	0.401	0.532	SUBCLONAL	1	TRUE	1	0.479218419994727	2		411	567	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590764	189590764	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	124	521	0	ENST00000264731.3:c.1329C>G	p.His443Gln	p.H443Q	ENST00000264731	NM_003722.4	443	caC/caG	10/14	1	2	FACETS	0.697	0.631	0.767	0.697	0.631	0.767	SUBCLONAL	1	TRUE	1	0.479218419994727	2		521	742	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740809	58740809	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs765769406	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	237	518	0	ENST00000305921.3:c.1714C>T	p.Arg572Ter	p.R572*	ENST00000305921	NM_003620.3	572	Cga/Tga	6/6	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.479218419994727	2		518	779	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400035	139400035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61751541	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	152	678	0	ENST00000277541.6:c.4313G>A	p.Arg1438His	p.R1438H	ENST00000277541	NM_017617.3	1438	cGc/cAc	25/34	1	2	FACETS	0.816	0.748	0.888	0.816	0.748	0.888	CLONAL	1	TRUE	1	0.479218419994727	2		678	777	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376187	225376187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773927741	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	88	564	1	ENST00000264414.4:c.767C>T	p.Thr256Met	p.T256M	ENST00000264414	NM_003590.4	256	aCg/aTg	6/16	0.479218419994727	2	FACETS	0.578	0.513	0.648	0.289	0.256	0.324	SUBCLONAL	1	TRUE	0	0.479218419994727	2		565	635	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225574	133225574	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	57	565	0	ENST00000320574.5:c.4090del	p.Arg1364ValfsTer5	p.R1364Vfs*5	ENST00000320574	NM_006231.2	1364	Cgt/gt	32/49	1	2	FACETS	0.312	0.267	0.361	0.312	0.267	0.361	SUBCLONAL	1	TRUE	1	0.479218419994727	2		565	763	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	57	740	3	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	1	2	FACETS	0.215	0.183	0.249	0.215	0.183	0.249	SUBCLONAL	1	TRUE	1	0.479218419994727	2		743	1109	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131403	17131403	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs758385503	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	51	605	0	ENST00000285071.4:c.49del	p.Arg17AlafsTer38	p.R17Afs*38	ENST00000285071	NM_144997.5	17	Cgc/gc	4/14	1	2	FACETS	0.303	0.257	0.354	0.303	0.257	0.354	SUBCLONAL	1	TRUE	1	0.479218419994727	2		605	703	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	55	525	3	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.31	0.264	0.36	0.31	0.264	0.36	SUBCLONAL	1	TRUE	1	0.479218419994727	2		528	741	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510684	38510684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762374504	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	160	505	0	ENST00000254066.5:c.938C>T	p.Ala313Val	p.A313V	ENST00000254066	NM_000964.3	313	gCc/gTc	7/9	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.479218419994727	2		505	629	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346085	89346085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1282116476	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	15	101	2	ENST00000301030.4:c.6865G>A	p.Gly2289Ser	p.G2289S	ENST00000301030	NM_001256183.1	2289	Ggc/Agc	9/13	1	2	FACETS	0.659	0.489	0.857	0.659	0.489	0.857	SUBCLONAL	1	TRUE	1	0.479218419994727	2		103	95	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249911	110249911	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	27	513	0	ENST00000374672.4:c.764C>A	p.Pro255His	p.P255H	ENST00000374672	NM_004235.4	255	cCt/cAt	3/5	1	2	FACETS	0.222	0.176	0.275	0.222	0.176	0.275	SUBCLONAL	1	TRUE	1	0.479218419994727	2		513	508	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103666	47103666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	24	332	0	ENST00000409792.3:c.6280del	p.Arg2094GlyfsTer53	p.R2094Gfs*53	ENST00000409792	NM_014159.6	2094	Agg/gg	14/21	1	2	FACETS	0.229	0.179	0.287	0.229	0.179	0.287	SUBCLONAL	1	TRUE	1	0.479218419994727	2		332	438	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603092	48603092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786201798	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	150	486	0	ENST00000342988.3:c.1393G>A	p.Val465Met	p.V465M	ENST00000342988	NM_005359.5	465	Gtg/Atg	11/12	1	2	FACETS	0.894	0.819	0.973	0.894	0.819	0.973	CLONAL	1	TRUE	1	0.479218419994727	2		486	700	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620387	43620387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748288493	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	138	515	1	ENST00000355710.3:c.2996C>T	p.Ala999Val	p.A999V	ENST00000355710	NM_020975.4	999	gCg/gTg	18/20	1	2	FACETS	0.742	0.676	0.812	0.742	0.676	0.812	SUBCLONAL	1	TRUE	1	0.479218419994727	2		516	776	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133797	2133797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747695245	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	162	530	0	ENST00000219476.3:c.3985C>T	p.Arg1329Cys	p.R1329C	ENST00000219476	NM_000548.3	1329	Cgc/Tgc	33/42	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.479218419994727	2		530	569	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260194	16260194	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1557761571	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	117	473	1	ENST00000375759.3:c.7464del	p.Ile2489SerfsTer10	p.I2489Sfs*10	ENST00000375759	NM_015001.2	2487	Ggg/gg	11/15	1	2	FACETS	0.934	0.846	1	0.934	0.846	1	CLONAL	1	TRUE	1	0.479218419994727	2		474	523	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807363	36807363	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369580497	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	117	546	1	ENST00000373129.3:c.1301G>A	p.Arg434Gln	p.R434Q	ENST00000373129	NM_032017.1	434	cGg/cAg	12/12	1	2	FACETS	0.751	0.679	0.828	0.751	0.679	0.828	SUBCLONAL	1	TRUE	1	0.479218419994727	2		547	650	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670503	246670503	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	49	384	1	ENST00000388985.4:c.17T>C	p.Val6Ala	p.V6A	ENST00000388985		6	gTg/gCg	1/12	1	2	FACETS	0.415	0.351	0.485	0.415	0.351	0.485	SUBCLONAL	1	TRUE	1	0.479218419994727	2		385	493	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100645	8100645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1218595084	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	184	679	0	ENST00000346208.3:c.619G>A	p.Ala207Thr	p.A207T	ENST00000346208		207	Gcc/Acc	3/6	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.479218419994727	2		679	716	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596144	43596144	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	103	514	0	ENST00000355710.3:c.311G>T	p.Ser104Ile	p.S104I	ENST00000355710	NM_020975.4	104	aGc/aTc	2/20	1	2	FACETS	0.725	0.65	0.804	0.725	0.65	0.804	SUBCLONAL	1	TRUE	1	0.479218419994727	2		514	593	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70360764	70360764	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	81	293	0	ENST00000373644.4:c.1941G>C	p.Gln647His	p.Q647H	ENST00000373644	NM_030625.2	647	caG/caC	3/12	1	2	FACETS	0.874	0.774	0.978	0.874	0.774	0.978	CLONAL	1	TRUE	1	0.479218419994727	2		293	387	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450999	70450999	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	51	502	0	ENST00000373644.4:c.5839A>G	p.Thr1947Ala	p.T1947A	ENST00000373644	NM_030625.2	1947	Acc/Gcc	12/12	1	2	FACETS	0.368	0.313	0.429	0.368	0.313	0.429	SUBCLONAL	1	TRUE	1	0.479218419994727	2		502	578	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154344	2154344	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	189	734	0	ENST00000434045.2:c.584del	p.Gly195ValfsTer20	p.G195Vfs*20	ENST00000434045	NM_001127598.1	195	gGt/gt	5/5	1	2	FACETS	0.885	0.819	0.954	0.885	0.819	0.954	CLONAL	1	TRUE	1	0.479218419994727	2		734	891	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742497	17742497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	140	588	0	ENST00000250003.3:c.679G>A	p.Glu227Lys	p.E227K	ENST00000250003	NM_002478.4	227	Gaa/Aaa	2/3	1	2	FACETS	0.904	0.826	0.986	0.904	0.826	0.986	CLONAL	1	TRUE	1	0.479218419994727	2		588	646	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201667	67201668	+	splice_acceptor_variant	Splice_Site	DEL	AG	AG	-	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	108	532	0	ENST00000312629.5:c.971_972del		p.X324_splice	ENST00000312629	NM_003952.2	324			1	2	FACETS	0.821	0.739	0.907	0.821	0.739	0.907	CLONAL	1	TRUE	1	0.479218419994727	2		532	549	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911874	94911874	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	66	513	0	ENST00000536441.1:c.1056G>T	p.Gln352His	p.Q352H	ENST00000536441	NM_144665.3	352	caG/caT	7/10	1	2	FACETS	0.528	0.458	0.602	0.528	0.458	0.602	SUBCLONAL	1	TRUE	1	0.479218419994727	2		513	522	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375125	118375125	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	70	384	0	ENST00000534358.1:c.8518A>G	p.Asn2840Asp	p.N2840D	ENST00000534358	NM_005933.3	2840	Aac/Gac	27/36	1	2	FACETS	0.753	0.66	0.852	0.753	0.66	0.852	SUBCLONAL	1	TRUE	1	0.479218419994727	2		384	388	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156187	119156187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1344210823	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	131	514	0	ENST00000264033.4:c.1852C>T	p.His618Tyr	p.H618Y	ENST00000264033	NM_005188.3	618	Cac/Tac	11/16	1	2	FACETS	0.817	0.743	0.895	0.817	0.743	0.895	CLONAL	1	TRUE	1	0.479218419994727	2		514	669	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230620	46230620	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	90	433	0	ENST00000334344.6:c.869C>A	p.Ala290Glu	p.A290E	ENST00000334344	NM_152641.2	290	gCa/gAa	8/21	1	2	FACETS	0.871	0.777	0.971	0.871	0.777	0.971	CLONAL	1	TRUE	1	0.479218419994727	2		433	431	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416600	49416600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	140	464	0	ENST00000301067.7:c.16111G>A	p.Glu5371Lys	p.E5371K	ENST00000301067	NM_003482.3	5371	Gag/Aag	51/54	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.479218419994727	2		464	562	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562556	21562556	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	26	113	0	ENST00000382592.4:c.1363C>T	p.Gln455Ter	p.Q455*	ENST00000382592	NM_014572.2	455	Cag/Tag	4/8	0.247922063002316	5	FACETS	1	0.829	1	0.347	0.277	0.426	INDETERMINATE	1	TRUE	2	0.479218419994727	5		113	179	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643719	38643719	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	105	647	1	ENST00000299084.4:c.1189G>A	p.Asp397Asn	p.D397N	ENST00000299084	NM_152594.2	397	Gac/Aac	7/7	1	2	FACETS	0.558	0.499	0.619	0.558	0.499	0.619	SUBCLONAL	1	TRUE	1	0.479218419994727	2		648	786	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034933	42034933	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	49	528	0	ENST00000219905.7:c.4775C>A	p.Pro1592His	p.P1592H	ENST00000219905	NM_001164273.1	1592	cCt/cAt	15/24	1	2	FACETS	0.323	0.273	0.378	0.323	0.273	0.378	SUBCLONAL	1	TRUE	1	0.479218419994727	2		528	633	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003770	45003770	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	91	398	0	ENST00000558401.1:c.26T>A	p.Val9Glu	p.V9E	ENST00000558401	NM_004048.2	9	gTg/gAg	1/4	1	2	FACETS	0.929	0.83	1	0.929	0.83	1	CLONAL	1	TRUE	1	0.479218419994727	2		398	409	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348127	348127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560238796	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	133	674	0	ENST00000262320.3:c.1379G>A	p.Arg460Gln	p.R460Q	ENST00000262320	NM_003502.3	460	cGg/cAg	6/11	1	2	FACETS	0.748	0.68	0.819	0.748	0.68	0.819	SUBCLONAL	1	TRUE	1	0.479218419994727	2		674	742	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827466	72827466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	44	636	1	ENST00000268489.5:c.9115G>A	p.Val3039Ile	p.V3039I	ENST00000268489	NM_006885.3	3039	Gta/Ata	9/10	1	2	FACETS	0.247	0.206	0.292	0.247	0.206	0.292	SUBCLONAL	1	TRUE	1	0.479218419994727	2		637	744	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969958	81969958	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	31	404	0	ENST00000359376.3:c.3027G>T	p.Met1009Ile	p.M1009I	ENST00000359376	NM_002661.3	1009	atG/atT	27/33	1	2	FACETS	0.231	0.186	0.282	0.231	0.186	0.282	SUBCLONAL	1	TRUE	1	0.479218419994727	2		404	560	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936262	78936262	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs777396934	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	116	519	1	ENST00000306801.3:c.3694G>A	p.Val1232Ile	p.V1232I	ENST00000306801	NM_020761.2	1232	Gtc/Atc	32/34	1	2	FACETS	0.912	0.825	1	0.912	0.825	1	CLONAL	1	TRUE	1	0.479218419994727	2		520	531	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210518	5210518	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	194	527	0	ENST00000357368.4:c.5449C>T	p.Gln1817Ter	p.Q1817*	ENST00000357368	NM_002850.3	1817	Cag/Tag	35/38	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.479218419994727	2		527	747	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144844	11144844	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568512220	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	186	556	0	ENST00000358026.2:c.3919G>A	p.Ala1307Thr	p.A1307T	ENST00000358026	NM_001128849.1	1307	Gcc/Acc	28/36	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.479218419994727	2		556	694	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349753	15349753	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	137	630	0	ENST00000263377.2:c.3821G>A	p.Arg1274Gln	p.R1274Q	ENST00000263377	NM_058243.2	1274	cGg/cAg	19/20	1	2	FACETS	0.958	0.874	1	0.958	0.874	1	CLONAL	1	TRUE	1	0.479218419994727	2		630	597	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952489	17952489	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	162	690	0	ENST00000458235.1:c.944A>G	p.His315Arg	p.H315R	ENST00000458235	NM_000215.3	315	cAc/cGc	7/24	1	2	FACETS	0.846	0.777	0.918	0.846	0.777	0.918	CLONAL	1	TRUE	1	0.479218419994727	2		690	799	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279562	18279562	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	138	615	0	ENST00000222254.8:c.1835A>G	p.Asp612Gly	p.D612G	ENST00000222254	NM_005027.3	612	gAc/gGc	15/16	1	2	FACETS	0.779	0.71	0.852	0.779	0.71	0.852	SUBCLONAL	1	TRUE	1	0.479218419994727	2		615	739	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798118	42798118	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	172	623	0	ENST00000575354.2:c.4072C>T	p.Arg1358Cys	p.R1358C	ENST00000575354	NM_015125.3	1358	Cgc/Tgc	17/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.479218419994727	2		623	590	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793291	242793291	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	48	781	0	ENST00000334409.5:c.786del	p.Ala263ProfsTer15	p.A263Pfs*15	ENST00000334409	NM_005018.2	262	ccC/cc	5/5	0.479218419994727	2	FACETS	0.237	0.199	0.279	0.119	0.099	0.14	SUBCLONAL	1	TRUE	0	0.479218419994727	2		781	845	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021590	31021590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs988568801	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	149	501	3	ENST00000375687.4:c.1589C>T	p.Ala530Val	p.A530V	ENST00000375687	NM_015338.5	530	gCg/gTg	12/13	0.114731072440708	5	FACETS	1	0.987	1	0.362	0.331	0.394	INDETERMINATE	1	TRUE	1	0.479218419994727	5		504	739	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29099521	29099521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	80	402	0	ENST00000328354.6:c.880G>A	p.Ala294Thr	p.A294T	ENST00000328354	NM_007194.3	294	Gca/Aca	8/15	1	2	FACETS	0.532	0.469	0.601	0.532	0.469	0.601	SUBCLONAL	1	TRUE	1	0.479218419994727	2		402	627	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430206	181430208	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	29	308	0	ENST00000325404.1:c.67_69del	p.Gly23del	p.G23del	ENST00000325404	NM_003106.3	20	GGC/-	1/1	1	2	FACETS	0.325	0.261	0.399	0.325	0.261	0.399	SUBCLONAL	1	TRUE	1	0.479218419994727	2		308	372	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430208	181430211	+	frameshift_variant	Frame_Shift_Del	DEL	CGGC	CGGC	GG	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	68	320	1	ENST00000325404.1:c.60_63delinsGG	p.Gly22ArgfsTer73	p.G22Rfs*73	ENST00000325404	NM_003106.3	20	ggCGGC/ggGG	1/1	1	2	FACETS	0.711	0.622	0.807	0.711	0.622	0.807	SUBCLONAL	1	TRUE	1	0.479218419994727	2		321	399	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447647	187447647	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	120	538	0	ENST00000232014.4:c.546del	p.Ser183AlafsTer141	p.S183Afs*141	ENST00000232014	NM_001130845.1	182	ccC/cc	5/10	1	2	FACETS	0.773	0.699	0.85	0.773	0.699	0.85	SUBCLONAL	1	TRUE	1	0.479218419994727	2		538	648	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213816	66213816	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	39	422	0	ENST00000273854.3:c.2614G>A	p.Val872Met	p.V872M	ENST00000273854	NM_004439.5	872	Gtg/Atg	15/18	1	2	FACETS	0.363	0.301	0.433	0.363	0.301	0.433	SUBCLONAL	1	TRUE	1	0.479218419994727	2		422	448	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156321	106156321	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	62	353	0	ENST00000380013.4:c.1226del	p.Pro409LeufsTer18	p.P409Lfs*18	ENST00000380013	NM_001127208.2	408	Ccc/cc	3/11	1	2	FACETS	0.628	0.544	0.718	0.628	0.544	0.718	SUBCLONAL	1	TRUE	1	0.479218419994727	2		353	412	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31421456	31421456	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	41	456	0	ENST00000344624.3:c.3448G>T	p.Gly1150Cys	p.G1150C	ENST00000344624		1150	Ggt/Tgt	27/33	1	2	FACETS	0.316	0.262	0.375	0.316	0.262	0.375	SUBCLONAL	1	TRUE	1	0.479218419994727	2		456	542	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31947331	31947331	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs752938149	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	119	386	0	ENST00000375333.2:c.815+1G>A		p.X272_splice	ENST00000375333	NM_032454.1	272			0.156188357583351	3	FACETS	1	0.931	1	0.517	0.468	0.569	INDETERMINATE	1	TRUE	1	0.479218419994727	3		386	595	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29195835	29195835	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	172	715	0	ENST00000240100.2:c.763A>G	p.Ile255Val	p.I255V	ENST00000240100	NM_001394.6	255	Atc/Gtc	3/4	1	2	FACETS	0.815	0.75	0.882	0.815	0.75	0.882	CLONAL	1	TRUE	1	0.479218419994727	2		715	881	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750889	128750891	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	rs765532126	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	53	599	0	ENST00000377970.2:c.433_435del	p.Ile145del	p.I145del	ENST00000377970	NM_002467.4	142	aaCATc/aac	2/3	1	2	FACETS	0.299	0.254	0.348	0.299	0.254	0.348	SUBCLONAL	1	TRUE	1	0.479218419994727	2		599	741	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738168	133738168	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	64	385	0	ENST00000318560.5:c.568A>C	p.Ser190Arg	p.S190R	ENST00000318560	NM_005157.4	190	Agc/Cgc	4/11	1	2	FACETS	0.5	0.433	0.572	0.5	0.433	0.572	SUBCLONAL	1	TRUE	1	0.479218419994727	2		385	534	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300836	137300836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	212	653	0	ENST00000481739.1:c.481C>T	p.Arg161Trp	p.R161W	ENST00000481739	NM_002957.4	161	Cgg/Tgg	4/10	1	2	FACETS	0.987	0.918	1	0.987	0.918	1	CLONAL	1	TRUE	1	0.479218419994727	2		653	896	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137323779	137323779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368400425	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	163	670	1	ENST00000481739.1:c.1072C>T	p.Arg358Trp	p.R358W	ENST00000481739	NM_002957.4	358	Cgg/Tgg	8/10	1	2	FACETS	0.849	0.78	0.921	0.849	0.78	0.921	CLONAL	1	TRUE	1	0.479218419994727	2		671	801	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361790	70361790	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	53	316	0	ENST00000374080.3:c.6466C>T	p.Arg2156Trp	p.R2156W	ENST00000374080		2156	Cgg/Tgg	44/45	1	1	FACETS	0.323	0.275	0.375	0.323	0.275	0.375	SUBCLONAL	1	TRUE	0	0.479218419994727	1		316	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0028015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	391	606	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.686667707333978	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.71114997682921	2		608	547	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0028015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	433	412	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.71114997682921	4	FACETS	0.998	0.963	1	0.998	0.963	1	CLONAL	3	TRUE	1	0.71114997682921	4		412	696	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347756	347756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769767245	NA	P-0028015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	236	788	2	ENST00000262320.3:c.1750G>A	p.Ala584Thr	p.A584T	ENST00000262320	NM_003502.3	584	Gct/Act	6/11	0.644594931432177	4	FACETS	0.968	0.903	1	0.484	0.451	0.518	CLONAL	1	TRUE	2	0.71114997682921	4		790	1173	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962553	100962553	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778032418	NA	P-0028015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	381	516	0	ENST00000325455.5:c.1844G>A	p.Arg615His	p.R615H	ENST00000325455	NM_001202474.3	615	cGc/cAc	3/8	0.71114997682921	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.71114997682921	3		516	693	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097802	27097802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	121	399	0	ENST00000324856.7:c.3391C>T	p.Gln1131Ter	p.Q1131*	ENST00000324856	NM_006015.4	1131	Cag/Tag	12/20	1	2	FACETS	0.93	0.849	1	0.93	0.849	1	CLONAL	1	TRUE	1	0.71114997682921	2		399	366	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140487359	140487359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs577372072	NA	P-0028015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	231	694	0	ENST00000288602.6:c.1166G>A	p.Arg389His	p.R389H	ENST00000288602	NM_004333.4	389	cGt/cAt	9/18	0.628317533395098	4	FACETS	1	0.937	1	0.503	0.468	0.539	CLONAL	1	TRUE	2	0.71114997682921	4		694	1105	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	141	210	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.935	0.858	1	0.935	0.858	1	CLONAL	1	TRUE	1	0.633388099541692	2		210	476	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720741	89720741	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs371387815	NA	P-0028018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	34	194	0	ENST00000371953.3:c.892C>T	p.Gln298Ter	p.Q298*	ENST00000371953	NM_000314.4	298	Caa/Taa	8/9	0.633388099541692	2	FACETS	1	0.922	1	0.583	0.492	0.679	CLONAL	1	TRUE	0	0.633388099541692	2		194	92	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325974	30325977	+	frameshift_variant	Frame_Shift_Del	DEL	AGAT	AGAT	-	rs747796605	NA	P-0028018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	81	433	0	ENST00000322652.5:c.2174_2177del	p.Asp725ValfsTer18	p.D725Vfs*18	ENST00000322652	NM_015355.2	724	acAGAT/ac	16/16	1	2	FACETS	0.894	0.797	0.996	0.894	0.797	0.996	CLONAL	1	TRUE	1	0.633388099541692	2		433	286	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792758	33792758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568419813	NA	P-0028018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	39	37	0	ENST00000498907.2:c.563C>T	p.Pro188Leu	p.P188L	ENST00000498907	NM_004364.3	188	cCg/cTg	1/1	0.480960975359905	3	FACETS	1	0.907	1	0.555	0.468	0.648	CLONAL	1	TRUE	1	0.633388099541692	3		37	146	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729927	47729927	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	208	444	0	ENST00000449228.1:c.462C>G	p.His154Gln	p.H154Q	ENST00000449228	NM_001127240.2	154	caC/caG	3/4	0.480960975359905	3	FACETS	0.972	0.903	1	0.486	0.451	0.522	CLONAL	1	TRUE	1	0.633388099541692	3		444	890	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427772	72427772	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	128	233	0	ENST00000477973.2:c.718G>A	p.Val240Met	p.V240M	ENST00000477973	NM_012234.5	240	Gtg/Atg	4/4	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.633388099541692	2		233	348	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979480	2979480	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	219	547	0	ENST00000396946.4:c.767A>G	p.Asp256Gly	p.D256G	ENST00000396946	NM_032415.4	256	gAc/gGc	6/25	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.486257852978822	2		547	867	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601927	43601927	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1278030644	NA	P-0028020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	289	716	1	ENST00000355710.3:c.971G>A	p.Trp324Ter	p.W324*	ENST00000355710	NM_020975.4	324	tGg/tAg	5/20	0.227302791592886	3	FACETS	1	0.993	1	0.693	0.652	0.735	INDETERMINATE	1	TRUE	1	0.486257852978822	3		717	1066	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579360	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0028020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	268	669	0	ENST00000269305.4:c.326_327dup	p.Arg110SerfsTer14	p.R110Sfs*14	ENST00000269305	NM_001126112.2	109	-/TC	4/11	0.486257852978822	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.486257852978822	1		669	692	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0028033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	81	643	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	0.24524803373973	3	FACETS	1	0.934	1	0.545	0.48	0.615	CLONAL	1	TRUE	1	0.24524803373973	3		643	680	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205684	128205684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	66	667	1	ENST00000341105.2:c.191C>T	p.Ala64Val	p.A64V	ENST00000341105	NM_032638.4	64	gCt/gTt	2/6	0.24524803373973	1	FACETS	0.551	0.477	0.632	0.551	0.477	0.632	SUBCLONAL	1	TRUE	0	0.24524803373973	1		668	857	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1952878	1952878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	88	785	0	ENST00000382891.5:c.1961C>T	p.Ser654Leu	p.S654L	ENST00000382891	NM_133335.3	654	tCa/tTa	10/22	0.24524803373973	1	FACETS	0.717	0.634	0.806	0.717	0.634	0.806	SUBCLONAL	1	TRUE	0	0.24524803373973	1		785	878	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	324	529	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.628629283294539	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.628629283294539	2		529	487	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	577	600	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.93	0.9	0.96	1	0.998	1	CLONAL	2	TRUE	1	0.628629283294539	2		606	987	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	319	338	2	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.849	0.81	0.887	1	0.996	1	CLONAL	2	TRUE	1	0.628629283294539	2		340	598	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	172	611	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.988	0.915	1	0.988	0.915	1	CLONAL	1	TRUE	1	0.628629283294539	2		611	554	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	329	546	4	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.97	0.918	1	0.97	0.918	1	CLONAL	1	TRUE	1	0.628629283294539	2		550	1079	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	229	434	0	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.628629283294539	2		434	723	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188823	32188823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs8192585	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	285	581	1	ENST00000375023.3:c.731C>T	p.Ser244Leu	p.S244L	ENST00000375023	NM_004557.3	244	tCg/tTg	4/30	1	2	FACETS	0.886	0.834	0.94	0.886	0.834	0.94	CLONAL	1	TRUE	1	0.628629283294539	2		582	1023	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	267	469	6	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.628629283294539	2		475	831	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	193	410	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.886	0.823	0.951	0.886	0.823	0.951	CLONAL	1	TRUE	1	0.628629283294539	2		410	693	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692790	89692790	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	259	362	1	ENST00000371953.3:c.274G>C	p.Asp92His	p.D92H	ENST00000371953	NM_000314.4	92	Gac/Cac	5/9	0.628629283294539	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.628629283294539	2		363	394	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	106	310	2	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	1	2	FACETS	0.955	0.865	1	0.955	0.865	1	CLONAL	1	TRUE	1	0.628629283294539	2		312	353	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293662	1293662	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1304418053	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	358	647	0	ENST00000310581.5:c.1339C>T	p.Arg447Cys	p.R447C	ENST00000310581	NM_198253.2	447	Cgc/Tgc	2/16	1	2	FACETS	0.995	0.943	1	0.995	0.943	1	CLONAL	1	TRUE	1	0.628629283294539	2		647	1145	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121805	2121807	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs137854104	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	280	667	0	ENST00000219476.3:c.1973_1975del	p.Lys658del	p.K658del	ENST00000219476	NM_000548.3	656	gAGAag/gag	19/42	1	2	FACETS	0.791	0.743	0.841	0.791	0.743	0.841	SUBCLONAL	1	TRUE	1	0.628629283294539	2		667	1126	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	416	621	0	ENST00000227507.2:c.859C>T	p.Pro287Ser	p.P287S	ENST00000227507	NM_053056.2	287	Ccc/Tcc	5/5	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.628629283294539	2		621	1289	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673750	176673750	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	209	443	2	ENST00000439151.2:c.4455del	p.Val1486Ter	p.V1486*	ENST00000439151	NM_022455.4	1484	Aaa/aa	10/23	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.628629283294539	2		445	661	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678508	88678508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs183806623	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	52	364	0	ENST00000360948.2:c.1028G>A	p.Arg343Gln	p.R343Q	ENST00000360948	NM_001012338.2	343	cGg/cAg	9/19	1	2	FACETS	0.26	0.221	0.303	0.26	0.221	0.303	SUBCLONAL	1	TRUE	1	0.628629283294539	2		364	637	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402537	20402537	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	204	344	0	ENST00000346618.3:c.74T>C	p.Val25Ala	p.V25A	ENST00000346618	NM_001949.4	25	gTc/gCc	1/7	1	2	FACETS	0.895	0.833	0.959	0.895	0.833	0.959	CLONAL	1	TRUE	1	0.628629283294539	2		344	725	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268379	142268380	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1559984993	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	147	421	0	ENST00000350721.4:c.3112dup	p.Ser1038PhefsTer11	p.S1038Ffs*11	ENST00000350721	NM_001184.3	1038	tct/tTct	15/47	1	2	FACETS	0.939	0.863	1	0.939	0.863	1	CLONAL	1	TRUE	1	0.628629283294539	2		421	498	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370236	40370236	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs761761205	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	195	667	12	ENST00000293328.3:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000293328	NM_012448.3	368	Cag/ag	9/19	1	2	FACETS	0.585	0.541	0.631	0.585	0.541	0.631	SUBCLONAL	1	TRUE	1	0.628629283294539	2		679	1060	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219487	133219487	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	307	672	0	ENST00000320574.5:c.4647del	p.Lys1550AsnfsTer12	p.K1550Nfs*12	ENST00000320574	NM_006231.2	1549	ccC/cc	36/49	NA	2	FACETS	0.955	0.901	1			1	INDETERMINATE	1	TRUE	NA	0.628629283294539	2		672	1023	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722761	49722761	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs62262682	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	10	22	2	ENST00000449682.2:c.1478G>T	p.Arg493Leu	p.R493L	ENST00000449682	NM_020998.3	493	cGt/cTt	13/18	1	2	FACETS	0.663	0.462	0.899	0.663	0.462	0.899	SUBCLONAL	1	TRUE	1	0.628629283294539	2		24	48	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431367	121431367	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	271	477	1	ENST00000257555.6:c.571G>T	p.Gly191Cys	p.G191C	ENST00000257555		191	Ggt/Tgt	3/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.628629283294539	2		478	839	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954643	17954643	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	388	730	2	ENST00000458235.1:c.251del	p.Pro84ArgfsTer63	p.P84Rfs*63	ENST00000458235	NM_000215.3	84	cCg/cg	3/24	1	2	FACETS	0.876	0.832	0.922	0.876	0.832	0.922	CLONAL	1	TRUE	1	0.628629283294539	2		732	1409	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149973	202149973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1272714323	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	265	475	0	ENST00000358485.4:c.1414C>T	p.Arg472Ter	p.R472*	ENST00000358485	NM_001080125.1	472	Cga/Tga	8/9	1	2	FACETS	0.952	0.894	1	0.952	0.894	1	CLONAL	1	TRUE	1	0.628629283294539	2		475	886	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563349	21563349	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	377	761	0	ENST00000382592.4:c.570del	p.Tyr191ThrfsTer49	p.Y191Tfs*49	ENST00000382592	NM_014572.2	190	ccC/cc	4/8	1	2	FACETS	0.98	0.93	1	0.98	0.93	1	CLONAL	1	TRUE	1	0.628629283294539	2		761	1224	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966873	25966873	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1271466699	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	37	512	2	ENST00000435504.4:c.2333del	p.Pro778GlnfsTer21	p.P778Qfs*21	ENST00000435504		778	cCa/ca	13/13	1	2	FACETS	0.166	0.136	0.199	0.166	0.136	0.199	SUBCLONAL	1	TRUE	1	0.628629283294539	2		514	710	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552143	29552144	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1555613558	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	79	267	0	ENST00000356175.3:c.1882dup	p.Tyr628LeufsTer6	p.Y628Lfs*6	ENST00000356175	NM_000267.3	626	ctt/cTtt	17/57	1	2	FACETS	0.997	0.89	1	0.997	0.89	1	CLONAL	1	TRUE	1	0.628629283294539	2		267	252	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339926	116339926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764052874	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	198	409	2	ENST00000397752.3:c.788C>T	p.Thr263Met	p.T263M	ENST00000397752	NM_000245.2	263	aCg/aTg	2/21	0.628629283294539	3	FACETS	1	0.972	1	0.545	0.506	0.586	CLONAL	1	TRUE	1	0.628629283294539	3		411	759	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625696	1625696	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	357	587	1	ENST00000344749.5:c.378del	p.Ser127GlnfsTer17	p.S127Qfs*17	ENST00000344749	NM_001136139.2	126	ctG/ct	7/19	NA	2	FACETS	0.97	0.92	1			1	INDETERMINATE	1	TRUE	NA	0.628629283294539	2		588	1171	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204992	128204992	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	263	525	2	ENST00000341105.2:c.449del	p.Gly150GlufsTer68	p.G150Efs*68	ENST00000341105	NM_032638.4	150	gGa/ga	3/6	1	2	FACETS	0.875	0.821	0.931	0.875	0.821	0.931	CLONAL	1	TRUE	1	0.628629283294539	2		527	956	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645975	215645975	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs587780033	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	159	354	0	ENST00000260947.4:c.623del	p.Lys208ArgfsTer4	p.K208Rfs*4	ENST00000260947	NM_000465.2	208	aAg/ag	4/11	1	2	FACETS	0.939	0.866	1	0.939	0.866	1	CLONAL	1	TRUE	1	0.628629283294539	2		354	539	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957496	175957496	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1326454203	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	154	492	1	ENST00000367669.3:c.1900C>T	p.Arg634Cys	p.R634C	ENST00000367669	NM_022457.5	634	Cgt/Tgt	17/20	1	2	FACETS	0.846	0.778	0.917	0.846	0.778	0.917	CLONAL	1	TRUE	1	0.628629283294539	2		493	579	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225632	26225632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	43	406	0	ENST00000360408.1:c.250C>T	p.Arg84Cys	p.R84C	ENST00000360408	NM_003532.2	84	Cgc/Tgc	1/1	1	2	FACETS	0.179	0.149	0.213	0.179	0.149	0.213	SUBCLONAL	1	TRUE	1	0.628629283294539	2		406	764	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340168	116340168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761768345	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	147	235	0	ENST00000397752.3:c.1030G>A	p.Gly344Arg	p.G344R	ENST00000397752	NM_000245.2	344	Ggg/Agg	2/21	0.628629283294539	3	FACETS	1	0.95	1	0.525	0.482	0.571	CLONAL	1	TRUE	1	0.628629283294539	3		235	585	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464881	120464881	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	209	384	0	ENST00000256646.2:c.5191G>T	p.Gly1731Ter	p.G1731*	ENST00000256646	NM_024408.3	1731	Gga/Tga	28/34	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.628629283294539	2		384	662	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940594	71940594	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	308	535	2	ENST00000298229.2:c.745C>T	p.Gln249Ter	p.Q249*	ENST00000298229	NM_001567.3	249	Cag/Tag	6/28	1	2	FACETS	0.955	0.902	1	0.955	0.902	1	CLONAL	1	TRUE	1	0.628629283294539	2		537	1026	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121532	108121532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760676955	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	180	409	0	ENST00000278616.4:c.1340G>A	p.Arg447Gln	p.R447Q	ENST00000278616	NM_000051.3	447	cGa/cAa	10/63	1	2	FACETS	0.948	0.879	1	0.948	0.879	1	CLONAL	1	TRUE	1	0.628629283294539	2		409	604	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425752	49425752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1320272329	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	269	545	0	ENST00000301067.7:c.12736C>T	p.Pro4246Ser	p.P4246S	ENST00000301067	NM_003482.3	4246	Cct/Tct	39/54	1	2	FACETS	0.967	0.909	1	0.967	0.909	1	CLONAL	1	TRUE	1	0.628629283294539	2		545	885	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209289	133209292	+	frameshift_variant	Frame_Shift_Del	DEL	GCTG	GCTG	-	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	69	629	0	ENST00000320574.5:c.6094_6097del	p.Gln2032SerfsTer15	p.Q2032Sfs*15	ENST00000320574	NM_006231.2	2032	CAGCtc/tc	44/49	1	2	FACETS	0.194	0.168	0.222	0.194	0.168	0.222	SUBCLONAL	1	TRUE	1	0.628629283294539	2		629	1133	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549227	21549227	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	376	771	0	ENST00000382592.4:c.3049G>T	p.Gly1017Cys	p.G1017C	ENST00000382592	NM_014572.2	1017	Ggt/Tgt	8/8	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.628629283294539	2		771	1176	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975408	26975408	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	136	455	0	ENST00000381527.3:c.1038del	p.Phe346LeufsTer14	p.F346Lfs*14	ENST00000381527	NM_001260.1	345	gTt/gt	11/13	1	2	FACETS	0.911	0.834	0.99	0.911	0.834	0.99	CLONAL	1	TRUE	1	0.628629283294539	2		455	475	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911472	32911472	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782223	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	121	392	0	ENST00000380152.3:c.2980G>A	p.Ala994Thr	p.A994T	ENST00000380152		994	Gca/Aca	11/27	1	2	FACETS	0.941	0.858	1	0.941	0.858	1	CLONAL	1	TRUE	1	0.628629283294539	2		392	409	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061541	38061541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	137	148	0	ENST00000250448.2:c.448C>T	p.Arg150Cys	p.R150C	ENST00000250448	NM_004496.3	150	Cgc/Tgc	2/2	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.628629283294539	2		148	345	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032402	42032402	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	191	387	0	ENST00000219905.7:c.4585+1G>T		p.X1529_splice	ENST00000219905	NM_001164273.1	1529			1	2	FACETS	0.933	0.867	1	0.933	0.867	1	CLONAL	1	TRUE	1	0.628629283294539	2		387	651	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483862	88483862	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	299	547	0	ENST00000360948.2:c.1708G>A	p.Ala570Thr	p.A570T	ENST00000360948	NM_001012338.2	570	Gct/Act	14/19	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.628629283294539	2		547	908	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350747	89350747	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	300	743	0	ENST00000301030.4:c.2203G>C	p.Glu735Gln	p.E735Q	ENST00000301030	NM_001256183.1	735	Gag/Cag	9/13	1	2	FACETS	0.975	0.92	1	0.975	0.92	1	CLONAL	1	TRUE	1	0.628629283294539	2		743	979	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351542	89351542	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	331	594	0	ENST00000301030.4:c.1408G>T	p.Gly470Ter	p.G470*	ENST00000301030	NM_001256183.1	470	Gga/Tga	9/13	1	2	FACETS	0.961	0.909	1	0.961	0.909	1	CLONAL	1	TRUE	1	0.628629283294539	2		594	1096	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435153	56435153	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768648593	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	339	598	1	ENST00000407977.2:c.1984G>A	p.Glu662Lys	p.E662K	ENST00000407977		662	Gag/Aag	9/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.628629283294539	2		599	992	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554039	63554039	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	296	509	0	ENST00000307078.5:c.700T>C	p.Trp234Arg	p.W234R	ENST00000307078	NM_004655.3	234	Tgg/Cgg	2/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.628629283294539	2		509	931	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39618740	39618740	+	splice_region_variant,intron_variant	Splice_Region	DEL	A	A	-	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	104	227	0	ENST00000262039.4:c.1969-2del		p.X657_splice	ENST00000262039	NM_002647.2	657			1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.628629283294539	2		227	317	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107184	11107186	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs1484395538	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	261	555	0	ENST00000358026.2:c.1778_1780del	p.Glu593del	p.E593del	ENST00000358026	NM_001128849.1	592	gcAGAa/gca	11/36	1	2	FACETS	0.878	0.824	0.933	0.878	0.824	0.933	CLONAL	1	TRUE	1	0.628629283294539	2		555	946	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627379	14627381	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	70	749	0	ENST00000254322.2:c.689_691del	p.Asn230del	p.N230del	ENST00000254322	NM_006145.1	230	aACAtt/att	2/3	1	2	FACETS	0.191	0.166	0.219	0.191	0.166	0.219	SUBCLONAL	1	TRUE	1	0.628629283294539	2		749	1165	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375451	15375451	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568388201	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	297	612	0	ENST00000263377.2:c.976C>T	p.Arg326Trp	p.R326W	ENST00000263377	NM_058243.2	326	Cgg/Tgg	6/20	1	2	FACETS	0.92	0.867	0.974	0.92	0.867	0.974	CLONAL	1	TRUE	1	0.628629283294539	2		612	1027	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212144	36212144	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	153	368	0	ENST00000222270.7:c.1898del	p.Pro633HisfsTer27	p.P633Hfs*27	ENST00000222270	NM_014727.1	632	tCc/tc	3/37	1	2	FACETS	0.749	0.687	0.813	0.749	0.687	0.813	SUBCLONAL	1	TRUE	1	0.628629283294539	2		368	650	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607691	46607692	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	299	620	0	ENST00000263734.3:c.1886_1887del	p.Ser629PhefsTer86	p.S629Ffs*86	ENST00000263734	NM_001430.4	627	cCT/c	12/16	1	2	FACETS	0.852	0.803	0.903	0.852	0.803	0.903	CLONAL	1	TRUE	1	0.628629283294539	2		620	1116	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128028913	128028913	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	267	467	3	ENST00000285398.2:c.1944del	p.Met650TrpfsTer32	p.M650Wfs*32	ENST00000285398	NM_000122.1	648	aaA/aa	12/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.628629283294539	2		470	783	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436362	52436362	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	289	535	0	ENST00000460680.1:c.2132A>C	p.Lys711Thr	p.K711T	ENST00000460680	NM_004656.3	711	aAg/aCg	17/17	1	2	FACETS	0.956	0.901	1	0.956	0.901	1	CLONAL	1	TRUE	1	0.628629283294539	2		535	962	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146575	185146575	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	220	507	0	ENST00000265026.3:c.206T>C	p.Leu69Ser	p.L69S	ENST00000265026	NM_004721.4	69	tTg/tCg	2/14	1	2	FACETS	0.849	0.792	0.908	0.849	0.792	0.908	CLONAL	1	TRUE	1	0.628629283294539	2		507	824	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164071	106164071	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	123	307	1	ENST00000380013.4:c.3581C>A	p.Pro1194His	p.P1194H	ENST00000380013	NM_001127208.2	1194	cCt/cAt	5/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.628629283294539	2		308	331	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518902	187518902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	230	549	0	ENST00000441802.2:c.12302G>A	p.Gly4101Asp	p.G4101D	ENST00000441802	NM_005245.3	4101	gGc/gAc	24/27	1	2	FACETS	0.87	0.813	0.929	0.87	0.813	0.929	CLONAL	1	TRUE	1	0.628629283294539	2		549	841	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645061	86645061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	96	330	0	ENST00000274376.6:c.1133C>T	p.Pro378Leu	p.P378L	ENST00000274376	NM_002890.2	378	cCc/cTc	8/25	1	2	FACETS	0.976	0.88	1	0.976	0.88	1	CLONAL	1	TRUE	1	0.628629283294539	2		330	313	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982059	93982059	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	168	445	1	ENST00000369303.4:c.1406C>A	p.Pro469His	p.P469H	ENST00000369303	NM_004440.3	469	cCc/cAc	6/17	1	2	FACETS	0.938	0.867	1	0.938	0.867	1	CLONAL	1	TRUE	1	0.628629283294539	2		446	570	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026834	6026834	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	225	467	0	ENST00000265849.7:c.1562C>T	p.Ala521Val	p.A521V	ENST00000265849	NM_000535.5	521	gCc/gTc	11/15	0.628629283294539	1	FACETS	0.884	0.831	0.939	0.884	0.831	0.939	CLONAL	1	TRUE	0	0.628629283294539	1		467	555	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6439775	6439775	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	254	458	0	ENST00000356142.4:c.301T>C	p.Phe101Leu	p.F101L	ENST00000356142	NM_018890.3	101	Ttt/Ctt	5/7	0.628629283294539	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.628629283294539	1		458	544	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874967	151874967	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	104	277	0	ENST00000262189.6:c.7571G>T	p.Arg2524Met	p.R2524M	ENST00000262189	NM_170606.2	2524	aGg/aTg	38/59	0.628629283294539	3	FACETS	0.76	0.683	0.842	0.38	0.341	0.421	SUBCLONAL	1	TRUE	1	0.628629283294539	3		277	572	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878634	151878634	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	196	475	1	ENST00000262189.6:c.6311C>T	p.Ala2104Val	p.A2104V	ENST00000262189	NM_170606.2	2104	gCa/gTa	36/59	0.628629283294539	3	FACETS	0.885	0.82	0.953	0.443	0.41	0.477	CLONAL	1	TRUE	1	0.628629283294539	3		476	926	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391536	139391536	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	385	682	0	ENST00000277541.6:c.6655C>G	p.Leu2219Val	p.L2219V	ENST00000277541	NM_017617.3	2219	Ctg/Gtg	34/34	1	2	FACETS	0.888	0.843	0.934	0.888	0.843	0.934	CLONAL	1	TRUE	1	0.628629283294539	2		682	1379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0028035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	121	578	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.2	2		578	1035	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913396	NA	P-0028035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	23	251	0	ENST00000349496.5:c.95A>G	p.Asp32Gly	p.D32G	ENST00000349496	NM_001904.3	32	gAc/gGc	3/15	1	2	FACETS	0.431	0.335	0.543	0.431	0.335	0.543	SUBCLONAL	1	TRUE	1	0.2	2		251	534	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016662	12016685	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAGGCCATACATGGCAGTAAGTGT	TAGGCCATACATGGCAGTAAGTGT	-	novel	NA	P-0028035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	43	214	0	ENST00000353533.5:c.800_813+10del		p.X267_splice	ENST00000353533	NM_003010.3	267		7/11	1	2	FACETS	0.869	0.727	1	0.869	0.727	1	CLONAL	1	TRUE	1	0.2	2		214	495	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933387	39933387	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs771322196	NA	P-0028035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	55	470	0	ENST00000378444.4:c.1212G>T	p.Gln404His	p.Q404H	ENST00000378444	NM_001123385.1	404	caG/caT	4/15	1	2	FACETS	0.531	0.452	0.617	0.531	0.452	0.617	SUBCLONAL	1	TRUE	1	0.2	2		470	1036	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50811826	50811826	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs886040872	NA	P-0028036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	62	742	0	ENST00000398568.2:c.1103C>A	p.Ser368Ter	p.S368*	ENST00000398568	NM_001042412.1	368	tCa/tAa	7/18	0.30819983349039	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.316307996043274	1		742	244	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778652	3778687	+	inframe_deletion	In_Frame_Del	DEL	GCCAGGCTGGGGTTGCATGCCGGGCTGGGACTGGAG	GCCAGGCTGGGGTTGCATGCCGGGCTGGGACTGGAG	-	rs761028983	NA	P-0028036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	105	475	1	ENST00000262367.5:c.6361_6396del	p.Leu2121_Gly2132del	p.L2121_G2132del	ENST00000262367	NM_004380.2	2121	CTCCAGTCCCAGCCCGGCATGCAACCCCAGCCTGGC/-	31/31	1	2	FACETS	0.841	0.754	0.935	0.841	0.754	0.935	CLONAL	1	TRUE	1	0.316307996043274	2		476	789	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399948	139399948	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1359387706	NA	P-0028036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	212	567	2	ENST00000277541.6:c.4400G>T	p.Cys1467Phe	p.C1467F	ENST00000277541	NM_017617.3	1467	tGc/tTc	25/34	1	2	FACETS	0.989	0.916	1	0.989	0.916	1	CLONAL	1	TRUE	1	0.316307996043274	2		569	1356	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413055	139413055	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	143	402	0	ENST00000277541.6:c.1087del	p.His363MetfsTer268	p.H363Mfs*268	ENST00000277541	NM_017617.3	363	Cat/at	6/34	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.316307996043274	2		402	806	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855985	68855985	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780759537	NA	P-0028037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	144	470	1	ENST00000261769.5:c.1793G>A	p.Arg598Gln	p.R598Q	ENST00000261769	NM_004360.3	598	cGa/cAa	12/16	0.836009632880601	1	FACETS	0.353	0.324	0.384	0.353	0.324	0.384	SUBCLONAL	1	TRUE	0	0.850300392900458	1		471	551	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430939	181430939	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	93	556	0	ENST00000325404.1:c.791C>A	p.Pro264His	p.P264H	ENST00000325404	NM_003106.3	264	cCc/cAc	1/1	1	2	FACETS	0.214	0.19	0.241	0.214	0.19	0.241	SUBCLONAL	1	TRUE	1	0.850300392900458	2		556	1020	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0028038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	206	497	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	0.57627710354299	2		497	695	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587780070	NA	P-0028038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	168	548	0	ENST00000269305.4:c.535C>G	p.His179Asp	p.H179D	ENST00000269305	NM_001126112.2	179	Cat/Gat	5/11	0.555761541761128	1	FACETS	0.986	0.917	1	0.986	0.917	1	CLONAL	1	TRUE	0	0.57627710354299	1		548	421	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99486169	99486169	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	180	390	0	ENST00000268035.6:c.3475G>C	p.Asp1159His	p.D1159H	ENST00000268035	NM_000875.3	1159	Gat/Cat	19/21	0.127278806685809	5	FACETS	0.834	0.772	0.899			1	INDETERMINATE	2	TRUE	NA	0.57627710354299	5		390	698	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0028041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	160	433	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.260333025814998	3	FACETS	0.864	0.795	0.936	0.864	0.795	0.936	CLONAL	2	TRUE	1	0.336416478262378	3		433	643	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0028041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	91	250	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.336416478262378	2		250	432	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145437	58145437	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1555201381	NA	P-0028041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	88	420	0	ENST00000257904.6:c.64A>C	p.Lys22Gln	p.K22Q	ENST00000257904	NM_000075.3	22	Aag/Cag	2/8	1	2	FACETS	0.923	0.819	1	0.923	0.819	1	CLONAL	1	TRUE	1	0.336416478262378	2		420	567	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981870	201981870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	328	692	4	ENST00000359651.3:c.581C>T	p.Ser194Phe	p.S194F	ENST00000359651		194	tCt/tTt	4/8	0.260333025814998	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.336416478262378	3		696	1084	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526251	189526251	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	155	584	0	ENST00000264731.3:c.515C>T	p.Pro172Leu	p.P172L	ENST00000264731	NM_003722.4	172	cCa/cTa	4/14	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.336416478262378	2		584	809	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358967	81358967	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	140	493	0	ENST00000222390.5:c.994C>T	p.Gln332Ter	p.Q332*	ENST00000222390	NM_000601.4	332	Cag/Tag	8/18	0.260333025814998	3	FACETS	1	0.983	1	0.666	0.607	0.727	CLONAL	1	TRUE	1	0.336416478262378	3		493	730	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141567331	141567331	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	101	415	2	ENST00000220592.5:c.883C>T	p.Pro295Ser	p.P295S	ENST00000220592	NM_012154.3	295	Ccg/Tcg	8/19	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.336416478262378	2		417	541	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0028051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	161	689	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.495463063824177	1	FACETS	0.986	0.911	1	0.986	0.911	1	CLONAL	1	TRUE	0	0.495463063824177	1		689	496	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692794	89692794	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121909238	NA	P-0028051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	82	377	0	ENST00000371953.3:c.278A>G	p.His93Arg	p.H93R	ENST00000371953	NM_000314.4	93	cAt/cGt	5/9	0.482108795639296	1	FACETS	0.909	0.812	1	0.909	0.812	1	CLONAL	1	TRUE	0	0.495463063824177	1		377	274	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971029	21971029	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519852	NA	P-0028051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	75	408	0	ENST00000304494.5:c.329G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tGg/tAg	2/3	0.495463063824177	1	FACETS	0.822	0.729	0.92	0.822	0.729	0.92	CLONAL	1	TRUE	0	0.495463063824177	1		408	277	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059260	27059260	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	170	514	0	ENST00000324856.7:c.1897C>T	p.Gln633Ter	p.Q633*	ENST00000324856	NM_006015.4	633	Cag/Tag	4/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.495463063824177	2		514	629	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0028051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	145	523	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.482108795639296	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.495463063824177	1		523	422	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436145	56436145	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	56	643	0	ENST00000407977.2:c.992C>G	p.Ser331Cys	p.S331C	ENST00000407977		331	tCt/tGt	9/10	1	2	FACETS	0.354	0.302	0.41	0.354	0.302	0.41	SUBCLONAL	1	TRUE	1	0.495463063824177	2		643	639	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685313	89685313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	114	382	0	ENST00000371953.3:c.208C>G	p.Leu70Val	p.L70V	ENST00000371953	NM_000314.4	70	Ctt/Gtt	3/9	0.482108795639296	1	FACETS	0.909	0.826	0.994	0.909	0.826	0.994	CLONAL	1	TRUE	0	0.495463063824177	1		382	381	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134245	2134245	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	55	542	0	ENST00000219476.3:c.4022G>T	p.Ser1341Ile	p.S1341I	ENST00000219476	NM_000548.3	1341	aGc/aTc	34/42	0.248119715866511	1	FACETS	0.347	0.296	0.401	0.347	0.296	0.401	INDETERMINATE	1	TRUE	0	0.495463063824177	1		542	482	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353820	40353820	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	134	570	0	ENST00000293328.3:c.2300G>T	p.Arg767Leu	p.R767L	ENST00000293328	NM_012448.3	767	cGg/cTg	19/19	1	2	FACETS	0.912	0.832	0.996	0.912	0.832	0.996	CLONAL	1	TRUE	1	0.495463063824177	2		570	593	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489782	40489782	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	76	515	0	ENST00000264657.5:c.644G>C	p.Arg215Thr	p.R215T	ENST00000264657	NM_139276.2	215	aGa/aCa	7/24	1	2	FACETS	0.512	0.449	0.58	0.512	0.449	0.58	SUBCLONAL	1	TRUE	1	0.495463063824177	2		515	599	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436052	56436052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	46	491	0	ENST00000407977.2:c.1085C>T	p.Ser362Phe	p.S362F	ENST00000407977		362	tCc/tTc	9/10	1	2	FACETS	0.452	0.381	0.53	0.452	0.381	0.53	SUBCLONAL	1	TRUE	1	0.495463063824177	2		491	411	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39537586	39537586	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	60	452	0	ENST00000262039.4:c.120A>T	p.Glu40Asp	p.E40D	ENST00000262039	NM_002647.2	40	gaA/gaT	2/25	0.220168502431767	1	FACETS	0.464	0.401	0.531	0.464	0.401	0.531	INDETERMINATE	1	TRUE	0	0.495463063824177	1		452	393	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916843	178916843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	96	674	1	ENST00000263967.3:c.230C>T	p.Ala77Val	p.A77V	ENST00000263967	NM_006218.2	77	gCa/gTa	2/21	0.495463063824177	3	FACETS	0.495	0.44	0.554	0.247	0.22	0.277	SUBCLONAL	1	TRUE	1	0.495463063824177	3		675	977	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927475	178927476	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0028051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	127	461	0	ENST00000263967.3:c.1241dup	p.Ala415CysfsTer2	p.A415Cfs*2	ENST00000263967	NM_006218.2	413	aag/aaGg	7/21	0.495463063824177	3	FACETS	0.962	0.873	1	0.481	0.436	0.528	CLONAL	1	TRUE	1	0.495463063824177	3		461	665	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196930	106196930	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	102	288	1	ENST00000380013.4:c.5263G>T	p.Glu1755Ter	p.E1755*	ENST00000380013	NM_001127208.2	1755	Gaa/Taa	11/11	0.495463063824177	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.495463063824177	1		289	279	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637762	176637763	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0028051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	152	693	0	ENST00000439151.2:c.2363dup	p.Ser789LysfsTer20	p.S789Kfs*20	ENST00000439151	NM_022455.4	788	cga/cGga	5/23	0.495463063824177	1	FACETS	0.806	0.74	0.873	0.806	0.74	0.873	CLONAL	1	TRUE	0	0.495463063824177	1		693	573	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490584	20490584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	124	618	0	ENST00000346618.3:c.1321G>A	p.Glu441Lys	p.E441K	ENST00000346618	NM_001949.4	441	Gag/Aag	7/7	0.248119715866511	1	FACETS	0.789	0.719	0.863	0.789	0.719	0.863	INDETERMINATE	1	TRUE	0	0.495463063824177	1		618	477	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358920	81358920	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0028051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	96	422	0	ENST00000222390.5:c.1040+1G>T		p.X347_splice	ENST00000222390	NM_000601.4	347			1	2	FACETS	0.889	0.796	0.986	0.889	0.796	0.986	CLONAL	1	TRUE	1	0.495463063824177	2		422	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0028052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	112	716	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.194642957021791	2	FACETS	0.837	0.754	0.926	0.419	0.377	0.463	INDETERMINATE	1	TRUE	0	0.368501454152741	2		716	726	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916929	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519931	NA	P-0028052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	118	572	0	ENST00000263967.3:c.316G>C	p.Gly106Arg	p.G106R	ENST00000263967	NM_006218.2	106	Ggc/Cgc	2/21	0.243304034746681	3	FACETS	0.866	0.787	0.948	0.577	0.524	0.632	CLONAL	2	TRUE	0	0.368501454152741	3		572	438	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428511	78428511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408536007	NA	P-0028052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	9	602	1	ENST00000370768.2:c.1288C>T	p.Arg430Cys	p.R430C	ENST00000370768	NM_003902.3	430	Cgt/Tgt	14/20	1	2	FACETS	0.114	0.074	0.164	0.114	0.074	0.164	SUBCLONAL	1	TRUE	1	0.368501454152741	2		603	430	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923216	26923216	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	19	346	0	ENST00000381527.3:c.212G>C	p.Arg71Pro	p.R71P	ENST00000381527	NM_001260.1	71	cGa/cCa	3/13	0.251088011428886	2	FACETS	0.448	0.341	0.574	0.224	0.17	0.287	SUBCLONAL	1	TRUE	0	0.368501454152741	2		346	230	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28897066	28897066	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	31	394	0	ENST00000282397.4:c.2814G>T	p.Met938Ile	p.M938I	ENST00000282397	NM_002019.4	938	atG/atT	21/30	0.251088011428886	2	FACETS	0.43	0.348	0.524	0.215	0.174	0.262	SUBCLONAL	1	TRUE	0	0.368501454152741	2		394	391	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591291	67591294	+	frameshift_variant	Frame_Shift_Del	DEL	TGGT	TGGT	-	novel	NA	P-0028052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	32	501	0	ENST00000274335.5:c.1792_1795del	p.Leu598AlafsTer63	p.L598Afs*63	ENST00000274335		597	TGGTtg/tg	13/15	1	2	FACETS	0.427	0.346	0.518	0.427	0.346	0.518	SUBCLONAL	1	TRUE	1	0.368501454152741	2		501	407	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722761	49722761	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs62262682	NA	P-0028055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	16	22	2	ENST00000449682.2:c.1478G>T	p.Arg493Leu	p.R493L	ENST00000449682	NM_020998.3	493	cGt/cTt	13/18	0.59941298914827	2	FACETS	1	0.913	1	0.72	0.566	0.876	CLONAL	1	TRUE	0	0.635358664627727	2		24	35	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256717	16256720	+	frameshift_variant	Frame_Shift_Del	DEL	CTAT	CTAT	-	novel	NA	P-0028055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	344	591	0	ENST00000375759.3:c.3984_3987del	p.Val1330Ter	p.V1330*	ENST00000375759	NM_015001.2	1328	CTATct/ct	11/15	0.635358664627727	3	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.635358664627727	3		591	613	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692787	89692787	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554898062	NA	P-0028055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	100	382	0	ENST00000371953.3:c.271G>T	p.Glu91Ter	p.E91*	ENST00000371953	NM_000314.4	91	Gaa/Taa	5/9	0.545044706626488	1	FACETS	0.87	0.791	0.95	0.87	0.791	0.95	CLONAL	1	TRUE	0	0.635358664627727	1		382	247	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940136	71940157	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CTCCCAATGGGCTGAGCACCGT	CTCCCAATGGGCTGAGCACCGT	-	novel	NA	P-0028055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	30	666	0	ENST00000298229.2:c.524_545del	p.Pro175ArgfsTer5	p.P175Rfs*5	ENST00000298229	NM_001567.3	174	gCTCCCAATGGGCTGAGCACCGTc/gc	5/28	0.635358664627727	1	FACETS	0.217	0.175	0.264	0.217	0.175	0.264	SUBCLONAL	1	TRUE	0	0.635358664627727	1		666	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0028057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	591	721	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.401824890724426	3	FACETS	1	0.996	1	0.817	0.788	0.847	CLONAL	2	TRUE	0	0.474559452308114	3		721	1257	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875920	76875920	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	431	389	3	ENST00000373344.5:c.5215C>T	p.Arg1739Ter	p.R1739*	ENST00000373344	NM_000489.3	1739	Cga/Tga	20/35	0.474559452308114	2	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.474559452308114	2		392	777	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149238733	149238733	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1716	224	1010	0	ENST00000360632.3:c.1062G>T	p.Gln354His	p.Q354H	ENST00000360632	NM_015472.4	354	caG/caT	7/7	0.267435778047401	3	FACETS	0.602	0.558	0.648	0.301	0.279	0.324	INDETERMINATE	1	TRUE	1	0.474559452308114	3		1010	1940	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149238774	149238774	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1436	168	814	0	ENST00000360632.3:c.1021G>C	p.Glu341Gln	p.E341Q	ENST00000360632	NM_015472.4	341	Gaa/Caa	7/7	0.267435778047401	3	FACETS	0.546	0.5	0.595	0.273	0.25	0.298	INDETERMINATE	1	TRUE	1	0.474559452308114	3		814	1604	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036917	180036917	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	149	811	0	ENST00000261937.6:c.3795C>A	p.Tyr1265Ter	p.Y1265*	ENST00000261937	NM_182925.4	1265	taC/taA	28/30	1	2	FACETS	0.638	0.582	0.696	0.638	0.582	0.696	SUBCLONAL	1	TRUE	1	0.474559452308114	2		811	985	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039625	47039626	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTGCAGATC	novel	NA	P-0028058-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	80	301	0	ENST00000377604.3:c.1084_1092dup	p.Ile362_Gln364dup	p.I362_Q364dup	ENST00000377604	NM_001204468.1	362	-/CTGCAGATC	11/24	1	1	FACETS	0.92	0.818	1	0.92	0.818	1	CLONAL	1	TRUE	0	0.433702037660987	1		301	314	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0028067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	44	250	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	FALSE	1	0.172834528668997	2		250	439	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230691	46230691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424958105	NA	P-0028067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	43	462	0	ENST00000334344.6:c.940C>T	p.Arg314Cys	p.R314C	ENST00000334344	NM_152641.2	314	Cgt/Tgt	8/21	1	2	FACETS	0.903	0.755	1	0.903	0.755	1	CLONAL	1	FALSE	1	0.172834528668997	2		462	551	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0028067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	102	477	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.164770158675099	3	FACETS	0.944	0.845	1	0.944	0.845	1	CLONAL	2	FALSE	1	0.172834528668997	3		477	679	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170486	108170486	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1565473651	NA	P-0028067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	36	361	0	ENST00000278616.4:c.5051C>G	p.Ser1684Cys	p.S1684C	ENST00000278616	NM_000051.3	1684	tCt/tGt	34/63	0.172834528668997	3	FACETS	0.788	0.647	0.948	0.394	0.323	0.474	CLONAL	1	FALSE	1	0.172834528668997	3		361	574	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561382	9561382	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1186089642	NA	P-0028067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	49	495	0	ENST00000353224.5:c.400G>A	p.Glu134Lys	p.E134K	ENST00000353224	NM_177990.2	134	Gaa/Aaa	4/10	1	2	FACETS	0.995	0.842	1	0.995	0.842	1	CLONAL	1	FALSE	1	0.172834528668997	2		495	570	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564795	86564795	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	76	703	0	ENST00000274376.6:c.527C>T	p.Pro176Leu	p.P176L	ENST00000274376	NM_002890.2	176	cCt/cTt	1/25	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	1	0.172834528668997	2		703	806	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942891	68942891	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	90	573	0	ENST00000288368.4:c.703G>A	p.Glu235Lys	p.E235K	ENST00000288368	NM_024870.2	235	Gag/Aag	6/40	0.164770158675099	3	FACETS	0.884	0.785	0.989	0.884	0.785	0.989	CLONAL	2	FALSE	1	0.172834528668997	3		573	640	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002814	69002814	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1213028913	NA	P-0028067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	43	281	0	ENST00000288368.4:c.2114G>A	p.Gly705Glu	p.G705E	ENST00000288368	NM_024870.2	705	gGa/gAa	20/40	0.164770158675099	3	FACETS	0.772	0.648	0.909	0.772	0.648	0.909	CLONAL	2	FALSE	1	0.172834528668997	3		281	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579714	7579714	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	381	582	1	ENST00000269305.4:c.82del	p.Glu28LysfsTer16	p.E28Kfs*16	ENST00000269305	NM_001126112.2	28	Gaa/aa	3/11	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	2	TRUE	NA	0.55370132237914	2		583	664	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0028091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	32	392	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	1	2	FACETS	0.217	0.175	0.264	0.217	0.175	0.264	SUBCLONAL	1	TRUE	1	0.386837820882345	2		392	763	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0028092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	169	581	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.230844330362546	3	FACETS	0.904	0.832	0.979	1	0.987	1	CLONAL	3	TRUE	1	0.16	3		581	841	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	43	534	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.187636738151589	1	FACETS	0.886	0.741	1	0.886	0.741	1	CLONAL	1	TRUE	0	0.16	1		534	558	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0028092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	38	430	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	0.896	0.74	1	0.896	0.74	1	CLONAL	1	TRUE	1	0.16	2		430	530	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607552	43607552	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	32	578	0	ENST00000355710.3:c.1528G>T	p.Ala510Ser	p.A510S	ENST00000355710	NM_020975.4	510	Gcc/Tcc	8/20	1	2	FACETS	0.759	0.615	0.922	0.759	0.615	0.922	CLONAL	1	TRUE	1	0.16	2		578	527	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038846	47038846	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	64	375	1	ENST00000377604.3:c.853C>T	p.Gln285Ter	p.Q285*	ENST00000377604	NM_001204468.1	285	Caa/Taa	9/24	1	1	FACETS	0.858	0.75	0.973	1	0.984	1	CLONAL	3	TRUE	0	0.16	1		376	286	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356175	66356175	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1162142172	NA	P-0028092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	45	554	0	ENST00000273854.3:c.1322T>C	p.Ile441Thr	p.I441T	ENST00000273854	NM_004439.5	441	aTt/aCt	5/18	1	2	FACETS	0.859	0.72	1	0.859	0.72	1	CLONAL	1	TRUE	1	0.16	2		554	655	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873670	35873670	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	32	427	0	ENST00000303115.3:c.626C>G	p.Pro209Arg	p.P209R	ENST00000303115	NM_002185.3	209	cCt/cGt	5/8	1	2	FACETS	0.795	0.645	0.966	0.795	0.645	0.966	CLONAL	1	TRUE	1	0.16	2		427	503	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513358	106513359	+	missense_variant	Missense_Mutation	DNP	TG	TG	GA	novel	NA	P-0028092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	63	358	0	ENST00000359195.3:c.2262_2263delinsGA	p.Glu755Lys	p.E755K	ENST00000359195	NM_002649.2	754	gcTGaa/gcGAaa	4/11	0.230844330362546	3	FACETS	1	0.968	1	0.717	0.62	0.822	CLONAL	1	TRUE	1	0.16	3		358	593	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974727	21974744	+	inframe_deletion	In_Frame_Del	DEL	CCTCCAGCAGCGCCCGCA	CCTCCAGCAGCGCCCGCA	-	novel	NA	P-0028093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	44	334	0	ENST00000304494.5:c.83_100del	p.Val28_Glu33del	p.V28_E33del	ENST00000304494	NM_000077.4	28	gTGCGGGCGCTGCTGGAGGcg/gcg	1/3	0.38374495104133	1	FACETS	0.669	0.564	0.783	0.669	0.564	0.783	SUBCLONAL	1	TRUE	0	0.38374495104133	1		334	277	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278099	15278099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139983430	NA	P-0028093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	93	665	2	ENST00000263388.2:c.5323G>A	p.Ala1775Thr	p.A1775T	ENST00000263388	NM_000435.2	1775	Gca/Aca	29/33	0.355292304772312	1	FACETS	0.558	0.496	0.624	0.558	0.496	0.624	SUBCLONAL	1	TRUE	0	0.38374495104133	1		667	702	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435469	49435469	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	50	649	1	ENST00000301067.7:c.6203G>A	p.Arg2068Gln	p.R2068Q	ENST00000301067	NM_003482.3	2068	cGg/cAg	30/54	1	2	FACETS	0.364	0.308	0.426	0.364	0.308	0.426	SUBCLONAL	1	TRUE	1	0.38374495104133	2		650	715	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059476	42059476	+	stop_lost	Nonstop_Mutation	SNP	T	T	C	novel	NA	P-0028093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	31	328	0	ENST00000219905.7:c.9196T>C	p.Ter3066ArgextTer51	p.*3066Rext*51	ENST00000219905	NM_001164273.1	3066	Tga/Cga	24/24	1	2	FACETS	0.366	0.296	0.446	0.366	0.296	0.446	SUBCLONAL	1	TRUE	1	0.38374495104133	2		328	441	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4097325	4097326	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CTATCCA	novel	NA	P-0028093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	52	668	0	ENST00000262948.5:c.929_935dup	p.Arg313GlyfsTer2	p.R313Gfs*2	ENST00000262948	NM_030662.3	312	agc/agTGGATAGc	8/11	0.355292304772312	1	FACETS	0.294	0.249	0.343	0.294	0.249	0.343	SUBCLONAL	1	TRUE	0	0.38374495104133	1		668	746	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920424	134920424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	55	609	1	ENST00000398015.3:c.2239G>T	p.Ala747Ser	p.A747S	ENST00000398015	NM_004441.4	747	Gct/Tct	12/16	1	2	FACETS	0.433	0.37	0.502	0.433	0.37	0.502	SUBCLONAL	1	TRUE	1	0.38374495104133	2		610	662	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579429	7579429	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	290	523	0	ENST00000269305.4:c.258del	p.Pro87GlnfsTer36	p.P87Qfs*36	ENST00000269305	NM_001126112.2	86	gcA/gc	4/11	0.599369031207764	2	FACETS	0.944	0.901	0.985	0.944	0.901	0.985	CLONAL	2	TRUE	0	0.632387498793527	2		523	486	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554186	63554186	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	119	640	0	ENST00000307078.5:c.553A>T	p.Asn185Tyr	p.N185Y	ENST00000307078	NM_004655.3	185	Aat/Tat	2/11	0.599369031207764	2	FACETS	0.582	0.526	0.64	0.291	0.263	0.32	SUBCLONAL	1	TRUE	0	0.632387498793527	2		640	647	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225666	225666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs575617625	NA	P-0028094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	130	637	0	ENST00000264932.6:c.445G>A	p.Ala149Thr	p.A149T	ENST00000264932	NM_004168.2	149	Gcc/Acc	4/15	0.300520844322176	4	FACETS	0.521	0.471	0.574	0.26	0.235	0.287	INDETERMINATE	1	TRUE	2	0.632387498793527	4		637	1289	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	159	210	0				ENST00000310581	NM_198253.2	-/1132			0.510153679420566	5	FACETS	1	0.938	1	1	0.938	1	CLONAL	3	TRUE	2	0.672664588491596	5		210	315	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063320	67063320	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	112	262	0	ENST00000412916.2:c.10G>T	p.Val4Phe	p.V4F	ENST00000412916		4	Gtc/Ttc	1/6	0.52784712426447	3	FACETS	0.916	0.841	0.991	0.61	0.56	0.661	CLONAL	2	TRUE	0	0.672664588491596	3		262	243	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971167	21971167	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	122	441	0	ENST00000304494.5:c.191T>C	p.Leu64Pro	p.L64P	ENST00000304494	NM_000077.4	64	cTg/cCg	2/3	0.672664588491596	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.672664588491596	1		441	176	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928935	44928935	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	218	263	1	ENST00000377967.4:c.2035C>T	p.Gln679Ter	p.Q679*	ENST00000377967	NM_021140.2	679	Cag/Tag	17/29	0.672664588491596	3	FACETS	1	0.992	1			1	CLONAL	3	TRUE	NA	0.672664588491596	3		264	260	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135882	64135959	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTACCAGGTGGGACCTCTGACGCGCCGCCTTCGCCTTCGCCTTCGCCTTCGCCTCCAGGACTCGCCCTTCTTCCAGCA	CTACCAGGTGGGACCTCTGACGCGCCGCCTTCGCCTTCGCCTTCGCCTTCGCCTCCAGGACTCGCCCTTCTTCCAGCA	GTACC	novel	NA	P-0028095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	46	590	2	ENST00000334205.4:c.1201-58_1220delinsGTACC		p.X401_splice	ENST00000334205	NM_003942.2	401		11/17	0.533367541472972	4	FACETS	0.451	0.38	0.53	0.226	0.19	0.265	SUBCLONAL	1	TRUE	2	0.672664588491596	4		592	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573968	7573978	+	frameshift_variant	Frame_Shift_Del	DEL	GGCATCCTTGA	GGCATCCTTGA	-	novel	NA	P-0028095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	134	694	0	ENST00000269305.4:c.1049_1059del	p.Leu350ProfsTer28	p.L350Pfs*28	ENST00000269305	NM_001126112.2	350	cTCAAGGATGCC/c	10/11	0.582073871908499	2	FACETS	0.841	0.783	0.897	0.841	0.783	0.897	CLONAL	2	TRUE	0	0.672664588491596	2		694	237	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299085	15299085	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0028095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	90	639	1	ENST00000263388.2:c.1453A>T	p.Lys485Ter	p.K485*	ENST00000263388	NM_000435.2	485	Aag/Tag	9/33	0.488017163952733	4	FACETS	0.908	0.809	1	0.454	0.404	0.507	CLONAL	1	TRUE	2	0.672664588491596	4		640	493	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218489	36218489	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	49	584	0	ENST00000222270.7:c.4268C>G	p.Ser1423Cys	p.S1423C	ENST00000222270	NM_014727.1	1423	tCc/tGc	16/37	0.510272919710765	3	FACETS	0.695	0.593	0.806	0.348	0.296	0.403	SUBCLONAL	1	TRUE	1	0.672664588491596	3		584	280	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652032	36652037	+	inframe_deletion	In_Frame_Del	DEL	GACTTT	GACTTT	-	novel	NA	P-0028095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	269	721	0	ENST00000244741.5:c.155_160del	p.Asp52_Phe53del	p.D52_F53del	ENST00000244741	NM_000389.4	52	GACTTT/-	2/3	0.672664588491596	5	FACETS	0.999	0.948	1	0.999	0.948	1	CLONAL	3	TRUE	2	0.672664588491596	5		721	536	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864623	56864623	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	71	672	0	ENST00000519728.1:c.586T>C	p.Ser196Pro	p.S196P	ENST00000519728	NM_002350.3	196	Tct/Cct	7/13	1	2	FACETS	0.409	0.357	0.465	0.409	0.357	0.465	SUBCLONAL	1	TRUE	1	0.672664588491596	2		672	516	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0028096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	180	559	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.219142373302284	3	FACETS	0.866	0.801	0.933	0.866	0.801	0.933	CLONAL	3	TRUE	0	0.219142373302284	3		559	702	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038783	47038783	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	107	351	0	ENST00000377604.3:c.790G>T	p.Glu264Ter	p.E264*	ENST00000377604	NM_001204468.1	264	Gag/Tag	9/24	1	1	FACETS	0.933	0.842	1	1	0.987	1	CLONAL	2	TRUE	0	0.219142373302284	1		351	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579485	7579485	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs869312782	NA	P-0028096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	93	601	0	ENST00000269305.4:c.202G>T	p.Glu68Ter	p.E68*	ENST00000269305	NM_001126112.2	68	Gag/Tag	4/11	0.219142373302284	1	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	0	0.219142373302284	1		601	751	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544091	18544091	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	142	405	0	ENST00000266497.5:c.1908A>T	p.Lys636Asn	p.K636N	ENST00000266497		636	aaA/aaT	13/31	0.219142373302284	3	FACETS	0.918	0.842	0.997	0.918	0.842	0.997	CLONAL	3	TRUE	0	0.219142373302284	3		405	522	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420852	49420852	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	165	504	0	ENST00000301067.7:c.14897G>T	p.Arg4966Leu	p.R4966L	ENST00000301067	NM_003482.3	4966	cGg/cTg	48/54	0.215879864581086	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.219142373302284	2		504	720	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135245	2135245	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199848388	NA	P-0028096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	125	743	1	ENST00000219476.3:c.4584G>T	p.Glu1528Asp	p.E1528D	ENST00000219476	NM_000548.3	1528	gaG/gaT	36/42	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.219142373302284	2		744	1022	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993856	72993856	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	44	377	1	ENST00000268489.5:c.189G>T	p.Glu63Asp	p.E63D	ENST00000268489	NM_006885.3	63	gaG/gaT	2/10	1	2	FACETS	0.954	0.801	1	0.954	0.801	1	CLONAL	1	TRUE	1	0.219142373302284	2		378	421	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560032	29560032	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	54	346	0	ENST00000356175.3:c.3509A>T	p.His1170Leu	p.H1170L	ENST00000356175	NM_000267.3	1170	cAc/cTc	27/57	0.178778420786227	3	FACETS	1	0.945	1	0.612	0.523	0.708	CLONAL	1	TRUE	1	0.219142373302284	3		346	447	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627721	37627721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1361723983	NA	P-0028096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	145	758	0	ENST00000447079.4:c.1636C>T	p.Pro546Ser	p.P546S	ENST00000447079	NM_015083.1	546	Cct/Tct	2/14	0.178778420786227	3	FACETS	1	0.982	1	0.657	0.598	0.719	CLONAL	1	TRUE	1	0.219142373302284	3		758	1117	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210935	36210935	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1393	97	692	1	ENST00000222270.7:c.686G>T	p.Gly229Val	p.G229V	ENST00000222270	NM_014727.1	229	gGc/gTc	3/37	0.219142373302284	7	FACETS	0.92	0.817	1	0.153	0.136	0.172	CLONAL	1	TRUE	1	0.219142373302284	7		693	1490	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168700	32168700	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	100	778	1	ENST00000375023.3:c.4223T>A	p.Leu1408Gln	p.L1408Q	ENST00000375023	NM_004557.3	1408	cTa/cAa	23/30	1	2	FACETS	0.947	0.844	1	0.947	0.844	1	CLONAL	1	TRUE	1	0.219142373302284	2		779	964	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463580	25463580	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	141	571	0	ENST00000264709.3:c.2102T>G	p.Phe701Cys	p.F701C	ENST00000264709	NM_175629.2	701	tTc/tGc	18/23	0.235929155140747	3	FACETS	1	0.985	1	0.701	0.64	0.766	CLONAL	1	TRUE	1	0.326070448626736	3		571	717	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250823	153250823	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0028098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	127	385	0	ENST00000281708.4:c.1236+1G>C		p.X412_splice	ENST00000281708	NM_033632.3	412			0.238696701302982	2	FACETS	1	0.982	1	0.664	0.603	0.727	CLONAL	1	TRUE	0	0.326070448626736	2		385	587	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0028100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	21	482	0	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	0.204468062171145	1	FACETS	1	0.776	1	1	0.776	1	CLONAL	1	TRUE	0	0.204468062171145	1		482	184	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939956	76939956	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0028100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	53	569	0	ENST00000373344.5:c.792T>A	p.Tyr264Ter	p.Y264*	ENST00000373344	NM_000489.3	264	taT/taA	9/35	0.204497471142623	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.204468062171145	1		569	372	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0028102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	268	581	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.200768239626621	0	FACETS	0.816	0.769	0.863			1	CLONAL	3	FALSE	0	0.237836588858469	0		583	702	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867546	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGC	GGCGGCGGC	-	rs11466445	NA	P-0028102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	10	27	0	ENST00000374994.4:c.70_78del	p.Ala24_Ala26del	p.A24_A26del	ENST00000374994	NM_004612.2	17	ctGGCGGCGGCg/ctg	1/9	0.173698600066048	3	FACETS	1	0.812	1	1	0.812	1	CLONAL	2	FALSE	1	0.237836588858469	3		27	38	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136825	55136825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1324781921	NA	P-0028102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	54	464	1	ENST00000257290.5:c.1147C>T	p.Arg383Cys	p.R383C	ENST00000257290	NM_006206.4	383	Cgt/Tgt	8/23	1	2	FACETS	0.577	0.492	0.671	0.577	0.492	0.671	SUBCLONAL	1	FALSE	1	0.237836588858469	2		465	787	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945591	151945591	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs771545679	NA	P-0028102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	29	252	0	ENST00000262189.6:c.1928T>C	p.Ile643Thr	p.I643T	ENST00000262189	NM_170606.2	643	aTt/aCt	14/59	0.132466330704843	4	FACETS	0.614	0.491	0.753	0.307	0.245	0.377	INDETERMINATE	1	FALSE	2	0.237836588858469	4		252	492	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188240	10188240	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	312	613	0	ENST00000256474.2:c.383T>A	p.Leu128His	p.L128H	ENST00000256474	NM_000551.3	128	cTt/cAt	2/3	0.322669046724689	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.384257881173287	2		613	781	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188187	32188187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754712190	NA	P-0028103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	229	446	1	ENST00000375023.3:c.1154G>A	p.Arg385His	p.R385H	ENST00000375023	NM_004557.3	385	cGc/cAc	6/30	0.384257881173287	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.384257881173287	2		447	555	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141557687	141557687	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	202	588	0	ENST00000220592.5:c.1628C>G	p.Ala543Gly	p.A543G	ENST00000220592	NM_012154.3	543	gCc/gGc	13/19	0.331639892798915	3	FACETS	1	0.986	1	0.625	0.579	0.672	CLONAL	1	TRUE	1	0.384257881173287	3		588	1003	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227632	53227672	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGCACCTTATGTGTGCCCTAACTCCTCACGCTGTCATACC	CAGCACCTTATGTGTGCCCTAACTCCTCACGCTGTCATACC	-	novel	NA	P-0028103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	190	135	0	ENST00000375401.3:c.2516_2516+40del		p.X839_splice	ENST00000375401	NM_004187.3	839		17/26	0.323699945541797	2	FACETS	1	0.987	1			1	CLONAL	3	TRUE	NA	0.384257881173287	2		135	291	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0028106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	101	298	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.20433681249849	3	FACETS	0.889	0.796	0.987	0.592	0.53	0.658	CLONAL	2	TRUE	0	0.20433681249849	3		298	613	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575200	48575200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500743	NA	P-0028106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	64	313	0	ENST00000342988.3:c.394C>T	p.His132Tyr	p.H132Y	ENST00000342988	NM_005359.5	132	Cac/Tac	3/12	0.20433681249849	1	FACETS	0.773	0.673	0.88	1	0.973	1	SUBCLONAL	2	TRUE	0	0.20433681249849	1		313	364	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672814	86672816	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	novel	NA	P-0028106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	84	367	0	ENST00000274376.6:c.2307_2309del	p.Leu770del	p.L770del	ENST00000274376	NM_002890.2	767	tcGTTg/tcg	17/25	1	2	FACETS	0.754	0.668	0.847	1	0.978	1	SUBCLONAL	2	TRUE	1	0.20433681249849	2		367	545	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553033	106553033	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1345016975	NA	P-0028106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	151	524	0	ENST00000369096.4:c.998C>T	p.Thr333Ile	p.T333I	ENST00000369096	NM_001198.3	333	aCc/aTc	5/7	1	2	FACETS	0.759	0.693	0.828	1	0.988	1	SUBCLONAL	2	TRUE	1	0.20433681249849	2		524	974	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820486	44820527	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	GGCTTTATTTTTTGCTTACATATTTGTATTTTTTTATTTCTA	GGCTTTATTTTTTGCTTACATATTTGTATTTTTTTATTTCTA	-	novel	NA	P-0028106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	21	96	0	ENST00000377967.4:c.226-39_228del		p.X76_splice	ENST00000377967	NM_021140.2	76			1	1	FACETS	0.847	0.662	1	1	0.933	1	CLONAL	2	TRUE	0	0.20433681249849	1		96	109	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0028107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	95	445	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.134422775268258	3	FACETS	0.951	0.852	1	0.634	0.568	0.704	INDETERMINATE	2	TRUE	0	0.262926568869143	3		445	430	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877387	28877387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747687298	NA	P-0028107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	65	461	0	ENST00000282397.4:c.3934G>A	p.Ala1312Thr	p.A1312T	ENST00000282397	NM_002019.4	1312	Gct/Act	30/30	0.262926568869143	1	FACETS	0.54	0.467	0.619	0.54	0.467	0.619	SUBCLONAL	1	TRUE	0	0.262926568869143	1		461	795	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0028109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	128	297	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.290579915865824	2		297	754	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0028109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	64	502	1	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.631	0.546	0.724	0.631	0.546	0.724	SUBCLONAL	1	TRUE	1	0.290579915865824	2		503	698	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0028109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	106	295	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	0.290579915865824	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.290579915865824	1		295	496	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845937	72845937	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	30	298	1	ENST00000268489.5:c.3530C>T	p.Ala1177Val	p.A1177V	ENST00000268489	NM_006885.3	1177	gCa/gTa	6/10	1	2	FACETS	0.363	0.291	0.444	0.363	0.291	0.444	SUBCLONAL	1	TRUE	1	0.290579915865824	2		299	569	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44935980	44935980	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0028109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	109	229	0	ENST00000377967.4:c.2741T>A	p.Leu914Ter	p.L914*	ENST00000377967	NM_021140.2	914	tTg/tAg	18/29	0.0892401518855364	2	FACETS	0.959	0.869	1			1	INDETERMINATE	2	TRUE	NA	0.290579915865824	2		229	391	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0028111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	77	586	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.91	0.799	1	0.91	0.799	1	CLONAL	1	TRUE	1	0.270346957215965	2		587	626	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77051721	77051721	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	133	484	0	ENST00000356341.3:c.1086T>G	p.Asp362Glu	p.D362E	ENST00000356341	NM_002576.4	362	gaT/gaG	11/15	0.270346957215965	1	FACETS	0.864	0.784	0.949	0.864	0.784	0.949	CLONAL	1	TRUE	0	0.270346957215965	1		484	985	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790183	40790183	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0028111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	94	290	1	ENST00000373198.4:c.2549-1G>T		p.X850_splice	ENST00000373198	NM_133170.3	850			1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.270346957215965	2		291	617	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165557	47165557	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs563907746	NA	P-0028111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	141	468	0	ENST00000409792.3:c.569C>T	p.Pro190Leu	p.P190L	ENST00000409792	NM_014159.6	190	cCg/cTg	3/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.270346957215965	2		468	886	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508995	106508995	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	95	344	0	ENST00000359195.3:c.989C>A	p.Thr330Lys	p.T330K	ENST00000359195	NM_002649.2	330	aCg/aAg	2/11	1	2	FACETS	0.984	0.877	1	0.984	0.877	1	CLONAL	1	TRUE	1	0.270346957215965	2		344	714	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370762	55370762	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	116	335	1	ENST00000297316.4:c.64G>T	p.Ala22Ser	p.A22S	ENST00000297316	NM_022454.3	22	Gcg/Tcg	1/2	0.270346957215965	3	FACETS	1	0.981	1	0.684	0.617	0.755	CLONAL	1	TRUE	1	0.270346957215965	3		336	712	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900329	101900329	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	49	326	0	ENST00000374994.4:c.763C>A	p.Arg255Ser	p.R255S	ENST00000374994	NM_004612.2	255	Cgt/Agt	4/9	1	2	FACETS	0.592	0.501	0.693	0.592	0.501	0.693	SUBCLONAL	1	TRUE	1	0.270346957215965	2		326	612	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291143	10291143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376894659	NA	P-0028113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	101	610	0	ENST00000340748.4:c.328G>A	p.Gly110Arg	p.G110R	ENST00000340748		110	Ggg/Agg	4/40	1	2	FACETS	0.981	0.875	1	0.981	0.875	1	CLONAL	1	TRUE	1	0.22	2		610	936	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465399	120465399	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	82	525	0	ENST00000256646.2:c.4862C>A	p.Ser1621Tyr	p.S1621Y	ENST00000256646	NM_024408.3	1621	tCt/tAt	27/34	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.22	2		525	745	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151871279	151871279	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	68	448	0	ENST00000262189.6:c.9311T>C	p.Leu3104Pro	p.L3104P	ENST00000262189	NM_170606.2	3104	cTt/cCt	39/59	1	2	FACETS	0.829	0.72	0.947	0.829	0.72	0.947	CLONAL	1	TRUE	1	0.22	2		448	746	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858000	152858001	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0028113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	13	203	0	ENST00000406277.2:c.614dup	p.Pro206AlafsTer7	p.P206Afs*7	ENST00000406277	NM_152274.4	205	gtg/gtTg	6/7	1	2	FACETS	0.512	0.365	0.691	0.512	0.365	0.691	SUBCLONAL	1	TRUE	1	0.22	2		203	231	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	451	210	0				ENST00000310581	NM_198253.2	-/1132			0.417724710520864	6	FACETS	1	0.983	1	1	0.983	1	CLONAL	4	TRUE	2	0.417724710520864	6		210	948	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0028117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	725	586	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.417724710520864	5	FACETS	1	0.992	1	1	0.997	1	CLONAL	4	TRUE	2	0.417724710520864	5		587	1331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578192	7578192	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	402	620	0	ENST00000269305.4:c.657del	p.Tyr220MetfsTer27	p.Y220Mfs*27	ENST00000269305	NM_001126112.2	219	ccC/cc	6/11	0.417724710520864	2	FACETS	0.987	0.942	1	0.987	0.942	1	CLONAL	2	TRUE	0	0.417724710520864	2		620	975	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632276	215632276	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	223	530	0	ENST00000260947.4:c.1498G>C	p.Asp500His	p.D500H	ENST00000260947	NM_000465.2	500	Gat/Cat	6/11	0.25151230708345	5	FACETS	1	0.947	1	0.679	0.633	0.726	CLONAL	2	TRUE	2	0.417724710520864	5		530	853	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127765	47127765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758473163	NA	P-0028117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	103	460	0	ENST00000409792.3:c.5317C>T	p.Arg1773Cys	p.R1773C	ENST00000409792	NM_014159.6	1773	Cgt/Tgt	11/21	0.417724710520864	3	FACETS	0.817	0.731	0.908	0.408	0.365	0.454	CLONAL	1	TRUE	1	0.417724710520864	3		460	730	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632383	1632383	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0028117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	196	706	0	ENST00000344749.5:c.167C>G	p.Ser56Ter	p.S56*	ENST00000344749	NM_001136139.2	56	tCa/tGa	4/19	0.417724710520864	3	FACETS	1	0.967	1	0.539	0.499	0.581	CLONAL	1	TRUE	1	0.417724710520864	3		706	1052	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041572	14041572	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	113	450	0	ENST00000311895.7:c.2119G>A	p.Glu707Lys	p.E707K	ENST00000311895	NM_005236.2	707	Gaa/Aaa	11/11	1	2	FACETS	0.993	0.897	1	0.993	0.897	1	CLONAL	1	TRUE	1	0.417724710520864	2		450	545	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809203	243809203	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	94	344	0	ENST00000263826.5:c.421A>G	p.Lys141Glu	p.K141E	ENST00000263826	NM_005465.4	141	Aaa/Gaa	4/13	0.417724710520864	5	FACETS	0.951	0.846	1	0.317	0.282	0.355	CLONAL	1	TRUE	2	0.417724710520864	5		344	770	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218035	108218035	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	237	398	1	ENST00000278616.4:c.8614C>A	p.His2872Asn	p.H2872N	ENST00000278616	NM_000051.3	2872	Cat/Aat	59/63	0.417724710520864	3	FACETS	0.863	0.813	0.912	0.863	0.813	0.912	CLONAL	3	TRUE	0	0.417724710520864	3		399	530	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508788	29508788	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	201	434	0	ENST00000356175.3:c.715C>T	p.Gln239Ter	p.Q239*	ENST00000356175	NM_000267.3	239	Cag/Tag	7/57	0.417724710520864	6	FACETS	0.801	0.741	0.862	0.4	0.37	0.431	CLONAL	2	TRUE	2	0.417724710520864	6		434	1103	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219778	36219778	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	117	704	0	ENST00000222270.7:c.4675G>A	p.Asp1559Asn	p.D1559N	ENST00000222270	NM_014727.1	1559	Gat/Aat	20/37	0.25151230708345	5	FACETS	0.828	0.745	0.916	0.276	0.248	0.306	CLONAL	1	TRUE	2	0.417724710520864	5		704	1101	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015243	128015243	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	115	520	0	ENST00000285398.2:c.2278G>T	p.Glu760Ter	p.E760*	ENST00000285398	NM_000122.1	760	Gag/Tag	15/15	0.25151230708345	5	FACETS	0.906	0.815	1	0.302	0.271	0.335	CLONAL	1	TRUE	2	0.417724710520864	5		520	988	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72842125	72842125	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	246	365	0	ENST00000325599.8:c.1123G>T	p.Ala375Ser	p.A375S	ENST00000325599	NM_018130.2	375	Gcg/Tcg	10/11	0.25151230708345	5	FACETS	1	0.972	1	0.712	0.667	0.759	CLONAL	2	TRUE	2	0.417724710520864	5		365	897	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081599	143081599	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	266	492	0	ENST00000262992.4:c.1475C>A	p.Thr492Lys	p.T492K	ENST00000262992	NM_001101669.1	492	aCa/aAa	15/24	0.417724710520864	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.417724710520864	2		492	618	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38957819	38957819	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	42	294	0	ENST00000357387.3:c.2434C>G	p.Pro812Ala	p.P812A	ENST00000357387	NM_152756.3	812	Cca/Gca	25/38	0.417724710520864	6	FACETS	0.501	0.417	0.595	0.125	0.104	0.149	SUBCLONAL	1	TRUE	2	0.417724710520864	6		294	737	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8525025	8525025	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	148	333	2	ENST00000356435.5:c.579G>T	p.Gln193His	p.Q193H	ENST00000356435		193	caG/caT	7/35	0.417724710520864	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	0	0.417724710520864	2		335	354	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0028118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	276	297	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.888	0.836	0.942	0.888	0.836	0.942	CLONAL	1	TRUE	1	0.683697149952707	2		297	909	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0028118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	381	623	1	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.641407946522229	1	FACETS	0.974	0.932	1	0.974	0.932	1	CLONAL	1	TRUE	0	0.683697149952707	1		624	753	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100080	157100094	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGCGGCCGC	GGCGGCGGCGGCCGC	-	rs775733700	NA	P-0028118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	92	59	0	ENST00000346085.5:c.1029_1043del	p.Ala346_Ala350del	p.A346_A350del	ENST00000346085	NM_020732.3	339	gtGGCGGCGGCGGCCGCg/gtg	1/20	0.683697149952707	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.683697149952707	1		59	156	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292797	91292798	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1489224386	NA	P-0028118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	156	532	0	ENST00000355112.3:c.303_304del	p.Gly102TrpfsTer40	p.G102Wfs*40	ENST00000355112	NM_000057.2	100	cAG/c	3/22	1	2	FACETS	0.433	0.396	0.472	0.433	0.396	0.472	SUBCLONAL	1	TRUE	1	0.683697149952707	2		532	1053	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40876321	40876321	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0028118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	304	534	0	ENST00000428826.2:c.366+2T>C		p.X122_splice	ENST00000428826		122			0.351334050501461	1	FACETS	0.744	0.704	0.784	0.744	0.704	0.784	INDETERMINATE	1	TRUE	0	0.683697149952707	1		534	787	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651430	52651430	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	349	593	0	ENST00000394830.3:c.1666C>A	p.Pro556Thr	p.P556T	ENST00000394830	NM_018313.4	556	Cct/Act	15/30	0.683697149952707	1	FACETS	0.963	0.919	1	0.963	0.919	1	CLONAL	1	TRUE	0	0.683697149952707	1		593	698	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578539	7578539	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782160	NA	P-0028119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	365	816	1	ENST00000269305.4:c.391A>T	p.Asn131Tyr	p.N131Y	ENST00000269305	NM_001126112.2	131	Aac/Tac	5/11	0.521111414183559	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	0	0.521713395858041	3		817	575	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50483670	50483670	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	47	310	0	ENST00000394963.4:c.775C>G	p.His259Asp	p.H259D	ENST00000394963	NM_003076.4	259	Cac/Gac	7/13	0.521713395858041	2	FACETS	0.905	0.774	1	0.453	0.387	0.523	CLONAL	1	TRUE	0	0.521713395858041	2		310	199	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211985	36211985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761171846	NA	P-0028119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	114	917	1	ENST00000222270.7:c.1736C>T	p.Pro579Leu	p.P579L	ENST00000222270	NM_014727.1	579	cCa/cTa	3/37	1	2	FACETS	0.984	0.892	1	0.984	0.892	1	CLONAL	1	TRUE	1	0.521713395858041	2		918	444	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128036933	128036933	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747849600	NA	P-0028119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	147	415	0	ENST00000285398.2:c.1546C>G	p.Pro516Ala	p.P516A	ENST00000285398	NM_000122.1	516	Cct/Gct	10/15	0.237694244706232	5	FACETS	1	0.973	1	0.751	0.691	0.812	INDETERMINATE	2	TRUE	2	0.521713395858041	5		415	446	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443314	187443314	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	54	305	0	ENST00000232014.4:c.1812C>G	p.Cys604Trp	p.C604W	ENST00000232014	NM_001130845.1	604	tgC/tgG	8/10	0.279731539751897	5	FACETS	1	0.924	1	0.373	0.32	0.43	INDETERMINATE	1	TRUE	2	0.521713395858041	5		305	330	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5557668	5557672	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTT	CCCTT	-	novel	NA	P-0028119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	158	549	0	ENST00000397747.3:c.683_687del	p.Pro228LeufsTer54	p.P228Lfs*54	ENST00000397747	NM_025239.3	228	CCCTTc/c	5/7	0.179113793221597	2	FACETS	0.785	0.728	0.842	0.785	0.728	0.842	INDETERMINATE	2	TRUE	0	0.521713395858041	2		549	386	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0028120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	59	412	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		412	1083	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0028120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	58	635	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		635	1027	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2220185	2220185	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	43	625	0	ENST00000398665.3:c.2770G>T	p.Gly924Cys	p.G924C	ENST00000398665	NM_032482.2	924	Ggt/Tgt	23/28	0.228386029211525	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		625	852	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974720	21974720	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	46	388	0	ENST00000304494.5:c.107del	p.Ala36GlyfsTer17	p.A36Gfs*17	ENST00000304494	NM_000077.4	36	gCg/gg	1/3	0.228386029211525	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		388	378	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	33	210	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.737	0.598	0.893	0.737	0.598	0.893	SUBCLONAL	1	TRUE	1	0.14	2		210	640	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099386	27099387	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0028121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	57	823	0	ENST00000324856.7:c.3625_3626dup	p.Gly1210LeufsTer7	p.G1210Lfs*7	ENST00000324856	NM_006015.4	1208	aac/aaCCc	14/20	1	2	FACETS	0.772	0.66	0.895	0.772	0.66	0.895	SUBCLONAL	1	TRUE	1	0.14	2		823	1055	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781290	135781291	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0028121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	47	609	0	ENST00000298552.3:c.1674dup	p.Cys559LeufsTer5	p.C559Lfs*5	ENST00000298552	NM_001162426.1	558	-/C	15/23	1	2	FACETS	0.745	0.627	0.877	0.745	0.627	0.877	SUBCLONAL	1	TRUE	1	0.14	2		609	901	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480075	120480075	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553195880	NA	P-0028123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	234	693	0	ENST00000256646.2:c.3352C>T	p.His1118Tyr	p.H1118Y	ENST00000256646	NM_024408.3	1118	Cac/Tac	21/34	1	2	FACETS	0.871	0.814	0.929	0.871	0.814	0.929	CLONAL	1	TRUE	1	0.65	2		693	827	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226276	2226276	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	64	873	0	ENST00000326181.6:c.1889T>C	p.Met630Thr	p.M630T	ENST00000326181	NM_032271.2	630	aTg/aCg	20/21	1	2	FACETS	0.243	0.209	0.279	0.243	0.209	0.279	SUBCLONAL	1	TRUE	1	0.65	2		873	812	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032762	30032762	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	198	536	0	ENST00000338641.4:c.137T>G	p.Leu46Arg	p.L46R	ENST00000338641	NM_000268.3	46	cTc/cGc	2/16	0.669894150163757	1	FACETS	0.941	0.883	1	0.941	0.883	1	CLONAL	1	TRUE	0	0.65	1		536	437	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593667	55593669	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	rs1060502543	NA	P-0028138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	496	529	0	ENST00000288135.5:c.1735_1737del	p.Asp579del	p.D579del	ENST00000288135	NM_000222.2	578	tATGat/tat	11/21	0.703906332132422	2	FACETS	0.931	0.901	0.96	0.931	0.901	0.96	CLONAL	2	TRUE	0	0.703906332132422	2		529	757	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	109	683	0	ENST00000397752.3:c.3028G>T	p.Asp1010Tyr	p.D1010Y	ENST00000397752	NM_000245.2	1010	Gat/Tat	14/21	0.145476025536121	1	FACETS	1	0.97	1	1	0.99	1	INDETERMINATE	2	TRUE	0	0.245076519449063	1		683	335	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268978	115268978	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs947495575	NA	P-0028139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	43	444	0	ENST00000438362.2:c.1632G>C	p.Arg544Ser	p.R544S	ENST00000438362	NM_001242891.1	544	agG/agC	14/20	0.183765655309745	3	FACETS	1	0.946	1	0.659	0.554	0.774	CLONAL	1	TRUE	1	0.245076519449063	3		444	299	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380831	118380831	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	15	300	0	ENST00000534358.1:c.11069A>G	p.Glu3690Gly	p.E3690G	ENST00000534358	NM_005933.3	3690	gAa/gGa	30/36	0.233754897694861	4	FACETS	0.663	0.485	0.876	0.221	0.161	0.292	SUBCLONAL	1	TRUE	1	0.245076519449063	4		300	230	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80343487	80343487	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	47	442	0	ENST00000286548.4:c.832C>G	p.Leu278Val	p.L278V	ENST00000286548	NM_002072.3	278	Ctt/Gtt	6/7	0.231716569303556	2	FACETS	0.827	0.704	0.959	0.827	0.704	0.959	CLONAL	2	TRUE	0	0.245076519449063	2		442	232	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0028140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	248	518	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.952	0.896	1	0.952	0.896	1	CLONAL	1	TRUE	1	0.821722011838417	2		518	634	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	252	488	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	0.975	0.919	1	0.975	0.919	1	CLONAL	1	TRUE	1	0.821722011838417	2		488	629	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913396	NA	P-0028140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	162	251	0	ENST00000349496.5:c.95A>G	p.Asp32Gly	p.D32G	ENST00000349496	NM_001904.3	32	gAc/gGc	3/15	1	2	FACETS	0.957	0.888	1	0.957	0.888	1	CLONAL	1	TRUE	1	0.821722011838417	2		251	412	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101300	27101300	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	271	613	0	ENST00000324856.7:c.4582C>T	p.Arg1528Ter	p.R1528*	ENST00000324856	NM_006015.4	1528	Cga/Tga	18/20	1	2	FACETS	0.964	0.911	1	0.964	0.911	1	CLONAL	1	TRUE	1	0.821722011838417	2		613	684	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984782	11984782	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1164096095	NA	P-0028140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	73	434	0	ENST00000353533.5:c.328C>T	p.Arg110Ter	p.R110*	ENST00000353533	NM_003010.3	110	Cga/Tga	3/11	0.761675491882418	1	FACETS	0.526	0.469	0.585	0.526	0.469	0.585	SUBCLONAL	1	TRUE	0	0.821722011838417	1		434	199	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425154	49425154	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	326	777	1	ENST00000301067.7:c.13334C>A	p.Thr4445Asn	p.T4445N	ENST00000301067	NM_003482.3	4445	aCc/aAc	39/54	1	2	FACETS	0.97	0.921	1	0.97	0.921	1	CLONAL	1	TRUE	1	0.821722011838417	2		778	818	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39570448	39570448	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	101	208	0	ENST00000262039.4:c.644T>G	p.Met215Arg	p.M215R	ENST00000262039	NM_002647.2	215	aTg/aGg	6/25	1	2	FACETS	0.825	0.747	0.905	0.825	0.747	0.905	CLONAL	1	TRUE	1	0.821722011838417	2		208	298	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163299	32163299	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	366	744	2	ENST00000375023.3:c.5927C>A	p.Pro1976Gln	p.P1976Q	ENST00000375023	NM_004557.3	1976	cCg/cAg	30/30	1	2	FACETS	0.953	0.907	0.999	0.953	0.907	0.999	CLONAL	1	TRUE	1	0.821722011838417	2		746	935	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339715	70339746	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTAGCCAAAAAGGTAAGGTACTGTTTCCTGT	ACTAGCCAAAAAGGTAAGGTACTGTTTCCTGT	-	novel	NA	P-0028140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	208	574	0	ENST00000374080.3:c.384_396+19del		p.X128_splice	ENST00000374080		128		3/45	1	2	FACETS	0.741	0.691	0.793	0.741	0.691	0.793	SUBCLONAL	1	TRUE	1	0.821722011838417	2		574	683	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0028141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	76	600	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.736	0.646	0.833	0.736	0.646	0.833	SUBCLONAL	1	TRUE	1	0.344141585077615	2		606	600	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0028141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	44	233	0	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.735	0.618	0.863	0.735	0.618	0.863	SUBCLONAL	1	TRUE	1	0.344141585077615	2		233	348	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0028141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	62	518	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.599	0.517	0.687	0.599	0.517	0.687	SUBCLONAL	1	TRUE	1	0.344141585077615	2		518	602	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0028141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	64	546	4	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.629	0.545	0.721	0.629	0.545	0.721	SUBCLONAL	1	TRUE	1	0.344141585077615	2		550	591	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0028141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	72	544	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.737	0.644	0.836	0.737	0.644	0.836	SUBCLONAL	1	TRUE	1	0.344141585077615	2		544	568	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913252	39913253	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs797044647	NA	P-0028141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	42	466	0	ENST00000378444.4:c.4862dup	p.Gly1622ArgfsTer7	p.G1622Rfs*7	ENST00000378444	NM_001123385.1	1621	cca/ccCa	14/15	1	2	FACETS	0.41	0.342	0.486	0.41	0.342	0.486	SUBCLONAL	1	TRUE	1	0.344141585077615	2		466	595	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781121	161781122	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	rs758718482	NA	P-0028141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	81	384	0	ENST00000366898.1:c.1283dup	p.Asn428LysfsTer141	p.N428Kfs*141	ENST00000366898	NM_004562.2	428	aat/aaAt	11/12	1	2	FACETS	0.777	0.685	0.875	0.777	0.685	0.875	SUBCLONAL	1	TRUE	1	0.344141585077615	2		384	606	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0028141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	130	370	1	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.344141585077615	2		371	530	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681119	117681120	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs748436511	NA	P-0028141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	54	407	0	ENST00000368508.3:c.3500dup	p.Leu1167PhefsTer26	p.L1167Ffs*26	ENST00000368508	NM_002944.2	1167	tta/ttTa	23/43	1	2	FACETS	0.569	0.485	0.659	0.569	0.485	0.659	SUBCLONAL	1	TRUE	1	0.344141585077615	2		407	552	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720721	89720721	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs786204905	NA	P-0028141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	18	137	0	ENST00000371953.3:c.875del	p.Asn292MetfsTer15	p.N292Mfs*15	ENST00000371953	NM_000314.4	291	gAa/ga	8/9	1	2	FACETS	0.581	0.44	0.747	0.581	0.44	0.747	SUBCLONAL	1	TRUE	1	0.344141585077615	2		137	180	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841258	15841258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763087055	NA	P-0028141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	81	399	0	ENST00000307771.7:c.1342C>T	p.Arg448Cys	p.R448C	ENST00000307771	NM_005089.3	448	Cgc/Tgc	11/11	1	2	FACETS	0.845	0.746	0.951	0.845	0.746	0.951	CLONAL	1	TRUE	1	0.344141585077615	2		399	557	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346157	89346158	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs878855327	NA	P-0028141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	19	215	0	ENST00000301030.4:c.6792dup	p.Ala2265ArgfsTer8	p.A2265Rfs*8	ENST00000301030	NM_001256183.1	2264	-/C	9/13	1	2	FACETS	0.489	0.372	0.625	0.489	0.372	0.625	SUBCLONAL	1	TRUE	1	0.344141585077615	2		215	226	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138382857	138382857	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142933486	NA	P-0028141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	63	365	0	ENST00000289153.2:c.2687G>A	p.Arg896Gln	p.R896Q	ENST00000289153	NM_006219.2	896	cGa/cAa	19/22	1	2	FACETS	0.714	0.618	0.817	0.714	0.618	0.817	SUBCLONAL	1	TRUE	1	0.344141585077615	2		365	513	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224440	39224440	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs727505016	NA	P-0028141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	60	449	0	ENST00000402219.2:c.2918A>T	p.Gln973Leu	p.Q973L	ENST00000402219	NM_005633.3	973	cAg/cTg	18/23	1	2	FACETS	0.547	0.47	0.63	0.547	0.47	0.63	SUBCLONAL	1	TRUE	1	0.344141585077615	2		449	638	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007551	62007551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751548429	NA	P-0028141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	80	560	0	ENST00000392795.3:c.316G>A	p.Ala106Thr	p.A106T	ENST00000392795	NM_001039933.1	106	Gcc/Acc	3/6	1	2	FACETS	0.676	0.595	0.763	0.676	0.595	0.763	SUBCLONAL	1	TRUE	1	0.344141585077615	2		560	688	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793363	242793363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	90	586	0	ENST00000334409.5:c.714del	p.Val239CysfsTer39	p.V239Cfs*39	ENST00000334409	NM_005018.2	238	ccC/cc	5/5	1	2	FACETS	0.709	0.629	0.794	0.709	0.629	0.794	SUBCLONAL	1	TRUE	1	0.344141585077615	2		586	738	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156169	106156169	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	55	326	0	ENST00000380013.4:c.1070G>A	p.Ser357Asn	p.S357N	ENST00000380013	NM_001127208.2	357	aGc/aAc	3/11	1	2	FACETS	0.679	0.581	0.785	0.679	0.581	0.785	SUBCLONAL	1	TRUE	1	0.344141585077615	2		326	471	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655481	67655481	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs34679888	NA	P-0028141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	68	391	0	ENST00000264010.4:c.1348del	p.Ser450ValfsTer61	p.S450Vfs*61	ENST00000264010	NM_006565.3	448	cgA/cg	7/12	1	2	FACETS	0.66	0.574	0.752	0.66	0.574	0.752	SUBCLONAL	1	TRUE	1	0.344141585077615	2		391	599	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101379	27101379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	86	410	0	ENST00000324856.7:c.4661C>T	p.Pro1554Leu	p.P1554L	ENST00000324856	NM_006015.4	1554	cCa/cTa	18/20	1	2	FACETS	0.844	0.748	0.947	0.844	0.748	0.947	CLONAL	1	TRUE	1	0.344141585077615	2		410	592	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942228	71942228	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	56	420	0	ENST00000298229.2:c.1492C>A	p.Arg498Ser	p.R498S	ENST00000298229	NM_001567.3	498	Cgc/Agc	12/28	1	2	FACETS	0.626	0.536	0.723	0.626	0.536	0.723	SUBCLONAL	1	TRUE	1	0.344141585077615	2		420	520	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719992	18719992	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs376472161	NA	P-0028141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	32	262	0	ENST00000266497.5:c.3888+1G>A		p.X1296_splice	ENST00000266497		1296			1	2	FACETS	0.443	0.359	0.537	0.443	0.359	0.537	SUBCLONAL	1	TRUE	1	0.344141585077615	2		262	420	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445202	49445203	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1555196984	NA	P-0028141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	92	636	0	ENST00000301067.7:c.2263dup	p.Arg755ProfsTer3	p.R755Pfs*3	ENST00000301067	NM_003482.3	755	cgg/cCgg	10/54	1	2	FACETS	0.718	0.637	0.803	0.718	0.637	0.803	SUBCLONAL	1	TRUE	1	0.344141585077615	2		636	745	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639728	3639728	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	91	656	0	ENST00000294008.3:c.3911T>C	p.Val1304Ala	p.V1304A	ENST00000294008	NM_032444.2	1304	gTc/gCc	12/15	1	2	FACETS	0.659	0.585	0.739	0.659	0.585	0.739	SUBCLONAL	1	TRUE	1	0.344141585077615	2		656	802	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830520	72830521	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	77	421	0	ENST00000268489.5:c.6060dup	p.Gln2021ThrfsTer8	p.Q2021Tfs*8	ENST00000268489	NM_006885.3	2020	-/A	9/10	1	2	FACETS	0.636	0.558	0.72	0.636	0.558	0.72	SUBCLONAL	1	TRUE	1	0.344141585077615	2		421	704	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30311741	30311741	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	41	343	0	ENST00000262643.3:c.595G>A	p.Ala199Thr	p.A199T	ENST00000262643	NM_001238.2	199	Gca/Aca	7/12	1	2	FACETS	0.447	0.372	0.531	0.447	0.372	0.531	SUBCLONAL	1	TRUE	1	0.344141585077615	2		343	533	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046937	128046937	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	77	457	0	ENST00000285398.2:c.798G>T	p.Gln266His	p.Q266H	ENST00000285398	NM_000122.1	266	caG/caT	6/15	1	2	FACETS	0.639	0.561	0.724	0.639	0.561	0.724	SUBCLONAL	1	TRUE	1	0.344141585077615	2		457	700	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047807	128047807	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	62	411	0	ENST00000285398.2:c.514C>T	p.His172Tyr	p.H172Y	ENST00000285398	NM_000122.1	172	Cac/Tac	4/15	1	2	FACETS	0.609	0.526	0.699	0.609	0.526	0.699	SUBCLONAL	1	TRUE	1	0.344141585077615	2		411	592	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845287	42845287	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	70	497	0	ENST00000398585.3:c.975del	p.Glu326SerfsTer4	p.E326Sfs*4	ENST00000398585	NM_001135099.1	325	ccC/cc	9/14	1	2	FACETS	0.589	0.513	0.671	0.589	0.513	0.671	SUBCLONAL	1	TRUE	1	0.344141585077615	2		497	691	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573407	41573407	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	82	590	0	ENST00000263253.7:c.5692C>T	p.Gln1898Ter	p.Q1898*	ENST00000263253	NM_001429.3	1898	Cag/Tag	31/31	1	2	FACETS	0.718	0.633	0.809	0.718	0.633	0.809	SUBCLONAL	1	TRUE	1	0.344141585077615	2		590	664	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444560	187444560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	91	399	0	ENST00000232014.4:c.1667G>A	p.Arg556His	p.R556H	ENST00000232014	NM_001130845.1	556	cGc/cAc	7/10	1	2	FACETS	0.794	0.705	0.889	0.794	0.705	0.889	SUBCLONAL	1	TRUE	1	0.344141585077615	2		399	666	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530441	187530441	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	41	258	0	ENST00000441802.2:c.10102A>G	p.Ser3368Gly	p.S3368G	ENST00000441802	NM_005245.3	3368	Agc/Ggc	16/27	1	2	FACETS	0.667	0.557	0.789	0.667	0.557	0.789	SUBCLONAL	1	TRUE	1	0.344141585077615	2		258	357	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41905089	41905089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	67	364	0	ENST00000372991.4:c.458C>T	p.Ala153Val	p.A153V	ENST00000372991	NM_001760.3	153	gCt/gTt	3/5	1	2	FACETS	0.743	0.647	0.847	0.743	0.647	0.847	SUBCLONAL	1	TRUE	1	0.344141585077615	2		364	524	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100328	157100328	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	32	176	0	ENST00000346085.5:c.1265T>C	p.Leu422Pro	p.L422P	ENST00000346085	NM_020732.3	422	cTg/cCg	1/20	1	2	FACETS	0.583	0.474	0.705	0.583	0.474	0.705	SUBCLONAL	1	TRUE	1	0.344141585077615	2		176	319	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74859050	74859050	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	61	341	0	ENST00000284811.8:c.154T>G	p.Phe52Val	p.F52V	ENST00000284811		52	Ttt/Gtt	4/4	1	2	FACETS	0.625	0.539	0.718	0.625	0.539	0.718	SUBCLONAL	1	TRUE	1	0.344141585077615	2		341	567	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932521	39932521	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	94	636	1	ENST00000378444.4:c.2078C>A	p.Pro693His	p.P693H	ENST00000378444	NM_001123385.1	693	cCt/cAt	4/15	1	2	FACETS	0.701	0.624	0.784	0.701	0.624	0.784	SUBCLONAL	1	TRUE	1	0.344141585077615	2		637	779	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0028143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	158	445	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.274441819301017	5	FACETS	1	0.963	1	0.717	0.66	0.775	CLONAL	2	TRUE	2	0.430066246977758	5		445	562	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0028143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	158	647	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	0.430066246977758	3	FACETS	1	0.942	1	0.517	0.474	0.562	CLONAL	1	TRUE	1	0.430066246977758	3		647	863	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265574	152265574	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	232	521	0	ENST00000206249.3:c.1027A>T	p.Met343Leu	p.M343L	ENST00000206249	NM_000125.3	343	Atg/Ttg	4/8	0.238170487182269	6	FACETS	0.886	0.829	0.944			1	INDETERMINATE	3	TRUE	NA	0.430066246977758	6		521	755	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410873	63410873	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	226	716	0	ENST00000330258.3:c.2294C>G	p.Ala765Gly	p.A765G	ENST00000330258	NM_152424.3	765	gCc/gGc	2/2	0.226099444629431	5	FACETS	0.886	0.825	0.948			1	INDETERMINATE	2	TRUE	NA	0.430066246977758	5		716	976	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	224	297	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.915	0.857	0.974	0.915	0.857	0.974	CLONAL	1	TRUE	1	0.77	2		297	636	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	390	846	1	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.913	0.869	0.957	0.913	0.869	0.957	CLONAL	1	TRUE	1	0.77	2		847	1110	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	270	338	2	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.786	0.75	0.822	1	0.995	1	SUBCLONAL	2	TRUE	1	0.77	2		340	446	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	670	546	4	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.958	0.935	0.981	1	0.998	1	CLONAL	2	TRUE	1	0.77	2		550	908	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	272	544	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.93	0.876	0.984	0.93	0.876	0.984	CLONAL	1	TRUE	1	0.77	2		544	760	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	418	600	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.77	2		600	1068	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509085	66509085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	103	372	1	ENST00000273854.3:c.242del	p.Asn81MetfsTer24	p.N81Mfs*24	ENST00000273854	NM_004439.5	81	aAt/at	2/18	1	2	FACETS	0.932	0.846	1	0.932	0.846	1	CLONAL	1	TRUE	1	0.77	2		373	287	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	317	578	0	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	1	2	FACETS	0.919	0.87	0.969	0.919	0.87	0.969	CLONAL	1	TRUE	1	0.77	2		578	896	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	256	661	3	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.941	0.885	0.997	0.941	0.885	0.997	CLONAL	1	TRUE	1	0.77	2		664	707	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121909229	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	230	548	0	ENST00000371953.3:c.389G>C	p.Arg130Pro	p.R130P	ENST00000371953	NM_000314.4	130	cGa/cCa	5/9	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.77	2		548	580	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133236047	133236047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs948001596	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	291	481	0	ENST00000320574.5:c.3109C>T	p.Arg1037Cys	p.R1037C	ENST00000320574	NM_006231.2	1037	Cgt/Tgt	26/49	1	2	FACETS	0.956	0.903	1	0.956	0.903	1	CLONAL	1	TRUE	1	0.77	2		481	791	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	109	117	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.77	2		117	222	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444659	78444659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs908264837	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	264	385	1	ENST00000370768.2:c.30del	p.Ser11LeufsTer43	p.S11Lfs*43	ENST00000370768	NM_003902.3	10	ccC/cc	1/20	1	2	FACETS	0.998	0.941	1	0.998	0.941	1	CLONAL	1	TRUE	1	0.77	2		386	687	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	261	496	3	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.77	2		499	664	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851230	63851230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1271514044	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	80	652	0	ENST00000279873.7:c.2008C>T	p.His670Tyr	p.H670Y	ENST00000279873	NM_032199.2	670	Cat/Tat	10/10	1	2	FACETS	0.237	0.208	0.268	0.237	0.208	0.268	SUBCLONAL	1	TRUE	1	0.77	2		652	878	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606273	93606273	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	94	726	3	ENST00000375746.1:c.98del	p.Gly33AlafsTer2	p.G33Afs*2	ENST00000375746	NM_001174167.1	31	caG/ca	2/14	1	2	FACETS	0.271	0.241	0.304	0.271	0.241	0.304	SUBCLONAL	1	TRUE	1	0.77	2		729	900	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100210	157100210	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	57	58	0	ENST00000346085.5:c.1151del	p.Gly384AlafsTer46	p.G384Afs*46	ENST00000346085	NM_020732.3	383	Ggg/gg	1/20	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.77	2		58	145	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6027156	6027157	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs267608159	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	10	19	0	ENST00000265849.7:c.1239dup	p.Asp414ArgfsTer44	p.D414Rfs*44	ENST00000265849	NM_000535.5	413	-/A	11/15	1	2	FACETS	0.999	0.721	1	0.999	0.721	1	CLONAL	1	TRUE	1	0.77	2		19	26	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776558	9776558	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	105	662	1	ENST00000377346.4:c.661C>A	p.Leu221Met	p.L221M	ENST00000377346	NM_005026.3	221	Ctg/Atg	6/24	1	2	FACETS	0.317	0.284	0.353	0.317	0.284	0.353	SUBCLONAL	1	TRUE	1	0.77	2		663	859	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023182	27023182	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	105	119	0	ENST00000324856.7:c.289del	p.Glu97SerfsTer4	p.E97Sfs*4	ENST00000324856	NM_006015.4	96	gcG/gc	1/20	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.77	2		119	261	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275301	115275301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1255615164	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	282	622	1	ENST00000438362.2:c.1112G>A	p.Arg371His	p.R371H	ENST00000438362	NM_001242891.1	371	cGt/cAt	10/20	1	2	FACETS	0.918	0.866	0.971	0.918	0.866	0.971	CLONAL	1	TRUE	1	0.77	2		623	798	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165656	118165656	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756798728	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	178	362	0	ENST00000369448.3:c.166C>T	p.Arg56Cys	p.R56C	ENST00000369448	NM_017709.3	56	Cgc/Tgc	2/2	1	2	FACETS	0.914	0.849	0.98	0.914	0.849	0.98	CLONAL	1	TRUE	1	0.77	2		362	506	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437755	110437755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768235363	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	387	605	0	ENST00000375856.3:c.646G>A	p.Val216Met	p.V216M	ENST00000375856	NM_003749.2	216	Gtg/Atg	1/2	0.0999805966297127	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.77	0		605	1105	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068312	30068312	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	27	378	0	ENST00000331968.5:c.2087A>G	p.His696Arg	p.H696R	ENST00000331968	NM_002742.2	696	cAc/cGc	15/18	1	2	FACETS	0.165	0.13	0.204	0.165	0.13	0.204	SUBCLONAL	1	TRUE	1	0.77	2		378	426	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061684	38061684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	183	322	0	ENST00000250448.2:c.305C>T	p.Thr102Met	p.T102M	ENST00000250448	NM_004496.3	102	aCg/aTg	2/2	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.77	2		322	446	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675482	40675482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	336	584	1	ENST00000249776.8:c.263G>A	p.Ser88Asn	p.S88N	ENST00000249776	NM_033286.3	88	aGc/aAc	2/9	1	2	FACETS	0.991	0.94	1	0.991	0.94	1	CLONAL	1	TRUE	1	0.77	2		585	881	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032078	10032078	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	309	632	0	ENST00000330684.3:c.745A>G	p.Thr249Ala	p.T249A	ENST00000330684	NM_001134407.1	249	Acc/Gcc	3/13	1	2	FACETS	0.97	0.919	1	0.97	0.919	1	CLONAL	1	TRUE	1	0.77	2		632	827	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349291	89349291	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	80	981	1	ENST00000301030.4:c.3659G>T	p.Arg1220Met	p.R1220M	ENST00000301030	NM_001256183.1	1220	aGg/aTg	9/13	1	2	FACETS	0.167	0.146	0.189	0.167	0.146	0.189	SUBCLONAL	1	TRUE	1	0.77	2		982	1247	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120318	70120318	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs80338688	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	584	814	1	ENST00000245479.2:c.1320C>A	p.Tyr440Ter	p.Y440*	ENST00000245479	NM_000346.3	440	taC/taA	3/3	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.77	2		815	1499	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223814	36223814	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	363	839	0	ENST00000222270.7:c.6368del	p.Gly2123ValfsTer30	p.G2123Vfs*30	ENST00000222270	NM_014727.1	2122	Ggg/gg	28/37	1	2	FACETS	0.863	0.819	0.907	0.863	0.819	0.907	CLONAL	1	TRUE	1	0.77	2		839	1093	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018081	48018083	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	277	576	0	ENST00000234420.5:c.278_280del	p.Gly93del	p.G93del	ENST00000234420	NM_000179.2	92	ccAGGa/cca	2/10	1	2	FACETS	0.999	0.944	1	0.999	0.944	1	CLONAL	1	TRUE	1	0.77	2		576	720	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468481	89468481	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	163	437	0	ENST00000336596.2:c.2015G>T	p.Ser672Ile	p.S672I	ENST00000336596	NM_005233.5	672	aGc/aTc	11/17	1	2	FACETS	0.811	0.749	0.874	0.811	0.749	0.874	CLONAL	1	TRUE	1	0.77	2		437	522	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260247	149260247	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs753225952	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	443	742	0	ENST00000360632.3:c.646G>T	p.Ala216Ser	p.A216S	ENST00000360632	NM_015472.4	216	Gca/Tca	4/7	1	2	FACETS	0.988	0.944	1	0.988	0.944	1	CLONAL	1	TRUE	1	0.77	2		742	1165	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858164	27858167	+	frameshift_variant	Frame_Shift_Del	DEL	GCTC	GCTC	-	novel	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	46	401	0	ENST00000359303.2:c.404_407del	p.Arg135HisfsTer?	p.R135Hfs*?	ENST00000359303	NM_003535.2	135	cGAGCa/ca	1/1	1	2	FACETS	0.218	0.183	0.256	0.218	0.183	0.256	SUBCLONAL	1	TRUE	1	0.77	2		401	549	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759710	133759710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752701660	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	255	546	0	ENST00000318560.5:c.2033G>A	p.Gly678Asp	p.G678D	ENST00000318560	NM_005157.4	678	gGc/gAc	11/11	1	2	FACETS	0.971	0.914	1	0.971	0.914	1	CLONAL	1	TRUE	1	0.77	2		546	682	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786481	135786481	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	259	577	0	ENST00000298552.3:c.1049C>G	p.Ser350Cys	p.S350C	ENST00000298552	NM_001162426.1	350	tCt/tGt	11/23	1	2	FACETS	0.925	0.871	0.981	0.925	0.871	0.981	CLONAL	1	TRUE	1	0.77	2		577	727	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466028	69466034	+	protein_altering_variant	In_Frame_Del	DEL	ACGTGCG	ACGTGCG	C	novel	NA	P-0028144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	412	655	0	ENST00000227507.2:c.866_872delinsC	p.Asp289_Arg291delinsAla	p.D289_R291delinsA	ENST00000227507	NM_053056.2	289	gACGTGCGg/gCg	5/5	1	2	FACETS	0.996	0.951	1	0.996	0.951	1	CLONAL	1	TRUE	1	0.77	2		655	1074	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0028145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	59	586	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.3	2	FACETS	0.771	0.672	0.876			1	SUBCLONAL	2	TRUE	NA	0.34	2		587	225	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409047	4409047	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	20	270	0	ENST00000261254.3:c.742G>T	p.Glu248Ter	p.E248*	ENST00000261254	NM_001759.3	248	Gag/Tag	5/5	0.389002512406926	3	FACETS	1	0.852	1	0.569	0.44	0.715	CLONAL	1	TRUE	1	0.34	3		270	121	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799378	88799378	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	19	258	0	ENST00000360948.2:c.7G>T	p.Val3Phe	p.V3F	ENST00000360948	NM_001012338.2	3	Gtc/Ttc	2/19	1	2	FACETS	0.47	0.357	0.601	0.47	0.357	0.601	SUBCLONAL	1	TRUE	1	0.34	2		258	238	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953124	81953124	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs767717794	NA	P-0028145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	10	249	0	ENST00000359376.3:c.2090G>C	p.Arg697Pro	p.R697P	ENST00000359376	NM_002661.3	697	cGg/cCg	20/33	0.135714076756205	2	FACETS	0.626	0.428	0.869	0.313	0.214	0.435	INDETERMINATE	1	TRUE	0	0.34	2		249	94	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0028145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	41	494	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.214016175960264	3	FACETS	0.457	0.379	0.543	0.228	0.189	0.272	SUBCLONAL	1	TRUE	1	0.34	3		494	618	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881483	111881483	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	42	426	0	ENST00000393256.3:c.161G>T	p.Ser54Ile	p.S54I	ENST00000393256	NM_006538.4	54	aGc/aTc	2/4	0.389002512406926	3	FACETS	0.693	0.579	0.819	0.347	0.289	0.41	SUBCLONAL	1	TRUE	1	0.34	3		426	417	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541859	187541859	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	15	409	0	ENST00000441802.2:c.5881G>T	p.Gly1961Cys	p.G1961C	ENST00000441802	NM_005245.3	1961	Ggc/Tgc	10/27	0.27633445527244	5	FACETS	0.932	0.686	1	0.311	0.228	0.408	CLONAL	1	TRUE	2	0.34	5		409	143	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90994967	90994967	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	13	330	0	ENST00000265433.3:c.154T>A	p.Phe52Ile	p.F52I	ENST00000265433	NM_002485.4	52	Ttt/Att	2/16	0.3	0	FACETS	0.515	0.372	0.685			1	SUBCLONAL	1	TRUE	0	0.34	0		330	98	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	93	210	0				ENST00000310581	NM_198253.2	-/1132			0.113470393307304	4	FACETS	0.847	0.76	0.937	0.847	0.76	0.937	INDETERMINATE	2	TRUE	2	0.469226497913488	4		210	344	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085917	16085917	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs140276895	NA	P-0028146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	26	475	0	ENST00000281043.3:c.1093C>G	p.Pro365Ala	p.P365A	ENST00000281043	NM_005378.4	365	Cca/Gca	3/3	0.469226497913488	2	FACETS	0.252	0.199	0.313	0.126	0.099	0.157	SUBCLONAL	1	TRUE	0	0.469226497913488	2		475	440	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	203	643	0	ENST00000269305.4:c.166del	p.Glu56LysfsTer67	p.E56Kfs*67	ENST00000269305	NM_001126112.2	56	Gaa/aa	4/11	0.469226497913488	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.469226497913488	1		643	506	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089718	27089718	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	89	613	1	ENST00000324856.7:c.2674C>T	p.Arg892Trp	p.R892W	ENST00000324856	NM_006015.4	892	Cgg/Tgg	8/20	0.14868520965599	2	FACETS	0.682	0.606	0.763	0.341	0.303	0.382	INDETERMINATE	1	TRUE	0	0.469226497913488	2		614	556	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720624	89720665	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTCTTTTCTTTTTTTTTTTTTTTAGGACAAAATGTTTCAC	TTTTCTTTTCTTTTTTTTTTTTTTTAGGACAAAATGTTTCAC	-	novel	NA	P-0028146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	36	350	0	ENST00000371953.3:c.802-23_820del		p.X268_splice	ENST00000371953	NM_000314.4	268		8/9	0.469226497913488	1	FACETS	0.57	0.473	0.677	0.57	0.473	0.677	SUBCLONAL	1	TRUE	0	0.469226497913488	1		350	206	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252038	133252038	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	20	567	0	ENST00000320574.5:c.1172A>G	p.Lys391Arg	p.K391R	ENST00000320574	NM_006231.2	391	aAg/aGg	12/49	0.469226497913488	1	FACETS	0.165	0.125	0.211	0.165	0.125	0.211	SUBCLONAL	1	TRUE	0	0.469226497913488	1		567	396	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436399	110436399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	45	535	0	ENST00000375856.3:c.2002G>A	p.Gly668Ser	p.G668S	ENST00000375856	NM_003749.2	668	Ggc/Agc	1/2	1	2	FACETS	0.487	0.41	0.572	0.487	0.41	0.572	SUBCLONAL	1	TRUE	1	0.469226497913488	2		535	394	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068966	30068966	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	73	658	0	ENST00000331968.5:c.1963G>C	p.Val655Leu	p.V655L	ENST00000331968	NM_002742.2	655	Gtg/Ctg	14/18	1	2	FACETS	0.624	0.546	0.706	0.624	0.546	0.706	SUBCLONAL	1	TRUE	1	0.469226497913488	2		658	499	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823822	3823822	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs749642688	NA	P-0028146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	85	471	0	ENST00000262367.5:c.2393A>G	p.Gln798Arg	p.Q798R	ENST00000262367	NM_004380.2	798	cAg/cGg	13/31	0.469226497913488	1	FACETS	0.643	0.571	0.72	0.643	0.571	0.72	SUBCLONAL	1	TRUE	0	0.469226497913488	1		471	431	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390107	89390107	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	129	354	1	ENST00000336596.2:c.856A>G	p.Lys286Glu	p.K286E	ENST00000336596	NM_005233.5	286	Aag/Gag	4/17	1	2	FACETS	0.823	0.757	0.891	1	0.989	1	CLONAL	2	TRUE	1	0.469226497913488	2		355	334	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851599	128851599	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	46	495	0	ENST00000249373.3:c.1924G>T	p.Val642Leu	p.V642L	ENST00000249373	NM_005631.4	642	Gtg/Ttg	11/12	0.469226497913488	1	FACETS	0.325	0.273	0.381	0.325	0.273	0.381	SUBCLONAL	1	TRUE	0	0.469226497913488	1		495	462	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608181	100608181	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0028146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	43	386	0	ENST00000308731.7:c.1908+1G>T		p.X636_splice	ENST00000308731	NM_000061.2	636			0.469226497913488	1	FACETS	0.389	0.326	0.458	0.389	0.326	0.458	SUBCLONAL	1	TRUE	0	0.469226497913488	1		386	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934575	NA	P-0028149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	272	529	0	ENST00000269305.4:c.733G>C	p.Gly245Arg	p.G245R	ENST00000269305	NM_001126112.2	245	Ggc/Cgc	7/11	0.499535991172719	1	FACETS	0.765	0.726	0.804	1	0.995	1	SUBCLONAL	2	TRUE	0	0.499535991172719	1		529	534	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076752	72076752	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	68	483	0	ENST00000357731.5:c.745G>T	p.Gly249Cys	p.G249C	ENST00000357731	NM_173808.2	249	Ggt/Tgt	5/7	0.213315477064446	2	FACETS	0.489	0.425	0.557	0.244	0.212	0.279	INDETERMINATE	1	TRUE	0	0.499535991172719	2		483	557	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257152	19257152	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	60	447	2	ENST00000162023.5:c.811C>A	p.Gln271Lys	p.Q271K	ENST00000162023		271	Cag/Aag	12/13	0.499535991172719	4	FACETS	0.573	0.493	0.66	0.143	0.123	0.165	SUBCLONAL	1	TRUE	0	0.499535991172719	4		449	629	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028218	48028218	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	102	435	0	ENST00000234420.5:c.3096C>A	p.Cys1032Ter	p.C1032*	ENST00000234420	NM_000179.2	1032	tgC/tgA	4/10	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.499535991172719	2		435	402	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0028153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	348	648	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.487045894205422	2	FACETS	0.968	0.924	1	0.968	0.924	1	CLONAL	2	TRUE	0	0.497025646090698	2		648	723	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986658	36986658	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	13	73	0	ENST00000354822.5:c.1031G>C	p.Gly344Ala	p.G344A	ENST00000354822	NM_001079668.2	344	gGc/gCc	3/3	1	2	FACETS	0.781	0.569	1	0.781	0.569	1	CLONAL	1	TRUE	1	0.497025646090698	2		73	67	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0028155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	176	493	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.213695801480866	4	FACETS	0.759	0.699	0.821	0.759	0.699	0.821	INDETERMINATE	2	TRUE	2	0.36	4		493	876	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0028155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	455	544	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.157378481886537	3	FACETS	0.951	0.911	0.991			1	INDETERMINATE	3	TRUE	NA	0.36	3		544	1046	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589599	67589604	+	inframe_deletion	In_Frame_Del	DEL	TCAGTT	TCAGTT	-	novel	NA	P-0028155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	39	341	0	ENST00000274335.5:c.1365_1370del	p.Phe456_Gln457del	p.F456_Q457del	ENST00000274335		454	acTCAGTTt/act	10/15	0.299409138407098	3	FACETS	0.987	0.823	1	0.494	0.411	0.584	CLONAL	1	TRUE	1	0.36	3		341	259	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141549490	141549490	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	76	390	0	ENST00000220592.5:c.2098C>A	p.Pro700Thr	p.P700T	ENST00000220592	NM_012154.3	700	Ccc/Acc	16/19	0.242434043484612	3	FACETS	0.748	0.656	0.847	0.374	0.328	0.424	SUBCLONAL	1	TRUE	1	0.36	3		390	666	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212839	27212839	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	121	574	0	ENST00000380036.4:c.2821C>G	p.Leu941Val	p.L941V	ENST00000380036	NM_000459.3	941	Ctc/Gtc	17/23	0.138075592403848	5	FACETS	0.938	0.845	1	0.313	0.281	0.346	INDETERMINATE	1	TRUE	2	0.36	5		574	1104	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440887	56440899	+	protein_altering_variant,splice_region_variant	In_Frame_Del	DEL	CTGCTCAGCAGCA	CTGCTCAGCAGCA	ATTT	novel	NA	P-0028155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	172	594	0	ENST00000407977.2:c.438_450delinsAAAT	p.Ala147_Gln150delinsAsn	p.A147_Q150delinsN	ENST00000407977		146	gcTGCTGCTGAGCAG/gcAAAT	4/10	0.299409138407098	2	FACETS	1	0.986	1	0.654	0.603	0.706	CLONAL	1	TRUE	0	0.36	2		594	731	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	72	210	0				ENST00000310581	NM_198253.2	-/1132			0.268346026269444	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.282195878415209	1		210	338	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0028156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	71	518	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.282195878415209	3	FACETS	0.844	0.737	0.961	0.422	0.368	0.481	CLONAL	1	TRUE	1	0.282195878415209	3		518	680	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910744	29910744	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0028156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	106	659	0	ENST00000376809.5:c.284C>G	p.Ser95Ter	p.S95*	ENST00000376809	NM_002116.7	95	tCa/tGa	2/8	1	2	FACETS	0.842	0.754	0.936	0.842	0.754	0.936	CLONAL	1	TRUE	1	0.282195878415209	2		659	892	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40490803	40490803	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	86	357	0	ENST00000264657.5:c.496G>C	p.Glu166Gln	p.E166Q	ENST00000264657	NM_139276.2	166	Gag/Cag	6/24	1	2	FACETS	0.946	0.838	1	0.946	0.838	1	CLONAL	1	TRUE	1	0.282195878415209	2		357	644	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910797	29910797	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs41559912	NA	P-0028156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	86	403	1	ENST00000376809.5:c.337G>T	p.Glu113Ter	p.E113*	ENST00000376809	NM_002116.7	113	Gag/Tag	2/8	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.282195878415209	2		404	544	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091193	29091193	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	50	219	0	ENST00000328354.6:c.1297C>G	p.Gln433Glu	p.Q433E	ENST00000328354	NM_007194.3	433	Caa/Gaa	12/15	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.282195878415209	2		219	310	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617424	43617424	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	65	367	0	ENST00000355710.3:c.2761G>A	p.Glu921Lys	p.E921K	ENST00000355710	NM_020975.4	921	Gaa/Aaa	16/20	1	2	FACETS	0.864	0.75	0.988	0.864	0.75	0.988	CLONAL	1	TRUE	1	0.282195878415209	2		367	533	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420241	49420241	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	117	543	0	ENST00000301067.7:c.15508C>T	p.Gln5170Ter	p.Q5170*	ENST00000301067	NM_003482.3	5170	Cag/Tag	48/54	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.282195878415209	2		543	808	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911663	32911663	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	79	454	0	ENST00000380152.3:c.3171G>C	p.Lys1057Asn	p.K1057N	ENST00000380152		1057	aaG/aaC	11/27	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.282195878415209	2		454	543	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061087	38061087	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	22	203	0	ENST00000250448.2:c.902C>T	p.Ser301Phe	p.S301F	ENST00000250448	NM_004496.3	301	tCt/tTt	2/2	1	2	FACETS	0.808	0.63	1	0.808	0.63	1	CLONAL	1	TRUE	1	0.282195878415209	2		203	193	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117515	4117515	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1427916025	NA	P-0028156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	34	206	0	ENST00000262948.5:c.205G>C	p.Asp69His	p.D69H	ENST00000262948	NM_030662.3	69	Gac/Cac	2/11	1	2	FACETS	0.803	0.658	0.965	0.803	0.658	0.965	CLONAL	1	TRUE	1	0.282195878415209	2		206	300	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61706029	61706029	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	103	506	0	ENST00000401558.2:c.3142G>C	p.Glu1048Gln	p.E1048Q	ENST00000401558	NM_003400.3	1048	Gag/Cag	25/25	1	2	FACETS	0.874	0.782	0.973	0.874	0.782	0.973	CLONAL	1	TRUE	1	0.282195878415209	2		506	835	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586422	189586423	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0028156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	71	356	0	ENST00000264731.3:c.1046_1047delinsAT	p.Gly349Asp	p.G349D	ENST00000264731	NM_003722.4	349	gGA/gAT	8/14	0.282195878415209	3	FACETS	0.925	0.807	1	0.462	0.403	0.526	CLONAL	1	TRUE	1	0.282195878415209	3		356	621	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910598	29910598	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	64	510	0	ENST00000376809.5:c.138C>G	p.Phe46Leu	p.F46L	ENST00000376809	NM_002116.7	46	ttC/ttG	2/8	1	2	FACETS	0.665	0.575	0.763	0.665	0.575	0.763	SUBCLONAL	1	TRUE	1	0.282195878415209	2		510	682	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977655	2977655	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	96	498	0	ENST00000396946.4:c.1029G>C	p.Glu343Asp	p.E343D	ENST00000396946	NM_032415.4	343	gaG/gaC	8/25	1	2	FACETS	0.81	0.721	0.905	0.81	0.721	0.905	CLONAL	1	TRUE	1	0.282195878415209	2		498	840	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845871	151845871	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	110	569	0	ENST00000262189.6:c.13141G>T	p.Glu4381Ter	p.E4381*	ENST00000262189	NM_170606.2	4381	Gaa/Taa	52/59	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.282195878415209	2		569	700	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879322	151879322	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	68	372	0	ENST00000262189.6:c.5623C>T	p.Gln1875Ter	p.Q1875*	ENST00000262189	NM_170606.2	1875	Cag/Tag	36/59	1	2	FACETS	0.891	0.776	1	0.891	0.776	1	CLONAL	1	TRUE	1	0.282195878415209	2		372	541	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0028157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	305	519	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.125148393544142	3	FACETS	0.965	0.918	1	1	0.995	1	INDETERMINATE	3	FALSE	1	0.406492338132972	3		519	624	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0028157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	97	581	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.406492338132972	1	FACETS	0.797	0.714	0.885	0.797	0.714	0.885	SUBCLONAL	1	FALSE	0	0.406492338132972	1		583	477	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112434	115112435	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	98	538	0	ENST00000257566.3:c.1305dup	p.Arg436ThrfsTer3	p.R436Tfs*3	ENST00000257566	NM_016569.3	435	-/A	7/8	1	2	FACETS	0.947	0.848	1	0.947	0.848	1	CLONAL	1	FALSE	1	0.406492338132972	2		538	509	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742803	145742803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	52	367	0	ENST00000428558.2:c.208G>A	p.Glu70Lys	p.E70K	ENST00000428558	NM_004260.3	70	Gaa/Aaa	3/22	1	2	FACETS	0.723	0.618	0.837	0.723	0.618	0.837	SUBCLONAL	1	FALSE	1	0.406492338132972	2		367	354	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056226	27056226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	123	581	0	ENST00000324856.7:c.1222C>T	p.Pro408Ser	p.P408S	ENST00000324856	NM_006015.4	408	Ccg/Tcg	2/20	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	FALSE	1	0.406492338132972	2		581	581	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056294	27056294	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0028157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	106	487	0	ENST00000324856.7:c.1290C>G	p.Tyr430Ter	p.Y430*	ENST00000324856	NM_006015.4	430	taC/taG	2/20	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	FALSE	1	0.406492338132972	2		487	490	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118713	115118717	+	frameshift_variant	Frame_Shift_Del	DEL	TGAGT	TGAGT	-	novel	NA	P-0028157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	99	493	0	ENST00000257566.3:c.624_628del	p.Lys208AsnfsTer17	p.K208Nfs*17	ENST00000257566	NM_016569.3	208	aaACTCAcc/aacc	2/8	1	2	FACETS	0.942	0.844	1	0.942	0.844	1	CLONAL	1	FALSE	1	0.406492338132972	2		493	517	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847232	68847233	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	88	470	0	ENST00000261769.5:c.1155dup	p.Glu386Ter	p.E386*	ENST00000261769	NM_004360.3	385	cct/ccTt	9/16	0.406492338132972	0	FACETS	0.73	0.652	0.812			1	SUBCLONAL	1	FALSE	0	0.406492338132972	0		470	352	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851097	151851097	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	61	215	0	ENST00000262189.6:c.12274G>A	p.Glu4092Lys	p.E4092K	ENST00000262189	NM_170606.2	4092	Gag/Aag	48/59	0.182440037604224	4	FACETS	1	0.957	1	0.42	0.364	0.48	INDETERMINATE	1	FALSE	1	0.406492338132972	4		215	335	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0028158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	490	491	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.140054231459269	6	FACETS	0.93	0.895	0.966			1	INDETERMINATE	4	TRUE	NA	0.581279057523399	6		491	980	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134234	11134234	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1085307769	NA	P-0028158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	240	487	0	ENST00000358026.2:c.2900G>A	p.Arg967His	p.R967H	ENST00000358026	NM_001128849.1	967	cGt/cAt	20/36	0.372237054506496	1	FACETS	0.838	0.786	0.891	0.838	0.786	0.891	CLONAL	1	TRUE	0	0.581279057523399	1		487	699	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253394	226253394	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	54	157	0	ENST00000366813.1:c.166C>T	p.Gln56Ter	p.Q56*	ENST00000366813		56	Cag/Tag	2/3	0.471116235539842	1	FACETS	0.534	0.46	0.612	0.534	0.46	0.612	SUBCLONAL	1	TRUE	0	0.581279057523399	1		157	247	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73334756	73334756	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	98	235	1	ENST00000377767.4:c.2704C>T	p.His902Tyr	p.H902Y	ENST00000377767	NM_014953.3	902	Cat/Tat	20/21	0.581279057523399	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.581279057523399	1		236	236	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579348	7579349	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	323	592	0	ENST00000269305.4:c.338_339insA	p.Phe113LeufsTer36	p.F113Lfs*36	ENST00000269305	NM_001126112.2	113	ttc/ttAc	4/11	0.512893171862906	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.581279057523399	1		592	766	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448396	56448396	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0028158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	283	603	0	ENST00000407977.2:c.253-2A>G		p.X85_splice	ENST00000407977		85			0.581279057523399	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.581279057523399	1		603	646	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561352	9561352	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	401	333	0	ENST00000353224.5:c.430G>T	p.Glu144Ter	p.E144*	ENST00000353224	NM_177990.2	144	Gaa/Taa	4/10	0.581279057523399	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.581279057523399	2		333	653	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067239	37067239	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	103	335	0	ENST00000231790.2:c.1150G>T	p.Val384Phe	p.V384F	ENST00000231790	NM_000249.3	384	Gtt/Ttt	12/19	0.305080959005483	2	FACETS	0.515	0.461	0.572	0.258	0.23	0.286	INDETERMINATE	1	TRUE	0	0.581279057523399	2		335	688	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294537	1294537	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	416	428	0	ENST00000310581.5:c.464G>A	p.Arg155His	p.R155H	ENST00000310581	NM_198253.2	155	cGc/cAc	2/16	NA	2	FACETS	0.854	0.819	0.889			1	INDETERMINATE	2	TRUE	NA	0.581279057523399	2		428	838	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0028161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	358	497	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.767452770959806	4	FACETS	0.776	0.737	0.815	0.776	0.737	0.815	SUBCLONAL	2	TRUE	2	0.907186230969169	4		497	970	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0028162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	305	581	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.3	4	FACETS	0.963	0.909	1	0.963	0.909	1	CLONAL	3	TRUE	1	0.27	4		581	993	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0028162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	182	525	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.229163370213567	2	FACETS	0.915	0.846	0.986	0.915	0.846	0.986	CLONAL	2	TRUE	0	0.27	2		525	737	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928906	49928906	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	90	808	0	ENST00000296474.3:c.3460G>C	p.Glu1154Gln	p.E1154Q	ENST00000296474	NM_002447.2	1154	Gag/Cag	16/20	1	2	FACETS	0.718	0.636	0.807	0.718	0.636	0.807	SUBCLONAL	1	TRUE	1	0.27	2		808	928	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402665	20402665	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	37	368	0	ENST00000346618.3:c.202del	p.Thr68ProfsTer12	p.T68Pfs*12	ENST00000346618	NM_001949.4	68	Acc/cc	1/7	0.246269948600665	2	FACETS	0.537	0.442	0.644	0.269	0.221	0.322	SUBCLONAL	1	TRUE	0	0.27	2		368	510	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740766	145740766	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	122	682	0	ENST00000428558.2:c.1334G>C	p.Ser445Thr	p.S445T	ENST00000428558	NM_004260.3	445	aGc/aCc	7/22	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.27	2		682	840	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519912	NA	P-0028163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	170	288	0	ENST00000374080.3:c.3670C>G	p.Leu1224Val	p.L1224V	ENST00000374080		1224	Ctc/Gtc	26/45	1	1	FACETS	1	0.973	1	1	0.994	1	CLONAL	3	TRUE	0	0.204789473894916	1		288	452	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165917	47165917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	32	352	0	ENST00000409792.3:c.209G>A	p.Arg70Gln	p.R70Q	ENST00000409792	NM_014159.6	70	cGa/cAa	3/21	1	2	FACETS	0.503	0.407	0.612	0.503	0.407	0.612	SUBCLONAL	1	TRUE	1	0.204789473894916	2		352	621	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492696	56492697	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0028163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	78	326	0	ENST00000407977.2:c.242_243del	p.Lys81IlefsTer14	p.K81Ifs*14	ENST00000407977		81	aAA/a	2/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.204789473894916	2		326	552	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980577	70980577	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	236	502	0	ENST00000276594.2:c.800G>C	p.Gly267Ala	p.G267A	ENST00000276594	NM_024504.3	267	gGt/gCt	4/8	0.204789473894916	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.204789473894916	3		502	1122	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0028164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	101	497	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.829	0.743	0.92	0.829	0.743	0.92	CLONAL	1	TRUE	1	0.426041495366812	2		497	572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0028164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	260	903	1	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.383585650028469	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.426041495366812	1		904	894	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023141	27023196	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCGGCGGCGGAGCCGGCAGCGGCGGCGGGCCCGGCGCGGAGCCGGACCTGAA	GGCGGCGGCGGCGGAGCCGGCAGCGGCGGCGGGCCCGGCGCGGAGCCGGACCTGAA	-	novel	NA	P-0028164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	90	56	0	ENST00000324856.7:c.248_303del	p.Gly83GlufsTer9	p.G83Efs*9	ENST00000324856	NM_006015.4	83	GGCGGCGGCGGCGGAGCCGGCAGCGGCGGCGGGCCCGGCGCGGAGCCGGACCTGAAg/g	1/20	0.369552996832533	1	FACETS	1	0.956	1	1	0.989	1	CLONAL	2	TRUE	0	0.426041495366812	1		56	156	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434580	49434580	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	162	523	0	ENST00000301067.7:c.6973del	p.Asp2325MetfsTer7	p.D2325Mfs*7	ENST00000301067	NM_003482.3	2325	Gat/at	31/54	1	2	FACETS	0.846	0.776	0.919	0.846	0.776	0.919	CLONAL	1	TRUE	1	0.426041495366812	2		523	899	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954180	32954180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45580035	NA	P-0028164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	177	405	0	ENST00000380152.3:c.9154C>T	p.Arg3052Trp	p.R3052W	ENST00000380152		3052	Cgg/Tgg	24/27	0.426041495366812	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.426041495366812	1		405	584	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252854	36252854	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	75	241	0	ENST00000300305.3:c.508G>C	p.Gly170Arg	p.G170R	ENST00000300305		170	Ggg/Cgg	4/8	0.413596494652447	2	FACETS	0.946	0.835	1	0.473	0.417	0.533	CLONAL	1	TRUE	0	0.426041495366812	2		241	372	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278850	1278850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	197	502	0	ENST00000310581.5:c.2192G>A	p.Ser731Asn	p.S731N	ENST00000310581	NM_198253.2	731	aGc/aAc	6/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.426041495366812	2		502	801	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0028165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	236	600	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.333267834247299	2	FACETS	0.952	0.894	1	0.952	0.894	1	CLONAL	2	TRUE	0	0.397359950387647	2		600	624	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713333	30713333	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	59	367	0	ENST00000295754.5:c.658C>A	p.Leu220Met	p.L220M	ENST00000295754	NM_003242.5	220	Ctg/Atg	4/7	0.333267834247299	2	FACETS	0.717	0.619	0.824	0.359	0.309	0.412	SUBCLONAL	1	TRUE	0	0.397359950387647	2		367	414	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120231	94120231	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	98	216	0	ENST00000369303.4:c.820G>C	p.Asp274His	p.D274H	ENST00000369303	NM_004440.3	274	Gac/Cac	3/17	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.397359950387647	2		216	363	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301837	65301838	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0028167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	59	281	1	ENST00000342505.4:c.3201_3202del	p.Phe1067LeufsTer6	p.F1067Lfs*6	ENST00000342505	NM_002227.2	1067	ttTGga/ttga	23/25	0.337676832050291	1	FACETS	0.938	0.814	1	0.938	0.814	1	CLONAL	1	TRUE	0	0.362709250392196	1		282	284	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870903	12871117	+	frameshift_variant	Frame_Shift_Del	DEL	GACTTGGAGAAGCACTGCAGAGACATGGAAGAGGCGAGCCAGCGCAAGTGGAATTTCGATTTTCAGAATCACAAACCCCTAGAGGGCAAGTACGAGTGGCAAGAGGTGGAGAAGGGCAGCTTGCCCGAGTTCTACTACAGACCCCCGCGGCCCCCCAAAGGTGCCTGCAAGGTGCCGGCGCAGGAGAGCCAGGATGTCAGCGGGAGCCGCCCGGC	GACTTGGAGAAGCACTGCAGAGACATGGAAGAGGCGAGCCAGCGCAAGTGGAATTTCGATTTTCAGAATCACAAACCCCTAGAGGGCAAGTACGAGTGGCAAGAGGTGGAGAAGGGCAGCTTGCCCGAGTTCTACTACAGACCCCCGCGGCCCCCCAAAGGTGCCTGCAAGGTGCCGGCGCAGGAGAGCCAGGATGTCAGCGGGAGCCGCCCGGC	-	novel	NA	P-0028167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	68	239	0	ENST00000228872.4:c.131_345del	p.Asp44GlyfsTer9	p.D44Gfs*9	ENST00000228872	NM_004064.3	44	GACTTGGAGAAGCACTGCAGAGACATGGAAGAGGCGAGCCAGCGCAAGTGGAATTTCGATTTTCAGAATCACAAACCCCTAGAGGGCAAGTACGAGTGGCAAGAGGTGGAGAAGGGCAGCTTGCCCGAGTTCTACTACAGACCCCCGCGGCCCCCCAAAGGTGCCTGCAAGGTGCCGGCGCAGGAGAGCCAGGATGTCAGCGGGAGCCGCCCGGCg/g	1/3	0.36117862351876	4	FACETS	1	0.969	1	0.685	0.599	0.777	CLONAL	1	TRUE	2	0.362709250392196	4		239	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577561	7577561	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	95	432	0	ENST00000269305.4:c.720T>A	p.Ser240Arg	p.S240R	ENST00000269305	NM_001126112.2	240	agT/agA	7/11	0.336551142754185	1	FACETS	0.926	0.829	1	0.926	0.829	1	CLONAL	1	TRUE	0	0.362709250392196	1		432	463	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592115	67592116	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CACTTTTCTTGTCCGGGAGAGCAGTAAACAGGGCTGCTATGCCTGCTCTGTAGTGTGA	novel	NA	P-0028167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	46	245	0	ENST00000274335.5:c.1985+2_1985+3insGACACTTTTCTTGTCCGGGAGAGCAGTAAACAGGGCTGCTATGCCTGCTCTGTAGTGT		p.G644GTFLVRESSKQGCYACSVV*X	ENST00000274335		644	ggc/ggCACTTTTCTTGTCCGGGAGAGCAGTAAACAGGGCTGCTATGCCTGCTCTGTAGTGTGAc	14/15	0.362709250392196	2	FACETS	0.669	0.565	0.784	0.335	0.282	0.392	SUBCLONAL	1	TRUE	0	0.362709250392196	2		245	379	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0028170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	108	497	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.855	0.769	0.946	0.855	0.769	0.946	CLONAL	1	TRUE	1	0.392832864285899	2		497	643	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0028170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	150	795	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.741	0.676	0.809	0.741	0.676	0.809	SUBCLONAL	1	TRUE	1	0.392832864285899	2		801	1031	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0028170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	76	281	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.963	0.849	1	0.963	0.849	1	CLONAL	1	TRUE	1	0.392832864285899	2		281	402	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965666	90965666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	78	306	0	ENST00000265433.3:c.1651del	p.Arg551GlyfsTer8	p.R551Gfs*8	ENST00000265433	NM_002485.4	551	Agg/gg	11/16	1	2	FACETS	0.731	0.644	0.825	0.731	0.644	0.825	SUBCLONAL	1	TRUE	1	0.392832864285899	2		306	543	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907692	111907692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775080943	NA	P-0028170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	108	326	0	ENST00000393256.3:c.466G>A	p.Gly156Arg	p.G156R	ENST00000393256	NM_006538.4	156	Gga/Aga	3/4	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.392832864285899	2		326	535	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	156	579	2	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	1	2	FACETS	0.824	0.754	0.897	0.824	0.754	0.897	CLONAL	1	TRUE	1	0.392832864285899	2		581	964	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0028170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	136	498	1	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	0.844	0.768	0.925	0.844	0.768	0.925	CLONAL	1	TRUE	1	0.392832864285899	2		499	820	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026204	48026204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750440	NA	P-0028170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	96	325	1	ENST00000234420.5:c.1082G>A	p.Arg361His	p.R361H	ENST00000234420	NM_000179.2	361	cGc/cAc	4/10	1	2	FACETS	0.949	0.849	1	0.949	0.849	1	CLONAL	1	TRUE	1	0.392832864285899	2		326	515	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131457	202131459	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0028170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	95	427	0	ENST00000358485.4:c.430_432del	p.Glu144del	p.E144del	ENST00000358485	NM_001080125.1	142	aAGGag/aag	2/9	1	2	FACETS	0.68	0.606	0.76	0.68	0.606	0.76	SUBCLONAL	1	TRUE	1	0.392832864285899	2		427	711	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30946592	30946594	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs752094508	NA	P-0028170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	53	254	4	ENST00000375687.4:c.25_27del	p.Lys9del	p.K9del	ENST00000375687	NM_015338.5	5	cAGAag/cag	1/13	1	2	FACETS	0.733	0.628	0.848	0.733	0.628	0.848	SUBCLONAL	1	TRUE	1	0.392832864285899	2		258	368	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023861	27023861	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1336228861	NA	P-0028170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	87	201	0	ENST00000324856.7:c.971del	p.Gly324AlafsTer39	p.G324Afs*39	ENST00000324856	NM_006015.4	323	Ggg/gg	1/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.392832864285899	2		201	401	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057747	27057747	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	229	625	0	ENST00000324856.7:c.1455C>A	p.Tyr485Ter	p.Y485*	ENST00000324856	NM_006015.4	485	taC/taA	3/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.392832864285899	2		625	1021	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39240630	39240630	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352826	NA	P-0028170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	102	306	0	ENST00000402219.2:c.2138G>A	p.Arg713Gln	p.R713Q	ENST00000402219	NM_005633.3	713	cGa/cAa	13/23	1	2	FACETS	0.892	0.8	0.99	0.892	0.8	0.99	CLONAL	1	TRUE	1	0.392832864285899	2		306	582	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50916690	50916690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	62	462	0	ENST00000440232.2:c.2162C>T	p.Thr721Met	p.T721M	ENST00000440232	NM_002691.3	721	aCg/aTg	18/27	1	2	FACETS	0.402	0.346	0.462	0.402	0.346	0.462	SUBCLONAL	1	TRUE	1	0.392832864285899	2		462	786	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043407	180043407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757396801	NA	P-0028170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	165	547	2	ENST00000261937.6:c.3179G>A	p.Arg1060Gln	p.R1060Q	ENST00000261937	NM_182925.4	1060	cGg/cAg	23/30	1	2	FACETS	0.962	0.884	1	0.962	0.884	1	CLONAL	1	TRUE	1	0.392832864285899	2		549	873	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395615	31395615	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	163	483	4	ENST00000328111.2:c.2468G>A	p.Arg823His	p.R823H	ENST00000328111	NM_006892.3	823	cGt/cAt	23/23	1	2	FACETS	0.95	0.872	1	0.95	0.872	1	CLONAL	1	TRUE	1	0.392832864285899	2		487	874	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434225	49434225	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780776865	NA	P-0028170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	222	665	1	ENST00000301067.7:c.7328G>A	p.Arg2443His	p.R2443H	ENST00000301067	NM_003482.3	2443	cGc/cAc	31/54	1	2	FACETS	0.901	0.837	0.967	0.901	0.837	0.967	CLONAL	1	TRUE	1	0.392832864285899	2		666	1255	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481620	56481620	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	139	533	0	ENST00000267101.3:c.655T>G	p.Phe219Val	p.F219V	ENST00000267101	NM_001982.3	219	Ttt/Gtt	6/28	1	2	FACETS	0.881	0.803	0.964	0.881	0.803	0.964	CLONAL	1	TRUE	1	0.392832864285899	2		533	803	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555739	21555739	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	152	474	0	ENST00000382592.4:c.2531A>G	p.Asp844Gly	p.D844G	ENST00000382592	NM_014572.2	844	gAt/gGt	6/8	1	2	FACETS	0.885	0.81	0.965	0.885	0.81	0.965	CLONAL	1	TRUE	1	0.392832864285899	2		474	874	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	69061265	69061265	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	28	192	0	ENST00000487270.1:c.1100A>G	p.Gln367Arg	p.Q367R	ENST00000487270	NM_133509.3	367	cAg/cGg	11/11	1	2	FACETS	0.393	0.314	0.483	0.393	0.314	0.483	SUBCLONAL	1	TRUE	1	0.392832864285899	2		192	363	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41022106	41022106	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532630164	NA	P-0028170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	174	506	0	ENST00000267868.3:c.830C>T	p.Ala277Val	p.A277V	ENST00000267868	NM_002875.4	277	gCg/gTg	9/10	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.392832864285899	2		506	880	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131668	2131668	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	67	589	0	ENST00000219476.3:c.3683T>C	p.Leu1228Pro	p.L1228P	ENST00000219476	NM_000548.3	1228	cTg/cCg	31/42	1	2	FACETS	0.364	0.316	0.418	0.364	0.316	0.418	SUBCLONAL	1	TRUE	1	0.392832864285899	2		589	936	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974754	15974754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	124	336	0	ENST00000268712.3:c.4121C>T	p.Thr1374Ile	p.T1374I	ENST00000268712	NM_006311.3	1374	aCa/aTa	30/46	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.392832864285899	2		336	627	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46608760	46608760	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	177	542	0	ENST00000263734.3:c.2071G>A	p.Gly691Ser	p.G691S	ENST00000263734	NM_001430.4	691	Ggc/Agc	13/16	1	2	FACETS	0.982	0.905	1	0.982	0.905	1	CLONAL	1	TRUE	1	0.392832864285899	2		542	918	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735359	204735359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553657387	NA	P-0028170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	54	173	0	ENST00000302823.3:c.160G>A	p.Ala54Thr	p.A54T	ENST00000302823	NM_005214.4	54	Gcc/Acc	2/4	1	2	FACETS	0.811	0.696	0.935	0.811	0.696	0.935	CLONAL	1	TRUE	1	0.392832864285899	2		173	339	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715596	30715596	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0028170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	80	205	0	ENST00000295754.5:c.1255-1G>A		p.X419_splice	ENST00000295754	NM_003242.5	419			0.380412055538295	2	FACETS	1	0.934	1	0.539	0.477	0.604	CLONAL	1	TRUE	0	0.392832864285899	2		205	378	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803353	1803353	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769124009	NA	P-0028170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	150	484	1	ENST00000260795.2:c.622C>T	p.His208Tyr	p.H208Y	ENST00000260795		208	Cat/Tat	5/17	1	2	FACETS	0.983	0.899	1	0.983	0.899	1	CLONAL	1	TRUE	1	0.392832864285899	2		485	777	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1941423	1941423	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1189008609	NA	P-0028170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	156	458	0	ENST00000382891.5:c.1799G>A	p.Arg600Gln	p.R600Q	ENST00000382891	NM_133335.3	600	cGa/cAa	9/22	1	2	FACETS	0.949	0.87	1	0.949	0.87	1	CLONAL	1	TRUE	1	0.392832864285899	2		458	837	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136880	55136880	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514549	NA	P-0028170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	113	427	0	ENST00000257290.5:c.1202C>T	p.Ala401Val	p.A401V	ENST00000257290	NM_006206.4	401	gCt/gTt	8/23	1	2	FACETS	0.774	0.697	0.856	0.774	0.697	0.856	SUBCLONAL	1	TRUE	1	0.392832864285899	2		427	743	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84390275	84390275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	111	360	0	ENST00000321945.7:c.506C>T	p.Ala169Val	p.A169V	ENST00000321945	NM_139076.2	169	gCc/gTc	6/9	1	2	FACETS	0.861	0.776	0.952	0.861	0.776	0.952	CLONAL	1	TRUE	1	0.392832864285899	2		360	656	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630906	187630906	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	127	406	1	ENST00000441802.2:c.76C>T	p.Arg26Ter	p.R26*	ENST00000441802	NM_005245.3	26	Cga/Tga	2/27	1	2	FACETS	0.921	0.836	1	0.921	0.836	1	CLONAL	1	TRUE	1	0.392832864285899	2		407	702	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553015	106553015	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	141	467	1	ENST00000369096.4:c.984del	p.Ile329PhefsTer49	p.I329Ffs*49	ENST00000369096	NM_001198.3	327	tCc/tc	5/7	1	2	FACETS	0.919	0.838	1	0.919	0.838	1	CLONAL	1	TRUE	1	0.392832864285899	2		468	781	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576890	7576890	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	627	598	0	ENST00000269305.4:c.956del	p.Lys319ArgfsTer26	p.K319Rfs*26	ENST00000269305	NM_001126112.2	319	aAg/ag	9/11	0.791207532581351	2	FACETS	0.975	0.952	0.997	0.975	0.952	0.997	CLONAL	2	TRUE	0	0.791207532581351	2		598	813	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-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	170	272	0	ENST00000267163.4:c.2490-6_2500del		p.X830_splice	ENST00000267163	NM_000321.2	830		24/27	0.791207532581351	2	FACETS	0.849	0.804	0.893	0.849	0.804	0.893	CLONAL	2	TRUE	0	0.791207532581351	2		272	253	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89865607	89865607	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	292	477	0	ENST00000389301.3:c.860A>G	p.Glu287Gly	p.E287G	ENST00000389301	NM_000135.2	287	gAg/gGg	10/43	0.791207532581351	2	FACETS	1	0.973	1	0.521	0.493	0.549	CLONAL	1	TRUE	0	0.791207532581351	2		477	708	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871916	45871916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	316	625	0	ENST00000391945.4:c.332C>T	p.Ser111Phe	p.S111F	ENST00000391945	NM_000400.3	111	tCc/tTc	5/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.791207532581351	2		625	775	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026066	48026066	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs63750491	NA	P-0028171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	204	414	0	ENST00000234420.5:c.944C>G	p.Ser315Cys	p.S315C	ENST00000234420	NM_000179.2	315	tCt/tGt	4/10	0.791207532581351	2	FACETS	1	0.959	1	0.516	0.483	0.549	CLONAL	1	TRUE	0	0.791207532581351	2		414	500	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12393170	12393170	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	444	471	0	ENST00000287820.6:c.79C>T	p.Gln27Ter	p.Q27*	ENST00000287820	NM_015869.4	27	Caa/Taa	1/7	0.791207532581351	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.791207532581351	2		471	552	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643764	52643764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	237	607	0	ENST00000394830.3:c.2132G>A	p.Ser711Asn	p.S711N	ENST00000394830	NM_018313.4	711	aGt/aAt	17/30	0.791207532581351	2	FACETS	0.894	0.839	0.95	0.447	0.419	0.475	CLONAL	1	TRUE	0	0.791207532581351	2		607	670	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629397	187629397	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	323	581	0	ENST00000441802.2:c.1585C>A	p.Leu529Met	p.L529M	ENST00000441802	NM_005245.3	529	Ctg/Atg	2/27	1	2	FACETS	0.892	0.845	0.94	0.892	0.845	0.94	CLONAL	1	TRUE	1	0.791207532581351	2		581	915	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727455	66727455	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs869025608	NA	P-0028173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	135	338	0	ENST00000307102.5:c.171G>T	p.Lys57Asn	p.K57N	ENST00000307102	NM_002755.3	57	aaG/aaT	2/11	1	2	FACETS	0.933	0.856	1	0.933	0.856	1	CLONAL	1	TRUE	1	0.666556954146411	2		338	434	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298716	46298716	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0028173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	92	238	0	ENST00000334344.6:c.5364-1G>T		p.X1788_splice	ENST00000334344	NM_152641.2	1788			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.666556954146411	2		238	248	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220641	1220642	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0028173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	232	596	0	ENST00000326873.7:c.659_660del	p.Gln220ProfsTer45	p.Q220Pfs*45	ENST00000326873	NM_000455.4	220	cAG/c	5/10	0.666556954146411	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.666556954146411	1		596	450	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602815	10602824	+	frameshift_variant	Frame_Shift_Del	DEL	ACTTGACCCA	ACTTGACCCA	-	novel	NA	P-0028173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	249	622	0	ENST00000171111.5:c.754_763del	p.Trp252ThrfsTer22	p.W252Tfs*22	ENST00000171111	NM_203500.1	252	TGGGTCAAGTac/ac	3/6	0.666556954146411	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.666556954146411	1		622	464	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714594	52714594	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	322	464	0	ENST00000322088.6:c.352G>T	p.Glu118Ter	p.E118*	ENST00000322088	NM_014225.5	118	Gag/Tag	4/15	0.601639060102139	3	FACETS	0.927	0.882	0.972	0.927	0.882	0.972	CLONAL	2	TRUE	1	0.666556954146411	3		464	695	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0028174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	460	534	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			NA	2	FACETS	1	0.985	1			1	INDETERMINATE	2	TRUE	NA	0.755459766727865	2		534	597	SUCCESS
APC	324	MSKCC	GRCh37	5	112174583	112174584	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs1064794228	NA	P-0028174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	179	424	0	ENST00000257430.4:c.3295_3296del	p.Val1099PhefsTer19	p.V1099Ffs*19	ENST00000257430	NM_000038.5	1098	TGt/t	16/16	0.755459766727865	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.755459766727865	1		424	278	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041121	180041121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770869636	NA	P-0028174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	753	868	0	ENST00000261937.6:c.3278C>T	p.Thr1093Met	p.T1093M	ENST00000261937	NM_182925.4	1093	aCg/aTg	24/30	0.755459766727865	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.755459766727865	2		868	979	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182881	123182881	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	154	188	0	ENST00000218089.9:c.846A>C	p.Glu282Asp	p.E282D	ENST00000218089	NM_001042749.1	282	gaA/gaC	10/35	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.755459766727865	1		188	204	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0028175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	91	487	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.2	2		487	907	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446160	49446160	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776768333	NA	P-0028175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	89	549	0	ENST00000301067.7:c.1306G>A	p.Glu436Lys	p.E436K	ENST00000301067	NM_003482.3	436	Gag/Aag	10/54	1	2	FACETS	0.989	0.875	1	0.989	0.875	1	CLONAL	1	TRUE	1	0.2	2		549	900	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578419	+	frameshift_variant	Frame_Shift_Del	DEL	CCTC	CCTC	-	novel	NA	P-0028175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	60	546	0	ENST00000269305.4:c.511_514del	p.Glu171LeufsTer2	p.E171Lfs*2	ENST00000269305	NM_001126112.2	171	GAGGtt/tt	5/11	0.3	2	FACETS	0.729	0.627	0.841			1	SUBCLONAL	1	TRUE	NA	0.2	2		546	823	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0028175-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	395	487	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.314852583538114	5	FACETS	0.951	0.906	0.997	0.951	0.906	0.997	CLONAL	3	TRUE	2	0.3928071527011	5		487	1120	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446160	49446160	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776768333	NA	P-0028175-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	378	549	0	ENST00000301067.7:c.1306G>A	p.Glu436Lys	p.E436K	ENST00000301067	NM_003482.3	436	Gag/Aag	10/54	0.3928071527011	4	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.3928071527011	4		549	1086	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578419	+	frameshift_variant	Frame_Shift_Del	DEL	CCTC	CCTC	-	novel	NA	P-0028175-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	252	546	0	ENST00000269305.4:c.511_514del	p.Glu171LeufsTer2	p.E171Lfs*2	ENST00000269305	NM_001126112.2	171	GAGGtt/tt	5/11	0.252568087822099	2	FACETS	0.918	0.863	0.973	0.918	0.863	0.973	CLONAL	2	TRUE	0	0.3928071527011	2		546	699	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458746	120458746	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028175-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	37	428	0	ENST00000256646.2:c.6599C>G	p.Ser2200Cys	p.S2200C	ENST00000256646	NM_024408.3	2200	tCt/tGt	34/34	0.349105602760345	3	FACETS	0.31	0.255	0.372	0.155	0.127	0.186	SUBCLONAL	1	TRUE	1	0.3928071527011	3		428	727	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322430	31322430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs956809791	NA	P-0028175-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	42	343	0	ENST00000412585.2:c.1025G>A	p.Gly342Glu	p.G342E	ENST00000412585	NM_005514.6	342	gGg/gAg	6/8	0.109506591895624	3	FACETS	0.374	0.311	0.444	0.187	0.155	0.222	INDETERMINATE	1	TRUE	1	0.3928071527011	3		343	684	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965527	15965527	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028175-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	20	231	0	ENST00000268712.3:c.5279C>A	p.Ser1760Ter	p.S1760*	ENST00000268712	NM_006311.3	1760	tCa/tAa	36/46	0.252568087822099	2	FACETS	0.283	0.216	0.362	0.141	0.108	0.181	SUBCLONAL	1	TRUE	0	0.3928071527011	2		231	360	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965581	15965581	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746171790	NA	P-0028175-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	13	144	0	ENST00000268712.3:c.5225C>T	p.Ser1742Leu	p.S1742L	ENST00000268712	NM_006311.3	1742	tCa/tTa	36/46	0.252568087822099	2	FACETS	0.321	0.229	0.433	0.161	0.114	0.217	SUBCLONAL	1	TRUE	0	0.3928071527011	2		144	206	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238950	5238950	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028175-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	32	343	0	ENST00000357368.4:c.1829G>T	p.Arg610Leu	p.R610L	ENST00000357368	NM_002850.3	610	cGg/cTg	13/38	0.106099050147661	5	FACETS	0.474	0.384	0.577	0.119	0.096	0.145	INDETERMINATE	1	TRUE	1	0.3928071527011	5		343	546	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43745379	43745379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334033917	NA	P-0028175-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	62	510	0	ENST00000523873.1:c.292G>A	p.Glu98Lys	p.E98K	ENST00000523873		98	Gag/Aag	3/8	0.109506591895624	3	FACETS	0.467	0.403	0.538	0.234	0.201	0.269	INDETERMINATE	1	TRUE	1	0.3928071527011	3		510	808	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93953260	93953260	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0028175-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	55	368	0	ENST00000369303.4:c.2883-2A>T		p.X961_splice	ENST00000369303	NM_004440.3	961			0.244065154812141	1	FACETS	0.434	0.372	0.503	0.434	0.372	0.503	SUBCLONAL	1	TRUE	0	0.3928071527011	1		368	518	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776376	76776376	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028175-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	40	349	0	ENST00000373344.5:c.7090C>G	p.Leu2364Val	p.L2364V	ENST00000373344	NM_000489.3	2364	Ctc/Gtc	34/35	0.238649679344605	3	FACETS	0.385	0.319	0.459	0.192	0.159	0.23	SUBCLONAL	1	TRUE	1	0.3928071527011	3		349	633	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938647	76938647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs533271695	NA	P-0028175-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	76	481	0	ENST00000373344.5:c.2101C>T	p.Arg701Cys	p.R701C	ENST00000373344	NM_000489.3	701	Cgt/Tgt	9/35	0.238649679344605	3	FACETS	0.593	0.519	0.672	0.296	0.259	0.336	SUBCLONAL	1	TRUE	1	0.3928071527011	3		481	781	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030378	49030378	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs267603840	NA	P-0028176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	346	395	0	ENST00000267163.4:c.1853C>A	p.Ser618Ter	p.S618*	ENST00000267163	NM_000321.2	618	tCa/tAa	19/27	0.555575541899288	3	FACETS	0.935	0.897	0.972	0.935	0.897	0.972	CLONAL	3	TRUE	0	0.558940219309917	3		395	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578610	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGGGGGTGTGGAATCAACCCACAGCTGCACAGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAA	CGGGGGTGTGGAATCAACCCACAGCTGCACAGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAA	-	novel	NA	P-0028176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	264	682	0	ENST00000269305.4:c.376-56_456del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	0.558940219309917	2	FACETS	1	0.993	1	0.719	0.678	0.76	CLONAL	1	TRUE	0	0.558940219309917	2		682	657	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054727	13054727	+	stop_lost	Nonstop_Mutation	SNP	G	G	T	novel	NA	P-0028176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	200	313	0	ENST00000316448.5:c.1254G>T	p.Ter418TyrextTer9	p.*418Yext*9	ENST00000316448	NM_004343.3	418	taG/taT	9/9	0.558940219309917	2	FACETS	0.944	0.89	0.998	0.944	0.89	0.998	CLONAL	2	TRUE	0	0.558940219309917	2		313	379	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090775	5090775	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1253373055	NA	P-0028176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	93	321	0	ENST00000381652.3:c.2923A>G	p.Arg975Gly	p.R975G	ENST00000381652	NM_004972.3	975	Agg/Ggg	22/25	1	2	FACETS	0.982	0.881	1	0.982	0.881	1	CLONAL	1	TRUE	1	0.558940219309917	2		321	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0028177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	46	789	1	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	1	2	FACETS	0.491	0.412	0.579	0.491	0.412	0.579	SUBCLONAL	1	TRUE	1	0.236545694631574	2		790	792	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0028177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	93	738	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.11800358383526	5	FACETS	0.797	0.709	0.891	0.399	0.354	0.446	INDETERMINATE	2	TRUE	1	0.236545694631574	5		738	668	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0028196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	619	581	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.185457981941509	8	FACETS	1	0.99	1			1	CLONAL	7	TRUE	NA	0.185457981941509	8		581	1392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578400	7578400	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs751477326	NA	P-0028196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	71	563	0	ENST00000269305.4:c.530C>G	p.Pro177Arg	p.P177R	ENST00000269305	NM_001126112.2	177	cCc/cGc	5/11	0.139953360709625	3	FACETS	0.98	0.853	1	0.49	0.426	0.559	CLONAL	1	TRUE	1	0.185457981941509	3		563	854	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430042	78430042	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0028196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	39	232	0	ENST00000370768.2:c.838-1G>T		p.X280_splice	ENST00000370768	NM_003902.3	280			1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.185457981941509	2		232	378	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285871	46285871	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	69	461	0	ENST00000334344.6:c.5140del	p.Ser1714LeufsTer7	p.S1714Lfs*7	ENST00000334344	NM_152641.2	1713	tcT/tc	18/21	1	2	FACETS	0.996	0.867	1	0.996	0.867	1	CLONAL	1	TRUE	1	0.185457981941509	2		461	747	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355315	81355315	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	43	283	0	ENST00000222390.5:c.1059C>A	p.Tyr353Ter	p.Y353*	ENST00000222390	NM_000601.4	353	taC/taA	9/18	0.185457981941509	3	FACETS	1	0.91	1	0.567	0.474	0.669	CLONAL	1	TRUE	1	0.185457981941509	3		283	447	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349625	70349625	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	52	605	1	ENST00000374080.3:c.3787C>A	p.Gln1263Lys	p.Q1263K	ENST00000374080		1263	Cag/Aag	27/45	1	2	FACETS	0.624	0.529	0.728	0.624	0.529	0.728	SUBCLONAL	1	TRUE	1	0.185457981941509	2		606	899	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0028198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	49	497	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.969	0.821	1	0.969	0.821	1	CLONAL	1	FALSE	1	0.186914922982761	2		497	541	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0028198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	57	277	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	1	0.186914922982761	2		277	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0028199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	814	837	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.724473605484355	4	FACETS	0.987	0.971	1	1	0.999	1	CLONAL	4	TRUE	2	0.771534943454758	4		837	947	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022766	31022766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs6058693	NA	P-0028199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	80	476	0	ENST00000375687.4:c.2251G>A	p.Val751Ile	p.V751I	ENST00000375687	NM_015338.5	751	Gtt/Att	13/13	0.675866557419132	6	FACETS	0.654	0.575	0.74	0.164	0.143	0.185	SUBCLONAL	1	TRUE	2	0.771534943454758	6		476	806	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544092	18544093	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0028199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	220	364	1	ENST00000266497.5:c.1909_1910delinsAA	p.Pro637Asn	p.P637N	ENST00000266497		637	CCt/AAt	13/31	0.752224706019262	3	FACETS	0.937	0.901	0.972	0.937	0.901	0.972	CLONAL	3	TRUE	0	0.771534943454758	3		365	281	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165818	47165818	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	378	389	0	ENST00000409792.3:c.308del	p.Pro103LeufsTer8	p.P103Lfs*8	ENST00000409792	NM_014159.6	103	cCt/ct	3/21	0.76521502701733	3	FACETS	0.949	0.922	0.975	0.949	0.922	0.975	CLONAL	3	TRUE	0	0.771534943454758	3		389	477	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935078	49935078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	96	705	0	ENST00000296474.3:c.1921G>A	p.Glu641Lys	p.E641K	ENST00000296474	NM_002447.2	641	Gaa/Aaa	6/20	0.76521502701733	3	FACETS	0.567	0.506	0.632	0.189	0.168	0.211	SUBCLONAL	1	TRUE	0	0.771534943454758	3		705	608	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71019957	71019957	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0028199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	125	121	0	ENST00000318789.4:c.1653-1G>T		p.X551_splice	ENST00000318789	NM_032682.5	551			0.76521502701733	3	FACETS	0.991	0.945	1	0.991	0.945	1	CLONAL	3	TRUE	0	0.771534943454758	3		121	151	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	231043	231043	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	148	651	0	ENST00000264932.6:c.823G>T	p.Asp275Tyr	p.D275Y	ENST00000264932	NM_004168.2	275	Gac/Tac	7/15	0.64137583828053	5	FACETS	1	0.937	1	0.344	0.314	0.375	CLONAL	1	TRUE	2	0.771534943454758	5		651	803	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165820	47165820	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	24	386	0	ENST00000409792.3:c.306C>A	p.Asn102Lys	p.N102K	ENST00000409792	NM_014159.6	102	aaC/aaA	3/21	0.76521502701733	3	FACETS	0.181	0.141	0.227	0.06	0.047	0.076	SUBCLONAL	1	TRUE	0	0.771534943454758	3		386	476	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033825	49033825	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	G	G	TT	novel	NA	P-0028199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	266	313	0	ENST00000267163.4:c.1962delinsTT	p.Tyr655LeufsTer13	p.Y655Lfs*13	ENST00000267163	NM_000321.2	654	gtG/gtTT	20/27	0.771534943454758	4	FACETS	0.937	0.906	0.965	0.937	0.906	0.965	CLONAL	4	TRUE	0	0.771534943454758	4		313	326	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0028200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	773	600	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	NA	2	FACETS	0.953	0.934	0.97			1	INDETERMINATE	2	TRUE	NA	0.85497618627838	2		606	949	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0028200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	535	795	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.898	0.862	0.935	0.898	0.862	0.935	CLONAL	1	TRUE	1	0.85497618627838	2		801	1393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0028200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	511	581	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.85497618627838	2		583	1145	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0028200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	298	412	3	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.842	0.796	0.889	0.842	0.796	0.889	CLONAL	1	TRUE	1	0.85497618627838	2		415	828	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0028200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	212	351	2	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	1	2	FACETS	0.838	0.783	0.893	0.838	0.783	0.893	CLONAL	1	TRUE	1	0.85497618627838	2		353	592	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0028200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	232	301	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.85497618627838	2		301	539	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959898	38959898	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	216	312	0	ENST00000357387.3:c.2034del	p.Lys678AsnfsTer14	p.K678Nfs*14	ENST00000357387	NM_152756.3	678	aaA/aa	21/38	1	2	FACETS	0.959	0.9	1	0.959	0.9	1	CLONAL	1	TRUE	1	0.85497618627838	2		312	527	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0028200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	452	651	3	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.962	0.921	1	0.962	0.921	1	CLONAL	1	TRUE	1	0.85497618627838	2		654	1099	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510805	157510806	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1289067120	NA	P-0028200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	379	525	0	ENST00000346085.5:c.3586dup	p.Gln1196ProfsTer14	p.Q1196Pfs*14	ENST00000346085	NM_020732.3	1194	acc/aCcc	14/20	1	2	FACETS	0.924	0.88	0.968	0.924	0.88	0.968	CLONAL	1	TRUE	1	0.85497618627838	2		525	960	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519966	NA	P-0028200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	763	512	0	ENST00000347630.2:c.397T>A	p.Phe133Ile	p.F133I	ENST00000347630	NM_001007230.1	133	Ttc/Atc	6/11	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	2	TRUE	NA	0.85497618627838	2		512	892	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578202	7578202	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520004	NA	P-0028200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	554	692	0	ENST00000269305.4:c.647T>G	p.Val216Gly	p.V216G	ENST00000269305	NM_001126112.2	216	gTg/gGg	6/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.85497618627838	2		692	1274	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600609	43600609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777221273	NA	P-0028200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	389	572	3	ENST00000355710.3:c.835G>A	p.Ala279Thr	p.A279T	ENST00000355710	NM_020975.4	279	Gcc/Acc	4/20	1	2	FACETS	0.993	0.948	1	0.993	0.948	1	CLONAL	1	TRUE	1	0.85497618627838	2		575	916	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0028200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	416	546	4	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.903	0.862	0.944	0.903	0.862	0.944	CLONAL	1	TRUE	1	0.85497618627838	2		550	1078	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427974	49427974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	450	587	0	ENST00000301067.7:c.10616G>A	p.Arg3539Gln	p.R3539Q	ENST00000301067	NM_003482.3	3539	cGg/cAg	38/54	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.85497618627838	2		587	988	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213358	36213359	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0028200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	451	840	1	ENST00000222270.7:c.2561_2562del	p.Glu854AlafsTer34	p.E854Afs*34	ENST00000222270	NM_014727.1	852	aAG/a	4/37	1	2	FACETS	0.78	0.745	0.816	0.78	0.745	0.816	SUBCLONAL	1	TRUE	1	0.85497618627838	2		841	1352	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614463	38614463	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	294	425	1	ENST00000299084.4:c.234del	p.Asp79ThrfsTer42	p.D79Tfs*42	ENST00000299084	NM_152594.2	77	Aaa/aa	3/7	1	2	FACETS	0.94	0.889	0.99	0.94	0.889	0.99	CLONAL	1	TRUE	1	0.85497618627838	2		426	732	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023003	27023007	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGA	GGCGA	-	novel	NA	P-0028200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	23	35	0	ENST00000324856.7:c.113_117del	p.Glu38GlyfsTer71	p.E38Gfs*71	ENST00000324856	NM_006015.4	37	GGCGAg/g	1/20	1	2	FACETS	0.803	0.649	0.968	0.803	0.649	0.968	CLONAL	1	TRUE	1	0.85497618627838	2		35	67	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106727	27106727	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	400	525	0	ENST00000324856.7:c.6341del	p.Pro2114ArgfsTer21	p.P2114Rfs*21	ENST00000324856	NM_006015.4	2113	tCc/tc	20/20	1	2	FACETS	0.964	0.92	1	0.964	0.92	1	CLONAL	1	TRUE	1	0.85497618627838	2		525	971	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720789	89720789	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1455551840	NA	P-0028200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	18	217	0	ENST00000371953.3:c.940G>T	p.Glu314Ter	p.E314*	ENST00000371953	NM_000314.4	314	Gaa/Taa	8/9	0.85497618627838	2	FACETS	0.561	0.433	0.705	0.281	0.216	0.353	SUBCLONAL	1	TRUE	0	0.85497618627838	2		217	75	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948755	71948755	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1565399032	NA	P-0028200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	509	712	2	ENST00000298229.2:c.3470del	p.Gly1157AspfsTer45	p.G1157Dfs*45	ENST00000298229	NM_001567.3	1156	cGg/cg	26/28	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.85497618627838	2		714	1118	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374279	118374279	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	335	476	0	ENST00000534358.1:c.7674del	p.Thr2559GlnfsTer43	p.T2559Qfs*43	ENST00000534358	NM_005933.3	2558	Ccc/cc	27/36	1	2	FACETS	0.992	0.943	1	0.992	0.943	1	CLONAL	1	TRUE	1	0.85497618627838	2		476	790	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416586	49416586	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555184893	NA	P-0028200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	374	445	0	ENST00000301067.7:c.16125del	p.Tyr5376ThrfsTer42	p.Y5376Tfs*42	ENST00000301067	NM_003482.3	5375	ccC/cc	51/54	1	2	FACETS	0.995	0.949	1	0.995	0.949	1	CLONAL	1	TRUE	1	0.85497618627838	2		445	879	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633500	3633500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199969428	NA	P-0028200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	463	712	2	ENST00000294008.3:c.4751G>A	p.Arg1584His	p.R1584H	ENST00000294008	NM_032444.2	1584	cGc/cAc	14/15	1	2	FACETS	0.948	0.907	0.988	0.948	0.907	0.988	CLONAL	1	TRUE	1	0.85497618627838	2		714	1143	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162659	47162659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752223546	NA	P-0028200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	282	339	2	ENST00000409792.3:c.3467G>A	p.Arg1156His	p.R1156H	ENST00000409792	NM_014159.6	1156	cGc/cAc	3/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.85497618627838	2		341	639	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948737	55948737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150847930	NA	P-0028200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	396	558	1	ENST00000263923.4:c.3728C>T	p.Pro1243Leu	p.P1243L	ENST00000263923	NM_002253.2	1243	cCg/cTg	28/30	1	2	FACETS	0.898	0.857	0.941	0.898	0.857	0.941	CLONAL	1	TRUE	1	0.85497618627838	2		559	1031	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043387	180043387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760757893	NA	P-0028200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	411	593	1	ENST00000261937.6:c.3199G>A	p.Asp1067Asn	p.D1067N	ENST00000261937	NM_182925.4	1067	Gac/Aac	23/30	1	2	FACETS	0.935	0.893	0.978	0.935	0.893	0.978	CLONAL	1	TRUE	1	0.85497618627838	2		594	1028	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053171	180053171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369939230	NA	P-0028200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	481	733	1	ENST00000261937.6:c.1198G>A	p.Ala400Thr	p.A400T	ENST00000261937	NM_182925.4	400	Gcc/Acc	9/30	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.85497618627838	2		734	1110	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099907	157099907	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	411	647	0	ENST00000346085.5:c.844C>A	p.Pro282Thr	p.P282T	ENST00000346085	NM_020732.3	282	Ccc/Acc	1/20	1	2	FACETS	0.98	0.936	1	0.98	0.936	1	CLONAL	1	TRUE	1	0.85497618627838	2		647	981	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845504	151845504	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	455	578	2	ENST00000262189.6:c.13508G>A	p.Cys4503Tyr	p.C4503Y	ENST00000262189	NM_170606.2	4503	tGc/tAc	52/59	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.85497618627838	2		580	1036	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864629	56864629	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	522	677	0	ENST00000519728.1:c.592C>T	p.Arg198Ter	p.R198*	ENST00000519728	NM_002350.3	198	Cga/Tga	7/13	0.85497618627838	3	FACETS	1	0.975	1	0.513	0.49	0.535	CLONAL	1	TRUE	1	0.85497618627838	3		677	1700	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045659	47045659	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	430	621	1	ENST00000377604.3:c.2540A>T	p.Asp847Val	p.D847V	ENST00000377604	NM_001204468.1	847	gAc/gTc	23/24	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.85497618627838	2		622	982	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224475	123224475	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	458	654	1	ENST00000218089.9:c.3328C>A	p.Leu1110Met	p.L1110M	ENST00000218089	NM_001042749.1	1110	Ctg/Atg	31/35	1	2	FACETS	0.956	0.915	0.997	0.956	0.915	0.997	CLONAL	1	TRUE	1	0.85497618627838	2		655	1121	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0028201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	226	518	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.396142338396103	6	FACETS	1	0.97	1	1	0.97	1	CLONAL	5	TRUE	1	0.396142338396103	6		518	396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1567548223	NA	P-0028201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	188	521	2	ENST00000269305.4:c.797del	p.Gly266AspfsTer79	p.G266Dfs*79	ENST00000269305	NM_001126112.2	266	gGa/ga	8/11	0.396528040084021	2	FACETS	0.831	0.773	0.891	0.831	0.773	0.891	CLONAL	2	TRUE	0	0.396142338396103	2		523	571	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971304	13971304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	213	369	0	ENST00000405192.2:c.625C>T	p.Pro209Ser	p.P209S	ENST00000405192	NM_001163147.1	209	Cct/Tct	8/12	0.329450816405721	4	FACETS	0.927	0.869	0.986	0.927	0.869	0.986	CLONAL	3	TRUE	1	0.396142338396103	4		369	540	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0028203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	145	433	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.469	0.429	0.511	0.469	0.429	0.511	SUBCLONAL	1	TRUE	1	0.920953843315744	2		433	671	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0028203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	128	298	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.451	0.41	0.494	0.451	0.41	0.494	SUBCLONAL	1	TRUE	1	0.920953843315744	2		298	616	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206585	108206585	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	126	357	0	ENST00000278616.4:c.8165del	p.Leu2722ArgfsTer29	p.L2722Rfs*29	ENST00000278616	NM_000051.3	2722	cTg/cg	56/63	NA	2	FACETS	0.594	0.541	0.648			1	INDETERMINATE	1	TRUE	NA	0.920953843315744	2		357	461	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665027	138665027	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	50	135	0	ENST00000330315.3:c.538G>C	p.Gly180Arg	p.G180R	ENST00000330315	NM_023067.3	180	Ggc/Cgc	1/1	1	2	FACETS	0.56	0.482	0.643	0.56	0.482	0.643	SUBCLONAL	1	TRUE	1	0.920953843315744	2		135	194	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55569972	55569972	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs386833402	NA	P-0028203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	128	380	0	ENST00000288135.5:c.839C>T	p.Ala280Val	p.A280V	ENST00000288135	NM_000222.2	280	gCg/gTg	5/21	1	2	FACETS	0.525	0.478	0.575	0.525	0.478	0.575	SUBCLONAL	1	TRUE	1	0.920953843315744	2		380	529	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259045	153259046	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0028203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	66	250	0	ENST00000281708.4:c.769_770del	p.Ile257Ter	p.I257*	ENST00000281708	NM_033632.3	257	ATt/t	5/12	1	2	FACETS	0.415	0.363	0.472	0.415	0.363	0.472	SUBCLONAL	1	TRUE	1	0.920953843315744	2		250	345	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100117	157100119	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs797045268	NA	P-0028204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	10	42	0	ENST00000346085.5:c.1069_1071del	p.Gly357del	p.G357del	ENST00000346085	NM_020732.3	352	GGC/-	1/20	1	2	FACETS	0.938	0.643	1	0.938	0.643	1	CLONAL	1	TRUE	1	0.26	2		42	82	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149893	202149893	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0028204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	40	418	0	ENST00000358485.4:c.1334C>G	p.Ser445Ter	p.S445*	ENST00000358485	NM_001080125.1	445	tCa/tGa	8/9	1	2	FACETS	0.4	0.331	0.477	0.4	0.331	0.477	SUBCLONAL	1	TRUE	1	0.26	2		418	769	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044713	47044713	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	77	335	0	ENST00000377604.3:c.2113G>T	p.Glu705Ter	p.E705*	ENST00000377604	NM_001204468.1	705	Gag/Tag	19/24	1	1	FACETS	0.845	0.742	0.955	0.845	0.742	0.955	CLONAL	1	TRUE	0	0.26	1		335	610	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411879	116411900	+	splice_region_variant,intron_variant	Splice_Region	DEL	CTCTTTCTTTCTCTCTGTTTTA	CTCTTTCTTTCTCTCTGTTTTA	-	novel	NA	P-0028204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	244	833	0	ENST00000397752.3:c.2888-24_2888-3del		p.X963_splice	ENST00000397752	NM_000245.2	963			0.3	3	FACETS	1	0.992	1	0.742	0.691	0.794	CLONAL	1	TRUE	1	0.26	3		833	1430	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204512035	204512035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879018393	NA	P-0028204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	31	323	0	ENST00000367182.3:c.635C>T	p.Pro212Leu	p.P212L	ENST00000367182	NM_001278516.1	212	cCt/cTt	8/11	1	2	FACETS	0.439	0.354	0.536	0.439	0.354	0.536	SUBCLONAL	1	TRUE	1	0.26	2		323	543	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557390	29557390	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	27	176	0	ENST00000356175.3:c.3103A>T	p.Met1035Leu	p.M1035L	ENST00000356175	NM_000267.3	1035	Atg/Ttg	23/57	1	2	FACETS	0.592	0.471	0.73	0.592	0.471	0.73	SUBCLONAL	1	TRUE	1	0.26	2		176	351	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0028205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	187	250	0				ENST00000310581	NM_198253.2	-/1132			0.628369706258698	3	FACETS	1	0.974	1			1	CLONAL	1	TRUE	NA	0.895094027115563	3		250	552	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0028205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	268	648	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	0.895094027115563	2		648	558	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188397	142188397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1169255490	NA	P-0028205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	127	331	2	ENST00000350721.4:c.6334C>T	p.Arg2112Cys	p.R2112C	ENST00000350721	NM_001184.3	2112	Cgt/Tgt	38/47	1	2	FACETS	0.91	0.837	0.984	0.91	0.837	0.984	CLONAL	1	TRUE	1	0.895094027115563	2		333	312	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259262	89259262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770780950	NA	P-0028205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	155	317	0	ENST00000336596.2:c.406C>T	p.Arg136Ter	p.R136*	ENST00000336596	NM_005233.5	136	Cga/Tga	3/17	1	2	FACETS	0.962	0.893	1	0.962	0.893	1	CLONAL	1	TRUE	1	0.895094027115563	2		317	360	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	165	427	0	ENST00000304494.5:c.143C>T	p.Pro48Leu	p.P48L	ENST00000304494	NM_000077.4	48	cCg/cTg	1/3	0.895094027115563	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.895094027115563	1		427	201	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220485	1220485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	579	767	0	ENST00000326873.7:c.578C>T	p.Ser193Phe	p.S193F	ENST00000326873	NM_000455.4	193	tCc/tTc	4/10	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.895094027115563	2		767	635	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392050	81392050	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	165	287	0	ENST00000222390.5:c.227G>A	p.Arg76Lys	p.R76K	ENST00000222390	NM_000601.4	76	aGg/aAg	2/18	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.895094027115563	2		287	345	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414251	32414251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121907910	NA	P-0028205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	200	463	2	ENST00000332351.3:c.1300C>T	p.Arg434Cys	p.R434C	ENST00000332351	NM_024426.4	434	Cgt/Tgt	8/10	1	2	FACETS	0.967	0.906	1	0.967	0.906	1	CLONAL	1	TRUE	1	0.895094027115563	2		465	462	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141561	11141561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	232	608	0	ENST00000358026.2:c.3538C>T	p.Pro1180Ser	p.P1180S	ENST00000358026	NM_001128849.1	1180	Cct/Tct	25/36	1	2	FACETS	0.951	0.895	1	0.951	0.895	1	CLONAL	1	TRUE	1	0.895094027115563	2		608	545	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681507	117681507	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	137	284	0	ENST00000368508.3:c.3443C>T	p.Ser1148Leu	p.S1148L	ENST00000368508	NM_002944.2	1148	tCa/tTa	22/43	NA	2	FACETS	0.969	0.895	1			1	INDETERMINATE	1	TRUE	NA	0.895094027115563	2		284	316	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858687	9858687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	159	378	0	ENST00000330684.3:c.2714C>T	p.Ser905Phe	p.S905F	ENST00000330684	NM_001134407.1	905	tCc/tTc	13/13	1	2	FACETS	0.979	0.91	1	0.979	0.91	1	CLONAL	1	TRUE	1	0.895094027115563	2		378	363	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409108	4409108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	203	467	0	ENST00000261254.3:c.803G>A	p.Gly268Glu	p.G268E	ENST00000261254	NM_001759.3	268	gGa/gAa	5/5	1	2	FACETS	0.965	0.905	1	0.965	0.905	1	CLONAL	1	TRUE	1	0.895094027115563	2		467	470	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222961	36222961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	591	817	3	ENST00000222270.7:c.5590C>T	p.Arg1864Ter	p.R1864*	ENST00000222270	NM_014727.1	1864	Cga/Tga	27/37	0.768153431250755	3	FACETS	0.966	0.936	0.996			1	CLONAL	2	TRUE	NA	0.895094027115563	3		820	989	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057767	180057767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	170	405	1	ENST00000261937.6:c.188G>A	p.Gly63Glu	p.G63E	ENST00000261937	NM_182925.4	63	gGa/gAa	3/30	0.895094027115563	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.895094027115563	1		406	200	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852154	63852154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	174	481	0	ENST00000279873.7:c.2932C>T	p.Pro978Ser	p.P978S	ENST00000279873	NM_032199.2	978	Cct/Tct	10/10	1	2	FACETS	0.882	0.82	0.944	0.882	0.82	0.944	CLONAL	1	TRUE	1	0.895094027115563	2		481	441	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588252	69588252	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1638	122	307	0	ENST00000168712.1:c.446C>T	p.Pro149Leu	p.P149L	ENST00000168712	NM_002007.2	149	cCc/cTc	3/3	0.895094027115563	11	FACETS	0.779	0.701	0.862			1	SUBCLONAL	1	TRUE	NA	0.895094027115563	11		307	1760	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372503	118372503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	226	539	0	ENST00000534358.1:c.6436C>T	p.Pro2146Ser	p.P2146S	ENST00000534358	NM_005933.3	2146	Ccc/Tcc	26/36	0.895094027115563	1	FACETS	0.986	0.949	1	0.986	0.949	1	CLONAL	1	TRUE	0	0.895094027115563	1		539	283	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037463	12037463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	185	395	0	ENST00000396373.4:c.1094C>T	p.Ser365Phe	p.S365F	ENST00000396373	NM_001987.4	365	tCc/tTc	6/8	1	2	FACETS	0.968	0.905	1	0.968	0.905	1	CLONAL	1	TRUE	1	0.895094027115563	2		395	427	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425230	49425230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199797812	NA	P-0028205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	288	688	0	ENST00000301067.7:c.13258C>T	p.Arg4420Trp	p.R4420W	ENST00000301067	NM_003482.3	4420	Cgg/Tgg	39/54	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.895094027115563	2		688	586	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445934	49445934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	319	877	0	ENST00000301067.7:c.1532C>T	p.Pro511Leu	p.P511L	ENST00000301067	NM_003482.3	511	cCt/cTt	10/54	1	2	FACETS	0.954	0.906	1	0.954	0.906	1	CLONAL	1	TRUE	1	0.895094027115563	2		877	747	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864513	57864513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150127797	NA	P-0028205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	270	562	1	ENST00000228682.2:c.1990C>T	p.His664Tyr	p.H664Y	ENST00000228682	NM_005269.2	664	Cat/Tat	12/12	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.895094027115563	2		563	548	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122859	2122859	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	238	553	0	ENST00000219476.3:c.2230C>T	p.Pro744Ser	p.P744S	ENST00000219476	NM_000548.3	744	Cca/Tca	21/42	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.895094027115563	2		553	510	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872613	37872613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	230	722	1	ENST00000269571.5:c.1573C>T	p.Pro525Ser	p.P525S	ENST00000269571		525	Ccc/Tcc	13/27	1	2	FACETS	0.898	0.844	0.953	0.898	0.844	0.953	CLONAL	1	TRUE	1	0.895094027115563	2		723	572	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753803	42753803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	367	793	0	ENST00000222329.4:c.461C>T	p.Ser154Phe	p.S154F	ENST00000222329	NM_006494.2	154	tCc/tTc	4/4	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.895094027115563	2		793	769	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371610	225371610	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	217	468	1	ENST00000264414.4:c.994G>A	p.Glu332Lys	p.E332K	ENST00000264414	NM_003590.4	332	Gaa/Aaa	7/16	1	2	FACETS	0.982	0.923	1	0.982	0.923	1	CLONAL	1	TRUE	1	0.895094027115563	2		469	494	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543602	9543602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	220	595	0	ENST00000353224.5:c.1552G>A	p.Glu518Lys	p.E518K	ENST00000353224	NM_177990.2	518	Gag/Aag	6/10	1	2	FACETS	0.955	0.897	1	0.955	0.897	1	CLONAL	1	TRUE	1	0.895094027115563	2		595	515	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546908	9546908	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	180	352	0	ENST00000353224.5:c.1114C>T	p.Gln372Ter	p.Q372*	ENST00000353224	NM_177990.2	372	Cag/Tag	5/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.895094027115563	2		352	388	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514567	41514567	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	173	404	0	ENST00000373198.4:c.94T>G	p.Cys32Gly	p.C32G	ENST00000373198	NM_133170.3	32	Tgt/Ggt	2/32	1	2	FACETS	0.996	0.93	1	0.996	0.93	1	CLONAL	1	TRUE	1	0.895094027115563	2		404	388	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62320936	62320936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	311	834	0	ENST00000360203.5:c.1960C>T	p.Pro654Ser	p.P654S	ENST00000360203	NM_001283009.1	654	Ccc/Tcc	23/35	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.895094027115563	2		834	679	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641222	12641222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	225	456	0	ENST00000251849.4:c.1076C>T	p.Ser359Phe	p.S359F	ENST00000251849	NM_002880.3	359	tCt/tTt	10/17	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.895094027115563	2		456	462	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182679097	182679097	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	190	487	0	ENST00000292782.4:c.437A>T	p.Gln146Leu	p.Q146L	ENST00000292782	NM_020640.2	146	cAa/cTa	4/7	1	2	FACETS	0.915	0.855	0.976	0.915	0.855	0.976	CLONAL	1	TRUE	1	0.895094027115563	2		487	464	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964361	55964361	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	190	463	1	ENST00000263923.4:c.2452G>A	p.Glu818Lys	p.E818K	ENST00000263923	NM_002253.2	818	Gaa/Aaa	17/30	1	2	FACETS	0.933	0.872	0.995	0.933	0.872	0.995	CLONAL	1	TRUE	1	0.895094027115563	2		464	455	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31466348	31466349	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0028205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	236	721	0	ENST00000344624.3:c.2406_2407delinsTT	p.Leu803Phe	p.L803F	ENST00000344624		802	caCCtc/caTTtc	16/33	0.536520401117143	4	FACETS	1	0.98	1	0.373	0.348	0.398	INDETERMINATE	1	TRUE	1	0.895094027115563	4		721	893	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771212	161771213	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0028205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	179	494	1	ENST00000366898.1:c.1316_1317delinsTT	p.Pro439Leu	p.P439L	ENST00000366898	NM_004562.2	439	cCC/cTT	12/12	1	2	FACETS	0.885	0.824	0.946	0.885	0.824	0.946	CLONAL	1	TRUE	1	0.895094027115563	2		495	452	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740618	145740618	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770371344	NA	P-0028205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	261	645	0	ENST00000428558.2:c.1399G>A	p.Ala467Thr	p.A467T	ENST00000428558	NM_004260.3	467	Gct/Act	8/22	0.768153431250755	3	FACETS	1	0.964	1			1	CLONAL	1	TRUE	NA	0.895094027115563	3		645	815	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	126	210	0				ENST00000310581	NM_198253.2	-/1132			0.3	4	FACETS	0.862	0.788	0.938	0.862	0.788	0.938	CLONAL	3	TRUE	1	0.32	4		210	402	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207009	1207009	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	109	646	2	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	0.32	NA		648	682	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322925	31322925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	147	819	0	ENST00000412585.2:c.971G>A	p.Gly324Glu	p.G324E	ENST00000412585	NM_005514.6	324	gGa/gAa	5/8	0.3	3	FACETS	0.874	0.796	0.956	0.437	0.398	0.478	CLONAL	1	TRUE	1	0.32	3		819	1220	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724694	112724694	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	108	460	0	ENST00000369452.4:c.578C>G	p.Ser193Cys	p.S193C	ENST00000369452	NM_007373.3	193	tCt/tGt	2/9	1	2	FACETS	0.959	0.861	1	0.959	0.861	1	CLONAL	1	TRUE	1	0.32	2		460	704	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641494	18641494	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	54	442	0	ENST00000266497.5:c.2493G>T	p.Glu831Asp	p.E831D	ENST00000266497		831	gaG/gaT	17/31	1	2	FACETS	0.703	0.601	0.814	0.703	0.601	0.814	SUBCLONAL	1	TRUE	1	0.32	2		442	480	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240240	41240240	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	44	296	0	ENST00000379561.5:c.110C>A	p.Ser37Ter	p.S37*	ENST00000379561	NM_002015.3	37	tCg/tAg	1/3	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.32	2		296	221	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49051507	49051507	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	49	371	0	ENST00000267163.4:c.2680G>C	p.Glu894Gln	p.E894Q	ENST00000267163	NM_000321.2	894	Gag/Cag	26/27	1	2	FACETS	0.678	0.574	0.791	0.678	0.574	0.791	SUBCLONAL	1	TRUE	1	0.32	2		371	452	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84384682	84384682	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs369385726	NA	P-0028206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	86	452	0	ENST00000321945.7:c.761T>C	p.Ile254Thr	p.I254T	ENST00000321945	NM_139076.2	254	aTt/aCt	8/9	1	2	FACETS	0.855	0.757	0.959	0.855	0.757	0.959	CLONAL	1	TRUE	1	0.32	2		452	629	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323201	31323201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	103	589	0	ENST00000412585.2:c.788G>A	p.Arg263Lys	p.R263K	ENST00000412585	NM_005514.6	263	aGa/aAa	4/8	0.3	3	FACETS	0.789	0.705	0.879	0.395	0.352	0.44	SUBCLONAL	1	TRUE	1	0.32	3		589	946	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323216	31323216	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	109	536	2	ENST00000412585.2:c.773G>A	p.Arg258Lys	p.R258K	ENST00000412585	NM_005514.6	258	aGa/aAa	4/8	0.3	3	FACETS	0.923	0.828	1	0.462	0.414	0.512	CLONAL	1	TRUE	1	0.32	3		538	856	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323283	31323283	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	51	151	0	ENST00000412585.2:c.706G>A	p.Glu236Lys	p.E236K	ENST00000412585	NM_005514.6	236	Gag/Aag	4/8	0.3	3	FACETS	1	0.956	1	0.667	0.571	0.771	CLONAL	1	TRUE	1	0.32	3		151	277	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965616	93965616	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	71	473	0	ENST00000369303.4:c.2312T>A	p.Val771Asp	p.V771D	ENST00000369303	NM_004440.3	771	gTt/gAt	13/17	1	2	FACETS	0.703	0.614	0.8	0.703	0.614	0.8	SUBCLONAL	1	TRUE	1	0.32	2		473	631	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567701	226567701	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	236	486	0	ENST00000366794.5:c.1465C>A	p.Pro489Thr	p.P489T	ENST00000366794	NM_001618.3	489	Cct/Act	10/23	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.771996455114831	2		486	565	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996076	73996076	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	339	840	0	ENST00000318443.5:c.810C>G	p.Phe270Leu	p.F270L	ENST00000318443	NM_001024736.1	270	ttC/ttG	5/10	NA	2	FACETS	0.996	0.946	1			1	INDETERMINATE	1	TRUE	NA	0.771996455114831	2		840	882	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989688	15989688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	185	384	0	ENST00000268712.3:c.3085C>T	p.Pro1029Ser	p.P1029S	ENST00000268712	NM_006311.3	1029	Cca/Tca	23/46	0.735810083530731	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.771996455114831	1		384	283	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40460232	40460232	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	449	638	0	ENST00000345506.4:c.1943C>G	p.Thr648Arg	p.T648R	ENST00000345506	NM_003152.3	648	aCg/aGg	17/20	0.684881241978882	3	FACETS	0.955	0.918	0.992			1	CLONAL	2	TRUE	NA	0.771996455114831	3		638	844	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122669	7123684	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTGCCAGGTCCCGATGCACAAACTTCTTGGCGTTCAGGTAGGCCATCCCGTCAGCAATCTCTGCCGCCATCTGAATCATCTCTTGAAGGGTAGGGGGAGGGCGGCCAGGATTATTCTAAAACAGAAACACGGGGTTGGTGTTTCAGCAGCACTGGGATCCGAGGAGGCCAGGAGCGGGTGCTCCACCGAGTACCCCGCTGGGTCCCCCGAAGCAGCTTACCTCAGCCTCTGGCCGCAGAGAACGGAGGTAGCTCTTCAGGTCTCCGTGAGCCATCAGCTCCATCACCACCAGCGTGGGCTGGCCCTTGGACACCACTCCCAGGAGGCGCACCTGCAGAGCAAGCAACCAGGGTTCTTGGAGGAGGGTCCGTGATTCGACTCACCAGGGTTCTCCTCCCTCCCTGGTGTCTATGTCACACACAGCACCCTGTGGCCTGGATGCAGCGTGCTCAGCCCTGGTCTAGGAGAGCAGACATACCTGCCCGGACAGCAGACAGATAGGCCTTTGTATTTTTTTTTTTTTAATTTTCGAGACGGAATCTTGCTGTTACCCAGGCTAGAGTGCAGTGGCGTGATCTCGGCTCACTGCAACCTTTGCCTCCCGGGTTCAAGCAATTCTCCTGCCTCAGTCTCCCGAGTAGCTGGGGTTACAGGTGCCCGCCTCCACACCCGGCTAATTTTTGTATTTTTAGTAGAGACAGGATTTCTCCATGTTGGTCAGGCTGGTCTTGAACTCCTGACCTCTGGTGATCCGCCTGCCTCAGCCTCCCAAAGTGCTGGGATTATAGCCACTGCACCCAGCCAGGCCTTTGTATTTTAATCATTCCCTCTGCCTGGCTCTCTGTTCCCTGCCACATCCACAGGGCCCAGCTCCTCATGTCCTCTAAGTCTTTGCTCAAATACACCCCTGTCCAACCCTCCTTTCCTCCCTTTCTTCATGTTTCCATAGCATTTGCTCCTAATGTATAAAGGGTTTGGAGTCAGCTGGGGGTGGTGGCTTATGCCTGTAATCCCA	GCTGCCAGGTCCCGATGCACAAACTTCTTGGCGTTCAGGTAGGCCATCCCGTCAGCAATCTCTGCCGCCATCTGAATCATCTCTTGAAGGGTAGGGGGAGGGCGGCCAGGATTATTCTAAAACAGAAACACGGGGTTGGTGTTTCAGCAGCACTGGGATCCGAGGAGGCCAGGAGCGGGTGCTCCACCGAGTACCCCGCTGGGTCCCCCGAAGCAGCTTACCTCAGCCTCTGGCCGCAGAGAACGGAGGTAGCTCTTCAGGTCTCCGTGAGCCATCAGCTCCATCACCACCAGCGTGGGCTGGCCCTTGGACACCACTCCCAGGAGGCGCACCTGCAGAGCAAGCAACCAGGGTTCTTGGAGGAGGGTCCGTGATTCGACTCACCAGGGTTCTCCTCCCTCCCTGGTGTCTATGTCACACACAGCACCCTGTGGCCTGGATGCAGCGTGCTCAGCCCTGGTCTAGGAGAGCAGACATACCTGCCCGGACAGCAGACAGATAGGCCTTTGTATTTTTTTTTTTTTAATTTTCGAGACGGAATCTTGCTGTTACCCAGGCTAGAGTGCAGTGGCGTGATCTCGGCTCACTGCAACCTTTGCCTCCCGGGTTCAAGCAATTCTCCTGCCTCAGTCTCCCGAGTAGCTGGGGTTACAGGTGCCCGCCTCCACACCCGGCTAATTTTTGTATTTTTAGTAGAGACAGGATTTCTCCATGTTGGTCAGGCTGGTCTTGAACTCCTGACCTCTGGTGATCCGCCTGCCTCAGCCTCCCAAAGTGCTGGGATTATAGCCACTGCACCCAGCCAGGCCTTTGTATTTTAATCATTCCCTCTGCCTGGCTCTCTGTTCCCTGCCACATCCACAGGGCCCAGCTCCTCATGTCCTCTAAGTCTTTGCTCAAATACACCCCTGTCCAACCCTCCTTTCCTCCCTTTCTTCATGTTTCCATAGCATTTGCTCCTAATGTATAAAGGGTTTGGAGTCAGCTGGGGGTGGTGGCTTATGCCTGTAATCCCA	-	novel	NA	P-0028208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	109	678	0	ENST00000302850.5:c.3259-684_3485del		p.X1087_splice	ENST00000302850	NM_000208.2	1087		18-19/22	1	2	FACETS	0.48	0.432	0.531	0.48	0.432	0.531	SUBCLONAL	1	TRUE	1	0.771996455114831	2		678	588	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10267157	10267157	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	224	502	0	ENST00000340748.4:c.1261C>G	p.Pro421Ala	p.P421A	ENST00000340748		421	Ccc/Gcc	17/40	1	2	FACETS	0.977	0.916	1	0.977	0.916	1	CLONAL	1	TRUE	1	0.771996455114831	2		502	594	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31495431	31495431	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	256	635	0	ENST00000344624.3:c.1717C>A	p.His573Asn	p.H573N	ENST00000344624		573	Cac/Aac	9/33	1	2	FACETS	0.952	0.896	1	0.952	0.896	1	CLONAL	1	TRUE	1	0.771996455114831	2		635	697	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31495447	31495447	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	251	636	0	ENST00000344624.3:c.1701T>A	p.Asn567Lys	p.N567K	ENST00000344624		567	aaT/aaA	9/33	1	2	FACETS	0.966	0.909	1	0.966	0.909	1	CLONAL	1	TRUE	1	0.771996455114831	2		636	673	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459900	149459900	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0028208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	260	560	1	ENST00000286301.3:c.308-1G>T		p.X103_splice	ENST00000286301	NM_005211.3	103			0.771996455114831	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.771996455114831	1		561	399	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099942	157099942	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	191	524	0	ENST00000346085.5:c.879C>G	p.Ser293Arg	p.S293R	ENST00000346085	NM_020732.3	293	agC/agG	1/20	0.771996455114831	1	FACETS	0.996	0.943	1	0.996	0.943	1	CLONAL	1	TRUE	0	0.771996455114831	1		524	305	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099340	27099356	+	frameshift_variant	Frame_Shift_Del	DEL	GATGGAAGTGACTCCAC	GATGGAAGTGACTCCAC	A	novel	NA	P-0028208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	220	620	0	ENST00000324856.7:c.3577_3593delinsA	p.Asp1193AsnfsTer8	p.D1193Nfs*8	ENST00000324856	NM_006015.4	1193	GATGGAAGTGACTCCACa/Aa	14/20	1	2	FACETS	0.844	0.789	0.9	0.844	0.789	0.9	CLONAL	1	TRUE	1	0.771996455114831	2		620	675	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0028209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	35	297	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.127863688715526	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		297	281	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038932	12038932	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	53	489	0	ENST00000396373.4:c.1225A>G	p.Lys409Glu	p.K409E	ENST00000396373	NM_001987.4	409	Aag/Gag	7/8	0.343062940297904	4	FACETS		NA	1			1	NA	NA	FALSE	2	NA	4		489	301	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648405	30648405	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	49	520	0	ENST00000295754.5:c.30G>A	p.Trp10Ter	p.W10*	ENST00000295754	NM_003242.5	10	tgG/tgA	1/7	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		520	391	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981462	55981462	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs545112274	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	41	536	0	ENST00000263923.4:c.475G>A	p.Val159Met	p.V159M	ENST00000263923	NM_002253.2	159	Gtg/Atg	4/30	1	2	FACETS	0.697	0.58	0.826	0.697	0.58	0.826	SUBCLONAL	1	TRUE	1	0.245206643574172	2		536	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934575	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	117	529	0	ENST00000269305.4:c.733G>C	p.Gly245Arg	p.G245R	ENST00000269305	NM_001126112.2	245	Ggc/Cgc	7/11	0.201652077631548	3	FACETS	0.761	0.687	0.839	0.761	0.687	0.839	SUBCLONAL	2	TRUE	1	0.245206643574172	3		529	704	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713609	30713609	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	68	505	0	ENST00000295754.5:c.934G>T	p.Glu312Ter	p.E312*	ENST00000295754	NM_003242.5	312	Gag/Tag	4/7	0.183260187582112	2	FACETS	1	0.938	1	0.564	0.491	0.642	CLONAL	1	TRUE	0	0.245206643574172	2		505	492	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867550	35867550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	36	434	0	ENST00000303115.3:c.364G>T	p.Asp122Tyr	p.D122Y	ENST00000303115	NM_002185.3	122	Gac/Tac	3/8	0.158398339075418	2	FACETS	0.612	0.502	0.734	0.306	0.251	0.367	SUBCLONAL	1	TRUE	0	0.245206643574172	2		434	480	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120699	115120699	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	82	781	0	ENST00000257566.3:c.307C>A	p.Pro103Thr	p.P103T	ENST00000257566	NM_016569.3	103	Ccc/Acc	1/8	1	2	FACETS	0.837	0.737	0.944	0.837	0.737	0.944	CLONAL	1	TRUE	1	0.245206643574172	2		781	799	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440334	187440334	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	51	500	1	ENST00000232014.4:c.2033G>A	p.Arg678His	p.R678H	ENST00000232014	NM_001130845.1	678	cGc/cAc	10/10	0.0726005010560908	4	FACETS	0.74	0.628	0.864	0.37	0.314	0.432	INDETERMINATE	1	TRUE	2	0.245206643574172	4		501	700	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259321	16259321	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	31	396	0	ENST00000375759.3:c.6586G>T	p.Glu2196Ter	p.E2196*	ENST00000375759	NM_015001.2	2196	Gag/Tag	11/15	0.158398339075418	2	FACETS	0.84	0.681	1	0.42	0.34	0.51	CLONAL	1	TRUE	0	0.245206643574172	2		396	301	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039464	49039464	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	120	568	0	ENST00000267163.4:c.2449G>T	p.Glu817Ter	p.E817*	ENST00000267163	NM_000321.2	817	Gaa/Taa	23/27	0.183260187582112	2	FACETS	1	0.981	1	0.675	0.61	0.744	CLONAL	1	TRUE	0	0.245206643574172	2		568	725	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244590	41244590	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	37	664	0	ENST00000357654.3:c.2958C>G	p.Ile986Met	p.I986M	ENST00000357654	NM_007294.3	986	atC/atG	10/23	0.201652077631548	3	FACETS	0.464	0.381	0.557	0.232	0.19	0.279	SUBCLONAL	1	TRUE	1	0.245206643574172	3		664	730	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122730	7122730	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	39	752	0	ENST00000302850.5:c.3424G>A	p.Glu1142Lys	p.E1142K	ENST00000302850	NM_000208.2	1142	Gag/Aag	19/22	0.158398339075418	2	FACETS	0.413	0.341	0.493	0.206	0.17	0.247	SUBCLONAL	1	TRUE	0	0.245206643574172	2		752	771	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101702	27101702	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	115	818	0	ENST00000324856.7:c.4984A>G	p.Lys1662Glu	p.K1662E	ENST00000324856	NM_006015.4	1662	Aaa/Gaa	18/20	0.158398339075418	2	FACETS	1	0.947	1	0.54	0.486	0.597	CLONAL	1	TRUE	0	0.245206643574172	2		818	869	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400857	72400857	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	54	415	0	ENST00000357731.5:c.314T>A	p.Ile105Lys	p.I105K	ENST00000357731	NM_173808.2	105	aTa/aAa	2/7	0.158398339075418	2	FACETS	1	0.903	1	0.536	0.459	0.62	CLONAL	1	TRUE	0	0.245206643574172	2		415	411	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736544	85736544	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	39	305	0	ENST00000370580.1:c.103G>C	p.Glu35Gln	p.E35Q	ENST00000370580	NM_003921.4	35	Gag/Cag	2/3	0.158398339075418	2	FACETS	0.944	0.785	1	0.472	0.392	0.56	CLONAL	1	TRUE	0	0.245206643574172	2		305	337	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050378	176050378	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	158	525	0	ENST00000367669.3:c.1187T>G	p.Leu396Trp	p.L396W	ENST00000367669	NM_022457.5	396	tTg/tGg	11/20	0.245206643574172	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	0	0.245206643574172	2		525	635	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252131	226252131	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	26	87	0	ENST00000366813.1:c.79C>T	p.Arg27Cys	p.R27C	ENST00000366813		27	Cgc/Tgc	1/3	0.245206643574172	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	2	TRUE	0	0.245206643574172	2		87	98	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852308	63852308	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	76	631	0	ENST00000279873.7:c.3088del	p.Ala1030GlnfsTer5	p.A1030Qfs*5	ENST00000279873	NM_032199.2	1029	cGg/cg	10/10	0.201652077631548	3	FACETS	1	0.944	1	0.568	0.498	0.642	CLONAL	1	TRUE	1	0.245206643574172	3		631	613	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276970	123276970	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	28	396	0	ENST00000358487.5:c.947G>C	p.Gly316Ala	p.G316A	ENST00000358487	NM_000141.4	316	gGt/gCt	8/18	0.245206643574172	1	FACETS	0.566	0.453	0.695	0.566	0.453	0.695	SUBCLONAL	1	TRUE	0	0.245206643574172	1		396	354	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373748	118373748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	48	442	0	ENST00000534358.1:c.7141G>A	p.Asp2381Asn	p.D2381N	ENST00000534358	NM_005933.3	2381	Gat/Aat	27/36	1	2	FACETS	0.799	0.676	0.935	0.799	0.676	0.935	CLONAL	1	TRUE	1	0.245206643574172	2		442	490	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380664	118380664	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	rs113003878	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	46	399	0	ENST00000534358.1:c.10902A>T	p.Glu3634Asp	p.E3634D	ENST00000534358	NM_005933.3	3634	gaA/gaT	30/36	1	2	FACETS	0.769	0.648	0.903	0.769	0.648	0.903	CLONAL	1	TRUE	1	0.245206643574172	2		399	488	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244263	46244263	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	49	409	0	ENST00000334344.6:c.2357G>T	p.Gly786Val	p.G786V	ENST00000334344	NM_152641.2	786	gGc/gTc	15/21	1	2	FACETS	0.958	0.813	1	0.958	0.813	1	CLONAL	1	TRUE	1	0.245206643574172	2		409	417	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434509	49434509	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	53	775	0	ENST00000301067.7:c.7044G>T	p.Arg2348Ser	p.R2348S	ENST00000301067	NM_003482.3	2348	agG/agT	31/54	1	2	FACETS	0.654	0.557	0.761	0.654	0.557	0.761	SUBCLONAL	1	TRUE	1	0.245206643574172	2		775	661	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219308	133219308	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	34	630	0	ENST00000320574.5:c.4736G>C	p.Arg1579Pro	p.R1579P	ENST00000320574	NM_006231.2	1579	cGc/cCc	37/49	1	2	FACETS	0.476	0.388	0.575	0.476	0.388	0.575	SUBCLONAL	1	TRUE	1	0.245206643574172	2		630	583	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250211	133250211	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	53	643	0	ENST00000320574.5:c.1309G>C	p.Val437Leu	p.V437L	ENST00000320574	NM_006231.2	437	Gtg/Ctg	13/49	NA	2	FACETS	0.668	0.569	0.777			1	INDETERMINATE	1	TRUE	NA	0.245206643574172	2		643	647	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396943	396943	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	45	784	0	ENST00000262320.3:c.83A>G	p.Glu28Gly	p.E28G	ENST00000262320	NM_003502.3	28	gAg/gGg	2/11	1	2	FACETS	0.5	0.419	0.59	0.5	0.419	0.59	SUBCLONAL	1	TRUE	1	0.245206643574172	2		784	734	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50827554	50827554	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	33	519	0	ENST00000398568.2:c.2439T>G	p.Phe813Leu	p.F813L	ENST00000398568	NM_001042412.1	813	ttT/ttG	16/18	1	2	FACETS	0.415	0.337	0.504	0.415	0.337	0.504	SUBCLONAL	1	TRUE	1	0.245206643574172	2		519	648	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40368037	40368037	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	91	594	0	ENST00000293328.3:c.1468G>T	p.Glu490Ter	p.E490*	ENST00000293328	NM_012448.3	490	Gag/Tag	12/19	0.201652077631548	3	FACETS	0.921	0.816	1	0.46	0.408	0.517	CLONAL	1	TRUE	1	0.245206643574172	3		594	905	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475042	40475042	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786205503	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	119	593	0	ENST00000264657.5:c.1868G>T	p.Trp623Leu	p.W623L	ENST00000264657	NM_139276.2	623	tGg/tTg	20/24	0.201652077631548	3	FACETS	0.879	0.795	0.967	0.879	0.795	0.967	CLONAL	2	TRUE	1	0.245206643574172	3		593	620	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243854	41243854	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	64	610	0	ENST00000357654.3:c.3694G>T	p.Gly1232Cys	p.G1232C	ENST00000357654	NM_007294.3	1232	Ggt/Tgt	10/23	0.201652077631548	3	FACETS	0.885	0.766	1	0.443	0.383	0.508	CLONAL	1	TRUE	1	0.245206643574172	3		610	662	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804358	46804358	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	98	542	1	ENST00000290295.7:c.649C>A	p.Arg217Ser	p.R217S	ENST00000290295	NM_006361.5	217	Cgc/Agc	2/2	0.201652077631548	3	FACETS	0.758	0.677	0.843	0.758	0.677	0.843	SUBCLONAL	2	TRUE	1	0.245206643574172	3		543	592	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752461	55752461	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	141	772	1	ENST00000284073.2:c.919G>T	p.Gly307Cys	p.G307C	ENST00000284073	NM_138962.2	307	Ggc/Tgc	12/14	0.201652077631548	3	FACETS	1	0.985	1	0.71	0.647	0.777	CLONAL	1	TRUE	1	0.245206643574172	3		773	909	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436071	56436071	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	92	564	0	ENST00000407977.2:c.1066G>T	p.Ala356Ser	p.A356S	ENST00000407977		356	Gcc/Tcc	9/10	0.201652077631548	3	FACETS	1	0.978	1	0.713	0.634	0.796	CLONAL	1	TRUE	1	0.245206643574172	3		564	591	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532440	63532440	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs752664902	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	154	630	0	ENST00000307078.5:c.2139G>T	p.Gln713His	p.Q713H	ENST00000307078	NM_004655.3	713	caG/caT	8/11	0.201652077631548	3	FACETS	0.772	0.706	0.841	0.772	0.706	0.841	SUBCLONAL	2	TRUE	1	0.245206643574172	3		630	913	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66521894	66521894	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	76	282	1	ENST00000358598.2:c.550-1G>T		p.X184_splice	ENST00000358598	NM_212471.2	184			0.201652077631548	3	FACETS	0.866	0.763	0.975	0.866	0.763	0.975	CLONAL	2	TRUE	1	0.245206643574172	3		283	402	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45422905	45422905	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	24	320	0	ENST00000262160.6:c.223G>T	p.Val75Phe	p.V75F	ENST00000262160	NM_005901.5	75	Gtt/Ttt	2/11	1	2	FACETS	0.473	0.37	0.592	0.473	0.37	0.592	SUBCLONAL	1	TRUE	1	0.245206643574172	2		320	414	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602863	10602863	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	183	883	2	ENST00000171111.5:c.715G>T	p.Val239Leu	p.V239L	ENST00000171111	NM_203500.1	239	Gtg/Ttg	3/6	0.158398339075418	2	FACETS	1	0.988	1	0.705	0.65	0.762	CLONAL	1	TRUE	0	0.245206643574172	2		885	1059	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082766	16082766	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1374212272	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	13	143	0	ENST00000281043.3:c.580C>A	p.Pro194Thr	p.P194T	ENST00000281043	NM_005378.4	194	Ccc/Acc	2/3	1	2	FACETS	0.655	0.468	0.879	0.655	0.468	0.879	SUBCLONAL	1	TRUE	1	0.245206643574172	2		143	162	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525109	9525109	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	37	523	1	ENST00000353224.5:c.1776A>T	p.Gln592His	p.Q592H	ENST00000353224	NM_177990.2	592	caA/caT	8/10	1	2	FACETS	0.58	0.478	0.695	0.58	0.478	0.695	SUBCLONAL	1	TRUE	1	0.245206643574172	2		524	520	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309749	30309749	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	67	499	0	ENST00000307677.4:c.273G>T	p.Arg91Ser	p.R91S	ENST00000307677	NM_138578.1	91	agG/agT	2/3	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.245206643574172	2		499	480	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259281	36259281	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	47	339	0	ENST00000300305.3:c.210G>T	p.Lys70Asn	p.K70N	ENST00000300305		70	aaG/aaT	3/8	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.245206643574172	2		339	311	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163212	47163212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751617319	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	81	449	0	ENST00000409792.3:c.2914G>A	p.Glu972Lys	p.E972K	ENST00000409792	NM_014159.6	972	Gaa/Aaa	3/21	0.183260187582112	2	FACETS	0.82	0.726	0.919	0.82	0.726	0.919	CLONAL	2	TRUE	0	0.245206643574172	2		449	403	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73096506	73096506	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	61	302	0	ENST00000356692.5:c.286G>C	p.Gly96Arg	p.G96R	ENST00000356692		96	Ggt/Cgt	3/9	0.183260187582112	2	FACETS	1	0.961	1	0.66	0.572	0.755	CLONAL	1	TRUE	0	0.245206643574172	2		302	377	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119642266	119642266	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	60	548	0	ENST00000316626.5:c.431G>C	p.Arg144Thr	p.R144T	ENST00000316626		144	aGa/aCa	4/12	0.0726005010560908	4	FACETS	0.836	0.719	0.964	0.418	0.359	0.482	INDETERMINATE	1	TRUE	2	0.245206643574172	4		548	729	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911502	134911502	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	126	609	0	ENST00000398015.3:c.1967G>C	p.Gly656Ala	p.G656A	ENST00000398015	NM_004441.4	656	gGg/gCg	11/16	0.0726005010560908	4	FACETS	0.81	0.734	0.89	0.81	0.734	0.89	INDETERMINATE	2	TRUE	2	0.245206643574172	4		609	790	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138382765	138382765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	81	506	1	ENST00000289153.2:c.2779G>A	p.Val927Ile	p.V927I	ENST00000289153	NM_006219.2	927	Gtc/Atc	19/22	0.0726005010560908	4	FACETS	1	0.977	1	0.741	0.654	0.834	INDETERMINATE	1	TRUE	2	0.245206643574172	4		507	555	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188232	142188232	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	63	435	1	ENST00000350721.4:c.6499G>T	p.Val2167Leu	p.V2167L	ENST00000350721	NM_001184.3	2167	Gta/Tta	38/47	0.0726005010560908	4	FACETS	1	0.945	1	0.592	0.513	0.679	INDETERMINATE	1	TRUE	2	0.245206643574172	4		436	540	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242756	66242756	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	28	384	0	ENST00000273854.3:c.1816G>T	p.Ala606Ser	p.A606S	ENST00000273854	NM_004439.5	606	Gct/Tct	9/18	1	2	FACETS	0.446	0.356	0.55	0.446	0.356	0.55	SUBCLONAL	1	TRUE	1	0.245206643574172	2		384	512	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398826	398826	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	76	421	0	ENST00000380956.4:c.638-2A>T		p.X213_splice	ENST00000380956	NM_001195286.1	213			NA	3	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.245206643574172	3		421	515	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045825	26045825	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	73	514	0	ENST00000540144.1:c.187A>G	p.Ile63Val	p.I63V	ENST00000540144	NM_003531.2	63	Atc/Gtc	1/1	0.153801255065801	5	FACETS	0.757	0.663	0.858	0.505	0.442	0.572	SUBCLONAL	2	TRUE	2	0.245206643574172	5		514	538	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704486	117704486	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	21	318	0	ENST00000368508.3:c.2490del	p.Lys832ArgfsTer2	p.K832Rfs*2	ENST00000368508	NM_002944.2	830	ggG/gg	16/43	1	2	FACETS	0.476	0.366	0.604	0.476	0.366	0.604	SUBCLONAL	1	TRUE	1	0.245206643574172	2		318	360	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963901	2963901	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	177	672	0	ENST00000396946.4:c.1906G>T	p.Val636Phe	p.V636F	ENST00000396946	NM_032415.4	636	Gtc/Ttc	15/25	0.153801255065801	5	FACETS	1	0.944	1	0.687	0.633	0.744	CLONAL	2	TRUE	2	0.245206643574172	5		672	958	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381533	81381533	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	93	291	0	ENST00000222390.5:c.528C>G	p.Tyr176Ter	p.Y176*	ENST00000222390	NM_000601.4	176	taC/taG	5/18	0.153801255065801	5	FACETS	1	0.96	1	0.772	0.69	0.859	CLONAL	2	TRUE	2	0.245206643574172	5		291	448	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509831	106509831	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	177	696	1	ENST00000359195.3:c.1825C>A	p.Gln609Lys	p.Q609K	ENST00000359195	NM_002649.2	609	Caa/Aaa	2/11	0.153801255065801	5	FACETS	0.849	0.784	0.917	0.849	0.784	0.917	CLONAL	3	TRUE	2	0.245206643574172	5		697	775	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845160	128845160	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	112	781	1	ENST00000249373.3:c.654G>T	p.Gln218His	p.Q218H	ENST00000249373	NM_005631.4	218	caG/caT	3/12	0.153801255065801	5	FACETS	1	0.982	1	0.48	0.431	0.532	CLONAL	1	TRUE	2	0.245206643574172	5		782	867	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187398	38187398	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	40	461	0	ENST00000317025.8:c.1079G>T	p.Arg360Leu	p.R360L	ENST00000317025	NM_023034.1	360	cGa/cTa	6/24	1	2	FACETS	0.706	0.587	0.839	0.706	0.587	0.839	SUBCLONAL	1	TRUE	1	0.245206643574172	2		461	462	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465465	8465465	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs200841828	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	36	435	0	ENST00000356435.5:c.3714+1G>A		p.X1238_splice	ENST00000356435		1238			0.158398339075418	2	FACETS	0.688	0.565	0.825	0.344	0.282	0.413	SUBCLONAL	1	TRUE	0	0.245206643574172	2		435	427	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202816	27202816	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	40	317	0	ENST00000380036.4:c.1910-2A>T		p.X637_splice	ENST00000380036	NM_000459.3	637			0.158398339075418	2	FACETS	0.901	0.751	1	0.451	0.375	0.534	CLONAL	1	TRUE	0	0.245206643574172	2		317	362	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730343	133730343	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	124	568	0	ENST00000318560.5:c.409G>C	p.Ala137Pro	p.A137P	ENST00000318560	NM_005157.4	137	Gct/Cct	3/11	0.158398339075418	2	FACETS	0.867	0.787	0.951	0.867	0.787	0.951	CLONAL	2	TRUE	0	0.245206643574172	2		568	583	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932643	39932643	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	46	889	0	ENST00000378444.4:c.1956del	p.Tyr653ThrfsTer16	p.Y653Tfs*16	ENST00000378444	NM_001123385.1	652	ccC/cc	4/15	0.245206643574172	1	FACETS	0.38	0.319	0.448	0.38	0.319	0.448	SUBCLONAL	1	TRUE	0	0.245206643574172	1		889	866	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006897	47006897	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	44	772	0	ENST00000377604.3:c.17G>T	p.Arg6Leu	p.R6L	ENST00000377604	NM_001204468.1	6	cGt/cTt	2/24	0.245206643574172	1	FACETS	0.43	0.359	0.508	0.43	0.359	0.508	SUBCLONAL	1	TRUE	0	0.245206643574172	1		772	733	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344910	70344910	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1487824889	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	96	793	0	ENST00000374080.3:c.2140C>A	p.Pro714Thr	p.P714T	ENST00000374080		714	Ccc/Acc	15/45	0.245206643574172	1	FACETS	0.895	0.797	0.999	0.895	0.797	0.999	CLONAL	1	TRUE	0	0.245206643574172	1		793	768	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357082	70357082	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	122	850	0	ENST00000374080.3:c.5597A>T	p.Gln1866Leu	p.Q1866L	ENST00000374080		1866	cAg/cTg	39/45	0.245206643574172	1	FACETS	0.902	0.814	0.995	0.902	0.814	0.995	CLONAL	1	TRUE	0	0.245206643574172	1		850	968	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438527	52438527	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	185	562	0	ENST00000460680.1:c.1192G>T	p.Glu398Ter	p.E398*	ENST00000460680	NM_004656.3	398	Gag/Tag	12/17	0.607172511149328	1	FACETS	0.997	0.933	1	0.997	0.933	1	CLONAL	1	TRUE	0	0.623174762005737	1		562	410	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372175	55372175	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	108	311	0	ENST00000297316.4:c.865C>A	p.Pro289Thr	p.P289T	ENST00000297316	NM_022454.3	289	Cca/Aca	2/2	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.623174762005737	2		311	343	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	147	210	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.839377389461662	2		210	346	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544169	18544169	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	177	421	0	ENST00000266497.5:c.1986G>C	p.Gln662His	p.Q662H	ENST00000266497		662	caG/caC	13/31	1	2	FACETS	0.897	0.835	0.961	0.897	0.835	0.961	CLONAL	1	TRUE	1	0.839377389461662	2		421	470	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480492	89480492	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	153	290	0	ENST00000336596.2:c.2329G>C	p.Ala777Pro	p.A777P	ENST00000336596	NM_005233.5	777	Gct/Cct	13/17	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.839377389461662	2		290	358	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220396	123220400	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GGTAT	GGTAT	-	novel	NA	P-0028241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	192	184	0	ENST00000218089.9:c.3054_3058del		p.X1018_splice	ENST00000218089	NM_001042749.1	1018		30/35	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.839377389461662	1		184	239	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725009	162725009	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	183	375	0	ENST00000367921.3:c.481G>T	p.Ala161Ser	p.A161S	ENST00000367921	NM_006182.2	161	Gcc/Tcc	6/18	0.37356794140435	4	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	2	0.382662613043188	4		375	653	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163298025	163298025	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	81	451	1	ENST00000271452.3:c.206T>A	p.Val69Glu	p.V69E	ENST00000271452	NM_145697.2	69	gTg/gAg	4/14	0.37356794140435	4	FACETS	0.827	0.728	0.933	0.413	0.364	0.467	CLONAL	1	TRUE	2	0.382662613043188	4		452	708	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110028	115110028	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200821102	NA	P-0028244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	358	596	1	ENST00000257566.3:c.1850C>A	p.Ala617Glu	p.A617E	ENST00000257566	NM_016569.3	617	gCg/gAg	8/8	0.37356794140435	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	2	0.382662613043188	4		597	1105	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562758	21562758	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	261	343	0	ENST00000382592.4:c.1161G>T	p.Glu387Asp	p.E387D	ENST00000382592	NM_014572.2	387	gaG/gaT	4/8	0.382662613043188	2	FACETS	0.842	0.798	0.887	1	0.992	1	CLONAL	3	TRUE	0	0.382662613043188	2		343	540	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052623	42052623	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	231	431	0	ENST00000219905.7:c.7294G>T	p.Glu2432Ter	p.E2432*	ENST00000219905	NM_001164273.1	2432	Gag/Tag	20/24	0.382662613043188	2	FACETS	0.993	0.932	1	0.993	0.932	1	CLONAL	2	TRUE	0	0.382662613043188	2		431	608	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577541	7577562	+	frameshift_variant	Frame_Shift_Del	DEL	TTCATGCCGCCCATGCAGGAAC	TTCATGCCGCCCATGCAGGAAC	-	novel	NA	P-0028244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	397	507	0	ENST00000269305.4:c.719_740del	p.Ser240ThrfsTer98	p.S240Tfs*98	ENST00000269305	NM_001126112.2	240	aGTTCCTGCATGGGCGGCATGAAc/ac	7/11	0.294669513015233	4	FACETS	1	0.99	1			1	CLONAL	3	TRUE	NA	0.382662613043188	4		507	858	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984779	11984779	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	86	365	0	ENST00000353533.5:c.325G>T	p.Gly109Ter	p.G109*	ENST00000353533	NM_003010.3	109	Gga/Tga	3/11	0.294669513015233	4	FACETS	1	0.896	1			1	CLONAL	1	TRUE	NA	0.382662613043188	4		365	614	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132501	11132501	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	346	577	0	ENST00000358026.2:c.2717G>T	p.Arg906Leu	p.R906L	ENST00000358026	NM_001128849.1	906	cGc/cTc	19/36	0.382662613043188	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.382662613043188	2		577	843	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919979	50919979	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	254	490	0	ENST00000440232.2:c.3066G>T	p.Gln1022His	p.Q1022H	ENST00000440232	NM_002691.3	1022	caG/caT	24/27	0.382662613043188	3	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	1	0.382662613043188	3		490	787	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99169353	99169353	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs960890310	NA	P-0028244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	254	395	0	ENST00000074304.5:c.1283A>G	p.Tyr428Cys	p.Y428C	ENST00000074304	NM_001134224.1	428	tAc/tGc	15/26	0.382662613043188	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.382662613043188	3		395	776	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127565	55127565	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	82	295	0	ENST00000257290.5:c.353A>T	p.Tyr118Phe	p.Y118F	ENST00000257290	NM_006206.4	118	tAc/tTc	3/23	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.382662613043188	2		295	360	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31435915	31435915	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	289	457	0	ENST00000344624.3:c.2999G>C	p.Arg1000Pro	p.R1000P	ENST00000344624		1000	cGg/cCg	22/33	0.382662613043188	5	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	TRUE	2	0.382662613043188	5		457	761	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592114	67592114	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	143	247	0	ENST00000274335.5:c.1930G>T	p.Gly644Cys	p.G644C	ENST00000274335		644	Ggc/Tgc	14/15	0.382662613043188	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.382662613043188	2		247	348	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476813	140476813	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs606231228	NA	P-0028244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	232	458	0	ENST00000288602.6:c.1593G>T	p.Trp531Cys	p.W531C	ENST00000288602	NM_004333.4	531	tgG/tgT	13/18	0.37356794140435	4	FACETS	0.991	0.926	1	0.991	0.926	1	CLONAL	2	TRUE	2	0.382662613043188	4		458	846	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981906	70981906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	484	583	1	ENST00000276594.2:c.190C>T	p.Pro64Ser	p.P64S	ENST00000276594	NM_024504.3	64	Ccc/Tcc	2/8	0.382662613043188	6	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	3	0.382662613043188	6		584	1403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579397	7579397	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs730881995	NA	P-0028245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	290	768	1	ENST00000269305.4:c.290T>A	p.Val97Asp	p.V97D	ENST00000269305	NM_001126112.2	97	gTc/gAc	4/11	0.534383130963184	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.534383130963184	1		769	682	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221946	1221946	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0028245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	316	684	0	ENST00000326873.7:c.863-2A>T		p.X288_splice	ENST00000326873	NM_000455.4	288			0.534383130963184	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.534383130963184	1		684	728	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-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	132	74	0	ENST00000394830.3:c.3756_3800+164del		p.X1252_splice	ENST00000394830	NM_018313.4	1252		24/30	0.534383130963184	1	FACETS	1	0.992	1	1	0.994	1	CLONAL	2	TRUE	0	0.534383130963184	1		74	146	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659320	86659320	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	54	199	0	ENST00000274376.6:c.1609A>G	p.Arg537Gly	p.R537G	ENST00000274376	NM_002890.2	537	Agg/Ggg	11/25	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.534383130963184	2		199	182	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349851	89349888	+	frameshift_variant	Frame_Shift_Del	DEL	ACTGGATTTCTCTTTGTATCTTTCTGGTTTTGTCTTCT	ACTGGATTTCTCTTTGTATCTTTCTGGTTTTGTCTTCT	C	novel	NA	P-0028245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	188	730	1	ENST00000301030.4:c.3062_3099delinsG	p.Glu1021GlyfsTer285	p.E1021Gfs*285	ENST00000301030	NM_001256183.1	1021	gAGAAGACAAAACCAGAAAGATACAAAGAGAAATCCAGT/gG	9/13	1	2	FACETS	0.805	0.744	0.868	0.805	0.744	0.868	CLONAL	1	TRUE	1	0.534383130963184	2		731	874	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597407	10597413	+	protein_altering_variant	In_Frame_Del	DEL	GATGTCA	GATGTCA	T	novel	NA	P-0028245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	308	811	0	ENST00000171111.5:c.1790_1796delinsA	p.Met597_Ser599delinsLys	p.M597_S599delinsK	ENST00000171111	NM_203500.1	597	aTGACATCg/aAg	6/6	0.534383130963184	1	FACETS	0.94	0.888	0.992	0.94	0.888	0.992	CLONAL	1	TRUE	0	0.534383130963184	1		811	899	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	85	210	0				ENST00000310581	NM_198253.2	-/1132			0.370085885042474	4	FACETS	0.813	0.724	0.907	0.813	0.724	0.907	CLONAL	2	TRUE	2	0.407675558573186	4		210	361	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0028246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	46	350	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	0.407675558573186	5	FACETS	0.935	0.789	1	0.312	0.263	0.365	CLONAL	1	TRUE	2	0.407675558573186	5		350	389	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097670	27097670	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	164	667	0	ENST00000324856.7:c.3259del	p.Ser1087ValfsTer6	p.S1087Vfs*6	ENST00000324856	NM_006015.4	1087	Agt/gt	12/20	0.342767773093751	3	FACETS	0.926	0.856	0.998	0.926	0.856	0.998	CLONAL	2	TRUE	1	0.407675558573186	3		667	523	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528581	89528581	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	97	311	0	ENST00000336596.2:c.2881C>A	p.Pro961Thr	p.P961T	ENST00000336596	NM_005233.5	961	Cca/Aca	17/17	0.407675558573186	5	FACETS	1	0.96	1	0.754	0.679	0.832	CLONAL	2	TRUE	2	0.407675558573186	5		311	339	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413151	63413151	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	138	308	0	ENST00000330258.3:c.16G>T	p.Asp6Tyr	p.D6Y	ENST00000330258	NM_152424.3	6	Gat/Tat	2/2	0.350525430684943	2	FACETS	0.861	0.801	0.921			1	CLONAL	3	TRUE	NA	0.407675558573186	2		308	262	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0028247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	156	716	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.245805747905093	2	FACETS	0.912	0.842	0.983	1	0.987	1	CLONAL	3	TRUE	0	0.245805747905093	2		716	464	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0028247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	122	656	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.119537443205858	4	FACETS	1	0.975	1	0.804	0.73	0.88	INDETERMINATE	2	TRUE	1	0.245805747905093	4		656	513	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604655	48604655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	42	303	0	ENST00000342988.3:c.1477G>A	p.Asp493Asn	p.D493N	ENST00000342988	NM_005359.5	493	Gat/Aat	12/12	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.245805747905093	2		303	245	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991602	72991602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs926058661	NA	P-0028247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	59	610	0	ENST00000268489.5:c.2443G>A	p.Val815Met	p.V815M	ENST00000268489	NM_006885.3	815	Gtg/Atg	2/10	0.148299515615806	2	FACETS	0.943	0.812	1	0.472	0.406	0.543	CLONAL	1	TRUE	0	0.245805747905093	2		610	509	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16041505	16041505	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	89	325	0	ENST00000268712.3:c.1374C>G	p.Asn458Lys	p.N458K	ENST00000268712	NM_006311.3	458	aaC/aaG	13/46	0.245805747905093	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.245805747905093	2		325	318	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495721	72495721	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	111	424	0	ENST00000477973.2:c.351C>G	p.Ser117Arg	p.S117R	ENST00000477973	NM_012234.5	117	agC/agG	1/4	0.207526054465947	3	FACETS	0.909	0.82	1	0.909	0.82	1	CLONAL	2	TRUE	1	0.245805747905093	3		424	558	SUCCESS
APC	324	MSKCC	GRCh37	5	112175760	112175760	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	31	345	0	ENST00000257430.4:c.4469del	p.His1490LeufsTer17	p.H1490Lfs*17	ENST00000257430	NM_000038.5	1490	cAt/ct	16/16	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.245805747905093	2		345	230	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0028248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	143	837	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.300794507917694	2	FACETS	0.935	0.85	1			1	CLONAL	1	TRUE	NA	0.26	2		837	1177	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0028248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	41	511	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.389	0.323	0.463	0.389	0.323	0.463	SUBCLONAL	1	TRUE	1	0.26	2		511	811	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0028248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	57	309	2	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	1	2	FACETS	0.703	0.602	0.812	0.703	0.602	0.812	SUBCLONAL	1	TRUE	1	0.26	2		311	624	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729844	41729844	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs908163566	NA	P-0028248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	30	293	1	ENST00000242208.4:c.685C>T	p.Arg229Trp	p.R229W	ENST00000242208	NM_002192.2	229	Cgg/Tgg	3/3	1	2	FACETS	0.391	0.314	0.479	0.391	0.314	0.479	SUBCLONAL	1	TRUE	1	0.26	2		294	590	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828882	26828882	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	72	363	0	ENST00000381527.3:c.104T>G	p.Val35Gly	p.V35G	ENST00000381527	NM_001260.1	35	gTc/gGc	1/13	0.137325165408267	3	FACETS	0.797	0.696	0.907	0.399	0.348	0.454	INDETERMINATE	1	TRUE	1	0.26	3		363	785	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119671	70119694	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTATTGTCCACAGGGCAATCCCAG	TTATTGTCCACAGGGCAATCCCAG	-	novel	NA	P-0028248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	49	515	1	ENST00000245479.2:c.686-13_696del		p.X229_splice	ENST00000245479	NM_000346.3	229		3/3	1	2	FACETS	0.432	0.365	0.507	0.432	0.365	0.507	SUBCLONAL	1	TRUE	1	0.26	2		516	872	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163469	47163469	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	32	259	0	ENST00000409792.3:c.2657T>G	p.Leu886Arg	p.L886R	ENST00000409792	NM_014159.6	886	cTt/cGt	3/21	1	2	FACETS	0.443	0.358	0.538	0.443	0.358	0.538	SUBCLONAL	1	TRUE	1	0.26	2		259	556	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0028249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	37	497	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.653	0.536	0.784	0.653	0.536	0.784	SUBCLONAL	1	TRUE	1	0.14	2		497	810	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225591	26225591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	96	466	0	ENST00000360408.1:c.209G>A	p.Arg70His	p.R70H	ENST00000360408	NM_003532.2	70	cGc/cAc	1/1	0.195931221168538	3	FACETS	1	0.923	1	1	0.923	1	CLONAL	2	TRUE	1	0.14	3		466	703	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475550	12475550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479145908	NA	P-0028249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	42	535	3	ENST00000287820.6:c.1424C>T	p.Thr475Met	p.T475M	ENST00000287820	NM_015869.4	475	aCg/aTg	7/7	1	2	FACETS	0.78	0.65	0.926	0.78	0.65	0.926	CLONAL	1	TRUE	1	0.14	2		538	769	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202630	108202630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	40	404	0	ENST00000278616.4:c.7654C>T	p.His2552Tyr	p.H2552Y	ENST00000278616	NM_000051.3	2552	Cac/Tac	52/63	1	2	FACETS	0.932	0.773	1	0.932	0.773	1	CLONAL	1	TRUE	1	0.14	2		404	613	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001429	29001429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753144948	NA	P-0028249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	41	311	0	ENST00000282397.4:c.1303G>A	p.Val435Met	p.V435M	ENST00000282397	NM_002019.4	435	Gtg/Atg	10/30	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.14	2		311	487	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027225	49027226	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0028249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	53	518	0	ENST00000267163.4:c.1794_1795dup	p.Asn599IlefsTer13	p.N599Ifs*13	ENST00000267163	NM_000321.2	598	aat/aATat	18/27	1	2	FACETS	0.956	0.813	1	0.956	0.813	1	CLONAL	1	TRUE	1	0.14	2		518	792	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0028251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	85	253	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.879	0.788	0.973	0.879	0.788	0.973	CLONAL	1	TRUE	1	0.740894615191157	2		253	261	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538913	23538913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	35	478	0	ENST00000380871.4:c.526C>T	p.Arg176Cys	p.R176C	ENST00000380871	NM_006167.3	176	Cgc/Tgc	2/2	0.221539747830791	1	FACETS	0.125	0.102	0.151	0.125	0.102	0.151	INDETERMINATE	1	TRUE	0	0.740894615191157	1		478	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577097	+	missense_variant	Missense_Mutation	DNP	TC	TC	GG	novel	NA	P-0028251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	616	759	1	ENST00000269305.4:c.841_842delinsCC	p.Asp281Pro	p.D281P	ENST00000269305	NM_001126112.2	281	GAc/CCc	8/11	NA	2	FACETS	0.97	0.945	0.995			1	INDETERMINATE	2	TRUE	NA	0.740894615191157	2		760	857	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940489	76940490	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0028251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	118	266	0	ENST00000373344.5:c.603dup	p.Lys202Ter	p.K202*	ENST00000373344	NM_000489.3	201	-/T	8/35	1	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.740894615191157	1		266	191	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43772110	43772110	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	61	690	0	ENST00000382044.4:c.605C>A	p.Ser202Ter	p.S202*	ENST00000382044	NM_001141980.1	202	tCa/tAa	6/28	1	2	FACETS	0.51	0.439	0.589	0.51	0.439	0.589	SUBCLONAL	1	TRUE	1	0.24	2		690	996	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534386	63534386	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1204	69	799	0	ENST00000307078.5:c.1135G>C	p.Glu379Gln	p.E379Q	ENST00000307078	NM_004655.3	379	Gaa/Caa	5/11	0.164345881999006	3	FACETS	0.714	0.619	0.817	0.238	0.206	0.273	SUBCLONAL	1	TRUE	0	0.164345881999006	3		799	1273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579329	7579329	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs121912658	NA	P-0028256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	193	646	0	ENST00000269305.4:c.358A>T	p.Lys120Ter	p.K120*	ENST00000269305	NM_001126112.2	120	Aag/Tag	4/11	0.163464827060958	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.164345881999006	2		646	1015	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210689	2210691	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs993985886	NA	P-0028256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	60	773	0	ENST00000398665.3:c.1192_1194del	p.Lys398del	p.K398del	ENST00000398665	NM_032482.2	396	AAG/-	14/28	1	2	FACETS	0.627	0.538	0.725	0.627	0.538	0.725	SUBCLONAL	1	TRUE	1	0.164345881999006	2		773	1164	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39744996	39744996	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	115	554	2	ENST00000361337.2:c.1786A>T	p.Ile596Phe	p.I596F	ENST00000361337	NM_003286.2	596	Atc/Ttc	17/21	0.143544561263108	4	FACETS	1	0.982	1	0.733	0.658	0.812	CLONAL	1	TRUE	2	0.164345881999006	4		556	1112	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0028257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	264	619	1	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.530133532824993	1	FACETS	0.929	0.874	0.985	0.929	0.874	0.985	CLONAL	1	TRUE	0	0.530133532824993	1		620	788	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0028257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	107	511	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.915	0.826	1	0.915	0.826	1	CLONAL	1	TRUE	1	0.530133532824993	2		511	441	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172408	108172409	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0028257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	213	403	0	ENST00000278616.4:c.5216dup	p.Asn1739LysfsTer10	p.N1739Kfs*10	ENST00000278616	NM_000051.3	1737	-/A	35/63	0.528832832291744	2	FACETS	0.764	0.716	0.812	0.764	0.716	0.812	SUBCLONAL	2	TRUE	0	0.530133532824993	2		403	526	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273938	10273938	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs768592036	NA	P-0028257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	210	805	2	ENST00000330684.3:c.331C>T	p.Gln111Ter	p.Q111*	ENST00000330684	NM_001134407.1	111	Cag/Tag	2/13	1	2	FACETS	0.886	0.824	0.951	0.886	0.824	0.951	CLONAL	1	TRUE	1	0.530133532824993	2		807	894	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979987	7979987	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746723399	NA	P-0028260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	170	576	3	ENST00000319144.4:c.1350del	p.Leu451SerfsTer16	p.L451Sfs*16	ENST00000319144	NM_001139.2	450	ggG/gg	10/15	NA	2	FACETS	0.459	0.422	0.498			1	INDETERMINATE	1	TRUE	NA	0.851235108852867	2		579	870	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0028260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	356	238	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.851235108852867	2	FACETS	0.977	0.951	1	0.977	0.951	1	CLONAL	2	TRUE	0	0.851235108852867	2		238	428	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659240	86659240	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	121	289	0	ENST00000274376.6:c.1533del	p.Lys511AsnfsTer9	p.K511Nfs*9	ENST00000274376	NM_002890.2	510	gAa/ga	11/25	1	2	FACETS	0.658	0.599	0.719	0.658	0.599	0.719	SUBCLONAL	1	TRUE	1	0.851235108852867	2		289	432	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0028260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	88	434	0	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	0.284	0.251	0.319	0.284	0.251	0.319	SUBCLONAL	1	TRUE	1	0.851235108852867	2		434	728	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100577	157100577	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1289149988	NA	P-0028260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	137	356	3	ENST00000346085.5:c.1518del	p.Gly507AspfsTer16	p.G507Dfs*16	ENST00000346085	NM_020732.3	505	aCc/ac	1/20	1	2	FACETS	0.534	0.487	0.582	0.534	0.487	0.582	SUBCLONAL	1	TRUE	1	0.851235108852867	2		359	603	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466019	69466019	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	409	680	1	ENST00000227507.2:c.857C>A	p.Thr286Lys	p.T286K	ENST00000227507	NM_053056.2	286	aCa/aAa	5/5	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.851235108852867	2		681	850	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925402	114925402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748822481	NA	P-0028260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	267	536	0	ENST00000543371.1:c.1485del	p.Ser496ProfsTer5	p.S496Pfs*5	ENST00000543371	NM_001198531.1	494	Ccc/cc	14/14	0.851235108852867	2	FACETS	0.711	0.668	0.755	0.356	0.334	0.378	SUBCLONAL	1	TRUE	0	0.851235108852867	2		536	882	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101254	27101267	+	frameshift_variant	Frame_Shift_Del	DEL	GAGCACGGGCTCTG	GAGCACGGGCTCTG	-	novel	NA	P-0028260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	605	492	0	ENST00000324856.7:c.4536_4549del	p.Gln1512HisfsTer15	p.Q1512Hfs*15	ENST00000324856	NM_006015.4	1512	caGAGCACGGGCTCTGcc/cacc	18/20	0.851235108852867	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.851235108852867	2		492	622	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560476	95560477	+	missense_variant	Missense_Mutation	DNP	CT	CT	TG	novel	NA	P-0028260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	248	418	1	ENST00000393063.1:c.5112_5113delinsCA	p.Leu1704_Glu1705delinsPheLys	p.L1704_E1705delinsFK	ENST00000393063	NM_030621.3	1704	ttAGaa/ttCAaa	25/28	1	2	FACETS	0.96	0.905	1	0.96	0.905	1	CLONAL	1	TRUE	1	0.851235108852867	2		419	607	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562977	95562978	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0028260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	168	284	0	ENST00000393063.1:c.4279dup	p.Leu1427ProfsTer11	p.L1427Pfs*11	ENST00000393063	NM_030621.3	1427	ctg/cCtg	24/28	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.851235108852867	2		284	391	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3113451	3113451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	163	577	1	ENST00000078429.4:c.445C>T	p.Arg149Cys	p.R149C	ENST00000078429	NM_002067.2	149	Cgc/Tgc	3/7	1	2	FACETS	0.451	0.413	0.489	0.451	0.413	0.489	SUBCLONAL	1	TRUE	1	0.851235108852867	2		578	850	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024381	31024381	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755522655	NA	P-0028260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	156	523	0	ENST00000375687.4:c.3866G>A	p.Arg1289Gln	p.R1289Q	ENST00000375687	NM_015338.5	1289	cGg/cAg	13/13	1	2	FACETS	0.466	0.427	0.507	0.466	0.427	0.507	SUBCLONAL	1	TRUE	1	0.851235108852867	2		523	786	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588174	67588175	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0028260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	238	339	0	ENST00000274335.5:c.1006_1007del	p.Gly336ArgfsTer9	p.G336Rfs*9	ENST00000274335		335	tGG/t	7/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.851235108852867	2		339	538	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591107	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0028260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	255	308	0	ENST00000274335.5:c.1700_1701del	p.Lys567ThrfsTer34	p.K567Tfs*34	ENST00000274335		567	AAa/a	12/15	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.851235108852867	2		308	510	SUCCESS
APC	324	MSKCC	GRCh37	5	112177224	112177224	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs863225368	NA	P-0028260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	149	268	0	ENST00000257430.4:c.5936del	p.Asn1979ThrfsTer65	p.N1979Tfs*65	ENST00000257430	NM_000038.5	1978	gAa/ga	16/16	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.851235108852867	2		268	339	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206599	27206599	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	153	380	0	ENST00000380036.4:c.2384A>G	p.Gln795Arg	p.Q795R	ENST00000380036	NM_000459.3	795	cAg/cGg	15/23	1	2	FACETS	0.598	0.549	0.649	0.598	0.549	0.649	SUBCLONAL	1	TRUE	1	0.851235108852867	2		380	601	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776116	135776116	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	136	334	0	ENST00000298552.3:c.2611T>C	p.Ser871Pro	p.S871P	ENST00000298552	NM_001162426.1	871	Tca/Cca	20/23	1	2	FACETS	0.612	0.56	0.667	0.612	0.56	0.667	SUBCLONAL	1	TRUE	1	0.851235108852867	2		334	522	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660569	67660569	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	CGAATGAGAAGC	novel	NA	P-0028260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	396	595	0	ENST00000264010.4:c.1469delinsCGAATGAGAAGC	p.Lys490ThrfsTer25	p.K490Tfs*25	ENST00000264010	NM_006565.3	490	aAg/aCGAATGAGAAGCg	8/12	1	2	FACETS	0.948	0.905	0.992	0.948	0.905	0.992	CLONAL	1	TRUE	1	0.851235108852867	2		595	981	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710670	114710670	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0028261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	120	475	0	ENST00000543371.1:c.155C>G	p.Ser52Ter	p.S52*	ENST00000543371	NM_001198531.1	52	tCa/tGa	1/14	1	2	FACETS	0.938	0.85	1	0.938	0.85	1	CLONAL	1	TRUE	1	0.437300303367153	2		475	585	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348882	118348882	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	173	235	0	ENST00000534358.1:c.3535T>G	p.Phe1179Val	p.F1179V	ENST00000534358	NM_005933.3	1179	Ttt/Gtt	5/36	0.437300303367153	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.437300303367153	2		235	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578538	7578538	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1131691037	NA	P-0028261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	399	791	2	ENST00000269305.4:c.392A>T	p.Asn131Ile	p.N131I	ENST00000269305	NM_001126112.2	131	aAc/aTc	5/11	0.437300303367153	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.437300303367153	1		793	1031	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0028261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	123	350	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	1	2	FACETS	0.992	0.901	1	0.992	0.901	1	CLONAL	1	TRUE	1	0.437300303367153	2		350	567	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864377	162864377	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs75860381	NA	P-0028261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	91	428	0	ENST00000366898.1:c.136G>A	p.Ala46Thr	p.A46T	ENST00000366898	NM_004562.2	46	Gca/Aca	2/12	0.153689540059392	2	FACETS	0.851	0.759	0.949	0.426	0.379	0.475	INDETERMINATE	1	TRUE	0	0.437300303367153	2		428	489	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236086	108236086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782292	NA	P-0028264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	26	548	3	ENST00000278616.4:c.9022C>T	p.Arg3008Cys	p.R3008C	ENST00000278616	NM_000051.3	3008	Cgt/Tgt	63/63	1	2	FACETS	0.222	0.174	0.276	0.222	0.174	0.276	SUBCLONAL	1	TRUE	1	0.3	2		551	782	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050691	30050691	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	69	449	0	ENST00000338641.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000338641	NM_000268.3	165	Caa/Taa	5/16	0.3	1	FACETS	0.879	0.768	0.998	0.879	0.768	0.998	CLONAL	1	TRUE	0	0.3	1		449	445	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156918	89156920	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	rs768142526	NA	P-0028268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	82	558	0	ENST00000336596.2:c.27_29del	p.Leu11del	p.L11del	ENST00000336596	NM_005233.5	7	aTCCtc/atc	1/17	1	2	FACETS	0.826	0.728	0.932	0.826	0.728	0.932	CLONAL	1	TRUE	1	0.24	2		558	827	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919271	48919272	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATGC	novel	NA	P-0028268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	18	313	0	ENST00000267163.4:c.437_440dup	p.Met148CysfsTer10	p.M148Cfs*10	ENST00000267163	NM_000321.2	146	aat/aATGCat	4/27	1	2	FACETS	0.602	0.454	0.777	0.602	0.454	0.777	SUBCLONAL	1	TRUE	1	0.24	2		313	249	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24129371	24129398	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGAGCAAGACCTTCGGGCAGAAGCCC	GCTGAGCAAGACCTTCGGGCAGAAGCCC	CAA	novel	NA	P-0028268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	159	437	2	ENST00000263121.7:c.15_42delinsCAA	p.Leu6LysfsTer2	p.L6Kfs*2	ENST00000263121	NM_003073.3	5	gcGCTGAGCAAGACCTTCGGGCAGAAGCCC/gcCAA	1/9	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.24	2		439	910	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0028269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	25	495	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.3	2	FACETS	0.774	0.609	0.966			1	CLONAL	1	TRUE	NA	0.12	2		495	538	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577138	7577138	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587780075	NA	P-0028269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	37	684	0	ENST00000269305.4:c.800G>C	p.Arg267Pro	p.R267P	ENST00000269305	NM_001126112.2	267	cGg/cCg	8/11	1	2	FACETS	0.91	0.748	1	0.91	0.748	1	CLONAL	1	TRUE	1	0.12	2		684	678	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427557	49427557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	46	587	0	ENST00000301067.7:c.10931C>T	p.Pro3644Leu	p.P3644L	ENST00000301067	NM_003482.3	3644	cCa/cTa	39/54	1	2	FACETS	0.753	0.634	0.884	1	0.96	1	SUBCLONAL	2	TRUE	1	0.12	2		587	509	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031912	10031912	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs771113247	NA	P-0028269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	32	678	0	ENST00000330684.3:c.911C>A	p.Ser304Tyr	p.S304Y	ENST00000330684	NM_001134407.1	304	tCt/tAt	3/13	1	2	FACETS	0.923	0.747	1	0.923	0.747	1	CLONAL	1	TRUE	1	0.12	2		678	578	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602722	10602772	+	inframe_deletion	In_Frame_Del	DEL	GCAGCTGCATCTGCAGGAAGTTCGGCGTCAACGAGTGGCAGCGCACGGCCC	GCAGCTGCATCTGCAGGAAGTTCGGCGTCAACGAGTGGCAGCGCACGGCCC	-	novel	NA	P-0028269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	47	805	1	ENST00000171111.5:c.806_856del	p.Arg269_Leu285del	p.R269_L285del	ENST00000171111	NM_203500.1	269	cGGGCCGTGCGCTGCCACTCGTTGACGCCGAACTTCCTGCAGATGCAGCTGCag/cag	3/6	1	2	FACETS	0.995	0.838	1	0.995	0.838	1	CLONAL	1	TRUE	1	0.12	2		806	787	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308049	30308050	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0028269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	31	471	0	ENST00000262643.3:c.186_187delinsTT	p.Trp62_Asp63delinsCysTyr	p.W62_D63delinsCY	ENST00000262643	NM_001238.2	62	tgGGac/tgTTac	5/12	1	2	FACETS	0.895	0.723	1	0.895	0.723	1	CLONAL	1	TRUE	1	0.12	2		471	577	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38641629	38641629	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	64	453	0	ENST00000299084.4:c.591del	p.Phe197LeufsTer27	p.F197Lfs*27	ENST00000299084	NM_152594.2	197	Ttt/tt	6/7	1	2	FACETS	0.276	0.239	0.317	0.276	0.239	0.317	SUBCLONAL	1	FALSE	1	0.732158159727801	2		453	633	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0028272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	225	380	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.574052459514766	3	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	1	0.568704893404947	3		380	503	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219225	133219241	+	frameshift_variant	Frame_Shift_Del	DEL	GGAATTCCTCCAAGACA	GGAATTCCTCCAAGACA	-	novel	NA	P-0028272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	55	702	0	ENST00000320574.5:c.4803_4819del	p.Val1602ThrfsTer8	p.V1602Tfs*8	ENST00000320574	NM_006231.2	1601	ccTGTCTTGGAGGAATTCCca/ccca	37/49	0.430606416443262	1	FACETS	0.372	0.319	0.429	0.372	0.319	0.429	SUBCLONAL	1	TRUE	0	0.568704893404947	1		702	372	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64288934	64288934	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0028272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	66	436	0	ENST00000370651.3:c.329+1G>A		p.X110_splice	ENST00000370651	NM_003463.4	110			0.551564468116181	1	FACETS	0.593	0.52	0.671	0.593	0.52	0.671	SUBCLONAL	1	TRUE	0	0.568704893404947	1		436	280	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630212	100630212	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	77	320	0	ENST00000308731.7:c.61T>A	p.Ser21Thr	p.S21T	ENST00000308731	NM_000061.2	21	Tca/Aca	2/19	0.22330376876808	4	FACETS	1	0.893	1	0.509	0.447	0.576	CLONAL	1	TRUE	2	0.324156107629109	4		320	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0028288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	24	345	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	1	2	FACETS	0.183	0.142	0.229	0.183	0.142	0.229	SUBCLONAL	1	TRUE	1	0.41	2		345	641	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489842	2489842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771517383	NA	P-0028288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	109	374	0	ENST00000355716.4:c.239C>T	p.Pro80Leu	p.P80L	ENST00000355716	NM_003820.2	80	cCa/cTa	3/8	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.41	2		374	517	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100876	27100877	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0028289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	180	353	0	ENST00000324856.7:c.4161_4162dup	p.Met1388ArgfsTer94	p.M1388Rfs*94	ENST00000324856	NM_006015.4	1386	-/GA	18/20	0.564569407617693	3	FACETS	1	0.99	1	0.731	0.679	0.785	CLONAL	1	TRUE	1	0.564569407617693	3		353	559	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988398	36988398	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	16	117	0	ENST00000354822.5:c.255G>T	p.Gln85His	p.Q85H	ENST00000354822	NM_001079668.2	85	caG/caT	2/3	0.564569407617693	6	FACETS	0.442	0.326	0.58	0.111	0.081	0.145	SUBCLONAL	1	TRUE	2	0.564569407617693	6		117	273	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872969	136872969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767830104	NA	P-0028291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	71	197	0	ENST00000241393.3:c.529G>A	p.Val177Ile	p.V177I	ENST00000241393	NM_003467.2	177	Gtc/Atc	2/2	1	2	FACETS	0.857	0.753	0.967	0.857	0.753	0.967	CLONAL	1	TRUE	1	0.487450312424172	2		197	340	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227940	123227946	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGATT	GAGGATT	-	novel	NA	P-0028291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	41	261	0	ENST00000218089.9:c.3657_3663del	p.Glu1220LeufsTer12	p.E1220Lfs*12	ENST00000218089	NM_001042749.1	1217	ggGAGGATT/gg	33/35	1	2	FACETS	0.424	0.353	0.502	0.424	0.353	0.502	SUBCLONAL	1	TRUE	1	0.487450312424172	2		261	397	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0028294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	29	298	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.771	0.624	0.935	0.771	0.624	0.935	CLONAL	1	TRUE	1	0.404442277264436	2		298	186	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0028294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	68	253	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.945	1	1	0.985	1	CLONAL	2	TRUE	1	0.404442277264436	2		253	154	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0028294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	498	580	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.404442277264436	2	FACETS	0.98	0.956	1	1	0.998	1	CLONAL	4	TRUE	0	0.404442277264436	2		580	628	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288811	15288811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	15	30	0	ENST00000263388.2:c.3928G>A	p.Gly1310Arg	p.G1310R	ENST00000263388	NM_000435.2	1310	Ggg/Agg	24/33	1	2	FACETS	0.662	0.49	0.865	0.662	0.49	0.865	SUBCLONAL	1	TRUE	1	0.404442277264436	2		30	112	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247531	53247531	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	183	422	0	ENST00000375401.3:c.278G>A	p.Trp93Ter	p.W93*	ENST00000375401	NM_004187.3	93	tGg/tAg	3/26	1	2	FACETS	0.891	0.829	0.954	1	0.993	1	CLONAL	2	TRUE	1	0.404442277264436	2		422	508	SUCCESS
AR	367	MSKCC	GRCh37	X	66942680	66942680	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	46	298	0	ENST00000374690.3:c.2461G>T	p.Gly821Trp	p.G821W	ENST00000374690	NM_000044.3	821	Ggg/Tgg	7/8	0.260670065229107	0	FACETS	0.479	0.405	0.558			1	SUBCLONAL	1	TRUE	0	0.404442277264436	0		298	283	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813058	76813058	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	76	416	0	ENST00000373344.5:c.6563G>A	p.Arg2188Gln	p.R2188Q	ENST00000373344	NM_000489.3	2188	cGa/cAa	30/35	0.260670065229107	0	FACETS	1	0.933	1			1	CLONAL	1	TRUE	0	0.404442277264436	0		416	211	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700253	117700253	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	45	408	0	ENST00000368508.3:c.2566C>T	p.His856Tyr	p.H856Y	ENST00000368508	NM_002944.2	856	Cac/Tac	17/43	0.261150683201735	1	FACETS	0.642	0.539	0.754	0.642	0.539	0.754	SUBCLONAL	1	TRUE	0	0.261150683201735	1		408	467	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636134	28636134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200841206	NA	P-0028296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	323	320	0	ENST00000241453.7:c.238G>A	p.Ala80Thr	p.A80T	ENST00000241453	NM_004119.2	80	Gct/Act	3/24	0.46205915877372	3	FACETS	0.983	0.934	1	0.983	0.934	1	CLONAL	2	TRUE	1	0.555051843108521	3		320	756	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0028296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	102	295	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.555051843108521	2		295	359	SUCCESS
APC	324	MSKCC	GRCh37	5	112175147	112175147	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	136	219	0	ENST00000257430.4:c.3856G>T	p.Glu1286Ter	p.E1286*	ENST00000257430	NM_000038.5	1286	Gaa/Taa	16/16	0.555051843108521	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.555051843108521	2		219	231	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748374	43748375	+	stop_gained	Nonsense_Mutation	DNP	TC	TC	CA	novel	NA	P-0028296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	208	419	0	ENST00000382044.4:c.2431_2432delinsTG	p.Glu811Ter	p.E811*	ENST00000382044	NM_001141980.1	811	GAa/TGa	12/28	0.33773761311804	2	FACETS	1	0.99	1	0.664	0.621	0.708	CLONAL	1	TRUE	0	0.555051843108521	2		419	564	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348083	348083	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1168676445	NA	P-0028296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	157	367	0	ENST00000262320.3:c.1423G>A	p.Val475Ile	p.V475I	ENST00000262320	NM_003502.3	475	Gta/Ata	6/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.555051843108521	2		367	523	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368209	45368209	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	60	259	0	ENST00000262160.6:c.1393A>C	p.Ser465Arg	p.S465R	ENST00000262160	NM_005901.5	465	Agc/Cgc	11/11	1	2	FACETS	0.855	0.744	0.972	0.855	0.744	0.972	CLONAL	1	TRUE	1	0.555051843108521	2		259	253	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395688	45395688	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	85	283	0	ENST00000262160.6:c.446G>T	p.Cys149Phe	p.C149F	ENST00000262160	NM_005901.5	149	tGc/tTc	4/11	1	2	FACETS	0.837	0.745	0.933	0.837	0.745	0.933	CLONAL	1	TRUE	1	0.555051843108521	2		283	366	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952146	178952147	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587776802	NA	P-0028297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	33	208	0	ENST00000263967.3:c.3203dup	p.Asn1068LysfsTer5	p.N1068Kfs*5	ENST00000263967	NM_006218.2	1067	-/A	21/21	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.499263897710777	2		208	114	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392733	118392733	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs782418508	NA	P-0028297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	121	356	0	ENST00000534358.1:c.11765A>G	p.Asn3922Ser	p.N3922S	ENST00000534358	NM_005933.3	3922	aAt/aGt	36/36	1	2	FACETS	0.981	0.891	1	0.981	0.891	1	CLONAL	1	TRUE	1	0.499263897710777	2		356	494	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847363	68847363	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	103	351	0	ENST00000261769.5:c.1286del	p.Pro429GlnfsTer2	p.P429Qfs*2	ENST00000261769	NM_004360.3	429	Cca/ca	9/16	0.499263897710777	1	FACETS	0.862	0.779	0.949	0.862	0.779	0.949	CLONAL	1	TRUE	0	0.499263897710777	1		351	359	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872191	45872191	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	143	586	0	ENST00000391945.4:c.243G>T	p.Glu81Asp	p.E81D	ENST00000391945	NM_000400.3	81	gaG/gaT	4/23	0.206232719876464	4	FACETS	0.723	0.659	0.79	0.361	0.329	0.395	INDETERMINATE	1	TRUE	2	0.810574974737304	4		586	884	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578467	7578467	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	367	650	2	ENST00000269305.4:c.463A>C	p.Thr155Pro	p.T155P	ENST00000269305	NM_001126112.2	155	Acc/Ccc	5/11	0.778057910843565	1	FACETS	0.979	0.941	1	0.979	0.941	1	CLONAL	1	TRUE	0	0.778057910843565	1		652	589	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947603	48947603	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0028302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	217	478	2	ENST00000267163.4:c.1190C>G	p.Ser397Ter	p.S397*	ENST00000267163	NM_000321.2	397	tCa/tGa	12/27	0.659818134589274	1	FACETS	0.902	0.854	0.949	0.902	0.854	0.949	CLONAL	1	TRUE	0	0.778057910843565	1		480	378	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129655	11129655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	364	569	0	ENST00000358026.2:c.2461G>A	p.Glu821Lys	p.E821K	ENST00000358026	NM_001128849.1	821	Gag/Aag	17/36	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.778057910843565	2		569	893	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717650	89717650	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs1057520900	NA	P-0028302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	281	551	0	ENST00000371953.3:c.675T>G	p.Tyr225Ter	p.Y225*	ENST00000371953	NM_000314.4	225	taT/taG	7/9	0.774862527419638	1	FACETS	0.904	0.862	0.946	0.904	0.862	0.946	CLONAL	1	TRUE	0	0.778057910843565	1		551	488	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117755	70117755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	358	624	1	ENST00000245479.2:c.223G>A	p.Glu75Lys	p.E75K	ENST00000245479	NM_000346.3	75	Gag/Aag	1/3	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.778057910843565	2		625	913	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005319	29005319	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	276	574	1	ENST00000282397.4:c.942G>T	p.Arg314Ser	p.R314S	ENST00000282397	NM_002019.4	314	agG/agT	7/30	0.778057910843565	1	FACETS	0.968	0.924	1	0.968	0.924	1	CLONAL	1	TRUE	0	0.778057910843565	1		575	448	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347584	89347584	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1048947362	NA	P-0028302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	288	568	0	ENST00000301030.4:c.5366G>T	p.Arg1789Leu	p.R1789L	ENST00000301030	NM_001256183.1	1789	cGc/cTc	9/13	1	2	FACETS	0.927	0.875	0.979	0.927	0.875	0.979	CLONAL	1	TRUE	1	0.778057910843565	2		568	799	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279998	18279998	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	317	496	0	ENST00000222254.8:c.2081T>G	p.Leu694Arg	p.L694R	ENST00000222254	NM_005027.3	694	cTg/cGg	16/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.778057910843565	2		496	754	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224259	36224259	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	273	480	2	ENST00000222270.7:c.6809G>T	p.Ser2270Ile	p.S2270I	ENST00000222270	NM_014727.1	2270	aGc/aTc	28/37	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.778057910843565	2		482	687	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416484	29416484	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	358	648	0	ENST00000389048.3:c.4469A>C	p.His1490Pro	p.H1490P	ENST00000389048	NM_004304.4	1490	cAc/cCc	29/29	NA	2	FACETS	0.926	0.88	0.973			1	INDETERMINATE	1	TRUE	NA	0.778057910843565	2		648	994	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293949	1293949	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	383	772	0	ENST00000310581.5:c.1052G>T	p.Arg351Met	p.R351M	ENST00000310581	NM_198253.2	351	aGg/aTg	2/16	NA	2	FACETS	0.989	0.943	1			1	INDETERMINATE	1	TRUE	NA	0.778057910843565	2		772	995	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704548	117704548	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	230	458	1	ENST00000368508.3:c.2428G>T	p.Glu810Ter	p.E810*	ENST00000368508	NM_002944.2	810	Gaa/Taa	16/43	1	2	FACETS	0.892	0.836	0.949	0.892	0.836	0.949	CLONAL	1	TRUE	1	0.778057910843565	2		459	663	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945106	151945106	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	49	380	0	ENST00000262189.6:c.2413A>G	p.Ser805Gly	p.S805G	ENST00000262189	NM_170606.2	805	Agt/Ggt	14/59	1	2	FACETS	0.328	0.278	0.382	0.328	0.278	0.382	SUBCLONAL	1	TRUE	1	0.778057910843565	2		380	384	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0028303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	147	297	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.98	0.9	1	0.98	0.9	1	CLONAL	1	TRUE	1	0.544234774888252	2		297	551	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0028303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	111	398	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.536062128643335	1	FACETS	0.928	0.845	1	0.928	0.845	1	CLONAL	1	TRUE	0	0.544234774888252	1		404	320	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0028303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	79	255	0	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	1	2	FACETS	0.893	0.793	0.999	0.893	0.793	0.999	CLONAL	1	TRUE	1	0.544234774888252	2		255	325	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720753	89720768	+	frameshift_variant	Frame_Shift_Del	DEL	AGCATTTGCAGTATAG	AGCATTTGCAGTATAG	-	novel	NA	P-0028303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	10	182	0	ENST00000371953.3:c.907_922del	p.Ile303ValfsTer9	p.I303Vfs*9	ENST00000371953	NM_000314.4	302	AGCATTTGCAGTATAGag/ag	8/9	0.536062128643335	1	FACETS	0.291	0.199	0.404	0.291	0.199	0.404	SUBCLONAL	1	TRUE	0	0.544234774888252	1		182	92	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465398	99465398	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	26	464	0	ENST00000268035.6:c.2223del	p.Asp741GlufsTer98	p.D741Efs*98	ENST00000268035	NM_000875.3	741	gaT/ga	11/21	1	2	FACETS	0.218	0.172	0.27	0.218	0.172	0.27	SUBCLONAL	1	TRUE	1	0.544234774888252	2		464	439	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414947	56414947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	134	575	0	ENST00000348428.3:c.2348C>T	p.Pro783Leu	p.P783L	ENST00000348428	NM_006785.3	783	cCa/cTa	17/17	0.536062128643335	1	FACETS	0.739	0.676	0.805	0.739	0.676	0.805	SUBCLONAL	1	TRUE	0	0.544234774888252	1		575	485	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519406	137519406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762165619	NA	P-0028303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	73	247	0	ENST00000367739.4:c.1232G>A	p.Gly411Asp	p.G411D	ENST00000367739	NM_000416.2	411	gGt/gAt	7/7	1	2	FACETS	0.994	0.879	1	0.994	0.879	1	CLONAL	1	TRUE	1	0.544234774888252	2		247	270	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0028305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	116	246	0	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	0.589662755279441	1	FACETS	0.788	0.718	0.86	0.788	0.718	0.86	SUBCLONAL	1	TRUE	0	0.589662755279441	1		246	352	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68301903	68301903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1231137726	NA	P-0028305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	140	476	0	ENST00000487270.1:c.305C>T	p.Ser102Phe	p.S102F	ENST00000487270	NM_133509.3	102	tCc/tTc	4/11	NA	2	FACETS	0.558	0.508	0.61			1	INDETERMINATE	1	TRUE	NA	0.589662755279441	2		476	851	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579406	7579409	+	frameshift_variant	Frame_Shift_Del	DEL	GACA	GACA	-	novel	NA	P-0028305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	346	552	1	ENST00000269305.4:c.278_281del	p.Leu93HisfsTer29	p.L93Hfs*29	ENST00000269305	NM_001126112.2	93	cTGTCa/ca	4/11	0.589662755279441	1	FACETS	0.936	0.89	0.983	0.936	0.89	0.983	CLONAL	1	TRUE	0	0.589662755279441	1		553	884	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410217	63410217	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs775915295	NA	P-0028305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	316	524	0	ENST00000330258.3:c.2950T>C	p.Ser984Pro	p.S984P	ENST00000330258	NM_152424.3	984	Tcc/Ccc	2/2	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.589662755279441	2		524	976	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0028306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	11	182	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.434458305247958	1	FACETS	0.195	0.135	0.27	0.195	0.135	0.27	SUBCLONAL	1	TRUE	0	0.501784184708506	1		182	168	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197362	106197362	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	78	364	0	ENST00000380013.4:c.5695C>G	p.Leu1899Val	p.L1899V	ENST00000380013	NM_001127208.2	1899	Ctc/Gtc	11/11	1	2	FACETS	0.49	0.431	0.554	0.49	0.431	0.554	SUBCLONAL	1	TRUE	1	0.501784184708506	2		364	634	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798882	42798882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	218	618	0	ENST00000575354.2:c.4454C>T	p.Pro1485Leu	p.P1485L	ENST00000575354	NM_015125.3	1485	cCg/cTg	19/20	1	2	FACETS	0.972	0.905	1	0.972	0.905	1	CLONAL	1	TRUE	1	0.501784184708506	2		618	894	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911618	134911618	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	179	459	0	ENST00000398015.3:c.2083A>T	p.Ile695Phe	p.I695F	ENST00000398015	NM_004441.4	695	Atc/Ttc	11/16	0.190636055583263	3	FACETS	1	0.974	1	0.563	0.519	0.608	INDETERMINATE	1	TRUE	1	0.501784184708506	3		459	793	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921374	178921374	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	93	649	0	ENST00000263967.3:c.856A>C	p.Met286Leu	p.M286L	ENST00000263967	NM_006218.2	286	Atg/Ctg	5/21	0.190636055583263	3	FACETS	0.513	0.456	0.575	0.257	0.228	0.288	INDETERMINATE	1	TRUE	1	0.501784184708506	3		649	903	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248166	110248166	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	53	435	0	ENST00000374672.4:c.1306A>G	p.Lys436Glu	p.K436E	ENST00000374672	NM_004235.4	436	Aaa/Gaa	5/5	1	2	FACETS	0.311	0.264	0.362	0.311	0.264	0.362	SUBCLONAL	1	TRUE	1	0.501784184708506	2		435	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0028308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	482	345	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.737727145594794	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.737727145594794	2		345	626	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052632	42052632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779811318	NA	P-0028308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	242	506	0	ENST00000219905.7:c.7303C>T	p.Arg2435Trp	p.R2435W	ENST00000219905	NM_001164273.1	2435	Cgg/Tgg	20/24	NA	2	FACETS	0.994	0.934	1			1	INDETERMINATE	1	TRUE	NA	0.737727145594794	2		506	660	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795279	42795280	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0028308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	191	555	2	ENST00000575354.2:c.2359_2360delinsCT	p.Gly787Leu	p.G787L	ENST00000575354	NM_015125.3	787	GGt/CTt	10/20	0.737727145594794	3	FACETS	0.949	0.88	1	0.474	0.44	0.51	CLONAL	1	TRUE	1	0.737727145594794	3		557	747	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165977	47165977	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	270	540	0	ENST00000409792.3:c.149C>T	p.Ala50Val	p.A50V	ENST00000409792	NM_014159.6	50	gCt/gTt	3/21	0.34440403090122	5	FACETS	1	0.993	1	0.488	0.458	0.519	INDETERMINATE	1	TRUE	2	0.737727145594794	5		540	1053	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191373	185191373	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	228	689	0	ENST00000265026.3:c.2254G>C	p.Gly752Arg	p.G752R	ENST00000265026	NM_004721.4	752	Ggg/Cgg	11/14	0.737727145594794	5	FACETS	1	0.955	1	0.345	0.32	0.37	CLONAL	1	TRUE	2	0.737727145594794	5		689	1259	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55229252	55229266	+	inframe_deletion	In_Frame_Del	DEL	CCAGGGACTGCGTCT	CCAGGGACTGCGTCT	-	novel	NA	P-0028308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	231	546	0	ENST00000275493.2:c.1560_1574del	p.Arg521_Ser525del	p.R521_S525del	ENST00000275493	NM_005228.3	520	cCCAGGGACTGCGTCTct/cct	13/28	0.696211133211545	4	FACETS	1	0.979	1	0.56	0.523	0.599	CLONAL	1	TRUE	2	0.737727145594794	4		546	971	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191480	10191480	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	128	438	0	ENST00000256474.2:c.473T>G	p.Leu158Arg	p.L158R	ENST00000256474	NM_000551.3	158	cTg/cGg	3/3	0.355072199976845	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.356244812432383	1		438	580	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582198	52582199	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0028313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	95	389	0	ENST00000394830.3:c.4629_4630del	p.His1544LeufsTer51	p.H1544Lfs*51	ENST00000394830	NM_018313.4	1543	tcTCac/tcac	30/30	0.355072199976845	1	FACETS	0.773	0.69	0.861	0.773	0.69	0.861	SUBCLONAL	1	TRUE	0	0.356244812432383	1		389	567	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913343	NA	P-0028314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	115	801	0	ENST00000269305.4:c.817C>A	p.Arg273Ser	p.R273S	ENST00000269305	NM_001126112.2	273	Cgt/Agt	8/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.31	2		801	696	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477837	140477851	+	inframe_deletion	In_Frame_Del	DEL	TAGGTGCTGTCACAT	TAGGTGCTGTCACAT	-	novel	NA	P-0028314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	89	674	0	ENST00000288602.6:c.1457_1471del	p.Asn486_Pro490del	p.N486_P490del	ENST00000288602	NM_004333.4	486	aATGTGACAGCACCTAca/aca	12/18	1	2	FACETS	0.656	0.581	0.737	0.656	0.581	0.737	SUBCLONAL	1	TRUE	1	0.31	2		674	875	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15826386	15826386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769746691	NA	P-0028314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	53	544	0	ENST00000307771.7:c.430G>A	p.Glu144Lys	p.E144K	ENST00000307771	NM_005089.3	144	Gaa/Aaa	6/11	0.295541029255907	1	FACETS	0.385	0.328	0.449	0.385	0.328	0.449	SUBCLONAL	1	TRUE	0	0.31	1		544	750	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981174	201981174	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	67	741	0	ENST00000359651.3:c.253del	p.Tyr85ThrfsTer70	p.Y85Tfs*70	ENST00000359651		85	Tac/ac	2/8	1	2	FACETS	0.625	0.542	0.714	0.625	0.542	0.714	SUBCLONAL	1	TRUE	1	0.31	2		741	692	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426387	49426388	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0028314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	107	861	2	ENST00000301067.7:c.12100dup	p.Ser4034PhefsTer6	p.S4034Ffs*6	ENST00000301067	NM_003482.3	4034	tct/tTct	39/54	1	2	FACETS	0.823	0.737	0.913	0.823	0.737	0.913	CLONAL	1	TRUE	1	0.31	2		863	839	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608466	28608466	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	113	664	0	ENST00000241453.7:c.1676C>A	p.Thr559Asn	p.T559N	ENST00000241453	NM_004119.2	559	aCc/aAc	13/24	NA	2	FACETS	0.871	0.783	0.964			1	INDETERMINATE	1	TRUE	NA	0.31	2		664	837	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971097	21971098	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGGGCAG	novel	NA	P-0028314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	36	249	0	ENST00000304494.5:c.254_260dup	p.Glu88CysfsTer34	p.E88Cfs*34	ENST00000304494	NM_000077.4	87	cgg/cgCTGCCCGg	2/3	1	2	FACETS	0.74	0.61	0.884	0.74	0.61	0.884	SUBCLONAL	1	TRUE	1	0.31	2		249	314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0028315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	403	681	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.427371845789075	2	FACETS	0.899	0.859	0.941	0.899	0.859	0.941	CLONAL	2	TRUE	0	0.454891731423475	2		681	985	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175796	176175796	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	160	466	0	ENST00000367669.3:c.319G>T	p.Gly107Cys	p.G107C	ENST00000367669	NM_022457.5	107	Ggc/Tgc	1/20	0.454891731423475	4	FACETS	0.996	0.912	1	0.332	0.304	0.361	CLONAL	1	TRUE	1	0.454891731423475	4		466	1028	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432296	432296	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	269	605	2	ENST00000399788.2:c.2227del	p.Val743SerfsTer18	p.V743Sfs*18	ENST00000399788	NM_001042603.1	743	Gtc/tc	16/28	0.251222699552503	5	FACETS	0.851	0.802	0.902			1	INDETERMINATE	3	TRUE	NA	0.454891731423475	5		607	779	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424972	49424973	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0028315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	352	621	0	ENST00000301067.7:c.13515_13516insAC	p.Pro4506ThrfsTer14	p.P4506Tfs*14	ENST00000301067	NM_003482.3	4505	-/AC	39/54	NA	2	FACETS	0.949	0.904	0.995			1	INDETERMINATE	2	TRUE	NA	0.454891731423475	2		621	815	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343492	343492	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	322	650	0	ENST00000262320.3:c.2182C>T	p.Gln728Ter	p.Q728*	ENST00000262320	NM_003502.3	728	Cag/Tag	8/11	0.427371845789075	2	FACETS	0.873	0.828	0.918	0.873	0.828	0.918	CLONAL	2	TRUE	0	0.454891731423475	2		650	811	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99203974	99203993	+	frameshift_variant	Frame_Shift_Del	DEL	TTGGAAGTCGCAAATATGCA	TTGGAAGTCGCAAATATGCA	-	novel	NA	P-0028315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	104	519	0	ENST00000074304.5:c.2839_2858del	p.Gly947Ter	p.G947*	ENST00000074304	NM_001134224.1	946	gTTGGAAGTCGCAAATATGCA/g	26/26	0.238230574312446	3	FACETS	0.833	0.746	0.924	0.416	0.373	0.462	INDETERMINATE	1	TRUE	1	0.454891731423475	3		519	674	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098809	178098809	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	508	714	0	ENST00000397062.3:c.236A>C	p.Glu79Ala	p.E79A	ENST00000397062	NM_006164.4	79	gAg/gCg	2/5	0.454891731423475	3	FACETS	0.994	0.959	1	0.994	0.959	1	CLONAL	3	TRUE	0	0.454891731423475	3		714	919	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020882	26020882	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0028315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	203	369	0	ENST00000357647.3:c.165T>G	p.Tyr55Ter	p.Y55*	ENST00000357647	NM_003529.2	55	taT/taG	1/1	0.286823557123816	4	FACETS	0.885	0.823	0.948	0.885	0.823	0.948	CLONAL	2	TRUE	2	0.454891731423475	4		369	734	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056440	26056440	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773914281	NA	P-0028315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	69	263	0	ENST00000343677.2:c.217G>A	p.Val73Met	p.V73M	ENST00000343677	NM_005319.3	73	Gtg/Atg	1/1	0.286823557123816	4	FACETS	0.8	0.697	0.91	0.4	0.348	0.455	CLONAL	1	TRUE	2	0.454891731423475	4		263	552	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324085	31324085	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	177	287	1	ENST00000412585.2:c.478G>T	p.Ala160Ser	p.A160S	ENST00000412585	NM_005514.6	160	Gcg/Tcg	3/8	0.286823557123816	4	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	2	0.454891731423475	4		288	550	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239083	98239083	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	316	639	0	ENST00000331920.6:c.1560C>G	p.His520Gln	p.H520Q	ENST00000331920	NM_000264.3	520	caC/caG	11/24	0.450362812177876	2	FACETS	0.97	0.922	1	0.97	0.922	1	CLONAL	2	TRUE	0	0.454891731423475	2		639	716	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0028316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	112	250	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.433420186726691	2		250	429	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0028316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	571	656	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.360825085275217	3	FACETS	0.896	0.863	0.928			1	CLONAL	3	TRUE	NA	0.433420186726691	3		656	1193	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1023835002	NA	P-0028316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	95	368	0	ENST00000558401.1:c.1A>G	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Gtg	1/4	0.433420186726691	1	FACETS	0.701	0.626	0.779	0.701	0.626	0.779	SUBCLONAL	1	TRUE	0	0.433420186726691	1		368	490	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445178	49445178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771291128	NA	P-0028316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	211	603	1	ENST00000301067.7:c.2288C>T	p.Pro763Leu	p.P763L	ENST00000301067	NM_003482.3	763	cCg/cTg	10/54	1	2	FACETS	0.911	0.845	0.979	0.911	0.845	0.979	CLONAL	1	TRUE	1	0.433420186726691	2		604	1069	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78599539	78599539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	195	560	0	ENST00000306801.3:c.211G>A	p.Asp71Asn	p.D71N	ENST00000306801	NM_020761.2	71	Gac/Aac	2/34	1	2	FACETS	0.838	0.775	0.903	0.838	0.775	0.903	CLONAL	1	TRUE	1	0.433420186726691	2		560	1074	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085798	16085798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	156	446	0	ENST00000281043.3:c.974C>T	p.Pro325Leu	p.P325L	ENST00000281043	NM_005378.4	325	cCc/cTc	3/3	0.432515993118113	3	FACETS	0.871	0.797	0.949	0.436	0.398	0.475	CLONAL	1	TRUE	1	0.433420186726691	3		446	1005	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969117	93969117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	117	352	0	ENST00000369303.4:c.1879G>A	p.Glu627Lys	p.E627K	ENST00000369303	NM_004440.3	627	Gag/Aag	10/17	1	2	FACETS	0.765	0.69	0.843	0.765	0.69	0.843	SUBCLONAL	1	TRUE	1	0.433420186726691	2		352	706	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0028317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	96	298	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.24	2		298	714	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023549	27023619	+	frameshift_variant	Frame_Shift_Del	DEL	CGCAGCGCCTACCCCCCGCCCGCCCCGGCCTACGCGCTGAGCTCCCCGAGAGGTGGCACTCCGGGCTCCGG	CGCAGCGCCTACCCCCCGCCCGCCCCGGCCTACGCGCTGAGCTCCCCGAGAGGTGGCACTCCGGGCTCCGG	-	novel	NA	P-0028317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	76	476	1	ENST00000324856.7:c.658_728del	p.Ser220GlyfsTer156	p.S220Gfs*156	ENST00000324856	NM_006015.4	219	CGCAGCGCCTACCCCCCGCCCGCCCCGGCCTACGCGCTGAGCTCCCCGAGAGGTGGCACTCCGGGCTCCGGc/c	1/20	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.24	2		477	570	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842754	68842758	+	splice_region_variant,intron_variant	Splice_Region	DEL	AAGTA	AAGTA	-	novel	NA	P-0028317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	61	494	0	ENST00000261769.5:c.687+3_687+7del		p.X229_splice	ENST00000261769	NM_004360.3	229			0.237647501476267	1	FACETS	0.859	0.741	0.986	0.859	0.741	0.986	CLONAL	1	TRUE	0	0.24	1		494	521	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991715	25991715	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs768626747	NA	P-0028317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	79	488	0	ENST00000435504.4:c.527A>G	p.Lys176Arg	p.K176R	ENST00000435504		176	aAg/aGg	7/13	1	2	FACETS	0.888	0.781	1	0.888	0.781	1	CLONAL	1	TRUE	1	0.24	2		488	741	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405977	49405977	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	89	629	0	ENST00000418115.1:c.161A>C	p.Glu54Ala	p.E54A	ENST00000418115	NM_001664.2	54	gAg/gCg	3/5	1	2	FACETS	0.876	0.775	0.983	0.876	0.775	0.983	CLONAL	1	TRUE	1	0.24	2		629	847	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499420	89499420	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	89	534	0	ENST00000336596.2:c.2590G>T	p.Asp864Tyr	p.D864Y	ENST00000336596	NM_005233.5	864	Gac/Tac	15/17	1	2	FACETS	0.902	0.799	1	0.902	0.799	1	CLONAL	1	TRUE	1	0.24	2		534	822	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349948	70349948	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	124	771	0	ENST00000374080.3:c.3931G>T	p.Val1311Leu	p.V1311L	ENST00000374080		1311	Gtg/Ttg	28/45	0.237647501476267	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.24	1		771	880	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0028318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	631	681	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.71350255866792	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.71350255866792	2		681	832	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519895	NA	P-0028318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	355	570	0	ENST00000281708.4:c.1394G>T	p.Arg465Leu	p.R465L	ENST00000281708	NM_033632.3	465	cGt/cTt	9/12	0.71350255866792	4	FACETS	0.924	0.886	0.962	0.924	0.886	0.962	CLONAL	3	TRUE	1	0.71350255866792	4		570	615	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070880	30070880	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315504	NA	P-0028318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	571	690	0	ENST00000338641.4:c.1396C>T	p.Arg466Ter	p.R466*	ENST00000338641	NM_000268.3	466	Cga/Tga	13/16	0.71350255866792	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.71350255866792	2		690	796	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	59	210	0				ENST00000310581	NM_198253.2	-/1132			0.615325324105794	3	FACETS	0.925	0.804	1	0.463	0.402	0.528	CLONAL	1	TRUE	1	0.615325324105794	3		210	271	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591085	67591085	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	193	358	0	ENST00000274335.5:c.1678G>C	p.Asp560His	p.D560H	ENST00000274335		560	Gac/Cac	12/15	0.386863671875836	5	FACETS	0.967	0.906	1	0.967	0.906	1	CLONAL	3	TRUE	2	0.615325324105794	5		358	416	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103261	119103262	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAGATATGAGGGGAAGATGGAGACACTTGGAGAAAATGAGTATTTTA	novel	NA	P-0028319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	52	559	0	ENST00000264033.4:c.300_346dup	p.Arg116LysfsTer23	p.R116Kfs*23	ENST00000264033	NM_005188.3	100	tca/tcAAGATATGAGGGGAAGATGGAGACACTTGGAGAAAATGAGTATTTTAa	2/16	1	2	FACETS	0.373	0.318	0.433	0.373	0.318	0.433	SUBCLONAL	1	TRUE	1	0.615325324105794	2		559	453	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0028320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	617	497	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.55815319704937	3	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.55815319704937	3		497	1337	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0028320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	167	324	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.553341310496005	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.55815319704937	1		324	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0028320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	646	633	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	0.503324226234302	3	FACETS	0.944	0.917	0.972	0.944	0.917	0.972	CLONAL	3	TRUE	0	0.55815319704937	3		633	1045	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968250	134968250	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs765393605	NA	P-0028320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	100	650	1	ENST00000398015.3:c.2763C>A	p.Ser921Arg	p.S921R	ENST00000398015	NM_004441.4	921	agC/agA	15/16	NA	2	FACETS	0.436	0.389	0.487			1	INDETERMINATE	1	TRUE	NA	0.55815319704937	2		651	821	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572709	141572709	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	418	499	0	ENST00000220592.5:c.361G>T	p.Gly121Ter	p.G121*	ENST00000220592	NM_012154.3	121	Gga/Tga	4/19	0.501774149937513	5	FACETS	0.855	0.816	0.894	0.855	0.816	0.894	CLONAL	3	TRUE	2	0.55815319704937	5		499	1073	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65323350	65323350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	221	556	0	ENST00000342505.4:c.1447G>A	p.Glu483Lys	p.E483K	ENST00000342505	NM_002227.2	483	Gag/Aag	10/25	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.55815319704937	2		556	741	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468328	120468328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	272	567	0	ENST00000256646.2:c.4111C>T	p.Pro1371Ser	p.P1371S	ENST00000256646	NM_024408.3	1371	Ccc/Tcc	25/34	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.55815319704937	2		567	822	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741830	17741830	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1446933595	NA	P-0028320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	100	213	0	ENST00000250003.3:c.501G>T	p.Gln167His	p.Q167H	ENST00000250003	NM_002478.4	167	caG/caT	1/3	0.550663486629869	2	FACETS	1	0.976	1	0.624	0.565	0.685	CLONAL	1	TRUE	0	0.55815319704937	2		213	287	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198983	67198983	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	108	426	0	ENST00000312629.5:c.454A>T	p.Ser152Cys	p.S152C	ENST00000312629	NM_003952.2	152	Agt/Tgt	5/15	0.55815319704937	3	FACETS	0.805	0.724	0.89	0.402	0.362	0.445	CLONAL	1	TRUE	1	0.55815319704937	3		426	615	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307630	118307631	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0028320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	142	418	0	ENST00000534358.1:c.406_407del	p.Ser136ArgfsTer10	p.S136Rfs*10	ENST00000534358	NM_005933.3	135	GAg/g	1/36	0.55815319704937	3	FACETS	0.961	0.878	1	0.481	0.439	0.524	CLONAL	1	TRUE	1	0.55815319704937	3		418	677	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034911	42034911	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	536	552	0	ENST00000219905.7:c.4753G>T	p.Glu1585Ter	p.E1585*	ENST00000219905	NM_001164273.1	1585	Gag/Tag	15/24	0.503324226234302	3	FACETS	0.938	0.908	0.968	0.938	0.908	0.968	CLONAL	3	TRUE	0	0.55815319704937	3		552	873	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2645846	2645846	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753410336	NA	P-0028320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	57	568	0	ENST00000342085.4:c.1396C>T	p.Arg466Trp	p.R466W	ENST00000342085	NM_002613.4	466	Cgg/Tgg	12/14	0.32243744532334	5	FACETS	0.341	0.291	0.395	0.114	0.097	0.132	INDETERMINATE	1	TRUE	2	0.55815319704937	5		568	1102	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222242	2222243	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0028320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	517	764	0	ENST00000398665.3:c.3077dup	p.Asp1027ArgfsTer12	p.D1027Rfs*12	ENST00000398665	NM_032482.2	1025	aag/aaGg	24/28	0.550663486629869	2	FACETS	0.909	0.875	0.943	0.909	0.875	0.943	CLONAL	2	TRUE	0	0.55815319704937	2		764	1019	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023558	31023558	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	212	572	0	ENST00000375687.4:c.3043G>A	p.Glu1015Lys	p.E1015K	ENST00000375687	NM_015338.5	1015	Gag/Aag	13/13	0.497171285354594	3	FACETS	1	0.953	1			1	CLONAL	1	TRUE	NA	0.55815319704937	3		572	941	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675418	30675418	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	147	519	0	ENST00000376406.3:c.2938A>G	p.Thr980Ala	p.T980A	ENST00000376406	NM_014641.2	980	Acc/Gcc	8/15	0.551453861462218	4	FACETS	0.847	0.773	0.925	0.282	0.257	0.309	CLONAL	1	TRUE	1	0.55815319704937	4		519	969	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323172	31323172	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	78	657	0	ENST00000412585.2:c.817G>C	p.Val273Leu	p.V273L	ENST00000412585	NM_005514.6	273	Gtg/Ctg	4/8	0.551453861462218	4	FACETS	0.361	0.316	0.41	0.12	0.105	0.137	SUBCLONAL	1	TRUE	1	0.55815319704937	4		657	1206	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168682	32168682	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1162	223	699	0	ENST00000375023.3:c.4241C>A	p.Ala1414Glu	p.A1414E	ENST00000375023	NM_004557.3	1414	gCg/gAg	23/30	0.551453861462218	4	FACETS	0.899	0.835	0.966	0.3	0.278	0.322	CLONAL	1	TRUE	1	0.55815319704937	4		699	1385	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206887	162206887	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	227	579	0	ENST00000366898.1:c.788G>T	p.Cys263Phe	p.C263F	ENST00000366898	NM_004562.2	263	tGt/tTt	7/12	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.55815319704937	2		579	811	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0028321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	351	606	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.45745200348112	2	FACETS	0.955	0.91	1	0.955	0.91	1	CLONAL	2	TRUE	0	0.458814489478777	2		608	801	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0028321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	219	518	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.235443553276452	5	FACETS	1	0.981	1	0.751	0.702	0.802	INDETERMINATE	2	TRUE	2	0.458814489478777	5		518	715	SUCCESS
AR	367	MSKCC	GRCh37	X	66942700	66942700	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs200801099	NA	P-0028321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	129	668	0	ENST00000374690.3:c.2481C>A	p.Phe827Leu	p.F827L	ENST00000374690	NM_000044.3	827	ttC/ttA	7/8	1	2	FACETS	0.684	0.62	0.751	0.684	0.62	0.751	SUBCLONAL	1	TRUE	1	0.458814489478777	2		668	822	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879904	44879904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs912069418	NA	P-0028321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	216	636	0	ENST00000377967.4:c.493C>T	p.Arg165Ter	p.R165*	ENST00000377967	NM_021140.2	165	Cga/Tga	6/29	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.458814489478777	2		636	730	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573127	64573127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs566593066	NA	P-0028321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	190	393	1	ENST00000312049.6:c.1165C>T	p.Arg389Trp	p.R389W	ENST00000312049	NM_130799.2	389	Cgg/Tgg	8/10	0.437082959319606	3	FACETS	0.992	0.925	1	0.992	0.925	1	CLONAL	2	TRUE	1	0.458814489478777	3		394	513	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0028322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	104	281	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.14756085835254	5	FACETS	1	0.967	1	0.779	0.702	0.859	INDETERMINATE	2	TRUE	2	0.311823850106244	5		281	419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0028322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	292	442	0	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	0.304762875424067	2	FACETS	0.97	0.915	1	0.97	0.915	1	CLONAL	2	TRUE	0	0.311823850106244	2		442	965	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43806149	43806149	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1468100591	NA	P-0028322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	133	632	0	ENST00000372470.3:c.945C>G	p.Phe315Leu	p.F315L	ENST00000372470	NM_005373.2	315	ttC/ttG	6/12	0.311823850106244	3	FACETS	1	0.973	1	0.594	0.539	0.651	CLONAL	1	TRUE	1	0.311823850106244	3		632	830	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872241	45872242	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CGGATATGCCTGCCGATAACAAGCGGACTCAGTCCCTGTCCCGCCC	novel	NA	P-0028322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	74	798	0	ENST00000391945.4:c.184-37_192dup	p.Leu65GlyfsTer6	p.L65Gfs*6	ENST00000391945	NM_000400.3	64	-/GGGCGGGACAGGGACTGAGTCCGCTTGTTATCGGCAGGCATATCCG	4/23	0.311823850106244	3	FACETS	0.492	0.43	0.561	0.246	0.215	0.281	SUBCLONAL	1	TRUE	1	0.311823850106244	3		798	1114	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0028323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	8	529	1	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	0.6642756129889	4	FACETS	0.094	0.06	0.138	0.031	0.02	0.046	SUBCLONAL	1	TRUE	1	0.800842847817492	4		530	384	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0028323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	570	493	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.624352978087744	6	FACETS	1	0.977	1			1	CLONAL	3	TRUE	NA	0.800842847817492	6		493	1212	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577528	7577536	+	frameshift_variant	Frame_Shift_Del	DEL	GATGGGCCT	GATGGGCCT	AC	novel	NA	P-0028323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	449	714	4	ENST00000269305.4:c.745_753delinsGT	p.Arg249ValfsTer94	p.R249Vfs*94	ENST00000269305	NM_001126112.2	249	AGGCCCATC/GT	7/11	0.738146288058281	2	FACETS	0.893	0.865	0.919	0.893	0.865	0.919	CLONAL	2	TRUE	0	0.800842847817492	2		718	628	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489849	40489849	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	455	616	0	ENST00000264657.5:c.577C>T	p.Gln193Ter	p.Q193*	ENST00000264657	NM_139276.2	193	Cag/Tag	7/24	0.663456423013808	3	FACETS	0.851	0.817	0.885	0.851	0.817	0.885	CLONAL	2	TRUE	1	0.800842847817492	3		616	935	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641747	12641747	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	513	528	0	ENST00000251849.4:c.894C>A	p.Asn298Lys	p.N298K	ENST00000251849	NM_002880.3	298	aaC/aaA	9/17	0.554149367208994	5	FACETS	0.877	0.844	0.91	0.877	0.844	0.91	CLONAL	3	TRUE	2	0.800842847817492	5		528	1072	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721264	176721264	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1464788039	NA	P-0028323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	168	450	0	ENST00000439151.2:c.6895C>G	p.Leu2299Val	p.L2299V	ENST00000439151	NM_022455.4	2299	Ctc/Gtc	23/23	0.707287914318505	4	FACETS	0.851	0.782	0.922	0.213	0.195	0.231	CLONAL	1	TRUE	0	0.800842847817492	4		450	888	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412623	139412624	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0028323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	571	685	0	ENST00000277541.6:c.1220dup	p.Ala408GlyfsTer8	p.A408Gfs*8	ENST00000277541	NM_017617.3	407	ccg/ccCg	7/34	0.698755944998513	3	FACETS	1	0.997	1	0.831	0.808	0.853	CLONAL	2	TRUE	0	0.800842847817492	3		685	801	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813051	76813052	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACAACTC	novel	NA	P-0028325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	136	784	0	ENST00000373344.5:c.6563_6569dup	p.Asp2191SerfsTer3	p.D2191Sfs*3	ENST00000373344	NM_000489.3	2190	gtt/gtGAGTTGTt	30/35	0.673806021213131	1	FACETS	0.819	0.755	0.883	0.819	0.755	0.883	CLONAL	1	TRUE	0	0.673806021213131	1		784	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764146326	NA	P-0028326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	548	579	0	ENST00000269305.4:c.841G>T	p.Asp281Tyr	p.D281Y	ENST00000269305	NM_001126112.2	281	Gac/Tac	8/11	0.541208351440189	3	FACETS	0.896	0.873	0.918	1	0.997	1	CLONAL	4	TRUE	0	0.541208351440189	3		579	718	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161363	185161363	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	293	485	0	ENST00000265026.3:c.790G>C	p.Ala264Pro	p.A264P	ENST00000265026	NM_004721.4	264	Gca/Cca	4/14	0.541208351440189	5	FACETS	1	0.979	1	0.719	0.678	0.76	CLONAL	2	TRUE	2	0.541208351440189	5		485	910	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156515	55156515	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	44	465	0	ENST00000257290.5:c.2916T>G	p.Ser972Arg	p.S972R	ENST00000257290	NM_006206.4	972	agT/agG	22/23	0.541208351440189	3	FACETS	0.278	0.232	0.329	0.139	0.116	0.165	SUBCLONAL	1	TRUE	1	0.541208351440189	3		465	743	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221889	98221889	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	31	439	0	ENST00000331920.6:c.2880G>T	p.Arg960Ser	p.R960S	ENST00000331920	NM_000264.3	960	agG/agT	17/24	1	2	FACETS	0.277	0.223	0.337	0.277	0.223	0.337	SUBCLONAL	1	TRUE	1	0.541208351440189	2		439	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578525	7578525	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519976	NA	P-0028327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	353	617	0	ENST00000269305.4:c.405C>G	p.Cys135Trp	p.C135W	ENST00000269305	NM_001126112.2	135	tgC/tgG	5/11	0.534137717082255	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.534137717082255	1		617	952	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325206	39325206	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	397	382	0	ENST00000373001.3:c.113C>G	p.Ala38Gly	p.A38G	ENST00000373001	NM_022157.3	38	gCg/gGg	1/7	0.296824323922678	3	FACETS	0.989	0.944	1	0.989	0.944	1	INDETERMINATE	2	TRUE	1	0.534137717082255	3		382	952	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428387	49428425	+	inframe_deletion	In_Frame_Del	DEL	TGGTTCTGCAGATCACTGCTAGGTCCCCCCGAGAGCCTC	TGGTTCTGCAGATCACTGCTAGGTCCCCCCGAGAGCCTC	-	novel	NA	P-0028327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	772	533	0	ENST00000301067.7:c.10380_10418del	p.Gln3460_Asn3472del	p.Q3460_N3472del	ENST00000301067	NM_003482.3	3460	caGAGGCTCTCGGGGGGACCTAGCAGTGATCTGCAGAACCAt/cat	36/54	0.534137717082255	3	FACETS	0.935	0.909	0.961	0.935	0.909	0.961	CLONAL	3	TRUE	0	0.534137717082255	3		533	1306	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954368	48954374	+	frameshift_variant	Frame_Shift_Del	DEL	ACATATA	ACATATA	-	novel	NA	P-0028327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	126	366	0	ENST00000267163.4:c.1489_1495del	p.Thr497AlafsTer20	p.T497Afs*20	ENST00000267163	NM_000321.2	497	ACATATAgc/gc	16/27	0.534137717082255	1	FACETS	0.932	0.853	1	0.932	0.853	1	CLONAL	1	TRUE	0	0.534137717082255	1		366	371	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526475	31526475	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2204	373	731	0	ENST00000344624.3:c.565C>T	p.Pro189Ser	p.P189S	ENST00000344624		189	Cct/Tct	2/33	0.534137717082255	5	FACETS	0.976	0.922	1	0.195	0.184	0.207	CLONAL	1	TRUE	0	0.534137717082255	5		731	2577	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367288	50367288	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	204	382	1	ENST00000331340.3:c.95C>G	p.Pro32Arg	p.P32R	ENST00000331340	NM_006060.4	32	cCg/cGg	3/8	1	2	FACETS	0.897	0.833	0.963	0.897	0.833	0.963	CLONAL	1	TRUE	1	0.534137717082255	2		383	852	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0028329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	449	662	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.833801798733407	2	FACETS	0.972	0.947	0.995	0.972	0.947	0.995	CLONAL	2	TRUE	0	0.83093449724939	2		662	556	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667819	37667819	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	1898	581	1	ENST00000447079.4:c.2704C>T	p.Arg902Ter	p.R902*	ENST00000447079	NM_015083.1	902	Cga/Tga	8/14	0.83093449724939	9	FACETS	0.992	0.985	0.998			1	CLONAL	9	TRUE	NA	0.83093449724939	9		582	2000	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480494	57480494	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	138	422	0	ENST00000371085.3:c.489C>A	p.Tyr163Ter	p.Y163*	ENST00000371085	NM_000516.4	163	taC/taA	6/13	0.622684009085285	4	FACETS	0.926	0.845	1	0.463	0.422	0.505	CLONAL	1	TRUE	2	0.83093449724939	4		422	657	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199842	108199842	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	395	264	0	ENST00000278616.4:c.7184A>G	p.Asp2395Gly	p.D2395G	ENST00000278616	NM_000051.3	2395	gAt/gGt	49/63	0.833801798733407	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	1	0.83093449724939	3		264	563	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650583	18650583	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	162	598	1	ENST00000266497.5:c.2794G>T	p.Val932Phe	p.V932F	ENST00000266497		932	Gtt/Ttt	20/31	0.767210223247206	4	FACETS	0.944	0.868	1	0.472	0.434	0.512	CLONAL	1	TRUE	2	0.83093449724939	4		599	756	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231178	46231178	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	289	473	0	ENST00000334344.6:c.1098G>C	p.Arg366Ser	p.R366S	ENST00000334344	NM_152641.2	366	agG/agC	9/21	0.83093449724939	7	FACETS	1	0.965	1			1	CLONAL	2	TRUE	NA	0.83093449724939	7		473	1035	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592653	28592653	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	399	637	0	ENST00000241453.7:c.2492G>T	p.Gly831Val	p.G831V	ENST00000241453	NM_004119.2	831	gGa/gTa	20/24	0.833801798733407	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.83093449724939	2		637	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0028330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	513	705	1	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.903676249568	1	FACETS	0.994	0.971	1	0.994	0.971	1	CLONAL	1	TRUE	0	0.903676249568	1		706	626	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258067	16258067	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	159	390	0	ENST00000375759.3:c.5332G>C	p.Asp1778His	p.D1778H	ENST00000375759	NM_015001.2	1778	Gac/Cac	11/15	0.541776538239199	1	FACETS	0.3	0.276	0.326	0.3	0.276	0.326	INDETERMINATE	1	TRUE	0	0.903676249568	1		390	642	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0028332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	47	497	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.803	0.676	0.945	0.803	0.676	0.945	CLONAL	1	TRUE	1	0.15	2		497	780	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0028332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	56	608	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	1	2	FACETS	0.796	0.68	0.924	0.796	0.68	0.924	CLONAL	1	TRUE	1	0.15	2		608	938	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544677	65544677	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	75	609	0	ENST00000358664.4:c.249A>T	p.Gln83His	p.Q83H	ENST00000358664	NM_002382.4	83	caA/caT	4/5	1	2	FACETS	0.992	0.867	1	0.992	0.867	1	CLONAL	1	TRUE	1	0.15	2		609	1008	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938554	76938554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	37	443	1	ENST00000373344.5:c.2194G>A	p.Asp732Asn	p.D732N	ENST00000373344	NM_000489.3	732	Gat/Aat	9/35	1	2	FACETS	0.831	0.683	0.996	0.831	0.683	0.996	CLONAL	1	TRUE	1	0.15	2		444	594	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0028334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	57	412	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.815	0.699	0.942	0.815	0.699	0.942	CLONAL	1	TRUE	1	0.239052099764089	2		412	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579463	7579463	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	73	478	0	ENST00000269305.4:c.224del	p.Pro75LeufsTer48	p.P75Lfs*48	ENST00000269305	NM_001126112.2	75	cCt/ct	4/11	0.239052099764089	1	FACETS	0.899	0.787	1	0.899	0.787	1	CLONAL	1	TRUE	0	0.239052099764089	1		478	598	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575209	48575209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767326	NA	P-0028334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	30	253	0	ENST00000342988.3:c.403C>T	p.Arg135Ter	p.R135*	ENST00000342988	NM_005359.5	135	Cga/Tga	3/12	0.239052099764089	1	FACETS	0.662	0.534	0.806	0.662	0.534	0.806	SUBCLONAL	1	TRUE	0	0.239052099764089	1		253	334	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244453	46244454	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0028334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	46	438	0	ENST00000334344.6:c.2552dup	p.Gln852ThrfsTer99	p.Q852Tfs*99	ENST00000334344	NM_152641.2	849	-/C	15/21	1	2	FACETS	0.617	0.518	0.726	0.617	0.518	0.726	SUBCLONAL	1	TRUE	1	0.239052099764089	2		438	624	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942029	44942030	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0028334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	37	165	0	ENST00000377967.4:c.3284dup	p.Trp1096ValfsTer7	p.W1096Vfs*7	ENST00000377967	NM_021140.2	1093	-/A	22/29	1	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.239052099764089	1		165	229	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143033774	143033774	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	62	424	0	ENST00000262992.4:c.2197A>G	p.Ile733Val	p.I733V	ENST00000262992	NM_001101669.1	733	Att/Gtt	20/24	1	2	FACETS	0.95	0.821	1	0.95	0.821	1	CLONAL	1	TRUE	1	0.239052099764089	2		424	546	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520512	176520512	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	57	574	1	ENST00000292408.4:c.1357G>A	p.Asp453Asn	p.D453N	ENST00000292408	NM_213647.1	453	Gat/Aat	10/18	1	2	FACETS	0.675	0.579	0.782	0.675	0.579	0.782	SUBCLONAL	1	TRUE	1	0.239052099764089	2		575	706	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970975	21970976	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0028334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	95	397	0	ENST00000304494.5:c.382_383insTA	p.Arg128LeufsTer19	p.R128Lfs*19	ENST00000304494	NM_000077.4	128	cgg/cTAgg	2/3	0.239052099764089	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.239052099764089	1		397	629	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0028337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	35	559	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.499	0.409	0.6	0.499	0.409	0.6	SUBCLONAL	1	TRUE	1	0.35	2		559	401	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186791	11186791	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	59	322	0	ENST00000361445.4:c.6414G>T	p.Leu2138Phe	p.L2138F	ENST00000361445	NM_004958.3	2138	ttG/ttT	46/58	1	2	FACETS	0.642	0.553	0.739	0.642	0.553	0.739	SUBCLONAL	1	TRUE	1	0.35	2		322	525	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106747	2106747	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167465	NA	P-0028337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	40	393	0	ENST00000219476.3:c.751G>T	p.Glu251Ter	p.E251*	ENST00000219476	NM_000548.3	251	Gag/Tag	8/42	1	2	FACETS	0.384	0.318	0.458	0.384	0.318	0.458	SUBCLONAL	1	TRUE	1	0.35	2		393	595	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577050	7577051	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	147	444	0	ENST00000269305.4:c.887dup	p.His296GlnfsTer10	p.H296Qfs*10	ENST00000269305	NM_001126112.2	296	cac/caAc	8/11	0.434549112074321	1	FACETS	0.994	0.912	1	0.994	0.912	1	CLONAL	1	TRUE	0	0.434549112074321	1		444	533	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0028342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	179	409	2	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.512315903638008	2		411	594	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191055	185191055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	140	449	2	ENST00000265026.3:c.1936C>T	p.Pro646Ser	p.P646S	ENST00000265026	NM_004721.4	646	Cct/Tct	11/14	0.361629110446258	3	FACETS	1	0.932	1	0.512	0.467	0.559	CLONAL	1	TRUE	1	0.512315903638008	3		451	670	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271254	26271254	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	83	347	0	ENST00000305910.3:c.359T>G	p.Ile120Ser	p.I120S	ENST00000305910	NM_003534.2	120	aTc/aGc	1/1	1	2	FACETS	0.665	0.589	0.747	0.665	0.589	0.747	SUBCLONAL	1	TRUE	1	0.512315903638008	2		347	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0028343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	526	567	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.771756308025484	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.771756308025484	2		568	601	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0028343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	123	253	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.771756308025484	2		253	317	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937611	76937615	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTT	CTTTT	-	novel	NA	P-0028343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	151	348	0	ENST00000373344.5:c.3133_3137del	p.Lys1045Ter	p.K1045*	ENST00000373344	NM_000489.3	1045	AAAAGt/t	9/35	1	2	FACETS	0.986	0.912	1	0.986	0.912	1	CLONAL	1	TRUE	1	0.771756308025484	2		348	397	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0028344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	598	586	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.56603038801178	4	FACETS	0.983	0.951	1	0.983	0.951	1	CLONAL	3	TRUE	1	0.578025841008903	4		587	1107	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0028344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	264	412	0	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.578025841008903	2		412	786	SUCCESS
APC	324	MSKCC	GRCh37	5	112163677	112163677	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0028344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	175	369	1	ENST00000257430.4:c.1600A>T	p.Lys534Ter	p.K534*	ENST00000257430	NM_000038.5	534	Aaa/Taa	13/16	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.578025841008903	2		370	540	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0028344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	161	301	1	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	0.991	0.914	1	0.991	0.914	1	CLONAL	1	TRUE	1	0.578025841008903	2		302	562	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0028344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	66	324	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.578025841008903	1	FACETS	0.338	0.293	0.385	0.338	0.293	0.385	SUBCLONAL	1	TRUE	0	0.578025841008903	1		324	481	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0028344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	70	611	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.332179495680013	1	FACETS	0.4	0.349	0.453	0.4	0.349	0.453	INDETERMINATE	1	TRUE	0	0.578025841008903	1		611	431	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524215	18524215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769408892	NA	P-0028344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	55	475	1	ENST00000266497.5:c.1727C>T	p.Ala576Val	p.A576V	ENST00000266497		576	gCg/gTg	11/31	0.56603038801178	4	FACETS	0.294	0.25	0.342	0.098	0.083	0.114	SUBCLONAL	1	TRUE	1	0.578025841008903	4		476	1022	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372184	55372184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs915105324	NA	P-0028344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	20	153	0	ENST00000297316.4:c.874G>A	p.Ala292Thr	p.A292T	ENST00000297316	NM_022454.3	292	Gcc/Acc	2/2	0.500895305484842	3	FACETS	0.236	0.18	0.302	0.118	0.09	0.151	SUBCLONAL	1	TRUE	1	0.578025841008903	3		153	378	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0028344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	67	397	2	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	1	2	FACETS	0.353	0.306	0.403	0.353	0.306	0.403	SUBCLONAL	1	TRUE	1	0.578025841008903	2		399	657	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912580	NA	P-0028344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	138	310	0	ENST00000342988.3:c.1157G>A	p.Gly386Asp	p.G386D	ENST00000342988	NM_005359.5	386	gGt/gAt	10/12	0.578025841008903	1	FACETS	0.935	0.862	1	0.935	0.862	1	CLONAL	1	TRUE	0	0.578025841008903	1		310	363	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686901	37686901	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	97	338	0	ENST00000447079.4:c.3810del	p.Gly1271AspfsTer23	p.G1271Dfs*23	ENST00000447079	NM_015083.1	1269	Ccc/cc	14/14	1	2	FACETS	0.486	0.434	0.542	0.486	0.434	0.542	SUBCLONAL	1	TRUE	1	0.578025841008903	2		338	690	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007825	45007825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	37	380	1	ENST00000558401.1:c.276del	p.Thr93LeufsTer10	p.T93Lfs*10	ENST00000558401	NM_004048.2	91	aCc/ac	2/4	0.578025841008903	1	FACETS	0.2	0.165	0.24	0.2	0.165	0.24	SUBCLONAL	1	TRUE	0	0.578025841008903	1		381	455	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743520	46743520	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141523334	NA	P-0028344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	93	398	0	ENST00000371975.4:c.1901G>A	p.Arg634His	p.R634H	ENST00000371975	NM_003579.3	634	cGt/cAt	17/18	1	2	FACETS	0.407	0.361	0.456	0.407	0.361	0.456	SUBCLONAL	1	TRUE	1	0.578025841008903	2		398	791	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503787	186503789	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs1560084666	NA	P-0028344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	54	435	0	ENST00000323963.5:c.470_472del	p.Val157del	p.V157del	ENST00000323963		155	aTTGtt/att	5/11	1	2	FACETS	0.231	0.196	0.269	0.231	0.196	0.269	SUBCLONAL	1	TRUE	1	0.578025841008903	2		435	809	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366389	15366389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs577973488	NA	P-0028344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	53	282	3	ENST00000263377.2:c.1766C>T	p.Ala589Val	p.A589V	ENST00000263377	NM_058243.2	589	gCg/gTg	10/20	1	2	FACETS	0.376	0.32	0.436	0.376	0.32	0.436	SUBCLONAL	1	TRUE	1	0.578025841008903	2		285	488	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911630	39911630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754470140	NA	P-0028344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	77	469	0	ENST00000378444.4:c.5000C>T	p.Ser1667Leu	p.S1667L	ENST00000378444	NM_001123385.1	1667	tCg/tTg	15/15	0.495421158181171	2	FACETS	0.409	0.359	0.462			1	SUBCLONAL	1	TRUE	NA	0.578025841008903	2		469	652	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515045	103515045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	34	294	0	ENST00000355739.4:c.1546C>T	p.Leu516Phe	p.L516F	ENST00000355739	NM_000123.3	516	Ctc/Ttc	8/15	1	2	FACETS	0.211	0.172	0.255	0.211	0.172	0.255	SUBCLONAL	1	TRUE	1	0.578025841008903	2		294	558	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609856	81609856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	101	290	1	ENST00000298171.2:c.1454C>T	p.Ala485Val	p.A485V	ENST00000298171	NM_000369.2	485	gCc/gTc	10/10	0.179552234846202	2	FACETS	0.654	0.587	0.726	0.327	0.293	0.363	INDETERMINATE	1	TRUE	0	0.578025841008903	2		291	534	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021525	42021525	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	66	488	0	ENST00000219905.7:c.3821C>A	p.Pro1274His	p.P1274H	ENST00000219905	NM_001164273.1	1274	cCt/cAt	11/24	0.578025841008903	1	FACETS	0.325	0.282	0.371	0.325	0.282	0.371	SUBCLONAL	1	TRUE	0	0.578025841008903	1		488	500	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712782	43712783	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0028344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	85	492	0	ENST00000382044.4:c.4401_4402del	p.Pro1468ArgfsTer12	p.P1468Rfs*12	ENST00000382044	NM_001141980.1	1467	tcTCca/tcca	21/28	0.578025841008903	1	FACETS	0.351	0.31	0.394	0.351	0.31	0.394	SUBCLONAL	1	TRUE	0	0.578025841008903	1		492	596	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43733754	43733754	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	33	385	0	ENST00000382044.4:c.3068G>T	p.Gly1023Val	p.G1023V	ENST00000382044	NM_001141980.1	1023	gGa/gTa	15/28	0.578025841008903	1	FACETS	0.187	0.152	0.227	0.187	0.152	0.227	SUBCLONAL	1	TRUE	0	0.578025841008903	1		385	434	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217409	7217411	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs776495886	NA	P-0028344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	81	376	0	ENST00000380728.2:c.385_387del	p.Leu129del	p.L129del	ENST00000380728		129	CTC/-	5/11	1	2	FACETS	0.384	0.338	0.434	0.384	0.338	0.434	SUBCLONAL	1	TRUE	1	0.578025841008903	2		376	729	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78858812	78858812	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	45	381	1	ENST00000306801.3:c.1847G>A	p.Arg616His	p.R616H	ENST00000306801	NM_020761.2	616	cGc/cAc	17/34	1	2	FACETS	0.221	0.185	0.261	0.221	0.185	0.261	SUBCLONAL	1	TRUE	1	0.578025841008903	2		382	705	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367902	15367902	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	78	457	1	ENST00000263377.2:c.1424del	p.Pro475LeufsTer109	p.P475Lfs*109	ENST00000263377	NM_058243.2	475	cCt/ct	8/20	1	2	FACETS	0.308	0.27	0.349	0.308	0.27	0.349	SUBCLONAL	1	TRUE	1	0.578025841008903	2		458	877	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009126	27009138	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCGACCCCCGG	CCCCGACCCCCGG	-	novel	NA	P-0028344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	61	125	0	ENST00000335756.4:c.66_78del	p.Thr23ProfsTer7	p.T23Pfs*7	ENST00000335756	NM_001809.3	21	aCCCCGACCCCCGGc/ac	1/5	1	2	FACETS	0.938	0.82	1	0.938	0.82	1	CLONAL	1	TRUE	1	0.578025841008903	2		125	225	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99181112	99181112	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	237	453	0	ENST00000074304.5:c.2053C>A	p.Leu685Ile	p.L685I	ENST00000074304	NM_001134224.1	685	Ctc/Atc	20/26	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.578025841008903	2		453	706	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215634033	215634033	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876658999	NA	P-0028344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	23	365	1	ENST00000260947.4:c.1318G>A	p.Asp440Asn	p.D440N	ENST00000260947	NM_000465.2	440	Gac/Aac	5/11	0.332179495680013	1	FACETS	0.163	0.126	0.205	0.163	0.126	0.205	INDETERMINATE	1	TRUE	0	0.578025841008903	1		366	348	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281315	46281315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1387775662	NA	P-0028344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	60	249	0	ENST00000371998.3:c.4112C>T	p.Ala1371Val	p.A1371V	ENST00000371998		1371	gCc/gTc	21/23	0.578025841008903	3	FACETS	0.388	0.333	0.447	0.194	0.166	0.224	SUBCLONAL	1	TRUE	1	0.578025841008903	3		249	690	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524474	44524474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	52	280	0	ENST00000291552.4:c.83G>A	p.Arg28His	p.R28H	ENST00000291552	NM_006758.2	28	cGt/cAt	2/8	1	2	FACETS	0.292	0.248	0.34	0.292	0.248	0.34	SUBCLONAL	1	TRUE	1	0.578025841008903	2		280	616	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707779	176707779	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	192	401	0	ENST00000439151.2:c.5836A>G	p.Ile1946Val	p.I1946V	ENST00000439151	NM_022455.4	1946	Att/Gtt	18/23	1	2	FACETS	0.95	0.882	1	0.95	0.882	1	CLONAL	1	TRUE	1	0.578025841008903	2		401	699	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205092	38205092	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	58	485	1	ENST00000317025.8:c.598del	p.Ser200AlafsTer20	p.S200Afs*20	ENST00000317025	NM_023034.1	200	Agc/gc	2/24	0.578025841008903	1	FACETS	0.306	0.263	0.353	0.306	0.263	0.353	SUBCLONAL	1	TRUE	0	0.578025841008903	1		486	466	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864745	68864745	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	38	268	0	ENST00000288368.4:c.116T>C	p.Val39Ala	p.V39A	ENST00000288368	NM_024870.2	39	gTg/gCg	1/40	0.500895305484842	3	FACETS	0.266	0.219	0.318	0.133	0.109	0.159	SUBCLONAL	1	TRUE	1	0.578025841008903	3		268	638	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222486	53222486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	461	236	0	ENST00000375401.3:c.4346G>A	p.Arg1449Gln	p.R1449Q	ENST00000375401	NM_004187.3	1449	cGg/cAg	26/26	0.495421158181171	2	FACETS	0.833	0.808	0.858			1	CLONAL	3	TRUE	NA	0.578025841008903	2		236	638	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673809	37673823	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTGAGTTTGGGGAA	TGTGAGTTTGGGGAA	G	novel	NA	P-0028344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	181	466	0	ENST00000447079.4:c.2963_2963+14delinsG		p.X988_splice	ENST00000447079	NM_015083.1	988		10/14	1	2	FACETS	0.845	0.781	0.911	0.845	0.781	0.911	CLONAL	1	TRUE	1	0.578025841008903	2		466	741	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0028346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	30	297	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.396	0.318	0.485	0.396	0.318	0.485	SUBCLONAL	1	FALSE	1	0.262301460794231	2		297	578	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0028346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	37	380	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.58	0.478	0.695	0.58	0.478	0.695	SUBCLONAL	1	FALSE	1	0.262301460794231	2		380	486	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0028350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	70	250	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.39147167068566	2		250	278	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546036	29546037	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs267606600	NA	P-0028350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	234	472	0	ENST00000356175.3:c.1541_1542del	p.Gln514ArgfsTer43	p.Q514Rfs*43	ENST00000356175	NM_000267.3	514	cAG/c	14/57	0.39147167068566	2	FACETS	0.876	0.822	0.932	0.876	0.822	0.932	CLONAL	2	TRUE	0	0.39147167068566	2		472	682	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280292	1280292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201927653	NA	P-0028350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	164	642	0	ENST00000310581.5:c.1931C>T	p.Thr644Met	p.T644M	ENST00000310581	NM_198253.2	644	aCg/aTg	4/16	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.39147167068566	2		642	835	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913255	NA	P-0028351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	97	687	0	ENST00000369535.4:c.183A>C	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caC	3/7	1	2	FACETS	0.877	0.781	0.98	0.877	0.781	0.98	CLONAL	1	TRUE	1	0.241357477258898	2		687	916	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	358	355	0	ENST00000269305.4:c.313G>T	p.Gly105Cys	p.G105C	ENST00000269305	NM_001126112.2	105	Ggc/Tgc	4/11	0.603993981646718	2	FACETS	0.952	0.914	0.989	0.952	0.914	0.989	CLONAL	2	TRUE	0	0.645163942360148	2		355	583	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455091	50455091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1422790468	NA	P-0028352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	60	224	0	ENST00000331340.3:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000331340	NM_006060.4	213	cGa/cAa	6/8	0.352459439635984	4	FACETS	0.442	0.38	0.51	0.221	0.19	0.255	INDETERMINATE	1	TRUE	2	0.645163942360148	4		224	692	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs730881677	NA	P-0028352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	198	188	0	ENST00000304494.5:c.151-1G>T		p.X51_splice	ENST00000304494	NM_000077.4	51			0.645163942360148	2	FACETS	0.897	0.848	0.946	0.897	0.848	0.946	CLONAL	2	TRUE	0	0.645163942360148	2		188	342	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533390	29533390	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0028352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	228	151	0	ENST00000356175.3:c.1392+1G>T		p.X464_splice	ENST00000356175	NM_000267.3	464			0.603993981646718	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.645163942360148	2		151	353	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436143	51436143	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	305	215	0	ENST00000262662.1:c.103A>T	p.Asn35Tyr	p.N35Y	ENST00000262662		35	Aat/Tat	3/4	0.645163942360148	2	FACETS	0.942	0.901	0.982	0.942	0.901	0.982	CLONAL	2	TRUE	0	0.645163942360148	2		215	502	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515104	103515104	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	210	225	0	ENST00000355739.4:c.1605G>T	p.Lys535Asn	p.K535N	ENST00000355739	NM_000123.3	535	aaG/aaT	8/15	0.618275786037656	2	FACETS	0.875	0.827	0.922	0.875	0.827	0.922	CLONAL	2	TRUE	0	0.645163942360148	2		225	372	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2194557	2194557	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	67	246	0	ENST00000398665.3:c.632A>T	p.Lys211Ile	p.K211I	ENST00000398665	NM_032482.2	211	aAa/aTa	7/28	0.448684131025209	1	FACETS	0.377	0.329	0.428	0.377	0.329	0.428	SUBCLONAL	1	TRUE	0	0.645163942360148	1		246	373	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081587	143081587	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	338	309	0	ENST00000262992.4:c.1487G>A	p.Ser496Asn	p.S496N	ENST00000262992	NM_001101669.1	496	aGt/aAt	15/24	0.603993981646718	2	FACETS	0.967	0.928	1	0.967	0.928	1	CLONAL	2	TRUE	0	0.645163942360148	2		309	542	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410154	139410154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	96	259	0	ENST00000277541.6:c.1684C>T	p.His562Tyr	p.H562Y	ENST00000277541	NM_017617.3	562	Cac/Tac	11/34	0.615788987355534	2	FACETS	0.836	0.752	0.924	0.418	0.376	0.462	CLONAL	1	TRUE	0	0.645163942360148	2		259	356	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922722	44922722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1340911940	NA	P-0028352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	300	253	0	ENST00000377967.4:c.1583C>T	p.Thr528Ile	p.T528I	ENST00000377967	NM_021140.2	528	aCa/aTa	16/29	0.600628214604755	2	FACETS	0.917	0.877	0.957	0.917	0.877	0.957	CLONAL	2	TRUE	0	0.645163942360148	2		253	507	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340084	116340084	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0121520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	92	321	0	ENST00000397752.3:c.946A>T	p.Ile316Leu	p.I316L	ENST00000397752	NM_000245.2	316	Ata/Tta	2/21	1	2	FACETS	0.879	0.787	0.976	0.879	0.787	0.976	CLONAL	1	NA	1	0.556630301792971	2		321	376	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0028356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	88	497	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	0.987	1	CLONAL	2	TRUE	1	0.17	2		497	426	SUCCESS
APC	324	MSKCC	GRCh37	5	112174112	112174112	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	64	413	0	ENST00000257430.4:c.2821G>T	p.Glu941Ter	p.E941*	ENST00000257430	NM_000038.5	941	Gaa/Taa	16/16	1	2	FACETS	1	0.922	1	1	0.981	1	CLONAL	2	TRUE	1	0.17	2		413	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578510	7578510	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	174	645	0	ENST00000269305.4:c.420del	p.Cys141AlafsTer29	p.C141Afs*29	ENST00000269305	NM_001126112.2	140	acC/ac	5/11	0.303731252718583	1	FACETS	1	0.979	1	1	0.993	1	CLONAL	2	TRUE	0	0.17	1		645	801	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114724358	114724358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200865074	NA	P-0028356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	72	479	1	ENST00000543371.1:c.425C>T	p.Thr142Met	p.T142M	ENST00000543371	NM_001198531.1	142	aCg/aTg	4/14	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.17	2		480	588	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114917829	114917829	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0028356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	115	544	0	ENST00000543371.1:c.1318+1G>A		p.X440_splice	ENST00000543371	NM_001198531.1	440			1	2	FACETS	1	0.953	1	1	0.989	1	CLONAL	2	TRUE	1	0.17	2		544	619	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267927	46267927	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	36	513	0	ENST00000371998.3:c.2688A>C	p.Glu896Asp	p.E896D	ENST00000371998		896	gaA/gaC	14/23	0.291261001275366	3	FACETS	0.762	0.625	0.916	0.381	0.312	0.458	CLONAL	1	TRUE	1	0.17	3		513	603	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249381	153249381	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	55	505	1	ENST00000281708.4:c.1397G>T	p.Cys466Phe	p.C466F	ENST00000281708	NM_033632.3	466	tGt/tTt	9/12	1	2	FACETS	0.899	0.772	1	1	0.974	1	CLONAL	2	TRUE	1	0.17	2		506	360	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0028357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	380	567	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.994	1	1	0.997	1	CLONAL	2	TRUE	1	0.384363251476194	2		568	799	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0028357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	180	253	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	0.994	1	CLONAL	2	TRUE	1	0.384363251476194	2		253	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0028357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	389	619	1	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	1	2	FACETS	1	0.994	1	1	0.997	1	CLONAL	2	TRUE	1	0.384363251476194	2		620	812	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73350131	73350131	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	301	561	2	ENST00000377767.4:c.754A>G	p.Arg252Gly	p.R252G	ENST00000377767	NM_014953.3	252	Aga/Gga	5/21	1	2	FACETS	1	0.986	1	1	0.996	1	CLONAL	2	TRUE	1	0.384363251476194	2		563	703	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514596	103514596	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769870058	NA	P-0028357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	35	360	1	ENST00000355739.4:c.1097G>A	p.Arg366Gln	p.R366Q	ENST00000355739	NM_000123.3	366	cGa/cAa	8/15	1	2	FACETS	0.401	0.328	0.483	0.401	0.328	0.483	SUBCLONAL	1	TRUE	1	0.384363251476194	2		361	454	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213895	2213895	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	110	629	0	ENST00000398665.3:c.1707G>C	p.Lys569Asn	p.K569N	ENST00000398665	NM_032482.2	569	aaG/aaC	18/28	1	2	FACETS	0.741	0.666	0.821	0.741	0.666	0.821	SUBCLONAL	1	TRUE	1	0.384363251476194	2		629	772	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894230	NA	P-0028358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	212	482	0	ENST00000451590.1:c.35G>T	p.Gly12Val	p.G12V	ENST00000451590	NM_001130442.1	12	gGc/gTc	2/5	1	2	FACETS	0.969	0.908	1	0.969	0.908	1	CLONAL	1	TRUE	1	0.798110693135146	2		482	548	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0028359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	77	297	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.210271723592676	1	FACETS	0.762	0.67	0.862	0.762	0.67	0.862	SUBCLONAL	1	TRUE	0	0.280573872444199	1		297	619	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0028359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	87	518	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.280573872444199	2		518	609	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226309	2226309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	54	771	1	ENST00000326181.6:c.1922G>A	p.Arg641His	p.R641H	ENST00000326181	NM_032271.2	641	cGt/cAt	20/21	1	2	FACETS	0.364	0.309	0.424	0.364	0.309	0.424	SUBCLONAL	1	TRUE	1	0.280573872444199	2		772	1058	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459879	149459879	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1432099970	NA	P-0028359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	157	750	2	ENST00000286301.3:c.328G>A	p.Val110Met	p.V110M	ENST00000286301	NM_005211.3	110	Gtg/Atg	4/22	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.280573872444199	2		752	1049	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0028359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	77	587	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.280573872444199	1	FACETS	0.889	0.782	1	0.889	0.782	1	CLONAL	1	TRUE	0	0.280573872444199	1		587	531	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467843	50467843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	120	448	1	ENST00000331340.3:c.1078C>T	p.Arg360Cys	p.R360C	ENST00000331340	NM_006060.4	360	Cgc/Tgc	8/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.280573872444199	2		449	645	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68982089	68982089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376775544	NA	P-0028359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	79	704	0	ENST00000288368.4:c.1463G>A	p.Arg488His	p.R488H	ENST00000288368	NM_024870.2	488	cGt/cAt	13/40	1	2	FACETS	0.653	0.573	0.739	0.653	0.573	0.739	SUBCLONAL	1	TRUE	1	0.280573872444199	2		704	863	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468167	50468167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	129	636	1	ENST00000331340.3:c.1402C>T	p.Arg468Trp	p.R468W	ENST00000331340	NM_006060.4	468	Cgg/Tgg	8/8	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.280573872444199	2		637	815	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871005	12871006	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0028359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	102	470	0	ENST00000228872.4:c.233dup	p.Val79GlyfsTer46	p.V79Gfs*46	ENST00000228872	NM_004064.3	78	gag/gAag	1/3	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.280573872444199	2		470	614	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864291	57864291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758959112	NA	P-0028359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	134	589	0	ENST00000228682.2:c.1768C>T	p.Arg590Trp	p.R590W	ENST00000228682	NM_005269.2	590	Cgg/Tgg	12/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.280573872444199	2		589	836	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245480	153245481	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0028359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	101	654	0	ENST00000281708.4:c.1710_1711del	p.Gly571GlufsTer33	p.G571Efs*33	ENST00000281708	NM_033632.3	570	acAGgg/acgg	11/12	1	2	FACETS	0.97	0.867	1	0.97	0.867	1	CLONAL	1	TRUE	1	0.280573872444199	2		654	742	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0028360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	38	445	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.272	0.224	0.326	0.272	0.224	0.326	SUBCLONAL	1	TRUE	1	0.381509088233892	2		445	732	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100658	67100658	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	167	613	1	ENST00000412916.2:c.356T>A	p.Leu119Gln	p.L119Q	ENST00000412916		119	cTg/cAg	4/6	0.381509088233892	1	FACETS	0.888	0.817	0.962	0.888	0.817	0.962	CLONAL	1	TRUE	0	0.381509088233892	1		614	798	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115111972	115111972	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	174	621	0	ENST00000257566.3:c.1768C>T	p.Gln590Ter	p.Q590*	ENST00000257566	NM_016569.3	590	Cag/Tag	7/8	1	2	FACETS	0.99	0.912	1	0.99	0.912	1	CLONAL	1	TRUE	1	0.381509088233892	2		621	921	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154760	2154760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143785521	NA	P-0028360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	164	675	1	ENST00000434045.2:c.461C>T	p.Pro154Leu	p.P154L	ENST00000434045	NM_001127598.1	154	cCg/cTg	4/5	NA	2	FACETS	0.816	0.749	0.888			1	INDETERMINATE	1	TRUE	NA	0.381509088233892	2		676	1053	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857311	68857312	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	110	357	0	ENST00000261769.5:c.1947dup	p.Ile650TyrfsTer13	p.I650Yfs*13	ENST00000261769	NM_004360.3	649	tct/tcTt	13/16	0.381509088233892	1	FACETS	0.95	0.858	1	0.95	0.858	1	CLONAL	1	TRUE	0	0.381509088233892	1		357	491	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070551	67070551	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	26	302	0	ENST00000412916.2:c.175G>T	p.Ala59Ser	p.A59S	ENST00000412916		59	Gcc/Tcc	3/6	0.381509088233892	1	FACETS	0.276	0.218	0.342	0.276	0.218	0.342	SUBCLONAL	1	TRUE	0	0.381509088233892	1		302	400	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105541	27105541	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	69	523	1	ENST00000324856.7:c.5152G>T	p.Glu1718Ter	p.E1718*	ENST00000324856	NM_006015.4	1718	Gaa/Taa	20/20	0.176311779317243	1	FACETS	0.89	0.774	1	0.89	0.774	1	CLONAL	1	FALSE	0	0.178868870582532	1		524	789	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871147	12871148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0028363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	35	321	0	ENST00000228872.4:c.375_376insTT	p.Glu126LeufsTer20	p.E126Lfs*20	ENST00000228872	NM_004064.3	125	tct/tcTTt	1/3	0.176311779317243	1	FACETS	0.747	0.612	0.899	0.747	0.612	0.899	SUBCLONAL	1	FALSE	0	0.178868870582532	1		321	477	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380269	25380270	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCCTCTTGACCTGCTGTGTCGAGAATA	novel	NA	P-0028363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	56	703	0	ENST00000311936.3:c.162_188dup	p.Asp54_Glu62dup	p.D54_E62dup	ENST00000311936	NM_004985.3	54	gag/gaTATTCTCGACACAGCAGGTCAAGAGGAg	3/5	0.176311779317243	1	FACETS	0.621	0.53	0.721	0.621	0.53	0.721	SUBCLONAL	1	FALSE	0	0.178868870582532	1		703	918	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0028365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	96	346	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.241836008239837	3	FACETS	0.786	0.703	0.872	0.786	0.703	0.872	SUBCLONAL	2	TRUE	1	0.307088686734639	3		346	459	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115779	8115780	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0028365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	111	814	2	ENST00000346208.3:c.1131dup	p.Val378SerfsTer3	p.V378Sfs*3	ENST00000346208		375	-/A	6/6	NA	2	FACETS	0.825	0.741	0.914			1	INDETERMINATE	1	TRUE	NA	0.307088686734639	2		816	876	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407525	407525	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs934318315	NA	P-0028365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	100	697	0	ENST00000380956.4:c.1283A>G	p.Tyr428Cys	p.Y428C	ENST00000380956	NM_001195286.1	428	tAc/tGc	9/9	0.226974434706788	4	FACETS	0.785	0.7	0.877	0.393	0.35	0.439	SUBCLONAL	1	TRUE	2	0.307088686734639	4		697	1084	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932368	36932368	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	76	565	1	ENST00000361632.4:c.2101G>T	p.Glu701Ter	p.E701*	ENST00000361632		701	Gag/Tag	16/16	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.468885998049452	2		566	311	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163425	108163425	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760542469	NA	P-0028367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	68	661	0	ENST00000278616.4:c.4516G>A	p.Val1506Met	p.V1506M	ENST00000278616	NM_000051.3	1506	Gtg/Atg	30/63	1	2	FACETS	0.786	0.688	0.891	0.786	0.688	0.891	SUBCLONAL	1	TRUE	1	0.468885998049452	2		661	369	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052615	42052615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	80	448	0	ENST00000219905.7:c.7286C>T	p.Thr2429Ile	p.T2429I	ENST00000219905	NM_001164273.1	2429	aCt/aTt	20/24	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.468885998049452	2		448	321	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348421	89348421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770592504	NA	P-0028367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	74	549	0	ENST00000301030.4:c.4529C>T	p.Pro1510Leu	p.P1510L	ENST00000301030	NM_001256183.1	1510	cCg/cTg	9/13	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.468885998049452	2		549	306	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578181	7578181	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138983188	NA	P-0028367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	83	692	0	ENST00000269305.4:c.668C>T	p.Pro223Leu	p.P223L	ENST00000269305	NM_001126112.2	223	cCt/cTt	6/11	1	2	FACETS	0.989	0.879	1	0.989	0.879	1	CLONAL	1	TRUE	1	0.468885998049452	2		692	358	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579378	7579378	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0028367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	87	671	0	ENST00000269305.4:c.309C>G	p.Tyr103Ter	p.Y103*	ENST00000269305	NM_001126112.2	103	taC/taG	4/11	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.468885998049452	2		671	343	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678008	117678008	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	79	548	1	ENST00000368508.3:c.3925T>A	p.Leu1309Met	p.L1309M	ENST00000368508	NM_002944.2	1309	Ttg/Atg	25/43	0.468885998049452	2	FACETS	1	0.889	1	0.501	0.444	0.562	CLONAL	1	TRUE	0	0.468885998049452	2		549	336	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0028367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	93	277	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	1	0.929	1	1	0.988	1	CLONAL	2	TRUE	1	0.468885998049452	2		277	194	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137325956	137325989	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCTCTCGAACCCGGCCGAGGTGGAGGCGCTGA	GGGCTCTCGAACCCGGCCGAGGTGGAGGCGCTGA	-	novel	NA	P-0028367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	59	578	0	ENST00000481739.1:c.1147_1180del	p.Leu383ArgfsTer68	p.L383Rfs*68	ENST00000481739	NM_002957.4	382	GGGCTCTCGAACCCGGCCGAGGTGGAGGCGCTGAgg/gg	9/10	1	2	FACETS	0.905	0.786	1	0.905	0.786	1	CLONAL	1	TRUE	1	0.468885998049452	2		578	278	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0028368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	601	596	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.87907283860934	2	FACETS	0.995	0.977	1	0.995	0.977	1	CLONAL	2	TRUE	0	0.87907283860934	2		596	687	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040961	42040961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758543910	NA	P-0028368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	287	648	4	ENST00000219905.7:c.5339C>T	p.Thr1780Ile	p.T1780I	ENST00000219905	NM_001164273.1	1780	aCa/aTa	16/24	0.87907283860934	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.87907283860934	1		652	359	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0028373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	173	689	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.220043116645883	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	0	0.220043116645883	1		689	983	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245465	46245466	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	53	436	0	ENST00000334344.6:c.3560dup	p.Ser1188GlufsTer53	p.S1188Efs*53	ENST00000334344	NM_152641.2	1187	gtg/gTtg	15/21	0.0536334495247077	4	FACETS	0.913	0.783	1	0.913	0.783	1	INDETERMINATE	2	FALSE	2	0.220043116645883	4		436	322	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349916	15349916	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	37	576	0	ENST00000263377.2:c.3736G>A	p.Glu1246Lys	p.E1246K	ENST00000263377	NM_058243.2	1246	Gag/Aag	18/20	0.205840503280979	4	FACETS	0.564	0.464	0.678	0.188	0.154	0.226	SUBCLONAL	1	FALSE	1	0.220043116645883	4		576	727	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865006	57865006	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	116	723	0	ENST00000228682.2:c.2483G>C	p.Gly828Ala	p.G828A	ENST00000228682	NM_005269.2	828	gGa/gCa	12/12	0.452754989623759	2	FACETS	0.63	0.567	0.696	0.315	0.283	0.348	SUBCLONAL	1	TRUE	0	0.454126547657598	2		723	811	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0028375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	481	760	0	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	0.446750134304235	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.446750134304235	2		760	1067	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905112	50905112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781132734	NA	P-0028375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	315	799	0	ENST00000440232.2:c.394G>A	p.Asp132Asn	p.D132N	ENST00000440232	NM_002691.3	132	Gat/Aat	4/27	0.2042380152612	5	FACETS	0.879	0.828	0.931	0.586	0.552	0.621	INDETERMINATE	2	TRUE	2	0.446750134304235	5		799	1340	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508860	106508860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1251220989	NA	P-0028375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	278	553	0	ENST00000359195.3:c.854C>T	p.Thr285Met	p.T285M	ENST00000359195	NM_002649.2	285	aCg/aTg	2/11	0.446750134304235	6	FACETS	0.964	0.905	1	0.482	0.452	0.513	CLONAL	2	TRUE	2	0.446750134304235	6		553	1222	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321216	65321216	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1306467125	NA	P-0028375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	288	444	0	ENST00000342505.4:c.1624C>T	p.Arg542Cys	p.R542C	ENST00000342505	NM_002227.2	542	Cgc/Tgc	11/25	0.446750134304235	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.446750134304235	2		444	605	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040892	42040892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1463241547	NA	P-0028375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	52	543	0	ENST00000219905.7:c.5270G>A	p.Arg1757His	p.R1757H	ENST00000219905	NM_001164273.1	1757	cGt/cAt	16/24	0.344137483140451	4	FACETS	0.344	0.292	0.402	0.172	0.146	0.201	SUBCLONAL	1	TRUE	2	0.446750134304235	4		543	978	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276825	15276825	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	277	742	1	ENST00000263388.2:c.5440G>A	p.Asp1814Asn	p.D1814N	ENST00000263388	NM_000435.2	1814	Gat/Aat	30/33	0.2042380152612	5	FACETS	0.846	0.794	0.9	0.564	0.529	0.6	INDETERMINATE	2	TRUE	2	0.446750134304235	5		743	1224	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349870	15349870	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	274	482	0	ENST00000263377.2:c.3782G>T	p.Arg1261Met	p.R1261M	ENST00000263377	NM_058243.2	1261	aGg/aTg	18/20	0.2042380152612	5	FACETS	1	0.99	1	0.814	0.766	0.862	INDETERMINATE	2	TRUE	2	0.446750134304235	5		482	839	SUCCESS
APC	324	MSKCC	GRCh37	5	112175496	112175506	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGCTCCGTT	CCAGCTCCGTT	A	novel	NA	P-0028375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	283	389	0	ENST00000257430.4:c.4205_4215delinsA	p.Ala1402AspfsTer10	p.A1402Dfs*10	ENST00000257430	NM_000038.5	1402	gCCAGCTCCGTT/gA	16/16	0.443560239864628	3	FACETS	0.936	0.89	0.982	0.936	0.89	0.982	CLONAL	3	TRUE	0	0.446750134304235	3		389	552	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0028376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	465	519	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.447658298785508	2		519	895	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7977017	7977017	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	206	752	0	ENST00000319144.4:c.1713C>G	p.Ile571Met	p.I571M	ENST00000319144	NM_001139.2	571	atC/atG	13/15	0.447658298785508	1	FACETS	0.835	0.776	0.897	0.835	0.776	0.897	CLONAL	1	TRUE	0	0.447658298785508	1		752	855	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67646006	67646006	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	319	547	0	ENST00000264010.4:c.934C>G	p.His312Asp	p.H312D	ENST00000264010	NM_006565.3	312	Cac/Gac	4/12	0.447658298785508	2	FACETS	0.881	0.835	0.927	0.881	0.835	0.927	CLONAL	2	TRUE	0	0.447658298785508	2		547	809	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012385	152012386	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	206	417	0	ENST00000262189.6:c.427dup	p.Ser143LysfsTer27	p.S143Kfs*27	ENST00000262189	NM_170606.2	143	agt/aAgt	4/59	0.447658298785508	2	FACETS	0.817	0.764	0.872	0.817	0.764	0.872	CLONAL	2	TRUE	0	0.447658298785508	2		417	563	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248998	55248999	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCCAGCG	rs727504263	NA	P-0028377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	160	580	0	ENST00000275493.2:c.2300_2308dup	p.Ala767_Val769dup	p.A767_V769dup	ENST00000275493	NM_005228.3	767	atg/aTGGCCAGCGtg	20/28	0.415246165884957	3	FACETS	1	0.988	1	0.711	0.655	0.77	CLONAL	1	TRUE	1	0.42629387855681	3		580	640	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7126642	7126642	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	72	760	1	ENST00000302850.5:c.2966G>T	p.Gly989Val	p.G989V	ENST00000302850	NM_000208.2	989	gGa/gTa	16/22	1	2	FACETS	0.402	0.35	0.458	0.402	0.35	0.458	SUBCLONAL	1	TRUE	1	0.42629387855681	2		761	841	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351993	70351993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	113	827	0	ENST00000374080.3:c.4190G>A	p.Gly1397Glu	p.G1397E	ENST00000374080		1397	gGg/gAg	30/45	0.378292061572225	3	FACETS	0.639	0.574	0.708	0.319	0.287	0.354	SUBCLONAL	1	TRUE	1	0.42629387855681	3		827	1007	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710673	114710673	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	167	568	0	ENST00000543371.1:c.160del	p.Thr54ArgfsTer54	p.T54Rfs*54	ENST00000543371	NM_001198531.1	53	gAa/ga	1/14	0.392383690609586	1	FACETS	0.436	0.402	0.471	0.436	0.402	0.471	INDETERMINATE	1	TRUE	0	0.778500466892137	1		568	601	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264377	46264378	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0028378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	107	463	0	ENST00000371998.3:c.1427dup	p.Asn476LysfsTer11	p.N476Kfs*11	ENST00000371998		475	cca/ccAa	11/23	0.379059918148766	5	FACETS	0.594	0.531	0.66	0.198	0.177	0.22	INDETERMINATE	1	TRUE	2	0.778500466892137	5		463	1004	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098424	47098425	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTGTACA	novel	NA	P-0028378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	251	577	0	ENST00000409792.3:c.6843_6849dup	p.Gln2284CysfsTer87	p.Q2284Cfs*87	ENST00000409792	NM_014159.6	2283	-/TGTACAG	15/21	0.778500466892137	1	FACETS	0.895	0.851	0.939	0.895	0.851	0.939	CLONAL	1	TRUE	0	0.778500466892137	1		577	440	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956626	93956626	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	286	496	0	ENST00000369303.4:c.2610G>T	p.Leu870Phe	p.L870F	ENST00000369303	NM_004440.3	870	ttG/ttT	15/17	0.778500466892137	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.778500466892137	1		496	417	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845128	128845128	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	200	844	2	ENST00000249373.3:c.622G>T	p.Glu208Ter	p.E208*	ENST00000249373	NM_005631.4	208	Gag/Tag	3/12	NA	2	FACETS	0.588	0.545	0.632			1	INDETERMINATE	1	TRUE	NA	0.778500466892137	2		846	874	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911494	32911494	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	226	491	0	ENST00000380152.3:c.3002C>T	p.Ser1001Leu	p.S1001L	ENST00000380152		1001	tCa/tTa	11/27	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.636602464238845	2		491	604	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0028381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	40	665	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	0.782	0.656	0.92	1	0.959	1	CLONAL	2	FALSE	1	0.229385043387619	2		665	223	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63760017	63760018	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0028381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	27	411	0	ENST00000279873.7:c.670_671del	p.Tyr224LeufsTer6	p.Y224Lfs*6	ENST00000279873	NM_032199.2	224	TAc/c	4/10	1	2	FACETS	0.755	0.607	0.919	1	0.938	1	CLONAL	2	FALSE	1	0.229385043387619	2		411	156	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267499	198267499	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	21	505	0	ENST00000335508.6:c.1858A>G	p.Met620Val	p.M620V	ENST00000335508	NM_012433.2	620	Atg/Gtg	14/25	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	FALSE	1	0.229385043387619	2		505	125	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	246	847	0	ENST00000269305.4:c.584del	p.Ile195ThrfsTer52	p.I195Tfs*52	ENST00000269305	NM_001126112.2	195	aTc/ac	6/11	0.154504289410299	3	FACETS	1	0.977	1	0.733	0.684	0.782	CLONAL	2	TRUE	0	0.220327060559911	3		847	1128	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251913	153251913	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	56	662	0	ENST00000281708.4:c.1093T>C	p.Trp365Arg	p.W365R	ENST00000281708	NM_033632.3	365	Tgg/Cgg	7/12	0.220327060559911	1	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	0	0.220327060559911	1		662	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0028388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	81	581	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.41616072958634	1	FACETS	0.551	0.488	0.618	0.551	0.488	0.618	SUBCLONAL	1	TRUE	0	0.544442131033423	1		583	393	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180551	56180555	+	frameshift_variant	Frame_Shift_Del	DEL	GAGAT	GAGAT	-	novel	NA	P-0028388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	54	582	0	ENST00000399503.3:c.3880_3884del	p.Glu1294LysfsTer13	p.E1294Kfs*13	ENST00000399503	NM_005921.1	1294	GAGATa/a	16/20	1	2	FACETS	0.737	0.635	0.847	0.737	0.635	0.847	SUBCLONAL	1	TRUE	1	0.544442131033423	2		582	269	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178643	56178643	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	49	396	0	ENST00000399503.3:c.3617del	p.Pro1206LeufsTer39	p.P1206Lfs*39	ENST00000399503	NM_005921.1	1206	Cct/ct	14/20	1	2	FACETS	0.756	0.647	0.874	0.756	0.647	0.874	SUBCLONAL	1	TRUE	1	0.544442131033423	2		396	238	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256159	16256159	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	75	765	1	ENST00000375759.3:c.3424G>T	p.Glu1142Ter	p.E1142*	ENST00000375759	NM_015001.2	1142	Gaa/Taa	11/15	1	2	FACETS	0.808	0.713	0.908	0.808	0.713	0.908	CLONAL	1	TRUE	1	0.544442131033423	2		766	341	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0028403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	331	518	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.259603257688982	5	FACETS	0.866	0.824	0.909			1	INDETERMINATE	3	TRUE	NA	0.668879544982875	5		518	763	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600378	10600378	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	748	576	0	ENST00000171111.5:c.1477G>A	p.Glu493Lys	p.E493K	ENST00000171111	NM_203500.1	493	Gag/Aag	4/6	0.668879544982875	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.668879544982875	2		576	1089	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106154	27106154	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	246	424	0	ENST00000324856.7:c.5765T>G	p.Leu1922Trp	p.L1922W	ENST00000324856	NM_006015.4	1922	tTg/tGg	20/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.668879544982875	2		424	734	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106178	27106178	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	246	414	0	ENST00000324856.7:c.5789C>A	p.Ser1930Ter	p.S1930*	ENST00000324856	NM_006015.4	1930	tCa/tAa	20/20	1	2	FACETS	0.995	0.934	1	0.995	0.934	1	CLONAL	1	TRUE	1	0.668879544982875	2		414	739	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107204	27107204	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1476138197	NA	P-0028403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	228	334	0	ENST00000324856.7:c.6815C>T	p.Ser2272Leu	p.S2272L	ENST00000324856	NM_006015.4	2272	tCa/tTa	20/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.668879544982875	2		334	654	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932254	36932254	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	133	484	0	ENST00000361632.4:c.2215C>A	p.Gln739Lys	p.Q739K	ENST00000361632		739	Cag/Aag	16/16	1	2	FACETS	0.44	0.399	0.483	0.44	0.399	0.483	SUBCLONAL	1	TRUE	1	0.668879544982875	2		484	903	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417916	138417916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	176	344	0	ENST00000289153.2:c.1603C>T	p.Leu535Phe	p.L535F	ENST00000289153	NM_006219.2	535	Ctt/Ttt	11/22	0.586511508066627	4	FACETS	0.987	0.909	1	0.493	0.454	0.534	CLONAL	1	TRUE	2	0.668879544982875	4		344	890	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0028405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	203	544	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.259463369966301	2	FACETS	0.881	0.823	0.94	1	0.989	1	CLONAL	3	TRUE	0	0.268598424375199	2		544	572	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0028405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	111	341	3	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.215339563280325	3	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	1	0.268598424375199	3		344	450	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0028405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	34	247	0	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	0.215339563280325	3	FACETS	0.977	0.801	1	0.488	0.4	0.587	CLONAL	1	TRUE	1	0.268598424375199	3		247	294	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622205	117622205	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	98	317	1	ENST00000368508.3:c.6665del	p.Phe2222SerfsTer2	p.F2222Sfs*2	ENST00000368508	NM_002944.2	2222	tTc/tc	42/43	0.199548745651891	4	FACETS	0.945	0.846	1	0.945	0.846	1	CLONAL	2	TRUE	2	0.268598424375199	4		318	490	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714391	40714391	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	327	419	0	ENST00000373198.4:c.4006T>C	p.Phe1336Leu	p.F1336L	ENST00000373198	NM_133170.3	1336	Ttc/Ctc	29/32	0.268598424375199	6	FACETS	0.923	0.879	0.966	1	0.988	1	CLONAL	6	TRUE	1	0.268598424375199	6		419	676	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409866	63409866	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	60	337	0	ENST00000330258.3:c.3301C>A	p.His1101Asn	p.H1101N	ENST00000330258	NM_152424.3	1101	Cac/Aac	2/2	0.176504766348615	5	FACETS	0.818	0.708	0.937	0.545	0.472	0.625	CLONAL	2	TRUE	2	0.268598424375199	5		337	383	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038257	30038258	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0028409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	211	324	0	ENST00000338641.4:c.431dup	p.Tyr144Ter	p.Y144*	ENST00000338641	NM_000268.3	144	tac/tAac	4/16	0.634743680726242	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.636561939870485	1		324	451	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225938	2225938	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	294	580	0	ENST00000326181.6:c.1730A>C	p.Tyr577Ser	p.Y577S	ENST00000326181	NM_032271.2	577	tAc/tCc	18/21	1	2	FACETS	0.897	0.845	0.95	0.897	0.845	0.95	CLONAL	1	TRUE	1	0.636561939870485	2		580	1030	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267722	7267722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752292214	NA	P-0028409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	352	574	0	ENST00000302850.5:c.286C>T	p.Leu96Phe	p.L96F	ENST00000302850	NM_000208.2	96	Ctc/Ttc	2/22	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.636561939870485	2		574	1046	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582319	119582319	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	175	310	0	ENST00000316626.5:c.1082T>G	p.Val361Gly	p.V361G	ENST00000316626		361	gTc/gGc	10/12	1	2	FACETS	0.956	0.886	1	0.956	0.886	1	CLONAL	1	TRUE	1	0.636561939870485	2		310	575	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0028410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	1216	445	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.248428428413734	28	FACETS	0.986	0.967	1			1	CLONAL	24	TRUE	NA	0.248428428413734	28		445	1749	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578410	7578410	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	262	582	0	ENST00000269305.4:c.520A>T	p.Arg174Trp	p.R174W	ENST00000269305	NM_001126112.2	174	Agg/Tgg	5/11	0.248428428413734	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	3	TRUE	0	0.248428428413734	3		582	764	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243237	123243237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55774317	NA	P-0028410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	107	716	0	ENST00000358487.5:c.2276G>A	p.Arg759Gln	p.R759Q	ENST00000358487	NM_000141.4	759	cGa/cAa	17/18	0.248428428413734	3	FACETS	0.977	0.875	1	0.489	0.437	0.543	CLONAL	1	TRUE	1	0.248428428413734	3		716	991	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867349	45867349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375415853	NA	P-0028410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	79	602	1	ENST00000391945.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000391945	NM_000400.3	282	Cgg/Tgg	10/23	0.248428428413734	3	FACETS	0.938	0.824	1	0.469	0.412	0.531	CLONAL	1	TRUE	1	0.248428428413734	3		603	762	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313343	65313343	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0028410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	153	373	0	ENST00000342505.4:c.1771A>T	p.Arg591Ter	p.R591*	ENST00000342505	NM_002227.2	591	Aga/Tga	13/25	0.248428428413734	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.248428428413734	3		373	590	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857950	9857950	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1555482433	NA	P-0028410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	89	529	0	ENST00000330684.3:c.3451T>A	p.Tyr1151Asn	p.Y1151N	ENST00000330684	NM_001134407.1	1151	Tac/Aac	13/13	0.248428428413734	2	FACETS	1	0.946	1	0.556	0.493	0.623	CLONAL	1	TRUE	0	0.248428428413734	2		529	644	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166356	7166356	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	61	611	0	ENST00000302850.5:c.1670C>G	p.Thr557Arg	p.T557R	ENST00000302850	NM_000208.2	557	aCg/aGg	8/22	0.248428428413734	3	FACETS	0.596	0.513	0.688	0.298	0.256	0.344	SUBCLONAL	1	TRUE	1	0.248428428413734	3		611	926	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0028412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	65	586	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.224629198216906	2		587	550	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220649	1220649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060499964	NA	P-0028412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	58	539	1	ENST00000326873.7:c.667G>A	p.Glu223Lys	p.E223K	ENST00000326873	NM_000455.4	223	Gag/Aag	5/10	0.224629198216906	0	FACETS	0.741	0.637	0.855			1	SUBCLONAL	1	TRUE	0	0.224629198216906	0		540	540	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211569	46211570	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	40	233	0	ENST00000334344.6:c.536dup	p.Cys180MetfsTer7	p.C180Mfs*7	ENST00000334344	NM_152641.2	179	gta/gTta	5/21	1	2	FACETS	0.96	0.799	1	0.96	0.799	1	CLONAL	1	TRUE	1	0.224629198216906	2		233	371	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426298	49426298	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1369666889	NA	P-0028412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	83	600	0	ENST00000301067.7:c.12190G>A	p.Glu4064Lys	p.E4064K	ENST00000301067	NM_003482.3	4064	Gag/Aag	39/54	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.224629198216906	2		600	723	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987091	36987091	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	125	436	1	ENST00000354822.5:c.598C>T	p.Gln200Ter	p.Q200*	ENST00000354822	NM_001079668.2	200	Cag/Tag	3/3	0.200315396761224	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.224629198216906	2		437	510	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509583	106509583	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs749714535	NA	P-0028412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	51	349	0	ENST00000359195.3:c.1577C>A	p.Pro526Gln	p.P526Q	ENST00000359195	NM_002649.2	526	cCg/cAg	2/11	1	2	FACETS	0.857	0.728	0.998	0.857	0.728	0.998	CLONAL	1	TRUE	1	0.224629198216906	2		349	530	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015069	37015069	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	46	374	0	ENST00000358127.4:c.335G>T	p.Trp112Leu	p.W112L	ENST00000358127	NM_001280556.1	112	tGg/tTg	3/10	1	2	FACETS	0.821	0.691	0.964	0.821	0.691	0.964	CLONAL	1	TRUE	1	0.224629198216906	2		374	499	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs767894241	NA	P-0028414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	277	495	0	ENST00000358127.4:c.76dup	p.Val26GlyfsTer49	p.V26Gfs*49	ENST00000358127	NM_001280556.1	26	gtt/gGtt	2/10	1	2	FACETS	0.832	0.784	0.882	0.832	0.784	0.882	CLONAL	1	TRUE	1	0.773195542112477	2		495	861	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0028421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	271	519	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.391713655093486	2	FACETS	0.887	0.836	0.939	0.887	0.836	0.939	CLONAL	2	TRUE	0	0.391713655093486	2		519	780	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553441	106553441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746535819	NA	P-0028421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	59	322	1	ENST00000369096.4:c.1406C>T	p.Ser469Leu	p.S469L	ENST00000369096	NM_001198.3	469	tCg/tTg	5/7	1	2	FACETS	0.819	0.708	0.938	0.819	0.708	0.938	CLONAL	1	TRUE	1	0.391713655093486	2		323	368	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416526	49416526	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	137	626	0	ENST00000301067.7:c.16185G>A	p.Trp5395Ter	p.W5395*	ENST00000301067	NM_003482.3	5395	tgG/tgA	51/54	0.361194168495546	1	FACETS	0.873	0.797	0.954	0.873	0.797	0.954	CLONAL	1	TRUE	0	0.391713655093486	1		626	644	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885939	111885939	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	128	579	0	ENST00000341259.2:c.1561C>A	p.Pro521Thr	p.P521T	ENST00000341259	NM_005475.2	521	Ccc/Acc	8/8	1	2	FACETS	0.839	0.761	0.921	0.839	0.761	0.921	CLONAL	1	TRUE	1	0.391713655093486	2		579	779	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562694	29562694	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	87	517	0	ENST00000356175.3:c.3774G>A	p.Trp1258Ter	p.W1258*	ENST00000356175	NM_000267.3	1258	tgG/tgA	28/57	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.234811152433054	2		517	666	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0028423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	55	351	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	0.884	0.756	1	0.884	0.756	1	CLONAL	1	TRUE	1	0.234811152433054	2		351	530	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115252204	115252204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	131	313	0	ENST00000369535.4:c.436G>A	p.Ala146Thr	p.A146T	ENST00000369535	NM_002524.4	146	Gcc/Acc	4/7	0.215506896691621	4	FACETS	1	0.975	1			1	CLONAL	2	TRUE	NA	0.234811152433054	4		313	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0028425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	167	658	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.461815750971163	1	FACETS	0.957	0.885	1	0.957	0.885	1	CLONAL	1	TRUE	0	0.467999802357001	1		658	571	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0028425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	70	297	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.898	0.789	1	0.898	0.789	1	CLONAL	1	TRUE	1	0.467999802357001	2		297	333	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607597	43607597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs545625150	NA	P-0028425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	135	954	4	ENST00000355710.3:c.1573C>T	p.Arg525Trp	p.R525W	ENST00000355710	NM_020975.4	525	Cgg/Tgg	8/20	0.142871666070727	1	FACETS	0.622	0.567	0.681	0.622	0.567	0.681	INDETERMINATE	1	TRUE	0	0.467999802357001	1		958	710	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082286	16082286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	222	983	0	ENST00000281043.3:c.100G>A	p.Asp34Asn	p.D34N	ENST00000281043	NM_005378.4	34	Gac/Aac	2/3	0.467999802357001	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.467999802357001	1		983	679	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44919308	44919311	+	frameshift_variant	Frame_Shift_Del	DEL	AACT	AACT	-	novel	NA	P-0028425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	93	254	0	ENST00000377967.4:c.1238_1241del	p.Thr413AsnfsTer25	p.T413Nfs*25	ENST00000377967	NM_021140.2	412	aaAACT/aa	13/29	1	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.467999802357001	1		254	208	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	114	210	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.228388707225411	2		210	717	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781904	9781904	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	66	626	0	ENST00000377346.4:c.2041G>C	p.Val681Leu	p.V681L	ENST00000377346	NM_005026.3	681	Gtg/Ctg	16/24	1	2	FACETS	0.568	0.491	0.651	0.568	0.491	0.651	SUBCLONAL	1	TRUE	1	0.228388707225411	2		626	1018	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55524245	55524245	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	60	532	0	ENST00000288135.5:c.64A>G	p.Thr22Ala	p.T22A	ENST00000288135	NM_000222.2	22	Aca/Gca	1/21	1	2	FACETS	0.629	0.541	0.726	0.629	0.541	0.726	SUBCLONAL	1	TRUE	1	0.228388707225411	2		532	835	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074335	8074335	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	268	395	1	ENST00000377482.5:c.324G>T	p.Glu108Asp	p.E108D	ENST00000377482	NM_018948.3	108	gaG/gaT	4/4	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.582137615376259	2		396	757	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303205	11303205	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	306	581	1	ENST00000361445.4:c.1378C>T	p.Arg460Ter	p.R460*	ENST00000361445	NM_004958.3	460	Cga/Tga	9/58	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.582137615376259	2		582	1022	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199319	16199319	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1460194680	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	169	275	0	ENST00000375759.3:c.92G>A	p.Arg31His	p.R31H	ENST00000375759	NM_015001.2	31	cGc/cAc	2/15	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.582137615376259	2		275	571	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101225	27101225	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	275	607	0	ENST00000324856.7:c.4507G>T	p.Asp1503Tyr	p.D1503Y	ENST00000324856	NM_006015.4	1503	Gac/Tac	18/20	1	2	FACETS	0.972	0.914	1	0.972	0.914	1	CLONAL	1	TRUE	1	0.582137615376259	2		607	972	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39317318	39317318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	263	651	1	ENST00000373001.3:c.868G>A	p.Asp290Asn	p.D290N	ENST00000373001	NM_022157.3	290	Gat/Aat	5/7	1	2	FACETS	0.914	0.857	0.972	0.914	0.857	0.972	CLONAL	1	TRUE	1	0.582137615376259	2		652	989	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39317430	39317430	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	310	596	0	ENST00000373001.3:c.757-1G>T		p.X253_splice	ENST00000373001	NM_022157.3	253			1	2	FACETS	0.995	0.939	1	0.995	0.939	1	CLONAL	1	TRUE	1	0.582137615376259	2		596	1070	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736474	85736474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	205	379	0	ENST00000370580.1:c.173G>A	p.Arg58Gln	p.R58Q	ENST00000370580	NM_003921.4	58	cGa/cAa	2/3	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.582137615376259	2		379	669	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724632	162724632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767283136	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	230	382	1	ENST00000367921.3:c.404G>A	p.Arg135His	p.R135H	ENST00000367921	NM_006182.2	135	cGt/cAt	5/18	1	2	FACETS	0.974	0.911	1	0.974	0.911	1	CLONAL	1	TRUE	1	0.582137615376259	2		383	811	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206943236	206943236	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs766492258	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	140	345	2	ENST00000423557.1:c.382C>T	p.Arg128Ter	p.R128*	ENST00000423557	NM_000572.2	128	Cga/Tga	4/5	1	2	FACETS	0.832	0.761	0.906	0.832	0.761	0.906	CLONAL	1	TRUE	1	0.582137615376259	2		347	578	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333143	70333143	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767493807	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	400	640	0	ENST00000373644.4:c.1048G>A	p.Glu350Lys	p.E350K	ENST00000373644	NM_030625.2	350	Gaa/Aaa	2/12	0.582137615376259	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.582137615376259	1		640	872	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405743	70405743	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	333	558	0	ENST00000373644.4:c.3257C>T	p.Ser1086Leu	p.S1086L	ENST00000373644	NM_030625.2	1086	tCg/tTg	4/12	0.582137615376259	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.582137615376259	1		558	758	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649869	88649869	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781556	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	203	411	1	ENST00000372037.3:c.118G>A	p.Asp40Asn	p.D40N	ENST00000372037	NM_004329.2	40	Gac/Aac	4/13	0.582137615376259	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.582137615376259	1		412	473	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88671996	88671996	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	288	643	0	ENST00000372037.3:c.531-1G>T		p.X177_splice	ENST00000372037	NM_004329.2	177			0.582137615376259	1	FACETS	0.974	0.922	1	0.974	0.922	1	CLONAL	1	TRUE	0	0.582137615376259	1		643	720	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154868	2154868	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768105151	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	321	746	1	ENST00000434045.2:c.353G>A	p.Arg118His	p.R118H	ENST00000434045	NM_001127598.1	118	cGc/cAc	4/5	1	2	FACETS	0.988	0.934	1	0.988	0.934	1	CLONAL	1	TRUE	1	0.582137615376259	2		747	1116	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316091	14316091	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	139	349	0	ENST00000256196.4:c.334C>A	p.Leu112Ile	p.L112I	ENST00000256196		112	Ctc/Atc	4/6	1	2	FACETS	0.989	0.906	1	0.989	0.906	1	CLONAL	1	TRUE	1	0.582137615376259	2		349	483	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102080254	102080254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193100333	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	170	482	1	ENST00000282441.5:c.991C>T	p.Arg331Trp	p.R331W	ENST00000282441	NM_001130145.2	331	Cgg/Tgg	6/9	1	2	FACETS	0.74	0.682	0.801	0.74	0.682	0.801	SUBCLONAL	1	TRUE	1	0.582137615376259	2		483	789	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115600	108115600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772821016	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	197	485	0	ENST00000278616.4:c.748C>T	p.Arg250Ter	p.R250*	ENST00000278616	NM_000051.3	250	Cga/Tga	7/63	1	2	FACETS	0.984	0.915	1	0.984	0.915	1	CLONAL	1	TRUE	1	0.582137615376259	2		485	688	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143494	108143494	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs766342338	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	232	536	0	ENST00000278616.4:c.3199G>T	p.Asp1067Tyr	p.D1067Y	ENST00000278616	NM_000051.3	1067	Gac/Tac	22/63	1	2	FACETS	0.963	0.9	1	0.963	0.9	1	CLONAL	1	TRUE	1	0.582137615376259	2		536	828	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190757	108190757	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1263398076	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	139	594	0	ENST00000278616.4:c.6424A>G	p.Thr2142Ala	p.T2142A	ENST00000278616	NM_000051.3	2142	Aca/Gca	44/63	1	2	FACETS	0.637	0.58	0.696	0.637	0.58	0.696	SUBCLONAL	1	TRUE	1	0.582137615376259	2		594	750	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352742	118352742	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	258	558	1	ENST00000534358.1:c.3947G>T	p.Arg1316Ile	p.R1316I	ENST00000534358	NM_005933.3	1316	aGa/aTa	7/36	1	2	FACETS	0.919	0.862	0.978	0.919	0.862	0.978	CLONAL	1	TRUE	1	0.582137615376259	2		559	964	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144604	119144604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	164	235	0	ENST00000264033.4:c.617G>A	p.Arg206Gln	p.R206Q	ENST00000264033	NM_005188.3	206	cGa/cAa	4/16	1	2	FACETS	0.892	0.822	0.964	0.892	0.822	0.964	CLONAL	1	TRUE	1	0.582137615376259	2		235	632	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155743	119155743	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	303	662	4	ENST00000264033.4:c.1496G>A	p.Arg499Gln	p.R499Q	ENST00000264033	NM_005188.3	499	cGa/cAa	10/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.582137615376259	2		666	1036	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	493277	493277	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	261	537	0	ENST00000399788.2:c.286A>C	p.Lys96Gln	p.K96Q	ENST00000399788	NM_001042603.1	96	Aaa/Caa	3/28	NA	2	FACETS	0.965	0.906	1			1	INDETERMINATE	1	TRUE	NA	0.582137615376259	2		537	929	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435082	18435082	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	222	436	0	ENST00000266497.5:c.67G>T	p.Glu23Ter	p.E23*	ENST00000266497		23	Gaa/Taa	1/31	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.582137615376259	2		436	758	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628732	21628732	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	196	529	0	ENST00000421138.2:c.976G>T	p.Asp326Tyr	p.D326Y	ENST00000421138		326	Gac/Tac	10/16	1	2	FACETS	0.957	0.889	1	0.957	0.889	1	CLONAL	1	TRUE	1	0.582137615376259	2		529	704	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944761	31944761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	134	220	0	ENST00000340398.3:c.340G>A	p.Ala114Thr	p.A114T	ENST00000340398	NM_001013699.2	114	Gct/Act	1/1	1	2	FACETS	0.953	0.872	1	0.953	0.872	1	CLONAL	1	TRUE	1	0.582137615376259	2		220	483	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231173	46231173	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	173	385	0	ENST00000334344.6:c.1093T>C	p.Ser365Pro	p.S365P	ENST00000334344	NM_152641.2	365	Tca/Cca	9/21	1	2	FACETS	0.906	0.837	0.977	0.906	0.837	0.977	CLONAL	1	TRUE	1	0.582137615376259	2		385	656	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424427	49424427	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs577303074	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	308	562	0	ENST00000301067.7:c.13796C>T	p.Ala4599Val	p.A4599V	ENST00000301067	NM_003482.3	4599	gCg/gTg	41/54	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.582137615376259	2		562	999	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884982	111884982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776733533	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	311	650	1	ENST00000341259.2:c.980C>T	p.Thr327Met	p.T327M	ENST00000341259	NM_005475.2	327	aCg/aTg	5/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.582137615376259	2		651	1001	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891037	112891037	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	195	369	0	ENST00000351677.2:c.371A>C	p.Lys124Thr	p.K124T	ENST00000351677	NM_002834.3	124	aAa/aCa	4/16	1	2	FACETS	0.919	0.853	0.987	0.919	0.853	0.987	CLONAL	1	TRUE	1	0.582137615376259	2		369	729	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249845	133249856	+	inframe_deletion	In_Frame_Del	DEL	CAGAATACGTGG	CAGAATACGTGG	-	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	212	520	0	ENST00000320574.5:c.1367_1378del	p.Ala456_Ser459del	p.A456_S459del	ENST00000320574	NM_006231.2	456	gCCACGTATTCTGtg/gtg	14/49	1	2	FACETS	0.917	0.854	0.982	0.917	0.854	0.982	CLONAL	1	TRUE	1	0.582137615376259	2		520	794	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620154	21620154	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	232	440	0	ENST00000382592.4:c.12G>T	p.Lys4Asn	p.K4N	ENST00000382592	NM_014572.2	4	aaG/aaT	2/8	1	2	FACETS	0.941	0.879	1	0.941	0.879	1	CLONAL	1	TRUE	1	0.582137615376259	2		440	847	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967503	26967503	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	141	327	0	ENST00000381527.3:c.647-1G>T		p.X216_splice	ENST00000381527	NM_001260.1	216			1	2	FACETS	0.973	0.892	1	0.973	0.892	1	CLONAL	1	TRUE	1	0.582137615376259	2		327	498	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913575	32913575	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	235	444	0	ENST00000380152.3:c.5083G>T	p.Glu1695Ter	p.E1695*	ENST00000380152		1695	Gaa/Taa	11/27	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.582137615376259	2		444	805	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913801	32913801	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	203	514	0	ENST00000380152.3:c.5309C>A	p.Ser1770Tyr	p.S1770Y	ENST00000380152		1770	tCt/tAt	11/27	1	2	FACETS	0.94	0.874	1	0.94	0.874	1	CLONAL	1	TRUE	1	0.582137615376259	2		514	742	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916833	48916834	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs869214358	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	137	461	0	ENST00000267163.4:c.368dup	p.Asn123LysfsTer8	p.N123Kfs*8	ENST00000267163	NM_000321.2	121	-/A	3/27	1	2	FACETS	0.875	0.8	0.953	0.875	0.8	0.953	CLONAL	1	TRUE	1	0.582137615376259	2		461	538	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919244	48919244	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913296	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	105	199	0	ENST00000267163.4:c.409G>T	p.Glu137Ter	p.E137*	ENST00000267163	NM_000321.2	137	Gaa/Taa	4/27	1	2	FACETS	0.999	0.904	1	0.999	0.904	1	CLONAL	1	TRUE	1	0.582137615376259	2		199	361	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504590	103504590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1400329743	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	136	350	0	ENST00000355739.4:c.211C>T	p.Arg71Cys	p.R71C	ENST00000355739	NM_000123.3	71	Cgt/Tgt	2/15	1	2	FACETS	0.799	0.729	0.871	0.799	0.729	0.871	SUBCLONAL	1	TRUE	1	0.582137615376259	2		350	585	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518233	103518233	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764873580	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	136	278	0	ENST00000355739.4:c.2171C>T	p.Ser724Leu	p.S724L	ENST00000355739	NM_000123.3	724	tCg/tTg	9/15	1	2	FACETS	0.897	0.82	0.977	0.897	0.82	0.977	CLONAL	1	TRUE	1	0.582137615376259	2		278	521	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435889	110435889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1329734454	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	239	551	0	ENST00000375856.3:c.2512C>T	p.Arg838Cys	p.R838C	ENST00000375856	NM_003749.2	838	Cgt/Tgt	1/2	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.582137615376259	2		551	816	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093456	30093456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1008608681	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	125	389	0	ENST00000331968.5:c.1807C>T	p.Arg603Cys	p.R603C	ENST00000331968	NM_002742.2	603	Cgt/Tgt	13/18	1	2	FACETS	0.938	0.855	1	0.938	0.855	1	CLONAL	1	TRUE	1	0.582137615376259	2		389	458	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988543	36988543	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	452	1003	0	ENST00000354822.5:c.110A>G	p.His37Arg	p.H37R	ENST00000354822	NM_001079668.2	37	cAc/cGc	2/3	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.582137615376259	2		1003	1436	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81557479	81557479	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	204	355	1	ENST00000298171.2:c.459C>A	p.Phe153Leu	p.F153L	ENST00000298171	NM_000369.2	153	ttC/ttA	5/10	1	2	FACETS	0.915	0.851	0.981	0.915	0.851	0.981	CLONAL	1	TRUE	1	0.582137615376259	2		356	766	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610399	81610399	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	250	437	0	ENST00000298171.2:c.1997T>C	p.Phe666Ser	p.F666S	ENST00000298171	NM_000369.2	666	tTc/tCc	10/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.582137615376259	2		437	765	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590877	95590877	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1161765608	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	129	310	0	ENST00000393063.1:c.1032T>G	p.Phe344Leu	p.F344L	ENST00000393063	NM_030621.3	344	ttT/ttG	9/28	1	2	FACETS	0.702	0.638	0.769	0.702	0.638	0.769	SUBCLONAL	1	TRUE	1	0.582137615376259	2		310	631	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022963	33022964	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	163	433	0	ENST00000300177.4:c.77dup	p.Lys27GlufsTer17	p.K27Efs*17	ENST00000300177	NM_001191322.1	24	-/A	2/2	1	2	FACETS	0.77	0.708	0.835	0.77	0.708	0.835	SUBCLONAL	1	TRUE	1	0.582137615376259	2		433	727	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708558	43708558	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	330	705	1	ENST00000382044.4:c.4738G>T	p.Glu1580Ter	p.E1580*	ENST00000382044	NM_001141980.1	1580	Gaa/Taa	22/28	1	2	FACETS	0.991	0.937	1	0.991	0.937	1	CLONAL	1	TRUE	1	0.582137615376259	2		706	1144	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43738669	43738669	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758253263	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	331	660	0	ENST00000382044.4:c.2956G>A	p.Val986Met	p.V986M	ENST00000382044	NM_001141980.1	986	Gtg/Atg	14/28	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.582137615376259	2		660	1098	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423573	88423573	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	295	593	0	ENST00000360948.2:c.2262G>T	p.Trp754Cys	p.W754C	ENST00000360948	NM_001012338.2	754	tgG/tgT	18/19	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.582137615376259	2		593	963	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293004	91293004	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1013299710	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	293	574	0	ENST00000355112.3:c.506T>G	p.Phe169Cys	p.F169C	ENST00000355112	NM_000057.2	169	tTt/tGt	3/22	1	2	FACETS	0.927	0.873	0.983	0.927	0.873	0.983	CLONAL	1	TRUE	1	0.582137615376259	2		574	1086	SUCCESS
BLM	641	MSKCC	GRCh37	15	91352370	91352370	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	148	280	0	ENST00000355112.3:c.3755C>A	p.Ser1252Tyr	p.S1252Y	ENST00000355112	NM_000057.2	1252	tCt/tAt	20/22	1	2	FACETS	0.97	0.892	1	0.97	0.892	1	CLONAL	1	TRUE	1	0.582137615376259	2		280	524	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110728	2110728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397515146	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	367	809	1	ENST00000219476.3:c.1033C>T	p.Leu345Phe	p.L345F	ENST00000219476	NM_000548.3	345	Ctc/Ttc	11/42	1	2	FACETS	0.947	0.898	0.998	0.947	0.898	0.998	CLONAL	1	TRUE	1	0.582137615376259	2		810	1331	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923482	9923482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	262	495	0	ENST00000330684.3:c.1805G>A	p.Gly602Glu	p.G602E	ENST00000330684	NM_001134407.1	602	gGa/gAa	9/13	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.582137615376259	2		495	839	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041599	14041599	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	251	446	0	ENST00000311895.7:c.2146T>G	p.Tyr716Asp	p.Y716D	ENST00000311895	NM_005236.2	716	Tac/Gac	11/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.582137615376259	2		446	824	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72833937	72833937	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199774638	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	221	442	0	ENST00000268489.5:c.3956G>A	p.Gly1319Glu	p.G1319E	ENST00000268489	NM_006885.3	1319	gGa/gAa	8/10	1	2	FACETS	0.978	0.913	1	0.978	0.913	1	CLONAL	1	TRUE	1	0.582137615376259	2		442	776	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944157	81944157	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761094228	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	302	551	0	ENST00000359376.3:c.1766G>A	p.Arg589His	p.R589H	ENST00000359376	NM_002661.3	589	cGc/cAc	18/33	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.582137615376259	2		551	978	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217654	7217654	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	233	429	0	ENST00000380728.2:c.273G>T	p.Lys91Asn	p.K91N	ENST00000380728		91	aaG/aaT	4/11	1	2	FACETS	0.94	0.878	1	0.94	0.878	1	CLONAL	1	TRUE	1	0.582137615376259	2		429	852	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	363	760	0	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.582137615376259	2		760	1236	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	387	717	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.582137615376259	2		718	1231	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16046956	16046956	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	225	491	0	ENST00000268712.3:c.1137G>T	p.Glu379Asp	p.E379D	ENST00000268712	NM_006311.3	379	gaG/gaT	11/46	1	2	FACETS	0.944	0.881	1	0.944	0.881	1	CLONAL	1	TRUE	1	0.582137615376259	2		491	819	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663680	29663680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761029453	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	253	431	0	ENST00000356175.3:c.6112G>A	p.Asp2038Asn	p.D2038N	ENST00000356175	NM_000267.3	2038	Gac/Aac	41/57	1	2	FACETS	0.954	0.894	1	0.954	0.894	1	CLONAL	1	TRUE	1	0.582137615376259	2		431	911	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243774	41243774	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs431825399	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	303	529	0	ENST00000357654.3:c.3774G>T	p.Glu1258Asp	p.E1258D	ENST00000357654	NM_007294.3	1258	gaG/gaT	10/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.582137615376259	2		529	995	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696636	47696636	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	327	489	1	ENST00000347630.2:c.312C>A	p.Phe104Leu	p.F104L	ENST00000347630	NM_001007230.1	104	ttC/ttA	5/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.582137615376259	2		490	1009	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59878810	59878810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867548960	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	148	283	0	ENST00000259008.2:c.944G>A	p.Gly315Glu	p.G315E	ENST00000259008	NM_032043.2	315	gGa/gAa	8/20	1	2	FACETS	0.93	0.854	1	0.93	0.854	1	CLONAL	1	TRUE	1	0.582137615376259	2		283	547	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943516	17943516	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	206	582	1	ENST00000458235.1:c.2492G>A	p.Gly831Asp	p.G831D	ENST00000458235	NM_000215.3	831	gGc/gAc	19/24	1	2	FACETS	0.765	0.71	0.822	0.765	0.71	0.822	SUBCLONAL	1	TRUE	1	0.582137615376259	2		583	925	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258520	19258520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376625415	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1212	72	800	2	ENST00000162023.5:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000162023		127	cGa/cAa	8/13	1	2	FACETS	0.193	0.167	0.22	0.193	0.167	0.22	SUBCLONAL	1	TRUE	1	0.582137615376259	2		802	1284	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30311662	30311662	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	237	485	0	ENST00000262643.3:c.516C>A	p.Phe172Leu	p.F172L	ENST00000262643	NM_001238.2	172	ttC/ttA	7/12	1	2	FACETS	0.9	0.841	0.96	0.9	0.841	0.96	CLONAL	1	TRUE	1	0.582137615376259	2		485	905	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218350	36218350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1454713201	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	323	798	0	ENST00000222270.7:c.4129G>A	p.Glu1377Lys	p.E1377K	ENST00000222270	NM_014727.1	1377	Gag/Aag	16/37	1	2	FACETS	0.959	0.906	1	0.959	0.906	1	CLONAL	1	TRUE	1	0.582137615376259	2		798	1157	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726565	41726565	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	279	533	0	ENST00000301178.4:c.110T>C	p.Phe37Ser	p.F37S	ENST00000301178	NM_021913.4	37	tTc/tCc	2/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.582137615376259	2		533	875	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416563	29416563	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs374135358	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	273	508	0	ENST00000389048.3:c.4390C>T	p.Arg1464Ter	p.R1464*	ENST00000389048	NM_004304.4	1464	Cga/Tga	29/29	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.582137615376259	2		508	917	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754886	29754886	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759426382	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	216	418	0	ENST00000389048.3:c.1049C>T	p.Ser350Leu	p.S350L	ENST00000389048	NM_004304.4	350	tCg/tTg	4/29	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.582137615376259	2		418	740	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637278	47637278	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553350673	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	311	577	0	ENST00000233146.2:c.412A>G	p.Asn138Asp	p.N138D	ENST00000233146	NM_000251.2	138	Aac/Gac	3/16	1	2	FACETS	0.991	0.935	1	0.991	0.935	1	CLONAL	1	TRUE	1	0.582137615376259	2		577	1078	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027958	48027958	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1558666905	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	174	337	0	ENST00000234420.5:c.2836G>T	p.Glu946Ter	p.E946*	ENST00000234420	NM_000179.2	946	Gaa/Taa	4/10	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.582137615376259	2		337	593	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030754	48030754	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	166	310	0	ENST00000234420.5:c.3368A>G	p.Glu1123Gly	p.E1123G	ENST00000234420	NM_000179.2	1123	gAa/gGa	5/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.582137615376259	2		310	549	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	220	508	1	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	1	2	FACETS	0.956	0.892	1	0.956	0.892	1	CLONAL	1	TRUE	1	0.582137615376259	2		509	791	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128028924	128028924	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1404157087	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	289	594	0	ENST00000285398.2:c.1933C>T	p.Arg645Ter	p.R645*	ENST00000285398	NM_000122.1	645	Cga/Tga	12/15	1	2	FACETS	0.977	0.92	1	0.977	0.92	1	CLONAL	1	TRUE	1	0.582137615376259	2		594	1016	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038043	128038043	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745884071	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	179	456	0	ENST00000285398.2:c.1507G>A	p.Ala503Thr	p.A503T	ENST00000285398	NM_000122.1	503	Gcc/Acc	9/15	1	2	FACETS	0.956	0.886	1	0.956	0.886	1	CLONAL	1	TRUE	1	0.582137615376259	2		456	643	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095691	178095691	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	198	433	0	ENST00000397062.3:c.1640A>G	p.Asp547Gly	p.D547G	ENST00000397062	NM_006164.4	547	gAc/gGc	5/5	1	2	FACETS	0.909	0.845	0.976	0.909	0.845	0.976	CLONAL	1	TRUE	1	0.582137615376259	2		433	748	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719617	190719617	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	113	197	0	ENST00000441310.2:c.1619A>C	p.Asn540Thr	p.N540T	ENST00000441310	NM_000534.4	540	aAt/aCt	9/13	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.582137615376259	2		197	365	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566803	212566803	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747093464	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	168	357	0	ENST00000342788.4:c.1378A>G	p.Ile460Val	p.I460V	ENST00000342788	NM_005235.2	460	Att/Gtt	12/28	1	2	FACETS	0.957	0.884	1	0.957	0.884	1	CLONAL	1	TRUE	1	0.582137615376259	2		357	603	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593410	215593410	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	28	194	0	ENST00000260947.4:c.2324T>C	p.Leu775Pro	p.L775P	ENST00000260947	NM_000465.2	775	cTt/cCt	11/11	1	2	FACETS	0.239	0.19	0.294	0.239	0.19	0.294	SUBCLONAL	1	TRUE	1	0.582137615376259	2		194	403	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016048	31016048	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771925643	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	873	613	2	ENST00000375687.4:c.370G>A	p.Asp124Asn	p.D124N	ENST00000375687	NM_015338.5	124	Gat/Aat	5/13	0.561410581733298	4	FACETS	0.997	0.97	1	0.997	0.97	1	CLONAL	3	TRUE	1	0.582137615376259	4		615	1586	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735548	40735548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	234	470	0	ENST00000373198.4:c.3325C>T	p.Arg1109Trp	p.R1109W	ENST00000373198	NM_133170.3	1109	Cgg/Tgg	25/32	0.561410581733298	4	FACETS	1	0.946	1	0.339	0.316	0.364	CLONAL	1	TRUE	1	0.582137615376259	4		470	1249	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100959	41100959	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	259	497	0	ENST00000373198.4:c.1397A>G	p.Asn466Ser	p.N466S	ENST00000373198	NM_133170.3	466	aAc/aGc	8/32	0.561410581733298	4	FACETS	1	0.974	1	0.359	0.335	0.383	CLONAL	1	TRUE	1	0.582137615376259	4		497	1307	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39774543	39774543	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	215	410	0	ENST00000288319.7:c.609G>T	p.Leu203Phe	p.L203F	ENST00000288319	NM_182918.3	203	ttG/ttT	5/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.582137615376259	2		410	698	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29099533	29099533	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	295	530	0	ENST00000328354.6:c.868A>C	p.Asn290His	p.N290H	ENST00000328354	NM_007194.3	290	Aac/Cac	8/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.582137615376259	2		530	885	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074282	30074282	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	234	474	0	ENST00000338641.4:c.1544A>C	p.Lys515Thr	p.K515T	ENST00000338641	NM_000268.3	515	aAg/aCg	14/16	1	2	FACETS	0.973	0.91	1	0.973	0.91	1	CLONAL	1	TRUE	1	0.582137615376259	2		474	826	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513353	41513353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147121738	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	342	649	1	ENST00000263253.7:c.257G>A	p.Arg86Gln	p.R86Q	ENST00000263253	NM_001429.3	86	cGa/cAa	2/31	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.582137615376259	2		650	1119	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545898	41545898	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774840930	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	334	846	5	ENST00000263253.7:c.2513G>A	p.Arg838His	p.R838H	ENST00000263253	NM_001429.3	838	cGt/cAt	14/31	1	2	FACETS	0.836	0.789	0.884	0.836	0.789	0.884	CLONAL	1	TRUE	1	0.582137615376259	2		851	1373	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37083763	37083763	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63751081	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	188	330	1	ENST00000231790.2:c.1672G>T	p.Glu558Ter	p.E558*	ENST00000231790	NM_000249.3	558	Gaa/Taa	15/19	1	2	FACETS	0.997	0.925	1	0.997	0.925	1	CLONAL	1	TRUE	1	0.582137615376259	2		331	648	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182637	38182637	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs748659894	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	167	275	0	ENST00000396334.3:c.790C>T	p.Arg264Ter	p.R264*	ENST00000396334	NM_002468.4	264	Cga/Tga	5/5	1	2	FACETS	0.977	0.903	1	0.977	0.903	1	CLONAL	1	TRUE	1	0.582137615376259	2		275	587	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164366	47164366	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1299511576	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	167	317	1	ENST00000409792.3:c.1760C>A	p.Ser587Tyr	p.S587Y	ENST00000409792	NM_014159.6	587	tCt/tAt	3/21	1	2	FACETS	0.898	0.828	0.97	0.898	0.828	0.97	CLONAL	1	TRUE	1	0.582137615376259	2		318	639	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49724690	49724690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	228	432	0	ENST00000449682.2:c.499G>A	p.Glu167Lys	p.E167K	ENST00000449682	NM_020998.3	167	Gaa/Aaa	5/18	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.582137615376259	2		432	727	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643474	52643474	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1194011743	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	245	433	0	ENST00000394830.3:c.2422C>A	p.Pro808Thr	p.P808T	ENST00000394830	NM_018313.4	808	Cct/Act	17/30	1	2	FACETS	0.965	0.904	1	0.965	0.904	1	CLONAL	1	TRUE	1	0.582137615376259	2		433	872	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014163	70014163	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868519483	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	376	695	2	ENST00000394351.3:c.1024G>A	p.Asp342Asn	p.D342N	ENST00000394351	NM_000248.3	342	Gat/Aat	9/9	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.582137615376259	2		697	1139	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73108259	73108259	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	70	204	0	ENST00000356692.5:c.359A>C	p.Lys120Thr	p.K120T	ENST00000356692		120	aAa/aCa	4/9	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.582137615376259	2		204	235	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445029	89445029	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	241	556	0	ENST00000336596.2:c.1349G>T	p.Arg450Ile	p.R450I	ENST00000336596	NM_005233.5	450	aGa/aTa	6/17	1	2	FACETS	0.952	0.891	1	0.952	0.891	1	CLONAL	1	TRUE	1	0.582137615376259	2		556	870	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457256	89457256	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	195	479	0	ENST00000336596.2:c.1737A>C	p.Lys579Asn	p.K579N	ENST00000336596	NM_005233.5	579	aaA/aaC	9/17	1	2	FACETS	0.975	0.906	1	0.975	0.906	1	CLONAL	1	TRUE	1	0.582137615376259	2		479	687	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119562186	119562186	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	178	345	1	ENST00000316626.5:c.1150C>T	p.Pro384Ser	p.P384S	ENST00000316626		384	Cca/Tca	11/12	1	2	FACETS	0.91	0.842	0.98	0.91	0.842	0.98	CLONAL	1	TRUE	1	0.582137615376259	2		346	672	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453482	138453482	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	178	352	0	ENST00000289153.2:c.966T>G	p.Ile322Met	p.I322M	ENST00000289153	NM_006219.2	322	atT/atG	5/22	1	2	FACETS	0.956	0.885	1	0.956	0.885	1	CLONAL	1	TRUE	1	0.582137615376259	2		352	640	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461462	138461462	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	270	535	0	ENST00000289153.2:c.559A>C	p.Asn187His	p.N187H	ENST00000289153	NM_006219.2	187	Aac/Cac	3/22	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.582137615376259	2		535	900	SUCCESS
ATR	545	MSKCC	GRCh37	3	142224146	142224146	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	115	233	0	ENST00000350721.4:c.5032-1G>T		p.X1678_splice	ENST00000350721	NM_001184.3	1678			1	2	FACETS	0.888	0.805	0.974	0.888	0.805	0.974	CLONAL	1	TRUE	1	0.582137615376259	2		233	445	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242849	142242849	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	258	446	0	ENST00000350721.4:c.4138G>T	p.Asp1380Tyr	p.D1380Y	ENST00000350721	NM_001184.3	1380	Gat/Tat	22/47	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.582137615376259	2		446	834	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916797	178916797	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	297	605	0	ENST00000263967.3:c.184C>A	p.Leu62Ile	p.L62I	ENST00000263967	NM_006218.2	62	Ctt/Att	2/21	0.582137615376259	3	FACETS	1	0.956	1	0.51	0.479	0.541	CLONAL	1	TRUE	1	0.582137615376259	3		605	1292	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	224	471	0	ENST00000263967.3:c.333G>T	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaT	2/21	0.582137615376259	3	FACETS	1	0.973	1	0.542	0.505	0.58	CLONAL	1	TRUE	1	0.582137615376259	3		471	917	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917562	178917562	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	186	508	0	ENST00000263967.3:c.437T>C	p.Val146Ala	p.V146A	ENST00000263967	NM_006218.2	146	gTt/gCt	3/21	0.582137615376259	3	FACETS	0.969	0.896	1	0.485	0.448	0.523	CLONAL	1	TRUE	1	0.582137615376259	3		508	851	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922301	178922301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	205	440	0	ENST00000263967.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000263967	NM_006218.2	357	cGa/cAa	6/21	0.582137615376259	3	FACETS	1	0.935	1	0.503	0.467	0.541	CLONAL	1	TRUE	1	0.582137615376259	3		440	903	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936068	178936068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	165	459	0	ENST00000263967.3:c.1610G>A	p.Arg537Gln	p.R537Q	ENST00000263967	NM_006218.2	537	cGa/cAa	10/21	0.582137615376259	3	FACETS	1	0.944	1	0.515	0.474	0.558	CLONAL	1	TRUE	1	0.582137615376259	3		459	710	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167750	185167750	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	260	505	0	ENST00000265026.3:c.1073C>A	p.Ser358Tyr	p.S358Y	ENST00000265026	NM_004721.4	358	tCt/tAt	6/14	0.582137615376259	3	FACETS	0.993	0.93	1	0.497	0.465	0.53	CLONAL	1	TRUE	1	0.582137615376259	3		505	1161	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612175	189612175	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1560311554	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	524	548	7	ENST00000264731.3:c.1927C>T	p.Arg643Ter	p.R643*	ENST00000264731	NM_003722.4	643	Cga/Tga	14/14	0.582137615376259	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.582137615376259	3		555	1111	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144549	55144549	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	197	426	0	ENST00000257290.5:c.2023G>T	p.Glu675Ter	p.E675*	ENST00000257290	NM_006206.4	675	Gag/Tag	15/23	1	2	FACETS	0.911	0.846	0.978	0.911	0.846	0.978	CLONAL	1	TRUE	1	0.582137615376259	2		426	743	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958788	55958788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780764266	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	597	569	0	ENST00000263923.4:c.3065G>A	p.Arg1022Gln	p.R1022Q	ENST00000263923	NM_002253.2	1022	cGa/cAa	22/30	1	2	FACETS	1	0.989	1	1	0.998	1	CLONAL	2	TRUE	1	0.582137615376259	2		569	983	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286219	66286219	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	154	444	0	ENST00000273854.3:c.1467G>T	p.Trp489Cys	p.W489C	ENST00000273854	NM_004439.5	489	tgG/tgT	6/18	1	2	FACETS	0.958	0.882	1	0.958	0.882	1	CLONAL	1	TRUE	1	0.582137615376259	2		444	552	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808276	99808276	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	267	482	0	ENST00000280892.6:c.413A>T	p.Asn138Ile	p.N138I	ENST00000280892	NM_001130678.1	138	aAc/aTc	5/7	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.582137615376259	2		482	908	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155583	106155583	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	186	369	0	ENST00000380013.4:c.484G>T	p.Asp162Tyr	p.D162Y	ENST00000380013	NM_001127208.2	162	Gat/Tat	3/11	1	2	FACETS	0.78	0.722	0.841	0.78	0.722	0.841	SUBCLONAL	1	TRUE	1	0.582137615376259	2		369	819	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106182921	106182921	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	107	399	0	ENST00000380013.4:c.3960G>T	p.Glu1320Asp	p.E1320D	ENST00000380013	NM_001127208.2	1320	gaG/gaT	8/11	1	2	FACETS	0.851	0.768	0.937	0.851	0.768	0.937	CLONAL	1	TRUE	1	0.582137615376259	2		399	432	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114337	143114337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747045725	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	195	461	1	ENST00000262992.4:c.1084G>A	p.Asp362Asn	p.D362N	ENST00000262992	NM_001101669.1	362	Gat/Aat	13/24	1	2	FACETS	0.94	0.873	1	0.94	0.873	1	CLONAL	1	TRUE	1	0.582137615376259	2		462	713	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531164	187531164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747163395	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	134	358	1	ENST00000441802.2:c.9859G>A	p.Val3287Ile	p.V3287I	ENST00000441802	NM_005245.3	3287	Gta/Ata	15/27	1	2	FACETS	0.712	0.648	0.778	0.712	0.648	0.778	SUBCLONAL	1	TRUE	1	0.582137615376259	2		359	647	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542633	187542633	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	226	433	0	ENST00000441802.2:c.5107G>T	p.Asp1703Tyr	p.D1703Y	ENST00000441802	NM_005245.3	1703	Gat/Tat	10/27	1	2	FACETS	0.987	0.922	1	0.987	0.922	1	CLONAL	1	TRUE	1	0.582137615376259	2		433	787	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542860	187542860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767331775	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	199	347	0	ENST00000441802.2:c.4880G>A	p.Arg1627Gln	p.R1627Q	ENST00000441802	NM_005245.3	1627	cGa/cAa	10/27	1	2	FACETS	0.955	0.888	1	0.955	0.888	1	CLONAL	1	TRUE	1	0.582137615376259	2		347	716	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950389	38950389	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	213	416	0	ENST00000357387.3:c.3561G>T	p.Lys1187Asn	p.K1187N	ENST00000357387	NM_152756.3	1187	aaG/aaT	31/38	1	2	FACETS	0.958	0.893	1	0.958	0.893	1	CLONAL	1	TRUE	1	0.582137615376259	2		416	764	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80021297	80021297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs963234468	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	208	502	0	ENST00000265081.6:c.1366G>A	p.Glu456Lys	p.E456K	ENST00000265081	NM_002439.4	456	Gaa/Aaa	9/24	1	2	FACETS	0.895	0.833	0.96	0.895	0.833	0.96	CLONAL	1	TRUE	1	0.582137615376259	2		502	798	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80160691	80160691	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	323	737	0	ENST00000265081.6:c.3060T>G	p.Asn1020Lys	p.N1020K	ENST00000265081	NM_002439.4	1020	aaT/aaG	22/24	1	2	FACETS	0.932	0.88	0.985	0.932	0.88	0.985	CLONAL	1	TRUE	1	0.582137615376259	2		737	1191	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633870	86633870	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	149	440	0	ENST00000274376.6:c.979G>T	p.Glu327Ter	p.E327*	ENST00000274376	NM_002890.2	327	Gaa/Taa	5/25	1	2	FACETS	0.809	0.741	0.879	0.809	0.741	0.879	CLONAL	1	TRUE	1	0.582137615376259	2		440	633	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86642527	86642527	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	101	345	0	ENST00000274376.6:c.1088A>C	p.Asn363Thr	p.N363T	ENST00000274376	NM_002890.2	363	aAt/aCt	7/25	1	2	FACETS	0.863	0.777	0.953	0.863	0.777	0.953	CLONAL	1	TRUE	1	0.582137615376259	2		345	402	SUCCESS
APC	324	MSKCC	GRCh37	5	112175118	112175118	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1060503299	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	153	189	0	ENST00000257430.4:c.3827C>A	p.Ser1276Ter	p.S1276*	ENST00000257430	NM_000038.5	1276	tCa/tAa	16/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.582137615376259	2		189	465	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	203	335	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.582137615376259	2		335	665	SUCCESS
APC	324	MSKCC	GRCh37	5	112177354	112177354	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	193	333	1	ENST00000257430.4:c.6063C>A	p.Phe2021Leu	p.F2021L	ENST00000257430	NM_000038.5	2021	ttC/ttA	16/16	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.582137615376259	2		334	660	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915107	131915107	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	298	579	0	ENST00000265335.6:c.464T>G	p.Ile155Ser	p.I155S	ENST00000265335		155	aTt/aGt	4/25	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.582137615376259	2		579	934	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176666781	176666781	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	187	468	1	ENST00000439151.2:c.4217G>T	p.Arg1406Ile	p.R1406I	ENST00000439151	NM_022455.4	1406	aGa/aTa	8/23	1	2	FACETS	0.907	0.841	0.976	0.907	0.841	0.976	CLONAL	1	TRUE	1	0.582137615376259	2		469	708	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176671259	176671259	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	151	322	0	ENST00000439151.2:c.4366G>T	p.Asp1456Tyr	p.D1456Y	ENST00000439151	NM_022455.4	1456	Gat/Tat	9/23	1	2	FACETS	0.774	0.71	0.841	0.774	0.71	0.841	SUBCLONAL	1	TRUE	1	0.582137615376259	2		322	670	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721223	176721223	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	202	372	1	ENST00000439151.2:c.6854G>T	p.Arg2285Ile	p.R2285I	ENST00000439151	NM_022455.4	2285	aGa/aTa	23/23	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.582137615376259	2		373	683	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047665	180047665	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757057248	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	362	821	0	ENST00000261937.6:c.2350G>A	p.Val784Ile	p.V784I	ENST00000261937	NM_182925.4	784	Gtc/Atc	16/30	1	2	FACETS	0.947	0.897	0.998	0.947	0.897	0.998	CLONAL	1	TRUE	1	0.582137615376259	2		821	1313	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047963	180047963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	382	685	0	ENST00000261937.6:c.2212G>A	p.Val738Met	p.V738M	ENST00000261937	NM_182925.4	738	Gtg/Atg	15/30	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.582137615376259	2		685	1119	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056286	180056286	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759344198	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	367	789	1	ENST00000261937.6:c.958C>T	p.Arg320Trp	p.R320W	ENST00000261937	NM_182925.4	320	Cgg/Tgg	7/30	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.582137615376259	2		790	1165	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163542	32163542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1187763031	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	190	515	1	ENST00000375023.3:c.5684C>T	p.Ser1895Phe	p.S1895F	ENST00000375023	NM_004557.3	1895	tCt/tTt	30/30	1	2	FACETS	0.977	0.907	1	0.977	0.907	1	CLONAL	1	TRUE	1	0.582137615376259	2		516	668	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169941	32169941	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1479628728	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	346	762	1	ENST00000375023.3:c.3667C>A	p.Leu1223Ile	p.L1223I	ENST00000375023	NM_004557.3	1223	Ctc/Atc	21/30	1	2	FACETS	0.986	0.933	1	0.986	0.933	1	CLONAL	1	TRUE	1	0.582137615376259	2		763	1206	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178537	32178537	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	274	501	0	ENST00000375023.3:c.2857C>A	p.Leu953Ile	p.L953I	ENST00000375023	NM_004557.3	953	Ctc/Atc	18/30	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.582137615376259	2		501	896	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289501	33289501	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1359646835	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	367	885	0	ENST00000374542.5:c.202G>A	p.Glu68Lys	p.E68K	ENST00000374542	NM_001141970.1	68	Gaa/Aaa	2/8	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.582137615376259	2		885	1256	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89791092	89791092	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	38	114	0	ENST00000336032.3:c.479C>A	p.Ala160Asp	p.A160D	ENST00000336032	NM_006813.2	160	gCc/gAc	1/2	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.582137615376259	2		114	126	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665230	117665230	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1258207555	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	125	254	0	ENST00000368508.3:c.4517G>T	p.Arg1506Ile	p.R1506I	ENST00000368508	NM_002944.2	1506	aGa/aTa	27/43	1	2	FACETS	0.985	0.898	1	0.985	0.898	1	CLONAL	1	TRUE	1	0.582137615376259	2		254	436	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001395	150001395	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	281	508	1	ENST00000253339.5:c.2209C>T	p.Arg737Ter	p.R737*	ENST00000253339		737	Cga/Tga	4/7	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.582137615376259	2		509	964	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004834	150004834	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	192	426	0	ENST00000253339.5:c.1391C>A	p.Ser464Tyr	p.S464Y	ENST00000253339		464	tCt/tAt	3/7	1	2	FACETS	0.832	0.771	0.895	0.832	0.771	0.895	CLONAL	1	TRUE	1	0.582137615376259	2		426	793	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163766	152163766	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	223	457	0	ENST00000206249.3:c.487G>T	p.Glu163Ter	p.E163*	ENST00000206249	NM_000125.3	163	Gaa/Taa	2/8	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.582137615376259	2		457	745	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382257	152382257	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	189	402	2	ENST00000206249.3:c.1367C>T	p.Ser456Phe	p.S456F	ENST00000206249	NM_000125.3	456	tCt/tTt	6/8	1	2	FACETS	0.979	0.909	1	0.979	0.909	1	CLONAL	1	TRUE	1	0.582137615376259	2		404	663	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100550	157100550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	133	348	0	ENST00000346085.5:c.1487G>T	p.Arg496Met	p.R496M	ENST00000346085	NM_020732.3	496	aGg/aTg	1/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.582137615376259	2		348	411	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951907	2951907	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	312	649	0	ENST00000396946.4:c.3043C>A	p.Leu1015Ile	p.L1015I	ENST00000396946	NM_032415.4	1015	Ctc/Atc	23/25	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.582137615376259	2		649	1009	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334740	81334740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	241	478	0	ENST00000222390.5:c.1976C>T	p.Ala659Val	p.A659V	ENST00000222390	NM_000601.4	659	gCt/gTt	17/18	1	2	FACETS	0.892	0.834	0.952	0.892	0.834	0.952	CLONAL	1	TRUE	1	0.582137615376259	2		478	928	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508152	106508152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1446853033	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	80	210	0	ENST00000359195.3:c.146G>A	p.Arg49His	p.R49H	ENST00000359195	NM_002649.2	49	cGc/cAc	2/11	1	2	FACETS	0.985	0.878	1	0.985	0.878	1	CLONAL	1	TRUE	1	0.582137615376259	2		210	279	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395562	116395562	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	222	424	0	ENST00000397752.3:c.1855A>G	p.Met619Val	p.M619V	ENST00000397752	NM_000245.2	619	Atg/Gtg	6/21	1	2	FACETS	0.956	0.892	1	0.956	0.892	1	CLONAL	1	TRUE	1	0.582137615376259	2		424	798	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525837	148525837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765147666	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	178	348	0	ENST00000320356.2:c.620G>A	p.Arg207Gln	p.R207Q	ENST00000320356	NM_004456.4	207	cGa/cAa	6/20	1	2	FACETS	0.897	0.829	0.966	0.897	0.829	0.966	CLONAL	1	TRUE	1	0.582137615376259	2		348	682	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873932	151873932	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	251	414	0	ENST00000262189.6:c.8606C>A	p.Ser2869Tyr	p.S2869Y	ENST00000262189	NM_170606.2	2869	tCt/tAt	38/59	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.582137615376259	2		414	820	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372534	55372534	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	442	974	2	ENST00000297316.4:c.1224C>A	p.Tyr408Ter	p.Y408*	ENST00000297316	NM_022454.3	408	taC/taA	2/2	1	2	FACETS	0.977	0.931	1	0.977	0.931	1	CLONAL	1	TRUE	1	0.582137615376259	2		976	1554	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995495	68995496	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	232	581	0	ENST00000288368.4:c.1904dup	p.Ile636AspfsTer5	p.I636Dfs*5	ENST00000288368	NM_024870.2	633	-/A	18/40	1	2	FACETS	0.896	0.836	0.956	0.896	0.836	0.956	CLONAL	1	TRUE	1	0.582137615376259	2		581	890	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69012038	69012038	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	316	604	0	ENST00000288368.4:c.2675G>T	p.Arg892Ile	p.R892I	ENST00000288368	NM_024870.2	892	aGa/aTa	23/40	1	2	FACETS	0.962	0.909	1	0.962	0.909	1	CLONAL	1	TRUE	1	0.582137615376259	2		604	1128	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117870651	117870651	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	192	425	0	ENST00000297338.2:c.421G>T	p.Glu141Ter	p.E141*	ENST00000297338	NM_006265.2	141	Gaa/Taa	5/14	1	2	FACETS	0.964	0.895	1	0.964	0.895	1	CLONAL	1	TRUE	1	0.582137615376259	2		425	684	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080620	5080620	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	372	541	0	ENST00000381652.3:c.2371G>T	p.Glu791Ter	p.E791*	ENST00000381652	NM_004972.3	791	Gaa/Taa	18/25	0.582137615376259	3	FACETS	0.942	0.898	0.986	0.942	0.898	0.986	CLONAL	2	TRUE	1	0.582137615376259	3		541	876	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090571	5090571	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	164	459	0	ENST00000381652.3:c.2886+1G>A		p.X962_splice	ENST00000381652	NM_004972.3	962			0.582137615376259	3	FACETS	0.994	0.914	1	0.497	0.457	0.538	CLONAL	1	TRUE	1	0.582137615376259	3		459	732	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158098	27158098	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	321	548	0	ENST00000380036.4:c.322G>T	p.Gly108Ter	p.G108*	ENST00000380036	NM_000459.3	108	Gga/Tga	2/23	0.582137615376259	3	FACETS	1	0.961	1	0.513	0.483	0.543	CLONAL	1	TRUE	1	0.582137615376259	3		548	1389	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197484	27197484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756064806	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	795	772	0	ENST00000380036.4:c.1796C>T	p.Ser599Leu	p.S599L	ENST00000380036	NM_000459.3	599	tCg/tTg	12/23	0.582137615376259	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.582137615376259	3		772	1740	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202881	27202881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	199	499	0	ENST00000380036.4:c.1973C>T	p.Ser658Phe	p.S658F	ENST00000380036	NM_000459.3	658	tCt/tTt	13/23	0.582137615376259	3	FACETS	0.698	0.645	0.753	0.349	0.322	0.377	SUBCLONAL	1	TRUE	1	0.582137615376259	3		499	1264	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27205015	27205015	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	647	575	0	ENST00000380036.4:c.2316G>T	p.Leu772Phe	p.L772F	ENST00000380036	NM_000459.3	772	ttG/ttT	14/23	0.582137615376259	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.582137615376259	3		575	1320	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206682	27206682	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	283	529	1	ENST00000380036.4:c.2467G>A	p.Asp823Asn	p.D823N	ENST00000380036	NM_000459.3	823	Gac/Aac	15/23	0.582137615376259	3	FACETS	0.958	0.899	1	0.479	0.449	0.51	CLONAL	1	TRUE	1	0.582137615376259	3		530	1310	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98003008	98003008	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	418	378	0	ENST00000289081.3:c.268C>A	p.Leu90Ile	p.L90I	ENST00000289081	NM_000136.2	90	Cta/Ata	4/15	0.582137615376259	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.582137615376259	3		378	881	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907155	101907155	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	144	424	1	ENST00000374994.4:c.1115G>A	p.Arg372Lys	p.R372K	ENST00000374994	NM_004612.2	372	aGa/aAa	6/9	0.582137615376259	3	FACETS	0.78	0.712	0.851	0.39	0.356	0.426	SUBCLONAL	1	TRUE	1	0.582137615376259	3		425	819	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128432165	128432165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1371596131	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	391	439	1	ENST00000265960.3:c.281G>A	p.Arg94Gln	p.R94Q	ENST00000265960	NM_001006617.1	94	cGa/cAa	3/12	0.582137615376259	3	FACETS	0.946	0.903	0.989	0.946	0.903	0.989	CLONAL	2	TRUE	1	0.582137615376259	3		440	917	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133761036	133761036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1456042173	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	624	598	1	ENST00000318560.5:c.3359C>T	p.Ser1120Leu	p.S1120L	ENST00000318560	NM_005157.4	1120	tCg/tTg	11/11	0.582137615376259	3	FACETS	0.956	0.921	0.99	0.956	0.921	0.99	CLONAL	2	TRUE	1	0.582137615376259	3		599	1448	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786007	135786007	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1502	93	662	0	ENST00000298552.3:c.1214A>C	p.Asp405Ala	p.D405A	ENST00000298552	NM_001162426.1	405	gAc/gCc	12/23	0.582137615376259	3	FACETS	0.259	0.229	0.291	0.129	0.114	0.146	SUBCLONAL	1	TRUE	1	0.582137615376259	3		662	1595	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15808651	15808651	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	281	698	0	ENST00000307771.7:c.33G>T	p.Glu11Asp	p.E11D	ENST00000307771	NM_005089.3	11	gaG/gaT	1/11	0.44177087065091	3	FACETS	1	0.983	1	0.559	0.525	0.594	CLONAL	1	TRUE	1	0.582137615376259	3		698	1114	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44919307	44919307	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	369	409	0	ENST00000377967.4:c.1235A>C	p.Lys412Thr	p.K412T	ENST00000377967	NM_021140.2	412	aAa/aCa	13/29	0.44177087065091	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.582137615376259	3		409	807	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44919316	44919316	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	157	425	0	ENST00000377967.4:c.1244T>G	p.Leu415Ter	p.L415*	ENST00000377967	NM_021140.2	415	tTa/tGa	13/29	0.44177087065091	3	FACETS	0.841	0.771	0.914	0.421	0.385	0.457	CLONAL	1	TRUE	1	0.582137615376259	3		425	828	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410130	63410130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	250	643	1	ENST00000330258.3:c.3037C>T	p.Pro1013Ser	p.P1013S	ENST00000330258	NM_152424.3	1013	Cct/Tct	2/2	0.44177087065091	3	FACETS	0.884	0.825	0.944	0.442	0.412	0.472	CLONAL	1	TRUE	1	0.582137615376259	3		644	1255	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411093	63411093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759613339	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	562	577	1	ENST00000330258.3:c.2074G>A	p.Glu692Lys	p.E692K	ENST00000330258	NM_152424.3	692	Gag/Aag	2/2	0.44177087065091	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.582137615376259	3		578	1216	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411186	63411186	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	59	553	0	ENST00000330258.3:c.1981C>A	p.Pro661Thr	p.P661T	ENST00000330258	NM_152424.3	661	Cca/Aca	2/2	0.44177087065091	3	FACETS	0.229	0.196	0.265	0.115	0.098	0.133	SUBCLONAL	1	TRUE	1	0.582137615376259	3		553	1142	SUCCESS
AR	367	MSKCC	GRCh37	X	66931257	66931257	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	221	410	0	ENST00000374690.3:c.1899G>T	p.Lys633Asn	p.K633N	ENST00000374690	NM_000044.3	633	aaG/aaT	4/8	0.44177087065091	3	FACETS	1	0.969	1	0.534	0.497	0.572	CLONAL	1	TRUE	1	0.582137615376259	3		410	918	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352002	70352002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1407	274	829	1	ENST00000374080.3:c.4199C>T	p.Ser1400Phe	p.S1400F	ENST00000374080		1400	tCt/tTt	30/45	0.44177087065091	3	FACETS	0.723	0.676	0.771	0.361	0.338	0.386	SUBCLONAL	1	TRUE	1	0.582137615376259	3		830	1681	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776955	76776955	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	341	590	0	ENST00000373344.5:c.6997G>T	p.Glu2333Ter	p.E2333*	ENST00000373344	NM_000489.3	2333	Gaa/Taa	33/35	0.44177087065091	3	FACETS	0.91	0.865	0.955	0.91	0.865	0.955	CLONAL	2	TRUE	1	0.582137615376259	3		590	831	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855018	76855018	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	324	505	0	ENST00000373344.5:c.5818G>T	p.Asp1940Tyr	p.D1940Y	ENST00000373344	NM_000489.3	1940	Gat/Tat	25/35	0.44177087065091	3	FACETS	0.801	0.759	0.844	0.801	0.759	0.844	CLONAL	2	TRUE	1	0.582137615376259	3		505	897	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937335	76937335	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	204	457	0	ENST00000373344.5:c.3413G>T	p.Arg1138Ile	p.R1138I	ENST00000373344	NM_000489.3	1138	aGa/aTa	9/35	0.44177087065091	3	FACETS	1	0.974	1	0.549	0.51	0.589	CLONAL	1	TRUE	1	0.582137615376259	3		457	824	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939699	76939699	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	613	669	0	ENST00000373344.5:c.1049A>C	p.Lys350Thr	p.K350T	ENST00000373344	NM_000489.3	350	aAa/aCa	9/35	0.44177087065091	3	FACETS	0.922	0.888	0.956	0.922	0.888	0.956	CLONAL	2	TRUE	1	0.582137615376259	3		669	1475	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76954099	76954099	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	141	554	3	ENST00000373344.5:c.152G>T	p.Gly51Val	p.G51V	ENST00000373344	NM_000489.3	51	gGa/gTa	3/35	0.44177087065091	3	FACETS	0.649	0.59	0.71	0.324	0.295	0.355	SUBCLONAL	1	TRUE	1	0.582137615376259	3		557	964	SUCCESS
BTK	695	MSKCC	GRCh37	X	100609658	100609658	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782740486	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	250	494	0	ENST00000308731.7:c.1591G>A	p.Asp531Asn	p.D531N	ENST00000308731	NM_000061.2	531	Gat/Aat	16/19	0.44177087065091	3	FACETS	0.938	0.877	1	0.469	0.438	0.501	CLONAL	1	TRUE	1	0.582137615376259	3		494	1182	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019576	123019576	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	422	544	0	ENST00000355640.3:c.64G>T	p.Glu22Ter	p.E22*	ENST00000355640		22	Gaa/Taa	2/7	0.44177087065091	3	FACETS	0.825	0.787	0.863	0.825	0.787	0.863	CLONAL	2	TRUE	1	0.582137615376259	3		544	1135	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020225	123020225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	328	606	1	ENST00000355640.3:c.713G>A	p.Arg238Gln	p.R238Q	ENST00000355640		238	cGa/cAa	2/7	0.44177087065091	3	FACETS	1	0.969	1	0.52	0.491	0.551	CLONAL	1	TRUE	1	0.582137615376259	3		607	1398	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220477	123220477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1372684971	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	331	646	0	ENST00000218089.9:c.3134G>A	p.Arg1045Gln	p.R1045Q	ENST00000218089	NM_001042749.1	1045	cGa/cAa	30/35	0.44177087065091	3	FACETS	1	0.984	1	0.554	0.523	0.586	CLONAL	1	TRUE	1	0.582137615376259	3		646	1324	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480538	123480538	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	481	597	0	ENST00000371139.4:c.46G>A	p.Gly16Ser	p.G16S	ENST00000371139	NM_001114937.2	16	Ggc/Agc	1/4	0.44177087065091	3	FACETS	0.988	0.948	1	0.988	0.948	1	CLONAL	2	TRUE	1	0.582137615376259	3		597	1080	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0028428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	300	497	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.442491124355103	2	FACETS	0.958	0.908	1	0.958	0.908	1	CLONAL	2	TRUE	0	0.442491124355103	2		497	708	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0028428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	335	324	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.442491124355103	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.442491124355103	2		324	646	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934874	NA	P-0028428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	479	291	0	ENST00000269305.4:c.451C>A	p.Pro151Thr	p.P151T	ENST00000269305	NM_001126112.2	151	Ccc/Acc	5/11	0.442491124355103	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.442491124355103	2		291	1018	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440946	56440946	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	334	618	0	ENST00000407977.2:c.391G>T	p.Glu131Ter	p.E131*	ENST00000407977		131	Gag/Tag	4/10	0.442491124355103	2	FACETS	0.752	0.712	0.792	0.752	0.712	0.792	SUBCLONAL	2	TRUE	0	0.442491124355103	2		618	1004	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0028431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	81	433	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.833	0.74	0.932	0.833	0.74	0.932	CLONAL	1	TRUE	1	0.57	2		433	341	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0028431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	86	250	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.57	2		250	283	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18576953	18576953	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	65	404	1	ENST00000266497.5:c.2361G>T	p.Gln787His	p.Q787H	ENST00000266497		787	caG/caT	16/31	0.184301273159772	0	FACETS	0.275	0.24	0.314			1	INDETERMINATE	1	TRUE	0	0.57	0		405	356	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831288	72831288	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	31	321	0	ENST00000268489.5:c.5293G>A	p.Ala1765Thr	p.A1765T	ENST00000268489	NM_006885.3	1765	Gcc/Acc	9/10	1	2	FACETS	0.301	0.244	0.366	0.301	0.244	0.366	SUBCLONAL	1	TRUE	1	0.57	2		321	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0028432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	628	494	1	ENST00000269305.4:c.376-1G>T		p.X126_splice	ENST00000269305	NM_001126112.2	126			NA	2	FACETS	1	0.981	1			1	INDETERMINATE	2	TRUE	NA	0.614072788522598	2		495	1008	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097695	27097699	+	frameshift_variant	Frame_Shift_Del	DEL	AGTAT	AGTAT	-	novel	NA	P-0028432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	223	435	0	ENST00000324856.7:c.3285_3289del	p.Gln1095HisfsTer8	p.Q1095Hfs*8	ENST00000324856	NM_006015.4	1095	cAGTAT/c	12/20	1	2	FACETS	0.965	0.901	1	0.965	0.901	1	CLONAL	1	TRUE	1	0.614072788522598	2		435	753	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048162	180048162	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773021479	NA	P-0028432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	591	557	0	ENST00000261937.6:c.2111C>T	p.Ala704Val	p.A704V	ENST00000261937	NM_182925.4	704	gCg/gTg	14/30	0.614072788522598	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.614072788522598	2		557	921	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943376	71943376	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	122	403	0	ENST00000298229.2:c.1708G>T	p.Ala570Ser	p.A570S	ENST00000298229	NM_001567.3	570	Gct/Tct	14/28	1	2	FACETS	0.517	0.467	0.57	0.517	0.467	0.57	SUBCLONAL	1	TRUE	1	0.575652951970216	2		403	820	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920734	100920734	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	117	465	0	ENST00000325455.5:c.2414C>A	p.Pro805Gln	p.P805Q	ENST00000325455	NM_001202474.3	805	cCa/cAa	6/8	1	2	FACETS	0.515	0.464	0.569	0.515	0.464	0.569	SUBCLONAL	1	TRUE	1	0.575652951970216	2		465	789	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808647	1808647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373425119	NA	P-0028436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	124	680	1	ENST00000260795.2:c.2260G>A	p.Val754Met	p.V754M	ENST00000260795		754	Gtg/Atg	16/17	0.128544827237391	6	FACETS	1	0.981	1	0.452	0.409	0.498	INDETERMINATE	1	TRUE	3	0.407084087889839	6		681	815	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106392	27106396	+	frameshift_variant	Frame_Shift_Del	DEL	GTCCA	GTCCA	CTC	novel	NA	P-0028436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	165	488	1	ENST00000324856.7:c.6003_6007delinsCTC	p.Met2001IlefsTer31	p.M2001Ifs*31	ENST00000324856	NM_006015.4	2001	atGTCCAaa/atCTCaa	20/20	0.407084087889839	3	FACETS	0.94	0.869	1	0.94	0.869	1	CLONAL	2	TRUE	1	0.407084087889839	3		489	519	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984723	11984724	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0028436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	73	244	0	ENST00000353533.5:c.269_270insAT	p.Pro91SerfsTer13	p.P91Sfs*13	ENST00000353533	NM_003010.3	90	tcc/tcATc	3/11	0.355960521244924	3	FACETS	1	0.943	1	0.727	0.648	0.808	CLONAL	2	TRUE	0	0.407084087889839	3		244	198	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183571	185183571	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	63	348	1	ENST00000265026.3:c.1425G>T	p.Lys475Asn	p.K475N	ENST00000265026	NM_004721.4	475	aaG/aaT	9/14	0.380904289821534	3	FACETS	0.902	0.783	1	0.451	0.391	0.515	CLONAL	1	TRUE	1	0.407084087889839	3		349	413	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0028439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	117	495	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.63911414147676	2		495	340	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0028439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	128	315	1	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	0.965	0.883	1	0.965	0.883	1	CLONAL	1	TRUE	1	0.63911414147676	2		316	415	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs121913292	NA	P-0028439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	94	346	0	ENST00000371953.3:c.389del	p.Arg130GlnfsTer4	p.R130Qfs*4	ENST00000371953	NM_000314.4	130	cGa/ca	5/9	0.63911414147676	3	FACETS	0.915	0.819	1	0.458	0.409	0.508	CLONAL	1	TRUE	1	0.63911414147676	3		346	424	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692778	89692778	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	158	249	0	ENST00000371953.3:c.262T>G	p.Tyr88Asp	p.Y88D	ENST00000371953	NM_000314.4	88	Tat/Gat	5/9	0.63911414147676	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.63911414147676	3		249	270	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28963980	28963980	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	121	284	0	ENST00000282397.4:c.1922T>C	p.Val641Ala	p.V641A	ENST00000282397	NM_002019.4	641	gTa/gCa	13/30	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.63911414147676	2		284	318	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349136	11349136	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	123	246	0	ENST00000332029.2:c.200T>G	p.Ile67Ser	p.I67S	ENST00000332029	NM_003745.1	67	aTc/aGc	2/2	1	2	FACETS	0.982	0.896	1	0.982	0.896	1	CLONAL	1	TRUE	1	0.63911414147676	2		246	392	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660513	67660513	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0028439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	226	393	0	ENST00000264010.4:c.1413C>G	p.Tyr471Ter	p.Y471*	ENST00000264010	NM_006565.3	471	taC/taG	8/12	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.63911414147676	2		393	596	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296181	15296181	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144935367	NA	P-0028439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	298	585	0	ENST00000263388.2:c.2183G>A	p.Arg728His	p.R728H	ENST00000263388	NM_000435.2	728	cGc/cAc	14/33	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.63911414147676	2		585	871	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591042	67591042	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	53	244	0	ENST00000274335.5:c.1636del	p.Glu546LysfsTer4	p.E546Kfs*4	ENST00000274335		545	ttG/tt	12/15	0.63911414147676	3	FACETS	0.973	0.839	1	0.486	0.419	0.558	CLONAL	1	TRUE	1	0.63911414147676	3		244	225	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591086	67591097	+	inframe_deletion	In_Frame_Del	DEL	ACAAACGTATGA	ACAAACGTATGA	-	novel	NA	P-0028439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	103	245	0	ENST00000274335.5:c.1682_1693del	p.Lys561_Asn564del	p.K561_N564del	ENST00000274335		560	gACAAACGTATGAac/gac	12/15	0.63911414147676	3	FACETS	0.868	0.792	0.946	0.868	0.792	0.946	CLONAL	2	TRUE	1	0.63911414147676	3		245	245	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965664	90965664	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	52	217	0	ENST00000265433.3:c.1653G>C	p.Arg551Ser	p.R551S	ENST00000265433	NM_002485.4	551	agG/agC	11/16	0.449984148269857	3	FACETS	1	0.92	1	0.548	0.473	0.627	CLONAL	1	TRUE	1	0.63911414147676	3		217	196	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057715	27057716	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0028439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	344	583	0	ENST00000324856.7:c.1423_1424del	p.Pro476SerfsTer146	p.P476Sfs*146	ENST00000324856	NM_006015.4	475	AGt/t	3/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.63911414147676	2		583	983	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	90	210	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.949	0.858	1	1	0.989	1	CLONAL	3	TRUE	1	0.273745286539914	2		210	231	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0028440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	96	433	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.953	0.856	1	1	0.987	1	CLONAL	2	TRUE	1	0.273745286539914	2		433	368	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915699	131915699	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	42	356	0	ENST00000265335.6:c.697C>T	p.Gln233Ter	p.Q233*	ENST00000265335		233	Cag/Tag	5/25	0.273745286539914	2	FACETS	0.838	0.702	0.989	0.419	0.351	0.495	CLONAL	1	TRUE	0	0.273745286539914	2		356	366	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0028441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	85	497	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.362475931701278	3	FACETS	0.939	0.84	1	0.939	0.84	1	CLONAL	2	TRUE	1	0.362475931701278	3		497	295	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578373	7578381	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TCGCTATCT	TCGCTATCT	-	novel	NA	P-0028441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	164	401	0	ENST00000269305.4:c.549_557del	p.Asp184_Asp186del	p.D184_D186del	ENST00000269305	NM_001126112.2	183	tcAGATAGCGAt/tct	5/11	0.28823375406987	2	FACETS	0.923	0.855	0.994	0.923	0.855	0.994	CLONAL	2	TRUE	0	0.362475931701278	2		401	490	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877427	40877427	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	170	347	0	ENST00000373198.4:c.2269G>T	p.Glu757Ter	p.E757*	ENST00000373198	NM_133170.3	757	Gag/Tag	15/32	0.362475931701278	5	FACETS	0.807	0.742	0.875	0.538	0.495	0.583	CLONAL	2	TRUE	2	0.362475931701278	5		347	897	SUCCESS
APC	324	MSKCC	GRCh37	5	112175440	112175441	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	116	245	0	ENST00000257430.4:c.4152dup	p.Ser1385Ter	p.S1385*	ENST00000257430	NM_000038.5	1383	-/T	16/16	0.332795033893875	3	FACETS	1	0.977	1	0.808	0.738	0.879	CLONAL	2	TRUE	0	0.362475931701278	3		245	312	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406288	406288	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	38	397	0	ENST00000399788.2:c.4153G>C	p.Glu1385Gln	p.E1385Q	ENST00000399788	NM_001042603.1	1385	Gag/Cag	25/28	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		397	349	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511673	38511673	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	35	356	0	ENST00000254066.5:c.1171G>A	p.Gly391Arg	p.G391R	ENST00000254066	NM_000964.3	391	Ggg/Agg	8/9	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		356	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913343	NA	P-0028443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	369	498	0	ENST00000269305.4:c.817C>G	p.Arg273Gly	p.R273G	ENST00000269305	NM_001126112.2	273	Cgt/Ggt	8/11	0.606049679368926	3	FACETS	0.851	0.821	0.879	0.851	0.821	0.879	CLONAL	3	TRUE	0	0.754289044206898	3		498	528	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447265	49447265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	308	337	0	ENST00000301067.7:c.833C>T	p.Ala278Val	p.A278V	ENST00000301067	NM_003482.3	278	gCc/gTc	6/54	0.754289044206898	6	FACETS	1	0.987	1	0.567	0.536	0.599	CLONAL	2	TRUE	2	0.754289044206898	6		337	903	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906426	32906426	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555281599	NA	P-0028443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	270	320	0	ENST00000380152.3:c.813del	p.Asn272IlefsTer5	p.N272Ifs*5	ENST00000380152		271	Ggg/gg	10/27	0.602693380129302	4	FACETS	0.915	0.884	0.945	0.915	0.884	0.945	CLONAL	4	TRUE	0	0.754289044206898	4		320	343	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647843	3647843	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768483565	NA	P-0028443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	215	530	0	ENST00000294008.3:c.1321C>T	p.Leu441Phe	p.L441F	ENST00000294008	NM_032444.2	441	Ctc/Ttc	6/15	0.697762793656179	5	FACETS	1	0.973	1	0.365	0.339	0.393	CLONAL	1	TRUE	2	0.754289044206898	5		530	1109	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828787	3828787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1013334018	NA	P-0028443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	518	491	0	ENST00000262367.5:c.1855G>A	p.Ala619Thr	p.A619T	ENST00000262367	NM_004380.2	619	Gca/Aca	9/31	0.697762793656179	5	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	2	0.754289044206898	5		491	970	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920346	134920346	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	386	333	0	ENST00000398015.3:c.2161C>A	p.Leu721Ile	p.L721I	ENST00000398015	NM_004441.4	721	Ctt/Att	12/16	0.754289044206898	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	2	0.754289044206898	4		333	750	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737817	145737817	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	644	584	0	ENST00000428558.2:c.3013C>G	p.Arg1005Gly	p.R1005G	ENST00000428558	NM_004260.3	1005	Cgg/Ggg	18/22	0.754289044206898	6	FACETS	0.911	0.887	0.935	1	0.996	1	CLONAL	5	TRUE	2	0.754289044206898	6		584	940	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023525	27023525	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	65	787	0	ENST00000324856.7:c.631C>T	p.Gln211Ter	p.Q211*	ENST00000324856	NM_006015.4	211	Cag/Tag	1/20	0.185395489915616	3	FACETS	0.884	0.764	1	0.442	0.382	0.507	CLONAL	1	FALSE	1	0.185395489915616	3		787	867	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111498	8111499	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0028446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	151	781	0	ENST00000346208.3:c.985dup	p.Arg329LysfsTer23	p.R329Kfs*23	ENST00000346208		328	-/A	5/6	0.165165499769826	4	FACETS	0.875	0.798	0.955	0.875	0.798	0.955	CLONAL	2	FALSE	2	0.185395489915616	4		781	1104	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169985714	169985714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	84	546	1	ENST00000295797.4:c.376C>T	p.Arg126Cys	p.R126C	ENST00000295797	NM_002740.5	126	Cgt/Tgt	5/18	0.185395489915616	3	FACETS	1	0.969	1	0.648	0.572	0.73	CLONAL	1	FALSE	1	0.185395489915616	3		547	764	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981408	70981408	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	72	863	0	ENST00000276594.2:c.688C>A	p.Pro230Thr	p.P230T	ENST00000276594	NM_024504.3	230	Cca/Aca	2/8	0.185395489915616	4	FACETS	0.744	0.647	0.849	0.186	0.161	0.213	SUBCLONAL	1	FALSE	0	0.185395489915616	4		863	1238	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375955	8375955	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	31	417	1	ENST00000356435.5:c.4642C>A	p.Pro1548Thr	p.P1548T	ENST00000356435		1548	Ccg/Acg	28/35	1	2	FACETS	0.672	0.542	0.818	0.672	0.542	0.818	SUBCLONAL	1	FALSE	1	0.185395489915616	2		418	498	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061250	38061250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1459219194	NA	P-0028450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	110	746	1	ENST00000250448.2:c.739C>T	p.His247Tyr	p.H247Y	ENST00000250448	NM_004496.3	247	Cac/Tac	2/2	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	FALSE	1	0.361724289496999	2		747	571	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391011	89391011	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	15	621	0	ENST00000336596.2:c.1077C>G	p.Phe359Leu	p.F359L	ENST00000336596	NM_005233.5	359	ttC/ttG	5/17	1	2	FACETS	0.453	0.332	0.597	0.453	0.332	0.597	SUBCLONAL	1	FALSE	1	0.361724289496999	2		621	183	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447037	187447037	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	114	676	0	ENST00000232014.4:c.1156C>G	p.Leu386Val	p.L386V	ENST00000232014	NM_001130845.1	386	Ctc/Gtc	5/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.361724289496999	2		676	498	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699360	47699360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	84	679	0	ENST00000347630.2:c.148G>A	p.Glu50Lys	p.E50K	ENST00000347630	NM_001007230.1	50	Gaa/Aaa	4/11	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.26	2		679	595	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	123	972	1	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	1	2	FACETS	0.955	0.862	1	0.955	0.862	1	CLONAL	1	TRUE	1	0.26	2		973	991	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846080	68846080	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555515726	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	143	907	4	ENST00000261769.5:c.1051C>T	p.Gln351Ter	p.Q351*	ENST00000261769	NM_004360.3	351	Caa/Taa	8/16	0.3	1	FACETS	0.994	0.905	1	0.994	0.905	1	CLONAL	1	TRUE	0	0.26	1		911	963	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061517	38061517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771653601	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	68	431	0	ENST00000250448.2:c.472G>A	p.Asp158Asn	p.D158N	ENST00000250448	NM_004496.3	158	Gac/Aac	2/2	1	2	FACETS	0.919	0.8	1	0.919	0.8	1	CLONAL	1	TRUE	1	0.26	2		431	569	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175942	176175942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs964768927	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	32	122	0	ENST00000367669.3:c.173C>T	p.Ser58Leu	p.S58L	ENST00000367669	NM_022457.5	58	tCg/tTg	1/20	0.3	3	FACETS	1	0.942	1	0.717	0.587	0.861	CLONAL	1	TRUE	1	0.26	3		122	194	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949356	71949356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	120	881	0	ENST00000298229.2:c.3736C>T	p.His1246Tyr	p.H1246Y	ENST00000298229	NM_001567.3	1246	Cac/Tac	28/28	1	2	FACETS	0.926	0.835	1	0.926	0.835	1	CLONAL	1	TRUE	1	0.26	2		881	997	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910756	29910756	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	92	1097	0	ENST00000376809.5:c.296G>C	p.Arg99Pro	p.R99P	ENST00000376809	NM_002116.7	99	cGa/cCa	2/8	1	2	FACETS	0.558	0.494	0.627	0.558	0.494	0.627	SUBCLONAL	1	TRUE	1	0.26	2		1097	1269	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637126	93637126	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	43	751	2	ENST00000375746.1:c.1176G>A	p.Met392Ile	p.M392I	ENST00000375746	NM_001174167.1	392	atG/atA	9/14	1	2	FACETS	0.447	0.373	0.53	0.447	0.373	0.53	SUBCLONAL	1	TRUE	1	0.26	2		753	740	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859702	151859702	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	41	350	0	ENST00000262189.6:c.10960C>T	p.Gln3654Ter	p.Q3654*	ENST00000262189	NM_170606.2	3654	Caa/Taa	43/59	1	2	FACETS	0.79	0.659	0.936	0.79	0.659	0.936	CLONAL	1	TRUE	1	0.26	2		350	399	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023307	27023307	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	26	234	0	ENST00000324856.7:c.413C>T	p.Ser138Leu	p.S138L	ENST00000324856	NM_006015.4	138	tCa/tTa	1/20	1	2	FACETS	0.524	0.414	0.649	0.524	0.414	0.649	SUBCLONAL	1	TRUE	1	0.26	2		234	382	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163295859	163295859	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	54	654	0	ENST00000271452.3:c.18C>G	p.Phe6Leu	p.F6L	ENST00000271452	NM_145697.2	6	ttC/ttG	2/14	0.3	3	FACETS	0.771	0.658	0.895	0.385	0.329	0.448	SUBCLONAL	1	TRUE	1	0.26	3		654	609	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649908	88649908	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	68	604	0	ENST00000372037.3:c.157G>C	p.Glu53Gln	p.E53Q	ENST00000372037	NM_004329.2	53	Gag/Cag	4/13	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.26	2		604	489	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711923	89711945	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTTAAAGAATCATCTGGATTA	CTGTTAAAGAATCATCTGGATTA	-	novel	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	27	755	0	ENST00000371953.3:c.541_563del	p.Leu181Ter	p.L181*	ENST00000371953	NM_000314.4	181	CTGTTAAAGAATCATCTGGATTAt/t	6/9	1	2	FACETS	0.403	0.32	0.499	0.403	0.32	0.499	SUBCLONAL	1	TRUE	1	0.26	2		755	515	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936176	71936176	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	44	579	0	ENST00000298229.2:c.148G>T	p.Glu50Ter	p.E50*	ENST00000298229	NM_001567.3	50	Gag/Tag	1/28	1	2	FACETS	0.456	0.381	0.539	0.456	0.381	0.539	SUBCLONAL	1	TRUE	1	0.26	2		579	742	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942656	71942656	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	122	844	0	ENST00000298229.2:c.1612C>G	p.Leu538Val	p.L538V	ENST00000298229	NM_001567.3	538	Ctg/Gtg	13/28	1	2	FACETS	0.966	0.872	1	0.966	0.872	1	CLONAL	1	TRUE	1	0.26	2		844	971	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94908775	94908775	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	72	763	1	ENST00000536441.1:c.1279C>T	p.Gln427Ter	p.Q427*	ENST00000536441	NM_144665.3	427	Caa/Taa	9/10	1	2	FACETS	0.81	0.707	0.921	0.81	0.707	0.921	CLONAL	1	TRUE	1	0.26	2		764	684	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807374	3807374	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	67	560	0	ENST00000262367.5:c.3613G>C	p.Glu1205Gln	p.E1205Q	ENST00000262367	NM_004380.2	1205	Gag/Cag	19/31	1	2	FACETS	0.83	0.721	0.948	0.83	0.721	0.948	CLONAL	1	TRUE	1	0.26	2		560	621	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671611	67671611	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	57	615	0	ENST00000264010.4:c.2020G>A	p.Glu674Lys	p.E674K	ENST00000264010	NM_006565.3	674	Gaa/Aaa	12/12	0.3	1	FACETS	0.713	0.612	0.823	0.713	0.612	0.823	SUBCLONAL	1	TRUE	0	0.26	1		615	535	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029406	16029406	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	45	676	0	ENST00000268712.3:c.1624G>C	p.Glu542Gln	p.E542Q	ENST00000268712	NM_006311.3	542	Gaa/Caa	15/46	0.3	1	FACETS	0.571	0.48	0.673	0.571	0.48	0.673	SUBCLONAL	1	TRUE	0	0.26	1		676	527	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029484	16029484	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	48	622	1	ENST00000268712.3:c.1546G>T	p.Glu516Ter	p.E516*	ENST00000268712	NM_006311.3	516	Gaa/Taa	15/46	0.3	1	FACETS	0.679	0.574	0.794	0.679	0.574	0.794	SUBCLONAL	1	TRUE	0	0.26	1		623	473	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793219	42793219	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	70	1175	0	ENST00000575354.2:c.1111C>T	p.Gln371Ter	p.Q371*	ENST00000575354	NM_015125.3	371	Cag/Tag	7/20	1	2	FACETS	0.457	0.397	0.523	0.457	0.397	0.523	SUBCLONAL	1	TRUE	1	0.26	2		1175	1178	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278424	39278424	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	81	773	0	ENST00000402219.2:c.725T>A	p.Val242Glu	p.V242E	ENST00000402219	NM_005633.3	242	gTa/gAa	6/23	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.26	2		773	607	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266024	41266024	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	14	275	0	ENST00000349496.5:c.21G>C	p.Leu7Phe	p.L7F	ENST00000349496	NM_001904.3	7	ttG/ttC	3/15	1	2	FACETS	0.392	0.283	0.524	0.392	0.283	0.524	SUBCLONAL	1	TRUE	1	0.26	2		275	275	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101690	71101690	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	22	388	0	ENST00000318789.4:c.508G>C	p.Glu170Gln	p.E170Q	ENST00000318789	NM_032682.5	170	Gag/Cag	9/21	1	2	FACETS	0.604	0.469	0.761	0.604	0.469	0.761	SUBCLONAL	1	TRUE	1	0.26	2		388	280	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101708	71101708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	27	412	0	ENST00000318789.4:c.490G>A	p.Ala164Thr	p.A164T	ENST00000318789	NM_032682.5	164	Gct/Act	9/21	1	2	FACETS	0.664	0.529	0.817	0.664	0.529	0.817	SUBCLONAL	1	TRUE	1	0.26	2		412	313	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101729	71101729	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	31	408	0	ENST00000318789.4:c.469C>T	p.Gln157Ter	p.Q157*	ENST00000318789	NM_032682.5	157	Caa/Taa	9/21	1	2	FACETS	0.814	0.66	0.987	0.814	0.66	0.987	CLONAL	1	TRUE	1	0.26	2		408	293	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143033788	143033788	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	44	632	1	ENST00000262992.4:c.2183C>T	p.Ser728Leu	p.S728L	ENST00000262992	NM_001101669.1	728	tCa/tTa	20/24	1	2	FACETS	0.637	0.534	0.752	0.637	0.534	0.752	SUBCLONAL	1	TRUE	1	0.26	2		633	531	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094931	143094931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	66	644	0	ENST00000262992.4:c.1213G>A	p.Glu405Lys	p.E405K	ENST00000262992	NM_001101669.1	405	Gaa/Aaa	14/24	1	2	FACETS	0.967	0.841	1	0.967	0.841	1	CLONAL	1	TRUE	1	0.26	2		644	525	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160564	56160564	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	50	359	0	ENST00000399503.3:c.838C>T	p.Gln280Ter	p.Q280*	ENST00000399503	NM_005921.1	280	Cag/Tag	4/20	1	2	FACETS	0.971	0.826	1	0.971	0.826	1	CLONAL	1	TRUE	1	0.26	2		359	396	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720958	176720958	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	93	573	0	ENST00000439151.2:c.6589G>A	p.Asp2197Asn	p.D2197N	ENST00000439151	NM_022455.4	2197	Gat/Aat	23/23	1	2	FACETS	0.992	0.882	1	0.992	0.882	1	CLONAL	1	TRUE	1	0.26	2		573	721	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032138	26032138	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	56	395	0	ENST00000244661.2:c.151G>C	p.Glu51Gln	p.E51Q	ENST00000244661	NM_003537.3	51	Gag/Cag	1/1	1	2	FACETS	0.832	0.713	0.961	0.832	0.713	0.961	CLONAL	1	TRUE	1	0.26	2		395	518	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813519	32813519	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	97	598	0	ENST00000354258.4:c.2264C>A	p.Ser755Ter	p.S755*	ENST00000354258	NM_000593.5	755	tCa/tAa	11/11	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.26	2		598	731	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946057	13946057	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	24	420	0	ENST00000405192.2:c.1039G>C	p.Glu347Gln	p.E347Q	ENST00000405192	NM_001163147.1	347	Gag/Cag	10/12	1	2	FACETS	0.431	0.337	0.54	0.431	0.337	0.54	SUBCLONAL	1	TRUE	1	0.26	2		420	428	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38153467	38153467	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1156943543	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	33	566	0	ENST00000317025.8:c.2762G>A	p.Gly921Glu	p.G921E	ENST00000317025	NM_023034.1	921	gGa/gAa	16/24	1	2	FACETS	0.435	0.354	0.528	0.435	0.354	0.528	SUBCLONAL	1	TRUE	1	0.26	2		566	583	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372500	55372500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1473687136	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1259	172	1424	3	ENST00000297316.4:c.1190C>T	p.Ser397Leu	p.S397L	ENST00000297316	NM_022454.3	397	tCg/tTg	2/2	1	2	FACETS	0.925	0.848	1	0.925	0.848	1	CLONAL	1	TRUE	1	0.26	2		1427	1431	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434737	128434737	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	97	846	0	ENST00000265960.3:c.117G>C	p.Glu39Asp	p.E39D	ENST00000265960	NM_001006617.1	39	gaG/gaC	2/12	1	2	FACETS	0.984	0.877	1	0.984	0.877	1	CLONAL	1	TRUE	1	0.26	2		846	758	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0028457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	259	298	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.179786345249034	5	FACETS	1	0.989	1	0.827	0.775	0.879	INDETERMINATE	2	TRUE	2	0.336594256250307	5		298	934	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952496	17952496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	90	687	2	ENST00000458235.1:c.937G>A	p.Gly313Arg	p.G313R	ENST00000458235	NM_000215.3	313	Gga/Aga	7/24	0.157337784098289	2	FACETS	0.466	0.412	0.524	0.233	0.206	0.262	INDETERMINATE	1	TRUE	0	0.336594256250307	2		689	1148	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149516600	149516600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144923639	NA	P-0028457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1480	113	711	1	ENST00000261799.4:c.11C>T	p.Pro4Leu	p.P4L	ENST00000261799	NM_002609.3	4	cCg/cTg	2/23	0.179786345249034	5	FACETS	0.634	0.568	0.705	0.211	0.189	0.235	INDETERMINATE	1	TRUE	2	0.336594256250307	5		712	1593	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604704	48604704	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	256	451	0	ENST00000342988.3:c.1526G>A	p.Trp509Ter	p.W509*	ENST00000342988	NM_005359.5	509	tGg/tAg	12/12	0.336594256250307	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.336594256250307	2		451	742	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178131	56178131	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	190	361	0	ENST00000399503.3:c.3107del	p.Asn1036ThrfsTer46	p.N1036Tfs*46	ENST00000399503	NM_005921.1	1035	gAa/ga	14/20	0.179786345249034	5	FACETS	1	0.972	1	0.734	0.68	0.789	INDETERMINATE	2	TRUE	2	0.336594256250307	5		361	772	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180648	56180649	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0028457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	152	429	0	ENST00000399503.3:c.3979dup	p.Ala1327GlyfsTer11	p.A1327Gfs*11	ENST00000399503	NM_005921.1	1326	atg/atGg	16/20	0.179786345249034	5	FACETS	0.846	0.775	0.921	0.564	0.516	0.614	INDETERMINATE	2	TRUE	2	0.336594256250307	5		429	803	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020764	26020765	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTG	novel	NA	P-0028457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	153	206	0	ENST00000357647.3:c.48_49insTGG	p.Ala16_Pro17insTrp	p.A16_P17insW	ENST00000357647	NM_003529.2	16	gcg/gcGTGg	1/1	0.320751637813637	3	FACETS	1	0.979	1	0.783	0.723	0.845	CLONAL	2	TRUE	0	0.336594256250307	3		206	452	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0028464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	52	335	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.280419782123117	2	FACETS	1	0.915	1	0.551	0.471	0.637	CLONAL	1	TRUE	0	0.284415796414084	2		335	332	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577146	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0028464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	183	429	0	ENST00000269305.4:c.792_794del	p.Leu265del	p.L265del	ENST00000269305	NM_001126112.2	264	ctACTg/ctg	8/11	0.284415796414084	3	FACETS	1	0.984	1	0.808	0.75	0.869	CLONAL	2	TRUE	0	0.284415796414084	3		429	606	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0028464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	285	529	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.284415796414084	7	FACETS	1	0.955	1			1	CLONAL	5	TRUE	NA	0.284415796414084	7		529	679	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6045573	6045573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148270248	NA	P-0028464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	96	300	0	ENST00000265849.7:c.113C>T	p.Ala38Val	p.A38V	ENST00000265849	NM_000535.5	38	gCg/gTg	2/15	0.273712271692923	4	FACETS	0.947	0.848	1	0.947	0.848	1	CLONAL	2	TRUE	2	0.284415796414084	4		300	458	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0028464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	90	364	2				ENST00000310581	NM_198253.2	-/1132			0.229187661267851	4	FACETS	0.945	0.843	1	0.945	0.843	1	CLONAL	2	TRUE	2	0.284415796414084	4		366	430	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486587	56486587	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	127	440	0	ENST00000267101.3:c.1166C>A	p.Thr389Lys	p.T389K	ENST00000267101	NM_001982.3	389	aCa/aAa	10/28	0.28449950426167	4	FACETS	0.837	0.76	0.919	0.837	0.76	0.919	CLONAL	2	TRUE	2	0.284415796414084	4		440	685	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	31	210	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.722	0.586	0.876	0.722	0.586	0.876	SUBCLONAL	1	TRUE	1	0.29	2		210	296	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0028465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	9	298	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.184007316848042	3	FACETS	0.178	0.117	0.256	0.089	0.058	0.128	SUBCLONAL	1	TRUE	1	0.29	3		298	400	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0028465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	41	586	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.3	1	FACETS	0.793	0.663	0.935	0.793	0.663	0.935	CLONAL	1	TRUE	0	0.29	1		587	305	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665213	138665213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	40	536	0	ENST00000330315.3:c.352G>A	p.Glu118Lys	p.E118K	ENST00000330315	NM_023067.3	118	Gag/Aag	1/1	0.184007316848042	3	FACETS	0.429	0.355	0.512	0.215	0.177	0.256	SUBCLONAL	1	TRUE	1	0.29	3		536	736	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0028465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	47	428	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	1	2	FACETS	0.65	0.548	0.761	0.65	0.548	0.761	SUBCLONAL	1	TRUE	1	0.29	2		428	499	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044595	47044595	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	72	340	0	ENST00000377604.3:c.2092G>T	p.Glu698Ter	p.E698*	ENST00000377604	NM_001204468.1	698	Gag/Tag	18/24	1	1	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	0	0.29	1		340	403	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023220	27023220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1167372383	NA	P-0028465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	19	163	0	ENST00000324856.7:c.326C>T	p.Pro109Leu	p.P109L	ENST00000324856	NM_006015.4	109	cCt/cTt	1/20	1	2	FACETS	0.645	0.492	0.825	0.645	0.492	0.825	SUBCLONAL	1	TRUE	1	0.29	2		163	203	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890157	76890158	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0028465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	14	218	0	ENST00000373344.5:c.4736_4737del	p.Val1579GlufsTer21	p.V1579Efs*21	ENST00000373344	NM_000489.3	1579	gTG/g	17/35	0.3	2	FACETS	0.406	0.293	0.542			1	SUBCLONAL	1	TRUE	NA	0.29	2		218	238	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690810	89690810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	18	244	0	ENST00000371953.3:c.217G>A	p.Glu73Lys	p.E73K	ENST00000371953	NM_000314.4	73	Gaa/Aaa	4/9	0.184007316848042	3	FACETS	0.602	0.454	0.777	0.301	0.227	0.389	SUBCLONAL	1	TRUE	1	0.29	3		244	236	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988085	85988085	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	16	231	0	ENST00000263360.6:c.1030A>G	p.Lys344Glu	p.K344E	ENST00000263360	NM_003797.3	344	Aaa/Gaa	10/12	1	2	FACETS	0.509	0.376	0.666	0.509	0.376	0.666	SUBCLONAL	1	TRUE	1	0.29	2		231	217	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606708	29606708	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	57	353	1	ENST00000389048.3:c.1172G>T	p.Gly391Val	p.G391V	ENST00000389048	NM_004304.4	391	gGa/gTa	5/29	1	2	FACETS	0.819	0.704	0.944	0.819	0.704	0.944	CLONAL	1	TRUE	1	0.29	2		354	480	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164660	47164660	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	21	234	0	ENST00000409792.3:c.1466C>G	p.Ser489Cys	p.S489C	ENST00000409792	NM_014159.6	489	tCt/tGt	3/21	0.184007316848042	3	FACETS	0.599	0.461	0.758	0.299	0.23	0.379	SUBCLONAL	1	TRUE	1	0.29	3		234	277	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890218	72890218	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0028465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	27	340	0	ENST00000325599.8:c.464C>G	p.Ser155Ter	p.S155*	ENST00000325599	NM_018130.2	155	tCa/tGa	4/11	0.184007316848042	3	FACETS	0.4	0.317	0.495	0.2	0.158	0.248	SUBCLONAL	1	TRUE	1	0.29	3		340	533	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272837	142272837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	42	274	0	ENST00000350721.4:c.2362C>T	p.His788Tyr	p.H788Y	ENST00000350721	NM_001184.3	788	Cat/Tat	11/47	0.184007316848042	3	FACETS	1	0.924	1	0.59	0.495	0.694	CLONAL	1	TRUE	1	0.29	3		274	281	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430383	181430383	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	46	481	0	ENST00000325404.1:c.235T>C	p.Trp79Arg	p.W79R	ENST00000325404	NM_003106.3	79	Tgg/Cgg	1/1	0.184007316848042	3	FACETS	0.574	0.482	0.675	0.287	0.241	0.338	SUBCLONAL	1	TRUE	1	0.29	3		481	633	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280058	66280058	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	35	204	0	ENST00000273854.3:c.1631C>A	p.Thr544Lys	p.T544K	ENST00000273854	NM_004439.5	544	aCa/aAa	7/18	1	2	FACETS	0.736	0.605	0.882	0.736	0.605	0.882	SUBCLONAL	1	TRUE	1	0.29	2		204	328	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0028466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	44	576	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	0.785	0.659	0.925	0.785	0.659	0.925	CLONAL	1	TRUE	1	0.24	2		576	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577093	7577093	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882008	NA	P-0028466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	149	616	0	ENST00000269305.4:c.845G>C	p.Arg282Pro	p.R282P	ENST00000269305	NM_001126112.2	282	cGg/cCg	8/11	1	2	FACETS	0.964	0.884	1	1	0.991	1	CLONAL	2	TRUE	1	0.24	2		616	644	SUCCESS
ATM	472	MSKCC	GRCh37	11	108128328	108128328	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	42	217	0	ENST00000278616.4:c.2371A>T	p.Thr791Ser	p.T791S	ENST00000278616	NM_000051.3	791	Acc/Tcc	15/63	0.193644909039755	3	FACETS	1	0.925	1	0.596	0.499	0.702	CLONAL	1	TRUE	1	0.24	3		217	329	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037374	12037394	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTAGACTGTAGACTGCTTTG	TGTAGACTGTAGACTGCTTTG	-	novel	NA	P-0028466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	62	670	0	ENST00000396373.4:c.1010-5_1025del		p.X337_splice	ENST00000396373	NM_001987.4	337		6/8	1	2	FACETS	0.843	0.728	0.968	0.843	0.728	0.968	CLONAL	1	TRUE	1	0.24	2		670	613	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473592	67473593	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0028466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	32	399	1	ENST00000327367.4:c.673dup	p.Thr225AsnfsTer86	p.T225Nfs*86	ENST00000327367	NM_005902.3	224	-/A	6/9	1	2	FACETS	0.654	0.53	0.793	0.654	0.53	0.793	SUBCLONAL	1	TRUE	1	0.24	2		400	408	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375255	15375255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	28	507	1	ENST00000263377.2:c.1172G>T	p.Cys391Phe	p.C391F	ENST00000263377	NM_058243.2	391	tGt/tTt	6/20	1	2	FACETS	0.477	0.38	0.588	0.477	0.38	0.588	SUBCLONAL	1	TRUE	1	0.24	2		508	489	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095986	178095986	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	20	386	0	ENST00000397062.3:c.1345C>G	p.Arg449Gly	p.R449G	ENST00000397062	NM_006164.4	449	Cgc/Ggc	5/5	0.170319685834733	3	FACETS	0.495	0.378	0.633	0.165	0.126	0.211	SUBCLONAL	1	TRUE	0	0.24	3		386	377	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624885	9624885	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	45	362	0	ENST00000353224.5:c.92del	p.Lys31SerfsTer13	p.K31Sfs*13	ENST00000353224	NM_177990.2	31	aAg/ag	3/10	1	2	FACETS	0.921	0.776	1	0.921	0.776	1	CLONAL	1	TRUE	1	0.24	2		362	407	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776892	76776892	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	40	451	0	ENST00000373344.5:c.7060A>G	p.Ile2354Val	p.I2354V	ENST00000373344	NM_000489.3	2354	Att/Gtt	33/35	1	2	FACETS	0.715	0.594	0.85	0.715	0.594	0.85	SUBCLONAL	1	TRUE	1	0.24	2		451	466	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0028470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	58	297	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.191595627730271	4	FACETS	0.855	0.738	0.982	0.855	0.738	0.982	CLONAL	2	TRUE	2	0.216596763177442	4		297	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934874	NA	P-0028470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	130	799	0	ENST00000269305.4:c.451C>G	p.Pro151Ala	p.P151A	ENST00000269305	NM_001126112.2	151	Ccc/Gcc	5/11	0.180552938041397	2	FACETS	0.992	0.903	1	0.992	0.903	1	CLONAL	2	TRUE	0	0.216596763177442	2		799	605	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971003	21971003	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	91	485	0	ENST00000304494.5:c.355G>T	p.Glu119Ter	p.E119*	ENST00000304494	NM_000077.4	119	Gag/Tag	2/3	0.181969392469079	2	FACETS	0.8	0.713	0.893	0.8	0.713	0.893	SUBCLONAL	2	TRUE	0	0.216596763177442	2		485	525	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18972860	18972860	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	42	460	0	ENST00000262803.5:c.2499G>C	p.Glu833Asp	p.E833D	ENST00000262803	NM_002911.3	833	gaG/gaC	18/24	0.216596763177442	6	FACETS	0.907	0.756	1			1	CLONAL	1	TRUE	NA	0.216596763177442	6		460	613	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144604	119144604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	90	235	0	ENST00000264033.4:c.617G>A	p.Arg206Gln	p.R206Q	ENST00000264033	NM_005188.3	206	cGa/cAa	4/16	1	2	FACETS	0.961	0.86	1	0.961	0.86	1	CLONAL	1	TRUE	1	0.535261958922136	2		235	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	58	716	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.307	0.263	0.355	0.307	0.263	0.355	SUBCLONAL	1	TRUE	1	0.535261958922136	2		716	706	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	94	301	0	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	1	2	FACETS	0.869	0.779	0.965	0.869	0.779	0.965	CLONAL	1	TRUE	1	0.535261958922136	2		301	404	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	139	648	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.839	0.766	0.915	0.839	0.766	0.915	CLONAL	1	TRUE	1	0.535261958922136	2		648	619	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	140	600	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.809	0.738	0.882	0.809	0.738	0.882	CLONAL	1	TRUE	1	0.535261958922136	2		606	647	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	136	571	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.881	0.804	0.96	0.881	0.804	0.96	CLONAL	1	TRUE	1	0.535261958922136	2		571	577	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	130	332	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.89	0.811	0.972	0.89	0.811	0.972	CLONAL	1	TRUE	1	0.535261958922136	2		332	546	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	183	456	1	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.535261958922136	2		457	653	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438316	110438317	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	rs532810290	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	36	196	1	ENST00000375856.3:c.82_84dup	p.Asn28dup	p.N28dup	ENST00000375856	NM_003749.2	28	-/AAC	1/2	1	2	FACETS	0.69	0.573	0.818	0.69	0.573	0.818	SUBCLONAL	1	TRUE	1	0.535261958922136	2		197	195	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	203	526	1	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.535261958922136	2		527	698	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402690	139402690	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs41309764	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	81	435	0	ENST00000277541.6:c.3319C>T	p.Arg1107Ter	p.R1107*	ENST00000277541	NM_017617.3	1107	Cga/Tga	20/34	1	2	FACETS	0.437	0.384	0.493	0.437	0.384	0.493	SUBCLONAL	1	TRUE	1	0.535261958922136	2		435	693	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088788	27088788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	147	399	0	ENST00000324856.7:c.2402del	p.Gly801ValfsTer32	p.G801Vfs*32	ENST00000324856	NM_006015.4	799	caG/ca	7/20	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.535261958922136	2		399	545	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140829	37140829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	128	386	0	ENST00000373509.5:c.665C>T	p.Ser222Leu	p.S222L	ENST00000373509	NM_002648.3	222	tCg/tTg	5/6	1	2	FACETS	0.945	0.861	1	0.945	0.861	1	CLONAL	1	TRUE	1	0.535261958922136	2		386	506	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566418	139566418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374930413	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	154	411	1	ENST00000308874.7:c.677C>T	p.Ser226Leu	p.S226L	ENST00000308874		226	tCg/tTg	9/10	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.535261958922136	2		412	572	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	115	228	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.535261958922136	2		228	343	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272336	15272337	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs771517374	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	187	591	3	ENST00000263388.2:c.6102dup	p.Gly2035ArgfsTer60	p.G2035Rfs*60	ENST00000263388	NM_000435.2	2034	-/C	33/33	1	2	FACETS	0.887	0.821	0.955	0.887	0.821	0.955	CLONAL	1	TRUE	1	0.535261958922136	2		594	788	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131895051	131895051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370769989	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	65	247	0	ENST00000265335.6:c.205G>A	p.Asp69Asn	p.D69N	ENST00000265335		69	Gat/Aat	2/25	1	2	FACETS	0.812	0.71	0.921	0.812	0.71	0.921	CLONAL	1	TRUE	1	0.535261958922136	2		247	299	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123837	46123837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	77	204	0	ENST00000334344.6:c.109del	p.Ile37SerfsTer21	p.I37Sfs*21	ENST00000334344	NM_152641.2	35	Aaa/aa	2/21	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.535261958922136	2		204	270	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120457933	120457933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769520444	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	93	268	0	ENST00000256646.2:c.7412C>T	p.Ala2471Val	p.A2471V	ENST00000256646	NM_024408.3	2471	gCg/gTg	34/34	1	2	FACETS	0.848	0.758	0.941	0.848	0.758	0.941	CLONAL	1	TRUE	1	0.535261958922136	2		268	410	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198852	67198852	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs185889430	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	96	264	0	ENST00000312629.5:c.323G>A	p.Arg108His	p.R108H	ENST00000312629	NM_003952.2	108	cGc/cAc	5/15	1	2	FACETS	0.823	0.737	0.913	0.823	0.737	0.913	CLONAL	1	TRUE	1	0.535261958922136	2		264	436	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116262	209116263	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs754375602	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	56	156	0	ENST00000345146.2:c.13dup	p.Ile5AsnfsTer13	p.I5Nfs*13	ENST00000345146	NM_005896.2	5	atc/aAtc	3/10	0.535261958922136	3	FACETS	0.858	0.74	0.986	0.429	0.37	0.493	CLONAL	1	TRUE	1	0.535261958922136	3		156	309	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30682856	30682856	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113702536	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	164	352	0	ENST00000376406.3:c.97C>T	p.Arg33Trp	p.R33W	ENST00000376406	NM_014641.2	33	Cgg/Tgg	2/15	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.535261958922136	2		352	592	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510806	157510806	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	136	352	2	ENST00000346085.5:c.3586del	p.Gln1196SerfsTer15	p.Q1196Sfs*15	ENST00000346085	NM_020732.3	1194	aCc/ac	14/20	1	2	FACETS	0.921	0.841	1	0.921	0.841	1	CLONAL	1	TRUE	1	0.535261958922136	2		354	552	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302277	15302277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137852641	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	78	503	0	ENST00000263388.2:c.994C>T	p.Arg332Cys	p.R332C	ENST00000263388	NM_000435.2	332	Cgc/Tgc	6/33	1	2	FACETS	0.389	0.341	0.44	0.389	0.341	0.44	SUBCLONAL	1	TRUE	1	0.535261958922136	2		503	750	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572092	64572093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs767319284	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	45	397	1	ENST00000312049.6:c.1546dup	p.Arg516ProfsTer15	p.R516Pfs*15	ENST00000312049	NM_130799.2	516	cgg/cCgg	10/10	1	2	FACETS	0.279	0.234	0.329	0.279	0.234	0.329	SUBCLONAL	1	TRUE	1	0.535261958922136	2		398	603	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936083	178936083	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519927	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	123	377	0	ENST00000263967.3:c.1625A>T	p.Glu542Val	p.E542V	ENST00000263967	NM_006218.2	542	gAa/gTa	10/21	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.535261958922136	2		377	454	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212230	5212230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367918810	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	180	373	1	ENST00000357368.4:c.4801G>A	p.Val1601Ile	p.V1601I	ENST00000357368	NM_002850.3	1601	Gtc/Atc	32/38	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.535261958922136	2		374	592	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	124	795	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.762	0.691	0.836	0.762	0.691	0.836	SUBCLONAL	1	TRUE	1	0.535261958922136	2		801	608	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976741	2976741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564294642	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	190	396	1	ENST00000396946.4:c.1271G>A	p.Arg424Gln	p.R424Q	ENST00000396946	NM_032415.4	424	cGg/cAg	9/25	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.535261958922136	2		397	668	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943789	71943789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773085707	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	179	457	1	ENST00000298229.2:c.1832G>A	p.Arg611His	p.R611H	ENST00000298229	NM_001567.3	611	cGc/cAc	15/28	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.535261958922136	2		458	635	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	174	564	2	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.818	0.754	0.884	0.818	0.754	0.884	CLONAL	1	TRUE	1	0.535261958922136	2		566	795	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31431691	31431691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	106	270	0	ENST00000344624.3:c.3137C>T	p.Ala1046Val	p.A1046V	ENST00000344624		1046	gCg/gTg	23/33	1	2	FACETS	0.945	0.853	1	0.945	0.853	1	CLONAL	1	TRUE	1	0.535261958922136	2		270	419	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500476	99500476	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	68	438	2	ENST00000268035.6:c.3913del	p.Leu1305TrpfsTer45	p.L1305Wfs*45	ENST00000268035	NM_000875.3	1303	gtC/gt	21/21	1	2	FACETS	0.406	0.353	0.463	0.406	0.353	0.463	SUBCLONAL	1	TRUE	1	0.535261958922136	2		440	626	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245474	133245474	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752076074	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	153	351	0	ENST00000320574.5:c.1846C>T	p.Arg616Cys	p.R616C	ENST00000320574	NM_006231.2	616	Cgc/Tgc	17/49	1	2	FACETS	0.987	0.908	1	0.987	0.908	1	CLONAL	1	TRUE	1	0.535261958922136	2		351	579	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574405	95574405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	67	177	0	ENST00000393063.1:c.2462G>A	p.Arg821His	p.R821H	ENST00000393063	NM_030621.3	821	cGc/cAc	17/28	1	2	FACETS	0.941	0.827	1	0.941	0.827	1	CLONAL	1	TRUE	1	0.535261958922136	2		177	266	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417616	139417616	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1228192276	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	244	502	0	ENST00000277541.6:c.428C>T	p.Pro143Leu	p.P143L	ENST00000277541	NM_017617.3	143	cCg/cTg	4/34	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.535261958922136	2		502	777	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230818	66230818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs910705978	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	94	245	0	ENST00000273854.3:c.2153G>A	p.Arg718His	p.R718H	ENST00000273854	NM_004439.5	718	cGc/cAc	12/18	1	2	FACETS	0.944	0.847	1	0.944	0.847	1	CLONAL	1	TRUE	1	0.535261958922136	2		245	372	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225510	26225510	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775230480	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	90	264	0	ENST00000360408.1:c.128G>A	p.Arg43His	p.R43H	ENST00000360408	NM_003532.2	43	cGc/cAc	1/1	1	2	FACETS	0.851	0.76	0.947	0.851	0.76	0.947	CLONAL	1	TRUE	1	0.535261958922136	2		264	395	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95578563	95578563	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886037684	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	100	259	0	ENST00000393063.1:c.2062C>T	p.Arg688Ter	p.R688*	ENST00000393063	NM_030621.3	688	Cga/Tga	14/28	1	2	FACETS	0.978	0.881	1	0.978	0.881	1	CLONAL	1	TRUE	1	0.535261958922136	2		259	382	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189882	11189883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	126	268	0	ENST00000361445.4:c.5626dup	p.Thr1876AsnfsTer37	p.T1876Nfs*37	ENST00000361445	NM_004958.3	1876	acc/aAcc	40/58	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.535261958922136	2		268	430	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11205036	11205036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	145	441	0	ENST00000361445.4:c.4753C>T	p.Arg1585Trp	p.R1585W	ENST00000361445	NM_004958.3	1585	Cgg/Tgg	33/58	1	2	FACETS	0.923	0.846	1	0.923	0.846	1	CLONAL	1	TRUE	1	0.535261958922136	2		441	587	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059206	27059207	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	105	336	0	ENST00000324856.7:c.1848dup	p.Ser617LeufsTer6	p.S617Lfs*6	ENST00000324856	NM_006015.4	615	gcc/gCcc	4/20	1	2	FACETS	0.809	0.728	0.894	0.809	0.728	0.894	CLONAL	1	TRUE	1	0.535261958922136	2		336	485	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456390	32456390	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	43	481	0	ENST00000332351.3:c.502T>C	p.Phe168Leu	p.F168L	ENST00000332351	NM_024426.4	168	Ttc/Ctc	1/10	1	2	FACETS	0.242	0.201	0.286	0.242	0.201	0.286	SUBCLONAL	1	TRUE	1	0.535261958922136	2		481	665	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577434	64577434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	164	404	0	ENST00000312049.6:c.148G>A	p.Val50Ile	p.V50I	ENST00000312049	NM_130799.2	50	Gtc/Atc	2/10	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.535261958922136	2		404	612	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942071	71942071	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	196	511	0	ENST00000298229.2:c.1335G>A	p.Trp445Ter	p.W445*	ENST00000298229	NM_001567.3	445	tgG/tgA	12/28	1	2	FACETS	0.97	0.9	1	0.97	0.9	1	CLONAL	1	TRUE	1	0.535261958922136	2		511	755	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230680	46230680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1325578765	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	30	299	1	ENST00000334344.6:c.929G>A	p.Arg310His	p.R310H	ENST00000334344	NM_152641.2	310	cGt/cAt	8/21	1	2	FACETS	0.298	0.24	0.364	0.298	0.24	0.364	SUBCLONAL	1	TRUE	1	0.535261958922136	2		300	376	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435998	49435998	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393276376	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	171	403	1	ENST00000301067.7:c.5983G>A	p.Gly1995Arg	p.G1995R	ENST00000301067	NM_003482.3	1995	Gga/Aga	28/54	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.535261958922136	2		404	556	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341278	341278	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780541699	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	64	456	0	ENST00000262320.3:c.2206C>T	p.Arg736Trp	p.R736W	ENST00000262320	NM_003502.3	736	Cgg/Tgg	9/11	1	2	FACETS	0.357	0.309	0.409	0.357	0.309	0.409	SUBCLONAL	1	TRUE	1	0.535261958922136	2		456	670	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3645617	3645617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs970090954	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	208	444	0	ENST00000294008.3:c.2002G>A	p.Gly668Ser	p.G668S	ENST00000294008	NM_032444.2	668	Ggc/Agc	9/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.535261958922136	2		444	686	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892212	9892212	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	143	377	0	ENST00000330684.3:c.2278G>T	p.Gly760Cys	p.G760C	ENST00000330684	NM_001134407.1	760	Ggt/Tgt	11/13	1	2	FACETS	0.883	0.808	0.961	0.883	0.808	0.961	CLONAL	1	TRUE	1	0.535261958922136	2		377	605	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944151	81944151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	115	402	1	ENST00000359376.3:c.1760G>A	p.Arg587Gln	p.R587Q	ENST00000359376	NM_002661.3	587	cGg/cAg	18/33	1	2	FACETS	0.863	0.781	0.948	0.863	0.781	0.948	CLONAL	1	TRUE	1	0.535261958922136	2		403	498	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351532	89351532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	181	467	0	ENST00000301030.4:c.1418G>A	p.Ser473Asn	p.S473N	ENST00000301030	NM_001256183.1	473	aGc/aAc	9/13	1	2	FACETS	0.982	0.909	1	0.982	0.909	1	CLONAL	1	TRUE	1	0.535261958922136	2		467	689	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16055260	16055260	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1446410092	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	95	281	0	ENST00000268712.3:c.842C>T	p.Thr281Ile	p.T281I	ENST00000268712	NM_006311.3	281	aCa/aTa	8/46	1	2	FACETS	0.97	0.871	1	0.97	0.871	1	CLONAL	1	TRUE	1	0.535261958922136	2		281	366	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40462643	40462643	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	34	353	0	ENST00000345506.4:c.2345del	p.Pro782LeufsTer34	p.P782Lfs*34	ENST00000345506	NM_003152.3	781	Ccc/cc	20/20	1	2	FACETS	0.255	0.207	0.308	0.255	0.207	0.308	SUBCLONAL	1	TRUE	1	0.535261958922136	2		353	499	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217906	2217906	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769883924	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	205	437	0	ENST00000398665.3:c.2680G>A	p.Ala894Thr	p.A894T	ENST00000398665	NM_032482.2	894	Gcc/Acc	22/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.535261958922136	2		437	699	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122732	7122732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	193	481	1	ENST00000302850.5:c.3422C>T	p.Ala1141Val	p.A1141V	ENST00000302850	NM_000208.2	1141	gCa/gTa	19/22	1	2	FACETS	0.941	0.873	1	0.941	0.873	1	CLONAL	1	TRUE	1	0.535261958922136	2		482	766	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097224	11097224	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761515593	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	176	434	1	ENST00000358026.2:c.715G>A	p.Gly239Ser	p.G239S	ENST00000358026	NM_001128849.1	239	Ggc/Agc	4/36	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.535261958922136	2		435	604	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214390	36214390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	166	437	0	ENST00000222270.7:c.3044G>A	p.Arg1015Gln	p.R1015Q	ENST00000222270	NM_014727.1	1015	cGa/cAa	7/37	1	2	FACETS	0.991	0.914	1	0.991	0.914	1	CLONAL	1	TRUE	1	0.535261958922136	2		437	626	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702319	47702319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28929484	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	142	302	0	ENST00000233146.2:c.1915C>T	p.His639Tyr	p.H639Y	ENST00000233146	NM_000251.2	639	Cat/Tat	12/16	0.535261958922136	3	FACETS	1	0.96	1	0.542	0.495	0.59	CLONAL	1	TRUE	1	0.535261958922136	3		302	621	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703543	47703552	+	frameshift_variant	Frame_Shift_Del	DEL	AACTGGGGTG	AACTGGGGTG	-	novel	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	204	372	0	ENST00000233146.2:c.2044_2053del	p.Thr682Ter	p.T682*	ENST00000233146	NM_000251.2	681	caAACTGGGGTG/ca	13/16	0.535261958922136	3	FACETS	0.792	0.739	0.846	0.792	0.739	0.846	SUBCLONAL	2	TRUE	1	0.535261958922136	3		372	610	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015296	128015296	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772307115	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	102	303	0	ENST00000285398.2:c.2225G>A	p.Arg742Gln	p.R742Q	ENST00000285398	NM_000122.1	742	cGg/cAg	15/15	0.535261958922136	3	FACETS	0.955	0.857	1	0.477	0.428	0.529	CLONAL	1	TRUE	1	0.535261958922136	3		303	506	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131200	202131200	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	165	194	0	ENST00000358485.4:c.171del	p.Phe57LeufsTer28	p.F57Lfs*28	ENST00000358485	NM_001080125.1	56	ccT/cc	2/9	0.535261958922136	3	FACETS	0.924	0.858	0.991	0.924	0.858	0.991	CLONAL	2	TRUE	1	0.535261958922136	3		194	423	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368442	225368444	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	37	296	0	ENST00000264414.4:c.1302_1304del	p.Gln434del	p.Q434del	ENST00000264414	NM_003590.4	434	caACAc/cac	9/16	0.535261958922136	3	FACETS	0.309	0.254	0.37	0.154	0.127	0.185	SUBCLONAL	1	TRUE	1	0.535261958922136	3		296	568	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538334	9538334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	122	324	0	ENST00000353224.5:c.1664C>T	p.Ala555Val	p.A555V	ENST00000353224	NM_177990.2	555	gCt/gTt	7/10	1	2	FACETS	0.962	0.875	1	0.962	0.875	1	CLONAL	1	TRUE	1	0.535261958922136	2		324	474	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46282157	46282157	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1170628032	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	85	209	0	ENST00000371998.3:c.4271G>A	p.Cys1424Tyr	p.C1424Y	ENST00000371998		1424	tGc/tAc	23/23	1	2	FACETS	0.892	0.795	0.994	0.892	0.795	0.994	CLONAL	1	TRUE	1	0.535261958922136	2		209	356	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655337	45655337	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	248	580	0	ENST00000407780.3:c.515T>A	p.Ile172Asn	p.I172N	ENST00000407780	NM_001283052.1	172	aTc/aAc	4/7	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.535261958922136	2		580	875	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643861	52643861	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764416320	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	149	311	1	ENST00000394830.3:c.2035C>T	p.Arg679Cys	p.R679C	ENST00000394830	NM_018313.4	679	Cgc/Tgc	17/30	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.535261958922136	2		312	473	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114283	73114285	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs1559572227	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	58	154	0	ENST00000356692.5:c.926_928del	p.Glu310del	p.E310del	ENST00000356692		307	GAA/-	8/9	1	2	FACETS	0.84	0.729	0.958	0.84	0.729	0.958	CLONAL	1	TRUE	1	0.535261958922136	2		154	258	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138400882	138400882	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	129	352	0	ENST00000289153.2:c.2431C>T	p.Arg811Ter	p.R811*	ENST00000289153	NM_006219.2	811	Cga/Tga	17/22	1	2	FACETS	0.861	0.784	0.941	0.861	0.784	0.941	CLONAL	1	TRUE	1	0.535261958922136	2		352	560	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242935	142242935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	152	338	0	ENST00000350721.4:c.4052G>A	p.Arg1351Gln	p.R1351Q	ENST00000350721	NM_001184.3	1351	cGg/cAg	22/47	1	2	FACETS	0.927	0.851	1	0.927	0.851	1	CLONAL	1	TRUE	1	0.535261958922136	2		338	613	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957425	1957425	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	89	259	1	ENST00000382891.5:c.2524A>G	p.Ser842Gly	p.S842G	ENST00000382891	NM_133335.3	842	Agc/Ggc	14/22	1	2	FACETS	0.868	0.775	0.966	0.868	0.775	0.966	CLONAL	1	TRUE	1	0.535261958922136	2		260	383	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509128	66509128	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1439062174	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	89	321	0	ENST00000273854.3:c.199C>T	p.Arg67Cys	p.R67C	ENST00000273854	NM_004439.5	67	Cgc/Tgc	2/18	1	2	FACETS	0.975	0.873	1	0.975	0.873	1	CLONAL	1	TRUE	1	0.535261958922136	2		321	341	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197299	106197299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	41	245	0	ENST00000380013.4:c.5632C>T	p.Arg1878Cys	p.R1878C	ENST00000380013	NM_001127208.2	1878	Cgt/Tgt	11/11	1	2	FACETS	0.441	0.369	0.522	0.441	0.369	0.522	SUBCLONAL	1	TRUE	1	0.535261958922136	2		245	347	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813523	32813523	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs563899405	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	29	304	0	ENST00000354258.4:c.2260C>T	p.Arg754Cys	p.R754C	ENST00000354258	NM_000593.5	754	Cgc/Tgc	11/11	1	2	FACETS	0.26	0.208	0.319	0.26	0.208	0.319	SUBCLONAL	1	TRUE	1	0.535261958922136	2		304	417	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482934	140482934	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	54	457	1	ENST00000288602.6:c.1201A>G	p.Thr401Ala	p.T401A	ENST00000288602	NM_004333.4	401	Acc/Gcc	10/18	1	2	FACETS	0.309	0.263	0.359	0.309	0.263	0.359	SUBCLONAL	1	TRUE	1	0.535261958922136	2		458	654	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412719	139412720	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	80	444	0	ENST00000277541.6:c.1124dup	p.Cys376MetfsTer7	p.C376Mfs*7	ENST00000277541	NM_017617.3	375	gca/gcCa	7/34	1	2	FACETS	0.438	0.386	0.495	0.438	0.386	0.495	SUBCLONAL	1	TRUE	1	0.535261958922136	2		444	682	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929281	44929281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	197	475	0	ENST00000377967.4:c.2381C>T	p.Thr794Ile	p.T794I	ENST00000377967	NM_021140.2	794	aCt/aTt	17/29	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.535261958922136	2		475	715	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200095	123200095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	28	300	0	ENST00000218089.9:c.2167G>A	p.Gly723Arg	p.G723R	ENST00000218089	NM_001042749.1	723	Gga/Aga	22/35	1	2	FACETS	0.213	0.169	0.262	0.213	0.169	0.262	SUBCLONAL	1	TRUE	1	0.535261958922136	2		300	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	341	689	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.462911695966686	3	FACETS	0.998	0.948	1	0.998	0.948	1	CLONAL	2	TRUE	1	0.462911695966686	3		689	909	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	146	548	0	ENST00000269305.4:c.859G>T	p.Glu287Ter	p.E287*	ENST00000269305	NM_001126112.2	287	Gag/Tag	8/11	0.462911695966686	3	FACETS	0.937	0.856	1	0.469	0.428	0.511	CLONAL	1	TRUE	1	0.462911695966686	3		548	829	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	212	351	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.462911695966686	3	FACETS	0.974	0.92	1	0.974	0.92	1	CLONAL	3	TRUE	0	0.462911695966686	3		351	386	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275179	41275179	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771596917	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	126	307	0	ENST00000349496.5:c.1345C>T	p.Arg449Cys	p.R449C	ENST00000349496	NM_001904.3	449	Cgt/Tgt	9/15	0.462911695966686	2	FACETS	0.881	0.81	0.953	0.881	0.81	0.953	CLONAL	2	TRUE	0	0.462911695966686	2		307	309	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644470	18644470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	55	343	0	ENST00000266497.5:c.2648G>A	p.Cys883Tyr	p.C883Y	ENST00000266497		883	tGt/tAt	18/31	0.209077421567381	2	FACETS	0.718	0.617	0.826	0.359	0.308	0.413	INDETERMINATE	1	TRUE	0	0.462911695966686	2		343	331	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520076	106520076	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	83	236	2	ENST00000359195.3:c.2504G>T	p.Gly835Val	p.G835V	ENST00000359195	NM_002649.2	835	gGt/gTt	6/11	0.453206440342762	3	FACETS	0.92	0.825	1	0.92	0.825	1	CLONAL	2	TRUE	1	0.462911695966686	3		238	240	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739332	46739332	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	177	323	0	ENST00000371975.4:c.1525del	p.Arg509GlufsTer8	p.R509Efs*8	ENST00000371975	NM_003579.3	508	aCc/ac	14/18	0.462911695966686	3	FACETS	0.929	0.863	0.996	0.929	0.863	0.996	CLONAL	2	TRUE	1	0.462911695966686	3		323	507	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658386	206658386	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	186	428	0	ENST00000367120.3:c.1480G>T	p.Glu494Ter	p.E494*	ENST00000367120	NM_014002.3	494	Gaa/Taa	14/22	0.462911695966686	3	FACETS	0.923	0.859	0.989	0.923	0.859	0.989	CLONAL	2	TRUE	1	0.462911695966686	3		428	536	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32439165	32439165	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	159	396	0	ENST00000332351.3:c.908G>T	p.Cys303Phe	p.C303F	ENST00000332351	NM_024426.4	303	tGc/tTc	4/10	0.462911695966686	3	FACETS	0.968	0.896	1	0.968	0.896	1	CLONAL	2	TRUE	1	0.462911695966686	3		396	437	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125499186	125499186	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	193	407	0	ENST00000428830.2:c.349G>T	p.Gly117Trp	p.G117W	ENST00000428830	NM_001114121.2	117	Ggg/Tgg	4/14	0.462911695966686	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.462911695966686	3		407	493	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103513875	103513875	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	125	248	0	ENST00000355739.4:c.691C>T	p.Gln231Ter	p.Q231*	ENST00000355739	NM_000123.3	231	Cag/Tag	7/15	0.341605027229012	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.462911695966686	4		248	350	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434565	110434565	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	233	555	1	ENST00000375856.3:c.3836G>T	p.Gly1279Val	p.G1279V	ENST00000375856	NM_003749.2	1279	gGa/gTa	1/2	0.341605027229012	4	FACETS	0.959	0.897	1	0.959	0.897	1	CLONAL	2	TRUE	2	0.462911695966686	4		556	768	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631833	90631833	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	247	420	0	ENST00000330062.3:c.520G>T	p.Ala174Ser	p.A174S	ENST00000330062	NM_002168.2	174	Gcc/Tcc	4/11	0.462911695966686	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.462911695966686	3		420	618	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992860	72992860	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	138	512	1	ENST00000268489.5:c.1185G>T	p.Leu395Phe	p.L395F	ENST00000268489	NM_006885.3	395	ttG/ttT	2/10	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.462911695966686	2		513	570	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16047001	16047001	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs752709448	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	136	320	0	ENST00000268712.3:c.1092G>T	p.Gln364His	p.Q364H	ENST00000268712	NM_006311.3	364	caG/caT	11/46	0.462911695966686	3	FACETS	0.98	0.902	1	0.98	0.902	1	CLONAL	2	TRUE	1	0.462911695966686	3		320	369	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763208	59763208	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	61	422	0	ENST00000259008.2:c.2894G>T	p.Arg965Ile	p.R965I	ENST00000259008	NM_032043.2	965	aGa/aTa	19/20	0.453206440342762	3	FACETS	0.803	0.696	0.92	0.402	0.348	0.46	CLONAL	1	TRUE	1	0.462911695966686	3		422	404	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857629	78857629	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	150	606	0	ENST00000306801.3:c.1699A>T	p.Asn567Tyr	p.N567Y	ENST00000306801	NM_020761.2	567	Aac/Tac	16/34	0.453206440342762	3	FACETS	1	0.926	1	0.506	0.463	0.552	CLONAL	1	TRUE	1	0.462911695966686	3		606	788	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610357	10610357	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	334	635	0	ENST00000171111.5:c.353A>T	p.Gln118Leu	p.Q118L	ENST00000171111	NM_203500.1	118	cAg/cTg	2/6	0.462911695966686	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.462911695966686	2		635	695	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135066	11135069	+	frameshift_variant	Frame_Shift_Del	DEL	GCAG	GCAG	-	novel	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	330	600	0	ENST00000358026.2:c.3035_3038del	p.Gln1012ProfsTer6	p.Q1012Pfs*6	ENST00000358026	NM_001128849.1	1011	atGCAG/at	21/36	0.462911695966686	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.462911695966686	2		600	686	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051114	13051114	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	247	450	0	ENST00000316448.5:c.550G>T	p.Val184Leu	p.V184L	ENST00000316448	NM_004343.3	184	Gtg/Ttg	5/9	0.410584017797328	4	FACETS	0.951	0.891	1			1	CLONAL	2	TRUE	NA	0.462911695966686	4		450	821	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220938	36220938	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	177	308	0	ENST00000222270.7:c.4988A>G	p.His1663Arg	p.H1663R	ENST00000222270	NM_014727.1	1663	cAc/cGc	23/37	0.454534856162661	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.462911695966686	4		308	522	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274533	198274533	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	183	373	0	ENST00000335508.6:c.865C>A	p.Arg289Ser	p.R289S	ENST00000335508	NM_012433.2	289	Cgt/Agt	7/25	0.3933764579199	4	FACETS	0.957	0.888	1	0.957	0.888	1	CLONAL	2	TRUE	2	0.462911695966686	4		373	604	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092893	29092893	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	159	336	0	ENST00000328354.6:c.1091T>A	p.Ile364Lys	p.I364K	ENST00000328354	NM_007194.3	364	aTa/aAa	10/15	0.462911695966686	3	FACETS	0.912	0.843	0.982	0.912	0.843	0.982	CLONAL	2	TRUE	1	0.462911695966686	3		336	464	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566442	41566442	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	159	312	0	ENST00000263253.7:c.4319C>G	p.Pro1440Arg	p.P1440R	ENST00000263253	NM_001429.3	1440	cCa/cGa	27/31	0.462911695966686	3	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	1	0.462911695966686	3		312	416	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182646	38182646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	141	292	0	ENST00000396334.3:c.799C>T	p.Pro267Ser	p.P267S	ENST00000396334	NM_002468.4	267	Ccc/Tcc	5/5	0.462911695966686	2	FACETS	0.979	0.907	1	0.979	0.907	1	CLONAL	2	TRUE	0	0.462911695966686	2		292	311	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911488	134911488	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	237	450	2	ENST00000398015.3:c.1953G>T	p.Lys651Asn	p.K651N	ENST00000398015	NM_004441.4	651	aaG/aaT	11/16	0.3933764579199	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	2	0.462911695966686	4		452	726	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228307	228307	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	84	201	0	ENST00000264932.6:c.629G>C	p.Arg210Pro	p.R210P	ENST00000264932	NM_004168.2	210	cGa/cCa	6/15	0.462911695966686	5	FACETS	0.878	0.782	0.98	0.586	0.521	0.653	CLONAL	2	TRUE	2	0.462911695966686	5		201	350	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752841	57752841	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	177	299	0	ENST00000274289.3:c.1087T>G	p.Phe363Val	p.F363V	ENST00000274289	NM_006622.3	363	Ttc/Gtc	8/14	0.462911695966686	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.462911695966686	2		299	351	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953921	131953921	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	65	295	0	ENST00000265335.6:c.3324G>T	p.Met1108Ile	p.M1108I	ENST00000265335		1108	atG/atT	21/25	0.462911695966686	3	FACETS	0.95	0.828	1	0.317	0.276	0.361	CLONAL	1	TRUE	0	0.462911695966686	3		295	364	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710637	117710637	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	79	286	0	ENST00000368508.3:c.1635G>T	p.Leu545Phe	p.L545F	ENST00000368508	NM_002944.2	545	ttG/ttT	12/43	0.0804271364471667	3	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.462911695966686	3		286	368	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525537	137525537	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	99	463	0	ENST00000367739.4:c.478del	p.Asp160IlefsTer17	p.D160Ifs*17	ENST00000367739	NM_000416.2	160	Gat/at	4/7	0.462911695966686	3	FACETS	1	0.91	1	0.508	0.455	0.564	CLONAL	1	TRUE	1	0.462911695966686	3		463	518	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509517	106509517	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	115	516	0	ENST00000359195.3:c.1511C>A	p.Ser504Tyr	p.S504Y	ENST00000359195	NM_002649.2	504	tCt/tAt	2/11	0.453206440342762	3	FACETS	0.976	0.881	1	0.488	0.44	0.538	CLONAL	1	TRUE	1	0.462911695966686	3		516	627	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151834005	151834005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	201	338	0	ENST00000262189.6:c.14648G>A	p.Cys4883Tyr	p.C4883Y	ENST00000262189	NM_170606.2	4883	tGc/tAc	59/59	0.453206440342762	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.462911695966686	3		338	504	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860124	151860124	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	104	360	0	ENST00000262189.6:c.10538C>A	p.Pro3513His	p.P3513H	ENST00000262189	NM_170606.2	3513	cCt/cAt	43/59	0.453206440342762	3	FACETS	1	0.962	1	0.572	0.514	0.632	CLONAL	1	TRUE	1	0.462911695966686	3		360	484	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028087	69028087	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	237	577	0	ENST00000288368.4:c.3246C>A	p.Ser1082Arg	p.S1082R	ENST00000288368	NM_024870.2	1082	agC/agA	26/40	0.3933764579199	4	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	2	0.462911695966686	4		577	735	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938830	76938830	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	221	295	0	ENST00000373344.5:c.1918G>T	p.Val640Phe	p.V640F	ENST00000373344	NM_000489.3	640	Gtt/Ttt	9/35	0.410584017797328	2	FACETS	0.931	0.886	0.974			1	CLONAL	3	TRUE	NA	0.462911695966686	2		295	342	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	113	433	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.463703341859834	3	FACETS	1	0.928	1	0.516	0.466	0.569	CLONAL	1	TRUE	1	0.507336568585582	3		433	541	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	173	600	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.996	0.919	1	0.996	0.919	1	CLONAL	1	TRUE	1	0.507336568585582	2		606	685	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	269	795	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.836	0.79	0.883	1	0.995	1	CLONAL	2	TRUE	1	0.507336568585582	2		801	634	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074381	8074381	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	120	291	0	ENST00000377482.5:c.278C>A	p.Pro93His	p.P93H	ENST00000377482	NM_018948.3	93	cCc/cAc	4/4	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.507336568585582	2		291	401	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807480	36807480	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	126	447	0	ENST00000373129.3:c.1184C>T	p.Ala395Val	p.A395V	ENST00000373129	NM_032017.1	395	gCc/gTc	12/12	1	2	FACETS	0.839	0.762	0.919	0.839	0.762	0.919	CLONAL	1	TRUE	1	0.507336568585582	2		447	592	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933161	36933161	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	146	458	0	ENST00000361632.4:c.1956del	p.Asn653ThrfsTer149	p.N653Tfs*149	ENST00000361632		652	ccC/cc	14/16	1	2	FACETS	0.947	0.867	1	0.947	0.867	1	CLONAL	1	TRUE	1	0.507336568585582	2		458	608	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46725744	46725744	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	115	320	0	ENST00000371975.4:c.380G>A	p.Ser127Asn	p.S127N	ENST00000371975	NM_003579.3	127	aGc/aAc	5/18	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.507336568585582	2		320	441	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726435	46726435	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142433634	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	97	263	0	ENST00000371975.4:c.514C>T	p.Arg172Cys	p.R172C	ENST00000371975	NM_003579.3	172	Cgc/Tgc	7/18	1	2	FACETS	0.947	0.85	1	0.947	0.85	1	CLONAL	1	TRUE	1	0.507336568585582	2		263	404	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206942061	206942061	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	59	239	0	ENST00000423557.1:c.457G>T	p.Gly153Cys	p.G153C	ENST00000423557	NM_000572.2	153	Ggc/Tgc	5/5	0.463703341859834	3	FACETS	0.688	0.593	0.79	0.344	0.296	0.395	SUBCLONAL	1	TRUE	1	0.507336568585582	3		239	424	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555308	226555308	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	85	268	0	ENST00000366794.5:c.2279C>T	p.Ala760Val	p.A760V	ENST00000366794	NM_001618.3	760	gCc/gTc	17/23	0.463703341859834	3	FACETS	0.87	0.772	0.974	0.435	0.386	0.487	CLONAL	1	TRUE	1	0.507336568585582	3		268	483	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263973	104263974	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776579	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	59	224	2	ENST00000369902.3:c.71dup	p.Ala25GlyfsTer23	p.A25Gfs*23	ENST00000369902	NM_016169.3	22	gcc/gCcc	1/12	1	2	FACETS	0.674	0.583	0.772	0.674	0.583	0.772	SUBCLONAL	1	TRUE	1	0.507336568585582	2		226	345	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114724349	114724349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780519218	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	112	308	2	ENST00000543371.1:c.416C>T	p.Ala139Val	p.A139V	ENST00000543371	NM_001198531.1	139	gCg/gTg	4/14	1	2	FACETS	0.881	0.796	0.97	0.881	0.796	0.97	CLONAL	1	TRUE	1	0.507336568585582	2		310	501	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	239	398	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.933	0.881	0.985	1	0.995	1	CLONAL	2	TRUE	1	0.507336568585582	2		404	505	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456509	32456509	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770618081	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	46	149	0	ENST00000332351.3:c.383C>T	p.Pro128Leu	p.P128L	ENST00000332351	NM_024426.4	128	cCg/cTg	1/10	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.507336568585582	2		149	180	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201725	67201725	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1353245033	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	133	400	2	ENST00000312629.5:c.1031del	p.Pro344LeufsTer12	p.P344Lfs*12	ENST00000312629	NM_003952.2	342	gaC/ga	12/15	1	2	FACETS	0.867	0.79	0.947	0.867	0.79	0.947	CLONAL	1	TRUE	1	0.507336568585582	2		402	605	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943359	71943359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775327646	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	118	335	0	ENST00000298229.2:c.1691C>T	p.Ser564Leu	p.S564L	ENST00000298229	NM_001567.3	564	tCg/tTg	14/28	1	2	FACETS	0.907	0.822	0.995	0.907	0.822	0.995	CLONAL	1	TRUE	1	0.507336568585582	2		335	513	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066866	77066866	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	69	197	0	ENST00000356341.3:c.619G>A	p.Glu207Lys	p.E207K	ENST00000356341	NM_002576.4	207	Gaa/Aaa	7/15	1	2	FACETS	0.845	0.741	0.955	0.845	0.741	0.955	CLONAL	1	TRUE	1	0.507336568585582	2		197	322	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216477	108216477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587782558	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	63	186	0	ENST00000278616.4:c.8432del	p.Lys2811SerfsTer46	p.K2811Sfs*46	ENST00000278616	NM_000051.3	2809	cAa/ca	58/63	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.507336568585582	2		186	214	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	128	311	0	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	0.507336568585582	2		311	420	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	102	378	5	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.764	0.686	0.847	0.764	0.686	0.847	SUBCLONAL	1	TRUE	1	0.507336568585582	2		383	526	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944698	31944699	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1332433212	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	12	87	0	ENST00000340398.3:c.402_403del	p.Arg134SerfsTer12	p.R134Sfs*12	ENST00000340398	NM_001013699.2	134	agAGct/agct	1/1	1	2	FACETS	0.498	0.354	0.671	0.498	0.354	0.671	SUBCLONAL	1	TRUE	1	0.507336568585582	2		87	95	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945024	31945024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	165	563	0	ENST00000340398.3:c.77C>T	p.Ala26Val	p.A26V	ENST00000340398	NM_001013699.2	26	gCc/gTc	1/1	1	2	FACETS	0.884	0.813	0.957	0.884	0.813	0.957	CLONAL	1	TRUE	1	0.507336568585582	2		563	736	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254666	46254666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	100	328	0	ENST00000334344.6:c.4856G>A	p.Ser1619Asn	p.S1619N	ENST00000334344	NM_152641.2	1619	aGt/aAt	16/21	1	2	FACETS	0.936	0.842	1	0.936	0.842	1	CLONAL	1	TRUE	1	0.507336568585582	2		328	421	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425611	49425611	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	196	539	0	ENST00000301067.7:c.12877C>T	p.Pro4293Ser	p.P4293S	ENST00000301067	NM_003482.3	4293	Cca/Tca	39/54	1	2	FACETS	0.997	0.925	1	0.997	0.925	1	CLONAL	1	TRUE	1	0.507336568585582	2		539	775	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218164	69218164	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	106	282	0	ENST00000462284.1:c.380C>A	p.Ser127Tyr	p.S127Y	ENST00000462284	NM_002392.5	127	tCt/tAt	6/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.507336568585582	2		282	391	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117423	115117423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	71	298	0	ENST00000257566.3:c.751C>T	p.Arg251Trp	p.R251W	ENST00000257566	NM_016569.3	251	Cgg/Tgg	4/8	1	2	FACETS	0.767	0.673	0.866	0.767	0.673	0.866	SUBCLONAL	1	TRUE	1	0.507336568585582	2		298	365	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416861	121416861	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	247	618	0	ENST00000257555.6:c.290C>A	p.Ala97Glu	p.A97E	ENST00000257555		97	gCg/gAg	1/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.507336568585582	2		618	937	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210965	133210965	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	108	283	0	ENST00000320574.5:c.5812-1G>A		p.X1938_splice	ENST00000320574	NM_006231.2	1938			1	2	FACETS	0.952	0.86	1	0.952	0.86	1	CLONAL	1	TRUE	1	0.507336568585582	2		283	447	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	130	378	1	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	1	2	FACETS	0.949	0.865	1	0.949	0.865	1	CLONAL	1	TRUE	1	0.507336568585582	2		379	540	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871856	35871856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	114	304	0	ENST00000216797.5:c.650G>A	p.Gly217Asp	p.G217D	ENST00000216797	NM_020529.2	217	gGc/gAc	5/6	1	2	FACETS	0.912	0.825	1	0.912	0.825	1	CLONAL	1	TRUE	1	0.507336568585582	2		304	493	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873766	35873766	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	120	339	0	ENST00000216797.5:c.85C>A	p.Arg29Ser	p.R29S	ENST00000216797	NM_020529.2	29	Cgc/Agc	1/6	1	2	FACETS	0.962	0.873	1	0.962	0.873	1	CLONAL	1	TRUE	1	0.507336568585582	2		339	492	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986774	36986774	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1448653785	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	41	101	0	ENST00000354822.5:c.915del	p.Ala306ArgfsTer75	p.A306Rfs*75	ENST00000354822	NM_001079668.2	305	ccC/cc	3/3	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.507336568585582	2		101	150	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986925	36986925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1192440323	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	166	403	0	ENST00000354822.5:c.764C>T	p.Ala255Val	p.A255V	ENST00000354822	NM_001079668.2	255	gCg/gTg	3/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.507336568585582	2		403	590	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241310	105241310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1176264024	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	164	527	0	ENST00000349310.3:c.598C>T	p.Arg200Cys	p.R200C	ENST00000349310	NM_001014432.1	200	Cgc/Tgc	8/15	1	2	FACETS	0.937	0.863	1	0.937	0.863	1	CLONAL	1	TRUE	1	0.507336568585582	2		527	690	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052626	42052626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	122	358	0	ENST00000219905.7:c.7297C>T	p.Arg2433Trp	p.R2433W	ENST00000219905	NM_001164273.1	2433	Cgg/Tgg	20/24	1	2	FACETS	0.984	0.894	1	0.984	0.894	1	CLONAL	1	TRUE	1	0.507336568585582	2		358	489	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707818	43707818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	169	506	1	ENST00000382044.4:c.5063G>A	p.Gly1688Asp	p.G1688D	ENST00000382044	NM_001141980.1	1688	gGt/gAt	23/28	1	2	FACETS	0.97	0.894	1	0.97	0.894	1	CLONAL	1	TRUE	1	0.507336568585582	2		507	687	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748384	43748384	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	75	570	0	ENST00000382044.4:c.2422G>A	p.Asp808Asn	p.D808N	ENST00000382044	NM_001141980.1	808	Gac/Aac	12/28	1	2	FACETS	0.381	0.333	0.432	0.381	0.333	0.432	SUBCLONAL	1	TRUE	1	0.507336568585582	2		570	777	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396507	396507	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	171	614	2	ENST00000262320.3:c.519G>A	p.Met173Ile	p.M173I	ENST00000262320	NM_003502.3	173	atG/atA	2/11	1	2	FACETS	0.815	0.751	0.882	0.815	0.751	0.882	CLONAL	1	TRUE	1	0.507336568585582	2		616	827	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096314	2096314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767591879	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	162	572	2	ENST00000219066.1:c.193C>T	p.Arg65Cys	p.R65C	ENST00000219066	NM_002528.5	65	Cgt/Tgt	2/6	1	2	FACETS	0.835	0.767	0.905	0.835	0.767	0.905	CLONAL	1	TRUE	1	0.507336568585582	2		574	765	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660509	67660509	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1259626314	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	122	329	0	ENST00000264010.4:c.1409G>A	p.Arg470His	p.R470H	ENST00000264010	NM_006565.3	470	cGt/cAt	8/12	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.507336568585582	2		329	474	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822539	72822540	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	94	373	0	ENST00000268489.5:c.9635dup	p.Pro3213AlafsTer26	p.P3213Afs*26	ENST00000268489	NM_006885.3	3212	ccg/ccCg	10/10	1	2	FACETS	0.755	0.674	0.84	0.755	0.674	0.84	SUBCLONAL	1	TRUE	1	0.507336568585582	2		373	491	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991976	72991976	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	137	416	0	ENST00000268489.5:c.2069T>C	p.Met690Thr	p.M690T	ENST00000268489	NM_006885.3	690	aTg/aCg	2/10	1	2	FACETS	0.986	0.901	1	0.986	0.901	1	CLONAL	1	TRUE	1	0.507336568585582	2		416	548	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350048	89350048	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1164325679	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	160	488	1	ENST00000301030.4:c.2902C>T	p.Pro968Ser	p.P968S	ENST00000301030	NM_001256183.1	968	Ccc/Tcc	9/13	1	2	FACETS	0.908	0.834	0.984	0.908	0.834	0.984	CLONAL	1	TRUE	1	0.507336568585582	2		489	695	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350611	89350613	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	rs1163513451	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	197	684	0	ENST00000301030.4:c.2337_2339del	p.Lys779del	p.K779del	ENST00000301030	NM_001256183.1	779	aaGAAt/aat	9/13	1	2	FACETS	0.87	0.806	0.936	0.87	0.806	0.936	CLONAL	1	TRUE	1	0.507336568585582	2		684	893	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352540	89352540	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	129	391	0	ENST00000301030.4:c.799G>T	p.Gly267Cys	p.G267C	ENST00000301030	NM_001256183.1	267	Ggc/Tgc	8/13	1	2	FACETS	0.984	0.897	1	0.984	0.897	1	CLONAL	1	TRUE	1	0.507336568585582	2		391	517	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216379	7216380	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1216832021	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	111	459	2	ENST00000380728.2:c.868dup	p.Gln290ProfsTer?	p.Q290Pfs*?	ENST00000380728		290	cag/cCag	10/11	1	2	FACETS	0.676	0.609	0.747	0.676	0.609	0.747	SUBCLONAL	1	TRUE	1	0.507336568585582	2		461	647	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217008	7217008	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	114	351	0	ENST00000380728.2:c.513del	p.Phe171LeufsTer174	p.F171Lfs*174	ENST00000380728		171	ttT/tt	7/11	1	2	FACETS	0.915	0.828	1	0.915	0.828	1	CLONAL	1	TRUE	1	0.507336568585582	2		351	491	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976476	7976476	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	140	369	0	ENST00000319144.4:c.1916del	p.Pro639LeufsTer24	p.P639Lfs*24	ENST00000319144	NM_001139.2	639	cCt/ct	14/15	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.507336568585582	2		369	536	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998898	11998898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	56	201	0	ENST00000353533.5:c.400C>T	p.Arg134Trp	p.R134W	ENST00000353533	NM_003010.3	134	Cgg/Tgg	4/11	1	2	FACETS	0.964	0.836	1	0.964	0.836	1	CLONAL	1	TRUE	1	0.507336568585582	2		201	229	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508503	29508503	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	88	330	0	ENST00000356175.3:c.653del	p.Lys218ArgfsTer7	p.K218Rfs*7	ENST00000356175	NM_000267.3	217	gAa/ga	6/57	1	2	FACETS	0.822	0.732	0.917	0.822	0.732	0.917	CLONAL	1	TRUE	1	0.507336568585582	2		330	422	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665778	29665778	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	73	302	0	ENST00000356175.3:c.6813A>C	p.Glu2271Asp	p.E2271D	ENST00000356175	NM_000267.3	2271	gaA/gaC	45/57	1	2	FACETS	0.827	0.728	0.932	0.827	0.728	0.932	CLONAL	1	TRUE	1	0.507336568585582	2		302	348	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884070	37884070	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776754071	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	188	549	0	ENST00000269571.5:c.3541G>A	p.Val1181Ile	p.V1181I	ENST00000269571		1181	Gtc/Atc	27/27	1	2	FACETS	0.953	0.882	1	0.953	0.882	1	CLONAL	1	TRUE	1	0.507336568585582	2		549	778	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40447790	40447790	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	127	391	0	ENST00000345506.4:c.529C>A	p.Gln177Lys	p.Q177K	ENST00000345506	NM_003152.3	177	Cag/Aag	6/20	1	2	FACETS	0.948	0.863	1	0.948	0.863	1	CLONAL	1	TRUE	1	0.507336568585582	2		391	528	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245587	41245587	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357522	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	132	470	1	ENST00000357654.3:c.1961del	p.Lys654SerfsTer47	p.K654Sfs*47	ENST00000357654	NM_007294.3	654	aAg/ag	10/23	1	2	FACETS	0.714	0.649	0.782	0.714	0.649	0.782	SUBCLONAL	1	TRUE	1	0.507336568585582	2		471	729	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857747	78857747	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	118	506	0	ENST00000306801.3:c.1817G>T	p.Ser606Ile	p.S606I	ENST00000306801	NM_020761.2	606	aGc/aTc	16/34	1	2	FACETS	0.75	0.678	0.826	0.75	0.678	0.826	SUBCLONAL	1	TRUE	1	0.507336568585582	2		506	620	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919466	78919466	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	146	363	0	ENST00000306801.3:c.3026-1G>T		p.X1009_splice	ENST00000306801	NM_020761.2	1009			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.507336568585582	2		363	521	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1650225	1650225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376780559	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	158	491	1	ENST00000344749.5:c.23C>T	p.Ala8Val	p.A8V	ENST00000344749	NM_001136139.2	8	gCg/gTg	2/19	1	2	FACETS	0.913	0.839	0.99	0.913	0.839	0.99	CLONAL	1	TRUE	1	0.507336568585582	2		492	682	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226382	2226382	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	202	655	1	ENST00000398665.3:c.3862C>A	p.Leu1288Met	p.L1288M	ENST00000398665	NM_032482.2	1288	Ctg/Atg	27/28	1	2	FACETS	0.949	0.881	1	0.949	0.881	1	CLONAL	1	TRUE	1	0.507336568585582	2		656	839	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3114988	3114988	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	156	514	0	ENST00000078429.4:c.523A>G	p.Thr175Ala	p.T175A	ENST00000078429	NM_002067.2	175	Acc/Gcc	4/7	1	2	FACETS	0.815	0.747	0.885	0.815	0.747	0.885	CLONAL	1	TRUE	1	0.507336568585582	2		514	755	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244068	5244068	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747170106	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	157	531	1	ENST00000357368.4:c.1414G>A	p.Val472Met	p.V472M	ENST00000357368	NM_002850.3	472	Gtg/Atg	11/38	1	2	FACETS	0.883	0.811	0.958	0.883	0.811	0.958	CLONAL	1	TRUE	1	0.507336568585582	2		532	701	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270594	10270594	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	133	452	0	ENST00000340748.4:c.1046A>G	p.His349Arg	p.H349R	ENST00000340748		349	cAc/cGc	15/40	1	2	FACETS	0.92	0.839	1	0.92	0.839	1	CLONAL	1	TRUE	1	0.507336568585582	2		452	570	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098363	11098363	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	186	511	0	ENST00000358026.2:c.885del	p.Thr296ArgfsTer7	p.T296Rfs*7	ENST00000358026	NM_001128849.1	294	gCc/gc	6/36	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.507336568585582	2		511	676	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101877	11101877	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	168	599	1	ENST00000358026.2:c.1297G>C	p.Ala433Pro	p.A433P	ENST00000358026	NM_001128849.1	433	Gcc/Ccc	8/36	1	2	FACETS	0.865	0.796	0.936	0.865	0.796	0.936	CLONAL	1	TRUE	1	0.507336568585582	2		600	766	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135006	11135006	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	92	434	0	ENST00000358026.2:c.2974-1G>T		p.X992_splice	ENST00000358026	NM_001128849.1	992			1	2	FACETS	0.711	0.634	0.793	0.711	0.634	0.793	SUBCLONAL	1	TRUE	1	0.507336568585582	2		434	510	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145645	11145645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	196	538	1	ENST00000358026.2:c.4007G>A	p.Arg1336His	p.R1336H	ENST00000358026	NM_001128849.1	1336	cGc/cAc	29/36	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.507336568585582	2		539	757	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152049	11152049	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558017726	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	163	405	0	ENST00000358026.2:c.4333C>T	p.Arg1445Cys	p.R1445C	ENST00000358026	NM_001128849.1	1445	Cgc/Tgc	31/36	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.507336568585582	2		405	576	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285206	15285206	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	193	538	0	ENST00000263388.2:c.4409T>G	p.Val1470Gly	p.V1470G	ENST00000263388	NM_000435.2	1470	gTg/gGg	25/33	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.507336568585582	2		538	722	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297972	15297972	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1433631796	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	227	635	0	ENST00000263388.2:c.1784G>A	p.Gly595Asp	p.G595D	ENST00000263388	NM_000435.2	595	gGc/gAc	11/33	1	2	FACETS	0.986	0.919	1	0.986	0.919	1	CLONAL	1	TRUE	1	0.507336568585582	2		635	908	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300125	15300125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201917592	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	167	513	0	ENST00000263388.2:c.1151C>T	p.Thr384Met	p.T384M	ENST00000263388	NM_000435.2	384	aCg/aTg	7/33	1	2	FACETS	0.858	0.79	0.929	0.858	0.79	0.929	CLONAL	1	TRUE	1	0.507336568585582	2		513	767	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349918	15349918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293348757	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	148	417	0	ENST00000263377.2:c.3734C>T	p.Ala1245Val	p.A1245V	ENST00000263377	NM_058243.2	1245	gCc/gTc	18/20	1	2	FACETS	0.986	0.904	1	0.986	0.904	1	CLONAL	1	TRUE	1	0.507336568585582	2		417	592	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376352	15376352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776261114	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	237	714	0	ENST00000263377.2:c.662C>T	p.Thr221Met	p.T221M	ENST00000263377	NM_058243.2	221	aCg/aTg	5/20	1	2	FACETS	0.945	0.882	1	0.945	0.882	1	CLONAL	1	TRUE	1	0.507336568585582	2		714	989	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955112	17955112	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755706305	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	180	573	4	ENST00000458235.1:c.115del	p.Gln39SerfsTer108	p.Q39Sfs*108	ENST00000458235	NM_000215.3	39	Cag/ag	2/24	1	2	FACETS	0.922	0.852	0.994	0.922	0.852	0.994	CLONAL	1	TRUE	1	0.507336568585582	2		577	770	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18963016	18963016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749622332	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	196	587	0	ENST00000262803.5:c.883C>T	p.Arg295Trp	p.R295W	ENST00000262803	NM_002911.3	295	Cgg/Tgg	6/24	1	2	FACETS	0.935	0.867	1	0.935	0.867	1	CLONAL	1	TRUE	1	0.507336568585582	2		587	826	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	217	846	1	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.868	0.808	0.931	0.868	0.808	0.931	CLONAL	1	TRUE	1	0.507336568585582	2		847	985	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223230	36223230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372039999	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	264	698	2	ENST00000222270.7:c.5780G>A	p.Arg1927Gln	p.R1927Q	ENST00000222270	NM_014727.1	1927	cGg/cAg	28/37	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.507336568585582	2		700	1001	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469540	25469540	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	198	548	0	ENST00000264709.3:c.1228G>C	p.Ala410Pro	p.A410P	ENST00000264709	NM_175629.2	410	Gcc/Ccc	10/23	0.483618030876634	2	FACETS	1	0.963	1	0.528	0.49	0.567	CLONAL	1	TRUE	0	0.507336568585582	2		548	739	SUCCESS
ALK	238	MSKCC	GRCh37	2	29450530	29450530	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	134	525	1	ENST00000389048.3:c.2824G>A	p.Ala942Thr	p.A942T	ENST00000389048	NM_004304.4	942	Gca/Aca	17/29	0.483618030876634	2	FACETS	0.804	0.732	0.879	0.402	0.366	0.44	CLONAL	1	TRUE	0	0.507336568585582	2		526	657	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46603887	46603887	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	127	402	0	ENST00000263734.3:c.1244A>T	p.Asp415Val	p.D415V	ENST00000263734	NM_001430.4	415	gAt/gTt	9/16	0.483618030876634	2	FACETS	1	0.912	1	0.501	0.456	0.547	CLONAL	1	TRUE	0	0.507336568585582	2		402	500	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607784	46607784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs112301187	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	188	614	1	ENST00000263734.3:c.1973G>A	p.Arg658His	p.R658H	ENST00000263734	NM_001430.4	658	cGc/cAc	12/16	0.483618030876634	2	FACETS	1	0.933	1	0.503	0.466	0.542	CLONAL	1	TRUE	0	0.507336568585582	2		615	736	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693895	47693895	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	161	328	0	ENST00000233146.2:c.1613del	p.Asn538ThrfsTer5	p.N538Tfs*5	ENST00000233146	NM_000251.2	537	Aaa/aa	10/16	0.483618030876634	2	FACETS	0.78	0.723	0.837	0.78	0.723	0.837	SUBCLONAL	2	TRUE	0	0.507336568585582	2		328	407	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149631	61149631	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	65	237	0	ENST00000295025.8:c.1821A>T	p.Gln607His	p.Q607H	ENST00000295025	NM_002908.2	607	caA/caT	11/11	0.483618030876634	2	FACETS	0.843	0.737	0.956	0.421	0.368	0.478	CLONAL	1	TRUE	0	0.507336568585582	2		237	304	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682810	190682810	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	101	323	2	ENST00000441310.2:c.492del	p.Lys164AsnfsTer6	p.K164Nfs*6	ENST00000441310	NM_000534.4	162	gcA/gc	5/13	0.483618030876634	2	FACETS	0.937	0.843	1	0.468	0.421	0.518	CLONAL	1	TRUE	0	0.507336568585582	2		325	425	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141631	202141631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs17860424	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	66	457	3	ENST00000358485.4:c.919C>T	p.Arg307Trp	p.R307W	ENST00000358485	NM_001080125.1	307	Cgg/Tgg	7/9	0.483618030876634	2	FACETS	0.541	0.47	0.617	0.27	0.235	0.309	SUBCLONAL	1	TRUE	0	0.507336568585582	2		460	481	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151290	202151290	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	117	326	0	ENST00000358485.4:c.1596del	p.Lys532AsnfsTer73	p.K532Nfs*73	ENST00000358485	NM_001080125.1	530	agA/ag	9/9	0.483618030876634	2	FACETS	1	0.926	1	0.511	0.464	0.561	CLONAL	1	TRUE	0	0.507336568585582	2		326	451	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578280	212578280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	89	364	0	ENST00000342788.4:c.977G>A	p.Cys326Tyr	p.C326Y	ENST00000342788	NM_005235.2	326	tGc/tAc	8/28	0.483618030876634	2	FACETS	0.751	0.669	0.839	0.376	0.334	0.42	SUBCLONAL	1	TRUE	0	0.507336568585582	2		364	467	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388021	31388021	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	101	298	0	ENST00000328111.2:c.1822G>A	p.Glu608Lys	p.E608K	ENST00000328111	NM_006892.3	608	Gag/Aag	17/23	1	2	FACETS	0.995	0.896	1	0.995	0.896	1	CLONAL	1	TRUE	1	0.507336568585582	2		298	400	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755554	39755554	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	98	350	1	ENST00000288319.7:c.1211del	p.Pro404ArgfsTer25	p.P404Rfs*25	ENST00000288319	NM_182918.3	404	cCg/cg	10/10	1	2	FACETS	0.87	0.781	0.964	0.87	0.781	0.964	CLONAL	1	TRUE	1	0.507336568585582	2		351	444	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764351	39764351	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	98	359	0	ENST00000288319.7:c.761C>A	p.Pro254His	p.P254H	ENST00000288319	NM_182918.3	254	cCc/cAc	7/10	1	2	FACETS	0.813	0.729	0.902	0.813	0.729	0.902	CLONAL	1	TRUE	1	0.507336568585582	2		359	475	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	76	251	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.801	0.707	0.901	0.801	0.707	0.901	CLONAL	1	TRUE	1	0.507336568585582	2		252	374	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277290	41277290	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064796453	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	73	250	2	ENST00000349496.5:c.1759C>T	p.Arg587Ter	p.R587*	ENST00000349496	NM_001904.3	587	Cga/Tga	11/15	1	2	FACETS	0.846	0.746	0.953	0.846	0.746	0.953	CLONAL	1	TRUE	1	0.507336568585582	2		252	340	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920370	134920370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542190087	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	101	362	0	ENST00000398015.3:c.2185G>A	p.Ala729Thr	p.A729T	ENST00000398015	NM_004441.4	729	Gct/Act	12/16	1	2	FACETS	0.92	0.827	1	0.92	0.827	1	CLONAL	1	TRUE	1	0.507336568585582	2		362	433	SUCCESS
ATR	545	MSKCC	GRCh37	3	142255002	142255002	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	57	188	1	ENST00000350721.4:c.3767C>A	p.Pro1256His	p.P1256H	ENST00000350721	NM_001184.3	1256	cCt/cAt	20/47	1	2	FACETS	0.775	0.67	0.887	0.775	0.67	0.887	SUBCLONAL	1	TRUE	1	0.507336568585582	2		189	290	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274740	142274741	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	94	317	0	ENST00000350721.4:c.2319_2320del	p.Lys773AsnfsTer3	p.K773Nfs*3	ENST00000350721	NM_001184.3	773	aaAAta/aata	10/47	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.507336568585582	2		317	353	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	85	529	1	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.868	0.772	0.969	0.868	0.772	0.969	CLONAL	1	TRUE	1	0.507336568585582	2		530	386	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535435	66535435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	111	348	0	ENST00000273854.3:c.26C>T	p.Ala9Val	p.A9V	ENST00000273854	NM_004439.5	9	gCg/gTg	1/18	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.507336568585582	2		348	396	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	105	368	0	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	0.804	0.723	0.889	0.804	0.723	0.889	CLONAL	1	TRUE	1	0.507336568585582	2		368	515	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251485	251485	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	21	31	0	ENST00000264932.6:c.1696C>A	p.Leu566Met	p.L566M	ENST00000264932	NM_004168.2	566	Ctg/Atg	13/15	1	2	FACETS	0.9	0.732	1	1	0.947	1	CLONAL	2	TRUE	1	0.507336568585582	2		31	46	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876588	35876588	+	stop_lost	Nonstop_Mutation	SNP	A	A	T	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	107	349	1	ENST00000303115.3:c.1380A>T	p.Ter460CysextTer7	p.*460Cext*7	ENST00000303115	NM_002185.3	460	tgA/tgT	8/8	1	2	FACETS	0.913	0.824	1	0.913	0.824	1	CLONAL	1	TRUE	1	0.507336568585582	2		350	462	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178257	56178258	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	68	239	0	ENST00000399503.3:c.3236dup	p.Asn1079LysfsTer2	p.N1079Kfs*2	ENST00000399503	NM_005921.1	1077	tca/tcAa	14/20	1	2	FACETS	0.786	0.688	0.89	0.786	0.688	0.89	SUBCLONAL	1	TRUE	1	0.507336568585582	2		239	341	SUCCESS
APC	324	MSKCC	GRCh37	5	112175559	112175559	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	151	245	0	ENST00000257430.4:c.4269del	p.Pro1424GlnfsTer49	p.P1424Qfs*49	ENST00000257430	NM_000038.5	1423	cTt/ct	16/16	NA	2	FACETS	0.846	0.784	0.908			1	INDETERMINATE	2	TRUE	NA	0.507336568585582	2		245	352	SUCCESS
APC	324	MSKCC	GRCh37	5	112178865	112178865	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762034315	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	75	269	0	ENST00000257430.4:c.7574G>A	p.Arg2525His	p.R2525H	ENST00000257430	NM_000038.5	2525	cGc/cAc	16/16	NA	2	FACETS	0.824	0.727	0.927			1	INDETERMINATE	1	TRUE	NA	0.507336568585582	2		269	359	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818391	170818391	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	43	134	0	ENST00000296930.5:c.221T>C	p.Val74Ala	p.V74A	ENST00000296930	NM_002520.6	74	gTa/gCa	3/11	0.483618030876634	2	FACETS	0.958	0.813	1	0.479	0.406	0.557	CLONAL	1	TRUE	0	0.507336568585582	2		134	177	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053023	180053023	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	180	604	1	ENST00000261937.6:c.1267del	p.Gln423ArgfsTer70	p.Q423Rfs*70	ENST00000261937	NM_182925.4	423	Cag/ag	10/30	0.483618030876634	2	FACETS	0.855	0.789	0.923	0.427	0.394	0.462	CLONAL	1	TRUE	0	0.507336568585582	2		605	830	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056464	26056464	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138308559	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	43	199	0	ENST00000343677.2:c.193G>A	p.Ala65Thr	p.A65T	ENST00000343677	NM_005319.3	65	Gcg/Acg	1/1	0.475209037246738	2	FACETS	0.75	0.633	0.877	0.375	0.316	0.439	SUBCLONAL	1	TRUE	0	0.507336568585582	2		199	226	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790978	89790978	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	89	229	0	ENST00000336032.3:c.365C>A	p.Pro122Gln	p.P122Q	ENST00000336032	NM_006813.2	122	cCg/cAg	1/2	1	2	FACETS	0.951	0.85	1	0.951	0.85	1	CLONAL	1	TRUE	1	0.507336568585582	2		229	369	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710605	117710605	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	65	251	0	ENST00000368508.3:c.1667C>A	p.Pro556His	p.P556H	ENST00000368508	NM_002944.2	556	cCt/cAt	12/43	1	2	FACETS	0.73	0.637	0.83	0.73	0.637	0.83	SUBCLONAL	1	TRUE	1	0.507336568585582	2		251	351	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138201360	138201360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	90	326	0	ENST00000237289.4:c.2059C>T	p.His687Tyr	p.H687Y	ENST00000237289	NM_001270507.1	687	Cat/Tat	8/9	1	2	FACETS	0.797	0.711	0.889	0.797	0.711	0.889	SUBCLONAL	1	TRUE	1	0.507336568585582	2		326	445	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851993	128851993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1200280970	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	186	605	0	ENST00000249373.3:c.2065C>T	p.Pro689Ser	p.P689S	ENST00000249373	NM_005631.4	689	Cct/Tct	12/12	0.463703341859834	3	FACETS	1	0.934	1	0.506	0.467	0.546	CLONAL	1	TRUE	1	0.507336568585582	3		605	909	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860697	151860697	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	101	377	0	ENST00000262189.6:c.9965G>A	p.Gly3322Asp	p.G3322D	ENST00000262189	NM_170606.2	3322	gGc/gAc	43/59	0.463703341859834	3	FACETS	0.865	0.775	0.96	0.433	0.387	0.48	CLONAL	1	TRUE	1	0.507336568585582	3		377	577	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136797	69136797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868748091	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	146	309	0	ENST00000288368.4:c.4711G>A	p.Ala1571Thr	p.A1571T	ENST00000288368	NM_024870.2	1571	Gca/Aca	39/40	0.463703341859834	3	FACETS	0.82	0.755	0.887	0.82	0.755	0.887	CLONAL	2	TRUE	1	0.507336568585582	3		309	440	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982742	90982742	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	97	230	0	ENST00000265433.3:c.746C>T	p.Ala249Val	p.A249V	ENST00000265433	NM_002485.4	249	gCt/gTt	7/16	0.463703341859834	3	FACETS	1	0.944	1	0.54	0.484	0.599	CLONAL	1	TRUE	1	0.507336568585582	3		230	444	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739855	145739855	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	166	566	1	ENST00000428558.2:c.1675A>G	p.Arg559Gly	p.R559G	ENST00000428558	NM_004260.3	559	Agg/Ggg	10/22	0.463703341859834	3	FACETS	0.838	0.769	0.91	0.419	0.384	0.455	CLONAL	1	TRUE	1	0.507336568585582	3		567	979	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460441	8460441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	81	301	0	ENST00000356435.5:c.3845G>A	p.Cys1282Tyr	p.C1282Y	ENST00000356435		1282	tGc/tAc	22/35	1	2	FACETS	0.882	0.783	0.987	0.882	0.783	0.987	CLONAL	1	TRUE	1	0.507336568585582	2		301	362	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	123	395	3	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.911	0.828	0.999	0.911	0.828	0.999	CLONAL	1	TRUE	1	0.507336568585582	2		398	532	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240416	98240416	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	92	336	0	ENST00000331920.6:c.1268C>G	p.Thr423Ser	p.T423S	ENST00000331920	NM_000264.3	423	aCc/aGc	9/24	1	2	FACETS	0.815	0.728	0.907	0.815	0.728	0.907	CLONAL	1	TRUE	1	0.507336568585582	2		336	445	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753838	133753838	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	277	435	1	ENST00000318560.5:c.1307G>A	p.Gly436Asp	p.G436D	ENST00000318560	NM_005157.4	436	gGc/gAc	8/11	0.483618030876634	2	FACETS	0.991	0.941	1	0.991	0.941	1	CLONAL	2	TRUE	0	0.507336568585582	2		436	551	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390736	139390736	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	179	625	1	ENST00000277541.6:c.7455del	p.Ser2486ArgfsTer103	p.S2486Rfs*103	ENST00000277541	NM_017617.3	2485	ccC/cc	34/34	0.483618030876634	2	FACETS	0.827	0.763	0.894	0.414	0.381	0.447	CLONAL	1	TRUE	0	0.507336568585582	2		626	853	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650793	48650793	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	211	271	0	ENST00000376670.3:c.662G>T	p.Gly221Val	p.G221V	ENST00000376670	NM_002049.3	221	gGc/gTc	4/6	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.507336568585582	1		271	419	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226112	53226112	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	151	250	2	ENST00000375401.3:c.2737del	p.Val913TrpfsTer22	p.V913Wfs*22	ENST00000375401	NM_004187.3	913	Gtg/tg	19/26	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.507336568585582	1		252	352	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279864	46279872	+	inframe_deletion	In_Frame_Del	DEL	CAACAGCAA	CAACAGCAA	-	rs778086744	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	28	205	0	ENST00000371998.3:c.3792_3800del	p.Gln1274_Gln1276del	p.Q1274_Q1276del	ENST00000371998		1264	CAACAGCAA/-	20/23	1	2	FACETS	0.379	0.304	0.465	0.379	0.304	0.465	SUBCLONAL	1	TRUE	1	0.507336568585582	2		205	291	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0028474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	153	463	3	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.892	0.819	0.969	0.892	0.819	0.969	CLONAL	1	TRUE	1	0.507336568585582	2		466	676	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0028475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	59	567	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.453509931988432	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	0	0.453509931988432	1		568	169	SUCCESS
APC	324	MSKCC	GRCh37	5	112175360	112175360	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	22	179	0	ENST00000257430.4:c.4069G>T	p.Gly1357Ter	p.G1357*	ENST00000257430	NM_000038.5	1357	Gga/Tga	16/16	0.453509931988432	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	2	FALSE	0	0.453509931988432	2		179	45	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0028478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	98	603	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.406565310999743	1	FACETS	0.975	0.876	1	0.975	0.876	1	CLONAL	1	TRUE	0	0.406565310999743	1		604	394	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121082	11121082	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	89	647	0	ENST00000358026.2:c.2149G>C	p.Glu717Gln	p.E717Q	ENST00000358026	NM_001128849.1	717	Gaa/Caa	15/36	0.347495384087982	3	FACETS	0.882	0.784	0.988	0.441	0.392	0.494	CLONAL	1	TRUE	1	0.406565310999743	3		647	597	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123199756	123199756	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	44	261	0	ENST00000218089.9:c.2056C>G	p.Gln686Glu	p.Q686E	ENST00000218089	NM_001042749.1	686	Cag/Gag	21/35	0.670864464408647	1	FACETS	0.369	0.312	0.431	0.369	0.312	0.431	SUBCLONAL	1	TRUE	0	0.670864464408647	1		261	236	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579368	7579368	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	223	724	0	ENST00000269305.4:c.319T>G	p.Tyr107Asp	p.Y107D	ENST00000269305	NM_001126112.2	107	Tac/Gac	4/11	0.670864464408647	1	FACETS	0.986	0.931	1	0.986	0.931	1	CLONAL	1	TRUE	0	0.670864464408647	1		724	448	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446746	49446746	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	196	470	0	ENST00000301067.7:c.1064G>T	p.Gly355Val	p.G355V	ENST00000301067	NM_003482.3	355	gGt/gTt	8/54	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.670864464408647	2		470	569	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99472808	99472808	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	179	367	0	ENST00000268035.6:c.2804A>G	p.His935Arg	p.H935R	ENST00000268035	NM_000875.3	935	cAt/cGt	14/21	0.508430526695868	1	FACETS	0.966	0.905	1	0.966	0.905	1	CLONAL	1	TRUE	0	0.670864464408647	1		367	367	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683976	29683976	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0028480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	155	405	0	ENST00000356175.3:c.7676-2A>G		p.X2559_splice	ENST00000356175	NM_000267.3	2559			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.670864464408647	2		405	420	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115027	3115027	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	141	736	0	ENST00000078429.4:c.562G>C	p.Gly188Arg	p.G188R	ENST00000078429	NM_002067.2	188	Ggc/Cgc	4/7	1	2	FACETS	0.543	0.495	0.593	0.543	0.495	0.593	SUBCLONAL	1	TRUE	1	0.670864464408647	2		736	774	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149245643	149245643	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	223	626	0	ENST00000360632.3:c.885C>G	p.Ser295Arg	p.S295R	ENST00000360632	NM_015472.4	295	agC/agG	5/7	0.396666148093406	1	FACETS	0.759	0.712	0.807	0.759	0.712	0.807	INDETERMINATE	1	TRUE	0	0.670864464408647	1		626	582	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392039	81392039	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	72	186	0	ENST00000222390.5:c.238C>G	p.Leu80Val	p.L80V	ENST00000222390	NM_000601.4	80	Ctt/Gtt	2/18	1	2	FACETS	0.781	0.689	0.876	0.781	0.689	0.876	SUBCLONAL	1	TRUE	1	0.670864464408647	2		186	275	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270514	98270514	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	148	428	0	ENST00000331920.6:c.130G>T	p.Ala44Ser	p.A44S	ENST00000331920	NM_000264.3	44	Gcg/Tcg	1/24	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.670864464408647	2		428	371	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412029	63412029	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	72	589	0	ENST00000330258.3:c.1138G>T	p.Glu380Ter	p.E380*	ENST00000330258	NM_152424.3	380	Gag/Tag	2/2	0.670864464408647	1	FACETS	0.411	0.361	0.464	0.411	0.361	0.464	SUBCLONAL	1	TRUE	0	0.670864464408647	1		589	347	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345907	70345907	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762905361	NA	P-0028480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	64	436	0	ENST00000374080.3:c.2444G>A	p.Arg815Gln	p.R815Q	ENST00000374080		815	cGg/cAg	18/45	0.670864464408647	1	FACETS	0.369	0.321	0.42	0.369	0.321	0.42	SUBCLONAL	1	TRUE	0	0.670864464408647	1		436	344	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907626	76907626	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	70	461	0	ENST00000373344.5:c.4535G>T	p.Arg1512Leu	p.R1512L	ENST00000373344	NM_000489.3	1512	cGt/cTt	15/35	0.670864464408647	1	FACETS	0.331	0.289	0.375	0.331	0.289	0.375	SUBCLONAL	1	TRUE	0	0.670864464408647	1		461	419	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	87	433	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	0.270474720178342	2		433	478	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	112	600	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.818	0.739	0.901	1	0.986	1	CLONAL	2	TRUE	1	0.270474720178342	2		606	506	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	118	795	6	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	0.270474720178342	2		801	674	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274740	142274741	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	46	317	0	ENST00000350721.4:c.2319_2320del	p.Lys773AsnfsTer3	p.K773Nfs*3	ENST00000350721	NM_001184.3	773	aaAAta/aata	10/47	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.270474720178342	2		317	295	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429978	78429978	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	75	341	0	ENST00000370768.2:c.901del	p.Ile301TyrfsTer22	p.I301Yfs*22	ENST00000370768	NM_003902.3	301	Ata/ta	11/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.270474720178342	2		341	444	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	112	661	2	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.789	0.712	0.869	1	0.985	1	SUBCLONAL	2	TRUE	1	0.270474720178342	2		663	525	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	103	445	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.865	0.779	0.956	1	0.986	1	CLONAL	2	TRUE	1	0.270474720178342	2		445	440	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	75	338	2	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.270474720178342	2		340	384	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223796	53223796	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	54	735	0	ENST00000375401.3:c.3563G>C	p.Cys1188Ser	p.C1188S	ENST00000375401	NM_004187.3	1188	tGt/tCt	23/26	0.270474720178342	1	FACETS	0.507	0.432	0.589	0.507	0.432	0.589	SUBCLONAL	1	TRUE	0	0.270474720178342	1		735	681	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	30	150	0	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	0.270474720178342	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.270474720178342	1		150	153	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584514	48584514	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	43	311	1	ENST00000342988.3:c.692del	p.Gly231AlafsTer10	p.G231Afs*10	ENST00000342988	NM_005359.5	229	ctG/ct	6/12	1	2	FACETS	0.919	0.772	1	0.919	0.772	1	CLONAL	1	TRUE	1	0.270474720178342	2		312	346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	99	556	2	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.270474720178342	2		558	533	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564642	55564642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	51	452	2	ENST00000288135.5:c.530G>A	p.Arg177His	p.R177H	ENST00000288135	NM_000222.2	177	cGc/cAc	3/21	1	2	FACETS	0.742	0.631	0.864	0.742	0.631	0.864	SUBCLONAL	1	TRUE	1	0.270474720178342	2		454	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	29	598	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	1	2	FACETS	0.28	0.223	0.345	0.28	0.223	0.345	SUBCLONAL	1	TRUE	1	0.270474720178342	2		598	766	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440943	56440943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786205215	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	118	445	1	ENST00000407977.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000407977		132	Cga/Tga	4/10	1	2	FACETS	0.845	0.766	0.928	1	0.987	1	CLONAL	2	TRUE	1	0.270474720178342	2		446	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	36	499	2	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	1	2	FACETS	0.399	0.327	0.48	0.399	0.327	0.48	SUBCLONAL	1	TRUE	1	0.270474720178342	2		501	667	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237689	133237689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500820	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	92	510	0	ENST00000320574.5:c.2926C>T	p.Arg976Cys	p.R976C	ENST00000320574	NM_006231.2	976	Cgc/Tgc	25/49	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.270474720178342	2		510	661	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	118	505	3	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	1	2	FACETS	0.82	0.743	0.901	1	0.987	1	CLONAL	2	TRUE	1	0.270474720178342	2		508	532	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874637	35874637	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	65	321	5	ENST00000303115.3:c.799del	p.Arg267GlyfsTer28	p.R267Gfs*28	ENST00000303115	NM_002185.3	265	Aaa/aa	6/8	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.270474720178342	2		326	393	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008054	29008054	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	27	305	0	ENST00000282397.4:c.715C>A	p.Pro239Thr	p.P239T	ENST00000282397	NM_002019.4	239	Cca/Aca	6/30	1	2	FACETS	0.574	0.457	0.707	0.574	0.457	0.707	SUBCLONAL	1	TRUE	1	0.270474720178342	2		305	348	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	14	233	0	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.417	0.301	0.558	0.417	0.301	0.558	SUBCLONAL	1	TRUE	1	0.270474720178342	2		233	248	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136070	64136070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	78	531	1	ENST00000334205.4:c.1331G>A	p.Arg444His	p.R444H	ENST00000334205	NM_003942.2	444	cGc/cAc	11/17	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.270474720178342	2		532	434	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169952	32169952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151325272	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	51	639	0	ENST00000375023.3:c.3656G>A	p.Arg1219Gln	p.R1219Q	ENST00000375023	NM_004557.3	1219	cGg/cAg	21/30	0.251731936128695	2	FACETS	0.573	0.486	0.669	0.287	0.243	0.335	SUBCLONAL	1	TRUE	0	0.270474720178342	2		639	658	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	40	423	0	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	0.484	0.401	0.577	0.484	0.401	0.577	SUBCLONAL	1	TRUE	1	0.270474720178342	2		423	611	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258979	153258979	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	30	223	0	ENST00000281708.4:c.836A>G	p.Asp279Gly	p.D279G	ENST00000281708	NM_033632.3	279	gAc/gGc	5/12	1	2	FACETS	0.765	0.618	0.93	0.765	0.618	0.93	CLONAL	1	TRUE	1	0.270474720178342	2		223	290	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422716	47422716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1413219188	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	41	437	3	ENST00000377045.4:c.188G>A	p.Arg63Gln	p.R63Q	ENST00000377045	NM_001654.4	63	cGa/cAa	3/16	0.270474720178342	1	FACETS	0.655	0.547	0.776	0.655	0.547	0.776	SUBCLONAL	1	TRUE	0	0.270474720178342	1		440	400	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097625	11097625	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	148	648	3	ENST00000358026.2:c.810del	p.Met272CysfsTer31	p.M272Cfs*31	ENST00000358026	NM_001128849.1	269	Ccc/cc	5/36	1	2	FACETS	0.86	0.788	0.935	1	0.99	1	CLONAL	2	TRUE	1	0.270474720178342	2		651	636	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954342	48954342	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780248969	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	38	279	0	ENST00000267163.4:c.1463C>T	p.Ala488Val	p.A488V	ENST00000267163	NM_000321.2	488	gCg/gTg	16/27	1	2	FACETS	0.65	0.538	0.776	0.65	0.538	0.776	SUBCLONAL	1	TRUE	1	0.270474720178342	2		279	432	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400005	139400005	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1479377696	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	133	629	1	ENST00000277541.6:c.4343C>T	p.Ala1448Val	p.A1448V	ENST00000277541	NM_017617.3	1448	gCg/gTg	25/34	1	2	FACETS	0.792	0.721	0.866	1	0.987	1	SUBCLONAL	2	TRUE	1	0.270474720178342	2		630	621	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979319	40979319	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1217327426	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	36	540	0	ENST00000373198.4:c.1814C>T	p.Thr605Met	p.T605M	ENST00000373198	NM_133170.3	605	aCg/aTg	11/32	1	2	FACETS	0.439	0.36	0.528	0.439	0.36	0.528	SUBCLONAL	1	TRUE	1	0.270474720178342	2		540	606	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627418	37627418	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	51	556	2	ENST00000447079.4:c.1337del	p.Lys446SerfsTer6	p.K446Sfs*6	ENST00000447079	NM_015083.1	445	Aaa/aa	2/14	1	2	FACETS	0.555	0.471	0.648	0.555	0.471	0.648	SUBCLONAL	1	TRUE	1	0.270474720178342	2		558	679	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955111	17955112	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755706305	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	119	590	2	ENST00000458235.1:c.115dup	p.Gln39ProfsTer13	p.Q39Pfs*13	ENST00000458235	NM_000215.3	39	cag/cCag	2/24	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.270474720178342	2		592	619	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256439	115256439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774832953	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	75	344	0	ENST00000369535.4:c.272C>T	p.Ala91Val	p.A91V	ENST00000369535	NM_002524.4	91	gCg/gTg	3/7	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.270474720178342	2		344	427	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905061	50905061	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	92	565	0	ENST00000440232.2:c.347del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	115	Ccc/cc	4/27	1	2	FACETS	0.818	0.731	0.909	1	0.983	1	CLONAL	2	TRUE	1	0.270474720178342	2		565	416	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346220	152346220	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	133	701	7	ENST00000359321.1:c.350del	p.Leu117TrpfsTer17	p.L117Wfs*17	ENST00000359321	NM_005431.1	117	tTg/tg	3/3	1	2	FACETS	0.796	0.725	0.87	1	0.988	1	SUBCLONAL	2	TRUE	1	0.270474720178342	2		708	618	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285630	46285630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	63	372	0	ENST00000334344.6:c.4990C>T	p.Pro1664Ser	p.P1664S	ENST00000334344	NM_152641.2	1664	Cca/Tca	17/21	1	2	FACETS	0.845	0.732	0.969	0.845	0.732	0.969	CLONAL	1	TRUE	1	0.270474720178342	2		372	551	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307280	65307283	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	28	274	0	ENST00000342505.4:c.2405_2408del	p.Lys802ArgfsTer11	p.K802Rfs*11	ENST00000342505	NM_002227.2	802	aAAGAg/ag	18/25	1	2	FACETS	0.737	0.591	0.903	0.737	0.591	0.903	CLONAL	1	TRUE	1	0.270474720178342	2		274	281	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295773	15295773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1248140755	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	144	784	3	ENST00000263388.2:c.2354G>A	p.Arg785His	p.R785H	ENST00000263388	NM_000435.2	785	cGc/cAc	15/33	1	2	FACETS	0.834	0.763	0.908	1	0.989	1	CLONAL	2	TRUE	1	0.270474720178342	2		787	638	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636766	8636766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776233840	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	102	401	0	ENST00000356435.5:c.143C>T	p.Thr48Met	p.T48M	ENST00000356435		48	aCg/aTg	2/35	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.270474720178342	2		401	559	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189472	94189473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs757691558	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	68	397	1	ENST00000323929.3:c.1532dup	p.Asn511LysfsTer3	p.N511Kfs*3	ENST00000323929	NM_005591.3	511	aat/aaAt	14/20	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.270474720178342	2		398	461	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164508	47164508	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs201756643	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	61	300	1	ENST00000409792.3:c.1618C>T	p.Arg540Ter	p.R540*	ENST00000409792	NM_014159.6	540	Cga/Tga	3/21	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.270474720178342	2		301	331	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	132	451	2	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.270474720178342	2		453	775	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556250	29556250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199474739	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	52	378	0	ENST00000356175.3:c.2617C>T	p.Arg873Cys	p.R873C	ENST00000356175	NM_000267.3	873	Cgt/Tgt	21/57	1	2	FACETS	0.991	0.846	1	0.991	0.846	1	CLONAL	1	TRUE	1	0.270474720178342	2		378	388	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431874	49431874	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	33	531	2	ENST00000301067.7:c.9265del	p.Val3089TrpfsTer30	p.V3089Wfs*30	ENST00000301067	NM_003482.3	3089	Gtg/tg	34/54	1	2	FACETS	0.449	0.365	0.545	0.449	0.365	0.545	SUBCLONAL	1	TRUE	1	0.270474720178342	2		533	543	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602518	10602518	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	93	519	1	ENST00000171111.5:c.1060C>T	p.Arg354Trp	p.R354W	ENST00000171111	NM_203500.1	354	Cgg/Tgg	3/6	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.270474720178342	2		520	470	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155654	56155654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746479827	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	50	307	0	ENST00000399503.3:c.746G>A	p.Arg249His	p.R249H	ENST00000399503	NM_005921.1	249	cGc/cAc	3/20	1	2	FACETS	0.844	0.717	0.983	0.844	0.717	0.983	CLONAL	1	TRUE	1	0.270474720178342	2		307	438	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218451	36218451	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs34078597	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	70	532	0	ENST00000222270.7:c.4235del	p.Gly1412AlafsTer10	p.G1412Afs*10	ENST00000222270	NM_014727.1	1410	caG/ca	16/37	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.270474720178342	2		532	403	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680722	88680722	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	81	488	0	ENST00000360948.2:c.535del	p.Glu179ArgfsTer24	p.E179Rfs*24	ENST00000360948	NM_001012338.2	179	Gag/ag	6/19	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.270474720178342	2		488	493	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707977	43707977	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	141	615	0	ENST00000382044.4:c.4904G>A	p.Arg1635His	p.R1635H	ENST00000382044	NM_001141980.1	1635	cGc/cAc	23/28	1	2	FACETS	0.78	0.713	0.851	1	0.988	1	SUBCLONAL	2	TRUE	1	0.270474720178342	2		615	668	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436815	110436815	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	65	606	2	ENST00000375856.3:c.1586del	p.Pro529ArgfsTer15	p.P529Rfs*15	ENST00000375856	NM_003749.2	529	cCg/cg	1/2	1	2	FACETS	0.608	0.526	0.697	0.608	0.526	0.697	SUBCLONAL	1	TRUE	1	0.270474720178342	2		608	791	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133898	41133898	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	57	286	0	ENST00000379561.5:c.1730del	p.Gly577AlafsTer5	p.G577Afs*5	ENST00000379561	NM_002015.3	577	gGc/gc	2/3	1	2	FACETS	0.798	0.691	0.913	1	0.972	1	CLONAL	2	TRUE	1	0.270474720178342	2		286	264	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40683721	40683721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757403176	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	126	467	0	ENST00000249776.8:c.713G>A	p.Arg238Gln	p.R238Q	ENST00000249776	NM_033286.3	238	cGa/cAa	7/9	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.270474720178342	2		467	700	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034427	47034427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	63	289	1	ENST00000377604.3:c.512G>A	p.Arg171Gln	p.R171Q	ENST00000377604	NM_001204468.1	171	cGg/cAg	6/24	0.270474720178342	1	FACETS	0.685	0.593	0.786	0.685	0.593	0.786	SUBCLONAL	1	TRUE	0	0.270474720178342	1		290	588	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795081	45795081	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778542	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	63	436	3	ENST00000450313.1:c.1547C>T	p.Pro516Leu	p.P516L	ENST00000450313	NM_012222.2	516	cCg/cTg	16/16	1	2	FACETS	0.858	0.743	0.983	0.858	0.743	0.983	CLONAL	1	TRUE	1	0.270474720178342	2		439	543	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828186	243828186	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	34	302	0	ENST00000263826.5:c.173-1G>A		p.X58_splice	ENST00000263826	NM_005465.4	58			1	2	FACETS	0.914	0.75	1	0.914	0.75	1	CLONAL	1	TRUE	1	0.270474720178342	2		302	275	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620390	43620390	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	94	429	0	ENST00000355710.3:c.2999A>G	p.Asp1000Gly	p.D1000G	ENST00000355710	NM_020975.4	1000	gAc/gGc	18/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.270474720178342	2		429	537	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571894	64571895	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	218	822	0	ENST00000312049.6:c.1744_1745del	p.Gln582ValfsTer14	p.Q582Vfs*14	ENST00000312049	NM_130799.2	582	CAg/g	10/10	1	2	FACETS	0.778	0.723	0.835	1	0.992	1	SUBCLONAL	2	TRUE	1	0.270474720178342	2		822	1036	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998423	100998423	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	39	326	0	ENST00000325455.5:c.1379G>A	p.Cys460Tyr	p.C460Y	ENST00000325455	NM_001202474.3	460	tGc/tAc	1/8	1	2	FACETS	0.836	0.695	0.992	0.836	0.695	0.992	CLONAL	1	TRUE	1	0.270474720178342	2		326	345	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199803	108199803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	67	221	1	ENST00000278616.4:c.7145G>A	p.Gly2382Glu	p.G2382E	ENST00000278616	NM_000051.3	2382	gGa/gAa	49/63	1	2	FACETS	0.845	0.741	0.956	1	0.978	1	CLONAL	2	TRUE	1	0.270474720178342	2		222	293	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870955	12870955	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	68	301	0	ENST00000228872.4:c.182A>C	p.Asn61Thr	p.N61T	ENST00000228872	NM_004064.3	61	aAt/aCt	1/3	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.270474720178342	2		301	352	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245225	46245225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529386166	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	33	396	0	ENST00000334344.6:c.3319G>A	p.Ala1107Thr	p.A1107T	ENST00000334344	NM_152641.2	1107	Gca/Aca	15/21	1	2	FACETS	0.634	0.516	0.766	0.634	0.516	0.766	SUBCLONAL	1	TRUE	1	0.270474720178342	2		396	385	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435295	121435296	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs776793516	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	102	475	0	ENST00000257555.6:c.1330_1331del	p.Gln444GlufsTer104	p.Q444Efs*104	ENST00000257555		443	gCA/g	7/10	1	2	FACETS	0.827	0.744	0.914	1	0.985	1	CLONAL	2	TRUE	1	0.270474720178342	2		475	456	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233811	133233811	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs575738148	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	44	467	1	ENST00000320574.5:c.3493G>A	p.Asp1165Asn	p.D1165N	ENST00000320574	NM_006231.2	1165	Gac/Aac	29/49	1	2	FACETS	0.521	0.436	0.615	0.521	0.436	0.615	SUBCLONAL	1	TRUE	1	0.270474720178342	2		468	625	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249748	133249748	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	56	314	0	ENST00000320574.5:c.1473+2T>C		p.X491_splice	ENST00000320574	NM_006231.2	491			1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.270474720178342	2		314	373	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562141	21562141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373012826	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	243	799	0	ENST00000382592.4:c.1778G>A	p.Arg593His	p.R593H	ENST00000382592	NM_014572.2	593	cGc/cAc	4/8	1	2	FACETS	0.815	0.761	0.871	1	0.993	1	CLONAL	2	TRUE	1	0.270474720178342	2		799	1102	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66779632	66779632	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	40	371	0	ENST00000307102.5:c.960+2T>C		p.X320_splice	ENST00000307102	NM_002755.3	320			1	2	FACETS	0.585	0.485	0.695	0.585	0.485	0.695	SUBCLONAL	1	TRUE	1	0.270474720178342	2		371	506	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99482547	99482547	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	62	475	0	ENST00000268035.6:c.3415C>T	p.Arg1139Trp	p.R1139W	ENST00000268035	NM_000875.3	1139	Cgg/Tgg	18/21	1	2	FACETS	0.8	0.691	0.918	0.8	0.691	0.918	CLONAL	1	TRUE	1	0.270474720178342	2		475	573	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807319	3807319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1315374383	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	53	383	0	ENST00000262367.5:c.3668G>A	p.Arg1223His	p.R1223H	ENST00000262367	NM_004380.2	1223	cGc/cAc	19/31	1	2	FACETS	0.696	0.593	0.809	0.696	0.593	0.809	SUBCLONAL	1	TRUE	1	0.270474720178342	2		383	563	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348869	11348869	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	22	209	0	ENST00000332029.2:c.467C>A	p.Ala156Glu	p.A156E	ENST00000332029	NM_003745.1	156	gCg/gAg	2/2	1	2	FACETS	0.764	0.594	0.958	0.764	0.594	0.958	CLONAL	1	TRUE	1	0.270474720178342	2		209	213	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644845	67644845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	125	414	0	ENST00000264010.4:c.110C>T	p.Ala37Val	p.A37V	ENST00000264010	NM_006565.3	37	gCc/gTc	3/12	1	2	FACETS	0.917	0.834	1	1	0.989	1	CLONAL	2	TRUE	1	0.270474720178342	2		414	504	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822127	72822127	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	37	395	0	ENST00000268489.5:c.10048C>T	p.Gln3350Ter	p.Q3350*	ENST00000268489	NM_006885.3	3350	Cag/Tag	10/10	1	2	FACETS	0.724	0.598	0.865	0.724	0.598	0.865	SUBCLONAL	1	TRUE	1	0.270474720178342	2		395	378	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831172	72831172	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	87	388	0	ENST00000268489.5:c.5409del	p.Ser1804ValfsTer10	p.S1804Vfs*10	ENST00000268489	NM_006885.3	1803	ccC/cc	9/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.270474720178342	2		388	439	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653022	29653022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555533342	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	51	310	1	ENST00000356175.3:c.4957G>A	p.Val1653Ile	p.V1653I	ENST00000356175	NM_000267.3	1653	Gtc/Atc	36/57	1	2	FACETS	0.836	0.712	0.972	0.836	0.712	0.972	CLONAL	1	TRUE	1	0.270474720178342	2		311	451	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245162	41245162	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	37	580	0	ENST00000357654.3:c.2386del	p.Thr796GlnfsTer7	p.T796Qfs*7	ENST00000357654	NM_007294.3	796	Aca/ca	10/23	1	2	FACETS	0.436	0.359	0.524	0.436	0.359	0.524	SUBCLONAL	1	TRUE	1	0.270474720178342	2		580	627	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532568	63532568	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	129	558	1	ENST00000307078.5:c.2011del	p.Arg671AlafsTer18	p.R671Afs*18	ENST00000307078	NM_004655.3	671	Cgc/gc	8/11	1	2	FACETS	0.834	0.759	0.912	1	0.988	1	CLONAL	2	TRUE	1	0.270474720178342	2		559	572	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534458	63534458	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	62	506	0	ENST00000307078.5:c.1063A>G	p.Thr355Ala	p.T355A	ENST00000307078	NM_004655.3	355	Acc/Gcc	5/11	1	2	FACETS	0.837	0.723	0.96	0.837	0.723	0.96	CLONAL	1	TRUE	1	0.270474720178342	2		506	548	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985752	60985754	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	24	213	0	ENST00000333681.4:c.146_148del	p.Phe49del	p.F49del	ENST00000333681		49	tTCTcc/tcc	2/3	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.270474720178342	2		213	158	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353791	15353791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1158865535	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	119	520	1	ENST00000263377.2:c.3089C>T	p.Pro1030Leu	p.P1030L	ENST00000263377	NM_058243.2	1030	cCg/cTg	14/20	1	2	FACETS	0.783	0.709	0.86	1	0.986	1	SUBCLONAL	2	TRUE	1	0.270474720178342	2		521	562	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213944	36213944	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs183764710	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	129	662	2	ENST00000222270.7:c.2770C>T	p.Arg924Trp	p.R924W	ENST00000222270	NM_014727.1	924	Cgg/Tgg	6/37	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.270474720178342	2		664	673	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216679	36216679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	105	477	0	ENST00000222270.7:c.3845C>T	p.Pro1282Leu	p.P1282L	ENST00000222270	NM_014727.1	1282	cCc/cTc	13/37	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.270474720178342	2		477	589	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218383	36218383	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	141	657	0	ENST00000222270.7:c.4162T>C	p.Tyr1388His	p.Y1388H	ENST00000222270	NM_014727.1	1388	Tac/Cac	16/37	1	2	FACETS	0.75	0.685	0.818	1	0.987	1	SUBCLONAL	2	TRUE	1	0.270474720178342	2		657	695	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220932	36220932	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	55	306	0	ENST00000222270.7:c.4982A>C	p.Asn1661Thr	p.N1661T	ENST00000222270	NM_014727.1	1661	aAc/aCc	23/37	1	2	FACETS	0.776	0.67	0.89	1	0.97	1	SUBCLONAL	2	TRUE	1	0.270474720178342	2		306	262	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791698	42791698	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1183958206	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	87	485	2	ENST00000575354.2:c.584G>A	p.Arg195Gln	p.R195Q	ENST00000575354	NM_015125.3	195	cGg/cAg	5/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.270474720178342	2		487	459	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796535	42796535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs539384322	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	122	639	1	ENST00000575354.2:c.3092C>T	p.Ser1031Leu	p.S1031L	ENST00000575354	NM_015125.3	1031	tCg/tTg	13/20	1	2	FACETS	0.787	0.714	0.864	1	0.986	1	SUBCLONAL	2	TRUE	1	0.270474720178342	2		640	573	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940533	29940533	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs749700096	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	136	532	0	ENST00000389048.3:c.698T>C	p.Met233Thr	p.M233T	ENST00000389048	NM_004304.4	233	aTg/aCg	2/29	1	2	FACETS	0.816	0.745	0.891	1	0.988	1	CLONAL	2	TRUE	1	0.270474720178342	2		532	616	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143223	30143223	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	80	564	0	ENST00000389048.3:c.303G>T	p.Leu101Phe	p.L101F	ENST00000389048	NM_004304.4	101	ttG/ttT	1/29	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.270474720178342	2		564	412	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574040	46574040	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	34	489	0	ENST00000263734.3:c.55T>A	p.Ser19Thr	p.S19T	ENST00000263734	NM_001430.4	19	Tcc/Acc	2/16	1	2	FACETS	0.462	0.377	0.559	0.462	0.377	0.559	SUBCLONAL	1	TRUE	1	0.270474720178342	2		489	544	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605131	46605131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762678739	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	43	585	0	ENST00000263734.3:c.1348G>A	p.Glu450Lys	p.E450K	ENST00000263734	NM_001430.4	450	Gag/Aag	10/16	1	2	FACETS	0.641	0.536	0.757	0.641	0.536	0.757	SUBCLONAL	1	TRUE	1	0.270474720178342	2		585	496	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251619	212251619	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	30	353	0	ENST00000342788.4:c.3440A>G	p.Glu1147Gly	p.E1147G	ENST00000342788	NM_005235.2	1147	gAg/gGg	27/28	1	2	FACETS	0.564	0.455	0.689	0.564	0.455	0.689	SUBCLONAL	1	TRUE	1	0.270474720178342	2		353	393	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021634	31021634	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs137920574	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	119	439	0	ENST00000375687.4:c.1633C>A	p.Arg545Ser	p.R545S	ENST00000375687	NM_015338.5	545	Cgt/Agt	12/13	1	2	FACETS	0.753	0.682	0.828	1	0.985	1	SUBCLONAL	2	TRUE	1	0.270474720178342	2		439	584	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023798	31023798	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	94	517	0	ENST00000375687.4:c.3283T>C	p.Ser1095Pro	p.S1095P	ENST00000375687	NM_015338.5	1095	Tcc/Ccc	13/13	1	2	FACETS	0.767	0.686	0.853	1	0.982	1	SUBCLONAL	2	TRUE	1	0.270474720178342	2		517	453	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46252731	46252731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	22	317	1	ENST00000371998.3:c.160G>A	p.Ala54Thr	p.A54T	ENST00000371998		54	Gcc/Acc	4/23	1	2	FACETS	0.416	0.322	0.526	0.416	0.322	0.526	SUBCLONAL	1	TRUE	1	0.270474720178342	2		318	391	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130637	29130637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142243299	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	21	418	0	ENST00000328354.6:c.73G>A	p.Val25Ile	p.V25I	ENST00000328354	NM_007194.3	25	Gtt/Att	2/15	1	2	FACETS	0.433	0.333	0.549	0.433	0.333	0.549	SUBCLONAL	1	TRUE	1	0.270474720178342	2		418	359	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37622751	37622751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	83	629	0	ENST00000249071.6:c.541C>T	p.Pro181Ser	p.P181S	ENST00000249071	NM_002872.4	181	Ccc/Tcc	6/7	1	2	FACETS	0.9	0.794	1	0.9	0.794	1	CLONAL	1	TRUE	1	0.270474720178342	2		629	682	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936430	49936430	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	155	664	0	ENST00000296474.3:c.1420-2A>G		p.X474_splice	ENST00000296474	NM_002447.2	474			1	2	FACETS	1	0.958	1	1	0.992	1	CLONAL	2	TRUE	1	0.270474720178342	2		664	540	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72842184	72842184	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	16	207	0	ENST00000325599.8:c.1064A>G	p.Lys355Arg	p.K355R	ENST00000325599	NM_018130.2	355	aAa/aGa	10/11	1	2	FACETS	0.415	0.306	0.545	0.415	0.306	0.545	SUBCLONAL	1	TRUE	1	0.270474720178342	2		207	285	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884858	134884858	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774975718	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	44	336	1	ENST00000398015.3:c.1634C>T	p.Ser545Leu	p.S545L	ENST00000398015	NM_004441.4	545	tCg/tTg	8/16	1	2	FACETS	0.644	0.54	0.76	0.644	0.54	0.76	SUBCLONAL	1	TRUE	1	0.270474720178342	2		337	505	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138402552	138402552	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	85	373	0	ENST00000289153.2:c.2393A>T	p.Asp798Val	p.D798V	ENST00000289153	NM_006219.2	798	gAt/gTt	16/22	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.270474720178342	2		373	427	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456712	138456712	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	30	363	0	ENST00000289153.2:c.638A>G	p.Gln213Arg	p.Q213R	ENST00000289153	NM_006219.2	213	cAa/cGa	4/22	1	2	FACETS	0.514	0.413	0.627	0.514	0.413	0.627	SUBCLONAL	1	TRUE	1	0.270474720178342	2		363	432	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430501	181430501	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1207683228	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	137	616	0	ENST00000325404.1:c.353C>T	p.Thr118Met	p.T118M	ENST00000325404	NM_003106.3	118	aCg/aTg	1/1	1	2	FACETS	0.789	0.72	0.861	1	0.988	1	SUBCLONAL	2	TRUE	1	0.270474720178342	2		616	642	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540670	187540670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530876083	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	93	309	0	ENST00000441802.2:c.7070C>T	p.Thr2357Met	p.T2357M	ENST00000441802	NM_005245.3	2357	aCg/aTg	10/27	1	2	FACETS	0.95	0.852	1	1	0.986	1	CLONAL	2	TRUE	1	0.270474720178342	2		309	362	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31429619	31429619	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	33	541	0	ENST00000344624.3:c.3179C>T	p.Ala1060Val	p.A1060V	ENST00000344624		1060	gCc/gTc	24/33	1	2	FACETS	0.371	0.301	0.45	0.371	0.301	0.45	SUBCLONAL	1	TRUE	1	0.270474720178342	2		541	658	SUCCESS
APC	324	MSKCC	GRCh37	5	112177731	112177731	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779469633	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	75	327	0	ENST00000257430.4:c.6440C>T	p.Pro2147Leu	p.P2147L	ENST00000257430	NM_000038.5	2147	cCa/cTa	16/16	1	2	FACETS	0.906	0.802	1	1	0.982	1	CLONAL	2	TRUE	1	0.270474720178342	2		327	306	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911125	29911125	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199474508	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	35	531	1	ENST00000376809.5:c.424T>C	p.Tyr142His	p.Y142H	ENST00000376809	NM_002116.7	142	Tac/Cac	3/8	0.251731936128695	2	FACETS	0.448	0.366	0.54	0.224	0.183	0.27	SUBCLONAL	1	TRUE	0	0.270474720178342	2		532	578	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157454234	157454234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150140314	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	136	447	1	ENST00000346085.5:c.2444C>T	p.Ser815Leu	p.S815L	ENST00000346085	NM_020732.3	815	tCg/tTg	8/20	0.0460267815941782	3	FACETS	1	0.954	1	1	0.954	1	INDETERMINATE	2	TRUE	1	0.270474720178342	3		448	535	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6037019	6037020	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs762540878	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	140	412	0	ENST00000265849.7:c.740dup	p.Ser248Ter	p.S248*	ENST00000265849	NM_000535.5	247	cct/ccCt	7/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.270474720178342	2		412	736	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249166	55249166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397517125	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	63	490	2	ENST00000275493.2:c.2464G>A	p.Ala822Thr	p.A822T	ENST00000275493	NM_005228.3	822	Gca/Aca	20/28	1	2	FACETS	0.861	0.745	0.986	0.861	0.745	0.986	CLONAL	1	TRUE	1	0.270474720178342	2		492	541	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750504	128750504	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	71	398	0	ENST00000377970.2:c.41C>T	p.Ala14Val	p.A14V	ENST00000377970	NM_002467.4	14	gCg/gTg	2/3	0.270474720178342	3	FACETS	1	0.956	1	0.606	0.53	0.687	CLONAL	1	TRUE	1	0.270474720178342	3		398	492	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212815	27212815	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1307510192	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	129	603	1	ENST00000380036.4:c.2797G>A	p.Ala933Thr	p.A933T	ENST00000380036	NM_000459.3	933	Gcg/Acg	17/23	1	2	FACETS	0.802	0.729	0.877	1	0.987	1	CLONAL	2	TRUE	1	0.270474720178342	2		604	595	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894950	101894950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777965779	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	68	288	1	ENST00000374994.4:c.503G>A	p.Arg168His	p.R168H	ENST00000374994	NM_004612.2	168	cGc/cAc	3/9	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.270474720178342	2		289	354	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738297	133738297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1394653602	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	71	417	0	ENST00000318560.5:c.697G>A	p.Asp233Asn	p.D233N	ENST00000318560	NM_005157.4	233	Gac/Aac	4/11	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.270474720178342	2		417	449	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938456	44938456	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	30	474	0	ENST00000377967.4:c.3004A>G	p.Thr1002Ala	p.T1002A	ENST00000377967	NM_021140.2	1002	Aca/Gca	20/29	0.270474720178342	1	FACETS	0.367	0.295	0.45	0.367	0.295	0.45	SUBCLONAL	1	TRUE	0	0.270474720178342	1		474	522	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411330	63411330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	37	601	0	ENST00000330258.3:c.1837G>A	p.Ala613Thr	p.A613T	ENST00000330258	NM_152424.3	613	Gcc/Acc	2/2	0.270474720178342	1	FACETS	0.525	0.432	0.628	0.525	0.432	0.628	SUBCLONAL	1	TRUE	0	0.270474720178342	1		601	451	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351416	70351416	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	44	549	0	ENST00000374080.3:c.4064C>T	p.Thr1355Ile	p.T1355I	ENST00000374080		1355	aCc/aTc	29/45	0.270474720178342	1	FACETS	0.564	0.473	0.665	0.564	0.473	0.665	SUBCLONAL	1	TRUE	0	0.270474720178342	1		549	499	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76777814	76777814	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	43	563	0	ENST00000373344.5:c.6902G>T	p.Ser2301Ile	p.S2301I	ENST00000373344	NM_000489.3	2301	aGt/aTt	32/35	0.270474720178342	1	FACETS	0.482	0.402	0.57	0.482	0.402	0.57	SUBCLONAL	1	TRUE	0	0.270474720178342	1		563	571	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0028486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	99	581	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.184938945873965	3	FACETS	1	0.902	1	0.506	0.451	0.565	CLONAL	1	TRUE	1	0.24	3		581	913	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913396	NA	P-0028486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	45	294	1	ENST00000349496.5:c.95A>T	p.Asp32Val	p.D32V	ENST00000349496	NM_001904.3	32	gAc/gTc	3/15	0.3	1	FACETS	0.851	0.716	0.998	0.851	0.716	0.998	CLONAL	1	TRUE	0	0.24	1		295	388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0028486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	66	736	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.3	1	FACETS	0.462	0.4	0.53	0.462	0.4	0.53	SUBCLONAL	1	TRUE	0	0.24	1		736	1047	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038828	47038828	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	109	333	0	ENST00000377604.3:c.835C>T	p.Gln279Ter	p.Q279*	ENST00000377604	NM_001204468.1	279	Cag/Tag	9/24	0.00192203091496879	2	FACETS	1	0.962	1			1	INDETERMINATE	2	TRUE	NA	0.24	2		333	404	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967567	26967567	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	71	488	0	ENST00000381527.3:c.710G>T	p.Arg237Leu	p.R237L	ENST00000381527	NM_001260.1	237	cGa/cTa	7/13	1	2	FACETS	0.706	0.615	0.805	0.706	0.615	0.805	SUBCLONAL	1	TRUE	1	0.24	2		488	838	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354941	70354941	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0028486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	26	239	0	ENST00000374080.3:c.4864-1G>T		p.X1622_splice	ENST00000374080		1622			0.00192203091496879	2	FACETS	0.626	0.496	0.775			1	INDETERMINATE	1	TRUE	NA	0.24	2		239	346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0028491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	254	581	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.369912079160645	2	FACETS	0.845	0.795	0.896	0.845	0.795	0.896	CLONAL	2	TRUE	0	0.429348046288787	2		583	700	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974695	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691187	NA	P-0028491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	247	395	0	ENST00000304494.5:c.132del	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	taC/ta	1/3	0.427180648443974	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.429348046288787	2		395	518	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716329	52716329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863225094	NA	P-0028491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	43	634	0	ENST00000322088.6:c.773G>A	p.Arg258His	p.R258H	ENST00000322088	NM_014225.5	258	cGc/cAc	6/15	0.338244226937725	4	FACETS	0.269	0.223	0.319			1	SUBCLONAL	1	TRUE	NA	0.429348046288787	4		634	1066	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118368709	118368722	+	frameshift_variant	Frame_Shift_Del	DEL	TGTGGTCAGCGGAA	TGTGGTCAGCGGAA	-	novel	NA	P-0028491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	68	560	1	ENST00000534358.1:c.5723_5736del	p.Leu1908CysfsTer3	p.L1908Cfs*3	ENST00000534358	NM_005933.3	1908	tTGTGGTCAGCGGAA/t	21/36	0.266948078713864	3	FACETS	0.628	0.546	0.716	0.314	0.273	0.358	SUBCLONAL	1	TRUE	1	0.429348046288787	3		561	613	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937691	44937691	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	80	355	1	ENST00000377967.4:c.2879G>T	p.Cys960Phe	p.C960F	ENST00000377967	NM_021140.2	960	tGt/tTt	19/29	0.374426370977974	2	FACETS	1	0.972	1			1	CLONAL	1	TRUE	NA	0.429348046288787	2		356	286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0028492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	643	567	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.361428937317137	3	FACETS	1	0.993	1	0.732	0.707	0.758	CLONAL	2	TRUE	0	0.547385652342073	3		568	1362	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690845	89690877	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTAGGTATGAATGTACTGTACTATGTTGTAT	AGGTAGGTATGAATGTACTGTACTATGTTGTAT	-	novel	NA	P-0028492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	93	379	2	ENST00000371953.3:c.253_253+32del		p.X85_splice	ENST00000371953	NM_000314.4	85		4/9	0.430093560947535	2	FACETS	0.887	0.795	0.984	0.444	0.397	0.492	CLONAL	1	TRUE	0	0.547385652342073	2		381	383	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924284	112924285	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACGGAGAGA	novel	NA	P-0028492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	158	663	1	ENST00000351677.2:c.1235_1243dup	p.Glu412_Thr414dup	p.E412_T414dup	ENST00000351677	NM_002834.3	412	-/ACGGAGAGA	11/16	0.430093560947535	2	FACETS	0.581	0.532	0.632	0.29	0.266	0.316	SUBCLONAL	1	TRUE	0	0.547385652342073	2		664	994	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955555	48955556	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0028492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	285	463	0	ENST00000267163.4:c.1672dup	p.Met558AsnfsTer14	p.M558Nfs*14	ENST00000267163	NM_000321.2	557	-/A	17/27	0.45733883614943	2	FACETS	0.803	0.761	0.846	0.803	0.761	0.846	CLONAL	2	TRUE	0	0.547385652342073	2		463	648	SUCCESS
APC	324	MSKCC	GRCh37	5	112179362	112179362	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1060503281	NA	P-0028492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	181	492	0	ENST00000257430.4:c.8071A>G	p.Asn2691Asp	p.N2691D	ENST00000257430	NM_000038.5	2691	Aat/Gat	16/16	0.325104942191925	1	FACETS	0.684	0.633	0.737	0.684	0.633	0.737	INDETERMINATE	1	TRUE	0	0.547385652342073	1		492	702	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942019	44942019	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	162	459	0	ENST00000377967.4:c.3269del	p.Leu1090HisfsTer14	p.L1090Hfs*14	ENST00000377967	NM_021140.2	1090	cTa/ca	22/29	0.534231800587809	1	FACETS	0.732	0.675	0.791	0.732	0.675	0.791	SUBCLONAL	1	TRUE	0	0.547385652342073	1		459	587	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0028495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	230	600	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.556816392892188	3	FACETS	1	0.934	1	0.501	0.467	0.536	CLONAL	1	TRUE	1	0.556816392892188	3		606	1054	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	194	338	2	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	0.556816392892188	2		340	514	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739820	46739820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555234707	NA	P-0028495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	165	428	0	ENST00000371975.4:c.1621G>A	p.Val541Ile	p.V541I	ENST00000371975	NM_003579.3	541	Gtc/Atc	15/18	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.556816392892188	2		428	537	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	47	609	1	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.222	0.186	0.261	0.222	0.186	0.261	SUBCLONAL	1	TRUE	1	0.556816392892188	2		610	761	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057937	27057937	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	113	663	0	ENST00000324856.7:c.1650del	p.Tyr551ThrfsTer68	p.Y551Tfs*68	ENST00000324856	NM_006015.4	549	Ccc/cc	3/20	1	2	FACETS	0.507	0.456	0.561	0.507	0.456	0.561	SUBCLONAL	1	TRUE	1	0.556816392892188	2		663	800	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161939	47161939	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	114	334	1	ENST00000409792.3:c.4187del	p.Asn1396MetfsTer16	p.N1396Mfs*16	ENST00000409792	NM_014159.6	1396	aAt/at	3/21	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.556816392892188	2		335	378	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168969	32168969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs567483221	NA	P-0028495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	286	892	0	ENST00000375023.3:c.4064G>A	p.Arg1355Gln	p.R1355Q	ENST00000375023	NM_004557.3	1355	cGg/cAg	22/30	1	2	FACETS	0.989	0.93	1	0.989	0.93	1	CLONAL	1	TRUE	1	0.556816392892188	2		892	1039	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591135	67591136	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0028495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	104	329	0	ENST00000274335.5:c.1732_1733del	p.Asp578ProfsTer23	p.D578Pfs*23	ENST00000274335		576	acGAga/acga	12/15	1	2	FACETS	0.892	0.804	0.983	0.892	0.804	0.983	CLONAL	1	TRUE	1	0.556816392892188	2		329	419	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0028495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	322	742	3	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.556816392892188	2		745	1156	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554341	141554341	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564077207	NA	P-0028495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	330	1084	0	ENST00000220592.5:c.1810G>A	p.Gly604Arg	p.G604R	ENST00000220592	NM_012154.3	604	Ggg/Agg	14/19	0.556816392892188	3	FACETS	1	0.949	1	0.503	0.474	0.533	CLONAL	1	TRUE	1	0.556816392892188	3		1084	1506	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830421	72830421	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	81	232	0	ENST00000268489.5:c.6160G>A	p.Ala2054Thr	p.A2054T	ENST00000268489	NM_006885.3	2054	Gcg/Acg	9/10	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.556816392892188	2		232	290	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272482	11272482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	71	555	0	ENST00000361445.4:c.3448G>A	p.Asp1150Asn	p.D1150N	ENST00000361445	NM_004958.3	1150	Gac/Aac	23/58	1	2	FACETS	0.393	0.343	0.447	0.393	0.343	0.447	SUBCLONAL	1	TRUE	1	0.556816392892188	2		555	649	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653802	89653802	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	179	401	0	ENST00000371953.3:c.100del	p.Ala34LeufsTer20	p.A34Lfs*20	ENST00000371953	NM_000314.4	34	Gct/ct	2/9	0.556816392892188	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	0	0.556816392892188	2		401	321	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996878	100996879	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0028495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	174	589	0	ENST00000325455.5:c.1648_1649del	p.Glu550SerfsTer23	p.E550Sfs*23	ENST00000325455	NM_001202474.3	550	GAa/a	2/8	0.556816392892188	2	FACETS	0.969	0.896	1	0.484	0.448	0.523	CLONAL	1	TRUE	0	0.556816392892188	2		589	645	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205314	46205314	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	134	479	0	ENST00000334344.6:c.398A>G	p.Tyr133Cys	p.Y133C	ENST00000334344	NM_152641.2	133	tAc/tGc	4/21	1	2	FACETS	0.949	0.868	1	0.949	0.868	1	CLONAL	1	TRUE	1	0.556816392892188	2		479	507	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066890	30066890	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	191	572	2	ENST00000331968.5:c.2241del	p.Ala748LeufsTer8	p.A748Lfs*8	ENST00000331968	NM_002742.2	747	ccC/cc	16/18	1	2	FACETS	0.962	0.893	1	0.962	0.893	1	CLONAL	1	TRUE	1	0.556816392892188	2		574	713	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630775	90630775	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	140	499	0	ENST00000330062.3:c.711G>T	p.Gln237His	p.Q237H	ENST00000330062	NM_002168.2	237	caG/caT	6/11	1	2	FACETS	0.861	0.787	0.938	0.861	0.787	0.938	CLONAL	1	TRUE	1	0.556816392892188	2		499	584	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130204	2130204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1437771620	NA	P-0028495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	267	822	0	ENST00000219476.3:c.3436G>A	p.Ala1146Thr	p.A1146T	ENST00000219476	NM_000548.3	1146	Gcc/Acc	30/42	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.556816392892188	2		822	917	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821812	72821812	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1213646160	NA	P-0028495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	174	654	0	ENST00000268489.5:c.10363C>A	p.Pro3455Thr	p.P3455T	ENST00000268489	NM_006885.3	3455	Ccc/Acc	10/10	1	2	FACETS	0.764	0.704	0.826	0.764	0.704	0.826	SUBCLONAL	1	TRUE	1	0.556816392892188	2		654	818	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828675	72828677	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs747990539	NA	P-0028495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	181	654	1	ENST00000268489.5:c.7904_7906del	p.Gly2635del	p.G2635del	ENST00000268489	NM_006885.3	2635	gGAGaa/gaa	9/10	1	2	FACETS	0.787	0.727	0.85	0.787	0.727	0.85	SUBCLONAL	1	TRUE	1	0.556816392892188	2		655	826	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586144	29586144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555618691	NA	P-0028495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	136	536	3	ENST00000356175.3:c.4364G>A	p.Arg1455His	p.R1455H	ENST00000356175	NM_000267.3	1455	cGc/cAc	32/57	0.556816392892188	3	FACETS	0.854	0.778	0.934	0.427	0.389	0.467	CLONAL	1	TRUE	1	0.556816392892188	3		539	731	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654716	29654716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	128	354	0	ENST00000356175.3:c.5405C>T	p.Ser1802Phe	p.S1802F	ENST00000356175	NM_000267.3	1802	tCt/tTt	37/57	0.556816392892188	3	FACETS	1	0.924	1	0.508	0.462	0.557	CLONAL	1	TRUE	1	0.556816392892188	3		354	578	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533117	63533117	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	202	544	0	ENST00000307078.5:c.1777C>G	p.Pro593Ala	p.P593A	ENST00000307078	NM_004655.3	593	Ccc/Gcc	7/11	0.556816392892188	3	FACETS	1	0.954	1	0.518	0.481	0.557	CLONAL	1	TRUE	1	0.556816392892188	3		544	895	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117191	7117191	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	175	616	1	ENST00000302850.5:c.4025del	p.Gly1342AlafsTer23	p.G1342Afs*23	ENST00000302850	NM_000208.2	1342	gGc/gc	22/22	1	2	FACETS	0.79	0.728	0.853	0.79	0.728	0.853	SUBCLONAL	1	TRUE	1	0.556816392892188	2		617	796	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791326	42791326	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	227	747	0	ENST00000575354.2:c.386A>C	p.Glu129Ala	p.E129A	ENST00000575354	NM_015125.3	129	gAg/gCg	3/20	1	2	FACETS	0.929	0.867	0.993	0.929	0.867	0.993	CLONAL	1	TRUE	1	0.556816392892188	2		747	878	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267335	198267337	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0028495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	152	510	0	ENST00000335508.6:c.2020_2022del	p.Leu674del	p.L674del	ENST00000335508	NM_012433.2	674	CTT/-	14/25	1	2	FACETS	0.892	0.819	0.968	0.892	0.819	0.968	CLONAL	1	TRUE	1	0.556816392892188	2		510	612	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663423	227663423	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	97	304	0	ENST00000305123.5:c.32C>A	p.Ser11Ter	p.S11*	ENST00000305123	NM_005544.2	11	tCg/tAg	1/2	1	2	FACETS	0.912	0.82	1	0.912	0.82	1	CLONAL	1	TRUE	1	0.556816392892188	2		304	382	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31372648	31372648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769220144	NA	P-0028495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	238	586	0	ENST00000328111.2:c.289C>T	p.Arg97Cys	p.R97C	ENST00000328111	NM_006892.3	97	Cgt/Tgt	4/23	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.556816392892188	2		586	818	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446252	187446252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	219	755	0	ENST00000232014.4:c.1436G>A	p.Gly479Asp	p.G479D	ENST00000232014	NM_001130845.1	479	gGc/gAc	6/10	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.556816392892188	2		755	786	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177987	56177987	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	102	409	0	ENST00000399503.3:c.2960C>G	p.Ser987Cys	p.S987C	ENST00000399503	NM_005921.1	987	tCt/tGt	14/20	1	2	FACETS	0.651	0.584	0.722	0.651	0.584	0.722	SUBCLONAL	1	TRUE	1	0.556816392892188	2		409	563	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591279	67591279	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	199	424	0	ENST00000274335.5:c.1778del	p.Lys593SerfsTer2	p.K593Sfs*2	ENST00000274335		593	Aag/ag	13/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.556816392892188	2		424	631	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911212	29911212	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199474544	NA	P-0028495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	29	210	0	ENST00000376809.5:c.511T>C	p.Trp171Arg	p.W171R	ENST00000376809	NM_002116.7	171	Tgg/Cgg	3/8	1	2	FACETS	0.496	0.401	0.603	0.496	0.401	0.603	SUBCLONAL	1	TRUE	1	0.556816392892188	2		210	210	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163752	152163752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757200716	NA	P-0028495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	139	475	0	ENST00000206249.3:c.473G>A	p.Arg158His	p.R158H	ENST00000206249	NM_000125.3	158	cGc/cAc	2/8	1	2	FACETS	0.9	0.823	0.979	0.9	0.823	0.979	CLONAL	1	TRUE	1	0.556816392892188	2		475	555	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752907	128752907	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	90	393	0	ENST00000377970.2:c.1068A>C	p.Lys356Asn	p.K356N	ENST00000377970	NM_002467.4	356	aaA/aaC	3/3	0.556816392892188	3	FACETS	0.669	0.594	0.748	0.334	0.297	0.374	SUBCLONAL	1	TRUE	1	0.556816392892188	3		393	618	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564648	139564650	+	frameshift_variant	Frame_Shift_Del	DEL	GCG	GCG	AA	novel	NA	P-0028495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	269	991	6	ENST00000308874.7:c.437_439delinsAA	p.Gly146GlufsTer51	p.G146Efs*51	ENST00000308874		146	gGCGgc/gAAgc	7/10	1	2	FACETS	0.882	0.828	0.939	0.882	0.828	0.939	CLONAL	1	TRUE	1	0.556816392892188	2		997	1095	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0028498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	35	497	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.702	0.574	0.847	0.702	0.574	0.847	SUBCLONAL	1	TRUE	1	0.15	2		497	665	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0028498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	73	689	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	1	2	FACETS	0.912	0.795	1	0.912	0.795	1	CLONAL	1	TRUE	1	0.15	2		689	1067	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0028498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	43	385	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	0.978	0.818	1	0.978	0.818	1	CLONAL	1	TRUE	1	0.15	2		385	586	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72842185	72842185	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	32	467	0	ENST00000325599.8:c.1063A>G	p.Lys355Glu	p.K355E	ENST00000325599	NM_018130.2	355	Aaa/Gaa	10/11	1	2	FACETS	0.865	0.702	1	0.865	0.702	1	CLONAL	1	TRUE	1	0.15	2		467	493	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417814	32417814	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs373176048	NA	P-0028498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	36	445	0	ENST00000332351.3:c.1238G>T	p.Arg413Met	p.R413M	ENST00000332351	NM_024426.4	413	aGg/aTg	7/10	1	2	FACETS	0.868	0.712	1	0.868	0.712	1	CLONAL	1	TRUE	1	0.15	2		445	553	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438196	438196	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0028498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	31	323	0	ENST00000399788.2:c.1774-1G>T		p.X592_splice	ENST00000399788	NM_001042603.1	592			NA	2	FACETS	0.804	0.649	0.98			1	INDETERMINATE	1	TRUE	NA	0.15	2		323	514	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988535	36989088	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGTCGTGTGCTTTGGACTCATCGACATGATTCGGCGGCGGCTGGAGGAGGAAGGAAGAGGAGGAAAAAAAAGGGAGAGGGGGAAGGCGAAGCCTCGCTGCTTTTTTTTTCTCCCTTTGCCAAATATTCTGGTGTTACCTTAACGCCGATCTTGTTGGATGTACACGTAACGGAGTGGACCGAGTCCTCCTTAATTGGCTTGAGTGGAGGCTCGGGGGCTGCCTCGCGTTTGTTTTAGCCCGGCGCCAGGTTTTAGGCAGCCACCAGAGGCGGGGCGTAAGCGCTAAAGCAACAAGACAATAGAAGCCTACATCTTGCCCGAGATAATTAGCTTACATGCTGATGACAAGGTAAACACCTTTAAGTTTCACTTGTCAGGATTTTTAGGTCTCAAAGAGAGAGAGAGAGAGGCAGAGACGAGACCCAAAGCATTTCCCCCCTCCCTTGGACACCCCCACCCCCATTTTTTGTGGGGTACCAGCGGAGCGCGGGGAGGAGGTGGAGGGGAGGGGAAGGAGGAGGGAACCGAGAGCGGGGAGGGCAGGAGGTGGGGT	GAGTCGTGTGCTTTGGACTCATCGACATGATTCGGCGGCGGCTGGAGGAGGAAGGAAGAGGAGGAAAAAAAAGGGAGAGGGGGAAGGCGAAGCCTCGCTGCTTTTTTTTTCTCCCTTTGCCAAATATTCTGGTGTTACCTTAACGCCGATCTTGTTGGATGTACACGTAACGGAGTGGACCGAGTCCTCCTTAATTGGCTTGAGTGGAGGCTCGGGGGCTGCCTCGCGTTTGTTTTAGCCCGGCGCCAGGTTTTAGGCAGCCACCAGAGGCGGGGCGTAAGCGCTAAAGCAACAAGACAATAGAAGCCTACATCTTGCCCGAGATAATTAGCTTACATGCTGATGACAAGGTAAACACCTTTAAGTTTCACTTGTCAGGATTTTTAGGTCTCAAAGAGAGAGAGAGAGAGGCAGAGACGAGACCCAAAGCATTTCCCCCCTCCCTTGGACACCCCCACCCCCATTTTTTGTGGGGTACCAGCGGAGCGCGGGGAGGAGGTGGAGGGGAGGGGAAGGAGGAGGGAACCGAGAGCGGGGAGGGCAGGAGGTGGGGT	-	novel	NA	P-0028498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	67	918	0	ENST00000354822.5:c.77+170_118del		p.X26_splice	ENST00000354822	NM_001079668.2	26		2/3	1	2	FACETS	0.688	0.595	0.789	0.688	0.595	0.789	SUBCLONAL	1	TRUE	1	0.15	2		918	1299	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042112	42042112	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0028498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	61	609	1	ENST00000219905.7:c.6307A>T	p.Lys2103Ter	p.K2103*	ENST00000219905	NM_001164273.1	2103	Aaa/Taa	17/24	1	2	FACETS	0.857	0.737	0.988	0.857	0.737	0.988	CLONAL	1	TRUE	1	0.15	2		610	949	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198303	138198303	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	37	348	0	ENST00000237289.4:c.896A>T	p.Lys299Met	p.K299M	ENST00000237289	NM_001270507.1	299	aAg/aTg	6/9	1	2	FACETS	0.91	0.749	1	0.91	0.749	1	CLONAL	1	TRUE	1	0.15	2		348	542	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	91	210	0				ENST00000310581	NM_198253.2	-/1132			0.0829937849261966	1	FACETS	1	0.935	1	1	0.991	1	CLONAL	6	FALSE	0	0.0829937849261966	1		210	331	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0028503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	108	433	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.971	0.882	1	1	0.992	1	CLONAL	8	FALSE	1	0.0829937849261966	2		433	335	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104712	193104712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	12	321	0	ENST00000367435.3:c.416G>A	p.Arg139Gln	p.R139Q	ENST00000367435	NM_024529.4	139	cGa/cAa	5/17	1	2	FACETS	1	0.806	1	1	0.806	1	CLONAL	1	FALSE	1	0.0829937849261966	2		321	238	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346364	73346364	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	37	470	0	ENST00000377767.4:c.1436A>G	p.Asp479Gly	p.D479G	ENST00000377767	NM_014953.3	479	gAc/gGc	10/21	0.0829937849261966	1	FACETS	0.925	0.765	1	1	0.972	1	CLONAL	3	FALSE	0	0.0829937849261966	1		470	308	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	275	584	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	1	2	FACETS	0.926	0.874	0.979	0.926	0.874	0.979	CLONAL	1	TRUE	1	0.803965075440722	2		584	739	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	95	315	1				ENST00000310581	NM_198253.2	-/1132			0.13670130216103	1	FACETS	0.645	0.587	0.705	0.645	0.587	0.705	INDETERMINATE	1	TRUE	0	0.803965075440722	1		316	219	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	298	796	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	0.803965075440722	2		796	686	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778899	9778899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	205	731	0	ENST00000377346.4:c.1168C>T	p.Leu390Phe	p.L390F	ENST00000377346	NM_005026.3	390	Ctc/Ttc	9/24	1	2	FACETS	0.97	0.907	1	0.97	0.907	1	CLONAL	1	TRUE	1	0.803965075440722	2		731	526	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932083	36932083	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	203	569	0	ENST00000361632.4:c.2386C>T	p.Pro796Ser	p.P796S	ENST00000361632		796	Ccc/Tcc	16/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.803965075440722	2		569	462	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805121	43805121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	196	679	1	ENST00000372470.3:c.571G>A	p.Glu191Lys	p.E191K	ENST00000372470	NM_005373.2	191	Gaa/Aaa	4/12	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.803965075440722	2		680	475	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263315	115263315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	282	755	0	ENST00000438362.2:c.2035C>T	p.Pro679Ser	p.P679S	ENST00000438362	NM_001242891.1	679	Cca/Tca	17/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.803965075440722	2		755	693	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874285	155874285	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs730881014	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	242	522	0	ENST00000368323.3:c.246T>A	p.Phe82Leu	p.F82L	ENST00000368323	NM_006912.5	82	ttT/ttA	5/6	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.803965075440722	2		522	574	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725057	162725057	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	198	481	0	ENST00000367921.3:c.529T>G	p.Cys177Gly	p.C177G	ENST00000367921	NM_006182.2	177	Tgt/Ggt	6/18	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.803965075440722	2		481	433	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729737	162729737	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	269	643	1	ENST00000367921.3:c.823T>A	p.Phe275Ile	p.F275I	ENST00000367921	NM_006182.2	275	Ttt/Att	8/18	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.803965075440722	2		644	627	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567300	226567300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	241	673	0	ENST00000366794.5:c.1586G>A	p.Gly529Glu	p.G529E	ENST00000366794	NM_001618.3	529	gGa/gAa	11/23	0.783138454454383	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.803965075440722	1		673	338	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589784	69589784	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	27	135	1	ENST00000168712.1:c.69G>A	p.Trp23Ter	p.W23*	ENST00000168712	NM_002007.2	23	tgG/tgA	1/3	0.13670130216103	1	FACETS	0.55	0.454	0.652	0.55	0.454	0.652	INDETERMINATE	1	TRUE	0	0.803965075440722	1		136	73	SUCCESS
EED	8726	MSKCC	GRCh37	11	85967550	85967550	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	231	460	0	ENST00000263360.6:c.548T>A	p.Ile183Lys	p.I183K	ENST00000263360	NM_003797.3	183	aTa/aAa	5/12	NA	2	FACETS	1	0.96	1			1	INDETERMINATE	1	TRUE	NA	0.803965075440722	2		460	560	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375152	118375152	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	223	466	0	ENST00000534358.1:c.8545C>T	p.Pro2849Ser	p.P2849S	ENST00000534358	NM_005933.3	2849	Cct/Tct	27/36	0.803965075440722	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.803965075440722	1		466	295	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375923	118375923	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	249	572	1	ENST00000534358.1:c.9316C>T	p.Gln3106Ter	p.Q3106*	ENST00000534358	NM_005933.3	3106	Caa/Taa	27/36	0.803965075440722	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.803965075440722	1		573	368	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435566	18435566	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	199	338	0	ENST00000266497.5:c.551G>C	p.Ser184Thr	p.S184T	ENST00000266497		184	aGt/aCt	1/31	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.803965075440722	2		338	470	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656272	18656272	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	227	686	0	ENST00000266497.5:c.2951G>A	p.Gly984Glu	p.G984E	ENST00000266497		984	gGa/gAa	21/31	1	2	FACETS	0.982	0.922	1	0.982	0.922	1	CLONAL	1	TRUE	1	0.803965075440722	2		686	575	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230638	46230641	+	missense_variant	Missense_Mutation	ONP	TTTC	TTTC	CTTT	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	256	656	0	ENST00000334344.6:c.887_890delinsCTTT	p.Leu296_Ser297delinsProPhe	p.L296_S297delinsPF	ENST00000334344	NM_152641.2	296	cTTTCc/cCTTTc	8/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.803965075440722	2		656	601	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861246	57861246	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745587766	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	218	644	0	ENST00000228682.2:c.1043G>A	p.Arg348Gln	p.R348Q	ENST00000228682	NM_005269.2	348	cGa/cAa	9/12	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.803965075440722	2		644	495	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352667	68352667	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	284	547	0	ENST00000487270.1:c.534T>A	p.His178Gln	p.H178Q	ENST00000487270	NM_133509.3	178	caT/caA	6/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.803965075440722	2		547	698	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675097	40675097	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	259	863	0	ENST00000249776.8:c.61G>A	p.Glu21Lys	p.E21K	ENST00000249776	NM_033286.3	21	Gag/Aag	1/9	1	2	FACETS	0.913	0.859	0.967	0.913	0.859	0.967	CLONAL	1	TRUE	1	0.803965075440722	2		863	706	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059474	42059474	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	125	358	0	ENST00000219905.7:c.9194A>T	p.Lys3065Ile	p.K3065I	ENST00000219905	NM_001164273.1	3065	aAa/aTa	24/24	1	2	FACETS	0.981	0.901	1	0.981	0.901	1	CLONAL	1	TRUE	1	0.803965075440722	2		358	317	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857482	9857482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148827608	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	154	466	0	ENST00000330684.3:c.3919C>T	p.Pro1307Ser	p.P1307S	ENST00000330684	NM_001134407.1	1307	Ccc/Tcc	13/13	0.13670130216103	1	FACETS	0.551	0.509	0.593	0.551	0.509	0.593	INDETERMINATE	1	TRUE	0	0.803965075440722	1		466	416	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984848	9984848	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	211	613	1	ENST00000330684.3:c.1117G>A	p.Glu373Lys	p.E373K	ENST00000330684	NM_001134407.1	373	Gaa/Aaa	4/13	0.13670130216103	1	FACETS	0.629	0.59	0.668	0.629	0.59	0.668	INDETERMINATE	1	TRUE	0	0.803965075440722	1		614	499	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979989	7979990	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	180	717	2	ENST00000319144.4:c.1347_1348delinsAA	p.Gly450Arg	p.G450R	ENST00000319144	NM_001139.2	449	ggGGgg/ggAAgg	10/15	0.165955315551907	2	FACETS	0.914	0.85	0.979	0.457	0.425	0.49	INDETERMINATE	1	TRUE	0	0.803965075440722	2		719	490	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560230	29560231	+	stop_gained,splice_region_variant	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	87	259	1	ENST00000356175.3:c.3707_3708delinsAA	p.Trp1236Ter	p.W1236*	ENST00000356175	NM_000267.3	1236	tGG/tAA	27/57	0.795249381860489	1	FACETS	0.988	0.914	1	0.988	0.914	1	CLONAL	1	TRUE	0	0.803965075440722	1		260	131	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41201146	41201146	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1064794662	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	226	813	0	ENST00000357654.3:c.5398del	p.Gly1801AlafsTer33	p.G1801Afs*33	ENST00000357654	NM_007294.3	1800	Ctt/tt	21/23	1	2	FACETS	0.955	0.896	1	0.955	0.896	1	CLONAL	1	TRUE	1	0.803965075440722	2		813	589	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622363	1622363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	208	893	1	ENST00000344749.5:c.601C>T	p.Pro201Ser	p.P201S	ENST00000344749	NM_001136139.2	201	Ccg/Tcg	9/19	0.803965075440722	3	FACETS	0.906	0.843	0.971	0.453	0.421	0.486	CLONAL	1	TRUE	1	0.803965075440722	3		894	801	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271976	15271976	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	392	733	0	ENST00000263388.2:c.6463G>A	p.Gly2155Arg	p.G2155R	ENST00000263388	NM_000435.2	2155	Gga/Aga	33/33	0.803965075440722	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.803965075440722	3		733	679	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284907	15284907	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs551991530	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	228	930	3	ENST00000263388.2:c.4708C>T	p.Arg1570Cys	p.R1570C	ENST00000263388	NM_000435.2	1570	Cgt/Tgt	25/33	0.803965075440722	3	FACETS	1	0.958	1	0.516	0.483	0.551	CLONAL	1	TRUE	1	0.803965075440722	3		933	770	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213965	36213965	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	241	942	2	ENST00000222270.7:c.2791G>A	p.Gly931Ser	p.G931S	ENST00000222270	NM_014727.1	931	Ggc/Agc	6/37	0.199927509403393	1	FACETS	0.619	0.583	0.656	0.619	0.583	0.656	INDETERMINATE	1	TRUE	0	0.803965075440722	1		944	579	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520168	9520168	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	178	532	0	ENST00000353224.5:c.2101A>T	p.Lys701Ter	p.K701*	ENST00000353224	NM_177990.2	701	Aaa/Taa	10/10	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.803965075440722	2		532	442	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561439	9561439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	197	632	0	ENST00000353224.5:c.343C>T	p.His115Tyr	p.H115Y	ENST00000353224	NM_177990.2	115	Cac/Tac	4/10	1	2	FACETS	0.98	0.916	1	0.98	0.916	1	CLONAL	1	TRUE	1	0.803965075440722	2		632	500	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827993	40827993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1328809133	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	152	550	0	ENST00000373198.4:c.2435G>A	p.Gly812Glu	p.G812E	ENST00000373198	NM_133170.3	812	gGa/gAa	17/32	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.803965075440722	2		550	373	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171760	36171760	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	154	392	0	ENST00000300305.3:c.806-1G>A		p.X269_splice	ENST00000300305		269			0.13670130216103	1	FACETS	0.616	0.571	0.661	0.616	0.571	0.661	INDETERMINATE	1	TRUE	0	0.803965075440722	1		392	372	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723109	49723109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1409765654	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	165	564	0	ENST00000449682.2:c.1307C>T	p.Pro436Leu	p.P436L	ENST00000449682	NM_020998.3	436	cCa/cTa	11/18	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.803965075440722	2		564	399	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723319	49723319	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs771999839	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	21	91	0	ENST00000449682.2:c.1224G>A	p.Trp408Ter	p.W408*	ENST00000449682	NM_020998.3	408	tgG/tgA	10/18	1	2	FACETS	0.829	0.662	1	0.829	0.662	1	CLONAL	1	TRUE	1	0.803965075440722	2		91	63	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932644	49932644	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	212	761	0	ENST00000296474.3:c.3227C>T	p.Pro1076Leu	p.P1076L	ENST00000296474	NM_002447.2	1076	cCc/cTc	14/20	1	2	FACETS	0.949	0.888	1	0.949	0.888	1	CLONAL	1	TRUE	1	0.803965075440722	2		761	556	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935601	49935601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	243	785	0	ENST00000296474.3:c.1763C>T	p.Thr588Ile	p.T588I	ENST00000296474	NM_002447.2	588	aCc/aTc	5/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.803965075440722	2		785	557	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390946	89390946	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	181	618	0	ENST00000336596.2:c.1012G>A	p.Glu338Lys	p.E338K	ENST00000336596	NM_005233.5	338	Gag/Aag	5/17	1	2	FACETS	0.938	0.873	1	0.938	0.873	1	CLONAL	1	TRUE	1	0.803965075440722	2		618	480	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1321583762	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	132	278	0	ENST00000257430.4:c.3925G>A	p.Glu1309Lys	p.E1309K	ENST00000257430	NM_000038.5	1309	Gaa/Aaa	16/16	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.803965075440722	2		278	318	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043441	180043441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56310180	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	176	862	0	ENST00000261937.6:c.3145G>A	p.Asp1049Asn	p.D1049N	ENST00000261937	NM_182925.4	1049	Gac/Aac	23/30	1	2	FACETS	0.903	0.839	0.968	0.903	0.839	0.968	CLONAL	1	TRUE	1	0.803965075440722	2		862	485	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839874	27839874	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	204	838	0	ENST00000328488.2:c.220G>A	p.Glu74Lys	p.E74K	ENST00000328488	NM_003533.2	74	Gag/Aag	1/1	1	2	FACETS	0.959	0.897	1	0.959	0.897	1	CLONAL	1	TRUE	1	0.803965075440722	2		838	529	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673803	30673803	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1387652060	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	216	587	0	ENST00000376406.3:c.3157C>T	p.Leu1053Phe	p.L1053F	ENST00000376406	NM_014641.2	1053	Ctt/Ttt	10/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.803965075440722	2		587	516	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188814	32188814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754461878	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	175	782	0	ENST00000375023.3:c.740G>A	p.Gly247Asp	p.G247D	ENST00000375023	NM_004557.3	247	gGc/gAc	4/30	1	2	FACETS	0.92	0.856	0.986	0.92	0.856	0.986	CLONAL	1	TRUE	1	0.803965075440722	2		782	473	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242449	55242449	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	183	625	0	ENST00000275493.2:c.2220del	p.Val742SerfsTer6	p.V742Sfs*6	ENST00000275493	NM_005228.3	740	aTt/at	19/28	1	2	FACETS	0.979	0.913	1	0.979	0.913	1	CLONAL	1	TRUE	1	0.803965075440722	2		625	465	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435763	116435763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267601244	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	241	714	1	ENST00000397752.3:c.3853C>T	p.Pro1285Ser	p.P1285S	ENST00000397752	NM_000245.2	1285	Cct/Tct	20/21	1	2	FACETS	0.946	0.889	1	0.946	0.889	1	CLONAL	1	TRUE	1	0.803965075440722	2		715	634	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434555	140434555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	138	229	0	ENST00000288602.6:c.2143G>A	p.Glu715Lys	p.E715K	ENST00000288602	NM_004333.4	715	Gag/Aag	18/18	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.803965075440722	2		229	273	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913351	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	235	519	1	ENST00000288602.6:c.1397G>A	p.Gly466Glu	p.G466E	ENST00000288602	NM_004333.4	466	gGa/gAa	11/18	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.803965075440722	2		520	544	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862986	117862986	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	305	595	0	ENST00000297338.2:c.1491G>A	p.Met497Ile	p.M497I	ENST00000297338	NM_006265.2	497	atG/atA	12/14	0.194151470692177	4	FACETS	1	0.974	1	1	0.974	1	INDETERMINATE	2	TRUE	2	0.803965075440722	4		595	659	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492889	8492889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778370224	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	160	607	0	ENST00000356435.5:c.2440C>T	p.Pro814Ser	p.P814S	ENST00000356435		814	Ccc/Tcc	16/35	1	2	FACETS	0.896	0.83	0.964	0.896	0.83	0.964	CLONAL	1	TRUE	1	0.803965075440722	2		607	444	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507381	8507381	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	153	460	1	ENST00000356435.5:c.1597T>A	p.Leu533Met	p.L533M	ENST00000356435		533	Ttg/Atg	11/35	1	2	FACETS	0.883	0.816	0.952	0.883	0.816	0.952	CLONAL	1	TRUE	1	0.803965075440722	2		461	431	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915886	127915886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	263	693	0	ENST00000373547.4:c.595C>T	p.Pro199Ser	p.P199S	ENST00000373547	NM_002721.4	199	Cct/Tct	6/7	0.427596277859891	1	FACETS	0.815	0.775	0.855	0.815	0.775	0.855	INDETERMINATE	1	TRUE	0	0.803965075440722	1		693	480	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402421	139402421	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	70	782	0	ENST00000277541.6:c.3496G>T	p.Gly1166Cys	p.G1166C	ENST00000277541	NM_017617.3	1166	Ggc/Tgc	21/34	0.427596277859891	1	FACETS	0.211	0.184	0.24	0.211	0.184	0.24	INDETERMINATE	1	TRUE	0	0.803965075440722	1		782	494	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195669	123195669	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1231750099	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	242	281	1	ENST00000218089.9:c.1583C>T	p.Thr528Ile	p.T528I	ENST00000218089	NM_001042749.1	528	aCc/aTc	17/35	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.803965075440722	1		282	307	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860053	152860055	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0001756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	214	334	0	ENST00000406277.2:c.373_375del	p.Leu125del	p.L125del	ENST00000406277	NM_152274.4	125	CTC/-	5/7	1		FACETS		0.994	1				CLONAL	1	TRUE	0	0.803965075440722	1		334	256	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913499	NA	P-0001975-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	155	366	0	ENST00000345146.2:c.394C>A	p.Arg132Ser	p.R132S	ENST00000345146	NM_005896.2	132	Cgt/Agt	4/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.876424034837874	2		366	324	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0001975-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	390	591	1	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.876424034837874	2		592	805	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937611	76937615	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTT	CTTTT	-	novel	NA	P-0001975-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	197	106	0	ENST00000373344.5:c.3133_3137del	p.Lys1045Ter	p.K1045*	ENST00000373344	NM_000489.3	1045	AAAAGt/t	9/35	1	1	FACETS	0.96	0.918	1	0.96	0.918	1	CLONAL	1	TRUE	0	0.876424034837874	1		106	263	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965595	25965595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001975-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	672	450	0	ENST00000435504.4:c.3611G>A	p.Ser1204Asn	p.S1204N	ENST00000435504		1204	aGt/aAt	13/13	0.876424034837874	3	FACETS	0.923	0.895	0.951			1	CLONAL	2	TRUE	NA	0.876424034837874	3		450	1195	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577157	7577157	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0001975-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	299	409	0	ENST00000269305.4:c.783-2A>C		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	0.95	0.901	1	0.95	0.901	1	CLONAL	1	TRUE	1	0.876424034837874	2		409	718	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978526	70978526	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001975-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	226	412	0	ENST00000276594.2:c.1127T>C	p.Ile376Thr	p.I376T	ENST00000276594	NM_024504.3	376	aTt/aCt	5/8	1	2	FACETS	0.895	0.841	0.951	0.895	0.841	0.951	CLONAL	1	TRUE	1	0.876424034837874	2		412	576	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0002294-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	345	326	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.144227304849497	3	FACETS	0.786	0.749	0.823	0.786	0.749	0.823	INDETERMINATE	2	TRUE	1	0.850176453248263	3		326	736	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578518	7578518	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934875	NA	P-0002294-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	508	299	0	ENST00000269305.4:c.412G>C	p.Ala138Pro	p.A138P	ENST00000269305	NM_001126112.2	138	Gcc/Ccc	5/11	0.0844360848327015	3	FACETS	0.959	0.939	0.978			1	INDETERMINATE	3	TRUE	NA	0.850176453248263	3		299	592	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970954	21970954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1182554152	NA	P-0002294-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	261	269	0	ENST00000304494.5:c.404G>A	p.Gly135Glu	p.G135E	ENST00000304494	NM_000077.4	135	gGg/gAg	2/3	0.710945740695278	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.850176453248263	1		269	332	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562363	21562363	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202040927	NA	P-0002294-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	10	219	0	ENST00000382592.4:c.1556C>T	p.Pro519Leu	p.P519L	ENST00000382592	NM_014572.2	519	cCg/cTg	4/8	0.850176453248263	1	FACETS	0.072	0.048	0.101	0.072	0.048	0.101	SUBCLONAL	1	TRUE	0	0.850176453248263	1		219	189	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916850	48916850	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1131690843	NA	P-0002294-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	230	256	0	ENST00000267163.4:c.380G>A	p.Ser127Asn	p.S127N	ENST00000267163	NM_000321.2	127	aGt/aAt	3/27	0.850176453248263	1	FACETS	0.899	0.858	0.939	0.899	0.858	0.939	CLONAL	1	TRUE	0	0.850176453248263	1		256	346	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591936	48591936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	103	354	0	ENST00000342988.3:c.1099C>T	p.Leu367Phe	p.L367F	ENST00000342988	NM_005359.5	367	Ctc/Ttc	9/12	0.850176453248263	3	FACETS	0.345	0.308	0.385	0.172	0.154	0.193	SUBCLONAL	1	TRUE	1	0.850176453248263	3		354	1001	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554257	29554275	+	frameshift_variant	Frame_Shift_Del	DEL	GAGTGATGGCACTGCTGAG	GAGTGATGGCACTGCTGAG	-	novel	NA	P-0002294-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	42	353	0	ENST00000356175.3:c.2274_2292del	p.Arg758SerfsTer27	p.R758Sfs*27	ENST00000356175	NM_000267.3	758	aGAGTGATGGCACTGCTGAGg/ag	19/57	0.144227304849497	3	FACETS	0.219	0.182	0.26	0.109	0.091	0.13	INDETERMINATE	1	TRUE	1	0.850176453248263	3		353	644	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912079	76912079	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002294-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	457	492	0	ENST00000373344.5:c.4185del	p.Glu1395AspfsTer95	p.E1395Dfs*95	ENST00000373344	NM_000489.3	1395	gaA/ga	13/35	0.850176453248263	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.850176453248263	1		492	617	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117737472	117737472	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002731-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	97	458	0	ENST00000368508.3:c.177A>T	p.Gln59His	p.Q59H	ENST00000368508	NM_002944.2	59	caA/caT	3/43	0.837313172428264	2	FACETS	0.433	0.387	0.482	0.217	0.193	0.241	SUBCLONAL	1	TRUE	0	0.847820699422963	2		458	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912657	NA	P-0002731-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	840	565	0	ENST00000269305.4:c.814G>C	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ctg	8/11	0.847820699422963	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.847820699422963	3		565	925	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653080	29653080	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002731-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	442	320	0	ENST00000356175.3:c.5015A>G	p.His1672Arg	p.H1672R	ENST00000356175	NM_000267.3	1672	cAt/cGt	36/57	0.847820699422963	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	0	0.847820699422963	3		320	494	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600417	10600417	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002731-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	756	719	1	ENST00000171111.5:c.1438G>T	p.Gly480Trp	p.G480W	ENST00000171111	NM_203500.1	480	Ggg/Tgg	4/6	0.847820699422963	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.847820699422963	2		720	852	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219412	1219422	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTGCGTGCGC	GGTGCGTGCGC	-	novel	NA	P-0002731-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	441	522	0	ENST00000326873.7:c.464+2_464+12del		p.X155_splice	ENST00000326873	NM_000455.4	155		3/10	0.847820699422963	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.847820699422963	2		522	520	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016322	150016322	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002731-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	412	402	1	ENST00000253339.5:c.384C>A	p.Asn128Lys	p.N128K	ENST00000253339		128	aaC/aaA	2/7	0.837313172428264	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.847820699422963	2		403	481	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738648	145738648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767102398	NA	P-0002731-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	385	605	0	ENST00000428558.2:c.2416G>A	p.Gly806Arg	p.G806R	ENST00000428558	NM_004260.3	806	Ggg/Agg	15/22	0.50348995047473	5	FACETS	0.896	0.852	0.941			1	INDETERMINATE	2	TRUE	NA	0.847820699422963	5		605	1151	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563201	21563201	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002731-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	328	724	0	ENST00000382592.4:c.718G>C	p.Glu240Gln	p.E240Q	ENST00000382592	NM_014572.2	240	Gag/Cag	4/8	0.505293228981433	1	FACETS	0.753	0.72	0.786	0.753	0.72	0.786	INDETERMINATE	1	TRUE	0	0.847820699422963	1		724	592	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058472	42058472	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002731-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	396	461	0	ENST00000219905.7:c.8193del	p.Asp2732ThrfsTer20	p.D2732Tfs*20	ENST00000219905	NM_001164273.1	2731	gTt/gt	24/24	0.847820699422963	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.847820699422963	1		461	482	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609601	81609601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002731-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	120	483	1	ENST00000298171.2:c.1199C>T	p.Pro400Leu	p.P400L	ENST00000298171	NM_000369.2	400	cCc/cTc	10/10	0.448398212579133	6	FACETS	0.618	0.556	0.683	0.154	0.139	0.171	INDETERMINATE	1	TRUE	2	0.847820699422963	6		484	1235	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95584093	95584093	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0002731-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	76	293	0	ENST00000393063.1:c.1377-2A>C		p.X459_splice	ENST00000393063	NM_030621.3	459			0.847820699422963	6	FACETS	0.466	0.408	0.53			1	SUBCLONAL	1	TRUE	NA	0.847820699422963	6		293	1036	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546137	29546137	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0002731-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	108	352	0	ENST00000356175.3:c.1641+1G>C		p.X547_splice	ENST00000356175	NM_000267.3	547			0.847820699422963	3	FACETS	0.535	0.481	0.593	0.178	0.16	0.198	SUBCLONAL	1	TRUE	0	0.847820699422963	3		352	678	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18964079	18964079	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002731-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	199	455	0	ENST00000262803.5:c.1076G>T	p.Gly359Val	p.G359V	ENST00000262803	NM_002911.3	359	gGg/gTg	8/24	0.234022772688789	3	FACETS	0.923	0.858	0.99	0.308	0.286	0.33	INDETERMINATE	1	TRUE	0	0.847820699422963	3		455	724	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42861439	42861439	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002731-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	102	461	0	ENST00000398585.3:c.431A>T	p.Lys144Met	p.K144M	ENST00000398585	NM_001135099.1	144	aAg/aTg	4/14	0.769757159138525	1	FACETS	0.3	0.269	0.332	0.3	0.269	0.332	SUBCLONAL	1	TRUE	0	0.847820699422963	1		461	462	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799521	72799522	+	missense_variant	Missense_Mutation	DNP	CT	CT	AA	novel	NA	P-0002731-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	147	547	1	ENST00000325599.8:c.1647_1648delinsTT	p.Val550Phe	p.V550F	ENST00000325599	NM_018130.2	549	acAGtt/acTTtt	11/11	0.847820699422963	1	FACETS	0.323	0.296	0.352	0.323	0.296	0.352	SUBCLONAL	1	TRUE	0	0.847820699422963	1		548	618	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431589	6431589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002731-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	33	107	0	ENST00000356142.4:c.142G>A	p.Gly48Arg	p.G48R	ENST00000356142	NM_018890.3	48	Gga/Aga	3/7	0.491259358836212	1	FACETS	0.356	0.295	0.421	0.356	0.295	0.421	INDETERMINATE	1	TRUE	0	0.847820699422963	1		107	126	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920191	76920191	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002731-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	108	445	1	ENST00000373344.5:c.3886C>A	p.Pro1296Thr	p.P1296T	ENST00000373344	NM_000489.3	1296	Cca/Aca	11/35	0.847820699422963	2	FACETS	0.491	0.442	0.542	0.245	0.221	0.271	SUBCLONAL	1	TRUE	0	0.847820699422963	2		446	519	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971029	21971029	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519852	NA	P-0004016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	22	208	0	ENST00000304494.5:c.329G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tGg/tAg	2/3	0.399674346452777	0	FACETS	0.944	0.755	1			1	CLONAL	1	TRUE	0	0.392862002590193	0		208	72	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375510	40375510	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768919211	NA	P-0004016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	37	491	0	ENST00000293328.3:c.440C>T	p.Thr147Met	p.T147M	ENST00000293328	NM_012448.3	147	aCg/aTg	5/19	0.353623426933068	1	FACETS	0.337	0.278	0.404	0.337	0.278	0.404	SUBCLONAL	1	TRUE	0	0.392862002590193	1		491	449	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044550	47044550	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	21	138	0	ENST00000377604.3:c.2047G>T	p.Glu683Ter	p.E683*	ENST00000377604	NM_001204468.1	683	Gag/Tag	18/24	0.399674346452777	0	FACETS	0.442	0.343	0.554			1	SUBCLONAL	1	TRUE	NA	0.392862002590193	0		138	147	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347822	70347822	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	101	227	0	ENST00000374080.3:c.3061T>C	p.Phe1021Leu	p.F1021L	ENST00000374080		1021	Ttc/Ctc	22/45	0.295729001724718	0	FACETS	0.853	0.785	0.92			1	CLONAL	2	TRUE	NA	0.392862002590193	0		227	183	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576890	7576890	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	197	201	0	ENST00000269305.4:c.956del	p.Lys319ArgfsTer26	p.K319Rfs*26	ENST00000269305	NM_001126112.2	319	aAg/ag	9/11	NA	2	FACETS	1	0.957	1			1	INDETERMINATE	3	TRUE	NA	0.392862002590193	2		201	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0005163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	446	630	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.597499821682523	2	FACETS	0.929	0.895	0.963	0.929	0.895	0.963	CLONAL	2	FALSE	0	0.625317900174067	2		632	768	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057230	180057230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780661773	NA	P-0005163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	131	657	0	ENST00000261937.6:c.508C>T	p.Arg170Cys	p.R170C	ENST00000261937	NM_182925.4	170	Cgc/Tgc	4/30	0.560846713581969	3	FACETS	0.766	0.696	0.839	0.255	0.232	0.28	SUBCLONAL	1	FALSE	0	0.625317900174067	3		657	718	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581157	48581157	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1555685624	NA	P-0005163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	227	297	0	ENST00000342988.3:c.461C>G	p.Ser154Ter	p.S154*	ENST00000342988	NM_005359.5	154	tCa/tGa	5/12	0.597499821682523	2	FACETS	0.958	0.91	1	0.958	0.91	1	CLONAL	2	FALSE	0	0.625317900174067	2		297	379	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0005163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	211	283	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.560846713581969	3	FACETS	0.834	0.79	0.877	0.834	0.79	0.877	CLONAL	3	FALSE	0	0.625317900174067	3		283	354	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821760	72821760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150891901	NA	P-0005163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	291	511	0	ENST00000268489.5:c.10415C>T	p.Ala3472Val	p.A3472V	ENST00000268489	NM_006885.3	3472	gCg/gTg	10/10	0.5861857422525	4	FACETS	0.934	0.882	0.986	0.467	0.441	0.493	CLONAL	2	FALSE	0	0.625317900174067	4		511	810	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864807	117864808	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCTGCTGT	novel	NA	P-0005163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1401	328	478	0	ENST00000297338.2:c.1293_1301dup	p.Gln431_Gln433dup	p.Q431_Q433dup	ENST00000297338	NM_006265.2	431	cat/caACAGCAGCAt	10/14	0.625317900174067	9	FACETS	0.967	0.911	1	0.276	0.26	0.293	CLONAL	2	FALSE	2	0.625317900174067	9		478	1729	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114901017	114901018	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0005163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	432	659	0	ENST00000543371.1:c.629_630del	p.His210LeufsTer117	p.H210Lfs*117	ENST00000543371	NM_001198531.1	209	gaACac/gaac	6/14	0.53928279232943	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	FALSE	2	0.625317900174067	4		659	1118	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227855	55227855	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	96	383	0	ENST00000275493.2:c.1322T>G	p.Val441Gly	p.V441G	ENST00000275493	NM_005228.3	441	gTc/gGc	12/28	0.625317900174067	6	FACETS	0.668	0.593	0.747	0.167	0.148	0.187	SUBCLONAL	1	FALSE	2	0.625317900174067	6		383	1035	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642791	3642791	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758785487	NA	P-0005163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1358	97	806	2	ENST00000294008.3:c.2236G>A	p.Glu746Lys	p.E746K	ENST00000294008	NM_032444.2	746	Gag/Aag	11/15	0.55973506354288	4	FACETS	0.347	0.307	0.389	0.087	0.076	0.098	SUBCLONAL	1	FALSE	0	0.625317900174067	4		808	1455	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227926	55227926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1395	104	534	0	ENST00000275493.2:c.1393G>A	p.Gly465Arg	p.G465R	ENST00000275493	NM_005228.3	465	Gga/Aga	12/28	0.625317900174067	6	FACETS	0.499	0.445	0.557	0.125	0.111	0.14	SUBCLONAL	1	FALSE	2	0.625317900174067	6		534	1499	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0005500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	48	359	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	0.3	1	FACETS	0.828	0.708	0.958	1	0.969	1	CLONAL	2	TRUE	0	0.23	1		359	223	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	53	423	3	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.23	2		426	395	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969884	81969884	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199840870	NA	P-0005500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	70	656	2	ENST00000359376.3:c.2953G>A	p.Val985Ile	p.V985I	ENST00000359376	NM_002661.3	985	Gtc/Atc	27/33	0.210972964597626	0	FACETS	0.737	0.642	0.839			1	SUBCLONAL	1	TRUE	0	0.23	0		658	636	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979987	7979987	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746723399	NA	P-0005500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	59	314	2	ENST00000319144.4:c.1350del	p.Leu451SerfsTer16	p.L451Sfs*16	ENST00000319144	NM_001139.2	450	ggG/gg	10/15	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.23	2		316	451	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793238	42793238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763699553	NA	P-0005500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	71	434	1	ENST00000575354.2:c.1130C>T	p.Thr377Met	p.T377M	ENST00000575354	NM_015125.3	377	aCg/aTg	7/20	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.23	2		435	615	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820836	36820836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1452017656	NA	P-0005500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	52	259	0	ENST00000373129.3:c.541G>A	p.Val181Met	p.V181M	ENST00000373129	NM_032017.1	181	Gtg/Atg	6/12	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.23	2		259	428	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118821	61118821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146326268	NA	P-0005500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	80	254	0	ENST00000295025.8:c.14C>T	p.Ala5Val	p.A5V	ENST00000295025	NM_002908.2	5	gCg/gTg	2/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.23	2		254	488	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437230	220437230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs960266462	NA	P-0005500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	96	568	1	ENST00000243786.2:c.134C>T	p.Ala45Val	p.A45V	ENST00000243786	NM_002191.3	45	gCg/gTg	1/2	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.23	2		569	592	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613132	52613132	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	79	456	0	ENST00000394830.3:c.3396G>A	p.Trp1132Ter	p.W1132*	ENST00000394830	NM_018313.4	1132	tgG/tgA	22/30	0.224553967720944	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.23	1		456	540	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947821	178947821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	80	427	1	ENST00000263967.3:c.2696G>A	p.Arg899His	p.R899H	ENST00000263967	NM_006218.2	899	cGt/cAt	19/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.23	2		428	606	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048788	180048788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375315719	NA	P-0005500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	63	457	0	ENST00000261937.6:c.1774C>T	p.Arg592Cys	p.R592C	ENST00000261937	NM_182925.4	592	Cgc/Tgc	13/30	0.3	1	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	0	0.23	1		457	461	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670332	30670332	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	61	451	0	ENST00000376406.3:c.6100A>C	p.Lys2034Gln	p.K2034Q	ENST00000376406	NM_014641.2	2034	Aag/Cag	14/15	0.114202232587281	4	FACETS	1	0.922	1	0.551	0.475	0.634	INDETERMINATE	1	TRUE	2	0.23	4		451	592	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725519	117725519	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	82	359	0	ENST00000368508.3:c.362C>A	p.Ser121Tyr	p.S121Y	ENST00000368508	NM_002944.2	121	tCt/tAt	5/43	NA	2	FACETS	1	0.963	1			1	INDETERMINATE	1	TRUE	NA	0.23	2		359	578	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502175	157502175	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	72	305	0	ENST00000346085.5:c.3208A>G	p.Lys1070Glu	p.K1070E	ENST00000346085	NM_020732.3	1070	Aag/Gag	12/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.23	2		305	511	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132836	64132836	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	82	522	0	ENST00000334205.4:c.970T>C	p.Ser324Pro	p.S324P	ENST00000334205	NM_003942.2	324	Tca/Cca	9/17	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.23	2		522	618	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434358	49434358	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167621447	NA	P-0005500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	58	437	2	ENST00000301067.7:c.7195C>T	p.Pro2399Ser	p.P2399S	ENST00000301067	NM_003482.3	2399	Ccc/Tcc	31/54	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.23	2		439	457	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098591	11098591	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854197	NA	P-0005500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	66	412	0	ENST00000358026.2:c.1109G>A	p.Arg370His	p.R370H	ENST00000358026	NM_001128849.1	370	cGc/cAc	6/36	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.23	2		412	479	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067900	30067900	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	72	534	0	ENST00000338641.4:c.1085A>G	p.Gln362Arg	p.Q362R	ENST00000338641	NM_000268.3	362	cAg/cGg	11/16	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.23	2		534	606	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505443	157505443	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554231830	NA	P-0005500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	80	360	0	ENST00000346085.5:c.3428del	p.Lys1143SerfsTer68	p.K1143Sfs*68	ENST00000346085	NM_020732.3	1142	Aaa/aa	13/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.23	2		360	605	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32931924	32931924	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	65	433	0	ENST00000380152.3:c.7667del	p.Asn2556MetfsTer92	p.N2556Mfs*92	ENST00000380152		2555	Aaa/aa	16/27	0.224553967720944	1	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	0	0.23	1		433	480	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127638	2127639	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0005500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	53	439	0	ENST00000219476.3:c.2880_2881del	p.Pro961ThrfsTer23	p.P961Tfs*23	ENST00000219476	NM_000548.3	959	aaCTct/aact	26/42	1	2	FACETS	0.852	0.727	0.989	0.852	0.727	0.989	CLONAL	1	TRUE	1	0.23	2		439	541	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0005500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	68	297	2	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.23	2		299	518	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0005500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	22	192	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	NA	2	FACETS	0.971	0.757	1			1	INDETERMINATE	1	TRUE	NA	0.23	2		192	197	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257366	19257366	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	47	398	0	ENST00000162023.5:c.767del	p.Pro256GlnfsTer?	p.P256Qfs*?	ENST00000162023		256	cCa/ca	11/13	1	2	FACETS	0.864	0.73	1	0.864	0.73	1	CLONAL	1	TRUE	1	0.23	2		398	473	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0006162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	65	541	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.203679945365882	4	FACETS	0.773	0.672	0.882	0.773	0.672	0.882	SUBCLONAL	2	FALSE	2	0.240267772704851	4		541	434	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0006162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	84	480	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.240267772704851	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	FALSE	1	0.240267772704851	3		480	325	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0006162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	59	408	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.186333709020152	3	FACETS	1	0.956	1	0.64	0.552	0.735	CLONAL	1	FALSE	1	0.240267772704851	3		408	430	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	64	619	0	ENST00000206249.3:c.1610A>G	p.Tyr537Cys	p.Y537C	ENST00000206249	NM_000125.3	537	tAt/tGt	8/8	0.186333709020152	3	FACETS	1	0.962	1	0.659	0.572	0.752	CLONAL	1	FALSE	1	0.240267772704851	3		619	453	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001539	150001539	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	50	518	0	ENST00000253339.5:c.2065G>C	p.Glu689Gln	p.E689Q	ENST00000253339		689	Gaa/Caa	4/7	0.186333709020152	3	FACETS	1	0.896	1	0.535	0.454	0.623	CLONAL	1	FALSE	1	0.240267772704851	3		518	436	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611806	100611806	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	37	533	1	ENST00000308731.7:c.1315G>A	p.Glu439Lys	p.E439K	ENST00000308731	NM_000061.2	439	Gaa/Aaa	14/19	0.240267772704851	1	FACETS	0.774	0.64	0.924	0.774	0.64	0.924	CLONAL	1	FALSE	0	0.240267772704851	1		534	350	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463300	25463301	+	protein_altering_variant	In_Frame_Ins	INS	-	-	TTT	novel	NA	P-0006162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	51	584	0	ENST00000264709.3:c.2192_2193insAAA	p.Phe731delinsLeuAsn	p.F731delinsLN	ENST00000264709	NM_175629.2	731	ttc/ttAAAc	19/23	0.191071838715731	3	FACETS	1	0.951	1	0.648	0.553	0.752	CLONAL	1	FALSE	1	0.240267772704851	3		584	367	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239715	53239715	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	59	674	0	ENST00000375401.3:c.1627G>A	p.Glu543Lys	p.E543K	ENST00000375401	NM_004187.3	543	Gaa/Aaa	12/26	0.240267772704851	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	FALSE	0	0.240267772704851	1		674	378	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	63	315	1				ENST00000310581	NM_198253.2	-/1132			0.47568008502982	1	FACETS	0.75	0.669	0.833	1	0.977	1	SUBCLONAL	2	TRUE	0	0.471688928074148	1		316	136	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584663	187584663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	246	669	0	ENST00000441802.2:c.3370G>A	p.Glu1124Lys	p.E1124K	ENST00000441802	NM_005245.3	1124	Gag/Aag	3/27	0.47568008502982	3	FACETS	1	0.988	1	0.616	0.576	0.658	CLONAL	1	TRUE	1	0.471688928074148	3		669	1046	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	494	310	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	0.47568008502982	2	FACETS	1	0.993	1			1	CLONAL	3	TRUE	NA	0.471688928074148	2		310	659	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974792	21974792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141798398	NA	P-0006190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	148	202	0	ENST00000304494.5:c.35C>T	p.Ser12Leu	p.S12L	ENST00000304494	NM_000077.4	12	tCg/tTg	1/3	0.199508240040854	4	FACETS	0.987	0.928	1			1	INDETERMINATE	4	TRUE	NA	0.471688928074148	4		202	234	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482552	56482552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	421	479	0	ENST00000267101.3:c.1009G>A	p.Gly337Arg	p.G337R	ENST00000267101	NM_001982.3	337	Ggg/Agg	9/28	0.471688928074148	6	FACETS	1	0.959	1			1	CLONAL	4	TRUE	NA	0.471688928074148	6		479	867	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023697	27023697	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1315912114	NA	P-0006190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	296	459	0	ENST00000324856.7:c.803A>G	p.Gln268Arg	p.Q268R	ENST00000324856	NM_006015.4	268	cAg/cGg	1/20	0.47568008502982	5	FACETS	1	0.986	1	0.756	0.713	0.8	CLONAL	2	TRUE	2	0.471688928074148	5		459	945	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131228	202131228	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	116	437	0	ENST00000358485.4:c.196C>G	p.Leu66Val	p.L66V	ENST00000358485	NM_001080125.1	66	Ctt/Gtt	2/9	0.47568008502982	4	FACETS	1	0.966	1	0.385	0.348	0.425	CLONAL	1	TRUE	1	0.471688928074148	4		437	626	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543809	212543809	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	173	423	0	ENST00000342788.4:c.1590G>C	p.Arg530Ser	p.R530S	ENST00000342788	NM_005235.2	530	agG/agC	13/28	0.47568008502982	4	FACETS	1	0.988	1	0.46	0.423	0.497	CLONAL	1	TRUE	1	0.471688928074148	4		423	783	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439667	220439667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1023987842	NA	P-0006190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	368	711	0	ENST00000243786.2:c.520C>T	p.Pro174Ser	p.P174S	ENST00000243786	NM_002191.3	174	Cct/Tct	2/2	0.297901316280996	4	FACETS	1	0.979	1			1	CLONAL	3	TRUE	NA	0.471688928074148	4		711	737	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723624	49723624	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1402163092	NA	P-0006190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	115	175	0	ENST00000449682.2:c.1018G>A	p.Asp340Asn	p.D340N	ENST00000449682	NM_020998.3	340	Gac/Aac	9/18	0.47568008502982	4	FACETS	0.889	0.815	0.964	1	0.984	1	CLONAL	3	TRUE	2	0.471688928074148	4		175	269	SUCCESS
ATR	545	MSKCC	GRCh37	3	142185319	142185319	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	273	306	0	ENST00000350721.4:c.6744G>T	p.Lys2248Asn	p.K2248N	ENST00000350721	NM_001184.3	2248	aaG/aaT	40/47	0.471688928074148	5	FACETS	1	0.99	1	0.831	0.783	0.88	CLONAL	2	TRUE	2	0.471688928074148	5		306	793	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526125	189526125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	453	490	0	ENST00000264731.3:c.389C>T	p.Ser130Phe	p.S130F	ENST00000264731	NM_003722.4	130	tCc/tTc	4/14	0.471688928074148	5	FACETS	0.903	0.863	0.943	0.903	0.863	0.943	CLONAL	3	TRUE	2	0.471688928074148	5		490	1211	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584693	187584693	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	434	662	2	ENST00000441802.2:c.3340C>T	p.Gln1114Ter	p.Q1114*	ENST00000441802	NM_005245.3	1114	Cag/Tag	3/27	0.47568008502982	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.471688928074148	3		664	989	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527481	157527481	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	519	758	0	ENST00000346085.5:c.5206G>A	p.Glu1736Lys	p.E1736K	ENST00000346085	NM_020732.3	1736	Gaa/Aaa	20/20	0.47568008502982	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.471688928074148	2		758	890	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750831	128750831	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	402	552	0	ENST00000377970.2:c.368G>A	p.Gly123Glu	p.G123E	ENST00000377970	NM_002467.4	123	gGa/gAa	2/3	0.276562765393618	5	FACETS	1	0.988	1			1	INDETERMINATE	3	TRUE	NA	0.471688928074148	5		552	894	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915883	127915883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	182	679	1	ENST00000373547.4:c.598G>A	p.Glu200Lys	p.E200K	ENST00000373547	NM_002721.4	200	Gaa/Aaa	6/7	0.151921957553376	3	FACETS	1	0.963	1	0.357	0.329	0.386	INDETERMINATE	1	TRUE	0	0.471688928074148	3		680	891	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710610	114710610	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	721	736	1	ENST00000543371.1:c.95C>T	p.Ser32Phe	p.S32F	ENST00000543371	NM_001198531.1	32	tCc/tTc	1/14	0.47568008502982	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	1	0.471688928074148	3		737	1556	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160489	108160489	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	442	459	0	ENST00000278616.4:c.4397G>C	p.Arg1466Pro	p.R1466P	ENST00000278616	NM_000051.3	1466	cGa/cCa	29/63	0.47568008502982	4	FACETS	0.851	0.814	0.889	0.851	0.814	0.889	CLONAL	3	TRUE	1	0.471688928074148	4		459	1080	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202753	108202753	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs781215442	NA	P-0006190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	197	438	0	ENST00000278616.4:c.7777C>T	p.Gln2593Ter	p.Q2593*	ENST00000278616	NM_000051.3	2593	Cag/Tag	52/63	0.47568008502982	4	FACETS	1	0.986	1	0.423	0.391	0.456	CLONAL	1	TRUE	1	0.471688928074148	4		438	969	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242635	46242635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	106	251	0	ENST00000334344.6:c.1597G>A	p.Glu533Lys	p.E533K	ENST00000334344	NM_152641.2	533	Gaa/Aaa	13/21	0.47568008502982	3	FACETS	0.988	0.889	1	0.494	0.444	0.547	CLONAL	1	TRUE	1	0.471688928074148	3		251	562	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444483	49444483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	111	424	1	ENST00000301067.7:c.2888C>T	p.Ala963Val	p.A963V	ENST00000301067	NM_003482.3	963	gCc/gTc	11/54	0.47568008502982	3	FACETS	1	0.952	1	0.546	0.492	0.602	CLONAL	1	TRUE	1	0.471688928074148	3		425	533	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060822	38060822	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	357	697	0	ENST00000250448.2:c.1167A>T	p.Lys389Asn	p.K389N	ENST00000250448	NM_004496.3	389	aaA/aaT	2/2	0.365745870291501	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.471688928074148	4		697	1021	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628554	90628554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	99	378	0	ENST00000330062.3:c.1033G>A	p.Glu345Lys	p.E345K	ENST00000330062	NM_002168.2	345	Gag/Aag	8/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.471688928074148	2		378	324	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636720	2636720	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779064858	NA	P-0006190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	99	425	0	ENST00000342085.4:c.1169C>T	p.Ser390Leu	p.S390L	ENST00000342085	NM_002613.4	390	tCg/tTg	11/14	0.225685657857513	2	FACETS	0.911	0.817	1	0.455	0.408	0.505	INDETERMINATE	1	TRUE	0	0.471688928074148	2		425	461	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843447	3843447	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783461	NA	P-0006190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	198	467	1	ENST00000262367.5:c.1156C>T	p.Arg386Ter	p.R386*	ENST00000262367	NM_004380.2	386	Cga/Tga	4/31	0.225685657857513	2	FACETS	0.899	0.842	0.957	0.899	0.842	0.957	INDETERMINATE	2	TRUE	0	0.471688928074148	2		468	467	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511611	38511611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs899025600	NA	P-0006190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	194	560	1	ENST00000254066.5:c.1109G>A	p.Arg370His	p.R370H	ENST00000254066	NM_000964.3	370	cGc/cAc	8/9	0.471688928074148	6	FACETS	0.934	0.865	1			1	CLONAL	2	TRUE	NA	0.471688928074148	6		561	856	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856343	45856343	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	118	575	0	ENST00000391945.4:c.1829T>A	p.Phe610Tyr	p.F610Y	ENST00000391945	NM_000400.3	610	tTt/tAt	19/23	0.388769790457439	4	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.471688928074148	4		575	498	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20150336	20150336	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	450	240	0	ENST00000379607.5:c.301A>G	p.Arg101Gly	p.R101G	ENST00000379607	NM_001412.3	101	Aga/Gga	5/7	0.47568008502982	2	FACETS	1	0.991	1			1	CLONAL	3	TRUE	NA	0.471688928074148	2		240	605	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611047	100611047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs128621202	NA	P-0006190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	367	354	0	ENST00000308731.7:c.1559G>A	p.Arg520Gln	p.R520Q	ENST00000308731	NM_000061.2	520	cGa/cAa	15/19	0.471688928074148	2	FACETS	1	0.967	1			1	CLONAL	3	TRUE	NA	0.471688928074148	2		354	518	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247247	153247267	+	frameshift_variant	Frame_Shift_Del	DEL	ATGCTCCACTAACAACCCTCC	ATGCTCCACTAACAACCCTCC	T	novel	NA	P-0006190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	163	503	0	ENST00000281708.4:c.1535_1555delinsA	p.Arg512LysfsTer2	p.R512Kfs*2	ENST00000281708	NM_033632.3	512	aGGAGGGTTGTTAGTGGAGCATat/aAat	10/12	0.47568008502982	4	FACETS	1	0.96	1	0.359	0.329	0.39	CLONAL	1	TRUE	1	0.471688928074148	4		503	944	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006589-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	221	528	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.893	0.833	0.956	0.893	0.833	0.956	CLONAL	1	TRUE	1	0.576577494320365	2		529	858	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0006589-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	446	583	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.576577494320365	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.576577494320365	1		583	987	SUCCESS
APC	324	MSKCC	GRCh37	5	112175541	112175541	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006589-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	203	317	0	ENST00000257430.4:c.4251del	p.Ile1418Ter	p.I1418*	ENST00000257430	NM_000038.5	1417	aTt/at	16/16	1	2	FACETS	0.943	0.877	1	0.943	0.877	1	CLONAL	1	TRUE	1	0.576577494320365	2		317	747	SUCCESS
APC	324	MSKCC	GRCh37	5	112163696	112163697	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1131691555	NA	P-0006589-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	195	408	0	ENST00000257430.4:c.1620dup	p.Gln541ThrfsTer19	p.Q541Tfs*19	ENST00000257430	NM_000038.5	540	tta/ttAa	13/16	1	2	FACETS	0.894	0.829	0.96	0.894	0.829	0.96	CLONAL	1	TRUE	1	0.576577494320365	2		408	757	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254460	10254461	+	missense_variant	Missense_Mutation	DNP	CG	CG	AC	novel	NA	P-0006589-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	40	519	1	ENST00000340748.4:c.3049_3050delinsGT	p.Arg1017Val	p.R1017V	ENST00000340748		1017	CGg/GTg	28/40	0.576577494320365	1	FACETS	0.128	0.105	0.153	0.128	0.105	0.153	SUBCLONAL	1	TRUE	0	0.576577494320365	1		520	773	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981282	68981282	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006589-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	307	361	1	ENST00000288368.4:c.1354C>T	p.Gln452Ter	p.Q452*	ENST00000288368	NM_024870.2	452	Caa/Taa	12/40	0.443215565555526	3	FACETS	0.901	0.854	0.949	0.901	0.854	0.949	CLONAL	2	TRUE	1	0.576577494320365	3		362	761	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028150	69028150	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006589-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	101	701	0	ENST00000288368.4:c.3309C>A	p.Ser1103Arg	p.S1103R	ENST00000288368	NM_024870.2	1103	agC/agA	26/40	0.443215565555526	3	FACETS	0.357	0.318	0.399	0.178	0.159	0.2	SUBCLONAL	1	TRUE	1	0.576577494320365	3		701	1265	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007179-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	65	528	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.157282453024788	3	FACETS	0.717	0.621	0.822	0.359	0.31	0.411	INDETERMINATE	1	TRUE	1	0.28	3		529	738	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576870	7576870	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs876659384	NA	P-0007179-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	85	621	0	ENST00000269305.4:c.976G>T	p.Glu326Ter	p.E326*	ENST00000269305	NM_001126112.2	326	Gaa/Taa	9/11	1	2	FACETS	0.649	0.573	0.732	0.649	0.573	0.732	SUBCLONAL	1	TRUE	1	0.28	2		621	935	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195511	102195511	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007179-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	35	412	0	ENST00000263464.3:c.271C>A	p.Pro91Thr	p.P91T	ENST00000263464	NM_001165.4	91	Cct/Act	2/9	1	2	FACETS	0.398	0.325	0.48	0.398	0.325	0.48	SUBCLONAL	1	TRUE	1	0.28	2		412	628	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023144	27023159	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCGGCGGAGCCG	GGCGGCGGCGGAGCCG	TC	novel	NA	P-0007179-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	47	62	0	ENST00000324856.7:c.250_265delinsTC	p.Gly84SerfsTer22	p.G84Sfs*22	ENST00000324856	NM_006015.4	84	GGCGGCGGCGGAGCCGgc/TCgc	1/20	1	2	FACETS	1	0.941	1	1	0.978	1	CLONAL	2	TRUE	1	0.28	2		62	142	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971075	21971101	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CCAGCGTGTCCAGGAAGCCCTCCCGGG	CCAGCGTGTCCAGGAAGCCCTCCCGGG	T	novel	NA	P-0007179-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	37	510	0	ENST00000579755.1:c.300_326delinsA	p.Cys100Ter	p.C100*	ENST00000579755		100	tgCCCGGGAGGGCTTCCTGGACACGCTGGt/tgAt	2/3	1	2	FACETS	0.423	0.348	0.507	0.423	0.348	0.507	SUBCLONAL	1	TRUE	1	0.28	2		510	625	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971029	21971029	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519852	NA	P-0007572-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	101	208	0	ENST00000304494.5:c.329G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tGg/tAg	2/3	0.241416810685333	2	FACETS	0.948	0.857	1	0.948	0.857	1	CLONAL	2	TRUE	0	0.315117450910017	2		208	338	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254656	16254656	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007572-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	119	596	0	ENST00000375759.3:c.1921A>G	p.Thr641Ala	p.T641A	ENST00000375759	NM_015001.2	641	Act/Gct	11/15	1	2	FACETS	0.978	0.883	1	0.978	0.883	1	CLONAL	1	TRUE	1	0.315117450910017	2		596	772	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447305	187447305	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0007572-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	42	238	0	ENST00000232014.4:c.888T>A	p.Cys296Ter	p.C296*	ENST00000232014	NM_001130845.1	296	tgT/tgA	5/10	0.292717504588853	3	FACETS	0.726	0.607	0.858	0.363	0.303	0.429	SUBCLONAL	1	TRUE	1	0.315117450910017	3		238	425	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356299	66356299	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007572-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	66	358	0	ENST00000273854.3:c.1198T>C	p.Ser400Pro	p.S400P	ENST00000273854	NM_004439.5	400	Tcc/Ccc	5/18	1	2	FACETS	0.784	0.682	0.895	0.784	0.682	0.895	SUBCLONAL	1	TRUE	1	0.315117450910017	2		358	534	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6048627	6048627	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs587782074	NA	P-0007572-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	128	370	0	ENST00000265849.7:c.23+1G>T		p.X8_splice	ENST00000265849	NM_000535.5	8			0.292717504588853	3	FACETS	0.766	0.696	0.839	0.766	0.696	0.839	SUBCLONAL	2	TRUE	1	0.315117450910017	3		370	614	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133804	41133804	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007572-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	222	694	0	ENST00000379561.5:c.1824G>C	p.Glu608Asp	p.E608D	ENST00000379561	NM_002015.3	608	gaG/gaC	2/3	0.256667300749499	4	FACETS	0.835	0.776	0.895	0.835	0.776	0.895	CLONAL	2	TRUE	2	0.315117450910017	4		694	1110	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032356	10032356	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763500409	NA	P-0007572-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	34	180	0	ENST00000330684.3:c.467C>T	p.Thr156Met	p.T156M	ENST00000330684	NM_001134407.1	156	aCg/aTg	3/13	0.292717504588853	3	FACETS	0.905	0.743	1	0.453	0.371	0.543	CLONAL	1	TRUE	1	0.315117450910017	3		180	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578441	7578441	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007572-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	116	329	0	ENST00000269305.4:c.489C>A	p.Tyr163Ter	p.Y163*	ENST00000269305	NM_001126112.2	163	taC/taA	5/11	0.276392141114364	2	FACETS	0.773	0.701	0.849	0.773	0.701	0.849	SUBCLONAL	2	TRUE	0	0.315117450910017	2		329	476	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59878735	59878735	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007572-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	92	476	0	ENST00000259008.2:c.1019T>G	p.Leu340Arg	p.L340R	ENST00000259008	NM_032043.2	340	cTt/cGt	8/20	0.261984149520615	4	FACETS	0.869	0.771	0.974	0.29	0.257	0.325	CLONAL	1	TRUE	1	0.315117450910017	4		476	884	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0008837-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	588	344	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.6146236684802	6	FACETS	0.956	0.933	0.977			1	CLONAL	6	TRUE	NA	0.6146236684802	6		345	744	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0008837-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	319	693	1	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.540282646669422	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.6146236684802	2		694	514	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972769	25972769	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008837-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	108	327	0	ENST00000435504.4:c.1656A>C	p.Lys552Asn	p.K552N	ENST00000435504		552	aaA/aaC	12/13	0.51986021129221	5	FACETS	0.933	0.846	1	0.622	0.564	0.682	CLONAL	2	TRUE	2	0.6146236684802	5		327	362	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361130	66361130	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008837-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	92	292	0	ENST00000273854.3:c.1042G>T	p.Asp348Tyr	p.D348Y	ENST00000273854	NM_004439.5	348	Gat/Tat	4/18	0.467651346524697	3	FACETS	0.955	0.868	1	0.955	0.868	1	CLONAL	2	TRUE	1	0.6146236684802	3		292	205	SUCCESS
APC	324	MSKCC	GRCh37	5	112177095	112177095	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1346125460	NA	P-0008837-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	70	407	0	ENST00000257430.4:c.5804A>T	p.Gln1935Leu	p.Q1935L	ENST00000257430	NM_000038.5	1935	cAg/cTg	16/16	0.44243404099677	4	FACETS	1	0.972	1	0.691	0.61	0.777	CLONAL	1	TRUE	2	0.6146236684802	4		407	266	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680734	30680734	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008837-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	61	431	1	ENST00000376406.3:c.985A>T	p.Ser329Cys	p.S329C	ENST00000376406	NM_014641.2	329	Agc/Tgc	5/15	0.6146236684802	7	FACETS	0.739	0.637	0.851	0.148	0.127	0.171	SUBCLONAL	1	TRUE	2	0.6146236684802	7		432	681	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8526642	8526642	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008837-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	72	448	2	ENST00000356435.5:c.553G>T	p.Gly185Cys	p.G185C	ENST00000356435		185	Ggt/Tgt	6/35	0.467651346524697	3	FACETS	1	0.976	1	0.719	0.639	0.802	CLONAL	1	TRUE	1	0.6146236684802	3		450	213	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346976	73346976	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008837-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	76	248	0	ENST00000377767.4:c.1241G>T	p.Gly414Val	p.G414V	ENST00000377767	NM_014953.3	414	gGa/gTa	9/21	0.415589029905599	3	FACETS	1	0.925	1	0.686	0.62	0.754	CLONAL	2	TRUE	0	0.6146236684802	3		248	157	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820576	3820576	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008837-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	340	579	0	ENST00000262367.5:c.2875A>G	p.Thr959Ala	p.T959A	ENST00000262367	NM_004380.2	959	Aca/Gca	14/31	0.6146236684802	5	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	3	0.6146236684802	5		579	881	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993714	72993714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1266350809	NA	P-0008837-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	68	441	0	ENST00000268489.5:c.331G>A	p.Glu111Lys	p.E111K	ENST00000268489	NM_006885.3	111	Gag/Aag	2/10	0.6146236684802	3	FACETS	0.898	0.788	1	0.449	0.394	0.508	CLONAL	1	TRUE	1	0.6146236684802	3		441	322	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972475	81972475	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008837-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	146	564	0	ENST00000359376.3:c.3268T>A	p.Cys1090Ser	p.C1090S	ENST00000359376	NM_002661.3	1090	Tgt/Agt	29/33	0.6146236684802	3	FACETS	0.989	0.918	1	0.989	0.918	1	CLONAL	2	TRUE	1	0.6146236684802	3		564	314	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770089	56770089	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008837-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	81	530	0	ENST00000337432.4:c.85T>C	p.Ser29Pro	p.S29P	ENST00000337432	NM_058216.2	29	Tct/Cct	1/9	0.6146236684802	7	FACETS	0.752	0.661	0.85	0.15	0.132	0.17	SUBCLONAL	1	TRUE	2	0.6146236684802	7		530	889	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897336	78897336	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs757484259	NA	P-0008837-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	504	691	0	ENST00000306801.3:c.2671G>T	p.Asp891Tyr	p.D891Y	ENST00000306801	NM_020761.2	891	Gat/Tat	23/34	0.6146236684802	7	FACETS	0.97	0.936	1	0.97	0.936	1	CLONAL	5	TRUE	2	0.6146236684802	7		691	858	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212059	5212059	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770983463	NA	P-0008837-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	88	583	1	ENST00000357368.4:c.4972G>A	p.Ala1658Thr	p.A1658T	ENST00000357368	NM_002850.3	1658	Gca/Aca	32/38	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.6146236684802	2		584	266	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781059	135781083	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTGTTTCCTTTTGCTTTCTTTAA	CTGTGTTTCCTTTTGCTTTCTTTAA	-	novel	NA	P-0008837-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	149	548	0	ENST00000298552.3:c.1882_1906del	p.Leu628ArgfsTer17	p.L628Rfs*17	ENST00000298552	NM_001162426.1	628	TTAAAGAAAGCAAAAGGAAACACAGag/ag	15/23	0.467651346524697	3	FACETS	0.841	0.778	0.905	0.841	0.778	0.905	CLONAL	2	TRUE	1	0.6146236684802	3		548	377	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533104	63533104	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008837-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	423	595	0	ENST00000307078.5:c.1790del	p.Gly597GlufsTer92	p.G597Efs*92	ENST00000307078	NM_004655.3	597	gGa/ga	7/11	0.6146236684802	7	FACETS	0.963	0.927	0.999	0.963	0.927	0.999	CLONAL	5	TRUE	2	0.6146236684802	7		595	725	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988508	36988508	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008837-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2336	190	932	0	ENST00000354822.5:c.145C>G	p.Pro49Ala	p.P49A	ENST00000354822	NM_001079668.2	49	Ccc/Gcc	2/3	0.6146236684802	13	FACETS	1	0.961	1			1	CLONAL	1	TRUE	NA	0.6146236684802	13		932	2526	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346951	89346951	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008837-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	45	288	0	ENST00000301030.4:c.5999T>G	p.Leu2000Arg	p.L2000R	ENST00000301030	NM_001256183.1	2000	cTc/cGc	9/13	0.6146236684802	3	FACETS	0.874	0.742	1	0.437	0.371	0.508	CLONAL	1	TRUE	1	0.6146236684802	3		288	219	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0009394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	444	574	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.669659288612806	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.669659288612806	2		576	607	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499393	89499393	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	179	386	0	ENST00000336596.2:c.2563C>T	p.Gln855Ter	p.Q855*	ENST00000336596	NM_005233.5	855	Cag/Tag	15/17	0.669659288612806	3	FACETS	1	0.972	1	0.551	0.51	0.594	CLONAL	1	TRUE	1	0.669659288612806	3		386	647	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156781	106156781	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	371	425	0	ENST00000380013.4:c.1682A>G	p.Lys561Arg	p.K561R	ENST00000380013	NM_001127208.2	561	aAa/aGa	3/11	0.668365042036382	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.669659288612806	2		425	543	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294069	1294069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs974018889	NA	P-0009394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	272	860	3	ENST00000310581.5:c.932C>T	p.Ser311Leu	p.S311L	ENST00000310581	NM_198253.2	311	tCg/tTg	2/16	1	2	FACETS	0.942	0.887	0.999	0.942	0.887	0.999	CLONAL	1	TRUE	1	0.669659288612806	2		863	862	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112884112	112884112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	223	412	1	ENST00000351677.2:c.47C>T	p.Ala16Val	p.A16V	ENST00000351677	NM_002834.3	16	gCa/gTa	2/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.669659288612806	2		413	589	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578498	7578499	+	missense_variant	Missense_Mutation	DNP	CT	CT	GG	novel	NA	P-0009450-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	413	918	2	ENST00000269305.4:c.431_432delinsCC	p.Gln144Pro	p.Q144P	ENST00000269305	NM_001126112.2	144	cAG/cCC	5/11	NA	2	FACETS	0.927	0.884	0.971			1	INDETERMINATE	2	TRUE	NA	0.395850965685253	2		920	1125	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48921906	48921975	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TATGACTTCTAAATTACGAAAAAATGTTAAAAAGTCATAATGTTTTTCTTTTCAGGACATGTGAACTTAT	TATGACTTCTAAATTACGAAAAAATGTTAAAAAGTCATAATGTTTTTCTTTTCAGGACATGTGAACTTAT	-	novel	NA	P-0009450-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	91	309	0	ENST00000267163.4:c.501-55_515del		p.X167_splice	ENST00000267163	NM_000321.2	167		5/27	0.395850965685253	2	FACETS	1	0.967	1	0.602	0.538	0.669	CLONAL	1	TRUE	0	0.395850965685253	2		309	382	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602789	10602789	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009450-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	143	967	0	ENST00000171111.5:c.789C>A	p.Tyr263Ter	p.Y263*	ENST00000171111	NM_203500.1	263	taC/taA	3/6	0.395850965685253	1	FACETS	0.599	0.546	0.656	0.599	0.546	0.656	SUBCLONAL	1	TRUE	0	0.395850965685253	1		967	967	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	139	315	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.881	0.812	0.951	0.881	0.812	0.951	CLONAL	1	TRUE	1	0.866829688783246	2		316	364	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	80	733	0	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	1	2	FACETS	0.188	0.165	0.213	0.188	0.165	0.213	SUBCLONAL	1	TRUE	1	0.866829688783246	2		733	982	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	156	326	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.994	0.924	1	0.994	0.924	1	CLONAL	1	TRUE	1	0.866829688783246	2		326	362	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	220	595	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	1	2	FACETS	0.636	0.593	0.68	0.636	0.593	0.68	SUBCLONAL	1	TRUE	1	0.866829688783246	2		595	798	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432411	78432412	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACCTTTCTGGAAGGCCACC	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	191	405	0	ENST00000370768.2:c.421_439dup	p.Ser147TrpfsTer15	p.S147Wfs*15	ENST00000370768	NM_003902.3	147	tcc/tGGTGGCCTTCCAGAAAGGTcc	7/20	0.866829688783246	1	FACETS	0.609	0.571	0.647	0.609	0.571	0.647	SUBCLONAL	1	TRUE	0	0.866829688783246	1		405	410	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599309	55599309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	68	471	0	ENST00000288135.5:c.2435G>A	p.Gly812Asp	p.G812D	ENST00000288135	NM_000222.2	812	gGt/gAt	17/21	1	2	FACETS	0.211	0.183	0.242	0.211	0.183	0.242	SUBCLONAL	1	TRUE	1	0.866829688783246	2		471	743	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212128	98212128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	29	357	0	ENST00000331920.6:c.3544C>T	p.Pro1182Ser	p.P1182S	ENST00000331920	NM_000264.3	1182	Cct/Tct	21/24	1	2	FACETS	0.139	0.111	0.171	0.139	0.111	0.171	SUBCLONAL	1	TRUE	1	0.866829688783246	2		357	480	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575153	64575153	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	131	366	0	ENST00000312049.6:c.655-1G>A		p.X219_splice	ENST00000312049	NM_130799.2	219			1	2	FACETS	0.583	0.532	0.637	0.583	0.532	0.637	SUBCLONAL	1	TRUE	1	0.866829688783246	2		366	518	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484280	120484280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	18	434	0	ENST00000256646.2:c.2850G>A	p.Met950Ile	p.M950I	ENST00000256646	NM_024408.3	950	atG/atA	18/34	0.866829688783246	1	FACETS	0.067	0.05	0.087	0.067	0.05	0.087	SUBCLONAL	1	TRUE	0	0.866829688783246	1		434	351	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247469	71247469	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs794727811	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	44	495	0	ENST00000318789.4:c.64G>A	p.Gly22Ser	p.G22S	ENST00000318789	NM_032682.5	22	Ggc/Agc	6/21	1	2	FACETS	0.133	0.111	0.158	0.133	0.111	0.158	SUBCLONAL	1	TRUE	1	0.866829688783246	2		495	764	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412203	139412203	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	40	546	1	ENST00000277541.6:c.1441+1G>A		p.X481_splice	ENST00000277541	NM_017617.3	481			1	2	FACETS	0.136	0.112	0.162	0.136	0.112	0.162	SUBCLONAL	1	TRUE	1	0.866829688783246	2		547	680	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022998	27022999	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	20	59	0	ENST00000324856.7:c.110dup	p.Glu38ArgfsTer73	p.E38Rfs*73	ENST00000324856	NM_006015.4	35	gcg/gcGg	1/20	0.866829688783246	1	FACETS	0.623	0.505	0.741	0.623	0.505	0.741	SUBCLONAL	1	TRUE	0	0.866829688783246	1		59	42	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598978	28598978	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	29	604	0	ENST00000253063.3:c.537+1G>A		p.X179_splice	ENST00000253063	NM_031459.4	179			0.866829688783246	1	FACETS	0.099	0.079	0.122	0.099	0.079	0.122	SUBCLONAL	1	TRUE	0	0.866829688783246	1		604	382	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939093	36939093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	67	674	0	ENST00000361632.4:c.616G>A	p.Glu206Lys	p.E206K	ENST00000361632		206	Gag/Aag	5/16	0.866829688783246	1	FACETS	0.203	0.177	0.232	0.203	0.177	0.232	SUBCLONAL	1	TRUE	0	0.866829688783246	1		674	431	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466588	120466588	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	15	328	2	ENST00000256646.2:c.4531G>A	p.Asp1511Asn	p.D1511N	ENST00000256646	NM_024408.3	1511	Gac/Aac	26/34	0.866829688783246	1	FACETS	0.069	0.05	0.092	0.069	0.05	0.092	SUBCLONAL	1	TRUE	0	0.866829688783246	1		330	284	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925681	114925681	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774145012	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	57	561	1	ENST00000543371.1:c.1759G>A	p.Ala587Thr	p.A587T	ENST00000543371	NM_001198531.1	587	Gcc/Acc	14/14	1	2	FACETS	0.172	0.147	0.2	0.172	0.147	0.2	SUBCLONAL	1	TRUE	1	0.866829688783246	2		562	763	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274662	123274662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	117	351	0	ENST00000358487.5:c.1256C>T	p.Thr419Ile	p.T419I	ENST00000358487	NM_000141.4	419	aCc/aTc	9/18	1	2	FACETS	0.505	0.457	0.555	0.505	0.457	0.555	SUBCLONAL	1	TRUE	1	0.866829688783246	2		351	535	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61213490	61213490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1300630237	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	137	426	0	ENST00000301761.2:c.448G>A	p.Glu150Lys	p.E150K	ENST00000301761	NM_017841.2	150	Gag/Aag	4/4	1	2	FACETS	0.476	0.434	0.52	0.476	0.434	0.52	SUBCLONAL	1	TRUE	1	0.866829688783246	2		426	664	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076707	102076707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747168208	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	39	470	0	ENST00000282441.5:c.886G>A	p.Gly296Ser	p.G296S	ENST00000282441	NM_001130145.2	296	Ggt/Agt	5/9	1	2	FACETS	0.147	0.121	0.176	0.147	0.121	0.176	SUBCLONAL	1	TRUE	1	0.866829688783246	2		470	611	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444487	49444487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	185	587	2	ENST00000301067.7:c.2884G>A	p.Gly962Ser	p.G962S	ENST00000301067	NM_003482.3	962	Ggt/Agt	11/54	1	2	FACETS	0.572	0.529	0.616	0.572	0.529	0.616	SUBCLONAL	1	TRUE	1	0.866829688783246	2		589	746	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777798	3777798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	92	782	0	ENST00000262367.5:c.7250G>A	p.Arg2417Lys	p.R2417K	ENST00000262367	NM_004380.2	2417	aGg/aAg	31/31	1	2	FACETS	0.201	0.177	0.225	0.201	0.177	0.225	SUBCLONAL	1	TRUE	1	0.866829688783246	2		782	1058	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134475	30134475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	42	390	0	ENST00000263025.4:c.56G>A	p.Gly19Glu	p.G19E	ENST00000263025	NM_002746.2	19	gGg/gAg	1/9	1	2	FACETS	0.218	0.182	0.258	0.218	0.182	0.258	SUBCLONAL	1	TRUE	1	0.866829688783246	2		390	445	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989394	7989394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	198	642	0	ENST00000319144.4:c.292C>T	p.His98Tyr	p.H98Y	ENST00000319144	NM_001139.2	98	Cac/Tac	2/15	1	2	FACETS	0.583	0.541	0.626	0.583	0.541	0.626	SUBCLONAL	1	TRUE	1	0.866829688783246	2		642	784	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12043202	12043202	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	30	323	0	ENST00000353533.5:c.1086+1G>A		p.X362_splice	ENST00000353533	NM_003010.3	362			1	2	FACETS	0.139	0.112	0.171	0.139	0.112	0.171	SUBCLONAL	1	TRUE	1	0.866829688783246	2		323	497	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475644	40475644	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	156	369	0	ENST00000264657.5:c.1601-1G>A		p.X534_splice	ENST00000264657	NM_139276.2	534			1	2	FACETS	0.644	0.593	0.697	0.644	0.593	0.697	SUBCLONAL	1	TRUE	1	0.866829688783246	2		369	559	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772330	56772330	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	136	404	0	ENST00000337432.4:c.184C>T	p.Gln62Ter	p.Q62*	ENST00000337432	NM_058216.2	62	Caa/Taa	2/9	1	2	FACETS	0.563	0.514	0.614	0.563	0.514	0.614	SUBCLONAL	1	TRUE	1	0.866829688783246	2		404	557	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761204	59761204	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	58	575	0	ENST00000259008.2:c.3203C>T	p.Pro1068Leu	p.P1068L	ENST00000259008	NM_032043.2	1068	cCt/cTt	20/20	1	2	FACETS	0.16	0.137	0.185	0.16	0.137	0.185	SUBCLONAL	1	TRUE	1	0.866829688783246	2		575	837	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926612	59926612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555616229	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	146	355	1	ENST00000259008.2:c.385C>T	p.Pro129Ser	p.P129S	ENST00000259008	NM_032043.2	129	Cct/Tct	5/20	1	2	FACETS	0.614	0.563	0.666	0.614	0.563	0.666	SUBCLONAL	1	TRUE	1	0.866829688783246	2		356	549	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296487	15296487	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	193	847	0	ENST00000263388.2:c.1955C>T	p.Pro652Leu	p.P652L	ENST00000263388	NM_000435.2	652	cCc/cTc	13/33	NA	2	FACETS	0.514	0.476	0.554			1	INDETERMINATE	1	TRUE	NA	0.866829688783246	2		847	866	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791736	42791736	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	296	512	0	ENST00000575354.2:c.622A>G	p.Met208Val	p.M208V	ENST00000575354	NM_015125.3	208	Atg/Gtg	5/20	0.866829688783246	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.866829688783246	1		512	383	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637237	47637237	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	131	370	1	ENST00000233146.2:c.371C>T	p.Ser124Phe	p.S124F	ENST00000233146	NM_000251.2	124	tCt/tTt	3/16	1	2	FACETS	0.554	0.504	0.605	0.554	0.504	0.605	SUBCLONAL	1	TRUE	1	0.866829688783246	2		371	546	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027287	48027287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	109	279	0	ENST00000234420.5:c.2165C>T	p.Ser722Phe	p.S722F	ENST00000234420	NM_000179.2	722	tCt/tTt	4/10	1	2	FACETS	0.554	0.5	0.61	0.554	0.5	0.61	SUBCLONAL	1	TRUE	1	0.866829688783246	2		279	454	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190742001	190742001	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	43	412	0	ENST00000441310.2:c.2638G>A	p.Glu880Lys	p.E880K	ENST00000441310	NM_000534.4	880	Gaa/Aaa	13/13	1	2	FACETS	0.157	0.131	0.187	0.157	0.131	0.187	SUBCLONAL	1	TRUE	1	0.866829688783246	2		412	630	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023735	31023735	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	56	526	0	ENST00000375687.4:c.3220C>T	p.Gln1074Ter	p.Q1074*	ENST00000375687	NM_015338.5	1074	Caa/Taa	13/13	1	2	FACETS	0.185	0.158	0.215	0.185	0.158	0.215	SUBCLONAL	1	TRUE	1	0.866829688783246	2		526	697	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383328	31383328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	164	520	0	ENST00000328111.2:c.1240G>A	p.Asp414Asn	p.D414N	ENST00000328111	NM_006892.3	414	Gat/Aat	11/23	1	2	FACETS	0.578	0.532	0.625	0.578	0.532	0.625	SUBCLONAL	1	TRUE	1	0.866829688783246	2		520	655	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164232	47164232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	33	320	0	ENST00000409792.3:c.1894G>A	p.Glu632Lys	p.E632K	ENST00000409792	NM_014159.6	632	Gaa/Aaa	3/21	1	2	FACETS	0.145	0.117	0.176	0.145	0.117	0.176	SUBCLONAL	1	TRUE	1	0.866829688783246	2		320	526	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940564	49940564	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	141	583	0	ENST00000296474.3:c.479C>T	p.Pro160Leu	p.P160L	ENST00000296474	NM_002447.2	160	cCa/cTa	1/20	1	2	FACETS	0.501	0.458	0.547	0.501	0.458	0.547	SUBCLONAL	1	TRUE	1	0.866829688783246	2		583	649	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191512	185191512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	63	576	0	ENST00000265026.3:c.2393C>T	p.Pro798Leu	p.P798L	ENST00000265026	NM_004721.4	798	cCt/cTt	11/14	1	2	FACETS	0.197	0.169	0.226	0.197	0.169	0.226	SUBCLONAL	1	TRUE	1	0.866829688783246	2		576	739	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447355	187447355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1210638938	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	61	466	0	ENST00000232014.4:c.838G>A	p.Gly280Ser	p.G280S	ENST00000232014	NM_001130845.1	280	Ggc/Agc	5/10	1	2	FACETS	0.198	0.17	0.228	0.198	0.17	0.228	SUBCLONAL	1	TRUE	1	0.866829688783246	2		466	711	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806623	1806623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	161	705	2	ENST00000260795.2:c.1339G>A	p.Glu447Lys	p.E447K	ENST00000260795		447	Gag/Aag	9/17	1	2	FACETS	0.506	0.465	0.549	0.506	0.465	0.549	SUBCLONAL	1	TRUE	1	0.866829688783246	2		707	734	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970876	55970876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	43	433	1	ENST00000263923.4:c.1921G>A	p.Val641Ile	p.V641I	ENST00000263923	NM_002253.2	641	Gtc/Atc	13/30	1	2	FACETS	0.158	0.132	0.188	0.158	0.132	0.188	SUBCLONAL	1	TRUE	1	0.866829688783246	2		434	626	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160661	56160661	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	42	335	0	ENST00000399503.3:c.935T>C	p.Met312Thr	p.M312T	ENST00000399503	NM_005921.1	312	aTg/aCg	4/20	1	2	FACETS	0.172	0.143	0.205	0.172	0.143	0.205	SUBCLONAL	1	TRUE	1	0.866829688783246	2		335	562	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177524	56177524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	107	370	1	ENST00000399503.3:c.2497G>A	p.Val833Met	p.V833M	ENST00000399503	NM_005921.1	833	Gtg/Atg	14/20	1	2	FACETS	0.511	0.461	0.564	0.511	0.461	0.564	SUBCLONAL	1	TRUE	1	0.866829688783246	2		371	483	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189451	56189451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	40	472	0	ENST00000399503.3:c.4483G>A	p.Asp1495Asn	p.D1495N	ENST00000399503	NM_005921.1	1495	Gac/Aac	20/20	1	2	FACETS	0.143	0.118	0.171	0.143	0.118	0.171	SUBCLONAL	1	TRUE	1	0.866829688783246	2		472	645	SUCCESS
APC	324	MSKCC	GRCh37	5	112179048	112179048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	31	273	0	ENST00000257430.4:c.7757G>A	p.Ser2586Asn	p.S2586N	ENST00000257430	NM_000038.5	2586	aGt/aAt	16/16	1	2	FACETS	0.125	0.101	0.153	0.125	0.101	0.153	SUBCLONAL	1	TRUE	1	0.866829688783246	2		273	570	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672011	30672011	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	176	637	1	ENST00000376406.3:c.4949C>T	p.Pro1650Leu	p.P1650L	ENST00000376406	NM_014641.2	1650	cCc/cTc	10/15	1	2	FACETS	0.504	0.465	0.545	0.504	0.465	0.545	SUBCLONAL	1	TRUE	1	0.866829688783246	2		638	805	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511229	148511229	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	126	347	0	ENST00000320356.2:c.1673G>A	p.Cys558Tyr	p.C558Y	ENST00000320356	NM_004456.4	558	tGt/tAt	15/20	1	2	FACETS	0.545	0.496	0.597	0.545	0.496	0.597	SUBCLONAL	1	TRUE	1	0.866829688783246	2		347	533	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008970	152008970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	62	429	0	ENST00000262189.6:c.652G>A	p.Asp218Asn	p.D218N	ENST00000262189	NM_170606.2	218	Gat/Aat	5/59	1	2	FACETS	0.209	0.18	0.241	0.209	0.18	0.241	SUBCLONAL	1	TRUE	1	0.866829688783246	2		429	684	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221930	98221930	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	145	483	0	ENST00000331920.6:c.2839G>A	p.Glu947Lys	p.E947K	ENST00000331920	NM_000264.3	947	Gaa/Aaa	17/24	1	2	FACETS	0.555	0.508	0.603	0.555	0.508	0.603	SUBCLONAL	1	TRUE	1	0.866829688783246	2		483	603	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128321978	128321978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	72	603	0	ENST00000265960.3:c.782C>T	p.Thr261Ile	p.T261I	ENST00000265960	NM_001006617.1	261	aCt/aTt	6/12	1	2	FACETS	0.201	0.175	0.229	0.201	0.175	0.229	SUBCLONAL	1	TRUE	1	0.866829688783246	2		603	826	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782220	135782220	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	123	325	0	ENST00000298552.3:c.1336G>A	p.Glu446Lys	p.E446K	ENST00000298552	NM_001162426.1	446	Gag/Aag	14/23	1	2	FACETS	0.545	0.495	0.597	0.545	0.495	0.597	SUBCLONAL	1	TRUE	1	0.866829688783246	2		325	521	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932269	39932269	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	88	421	1	ENST00000378444.4:c.2330C>T	p.Pro777Leu	p.P777L	ENST00000378444	NM_001123385.1	777	cCa/cTa	4/15	1	1	FACETS	0.21	0.186	0.235	0.21	0.186	0.235	SUBCLONAL	1	TRUE	0	0.866829688783246	1		422	549	SUCCESS
AR	367	MSKCC	GRCh37	X	66766315	66766315	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196177599	NA	P-0009511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	16	155	0	ENST00000374690.3:c.1327G>A	p.Glu443Lys	p.E443K	ENST00000374690	NM_000044.3	443	Gaa/Aaa	1/8	1	1	FACETS	0.122	0.09	0.16	0.122	0.09	0.16	SUBCLONAL	1	TRUE	0	0.866829688783246	1		155	171	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0009689-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	376	412	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.298971646376945	3	FACETS	1	0.99	1	0.754	0.72	0.789	CLONAL	2	FALSE	0	0.486768836636961	3		412	849	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446324	187446324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs541016998	NA	P-0009689-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	78	266	0	ENST00000232014.4:c.1364C>T	p.Thr455Met	p.T455M	ENST00000232014	NM_001130845.1	455	aCg/aTg	6/10	0.486768836636961	6	FACETS	0.808	0.709	0.914	0.162	0.141	0.183	CLONAL	1	FALSE	1	0.486768836636961	6		266	783	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059176	27059176	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009689-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	164	649	1	ENST00000324856.7:c.1813C>T	p.Gln605Ter	p.Q605*	ENST00000324856	NM_006015.4	605	Caa/Taa	4/20	0.363372505815785	2	FACETS	0.726	0.666	0.788	0.363	0.333	0.394	SUBCLONAL	1	FALSE	0	0.486768836636961	2		650	928	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098954	178098954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553488015	NA	P-0009689-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	246	431	0	ENST00000397062.3:c.91G>A	p.Gly31Arg	p.G31R	ENST00000397062	NM_006164.4	31	Gga/Aga	2/5	0.400939268220592	4	FACETS	0.814	0.762	0.868			1	CLONAL	2	FALSE	NA	0.486768836636961	4		431	923	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057860	27057860	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009689-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	190	678	0	ENST00000324856.7:c.1568C>G	p.Ser523Cys	p.S523C	ENST00000324856	NM_006015.4	523	tCc/tGc	3/20	0.363372505815785	2	FACETS	0.811	0.75	0.875	0.406	0.375	0.438	CLONAL	1	FALSE	0	0.486768836636961	2		678	962	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99163121	99163121	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009689-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	136	526	1	ENST00000074304.5:c.1127G>T	p.Arg376Leu	p.R376L	ENST00000074304	NM_001134224.1	376	cGc/cTc	13/26	0.345909407847848	3	FACETS	0.709	0.644	0.778	0.354	0.322	0.389	SUBCLONAL	1	FALSE	1	0.486768836636961	3		527	980	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164320	47164320	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009689-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	133	504	0	ENST00000409792.3:c.1806G>C	p.Met602Ile	p.M602I	ENST00000409792	NM_014159.6	602	atG/atC	3/21	0.363372505815785	2	FACETS	0.686	0.623	0.752	0.343	0.311	0.376	SUBCLONAL	1	FALSE	0	0.486768836636961	2		504	797	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934923	9934923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009689-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	115	526	0	ENST00000330684.3:c.1367G>A	p.Cys456Tyr	p.C456Y	ENST00000330684	NM_001134407.1	456	tGc/tAc	6/13	0.363372505815785	2	FACETS	0.735	0.663	0.81	0.367	0.331	0.405	SUBCLONAL	1	FALSE	0	0.486768836636961	2		526	643	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348800	11348800	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009689-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	115	164	0	ENST00000332029.2:c.536G>T	p.Arg179Leu	p.R179L	ENST00000332029	NM_003745.1	179	cGc/cTc	2/2	0.363372505815785	2	FACETS	0.869	0.796	0.942	0.869	0.796	0.942	CLONAL	2	FALSE	0	0.486768836636961	2		164	272	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974748	21974748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009689-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	392	294	0	ENST00000304494.5:c.79del	p.Glu27ArgfsTer26	p.E27Rfs*26	ENST00000304494	NM_000077.4	27	Gag/ag	1/3	0.486768836636961	3	FACETS	0.947	0.909	0.985	0.947	0.909	0.985	CLONAL	3	FALSE	0	0.486768836636961	3		294	705	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0010207-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	365	583	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.335379845494206	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.366473749563291	2		583	948	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0010207-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	77	362	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.366473749563291	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	TRUE	0	0.366473749563291	2		363	201	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495336	149495336	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010207-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	126	467	0	ENST00000261799.4:c.3311G>A	p.Ser1104Asn	p.S1104N	ENST00000261799	NM_002609.3	1104	aGc/aAc	23/23	0.219024691715742	4	FACETS	1	0.954	1	0.544	0.492	0.598	INDETERMINATE	1	TRUE	2	0.366473749563291	4		467	864	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412164	63412164	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010207-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	328	367	0	ENST00000330258.3:c.1003C>T	p.Gln335Ter	p.Q335*	ENST00000330258	NM_152424.3	335	Cag/Tag	2/2	0.25366762193729	2	FACETS	1	0.991	1			1	CLONAL	3	TRUE	NA	0.366473749563291	2		367	528	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0010269-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	57	650	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.25394993611932	4	FACETS	0.492	0.421	0.57	0.246	0.21	0.285	SUBCLONAL	1	TRUE	2	0.310922822601165	4		651	977	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0010269-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	126	519	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.25394993611932	4	FACETS	1	0.972	1	0.596	0.539	0.656	CLONAL	1	TRUE	2	0.310922822601165	4		519	891	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302983	15302983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142492710	NA	P-0010269-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	124	724	0	ENST00000263388.2:c.467G>A	p.Arg156Gln	p.R156Q	ENST00000263388	NM_000435.2	156	cGa/cAa	4/33	0.281046963032417	3	FACETS	0.86	0.776	0.948	0.43	0.388	0.474	CLONAL	1	TRUE	1	0.310922822601165	3		724	1072	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0010689-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	151	528	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.341120622383744	3	FACETS	0.944	0.862	1	0.472	0.431	0.516	CLONAL	1	TRUE	1	0.34757154154386	3		529	1080	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994138	21994138	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010689-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	194	517	0	ENST00000579755.1:c.193G>A	p.Gly65Ser	p.G65S	ENST00000579755		65	Ggt/Agt	1/3	0.335859846900092		FACETS		0.832	0.97				CLONAL	1	TRUE	0	0.34757154154386	1		517	1025	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578286	7578286	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010689-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	186	434	0	ENST00000269305.4:c.563T>A	p.Leu188Gln	p.L188Q	ENST00000269305	NM_001126112.2	188	cTg/cAg	6/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.34757154154386	2		434	967	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0010980-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	336	344	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.516072962592903	3	FACETS	0.949	0.901	0.998	0.949	0.901	0.998	CLONAL	2	TRUE	1	0.516072962592903	3		345	863	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11552822	NA	P-0010980-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	202	439	0	ENST00000304494.5:c.250G>T	p.Asp84Tyr	p.D84Y	ENST00000304494	NM_000077.4	84	Gac/Tac	2/3	0.516072962592903	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.516072962592903	1		439	504	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222987	1222987	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010980-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	159	506	0	ENST00000326873.7:c.924G>T	p.Trp308Cys	p.W308C	ENST00000326873	NM_000455.4	308	tgG/tgT	8/10	0.516072962592903	1	FACETS	0.96	0.888	1	0.96	0.888	1	CLONAL	1	TRUE	0	0.516072962592903	1		506	476	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098601	11098601	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0010980-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	248	612	0	ENST00000358026.2:c.1118+1G>T		p.X373_splice	ENST00000358026	NM_001128849.1	373			0.516072962592903	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.516072962592903	1		612	706	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164513	47164513	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010980-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	126	282	0	ENST00000409792.3:c.1613G>T	p.Gly538Val	p.G538V	ENST00000409792	NM_014159.6	538	gGa/gTa	3/21	1	2	FACETS	0.889	0.809	0.974	0.889	0.809	0.974	CLONAL	1	TRUE	1	0.516072962592903	2		282	549	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288645	33288645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs865973372	NA	P-0010980-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	277	307	0	ENST00000374542.5:c.907G>A	p.Gly303Ser	p.G303S	ENST00000374542	NM_001141970.1	303	Ggc/Agc	3/8	0.516072962592903	3	FACETS	0.947	0.895	1	0.947	0.895	1	CLONAL	2	TRUE	1	0.516072962592903	3		307	713	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602737	10602737	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010980-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	319	740	0	ENST00000171111.5:c.841C>A	p.Leu281Met	p.L281M	ENST00000171111	NM_203500.1	281	Ctg/Atg	3/6	0.516072962592903	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.516072962592903	1		740	827	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411922	63411922	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010980-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	357	822	1	ENST00000330258.3:c.1245G>T	p.Met415Ile	p.M415I	ENST00000330258	NM_152424.3	415	atG/atT	2/2	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.516072962592903	2		823	1282	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845854	72845855	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010980-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	206	526	0	ENST00000268489.5:c.3612dup	p.Pro1205SerfsTer11	p.P1205Sfs*11	ENST00000268489	NM_006885.3	1204	-/T	6/10	1	2	FACETS	0.969	0.901	1	0.969	0.901	1	CLONAL	1	TRUE	1	0.516072962592903	2		526	824	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913381	NA	P-0011147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	340	279	0	ENST00000304494.5:c.322G>T	p.Asp108Tyr	p.D108Y	ENST00000304494	NM_000077.4	108	Gat/Tat	2/3	0.759266489713847	2	FACETS	0.993	0.96	1	0.993	0.96	1	CLONAL	2	TRUE	0	0.759266489713847	2		279	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913343	NA	P-0011147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	809	520	0	ENST00000269305.4:c.817C>A	p.Arg273Ser	p.R273S	ENST00000269305	NM_001126112.2	273	Cgt/Agt	8/11	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	2	TRUE	NA	0.759266489713847	2		520	1057	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425644	49425644	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057517992	NA	P-0011147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	565	551	1	ENST00000301067.7:c.12844C>T	p.Arg4282Ter	p.R4282*	ENST00000301067	NM_003482.3	4282	Cga/Tga	39/54	0.750309130704387	4	FACETS	0.944	0.908	0.98	0.944	0.908	0.98	CLONAL	2	TRUE	2	0.759266489713847	4		552	1387	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716082	243716082	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1303	284	557	0	ENST00000263826.5:c.1112C>A	p.Ser371Ter	p.S371*	ENST00000263826	NM_005465.4	371	tCa/tAa	10/13	0.759266489713847	4	FACETS	0.829	0.777	0.883	0.276	0.259	0.295	CLONAL	1	TRUE	1	0.759266489713847	4		557	1587	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488678	212488678	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	291	504	0	ENST00000342788.4:c.2171T>A	p.Leu724His	p.L724H	ENST00000342788	NM_005235.2	724	cTt/cAt	18/28	0.759266489713847	3	FACETS	0.938	0.883	0.995	0.469	0.441	0.498	CLONAL	1	TRUE	1	0.759266489713847	3		504	1127	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610446	215610446	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1553615089	NA	P-0011147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	255	474	0	ENST00000260947.4:c.1810G>A	p.Val604Ile	p.V604I	ENST00000260947	NM_000465.2	604	Gta/Ata	8/11	0.759266489713847	3	FACETS	0.918	0.86	0.978	0.459	0.43	0.489	CLONAL	1	TRUE	1	0.759266489713847	3		474	1009	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138375112	138375112	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	203	345	0	ENST00000289153.2:c.2947C>G	p.Arg983Gly	p.R983G	ENST00000289153	NM_006219.2	983	Cgc/Ggc	21/22	0.749483060672662	4	FACETS	1	0.969	1	0.269	0.25	0.29	CLONAL	1	TRUE	0	0.759266489713847	4		345	873	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117730753	117730753	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs576811751	NA	P-0011147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	371	756	0	ENST00000368508.3:c.281A>C	p.Glu94Ala	p.E94A	ENST00000368508	NM_002944.2	94	gAa/gCa	4/43	1	2	FACETS	0.914	0.869	0.96	0.914	0.869	0.96	CLONAL	1	TRUE	1	0.759266489713847	2		756	1069	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244406	46244406	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	351	534	1	ENST00000334344.6:c.2500C>T	p.Gln834Ter	p.Q834*	ENST00000334344	NM_152641.2	834	Caa/Taa	15/21	0.759266489713847	3	FACETS	1	0.977	1	0.527	0.499	0.556	CLONAL	1	TRUE	1	0.759266489713847	3		535	1210	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289947	15289947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779780504	NA	P-0011147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	382	602	0	ENST00000263388.2:c.3607G>A	p.Glu1203Lys	p.E1203K	ENST00000263388	NM_000435.2	1203	Gag/Aag	22/33	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.759266489713847	2		602	910	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0012160-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	165	451	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.280396462277777	3	FACETS	1	0.988	1	0.716	0.657	0.777	CLONAL	1	TRUE	1	0.280396462277777	3		451	937	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013745-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	93	315	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.938	0.842	1	0.938	0.842	1	CLONAL	1	TRUE	1	0.56	2		316	354	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0013745-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	124	456	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.882	0.802	0.965	0.882	0.802	0.965	CLONAL	1	TRUE	1	0.56	2		456	502	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252155	226252155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013745-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	29	84	0	ENST00000366813.1:c.103G>T	p.Gly35Trp	p.G35W	ENST00000366813		35	Ggg/Tgg	1/3	1	2	FACETS	0.977	0.802	1	0.977	0.802	1	CLONAL	1	TRUE	1	0.56	2		84	106	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302592	15302592	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013745-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	164	746	0	ENST00000263388.2:c.766A>T	p.Asn256Tyr	p.N256Y	ENST00000263388	NM_000435.2	256	Aac/Tac	5/33	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.56	2		746	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0013895-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	224	780	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.686303788164054	1	FACETS	0.818	0.769	0.868	0.818	0.769	0.868	CLONAL	1	TRUE	0	0.686303788164054	1		780	524	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0013895-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	113	583	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.686303788164054	2		583	305	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0013895-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	67	404	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.751	0.66	0.847	0.751	0.66	0.847	SUBCLONAL	1	TRUE	1	0.686303788164054	2		404	260	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650748	67650748	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013895-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	185	676	0	ENST00000264010.4:c.1053C>G	p.Phe351Leu	p.F351L	ENST00000264010	NM_006565.3	351	ttC/ttG	5/12	0.661055786983669	1	FACETS	0.857	0.802	0.913	0.857	0.802	0.913	CLONAL	1	TRUE	0	0.686303788164054	1		676	413	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0013895-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	113	444	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	0.661055786983669	1	FACETS	0.928	0.854	1	0.928	0.854	1	CLONAL	1	TRUE	0	0.686303788164054	1		444	233	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061191	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013895-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	88	496	0	ENST00000250448.2:c.798C>G	p.Phe266Leu	p.F266L	ENST00000250448	NM_004496.3	266	ttC/ttG	2/2	1	2	FACETS	0.926	0.831	1	0.926	0.831	1	CLONAL	1	TRUE	1	0.686303788164054	2		496	277	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772269	68772290	+	frameshift_variant	Frame_Shift_Del	DEL	ACGGTGCCCCGGCGCCACCTGG	ACGGTGCCCCGGCGCCACCTGG	-	novel	NA	P-0013895-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	205	749	1	ENST00000261769.5:c.119_140del	p.Thr40ArgfsTer9	p.T40Rfs*9	ENST00000261769	NM_004360.3	40	ACGGTGCCCCGGCGCCACCTGGag/ag	2/16	0.661055786983669	1	FACETS	0.957	0.901	1	0.957	0.901	1	CLONAL	1	TRUE	0	0.686303788164054	1		750	410	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216899	7216899	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013895-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	119	566	0	ENST00000380728.2:c.622C>T	p.Gln208Ter	p.Q208*	ENST00000380728		208	Cag/Tag	7/11	0.686303788164054	1	FACETS	0.953	0.88	1	0.953	0.88	1	CLONAL	1	TRUE	0	0.686303788164054	1		566	239	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524466	44524466	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013895-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	120	443	0	ENST00000291552.4:c.91G>C	p.Asp31His	p.D31H	ENST00000291552	NM_006758.2	31	Gac/Cac	2/8	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.686303788164054	2		443	321	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26046026	26046026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013895-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	81	359	0	ENST00000540144.1:c.388C>T	p.Arg130Cys	p.R130C	ENST00000540144	NM_003531.2	130	Cgc/Tgc	1/1	1	2	FACETS	0.731	0.65	0.816	0.731	0.65	0.816	SUBCLONAL	1	TRUE	1	0.686303788164054	2		359	323	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5081808	5081808	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013895-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	76	400	0	ENST00000381652.3:c.2518G>C	p.Asp840His	p.D840H	ENST00000381652	NM_004972.3	840	Gat/Cat	19/25	1	2	FACETS	0.817	0.725	0.913	0.817	0.725	0.913	CLONAL	1	TRUE	1	0.686303788164054	2		400	271	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0014066-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	402	629	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.651955795357898	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.653135367988256	2		630	573	SUCCESS
APC	324	MSKCC	GRCh37	5	112137030	112137030	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014066-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	375	570	0	ENST00000257430.4:c.784G>T	p.Glu262Ter	p.E262*	ENST00000257430	NM_000038.5	262	Gaa/Taa	8/16	0.651955795357898	2	FACETS	0.967	0.93	1	0.967	0.93	1	CLONAL	2	TRUE	0	0.653135367988256	2		570	594	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225788	26225788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs911990384	NA	P-0014066-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	121	409	0	ENST00000360408.1:c.406G>A	p.Ala136Thr	p.A136T	ENST00000360408	NM_003532.2	136	Gcg/Acg	1/1	0.653135367988256	3	FACETS	0.884	0.802	0.97	0.442	0.401	0.485	CLONAL	1	TRUE	1	0.653135367988256	3		409	556	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0014468-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	59	487	2	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.265402965703851	4	FACETS	1	0.966	1	0.706	0.61	0.811	CLONAL	1	TRUE	2	0.271628896698406	4		489	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0014468-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	91	872	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.271628896698406	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	2	TRUE	0	0.271628896698406	2		872	328	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014468-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	27	660	0	ENST00000304494.5:c.247C>A	p.His83Asn	p.H83N	ENST00000304494	NM_000077.4	83	Cac/Aac	2/3	0.214431778032053	1	FACETS	0.795	0.637	0.975	0.795	0.637	0.975	CLONAL	1	TRUE	0	0.271628896698406	1		660	216	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864262	151864262	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014468-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	49	507	0	ENST00000262189.6:c.9719A>C	p.Gln3240Pro	p.Q3240P	ENST00000262189	NM_170606.2	3240	cAg/cCg	42/59	0.160938505398931	4	FACETS	0.813	0.694	0.943	0.813	0.694	0.943	INDETERMINATE	2	TRUE	2	0.271628896698406	4		507	282	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0014997-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	545	487	2	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.47856689706633	7	FACETS	1	0.984	1	0.788	0.755	0.82	CLONAL	3	TRUE	3	0.47856689706633	7		489	1588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0014997-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	292	500	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.382146078560742	3	FACETS	1	0.961	1	0.679	0.643	0.717	CLONAL	2	TRUE	0	0.47856689706633	3		500	742	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436117	51436117	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014997-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	79	387	0	ENST00000262662.1:c.77A>G	p.Gln26Arg	p.Q26R	ENST00000262662		26	cAa/cGa	3/4	0.359223568342779	6	FACETS	0.724	0.635	0.819	0.181	0.158	0.205	SUBCLONAL	1	TRUE	2	0.47856689706633	6		387	893	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435692	110435692	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014997-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	106	525	0	ENST00000375856.3:c.2709C>A	p.Ser903Arg	p.S903R	ENST00000375856	NM_003749.2	903	agC/agA	1/2	0.428967383491718	3	FACETS	0.885	0.795	0.981	0.443	0.397	0.491	CLONAL	1	TRUE	1	0.47856689706633	3		525	620	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577508	7577508	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060501201	NA	P-0016317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	397	536	0	ENST00000269305.4:c.773A>G	p.Glu258Gly	p.E258G	ENST00000269305	NM_001126112.2	258	gAa/gGa	7/11	0.518102212535442	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.518102212535442	2		536	718	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726275	46726275	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	134	565	0	ENST00000371975.4:c.469C>G	p.Gln157Glu	p.Q157E	ENST00000371975	NM_003579.3	157	Cag/Gag	6/18	0.318943523285115	4	FACETS	0.768	0.696	0.843	0.384	0.348	0.422	SUBCLONAL	1	TRUE	2	0.518102212535442	4		565	1023	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46733270	46733270	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	129	461	0	ENST00000371975.4:c.1031C>G	p.Ser344Cys	p.S344C	ENST00000371975	NM_003579.3	344	tCc/tGc	9/18	0.318943523285115	4	FACETS	0.919	0.833	1	0.459	0.416	0.505	CLONAL	1	TRUE	2	0.518102212535442	4		461	823	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636116	28636116	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs758850662	NA	P-0016317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	404	541	0	ENST00000241453.7:c.256T>C	p.Ser86Pro	p.S86P	ENST00000241453	NM_004119.2	86	Tct/Cct	3/24	0.243223599399487	6	FACETS	1	0.987	1	0.554	0.526	0.582	INDETERMINATE	2	TRUE	2	0.518102212535442	6		541	1434	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772850	135772850	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	479	630	0	ENST00000298552.3:c.2773G>T	p.Glu925Ter	p.E925*	ENST00000298552	NM_001162426.1	925	Gaa/Taa	21/23	0.518102212535442	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.518102212535442	2		630	793	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476264	88476264	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016507-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	337	632	1	ENST00000360948.2:c.1868G>A	p.Gly623Glu	p.G623E	ENST00000360948	NM_001012338.2	623	gGa/gAa	15/19	0.423519523902318	4	FACETS	0.962	0.91	1	0.642	0.607	0.677	CLONAL	2	TRUE	1	0.423519523902318	4		633	1177	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751095	57751141	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAAGCCACAGTACTTACATCCATGAGGTTCTCCTCCATGTAATGAGA	AAAGCCACAGTACTTACATCCATGAGGTTCTCCTCCATGTAATGAGA	-	novel	NA	P-0016507-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	60	280	0	ENST00000274289.3:c.1726_1755+17del		p.X576_splice	ENST00000274289	NM_006622.3	576		12/14	1	2	FACETS	0.703	0.608	0.806	0.703	0.608	0.806	SUBCLONAL	1	TRUE	1	0.423519523902318	2		280	403	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971155	21971164	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCCGTGGA	GCGCCGTGGA	-	novel	NA	P-0016507-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	244	378	0	ENST00000304494.5:c.194_203del	p.Leu65ArgfsTer78	p.L65Rfs*78	ENST00000304494	NM_000077.4	65	cTCCACGGCGCg/cg	2/3	0.423519523902318	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.423519523902318	2		378	477	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0017386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	1385	451	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.516222300915824	15	FACETS	0.984	0.965	1	0.902	0.884	0.92	CLONAL	11	TRUE	3	0.516222300915824	15		451	2159	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577088	7577088	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1204379654	NA	P-0017386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	695	656	0	ENST00000269305.4:c.850A>C	p.Thr284Pro	p.T284P	ENST00000269305	NM_001126112.2	284	Aca/Cca	8/11	0.505012360471364	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	0	0.516222300915824	3		656	1128	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521327	8521327	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	246	265	0	ENST00000356435.5:c.911C>G	p.Ala304Gly	p.A304G	ENST00000356435		304	gCt/gGt	9/35	0.516222300915824	2	FACETS	0.999	0.946	1	0.999	0.946	1	CLONAL	2	TRUE	0	0.516222300915824	2		265	477	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717684	89717684	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0017386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	290	360	0	ENST00000371953.3:c.709A>T	p.Lys237Ter	p.K237*	ENST00000371953	NM_000314.4	237	Aag/Tag	7/9	0.516222300915824	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.516222300915824	2		360	551	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143087	7143087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	167	517	0	ENST00000302850.5:c.2282G>A	p.Arg761His	p.R761H	ENST00000302850	NM_000208.2	761	cGc/cAc	12/22	0.426189891141781	4	FACETS	0.989	0.908	1			1	CLONAL	1	TRUE	NA	0.516222300915824	4		517	992	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0017971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	365	1030	3	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	0.467265745581925	3	FACETS	0.905	0.861	0.95			1	CLONAL	2	TRUE	NA	0.512698987637468	3		1033	988	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128559	30128559	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	164	842	0	ENST00000263025.4:c.823A>G	p.Met275Val	p.M275V	ENST00000263025	NM_002746.2	275	Atg/Gtg	6/9	1	2	FACETS	0.917	0.844	0.992	0.917	0.844	0.992	CLONAL	1	TRUE	1	0.512698987637468	2		842	698	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56872946	56872951	+	inframe_deletion	In_Frame_Del	DEL	GAGTAT	GAGTAT	-	novel	NA	P-0017971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	103	685	0	ENST00000308159.5:c.2101_2106del	p.Glu701_Tyr702del	p.E701_Y702del	ENST00000308159	NM_014669.4	701	GAGTAT/-	19/22	1	2	FACETS	0.913	0.822	1	0.913	0.822	1	CLONAL	1	TRUE	1	0.512698987637468	2		685	440	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441261	52441261	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	178	822	0	ENST00000460680.1:c.509T>G	p.Phe170Cys	p.F170C	ENST00000460680	NM_004656.3	170	tTt/tGt	7/17	0.512698987637468	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.512698987637468	1		822	486	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120219	94120219	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	78	510	3	ENST00000369303.4:c.832C>A	p.Pro278Thr	p.P278T	ENST00000369303	NM_004440.3	278	Ccc/Acc	3/17	0.512698987637468	1	FACETS	0.901	0.803	1	0.901	0.803	1	CLONAL	1	TRUE	0	0.512698987637468	1		513	251	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0018092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	114	575	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.342084687408973	2		575	645	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579408	7579460	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTG	CAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTG	-	rs1555526610	NA	P-0018092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	193	627	0	ENST00000269305.4:c.227_279del	p.Ala76ValfsTer55	p.A76Vfs*55	ENST00000269305	NM_001126112.2	76	gCACCAGCAGCTCCTACACCGGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTG/g	4/11	0.263471046411315	2	FACETS	0.919	0.855	0.985	0.919	0.855	0.985	CLONAL	2	TRUE	0	0.342084687408973	2		627	614	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509084	66509085	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	25	321	0	ENST00000273854.3:c.242dup	p.Asn81LysfsTer8	p.N81Kfs*8	ENST00000273854	NM_004439.5	81	aat/aaAt	2/18	1	2	FACETS	0.425	0.335	0.528	0.425	0.335	0.528	SUBCLONAL	1	TRUE	1	0.342084687408973	2		321	344	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023381	27023381	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	75	390	0	ENST00000324856.7:c.487del	p.Ala163ProfsTer69	p.A163Pfs*69	ENST00000324856	NM_006015.4	163	Gcc/cc	1/20	1	2	FACETS	0.985	0.867	1	0.985	0.867	1	CLONAL	1	TRUE	1	0.342084687408973	2		390	445	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861825	57861825	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1430036137	NA	P-0018092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	78	558	0	ENST00000228682.2:c.1126C>A	p.Pro376Thr	p.P376T	ENST00000228682	NM_005269.2	376	Cct/Act	10/12	1	2	FACETS	0.919	0.81	1	0.919	0.81	1	CLONAL	1	TRUE	1	0.342084687408973	2		558	496	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106543594	106543594	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	74	502	0	ENST00000369096.4:c.396G>C	p.Arg132Ser	p.R132S	ENST00000369096	NM_001198.3	132	agG/agC	3/7	0.293475078100291	2	FACETS	0.909	0.798	1	0.454	0.399	0.514	CLONAL	1	TRUE	0	0.340064802298275	2		502	479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	262	897	0	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	0.272352665667039	2	FACETS	0.817	0.767	0.869	0.817	0.767	0.869	CLONAL	2	TRUE	0	0.340064802298275	2		897	943	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285243	212285243	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1332523099	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	92	772	1	ENST00000342788.4:c.3058G>A	p.Glu1020Lys	p.E1020K	ENST00000342788	NM_005235.2	1020	Gag/Aag	25/28	0.277100586010506	4	FACETS	0.803	0.712	0.9	0.401	0.356	0.45	CLONAL	1	TRUE	2	0.340064802298275	4		773	903	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293295	91293295	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	61	397	0	ENST00000355112.3:c.797G>C	p.Arg266Thr	p.R266T	ENST00000355112	NM_000057.2	266	aGa/aCa	3/22	0.277063619941083	4	FACETS	0.74	0.638	0.851	0.247	0.212	0.284	SUBCLONAL	1	TRUE	1	0.340064802298275	4		397	650	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663346	227663346	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1024227751	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	37	467	0	ENST00000305123.5:c.109G>C	p.Glu37Gln	p.E37Q	ENST00000305123	NM_005544.2	37	Gag/Cag	1/2	0.275954490913902	4	FACETS	0.436	0.358	0.523			1	SUBCLONAL	1	TRUE	NA	0.340064802298275	4		467	669	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46738417	46738417	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	189	790	0	ENST00000371975.4:c.1318G>T	p.Gly440Cys	p.G440C	ENST00000371975	NM_003579.3	440	Ggc/Tgc	12/18	0.272352665667039	2	FACETS	0.793	0.735	0.852	0.793	0.735	0.852	SUBCLONAL	2	TRUE	0	0.340064802298275	2		790	701	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439671	51439671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	74	508	0	ENST00000262662.1:c.236G>T	p.Arg79Ile	p.R79I	ENST00000262662		79	aGa/aTa	4/4	0.272352665667039	2	FACETS	0.858	0.753	0.971	0.429	0.376	0.486	CLONAL	1	TRUE	0	0.340064802298275	2		508	507	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248366	59248366	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	75	288	0	ENST00000371222.2:c.377C>T	p.Thr126Met	p.T126M	ENST00000371222	NM_002228.3	126	aCg/aTg	1/1	0.272352665667039	2	FACETS	1	0.974	1	0.7	0.619	0.786	CLONAL	1	TRUE	0	0.340064802298275	2		288	315	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65349065	65349065	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	102	706	0	ENST00000342505.4:c.100C>T	p.Pro34Ser	p.P34S	ENST00000342505	NM_002227.2	34	Cca/Tca	3/25	0.272352665667039	2	FACETS	0.801	0.716	0.891	0.4	0.358	0.446	CLONAL	1	TRUE	0	0.340064802298275	2		706	749	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741901	162741901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	157	575	0	ENST00000367921.3:c.1592G>A	p.Gly531Glu	p.G531E	ENST00000367921	NM_006182.2	531	gGa/gAa	13/18	0.32745619723194	4	FACETS	0.848	0.778	0.92	0.565	0.518	0.613	CLONAL	2	TRUE	1	0.340064802298275	4		575	730	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94169032	94169032	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1264567817	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	175	598	1	ENST00000323929.3:c.1960G>T	p.Asp654Tyr	p.D654Y	ENST00000323929	NM_005591.3	654	Gac/Tac	18/20	0.277063619941083	4	FACETS	0.787	0.725	0.852	0.525	0.483	0.568	SUBCLONAL	2	TRUE	1	0.340064802298275	4		599	876	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998841	100998841	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	91	899	0	ENST00000325455.5:c.961C>G	p.Arg321Gly	p.R321G	ENST00000325455	NM_001202474.3	321	Cgg/Ggg	1/8	0.277063619941083	4	FACETS	0.769	0.681	0.862	0.256	0.227	0.288	SUBCLONAL	1	TRUE	1	0.340064802298275	4		899	933	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981889	101981889	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	128	1005	0	ENST00000282441.5:c.310C>G	p.His104Asp	p.H104D	ENST00000282441	NM_001130145.2	104	Cac/Gac	1/9	0.277063619941083	4	FACETS	0.854	0.772	0.941	0.285	0.257	0.314	CLONAL	1	TRUE	1	0.340064802298275	4		1005	1181	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196122	108196122	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	155	812	1	ENST00000278616.4:c.6658C>G	p.Gln2220Glu	p.Q2220E	ENST00000278616	NM_000051.3	2220	Cag/Gag	46/63	0.277063619941083	4	FACETS	1	0.986	1	0.466	0.427	0.508	CLONAL	1	TRUE	1	0.340064802298275	4		813	873	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	461416	461416	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	124	768	0	ENST00000399788.2:c.1104G>C	p.Glu368Asp	p.E368D	ENST00000399788	NM_001042603.1	368	gaG/gaC	9/28	0.340064802298275	6	FACETS	0.945	0.853	1			1	CLONAL	1	TRUE	NA	0.340064802298275	6		768	1296	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437211	49437211	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	97	767	0	ENST00000301067.7:c.5468G>C	p.Gly1823Ala	p.G1823A	ENST00000301067	NM_003482.3	1823	gGa/gCa	24/54	0.274637520311558	3	FACETS	0.81	0.722	0.904	0.405	0.361	0.452	CLONAL	1	TRUE	1	0.340064802298275	3		767	824	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112910751	112910751	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	109	765	0	ENST00000351677.2:c.760C>G	p.Leu254Val	p.L254V	ENST00000351677	NM_002834.3	254	Cta/Gta	7/16	0.272352665667039	2	FACETS	0.889	0.799	0.985	0.445	0.399	0.493	CLONAL	1	TRUE	0	0.340064802298275	2		765	721	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601288	28601288	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	303	840	2	ENST00000241453.7:c.2144C>A	p.Thr715Lys	p.T715K	ENST00000241453	NM_004119.2	715	aCa/aAa	17/24	0.269435947049884	3	FACETS	1	0.989	1	0.785	0.742	0.829	CLONAL	2	TRUE	0	0.340064802298275	3		842	885	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437616	110437616	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	104	883	0	ENST00000375856.3:c.785C>G	p.Ser262Trp	p.S262W	ENST00000375856	NM_003749.2	262	tCg/tGg	1/2	0.293475078100291	2	FACETS	0.783	0.701	0.87	0.392	0.35	0.435	SUBCLONAL	1	TRUE	0	0.340064802298275	2		883	781	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472658	88472659	+	missense_variant	Missense_Mutation	DNP	CA	CA	AT	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	66	406	0	ENST00000360948.2:c.1896_1897delinsAT	p.His632_Gly633delinsGlnTrp	p.H632_G633delinsQW	ENST00000360948	NM_001012338.2	632	caTGgg/caATgg	16/19	0.277063619941083	4	FACETS	0.98	0.851	1	0.327	0.283	0.373	CLONAL	1	TRUE	1	0.340064802298275	4		406	531	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680742	88680742	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	127	848	0	ENST00000360948.2:c.515A>T	p.Gln172Leu	p.Q172L	ENST00000360948	NM_001012338.2	172	cAg/cTg	6/19	0.277063619941083	4	FACETS	0.911	0.823	1	0.304	0.274	0.335	CLONAL	1	TRUE	1	0.340064802298275	4		848	1099	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779388	3779388	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	67	658	0	ENST00000262367.5:c.5660C>A	p.Ser1887Ter	p.S1887*	ENST00000262367	NM_004380.2	1887	tCa/tAa	31/31	0.272352665667039	2	FACETS	0.731	0.636	0.834	0.366	0.318	0.417	SUBCLONAL	1	TRUE	0	0.340064802298275	2		658	539	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81892769	81892769	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	86	624	0	ENST00000359376.3:c.479+1G>T		p.X160_splice	ENST00000359376	NM_002661.3	160			1	2	FACETS	0.836	0.74	0.938	0.836	0.74	0.938	CLONAL	1	TRUE	1	0.340064802298275	2		624	605	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81922868	81922868	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	91	515	1	ENST00000359376.3:c.857T>G	p.Phe286Cys	p.F286C	ENST00000359376	NM_002661.3	286	tTt/tGt	10/33	1	2	FACETS	0.991	0.882	1	0.991	0.882	1	CLONAL	1	TRUE	1	0.340064802298275	2		516	540	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925180	81925180	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs759069790	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	113	645	0	ENST00000359376.3:c.971C>G	p.Ser324Cys	p.S324C	ENST00000359376	NM_002661.3	324	tCc/tGc	11/33	1	2	FACETS	0.869	0.782	0.961	0.869	0.782	0.961	CLONAL	1	TRUE	1	0.340064802298275	2		645	765	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56787224	56787224	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	151	705	0	ENST00000337432.4:c.710G>T	p.Arg237Leu	p.R237L	ENST00000337432	NM_058216.2	237	cGa/cTa	5/9	0.320742155463988	3	FACETS	1	0.985	1	0.676	0.618	0.735	CLONAL	1	TRUE	1	0.340064802298275	3		705	769	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240284	5240284	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	178	980	0	ENST00000357368.4:c.1630T>C	p.Ser544Pro	p.S544P	ENST00000357368	NM_002850.3	544	Tcc/Ccc	12/38	0.272352665667039	2	FACETS	1	0.983	1	0.619	0.571	0.669	CLONAL	1	TRUE	0	0.340064802298275	2		980	846	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274221	5274221	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	240	918	0	ENST00000357368.4:c.226C>G	p.Gln76Glu	p.Q76E	ENST00000357368	NM_002850.3	76	Cag/Gag	3/38	0.272352665667039	2	FACETS	0.859	0.804	0.915	0.859	0.804	0.915	CLONAL	2	TRUE	0	0.340064802298275	2		918	822	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212164	36212164	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs747737343	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	60	538	0	ENST00000222270.7:c.1915A>G	p.Thr639Ala	p.T639A	ENST00000222270	NM_014727.1	639	Acc/Gcc	3/37	0.236591280873298	5	FACETS	0.857	0.738	0.986	0.286	0.246	0.329	CLONAL	1	TRUE	2	0.340064802298275	5		538	622	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085894	16085894	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	67	722	0	ENST00000281043.3:c.1070G>C	p.Arg357Pro	p.R357P	ENST00000281043	NM_005378.4	357	cGt/cCt	3/3	0.320742155463988	3	FACETS	0.587	0.509	0.672	0.294	0.254	0.336	SUBCLONAL	1	TRUE	1	0.340064802298275	3		722	785	SUCCESS
ALK	238	MSKCC	GRCh37	2	29448368	29448368	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	176	1021	2	ENST00000389048.3:c.3131T>A	p.Leu1044His	p.L1044H	ENST00000389048	NM_004304.4	1044	cTc/cAc	19/29	0.320742155463988	3	FACETS	0.945	0.869	1	0.473	0.434	0.513	CLONAL	1	TRUE	1	0.340064802298275	3		1023	1281	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609582	46609582	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	107	948	0	ENST00000263734.3:c.2306C>G	p.Pro769Arg	p.P769R	ENST00000263734	NM_001430.4	769	cCc/cGc	15/16	0.320742155463988	3	FACETS	0.682	0.611	0.759	0.341	0.305	0.38	SUBCLONAL	1	TRUE	1	0.340064802298275	3		948	1079	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99169382	99169382	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	82	573	0	ENST00000074304.5:c.1312G>T	p.Asp438Tyr	p.D438Y	ENST00000074304	NM_001134224.1	438	Gac/Tac	15/26	0.320742155463988	3	FACETS	0.789	0.696	0.89	0.395	0.348	0.445	SUBCLONAL	1	TRUE	1	0.340064802298275	3		573	715	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634777	158634777	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	61	619	0	ENST00000263640.3:c.409C>G	p.Leu137Val	p.L137V	ENST00000263640	NM_001105.4	137	Ctt/Gtt	5/11	0.277100586010506	4	FACETS	0.592	0.51	0.682	0.296	0.255	0.341	SUBCLONAL	1	TRUE	2	0.340064802298275	4		619	812	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566848	212566848	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	66	388	0	ENST00000342788.4:c.1333C>A	p.Leu445Ile	p.L445I	ENST00000342788	NM_005235.2	445	Cta/Ata	12/28	0.277100586010506	4	FACETS	1	0.956	1	0.615	0.535	0.7	CLONAL	1	TRUE	2	0.340064802298275	4		388	423	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587239	212587239	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	121	587	0	ENST00000342788.4:c.762C>G	p.Asp254Glu	p.D254E	ENST00000342788	NM_005235.2	254	gaC/gaG	7/28	0.277100586010506	4	FACETS	1	0.98	1	0.659	0.595	0.725	CLONAL	1	TRUE	2	0.340064802298275	4		587	724	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376164	225376164	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	124	912	0	ENST00000264414.4:c.790G>T	p.Val264Phe	p.V264F	ENST00000264414	NM_003590.4	264	Gtt/Ttt	6/16	NA	2	FACETS	0.9	0.815	0.991			1	INDETERMINATE	1	TRUE	NA	0.340064802298275	2		912	810	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378309	225378309	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	105	695	0	ENST00000264414.4:c.586G>T	p.Glu196Ter	p.E196*	ENST00000264414	NM_003590.4	196	Gaa/Taa	5/16	NA	2	FACETS	0.947	0.85	1			1	INDETERMINATE	1	TRUE	NA	0.340064802298275	2		695	652	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714381	40714383	+	missense_variant	Missense_Mutation	TNP	CAG	CAG	AGT	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	67	625	1	ENST00000373198.4:c.4014_4016delinsACT	p.Cys1339Leu	p.C1339L	ENST00000373198	NM_133170.3	1338	atCTGt/atACTt	29/32	0.320742155463988	3	FACETS	0.581	0.504	0.665	0.291	0.252	0.333	SUBCLONAL	1	TRUE	1	0.340064802298275	3		626	793	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306677	41306677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs724159835	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	97	684	0	ENST00000373198.4:c.982C>G	p.Arg328Gly	p.R328G	ENST00000373198	NM_133170.3	328	Cgc/Ggc	7/32	0.320742155463988	3	FACETS	0.774	0.689	0.865	0.387	0.344	0.433	SUBCLONAL	1	TRUE	1	0.340064802298275	3		684	862	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319506	62319506	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1641	191	865	2	ENST00000360203.5:c.1610G>T	p.Cys537Phe	p.C537F	ENST00000360203	NM_001283009.1	537	tGc/tTc	19/35	0.340064802298275	9	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.340064802298275	9		867	1832	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436631	52436631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	96	795	0	ENST00000460680.1:c.2043G>A	p.Met681Ile	p.M681I	ENST00000460680	NM_004656.3	681	atG/atA	16/17	0.293475078100291	2	FACETS	0.789	0.703	0.88	0.394	0.351	0.44	SUBCLONAL	1	TRUE	0	0.340064802298275	2		795	716	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498442	89498442	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765969815	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	113	451	1	ENST00000336596.2:c.2414G>A	p.Ser805Asn	p.S805N	ENST00000336596	NM_005233.5	805	aGc/aAc	14/17	0.293475078100291	2	FACETS	1	0.98	1	0.67	0.606	0.737	CLONAL	1	TRUE	0	0.340064802298275	2		452	496	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200121	128200121	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	112	860	0	ENST00000341105.2:c.1184C>G	p.Thr395Ser	p.T395S	ENST00000341105	NM_032638.4	395	aCt/aGt	6/6	0.306711516330569	3	FACETS	0.748	0.671	0.829	0.249	0.223	0.277	SUBCLONAL	1	TRUE	0	0.340064802298275	3		860	1031	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670399	134670399	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	67	607	0	ENST00000398015.3:c.310G>T	p.Gly104Ter	p.G104*	ENST00000398015	NM_004441.4	104	Gga/Tga	3/16	0.306711516330569	3	FACETS	0.617	0.535	0.706	0.206	0.178	0.236	SUBCLONAL	1	TRUE	0	0.340064802298275	3		607	747	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599301	55599301	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	114	720	0	ENST00000288135.5:c.2427T>A	p.Cys809Ter	p.C809*	ENST00000288135	NM_000222.2	809	tgT/tgA	17/21	0.275954490913902	4	FACETS	1	0.922	1			1	CLONAL	1	TRUE	NA	0.340064802298275	4		720	873	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803432	32803432	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	120	891	0	ENST00000374899.4:c.727G>T	p.Glu243Ter	p.E243*	ENST00000374899	NM_018833.2	243	Gag/Tag	4/12	0.274637520311558	3	FACETS	0.832	0.75	0.918	0.416	0.375	0.459	CLONAL	1	TRUE	1	0.340064802298275	3		891	993	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501294	140501294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	85	658	0	ENST00000288602.6:c.778C>T	p.Arg260Cys	p.R260C	ENST00000288602	NM_004333.4	260	Cgc/Tgc	6/18	1	2	FACETS	0.853	0.755	0.958	0.853	0.755	0.958	CLONAL	1	TRUE	1	0.340064802298275	2		658	586	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873944	151873944	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1191272660	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	72	711	0	ENST00000262189.6:c.8594G>C	p.Gly2865Ala	p.G2865A	ENST00000262189	NM_170606.2	2865	gGa/gCa	38/59	1	2	FACETS	0.596	0.52	0.677	0.596	0.52	0.677	SUBCLONAL	1	TRUE	1	0.340064802298275	2		711	711	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285909	38285909	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs775228360	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	97	695	1	ENST00000425967.3:c.502T>A	p.Ser168Thr	p.S168T	ENST00000425967	NM_001174067.1	168	Tct/Act	5/19	0.340064802298275	6	FACETS	0.79	0.702	0.884			1	SUBCLONAL	1	TRUE	NA	0.340064802298275	6		696	1213	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5070016	5070016	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	111	712	0	ENST00000381652.3:c.1605G>C	p.Met535Ile	p.M535I	ENST00000381652	NM_004972.3	535	atG/atC	12/25	0.29800699096628	1	FACETS	0.937	0.845	1	0.937	0.845	1	CLONAL	1	TRUE	0	0.340064802298275	1		712	578	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563419	87563419	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	205	800	2	ENST00000277120.3:c.1807C>A	p.Arg603Ser	p.R603S	ENST00000277120		603	Cgt/Agt	16/19	0.272352665667039	2	FACETS	0.773	0.719	0.829	0.773	0.719	0.829	SUBCLONAL	2	TRUE	0	0.340064802298275	2		802	780	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209669	98209669	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	61	632	0	ENST00000331920.6:c.3869C>A	p.Ser1290Ter	p.S1290*	ENST00000331920	NM_000264.3	1290	tCa/tAa	23/24	0.272352665667039	2	FACETS	0.54	0.466	0.622	0.27	0.233	0.311	SUBCLONAL	1	TRUE	0	0.340064802298275	2		632	664	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412996	63412996	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs965178548	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	127	557	1	ENST00000330258.3:c.171G>T	p.Met57Ile	p.M57I	ENST00000330258	NM_152424.3	57	atG/atT	2/2	0.275954490913902	2	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.340064802298275	2		558	608	SUCCESS
AR	367	MSKCC	GRCh37	X	66942718	66942718	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	108	506	3	ENST00000374690.3:c.2499G>T	p.Met833Ile	p.M833I	ENST00000374690	NM_000044.3	833	atG/atT	7/8	0.275954490913902	2	FACETS	1	0.97	1			1	CLONAL	1	TRUE	NA	0.340064802298275	2		509	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0018403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	433	483	1	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	0.776162428817175	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.776162428817175	1		484	584	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557642	95557642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	477	526	1	ENST00000393063.1:c.5425G>A	p.Gly1809Arg	p.G1809R	ENST00000393063	NM_030621.3	1809	Ggg/Agg	26/28	0.184289702519169	3	FACETS	0.904	0.869	0.938	0.602	0.579	0.626	INDETERMINATE	2	TRUE	0	0.776162428817175	3		527	944	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784440	9784440	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	167	482	0	ENST00000377346.4:c.2825T>C	p.Ile942Thr	p.I942T	ENST00000377346	NM_005026.3	942	aTt/aCt	22/24	0.274398558286837	2	FACETS	0.6	0.553	0.649	0.3	0.276	0.325	INDETERMINATE	1	TRUE	0	0.776162428817175	2		482	717	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226573273	226573273	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	414	484	1	ENST00000366794.5:c.943G>T	p.Val315Phe	p.V315F	ENST00000366794	NM_001618.3	315	Gtc/Ttc	7/23	0.274398558286837	2	FACETS	1	0.996	1	0.695	0.667	0.722	INDETERMINATE	1	TRUE	0	0.776162428817175	2		485	768	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104375131	104375131	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	354	499	0	ENST00000369902.3:c.1129T>C	p.Ser377Pro	p.S377P	ENST00000369902	NM_016169.3	377	Tcc/Ccc	9/12	0.433472750264803	4	FACETS	1	0.987	1	1	0.987	1	INDETERMINATE	2	TRUE	2	0.776162428817175	4		499	744	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201860	67201860	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	359	493	0	ENST00000312629.5:c.1060G>A	p.Asp354Asn	p.D354N	ENST00000312629	NM_003952.2	354	Gac/Aac	13/15	0.245132963583348	3	FACETS	0.893	0.853	0.933	0.595	0.569	0.622	INDETERMINATE	2	TRUE	0	0.776162428817175	3		493	719	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936803	32936803	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	176	345	0	ENST00000380152.3:c.7949A>G	p.Glu2650Gly	p.E2650G	ENST00000380152		2650	gAa/gGa	17/27	0.776162428817175	4	FACETS	0.678	0.623	0.735	0.226	0.207	0.245	SUBCLONAL	1	TRUE	1	0.776162428817175	4		345	1188	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557538	95557538	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0018403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	126	265	0	ENST00000393063.1:c.5527+2T>C		p.X1843_splice	ENST00000393063	NM_030621.3	1843			0.184289702519169	3	FACETS	0.978	0.891	1	0.326	0.297	0.356	INDETERMINATE	1	TRUE	0	0.776162428817175	3		265	461	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90634864	90634864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	342	396	0	ENST00000330062.3:c.128G>A	p.Arg43Lys	p.R43K	ENST00000330062	NM_002168.2	43	aGg/aAg	2/11	0.240074743906007	4	FACETS	1	0.975	1	1	0.975	1	INDETERMINATE	2	TRUE	2	0.776162428817175	4		396	755	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223509	36223509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867769309	NA	P-0018403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	337	558	3	ENST00000222270.7:c.6059C>T	p.Pro2020Leu	p.P2020L	ENST00000222270	NM_014727.1	2020	cCg/cTg	28/37	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.776162428817175	2		561	732	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799261	42799261	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	254	517	0	ENST00000575354.2:c.4745G>A	p.Gly1582Glu	p.G1582E	ENST00000575354	NM_015125.3	1582	gGg/gAg	20/20	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.776162428817175	2		517	652	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191065	185191065	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	226	550	0	ENST00000265026.3:c.1946C>T	p.Ser649Phe	p.S649F	ENST00000265026	NM_004721.4	649	tCc/tTc	11/14	0.478741778940738	3	FACETS	0.768	0.715	0.823	0.256	0.238	0.275	SUBCLONAL	1	TRUE	0	0.776162428817175	3		550	1052	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446181	187446181	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1488877472	NA	P-0018403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	256	663	0	ENST00000232014.4:c.1507G>A	p.Glu503Lys	p.E503K	ENST00000232014	NM_001130845.1	503	Gag/Aag	6/10	0.478741778940738	3	FACETS	0.694	0.649	0.741	0.231	0.216	0.247	SUBCLONAL	1	TRUE	0	0.776162428817175	3		663	1319	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637423	176637423	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	251	412	0	ENST00000439151.2:c.2023A>G	p.Met675Val	p.M675V	ENST00000439151	NM_022455.4	675	Atg/Gtg	5/23	0.274398558286837	2	FACETS	1	0.989	1	0.588	0.555	0.621	INDETERMINATE	1	TRUE	0	0.776162428817175	2		412	550	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169251	32169251	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	222	486	0	ENST00000375023.3:c.3782A>G	p.Asp1261Gly	p.D1261G	ENST00000375023	NM_004557.3	1261	gAt/gGt	22/30	0.754367305418649	3	FACETS	1	0.947	1	0.508	0.474	0.543	CLONAL	1	TRUE	1	0.776162428817175	3		486	781	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226039	53226039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	292	646	0	ENST00000375401.3:c.2810C>T	p.Thr937Ile	p.T937I	ENST00000375401	NM_004187.3	937	aCa/aTa	19/26	1	2	FACETS	0.927	0.875	0.979	0.927	0.875	0.979	CLONAL	1	TRUE	1	0.776162428817175	2		646	812	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107299	193107299	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	128	188	0	ENST00000367435.3:c.508A>C	p.Ile170Leu	p.I170L	ENST00000367435	NM_024529.4	170	Att/Ctt	6/17	0.274398558286837	2	FACETS	0.73	0.666	0.796	0.365	0.333	0.398	INDETERMINATE	1	TRUE	0	0.776162428817175	2		188	452	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18276978	18276978	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	53	321	0	ENST00000222254.8:c.1425G>T	p.Gln475His	p.Q475H	ENST00000222254	NM_005027.3	475	caG/caT	12/16	0.57736778916034	3	FACETS	0.302	0.257	0.351	0.151	0.128	0.176	SUBCLONAL	1	TRUE	1	0.776162428817175	3		321	628	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	523	315	1				ENST00000310581	NM_198253.2	-/1132			0.259543701330285	4	FACETS	0.888	0.855	0.922	0.888	0.855	0.922	CLONAL	4	TRUE	0	0.370865990785465	4		316	1088	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0018814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	360	344	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.370865990785465	2	FACETS	0.971	0.922	1	0.971	0.922	1	CLONAL	2	TRUE	0	0.370865990785465	2		345	1000	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746117	162746117	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	141	406	1	ENST00000367921.3:c.2240C>A	p.Ala747Glu	p.A747E	ENST00000367921	NM_006182.2	747	gCa/gAa	16/18	0.367778939234001	3	FACETS	1	0.953	1	0.535	0.487	0.585	CLONAL	1	TRUE	1	0.370865990785465	3		407	843	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373683	118373683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	197	676	0	ENST00000534358.1:c.7076C>T	p.Ser2359Leu	p.S2359L	ENST00000534358	NM_005933.3	2359	tCa/tTa	27/36	0.367778939234001	3	FACETS	1	0.935	1	0.506	0.468	0.546	CLONAL	1	TRUE	1	0.370865990785465	3		676	1244	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281146	49281146	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	111	893	1	ENST00000282018.3:c.193C>A	p.Gln65Lys	p.Q65K	ENST00000282018	NM_020377.2	65	Cag/Aag	1/1	1	2	FACETS	0.547	0.49	0.607	0.547	0.49	0.607	SUBCLONAL	1	TRUE	1	0.370865990785465	2		894	1095	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420245	88420245	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	223	585	0	ENST00000360948.2:c.2441G>T	p.Arg814Leu	p.R814L	ENST00000360948	NM_001012338.2	814	cGg/cTg	19/19	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.370865990785465	2		585	1099	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836351	89836351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1210	103	777	0	ENST00000389301.3:c.2398G>A	p.Glu800Lys	p.E800K	ENST00000389301	NM_000135.2	800	Gag/Aag	26/43	0.2891124269342	1	FACETS	0.345	0.307	0.385	0.345	0.307	0.385	SUBCLONAL	1	TRUE	0	0.370865990785465	1		777	1313	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100043	11100043	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1214	306	896	0	ENST00000358026.2:c.1169G>T	p.Gly390Val	p.G390V	ENST00000358026	NM_001128849.1	390	gGg/gTg	7/36	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.370865990785465	2		896	1520	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55130019	55130019	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1489	120	829	0	ENST00000257290.5:c.553G>C	p.Gly185Arg	p.G185R	ENST00000257290	NM_006206.4	185	Ggg/Cgg	4/23	0.370865990785465	3	FACETS	0.477	0.429	0.528	0.159	0.143	0.176	SUBCLONAL	1	TRUE	0	0.370865990785465	3		829	1609	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594094	55594094	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0018814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	80	391	0	ENST00000288135.5:c.1879+1G>T		p.X627_splice	ENST00000288135	NM_000222.2	627			0.370865990785465	3	FACETS	0.548	0.481	0.62	0.183	0.16	0.207	SUBCLONAL	1	TRUE	0	0.370865990785465	3		391	934	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279519	1279519	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1806	135	797	0	ENST00000310581.5:c.2017C>A	p.Pro673Thr	p.P673T	ENST00000310581	NM_198253.2	673	Ccc/Acc	5/16	0.259543701330285	4	FACETS	0.514	0.465	0.566	0.129	0.116	0.142	SUBCLONAL	1	TRUE	0	0.370865990785465	4		797	1941	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225777	26225777	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	162	432	0	ENST00000360408.1:c.395G>C	p.Arg132Pro	p.R132P	ENST00000360408	NM_003532.2	132	cGt/cCt	1/1	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.370865990785465	2		432	845	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964345	70964345	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1423232475	NA	P-0018814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	58	328	0	ENST00000276594.2:c.1683C>G	p.Phe561Leu	p.F561L	ENST00000276594	NM_024504.3	561	ttC/ttG	8/8	0.367778939234001	3	FACETS	0.527	0.452	0.609	0.263	0.226	0.305	SUBCLONAL	1	TRUE	1	0.370865990785465	3		328	704	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523578	148523589	+	frameshift_variant	Frame_Shift_Del	DEL	TATTTAAAACAT	TATTTAAAACAT	C	novel	NA	P-0018814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	183	453	0	ENST00000320356.2:c.864_875delinsG	p.Cys289Ter	p.C289*	ENST00000320356	NM_004456.4	288	cgATGTTTTAAATAt/cgGt	8/20	0.370865990785465	3	FACETS	1	0.988	1	0.693	0.64	0.748	CLONAL	1	TRUE	1	0.370865990785465	3		453	844	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0019082-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	67	321	2	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.300386819133226	3	FACETS	0.402	0.349	0.46	0.201	0.174	0.23	INDETERMINATE	1	TRUE	1	0.556270967633356	3		323	766	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0019082-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	344	519	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.556270967633356	4	FACETS	1	0.995	1			1	CLONAL	1	TRUE	NA	0.556270967633356	4		519	1288	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0019082-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	363	761	0	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	0.530549064555302	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.556270967633356	1		761	941	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187483	32187483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019082-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1567	123	705	4	ENST00000375023.3:c.1396G>A	p.Gly466Ser	p.G466S	ENST00000375023	NM_004557.3	466	Ggc/Agc	8/30	0.556270967633356	4	FACETS	0.407	0.366	0.451	0.204	0.183	0.226	SUBCLONAL	1	TRUE	2	0.556270967633356	4		709	1690	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	262	443	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.162883623111711	9	FACETS	0.988	0.933	1	1	0.995	1	CLONAL	8	FALSE	5	0.162883623111711	9		443	639	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0019458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	175	404	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.162883623111711	9	FACETS	1	0.947	1	1	0.991	1	CLONAL	6	FALSE	5	0.162883623111711	9		404	548	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189412	56189412	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	515	518	0	ENST00000399503.3:c.4444C>T	p.Arg1482Ter	p.R1482*	ENST00000399503	NM_005921.1	1482	Cga/Tga	20/20	0.162883623111711	7	FACETS	1	0.985	1			1	CLONAL	12	FALSE	NA	0.162883623111711	7		518	726	SUCCESS
AR	367	MSKCC	GRCh37	X	66943543	66943543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852581	NA	P-0019458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	271	368	1	ENST00000374690.3:c.2623C>T	p.His875Tyr	p.H875Y	ENST00000374690	NM_000044.3	875	Cat/Tat	8/8	0.162883623111711	2	FACETS	1	0.961	1	1	0.997	1	CLONAL	7	FALSE	0	0.162883623111711	2		369	471	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061463	38061463	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	168	459	0	ENST00000250448.2:c.526A>G	p.Ile176Val	p.I176V	ENST00000250448	NM_004496.3	176	Atc/Gtc	2/2	0.162883623111711	6	FACETS	1	0.967	1	0.87	0.803	0.939	CLONAL	4	FALSE	1	0.162883623111711	6		459	629	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0020564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	395	321	2	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.86242439676365	3	FACETS	0.958	0.921	0.996	0.958	0.921	0.996	CLONAL	2	TRUE	1	0.86242439676365	3		323	684	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0020564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	176	449	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.956	0.891	1	0.956	0.891	1	CLONAL	1	TRUE	1	0.86242439676365	2		449	427	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436146	110436146	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1308299093	NA	P-0020564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	642	826	0	ENST00000375856.3:c.2255C>T	p.Ser752Phe	p.S752F	ENST00000375856	NM_003749.2	752	tCc/tTc	1/2	0.86242439676365	3	FACETS	0.99	0.96	1	0.99	0.96	1	CLONAL	2	TRUE	1	0.86242439676365	3		826	1076	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9787030	9787030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397518423	NA	P-0020564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	228	633	4	ENST00000377346.4:c.3061G>A	p.Glu1021Lys	p.E1021K	ENST00000377346	NM_005026.3	1021	Gaa/Aaa	24/24	1	2	FACETS	0.951	0.894	1	0.951	0.894	1	CLONAL	1	TRUE	1	0.86242439676365	2		637	556	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553501	29553501	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	306	618	0	ENST00000356175.3:c.2050C>T	p.Gln684Ter	p.Q684*	ENST00000356175	NM_000267.3	684	Cag/Tag	18/57	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.86242439676365	2		618	692	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412689	63412689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760337524	NA	P-0020564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	223	531	1	ENST00000330258.3:c.478C>T	p.Pro160Ser	p.P160S	ENST00000330258	NM_152424.3	160	Ccc/Tcc	2/2	1	2	FACETS	0.93	0.873	0.988	0.93	0.873	0.988	CLONAL	1	TRUE	1	0.86242439676365	2		532	556	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287309	33287310	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	179	543	1	ENST00000374542.5:c.1787_1788delinsTT	p.Pro596Leu	p.P596L	ENST00000374542	NM_001141970.1	596	cCC/cTT	6/8	0.86242439676365	3	FACETS	0.854	0.789	0.92	0.427	0.394	0.46	CLONAL	1	TRUE	1	0.86242439676365	3		544	696	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032032	10032032	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	254	518	0	ENST00000330684.3:c.791A>G	p.Asn264Ser	p.N264S	ENST00000330684	NM_001134407.1	264	aAc/aGc	3/13	1	2	FACETS	0.861	0.811	0.912	0.861	0.811	0.912	CLONAL	1	TRUE	1	0.86242439676365	2		518	684	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259322	89259322	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866821420	NA	P-0020564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	179	396	1	ENST00000336596.2:c.466G>A	p.Asp156Asn	p.D156N	ENST00000336596	NM_005233.5	156	Gat/Aat	3/17	1	2	FACETS	0.943	0.879	1	0.943	0.879	1	CLONAL	1	TRUE	1	0.86242439676365	2		397	440	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716366	18716366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs935135637	NA	P-0020564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	210	449	0	ENST00000266497.5:c.3713C>T	p.Ser1238Leu	p.S1238L	ENST00000266497		1238	tCa/tTa	26/31	1	2	FACETS	0.905	0.848	0.964	0.905	0.848	0.964	CLONAL	1	TRUE	1	0.86242439676365	2		449	538	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392143	81392143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	130	286	0	ENST00000222390.5:c.134C>T	p.Ser45Leu	p.S45L	ENST00000222390	NM_000601.4	45	tCa/tTa	2/18	0.86242439676365	3	FACETS	0.908	0.829	0.99	0.454	0.414	0.495	CLONAL	1	TRUE	1	0.86242439676365	3		286	475	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223283	2223283	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	312	758	1	ENST00000326181.6:c.895C>T	p.His299Tyr	p.H299Y	ENST00000326181	NM_032271.2	299	Cac/Tac	10/21	1	2	FACETS	0.983	0.933	1	0.983	0.933	1	CLONAL	1	TRUE	1	0.86242439676365	2		759	736	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372554	118372554	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555045816	NA	P-0020564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	261	487	0	ENST00000534358.1:c.6487C>T	p.Arg2163Ter	p.R2163*	ENST00000534358	NM_005933.3	2163	Cga/Tga	26/36	0.834474361000887	1	FACETS	0.998	0.961	1	0.998	0.961	1	CLONAL	1	TRUE	0	0.86242439676365	1		487	345	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373665	118373665	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	186	460	0	ENST00000534358.1:c.7058C>T	p.Ser2353Phe	p.S2353F	ENST00000534358	NM_005933.3	2353	tCc/tTc	27/36	0.834474361000887	1	FACETS	0.936	0.891	0.979	0.936	0.891	0.979	CLONAL	1	TRUE	0	0.86242439676365	1		460	262	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28631541	28631541	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	175	422	0	ENST00000241453.7:c.427C>G	p.Leu143Val	p.L143V	ENST00000241453	NM_004119.2	143	Ctt/Gtt	4/24	0.86242439676365	3	FACETS	0.792	0.731	0.856	0.396	0.365	0.428	SUBCLONAL	1	TRUE	1	0.86242439676365	3		422	733	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2125869	2125870	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0020564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	272	804	3	ENST00000219476.3:c.2615_2616delinsTT	p.Ser872Phe	p.S872F	ENST00000219476	NM_000548.3	872	tCC/tTT	23/42	1	2	FACETS	0.909	0.858	0.96	0.909	0.858	0.96	CLONAL	1	TRUE	1	0.86242439676365	2		807	694	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134464	30134464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	224	573	0	ENST00000263025.4:c.67G>A	p.Gly23Arg	p.G23R	ENST00000263025	NM_002746.2	23	Ggg/Agg	1/9	1	2	FACETS	0.944	0.887	1	0.944	0.887	1	CLONAL	1	TRUE	1	0.86242439676365	2		573	550	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667646	29667646	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56013763	NA	P-0020564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	199	428	0	ENST00000356175.3:c.6982C>T	p.Arg2328Cys	p.R2328C	ENST00000356175	NM_000267.3	2328	Cgt/Tgt	46/57	1	2	FACETS	0.917	0.858	0.978	0.917	0.858	0.978	CLONAL	1	TRUE	1	0.86242439676365	2		428	503	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761243	59761243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	258	571	0	ENST00000259008.2:c.3164C>T	p.Ser1055Phe	p.S1055F	ENST00000259008	NM_032043.2	1055	tCc/tTc	20/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.86242439676365	2		571	580	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383628	15383628	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1409879003	NA	P-0020564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	137	342	0	ENST00000263377.2:c.283C>T	p.Pro95Ser	p.P95S	ENST00000263377	NM_058243.2	95	Cct/Tct	2/20	1	2	FACETS	0.929	0.857	1	0.929	0.857	1	CLONAL	1	TRUE	1	0.86242439676365	2		342	342	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736110	204736110	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	140	316	0	ENST00000302823.3:c.467C>A	p.Pro156Gln	p.P156Q	ENST00000302823	NM_005214.4	156	cCg/cAg	3/4	1	2	FACETS	0.93	0.859	1	0.93	0.859	1	CLONAL	1	TRUE	1	0.86242439676365	2		316	349	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543876	212543876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	230	474	0	ENST00000342788.4:c.1523C>T	p.Ser508Phe	p.S508F	ENST00000342788	NM_005235.2	508	tCc/tTc	13/28	1	2	FACETS	0.944	0.887	1	0.944	0.887	1	CLONAL	1	TRUE	1	0.86242439676365	2		474	565	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268407	46268407	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	190	391	0	ENST00000371998.3:c.2794C>T	p.Pro932Ser	p.P932S	ENST00000371998		932	Cct/Tct	15/23	1	2	FACETS	0.903	0.843	0.964	0.903	0.843	0.964	CLONAL	1	TRUE	1	0.86242439676365	2		391	488	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721578	49721579	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0020564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	148	418	0	ENST00000449682.2:c.2060_2061delinsAA	p.Trp687Ter	p.W687*	ENST00000449682	NM_020998.3	687	tGG/tAA	18/18	1	2	FACETS	0.943	0.873	1	0.943	0.873	1	CLONAL	1	TRUE	1	0.86242439676365	2		418	364	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403480	138403480	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1316933213	NA	P-0020564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	203	435	0	ENST00000289153.2:c.2302C>T	p.Leu768Phe	p.L768F	ENST00000289153	NM_006219.2	768	Ctc/Ttc	15/22	1	2	FACETS	0.975	0.913	1	0.975	0.913	1	CLONAL	1	TRUE	1	0.86242439676365	2		435	483	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196355	106196355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	184	356	0	ENST00000380013.4:c.4688C>T	p.Ser1563Phe	p.S1563F	ENST00000380013	NM_001127208.2	1563	tCt/tTt	11/11	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.86242439676365	2		356	422	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177670	56177671	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0020564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	165	404	0	ENST00000399503.3:c.2644_2645dup	p.Asp882GlufsTer28	p.D882Efs*28	ENST00000399503	NM_005921.1	881	-/GA	14/20	1	2	FACETS	0.9	0.836	0.966	0.9	0.836	0.966	CLONAL	1	TRUE	1	0.86242439676365	2		404	425	SUCCESS
APC	324	MSKCC	GRCh37	5	112174245	112174245	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	164	382	0	ENST00000257430.4:c.2954C>T	p.Ser985Phe	p.S985F	ENST00000257430	NM_000038.5	985	tCc/tTc	16/16	1	2	FACETS	0.965	0.897	1	0.965	0.897	1	CLONAL	1	TRUE	1	0.86242439676365	2		382	394	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979427	2979427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	277	572	0	ENST00000396946.4:c.820G>A	p.Glu274Lys	p.E274K	ENST00000396946	NM_032415.4	274	Gaa/Aaa	6/25	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.86242439676365	2		572	621	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987238	2987238	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	224	469	0	ENST00000396946.4:c.191C>T	p.Pro64Leu	p.P64L	ENST00000396946	NM_032415.4	64	cCt/cTt	3/25	1	2	FACETS	0.926	0.869	0.983	0.926	0.869	0.983	CLONAL	1	TRUE	1	0.86242439676365	2		469	561	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55269447	55269447	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	380	835	1	ENST00000275493.2:c.3134C>T	p.Ser1045Phe	p.S1045F	ENST00000275493	NM_005228.3	1045	tCc/tTc	26/28	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.86242439676365	2		836	853	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485798	8485798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750659786	NA	P-0020564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	140	260	0	ENST00000356435.5:c.3019C>T	p.Pro1007Ser	p.P1007S	ENST00000356435		1007	Ccc/Tcc	17/35	0.855560361052678	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.86242439676365	1		260	178	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345918	70345918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751774081	NA	P-0020564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	270	533	2	ENST00000374080.3:c.2455C>T	p.Arg819Trp	p.R819W	ENST00000374080		819	Cgg/Tgg	18/45	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.86242439676365	2		535	618	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019768	123019768	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	251	540	1	ENST00000355640.3:c.256G>A	p.Val86Ile	p.V86I	ENST00000355640		86	Gta/Ata	2/7	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	1	TRUE	NA	0.86242439676365	2		541	552	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	215	345	8	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	FALSE	1	0.314156104534388	2		353	955	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1157	145	754	7	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	0.10068985163622	0	FACETS	0.486	0.442	0.533			1	INDETERMINATE	1	FALSE	0	0.314156104534388	0		761	1302	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	47	320	1	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.314156104534388	2		321	210	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	60	418	1	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.446	0.383	0.515	0.446	0.383	0.515	SUBCLONAL	1	FALSE	1	0.314156104534388	2		419	856	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1500	118	976	5	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.464	0.417	0.515	0.464	0.417	0.515	SUBCLONAL	1	FALSE	1	0.314156104534388	2		981	1618	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	23	539	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.318	0.247	0.4	0.318	0.247	0.4	SUBCLONAL	1	FALSE	1	0.314156104534388	2		539	461	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	169	556	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	0.161503905050332	3	FACETS	1	0.985	1	0.653	0.6	0.708	INDETERMINATE	1	FALSE	1	0.314156104534388	3		556	953	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552144	29552144	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	20	241	0	ENST00000356175.3:c.1882del	p.Tyr628ThrfsTer3	p.Y628Tfs*3	ENST00000356175	NM_000267.3	626	cTt/ct	17/57	1	2	FACETS	1	0.776	1	1	0.776	1	CLONAL	1	FALSE	1	0.314156104534388	2		241	127	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	120	446	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.161503905050332	3	FACETS	1	0.978	1	0.647	0.585	0.712	INDETERMINATE	1	FALSE	1	0.314156104534388	3		446	683	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	63	337	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.314156104534388	2		337	333	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216477	108216477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587782558	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	24	162	0	ENST00000278616.4:c.8432del	p.Lys2811SerfsTer46	p.K2811Sfs*46	ENST00000278616	NM_000051.3	2809	cAa/ca	58/63	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	FALSE	1	0.314156104534388	2		162	126	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	79	604	3	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	FALSE	1	0.314156104534388	2		607	471	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100728	8100728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs771019738	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	202	535	3	ENST00000346208.3:c.708del	p.Ser237AlafsTer28	p.S237Afs*28	ENST00000346208		234	ttC/tt	3/6	0.10068985163622	0	FACETS	0.744	0.689	0.802			1	INDETERMINATE	1	FALSE	0	0.314156104534388	0		538	1185	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	114	457	3	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.966	0.87	1	0.966	0.87	1	CLONAL	1	FALSE	1	0.314156104534388	2		460	751	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785963	135785964	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs118203506	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	48	522	0	ENST00000298552.3:c.1257dup	p.Arg420GlnfsTer22	p.R420Qfs*22	ENST00000298552	NM_001162426.1	419	-/C	12/23	1	2	FACETS	0.362	0.305	0.425	0.362	0.305	0.425	SUBCLONAL	1	FALSE	1	0.314156104534388	2		522	844	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	34	469	2	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	0.161503905050332	3	FACETS	0.447	0.365	0.541	0.224	0.182	0.271	INDETERMINATE	1	FALSE	1	0.314156104534388	3		471	560	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28979946	28979946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764045713	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	73	530	0	ENST00000282397.4:c.1522C>T	p.Arg508Cys	p.R508C	ENST00000282397	NM_002019.4	508	Cgc/Tgc	11/30	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.314156104534388	2		530	380	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306553	41306553	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	105	459	1	ENST00000373198.4:c.1106del	p.Gly369ValfsTer28	p.G369Vfs*28	ENST00000373198	NM_133170.3	369	gGt/gt	7/32	0.161503905050332	3	FACETS	0.988	0.885	1	0.494	0.442	0.549	INDETERMINATE	1	FALSE	1	0.314156104534388	3		460	783	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821425	72821425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769841511	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	61	666	0	ENST00000268489.5:c.10750G>A	p.Ala3584Thr	p.A3584T	ENST00000268489	NM_006885.3	3584	Gca/Aca	10/10	0.161503905050332	3	FACETS	0.406	0.349	0.469	0.203	0.174	0.235	INDETERMINATE	1	FALSE	1	0.314156104534388	3		666	1107	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060912	38060912	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	54	492	1	ENST00000250448.2:c.1077del	p.Ile360Ter	p.I360*	ENST00000250448	NM_004496.3	359	ccC/cc	2/2	1	2	FACETS	0.476	0.406	0.553	0.476	0.406	0.553	SUBCLONAL	1	FALSE	1	0.314156104534388	2		493	722	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	78	638	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.443	0.388	0.503	0.443	0.388	0.503	SUBCLONAL	1	FALSE	1	0.314156104534388	2		640	1120	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797892	42797892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1227	84	839	0	ENST00000575354.2:c.3944C>T	p.Ala1315Val	p.A1315V	ENST00000575354	NM_015125.3	1315	gCc/gTc	16/20	0.161503905050332	3	FACETS	0.472	0.415	0.533	0.236	0.207	0.267	INDETERMINATE	1	FALSE	1	0.314156104534388	3		839	1311	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562271	21562271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1256	196	726	0	ENST00000382592.4:c.1648G>A	p.Glu550Lys	p.E550K	ENST00000382592	NM_014572.2	550	Gag/Aag	4/8	1	2	FACETS	0.859	0.793	0.929	0.859	0.793	0.929	CLONAL	1	FALSE	1	0.314156104534388	2		726	1452	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45422934	45422934	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	31	311	0	ENST00000262160.6:c.194T>C	p.Ile65Thr	p.I65T	ENST00000262160	NM_005901.5	65	aTc/aCc	2/11	0.10068985163622	0	FACETS	0.351	0.283	0.427			1	INDETERMINATE	1	FALSE	0	0.314156104534388	0		311	386	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023315	27023322	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGCCTT	GCCGCCTT	-	novel	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	97	395	0	ENST00000324856.7:c.427_434del	p.Leu143ProfsTer254	p.L143Pfs*254	ENST00000324856	NM_006015.4	141	GCCGCCTTg/g	1/20	0.161503905050332	3	FACETS	1	0.964	1	0.592	0.529	0.66	INDETERMINATE	1	FALSE	1	0.314156104534388	3		395	603	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606881	43606881	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1261	92	849	0	ENST00000355710.3:c.1490A>G	p.Gln497Arg	p.Q497R	ENST00000355710	NM_020975.4	497	cAg/cGg	7/20	1	2	FACETS	0.433	0.383	0.487	0.433	0.383	0.487	SUBCLONAL	1	FALSE	1	0.314156104534388	2		849	1353	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236084	108236084	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	52	421	0	ENST00000278616.4:c.9020A>G	p.Glu3007Gly	p.E3007G	ENST00000278616	NM_000051.3	3007	gAa/gGa	63/63	1	2	FACETS	0.783	0.668	0.908	0.783	0.668	0.908	CLONAL	1	FALSE	1	0.314156104534388	2		421	423	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236190	108236191	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	89	510	0	ENST00000278616.4:c.9131dup	p.Asn3044LysfsTer19	p.N3044Kfs*19	ENST00000278616	NM_000051.3	3042	-/A	63/63	1	2	FACETS	0.766	0.679	0.859	0.766	0.679	0.859	SUBCLONAL	1	FALSE	1	0.314156104534388	2		510	740	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432599	49432599	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776779364	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	152	753	2	ENST00000301067.7:c.8540G>A	p.Arg2847His	p.R2847H	ENST00000301067	NM_003482.3	2847	cGc/cAc	34/54	0.161503905050332	3	FACETS	0.943	0.861	1	0.472	0.43	0.515	INDETERMINATE	1	FALSE	1	0.314156104534388	3		755	1187	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433956	49433957	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	161	709	0	ENST00000301067.7:c.7596_7597del	p.Pro2533HisfsTer121	p.P2533Hfs*121	ENST00000301067	NM_003482.3	2532	tcTCcc/tccc	31/54	0.161503905050332	3	FACETS	1	0.954	1	0.531	0.486	0.578	INDETERMINATE	1	FALSE	1	0.314156104534388	3		709	1117	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422091	81422091	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	80	492	1	ENST00000298171.2:c.67G>T	p.Gly23Trp	p.G23W	ENST00000298171	NM_000369.2	23	Ggg/Tgg	1/10	1	2	FACETS	0.693	0.609	0.783	0.693	0.609	0.783	SUBCLONAL	1	FALSE	1	0.314156104534388	2		493	735	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562982	95562984	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs751284020	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	26	293	0	ENST00000393063.1:c.4273_4275del	p.Glu1425del	p.E1425del	ENST00000393063	NM_030621.3	1425	GAG/-	24/28	1	2	FACETS	0.364	0.287	0.452	0.364	0.287	0.452	SUBCLONAL	1	FALSE	1	0.314156104534388	2		293	455	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807988	3807988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	130	461	0	ENST00000262367.5:c.3431C>T	p.Thr1144Ile	p.T1144I	ENST00000262367	NM_004380.2	1144	aCa/aTa	18/31	0.161503905050332	3	FACETS	1	0.983	1	0.685	0.622	0.751	INDETERMINATE	1	FALSE	1	0.314156104534388	3		461	699	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805534	46805534	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556045007	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	85	860	0	ENST00000290295.7:c.422C>T	p.Ala141Val	p.A141V	ENST00000290295	NM_006361.5	141	gCc/gTc	1/2	1	2	FACETS	0.42	0.37	0.474	0.42	0.37	0.474	SUBCLONAL	1	FALSE	1	0.314156104534388	2		860	1288	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371780	45371780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	18	346	0	ENST00000262160.6:c.1211C>T	p.Ala404Val	p.A404V	ENST00000262160	NM_005901.5	404	gCc/gTc	10/11	0.10068985163622	0	FACETS	0.243	0.183	0.315			1	INDETERMINATE	1	FALSE	0	0.314156104534388	0		346	323	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652793	212652793	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	18	355	0	ENST00000342788.4:c.513G>A	p.Trp171Ter	p.W171*	ENST00000342788	NM_005235.2	171	tgG/tgA	4/28	0.10068985163622	0	FACETS	0.342	0.258	0.441			1	INDETERMINATE	1	FALSE	0	0.314156104534388	0		355	230	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852418	42852418	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	49	567	1	ENST00000398585.3:c.668G>T	p.Arg223Met	p.R223M	ENST00000398585	NM_001135099.1	223	aGg/aTg	6/14	1	2	FACETS	0.33	0.279	0.388	0.33	0.279	0.388	SUBCLONAL	1	FALSE	1	0.314156104534388	2		568	944	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162061	22162061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	98	453	0	ENST00000215832.6:c.194G>A	p.Cys65Tyr	p.C65Y	ENST00000215832	NM_002745.4	65	tGc/tAc	2/9	0.10068985163622	0	FACETS	0.829	0.742	0.921			1	INDETERMINATE	1	FALSE	0	0.314156104534388	0		453	516	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090096	37090107	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGAGGTCAGTG	CTGAGGTCAGTG	-	novel	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	83	377	0	ENST00000231790.2:c.1985_1989+7del		p.X662_splice	ENST00000231790	NM_000249.3	662		17/19	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	FALSE	1	0.314156104534388	2		377	489	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129960	55129960	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	59	469	0	ENST00000257290.5:c.494A>G	p.Glu165Gly	p.E165G	ENST00000257290	NM_006206.4	165	gAg/gGg	4/23	1	2	FACETS	0.483	0.415	0.558	0.483	0.415	0.558	SUBCLONAL	1	FALSE	1	0.314156104534388	2		469	777	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958387	90958387	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	26	243	0	ENST00000265433.3:c.2051del	p.Asn684IlefsTer25	p.N684Ifs*25	ENST00000265433	NM_002485.4	684	aAt/at	13/16	0.10068985163622	0	FACETS	0.645	0.515	0.791			1	INDETERMINATE	1	FALSE	0	0.314156104534388	0		243	176	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741623	145741625	+	inframe_deletion	In_Frame_Del	DEL	CTG	CTG	-	novel	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	127	675	0	ENST00000428558.2:c.878_880del	p.Ala293del	p.A293del	ENST00000428558	NM_004260.3	293	gCAGtt/gtt	5/22	0.10068985163622	0	FACETS	0.511	0.461	0.563			1	INDETERMINATE	1	FALSE	0	0.314156104534388	0		675	1086	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504278	8504278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	48	382	0	ENST00000356435.5:c.1805C>T	p.Ala602Val	p.A602V	ENST00000356435		602	gCt/gTt	12/35	1	2	FACETS	0.582	0.492	0.681	0.582	0.492	0.681	SUBCLONAL	1	FALSE	1	0.314156104534388	2		382	525	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019697	123019697	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755189208	NA	P-0020633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	73	457	1	ENST00000355640.3:c.185G>A	p.Arg62Gln	p.R62Q	ENST00000355640		62	cGg/cAg	2/7	0.314156104534388	0	FACETS	0.683	0.599	0.772			1	SUBCLONAL	1	FALSE	0	0.314156104534388	0		458	467	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0020825-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1225	154	650	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.509832762714447	3	FACETS	0.518	0.473	0.566	0.259	0.236	0.283	SUBCLONAL	1	FALSE	1	0.549376980317142	3		651	1379	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0020825-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	337	487	2	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.509832762714447	3	FACETS	1	0.976	1	0.529	0.499	0.56	CLONAL	1	FALSE	1	0.549376980317142	3		489	1477	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404576	8404576	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146844299	NA	P-0020825-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	147	345	0	ENST00000356435.5:c.4171G>A	p.Ala1391Thr	p.A1391T	ENST00000356435		1391	Gca/Aca	25/35	NA	2	FACETS	0.973	0.893	1			1	INDETERMINATE	1	FALSE	NA	0.549376980317142	2		345	550	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653780	89653781	+	splice_acceptor_variant	Splice_Site	DEL	AG	AG	-	rs1554893747	NA	P-0020825-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	235	405	0	ENST00000371953.3:c.80-1_80del		p.X27_splice	ENST00000371953	NM_000314.4	27			0.536278512933678	2	FACETS	0.827	0.78	0.875	0.827	0.78	0.875	CLONAL	2	FALSE	0	0.549376980317142	2		405	517	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679790	88679790	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020825-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	260	696	0	ENST00000360948.2:c.673G>T	p.Asp225Tyr	p.D225Y	ENST00000360948	NM_001012338.2	225	Gac/Tac	7/19	1	2	FACETS	0.899	0.842	0.957	0.899	0.842	0.957	CLONAL	1	FALSE	1	0.549376980317142	2		696	1053	SUCCESS
APC	324	MSKCC	GRCh37	5	112154966	112154970	+	frameshift_variant	Frame_Shift_Del	DEL	ATACG	ATACG	C	novel	NA	P-0020825-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	258	749	0	ENST00000257430.4:c.1237_1241delinsC	p.Ile413ProfsTer40	p.I413Pfs*40	ENST00000257430	NM_000038.5	413	ATACGc/Cc	10/16	0.549376980317142	1	FACETS	0.868	0.816	0.921	0.868	0.816	0.921	CLONAL	1	FALSE	0	0.549376980317142	1		749	785	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	51	315	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.958	0.815	1	0.958	0.815	1	CLONAL	1	TRUE	1	0.209980893697532	2		316	507	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982323	201982324	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	105	1076	0	ENST00000359651.3:c.703dup	p.Cys235LeufsTer66	p.C235Lfs*66	ENST00000359651		234	-/T	6/8	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.209980893697532	2		1076	894	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245826	46245826	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0020835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	27	688	0	ENST00000334344.6:c.3920C>G	p.Ser1307Ter	p.S1307*	ENST00000334344	NM_152641.2	1307	tCa/tGa	15/21	1	2	FACETS	0.772	0.615	0.952	0.772	0.615	0.952	CLONAL	1	TRUE	1	0.209980893697532	2		688	333	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287287	46287300	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGAGAGGATCAA	GAGGAGAGGATCAA	-	novel	NA	P-0020835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	40	870	0	ENST00000334344.6:c.5234_5247del	p.Arg1745LysfsTer10	p.R1745Kfs*10	ENST00000334344	NM_152641.2	1744	ctGAGGAGAGGATCAAga/ctga	19/21	1	2	FACETS	0.776	0.644	0.922	0.776	0.644	0.922	CLONAL	1	TRUE	1	0.209980893697532	2		870	491	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458321	12458321	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	54	917	2	ENST00000287820.6:c.938G>T	p.Cys313Phe	p.C313F	ENST00000287820	NM_015869.4	313	tGc/tTc	6/7	1	2	FACETS	0.647	0.551	0.752	0.647	0.551	0.752	SUBCLONAL	1	TRUE	1	0.209980893697532	2		919	795	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs149680468	NA	P-0020835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	46	702	0	ENST00000281708.4:c.1513C>A	p.Arg505Ser	p.R505S	ENST00000281708	NM_033632.3	505	Cgc/Agc	10/12	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.209980893697532	2		702	392	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651906	36651906	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	137	825	1	ENST00000244741.5:c.28C>T	p.Gln10Ter	p.Q10*	ENST00000244741	NM_000389.4	10	Cag/Tag	2/3	0.209980893697532	3	FACETS	0.968	0.881	1	0.645	0.587	0.706	CLONAL	2	TRUE	0	0.209980893697532	3		826	745	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179050	123179050	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	43	575	1	ENST00000218089.9:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000218089	NM_001042749.1	167	Cag/Tag	8/35	1	1	FACETS	0.757	0.639	0.886	1	0.96	1	SUBCLONAL	2	TRUE	0	0.209980893697532	1		576	242	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0020835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	36	431	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	0.875	0.72	1	0.875	0.72	1	CLONAL	1	TRUE	1	0.209980893697532	2		431	392	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020990-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	19	528	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.148211162482021	3	FACETS	0.69	0.524	0.884	0.345	0.262	0.442	SUBCLONAL	1	TRUE	1	0.244403461857735	3		529	253	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0020990-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	23	166	1	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.148211162482021	3	FACETS	0.845	0.661	1	0.422	0.33	0.529	CLONAL	1	TRUE	1	0.244403461857735	3		167	250	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486587	56486587	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020990-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	59	626	0	ENST00000267101.3:c.1166C>A	p.Thr389Lys	p.T389K	ENST00000267101	NM_001982.3	389	aCa/aAa	10/28	0.148211162482021	3	FACETS	1	0.955	1	0.634	0.547	0.729	CLONAL	1	TRUE	1	0.244403461857735	3		626	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578391	7578393	+	frameshift_variant	Frame_Shift_Del	DEL	TCA	TCA	AT	novel	NA	P-0020990-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	77	533	1	ENST00000269305.4:c.537_539delinsAT	p.His179GlnfsTer68	p.H179Qfs*68	ENST00000269305	NM_001126112.2	179	caTGAg/caATg	5/11	0.244403461857735	2	FACETS	0.978	0.867	1	0.978	0.867	1	CLONAL	2	TRUE	0	0.244403461857735	2		534	322	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	29	423	3	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.265	0.212	0.326	0.265	0.212	0.326	SUBCLONAL	1	TRUE	1	0.420978109754604	2		426	519	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053022	180053023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750808726	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	64	703	2	ENST00000261937.6:c.1267dup	p.Gln423ProfsTer4	p.Q423Pfs*4	ENST00000261937	NM_182925.4	423	cag/cCag	10/30	1	2	FACETS	0.449	0.388	0.515	0.449	0.388	0.515	SUBCLONAL	1	TRUE	1	0.420978109754604	2		705	677	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	146	613	2	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.987	0.902	1	0.987	0.902	1	CLONAL	1	TRUE	1	0.420978109754604	2		615	703	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436393	52436393	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1244342890	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	138	595	0	ENST00000460680.1:c.2101C>T	p.Arg701Cys	p.R701C	ENST00000460680	NM_004656.3	701	Cgc/Tgc	17/17	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.420978109754604	2		595	609	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	141	394	0	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.420978109754604	2		394	506	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	100	705	2	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	0.667	0.596	0.743	0.667	0.596	0.743	SUBCLONAL	1	TRUE	1	0.420978109754604	2		707	712	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337296	89337296	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567537413	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	143	516	2	ENST00000301030.4:c.7735C>T	p.Arg2579Cys	p.R2579C	ENST00000301030	NM_001256183.1	2579	Cgc/Tgc	12/13	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.420978109754604	2		518	603	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835781	68835781	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060501215	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	151	515	0	ENST00000261769.5:c.377del	p.Pro126ArgfsTer89	p.P126Rfs*89	ENST00000261769	NM_004360.3	124	cgC/cg	3/16	1	2	FACETS	0.94	0.861	1	0.94	0.861	1	CLONAL	1	TRUE	1	0.420978109754604	2		515	763	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871053	12871053	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	97	382	0	ENST00000228872.4:c.285del	p.Gly97ValfsTer22	p.G97Vfs*22	ENST00000228872	NM_004064.3	94	Ccc/cc	1/3	0.420978109754604	1	FACETS	0.957	0.86	1	0.957	0.86	1	CLONAL	1	TRUE	0	0.420978109754604	1		382	380	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348566	89348568	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs753054998	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	214	850	1	ENST00000301030.4:c.4382_4384del	p.Lys1461del	p.K1461del	ENST00000301030	NM_001256183.1	1461	aAGAga/aga	9/13	1	2	FACETS	0.938	0.871	1	0.938	0.871	1	CLONAL	1	TRUE	1	0.420978109754604	2		851	1084	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857925	9857925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs534440095	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	126	576	0	ENST00000330684.3:c.3476G>A	p.Arg1159His	p.R1159H	ENST00000330684	NM_001134407.1	1159	cGc/cAc	13/13	1	2	FACETS	0.927	0.841	1	0.927	0.841	1	CLONAL	1	TRUE	1	0.420978109754604	2		576	646	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713407	40713407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768298187	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	44	596	3	ENST00000373198.4:c.4108C>T	p.Arg1370Cys	p.R1370C	ENST00000373198	NM_133170.3	1370	Cgc/Tgc	30/32	1	2	FACETS	0.27	0.226	0.32	0.27	0.226	0.32	SUBCLONAL	1	TRUE	1	0.420978109754604	2		599	774	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81927315	81927315	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	161	643	0	ENST00000359376.3:c.988T>C	p.Tyr330His	p.Y330H	ENST00000359376	NM_002661.3	330	Tac/Cac	12/33	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.420978109754604	2		643	708	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845477	72845477	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1395722106	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	132	461	0	ENST00000268489.5:c.3863C>T	p.Thr1288Met	p.T1288M	ENST00000268489	NM_006885.3	1288	aCg/aTg	7/10	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.420978109754604	2		461	591	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954379	48954379	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	98	408	0	ENST00000267163.4:c.1498+2T>C		p.X500_splice	ENST00000267163	NM_000321.2	500			0.420649329616918	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.420978109754604	1		408	356	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935322	36935323	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs747437399	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	67	727	1	ENST00000361632.4:c.1404dup	p.Ser469GlnfsTer5	p.S469Qfs*5	ENST00000361632		468	-/C	10/16	1	2	FACETS	0.432	0.375	0.494	0.432	0.375	0.494	SUBCLONAL	1	TRUE	1	0.420978109754604	2		728	737	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	131	589	1	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	1	2	FACETS	0.919	0.836	1	0.919	0.836	1	CLONAL	1	TRUE	1	0.420978109754604	2		590	677	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222475	53222475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782302305	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	166	357	0	ENST00000375401.3:c.4357C>T	p.Arg1453Trp	p.R1453W	ENST00000375401	NM_004187.3	1453	Cgg/Tgg	26/26	1	1	FACETS	0.828	0.771	0.885	1	0.992	1	CLONAL	2	TRUE	0	0.420978109754604	1		357	376	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061168	38061195	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCCCGGCTGCTTCTCGCACTTGAAGC	GCCCCCGGCTGCTTCTCGCACTTGAAGC	-	novel	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	85	180	0	ENST00000250448.2:c.794_821del	p.Arg265ProfsTer47	p.R265Pfs*47	ENST00000250448	NM_004496.3	265	cGCTTCAAGTGCGAGAAGCAGCCGGGGGCc/cc	2/2	1	2	FACETS	0.771	0.691	0.853	1	0.982	1	SUBCLONAL	2	TRUE	1	0.420978109754604	2		180	262	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705557	47705561	+	frameshift_variant	Frame_Shift_Del	DEL	AACTT	AACTT	-	novel	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	97	442	0	ENST00000233146.2:c.2358_2362del	p.Glu786AspfsTer11	p.E786Dfs*11	ENST00000233146	NM_000251.2	786	gAACTT/g	14/16	0.420649329616918	1	FACETS	0.95	0.854	1	0.95	0.854	1	CLONAL	1	TRUE	0	0.420978109754604	1		442	383	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042482	16042482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	84	461	4	ENST00000268712.3:c.1192C>T	p.Arg398Trp	p.R398W	ENST00000268712	NM_006311.3	398	Cgg/Tgg	12/46	1	2	FACETS	0.782	0.693	0.878	0.782	0.693	0.878	SUBCLONAL	1	TRUE	1	0.420978109754604	2		465	510	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16248837	16248837	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767352538	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	115	574	0	ENST00000375759.3:c.1843G>A	p.Glu615Lys	p.E615K	ENST00000375759	NM_015001.2	615	Gaa/Aaa	10/15	1	2	FACETS	0.883	0.797	0.973	0.883	0.797	0.973	CLONAL	1	TRUE	1	0.420978109754604	2		574	619	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778953	9778955	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs1259321686	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	70	604	0	ENST00000377346.4:c.1228_1230del	p.Lys410del	p.K410del	ENST00000377346	NM_005026.3	408	AAG/-	9/24	1	2	FACETS	0.521	0.454	0.594	0.521	0.454	0.594	SUBCLONAL	1	TRUE	1	0.420978109754604	2		604	638	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128044	64128044	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	69	659	0	ENST00000334205.4:c.442G>C	p.Ala148Pro	p.A148P	ENST00000334205	NM_003942.2	148	Gcc/Ccc	4/17	1	2	FACETS	0.414	0.36	0.473	0.414	0.36	0.473	SUBCLONAL	1	TRUE	1	0.420978109754604	2		659	792	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394816	394816	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	29	461	0	ENST00000399788.2:c.4879C>T	p.Gln1627Ter	p.Q1627*	ENST00000399788	NM_001042603.1	1627	Caa/Taa	28/28	NA	2	FACETS	0.25	0.2	0.307			1	INDETERMINATE	1	TRUE	NA	0.420978109754604	2		461	551	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432560	49432560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377747403	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	54	652	0	ENST00000301067.7:c.8579G>A	p.Arg2860His	p.R2860H	ENST00000301067	NM_003482.3	2860	cGt/cAt	34/54	1	2	FACETS	0.329	0.28	0.383	0.329	0.28	0.383	SUBCLONAL	1	TRUE	1	0.420978109754604	2		652	779	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434618	49434620	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	71	766	1	ENST00000301067.7:c.6933_6935del	p.Ser2312del	p.S2312del	ENST00000301067	NM_003482.3	2311	tcCTCa/tca	31/54	1	2	FACETS	0.426	0.371	0.486	0.426	0.371	0.486	SUBCLONAL	1	TRUE	1	0.420978109754604	2		767	791	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436360	110436360	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1201419105	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	96	467	1	ENST00000375856.3:c.2041G>A	p.Ala681Thr	p.A681T	ENST00000375856	NM_003749.2	681	Gcc/Acc	1/2	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.420978109754604	2		468	394	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355204	15355204	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147958185	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	157	701	2	ENST00000263377.2:c.2419G>A	p.Val807Ile	p.V807I	ENST00000263377	NM_058243.2	807	Gtc/Atc	13/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.420978109754604	2		703	683	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946803	17946803	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764977510	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	156	705	1	ENST00000458235.1:c.1844G>A	p.Arg615His	p.R615H	ENST00000458235	NM_000215.3	615	cGt/cAt	14/24	1	2	FACETS	0.989	0.908	1	0.989	0.908	1	CLONAL	1	TRUE	1	0.420978109754604	2		706	749	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266717	18266717	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765334654	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	61	641	1	ENST00000222254.8:c.28C>T	p.Arg10Cys	p.R10C	ENST00000222254	NM_005027.3	10	Cgc/Tgc	2/16	1	2	FACETS	0.466	0.402	0.536	0.466	0.402	0.536	SUBCLONAL	1	TRUE	1	0.420978109754604	2		642	622	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219933	36219933	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	83	695	0	ENST00000222270.7:c.4735C>T	p.Arg1579Cys	p.R1579C	ENST00000222270	NM_014727.1	1579	Cgt/Tgt	21/37	1	2	FACETS	0.53	0.467	0.597	0.53	0.467	0.597	SUBCLONAL	1	TRUE	1	0.420978109754604	2		695	744	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99169415	99169415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs909251709	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	34	391	0	ENST00000074304.5:c.1345G>A	p.Ala449Thr	p.A449T	ENST00000074304	NM_001134224.1	449	Gcc/Acc	15/26	1	2	FACETS	0.299	0.243	0.361	0.299	0.243	0.361	SUBCLONAL	1	TRUE	1	0.420978109754604	2		391	541	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267324	198267324	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	152	641	0	ENST00000335508.6:c.2033C>T	p.Ala678Val	p.A678V	ENST00000335508	NM_012433.2	678	gCc/gTc	14/25	1	2	FACETS	0.955	0.875	1	0.955	0.875	1	CLONAL	1	TRUE	1	0.420978109754604	2		641	756	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755719	39755719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	142	554	0	ENST00000288319.7:c.1046G>A	p.Arg349Gln	p.R349Q	ENST00000288319	NM_182918.3	349	cGg/cAg	10/10	1	2	FACETS	0.999	0.913	1	0.999	0.913	1	CLONAL	1	TRUE	1	0.420978109754604	2		554	675	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259150	89259150	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	107	451	0	ENST00000336596.2:c.294G>T	p.Glu98Asp	p.E98D	ENST00000336596	NM_005233.5	98	gaG/gaT	3/17	1	2	FACETS	0.983	0.886	1	0.983	0.886	1	CLONAL	1	TRUE	1	0.420978109754604	2		451	517	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157730	106157732	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs750024433	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	103	348	0	ENST00000380013.4:c.2636_2638del	p.Leu879del	p.L879del	ENST00000380013	NM_001127208.2	877	gaTCTt/gat	3/11	1	2	FACETS	0.915	0.821	1	0.915	0.821	1	CLONAL	1	TRUE	1	0.420978109754604	2		348	535	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39021189	39021189	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	81	615	0	ENST00000357387.3:c.147G>T	p.Gln49His	p.Q49H	ENST00000357387	NM_152756.3	49	caG/caT	3/38	1	2	FACETS	0.619	0.545	0.697	0.619	0.545	0.697	SUBCLONAL	1	TRUE	1	0.420978109754604	2		615	622	SUCCESS
APC	324	MSKCC	GRCh37	5	112175926	112175927	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	74	359	0	ENST00000257430.4:c.4636_4637del	p.Asn1546Ter	p.N1546*	ENST00000257430	NM_000038.5	1545	tcAAat/tcat	16/16	0.420978109754604	1	FACETS	0.789	0.695	0.888	0.789	0.695	0.888	SUBCLONAL	1	TRUE	0	0.420978109754604	1		359	352	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721772	176721772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587784217	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	42	487	1	ENST00000439151.2:c.7403G>A	p.Arg2468Gln	p.R2468Q	ENST00000439151	NM_022455.4	2468	cGg/cAg	23/23	1	2	FACETS	0.332	0.276	0.394	0.332	0.276	0.394	SUBCLONAL	1	TRUE	1	0.420978109754604	2		488	601	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840604	36840604	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs377685637	NA	P-0021894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	177	662	2	ENST00000358127.4:c.1129C>T	p.Arg377Ter	p.R377*	ENST00000358127	NM_001280556.1	377	Cga/Tga	10/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.420978109754604	2		664	677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0022151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	390	872	0	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.519145146319953	2	FACETS	0.844	0.809	0.879	0.844	0.809	0.879	CLONAL	2	TRUE	0	0.63466847037102	2		872	728	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0022151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	356	522	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.63466847037102	3	FACETS	0.971	0.926	1	0.647	0.617	0.677	CLONAL	2	TRUE	0	0.63466847037102	3		522	761	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29107902	29107902	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730881686	NA	P-0022151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	38	577	0	ENST00000328354.6:c.787G>C	p.Glu263Gln	p.E263Q	ENST00000328354	NM_007194.3	263	Gag/Cag	6/15	0.558987079317775	2	FACETS	0.193	0.159	0.231	0.096	0.079	0.116	SUBCLONAL	1	TRUE	0	0.63466847037102	2		577	621	SUCCESS
REL	5966	MSKCC	GRCh37	2	61121601	61121601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	154	576	0	ENST00000295025.8:c.223C>T	p.His75Tyr	p.H75Y	ENST00000295025	NM_002908.2	75	Cat/Tat	3/11	0.519145146319953	2	FACETS	0.85	0.782	0.92	0.425	0.391	0.46	CLONAL	1	TRUE	0	0.63466847037102	2		576	571	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435582	110435582	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	98	300	4	ENST00000375856.3:c.2819C>T	p.Ala940Val	p.A940V	ENST00000375856	NM_003749.2	940	gCg/gTg	1/2	NA	2	FACETS	1	0.95	1			1	INDETERMINATE	1	TRUE	NA	0.63466847037102	2		304	286	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743895	41743895	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	191	929	0	ENST00000301178.4:c.830del	p.Asp277AlafsTer20	p.D277Afs*20	ENST00000301178	NM_021913.4	277	gAc/gc	7/20	0.610975577801613	1	FACETS	0.734	0.683	0.786	0.734	0.683	0.786	SUBCLONAL	1	TRUE	0	0.63466847037102	1		929	560	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499434	89499434	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	136	566	0	ENST00000336596.2:c.2604A>C	p.Arg868Ser	p.R868S	ENST00000336596	NM_005233.5	868	agA/agC	15/17	1	2	FACETS	0.72	0.657	0.786	0.72	0.657	0.786	SUBCLONAL	1	TRUE	1	0.63466847037102	2		566	595	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979613	55979613	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	186	652	0	ENST00000263923.4:c.834A>T	p.Lys278Asn	p.K278N	ENST00000263923	NM_002253.2	278	aaA/aaT	7/30	0.269323342264101	6	FACETS	1	0.968	1	0.182	0.168	0.198	INDETERMINATE	1	TRUE	0	0.63466847037102	6		652	1216	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84388689	84388689	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	121	580	0	ENST00000321945.7:c.599C>A	p.Ser200Tyr	p.S200Y	ENST00000321945	NM_139076.2	200	tCt/tAt	7/9	0.486736034591258	3	FACETS	0.848	0.769	0.932	0.283	0.256	0.311	CLONAL	1	TRUE	0	0.63466847037102	3		580	592	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541351	187541351	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	52	477	0	ENST00000441802.2:c.6389G>T	p.Gly2130Val	p.G2130V	ENST00000441802	NM_005245.3	2130	gGa/gTa	10/27	0.63466847037102	1	FACETS	0.421	0.361	0.485	0.421	0.361	0.485	SUBCLONAL	1	TRUE	0	0.63466847037102	1		477	266	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752357	57752357	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs758394491	NA	P-0022151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	163	543	0	ENST00000274289.3:c.1216T>G	p.Ser406Ala	p.S406A	ENST00000274289	NM_006622.3	406	Tca/Gca	9/14	0.575753490169959	3	FACETS	1	0.951	1	0.522	0.481	0.565	CLONAL	1	TRUE	1	0.63466847037102	3		543	648	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	140	315	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.65012995549836	2		316	391	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306536	41306536	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	110	570	0	ENST00000373198.4:c.1123C>A	p.Pro375Thr	p.P375T	ENST00000373198	NM_133170.3	375	Cct/Act	7/32	1	2	FACETS	0.726	0.656	0.799	0.726	0.656	0.799	SUBCLONAL	1	TRUE	1	0.65012995549836	2		570	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579505	7579512	+	frameshift_variant	Frame_Shift_Del	DEL	TCTGGACC	TCTGGACC	-	novel	NA	P-0022322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	141	734	0	ENST00000269305.4:c.175_182del	p.Gly59Ter	p.G59*	ENST00000269305	NM_001126112.2	59	GGTCCAGAt/t	4/11	0.608025133281262	2	FACETS	0.875	0.802	0.95	0.437	0.401	0.475	CLONAL	1	TRUE	0	0.65012995549836	2		734	496	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673380	30673380	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	54	723	0	ENST00000376406.3:c.3580T>A	p.Ser1194Thr	p.S1194T	ENST00000376406	NM_014641.2	1194	Tcc/Acc	10/15	0.285335207036891	3	FACETS	0.309	0.263	0.359	0.154	0.131	0.18	INDETERMINATE	1	TRUE	1	0.65012995549836	3		723	713	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0022456-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	159	473	1	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	0.620033167520688	2		474	493	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022456-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	100	237	0	ENST00000257430.4:c.3919dup	p.Ile1307AsnfsTer8	p.I1307Nfs*8	ENST00000257430	NM_000038.5	1306	gaa/gAaa	16/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.620033167520688	2		237	296	SUCCESS
RET	5979	MSKCC	GRCh37	10	43595926	43595926	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022456-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1899	262	927	0	ENST00000355710.3:c.93C>G	p.Phe31Leu	p.F31L	ENST00000355710	NM_020975.4	31	ttC/ttG	2/20	0.620033167520688	7	FACETS	0.997	0.93	1			1	CLONAL	1	TRUE	NA	0.620033167520688	7		927	2161	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562493	21562493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1417916199	NA	P-0022456-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	27	67	0	ENST00000382592.4:c.1426G>A	p.Ala476Thr	p.A476T	ENST00000382592	NM_014572.2	476	Gcc/Acc	4/8	0.620033167520688	5	FACETS	1	0.855	1	0.359	0.289	0.438	CLONAL	1	TRUE	2	0.620033167520688	5		67	156	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041546	42041546	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022456-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	201	684	1	ENST00000219905.7:c.5741G>T	p.Ser1914Ile	p.S1914I	ENST00000219905	NM_001164273.1	1914	aGt/aTt	17/24	0.620033167520688	3	FACETS	0.918	0.851	0.987			1	CLONAL	1	TRUE	NA	0.620033167520688	3		685	925	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022456-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	846	935	1	ENST00000269305.4:c.159del	p.Trp53CysfsTer70	p.W53Cfs*70	ENST00000269305	NM_001126112.2	53	tgG/tg	4/11	0.620033167520688	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.620033167520688	3		936	1137	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240320	5240320	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1456886552	NA	P-0022456-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	234	1025	2	ENST00000357368.4:c.1594C>T	p.Arg532Trp	p.R532W	ENST00000357368	NM_002850.3	532	Cgg/Tgg	12/38	0.611833455814523	3	FACETS	0.905	0.843	0.968	0.452	0.421	0.484	CLONAL	1	TRUE	1	0.620033167520688	3		1027	1093	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379420	225379420	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022456-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	283	818	0	ENST00000264414.4:c.448C>A	p.Gln150Lys	p.Q150K	ENST00000264414	NM_003590.4	150	Caa/Aaa	4/16	0.611833455814523	3	FACETS	1	0.98	1	0.547	0.514	0.581	CLONAL	1	TRUE	1	0.620033167520688	3		818	1093	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466808	57466822	+	inframe_deletion	In_Frame_Del	DEL	CGAGGACCAGCGCAA	CGAGGACCAGCGCAA	-	novel	NA	P-0022456-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	114	406	1	ENST00000371085.3:c.33_47del	p.Asp11_Glu15del	p.D11_E15del	ENST00000371085	NM_000516.4	9	acCGAGGACCAGCGCAAc/acc	1/13	0.620033167520688	9	FACETS	0.887	0.796	0.984	0.127	0.113	0.141	CLONAL	1	TRUE	2	0.620033167520688	9		407	1314	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753960	57753960	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022456-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	150	495	0	ENST00000274289.3:c.664G>T	p.Gly222Trp	p.G222W	ENST00000274289	NM_006622.3	222	Ggg/Tgg	5/14	1	2	FACETS	0.981	0.903	1	0.981	0.903	1	CLONAL	1	TRUE	1	0.620033167520688	2		495	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579406	7579406	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0022870-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	294	672	0	ENST00000269305.4:c.281C>G	p.Ser94Ter	p.S94*	ENST00000269305	NM_001126112.2	94	tCa/tGa	4/11	0.386240774869486	3	FACETS	0.854	0.811	0.896	0.854	0.811	0.896	CLONAL	3	TRUE	0	0.470196063677887	3		672	603	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720676	89720677	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0022870-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	135	205	0	ENST00000371953.3:c.828_829del	p.Thr277IlefsTer20	p.T277Ifs*20	ENST00000371953	NM_000314.4	276	aAT/a	8/9	0.470196063677887	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.470196063677887	1		205	389	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141621	202141621	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022870-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	249	513	1	ENST00000358485.4:c.909T>A	p.Phe303Leu	p.F303L	ENST00000358485	NM_001080125.1	303	ttT/ttA	7/9	0.470196063677887	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.470196063677887	1		514	711	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577101	7577102	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCAGGACAGGCACAAACACGCACCTCAAAGCTGTTCCGTCCCAGTAGATTACCA	novel	NA	P-0023212-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	97	621	0	ENST00000269305.4:c.783_836dup	p.Gly262_Gly279dup	p.G262_G279dup	ENST00000269305	NM_001126112.2	262	ggg/ggTGGTAATCTACTGGGACGGAACAGCTTTGAGGTGCGTGTTTGTGCCTGTCCTGGg	8/11	0.457509247392711	1	FACETS	0.408	0.363	0.455	0.408	0.363	0.455	SUBCLONAL	1	TRUE	0	0.457509247392711	1		621	802	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350061	15350061	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023212-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	207	571	0	ENST00000263377.2:c.3591G>C	p.Lys1197Asn	p.K1197N	ENST00000263377	NM_058243.2	1197	aaG/aaC	18/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.457509247392711	2		571	713	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111741	56111741	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023212-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	33	116	0	ENST00000399503.3:c.341A>T	p.His114Leu	p.H114L	ENST00000399503	NM_005921.1	114	cAc/cTc	1/20	0.457509247392711	3	FACETS	0.828	0.691	0.974			1	CLONAL	2	TRUE	NA	0.457509247392711	3		116	107	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952146	178952147	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587776802	NA	P-0023283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	88	502	0	ENST00000263967.3:c.3203dup	p.Asn1068LysfsTer5	p.N1068Kfs*5	ENST00000263967	NM_006218.2	1067	-/A	21/21	0.521866733098674	4	FACETS	0.841	0.753	0.932	0.841	0.753	0.932	CLONAL	2	TRUE	2	0.522426901784265	4		502	305	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612061	189612061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777373892	NA	P-0023283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	126	810	1	ENST00000264731.3:c.1813C>T	p.Arg605Trp	p.R605W	ENST00000264731	NM_003722.4	605	Cgg/Tgg	14/14	0.521866733098674	4	FACETS	1	0.952	1	0.538	0.488	0.591	CLONAL	1	TRUE	2	0.522426901784265	4		811	682	SUCCESS
FH	2271	MSKCC	GRCh37	1	241669468	241669468	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	317	530	0	ENST00000366560.3:c.739G>A	p.Glu247Lys	p.E247K	ENST00000366560	NM_000143.3	247	Gaa/Aaa	6/10	0.522426901784265	8	FACETS	0.911	0.866	0.956	0.911	0.866	0.956	CLONAL	5	TRUE	3	0.522426901784265	8		530	684	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56857629	56857629	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	86	648	0	ENST00000308159.5:c.665A>C	p.Asp222Ala	p.D222A	ENST00000308159	NM_014669.4	222	gAc/gCc	8/22	0.521866733098674	4	FACETS	0.842	0.746	0.945	0.421	0.373	0.473	CLONAL	1	TRUE	2	0.522426901784265	4		648	595	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302252	15302252	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	74	861	0	ENST00000263388.2:c.1019G>T	p.Cys340Phe	p.C340F	ENST00000263388	NM_000435.2	340	tGc/tTc	6/33	0.446272758629342	4	FACETS	0.562	0.491	0.638	0.281	0.245	0.319	SUBCLONAL	1	TRUE	2	0.522426901784265	4		861	768	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0023530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	242	596	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.628645241291028	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.628645241291028	1		597	507	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0023530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	213	429	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.143745326411062	3	FACETS	1	0.986	1	0.612	0.57	0.654	INDETERMINATE	1	TRUE	1	0.628645241291028	3		429	728	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0023530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	250	796	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.628645241291028	2		796	793	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593491	48593494	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	rs80338965	NA	P-0023530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	132	448	0	ENST00000342988.3:c.1245_1248del	p.Asp415GlufsTer20	p.D415Efs*20	ENST00000342988	NM_005359.5	414	ttAGAC/tt	10/12	0.628645241291028	1	FACETS	0.929	0.857	1	0.929	0.857	1	CLONAL	1	TRUE	0	0.628645241291028	1		448	310	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974783	21974786	+	frameshift_variant	Frame_Shift_Del	DEL	CAGT	CAGT	-	novel	NA	P-0023530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	64	275	0	ENST00000304494.5:c.41_44del	p.Asp14GlyfsTer11	p.D14Gfs*11	ENST00000304494	NM_000077.4	14	gACTGg/gg	1/3	0.628645241291028	1	FACETS	0.812	0.718	0.908	0.812	0.718	0.908	CLONAL	1	TRUE	0	0.628645241291028	1		275	172	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063321	67063321	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023676-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	44	272	0	ENST00000412916.2:c.11T>G	p.Val4Gly	p.V4G	ENST00000412916		4	gTc/gGc	1/6	0.286429205509709	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	0	0.286429205509709	1		272	239	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0023676-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	67	455	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			0.286429205509709	1	FACETS	0.791	0.688	0.901	0.791	0.688	0.901	CLONAL	1	TRUE	0	0.286429205509709	1		455	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0023737-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	382	804	1	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.360302787403764	3	FACETS	1	0.989	1	0.732	0.7	0.764	CLONAL	2	TRUE	0	0.586657882229014	3		805	767	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512269	120512269	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023737-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	95	429	0	ENST00000256646.2:c.973G>C	p.Val325Leu	p.V325L	ENST00000256646	NM_024408.3	325	Gta/Cta	6/34	1	2	FACETS	0.581	0.519	0.648	0.581	0.519	0.648	SUBCLONAL	1	TRUE	1	0.586657882229014	2		429	557	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62311283	62311283	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023737-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	32	265	0	ENST00000360203.5:c.1119C>G	p.Ile373Met	p.I373M	ENST00000360203	NM_001283009.1	373	atC/atG	13/35	0.586657882229014	3	FACETS	0.337	0.273	0.409	0.168	0.136	0.205	SUBCLONAL	1	TRUE	1	0.586657882229014	3		265	419	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864407	162864407	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023737-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	70	480	1	ENST00000366898.1:c.106G>T	p.Val36Phe	p.V36F	ENST00000366898	NM_004562.2	36	Gtt/Ttt	2/12	1	2	FACETS	0.439	0.383	0.5	0.439	0.383	0.5	SUBCLONAL	1	TRUE	1	0.586657882229014	2		481	543	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0023919-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	119	443	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.501	0.453	0.552	0.501	0.453	0.552	SUBCLONAL	1	TRUE	1	0.689152664792405	2		443	689	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922364	178922364	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397514565	NA	P-0023919-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	146	445	0	ENST00000263967.3:c.1133G>A	p.Cys378Tyr	p.C378Y	ENST00000263967	NM_006218.2	378	tGt/tAt	6/21	1	2	FACETS	0.553	0.505	0.603	0.553	0.505	0.603	SUBCLONAL	1	TRUE	1	0.689152664792405	2		445	766	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117593	70117599	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCCCA	GCCCCCA	-	novel	NA	P-0023919-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	117	579	0	ENST00000245479.2:c.66_72del	p.Ser23ProfsTer36	p.S23Pfs*36	ENST00000245479	NM_000346.3	21	GCCCCCAgc/gc	1/3	1	2	FACETS	0.362	0.326	0.4	0.362	0.326	0.4	SUBCLONAL	1	TRUE	1	0.689152664792405	2		579	938	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539785	187539785	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1319757634	NA	P-0023919-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	83	366	0	ENST00000441802.2:c.7955C>T	p.Ser2652Phe	p.S2652F	ENST00000441802	NM_005245.3	2652	tCc/tTc	10/27	1	2	FACETS	0.444	0.393	0.499	0.444	0.393	0.499	SUBCLONAL	1	TRUE	1	0.689152664792405	2		366	542	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412443	80412443	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023919-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	79	269	0	ENST00000286548.4:c.598A>G	p.Ile200Val	p.I200V	ENST00000286548	NM_002072.3	200	Att/Gtt	4/7	1	2	FACETS	0.409	0.36	0.461	0.409	0.36	0.461	SUBCLONAL	1	TRUE	1	0.689152664792405	2		269	561	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952146	178952147	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587776802	NA	P-0024119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	12	502	0	ENST00000263967.3:c.3203dup	p.Asn1068LysfsTer5	p.N1068Kfs*5	ENST00000263967	NM_006218.2	1067	-/A	21/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		502	150	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112025222	112025222	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866100904	NA	P-0024165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	77	785	2	ENST00000368678.4:c.527G>A	p.Arg176His	p.R176H	ENST00000368678		176	cGc/cAc	6/13	1	2	FACETS	0.783	0.689	0.883	0.783	0.689	0.883	SUBCLONAL	1	TRUE	1	0.382699163607467	2		787	514	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954222	48954222	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0024182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	49	460	0	ENST00000267163.4:c.1421+2T>A		p.X474_splice	ENST00000267163	NM_000321.2	474			0.876513783239097	1	FACETS	0.208	0.177	0.242	0.208	0.177	0.242	SUBCLONAL	1	TRUE	0	0.876513783239097	1		460	302	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575051	64575051	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	231	565	0	ENST00000312049.6:c.756del	p.Ser253ArgfsTer28	p.S253Rfs*28	ENST00000312049	NM_130799.2	252	gaC/ga	4/10	0.81519929842208	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.876513783239097	1		565	292	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	70	528	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.335533887122891	5	FACETS	0.839	0.735	0.949	0.559	0.49	0.633	CLONAL	2	TRUE	2	0.335533887122891	5		529	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934573	NA	P-0024354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	40	808	0	ENST00000269305.4:c.722C>A	p.Ser241Tyr	p.S241Y	ENST00000269305	NM_001126112.2	241	tCc/tAc	7/11	0.247799612405275	2	FACETS	1	0.935	1	0.618	0.519	0.725	CLONAL	1	TRUE	0	0.335533887122891	2		808	193	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142475	119142475	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	336	610	0	ENST00000264033.4:c.474del	p.Phe158LeufsTer8	p.F158Lfs*8	ENST00000264033	NM_005188.3	158	ttC/tt	3/16	0.719654626691588	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.716419299987908	4		610	797	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058866	42058866	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	232	463	3	ENST00000219905.7:c.8589del	p.Phe2863LeufsTer22	p.F2863Lfs*22	ENST00000219905	NM_001164273.1	2862	gcT/gc	24/24	0.719654626691588	4	FACETS	0.98	0.922	1	0.98	0.922	1	CLONAL	2	TRUE	2	0.716419299987908	4		466	567	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039290	47039290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	146	983	3	ENST00000377604.3:c.913C>T	p.Arg305Cys	p.R305C	ENST00000377604	NM_001204468.1	305	Cgc/Tgc	10/24	0.346532489483061	5	FACETS	0.924	0.843	1	0.308	0.281	0.337	INDETERMINATE	1	TRUE	2	0.716419299987908	5		986	915	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509978	106509978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764518673	NA	P-0024538-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	119	541	0	ENST00000359195.3:c.1972C>T	p.His658Tyr	p.H658Y	ENST00000359195	NM_002649.2	658	Cat/Tat	2/11	0.465288120566547	3	FACETS	0.554	0.499	0.613	0.277	0.249	0.307	SUBCLONAL	1	FALSE	1	0.465288120566547	3		541	1138	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519886	NA	P-0024538-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	159	359	0	ENST00000349496.5:c.97T>G	p.Ser33Ala	p.S33A	ENST00000349496	NM_001904.3	33	Tct/Gct	3/15	1	2	FACETS	0.955	0.877	1	0.955	0.877	1	CLONAL	1	FALSE	1	0.465288120566547	2		359	716	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807914	3807914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	57	877	0	ENST00000262367.5:c.3505C>T	p.Arg1169Cys	p.R1169C	ENST00000262367	NM_004380.2	1169	Cgc/Tgc	18/31	0.376414921454646	6	FACETS	0.416	0.355	0.482	0.139	0.118	0.161	INDETERMINATE	1	TRUE	3	0.793743150400196	6		877	894	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248525	59248525	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	178	888	0	ENST00000371222.2:c.218C>T	p.Ser73Leu	p.S73L	ENST00000371222	NM_002228.3	73	tCg/tTg	1/1	0.793743150400196	3	FACETS	1	0.953	1	0.519	0.48	0.558	CLONAL	1	TRUE	1	0.793743150400196	3		888	604	SUCCESS
BLM	641	MSKCC	GRCh37	15	91298070	91298070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	189	702	0	ENST00000355112.3:c.989G>A	p.Arg330Lys	p.R330K	ENST00000355112	NM_000057.2	330	aGa/aAa	5/22	0.431138559871473	6	FACETS	0.834	0.773	0.897	0.556	0.515	0.598	INDETERMINATE	2	TRUE	3	0.793743150400196	6		702	739	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785527	50785527	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs965699210	NA	P-0024546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	170	784	0	ENST00000398568.2:c.517G>A	p.Gly173Ser	p.G173S	ENST00000398568	NM_001042412.1	173	Ggt/Agt	4/18	0.793743150400196	6	FACETS	0.921	0.845	1			1	CLONAL	1	TRUE	NA	0.793743150400196	6		784	1204	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838103	89838103	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	536	826	0	ENST00000389301.3:c.2134G>T	p.Glu712Ter	p.E712*	ENST00000389301	NM_000135.2	712	Gag/Tag	23/43	0.793743150400196	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	0	0.793743150400196	3		826	628	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39535278	39535278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	78	412	0	ENST00000262039.4:c.22C>T	p.His8Tyr	p.H8Y	ENST00000262039	NM_002647.2	8	Cac/Tac	1/25	0.793743150400196	3	FACETS	0.832	0.737	0.932	0.416	0.368	0.466	CLONAL	1	TRUE	1	0.793743150400196	3		412	330	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549701	187549701	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	154	747	0	ENST00000441802.2:c.4540C>G	p.Leu1514Val	p.L1514V	ENST00000441802	NM_005245.3	1514	Ctc/Gtc	8/27	0.431138559871473	6	FACETS	1	0.98	1	0.411	0.376	0.448	INDETERMINATE	1	TRUE	3	0.793743150400196	6		747	814	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225626	26225626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373685271	NA	P-0024546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	649	834	0	ENST00000360408.1:c.244G>A	p.Asp82Asn	p.D82N	ENST00000360408	NM_003532.2	82	Gac/Aac	1/1	0.793743150400196	3	FACETS	0.959	0.939	0.978	0.959	0.939	0.978	CLONAL	3	TRUE	0	0.793743150400196	3		834	794	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087503	27087503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024608-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	271	722	1	ENST00000324856.7:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000324856	NM_006015.4	693	Cga/Tga	5/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.602510999731542	2		723	887	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	54	315	1				ENST00000310581	NM_198253.2	-/1132			0.351358335560238	3	FACETS	1	0.912	1	1	0.912	1	CLONAL	2	TRUE	1	0.453074865681593	3		316	139	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952138	178952139	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	79	283	0	ENST00000263967.3:c.3193_3194insT	p.His1065LeufsTer8	p.H1065Lfs*8	ENST00000263967	NM_006218.2	1065	cat/cTat	21/21	1	2	FACETS	0.878	0.777	0.986	0.878	0.777	0.986	CLONAL	1	TRUE	1	0.453074865681593	2		283	397	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0024791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	157	692	1	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	1	2	FACETS	0.763	0.698	0.831	1	0.988	1	SUBCLONAL	2	TRUE	1	0.21	2		693	980	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896990	28896990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753953796	NA	P-0024791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	75	547	1	ENST00000282397.4:c.2890G>A	p.Glu964Lys	p.E964K	ENST00000282397	NM_002019.4	964	Gaa/Aaa	21/30	1	2	FACETS	0.946	0.828	1	0.946	0.828	1	CLONAL	1	TRUE	1	0.21	2		548	755	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855202	76855207	+	stop_gained,frameshift_variant,splice_region_variant	Nonsense_Mutation	DEL	TTGTAT	TTGTAT	C	novel	NA	P-0024791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	52	634	0	ENST00000373344.5:c.5780_5785delinsG	p.Tyr1927Ter	p.Y1927*	ENST00000373344	NM_000489.3	1927	tATACAAaa/tGaa	24/35	1	2	FACETS	0.727	0.618	0.847	0.727	0.618	0.847	SUBCLONAL	1	TRUE	1	0.21	2		634	681	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	944	315	1				ENST00000310581	NM_198253.2	-/1132			0.77979864594702	8	FACETS	1	0.983	1	1	0.983	1	CLONAL	6	TRUE	2	0.77979864594702	8		316	1340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0024797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	773	570	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.77979864594702	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	0	0.77979864594702	3		570	913	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934194	48934194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	229	503	0	ENST00000267163.4:c.649C>T	p.Gln217Ter	p.Q217*	ENST00000267163	NM_000321.2	217	Cag/Tag	7/27	0.77979864594702	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.77979864594702	1		503	325	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438587	49438587	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	243	467	0	ENST00000301067.7:c.4903del	p.Gly1636AlafsTer86	p.G1636Afs*86	ENST00000301067	NM_003482.3	1635	Ctt/tt	19/54	0.765905872583166	3	FACETS	1	0.947	1	0.506	0.474	0.539	CLONAL	1	TRUE	1	0.77979864594702	3		467	856	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046521	30046521	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	234	518	0	ENST00000331968.5:c.2662A>G	p.Ser888Gly	p.S888G	ENST00000331968	NM_002742.2	888	Agt/Ggt	18/18	0.7582043888118	4	FACETS	1	0.954	1	0.515	0.48	0.55	CLONAL	1	TRUE	2	0.77979864594702	4		518	1038	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095002	11095002	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1315494799	NA	P-0024797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	550	597	0	ENST00000358026.2:c.175C>T	p.Gln59Ter	p.Q59*	ENST00000358026	NM_001128849.1	59	Cag/Tag	2/36	0.773065538532559	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.77979864594702	2		597	692	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207631	29207632	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0024797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	215	451	0	ENST00000240100.2:c.164dup	p.His56AlafsTer15	p.H56Afs*15	ENST00000240100	NM_001394.6	55	gcg/gcCg	1/4	1	2	FACETS	0.952	0.892	1	0.952	0.892	1	CLONAL	1	TRUE	1	0.77979864594702	2		451	579	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0025160-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	446	570	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	0.467493322199202	2	FACETS	0.946	0.906	0.985	0.946	0.906	0.985	CLONAL	2	TRUE	0	0.471173308289522	2		570	1001	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482425	56482425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025160-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	230	518	0	ENST00000267101.3:c.973G>A	p.Gly325Arg	p.G325R	ENST00000267101	NM_001982.3	325	Gga/Aga	8/28	0.467493322199202	2	FACETS	1	0.97	1	0.533	0.498	0.57	CLONAL	1	TRUE	0	0.471173308289522	2		518	915	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900288	101900288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111854391	NA	P-0025160-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	144	358	1	ENST00000374994.4:c.722C>T	p.Ser241Leu	p.S241L	ENST00000374994	NM_004612.2	241	tCg/tTg	4/9	1	2	FACETS	0.869	0.795	0.948	0.869	0.795	0.948	CLONAL	1	TRUE	1	0.471173308289522	2		359	703	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0025160-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	237	590	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	1	2	FACETS	0.925	0.863	0.989	0.925	0.863	0.989	CLONAL	1	TRUE	1	0.471173308289522	2		590	1088	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023873	27023873	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0025160-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	108	230	0	ENST00000324856.7:c.979A>T	p.Lys327Ter	p.K327*	ENST00000324856	NM_006015.4	327	Aag/Tag	1/20	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.471173308289522	2		230	427	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094744	2094744	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025160-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	264	613	0	ENST00000219066.1:c.436G>T	p.Val146Leu	p.V146L	ENST00000219066	NM_002528.5	146	Gtg/Ttg	3/6	1	2	FACETS	0.994	0.932	1	0.994	0.932	1	CLONAL	1	TRUE	1	0.471173308289522	2		613	1127	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266041	41266672	+	splice_donor_variant,splice_acceptor_variant,stop_lost,protein_altering_variant,intron_variant	Splice_Site	DEL	CCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCAAGATGATGCAGAACTTGCCACACGTGCAATCCCTGAACTGA	CCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCAAGATGATGCAGAACTTGCCACACGTGCAATCCCTGAACTGA	-	novel	NA	P-0025160-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	66	223	0	ENST00000349496.5:c.39_470del		p.X13_splice	ENST00000349496	NM_001904.3	13	gCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCAAGATGATGCAGAACTTGCCACACGTGCAATCCCTGAACTGAca/gca	3-4/15	1	2	FACETS	0.617	0.537	0.703	0.617	0.537	0.703	SUBCLONAL	1	TRUE	1	0.471173308289522	2		223	454	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70005682	70005682	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1559749017	NA	P-0025160-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	144	379	0	ENST00000394351.3:c.710+1G>A		p.X237_splice	ENST00000394351	NM_000248.3	237			1	2	FACETS	0.892	0.816	0.972	0.892	0.816	0.972	CLONAL	1	TRUE	1	0.471173308289522	2		379	685	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908891	101908891	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025160-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	128	448	0	ENST00000374994.4:c.1255G>C	p.Gly419Arg	p.G419R	ENST00000374994	NM_004612.2	419	Gga/Cga	7/9	1	2	FACETS	0.693	0.628	0.761	0.693	0.628	0.761	SUBCLONAL	1	TRUE	1	0.471173308289522	2		448	784	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40864896	40864896	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	523	466	0	ENST00000373198.4:c.2372G>A	p.Arg791Lys	p.R791K	ENST00000373198	NM_133170.3	791	aGa/aAa	16/32	0.7295807011412	3	FACETS	0.897	0.864	0.93	0.897	0.864	0.93	CLONAL	2	TRUE	1	0.7740970263939	3		466	1045	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692969	89692979	+	frameshift_variant	Frame_Shift_Del	DEL	CCTAGATTTCT	CCTAGATTTCT	-	novel	NA	P-0025275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	40	562	0	ENST00000371953.3:c.453_463del	p.Leu152TrpfsTer24	p.L152Wfs*24	ENST00000371953	NM_000314.4	151	gcCCTAGATTTCTat/gcat	5/9	0.7740970263939	1	FACETS	0.116	0.096	0.139	0.116	0.096	0.139	SUBCLONAL	1	TRUE	0	0.7740970263939	1		562	544	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207831	102207831	+	stop_lost	Nonstop_Mutation	SNP	T	T	G	novel	NA	P-0025275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	85	273	0	ENST00000263464.3:c.1813T>G	p.Ter605GlyextTer10	p.*605Gext*10	ENST00000263464	NM_001165.4	605	Tga/Gga	9/9	1	2	FACETS	0.412	0.365	0.462	0.412	0.365	0.462	SUBCLONAL	1	TRUE	1	0.7740970263939	2		273	533	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955480	48955506	+	inframe_deletion	In_Frame_Del	DEL	CGAAAGTTTTATCAAAGCAGAAGGCAA	CGAAAGTTTTATCAAAGCAGAAGGCAA	-	novel	NA	P-0025275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	238	497	0	ENST00000267163.4:c.1597_1623del	p.Glu533_Asn541del	p.E533_N541del	ENST00000267163	NM_000321.2	532	atCGAAAGTTTTATCAAAGCAGAAGGCAAc/atc	17/27	0.7740970263939	1	FACETS	0.954	0.907	1	0.954	0.907	1	CLONAL	1	TRUE	0	0.7740970263939	1		497	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573897	7573993	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAGGGCCAGGAAGGGGCTGAGGTCACTCACCTGGAGTGAGCCCTGCTCCCCCCTGGCTCCTTCCCAGCCTGGGCATCCTTGAGTTCCAAGGCCTCAT	TAGGGCCAGGAAGGGGCTGAGGTCACTCACCTGGAGTGAGCCCTGCTCCCCCCTGGCTCCTTCCCAGCCTGGGCATCCTTGAGTTCCAAGGCCTCAT	-	novel	NA	P-0025275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	310	347	0	ENST00000269305.4:c.1034_1100+30del		p.X345_splice	ENST00000269305	NM_001126112.2	345		10/11	0.75275459930236	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.7740970263939	1		347	475	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40864899	40864899	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs746035795	NA	P-0025275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	514	455	0	ENST00000373198.4:c.2370-1G>A		p.X790_splice	ENST00000373198	NM_133170.3	790			0.7295807011412	3	FACETS	0.904	0.87	0.937	0.904	0.87	0.937	CLONAL	2	TRUE	1	0.7740970263939	3		455	1019	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047507	49047507	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1131690906	NA	P-0025650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	257	369	0	ENST00000267163.4:c.2501C>A	p.Ser834Ter	p.S834*	ENST00000267163	NM_000321.2	834	tCa/tAa	24/27	0.898447912481163	1	FACETS	0.982	0.948	1	0.982	0.948	1	CLONAL	1	TRUE	0	0.898447912481163	1		369	321	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560468	65560468	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	354	465	0	ENST00000358664.4:c.129del	p.His44ThrfsTer21	p.H44Tfs*21	ENST00000358664	NM_002382.4	43	ttT/tt	3/5	NA	2	FACETS	0.929	0.885	0.974			1	INDETERMINATE	1	TRUE	NA	0.898447912481163	2		465	848	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341195	8341195	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755582635	NA	P-0025650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	330	447	0	ENST00000356435.5:c.5021G>A	p.Arg1674His	p.R1674H	ENST00000356435		1674	cGc/cAc	30/35	1	2	FACETS	0.993	0.944	1	0.993	0.944	1	CLONAL	1	TRUE	1	0.898447912481163	2		447	740	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776583	9776584	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCAGCCGCCA	novel	NA	P-0025650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	434	626	0	ENST00000377346.4:c.694_695insCAGCAGCCGC	p.Leu232ProfsTer20	p.L232Pfs*20	ENST00000377346	NM_005026.3	229	cgg/cgGCAGCCGCCAg	6/24	0.898447912481163	1	FACETS	0.423	0.403	0.443	0.423	0.403	0.443	SUBCLONAL	1	TRUE	0	0.898447912481163	1		626	1259	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70971077	70971077	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	424	589	0	ENST00000276594.2:c.1184A>G	p.Glu395Gly	p.E395G	ENST00000276594	NM_024504.3	395	gAg/gGg	6/8	1	2	FACETS	0.893	0.853	0.933	0.893	0.853	0.933	CLONAL	1	TRUE	1	0.898447912481163	2		589	1057	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025670-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	14	315	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.922	0.667	1	0.922	0.667	1	CLONAL	1	TRUE	1	0.14	2		316	217	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521298	187521299	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0025670-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	35	484	1	ENST00000441802.2:c.11856dup	p.Gly3953TrpfsTer19	p.G3953Wfs*19	ENST00000441802	NM_005245.3	3952	-/T	22/27	1	2	FACETS	0.88	0.72	1	0.88	0.72	1	CLONAL	1	TRUE	1	0.14	2		485	568	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137620	202137620	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0025670-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	39	364	0	ENST00000358485.4:c.728-1G>C		p.X243_splice	ENST00000358485	NM_001080125.1	243			1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.14	2		364	473	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227057	2227057	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025670-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	37	536	3	ENST00000398665.3:c.4537G>A	p.Ala1513Thr	p.A1513T	ENST00000398665	NM_032482.2	1513	Gct/Act	27/28	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.14	2		539	481	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512271	120512271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025670-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	27	449	0	ENST00000256646.2:c.971G>A	p.Cys324Tyr	p.C324Y	ENST00000256646	NM_024408.3	324	tGt/tAt	6/34	1	2	FACETS	0.812	0.645	1	0.812	0.645	1	CLONAL	1	TRUE	1	0.14	2		449	475	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918501	94918502	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0025670-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	30	481	0	ENST00000536441.1:c.680dup	p.Ser228IlefsTer9	p.S228Ifs*9	ENST00000536441	NM_144665.3	227	ata/atTa	5/10	1	2	FACETS	0.887	0.714	1	0.887	0.714	1	CLONAL	1	TRUE	1	0.14	2		481	483	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344720	118344721	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0025670-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	21	298	0	ENST00000534358.1:c.2848_2849del	p.Leu950TrpfsTer47	p.L950Wfs*47	ENST00000534358	NM_005933.3	949	aCT/a	3/36	1	2	FACETS	0.826	0.636	1	0.826	0.636	1	CLONAL	1	TRUE	1	0.14	2		298	363	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372411	118372412	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0025670-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	33	471	0	ENST00000534358.1:c.6347_6348del	p.Thr2116SerfsTer2	p.T2116Sfs*2	ENST00000534358	NM_005933.3	2115	aAC/a	26/36	1	2	FACETS	0.817	0.664	0.99	0.817	0.664	0.99	CLONAL	1	TRUE	1	0.14	2		471	577	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996808	73996808	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025670-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	23	223	0	ENST00000318443.5:c.1364T>G	p.Ile455Ser	p.I455S	ENST00000318443	NM_001024736.1	455	aTc/aGc	6/10	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.14	2		223	294	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211975	36211975	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025670-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	39	779	0	ENST00000222270.7:c.1726G>T	p.Glu576Ter	p.E576*	ENST00000222270	NM_014727.1	576	Gag/Tag	3/37	1	2	FACETS	0.817	0.675	0.976	0.817	0.675	0.976	CLONAL	1	TRUE	1	0.14	2		779	682	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215611	36215611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025670-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	41	594	0	ENST00000222270.7:c.3409del	p.Ala1137ProfsTer45	p.A1137Pfs*45	ENST00000222270	NM_014727.1	1136	aaG/aa	9/37	1	2	FACETS	1	0.84	1	1	0.84	1	CLONAL	1	TRUE	1	0.14	2		594	580	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519244	187519245	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0025670-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	34	479	0	ENST00000441802.2:c.12138dup	p.Thr4047AspfsTer4	p.T4047Dfs*4	ENST00000441802	NM_005245.3	4046	-/G	23/27	1	2	FACETS	0.875	0.714	1	0.875	0.714	1	CLONAL	1	TRUE	1	0.14	2		479	555	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395101	139395108	+	frameshift_variant	Frame_Shift_Del	DEL	CGCTTGGC	CGCTTGGC	-	novel	NA	P-0025670-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	30	530	0	ENST00000277541.6:c.5830_5837del	p.Ala1944ProfsTer48	p.A1944Pfs*48	ENST00000277541	NM_017617.3	1944	GCCAAGCGc/c	31/34	1	2	FACETS	0.873	0.702	1	0.873	0.702	1	CLONAL	1	TRUE	1	0.14	2		530	491	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0025688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	74	321	2	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.434868232841252	3	FACETS	0.844	0.741	0.954	0.422	0.37	0.477	CLONAL	1	TRUE	1	0.434868232841252	3		323	491	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0025688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	45	278	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.739	0.625	0.864	0.739	0.625	0.864	SUBCLONAL	1	TRUE	1	0.434868232841252	2		278	280	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203436	NA	P-0025688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	126	590	0	ENST00000269305.4:c.487T>C	p.Tyr163His	p.Y163H	ENST00000269305	NM_001126112.2	163	Tac/Cac	5/11	0.384791093068744	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.434868232841252	1		590	442	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0025688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	62	473	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.794	0.69	0.907	0.794	0.69	0.907	CLONAL	1	TRUE	1	0.434868232841252	2		474	359	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561309	9561309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760330867	NA	P-0025688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	47	389	0	ENST00000353224.5:c.473C>T	p.Pro158Leu	p.P158L	ENST00000353224	NM_177990.2	158	cCg/cTg	4/10	NA	2	FACETS	0.688	0.584	0.803			1	INDETERMINATE	1	TRUE	NA	0.434868232841252	2		389	314	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777676	9777676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	122	529	0	ENST00000377346.4:c.1012C>T	p.Arg338Trp	p.R338W	ENST00000377346	NM_005026.3	338	Cgg/Tgg	8/24	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.434868232841252	2		529	552	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610695	52610695	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	70	447	0	ENST00000394830.3:c.3478C>T	p.Arg1160Ter	p.R1160*	ENST00000394830	NM_018313.4	1160	Cga/Tga	23/30	1	2	FACETS	0.882	0.774	0.998	0.882	0.774	0.998	CLONAL	1	TRUE	1	0.434868232841252	2		447	365	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066648	94066648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371089003	NA	P-0025688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	83	504	0	ENST00000369303.4:c.1111C>T	p.Arg371Trp	p.R371W	ENST00000369303	NM_004440.3	371	Cgg/Tgg	5/17	0.43393917040379	1	FACETS	0.766	0.68	0.857	0.766	0.68	0.857	SUBCLONAL	1	TRUE	0	0.434868232841252	1		504	390	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620674	52620674	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	63	303	0	ENST00000394830.3:c.3079C>T	p.Arg1027Ter	p.R1027*	ENST00000394830	NM_018313.4	1027	Cga/Tga	21/30	1	2	FACETS	0.798	0.694	0.91	0.798	0.694	0.91	CLONAL	1	TRUE	1	0.434868232841252	2		303	363	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828384	72828384	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759038643	NA	P-0025688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	70	429	1	ENST00000268489.5:c.8197C>T	p.Arg2733Cys	p.R2733C	ENST00000268489	NM_006885.3	2733	Cgt/Tgt	9/10	1	2	FACETS	0.925	0.812	1	0.925	0.812	1	CLONAL	1	TRUE	1	0.434868232841252	2		430	348	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242444	55242445	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAAATTCCCGTCGCTATC	rs397517090	NA	P-0026045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	150	547	0	ENST00000275493.2:c.2217_2234dup	p.Ile740_Lys745dup	p.I740_K745dup	ENST00000275493	NM_005228.3	740	-/AAAATTCCCGTCGCTATC	19/28	0.328719123362289	4	FACETS	0.86	0.788	0.935	0.573	0.525	0.624	CLONAL	2	TRUE	1	0.328719123362289	4		547	705	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951939	178951943	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CATAA	CATAA	ATG	novel	NA	P-0026045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	112	513	0	ENST00000263967.3:c.2994_2998delinsATG	p.Phe998LeufsTer2	p.F998Lfs*2	ENST00000263967	NM_006218.2	998	ttCATAAat/ttATGat	21/21	0.281494288007849	4	FACETS	0.888	0.802	0.977	0.888	0.802	0.977	CLONAL	2	TRUE	2	0.328719123362289	4		513	510	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753316	57753316	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	170	418	0	ENST00000274289.3:c.808A>T	p.Met270Leu	p.M270L	ENST00000274289	NM_006622.3	270	Atg/Ttg	6/14	0.328719123362289	5	FACETS	0.908	0.84	0.978	0.908	0.84	0.978	CLONAL	3	TRUE	2	0.328719123362289	5		418	567	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593578	55593606	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	In_Frame_Del	DEL	ACAGAAACCCATGTATGAAGTACAGTGGA	ACAGAAACCCATGTATGAAGTACAGTGGA	-	novel	NA	P-0026071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	169	301	0	ENST00000288135.5:c.1648-3_1673del		p.K550_K558del	ENST00000288135	NM_000222.2	550		11/21	1	2	FACETS	0.921	0.85	0.995	0.921	0.85	0.995	CLONAL	1	TRUE	1	0.553329650909608	2		301	663	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924204	11924204	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0026071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	10	18	0	ENST00000353533.5:c.1A>G	p.Met1?	p.M1?	ENST00000353533	NM_003010.3	1	Atg/Gtg	1/11	1	2	FACETS	0.821	0.574	1	0.821	0.574	1	CLONAL	1	TRUE	1	0.553329650909608	2		18	44	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593578	55593606	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	In_Frame_Del	DEL	ACAGAAACCCATGTATGAAGTACAGTGGA	ACAGAAACCCATGTATGAAGTACAGTGGA	-	novel	NA	P-0026071-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	50	301	0	ENST00000288135.5:c.1648-3_1673del		p.K550_K558del	ENST00000288135	NM_000222.2	550		11/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		301	313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0026231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	324	601	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.278838394424317	2	FACETS	0.82	0.779	0.861	0.82	0.779	0.861	INDETERMINATE	2	TRUE	0	0.528244636163553	2		603	748	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0026231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	34	591	1	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.278838394424317	2	FACETS	0.216	0.176	0.262	0.108	0.088	0.131	INDETERMINATE	1	TRUE	0	0.528244636163553	2		592	595	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40856625	40856625	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	204	525	2	ENST00000428826.2:c.2012A>G	p.Asn671Ser	p.N671S	ENST00000428826		671	aAt/aGt	18/21	0.278838394424317	2	FACETS	1	0.99	1	0.667	0.623	0.712	INDETERMINATE	1	TRUE	0	0.528244636163553	2		527	579	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661268	227661268	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	270	670	0	ENST00000305123.5:c.2187del	p.Gly730ValfsTer4	p.G730Vfs*4	ENST00000305123	NM_005544.2	729	acA/ac	1/2	0.301709551533886	3	FACETS	0.781	0.735	0.828	0.781	0.735	0.828	INDETERMINATE	2	TRUE	1	0.528244636163553	3		670	827	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860704	3860704	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs752252706	NA	P-0026231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	44	594	0	ENST00000262367.5:c.875G>T	p.Gly292Val	p.G292V	ENST00000262367	NM_004380.2	292	gGa/gTa	3/31	0.301709551533886	3	FACETS	0.283	0.236	0.334	0.141	0.118	0.167	INDETERMINATE	1	TRUE	1	0.528244636163553	3		594	745	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0026262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	28	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.441	0.351	0.544	0.441	0.351	0.544	SUBCLONAL	1	TRUE	1	0.21	2		509	605	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691025	NA	P-0026262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	60	439	0	ENST00000269305.4:c.785G>T	p.Gly262Val	p.G262V	ENST00000269305	NM_001126112.2	262	gGt/gTt	8/11	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.21	2		439	506	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600324	10600324	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	25	462	0	ENST00000171111.5:c.1531G>T	p.Gly511Cys	p.G511C	ENST00000171111	NM_203500.1	511	Ggc/Tgc	4/6	0.184745296377109	1	FACETS	0.541	0.426	0.673	0.541	0.426	0.673	SUBCLONAL	1	TRUE	0	0.21	1		462	394	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678622	88678622	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	17	291	0	ENST00000360948.2:c.914C>A	p.Pro305Gln	p.P305Q	ENST00000360948	NM_001012338.2	305	cCa/cAa	9/19	1	2	FACETS	0.62	0.463	0.807	0.62	0.463	0.807	SUBCLONAL	1	TRUE	1	0.21	2		291	261	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133825	55133825	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	32	389	0	ENST00000257290.5:c.1038G>T	p.Arg346Ser	p.R346S	ENST00000257290	NM_006206.4	346	agG/agT	7/23	1	2	FACETS	0.606	0.491	0.736	0.606	0.491	0.736	SUBCLONAL	1	TRUE	1	0.21	2		389	503	SUCCESS
RET	5979	MSKCC	GRCh37	10	43598056	43598056	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	27	549	0	ENST00000355710.3:c.604G>T	p.Val202Leu	p.V202L	ENST00000355710	NM_020975.4	202	Gtg/Ttg	3/20	0.3	2	FACETS	0.513	0.407	0.635			1	SUBCLONAL	1	TRUE	NA	0.21	2		549	501	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657408	29657408	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	39	492	0	ENST00000356175.3:c.5641G>T	p.Ala1881Ser	p.A1881S	ENST00000356175	NM_000267.3	1881	Gcc/Tcc	38/57	1	2	FACETS	0.498	0.411	0.595	0.498	0.411	0.595	SUBCLONAL	1	TRUE	1	0.21	2		492	746	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246699	41246699	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	26	406	0	ENST00000357654.3:c.849A>T	p.Leu283Phe	p.L283F	ENST00000357654	NM_007294.3	283	ttA/ttT	10/23	1	2	FACETS	0.489	0.387	0.608	0.489	0.387	0.608	SUBCLONAL	1	TRUE	1	0.21	2		406	506	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376794	31376794	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	31	482	0	ENST00000328111.2:c.789G>T	p.Trp263Cys	p.W263C	ENST00000328111	NM_006892.3	263	tgG/tgT	7/23	1	2	FACETS	0.698	0.564	0.849	0.698	0.564	0.849	SUBCLONAL	1	TRUE	1	0.21	2		482	423	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057001	180057001	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	45	660	0	ENST00000261937.6:c.618C>A	p.Cys206Ter	p.C206*	ENST00000261937	NM_182925.4	206	tgC/tgA	5/30	0.3	0	FACETS	0.673	0.566	0.792			1	SUBCLONAL	1	TRUE	0	0.21	0		660	503	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0026363-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	175	344	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.164332324200698	3	FACETS	0.921	0.852	0.992	0.921	0.852	0.992	INDETERMINATE	2	TRUE	1	0.364656852699214	3		345	616	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003496	42003496	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026363-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	143	541	0	ENST00000219905.7:c.3033C>A	p.Tyr1011Ter	p.Y1011*	ENST00000219905	NM_001164273.1	1011	taC/taA	8/24	0.364656852699214	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.364656852699214	1		541	550	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039842	47039846	+	frameshift_variant	Frame_Shift_Del	DEL	TCGCA	TCGCA	-	novel	NA	P-0026363-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	223	975	0	ENST00000377604.3:c.1187_1191del	p.Arg396GlnfsTer45	p.R396Qfs*45	ENST00000377604	NM_001204468.1	395	agTCGCAtc/agtc	12/24	0.364656852699214	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.364656852699214	1		975	985	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39595507	39595507	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1442062086	NA	P-0026363-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	79	340	0	ENST00000262039.4:c.1393G>T	p.Val465Phe	p.V465F	ENST00000262039	NM_002647.2	465	Gtt/Ttt	12/25	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.364656852699214	2		340	321	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945009	151945009	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026363-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	15	86	0	ENST00000262189.6:c.2510C>A	p.Pro837His	p.P837H	ENST00000262189	NM_170606.2	837	cCt/cAt	14/59	1	2	FACETS	0.433	0.317	0.571	0.433	0.317	0.571	SUBCLONAL	1	TRUE	1	0.364656852699214	2		86	190	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776393	76776393	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026363-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	41	436	0	ENST00000373344.5:c.7073G>T	p.Trp2358Leu	p.W2358L	ENST00000373344	NM_000489.3	2358	tGg/tTg	34/35	0.364656852699214	1	FACETS	0.666	0.558	0.785	0.666	0.558	0.785	SUBCLONAL	1	TRUE	0	0.364656852699214	1		436	276	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0026370-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	385	650	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.696014458329234	4	FACETS	1	0.983	1	0.36	0.341	0.38	CLONAL	1	TRUE	1	0.848501963583241	4		651	1552	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0026370-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	644	519	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.696014458329234	4	FACETS	0.84	0.814	0.866	0.84	0.814	0.866	CLONAL	3	TRUE	1	0.848501963583241	4		519	1113	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0026370-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	354	372	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.848501963583241	2	FACETS	0.986	0.96	1	0.986	0.96	1	CLONAL	2	TRUE	0	0.848501963583241	2		372	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0026370-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	669	632	0	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.848501963583241	2		632	768	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729814	41729814	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026370-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	232	292	0	ENST00000242208.4:c.715G>T	p.Asp239Tyr	p.D239Y	ENST00000242208	NM_002192.2	239	Gac/Tac	3/3	0.696014458329234	4	FACETS	1	0.975	1	0.363	0.339	0.389	CLONAL	1	TRUE	1	0.848501963583241	4		292	927	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32439142	32439142	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026370-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	221	615	0	ENST00000332351.3:c.931T>G	p.Leu311Val	p.L311V	ENST00000332351	NM_024426.4	311	Tta/Gta	4/10	0.186658920885896	4	FACETS	0.969	0.902	1	0.242	0.225	0.26	INDETERMINATE	1	TRUE	0	0.848501963583241	4		615	994	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348456	89348456	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026370-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	259	780	1	ENST00000301030.4:c.4494C>A	p.Asp1498Glu	p.D1498E	ENST00000301030	NM_001256183.1	1498	gaC/gaA	9/13	0.848501963583241	2	FACETS	0.61	0.572	0.65	0.305	0.286	0.325	SUBCLONAL	1	TRUE	0	0.848501963583241	2		781	1000	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209306	98209306	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026370-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	106	672	1	ENST00000331920.6:c.4232A>T	p.Asp1411Val	p.D1411V	ENST00000331920	NM_000264.3	1411	gAc/gTc	23/24	0.843202983622327	3	FACETS	0.295	0.263	0.329	0.098	0.087	0.11	SUBCLONAL	1	TRUE	0	0.848501963583241	3		673	1206	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0026432-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	22	480	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		480	720	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720709	89720709	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs863224909	NA	P-0026432-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	11	118	0	ENST00000371953.3:c.860C>G	p.Ser287Ter	p.S287*	ENST00000371953	NM_000314.4	287	tCa/tGa	8/9	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		118	192	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0026530-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	86	429	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.991	0.877	1	0.991	0.877	1	CLONAL	1	TRUE	1	0.25	2		429	694	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560434	65560434	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026530-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	44	260	0	ENST00000358664.4:c.163G>T	p.Gly55Ter	p.G55*	ENST00000358664	NM_002382.4	55	Gga/Tga	3/5	0.250749443859937	1	FACETS	0.846	0.712	0.994	0.846	0.712	0.994	CLONAL	1	TRUE	0	0.25	1		260	364	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506289	120506289	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553199299	NA	P-0026530-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	28	432	0	ENST00000256646.2:c.1823T>C	p.Ile608Thr	p.I608T	ENST00000256646	NM_024408.3	608	aTt/aCt	11/34	1	2	FACETS	0.415	0.331	0.511	0.415	0.331	0.511	SUBCLONAL	1	TRUE	1	0.25	2		432	540	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639174	3639174	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026530-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	79	608	3	ENST00000294008.3:c.4465C>T	p.Gln1489Ter	p.Q1489*	ENST00000294008	NM_032444.2	1489	Caa/Taa	12/15	1	2	FACETS	0.762	0.669	0.863	0.762	0.669	0.863	SUBCLONAL	1	TRUE	1	0.25	2		611	829	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579312	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CG	CG	AT	novel	NA	P-0026530-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	74	483	1	ENST00000269305.4:c.374_375delinsAT	p.Thr125Asn	p.T125N	ENST00000269305	NM_001126112.2	125	aCG/aAT	4/11	NA	2	FACETS	1	0.913	1			1	INDETERMINATE	1	TRUE	NA	0.25	2		484	563	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37622729	37622729	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026530-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	62	547	0	ENST00000249071.6:c.563C>T	p.Ala188Val	p.A188V	ENST00000249071	NM_002872.4	188	gCc/gTc	6/7	1	2	FACETS	0.676	0.583	0.777	0.676	0.583	0.777	SUBCLONAL	1	TRUE	1	0.25	2		547	734	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628482	187628482	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026530-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	120	583	0	ENST00000441802.2:c.2500G>T	p.Asp834Tyr	p.D834Y	ENST00000441802	NM_005245.3	834	Gac/Tac	2/27	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.25	2		583	927	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912278	29912278	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1274693904	NA	P-0026530-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	94	733	1	ENST00000376809.5:c.897G>T	p.Glu299Asp	p.E299D	ENST00000376809	NM_002116.7	299	gaG/gaT	5/8	0.107850437392965	4	FACETS	1	0.91	1	0.514	0.456	0.575	INDETERMINATE	1	TRUE	2	0.25	4		734	915	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035986	47035986	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0026530-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	92	349	0	ENST00000377604.3:c.663+1G>T		p.X221_splice	ENST00000377604	NM_001204468.1	221			1	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.25	1		349	446	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0026622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	368	583	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.582988151723473	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.582988151723473	3		583	777	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0026622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	213	530	3	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	0.582988151723473	1	FACETS	0.935	0.875	0.995	0.935	0.875	0.995	CLONAL	1	TRUE	0	0.582988151723473	1		533	554	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111458	8111459	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	170	490	0	ENST00000346208.3:c.945dup	p.Ser316ValfsTer36	p.S316Vfs*36	ENST00000346208		315	acg/acGg	5/6	1	2	FACETS	0.897	0.828	0.968	0.897	0.828	0.968	CLONAL	1	TRUE	1	0.582988151723473	2		490	650	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855029	76855029	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1557085898	NA	P-0026646-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	9	301	1	ENST00000373344.5:c.5807A>G	p.Lys1936Arg	p.K1936R	ENST00000373344	NM_000489.3	1936	aAg/aGg	25/35	1	2	FACETS	0.053	0.034	0.076	0.053	0.034	0.076	SUBCLONAL	1	TRUE	1	0.838960251663746	2		302	408	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186608	108186608	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026646-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	170	312	0	ENST00000278616.4:c.6065G>C	p.Gly2022Ala	p.G2022A	ENST00000278616	NM_000051.3	2022	gGt/gCt	41/63	0.831270953485373	3	FACETS	0.872	0.804	0.941	0.436	0.402	0.471	CLONAL	1	TRUE	1	0.838960251663746	3		312	660	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884935	111884935	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	71	467	1	ENST00000341259.2:c.933G>T	p.Glu311Asp	p.E311D	ENST00000341259	NM_005475.2	311	gaG/gaT	5/8	0.264574858685483	3	FACETS	0.543	0.474	0.618	0.271	0.237	0.309	INDETERMINATE	1	TRUE	1	0.509769404561923	3		468	644	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527478	157527478	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	184	538	0	ENST00000346085.5:c.5203G>C	p.Ala1735Pro	p.A1735P	ENST00000346085	NM_020732.3	1735	Gct/Cct	20/20	0.48885355021982	3	FACETS	1	0.986	1	0.428	0.396	0.461	CLONAL	1	TRUE	0	0.509769404561923	3		538	706	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	219	469	2	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.654	0.608	0.701	0.654	0.608	0.701	SUBCLONAL	1	TRUE	1	0.688708335034115	2		471	973	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0026714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	471	638	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.688708335034115	2		640	1020	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0026714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	294	675	0	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	1	2	FACETS	0.735	0.692	0.78	0.735	0.692	0.78	SUBCLONAL	1	TRUE	1	0.688708335034115	2		675	1161	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0026714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	342	505	2	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.688708335034115	2		507	993	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0026714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	205	295	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.688708335034115	2	FACETS	1	0.951	1	0.511	0.477	0.545	CLONAL	1	TRUE	0	0.688708335034115	2		295	583	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916648	178916648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	304	409	0	ENST00000263967.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000263967	NM_006218.2	12	gGc/gAc	2/21	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.688708335034115	2		409	703	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793211	139793212	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs748531430	NA	P-0026714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	374	588	0	ENST00000247668.2:c.26dup	p.Gly10TrpfsTer70	p.G10Wfs*70	ENST00000247668	NM_021138.3	7	acc/aCcc	2/11	1	2	FACETS	0.913	0.867	0.96	0.913	0.867	0.96	CLONAL	1	TRUE	1	0.688708335034115	2		588	1189	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029445	16029446	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0026714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	243	509	4	ENST00000268712.3:c.1584dup	p.Glu529ArgfsTer7	p.E529Rfs*7	ENST00000268712	NM_006311.3	528	-/A	15/46	1	2	FACETS	0.899	0.843	0.956	0.899	0.843	0.956	CLONAL	1	TRUE	1	0.688708335034115	2		513	785	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955043	17955043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs199602590	NA	P-0026714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	449	696	1	ENST00000458235.1:c.184G>A	p.Gly62Ser	p.G62S	ENST00000458235	NM_000215.3	62	Ggc/Agc	2/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.688708335034115	2		697	1225	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512402	38512402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	135	560	0	ENST00000254066.5:c.1319del	p.Pro440ArgfsTer203	p.P440Rfs*203	ENST00000254066	NM_000964.3	438	gCc/gc	9/9	1	2	FACETS	0.373	0.338	0.41	0.373	0.338	0.41	SUBCLONAL	1	TRUE	1	0.688708335034115	2		560	1051	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711879	89711880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	358	429	0	ENST00000371953.3:c.499dup	p.Thr167AsnfsTer13	p.T167Nfs*13	ENST00000371953	NM_000314.4	166	gta/gtAa	6/9	0.688708335034115	2	FACETS	0.983	0.947	1	0.983	0.947	1	CLONAL	2	TRUE	0	0.688708335034115	2		429	529	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0026714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	301	577	6	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.84	0.792	0.89	0.84	0.792	0.89	CLONAL	1	TRUE	1	0.688708335034115	2		583	1040	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346437	89346437	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555525603	NA	P-0026714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	376	630	4	ENST00000301030.4:c.6513del	p.Val2173SerfsTer2	p.V2173Sfs*2	ENST00000301030	NM_001256183.1	2171	ccC/cc	9/13	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.688708335034115	2		634	1088	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439784	51439784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1321555751	NA	P-0026714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	252	370	0	ENST00000262662.1:c.349C>T	p.Arg117Trp	p.R117W	ENST00000262662		117	Cgg/Tgg	4/4	1	2	FACETS	0.99	0.931	1	0.99	0.931	1	CLONAL	1	TRUE	1	0.688708335034115	2		370	739	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073457	8073457	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	276	506	0	ENST00000377482.5:c.1202C>A	p.Pro401Gln	p.P401Q	ENST00000377482	NM_018948.3	401	cCa/cAa	4/4	1	2	FACETS	0.972	0.915	1	0.972	0.915	1	CLONAL	1	TRUE	1	0.688708335034115	2		506	825	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736510	85736510	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	34	382	0	ENST00000370580.1:c.137T>A	p.Ile46Lys	p.I46K	ENST00000370580	NM_003921.4	46	aTa/aAa	2/3	1	2	FACETS	0.162	0.132	0.197	0.162	0.132	0.197	SUBCLONAL	1	TRUE	1	0.688708335034115	2		382	608	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945433	71945433	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	367	635	0	ENST00000298229.2:c.2321T>C	p.Leu774Pro	p.L774P	ENST00000298229	NM_001567.3	774	cTg/cCg	20/28	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.688708335034115	2		635	1059	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998612	100998622	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGCCTCCGC	GAGGCCTCCGC	-	novel	NA	P-0026714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	378	564	0	ENST00000325455.5:c.1180_1190del	p.Ala394ArgfsTer176	p.A394Rfs*176	ENST00000325455	NM_001202474.3	394	GCGGAGGCCTCc/c	1/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.688708335034115	2		564	991	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007741	45007744	+	frameshift_variant	Frame_Shift_Del	DEL	GAGA	GAGA	-	novel	NA	P-0026714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	93	490	0	ENST00000558401.1:c.192_195del	p.Arg65LeufsTer37	p.R65Lfs*37	ENST00000558401	NM_004048.2	63	gGAGAg/gg	2/4	1	2	FACETS	0.38	0.338	0.426	0.38	0.338	0.426	SUBCLONAL	1	TRUE	1	0.688708335034115	2		490	710	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134425	30134425	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	406	669	0	ENST00000263025.4:c.106T>G	p.Phe36Val	p.F36V	ENST00000263025	NM_002746.2	36	Ttc/Gtc	1/9	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.688708335034115	2		669	1149	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830482	72830482	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	54	594	0	ENST00000268489.5:c.6099G>T	p.Arg2033Ser	p.R2033S	ENST00000268489	NM_006885.3	2033	agG/agT	9/10	1	2	FACETS	0.153	0.13	0.179	0.153	0.13	0.179	SUBCLONAL	1	TRUE	1	0.688708335034115	2		594	1023	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836581	89836581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145552439	NA	P-0026714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	382	648	3	ENST00000389301.3:c.2309G>A	p.Arg770His	p.R770H	ENST00000389301	NM_000135.2	770	cGt/cAt	25/43	1	2	FACETS	0.983	0.935	1	0.983	0.935	1	CLONAL	1	TRUE	1	0.688708335034115	2		651	1128	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574101	46574101	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	402	734	0	ENST00000263734.3:c.116A>C	p.His39Pro	p.H39P	ENST00000263734	NM_001430.4	39	cAt/cCt	2/16	0.262730374898077	1	FACETS	0.648	0.617	0.68	0.648	0.617	0.68	INDETERMINATE	1	TRUE	0	0.688708335034115	1		734	1181	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927987	178927987	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	125	319	0	ENST00000263967.3:c.1265T>G	p.Leu422Trp	p.L422W	ENST00000263967	NM_006218.2	422	tTg/tGg	8/21	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.688708335034115	2		319	358	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821583	32821583	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	213	717	0	ENST00000354258.4:c.11T>C	p.Leu4Pro	p.L4P	ENST00000354258	NM_000593.5	4	cTt/cCt	1/11	1	2	FACETS	0.556	0.516	0.598	0.556	0.516	0.598	SUBCLONAL	1	TRUE	1	0.688708335034115	2		717	1112	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984060	2984060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781530962	NA	P-0026714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	336	506	0	ENST00000396946.4:c.470G>A	p.Arg157Gln	p.R157Q	ENST00000396946	NM_032415.4	157	cGg/cAg	5/25	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.688708335034115	2		506	850	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922283	39922283	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	37	421	0	ENST00000378444.4:c.3889T>C	p.Ser1297Pro	p.S1297P	ENST00000378444	NM_001123385.1	1297	Tca/Cca	9/15	1	2	FACETS	0.152	0.125	0.183	0.152	0.125	0.183	SUBCLONAL	1	TRUE	1	0.688708335034115	2		421	706	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70353032	70353032	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	351	634	1	ENST00000374080.3:c.4587G>A	p.Met1529Ile	p.M1529I	ENST00000374080		1529	atG/atA	33/45	1	2	FACETS	0.96	0.91	1	0.96	0.91	1	CLONAL	1	TRUE	1	0.688708335034115	2		635	1062	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357694	70357694	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1216	123	769	0	ENST00000374080.3:c.5945C>A	p.Pro1982His	p.P1982H	ENST00000374080		1982	cCt/cAt	41/45	1	2	FACETS	0.267	0.24	0.295	0.267	0.24	0.295	SUBCLONAL	1	TRUE	1	0.688708335034115	2		769	1339	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0026721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	146	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.335494170411141	3	FACETS	1	0.934	1	0.514	0.469	0.562	CLONAL	1	TRUE	1	0.369688293050254	3		509	910	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0026721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	209	403	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.369688293050254	2	FACETS	0.881	0.822	0.941	0.881	0.822	0.941	CLONAL	2	TRUE	0	0.369688293050254	2		403	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0026721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	326	676	0	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	NA	2	FACETS	0.972	0.921	1			1	INDETERMINATE	2	TRUE	NA	0.369688293050254	2		676	907	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0026721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	27	526	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	0.182	0.144	0.226	0.182	0.144	0.226	SUBCLONAL	1	TRUE	1	0.369688293050254	2		526	802	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730876	40730876	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372862828	NA	P-0026721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	333	752	0	ENST00000373198.4:c.3659G>A	p.Arg1220Gln	p.R1220Q	ENST00000373198	NM_133170.3	1220	cGg/cAg	27/32	0.322617201616421	4	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	2	0.369688293050254	4		752	1234	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135409	30135409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780784905	NA	P-0026721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	96	424	0	ENST00000331968.5:c.409G>A	p.Ala137Thr	p.A137T	ENST00000331968	NM_002742.2	137	Gcc/Acc	3/18	1	2	FACETS	0.809	0.722	0.902	0.809	0.722	0.902	CLONAL	1	TRUE	1	0.369688293050254	2		424	642	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057702	27057702	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0026721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	220	806	0	ENST00000324856.7:c.1410T>G	p.Tyr470Ter	p.Y470*	ENST00000324856	NM_006015.4	470	taT/taG	3/20	1	2	FACETS	0.98	0.91	1	0.98	0.91	1	CLONAL	1	TRUE	1	0.369688293050254	2		806	1215	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154290	2154290	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	187	876	0	ENST00000434045.2:c.638C>T	p.Pro213Leu	p.P213L	ENST00000434045	NM_001127598.1	213	cCc/cTc	5/5	0.218206721178375	3	FACETS	0.957	0.882	1	0.319	0.294	0.345	INDETERMINATE	1	TRUE	0	0.369688293050254	3		876	1253	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741897	17741897	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752898631	NA	P-0026721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	21	121	0	ENST00000250003.3:c.568G>A	p.Gly190Ser	p.G190S	ENST00000250003	NM_002478.4	190	Ggc/Agc	1/3	0.218206721178375	3	FACETS	0.609	0.471	0.769	0.203	0.157	0.257	INDETERMINATE	1	TRUE	0	0.369688293050254	3		121	221	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741924	17741924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444003943	NA	P-0026721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	98	235	0	ENST00000250003.3:c.595G>A	p.Ala199Thr	p.A199T	ENST00000250003	NM_002478.4	199	Gcg/Acg	1/3	0.218206721178375	3	FACETS	1	0.978	1	0.457	0.41	0.507	INDETERMINATE	1	TRUE	0	0.369688293050254	3		235	458	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446455	49446455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	224	461	1	ENST00000301067.7:c.1150G>A	p.Glu384Lys	p.E384K	ENST00000301067	NM_003482.3	384	Gag/Aag	9/54	0.335494170411141	3	FACETS	0.812	0.757	0.869	0.812	0.757	0.869	CLONAL	2	TRUE	1	0.369688293050254	3		462	884	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63545728	63545731	+	protein_altering_variant	In_Frame_Ins	INS	TAGC	TAGC	CTATGTG	novel	NA	P-0026721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	338	636	0	ENST00000307078.5:c.863_866delinsCACATAG	p.Gly288_Tyr289delinsAlaHisSer	p.G288_Y289delinsAHS	ENST00000307078	NM_004655.3	288	gGCTAt/gCACATAGt	3/11	0.327478549819754	3	FACETS	1	0.991	1	0.802	0.761	0.843	CLONAL	2	TRUE	0	0.369688293050254	3		636	901	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	123	528	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.311068173083283	1	FACETS	0.981	0.889	1	0.981	0.889	1	CLONAL	1	TRUE	0	0.336984421009335	1		529	619	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484595	57484595	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	129	466	0	ENST00000371085.3:c.679C>G	p.Gln227Glu	p.Q227E	ENST00000371085	NM_000516.4	227	Cag/Gag	9/13	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.336984421009335	2		466	682	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591891	48591891	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	103	432	0	ENST00000342988.3:c.1055del	p.Gly352AspfsTer32	p.G352Dfs*32	ENST00000342988	NM_005359.5	352	Gga/ga	9/12	0.336984421009335	1	FACETS	0.808	0.724	0.897	0.808	0.724	0.897	CLONAL	1	TRUE	0	0.336984421009335	1		432	629	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710521	40710521	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0026726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	105	530	0	ENST00000373198.4:c.4329+1G>T		p.X1443_splice	ENST00000373198	NM_133170.3	1443			1	2	FACETS	0.832	0.746	0.924	0.832	0.746	0.924	CLONAL	1	TRUE	1	0.336984421009335	2		530	749	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0026731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	280	583	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	0.65310024061325	2		583	838	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0026731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	397	781	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	0.641427056960745	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.65310024061325	1		781	806	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416245	416245	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	229	453	0	ENST00000399788.2:c.3941C>G	p.Pro1314Arg	p.P1314R	ENST00000399788	NM_001042603.1	1314	cCt/cGt	24/28	0.636271720850766	3	FACETS	0.892	0.831	0.955			1	CLONAL	1	TRUE	NA	0.65310024061325	3		453	1043	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243999	41243999	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	380	579	0	ENST00000357654.3:c.3549del	p.Gly1184GlufsTer26	p.G1184Efs*26	ENST00000357654	NM_007294.3	1183	aaA/aa	10/23	0.641427056960745	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.65310024061325	1		579	725	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54956509	54956509	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	264	508	0	ENST00000312783.6:c.685G>C	p.Asp229His	p.D229H	ENST00000312783	NM_198436.1	229	Gat/Cat	7/10	0.642456046856535	3	FACETS	0.821	0.768	0.876	0.411	0.384	0.438	CLONAL	1	TRUE	1	0.65310024061325	3		508	1306	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92244551	92244551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	239	442	0	ENST00000265734.4:c.884T>C	p.Leu295Pro	p.L295P	ENST00000265734	NM_001259.6	295	cTg/cCg	8/8	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.65310024061325	2		442	732	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255788	16255790	+	stop_gained	Nonsense_Mutation	TNP	AGC	AGC	TGT	novel	NA	P-0026731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	269	438	0	ENST00000375759.3:c.3053_3055delinsTGT	p.Lys1018_Gln1019delinsMetTer	p.K1018_Q1019delinsM*	ENST00000375759	NM_015001.2	1018	aAGCag/aTGTag	11/15	0.39185694328566	4	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.65310024061325	4		438	1093	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	69	528	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.874	0.762	0.996	0.874	0.762	0.996	CLONAL	1	TRUE	1	0.26	2		529	607	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0026778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	24	397	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.406	0.317	0.508	0.406	0.317	0.508	SUBCLONAL	1	TRUE	1	0.26	2		397	455	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0026778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	26	487	2	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.282	0.223	0.352	0.282	0.223	0.352	SUBCLONAL	1	TRUE	1	0.26	2		489	708	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045136	47045136	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	49	477	1	ENST00000377604.3:c.2377C>T	p.Arg793Ter	p.R793*	ENST00000377604	NM_001204468.1	793	Cga/Tga	21/24	1	2	FACETS	0.542	0.458	0.635	0.542	0.458	0.635	SUBCLONAL	1	TRUE	1	0.26	2		478	695	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045533	47045533	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0026778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	46	517	1	ENST00000377604.3:c.2500A>T	p.Lys834Ter	p.K834*	ENST00000377604	NM_001204468.1	834	Aag/Tag	22/24	1	2	FACETS	0.596	0.501	0.701	0.596	0.501	0.701	SUBCLONAL	1	TRUE	1	0.26	2		518	594	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28880903	28880903	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	37	352	0	ENST00000282397.4:c.3727C>A	p.Gln1243Lys	p.Q1243K	ENST00000282397	NM_002019.4	1243	Cag/Aag	29/30	1	2	FACETS	0.724	0.598	0.865	0.724	0.598	0.865	SUBCLONAL	1	TRUE	1	0.26	2		352	393	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143033804	143033804	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	37	285	0	ENST00000262992.4:c.2167G>T	p.Ala723Ser	p.A723S	ENST00000262992	NM_001101669.1	723	Gcc/Tcc	20/24	1	2	FACETS	0.529	0.435	0.634	0.529	0.435	0.634	SUBCLONAL	1	TRUE	1	0.26	2		285	538	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777798	3777798	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	88	722	0	ENST00000262367.5:c.7250G>T	p.Arg2417Met	p.R2417M	ENST00000262367	NM_004380.2	2417	aGg/aTg	31/31	1	2	FACETS	0.81	0.716	0.91	0.81	0.716	0.91	CLONAL	1	TRUE	1	0.26	2		722	836	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273863	10273863	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555491437	NA	P-0026778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	53	541	0	ENST00000330684.3:c.406G>T	p.Ala136Ser	p.A136S	ENST00000330684	NM_001134407.1	136	Gct/Tct	2/13	1	2	FACETS	0.654	0.557	0.761	0.654	0.557	0.761	SUBCLONAL	1	TRUE	1	0.26	2		541	623	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953196	17953196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	47	648	1	ENST00000458235.1:c.790G>A	p.Gly264Ser	p.G264S	ENST00000458235	NM_000215.3	264	Ggc/Agc	6/24	1	2	FACETS	0.596	0.502	0.699	0.596	0.502	0.699	SUBCLONAL	1	TRUE	1	0.26	2		649	607	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464491	25464491	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	29	440	1	ENST00000264709.3:c.2022G>T	p.Met674Ile	p.M674I	ENST00000264709	NM_175629.2	674	atG/atT	17/23	1	2	FACETS	0.391	0.313	0.481	0.391	0.313	0.481	SUBCLONAL	1	TRUE	1	0.26	2		441	570	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445402	29445402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	44	579	0	ENST00000389048.3:c.3431C>T	p.Pro1144Leu	p.P1144L	ENST00000389048	NM_004304.4	1144	cCc/cTc	21/29	1	2	FACETS	0.496	0.414	0.586	0.496	0.414	0.586	SUBCLONAL	1	TRUE	1	0.26	2		579	683	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388641	31388641	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	32	366	0	ENST00000328111.2:c.1906A>T	p.Ile636Phe	p.I636F	ENST00000328111	NM_006892.3	636	Att/Ttt	18/23	1	2	FACETS	0.52	0.422	0.632	0.52	0.422	0.632	SUBCLONAL	1	TRUE	1	0.26	2		366	473	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280153	66280153	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	30	216	0	ENST00000273854.3:c.1536G>C	p.Glu512Asp	p.E512D	ENST00000273854	NM_004439.5	512	gaG/gaC	7/18	1	2	FACETS	0.648	0.523	0.79	0.648	0.523	0.79	SUBCLONAL	1	TRUE	1	0.26	2		216	356	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27190620	27190620	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	36	495	0	ENST00000380036.4:c.1421G>C	p.Gly474Ala	p.G474A	ENST00000380036	NM_000459.3	474	gGa/gCa	10/23	1	2	FACETS	0.398	0.326	0.479	0.398	0.326	0.479	SUBCLONAL	1	TRUE	1	0.26	2		495	696	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27218786	27218786	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	50	371	0	ENST00000380036.4:c.3074G>T	p.Gly1025Val	p.G1025V	ENST00000380036	NM_000459.3	1025	gGt/gTt	20/23	1	2	FACETS	0.687	0.582	0.802	0.687	0.582	0.802	SUBCLONAL	1	TRUE	1	0.26	2		371	560	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032548	47032548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	57	567	1	ENST00000377604.3:c.454C>T	p.His152Tyr	p.H152Y	ENST00000377604	NM_001204468.1	152	Cac/Tac	5/24	1	2	FACETS	0.659	0.565	0.763	0.659	0.565	0.763	SUBCLONAL	1	TRUE	1	0.26	2		568	665	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0026778-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	41	397	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.62	0.516	0.736	0.62	0.516	0.736	SUBCLONAL	1	TRUE	1	0.25	2		397	529	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0026778-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	85	487	2	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.962	0.85	1	0.962	0.85	1	CLONAL	1	TRUE	1	0.25	2		489	707	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045136	47045136	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026778-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	77	477	1	ENST00000377604.3:c.2377C>T	p.Arg793Ter	p.R793*	ENST00000377604	NM_001204468.1	793	Cga/Tga	21/24	1	2	FACETS	0.853	0.749	0.966	0.853	0.749	0.966	CLONAL	1	TRUE	1	0.25	2		478	722	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0026783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	198	604	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.520926627677718	1	FACETS	0.671	0.627	0.715	0.671	0.627	0.715	SUBCLONAL	1	TRUE	0	0.756677481695319	1		604	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578506	7578507	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	426	857	0	ENST00000269305.4:c.423_424insT	p.Pro142SerfsTer7	p.P142Sfs*7	ENST00000269305	NM_001126112.2	141	-/T	5/11	0.756677481695319	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.756677481695319	1		857	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0026828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	150	633	1	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		634	988	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276713	15276713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238520484	NA	P-0026828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	82	633	0	ENST00000263388.2:c.5552G>A	p.Arg1851His	p.R1851H	ENST00000263388	NM_000435.2	1851	cGt/cAt	30/33	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		633	942	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0026829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	125	583	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	0.993	1	CLONAL	4	TRUE	1	0.179462638135421	2		583	341	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	166	593	1	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	0.9	0.833	0.969	1	0.994	1	CLONAL	4	TRUE	1	0.179462638135421	2		594	514	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106058	8106058	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	187	506	0	ENST00000346208.3:c.878T>A	p.Met293Lys	p.M293K	ENST00000346208		293	aTg/aAg	4/6	1	2	FACETS	0.965	0.898	1	1	0.995	1	CLONAL	4	TRUE	1	0.179462638135421	2		506	540	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270593	98270595	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	rs756897237	NA	P-0026829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	16	109	1	ENST00000331920.6:c.49_51del	p.Gly17del	p.G17del	ENST00000331920	NM_000264.3	17	GGC/-	1/24	1	2	FACETS	0.803	0.595	1	0.803	0.595	1	CLONAL	1	TRUE	1	0.179462638135421	2		110	222	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428511	78428511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408536007	NA	P-0026829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	10	487	0	ENST00000370768.2:c.1288C>T	p.Arg430Cys	p.R430C	ENST00000370768	NM_003902.3	430	Cgt/Tgt	14/20	1	2	FACETS	0.283	0.19	0.4	0.283	0.19	0.4	SUBCLONAL	1	TRUE	1	0.179462638135421	2		487	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782177	NA	P-0026830-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	108	673	0	ENST00000269305.4:c.644G>C	p.Ser215Thr	p.S215T	ENST00000269305	NM_001126112.2	215	aGt/aCt	6/11	1	2	FACETS	0.784	0.703	0.87	0.784	0.703	0.87	SUBCLONAL	1	TRUE	1	0.31	2		673	889	SUCCESS
APC	324	MSKCC	GRCh37	5	112174438	112174438	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs863225340	NA	P-0026830-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	65	285	0	ENST00000257430.4:c.3147G>A	p.Trp1049Ter	p.W1049*	ENST00000257430	NM_000038.5	1049	tgG/tgA	16/16	0.29889984977395	1	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	0	0.31	1		285	340	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930687	32930687	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs80358981	NA	P-0026830-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	64	472	0	ENST00000380152.3:c.7558C>T	p.Arg2520Ter	p.R2520*	ENST00000380152		2520	Cga/Tga	15/27	1	2	FACETS	0.608	0.526	0.697	0.608	0.526	0.697	SUBCLONAL	1	TRUE	1	0.31	2		472	679	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577562	7577563	+	missense_variant	Missense_Mutation	DNP	CT	CT	AA	novel	NA	P-0026830-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	106	486	2	ENST00000269305.4:c.718_719delinsTT	p.Ser240Phe	p.S240F	ENST00000269305	NM_001126112.2	240	AGt/TTt	7/11	1	2	FACETS	0.929	0.833	1	0.929	0.833	1	CLONAL	1	TRUE	1	0.31	2		488	736	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451194	70451194	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1202179982	NA	P-0026830-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	97	506	0	ENST00000373644.4:c.6034G>A	p.Ala2012Thr	p.A2012T	ENST00000373644	NM_030625.2	2012	Gca/Aca	12/12	0.164369594875369	1	FACETS	0.857	0.765	0.954	0.857	0.765	0.954	INDETERMINATE	1	TRUE	0	0.31	1		506	617	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112098	115112098	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026830-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	98	690	0	ENST00000257566.3:c.1642G>T	p.Gly548Trp	p.G548W	ENST00000257566	NM_016569.3	548	Ggg/Tgg	7/8	1	2	FACETS	0.945	0.844	1	0.945	0.844	1	CLONAL	1	TRUE	1	0.31	2		690	669	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22405018	22405018	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026830-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	18	118	0	ENST00000344548.3:c.47A>C	p.Lys16Thr	p.K16T	ENST00000344548	NM_001039802.1	16	aAa/aCa	3/7	1	2	FACETS	0.664	0.502	0.852	0.664	0.502	0.852	SUBCLONAL	1	TRUE	1	0.31	2		118	175	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797736	45797736	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026830-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	59	570	1	ENST00000450313.1:c.956C>T	p.Ala319Val	p.A319V	ENST00000450313	NM_012222.2	319	gCc/gTc	11/16	1	2	FACETS	0.508	0.436	0.587	0.508	0.436	0.587	SUBCLONAL	1	TRUE	1	0.31	2		571	749	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838025	156838025	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026830-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	130	699	0	ENST00000524377.1:c.558G>T	p.Met186Ile	p.M186I	ENST00000524377	NM_002529.3	186	atG/atT	5/17	1	2	FACETS	0.97	0.879	1	0.97	0.879	1	CLONAL	1	TRUE	1	0.31	2		699	865	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612990	228612990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1397772335	NA	P-0026830-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	65	304	0	ENST00000366696.1:c.37G>A	p.Gly13Ser	p.G13S	ENST00000366696	NM_003493.2	13	Ggt/Agt	1/1	1	2	FACETS	0.928	0.807	1	0.928	0.807	1	CLONAL	1	TRUE	1	0.31	2		304	452	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110067	115110067	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026830-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	136	769	0	ENST00000257566.3:c.1811C>A	p.Pro604His	p.P604H	ENST00000257566	NM_016569.3	604	cCc/cAc	8/8	1	2	FACETS	0.972	0.883	1	0.972	0.883	1	CLONAL	1	TRUE	1	0.31	2		769	903	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244988	41244988	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026830-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	69	622	0	ENST00000357654.3:c.2560G>A	p.Ala854Thr	p.A854T	ENST00000357654	NM_007294.3	854	Gct/Act	10/23	1	2	FACETS	0.591	0.514	0.675	0.591	0.514	0.675	SUBCLONAL	1	TRUE	1	0.31	2		622	753	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881594	111881594	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs778682749	NA	P-0026830-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	122	597	0	ENST00000393256.3:c.272G>T	p.Arg91Leu	p.R91L	ENST00000393256	NM_006538.4	91	cGa/cTa	2/4	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.31	2		597	724	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224532	224532	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026830-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	230	351	2	ENST00000264932.6:c.208G>T	p.Gly70Ter	p.G70*	ENST00000264932	NM_004168.2	70	Gga/Tga	3/15	0.29889984977395	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	1	0.31	4		353	596	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471026	8471026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026830-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	83	449	1	ENST00000356435.5:c.3473G>T	p.Trp1158Leu	p.W1158L	ENST00000356435		1158	tGg/tTg	20/35	0.29889984977395	1	FACETS	0.961	0.851	1	0.961	0.851	1	CLONAL	1	TRUE	0	0.31	1		450	471	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410888	63410888	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026830-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	63	590	0	ENST00000330258.3:c.2279A>T	p.Glu760Val	p.E760V	ENST00000330258	NM_152424.3	760	gAg/gTg	2/2	0.245336072518929	1	FACETS	0.522	0.451	0.599	0.522	0.451	0.599	SUBCLONAL	1	TRUE	0	0.31	1		590	658	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338608	70338608	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026830-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	26	438	1	ENST00000374080.3:c.4G>T	p.Ala2Ser	p.A2S	ENST00000374080		2	Gcg/Tcg	1/45	0.245336072518929	1	FACETS	0.274	0.216	0.341	0.274	0.216	0.341	SUBCLONAL	1	TRUE	0	0.31	1		439	517	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453141	+	protein_altering_variant	In_Frame_Del	DEL	ACTGTA	ACTGTA	CGT	novel	NA	P-0026830-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	105	448	2	ENST00000288602.6:c.1794_1799delinsACG	p.Thr599_Val600delinsArg	p.T599_V600delinsR	ENST00000288602	NM_004333.4	598	gcTACAGTg/gcACGg	15/18	1	2	FACETS	0.887	0.795	0.984	0.887	0.795	0.984	CLONAL	1	TRUE	1	0.32987736141808	2		450	718	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	156	528	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.793	0.728	0.861	1	0.989	1	SUBCLONAL	2	TRUE	1	0.289608432731766	2		529	679	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947603	48947603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	44	418	0	ENST00000267163.4:c.1190C>T	p.Ser397Leu	p.S397L	ENST00000267163	NM_000321.2	397	tCa/tTa	12/27	1	2	FACETS	0.492	0.412	0.582	0.492	0.412	0.582	SUBCLONAL	1	TRUE	1	0.289608432731766	2		418	617	SUCCESS
EED	8726	MSKCC	GRCh37	11	85961354	85961354	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1420554958	NA	P-0026831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	54	316	0	ENST00000263360.6:c.131T>C	p.Ile44Thr	p.I44T	ENST00000263360	NM_003797.3	44	aTa/aCa	2/12	0.201165971469984	2	FACETS	0.783	0.67	0.907	0.392	0.335	0.454	CLONAL	1	TRUE	0	0.289608432731766	2		316	476	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226080	2226080	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1397292006	NA	P-0026831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	46	665	2	ENST00000326181.6:c.1777C>T	p.Arg593Trp	p.R593W	ENST00000326181	NM_032271.2	593	Cgg/Tgg	19/21	1	2	FACETS	0.389	0.326	0.458	0.389	0.326	0.458	SUBCLONAL	1	TRUE	1	0.289608432731766	2		667	817	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577145	+	frameshift_variant	Frame_Shift_Del	DEL	GTCCCAG	GTCCCAG	-	novel	NA	P-0026831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	98	589	0	ENST00000269305.4:c.793_799del	p.Leu265GlyfsTer78	p.L265Gfs*78	ENST00000269305	NM_001126112.2	265	CTGGGACgg/gg	8/11	0.289608432731766	1	FACETS	0.801	0.714	0.892	0.801	0.714	0.892	CLONAL	1	TRUE	0	0.289608432731766	1		589	723	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055686	152055686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748418114	NA	P-0026831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	53	570	0	ENST00000262189.6:c.236C>T	p.Thr79Met	p.T79M	ENST00000262189	NM_170606.2	79	aCg/aTg	2/59	1	2	FACETS	0.388	0.33	0.453	0.388	0.33	0.453	SUBCLONAL	1	TRUE	1	0.289608432731766	2		570	943	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945043	31945043	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	108	463	0	ENST00000340398.3:c.58C>T	p.Gln20Ter	p.Q20*	ENST00000340398	NM_001013699.2	20	Cag/Tag	1/1	0.517901378778611	3	FACETS	0.822	0.739	0.909	0.411	0.369	0.455	CLONAL	1	TRUE	1	0.517901378778611	3		463	639	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845634	63845634	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	35	308	0	ENST00000279873.7:c.1376del	p.Pro459GlnfsTer20	p.P459Qfs*20	ENST00000279873	NM_032199.2	458	gCc/gc	9/10	1	2	FACETS	0.194	0.159	0.234	0.194	0.159	0.234	SUBCLONAL	1	TRUE	1	0.80352710138035	2		308	449	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	480	466	0	ENST00000330062.3:c.515G>C	p.Arg172Thr	p.R172T	ENST00000330062	NM_002168.2	172	aGg/aCg	4/11	0.54242494074591	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.54242494074591	3		466	1028	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656213	18656213	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0026837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	306	303	0	ENST00000266497.5:c.2894-2A>G		p.X965_splice	ENST00000266497		965			0.54242494074591	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	1	0.54242494074591	3		303	717	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272266	15272266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1363323415	NA	P-0026838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	183	544	0	ENST00000263388.2:c.6173C>T	p.Ser2058Leu	p.S2058L	ENST00000263388	NM_000435.2	2058	tCg/tTg	33/33	1	2	FACETS	0.838	0.774	0.904	1	0.991	1	CLONAL	2	FALSE	1	0.262087393194131	2		544	833	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78811759	78811759	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	191	542	1	ENST00000306801.3:c.1174C>T	p.Gln392Ter	p.Q392*	ENST00000306801	NM_020761.2	392	Cag/Tag	10/34	1	2	FACETS	0.837	0.774	0.901	1	0.992	1	CLONAL	2	FALSE	1	0.262087393194131	2		543	871	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624295	89624298	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	novel	NA	P-0026838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	122	496	0	ENST00000371953.3:c.69_72del	p.Leu23PhefsTer2	p.L23Ffs*2	ENST00000371953	NM_000314.4	23	ttAGAC/tt	1/9	0.262087393194131	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	0	0.262087393194131	1		496	614	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	152	315	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.540562026680129	2		316	520	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0026839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	43	521	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	NA	2	FACETS	0.266	0.222	0.315			1	INDETERMINATE	1	TRUE	NA	0.540562026680129	2		521	598	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652147	36652148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	172	583	0	ENST00000244741.5:c.270dup	p.Gly91ArgfsTer38	p.G91Rfs*38	ENST00000244741	NM_000389.4	90	gga/ggAa	2/3	1	2	FACETS	0.845	0.779	0.913	0.845	0.779	0.913	CLONAL	1	TRUE	1	0.540562026680129	2		583	753	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651893	36651894	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	206	472	0	ENST00000244741.5:c.19dup	p.Asp7GlyfsTer29	p.D7Gfs*29	ENST00000244741	NM_000389.4	5	-/G	2/3	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.540562026680129	2		472	755	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281768	49281768	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148425155	NA	P-0026839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	229	640	1	ENST00000282018.3:c.815C>T	p.Thr272Met	p.T272M	ENST00000282018	NM_020377.2	272	aCg/aTg	1/1	1	2	FACETS	0.996	0.93	1	0.996	0.93	1	CLONAL	1	TRUE	1	0.540562026680129	2		641	851	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	104	528	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.997	0.896	1	0.997	0.896	1	CLONAL	1	TRUE	1	0.422494462049181	2		529	494	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0026840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	35	397	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.31	0.253	0.373	0.31	0.253	0.373	SUBCLONAL	1	TRUE	1	0.422494462049181	2		397	535	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0026840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	114	439	1	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.422494462049181	2		440	513	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720735	89720736	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0026840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	44	105	0	ENST00000371953.3:c.888_889del	p.Cys296Ter	p.C296*	ENST00000371953	NM_000314.4	296	TGt/t	8/9	0.422494462049181	2	FACETS	1	0.959	1	0.699	0.598	0.806	CLONAL	1	TRUE	0	0.422494462049181	2		105	149	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481400	140481400	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	81	391	0	ENST00000288602.6:c.1408A>C	p.Thr470Pro	p.T470P	ENST00000288602	NM_004333.4	470	Aca/Cca	11/18	1	2	FACETS	0.846	0.749	0.95	0.846	0.749	0.95	CLONAL	1	TRUE	1	0.422494462049181	2		391	453	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0026855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	140	303	4	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.818	0.753	0.885	0.818	0.753	0.885	CLONAL	1	TRUE	1	0.859751153149282	2		307	398	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs371769427	NA	P-0026855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	274	432	0	ENST00000291552.4:c.101C>A	p.Ser34Tyr	p.S34Y	ENST00000291552	NM_006758.2	34	tCt/tAt	2/8	1	2	FACETS	0.891	0.842	0.942	0.891	0.842	0.942	CLONAL	1	TRUE	1	0.859751153149282	2		432	715	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118744	115118745	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAT	novel	NA	P-0026855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1439	374	666	0	ENST00000257566.3:c.596_597insATC	p.Ser199dup	p.S199dup	ENST00000257566	NM_016569.3	199	tcc/tcATCc	2/8	0.821450157092022	4	FACETS	0.892	0.844	0.942	0.446	0.422	0.471	CLONAL	1	TRUE	2	0.859751153149282	4		666	1813	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046524	30046524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	398	616	2	ENST00000331968.5:c.2659C>T	p.Pro887Ser	p.P887S	ENST00000331968	NM_002742.2	887	Cca/Tca	18/18	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.859751153149282	2		618	886	SUCCESS
APC	324	MSKCC	GRCh37	5	112176520	112176521	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554086550	NA	P-0026855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	307	429	0	ENST00000257430.4:c.5234dup	p.Ile1746AspfsTer23	p.I1746Dfs*23	ENST00000257430	NM_000038.5	1743	-/A	16/16	0.83140280563596	1	FACETS	0.899	0.864	0.933	0.899	0.864	0.933	CLONAL	1	TRUE	0	0.859751153149282	1		429	453	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400023	139400023	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	45	656	0	ENST00000277541.6:c.4325del	p.Pro1442ArgfsTer3	p.P1442Rfs*3	ENST00000277541	NM_017617.3	1442	cCg/cg	25/34	1	2	FACETS	0.403	0.339	0.472	0.403	0.339	0.472	SUBCLONAL	1	TRUE	1	0.602615055266017	2		656	371	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577525	7577548	+	inframe_deletion	In_Frame_Del	DEL	GAGGATGGGCCTCCGGTTCATGCC	GAGGATGGGCCTCCGGTTCATGCC	-	novel	NA	P-0026882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	207	671	0	ENST00000269305.4:c.733_756del	p.Gly245_Leu252del	p.G245_L252del	ENST00000269305	NM_001126112.2	245	GGCATGAACCGGAGGCCCATCCTC/-	7/11	0.578471236721257	2	FACETS	0.844	0.795	0.893	0.844	0.795	0.893	CLONAL	2	TRUE	0	0.602615055266017	2		671	407	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411440	63411441	+	missense_variant	Missense_Mutation	DNP	TC	TC	CT	novel	NA	P-0026882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	30	629	0	ENST00000330258.3:c.1726_1727delinsAG	p.Glu576Arg	p.E576R	ENST00000330258	NM_152424.3	576	GAg/AGg	2/2	0.122832898197575	1	FACETS	0.219	0.176	0.267	0.219	0.176	0.267	INDETERMINATE	1	TRUE	0	0.602615055266017	1		629	318	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0026883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	229	519	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.249043570764163	4	FACETS	0.879	0.821	0.939	0.879	0.821	0.939	CLONAL	3	TRUE	1	0.249043570764163	4		519	871	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951171	48951171	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587778846	NA	P-0026883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	46	391	0	ENST00000267163.4:c.1332+1G>A		p.X444_splice	ENST00000267163	NM_000321.2	444			0.249043570764163	1	FACETS	0.983	0.831	1	0.983	0.831	1	CLONAL	1	TRUE	0	0.249043570764163	1		391	329	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218910	193218910	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	88	308	0	ENST00000367435.3:c.1468C>T	p.Gln490Ter	p.Q490*	ENST00000367435	NM_024529.4	490	Cag/Tag	16/17	0.107700691701376	3	FACETS	0.833	0.741	0.931	0.833	0.741	0.931	INDETERMINATE	2	TRUE	1	0.249043570764163	3		308	477	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578245	7578271	+	inframe_deletion	In_Frame_Del	DEL	GCAAATTTCCTTCCACTCGGATAAGAT	GCAAATTTCCTTCCACTCGGATAAGAT	-	novel	NA	P-0026883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	79	627	0	ENST00000269305.4:c.578_604del	p.His193_Leu201del	p.H193_L201del	ENST00000269305	NM_001126112.2	193	cATCTTATCCGAGTGGAAGGAAATTTGCgt/cgt	6/11	0.249043570764163	1	FACETS	0.769	0.676	0.869	0.769	0.676	0.869	SUBCLONAL	1	TRUE	0	0.249043570764163	1		627	722	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728906	190728907	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0026883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	53	398	0	ENST00000441310.2:c.2295_2296del	p.His765GlnfsTer19	p.H765Qfs*19	ENST00000441310	NM_000534.4	765	cAT/c	10/13	1	2	FACETS	0.952	0.813	1	0.952	0.813	1	CLONAL	1	TRUE	1	0.249043570764163	2		398	447	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94067979	94067979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	118	249	0	ENST00000369303.4:c.983G>A	p.Cys328Tyr	p.C328Y	ENST00000369303	NM_004440.3	328	tGc/tAc	4/17	0.181109386407556	3	FACETS	0.838	0.762	0.917	0.838	0.762	0.917	CLONAL	3	TRUE	0	0.249043570764163	3		249	424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0026884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	868	596	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.731676144835369	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.731676144835369	3		597	1052	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255995	16255995	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	475	579	0	ENST00000375759.3:c.3260G>C	p.Arg1087Thr	p.R1087T	ENST00000375759	NM_015001.2	1087	aGa/aCa	11/15	0.731676144835369	2	FACETS	0.987	0.958	1	0.987	0.958	1	CLONAL	2	TRUE	0	0.731676144835369	2		579	658	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932990	39932991	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0026884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	505	338	0	ENST00000378444.4:c.1608dup	p.Pro537ThrfsTer20	p.P537Tfs*20	ENST00000378444	NM_001123385.1	536	-/A	4/15	0.461181013721689	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.731676144835369	2		338	636	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	161	443	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	0.493323918174281	2		443	642	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	181	444	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	0.493323918174281	1	FACETS	0.966	0.897	1	0.966	0.897	1	CLONAL	1	TRUE	0	0.493323918174281	1		444	572	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784049	9784049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	105	659	0	ENST00000377346.4:c.2617G>A	p.Glu873Lys	p.E873K	ENST00000377346	NM_005026.3	873	Gag/Aag	21/24	0.487793525716466	2	FACETS	0.4	0.357	0.446	0.2	0.178	0.223	SUBCLONAL	1	TRUE	0	0.493323918174281	2		659	1064	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184649	11184649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	99	549	0	ENST00000361445.4:c.6568G>A	p.Glu2190Lys	p.E2190K	ENST00000361445	NM_004958.3	2190	Gaa/Aaa	47/58	0.487793525716466	2	FACETS	0.445	0.396	0.497	0.222	0.198	0.249	SUBCLONAL	1	TRUE	0	0.493323918174281	2		549	902	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16203049	16203049	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	101	539	0	ENST00000375759.3:c.757C>T	p.Gln253Ter	p.Q253*	ENST00000375759	NM_015001.2	253	Cag/Tag	3/15	0.363078014834177	2	FACETS	0.41	0.365	0.457	0.205	0.182	0.229	SUBCLONAL	1	TRUE	0	0.493323918174281	2		539	999	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257893	16257893	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748198500	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	106	612	0	ENST00000375759.3:c.5158G>A	p.Glu1720Lys	p.E1720K	ENST00000375759	NM_015001.2	1720	Gag/Aag	11/15	0.363078014834177	2	FACETS	0.469	0.42	0.522	0.235	0.21	0.261	SUBCLONAL	1	TRUE	0	0.493323918174281	2		612	916	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260551	16260551	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	132	588	0	ENST00000375759.3:c.7816G>A	p.Asp2606Asn	p.D2606N	ENST00000375759	NM_015001.2	2606	Gac/Aac	11/15	0.363078014834177	2	FACETS	0.511	0.463	0.561	0.255	0.231	0.281	SUBCLONAL	1	TRUE	0	0.493323918174281	2		588	1048	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264060	16264060	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1330	156	848	0	ENST00000375759.3:c.10429G>A	p.Glu3477Lys	p.E3477K	ENST00000375759	NM_015001.2	3477	Gaa/Aaa	12/15	0.363078014834177	2	FACETS	0.426	0.388	0.465	0.213	0.194	0.233	SUBCLONAL	1	TRUE	0	0.493323918174281	2		848	1486	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087504	27087504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770764901	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	303	676	0	ENST00000324856.7:c.2078G>A	p.Arg693Gln	p.R693Q	ENST00000324856	NM_006015.4	693	cGa/cAa	5/20	0.363078014834177	2	FACETS	1	0.955	1	0.508	0.478	0.539	CLONAL	1	TRUE	0	0.493323918174281	2		676	1209	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099408	27099408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	147	707	1	ENST00000324856.7:c.3645G>A	p.Met1215Ile	p.M1215I	ENST00000324856	NM_006015.4	1215	atG/atA	14/20	0.363078014834177	2	FACETS	0.531	0.484	0.581	0.266	0.242	0.291	SUBCLONAL	1	TRUE	0	0.493323918174281	2		708	1122	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812154	43812154	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	225	536	0	ENST00000372470.3:c.1019C>G	p.Thr340Arg	p.T340R	ENST00000372470	NM_005373.2	340	aCa/aGa	7/12	0.363078014834177	2	FACETS	1	0.937	1	0.502	0.468	0.538	CLONAL	1	TRUE	0	0.493323918174281	2		536	908	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65304159	65304159	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	79	453	0	ENST00000342505.4:c.2956C>T	p.Gln986Ter	p.Q986*	ENST00000342505	NM_002227.2	986	Cag/Tag	21/25	0.493323918174281	1	FACETS	0.416	0.366	0.469	0.416	0.366	0.469	SUBCLONAL	1	TRUE	0	0.493323918174281	1		453	580	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307188	65307188	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	94	534	0	ENST00000342505.4:c.2500C>T	p.Gln834Ter	p.Q834*	ENST00000342505	NM_002227.2	834	Cag/Tag	18/25	0.493323918174281	1	FACETS	0.442	0.393	0.493	0.442	0.393	0.493	SUBCLONAL	1	TRUE	0	0.493323918174281	1		534	650	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258691	115258691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	142	330	0	ENST00000369535.4:c.91G>A	p.Glu31Lys	p.E31K	ENST00000369535	NM_002524.4	31	Gaa/Aaa	2/7	1	2	FACETS	0.876	0.801	0.955	0.876	0.801	0.955	CLONAL	1	TRUE	1	0.493323918174281	2		330	657	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120467998	120467998	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	143	751	2	ENST00000256646.2:c.4441G>A	p.Asp1481Asn	p.D1481N	ENST00000256646	NM_024408.3	1481	Gat/Aat	25/34	1	2	FACETS	0.466	0.424	0.511	0.466	0.424	0.511	SUBCLONAL	1	TRUE	1	0.493323918174281	2		753	1243	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480519	120480519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782536553	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	201	471	2	ENST00000256646.2:c.3298G>A	p.Val1100Met	p.V1100M	ENST00000256646	NM_024408.3	1100	Gtg/Atg	20/34	1	2	FACETS	0.926	0.859	0.995	0.926	0.859	0.995	CLONAL	1	TRUE	1	0.493323918174281	2		473	880	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745460	162745460	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	139	375	0	ENST00000367921.3:c.1875G>C	p.Glu625Asp	p.E625D	ENST00000367921	NM_006182.2	625	gaG/gaC	15/18	1	2	FACETS	0.958	0.876	1	0.958	0.876	1	CLONAL	1	TRUE	1	0.493323918174281	2		375	588	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745524	162745524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	212	533	0	ENST00000367921.3:c.1939G>A	p.Asp647Asn	p.D647N	ENST00000367921	NM_006182.2	647	Gat/Aat	15/18	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.493323918174281	2		533	839	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745985	162745985	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	75	380	0	ENST00000367921.3:c.2108C>T	p.Ser703Phe	p.S703F	ENST00000367921	NM_006182.2	703	tCt/tTt	16/18	1	2	FACETS	0.489	0.428	0.554	0.489	0.428	0.554	SUBCLONAL	1	TRUE	1	0.493323918174281	2		380	622	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094321	193094321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	65	426	0	ENST00000367435.3:c.211C>T	p.His71Tyr	p.H71Y	ENST00000367435	NM_024529.4	71	Cat/Tat	2/17	1	2	FACETS	0.42	0.363	0.48	0.42	0.363	0.48	SUBCLONAL	1	TRUE	1	0.493323918174281	2		426	628	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667372	241667372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	92	607	0	ENST00000366560.3:c.1078G>A	p.Glu360Lys	p.E360K	ENST00000366560	NM_000143.3	360	Gaa/Aaa	7/10	1	2	FACETS	0.456	0.405	0.511	0.456	0.405	0.511	SUBCLONAL	1	TRUE	1	0.493323918174281	2		607	818	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615593	43615593	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	120	641	0	ENST00000355710.3:c.2672C>T	p.Ser891Leu	p.S891L	ENST00000355710	NM_020975.4	891	tCg/tTg	15/20	1	2	FACETS	0.498	0.449	0.55	0.498	0.449	0.55	SUBCLONAL	1	TRUE	1	0.493323918174281	2		641	977	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88651883	88651883	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs1564715427	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	168	447	0	ENST00000372037.3:c.231-1G>C		p.X77_splice	ENST00000372037	NM_004329.2	77			1	2	FACETS	0.977	0.901	1	0.977	0.901	1	CLONAL	1	TRUE	1	0.493323918174281	2		447	697	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692918	89692918	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	78	559	0	ENST00000371953.3:c.402G>A	p.Met134Ile	p.M134I	ENST00000371953	NM_000314.4	134	atG/atA	5/9	1	2	FACETS	0.437	0.384	0.495	0.437	0.384	0.495	SUBCLONAL	1	TRUE	1	0.493323918174281	2		559	723	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710987	114710987	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	72	514	1	ENST00000543371.1:c.211C>T	p.Arg71Cys	p.R71C	ENST00000543371	NM_001198531.1	71	Cgc/Tgc	2/14	1	2	FACETS	0.324	0.282	0.369	0.324	0.282	0.369	SUBCLONAL	1	TRUE	1	0.493323918174281	2		515	902	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911512	114911512	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	66	390	0	ENST00000543371.1:c.1030G>A	p.Glu344Lys	p.E344K	ENST00000543371	NM_001198531.1	344	Gaa/Aaa	10/14	1	2	FACETS	0.493	0.428	0.563	0.493	0.428	0.563	SUBCLONAL	1	TRUE	1	0.493323918174281	2		390	543	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244999	123244999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150015885	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	123	616	1	ENST00000358487.5:c.2105C>T	p.Ser702Leu	p.S702L	ENST00000358487	NM_000141.4	702	tCg/tTg	16/18	1	2	FACETS	0.532	0.481	0.587	0.532	0.481	0.587	SUBCLONAL	1	TRUE	1	0.493323918174281	2		617	937	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247543	123247543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	106	663	1	ENST00000358487.5:c.1948G>A	p.Asp650Asn	p.D650N	ENST00000358487	NM_000141.4	650	Gat/Aat	14/18	1	2	FACETS	0.389	0.347	0.433	0.389	0.347	0.433	SUBCLONAL	1	TRUE	1	0.493323918174281	2		664	1105	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121744	108121744	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	80	552	0	ENST00000278616.4:c.1552G>A	p.Glu518Lys	p.E518K	ENST00000278616	NM_000051.3	518	Gag/Aag	10/63	1	2	FACETS	0.415	0.364	0.469	0.415	0.364	0.469	SUBCLONAL	1	TRUE	1	0.493323918174281	2		552	782	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343273	118343273	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	61	332	0	ENST00000534358.1:c.1399C>T	p.Gln467Ter	p.Q467*	ENST00000534358	NM_005933.3	467	Cag/Tag	3/36	1	2	FACETS	0.424	0.366	0.488	0.424	0.366	0.488	SUBCLONAL	1	TRUE	1	0.493323918174281	2		332	583	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380677	118380677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	152	478	0	ENST00000534358.1:c.10915G>A	p.Glu3639Lys	p.E3639K	ENST00000534358	NM_005933.3	3639	Gaa/Aaa	30/36	1	2	FACETS	0.952	0.874	1	0.952	0.874	1	CLONAL	1	TRUE	1	0.493323918174281	2		478	647	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155695	119155695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	95	473	0	ENST00000264033.4:c.1448C>T	p.Ser483Phe	p.S483F	ENST00000264033	NM_005188.3	483	tCt/tTt	10/16	1	2	FACETS	0.445	0.395	0.498	0.445	0.395	0.498	SUBCLONAL	1	TRUE	1	0.493323918174281	2		473	866	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170291	119170291	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	146	318	0	ENST00000264033.4:c.2521C>T	p.Gln841Ter	p.Q841*	ENST00000264033	NM_005188.3	841	Cag/Tag	16/16	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.493323918174281	2		318	574	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125523707	125523707	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	134	407	0	ENST00000428830.2:c.1300G>C	p.Asp434His	p.D434H	ENST00000428830	NM_001114121.2	434	Gat/Cat	12/14	1	2	FACETS	0.938	0.856	1	0.938	0.856	1	CLONAL	1	TRUE	1	0.493323918174281	2		407	579	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416910	416910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	95	470	0	ENST00000399788.2:c.3640C>T	p.Leu1214Phe	p.L1214F	ENST00000399788	NM_001042603.1	1214	Ctt/Ttt	23/28	1	2	FACETS	0.505	0.45	0.565	0.505	0.45	0.565	SUBCLONAL	1	TRUE	1	0.493323918174281	2		470	762	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417122	417122	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	64	354	0	ENST00000399788.2:c.3428C>T	p.Ser1143Phe	p.S1143F	ENST00000399788	NM_001042603.1	1143	tCt/tTt	23/28	1	2	FACETS	0.407	0.352	0.466	0.407	0.352	0.466	SUBCLONAL	1	TRUE	1	0.493323918174281	2		354	638	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	422224	422224	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	89	569	0	ENST00000399788.2:c.3034C>T	p.Gln1012Ter	p.Q1012*	ENST00000399788	NM_001042603.1	1012	Cag/Tag	20/28	1	2	FACETS	0.41	0.363	0.461	0.41	0.363	0.461	SUBCLONAL	1	TRUE	1	0.493323918174281	2		569	879	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006424	12006424	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	114	540	0	ENST00000396373.4:c.392C>T	p.Ser131Leu	p.S131L	ENST00000396373	NM_001987.4	131	tCa/tTa	4/8	1	2	FACETS	0.472	0.424	0.523	0.472	0.424	0.523	SUBCLONAL	1	TRUE	1	0.493323918174281	2		540	979	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658367	18658367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	59	447	0	ENST00000266497.5:c.3172C>T	p.His1058Tyr	p.H1058Y	ENST00000266497		1058	Cat/Tat	22/31	1	2	FACETS	0.413	0.355	0.476	0.413	0.355	0.476	SUBCLONAL	1	TRUE	1	0.493323918174281	2		447	579	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793483	18793483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267603405	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	45	317	0	ENST00000266497.5:c.4180G>A	p.Glu1394Lys	p.E1394K	ENST00000266497		1394	Gaa/Aaa	30/31	1	2	FACETS	0.417	0.351	0.491	0.417	0.351	0.491	SUBCLONAL	1	TRUE	1	0.493323918174281	2		317	437	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230613	46230613	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	100	527	0	ENST00000334344.6:c.862C>T	p.Gln288Ter	p.Q288*	ENST00000334344	NM_152641.2	288	Cag/Tag	8/21	1	2	FACETS	0.515	0.46	0.574	0.515	0.46	0.574	SUBCLONAL	1	TRUE	1	0.493323918174281	2		527	787	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478821	56478821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	163	692	1	ENST00000267101.3:c.277G>A	p.Glu93Lys	p.E93K	ENST00000267101	NM_001982.3	93	Gaa/Aaa	3/28	1	2	FACETS	0.574	0.526	0.625	0.574	0.526	0.625	SUBCLONAL	1	TRUE	1	0.493323918174281	2		693	1151	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858567	57858567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	142	749	1	ENST00000228682.2:c.305C>T	p.Ser102Leu	p.S102L	ENST00000228682	NM_005269.2	102	tCa/tTa	4/12	1	2	FACETS	0.463	0.42	0.507	0.463	0.42	0.507	SUBCLONAL	1	TRUE	1	0.493323918174281	2		750	1244	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58142997	58142997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	149	749	0	ENST00000257904.6:c.787G>A	p.Glu263Lys	p.E263K	ENST00000257904	NM_000075.3	263	Gag/Aag	7/8	1	2	FACETS	0.478	0.435	0.522	0.478	0.435	0.522	SUBCLONAL	1	TRUE	1	0.493323918174281	2		749	1265	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69229711	69229711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	36	422	0	ENST00000462284.1:c.787G>A	p.Glu263Lys	p.E263K	ENST00000462284	NM_002392.5	263	Gaa/Aaa	9/11	1	2	FACETS	0.228	0.187	0.275	0.228	0.187	0.275	SUBCLONAL	1	TRUE	1	0.493323918174281	2		422	640	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26927938	26927938	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	135	466	0	ENST00000381527.3:c.377G>A	p.Gly126Glu	p.G126E	ENST00000381527	NM_001260.1	126	gGa/gAa	4/13	NA	2	FACETS	0.988	0.902	1			1	INDETERMINATE	1	TRUE	NA	0.493323918174281	2		466	554	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240285	41240285	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	121	484	1	ENST00000379561.5:c.65C>T	p.Ser22Leu	p.S22L	ENST00000379561	NM_002015.3	22	tCg/tTg	1/3	1	2	FACETS	0.565	0.51	0.623	0.565	0.51	0.623	SUBCLONAL	1	TRUE	1	0.493323918174281	2		485	868	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281386	49281386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139045217	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	320	781	0	ENST00000282018.3:c.433C>T	p.Arg145Trp	p.R145W	ENST00000282018	NM_020377.2	145	Cgg/Tgg	1/1	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.493323918174281	2		781	1162	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346883	73346883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	107	330	1	ENST00000377767.4:c.1334C>T	p.Ser445Leu	p.S445L	ENST00000377767	NM_014953.3	445	tCa/tTa	9/21	1	2	FACETS	0.958	0.864	1	0.958	0.864	1	CLONAL	1	TRUE	1	0.493323918174281	2		331	453	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346932	73346932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	48	383	1	ENST00000377767.4:c.1285G>A	p.Glu429Lys	p.E429K	ENST00000377767	NM_014953.3	429	Gaa/Aaa	9/21	1	2	FACETS	0.4	0.338	0.468	0.4	0.338	0.468	SUBCLONAL	1	TRUE	1	0.493323918174281	2		384	487	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527672	103527672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	44	262	0	ENST00000355739.4:c.2980G>A	p.Asp994Asn	p.D994N	ENST00000355739	NM_000123.3	994	Gat/Aat	15/15	1	2	FACETS	0.389	0.327	0.459	0.389	0.327	0.459	SUBCLONAL	1	TRUE	1	0.493323918174281	2		262	458	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061532	38061532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781269308	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	189	308	0	ENST00000250448.2:c.457G>A	p.Ala153Thr	p.A153T	ENST00000250448	NM_004496.3	153	Gcg/Acg	2/2	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.493323918174281	2		308	569	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331767	68331767	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	85	467	0	ENST00000487270.1:c.363G>A	p.Met121Ile	p.M121I	ENST00000487270	NM_133509.3	121	atG/atA	5/11	1	2	FACETS	0.525	0.464	0.59	0.525	0.464	0.59	SUBCLONAL	1	TRUE	1	0.493323918174281	2		467	657	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352593	68352593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	58	362	0	ENST00000487270.1:c.460G>A	p.Glu154Lys	p.E154K	ENST00000487270	NM_133509.3	154	Gaa/Aaa	6/11	1	2	FACETS	0.477	0.41	0.55	0.477	0.41	0.55	SUBCLONAL	1	TRUE	1	0.493323918174281	2		362	493	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574303	95574303	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	166	388	0	ENST00000393063.1:c.2564C>T	p.Ser855Leu	p.S855L	ENST00000393063	NM_030621.3	855	tCa/tTa	17/28	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.493323918174281	2		388	645	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574663	95574663	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	125	302	0	ENST00000393063.1:c.2434C>G	p.Gln812Glu	p.Q812E	ENST00000393063	NM_030621.3	812	Cag/Gag	16/28	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.493323918174281	2		302	482	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582900	95582900	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	73	415	0	ENST00000393063.1:c.1642C>T	p.Gln548Ter	p.Q548*	ENST00000393063	NM_030621.3	548	Caa/Taa	11/28	1	2	FACETS	0.491	0.429	0.557	0.491	0.429	0.557	SUBCLONAL	1	TRUE	1	0.493323918174281	2		415	603	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003545	42003545	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	65	398	0	ENST00000219905.7:c.3082C>T	p.Gln1028Ter	p.Q1028*	ENST00000219905	NM_001164273.1	1028	Caa/Taa	8/24	1	2	FACETS	0.419	0.363	0.48	0.419	0.363	0.48	SUBCLONAL	1	TRUE	1	0.493323918174281	2		398	629	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748474	43748474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	263	718	1	ENST00000382044.4:c.2332G>A	p.Glu778Lys	p.E778K	ENST00000382044	NM_001141980.1	778	Gaa/Aaa	12/28	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.493323918174281	2		719	1051	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43783907	43783907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	132	690	2	ENST00000382044.4:c.331C>T	p.Gln111Ter	p.Q111*	ENST00000382044	NM_001141980.1	111	Cag/Tag	4/28	1	2	FACETS	0.49	0.443	0.538	0.49	0.443	0.538	SUBCLONAL	1	TRUE	1	0.493323918174281	2		692	1093	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784619	43784619	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1323524336	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	86	614	0	ENST00000382044.4:c.55C>T	p.Gln19Ter	p.Q19*	ENST00000382044	NM_001141980.1	19	Cag/Tag	2/28	1	2	FACETS	0.335	0.295	0.378	0.335	0.295	0.378	SUBCLONAL	1	TRUE	1	0.493323918174281	2		614	1041	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727501	66727501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	115	580	1	ENST00000307102.5:c.217G>A	p.Glu73Lys	p.E73K	ENST00000307102	NM_002755.3	73	Gag/Aag	2/11	1	2	FACETS	0.456	0.41	0.505	0.456	0.41	0.505	SUBCLONAL	1	TRUE	1	0.493323918174281	2		581	1023	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66777349	66777349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	103	569	3	ENST00000307102.5:c.715C>T	p.His239Tyr	p.H239Y	ENST00000307102	NM_002755.3	239	Cat/Tat	7/11	1	2	FACETS	0.434	0.388	0.484	0.434	0.388	0.484	SUBCLONAL	1	TRUE	1	0.493323918174281	2		572	962	SUCCESS
BLM	641	MSKCC	GRCh37	15	91341500	91341500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	80	548	2	ENST00000355112.3:c.3291G>A	p.Met1097Ile	p.M1097I	ENST00000355112	NM_000057.2	1097	atG/atA	17/22	1	2	FACETS	0.397	0.349	0.449	0.397	0.349	0.449	SUBCLONAL	1	TRUE	1	0.493323918174281	2		550	816	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434793	99434793	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201529410	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	248	607	2	ENST00000268035.6:c.880G>A	p.Glu294Lys	p.E294K	ENST00000268035	NM_000875.3	294	Gag/Aag	3/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.493323918174281	2		609	944	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99473531	99473531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	50	290	0	ENST00000268035.6:c.2953G>A	p.Asp985Asn	p.D985N	ENST00000268035	NM_000875.3	985	Gat/Aat	15/21	1	2	FACETS	0.411	0.349	0.48	0.411	0.349	0.48	SUBCLONAL	1	TRUE	1	0.493323918174281	2		290	493	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3799647	3799647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	73	492	0	ENST00000262367.5:c.3817G>A	p.Asp1273Asn	p.D1273N	ENST00000262367	NM_004380.2	1273	Gat/Aat	21/31	1	2	FACETS	0.363	0.316	0.413	0.363	0.316	0.413	SUBCLONAL	1	TRUE	1	0.493323918174281	2		492	816	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817911	3817911	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	73	392	0	ENST00000262367.5:c.3061-1G>A		p.X1021_splice	ENST00000262367	NM_004380.2	1021			1	2	FACETS	0.479	0.419	0.544	0.479	0.419	0.544	SUBCLONAL	1	TRUE	1	0.493323918174281	2		392	618	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3824580	3824580	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	191	353	0	ENST00000262367.5:c.2273C>T	p.Ser758Leu	p.S758L	ENST00000262367	NM_004380.2	758	tCa/tTa	12/31	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.493323918174281	2		353	708	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857021	9857021	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs769629103	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	69	294	0	ENST00000330684.3:c.4380C>G	p.Ile1460Met	p.I1460M	ENST00000330684	NM_001134407.1	1460	atC/atG	13/13	1	2	FACETS	0.76	0.666	0.861	0.76	0.666	0.861	SUBCLONAL	1	TRUE	1	0.493323918174281	2		294	368	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029128	14029128	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748206066	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	71	328	0	ENST00000311895.7:c.1339G>A	p.Glu447Lys	p.E447K	ENST00000311895	NM_005236.2	447	Gaa/Aaa	8/11	1	2	FACETS	0.504	0.44	0.573	0.504	0.44	0.573	SUBCLONAL	1	TRUE	1	0.493323918174281	2		328	571	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50811745	50811745	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749160760	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	66	390	0	ENST00000398568.2:c.1022C>T	p.Ser341Leu	p.S341L	ENST00000398568	NM_001042412.1	341	tCa/tTa	7/18	NA	2	FACETS	0.498	0.433	0.569			1	INDETERMINATE	1	TRUE	NA	0.493323918174281	2		390	537	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849663	68849663	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587780113	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	150	482	0	ENST00000261769.5:c.1565+1G>T		p.X522_splice	ENST00000261769	NM_004360.3	522			0.493323918174281	1	FACETS	0.858	0.789	0.929	0.858	0.789	0.929	CLONAL	1	TRUE	0	0.493323918174281	1		482	534	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867307	68867307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	228	567	0	ENST00000261769.5:c.2554G>A	p.Glu852Lys	p.E852K	ENST00000261769	NM_004360.3	852	Gag/Aag	16/16	0.493323918174281	1	FACETS	0.998	0.934	1	0.998	0.934	1	CLONAL	1	TRUE	0	0.493323918174281	1		567	698	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350486	89350486	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	181	787	1	ENST00000301030.4:c.2464C>T	p.Gln822Ter	p.Q822*	ENST00000301030	NM_001256183.1	822	Cag/Tag	9/13	NA	2	FACETS	0.544	0.5	0.59			1	INDETERMINATE	1	TRUE	NA	0.493323918174281	2		788	1349	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350858	89350858	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1422731618	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	147	720	0	ENST00000301030.4:c.2092G>A	p.Glu698Lys	p.E698K	ENST00000301030	NM_001256183.1	698	Gag/Aag	9/13	NA	2	FACETS	0.531	0.483	0.58			1	INDETERMINATE	1	TRUE	NA	0.493323918174281	2		720	1123	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976471	7976471	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	206	491	1	ENST00000319144.4:c.1921G>A	p.Asp641Asn	p.D641N	ENST00000319144	NM_001139.2	641	Gac/Aac	14/15	0.493323918174281	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.493323918174281	1		492	597	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990631	7990631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	290	593	1	ENST00000319144.4:c.130G>A	p.Asp44Asn	p.D44N	ENST00000319144	NM_001139.2	44	Gac/Aac	1/15	0.493323918174281	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.493323918174281	1		594	858	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004664	16004664	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	123	571	1	ENST00000268712.3:c.2590C>T	p.Gln864Ter	p.Q864*	ENST00000268712	NM_006311.3	864	Cag/Tag	20/46	0.493323918174281	1	FACETS	0.498	0.45	0.548	0.498	0.45	0.548	SUBCLONAL	1	TRUE	0	0.493323918174281	1		572	755	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004673	16004673	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	247	570	0	ENST00000268712.3:c.2581G>C	p.Val861Leu	p.V861L	ENST00000268712	NM_006311.3	861	Gtg/Ctg	20/46	0.493323918174281	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.493323918174281	1		570	748	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627496	37627496	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1245449401	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	235	655	0	ENST00000447079.4:c.1411G>A	p.Glu471Lys	p.E471K	ENST00000447079	NM_015083.1	471	Gag/Aag	2/14	1	2	FACETS	0.878	0.819	0.939	0.878	0.819	0.939	CLONAL	1	TRUE	1	0.493323918174281	2		655	1085	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687366	37687366	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	245	557	0	ENST00000447079.4:c.4270G>A	p.Glu1424Lys	p.E1424K	ENST00000447079	NM_015083.1	1424	Gag/Aag	14/14	1	2	FACETS	0.993	0.929	1	0.993	0.929	1	CLONAL	1	TRUE	1	0.493323918174281	2		557	1000	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441993	40441993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	98	815	0	ENST00000345506.4:c.238G>A	p.Gly80Arg	p.G80R	ENST00000345506	NM_003152.3	80	Ggg/Agg	4/20	1	2	FACETS	0.324	0.288	0.363	0.324	0.288	0.363	SUBCLONAL	1	TRUE	1	0.493323918174281	2		815	1225	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226507	41226507	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	121	573	0	ENST00000357654.3:c.4516G>A	p.Asp1506Asn	p.D1506N	ENST00000357654	NM_007294.3	1506	Gat/Aat	14/23	1	2	FACETS	0.566	0.511	0.625	0.566	0.511	0.625	SUBCLONAL	1	TRUE	1	0.493323918174281	2		573	866	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677814	47677814	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	108	594	1	ENST00000347630.2:c.1051G>A	p.Glu351Lys	p.E351K	ENST00000347630	NM_001007230.1	351	Gag/Aag	11/11	1	2	FACETS	0.448	0.401	0.498	0.448	0.401	0.498	SUBCLONAL	1	TRUE	1	0.493323918174281	2		595	977	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47700168	47700168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	63	444	0	ENST00000347630.2:c.5C>T	p.Ser2Leu	p.S2L	ENST00000347630	NM_001007230.1	2	tCa/tTa	3/11	1	2	FACETS	0.36	0.31	0.413	0.36	0.31	0.413	SUBCLONAL	1	TRUE	1	0.493323918174281	2		444	710	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740674	58740674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs564827577	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	124	623	0	ENST00000305921.3:c.1579G>A	p.Glu527Lys	p.E527K	ENST00000305921	NM_003620.3	527	Gaa/Aaa	6/6	1	2	FACETS	0.479	0.432	0.528	0.479	0.432	0.528	SUBCLONAL	1	TRUE	1	0.493323918174281	2		623	1050	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581234	48581234	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767332	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	105	642	0	ENST00000342988.3:c.538C>T	p.Gln180Ter	p.Q180*	ENST00000342988	NM_005359.5	180	Caa/Taa	5/12	0.493323918174281	1	FACETS	0.472	0.423	0.524	0.472	0.423	0.524	SUBCLONAL	1	TRUE	0	0.493323918174281	1		642	679	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625645	1625645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759137601	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	132	870	0	ENST00000344749.5:c.429G>A	p.Met143Ile	p.M143I	ENST00000344749	NM_001136139.2	143	atG/atA	7/19	1	2	FACETS	0.432	0.39	0.475	0.432	0.39	0.475	SUBCLONAL	1	TRUE	1	0.493323918174281	2		870	1240	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2206785	2206785	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	222	562	0	ENST00000398665.3:c.845G>A	p.Arg282Lys	p.R282K	ENST00000398665	NM_032482.2	282	aGa/aAa	10/28	1	2	FACETS	0.953	0.888	1	0.953	0.888	1	CLONAL	1	TRUE	1	0.493323918174281	2		562	944	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217909	2217909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1230117726	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	138	699	1	ENST00000398665.3:c.2683G>A	p.Glu895Lys	p.E895K	ENST00000398665	NM_032482.2	895	Gag/Aag	22/28	1	2	FACETS	0.474	0.43	0.52	0.474	0.43	0.52	SUBCLONAL	1	TRUE	1	0.493323918174281	2		700	1181	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223443	2223443	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	189	527	0	ENST00000398665.3:c.3554C>G	p.Ser1185Ter	p.S1185*	ENST00000398665	NM_032482.2	1185	tCa/tGa	25/28	1	2	FACETS	0.971	0.899	1	0.971	0.899	1	CLONAL	1	TRUE	1	0.493323918174281	2		527	789	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5207935	5207935	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	242	613	0	ENST00000357368.4:c.5776G>A	p.Glu1926Lys	p.E1926K	ENST00000357368	NM_002850.3	1926	Gag/Aag	37/38	1	2	FACETS	0.942	0.88	1	0.942	0.88	1	CLONAL	1	TRUE	1	0.493323918174281	2		613	1041	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097233	11097233	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555753773	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	152	661	0	ENST00000358026.2:c.724C>T	p.Pro242Ser	p.P242S	ENST00000358026	NM_001128849.1	242	Ccc/Tcc	4/36	1	2	FACETS	0.554	0.506	0.605	0.554	0.506	0.605	SUBCLONAL	1	TRUE	1	0.493323918174281	2		661	1112	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272444	15272444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	401	986	0	ENST00000263388.2:c.5995G>A	p.Glu1999Lys	p.E1999K	ENST00000263388	NM_000435.2	1999	Gag/Aag	33/33	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.493323918174281	2		986	1534	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278090	15278090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1487561873	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	267	777	0	ENST00000263388.2:c.5332G>A	p.Asp1778Asn	p.D1778N	ENST00000263388	NM_000435.2	1778	Gat/Aat	29/33	1	2	FACETS	0.928	0.869	0.988	0.928	0.869	0.988	CLONAL	1	TRUE	1	0.493323918174281	2		777	1167	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943367	17943367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	292	694	1	ENST00000458235.1:c.2641G>A	p.Asp881Asn	p.D881N	ENST00000458235	NM_000215.3	881	Gat/Aat	19/24	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.493323918174281	2		695	1119	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976499	18976499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	340	804	0	ENST00000262803.5:c.3149C>T	p.Ser1050Phe	p.S1050F	ENST00000262803	NM_002911.3	1050	tCt/tTt	22/24	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.493323918174281	2		804	1295	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792825	33792825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755311871	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	90	284	0	ENST00000498907.2:c.496G>A	p.Glu166Lys	p.E166K	ENST00000498907	NM_004364.3	166	Gag/Aag	1/1	1	2	FACETS	0.597	0.53	0.668	0.597	0.53	0.668	SUBCLONAL	1	TRUE	1	0.493323918174281	2		284	611	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765795	41765795	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	96	418	0	ENST00000301178.4:c.2671G>A	p.Glu891Lys	p.E891K	ENST00000301178	NM_021913.4	891	Gag/Aag	20/20	1	2	FACETS	0.509	0.454	0.569	0.509	0.454	0.569	SUBCLONAL	1	TRUE	1	0.493323918174281	2		418	764	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793342	42793342	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343848845	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	218	650	1	ENST00000575354.2:c.1144G>A	p.Gly382Ser	p.G382S	ENST00000575354	NM_015125.3	382	Ggc/Agc	8/20	1	2	FACETS	0.865	0.804	0.927	0.865	0.804	0.927	CLONAL	1	TRUE	1	0.493323918174281	2		651	1022	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793358	42793358	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	128	635	0	ENST00000575354.2:c.1160C>T	p.Ser387Phe	p.S387F	ENST00000575354	NM_015125.3	387	tCt/tTt	8/20	1	2	FACETS	0.517	0.468	0.569	0.517	0.468	0.569	SUBCLONAL	1	TRUE	1	0.493323918174281	2		635	1004	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25459852	25459852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	107	739	1	ENST00000264709.3:c.2431G>A	p.Asp811Asn	p.D811N	ENST00000264709	NM_175629.2	811	Gat/Aat	21/23	0.493323918174281	1	FACETS	0.354	0.317	0.394	0.354	0.317	0.394	SUBCLONAL	1	TRUE	0	0.493323918174281	1		740	923	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416698	29416698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56181542	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	112	458	1	ENST00000389048.3:c.4255G>A	p.Glu1419Lys	p.E1419K	ENST00000389048	NM_004304.4	1419	Gag/Aag	29/29	1	2	FACETS	0.67	0.603	0.74	0.67	0.603	0.74	SUBCLONAL	1	TRUE	1	0.493323918174281	2		459	678	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39237792	39237792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	76	536	0	ENST00000402219.2:c.2443G>A	p.Glu815Lys	p.E815K	ENST00000402219	NM_005633.3	815	Gaa/Aaa	15/23	1	2	FACETS	0.349	0.305	0.396	0.349	0.305	0.396	SUBCLONAL	1	TRUE	1	0.493323918174281	2		536	883	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47600981	47600981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	112	698	0	ENST00000263735.4:c.219G>A	p.Met73Ile	p.M73I	ENST00000263735	NM_002354.2	73	atG/atA	3/9	1	2	FACETS	0.421	0.378	0.467	0.421	0.378	0.467	SUBCLONAL	1	TRUE	1	0.493323918174281	2		698	1078	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010526	48010526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	99	384	0	ENST00000234420.5:c.154G>A	p.Glu52Lys	p.E52K	ENST00000234420	NM_000179.2	52	Gag/Aag	1/10	1	2	FACETS	0.59	0.527	0.657	0.59	0.527	0.657	SUBCLONAL	1	TRUE	1	0.493323918174281	2		384	680	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025904	48025904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876661250	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	122	512	0	ENST00000234420.5:c.782C>T	p.Ser261Phe	p.S261F	ENST00000234420	NM_000179.2	261	tCt/tTt	4/10	1	2	FACETS	0.562	0.507	0.62	0.562	0.507	0.62	SUBCLONAL	1	TRUE	1	0.493323918174281	2		512	880	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61725918	61725918	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	169	458	1	ENST00000401558.2:c.649C>T	p.Gln217Ter	p.Q217*	ENST00000401558	NM_003400.3	217	Caa/Taa	9/25	1	2	FACETS	0.871	0.802	0.942	0.871	0.802	0.942	CLONAL	1	TRUE	1	0.493323918174281	2		459	787	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919703	96919703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	107	565	0	ENST00000258439.3:c.560C>T	p.Ser187Leu	p.S187L	ENST00000258439	NM_001193304.2	187	tCa/tTa	4/4	1	2	FACETS	0.506	0.453	0.562	0.506	0.453	0.562	SUBCLONAL	1	TRUE	1	0.493323918174281	2		565	857	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732616	190732616	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	161	623	0	ENST00000441310.2:c.2434C>A	p.Arg812Ser	p.R812S	ENST00000441310	NM_000534.4	812	Cgt/Agt	11/13	1	2	FACETS	0.947	0.871	1	0.947	0.871	1	CLONAL	1	TRUE	1	0.493323918174281	2		623	689	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270054	198270054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	122	453	0	ENST00000335508.6:c.1382C>T	p.Ser461Phe	p.S461F	ENST00000335508	NM_012433.2	461	tCt/tTt	10/25	1	2	FACETS	0.631	0.57	0.695	0.631	0.57	0.695	SUBCLONAL	1	TRUE	1	0.493323918174281	2		453	784	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136300	202136300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	53	649	0	ENST00000358485.4:c.544C>T	p.Leu182Phe	p.L182F	ENST00000358485	NM_001080125.1	182	Ctt/Ttt	3/9	1	2	FACETS	0.223	0.189	0.26	0.223	0.189	0.26	SUBCLONAL	1	TRUE	1	0.493323918174281	2		649	964	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663346	227663346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024227751	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	95	504	0	ENST00000305123.5:c.109G>A	p.Glu37Lys	p.E37K	ENST00000305123	NM_005544.2	37	Gag/Aag	1/2	1	2	FACETS	0.524	0.466	0.585	0.524	0.466	0.585	SUBCLONAL	1	TRUE	1	0.493323918174281	2		504	735	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538320	9538320	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	186	575	0	ENST00000353224.5:c.1678C>T	p.His560Tyr	p.H560Y	ENST00000353224	NM_177990.2	560	Cat/Tat	7/10	1	2	FACETS	0.934	0.864	1	0.934	0.864	1	CLONAL	1	TRUE	1	0.493323918174281	2		575	807	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750694	39750694	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	131	309	0	ENST00000361337.2:c.2094G>C	p.Leu698Phe	p.L698F	ENST00000361337	NM_003286.2	698	ttG/ttC	20/21	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.493323918174281	2		309	489	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264878	46264878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	95	464	0	ENST00000371998.3:c.1748C>T	p.Ser583Leu	p.S583L	ENST00000371998		583	tCa/tTa	12/23	1	2	FACETS	0.488	0.434	0.545	0.488	0.434	0.545	SUBCLONAL	1	TRUE	1	0.493323918174281	2		464	790	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265037	46265037	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	117	469	0	ENST00000371998.3:c.1907C>T	p.Ser636Phe	p.S636F	ENST00000371998		636	tCc/tTc	12/23	1	2	FACETS	0.534	0.481	0.59	0.534	0.481	0.59	SUBCLONAL	1	TRUE	1	0.493323918174281	2		469	888	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958078	54958078	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	124	297	0	ENST00000312783.6:c.529C>T	p.Gln177Ter	p.Q177*	ENST00000312783	NM_198436.1	177	Cag/Tag	6/10	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.493323918174281	2		297	484	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39762954	39762954	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	203	499	0	ENST00000288319.7:c.882G>C	p.Gln294His	p.Q294H	ENST00000288319	NM_182918.3	294	caG/caC	9/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.493323918174281	2		499	733	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42870089	42870089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	159	696	2	ENST00000398585.3:c.83C>T	p.Ser28Leu	p.S28L	ENST00000398585	NM_001135099.1	28	tCa/tTa	2/14	1	2	FACETS	0.59	0.54	0.642	0.59	0.54	0.642	SUBCLONAL	1	TRUE	1	0.493323918174281	2		698	1093	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221645	22221645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	105	358	0	ENST00000215832.6:c.86C>T	p.Ser29Leu	p.S29L	ENST00000215832	NM_002745.4	29	tCg/tTg	1/9	1	2	FACETS	0.588	0.527	0.653	0.588	0.527	0.653	SUBCLONAL	1	TRUE	1	0.493323918174281	2		358	724	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573903	41573903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	106	717	1	ENST00000263253.7:c.6188C>T	p.Ser2063Phe	p.S2063F	ENST00000263253	NM_001429.3	2063	tCt/tTt	31/31	1	2	FACETS	0.358	0.32	0.399	0.358	0.32	0.399	SUBCLONAL	1	TRUE	1	0.493323918174281	2		718	1200	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41279543	41279543	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762655300	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	117	496	1	ENST00000349496.5:c.2113G>A	p.Glu705Lys	p.E705K	ENST00000349496	NM_001904.3	705	Gaa/Aaa	14/15	0.493323918174281	1	FACETS	0.563	0.508	0.62	0.563	0.508	0.62	SUBCLONAL	1	TRUE	0	0.493323918174281	1		497	635	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164553	47164553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	67	295	0	ENST00000409792.3:c.1573G>A	p.Glu525Lys	p.E525K	ENST00000409792	NM_014159.6	525	Gaa/Aaa	3/21	0.493323918174281	1	FACETS	0.553	0.483	0.628	0.553	0.483	0.628	SUBCLONAL	1	TRUE	0	0.493323918174281	1		295	370	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73047278	73047278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	178	522	0	ENST00000356692.5:c.85C>T	p.Leu29Phe	p.L29F	ENST00000356692		29	Ctt/Ttt	2/9	0.493323918174281	1	FACETS	0.884	0.819	0.951	0.884	0.819	0.951	CLONAL	1	TRUE	0	0.493323918174281	1		522	615	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474668	138474668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	100	566	0	ENST00000289153.2:c.325C>T	p.Leu109Phe	p.L109F	ENST00000289153	NM_006219.2	109	Ctc/Ttc	2/22	1	2	FACETS	0.562	0.502	0.626	0.562	0.502	0.626	SUBCLONAL	1	TRUE	1	0.493323918174281	2		566	721	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938922	178938922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	74	436	0	ENST00000263967.3:c.2164G>A	p.Glu722Lys	p.E722K	ENST00000263967	NM_006218.2	722	Gag/Aag	14/21	1	2	FACETS	0.45	0.394	0.511	0.45	0.394	0.511	SUBCLONAL	1	TRUE	1	0.493323918174281	2		436	666	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	75	628	0	ENST00000263967.3:c.3012G>A	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atA	21/21	1	2	FACETS	0.419	0.366	0.475	0.419	0.366	0.475	SUBCLONAL	1	TRUE	1	0.493323918174281	2		628	726	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608654	189608654	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	176	539	0	ENST00000264731.3:c.1729G>A	p.Glu577Lys	p.E577K	ENST00000264731	NM_003722.4	577	Gag/Aag	13/14	1	2	FACETS	0.94	0.868	1	0.94	0.868	1	CLONAL	1	TRUE	1	0.493323918174281	2		539	759	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1978221	1978221	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	302	726	1	ENST00000382891.5:c.3641C>T	p.Ser1214Leu	p.S1214L	ENST00000382891	NM_133335.3	1214	tCa/tTa	21/22	NA	2	FACETS	0.973	0.916	1			1	INDETERMINATE	1	TRUE	NA	0.493323918174281	2		727	1258	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136887	55136887	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	192	557	0	ENST00000257290.5:c.1209G>C	p.Lys403Asn	p.K403N	ENST00000257290	NM_006206.4	403	aaG/aaC	8/23	NA	2	FACETS	0.99	0.918	1			1	INDETERMINATE	1	TRUE	NA	0.493323918174281	2		557	786	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196697	106196697	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	102	545	0	ENST00000380013.4:c.5030C>T	p.Thr1677Ile	p.T1677I	ENST00000380013	NM_001127208.2	1677	aCa/aTa	11/11	1	2	FACETS	0.512	0.458	0.57	0.512	0.458	0.57	SUBCLONAL	1	TRUE	1	0.493323918174281	2		545	807	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197635	106197635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	75	355	0	ENST00000380013.4:c.5968G>A	p.Ala1990Thr	p.A1990T	ENST00000380013	NM_001127208.2	1990	Gcc/Acc	11/11	1	2	FACETS	0.425	0.372	0.483	0.425	0.372	0.483	SUBCLONAL	1	TRUE	1	0.493323918174281	2		355	715	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332589	153332589	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	83	360	1	ENST00000281708.4:c.367G>A	p.Asp123Asn	p.D123N	ENST00000281708	NM_033632.3	123	Gac/Aac	2/12	1	2	FACETS	0.552	0.487	0.621	0.552	0.487	0.621	SUBCLONAL	1	TRUE	1	0.493323918174281	2		361	610	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517867	187517867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	52	500	1	ENST00000441802.2:c.12827C>T	p.Ser4276Phe	p.S4276F	ENST00000441802	NM_005245.3	4276	tCt/tTt	25/27	0.493323918174281	1	FACETS	0.306	0.26	0.356	0.306	0.26	0.356	SUBCLONAL	1	TRUE	0	0.493323918174281	1		501	519	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945147	38945147	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561436214	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	43	367	0	ENST00000357387.3:c.4657G>A	p.Asp1553Asn	p.D1553N	ENST00000357387	NM_152756.3	1553	Gat/Aat	35/38	1	2	FACETS	0.31	0.259	0.366	0.31	0.259	0.366	SUBCLONAL	1	TRUE	1	0.493323918174281	2		367	563	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39074433	39074433	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	228	557	1	ENST00000357387.3:c.47G>A	p.Arg16Gln	p.R16Q	ENST00000357387	NM_152756.3	16	cGa/cAa	1/38	1	2	FACETS	0.922	0.859	0.986	0.922	0.859	0.986	CLONAL	1	TRUE	1	0.493323918174281	2		558	1003	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178058	56178058	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	139	310	0	ENST00000399503.3:c.3031C>T	p.Pro1011Ser	p.P1011S	ENST00000399503	NM_005921.1	1011	Ccc/Tcc	14/20	1	2	FACETS	0.99	0.906	1	0.99	0.906	1	CLONAL	1	TRUE	1	0.493323918174281	2		310	569	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178544	56178544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781361183	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	74	306	0	ENST00000399503.3:c.3517C>T	p.His1173Tyr	p.H1173Y	ENST00000399503	NM_005921.1	1173	Cat/Tat	14/20	1	2	FACETS	0.565	0.495	0.64	0.565	0.495	0.64	SUBCLONAL	1	TRUE	1	0.493323918174281	2		306	531	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696790	176696790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	65	355	0	ENST00000439151.2:c.5491G>A	p.Asp1831Asn	p.D1831N	ENST00000439151	NM_022455.4	1831	Gat/Aat	16/23	1	2	FACETS	0.434	0.376	0.497	0.434	0.376	0.497	SUBCLONAL	1	TRUE	1	0.493323918174281	2		355	607	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048007	180048007	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs761339590	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	247	657	0	ENST00000261937.6:c.2168G>A	p.Gly723Glu	p.G723E	ENST00000261937	NM_182925.4	723	gGa/gAa	15/30	0.122881308980097	0	FACETS	0.553	0.518	0.59			1	INDETERMINATE	1	TRUE	0	0.493323918174281	0		657	917	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393279	393279	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	262	728	0	ENST00000380956.4:c.127G>C	p.Glu43Gln	p.E43Q	ENST00000380956	NM_001195286.1	43	Gag/Cag	2/9	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.493323918174281	2		728	1059	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671596	30671597	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	207	586	1	ENST00000376406.3:c.5363_5364delinsAT	p.Ile1788Asn	p.I1788N	ENST00000376406	NM_014641.2	1788	aTC/aAT	10/15	1	2	FACETS	0.837	0.776	0.899	0.837	0.776	0.899	CLONAL	1	TRUE	1	0.493323918174281	2		587	1003	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681006	30681006	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	220	541	0	ENST00000376406.3:c.713G>C	p.Arg238Thr	p.R238T	ENST00000376406	NM_014641.2	238	aGa/aCa	5/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.493323918174281	2		541	862	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163720	32163720	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253487294	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	115	484	0	ENST00000375023.3:c.5506G>A	p.Glu1836Lys	p.E1836K	ENST00000375023	NM_004557.3	1836	Gag/Aag	30/30	1	2	FACETS	0.617	0.556	0.681	0.617	0.556	0.681	SUBCLONAL	1	TRUE	1	0.493323918174281	2		484	756	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164807	32164807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	102	642	0	ENST00000375023.3:c.5095G>A	p.Glu1699Lys	p.E1699K	ENST00000375023	NM_004557.3	1699	Gag/Aag	28/30	1	2	FACETS	0.379	0.338	0.423	0.379	0.338	0.423	SUBCLONAL	1	TRUE	1	0.493323918174281	2		642	1092	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170046	32170046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768387019	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	138	829	0	ENST00000375023.3:c.3562G>A	p.Asp1188Asn	p.D1188N	ENST00000375023	NM_004557.3	1188	Gat/Aat	21/30	1	2	FACETS	0.444	0.402	0.487	0.444	0.402	0.487	SUBCLONAL	1	TRUE	1	0.493323918174281	2		829	1261	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821535	32821535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868484039	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	116	690	3	ENST00000354258.4:c.59C>T	p.Pro20Leu	p.P20L	ENST00000354258	NM_000593.5	20	cCg/cTg	1/11	1	2	FACETS	0.383	0.344	0.425	0.383	0.344	0.425	SUBCLONAL	1	TRUE	1	0.493323918174281	2		693	1227	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974394	93974394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	137	541	0	ENST00000369303.4:c.1660C>T	p.Pro554Ser	p.P554S	ENST00000369303	NM_004440.3	554	Cct/Tct	8/17	0.493323918174281	1	FACETS	0.908	0.832	0.986	0.908	0.832	0.986	CLONAL	1	TRUE	0	0.493323918174281	1		541	461	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555335	106555335	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	182	491	0	ENST00000369096.4:c.2452G>C	p.Glu818Gln	p.E818Q	ENST00000369096	NM_001198.3	818	Gaa/Caa	7/7	0.493323918174281	1	FACETS	0.907	0.841	0.975	0.907	0.841	0.975	CLONAL	1	TRUE	0	0.493323918174281	1		491	613	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681103	117681103	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	197	628	2	ENST00000368508.3:c.3517C>T	p.Gln1173Ter	p.Q1173*	ENST00000368508	NM_002944.2	1173	Caa/Taa	23/43	0.493323918174281	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.493323918174281	1		630	571	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14027714	14027714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	169	404	0	ENST00000405192.2:c.130G>A	p.Glu44Lys	p.E44K	ENST00000405192	NM_001163147.1	44	Gaa/Aaa	3/12	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.493323918174281	2		404	639	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259560	55259560	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	121	601	0	ENST00000275493.2:c.2618G>A	p.Gly873Glu	p.G873E	ENST00000275493	NM_005228.3	873	gGa/gAa	21/28	1	2	FACETS	0.516	0.465	0.569	0.516	0.465	0.569	SUBCLONAL	1	TRUE	1	0.493323918174281	2		601	951	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339829	116339829	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	68	508	0	ENST00000397752.3:c.691G>A	p.Asp231Asn	p.D231N	ENST00000397752	NM_000245.2	231	Gac/Aac	2/21	1	2	FACETS	0.399	0.347	0.456	0.399	0.347	0.456	SUBCLONAL	1	TRUE	1	0.493323918174281	2		508	691	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852161	128852161	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	171	831	0	ENST00000249373.3:c.2233C>T	p.Gln745Ter	p.Q745*	ENST00000249373	NM_005631.4	745	Cag/Tag	12/12	1	2	FACETS	0.543	0.498	0.59	0.543	0.498	0.59	SUBCLONAL	1	TRUE	1	0.493323918174281	2		831	1276	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851156	151851156	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	81	429	0	ENST00000262189.6:c.12215C>T	p.Pro4072Leu	p.P4072L	ENST00000262189	NM_170606.2	4072	cCa/cTa	48/59	1	2	FACETS	0.494	0.435	0.557	0.494	0.435	0.557	SUBCLONAL	1	TRUE	1	0.493323918174281	2		429	665	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949138	151949138	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	48	462	0	ENST00000262189.6:c.1507G>A	p.Glu503Lys	p.E503K	ENST00000262189	NM_170606.2	503	Gaa/Aaa	11/59	1	2	FACETS	0.243	0.204	0.285	0.243	0.204	0.285	SUBCLONAL	1	TRUE	1	0.493323918174281	2		462	802	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540306	23540306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	112	537	1	ENST00000380871.4:c.97G>A	p.Asp33Asn	p.D33N	ENST00000380871	NM_006167.3	33	Gac/Aac	1/2	1	2	FACETS	0.562	0.505	0.622	0.562	0.505	0.622	SUBCLONAL	1	TRUE	1	0.493323918174281	2		538	808	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29195831	29195831	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748514096	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	321	763	0	ENST00000240100.2:c.767G>A	p.Ser256Asn	p.S256N	ENST00000240100	NM_001394.6	256	aGc/aAc	3/4	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.493323918174281	2		763	1267	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207402	29207402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	259	490	0	ENST00000240100.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000240100	NM_001394.6	132	Cgc/Tgc	1/4	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.493323918174281	2		490	905	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005901	69005901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	102	634	0	ENST00000288368.4:c.2312C>T	p.Ser771Phe	p.S771F	ENST00000288368	NM_024870.2	771	tCt/tTt	21/40	NA	2	FACETS	0.476	0.425	0.531			1	INDETERMINATE	1	TRUE	NA	0.493323918174281	2		634	868	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5463077	5463077	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	140	342	0	ENST00000381577.3:c.638G>T	p.Arg213Ile	p.R213I	ENST00000381577	NM_014143.3	213	aGa/aTa	4/7	1	2	FACETS	0.951	0.869	1	0.951	0.869	1	CLONAL	1	TRUE	1	0.493323918174281	2		342	597	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465582	8465582	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	128	609	0	ENST00000356435.5:c.3598C>T	p.Pro1200Ser	p.P1200S	ENST00000356435		1200	Ccc/Tcc	21/35	1	2	FACETS	0.599	0.543	0.659	0.599	0.543	0.659	SUBCLONAL	1	TRUE	1	0.493323918174281	2		609	866	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221935	98221935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201118857	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	108	613	2	ENST00000331920.6:c.2834G>A	p.Arg945Gln	p.R945Q	ENST00000331920	NM_000264.3	945	cGa/cAa	17/24	1	2	FACETS	0.486	0.436	0.54	0.486	0.436	0.54	SUBCLONAL	1	TRUE	1	0.493323918174281	2		615	900	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753861	133753861	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	135	648	0	ENST00000318560.5:c.1330G>A	p.Asp444Asn	p.D444N	ENST00000318560	NM_005157.4	444	Gac/Aac	8/11	1	2	FACETS	0.562	0.51	0.617	0.562	0.51	0.617	SUBCLONAL	1	TRUE	1	0.493323918174281	2		648	974	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772916	135772916	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	154	600	0	ENST00000298552.3:c.2707G>A	p.Asp903Asn	p.D903N	ENST00000298552	NM_001162426.1	903	Gat/Aat	21/23	1	2	FACETS	0.676	0.618	0.736	0.676	0.618	0.736	SUBCLONAL	1	TRUE	1	0.493323918174281	2		600	924	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782153	135782153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	109	610	0	ENST00000298552.3:c.1403C>T	p.Ser468Phe	p.S468F	ENST00000298552	NM_001162426.1	468	tCt/tTt	14/23	1	2	FACETS	0.483	0.433	0.537	0.483	0.433	0.537	SUBCLONAL	1	TRUE	1	0.493323918174281	2		610	914	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796796	135796796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	134	409	0	ENST00000298552.3:c.691C>T	p.Pro231Ser	p.P231S	ENST00000298552	NM_001162426.1	231	Ccg/Tcg	8/23	1	2	FACETS	0.908	0.828	0.992	0.908	0.828	0.992	CLONAL	1	TRUE	1	0.493323918174281	2		409	598	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801054	135801054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	202	608	1	ENST00000298552.3:c.283C>T	p.His95Tyr	p.H95Y	ENST00000298552	NM_001162426.1	95	Cat/Tat	5/23	1	2	FACETS	0.93	0.863	0.999	0.93	0.863	0.999	CLONAL	1	TRUE	1	0.493323918174281	2		609	881	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300932	137300932	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	155	747	0	ENST00000481739.1:c.577C>T	p.Gln193Ter	p.Q193*	ENST00000481739	NM_002957.4	193	Cag/Tag	4/10	1	2	FACETS	0.514	0.469	0.561	0.514	0.469	0.561	SUBCLONAL	1	TRUE	1	0.493323918174281	2		747	1222	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15840862	15840862	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	166	432	0	ENST00000307771.7:c.946G>C	p.Glu316Gln	p.E316Q	ENST00000307771	NM_005089.3	316	Gaa/Caa	11/11	0.359452772098345	1	FACETS	0.902	0.833	0.973	0.902	0.833	0.973	CLONAL	1	TRUE	0	0.493323918174281	1		432	562	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932926	39932926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	74	524	0	ENST00000378444.4:c.1673C>T	p.Ser558Leu	p.S558L	ENST00000378444	NM_001123385.1	558	tCa/tTa	4/15	0.359452772098345	1	FACETS	0.323	0.283	0.367	0.323	0.283	0.367	SUBCLONAL	1	TRUE	0	0.493323918174281	1		524	699	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028824	47028824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	107	816	0	ENST00000377604.3:c.128C>T	p.Ser43Leu	p.S43L	ENST00000377604	NM_001204468.1	43	tCa/tTa	3/24	0.359452772098345	1	FACETS	0.317	0.284	0.353	0.317	0.284	0.353	SUBCLONAL	1	TRUE	0	0.493323918174281	1		816	1030	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430373	47430373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	115	734	0	ENST00000377045.4:c.1648C>T	p.Leu550Phe	p.L550F	ENST00000377045	NM_001654.4	550	Ctc/Ttc	15/16	0.359452772098345	1	FACETS	0.35	0.314	0.388	0.35	0.314	0.388	SUBCLONAL	1	TRUE	0	0.493323918174281	1		734	1004	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227021	53227021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	65	636	0	ENST00000375401.3:c.2554G>A	p.Glu852Lys	p.E852K	ENST00000375401	NM_004187.3	852	Gag/Aag	18/26	0.359452772098345	1	FACETS	0.216	0.186	0.248	0.216	0.186	0.248	SUBCLONAL	1	TRUE	0	0.493323918174281	1		636	919	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854916	76854916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1013126734	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	70	723	0	ENST00000373344.5:c.5920G>A	p.Gly1974Arg	p.G1974R	ENST00000373344	NM_000489.3	1974	Gga/Aga	25/35	0.359452772098345	1	FACETS	0.344	0.299	0.392	0.344	0.299	0.392	SUBCLONAL	1	TRUE	0	0.493323918174281	1		723	622	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939520	76939520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	71	553	1	ENST00000373344.5:c.1228G>A	p.Glu410Lys	p.E410K	ENST00000373344	NM_000489.3	410	Gaa/Aaa	9/35	0.359452772098345	1	FACETS	0.331	0.289	0.377	0.331	0.289	0.377	SUBCLONAL	1	TRUE	0	0.493323918174281	1		554	655	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939532	76939532	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	122	552	0	ENST00000373344.5:c.1216C>T	p.His406Tyr	p.H406Y	ENST00000373344	NM_000489.3	406	Cat/Tat	9/35	0.359452772098345	1	FACETS	0.572	0.518	0.629	0.572	0.518	0.629	SUBCLONAL	1	TRUE	0	0.493323918174281	1		552	651	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0026888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	98	480	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	FALSE	1	0.219258987809854	2		480	780	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0026888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	69	574	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.219258987809854	1	FACETS	0.793	0.69	0.904	0.793	0.69	0.904	CLONAL	1	FALSE	0	0.219258987809854	1		576	707	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405953	49405953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	66	305	0	ENST00000418115.1:c.185G>A	p.Gly62Glu	p.G62E	ENST00000418115	NM_001664.2	62	gGg/gAg	3/5	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.219258987809854	2		305	500	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876422	35876422	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	54	636	0	ENST00000303115.3:c.1214T>A	p.Leu405Gln	p.L405Q	ENST00000303115	NM_002185.3	405	cTg/cAg	8/8	1	2	FACETS	0.539	0.459	0.627	0.539	0.459	0.627	SUBCLONAL	1	FALSE	1	0.219258987809854	2		636	914	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0026889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	213	686	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.525655609007156	1	FACETS	0.957	0.895	1	0.957	0.895	1	CLONAL	1	TRUE	0	0.525655609007156	1		686	624	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812538	43812538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772102737	NA	P-0026889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	205	613	0	ENST00000372470.3:c.1241C>T	p.Ser414Leu	p.S414L	ENST00000372470	NM_005373.2	414	tCg/tTg	8/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.525655609007156	2		613	730	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115111972	115111972	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	165	706	0	ENST00000257566.3:c.1768C>T	p.Gln590Ter	p.Q590*	ENST00000257566	NM_016569.3	590	Cag/Tag	7/8	1	2	FACETS	0.894	0.823	0.968	0.894	0.823	0.968	CLONAL	1	TRUE	1	0.525655609007156	2		706	702	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023696	27023696	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	136	430	0	ENST00000324856.7:c.802C>T	p.Gln268Ter	p.Q268*	ENST00000324856	NM_006015.4	268	Cag/Tag	1/20	1	2	FACETS	0.995	0.91	1	0.995	0.91	1	CLONAL	1	TRUE	1	0.525655609007156	2		430	520	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620429	43620429	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	148	516	0	ENST00000355710.3:c.3038G>C	p.Arg1013Thr	p.R1013T	ENST00000355710	NM_020975.4	1013	aGa/aCa	18/20	1	2	FACETS	0.969	0.889	1	0.969	0.889	1	CLONAL	1	TRUE	1	0.525655609007156	2		516	581	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523318	176523318	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	193	637	1	ENST00000292408.4:c.1975G>A	p.Glu659Lys	p.E659K	ENST00000292408	NM_213647.1	659	Gag/Aag	15/18	1	2	FACETS	0.998	0.926	1	0.998	0.926	1	CLONAL	1	TRUE	1	0.525655609007156	2		638	736	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091415	193091415	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	156	458	0	ENST00000367435.3:c.85G>A	p.Glu29Lys	p.E29K	ENST00000367435	NM_024529.4	29	Gag/Aag	1/17	0.477927381971836	3	FACETS	0.897	0.822	0.975	0.448	0.411	0.488	CLONAL	1	TRUE	1	0.525655609007156	3		458	836	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248409	59248409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184098204	NA	P-0026889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	112	401	1	ENST00000371222.2:c.334G>A	p.Glu112Lys	p.E112K	ENST00000371222	NM_002228.3	112	Gag/Aag	1/1	1	2	FACETS	0.839	0.758	0.924	0.839	0.758	0.924	CLONAL	1	TRUE	1	0.525655609007156	2		402	508	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524966	8524966	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764474694	NA	P-0026889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	123	406	0	ENST00000356435.5:c.638C>T	p.Ala213Val	p.A213V	ENST00000356435		213	gCg/gTg	7/35	1	2	FACETS	0.912	0.829	0.999	0.912	0.829	0.999	CLONAL	1	TRUE	1	0.525655609007156	2		406	513	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265533	152265533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	177	460	0	ENST00000206249.3:c.986C>T	p.Ser329Phe	p.S329F	ENST00000206249	NM_000125.3	329	tCc/tTc	4/8	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.525655609007156	2		460	660	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828845	26828845	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	146	467	0	ENST00000381527.3:c.67G>A	p.Glu23Lys	p.E23K	ENST00000381527	NM_001260.1	23	Gag/Aag	1/13	1	2	FACETS	0.895	0.819	0.973	0.895	0.819	0.973	CLONAL	1	TRUE	1	0.525655609007156	2		467	621	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335903	73335903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	126	465	0	ENST00000377767.4:c.2392G>A	p.Asp798Asn	p.D798N	ENST00000377767	NM_014953.3	798	Gac/Aac	18/21	1	2	FACETS	0.821	0.746	0.899	0.821	0.746	0.899	CLONAL	1	TRUE	1	0.525655609007156	2		465	584	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482835	67482835	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	111	576	0	ENST00000327367.4:c.1239G>C	p.Gln413His	p.Q413H	ENST00000327367	NM_005902.3	413	caG/caC	9/9	1	2	FACETS	0.616	0.554	0.681	0.616	0.554	0.681	SUBCLONAL	1	TRUE	1	0.525655609007156	2		576	686	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641274	23641274	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	168	612	0	ENST00000261584.4:c.2201C>T	p.Thr734Ile	p.T734I	ENST00000261584	NM_024675.3	734	aCt/aTt	5/13	1	2	FACETS	0.884	0.815	0.956	0.884	0.815	0.956	CLONAL	1	TRUE	1	0.525655609007156	2		612	723	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772202	68772203	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0026889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	142	579	0	ENST00000261769.5:c.52dup	p.Ser18PhefsTer16	p.S18Ffs*16	ENST00000261769	NM_004360.3	17	-/T	2/16	0.525655609007156	1	FACETS	0.907	0.834	0.982	0.907	0.834	0.982	CLONAL	1	TRUE	0	0.525655609007156	1		579	439	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663415	29663415	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	188	510	0	ENST00000356175.3:c.6008G>A	p.Gly2003Glu	p.G2003E	ENST00000356175	NM_000267.3	2003	gGa/gAa	40/57	1	2	FACETS	0.935	0.866	1	0.935	0.866	1	CLONAL	1	TRUE	1	0.525655609007156	2		510	765	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937667	17937667	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	143	577	1	ENST00000458235.1:c.3260C>A	p.Ser1087Ter	p.S1087*	ENST00000458235	NM_000215.3	1087	tCa/tAa	24/24	0.311335994817666	3	FACETS	0.841	0.767	0.918			1	INDETERMINATE	1	TRUE	NA	0.525655609007156	3		578	817	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413689	138413689	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	190	481	0	ENST00000289153.2:c.1831G>T	p.Asp611Tyr	p.D611Y	ENST00000289153	NM_006219.2	611	Gat/Tat	12/22	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.525655609007156	2		481	700	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948096	178948096	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	112	280	0	ENST00000263967.3:c.2868G>C	p.Leu956Phe	p.L956F	ENST00000263967	NM_006218.2	956	ttG/ttC	20/21	1	2	FACETS	0.829	0.749	0.913	0.829	0.749	0.913	CLONAL	1	TRUE	1	0.525655609007156	2		280	514	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510060	187510060	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	160	453	0	ENST00000441802.2:c.13453A>C	p.Asn4485His	p.N4485H	ENST00000441802	NM_005245.3	4485	Aac/Cac	27/27	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.525655609007156	2		453	564	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879019	151879019	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	178	509	0	ENST00000262189.6:c.5926G>T	p.Asp1976Tyr	p.D1976Y	ENST00000262189	NM_170606.2	1976	Gat/Tat	36/59	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.525655609007156	2		509	667	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539034	23539034	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	131	479	0	ENST00000380871.4:c.405G>C	p.Gln135His	p.Q135H	ENST00000380871	NM_006167.3	135	caG/caC	2/2	1	2	FACETS	0.94	0.858	1	0.94	0.858	1	CLONAL	1	TRUE	1	0.525655609007156	2		479	530	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965642	90965642	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	116	338	0	ENST00000265433.3:c.1675G>C	p.Glu559Gln	p.E559Q	ENST00000265433	NM_002485.4	559	Gaa/Caa	11/16	1	2	FACETS	0.899	0.814	0.987	0.899	0.814	0.987	CLONAL	1	TRUE	1	0.525655609007156	2		338	491	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869542	117869542	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	90	438	0	ENST00000297338.2:c.652G>A	p.Asp218Asn	p.D218N	ENST00000297338	NM_006265.2	218	Gat/Aat	6/14	1	2	FACETS	0.628	0.559	0.702	0.628	0.559	0.702	SUBCLONAL	1	TRUE	1	0.525655609007156	2		438	545	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5077542	5077542	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1478094766	NA	P-0026889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	110	405	0	ENST00000381652.3:c.1954G>C	p.Glu652Gln	p.E652Q	ENST00000381652	NM_004972.3	652	Gaa/Caa	15/25	1	2	FACETS	0.754	0.68	0.832	0.754	0.68	0.832	SUBCLONAL	1	TRUE	1	0.525655609007156	2		405	555	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226184	53226184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	40	636	0	ENST00000375401.3:c.2665G>A	p.Glu889Lys	p.E889K	ENST00000375401	NM_004187.3	889	Gag/Aag	19/26	1	2	FACETS	0.229	0.19	0.273	0.229	0.19	0.273	SUBCLONAL	1	TRUE	1	0.525655609007156	2		636	664	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0026890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	158	583	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.266489473137577	2	FACETS	0.918	0.844	0.994	0.918	0.844	0.994	CLONAL	2	TRUE	0	0.266489473137577	2		583	646	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0026890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	34	283	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	0.69	1	0.842	0.69	1	CLONAL	1	TRUE	1	0.266489473137577	2		283	303	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761459	59761460	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs774684620	NA	P-0026890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	82	505	0	ENST00000259008.2:c.2947dup	p.Ile983AsnfsTer19	p.I983Nfs*19	ENST00000259008	NM_032043.2	983	att/aAtt	20/20	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.266489473137577	2		505	554	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120373	70120374	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0026890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	139	1005	0	ENST00000245479.2:c.1376_1377dup	p.Thr460AlafsTer11	p.T460Afs*11	ENST00000245479	NM_000346.3	459	ggc/gGCgc	3/3	1	2	FACETS	0.928	0.843	1	0.928	0.843	1	CLONAL	1	TRUE	1	0.266489473137577	2		1005	1124	SUCCESS
APC	324	MSKCC	GRCh37	5	112175074	112175074	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	42	243	0	ENST00000257430.4:c.3784del	p.Tyr1262IlefsTer3	p.Y1262Ifs*3	ENST00000257430	NM_000038.5	1261	acT/ac	16/16	1	2	FACETS	1	0.839	1	1	0.839	1	CLONAL	1	TRUE	1	0.266489473137577	2		243	315	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121508	108121508	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	127	535	0	ENST00000278616.4:c.1316T>C	p.Leu439Pro	p.L439P	ENST00000278616	NM_000051.3	439	cTa/cCa	10/63	0.254303408920512	2	FACETS	0.934	0.851	1	0.934	0.851	1	CLONAL	2	TRUE	0	0.266489473137577	2		535	510	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730778	40730778	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	98	571	0	ENST00000373198.4:c.3757G>A	p.Ala1253Thr	p.A1253T	ENST00000373198	NM_133170.3	1253	Gca/Aca	27/32	0.266489473137577	4	FACETS	1	0.932	1	0.354	0.315	0.396	CLONAL	1	TRUE	1	0.266489473137577	4		571	877	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393198	393198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	100	493	1	ENST00000380956.4:c.46G>A	p.Ala16Thr	p.A16T	ENST00000380956	NM_001195286.1	16	Gcg/Acg	2/9	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.266489473137577	2		494	651	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820624	3820624	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	85	777	1	ENST00000262367.5:c.2827C>T	p.Gln943Ter	p.Q943*	ENST00000262367	NM_004380.2	943	Cag/Tag	14/31	0.333842737040356	1	FACETS	0.977	0.868	1	0.977	0.868	1	CLONAL	1	TRUE	0	0.333842737040356	1		778	434	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597862	43597862	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	125	758	4	ENST00000355710.3:c.410G>A	p.Cys137Tyr	p.C137Y	ENST00000355710	NM_020975.4	137	tGc/tAc	3/20	0.333842737040356	3	FACETS	0.794	0.722	0.87	0.794	0.722	0.87	SUBCLONAL	2	TRUE	1	0.333842737040356	3		762	550	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352618	68352618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	37	362	0	ENST00000487270.1:c.485G>A	p.Arg162Lys	p.R162K	ENST00000487270	NM_133509.3	162	aGa/aAa	6/11	1	2	FACETS	0.387	0.318	0.464	0.387	0.318	0.464	SUBCLONAL	1	TRUE	1	0.333842737040356	2		362	573	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973652	15973652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375150524	NA	P-0026892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	32	373	0	ENST00000268712.3:c.4340G>A	p.Arg1447Gln	p.R1447Q	ENST00000268712	NM_006311.3	1447	cGg/cAg	31/46	0.333842737040356	1	FACETS	0.493	0.401	0.597	0.493	0.401	0.597	SUBCLONAL	1	TRUE	0	0.333842737040356	1		373	324	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282709	1282709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768398955	NA	P-0026892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	36	579	0	ENST00000310581.5:c.1604G>A	p.Arg535His	p.R535H	ENST00000310581	NM_198253.2	535	cGt/cAt	3/16	0.333842737040356	1	FACETS	0.483	0.397	0.579	0.483	0.397	0.579	SUBCLONAL	1	TRUE	0	0.333842737040356	1		579	372	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520504	176520504	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	45	626	1	ENST00000292408.4:c.1349T>C	p.Val450Ala	p.V450A	ENST00000292408	NM_213647.1	450	gTg/gCg	10/18	0.257942419599557	1	FACETS	0.548	0.461	0.643	0.548	0.461	0.643	SUBCLONAL	1	TRUE	0	0.333842737040356	1		627	410	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853118	151853118	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	98	437	0	ENST00000262189.6:c.11837C>T	p.Pro3946Leu	p.P3946L	ENST00000262189	NM_170606.2	3946	cCa/cTa	46/59	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.333842737040356	2		437	541	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0026907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	288	541	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.213276247017545	5	FACETS	1	0.989	1	0.775	0.734	0.816	INDETERMINATE	2	TRUE	2	0.819225612425985	5		541	674	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549428	187549428	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2304867	NA	P-0026907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	138	533	3	ENST00000441802.2:c.4690G>A	p.Ala1564Thr	p.A1564T	ENST00000441802	NM_005245.3	1564	Gct/Act	9/27	0.819225612425985	1	FACETS	0.884	0.828	0.939	0.884	0.828	0.939	CLONAL	1	TRUE	0	0.819225612425985	1		536	225	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685281	89685281	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1060500116	NA	P-0026907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	166	319	0	ENST00000371953.3:c.176C>G	p.Ser59Ter	p.S59*	ENST00000371953	NM_000314.4	59	tCa/tGa	3/9	0.221032338210749	4	FACETS	0.817	0.758	0.878	0.817	0.758	0.878	INDETERMINATE	2	TRUE	2	0.819225612425985	4		319	451	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087549	27087550	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	374	627	1	ENST00000324856.7:c.2124dup	p.Ser709ValfsTer108	p.S709Vfs*108	ENST00000324856	NM_006015.4	708	cag/caGg	5/20	0.644212584001098	4	FACETS	0.889	0.847	0.932	0.889	0.847	0.932	CLONAL	2	TRUE	2	0.819225612425985	4		628	934	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186583	108186583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375783941	NA	P-0026907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	115	364	1	ENST00000278616.4:c.6040G>A	p.Glu2014Lys	p.E2014K	ENST00000278616	NM_000051.3	2014	Gag/Aag	41/63	0.660395010298433	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.819225612425985	1		365	160	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753584	42753584	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	580	766	0	ENST00000222329.4:c.680A>G	p.His227Arg	p.H227R	ENST00000222329	NM_006494.2	227	cAt/cGt	4/4	0.213276247017545	5	FACETS	1	0.994	1	0.766	0.737	0.795	INDETERMINATE	2	TRUE	2	0.819225612425985	5		766	1373	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971369	13971369	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779937870	NA	P-0026907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	142	351	2	ENST00000405192.2:c.560G>A	p.Arg187His	p.R187H	ENST00000405192	NM_001163147.1	187	cGc/cAc	8/12	0.279795569908381	3	FACETS	1	0.982	1	0.617	0.568	0.667	INDETERMINATE	1	TRUE	1	0.819225612425985	3		353	396	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500985	8500985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	64	322	0	ENST00000356435.5:c.1897C>T	p.Pro633Ser	p.P633S	ENST00000356435		633	Cca/Tca	13/35	0.215387131998711	1	FACETS	0.48	0.423	0.54	0.48	0.423	0.54	INDETERMINATE	1	TRUE	0	0.819225612425985	1		322	192	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	82	321	2	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.864	0.764	0.971	0.864	0.764	0.971	CLONAL	1	TRUE	1	0.360893801280769	2		323	526	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	164	768	1	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	1	2	FACETS	0.91	0.835	0.988	0.91	0.835	0.988	CLONAL	1	TRUE	1	0.360893801280769	2		769	999	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	55	359	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.776	0.666	0.895	0.776	0.666	0.895	SUBCLONAL	1	TRUE	1	0.360893801280769	2		359	393	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	81	423	3	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.909	0.803	1	0.909	0.803	1	CLONAL	1	TRUE	1	0.360893801280769	2		426	494	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	22	293	1	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.286	0.221	0.361	0.286	0.221	0.361	SUBCLONAL	1	TRUE	1	0.360893801280769	2		294	427	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	109	604	3	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.891	0.801	0.986	0.891	0.801	0.986	CLONAL	1	TRUE	1	0.360893801280769	2		607	678	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255281	16255281	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	136	624	0	ENST00000375759.3:c.2549del	p.Lys850SerfsTer8	p.K850Sfs*8	ENST00000375759	NM_015001.2	849	gAa/ga	11/15	1	2	FACETS	0.854	0.776	0.935	0.854	0.776	0.935	CLONAL	1	TRUE	1	0.360893801280769	2		624	883	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057937	27057937	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	129	635	1	ENST00000324856.7:c.1650del	p.Tyr551ThrfsTer68	p.Y551Tfs*68	ENST00000324856	NM_006015.4	549	Ccc/cc	3/20	1	2	FACETS	0.936	0.849	1	0.936	0.849	1	CLONAL	1	TRUE	1	0.360893801280769	2		636	764	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748053	72748053	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	144	638	1	ENST00000357731.5:c.125G>T	p.Trp42Leu	p.W42L	ENST00000357731	NM_173808.2	42	tGg/tTg	1/7	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.360893801280769	2		639	743	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432759	78432759	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs200979131	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	110	454	0	ENST00000370768.2:c.317A>G	p.Lys106Arg	p.K106R	ENST00000370768	NM_003902.3	106	aAa/aGa	5/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.360893801280769	2		454	493	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880515	155880515	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	159	627	1	ENST00000368323.3:c.38G>T	p.Ser13Ile	p.S13I	ENST00000368323	NM_006912.5	13	aGc/aTc	2/6	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.360893801280769	2		628	825	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456626	32456626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1417614394	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	91	323	0	ENST00000332351.3:c.266G>A	p.Gly89Asp	p.G89D	ENST00000332351	NM_024426.4	89	gGc/gAc	1/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.360893801280769	2		323	429	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197281	94197282	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs774440500	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	49	374	0	ENST00000323929.3:c.1222dup	p.Thr408AsnfsTer49	p.T408Nfs*49	ENST00000323929	NM_005591.3	408	aca/aAca	11/20	1	2	FACETS	0.732	0.622	0.852	0.732	0.622	0.852	SUBCLONAL	1	TRUE	1	0.360893801280769	2		374	371	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998709	100998709	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	181	776	0	ENST00000325455.5:c.1093C>T	p.Pro365Ser	p.P365S	ENST00000325455	NM_001202474.3	365	Ccc/Tcc	1/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.360893801280769	2		776	899	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205757	108205757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658385	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	82	474	0	ENST00000278616.4:c.8072G>A	p.Arg2691His	p.R2691H	ENST00000278616	NM_000051.3	2691	cGc/cAc	55/63	1	2	FACETS	0.896	0.793	1	0.896	0.793	1	CLONAL	1	TRUE	1	0.360893801280769	2		474	507	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120546244	120546244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	169	695	1	ENST00000229340.5:c.80G>A	p.Arg27His	p.R27H	ENST00000229340	NM_006861.6	27	cGt/cAt	2/6	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.360893801280769	2		696	926	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046602	30046602	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	107	575	0	ENST00000331968.5:c.2581A>G	p.Thr861Ala	p.T861A	ENST00000331968	NM_002742.2	861	Acc/Gcc	18/18	1	2	FACETS	0.862	0.774	0.955	0.862	0.774	0.955	CLONAL	1	TRUE	1	0.360893801280769	2		575	688	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872461	35872461	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	136	510	1	ENST00000216797.5:c.442del	p.Leu148TyrfsTer16	p.L148Yfs*16	ENST00000216797	NM_020529.2	148	Cta/ta	3/6	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.360893801280769	2		511	740	SUCCESS
BLM	641	MSKCC	GRCh37	15	91306293	91306294	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	84	465	1	ENST00000355112.3:c.1986dup	p.Phe663IlefsTer5	p.F663Ifs*5	ENST00000355112	NM_000057.2	660	-/A	8/22	1	2	FACETS	0.86	0.762	0.966	0.86	0.762	0.966	CLONAL	1	TRUE	1	0.360893801280769	2		466	541	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396234	396234	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	112	652	2	ENST00000262320.3:c.792del	p.Gly265GlufsTer149	p.G265Efs*149	ENST00000262320	NM_003502.3	264	ccC/cc	2/11	1	2	FACETS	0.8	0.719	0.885	0.8	0.719	0.885	SUBCLONAL	1	TRUE	1	0.360893801280769	2		654	776	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094711	2094711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376048896	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	191	872	1	ENST00000219066.1:c.469C>T	p.Arg157Trp	p.R157W	ENST00000219066	NM_002528.5	157	Cgg/Tgg	3/6	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.360893801280769	2		873	985	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858637	9858637	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	105	437	0	ENST00000330684.3:c.2764G>A	p.Ala922Thr	p.A922T	ENST00000330684	NM_001134407.1	922	Gct/Act	13/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.360893801280769	2		437	523	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128304	30128304	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	63	691	0	ENST00000263025.4:c.928A>G	p.Met310Val	p.M310V	ENST00000263025	NM_002746.2	310	Atg/Gtg	7/9	1	2	FACETS	0.414	0.357	0.476	0.414	0.357	0.476	SUBCLONAL	1	TRUE	1	0.360893801280769	2		691	843	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825518	50825518	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	84	528	1	ENST00000398568.2:c.2149G>A	p.Glu717Lys	p.E717K	ENST00000398568	NM_001042412.1	717	Gaa/Aaa	14/18	1	2	FACETS	0.875	0.775	0.982	0.875	0.775	0.982	CLONAL	1	TRUE	1	0.360893801280769	2		529	532	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961294	15961294	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	50	555	1	ENST00000268712.3:c.6095del	p.Pro2032LeufsTer17	p.P2032Lfs*17	ENST00000268712	NM_006311.3	2032	cCt/ct	39/46	1	2	FACETS	0.419	0.354	0.489	0.419	0.354	0.489	SUBCLONAL	1	TRUE	1	0.360893801280769	2		556	662	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	57	515	1	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	1	2	FACETS	0.514	0.44	0.594	0.514	0.44	0.594	SUBCLONAL	1	TRUE	1	0.360893801280769	2		516	615	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16047005	16047005	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	78	455	0	ENST00000268712.3:c.1088G>T	p.Gly363Val	p.G363V	ENST00000268712	NM_006311.3	363	gGg/gTg	11/46	1	2	FACETS	0.952	0.84	1	0.952	0.84	1	CLONAL	1	TRUE	1	0.360893801280769	2		455	454	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16052795	16052795	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	66	458	0	ENST00000268712.3:c.879del	p.Phe293LeufsTer33	p.F293Lfs*33	ENST00000268712	NM_006311.3	293	ttT/tt	9/46	1	2	FACETS	0.787	0.684	0.897	0.787	0.684	0.897	SUBCLONAL	1	TRUE	1	0.360893801280769	2		458	465	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683546	29683546	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	82	545	0	ENST00000356175.3:c.7621G>T	p.Gly2541Trp	p.G2541W	ENST00000356175	NM_000267.3	2541	Ggg/Tgg	51/57	1	2	FACETS	0.862	0.762	0.969	0.862	0.762	0.969	CLONAL	1	TRUE	1	0.360893801280769	2		545	527	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512401	38512402	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs745553450	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	50	635	2	ENST00000254066.5:c.1319dup	p.Pro441AlafsTer5	p.P441Afs*5	ENST00000254066	NM_000964.3	438	gcc/gCcc	9/9	1	2	FACETS	0.374	0.317	0.438	0.374	0.317	0.438	SUBCLONAL	1	TRUE	1	0.360893801280769	2		637	740	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858095	40858095	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	218	773	0	ENST00000428826.2:c.1769G>T	p.Gly590Val	p.G590V	ENST00000428826		590	gGg/gTg	16/21	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.360893801280769	2		773	954	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760676	59760676	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	35	617	0	ENST00000259008.2:c.3731T>G	p.Met1244Arg	p.M1244R	ENST00000259008	NM_032043.2	1244	aTg/aGg	20/20	1	2	FACETS	0.289	0.236	0.349	0.289	0.236	0.349	SUBCLONAL	1	TRUE	1	0.360893801280769	2		617	671	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119910	70119910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1297203260	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	155	555	2	ENST00000245479.2:c.916del	p.Val306CysfsTer77	p.V306Cfs*77	ENST00000245479	NM_000346.3	304	ccG/cc	3/3	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.360893801280769	2		557	835	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223239	5223239	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	202	752	3	ENST00000357368.4:c.2564del	p.Pro855ArgfsTer67	p.P855Rfs*67	ENST00000357368	NM_002850.3	855	cCg/cg	18/38	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.360893801280769	2		755	924	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303663	30303663	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1443126704	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	164	618	0	ENST00000262643.3:c.91A>G	p.Arg31Gly	p.R31G	ENST00000262643	NM_001238.2	31	Agg/Ggg	3/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.360893801280769	2		618	805	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791591	42791592	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	160	561	0	ENST00000575354.2:c.576dup	p.Asn193GlnfsTer122	p.N193Qfs*122	ENST00000575354	NM_015125.3	191	agc/agCc	4/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.360893801280769	2		561	802	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	236	499	7	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	0.991	0.93	1	1	0.995	1	CLONAL	2	TRUE	1	0.360893801280769	2		506	660	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147602	61147602	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	11	55	0	ENST00000295025.8:c.1007C>A	p.Ala336Asp	p.A336D	ENST00000295025	NM_002908.2	336	gCt/gAt	9/11	1	2	FACETS	0.968	0.682	1	0.968	0.682	1	CLONAL	1	TRUE	1	0.360893801280769	2		55	63	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795103	242795104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs768249210	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	127	763	1	ENST00000334409.5:c.105dup	p.Thr36HisfsTer70	p.T36Hfs*70	ENST00000334409	NM_005018.2	35	-/C	2/5	1	2	FACETS	0.72	0.652	0.793	0.72	0.652	0.793	SUBCLONAL	1	TRUE	1	0.360893801280769	2		764	977	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164218	47164218	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	72	420	0	ENST00000409792.3:c.1908del	p.Phe636LeufsTer6	p.F636Lfs*6	ENST00000409792	NM_014159.6	636	ttT/tt	3/21	1	2	FACETS	0.998	0.876	1	0.998	0.876	1	CLONAL	1	TRUE	1	0.360893801280769	2		420	400	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940111	49940111	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	122	653	3	ENST00000296474.3:c.932C>G	p.Ala311Gly	p.A311G	ENST00000296474	NM_002447.2	311	gCc/gGc	1/20	1	2	FACETS	0.847	0.766	0.933	0.847	0.766	0.933	CLONAL	1	TRUE	1	0.360893801280769	2		656	798	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595976	52595977	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	93	410	0	ENST00000394830.3:c.3938dup	p.Ser1315ValfsTer26	p.S1315Vfs*26	ENST00000394830	NM_018313.4	1313	cca/ccCa	26/30	1	2	FACETS	0.965	0.861	1	0.965	0.861	1	CLONAL	1	TRUE	1	0.360893801280769	2		410	534	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021754	71021754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	95	453	0	ENST00000318789.4:c.1604C>T	p.Thr535Ile	p.T535I	ENST00000318789	NM_032682.5	535	aCa/aTa	18/21	1	2	FACETS	0.971	0.867	1	0.971	0.867	1	CLONAL	1	TRUE	1	0.360893801280769	2		453	542	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508780	31508780	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	178	698	0	ENST00000344624.3:c.1535del	p.Lys512ArgfsTer19	p.K512Rfs*19	ENST00000344624		512	aAg/ag	7/33	1	2	FACETS	0.971	0.894	1	0.971	0.894	1	CLONAL	1	TRUE	1	0.360893801280769	2		698	1016	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	90	579	1	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.91	0.81	1	0.91	0.81	1	CLONAL	1	TRUE	1	0.360893801280769	2		580	548	SUCCESS
APC	324	MSKCC	GRCh37	5	112175945	112175945	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	61	274	0	ENST00000257430.4:c.4654G>T	p.Glu1552Ter	p.E1552*	ENST00000257430	NM_000038.5	1552	Gag/Tag	16/16	1	2	FACETS	0.921	0.799	1	0.921	0.799	1	CLONAL	1	TRUE	1	0.360893801280769	2		274	367	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433745	149433745	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537011691	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	158	772	0	ENST00000286301.3:c.2806G>A	p.Gly936Ser	p.G936S	ENST00000286301	NM_005211.3	936	Ggc/Agc	22/22	1	2	FACETS	0.966	0.886	1	0.966	0.886	1	CLONAL	1	TRUE	1	0.360893801280769	2		772	906	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324917	31324917	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	127	288	0	ENST00000412585.2:c.19del	p.Arg7GlufsTer13	p.R7Efs*13	ENST00000412585	NM_005514.6	7	Cga/ga	1/8	0.360893801280769	2	FACETS	0.978	0.896	1	0.978	0.896	1	CLONAL	2	TRUE	0	0.360893801280769	2		288	360	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27213579	27213579	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	114	599	0	ENST00000380036.4:c.2975A>T	p.Tyr992Phe	p.Y992F	ENST00000380036	NM_000459.3	992	tAt/tTt	18/23	1	2	FACETS	0.904	0.815	0.998	0.904	0.815	0.998	CLONAL	1	TRUE	1	0.360893801280769	2		599	699	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635191	87635191	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367769334	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	134	561	3	ENST00000277120.3:c.2243C>T	p.Thr748Met	p.T748M	ENST00000277120		748	aCg/aTg	18/19	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.360893801280769	2		564	704	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041561	47041561	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	132	332	0	ENST00000377604.3:c.1786T>C	p.Tyr596His	p.Y596H	ENST00000377604	NM_001204468.1	596	Tat/Cat	17/24	1	1	FACETS	0.795	0.73	0.862	1	0.989	1	SUBCLONAL	2	TRUE	0	0.360893801280769	1		332	377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0026909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1239	434	655	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.3	3	FACETS	0.951	0.905	0.998			1	CLONAL	3	TRUE	NA	0.2	3		655	1673	SUCCESS
APC	324	MSKCC	GRCh37	5	112175952	112175952	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587783031	NA	P-0026909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	65	284	0	ENST00000257430.4:c.4666del	p.Thr1556LeufsTer9	p.T1556Lfs*9	ENST00000257430	NM_000038.5	1554	gAa/ga	16/16	0.194584144302108	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.2	1		284	535	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99454555	99454555	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61740877	NA	P-0026909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	95	498	0	ENST00000268035.6:c.1474G>A	p.Val492Ile	p.V492I	ENST00000268035	NM_000875.3	492	Gtc/Atc	7/21	1	2	FACETS	0.879	0.78	0.984	0.879	0.78	0.984	CLONAL	1	TRUE	1	0.2	2		498	1081	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40458299	40458299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757085900	NA	P-0026909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	102	628	1	ENST00000345506.4:c.1514C>T	p.Pro505Leu	p.P505L	ENST00000345506	NM_003152.3	505	cCg/cTg	14/20	1	2	FACETS	0.969	0.864	1	0.969	0.864	1	CLONAL	1	TRUE	1	0.2	2		629	1053	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0026911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	169	509	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	0.402897093157114	2		509	758	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0026911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	246	570	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.402897093157114	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.402897093157114	1		570	953	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171735	36171735	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	108	375	1	ENST00000300305.3:c.830del	p.Pro277HisfsTer34	p.P277Hfs*34	ENST00000300305		277	cCa/ca	7/8	1	2	FACETS	0.906	0.815	1	0.906	0.815	1	CLONAL	1	TRUE	1	0.402897093157114	2		376	592	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	237	315	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.947	0.89	1	0.947	0.89	1	CLONAL	1	TRUE	1	0.786757708620993	2		316	636	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0026914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16222	721	714	3	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.786757708620993	21	FACETS	0.917	0.877	0.957	0.044	0.041	0.046	CLONAL	1	TRUE	0	0.786757708620993	21		717	16943	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612777	228612777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758908744	NA	P-0026914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	206	555	2	ENST00000366696.1:c.250C>T	p.Arg84Cys	p.R84C	ENST00000366696	NM_003493.2	84	Cgc/Tgc	1/1	0.621859470381651	3	FACETS	0.581	0.538	0.626	0.29	0.269	0.313	SUBCLONAL	1	TRUE	1	0.786757708620993	3		557	1256	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	G	rs11575997	NA	P-0026914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	696	535	0	ENST00000269305.4:c.993+1G>C		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.786757708620993	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.786757708620993	2		535	869	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114129	115114129	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	319	509	1	ENST00000257566.3:c.1088C>A	p.Ser363Ter	p.S363*	ENST00000257566	NM_016569.3	363	tCg/tAg	6/8	1	2	FACETS	0.988	0.937	1	0.988	0.937	1	CLONAL	1	TRUE	1	0.786757708620993	2		510	821	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421415	12421415	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	545	496	0	ENST00000287820.6:c.295C>T	p.Leu99Phe	p.L99F	ENST00000287820	NM_015869.4	99	Ctt/Ttt	2/7	0.621859470381651	3	FACETS	0.9	0.868	0.933	0.9	0.868	0.933	CLONAL	2	TRUE	1	0.786757708620993	3		496	1072	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447282	49447289	+	frameshift_variant	Frame_Shift_Del	DEL	TTCAGGGC	TTCAGGGC	-	novel	NA	P-0026916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	108	476	0	ENST00000301067.7:c.809_816del	p.Cys270LeufsTer13	p.C270Lfs*13	ENST00000301067	NM_003482.3	270	tGCCCTGAA/t	6/54	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		476	705	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519999	NA	P-0026917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	217	589	1	ENST00000269305.4:c.716A>G	p.Asn239Ser	p.N239S	ENST00000269305	NM_001126112.2	239	aAc/aGc	7/11	0.710400314062777	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.710400314062777	1		590	383	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023006	27023006	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	75	53	0	ENST00000324856.7:c.112G>T	p.Glu38Ter	p.E38*	ENST00000324856	NM_006015.4	38	Gag/Tag	1/20	1	2	FACETS	0.771	0.699	0.841	1	0.983	1	SUBCLONAL	2	TRUE	1	0.710400314062777	2		53	137	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916926	178916937	+	inframe_deletion	In_Frame_Del	DEL	GTAGGCAACCGT	GTAGGCAACCGT	-	novel	NA	P-0026917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	61	511	0	ENST00000263967.3:c.314_325del	p.Val105_Arg108del	p.V105_R108del	ENST00000263967	NM_006218.2	105	GTAGGCAACCGT/-	2/21	1	2	FACETS	0.846	0.742	0.956	0.846	0.742	0.956	CLONAL	1	TRUE	1	0.710400314062777	2		511	203	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748389	43748389	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	38	648	0	ENST00000382044.4:c.2417G>C	p.Arg806Thr	p.R806T	ENST00000382044	NM_001141980.1	806	aGa/aCa	12/28	1	2	FACETS	0.348	0.289	0.414	0.348	0.289	0.414	SUBCLONAL	1	TRUE	1	0.710400314062777	2		648	307	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66777399	66777399	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	34	640	0	ENST00000307102.5:c.765G>C	p.Glu255Asp	p.E255D	ENST00000307102	NM_002755.3	255	gaG/gaC	7/11	1	2	FACETS	0.165	0.134	0.2	0.165	0.134	0.2	SUBCLONAL	1	TRUE	1	0.710400314062777	2		640	579	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0026926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	25	443	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.335292830189168	3	FACETS	1	0.822	1	0.518	0.412	0.638	CLONAL	1	TRUE	1	0.335292830189168	3		443	168	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111503	8111504	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAATGCCAATGGGGACCCT	novel	NA	P-0026926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	89	690	0	ENST00000346208.3:c.991_1009dup	p.Val337GlufsTer21	p.V337Efs*21	ENST00000346208		330	agg/agGAATGCCAATGGGGACCCTg	5/6	NA	2	FACETS	0.792	0.709	0.879			1	INDETERMINATE	2	TRUE	NA	0.335292830189168	2		690	335	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426771	212426771	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879060634	NA	P-0026926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	22	577	0	ENST00000342788.4:c.2344C>T	p.Arg782Trp	p.R782W	ENST00000342788	NM_005235.2	782	Cgg/Tgg	20/28	0.159622730147679	2	FACETS	0.64	0.498	0.803	0.32	0.249	0.402	INDETERMINATE	1	TRUE	0	0.335292830189168	2		577	205	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0026928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	70	443	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.782	0.682	0.891	0.782	0.682	0.891	SUBCLONAL	1	TRUE	1	0.277047215057438	2		443	646	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0026928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	85	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.277047215057438	1	FACETS	0.733	0.648	0.825	0.733	0.648	0.825	SUBCLONAL	1	TRUE	0	0.277047215057438	1		509	721	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0026928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	92	372	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.902	0.802	1	0.902	0.802	1	CLONAL	1	TRUE	1	0.277047215057438	2		372	736	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233140	66233140	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs769393148	NA	P-0026928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	64	447	0	ENST00000273854.3:c.1859G>A	p.Arg620Gln	p.R620Q	ENST00000273854	NM_004439.5	620	cGg/cAg	10/18	1	2	FACETS	0.549	0.475	0.631	0.549	0.475	0.631	SUBCLONAL	1	TRUE	1	0.277047215057438	2		447	841	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121762	108121762	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	79	485	0	ENST00000278616.4:c.1570T>C	p.Trp524Arg	p.W524R	ENST00000278616	NM_000051.3	524	Tgg/Cgg	10/63	1	2	FACETS	0.701	0.615	0.793	0.701	0.615	0.793	SUBCLONAL	1	TRUE	1	0.277047215057438	2		485	814	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99482477	99482477	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	111	604	0	ENST00000268035.6:c.3345G>A	p.Met1115Ile	p.M1115I	ENST00000268035	NM_000875.3	1115	atG/atA	18/21	1	2	FACETS	0.783	0.703	0.869	0.783	0.703	0.869	SUBCLONAL	1	TRUE	1	0.277047215057438	2		604	1023	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533838	63533838	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	115	548	0	ENST00000307078.5:c.1316T>C	p.Leu439Pro	p.L439P	ENST00000307078	NM_004655.3	439	cTg/cCg	6/11	1	2	FACETS	0.964	0.868	1	0.964	0.868	1	CLONAL	1	TRUE	1	0.277047215057438	2		548	861	SUCCESS
APC	324	MSKCC	GRCh37	5	112157642	112157643	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	81	538	0	ENST00000257430.4:c.1365dup	p.Leu456ThrfsTer4	p.L456Tfs*4	ENST00000257430	NM_000038.5	454	-/A	11/16	1	2	FACETS	0.931	0.821	1	0.931	0.821	1	CLONAL	1	TRUE	1	0.277047215057438	2		538	628	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041379	47041379	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	103	755	1	ENST00000377604.3:c.1723G>A	p.Asp575Asn	p.D575N	ENST00000377604	NM_001204468.1	575	Gat/Aat	16/24	1	2	FACETS	0.688	0.614	0.767	0.688	0.614	0.767	SUBCLONAL	1	TRUE	1	0.277047215057438	2		756	1081	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0026930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	214	344	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.472825536588637	3	FACETS	0.95	0.889	1	0.95	0.889	1	CLONAL	2	TRUE	1	0.472825536588637	3		345	589	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0026930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	356	601	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.472825536588637	2	FACETS	0.951	0.906	0.995	0.951	0.906	0.995	CLONAL	2	TRUE	0	0.472825536588637	2		603	792	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12629100	12629100	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	220	414	2	ENST00000251849.4:c.1407G>A	p.Met469Ile	p.M469I	ENST00000251849	NM_002880.3	469	atG/atA	13/17	0.472825536588637	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.472825536588637	3		416	542	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222953	36222953	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753685124	NA	P-0026930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	219	776	0	ENST00000222270.7:c.5582C>T	p.Ser1861Leu	p.S1861L	ENST00000222270	NM_014727.1	1861	tCg/tTg	27/37	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.472825536588637	2		776	869	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971114	21971131	+	inframe_deletion	In_Frame_Del	DEL	CGGGTCGGGTGAGAGTGG	CGGGTCGGGTGAGAGTGG	-	novel	NA	P-0026930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	60	531	0	ENST00000304494.5:c.227_244del	p.Ala76_Pro81del	p.A76_P81del	ENST00000304494	NM_000077.4	76	gCCACTCTCACCCGACCCGtg/gtg	2/3	0.472825536588637	1	FACETS	0.45	0.388	0.516	0.45	0.388	0.516	SUBCLONAL	1	TRUE	0	0.472825536588637	1		531	431	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891337	101891337	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	280	656	0	ENST00000374994.4:c.298T>C	p.Cys100Arg	p.C100R	ENST00000374994	NM_004612.2	100	Tgc/Cgc	2/9	0.472825536588637	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.472825536588637	2		656	575	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913286	NA	P-0026931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	34	621	0	ENST00000263967.3:c.1636C>G	p.Gln546Glu	p.Q546E	ENST00000263967	NM_006218.2	546	Cag/Gag	10/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		621	1136	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006898	47006898	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1556762493	NA	P-0026932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	159	706	0	ENST00000377604.3:c.17+1G>T		p.X6_splice	ENST00000377604	NM_001204468.1	6			1	2	FACETS	0.874	0.8	0.952	0.874	0.8	0.952	CLONAL	1	TRUE	1	0.339056095345578	2		706	1073	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720876	89720876	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs786201041	NA	P-0026932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	28	305	0	ENST00000371953.3:c.1026+1G>A		p.X342_splice	ENST00000371953	NM_000314.4	342			0.339056095345578	1	FACETS	0.502	0.403	0.615	0.502	0.403	0.615	SUBCLONAL	1	TRUE	0	0.339056095345578	1		305	273	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219552	133219552	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	121	558	0	ENST00000320574.5:c.4582G>C	p.Ala1528Pro	p.A1528P	ENST00000320574	NM_006231.2	1528	Gcc/Ccc	36/49	0.207878531468795	1	FACETS	0.749	0.677	0.826	0.749	0.677	0.826	SUBCLONAL	1	TRUE	0	0.339056095345578	1		558	791	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162374	47162374	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	82	316	0	ENST00000409792.3:c.3752C>A	p.Ser1251Ter	p.S1251*	ENST00000409792	NM_014159.6	1251	tCa/tAa	3/21	0.31176757412281	1	FACETS	0.97	0.86	1	0.97	0.86	1	CLONAL	1	TRUE	0	0.339056095345578	1		316	414	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450244	50450244	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	93	404	0	ENST00000331340.3:c.428G>C	p.Arg143Pro	p.R143P	ENST00000331340	NM_006060.4	143	cGg/cCg	5/8	1	2	FACETS	0.835	0.743	0.933	0.835	0.743	0.933	CLONAL	1	TRUE	1	0.339056095345578	2		404	657	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730188	133730188	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	119	468	0	ENST00000318560.5:c.254G>T	p.Gly85Val	p.G85V	ENST00000318560	NM_005157.4	85	gGt/gTt	3/11	1	2	FACETS	0.938	0.848	1	0.938	0.848	1	CLONAL	1	TRUE	1	0.339056095345578	2		468	748	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0026933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	494	644	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.705403919968411	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.705598049181769	2		644	644	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0026933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	38	271	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	0.519388702356553	3	FACETS	0.376	0.311	0.448	0.125	0.103	0.15	SUBCLONAL	1	TRUE	0	0.705598049181769	3		271	388	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916205	9916205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555491654	NA	P-0026933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	161	500	1	ENST00000330684.3:c.2084G>A	p.Arg695Gln	p.R695Q	ENST00000330684	NM_001134407.1	695	cGg/cAg	10/13	0.705598049181769	3	FACETS	1	0.983	1	0.616	0.569	0.664	CLONAL	1	TRUE	1	0.705598049181769	3		501	501	SUCCESS
APC	324	MSKCC	GRCh37	5	112174949	112174949	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	135	222	0	ENST00000257430.4:c.3658del	p.Thr1220HisfsTer45	p.T1220Hfs*45	ENST00000257430	NM_000038.5	1220	Aca/ca	16/16	0.519388702356553	3	FACETS	1	0.963	1	0.701	0.653	0.749	CLONAL	2	TRUE	0	0.705598049181769	3		222	246	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0026935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	87	541	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.839	0.743	0.943	0.839	0.743	0.943	CLONAL	1	TRUE	1	0.282037432844371	2		541	735	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0026935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	48	344	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.513	0.433	0.602	0.513	0.433	0.602	SUBCLONAL	1	TRUE	1	0.282037432844371	2		345	663	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100728	8100728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs771019738	NA	P-0026935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	76	535	3	ENST00000346208.3:c.708del	p.Ser237AlafsTer28	p.S237Afs*28	ENST00000346208		234	ttC/tt	3/6	1	2	FACETS	0.762	0.668	0.864	0.762	0.668	0.864	SUBCLONAL	1	TRUE	1	0.282037432844371	2		538	707	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	46	469	2	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.545	0.459	0.642	0.545	0.459	0.642	SUBCLONAL	1	TRUE	1	0.282037432844371	2		471	598	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256768	19256769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1202792889	NA	P-0026935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	53	509	0	ENST00000162023.5:c.944dup	p.Val316SerfsTer6	p.V316Sfs*6	ENST00000162023		315	cca/ccCa	13/13	1	2	FACETS	0.617	0.526	0.717	0.617	0.526	0.717	SUBCLONAL	1	TRUE	1	0.282037432844371	2		509	609	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0026935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	75	431	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	0.985	0.865	1	0.985	0.865	1	CLONAL	1	TRUE	1	0.282037432844371	2		431	540	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560514	65560514	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	95	392	0	ENST00000358664.4:c.83A>G	p.His28Arg	p.H28R	ENST00000358664	NM_002382.4	28	cAt/cGt	3/5	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.282037432844371	2		392	649	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0026935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	24	68	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	1	2	FACETS	0.799	0.63	0.992	0.799	0.63	0.992	CLONAL	1	TRUE	1	0.282037432844371	2		68	213	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366129	15366129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1468704458	NA	P-0026935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	62	412	1	ENST00000263377.2:c.2026C>T	p.Arg676Trp	p.R676W	ENST00000263377	NM_058243.2	676	Cgg/Tgg	10/20	1	2	FACETS	0.67	0.578	0.77	0.67	0.578	0.77	SUBCLONAL	1	TRUE	1	0.282037432844371	2		413	656	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791393	42791393	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0026935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	101	598	0	ENST00000575354.2:c.452+1G>A		p.X151_splice	ENST00000575354	NM_015125.3	151			1	2	FACETS	0.894	0.799	0.996	0.894	0.799	0.996	CLONAL	1	TRUE	1	0.282037432844371	2		598	801	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0026935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	107	628	4	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	1	2	FACETS	0.773	0.692	0.859	0.773	0.692	0.859	SUBCLONAL	1	TRUE	1	0.282037432844371	2		632	982	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36814324	36814324	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	81	528	0	ENST00000373129.3:c.716A>G	p.Tyr239Cys	p.Y239C	ENST00000373129	NM_032017.1	239	tAc/tGc	8/12	1	2	FACETS	0.809	0.712	0.913	0.809	0.712	0.913	CLONAL	1	TRUE	1	0.282037432844371	2		528	710	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0026935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	66	600	1	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.716	0.621	0.818	0.716	0.621	0.818	SUBCLONAL	1	TRUE	1	0.282037432844371	2		601	654	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352727	70352727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1488661030	NA	P-0026935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	83	509	0	ENST00000374080.3:c.4448C>T	p.Ser1483Leu	p.S1483L	ENST00000374080		1483	tCg/tTg	32/45	1	2	FACETS	0.822	0.725	0.926	0.822	0.725	0.926	CLONAL	1	TRUE	1	0.282037432844371	2		509	716	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692809	89692809	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	90	282	1	ENST00000371953.3:c.293del	p.Leu98GlnfsTer15	p.L98Qfs*15	ENST00000371953	NM_000314.4	98	cTa/ca	5/9	0.228107359777135	2	FACETS	0.8	0.714	0.89	0.8	0.714	0.89	SUBCLONAL	2	TRUE	0	0.282037432844371	2		283	399	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519135	103519136	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0026935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	86	427	0	ENST00000355739.4:c.2477_2478del	p.Phe826Ter	p.F826*	ENST00000355739	NM_000123.3	825	TTt/t	11/15	1	2	FACETS	0.82	0.725	0.921	0.82	0.725	0.921	CLONAL	1	TRUE	1	0.282037432844371	2		427	744	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99454619	99454619	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373427868	NA	P-0026935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	100	573	0	ENST00000268035.6:c.1538G>A	p.Arg513Gln	p.R513Q	ENST00000268035	NM_000875.3	513	cGg/cAg	7/21	1	2	FACETS	0.933	0.833	1	0.933	0.833	1	CLONAL	1	TRUE	1	0.282037432844371	2		573	760	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858351	9858351	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	45	379	0	ENST00000330684.3:c.3050C>T	p.Ser1017Phe	p.S1017F	ENST00000330684	NM_001134407.1	1017	tCc/tTc	13/13	1	2	FACETS	0.769	0.647	0.903	0.769	0.647	0.903	CLONAL	1	TRUE	1	0.282037432844371	2		379	415	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287371	33287371	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	44	429	0	ENST00000374542.5:c.1726C>A	p.Leu576Met	p.L576M	ENST00000374542	NM_001141970.1	576	Ctg/Atg	6/8	1	2	FACETS	0.568	0.476	0.671	0.568	0.476	0.671	SUBCLONAL	1	TRUE	1	0.282037432844371	2		429	549	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484152	8484152	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	66	453	0	ENST00000356435.5:c.3380A>G	p.Gln1127Arg	p.Q1127R	ENST00000356435		1127	cAa/cGa	19/35	1	2	FACETS	0.75	0.651	0.857	0.75	0.651	0.857	SUBCLONAL	1	TRUE	1	0.282037432844371	2		453	624	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8733812	8733814	+	inframe_deletion	In_Frame_Del	DEL	AGC	AGC	-	rs753684147	NA	P-0026935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	56	487	2	ENST00000356435.5:c.30_32del	p.Leu12del	p.L12del	ENST00000356435		10	ctGCTc/ctc	1/35	1	2	FACETS	0.659	0.564	0.762	0.659	0.564	0.762	SUBCLONAL	1	TRUE	1	0.282037432844371	2		489	603	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778059	135778059	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	87	510	1	ENST00000298552.3:c.2324T>C	p.Leu775Pro	p.L775P	ENST00000298552	NM_001162426.1	775	cTc/cCc	18/23	1	2	FACETS	0.828	0.733	0.93	0.828	0.733	0.93	CLONAL	1	TRUE	1	0.282037432844371	2		511	745	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0026936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	154	443	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.488837627296303	2		443	627	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0026936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	190	626	0	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	0.439808991674611	1	FACETS	0.957	0.889	1	0.957	0.889	1	CLONAL	1	TRUE	0	0.488837627296303	1		626	614	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0026936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	242	804	1	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.439808991674611	1	FACETS	0.935	0.876	0.995	0.935	0.876	0.995	CLONAL	1	TRUE	0	0.488837627296303	1		805	800	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037944	49037944	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	106	541	0	ENST00000267163.4:c.2184C>A	p.Tyr728Ter	p.Y728*	ENST00000267163	NM_000321.2	728	taC/taA	21/27	0.320928741689772	1	FACETS	1	0.961	1	1	0.99	1	CLONAL	2	TRUE	0	0.320928741689772	1		541	253	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633115	3633115	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	112	514	0	ENST00000294008.3:c.5136C>A	p.Ser1712Arg	p.S1712R	ENST00000294008	NM_032444.2	1712	agC/agA	14/15	0.307764066605522	2	FACETS	1	0.904	1	0.502	0.452	0.555	CLONAL	1	TRUE	0	0.320928741689772	2		514	695	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823901	3823901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	78	673	1	ENST00000262367.5:c.2314C>T	p.Pro772Ser	p.P772S	ENST00000262367	NM_004380.2	772	Cct/Tct	13/31	0.307764066605522	2	FACETS	0.536	0.47	0.607	0.268	0.235	0.304	SUBCLONAL	1	TRUE	0	0.320928741689772	2		674	907	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577555	7577555	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	411	583	0	ENST00000269305.4:c.726C>A	p.Cys242Ter	p.C242*	ENST00000269305	NM_001126112.2	242	tgC/tgA	7/11	0.320928741689772	2	FACETS	0.971	0.93	1	1	0.996	1	CLONAL	3	TRUE	0	0.320928741689772	2		583	879	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589577	67589591	+	inframe_deletion	In_Frame_Del	DEL	AAAAATTACATGAAT	AAAAATTACATGAAT	-	novel	NA	P-0026937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	60	339	0	ENST00000274335.5:c.1341_1355del	p.Lys447_Tyr452delinsAsn	p.K447_Y452delinsN	ENST00000274335		447	aAAAAATTACATGAATat/aat	10/15	0.204963619981272	4	FACETS	1	0.92	1	1	0.92	1	CLONAL	2	TRUE	2	0.320928741689772	4		339	230	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393285	393285	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	100	698	0	ENST00000380956.4:c.133G>A	p.Glu45Lys	p.E45K	ENST00000380956	NM_001195286.1	45	Gag/Aag	2/9	0.320928741689772	5	FACETS	0.717	0.639	0.802			1	SUBCLONAL	1	TRUE	NA	0.320928741689772	5		698	1287	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650547	48650547	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	82	710	1	ENST00000376670.3:c.517T>C	p.Phe173Leu	p.F173L	ENST00000376670	NM_002049.3	173	Ttt/Ctt	3/6	NA	2	FACETS	0.512	0.45	0.578			1	INDETERMINATE	1	TRUE	NA	0.320928741689772	2		711	999	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872192	76872192	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	33	398	0	ENST00000373344.5:c.5455G>C	p.Asp1819His	p.D1819H	ENST00000373344	NM_000489.3	1819	Gat/Cat	22/35	0.320928741689772	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.320928741689772	1		398	144	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0026938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	362	630	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.593668285310726	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.593668285310726	1		632	777	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0026938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	227	279	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.593668285310726	6	FACETS	1	0.959	1	0.518	0.483	0.553	CLONAL	2	TRUE	2	0.593668285310726	6		279	808	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716326	52716326	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	309	530	1	ENST00000322088.6:c.770G>T	p.Trp257Leu	p.W257L	ENST00000322088	NM_014225.5	257	tGg/tTg	6/15	0.361415242140771	1	FACETS	0.851	0.805	0.898	0.851	0.805	0.898	CLONAL	1	TRUE	0	0.593668285310726	1		531	860	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3650990	3650990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	62	282	0	ENST00000294008.3:c.1153C>T	p.Pro385Ser	p.P385S	ENST00000294008	NM_032444.2	385	Ccc/Tcc	5/15	0.446506809377261	1	FACETS	0.422	0.366	0.482	0.422	0.366	0.482	SUBCLONAL	1	TRUE	0	0.593668285310726	1		282	348	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134230	2134230	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs148527903	NA	P-0026944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	94	403	0	ENST00000219476.3:c.4007C>T	p.Ser1336Leu	p.S1336L	ENST00000219476	NM_000548.3	1336	tCg/tTg	34/42	1	2	FACETS	0.681	0.61	0.757	0.681	0.61	0.757	SUBCLONAL	1	TRUE	1	0.64313495179615	2		403	429	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437795	52437795	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	109	497	0	ENST00000460680.1:c.1366del	p.Gln456ArgfsTer115	p.Q456Rfs*115	ENST00000460680	NM_004656.3	456	Cag/ag	13/17	1	2	FACETS	0.607	0.547	0.671	0.607	0.547	0.671	SUBCLONAL	1	TRUE	1	0.64313495179615	2		497	558	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911534	101911534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111426349	NA	P-0026945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	103	418	0	ENST00000374994.4:c.1459C>T	p.Arg487Trp	p.R487W	ENST00000374994	NM_004612.2	487	Cgg/Tgg	9/9	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.35510837130306	2		418	519	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	132	500	0	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	1	2	FACETS	0.991	0.901	1	0.991	0.901	1	CLONAL	1	TRUE	1	0.35510837130306	2		500	750	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489564	56489564	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	127	454	0	ENST00000267101.3:c.2029A>G	p.Met677Val	p.M677V	ENST00000267101	NM_001982.3	677	Atg/Gtg	17/28	1	2	FACETS	0.89	0.806	0.978	0.89	0.806	0.978	CLONAL	1	TRUE	1	0.35510837130306	2		454	804	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339817	116339817	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	106	363	0	ENST00000397752.3:c.679A>G	p.Met227Val	p.M227V	ENST00000397752	NM_000245.2	227	Atg/Gtg	2/21	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.35510837130306	2		363	572	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0026954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	2500	487	2	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.244500202457897	33	FACETS	0.994	0.982	1			1	CLONAL	31	TRUE	NA	0.244500202457897	33		489	3179	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038563	47038563	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0026954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	81	472	0	ENST00000377604.3:c.724+1G>T		p.X242_splice	ENST00000377604	NM_001204468.1	242			1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.244500202457897	2		472	616	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037866	49037866	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs587778860	NA	P-0026954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	42	225	0	ENST00000267163.4:c.2107-1G>C		p.X703_splice	ENST00000267163	NM_000321.2	703			1	2	FACETS	0.77	0.643	0.911	0.77	0.643	0.911	CLONAL	1	TRUE	1	0.244500202457897	2		225	446	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578220	7578220	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	117	467	0	ENST00000269305.4:c.629del	p.Asn210ThrfsTer37	p.N210Tfs*37	ENST00000269305	NM_001126112.2	210	aAc/ac	6/11	0.244500202457897	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.244500202457897	1		467	696	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223928	2223928	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	63	415	0	ENST00000326181.6:c.1142A>T	p.Asp381Val	p.D381V	ENST00000326181	NM_032271.2	381	gAc/gTc	13/21	1	2	FACETS	0.892	0.771	1	0.892	0.771	1	CLONAL	1	TRUE	1	0.244500202457897	2		415	578	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786417	135786418	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0026954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	55	437	0	ENST00000298552.3:c.1112_1113del	p.His371ProfsTer4	p.H371Pfs*4	ENST00000298552	NM_001162426.1	371	cAC/c	11/23	0.149536055137008	1	FACETS	0.599	0.512	0.695	0.599	0.512	0.695	SUBCLONAL	1	TRUE	0	0.244500202457897	1		437	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0026955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	199	574	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.315678801314953	2	FACETS	0.96	0.894	1	0.96	0.894	1	CLONAL	2	TRUE	0	0.316911125871773	2		576	654	SUCCESS
APC	324	MSKCC	GRCh37	5	112175240	112175240	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	101	200	0	ENST00000257430.4:c.3949G>T	p.Glu1317Ter	p.E1317*	ENST00000257430	NM_000038.5	1317	Gaa/Taa	16/16	0.241666337160738	3	FACETS	1	0.974	1	0.815	0.738	0.895	CLONAL	2	TRUE	0	0.316911125871773	3		200	302	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606814	43606814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746512075	NA	P-0026955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	164	594	0	ENST00000355710.3:c.1423C>T	p.Arg475Trp	p.R475W	ENST00000355710	NM_020975.4	475	Cgg/Tgg	7/20	0.316911125871773	3	FACETS	0.751	0.69	0.815	0.751	0.69	0.815	SUBCLONAL	2	TRUE	1	0.316911125871773	3		594	798	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710677	114710678	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	135	374	0	ENST00000543371.1:c.164dup	p.Asn55LysfsTer42	p.N55Kfs*42	ENST00000543371	NM_001198531.1	54	-/A	1/14	0.252396318059176	3	FACETS	0.851	0.776	0.928	0.851	0.776	0.928	CLONAL	2	TRUE	1	0.316911125871773	3		374	580	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198486	108198486	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0026955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	171	287	0	ENST00000278616.4:c.7089+1G>C		p.X2363_splice	ENST00000278616	NM_000051.3	2363			0.316911125871773	3	FACETS	0.877	0.814	0.942	0.877	0.814	0.942	CLONAL	3	TRUE	0	0.316911125871773	3		287	475	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945418	17945419	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0026955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	84	562	0	ENST00000458235.1:c.2311_2312del	p.Arg771SerfsTer5	p.R771Sfs*5	ENST00000458235	NM_000215.3	771	CGa/a	17/24	0.316911125871773	3	FACETS	0.673	0.593	0.759	0.337	0.296	0.38	SUBCLONAL	1	TRUE	1	0.316911125871773	3		562	912	SUCCESS
APC	324	MSKCC	GRCh37	5	112176200	112176200	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	28	339	0	ENST00000257430.4:c.4909G>T	p.Asp1637Tyr	p.D1637Y	ENST00000257430	NM_000038.5	1637	Gat/Tat	16/16	0.241666337160738	3	FACETS	0.41	0.327	0.505	0.137	0.109	0.169	SUBCLONAL	1	TRUE	0	0.316911125871773	3		339	499	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0026957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	64	443	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.89	0.773	1	0.89	0.773	1	CLONAL	1	TRUE	1	0.328323359158242	2		443	438	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921567	178921567	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553821144	NA	P-0026957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	46	199	0	ENST00000263967.3:c.1049A>G	p.Asp350Gly	p.D350G	ENST00000263967	NM_006218.2	350	gAc/gGc	5/21	1	2	FACETS	0.768	0.648	0.899	0.768	0.648	0.899	SUBCLONAL	1	TRUE	1	0.328323359158242	2		199	365	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851315	156851315	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs62640939	NA	P-0026957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	82	504	1	ENST00000524377.1:c.2272G>A	p.Ala758Thr	p.A758T	ENST00000524377	NM_002529.3	758	Gcc/Acc	17/17	0.328323359158242	3	FACETS	0.939	0.829	1	0.47	0.414	0.529	CLONAL	1	TRUE	1	0.328323359158242	3		505	619	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211360	36211360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779453478	NA	P-0026957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	136	617	0	ENST00000222270.7:c.1111G>A	p.Glu371Lys	p.E371K	ENST00000222270	NM_014727.1	371	Gaa/Aaa	3/37	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.328323359158242	2		617	771	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961351	1961351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	115	462	0	ENST00000382891.5:c.3139C>T	p.Pro1047Ser	p.P1047S	ENST00000382891	NM_133335.3	1047	Ccc/Tcc	17/22	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.328323359158242	2		462	625	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0026958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	110	344	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.879	0.792	0.97	1	0.987	1	CLONAL	2	TRUE	1	0.22	2		345	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0026958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	25	601	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.224	0.175	0.28	0.224	0.175	0.28	SUBCLONAL	1	TRUE	1	0.22	2		603	1016	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246290	46246290	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	33	281	0	ENST00000334344.6:c.4384C>T	p.Gln1462Ter	p.Q1462*	ENST00000334344	NM_152641.2	1462	Cag/Tag	15/21	0.121441049439278	3	FACETS	0.638	0.519	0.773	0.319	0.259	0.387	INDETERMINATE	1	TRUE	1	0.22	3		281	522	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097858	8097858	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	45	378	0	ENST00000346208.3:c.240C>A	p.His80Gln	p.H80Q	ENST00000346208		80	caC/caA	2/6	0.236167410583292	1	FACETS	0.575	0.482	0.678	0.575	0.482	0.678	SUBCLONAL	1	TRUE	0	0.22	1		378	633	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523026	25523026	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	89	573	0	ENST00000264709.3:c.159G>C	p.Arg53Ser	p.R53S	ENST00000264709	NM_175629.2	53	agG/agC	3/23	1	2	FACETS	0.744	0.658	0.837	0.744	0.658	0.837	SUBCLONAL	1	TRUE	1	0.22	2		573	1087	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39240676	39240676	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	24	330	0	ENST00000402219.2:c.2092G>C	p.Glu698Gln	p.E698Q	ENST00000402219	NM_005633.3	698	Gag/Cag	13/23	1	2	FACETS	0.47	0.368	0.589	0.47	0.368	0.589	SUBCLONAL	1	TRUE	1	0.22	2		330	464	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635547	47635547	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	28	252	0	ENST00000233146.2:c.219G>C	p.Lys73Asn	p.K73N	ENST00000233146	NM_000251.2	73	aaG/aaC	2/16	1	2	FACETS	0.503	0.401	0.62	0.503	0.401	0.62	SUBCLONAL	1	TRUE	1	0.22	2		252	506	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442821	187442821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	43	468	0	ENST00000232014.4:c.1885C>T	p.Pro629Ser	p.P629S	ENST00000232014	NM_001130845.1	629	Ccc/Tcc	9/10	1	2	FACETS	0.495	0.413	0.587	0.495	0.413	0.587	SUBCLONAL	1	TRUE	1	0.22	2		468	789	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196156	138196156	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	36	282	0	ENST00000237289.4:c.470T>G	p.Leu157Arg	p.L157R	ENST00000237289	NM_001270507.1	157	cTt/cGt	3/9	1	2	FACETS	0.653	0.536	0.784	0.653	0.536	0.784	SUBCLONAL	1	TRUE	1	0.22	2		282	501	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2966412	2966412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1368676658	NA	P-0026958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	98	489	0	ENST00000396946.4:c.1768G>A	p.Asp590Asn	p.D590N	ENST00000396946	NM_032415.4	590	Gac/Aac	14/25	0.121441049439278	3	FACETS	1	0.918	1	0.518	0.461	0.579	INDETERMINATE	1	TRUE	1	0.22	3		489	954	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976787	2976787	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	144	638	0	ENST00000396946.4:c.1225G>T	p.Glu409Ter	p.E409*	ENST00000396946	NM_032415.4	409	Gag/Tag	9/25	0.121441049439278	3	FACETS	1	0.984	1	0.693	0.631	0.758	INDETERMINATE	1	TRUE	1	0.22	3		638	1049	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577587	7577587	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	371	498	0	ENST00000269305.4:c.694del	p.Ile232SerfsTer15	p.I232Sfs*15	ENST00000269305	NM_001126112.2	232	Atc/tc	7/11	0.444073784893618	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.444073784893618	2		498	794	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346277	89346277	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	49	250	0	ENST00000301030.4:c.6673A>C	p.Thr2225Pro	p.T2225P	ENST00000301030	NM_001256183.1	2225	Acg/Ccg	9/13	1	2	FACETS	0.556	0.472	0.648	0.556	0.472	0.648	SUBCLONAL	1	TRUE	1	0.444073784893618	2		250	397	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913343	NA	P-0026960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	41	520	0	ENST00000269305.4:c.817C>A	p.Arg273Ser	p.R273S	ENST00000269305	NM_001126112.2	273	Cgt/Agt	8/11	1	2	FACETS	0.908	0.76	1	0.908	0.76	1	CLONAL	1	FALSE	1	0.3	2		520	301	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92462547	92462547	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	31	521	0	ENST00000265734.4:c.91C>A	p.Arg31Ser	p.R31S	ENST00000265734	NM_001259.6	31	Cgc/Agc	2/8	0.1204899318738	4	FACETS	1	0.914	1	0.616	0.502	0.744	INDETERMINATE	1	FALSE	2	0.3	4		521	218	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0026961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	133	341	1	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.31	2		342	730	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0026961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	204	426	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.3	3	FACETS	0.906	0.842	0.972	0.906	0.842	0.972	CLONAL	2	TRUE	1	0.31	3		426	839	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421590	32421590	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	100	324	0	ENST00000332351.3:c.1002C>A	p.Asn334Lys	p.N334K	ENST00000332351	NM_024426.4	334	aaC/aaA	6/10	1	2	FACETS	0.994	0.889	1	0.994	0.889	1	CLONAL	1	TRUE	1	0.31	2		324	649	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30047528	30047528	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0026961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	70	286	0	ENST00000331968.5:c.2473A>T	p.Arg825Ter	p.R825*	ENST00000331968	NM_002742.2	825	Aga/Tga	17/18	0.236235459602568	3	FACETS	0.659	0.574	0.752	0.33	0.287	0.376	SUBCLONAL	1	TRUE	1	0.31	3		286	791	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242036	105242046	+	frameshift_variant	Frame_Shift_Del	DEL	CTGAGTTGTCA	CTGAGTTGTCA	-	novel	NA	P-0026961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	43	505	0	ENST00000349310.3:c.378_388del	p.Ser126ArgfsTer3	p.S126Rfs*3	ENST00000349310	NM_001014432.1	126	agTGACAACTCAGgg/aggg	6/15	1	2	FACETS	0.378	0.315	0.448	0.378	0.315	0.448	SUBCLONAL	1	TRUE	1	0.31	2		505	734	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678587	88678587	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	17	223	0	ENST00000360948.2:c.949C>A	p.Leu317Met	p.L317M	ENST00000360948	NM_001012338.2	317	Ctg/Atg	9/19	1	2	FACETS	0.329	0.245	0.43	0.329	0.245	0.43	SUBCLONAL	1	TRUE	1	0.31	2		223	333	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680793	88680793	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0026961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	44	403	0	ENST00000360948.2:c.465-1G>T		p.X155_splice	ENST00000360948	NM_001012338.2	155			1	2	FACETS	0.428	0.358	0.505	0.428	0.358	0.505	SUBCLONAL	1	TRUE	1	0.31	2		403	664	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561364	9561364	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	61	280	0	ENST00000353224.5:c.418G>T	p.Asp140Tyr	p.D140Y	ENST00000353224	NM_177990.2	140	Gac/Tac	4/10	1	2	FACETS	0.658	0.568	0.757	0.658	0.568	0.757	SUBCLONAL	1	TRUE	1	0.31	2		280	598	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468458	89468458	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	39	241	0	ENST00000336596.2:c.1992G>T	p.Arg664Ser	p.R664S	ENST00000336596	NM_005233.5	664	agG/agT	11/17	0.198029515714057	2	FACETS	0.53	0.439	0.631	0.265	0.219	0.316	SUBCLONAL	1	TRUE	0	0.31	2		241	475	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344164	70344164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	46	356	0	ENST00000374080.3:c.1900C>T	p.Pro634Ser	p.P634S	ENST00000374080		634	Ccc/Tcc	13/45	1	2	FACETS	0.487	0.41	0.573	0.487	0.41	0.573	SUBCLONAL	1	TRUE	1	0.31	2		356	609	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0026961-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	39	344	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.78	0.645	0.931	0.78	0.645	0.931	CLONAL	1	TRUE	1	0.15	2		345	667	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874263	155874263	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1557960039	NA	P-0026961-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	37	380	0	ENST00000368323.3:c.268A>G	p.Met90Val	p.M90V	ENST00000368323	NM_006912.5	90	Atg/Gtg	5/6	1	2	FACETS	0.71	0.584	0.852	0.71	0.584	0.852	SUBCLONAL	1	TRUE	1	0.15	2		380	695	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750483	41750483	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026961-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	29	394	0	ENST00000226382.2:c.145A>T	p.Thr49Ser	p.T49S	ENST00000226382	NM_003924.3	49	Acc/Tcc	1/3	1	2	FACETS	0.832	0.667	1	0.832	0.667	1	CLONAL	1	TRUE	1	0.15	2		394	465	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955969	55955969	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026961-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	40	248	0	ENST00000263923.4:c.3193G>T	p.Ala1065Ser	p.A1065S	ENST00000263923	NM_002253.2	1065	Gct/Tct	24/30	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.15	2		248	510	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272306	38272306	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026961-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	37	350	1	ENST00000425967.3:c.2061G>T	p.Lys687Asn	p.K687N	ENST00000425967	NM_001174067.1	687	aaG/aaT	15/19	1	2	FACETS	0.843	0.694	1	0.843	0.694	1	CLONAL	1	TRUE	1	0.15	2		351	585	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287277	38287277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026961-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	40	503	0	ENST00000425967.3:c.380C>T	p.Ala127Val	p.A127V	ENST00000425967	NM_001174067.1	127	gCa/gTa	4/19	1	2	FACETS	0.774	0.642	0.922	0.774	0.642	0.922	CLONAL	1	TRUE	1	0.15	2		503	689	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410930	63410930	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026961-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	33	414	0	ENST00000330258.3:c.2237C>A	p.Pro746His	p.P746H	ENST00000330258	NM_152424.3	746	cCt/cAt	2/2	1	2	FACETS	0.735	0.597	0.891	0.735	0.597	0.891	SUBCLONAL	1	TRUE	1	0.15	2		414	599	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	71	321	2	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.751	0.656	0.853	1	0.974	1	SUBCLONAL	2	TRUE	1	0.16	2		323	591	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	43	293	0	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.16	2		293	495	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	53	583	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	0.16	2		583	506	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	49	337	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		337	542	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007806	45007807	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	78	327	0	ENST00000558401.1:c.253_254del	p.Leu85ValfsTer4	p.L85Vfs*4	ENST00000558401	NM_004048.2	85	TTg/g	2/4	1	2	FACETS	0.863	0.759	0.974	1	0.98	1	CLONAL	2	TRUE	1	0.16	2		327	565	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	16	68	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	1	2	FACETS	0.813	0.607	1	1	0.907	1	CLONAL	2	TRUE	1	0.16	2		68	123	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	46	310	1	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.16	2		311	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	49	496	1	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	1	2	FACETS	0.941	0.796	1	0.941	0.796	1	CLONAL	1	TRUE	1	0.16	2		497	651	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	52	351	1	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.16	2		352	508	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574678	41574679	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs754418509	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	90	606	2	ENST00000263253.7:c.6970dup	p.His2324ProfsTer55	p.H2324Pfs*55	ENST00000263253	NM_001429.3	2321	-/C	31/31	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.16	2		608	790	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	166	503	2	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	0.266423799889853	2	FACETS	0.963	0.887	1	1	0.988	1	CLONAL	3	TRUE	0	0.16	2		505	718	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748552	43748552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774318829	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	70	365	0	ENST00000523873.1:c.506C>T	p.Ala169Val	p.A169V	ENST00000523873		169	gCc/gTc	6/8	1	2	FACETS	0.84	0.733	0.954	1	0.978	1	CLONAL	2	TRUE	1	0.16	2		365	521	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952088	178952088	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553826184	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	45	276	0	ENST00000263967.3:c.3143A>G	p.His1048Arg	p.H1048R	ENST00000263967	NM_006218.2	1048	cAt/cGt	21/21	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.16	2		276	453	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017724	31017724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1005458245	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	45	363	0	ENST00000375687.4:c.586G>A	p.Asp196Asn	p.D196N	ENST00000375687	NM_015338.5	196	Gat/Aat	8/13	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.16	2		363	399	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991706	72991706	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540253425	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	53	191	0	ENST00000268489.5:c.2339C>T	p.Ala780Val	p.A780V	ENST00000268489	NM_006885.3	780	gCg/gTg	2/10	1	2	FACETS	0.883	0.761	1	1	0.98	1	CLONAL	3	TRUE	1	0.16	2		191	250	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100302	157100302	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1417035592	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	23	262	0	ENST00000346085.5:c.1243del	p.Ala415ProfsTer15	p.A415Pfs*15	ENST00000346085	NM_020732.3	413	tcG/tc	1/20	1	2	FACETS	0.927	0.724	1	0.927	0.724	1	CLONAL	1	TRUE	1	0.16	2		262	310	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243878	46243878	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	46	227	0	ENST00000334344.6:c.1972C>T	p.Gln658Ter	p.Q658*	ENST00000334344	NM_152641.2	658	Caa/Taa	15/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.16	2		227	451	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538941	187538941	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs113224498	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	58	305	2	ENST00000441802.2:c.8799del	p.Gly2934ValfsTer3	p.G2934Vfs*3	ENST00000441802	NM_005245.3	2933	caA/ca	10/27	1	2	FACETS	0.79	0.68	0.909	1	0.971	1	CLONAL	2	TRUE	1	0.16	2		307	459	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466824	57466824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	66	334	0	ENST00000371085.3:c.43G>A	p.Glu15Lys	p.E15K	ENST00000371085	NM_000516.4	15	Gag/Aag	1/13	1	2	FACETS	0.762	0.662	0.871	1	0.972	1	SUBCLONAL	2	TRUE	1	0.16	2		334	541	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	74	675	0	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.16	2		675	864	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214871	36214871	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	113	561	3	ENST00000222270.7:c.3302del	p.Pro1101LeufsTer81	p.P1101Lfs*81	ENST00000222270	NM_014727.1	1099	ggC/gg	8/37	1	2	FACETS	0.891	0.801	0.985	1	0.987	1	CLONAL	2	TRUE	1	0.16	2		564	793	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325282	39325282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1266744229	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	65	395	0	ENST00000373001.3:c.37G>A	p.Ala13Thr	p.A13T	ENST00000373001	NM_022157.3	13	Gcc/Acc	1/7	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.16	2		395	577	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444987	49444987	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	82	419	2	ENST00000301067.7:c.2479del	p.Gln827AsnfsTer103	p.Q827Nfs*103	ENST00000301067	NM_003482.3	827	Caa/aa	10/54	1	2	FACETS	0.854	0.754	0.961	1	0.981	1	CLONAL	2	TRUE	1	0.16	2		421	600	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343445	70343445	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs774363039	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	58	318	0	ENST00000374080.3:c.1619G>A	p.Arg540His	p.R540H	ENST00000374080		540	cGt/cAt	12/45	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.16	2		318	517	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087536	27087536	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760364683	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	155	487	0	ENST00000324856.7:c.2110G>A	p.Ala704Thr	p.A704T	ENST00000324856	NM_006015.4	704	Gcc/Acc	5/20	1	2	FACETS	0.967	0.888	1	1	0.993	1	CLONAL	3	TRUE	1	0.16	2		487	668	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105988	27105988	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	53	342	0	ENST00000324856.7:c.5599C>T	p.Pro1867Ser	p.P1867S	ENST00000324856	NM_006015.4	1867	Cct/Tct	20/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.16	2		342	457	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106063	8106063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	44	452	0	ENST00000346208.3:c.883G>A	p.Gly295Arg	p.G295R	ENST00000346208		295	Gga/Aga	4/6	1	2	FACETS	0.934	0.782	1	0.934	0.782	1	CLONAL	1	TRUE	1	0.16	2		452	589	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456824	32456824	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751641518	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	57	521	1	ENST00000332351.3:c.68G>A	p.Gly23Glu	p.G23E	ENST00000332351	NM_024426.4	23	gGg/gAg	1/10	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.16	2		522	628	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922177	100922177	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	34	355	0	ENST00000325455.5:c.2335G>T	p.Ala779Ser	p.A779S	ENST00000325455	NM_001202474.3	779	Gca/Tca	5/8	1	2	FACETS	0.799	0.652	0.965	0.799	0.652	0.965	CLONAL	1	TRUE	1	0.16	2		355	532	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117840	108117841	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	32	247	1	ENST00000278616.4:c.1051_1052delinsTT	p.Asp351Phe	p.D351F	ENST00000278616	NM_000051.3	351	GAt/TTt	8/63	1	2	FACETS	0.926	0.751	1	0.926	0.751	1	CLONAL	1	TRUE	1	0.16	2		248	432	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192057	108192057	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756626462	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	78	361	1	ENST00000278616.4:c.6482G>A	p.Arg2161His	p.R2161H	ENST00000278616	NM_000051.3	2161	cGc/cAc	45/63	1	2	FACETS	0.829	0.729	0.936	1	0.979	1	CLONAL	2	TRUE	1	0.16	2		362	588	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893647	28893647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	56	324	0	ENST00000282397.4:c.3199G>A	p.Ala1067Thr	p.A1067T	ENST00000282397	NM_002019.4	1067	Gct/Act	24/30	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.16	2		324	537	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133968	41133968	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767908809	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	79	366	0	ENST00000379561.5:c.1660C>T	p.Arg554Cys	p.R554C	ENST00000379561	NM_002015.3	554	Cgc/Tgc	2/3	1	2	FACETS	0.909	0.801	1	1	0.982	1	CLONAL	2	TRUE	1	0.16	2		366	543	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774177	66774177	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	111	744	0	ENST00000307102.5:c.653C>A	p.Ser218Tyr	p.S218Y	ENST00000307102	NM_002755.3	218	tCc/tAc	6/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.16	2		744	1032	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993602	72993602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	56	389	0	ENST00000268489.5:c.443G>A	p.Ser148Asn	p.S148N	ENST00000268489	NM_006885.3	148	aGc/aAc	2/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.16	2		389	510	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266124	198266124	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	54	259	0	ENST00000335508.6:c.2496G>T	p.Gln832His	p.Q832H	ENST00000335508	NM_012433.2	832	caG/caT	17/25	1	2	FACETS	0.879	0.753	1	1	0.973	1	CLONAL	2	TRUE	1	0.16	2		259	384	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149789	202149789	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	83	390	0	ENST00000358485.4:c.1230A>C	p.Lys410Asn	p.K410N	ENST00000358485	NM_001080125.1	410	aaA/aaC	8/9	1	2	FACETS	0.822	0.726	0.925	1	0.98	1	CLONAL	2	TRUE	1	0.16	2		390	631	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017142	31017142	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1259109293	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	60	228	0	ENST00000375687.4:c.473C>T	p.Ala158Val	p.A158V	ENST00000375687	NM_015338.5	158	gCg/gTg	7/13	1	2	FACETS	1	0.928	1	1	0.98	1	CLONAL	2	TRUE	1	0.16	2		228	338	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259387	36259387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1569084822	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	95	388	0	ENST00000300305.3:c.104G>A	p.Ser35Asn	p.S35N	ENST00000300305		35	aGc/aAc	3/8	1	2	FACETS	0.871	0.776	0.972	1	0.984	1	CLONAL	2	TRUE	1	0.16	2		388	682	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41525977	41525977	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	75	395	0	ENST00000263253.7:c.1256del	p.Asn419MetfsTer12	p.N419Mfs*12	ENST00000263253	NM_001429.3	418	Aaa/aa	5/31	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.16	2		395	626	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665540	138665540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	42	289	0	ENST00000330315.3:c.25G>A	p.Glu9Lys	p.E9K	ENST00000330315	NM_023067.3	9	Gag/Aag	1/1	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.16	2		289	365	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928284	178928285	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	63	313	0	ENST00000263967.3:c.1470_1471del	p.Val491AspfsTer2	p.V491Dfs*2	ENST00000263967	NM_006218.2	490	tcAGtg/tctg	9/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.16	2		313	566	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80057422	80057423	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	60	279	0	ENST00000265081.6:c.1824dup	p.Gly609TrpfsTer9	p.G609Wfs*9	ENST00000265081	NM_002439.4	607	-/T	13/24	1	2	FACETS	0.793	0.684	0.91	1	0.972	1	CLONAL	2	TRUE	1	0.16	2		279	473	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982045	93982045	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	47	272	0	ENST00000369303.4:c.1420A>G	p.Thr474Ala	p.T474A	ENST00000369303	NM_004440.3	474	Aca/Gca	6/17	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.16	2		272	533	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465503	8465503	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	50	400	1	ENST00000356435.5:c.3677T>C	p.Val1226Ala	p.V1226A	ENST00000356435		1226	gTc/gCc	21/35	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.16	2		401	574	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002660	37002660	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	69	322	0	ENST00000358127.4:c.589C>T	p.Arg197Cys	p.R197C	ENST00000358127	NM_001280556.1	197	Cgc/Tgc	5/10	1	2	FACETS	0.826	0.721	0.94	1	0.977	1	CLONAL	2	TRUE	1	0.16	2		322	522	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759980	133759980	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	115	673	1	ENST00000318560.5:c.2303G>T	p.Gly768Val	p.G768V	ENST00000318560	NM_005157.4	768	gGg/gTg	11/11	1	2	FACETS	0.904	0.814	0.999	1	0.987	1	CLONAL	2	TRUE	1	0.16	2		674	795	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411476	63411476	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	63	604	0	ENST00000330258.3:c.1691T>C	p.Ile564Thr	p.I564T	ENST00000330258	NM_152424.3	564	aTc/aCc	2/2	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.16	2		604	717	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344934	70344934	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	63	486	1	ENST00000374080.3:c.2164C>A	p.Leu722Ile	p.L722I	ENST00000374080		722	Ctt/Att	15/45	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.16	2		487	630	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938395	76938395	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	89	461	0	ENST00000373344.5:c.2353A>G	p.Thr785Ala	p.T785A	ENST00000373344	NM_000489.3	785	Aca/Gca	9/35	1	2	FACETS	0.833	0.739	0.933	1	0.982	1	CLONAL	2	TRUE	1	0.16	2		461	668	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0026964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	615	598	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.255647336660311	6	FACETS	0.948	0.913	0.982			1	CLONAL	4	TRUE	NA	0.41815781576497	6		598	1425	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111449	8111450	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	336	566	0	ENST00000346208.3:c.936dup	p.Ala313SerfsTer39	p.A313Sfs*39	ENST00000346208		312	aga/agAa	5/6	0.189390854757026	3	FACETS	1	0.979	1	0.7	0.666	0.734	INDETERMINATE	2	TRUE	0	0.545970840021214	3		566	746	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573344	55573346	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0026965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	121	536	0	ENST00000288135.5:c.1006_1008del	p.Glu336del	p.E336del	ENST00000288135	NM_000222.2	336	GAA/-	6/21	0.477703946223939	4	FACETS	0.78	0.704	0.86	0.39	0.352	0.43	SUBCLONAL	1	TRUE	2	0.545970840021214	4		536	879	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382150	152382152	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	novel	NA	P-0026965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	93	381	0	ENST00000206249.3:c.1260_1262del	p.Met421del	p.M421del	ENST00000206249	NM_000125.3	420	ggCATg/ggg	6/8	0.545970840021214	2	FACETS	0.949	0.851	1	0.474	0.425	0.526	CLONAL	1	TRUE	0	0.545970840021214	2		381	359	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	191	315	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.945	0.879	1	0.945	0.879	1	CLONAL	1	TRUE	1	0.714488769382912	2		316	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0026966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	225	574	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.855	0.799	0.912	0.855	0.799	0.912	CLONAL	1	TRUE	1	0.714488769382912	2		576	737	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807889	1807889	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs78311289	NA	P-0026966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	1332	669	1	ENST00000260795.2:c.1948A>G	p.Lys650Glu	p.K650E	ENST00000260795		650	Aag/Gag	13/17	0.714488769382912	5	FACETS	1	0.998	1			1	CLONAL	4	TRUE	NA	0.714488769382912	5		670	1742	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591099	67591099	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs773686816	NA	P-0026966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	138	315	0	ENST00000274335.5:c.1692C>A	p.Asn564Lys	p.N564K	ENST00000274335		564	aaC/aaA	12/15	1	2	FACETS	0.973	0.895	1	0.973	0.895	1	CLONAL	1	TRUE	1	0.714488769382912	2		315	397	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609708	28609708	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1275935565	NA	P-0026966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	235	626	0	ENST00000241453.7:c.1521A>G	p.Ile507Met	p.I507M	ENST00000241453	NM_004119.2	507	atA/atG	12/24	1	2	FACETS	0.904	0.847	0.962	0.904	0.847	0.962	CLONAL	1	TRUE	1	0.714488769382912	2		626	728	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822066	72822067	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0026966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	116	334	0	ENST00000268489.5:c.10108_10109del	p.Leu3371AlafsTer59	p.L3371Afs*59	ENST00000268489	NM_006885.3	3370	AGt/t	10/10	1	2	FACETS	0.828	0.753	0.906	0.828	0.753	0.906	CLONAL	1	TRUE	1	0.714488769382912	2		334	392	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89825087	89825087	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1460469198	NA	P-0026966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	200	533	0	ENST00000389301.3:c.2879A>G	p.His960Arg	p.H960R	ENST00000389301	NM_000135.2	960	cAt/cGt	30/43	1	2	FACETS	0.801	0.745	0.859	0.801	0.745	0.859	CLONAL	1	TRUE	1	0.714488769382912	2		533	699	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0026968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	71	344	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.242825160173405	1	FACETS	0.914	0.799	1	0.914	0.799	1	CLONAL	1	TRUE	0	0.242825160173405	1		345	562	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923308	26923308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1436081889	NA	P-0026968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	51	330	0	ENST00000381527.3:c.304C>T	p.His102Tyr	p.H102Y	ENST00000381527	NM_001260.1	102	Cat/Tat	3/13	1	2	FACETS	0.955	0.813	1	0.955	0.813	1	CLONAL	1	TRUE	1	0.242825160173405	2		330	440	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221239	1221240	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	122	706	0	ENST00000326873.7:c.762_763insG	p.Phe255ValfsTer11	p.F255Vfs*11	ENST00000326873	NM_000455.4	254	-/G	6/10	0.242825160173405	1	FACETS	0.937	0.846	1	0.937	0.846	1	CLONAL	1	TRUE	0	0.242825160173405	1		706	942	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158636945	158636945	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	168	485	0	ENST00000263640.3:c.235A>T	p.Met79Leu	p.M79L	ENST00000263640	NM_001105.4	79	Atg/Ttg	4/11	0.242825160173405	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.242825160173405	3		485	732	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225360642	225360648	+	frameshift_variant	Frame_Shift_Del	DEL	AGTTACT	AGTTACT	-	novel	NA	P-0026968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	86	375	0	ENST00000264414.4:c.1743_1749del	p.Val582AlafsTer16	p.V582Afs*16	ENST00000264414	NM_003590.4	581	caAGTAACT/ca	13/16	0.242825160173405	3	FACETS	0.811	0.719	0.907	0.811	0.719	0.907	CLONAL	2	TRUE	1	0.242825160173405	3		375	490	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163824	47163824	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	59	473	0	ENST00000409792.3:c.2302G>T	p.Val768Leu	p.V768L	ENST00000409792	NM_014159.6	768	Gtg/Ttg	3/21	1	2	FACETS	0.853	0.734	0.982	0.853	0.734	0.982	CLONAL	1	TRUE	1	0.242825160173405	2		473	570	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55569980	55569980	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	62	451	0	ENST00000288135.5:c.847A>T	p.Asn283Tyr	p.N283Y	ENST00000288135	NM_000222.2	283	Aat/Tat	5/21	1	2	FACETS	0.953	0.824	1	0.953	0.824	1	CLONAL	1	TRUE	1	0.242825160173405	2		451	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578520	7578520	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	380	771	2	ENST00000269305.4:c.410T>A	p.Leu137Gln	p.L137Q	ENST00000269305	NM_001126112.2	137	cTg/cAg	5/11	0.561596099162833	4	FACETS	0.863	0.82	0.907			1	CLONAL	2	TRUE	NA	0.596784372037663	4		773	1178	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546581	9546581	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	48	474	0	ENST00000353224.5:c.1441G>T	p.Asp481Tyr	p.D481Y	ENST00000353224	NM_177990.2	481	Gac/Tac	5/10	1	2	FACETS	0.288	0.243	0.337	0.288	0.243	0.337	SUBCLONAL	1	TRUE	1	0.596784372037663	2		474	559	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0026970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	272	449	0				ENST00000310581	NM_198253.2	-/1132			0.353265061195144	3	FACETS	1	0.972	1	0.526	0.495	0.558	INDETERMINATE	1	TRUE	1	0.856034144117587	3		449	862	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0026970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	456	521	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.844833237251611	2	FACETS	0.939	0.915	0.962	0.939	0.915	0.962	CLONAL	2	TRUE	0	0.856034144117587	2		521	567	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974792	21974792	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs141798398	NA	P-0026970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	218	200	0	ENST00000304494.5:c.35C>A	p.Ser12Ter	p.S12*	ENST00000304494	NM_000077.4	12	tCg/tAg	1/3	0.813827524113432	2	FACETS	0.961	0.927	0.992	0.961	0.927	0.992	CLONAL	2	TRUE	0	0.856034144117587	2		200	265	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547924	41547924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367954257	NA	P-0026970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	511	570	0	ENST00000263253.7:c.2905G>A	p.Glu969Lys	p.E969K	ENST00000263253	NM_001429.3	969	Gag/Aag	15/31	0.840496799335029	3	FACETS	0.923	0.89	0.955	0.923	0.89	0.955	CLONAL	2	TRUE	1	0.856034144117587	3		570	924	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056241	27056241	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	469	597	1	ENST00000324856.7:c.1237C>T	p.Gln413Ter	p.Q413*	ENST00000324856	NM_006015.4	413	Caa/Taa	2/20	0.425610253849445	2	FACETS	1	0.997	1	0.711	0.686	0.735	INDETERMINATE	1	TRUE	0	0.856034144117587	2		598	771	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451131	70451131	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	163	596	0	ENST00000373644.4:c.5971G>C	p.Asp1991His	p.D1991H	ENST00000373644	NM_030625.2	1991	Gat/Cat	12/12	0.255363231150734	5	FACETS	0.746	0.683	0.812			1	INDETERMINATE	1	TRUE	NA	0.856034144117587	5		596	1166	SUCCESS
ATM	472	MSKCC	GRCh37	11	108128292	108128292	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	86	447	2	ENST00000278616.4:c.2335A>G	p.Met779Val	p.M779V	ENST00000278616	NM_000051.3	779	Atg/Gtg	15/63	NA	2	FACETS	0.475	0.422	0.531			1	INDETERMINATE	1	TRUE	NA	0.856034144117587	2		449	423	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344147	118344147	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	510	426	0	ENST00000534358.1:c.2273G>C	p.Arg758Thr	p.R758T	ENST00000534358	NM_005933.3	758	aGa/aCa	3/36	0.854842079664454	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.856034144117587	2		426	594	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426694	49426694	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	233	228	0	ENST00000301067.7:c.11794C>T	p.Gln3932Ter	p.Q3932*	ENST00000301067	NM_003482.3	3932	Caa/Taa	39/54	0.409423917627912	3	FACETS	1	0.991	1	0.774	0.74	0.806	INDETERMINATE	2	TRUE	0	0.856034144117587	3		228	335	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281451	49281451	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	284	532	0	ENST00000282018.3:c.498C>G	p.Ile166Met	p.I166M	ENST00000282018	NM_020377.2	166	atC/atG	1/1	1	2	FACETS	0.977	0.925	1	0.977	0.925	1	CLONAL	1	TRUE	1	0.856034144117587	2		532	679	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641335	23641335	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45537237	NA	P-0026970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	169	715	3	ENST00000261584.4:c.2140G>A	p.Asp714Asn	p.D714N	ENST00000261584	NM_024675.3	714	Gat/Aat	5/13	0.430471811677146	1	FACETS	0.332	0.306	0.359	0.332	0.306	0.359	INDETERMINATE	1	TRUE	0	0.856034144117587	1		718	681	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351208	89351208	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1376769382	NA	P-0026970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	301	617	1	ENST00000301030.4:c.1742C>T	p.Ser581Phe	p.S581F	ENST00000301030	NM_001256183.1	581	tCt/tTt	9/13	0.430471811677146	1	FACETS	0.706	0.672	0.739	0.706	0.672	0.739	INDETERMINATE	1	TRUE	0	0.856034144117587	1		618	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573960	7573960	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	335	687	0	ENST00000269305.4:c.1067G>C	p.Gly356Ala	p.G356A	ENST00000269305	NM_001126112.2	356	gGg/gCg	10/11	0.450792381835496	3	FACETS	1	0.988	1	0.569	0.539	0.6	INDETERMINATE	1	TRUE	1	0.856034144117587	3		687	982	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677846	47677846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	138	582	0	ENST00000347630.2:c.1019C>T	p.Ser340Leu	p.S340L	ENST00000347630	NM_001007230.1	340	tCa/tTa	11/11	0.425610253849445	2	FACETS	0.456	0.415	0.498	0.228	0.207	0.249	INDETERMINATE	1	TRUE	0	0.856034144117587	2		582	707	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118870	70118870	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	420	507	0	ENST00000245479.2:c.442G>A	p.Glu148Lys	p.E148K	ENST00000245479	NM_000346.3	148	Gag/Aag	2/3	0.425610253849445	2	FACETS	1	0.997	1	0.73	0.704	0.756	INDETERMINATE	1	TRUE	0	0.856034144117587	2		507	672	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184568	7184568	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	339	416	0	ENST00000302850.5:c.733C>G	p.Gln245Glu	p.Q245E	ENST00000302850	NM_000208.2	245	Cag/Gag	3/22	0.450792381835496	3	FACETS	0.837	0.798	0.875	0.837	0.798	0.875	INDETERMINATE	2	TRUE	1	0.856034144117587	3		416	676	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272301	18272301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	15	26	0	ENST00000222254.8:c.811G>A	p.Asp271Asn	p.D271N	ENST00000222254	NM_005027.3	271	Gac/Aac	6/16	0.450792381835496	3	FACETS	0.944	0.715	1	0.472	0.357	0.6	INDETERMINATE	1	TRUE	1	0.856034144117587	3		26	53	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547972	41547972	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	580	632	0	ENST00000263253.7:c.2953G>C	p.Asp985His	p.D985H	ENST00000263253	NM_001429.3	985	Gat/Cat	15/31	0.840496799335029	3	FACETS	0.929	0.899	0.96	0.929	0.899	0.96	CLONAL	2	TRUE	1	0.856034144117587	3		632	1041	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548254	41548256	+	frameshift_variant	Frame_Shift_Del	DEL	GAG	GAG	AA	novel	NA	P-0026970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	324	387	1	ENST00000263253.7:c.3042_3044delinsAA	p.Arg1015LysfsTer5	p.R1015Kfs*5	ENST00000263253	NM_001429.3	1014	gaGAGa/gaAAa	16/31	0.840496799335029	3	FACETS	0.896	0.856	0.937	0.896	0.856	0.937	CLONAL	2	TRUE	1	0.856034144117587	3		388	603	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548276	41548276	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	338	378	0	ENST00000263253.7:c.3064G>A	p.Glu1022Lys	p.E1022K	ENST00000263253	NM_001429.3	1022	Gaa/Aaa	16/31	0.840496799335029	3	FACETS	0.944	0.904	0.985	0.944	0.904	0.985	CLONAL	2	TRUE	1	0.856034144117587	3		378	597	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548294	41548294	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	365	396	0	ENST00000263253.7:c.3082G>C	p.Asp1028His	p.D1028H	ENST00000263253	NM_001429.3	1028	Gac/Cac	16/31	0.840496799335029	3	FACETS	0.984	0.944	1	0.984	0.944	1	CLONAL	2	TRUE	1	0.856034144117587	3		396	619	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434161	12434161	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	326	440	0	ENST00000287820.6:c.529G>C	p.Asp177His	p.D177H	ENST00000287820	NM_015869.4	177	Gat/Cat	4/7	0.840496799335029	3	FACETS	0.925	0.884	0.965	0.925	0.884	0.965	CLONAL	2	TRUE	1	0.856034144117587	3		440	588	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119642275	119642275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	144	516	0	ENST00000316626.5:c.422G>A	p.Arg141Lys	p.R141K	ENST00000316626		141	aGa/aAa	4/12	0.840496799335029	3	FACETS	0.951	0.873	1	0.476	0.436	0.516	CLONAL	1	TRUE	1	0.856034144117587	3		516	505	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176678842	176678842	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	178	381	0	ENST00000439151.2:c.4753G>C	p.Glu1585Gln	p.E1585Q	ENST00000439151	NM_022455.4	1585	Gaa/Caa	12/23	0.700605225429357	3	FACETS	1	0.96	1	0.526	0.488	0.566	CLONAL	1	TRUE	1	0.856034144117587	3		381	564	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511196	148511196	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1443131834	NA	P-0026970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	1193	458	0	ENST00000320356.2:c.1706C>T	p.Ala569Val	p.A569V	ENST00000320356	NM_004456.4	569	gCa/gTa	15/20	0.84853453371969	5	FACETS	0.985	0.975	0.995	0.985	0.975	0.995	CLONAL	5	TRUE	0	0.856034144117587	5		458	1292	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859702	151859702	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	753	301	0	ENST00000262189.6:c.10960C>T	p.Gln3654Ter	p.Q3654*	ENST00000262189	NM_170606.2	3654	Caa/Taa	43/59	0.84853453371969	5	FACETS	1	0.99	1	1	0.99	1	CLONAL	5	TRUE	0	0.856034144117587	5		301	802	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209301	98209301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772886108	NA	P-0026970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	340	649	0	ENST00000331920.6:c.4237C>T	p.His1413Tyr	p.H1413Y	ENST00000331920	NM_000264.3	1413	Cac/Tac	23/24	0.813827524113432	2	FACETS	1	0.993	1	0.6	0.573	0.627	CLONAL	1	TRUE	0	0.856034144117587	2		649	662	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911488	101911488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	189	281	0	ENST00000374994.4:c.1413G>A	p.Met471Ile	p.M471I	ENST00000374994	NM_004612.2	471	atG/atA	9/9	0.813827524113432	2	FACETS	0.948	0.91	0.982	0.948	0.91	0.982	CLONAL	2	TRUE	0	0.856034144117587	2		281	233	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802682	135802682	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	251	350	0	ENST00000298552.3:c.116C>T	p.Pro39Leu	p.P39L	ENST00000298552	NM_001162426.1	39	cCt/cTt	4/23	0.813827524113432	2	FACETS	0.949	0.917	0.979	0.949	0.917	0.979	CLONAL	2	TRUE	0	0.856034144117587	2		350	309	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922921	39922921	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	307	344	0	ENST00000378444.4:c.3787G>C	p.Glu1263Gln	p.E1263Q	ENST00000378444	NM_001123385.1	1263	Gag/Cag	8/15	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.856034144117587	1		344	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0026971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	528	583	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.449175208269705	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	4	FALSE	0	0.449249420903442	4		583	839	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184670	185184670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188669013	NA	P-0026971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	101	419	2	ENST00000265026.3:c.1562G>A	p.Arg521His	p.R521H	ENST00000265026	NM_004721.4	521	cGt/cAt	10/14	0.449249420903442	5	FACETS	1	0.893	1	0.333	0.297	0.371	CLONAL	1	FALSE	2	0.449249420903442	5		421	753	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263191	115263191	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	121	459	0	ENST00000438362.2:c.2159G>C	p.Arg720Pro	p.R720P	ENST00000438362	NM_001242891.1	720	cGc/cCc	17/20	0.449249420903442	6	FACETS	1	0.967	1			1	CLONAL	1	FALSE	NA	0.449249420903442	6		459	878	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246021918	246021918	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1438	100	539	0	ENST00000388985.4:c.956G>C	p.Arg319Pro	p.R319P	ENST00000388985		319	cGg/cCg	10/12	0.449249420903442	8	FACETS	0.68	0.604	0.76			1	SUBCLONAL	1	FALSE	NA	0.449249420903442	8		539	1538	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478899	56478899	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	272	601	0	ENST00000267101.3:c.355G>C	p.Val119Leu	p.V119L	ENST00000267101	NM_001982.3	119	Gtc/Ctc	3/28	0.449175208269705	3	FACETS	0.906	0.854	0.96	0.604	0.569	0.64	CLONAL	2	FALSE	0	0.449249420903442	3		601	818	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0026972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	97	341	3	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.271010498441479	2	FACETS	0.891	0.8	0.985	0.891	0.8	0.985	CLONAL	2	TRUE	0	0.280683306807696	2		344	388	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736165	204736166	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0026972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	58	348	1	ENST00000302823.3:c.529dup	p.Tyr177LeufsTer2	p.Y177Lfs*2	ENST00000302823	NM_005214.4	174	-/T	3/4	0.27617578137351	3	FACETS	0.848	0.728	0.977	0.424	0.364	0.489	CLONAL	1	TRUE	1	0.280683306807696	3		349	556	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280081	18280081	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778796616	NA	P-0026972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	80	167	2	ENST00000222254.8:c.2164G>A	p.Gly722Ser	p.G722S	ENST00000222254	NM_005027.3	722	Ggc/Agc	16/16	0.280683306807696	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.280683306807696	2		169	252	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494900	56494900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs930167600	NA	P-0026972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	95	452	3	ENST00000267101.3:c.3257C>T	p.Pro1086Leu	p.P1086L	ENST00000267101	NM_001982.3	1086	cCa/cTa	27/28	0.0974404529917612	4	FACETS	1	0.961	1	0.589	0.524	0.658	INDETERMINATE	1	TRUE	2	0.280683306807696	4		455	736	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438145	56438145	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	217	692	4	ENST00000407977.2:c.848A>C	p.Gln283Pro	p.Q283P	ENST00000407977		283	cAg/cCg	7/10	NA	2	FACETS	0.964	0.899	1			1	INDETERMINATE	2	TRUE	NA	0.280683306807696	2		696	802	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120193	70120193	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	71	497	1	ENST00000245479.2:c.1195A>G	p.Thr399Ala	p.T399A	ENST00000245479	NM_000346.3	399	Acg/Gcg	3/3	0.189972619608656	5	FACETS	0.911	0.794	1	0.304	0.264	0.346	CLONAL	1	TRUE	2	0.280683306807696	5		498	789	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467734	66467734	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	17	285	0	ENST00000273854.3:c.535G>T	p.Ala179Ser	p.A179S	ENST00000273854	NM_004439.5	179	Gcc/Tcc	3/18	0.271010498441479	2	FACETS	0.382	0.285	0.498	0.191	0.142	0.249	SUBCLONAL	1	TRUE	0	0.280683306807696	2		285	317	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176662833	176662833	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	26	331	0	ENST00000439151.2:c.3808G>T	p.Glu1270Ter	p.E1270*	ENST00000439151	NM_022455.4	1270	Gag/Tag	6/23	0.271010498441479	2	FACETS	0.49	0.388	0.607	0.245	0.194	0.304	SUBCLONAL	1	TRUE	0	0.280683306807696	2		331	378	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845610	128845610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748021309	NA	P-0026972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	114	338	0	ENST00000249373.3:c.907C>T	p.Leu303Phe	p.L303F	ENST00000249373	NM_005631.4	303	Ctt/Ttt	4/12	0.189972619608656	5	FACETS	1	0.965	1	0.762	0.689	0.838	CLONAL	2	TRUE	2	0.280683306807696	5		338	505	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0026973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	97	541	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.938	0.838	1	0.938	0.838	1	CLONAL	1	TRUE	1	0.351768189547625	2		541	588	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692901	89692901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786204929	NA	P-0026973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	210	536	2	ENST00000371953.3:c.385G>A	p.Gly129Arg	p.G129R	ENST00000371953	NM_000314.4	129	Gga/Aga	5/9	0.351768189547625	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.351768189547625	2		538	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0026973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	148	644	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.351300563162611	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.351768189547625	1		644	687	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0026973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	65	344	2	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	0.351300563162611	1	FACETS	0.858	0.748	0.975	0.858	0.748	0.975	CLONAL	1	TRUE	0	0.351768189547625	1		346	355	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573312	41573312	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763290593	NA	P-0026973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	147	835	1	ENST00000263253.7:c.5597C>T	p.Pro1866Leu	p.P1866L	ENST00000263253	NM_001429.3	1866	cCg/cTg	31/31	0.351300563162611	1	FACETS	0.89	0.813	0.97	0.89	0.813	0.97	CLONAL	1	TRUE	0	0.351768189547625	1		836	774	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913326	28913326	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs758430941	NA	P-0026973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	129	704	0	ENST00000282397.4:c.2467G>T	p.Ala823Ser	p.A823S	ENST00000282397	NM_002019.4	823	Gcc/Tcc	17/30	0.351768189547625	2	FACETS	0.887	0.804	0.974	0.443	0.402	0.487	CLONAL	1	TRUE	0	0.351768189547625	2		704	827	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211667	5211667	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	138	644	0	ENST00000357368.4:c.5168G>A	p.Cys1723Tyr	p.C1723Y	ENST00000357368	NM_002850.3	1723	tGt/tAt	33/38	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.351768189547625	2		644	710	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428411	49428411	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	83	639	0	ENST00000301067.7:c.10394G>C	p.Gly3465Ala	p.G3465A	ENST00000301067	NM_003482.3	3465	gGa/gCa	36/54	1	2	FACETS	0.765	0.673	0.863	0.765	0.673	0.863	SUBCLONAL	1	TRUE	1	0.221722853677143	2		639	979	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562768	95562768	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	63	369	0	ENST00000393063.1:c.4489G>T	p.Asp1497Tyr	p.D1497Y	ENST00000393063	NM_030621.3	1497	Gat/Tat	24/28	1	2	FACETS	0.905	0.782	1	0.905	0.782	1	CLONAL	1	TRUE	1	0.221722853677143	2		369	628	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659675	NA	P-0026974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	88	585	0	ENST00000269305.4:c.764T>C	p.Ile255Thr	p.I255T	ENST00000269305	NM_001126112.2	255	aTc/aCc	7/11	0.19818258008935	1	FACETS	0.803	0.71	0.902	0.803	0.71	0.902	CLONAL	1	TRUE	0	0.221722853677143	1		585	879	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242442	55242443	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTAAAATTCCCGTCGCTA	novel	NA	P-0026974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	100	504	0	ENST00000275493.2:c.2214_2231dup	p.Ile740_Lys745dup	p.I740_K745dup	ENST00000275493	NM_005228.3	740	gtt/gTTAAAATTCCCGTCGCTAtt	19/28	0.221722853677143	3	FACETS	0.921	0.821	1	0.46	0.41	0.514	CLONAL	1	TRUE	1	0.221722853677143	3		504	1088	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0026975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	1716	519	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.471075271023157	19	FACETS	0.98	0.965	0.995			1	CLONAL	16	TRUE	NA	0.471075271023157	19		519	2325	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120802559	120802559	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0026975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	88	521	0	ENST00000257552.2:c.268-1G>A		p.X90_splice	ENST00000257552	NM_002442.3	90			0.36300004173899	3	FACETS	0.696	0.617	0.781	0.232	0.205	0.261	SUBCLONAL	1	TRUE	0	0.471075271023157	3		521	663	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100181	30100181	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	74	433	1	ENST00000331968.5:c.1439C>T	p.Ser480Leu	p.S480L	ENST00000331968	NM_002742.2	480	tCa/tTa	10/18	0.36300004173899	3	FACETS	0.569	0.498	0.646	0.19	0.166	0.216	SUBCLONAL	1	TRUE	0	0.471075271023157	3		434	682	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165699	47165699	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	26	401	0	ENST00000409792.3:c.427C>G	p.His143Asp	p.H143D	ENST00000409792	NM_014159.6	143	Cat/Gat	3/21	0.398779361629199	2	FACETS	0.262	0.207	0.325	0.131	0.103	0.163	SUBCLONAL	1	TRUE	0	0.471075271023157	2		401	421	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679454	30679454	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	89	508	0	ENST00000376406.3:c.2118G>T	p.Gln706His	p.Q706H	ENST00000376406	NM_014641.2	706	caG/caT	6/15	0.280742466827098	4	FACETS	0.678	0.6	0.761	0.339	0.3	0.381	INDETERMINATE	1	TRUE	2	0.471075271023157	4		508	820	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890174	76890174	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	23	195	0	ENST00000373344.5:c.4720del	p.Cys1574AlafsTer6	p.C1574Afs*6	ENST00000373344	NM_000489.3	1574	Tgc/gc	17/35	0.471075271023157	2	FACETS	0.223	0.174	0.281			1	SUBCLONAL	1	TRUE	NA	0.471075271023157	2		195	437	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860063	152860067	+	frameshift_variant	Frame_Shift_Del	DEL	CACTG	CACTG	-	novel	NA	P-0026975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	25	254	0	ENST00000406277.2:c.361_365del	p.Gln121Ter	p.Q121*	ENST00000406277	NM_152274.4	121	CAGTGt/t	5/7	0.471075271023157		FACETS		0.185	0.294				SUBCLONAL	1	TRUE	NA	0.471075271023157	2		254	451	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0026986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	53	278	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.796	0.681	0.922	0.796	0.681	0.922	CLONAL	1	TRUE	1	0.326248085575109	2		278	408	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0026986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	106	524	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	0.326248085575109	2		524	484	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0026986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	85	371	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.981	0.87	1	0.981	0.87	1	CLONAL	1	TRUE	1	0.326248085575109	2		371	531	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70441157	70441157	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	rs764225020	NA	P-0026986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	43	432	2	ENST00000373644.4:c.4832del	p.Asn1611ThrfsTer13	p.N1611Tfs*13	ENST00000373644	NM_030625.2	1609	gAa/ga	9/12	1	2	FACETS	0.45	0.376	0.532	0.45	0.376	0.532	SUBCLONAL	1	TRUE	1	0.326248085575109	2		434	586	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717630	89717630	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554825168	NA	P-0026986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	84	414	0	ENST00000371953.3:c.655C>T	p.Gln219Ter	p.Q219*	ENST00000371953	NM_000314.4	219	Cag/Tag	7/9	1	2	FACETS	0.918	0.812	1	0.918	0.812	1	CLONAL	1	TRUE	1	0.326248085575109	2		414	561	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0026986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	105	461	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.326248085575109	2		461	611	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0026986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	104	478	0	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	1	2	FACETS	0.863	0.773	0.958	0.863	0.773	0.958	CLONAL	1	TRUE	1	0.326248085575109	2		478	739	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466019	69466019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	179	862	0	ENST00000227507.2:c.857C>T	p.Thr286Ile	p.T286I	ENST00000227507	NM_053056.2	286	aCa/aTa	5/5	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.326248085575109	2		862	1057	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115780	8115780	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	150	654	0	ENST00000346208.3:c.1131del	p.Val378CysfsTer26	p.V378Cfs*26	ENST00000346208		376	Aaa/aa	6/6	1	2	FACETS	0.925	0.845	1	0.925	0.845	1	CLONAL	1	TRUE	1	0.326248085575109	2		654	994	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664651	138664651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	14	72	0	ENST00000330315.3:c.914C>T	p.Pro305Leu	p.P305L	ENST00000330315	NM_023067.3	305	cCg/cTg	1/1	1	2	FACETS	0.485	0.351	0.645	0.485	0.351	0.645	SUBCLONAL	1	TRUE	1	0.326248085575109	2		72	177	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	136	819	1	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.83	0.754	0.911	0.83	0.754	0.911	CLONAL	1	TRUE	1	0.326248085575109	2		820	1004	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748356	43748356	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	169	717	0	ENST00000382044.4:c.2450A>G	p.Tyr817Cys	p.Y817C	ENST00000382044	NM_001141980.1	817	tAt/tGt	12/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.326248085575109	2		717	907	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226560	1226560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1330230723	NA	P-0026986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	152	612	2	ENST00000326873.7:c.1216G>A	p.Ala406Thr	p.A406T	ENST00000326873	NM_000455.4	406	Gcg/Acg	9/10	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.326248085575109	2		614	909	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214094	36214094	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253599925	NA	P-0026986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	200	816	1	ENST00000222270.7:c.2920C>T	p.Arg974Cys	p.R974C	ENST00000222270	NM_014727.1	974	Cgt/Tgt	6/37	1	2	FACETS	0.946	0.875	1	0.946	0.875	1	CLONAL	1	TRUE	1	0.326248085575109	2		817	1296	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457226	25457227	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0026986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	158	670	0	ENST00000264709.3:c.2660_2661del	p.Arg887ThrfsTer33	p.R887Tfs*33	ENST00000264709	NM_175629.2	887	aGA/a	23/23	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.326248085575109	2		670	960	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591129	67591130	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAGACG	novel	NA	P-0026986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	64	373	0	ENST00000274335.5:c.1724_1729dup	p.Lys575_Thr576dup	p.K575_T576dup	ENST00000274335		575	-/AAGACG	12/15	1	2	FACETS	0.864	0.75	0.987	0.864	0.75	0.987	CLONAL	1	TRUE	1	0.326248085575109	2		373	454	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270595	98270595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217844666	NA	P-0026986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	28	68	0	ENST00000331920.6:c.49G>A	p.Gly17Ser	p.G17S	ENST00000331920	NM_000264.3	17	Ggc/Agc	1/24	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.326248085575109	2		68	156	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220488	1220488	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	218	670	0	ENST00000326873.7:c.581A>G	p.Asp194Gly	p.D194G	ENST00000326873	NM_000455.4	194	gAc/gGc	4/10	0.498191671683331	1	FACETS	0.981	0.917	1	0.981	0.917	1	CLONAL	1	TRUE	0	0.506032808262455	1		670	656	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026096	71026096	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	191	383	0	ENST00000318789.4:c.1526G>T	p.Trp509Leu	p.W509L	ENST00000318789	NM_032682.5	509	tGg/tTg	17/21	0.498191671683331	1	FACETS	0.966	0.898	1	0.966	0.898	1	CLONAL	1	TRUE	0	0.506032808262455	1		383	584	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874263	155874263	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1557960039	NA	P-0026987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	216	380	0	ENST00000368323.3:c.268A>G	p.Met90Val	p.M90V	ENST00000368323	NM_006912.5	90	Atg/Gtg	5/6	1	2	FACETS	0.973	0.906	1	0.973	0.906	1	CLONAL	1	TRUE	1	0.506032808262455	2		380	877	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226549740	226549740	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	181	592	0	ENST00000366794.5:c.2893G>T	p.Asp965Tyr	p.D965Y	ENST00000366794	NM_001618.3	965	Gat/Tat	22/23	1	2	FACETS	0.858	0.792	0.926	0.858	0.792	0.926	CLONAL	1	TRUE	1	0.506032808262455	2		592	834	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657391	29657391	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1135402879	NA	P-0026987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	205	639	1	ENST00000356175.3:c.5624C>G	p.Ser1875Ter	p.S1875*	ENST00000356175	NM_000267.3	1875	tCa/tGa	38/57	0.457506175399289	1	FACETS	0.897	0.835	0.959	0.897	0.835	0.959	CLONAL	1	TRUE	0	0.506032808262455	1		640	675	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59871029	59871029	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	165	532	0	ENST00000259008.2:c.1402T>A	p.Trp468Arg	p.W468R	ENST00000259008	NM_032043.2	468	Tgg/Agg	10/20	1	2	FACETS	0.896	0.824	0.97	0.896	0.824	0.97	CLONAL	1	TRUE	1	0.506032808262455	2		532	728	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18972882	18972882	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	293	678	0	ENST00000262803.5:c.2521T>G	p.Cys841Gly	p.C841G	ENST00000262803	NM_002911.3	841	Tgt/Ggt	18/24	0.498191671683331	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.506032808262455	1		678	802	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540397	23540434	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	GAGCATCCCGGCGGCCCCGCCTTGGCCTGAATGCACCC	GAGCATCCCGGCGGCCCCGCCTTGGCCTGAATGCACCC	-	novel	NA	P-0026987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	53	359	0	ENST00000380871.4:c.-32_6del		p.*11*	ENST00000380871	NM_006167.3	?-2/234		1/2	0.457506175399289	1	FACETS	0.559	0.48	0.644	0.559	0.48	0.644	SUBCLONAL	1	TRUE	0	0.506032808262455	1		359	280	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	172	528	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.221755291760436	3	FACETS	0.861	0.793	0.933	0.861	0.793	0.933	CLONAL	2	TRUE	1	0.235113959957916	3		529	949	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0026988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	324	686	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.235113959957916	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.235113959957916	2		686	1170	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0026988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	257	564	1	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	0.235113959957916	5	FACETS	0.905	0.847	0.965	0.905	0.847	0.965	CLONAL	3	TRUE	2	0.235113959957916	5		565	1089	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639726	3639726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763524714	NA	P-0026988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1523	185	850	2	ENST00000294008.3:c.3913G>A	p.Ala1305Thr	p.A1305T	ENST00000294008	NM_032444.2	1305	Gca/Aca	12/15	0.221755291760436	3	FACETS	1	0.942	1	0.515	0.473	0.558	CLONAL	1	TRUE	1	0.235113959957916	3		852	1708	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480529	57480529	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	72	370	1	ENST00000371085.3:c.524C>A	p.Ala175Asp	p.A175D	ENST00000371085	NM_000516.4	175	gCc/gAc	6/13	0.214012472238722	4	FACETS	0.886	0.772	1	0.443	0.386	0.505	CLONAL	1	TRUE	2	0.235113959957916	4		371	854	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265762	41266317	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAA	TGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAA	-	novel	NA	P-0026988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	35	35	0	ENST00000349496.5:c.13+191_241+74del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.235113959957916	2	FACETS	1	0.846	1	1	0.957	1	CLONAL	3	TRUE	0	0.235113959957916	2		35	99	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350164	81350164	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0026988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	41	341	0	ENST00000222390.5:c.1169-1G>T		p.X390_splice	ENST00000222390	NM_000601.4	390			0.221755291760436	3	FACETS	0.64	0.532	0.76	0.32	0.266	0.38	SUBCLONAL	1	TRUE	1	0.235113959957916	3		341	609	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0026989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	131	344	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.327090666851382	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.33171658363134	1		345	639	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216476	108216477	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587782558	NA	P-0026989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	64	203	1	ENST00000278616.4:c.8432dup	p.Ser2812ValfsTer3	p.S2812Vfs*3	ENST00000278616	NM_000051.3	2809	caa/cAaa	58/63	1	2	FACETS	0.982	0.854	1	0.982	0.854	1	CLONAL	1	TRUE	1	0.33171658363134	2		204	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0026989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	269	938	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.327090666851382	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.33171658363134	1		938	1294	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125088	46125089	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0026989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	112	261	0	ENST00000334344.6:c.277dup	p.Tyr93LeufsTer18	p.Y93Lfs*18	ENST00000334344	NM_152641.2	92	tat/taTt	3/21	0.33171658363134	2	FACETS	0.984	0.895	1	0.984	0.895	1	CLONAL	2	TRUE	0	0.33171658363134	2		261	343	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986656	36986657	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	28	89	0	ENST00000354822.5:c.1032dup	p.Ala345ArgfsTer94	p.A345Rfs*94	ENST00000354822	NM_001079668.2	344	-/C	3/3	0.327090666851382	1	FACETS	1	0.827	1	1	0.827	1	CLONAL	1	TRUE	0	0.33171658363134	1		89	138	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870055	40870055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	104	473	0	ENST00000428826.2:c.962G>A	p.Arg321His	p.R321H	ENST00000428826		321	cGc/cAc	10/21	1	2	FACETS	0.79	0.707	0.878	0.79	0.707	0.878	SUBCLONAL	1	TRUE	1	0.33171658363134	2		473	794	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449521	31449521	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	57	238	0	ENST00000344624.3:c.2688del	p.Met897Ter	p.M897*	ENST00000344624		896	gcC/gc	19/33	1	2	FACETS	0.737	0.634	0.85	0.737	0.634	0.85	SUBCLONAL	1	TRUE	1	0.33171658363134	2		238	466	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	86	528	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.394340409492078	1	FACETS	0.37	0.328	0.414	0.37	0.328	0.414	SUBCLONAL	1	TRUE	0	0.617487142292673	1		529	521	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0026990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	82	372	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.519	0.458	0.583	0.519	0.458	0.583	SUBCLONAL	1	TRUE	1	0.617487142292673	2		372	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579321	7579322	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs587780067	NA	P-0026990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	178	691	0	ENST00000269305.4:c.365_366del	p.Val122AspfsTer26	p.V122Dfs*26	ENST00000269305	NM_001126112.2	122	gTG/g	4/11	0.331154012173317	1	FACETS	0.515	0.475	0.556	0.515	0.475	0.556	INDETERMINATE	1	TRUE	0	0.617487142292673	1		691	774	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358955	81358955	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs549654942	NA	P-0026990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	79	593	1	ENST00000222390.5:c.1006G>A	p.Glu336Lys	p.E336K	ENST00000222390	NM_000601.4	336	Gag/Aag	8/18	1	2	FACETS	0.37	0.325	0.418	0.37	0.325	0.418	SUBCLONAL	1	TRUE	1	0.617487142292673	2		594	692	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623903	28623903	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1707	97	473	0	ENST00000241453.7:c.751C>T	p.Gln251Ter	p.Q251*	ENST00000241453	NM_004119.2	251	Caa/Taa	7/24	0.617487142292673	11	FACETS	0.658	0.584	0.738			1	SUBCLONAL	1	TRUE	NA	0.617487142292673	11		473	1804	SUCCESS
APC	324	MSKCC	GRCh37	5	112174031	112174032	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0026990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	48	410	0	ENST00000257430.4:c.2744_2745del	p.Val915AspfsTer3	p.V915Dfs*3	ENST00000257430	NM_000038.5	914	TGt/t	16/16	1	2	FACETS	0.328	0.277	0.384	0.328	0.277	0.384	SUBCLONAL	1	TRUE	1	0.617487142292673	2		410	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0026993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	113	570	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.169082867593379	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.17	1		570	1030	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664448	138664448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	78	519	2	ENST00000330315.3:c.1117C>T	p.Arg373Cys	p.R373C	ENST00000330315	NM_023067.3	373	Cgc/Tgc	1/1	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.17	2		521	856	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578490	7578490	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	168	745	1	ENST00000269305.4:c.440T>A	p.Val147Asp	p.V147D	ENST00000269305	NM_001126112.2	147	gTt/gAt	5/11	0.358699959808839	1	FACETS	0.808	0.743	0.877	0.808	0.743	0.877	CLONAL	1	TRUE	0	0.358699959808839	1		746	951	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476283	88476283	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	423	684	0	ENST00000360948.2:c.1849T>A	p.Phe617Ile	p.F617I	ENST00000360948	NM_001012338.2	617	Ttt/Att	15/19	1	2	FACETS	0.94	0.899	0.981	0.94	0.899	0.981	CLONAL	1	TRUE	1	0.919227299206886	2		684	979	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634812	158634812	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	268	439	0	ENST00000263640.3:c.374G>C	p.Gly125Ala	p.G125A	ENST00000263640	NM_001105.4	125	gGc/gCc	5/11	0.919227299206886	2	FACETS	0.948	0.897	1	0.474	0.448	0.5	CLONAL	1	TRUE	0	0.919227299206886	2		439	615	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191316	185191316	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	429	547	0	ENST00000265026.3:c.2197C>G	p.Leu733Val	p.L733V	ENST00000265026	NM_004721.4	733	Ctt/Gtt	11/14	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.919227299206886	2		547	891	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971169	21971176	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCAGCT	CAGCAGCT	-	novel	NA	P-0027006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	608	538	0	ENST00000304494.5:c.182_189del	p.Glu61AlafsTer56	p.E61Afs*56	ENST00000304494	NM_000077.4	61	gAGCTGCTG/g	2/3	0.919227299206886	2	FACETS	0.986	0.97	1	0.986	0.97	1	CLONAL	2	TRUE	0	0.919227299206886	2		538	671	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0027008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	31	397	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.979	0.79	1	0.979	0.79	1	CLONAL	1	TRUE	1	0.1	2		397	633	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95579529	95579529	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	32	353	0	ENST00000393063.1:c.1940C>T	p.Thr647Ile	p.T647I	ENST00000393063	NM_030621.3	647	aCt/aTt	13/28	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.1	2		353	479	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220443	1220444	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1131690939	NA	P-0027008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1218	65	618	0	ENST00000326873.7:c.540dup	p.Asn181GlufsTer85	p.N181Efs*85	ENST00000326873	NM_000455.4	179	ccg/ccGg	4/10	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.1	2		618	1283	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610541	10610541	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1202	86	595	1	ENST00000171111.5:c.169del	p.Glu57ArgfsTer11	p.E57Rfs*11	ENST00000171111	NM_203500.1	57	Gag/ag	2/6	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.1	2		596	1288	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175850	24175850	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	62	552	0	ENST00000263121.7:c.1078G>A	p.Glu360Lys	p.E360K	ENST00000263121	NM_003073.3	360	Gag/Aag	8/9	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.1	2		552	1205	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712516	52712516	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	57	406	3	ENST00000394830.3:c.236G>A	p.Arg79Lys	p.R79K	ENST00000394830	NM_018313.4	79	aGa/aAa	3/30	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.1	2		409	878	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0027010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	190	480	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.3	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.26	3		480	760	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0027011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	115	541	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.786	0.714	0.861	0.786	0.714	0.861	SUBCLONAL	1	TRUE	1	0.715072304342434	2		541	409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0027011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	321	500	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.662794616344684	2	FACETS	0.877	0.841	0.912	0.877	0.841	0.912	CLONAL	2	TRUE	0	0.715072304342434	2		500	512	SUCCESS
FH	2271	MSKCC	GRCh37	1	241669450	241669450	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1131691239	NA	P-0027011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	108	273	1	ENST00000366560.3:c.757C>T	p.Gln253Ter	p.Q253*	ENST00000366560	NM_000143.3	253	Caa/Taa	6/10	0.683214147587311	4	FACETS	0.932	0.839	1	0.233	0.209	0.258	CLONAL	1	TRUE	0	0.715072304342434	4		274	556	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871837	12871837	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	118	342	0	ENST00000228872.4:c.554A>T	p.Glu185Val	p.E185V	ENST00000228872	NM_004064.3	185	gAg/gTg	2/3	1	2	FACETS	0.831	0.757	0.909	0.831	0.757	0.909	CLONAL	1	TRUE	1	0.715072304342434	2		342	397	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445961	49445961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1449395575	NA	P-0027011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	192	616	1	ENST00000301067.7:c.1505C>T	p.Pro502Leu	p.P502L	ENST00000301067	NM_003482.3	502	cCt/cTt	10/54	1	2	FACETS	0.909	0.846	0.973	0.909	0.846	0.973	CLONAL	1	TRUE	1	0.715072304342434	2		617	591	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281214	49281214	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	188	533	1	ENST00000282018.3:c.261C>A	p.Phe87Leu	p.F87L	ENST00000282018	NM_020377.2	87	ttC/ttA	1/1	0.66013480117218	2	FACETS	1	0.969	1	0.534	0.498	0.571	CLONAL	1	TRUE	0	0.715072304342434	2		534	492	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346978	89346978	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	114	324	0	ENST00000301030.4:c.5972C>A	p.Pro1991Gln	p.P1991Q	ENST00000301030	NM_001256183.1	1991	cCa/cAa	9/13	0.670307554294989	2	FACETS	0.966	0.881	1	0.483	0.44	0.527	CLONAL	1	TRUE	0	0.715072304342434	2		324	330	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881370	37881370	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	151	608	0	ENST00000269571.5:c.2562G>C	p.Lys854Asn	p.K854N	ENST00000269571		854	aaG/aaC	21/27	0.697456959998442	3	FACETS	0.811	0.743	0.882	0.405	0.371	0.441	CLONAL	1	TRUE	1	0.715072304342434	3		608	707	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459460	40459460	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	161	531	0	ENST00000345506.4:c.1721T>G	p.Phe574Cys	p.F574C	ENST00000345506	NM_003152.3	574	tTt/tGt	15/20	0.715072304342434	3	FACETS	0.846	0.777	0.917			1	CLONAL	1	TRUE	NA	0.715072304342434	3		531	723	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602757	10602757	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	367	604	0	ENST00000171111.5:c.821A>G	p.His274Arg	p.H274R	ENST00000171111	NM_203500.1	274	cAc/cGc	3/6	0.670307554294989	2	FACETS	0.865	0.832	0.899	0.865	0.832	0.899	CLONAL	2	TRUE	0	0.715072304342434	2		604	593	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731679	47731679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	81	343	0	ENST00000449228.1:c.113G>A	p.Arg38His	p.R38H	ENST00000449228	NM_001127240.2	38	cGc/cAc	2/4	0.715072304342434	3	FACETS	0.805	0.714	0.902	0.403	0.357	0.451	CLONAL	1	TRUE	1	0.715072304342434	3		343	382	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39234297	39234297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	135	402	0	ENST00000402219.2:c.2548G>A	p.Ala850Thr	p.A850T	ENST00000402219	NM_005633.3	850	Gct/Act	16/23	1	2	FACETS	0.944	0.867	1	0.944	0.867	1	CLONAL	1	TRUE	1	0.715072304342434	2		402	400	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149077	61149077	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	136	410	1	ENST00000295025.8:c.1267G>T	p.Gly423Cys	p.G423C	ENST00000295025	NM_002908.2	423	Ggc/Tgc	11/11	0.250962587773003	3	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.715072304342434	3		411	437	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043408	180043408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778806900	NA	P-0027011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	331	585	0	ENST00000261937.6:c.3178C>T	p.Arg1060Trp	p.R1060W	ENST00000261937	NM_182925.4	1060	Cgg/Tgg	23/30	NA	2	FACETS	0.924	0.888	0.959			1	INDETERMINATE	2	TRUE	NA	0.715072304342434	2		585	501	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92244481	92244481	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	81	269	0	ENST00000265734.4:c.954G>C	p.Gln318His	p.Q318H	ENST00000265734	NM_001259.6	318	caG/caC	8/8	1	2	FACETS	0.781	0.696	0.87	0.781	0.696	0.87	SUBCLONAL	1	TRUE	1	0.715072304342434	2		269	290	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955492	90955492	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	24	358	0	ENST00000265433.3:c.2173C>T	p.Gln725Ter	p.Q725*	ENST00000265433	NM_002485.4	725	Cag/Tag	14/16	0.250962587773003	3	FACETS	0.221	0.172	0.276			1	INDETERMINATE	1	TRUE	NA	0.715072304342434	3		358	413	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500833	8500833	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0027011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	123	391	0	ENST00000356435.5:c.2049C>G	p.Tyr683Ter	p.Y683*	ENST00000356435		683	taC/taG	13/35	NA	2	FACETS	0.948	0.867	1			1	INDETERMINATE	1	TRUE	NA	0.715072304342434	2		391	363	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820290	139820290	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1265393184	NA	P-0027011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	175	538	0	ENST00000247668.2:c.1443G>T	p.Lys481Asn	p.K481N	ENST00000247668	NM_021138.3	481	aaG/aaT	11/11	0.634460157628198	4	FACETS	0.998	0.92	1			1	CLONAL	1	TRUE	NA	0.715072304342434	4		538	841	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692937	89692937	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500129	NA	P-0027011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	94	453	0	ENST00000371953.3:c.421C>T	p.His141Tyr	p.H141Y	ENST00000371953	NM_000314.4	141	Cat/Tat	5/9	0.670307554294989	2	FACETS	1	0.928	1	0.516	0.466	0.566	CLONAL	1	TRUE	0	0.715072304342434	2		453	255	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692940	89692941	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0027011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	99	439	0	ENST00000371953.3:c.424_425del	p.Arg142GlyfsTer37	p.R142Gfs*37	ENST00000371953	NM_000314.4	142	CGg/g	5/9	0.670307554294989	2	FACETS	1	0.96	1	0.552	0.501	0.603	CLONAL	1	TRUE	0	0.715072304342434	2		439	251	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155365	47155365	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0027013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	103	408	1	ENST00000409792.3:c.4715+1G>A		p.X1572_splice	ENST00000409792	NM_014159.6	1572			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		409	580	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440925	52440925	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1430317959	NA	P-0027013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	185	531	0	ENST00000460680.1:c.581-2A>G		p.X194_splice	ENST00000460680	NM_004656.3	194			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		531	734	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051572	30051605	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTTTGGTAGGTAATAAATCTGTATCAGATGAC	TTTTTTGGTAGGTAATAAATCTGTATCAGATGAC	-	novel	NA	P-0027013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	35	322	0	ENST00000338641.4:c.517-10_540del		p.X173_splice	ENST00000338641	NM_000268.3	173		6/16	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		322	352	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0027016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	301	574	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.326608847642739	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.326608847642739	2		576	838	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0027016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	79	226	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.326608847642739	2		226	445	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0027016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	82	259	2	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	1	2	FACETS	0.979	0.865	1	0.979	0.865	1	CLONAL	1	TRUE	1	0.326608847642739	2		261	513	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48586237	48586237	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs878854769	NA	P-0027016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	93	423	0	ENST00000342988.3:c.906G>A	p.Trp302Ter	p.W302*	ENST00000342988	NM_005359.5	302	tgG/tgA	8/12	0.326608847642739	1	FACETS	0.884	0.788	0.986	0.884	0.788	0.986	CLONAL	1	TRUE	0	0.326608847642739	1		423	539	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203493	108203493	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs140263969	NA	P-0027016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	77	209	0	ENST00000278616.4:c.7793G>T	p.Arg2598Leu	p.R2598L	ENST00000278616	NM_000051.3	2598	cGa/cTa	53/63	0.326608847642739	3	FACETS	1	0.938	1	0.553	0.487	0.624	CLONAL	1	TRUE	1	0.326608847642739	3		209	496	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007842	45007842	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	58	385	0	ENST00000558401.1:c.289G>A	p.Glu97Lys	p.E97K	ENST00000558401	NM_004048.2	97	Gag/Aag	2/4	1	2	FACETS	0.537	0.461	0.621	0.537	0.461	0.621	SUBCLONAL	1	TRUE	1	0.326608847642739	2		385	661	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556362	29556362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	108	412	2	ENST00000356175.3:c.2729G>A	p.Gly910Glu	p.G910E	ENST00000356175	NM_000267.3	910	gGa/gAa	21/57	0.326608847642739	2	FACETS	0.971	0.873	1	0.486	0.436	0.538	CLONAL	1	TRUE	0	0.326608847642739	2		414	681	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285227	212285227	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	111	454	3	ENST00000342788.4:c.3074C>A	p.Pro1025His	p.P1025H	ENST00000342788	NM_005235.2	1025	cCt/cAt	25/28	0.326608847642739	3	FACETS	1	0.931	1	0.522	0.469	0.578	CLONAL	1	TRUE	1	0.326608847642739	3		457	757	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374306	31374306	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0027016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	237	424	0	ENST00000328111.2:c.307-2A>G		p.X103_splice	ENST00000328111	NM_006892.3	103			0.326608847642739	6	FACETS	1	0.958	1	0.518	0.483	0.555	CLONAL	2	TRUE	2	0.326608847642739	6		424	1157	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43745226	43745228	+	missense_variant	Missense_Mutation	TNP	TAT	TAT	CAG	novel	NA	P-0027016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	77	428	0	ENST00000523873.1:c.139_141delinsCAG	p.Tyr47Gln	p.Y47Q	ENST00000523873		47	TAT/CAG	3/8	0.314735252187729	3	FACETS	0.607	0.531	0.688	0.202	0.177	0.23	SUBCLONAL	1	TRUE	0	0.326608847642739	3		428	904	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0027018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	162	583	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.269486109416607	4	FACETS	0.942	0.868	1	0.942	0.868	1	CLONAL	2	TRUE	2	0.390208992371519	4		583	613	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165084	47165084	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	41	290	1	ENST00000409792.3:c.1042G>T	p.Glu348Ter	p.E348*	ENST00000409792	NM_014159.6	348	Gaa/Taa	3/21	1	2	FACETS	0.685	0.573	0.808	0.685	0.573	0.808	SUBCLONAL	1	TRUE	1	0.390208992371519	2		291	307	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40742005	40742005	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	189	485	0	ENST00000392038.2:c.967G>C	p.Glu323Gln	p.E323Q	ENST00000392038	NM_001626.4	323	Gag/Cag	11/14	0.348153289137365	2	FACETS	0.965	0.9	1	0.965	0.9	1	CLONAL	2	TRUE	0	0.390208992371519	2		485	502	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219161	133219161	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	85	622	0	ENST00000320574.5:c.4883G>T	p.Gly1628Val	p.G1628V	ENST00000320574	NM_006231.2	1628	gGa/gTa	37/49	1	2	FACETS	0.618	0.546	0.695	0.618	0.546	0.695	SUBCLONAL	1	TRUE	1	0.390208992371519	2		622	705	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947628	48947628	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	62	269	0	ENST00000267163.4:c.1215C>A	p.Asn405Lys	p.N405K	ENST00000267163	NM_000321.2	405	aaC/aaA	12/27	1	2	FACETS	0.843	0.731	0.963	0.843	0.731	0.963	CLONAL	1	TRUE	1	0.390208992371519	2		269	377	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118339	17118339	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	258	558	0	ENST00000285071.4:c.1498del	p.Val500TrpfsTer13	p.V500Wfs*13	ENST00000285071	NM_144997.5	500	Gtg/tg	13/14	0.348135666126617	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.390208992371519	3		558	721	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602761	10602761	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	208	647	0	ENST00000171111.5:c.817T>C	p.Cys273Arg	p.C273R	ENST00000171111	NM_203500.1	273	Tgc/Cgc	3/6	0.348350814810356	2	FACETS	1	0.991	1	0.735	0.685	0.787	CLONAL	1	TRUE	0	0.390208992371519	2		647	725	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285875	39285875	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	89	429	0	ENST00000402219.2:c.284A>G	p.Glu95Gly	p.E95G	ENST00000402219	NM_005633.3	95	gAa/gGa	3/23	0.348135666126617	3	FACETS	0.909	0.807	1	0.454	0.403	0.509	CLONAL	1	TRUE	1	0.390208992371519	3		429	600	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62317148	62317148	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	287	587	0	ENST00000360203.5:c.1271A>G	p.His424Arg	p.H424R	ENST00000360203	NM_001283009.1	424	cAc/cGc	16/35	0.329000131189108	5	FACETS	0.886	0.836	0.938	0.886	0.836	0.938	CLONAL	3	TRUE	2	0.390208992371519	5		587	877	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098547	47098547	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	63	363	0	ENST00000409792.3:c.6727C>T	p.Gln2243Ter	p.Q2243*	ENST00000409792	NM_014159.6	2243	Cag/Tag	15/21	1	2	FACETS	0.726	0.629	0.83	0.726	0.629	0.83	SUBCLONAL	1	TRUE	1	0.390208992371519	2		363	445	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041432	47041433	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	159	223	0	ENST00000377604.3:c.1776_1777insT	p.Asn593Ter	p.N593*	ENST00000377604	NM_001204468.1	592	-/T	16/24	0.287363301057235	2	FACETS	1	0.978	1			1	CLONAL	2	TRUE	NA	0.390208992371519	2		223	361	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	46	315	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	FALSE	1	0.706648305553319	2		316	124	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245843	46245843	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	26	440	0	ENST00000334344.6:c.3937C>G	p.Gln1313Glu	p.Q1313E	ENST00000334344	NM_152641.2	1313	Caa/Gaa	15/21	1	2	FACETS	0.887	0.723	1	0.887	0.723	1	CLONAL	1	FALSE	1	0.706648305553319	2		440	83	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0027024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	409	583	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.454321185492183	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	0	0.452805343954592	3		583	699	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022465	12022465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	215	564	0	ENST00000396373.4:c.571C>T	p.Arg191Trp	p.R191W	ENST00000396373	NM_001987.4	191	Cgg/Tgg	5/8	0.454321185492183	4	FACETS	1	0.99	1	0.461	0.429	0.495	CLONAL	1	TRUE	1	0.452805343954592	4		564	997	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584585	189584585	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	128	373	0	ENST00000264731.3:c.881A>T	p.Gln294Leu	p.Q294L	ENST00000264731	NM_003722.4	294	cAg/cTg	6/14	0.454321185492183	4	FACETS	1	0.984	1	0.466	0.423	0.51	CLONAL	1	TRUE	1	0.452805343954592	4		373	588	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0027027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	54	626	0	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	1	2	FACETS	0.874	0.744	1	0.874	0.744	1	CLONAL	1	TRUE	1	0.15	2		626	824	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937671	36937671	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	97	627	2	ENST00000361632.4:c.1067G>A	p.Trp356Ter	p.W356*	ENST00000361632		356	tGg/tAg	8/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.15	2		629	1010	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651956	36651957	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	49	533	0	ENST00000244741.5:c.79dup	p.Ser27LysfsTer9	p.S27Kfs*9	ENST00000244741	NM_000389.4	26	-/A	2/3	1	2	FACETS	0.839	0.709	0.983	0.839	0.709	0.983	CLONAL	1	TRUE	1	0.15	2		533	779	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0027028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	61	226	1	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.162190674068025	3	FACETS	1	0.962	1	0.678	0.584	0.779	CLONAL	1	FALSE	1	0.169247000307156	3		227	577	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087513	27087513	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	105	497	0	ENST00000324856.7:c.2090del	p.Pro697ArgfsTer45	p.P697Rfs*45	ENST00000324856	NM_006015.4	696	tCc/tc	5/20	0.169247000307156	1	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	FALSE	0	0.169247000307156	1		497	1121	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40678619	40678619	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761636030	NA	P-0027028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	107	469	1	ENST00000249776.8:c.361G>A	p.Asp121Asn	p.D121N	ENST00000249776	NM_033286.3	121	Gat/Aat	3/9	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	FALSE	1	0.169247000307156	2		470	1247	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0027029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	22	635	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	1	2	FACETS	0.626	0.483	0.793	0.626	0.483	0.793	SUBCLONAL	1	TRUE	1	0.11	2		635	639	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0027029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	36	429	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.844	1	1	0.844	1	CLONAL	1	TRUE	1	0.11	2		429	634	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0027029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	20	409	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	0.914	0.698	1	0.914	0.698	1	CLONAL	1	TRUE	1	0.11	2		409	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057520000	NA	P-0027030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	83	647	0	ENST00000269305.4:c.452C>G	p.Pro151Arg	p.P151R	ENST00000269305	NM_001126112.2	151	cCc/cGc	5/11	1	2	FACETS	0.56	0.492	0.632	0.56	0.492	0.632	SUBCLONAL	1	TRUE	1	0.282683204215426	2		647	1049	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577035	7577036	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0027030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	54	604	0	ENST00000269305.4:c.902dup	p.Gly302ArgfsTer4	p.G302Rfs*4	ENST00000269305	NM_001126112.2	301	cca/ccCa	8/11	1	2	FACETS	0.429	0.365	0.499	0.429	0.365	0.499	SUBCLONAL	1	TRUE	1	0.282683204215426	2		604	891	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624275	89624275	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204910	NA	P-0027030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	54	370	1	ENST00000371953.3:c.49C>T	p.Gln17Ter	p.Q17*	ENST00000371953	NM_000314.4	17	Caa/Taa	1/9	1	2	FACETS	0.704	0.601	0.816	0.704	0.601	0.816	SUBCLONAL	1	TRUE	1	0.282683204215426	2		371	543	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78420988	78420988	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	52	380	0	ENST00000370768.2:c.1732G>T	p.Gly578Ter	p.G578*	ENST00000370768	NM_003902.3	578	Gga/Tga	18/20	1	2	FACETS	0.557	0.474	0.649	0.557	0.474	0.649	SUBCLONAL	1	TRUE	1	0.282683204215426	2		380	660	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713306	30713306	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	32	398	0	ENST00000295754.5:c.631G>T	p.Glu211Ter	p.E211*	ENST00000295754	NM_003242.5	211	Gag/Tag	4/7	1	2	FACETS	0.376	0.304	0.458	0.376	0.304	0.458	SUBCLONAL	1	TRUE	1	0.282683204215426	2		398	602	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974726	21975235	+	coding_sequence_variant,5_prime_UTR_variant	In_Frame_Del	DEL	GCCTCCAGCAGCGCCCGCACCTCCTCTACCCGACCCCGGGCCGCGGCCGTGGCCAGCCAGTCAGCCGAAGGCTCCATGCTGCTCCCCGCCGCCGGCTCCATGCTGCTCCCCGCCGCCCGCTGCCTGCTCTCCCCCTCTCCGCAGCCGCCGAGCGCACGCGGTCCGCCCCACCCTCTGGTGACCAGCCAGCCCCTCCTCTTTCTTCCTCCGGTGCTGGCGGAAGAGCCCCCTCCGACCCTGTCCCTCAAATCCTCTGGAGGGACCGCGGTATCTTTCCAGGCAAGGGGACGCCGTGAGCGAGTGCTCGGAGGAGGTGCTATTAACTCCGAGCACTTAGCGAATGTGGCACCCCTGAAGTCGCCCCAGGTTGGGTCTCCCCCGGGGGCACCAGCCGGAAGCAGCCCTCGCCAGAGCCAGCGTTGGCAAGGAAGGAGGACTGGGCTCCTCCCCACCTGCCCCCCACACCGCCCTCCGGCCTCCCTGCTCCCAGCCGCGCTCCCCCGCCTGCCA	GCCTCCAGCAGCGCCCGCACCTCCTCTACCCGACCCCGGGCCGCGGCCGTGGCCAGCCAGTCAGCCGAAGGCTCCATGCTGCTCCCCGCCGCCGGCTCCATGCTGCTCCCCGCCGCCCGCTGCCTGCTCTCCCCCTCTCCGCAGCCGCCGAGCGCACGCGGTCCGCCCCACCCTCTGGTGACCAGCCAGCCCCTCCTCTTTCTTCCTCCGGTGCTGGCGGAAGAGCCCCCTCCGACCCTGTCCCTCAAATCCTCTGGAGGGACCGCGGTATCTTTCCAGGCAAGGGGACGCCGTGAGCGAGTGCTCGGAGGAGGTGCTATTAACTCCGAGCACTTAGCGAATGTGGCACCCCTGAAGTCGCCCCAGGTTGGGTCTCCCCCGGGGGCACCAGCCGGAAGCAGCCCTCGCCAGAGCCAGCGTTGGCAAGGAAGGAGGACTGGGCTCCTCCCCACCTGCCCCCCACACCGCCCTCCGGCCTCCCTGCTCCCAGCCGCGCTCCCCCGCCTGCCA	-	novel	NA	P-0027030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	31	343	0				ENST00000304494	NM_000077.4	?-34/156		1/3	1	2	FACETS	0.528	0.427	0.643	0.528	0.427	0.643	SUBCLONAL	1	TRUE	1	0.282683204215426	2		343	415	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0027031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	129	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.26548475342076	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.26	3		509	493	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438566	52438566	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1553645164	NA	P-0027031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	50	367	0	ENST00000460680.1:c.1153C>T	p.Arg385Ter	p.R385*	ENST00000460680	NM_004656.3	385	Cga/Tga	12/17	0.271881724274548	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	0	0.26	1		367	309	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846068	68846070	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	novel	NA	P-0027031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	146	521	2	ENST00000261769.5:c.1043_1045del	p.Ala348del	p.A348del	ENST00000261769	NM_004360.3	347	GCT/-	8/16	0.266043232862028	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.26	2		523	526	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0027032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	22	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.121883630640256	3	FACETS	0.66	0.51	0.836	0.33	0.255	0.418	SUBCLONAL	1	TRUE	1	0.13	3		509	546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0027032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	12	417	0	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	1	2	FACETS	0.517	0.362	0.709	0.517	0.362	0.709	SUBCLONAL	1	TRUE	1	0.13	2		417	357	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11999013	11999013	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0027032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	14	272	0	ENST00000353533.5:c.513+2T>A		p.X171_splice	ENST00000353533	NM_003010.3	171			1	2	FACETS	0.928	0.671	1	0.928	0.671	1	CLONAL	1	TRUE	1	0.13	2		272	232	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0027033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	646	570	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.742423974115394	2	FACETS	0.984	0.962	1	0.984	0.962	1	CLONAL	2	TRUE	0	0.790709658324063	2		570	830	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603038	48603039	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCAGCAGCAGGCGGCTACTGCACAAGC	rs876660720	NA	P-0027033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	87	350	0	ENST00000342988.3:c.1349_1376dup	p.Ala460GlyfsTer43	p.A460Gfs*43	ENST00000342988	NM_005359.5	447	atg/aTGCAGCAGCAGGCGGCTACTGCACAAGCtg	11/12	0.762770976945641	1	FACETS	0.39	0.348	0.434	0.39	0.348	0.434	SUBCLONAL	1	TRUE	0	0.790709658324063	1		350	341	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0027033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1961	1778	556	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.790709658324063	6	FACETS	1	0.994	1			1	CLONAL	3	TRUE	NA	0.790709658324063	6		556	3739	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970977	21970978	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0027033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	372	595	0	ENST00000304494.5:c.380dup	p.Arg128ThrfsTer14	p.R128Tfs*14	ENST00000304494	NM_000077.4	127	gca/gcCa	2/3	0.549769657832318	1	FACETS	0.984	0.948	1	0.984	0.948	1	CLONAL	1	TRUE	0	0.790709658324063	1		595	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578189	7578189	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0027035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	937	583	0	ENST00000269305.4:c.660T>G	p.Tyr220Ter	p.Y220*	ENST00000269305	NM_001126112.2	220	taT/taG	6/11	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.814798228295267	2		583	1122	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467464	66467464	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773032839	NA	P-0027035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	158	335	1	ENST00000273854.3:c.805G>A	p.Asp269Asn	p.D269N	ENST00000273854	NM_004439.5	269	Gat/Aat	3/18	0.804803607755959	1	FACETS	0.901	0.848	0.953	0.901	0.848	0.953	CLONAL	1	TRUE	0	0.814798228295267	1		336	255	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870978	12870978	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	53	384	0	ENST00000228872.4:c.208del	p.Leu70Ter	p.L70*	ENST00000228872	NM_004064.3	69	Ccc/cc	1/3	1	2	FACETS	0.23	0.196	0.267	0.23	0.196	0.267	SUBCLONAL	1	TRUE	1	0.814798228295267	2		384	566	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138452	2138452	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	393	570	0	ENST00000219476.3:c.5265C>A	p.Cys1755Ter	p.C1755*	ENST00000219476	NM_000548.3	1755	tgC/tgA	42/42	0.814798228295267	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.814798228295267	1		570	549	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881629	111881630	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0027035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	290	589	0	ENST00000393256.3:c.307_308del	p.Arg103GlufsTer8	p.R103Efs*8	ENST00000393256	NM_006538.4	103	AGg/g	2/4	1	2	FACETS	0.906	0.856	0.956	0.906	0.856	0.956	CLONAL	1	TRUE	1	0.814798228295267	2		589	786	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685307	89685307	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs398123317	NA	P-0027036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	83	336	0	ENST00000371953.3:c.202T>A	p.Tyr68Asn	p.Y68N	ENST00000371953	NM_000314.4	68	Tac/Aac	3/9	0.41689128677531	1	FACETS	0.84	0.747	0.939	0.84	0.747	0.939	CLONAL	1	TRUE	0	0.41689128677531	1		336	375	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634842	158634842	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	74	328	0	ENST00000263640.3:c.344C>G	p.Pro115Arg	p.P115R	ENST00000263640	NM_001105.4	115	cCt/cGt	5/11	1	2	FACETS	0.822	0.722	0.928	0.822	0.722	0.928	CLONAL	1	TRUE	1	0.41689128677531	2		328	432	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112029222	112029222	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	25	356	0	ENST00000368678.4:c.346del	p.Glu116LysfsTer10	p.E116Kfs*10	ENST00000368678		116	Gaa/aa	5/13	1	2	FACETS	0.248	0.195	0.31	0.248	0.195	0.31	SUBCLONAL	1	TRUE	1	0.41689128677531	2		356	483	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6038842	6038842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	53	607	0	ENST00000265849.7:c.602G>A	p.Ser201Asn	p.S201N	ENST00000265849	NM_000535.5	201	aGt/aAt	6/15	1	2	FACETS	0.259	0.22	0.303	0.259	0.22	0.303	SUBCLONAL	1	TRUE	1	0.41689128677531	2		607	980	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139642	202139642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1351320412	NA	P-0027037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	77	359	1	ENST00000358485.4:c.803C>T	p.Ser268Leu	p.S268L	ENST00000358485	NM_001080125.1	268	tCg/tTg	6/9	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.326218090044241	2		360	388	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661126	227661126	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	89	544	1	ENST00000305123.5:c.2329C>A	p.Pro777Thr	p.P777T	ENST00000305123	NM_005544.2	777	Ccc/Acc	1/2	1	2	FACETS	0.884	0.785	0.99	0.884	0.785	0.99	CLONAL	1	TRUE	1	0.326218090044241	2		545	617	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348538	70348538	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	37	257	0	ENST00000374080.3:c.3445T>C	p.Cys1149Arg	p.C1149R	ENST00000374080		1149	Tgt/Cgt	24/45	1	1	FACETS	0.62	0.513	0.739	0.62	0.513	0.739	SUBCLONAL	1	TRUE	0	0.326218090044241	1		257	306	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78519468	78519468	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	50	508	2	ENST00000306801.3:c.43del	p.Glu15ArgfsTer17	p.E15Rfs*17	ENST00000306801	NM_020761.2	13	ctG/ct	1/34	0.221726706905727	0	FACETS	0.782	0.664	0.911			1	CLONAL	1	FALSE	0	0.221726706905727	0		510	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579386	7579386	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0027041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1192	96	672	0	ENST00000269305.4:c.301A>T	p.Lys101Ter	p.K101*	ENST00000269305	NM_001126112.2	101	Aaa/Taa	4/11	1	2	FACETS	0.785	0.697	0.879	0.785	0.697	0.879	SUBCLONAL	1	TRUE	1	0.19	2		672	1288	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420291	88420291	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	177	517	0	ENST00000360948.2:c.2395G>T	p.Val799Leu	p.V799L	ENST00000360948	NM_001012338.2	799	Gtg/Ttg	19/19	0.182689097370622	3	FACETS	0.802	0.737	0.87	0.802	0.737	0.87	CLONAL	2	TRUE	1	0.19	3		517	1272	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938193	36938193	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	122	664	0	ENST00000361632.4:c.768G>C	p.Trp256Cys	p.W256C	ENST00000361632		256	tgG/tgC	6/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.19	2		664	1122	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068881	30068881	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	44	588	0	ENST00000331968.5:c.2048C>G	p.Thr683Arg	p.T683R	ENST00000331968	NM_002742.2	683	aCg/aGg	14/18	1	2	FACETS	0.534	0.446	0.631	0.534	0.446	0.631	SUBCLONAL	1	TRUE	1	0.19	2		588	868	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786036	3786036	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0027041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	85	580	0	ENST00000262367.5:c.4728+1G>A		p.X1576_splice	ENST00000262367	NM_004380.2	1576			0.182689097370622	3	FACETS	0.848	0.747	0.956	0.424	0.373	0.478	CLONAL	1	TRUE	1	0.19	3		580	1156	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610129	10610129	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1298	117	629	0	ENST00000171111.5:c.581T>G	p.Ile194Ser	p.I194S	ENST00000171111	NM_203500.1	194	aTt/aGt	2/6	1	2	FACETS	0.87	0.782	0.964	0.87	0.782	0.964	CLONAL	1	TRUE	1	0.19	2		629	1415	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223799	36223799	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1440	103	745	0	ENST00000222270.7:c.6349G>T	p.Val2117Leu	p.V2117L	ENST00000222270	NM_014727.1	2117	Gtg/Ttg	28/37	1	2	FACETS	0.703	0.626	0.785	0.703	0.626	0.785	SUBCLONAL	1	TRUE	1	0.19	2		745	1543	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0027042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	80	559	3	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.15	2		562	983	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023008	27023010	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs587779737	NA	P-0027042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	10	99	0	ENST00000324856.7:c.126_128del	p.Ala45del	p.A45del	ENST00000324856	NM_006015.4	38	gaGGCg/gag	1/20	1	2	FACETS	0.926	0.629	1	0.926	0.629	1	CLONAL	1	TRUE	1	0.15	2		99	144	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141534	11141534	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	35	658	0	ENST00000358026.2:c.3511G>A	p.Val1171Met	p.V1171M	ENST00000358026	NM_001128849.1	1171	Gtg/Atg	25/36	1	2	FACETS	0.712	0.582	0.859	0.712	0.582	0.859	SUBCLONAL	1	TRUE	1	0.15	2		658	655	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578541	7578541	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1131691013	NA	P-0027042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	63	751	0	ENST00000269305.4:c.389T>C	p.Leu130Pro	p.L130P	ENST00000269305	NM_001126112.2	130	cTc/cCc	5/11	0.200385682658559	1	FACETS	0.845	0.728	0.971	0.845	0.728	0.971	CLONAL	1	TRUE	0	0.15	1		751	920	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540442	187540442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs183723851	NA	P-0027043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	166	416	0	ENST00000441802.2:c.7298A>G	p.Asn2433Ser	p.N2433S	ENST00000441802	NM_005245.3	2433	aAt/aGt	10/27	1	2	FACETS	0.969	0.891	1	0.969	0.891	1	CLONAL	1	TRUE	1	0.45035338533854	2		416	761	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650414	12650417	+	protein_altering_variant	In_Frame_Del	DEL	CTTC	CTTC	A	novel	NA	P-0027043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	91	373	0	ENST00000251849.4:c.429_432delinsT	p.Lys144del	p.K144del	ENST00000251849	NM_002880.3	143	cgGAAG/cgT	5/17	1	2	FACETS	0.537	0.476	0.601	0.537	0.476	0.601	SUBCLONAL	1	TRUE	1	0.45035338533854	2		373	753	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0027044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	126	321	2	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.87	0.793	0.95	0.87	0.793	0.95	CLONAL	1	TRUE	1	0.61	2		323	475	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0027044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	121	583	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.989	0.902	1	0.989	0.902	1	CLONAL	1	TRUE	1	0.61	2		583	401	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164163	108164163	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs869312755	NA	P-0027044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	105	337	0	ENST00000278616.4:c.4735C>T	p.Gln1579Ter	p.Q1579*	ENST00000278616	NM_000051.3	1579	Caa/Taa	31/63	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.61	2		337	338	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021142	31021142	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	168	691	0	ENST00000375687.4:c.1141G>A	p.Glu381Lys	p.E381K	ENST00000375687	NM_015338.5	381	Gaa/Aaa	12/13	1	2	FACETS	0.79	0.728	0.854	0.79	0.728	0.854	SUBCLONAL	1	TRUE	1	0.61	2		691	697	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158208	106158208	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748334095	NA	P-0027044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	91	439	7	ENST00000380013.4:c.3109G>A	p.Ala1037Thr	p.A1037T	ENST00000380013	NM_001127208.2	1037	Gcc/Acc	3/11	1	2	FACETS	0.709	0.633	0.789	0.709	0.633	0.789	SUBCLONAL	1	TRUE	1	0.61	2		446	421	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0027046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	14	556	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	1	2	FACETS	1	0.812	1	1	0.926	1	CLONAL	2	TRUE	1	0.29	2		556	44	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793385	242793385	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750496363	NA	P-0027046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	13	769	1	ENST00000334409.5:c.692G>A	p.Arg231Gln	p.R231Q	ENST00000334409	NM_005018.2	231	cGa/cAa	5/5	1	2	FACETS	0.897	0.647	1	0.897	0.647	1	CLONAL	1	TRUE	1	0.29	2		770	100	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0027047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	660	693	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.845631250929542	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.858420010369436	2		693	756	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46251038	46251038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1348905384	NA	P-0027047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1238	435	498	0	ENST00000371998.3:c.47G>A	p.Arg16Gln	p.R16Q	ENST00000371998		16	cGa/cAa	3/23	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.858420010369436	NA		498	1673	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622457	28622457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751562024	NA	P-0027047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	442	642	0	ENST00000241453.7:c.1160G>A	p.Arg387Gln	p.R387Q	ENST00000241453	NM_004119.2	387	cGa/cAa	9/24	0.747367774471848	4	FACETS	0.976	0.936	1	0.976	0.936	1	CLONAL	2	TRUE	2	0.858420010369436	4		642	980	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692790	89692790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	246	384	0	ENST00000371953.3:c.274G>A	p.Asp92Asn	p.D92N	ENST00000371953	NM_000314.4	92	Gac/Aac	5/9	0.839229831492222	3	FACETS	0.939	0.892	0.986	0.939	0.892	0.986	CLONAL	2	TRUE	1	0.858420010369436	3		384	436	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638725	176638725	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	562	723	1	ENST00000439151.2:c.3325C>A	p.His1109Asn	p.H1109N	ENST00000439151	NM_022455.4	1109	Cat/Aat	5/23	0.858420010369436	2	FACETS	0.992	0.972	1	0.992	0.972	1	CLONAL	2	TRUE	0	0.858420010369436	2		724	660	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41558779	41558779	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	342	538	0	ENST00000263253.7:c.3724G>A	p.Glu1242Lys	p.E1242K	ENST00000263253	NM_001429.3	1242	Gaa/Aaa	21/31	0.446665913259193	6	FACETS	1	0.989	1	0.769	0.73	0.809	INDETERMINATE	2	TRUE	3	0.858420010369436	6		538	938	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932158	36932158	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	709	543	0	ENST00000361632.4:c.2311G>C	p.Asp771His	p.D771H	ENST00000361632		771	Gac/Cac	16/16	0.858420010369436	5	FACETS	0.982	0.952	1	0.982	0.952	1	CLONAL	3	TRUE	2	0.858420010369436	5		543	1283	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425670	49425679	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCCTGTCT	GGGCCTGTCT	-	novel	NA	P-0027047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	521	600	0	ENST00000301067.7:c.12809_12818del	p.Gln4270ProfsTer5	p.Q4270Pfs*5	ENST00000301067	NM_003482.3	4270	cAGACAGGCCCc/cc	39/54	0.747367774471848	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.858420010369436	4		600	1121	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37871782	37871782	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	522	698	0	ENST00000269571.5:c.1306C>G	p.Leu436Val	p.L436V	ENST00000269571		436	Ctg/Gtg	11/27	0.858420010369436	4	FACETS	0.906	0.87	0.942	0.453	0.435	0.471	CLONAL	2	TRUE	0	0.858420010369436	4		698	1247	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282089	38282089	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	627	720	0	ENST00000425967.3:c.967C>A	p.His323Asn	p.H323N	ENST00000425967	NM_001174067.1	323	Cac/Aac	8/19	0.560302909041265	3	FACETS	0.766	0.739	0.793			1	SUBCLONAL	2	TRUE	NA	0.858420010369436	3		720	1363	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300846	137300846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	291	700	4	ENST00000481739.1:c.491G>A	p.Arg164His	p.R164H	ENST00000481739	NM_002957.4	164	cGc/cAc	4/10	0.858420010369436	3	FACETS	0.958	0.903	1	0.479	0.451	0.508	CLONAL	1	TRUE	1	0.858420010369436	3		704	1011	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0027048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	303	574	0	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.469416621159405	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.469416621159405	1		574	903	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499483	89499483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1426641543	NA	P-0027048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	62	448	0	ENST00000336596.2:c.2653C>T	p.Pro885Ser	p.P885S	ENST00000336596	NM_005233.5	885	Ccc/Tcc	15/17	0.362014394178872	4	FACETS	0.377	0.324	0.434			1	SUBCLONAL	1	TRUE	NA	0.469416621159405	4		448	1030	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813092	76813092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	73	524	0	ENST00000373344.5:c.6529G>A	p.Asp2177Asn	p.D2177N	ENST00000373344	NM_000489.3	2177	Gat/Aat	30/35	1	2	FACETS	0.467	0.408	0.531	0.467	0.408	0.531	SUBCLONAL	1	TRUE	1	0.469416621159405	2		524	666	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465638	8465638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781067774	NA	P-0027048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	35	425	0	ENST00000356435.5:c.3542G>A	p.Arg1181His	p.R1181H	ENST00000356435		1181	cGt/cAt	21/35	0.469416621159405	1	FACETS	0.203	0.166	0.245	0.203	0.166	0.245	SUBCLONAL	1	TRUE	0	0.469416621159405	1		425	562	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727982	78727982	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	157	291	0	ENST00000306801.3:c.827G>T	p.Arg276Leu	p.R276L	ENST00000306801	NM_020761.2	276	cGc/cTc	6/34	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.469416621159405	2		291	573	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248085	98248085	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	194	515	1	ENST00000331920.6:c.466C>T	p.Gln156Ter	p.Q156*	ENST00000331920	NM_000264.3	156	Caa/Taa	3/24	0.469416621159405	1	FACETS	0.881	0.818	0.946	0.881	0.818	0.946	CLONAL	1	TRUE	0	0.469416621159405	1		516	718	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992258	72992258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1342834308	NA	P-0027048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	221	680	0	ENST00000268489.5:c.1787A>G	p.Asn596Ser	p.N596S	ENST00000268489	NM_006885.3	596	aAt/aGt	2/10	0.256970776561258	1	FACETS	0.576	0.535	0.619	0.576	0.535	0.619	INDETERMINATE	1	TRUE	0	0.469416621159405	1		680	1250	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025871	48025871	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	90	398	1	ENST00000234420.5:c.749T>A	p.Val250Asp	p.V250D	ENST00000234420	NM_000179.2	250	gTc/gAc	4/10	0.333720448111021	3	FACETS	0.756	0.672	0.846	0.378	0.336	0.423	SUBCLONAL	1	TRUE	1	0.469416621159405	3		399	626	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098933	178098933	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	145	345	0	ENST00000397062.3:c.112G>C	p.Asp38His	p.D38H	ENST00000397062	NM_006164.4	38	Gac/Cac	2/5	0.333720448111021	3	FACETS	1	0.983	1	0.643	0.589	0.699	CLONAL	1	TRUE	1	0.469416621159405	3		345	593	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100998	41100998	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs772057709	NA	P-0027048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	267	485	1	ENST00000373198.4:c.1358G>T	p.Arg453Leu	p.R453L	ENST00000373198	NM_133170.3	453	cGc/cTc	8/32	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.469416621159405	2		486	959	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462338	89462338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	62	530	0	ENST00000336596.2:c.1810G>A	p.Asp604Asn	p.D604N	ENST00000336596	NM_005233.5	604	Gac/Aac	10/17	0.362014394178872	4	FACETS	0.424	0.365	0.488			1	SUBCLONAL	1	TRUE	NA	0.469416621159405	4		530	916	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231120	142231120	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	314	437	0	ENST00000350721.4:c.4834A>C	p.Asn1612His	p.N1612H	ENST00000350721	NM_001184.3	1612	Aat/Cat	27/47	0.463728247477199	2	FACETS	0.924	0.877	0.971	0.924	0.877	0.971	CLONAL	2	TRUE	0	0.469416621159405	2		437	724	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928069	178928098	+	inframe_deletion	In_Frame_Del	DEL	TCATGGATTAGAAGATTTGCTGAACCCTAT	TCATGGATTAGAAGATTTGCTGAACCCTAT	-	novel	NA	P-0027048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	237	511	0	ENST00000263967.3:c.1348_1377del	p.His450_Ile459del	p.H450_I459del	ENST00000263967	NM_006218.2	449	ccTCATGGATTAGAAGATTTGCTGAACCCTATt/cct	8/21	0.469416621159405	6	FACETS	0.921	0.859	0.984			1	CLONAL	2	TRUE	NA	0.469416621159405	6		511	1063	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70350065	70350065	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0027048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	219	345	0	ENST00000374080.3:c.4047+1G>T		p.X1349_splice	ENST00000374080		1349			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.469416621159405	2		345	822	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179167	123179168	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0027048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	49	453	0	ENST00000218089.9:c.616_617delinsTT	p.Gly206Leu	p.G206L	ENST00000218089	NM_001042749.1	206	GGa/TTa	8/35	1	2	FACETS	0.421	0.356	0.492	0.421	0.356	0.492	SUBCLONAL	1	TRUE	1	0.469416621159405	2		453	496	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928100	178928100	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	241	463	0	ENST00000263967.3:c.1378G>A	p.Gly460Ser	p.G460S	ENST00000263967	NM_006218.2	460	Ggt/Agt	8/21	0.469416621159405	6	FACETS	1	0.98	1			1	CLONAL	2	TRUE	NA	0.469416621159405	6		463	896	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0027050-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	3028	487	2	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.3	22	FACETS	1	0.996	1			1	CLONAL	26	TRUE	NA	0.15	22		489	3823	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038867	47038867	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027050-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	70	915	1	ENST00000377604.3:c.874G>T	p.Glu292Ter	p.E292*	ENST00000377604	NM_001204468.1	292	Gag/Tag	9/24	0.0771100323170275	0	FACETS	0.948	0.825	1			1	INDETERMINATE	1	TRUE	0	0.15	0		916	837	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577567	7577637	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACACATGTAGTTGTAGTGGATGGTGGTACAGTCAGAGCCAACCTAGGAGATAACACAGGCCCAAGATGAGG	ACACATGTAGTTGTAGTGGATGGTGGTACAGTCAGAGCCAACCTAGGAGATAACACAGGCCCAAGATGAGG	-	novel	NA	P-0027050-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	50	776	0	ENST00000269305.4:c.673-29_714del		p.X225_splice	ENST00000269305	NM_001126112.2	225		7/11	1	2	FACETS	0.892	0.756	1	0.892	0.756	1	CLONAL	1	TRUE	1	0.15	2		776	747	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579346	7579346	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	297	653	0	ENST00000269305.4:c.341del	p.Leu114CysfsTer9	p.L114Cfs*9	ENST00000269305	NM_001126112.2	114	tTg/tg	4/11	0.582314105497393	1	FACETS	0.982	0.93	1	0.982	0.93	1	CLONAL	1	TRUE	0	0.582314105497393	1		653	736	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444048	49444059	+	inframe_deletion	In_Frame_Del	DEL	GGGCTGGGGGCG	GGGCTGGGGGCG	-	novel	NA	P-0027069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	205	469	1	ENST00000301067.7:c.3312_3323del	p.Ser1107_Pro1110del	p.S1107_P1110del	ENST00000301067	NM_003482.3	1104	ccCGCCCCCAGCCCt/cct	11/54	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.582314105497393	2		470	664	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41258501	41258501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	125	465	0	ENST00000357654.3:c.184C>T	p.Pro62Ser	p.P62S	ENST00000357654	NM_007294.3	62	Cct/Tct	4/23	0.582314105497393	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.582314105497393	1		465	291	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183794	10183794	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	173	676	0	ENST00000256474.2:c.264del	p.Trp88CysfsTer71	p.W88Cfs*71	ENST00000256474	NM_000551.3	88	tGg/tg	1/3	0.491127408453471	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.491127408453471	1		676	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578374	7578375	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0027075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	197	489	0	ENST00000269305.4:c.555_556del	p.Ser185ArgfsTer23	p.S185Rfs*23	ENST00000269305	NM_001126112.2	185	agCGat/agat	5/11	0.829903110593939	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.829903110593939	1		489	275	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805807	46805807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	151	498	1	ENST00000290295.7:c.149C>A	p.Pro50His	p.P50H	ENST00000290295	NM_006361.5	50	cCc/cAc	1/2	NA	2	FACETS	0.888	0.82	0.956			1	INDETERMINATE	1	TRUE	NA	0.829903110593939	2		499	410	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158626878	158626878	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0027075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	166	322	0	ENST00000263640.3:c.790+2T>G		p.X264_splice	ENST00000263640	NM_001105.4	264			0.830316352946118	3	FACETS	0.963	0.889	1	0.481	0.444	0.52	CLONAL	1	TRUE	1	0.829903110593939	3		322	588	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670718	134670718	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	161	452	0	ENST00000398015.3:c.629T>G	p.Met210Arg	p.M210R	ENST00000398015	NM_004441.4	210	aTg/aGg	3/16	0.77519808667064	3	FACETS	0.87	0.801	0.941	0.435	0.4	0.471	CLONAL	1	TRUE	1	0.829903110593939	3		452	631	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0027077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	108	601	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.18	2		603	846	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005896	69005896	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	47	504	0	ENST00000288368.4:c.2307A>T	p.Gln769His	p.Q769H	ENST00000288368	NM_024870.2	769	caA/caT	21/40	1	2	FACETS	0.635	0.534	0.746	0.635	0.534	0.746	SUBCLONAL	1	TRUE	1	0.18	2		504	823	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	158	528	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.387082068990431	3	FACETS	0.928	0.856	1	0.928	0.856	1	CLONAL	2	TRUE	1	0.387082068990431	3		529	525	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0027078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	53	283	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.989	0.85	1	0.989	0.85	1	CLONAL	1	TRUE	1	0.387082068990431	2		283	277	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911684	32911687	+	frameshift_variant	Frame_Shift_Del	DEL	AATT	AATT	-	rs80359375	NA	P-0027078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	91	373	1	ENST00000380152.3:c.3195_3198del	p.Asn1066LeufsTer10	p.N1066Lfs*10	ENST00000380152		1064	tcAATT/tc	11/27	0.387082068990431	4	FACETS	0.84	0.746	0.942	0.28	0.248	0.314	CLONAL	1	TRUE	1	0.387082068990431	4		374	776	SUCCESS
APC	324	MSKCC	GRCh37	5	112175350	112175351	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	46	190	0	ENST00000257430.4:c.4063dup	p.Ser1355PhefsTer20	p.S1355Ffs*20	ENST00000257430	NM_000038.5	1353	-/T	16/16	1	2	FACETS	0.837	0.709	0.976	0.837	0.709	0.976	CLONAL	1	TRUE	1	0.387082068990431	2		190	284	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961132	79961132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372073889	NA	P-0027078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	99	434	1	ENST00000265081.6:c.529G>A	p.Ala177Thr	p.A177T	ENST00000265081	NM_002439.4	177	Gca/Aca	3/24	1	2	FACETS	0.873	0.781	0.97	0.873	0.781	0.97	CLONAL	1	TRUE	1	0.387082068990431	2		435	586	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434890	110434890	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	533	893	0	ENST00000375856.3:c.3511C>T	p.Arg1171Cys	p.R1171C	ENST00000375856	NM_003749.2	1171	Cgc/Tgc	1/2	0.387082068990431	4	FACETS	0.94	0.902	0.978	0.94	0.902	0.978	CLONAL	3	TRUE	1	0.387082068990431	4		893	1355	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821376	72821376	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1305097746	NA	P-0027078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	23	359	0	ENST00000268489.5:c.10799C>T	p.Pro3600Leu	p.P3600L	ENST00000268489	NM_006885.3	3600	cCg/cTg	10/10	0.387082068990431	3	FACETS	0.327	0.254	0.411	0.163	0.127	0.206	SUBCLONAL	1	TRUE	1	0.387082068990431	3		359	434	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096024	11096024	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	140	764	0	ENST00000358026.2:c.298T>G	p.Ser100Ala	p.S100A	ENST00000358026	NM_001128849.1	100	Tca/Gca	3/36	0.387082068990431	3	FACETS	1	0.92	1	0.505	0.46	0.553	CLONAL	1	TRUE	1	0.387082068990431	3		764	854	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264794	46264794	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1352253223	NA	P-0027078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	224	389	0	ENST00000371998.3:c.1664A>G	p.Asn555Ser	p.N555S	ENST00000371998		555	aAt/aGt	12/23	0.27290864204063	5	FACETS	1	0.986	1	0.804	0.752	0.859	CLONAL	2	TRUE	2	0.387082068990431	5		389	758	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272344	38272344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	88	510	0	ENST00000425967.3:c.2023C>T	p.Leu675Phe	p.L675F	ENST00000425967	NM_001174067.1	675	Ctc/Ttc	15/19	0.387082068990431	3	FACETS	0.749	0.663	0.84	0.374	0.331	0.42	SUBCLONAL	1	TRUE	1	0.387082068990431	3		510	725	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0027079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	274	525	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	1	2	FACETS	0.905	0.852	0.958	0.905	0.852	0.958	CLONAL	1	TRUE	1	0.737593815829806	2		525	821	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683680	162683680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373593750	NA	P-0027079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	61	440	2	ENST00000366898.1:c.289C>T	p.Arg97Trp	p.R97W	ENST00000366898	NM_004562.2	97	Cgg/Tgg	3/12	0.737593815829806	1	FACETS	0.209	0.18	0.24	0.209	0.18	0.24	SUBCLONAL	1	TRUE	0	0.737593815829806	1		442	499	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925700	114925700	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1003928208	NA	P-0027079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	54	511	0	ENST00000543371.1:c.1778C>T	p.Pro593Leu	p.P593L	ENST00000543371	NM_001198531.1	593	cCg/cTg	14/14	1	2	FACETS	0.187	0.159	0.218	0.187	0.159	0.218	SUBCLONAL	1	TRUE	1	0.737593815829806	2		511	782	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120812	94120812	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs200883289	NA	P-0027079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	54	402	0	ENST00000369303.4:c.239A>G	p.Asn80Ser	p.N80S	ENST00000369303	NM_004440.3	80	aAc/aGc	3/17	1	2	FACETS	0.211	0.18	0.246	0.211	0.18	0.246	SUBCLONAL	1	TRUE	1	0.737593815829806	2		402	693	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151947980	151947981	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	267	452	0	ENST00000262189.6:c.1692dup	p.Asp565ArgfsTer21	p.D565Rfs*21	ENST00000262189	NM_170606.2	564	-/A	12/59	0.706789799508051	3	FACETS	0.881	0.826	0.938	0.44	0.413	0.469	CLONAL	1	TRUE	1	0.737593815829806	3		452	1125	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395158	139395158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554826860	NA	P-0027079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	99	743	1	ENST00000277541.6:c.5780C>T	p.Thr1927Met	p.T1927M	ENST00000277541	NM_017617.3	1927	aCg/aTg	31/34	1	2	FACETS	0.265	0.236	0.296	0.265	0.236	0.296	SUBCLONAL	1	TRUE	1	0.737593815829806	2		744	1013	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0027080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	472	630	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.62102639683043	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.62102639683043	1		632	996	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870985	12870986	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1555085549	NA	P-0027080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	215	391	0	ENST00000228872.4:c.215dup	p.Lys73GlnfsTer52	p.K73Qfs*52	ENST00000228872	NM_004064.3	71	gag/gaGg	1/3	1	2	FACETS	0.991	0.925	1	0.991	0.925	1	CLONAL	1	TRUE	1	0.62102639683043	2		391	699	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881392	37881392	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	537	674	0	ENST00000269571.5:c.2584A>G	p.Thr862Ala	p.T862A	ENST00000269571		862	Aca/Gca	21/27	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.62102639683043	2		674	1432	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750681	128750681	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756091827	NA	P-0027080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	546	460	0	ENST00000377970.2:c.218C>T	p.Thr73Ile	p.T73I	ENST00000377970	NM_002467.4	73	aCc/aTc	2/3	0.62102639683043	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.62102639683043	3		460	1090	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106670	27106670	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	194	584	0	ENST00000324856.7:c.6281G>T	p.Cys2094Phe	p.C2094F	ENST00000324856	NM_006015.4	2094	tGc/tTc	20/20	1	2	FACETS	0.671	0.621	0.723	0.671	0.621	0.723	SUBCLONAL	1	TRUE	1	0.62102639683043	2		584	931	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146451	185146452	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	247	410	0	ENST00000265026.3:c.84dup	p.Asp29ArgfsTer2	p.D29Rfs*2	ENST00000265026	NM_004721.4	28	caa/cAaa	2/14	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.62102639683043	2		410	706	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973939	55973939	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0027080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	313	554	0	ENST00000263923.4:c.1377T>A	p.Tyr459Ter	p.Y459*	ENST00000263923	NM_002253.2	459	taT/taA	10/30	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.62102639683043	2		554	973	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1268653	1268653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775014633	NA	P-0027080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	891	674	1	ENST00000310581.5:c.2564C>T	p.Ala855Val	p.A855V	ENST00000310581	NM_198253.2	855	gCg/gTg	9/16	0.62102639683043	3	FACETS	0.967	0.939	0.996	0.967	0.939	0.996	CLONAL	2	TRUE	1	0.62102639683043	3		675	1944	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486273	8486273	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	168	295	0	ENST00000356435.5:c.2544C>A	p.Asp848Glu	p.D848E	ENST00000356435		848	gaC/gaA	17/35	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.62102639683043	2		295	541	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448299	56448300	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	C	novel	NA	P-0027080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	485	622	0	ENST00000407977.2:c.347_348delinsG	p.Pro116ArgfsTer42	p.P116Rfs*42	ENST00000407977		116	cCC/cG	3/10	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.62102639683043	2		622	1373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0027081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	392	523	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.465936481634355	3	FACETS	1	0.982	1			1	CLONAL	3	TRUE	NA	0.514822925462556	3		523	619	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110028	115110028	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200821102	NA	P-0027081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	105	737	3	ENST00000257566.3:c.1850C>T	p.Ala617Val	p.A617V	ENST00000257566	NM_016569.3	617	gCg/gTg	8/8	0.442017474025163	2	FACETS	0.813	0.731	0.898	0.406	0.365	0.449	CLONAL	1	TRUE	0	0.514822925462556	2		740	502	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259187	16259187	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	81	494	0	ENST00000375759.3:c.6452A>C	p.Glu2151Ala	p.E2151A	ENST00000375759	NM_015001.2	2151	gAa/gCa	11/15	0.425719503726689	2	FACETS	0.71	0.628	0.797	0.355	0.314	0.399	SUBCLONAL	1	TRUE	0	0.514822925462556	2		494	443	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265833	16265834	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	rs972442854	NA	P-0027081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	221	561	0	ENST00000375759.3:c.10909_10910del	p.His3638ProfsTer7	p.H3638Pfs*7	ENST00000375759	NM_015001.2	3636	GAg/g	15/15	0.425719503726689	2	FACETS	0.786	0.738	0.835	0.786	0.738	0.835	SUBCLONAL	2	TRUE	0	0.514822925462556	2		561	546	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405514	70405515	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0027081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	92	456	0	ENST00000373644.4:c.3029dup	p.Asn1011LysfsTer6	p.N1011Kfs*6	ENST00000373644	NM_030625.2	1010	tca/tCca	4/12	0.466199631221034	3	FACETS	0.727	0.647	0.813	0.364	0.323	0.407	SUBCLONAL	1	TRUE	1	0.514822925462556	3		456	618	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43749601	43749756	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCGGACATGTTAGGGGGTGTTGCATGGTGATTTTTTTTCTCTCTCTCTGCTGATGCTCTAGCTTAGATGTCTTTCCTTTTGCCTTTTTGCAGTCCCTGTGGGCCTTGCTCAGAGCGGAGAAAGCATTTGTTTGTACAAGATCCGCAGACGTGTAAA	GCGGACATGTTAGGGGGTGTTGCATGGTGATTTTTTTTCTCTCTCTCTGCTGATGCTCTAGCTTAGATGTCTTTCCTTTTGCCTTTTTGCAGTCCCTGTGGGCCTTGCTCAGAGCGGAGAAAGCATTTGTTTGTACAAGATCCGCAGACGTGTAAA	-	novel	NA	P-0027081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	45	66	0	ENST00000523873.1:c.546-92_609del		p.X182_splice	ENST00000523873		182		7/8	0.514822925462556	7	FACETS	0.865	0.741	0.997			1	CLONAL	3	TRUE	NA	0.514822925462556	7		66	154	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577520	7577521	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0027082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	145	603	0	ENST00000269305.4:c.760_761insG	p.Ile254SerfsTer10	p.I254Sfs*10	ENST00000269305	NM_001126112.2	254	atc/aGtc	7/11	0.338558746115583	4	FACETS	1	0.956	1	0.539	0.491	0.588	CLONAL	1	FALSE	2	0.431604150532888	4		603	893	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579590	7579590	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	98	467	2	ENST00000269305.4:c.97del	p.Ser33ProfsTer11	p.S33Pfs*11	ENST00000269305	NM_001126112.2	33	Tcc/cc	4/11	0.338558746115583	4	FACETS	0.82	0.731	0.914	0.41	0.365	0.457	CLONAL	1	FALSE	2	0.431604150532888	4		469	793	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945618	54945618	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	31	322	0	ENST00000312783.6:c.952C>A	p.Leu318Ile	p.L318I	ENST00000312783	NM_198436.1	318	Ctt/Att	9/10	0.431604150532888	5	FACETS	0.397	0.32	0.485	0.132	0.106	0.162	SUBCLONAL	1	FALSE	2	0.431604150532888	5		322	596	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0027083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	220	399	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	1	2	FACETS	0.766	0.713	0.821	0.766	0.713	0.821	SUBCLONAL	1	TRUE	1	0.60379696569686	2		399	951	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115267955	115267955	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0027083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	29	386	0	ENST00000438362.2:c.1779-1G>C		p.X593_splice	ENST00000438362	NM_001242891.1	593			0.60379696569686	1	FACETS	0.138	0.11	0.17	0.138	0.11	0.17	SUBCLONAL	1	TRUE	0	0.60379696569686	1		386	486	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280598	115280598	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	218	429	1	ENST00000438362.2:c.433C>T	p.Arg145Ter	p.R145*	ENST00000438362	NM_001242891.1	145	Cga/Tga	4/20	0.60379696569686	1	FACETS	0.847	0.793	0.902	0.847	0.793	0.902	CLONAL	1	TRUE	0	0.60379696569686	1		430	595	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	133	528	1	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	0.991	1	CLONAL	2	TRUE	1	0.258151395773203	2		529	510	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0027085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	102	570	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.258151395773203	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.258151395773203	1		570	519	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0027085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	54	403	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.258151395773203	1	FACETS	0.982	0.842	1	0.982	0.842	1	CLONAL	1	TRUE	0	0.258151395773203	1		403	371	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974721	21974721	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	121	309	1	ENST00000304494.5:c.106del	p.Ala36ArgfsTer17	p.A36Rfs*17	ENST00000304494	NM_000077.4	36	Gcg/cg	1/3	1	2	FACETS	1	0.962	1	1	0.99	1	CLONAL	2	TRUE	1	0.258151395773203	2		310	425	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132542	11132542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	65	580	0	ENST00000358026.2:c.2758G>A	p.Glu920Lys	p.E920K	ENST00000358026	NM_001128849.1	920	Gag/Aag	19/36	0.258151395773203	1	FACETS	0.619	0.536	0.71	0.619	0.536	0.71	SUBCLONAL	1	TRUE	0	0.258151395773203	1		580	708	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727066	40727066	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	55	429	0	ENST00000373198.4:c.3898G>T	p.Ala1300Ser	p.A1300S	ENST00000373198	NM_133170.3	1300	Gcc/Tcc	28/32	1	2	FACETS	0.796	0.682	0.922	0.796	0.682	0.922	CLONAL	1	TRUE	1	0.258151395773203	2		429	535	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174416	11174416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	157	563	0	ENST00000361445.4:c.7259C>T	p.Ala2420Val	p.A2420V	ENST00000361445	NM_004958.3	2420	gCc/gTc	53/58	0.341542853241578	3	FACETS	0.857	0.788	0.928	0.857	0.788	0.928	CLONAL	2	TRUE	1	0.341542853241578	3		563	628	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418376	49418376	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	38	360	0	ENST00000301067.7:c.16037T>G	p.Leu5346Arg	p.L5346R	ENST00000301067	NM_003482.3	5346	cTc/cGc	50/54	0.294383172255357	3	FACETS	0.555	0.459	0.663	0.278	0.229	0.332	SUBCLONAL	1	TRUE	1	0.341542853241578	3		360	469	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680655	88680655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142726068	NA	P-0027086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	65	434	1	ENST00000360948.2:c.602G>A	p.Arg201His	p.R201H	ENST00000360948	NM_001012338.2	201	cGc/cAc	6/19	1	2	FACETS	0.889	0.774	1	0.889	0.774	1	CLONAL	1	TRUE	1	0.341542853241578	2		435	428	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0027086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	218	543	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.341542853241578	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.341542853241578	2		543	550	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281279	46281279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	56	258	0	ENST00000371998.3:c.4076C>T	p.Ser1359Phe	p.S1359F	ENST00000371998		1359	tCc/tTc	21/23	0.341542853241578	3	FACETS	1	0.869	1	0.505	0.434	0.582	CLONAL	1	TRUE	1	0.341542853241578	3		258	380	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84390204	84390204	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs201698934	NA	P-0027086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	77	369	0	ENST00000321945.7:c.577C>T	p.Arg193Ter	p.R193*	ENST00000321945	NM_139076.2	193	Cga/Tga	6/9	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.341542853241578	2		369	363	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0027088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	154	499	0	ENST00000269305.4:c.375+1G>T		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.291196068713392	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	0	0.291209193985398	2		499	515	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865621	57865621	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	122	728	1	ENST00000228682.2:c.3098T>A	p.Val1033Glu	p.V1033E	ENST00000228682	NM_005269.2	1033	gTa/gAa	12/12	0.291209193985398	3	FACETS	1	0.959	1	0.557	0.503	0.614	CLONAL	1	TRUE	1	0.291209193985398	3		729	861	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120783979	120783979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112244011	NA	P-0027089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	138	690	1	ENST00000257552.2:c.1006G>A	p.Ala336Thr	p.A336T	ENST00000257552	NM_002442.3	336	Gcc/Acc	13/15	0.460309306416776	3	FACETS	0.503	0.457	0.551	0.251	0.228	0.276	INDETERMINATE	1	TRUE	1	0.849508384307544	3		691	921	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592280	29592280	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	153	233	0	ENST00000356175.3:c.4697del	p.Leu1566Ter	p.L1566*	ENST00000356175	NM_000267.3	1565	gcT/gc	35/57	1	2	FACETS	0.992	0.921	1	0.992	0.921	1	CLONAL	1	TRUE	1	0.849508384307544	2		233	363	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652936	29652936	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	206	378	0	ENST00000356175.3:c.4872del	p.Thr1625ProfsTer52	p.T1625Pfs*52	ENST00000356175	NM_000267.3	1624	cTt/ct	36/57	1	2	FACETS	0.895	0.837	0.954	0.895	0.837	0.954	CLONAL	1	TRUE	1	0.849508384307544	2		378	542	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	103	528	1	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	0.230113980280558	2		529	657	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714711	52714711	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs780485104	NA	P-0027090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	39	517	1	ENST00000322088.6:c.469C>T	p.Arg157Ter	p.R157*	ENST00000322088	NM_014225.5	157	Cga/Tga	4/15	0.137944088085418	1	FACETS	0.403	0.333	0.482	0.403	0.333	0.482	INDETERMINATE	1	TRUE	0	0.230113980280558	1		518	744	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs863224499	NA	P-0027090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	60	641	1	ENST00000269305.4:c.672+1G>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.21439209107095	1	FACETS	0.498	0.428	0.575	0.498	0.428	0.575	SUBCLONAL	1	TRUE	0	0.230113980280558	1		642	926	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432178	49432179	+	missense_variant	Missense_Mutation	DNP	GG	GG	TA	novel	NA	P-0027090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	55	694	1	ENST00000301067.7:c.8960_8961delinsTA	p.Pro2987Leu	p.P2987L	ENST00000301067	NM_003482.3	2987	cCC/cTA	34/54	1	2	FACETS	0.478	0.407	0.556	0.478	0.407	0.556	SUBCLONAL	1	TRUE	1	0.230113980280558	2		695	1000	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504374	149504374	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	96	531	0	ENST00000261799.4:c.1828del	p.Ala610ProfsTer13	p.A610Pfs*13	ENST00000261799	NM_002609.3	610	Gcc/cc	13/23	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.230113980280558	2		531	815	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986707	36986707	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	17	21	0	ENST00000354822.5:c.982C>T	p.Gln328Ter	p.Q328*	ENST00000354822	NM_001079668.2	328	Cag/Tag	3/3	0.319175950920103	2	FACETS	0.965	0.764	1	0.965	0.764	1	CLONAL	2	TRUE	0	0.463643228465042	2		21	38	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16056664	16056664	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs762815933	NA	P-0027092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	117	317	0	ENST00000268712.3:c.778A>G	p.Lys260Glu	p.K260E	ENST00000268712	NM_006311.3	260	Aaa/Gaa	7/46	0.319175950920103	2	FACETS	0.898	0.824	0.974	0.898	0.824	0.974	CLONAL	2	TRUE	0	0.463643228465042	2		317	281	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0027093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	105	574	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.252119721285326	2		574	564	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89869671	89869671	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768965612	NA	P-0027093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	81	556	0	ENST00000389301.3:c.788C>T	p.Pro263Leu	p.P263L	ENST00000389301	NM_000135.2	263	cCg/cTg	8/43	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.252119721285326	2		556	559	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659566	88659566	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	50	443	1	ENST00000372037.3:c.349C>T	p.Gln117Ter	p.Q117*	ENST00000372037	NM_004329.2	117	Cag/Tag	6/13	0.189529396723273	1	FACETS	0.677	0.574	0.79	0.677	0.574	0.79	SUBCLONAL	1	TRUE	0	0.252119721285326	1		444	512	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042454	42042454	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	40	505	0	ENST00000219905.7:c.6649C>T	p.Gln2217Ter	p.Q2217*	ENST00000219905	NM_001164273.1	2217	Caa/Taa	17/24	0.252119721285326	2	FACETS	0.546	0.453	0.65	0.273	0.226	0.325	SUBCLONAL	1	TRUE	0	0.252119721285326	2		505	581	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058886	42058902	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGAAGCAGAGCAACT	CTGGAAGCAGAGCAACT	-	novel	NA	P-0027093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	89	295	0	ENST00000219905.7:c.8606_8622del	p.Pro2869LeufsTer4	p.P2869Lfs*4	ENST00000219905	NM_001164273.1	2869	cCTGGAAGCAGAGCAACT/c	24/24	0.252119721285326	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	0	0.252119721285326	2		295	323	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533390	29533390	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0027093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	38	171	0	ENST00000356175.3:c.1392+1G>T		p.X464_splice	ENST00000356175	NM_000267.3	464			1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.252119721285326	2		171	220	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37871573	37871573	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	109	715	0	ENST00000269571.5:c.1183G>T	p.Glu395Ter	p.E395*	ENST00000269571		395	Gag/Tag	10/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.252119721285326	2		715	629	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420038	41420038	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	55	342	3	ENST00000373198.4:c.283C>A	p.Leu95Met	p.L95M	ENST00000373198	NM_133170.3	95	Ctg/Atg	3/32	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.252119721285326	2		345	328	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803455	32803455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148976382	NA	P-0027093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	120	665	1	ENST00000374899.4:c.704G>A	p.Arg235His	p.R235H	ENST00000374899	NM_018833.2	235	cGc/cAc	4/12	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.252119721285326	2		666	640	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864525	56864525	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	46	399	0	ENST00000519728.1:c.488G>C	p.Gly163Ala	p.G163A	ENST00000519728	NM_002350.3	163	gGa/gCa	7/13	1	2	FACETS	0.642	0.54	0.755	0.642	0.54	0.755	SUBCLONAL	1	TRUE	1	0.252119721285326	2		399	568	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730389	133730389	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	56	421	0	ENST00000318560.5:c.455G>C	p.Arg152Pro	p.R152P	ENST00000318560	NM_005157.4	152	cGt/cCt	3/11	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.252119721285326	2		421	373	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028784	47028784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782008653	NA	P-0027093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	49	721	2	ENST00000377604.3:c.88C>T	p.Arg30Cys	p.R30C	ENST00000377604	NM_001204468.1	30	Cgc/Tgc	3/24	0.189529396723273	1	FACETS	0.603	0.511	0.706	0.603	0.511	0.706	SUBCLONAL	1	TRUE	0	0.252119721285326	1		723	563	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038828	47038828	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	99	702	1	ENST00000377604.3:c.835C>T	p.Gln279Ter	p.Q279*	ENST00000377604	NM_001204468.1	279	Cag/Tag	9/24	0.189529396723273	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.252119721285326	1		703	496	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652476	48652476	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	27	720	0	ENST00000376670.3:c.1147C>A	p.Pro383Thr	p.P383T	ENST00000376670	NM_002049.3	383	Cct/Act	6/6	0.189529396723273	1	FACETS	0.365	0.289	0.451	0.365	0.289	0.451	SUBCLONAL	1	TRUE	0	0.252119721285326	1		720	513	SUCCESS
AR	367	MSKCC	GRCh37	X	66943600	66943600	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	31	496	0	ENST00000374690.3:c.2680G>T	p.Glu894Ter	p.E894*	ENST00000374690	NM_000044.3	894	Gaa/Taa	8/8	0.189529396723273	1	FACETS	0.532	0.43	0.647	0.532	0.43	0.647	SUBCLONAL	1	TRUE	0	0.252119721285326	1		496	404	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349965	70349965	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	36	635	0	ENST00000374080.3:c.3948G>T	p.Gln1316His	p.Q1316H	ENST00000374080		1316	caG/caT	28/45	0.189529396723273	1	FACETS	0.473	0.388	0.568	0.473	0.388	0.568	SUBCLONAL	1	TRUE	0	0.252119721285326	1		635	528	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182920	123182921	+	missense_variant	Missense_Mutation	DNP	TA	TA	AG	novel	NA	P-0027093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	34	290	2	ENST00000218089.9:c.885_886delinsAG	p.His295_Arg296delinsGlnGly	p.H295_R296delinsQG	ENST00000218089	NM_001042749.1	295	caTAga/caAGga	10/35	0.189529396723273	1	FACETS	0.546	0.446	0.658	0.546	0.446	0.658	SUBCLONAL	1	TRUE	0	0.252119721285326	1		292	432	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015840	112015842	+	missense_variant	Missense_Mutation	TNP	CAT	CAT	AAA	novel	NA	P-0027093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	68	452	0	ENST00000368678.4:c.1099_1101delinsTTT	p.Met367Phe	p.M367F	ENST00000368678		367	ATG/TTT	10/13	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.252119721285326	2		452	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0027094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	132	596	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.166564817916158	2	FACETS	0.789	0.717	0.864	0.789	0.717	0.864	SUBCLONAL	2	TRUE	0	0.238121525434362	2		597	703	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412898	49412898	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519954	NA	P-0027094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	70	531	0	ENST00000418115.1:c.125A>G	p.Tyr42Cys	p.Y42C	ENST00000418115	NM_001664.2	42	tAt/tGt	2/5	1	2	FACETS	0.629	0.547	0.719	0.629	0.547	0.719	SUBCLONAL	1	TRUE	1	0.238121525434362	2		531	934	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220895	36220895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	48	189	0	ENST00000222270.7:c.4945G>A	p.Ala1649Thr	p.A1649T	ENST00000222270	NM_014727.1	1649	Gcc/Acc	23/37	0.190398729645587	3	FACETS	0.94	0.802	1	0.94	0.802	1	CLONAL	2	TRUE	1	0.238121525434362	3		189	240	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	90	528	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.247956795567628	4	FACETS	1	0.927	1	0.527	0.469	0.589	INDETERMINATE	1	TRUE	2	0.499879960246206	4		529	512	SUCCESS
APC	324	MSKCC	GRCh37	5	112174973	112174973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085227	NA	P-0027098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	116	211	1	ENST00000257430.4:c.3682C>T	p.Gln1228Ter	p.Q1228*	ENST00000257430	NM_000038.5	1228	Cag/Tag	16/16	0.499270538651486	3	FACETS	0.908	0.84	0.975	0.908	0.84	0.975	CLONAL	3	TRUE	0	0.499879960246206	3		212	213	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911538	32911538	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs748508287	NA	P-0027098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	83	294	0	ENST00000380152.3:c.3046G>T	p.Glu1016Ter	p.E1016*	ENST00000380152		1016	Gaa/Taa	11/27	0.455237171771269	5	FACETS	1	0.953	1	0.384	0.339	0.431	CLONAL	1	TRUE	2	0.499879960246206	5		294	505	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348077	348077	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	420	605	0	ENST00000262320.3:c.1429C>G	p.Arg477Gly	p.R477G	ENST00000262320	NM_003502.3	477	Cgt/Ggt	6/11	0.499879960246206	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.499879960246206	3		605	1038	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576860	7576873	+	frameshift_variant	Frame_Shift_Del	DEL	GTGAAATATTCTCC	GTGAAATATTCTCC	-	novel	NA	P-0027098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	110	479	0	ENST00000269305.4:c.973_986del	p.Gly325ProfsTer7	p.G325Pfs*7	ENST00000269305	NM_001126112.2	325	GGAGAATATTTCACc/c	9/11	0.499879960246206	1	FACETS	0.84	0.761	0.922	0.84	0.761	0.922	CLONAL	1	TRUE	0	0.499879960246206	1		479	393	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959091	2959091	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	106	631	0	ENST00000396946.4:c.2425C>T	p.Gln809Ter	p.Q809*	ENST00000396946	NM_032415.4	809	Cag/Tag	18/25	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.361378325075962	2		631	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0027100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	274	570	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.949	0.895	1	0.949	0.895	1	CLONAL	1	TRUE	1	0.792340279817841	2		570	729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578471	7578471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	372	744	0	ENST00000269305.4:c.459del	p.Gly154AlafsTer16	p.G154Afs*16	ENST00000269305	NM_001126112.2	153	ccC/cc	5/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.792340279817841	2		744	926	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041022	112041022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376255649	NA	P-0027100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	181	334	1	ENST00000368678.4:c.233C>T	p.Thr78Met	p.T78M	ENST00000368678		78	aCg/aTg	3/13	0.436624747300557	3	FACETS	1	0.988	1	0.65	0.604	0.696	INDETERMINATE	1	TRUE	1	0.792340279817841	3		335	491	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105703	27105710	+	frameshift_variant	Frame_Shift_Del	DEL	AAACTAGA	AAACTAGA	-	novel	NA	P-0027102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	101	280	0	ENST00000324856.7:c.5315_5322del	p.Lys1772ArgfsTer9	p.K1772Rfs*9	ENST00000324856	NM_006015.4	1772	AAACTAGAa/a	20/20	0.513835821910852	1	FACETS	0.919	0.831	1	0.919	0.831	1	CLONAL	1	TRUE	0	0.513835821910852	1		280	318	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031237	11031237	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	173	592	0	ENST00000327064.4:c.1322T>G	p.Ile441Ser	p.I441S	ENST00000327064	NM_199141.1	441	aTt/aGt	11/16	1	2	FACETS	0.805	0.742	0.871	0.805	0.742	0.871	CLONAL	1	TRUE	1	0.513835821910852	2		592	836	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551934	150551934	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	181	496	0	ENST00000369026.2:c.73A>G	p.Ser25Gly	p.S25G	ENST00000369026	NM_021960.4	25	Agc/Ggc	1/3	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.652046108630874	2		496	498	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534385	63534386	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0027103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	246	708	1	ENST00000307078.5:c.1135_1136delinsTT	p.Glu379Leu	p.E379L	ENST00000307078	NM_004655.3	379	GAa/TTa	5/11	1	2	FACETS	0.961	0.902	1	0.961	0.902	1	CLONAL	1	TRUE	1	0.652046108630874	2		709	785	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440186	220440186	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	522	760	0	ENST00000243786.2:c.1039G>C	p.Gly347Arg	p.G347R	ENST00000243786	NM_002191.3	347	Ggt/Cgt	2/2	0.403426201153644	3	FACETS	1	0.979	1			1	CLONAL	2	TRUE	NA	0.652046108630874	3		760	1038	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0027104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	663	449	0				ENST00000310581	NM_198253.2	-/1132			0.423594196179796	2	FACETS	0.815	0.793	0.837	0.815	0.793	0.837	INDETERMINATE	2	TRUE	0	0.824898492298966	2		449	986	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0027104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	691	574	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.814641431531979	2	FACETS	0.963	0.942	0.983	0.963	0.942	0.983	CLONAL	2	TRUE	0	0.824898492298966	2		574	870	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800900	18800900	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs372507637	NA	P-0027104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	122	401	0	ENST00000266497.5:c.4276C>T	p.Arg1426Ter	p.R1426*	ENST00000266497		1426	Cga/Tga	31/31	0.410963072387279	1	FACETS	0.73	0.675	0.785	0.73	0.675	0.785	INDETERMINATE	1	TRUE	0	0.824898492298966	1		401	238	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591086	67591086	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	47	295	0	ENST00000274335.5:c.1679A>G	p.Asp560Gly	p.D560G	ENST00000274335		560	gAc/gGc	12/15	0.423594196179796	2	FACETS	0.259	0.218	0.304	0.129	0.109	0.152	INDETERMINATE	1	TRUE	0	0.824898492298966	2		295	440	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546559	9546559	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs958970085	NA	P-0027104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	430	362	0	ENST00000353224.5:c.1463G>A	p.Arg488Gln	p.R488Q	ENST00000353224	NM_177990.2	488	cGa/cAa	5/10	0.370942032649273	3	FACETS	1	0.995	1	0.777	0.751	0.802	INDETERMINATE	2	TRUE	0	0.824898492298966	3		362	632	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71947003	71947003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	645	811	1	ENST00000298229.2:c.2852C>T	p.Ala951Val	p.A951V	ENST00000298229	NM_001567.3	951	gCt/gTt	25/28	0.410963072387279	1	FACETS	0.782	0.757	0.807	0.782	0.757	0.807	INDETERMINATE	1	TRUE	0	0.824898492298966	1		812	1175	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118745	115118745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	297	520	1	ENST00000257566.3:c.596C>T	p.Ser199Phe	p.S199F	ENST00000257566	NM_016569.3	199	tCc/tTc	2/8	0.410963072387279	1	FACETS	0.678	0.644	0.712	0.678	0.644	0.712	INDETERMINATE	1	TRUE	0	0.824898492298966	1		521	624	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219688	36219688	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	469	618	0	ENST00000222270.7:c.4585A>G	p.Asn1529Asp	p.N1529D	ENST00000222270	NM_014727.1	1529	Aat/Gat	20/37	1	2	FACETS	0.881	0.842	0.92	0.881	0.842	0.92	CLONAL	1	TRUE	1	0.824898492298966	2		618	1291	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279217	142279218	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0027104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	254	544	2	ENST00000350721.4:c.1428_1429delinsTT	p.Leu477Phe	p.L477F	ENST00000350721	NM_001184.3	476	tcCCtt/tcTTtt	6/47	0.4095382440608	1	FACETS	0.717	0.679	0.754	0.717	0.679	0.754	INDETERMINATE	1	TRUE	0	0.824898492298966	1		546	505	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294775	1294775	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	454	448	0	ENST00000310581.5:c.226T>G	p.Cys76Gly	p.C76G	ENST00000310581	NM_198253.2	76	Tgc/Ggc	2/16	0.423594196179796	2	FACETS	1	0.997	1	0.725	0.699	0.751	INDETERMINATE	1	TRUE	0	0.824898492298966	2		448	759	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971035	21971035	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	488	382	0	ENST00000304494.5:c.323A>G	p.Asp108Gly	p.D108G	ENST00000304494	NM_000077.4	108	gAt/gGt	2/3	0.810660790969378	2	FACETS	0.89	0.864	0.914	0.89	0.864	0.914	CLONAL	2	TRUE	0	0.824898492298966	2		382	665	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0027106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	125	555	1	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.609073166140892	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.609073166140892	1		556	263	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707647	176707647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	65	461	0	ENST00000439151.2:c.5704G>A	p.Glu1902Lys	p.E1902K	ENST00000439151	NM_022455.4	1902	Gag/Aag	18/23	0.274026945984217	0	FACETS	0.335	0.294	0.379			1	INDETERMINATE	1	TRUE	0	0.609073166140892	0		461	249	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	156	478	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	0.191265937931744	5	FACETS	0.858	0.796	0.921			1	INDETERMINATE	3	TRUE	NA	0.609073166140892	5		478	381	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007146	152007146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	126	454	0	ENST00000262189.6:c.754C>T	p.His252Tyr	p.H252Y	ENST00000262189	NM_170606.2	252	Cat/Tat	6/59	0.343520475179493	3	FACETS	1	0.985	1	0.696	0.636	0.757	INDETERMINATE	1	TRUE	1	0.609073166140892	3		454	388	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343499	118343499	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782614654	NA	P-0027106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	82	410	0	ENST00000534358.1:c.1625C>T	p.Thr542Met	p.T542M	ENST00000534358	NM_005933.3	542	aCg/aTg	3/36	0.186904050420082	2	FACETS	1	0.936	1	0.532	0.476	0.591	INDETERMINATE	1	TRUE	0	0.609073166140892	2		410	253	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2097772	2097772	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	36	613	0	ENST00000219066.1:c.77G>C	p.Gly26Ala	p.G26A	ENST00000219066	NM_002528.5	26	gGg/gCg	1/6	0.257403000554162	3	FACETS	0.431	0.355	0.516	0.215	0.177	0.258	INDETERMINATE	1	TRUE	1	0.609073166140892	3		613	358	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226569	2226569	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	30	691	0	ENST00000326181.6:c.2008del	p.Cys670AlafsTer105	p.C670Afs*105	ENST00000326181	NM_032271.2	669	acT/ac	21/21	0.257403000554162	3	FACETS	0.332	0.267	0.405	0.166	0.133	0.203	INDETERMINATE	1	TRUE	1	0.609073166140892	3		691	387	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868417	117868417	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	183	475	0	ENST00000297338.2:c.925A>G	p.Ile309Val	p.I309V	ENST00000297338	NM_006265.2	309	Att/Gtt	8/14	0.515755033460175	3	FACETS	0.827	0.771	0.884	0.827	0.771	0.884	CLONAL	2	TRUE	1	0.609073166140892	3		475	474	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	45	315	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.861	0.726	1	0.861	0.726	1	CLONAL	1	TRUE	1	0.276479234065484	2		316	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0027107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	86	804	1	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	1	2	FACETS	0.742	0.656	0.835	0.742	0.656	0.835	SUBCLONAL	1	TRUE	1	0.276479234065484	2		805	838	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0027107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	143	717	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.276479234065484	2		717	853	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724541	162724541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759709680	NA	P-0027107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	49	578	0	ENST00000367921.3:c.313C>T	p.Arg105Cys	p.R105C	ENST00000367921	NM_006182.2	105	Cgc/Tgc	5/18	1	2	FACETS	0.734	0.622	0.857	0.734	0.622	0.857	SUBCLONAL	1	TRUE	1	0.276479234065484	2		578	483	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784592	43784592	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	71	570	0	ENST00000382044.4:c.82G>C	p.Glu28Gln	p.E28Q	ENST00000382044	NM_001141980.1	28	Gaa/Caa	2/28	1	2	FACETS	0.772	0.674	0.879	0.772	0.674	0.879	SUBCLONAL	1	TRUE	1	0.276479234065484	2		570	665	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129620	2129620	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878854092	NA	P-0027107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	131	819	1	ENST00000219476.3:c.3347C>T	p.Ala1116Val	p.A1116V	ENST00000219476	NM_000548.3	1116	gCt/gTt	29/42	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.276479234065484	2		820	757	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136292	202136292	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	75	607	0	ENST00000358485.4:c.536T>C	p.Phe179Ser	p.F179S	ENST00000358485	NM_001080125.1	179	tTt/tCt	3/9	1	2	FACETS	0.722	0.632	0.82	0.722	0.632	0.82	SUBCLONAL	1	TRUE	1	0.276479234065484	2		607	751	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149659	202149659	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	45	439	0	ENST00000358485.4:c.1100A>G	p.Asp367Gly	p.D367G	ENST00000358485	NM_001080125.1	367	gAc/gGc	8/9	1	2	FACETS	0.761	0.64	0.893	0.761	0.64	0.893	SUBCLONAL	1	TRUE	1	0.276479234065484	2		439	428	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910708	29910709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0027107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	188	976	0	ENST00000376809.5:c.249_250dup	p.Trp84PhefsTer9	p.W84Ffs*9	ENST00000376809	NM_002116.7	83	tat/taTTt	2/8	0.227704636384617	2	FACETS	0.864	0.8	0.93	0.864	0.8	0.93	CLONAL	2	TRUE	0	0.276479234065484	2		976	787	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0027108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	323	583	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.4013438132567	2	FACETS	0.896	0.849	0.943	0.896	0.849	0.943	CLONAL	2	TRUE	0	0.426257906904171	2		583	846	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445269	49445269	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1198	177	960	1	ENST00000301067.7:c.2197C>T	p.Gln733Ter	p.Q733*	ENST00000301067	NM_003482.3	733	Caa/Taa	10/54	0.254415247028643	5	FACETS	0.99	0.91	1	0.248	0.227	0.269	INDETERMINATE	1	TRUE	1	0.426257906904171	5		961	1375	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218803	133218803	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	104	639	1	ENST00000320574.5:c.5133A>T	p.Gln1711His	p.Q1711H	ENST00000320574	NM_006231.2	1711	caA/caT	38/49	0.254415247028643	5	FACETS	0.833	0.745	0.928	0.208	0.186	0.232	INDETERMINATE	1	TRUE	1	0.426257906904171	5		640	960	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0027109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	291	629	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.307270624855802	3	FACETS	0.929	0.881	0.978	0.929	0.881	0.978	CLONAL	3	TRUE	0	0.365254507132744	3		630	676	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087554	27087554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs935971471	NA	P-0027109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	89	597	0	ENST00000324856.7:c.2128C>T	p.Arg710Cys	p.R710C	ENST00000324856	NM_006015.4	710	Cgc/Tgc	5/20	0.365254507132744	3	FACETS	0.783	0.694	0.878	0.392	0.347	0.439	SUBCLONAL	1	TRUE	1	0.365254507132744	3		597	736	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121692	108121692	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	42	498	0	ENST00000278616.4:c.1500A>G	p.Ile500Met	p.I500M	ENST00000278616	NM_000051.3	500	atA/atG	10/63	0.365254507132744	3	FACETS	0.497	0.415	0.589	0.249	0.207	0.295	SUBCLONAL	1	TRUE	1	0.365254507132744	3		498	547	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431633	49431633	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs529813839	NA	P-0027109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	46	575	1	ENST00000301067.7:c.9506G>T	p.Gly3169Val	p.G3169V	ENST00000301067	NM_003482.3	3169	gGc/gTc	34/54	0.365254507132744	4	FACETS	0.586	0.493	0.689	0.195	0.164	0.23	SUBCLONAL	1	TRUE	1	0.365254507132744	4		576	587	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541829	187541829	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	52	381	0	ENST00000441802.2:c.5911G>C	p.Glu1971Gln	p.E1971Q	ENST00000441802	NM_005245.3	1971	Gaa/Caa	10/27	0.365254507132744	2	FACETS	0.745	0.637	0.864	0.373	0.318	0.432	SUBCLONAL	1	TRUE	0	0.365254507132744	2		381	382	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	140	528	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.882	0.805	0.964	0.882	0.805	0.964	CLONAL	1	FALSE	1	0.431155759050798	2		529	736	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0027112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	164	541	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.9	0.827	0.977	0.9	0.827	0.977	CLONAL	1	FALSE	1	0.431155759050798	2		541	845	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226443	2226443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773019943	NA	P-0027112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	261	595	1	ENST00000398665.3:c.3923C>T	p.Pro1308Leu	p.P1308L	ENST00000398665	NM_032482.2	1308	cCg/cTg	27/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.431155759050798	2		596	1058	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899066	40899066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199994862	NA	P-0027112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	181	504	0	ENST00000373198.4:c.2204C>T	p.Pro735Leu	p.P735L	ENST00000373198	NM_133170.3	735	cCg/cTg	14/32	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.431155759050798	2		504	766	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795109	242795109	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs763228671	NA	P-0027112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	218	594	0	ENST00000334409.5:c.100C>A	p.Pro34Thr	p.P34T	ENST00000334409	NM_005018.2	34	Ccc/Acc	2/5	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.431155759050798	2		594	996	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998186	100998186	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745472229	NA	P-0027112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	123	416	0	ENST00000325455.5:c.1616C>T	p.Pro539Leu	p.P539L	ENST00000325455	NM_001202474.3	539	cCg/cTg	1/8	1	2	FACETS	0.946	0.858	1	0.946	0.858	1	CLONAL	1	FALSE	1	0.431155759050798	2		416	603	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984345	201984348	+	frameshift_variant	Frame_Shift_Del	DEL	ACAA	ACAA	-	novel	NA	P-0027112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	167	510	2	ENST00000359651.3:c.1012_1015del	p.Lys338GlyfsTer108	p.K338Gfs*108	ENST00000359651		337	tACAAa/ta	8/8	1	2	FACETS	0.879	0.808	0.953	0.879	0.808	0.953	CLONAL	1	FALSE	1	0.431155759050798	2		512	881	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245376	46245376	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	174	387	0	ENST00000334344.6:c.3470C>A	p.Ser1157Ter	p.S1157*	ENST00000334344	NM_152641.2	1157	tCa/tAa	15/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.431155759050798	2		387	713	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645147	67645148	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0027112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	204	479	1	ENST00000264010.4:c.413dup	p.Tyr138Ter	p.Y138*	ENST00000264010	NM_006565.3	138	tat/tAat	3/12	1	2	FACETS	0.996	0.924	1	0.996	0.924	1	CLONAL	1	FALSE	1	0.431155759050798	2		480	950	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434942	56434943	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0027112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	373	475	0	ENST00000407977.2:c.2193_2194dup	p.Arg732LeufsTer96	p.R732Lfs*96	ENST00000407977		732	cgc/cTCgc	9/10	0.431155759050798	2	FACETS	0.971	0.926	1	0.971	0.926	1	CLONAL	2	FALSE	0	0.431155759050798	2		475	891	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713520	30713537	+	inframe_deletion	In_Frame_Del	DEL	AGGAGTATGCCTCTTGGA	AGGAGTATGCCTCTTGGA	-	novel	NA	P-0027112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	122	392	0	ENST00000295754.5:c.847_864del	p.Glu283_Lys288del	p.E283_K288del	ENST00000295754	NM_003242.5	282	gAGGAGTATGCCTCTTGGAag/gag	4/7	1	2	FACETS	0.881	0.799	0.969	0.881	0.799	0.969	CLONAL	1	FALSE	1	0.431155759050798	2		392	642	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507414	8507414	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	97	235	0	ENST00000356435.5:c.1564T>C	p.Phe522Leu	p.F522L	ENST00000356435		522	Ttc/Ctc	11/35	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	FALSE	1	0.431155759050798	2		235	447	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0027113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	51	226	1	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.267349522405497	4	FACETS	1	0.962	1	0.709	0.607	0.818	CLONAL	1	TRUE	2	0.376724613705595	4		227	263	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0027113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	107	372	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.376724613705595	2	FACETS	0.802	0.727	0.88	0.802	0.727	0.88	CLONAL	2	TRUE	0	0.376724613705595	2		372	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579359	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587780066	NA	P-0027113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	131	584	0	ENST00000269305.4:c.328del	p.Arg110ValfsTer13	p.R110Vfs*13	ENST00000269305	NM_001126112.2	110	Cgt/gt	4/11	0.376724613705595	3	FACETS	1	0.975	1	0.602	0.547	0.66	CLONAL	1	TRUE	1	0.376724613705595	3		584	686	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578412	7578412	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519747	NA	P-0027113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	107	520	0	ENST00000269305.4:c.518T>C	p.Val173Ala	p.V173A	ENST00000269305	NM_001126112.2	173	gTg/gCg	5/11	0.376724613705595	3	FACETS	1	0.972	1	0.611	0.55	0.676	CLONAL	1	TRUE	1	0.376724613705595	3		520	552	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534431	63534431	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567757528	NA	P-0027113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	53	581	1	ENST00000307078.5:c.1090C>T	p.Pro364Ser	p.P364S	ENST00000307078	NM_004655.3	364	Ccc/Tcc	5/11	0.376724613705595	3	FACETS	0.373	0.317	0.435	0.187	0.158	0.218	SUBCLONAL	1	TRUE	1	0.376724613705595	3		582	896	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943447	17943447	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	99	611	0	ENST00000458235.1:c.2561T>A	p.Val854Glu	p.V854E	ENST00000458235	NM_000215.3	854	gTg/gAg	19/24	1	2	FACETS	0.908	0.812	1	0.908	0.812	1	CLONAL	1	TRUE	1	0.376724613705595	2		611	579	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944484	71944484	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0027117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	117	491	0	ENST00000298229.2:c.2041-1G>C		p.X681_splice	ENST00000298229	NM_001567.3	681			0.278393106017363	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.278393106017363	1		491	697	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720833	89720836	+	frameshift_variant	Frame_Shift_Del	DEL	AAAT	AAAT	-	rs587782304	NA	P-0027117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	55	295	0	ENST00000371953.3:c.987_990del	p.Asn329LysfsTer14	p.N329Kfs*14	ENST00000371953	NM_000314.4	328	gcAAAT/gc	8/9	0.278393106017363	1	FACETS	0.787	0.675	0.909	0.787	0.675	0.909	CLONAL	1	TRUE	0	0.278393106017363	1		295	432	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961795	15961795	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	95	363	0	ENST00000268712.3:c.6000T>A	p.Asn2000Lys	p.N2000K	ENST00000268712	NM_006311.3	2000	aaT/aaA	38/46	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.278393106017363	2		363	573	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944484	71944484	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0027117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	16	491	0	ENST00000298229.2:c.2041-1G>C		p.X681_splice	ENST00000298229	NM_001567.3	681			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		491	64	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162920	47162920	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1302035546	NA	P-0027118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	41	380	0	ENST00000409792.3:c.3206T>C	p.Val1069Ala	p.V1069A	ENST00000409792	NM_014159.6	1069	gTt/gCt	3/21	0.189563009005336	3	FACETS	0.611	0.508	0.725	0.305	0.254	0.363	SUBCLONAL	1	TRUE	1	0.251555227892911	3		380	601	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928975	49928975	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	105	664	0	ENST00000296474.3:c.3391G>A	p.Glu1131Lys	p.E1131K	ENST00000296474	NM_002447.2	1131	Gag/Aag	16/20	0.189563009005336	3	FACETS	0.96	0.859	1	0.48	0.429	0.534	CLONAL	1	TRUE	1	0.251555227892911	3		664	979	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220579	1220594	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GGCACTGCACCCGTTC	GGCACTGCACCCGTTC	-	novel	NA	P-0027118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	156	559	0	ENST00000326873.7:c.598_613del		p.X200_splice	ENST00000326873	NM_000455.4	200		5/10	0.182769248196189	2	FACETS	1	0.988	1	0.744	0.681	0.809	CLONAL	1	TRUE	0	0.251555227892911	2		559	834	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0027119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	262	449	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		449	512	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0027120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	246	541	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.62415339971581	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.62415339971581	1		541	499	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163720	32163720	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	307	370	0	ENST00000375023.3:c.5506G>C	p.Glu1836Gln	p.E1836Q	ENST00000375023	NM_004557.3	1836	Gag/Cag	30/30	0.62415339971581	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.62415339971581	1		370	624	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577260	64577260	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs794728647	NA	P-0027120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	380	589	0	ENST00000312049.6:c.322C>T	p.Arg108Ter	p.R108*	ENST00000312049	NM_130799.2	108	Cga/Tga	2/10	0.62415339971581	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.62415339971581	1		589	827	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63760051	63760051	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1016216781	NA	P-0027120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	174	319	0	ENST00000279873.7:c.704T>C	p.Ile235Thr	p.I235T	ENST00000279873	NM_032199.2	235	aTa/aCa	4/10	0.62415339971581	1	FACETS	0.969	0.904	1	0.969	0.904	1	CLONAL	1	TRUE	0	0.62415339971581	1		319	396	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690801	89690801	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1564828914	NA	P-0027120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	136	274	0	ENST00000371953.3:c.210-2A>G		p.X70_splice	ENST00000371953	NM_000314.4	70			0.62415339971581	1	FACETS	0.955	0.882	1	0.955	0.882	1	CLONAL	1	TRUE	0	0.62415339971581	1		274	314	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165711	108165711	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	209	378	0	ENST00000278616.4:c.4834G>C	p.Glu1612Gln	p.E1612Q	ENST00000278616	NM_000051.3	1612	Gaa/Caa	32/63	0.62415339971581	1	FACETS	0.868	0.813	0.924	0.868	0.813	0.924	CLONAL	1	TRUE	0	0.62415339971581	1		378	531	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289559	33289559	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	401	612	0	ENST00000374542.5:c.144del	p.Gly49GlufsTer95	p.G49Efs*95	ENST00000374542	NM_001141970.1	48	agA/ag	2/8	0.62415339971581	1	FACETS	0.984	0.941	1	0.984	0.941	1	CLONAL	1	TRUE	0	0.62415339971581	1		612	898	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29195874	29195874	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	432	723	0	ENST00000240100.2:c.724T>C	p.Tyr242His	p.Y242H	ENST00000240100	NM_001394.6	242	Tac/Cac	3/4	0.62415339971581	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.62415339971581	1		723	909	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032205	26032205	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	175	254	0	ENST00000244661.2:c.84G>C	p.Lys28Asn	p.K28N	ENST00000244661	NM_003537.3	28	aaG/aaC	1/1	0.434389428896967	2	FACETS	0.921	0.857	0.985	0.921	0.857	0.985	CLONAL	2	TRUE	0	0.436975445276945	2		254	435	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356149	66356149	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs142589245	NA	P-0027124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	231	550	0	ENST00000273854.3:c.1348T>G	p.Leu450Val	p.L450V	ENST00000273854	NM_004439.5	450	Ttg/Gtg	5/18	0.436975445276945	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.436975445276945	1		550	818	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619834	1619834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761441337	NA	P-0027124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	336	784	1	ENST00000344749.5:c.1112G>A	p.Arg371Gln	p.R371Q	ENST00000344749	NM_001136139.2	371	cGa/cAa	14/19	0.436975445276945	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.436975445276945	1		785	1086	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154241	2154242	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755455183	NA	P-0027124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	149	620	0	ENST00000434045.2:c.686dup	p.Glu230ArgfsTer50	p.E230Rfs*50	ENST00000434045	NM_001127598.1	229	cca/ccCa	5/5	1	2	FACETS	0.636	0.58	0.695	0.636	0.58	0.695	SUBCLONAL	1	TRUE	1	0.436975445276945	2		620	1072	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954022	32954023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs397507419	NA	P-0027124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	215	531	7	ENST00000380152.3:c.9097dup	p.Thr3033AsnfsTer11	p.T3033Nfs*11	ENST00000380152		3030	aca/acAa	23/27	1	2	FACETS	0.931	0.865	0.999	0.931	0.865	0.999	CLONAL	1	TRUE	1	0.436975445276945	2		538	1057	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36208923	36208925	+	start_lost,inframe_deletion	Translation_Start_Site	DEL	GGC	GGC	-	rs898578503	NA	P-0027124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	12	38	0	ENST00000222270.7:c.14_16del	p.Ala5?	p.A5?	ENST00000222270	NM_014727.1	1	atGGCg/atg	1/37	0.257333289939059	2	FACETS	0.858	0.616	1	0.429	0.308	0.571	INDETERMINATE	1	TRUE	0	0.436975445276945	2		38	64	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373422	118373422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	269	405	0	ENST00000534358.1:c.6815C>T	p.Thr2272Ile	p.T2272I	ENST00000534358	NM_005933.3	2272	aCa/aTa	27/36	0.253510007782778	3	FACETS	0.795	0.747	0.845			1	INDETERMINATE	2	TRUE	NA	0.436975445276945	3		405	943	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43738590	43738605	+	frameshift_variant	Frame_Shift_Del	DEL	AGGTTGAACTGCAAAG	AGGTTGAACTGCAAAG	-	novel	NA	P-0027124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	149	481	0	ENST00000382044.4:c.3020_3035del	p.Ser1007TrpfsTer30	p.S1007Wfs*30	ENST00000382044	NM_001141980.1	1007	tCTTTGCAGTTCAACCTg/tg	14/28	1	2	FACETS	0.787	0.719	0.859	0.787	0.719	0.859	SUBCLONAL	1	TRUE	1	0.436975445276945	2		481	866	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90634823	90634823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	150	649	0	ENST00000330062.3:c.169G>A	p.Glu57Lys	p.E57K	ENST00000330062	NM_002168.2	57	Gag/Aag	2/11	1	2	FACETS	0.632	0.576	0.69	0.632	0.576	0.69	SUBCLONAL	1	TRUE	1	0.436975445276945	2		649	1087	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572949	7572961	+	frameshift_variant	Frame_Shift_Del	DEL	GTCTTGAACATGA	GTCTTGAACATGA	-	novel	NA	P-0027124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	218	622	1	ENST00000269305.4:c.1148_1160del	p.Leu383GlnfsTer35	p.L383Qfs*35	ENST00000269305	NM_001126112.2	383	cTCATGTTCAAGACa/ca	11/11	0.436975445276945	1	FACETS	0.953	0.889	1	0.953	0.889	1	CLONAL	1	TRUE	0	0.436975445276945	1		623	818	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244957	41244957	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs80357003	NA	P-0027124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	154	628	0	ENST00000357654.3:c.2591C>G	p.Ser864Ter	p.S864*	ENST00000357654	NM_007294.3	864	tCa/tGa	10/23	1	2	FACETS	0.647	0.591	0.705	0.647	0.591	0.705	SUBCLONAL	1	TRUE	1	0.436975445276945	2		628	1090	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100015	11100015	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	281	680	0	ENST00000358026.2:c.1141C>G	p.Arg381Gly	p.R381G	ENST00000358026	NM_001128849.1	381	Cga/Gga	7/36	0.436975445276945	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.436975445276945	1		680	1001	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439994	220439994	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1271	329	896	2	ENST00000243786.2:c.847C>A	p.Pro283Thr	p.P283T	ENST00000243786	NM_002191.3	283	Cct/Act	2/2	1	2	FACETS	0.941	0.887	0.997	0.941	0.887	0.997	CLONAL	1	TRUE	1	0.436975445276945	2		898	1600	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511330	157511330	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	156	346	0	ENST00000346085.5:c.3848G>T	p.Gly1283Val	p.G1283V	ENST00000346085	NM_020732.3	1283	gGg/gTg	15/20	0.436975445276945	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.436975445276945	1		346	528	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934344	68934344	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1173	298	780	0	ENST00000288368.4:c.410A>C	p.Asn137Thr	p.N137T	ENST00000288368	NM_024870.2	137	aAc/aCc	4/40	1	2	FACETS	0.927	0.871	0.985	0.927	0.871	0.985	CLONAL	1	TRUE	1	0.436975445276945	2		780	1471	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349059	70349059	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs778961820	NA	P-0027124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	240	265	0	ENST00000374080.3:c.3571G>C	p.Asp1191His	p.D1191H	ENST00000374080		1191	Gat/Cat	25/45	1	1	FACETS	0.753	0.709	0.797	1	0.993	1	SUBCLONAL	2	TRUE	0	0.436975445276945	1		265	570	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0027126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	207	449	0				ENST00000310581	NM_198253.2	-/1132			0.312207051506932	3	FACETS	0.891	0.83	0.955	0.891	0.83	0.955	CLONAL	2	TRUE	1	0.373451937218502	3		449	738	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	212	528	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.373451937218502	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.373451937218502	1		529	668	SUCCESS
APC	324	MSKCC	GRCh37	5	112175770	112175770	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	244	344	0	ENST00000257430.4:c.4480del	p.Glu1494LysfsTer13	p.E1494Kfs*13	ENST00000257430	NM_000038.5	1493	acG/ac	16/16	0.255479192386238	3	FACETS	0.846	0.796	0.896			1	CLONAL	3	TRUE	NA	0.373451937218502	3		344	611	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0027126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	391	862	1	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.236461156777822	2	FACETS	0.825	0.784	0.867	0.825	0.784	0.867	CLONAL	2	TRUE	0	0.373451937218502	2		863	1269	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058476	69058476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267601977	NA	P-0027126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	176	624	1	ENST00000288368.4:c.4120C>T	p.Arg1374Trp	p.R1374W	ENST00000288368	NM_024870.2	1374	Cgg/Tgg	34/40	0.236461156777822	2	FACETS	1	0.987	1	0.67	0.619	0.723	CLONAL	1	TRUE	0	0.373451937218502	2		625	703	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352612	118352612	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	148	586	0	ENST00000534358.1:c.3817G>C	p.Glu1273Gln	p.E1273Q	ENST00000534358	NM_005933.3	1273	Gaa/Caa	7/36	1	2	FACETS	0.845	0.771	0.922	0.845	0.771	0.922	CLONAL	1	TRUE	1	0.373451937218502	2		586	938	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052646	42052646	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs892952161	NA	P-0027126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	185	586	0	ENST00000219905.7:c.7317G>A	p.Met2439Ile	p.M2439I	ENST00000219905	NM_001164273.1	2439	atG/atA	20/24	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.373451937218502	2		586	980	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21272334	21272334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	142	715	0	ENST00000354336.3:c.112G>A	p.Val38Ile	p.V38I	ENST00000354336	NM_005207.3	38	Gtc/Atc	1/3	1	2	FACETS	0.785	0.714	0.859	0.785	0.714	0.859	SUBCLONAL	1	TRUE	1	0.373451937218502	2		715	969	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045880	26045887	+	frameshift_variant	Frame_Shift_Del	DEL	CCGACCTG	CCGACCTG	-	novel	NA	P-0027126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	95	635	0	ENST00000540144.1:c.243_250del	p.Asp82PhefsTer14	p.D82Ffs*14	ENST00000540144	NM_003531.2	81	aCCGACCTG/a	1/1	1	2	FACETS	0.475	0.422	0.532	0.475	0.422	0.532	SUBCLONAL	1	TRUE	1	0.373451937218502	2		635	1071	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997831	149997831	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1408705745	NA	P-0027126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	218	665	0	ENST00000253339.5:c.2636G>A	p.Trp879Ter	p.W879*	ENST00000253339		879	tGg/tAg	5/7	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.373451937218502	2		665	966	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0027128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	111	780	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.17	2		780	1252	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	122	528	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.153041305164878	3	FACETS	0.809	0.73	0.892	0.809	0.73	0.892	CLONAL	2	TRUE	1	0.17	3		529	963	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0027128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	55	443	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.775	0.661	0.9	0.775	0.661	0.9	SUBCLONAL	1	TRUE	1	0.17	2		443	835	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610695	52610695	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	51	447	0	ENST00000394830.3:c.3478C>T	p.Arg1160Ter	p.R1160*	ENST00000394830	NM_018313.4	1160	Cga/Tga	23/30	1	2	FACETS	0.739	0.626	0.863	0.739	0.626	0.863	SUBCLONAL	1	TRUE	1	0.17	2		447	812	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794743	120794743	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1296	219	801	0	ENST00000257552.2:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000257552	NM_002442.3	205	tAc/tGc	9/15	0.153041305164878	3	FACETS	0.923	0.856	0.992	0.923	0.856	0.992	CLONAL	2	TRUE	1	0.17	3		801	1515	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161725	47161725	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	32	351	0	ENST00000409792.3:c.4401del	p.Met1469CysfsTer14	p.M1469Cfs*14	ENST00000409792	NM_014159.6	1467	ggG/gg	3/21	1	2	FACETS	0.656	0.531	0.797	0.656	0.531	0.797	SUBCLONAL	1	TRUE	1	0.17	2		351	574	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630176	187630176	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	80	576	0	ENST00000441802.2:c.806G>T	p.Arg269Met	p.R269M	ENST00000441802	NM_005245.3	269	aGg/aTg	2/27	1	2	FACETS	0.962	0.845	1	0.962	0.845	1	CLONAL	1	TRUE	1	0.17	2		576	978	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293573	137293573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754539654	NA	P-0027128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1500	131	891	2	ENST00000481739.1:c.124G>A	p.Gly42Ser	p.G42S	ENST00000481739	NM_002957.4	42	Ggc/Agc	2/10	1	2	FACETS	0.945	0.854	1	0.945	0.854	1	CLONAL	1	TRUE	1	0.17	2		893	1631	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964398	70964398	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	92	448	1	ENST00000276594.2:c.1630G>T	p.Asp544Tyr	p.D544Y	ENST00000276594	NM_024504.3	544	Gat/Tat	8/8	0.153041305164878	3	FACETS	1	0.975	1	0.682	0.605	0.764	CLONAL	1	TRUE	1	0.17	3		449	861	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162135	47162136	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	T	novel	NA	P-0027128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	51	460	0	ENST00000409792.3:c.3990_3991delinsA	p.Leu1331Ter	p.L1331*	ENST00000409792	NM_014159.6	1330	tcCCta/tcAta	3/21	1	2	FACETS	0.756	0.641	0.883	0.756	0.641	0.883	SUBCLONAL	1	TRUE	1	0.17	2		460	794	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0027131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	73	714	3	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	1	2	FACETS	0.393	0.342	0.448	0.393	0.342	0.448	SUBCLONAL	1	TRUE	1	0.322877361538556	2		717	1152	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0027131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	219	487	2	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.322877361538556	2		489	1070	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577562	7577563	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGT	novel	NA	P-0027131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	83	652	0	ENST00000269305.4:c.716_718dup	p.Asn239dup	p.N239dup	ENST00000269305	NM_001126112.2	239	agt/aACAgt	7/11	0.322877361538556	1	FACETS	0.564	0.497	0.635	0.564	0.497	0.635	SUBCLONAL	1	TRUE	0	0.322877361538556	1		652	765	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182158	11182158	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	157	743	0	ENST00000361445.4:c.6688T>G	p.Leu2230Val	p.L2230V	ENST00000361445	NM_004958.3	2230	Tta/Gta	48/58	1	2	FACETS	0.955	0.874	1	0.955	0.874	1	CLONAL	1	TRUE	1	0.322877361538556	2		743	1018	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954301	48954301	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	51	389	0	ENST00000267163.4:c.1422C>A	p.Ser474Arg	p.S474R	ENST00000267163	NM_000321.2	474	agC/agA	16/27	0.322877361538556	1	FACETS	0.634	0.54	0.736	0.634	0.54	0.736	SUBCLONAL	1	TRUE	0	0.322877361538556	1		389	418	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045017	47045032	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGGCTCCACAAGGTA	AGGGCTCCACAAGGTA	-	novel	NA	P-0027131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	145	849	0	ENST00000377604.3:c.2344_2355+4del		p.X782_splice	ENST00000377604	NM_001204468.1	782		20/24	0.322877361538556	1	FACETS	0.914	0.834	0.998	0.914	0.834	0.998	CLONAL	1	TRUE	0	0.322877361538556	1		849	824	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0027132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	119	480	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.904	0.817	0.996	0.904	0.817	0.996	CLONAL	1	TRUE	1	0.367799678193393	2		480	716	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs985033810	NA	P-0027132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	200	714	0	ENST00000269305.4:c.731G>C	p.Gly244Ala	p.G244A	ENST00000269305	NM_001126112.2	244	gGc/gCc	7/11	0.367799678193393	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.367799678193393	1		714	736	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0027133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	507	397	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.179096186578168	9	FACETS	1	0.985	1	0.923	0.886	0.961	CLONAL	7	TRUE	1	0.179096186578168	9		397	1247	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934574	NA	P-0027133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	83	712	0	ENST00000269305.4:c.844C>G	p.Arg282Gly	p.R282G	ENST00000269305	NM_001126112.2	282	Cgg/Ggg	8/11	0.231867563621628	3	FACETS	0.841	0.74	0.95	0.42	0.37	0.475	CLONAL	1	TRUE	1	0.179096186578168	3		712	1201	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579503	7579503	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567556752	NA	P-0027133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	156	751	0	ENST00000269305.4:c.184G>T	p.Glu62Ter	p.E62*	ENST00000269305	NM_001126112.2	62	Gaa/Taa	4/11	0.231867563621628	3	FACETS	0.837	0.765	0.912	0.837	0.765	0.912	CLONAL	2	TRUE	1	0.179096186578168	3		751	1134	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176132113	176132113	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	117	576	0	ENST00000367669.3:c.654G>T	p.Arg218Ser	p.R218S	ENST00000367669	NM_022457.5	218	agG/agT	5/20	0.231867563621628	3	FACETS	0.769	0.692	0.85	0.769	0.692	0.85	SUBCLONAL	2	TRUE	1	0.179096186578168	3		576	926	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612901	228612901	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	69	572	0	ENST00000366696.1:c.126C>A	p.Tyr42Ter	p.Y42*	ENST00000366696	NM_003493.2	42	taC/taA	1/1	0.231867563621628	3	FACETS	0.962	0.836	1	0.481	0.418	0.549	CLONAL	1	TRUE	1	0.179096186578168	3		572	873	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988331	41988331	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	179	614	0	ENST00000219905.7:c.1123G>T	p.Gly375Ter	p.G375*	ENST00000219905	NM_001164273.1	375	Gga/Tga	3/24	0.231867563621628	3	FACETS	0.945	0.87	1	0.945	0.87	1	CLONAL	2	TRUE	1	0.179096186578168	3		614	1152	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953224	17953224	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	149	749	0	ENST00000458235.1:c.762C>A	p.Phe254Leu	p.F254L	ENST00000458235	NM_000215.3	254	ttC/ttA	6/24	0.157259922143745	2	FACETS	0.789	0.72	0.862	0.789	0.72	0.862	SUBCLONAL	2	TRUE	0	0.179096186578168	2		749	1054	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523322	9523323	+	missense_variant	Missense_Mutation	DNP	CA	CA	AT	novel	NA	P-0027133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	135	493	0	ENST00000353224.5:c.1914_1915delinsAT	p.Asp638_Gly639delinsGluCys	p.D638_G639delinsEC	ENST00000353224	NM_177990.2	638	gaTGgc/gaATgc	9/10	0.231867563621628	3	FACETS	0.804	0.73	0.883	0.804	0.73	0.883	CLONAL	2	TRUE	1	0.179096186578168	3		493	1021	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546795	9546795	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	97	325	1	ENST00000353224.5:c.1227C>A	p.Ser409Arg	p.S409R	ENST00000353224	NM_177990.2	409	agC/agA	5/10	0.231867563621628	3	FACETS	1	0.909	1	1	0.909	1	CLONAL	2	TRUE	1	0.179096186578168	3		326	579	SUCCESS
ATR	545	MSKCC	GRCh37	3	142183977	142183977	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	152	590	0	ENST00000350721.4:c.7003G>C	p.Asp2335His	p.D2335H	ENST00000350721	NM_001184.3	2335	Gat/Cat	41/47	0.231867563621628	3	FACETS	0.803	0.733	0.877	0.803	0.733	0.877	CLONAL	2	TRUE	1	0.179096186578168	3		590	1151	SUCCESS
ATR	545	MSKCC	GRCh37	3	142183992	142183992	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	147	607	0	ENST00000350721.4:c.6988G>C	p.Asp2330His	p.D2330H	ENST00000350721	NM_001184.3	2330	Gat/Cat	41/47	0.231867563621628	3	FACETS	0.762	0.694	0.834	0.762	0.694	0.834	SUBCLONAL	2	TRUE	1	0.179096186578168	3		607	1173	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845998	128845998	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	137	498	0	ENST00000249373.3:c.928G>A	p.Glu310Lys	p.E310K	ENST00000249373	NM_005631.4	310	Gag/Aag	5/12	0.231867563621628	3	FACETS	0.995	0.905	1	0.995	0.905	1	CLONAL	2	TRUE	1	0.179096186578168	3		498	838	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187246	38187246	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1228	196	706	0	ENST00000317025.8:c.1231G>T	p.Ala411Ser	p.A411S	ENST00000317025	NM_023034.1	411	Gcc/Tcc	6/24	0.179096186578168	5	FACETS	0.975	0.9	1			1	CLONAL	2	TRUE	NA	0.179096186578168	5		706	1424	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227763	53227763	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	105	689	2	ENST00000375401.3:c.2425A>G	p.Ser809Gly	p.S809G	ENST00000375401	NM_004187.3	809	Agt/Ggt	17/26	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.179096186578168	2		691	1078	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982814	7982814	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	171	865	0	ENST00000319144.4:c.971T>A	p.Ile324Asn	p.I324N	ENST00000319144	NM_001139.2	324	aTc/aAc	8/15	1	2	FACETS	0.957	0.885	1	1	0.992	1	CLONAL	2	FALSE	1	0.314682966016657	2		865	568	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549880	187549880	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	84	510	0	ENST00000441802.2:c.4361C>G	p.Pro1454Arg	p.P1454R	ENST00000441802	NM_005245.3	1454	cCt/cGt	8/27	0.135035511263745	3	FACETS	0.87	0.775	0.971	0.87	0.775	0.971	INDETERMINATE	2	FALSE	1	0.314682966016657	3		510	355	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876974	151876974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750213944	NA	P-0027134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	84	481	1	ENST00000262189.6:c.7387C>T	p.Arg2463Cys	p.R2463C	ENST00000262189	NM_170606.2	2463	Cgt/Tgt	37/59	0.135035511263745	3	FACETS	0.99	0.884	1	0.99	0.884	1	INDETERMINATE	2	FALSE	1	0.314682966016657	3		482	312	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913499	NA	P-0027135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	203	366	0	ENST00000345146.2:c.394C>A	p.Arg132Ser	p.R132S	ENST00000345146	NM_005896.2	132	Cgt/Agt	4/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.768277861638415	2		366	481	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0027135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	532	740	2	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.58184654736812	4	FACETS	0.772	0.739	0.804			1	SUBCLONAL	2	TRUE	NA	0.768277861638415	4		742	1587	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938029	76938029	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	443	689	0	ENST00000373344.5:c.2719C>T	p.Arg907Ter	p.R907*	ENST00000373344	NM_000489.3	907	Cga/Tga	9/35	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.768277861638415	2		689	980	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578213	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0027135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1347	417	867	0	ENST00000269305.4:c.636_637insAC	p.Arg213ThrfsTer35	p.R213Tfs*35	ENST00000269305	NM_001126112.2	212	-/AC	6/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.768277861638415	NA		867	1764	SUCCESS
ATR	545	MSKCC	GRCh37	3	142286910	142286910	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	277	465	0	ENST00000350721.4:c.146A>G	p.Asn49Ser	p.N49S	ENST00000350721	NM_001184.3	49	aAt/aGt	2/47	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.768277861638415	2		465	678	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923850	39923850	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	240	654	1	ENST00000378444.4:c.3241G>T	p.Glu1081Ter	p.E1081*	ENST00000378444	NM_001123385.1	1081	Gag/Tag	7/15	1	2	FACETS	0.632	0.591	0.675	0.632	0.591	0.675	SUBCLONAL	1	TRUE	1	0.768277861638415	2		655	988	SUCCESS
AR	367	MSKCC	GRCh37	X	66765149	66765151	+	inframe_deletion	In_Frame_Del	DEL	TGC	TGC	-	rs752055010	NA	P-0027136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	27	304	0	ENST00000374690.3:c.170_172del	p.Leu57del	p.L57del	ENST00000374690	NM_000044.3	54	tTGCtg/ttg	1/8	0.912776888278437	1	FACETS	0.266	0.215	0.322	0.266	0.215	0.322	SUBCLONAL	1	TRUE	0	0.912776888278437	1		304	121	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185819	32185819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145916093	NA	P-0027136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	340	683	0	ENST00000375023.3:c.1577C>T	p.Ala526Val	p.A526V	ENST00000375023	NM_004557.3	526	gCg/gTg	9/30	1	2	FACETS	0.996	0.949	1	0.996	0.949	1	CLONAL	1	TRUE	1	0.912776888278437	2		683	748	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422847	49422850	+	frameshift_variant	Frame_Shift_Del	DEL	GGAT	GGAT	-	novel	NA	P-0027136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	276	513	0	ENST00000301067.7:c.14245_14248del	p.Ile4749GlnfsTer47	p.I4749Qfs*47	ENST00000301067	NM_003482.3	4749	ATCCca/ca	44/54	0.279152623484853	5	FACETS	0.84	0.791	0.89			1	INDETERMINATE	2	TRUE	NA	0.912776888278437	5		513	853	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0027137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	184	473	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.351884214966029	1	FACETS	0.784	0.73	0.84	0.784	0.73	0.84	INDETERMINATE	1	TRUE	0	0.626001551833904	1		474	515	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588231	69588231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750386794	NA	P-0027137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	253	468	1	ENST00000168712.1:c.467C>T	p.Thr156Met	p.T156M	ENST00000168712	NM_002007.2	156	aCg/aTg	3/3	0.396412085221812	1	FACETS	0.888	0.838	0.94	0.888	0.838	0.94	CLONAL	1	TRUE	0	0.626001551833904	1		469	625	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578549	7578550	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGTACTGTA	novel	NA	P-0027137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	413	889	0	ENST00000269305.4:c.376-5_380dup	p.Pro128ThrfsTer24	p.P128Tfs*24	ENST00000269305	NM_001126112.2	127	tcc/tcTACAGTACTCc	5/11	0.626001551833904	1	FACETS	0.802	0.765	0.84	0.802	0.765	0.84	CLONAL	1	TRUE	0	0.626001551833904	1		889	1130	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40857171	40857171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1287411309	NA	P-0027137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	247	426	0	ENST00000428826.2:c.1870G>A	p.Gly624Arg	p.G624R	ENST00000428826		624	Gga/Aga	17/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.626001551833904	2		426	732	SUCCESS
APC	324	MSKCC	GRCh37	5	112175211	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	TAAAAG	TAAAAG	AAAAA	novel	NA	P-0027137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	53	248	0	ENST00000257430.4:c.3920_3925delinsAAAAA	p.Ile1307LysfsTer14	p.I1307Kfs*14	ENST00000257430	NM_000038.5	1307	aTAAAAGaa/aAAAAAaa	16/16	0.351884214966029	1	FACETS	0.337	0.289	0.39	0.337	0.289	0.39	INDETERMINATE	1	TRUE	0	0.626001551833904	1		248	345	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	412	528	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.585851848365863	3	FACETS	0.993	0.953	1			1	CLONAL	2	FALSE	NA	0.721734507773139	3		529	782	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0027138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	323	694	1	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.721734507773139	1	FACETS	0.949	0.906	0.991	0.949	0.906	0.991	CLONAL	1	FALSE	0	0.721734507773139	1		695	603	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363821	118363821	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	298	585	1	ENST00000534358.1:c.5054C>A	p.Ser1685Tyr	p.S1685Y	ENST00000534358	NM_005933.3	1685	tCc/tAc	16/36	1	2	FACETS	0.967	0.914	1	0.967	0.914	1	CLONAL	1	FALSE	1	0.721734507773139	2		586	854	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593415	48593415	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0027138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	243	430	0	ENST00000342988.3:c.1166T>A	p.Leu389Ter	p.L389*	ENST00000342988	NM_005359.5	389	tTg/tAg	10/12	0.721734507773139	1	FACETS	0.985	0.935	1	0.985	0.935	1	CLONAL	1	FALSE	0	0.721734507773139	1		430	437	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0027139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	225	443	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	0.715686604404688	2		443	588	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0027139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	234	408	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	NA	2	FACETS	0.893	0.837	0.951			1	INDETERMINATE	1	TRUE	NA	0.715686604404688	2		408	732	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844109	68844110	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	272	460	0	ENST00000261769.5:c.698dup	p.His233GlnfsTer11	p.H233Qfs*11	ENST00000261769	NM_004360.3	233	cac/cAac	6/16	0.699214693708191	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.715686604404688	1		460	470	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057303	30057303	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1450914413	NA	P-0027139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	273	401	0	ENST00000338641.4:c.785G>A	p.Arg262Gln	p.R262Q	ENST00000338641	NM_000268.3	262	cGa/cAa	8/16	1	2	FACETS	0.899	0.846	0.952	0.899	0.846	0.952	CLONAL	1	TRUE	1	0.715686604404688	2		401	849	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958295	11958295	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	100	339	0	ENST00000353533.5:c.205C>T	p.Gln69Ter	p.Q69*	ENST00000353533	NM_003010.3	69	Caa/Taa	2/11	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.715686604404688	2		339	276	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272118	18272118	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	22	51	0	ENST00000222254.8:c.628G>A	p.Glu210Lys	p.E210K	ENST00000222254	NM_005027.3	210	Gag/Aag	6/16	1	2	FACETS	0.647	0.512	0.797	0.647	0.512	0.797	SUBCLONAL	1	TRUE	1	0.715686604404688	2		51	95	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307941	11307941	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	260	492	0	ENST00000361445.4:c.1051C>G	p.Pro351Ala	p.P351A	ENST00000361445	NM_004958.3	351	Cca/Gca	7/58	0.699214693708191	1	FACETS	0.968	0.919	1	0.968	0.919	1	CLONAL	1	TRUE	0	0.715686604404688	1		492	482	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057799	27057799	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	420	770	1	ENST00000324856.7:c.1507C>T	p.Gln503Ter	p.Q503*	ENST00000324856	NM_006015.4	503	Cag/Tag	3/20	1	2	FACETS	0.934	0.89	0.978	0.934	0.89	0.978	CLONAL	1	TRUE	1	0.715686604404688	2		771	1257	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932167	36932167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	250	452	0	ENST00000361632.4:c.2302C>T	p.Leu768Phe	p.L768F	ENST00000361632		768	Ctc/Ttc	16/16	1	2	FACETS	0.907	0.852	0.964	0.907	0.852	0.964	CLONAL	1	TRUE	1	0.715686604404688	2		452	770	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981162	201981162	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1523	403	681	0	ENST00000359651.3:c.241G>C	p.Glu81Gln	p.E81Q	ENST00000359651		81	Gag/Cag	2/8	0.696171808715596	4	FACETS	1	0.951	1	0.334	0.317	0.353	CLONAL	1	TRUE	1	0.715686604404688	4		681	1926	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982122	201982122	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1447	379	645	0	ENST00000359651.3:c.646G>C	p.Asp216His	p.D216H	ENST00000359651		216	Gac/Cac	5/8	0.696171808715596	4	FACETS	0.995	0.942	1	0.332	0.314	0.35	CLONAL	1	TRUE	1	0.715686604404688	4		645	1826	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982361	201982361	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1710	412	684	0	ENST00000359651.3:c.740G>C	p.Arg247Pro	p.R247P	ENST00000359651		247	cGa/cCa	6/8	0.696171808715596	4	FACETS	0.931	0.883	0.98	0.31	0.294	0.327	CLONAL	1	TRUE	1	0.715686604404688	4		684	2122	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982416	201982416	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1594	403	671	1	ENST00000359651.3:c.795G>C	p.Lys265Asn	p.K265N	ENST00000359651		265	aaG/aaC	6/8	0.696171808715596	4	FACETS	0.968	0.917	1	0.323	0.305	0.34	CLONAL	1	TRUE	1	0.715686604404688	4		672	1997	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15952217	15952217	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	355	508	0	ENST00000268712.3:c.6478G>T	p.Glu2160Ter	p.E2160*	ENST00000268712	NM_006311.3	2160	Gag/Tag	41/46	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.715686604404688	2		508	964	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687547	37687547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2620	178	285	0	ENST00000447079.4:c.4451G>A	p.Arg1484Lys	p.R1484K	ENST00000447079	NM_015083.1	1484	aGa/aAa	14/14	0.715686604404688	12	FACETS	0.814	0.746	0.886			1	CLONAL	1	TRUE	NA	0.715686604404688	12		285	2798	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879854	37879854	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4359	318	515	0	ENST00000269571.5:c.2149G>T	p.Glu717Ter	p.E717*	ENST00000269571		717	Gag/Tag	18/27	0.715686604404688	12	FACETS	0.87	0.815	0.927			1	CLONAL	1	TRUE	NA	0.715686604404688	12		515	4677	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696399	47696399	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2423	305	520	0	ENST00000347630.2:c.424C>G	p.Leu142Val	p.L142V	ENST00000347630	NM_001007230.1	142	Ctt/Gtt	6/11	0.715686604404688	7	FACETS	0.871	0.817	0.928			1	CLONAL	1	TRUE	NA	0.715686604404688	7		520	2728	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645363	215645363	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	264	480	0	ENST00000260947.4:c.1235C>A	p.Ser412Ter	p.S412*	ENST00000260947	NM_000465.2	412	tCa/tAa	4/11	1	2	FACETS	0.896	0.843	0.951	0.896	0.843	0.951	CLONAL	1	TRUE	1	0.715686604404688	2		480	823	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388662	31388662	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	295	507	0	ENST00000328111.2:c.1927G>C	p.Asp643His	p.D643H	ENST00000328111	NM_006892.3	643	Gac/Cac	18/23	1	2	FACETS	0.896	0.845	0.948	0.896	0.845	0.948	CLONAL	1	TRUE	1	0.715686604404688	2		507	920	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103767	47103767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745410359	NA	P-0027139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	327	466	2	ENST00000409792.3:c.6179C>T	p.Ser2060Leu	p.S2060L	ENST00000409792	NM_014159.6	2060	tCa/tTa	14/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.715686604404688	2		468	912	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953884	55953884	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	251	457	0	ENST00000263923.4:c.3552G>T	p.Leu1184Phe	p.L1184F	ENST00000263923	NM_002253.2	1184	ttG/ttT	27/30	1	2	FACETS	0.998	0.938	1	0.998	0.938	1	CLONAL	1	TRUE	1	0.715686604404688	2		457	703	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665400	176665401	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0027139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	192	292	0	ENST00000439151.2:c.4084_4085delinsAA	p.Gly1362Lys	p.G1362K	ENST00000439151	NM_022455.4	1362	GGa/AAa	7/23	1	2	FACETS	0.927	0.863	0.992	0.927	0.863	0.992	CLONAL	1	TRUE	1	0.715686604404688	2		292	579	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045670	26045670	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	99	219	0	ENST00000540144.1:c.32C>A	p.Ser11Tyr	p.S11Y	ENST00000540144	NM_003531.2	11	tCt/tAt	1/1	1	2	FACETS	0.826	0.745	0.91	0.826	0.745	0.91	CLONAL	1	TRUE	1	0.715686604404688	2		219	335	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015605	112015605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1323	286	455	0	ENST00000368678.4:c.1237G>A	p.Glu413Lys	p.E413K	ENST00000368678		413	Gaa/Aaa	11/13	0.715686604404688	5	FACETS	1	0.959	1	0.257	0.241	0.275	CLONAL	1	TRUE	1	0.715686604404688	5		455	1609	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534506	140534506	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	279	371	0	ENST00000288602.6:c.407C>T	p.Ser136Leu	p.S136L	ENST00000288602	NM_004333.4	136	tCa/tTa	3/18	0.695259860643067	3	FACETS	1	0.974	1	0.531	0.5	0.564	CLONAL	1	TRUE	1	0.715686604404688	3		371	996	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787792	135787792	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	237	468	0	ENST00000298552.3:c.790C>G	p.Leu264Val	p.L264V	ENST00000298552	NM_001162426.1	264	Ctg/Gtg	9/23	1	2	FACETS	0.932	0.873	0.991	0.932	0.873	0.991	CLONAL	1	TRUE	1	0.715686604404688	2		468	711	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0027141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	369	434	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.617720051914282	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.617720051914282	1		434	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577088	7577088	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1204379654	NA	P-0027141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	660	656	0	ENST00000269305.4:c.850A>C	p.Thr284Pro	p.T284P	ENST00000269305	NM_001126112.2	284	Aca/Cca	8/11	0.616718187508609	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.617720051914282	2		656	1061	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981174	201981215	+	inframe_deletion	In_Frame_Del	DEL	TACGACGCAAGCGCCATTGACTTCTCACGATGTGACATGGAT	TACGACGCAAGCGCCATTGACTTCTCACGATGTGACATGGAT	-	novel	NA	P-0027141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	466	767	0	ENST00000359651.3:c.253_294del	p.Tyr85_Asp98del	p.Y85_D98del	ENST00000359651		85	TACGACGCAAGCGCCATTGACTTCTCACGATGTGACATGGAT/-	2/8	0.163688273729069	6	FACETS	1	0.992	1	0.78	0.745	0.816	INDETERMINATE	2	TRUE	3	0.617720051914282	6		767	1441	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0027142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	28	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.3	2	FACETS	0.697	0.555	0.858			1	SUBCLONAL	1	TRUE	NA	0.15	2		509	536	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132542	11132542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	38	580	0	ENST00000358026.2:c.2758G>A	p.Glu920Lys	p.E920K	ENST00000358026	NM_001128849.1	920	Gag/Aag	19/36	1	2	FACETS	0.762	0.628	0.912	0.762	0.628	0.912	CLONAL	1	TRUE	1	0.15	2		580	665	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0027142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	19	192	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	0.175155732018418	1	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	0	0.15	1		192	199	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578410	7578410	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	42	579	0	ENST00000269305.4:c.520A>T	p.Arg174Trp	p.R174W	ENST00000269305	NM_001126112.2	174	Agg/Tgg	5/11	1	2	FACETS	0.911	0.759	1	0.911	0.759	1	CLONAL	1	TRUE	1	0.15	2		579	615	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900239	32900239	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	27	312	0	ENST00000380152.3:c.427C>G	p.Pro143Ala	p.P143A	ENST00000380152		143	Cct/Gct	5/27	0.115299006981151	3	FACETS	0.749	0.594	0.926	0.374	0.297	0.463	CLONAL	1	TRUE	1	0.15	3		312	517	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0027143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	142	443	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	0.440731960058592	2		443	637	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106596	27106607	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGTTGGACCT	GCAGTTGGACCT	AC	novel	NA	P-0027143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	193	596	3	ENST00000324856.7:c.6207_6218delinsAC	p.Gln2070HisfsTer62	p.Q2070Hfs*62	ENST00000324856	NM_006015.4	2069	ggGCAGTTGGACCTa/ggACa	20/20	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.440731960058592	2		599	867	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050298	176050298	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	128	422	0	ENST00000367669.3:c.1267A>G	p.Ile423Val	p.I423V	ENST00000367669	NM_022457.5	423	Ata/Gta	11/20	0.39718892879605	3	FACETS	1	0.928	1	0.513	0.465	0.563	CLONAL	1	TRUE	1	0.440731960058592	3		422	691	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842746	68842747	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0027143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	139	431	0	ENST00000261769.5:c.685_686dup	p.Phe231SerfsTer20	p.F231Sfs*20	ENST00000261769	NM_004360.3	228	tac/tACac	5/16	0.440731960058592	1	FACETS	0.987	0.905	1	0.987	0.905	1	CLONAL	1	TRUE	0	0.440731960058592	1		431	498	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944257	206944257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	339	360	0	ENST00000423557.1:c.373C>T	p.Arg125Cys	p.R125C	ENST00000423557	NM_000572.2	125	Cgc/Tgc	3/5	0.739666447515842	4	FACETS	0.888	0.844	0.934	0.888	0.844	0.934	CLONAL	2	TRUE	2	0.770210274955461	4		360	877	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046500	30046500	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1183967758	NA	P-0027145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	217	511	1	ENST00000331968.5:c.2683C>T	p.Pro895Ser	p.P895S	ENST00000331968	NM_002742.2	895	Cct/Tct	18/18	0.748570417769332	3	FACETS	0.878	0.817	0.94	0.439	0.408	0.47	CLONAL	1	TRUE	1	0.770210274955461	3		512	889	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562821	95562821	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1218181729	NA	P-0027145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	296	362	0	ENST00000393063.1:c.4436A>G	p.Tyr1479Cys	p.Y1479C	ENST00000393063	NM_030621.3	1479	tAt/tGt	24/28	0.739666447515842	4	FACETS	0.924	0.875	0.974	0.924	0.875	0.974	CLONAL	2	TRUE	2	0.770210274955461	4		362	736	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274232	10274232	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1201806901	NA	P-0027145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	146	314	1	ENST00000330684.3:c.37C>A	p.Pro13Thr	p.P13T	ENST00000330684	NM_001134407.1	13	Ccg/Acg	2/13	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.770210274955461	2		315	370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0027145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	546	535	0	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.770210274955461	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.770210274955461	2		535	691	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732349	74732349	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	380	338	0	ENST00000359995.5:c.560C>T	p.Ser187Phe	p.S187F	ENST00000359995	NM_001195427.1	187	tCt/tTt	2/3	0.748570417769332	3	FACETS	0.952	0.912	0.992	0.952	0.912	0.992	CLONAL	2	TRUE	1	0.770210274955461	3		338	718	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940480	29940480	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	334	483	0	ENST00000389048.3:c.751G>C	p.Asp251His	p.D251H	ENST00000389048	NM_004304.4	251	Gac/Cac	2/29	0.532036725852307	5	FACETS	0.989	0.938	1	0.659	0.625	0.694	CLONAL	2	TRUE	2	0.770210274955461	5		483	945	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230832	66230832	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0027145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	165	401	0	ENST00000273854.3:c.2139T>A	p.Tyr713Ter	p.Y713*	ENST00000273854	NM_004439.5	713	taT/taA	12/18	0.626848957250397	3	FACETS	0.986	0.91	1			1	CLONAL	1	TRUE	NA	0.770210274955461	3		401	602	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858437	27858437	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	177	322	1	ENST00000359303.2:c.134G>A	p.Gly45Asp	p.G45D	ENST00000359303	NM_003535.2	45	gGc/gAc	1/1	1	2	FACETS	0.95	0.883	1	0.95	0.883	1	CLONAL	1	TRUE	1	0.770210274955461	2		323	484	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500808	8500808	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs376837190	NA	P-0027145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	421	410	0	ENST00000356435.5:c.2074G>C	p.Asp692His	p.D692H	ENST00000356435		692	Gat/Cat	13/35	0.770210274955461	2	FACETS	0.985	0.956	1	0.985	0.956	1	CLONAL	2	TRUE	0	0.770210274955461	2		410	555	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740560	145740571	+	frameshift_variant	Frame_Shift_Del	DEL	TCCTGCCCAGGG	TCCTGCCCAGGG	C	novel	NA	P-0027145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	281	655	0	ENST00000428558.2:c.1446_1457delinsG	p.Pro483AlafsTer53	p.P483Afs*53	ENST00000428558	NM_004260.3	482	cgCCCTGGGCAGGAg/cgGg	8/22	0.770210274955461	4	FACETS	0.875	0.82	0.931	0.292	0.273	0.311	CLONAL	1	TRUE	1	0.770210274955461	4		655	1477	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0027146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	77	570	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.935	0.82	1	0.935	0.82	1	CLONAL	1	TRUE	1	0.197860228466018	2		570	832	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231707	66231707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1211795184	NA	P-0027146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	31	481	1	ENST00000273854.3:c.1993G>A	p.Glu665Lys	p.E665K	ENST00000273854	NM_004439.5	665	Gaa/Aaa	11/18	1	2	FACETS	0.612	0.494	0.746	0.612	0.494	0.746	SUBCLONAL	1	TRUE	1	0.197860228466018	2		482	512	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952086	178952086	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	72	338	0	ENST00000263967.3:c.3141T>A	p.His1047Gln	p.H1047Q	ENST00000263967	NM_006218.2	1047	caT/caA	21/21	0.197860228466018	5	FACETS	1	0.961	1	0.422	0.368	0.481	CLONAL	1	TRUE	2	0.197860228466018	5		338	745	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0027146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	1238	562	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.197860228466018	26	FACETS	0.977	0.956	0.998			1	CLONAL	21	TRUE	NA	0.197860228466018	26		562	2058	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044850	47044850	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	220	640	1	ENST00000377604.3:c.2176C>T	p.Arg726Ter	p.R726*	ENST00000377604	NM_001204468.1	726	Cga/Tga	20/24	0.187359813837008	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.197860228466018	2		641	1056	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940045	76940045	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	138	463	0	ENST00000373344.5:c.703T>C	p.Cys235Arg	p.C235R	ENST00000373344	NM_000489.3	235	Tgc/Cgc	9/35	0.187359813837008	2	FACETS	0.848	0.772	0.928	0.848	0.772	0.928	CLONAL	2	TRUE	0	0.197860228466018	2		463	822	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0027147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	53	397	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.572	0.488	0.665	0.572	0.488	0.665	SUBCLONAL	1	TRUE	1	0.33750220265711	2		397	549	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0027147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	180	406	2	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	1	2	FACETS	1	0.977	1	1	0.994	1	CLONAL	2	TRUE	1	0.33750220265711	2		408	478	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0027147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	185	458	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	0.934	0.867	1	1	0.993	1	CLONAL	2	TRUE	1	0.33750220265711	2		458	587	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144148	55144148	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519700	NA	P-0027147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	205	493	0	ENST00000257290.5:c.1977C>G	p.Asn659Lys	p.N659K	ENST00000257290	NM_006206.4	659	aaC/aaG	14/23	1	2	FACETS	0.826	0.769	0.885	1	0.992	1	CLONAL	2	TRUE	1	0.33750220265711	2		493	735	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs967461896	NA	P-0027147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	29	559	1	ENST00000269305.4:c.526T>A	p.Cys176Ser	p.C176S	ENST00000269305	NM_001126112.2	176	Tgc/Agc	5/11	1	2	FACETS	0.245	0.196	0.302	0.245	0.196	0.302	SUBCLONAL	1	TRUE	1	0.33750220265711	2		560	701	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151882	108151891	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTTGTGAA	ACCTTGTGAA	-	novel	NA	P-0027147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	134	346	1	ENST00000278616.4:c.3564_3573del	p.His1188GlnfsTer4	p.H1188Qfs*4	ENST00000278616	NM_000051.3	1188	cACCTTGTGAAa/ca	24/63	1	2	FACETS	0.836	0.765	0.91	1	0.989	1	CLONAL	2	TRUE	1	0.33750220265711	2		347	475	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16235946	16235946	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0027149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	167	514	0	ENST00000375759.3:c.1012A>T	p.Lys338Ter	p.K338*	ENST00000375759	NM_015001.2	338	Aag/Tag	4/15	0.376801176823221	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.376801176823221	1		514	658	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094365	27094374	+	frameshift_variant	Frame_Shift_Del	DEL	GACCGTTATC	GACCGTTATC	-	novel	NA	P-0027149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	211	551	0	ENST00000324856.7:c.3073_3082del	p.Asp1025TrpfsTer11	p.D1025Wfs*11	ENST00000324856	NM_006015.4	1025	GACCGTTATCtg/tg	11/20	0.376801176823221	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.376801176823221	1		551	746	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436112	51436112	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	130	451	0	ENST00000262662.1:c.72G>T	p.Leu24Phe	p.L24F	ENST00000262662		24	ttG/ttT	3/4	0.376801176823221	1	FACETS	0.824	0.748	0.902	0.824	0.748	0.902	CLONAL	1	TRUE	0	0.376801176823221	1		451	680	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572576	64572576	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	227	654	1	ENST00000312049.6:c.1280G>T	p.Ser427Ile	p.S427I	ENST00000312049	NM_130799.2	427	aGt/aTt	9/10	0.376801176823221	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.376801176823221	1		655	776	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478847	56478847	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	93	697	1	ENST00000267101.3:c.303C>A	p.Asn101Lys	p.N101K	ENST00000267101	NM_001982.3	101	aaC/aaA	3/28	1	2	FACETS	0.427	0.379	0.48	0.427	0.379	0.48	SUBCLONAL	1	TRUE	1	0.376801176823221	2		698	1155	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514441	103514441	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	53	236	0	ENST00000355739.4:c.942G>T	p.Met314Ile	p.M314I	ENST00000355739	NM_000123.3	314	atG/atT	8/15	1	2	FACETS	0.754	0.645	0.872	0.754	0.645	0.872	SUBCLONAL	1	TRUE	1	0.376801176823221	2		236	373	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250927	99250927	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	172	513	1	ENST00000268035.6:c.231G>T	p.Lys77Asn	p.K77N	ENST00000268035	NM_000875.3	77	aaG/aaT	2/21	0.376801176823221	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.376801176823221	1		514	647	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351788	89351788	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	75	815	0	ENST00000301030.4:c.1162G>T	p.Val388Phe	p.V388F	ENST00000301030	NM_001256183.1	388	Gtt/Ttt	9/13	0.376801176823221	1	FACETS	0.33	0.288	0.375	0.33	0.288	0.375	SUBCLONAL	1	TRUE	0	0.376801176823221	1		815	980	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990651	7990651	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	242	668	0	ENST00000319144.4:c.110T>A	p.Leu37Gln	p.L37Q	ENST00000319144	NM_001139.2	37	cTg/cAg	1/15	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.376801176823221	2		668	1079	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42843834	42843834	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	75	607	0	ENST00000398585.3:c.1085G>A	p.Gly362Glu	p.G362E	ENST00000398585	NM_001135099.1	362	gGa/gAa	10/14	0.376801176823221	1	FACETS	0.466	0.408	0.529	0.466	0.408	0.529	SUBCLONAL	1	TRUE	0	0.376801176823221	1		607	693	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956747	68956747	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	169	606	0	ENST00000288368.4:c.865A>T	p.Thr289Ser	p.T289S	ENST00000288368	NM_024870.2	289	Aca/Tca	8/40	0.376801176823221	1	FACETS	0.899	0.827	0.973	0.899	0.827	0.973	CLONAL	1	TRUE	0	0.376801176823221	1		606	810	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798803	135798803	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	105	390	0	ENST00000298552.3:c.440G>T	p.Gly147Val	p.G147V	ENST00000298552	NM_001162426.1	147	gGg/gTg	6/23	1	2	FACETS	0.902	0.81	0.999	0.902	0.81	0.999	CLONAL	1	TRUE	1	0.376801176823221	2		390	618	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909636	76909636	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	94	270	0	ENST00000373344.5:c.4269del	p.Arg1425GlyfsTer65	p.R1425Gfs*65	ENST00000373344	NM_000489.3	1423	aaG/aa	14/35	1	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.376801176823221	1		270	312	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0027151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	142	294	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.173617993297005	4	FACETS	0.75	0.689	0.813	0.75	0.689	0.813	INDETERMINATE	2	TRUE	2	0.71	4		294	456	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797312	42797312	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	304	614	1	ENST00000575354.2:c.3674G>A	p.Gly1225Glu	p.G1225E	ENST00000575354	NM_015125.3	1225	gGg/gAg	15/20	0.173617993297005	4	FACETS	0.894	0.846	0.943	0.894	0.846	0.943	INDETERMINATE	2	TRUE	2	0.71	4		615	819	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196468	106196468	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	216	356	0	ENST00000380013.4:c.4801T>G	p.Ser1601Ala	p.S1601A	ENST00000380013	NM_001127208.2	1601	Tca/Gca	11/11	0.173617993297005	4	FACETS	0.858	0.803	0.915	0.858	0.803	0.915	INDETERMINATE	2	TRUE	2	0.71	4		356	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576900	7576901	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	176	613	0	ENST00000269305.4:c.945dup	p.Pro316SerfsTer21	p.P316Sfs*21	ENST00000269305	NM_001126112.2	315	-/T	9/11	0.194908385288241	2	FACETS	1	0.986	1	0.664	0.611	0.719	CLONAL	1	TRUE	0	0.266815622551451	2		613	993	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376382	15376382	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1490	142	953	0	ENST00000263377.2:c.632C>G	p.Pro211Arg	p.P211R	ENST00000263377	NM_058243.2	211	cCt/cGt	5/20	1	2	FACETS	0.652	0.592	0.716	0.652	0.592	0.716	SUBCLONAL	1	TRUE	1	0.266815622551451	2		953	1632	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085978	16085978	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	185	539	0	ENST00000281043.3:c.1154A>G	p.Asn385Ser	p.N385S	ENST00000281043	NM_005378.4	385	aAc/aGc	3/3	0.194908385288241	2	FACETS	0.883	0.817	0.952	0.883	0.817	0.952	CLONAL	2	TRUE	0	0.266815622551451	2		539	785	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394431	162394431	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	47	388	1	ENST00000366898.1:c.637G>T	p.Gly213Ter	p.G213*	ENST00000366898	NM_004562.2	213	Gga/Tga	6/12	0.266815622551451	3	FACETS	0.637	0.536	0.748	0.212	0.178	0.25	SUBCLONAL	1	TRUE	0	0.266815622551451	3		389	627	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411327	63411327	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	77	608	1	ENST00000330258.3:c.1840C>A	p.His614Asn	p.H614N	ENST00000330258	NM_152424.3	614	Cac/Aac	2/2	NA	2	FACETS	0.802	0.703	0.908			1	INDETERMINATE	1	TRUE	NA	0.266815622551451	2		609	720	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532912	187532914	+	missense_variant	Missense_Mutation	TNP	AAA	AAA	TAC	novel	NA	P-0027153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	35	379	0	ENST00000441802.2:c.9479_9481delinsGTA	p.Ile3160_Leu3161delinsSerIle	p.I3160_L3161delinsSI	ENST00000441802	NM_005245.3	3160	aTTTta/aGTAta	14/27	1	2	FACETS	0.632	0.518	0.76	0.632	0.518	0.76	SUBCLONAL	1	TRUE	1	0.266815622551451	2		379	415	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204512017	204512018	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	A	novel	NA	P-0027153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	63	408	0	ENST00000367182.3:c.617_618delinsA	p.Leu206Ter	p.L206*	ENST00000367182	NM_001278516.1	206	tTG/tA	8/11	1	2	FACETS	0.596	0.515	0.685	0.596	0.515	0.685	SUBCLONAL	1	TRUE	1	0.266815622551451	2		408	792	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0027154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	181	449	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.362764827154864	2		449	674	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0027154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	194	488	1	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.362764827154864	2		489	968	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915952	127915952	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs865855853	NA	P-0027154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	359	571	1	ENST00000373547.4:c.529C>T	p.Arg177Ter	p.R177*	ENST00000373547	NM_002721.4	177	Cga/Tga	6/7	0.362764827154864	2	FACETS	0.914	0.867	0.961	0.914	0.867	0.961	CLONAL	2	TRUE	0	0.362764827154864	2		572	1083	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420093	41420093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	68	340	0	ENST00000373198.4:c.228G>A	p.Met76Ile	p.M76I	ENST00000373198	NM_133170.3	76	atG/atA	3/32	0.362764827154864	1	FACETS	0.697	0.609	0.793	0.697	0.609	0.793	SUBCLONAL	1	TRUE	0	0.362764827154864	1		340	440	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007806	45007807	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0027154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	114	327	0	ENST00000558401.1:c.253_254del	p.Leu85ValfsTer4	p.L85Vfs*4	ENST00000558401	NM_004048.2	85	TTg/g	2/4	0.345522868220068	1	FACETS	0.617	0.555	0.682	0.617	0.555	0.682	SUBCLONAL	1	TRUE	0	0.362764827154864	1		327	834	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864663	68864663	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773560075	NA	P-0027154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	74	263	0	ENST00000288368.4:c.34G>A	p.Glu12Lys	p.E12K	ENST00000288368	NM_024870.2	12	Gag/Aag	1/40	1	2	FACETS	0.974	0.856	1	0.974	0.856	1	CLONAL	1	TRUE	1	0.362764827154864	2		263	419	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139148	108139148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	154	498	1	ENST00000278616.4:c.2650C>T	p.Pro884Ser	p.P884S	ENST00000278616	NM_000051.3	884	Cct/Tct	18/63	1	2	FACETS	0.949	0.868	1	0.949	0.868	1	CLONAL	1	TRUE	1	0.362764827154864	2		499	895	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420079	49420079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778198600	NA	P-0027154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	168	629	1	ENST00000301067.7:c.15670C>T	p.Arg5224Cys	p.R5224C	ENST00000301067	NM_003482.3	5224	Cgt/Tgt	48/54	1	2	FACETS	0.889	0.816	0.965	0.889	0.816	0.965	CLONAL	1	TRUE	1	0.362764827154864	2		630	1042	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431892	49431892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	236	846	0	ENST00000301067.7:c.9247G>A	p.Glu3083Lys	p.E3083K	ENST00000301067	NM_003482.3	3083	Gag/Aag	34/54	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.362764827154864	2		846	1244	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557701	21557701	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	209	697	0	ENST00000382592.4:c.2144C>T	p.Ala715Val	p.A715V	ENST00000382592	NM_014572.2	715	gCc/gTc	5/8	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.362764827154864	2		697	1065	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155659	106155659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	134	416	0	ENST00000380013.4:c.560G>A	p.Gly187Glu	p.G187E	ENST00000380013	NM_001127208.2	187	gGg/gAg	3/11	1	2	FACETS	0.913	0.83	1	0.913	0.83	1	CLONAL	1	TRUE	1	0.362764827154864	2		416	809	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140118	50140118	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745911237	NA	P-0027156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	459	788	1	ENST00000246792.3:c.307G>A	p.Gly103Ser	p.G103S	ENST00000246792	NM_006270.3	103	Ggc/Agc	3/6	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.701570732993162	2		789	1295	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440896	52440906	+	frameshift_variant	Frame_Shift_Del	DEL	GTCCACTCCTC	GTCCACTCCTC	-	novel	NA	P-0027156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	334	763	0	ENST00000460680.1:c.598_608del	p.Glu200ArgfsTer39	p.E200Rfs*39	ENST00000460680	NM_004656.3	200	GAGGAGTGGACa/a	8/17	0.701570732993162	1	FACETS	0.816	0.776	0.855	0.816	0.776	0.855	CLONAL	1	TRUE	0	0.701570732993162	1		763	758	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623266	52623266	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	170	311	0	ENST00000394830.3:c.2785G>T	p.Glu929Ter	p.E929*	ENST00000394830	NM_018313.4	929	Gaa/Taa	19/30	0.701570732993162	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.701570732993162	1		311	303	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	42	528	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.150916056032553	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		529	497	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0027157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	34	403	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		403	302	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526152	189526152	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751300168	NA	P-0027157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	92	656	0	ENST00000264731.3:c.416C>T	p.Ala139Val	p.A139V	ENST00000264731	NM_003722.4	139	gCg/gTg	4/14	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		656	742	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425533	49425533	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0027157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	33	957	1	ENST00000301067.7:c.12955A>T	p.Arg4319Ter	p.R4319*	ENST00000301067	NM_003482.3	4319	Aga/Tga	39/54	0.150916056032553	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		958	602	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477073	67477073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223744	NA	P-0027157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	26	442	0	ENST00000327367.4:c.880G>A	p.Val294Met	p.V294M	ENST00000327367	NM_005902.3	294	Gtg/Atg	7/9	0.150916056032553	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		442	421	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101932	11101932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0121559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1625	99	693	3	ENST00000358026.2:c.1352G>A	p.Arg451His	p.R451H	ENST00000358026	NM_001128849.1	451	cGc/cAc	8/36	1	2	FACETS	0.883	0.785	0.989	0.883	0.785	0.989	CLONAL	1	NA	1	0.13	2		696	1724	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435155	56435155	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0121559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1561	96	612	3	ENST00000407977.2:c.1982C>T	p.Ser661Phe	p.S661F	ENST00000407977		661	tCc/tTc	9/10	1	2	FACETS	0.891	0.791	1	0.891	0.791	1	CLONAL	1	NA	1	0.13	2		615	1657	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974676	21974676	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0121559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	52	464	2	ENST00000304494.5:c.150+1G>A		p.X50_splice	ENST00000304494	NM_000077.4	50			1	2	FACETS	0.8	0.679	0.934	0.8	0.679	0.934	CLONAL	1	NA	1	0.13	2		466	1000	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794950	42794950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141594034	NA	P-0121559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1325	85	658	0	ENST00000575354.2:c.2030G>A	p.Arg677Gln	p.R677Q	ENST00000575354	NM_015125.3	677	cGg/cAg	10/20	1	2	FACETS	0.927	0.817	1	0.927	0.817	1	CLONAL	1	NA	1	0.13	2		658	1410	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948835	71948837	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs777012152	NA	P-0121559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1606	94	869	0	ENST00000298229.2:c.3551_3552+1del		p.Edel	ENST00000298229	NM_001567.3	1183	GAG/-	26/28	1	2	FACETS	0.851	0.753	0.955	0.851	0.753	0.955	CLONAL	1	NA	1	0.13	2		869	1700	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005649	42005649	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0121559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	35	293	0	ENST00000219905.7:c.3385G>A	p.Glu1129Lys	p.E1129K	ENST00000219905	NM_001164273.1	1129	Gag/Aag	9/24	1	2	FACETS	0.798	0.652	0.962	0.798	0.652	0.962	CLONAL	1	NA	1	0.13	2		293	675	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15967414	15967414	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0121559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	67	501	2	ENST00000268712.3:c.5189C>T	p.Ala1730Val	p.A1730V	ENST00000268712	NM_006311.3	1730	gCt/gTt	35/46	1	2	FACETS	0.928	0.804	1	0.928	0.804	1	CLONAL	1	NA	1	0.13	2		503	1111	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677244	29677244	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0121559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	39	400	3	ENST00000356175.3:c.7305del	p.Lys2435AsnfsTer33	p.K2435Nfs*33	ENST00000356175	NM_000267.3	2434	ctA/ct	49/57	1	2	FACETS	0.839	0.694	1	0.839	0.694	1	CLONAL	1	NA	1	0.13	2		403	715	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40491423	40491423	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777883261	NA	P-0121559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	60	527	1	ENST00000264657.5:c.377G>A	p.Gly126Glu	p.G126E	ENST00000264657	NM_139276.2	126	gGg/gAg	5/24	1	2	FACETS	0.918	0.788	1	0.918	0.788	1	CLONAL	1	NA	1	0.13	2		528	1006	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1268704	1268704	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1575	113	720	3	ENST00000310581.5:c.2513C>A	p.Ser838Tyr	p.S838Y	ENST00000310581	NM_198253.2	838	tCc/tAc	9/16	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	NA	1	0.13	2		723	1688	SUCCESS
RET	5979	MSKCC	GRCh37	10	43602019	43602019	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	rs145402131	NA	P-0027159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	303	789	0	ENST00000355710.3:c.1063A>T	p.Arg355Trp	p.R355W	ENST00000355710	NM_020975.4	355	Agg/Tgg	5/20	1	2	FACETS	0.712	0.67	0.755	0.712	0.67	0.755	SUBCLONAL	1	TRUE	1	0.688316561808326	2		789	1237	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577460	64577460	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	723	701	0	ENST00000312049.6:c.122T>G	p.Leu41Arg	p.L41R	ENST00000312049	NM_130799.2	41	cTg/cGg	2/10	0.688316561808326	2	FACETS	0.981	0.956	1	0.981	0.956	1	CLONAL	2	TRUE	0	0.688316561808326	2		701	1071	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657524	37657524	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	32	497	0	ENST00000447079.4:c.2441A>T	p.Glu814Val	p.E814V	ENST00000447079	NM_015083.1	814	gAg/gTg	6/14	1	2	FACETS	0.154	0.124	0.188	0.154	0.124	0.188	SUBCLONAL	1	TRUE	1	0.688316561808326	2		497	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0027160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	143	669	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.597122127545378	1	FACETS	0.843	0.779	0.908	0.843	0.779	0.908	CLONAL	1	TRUE	0	0.646495173305777	1		669	355	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006009	22006009	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	36	797	0	ENST00000276925.6:c.394C>A	p.Leu132Met	p.L132M	ENST00000276925	NM_004936.3	132	Ctg/Atg	2/2	0.136086110447599	0	FACETS	0.063	0.051	0.076			1	INDETERMINATE	1	TRUE	0	0.646495173305777	0		797	627	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441431	52441431	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	105	557	0	ENST00000460680.1:c.421C>G	p.His141Asp	p.H141D	ENST00000460680	NM_004656.3	141	Cat/Gat	6/17	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.21	2		557	907	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0027162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	313	433	0	ENST00000374080.3:c.3670C>T	p.Leu1224Phe	p.L1224F	ENST00000374080		1224	Ctc/Ttc	26/45	1	1	FACETS	1	0.972	1	1	0.997	1	CLONAL	3	TRUE	0	0.276590745109746	1		433	632	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216476	108216477	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587782558	NA	P-0027162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	121	203	1	ENST00000278616.4:c.8432dup	p.Ser2812ValfsTer3	p.S2812Vfs*3	ENST00000278616	NM_000051.3	2809	caa/cAaa	58/63	0.276590745109746	1	FACETS	1	0.976	1	1	0.991	1	CLONAL	2	TRUE	0	0.276590745109746	1		204	318	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0027163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	632	671	2	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.700245635569674	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.700245635569674	2		673	900	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888165	112888165	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397507510	NA	P-0027163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	327	760	0	ENST00000351677.2:c.181G>T	p.Asp61Tyr	p.D61Y	ENST00000351677	NM_002834.3	61	Gat/Tat	3/16	0.700245635569674	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.700245635569674	1		760	578	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163707	47163707	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	202	414	0	ENST00000409792.3:c.2419T>C	p.Ser807Pro	p.S807P	ENST00000409792	NM_014159.6	807	Tct/Cct	3/21	0.700245635569674	3	FACETS	0.942	0.875	1	0.471	0.437	0.506	CLONAL	1	TRUE	1	0.700245635569674	3		414	827	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627296	86627296	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	161	346	0	ENST00000274376.6:c.671T>C	p.Met224Thr	p.M224T	ENST00000274376	NM_002890.2	224	aTg/aCg	2/25	NA	2	FACETS	0.974	0.901	1			1	INDETERMINATE	1	TRUE	NA	0.700245635569674	2		346	472	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618689	37618690	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	105	576	1	ENST00000447079.4:c.366dup	p.Leu123ThrfsTer4	p.L123Tfs*4	ENST00000447079	NM_015083.1	122	tta/ttAa	1/14	1	2	FACETS	0.71	0.637	0.789	0.71	0.637	0.789	SUBCLONAL	1	FALSE	1	0.398945376093435	2		577	741	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911617	134911617	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	37	482	0	ENST00000398015.3:c.2082G>T	p.Met694Ile	p.M694I	ENST00000398015	NM_004441.4	694	atG/atT	11/16	1	2	FACETS	0.325	0.267	0.39	0.325	0.267	0.39	SUBCLONAL	1	FALSE	1	0.398945376093435	2		482	571	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	31	528	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.694	0.56	0.848	0.694	0.56	0.848	SUBCLONAL	1	TRUE	1	0.12	2		529	744	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0027186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	46	750	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	1	2	FACETS	0.861	0.723	1	0.861	0.723	1	CLONAL	1	TRUE	1	0.12	2		750	890	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190905	106190905	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0027186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	22	340	0	ENST00000380013.4:c.4182+1G>T		p.X1394_splice	ENST00000380013	NM_001127208.2	1394			1	2	FACETS	0.921	0.713	1	0.921	0.713	1	CLONAL	1	TRUE	1	0.12	2		340	398	SUCCESS
APC	324	MSKCC	GRCh37	5	112176254	112176254	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs759441332	NA	P-0027186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	41	443	0	ENST00000257430.4:c.4963A>G	p.Thr1655Ala	p.T1655A	ENST00000257430	NM_000038.5	1655	Aca/Gca	16/16	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.12	2		443	604	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0027187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	164	483	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.395342319722173	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.395342319722173	1		483	577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	109	632	3	ENST00000269305.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	336	Gag/Tag	10/11	0.395342319722173	1	FACETS	0.546	0.49	0.606	0.546	0.49	0.606	SUBCLONAL	1	TRUE	0	0.395342319722173	1		635	810	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577573	7577573	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	57	601	1	ENST00000269305.4:c.708C>A	p.Tyr236Ter	p.Y236*	ENST00000269305	NM_001126112.2	236	taC/taA	7/11	0.395342319722173	1	FACETS	0.295	0.253	0.342	0.295	0.253	0.342	SUBCLONAL	1	TRUE	0	0.395342319722173	1		602	783	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32438072	32438072	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	143	487	1	ENST00000332351.3:c.965G>T	p.Ser322Ile	p.S322I	ENST00000332351	NM_024426.4	322	aGc/aTc	5/10	1	2	FACETS	0.947	0.864	1	0.947	0.864	1	CLONAL	1	TRUE	1	0.395342319722173	2		488	764	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119433	193119433	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0027187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1766	126	353	0	ENST00000367435.3:c.829-1G>T		p.X277_splice	ENST00000367435	NM_024529.4	277			0.395342319722173	14	FACETS	1	0.962	1			1	CLONAL	1	TRUE	NA	0.395342319722173	14		353	1892	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111958607	111958607	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0027187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	70	462	2	ENST00000375549.3:c.79A>T	p.Arg27Ter	p.R27*	ENST00000375549	NM_003002.3	27	Aga/Tga	2/4	1	2	FACETS	0.602	0.525	0.685	0.602	0.525	0.685	SUBCLONAL	1	TRUE	1	0.395342319722173	2		464	588	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484300	8484300	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	151	480	0	ENST00000356435.5:c.3232G>T	p.Glu1078Ter	p.E1078*	ENST00000356435		1078	Gag/Tag	19/35	1	2	FACETS	0.987	0.903	1	0.987	0.903	1	CLONAL	1	TRUE	1	0.395342319722173	2		480	774	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0027188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	136	559	3	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	0.875	0.798	0.957	0.875	0.798	0.957	CLONAL	1	TRUE	1	0.454984991720003	2		562	683	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0027188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	70	410	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	1	2	FACETS	0.838	0.735	0.948	0.838	0.735	0.948	CLONAL	1	TRUE	1	0.454984991720003	2		410	367	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913351	NA	P-0027188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	143	352	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	0.454984991720003	2		352	517	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098894	178098895	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	122	429	0	ENST00000397062.3:c.150dup	p.Gln51ThrfsTer5	p.Q51Tfs*5	ENST00000397062	NM_006164.4	50	-/A	2/5	1	2	FACETS	0.727	0.657	0.8	0.727	0.657	0.8	SUBCLONAL	1	TRUE	1	0.454984991720003	2		429	738	SUCCESS
APC	324	MSKCC	GRCh37	5	112111408	112111411	+	frameshift_variant	Frame_Shift_Del	DEL	ATAG	ATAG	-	rs387906231	NA	P-0027188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	57	328	0	ENST00000257430.4:c.509_512del	p.Asp170ValfsTer4	p.D170Vfs*4	ENST00000257430	NM_000038.5	169	ATAGat/at	5/16	1	2	FACETS	0.852	0.737	0.976	0.852	0.737	0.976	CLONAL	1	TRUE	1	0.454984991720003	2		328	294	SUCCESS
APC	324	MSKCC	GRCh37	5	112175761	112175761	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	86	258	0	ENST00000257430.4:c.4473del	p.Phe1491LeufsTer16	p.F1491Lfs*16	ENST00000257430	NM_000038.5	1490	caT/ca	16/16	1	2	FACETS	0.816	0.725	0.913	0.816	0.725	0.913	CLONAL	1	TRUE	1	0.454984991720003	2		258	463	SUCCESS
APC	324	MSKCC	GRCh37	5	112174113	112174114	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0027188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	93	326	0	ENST00000257430.4:c.2824_2825del	p.Asn942PhefsTer3	p.N942Ffs*3	ENST00000257430	NM_000038.5	941	gAA/g	16/16	1	2	FACETS	0.879	0.785	0.978	0.879	0.785	0.978	CLONAL	1	TRUE	1	0.454984991720003	2		326	465	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226318	133226318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572986717	NA	P-0027188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	246	644	1	ENST00000320574.5:c.3740C>T	p.Pro1247Leu	p.P1247L	ENST00000320574	NM_006231.2	1247	cCg/cTg	30/49	1	2	FACETS	0.978	0.914	1	0.978	0.914	1	CLONAL	1	TRUE	1	0.454984991720003	2		645	1106	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715724	30715724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782979	NA	P-0027188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	263	347	0	ENST00000295754.5:c.1382G>A	p.Cys461Tyr	p.C461Y	ENST00000295754	NM_003242.5	461	tGt/tAt	5/7	0.454984991720003	2	FACETS	0.965	0.912	1	0.965	0.912	1	CLONAL	2	TRUE	0	0.454984991720003	2		347	599	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17743018	17743018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471293207	NA	P-0027188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	242	533	1	ENST00000250003.3:c.926C>T	p.Ala309Val	p.A309V	ENST00000250003	NM_002478.4	309	gCg/gTg	3/3	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.454984991720003	2		534	998	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645373	67645373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1390969954	NA	P-0027188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	132	350	1	ENST00000264010.4:c.638G>A	p.Arg213His	p.R213H	ENST00000264010	NM_006565.3	213	cGt/cAt	3/12	1	2	FACETS	0.887	0.807	0.971	0.887	0.807	0.971	CLONAL	1	TRUE	1	0.454984991720003	2		351	654	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991999	72991999	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0027188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	201	472	0	ENST00000268489.5:c.2046C>G	p.Tyr682Ter	p.Y682*	ENST00000268489	NM_006885.3	682	taC/taG	2/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.454984991720003	2		472	846	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944174	81944174	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758138167	NA	P-0027188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	234	570	0	ENST00000359376.3:c.1783G>A	p.Gly595Arg	p.G595R	ENST00000359376	NM_002661.3	595	Ggg/Agg	18/33	1	2	FACETS	0.96	0.895	1	0.96	0.895	1	CLONAL	1	TRUE	1	0.454984991720003	2		570	1072	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120280	70120289	+	frameshift_variant	Frame_Shift_Del	DEL	TACAGCCCCT	TACAGCCCCT	-	novel	NA	P-0027188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	655	683	0	ENST00000245479.2:c.1282_1291del	p.Tyr428ProfsTer39	p.Y428Pfs*39	ENST00000245479	NM_000346.3	428	TACAGCCCCTcc/cc	3/3	0.454984991720003	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.454984991720003	2		683	1363	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946427	2946427	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200963550	NA	P-0027188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	239	654	0	ENST00000396946.4:c.3310C>T	p.Arg1104Trp	p.R1104W	ENST00000396946	NM_032415.4	1104	Cgg/Tgg	25/25	1	2	FACETS	0.953	0.89	1	0.953	0.89	1	CLONAL	1	TRUE	1	0.454984991720003	2		654	1102	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098390	11098414	+	frameshift_variant	Frame_Shift_Del	DEL	TTCCCCCGCAGCCAACGGGCCGCCC	TTCCCCCGCAGCCAACGGGCCGCCC	-	novel	NA	P-0027190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	325	611	0	ENST00000358026.2:c.917_941del	p.Gln306ArgfsTer12	p.Q306Rfs*12	ENST00000358026	NM_001128849.1	303	aTTCCCCCGCAGCCAACGGGCCGCCCt/at	6/36	0.576571208549205	1	FACETS	0.589	0.561	0.618	0.589	0.561	0.618	SUBCLONAL	1	TRUE	0	0.877135001905847	1		611	706	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037144	71037144	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0027190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	131	307	1	ENST00000318789.4:c.1146+1G>A		p.X382_splice	ENST00000318789	NM_032682.5	382			0.442654731045016	1	FACETS	0.382	0.349	0.416	0.382	0.349	0.416	INDETERMINATE	1	TRUE	0	0.877135001905847	1		308	439	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414278	32414278	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	155	479	0	ENST00000332351.3:c.1273T>C	p.Phe425Leu	p.F425L	ENST00000332351	NM_024426.4	425	Ttc/Ctc	8/10	1	2	FACETS	0.478	0.438	0.519	0.478	0.438	0.519	SUBCLONAL	1	TRUE	1	0.877135001905847	2		479	740	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108067	30108067	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	176	563	0	ENST00000331968.5:c.740C>T	p.Ser247Leu	p.S247L	ENST00000331968	NM_002742.2	247	tCa/tTa	5/18	1	2	FACETS	0.458	0.422	0.496	0.458	0.422	0.496	SUBCLONAL	1	TRUE	1	0.877135001905847	2		563	876	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031897	10031897	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs748601438	NA	P-0027190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	185	559	0	ENST00000330684.3:c.926A>G	p.Lys309Arg	p.K309R	ENST00000330684	NM_001134407.1	309	aAg/aGg	3/13	0.877135001905847	3	FACETS	0.489	0.45	0.529	0.244	0.225	0.265	SUBCLONAL	1	TRUE	1	0.877135001905847	3		559	1241	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14031642	14031642	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749814308	NA	P-0027190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	162	469	1	ENST00000311895.7:c.1831G>A	p.Gly611Arg	p.G611R	ENST00000311895	NM_005236.2	611	Gga/Aga	9/11	0.877135001905847	3	FACETS	0.491	0.449	0.534	0.245	0.224	0.267	SUBCLONAL	1	TRUE	1	0.877135001905847	3		470	1083	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382128	152382128	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	107	292	0	ENST00000206249.3:c.1238A>G	p.Asn413Ser	p.N413S	ENST00000206249	NM_000125.3	413	aAc/aGc	6/8	0.467570109130397	1	FACETS	0.37	0.335	0.407	0.37	0.335	0.407	INDETERMINATE	1	TRUE	0	0.877135001905847	1		292	370	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106632	27106632	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	171	527	0	ENST00000324856.7:c.6243C>A	p.Cys2081Ter	p.C2081*	ENST00000324856	NM_006015.4	2081	tgC/tgA	20/20	0.171464073059304	1	FACETS	0.653	0.601	0.706	0.653	0.601	0.706	INDETERMINATE	1	FALSE	0	0.514804841413796	1		527	756	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180982	108180982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781963	NA	P-0027191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	118	297	0	ENST00000278616.4:c.5858C>T	p.Thr1953Ile	p.T1953I	ENST00000278616	NM_000051.3	1953	aCa/aTa	39/63	0.514804841413796	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	FALSE	0	0.514804841413796	1		297	338	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989112	41989113	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	208	457	0	ENST00000219905.7:c.1907dup	p.Leu636PhefsTer21	p.L636Ffs*21	ENST00000219905	NM_001164273.1	635	tct/tcTt	3/24	0.287615527212794	1	FACETS	0.846	0.789	0.906	0.846	0.789	0.906	INDETERMINATE	1	FALSE	0	0.514804841413796	1		457	709	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581183	48581183	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	88	325	0	ENST00000342988.3:c.487G>A	p.Val163Met	p.V163M	ENST00000342988	NM_005359.5	163	Gtg/Atg	5/12	NA	2	FACETS	0.656	0.583	0.734			1	INDETERMINATE	1	FALSE	NA	0.514804841413796	2		325	521	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	150	528	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.49269648596002	1	FACETS	0.853	0.784	0.924	0.853	0.784	0.924	CLONAL	1	TRUE	0	0.49269648596002	1		529	538	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0027192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	154	397	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.49269648596002	2		397	609	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822354	72822354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs563030073	NA	P-0027192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	253	620	1	ENST00000268489.5:c.9821C>T	p.Ala3274Val	p.A3274V	ENST00000268489	NM_006885.3	3274	gCc/gTc	10/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.49269648596002	2		621	971	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143033783	143033783	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	160	402	0	ENST00000262992.4:c.2188C>G	p.Pro730Ala	p.P730A	ENST00000262992	NM_001101669.1	730	Cct/Gct	20/24	1	2	FACETS	0.989	0.91	1	0.989	0.91	1	CLONAL	1	TRUE	1	0.49269648596002	2		402	657	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711873	89711873	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs587781784	NA	P-0027193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	66	305	2	ENST00000371953.3:c.493-2A>G		p.X165_splice	ENST00000371953	NM_000314.4	165			1	2	FACETS	0.882	0.767	1	0.882	0.767	1	CLONAL	1	TRUE	1	0.3	2		307	499	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37863257	37863261	+	frameshift_variant	Frame_Shift_Del	DEL	GACAT	GACAT	-	novel	NA	P-0027193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	213	533	5	ENST00000269571.5:c.90_94del	p.Asp30GlufsTer78	p.D30Efs*78	ENST00000269571		30	GACATg/g	2/27	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.3	2		538	1030	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438288	56438289	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0027193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	104	556	8	ENST00000407977.2:c.704_705del	p.Arg235AsnfsTer23	p.R235Nfs*23	ENST00000407977		235	aGA/a	7/10	1	2	FACETS	0.818	0.731	0.909	0.818	0.731	0.909	CLONAL	1	TRUE	1	0.3	2		564	848	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57470700	57470700	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	255	352	0	ENST00000371085.3:c.173A>G	p.Lys58Arg	p.K58R	ENST00000371085	NM_000516.4	58	aAg/aGg	2/13	1	2	FACETS	0.887	0.835	0.94	0.887	0.835	0.94	CLONAL	1	TRUE	1	0.814441423708388	2		352	706	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593592	55593608	+	protein_altering_variant	In_Frame_Del	DEL	ATGAAGTACAGTGGAAG	ATGAAGTACAGTGGAAG	CT	novel	NA	P-0027195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	158	425	1	ENST00000288135.5:c.1658_1674delinsCT	p.Tyr553_Lys558delinsSer	p.Y553_K558delinsS	ENST00000288135	NM_000222.2	553	tATGAAGTACAGTGGAAG/tCT	11/21	1	2	FACETS	0.715	0.659	0.772	0.715	0.659	0.772	SUBCLONAL	1	TRUE	1	0.814441423708388	2		426	543	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944503	40944503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	79	542	1	ENST00000373198.4:c.1999G>A	p.Glu667Lys	p.E667K	ENST00000373198	NM_133170.3	667	Gag/Aag	12/32	1	2	FACETS	0.829	0.73	0.935	0.829	0.73	0.935	CLONAL	1	TRUE	1	0.323686735852204	2		543	589	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271910	18271910	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	95	565	0	ENST00000222254.8:c.513del	p.Asp172ThrfsTer15	p.D172Tfs*15	ENST00000222254	NM_005027.3	171	gcT/gc	5/16	1	2	FACETS	0.965	0.861	1	0.965	0.861	1	CLONAL	1	TRUE	1	0.323686735852204	2		565	608	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0027198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	250	480	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.446897074785511	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.446897074785511	2		480	545	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155721	56155722	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0027198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	145	299	0	ENST00000399503.3:c.816_817del	p.Arg273SerfsTer27	p.R273Sfs*27	ENST00000399503	NM_005921.1	271	agAAaa/agaa	3/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.446897074785511	2		299	597	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292896	91292896	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	158	512	0	ENST00000355112.3:c.398A>T	p.Asp133Val	p.D133V	ENST00000355112	NM_000057.2	133	gAt/gTt	3/22	1	2	FACETS	0.883	0.81	0.959	0.883	0.81	0.959	CLONAL	1	TRUE	1	0.446897074785511	2		512	801	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645883	67645883	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	202	435	1	ENST00000264010.4:c.811T>C	p.Cys271Arg	p.C271R	ENST00000264010	NM_006565.3	271	Tgc/Cgc	4/12	0.446897074785511	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.446897074785511	1		436	594	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155595	56155596	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	C	novel	NA	P-0027198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	170	350	0	ENST00000399503.3:c.687_688delinsC	p.Ala230LeufsTer33	p.A230Lfs*33	ENST00000399503	NM_005921.1	229	gcAGct/gcCct	3/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.446897074785511	2		350	683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0027203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	240	630	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.406761350049448	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.406761350049448	1		632	810	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469669	NA	P-0027203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	145	584	0	ENST00000374080.3:c.130G>A	p.Gly44Ser	p.G44S	ENST00000374080		44	Ggt/Agt	2/45	0.253284991679849	1	FACETS	0.571	0.52	0.624	0.571	0.52	0.624	SUBCLONAL	1	TRUE	0	0.406761350049448	1		584	995	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588143	67588144	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0027203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	128	455	0	ENST00000274335.5:c.973_974del	p.Asn325TyrfsTer7	p.N325Yfs*7	ENST00000274335		325	AAt/t	7/15	0.181943645196425	3	FACETS	1	0.982	1	0.667	0.606	0.73	INDETERMINATE	1	TRUE	1	0.406761350049448	3		455	568	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30733045	30733045	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	27	376	0	ENST00000295754.5:c.1658C>G	p.Ser553Trp	p.S553W	ENST00000295754	NM_003242.5	553	tCg/tGg	7/7	0.406761350049448	1	FACETS	0.209	0.166	0.259	0.209	0.166	0.259	SUBCLONAL	1	TRUE	0	0.406761350049448	1		376	506	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0027206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	185	246	1	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.74306480060277	3	FACETS	0.97	0.912	1	0.97	0.912	1	CLONAL	2	TRUE	1	0.74306480060277	3		247	352	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112287	115112287	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	387	202	0	ENST00000257566.3:c.1453C>T	p.Gln485Ter	p.Q485*	ENST00000257566	NM_016569.3	485	Cag/Tag	7/8	0.7428678500633	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.74306480060277	3		202	434	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551558	150551558	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	292	502	0	ENST00000369026.2:c.449C>A	p.Ser150Tyr	p.S150Y	ENST00000369026	NM_021960.4	150	tCt/tAt	1/3	0.733390199522025	4	FACETS	1	0.978	1	0.361	0.339	0.383	CLONAL	1	TRUE	1	0.74306480060277	4		502	1266	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419921	152419922	+	missense_variant	Missense_Mutation	DNP	CT	CT	TA	novel	NA	P-0027206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	219	494	2	ENST00000206249.3:c.1608_1609delinsTA	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	536	ctCTat/ctTAat	8/8	0.740210977209625	2	FACETS	0.979	0.917	1	0.49	0.458	0.521	CLONAL	1	TRUE	0	0.74306480060277	2		496	602	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877181	151877181	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	143	284	0	ENST00000262189.6:c.7180C>T	p.Gln2394Ter	p.Q2394*	ENST00000262189	NM_170606.2	2394	Cag/Tag	37/59	0.611931622641831	4	FACETS	0.964	0.881	1	0.482	0.44	0.526	CLONAL	1	TRUE	2	0.74306480060277	4		284	696	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945402	151945403	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	287	346	0	ENST00000262189.6:c.2116dup	p.Ser706LysfsTer7	p.S706Kfs*7	ENST00000262189	NM_170606.2	706	agt/aAgt	14/59	0.611931622641831	4	FACETS	0.816	0.77	0.863	0.816	0.77	0.863	CLONAL	2	TRUE	2	0.74306480060277	4		346	825	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692896	89692896	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs398123322	NA	P-0027208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	17	370	0	ENST00000371953.3:c.380G>T	p.Gly127Val	p.G127V	ENST00000371953	NM_000314.4	127	gGa/gTa	5/9	0.421557175507288	0	FACETS	0.276	0.207	0.357			1	SUBCLONAL	1	TRUE	0	0.421557175507288	0		370	169	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112272	115112272	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs544562535	NA	P-0027208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	49	180	1	ENST00000257566.3:c.1468G>T	p.Ala490Ser	p.A490S	ENST00000257566	NM_016569.3	490	Gcc/Tcc	7/8	0.421557175507288	0	FACETS	0.451	0.384	0.524			1	SUBCLONAL	1	TRUE	0	0.421557175507288	0		181	298	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120776	115120776	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	144	434	1	ENST00000257566.3:c.230del	p.Pro77ArgfsTer11	p.P77Rfs*11	ENST00000257566	NM_016569.3	77	cCg/cg	1/8	0.421557175507288	0	FACETS	0.627	0.574	0.683			1	SUBCLONAL	1	TRUE	0	0.421557175507288	0		435	630	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842595	68842595	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs771085839	NA	P-0027208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	43	430	0	ENST00000261769.5:c.532-1G>C		p.X178_splice	ENST00000261769	NM_004360.3	178			0.421557175507288	1	FACETS	0.703	0.594	0.822	0.703	0.594	0.822	SUBCLONAL	1	TRUE	0	0.421557175507288	1		430	229	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259261	16259261	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	166	367	1	ENST00000375759.3:c.6526G>A	p.Glu2176Lys	p.E2176K	ENST00000375759	NM_015001.2	2176	Gaa/Aaa	11/15	0.319466077001165	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.319466077001165	3		368	545	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933540	36933541	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	115	577	3	ENST00000361632.4:c.1746_1747delinsTT	p.Arg583Cys	p.R583C	ENST00000361632		582	tcCCgt/tcTTgt	13/16	1	2	FACETS	0.951	0.857	1	0.951	0.857	1	CLONAL	1	TRUE	1	0.319466077001165	2		580	757	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46725735	46725735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	95	446	0	ENST00000371975.4:c.371C>T	p.Pro124Leu	p.P124L	ENST00000371975	NM_003579.3	124	cCc/cTc	5/18	1	2	FACETS	0.897	0.799	1	0.897	0.799	1	CLONAL	1	TRUE	1	0.319466077001165	2		446	663	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468346	120468346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs987757552	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	111	597	0	ENST00000256646.2:c.4093C>T	p.Arg1365Cys	p.R1365C	ENST00000256646	NM_024408.3	1365	Cgc/Tgc	25/34	1	2	FACETS	0.948	0.853	1	0.948	0.853	1	CLONAL	1	TRUE	1	0.319466077001165	2		597	733	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100511	8100512	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	134	647	1	ENST00000346208.3:c.485_486delinsTT	p.Ser162Phe	p.S162F	ENST00000346208		162	tCC/tTT	3/6	0.319466077001165	1	FACETS	0.815	0.74	0.894	0.815	0.74	0.894	CLONAL	1	TRUE	0	0.319466077001165	1		648	865	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112767406	112767406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	70	386	0	ENST00000369452.4:c.1279C>T	p.Leu427Phe	p.L427F	ENST00000369452	NM_007373.3	427	Ctt/Ttt	6/9	0.319466077001165	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.319466077001165	1		386	323	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925434	114925435	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	115	602	2	ENST00000543371.1:c.1512_1513delinsTT	p.Arg505Ter	p.R505*	ENST00000543371	NM_001198531.1	504	ccCCga/ccTTga	14/14	0.319466077001165	1	FACETS	0.982	0.887	1	0.982	0.887	1	CLONAL	1	TRUE	0	0.319466077001165	1		604	616	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196788	108196788	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	36	246	0	ENST00000278616.4:c.6811C>T	p.Pro2271Ser	p.P2271S	ENST00000278616	NM_000051.3	2271	Cct/Tct	47/63	1	2	FACETS	0.665	0.548	0.795	0.665	0.548	0.795	SUBCLONAL	1	TRUE	1	0.319466077001165	2		246	339	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	401941	401941	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375859999	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	64	263	0	ENST00000399788.2:c.4850G>A	p.Arg1617Lys	p.R1617K	ENST00000399788	NM_001042603.1	1617	aGg/aAg	27/28	0.283088159434166	4	FACETS	0.902	0.781	1	0.301	0.26	0.345	CLONAL	1	TRUE	1	0.319466077001165	4		263	586	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12043888	12043888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	82	410	0	ENST00000396373.4:c.1267C>T	p.Pro423Ser	p.P423S	ENST00000396373	NM_001987.4	423	Cca/Tca	8/8	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.319466077001165	NA		410	825	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442998	49442998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375144626	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	97	476	0	ENST00000301067.7:c.3910C>T	p.Arg1304Cys	p.R1304C	ENST00000301067	NM_003482.3	1304	Cgc/Tgc	12/54	1	2	FACETS	0.881	0.786	0.983	0.881	0.786	0.983	CLONAL	1	TRUE	1	0.319466077001165	2		476	689	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446193	49446193	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	117	492	0	ENST00000301067.7:c.1273C>T	p.Gln425Ter	p.Q425*	ENST00000301067	NM_003482.3	425	Caa/Taa	10/54	1	2	FACETS	0.963	0.868	1	0.963	0.868	1	CLONAL	1	TRUE	1	0.319466077001165	2		492	761	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865705	57865705	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	141	644	0	ENST00000228682.2:c.3182C>T	p.Pro1061Leu	p.P1061L	ENST00000228682	NM_005269.2	1061	cCt/cTt	12/12	1	2	FACETS	0.987	0.899	1	0.987	0.899	1	CLONAL	1	TRUE	1	0.319466077001165	2		644	894	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218338	69218338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	88	410	0	ENST00000462284.1:c.430C>T	p.Leu144Phe	p.L144F	ENST00000462284	NM_002392.5	144	Ctt/Ttt	7/11	1	2	FACETS	0.88	0.781	0.986	0.88	0.781	0.986	CLONAL	1	TRUE	1	0.319466077001165	2		410	626	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416803	121416803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	121	734	0	ENST00000257555.6:c.232G>A	p.Gly78Arg	p.G78R	ENST00000257555		78	Ggg/Agg	1/10	1	2	FACETS	0.804	0.726	0.887	0.804	0.726	0.887	CLONAL	1	TRUE	1	0.319466077001165	2		734	942	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911065	32911065	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	92	487	0	ENST00000380152.3:c.2573G>A	p.Arg858Lys	p.R858K	ENST00000380152		858	aGa/aAa	11/27	1	2	FACETS	0.944	0.84	1	0.944	0.84	1	CLONAL	1	TRUE	1	0.319466077001165	2		487	610	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32932053	32932053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	38	301	1	ENST00000380152.3:c.7792G>A	p.Glu2598Lys	p.E2598K	ENST00000380152		2598	Gaa/Aaa	16/27	1	2	FACETS	0.67	0.555	0.798	0.67	0.555	0.798	SUBCLONAL	1	TRUE	1	0.319466077001165	2		302	355	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133889	41133889	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	43	296	0	ENST00000379561.5:c.1739C>T	p.Ser580Phe	p.S580F	ENST00000379561	NM_002015.3	580	tCc/tTc	2/3	1	2	FACETS	0.847	0.711	0.995	0.847	0.711	0.995	CLONAL	1	TRUE	1	0.319466077001165	2		296	318	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242034	105242035	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	260	721	1	ENST00000349310.3:c.389_390delinsAA	p.Gly130Glu	p.G130E	ENST00000349310	NM_001014432.1	130	gGG/gAA	6/15	0.316489538528586	2	FACETS	0.913	0.857	0.971	0.913	0.857	0.971	CLONAL	2	TRUE	0	0.319466077001165	2		722	891	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023180	33023180	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	125	590	1	ENST00000300177.4:c.289C>T	p.Gln97Ter	p.Q97*	ENST00000300177	NM_001191322.1	97	Cag/Tag	2/2	0.319466077001165	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.319466077001165	1		591	625	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019587	42019587	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	109	469	0	ENST00000219905.7:c.3640C>T	p.Pro1214Ser	p.P1214S	ENST00000219905	NM_001164273.1	1214	Ccc/Tcc	10/24	0.319466077001165	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.319466077001165	1		469	504	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482750	67482750	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	97	383	0	ENST00000327367.4:c.1155-1G>A		p.X385_splice	ENST00000327367	NM_005902.3	385			0.319466077001165	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.319466077001165	1		383	424	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310143	91310143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs940792839	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	56	329	0	ENST00000355112.3:c.2197C>T	p.Pro733Ser	p.P733S	ENST00000355112	NM_000057.2	733	Cca/Tca	10/22	1	2	FACETS	0.833	0.715	0.96	0.833	0.715	0.96	CLONAL	1	TRUE	1	0.319466077001165	2		329	421	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310246	91310246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	74	355	0	ENST00000355112.3:c.2300C>T	p.Pro767Leu	p.P767L	ENST00000355112	NM_000057.2	767	cCa/cTa	10/22	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.319466077001165	2		355	452	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396184	396184	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	101	416	0	ENST00000262320.3:c.842C>T	p.Ser281Phe	p.S281F	ENST00000262320	NM_003502.3	281	tCc/tTc	2/11	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.319466077001165	2		416	632	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134356	2134356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	131	593	1	ENST00000219476.3:c.4133C>T	p.Pro1378Leu	p.P1378L	ENST00000219476	NM_000548.3	1378	cCc/cTc	34/42	1	2	FACETS	0.985	0.893	1	0.985	0.893	1	CLONAL	1	TRUE	1	0.319466077001165	2		594	833	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134500	2134500	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	133	666	0	ENST00000219476.3:c.4277A>C	p.Glu1426Ala	p.E1426A	ENST00000219476	NM_000548.3	1426	gAa/gCa	34/42	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.319466077001165	2		666	814	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647663	3647663	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs896917989	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	207	740	2	ENST00000294008.3:c.1400C>T	p.Ser467Phe	p.S467F	ENST00000294008	NM_032444.2	467	tCc/tTc	7/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.319466077001165	2		742	1028	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	174	607	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.319466077001165	2		607	969	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579312	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	102	475	1	ENST00000269305.4:c.375_375+1delinsAA		p.X125_splice	ENST00000269305	NM_001126112.2	125		4/11	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.319466077001165	2		476	629	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805864	46805864	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	73	427	1	ENST00000290295.7:c.92C>T	p.Ser31Phe	p.S31F	ENST00000290295	NM_006361.5	31	tCc/tTc	1/2	1	2	FACETS	0.923	0.809	1	0.923	0.809	1	CLONAL	1	TRUE	1	0.319466077001165	2		428	495	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740723	58740723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	140	620	1	ENST00000305921.3:c.1628C>T	p.Ser543Phe	p.S543F	ENST00000305921	NM_003620.3	543	tCt/tTt	6/6	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.319466077001165	2		621	797	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955096	17955096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201650430	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	442	616	3	ENST00000458235.1:c.131C>T	p.Ser44Phe	p.S44F	ENST00000458235	NM_000215.3	44	tCc/tTc	2/24	0.319466077001165	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	1	0.319466077001165	4		619	1165	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149777	202149778	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	100	543	1	ENST00000358485.4:c.1218_1219delinsTT	p.Leu407Phe	p.L407F	ENST00000358485	NM_001080125.1	406	tcCCtt/tcTTtt	8/9	0.319466077001165	1	FACETS	0.861	0.77	0.957	0.861	0.77	0.957	CLONAL	1	TRUE	0	0.319466077001165	1		544	611	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546931	9546931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs562732119	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	69	387	0	ENST00000353224.5:c.1091C>T	p.Ser364Leu	p.S364L	ENST00000353224	NM_177990.2	364	tCg/tTg	5/10	1	2	FACETS	0.77	0.671	0.877	0.77	0.671	0.877	SUBCLONAL	1	TRUE	1	0.319466077001165	2		387	561	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560797	9560797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	67	305	0	ENST00000353224.5:c.985C>T	p.Pro329Ser	p.P329S	ENST00000353224	NM_177990.2	329	Cca/Tca	4/10	1	2	FACETS	0.846	0.736	0.964	0.846	0.736	0.964	CLONAL	1	TRUE	1	0.319466077001165	2		305	496	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023882	31023882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	116	524	1	ENST00000375687.4:c.3367C>T	p.Pro1123Ser	p.P1123S	ENST00000375687	NM_015338.5	1123	Cca/Tca	13/13	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.319466077001165	2		525	703	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827885	40827885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	95	417	0	ENST00000373198.4:c.2543G>A	p.Gly848Glu	p.G848E	ENST00000373198	NM_133170.3	848	gGa/gAa	17/32	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.319466077001165	2		417	576	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076902	41076902	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	67	518	0	ENST00000373198.4:c.1518G>A	p.Trp506Ter	p.W506*	ENST00000373198	NM_133170.3	506	tgG/tgA	9/32	1	2	FACETS	0.675	0.587	0.771	0.675	0.587	0.771	SUBCLONAL	1	TRUE	1	0.319466077001165	2		518	621	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076929	41076930	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	56	556	1	ENST00000373198.4:c.1490_1491delinsTT	p.Pro497Leu	p.P497L	ENST00000373198	NM_133170.3	497	cCC/cTT	9/32	1	2	FACETS	0.559	0.478	0.647	0.559	0.478	0.647	SUBCLONAL	1	TRUE	1	0.319466077001165	2		557	627	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319071	62319071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	129	682	1	ENST00000360203.5:c.1429C>T	p.Leu477Phe	p.L477F	ENST00000360203	NM_001283009.1	477	Ctt/Ttt	17/35	1	2	FACETS	0.925	0.838	1	0.925	0.838	1	CLONAL	1	TRUE	1	0.319466077001165	2		683	873	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127716	47127716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	158	479	4	ENST00000409792.3:c.5366G>A	p.Gly1789Asp	p.G1789D	ENST00000409792	NM_014159.6	1789	gGc/gAc	11/21	0.256767987679886	2	FACETS	1	0.988	1	0.735	0.675	0.797	CLONAL	1	TRUE	0	0.319466077001165	2		483	673	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441297	52441297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	148	485	0	ENST00000460680.1:c.473G>A	p.Gly158Asp	p.G158D	ENST00000460680	NM_004656.3	158	gGc/gAc	7/17	0.256767987679886	2	FACETS	1	0.987	1	0.725	0.664	0.788	CLONAL	1	TRUE	0	0.319466077001165	2		485	639	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205082	128205082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1330673412	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	130	712	0	ENST00000341105.2:c.359C>T	p.Pro120Leu	p.P120L	ENST00000341105	NM_032638.4	120	cCc/cTc	3/6	1	2	FACETS	0.974	0.883	1	0.974	0.883	1	CLONAL	1	TRUE	1	0.319466077001165	2		712	836	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644712	134644712	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	95	498	0	ENST00000398015.3:c.113C>T	p.Pro38Leu	p.P38L	ENST00000398015	NM_004441.4	38	cCt/cTt	2/16	1	2	FACETS	0.85	0.757	0.949	0.85	0.757	0.949	CLONAL	1	TRUE	1	0.319466077001165	2		498	700	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956220	55956220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190050670	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	103	522	0	ENST00000263923.4:c.3095G>A	p.Arg1032Gln	p.R1032Q	ENST00000263923	NM_002253.2	1032	cGa/cAa	23/30	1	2	FACETS	0.894	0.801	0.994	0.894	0.801	0.994	CLONAL	1	TRUE	1	0.319466077001165	2		522	721	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201746	66201746	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	95	468	0	ENST00000273854.3:c.2756G>A	p.Arg919Gln	p.R919Q	ENST00000273854	NM_004439.5	919	cGa/cAa	16/18	1	2	FACETS	0.941	0.839	1	0.941	0.839	1	CLONAL	1	TRUE	1	0.319466077001165	2		468	632	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541900	187541900	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs765843504	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	93	464	0	ENST00000441802.2:c.5840G>T	p.Arg1947Leu	p.R1947L	ENST00000441802	NM_005245.3	1947	cGc/cTc	10/27	1	2	FACETS	0.796	0.708	0.891	0.796	0.708	0.891	SUBCLONAL	1	TRUE	1	0.319466077001165	2		464	731	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630081	187630081	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	119	487	0	ENST00000441802.2:c.901C>T	p.Gln301Ter	p.Q301*	ENST00000441802	NM_005245.3	301	Cag/Tag	2/27	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.319466077001165	2		487	605	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295242	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	89	411	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.319466077001165	2		411	526	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526418	31526418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	162	810	0	ENST00000344624.3:c.622C>T	p.Pro208Ser	p.P208S	ENST00000344624		208	Cct/Tct	2/33	1	2	FACETS	0.919	0.842	1	0.919	0.842	1	CLONAL	1	TRUE	1	0.319466077001165	2		810	1103	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35860954	35860954	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	62	298	0	ENST00000303115.3:c.83G>A	p.Gly28Glu	p.G28E	ENST00000303115	NM_002185.3	28	gGa/gAa	2/8	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.319466077001165	2		298	373	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674233	86674233	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1463885690	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	62	350	0	ENST00000274376.6:c.2365C>T	p.Arg789Ter	p.R789*	ENST00000274376	NM_002890.2	789	Cga/Tga	18/25	0.319466077001165	1	FACETS	0.894	0.776	1	0.894	0.776	1	CLONAL	1	TRUE	0	0.319466077001165	1		350	365	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722165	176722165	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	97	472	1	ENST00000439151.2:c.7796C>T	p.Ser2599Phe	p.S2599F	ENST00000439151	NM_022455.4	2599	tCt/tTt	23/23	0.319466077001165	1	FACETS	0.965	0.863	1	0.965	0.863	1	CLONAL	1	TRUE	0	0.319466077001165	1		473	529	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909282	41909282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	129	582	0	ENST00000372991.4:c.106G>A	p.Glu36Lys	p.E36K	ENST00000372991	NM_001760.3	36	Gag/Aag	1/5	0.319466077001165	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.319466077001165	1		582	663	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967865	93967865	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	100	506	0	ENST00000369303.4:c.2062C>T	p.Gln688Ter	p.Q688*	ENST00000369303	NM_004440.3	688	Cag/Tag	11/17	1	2	FACETS	0.915	0.818	1	0.915	0.818	1	CLONAL	1	TRUE	1	0.319466077001165	2		506	684	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706901	117706901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	99	474	0	ENST00000368508.3:c.2249C>T	p.Ala750Val	p.A750V	ENST00000368508	NM_002944.2	750	gCt/gTt	15/43	1	2	FACETS	0.915	0.818	1	0.915	0.818	1	CLONAL	1	TRUE	1	0.319466077001165	2		474	677	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359035	81359035	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	81	462	0	ENST00000222390.5:c.926A>G	p.Gln309Arg	p.Q309R	ENST00000222390	NM_000601.4	309	cAa/cGa	8/18	1	2	FACETS	0.78	0.688	0.879	0.78	0.688	0.879	SUBCLONAL	1	TRUE	1	0.319466077001165	2		462	650	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525841	148525841	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	61	348	1	ENST00000320356.2:c.616C>A	p.His206Asn	p.H206N	ENST00000320356	NM_004456.4	206	Cac/Aac	6/20	1	2	FACETS	0.92	0.797	1	0.92	0.797	1	CLONAL	1	TRUE	1	0.319466077001165	2		349	415	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542660	141542660	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	142	625	0	ENST00000220592.5:c.2326T>C	p.Ser776Pro	p.S776P	ENST00000220592	NM_012154.3	776	Tct/Cct	18/19	0.319466077001165	5	FACETS	1	0.915	1	0.252	0.228	0.276	CLONAL	1	TRUE	1	0.319466077001165	5		625	1306	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396359	139396359	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	222	533	1	ENST00000277541.6:c.5479G>T	p.Glu1827Ter	p.E1827*	ENST00000277541	NM_017617.3	1827	Gag/Tag	30/34	0.316489538528586	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.319466077001165	2		534	686	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626661	100626661	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	94	237	0	ENST00000308731.7:c.269A>T	p.Glu90Val	p.E90V	ENST00000308731	NM_000061.2	90	gAg/gTg	4/19	1	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.319466077001165	1		237	331	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0027210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	200	565	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.998	0.927	1	0.998	0.927	1	CLONAL	1	TRUE	1	0.511800059247786	2		565	783	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060661	38060673	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGCGCTGCCTA	GAGGCGCTGCCTA	-	novel	NA	P-0027210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	279	620	0	ENST00000250448.2:c.1316_1328del	p.Leu439ArgfsTer2	p.L439Rfs*2	ENST00000250448	NM_004496.3	439	cTAGGCAGCGCCTCg/cg	2/2	1	2	FACETS	0.803	0.753	0.855	0.803	0.753	0.855	CLONAL	1	TRUE	1	0.511800059247786	2		620	1357	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226368	2226368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	231	603	1	ENST00000326181.6:c.1981G>A	p.Val661Met	p.V661M	ENST00000326181	NM_032271.2	661	Gtg/Atg	20/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.511800059247786	2		604	864	SUCCESS
APC	324	MSKCC	GRCh37	5	112176582	112176585	+	frameshift_variant	Frame_Shift_Del	DEL	AGTT	AGTT	-	rs1561599054	NA	P-0027210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	124	316	0	ENST00000257430.4:c.5293_5296del	p.Leu1765MetfsTer11	p.L1765Mfs*11	ENST00000257430	NM_000038.5	1764	cAGTTa/ca	16/16	0.512870144122942	1	FACETS	0.991	0.906	1	0.991	0.906	1	CLONAL	1	TRUE	0	0.511800059247786	1		316	364	SUCCESS
AR	367	MSKCC	GRCh37	X	66943552	66943552	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	16	205	0	ENST00000374690.3:c.2632A>T	p.Thr878Ser	p.T878S	ENST00000374690	NM_000044.3	878	Act/Tct	8/8	1	1	FACETS	0.156	0.115	0.205	0.156	0.115	0.205	SUBCLONAL	1	TRUE	0	0.511800059247786	1		205	298	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	63	315	1				ENST00000310581	NM_198253.2	-/1132			0.766475955672477	1	FACETS	0.474	0.415	0.537	0.474	0.415	0.537	SUBCLONAL	1	TRUE	0	0.724058137524221	1		316	234	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259408	89259408	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	218	416	0	ENST00000336596.2:c.552A>T	p.Gln184His	p.Q184H	ENST00000336596	NM_005233.5	184	caA/caT	3/17	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.724058137524221	2		416	521	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102196200	102196200	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs894701627	NA	P-0027216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	89	255	0	ENST00000263464.3:c.857A>G	p.Asn286Ser	p.N286S	ENST00000263464	NM_001165.4	286	aAc/aGc	3/9	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.307435134971411	2		255	442	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031209	36031209	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	157	727	0	ENST00000358208.4:c.1328C>T	p.Thr443Ile	p.T443I	ENST00000358208		443	aCc/aTc	11/12	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.307435134971411	2		727	761	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31421465	31421465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	186	550	0	ENST00000344624.3:c.3439G>A	p.Glu1147Lys	p.E1147K	ENST00000344624		1147	Gaa/Aaa	27/33	1	2	FACETS	0.89	0.826	0.955	0.89	0.826	0.955	CLONAL	1	TRUE	1	0.669016530944844	2		550	625	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913499	NA	P-0027218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	120	366	0	ENST00000345146.2:c.394C>A	p.Arg132Ser	p.R132S	ENST00000345146	NM_005896.2	132	Cgt/Agt	4/10	0.292195301323667	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.32315298788046	3		366	368	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913499	NA	P-0027218-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	205	366	0	ENST00000345146.2:c.394C>A	p.Arg132Ser	p.R132S	ENST00000345146	NM_005896.2	132	Cgt/Agt	4/10	0.47378572120348	3	FACETS	0.966	0.903	1	0.966	0.903	1	CLONAL	2	TRUE	1	0.480141688671719	3		366	548	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	182	315	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		316	511	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355846	73355846	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	47	360	0	ENST00000377767.4:c.125C>G	p.Ala42Gly	p.A42G	ENST00000377767	NM_014953.3	42	gCg/gGg	1/21	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		360	606	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0027223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	59	467	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.914	0.785	1	0.914	0.785	1	CLONAL	1	TRUE	1	0.16	2		468	807	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223059	1223059	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913325	NA	P-0027223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	83	684	1	ENST00000326873.7:c.996G>A	p.Trp332Ter	p.W332*	ENST00000326873	NM_000455.4	332	tgG/tgA	8/10	1	2	FACETS	0.961	0.845	1	0.961	0.845	1	CLONAL	1	TRUE	1	0.16	2		685	1080	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477837	140477851	+	inframe_deletion	In_Frame_Del	DEL	TAGGTGCTGTCACAT	TAGGTGCTGTCACAT	-	novel	NA	P-0027223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	48	677	0	ENST00000288602.6:c.1457_1471del	p.Asn486_Pro490del	p.N486_P490del	ENST00000288602	NM_004333.4	486	aATGTGACAGCACCTAca/aca	12/18	1	2	FACETS	0.782	0.66	0.918	0.782	0.66	0.918	CLONAL	1	TRUE	1	0.16	2		677	767	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62309700	62309700	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs895722334	NA	P-0027223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	41	474	0	ENST00000360203.5:c.1037+1G>T		p.X346_splice	ENST00000360203	NM_001283009.1	346			1	2	FACETS	0.703	0.584	0.836	0.703	0.584	0.836	SUBCLONAL	1	TRUE	1	0.16	2		474	729	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	92	315	1				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		316	370	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0027227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	352	321	2	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.214886630552867	3	FACETS	0.883	0.844	0.922	1	0.992	1	CLONAL	4	FALSE	0	0.342689614467273	3		323	681	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	151	315	1				ENST00000310581	NM_198253.2	-/1132			0.296984585772318	3	FACETS	0.93	0.861	0.999	1	0.988	1	CLONAL	3	FALSE	1	0.342689614467273	3		316	370	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321372	1321372	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1319865856	NA	P-0027227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	269	500	0	ENST00000400841.2:c.383C>T	p.Ser128Leu	p.S128L	ENST00000400841		128	tCg/tTg	4/6	1	2	FACETS	1	0.957	1	1	0.995	1	CLONAL	2	FALSE	1	0.342689614467273	2		500	770	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836312	89836312	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	268	769	0	ENST00000389301.3:c.2437C>T	p.Pro813Ser	p.P813S	ENST00000389301	NM_000135.2	813	Cct/Tct	26/43	0.342689614467273	0	FACETS	0.845	0.8	0.892			1	CLONAL	2	FALSE	0	0.342689614467273	0		769	608	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293875	1293875	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	445	848	1	ENST00000310581.5:c.1126C>T	p.Pro376Ser	p.P376S	ENST00000310581	NM_198253.2	376	Ccc/Tcc	2/16	0.296984585772318	3	FACETS	1	0.971	1	1	0.996	1	CLONAL	3	FALSE	1	0.342689614467273	3		849	998	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188238	32188238	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	120	716	0	ENST00000375023.3:c.1103C>T	p.Ser368Phe	p.S368F	ENST00000375023	NM_004557.3	368	tCc/tTc	6/30	1	2	FACETS	0.834	0.753	0.919	0.834	0.753	0.919	CLONAL	1	FALSE	1	0.342689614467273	2		716	840	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143326451	143326451	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs776542387	NA	P-0027227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	119	362	0	ENST00000262992.4:c.163C>G	p.Arg55Gly	p.R55G	ENST00000262992	NM_001101669.1	55	Cgt/Ggt	4/24	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.342689614467273	2		362	507	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061852	38061852	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	297	986	0	ENST00000250448.2:c.137C>T	p.Thr46Ile	p.T46I	ENST00000250448	NM_004496.3	46	aCc/aTc	2/2	1	2	FACETS	0.815	0.767	0.863	1	0.995	1	CLONAL	2	FALSE	1	0.342689614467273	2		986	1064	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740663	58740663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	220	626	0	ENST00000305921.3:c.1568C>T	p.Ala523Val	p.A523V	ENST00000305921	NM_003620.3	523	gCc/gTc	6/6	1	2	FACETS	0.873	0.816	0.933	1	0.993	1	CLONAL	2	FALSE	1	0.342689614467273	2		626	735	SUCCESS
CALR	811	MSKCC	GRCh37	19	13049566	13049566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	196	685	1	ENST00000316448.5:c.73G>A	p.Glu25Lys	p.E25K	ENST00000316448	NM_004343.3	25	Gag/Aag	1/9	1	2	FACETS	0.872	0.811	0.935	1	0.993	1	CLONAL	2	FALSE	1	0.342689614467273	2		686	656	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943705	17943705	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	103	660	1	ENST00000458235.1:c.2384C>T	p.Ala795Val	p.A795V	ENST00000458235	NM_000215.3	795	gCc/gTc	18/24	1	2	FACETS	0.876	0.785	0.973	0.876	0.785	0.973	CLONAL	1	FALSE	1	0.342689614467273	2		661	686	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933776	49933776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372453584	NA	P-0027227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	222	702	0	ENST00000296474.3:c.2501C>T	p.Pro834Leu	p.P834L	ENST00000296474	NM_002447.2	834	cCc/cTc	10/20	1	2	FACETS	0.931	0.87	0.993	1	0.994	1	CLONAL	2	FALSE	1	0.342689614467273	2		702	696	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170814992	170814992	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	122	366	0	ENST00000296930.5:c.40C>T	p.Pro14Ser	p.P14S	ENST00000296930	NM_002520.6	14	Ccc/Tcc	1/11	1	2	FACETS	0.85	0.774	0.928	1	0.988	1	CLONAL	2	FALSE	1	0.342689614467273	2		366	419	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0027238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	129	255	3	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	0.593254929839272	2	FACETS	0.814	0.754	0.875	0.814	0.754	0.875	CLONAL	2	TRUE	0	0.604868143959669	2		258	262	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0027238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	524	583	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.604868143959669	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.604868143959669	2		583	844	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0027238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	378	524	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.596263770019954	2	FACETS	0.966	0.927	1	0.966	0.927	1	CLONAL	2	TRUE	0	0.604868143959669	2		524	647	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0027238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	356	488	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	0.604868143959669	2	FACETS	0.894	0.856	0.933	0.894	0.856	0.933	CLONAL	2	TRUE	0	0.604868143959669	2		488	658	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469984	25469984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1326972729	NA	P-0027238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	171	583	1	ENST00000264709.3:c.1058C>T	p.Ala353Val	p.A353V	ENST00000264709	NM_175629.2	353	gCg/gTg	9/23	0.604868143959669	2	FACETS	0.782	0.721	0.845	0.391	0.36	0.423	SUBCLONAL	1	TRUE	0	0.604868143959669	2		584	723	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0027238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	304	320	0	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	0.604868143959669	2	FACETS	0.885	0.844	0.926	0.885	0.844	0.926	CLONAL	2	TRUE	0	0.604868143959669	2		320	568	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278069	15278069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771486133	NA	P-0027238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	181	562	0	ENST00000263388.2:c.5353C>T	p.Arg1785Cys	p.R1785C	ENST00000263388	NM_000435.2	1785	Cgt/Tgt	29/33	0.604868143959669	2	FACETS	0.919	0.852	0.989	0.46	0.426	0.495	CLONAL	1	TRUE	0	0.604868143959669	2		562	651	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439700	220439701	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0027238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	206	750	1	ENST00000243786.2:c.562_563dup	p.Leu189CysfsTer2	p.L189Cfs*2	ENST00000243786	NM_002191.3	185	gct/gCTct	2/2	0.604868143959669	2	FACETS	0.831	0.772	0.891	0.415	0.386	0.446	CLONAL	1	TRUE	0	0.604868143959669	2		751	820	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354152	15354152	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs868796773	NA	P-0027238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	101	508	2	ENST00000263377.2:c.2728del	p.Gln910LysfsTer39	p.Q910Kfs*39	ENST00000263377	NM_058243.2	910	Caa/aa	14/20	0.604868143959669	2	FACETS	0.561	0.503	0.623	0.281	0.251	0.312	SUBCLONAL	1	TRUE	0	0.604868143959669	2		510	595	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0027238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	415	567	7	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	0.604868143959669	2	FACETS	0.922	0.886	0.958	0.922	0.886	0.958	CLONAL	2	TRUE	0	0.604868143959669	2		574	744	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971053	21971053	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137854598	NA	P-0027238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	250	258	0	ENST00000304494.5:c.305C>T	p.Ala102Val	p.A102V	ENST00000304494	NM_000077.4	102	gCg/gTg	2/3	0.593254929839272	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.604868143959669	2		258	388	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	492	976	5	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	0.604868143959669	2	FACETS	0.949	0.916	0.982	0.949	0.916	0.982	CLONAL	2	TRUE	0	0.604868143959669	2		981	857	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137321073	137321073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768721235	NA	P-0027238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	351	531	1	ENST00000481739.1:c.1030G>A	p.Ala344Thr	p.A344T	ENST00000481739	NM_002957.4	344	Gcc/Acc	7/10	0.604868143959669	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.604868143959669	2		532	547	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589576	67589576	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1289537429	NA	P-0027238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	630	331	0	ENST00000274335.5:c.1344del	p.Lys448AsnfsTer32	p.K448Nfs*32	ENST00000274335		447	Aaa/aa	10/15	0.587662474857677	4	FACETS	0.937	0.912	0.961	0.937	0.912	0.961	CLONAL	4	TRUE	0	0.604868143959669	4		331	892	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736511	85736511	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs387906351	NA	P-0027238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	339	311	10	ENST00000370580.1:c.136del	p.Ile46TyrfsTer24	p.I46Yfs*24	ENST00000370580	NM_003921.4	46	Ata/ta	2/3	0.604868143959669	2	FACETS	0.929	0.889	0.969	0.929	0.889	0.969	CLONAL	2	TRUE	0	0.604868143959669	2		321	603	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665109	182665109	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	360	365	0	ENST00000292782.4:c.617G>A	p.Arg206Gln	p.R206Q	ENST00000292782	NM_020640.2	206	cGa/cAa	6/7	0.604868143959669	2	FACETS	0.981	0.941	1	0.981	0.941	1	CLONAL	2	TRUE	0	0.604868143959669	2		365	607	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260194	16260194	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1557761571	NA	P-0027238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	353	493	0	ENST00000375759.3:c.7464del	p.Ile2489SerfsTer10	p.I2489Sfs*10	ENST00000375759	NM_015001.2	2487	Ggg/gg	11/15	0.604868143959669	2	FACETS	0.935	0.896	0.974	0.935	0.896	0.974	CLONAL	2	TRUE	0	0.604868143959669	2		493	624	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724605	162724605	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756942296	NA	P-0027238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	328	533	1	ENST00000367921.3:c.377G>A	p.Gly126Asp	p.G126D	ENST00000367921	NM_006182.2	126	gGc/gAc	5/18	0.604868143959669	2	FACETS	0.919	0.879	0.959	0.919	0.879	0.959	CLONAL	2	TRUE	0	0.604868143959669	2		534	590	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946922	71946924	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-	novel	NA	P-0027238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	487	713	0	ENST00000298229.2:c.2774_2776del	p.Ser925del	p.S925del	ENST00000298229	NM_001567.3	924	gCCTcc/gcc	25/28	0.604868143959669	2	FACETS	0.939	0.906	0.973	0.939	0.906	0.973	CLONAL	2	TRUE	0	0.604868143959669	2		713	857	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434781	49434781	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770272063	NA	P-0027238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	192	748	1	ENST00000301067.7:c.6772C>T	p.Pro2258Ser	p.P2258S	ENST00000301067	NM_003482.3	2258	Cct/Tct	31/54	0.578222014834381	4	FACETS	0.732	0.675	0.792	0.366	0.337	0.396	SUBCLONAL	1	TRUE	2	0.604868143959669	4		749	1391	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435979	49435979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	399	665	1	ENST00000301067.7:c.6002G>A	p.Arg2001Gln	p.R2001Q	ENST00000301067	NM_003482.3	2001	cGg/cAg	28/54	0.578222014834381	4	FACETS	0.929	0.884	0.974	0.929	0.884	0.974	CLONAL	2	TRUE	2	0.604868143959669	4		666	1140	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491690	56491690	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	334	419	0	ENST00000267101.3:c.2582C>A	p.Pro861His	p.P861H	ENST00000267101	NM_001982.3	861	cCt/cAt	21/28	0.578222014834381	4	FACETS	0.992	0.942	1	0.992	0.942	1	CLONAL	2	TRUE	2	0.604868143959669	4		419	893	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281194	49281194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	520	633	2	ENST00000282018.3:c.241G>A	p.Ala81Thr	p.A81T	ENST00000282018	NM_020377.2	81	Gcc/Acc	1/1	0.604868143959669	2	FACETS	0.981	0.948	1	0.981	0.948	1	CLONAL	2	TRUE	0	0.604868143959669	2		635	876	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749148	43749148	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758857922	NA	P-0027238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	238	634	3	ENST00000382044.4:c.1658C>T	p.Thr553Met	p.T553M	ENST00000382044	NM_001141980.1	553	aCg/aTg	12/28	0.604868143959669	2	FACETS	0.859	0.803	0.917	0.43	0.401	0.459	CLONAL	1	TRUE	0	0.604868143959669	2		637	916	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72833965	72833965	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1192089213	NA	P-0027238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	454	467	0	ENST00000268489.5:c.3928G>A	p.Asp1310Asn	p.D1310N	ENST00000268489	NM_006885.3	1310	Gat/Aat	8/10	0.604868143959669	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.604868143959669	2		467	746	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075132	16075134	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0027238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	298	366	0	ENST00000268712.3:c.418_420del	p.Ser140del	p.S140del	ENST00000268712	NM_006311.3	140	TCT/-	4/46	0.604868143959669	2	FACETS	0.999	0.956	1	0.999	0.956	1	CLONAL	2	TRUE	0	0.604868143959669	2		366	493	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213612	2213612	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	483	697	0	ENST00000398665.3:c.1632G>C	p.Arg544Ser	p.R544S	ENST00000398665	NM_032482.2	544	agG/agC	17/28	0.604868143959669	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.604868143959669	2		697	798	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600417	10600417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	529	713	3	ENST00000171111.5:c.1438G>A	p.Gly480Arg	p.G480R	ENST00000171111	NM_203500.1	480	Ggg/Agg	4/6	0.604868143959669	2	FACETS	0.969	0.936	1	0.969	0.936	1	CLONAL	2	TRUE	0	0.604868143959669	2		716	903	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215588	36215588	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	554	771	1	ENST00000222270.7:c.3385C>A	p.Leu1129Met	p.L1129M	ENST00000222270	NM_014727.1	1129	Ctg/Atg	9/37	0.604868143959669	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.604868143959669	2		772	895	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912784	50912784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	203	651	2	ENST00000440232.2:c.2015C>T	p.Ala672Val	p.A672V	ENST00000440232	NM_002691.3	672	gCc/gTc	17/27	0.604868143959669	2	FACETS	0.921	0.857	0.987	0.46	0.428	0.494	CLONAL	1	TRUE	0	0.604868143959669	2		653	729	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690264	47690264	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs370970617	NA	P-0027238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	446	498	0	ENST00000233146.2:c.1481C>G	p.Ser494Ter	p.S494*	ENST00000233146	NM_000251.2	494	tCa/tGa	9/16	0.604868143959669	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.604868143959669	2		498	735	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280061	66280061	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	295	345	0	ENST00000273854.3:c.1628G>C	p.Arg543Pro	p.R543P	ENST00000273854	NM_004439.5	543	cGt/cCt	7/18	0.593254929839272	2	FACETS	0.938	0.895	0.98	0.938	0.895	0.98	CLONAL	2	TRUE	0	0.604868143959669	2		345	520	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410948	31410948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758133428	NA	P-0027238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	183	663	2	ENST00000344624.3:c.3572C>T	p.Ala1191Val	p.A1191V	ENST00000344624		1191	gCg/gTg	28/33	0.587662474857677	4	FACETS	0.729	0.67	0.789	0.182	0.167	0.198	SUBCLONAL	1	TRUE	0	0.604868143959669	4		665	1333	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042169	6042169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35629870	NA	P-0027238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	299	481	2	ENST00000265849.7:c.452G>A	p.Arg151His	p.R151H	ENST00000265849	NM_000535.5	151	cGc/cAc	5/15	0.578222014834381	4	FACETS	0.883	0.834	0.934	0.883	0.834	0.934	CLONAL	2	TRUE	2	0.604868143959669	4		483	898	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932028	39932029	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0027238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	415	351	0	ENST00000378444.4:c.2570_2571del	p.Glu857GlyfsTer7	p.E857Gfs*7	ENST00000378444	NM_001123385.1	857	gAG/g	4/15	0.540179753722423	2	FACETS	1	0.98	1			1	CLONAL	2	TRUE	NA	0.604868143959669	2		351	669	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0027240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	351	629	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.533029496113151	1	FACETS	0.936	0.889	0.984	0.936	0.889	0.984	CLONAL	1	TRUE	0	0.553898517820137	1		630	979	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088788	27088788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	124	583	2	ENST00000324856.7:c.2402del	p.Gly801ValfsTer32	p.G801Vfs*32	ENST00000324856	NM_006015.4	799	caG/ca	7/20	0.224864528361086	3	FACETS	0.528	0.477	0.583	0.264	0.238	0.292	INDETERMINATE	1	TRUE	1	0.553898517820137	3		585	1082	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263941	104263941	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1227379293	NA	P-0027240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	53	89	1	ENST00000369902.3:c.32G>A	p.Gly11Asp	p.G11D	ENST00000369902	NM_016169.3	11	gGc/gAc	1/12	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.553898517820137	2		90	160	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115048	3115048	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769982397	NA	P-0027240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	86	751	1	ENST00000078429.4:c.583G>A	p.Asp195Asn	p.D195N	ENST00000078429	NM_002067.2	195	Gac/Aac	4/7	0.533029496113151	1	FACETS	0.238	0.21	0.269	0.238	0.21	0.269	SUBCLONAL	1	TRUE	0	0.553898517820137	1		752	942	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748150	72748150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	243	447	3	ENST00000357731.5:c.28G>A	p.Ala10Thr	p.A10T	ENST00000357731	NM_173808.2	10	Gct/Act	1/7	0.153652292153384	2	FACETS	1	0.987	1	0.592	0.555	0.63	INDETERMINATE	1	TRUE	0	0.553898517820137	2		450	741	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114799886	114799886	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs377242639	NA	P-0027240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	344	497	0	ENST00000543371.1:c.552+1G>A		p.X184_splice	ENST00000543371	NM_001198531.1	184			1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.553898517820137	2		497	1125	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251753	212251753	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	56	304	0	ENST00000342788.4:c.3306T>G	p.Phe1102Leu	p.F1102L	ENST00000342788	NM_005235.2	1102	ttT/ttG	27/28	1	2	FACETS	0.299	0.256	0.347	0.299	0.256	0.347	SUBCLONAL	1	TRUE	1	0.553898517820137	2		304	676	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023726	31023732	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGTCC	GCGGTCC	-	novel	NA	P-0027240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	299	625	0	ENST00000375687.4:c.3213_3219del	p.Val1072LysfsTer35	p.V1072Kfs*35	ENST00000375687	NM_015338.5	1071	GCGGTCCgc/gc	13/13	0.153652292153384	2	FACETS	0.898	0.845	0.952	0.449	0.422	0.476	INDETERMINATE	1	TRUE	0	0.553898517820137	2		625	1202	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504347	186504347	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	152	306	0	ENST00000323963.5:c.684C>A	p.Phe228Leu	p.F228L	ENST00000323963		228	ttC/ttA	7/11	1	2	FACETS	0.811	0.743	0.881	0.811	0.743	0.881	CLONAL	1	TRUE	1	0.553898517820137	2		306	677	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155579	106155580	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	244	449	0	ENST00000380013.4:c.483dup	p.Asp162ArgfsTer9	p.D162Rfs*9	ENST00000380013	NM_001127208.2	160	-/A	3/11	0.368117300313443	1	FACETS	0.757	0.709	0.806	0.757	0.709	0.806	SUBCLONAL	1	TRUE	0	0.553898517820137	1		449	842	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793346	139793347	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0027240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	76	569	0	ENST00000247668.2:c.156dup	p.Tyr53ValfsTer27	p.Y53Vfs*27	ENST00000247668	NM_021138.3	52	cgg/cGgg	2/11	1	2	FACETS	0.242	0.211	0.276	0.242	0.211	0.276	SUBCLONAL	1	TRUE	1	0.553898517820137	2		569	1133	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390467	118390467	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	51	524	0	ENST00000534358.1:c.11281T>G	p.Leu3761Val	p.L3761V	ENST00000534358	NM_005933.3	3761	Ttg/Gtg	32/36	0.272301465673038	1	FACETS	0.141	0.119	0.165	0.141	0.119	0.165	INDETERMINATE	1	TRUE	0	0.553898517820137	1		524	943	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0027243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	307	671	2	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.645894442101198	3	FACETS	1	0.995	1			1	CLONAL	3	TRUE	NA	0.6562783855858	3		673	362	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295251	1295251	+	upstream_gene_variant	5'Flank	SNP	A	A	C	novel	NA	P-0027243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	58	235	0				ENST00000310581	NM_198253.2	-/1132			0.509807339600619	4	FACETS	1	0.934	1	0.723	0.639	0.808	CLONAL	2	TRUE	1	0.6562783855858	4		235	135	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38975681	38975681	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	10	511	0	ENST00000357387.3:c.847G>T	p.Ala283Ser	p.A283S	ENST00000357387	NM_152756.3	283	Gcc/Tcc	10/38	0.509807339600619	4	FACETS	0.297	0.201	0.417	0.099	0.067	0.139	SUBCLONAL	1	TRUE	1	0.6562783855858	4		511	170	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343639	118343639	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	129	453	0	ENST00000534358.1:c.1765A>G	p.Thr589Ala	p.T589A	ENST00000534358	NM_005933.3	589	Aca/Gca	3/36	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.470260810979567	2		453	522	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0027244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	336	595	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.470260810979567	3	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	1	0.470260810979567	3		595	882	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954347	48954347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201458896	NA	P-0027244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	150	485	0	ENST00000267163.4:c.1468G>A	p.Ala490Thr	p.A490T	ENST00000267163	NM_000321.2	490	Gct/Act	16/27	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.470260810979567	2		485	594	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678623	88678623	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	95	372	0	ENST00000360948.2:c.913C>A	p.Pro305Thr	p.P305T	ENST00000360948	NM_001012338.2	305	Cca/Aca	9/19	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.470260810979567	2		372	401	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245146	41245146	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	216	688	0	ENST00000357654.3:c.2402G>T	p.Cys801Phe	p.C801F	ENST00000357654	NM_007294.3	801	tGt/tTt	10/23	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.470260810979567	2		688	911	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207021	1207021	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913324	NA	P-0027244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	414	687	0	ENST00000326873.7:c.109C>T	p.Gln37Ter	p.Q37*	ENST00000326873	NM_000455.4	37	Cag/Tag	1/10	0.470260810979567	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.470260810979567	2		687	825	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600365	10600365	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	390	744	0	ENST00000171111.5:c.1490G>T	p.Trp497Leu	p.W497L	ENST00000171111	NM_203500.1	497	tGg/tTg	4/6	0.470260810979567	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.470260810979567	2		744	779	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584488	189584488	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	115	453	0	ENST00000264731.3:c.784A>G	p.Ser262Gly	p.S262G	ENST00000264731	NM_003722.4	262	Agt/Ggt	6/14	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.470260810979567	2		453	479	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286235	66286235	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	106	552	0	ENST00000273854.3:c.1451G>T	p.Ser484Ile	p.S484I	ENST00000273854	NM_004439.5	484	aGc/aTc	6/18	1	2	FACETS	0.891	0.802	0.984	0.891	0.802	0.984	CLONAL	1	TRUE	1	0.470260810979567	2		552	506	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111429	56111429	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	67	293	0	ENST00000399503.3:c.29C>G	p.Ser10Trp	p.S10W	ENST00000399503	NM_005921.1	10	tCg/tGg	1/20	1	2	FACETS	0.787	0.688	0.893	0.787	0.688	0.893	SUBCLONAL	1	TRUE	1	0.470260810979567	2		293	362	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997696	149997696	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	108	386	0	ENST00000253339.5:c.2771G>T	p.Arg924Leu	p.R924L	ENST00000253339		924	cGa/cTa	5/7	0.456046824547519	1	FACETS	0.981	0.89	1	0.981	0.89	1	CLONAL	1	TRUE	0	0.470260810979567	1		386	358	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449760	8449760	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	157	573	1	ENST00000356435.5:c.3953C>A	p.Pro1318His	p.P1318H	ENST00000356435		1318	cCt/cAt	23/35	0.456046824547519	1	FACETS	0.839	0.771	0.908	0.839	0.771	0.908	CLONAL	1	TRUE	0	0.470260810979567	1		574	609	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041259	47041259	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	202	375	0	ENST00000377604.3:c.1687C>T	p.Gln563Ter	p.Q563*	ENST00000377604	NM_001204468.1	563	Cag/Tag	15/24	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.470260810979567	1		375	448	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0027245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	25	583	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.169967703341769	4	FACETS	0.346	0.272	0.433	0.173	0.136	0.217	SUBCLONAL	1	TRUE	2	0.268421445099544	4		583	682	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0027245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	134	570	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.268421445099544	1	FACETS	0.879	0.798	0.965	0.879	0.798	0.965	CLONAL	1	TRUE	0	0.268421445099544	1		570	983	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0027245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	38	601	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.268421445099544	1	FACETS	0.226	0.186	0.272	0.226	0.186	0.272	SUBCLONAL	1	TRUE	0	0.268421445099544	1		603	1083	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690806	89690806	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	98	399	0	ENST00000371953.3:c.213T>G	p.Cys71Trp	p.C71W	ENST00000371953	NM_000314.4	71	tgT/tgG	4/9	0.268421445099544	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.268421445099544	1		399	534	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0027246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	76	321	2	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.12767782975229	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		323	914	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0027247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	681	761	0	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	0.475230287400005	3	FACETS	0.912	0.883	0.94	0.912	0.883	0.94	CLONAL	3	TRUE	0	0.475230287400005	3		761	1297	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483347	120483347	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782036233	NA	P-0027247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	149	540	0	ENST00000256646.2:c.3014G>A	p.Gly1005Glu	p.G1005E	ENST00000256646	NM_024408.3	1005	gGg/gAg	19/34	0.267373178247211	5	FACETS	0.988	0.901	1	0.329	0.3	0.36	INDETERMINATE	1	TRUE	2	0.475230287400005	5		540	1087	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262508	16262508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	82	260	1	ENST00000375759.3:c.9773C>T	p.Ala3258Val	p.A3258V	ENST00000375759	NM_015001.2	3258	gCc/gTc	11/15	0.426270542765795	3	FACETS	0.804	0.711	0.904	0.402	0.355	0.452	CLONAL	1	TRUE	1	0.475230287400005	3		261	531	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426890	70426890	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	322	449	0	ENST00000373644.4:c.4550T>A	p.Val1517Glu	p.V1517E	ENST00000373644	NM_030625.2	1517	gTg/gAg	7/12	0.267373178247211	5	FACETS	1	0.986	1	0.745	0.704	0.786	INDETERMINATE	2	TRUE	2	0.475230287400005	5		449	1039	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77048452	77048452	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	327	503	0	ENST00000356341.3:c.1133A>C	p.Glu378Ala	p.E378A	ENST00000356341	NM_002576.4	378	gAg/gCg	12/15	0.394902918320108	3	FACETS	0.947	0.898	0.997	0.632	0.598	0.665	CLONAL	2	TRUE	0	0.475230287400005	3		503	899	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107898	30107898	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0027247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	131	412	0	ENST00000331968.5:c.907+2T>C		p.X303_splice	ENST00000331968	NM_002742.2	303			0.267373178247211	5	FACETS	0.919	0.832	1	0.306	0.277	0.337	INDETERMINATE	1	TRUE	2	0.475230287400005	5		412	1028	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061678	38061678	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs769896071	NA	P-0027247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	113	178	1	ENST00000250448.2:c.311T>A	p.Met104Lys	p.M104K	ENST00000250448	NM_004496.3	104	aTg/aAg	2/2	0.267373178247211	5	FACETS	0.956	0.867	1	0.637	0.578	0.7	INDETERMINATE	2	TRUE	2	0.475230287400005	5		179	426	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129196	2129196	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	259	677	0	ENST00000219476.3:c.3130A>G	p.Arg1044Gly	p.R1044G	ENST00000219476	NM_000548.3	1044	Agg/Ggg	27/42	0.399933871387404	2	FACETS	0.932	0.873	0.994	0.466	0.436	0.497	CLONAL	1	TRUE	0	0.475230287400005	2		677	1169	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610348	10610348	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	234	804	1	ENST00000171111.5:c.362A>T	p.Glu121Val	p.E121V	ENST00000171111	NM_203500.1	121	gAg/gTg	2/6	0.475230287400005	3	FACETS	0.89	0.829	0.954	0.445	0.414	0.477	CLONAL	1	TRUE	1	0.475230287400005	3		805	1369	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945429	17945429	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1408	250	746	0	ENST00000458235.1:c.2301G>T	p.Arg767Ser	p.R767S	ENST00000458235	NM_000215.3	767	agG/agT	17/24	0.412913349253235	4	FACETS	0.936	0.873	1	0.312	0.291	0.334	CLONAL	1	TRUE	1	0.475230287400005	4		746	1658	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708977	117708977	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs993831048	NA	P-0027247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	126	606	0	ENST00000368508.3:c.1980G>A	p.Trp660Ter	p.W660*	ENST00000368508	NM_002944.2	660	tgG/tgA	13/43	0.235531985048836	4	FACETS	0.955	0.865	1	0.318	0.288	0.35	INDETERMINATE	1	TRUE	1	0.475230287400005	4		606	819	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020704	37020704	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	147	554	0	ENST00000358127.4:c.141A>C	p.Gln47His	p.Q47H	ENST00000358127	NM_001280556.1	47	caA/caC	2/10	0.475230287400005	3	FACETS	0.599	0.545	0.655	0.2	0.181	0.219	SUBCLONAL	1	TRUE	0	0.475230287400005	3		554	1279	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0027248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	531	784	1	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.749617753423462	2	FACETS	0.988	0.962	1	0.988	0.962	1	CLONAL	2	TRUE	0	0.751301487434845	2		785	715	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0027251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	195	541	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	0.6944108453822	2		541	523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0027251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	419	583	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.6944108453822	1	FACETS	0.968	0.928	1	0.968	0.928	1	CLONAL	1	TRUE	0	0.6944108453822	1		583	814	SUCCESS
EED	8726	MSKCC	GRCh37	11	85963188	85963188	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0027251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	92	292	0	ENST00000263360.6:c.268-2A>G		p.X90_splice	ENST00000263360	NM_003797.3	90			0.6944108453822	1	FACETS	0.901	0.821	0.981	0.901	0.821	0.981	CLONAL	1	TRUE	0	0.6944108453822	1		292	192	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	101	535	0	ENST00000269305.4:c.584del	p.Ile195ThrfsTer52	p.I195Tfs*52	ENST00000269305	NM_001126112.2	195	aTc/ac	6/11	0.441428356621785	2	FACETS	0.893	0.801	0.989	0.446	0.4	0.495	CLONAL	1	TRUE	0	0.450641890925635	2		535	502	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035184	30035185	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	192	470	0	ENST00000338641.4:c.347dup	p.His116GlnfsTer14	p.H116Qfs*14	ENST00000338641	NM_000268.3	116	cat/cAat	3/16	0.425433463716889	2	FACETS	0.897	0.838	0.957	0.897	0.838	0.957	CLONAL	2	TRUE	0	0.450641890925635	2		470	475	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188197	10188197	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0027252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	113	427	0	ENST00000256474.2:c.341-1G>A		p.X114_splice	ENST00000256474	NM_000551.3	114			0.43241744681463	2	FACETS	1	0.979	1	0.641	0.582	0.703	CLONAL	1	TRUE	0	0.450641890925635	2		427	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0027254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	43	644	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.824	0.688	0.976	0.824	0.688	0.976	CLONAL	1	TRUE	1	0.16	2		644	652	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0027254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	35	671	2	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	1	2	FACETS	0.727	0.594	0.876	0.727	0.594	0.876	SUBCLONAL	1	TRUE	1	0.16	2		673	602	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057682	27057682	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520585	NA	P-0027254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	43	592	0	ENST00000324856.7:c.1390C>T	p.Gln464Ter	p.Q464*	ENST00000324856	NM_006015.4	464	Caa/Taa	3/20	1	2	FACETS	0.84	0.701	0.994	0.84	0.701	0.994	CLONAL	1	TRUE	1	0.16	2		592	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0027254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	17	488	1	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	1	2	FACETS	0.399	0.296	0.521	0.399	0.296	0.521	SUBCLONAL	1	TRUE	1	0.16	2		489	533	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8111095	8111095	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	75	633	1	ENST00000585124.1:c.112G>T	p.Ala38Ser	p.A38S	ENST00000585124	NM_004217.3	38	Gca/Tca	3/9	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.16	2		634	683	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971170	21971170	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	25	414	0	ENST00000304494.5:c.188T>G	p.Leu63Arg	p.L63R	ENST00000304494	NM_000077.4	63	cTg/cGg	2/3	0.122887606572353	0	FACETS	0.68	0.536	0.846			1	SUBCLONAL	1	TRUE	0	0.16	0		414	386	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs786201838	NA	P-0027259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	436	636	0	ENST00000269305.4:c.578A>C	p.His193Pro	p.H193P	ENST00000269305	NM_001126112.2	193	cAt/cCt	6/11	0.688558928068854	2	FACETS	0.942	0.91	0.974	0.942	0.91	0.974	CLONAL	2	TRUE	0	0.688558928068854	2		636	672	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957419	1957419	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0027259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	158	467	1	ENST00000382891.5:c.2523del		p.X841_splice	ENST00000382891	NM_133335.3	841			0.688558928068854	3	FACETS	1	0.923	1			1	CLONAL	1	TRUE	NA	0.688558928068854	3		468	615	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285039	15285039	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	223	616	2	ENST00000263388.2:c.4576C>A	p.Arg1526Ser	p.R1526S	ENST00000263388	NM_000435.2	1526	Cgt/Agt	25/33	0.688558928068854	2	FACETS	0.975	0.913	1	0.488	0.456	0.52	CLONAL	1	TRUE	0	0.688558928068854	2		618	664	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233268	46233268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1246	193	429	0	ENST00000334344.6:c.1487C>T	p.Ala496Val	p.A496V	ENST00000334344	NM_152641.2	496	gCa/gTa	11/21	0.688558928068854	13	FACETS	0.932	0.86	1			1	CLONAL	2	TRUE	NA	0.688558928068854	13		429	1439	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438272	49438272	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	442	570	0	ENST00000301067.7:c.4997T>G	p.Leu1666Arg	p.L1666R	ENST00000301067	NM_003482.3	1666	cTg/cGg	20/54	0.586451607881382	3	FACETS	0.884	0.855	0.912	0.884	0.855	0.912	CLONAL	3	TRUE	0	0.688558928068854	3		570	651	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445059	49445059	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	195	587	0	ENST00000301067.7:c.2407G>T	p.Glu803Ter	p.E803*	ENST00000301067	NM_003482.3	803	Gaa/Taa	10/54	0.586451607881382	3	FACETS	1	0.986	1	0.412	0.383	0.442	CLONAL	1	TRUE	0	0.688558928068854	3		587	616	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109822	115109822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762726425	NA	P-0027259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	194	602	0	ENST00000257566.3:c.2056G>A	p.Val686Met	p.V686M	ENST00000257566	NM_016569.3	686	Gtg/Atg	8/8	0.512082528749649	4	FACETS	0.93	0.86	1	0.465	0.43	0.502	CLONAL	1	TRUE	2	0.688558928068854	4		602	1023	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28644651	28644651	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	235	671	0	ENST00000241453.7:c.142G>C	p.Gly48Arg	p.G48R	ENST00000241453	NM_004119.2	48	Ggg/Cgg	2/24	0.4177189239072	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.688558928068854	1		671	355	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667552	29667552	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	468	580	0	ENST00000356175.3:c.6888G>A	p.Trp2296Ter	p.W2296*	ENST00000356175	NM_000267.3	2296	tgG/tgA	46/57	0.688558928068854	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.688558928068854	2		580	671	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276699	15276699	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0027259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	526	758	1	ENST00000263388.2:c.5566A>T	p.Lys1856Ter	p.K1856*	ENST00000263388	NM_000435.2	1856	Aag/Tag	30/33	0.688558928068854	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.688558928068854	2		759	764	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712615	52712615	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0027259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	291	352	0	ENST00000394830.3:c.139-2A>T		p.X47_splice	ENST00000394830	NM_018313.4	47			0.68088199098622	2	FACETS	0.983	0.943	1	0.983	0.943	1	CLONAL	2	TRUE	0	0.688558928068854	2		352	430	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158482	106158482	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	163	331	0	ENST00000380013.4:c.3383A>G	p.Tyr1128Cys	p.Y1128C	ENST00000380013	NM_001127208.2	1128	tAt/tGt	3/11	0.688558928068854	3	FACETS	0.912	0.85	0.974	0.912	0.85	0.974	CLONAL	2	TRUE	1	0.688558928068854	3		331	349	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557740	187557740	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs777497306	NA	P-0027259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	224	292	0	ENST00000441802.2:c.3971C>T	p.Ser1324Leu	p.S1324L	ENST00000441802	NM_005245.3	1324	tCa/tTa	5/27	0.688558928068854	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.688558928068854	3		292	426	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627199	86627200	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	214	282	0	ENST00000274376.6:c.576dup	p.Glu193ArgfsTer18	p.E193Rfs*18	ENST00000274376	NM_002890.2	192	gaa/gAaa	2/25	0.679231863944082	2	FACETS	0.974	0.928	1	0.974	0.928	1	CLONAL	2	TRUE	0	0.688558928068854	2		282	319	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486253	8486253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1256737547	NA	P-0027259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	167	381	0	ENST00000356435.5:c.2564G>A	p.Gly855Asp	p.G855D	ENST00000356435		855	gGc/gAc	17/35	0.679231863944082	2	FACETS	0.869	0.818	0.919	0.869	0.818	0.919	CLONAL	2	TRUE	0	0.688558928068854	2		381	279	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321407	1321407	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0027259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	131	372	0	ENST00000400841.2:c.350-2A>T		p.X117_splice	ENST00000400841		117			1	1	FACETS	0.65	0.596	0.705	0.65	0.596	0.705	SUBCLONAL	1	TRUE	0	0.688558928068854	1		372	384	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148931	119148931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs985412813	NA	P-0027261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	303	519	0	ENST00000264033.4:c.1151G>A	p.Cys384Tyr	p.C384Y	ENST00000264033	NM_005188.3	384	tGt/tAt	8/16	0.632855735131558	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.632855735131558	1		519	651	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69788788	69788788	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	253	416	0	ENST00000352241.4:c.40G>C	p.Gly14Arg	p.G14R	ENST00000352241	NM_198159.2	14	Ggg/Cgg	1/10	1	2	FACETS	0.945	0.887	1	0.945	0.887	1	CLONAL	1	TRUE	1	0.632855735131558	2		416	846	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241717	55241717	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762494280	NA	P-0027261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	175	571	0	ENST00000275493.2:c.2165C>T	p.Ala722Val	p.A722V	ENST00000275493	NM_005228.3	722	gCg/gTg	18/28	NA	2	FACETS	0.631	0.582	0.683			1	INDETERMINATE	1	TRUE	NA	0.632855735131558	2		571	876	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0027263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	32	434	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	0.761	0.617	0.924	0.761	0.617	0.924	CLONAL	1	TRUE	1	0.168584326653645	2		434	499	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727451	66727451	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519729	NA	P-0027263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	68	421	0	ENST00000307102.5:c.167A>C	p.Gln56Pro	p.Q56P	ENST00000307102	NM_002755.3	56	cAg/cCg	2/11	0.168584326653645	3	FACETS	1	0.972	1	0.497	0.432	0.566	CLONAL	1	TRUE	0	0.168584326653645	3		421	587	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335014	65335036	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCAACTGCATCTTCTTCATCA	TGGCAACTGCATCTTCTTCATCA	-	novel	NA	P-0027263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	33	372	0	ENST00000342505.4:c.605_627del	p.Met202ArgfsTer18	p.M202Rfs*18	ENST00000342505	NM_002227.2	202	aTGATGAAGAAGATGCAGTTGCCA/a	6/25	1	2	FACETS	0.986	0.804	1	0.986	0.804	1	CLONAL	1	TRUE	1	0.168584326653645	2		372	397	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528152	103528152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760309416	NA	P-0027263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	87	348	1	ENST00000355739.4:c.3460G>A	p.Asp1154Asn	p.D1154N	ENST00000355739	NM_000123.3	1154	Gat/Aat	15/15	1	2	FACETS	1	0.922	1	1	0.986	1	CLONAL	2	TRUE	1	0.168584326653645	2		349	493	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396438	396458	+	inframe_deletion	In_Frame_Del	DEL	GTTTTCCTCCATAGTGGCCTG	GTTTTCCTCCATAGTGGCCTG	-	novel	NA	P-0027263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	51	561	0	ENST00000262320.3:c.568_588del	p.Gln190_Asn196del	p.Q190_N196del	ENST00000262320	NM_003502.3	190	CAGGCCACTATGGAGGAAAAC/-	2/11	0.148836957210878	1	FACETS	0.875	0.743	1	0.875	0.743	1	CLONAL	1	TRUE	0	0.168584326653645	1		561	633	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010592	48010592	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1553408388	NA	P-0027263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	59	447	0	ENST00000234420.5:c.220G>T	p.Gly74Ter	p.G74*	ENST00000234420	NM_000179.2	74	Gga/Tga	1/10	0.168584326653645	3	FACETS	1	0.959	1	0.665	0.572	0.766	CLONAL	1	TRUE	1	0.168584326653645	3		447	571	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945707	54945707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	32	324	0	ENST00000312783.6:c.863C>T	p.Thr288Ile	p.T288I	ENST00000312783	NM_198436.1	288	aCt/aTt	9/10	0.168584326653645	4	FACETS	0.956	0.775	1	0.478	0.387	0.581	CLONAL	1	TRUE	2	0.168584326653645	4		324	464	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	TCGGG	novel	NA	P-0027263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	82	570	0	ENST00000269305.4:c.461delinsCCCGA	p.Gly154AlafsTer28	p.G154Afs*28	ENST00000269305	NM_001126112.2	154	gGc/gCCCGAc	5/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.168584326653645	2		570	702	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094453	27094456	+	frameshift_variant	Frame_Shift_Del	DEL	TCTA	TCTA	-	novel	NA	P-0027268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	104	504	0	ENST00000324856.7:c.3162_3165del	p.Tyr1055CysfsTer3	p.Y1055Cfs*3	ENST00000324856	NM_006015.4	1054	cTCTAt/ct	11/20	0.196377896155324	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.219585810937469	1		504	799	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291492	15291492	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs764352557	NA	P-0027268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	148	380	5	ENST00000263388.2:c.3142G>A	p.Gly1048Arg	p.G1048R	ENST00000263388	NM_000435.2	1048	Ggg/Agg	19/33	0.151681104553904	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.219585810937469	3		385	664	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218824	36218824	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	246	645	0	ENST00000222270.7:c.4435T>C	p.Ser1479Pro	p.S1479P	ENST00000222270	NM_014727.1	1479	Tcg/Ccg	18/37	0.151681104553904	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	1	0.219585810937469	3		645	1199	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032831	30032837	+	frameshift_variant	Frame_Shift_Del	DEL	AGGACAC	AGGACAC	-	novel	NA	P-0027268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	88	321	0	ENST00000338641.4:c.208_214del	p.Asp70TrpfsTer51	p.D70Wfs*51	ENST00000338641	NM_000268.3	69	aAGGACACa/aa	2/16	0.196377896155324	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.219585810937469	1		321	660	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038837	47038837	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	101	323	0	ENST00000377604.3:c.844C>G	p.Leu282Val	p.L282V	ENST00000377604	NM_001204468.1	282	Ctg/Gtg	9/24	1	1	FACETS	0.8	0.718	0.886	1	0.984	1	SUBCLONAL	2	TRUE	0	0.219585810937469	1		323	512	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370798	55370798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1406469266	NA	P-0027269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	134	538	0	ENST00000297316.4:c.100G>A	p.Glu34Lys	p.E34K	ENST00000297316	NM_022454.3	34	Gag/Aag	1/2	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.36486829933862	2		538	720	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519990	NA	P-0027269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	100	499	0	ENST00000269305.4:c.796G>C	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Cga	8/11	0.36486829933862	1	FACETS	0.695	0.621	0.773	0.695	0.621	0.773	SUBCLONAL	1	TRUE	0	0.36486829933862	1		499	645	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873248	71873248	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	90	376	0	ENST00000357731.5:c.946A>C	p.Ser316Arg	p.S316R	ENST00000357731	NM_173808.2	316	Agt/Cgt	7/7	1	2	FACETS	0.858	0.763	0.959	0.858	0.763	0.959	CLONAL	1	TRUE	1	0.36486829933862	2		376	575	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047258	77047258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1565583382	NA	P-0027269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	152	471	0	ENST00000356341.3:c.1286A>G	p.Tyr429Cys	p.Y429C	ENST00000356341	NM_002576.4	429	tAc/tGc	13/15	0.341590756952283	2	FACETS	1	0.915	1	0.5	0.457	0.545	CLONAL	1	TRUE	0	0.36486829933862	2		471	833	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2089975	2089975	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	157	611	1	ENST00000219066.1:c.889T>A	p.Cys297Ser	p.C297S	ENST00000219066	NM_002528.5	297	Tgc/Agc	6/6	1	2	FACETS	0.923	0.846	1	0.923	0.846	1	CLONAL	1	TRUE	1	0.36486829933862	2		612	932	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341328	89341328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	72	300	1	ENST00000301030.4:c.7607G>A	p.Arg2536Gln	p.R2536Q	ENST00000301030	NM_001256183.1	2536	cGg/cAg	11/13	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.36486829933862	2		301	377	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591826	48591826	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs281875324	NA	P-0027269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	86	328	0	ENST00000342988.3:c.989A>C	p.Glu330Ala	p.E330A	ENST00000342988	NM_005359.5	330	gAa/gCa	9/12	0.3152904673081	1	FACETS	0.771	0.684	0.863	0.771	0.684	0.863	SUBCLONAL	1	TRUE	0	0.36486829933862	1		328	500	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300092	15300092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	160	508	2	ENST00000263388.2:c.1184G>A	p.Cys395Tyr	p.C395Y	ENST00000263388	NM_000435.2	395	tGc/tAc	7/33	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.36486829933862	2		510	821	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15378230	15378230	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	78	437	0	ENST00000263377.2:c.556A>T	p.Thr186Ser	p.T186S	ENST00000263377	NM_058243.2	186	Aca/Tca	4/20	1	2	FACETS	0.714	0.628	0.806	0.714	0.628	0.806	SUBCLONAL	1	TRUE	1	0.36486829933862	2		437	599	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46254154	46254154	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	112	443	0	ENST00000371998.3:c.286C>A	p.Gln96Lys	p.Q96K	ENST00000371998		96	Caa/Aaa	5/23	0.36486829933862	3	FACETS	0.825	0.741	0.914	0.412	0.37	0.457	CLONAL	1	TRUE	1	0.36486829933862	3		443	880	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0027270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	294	449	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.638489063385336	2		449	847	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0027270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	150	226	1	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.638489063385336	2		227	451	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0027270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	231	443	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	0.638489063385336	2		443	721	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729163	66729163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516792	NA	P-0027270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	339	552	1	ENST00000307102.5:c.371C>T	p.Pro124Leu	p.P124L	ENST00000307102	NM_002755.3	124	cCg/cTg	3/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.638489063385336	2		553	1003	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481403	+	missense_variant	Missense_Mutation	DNP	CC	CC	GA	rs1057519720	NA	P-0027270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	353	370	1	ENST00000288602.6:c.1405_1406delinsTC	p.Gly469Ser	p.G469S	ENST00000288602	NM_004333.4	469	GGa/TCa	11/18	0.145511117028368	3	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.638489063385336	3		371	592	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622436	28622436	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587778372	NA	P-0027270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	253	437	0	ENST00000241453.7:c.1181A>G	p.Gln394Arg	p.Q394R	ENST00000241453	NM_004119.2	394	cAa/cGa	9/24	1	2	FACETS	0.978	0.919	1	0.978	0.919	1	CLONAL	1	TRUE	1	0.638489063385336	2		437	810	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289247	33289247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1455644209	NA	P-0027270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	255	377	1	ENST00000374542.5:c.305C>T	p.Ser102Leu	p.S102L	ENST00000374542	NM_001141970.1	102	tCg/tTg	3/8	0.638489063385336	3	FACETS	0.985	0.922	1	0.492	0.461	0.525	CLONAL	1	TRUE	1	0.638489063385336	3		378	1070	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940120	31940120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1212	370	610	0	ENST00000375333.2:c.262G>A	p.Glu88Lys	p.E88K	ENST00000375333	NM_032454.1	88	Gaa/Aaa	2/8	0.638489063385336	3	FACETS	0.966	0.915	1	0.483	0.457	0.51	CLONAL	1	TRUE	1	0.638489063385336	3		610	1582	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546788	9546788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772481025	NA	P-0027270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	181	305	0	ENST00000353224.5:c.1234C>T	p.Pro412Ser	p.P412S	ENST00000353224	NM_177990.2	412	Ccg/Tcg	5/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.638489063385336	2		305	504	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527596	41527596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	285	481	0	ENST00000263253.7:c.1487C>T	p.Pro496Leu	p.P496L	ENST00000263253	NM_001429.3	496	cCt/cTt	6/31	0.618045882226927	3	FACETS	1	0.962	1			1	CLONAL	1	TRUE	NA	0.638489063385336	3		481	1142	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631443	117631443	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	133	306	0	ENST00000368508.3:c.6235G>A	p.Asp2079Asn	p.D2079N	ENST00000368508	NM_002944.2	2079	Gat/Aat	40/43	1	2	FACETS	0.864	0.79	0.941	0.864	0.79	0.941	CLONAL	1	TRUE	1	0.638489063385336	2		306	482	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658501	117658501	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	166	440	1	ENST00000368508.3:c.5082G>A	p.Trp1694Ter	p.W1694*	ENST00000368508	NM_002944.2	1694	tgG/tgA	31/43	1	2	FACETS	0.852	0.787	0.92	0.852	0.787	0.92	CLONAL	1	TRUE	1	0.638489063385336	2		441	610	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275813	38275813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs575766741	NA	P-0027270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	266	560	0	ENST00000425967.3:c.1456C>T	p.Pro486Ser	p.P486S	ENST00000425967	NM_001174067.1	486	Ccc/Tcc	11/19	1	2	FACETS	0.884	0.83	0.939	0.884	0.83	0.939	CLONAL	1	TRUE	1	0.638489063385336	2		560	943	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023949	27023949	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	106	153	0	ENST00000324856.7:c.1055G>A	p.Gly352Glu	p.G352E	ENST00000324856	NM_006015.4	352	gGg/gAg	1/20	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.638489063385336	2		153	312	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445611	49445611	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	454	811	0	ENST00000301067.7:c.1855C>T	p.Pro619Ser	p.P619S	ENST00000301067	NM_003482.3	619	Cca/Tca	10/54	1	2	FACETS	0.99	0.945	1	0.99	0.945	1	CLONAL	1	TRUE	1	0.638489063385336	2		811	1436	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562531	21562531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	68	77	0	ENST00000382592.4:c.1388C>T	p.Pro463Leu	p.P463L	ENST00000382592	NM_014572.2	463	cCc/cTc	4/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.638489063385336	2		77	160	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649275	23649275	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs730881897	NA	P-0027270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	177	285	0	ENST00000261584.4:c.109-2A>G		p.X37_splice	ENST00000261584	NM_024675.3	37			1	2	FACETS	0.918	0.85	0.988	0.918	0.85	0.988	CLONAL	1	TRUE	1	0.638489063385336	2		285	604	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149506164	149506164	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	283	482	0	ENST00000261799.4:c.1593G>C	p.Lys531Asn	p.K531N	ENST00000261799	NM_002609.3	531	aaG/aaC	11/23	0.638489063385336	1	FACETS	0.966	0.915	1	0.966	0.915	1	CLONAL	1	TRUE	0	0.638489063385336	1		482	625	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190580	32190580	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	277	545	1	ENST00000375023.3:c.159T>G	p.Cys53Trp	p.C53W	ENST00000375023	NM_004557.3	53	tgT/tgG	3/30	0.638489063385336	3	FACETS	0.886	0.831	0.943	0.443	0.415	0.472	CLONAL	1	TRUE	1	0.638489063385336	3		546	1292	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38148059	38148059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	344	599	0	ENST00000317025.8:c.3052C>T	p.Pro1018Ser	p.P1018S	ENST00000317025	NM_023034.1	1018	Cct/Tct	17/24	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.638489063385336	2		599	1027	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578316	226578316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs193238922	NA	P-0027273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	49	354	0	ENST00000366794.5:c.412C>T	p.Arg138Cys	p.R138C	ENST00000366794	NM_001618.3	138	Cgc/Tgc	4/23	0.315910120336755	5	FACETS	0.884	0.749	1	0.221	0.187	0.259	CLONAL	1	FALSE	1	0.315910120336755	5		354	517	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0027273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	166	525	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	1	2	FACETS	0.98	0.906	1	1	0.992	1	CLONAL	2	FALSE	1	0.315910120336755	2		525	536	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0027274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	151	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.440870654005408	3	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	1	0.493740099482273	3		509	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0027274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	249	601	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.493740099482273	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.493740099482273	1		603	621	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992154	11992154	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs202244621	NA	P-0027274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	291	532	0	ENST00000396373.4:c.244A>G	p.Ile82Val	p.I82V	ENST00000396373	NM_001987.4	82	Att/Gtt	3/8	0.397932517952239	4	FACETS	1	0.99	1	0.79	0.747	0.833	CLONAL	2	TRUE	1	0.493740099482273	4		532	743	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244282	5244282	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	48	721	0	ENST00000357368.4:c.1200C>G	p.Ile400Met	p.I400M	ENST00000357368	NM_002850.3	400	atC/atG	11/38	0.41001933621404	1	FACETS	0.224	0.189	0.263	0.224	0.189	0.263	SUBCLONAL	1	TRUE	0	0.493740099482273	1		721	653	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316223	11316223	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	299	392	0	ENST00000361445.4:c.531C>G	p.Ile177Met	p.I177M	ENST00000361445	NM_004958.3	177	atC/atG	5/58	0.334357644642377	3	FACETS	1	0.985	1	1	0.995	1	CLONAL	3	TRUE	1	0.353099608055702	3		392	611	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172247	99172247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755705596	NA	P-0027277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	114	514	0	ENST00000074304.5:c.1813G>A	p.Ala605Thr	p.A605T	ENST00000074304	NM_001134224.1	605	Gca/Aca	17/26	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.353099608055702	2		514	539	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560844	9560844	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	86	338	0	ENST00000353224.5:c.938A>G	p.Tyr313Cys	p.Y313C	ENST00000353224	NM_177990.2	313	tAc/tGc	4/10	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.353099608055702	2		338	480	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201731	66201731	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	160	411	0	ENST00000273854.3:c.2771A>G	p.Lys924Arg	p.K924R	ENST00000273854	NM_004439.5	924	aAg/aGg	16/18	0.339590487848645	3	FACETS	0.954	0.879	1	0.954	0.879	1	CLONAL	2	TRUE	1	0.353099608055702	3		411	559	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622284	162622284	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	53	277	0	ENST00000366898.1:c.413C>A	p.Ala138Glu	p.A138E	ENST00000366898	NM_004562.2	138	gCa/gAa	4/12	0.353099608055702	1	FACETS	0.772	0.662	0.892	0.772	0.662	0.892	SUBCLONAL	1	TRUE	0	0.353099608055702	1		277	320	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0027277-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	27	725	1	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.239986091389631	3	FACETS	0.236	0.187	0.293	0.118	0.093	0.147	SUBCLONAL	1	TRUE	1	0.239986091389631	3		726	1067	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0027277-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	79	448	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.239986091389631	3	FACETS	0.765	0.671	0.866	0.382	0.335	0.433	SUBCLONAL	1	TRUE	1	0.239986091389631	3		448	964	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0027277-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	207	644	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.239986091389631	3	FACETS	0.854	0.792	0.919	0.854	0.792	0.919	CLONAL	2	TRUE	1	0.239986091389631	3		644	1131	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098969	178098969	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027277-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	34	237	0	ENST00000397062.3:c.76C>A	p.Gln26Lys	p.Q26K	ENST00000397062	NM_006164.4	26	Caa/Aaa	2/5	1	2	FACETS	0.667	0.545	0.804	0.667	0.545	0.804	SUBCLONAL	1	TRUE	1	0.239986091389631	2		237	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0027277-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	121	671	2	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.239986091389631	3	FACETS	1	0.977	1	0.637	0.575	0.702	CLONAL	1	TRUE	1	0.239986091389631	3		673	887	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165725	118165725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1211776583	NA	P-0027277-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	27	377	0	ENST00000369448.3:c.235G>A	p.Val79Ile	p.V79I	ENST00000369448	NM_017709.3	79	Gtt/Att	2/2	1	2	FACETS	0.49	0.389	0.606	0.49	0.389	0.606	SUBCLONAL	1	TRUE	1	0.239986091389631	2		377	459	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608633	189608633	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027277-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	53	576	1	ENST00000264731.3:c.1708C>A	p.Leu570Met	p.L570M	ENST00000264731	NM_003722.4	570	Ctg/Atg	13/14	0.239986091389631	3	FACETS	0.502	0.426	0.585	0.251	0.213	0.293	SUBCLONAL	1	TRUE	1	0.239986091389631	3		577	986	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629608	187629609	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0027277-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	58	635	0	ENST00000441802.2:c.1373_1374del	p.Ser458LysfsTer4	p.S458Kfs*4	ENST00000441802	NM_005245.3	458	aGC/a	2/27	0.239986091389631	1	FACETS	0.588	0.504	0.679	0.588	0.504	0.679	SUBCLONAL	1	TRUE	0	0.239986091389631	1		635	724	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0027279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	70	370	1	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.295272510676799	1	FACETS	0.606	0.528	0.689	0.606	0.528	0.689	SUBCLONAL	1	TRUE	0	0.33	1		371	585	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0027279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	180	456	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.789	0.73	0.85	1	0.991	1	SUBCLONAL	2	TRUE	1	0.33	2		456	691	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845901	156845901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769486223	NA	P-0027279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	174	667	1	ENST00000524377.1:c.1531G>A	p.Val511Met	p.V511M	ENST00000524377	NM_002529.3	511	Gtg/Atg	13/17	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.33	2		668	1005	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593504	48593504	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	26	237	0	ENST00000342988.3:c.1255G>T	p.Gly419Trp	p.G419W	ENST00000342988	NM_005359.5	419	Ggg/Tgg	10/12	0.295272510676799	1	FACETS	0.332	0.263	0.412	0.332	0.263	0.412	SUBCLONAL	1	TRUE	0	0.33	1		237	396	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69000005	69000005	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561299451	NA	P-0027279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	160	496	1	ENST00000288368.4:c.2074C>T	p.Arg692Trp	p.R692W	ENST00000288368	NM_024870.2	692	Cgg/Tgg	19/40	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.33	2		497	805	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260103	19260103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369287078	NA	P-0027279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	79	596	1	ENST00000162023.5:c.190C>T	p.Arg64Cys	p.R64C	ENST00000162023		64	Cgt/Tgt	7/13	1	2	FACETS	0.484	0.424	0.549	0.484	0.424	0.549	SUBCLONAL	1	TRUE	1	0.33	2		597	989	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266853	41266853	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	86	275	1	ENST00000349496.5:c.524T>A	p.Val175Asp	p.V175D	ENST00000349496	NM_001904.3	175	gTc/gAc	5/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.33	2		276	432	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430234	181430234	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	67	293	0	ENST00000325404.1:c.86C>T	p.Ala29Val	p.A29V	ENST00000325404	NM_003106.3	29	gCg/gTg	1/1	1	2	FACETS	0.756	0.658	0.862	0.756	0.658	0.862	SUBCLONAL	1	TRUE	1	0.33	2		293	537	SUCCESS
APC	324	MSKCC	GRCh37	5	112175615	112175615	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	87	329	0	ENST00000257430.4:c.4325del	p.Pro1442LeufsTer31	p.P1442Lfs*31	ENST00000257430	NM_000038.5	1442	Cct/ct	16/16	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.33	2		329	508	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911483	114911483	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0027280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	41	148	0	ENST00000543371.1:c.1002-1G>A		p.X334_splice	ENST00000543371	NM_001198531.1	334			1	2	FACETS	0.686	0.573	0.809	0.686	0.573	0.809	SUBCLONAL	1	TRUE	1	0.380853534475123	2		148	314	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50830275	50830275	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	137	393	0	ENST00000398568.2:c.2720del	p.Pro907GlnfsTer3	p.P907Qfs*3	ENST00000398568	NM_001042412.1	906	tgC/tg	18/18	0.342544692960622	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.380853534475123	1		393	526	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470588	25470588	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	191	610	0	ENST00000264709.3:c.886G>T	p.Val296Leu	p.V296L	ENST00000264709	NM_175629.2	296	Gtg/Ttg	8/23	1	2	FACETS	0.964	0.891	1	0.964	0.891	1	CLONAL	1	TRUE	1	0.380853534475123	2		610	1040	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097171	178097171	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	150	366	0	ENST00000397062.3:c.543A>T	p.Gln181His	p.Q181H	ENST00000397062	NM_006164.4	181	caA/caT	4/5	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.380853534475123	2		366	747	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003189	143003189	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764114435	NA	P-0027280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	95	268	0	ENST00000262992.4:c.2637G>A	p.Met879Ile	p.M879I	ENST00000262992	NM_001101669.1	879	atG/atA	23/24	1	2	FACETS	0.875	0.781	0.975	0.875	0.781	0.975	CLONAL	1	TRUE	1	0.380853534475123	2		268	570	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0027281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	59	487	2	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.36	0.309	0.416	0.36	0.309	0.416	SUBCLONAL	1	TRUE	1	0.393326709320091	2		489	833	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0027281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	61	669	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	1	2	FACETS	0.411	0.354	0.473	0.411	0.354	0.473	SUBCLONAL	1	TRUE	1	0.393326709320091	2		669	755	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426115	47426115	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	71	644	0	ENST00000377045.4:c.635C>A	p.Ser212Tyr	p.S212Y	ENST00000377045	NM_001654.4	212	tCc/tAc	7/16	1	2	FACETS	0.305	0.265	0.349	0.305	0.265	0.349	SUBCLONAL	1	TRUE	1	0.393326709320091	2		644	1182	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	628	715	0	ENST00000269305.4:c.472C>G	p.Arg158Gly	p.R158G	ENST00000269305	NM_001126112.2	158	Cgc/Ggc	5/11	0.657659357386416	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.657659357386416	2		715	898	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346365	73346365	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	251	407	0	ENST00000377767.4:c.1435G>T	p.Asp479Tyr	p.D479Y	ENST00000377767	NM_014953.3	479	Gac/Tac	10/21	0.657659357386416	2	FACETS	0.969	0.924	1	0.969	0.924	1	CLONAL	2	TRUE	0	0.657659357386416	2		407	394	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220382	1220382	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	651	563	0	ENST00000326873.7:c.475C>T	p.Gln159Ter	p.Q159*	ENST00000326873	NM_000455.4	159	Cag/Tag	4/10	0.657659357386416	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.657659357386416	3		563	846	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602580	10602580	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	713	600	1	ENST00000171111.5:c.998G>T	p.Gly333Val	p.G333V	ENST00000171111	NM_203500.1	333	gGc/gTc	3/6	0.657659357386416	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.657659357386416	3		601	919	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551687	150551687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	219	318	0	ENST00000369026.2:c.320C>T	p.Pro107Leu	p.P107L	ENST00000369026	NM_021960.4	107	cCg/cTg	1/3	0.440487653337647	5	FACETS	1	0.983	1	0.755	0.708	0.804	CLONAL	2	TRUE	2	0.657659357386416	5		318	584	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667501	241667501	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	245	268	0	ENST00000366560.3:c.949G>T	p.Ala317Ser	p.A317S	ENST00000366560	NM_000143.3	317	Gct/Tct	7/10	0.657659357386416	3	FACETS	0.973	0.919	1	0.973	0.919	1	CLONAL	2	TRUE	1	0.657659357386416	3		268	509	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279530	123279530	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	267	534	0	ENST00000358487.5:c.902A>T	p.Tyr301Phe	p.Y301F	ENST00000358487	NM_000141.4	301	tAc/tTc	7/18	0.5329103310967	3	FACETS	1	0.991	1	0.645	0.606	0.684	CLONAL	1	TRUE	1	0.657659357386416	3		534	837	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67197033	67197033	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1263141252	NA	P-0027284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	210	466	0	ENST00000312629.5:c.276G>T	p.Leu92Phe	p.L92F	ENST00000312629	NM_003952.2	92	ttG/ttT	4/15	0.470675300662407	5	FACETS	0.858	0.8	0.919	0.572	0.533	0.613	CLONAL	2	TRUE	2	0.657659357386416	5		466	739	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870933	12870933	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	957	328	0	ENST00000228872.4:c.160G>T	p.Glu54Ter	p.E54*	ENST00000228872	NM_004064.3	54	Gag/Tag	1/3	0.657659357386416	8	FACETS	0.948	0.929	0.967			1	CLONAL	7	TRUE	NA	0.657659357386416	8		328	1304	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210886	133210886	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	601	650	0	ENST00000320574.5:c.5890G>T	p.Glu1964Ter	p.E1964*	ENST00000320574	NM_006231.2	1964	Gag/Tag	43/49	0.628454119932605	4	FACETS	0.877	0.848	0.907	0.877	0.848	0.907	CLONAL	3	TRUE	1	0.657659357386416	4		650	1151	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679724	88679725	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	282	514	0	ENST00000360948.2:c.738dup	p.Gly247TrpfsTer30	p.G247Wfs*30	ENST00000360948	NM_001012338.2	246	-/T	7/19	0.643369628407707	2	FACETS	0.907	0.865	0.947	0.907	0.865	0.947	CLONAL	2	TRUE	0	0.657659357386416	2		514	473	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2097817	2097817	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	398	671	1	ENST00000219066.1:c.32C>A	p.Ala11Asp	p.A11D	ENST00000219066	NM_002528.5	11	gCc/gAc	1/6	0.5329103310967	3	FACETS	0.945	0.904	0.986	0.945	0.904	0.986	CLONAL	2	TRUE	1	0.657659357386416	3		672	851	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640076	3640076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	482	855	0	ENST00000294008.3:c.3563C>T	p.Ser1188Phe	p.S1188F	ENST00000294008	NM_032444.2	1188	tCc/tTc	12/15	0.5329103310967	3	FACETS	0.845	0.81	0.881	0.845	0.81	0.881	CLONAL	2	TRUE	1	0.657659357386416	3		855	1152	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820934	3820934	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	410	617	0	ENST00000262367.5:c.2517G>T	p.Gln839His	p.Q839H	ENST00000262367	NM_004380.2	839	caG/caT	14/31	0.657659357386416	3	FACETS	0.866	0.827	0.904	0.866	0.827	0.904	CLONAL	2	TRUE	1	0.657659357386416	3		617	957	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902271	50902271	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	772	936	0	ENST00000440232.2:c.163G>T	p.Glu55Ter	p.E55*	ENST00000440232	NM_002691.3	55	Gag/Tag	2/27	0.514866901558649	4	FACETS	0.978	0.951	1			1	CLONAL	3	TRUE	NA	0.657659357386416	4		936	1326	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342966	225342967	+	missense_variant	Missense_Mutation	DNP	CG	CG	AA	novel	NA	P-0027284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	301	516	1	ENST00000264414.4:c.2125_2126delinsTT	p.Arg709Leu	p.R709L	ENST00000264414	NM_003590.4	709	CGg/TTg	15/16	0.657659357386416	3	FACETS	0.93	0.883	0.977	0.93	0.883	0.977	CLONAL	2	TRUE	1	0.657659357386416	3		517	654	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157428	106157428	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	319	369	0	ENST00000380013.4:c.2329G>T	p.Gly777Cys	p.G777C	ENST00000380013	NM_001127208.2	777	Ggc/Tgc	3/11	0.657659357386416	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	2	0.657659357386416	4		369	786	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	256523	256523	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	21	119	0	ENST00000264932.6:c.1983T>G	p.Ile661Met	p.I661M	ENST00000264932	NM_004168.2	661	atT/atG	15/15	0.657659357386416	2	FACETS	0.331	0.256	0.417	0.165	0.128	0.209	SUBCLONAL	1	TRUE	0	0.657659357386416	2		119	193	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148544377	148544377	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	448	510	0	ENST00000320356.2:c.14G>T	p.Gly5Val	p.G5V	ENST00000320356	NM_004456.4	5	gGg/gTg	2/20	0.551519753485819	4	FACETS	0.86	0.826	0.894	0.86	0.826	0.894	CLONAL	3	TRUE	1	0.657659357386416	4		510	875	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133879	38133879	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	874	723	1	ENST00000317025.8:c.4007G>T	p.Cys1336Phe	p.C1336F	ENST00000317025	NM_023034.1	1336	tGt/tTt	23/24	0.657428185849863	5	FACETS	0.951	0.923	0.979	0.951	0.923	0.979	CLONAL	3	TRUE	2	0.657659357386416	5		724	1850	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319837	8319837	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	134	345	0	ENST00000356435.5:c.5664G>C	p.Gln1888His	p.Q1888H	ENST00000356435		1888	caG/caC	34/35	0.657659357386416	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.657659357386416	1		345	246	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0027286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	80	425	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.836	0.738	0.941	0.836	0.738	0.941	CLONAL	1	TRUE	1	0.369550029610228	2		425	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0027286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	183	601	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.941	0.867	1	0.941	0.867	1	CLONAL	1	TRUE	1	0.369550029610228	2		603	1053	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873587	151873588	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	107	400	0	ENST00000262189.6:c.8950dup	p.Ser2984PhefsTer18	p.S2984Ffs*18	ENST00000262189	NM_170606.2	2984	tct/tTct	38/59	0.347571700629864	3	FACETS	0.861	0.772	0.955	0.43	0.386	0.478	CLONAL	1	TRUE	1	0.369550029610228	3		400	797	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711269	114711271	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	TTA	TTA	-	novel	NA	P-0027286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	133	423	3	ENST00000543371.1:c.284_286del	p.Phe95_Lys96delinsTer	p.F95_K96delins*	ENST00000543371	NM_001198531.1	95	tTTAag/tag	3/14	1	2	FACETS	0.916	0.832	1	0.916	0.832	1	CLONAL	1	TRUE	1	0.369550029610228	2		426	786	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46583310	46583310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770783327	NA	P-0027286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	45	279	0	ENST00000263734.3:c.238G>A	p.Glu80Lys	p.E80K	ENST00000263734	NM_001430.4	80	Gaa/Aaa	3/16	0.234469260648316	1	FACETS	0.505	0.425	0.593	0.505	0.425	0.593	SUBCLONAL	1	TRUE	0	0.369550029610228	1		279	393	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111736	56111737	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0027286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	20	58	0	ENST00000399503.3:c.340dup	p.His114ProfsTer50	p.H114Pfs*50	ENST00000399503	NM_005921.1	112	-/C	1/20	1	2	FACETS	0.846	0.654	1	0.846	0.654	1	CLONAL	1	TRUE	1	0.369550029610228	2		58	128	SUCCESS
APC	324	MSKCC	GRCh37	5	112175155	112175159	+	frameshift_variant	Frame_Shift_Del	DEL	ATGTA	ATGTA	-	novel	NA	P-0027286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	48	174	0	ENST00000257430.4:c.3866_3870del	p.Cys1289SerfsTer10	p.C1289Sfs*10	ENST00000257430	NM_000038.5	1288	ggATGTAat/ggat	16/16	0.369550029610228	1	FACETS	0.894	0.763	1	0.894	0.763	1	CLONAL	1	TRUE	0	0.369550029610228	1		174	237	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431408	121431408	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	68	531	0	ENST00000257555.6:c.612C>A	p.Phe204Leu	p.F204L	ENST00000257555		204	ttC/ttA	3/10	1	2	FACETS	0.25	0.217	0.286	0.25	0.217	0.286	SUBCLONAL	1	TRUE	1	0.619825745884231	2		531	877	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124442	94124442	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	27	446	0	ENST00000369303.4:c.141G>T	p.Trp47Cys	p.W47C	ENST00000369303	NM_004440.3	47	tgG/tgT	2/17	0.602482776698775	1	FACETS	0.138	0.109	0.171	0.138	0.109	0.171	SUBCLONAL	1	TRUE	0	0.619825745884231	1		446	435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0027288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	107	570	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.30787395695804	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.380266734120991	1		570	398	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0027288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	66	796	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.787	0.685	0.897	0.787	0.685	0.897	SUBCLONAL	1	TRUE	1	0.380266734120991	2		796	441	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0027288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	139	337	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.380266734120991	2	FACETS	0.914	0.841	0.989	0.914	0.841	0.989	CLONAL	2	TRUE	0	0.380266734120991	2		337	400	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0027288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	137	539	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.380266734120991	2		539	491	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023702	31023702	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1311033207	NA	P-0027288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	158	540	1	ENST00000375687.4:c.3187C>T	p.Gln1063Ter	p.Q1063*	ENST00000375687	NM_015338.5	1063	Cag/Tag	13/13	0.302778957208242	3	FACETS	0.872	0.803	0.943	0.872	0.803	0.943	CLONAL	2	TRUE	1	0.380266734120991	3		541	567	SUCCESS
APC	324	MSKCC	GRCh37	5	112175760	112175761	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs398123122	NA	P-0027288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	36	249	0	ENST00000257430.4:c.4473dup	p.Ala1492CysfsTer22	p.A1492Cfs*22	ENST00000257430	NM_000038.5	1490	cat/caTt	16/16	1	2	FACETS	0.74	0.611	0.881	0.74	0.611	0.881	SUBCLONAL	1	TRUE	1	0.380266734120991	2		249	256	SUCCESS
APC	324	MSKCC	GRCh37	5	112174223	112174223	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	61	321	0	ENST00000257430.4:c.2932C>T	p.Gln978Ter	p.Q978*	ENST00000257430	NM_000038.5	978	Caa/Taa	16/16	1	2	FACETS	0.874	0.758	0.999	0.874	0.758	0.999	CLONAL	1	TRUE	1	0.380266734120991	2		321	367	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248633	59248634	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0027293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	193	913	0	ENST00000371222.2:c.109_110del	p.Ser37HisfsTer69	p.S37Hfs*69	ENST00000371222	NM_002228.3	37	AGc/c	1/1	0.195421330883462	3	FACETS	1	0.976	1	0.567	0.524	0.613	INDETERMINATE	1	TRUE	1	0.334180228235642	3		913	1188	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435201	18435202	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1565550462	NA	P-0027293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	58	316	0	ENST00000266497.5:c.192dup	p.Val65CysfsTer16	p.V65Cfs*16	ENST00000266497		62	-/T	1/31	0.0870828542029076	4	FACETS	0.884	0.767	1	0.884	0.767	1	INDETERMINATE	2	TRUE	2	0.334180228235642	4		316	262	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0027293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	489	876	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.334180228235642	1	FACETS	1	0.981	1	1	0.997	1	CLONAL	2	TRUE	0	0.334180228235642	1		876	1175	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920495	134920495	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	116	670	0	ENST00000398015.3:c.2310G>T	p.Gln770His	p.Q770H	ENST00000398015	NM_004441.4	770	caG/caT	12/16	0.0776234971171268	4	FACETS	0.808	0.727	0.895	0.404	0.363	0.448	INDETERMINATE	1	TRUE	2	0.334180228235642	4		670	1146	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509850	187509850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	155	301	0	ENST00000441802.2:c.13663G>A	p.Val4555Met	p.V4555M	ENST00000441802	NM_005245.3	4555	Gtg/Atg	27/27	0.0776234971171268	4	FACETS	1	0.983	1	1	0.983	1	INDETERMINATE	2	TRUE	2	0.334180228235642	4		301	497	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	22	528	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.247	0.191	0.312	0.247	0.191	0.312	SUBCLONAL	1	TRUE	1	0.559781545194129	2		529	318	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0027294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	45	278	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.559781545194129	2		278	143	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0027294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	474	601	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.559781545194129	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.559781545194129	1		603	991	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0027294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	78	305	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.761	0.674	0.854	0.761	0.674	0.854	SUBCLONAL	1	TRUE	1	0.559781545194129	2		305	366	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0027294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	306	416	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	0.442108240522398	5	FACETS	1	0.976	1	0.823	0.788	0.857	CLONAL	4	TRUE	0	0.559781545194129	5		416	489	SUCCESS
APC	324	MSKCC	GRCh37	5	112174096	112174096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs137854575	NA	P-0027294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	48	276	0	ENST00000257430.4:c.2805C>A	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	taC/taA	16/16	1	2	FACETS	0.837	0.716	0.966	0.837	0.716	0.966	CLONAL	1	TRUE	1	0.559781545194129	2		276	205	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557927	187557927	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs369805914	NA	P-0027294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	149	397	0	ENST00000441802.2:c.3784C>T	p.Arg1262Ter	p.R1262*	ENST00000441802	NM_005245.3	1262	Cga/Tga	5/27	1	2	FACETS	0.902	0.828	0.979	0.902	0.828	0.979	CLONAL	1	TRUE	1	0.559781545194129	2		397	590	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981167	201981168	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	702	841	1	ENST00000359651.3:c.248dup	p.Asn83LysfsTer9	p.N83Kfs*9	ENST00000359651		82	-/A	2/8	0.542609727034219	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.559781545194129	2		842	1199	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343382	118343382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782313746	NA	P-0027294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	23	345	1	ENST00000534358.1:c.1508G>A	p.Arg503Gln	p.R503Q	ENST00000534358	NM_005933.3	503	cGg/cAg	3/36	1	2	FACETS	0.211	0.164	0.266	0.211	0.164	0.266	SUBCLONAL	1	TRUE	1	0.559781545194129	2		346	389	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271926	15271926	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	459	781	0	ENST00000263388.2:c.6513T>G	p.Asp2171Glu	p.D2171E	ENST00000263388	NM_000435.2	2171	gaT/gaG	33/33	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.559781545194129	2		781	1354	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719838	61719838	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	19	471	0	ENST00000401558.2:c.1430C>T	p.Thr477Ile	p.T477I	ENST00000401558	NM_003400.3	477	aCa/aTa	14/25	1	2	FACETS	0.203	0.153	0.261	0.203	0.153	0.261	SUBCLONAL	1	TRUE	1	0.559781545194129	2		471	335	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860272	151860289	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	GCATAAAATCACAAGGTA	GCATAAAATCACAAGGTA	-	novel	NA	P-0027294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	85	428	0	ENST00000262189.6:c.10373_10390del	p.Leu3458_Gln3464delinsTer	p.L3458_Q3464delins*	ENST00000262189	NM_170606.2	3458	tTACCTTGTGATTTTATGCaa/taa	43/59	0.442108240522398	5	FACETS	1	0.945	1	0.222	0.196	0.249	CLONAL	1	TRUE	0	0.559781545194129	5		428	504	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410922	63410923	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	132	566	0	ENST00000330258.3:c.2244_2245insA	p.Ser749IlefsTer4	p.S749Ifs*4	ENST00000330258	NM_152424.3	748	-/A	2/2	0.559781545194129	1	FACETS	0.853	0.782	0.926	0.853	0.782	0.926	CLONAL	1	TRUE	0	0.559781545194129	1		566	398	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	29	528	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.576	0.461	0.708	0.576	0.461	0.708	SUBCLONAL	1	TRUE	1	0.16	2		529	629	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026253	48026253	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	123	355	0	ENST00000234420.5:c.1131G>C	p.Lys377Asn	p.K377N	ENST00000234420	NM_000179.2	377	aaG/aaC	4/10	1	2	FACETS	0.89	0.81	0.974	0.89	0.81	0.974	CLONAL	1	TRUE	1	0.583012888457722	2		355	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0027298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	749	644	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.743396257982002	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.743396257982002	3		644	871	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519896	NA	P-0027298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	119	334	0	ENST00000281708.4:c.1514G>T	p.Arg505Leu	p.R505L	ENST00000281708	NM_033632.3	505	cGc/cTc	10/12	0.743396257982002	3	FACETS	0.825	0.748	0.906	0.413	0.374	0.453	CLONAL	1	TRUE	1	0.743396257982002	3		334	532	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120318	94120318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41273629	NA	P-0027298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	204	242	0	ENST00000369303.4:c.733G>A	p.Ala245Thr	p.A245T	ENST00000369303	NM_004440.3	245	Gcc/Acc	3/17	0.589438273756737	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.743396257982002	4		242	428	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741660	17741660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	246	646	1	ENST00000250003.3:c.331C>T	p.Arg111Cys	p.R111C	ENST00000250003	NM_002478.4	111	Cgc/Tgc	1/3	0.589438273756737	4	FACETS	1	0.976	1	0.544	0.509	0.581	CLONAL	1	TRUE	2	0.743396257982002	4		647	1060	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482439	56482446	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTGGGT	AGGTGGGT	-	novel	NA	P-0027298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	101	533	0	ENST00000267101.3:c.988+2_988+9del		p.X330_splice	ENST00000267101	NM_001982.3	330		8/28	0.743396257982002	3	FACETS	0.684	0.613	0.759	0.342	0.306	0.38	SUBCLONAL	1	TRUE	1	0.743396257982002	3		533	545	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120169	70120169	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	432	455	0	ENST00000245479.2:c.1171C>T	p.Gln391Ter	p.Q391*	ENST00000245479	NM_000346.3	391	Cag/Tag	3/3	0.743396257982002	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.743396257982002	3		455	512	SUCCESS
APC	324	MSKCC	GRCh37	5	112174276	112174276	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	124	315	1	ENST00000257430.4:c.2985C>A	p.Cys995Ter	p.C995*	ENST00000257430	NM_000038.5	995	tgC/tgA	16/16	0.743396257982002	2	FACETS	0.948	0.891	1	0.948	0.891	1	CLONAL	2	TRUE	0	0.743396257982002	2		316	176	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738497	145738497	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs771492637	NA	P-0027298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1574	221	613	0	ENST00000428558.2:c.2488A>G	p.Arg830Gly	p.R830G	ENST00000428558	NM_004260.3	830	Aga/Gga	16/22	0.743396257982002	6	FACETS	0.824	0.763	0.887	0.165	0.152	0.178	CLONAL	1	TRUE	1	0.743396257982002	6		613	1795	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0027299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	75	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.329590176091831	2		509	420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0027299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	107	448	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.202269112160444	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.329590176091831	1		448	455	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937723	36937723	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1251017589	NA	P-0027299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	75	350	0	ENST00000361632.4:c.1015G>A	p.Asp339Asn	p.D339N	ENST00000361632		339	Gac/Aac	8/16	1	2	FACETS	0.865	0.76	0.978	0.865	0.76	0.978	CLONAL	1	TRUE	1	0.329590176091831	2		350	526	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435460	18435460	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	19	219	0	ENST00000266497.5:c.445A>T	p.Thr149Ser	p.T149S	ENST00000266497		149	Aca/Tca	1/31	1	2	FACETS	0.443	0.337	0.568	0.443	0.337	0.568	SUBCLONAL	1	TRUE	1	0.329590176091831	2		219	260	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30098267	30098267	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	27	422	0	ENST00000331968.5:c.1705T>G	p.Cys569Gly	p.C569G	ENST00000331968	NM_002742.2	569	Tgc/Ggc	11/18	0.202269112160444	1	FACETS	0.291	0.231	0.36	0.291	0.231	0.36	SUBCLONAL	1	TRUE	0	0.329590176091831	1		422	470	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950288	15950288	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	25	588	0	ENST00000268712.3:c.6656C>G	p.Ser2219Cys	p.S2219C	ENST00000268712	NM_006311.3	2219	tCt/tGt	42/46	0.202269112160444	1	FACETS	0.273	0.214	0.341	0.273	0.214	0.341	SUBCLONAL	1	TRUE	0	0.329590176091831	1		588	464	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222999	5222999	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	49	473	0	ENST00000357368.4:c.2804T>G	p.Leu935Arg	p.L935R	ENST00000357368	NM_002850.3	935	cTg/cGg	18/38	0.217961037295896	1	FACETS	0.461	0.39	0.539	0.461	0.39	0.539	SUBCLONAL	1	TRUE	0	0.329590176091831	1		473	539	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249523	153249523	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	29	389	0	ENST00000281708.4:c.1255G>T	p.Gly419Ter	p.G419*	ENST00000281708	NM_033632.3	419	Gga/Tga	9/12	0.202269112160444	1	FACETS	0.343	0.274	0.42	0.343	0.274	0.42	SUBCLONAL	1	TRUE	0	0.329590176091831	1		389	429	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663678	117663678	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	15	267	0	ENST00000368508.3:c.4554A>C	p.Glu1518Asp	p.E1518D	ENST00000368508	NM_002944.2	1518	gaA/gaC	28/43	1	2	FACETS	0.306	0.224	0.406	0.306	0.224	0.406	SUBCLONAL	1	TRUE	1	0.329590176091831	2		267	297	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564852	41564852	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	203	543	0	ENST00000263253.7:c.4153T>C	p.Cys1385Arg	p.C1385R	ENST00000263253	NM_001429.3	1385	Tgc/Cgc	25/31	0.239431503787207	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.239431503787207	2		543	816	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289143	33289151	+	inframe_deletion	In_Frame_Del	DEL	GGGCCTTGA	GGGCCTTGA	-	novel	NA	P-0027300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	78	562	0	ENST00000374542.5:c.401_409del	p.Leu134_Ala136del	p.L134_A136del	ENST00000374542	NM_001141970.1	134	cTCAAGGCCCac/cac	3/8	1	2	FACETS	0.902	0.792	1	0.902	0.792	1	CLONAL	1	TRUE	1	0.239431503787207	2		562	722	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0027304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	245	487	2	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.303268731591742	5	FACETS	0.958	0.894	1	0.638	0.596	0.683	CLONAL	2	TRUE	2	0.29	5		489	1266	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579470	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	110	645	0	ENST00000269305.4:c.217G>C	p.Val73Leu	p.V73L	ENST00000269305	NM_001126112.2	73	Gtg/Ctg	4/11	0.303268731591742	2	FACETS	1	0.903	1	0.502	0.451	0.557	CLONAL	1	TRUE	0	0.29	2		645	755	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041429	47041429	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	178	645	0	ENST00000377604.3:c.1776del	p.Asn593ThrfsTer111	p.N593Tfs*111	ENST00000377604	NM_001204468.1	591	gaC/ga	16/24	0.303268731591742	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.29	1		645	839	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0027305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	67	574	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.254739008221718	1	FACETS	0.695	0.604	0.795	0.695	0.604	0.795	SUBCLONAL	1	TRUE	0	0.254739008221718	1		576	660	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412898	49412898	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519954	NA	P-0027305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	116	91	0	ENST00000418115.1:c.125A>T	p.Tyr42Phe	p.Y42F	ENST00000418115	NM_001664.2	42	tAt/tTt	2/5	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.254739008221718	2		91	901	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910668	29910668	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	244	174	0	ENST00000376809.5:c.208G>C	p.Glu70Gln	p.E70Q	ENST00000376809	NM_002116.7	70	Gag/Cag	2/8	0.202122611756808	2	FACETS	1	0.991	1	0.7	0.653	0.749	CLONAL	1	TRUE	0	0.254739008221718	2		174	1368	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582990	95582990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	30	151	0	ENST00000393063.1:c.1552G>A	p.Ala518Thr	p.A518T	ENST00000393063	NM_030621.3	518	Gca/Aca	11/28	0.346831045495992	3	FACETS	0.873	0.709	1	0.437	0.354	0.529	CLONAL	1	TRUE	1	0.393464757517448	3		151	209	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304069	91304069	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	47	361	0	ENST00000355112.3:c.1467del	p.Arg489SerfsTer13	p.R489Sfs*13	ENST00000355112	NM_000057.2	489	aGg/ag	7/22	0.355549617399937	2	FACETS	0.655	0.554	0.765	0.327	0.277	0.383	SUBCLONAL	1	TRUE	0	0.393464757517448	2		361	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578266	7578266	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs942158624	NA	P-0027307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	58	386	0	ENST00000269305.4:c.583A>T	p.Ile195Phe	p.I195F	ENST00000269305	NM_001126112.2	195	Atc/Ttc	6/11	1	2	FACETS	0.902	0.779	1	0.902	0.779	1	CLONAL	1	TRUE	1	0.393464757517448	2		386	327	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855832	45855832	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs761085729	NA	P-0027307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	94	521	0	ENST00000391945.4:c.1978G>T	p.Ala660Ser	p.A660S	ENST00000391945	NM_000400.3	660	Gcg/Tcg	21/23	1	2	FACETS	0.888	0.793	0.989	0.888	0.793	0.989	CLONAL	1	TRUE	1	0.393464757517448	2		521	538	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141680	202141680	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	31	190	0	ENST00000358485.4:c.968A>T	p.His323Leu	p.H323L	ENST00000358485	NM_001080125.1	323	cAc/cTc	7/9	0.338792105842731	1	FACETS	0.673	0.55	0.81	0.673	0.55	0.81	SUBCLONAL	1	TRUE	0	0.393464757517448	1		190	188	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790179	40790179	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs762081981	NA	P-0027307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	25	251	0	ENST00000373198.4:c.2552A>T	p.Asp851Val	p.D851V	ENST00000373198	NM_133170.3	851	gAt/gTt	18/32	0.334470774471156	1	FACETS	0.458	0.362	0.566	0.458	0.362	0.566	SUBCLONAL	1	TRUE	0	0.393464757517448	1		251	223	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24135779	24135779	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	45	295	0	ENST00000263121.7:c.266C>G	p.Thr89Ser	p.T89S	ENST00000263121	NM_003073.3	89	aCc/aGc	3/9	1	2	FACETS	0.63	0.531	0.739	0.63	0.531	0.739	SUBCLONAL	1	TRUE	1	0.393464757517448	2		295	363	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	88	305	0	ENST00000263967.3:c.278G>T	p.Arg93Leu	p.R93L	ENST00000263967	NM_006218.2	93	cGg/cTg	2/21	0.393464757517448	7	FACETS	1	0.966	1			1	CLONAL	1	TRUE	NA	0.393464757517448	7		305	716	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148507443	148507443	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	43	310	0	ENST00000320356.2:c.2011C>G	p.Leu671Val	p.L671V	ENST00000320356	NM_004456.4	671	Ctg/Gtg	17/20	0.338792105842731	1	FACETS	0.663	0.558	0.777	0.663	0.558	0.777	SUBCLONAL	1	TRUE	0	0.393464757517448	1		310	265	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968096	68968096	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	74	273	0	ENST00000288368.4:c.1125G>C	p.Trp375Cys	p.W375C	ENST00000288368	NM_024870.2	375	tgG/tgC	10/40	0.297355822354033	2	FACETS	0.765	0.679	0.854	0.765	0.679	0.854	SUBCLONAL	2	TRUE	0	0.393464757517448	2		273	246	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045134	47045134	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	85	208	0	ENST00000377604.3:c.2375G>T	p.Arg792Leu	p.R792L	ENST00000377604	NM_001204468.1	792	cGg/cTg	21/24	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.393464757517448	1		208	236	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0027309-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	11	443	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.838	1	1	0.838	1	CLONAL	1	TRUE	1	0.28	2		443	59	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0027309-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	13	487	2	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.537	0.384	0.722	0.537	0.384	0.722	SUBCLONAL	1	TRUE	1	0.28	2		489	173	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741459	39741459	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027309-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	14	378	2	ENST00000361337.2:c.1346G>T	p.Arg449Leu	p.R449L	ENST00000361337	NM_003286.2	449	cGg/cTg	14/21	1	2	FACETS	0.885	0.646	1	0.885	0.646	1	CLONAL	1	TRUE	1	0.28	2		380	113	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0027310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	63	443	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.222061221687158	3	FACETS	1	0.906	1	0.53	0.458	0.608	CLONAL	1	TRUE	1	0.222061221687158	3		443	595	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0027310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	132	403	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.222061221687158	3	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	1	0.222061221687158	3		403	637	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022913	27022938	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGCCGCCGCCAGCAGCCTGGGCAA	CCCGCCGCCGCCAGCAGCCTGGGCAA	-	rs797045262	NA	P-0027310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	14	69	0	ENST00000324856.7:c.31_56del	p.Ser11AlafsTer91	p.S11Afs*91	ENST00000324856	NM_006015.4	7	CCCGCCGCCGCCAGCAGCCTGGGCAAc/c	1/20	1	2	FACETS	0.733	0.532	0.975	0.733	0.532	0.975	CLONAL	1	TRUE	1	0.222061221687158	2		69	172	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0027310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	69	362	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.222061221687158	3	FACETS	1	0.955	1	0.612	0.533	0.697	CLONAL	1	TRUE	1	0.222061221687158	3		363	564	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945948	17945948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373027121	NA	P-0027310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1321	169	740	1	ENST00000458235.1:c.1991C>T	p.Pro664Leu	p.P664L	ENST00000458235	NM_000215.3	664	cCg/cTg	15/24	0.222061221687158	3	FACETS	1	0.972	1	0.567	0.52	0.618	CLONAL	1	TRUE	1	0.222061221687158	3		741	1490	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118941	70118942	+	inframe_insertion	In_Frame_Ins	INS	-	-	TAC	novel	NA	P-0027310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	329	731	0	ENST00000245479.2:c.514_516dup	p.Tyr172dup	p.Y172dup	ENST00000245479	NM_000346.3	172	-/TAC	2/3	0.222061221687158	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.222061221687158	3		731	1468	SUCCESS
APC	324	MSKCC	GRCh37	5	112175463	112175464	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	101	240	0	ENST00000257430.4:c.4174dup	p.Ser1392PhefsTer3	p.S1392Ffs*3	ENST00000257430	NM_000038.5	1391	agt/agTt	16/16	0.222061221687158	3	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	1	0.222061221687158	3		240	478	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0027311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	101	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.986	0.881	1	0.986	0.881	1	CLONAL	1	TRUE	1	0.271816617727381	2		509	754	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0027311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	126	686	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.271816617727381	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.271816617727381	1		686	761	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121912580	NA	P-0027311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	53	321	0	ENST00000342988.3:c.1157G>T	p.Gly386Val	p.G386V	ENST00000342988	NM_005359.5	386	gGt/gTt	10/12	0.271816617727381	1	FACETS	0.722	0.616	0.837	0.722	0.616	0.837	SUBCLONAL	1	TRUE	0	0.271816617727381	1		321	467	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0027312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	153	321	2	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.881	0.808	0.956	0.881	0.808	0.956	CLONAL	1	TRUE	1	0.531276542377308	2		323	654	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	206	375	0	ENST00000269305.4:c.528C>A	p.Cys176Ter	p.C176*	ENST00000269305	NM_001126112.2	176	tgC/tgA	5/11	0.531276542377308	1	FACETS	0.943	0.88	1	0.943	0.88	1	CLONAL	1	TRUE	0	0.531276542377308	1		375	604	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45800156	45800156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3219484	NA	P-0027313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1519	188	653	0	ENST00000450313.1:c.64G>A	p.Val22Met	p.V22M	ENST00000450313	NM_012222.2	22	Gtg/Atg	2/16	0.755273857592361	6	FACETS	0.732	0.674	0.793			1	SUBCLONAL	1	FALSE	NA	0.755273857592361	6		653	1707	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246027173	246027173	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	55	429	0	ENST00000388985.4:c.829A>G	p.Thr277Ala	p.T277A	ENST00000388985		277	Act/Gct	9/12	1	2	FACETS	0.462	0.394	0.536	0.462	0.394	0.536	SUBCLONAL	1	TRUE	1	0.362069975694031	2		429	658	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343871	118343871	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs782290578	NA	P-0027317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	48	411	0	ENST00000534358.1:c.1997G>C	p.Gly666Ala	p.G666A	ENST00000534358	NM_005933.3	666	gGt/gCt	3/36	1	2	FACETS	0.451	0.381	0.528	0.451	0.381	0.528	SUBCLONAL	1	TRUE	1	0.362069975694031	2		411	588	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954626	17954626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1016346013	NA	P-0027317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	79	868	2	ENST00000458235.1:c.268G>A	p.Val90Met	p.V90M	ENST00000458235	NM_000215.3	90	Gtg/Atg	3/24	1	2	FACETS	0.379	0.332	0.43	0.379	0.332	0.43	SUBCLONAL	1	TRUE	1	0.362069975694031	2		870	1151	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217458	142217458	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	90	365	1	ENST00000350721.4:c.5539G>A	p.Gly1847Arg	p.G1847R	ENST00000350721	NM_001184.3	1847	Gga/Aga	32/47	0.168943561010565	3	FACETS	0.767	0.685	0.852	0.767	0.685	0.852	INDETERMINATE	2	TRUE	1	0.362069975694031	3		366	383	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652246	36652246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1167588781	NA	P-0027317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	129	567	0	ENST00000244741.5:c.368C>T	p.Ser123Leu	p.S123L	ENST00000244741	NM_000389.4	123	tCa/tTa	2/3	1	2	FACETS	0.928	0.842	1	0.928	0.842	1	CLONAL	1	TRUE	1	0.362069975694031	2		567	768	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0027318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	355	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.977	0.943	1	1	0.997	1	CLONAL	2	TRUE	1	0.719403366787086	2		509	505	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514780	44514780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769567889	NA	P-0027318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	31	442	0	ENST00000291552.4:c.467G>A	p.Arg156His	p.R156H	ENST00000291552	NM_006758.2	156	cGt/cAt	6/8	1	2	FACETS	0.184	0.148	0.225	0.184	0.148	0.225	SUBCLONAL	1	TRUE	1	0.719403366787086	2		442	468	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338671	70338671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	240	656	0	ENST00000374080.3:c.67G>T	p.Asp23Tyr	p.D23Y	ENST00000374080		23	Gat/Tat	1/45	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.719403366787086	2		656	602	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092947	29092947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881688	NA	P-0027318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	122	407	1	ENST00000328354.6:c.1037G>A	p.Arg346His	p.R346H	ENST00000328354	NM_007194.3	346	cGt/cAt	10/15	0.300474519844455	1	FACETS	0.421	0.382	0.461	0.421	0.382	0.461	INDETERMINATE	1	TRUE	0	0.719403366787086	1		408	516	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023204	27023232	+	frameshift_variant	Frame_Shift_Del	DEL	AACGGGAACGCGGGCCCTAGGCCCGCCCT	AACGGGAACGCGGGCCCTAGGCCCGCCCT	-	novel	NA	P-0027318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	60	357	0	ENST00000324856.7:c.310_338del	p.Asn104GlufsTer3	p.N104Efs*3	ENST00000324856	NM_006015.4	104	AACGGGAACGCGGGCCCTAGGCCCGCCCTg/g	1/20	0.719403366787086	1	FACETS	0.506	0.442	0.573	0.506	0.442	0.573	SUBCLONAL	1	TRUE	0	0.719403366787086	1		357	211	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993912	72993912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1187392987	NA	P-0027318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	161	457	0	ENST00000268489.5:c.133G>A	p.Glu45Lys	p.E45K	ENST00000268489	NM_006885.3	45	Gag/Aag	2/10	1	2	FACETS	0.904	0.836	0.975	0.904	0.836	0.975	CLONAL	1	TRUE	1	0.719403366787086	2		457	495	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	47	528	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.676	0.572	0.79	0.676	0.572	0.79	SUBCLONAL	1	TRUE	1	0.37	2		529	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0027319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	82	601	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.543	0.478	0.612	0.543	0.478	0.612	SUBCLONAL	1	TRUE	1	0.37	2		603	817	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0027319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	73	434	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.10959834810309	0	FACETS	0.453	0.396	0.514			1	INDETERMINATE	1	TRUE	0	0.37	0		434	549	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593399	48593400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0027319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	13	267	0	ENST00000342988.3:c.1151_1152dup	p.Lys385AlafsTer31	p.K385Afs*31	ENST00000342988	NM_005359.5	384	ggc/gGCgc	10/12	1	2	FACETS	0.317	0.226	0.427	0.317	0.226	0.427	SUBCLONAL	1	TRUE	1	0.37	2		267	222	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879131	151879131	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	48	488	1	ENST00000262189.6:c.5814G>A	p.Met1938Ile	p.M1938I	ENST00000262189	NM_170606.2	1938	atG/atA	36/59	1	2	FACETS	0.569	0.481	0.665	0.569	0.481	0.665	SUBCLONAL	1	TRUE	1	0.37	2		489	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0027322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	297	675	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.417994960847053	2	FACETS	0.91	0.863	0.957	0.91	0.863	0.957	CLONAL	2	TRUE	0	0.476508669862794	2		675	685	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0027322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	78	283	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.417994960847053	2	FACETS	1	0.976	1	0.691	0.616	0.768	CLONAL	1	TRUE	0	0.476508669862794	2		283	237	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	164	367	0	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	0.417994960847053	2	FACETS	0.86	0.8	0.922	0.86	0.8	0.922	CLONAL	2	TRUE	0	0.476508669862794	2		367	400	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903718	114903718	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241370314	NA	P-0027322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	177	793	0	ENST00000543371.1:c.722C>T	p.Pro241Leu	p.P241L	ENST00000543371	NM_001198531.1	241	cCg/cTg	7/14	1	2	FACETS	0.804	0.741	0.87	0.804	0.741	0.87	CLONAL	1	TRUE	1	0.476508669862794	2		793	924	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546832	9546832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1018346655	NA	P-0027322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	102	434	0	ENST00000353224.5:c.1190C>T	p.Thr397Met	p.T397M	ENST00000353224	NM_177990.2	397	aCg/aTg	5/10	0.476508669862794	6	FACETS	0.874	0.78	0.974	0.218	0.195	0.244	CLONAL	1	TRUE	2	0.476508669862794	6		434	957	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158129	47158129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	98	561	0	ENST00000409792.3:c.4570C>T	p.Leu1524Phe	p.L1524F	ENST00000409792	NM_014159.6	1524	Ctt/Ttt	4/21	0.442396278430924	3	FACETS	0.677	0.604	0.755	0.339	0.302	0.378	SUBCLONAL	1	TRUE	1	0.476508669862794	3		561	752	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0027323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	125	429	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.230742488769557	3	FACETS	1	0.918	1	1	0.918	1	CLONAL	2	TRUE	1	0.230742488769557	3		429	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782144	NA	P-0027323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	98	810	0	ENST00000269305.4:c.473G>C	p.Arg158Pro	p.R158P	ENST00000269305	NM_001126112.2	158	cGc/cCc	5/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.230742488769557	2		810	709	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936802	32936802	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	69	390	0	ENST00000380152.3:c.7948G>C	p.Glu2650Gln	p.E2650Q	ENST00000380152		2650	Gaa/Caa	17/27	0.230742488769557	3	FACETS	0.869	0.76	0.984	0.579	0.507	0.656	CLONAL	2	TRUE	0	0.230742488769557	3		390	384	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	146	275	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.425274242397088	2		278	667	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	172	345	8	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.896	0.824	0.97	0.896	0.824	0.97	CLONAL	1	TRUE	1	0.425274242397088	2		353	903	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211899	36211899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1301	294	761	0	ENST00000222270.7:c.1656del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	550	gaC/ga	3/37	1	2	FACETS	0.867	0.813	0.922	0.867	0.813	0.922	CLONAL	1	TRUE	1	0.425274242397088	2		761	1595	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	65	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.7	0.608	0.798	0.7	0.608	0.798	SUBCLONAL	1	TRUE	1	0.425274242397088	2		509	437	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	78	166	1	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.425274242397088	2		167	344	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954198	48954198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123331	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	28	106	0	ENST00000267163.4:c.1399C>T	p.Arg467Ter	p.R467*	ENST00000267163	NM_000321.2	467	Cga/Tga	15/27	1	2	FACETS	0.549	0.44	0.671	0.549	0.44	0.671	SUBCLONAL	1	TRUE	1	0.425274242397088	2		106	240	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256768	19256769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1202792889	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	122	509	0	ENST00000162023.5:c.944dup	p.Val316SerfsTer6	p.V316Sfs*6	ENST00000162023		315	cca/ccCa	13/13	1	2	FACETS	0.681	0.615	0.75	0.681	0.615	0.75	SUBCLONAL	1	TRUE	1	0.425274242397088	2		509	843	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087503	27087503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	252	722	1	ENST00000324856.7:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000324856	NM_006015.4	693	Cga/Tga	5/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.425274242397088	2		723	1105	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	55	246	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.834	0.718	0.959	0.834	0.718	0.959	CLONAL	1	TRUE	1	0.425274242397088	2		246	310	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	86	208	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.83	0.737	0.929	0.83	0.737	0.929	CLONAL	1	TRUE	1	0.425274242397088	2		208	487	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31381362	31381362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113400552	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	183	284	0	ENST00000328111.2:c.1087C>T	p.Arg363Cys	p.R363C	ENST00000328111	NM_006892.3	363	Cgt/Tgt	10/23	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.425274242397088	2		284	793	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950546	38950546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371456052	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	69	278	0	ENST00000357387.3:c.3404C>T	p.Thr1135Met	p.T1135M	ENST00000357387	NM_152756.3	1135	aCg/aTg	31/38	1	2	FACETS	0.872	0.764	0.988	0.872	0.764	0.988	CLONAL	1	TRUE	1	0.425274242397088	2		278	372	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188317	32188317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144492578	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	267	471	0	ENST00000375023.3:c.1024G>A	p.Val342Met	p.V342M	ENST00000375023	NM_004557.3	342	Gtg/Atg	6/30	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.425274242397088	2		471	1105	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	99	176	1	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.425274242397088	2		177	441	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372184	55372184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs915105324	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	196	419	2	ENST00000297316.4:c.874G>A	p.Ala292Thr	p.A292T	ENST00000297316	NM_022454.3	292	Gcc/Acc	2/2	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.425274242397088	2		421	894	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514619	103514619	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759875052	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	62	275	0	ENST00000355739.4:c.1120G>A	p.Ala374Thr	p.A374T	ENST00000355739	NM_000123.3	374	Gca/Aca	8/15	1	2	FACETS	0.532	0.46	0.611	0.532	0.46	0.611	SUBCLONAL	1	TRUE	1	0.425274242397088	2		275	548	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531024	187531025	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	48	291	0	ENST00000441802.2:c.9998_9999del	p.Pro3333ArgfsTer13	p.P3333Rfs*13	ENST00000441802	NM_005245.3	3333	cCT/c	15/27	1	2	FACETS	0.28	0.235	0.329	0.28	0.235	0.329	SUBCLONAL	1	TRUE	1	0.425274242397088	2		291	807	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	131	286	0	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.425274242397088	2		286	604	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	232	502	2	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	0.902	0.84	0.967	0.902	0.84	0.967	CLONAL	1	TRUE	1	0.425274242397088	2		504	1209	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005515	150005515	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	125	207	0	ENST00000253339.5:c.710del	p.Pro237HisfsTer6	p.P237Hfs*6	ENST00000253339		237	cCa/ca	3/7	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.425274242397088	2		207	536	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244133	133244133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759398253	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	60	310	1	ENST00000320574.5:c.2275C>T	p.Arg759Cys	p.R759C	ENST00000320574	NM_006231.2	759	Cgt/Tgt	20/49	1	2	FACETS	0.334	0.287	0.386	0.334	0.287	0.386	SUBCLONAL	1	TRUE	1	0.425274242397088	2		311	844	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576120	88576120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147160868	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	201	498	1	ENST00000360948.2:c.1553G>A	p.Arg518His	p.R518H	ENST00000360948	NM_001012338.2	518	cGt/cAt	13/19	1	2	FACETS	0.926	0.858	0.997	0.926	0.858	0.997	CLONAL	1	TRUE	1	0.425274242397088	2		499	1021	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470498	25470498	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747448117	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	236	468	0	ENST00000264709.3:c.976C>T	p.Arg326Cys	p.R326C	ENST00000264709	NM_175629.2	326	Cgc/Tgc	8/23	1	2	FACETS	0.955	0.89	1	0.955	0.89	1	CLONAL	1	TRUE	1	0.425274242397088	2		468	1162	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664856	138664856	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	112	176	0	ENST00000330315.3:c.709G>T	p.Gly237Cys	p.G237C	ENST00000330315	NM_023067.3	237	Ggt/Tgt	1/1	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.425274242397088	2		176	414	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399976	139399976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200495793	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	263	595	1	ENST00000277541.6:c.4372G>A	p.Ala1458Thr	p.A1458T	ENST00000277541	NM_017617.3	1458	Gcg/Acg	25/34	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.425274242397088	2		596	1213	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324892	31324892	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs765875917	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	89	105	0	ENST00000412585.2:c.44del	p.Ala15GlyfsTer5	p.A15Gfs*5	ENST00000412585	NM_005514.6	15	gCg/gg	1/8	1	2	FACETS	0.758	0.681	0.838	1	0.982	1	SUBCLONAL	2	TRUE	1	0.425274242397088	2		105	276	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	191	444	4	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	1	2	FACETS	0.905	0.837	0.977	0.905	0.837	0.977	CLONAL	1	TRUE	1	0.425274242397088	2		448	992	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467906	99467906	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	85	162	0	ENST00000268035.6:c.2775G>T	p.Gln925His	p.Q925H	ENST00000268035	NM_000875.3	925	caG/caT	13/21	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.425274242397088	2		162	383	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40476813	40476813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	153	337	1	ENST00000264657.5:c.1516G>A	p.Glu506Lys	p.E506K	ENST00000264657	NM_139276.2	506	Gag/Aag	17/24	1	2	FACETS	0.842	0.77	0.916	0.842	0.77	0.916	CLONAL	1	TRUE	1	0.425274242397088	2		338	855	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383227	31383227	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148132847	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	159	284	0	ENST00000328111.2:c.1139G>A	p.Arg380Gln	p.R380Q	ENST00000328111	NM_006892.3	380	cGa/cAa	11/23	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.425274242397088	2		284	735	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564768	139564768	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	244	507	0	ENST00000308874.7:c.561del	p.Asn188ThrfsTer9	p.N188Tfs*9	ENST00000308874		186	gCc/gc	7/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.425274242397088	2		507	1038	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021818	71021818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs869025203	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	50	89	0	ENST00000318789.4:c.1540C>T	p.Arg514Cys	p.R514C	ENST00000318789	NM_032682.5	514	Cgt/Tgt	18/21	1	2	FACETS	0.901	0.771	1	0.901	0.771	1	CLONAL	1	TRUE	1	0.425274242397088	2		89	261	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212371	36212371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753909605	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	237	527	1	ENST00000222270.7:c.2122G>A	p.Ala708Thr	p.A708T	ENST00000222270	NM_014727.1	708	Gcc/Acc	3/37	1	2	FACETS	0.985	0.918	1	0.985	0.918	1	CLONAL	1	TRUE	1	0.425274242397088	2		528	1132	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31466354	31466354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376262500	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	150	416	0	ENST00000344624.3:c.2401C>T	p.Arg801Cys	p.R801C	ENST00000344624		801	Cgc/Tgc	16/33	1	2	FACETS	0.864	0.791	0.942	0.864	0.791	0.942	CLONAL	1	TRUE	1	0.425274242397088	2		416	816	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578316	226578316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs193238922	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	166	354	0	ENST00000366794.5:c.412C>T	p.Arg138Cys	p.R138C	ENST00000366794	NM_001618.3	138	Cgc/Tgc	4/23	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.425274242397088	2		354	682	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726495	46726495	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	92	216	0	ENST00000371975.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000371975	NM_003579.3	192	Cag/Tag	7/18	1	2	FACETS	0.86	0.767	0.959	0.86	0.767	0.959	CLONAL	1	TRUE	1	0.425274242397088	2		216	503	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193121534	193121534	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	25	183	0	ENST00000367435.3:c.932C>G	p.Thr311Ser	p.T311S	ENST00000367435	NM_024529.4	311	aCt/aGt	10/17	1	2	FACETS	0.404	0.319	0.502	0.404	0.319	0.502	SUBCLONAL	1	TRUE	1	0.425274242397088	2		183	291	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980293	201980293	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	88	473	0	ENST00000359651.3:c.33del	p.Phe11LeufsTer32	p.F11Lfs*32	ENST00000359651		10	aTt/at	1/8	1	2	FACETS	0.398	0.352	0.448	0.398	0.352	0.448	SUBCLONAL	1	TRUE	1	0.425274242397088	2		473	1039	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310895	123310895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141796960	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	160	313	1	ENST00000358487.5:c.533G>A	p.Arg178His	p.R178H	ENST00000358487	NM_000141.4	178	cGc/cAc	5/18	1	2	FACETS	0.989	0.908	1	0.989	0.908	1	CLONAL	1	TRUE	1	0.425274242397088	2		314	761	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948832	71948832	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1174	303	679	2	ENST00000298229.2:c.3544G>T	p.Ala1182Ser	p.A1182S	ENST00000298229	NM_001567.3	1182	Gca/Tca	26/28	1	2	FACETS	0.965	0.907	1	0.965	0.907	1	CLONAL	1	TRUE	1	0.425274242397088	2		681	1477	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090406	77090406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	150	269	0	ENST00000356341.3:c.319C>T	p.Leu107Phe	p.L107F	ENST00000356341	NM_002576.4	107	Ctt/Ttt	4/15	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.425274242397088	2		269	665	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409065	4409065	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	56	258	0	ENST00000261254.3:c.760C>T	p.Leu254Phe	p.L254F	ENST00000261254	NM_001759.3	254	Ctc/Ttc	5/5	1	2	FACETS	0.49	0.419	0.566	0.49	0.419	0.566	SUBCLONAL	1	TRUE	1	0.425274242397088	2		258	538	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478927	56478927	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	217	489	1	ENST00000267101.3:c.383G>A	p.Ser128Asn	p.S128N	ENST00000267101	NM_001982.3	128	aGc/aAc	3/28	1	2	FACETS	0.967	0.899	1	0.967	0.899	1	CLONAL	1	TRUE	1	0.425274242397088	2		490	1055	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112910829	112910829	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	173	304	1	ENST00000351677.2:c.842del	p.Asn281ThrfsTer58	p.N281Tfs*58	ENST00000351677	NM_002834.3	280	Aaa/aa	7/16	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.425274242397088	2		305	795	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435774	110435774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1428455100	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	136	276	2	ENST00000375856.3:c.2627G>A	p.Arg876His	p.R876H	ENST00000375856	NM_003749.2	876	cGc/cAc	1/2	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.425274242397088	2		278	567	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437104	110437104	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	33	166	0	ENST00000375856.3:c.1297A>G	p.Met433Val	p.M433V	ENST00000375856	NM_003749.2	433	Atg/Gtg	1/2	1	2	FACETS	0.379	0.309	0.459	0.379	0.309	0.459	SUBCLONAL	1	TRUE	1	0.425274242397088	2		166	409	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986526	36986526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	163	615	2	ENST00000354822.5:c.1163G>A	p.Gly388Asp	p.G388D	ENST00000354822	NM_001079668.2	388	gGc/gAc	3/3	1	2	FACETS	0.567	0.518	0.617	0.567	0.518	0.617	SUBCLONAL	1	TRUE	1	0.425274242397088	2		617	1353	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422191	81422192	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CT	CT	-	rs766597914	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	49	255	0	ENST00000298171.2:c.169_170del	p.Leu57GlufsTer4	p.L57Efs*4	ENST00000298171	NM_000369.2	56	aCT/a	1/10	1	2	FACETS	0.397	0.335	0.464	0.397	0.335	0.464	SUBCLONAL	1	TRUE	1	0.425274242397088	2		255	581	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43767762	43767762	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	152	226	0	ENST00000382044.4:c.1085+1G>A		p.X362_splice	ENST00000382044	NM_001141980.1	362			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.425274242397088	2		226	578	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358460	91358460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770313956	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	149	396	0	ENST00000355112.3:c.4205C>T	p.Pro1402Leu	p.P1402L	ENST00000355112	NM_000057.2	1402	cCg/cTg	22/22	1	2	FACETS	0.859	0.785	0.936	0.859	0.785	0.936	CLONAL	1	TRUE	1	0.425274242397088	2		396	816	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984828	72984828	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	47	314	0	ENST00000268489.5:c.2756del	p.Gly919AlafsTer9	p.G919Afs*9	ENST00000268489	NM_006885.3	919	gGc/gc	3/10	1	2	FACETS	0.28	0.235	0.329	0.28	0.235	0.329	SUBCLONAL	1	TRUE	1	0.425274242397088	2		314	790	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993737	72993737	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	127	286	0	ENST00000268489.5:c.308G>C	p.Arg103Pro	p.R103P	ENST00000268489	NM_006885.3	103	cGc/cCc	2/10	1	2	FACETS	0.953	0.865	1	0.953	0.865	1	CLONAL	1	TRUE	1	0.425274242397088	2		286	627	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89815165	89815165	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764206631	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	207	460	0	ENST00000389301.3:c.3250C>T	p.Arg1084Cys	p.R1084C	ENST00000389301	NM_000135.2	1084	Cgc/Tgc	33/43	1	2	FACETS	0.953	0.885	1	0.953	0.885	1	CLONAL	1	TRUE	1	0.425274242397088	2		460	1021	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120042	70120043	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	33	51	0	ENST00000245479.2:c.1049dup	p.Gln351ThrfsTer227	p.Q351Tfs*227	ENST00000245479	NM_000346.3	348	-/C	3/3	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.425274242397088	2		51	135	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727982	78727982	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749898610	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	105	217	1	ENST00000306801.3:c.827G>A	p.Arg276His	p.R276H	ENST00000306801	NM_020761.2	276	cGc/cAc	6/34	1	2	FACETS	0.988	0.889	1	0.988	0.889	1	CLONAL	1	TRUE	1	0.425274242397088	2		218	500	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227036	2227036	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	294	543	0	ENST00000398665.3:c.4516G>T	p.Gly1506Cys	p.G1506C	ENST00000398665	NM_032482.2	1506	Ggc/Tgc	27/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.425274242397088	2		543	1284	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110631	4110631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs544242665	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	199	390	0	ENST00000262948.5:c.326C>T	p.Pro109Leu	p.P109L	ENST00000262948	NM_030662.3	109	cCg/cTg	3/11	1	2	FACETS	0.929	0.861	1	0.929	0.861	1	CLONAL	1	TRUE	1	0.425274242397088	2		390	1007	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280067	18280067	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	152	231	1	ENST00000222254.8:c.2150G>A	p.Arg717His	p.R717H	ENST00000222254	NM_005027.3	717	cGc/cAc	16/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.425274242397088	2		232	591	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214714	36214714	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	128	343	1	ENST00000222270.7:c.3145del	p.Ala1049ArgfsTer133	p.A1049Rfs*133	ENST00000222270	NM_014727.1	1047	cGg/cg	8/37	1	2	FACETS	0.939	0.853	1	0.939	0.853	1	CLONAL	1	TRUE	1	0.425274242397088	2		344	641	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383649	42383649	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	152	403	0	ENST00000221972.3:c.424A>C	p.Asn142His	p.N142H	ENST00000221972	NM_021601.3	142	Aac/Cac	3/5	1	2	FACETS	0.777	0.71	0.847	0.777	0.71	0.847	SUBCLONAL	1	TRUE	1	0.425274242397088	2		403	920	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791528	42791528	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1306556657	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	255	561	0	ENST00000575354.2:c.509G>A	p.Arg170Gln	p.R170Q	ENST00000575354	NM_015125.3	170	cGg/cAg	4/20	1	2	FACETS	0.959	0.896	1	0.959	0.896	1	CLONAL	1	TRUE	1	0.425274242397088	2		561	1251	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705445	47705445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63751477	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	69	170	0	ENST00000233146.2:c.2245G>A	p.Glu749Lys	p.E749K	ENST00000233146	NM_000251.2	749	Gaa/Aaa	14/16	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.425274242397088	2		170	285	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99179943	99179943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	111	441	0	ENST00000074304.5:c.1886C>T	p.Ala629Val	p.A629V	ENST00000074304	NM_001134224.1	629	gCc/gTc	19/26	1	2	FACETS	0.472	0.423	0.524	0.472	0.423	0.524	SUBCLONAL	1	TRUE	1	0.425274242397088	2		441	1107	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47205398	47205398	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773983305	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	145	361	1	ENST00000409792.3:c.17C>T	p.Pro6Leu	p.P6L	ENST00000409792	NM_014159.6	6	cCg/cTg	1/21	1	2	FACETS	0.759	0.693	0.829	0.759	0.693	0.829	SUBCLONAL	1	TRUE	1	0.425274242397088	2		362	898	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164884	106164884	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1339287432	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	137	260	0	ENST00000380013.4:c.3752C>T	p.Thr1251Met	p.T1251M	ENST00000380013	NM_001127208.2	1251	aCg/aTg	6/11	1	2	FACETS	0.956	0.872	1	0.956	0.872	1	CLONAL	1	TRUE	1	0.425274242397088	2		260	674	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31406979	31406979	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	84	390	0	ENST00000344624.3:c.3928G>T	p.Gly1310Cys	p.G1310C	ENST00000344624		1310	Ggc/Tgc	31/33	1	2	FACETS	0.478	0.421	0.538	0.478	0.421	0.538	SUBCLONAL	1	TRUE	1	0.425274242397088	2		390	827	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674330	86674330	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	40	129	0	ENST00000274376.6:c.2462T>C	p.Ile821Thr	p.I821T	ENST00000274376	NM_002890.2	821	aTa/aCa	18/25	1	2	FACETS	0.844	0.707	0.992	0.844	0.707	0.992	CLONAL	1	TRUE	1	0.425274242397088	2		129	223	SUCCESS
APC	324	MSKCC	GRCh37	5	112177565	112177565	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	62	197	0	ENST00000257430.4:c.6274C>A	p.Leu2092Ile	p.L2092I	ENST00000257430	NM_000038.5	2092	Cta/Ata	16/16	1	2	FACETS	0.873	0.759	0.995	0.873	0.759	0.995	CLONAL	1	TRUE	1	0.425274242397088	2		197	334	SUCCESS
APC	324	MSKCC	GRCh37	5	112177672	112177672	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	26	176	0	ENST00000257430.4:c.6381A>C	p.Gln2127His	p.Q2127H	ENST00000257430	NM_000038.5	2127	caA/caC	16/16	1	2	FACETS	0.371	0.293	0.459	0.371	0.293	0.459	SUBCLONAL	1	TRUE	1	0.425274242397088	2		176	330	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816452	32816452	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765271187	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	238	486	2	ENST00000354258.4:c.1723C>T	p.Arg575Cys	p.R575C	ENST00000354258	NM_000593.5	575	Cgc/Tgc	7/11	1	2	FACETS	0.955	0.891	1	0.955	0.891	1	CLONAL	1	TRUE	1	0.425274242397088	2		488	1172	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124485	94124485	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	22	248	0	ENST00000369303.4:c.98T>G	p.Val33Gly	p.V33G	ENST00000369303	NM_004440.3	33	gTa/gGa	2/17	1	2	FACETS	0.428	0.332	0.538	0.428	0.332	0.538	SUBCLONAL	1	TRUE	1	0.425274242397088	2		248	242	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207401	29207401	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	184	315	1	ENST00000240100.2:c.395G>A	p.Arg132His	p.R132H	ENST00000240100	NM_001394.6	132	cGc/cAc	1/4	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.425274242397088	2		316	685	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908871	101908871	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	112	274	1	ENST00000374994.4:c.1235C>T	p.Ala412Val	p.A412V	ENST00000374994	NM_004612.2	412	gCt/gTt	7/9	1	2	FACETS	0.897	0.809	0.99	0.897	0.809	0.99	CLONAL	1	TRUE	1	0.425274242397088	2		275	587	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128347904	128347904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377752331	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	223	472	2	ENST00000265960.3:c.601G>A	p.Ala201Thr	p.A201T	ENST00000265960	NM_001006617.1	201	Gcc/Acc	5/12	1	2	FACETS	0.971	0.904	1	0.971	0.904	1	CLONAL	1	TRUE	1	0.425274242397088	2		474	1080	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802685	135802685	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	103	168	0	ENST00000298552.3:c.113G>T	p.Gly38Val	p.G38V	ENST00000298552	NM_001162426.1	38	gGc/gTc	4/23	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.425274242397088	2		168	386	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613671	100613673	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-	rs1064794285	NA	P-0027324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	99	126	0	ENST00000308731.7:c.906_908del	p.Gly303del	p.G303del	ENST00000308731	NM_000061.2	302	ggAGGt/ggt	11/19	1	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.425274242397088	1		126	313	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0027326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	60	246	1	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.861	0.746	0.986	0.861	0.746	0.986	CLONAL	1	TRUE	1	0.389124318536106	2		247	358	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032574	12032574	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	98	483	0	ENST00000353533.5:c.1013del	p.Pro338ArgfsTer25	p.P338Rfs*25	ENST00000353533	NM_003010.3	337	tCc/tc	9/11	0.389124318536106	1	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	0	0.389124318536106	1		483	403	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0027336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	141	321	2	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.959	0.879	1	0.959	0.879	1	CLONAL	1	TRUE	1	0.575363793086141	2		323	511	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	95	315	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.876	0.786	0.97	0.876	0.786	0.97	CLONAL	1	TRUE	1	0.575363793086141	2		316	377	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174873	11174873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	162	494	0	ENST00000361445.4:c.7161G>A	p.Met2387Ile	p.M2387I	ENST00000361445	NM_004958.3	2387	atG/atA	52/58	1	2	FACETS	0.922	0.849	0.996	0.922	0.849	0.996	CLONAL	1	TRUE	1	0.575363793086141	2		494	611	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972418	32972418	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	148	589	0	ENST00000380152.3:c.9768G>C	p.Glu3256Asp	p.E3256D	ENST00000380152		3256	gaG/gaC	27/27	1	2	FACETS	0.869	0.797	0.944	0.869	0.797	0.944	CLONAL	1	TRUE	1	0.575363793086141	2		589	592	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196580	106196580	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1372410810	NA	P-0027336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	87	382	0	ENST00000380013.4:c.4913C>G	p.Ser1638Ter	p.S1638*	ENST00000380013	NM_001127208.2	1638	tCa/tGa	11/11	1	2	FACETS	0.879	0.785	0.978	0.879	0.785	0.978	CLONAL	1	TRUE	1	0.575363793086141	2		382	344	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518143	187518143	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	174	450	0	ENST00000441802.2:c.12551G>C	p.Gly4184Ala	p.G4184A	ENST00000441802	NM_005245.3	4184	gGa/gCa	25/27	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.575363793086141	2		450	564	SUCCESS
BTK	695	MSKCC	GRCh37	X	100609625	100609625	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	157	199	0	ENST00000308731.7:c.1624C>A	p.Leu542Met	p.L542M	ENST00000308731	NM_000061.2	542	Ctg/Atg	16/19	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.575363793086141	1		199	310	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200063	123200064	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	152	173	0	ENST00000218089.9:c.2137dup	p.Tyr713LeufsTer15	p.Y713Lfs*15	ENST00000218089	NM_001042749.1	712	aat/aaTt	22/35	1	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.575363793086141	1		173	332	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863433	57863433	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149817893	NA	P-0027337-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	246	785	3	ENST00000228682.2:c.1528C>T	p.Arg510Trp	p.R510W	ENST00000228682	NM_005269.2	510	Cgg/Tgg	11/12	1	2	FACETS	0.974	0.909	1	0.974	0.909	1	CLONAL	1	FALSE	1	0.362975255503776	2		788	1391	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400138	41400138	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs755588862	NA	P-0027337-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	383	726	0	ENST00000373198.4:c.621G>C	p.Gln207His	p.Q207H	ENST00000373198	NM_133170.3	207	caG/caC	5/32	1	2	FACETS	0.995	0.947	1	1	0.997	1	CLONAL	2	FALSE	1	0.362975255503776	2		726	1060	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0027340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	207	678	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.440364961805106	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.440364961805106	1		678	685	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0027341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	40	443	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.606	0.504	0.72	0.606	0.504	0.72	SUBCLONAL	1	FALSE	1	0.3	2		443	440	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013744	12013744	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0027341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	42	339	0	ENST00000353533.5:c.685+1G>C		p.X229_splice	ENST00000353533	NM_003010.3	229			0.129927323707685	0	FACETS	0.383	0.319	0.453			1	INDETERMINATE	1	FALSE	0	0.3	0		339	512	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075157	16075157	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	55	316	0	ENST00000268712.3:c.395del	p.Pro132ArgfsTer6	p.P132Rfs*6	ENST00000268712	NM_006311.3	132	cCg/cg	4/46	0.129927323707685	0	FACETS	0.564	0.483	0.652			1	INDETERMINATE	1	FALSE	0	0.3	0		316	455	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966610	36966610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760031382	NA	P-0027341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	57	523	0	ENST00000358127.4:c.716G>A	p.Arg239His	p.R239H	ENST00000358127	NM_001280556.1	239	cGc/cAc	6/10	1	2	FACETS	0.667	0.572	0.77	0.667	0.572	0.77	SUBCLONAL	1	FALSE	1	0.3	2		523	570	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0027342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	770	541	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.49936951999013	11	FACETS	1	0.993	1			1	CLONAL	9	TRUE	NA	0.49936951999013	11		541	1065	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857082	9857082	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs752489703	NA	P-0027342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	62	241	0	ENST00000330684.3:c.4319C>G	p.Ser1440Cys	p.S1440C	ENST00000330684	NM_001134407.1	1440	tCt/tGt	13/13	0.49936951999013	5	FACETS	0.879	0.761	1	0.293	0.253	0.336	CLONAL	1	TRUE	2	0.49936951999013	5		241	494	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027167	48027167	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587779225	NA	P-0027342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	140	516	0	ENST00000234420.5:c.2045C>G	p.Ser682Cys	p.S682C	ENST00000234420	NM_000179.2	682	tCt/tGt	4/10	0.49936951999013	4	FACETS	1	0.963	1	0.553	0.504	0.604	CLONAL	1	TRUE	2	0.49936951999013	4		516	760	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163315571	163315571	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	51	445	0	ENST00000271452.3:c.911C>T	p.Ser304Leu	p.S304L	ENST00000271452	NM_145697.2	304	tCa/tTa	11/14	0.49936951999013	4	FACETS	0.707	0.602	0.822	0.354	0.301	0.411	SUBCLONAL	1	TRUE	2	0.49936951999013	4		445	433	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239754	53239754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	241	467	0	ENST00000375401.3:c.1588G>A	p.Glu530Lys	p.E530K	ENST00000375401	NM_004187.3	530	Gag/Aag	12/26	0.465339334932988	4	FACETS	0.99	0.929	1	0.99	0.929	1	CLONAL	2	TRUE	2	0.49936951999013	4		467	731	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103245	119103245	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	119	520	0	ENST00000264033.4:c.283C>G	p.Leu95Val	p.L95V	ENST00000264033	NM_005188.3	95	Ctc/Gtc	2/16	1	2	FACETS	0.955	0.867	1	0.955	0.867	1	CLONAL	1	TRUE	1	0.49936951999013	2		520	499	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233271	69233271	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0027342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	51	285	0	ENST00000462284.1:c.1136C>G	p.Ser379Ter	p.S379*	ENST00000462284	NM_002392.5	379	tCa/tGa	11/11	0.49936951999013	7	FACETS	0.73	0.62	0.852			1	SUBCLONAL	1	TRUE	NA	0.49936951999013	7		285	629	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292603	91292603	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	36	171	0	ENST00000355112.3:c.105C>A	p.Phe35Leu	p.F35L	ENST00000355112	NM_000057.2	35	ttC/ttA	3/22	0.49936951999013	4	FACETS	0.759	0.626	0.905	0.19	0.156	0.227	CLONAL	1	TRUE	0	0.49936951999013	4		171	285	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632372	3632372	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199736788	NA	P-0027342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	246	667	0	ENST00000294008.3:c.5476C>T	p.Arg1826Trp	p.R1826W	ENST00000294008	NM_032444.2	1826	Cgg/Tgg	15/15	0.49936951999013	5	FACETS	1	0.987	1	0.411	0.383	0.441	CLONAL	1	TRUE	2	0.49936951999013	5		667	1396	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857522	9857522	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	105	356	0	ENST00000330684.3:c.3879T>G	p.Asp1293Glu	p.D1293E	ENST00000330684	NM_001134407.1	1293	gaT/gaG	13/13	0.49936951999013	5	FACETS	1	0.924	1	0.346	0.31	0.384	CLONAL	1	TRUE	2	0.49936951999013	5		356	709	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576916	7576957	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAAAG	GTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAAAG	-	novel	NA	P-0027342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	388	587	0	ENST00000269305.4:c.920-31_930del		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	0.49936951999013	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.49936951999013	3		587	616	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935647	15935647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	93	333	0	ENST00000268712.3:c.7286C>T	p.Ser2429Leu	p.S2429L	ENST00000268712	NM_006311.3	2429	tCa/tTa	46/46	0.49936951999013	3	FACETS	1	0.944	1	0.362	0.323	0.402	CLONAL	1	TRUE	0	0.49936951999013	3		333	429	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082739	16082739	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	51	133	1	ENST00000281043.3:c.553G>T	p.Glu185Ter	p.E185*	ENST00000281043	NM_005378.4	185	Gag/Tag	2/3	0.49936951999013	2	FACETS	0.869	0.746	1	0.435	0.373	0.501	CLONAL	1	TRUE	0	0.49936951999013	2		134	235	SUCCESS
APC	324	MSKCC	GRCh37	5	112174529	112174529	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	111	357	1	ENST00000257430.4:c.3238G>A	p.Glu1080Lys	p.E1080K	ENST00000257430	NM_000038.5	1080	Gag/Aag	16/16	0.49936951999013	4	FACETS	1	0.936	1	0.526	0.473	0.581	CLONAL	1	TRUE	2	0.49936951999013	4		358	634	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687254	117687254	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	64	269	0	ENST00000368508.3:c.2797C>T	p.Leu933Phe	p.L933F	ENST00000368508	NM_002944.2	933	Ctt/Ttt	18/43	0.49936951999013	5	FACETS	0.832	0.721	0.952	0.277	0.24	0.318	CLONAL	1	TRUE	2	0.49936951999013	5		269	539	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001217	150001217	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	114	530	0	ENST00000253339.5:c.2387G>C	p.Arg796Thr	p.R796T	ENST00000253339		796	aGa/aCa	4/7	0.49936951999013	5	FACETS	0.99	0.891	1	0.33	0.297	0.365	CLONAL	1	TRUE	2	0.49936951999013	5		530	807	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750924	128750924	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2371	144	491	0	ENST00000377970.2:c.461C>G	p.Ser154Trp	p.S154W	ENST00000377970	NM_002467.4	154	tCg/tGg	2/3	0.49936951999013	18	FACETS	1	0.968	1			1	CLONAL	1	TRUE	NA	0.49936951999013	18		491	2515	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040991	47040991	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	152	657	0	ENST00000377604.3:c.1521C>G	p.Ile507Met	p.I507M	ENST00000377604	NM_001204468.1	507	atC/atG	14/24	0.465339334932988	4	FACETS	0.84	0.767	0.917	0.42	0.383	0.459	CLONAL	1	TRUE	2	0.49936951999013	4		657	1086	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0027343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	166	344	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.516797376880514	1	FACETS	0.836	0.772	0.902	0.836	0.772	0.902	CLONAL	1	TRUE	0	0.516797376880514	1		345	570	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0027343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	203	439	0	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	1				0.87	1				CLONAL	1	TRUE	1	0.516797376880514	2		439	839	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0027343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	244	694	1	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.516797376880514	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.516797376880514	1		695	676	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971029	21971029	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519852	NA	P-0027343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	206	208	0	ENST00000304494.5:c.329G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tGg/tAg	2/3	1	2	FACETS	0.93	0.864	0.998	0.93	0.864	0.998	CLONAL	1	TRUE	1	0.516797376880514	2		208	857	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021655	31021655	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs143952412	NA	P-0027343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	249	425	0	ENST00000375687.4:c.1654A>G	p.Ile552Val	p.I552V	ENST00000375687	NM_015338.5	552	Att/Gtt	12/13	1	2	FACETS	0.995	0.932	1	0.995	0.932	1	CLONAL	1	TRUE	1	0.516797376880514	2		425	968	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430574	78430574	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	101	358	0	ENST00000370768.2:c.716G>A	p.Gly239Glu	p.G239E	ENST00000370768	NM_003902.3	239	gGa/gAa	9/20	0.240356190112448	1	FACETS	0.423	0.378	0.471	0.423	0.378	0.471	INDETERMINATE	1	TRUE	0	0.516797376880514	1		358	685	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624290	89624290	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876660420	NA	P-0027343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	208	397	0	ENST00000371953.3:c.64G>C	p.Asp22His	p.D22H	ENST00000371953	NM_000314.4	22	Gac/Cac	1/9	0.240356190112448	1	FACETS	0.825	0.768	0.883	0.825	0.768	0.883	INDETERMINATE	1	TRUE	0	0.516797376880514	1		397	724	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1036417	1036417	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	220	488	0	ENST00000358495.3:c.361C>T	p.His121Tyr	p.H121Y	ENST00000358495	NM_134424.2	121	Cat/Tat	6/12	0.516797376880514	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.516797376880514	1		488	615	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041075	42041075	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1309775039	NA	P-0027343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	301	450	1	ENST00000219905.7:c.5453G>A	p.Arg1818Gln	p.R1818Q	ENST00000219905	NM_001164273.1	1818	cGa/cAa	16/24	0.516797376880514	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.516797376880514	1		451	763	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098547	11098547	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	281	576	0	ENST00000358026.2:c.1065C>G	p.Ile355Met	p.I355M	ENST00000358026	NM_001128849.1	355	atC/atG	6/36	1	2	FACETS	0.934	0.877	0.993	0.934	0.877	0.993	CLONAL	1	TRUE	1	0.516797376880514	2		576	1164	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128420028	128420028	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	242	581	0	ENST00000265960.3:c.400C>G	p.Pro134Ala	p.P134A	ENST00000265960	NM_001006617.1	134	Cca/Gca	4/12	1	2	FACETS	0.879	0.821	0.938	0.879	0.821	0.938	CLONAL	1	TRUE	1	0.516797376880514	2		581	1066	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0027346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	244	500	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.27342929890859	3	FACETS	0.96	0.903	1	0.96	0.903	1	CLONAL	3	TRUE	0	0.305206855234064	3		500	640	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435116	49435117	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	GCGGCTTCAGGAACCCGTCC	novel	NA	P-0027346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	148	457	0	ENST00000301067.7:c.6417_6436dup	p.Pro2146ArgfsTer5	p.P2146Rfs*5	ENST00000301067	NM_003482.3	2146	ccg/cGGACGGGTTCCTGAAGCCGCcg	31/54	0.305206855234064	3	FACETS	1	0.982	1	0.642	0.586	0.7	CLONAL	1	TRUE	1	0.305206855234064	3		457	871	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916802	48916803	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	57	405	0	ENST00000267163.4:c.333dup	p.Glu112Ter	p.E112*	ENST00000267163	NM_000321.2	111	gat/gaTt	3/27	1	2	FACETS	0.83	0.721	0.946	1	0.974	1	CLONAL	2	TRUE	1	0.305206855234064	2		405	225	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222991	1222991	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750366043	NA	P-0027346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	158	506	2	ENST00000326873.7:c.928C>T	p.Arg310Trp	p.R310W	ENST00000326873	NM_000455.4	310	Cgg/Tgg	8/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.305206855234064	2		508	752	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982355	25982355	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	31	183	0	ENST00000435504.4:c.935G>C	p.Arg312Pro	p.R312P	ENST00000435504		312	cGa/cCa	9/13	0.305206855234064	3	FACETS	1	0.814	1	0.5	0.407	0.605	CLONAL	1	TRUE	1	0.305206855234064	3		183	234	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098921	178098921	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs769685782	NA	P-0027346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	18	284	2	ENST00000397062.3:c.124C>T	p.Arg42Ter	p.R42*	ENST00000397062	NM_006164.4	42	Cga/Tga	2/5	0.296265218591774	2	FACETS	0.427	0.322	0.552	0.214	0.161	0.276	SUBCLONAL	1	TRUE	0	0.305206855234064	2		286	276	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840603	36840603	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	156	561	1	ENST00000358127.4:c.1130G>T	p.Arg377Leu	p.R377L	ENST00000358127	NM_001280556.1	377	cGa/cTa	10/10	0.305206855234064	3	FACETS	1	0.975	1	0.584	0.534	0.636	CLONAL	1	TRUE	1	0.305206855234064	3		562	1009	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0027347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	62	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.245928289776777	4	FACETS	1	0.947	1	0.768	0.674	0.867	CLONAL	2	TRUE	1	0.35810477905585	4		509	204	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156715	20156715	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	73	456	1	ENST00000379607.5:c.42G>T	p.Arg14Ser	p.R14S	ENST00000379607	NM_001412.3	14	agG/agT	2/7	0.32891579098795	0	FACETS	0.884	0.797	0.971			1	CLONAL	2	TRUE	0	0.35810477905585	0		457	148	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117757	108117757	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	25	402	0	ENST00000278616.4:c.968T>G	p.Ile323Arg	p.I323R	ENST00000278616	NM_000051.3	323	aTa/aGa	8/63	0.35810477905585	1	FACETS	0.997	0.799	1	0.997	0.799	1	CLONAL	1	TRUE	0	0.35810477905585	1		402	115	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109962	115109962	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	19	959	0	ENST00000257566.3:c.1916G>T	p.Arg639Leu	p.R639L	ENST00000257566	NM_016569.3	639	cGc/cTc	8/8	0.35810477905585	1	FACETS	0.636	0.487	0.807	0.636	0.487	0.807	SUBCLONAL	1	TRUE	0	0.35810477905585	1		959	137	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870504	40870504	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	99	542	0	ENST00000428826.2:c.899G>C	p.Arg300Pro	p.R300P	ENST00000428826		300	cGg/cCg	9/21	0.35810477905585	7	FACETS	0.885	0.801	0.972	0.885	0.801	0.972	CLONAL	4	TRUE	3	0.35810477905585	7		542	296	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740709	58740709	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	50	626	1	ENST00000305921.3:c.1614A>T	p.Leu538Phe	p.L538F	ENST00000305921	NM_003620.3	538	ttA/ttT	6/6	0.347186917963498	4	FACETS	0.886	0.761	1	0.886	0.761	1	CLONAL	2	TRUE	2	0.35810477905585	4		627	214	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526078	189526079	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0027347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	44	548	1	ENST00000264731.3:c.342_343delinsTT	p.Gly115Trp	p.G115W	ENST00000264731	NM_003722.4	114	ctGGgg/ctTTgg	4/14	0.245928289776777	4	FACETS	0.795	0.674	0.925	0.53	0.449	0.617	CLONAL	2	TRUE	1	0.35810477905585	4		549	210	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636677	176636677	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	18	432	0	ENST00000439151.2:c.1277G>T	p.Gly426Val	p.G426V	ENST00000439151	NM_022455.4	426	gGa/gTa	5/23	0.35810477905585	1	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	0	0.35810477905585	1		432	69	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36653554	36653554	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	79	550	0	ENST00000244741.5:c.472A>G	p.Ile158Val	p.I158V	ENST00000244741	NM_000389.4	158	Atc/Gtc	3/3	0.35810477905585	7	FACETS	0.978	0.87	1	0.734	0.652	0.818	CLONAL	3	TRUE	3	0.35810477905585	7		550	285	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951835	2951836	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0027347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	51	759	1	ENST00000396946.4:c.3114_3115delinsAA	p.Pro1039Thr	p.P1039T	ENST00000396946	NM_032415.4	1038	gcCCct/gcAAct	23/25	NA	2	FACETS	0.766	0.661	0.877			1	INDETERMINATE	2	TRUE	NA	0.35810477905585	2		760	186	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937040	48937046	+	frameshift_variant	Frame_Shift_Del	DEL	GATACAA	GATACAA	-	novel	NA	P-0027350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	186	478	0	ENST00000267163.4:c.810_816del	p.Asp270GlufsTer14	p.D270Efs*14	ENST00000267163	NM_000321.2	270	GATACAAga/ga	8/27	0.757093460495946	1	FACETS	0.872	0.82	0.924	0.872	0.82	0.924	CLONAL	1	TRUE	0	0.757093460495946	1		478	350	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396664	396664	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	274	555	0	ENST00000262320.3:c.362G>T	p.Cys121Phe	p.C121F	ENST00000262320	NM_003502.3	121	tGc/tTc	2/11	0.757093460495946	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.757093460495946	1		555	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577142	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TA	novel	NA	P-0027350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	301	644	2	ENST00000269305.4:c.796_797delinsTA	p.Gly266Ter	p.G266*	ENST00000269305	NM_001126112.2	266	GGa/TAa	8/11	0.757093460495946	1	FACETS	0.954	0.911	0.996	0.954	0.911	0.996	CLONAL	1	TRUE	0	0.757093460495946	1		646	518	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0027351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	385	487	2	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.540533443043169	4	FACETS	0.982	0.934	1	0.982	0.934	1	CLONAL	2	TRUE	2	0.540533443043169	4		489	1117	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0027351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	118	370	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	0.540533443043169	3	FACETS	0.945	0.855	1	0.472	0.427	0.52	CLONAL	1	TRUE	1	0.540533443043169	3		370	587	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087528	27087528	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	448	733	0	ENST00000324856.7:c.2102G>T	p.Gly701Val	p.G701V	ENST00000324856	NM_006015.4	701	gGc/gTc	5/20	0.540533443043169	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.540533443043169	4		733	1262	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039344	47039344	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	477	881	0	ENST00000377604.3:c.967T>G	p.Tyr323Asp	p.Y323D	ENST00000377604	NM_001204468.1	323	Tac/Gac	10/24	0.522041534828587	4	FACETS	0.965	0.922	1	0.965	0.922	1	CLONAL	2	TRUE	2	0.540533443043169	4		881	1409	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	189	528	1	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	0.53459825376816	2		529	679	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984424	201984424	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	256	719	0	ENST00000359651.3:c.1090del	p.Glu364LysfsTer83	p.E364Kfs*83	ENST00000359651		363	gaG/ga	8/8	1	2	FACETS	0.759	0.71	0.811	0.759	0.71	0.811	SUBCLONAL	1	TRUE	1	0.53459825376816	2		719	1261	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717640	89717646	+	frameshift_variant	Frame_Shift_Del	DEL	TGAAGAT	TGAAGAT	-	novel	NA	P-0027352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	39	497	0	ENST00000371953.3:c.665_671del	p.Val222AspfsTer32	p.V222Dfs*32	ENST00000371953	NM_000314.4	222	gTGAAGATa/ga	7/9	0.53459825376816	1	FACETS	0.301	0.25	0.358	0.301	0.25	0.358	SUBCLONAL	1	TRUE	0	0.53459825376816	1		497	355	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225558	2225558	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1182	90	936	1	ENST00000326181.6:c.1561C>A	p.His521Asn	p.H521N	ENST00000326181	NM_032271.2	521	Cac/Aac	17/21	1	2	FACETS	0.265	0.234	0.298	0.265	0.234	0.298	SUBCLONAL	1	TRUE	1	0.53459825376816	2		937	1272	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3799627	3799627	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs200782888	NA	P-0027352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	204	657	1	ENST00000262367.5:c.3836+1G>A		p.X1279_splice	ENST00000262367	NM_004380.2	1279			1	2	FACETS	0.818	0.759	0.879	0.818	0.759	0.879	CLONAL	1	TRUE	1	0.53459825376816	2		658	933	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0027352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	297	817	1	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	0.446173683618183	1	FACETS	0.753	0.709	0.798	0.753	0.709	0.798	SUBCLONAL	1	TRUE	0	0.53459825376816	1		818	1081	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368223	45368223	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	26	460	0	ENST00000262160.6:c.1379C>A	p.Ser460Ter	p.S460*	ENST00000262160	NM_005901.5	460	tCa/tAa	11/11	0.53459825376816	1	FACETS	0.167	0.132	0.207	0.167	0.132	0.207	SUBCLONAL	1	TRUE	0	0.53459825376816	1		460	427	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395753	45395753	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	124	464	0	ENST00000262160.6:c.381del	p.Tyr128IlefsTer35	p.Y128Ifs*35	ENST00000262160	NM_005901.5	127	atA/at	4/11	0.53459825376816	1	FACETS	0.681	0.62	0.745	0.681	0.62	0.745	SUBCLONAL	1	TRUE	0	0.53459825376816	1		464	499	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744489	41744489	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767925068	NA	P-0027352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1241	117	990	1	ENST00000301178.4:c.1109C>T	p.Ala370Val	p.A370V	ENST00000301178	NM_021913.4	370	gCg/gTg	8/20	1	2	FACETS	0.322	0.289	0.357	0.322	0.289	0.357	SUBCLONAL	1	TRUE	1	0.53459825376816	2		991	1358	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259207	36259207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	260	916	0	ENST00000300305.3:c.284C>T	p.Pro95Leu	p.P95L	ENST00000300305		95	cCc/cTc	3/8	1	2	FACETS	0.817	0.764	0.871	0.817	0.764	0.871	CLONAL	1	TRUE	1	0.53459825376816	2		916	1191	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278082	41278082	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	156	418	0	ENST00000349496.5:c.1958C>G	p.Thr653Arg	p.T653R	ENST00000349496	NM_001904.3	653	aCa/aGa	13/15	1	2	FACETS	0.949	0.873	1	0.949	0.873	1	CLONAL	1	TRUE	1	0.53459825376816	2		418	615	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0027352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	177	539	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.704	0.649	0.762	0.704	0.649	0.762	SUBCLONAL	1	TRUE	1	0.53459825376816	2		539	940	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591102	67591102	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	33	421	1	ENST00000274335.5:c.1695C>A	p.Ser565Arg	p.S565R	ENST00000274335		565	agC/agA	12/15	0.53459825376816	1	FACETS	0.226	0.183	0.273	0.226	0.183	0.273	SUBCLONAL	1	TRUE	0	0.53459825376816	1		422	401	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591128	67591128	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	29	434	0	ENST00000274335.5:c.1721G>T	p.Arg574Ile	p.R574I	ENST00000274335		574	aGa/aTa	12/15	0.53459825376816	1	FACETS	0.205	0.164	0.252	0.205	0.164	0.252	SUBCLONAL	1	TRUE	0	0.53459825376816	1		434	387	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741440	145741440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368601097	NA	P-0027352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	296	1036	2	ENST00000428558.2:c.1063C>T	p.Arg355Trp	p.R355W	ENST00000428558	NM_004260.3	355	Cgg/Tgg	5/22	1	2	FACETS	0.76	0.714	0.808	0.76	0.714	0.808	SUBCLONAL	1	TRUE	1	0.53459825376816	2		1038	1457	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966741	44966741	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	66	364	0	ENST00000377967.4:c.3965G>A	p.Arg1322Gln	p.R1322Q	ENST00000377967	NM_021140.2	1322	cGg/cAg	27/29	1	1	FACETS	0.391	0.34	0.446	0.391	0.34	0.446	SUBCLONAL	1	TRUE	0	0.53459825376816	1		364	463	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0027353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	192	487	2	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.38	2		489	806	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0027353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	94	886	4	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.299456815224096	1	FACETS	0.474	0.421	0.531	0.474	0.421	0.531	SUBCLONAL	1	TRUE	0	0.38	1		890	845	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210075	55210075	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	206	623	0	ENST00000275493.2:c.185T>G	p.Leu62Arg	p.L62R	ENST00000275493	NM_005228.3	62	cTt/cGt	2/28	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.38	2		623	911	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705596	47705596	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	97	419	0	ENST00000233146.2:c.2396A>G	p.Asn799Ser	p.N799S	ENST00000233146	NM_000251.2	799	aAt/aGt	14/16	1	2	FACETS	0.796	0.711	0.887	0.796	0.711	0.887	SUBCLONAL	1	TRUE	1	0.38	2		419	641	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0027357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	214	541	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.338568758137903	3	FACETS	0.992	0.926	1	0.992	0.926	1	CLONAL	2	TRUE	1	0.375294789328078	3		541	683	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499354	89499354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	55	358	1	ENST00000336596.2:c.2524C>T	p.Arg842Ter	p.R842*	ENST00000336596	NM_005233.5	842	Cga/Tga	15/17	0.338568758137903	3	FACETS	0.471	0.402	0.547	0.236	0.201	0.274	SUBCLONAL	1	TRUE	1	0.375294789328078	3		359	739	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100696	67100696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	248	564	0	ENST00000412916.2:c.394G>A	p.Ala132Thr	p.A132T	ENST00000412916		132	Gcc/Acc	4/6	0.314813158744284	2	FACETS	0.779	0.73	0.829	0.779	0.73	0.829	SUBCLONAL	2	TRUE	0	0.375294789328078	2		564	848	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842334	68842334	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	227	464	0	ENST00000261769.5:c.397del	p.Ser133LeufsTer82	p.S133Lfs*82	ENST00000261769	NM_004360.3	132	gTt/gt	4/16	0.314813158744284	2	FACETS	0.922	0.864	0.981	0.922	0.864	0.981	CLONAL	2	TRUE	0	0.375294789328078	2		464	656	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883105	37883105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	160	807	0	ENST00000269571.5:c.3008C>T	p.Thr1003Ile	p.T1003I	ENST00000269571		1003	aCc/aTc	25/27	1	2	FACETS	0.756	0.692	0.823	0.756	0.692	0.823	SUBCLONAL	1	TRUE	1	0.375294789328078	2		807	1128	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395496	116395496	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	62	501	1	ENST00000397752.3:c.1789G>A	p.Asp597Asn	p.D597N	ENST00000397752	NM_000245.2	597	Gat/Aat	6/21	0.299097927431104	4	FACETS	0.507	0.437	0.584	0.169	0.145	0.195	SUBCLONAL	1	TRUE	1	0.375294789328078	4		502	896	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44970656	44970656	+	frameshift_variant,stop_lost	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	190	516	0	ENST00000377967.4:c.4206del	p.Ter1402CysfsTer136	p.*1402Cfs*136	ENST00000377967	NM_021140.2	1402	tgA/tg	29/29	0.338568758137903	3	FACETS	0.773	0.716	0.832	0.773	0.716	0.832	SUBCLONAL	2	TRUE	1	0.375294789328078	3		516	778	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453136	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	rs397516897	NA	P-0027358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	124	551	0	ENST00000288602.6:c.1799_1801del	p.Val600_Lys601delinsGlu	p.V600_K601delinsE	ENST00000288602	NM_004333.4	600	gTGAaa/gaa	15/18	0.299972438532331	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		551	324	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	153	321	2	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.958	0.879	1	0.958	0.879	1	CLONAL	1	TRUE	1	0.5	2		323	639	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	305	345	8	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.926	0.88	0.972	1	0.996	1	CLONAL	2	TRUE	1	0.5	2		353	659	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	123	403	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.996	0.906	1	0.996	0.906	1	CLONAL	1	TRUE	1	0.5	2		403	494	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584514	48584514	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	142	343	0	ENST00000342988.3:c.692del	p.Gly231AlafsTer10	p.G231Afs*10	ENST00000342988	NM_005359.5	229	ctG/ct	6/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.5	2		343	501	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070349	37070349	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs63750855	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	115	449	2	ENST00000231790.2:c.1489del	p.Arg497GlyfsTer11	p.R497Gfs*11	ENST00000231790	NM_000249.3	495	aCc/ac	13/19	1	2	FACETS	0.796	0.719	0.876	0.796	0.719	0.876	SUBCLONAL	1	TRUE	1	0.5	2		451	578	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	91	256	3	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	1	2	FACETS	0.899	0.803	0.999	0.899	0.803	0.999	CLONAL	1	TRUE	1	0.5	2		259	405	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	186	607	2	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.896	0.829	0.966	0.896	0.829	0.966	CLONAL	1	TRUE	1	0.5	2		609	830	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	117	333	4	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.994	0.901	1	0.994	0.901	1	CLONAL	1	TRUE	1	0.5	2		337	471	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	68	293	1	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.741	0.648	0.84	0.741	0.648	0.84	SUBCLONAL	1	TRUE	1	0.5	2		294	367	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857524	9857524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778230379	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	89	392	1	ENST00000330684.3:c.3877G>A	p.Asp1293Asn	p.D1293N	ENST00000330684	NM_001134407.1	1293	Gat/Aat	13/13	1	2	FACETS	0.832	0.741	0.927	0.832	0.741	0.927	CLONAL	1	TRUE	1	0.5	2		393	428	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814539	43814539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	131	396	0	ENST00000372470.3:c.1334G>A	p.Arg445Gln	p.R445Q	ENST00000372470	NM_005373.2	445	cGa/cAa	9/12	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.5	2		396	502	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256341	46256341	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	157	467	0	ENST00000371998.3:c.574del	p.Ser192AlafsTer9	p.S192Afs*9	ENST00000371998		190	cAa/ca	7/23	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.5	2		467	605	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6031648	6031648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs116314131	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	176	465	1	ENST00000265849.7:c.944G>A	p.Arg315Gln	p.R315Q	ENST00000265849	NM_000535.5	315	cGa/cAa	9/15	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.5	2		466	697	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547004	9547004	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	53	235	0	ENST00000353224.5:c.1018C>T	p.Leu340Phe	p.L340F	ENST00000353224	NM_177990.2	340	Ctc/Ttc	5/10	1	2	FACETS	0.774	0.665	0.891	0.774	0.665	0.891	SUBCLONAL	1	TRUE	1	0.5	2		235	274	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043349	6043349	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781716	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	60	201	0	ENST00000265849.7:c.325del	p.Glu109LysfsTer3	p.E109Kfs*3	ENST00000265849	NM_000535.5	109	Gaa/aa	4/15	1	2	FACETS	0.822	0.714	0.937	0.822	0.714	0.937	CLONAL	1	TRUE	1	0.5	2		201	292	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981721	101981721	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555075353	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	70	277	1	ENST00000282441.5:c.147del	p.Ala50ProfsTer24	p.A50Pfs*24	ENST00000282441	NM_001130145.2	48	Ccc/cc	1/9	1	2	FACETS	0.838	0.736	0.947	0.838	0.736	0.947	CLONAL	1	TRUE	1	0.5	2		278	334	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274304	5274304	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	198	614	0	ENST00000357368.4:c.143del	p.Gly48ValfsTer17	p.G48Vfs*17	ENST00000357368	NM_002850.3	48	gGt/gt	3/38	1	2	FACETS	0.931	0.863	1	0.931	0.863	1	CLONAL	1	TRUE	1	0.5	2		614	851	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933594	39933594	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	88	486	0	ENST00000378444.4:c.1005del	p.Ser336ArgfsTer42	p.S336Rfs*42	ENST00000378444	NM_001123385.1	335	ccC/cc	4/15	1	2	FACETS	0.626	0.556	0.701	0.626	0.556	0.701	SUBCLONAL	1	TRUE	1	0.5	2		486	562	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251949	153251949	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	177	490	0	ENST00000281708.4:c.1057del	p.Ser353ValfsTer24	p.S353Vfs*24	ENST00000281708	NM_033632.3	353	Agt/gt	7/12	1	2	FACETS	0.989	0.914	1	0.989	0.914	1	CLONAL	1	TRUE	1	0.5	2		490	716	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151310	202151310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1328890647	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	147	391	0	ENST00000358485.4:c.1610C>T	p.Ser537Phe	p.S537F	ENST00000358485	NM_001080125.1	537	tCt/tTt	9/9	1	2	FACETS	0.947	0.868	1	0.947	0.868	1	CLONAL	1	TRUE	1	0.5	2		391	621	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738351	133738351	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	175	497	1	ENST00000318560.5:c.751G>T	p.Gly251Cys	p.G251C	ENST00000318560	NM_005157.4	251	Ggc/Tgc	4/11	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.5	2		498	694	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453399	40453399	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs759027671	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	231	777	12	ENST00000345506.4:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000345506	NM_003152.3	366	Ccc/cc	10/20	1	2	FACETS	0.909	0.847	0.972	0.909	0.847	0.972	CLONAL	1	TRUE	1	0.5	2		789	1017	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429367	78429367	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	169	403	1	ENST00000370768.2:c.1075C>T	p.Arg359Ter	p.R359*	ENST00000370768	NM_003902.3	359	Cga/Tga	13/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.5	2		404	638	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317707	163317707	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1241407588	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	102	392	0	ENST00000271452.3:c.1103A>G	p.Gln368Arg	p.Q368R	ENST00000271452	NM_145697.2	368	cAa/cGa	12/14	1	2	FACETS	0.874	0.785	0.966	0.874	0.785	0.966	CLONAL	1	TRUE	1	0.5	2		392	467	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981596	101981596	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	81	269	0	ENST00000282441.5:c.17A>C	p.Gln6Pro	p.Q6P	ENST00000282441	NM_001130145.2	6	cAg/cCg	1/9	1	2	FACETS	0.757	0.67	0.849	0.757	0.67	0.849	SUBCLONAL	1	TRUE	1	0.5	2		269	428	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376673	118376673	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	151	477	0	ENST00000534358.1:c.10066A>G	p.Thr3356Ala	p.T3356A	ENST00000534358	NM_005933.3	3356	Aca/Gca	27/36	1	2	FACETS	0.948	0.87	1	0.948	0.87	1	CLONAL	1	TRUE	1	0.5	2		477	637	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884931	111884931	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	39	429	0	ENST00000341259.2:c.929T>C	p.Leu310Pro	p.L310P	ENST00000341259	NM_005475.2	310	cTg/cCg	5/8	1	2	FACETS	0.303	0.251	0.361	0.303	0.251	0.361	SUBCLONAL	1	TRUE	1	0.5	2		429	515	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912742	32912743	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	113	349	0	ENST00000380152.3:c.4253_4254del	p.Ile1418LysfsTer4	p.I1418Kfs*4	ENST00000380152		1417	aAT/a	11/27	1	2	FACETS	0.866	0.783	0.953	0.866	0.783	0.953	CLONAL	1	TRUE	1	0.5	2		349	522	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060738	38060738	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	253	829	2	ENST00000250448.2:c.1251C>A	p.Phe417Leu	p.F417L	ENST00000250448	NM_004496.3	417	ttC/ttA	2/2	1	2	FACETS	0.943	0.883	1	0.943	0.883	1	CLONAL	1	TRUE	1	0.5	2		831	1073	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645054	67645054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	174	548	0	ENST00000264010.4:c.319C>T	p.Pro107Ser	p.P107S	ENST00000264010	NM_006565.3	107	Ccc/Tcc	3/12	1	2	FACETS	0.857	0.79	0.927	0.857	0.79	0.927	CLONAL	1	TRUE	1	0.5	2		548	812	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81892753	81892753	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	130	362	0	ENST00000359376.3:c.464A>G	p.Gln155Arg	p.Q155R	ENST00000359376	NM_002661.3	155	cAa/cGa	5/33	1	2	FACETS	0.914	0.832	0.999	0.914	0.832	0.999	CLONAL	1	TRUE	1	0.5	2		362	569	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352037	89352037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138353708	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	199	603	1	ENST00000301030.4:c.913G>A	p.Ala305Thr	p.A305T	ENST00000301030	NM_001256183.1	305	Gca/Aca	9/13	1	2	FACETS	0.952	0.883	1	0.952	0.883	1	CLONAL	1	TRUE	1	0.5	2		604	836	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866098	37866098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs971655376	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	96	625	0	ENST00000269571.5:c.607C>T	p.Arg203Cys	p.R203C	ENST00000269571		203	Cgc/Tgc	5/27	1	2	FACETS	0.463	0.412	0.518	0.463	0.412	0.518	SUBCLONAL	1	TRUE	1	0.5	2		625	829	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492764	56492764	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	206	644	0	ENST00000407977.2:c.175G>T	p.Gly59Ter	p.G59*	ENST00000407977		59	Gga/Tga	2/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.5	2		644	770	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254505	10254505	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	163	504	0	ENST00000340748.4:c.3005C>A	p.Pro1002His	p.P1002H	ENST00000340748		1002	cCc/cAc	28/40	1	2	FACETS	0.888	0.817	0.962	0.888	0.817	0.962	CLONAL	1	TRUE	1	0.5	2		504	734	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946749	17946749	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1049658753	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	226	679	0	ENST00000458235.1:c.1898A>G	p.Tyr633Cys	p.Y633C	ENST00000458235	NM_000215.3	633	tAc/tGc	14/24	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.5	2		679	863	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752694	42752695	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	153	628	0	ENST00000222329.4:c.1569dup	p.Pro524AlafsTer10	p.P524Afs*10	ENST00000222329	NM_006494.2	523	-/G	4/4	1	2	FACETS	0.964	0.885	1	0.964	0.885	1	CLONAL	1	TRUE	1	0.5	2		628	635	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164678	47164678	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	97	282	0	ENST00000409792.3:c.1448T>C	p.Leu483Pro	p.L483P	ENST00000409792	NM_014159.6	483	cTa/cCa	3/21	1	2	FACETS	0.99	0.889	1	0.99	0.889	1	CLONAL	1	TRUE	1	0.5	2		282	392	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799565	72799565	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	89	507	0	ENST00000325599.8:c.1604C>A	p.Ser535Tyr	p.S535Y	ENST00000325599	NM_018130.2	535	tCt/tAt	11/11	1	2	FACETS	0.539	0.478	0.604	0.539	0.478	0.604	SUBCLONAL	1	TRUE	1	0.5	2		507	661	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462366	89462366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	149	586	0	ENST00000336596.2:c.1838C>T	p.Ala613Val	p.A613V	ENST00000336596	NM_005233.5	613	gCc/gTc	10/17	1	2	FACETS	0.844	0.773	0.919	0.844	0.773	0.919	CLONAL	1	TRUE	1	0.5	2		586	706	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911580	134911580	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766084445	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	73	503	0	ENST00000398015.3:c.2045G>A	p.Arg682His	p.R682H	ENST00000398015	NM_004441.4	682	cGc/cAc	11/16	1	2	FACETS	0.447	0.391	0.508	0.447	0.391	0.508	SUBCLONAL	1	TRUE	1	0.5	2		503	653	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748294	41748294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	63	725	3	ENST00000226382.2:c.475G>A	p.Ala159Thr	p.A159T	ENST00000226382	NM_003924.3	159	Gca/Aca	3/3	1	2	FACETS	0.276	0.238	0.318	0.276	0.238	0.318	SUBCLONAL	1	TRUE	1	0.5	2		728	913	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143066999	143066999	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	77	305	1	ENST00000262992.4:c.1714C>A	p.Pro572Thr	p.P572T	ENST00000262992	NM_001101669.1	572	Cca/Aca	16/24	1	2	FACETS	0.744	0.656	0.837	0.744	0.656	0.837	SUBCLONAL	1	TRUE	1	0.5	2		306	414	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535408	187535408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1310770864	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	140	448	1	ENST00000441802.2:c.9166G>A	p.Ala3056Thr	p.A3056T	ENST00000441802	NM_005245.3	3056	Gct/Act	12/27	1	2	FACETS	0.838	0.765	0.915	0.838	0.765	0.915	CLONAL	1	TRUE	1	0.5	2		449	668	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481473	20481473	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138776759	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	45	313	0	ENST00000346618.3:c.542C>T	p.Thr181Met	p.T181M	ENST00000346618	NM_001949.4	181	aCg/aTg	3/7	1	2	FACETS	0.402	0.338	0.472	0.402	0.338	0.472	SUBCLONAL	1	TRUE	1	0.5	2		313	448	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017558	112017558	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	131	451	0	ENST00000368678.4:c.955A>G	p.Lys319Glu	p.K319E	ENST00000368678		319	Aag/Gag	9/13	1	2	FACETS	0.939	0.856	1	0.939	0.856	1	CLONAL	1	TRUE	1	0.5	2		451	558	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148513817	148513817	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	140	415	0	ENST00000320356.2:c.1464G>T	p.Glu488Asp	p.E488D	ENST00000320356	NM_004456.4	488	gaG/gaT	12/20	1	2	FACETS	0.862	0.787	0.94	0.862	0.787	0.94	CLONAL	1	TRUE	1	0.5	2		415	650	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540207	23540207	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55910090	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	165	477	1	ENST00000380871.4:c.196C>T	p.Arg66Cys	p.R66C	ENST00000380871	NM_006167.3	66	Cgc/Tgc	1/2	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.5	2		478	587	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981857	70981857	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1243625483	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	152	649	0	ENST00000276594.2:c.239C>T	p.Pro80Leu	p.P80L	ENST00000276594	NM_024504.3	80	cCg/cTg	2/8	1	2	FACETS	0.842	0.772	0.916	0.842	0.772	0.916	CLONAL	1	TRUE	1	0.5	2		649	722	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866605	117866605	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	155	482	0	ENST00000297338.2:c.1040T>A	p.Ile347Asn	p.I347N	ENST00000297338	NM_006265.2	347	aTt/aAt	9/14	1	2	FACETS	0.995	0.915	1	0.995	0.915	1	CLONAL	1	TRUE	1	0.5	2		482	623	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923729	39923729	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	205	652	0	ENST00000378444.4:c.3362C>T	p.Ala1121Val	p.A1121V	ENST00000378444	NM_001123385.1	1121	gCc/gTc	7/15	1	2	FACETS	0.977	0.908	1	0.977	0.908	1	CLONAL	1	TRUE	1	0.5	2		652	839	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0027376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	208	397	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.972	0.908	1	0.972	0.908	1	CLONAL	1	TRUE	1	0.70377098216288	2		397	608	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0027376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	479	441	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.703734552933329	2	FACETS	0.978	0.948	1	0.978	0.948	1	CLONAL	2	TRUE	0	0.70377098216288	2		441	696	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0027377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	56	449	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.726	0.622	0.841	0.726	0.622	0.841	SUBCLONAL	1	TRUE	1	0.26	2		449	593	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0027377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	99	630	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.178558941031713	1	FACETS	0.707	0.63	0.789	0.707	0.63	0.789	SUBCLONAL	1	TRUE	0	0.26	1		632	937	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624271	89624271	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1064794096	NA	P-0027377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	40	376	0	ENST00000371953.3:c.45A>C	p.Arg15Ser	p.R15S	ENST00000371953	NM_000314.4	15	agA/agC	1/9	0.178558941031713	1	FACETS	0.494	0.41	0.588	0.494	0.41	0.588	SUBCLONAL	1	TRUE	0	0.26	1		376	542	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450105	32450105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1190263054	NA	P-0027378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	91	760	0	ENST00000332351.3:c.707C>T	p.Ala236Val	p.A236V	ENST00000332351	NM_024426.4	236	gCg/gTg	2/10	1	2	FACETS	0.814	0.722	0.912	0.814	0.722	0.912	CLONAL	1	TRUE	1	0.282221655796971	2		760	792	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162942	47162943	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	58	440	0	ENST00000409792.3:c.3183dup	p.Pro1062SerfsTer34	p.P1062Sfs*34	ENST00000409792	NM_014159.6	1061	-/T	3/21	0.282221655796971	1	FACETS	0.797	0.686	0.917	0.797	0.686	0.917	CLONAL	1	TRUE	0	0.282221655796971	1		440	443	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	137	595	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.692499950101901	2	FACETS	0.573	0.523	0.626	0.287	0.261	0.313	SUBCLONAL	1	TRUE	0	0.741890868487996	2		595	644	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15827432	15827432	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	95	448	0	ENST00000307771.7:c.548T>G	p.Phe183Cys	p.F183C	ENST00000307771	NM_005089.3	183	tTt/tGt	7/11	1	2	FACETS	0.396	0.353	0.442	0.396	0.353	0.442	SUBCLONAL	1	TRUE	1	0.741890868487996	2		448	647	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	100	345	8	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.29	2		353	641	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	27	359	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.739	0.59	0.907	0.739	0.59	0.907	CLONAL	1	TRUE	1	0.29	2		359	252	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	59	418	1	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.763	0.657	0.879	0.763	0.657	0.879	SUBCLONAL	1	TRUE	1	0.29	2		419	533	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	53	423	3	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.914	0.782	1	0.914	0.782	1	CLONAL	1	TRUE	1	0.29	2		426	400	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278061	18278061	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519801	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	94	607	0	ENST00000222254.8:c.1681A>G	p.Asn561Asp	p.N561D	ENST00000222254	NM_005027.3	561	Aac/Gac	13/16	1	2	FACETS	0.838	0.745	0.937	0.838	0.745	0.937	CLONAL	1	TRUE	1	0.29	2		607	774	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101268	27101268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	59	571	0	ENST00000324856.7:c.4555del	p.Gln1519ArgfsTer8	p.Q1519Rfs*8	ENST00000324856	NM_006015.4	1517	gCc/gc	18/20	1	2	FACETS	0.693	0.596	0.799	0.693	0.596	0.799	SUBCLONAL	1	TRUE	1	0.29	2		571	587	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606382	93606382	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764942726	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	55	572	0	ENST00000375746.1:c.202C>T	p.Arg68Trp	p.R68W	ENST00000375746	NM_001174167.1	68	Cgg/Tgg	2/14	0.125156044051949	0	FACETS	0.578	0.495	0.668			1	INDETERMINATE	1	TRUE	0	0.29	0		572	466	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696432	47696432	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519968	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	77	502	0	ENST00000347630.2:c.391T>G	p.Trp131Gly	p.W131G	ENST00000347630	NM_001007230.1	131	Tgg/Ggg	6/11	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.29	2		502	510	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	93	672	6	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	0.125156044051949	3	FACETS	0.957	0.851	1	0.479	0.425	0.536	INDETERMINATE	1	TRUE	1	0.29	3		678	767	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960032	134960032	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779665397	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	49	495	0	ENST00000398015.3:c.2389G>A	p.Ala797Thr	p.A797T	ENST00000398015	NM_004441.4	797	Gcc/Acc	13/16	0.3	1	FACETS	0.701	0.595	0.818	0.701	0.595	0.818	SUBCLONAL	1	TRUE	0	0.29	1		495	412	SUCCESS
APC	324	MSKCC	GRCh37	5	112175952	112175952	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587783031	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	30	284	0	ENST00000257430.4:c.4666del	p.Thr1556LeufsTer9	p.T1556Lfs*9	ENST00000257430	NM_000038.5	1554	gAa/ga	16/16	1	2	FACETS	1	0.834	1	1	0.834	1	CLONAL	1	TRUE	1	0.29	2		284	201	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56832410	56832410	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	29	406	0	ENST00000308159.5:c.320A>G	p.Asp107Gly	p.D107G	ENST00000308159	NM_014669.4	107	gAc/gGc	4/22	0.125156044051949	3	FACETS	0.587	0.471	0.719	0.294	0.235	0.36	INDETERMINATE	1	TRUE	1	0.29	3		406	390	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878596	151878596	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	52	489	4	ENST00000262189.6:c.6349del	p.Ser2117ProfsTer26	p.S2117Pfs*26	ENST00000262189	NM_170606.2	2117	Tcc/cc	36/59	0.3	3	FACETS	0.802	0.683	0.932			1	CLONAL	1	TRUE	NA	0.29	3		493	512	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433689	49433689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760968358	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	108	801	1	ENST00000301067.7:c.7864G>A	p.Asp2622Asn	p.D2622N	ENST00000301067	NM_003482.3	2622	Gac/Aac	31/54	0.125156044051949	3	FACETS	1	0.912	1	0.509	0.457	0.565	INDETERMINATE	1	TRUE	1	0.29	3		802	837	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11027412	11027412	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	107	694	1	ENST00000327064.4:c.979C>T	p.Arg327Ter	p.R327*	ENST00000327064	NM_199141.1	327	Cga/Tga	8/16	1	2	FACETS	0.995	0.892	1	0.995	0.892	1	CLONAL	1	TRUE	1	0.29	2		695	742	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350006	89350006	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779463117	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	63	511	1	ENST00000301030.4:c.2944G>A	p.Glu982Lys	p.E982K	ENST00000301030	NM_001256183.1	982	Gag/Aag	9/13	1	2	FACETS	0.727	0.628	0.833	0.727	0.628	0.833	SUBCLONAL	1	TRUE	1	0.29	2		512	598	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188343	142188343	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	27	469	0	ENST00000350721.4:c.6388A>G	p.Thr2130Ala	p.T2130A	ENST00000350721	NM_001184.3	2130	Aca/Gca	38/47	1	2	FACETS	0.607	0.483	0.747	0.607	0.483	0.747	SUBCLONAL	1	TRUE	1	0.29	2		469	307	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245820	5245820	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746218785	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	95	768	2	ENST00000357368.4:c.955G>A	p.Val319Ile	p.V319I	ENST00000357368	NM_002850.3	319	Gtc/Atc	10/38	1	2	FACETS	0.932	0.83	1	0.932	0.83	1	CLONAL	1	TRUE	1	0.29	2		770	703	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662610	227662610	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	57	410	1	ENST00000305123.5:c.845T>C	p.Val282Ala	p.V282A	ENST00000305123	NM_005544.2	282	gTc/gCc	1/2	1	2	FACETS	0.817	0.702	0.942	0.817	0.702	0.942	CLONAL	1	TRUE	1	0.29	2		411	481	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955920	55955920	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	58	475	0	ENST00000263923.4:c.3242T>C	p.Val1081Ala	p.V1081A	ENST00000263923	NM_002253.2	1081	gTg/gCg	24/30	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.29	2		475	379	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832266	72832266	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	68	379	0	ENST00000268489.5:c.4315C>T	p.Arg1439Ter	p.R1439*	ENST00000268489	NM_006885.3	1439	Cga/Tga	9/10	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.29	2		379	455	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885673	23885673	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	108	493	0	ENST00000374561.5:c.245T>C	p.Val82Ala	p.V82A	ENST00000374561	NM_002167.4	82	gTa/gCa	1/3	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.29	2		493	707	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743866	46743866	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	69	604	0	ENST00000371975.4:c.2156T>C	p.Val719Ala	p.V719A	ENST00000371975	NM_003579.3	719	gTa/gCa	18/18	1	2	FACETS	0.765	0.666	0.872	0.765	0.666	0.872	SUBCLONAL	1	TRUE	1	0.29	2		604	622	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166413	118166413	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs770016455	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	29	324	0	ENST00000369448.3:c.923T>C	p.Met308Thr	p.M308T	ENST00000369448	NM_017709.3	308	aTg/aCg	2/2	1	2	FACETS	0.48	0.385	0.588	0.48	0.385	0.588	SUBCLONAL	1	TRUE	1	0.29	2		324	417	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650046	206650046	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	51	521	0	ENST00000367120.3:c.566T>C	p.Val189Ala	p.V189A	ENST00000367120	NM_014002.3	189	gTg/gCg	7/22	1	2	FACETS	0.624	0.53	0.727	0.624	0.53	0.727	SUBCLONAL	1	TRUE	1	0.29	2		521	564	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63829477	63829477	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	37	349	0	ENST00000279873.7:c.1120T>C	p.Trp374Arg	p.W374R	ENST00000279873	NM_032199.2	374	Tgg/Cgg	8/10	0.3	4	FACETS	0.679	0.559	0.813			1	SUBCLONAL	1	TRUE	NA	0.29	4		349	485	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681341	88681341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786202611	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	14	175	1	ENST00000372037.3:c.1231G>A	p.Glu411Lys	p.E411K	ENST00000372037	NM_004329.2	411	Gaa/Aaa	11/13	1	2	FACETS	0.447	0.323	0.596	0.447	0.323	0.596	SUBCLONAL	1	TRUE	1	0.29	2		176	216	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263346	123263346	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	58	433	2	ENST00000358487.5:c.1397A>T	p.Tyr466Phe	p.Y466F	ENST00000358487	NM_000141.4	466	tAt/tTt	10/18	1	2	FACETS	0.985	0.849	1	0.985	0.849	1	CLONAL	1	TRUE	1	0.29	2		435	406	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918457	94918457	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	49	564	0	ENST00000536441.1:c.725A>G	p.Asn242Ser	p.N242S	ENST00000536441	NM_144665.3	242	aAc/aGc	5/10	1	2	FACETS	0.807	0.684	0.94	0.807	0.684	0.94	CLONAL	1	TRUE	1	0.29	2		564	419	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106526	108106526	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	66	356	0	ENST00000278616.4:c.461A>G	p.Lys154Arg	p.K154R	ENST00000278616	NM_000051.3	154	aAa/aGa	5/63	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.29	2		356	422	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359477	118359477	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	46	319	0	ENST00000534358.1:c.4479+2T>C		p.X1493_splice	ENST00000534358	NM_005933.3	1493			1	2	FACETS	0.795	0.671	0.932	0.795	0.671	0.932	CLONAL	1	TRUE	1	0.29	2		319	399	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420783	49420783	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766918626	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	84	502	1	ENST00000301067.7:c.14966G>A	p.Arg4989Gln	p.R4989Q	ENST00000301067	NM_003482.3	4989	cGg/cAg	48/54	0.125156044051949	3	FACETS	1	0.95	1	0.568	0.502	0.638	INDETERMINATE	1	TRUE	1	0.29	3		503	584	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133208998	133208998	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745721448	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	69	585	0	ENST00000320574.5:c.6233G>A	p.Arg2078Gln	p.R2078Q	ENST00000320574	NM_006231.2	2078	cGg/cAg	45/49	1	2	FACETS	0.893	0.779	1	0.893	0.779	1	CLONAL	1	TRUE	1	0.29	2		585	533	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913624	32913624	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	14	369	0	ENST00000380152.3:c.5132T>C	p.Val1711Ala	p.V1711A	ENST00000380152		1711	gTa/gCa	11/27	1	2	FACETS	0.435	0.314	0.58	0.435	0.314	0.58	SUBCLONAL	1	TRUE	1	0.29	2		369	222	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873625	35873625	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	41	263	0	ENST00000216797.5:c.226T>C	p.Ser76Pro	p.S76P	ENST00000216797	NM_020529.2	76	Tcg/Ccg	1/6	1	2	FACETS	0.707	0.59	0.837	0.707	0.59	0.837	SUBCLONAL	1	TRUE	1	0.29	2		263	400	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987102	36987102	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	62	664	0	ENST00000354822.5:c.587T>C	p.Val196Ala	p.V196A	ENST00000354822	NM_001079668.2	196	gTg/gCg	3/3	1	2	FACETS	0.757	0.654	0.868	0.757	0.654	0.868	SUBCLONAL	1	TRUE	1	0.29	2		664	565	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562710	95562710	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	46	436	0	ENST00000393063.1:c.4547A>G	p.Lys1516Arg	p.K1516R	ENST00000393063	NM_030621.3	1516	aAa/aGa	24/28	1	2	FACETS	0.822	0.694	0.963	0.822	0.694	0.963	CLONAL	1	TRUE	1	0.29	2		436	386	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243045	105243045	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	91	741	0	ENST00000349310.3:c.238T>A	p.Trp80Arg	p.W80R	ENST00000349310	NM_001014432.1	80	Tgg/Agg	5/15	1	2	FACETS	0.795	0.706	0.891	0.795	0.706	0.891	SUBCLONAL	1	TRUE	1	0.29	2		741	789	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720290	43720290	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	56	531	0	ENST00000382044.4:c.3752T>C	p.Val1251Ala	p.V1251A	ENST00000382044	NM_001141980.1	1251	gTa/gCa	18/28	1	2	FACETS	0.729	0.625	0.842	0.729	0.625	0.842	SUBCLONAL	1	TRUE	1	0.29	2		531	530	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99473516	99473516	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	26	265	0	ENST00000268035.6:c.2938T>C	p.Tyr980His	p.Y980H	ENST00000268035	NM_000875.3	980	Tac/Cac	15/21	0.3	2	FACETS	0.61	0.484	0.754			1	SUBCLONAL	1	TRUE	NA	0.29	2		265	294	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129647	2129647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs796053475	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	84	641	4	ENST00000219476.3:c.3374G>A	p.Arg1125Gln	p.R1125Q	ENST00000219476	NM_000548.3	1125	cGg/cAg	29/42	1	2	FACETS	0.92	0.813	1	0.92	0.813	1	CLONAL	1	TRUE	1	0.29	2		645	630	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222333	2222333	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	69	661	0	ENST00000326181.6:c.617A>G	p.Asp206Gly	p.D206G	ENST00000326181	NM_032271.2	206	gAc/gGc	8/21	1	2	FACETS	0.739	0.643	0.842	0.739	0.643	0.842	SUBCLONAL	1	TRUE	1	0.29	2		661	644	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527615	29527615	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	27	325	0	ENST00000356175.3:c.1062+2T>C		p.X354_splice	ENST00000356175	NM_000267.3	354			1	2	FACETS	0.595	0.474	0.733	0.595	0.474	0.733	SUBCLONAL	1	TRUE	1	0.29	2		325	313	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670154	29670154	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1555535455	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	22	316	0	ENST00000356175.3:c.7126+1G>A		p.X2376_splice	ENST00000356175	NM_000267.3	2376			1	2	FACETS	0.584	0.453	0.734	0.584	0.453	0.734	SUBCLONAL	1	TRUE	1	0.29	2		316	260	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40478163	40478163	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	76	630	1	ENST00000264657.5:c.1336T>C	p.Tyr446His	p.Y446H	ENST00000264657	NM_139276.2	446	Tat/Cat	15/24	1	2	FACETS	0.748	0.655	0.847	0.748	0.655	0.847	SUBCLONAL	1	TRUE	1	0.29	2		631	701	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678049	58678049	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1391305414	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	52	323	0	ENST00000305921.3:c.274T>C	p.Cys92Arg	p.C92R	ENST00000305921	NM_003620.3	92	Tgc/Cgc	1/6	1	2	FACETS	0.87	0.743	1	0.87	0.743	1	CLONAL	1	TRUE	1	0.29	2		323	412	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732932	74732932	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	45	353	0	ENST00000359995.5:c.311del	p.Gly104AspfsTer128	p.G104Dfs*128	ENST00000359995	NM_001195427.1	104	gGa/ga	1/3	1	2	FACETS	0.622	0.523	0.732	0.622	0.523	0.732	SUBCLONAL	1	TRUE	1	0.29	2		353	499	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226299	2226299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780498768	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	114	736	1	ENST00000398665.3:c.3779C>T	p.Pro1260Leu	p.P1260L	ENST00000398665	NM_032482.2	1260	cCg/cTg	27/28	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.29	2		737	693	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298069	15298069	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	99	765	0	ENST00000263388.2:c.1687A>G	p.Ile563Val	p.I563V	ENST00000263388	NM_000435.2	563	Atc/Gtc	11/33	1	2	FACETS	0.955	0.853	1	0.955	0.853	1	CLONAL	1	TRUE	1	0.29	2		765	715	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741180	40741180	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	96	619	0	ENST00000392038.2:c.1253T>C	p.Val418Ala	p.V418A	ENST00000392038	NM_001626.4	418	gTc/gCc	12/14	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.29	2		619	619	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741244	40741244	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	71	596	0	ENST00000392038.2:c.1189C>G	p.Pro397Ala	p.P397A	ENST00000392038	NM_001626.4	397	Ccc/Gcc	12/14	1	2	FACETS	0.826	0.721	0.939	0.826	0.721	0.939	CLONAL	1	TRUE	1	0.29	2		596	593	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919024	50919024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868146189	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	111	630	0	ENST00000440232.2:c.2761C>T	p.Arg921Cys	p.R921C	ENST00000440232	NM_002691.3	921	Cgc/Tgc	22/27	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.29	2		630	685	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635517	47635556	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AATGTACTTTTTTTTTTTTTAAGGAGCAAAGAATCTGCAG	AATGTACTTTTTTTTTTTTTAAGGAGCAAAGAATCTGCAG	-	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	41	218	0	ENST00000233146.2:c.212-22_229del		p.X71_splice	ENST00000233146	NM_000251.2	71		2/16	0.209874045524863	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.29	1		218	163	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403197	213403197	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	85	455	0	ENST00000342788.4:c.58G>C	p.Val20Leu	p.V20L	ENST00000342788	NM_005235.2	20	Gtc/Ctc	1/28	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.29	2		455	476	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742743	39742743	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	77	493	2	ENST00000361337.2:c.1586T>A	p.Phe529Tyr	p.F529Y	ENST00000361337	NM_003286.2	529	tTc/tAc	15/21	1	2	FACETS	0.962	0.846	1	0.962	0.846	1	CLONAL	1	TRUE	1	0.29	2		495	552	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164716	36164716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1285485702	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	78	678	2	ENST00000300305.3:c.1159G>A	p.Gly387Ser	p.G387S	ENST00000300305		387	Ggc/Agc	8/8	1	2	FACETS	0.766	0.673	0.867	0.766	0.673	0.867	SUBCLONAL	1	TRUE	1	0.29	2		680	702	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091746	29091746	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	18	258	1	ENST00000328354.6:c.1211A>T	p.Tyr404Phe	p.Y404F	ENST00000328354	NM_007194.3	404	tAt/tTt	11/15	1	2	FACETS	0.54	0.407	0.696	0.54	0.407	0.696	SUBCLONAL	1	TRUE	1	0.29	2		259	230	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29115404	29115404	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs113947614	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	51	466	0	ENST00000328354.6:c.662T>C	p.Ile221Thr	p.I221T	ENST00000328354	NM_007194.3	221	aTc/aCc	5/15	1	2	FACETS	0.783	0.667	0.911	0.783	0.667	0.911	CLONAL	1	TRUE	1	0.29	2		466	449	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277574	142277574	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	36	462	0	ENST00000350721.4:c.1777del	p.Met593CysfsTer16	p.M593Cfs*16	ENST00000350721	NM_001184.3	593	Atg/tg	8/47	1	2	FACETS	0.859	0.709	1	0.859	0.709	1	CLONAL	1	TRUE	1	0.29	2		462	289	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1932462	1932462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	63	696	0	ENST00000382891.5:c.1520C>T	p.Ala507Val	p.A507V	ENST00000382891	NM_133335.3	507	gCc/gTc	6/22	1	2	FACETS	0.599	0.517	0.688	0.599	0.517	0.688	SUBCLONAL	1	TRUE	1	0.29	2		696	725	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143181707	143181707	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	36	348	0	ENST00000262992.4:c.626T>C	p.Val209Ala	p.V209A	ENST00000262992	NM_001101669.1	209	gTa/gCa	9/24	1	2	FACETS	0.839	0.692	1	0.839	0.692	1	CLONAL	1	TRUE	1	0.29	2		348	296	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268195	153268195	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	50	294	0	ENST00000281708.4:c.613A>G	p.Thr205Ala	p.T205A	ENST00000281708	NM_033632.3	205	Aca/Gca	4/12	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.29	2		294	305	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541693	187541693	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	54	333	0	ENST00000441802.2:c.6047T>C	p.Ile2016Thr	p.I2016T	ENST00000441802	NM_005245.3	2016	aTc/aCc	10/27	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.29	2		333	349	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1253911	1253911	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	46	547	0	ENST00000310581.5:c.3331A>T	p.Thr1111Ser	p.T1111S	ENST00000310581	NM_198253.2	1111	Acg/Tcg	16/16	0.3	2	FACETS	0.536	0.451	0.63			1	SUBCLONAL	1	TRUE	NA	0.29	2		547	592	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31401628	31401628	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	44	484	0	ENST00000344624.3:c.4036C>G	p.Arg1346Gly	p.R1346G	ENST00000344624		1346	Cgg/Ggg	33/33	0.3	2	FACETS	0.79	0.664	0.929			1	CLONAL	1	TRUE	NA	0.29	2		484	384	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31423005	31423005	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	59	554	0	ENST00000344624.3:c.3308T>C	p.Val1103Ala	p.V1103A	ENST00000344624		1103	gTt/gCt	26/33	0.3	2	FACETS	0.888	0.766	1			1	CLONAL	1	TRUE	NA	0.29	2		554	458	SUCCESS
APC	324	MSKCC	GRCh37	5	112179144	112179144	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	27	256	0	ENST00000257430.4:c.7853A>G	p.Asn2618Ser	p.N2618S	ENST00000257430	NM_000038.5	2618	aAt/aGt	16/16	1	2	FACETS	0.97	0.778	1	0.97	0.778	1	CLONAL	1	TRUE	1	0.29	2		256	192	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032066	26032066	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs748472587	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	44	358	0	ENST00000244661.2:c.223A>G	p.Ile75Val	p.I75V	ENST00000244661	NM_003537.3	75	Atc/Gtc	1/1	0.3	4	FACETS	0.816	0.684	0.961			1	CLONAL	1	TRUE	NA	0.29	4		358	480	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250719	26250719	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	48	439	0	ENST00000446824.2:c.115C>T	p.Pro39Ser	p.P39S	ENST00000446824	NM_021018.2	39	Ccc/Tcc	1/1	0.3	4	FACETS	0.739	0.624	0.865			1	SUBCLONAL	1	TRUE	NA	0.29	4		439	578	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117707000	117707000	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	49	538	0	ENST00000368508.3:c.2150T>C	p.Leu717Pro	p.L717P	ENST00000368508	NM_002944.2	717	cTc/cCc	15/43	0.209874045524863	0	FACETS	0.51	0.433	0.596			1	SUBCLONAL	1	TRUE	0	0.29	0		538	470	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012392	152012392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	34	305	2	ENST00000262189.6:c.421G>A	p.Glu141Lys	p.E141K	ENST00000262189	NM_170606.2	141	Gaa/Aaa	4/59	0.3	2	FACETS	0.885	0.727	1			1	CLONAL	1	TRUE	NA	0.29	2		307	265	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38194827	38194828	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	68	446	0	ENST00000317025.8:c.905dup	p.Arg303LysfsTer12	p.R303Kfs*12	ENST00000317025	NM_023034.1	302	aca/acCa	4/24	1	2	FACETS	0.983	0.857	1	0.983	0.857	1	CLONAL	1	TRUE	1	0.29	2		446	477	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275465	38275465	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	103	638	1	ENST00000425967.3:c.1568T>C	p.Val523Ala	p.V523A	ENST00000425967	NM_001174067.1	523	gTg/gCg	12/19	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.29	2		639	702	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912200	127912200	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	19	208	0	ENST00000373547.4:c.670T>C	p.Phe224Leu	p.F224L	ENST00000373547	NM_002721.4	224	Ttt/Ctt	7/7	1	2	FACETS	0.621	0.473	0.794	0.621	0.473	0.794	SUBCLONAL	1	TRUE	1	0.29	2		208	211	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650389	48650389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782377129	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	77	336	1	ENST00000376670.3:c.359C>T	p.Ala120Val	p.A120V	ENST00000376670	NM_002049.3	120	gCc/gTc	3/6	1	1	FACETS	0.777	0.69	0.87	1	0.979	1	SUBCLONAL	2	TRUE	0	0.29	1		337	292	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411698	63411698	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	64	364	0	ENST00000330258.3:c.1469T>C	p.Val490Ala	p.V490A	ENST00000330258	NM_152424.3	490	gTc/gCc	2/2	1	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.29	1		364	298	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188210	10188210	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs5030830	NA	P-0027381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	120	523	0	ENST00000256474.2:c.353T>C	p.Leu118Pro	p.L118P	ENST00000256474	NM_000551.3	118	cTc/cCc	2/3	0.347373131195134	1	FACETS	0.919	0.832	1	0.919	0.832	1	CLONAL	1	TRUE	0	0.347373131195134	1		523	621	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40856641	40856641	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	133	484	2	ENST00000428826.2:c.1996T>A	p.Phe666Ile	p.F666I	ENST00000428826		666	Ttc/Atc	18/21	1	2	FACETS	0.973	0.884	1	0.973	0.884	1	CLONAL	1	TRUE	1	0.347373131195134	2		486	787	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280386	1280386	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	137	701	0	ENST00000310581.5:c.1837A>T	p.Arg613Trp	p.R613W	ENST00000310581	NM_198253.2	613	Agg/Tgg	4/16	1	2	FACETS	0.942	0.857	1	0.942	0.857	1	CLONAL	1	TRUE	1	0.347373131195134	2		701	837	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	117	315	1				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.967	1			1	INDETERMINATE	1	TRUE	NA	0.394273601483079	2		316	517	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0027383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	695	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.394273601483079	7	FACETS	1	0.992	1			1	CLONAL	5	TRUE	NA	0.394273601483079	7		509	1314	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492926	56492926	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	44	185	0	ENST00000407977.2:c.13del	p.His5ThrfsTer13	p.H5Tfs*13	ENST00000407977		5	Cac/ac	2/10	0.381238196779477	3	FACETS	1	0.933	1	0.599	0.507	0.699	CLONAL	1	TRUE	1	0.394273601483079	3		185	223	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754605	57754605	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	86	343	0	ENST00000274289.3:c.442T>C	p.Tyr148His	p.Y148H	ENST00000274289	NM_006622.3	148	Tac/Cac	3/14	1	2	FACETS	0.619	0.547	0.695	0.619	0.547	0.695	SUBCLONAL	1	TRUE	1	0.394273601483079	2		343	705	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969407	44969407	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	249	312	0	ENST00000377967.4:c.4093del	p.Thr1365GlnfsTer11	p.T1365Qfs*11	ENST00000377967	NM_021140.2	1363	cgA/cg	28/29	1	1	FACETS	0.924	0.872	0.975	1	0.995	1	CLONAL	2	TRUE	0	0.394273601483079	1		312	549	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247367	153247367	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747241612	NA	P-0027386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	80	287	0	ENST00000281708.4:c.1435C>G	p.Arg479Gly	p.R479G	ENST00000281708	NM_033632.3	479	Cga/Gga	10/12	0.236548635981871	1	FACETS	0.43	0.38	0.483	0.43	0.38	0.483	INDETERMINATE	1	TRUE	0	0.588580928179182	1		287	446	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188134	11188134	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	215	433	2	ENST00000361445.4:c.5960G>T	p.Arg1987Leu	p.R1987L	ENST00000361445	NM_004958.3	1987	cGg/cTg	43/58	NA	2	FACETS	0.852	0.794	0.913			1	INDETERMINATE	1	TRUE	NA	0.588580928179182	2		435	857	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922197	100922197	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	157	434	0	ENST00000325455.5:c.2315G>T	p.Ser772Ile	p.S772I	ENST00000325455	NM_001202474.3	772	aGt/aTt	5/8	0.560169678812857	3	FACETS	0.896	0.822	0.973	0.448	0.411	0.487	CLONAL	1	TRUE	1	0.588580928179182	3		434	771	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56377305	56377305	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0027386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	115	254	0	ENST00000348428.3:c.925+1G>T		p.X309_splice	ENST00000348428	NM_006785.3	309			0.575058546671732	1	FACETS	0.985	0.902	1	0.985	0.902	1	CLONAL	1	TRUE	0	0.588580928179182	1		254	280	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350207	15350207	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	425	561	0	ENST00000263377.2:c.3572A>T	p.Lys1191Ile	p.K1191I	ENST00000263377	NM_058243.2	1191	aAa/aTa	17/20	0.284530490209844	6	FACETS	1	0.989	1	0.751	0.715	0.788	INDETERMINATE	2	TRUE	3	0.588580928179182	6		561	1395	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430269	181430269	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1225885626	NA	P-0027386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	203	463	0	ENST00000325404.1:c.121G>C	p.Val41Leu	p.V41L	ENST00000325404	NM_003106.3	41	Gtc/Ctc	1/1	0.288147306066053	5	FACETS	1	0.987	1	0.435	0.403	0.468	INDETERMINATE	1	TRUE	2	0.588580928179182	5		463	996	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356139	66356139	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	147	439	0	ENST00000273854.3:c.1358G>T	p.Gly453Val	p.G453V	ENST00000273854	NM_004439.5	453	gGa/gTa	5/18	0.236548635981871	1	FACETS	0.671	0.617	0.728	0.671	0.617	0.728	INDETERMINATE	1	TRUE	0	0.588580928179182	1		439	525	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467590	66467590	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	99	316	0	ENST00000273854.3:c.679C>A	p.Arg227Ser	p.R227S	ENST00000273854	NM_004439.5	227	Cgt/Agt	3/18	0.236548635981871	1	FACETS	0.528	0.473	0.585	0.528	0.473	0.585	INDETERMINATE	1	TRUE	0	0.588580928179182	1		316	450	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258956	153258956	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	97	234	1	ENST00000281708.4:c.859G>A	p.Glu287Lys	p.E287K	ENST00000281708	NM_033632.3	287	Gag/Aag	5/12	0.236548635981871	1	FACETS	0.703	0.633	0.775	0.703	0.633	0.775	INDETERMINATE	1	TRUE	0	0.588580928179182	1		235	331	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228366	228366	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	82	323	0	ENST00000264932.6:c.688G>T	p.Glu230Ter	p.E230*	ENST00000264932	NM_004168.2	230	Gag/Tag	6/15	0.359118604686111	1	FACETS	0.389	0.343	0.437	0.389	0.343	0.437	SUBCLONAL	1	TRUE	0	0.588580928179182	1		323	506	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294938	1294938	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	22	123	0	ENST00000310581.5:c.167T>A	p.Val56Glu	p.V56E	ENST00000310581	NM_198253.2	56	gTg/gAg	1/16	0.359118604686111	1	FACETS	0.328	0.256	0.41	0.328	0.256	0.41	SUBCLONAL	1	TRUE	0	0.588580928179182	1		123	161	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940483	31940483	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	323	592	2	ENST00000375333.2:c.516G>T	p.Arg172Ser	p.R172S	ENST00000375333	NM_032454.1	172	agG/agT	3/8	0.298183321083739	3	FACETS	1	0.992	1	0.631	0.596	0.667	INDETERMINATE	1	TRUE	1	0.588580928179182	3		594	1126	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0027388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	13	694	1	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		695	439	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0027388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	15	477	0	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	0.157308054667079	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		477	259	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870260	44870260	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	26	284	0	ENST00000377967.4:c.439C>T	p.Gln147Ter	p.Q147*	ENST00000377967	NM_021140.2	147	Cag/Tag	5/29	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		284	230	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802635	135802635	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203343	NA	P-0027388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	24	534	1	ENST00000298552.3:c.163C>T	p.Gln55Ter	p.Q55*	ENST00000298552	NM_001162426.1	55	Cag/Tag	4/23	0.157308054667079	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		535	405	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224595	123224595	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	29	310	0	ENST00000218089.9:c.3448C>G	p.Gln1150Glu	p.Q1150E	ENST00000218089	NM_001042749.1	1150	Caa/Gaa	31/35	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		310	327	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0027390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	163	321	2	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.315361473382981	3	FACETS	1	0.971	1	0.564	0.517	0.614	CLONAL	1	TRUE	1	0.315361473382981	3		323	1060	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0027390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	193	448	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.315361473382981	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.315361473382981	1		448	838	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0027390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	214	492	0	ENST00000262160.6:c.1391C>G	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tGa	11/11	0.287876526025897	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.315361473382981	2		492	669	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969884	81969884	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199840870	NA	P-0027390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	193	656	2	ENST00000359376.3:c.2953G>A	p.Val985Ile	p.V985I	ENST00000359376	NM_002661.3	985	Gtc/Atc	27/33	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.315361473382981	2		658	1022	SUCCESS
APC	324	MSKCC	GRCh37	5	112175350	112175351	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0027390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	61	325	0	ENST00000257430.4:c.4059_4060del	p.Glu1353AspfsTer21	p.E1353Dfs*21	ENST00000257430	NM_000038.5	1353	gaATtt/gatt	16/16	1	2	FACETS	0.836	0.722	0.958	0.836	0.722	0.958	CLONAL	1	TRUE	1	0.315361473382981	2		325	463	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031859	10031859	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374637415	NA	P-0027390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	177	730	1	ENST00000330684.3:c.964G>A	p.Gly322Arg	p.G322R	ENST00000330684	NM_001134407.1	322	Ggg/Agg	3/13	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.315361473382981	2		731	1019	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133553	55133553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	102	692	0	ENST00000257290.5:c.857G>A	p.Gly286Glu	p.G286E	ENST00000257290	NM_006206.4	286	gGa/gAa	6/23	1	2	FACETS	0.627	0.56	0.7	0.627	0.56	0.7	SUBCLONAL	1	TRUE	1	0.315361473382981	2		692	1031	SUCCESS
APC	324	MSKCC	GRCh37	5	112175643	112175643	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554085817	NA	P-0027390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	101	510	0	ENST00000257430.4:c.4353del	p.Val1452TyrfsTer21	p.V1452Yfs*21	ENST00000257430	NM_000038.5	1451	gAa/ga	16/16	1	2	FACETS	0.897	0.802	0.998	0.897	0.802	0.998	CLONAL	1	TRUE	1	0.315361473382981	2		510	714	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0027391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	249	634	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.300064885325588	2	FACETS	1	0.991	1	0.69	0.646	0.735	CLONAL	1	TRUE	0	0.394907271516576	2		634	914	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696461	47696461	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	87	493	0	ENST00000347630.2:c.362G>C	p.Arg121Pro	p.R121P	ENST00000347630	NM_001007230.1	121	cGg/cCg	6/11	1	2	FACETS	0.854	0.758	0.956	0.854	0.758	0.956	CLONAL	1	TRUE	1	0.394907271516576	2		493	516	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531024	187531025	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0027391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	115	625	0	ENST00000441802.2:c.9998dup	p.Val3334CysfsTer13	p.V3334Cfs*13	ENST00000441802	NM_005245.3	3333	cct/ccCt	15/27	1	2	FACETS	0.663	0.597	0.734	0.663	0.597	0.734	SUBCLONAL	1	TRUE	1	0.394907271516576	2		625	878	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057739	180057739	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	165	641	0	ENST00000261937.6:c.216C>A	p.Asp72Glu	p.D72E	ENST00000261937	NM_182925.4	72	gaC/gaA	3/30	0.394907271516576	1	FACETS	0.731	0.671	0.793	0.731	0.671	0.793	SUBCLONAL	1	TRUE	0	0.394907271516576	1		641	918	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0027395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	115	480	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.157107771019297	2	FACETS	0.97	0.874	1	0.97	0.874	1	CLONAL	2	TRUE	0	0.157107771019297	2		480	755	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871827	12871833	+	frameshift_variant	Frame_Shift_Del	DEL	GGTTCTG	GGTTCTG	-	novel	NA	P-0027395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	40	361	2	ENST00000228872.4:c.544_550del	p.Gly182TrpfsTer41	p.G182Wfs*41	ENST00000228872	NM_004064.3	182	GGTTCTGtg/tg	2/3	1	2	FACETS	0.796	0.66	0.948	0.796	0.66	0.948	CLONAL	1	TRUE	1	0.157107771019297	2		363	640	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842387	68842387	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0027395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	163	666	5	ENST00000261769.5:c.448A>T	p.Arg150Ter	p.R150*	ENST00000261769	NM_004360.3	150	Aga/Tga	4/16	0.157107771019297	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	2	TRUE	0	0.157107771019297	2		671	1036	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	170	315	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.933	0.868	1	0.933	0.868	1	CLONAL	1	TRUE	1	0.855128239468809	2		316	426	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0027397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	207	326	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.855128239468809	2		326	474	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130342	11130342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	85	764	2	ENST00000358026.2:c.2581G>A	p.Glu861Lys	p.E861K	ENST00000358026	NM_001128849.1	861	Gag/Aag	18/36	0.327026459068095	3	FACETS	0.27	0.237	0.304	0.135	0.118	0.152	INDETERMINATE	1	TRUE	1	0.855128239468809	3		766	1053	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791797	42791797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	34	700	0	ENST00000575354.2:c.683G>A	p.Arg228Gln	p.R228Q	ENST00000575354	NM_015125.3	228	cGg/cAg	5/20	0.855128239468809	1	FACETS	0.098	0.08	0.119	0.098	0.08	0.119	SUBCLONAL	1	TRUE	0	0.855128239468809	1		700	464	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740469	58740469	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	365	780	0	ENST00000305921.3:c.1374del	p.Glu459ArgfsTer6	p.E459Rfs*6	ENST00000305921	NM_003620.3	458	cgA/cg	6/6	1	2	FACETS	0.943	0.898	0.989	0.943	0.898	0.989	CLONAL	1	TRUE	1	0.855128239468809	2		780	905	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121205	11121205	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	309	646	0	ENST00000358026.2:c.2272C>G	p.Gln758Glu	p.Q758E	ENST00000358026	NM_001128849.1	758	Cag/Gag	15/36	0.327026459068095	3	FACETS	1	0.991	1	0.605	0.573	0.639	INDETERMINATE	1	TRUE	1	0.855128239468809	3		646	852	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99162450	99162450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	322	614	0	ENST00000074304.5:c.968G>A	p.Ser323Asn	p.S323N	ENST00000074304	NM_001134224.1	323	aGc/aAc	12/26	1	2	FACETS	0.932	0.884	0.98	0.932	0.884	0.98	CLONAL	1	TRUE	1	0.855128239468809	2		614	808	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0027408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	113	397	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.275073465670287	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.275073465670287	1		397	690	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610154	10610154	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	150	682	1	ENST00000171111.5:c.556G>T	p.Gly186Cys	p.G186C	ENST00000171111	NM_203500.1	186	Ggc/Tgc	2/6	0.275073465670287	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.275073465670287	1		683	915	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644404	18644404	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs539703060	NA	P-0027408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	77	399	0	ENST00000266497.5:c.2582T>C	p.Ile861Thr	p.I861T	ENST00000266497		861	aTt/aCt	18/31	0.275073465670287	1	FACETS	0.96	0.845	1	0.96	0.845	1	CLONAL	1	TRUE	0	0.275073465670287	1		399	503	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503852	149503852	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	116	602	1	ENST00000261799.4:c.1984C>A	p.Leu662Met	p.L662M	ENST00000261799	NM_002609.3	662	Ctg/Atg	14/23	0.275073465670287	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.275073465670287	1		603	664	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275233	115275233	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	115	540	0	ENST00000438362.2:c.1180C>T	p.Arg394Ter	p.R394*	ENST00000438362	NM_001242891.1	394	Cga/Tga	10/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.275073465670287	2		540	708	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	495141	495141	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0027408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	82	429	0	ENST00000399788.2:c.166-1G>T		p.X56_splice	ENST00000399788	NM_001042603.1	56			0.275073465670287	1	FACETS	0.915	0.808	1	0.915	0.808	1	CLONAL	1	TRUE	0	0.275073465670287	1		429	562	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633248	3633248	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	72	962	0	ENST00000294008.3:c.5003A>T	p.Gln1668Leu	p.Q1668L	ENST00000294008	NM_032444.2	1668	cAa/cTa	14/15	1	2	FACETS	0.446	0.388	0.508	0.446	0.388	0.508	SUBCLONAL	1	TRUE	1	0.275073465670287	2		962	1175	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786141	3786141	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	76	812	0	ENST00000262367.5:c.4624G>C	p.Gly1542Arg	p.G1542R	ENST00000262367	NM_004380.2	1542	Ggt/Cgt	28/31	1	2	FACETS	0.531	0.464	0.603	0.531	0.464	0.603	SUBCLONAL	1	TRUE	1	0.275073465670287	2		812	1041	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50784039	50784040	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0027408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	109	699	0	ENST00000398568.2:c.430_431delinsTT	p.Gly144Leu	p.G144L	ENST00000398568	NM_001042412.1	144	GGa/TTa	3/18	1	2	FACETS	0.81	0.726	0.899	0.81	0.726	0.899	CLONAL	1	TRUE	1	0.275073465670287	2		699	979	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578409	7578410	+	missense_variant	Missense_Mutation	DNP	CT	CT	TC	novel	NA	P-0027408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	126	638	0	ENST00000269305.4:c.520_521delinsGA	p.Arg174Glu	p.R174E	ENST00000269305	NM_001126112.2	174	AGg/GAg	5/11	0.275073465670287	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.275073465670287	1		638	746	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116217	209116217	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	83	464	0	ENST00000345146.2:c.59G>C	p.Arg20Pro	p.R20P	ENST00000345146	NM_005896.2	20	cGa/cCa	3/10	1	2	FACETS	0.91	0.804	1	0.91	0.804	1	CLONAL	1	TRUE	1	0.275073465670287	2		464	663	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40709556	40709556	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	98	654	0	ENST00000373198.4:c.4346T>C	p.Val1449Ala	p.V1449A	ENST00000373198	NM_133170.3	1449	gTa/gCa	32/32	1	2	FACETS	0.869	0.775	0.97	0.869	0.775	0.97	CLONAL	1	TRUE	1	0.275073465670287	2		654	820	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730803	40730803	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	134	666	0	ENST00000373198.4:c.3732C>A	p.Asp1244Glu	p.D1244E	ENST00000373198	NM_133170.3	1244	gaC/gaA	27/32	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.275073465670287	2		666	839	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100980	41100980	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs868706902	NA	P-0027408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	97	567	0	ENST00000373198.4:c.1376G>T	p.Arg459Leu	p.R459L	ENST00000373198	NM_133170.3	459	cGg/cTg	8/32	1	2	FACETS	0.928	0.827	1	0.928	0.827	1	CLONAL	1	TRUE	1	0.275073465670287	2		567	760	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183854	10183854	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs367594943	NA	P-0027408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	133	525	0	ENST00000256474.2:c.323G>T	p.Arg108Leu	p.R108L	ENST00000256474	NM_000551.3	108	cGc/cTc	1/3	0.19741824179709	2	FACETS	1	0.984	1	0.7	0.637	0.766	CLONAL	1	TRUE	0	0.275073465670287	2		525	691	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961083	55961083	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	141	772	0	ENST00000263923.4:c.2857G>T	p.Gly953Ter	p.G953*	ENST00000263923	NM_002253.2	953	Gga/Tga	21/30	1	2	FACETS	0.997	0.907	1	0.997	0.907	1	CLONAL	1	TRUE	1	0.275073465670287	2		772	1028	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522294	157522294	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0027408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	139	743	0	ENST00000346085.5:c.4566T>G	p.Tyr1522Ter	p.Y1522*	ENST00000346085	NM_020732.3	1522	taT/taG	18/20	0.275073465670287	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.275073465670287	1		743	838	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974713	21974714	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCAGCGCCCCCGCCTCC	novel	NA	P-0027408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	22	352	0	ENST00000304494.5:c.96_113dup	p.Glu33_Pro38dup	p.E33_P38dup	ENST00000304494	NM_000077.4	33	ccc/ccGGAGGCGGGGGCGCTGCCc	1/3	0.275073465670287	1	FACETS	0.329	0.254	0.416	0.329	0.254	0.416	SUBCLONAL	1	TRUE	0	0.275073465670287	1		352	419	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759457	133759457	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	142	718	0	ENST00000318560.5:c.1780G>T	p.Asp594Tyr	p.D594Y	ENST00000318560	NM_005157.4	594	Gac/Tac	11/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.275073465670287	2		718	778	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356750	70356750	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372271659	NA	P-0027408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	66	591	1	ENST00000374080.3:c.5422C>T	p.Arg1808Trp	p.R1808W	ENST00000374080		1808	Cgg/Tgg	38/45	0.275073465670287	1	FACETS	0.565	0.49	0.647	0.565	0.49	0.647	SUBCLONAL	1	TRUE	0	0.275073465670287	1		592	732	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528472	29528472	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1376759287	NA	P-0027410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	103	586	0	ENST00000356175.3:c.1229T>G	p.Leu410Arg	p.L410R	ENST00000356175	NM_000267.3	410	cTg/cGg	11/57	0.605765599465982	1	FACETS	0.796	0.722	0.872	0.796	0.722	0.872	SUBCLONAL	1	TRUE	0	0.605765599465982	1		586	298	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995553	68995553	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771763123	NA	P-0027410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	40	690	0	ENST00000288368.4:c.1957G>A	p.Asp653Asn	p.D653N	ENST00000288368	NM_024870.2	653	Gat/Aat	18/40	1	2	FACETS	0.27	0.224	0.321	0.27	0.224	0.321	SUBCLONAL	1	TRUE	1	0.605765599465982	2		690	489	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0027411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	341	397	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.26899959969101	5	FACETS	0.879	0.833	0.926	0.879	0.833	0.926	CLONAL	4	TRUE	1	0.26899959969101	5		397	1012	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587780070	NA	P-0027411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	129	587	0	ENST00000269305.4:c.535C>A	p.His179Asn	p.H179N	ENST00000269305	NM_001126112.2	179	Cat/Aat	5/11	0.26899959969101	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.26899959969101	1		587	650	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974697	21974699	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	novel	NA	P-0027411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	84	449	0	ENST00000304494.5:c.128_130del	p.Ser43_Tyr44delinsAsn	p.S43_Y44delinsN	ENST00000304494	NM_000077.4	43	aGTTac/aac	1/3	0.26899959969101	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.26899959969101	1		449	407	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0027412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	127	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.34	2		509	740	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0027412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	135	596	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.29461778193289	1	FACETS	0.852	0.775	0.932	0.852	0.775	0.932	CLONAL	1	TRUE	0	0.34	1		597	774	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610608	52610608	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	150	618	0	ENST00000394830.3:c.3565G>T	p.Glu1189Ter	p.E1189*	ENST00000394830	NM_018313.4	1189	Gaa/Taa	23/30	0.29461778193289	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.34	1		618	727	SUCCESS
BLM	641	MSKCC	GRCh37	15	91328208	91328208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367953471	NA	P-0027412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	112	546	0	ENST00000355112.3:c.2720C>T	p.Thr907Met	p.T907M	ENST00000355112	NM_000057.2	907	aCg/aTg	14/22	1	2	FACETS	0.82	0.738	0.908	0.82	0.738	0.908	CLONAL	1	TRUE	1	0.34	2		546	803	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0027414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	243	760	1	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.53609977872687	1	FACETS	0.938	0.883	0.994	0.938	0.883	0.994	CLONAL	1	TRUE	0	0.586735699145289	1		761	624	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430633	80430633	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	153	305	0	ENST00000286548.4:c.375G>T	p.Glu125Asp	p.E125D	ENST00000286548	NM_002072.3	125	gaG/gaT	3/7	0.550558945777977	2	FACETS	0.878	0.819	0.937	0.878	0.819	0.937	CLONAL	2	TRUE	0	0.586735699145289	2		305	297	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106321	27106322	+	missense_variant	Missense_Mutation	DNP	GC	GC	AT	novel	NA	P-0027414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	111	565	2	ENST00000324856.7:c.5932_5933delinsAT	p.Ala1978Ile	p.A1978I	ENST00000324856	NM_006015.4	1978	GCc/ATc	20/20	0.586735699145289	1	FACETS	0.435	0.392	0.481	0.435	0.392	0.481	SUBCLONAL	1	TRUE	0	0.586735699145289	1		567	614	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012898	176012898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	205	644	1	ENST00000367669.3:c.1478G>A	p.Gly493Asp	p.G493D	ENST00000367669	NM_022457.5	493	gGc/gAc	13/20	1	2	FACETS	0.993	0.924	1	0.993	0.924	1	CLONAL	1	TRUE	1	0.586735699145289	2		645	704	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828096	243828096	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	198	548	0	ENST00000263826.5:c.262C>A	p.His88Asn	p.H88N	ENST00000263826	NM_005465.4	88	Cat/Aat	3/13	1	2	FACETS	0.91	0.845	0.976	0.91	0.845	0.976	CLONAL	1	TRUE	1	0.586735699145289	2		548	742	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712793	43712793	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	238	761	0	ENST00000382044.4:c.4391G>T	p.Arg1464Leu	p.R1464L	ENST00000382044	NM_001141980.1	1464	cGt/cTt	21/28	1	2	FACETS	0.917	0.857	0.978	0.917	0.857	0.978	CLONAL	1	TRUE	1	0.586735699145289	2		761	885	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719125	52719125	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	199	669	0	ENST00000322088.6:c.901G>T	p.Ala301Ser	p.A301S	ENST00000322088	NM_014225.5	301	Gca/Tca	7/15	1	2	FACETS	0.932	0.866	1	0.932	0.866	1	CLONAL	1	TRUE	1	0.586735699145289	2		669	728	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967293	134967293	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	236	728	1	ENST00000398015.3:c.2632C>A	p.Leu878Ile	p.L878I	ENST00000398015	NM_004441.4	878	Cta/Ata	14/16	0.413101754634286	3	FACETS	1	0.983	1	0.575	0.537	0.614	CLONAL	1	TRUE	1	0.586735699145289	3		729	905	SUCCESS
ATR	545	MSKCC	GRCh37	3	142177868	142177868	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	406	549	0	ENST00000350721.4:c.7435G>A	p.Glu2479Lys	p.E2479K	ENST00000350721	NM_001184.3	2479	Gaa/Aaa	44/47	0.413101754634286	3	FACETS	0.912	0.871	0.954	0.912	0.871	0.954	CLONAL	2	TRUE	1	0.586735699145289	3		549	981	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295276	1295276	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0027414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	127	446	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.586735699145289	2		446	338	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0027415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	25	425	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.507	0.398	0.634	0.507	0.398	0.634	SUBCLONAL	1	TRUE	1	0.15	2		425	657	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	133	345	8	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.879	0.797	0.965	1	0.989	1	CLONAL	2	TRUE	1	0.16	2		353	946	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	45	359	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.825	0.692	0.973	0.825	0.692	0.973	CLONAL	1	TRUE	1	0.16	2		359	682	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	38	320	1	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	1	0.826	1	1	0.826	1	CLONAL	1	TRUE	1	0.16	2		321	475	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	55	573	8	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.878	0.749	1	0.878	0.749	1	CLONAL	1	TRUE	1	0.16	2		581	783	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	70	654	0	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	0.842	0.732	0.962	0.842	0.732	0.962	CLONAL	1	TRUE	1	0.16	2		654	1039	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40743950	40743950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781527200	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	87	769	1	ENST00000392038.2:c.757C>T	p.Arg253Trp	p.R253W	ENST00000392038	NM_001626.4	253	Cgg/Tgg	9/14	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.16	2		770	1062	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160451	108160451	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	79	718	2	ENST00000278616.4:c.4363del	p.Ser1455ValfsTer3	p.S1455Vfs*3	ENST00000278616	NM_000051.3	1453	atA/at	29/63	1	2	FACETS	0.819	0.718	0.928	0.819	0.718	0.928	CLONAL	1	TRUE	1	0.16	2		720	1206	SUCCESS
AR	367	MSKCC	GRCh37	X	66766357	66766389	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	-	rs746853821	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	13	177	1	ENST00000374690.3:c.1388_1420del	p.Gly463_Gly473del	p.G463_G473del	ENST00000374690	NM_000044.3	457	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC/-	1/8	1	1	FACETS	0.579	0.413	0.783	0.579	0.413	0.783	SUBCLONAL	1	TRUE	0	0.16	1		178	258	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	35	519	0	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	0.683	0.558	0.823	0.683	0.558	0.823	SUBCLONAL	1	TRUE	1	0.16	2		519	641	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149596	202149596	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	60	517	0	ENST00000358485.4:c.1037G>A	p.Cys346Tyr	p.C346Y	ENST00000358485	NM_001080125.1	346	tGc/tAc	8/9	1	2	FACETS	0.872	0.75	1	0.872	0.75	1	CLONAL	1	TRUE	1	0.16	2		517	860	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261555	142261555	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	81	576	3	ENST00000350721.4:c.3402del	p.Phe1134LeufsTer6	p.F1134Lfs*6	ENST00000350721	NM_001184.3	1134	ttT/tt	17/47	1	2	FACETS	0.841	0.738	0.952	0.841	0.738	0.952	CLONAL	1	TRUE	1	0.16	2		579	1204	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412898	49412898	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519954	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	71	531	0	ENST00000418115.1:c.125A>G	p.Tyr42Cys	p.Y42C	ENST00000418115	NM_001664.2	42	tAt/tGt	2/5	1	2	FACETS	0.692	0.602	0.791	0.692	0.602	0.791	SUBCLONAL	1	TRUE	1	0.16	2		531	1282	SUCCESS
APC	324	MSKCC	GRCh37	5	112174751	112174753	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs386833391	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	44	437	0	ENST00000257430.4:c.3468_3470del	p.Glu1157del	p.E1157del	ENST00000257430	NM_000038.5	1154	GAA/-	16/16	1	2	FACETS	0.744	0.622	0.88	0.744	0.622	0.88	SUBCLONAL	1	TRUE	1	0.16	2		437	739	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599234	28599234	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	62	743	1	ENST00000253063.3:c.685del	p.Gln229ArgfsTer18	p.Q229Rfs*18	ENST00000253063	NM_031459.4	227	gCc/gc	5/10	1	2	FACETS	0.818	0.704	0.941	0.818	0.704	0.941	CLONAL	1	TRUE	1	0.16	2		744	948	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	54	699	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	0.638	0.543	0.743	0.638	0.543	0.743	SUBCLONAL	1	TRUE	1	0.16	2		699	1058	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391358	84391358	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1560574509	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	70	654	0	ENST00000321945.7:c.474del	p.Gly159AspfsTer8	p.G159Dfs*8	ENST00000321945	NM_139076.2	158	aaA/aa	5/9	1	2	FACETS	0.773	0.672	0.883	0.773	0.672	0.883	SUBCLONAL	1	TRUE	1	0.16	2		654	1132	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527398	157527398	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	71	624	0	ENST00000346085.5:c.5127del	p.Ala1710HisfsTer56	p.A1710Hfs*56	ENST00000346085	NM_020732.3	1708	cAa/ca	20/20	1	2	FACETS	0.966	0.841	1	0.966	0.841	1	CLONAL	1	TRUE	1	0.16	2		624	919	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131978019	131978019	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs201766077	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	69	659	0	ENST00000265335.6:c.3902A>G	p.Lys1301Arg	p.K1301R	ENST00000265335		1301	aAa/aGa	25/25	1	2	FACETS	0.804	0.698	0.919	0.804	0.698	0.919	CLONAL	1	TRUE	1	0.16	2		659	1073	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599271	28599271	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs770146088	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	73	774	0	ENST00000253063.3:c.722del	p.Pro241GlnfsTer6	p.P241Qfs*6	ENST00000253063	NM_031459.4	239	agC/ag	5/10	1	2	FACETS	0.812	0.708	0.925	0.812	0.708	0.925	CLONAL	1	TRUE	1	0.16	2		774	1124	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226465	133226465	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1024652254	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	43	426	0	ENST00000320574.5:c.3593C>T	p.Ala1198Val	p.A1198V	ENST00000320574	NM_006231.2	1198	gCc/gTc	30/49	1	2	FACETS	0.902	0.754	1	0.902	0.754	1	CLONAL	1	TRUE	1	0.16	2		426	596	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371824	55371824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	16	90	1	ENST00000297316.4:c.514G>A	p.Gly172Ser	p.G172S	ENST00000297316	NM_022454.3	172	Ggc/Agc	2/2	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.16	2		91	134	SUCCESS
AR	367	MSKCC	GRCh37	X	66905906	66905906	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137852573	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	60	318	0	ENST00000374690.3:c.1823G>A	p.Arg608Gln	p.R608Q	ENST00000374690	NM_000044.3	608	cGa/cAa	3/8	1	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.16	1		318	530	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129156	152129156	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	61	772	3	ENST00000206249.3:c.109C>T	p.Arg37Trp	p.R37W	ENST00000206249	NM_000125.3	37	Cgg/Tgg	1/8	1	2	FACETS	0.816	0.702	0.941	0.816	0.702	0.941	CLONAL	1	TRUE	1	0.16	2		775	934	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741657	17741657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	55	398	1	ENST00000250003.3:c.328C>T	p.Arg110Cys	p.R110C	ENST00000250003	NM_002478.4	110	Cgc/Tgc	1/3	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.16	2		399	563	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190639	11190639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150639035	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	58	563	0	ENST00000361445.4:c.5560G>A	p.Glu1854Lys	p.E1854K	ENST00000361445	NM_004958.3	1854	Gag/Aag	39/58	1	2	FACETS	0.823	0.705	0.952	0.823	0.705	0.952	CLONAL	1	TRUE	1	0.16	2		563	881	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201703	67201703	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	55	756	0	ENST00000312629.5:c.1004A>G	p.Asp335Gly	p.D335G	ENST00000312629	NM_003952.2	335	gAc/gGc	12/15	1	2	FACETS	0.701	0.597	0.815	0.701	0.597	0.815	SUBCLONAL	1	TRUE	1	0.16	2		756	981	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924702	94924702	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1292	108	752	1	ENST00000536441.1:c.208G>T	p.Gly70Cys	p.G70C	ENST00000536441	NM_144665.3	70	Ggt/Tgt	3/10	1	2	FACETS	0.964	0.862	1	0.964	0.862	1	CLONAL	1	TRUE	1	0.16	2		753	1400	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524232	18524232	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	76	648	1	ENST00000266497.5:c.1744C>A	p.Leu582Met	p.L582M	ENST00000266497		582	Ctg/Atg	11/31	0.3	2	FACETS	0.846	0.74	0.961			1	CLONAL	1	TRUE	NA	0.16	2		649	1123	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431159	49431160	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1555190198	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	67	702	0	ENST00000301067.7:c.9979dup	p.Gln3327ProfsTer96	p.Q3327Pfs*96	ENST00000301067	NM_003482.3	3327	cag/cCag	34/54	1	2	FACETS	0.926	0.803	1	0.926	0.803	1	CLONAL	1	TRUE	1	0.16	2		702	904	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572385	95572385	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	47	497	0	ENST00000393063.1:c.2980T>G	p.Ser994Ala	p.S994A	ENST00000393063	NM_030621.3	994	Tct/Gct	19/28	1	2	FACETS	0.738	0.621	0.868	0.738	0.621	0.868	SUBCLONAL	1	TRUE	1	0.16	2		497	796	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105238776	105238776	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	61	674	0	ENST00000349310.3:c.1186T>C	p.Ser396Pro	p.S396P	ENST00000349310	NM_001014432.1	396	Tcc/Ccc	13/15	1	2	FACETS	0.852	0.733	0.982	0.852	0.733	0.982	CLONAL	1	TRUE	1	0.16	2		674	895	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994778	73994778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11574476	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	64	610	0	ENST00000318443.5:c.262G>A	p.Ala88Thr	p.A88T	ENST00000318443	NM_001024736.1	88	Gcc/Acc	3/10	1	2	FACETS	0.886	0.765	1	0.886	0.765	1	CLONAL	1	TRUE	1	0.16	2		610	903	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120560	2120560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397515296	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	89	794	0	ENST00000219476.3:c.1820C>T	p.Ala607Val	p.A607V	ENST00000219476	NM_000548.3	607	gCg/gTg	17/42	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.16	2		794	1057	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639276	3639276	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	70	710	0	ENST00000294008.3:c.4363A>G	p.Ser1455Gly	p.S1455G	ENST00000294008	NM_032444.2	1455	Agc/Ggc	12/15	1	2	FACETS	0.954	0.83	1	0.954	0.83	1	CLONAL	1	TRUE	1	0.16	2		710	917	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070597	67070597	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	40	390	0	ENST00000412916.2:c.221A>G	p.Gln74Arg	p.Q74R	ENST00000412916		74	cAg/cGg	3/6	1	2	FACETS	0.732	0.607	0.872	0.732	0.607	0.872	SUBCLONAL	1	TRUE	1	0.16	2		390	683	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89383342	89383342	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	71	658	6	ENST00000301030.4:c.86del	p.Lys29ArgfsTer8	p.K29Rfs*8	ENST00000301030	NM_001256183.1	29	aAg/ag	3/13	1	2	FACETS	0.98	0.853	1	0.98	0.853	1	CLONAL	1	TRUE	1	0.16	2		664	906	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485960	40485960	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1161466672	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	98	731	2	ENST00000264657.5:c.905G>A	p.Arg302Gln	p.R302Q	ENST00000264657	NM_139276.2	302	cGg/cAg	9/24	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.16	2		733	1166	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699382	47699382	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	57	509	0	ENST00000347630.2:c.126C>G	p.Ser42Arg	p.S42R	ENST00000347630	NM_001007230.1	42	agC/agG	4/11	1	2	FACETS	0.713	0.61	0.827	0.713	0.61	0.827	SUBCLONAL	1	TRUE	1	0.16	2		509	999	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600424	10600425	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	84	797	1	ENST00000171111.5:c.1430dup	p.Phe478LeufsTer2	p.F478Lfs*2	ENST00000171111	NM_203500.1	477	ggc/ggGc	4/6	1	2	FACETS	0.973	0.857	1	0.973	0.857	1	CLONAL	1	TRUE	1	0.16	2		798	1079	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383639	42383639	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	57	625	0	ENST00000221972.3:c.414G>T	p.Glu138Asp	p.E138D	ENST00000221972	NM_021601.3	138	gaG/gaT	3/5	1	2	FACETS	0.919	0.787	1	0.919	0.787	1	CLONAL	1	TRUE	1	0.16	2		625	775	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936572	49936572	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	85	819	0	ENST00000296474.3:c.1355A>G	p.Tyr452Cys	p.Y452C	ENST00000296474	NM_002447.2	452	tAt/tGt	2/20	1	2	FACETS	0.958	0.844	1	0.958	0.844	1	CLONAL	1	TRUE	1	0.16	2		819	1109	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	256507	256507	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	62	556	0	ENST00000264932.6:c.1967C>T	p.Thr656Ile	p.T656I	ENST00000264932	NM_004168.2	656	aCc/aTc	15/15	1	2	FACETS	0.855	0.737	0.985	0.855	0.737	0.985	CLONAL	1	TRUE	1	0.16	2		556	906	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962991	38962991	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs757361003	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	40	339	0	ENST00000357387.3:c.1553T>C	p.Ile518Thr	p.I518T	ENST00000357387	NM_152756.3	518	aTa/aCa	17/38	1	2	FACETS	0.846	0.702	1	0.846	0.702	1	CLONAL	1	TRUE	1	0.16	2		339	591	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047668	180047668	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs527697511	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	61	795	3	ENST00000261937.6:c.2347G>A	p.Gly783Ser	p.G783S	ENST00000261937	NM_182925.4	783	Ggc/Agc	16/30	0.3	2	FACETS	0.741	0.637	0.855			1	SUBCLONAL	1	TRUE	NA	0.16	2		798	1029	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401690	401690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1182121626	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	56	612	0	ENST00000380956.4:c.1012G>A	p.Gly338Arg	p.G338R	ENST00000380956	NM_001195286.1	338	Ggg/Agg	7/9	1	2	FACETS	0.858	0.733	0.995	0.858	0.733	0.995	CLONAL	1	TRUE	1	0.16	2		612	816	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951811	2951811	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146334064	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	115	661	2	ENST00000396946.4:c.3139G>A	p.Ala1047Thr	p.A1047T	ENST00000396946	NM_032415.4	1047	Gcc/Acc	23/25	1	2	FACETS	0.765	0.689	0.847	1	0.984	1	SUBCLONAL	2	TRUE	1	0.16	2		663	939	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467987	50467987	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	45	541	0	ENST00000331340.3:c.1222C>T	p.Arg408Cys	p.R408C	ENST00000331340	NM_006060.4	408	Cgc/Tgc	8/8	1	2	FACETS	0.726	0.608	0.857	0.726	0.608	0.857	SUBCLONAL	1	TRUE	1	0.16	2		541	775	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141557712	141557712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767897587	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	73	605	0	ENST00000220592.5:c.1603G>A	p.Val535Met	p.V535M	ENST00000220592	NM_012154.3	535	Gtg/Atg	13/19	1	2	FACETS	0.923	0.805	1	0.923	0.805	1	CLONAL	1	TRUE	1	0.16	2		605	989	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97869538	97869538	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	39	553	0	ENST00000289081.3:c.1343C>T	p.Ala448Val	p.A448V	ENST00000289081	NM_000136.2	448	gCc/gTc	14/15	1	2	FACETS	0.678	0.56	0.81	0.678	0.56	0.81	SUBCLONAL	1	TRUE	1	0.16	2		553	719	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0027417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	274	597	2	ENST00000311936.3:c.34_35delinsCT	p.Gly12Leu	p.G12L	ENST00000311936	NM_004985.3	12	GGt/CTt	2/5	0.350857149514453	3	FACETS	0.931	0.875	0.988	0.931	0.875	0.988	CLONAL	2	TRUE	1	0.350857149514453	3		599	986	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0027417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	177	560	0	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.350857149514453	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.350857149514453	1		560	769	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522359	157522359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1333892657	NA	P-0027417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	198	694	0	ENST00000346085.5:c.4631C>T	p.Pro1544Leu	p.P1544L	ENST00000346085	NM_020732.3	1544	cCg/cTg	18/20	1	2	FACETS	0.921	0.851	0.993	0.921	0.851	0.993	CLONAL	1	TRUE	1	0.350857149514453	2		694	1226	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0027420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	53	429	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.216246442290258	3	FACETS	1	0.877	1	0.516	0.44	0.599	CLONAL	1	TRUE	1	0.219771481315223	3		429	519	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0027420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	78	673	0	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.219771481315223	1	FACETS	0.842	0.745	0.946	1	0.981	1	CLONAL	2	TRUE	0	0.219771481315223	1		673	375	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603038	48603039	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCAGCAGCAGGCGGCTACTGCACAAGC	rs876660720	NA	P-0027420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	17	350	0	ENST00000342988.3:c.1349_1376dup	p.Ala460GlyfsTer43	p.A460Gfs*43	ENST00000342988	NM_005359.5	447	atg/aTGCAGCAGCAGGCGGCTACTGCACAAGCtg	11/12	0.219771481315223	1	FACETS	0.569	0.425	0.74	0.569	0.425	0.74	SUBCLONAL	1	TRUE	0	0.219771481315223	1		350	242	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214395	5214395	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772384138	NA	P-0027420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	41	502	0	ENST00000357368.4:c.4591G>A	p.Val1531Ile	p.V1531I	ENST00000357368	NM_002850.3	1531	Gtc/Atc	30/38	0.219771481315223	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.219771481315223	1		502	284	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016166	31016166	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	49	576	0	ENST00000375687.4:c.412A>G	p.Thr138Ala	p.T138A	ENST00000375687	NM_015338.5	138	Aca/Gca	6/13	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.219771481315223	2		576	373	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0027421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	118	429	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.0931937807313843	3	FACETS	0.97	0.877	1	1	0.984	1	CLONAL	3	TRUE	1	0.14	3		429	620	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057520000	NA	P-0027421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	53	647	0	ENST00000269305.4:c.452C>G	p.Pro151Arg	p.P151R	ENST00000269305	NM_001126112.2	151	cCc/cGc	5/11	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.14	2		647	757	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81574763	81574763	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs530605964	NA	P-0027421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	34	534	0	ENST00000298171.2:c.659C>A	p.Ala220Glu	p.A220E	ENST00000298171	NM_000369.2	220	gCa/gAa	8/10	1	2	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	TRUE	1	0.14	2		534	466	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295198	1295198	+	upstream_gene_variant	5'Flank	SNP	A	A	C	novel	NA	P-0027421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	16	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.822	0.608	1	0.822	0.608	1	CLONAL	1	TRUE	1	0.14	2		215	278	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306977	65306977	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	161	446	0	ENST00000342505.4:c.2600C>A	p.Pro867His	p.P867H	ENST00000342505	NM_002227.2	867	cCc/cAc	19/25	0.351818711963131	1	FACETS	0.993	0.912	1	0.993	0.912	1	CLONAL	1	TRUE	0	0.354034574630919	1		446	754	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273016	115273016	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	118	510	0	ENST00000438362.2:c.1357G>A	p.Ala453Thr	p.A453T	ENST00000438362	NM_001242891.1	453	Gct/Act	12/20	0.351818711963131	1	FACETS	0.759	0.685	0.836	0.759	0.685	0.836	SUBCLONAL	1	TRUE	0	0.354034574630919	1		510	723	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005535	42005535	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0027423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	188	510	0	ENST00000219905.7:c.3271A>T	p.Lys1091Ter	p.K1091*	ENST00000219905	NM_001164273.1	1091	Aaa/Taa	9/24	0.351818711963131	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.354034574630919	1		510	868	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978984	25978984	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0027423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	97	414	0	ENST00000435504.4:c.940-1G>A		p.X314_splice	ENST00000435504		314			0.351818711963131	1	FACETS	0.808	0.722	0.899	0.808	0.722	0.899	CLONAL	1	TRUE	0	0.354034574630919	1		414	558	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0027424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	56	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.12	2		509	906	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0027424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	37	500	2	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.774	0.636	0.929	0.774	0.636	0.929	CLONAL	1	TRUE	1	0.12	2		502	797	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533552	533552	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	575	763	0	ENST00000451590.1:c.351G>C	p.Lys117Asn	p.K117N	ENST00000451590	NM_001130442.1	117	aaG/aaC	4/5	0.728196106499275	4	FACETS	0.993	0.956	1	0.993	0.956	1	CLONAL	2	TRUE	2	0.862521902309153	4		763	1251	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597495	52597495	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	315	377	0	ENST00000394830.3:c.3815del	p.Pro1272LeufsTer16	p.P1272Lfs*16	ENST00000394830	NM_018313.4	1272	cCt/ct	25/30	0.862521902309153	2	FACETS	0.974	0.947	0.999	0.974	0.947	0.999	CLONAL	2	TRUE	0	0.862521902309153	2		377	375	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	242	528	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.136790284678052	3	FACETS	1	0.992	1	0.747	0.698	0.797	INDETERMINATE	1	TRUE	1	0.400713076083765	3		529	971	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0027427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	141	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.136790284678052	3	FACETS	0.87	0.792	0.952	0.435	0.396	0.476	INDETERMINATE	1	TRUE	1	0.400713076083765	3		509	971	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0027427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	32	480	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.158	0.127	0.193	0.158	0.127	0.193	SUBCLONAL	1	TRUE	1	0.400713076083765	2		480	1013	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214594	5214594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768496731	NA	P-0027427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	280	773	0	ENST00000357368.4:c.4472C>T	p.Thr1491Met	p.T1491M	ENST00000357368	NM_002850.3	1491	aCg/aTg	29/38	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.400713076083765	2		773	1362	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0027427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	326	302	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	0.400713076083765	2	FACETS	1	0.993	1	1	0.997	1	CLONAL	3	TRUE	0	0.400713076083765	2		302	468	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	360	694	0	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	1	2	FACETS	0.792	0.751	0.833	1	0.995	1	SUBCLONAL	2	TRUE	1	0.400713076083765	2		694	1135	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094327	27094327	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	333	615	1	ENST00000324856.7:c.3035del	p.Tyr1012LeufsTer27	p.Y1012Lfs*27	ENST00000324856	NM_006015.4	1012	tAt/tt	11/20	1	2	FACETS	0.827	0.783	0.871	1	0.995	1	CLONAL	2	TRUE	1	0.400713076083765	2		616	1005	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119877	70119878	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1237	66	671	0	ENST00000245479.2:c.882dup	p.Asp295Ter	p.D295*	ENST00000245479	NM_000346.3	293	-/T	3/3	1	2	FACETS	0.253	0.218	0.291	0.253	0.218	0.291	SUBCLONAL	1	TRUE	1	0.400713076083765	2		671	1303	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247253	153247253	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	357	578	0	ENST00000281708.4:c.1549G>A	p.Gly517Arg	p.G517R	ENST00000281708	NM_033632.3	517	Gga/Aga	10/12	1	2	FACETS	0.939	0.892	0.986	1	0.996	1	CLONAL	2	TRUE	1	0.400713076083765	2		578	949	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0027430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	295	574	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.474248378786082	2	FACETS	0.947	0.898	0.996	0.947	0.898	0.996	CLONAL	2	TRUE	0	0.474248378786082	2		576	657	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0027430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	377	370	1	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.474248378786082	3	FACETS	0.99	0.95	1	0.99	0.95	1	CLONAL	3	TRUE	0	0.474248378786082	3		371	662	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247294	153247294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	580	468	0	ENST00000281708.4:c.1508C>T	p.Ala503Val	p.A503V	ENST00000281708	NM_033632.3	503	gCa/gTa	10/12	0.474248378786082	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	4	TRUE	0	0.474248378786082	4		468	886	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942515	17942515	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149452625	NA	P-0027430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	383	651	0	ENST00000458235.1:c.2773C>T	p.Arg925Cys	p.R925C	ENST00000458235	NM_000215.3	925	Cgc/Tgc	20/24	0.474248378786082	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.474248378786082	3		651	920	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647026	23647026	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs751882053	NA	P-0027430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	164	682	0	ENST00000261584.4:c.841A>T	p.Ile281Phe	p.I281F	ENST00000261584	NM_024675.3	281	Att/Ttt	4/13	0.368710333844884	4	FACETS	0.936	0.858	1	0.468	0.429	0.509	CLONAL	1	TRUE	2	0.474248378786082	4		682	1089	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26046009	26046009	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	111	348	0	ENST00000540144.1:c.371A>G	p.Asp124Gly	p.D124G	ENST00000540144	NM_003531.2	124	gAt/gGt	1/1	0.446120546510431	4	FACETS	1	0.972	1	0.605	0.546	0.668	CLONAL	1	TRUE	2	0.474248378786082	4		348	570	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0027432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	136	449	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.739104727642864	2		449	349	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942515	17942515	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149452625	NA	P-0027432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	59	651	0	ENST00000458235.1:c.2773C>T	p.Arg925Cys	p.R925C	ENST00000458235	NM_000215.3	925	Cgc/Tgc	20/24	0.739104727642864	3	FACETS	0.23	0.197	0.267	0.115	0.098	0.134	SUBCLONAL	1	TRUE	1	0.739104727642864	3		651	949	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0027432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5590	15040	714	3	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.739104727642864	37	FACETS	1	0.999	1			1	CLONAL	27	TRUE	NA	0.739104727642864	37		717	20630	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755351	39755351	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	191	502	0	ENST00000288319.7:c.1414C>T	p.Pro472Ser	p.P472S	ENST00000288319	NM_182918.3	472	Cct/Tct	10/10	1	2	FACETS	0.947	0.882	1	0.947	0.882	1	CLONAL	1	TRUE	1	0.739104727642864	2		502	546	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0027434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	144	650	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.442501732639557	3	FACETS	0.997	0.91	1	0.499	0.455	0.544	CLONAL	1	TRUE	1	0.442501732639557	3		651	797	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0027434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	133	487	2	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.442501732639557	3	FACETS	0.853	0.774	0.935	0.426	0.387	0.468	CLONAL	1	TRUE	1	0.442501732639557	3		489	861	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584513	48584514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs377767334	NA	P-0027434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	110	360	0	ENST00000342988.3:c.692dup	p.Ser232GlnfsTer3	p.S232Qfs*3	ENST00000342988	NM_005359.5	229	ctg/ctGg	6/12	0.425728249236243	1	FACETS	0.954	0.864	1	0.954	0.864	1	CLONAL	1	TRUE	0	0.442501732639557	1		360	406	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856604	111856604	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1177556874	NA	P-0027434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	124	423	4	ENST00000341259.2:c.655C>T	p.Arg219Cys	p.R219C	ENST00000341259	NM_005475.2	219	Cgc/Tgc	2/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.442501732639557	2		427	389	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424206	47424206	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs756771141	NA	P-0027434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	57	542	0	ENST00000377045.4:c.211G>T	p.Val71Phe	p.V71F	ENST00000377045	NM_001654.4	71	Gtc/Ttc	4/16	1	2	FACETS	0.504	0.433	0.582	0.504	0.433	0.582	SUBCLONAL	1	TRUE	1	0.442501732639557	2		542	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579575	7579575	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	38	613	0	ENST00000269305.4:c.112C>T	p.Gln38Ter	p.Q38*	ENST00000269305	NM_001126112.2	38	Caa/Taa	4/11	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.13	2		613	524	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0027435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	25	439	0	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	1	2	FACETS	0.787	0.619	0.981	0.787	0.619	0.981	CLONAL	1	TRUE	1	0.13	2		439	489	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486292	8486292	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	24	313	0	ENST00000356435.5:c.2525A>G	p.Gln842Arg	p.Q842R	ENST00000356435		842	cAg/cGg	17/35	1	2	FACETS	0.881	0.69	1	0.881	0.69	1	CLONAL	1	TRUE	1	0.13	2		313	419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0027436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	321	857	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	0.448286538779614	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	FALSE	0	0.44312187775992	3		857	551	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0027436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	153	467	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.179446909557712	6	FACETS	1	0.969	1			1	INDETERMINATE	3	FALSE	NA	0.44312187775992	6		468	399	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256265	16256265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	105	612	0	ENST00000375759.3:c.3530G>A	p.Arg1177His	p.R1177H	ENST00000375759	NM_015001.2	1177	cGt/cAt	11/15	0.44312187775992	6	FACETS	1	0.98	1			1	CLONAL	1	FALSE	NA	0.44312187775992	6		612	640	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135804188	135804188	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	33	573	0	ENST00000298552.3:c.72C>A	p.Asp24Glu	p.D24E	ENST00000298552	NM_001162426.1	24	gaC/gaA	3/23	1	2	FACETS	0.254	0.206	0.308	0.254	0.206	0.308	SUBCLONAL	1	NA	1	0.445515374062568	2		573	583	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0027440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	277	718	0	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	0.673324339396985	1	FACETS	0.933	0.885	0.981	0.933	0.885	0.981	CLONAL	1	TRUE	0	0.681658918338978	1		718	574	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481659	56481659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140656187	NA	P-0027440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	310	769	1	ENST00000267101.3:c.694G>A	p.Ala232Thr	p.A232T	ENST00000267101	NM_001982.3	232	Gcc/Acc	6/28	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.681658918338978	2		770	886	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654858	29654858	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0027440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	71	234	0	ENST00000356175.3:c.5546+1G>T		p.X1849_splice	ENST00000356175	NM_000267.3	1849			0.673324339396985	1	FACETS	0.776	0.693	0.861	0.776	0.693	0.861	SUBCLONAL	1	TRUE	0	0.681658918338978	1		234	177	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155977	119155977	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	272	676	0	ENST00000264033.4:c.1642C>A	p.Pro548Thr	p.P548T	ENST00000264033	NM_005188.3	548	Cca/Aca	11/16	0.681658918338978	2	FACETS	0.929	0.874	0.985	0.465	0.437	0.493	CLONAL	1	TRUE	0	0.681658918338978	2		676	859	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986730	36986730	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	68	146	0	ENST00000354822.5:c.959C>T	p.Ala320Val	p.A320V	ENST00000354822	NM_001079668.2	320	gCg/gTg	3/3	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.681658918338978	2		146	171	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492758	56492758	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2280	226	720	0	ENST00000407977.2:c.181C>G	p.Leu61Val	p.L61V	ENST00000407977		61	Ctg/Gtg	2/10	0.681658918338978	9	FACETS	0.896	0.83	0.965			1	CLONAL	1	TRUE	NA	0.681658918338978	9		720	2506	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763472	41763472	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	270	672	0	ENST00000301178.4:c.2271G>C	p.Glu757Asp	p.E757D	ENST00000301178	NM_021913.4	757	gaG/gaC	19/20	1	2	FACETS	0.956	0.899	1	0.956	0.899	1	CLONAL	1	TRUE	1	0.681658918338978	2		672	829	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368382	225368382	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	145	398	0	ENST00000264414.4:c.1364T>C	p.Ile455Thr	p.I455T	ENST00000264414	NM_003590.4	455	aTa/aCa	9/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.681658918338978	2		398	389	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30733006	30733006	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	174	460	0	ENST00000295754.5:c.1619A>C	p.Glu540Ala	p.E540A	ENST00000295754	NM_003242.5	540	gAg/gCg	7/7	1	2	FACETS	0.98	0.909	1	0.98	0.909	1	CLONAL	1	TRUE	1	0.681658918338978	2		460	521	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447278	187447279	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0027440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	182	582	0	ENST00000232014.4:c.914_915del	p.Arg305ThrfsTer6	p.R305Tfs*6	ENST00000232014	NM_001130845.1	305	aGA/a	5/10	1	2	FACETS	0.782	0.724	0.842	0.782	0.724	0.842	SUBCLONAL	1	TRUE	1	0.681658918338978	2		582	683	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180035985	180035985	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	280	818	0	ENST00000261937.6:c.3876A>C	p.Arg1292Ser	p.R1292S	ENST00000261937	NM_182925.4	1292	agA/agC	29/30	1	2	FACETS	0.934	0.879	0.989	0.934	0.879	0.989	CLONAL	1	TRUE	1	0.681658918338978	2		818	880	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0027441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	680	443	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.863288698042111	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.863288698042111	3		443	740	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257339	16257339	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	646	653	1	ENST00000375759.3:c.4604T>A	p.Ile1535Asn	p.I1535N	ENST00000375759	NM_015001.2	1535	aTc/aAc	11/15	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.863288698042111	2		654	737	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361125	70361125	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	275	564	1	ENST00000374080.3:c.6313C>A	p.Gln2105Lys	p.Q2105K	ENST00000374080		2105	Caa/Aaa	43/45	0.70073019827544	3	FACETS	1	0.966	1	0.519	0.488	0.55	CLONAL	1	TRUE	1	0.863288698042111	3		565	879	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0027442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	156	344	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.265660028422143	3	FACETS	0.951	0.874	1	0.951	0.874	1	CLONAL	2	TRUE	1	0.292020456137369	3		345	644	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0027442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	89	467	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.292020456137369	3	FACETS	0.984	0.872	1	0.492	0.436	0.552	CLONAL	1	TRUE	1	0.292020456137369	3		468	710	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933047	39933047	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	39	359	2	ENST00000378444.4:c.1552G>T	p.Glu518Ter	p.E518*	ENST00000378444	NM_001123385.1	518	Gaa/Taa	4/15	1	1	FACETS	0.425	0.351	0.507	0.425	0.351	0.507	SUBCLONAL	1	TRUE	0	0.292020456137369	1		361	537	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259044	89259044	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	108	260	0	ENST00000336596.2:c.188C>A	p.Thr63Lys	p.T63K	ENST00000336596	NM_005233.5	63	aCa/aAa	3/17	0.265660028422143	3	FACETS	1	0.921	1	1	0.921	1	CLONAL	2	TRUE	1	0.292020456137369	3		260	415	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987025	36987025	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1555349209	NA	P-0027442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	369	556	0	ENST00000354822.5:c.664G>T	p.Glu222Ter	p.E222*	ENST00000354822	NM_001079668.2	222	Gag/Tag	3/3	0.292020456137369	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.292020456137369	3		556	860	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023145	27023162	+	inframe_deletion	In_Frame_Del	DEL	GCGGCGGCGGAGCCGGCA	GCGGCGGCGGAGCCGGCA	-	rs749452696	NA	P-0027442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	108	123	2	ENST00000324856.7:c.261_278del	p.Ala88_Gly93del	p.A88_G93del	ENST00000324856	NM_006015.4	84	gGCGGCGGCGGAGCCGGCAgc/ggc	1/20	1	2	FACETS	1	0.941	1	1	0.989	1	CLONAL	2	TRUE	1	0.292020456137369	2		125	352	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575193	48575193	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	97	329	0	ENST00000342988.3:c.387T>G	p.Asn129Lys	p.N129K	ENST00000342988	NM_005359.5	129	aaT/aaG	3/12	0.292020456137369	3	FACETS	0.873	0.783	0.968	0.582	0.522	0.645	CLONAL	2	TRUE	0	0.292020456137369	3		329	436	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028024	48028029	+	inframe_deletion	In_Frame_Del	DEL	GTCTAT	GTCTAT	-	novel	NA	P-0027442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	124	321	0	ENST00000234420.5:c.2902_2907del	p.Val968_Tyr969del	p.V968_Y969del	ENST00000234420	NM_000179.2	968	GTCTAT/-	4/10	0.292020456137369	3	FACETS	0.871	0.791	0.954	0.871	0.791	0.954	CLONAL	2	TRUE	1	0.292020456137369	3		321	559	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295045	1295045	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	46	198	0	ENST00000310581.5:c.60G>T	p.Glu20Asp	p.E20D	ENST00000310581	NM_198253.2	20	gaG/gaT	1/16	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.292020456137369	2		198	299	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858188	27858188	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	104	496	1	ENST00000359303.2:c.383C>A	p.Ala128Glu	p.A128E	ENST00000359303	NM_003535.2	128	gCg/gAg	1/1	0.292020456137369	3	FACETS	1	0.902	1	0.504	0.451	0.56	CLONAL	1	TRUE	1	0.292020456137369	3		497	810	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646186	3646186	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	234	691	0	ENST00000294008.3:c.1892G>C	p.Ser631Thr	p.S631T	ENST00000294008	NM_032444.2	631	aGt/aCt	8/15	0.561967954827736	3	FACETS	0.947	0.883	1	0.474	0.441	0.507	CLONAL	1	TRUE	1	0.572403497042196	3		691	1110	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40447672	40447672	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754394984	NA	P-0027443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	211	580	1	ENST00000345506.4:c.411G>A	p.Met137Ile	p.M137I	ENST00000345506	NM_003152.3	137	atG/atA	6/20	0.5522739714822	3	FACETS	1	0.939	1	0.505	0.47	0.543	CLONAL	1	TRUE	1	0.572403497042196	3		581	938	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39726922	39726922	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	78	367	0	ENST00000361337.2:c.920A>G	p.Gln307Arg	p.Q307R	ENST00000361337	NM_003286.2	307	cAg/cGg	11/21	1	2	FACETS	0.984	0.875	1	0.984	0.875	1	CLONAL	1	TRUE	1	0.572403497042196	2		367	277	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167520	24167520	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	250	640	1	ENST00000263121.7:c.904G>T	p.Gly302Trp	p.G302W	ENST00000263121	NM_003073.3	302	Ggg/Tgg	7/9	1	2	FACETS	0.997	0.935	1	0.997	0.935	1	CLONAL	1	TRUE	1	0.572403497042196	2		641	876	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421255	12421255	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	179	561	0	ENST00000287820.6:c.135del	p.Ser46AlafsTer7	p.S46Afs*7	ENST00000287820	NM_015869.4	45	atC/at	2/7	0.5522739714822	3	FACETS	0.976	0.901	1	0.488	0.45	0.527	CLONAL	1	TRUE	1	0.572403497042196	3		561	824	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251527	251527	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	181	325	0	ENST00000264932.6:c.1738T>G	p.Tyr580Asp	p.Y580D	ENST00000264932	NM_004168.2	580	Tac/Gac	13/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.572403497042196	2		325	501	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878933	151878933	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	130	555	1	ENST00000262189.6:c.6012T>A	p.Ser2004Arg	p.S2004R	ENST00000262189	NM_170606.2	2004	agT/agA	36/59	0.5522739714822	3	FACETS	0.932	0.848	1	0.466	0.424	0.51	CLONAL	1	TRUE	1	0.572403497042196	3		556	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579366	7579366	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs770776262	NA	P-0027448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	193	820	0	ENST00000269305.4:c.321C>A	p.Tyr107Ter	p.Y107*	ENST00000269305	NM_001126112.2	107	taC/taA	4/11	0.256332102441066	1	FACETS	0.96	0.886	1	0.96	0.886	1	CLONAL	1	TRUE	0	0.281868947937583	1		820	1226	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396929	396929	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1411	145	867	0	ENST00000262320.3:c.97G>C	p.Val33Leu	p.V33L	ENST00000262320	NM_003502.3	33	Gtg/Ctg	2/11	1	2	FACETS	0.661	0.601	0.725	0.661	0.601	0.725	SUBCLONAL	1	TRUE	1	0.281868947937583	2		867	1556	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750387	39750388	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTAA	novel	NA	P-0027448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	44	522	0	ENST00000361337.2:c.2003_2006dup	p.Lys669AsnfsTer2	p.K669Nfs*2	ENST00000361337	NM_003286.2	668	gct/gCTAAct	19/21	0.281868947937583	1	FACETS	0.346	0.289	0.409	0.346	0.289	0.409	SUBCLONAL	1	TRUE	0	0.281868947937583	1		522	775	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054648	5054648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765286468	NA	P-0027448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	95	424	1	ENST00000381652.3:c.700C>T	p.Arg234Cys	p.R234C	ENST00000381652	NM_004972.3	234	Cgc/Tgc	7/25	1	2	FACETS	0.91	0.81	1	0.91	0.81	1	CLONAL	1	TRUE	1	0.281868947937583	2		425	741	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	269	315	1				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		316	554	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0027453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	369	574	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.498687036047356	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.498687036047356	2		576	683	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0027454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	87	583	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.807	0.716	0.905	0.807	0.716	0.905	CLONAL	1	TRUE	1	0.362341699413894	2		583	595	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038935	12038935	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	122	436	0	ENST00000396373.4:c.1228G>T	p.Glu410Ter	p.E410*	ENST00000396373	NM_001987.4	410	Gag/Tag	7/8	0.362341699413894	1	FACETS	0.946	0.858	1	0.946	0.858	1	CLONAL	1	TRUE	0	0.362341699413894	1		436	583	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579329	7579329	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912658	NA	P-0027456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	742	699	2	ENST00000269305.4:c.358A>G	p.Lys120Glu	p.K120E	ENST00000269305	NM_001126112.2	120	Aag/Gag	4/11	0.888537452523112	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.893505055515714	1		701	897	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0027456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	543	574	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.446654414301171	1	FACETS	0.69	0.666	0.713	0.69	0.666	0.713	INDETERMINATE	1	TRUE	0	0.893505055515714	1		574	975	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230397	46230397	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	167	467	1	ENST00000334344.6:c.731A>T	p.Asn244Ile	p.N244I	ENST00000334344	NM_152641.2	244	aAt/aTt	7/21	NA	2	FACETS	0.571	0.526	0.617			1	INDETERMINATE	1	TRUE	NA	0.893505055515714	2		468	655	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120803	115120803	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	248	582	0	ENST00000257566.3:c.203T>G	p.Leu68Trp	p.L68W	ENST00000257566	NM_016569.3	68	tTg/tGg	1/8	0.864065115758091	2	FACETS	0.584	0.547	0.623	0.292	0.273	0.312	SUBCLONAL	1	TRUE	0	0.893505055515714	2		582	950	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736924	736924	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	431	581	1	ENST00000314574.4:c.1175A>G	p.Tyr392Cys	p.Y392C	ENST00000314574	NM_005433.3	392	tAt/tGt	10/12	0.888537452523112	1	FACETS	0.99	0.964	1	0.99	0.964	1	CLONAL	1	TRUE	0	0.893505055515714	1		582	539	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56402522	56402522	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	172	293	0	ENST00000348428.3:c.1564G>T	p.Asp522Tyr	p.D522Y	ENST00000348428	NM_006785.3	522	Gat/Tat	13/17	0.888537452523112	1	FACETS	0.859	0.815	0.901	0.859	0.815	0.901	CLONAL	1	TRUE	0	0.893505055515714	1		293	248	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261477	142261518	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTTAGCACTCTGGAACTATCACCACTTACCATTTTCTTATC	TCTTAGCACTCTGGAACTATCACCACTTACCATTTTCTTATC	-	novel	NA	P-0027456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	101	347	0	ENST00000350721.4:c.3439_3450+30del		p.X1147_splice	ENST00000350721	NM_001184.3	1147		17/47	0.439195195092033	4	FACETS	0.615	0.55	0.684	0.154	0.137	0.171	INDETERMINATE	1	TRUE	0	0.893505055515714	4		347	696	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875944	76875944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	356	621	0	ENST00000373344.5:c.5191G>A	p.Val1731Ile	p.V1731I	ENST00000373344	NM_000489.3	1731	Gtt/Att	20/35	1	2	FACETS	0.749	0.709	0.789	0.749	0.709	0.789	SUBCLONAL	1	TRUE	1	0.76	2		621	1251	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0027459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	257	321	2	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		323	721	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0027468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	103	443	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.947	0.861	1	1	0.988	1	CLONAL	2	FALSE	1	0.407484259377965	2		443	267	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0027468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	105	326	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.974	1	1	0.99	1	CLONAL	2	FALSE	1	0.407484259377965	2		326	221	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577561	7577561	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs764342812	NA	P-0027468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	416	431	0	ENST00000269305.4:c.720T>G	p.Ser240Arg	p.S240R	ENST00000269305	NM_001126112.2	240	agT/agG	7/11	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	4	FALSE	NA	0.407484259377965	2		431	481	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890149	76890150	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	145	222	0	ENST00000373344.5:c.4744dup	p.Thr1582AsnfsTer19	p.T1582Nfs*19	ENST00000373344	NM_000489.3	1582	aca/aAca	17/35	1	1	FACETS	1	0.96	1	1	0.994	1	CLONAL	3	FALSE	0	0.407484259377965	1		222	187	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568656	41568656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	208	344	0	ENST00000263253.7:c.4606G>A	p.Glu1536Lys	p.E1536K	ENST00000263253	NM_001429.3	1536	Gaa/Aaa	28/31	1	2	FACETS	0.925	0.865	0.985	0.925	0.865	0.985	CLONAL	1	TRUE	1	0.820790060074999	2		344	548	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285014	15285014	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	198	569	0	ENST00000263388.2:c.4601G>A	p.Arg1534Gln	p.R1534Q	ENST00000263388	NM_000435.2	1534	cGg/cAg	25/33	0.297501596233493	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.820790060074999	0		569	566	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568662	41568662	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	191	320	0	ENST00000263253.7:c.4612A>T	p.Thr1538Ser	p.T1538S	ENST00000263253	NM_001429.3	1538	Aca/Tca	28/31	1	2	FACETS	0.904	0.843	0.966	0.904	0.843	0.966	CLONAL	1	TRUE	1	0.820790060074999	2		320	515	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444413	50444413	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	179	321	0	ENST00000331340.3:c.343G>T	p.Gly115Ter	p.G115*	ENST00000331340	NM_006060.4	115	Gga/Tga	4/8	1	2	FACETS	0.946	0.881	1	0.946	0.881	1	CLONAL	1	TRUE	1	0.820790060074999	2		321	461	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444481	50444481	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	125	252	0	ENST00000331340.3:c.411A>C	p.Arg137Ser	p.R137S	ENST00000331340	NM_006060.4	137	agA/agC	4/8	1	2	FACETS	0.878	0.804	0.953	0.878	0.804	0.953	CLONAL	1	TRUE	1	0.820790060074999	2		252	347	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	378	595	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	0.987	0.941	1	0.987	0.941	1	CLONAL	1	TRUE	1	0.86668369000638	2		595	884	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573963	18573963	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	249	235	0	ENST00000266497.5:c.2281G>T	p.Val761Phe	p.V761F	ENST00000266497		761	Gtt/Ttt	15/31	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.86668369000638	2		235	527	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465459	99465459	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	321	405	0	ENST00000268035.6:c.2284del	p.Thr762ProfsTer77	p.T762Pfs*77	ENST00000268035	NM_000875.3	762	Acc/cc	11/21	1	2	FACETS	0.85	0.806	0.896	0.85	0.806	0.896	CLONAL	1	TRUE	1	0.86668369000638	2		405	871	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460537	149460537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	456	529	0	ENST00000286301.3:c.100C>T	p.Pro34Ser	p.P34S	ENST00000286301	NM_005211.3	34	Cca/Tca	3/22	1	2	FACETS	0.93	0.89	0.97	0.93	0.89	0.97	CLONAL	1	TRUE	1	0.86668369000638	2		529	1132	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265284	10265284	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	316	357	0	ENST00000340748.4:c.1762del	p.Ala588LeufsTer109	p.A588Lfs*109	ENST00000340748		588	Gct/ct	20/40	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.86668369000638	2		357	712	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0027479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	8	397	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.360669201736078	3	FACETS	0.136	0.087	0.2	0.068	0.043	0.1	SUBCLONAL	1	TRUE	1	0.360669201736078	3		397	386	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0027479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	243	574	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.228226375656977	4	FACETS	1	0.985	1	0.844	0.796	0.892	CLONAL	3	TRUE	0	0.360669201736078	4		576	543	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968322	2968323	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs762770988	NA	P-0027479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	114	512	3	ENST00000396946.4:c.1663dup	p.Arg555ProfsTer38	p.R555Pfs*38	ENST00000396946	NM_032415.4	555	cgg/cCgg	13/25	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.360669201736078	2		515	463	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247367	153247367	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	103	266	0	ENST00000281708.4:c.1435C>T	p.Arg479Ter	p.R479*	ENST00000281708	NM_033632.3	479	Cga/Tga	10/12	0.347609606840527	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.360669201736078	2		266	271	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18276986	18276986	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748211099	NA	P-0027479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	90	451	0	ENST00000222254.8:c.1433G>A	p.Arg478His	p.R478H	ENST00000222254	NM_005027.3	478	cGt/cAt	12/16	0.360669201736078	3	FACETS	1	0.968	1	0.619	0.551	0.69	CLONAL	1	TRUE	1	0.360669201736078	3		451	476	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778100	27778100	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	141	519	1	ENST00000369163.2:c.249G>T	p.Leu83Phe	p.L83F	ENST00000369163	NM_003536.2	83	ttG/ttT	1/1	0.360669201736078	5	FACETS	1	0.949	1			1	CLONAL	2	TRUE	NA	0.360669201736078	5		520	573	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436152	51436152	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	66	388	0	ENST00000262662.1:c.112G>A	p.Gly38Arg	p.G38R	ENST00000262662		38	Gga/Aga	3/4	0.360669201736078	5	FACETS	1	0.966	1	0.337	0.293	0.383	CLONAL	1	TRUE	1	0.360669201736078	5		388	419	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154794	2154794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	135	779	1	ENST00000434045.2:c.427C>T	p.Pro143Ser	p.P143S	ENST00000434045	NM_001127598.1	143	Ccc/Tcc	4/5	0.360669201736078	3	FACETS	1	0.937	1	0.519	0.472	0.569	CLONAL	1	TRUE	1	0.360669201736078	3		780	851	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18439843	18439843	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	32	433	0	ENST00000266497.5:c.745del	p.Cys249AlafsTer4	p.C249Afs*4	ENST00000266497		247	tcT/tc	2/31	0.360669201736078	3	FACETS	0.592	0.481	0.717	0.296	0.24	0.359	SUBCLONAL	1	TRUE	1	0.360669201736078	3		433	354	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873248	136873248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368016542	NA	P-0027479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	103	320	0	ENST00000241393.3:c.250G>A	p.Asp84Asn	p.D84N	ENST00000241393	NM_003467.2	84	Gac/Aac	2/2	0.353987141062822	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.360669201736078	3		320	301	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939979	49939979	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	133	732	0	ENST00000296474.3:c.1064A>T	p.Asp355Val	p.D355V	ENST00000296474	NM_002447.2	355	gAt/gTt	1/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.360669201736078	2		732	644	SUCCESS
APC	324	MSKCC	GRCh37	5	112175229	112175238	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	CTAGGTCAGC	CTAGGTCAGC	TAAAATAAAATAAAATAAAATAAGATAAAATAAAATAAA	novel	NA	P-0027479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	32	212	0	ENST00000257430.4:c.3938_3947delinsTAAAATAAAATAAAATAAAATAAGATAAAATAAAATAAA	p.Thr1313IlefsTer3	p.T1313Ifs*3	ENST00000257430	NM_000038.5	1313	aCTAGGTCAGCt/aTAAAATAAAATAAAATAAAATAAGATAAAATAAAATAAAt	16/16	0.360669201736078	3	FACETS	1	0.934	1	0.442	0.363	0.528	CLONAL	1	TRUE	0	0.360669201736078	3		212	158	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0027487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	307	403	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.51999196876474	3	FACETS	0.891	0.853	0.928	0.891	0.853	0.928	CLONAL	3	TRUE	0	0.600843775985546	3		403	497	SUCCESS
ATM	472	MSKCC	GRCh37	11	108213985	108213985	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	123	310	0	ENST00000278616.4:c.8305T>C	p.Trp2769Arg	p.W2769R	ENST00000278616	NM_000051.3	2769	Tgg/Cgg	57/63	0.580128513649158	1	FACETS	0.968	0.889	1	0.968	0.889	1	CLONAL	1	TRUE	0	0.600843775985546	1		310	296	SUCCESS
APC	324	MSKCC	GRCh37	5	112173283	112173284	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0027487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	83	183	0	ENST00000257430.4:c.1993_1994del	p.Leu665IlefsTer8	p.L665Ifs*8	ENST00000257430	NM_000038.5	664	acTTta/acta	16/16	1	2	FACETS	0.949	0.848	1	0.949	0.848	1	CLONAL	1	TRUE	1	0.600843775985546	2		183	291	SUCCESS
APC	324	MSKCC	GRCh37	5	112175745	112175746	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGATACTTTATTACATTTTGCCACAGAAAGTACTCCAGATGGAT	novel	NA	P-0027487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	32	235	0	ENST00000257430.4:c.4478_4479insAGAAAGTACTCCAGATGGATTGATACTTTATTACATTTTGCCAC	p.Phe1500LeufsTer22	p.F1500Lfs*22	ENST00000257430	NM_000038.5	1485	gct/gcTGATACTTTATTACATTTTGCCACAGAAAGTACTCCAGATGGATt	16/16	1	2	FACETS	0.259	0.21	0.315	0.259	0.21	0.315	SUBCLONAL	1	TRUE	1	0.600843775985546	2		235	411	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638783	176638783	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559441081	NA	P-0027487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	257	569	0	ENST00000439151.2:c.3383C>T	p.Ser1128Phe	p.S1128F	ENST00000439151	NM_022455.4	1128	tCt/tTt	5/23	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.600843775985546	2		569	839	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190344	32190344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146490163	NA	P-0027487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	182	575	1	ENST00000375023.3:c.395G>A	p.Arg132His	p.R132H	ENST00000375023	NM_004557.3	132	cGc/cAc	3/30	0.52474731787437	3	FACETS	0.945	0.873	1	0.472	0.436	0.51	CLONAL	1	TRUE	1	0.600843775985546	3		576	834	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182641	38182641	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs387907272	NA	P-0027488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	8	286	0	ENST00000396334.3:c.794T>C	p.Leu265Pro	p.L265P	ENST00000396334	NM_002468.4	265	cTg/cCg	5/5	1	2	FACETS	0.3	0.192	0.441	0.3	0.192	0.441	SUBCLONAL	1	TRUE	1	0.14	2		286	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577102	7577102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793881	NA	P-0027488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	54	613	0	ENST00000269305.4:c.836G>A	p.Gly279Glu	p.G279E	ENST00000269305	NM_001126112.2	279	gGg/gAg	8/11	1	2	FACETS	0.926	0.789	1	0.926	0.789	1	CLONAL	1	TRUE	1	0.14	2		613	833	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004217	150004217	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1431439182	NA	P-0027489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	84	310	0	ENST00000253339.5:c.2008C>T	p.Arg670Trp	p.R670W	ENST00000253339		670	Cgg/Tgg	3/7	0.38514692727833	1	FACETS	0.859	0.763	0.961	0.859	0.763	0.961	CLONAL	1	TRUE	0	0.38514692727833	1		310	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0027489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	153	675	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.38514692727833	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.38514692727833	1		675	508	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868134	45868134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143960980	NA	P-0027489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	192	741	0	ENST00000391945.4:c.556C>T	p.Arg186Cys	p.R186C	ENST00000391945	NM_000400.3	186	Cgc/Tgc	7/23	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.38514692727833	2		741	716	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020768	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs926053251	NA	P-0027490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	94	459	1	ENST00000358127.4:c.77T>G	p.Val26Gly	p.V26G	ENST00000358127	NM_001280556.1	26	gTt/gGt	2/10	0.408970711267516	3	FACETS	0.864	0.77	0.963	0.288	0.256	0.321	CLONAL	1	TRUE	0	0.460955574826237	3		460	581	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158771	26158771	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	157	574	0	ENST00000289316.2:c.375del	p.Lys126SerfsTer9	p.K126Sfs*9	ENST00000289316	NM_138720.2	125	tCc/tc	1/2	0.460955574826237	5	FACETS	0.892	0.815	0.974	0.297	0.271	0.325	CLONAL	1	TRUE	2	0.460955574826237	5		574	1291	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0027490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	217	431	0	ENST00000269305.4:c.560-2A>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.404509596318961	2	FACETS	0.89	0.835	0.945	0.89	0.835	0.945	CLONAL	2	TRUE	0	0.460955574826237	2		431	529	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309018	137309018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771883272	NA	P-0027490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	101	633	4	ENST00000481739.1:c.625C>T	p.Arg209Trp	p.R209W	ENST00000481739	NM_002957.4	209	Cgg/Tgg	5/10	0.408970711267516	3	FACETS	0.722	0.645	0.803	0.241	0.215	0.268	SUBCLONAL	1	TRUE	0	0.460955574826237	3		637	747	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864333	117864333	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	69	252	0	ENST00000297338.2:c.1324G>T	p.Glu442Ter	p.E442*	ENST00000297338	NM_006265.2	442	Gag/Tag	11/14	0.460955574826237	7	FACETS	0.822	0.715	0.938	0.164	0.143	0.188	CLONAL	1	TRUE	2	0.460955574826237	7		252	784	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0027491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	157	321	2	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.59	2		323	530	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664864	138664893	+	inframe_deletion	In_Frame_Del	DEL	GCGGCTGCAGCCGCAGCTGCTGCAGCCGCT	GCGGCTGCAGCCGCAGCTGCTGCAGCCGCT	-	rs387906321	NA	P-0027491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	97	176	5	ENST00000330315.3:c.672_701del	p.Ala225_Ala234del	p.A225_A234del	ENST00000330315	NM_023067.3	224	gcAGCGGCTGCAGCAGCTGCGGCTGCAGCCGCg/gcg	1/1	1	2	FACETS	0.847	0.775	0.919	1	0.987	1	CLONAL	2	TRUE	1	0.59	2		181	194	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339943	116339943	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs781257386	NA	P-0027491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	37	348	0	ENST00000397752.3:c.805C>G	p.Leu269Val	p.L269V	ENST00000397752	NM_000245.2	269	Cta/Gta	2/21	0.3	5	FACETS	0.342	0.281	0.411			1	INDETERMINATE	1	TRUE	NA	0.59	5		348	691	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0027492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	255	344	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.352807510304798	3	FACETS	0.934	0.877	0.992	0.934	0.877	0.992	CLONAL	2	TRUE	1	0.413326189965164	3		345	797	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371785	55371785	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	227	221	0	ENST00000297316.4:c.475C>A	p.Leu159Met	p.L159M	ENST00000297316	NM_022454.3	159	Ctg/Atg	2/2	0.384697193999673	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	0	0.413326189965164	3		221	406	SUCCESS
ATM	472	MSKCC	GRCh37	11	108099912	108099912	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775248597	NA	P-0027492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	142	206	0	ENST00000278616.4:c.193C>T	p.Gln65Ter	p.Q65*	ENST00000278616	NM_000051.3	65	Cag/Tag	4/63	0.41120248765166	3	FACETS	0.969	0.891	1	0.969	0.891	1	CLONAL	2	TRUE	1	0.413326189965164	3		206	428	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420330	88420330	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	84	365	0	ENST00000360948.2:c.2356G>T	p.Gly786Cys	p.G786C	ENST00000360948	NM_001012338.2	786	Ggt/Tgt	19/19	0.222345252399924	1	FACETS	0.552	0.488	0.62	0.552	0.488	0.62	INDETERMINATE	1	TRUE	0	0.413326189965164	1		365	584	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525075	9525075	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	138	529	0	ENST00000353224.5:c.1810G>T	p.Val604Phe	p.V604F	ENST00000353224	NM_177990.2	604	Gtt/Ttt	8/10	1	2	FACETS	0.879	0.8	0.961	0.879	0.8	0.961	CLONAL	1	TRUE	1	0.413326189965164	2		529	760	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36022660	36022660	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	127	569	0	ENST00000358208.4:c.533G>T	p.Arg178Leu	p.R178L	ENST00000358208		178	cGa/cTa	5/12	1	2	FACETS	0.828	0.751	0.909	0.828	0.751	0.909	CLONAL	1	TRUE	1	0.413326189965164	2		569	742	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665385	176665385	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	210	307	0	ENST00000439151.2:c.4069G>C	p.Ala1357Pro	p.A1357P	ENST00000439151	NM_022455.4	1357	Gct/Cct	7/23	0.41120248765166	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.413326189965164	3		307	592	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111995788	111995788	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	149	380	0	ENST00000368678.4:c.1310A>T	p.Tyr437Phe	p.Y437F	ENST00000368678		437	tAc/tTc	12/13	0.413326189965164	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.413326189965164	1		380	501	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984016	2984016	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	266	474	0	ENST00000396946.4:c.514G>T	p.Glu172Ter	p.E172*	ENST00000396946	NM_032415.4	172	Gag/Tag	5/25	0.41120248765166	3	FACETS	0.982	0.924	1	0.982	0.924	1	CLONAL	2	TRUE	1	0.413326189965164	3		474	791	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970999	21971450	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCTCAGCCAGGTCCACGGGCAGACGGCCCCAGGCATCGCGCACGTCCAGCCGCGCCCCGGCCCGGTGCAGCACCACCAGCGTGTCCAGGAAGCCCTCCCGGGCAGCGTCGTGCACGGGTCGGGTGAGAGTGGCGGGGTCGGCGCAGTTGGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCTGCCCATCATCATGACCTGCCAGAGAGAACAGAATGGTCAGAGCCAGGGTGGGGGCCGGCATGACGGAAAGGAAGCTTGTGTAGAGCCCCCTCACCGCCAAGCAGACCCCCACACAAGCCCCAGGTGTCTAATTACCCCTACATTTGCTTCCAGTTTCCAATTTCCTTCTTGAGTTCTCTATCCATTCTTCAGTACACAATGAATTCCATTATATCCTCCGAACTTCTGCGGAGCTGTCGTCACAGGCAGAGAGCACTG	TCCTCAGCCAGGTCCACGGGCAGACGGCCCCAGGCATCGCGCACGTCCAGCCGCGCCCCGGCCCGGTGCAGCACCACCAGCGTGTCCAGGAAGCCCTCCCGGGCAGCGTCGTGCACGGGTCGGGTGAGAGTGGCGGGGTCGGCGCAGTTGGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCTGCCCATCATCATGACCTGCCAGAGAGAACAGAATGGTCAGAGCCAGGGTGGGGGCCGGCATGACGGAAAGGAAGCTTGTGTAGAGCCCCCTCACCGCCAAGCAGACCCCCACACAAGCCCCAGGTGTCTAATTACCCCTACATTTGCTTCCAGTTTCCAATTTCCTTCTTGAGTTCTCTATCCATTCTTCAGTACACAATGAATTCCATTATATCCTCCGAACTTCTGCGGAGCTGTCGTCACAGGCAGAGAGCACTG	-	novel	NA	P-0027492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	94	561	0	ENST00000304494.5:c.151-243_359del		p.X51_splice	ENST00000304494	NM_000077.4	51		2/3	0.413326189965164	1	FACETS	0.665	0.593	0.741	0.665	0.593	0.741	SUBCLONAL	1	TRUE	0	0.413326189965164	1		561	543	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341479	70341479	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	71	530	0	ENST00000374080.3:c.914T>A	p.Leu305Gln	p.L305Q	ENST00000374080		305	cTg/cAg	7/45	0.373582880524758	1	FACETS	0.398	0.347	0.454	0.398	0.347	0.454	SUBCLONAL	1	TRUE	0	0.413326189965164	1		530	684	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938929	76938929	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	79	612	0	ENST00000373344.5:c.1819G>T	p.Glu607Ter	p.E607*	ENST00000373344	NM_000489.3	607	Gaa/Taa	9/35	0.373582880524758	1	FACETS	0.356	0.312	0.403	0.356	0.312	0.403	SUBCLONAL	1	TRUE	0	0.413326189965164	1		612	853	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0027493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	149	517	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.287656800637203	4	FACETS	1	0.976	1	0.598	0.546	0.653	CLONAL	1	TRUE	2	0.364423151322697	4		517	933	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0027493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	166	633	1	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.359627707469367	1	FACETS	0.958	0.881	1	0.958	0.881	1	CLONAL	1	TRUE	0	0.364423151322697	1		634	778	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242494	55242494	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	150	466	1	ENST00000275493.2:c.2264C>A	p.Ala755Asp	p.A755D	ENST00000275493	NM_005228.3	755	gCc/gAc	19/28	0.287656800637203	4	FACETS	1	0.983	1	0.65	0.594	0.709	CLONAL	1	TRUE	2	0.364423151322697	4		467	864	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916136	9916136	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	90	351	0	ENST00000330684.3:c.2153T>G	p.Val718Gly	p.V718G	ENST00000330684	NM_001134407.1	718	gTc/gGc	10/13	0.278203643582907	4	FACETS	0.826	0.732	0.926	0.413	0.366	0.463	CLONAL	1	TRUE	2	0.364423151322697	4		351	816	SUCCESS
ATR	545	MSKCC	GRCh37	3	142171989	142171989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	115	538	0	ENST00000350721.4:c.7742G>A	p.Gly2581Glu	p.G2581E	ENST00000350721	NM_001184.3	2581	gGa/gAa	46/47	0.326481708064049	2	FACETS	0.7	0.63	0.774	0.35	0.315	0.387	SUBCLONAL	1	TRUE	0	0.364423151322697	2		538	902	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0027494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	113	403	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.271791980929215	1	FACETS	0.833	0.751	0.92	0.833	0.751	0.92	CLONAL	1	TRUE	0	0.341292134871779	1		403	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0027494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	160	436	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.310020266526808	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.341292134871779	1		436	652	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609934	81609934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369995834	NA	P-0027494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	44	177	0	ENST00000298171.2:c.1532C>T	p.Thr511Met	p.T511M	ENST00000298171	NM_000369.2	511	aCg/aTg	10/10	1	2	FACETS	0.914	0.771	1	0.914	0.771	1	CLONAL	1	TRUE	1	0.341292134871779	2		177	282	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911510	114911514	+	frameshift_variant	Frame_Shift_Del	DEL	AAGAA	AAGAA	-	novel	NA	P-0027494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	57	211	0	ENST00000543371.1:c.1033_1037del	p.Lys345GlufsTer9	p.K345Efs*9	ENST00000543371	NM_001198531.1	343	gAAGAA/g	10/14	1	2	FACETS	0.715	0.615	0.825	0.715	0.615	0.825	SUBCLONAL	1	TRUE	1	0.341292134871779	2		211	467	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106556	108106556	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	77	315	0	ENST00000278616.4:c.491G>A	p.Trp164Ter	p.W164*	ENST00000278616	NM_000051.3	164	tGg/tAg	5/63	0.341292134871779	3	FACETS	0.897	0.788	1	0.448	0.394	0.507	CLONAL	1	TRUE	1	0.341292134871779	3		315	589	SUCCESS
APC	324	MSKCC	GRCh37	5	112173783	112173783	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0027494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	67	284	0	ENST00000257430.4:c.2492T>G	p.Leu831Ter	p.L831*	ENST00000257430	NM_000038.5	831	tTa/tGa	16/16	1	2	FACETS	0.919	0.802	1	0.919	0.802	1	CLONAL	1	TRUE	1	0.341292134871779	2		284	427	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266831	198266831	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	210	572	0	ENST00000335508.6:c.2101G>T	p.Val701Phe	p.V701F	ENST00000335508	NM_012433.2	701	Gtt/Ttt	15/25	1	2	FACETS	0.563	0.523	0.605	0.563	0.523	0.605	SUBCLONAL	1	TRUE	1	0.771328194066565	2		572	967	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0027499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	77	443	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.300293524245829	4	FACETS	1	0.975	1	0.705	0.624	0.791	CLONAL	1	TRUE	2	0.468834224942	4		443	342	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844244	68844244	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	146	386	0	ENST00000261769.5:c.832G>T	p.Gly278Ter	p.G278*	ENST00000261769	NM_004360.3	278	Gga/Tga	6/16	NA	2	FACETS	0.949	0.88	1			1	INDETERMINATE	2	TRUE	NA	0.468834224942	2		386	328	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0027501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	80	278	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.851	0.755	0.952	0.851	0.755	0.952	CLONAL	1	TRUE	1	0.543334294975414	2		278	346	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0027501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	234	403	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.543334294975414	2	FACETS	0.848	0.8	0.896	0.848	0.8	0.896	CLONAL	2	TRUE	0	0.543334294975414	2		403	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0027501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	342	601	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.543334294975414	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.543334294975414	1		603	916	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366308	15366308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	216	332	0	ENST00000263377.2:c.1847G>A	p.Arg616Gln	p.R616Q	ENST00000263377	NM_058243.2	616	cGg/cAg	10/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.543334294975414	2		332	788	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468282	50468282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	279	429	0	ENST00000331340.3:c.1517C>T	p.Ser506Leu	p.S506L	ENST00000331340	NM_006060.4	506	tCg/tTg	8/8	0.529827422134545	3	FACETS	1	0.97	1	0.527	0.495	0.561	CLONAL	1	TRUE	1	0.543334294975414	3		429	1238	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209585	98209585	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536440590	NA	P-0027501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	157	316	0	ENST00000331920.6:c.3953C>T	p.Pro1318Leu	p.P1318L	ENST00000331920	NM_000264.3	1318	cCg/cTg	23/24	1	2	FACETS	0.923	0.849	1	0.923	0.849	1	CLONAL	1	TRUE	1	0.543334294975414	2		316	626	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456509	32456509	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770618081	NA	P-0027501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	121	122	0	ENST00000332351.3:c.383C>T	p.Pro128Leu	p.P128L	ENST00000332351	NM_024426.4	128	cCg/cTg	1/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.543334294975414	2		122	325	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211057	36211057	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	377	688	1	ENST00000222270.7:c.808G>T	p.Glu270Ter	p.E270*	ENST00000222270	NM_014727.1	270	Gag/Tag	3/37	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.543334294975414	2		689	1263	SUCCESS
APC	324	MSKCC	GRCh37	5	112173581	112173581	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	105	223	0	ENST00000257430.4:c.2291del	p.Leu764Ter	p.L764*	ENST00000257430	NM_000038.5	764	Tta/ta	16/16	1	2	FACETS	0.802	0.722	0.886	0.802	0.722	0.886	CLONAL	1	TRUE	1	0.543334294975414	2		223	482	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412072	63412072	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	308	276	1	ENST00000330258.3:c.1095C>A	p.Tyr365Ter	p.Y365*	ENST00000330258	NM_152424.3	365	taC/taA	2/2	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.543334294975414	1		277	552	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	212	315	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.921	0.861	0.982	0.921	0.861	0.982	CLONAL	1	TRUE	1	0.754634677414394	2		316	610	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755656	39755656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	285	522	1	ENST00000288319.7:c.1109G>A	p.Arg370His	p.R370H	ENST00000288319	NM_182918.3	370	cGt/cAt	10/10	1	2	FACETS	0.929	0.877	0.982	0.929	0.877	0.982	CLONAL	1	TRUE	1	0.754634677414394	2		523	813	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133455	55133455	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0027502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1553	8441	359	0	ENST00000257290.5:c.760-1G>T		p.X254_splice	ENST00000257290	NM_006206.4	254			0.754634677414394	28	FACETS	1	0.998	1			1	CLONAL	24	TRUE	NA	0.754634677414394	28		359	9994	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196568	106196568	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs765001214	NA	P-0027502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	186	323	0	ENST00000380013.4:c.4901A>G	p.Asn1634Ser	p.N1634S	ENST00000380013	NM_001127208.2	1634	aAt/aGt	11/11	1	2	FACETS	0.952	0.886	1	0.952	0.886	1	CLONAL	1	TRUE	1	0.754634677414394	2		323	518	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111510	8111511	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0027503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	142	521	0	ENST00000346208.3:c.996_997del	p.Asn333TrpfsTer18	p.N333Wfs*18	ENST00000346208		332	gcCAat/gcat	5/6	0.586368264477042	3	FACETS	1	0.982	1	0.631	0.579	0.685	CLONAL	1	TRUE	1	0.586368264477042	3		521	496	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350025	89350025	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	148	525	0	ENST00000301030.4:c.2925G>C	p.Glu975Asp	p.E975D	ENST00000301030	NM_001256183.1	975	gaG/gaC	9/13	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.586368264477042	2		525	372	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412967	49412967	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	29	518	0	ENST00000418115.1:c.56C>A	p.Thr19Lys	p.T19K	ENST00000418115	NM_001664.2	19	aCa/aAa	2/5	0.586368264477042	2	FACETS	0.213	0.17	0.261	0.106	0.085	0.131	SUBCLONAL	1	TRUE	0	0.586368264477042	2		518	465	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981450	70981450	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	379	687	2	ENST00000276594.2:c.646C>A	p.Pro216Thr	p.P216T	ENST00000276594	NM_024504.3	216	Cca/Aca	2/8	0.586368264477042	7	FACETS	1	0.991	1	0.479	0.454	0.504	CLONAL	2	TRUE	2	0.586368264477042	7		689	1331	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17355133	17355133	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1553177740	NA	P-0027504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	69	452	0	ENST00000375499.3:c.385C>G	p.Pro129Ala	p.P129A	ENST00000375499	NM_003000.2	129	Cct/Gct	4/8	0.716920562314285	2	FACETS	0.795	0.702	0.893	0.398	0.351	0.447	SUBCLONAL	1	FALSE	0	0.716920562314285	2		452	242	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087931	27087934	+	frameshift_variant	Frame_Shift_Del	DEL	TCCA	TCCA	GCT	novel	NA	P-0027504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	178	554	1	ENST00000324856.7:c.2218_2221delinsGCT	p.Ser740AlafsTer2	p.S740Afs*2	ENST00000324856	NM_006015.4	740	TCCAtg/GCTtg	6/20	0.716920562314285	2	FACETS	0.859	0.811	0.906	0.859	0.811	0.906	CLONAL	2	FALSE	0	0.716920562314285	2		555	289	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900689	32900689	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	203	399	0	ENST00000380152.3:c.570del	p.Asp191IlefsTer8	p.D191Ifs*8	ENST00000380152		190	ccT/cc	7/27	0.716920562314285	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	FALSE	0	0.716920562314285	2		399	253	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348006	89348129	+	frameshift_variant	Frame_Shift_Del	DEL	TGGAGGGTCCAGCCCCGGCGGTTTCTTAGCAGGAATGTCCAGACCCTTCTTCCGCCCGTCGTCTGCCGGCTTCGCCTTCTCCTTGAGCTTGGGGTCTCCGGACCGGTGCCTCAGCTTCTCCATT	TGGAGGGTCCAGCCCCGGCGGTTTCTTAGCAGGAATGTCCAGACCCTTCTTCCGCCCGTCGTCTGCCGGCTTCGCCTTCTCCTTGAGCTTGGGGTCTCCGGACCGGTGCCTCAGCTTCTCCATT	-	novel	NA	P-0027504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	47	734	0	ENST00000301030.4:c.4821_4944del	p.Gln1607HisfsTer38	p.Q1607Hfs*38	ENST00000301030	NM_001256183.1	1607	caAATGGAGAAGCTGAGGCACCGGTCCGGAGACCCCAAGCTCAAGGAGAAGGCGAAGCCGGCAGACGACGGGCGGAAGAAGGGTCTGGACATTCCTGCTAAGAAACCGCCGGGGCTGGACCCTCCA/ca	9/13	0.716920562314285	2	FACETS	0.771	0.662	0.888	0.386	0.331	0.444	SUBCLONAL	1	FALSE	0	0.716920562314285	2		734	170	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31369200	31369200	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	176	475	0	ENST00000328111.2:c.184A>T	p.Ser62Cys	p.S62C	ENST00000328111	NM_006892.3	62	Agt/Tgt	3/23	0.590385923802687	4	FACETS	0.971	0.905	1	0.971	0.905	1	CLONAL	2	FALSE	2	0.716920562314285	4		475	434	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760628	133760628	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779677715	NA	P-0027504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	55	780	0	ENST00000318560.5:c.2951C>T	p.Thr984Met	p.T984M	ENST00000318560	NM_005157.4	984	aCg/aTg	11/11	0.669523644666398	4	FACETS	0.768	0.66	0.885	0.384	0.33	0.443	SUBCLONAL	1	FALSE	2	0.716920562314285	4		780	343	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0027506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	32	449	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.862	0.704	1	0.862	0.704	1	CLONAL	1	TRUE	1	0.33	2		449	225	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0027506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	51	574	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.994	0.85	1	0.994	0.85	1	CLONAL	1	TRUE	1	0.33	2		576	311	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0027506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	84	565	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.227125402592391	3	FACETS	0.862	0.761	0.97	0.431	0.38	0.485	CLONAL	1	TRUE	1	0.33	3		565	688	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	121	528	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.369653697295678	3	FACETS	1	0.967	1	0.577	0.522	0.635	CLONAL	1	TRUE	1	0.369653697295678	3		529	672	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862749	9862749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150316865	NA	P-0027508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	211	495	2	ENST00000330684.3:c.2554G>A	p.Val852Met	p.V852M	ENST00000330684	NM_001134407.1	852	Gtg/Atg	12/13	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.369653697295678	2		497	836	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578232	7578234	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	AAA	AAA	-	novel	NA	P-0027508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	240	569	0	ENST00000269305.4:c.615_617del	p.Tyr205_Leu206delinsTer	p.Y205_L206delins*	ENST00000269305	NM_001126112.2	205	taTTTg/tag	6/11	0.369653697295678	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.369653697295678	1		569	871	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649598	206649598	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373699027	NA	P-0027508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	114	536	0	ENST00000367120.3:c.433G>A	p.Val145Ile	p.V145I	ENST00000367120	NM_014002.3	145	Gta/Ata	6/22	0.367529644825873	2	FACETS	0.691	0.621	0.764	0.345	0.31	0.382	SUBCLONAL	1	TRUE	0	0.369653697295678	2		536	893	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939682	131939682	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	114	429	0	ENST00000265335.6:c.2468G>T	p.Arg823Leu	p.R823L	ENST00000265335		823	cGa/cTa	15/25	1	2	FACETS	0.797	0.718	0.881	0.797	0.718	0.881	SUBCLONAL	1	TRUE	1	0.369653697295678	2		429	774	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923140	39923140	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555915488	NA	P-0027508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	110	557	0	ENST00000378444.4:c.3568G>A	p.Glu1190Lys	p.E1190K	ENST00000378444	NM_001123385.1	1190	Gag/Aag	8/15	1	2	FACETS	0.639	0.573	0.709	0.639	0.573	0.709	SUBCLONAL	1	TRUE	1	0.369653697295678	2		557	931	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111495	8111496	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGGAGGA	novel	NA	P-0027514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	198	562	0	ENST00000346208.3:c.982_988dup	p.Arg330MetfsTer24	p.R330Mfs*24	ENST00000346208		327	-/TGGAGGA	5/6	1	2	FACETS	0.988	0.918	1	0.988	0.918	1	CLONAL	1	FALSE	1	0.562874366664852	2		562	712	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131478	202131478	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	91	437	0	ENST00000358485.4:c.446T>G	p.Leu149Arg	p.L149R	ENST00000358485	NM_001080125.1	149	cTt/cGt	2/9	1	2	FACETS	0.846	0.757	0.94	0.846	0.757	0.94	CLONAL	1	FALSE	1	0.562874366664852	2		437	382	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42851141	42851141	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	76	433	0	ENST00000398585.3:c.752C>T	p.Thr251Ile	p.T251I	ENST00000398585	NM_001135099.1	251	aCa/aTa	7/14	0.562874366664852	3	FACETS	0.857	0.755	0.964	0.428	0.377	0.482	CLONAL	1	FALSE	1	0.562874366664852	3		433	404	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0027523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	240	598	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.34698429110133	2	FACETS	0.793	0.742	0.846	0.793	0.742	0.846	SUBCLONAL	2	TRUE	0	0.34698429110133	2		598	872	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0027524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	452	429	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.531706148554362	3	FACETS	0.992	0.95	1	0.992	0.95	1	CLONAL	2	TRUE	1	0.531706148554362	3		429	1085	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900171	101900171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564161322	NA	P-0027524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	143	223	0	ENST00000374994.4:c.605C>T	p.Ala202Val	p.A202V	ENST00000374994	NM_004612.2	202	gCg/gTg	4/9	0.531706148554362	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.531706148554362	1		223	379	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971133	21971133	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	170	436	0	ENST00000304494.5:c.225del	p.Ala76ProfsTer70	p.A76Pfs*70	ENST00000304494	NM_000077.4	75	ccC/cc	2/3	0.531706148554362	1	FACETS	0.892	0.827	0.96	0.892	0.827	0.96	CLONAL	1	TRUE	0	0.531706148554362	1		436	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0027524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	256	659	1	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.531706148554362	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.531706148554362	1		660	568	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870214	44870215	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	298	192	0	ENST00000377967.4:c.398dup	p.Leu133PhefsTer12	p.L133Ffs*12	ENST00000377967	NM_021140.2	131	-/T	5/29	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.531706148554362	1		192	591	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0027525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	109	583	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.967	0.868	1	0.967	0.868	1	CLONAL	1	TRUE	1	0.276577745677699	2		583	815	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0027525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	118	208	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	0.24119406486045	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.276577745677699	2		208	394	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692831	89692831	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	33	201	0	ENST00000371953.3:c.315T>G	p.Cys105Trp	p.C105W	ENST00000371953	NM_000314.4	105	tgT/tgG	5/9	0.207979094217218	1	FACETS	0.857	0.702	1	0.857	0.702	1	CLONAL	1	TRUE	0	0.276577745677699	1		201	240	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579871	7579886	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAGGGGGCTCGACG	CAGAGGGGGCTCGACG	-	novel	NA	P-0027525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	181	598	1	ENST00000269305.4:c.27_42del	p.Ser9ArgfsTer30	p.S9Rfs*30	ENST00000269305	NM_001126112.2	9	agCGTCGAGCCCCCTCTG/ag	2/11	0.170502744366723	2	FACETS	1	0.985	1	0.642	0.591	0.694	CLONAL	1	TRUE	0	0.276577745677699	2		599	1020	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17949094	17949094	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	75	627	0	ENST00000458235.1:c.1547T>C	p.Ile516Thr	p.I516T	ENST00000458235	NM_000215.3	516	aTc/aCc	11/24	1	2	FACETS	0.501	0.438	0.57	0.501	0.438	0.57	SUBCLONAL	1	TRUE	1	0.276577745677699	2		627	1082	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077472	30077472	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs774824164	NA	P-0027525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	121	452	0	ENST00000338641.4:c.1619A>G	p.Asn540Ser	p.N540S	ENST00000338641	NM_000268.3	540	aAt/aGt	15/16	0.170502744366723	2	FACETS	1	0.971	1	0.596	0.539	0.656	CLONAL	1	TRUE	0	0.276577745677699	2		452	734	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0027528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	182	341	1	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	0.206131344134903	3	FACETS	0.884	0.814	0.956	0.884	0.814	0.956	CLONAL	2	TRUE	1	0.206131344134903	3		342	1102	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	146	565	0	ENST00000397752.3:c.3028G>A	p.Asp1010Asn	p.D1010N	ENST00000397752	NM_000245.2	1010	Gat/Aat	14/21	0.206131344134903	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.206131344134903	1		565	1152	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579329	7579329	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912658	NA	P-0027528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	104	699	2	ENST00000269305.4:c.358A>G	p.Lys120Glu	p.K120E	ENST00000269305	NM_001126112.2	120	Aag/Gag	4/11	0.206131344134903	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.206131344134903	1		701	819	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11270894	11270894	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	68	430	1	ENST00000361445.4:c.3631G>A	p.Val1211Met	p.V1211M	ENST00000361445	NM_004958.3	1211	Gtg/Atg	24/58	1	2	FACETS	0.814	0.706	0.93	0.814	0.706	0.93	CLONAL	1	TRUE	1	0.206131344134903	2		431	811	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333721	70333721	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	40	432	0	ENST00000373644.4:c.1626C>G	p.Asp542Glu	p.D542E	ENST00000373644	NM_030625.2	542	gaC/gaG	2/12	1	2	FACETS	0.563	0.467	0.671	0.563	0.467	0.671	SUBCLONAL	1	TRUE	1	0.206131344134903	2		432	689	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039435	49039435	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	101	562	0	ENST00000267163.4:c.2420C>A	p.Ser807Ter	p.S807*	ENST00000267163	NM_000321.2	807	tCa/tAa	23/27	0.206131344134903	1	FACETS	0.938	0.837	1	0.938	0.837	1	CLONAL	1	TRUE	0	0.206131344134903	1		562	937	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647167	23647167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1260	75	645	0	ENST00000261584.4:c.700G>A	p.Asp234Asn	p.D234N	ENST00000261584	NM_024675.3	234	Gat/Aat	4/13	0.193132393995756	3	FACETS	0.601	0.525	0.684	0.301	0.262	0.342	SUBCLONAL	1	TRUE	1	0.206131344134903	3		645	1335	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376036	8376036	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	66	311	0	ENST00000356435.5:c.4561G>T	p.Asp1521Tyr	p.D1521Y	ENST00000356435		1521	Gat/Tat	28/35	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.206131344134903	2		311	579	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440899	52440899	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	234	670	0	ENST00000460680.1:c.605G>C	p.Trp202Ser	p.W202S	ENST00000460680	NM_004656.3	202	tGg/tCg	8/17	0.437669868806052	1	FACETS	0.999	0.934	1	0.999	0.934	1	CLONAL	1	TRUE	0	0.444386314884734	1		670	820	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655359	67655359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	55	374	0	ENST00000264010.4:c.1222G>A	p.Glu408Lys	p.E408K	ENST00000264010	NM_006565.3	408	Gaa/Aaa	7/12	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.1	2		374	830	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295173	1295173	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0027530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	41	422	0				ENST00000310581	NM_198253.2	-/1132			0.124397648134548	1	FACETS	0.981	0.815	1	0.981	0.815	1	CLONAL	1	TRUE	0	0.1	1		422	794	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460543	149460543	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	63	614	0	ENST00000286301.3:c.94G>T	p.Val32Leu	p.V32L	ENST00000286301	NM_005211.3	32	Gtg/Ttg	3/22	0.124397648134548	1	FACETS	0.971	0.836	1	0.971	0.836	1	CLONAL	1	TRUE	0	0.1	1		614	1233	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0027531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	24	650	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.283921619682233	4	FACETS	0.183	0.142	0.23	0.091	0.071	0.115	SUBCLONAL	1	TRUE	2	0.294592477193142	4		651	1154	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0027531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	155	517	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.283921619682233	4	FACETS	1	0.987	1	0.719	0.658	0.783	CLONAL	1	TRUE	2	0.294592477193142	4		517	947	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757274881	NA	P-0027531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	374	759	3	ENST00000269305.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	144	Cag/Tag	5/11	0.260277006414857	2	FACETS	0.978	0.928	1	0.978	0.928	1	CLONAL	2	TRUE	0	0.294592477193142	2		762	1298	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797314	135797314	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0027531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	25	328	0	ENST00000298552.3:c.555C>G	p.Tyr185Ter	p.Y185*	ENST00000298552	NM_001162426.1	185	taC/taG	7/23	0.294592477193142	1	FACETS	0.323	0.254	0.403	0.323	0.254	0.403	SUBCLONAL	1	TRUE	0	0.294592477193142	1		328	448	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0027534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	108	397	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.208219869285756	2	FACETS	0.774	0.7	0.851	0.387	0.35	0.426	INDETERMINATE	1	TRUE	0	0.686053602056725	2		397	407	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236086	108236086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782292	NA	P-0027534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	222	409	0	ENST00000278616.4:c.9022C>T	p.Arg3008Cys	p.R3008C	ENST00000278616	NM_000051.3	3008	Cgt/Tgt	63/63	0.58178126352069	1	FACETS	0.91	0.858	0.963	0.91	0.858	0.963	CLONAL	1	TRUE	0	0.686053602056725	1		409	467	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106489	27106489	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	520	641	1	ENST00000324856.7:c.6100G>T	p.Glu2034Ter	p.E2034*	ENST00000324856	NM_006015.4	2034	Gag/Tag	20/20	0.362242874102221	2	FACETS	0.868	0.839	0.897	0.868	0.839	0.897	INDETERMINATE	2	TRUE	0	0.686053602056725	2		642	873	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6439802	6439802	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	71	391	0	ENST00000356142.4:c.328G>C	p.Glu110Gln	p.E110Q	ENST00000356142	NM_018890.3	110	Gaa/Caa	5/7	0.384585041887629	3	FACETS	0.517	0.451	0.587	0.258	0.225	0.294	INDETERMINATE	1	TRUE	1	0.686053602056725	3		391	538	SUCCESS
ATM	472	MSKCC	GRCh37	11	108225525	108225538	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTTTGACTCTAGA	TGTTTGACTCTAGA	-	novel	NA	P-0027534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	70	364	0	ENST00000278616.4:c.8787-11_8789del		p.X2929_splice	ENST00000278616	NM_000051.3	2929		61/63	0.58178126352069	1	FACETS	0.466	0.41	0.525	0.466	0.41	0.525	SUBCLONAL	1	TRUE	0	0.686053602056725	1		364	288	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996149	73996149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	252	776	0	ENST00000318443.5:c.883C>T	p.His295Tyr	p.H295Y	ENST00000318443	NM_001024736.1	295	Cac/Tac	5/10	0.344499228330552	1	FACETS	0.484	0.453	0.516	0.484	0.453	0.516	INDETERMINATE	1	TRUE	0	0.686053602056725	1		776	997	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89355061	89355061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	164	561	0	ENST00000301030.4:c.619G>A	p.Glu207Lys	p.E207K	ENST00000301030	NM_001256183.1	207	Gag/Aag	7/13	0.275792570977293	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.686053602056725	0		561	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0027543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	271	533	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.742544973136891	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.742544973136891	1		533	455	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	78	489	1	ENST00000346208.3:c.1220_1221insA	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcAg	6/6	1	2	FACETS	0.222	0.194	0.252	0.222	0.194	0.252	SUBCLONAL	1	TRUE	1	0.742544973136891	2		490	946	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877876	151877876	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	155	342	0	ENST00000262189.6:c.7069G>T	p.Gly2357Ter	p.G2357*	ENST00000262189	NM_170606.2	2357	Gga/Tga	36/59	1	2	FACETS	0.87	0.803	0.939	0.87	0.803	0.939	CLONAL	1	TRUE	1	0.742544973136891	2		342	480	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252994	36252995	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0027545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	183	336	0	ENST00000300305.3:c.367dup	p.Asp123GlyfsTer15	p.D123Gfs*15	ENST00000300305		123	gat/gGat	4/8	0.295067506990048	2	FACETS	0.959	0.889	1	0.959	0.889	1	CLONAL	2	TRUE	0	0.29	2		336	658	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573976	7573991	+	frameshift_variant	Frame_Shift_Del	DEL	TGAGTTCCAAGGCCTC	TGAGTTCCAAGGCCTC	-	novel	NA	P-0027545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	178	651	0	ENST00000269305.4:c.1036_1051del	p.Glu346ArgfsTer19	p.E346Rfs*19	ENST00000269305	NM_001126112.2	346	GAGGCCTTGGAACTCAag/ag	10/11	0.295067506990048	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.29	1		651	945	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184096	56184097	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGT	novel	NA	P-0027545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	98	313	0	ENST00000399503.3:c.4304_4306dup	p.Val1435dup	p.V1435dup	ENST00000399503	NM_005921.1	1435	agt/agTGTt	19/20	0.295067506990048	1	FACETS	0.916	0.818	1	0.916	0.818	1	CLONAL	1	TRUE	0	0.29	1		313	631	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0027546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	296	443	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.21094422587477	7	FACETS	1	0.963	1			1	CLONAL	6	TRUE	NA	0.21094422587477	7		443	701	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0027546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	72	604	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.819	0.714	0.932	0.819	0.714	0.932	CLONAL	1	TRUE	1	0.21094422587477	2		604	834	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0027546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	133	594	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.21094422587477	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.21094422587477	1		594	820	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs199469669	NA	P-0027546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	79	605	0	ENST00000374080.3:c.130G>C	p.Gly44Arg	p.G44R	ENST00000374080		44	Ggt/Cgt	2/45	1	2	FACETS	0.829	0.727	0.938	0.829	0.727	0.938	CLONAL	1	TRUE	1	0.21094422587477	2		605	904	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797482	45797482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778538	NA	P-0027546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	54	664	0	ENST00000450313.1:c.1037C>T	p.Ser346Leu	p.S346L	ENST00000450313	NM_012222.2	346	tCg/tTg	12/16	1	2	FACETS	0.531	0.451	0.618	0.531	0.451	0.618	SUBCLONAL	1	TRUE	1	0.21094422587477	2		664	965	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0027547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	383	321	2	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.80148467595341	3	FACETS	0.988	0.949	1	0.988	0.949	1	CLONAL	2	TRUE	1	0.828231880431263	3		323	662	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0027547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	438	629	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.77713703558857	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.828231880431263	1		630	618	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175951	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1392778905	NA	P-0027547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	144	223	0	ENST00000257430.4:c.4660G>T	p.Glu1554Ter	p.E1554*	ENST00000257430	NM_000038.5	1554	Gaa/Taa	16/16	1	2	FACETS	0.971	0.898	1	0.971	0.898	1	CLONAL	1	TRUE	1	0.828231880431263	2		223	358	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843535	156843535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369367198	NA	P-0027547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	331	512	2	ENST00000524377.1:c.961G>A	p.Val321Met	p.V321M	ENST00000524377	NM_002529.3	321	Gtg/Atg	8/17	1	2	FACETS	0.927	0.88	0.975	0.927	0.88	0.975	CLONAL	1	TRUE	1	0.828231880431263	2		514	862	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932171	39932171	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555918056	NA	P-0027547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	412	578	5	ENST00000378444.4:c.2428C>T	p.Arg810Ter	p.R810*	ENST00000378444	NM_001123385.1	810	Cga/Tga	4/15	1	2	FACETS	0.946	0.903	0.989	0.946	0.903	0.989	CLONAL	1	TRUE	1	0.828231880431263	2		583	1052	SUCCESS
APC	324	MSKCC	GRCh37	5	112175706	112175706	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	186	254	0	ENST00000257430.4:c.4415del	p.Val1472GlufsTer35	p.V1472Efs*35	ENST00000257430	NM_000038.5	1472	gTa/ga	16/16	1	2	FACETS	0.919	0.856	0.982	0.919	0.856	0.982	CLONAL	1	TRUE	1	0.828231880431263	2		254	489	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174420	11174420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587777900	NA	P-0027547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	853	495	0	ENST00000361445.4:c.7255G>A	p.Glu2419Lys	p.E2419K	ENST00000361445	NM_004958.3	2419	Gaa/Aaa	53/58	NA	2	FACETS	0.999	0.981	1			1	INDETERMINATE	2	TRUE	NA	0.828231880431263	2		495	1031	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717741	89717741	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121909228	NA	P-0027547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	244	299	0	ENST00000371953.3:c.766G>T	p.Glu256Ter	p.E256*	ENST00000371953	NM_000314.4	256	Gag/Tag	7/9	0.828231880431263	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.828231880431263	1		299	334	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659596	88659596	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	300	415	2	ENST00000372037.3:c.379A>G	p.Thr127Ala	p.T127A	ENST00000372037	NM_004329.2	127	Acc/Gcc	6/13	0.828231880431263	1	FACETS	0.992	0.954	1	0.992	0.954	1	CLONAL	1	TRUE	0	0.828231880431263	1		417	428	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279920	18279920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	535	558	2	ENST00000222254.8:c.2003G>A	p.Cys668Tyr	p.C668Y	ENST00000222254	NM_005027.3	668	tGc/tAc	16/16	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.828231880431263	NA		560	714	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675579	86675579	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	120	233	0	ENST00000274376.6:c.2515G>T	p.Glu839Ter	p.E839*	ENST00000274376	NM_002890.2	839	Gaa/Taa	19/25	1	2	FACETS	0.923	0.845	1	0.923	0.845	1	CLONAL	1	TRUE	1	0.828231880431263	2		233	314	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0027551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	59	541	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.68391039667669	2		541	165	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0027551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	51	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.944	0.819	1	0.944	0.819	1	CLONAL	1	TRUE	1	0.68391039667669	2		509	158	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0027551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	59	470	6	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.899	0.786	1	0.899	0.786	1	CLONAL	1	TRUE	1	0.68391039667669	2		476	192	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16040642	16040642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	96	368	0	ENST00000268712.3:c.1492C>T	p.Arg498Cys	p.R498C	ENST00000268712	NM_006311.3	498	Cgc/Tgc	14/46	0.623202596097292	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.68391039667669	1		368	157	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748338	43748338	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0027551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	74	569	8	ENST00000382044.4:c.2468C>G	p.Ser823Ter	p.S823*	ENST00000382044	NM_001141980.1	823	tCa/tGa	12/28	0.308931159268885	1	FACETS	0.685	0.61	0.761	0.685	0.61	0.761	INDETERMINATE	1	TRUE	0	0.68391039667669	1		577	208	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120254	70120254	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	553	749	21	ENST00000245479.2:c.1257del	p.Tyr420ThrfsTer50	p.Y420Tfs*50	ENST00000245479	NM_000346.3	419	gCc/gc	3/3	0.68391039667669	4	FACETS		NA	1	1	0.998	1	NA	5	TRUE	0	0.68391039667669	4		770	586	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046396	128046396	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	32	361	5	ENST00000285398.2:c.867C>A	p.Tyr289Ter	p.Y289*	ENST00000285398	NM_000122.1	289	taC/taA	7/15	0.68391039667669	2	FACETS	0.761	0.63	0.902	0.38	0.315	0.451	CLONAL	1	TRUE	0	0.68391039667669	2		366	123	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511205	148511205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	79	405	3	ENST00000320356.2:c.1697G>A	p.Arg566His	p.R566H	ENST00000320356	NM_004456.4	566	cGc/cAc	15/20	1	2	FACETS	0.983	0.879	1	0.983	0.879	1	CLONAL	1	TRUE	1	0.68391039667669	2		408	235	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0027552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	277	425	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.821172587322872	2	FACETS	0.986	0.954	1	0.986	0.954	1	CLONAL	2	TRUE	0	0.821172587322872	2		425	342	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0027553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	57	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.844	0.727	0.971	0.844	0.727	0.971	CLONAL	1	TRUE	1	0.345358410758048	2		509	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0027553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	94	574	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.943	0.841	1	0.943	0.841	1	CLONAL	1	TRUE	1	0.345358410758048	2		576	577	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974744	21974775	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTCCTCTACCCGACCCCGGGCCGCGGCCGT	ACCTCCTCTACCCGACCCCGGGCCGCGGCCGT	-	novel	NA	P-0027553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	36	262	0	ENST00000304494.5:c.52_83del	p.Thr18AlafsTer15	p.T18Afs*15	ENST00000304494	NM_000077.4	18	ACGGCCGCGGCCCGGGGTCGGGTAGAGGAGGTg/g	1/3	0.345358410758048	1	FACETS	0.81	0.671	0.962	0.81	0.671	0.962	CLONAL	1	TRUE	0	0.345358410758048	1		262	213	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0027554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	83	541	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.928	0.819	1	0.928	0.819	1	CLONAL	1	TRUE	1	0.236518102705336	2		541	756	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067192	37067192	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201673334	NA	P-0027554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	79	366	0	ENST00000231790.2:c.1103C>T	p.Ser368Leu	p.S368L	ENST00000231790	NM_000249.3	368	tCg/tTg	12/19	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.236518102705336	2		366	630	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874261	155874261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352822	NA	P-0027554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	115	457	1	ENST00000368323.3:c.270G>A	p.Met90Ile	p.M90I	ENST00000368323	NM_006912.5	90	atG/atA	5/6	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.236518102705336	2		458	863	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650562	18650562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	73	343	0	ENST00000266497.5:c.2773G>A	p.Asp925Asn	p.D925N	ENST00000266497		925	Gat/Aat	20/31	0.236518102705336	1	FACETS	0.901	0.789	1	0.901	0.789	1	CLONAL	1	TRUE	0	0.236518102705336	1		343	604	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402057	402057	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	88	367	0	ENST00000399788.2:c.4734G>C	p.Glu1578Asp	p.E1578D	ENST00000399788	NM_001042603.1	1578	gaG/gaC	27/28	0.236518102705336	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.236518102705336	1		367	578	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924285	112924285	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	127	446	0	ENST00000351677.2:c.1231A>G	p.Thr411Ala	p.T411A	ENST00000351677	NM_002834.3	411	Acg/Gcg	11/16	0.236518102705336	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.236518102705336	1		446	859	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573344	55573344	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	87	410	0	ENST00000288135.5:c.1006G>C	p.Glu336Gln	p.E336Q	ENST00000288135	NM_000222.2	336	Gaa/Caa	6/21	1	2	FACETS	0.924	0.817	1	0.924	0.817	1	CLONAL	1	TRUE	1	0.236518102705336	2		410	796	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142950031	142950031	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	85	381	0	ENST00000262992.4:c.2679C>G	p.Ile893Met	p.I893M	ENST00000262992	NM_001101669.1	893	atC/atG	24/24	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.236518102705336	2		381	690	SUCCESS
AR	367	MSKCC	GRCh37	X	66765955	66765955	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1021234843	NA	P-0027554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	171	621	1	ENST00000374690.3:c.967G>A	p.Glu323Lys	p.E323K	ENST00000374690	NM_000044.3	323	Gag/Aag	1/8	0.236518102705336	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.236518102705336	1		622	1061	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344096	70344098	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0027554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	140	582	0	ENST00000374080.3:c.1835_1837del	p.Asn612del	p.N612del	ENST00000374080		611	cACAac/cac	13/45	0.236518102705336	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.236518102705336	1		582	947	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	204	315	1				ENST00000310581	NM_198253.2	-/1132			0.671240323549172	3	FACETS	0.908	0.843	0.975	0.454	0.421	0.488	CLONAL	1	TRUE	1	0.671240323549172	3		316	894	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984224	7984224	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1470190596	NA	P-0027584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	214	476	0	ENST00000319144.4:c.505C>T	p.His169Tyr	p.H169Y	ENST00000319144	NM_001139.2	169	Cat/Tat	4/15	0.323912337264394	6	FACETS	1	0.967	1	0.358	0.332	0.386	INDETERMINATE	1	TRUE	3	0.671240323549172	6		476	1389	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217299	11217299	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519779	NA	P-0027585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	195	678	1	ENST00000361445.4:c.4379T>C	p.Leu1460Pro	p.L1460P	ENST00000361445	NM_004958.3	1460	cTt/cCt	30/58	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.390992794102744	2		679	886	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183799	10183799	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs869025623	NA	P-0027585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	163	531	0	ENST00000256474.2:c.269del	p.Asn90ThrfsTer69	p.N90Tfs*69	ENST00000256474	NM_000551.3	90	Aac/ac	1/3	0.390992794102744	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.390992794102744	1		531	658	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147486	47147486	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0027585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	110	472	0	ENST00000409792.3:c.4839+1G>C		p.X1613_splice	ENST00000409792	NM_014159.6	1613			0.390992794102744	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.390992794102744	1		472	403	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879125	151879125	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	45	526	0	ENST00000262189.6:c.5820G>C	p.Glu1940Asp	p.E1940D	ENST00000262189	NM_170606.2	1940	gaG/gaC	36/59	1	2	FACETS	0.338	0.283	0.399	0.338	0.283	0.399	SUBCLONAL	1	TRUE	1	0.390992794102744	2		526	681	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944256	206944256	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374619208	NA	P-0027586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	253	286	1	ENST00000423557.1:c.374G>A	p.Arg125His	p.R125H	ENST00000423557	NM_000572.2	125	cGc/cAc	3/5	0.255820877537495	5	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.877662397506212	5		287	1036	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0027586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	334	560	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	0.877662397506212	2	FACETS	0.66	0.624	0.696	0.33	0.312	0.348	SUBCLONAL	1	TRUE	0	0.877662397506212	2		560	1154	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0027586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	783	626	0	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	0.877662397506212	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.877662397506212	2		626	875	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063717	+	splice_donor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0027586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	262	281	0	ENST00000412916.2:c.165+1del		p.X55_splice	ENST00000412916		55			0.877662397506212	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.877662397506212	1		281	315	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112553	115112555	+	frameshift_variant	Frame_Shift_Del	DEL	GAG	GAG	AT	novel	NA	P-0027586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	539	603	2	ENST00000257566.3:c.1185_1187delinsAT	p.Thr397ProfsTer235	p.T397Pfs*235	ENST00000257566	NM_016569.3	395	atCTCc/atATc	7/8	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.877662397506212	2		605	1063	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842438	68842439	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	723	582	0	ENST00000261769.5:c.504dup	p.Gly169ArgfsTer5	p.G169Rfs*5	ENST00000261769	NM_004360.3	167	gaa/gAaa	4/16	0.877662397506212	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.877662397506212	1		582	902	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045934	47045934	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	536	525	1	ENST00000377604.3:c.2729C>A	p.Ser910Ter	p.S910*	ENST00000377604	NM_001204468.1	910	tCa/tAa	24/24	0.351559257540251	1	FACETS	0.735	0.71	0.759	0.735	0.71	0.759	INDETERMINATE	1	TRUE	0	0.877662397506212	1		526	933	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023307	27023307	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0027589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	99	273	0	ENST00000324856.7:c.413C>G	p.Ser138Ter	p.S138*	ENST00000324856	NM_006015.4	138	tCa/tGa	1/20	1	2	FACETS	0.869	0.781	0.961	0.869	0.781	0.961	CLONAL	1	TRUE	1	0.556867559647219	2		273	409	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0027589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	296	559	3	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	0.969	0.913	1	0.969	0.913	1	CLONAL	1	TRUE	1	0.556867559647219	2		562	1097	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53241055	53241055	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	110	574	0	ENST00000375401.3:c.1156G>C	p.Glu386Gln	p.E386Q	ENST00000375401	NM_004187.3	386	Gag/Cag	9/26	1	2	FACETS	0.425	0.381	0.471	0.425	0.381	0.471	SUBCLONAL	1	TRUE	1	0.556867559647219	2		574	930	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770065	56770065	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs752608224	NA	P-0027589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	124	466	0	ENST00000337432.4:c.61C>G	p.Pro21Ala	p.P21A	ENST00000337432	NM_058216.2	21	Cca/Gca	1/9	1	2	FACETS	0.512	0.463	0.565	0.512	0.463	0.565	SUBCLONAL	1	TRUE	1	0.556867559647219	2		466	869	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805979	32805979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293561966	NA	P-0027589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	137	682	0	ENST00000374899.4:c.32C>T	p.Ser11Phe	p.S11F	ENST00000374899	NM_018833.2	11	tCc/tTc	2/12	1	2	FACETS	0.466	0.423	0.512	0.466	0.423	0.512	SUBCLONAL	1	TRUE	1	0.556867559647219	2		682	1055	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105664	27105665	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	187	383	0	ENST00000324856.7:c.5276dup	p.Met1759IlefsTer14	p.M1759Ifs*14	ENST00000324856	NM_006015.4	1759	atg/aTtg	20/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.556867559647219	2		383	652	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842363	68842363	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	288	576	0	ENST00000261769.5:c.426del	p.Asn144ThrfsTer71	p.N144Tfs*71	ENST00000261769	NM_004360.3	142	Ttt/tt	4/16	0.556867559647219	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.556867559647219	1		576	697	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165545	47165545	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	213	481	0	ENST00000409792.3:c.581C>G	p.Pro194Arg	p.P194R	ENST00000409792	NM_014159.6	194	cCt/cGt	3/21	0.556867559647219	1	FACETS	0.905	0.846	0.965	0.905	0.846	0.965	CLONAL	1	TRUE	0	0.556867559647219	1		481	610	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165572	47165572	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	222	479	0	ENST00000409792.3:c.554C>A	p.Ser185Ter	p.S185*	ENST00000409792	NM_014159.6	185	tCa/tAa	3/21	0.556867559647219	1	FACETS	0.957	0.897	1	0.957	0.897	1	CLONAL	1	TRUE	0	0.556867559647219	1		479	601	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161673	56161673	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	82	453	0	ENST00000399503.3:c.1170G>T	p.Gln390His	p.Q390H	ENST00000399503	NM_005921.1	390	caG/caT	6/20	1	2	FACETS	0.288	0.253	0.326	0.288	0.253	0.326	SUBCLONAL	1	TRUE	1	0.556867559647219	2		453	1022	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372448	55372448	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	136	756	0	ENST00000297316.4:c.1138C>T	p.Gln380Ter	p.Q380*	ENST00000297316	NM_022454.3	380	Cag/Tag	2/2	1	2	FACETS	0.391	0.355	0.43	0.391	0.355	0.43	SUBCLONAL	1	TRUE	1	0.556867559647219	2		756	1248	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061261	38061264	+	missense_variant	Missense_Mutation	ONP	TAGG	TAGG	GAGC	novel	NA	P-0027591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	187	741	0	ENST00000250448.2:c.725_728delinsGCTC	p.Ser242_Tyr243delinsCysSer	p.S242_Y243delinsCS	ENST00000250448	NM_004496.3	242	tCCTAc/tGCTCc	2/2	0.16691834256496	6	FACETS	0.952	0.885	1	0.952	0.885	1	INDETERMINATE	3	TRUE	3	0.423354108522803	6		741	571	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230692	46230692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs916056847	NA	P-0027591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	11	545	1	ENST00000334344.6:c.941G>A	p.Arg314His	p.R314H	ENST00000334344	NM_152641.2	314	cGt/cAt	8/21	0.423354108522803	5	FACETS	0.164	0.112	0.228	0.055	0.037	0.076	SUBCLONAL	1	TRUE	2	0.423354108522803	5		546	519	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115880	8115881	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGC	novel	NA	P-0027591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	149	659	0	ENST00000346208.3:c.1229_1232dup	p.His411GlnfsTer97	p.H411Qfs*97	ENST00000346208		409	ttc/ttCAGCc	6/6	0.094207231292734	4	FACETS	0.768	0.704	0.835	0.768	0.704	0.835	INDETERMINATE	2	TRUE	2	0.423354108522803	4		659	652	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577140	64577142	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0027591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	173	797	0	ENST00000312049.6:c.440_442del	p.Ile147del	p.I147del	ENST00000312049	NM_130799.2	147	aTCAca/aca	2/10	NA	2	FACETS	0.826	0.766	0.886			1	INDETERMINATE	2	TRUE	NA	0.423354108522803	2		797	495	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188272	10188272	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	95	825	1	ENST00000256474.2:c.415T>A	p.Ser139Thr	p.S139T	ENST00000256474	NM_000551.3	139	Tct/Act	2/3	0.423354108522803	4	FACETS	0.879	0.782	0.981	0.439	0.391	0.491	CLONAL	1	TRUE	2	0.423354108522803	4		826	727	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921411	39921411	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	21	494	0	ENST00000378444.4:c.4409C>T	p.Ala1470Val	p.A1470V	ENST00000378444	NM_001123385.1	1470	gCa/gTa	10/15	0.293611251979599	3	FACETS	0.416	0.32	0.527	0.208	0.16	0.264	SUBCLONAL	1	TRUE	1	0.423354108522803	3		494	289	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064794618	NA	P-0027596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	411	722	0	ENST00000269305.4:c.159G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgG/tgA	4/11	0.455008651397216	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.455008651397216	2		722	894	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031950	26031950	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	95	383	0	ENST00000244661.2:c.339C>G	p.Ile113Met	p.I113M	ENST00000244661	NM_003537.3	113	atC/atG	1/1	0.455008651397216	2	FACETS	0.835	0.746	0.929	0.418	0.373	0.465	CLONAL	1	TRUE	0	0.455008651397216	2		383	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0027599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	717	857	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	0.659988867814105	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.659988867814105	2		857	1072	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690805	89690805	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	138	427	0	ENST00000371953.3:c.212G>A	p.Cys71Tyr	p.C71Y	ENST00000371953	NM_000314.4	71	tGt/tAt	4/9	0.174543816752417	5	FACETS	1	0.987	1	0.368	0.336	0.401	INDETERMINATE	1	TRUE	1	0.659988867814105	5		427	565	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720727	89720727	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	50	154	0	ENST00000371953.3:c.878G>T	p.Gly293Val	p.G293V	ENST00000371953	NM_000314.4	293	gGa/gTa	8/9	0.174543816752417	5	FACETS	0.985	0.854	1	0.493	0.427	0.562	INDETERMINATE	2	TRUE	1	0.659988867814105	5		154	153	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248415	59248415	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2119	208	445	0	ENST00000371222.2:c.328T>G	p.Phe110Val	p.F110V	ENST00000371222	NM_002228.3	110	Ttc/Gtc	1/1	0.659988867814105	9	FACETS	0.897	0.828	0.969	0.112	0.103	0.122	CLONAL	1	TRUE	1	0.659988867814105	9		445	2327	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788618	3788618	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs398124146	NA	P-0027599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	231	612	0	ENST00000262367.5:c.4336C>G	p.Arg1446Gly	p.R1446G	ENST00000262367	NM_004380.2	1446	Cgc/Ggc	26/31	1	2	FACETS	0.705	0.657	0.754	0.705	0.657	0.754	SUBCLONAL	1	TRUE	1	0.659988867814105	2		612	993	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993459	72993461	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0027599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	234	851	0	ENST00000268489.5:c.584_586del	p.Ile195del	p.I195del	ENST00000268489	NM_006885.3	195	aTCAac/aac	2/10	1	2	FACETS	0.62	0.578	0.664	0.62	0.578	0.664	SUBCLONAL	1	TRUE	1	0.659988867814105	2		851	1144	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983564	7983564	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	229	665	0	ENST00000319144.4:c.743C>A	p.Ser248Tyr	p.S248Y	ENST00000319144	NM_001139.2	248	tCt/tAt	6/15	0.659988867814105	2	FACETS	0.885	0.827	0.944	0.443	0.413	0.472	CLONAL	1	TRUE	0	0.659988867814105	2		665	784	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742680	39742680	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	301	523	0	ENST00000361337.2:c.1523G>T	p.Arg508Leu	p.R508L	ENST00000361337	NM_003286.2	508	cGt/cTt	15/21	0.107694903535637	4	FACETS	0.869	0.821	0.918	0.869	0.821	0.918	INDETERMINATE	2	TRUE	2	0.659988867814105	4		523	871	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0027601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	166	419	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	0.767	0.708	0.828	0.767	0.708	0.828	SUBCLONAL	1	TRUE	1	0.73145981837452	2		419	592	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2955004	2955004	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	132	521	0	ENST00000396946.4:c.2706del	p.Phe902LeufsTer12	p.F902Lfs*12	ENST00000396946	NM_032415.4	902	ttC/tt	21/25	0.30488952368347	6	FACETS	0.691	0.625	0.76	0.173	0.156	0.19	INDETERMINATE	1	TRUE	2	0.73145981837452	6		521	1287	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	989	528	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.268320662912348	8	FACETS	0.947	0.923	0.971	1	0.995	1	CLONAL	8	FALSE	1	0.268320662912348	8		529	1757	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0027602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	264	570	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.268320662912348	1	FACETS	0.918	0.862	0.975	1	0.995	1	CLONAL	2	FALSE	0	0.268320662912348	1		570	928	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28624327	28624327	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	217	583	0	ENST00000241453.7:c.647A>G	p.Lys216Arg	p.K216R	ENST00000241453	NM_004119.2	216	aAg/aGg	6/24	1	2	FACETS	0.777	0.722	0.834	1	0.992	1	SUBCLONAL	2	FALSE	1	0.268320662912348	2		583	1041	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	1084	541	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.549117184205033	6	FACETS	1	0.997	1			1	CLONAL	5	TRUE	NA	0.549117184205033	6		541	1523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	244	583	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.54825271928661	1	FACETS	0.887	0.832	0.942	0.887	0.832	0.942	CLONAL	1	TRUE	0	0.549117184205033	1		583	727	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158626	26158626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772836222	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	23	239	1	ENST00000289316.2:c.229G>A	p.Glu77Lys	p.E77K	ENST00000289316	NM_138720.2	77	Gag/Aag	1/2	1	2	FACETS	0.261	0.203	0.328	0.261	0.203	0.328	SUBCLONAL	1	TRUE	1	0.549117184205033	2		240	321	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201686	66201686	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	116	509	0	ENST00000273854.3:c.2816C>G	p.Pro939Arg	p.P939R	ENST00000273854	NM_004439.5	939	cCa/cGa	16/18	1	2	FACETS	0.544	0.49	0.601	0.544	0.49	0.601	SUBCLONAL	1	TRUE	1	0.549117184205033	2		509	777	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796616	42796616	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	91	568	0	ENST00000575354.2:c.3173C>G	p.Ser1058Ter	p.S1058*	ENST00000575354	NM_015125.3	1058	tCa/tGa	13/20	0.413117051254333	1	FACETS	0.428	0.38	0.478	0.428	0.38	0.478	SUBCLONAL	1	TRUE	0	0.549117184205033	1		568	562	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031939	26031939	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	48	366	1	ENST00000244661.2:c.350G>A	p.Arg117Gln	p.R117Q	ENST00000244661	NM_003537.3	117	cGa/cAa	1/1	1	2	FACETS	0.295	0.249	0.346	0.295	0.249	0.346	SUBCLONAL	1	TRUE	1	0.549117184205033	2		367	592	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106543594	106543594	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	486	502	0	ENST00000369096.4:c.396G>C	p.Arg132Ser	p.R132S	ENST00000369096	NM_001198.3	132	agG/agC	3/7	0.549117184205033	6	FACETS	1	0.974	1			1	CLONAL	4	TRUE	NA	0.549117184205033	6		502	915	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390751	118390751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	46	517	0	ENST00000534358.1:c.11401G>A	p.Glu3801Lys	p.E3801K	ENST00000534358	NM_005933.3	3801	Gag/Aag	33/36	1	2	FACETS	0.202	0.169	0.238	0.202	0.169	0.238	SUBCLONAL	1	TRUE	1	0.549117184205033	2		517	830	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174908	11174908	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	73	603	0	ENST00000361445.4:c.7126C>G	p.Pro2376Ala	p.P2376A	ENST00000361445	NM_004958.3	2376	Cca/Gca	52/58	0.325760823805756	1	FACETS	0.213	0.185	0.242	0.213	0.185	0.242	INDETERMINATE	1	TRUE	0	0.549117184205033	1		603	907	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322653	39322653	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1297460348	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	212	621	0	ENST00000373001.3:c.339G>C	p.Gln113His	p.Q113H	ENST00000373001	NM_022157.3	113	caG/caC	2/7	1	2	FACETS	0.92	0.856	0.986	0.92	0.856	0.986	CLONAL	1	TRUE	1	0.549117184205033	2		621	839	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273231	115273231	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	79	636	0	ENST00000438362.2:c.1227C>G	p.Ile409Met	p.I409M	ENST00000438362	NM_001242891.1	409	atC/atG	11/20	1	2	FACETS	0.291	0.255	0.33	0.291	0.255	0.33	SUBCLONAL	1	TRUE	1	0.549117184205033	2		636	988	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63699984	63699984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	54	330	0	ENST00000279873.7:c.319G>A	p.Glu107Lys	p.E107K	ENST00000279873	NM_032199.2	107	Gaa/Aaa	3/10	1	2	FACETS	0.411	0.352	0.477	0.411	0.352	0.477	SUBCLONAL	1	TRUE	1	0.549117184205033	2		330	478	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845593	63845593	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	46	387	0	ENST00000279873.7:c.1332C>G	p.Ile444Met	p.I444M	ENST00000279873	NM_032199.2	444	atC/atG	9/10	1	2	FACETS	0.252	0.211	0.296	0.252	0.211	0.296	SUBCLONAL	1	TRUE	1	0.549117184205033	2		387	666	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14317377	14317377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	64	457	0	ENST00000256196.4:c.133C>T	p.Pro45Ser	p.P45S	ENST00000256196		45	Cca/Tca	2/6	1	2	FACETS	0.312	0.269	0.358	0.312	0.269	0.358	SUBCLONAL	1	TRUE	1	0.549117184205033	2		457	748	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924635	94924635	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1384345368	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	122	708	1	ENST00000536441.1:c.275G>A	p.Ser92Asn	p.S92N	ENST00000536441	NM_144665.3	92	aGc/aAc	3/10	1	2	FACETS	0.4	0.36	0.441	0.4	0.36	0.441	SUBCLONAL	1	TRUE	1	0.549117184205033	2		709	1112	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207738	102207738	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	47	500	0	ENST00000263464.3:c.1720C>A	p.His574Asn	p.H574N	ENST00000263464	NM_001165.4	574	Cat/Aat	9/9	1	2	FACETS	0.236	0.198	0.277	0.236	0.198	0.277	SUBCLONAL	1	TRUE	1	0.549117184205033	2		500	726	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929380	32929380	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs572945276	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	71	576	0	ENST00000380152.3:c.7390C>G	p.Gln2464Glu	p.Q2464E	ENST00000380152		2464	Caa/Gaa	14/27	0.549117184205033	1	FACETS	0.284	0.248	0.324	0.284	0.248	0.324	SUBCLONAL	1	TRUE	0	0.549117184205033	1		576	660	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435769	110435769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745351480	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	33	314	0	ENST00000375856.3:c.2632G>A	p.Glu878Lys	p.E878K	ENST00000375856	NM_003749.2	878	Gag/Aag	1/2	0.549117184205033	1	FACETS	0.272	0.221	0.328	0.272	0.221	0.328	SUBCLONAL	1	TRUE	0	0.549117184205033	1		314	321	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748128	43748128	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	76	579	0	ENST00000382044.4:c.2678C>G	p.Ser893Cys	p.S893C	ENST00000382044	NM_001141980.1	893	tCt/tGt	12/28	0.549117184205033	1	FACETS	0.286	0.251	0.325	0.286	0.251	0.325	SUBCLONAL	1	TRUE	0	0.549117184205033	1		579	701	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81960704	81960704	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	92	617	0	ENST00000359376.3:c.2435G>A	p.Gly812Glu	p.G812E	ENST00000359376	NM_002661.3	812	gGa/gAa	23/33	0.549117184205033	1	FACETS	0.384	0.341	0.429	0.384	0.341	0.429	SUBCLONAL	1	TRUE	0	0.549117184205033	1		617	633	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998902	11998902	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	34	298	0	ENST00000353533.5:c.404C>G	p.Ser135Ter	p.S135*	ENST00000353533	NM_003010.3	135	tCa/tGa	4/11	0.54825271928661	1	FACETS	0.263	0.215	0.316	0.263	0.215	0.316	SUBCLONAL	1	TRUE	0	0.549117184205033	1		298	342	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490279	29490279	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	102	485	0	ENST00000356175.3:c.364C>A	p.His122Asn	p.H122N	ENST00000356175	NM_000267.3	122	Cac/Aac	4/57	1	2	FACETS	0.381	0.34	0.425	0.381	0.34	0.425	SUBCLONAL	1	TRUE	1	0.549117184205033	2		485	975	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37680979	37680979	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	55	583	1	ENST00000447079.4:c.3148C>T	p.Gln1050Ter	p.Q1050*	ENST00000447079	NM_015083.1	1050	Cag/Tag	12/14	1	2	FACETS	0.231	0.197	0.269	0.231	0.197	0.269	SUBCLONAL	1	TRUE	1	0.549117184205033	2		584	866	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760893	59760893	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1419	76	630	0	ENST00000259008.2:c.3514G>A	p.Glu1172Lys	p.E1172K	ENST00000259008	NM_032043.2	1172	Gaa/Aaa	20/20	0.325106025587562	5	FACETS	0.338	0.295	0.384			1	INDETERMINATE	1	TRUE	NA	0.549117184205033	5		630	1495	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222034	2222034	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	88	789	0	ENST00000398665.3:c.2866C>G	p.Leu956Val	p.L956V	ENST00000398665	NM_032482.2	956	Ctc/Gtc	24/28	1	2	FACETS	0.339	0.3	0.382	0.339	0.3	0.382	SUBCLONAL	1	TRUE	1	0.549117184205033	2		789	945	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222181	2222181	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	95	807	1	ENST00000398665.3:c.3013C>T	p.Gln1005Ter	p.Q1005*	ENST00000398665	NM_032482.2	1005	Cag/Tag	24/28	1	2	FACETS	0.356	0.316	0.399	0.356	0.316	0.399	SUBCLONAL	1	TRUE	1	0.549117184205033	2		808	972	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794475	42794475	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	62	825	0	ENST00000575354.2:c.1555G>A	p.Asp519Asn	p.D519N	ENST00000575354	NM_015125.3	519	Gat/Aat	10/20	0.413117051254333	1	FACETS	0.174	0.149	0.201	0.174	0.149	0.201	SUBCLONAL	1	TRUE	0	0.549117184205033	1		825	942	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416281	29416281	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	79	588	0	ENST00000389048.3:c.4672G>C	p.Glu1558Gln	p.E1558Q	ENST00000389048	NM_004304.4	1558	Gag/Cag	29/29	1	2	FACETS	0.317	0.278	0.359	0.317	0.278	0.359	SUBCLONAL	1	TRUE	1	0.549117184205033	2		588	908	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190742130	190742130	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	43	483	0	ENST00000441310.2:c.2767C>A	p.His923Asn	p.H923N	ENST00000441310	NM_000534.4	923	Cat/Aat	13/13	1	2	FACETS	0.208	0.173	0.247	0.208	0.173	0.247	SUBCLONAL	1	TRUE	1	0.549117184205033	2		483	752	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12653520	12653520	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1294	70	572	0	ENST00000251849.4:c.249G>T	p.Met83Ile	p.M83I	ENST00000251849	NM_002880.3	83	atG/atT	3/17	0.241310911984298	5	FACETS	0.341	0.296	0.39			1	INDETERMINATE	1	TRUE	NA	0.549117184205033	5		572	1364	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612142	189612142	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1431	495	550	0	ENST00000264731.3:c.1894G>A	p.Glu632Lys	p.E632K	ENST00000264731	NM_003722.4	632	Gag/Aag	14/14	0.549117184205033	6	FACETS	0.982	0.937	1	0.491	0.468	0.514	CLONAL	2	TRUE	2	0.549117184205033	6		550	1926	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535423	187535423	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs753744492	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	74	463	0	ENST00000441802.2:c.9151G>C	p.Asp3051His	p.D3051H	ENST00000441802	NM_005245.3	3051	Gac/Cac	12/27	1	2	FACETS	0.329	0.287	0.374	0.329	0.287	0.374	SUBCLONAL	1	TRUE	1	0.549117184205033	2		463	819	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554912	187554912	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	44	485	0	ENST00000441802.2:c.4249C>G	p.Leu1417Val	p.L1417V	ENST00000441802	NM_005245.3	1417	Ctt/Gtt	7/27	1	2	FACETS	0.21	0.175	0.249	0.21	0.175	0.249	SUBCLONAL	1	TRUE	1	0.549117184205033	2		485	763	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976688	2976688	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	36	431	0	ENST00000396946.4:c.1324A>G	p.Ser442Gly	p.S442G	ENST00000396946	NM_032415.4	442	Agc/Ggc	9/25	1	2	FACETS	0.192	0.157	0.231	0.192	0.157	0.231	SUBCLONAL	1	TRUE	1	0.549117184205033	2		431	684	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240811	55240811	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	89	796	0	ENST00000275493.2:c.2055G>C	p.Glu685Asp	p.E685D	ENST00000275493	NM_005228.3	685	gaG/gaC	17/28	0.549117184205033	1	FACETS	0.293	0.259	0.329	0.293	0.259	0.329	SUBCLONAL	1	TRUE	0	0.549117184205033	1		796	802	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334756	81334756	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	62	489	0	ENST00000222390.5:c.1960G>C	p.Glu654Gln	p.E654Q	ENST00000222390	NM_000601.4	654	Gag/Cag	17/18	1	2	FACETS	0.283	0.244	0.326	0.283	0.244	0.326	SUBCLONAL	1	TRUE	1	0.549117184205033	2		489	798	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117874102	117874102	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	51	467	0	ENST00000297338.2:c.352G>C	p.Asp118His	p.D118H	ENST00000297338	NM_006265.2	118	Gat/Cat	4/14	1	2	FACETS	0.275	0.233	0.321	0.275	0.233	0.321	SUBCLONAL	1	TRUE	1	0.549117184205033	2		467	675	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139438542	139438542	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	80	711	0	ENST00000277541.6:c.74C>A	p.Ser25Tyr	p.S25Y	ENST00000277541	NM_017617.3	25	tCc/tAc	2/34	1	2	FACETS	0.319	0.28	0.361	0.319	0.28	0.361	SUBCLONAL	1	TRUE	1	0.549117184205033	2		711	914	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920185	76920185	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	65	604	0	ENST00000373344.5:c.3892G>A	p.Glu1298Lys	p.E1298K	ENST00000373344	NM_000489.3	1298	Gaa/Aaa	11/35	1	2	FACETS	0.255	0.22	0.293	0.255	0.22	0.293	SUBCLONAL	1	TRUE	1	0.549117184205033	2		604	928	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100046	157100046	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	12	133	0	ENST00000346085.5:c.983G>A	p.Gly328Glu	p.G328E	ENST00000346085	NM_020732.3	328	gGa/gAa	1/20	1	2	FACETS	0.241	0.17	0.329	0.241	0.17	0.329	SUBCLONAL	1	TRUE	1	0.549117184205033	2		133	181	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0027608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	97	583	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.331832842234526	1	FACETS	0.489	0.438	0.543	0.489	0.438	0.543	INDETERMINATE	1	TRUE	0	0.596944384459342	1		583	466	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793663	NA	P-0027608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	327	646	1	ENST00000263967.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000263967	NM_006218.2	93	cGg/cAg	2/21	0.331832842234526	1	FACETS	0.985	0.936	1	0.985	0.936	1	INDETERMINATE	1	TRUE	0	0.596944384459342	1		647	780	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0027608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	277	372	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.240768053490845	2	FACETS	1	0.993	1	0.676	0.639	0.714	INDETERMINATE	1	TRUE	0	0.596944384459342	2		372	686	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911295	32911295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28897716	NA	P-0027608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	269	597	2	ENST00000380152.3:c.2803G>A	p.Asp935Asn	p.D935N	ENST00000380152		935	Gat/Aat	11/27	0.597890007963524	3	FACETS	1	0.985	1	0.573	0.537	0.609	CLONAL	1	TRUE	1	0.596944384459342	3		599	1022	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814313	76814313	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	88	352	1	ENST00000373344.5:c.6331C>T	p.Arg2111Ter	p.R2111*	ENST00000373344	NM_000489.3	2111	Cga/Tga	29/35	1	2	FACETS	0.533	0.473	0.597	0.533	0.473	0.597	SUBCLONAL	1	TRUE	1	0.596944384459342	2		353	553	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0027608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	366	583	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.326669035410927	3	FACETS	0.857	0.816	0.899	0.857	0.816	0.899	INDETERMINATE	2	TRUE	1	0.596944384459342	3		583	929	SUCCESS
APC	324	MSKCC	GRCh37	5	112174094	112174095	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs863225332	NA	P-0027608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	74	391	0	ENST00000257430.4:c.2804dup	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	tac/tAac	16/16	0.240768053490845	2	FACETS	0.425	0.372	0.481	0.212	0.186	0.241	INDETERMINATE	1	TRUE	0	0.596944384459342	2		391	584	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615539	43615539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1451004715	NA	P-0027608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	291	481	0	ENST00000355710.3:c.2618G>A	p.Arg873Gln	p.R873Q	ENST00000355710	NM_020975.4	873	cGg/cAg	15/20	1	2	FACETS	0.973	0.917	1	0.973	0.917	1	CLONAL	1	TRUE	1	0.596944384459342	2		481	1002	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117872	70117872	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	336	504	1	ENST00000245479.2:c.340G>C	p.Val114Leu	p.V114L	ENST00000245479	NM_000346.3	114	Gtg/Ctg	1/3	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.596944384459342	2		505	927	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248091	59248091	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1425026692	NA	P-0027608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	254	247	2	ENST00000371222.2:c.652C>T	p.Gln218Ter	p.Q218*	ENST00000371222	NM_002228.3	218	Cag/Tag	1/1	0.596944384459342	2	FACETS	0.9	0.854	0.945	0.9	0.854	0.945	CLONAL	2	TRUE	0	0.596944384459342	2		249	473	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554196	63554197	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	364	653	0	ENST00000307078.5:c.542dup	p.Met182AspfsTer13	p.M182Dfs*13	ENST00000307078	NM_004655.3	181	gtg/gtTg	2/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.596944384459342	2		653	1205	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1650179	1650179	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	73	657	0	ENST00000344749.5:c.69C>G	p.Ser23Arg	p.S23R	ENST00000344749	NM_001136139.2	23	agC/agG	2/19	1	2	FACETS	0.202	0.176	0.231	0.202	0.176	0.231	SUBCLONAL	1	TRUE	1	0.596944384459342	2		657	1208	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5286082	5286082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200430287	NA	P-0027608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1265	202	766	0	ENST00000357368.4:c.70G>A	p.Val24Ile	p.V24I	ENST00000357368	NM_002850.3	24	Gtt/Att	2/38	1	2	FACETS	0.461	0.426	0.498	0.461	0.426	0.498	SUBCLONAL	1	TRUE	1	0.596944384459342	2		766	1467	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109315795	109315798	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	rs779935597	NA	P-0027608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	303	594	2	ENST00000436639.2:c.987_990del	p.Phe329LeufsTer10	p.F329Lfs*10	ENST00000436639	NM_014454.2	329	ttCTTT/tt	6/10	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.596944384459342	2		596	1011	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390975	139390975	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	497	784	3	ENST00000277541.6:c.7216C>T	p.Gln2406Ter	p.Q2406*	ENST00000277541	NM_017617.3	2406	Caa/Taa	34/34	0.331832842234526	1	FACETS	0.94	0.901	0.979	0.94	0.901	0.979	INDETERMINATE	1	TRUE	0	0.596944384459342	1		787	1243	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0027609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	143	678	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.21782012468287	2		678	1206	SUCCESS
APC	324	MSKCC	GRCh37	5	112175219	112175219	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0027609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	53	221	0	ENST00000257430.4:c.3928A>T	p.Lys1310Ter	p.K1310*	ENST00000257430	NM_000038.5	1310	Aag/Tag	16/16	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.21782012468287	2		221	486	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250779	10250779	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	142	630	0	ENST00000340748.4:c.3701G>A	p.Arg1234His	p.R1234H	ENST00000340748		1234	cGc/cAc	32/40	1	2	FACETS	0.996	0.905	1	0.996	0.905	1	CLONAL	1	TRUE	1	0.21782012468287	2		630	1309	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739013	40739013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	378	551	1	ENST00000373198.4:c.3271C>T	p.Leu1091Phe	p.L1091F	ENST00000373198	NM_133170.3	1091	Ctc/Ttc	24/32	0.170554379013243	3	FACETS	0.972	0.922	1	1	0.995	1	CLONAL	3	TRUE	1	0.21782012468287	3		552	1320	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097687	27097688	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027614-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	103	599	0	ENST00000324856.7:c.3281dup	p.Gln1095AlafsTer10	p.Q1095Afs*10	ENST00000324856	NM_006015.4	1092	-/A	12/20	1	2	FACETS	0.664	0.593	0.74	0.664	0.593	0.74	SUBCLONAL	1	TRUE	1	0.3	2		599	1034	SUCCESS
ATR	545	MSKCC	GRCh37	3	142204030	142204030	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	305	635	0	ENST00000350721.4:c.6173T>C	p.Met2058Thr	p.M2058T	ENST00000350721	NM_001184.3	2058	aTg/aCg	36/47	0.603166913971645	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.603166913971645	1		635	653	SUCCESS
ALK	238	MSKCC	GRCh37	2	29436860	29436860	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs281864720	NA	P-0121522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	224	532	0	ENST00000389048.3:c.3733T>G	p.Phe1245Val	p.F1245V	ENST00000389048	NM_004304.4	1245	Ttc/Gtc	24/29	0.162666582445309	5	FACETS	0.789	0.735	0.845	0.526	0.49	0.563	INDETERMINATE	2	NA	2	0.557377774326908	5		532	935	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441972	52441972	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0027623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	145	398	0	ENST00000460680.1:c.375+2T>C		p.X125_splice	ENST00000460680	NM_004656.3	125			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		398	391	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	148	315	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.897	0.827	0.97	0.897	0.827	0.97	CLONAL	1	TRUE	1	0.734645089663723	2		316	449	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755612	39755612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776452839	NA	P-0027624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	184	511	1	ENST00000288319.7:c.1153C>T	p.Arg385Cys	p.R385C	ENST00000288319	NM_182918.3	385	Cgc/Tgc	10/10	1	2	FACETS	0.899	0.836	0.964	0.899	0.836	0.964	CLONAL	1	TRUE	1	0.734645089663723	2		512	557	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6036981	6036981	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777286241	NA	P-0027624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	279	609	0	ENST00000265849.7:c.779C>T	p.Ser260Phe	p.S260F	ENST00000265849	NM_000535.5	260	tCc/tTc	7/15	0.711949535822423	3	FACETS	0.987	0.928	1	0.494	0.464	0.524	CLONAL	1	TRUE	1	0.734645089663723	3		609	1052	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692868	89692868	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	69	271	0	ENST00000371953.3:c.352C>G	p.His118Asp	p.H118D	ENST00000371953	NM_000314.4	118	Cat/Gat	5/9	0.734645089663723	1	FACETS	0.928	0.838	1	0.928	0.838	1	CLONAL	1	TRUE	0	0.734645089663723	1		271	128	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0027625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	367	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.369066529959032	1	FACETS	0.756	0.721	0.791	0.756	0.721	0.791	INDETERMINATE	1	TRUE	0	0.744494741723503	1		509	819	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0027625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	143	397	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.369066529959032	1	FACETS	0.334	0.304	0.364	0.334	0.304	0.364	INDETERMINATE	1	TRUE	0	0.744494741723503	1		397	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0027625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	437	629	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.744494741723503	1	FACETS	0.983	0.946	1	0.983	0.946	1	CLONAL	1	TRUE	0	0.744494741723503	1		630	750	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0027625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	351	486	2	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.744494741723503	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.744494741723503	1		488	574	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001524	150001524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	390	533	1	ENST00000253339.5:c.2080C>T	p.Arg694Cys	p.R694C	ENST00000253339		694	Cgt/Tgt	4/7	0.380572801399781	1	FACETS	0.773	0.739	0.807	0.773	0.739	0.807	INDETERMINATE	1	TRUE	0	0.744494741723503	1		534	851	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0027626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	109	796	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.16	2		796	1246	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250883	153250883	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	58	560	1	ENST00000281708.4:c.1177C>T	p.Arg393Ter	p.R393*	ENST00000281708	NM_033632.3	393	Cga/Tga	8/12	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.16	2		561	693	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0027626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1614	148	1052	0	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.16	2		1052	1762	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260581	16260581	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	98	686	0	ENST00000375759.3:c.7846C>T	p.Pro2616Ser	p.P2616S	ENST00000375759	NM_015001.2	2616	Ccc/Tcc	11/15	1	2	FACETS	0.988	0.879	1	0.988	0.879	1	CLONAL	1	TRUE	1	0.16	2		686	1240	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156328	106156328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1224621491	NA	P-0027626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	44	410	0	ENST00000380013.4:c.1229C>T	p.Pro410Leu	p.P410L	ENST00000380013	NM_001127208.2	410	cCt/cTt	3/11	1	2	FACETS	0.688	0.575	0.813	0.688	0.575	0.813	SUBCLONAL	1	TRUE	1	0.16	2		410	800	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500573	99500573	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	115	597	2	ENST00000268035.6:c.4006C>T	p.Leu1336Phe	p.L1336F	ENST00000268035	NM_000875.3	1336	Ctc/Ttc	21/21	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.16	2		599	997	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326786	62326786	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs971908780	NA	P-0027626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1324	115	824	2	ENST00000360203.5:c.3605C>T	p.Pro1202Leu	p.P1202L	ENST00000360203	NM_001283009.1	1202	cCc/cTc	34/35	1	2	FACETS	0.999	0.897	1	0.999	0.897	1	CLONAL	1	TRUE	1	0.16	2		826	1439	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549873	187549873	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	72	543	0	ENST00000441802.2:c.4368T>A	p.Phe1456Leu	p.F1456L	ENST00000441802	NM_005245.3	1456	ttT/ttA	8/27	1	2	FACETS	0.959	0.836	1	0.959	0.836	1	CLONAL	1	TRUE	1	0.16	2		543	938	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131895022	131895022	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660895	NA	P-0027626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	57	459	0	ENST00000265335.6:c.176C>T	p.Pro59Leu	p.P59L	ENST00000265335		59	cCt/cTt	2/25	1	2	FACETS	0.99	0.848	1	0.99	0.848	1	CLONAL	1	TRUE	1	0.16	2		459	720	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0027627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	96	655	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.313518237780556	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.318890459613407	1		655	470	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0027627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	77	456	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.886	0.779	1	0.886	0.779	1	CLONAL	1	TRUE	1	0.318890459613407	2		456	545	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022898	27022950	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGCGCAGGTCGCCCCCGCCGCCGCCAGCAGCCTGGGCAACCCGCCGCCGCC	GCCGCGCAGGTCGCCCCCGCCGCCGCCAGCAGCCTGGGCAACCCGCCGCCGCC	-	novel	NA	P-0027627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	16	73	0	ENST00000324856.7:c.9_61del	p.Gln4LeufsTer89	p.Q4Lfs*89	ENST00000324856	NM_006015.4	2	GCCGCGCAGGTCGCCCCCGCCGCCGCCAGCAGCCTGGGCAACCCGCCGCCGCCg/g	1/20	1	2	FACETS	0.921	0.689	1	0.921	0.689	1	CLONAL	1	TRUE	1	0.318890459613407	2		73	109	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147181	61147182	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs778615617	NA	P-0027627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	69	477	0	ENST00000295025.8:c.860dup	p.Tyr287Ter	p.Y287*	ENST00000295025	NM_002908.2	287	tac/tAac	8/11	1	2	FACETS	0.919	0.802	1	0.919	0.802	1	CLONAL	1	TRUE	1	0.318890459613407	2		477	471	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273066	18273066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	52	700	0	ENST00000222254.8:c.956G>A	p.Gly319Glu	p.G319E	ENST00000222254	NM_005027.3	319	gGa/gAa	8/16	0.474232952087589	4	FACETS	0.298	0.253	0.349	0.149	0.126	0.175	SUBCLONAL	1	TRUE	2	0.54268465923575	4		700	991	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923776	131923776	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	109	446	0	ENST00000265335.6:c.1046A>G	p.Glu349Gly	p.E349G	ENST00000265335		349	gAa/gGa	7/25	0.54268465923575	4	FACETS	0.837	0.752	0.928	0.419	0.376	0.464	CLONAL	1	TRUE	2	0.54268465923575	4		446	740	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350134	81350134	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	254	435	0	ENST00000222390.5:c.1198A>G	p.Met400Val	p.M400V	ENST00000222390	NM_000601.4	400	Atg/Gtg	10/18	1	2	FACETS	0.972	0.915	1	0.972	0.915	1	CLONAL	1	TRUE	1	0.767721955068334	2		435	681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0027630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	159	659	1	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.355544491797232	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.355544491797232	1		660	714	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123688	11123688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	182	762	0	ENST00000358026.2:c.2338G>A	p.Glu780Lys	p.E780K	ENST00000358026	NM_001128849.1	780	Gag/Aag	16/36	0.355544491797232	1	FACETS	0.986	0.91	1	0.986	0.91	1	CLONAL	1	TRUE	0	0.355544491797232	1		762	854	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243778429	243778429	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	160	570	0	ENST00000263826.5:c.596T>C	p.Val199Ala	p.V199A	ENST00000263826	NM_005465.4	199	gTa/gCa	6/13	0.299820278560459	3	FACETS	0.87	0.801	0.942	0.87	0.801	0.942	CLONAL	2	TRUE	1	0.355544491797232	3		570	609	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0027633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	105	344	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.300537392515543	1	FACETS	0.865	0.775	0.96	0.865	0.775	0.96	CLONAL	1	TRUE	0	0.29	1		345	716	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967293	134967293	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	142	728	1	ENST00000398015.3:c.2632C>A	p.Leu878Ile	p.L878I	ENST00000398015	NM_004441.4	878	Cta/Ata	14/16	1	2	FACETS	0.986	0.898	1	0.986	0.898	1	CLONAL	1	TRUE	1	0.29	2		729	993	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0027633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	219	725	1	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.300537392515543	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.29	1		726	1051	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400822	72400822	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	78	411	0	ENST00000357731.5:c.349A>G	p.Thr117Ala	p.T117A	ENST00000357731	NM_173808.2	117	Acg/Gcg	2/7	1	2	FACETS	0.944	0.83	1	0.944	0.83	1	CLONAL	1	TRUE	1	0.29	2		411	570	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149450021	149450021	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs775029262	NA	P-0027633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	91	568	1	ENST00000286301.3:c.1196G>A	p.Arg399Gln	p.R399Q	ENST00000286301	NM_005211.3	399	cGa/cAa	8/22	1	2	FACETS	0.878	0.779	0.983	0.878	0.779	0.983	CLONAL	1	TRUE	1	0.29	2		569	715	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575055	48575055	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs1555685149	NA	P-0027633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	57	362	0	ENST00000342988.3:c.250-1G>C		p.X84_splice	ENST00000342988	NM_005359.5	84			1	2	FACETS	0.701	0.601	0.809	0.701	0.601	0.809	SUBCLONAL	1	TRUE	1	0.29	2		362	561	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11276228	11276228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	73	563	0	ENST00000361445.4:c.3094G>A	p.Asp1032Asn	p.D1032N	ENST00000361445	NM_004958.3	1032	Gat/Aat	20/58	1	2	FACETS	0.646	0.564	0.735	0.646	0.564	0.735	SUBCLONAL	1	TRUE	1	0.29	2		563	779	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649891	88649891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368595543	NA	P-0027633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	44	454	0	ENST00000372037.3:c.140G>A	p.Gly47Glu	p.G47E	ENST00000372037	NM_004329.2	47	gGa/gAa	4/13	1	2	FACETS	0.565	0.473	0.667	0.565	0.473	0.667	SUBCLONAL	1	TRUE	1	0.29	2		454	537	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104353466	104353466	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	67	778	2	ENST00000369902.3:c.671G>T	p.Arg224Leu	p.R224L	ENST00000369902	NM_016169.3	224	cGg/cTg	5/12	1	2	FACETS	0.489	0.424	0.561	0.489	0.424	0.561	SUBCLONAL	1	TRUE	1	0.29	2		780	944	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589729	69589729	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	46	280	0	ENST00000168712.1:c.124G>T	p.Glu42Ter	p.E42*	ENST00000168712	NM_002007.2	42	Gag/Tag	1/3	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.29	2		280	309	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922274	100922274	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	64	558	0	ENST00000325455.5:c.2238C>G	p.Asp746Glu	p.D746E	ENST00000325455	NM_001202474.3	746	gaC/gaG	5/8	1	2	FACETS	0.738	0.639	0.845	0.738	0.639	0.845	SUBCLONAL	1	TRUE	1	0.29	2		558	598	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478882	56478882	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	261	838	1	ENST00000267101.3:c.338G>T	p.Gly113Val	p.G113V	ENST00000267101	NM_001982.3	113	gGg/gTg	3/28	0.300537392515543	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.29	1		839	1088	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233524	69233536	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTATGGCCTGC	TCTTATGGCCTGC	-	novel	NA	P-0027633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	94	458	0	ENST00000462284.1:c.1390_1402del	p.Met465HisfsTer6	p.M465Hfs*6	ENST00000462284	NM_002392.5	463	caTCTTATGGCCTGC/ca	11/11	0.300537392515543	1	FACETS	0.941	0.839	1	0.941	0.839	1	CLONAL	1	TRUE	0	0.29	1		458	589	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879747	123879747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1235814187	NA	P-0027633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	28	166	1	ENST00000330479.4:c.443C>T	p.Thr148Ile	p.T148I	ENST00000330479	NM_020382.3	148	aCc/aTc	4/9	0.300537392515543	1	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	TRUE	0	0.29	1		167	155	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225522	133225522	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	145	608	0	ENST00000320574.5:c.4142A>C	p.Tyr1381Ser	p.Y1381S	ENST00000320574	NM_006231.2	1381	tAt/tCt	32/49	0.300537392515543	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.29	1		608	704	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626686	28626686	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	102	456	0	ENST00000241453.7:c.610G>T	p.Glu204Ter	p.E204*	ENST00000241453	NM_004119.2	204	Gaa/Taa	5/24	0.300537392515543	1	FACETS	0.943	0.844	1	0.943	0.844	1	CLONAL	1	TRUE	0	0.29	1		456	638	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961683	41961683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	89	493	0	ENST00000219905.7:c.591G>A	p.Met197Ile	p.M197I	ENST00000219905	NM_001164273.1	197	atG/atA	2/24	0.300537392515543	1	FACETS	0.853	0.758	0.955	0.853	0.758	0.955	CLONAL	1	TRUE	0	0.29	1		493	615	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726682	88726682	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	144	568	0	ENST00000360948.2:c.362G>T	p.Arg121Ile	p.R121I	ENST00000360948	NM_001012338.2	121	aGa/aTa	4/19	0.300537392515543	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.29	1		568	707	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969980	81969980	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	78	399	0	ENST00000359376.3:c.3049G>T	p.Ala1017Ser	p.A1017S	ENST00000359376	NM_002661.3	1017	Gca/Tca	27/33	1	2	FACETS	0.936	0.823	1	0.936	0.823	1	CLONAL	1	TRUE	1	0.29	2		399	575	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562762	29562762	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1060500341	NA	P-0027633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	103	490	0	ENST00000356175.3:c.3842C>G	p.Ala1281Gly	p.A1281G	ENST00000356175	NM_000267.3	1281	gCc/gGc	28/57	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.29	2		490	707	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602721	10602721	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	144	781	1	ENST00000171111.5:c.857A>T	p.Gln286Leu	p.Q286L	ENST00000171111	NM_203500.1	286	cAg/cTg	3/6	0.300537392515543	1	FACETS	0.821	0.748	0.898	0.821	0.748	0.898	CLONAL	1	TRUE	0	0.29	1		782	1034	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505417	25505418	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1553423604	NA	P-0027633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	121	494	0	ENST00000264709.3:c.340dup	p.Ala114GlyfsTer10	p.A114Gfs*10	ENST00000264709	NM_175629.2	114	gcc/gGcc	4/23	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.29	2		494	792	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728682	190728682	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	73	498	0	ENST00000441310.2:c.2070G>T	p.Arg690Ser	p.R690S	ENST00000441310	NM_000534.4	690	agG/agT	10/13	1	2	FACETS	0.658	0.575	0.748	0.658	0.575	0.748	SUBCLONAL	1	TRUE	1	0.29	2		498	765	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730916	40730916	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	88	587	0	ENST00000373198.4:c.3619C>A	p.Arg1207Ser	p.R1207S	ENST00000373198	NM_133170.3	1207	Cgt/Agt	27/32	1	2	FACETS	0.774	0.685	0.869	0.774	0.685	0.869	SUBCLONAL	1	TRUE	1	0.29	2		587	784	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427702	72427702	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	96	511	0	ENST00000477973.2:c.788A>T	p.Lys263Met	p.K263M	ENST00000477973	NM_012234.5	263	aAg/aTg	4/4	NA	2	FACETS	1	0.895	1			1	INDETERMINATE	1	TRUE	NA	0.29	2		511	660	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390928	89390928	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	86	448	0	ENST00000336596.2:c.994G>T	p.Val332Phe	p.V332F	ENST00000336596	NM_005233.5	332	Gtt/Ttt	5/17	1	2	FACETS	0.938	0.831	1	0.938	0.831	1	CLONAL	1	TRUE	1	0.29	2		448	632	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593617	55593617	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	84	568	0	ENST00000288135.5:c.1683G>T	p.Glu561Asp	p.E561D	ENST00000288135	NM_000222.2	561	gaG/gaT	11/21	1	2	FACETS	0.75	0.662	0.845	0.75	0.662	0.845	SUBCLONAL	1	TRUE	1	0.29	2		568	772	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171552	32171552	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	244	611	0	ENST00000375023.3:c.3226C>A	p.Pro1076Thr	p.P1076T	ENST00000375023	NM_004557.3	1076	Ccc/Acc	20/30	0.124074741735249	5	FACETS	0.841	0.787	0.897	0.631	0.59	0.673	INDETERMINATE	3	TRUE	1	0.29	5		611	957	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066704	94066704	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	104	554	0	ENST00000369303.4:c.1055G>T	p.Ser352Ile	p.S352I	ENST00000369303	NM_004440.3	352	aGt/aTt	5/17	0.300537392515543	1	FACETS	0.975	0.875	1	0.975	0.875	1	CLONAL	1	TRUE	0	0.29	1		554	629	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874863	151874863	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	88	372	0	ENST00000262189.6:c.7675A>G	p.Ile2559Val	p.I2559V	ENST00000262189	NM_170606.2	2559	Att/Gtt	38/59	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.29	2		372	559	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430289	47430289	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	148	771	3	ENST00000377045.4:c.1564G>T	p.Val522Leu	p.V522L	ENST00000377045	NM_001654.4	522	Gtg/Ttg	15/16	0.300537392515543	1	FACETS	0.964	0.88	1	0.964	0.88	1	CLONAL	1	TRUE	0	0.29	1		774	905	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0027636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	341	565	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.947	0.898	0.996	0.947	0.898	0.996	CLONAL	1	TRUE	1	0.741732240586909	2		565	971	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426373	49426373	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	467	908	0	ENST00000301067.7:c.12115G>T	p.Glu4039Ter	p.E4039*	ENST00000301067	NM_003482.3	4039	Gag/Tag	39/54	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.741732240586909	2		908	1211	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911203	32911203	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	261	642	0	ENST00000380152.3:c.2711G>C	p.Gly904Ala	p.G904A	ENST00000380152		904	gGa/gCa	11/27	1	2	FACETS	0.915	0.861	0.97	0.915	0.861	0.97	CLONAL	1	TRUE	1	0.741732240586909	2		642	769	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057800	180057800	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0027636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	159	366	0	ENST00000261937.6:c.156-1G>T		p.X52_splice	ENST00000261937	NM_182925.4	52			1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.741732240586909	2		366	428	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209622	98209622	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1169961504	NA	P-0027636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	324	477	0	ENST00000331920.6:c.3916C>T	p.Pro1306Ser	p.P1306S	ENST00000331920	NM_000264.3	1306	Ccc/Tcc	23/24	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.741732240586909	2		477	776	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37665992	37665992	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	19	430	0	ENST00000447079.4:c.2644C>T	p.Arg882Trp	p.R882W	ENST00000447079	NM_015083.1	882	Cgg/Tgg	7/14	0.306194648913597	4	FACETS	0.458	0.348	0.588	0.229	0.174	0.294	SUBCLONAL	1	TRUE	2	0.380130314419482	4		430	301	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696434	47696434	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	16	581	0	ENST00000347630.2:c.389A>T	p.Asp130Val	p.D130V	ENST00000347630	NM_001007230.1	130	gAc/gTc	6/11	0.380130314419482	6	FACETS	0.487	0.36	0.64	0.162	0.12	0.214	SUBCLONAL	1	TRUE	3	0.380130314419482	6		581	304	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204864	NA	P-0027638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	80	541	4	ENST00000371953.3:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000371953	NM_000314.4	171	Cag/Tag	6/9	0.260471392379861	1	FACETS	0.941	0.829	1	0.941	0.829	1	CLONAL	1	TRUE	0	0.260471392379861	1		545	568	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907692	111907692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775080943	NA	P-0027638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	160	566	0	ENST00000393256.3:c.466G>A	p.Gly156Arg	p.G156R	ENST00000393256	NM_006538.4	156	Gga/Aga	3/4	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.260471392379861	2		566	1202	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746132	162746132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1374086542	NA	P-0027638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	101	310	0	ENST00000367921.3:c.2255G>A	p.Arg752His	p.R752H	ENST00000367921	NM_006182.2	752	cGc/cAc	16/18	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.260471392379861	2		310	716	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936728	32936728	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs864622552	NA	P-0027638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	109	520	0	ENST00000380152.3:c.7874G>A	p.Arg2625Lys	p.R2625K	ENST00000380152		2625	aGa/aAa	17/27	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.260471392379861	2		520	746	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68301861	68301861	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	103	614	0	ENST00000487270.1:c.263C>G	p.Ser88Cys	p.S88C	ENST00000487270	NM_133509.3	88	tCt/tGt	4/11	1	2	FACETS	0.753	0.672	0.839	0.753	0.672	0.839	SUBCLONAL	1	TRUE	1	0.260471392379861	2		614	1050	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796469	42796469	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1363	186	852	1	ENST00000575354.2:c.3026C>T	p.Ser1009Leu	p.S1009L	ENST00000575354	NM_015125.3	1009	tCa/tTa	13/20	1	2	FACETS	0.922	0.849	0.999	0.922	0.849	0.999	CLONAL	1	TRUE	1	0.260471392379861	2		853	1549	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0027639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	1376	780	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.689566897286303	6	FACETS	1	0.993	1	1	0.993	1	CLONAL	6	TRUE	0	0.689566897286303	6		780	1571	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0027639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	2532	344	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.689566897286303	10	FACETS	0.988	0.977	0.998			1	CLONAL	9	TRUE	NA	0.689566897286303	10		345	3105	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260672	1260672	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201272197	NA	P-0027639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1268	147	654	0	ENST00000310581.5:c.2887G>A	p.Gly963Ser	p.G963S	ENST00000310581	NM_198253.2	963	Ggc/Agc	12/16	0.689566897286303	7	FACETS	0.821	0.747	0.899	0.164	0.149	0.18	CLONAL	1	TRUE	2	0.689566897286303	7		654	1415	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5258034	5258034	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	321	428	1	ENST00000357368.4:c.700G>T	p.Val234Leu	p.V234L	ENST00000357368	NM_002850.3	234	Gtg/Ttg	8/38	0.662093206734194	3	FACETS	0.899	0.866	0.932	0.899	0.866	0.932	CLONAL	3	TRUE	0	0.689566897286303	3		429	464	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356281	66356282	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CA	CA	-	novel	NA	P-0027639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	440	594	0	ENST00000273854.3:c.1215_1216del	p.Cys405Ter	p.C405*	ENST00000273854	NM_004439.5	405	tgTGag/tgag	5/18	0.642443278306317	4	FACETS	0.995	0.951	1	0.995	0.951	1	CLONAL	2	TRUE	2	0.689566897286303	4		594	1084	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841470	156841470	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	358	729	2	ENST00000524377.1:c.773T>A	p.Leu258His	p.L258H	ENST00000524377	NM_002529.3	258	cTc/cAc	7/17	0.689566897286303	5	FACETS	0.991	0.94	1	0.661	0.627	0.695	CLONAL	2	TRUE	2	0.689566897286303	5		731	1066	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615117	43615117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55947360	NA	P-0027639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	195	770	1	ENST00000355710.3:c.2531G>A	p.Arg844Gln	p.R844Q	ENST00000355710	NM_020975.4	844	cGg/cAg	14/20	0.642443278306317	4	FACETS	1	0.949	1	0.515	0.477	0.555	CLONAL	1	TRUE	2	0.689566897286303	4		771	927	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724286	112724286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536611911	NA	P-0027639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	560	717	0	ENST00000369452.4:c.170C>T	p.Ser57Phe	p.S57F	ENST00000369452	NM_007373.3	57	tCc/tTc	2/9	0.689566897286303	3	FACETS	0.961	0.927	0.996	0.961	0.927	0.996	CLONAL	2	TRUE	1	0.689566897286303	3		717	1136	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29007964	29007964	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	204	304	0	ENST00000282397.4:c.805C>A	p.Pro269Thr	p.P269T	ENST00000282397	NM_002019.4	269	Cct/Act	6/30	0.642443278306317	4	FACETS	0.902	0.843	0.962	0.902	0.843	0.962	CLONAL	2	TRUE	2	0.689566897286303	4		304	554	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609556	81609556	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1224730822	NA	P-0027639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	370	525	0	ENST00000298171.2:c.1154A>G	p.Tyr385Cys	p.Y385C	ENST00000298171	NM_000369.2	385	tAt/tGt	10/10	0.629171992604469	5	FACETS	1	0.951	1			1	CLONAL	2	TRUE	NA	0.689566897286303	5		525	1091	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849653	68849653	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	431	583	0	ENST00000261769.5:c.1556A>T	p.Gln519Leu	p.Q519L	ENST00000261769	NM_004360.3	519	cAg/cTg	10/16	0.550491693184356	4	FACETS	1	0.973	1			1	CLONAL	2	TRUE	NA	0.689566897286303	4		583	1032	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016654	12016654	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200798818	NA	P-0027639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	280	390	0	ENST00000353533.5:c.790G>T	p.Ala264Ser	p.A264S	ENST00000353533	NM_003010.3	264	Gct/Tct	7/11	0.689566897286303	6	FACETS	0.904	0.849	0.96	0.301	0.283	0.32	CLONAL	2	TRUE	0	0.689566897286303	6		390	1069	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223087	5223087	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	513	753	1	ENST00000357368.4:c.2716G>T	p.Ala906Ser	p.A906S	ENST00000357368	NM_002850.3	906	Gcg/Tcg	18/38	0.662093206734194	3	FACETS	0.92	0.893	0.946	0.92	0.893	0.946	CLONAL	3	TRUE	0	0.689566897286303	3		754	725	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240307	5240307	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	542	816	0	ENST00000357368.4:c.1607G>T	p.Arg536Met	p.R536M	ENST00000357368	NM_002850.3	536	aGg/aTg	12/38	0.662093206734194	3	FACETS	0.972	0.946	0.997	0.972	0.946	0.997	CLONAL	3	TRUE	0	0.689566897286303	3		816	725	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244133	5244133	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	475	825	0	ENST00000357368.4:c.1349C>A	p.Pro450Gln	p.P450Q	ENST00000357368	NM_002850.3	450	cCg/cAg	11/38	0.662093206734194	3	FACETS	0.953	0.926	0.98	0.953	0.926	0.98	CLONAL	3	TRUE	0	0.689566897286303	3		825	648	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727183	40727183	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	150	559	0	ENST00000373198.4:c.3781C>A	p.Gln1261Lys	p.Q1261K	ENST00000373198	NM_133170.3	1261	Cag/Aag	28/32	0.689566897286303	5	FACETS	0.931	0.85	1	0.31	0.283	0.339	CLONAL	1	TRUE	2	0.689566897286303	5		559	951	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267790	46267790	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	483	601	0	ENST00000371998.3:c.2551C>T	p.Pro851Ser	p.P851S	ENST00000371998		851	Cca/Tca	14/23	0.689566897286303	5	FACETS	1	0.975	1	0.684	0.655	0.715	CLONAL	2	TRUE	2	0.689566897286303	5		601	1388	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817378	39817445	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGGGGGTTGAGACAGCCAATCCTGCTGAGGGACGCGTGGGCTCATCTTGGAAGTCTGTCCATAGTC	GCTGGGGGTTGAGACAGCCAATCCTGCTGAGGGACGCGTGGGCTCATCTTGGAAGTCTGTCCATAGTC	-	novel	NA	P-0027639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	321	557	0	ENST00000288319.7:c.118_185del	p.Asp40GlnfsTer9	p.D40Qfs*9	ENST00000288319	NM_182918.3	40	GACTATGGACAGACTTCCAAGATGAGCCCACGCGTCCCTCAGCAGGATTGGCTGTCTCAACCCCCAGCc/c	2/10	0.689566897286303	2	FACETS	0.954	0.916	0.991	0.954	0.916	0.991	CLONAL	2	TRUE	0	0.689566897286303	2		557	488	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564455	55564455	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	289	386	0	ENST00000288135.5:c.343G>T	p.Ala115Ser	p.A115S	ENST00000288135	NM_000222.2	115	Gcc/Tcc	3/21	0.642443278306317	4	FACETS	0.884	0.835	0.934	0.884	0.835	0.934	CLONAL	2	TRUE	2	0.689566897286303	4		386	801	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467662	66467662	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	373	435	0	ENST00000273854.3:c.607G>T	p.Gly203Ter	p.G203*	ENST00000273854	NM_004439.5	203	Gga/Tga	3/18	0.642443278306317	4	FACETS	0.924	0.879	0.969	0.924	0.879	0.969	CLONAL	2	TRUE	2	0.689566897286303	4		435	989	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067121	143067121	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	365	441	2	ENST00000262992.4:c.1592G>T	p.Ser531Ile	p.S531I	ENST00000262992	NM_001101669.1	531	aGc/aTc	16/24	0.642443278306317	4	FACETS	0.921	0.876	0.967	0.921	0.876	0.967	CLONAL	2	TRUE	2	0.689566897286303	4		443	971	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143129589	143129589	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	364	437	0	ENST00000262992.4:c.1061C>A	p.Pro354His	p.P354H	ENST00000262992	NM_001101669.1	354	cCt/cAt	12/24	0.642443278306317	4	FACETS	0.979	0.932	1	0.979	0.932	1	CLONAL	2	TRUE	2	0.689566897286303	4		437	911	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531091	187531091	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	332	561	0	ENST00000441802.2:c.9932G>T	p.Gly3311Val	p.G3311V	ENST00000441802	NM_005245.3	3311	gGc/gTc	15/27	0.642443278306317	4	FACETS	0.917	0.87	0.965	0.917	0.87	0.965	CLONAL	2	TRUE	2	0.689566897286303	4		561	887	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939526	68939526	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	125	510	0	ENST00000288368.4:c.511C>A	p.Gln171Lys	p.Q171K	ENST00000288368	NM_024870.2	171	Caa/Aaa	5/40	0.51202193174241	4	FACETS	0.616	0.557	0.679	0.308	0.278	0.34	SUBCLONAL	1	TRUE	2	0.689566897286303	4		510	994	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021830	69021830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	589	675	1	ENST00000288368.4:c.3118G>A	p.Val1040Met	p.V1040M	ENST00000288368	NM_024870.2	1040	Gtg/Atg	25/40	0.51202193174241	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	2	0.689566897286303	4		676	1332	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340361	8340361	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	405	560	0	ENST00000356435.5:c.5235G>T	p.Lys1745Asn	p.K1745N	ENST00000356435		1745	aaG/aaT	31/35	0.689566897286303	5	FACETS	0.995	0.947	1	0.663	0.631	0.696	CLONAL	2	TRUE	2	0.689566897286303	5		560	1201	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341976	8341976	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	187	342	0	ENST00000356435.5:c.4664C>A	p.Ala1555Glu	p.A1555E	ENST00000356435		1555	gCg/gAg	29/35	0.689566897286303	5	FACETS	0.778	0.721	0.837	0.519	0.481	0.558	SUBCLONAL	2	TRUE	2	0.689566897286303	5		342	709	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486014	8486014	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	381	600	0	ENST00000356435.5:c.2803G>C	p.Val935Leu	p.V935L	ENST00000356435		935	Gtc/Ctc	17/35	0.689566897286303	5	FACETS	0.93	0.883	0.977	0.62	0.589	0.652	CLONAL	2	TRUE	2	0.689566897286303	5		600	1209	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0027640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	39	636	0	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	1	2	FACETS	0.504	0.416	0.603	0.504	0.416	0.603	SUBCLONAL	1	TRUE	1	0.16	2		636	967	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965936	25965936	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	85	549	0	ENST00000435504.4:c.3270del	p.Phe1090LeufsTer37	p.F1090Lfs*37	ENST00000435504		1090	ttC/tt	13/13	1	2	FACETS	0.482	0.426	0.542	0.482	0.426	0.542	SUBCLONAL	1	TRUE	1	0.494919257509737	2		549	713	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0027646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	33	434	2	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.240002682335325	2		436	253	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106282	27106282	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	83	627	0	ENST00000324856.7:c.5893del	p.Thr1965ProfsTer50	p.T1965Pfs*50	ENST00000324856	NM_006015.4	1965	Acc/cc	20/20	0.240002682335325	1	FACETS	0.896	0.791	1	0.896	0.791	1	CLONAL	1	TRUE	0	0.240002682335325	1		627	679	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0027648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	200	780	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.263133343947919	3	FACETS	1	0.933	1	1	0.933	1	CLONAL	2	TRUE	1	0.263133343947919	3		780	855	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	230	528	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.263133343947919	4	FACETS	1	0.987	1	0.817	0.763	0.873	CLONAL	2	TRUE	1	0.263133343947919	4		529	901	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435399	110435399	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1264962918	NA	P-0027648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	103	588	1	ENST00000375856.3:c.3002C>T	p.Ser1001Phe	p.S1001F	ENST00000375856	NM_003749.2	1001	tCc/tTc	1/2	0.263133343947919	3	FACETS	0.876	0.783	0.976	0.438	0.391	0.488	CLONAL	1	TRUE	1	0.263133343947919	3		589	1011	SUCCESS
APC	324	MSKCC	GRCh37	5	112173600	112173600	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1060503310	NA	P-0027648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	114	275	0	ENST00000257430.4:c.2309C>G	p.Ser770Ter	p.S770*	ENST00000257430	NM_000038.5	770	tCa/tGa	16/16	0.227701104517858	2	FACETS	0.843	0.762	0.927	0.843	0.762	0.927	CLONAL	2	TRUE	0	0.263133343947919	2		275	514	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0027650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	8	344	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.662	0.426	0.967	0.662	0.426	0.967	SUBCLONAL	1	TRUE	1	0.13	2		345	186	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0027650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	13	294	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.478	0.34	0.649	0.478	0.34	0.649	SUBCLONAL	1	TRUE	1	0.13	2		294	418	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247911	59247912	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0027653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	152	695	0	ENST00000371222.2:c.831dup	p.Ala278ArgfsTer32	p.A278Rfs*32	ENST00000371222	NM_002228.3	277	-/C	1/1	0.44352086671227	1	FACETS	0.679	0.622	0.738	0.679	0.622	0.738	SUBCLONAL	1	TRUE	0	0.468636556118579	1		695	732	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980337	201980338	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0027653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	137	741	0	ENST00000359651.3:c.76dup	p.Leu26ProfsTer14	p.L26Pfs*14	ENST00000359651		25	acc/aCcc	1/8	0.389508741024717	3	FACETS	0.733	0.666	0.804	0.367	0.333	0.402	SUBCLONAL	1	TRUE	1	0.468636556118579	3		741	984	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984364	201984365	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0027653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	344	606	0	ENST00000359651.3:c.1030dup	p.Arg344ProfsTer127	p.R344Pfs*127	ENST00000359651		343	-/C	8/8	0.389508741024717	3	FACETS	0.887	0.841	0.934	0.887	0.841	0.934	CLONAL	2	TRUE	1	0.468636556118579	3		606	1021	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574000	7574000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	368	576	0	ENST00000269305.4:c.1027G>T	p.Glu343Ter	p.E343*	ENST00000269305	NM_001126112.2	343	Gag/Tag	10/11	0.49932474785602	2	FACETS	0.962	0.919	1	0.962	0.919	1	CLONAL	2	TRUE	0	0.49932474785602	2		576	766	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657313	29657313	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	246	456	1	ENST00000356175.3:c.5547-1G>T		p.X1849_splice	ENST00000356175	NM_000267.3	1849			0.478489428549274	5	FACETS	1	0.974	1	0.714	0.67	0.76	CLONAL	2	TRUE	2	0.49932474785602	5		457	804	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483000	29483000	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs1263745475	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	229	308	2	ENST00000356175.3:c.61-1G>T		p.X21_splice	ENST00000356175	NM_000267.3	21			0.478489428549274	5	FACETS	0.871	0.817	0.925	0.871	0.817	0.925	CLONAL	3	TRUE	2	0.49932474785602	5		310	614	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846343	156846343	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	299	575	0	ENST00000524377.1:c.1784G>A	p.Gly595Glu	p.G595E	ENST00000524377	NM_002529.3	595	gGg/gAg	14/17	0.472926762970155	4	FACETS	0.969	0.914	1	0.969	0.914	1	CLONAL	2	TRUE	2	0.49932474785602	4		575	927	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162722964	162722964	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	271	502	0	ENST00000367921.3:c.162G>T	p.Glu54Asp	p.E54D	ENST00000367921	NM_006182.2	54	gaG/gaT	4/18	0.472926762970155	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	2	0.49932474785602	4		502	795	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809322	243809322	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	215	343	0	ENST00000263826.5:c.302C>A	p.Ala101Asp	p.A101D	ENST00000263826	NM_005465.4	101	gCt/gAt	4/13	0.472926762970155	4	FACETS	0.965	0.901	1	0.965	0.901	1	CLONAL	2	TRUE	2	0.49932474785602	4		343	669	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996861	100996861	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	336	527	0	ENST00000325455.5:c.1666C>G	p.Gln556Glu	p.Q556E	ENST00000325455	NM_001202474.3	556	Caa/Gaa	2/8	0.463288682184856	4	FACETS	1	0.992	1	0.815	0.775	0.856	CLONAL	2	TRUE	1	0.49932474785602	4		527	825	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	443491	443491	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	127	446	0	ENST00000399788.2:c.1406C>A	p.Pro469Gln	p.P469Q	ENST00000399788	NM_001042603.1	469	cCg/cAg	11/28	0.444162147308822	3	FACETS	0.898	0.815	0.985	0.449	0.407	0.493	CLONAL	1	TRUE	1	0.49932474785602	3		446	708	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	461394	461394	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	116	377	0	ENST00000399788.2:c.1126G>T	p.Asp376Tyr	p.D376Y	ENST00000399788	NM_001042603.1	376	Gat/Tat	9/28	0.444162147308822	3	FACETS	0.914	0.826	1	0.457	0.413	0.504	CLONAL	1	TRUE	1	0.49932474785602	3		377	635	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111886054	111886054	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	253	456	0	ENST00000341259.2:c.1676C>A	p.Ser559Ter	p.S559*	ENST00000341259	NM_005475.2	559	tCa/tAa	8/8	0.444162147308822	3	FACETS	0.914	0.86	0.969	0.914	0.86	0.969	CLONAL	2	TRUE	1	0.49932474785602	3		456	693	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432040	121432040	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	181	602	0	ENST00000257555.6:c.787C>A	p.Arg263Ser	p.R263S	ENST00000257555		263	Cgt/Agt	4/10	0.444162147308822	3	FACETS	0.986	0.91	1	0.493	0.455	0.533	CLONAL	1	TRUE	1	0.49932474785602	3		602	919	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134297	41134297	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	197	384	1	ENST00000379561.5:c.1331A>T	p.Asp444Val	p.D444V	ENST00000379561	NM_002015.3	444	gAc/gTc	2/3	0.492224171734581	2	FACETS	0.944	0.886	1	0.944	0.886	1	CLONAL	2	TRUE	0	0.49932474785602	2		385	418	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566164	95566164	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	232	460	0	ENST00000393063.1:c.4159G>T	p.Val1387Leu	p.V1387L	ENST00000393063	NM_030621.3	1387	Gta/Tta	23/28	0.303199112666853	5	FACETS	1	0.98	1	0.741	0.694	0.789	CLONAL	2	TRUE	2	0.49932474785602	5		460	731	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680725	88680725	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	282	566	0	ENST00000360948.2:c.532G>T	p.Gly178Trp	p.G178W	ENST00000360948	NM_001012338.2	178	Ggg/Tgg	6/19	0.49932474785602	5	FACETS	0.867	0.815	0.921	0.578	0.543	0.614	CLONAL	2	TRUE	2	0.49932474785602	5		566	1139	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031880	10031880	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs765104792	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	222	499	1	ENST00000330684.3:c.943G>T	p.Glu315Ter	p.E315*	ENST00000330684	NM_001134407.1	315	Gag/Tag	3/13	0.346079777827422	6	FACETS	0.911	0.849	0.976	0.456	0.424	0.488	CLONAL	2	TRUE	2	0.49932474785602	6		500	975	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10259662	10259662	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	203	393	0	ENST00000340748.4:c.2570G>T	p.Gly857Val	p.G857V	ENST00000340748		857	gGg/gTg	26/40	0.444162147308822	3	FACETS	0.902	0.843	0.963	0.902	0.843	0.963	CLONAL	2	TRUE	1	0.49932474785602	3		393	563	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872238	45872238	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs761965639	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	171	537	2	ENST00000391945.4:c.196G>T	p.Glu66Ter	p.E66*	ENST00000391945	NM_000400.3	66	Gag/Tag	4/23	0.444162147308822	3	FACETS	1	0.957	1	0.529	0.487	0.573	CLONAL	1	TRUE	1	0.49932474785602	3		539	809	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965665	25965665	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	165	470	0	ENST00000435504.4:c.3541A>G	p.Thr1181Ala	p.T1181A	ENST00000435504		1181	Act/Gct	13/13	0.499767461547306	4	FACETS	0.863	0.791	0.939	0.288	0.263	0.313	CLONAL	1	TRUE	1	0.49932474785602	4		470	1148	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966954	25966954	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	516	499	0	ENST00000435504.4:c.2252A>T	p.Gln751Leu	p.Q751L	ENST00000435504		751	cAg/cTg	13/13	0.499767461547306	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	1	0.49932474785602	4		499	970	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190742002	190742002	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	233	403	0	ENST00000441310.2:c.2639A>T	p.Glu880Val	p.E880V	ENST00000441310	NM_000534.4	880	gAa/gTa	13/13	0.499767461547306	3	FACETS	0.982	0.923	1	0.982	0.923	1	CLONAL	2	TRUE	1	0.49932474785602	3		403	594	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439155	52439155	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	282	572	1	ENST00000460680.1:c.1087A>T	p.Asn363Tyr	p.N363Y	ENST00000460680	NM_004656.3	363	Aat/Tat	11/17	0.492224171734581	2	FACETS	0.941	0.893	0.99	0.941	0.893	0.99	CLONAL	2	TRUE	0	0.49932474785602	2		573	600	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468442	89468443	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	145	347	0	ENST00000336596.2:c.1979_1980del	p.Thr660ArgfsTer18	p.T660Rfs*18	ENST00000336596	NM_005233.5	659	tAC/t	11/17	0.492224171734581	2	FACETS	0.816	0.754	0.878	0.816	0.754	0.878	CLONAL	2	TRUE	0	0.49932474785602	2		347	356	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644656	134644656	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	189	393	0	ENST00000398015.3:c.59-2A>G		p.X20_splice	ENST00000398015	NM_004441.4	20			0.472926762970155	4	FACETS	0.892	0.829	0.958	0.892	0.829	0.958	CLONAL	2	TRUE	2	0.49932474785602	4		393	636	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169940465	169940465	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	220	354	0	ENST00000295797.4:c.8C>A	p.Thr3Asn	p.T3N	ENST00000295797	NM_002740.5	3	aCc/aAc	1/18	0.472926762970155	4	FACETS	0.933	0.872	0.996	0.933	0.872	0.996	CLONAL	2	TRUE	2	0.49932474785602	4		354	708	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607266	189607266	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	275	569	0	ENST00000264731.3:c.1645A>T	p.Ile549Phe	p.I549F	ENST00000264731	NM_003722.4	549	Att/Ttt	12/14	0.472926762970155	4	FACETS	0.95	0.895	1	0.95	0.895	1	CLONAL	2	TRUE	2	0.49932474785602	4		569	869	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981537	55981537	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	115	383	0	ENST00000263923.4:c.400G>T	p.Gly134Ter	p.G134*	ENST00000263923	NM_002253.2	134	Gga/Tga	4/30	0.499767461547306	3	FACETS	1	0.929	1	0.517	0.467	0.569	CLONAL	1	TRUE	1	0.49932474785602	3		383	557	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629155	86629155	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	183	380	0	ENST00000274376.6:c.899+1G>T		p.X300_splice	ENST00000274376	NM_002890.2	300			0.49932474785602	2	FACETS	0.937	0.878	0.997	0.937	0.878	0.997	CLONAL	2	TRUE	0	0.49932474785602	2		380	391	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501445	149501445	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	314	482	0	ENST00000261799.4:c.2342C>A	p.Ser781Tyr	p.S781Y	ENST00000261799	NM_002609.3	781	tCt/tAt	16/23	0.49932474785602	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.49932474785602	2		482	618	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158689	26158689	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	10	92	0	ENST00000289316.2:c.292G>T	p.Ala98Ser	p.A98S	ENST00000289316	NM_138720.2	98	Gcc/Tcc	1/2	0.303199112666853	5	FACETS	0.438	0.297	0.614	0.146	0.099	0.205	SUBCLONAL	1	TRUE	2	0.49932474785602	5		92	160	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197348	26197348	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	162	331	0	ENST00000356476.2:c.131C>A	p.Pro44His	p.P44H	ENST00000356476		44	cCc/cAc	1/1	0.303199112666853	5	FACETS	1	0.938	1	0.679	0.627	0.733	CLONAL	2	TRUE	2	0.49932474785602	5		331	557	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181885	32181885	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	216	511	0	ENST00000375023.3:c.2167+2T>A		p.X723_splice	ENST00000375023	NM_004557.3	723			0.303199112666853	5	FACETS	0.964	0.899	1	0.643	0.599	0.687	CLONAL	2	TRUE	2	0.49932474785602	5		511	785	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6027077	6027077	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	239	232	0	ENST00000265849.7:c.1319del	p.Pro440GlnfsTer8	p.P440Qfs*8	ENST00000265849	NM_000535.5	440	cCa/ca	11/15	0.49932474785602	5	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	TRUE	2	0.49932474785602	5		232	532	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845982	151845982	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	74	441	0	ENST00000262189.6:c.13030G>C	p.Asp4344His	p.D4344H	ENST00000262189	NM_170606.2	4344	Gat/Cat	52/59	0.472926762970155	4	FACETS	0.564	0.493	0.641	0.282	0.246	0.321	SUBCLONAL	1	TRUE	2	0.49932474785602	4		441	788	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538747	23538747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752426352	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	171	283	0	ENST00000380871.4:c.692C>T	p.Pro231Leu	p.P231L	ENST00000380871	NM_006167.3	231	cCa/cTa	2/2	NA	2	FACETS	0.97	0.907	1			1	INDETERMINATE	2	TRUE	NA	0.49932474785602	2		283	353	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5557738	5557738	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	175	350	0	ENST00000397747.3:c.752T>G	p.Leu251Arg	p.L251R	ENST00000397747	NM_025239.3	251	cTg/cGg	5/7	NA	2	FACETS	0.945	0.883	1			1	INDETERMINATE	2	TRUE	NA	0.49932474785602	2		350	371	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314940	1314940	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	129	515	0	ENST00000400841.2:c.721C>A	p.Leu241Ile	p.L241I	ENST00000400841		241	Ctt/Att	6/6	0.499767461547306	0	FACETS	0.619	0.566	0.674			1	SUBCLONAL	1	TRUE	NA	0.49932474785602	0		515	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0027656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	346	630	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.429661238997238	2	FACETS	0.899	0.854	0.943	0.899	0.854	0.943	CLONAL	2	TRUE	0	0.443611781420429	2		632	868	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912092	114912101	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TGGCATGCAC	TGGCATGCAC	-	novel	NA	P-0027656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	104	338	0	ENST00000543371.1:c.1164_1173del	p.Trp388CysfsTer100	p.W388Cfs*100	ENST00000543371	NM_001198531.1	388	TGGCATGCACtg/tg	11/14	1	2	FACETS	0.851	0.764	0.942	0.851	0.764	0.942	CLONAL	1	TRUE	1	0.443611781420429	2		338	551	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584731	48584732	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	113	351	0	ENST00000342988.3:c.811dup	p.Ser271LysfsTer2	p.S271Kfs*2	ENST00000342988	NM_005359.5	270	gga/ggAa	7/12	0.443611781420429	1	FACETS	0.868	0.785	0.953	0.868	0.785	0.953	CLONAL	1	TRUE	0	0.443611781420429	1		351	457	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249469	153249469	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	560	485	0	ENST00000281708.4:c.1309G>A	p.Gly437Arg	p.G437R	ENST00000281708	NM_033632.3	437	Gga/Aga	9/12	0.412759711637695	4	FACETS	0.943	0.912	0.974	0.943	0.912	0.974	CLONAL	4	TRUE	0	0.443611781420429	4		485	966	SUCCESS
APC	324	MSKCC	GRCh37	5	112111390	112111390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs863225362	NA	P-0027656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	88	311	0	ENST00000257430.4:c.487C>T	p.Gln163Ter	p.Q163*	ENST00000257430	NM_000038.5	163	Cag/Tag	5/16	1	2	FACETS	0.81	0.72	0.905	0.81	0.72	0.905	CLONAL	1	TRUE	1	0.443611781420429	2		311	490	SUCCESS
APC	324	MSKCC	GRCh37	5	112175467	112175471	+	frameshift_variant	Frame_Shift_Del	DEL	ACTTG	ACTTG	-	novel	NA	P-0027656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	84	242	0	ENST00000257430.4:c.4177_4181del	p.Leu1393Ter	p.L1393*	ENST00000257430	NM_000038.5	1392	tcACTTGat/tcat	16/16	1	2	FACETS	0.879	0.78	0.983	0.879	0.78	0.983	CLONAL	1	TRUE	1	0.443611781420429	2		242	431	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0027657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	90	509	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.254604395773207	2		509	653	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0027660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	273	781	1	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.169984349005552	2	FACETS	1	0.992	1	0.693	0.649	0.738	INDETERMINATE	1	FALSE	0	0.3	2		782	1314	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878061	48878062	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1131690852	NA	P-0027660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	149	293	0	ENST00000267163.4:c.19dup	p.Arg7ProfsTer24	p.R7Pfs*24	ENST00000267163	NM_000321.2	5	acc/aCcc	1/27	0.3	3	FACETS	0.933	0.856	1	0.622	0.57	0.676	CLONAL	2	FALSE	0	0.3	3		293	612	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771155	161771155	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs757263675	NA	P-0027660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	91	563	0	ENST00000366898.1:c.1374G>T	p.Met458Ile	p.M458I	ENST00000366898	NM_004562.2	458	atG/atT	12/12	0.173692553603203	3	FACETS	0.659	0.583	0.74	0.329	0.291	0.37	INDETERMINATE	1	FALSE	1	0.3	3		563	1059	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551886	150551886	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	94	362	2	ENST00000369026.2:c.121G>C	p.Glu41Gln	p.E41Q	ENST00000369026	NM_021960.4	41	Gag/Cag	1/3	0.3	3	FACETS	0.993	0.883	1	0.496	0.441	0.555	CLONAL	1	FALSE	1	0.3	3		364	726	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70432741	70432741	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	124	576	0	ENST00000373644.4:c.4763G>A	p.Cys1588Tyr	p.C1588Y	ENST00000373644	NM_030625.2	1588	tGt/tAt	8/12	0.169984349005552	2	FACETS	1	0.96	1	0.556	0.503	0.611	INDETERMINATE	1	FALSE	0	0.3	2		576	744	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864234	57864234	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	125	492	0	ENST00000228682.2:c.1711C>G	p.Pro571Ala	p.P571A	ENST00000228682	NM_005269.2	571	Cca/Gca	12/12	0.173692553603203	3	FACETS	1	0.97	1	0.586	0.531	0.645	INDETERMINATE	1	FALSE	1	0.3	3		492	817	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888210	112888210	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	65	539	0	ENST00000351677.2:c.226G>T	p.Glu76Ter	p.E76*	ENST00000351677	NM_002834.3	76	Gag/Tag	3/16	0.154711263419678	3	FACETS	0.603	0.521	0.691	0.201	0.173	0.231	INDETERMINATE	1	FALSE	0	0.3	3		539	827	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467760	99467760	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs150221450	NA	P-0027660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	81	308	2	ENST00000268035.6:c.2629C>T	p.Arg877Ter	p.R877*	ENST00000268035	NM_000875.3	877	Cga/Tga	13/21	0.3	3	FACETS	1	0.911	1	0.346	0.305	0.39	CLONAL	1	FALSE	0	0.3	3		310	598	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825537	50825537	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	85	450	0	ENST00000398568.2:c.2168G>T	p.Gly723Val	p.G723V	ENST00000398568	NM_001042412.1	723	gGc/gTc	14/18	0.144700522164626	4	FACETS	1	0.951	1	0.572	0.506	0.643	INDETERMINATE	1	FALSE	2	0.3	4		450	644	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228154	36228154	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	92	626	0	ENST00000222270.7:c.7540G>C	p.Val2514Leu	p.V2514L	ENST00000222270	NM_014727.1	2514	Gtc/Ctc	33/37	0.144700522164626	4	FACETS	0.74	0.655	0.83	0.37	0.327	0.415	INDETERMINATE	1	FALSE	2	0.3	4		626	1078	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1959722	1959722	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	84	333	0	ENST00000382891.5:c.2944C>A	p.Gln982Lys	p.Q982K	ENST00000382891	NM_133335.3	982	Cag/Aag	16/22	0.169984349005552	2	FACETS	0.876	0.775	0.985	0.438	0.387	0.493	INDETERMINATE	1	FALSE	0	0.3	2		333	639	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628326	187628326	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	128	516	0	ENST00000441802.2:c.2656G>T	p.Glu886Ter	p.E886*	ENST00000441802	NM_005245.3	886	Gag/Tag	2/27	0.169984349005552	2	FACETS	1	0.938	1	0.523	0.474	0.575	INDETERMINATE	1	FALSE	0	0.3	2		516	816	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332865	152332865	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	39	410	0	ENST00000206249.3:c.1171C>A	p.Leu391Ile	p.L391I	ENST00000206249	NM_000125.3	391	Ctc/Atc	5/8	0.173692553603203	3	FACETS	0.448	0.37	0.535	0.224	0.185	0.268	INDETERMINATE	1	FALSE	1	0.3	3		410	668	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877975	151877975	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	93	324	0	ENST00000262189.6:c.6970G>T	p.Asp2324Tyr	p.D2324Y	ENST00000262189	NM_170606.2	2324	Gat/Tat	36/59	0.169984349005552	2	FACETS	1	0.968	1	0.614	0.548	0.684	INDETERMINATE	1	FALSE	0	0.3	2		324	505	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981355	68981355	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	67	382	0	ENST00000288368.4:c.1427A>T	p.Gln476Leu	p.Q476L	ENST00000288368	NM_024870.2	476	cAg/cTg	12/40	0.169984349005552	2	FACETS	1	0.912	1	0.529	0.461	0.602	INDETERMINATE	1	FALSE	0	0.3	2		382	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519980	NA	P-0027661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	300	604	0	ENST00000269305.4:c.528C>G	p.Cys176Trp	p.C176W	ENST00000269305	NM_001126112.2	176	tgC/tgG	5/11	0.558184790102362	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.558184790102362	1		604	699	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0027664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	300	872	0	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.322193261259797	2	FACETS	0.884	0.834	0.936	0.884	0.834	0.936	CLONAL	2	TRUE	0	0.322193261259797	2		872	1053	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589755	69589755	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	24	177	0	ENST00000168712.1:c.98C>A	p.Thr33Asn	p.T33N	ENST00000168712	NM_002007.2	33	aCt/aAt	1/3	0.268092540445876	4	FACETS	0.604	0.474	0.754	0.302	0.237	0.377	SUBCLONAL	1	TRUE	2	0.322193261259797	4		177	326	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66468001	66468001	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	37	241	0	ENST00000273854.3:c.268G>C	p.Asp90His	p.D90H	ENST00000273854	NM_004439.5	90	Gat/Cat	3/18	0.247399481739769	2	FACETS	0.601	0.496	0.718	0.301	0.248	0.359	SUBCLONAL	1	TRUE	0	0.322193261259797	2		241	382	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099569	157099569	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	52	179	0	ENST00000346085.5:c.506G>T	p.Gly169Val	p.G169V	ENST00000346085	NM_020732.3	169	gGc/gTc	1/20	1	2	FACETS	0.724	0.617	0.84	0.724	0.617	0.84	SUBCLONAL	1	TRUE	1	0.322193261259797	2		179	446	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372553	55372553	+	stop_lost	Nonstop_Mutation	SNP	T	T	A	novel	NA	P-0027664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	95	550	1	ENST00000297316.4:c.1243T>A	p.Ter415ArgextTer48	p.*415Rext*48	ENST00000297316	NM_022454.3	415	Tga/Aga	2/2	1	2	FACETS	0.507	0.45	0.568	0.507	0.45	0.568	SUBCLONAL	1	TRUE	1	0.322193261259797	2		551	1164	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953760	48953760	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913302	NA	P-0027673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	262	228	0	ENST00000267163.4:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000267163	NM_000321.2	455	Cga/Tga	14/27	0.520730904081187	3	FACETS	0.877	0.833	0.921	0.877	0.833	0.921	CLONAL	3	TRUE	0	0.520730904081187	3		228	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1427441061	NA	P-0027673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	315	512	0	ENST00000269305.4:c.560-2A>G		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.510468159100926	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.520730904081187	2		512	585	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619238	37619238	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1461056187	NA	P-0027673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	147	395	0	ENST00000447079.4:c.914A>G	p.Tyr305Cys	p.Y305C	ENST00000447079	NM_015083.1	305	tAt/tGt	1/14	0.520730904081187	3	FACETS	0.994	0.909	1	0.497	0.454	0.541	CLONAL	1	TRUE	1	0.520730904081187	3		395	716	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012929	176012929	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0027673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	143	431	0	ENST00000367669.3:c.1447A>T	p.Lys483Ter	p.K483*	ENST00000367669	NM_022457.5	483	Aag/Tag	13/20	0.520730904081187	4	FACETS	0.882	0.803	0.964	0.294	0.267	0.322	CLONAL	1	TRUE	1	0.520730904081187	4		431	947	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	443499	443499	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	168	424	0	ENST00000399788.2:c.1398G>T	p.Met466Ile	p.M466I	ENST00000399788	NM_001042603.1	466	atG/atT	11/28	0.520730904081187	3	FACETS	0.902	0.829	0.978	0.451	0.414	0.489	CLONAL	1	TRUE	1	0.520730904081187	3		424	902	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21553911	21553911	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	425	441	0	ENST00000382592.4:c.2691G>C	p.Trp897Cys	p.W897C	ENST00000382592	NM_014572.2	897	tgG/tgC	7/8	0.520730904081187	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	3	TRUE	0	0.520730904081187	3		441	684	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223343	2223343	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	304	562	0	ENST00000326181.6:c.955C>G	p.Leu319Val	p.L319V	ENST00000326181	NM_032271.2	319	Ctg/Gtg	10/21	0.520730904081187	3	FACETS	0.98	0.929	1	0.98	0.929	1	CLONAL	2	TRUE	1	0.520730904081187	3		562	751	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865840	56865840	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	110	365	0	ENST00000308159.5:c.1172A>G	p.Tyr391Cys	p.Y391C	ENST00000308159	NM_014669.4	391	tAc/tGc	11/22	1	2	FACETS	0.888	0.802	0.977	0.888	0.802	0.977	CLONAL	1	TRUE	1	0.520730904081187	2		365	476	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677834	58677834	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	354	611	1	ENST00000305921.3:c.59A>T	p.Tyr20Phe	p.Y20F	ENST00000305921	NM_003620.3	20	tAc/tTc	1/6	0.520730904081187	3	FACETS	0.912	0.867	0.958	0.912	0.867	0.958	CLONAL	2	TRUE	1	0.520730904081187	3		612	939	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098975	178098975	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	176	214	0	ENST00000397062.3:c.70T>G	p.Trp24Gly	p.W24G	ENST00000397062	NM_006164.4	24	Tgg/Ggg	2/5	0.500341251468426	4	FACETS	0.919	0.852	0.988	0.919	0.852	0.988	CLONAL	2	TRUE	2	0.520730904081187	4		214	559	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42838075	42838075	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	142	370	0	ENST00000398585.3:c.1584C>A	p.Asp528Glu	p.D528E	ENST00000398585	NM_001135099.1	528	gaC/gaA	14/14	1	2	FACETS	0.915	0.837	0.996	0.915	0.837	0.996	CLONAL	1	TRUE	1	0.520730904081187	2		370	596	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131163	55131163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	351	578	0	ENST00000257290.5:c.706G>A	p.Ala236Thr	p.A236T	ENST00000257290	NM_006206.4	236	Gct/Act	5/23	0.520730904081187	4	FACETS	0.833	0.789	0.879			1	CLONAL	2	TRUE	NA	0.520730904081187	4		578	1230	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950528	38950528	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	139	367	0	ENST00000357387.3:c.3422T>G	p.Phe1141Cys	p.F1141C	ENST00000357387	NM_152756.3	1141	tTt/tGt	31/38	0.520730904081187	6	FACETS	0.922	0.837	1	0.231	0.209	0.253	CLONAL	1	TRUE	2	0.520730904081187	6		367	1182	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829009	128829009	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	43	66	0	ENST00000249373.3:c.17C>T	p.Pro6Leu	p.P6L	ENST00000249373	NM_005631.4	6	cCa/cTa	1/12	0.520730904081187	3	FACETS	1	0.959	1	0.713	0.608	0.824	CLONAL	1	TRUE	1	0.520730904081187	3		66	146	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878898	117878898	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	139	424	0	ENST00000297338.2:c.71A>T	p.Asp24Val	p.D24V	ENST00000297338	NM_006265.2	24	gAt/gTt	2/14	0.520730904081187	6	FACETS	0.946	0.859	1			1	CLONAL	1	TRUE	NA	0.520730904081187	6		424	1152	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76949319	76949319	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	158	432	0	ENST00000373344.5:c.478C>T	p.Arg160Cys	p.R160C	ENST00000373344	NM_000489.3	160	Cgc/Tgc	6/35	NA	2	FACETS	0.879	0.808	0.954			1	INDETERMINATE	1	TRUE	NA	0.520730904081187	2		432	690	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0027675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	541	635	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.942910749915518	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.942910749915518	1		635	567	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447343	49447343	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	543	646	1	ENST00000301067.7:c.755A>C	p.His252Pro	p.H252P	ENST00000301067	NM_003482.3	252	cAc/cCc	6/54	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.942910749915518	2		647	1105	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416836	121416836	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs755294539	NA	P-0027675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	69	772	0	ENST00000257555.6:c.265C>A	p.Leu89Met	p.L89M	ENST00000257555		89	Ctg/Atg	1/10	1	2	FACETS	0.121	0.104	0.138	0.121	0.104	0.138	SUBCLONAL	1	TRUE	1	0.942910749915518	2		772	1213	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220014	133220014	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	366	537	1	ENST00000320574.5:c.4423C>A	p.Gln1475Lys	p.Q1475K	ENST00000320574	NM_006231.2	1475	Cag/Aag	34/49	1	2	FACETS	0.995	0.95	1	0.995	0.95	1	CLONAL	1	TRUE	1	0.942910749915518	2		538	780	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936943	48936959	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTACAGAAACAGCTG	TTTTACAGAAACAGCTG	-	novel	NA	P-0027675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	172	349	0	ENST00000267163.4:c.719-6_729del		p.X240_splice	ENST00000267163	NM_000321.2	240		8/27	0.942910749915518	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.942910749915518	2		349	177	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126115	2126115	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	812	769	0	ENST00000219476.3:c.2686T>A	p.Trp896Arg	p.W896R	ENST00000219476	NM_000548.3	896	Tgg/Agg	24/42	0.615783728150971	2	FACETS	0.872	0.856	0.887	0.872	0.856	0.887	CLONAL	2	TRUE	0	0.942910749915518	2		769	988	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682135	37682135	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	292	462	0	ENST00000447079.4:c.3326A>C	p.Gln1109Pro	p.Q1109P	ENST00000447079	NM_015083.1	1109	cAa/cCa	13/14	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.942910749915518	2		462	582	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281232	15281232	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	588	716	0	ENST00000263388.2:c.5024G>T	p.Trp1675Leu	p.W1675L	ENST00000263388	NM_000435.2	1675	tGg/tTg	27/33	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.942910749915518	2		716	1199	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799267	42799267	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	366	499	2	ENST00000575354.2:c.4751G>T	p.Gly1584Val	p.G1584V	ENST00000575354	NM_015125.3	1584	gGa/gTa	20/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.942910749915518	2		501	776	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881389	111881389	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	293	469	2	ENST00000393256.3:c.67G>T	p.Glu23Ter	p.E23*	ENST00000393256	NM_006538.4	23	Gag/Tag	2/4	1	2	FACETS	0.942	0.893	0.991	0.942	0.893	0.991	CLONAL	1	TRUE	1	0.942910749915518	2		471	660	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670622	134670622	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs748011668	NA	P-0027675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	361	718	0	ENST00000398015.3:c.533A>T	p.Gln178Leu	p.Q178L	ENST00000398015	NM_004441.4	178	cAg/cTg	3/16	0.942910749915518	3	FACETS	1	0.966	1	0.512	0.485	0.538	CLONAL	1	TRUE	1	0.942910749915518	3		718	1101	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1978322	1978322	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	590	668	0	ENST00000382891.5:c.3742G>C	p.Gly1248Arg	p.G1248R	ENST00000382891	NM_133335.3	1248	Ggc/Cgc	21/22	0.127078590663993	3	FACETS	0.779	0.752	0.806	0.779	0.752	0.806	INDETERMINATE	2	TRUE	1	0.942910749915518	3		668	1182	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356320	66356320	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	426	441	0	ENST00000273854.3:c.1177A>G	p.Ile393Val	p.I393V	ENST00000273854	NM_004439.5	393	Att/Gtt	5/18	0.867857007009012	4	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.942910749915518	4		441	791	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467833	66467833	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	170	296	0	ENST00000273854.3:c.436A>T	p.Thr146Ser	p.T146S	ENST00000273854	NM_004439.5	146	Acc/Tcc	3/18	0.867857007009012	4	FACETS	0.878	0.818	0.939			1	CLONAL	2	TRUE	NA	0.942910749915518	4		296	399	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032202	26032202	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	171	243	0	ENST00000244661.2:c.87C>A	p.Ser29Arg	p.S29R	ENST00000244661	NM_003537.3	29	agC/agA	1/1	1	2	FACETS	0.962	0.898	1	0.962	0.898	1	CLONAL	1	TRUE	1	0.942910749915518	2		243	377	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56860224	56860224	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1370509547	NA	P-0027675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	36	519	0	ENST00000519728.1:c.226G>A	p.Gly76Ser	p.G76S	ENST00000519728	NM_002350.3	76	Ggc/Agc	4/13	1	2	FACETS	0.126	0.103	0.152	0.126	0.103	0.152	SUBCLONAL	1	TRUE	1	0.942910749915518	2		519	606	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751238	128751238	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	286	366	0	ENST00000377970.2:c.775A>T	p.Thr259Ser	p.T259S	ENST00000377970	NM_002467.4	259	Aca/Tca	2/3	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.942910749915518	2		366	547	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224517	53224518	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AG	novel	NA	P-0027675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	878	707	1	ENST00000375401.3:c.3195_3196delinsCT	p.Glu1066Ter	p.E1066*	ENST00000375401	NM_004187.3	1065	ctGGag/ctCTag	21/26	0.942910749915518	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	1	0.942910749915518	3		708	1252	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034437	123034437	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	157	583	0	ENST00000355640.3:c.1194G>C	p.Gln398His	p.Q398H	ENST00000355640		398	caG/caC	6/7	1	2	FACETS	0.928	0.862	0.994	0.928	0.862	0.994	CLONAL	1	TRUE	1	0.942910749915518	2		583	359	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954210	48954210	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1354030520	NA	P-0027676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	65	341	0	ENST00000267163.4:c.1411C>T	p.Gln471Ter	p.Q471*	ENST00000267163	NM_000321.2	471	Caa/Taa	15/27	0.176054665542856	1	FACETS	0.624	0.54	0.715	0.624	0.54	0.715	SUBCLONAL	1	TRUE	0	0.23	1		341	802	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	157	653	0	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	0.176054665542856	1	FACETS	0.89	0.813	0.972	0.89	0.813	0.972	CLONAL	1	TRUE	0	0.23	1		653	1357	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023153	27023153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	24	96	0	ENST00000324856.7:c.259G>A	p.Gly87Arg	p.G87R	ENST00000324856	NM_006015.4	87	Gga/Aga	1/20	1	2	FACETS	0.862	0.679	1	0.862	0.679	1	CLONAL	1	TRUE	1	0.23	2		96	242	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445028	89445028	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0027676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	87	579	0	ENST00000336596.2:c.1348A>T	p.Arg450Ter	p.R450*	ENST00000336596	NM_005233.5	450	Aga/Tga	6/17	0.176054665542856	1	FACETS	0.584	0.515	0.658	0.584	0.515	0.658	SUBCLONAL	1	TRUE	0	0.23	1		579	1147	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440534	49440534	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1637	215	836	0	ENST00000301067.7:c.4276G>C	p.Glu1426Gln	p.E1426Q	ENST00000301067	NM_003482.3	1426	Gag/Cag	15/54	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.23	2		836	1852	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336062	73336062	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	51	198	0	ENST00000377767.4:c.2341A>G	p.Arg781Gly	p.R781G	ENST00000377767	NM_014953.3	781	Aga/Gga	17/21	0.176054665542856	1	FACETS	0.825	0.701	0.959	0.825	0.701	0.959	CLONAL	1	TRUE	0	0.23	1		198	476	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207203	1207203	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs1131690950	NA	P-0027676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	141	666	0	ENST00000326873.7:c.290+1G>C		p.X97_splice	ENST00000326873	NM_000455.4	97			0.176054665542856	1	FACETS	0.79	0.718	0.867	0.79	0.718	0.867	SUBCLONAL	1	TRUE	0	0.23	1		666	1373	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591115	67591123	+	inframe_deletion	In_Frame_Del	DEL	CTTATCCAG	CTTATCCAG	-	novel	NA	P-0027678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	59	332	0	ENST00000274335.5:c.1710_1718del	p.Ile571_Leu573del	p.I571_L573del	ENST00000274335		570	CTTATCCAG/-	12/15	0.34249884019833	2	FACETS	0.666	0.576	0.763	0.333	0.288	0.382	SUBCLONAL	1	TRUE	0	0.496517994509498	2		332	357	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138473	11138473	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	180	461	2	ENST00000358026.2:c.3229C>T	p.Arg1077Ter	p.R1077*	ENST00000358026	NM_001128849.1	1077	Cga/Tga	24/36	0.438972471144996	2	FACETS	1	0.991	1	0.747	0.695	0.8	CLONAL	1	TRUE	0	0.496517994509498	2		463	485	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431184	49431184	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	122	619	0	ENST00000301067.7:c.9955G>C	p.Gly3319Arg	p.G3319R	ENST00000301067	NM_003482.3	3319	Ggt/Cgt	34/54	0.438972471144996	2	FACETS	0.775	0.702	0.852	0.388	0.351	0.426	SUBCLONAL	1	TRUE	0	0.496517994509498	2		619	634	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041727	29041727	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	28	372	0	ENST00000282397.4:c.92A>G	p.Asp31Gly	p.D31G	ENST00000282397	NM_002019.4	31	gAt/gGt	2/30	NA	2	FACETS	0.265	0.211	0.326			1	INDETERMINATE	1	TRUE	NA	0.496517994509498	2		372	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578504	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGGGCAGG	novel	NA	P-0027678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	292	887	0	ENST00000269305.4:c.419_426dup	p.Val143ProfsTer30	p.V143Pfs*30	ENST00000269305	NM_001126112.2	142	-/CCTGCCCT	5/11	0.305180656352638	3	FACETS	0.806	0.76	0.853	0.537	0.507	0.569	CLONAL	2	TRUE	0	0.496517994509498	3		887	911	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41228518	41228518	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs111034213	NA	P-0027678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	420	604	0	ENST00000357654.3:c.4471C>G	p.Pro1491Ala	p.P1491A	ENST00000357654	NM_007294.3	1491	Cca/Gca	13/23	0.496517994509498	3	FACETS	0.98	0.943	1	0.98	0.943	1	CLONAL	3	TRUE	0	0.496517994509498	3		604	718	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314635	30314635	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	128	531	0	ENST00000262643.3:c.1184C>A	p.Thr395Asn	p.T395N	ENST00000262643	NM_001238.2	395	aCc/aAc	12/12	0.337399800747678	4	FACETS	0.864	0.783	0.95	0.432	0.391	0.475	CLONAL	1	TRUE	2	0.496517994509498	4		531	893	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24129358	24129358	+	start_lost	Translation_Start_Site	SNP	T	T	G	novel	NA	P-0027678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	107	404	0	ENST00000263121.7:c.2T>G	p.Met1?	p.M1?	ENST00000263121	NM_003073.3	1	aTg/aGg	1/9	0.496517994509498	3	FACETS	0.808	0.725	0.895	0.404	0.362	0.448	CLONAL	1	TRUE	1	0.496517994509498	3		404	666	SUCCESS
APC	324	MSKCC	GRCh37	5	112174868	112174898	+	protein_altering_variant	In_Frame_Del	DEL	CAGTCATTTTCATTCTCAAAGAGTTCATCTG	CAGTCATTTTCATTCTCAAAGAGTTCATCTG	ACTC	novel	NA	P-0027678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	55	264	1	ENST00000257430.4:c.3577_3607delinsACTC	p.Gln1193_Gly1203delinsThrArg	p.Q1193_G1203delinsTR	ENST00000257430	NM_000038.5	1193	CAGTCATTTTCATTCTCAAAGAGTTCATCTGga/ACTCga	16/16	0.34249884019833	2	FACETS	0.879	0.76	1	0.44	0.38	0.504	CLONAL	1	TRUE	0	0.496517994509498	2		265	252	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120594	94120594	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	57	380	0	ENST00000369303.4:c.457G>T	p.Glu153Ter	p.E153*	ENST00000369303	NM_004440.3	153	Gaa/Taa	3/17	0.430460693544268	1	FACETS	0.429	0.369	0.494	0.429	0.369	0.494	SUBCLONAL	1	TRUE	0	0.496517994509498	1		380	402	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034460	47034460	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	80	712	0	ENST00000377604.3:c.545A>C	p.Gln182Pro	p.Q182P	ENST00000377604	NM_001204468.1	182	cAg/cCg	6/24	1	2	FACETS	0.361	0.317	0.408	0.361	0.317	0.408	SUBCLONAL	1	TRUE	1	0.496517994509498	2		712	893	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0027680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	80	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.807	0.717	0.902	0.807	0.717	0.902	CLONAL	1	TRUE	1	0.598901870977265	2		509	331	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0027680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	68	261	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	0.598901870977265	3	FACETS	0.863	0.756	0.977	0.431	0.378	0.489	CLONAL	1	TRUE	1	0.598901870977265	3		261	342	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691025	NA	P-0027680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	226	439	0	ENST00000269305.4:c.785G>T	p.Gly262Val	p.G262V	ENST00000269305	NM_001126112.2	262	gGt/gTt	8/11	0.598901870977265	1	FACETS	0.904	0.848	0.96	0.904	0.848	0.96	CLONAL	1	TRUE	0	0.598901870977265	1		439	585	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0027680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	165	166	1	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.598901870977265	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	1	0.598901870977265	3		167	349	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575090	48575090	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	95	393	0	ENST00000342988.3:c.284A>G	p.Tyr95Cys	p.Y95C	ENST00000342988	NM_005359.5	95	tAt/tGt	3/12	0.598901870977265	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.598901870977265	1		393	218	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829128	128829128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	62	64	0	ENST00000249373.3:c.136G>A	p.Gly46Arg	p.G46R	ENST00000249373	NM_005631.4	46	Ggg/Agg	1/12	1	2	FACETS	0.856	0.748	0.969	0.856	0.748	0.969	CLONAL	1	TRUE	1	0.598901870977265	2		64	242	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0027683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	340	655	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.878179103115863	2		655	704	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0027683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	349	630	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.878179103115863	2		632	731	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259012	153259013	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0027683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	122	336	0	ENST00000281708.4:c.802_803del	p.Met268AspfsTer18	p.M268Dfs*18	ENST00000281708	NM_033632.3	268	ATg/g	5/12	0.878179103115863	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	0	0.878179103115863	1		336	144	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252155	226252155	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	53	129	0	ENST00000366813.1:c.103G>C	p.Gly35Arg	p.G35R	ENST00000366813		35	Ggg/Cgg	1/3	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	FALSE	1	0.878179103115863	2		129	120	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136816	2136817	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	rs137854141	NA	P-0027683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	426	790	0	ENST00000219476.3:c.4934_4935del	p.Phe1645CysfsTer7	p.F1645Cfs*7	ENST00000219476	NM_000548.3	1645	TTt/t	38/42	0.760506587906797	1	FACETS	0.988	0.96	1	0.988	0.96	1	CLONAL	1	FALSE	0	0.878179103115863	1		790	551	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945069	151945069	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	65	588	1	ENST00000262189.6:c.2450T>A	p.Ile817Asn	p.I817N	ENST00000262189	NM_170606.2	817	aTc/aAc	14/59	1	2	FACETS	0.378	0.329	0.43	0.378	0.329	0.43	SUBCLONAL	1	FALSE	1	0.878179103115863	2		589	392	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938573	76938574	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0027683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	171	246	0	ENST00000373344.5:c.2174_2175del	p.Val725GlyfsTer7	p.V725Gfs*7	ENST00000373344	NM_000489.3	725	gTG/g	9/35	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	FALSE	0	0.878179103115863	1		246	191	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223251	5223251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199604489	NA	P-0027685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	139	742	0	ENST00000357368.4:c.2552G>A	p.Arg851His	p.R851H	ENST00000357368	NM_002850.3	851	cGc/cAc	18/38	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.39514122705542	2		742	658	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165024	47165024	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	51	380	1	ENST00000409792.3:c.1102C>T	p.Arg368Ter	p.R368*	ENST00000409792	NM_014159.6	368	Cga/Tga	3/21	0.39514122705542	1	FACETS	0.666	0.569	0.771	0.666	0.569	0.771	SUBCLONAL	1	TRUE	0	0.39514122705542	1		381	311	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430390	181430390	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	148	784	0	ENST00000325404.1:c.245del	p.Leu82CysfsTer21	p.L82Cfs*21	ENST00000325404	NM_003106.3	81	cTt/ct	1/1	0.39514122705542	1	FACETS	0.859	0.786	0.935	0.859	0.786	0.935	CLONAL	1	TRUE	0	0.39514122705542	1		784	700	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953861	55953861	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	98	533	0	ENST00000263923.4:c.3575T>G	p.Leu1192Arg	p.L1192R	ENST00000263923	NM_002253.2	1192	cTc/cGc	27/30	1	2	FACETS	0.799	0.714	0.889	0.799	0.714	0.889	SUBCLONAL	1	TRUE	1	0.39514122705542	2		533	621	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0027686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	37	278	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.216861572784993	1	FACETS	0.808	0.668	0.964	0.808	0.668	0.964	CLONAL	1	TRUE	0	0.23805029444324	1		278	339	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205323	38205323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	107	786	0	ENST00000317025.8:c.367G>A	p.Glu123Lys	p.E123K	ENST00000317025	NM_023034.1	123	Gaa/Aaa	2/24	1	2	FACETS	0.936	0.839	1	0.936	0.839	1	CLONAL	1	TRUE	1	0.23805029444324	2		786	960	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112910749	112910750	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	80	441	0	ENST00000351677.2:c.759dup	p.Leu254ThrfsTer25	p.L254Tfs*25	ENST00000351677	NM_002834.3	253	aca/acAa	7/16	0.23805029444324	2	FACETS	0.957	0.843	1	0.479	0.421	0.541	CLONAL	1	TRUE	0	0.23805029444324	2		441	702	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457251	67457251	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	44	543	0	ENST00000327367.4:c.225G>T	p.Leu75Phe	p.L75F	ENST00000327367	NM_005902.3	75	ttG/ttT	2/9	1	2	FACETS	0.638	0.535	0.754	0.638	0.535	0.754	SUBCLONAL	1	TRUE	1	0.23805029444324	2		543	579	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647391	3647391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372264472	NA	P-0027686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	38	553	0	ENST00000294008.3:c.1672C>T	p.Arg558Trp	p.R558W	ENST00000294008	NM_032444.2	558	Cgg/Tgg	7/15	0.195396641795921	3	FACETS	0.641	0.529	0.767	0.321	0.264	0.384	SUBCLONAL	1	TRUE	1	0.23805029444324	3		553	557	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0027714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	332	321	2	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.634514265910611	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.634514265910611	3		323	684	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852248	63852248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145564601	NA	P-0027715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	55	584	1	ENST00000279873.7:c.3026C>T	p.Ala1009Val	p.A1009V	ENST00000279873	NM_032199.2	1009	gCg/gTg	10/10	1	2	FACETS	0.464	0.396	0.539	0.464	0.396	0.539	SUBCLONAL	1	TRUE	1	0.272530221790434	2		585	870	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549364	187549364	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs111886222	NA	P-0027715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	54	724	3	ENST00000441802.2:c.4754C>T	p.Thr1585Met	p.T1585M	ENST00000441802	NM_005245.3	1585	aCg/aTg	9/27	1	2	FACETS	0.377	0.321	0.44	0.377	0.321	0.44	SUBCLONAL	1	TRUE	1	0.272530221790434	2		727	1050	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845814	151845814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	42	826	2	ENST00000262189.6:c.13198C>T	p.Arg4400Trp	p.R4400W	ENST00000262189	NM_170606.2	4400	Cgg/Tgg	52/59	1	2	FACETS	0.394	0.328	0.468	0.394	0.328	0.468	SUBCLONAL	1	TRUE	1	0.272530221790434	2		828	782	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653405	206653405	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782442134	NA	P-0027715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	55	853	0	ENST00000367120.3:c.1289G>A	p.Arg430Gln	p.R430Q	ENST00000367120	NM_014002.3	430	cGg/cAg	12/22	1	2	FACETS	0.373	0.318	0.434	0.373	0.318	0.434	SUBCLONAL	1	TRUE	1	0.272530221790434	2		853	1082	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915481	112915481	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376007642	NA	P-0027715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	30	727	2	ENST00000351677.2:c.880G>A	p.Asp294Asn	p.D294N	ENST00000351677	NM_002834.3	294	Gat/Aat	8/16	1	2	FACETS	0.378	0.303	0.462	0.378	0.303	0.462	SUBCLONAL	1	TRUE	1	0.272530221790434	2		729	583	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961204	41961204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	46	478	2	ENST00000219905.7:c.112C>T	p.Gln38Ter	p.Q38*	ENST00000219905	NM_001164273.1	38	Caa/Taa	2/24	1	2	FACETS	0.689	0.58	0.809	0.689	0.58	0.809	SUBCLONAL	1	TRUE	1	0.272530221790434	2		480	490	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006075	22006075	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	37	697	0	ENST00000276925.6:c.328G>C	p.Asp110His	p.D110H	ENST00000276925	NM_004936.3	110	Gat/Cat	2/2	1	2	FACETS	0.381	0.313	0.457	0.381	0.313	0.457	SUBCLONAL	1	TRUE	1	0.272530221790434	2		697	713	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0027716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	780	449	0				ENST00000310581	NM_198253.2	-/1132			0.65490097584871	3	FACETS	0.864	0.837	0.891	0.864	0.837	0.891	CLONAL	2	TRUE	1	0.723200990723164	3		449	1700	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0027716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	889	780	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	2	TRUE	NA	0.723200990723164	2		780	1150	SUCCESS
APC	324	MSKCC	GRCh37	5	112175876	112175876	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085992	NA	P-0027716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	227	359	0	ENST00000257430.4:c.4585C>T	p.Gln1529Ter	p.Q1529*	ENST00000257430	NM_000038.5	1529	Cag/Tag	16/16	0.723200990723164	2	FACETS	0.94	0.897	0.981	0.94	0.897	0.981	CLONAL	2	TRUE	0	0.723200990723164	2		359	334	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145430	58145430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894340	NA	P-0027716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	663	627	1	ENST00000257904.6:c.71G>A	p.Arg24His	p.R24H	ENST00000257904	NM_000075.3	24	cGt/cAt	2/8	0.629176937223354	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	2	0.723200990723164	4		628	1463	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0027716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	214	488	1	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.723200990723164	6	FACETS	0.991	0.931	1	0.743	0.698	0.789	CLONAL	3	TRUE	2	0.723200990723164	6		489	487	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541715	120541715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1261521534	NA	P-0027716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	629	803	2	ENST00000229340.5:c.142C>T	p.Arg48Trp	p.R48W	ENST00000229340	NM_006861.6	48	Cgg/Tgg	3/6	0.629176937223354	4	FACETS	0.991	0.955	1	0.991	0.955	1	CLONAL	2	TRUE	2	0.723200990723164	4		805	1513	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656259	18656259	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201569993	NA	P-0027716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	131	714	1	ENST00000266497.5:c.2938C>T	p.His980Tyr	p.H980Y	ENST00000266497		980	Cat/Tat	21/31	0.40331884899767	4	FACETS	1	0.981	1	0.644	0.588	0.702	INDETERMINATE	1	TRUE	2	0.723200990723164	4		715	485	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349918	15349918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293348757	NA	P-0027716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	610	671	1	ENST00000263377.2:c.3734C>T	p.Ala1245Val	p.A1245V	ENST00000263377	NM_058243.2	1245	gCc/gTc	18/20	0.629176937223354	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.723200990723164	4		672	1392	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977594	2977594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1576	807	987	1	ENST00000396946.4:c.1090C>T	p.Arg364Cys	p.R364C	ENST00000396946	NM_032415.4	364	Cgc/Tgc	8/25	0.715569583536344	5	FACETS	0.976	0.943	1	0.488	0.471	0.505	CLONAL	2	TRUE	1	0.723200990723164	5		988	2383	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007575	62007575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	345	1015	0	ENST00000392795.3:c.292G>A	p.Glu98Lys	p.E98K	ENST00000392795	NM_001039933.1	98	Gaa/Aaa	3/6	0.723200990723164	3	FACETS	0.921	0.871	0.973	0.461	0.435	0.487	CLONAL	1	TRUE	1	0.723200990723164	3		1015	1410	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331723	8331723	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367558329	NA	P-0027716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	473	488	0	ENST00000356435.5:c.5393G>A	p.Arg1798Gln	p.R1798Q	ENST00000356435		1798	cGa/cAa	33/35	0.723200990723164	3	FACETS	0.991	0.953	1	0.991	0.953	1	CLONAL	2	TRUE	1	0.723200990723164	3		488	899	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0027716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1827	679	1009	0	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	0.723200990723164	3	FACETS	1	0.976	1	0.51	0.49	0.53	CLONAL	1	TRUE	1	0.723200990723164	3		1009	2506	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243965	5243965	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	943	778	1	ENST00000357368.4:c.1517C>T	p.Ser506Phe	p.S506F	ENST00000357368	NM_002850.3	506	tCc/tTc	11/38	0.723200990723164	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	2	0.723200990723164	4		779	2119	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265890	16265890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	517	836	1	ENST00000375759.3:c.10963C>T	p.Pro3655Ser	p.P3655S	ENST00000375759	NM_015001.2	3655	Ccc/Tcc	15/15	0.351159502798088	6	FACETS	0.878	0.842	0.914	0.878	0.842	0.914	INDETERMINATE	3	TRUE	3	0.723200990723164	6		837	1328	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486550	56486550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1452978964	NA	P-0027716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	640	858	0	ENST00000267101.3:c.1129C>T	p.Pro377Ser	p.P377S	ENST00000267101	NM_001982.3	377	Cct/Tct	10/28	0.629176937223354	4	FACETS	0.95	0.915	0.985	0.95	0.915	0.985	CLONAL	2	TRUE	2	0.723200990723164	4		858	1605	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416758	121416758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1457	1033	1043	2	ENST00000257555.6:c.187G>A	p.Gly63Arg	p.G63R	ENST00000257555		63	Ggg/Agg	1/10	0.629176937223354	4	FACETS	0.989	0.96	1	0.989	0.96	1	CLONAL	2	TRUE	2	0.723200990723164	4		1045	2490	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66737004	66737004	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	369	680	0	ENST00000307102.5:c.527G>T	p.Gly176Val	p.G176V	ENST00000307102	NM_002755.3	176	gGc/gTc	5/11	0.629176937223354	4	FACETS	0.88	0.837	0.924	0.88	0.837	0.924	CLONAL	2	TRUE	2	0.723200990723164	4		680	999	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210843	2210843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	419	512	0	ENST00000398665.3:c.1340C>T	p.Ser447Phe	p.S447F	ENST00000398665	NM_032482.2	447	tCc/tTc	14/28	0.667659435722288	4	FACETS	0.935	0.893	0.977			1	CLONAL	2	TRUE	NA	0.723200990723164	4		512	1068	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754478	41754478	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144179986	NA	P-0027716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1238	1003	957	5	ENST00000301178.4:c.1597C>T	p.Arg533Trp	p.R533W	ENST00000301178	NM_021913.4	533	Cgg/Tgg	13/20	0.629176937223354	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	2	0.723200990723164	4		962	2241	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39746936	39746937	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0027716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	317	695	0	ENST00000361337.2:c.1950_1950+1delinsAA		p.X650_splice	ENST00000361337	NM_003286.2	650		18/21	0.351159502798088	6	FACETS	1	0.986	1	0.748	0.707	0.789	INDETERMINATE	2	TRUE	3	0.723200990723164	6		695	956	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739123	40739123	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	411	714	0	ENST00000373198.4:c.3161G>A	p.Gly1054Asp	p.G1054D	ENST00000373198	NM_133170.3	1054	gGc/gAc	24/32	0.223681706935435	5	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.723200990723164	5		714	1060	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157087	106157087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	449	689	0	ENST00000380013.4:c.1988C>T	p.Ser663Phe	p.S663F	ENST00000380013	NM_001127208.2	663	tCc/tTc	3/11	0.629176937223354	4	FACETS	0.935	0.894	0.976	0.935	0.894	0.976	CLONAL	2	TRUE	2	0.723200990723164	4		689	1144	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163857	152163857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	238	667	1	ENST00000206249.3:c.578C>T	p.Ser193Leu	p.S193L	ENST00000206249	NM_000125.3	193	tCa/tTa	2/8	1	2	FACETS	0.914	0.857	0.972	0.914	0.857	0.972	CLONAL	1	TRUE	1	0.723200990723164	2		668	720	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69000021	69000021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1048744323	NA	P-0027716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	213	880	1	ENST00000288368.4:c.2090C>T	p.Ser697Phe	p.S697F	ENST00000288368	NM_024870.2	697	tCt/tTt	19/40	0.66945391202074	4	FACETS	0.797	0.739	0.857	0.266	0.246	0.286	SUBCLONAL	1	TRUE	1	0.723200990723164	4		881	1274	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129892	69129892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	530	415	1	ENST00000288368.4:c.4646C>T	p.Ala1549Val	p.A1549V	ENST00000288368	NM_024870.2	1549	gCc/gTc	38/40	0.66945391202074	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	1	0.723200990723164	4		416	804	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90976721	90976721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536965870	NA	P-0027716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	59	597	0	ENST00000265433.3:c.911C>T	p.Pro304Leu	p.P304L	ENST00000265433	NM_002485.4	304	cCt/cTt	8/16	0.66945391202074	4	FACETS	0.613	0.528	0.704	0.204	0.176	0.235	SUBCLONAL	1	TRUE	1	0.723200990723164	4		597	459	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211431	98211431	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779417284	NA	P-0027716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	761	735	0	ENST00000331920.6:c.3724G>A	p.Glu1242Lys	p.E1242K	ENST00000331920	NM_000264.3	1242	Gag/Aag	22/24	0.723200990723164	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.723200990723164	3		735	1363	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	87	528	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.954	0.844	1	0.954	0.844	1	CLONAL	1	FALSE	1	0.248811468012482	2		529	733	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0027737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	139	541	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	FALSE	1	0.248811468012482	2		541	859	SUCCESS
APC	324	MSKCC	GRCh37	5	112173847	112173848	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0027737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	77	299	0	ENST00000257430.4:c.2563_2564dup	p.Arg856AsnfsTer6	p.R856Nfs*6	ENST00000257430	NM_000038.5	852	-/GA	16/16	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	FALSE	1	0.248811468012482	2		299	606	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014170	70014170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769488988	NA	P-0027737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	71	523	1	ENST00000394351.3:c.1031C>T	p.Thr344Met	p.T344M	ENST00000394351	NM_000248.3	344	aCg/aTg	9/9	0.201433330785027	1	FACETS	0.517	0.45	0.59	0.517	0.45	0.59	SUBCLONAL	1	FALSE	0	0.248811468012482	1		524	966	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099329	27099333	+	frameshift_variant	Frame_Shift_Del	DEL	ATGCC	ATGCC	-	novel	NA	P-0027737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	137	450	2	ENST00000324856.7:c.3566_3570del	p.Asp1189ValfsTer2	p.D1189Vfs*2	ENST00000324856	NM_006015.4	1189	gATGCC/g	14/20	0.201433330785027	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	0	0.248811468012482	1		452	835	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0027739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	103	321	2	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.346400204065491	3	FACETS	1	0.938	1	0.533	0.478	0.592	CLONAL	1	TRUE	1	0.346400204065491	3		323	654	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0027739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	76	449	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.346400204065491	2		449	433	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0027739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	117	584	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.346400204065491	3	FACETS	1	0.949	1	0.54	0.487	0.596	CLONAL	1	TRUE	1	0.346400204065491	3		584	734	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0027739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	68	226	1	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	0.346400204065491	2		227	323	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265535	152265535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571716552	NA	P-0027739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	78	415	0	ENST00000206249.3:c.988G>A	p.Glu330Lys	p.E330K	ENST00000206249	NM_000125.3	330	Gag/Aag	4/8	1	2	FACETS	0.832	0.733	0.939	0.832	0.733	0.939	CLONAL	1	TRUE	1	0.346400204065491	2		415	541	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370868	55370868	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757855527	NA	P-0027739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	185	466	0	ENST00000297316.4:c.170G>A	p.Gly57Glu	p.G57E	ENST00000297316	NM_022454.3	57	gGg/gAg	1/2	0.346400204065491	3	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	1	0.346400204065491	3		466	622	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804995	43804995	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267598615	NA	P-0027739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	72	376	0	ENST00000372470.3:c.445G>A	p.Glu149Lys	p.E149K	ENST00000372470	NM_005373.2	149	Gaa/Aaa	4/12	1	2	FACETS	0.924	0.81	1	0.924	0.81	1	CLONAL	1	TRUE	1	0.346400204065491	2		376	450	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434747	49434747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	134	567	0	ENST00000301067.7:c.6806C>T	p.Ser2269Phe	p.S2269F	ENST00000301067	NM_003482.3	2269	tCc/tTc	31/54	1	2	FACETS	0.997	0.907	1	0.997	0.907	1	CLONAL	1	TRUE	1	0.346400204065491	2		567	776	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784117	120784117	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	60	677	0	ENST00000257552.2:c.868C>T	p.Pro290Ser	p.P290S	ENST00000257552	NM_002442.3	290	Ccc/Tcc	13/15	1	2	FACETS	0.435	0.374	0.502	0.435	0.374	0.502	SUBCLONAL	1	TRUE	1	0.346400204065491	2		677	796	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835885	151835885	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	84	319	0	ENST00000262189.6:c.14639A>G	p.Glu4880Gly	p.E4880G	ENST00000262189	NM_170606.2	4880	gAa/gGa	58/59	0.346400204065491	3	FACETS	0.918	0.811	1	0.459	0.405	0.516	CLONAL	1	TRUE	1	0.346400204065491	3		319	620	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500810	8500811	+	missense_variant	Missense_Mutation	DNP	GT	GT	AA	novel	NA	P-0027739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	67	383	1	ENST00000356435.5:c.2071_2072delinsTT	p.Thr691Leu	p.T691L	ENST00000356435		691	ACa/TTa	13/35	1	2	FACETS	0.718	0.624	0.818	0.718	0.624	0.818	SUBCLONAL	1	TRUE	1	0.346400204065491	2		384	539	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272422	11272422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746532612	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	132	419	0	ENST00000361445.4:c.3508C>T	p.Arg1170Cys	p.R1170C	ENST00000361445	NM_004958.3	1170	Cgc/Tgc	23/58	1	2	FACETS	0.745	0.678	0.816	0.745	0.678	0.816	SUBCLONAL	1	TRUE	1	0.519317402053224	2		419	682	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057936	27057937	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1415146710	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	181	424	0	ENST00000324856.7:c.1650dup	p.Tyr551LeufsTer72	p.Y551Lfs*72	ENST00000324856	NM_006015.4	548	-/C	3/20	1	2	FACETS	0.997	0.923	1	0.997	0.923	1	CLONAL	1	TRUE	1	0.519317402053224	2		424	699	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099914	27099914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs953652494	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	152	402	0	ENST00000324856.7:c.3793G>A	p.Gly1265Ser	p.G1265S	ENST00000324856	NM_006015.4	1265	Ggc/Agc	15/20	1	2	FACETS	0.931	0.854	1	0.931	0.854	1	CLONAL	1	TRUE	1	0.519317402053224	2		402	629	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101282	27101282	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199776442	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	163	411	1	ENST00000324856.7:c.4564G>A	p.Ala1522Thr	p.A1522T	ENST00000324856	NM_006015.4	1522	Gcc/Acc	18/20	1	2	FACETS	0.998	0.92	1	0.998	0.92	1	CLONAL	1	TRUE	1	0.519317402053224	2		412	629	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101375	27101375	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	171	393	0	ENST00000324856.7:c.4661del	p.Pro1554HisfsTer11	p.P1554Hfs*11	ENST00000324856	NM_006015.4	1553	Ccc/cc	18/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.519317402053224	2		393	616	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598252	28598252	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs994631336	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	219	573	0	ENST00000253063.3:c.224G>A	p.Arg75Gln	p.R75Q	ENST00000253063	NM_031459.4	75	cGa/cAa	3/10	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.519317402053224	2		573	838	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246518359	246518359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746219350	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	139	313	1	ENST00000388985.4:c.202G>A	p.Ala68Thr	p.A68T	ENST00000388985		68	Gcc/Acc	2/12	1	2	FACETS	0.839	0.766	0.915	0.839	0.766	0.915	CLONAL	1	TRUE	1	0.519317402053224	2		314	638	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604533	43604533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs546866208	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	183	487	2	ENST00000355710.3:c.1118C>T	p.Ala373Val	p.A373V	ENST00000355710	NM_020975.4	373	gCg/gTg	6/20	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.519317402053224	2		489	685	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63829504	63829504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529464997	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	155	384	0	ENST00000279873.7:c.1147G>A	p.Gly383Ser	p.G383S	ENST00000279873	NM_032199.2	383	Ggt/Agt	8/10	1	2	FACETS	0.985	0.906	1	0.985	0.906	1	CLONAL	1	TRUE	1	0.519317402053224	2		384	606	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	131	275	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.987	0.901	1	0.987	0.901	1	CLONAL	1	TRUE	1	0.519317402053224	2		278	511	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533860	533860	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	220	602	0	ENST00000451590.1:c.196G>A	p.Ala66Thr	p.A66T	ENST00000451590	NM_001130442.1	66	Gcc/Acc	3/5	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.519317402053224	2		602	833	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421570	32421570	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	155	373	0	ENST00000332351.3:c.1022G>T	p.Ser341Ile	p.S341I	ENST00000332351	NM_024426.4	341	aGc/aTc	6/10	1	2	FACETS	0.842	0.772	0.914	0.842	0.772	0.914	CLONAL	1	TRUE	1	0.519317402053224	2		373	709	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999059	100999059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	120	410	1	ENST00000325455.5:c.743C>T	p.Ala248Val	p.A248V	ENST00000325455	NM_001202474.3	248	gCg/gTg	1/8	1	2	FACETS	0.919	0.834	1	0.919	0.834	1	CLONAL	1	TRUE	1	0.519317402053224	2		411	503	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149358	119149358	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs886041472	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	118	296	0	ENST00000264033.4:c.1366G>T	p.Asp456Tyr	p.D456Y	ENST00000264033	NM_005188.3	456	Gat/Tat	9/16	1	2	FACETS	0.997	0.905	1	0.997	0.905	1	CLONAL	1	TRUE	1	0.519317402053224	2		296	456	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	129	293	0	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.998	0.91	1	0.998	0.91	1	CLONAL	1	TRUE	1	0.519317402053224	2		293	498	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885578	111885578	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs751470371	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	180	529	0	ENST00000341259.2:c.1355C>G	p.Ala452Gly	p.A452G	ENST00000341259	NM_005475.2	452	gCc/gGc	7/8	0.519317402053224	3	FACETS	0.914	0.843	0.989	0.457	0.421	0.495	CLONAL	1	TRUE	1	0.519317402053224	3		529	955	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112326	115112326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1302202171	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	74	143	0	ENST00000257566.3:c.1414G>A	p.Ala472Thr	p.A472T	ENST00000257566	NM_016569.3	472	Gcg/Acg	7/8	0.519317402053224	3	FACETS	1	0.958	1	0.594	0.525	0.667	CLONAL	1	TRUE	1	0.519317402053224	3		143	302	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	127	414	2	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	0.519317402053224	3	FACETS	0.731	0.662	0.804	0.365	0.331	0.402	SUBCLONAL	1	TRUE	1	0.519317402053224	3		416	843	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874019	123874019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424196684	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	26	36	0	ENST00000330479.4:c.50C>T	p.Ala17Val	p.A17V	ENST00000330479	NM_020382.3	17	gCg/gTg	2/9	0.519317402053224	3	FACETS	0.751	0.612	0.9	0.751	0.612	0.9	SUBCLONAL	2	TRUE	1	0.519317402053224	3		36	84	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123875244	123875244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	36	100	0	ENST00000330479.4:c.200G>A	p.Arg67His	p.R67H	ENST00000330479	NM_020382.3	67	cGt/cAt	3/9	0.519317402053224	3	FACETS	0.865	0.718	1	0.432	0.359	0.513	CLONAL	1	TRUE	1	0.519317402053224	3		100	202	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913316	28913316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	382	477	0	ENST00000282397.4:c.2477G>A	p.Arg826Lys	p.R826K	ENST00000282397	NM_002019.4	826	aGa/aAa	17/30	0.519317402053224	3	FACETS	0.894	0.851	0.937	0.894	0.851	0.937	CLONAL	2	TRUE	1	0.519317402053224	3		477	1037	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005429	29005429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372354806	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	106	240	0	ENST00000282397.4:c.832G>A	p.Val278Ile	p.V278I	ENST00000282397	NM_002019.4	278	Gta/Ata	7/30	0.519317402053224	3	FACETS	1	0.944	1	0.536	0.482	0.591	CLONAL	1	TRUE	1	0.519317402053224	3		240	480	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514821	103514821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112825485	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	187	281	0	ENST00000355739.4:c.1322C>T	p.Pro441Leu	p.P441L	ENST00000355739	NM_000123.3	441	cCg/cTg	8/15	0.519317402053224	3	FACETS	0.825	0.767	0.884	0.825	0.767	0.884	CLONAL	2	TRUE	1	0.519317402053224	3		281	550	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434736	110434736	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757728267	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	383	496	2	ENST00000375856.3:c.3665C>T	p.Pro1222Leu	p.P1222L	ENST00000375856	NM_003749.2	1222	cCg/cTg	1/2	0.519317402053224	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.519317402053224	3		498	921	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434766	110434766	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	384	522	0	ENST00000375856.3:c.3635del	p.Pro1212LeufsTer47	p.P1212Lfs*47	ENST00000375856	NM_003749.2	1212	cCt/ct	1/2	0.519317402053224	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.519317402053224	3		522	927	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614440	38614440	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	104	282	0	ENST00000299084.4:c.208-2A>G		p.X70_splice	ENST00000299084	NM_152594.2	70			1	2	FACETS	0.979	0.883	1	0.979	0.883	1	CLONAL	1	TRUE	1	0.519317402053224	2		282	409	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576240	88576240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	118	313	0	ENST00000360948.2:c.1433C>T	p.Ala478Val	p.A478V	ENST00000360948	NM_001012338.2	478	gCc/gTc	13/19	1	2	FACETS	0.837	0.758	0.919	0.837	0.758	0.919	CLONAL	1	TRUE	1	0.519317402053224	2		313	543	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	203	768	1	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	1	2	FACETS	0.897	0.832	0.963	0.897	0.832	0.963	CLONAL	1	TRUE	1	0.519317402053224	2		769	872	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813825	50813825	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	217	540	0	ENST00000398568.2:c.1379C>A	p.Pro460His	p.P460H	ENST00000398568	NM_001042412.1	460	cCt/cAt	8/18	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.519317402053224	2		540	819	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063359	67063359	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	132	307	1	ENST00000412916.2:c.54del	p.Phe18LeufsTer4	p.F18Lfs*4	ENST00000412916		17	Ttt/tt	1/6	1	2	FACETS	0.914	0.834	0.998	0.914	0.834	0.998	CLONAL	1	TRUE	1	0.519317402053224	2		308	556	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662385	67662385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1436030657	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	248	502	0	ENST00000264010.4:c.1631G>A	p.Arg544His	p.R544H	ENST00000264010	NM_006565.3	544	cGc/cAc	9/12	1	2	FACETS	0.995	0.931	1	0.995	0.931	1	CLONAL	1	TRUE	1	0.519317402053224	2		502	960	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844140	68844140	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	198	465	0	ENST00000261769.5:c.728A>G	p.Glu243Gly	p.E243G	ENST00000261769	NM_004360.3	243	gAg/gGg	6/16	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.519317402053224	2		465	750	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822240	72822240	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	220	530	0	ENST00000268489.5:c.9935T>C	p.Val3312Ala	p.V3312A	ENST00000268489	NM_006885.3	3312	gTa/gCa	10/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.519317402053224	2		530	809	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993885	72993885	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	110	324	0	ENST00000268489.5:c.160A>T	p.Arg54Trp	p.R54W	ENST00000268489	NM_006885.3	54	Agg/Tgg	2/10	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.519317402053224	2		324	416	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346424	89346424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1228696930	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	172	471	2	ENST00000301030.4:c.6526G>A	p.Gly2176Ser	p.G2176S	ENST00000301030	NM_001256183.1	2176	Ggt/Agt	9/13	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.519317402053224	2		473	662	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347762	89347762	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748736120	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	139	396	1	ENST00000301030.4:c.5188G>A	p.Asp1730Asn	p.D1730N	ENST00000301030	NM_001256183.1	1730	Gat/Aat	9/13	1	2	FACETS	0.991	0.907	1	0.991	0.907	1	CLONAL	1	TRUE	1	0.519317402053224	2		397	540	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127243	17127243	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	124	381	0	ENST00000285071.4:c.611del	p.Ala204GlyfsTer19	p.A204Gfs*19	ENST00000285071	NM_144997.5	204	gCg/gg	6/14	1	2	FACETS	0.983	0.894	1	0.983	0.894	1	CLONAL	1	TRUE	1	0.519317402053224	2		381	486	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487510	38487510	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567751372	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	118	342	0	ENST00000254066.5:c.40G>A	p.Gly14Arg	p.G14R	ENST00000254066	NM_000964.3	14	Ggg/Agg	2/9	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.519317402053224	2		342	436	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40468917	40468917	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs869312892	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	85	176	0	ENST00000264657.5:c.2147C>T	p.Thr716Met	p.T716M	ENST00000264657	NM_139276.2	716	aCg/aTg	23/24	1	2	FACETS	0.875	0.779	0.977	0.875	0.779	0.977	CLONAL	1	TRUE	1	0.519317402053224	2		176	374	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	312	345	8	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.96	0.914	1	1	0.996	1	CLONAL	2	TRUE	1	0.519317402053224	2		353	626	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740506	58740506	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	142	471	2	ENST00000305921.3:c.1411C>A	p.Pro471Thr	p.P471T	ENST00000305921	NM_003620.3	471	Cca/Aca	6/6	1	2	FACETS	0.843	0.77	0.918	0.843	0.77	0.918	CLONAL	1	TRUE	1	0.519317402053224	2		473	649	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78865613	78865613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752600548	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	155	371	0	ENST00000306801.3:c.2077G>A	p.Ala693Thr	p.A693T	ENST00000306801	NM_020761.2	693	Gcc/Acc	18/34	1	2	FACETS	0.854	0.784	0.927	0.854	0.784	0.927	CLONAL	1	TRUE	1	0.519317402053224	2		371	699	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243923	5243923	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778260386	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	107	305	0	ENST00000357368.4:c.1559C>T	p.Thr520Met	p.T520M	ENST00000357368	NM_002850.3	520	aCg/aTg	11/38	1	2	FACETS	0.839	0.756	0.926	0.839	0.756	0.926	CLONAL	1	TRUE	1	0.519317402053224	2		305	491	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251482	10251482	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	170	442	1	ENST00000340748.4:c.3450del	p.Leu1151CysfsTer29	p.L1151Cfs*29	ENST00000340748		1150	ggG/gg	31/40	1	2	FACETS	0.917	0.846	0.991	0.917	0.846	0.991	CLONAL	1	TRUE	1	0.519317402053224	2		443	714	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170474	11170474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749700321	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	232	527	0	ENST00000358026.2:c.4777C>T	p.Arg1593Trp	p.R1593W	ENST00000358026	NM_001128849.1	1593	Cgg/Tgg	34/36	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.519317402053224	2		527	872	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289862	15289862	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778176344	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	236	581	1	ENST00000263388.2:c.3692G>A	p.Arg1231His	p.R1231H	ENST00000263388	NM_000435.2	1231	cGt/cAt	22/33	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.519317402053224	2		582	909	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300240	15300240	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	203	476	0	ENST00000263388.2:c.1037-1G>A		p.X346_splice	ENST00000263388	NM_000435.2	346			1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.519317402053224	2		476	781	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974365	18974365	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	157	514	2	ENST00000262803.5:c.2719C>T	p.Arg907Cys	p.R907C	ENST00000262803	NM_002911.3	907	Cgt/Tgt	19/24	1	2	FACETS	0.842	0.773	0.914	0.842	0.773	0.914	CLONAL	1	TRUE	1	0.519317402053224	2		516	718	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210845	36210845	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	236	596	1	ENST00000222270.7:c.596G>A	p.Arg199Gln	p.R199Q	ENST00000222270	NM_014727.1	199	cGg/cAg	3/37	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.519317402053224	2		597	865	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211899	36211899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	223	761	0	ENST00000222270.7:c.1656del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	550	gaC/ga	3/37	1	2	FACETS	0.846	0.788	0.907	0.846	0.788	0.907	CLONAL	1	TRUE	1	0.519317402053224	2		761	1015	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218425	36218425	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555730957	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	186	417	1	ENST00000222270.7:c.4204C>T	p.Arg1402Ter	p.R1402*	ENST00000222270	NM_014727.1	1402	Cga/Tga	16/37	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.519317402053224	2		418	653	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223191	36223191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373804780	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	288	675	2	ENST00000222270.7:c.5741G>A	p.Arg1914His	p.R1914H	ENST00000222270	NM_014727.1	1914	cGt/cAt	28/37	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.519317402053224	2		677	1099	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762376	41762377	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	161	438	0	ENST00000301178.4:c.2063_2064del	p.Val688GlyfsTer31	p.V688Gfs*31	ENST00000301178	NM_021913.4	686	GTg/g	18/20	1	2	FACETS	0.938	0.863	1	0.938	0.863	1	CLONAL	1	TRUE	1	0.519317402053224	2		438	661	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	193	563	0	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.837	0.775	0.901	0.837	0.775	0.901	CLONAL	1	TRUE	1	0.519317402053224	2		563	888	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910319	50910319	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372190244	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	206	577	2	ENST00000440232.2:c.1574G>A	p.Arg525Gln	p.R525Q	ENST00000440232	NM_002691.3	525	cGg/cAg	13/27	1	2	FACETS	0.97	0.902	1	0.97	0.902	1	CLONAL	1	TRUE	1	0.519317402053224	2		579	818	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47672797	47672797	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs267607957	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	95	353	0	ENST00000233146.2:c.1386+1G>A		p.X462_splice	ENST00000233146	NM_000251.2	462			1	2	FACETS	0.732	0.654	0.814	0.732	0.654	0.814	SUBCLONAL	1	TRUE	1	0.519317402053224	2		353	500	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026782	48026782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775716798	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	139	322	0	ENST00000234420.5:c.1660C>T	p.Arg554Cys	p.R554C	ENST00000234420	NM_000179.2	554	Cgt/Tgt	4/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.519317402053224	2		322	483	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026852	48026852	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376220212	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	112	293	0	ENST00000234420.5:c.1730G>A	p.Arg577His	p.R577H	ENST00000234420	NM_000179.2	577	cGc/cAc	4/10	1	2	FACETS	0.884	0.799	0.973	0.884	0.799	0.973	CLONAL	1	TRUE	1	0.519317402053224	2		293	488	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919780	96919781	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGC	rs777748763	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	131	425	0	ENST00000258439.3:c.480_482dup	p.Gln160dup	p.Q160dup	ENST00000258439	NM_001193304.2	160	cat/caGCAt	4/4	1	2	FACETS	0.705	0.64	0.772	0.705	0.64	0.772	SUBCLONAL	1	TRUE	1	0.519317402053224	2		425	716	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920700	96920700	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908824	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	199	400	0	ENST00000258439.3:c.280C>T	p.Arg94Trp	p.R94W	ENST00000258439	NM_001193304.2	94	Cgg/Tgg	3/4	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.519317402053224	2		400	709	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735354	204735354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	60	175	0	ENST00000302823.3:c.155G>A	p.Gly52Asp	p.G52D	ENST00000302823	NM_005214.4	52	gGc/gAc	2/4	1	2	FACETS	0.943	0.822	1	0.943	0.822	1	CLONAL	1	TRUE	1	0.519317402053224	2		175	245	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566818	212566818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762866612	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	98	220	0	ENST00000342788.4:c.1363G>A	p.Ala455Thr	p.A455T	ENST00000342788	NM_005235.2	455	Gca/Aca	12/28	1	2	FACETS	0.939	0.844	1	0.939	0.844	1	CLONAL	1	TRUE	1	0.519317402053224	2		220	402	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646085	215646085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	153	435	1	ENST00000260947.4:c.513del	p.Asp172MetfsTer40	p.D172Mfs*40	ENST00000260947	NM_000465.2	171	aaA/aa	4/11	1	2	FACETS	0.994	0.913	1	0.994	0.913	1	CLONAL	1	TRUE	1	0.519317402053224	2		436	593	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439742	220439742	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257387062	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	183	481	0	ENST00000243786.2:c.595C>T	p.Arg199Cys	p.R199C	ENST00000243786	NM_002191.3	199	Cgc/Tgc	2/2	1	2	FACETS	0.95	0.879	1	0.95	0.879	1	CLONAL	1	TRUE	1	0.519317402053224	2		481	742	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370741	225370741	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	126	358	1	ENST00000264414.4:c.1138C>A	p.Leu380Ile	p.L380I	ENST00000264414	NM_003590.4	380	Ctc/Atc	8/16	1	2	FACETS	0.899	0.817	0.983	0.899	0.817	0.983	CLONAL	1	TRUE	1	0.519317402053224	2		359	540	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661726	227661726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760281604	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	137	351	1	ENST00000305123.5:c.1729G>A	p.Val577Met	p.V577M	ENST00000305123	NM_005544.2	577	Gtg/Atg	1/2	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.519317402053224	2		352	483	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	205	754	7	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.92	0.855	0.988	0.92	0.855	0.988	CLONAL	1	TRUE	1	0.519317402053224	2		761	858	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	110	255	3	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	0.516696156886364	3	FACETS	0.97	0.886	1	0.97	0.886	1	CLONAL	2	TRUE	1	0.519317402053224	3		258	275	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742680	39742680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	105	304	0	ENST00000361337.2:c.1523G>A	p.Arg508His	p.R508H	ENST00000361337	NM_003286.2	508	cGt/cAt	15/21	0.516696156886364	3	FACETS	0.828	0.744	0.918	0.414	0.372	0.459	CLONAL	1	TRUE	1	0.519317402053224	3		304	615	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961526	54961526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1211313151	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	265	378	0	ENST00000312783.6:c.106C>T	p.Pro36Ser	p.P36S	ENST00000312783	NM_198436.1	36	Cca/Tca	4/10	0.516696156886364	3	FACETS	0.972	0.918	1	0.972	0.918	1	CLONAL	2	TRUE	1	0.519317402053224	3		378	661	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167410	24167410	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	141	417	0	ENST00000263121.7:c.796-2A>G		p.X266_splice	ENST00000263121	NM_003073.3	266			1	2	FACETS	0.987	0.904	1	0.987	0.904	1	CLONAL	1	TRUE	1	0.519317402053224	2		417	550	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057302	30057302	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315496	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	136	384	0	ENST00000338641.4:c.784C>T	p.Arg262Ter	p.R262*	ENST00000338641	NM_000268.3	262	Cga/Tga	8/16	1	2	FACETS	0.905	0.826	0.987	0.905	0.826	0.987	CLONAL	1	TRUE	1	0.519317402053224	2		384	579	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077462	30077462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	145	312	0	ENST00000338641.4:c.1609G>A	p.Glu537Lys	p.E537K	ENST00000338641	NM_000268.3	537	Gag/Aag	15/16	1	2	FACETS	0.985	0.903	1	0.985	0.903	1	CLONAL	1	TRUE	1	0.519317402053224	2		312	567	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627233	12627233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs941573221	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	169	397	0	ENST00000251849.4:c.1483C>T	p.Arg495Cys	p.R495C	ENST00000251849	NM_002880.3	495	Cgc/Tgc	14/17	1	2	FACETS	0.998	0.921	1	0.998	0.921	1	CLONAL	1	TRUE	1	0.519317402053224	2		397	652	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928834	49928834	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs878910700	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	196	502	0	ENST00000296474.3:c.3532C>T	p.Arg1178Trp	p.R1178W	ENST00000296474	NM_002447.2	1178	Cgg/Tgg	16/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.519317402053224	2		502	745	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499363	89499363	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1317589623	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	100	305	0	ENST00000336596.2:c.2538del	p.Met847TrpfsTer10	p.M847Wfs*10	ENST00000336596	NM_005233.5	845	Ccc/cc	15/17	1	2	FACETS	0.86	0.772	0.951	0.86	0.772	0.951	CLONAL	1	TRUE	1	0.519317402053224	2		305	448	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612212	189612212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764601563	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	153	356	0	ENST00000264731.3:c.1964G>A	p.Arg655Gln	p.R655Q	ENST00000264731	NM_003722.4	655	cGa/cAa	14/14	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.519317402053224	2		356	573	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806234	1806234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781361431	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	194	485	0	ENST00000260795.2:c.1253C>T	p.Pro418Leu	p.P418L	ENST00000260795		418	cCg/cTg	8/17	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.519317402053224	2		485	716	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980458	1980458	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	256	610	0	ENST00000382891.5:c.3920A>G	p.His1307Arg	p.H1307R	ENST00000382891	NM_133335.3	1307	cAc/cGc	22/22	1	2	FACETS	0.974	0.913	1	0.974	0.913	1	CLONAL	1	TRUE	1	0.519317402053224	2		610	1012	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980581	1980581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370127436	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	169	443	0	ENST00000382891.5:c.4043C>T	p.Pro1348Leu	p.P1348L	ENST00000382891	NM_133335.3	1348	cCg/cTg	22/22	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.519317402053224	2		443	645	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538991	187538991	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	278	310	0	ENST00000441802.2:c.8749C>T	p.Arg2917Ter	p.R2917*	ENST00000441802	NM_005245.3	2917	Cga/Tga	10/27	0.519317402053224	3	FACETS	0.958	0.905	1	0.958	0.905	1	CLONAL	2	TRUE	1	0.519317402053224	3		310	704	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630099	187630099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61733573	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	328	406	0	ENST00000441802.2:c.883G>A	p.Val295Met	p.V295M	ENST00000441802	NM_005245.3	295	Gtg/Atg	2/27	0.519317402053224	3	FACETS	0.967	0.918	1	0.967	0.918	1	CLONAL	2	TRUE	1	0.519317402053224	3		406	823	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592108	67592108	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1419325070	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	105	240	0	ENST00000274335.5:c.1924C>T	p.Arg642Ter	p.R642*	ENST00000274335		642	Cga/Tga	14/15	1	2	FACETS	0.925	0.834	1	0.925	0.834	1	CLONAL	1	TRUE	1	0.519317402053224	2		240	437	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79965934	79965934	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	107	383	0	ENST00000265081.6:c.598C>G	p.Leu200Val	p.L200V	ENST00000265081	NM_002439.4	200	Ctc/Gtc	4/24	1	2	FACETS	0.763	0.687	0.843	0.763	0.687	0.843	SUBCLONAL	1	TRUE	1	0.519317402053224	2		383	540	SUCCESS
APC	324	MSKCC	GRCh37	5	112102931	112102932	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	131	308	0	ENST00000257430.4:c.271dup	p.Met91AsnfsTer48	p.M91Nfs*48	ENST00000257430	NM_000038.5	89	tca/tcAa	4/16	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.519317402053224	2		308	493	SUCCESS
APC	324	MSKCC	GRCh37	5	112162852	112162852	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	101	393	0	ENST00000257430.4:c.1456T>G	p.Tyr486Asp	p.Y486D	ENST00000257430	NM_000038.5	486	Tat/Gat	12/16	1	2	FACETS	0.81	0.728	0.897	0.81	0.728	0.897	CLONAL	1	TRUE	1	0.519317402053224	2		393	480	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	122	274	1	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.519317402053224	2		275	420	SUCCESS
APC	324	MSKCC	GRCh37	5	112179674	112179674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369264968	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	97	296	0	ENST00000257430.4:c.8383G>A	p.Ala2795Thr	p.A2795T	ENST00000257430	NM_000038.5	2795	Gca/Aca	16/16	1	2	FACETS	0.838	0.751	0.929	0.838	0.751	0.929	CLONAL	1	TRUE	1	0.519317402053224	2		296	446	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665377	176665377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	90	264	1	ENST00000439151.2:c.4061G>A	p.Gly1354Asp	p.G1354D	ENST00000439151	NM_022455.4	1354	gGc/gAc	7/23	1	2	FACETS	0.845	0.755	0.941	0.845	0.755	0.941	CLONAL	1	TRUE	1	0.519317402053224	2		265	410	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721713	176721713	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	120	362	2	ENST00000439151.2:c.7349del	p.Asn2450IlefsTer6	p.N2450Ifs*6	ENST00000439151	NM_022455.4	2448	tcA/tc	23/23	1	2	FACETS	0.91	0.826	0.997	0.91	0.826	0.997	CLONAL	1	TRUE	1	0.519317402053224	2		364	508	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057064	180057064	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	191	491	0	ENST00000261937.6:c.555G>A	p.Trp185Ter	p.W185*	ENST00000261937	NM_182925.4	185	tgG/tgA	5/30	1	2	FACETS	0.995	0.923	1	0.995	0.923	1	CLONAL	1	TRUE	1	0.519317402053224	2		491	739	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858551	27858551	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	88	199	0	ENST00000359303.2:c.20C>T	p.Thr7Ile	p.T7I	ENST00000359303	NM_003535.2	7	aCa/aTa	1/1	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.519317402053224	2		199	339	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288857	33288857	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	88	245	0	ENST00000374542.5:c.695T>G	p.Leu232Arg	p.L232R	ENST00000374542	NM_001141970.1	232	cTg/cGg	3/8	1	2	FACETS	0.971	0.868	1	0.971	0.868	1	CLONAL	1	TRUE	1	0.519317402053224	2		245	349	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790873	89790873	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	136	463	0	ENST00000336032.3:c.260G>A	p.Gly87Glu	p.G87E	ENST00000336032	NM_006813.2	87	gGa/gAa	1/2	1	2	FACETS	0.932	0.851	1	0.932	0.851	1	CLONAL	1	TRUE	1	0.519317402053224	2		463	562	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511194	157511194	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1476545892	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	130	436	2	ENST00000346085.5:c.3712G>A	p.Asp1238Asn	p.D1238N	ENST00000346085	NM_020732.3	1238	Gac/Aac	15/20	1	2	FACETS	0.806	0.733	0.882	0.806	0.733	0.882	CLONAL	1	TRUE	1	0.519317402053224	2		438	621	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522076	157522076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376207220	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	107	355	0	ENST00000346085.5:c.4348G>A	p.Gly1450Ser	p.G1450S	ENST00000346085	NM_020732.3	1450	Ggc/Agc	18/20	1	2	FACETS	0.829	0.747	0.915	0.829	0.747	0.915	CLONAL	1	TRUE	1	0.519317402053224	2		355	497	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864448	162864448	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	139	374	0	ENST00000366898.1:c.65G>T	p.Ser22Ile	p.S22I	ENST00000366898	NM_004562.2	22	aGc/aTc	2/12	1	2	FACETS	0.878	0.802	0.957	0.878	0.802	0.957	CLONAL	1	TRUE	1	0.519317402053224	2		374	610	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6038813	6038813	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs760228510	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	206	512	0	ENST00000265849.7:c.631C>T	p.Arg211Ter	p.R211*	ENST00000265849	NM_000535.5	211	Cga/Tga	6/15	1	2	FACETS	0.977	0.908	1	0.977	0.908	1	CLONAL	1	TRUE	1	0.519317402053224	2		512	812	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534620	140534622	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	132	314	0	ENST00000288602.6:c.291_293del	p.Gln98del	p.Q98del	ENST00000288602	NM_004333.4	97	caACAg/cag	3/18	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.519317402053224	2		314	493	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523690	148523690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	98	213	0	ENST00000320356.2:c.763G>A	p.Ala255Thr	p.A255T	ENST00000320356	NM_004456.4	255	Gca/Aca	8/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.519317402053224	2		213	350	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371734	55371734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	176	371	0	ENST00000297316.4:c.424C>T	p.Arg142Cys	p.R142C	ENST00000297316	NM_022454.3	142	Cgc/Tgc	2/2	1	2	FACETS	0.992	0.917	1	0.992	0.917	1	CLONAL	1	TRUE	1	0.519317402053224	2		371	683	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942744	68942744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755013538	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	122	312	1	ENST00000288368.4:c.556C>T	p.Arg186Trp	p.R186W	ENST00000288368	NM_024870.2	186	Cgg/Tgg	6/40	1	2	FACETS	0.969	0.881	1	0.969	0.881	1	CLONAL	1	TRUE	1	0.519317402053224	2		313	485	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129868	69129868	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776942401	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	85	222	0	ENST00000288368.4:c.4622C>T	p.Thr1541Met	p.T1541M	ENST00000288368	NM_024870.2	1541	aCg/aTg	38/40	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.519317402053224	2		222	323	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864938	117864938	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1259968025	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	86	198	0	ENST00000297338.2:c.1171C>T	p.Arg391Cys	p.R391C	ENST00000297338	NM_006265.2	391	Cgc/Tgc	10/14	0.45552051805006	3	FACETS	0.935	0.831	1			1	CLONAL	1	TRUE	NA	0.519317402053224	3		198	446	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737400	145737400	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765087683	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	184	479	1	ENST00000428558.2:c.3287G>A	p.Arg1096His	p.R1096H	ENST00000428558	NM_004260.3	1096	cGc/cAc	20/22	NA	2	FACETS	1	0.931	1			1	INDETERMINATE	1	TRUE	NA	0.519317402053224	2		480	705	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050689	5050689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765494796	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	95	277	0	ENST00000381652.3:c.472C>T	p.Arg158Trp	p.R158W	ENST00000381652	NM_004972.3	158	Cgg/Tgg	6/25	1	2	FACETS	0.888	0.796	0.985	0.888	0.796	0.985	CLONAL	1	TRUE	1	0.519317402053224	2		277	412	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090449	5090449	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs888369460	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	70	206	0	ENST00000381652.3:c.2765G>A	p.Arg922Gln	p.R922Q	ENST00000381652	NM_004972.3	922	cGg/cAg	21/25	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.519317402053224	2		206	252	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521420	8521421	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	195	500	0	ENST00000356435.5:c.817dup	p.Ala273GlyfsTer7	p.A273Gfs*7	ENST00000356435		273	gca/gGca	9/35	1	2	FACETS	0.909	0.843	0.978	0.909	0.843	0.978	CLONAL	1	TRUE	1	0.519317402053224	2		500	826	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212783	27212783	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754385594	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	201	527	2	ENST00000380036.4:c.2765C>T	p.Thr922Met	p.T922M	ENST00000380036	NM_000459.3	922	aCg/aTg	17/23	1	2	FACETS	0.953	0.885	1	0.953	0.885	1	CLONAL	1	TRUE	1	0.519317402053224	2		529	812	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137326005	137326005	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11542209	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	234	529	3	ENST00000481739.1:c.1193C>T	p.Ala398Val	p.A398V	ENST00000481739	NM_002957.4	398	gCg/gTg	9/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.519317402053224	2		532	865	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030463	47030463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781862400	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	221	535	1	ENST00000377604.3:c.238C>T	p.Arg80Cys	p.R80C	ENST00000377604	NM_001204468.1	80	Cgt/Tgt	4/24	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.519317402053224	2		536	800	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222454	53222454	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	170	523	0	ENST00000375401.3:c.4378C>G	p.Arg1460Gly	p.R1460G	ENST00000375401	NM_004187.3	1460	Cgg/Ggg	26/26	1	2	FACETS	0.898	0.828	0.971	0.898	0.828	0.971	CLONAL	1	TRUE	1	0.519317402053224	2		523	729	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611203	100611203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555977836	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	132	444	1	ENST00000308731.7:c.1403G>A	p.Arg468His	p.R468H	ENST00000308731	NM_000061.2	468	cGc/cAc	15/19	1	2	FACETS	0.918	0.837	1	0.918	0.837	1	CLONAL	1	TRUE	1	0.519317402053224	2		445	554	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630173	100630173	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141488935	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	153	403	0	ENST00000308731.7:c.100G>A	p.Val34Met	p.V34M	ENST00000308731	NM_000061.2	34	Gtg/Atg	2/19	1	2	FACETS	0.907	0.832	0.984	0.907	0.832	0.984	CLONAL	1	TRUE	1	0.519317402053224	2		403	650	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860097	152860097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201043377	NA	P-0027740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	226	597	1	ENST00000406277.2:c.331C>T	p.Arg111Cys	p.R111C	ENST00000406277	NM_152274.4	111	Cgc/Tgc	5/7	1		FACETS		0.965	1				CLONAL	1	TRUE	1	0.519317402053224	2		598	829	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627234	86627238	+	frameshift_variant	Frame_Shift_Del	DEL	TTATC	TTATC	-	rs1060503441	NA	P-0027741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	116	272	0	ENST00000274376.6:c.613_617del	p.Leu205LysfsTer4	p.L205Kfs*4	ENST00000274376	NM_002890.2	203	agTTATCtt/agtt	2/25	0.652807880519019	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	0	0.651408329156238	1		272	229	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109753	115109753	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	107	602	0	ENST00000257566.3:c.2125A>G	p.Lys709Glu	p.K709E	ENST00000257566	NM_016569.3	709	Aaa/Gaa	8/8	0.569873708634091	4	FACETS	0.705	0.632	0.782	0.352	0.316	0.391	SUBCLONAL	1	FALSE	2	0.651408329156238	4		602	770	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035307	42035307	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	128	393	0	ENST00000219905.7:c.5149C>G	p.Leu1717Val	p.L1717V	ENST00000219905	NM_001164273.1	1717	Ctg/Gtg	15/24	0.652807880519019	4	FACETS	1	0.958	1	0.546	0.497	0.598	CLONAL	1	FALSE	2	0.651408329156238	4		393	594	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135777055	135777055	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756514375	NA	P-0027741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	97	432	1	ENST00000298552.3:c.2423C>T	p.Ala808Val	p.A808V	ENST00000298552	NM_001162426.1	808	gCg/gTg	19/23	0.652807880519019	2	FACETS	1	0.962	1	0.562	0.509	0.617	CLONAL	1	FALSE	0	0.651408329156238	2		433	265	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38960078	38960090	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATCCTAAAAGTAA	ATCCTAAAAGTAA	-	novel	NA	P-0027741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	19	197	0	ENST00000357387.3:c.1852-10_1854del		p.X618_splice	ENST00000357387	NM_152756.3	618		21/38	0.652807880519019	3	FACETS	0.344	0.261	0.44			1	SUBCLONAL	1	FALSE	NA	0.651408329156238	3		197	225	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012465	29012465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373801409	NA	P-0027743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	66	324	0	ENST00000282397.4:c.406G>A	p.Val136Ile	p.V136I	ENST00000282397	NM_002019.4	136	Gta/Ata	4/30	0.185664549280389	5	FACETS	1	0.961	1	0.435	0.377	0.498	CLONAL	1	TRUE	2	0.185664549280389	5		324	696	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288843	15288843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	44	186	0	ENST00000263388.2:c.3896C>T	p.Pro1299Leu	p.P1299L	ENST00000263388	NM_000435.2	1299	cCg/cTg	24/33	1	2	FACETS	0.752	0.634	0.882	1	0.959	1	SUBCLONAL	2	TRUE	1	0.185664549280389	2		186	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579315	7579315	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1555526478	NA	P-0027743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	86	408	0	ENST00000269305.4:c.372C>A	p.Cys124Ter	p.C124*	ENST00000269305	NM_001126112.2	124	tgC/tgA	4/11	NA	2	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.185664549280389	2		408	676	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300565	11300565	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	125	576	0	ENST00000361445.4:c.1581G>T	p.Gln527His	p.Q527H	ENST00000361445	NM_004958.3	527	caG/caT	11/58	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.185664549280389	2		576	1000	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291193	10291193	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	104	473	0	ENST00000340748.4:c.278A>T	p.Glu93Val	p.E93V	ENST00000340748		93	gAg/gTg	4/40	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.185664549280389	2		473	900	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646191	215646191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553622698	NA	P-0027743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	43	314	0	ENST00000260947.4:c.407C>T	p.Ala136Val	p.A136V	ENST00000260947	NM_000465.2	136	gCa/gTa	4/11	1	2	FACETS	0.93	0.778	1	0.93	0.778	1	CLONAL	1	TRUE	1	0.185664549280389	2		314	498	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064749	80064749	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	64	478	1	ENST00000265081.6:c.2180G>T	p.Arg727Leu	p.R727L	ENST00000265081	NM_002439.4	727	cGa/cTa	15/24	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.185664549280389	2		479	598	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0027744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	18	583	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.272	0.204	0.354	0.272	0.204	0.354	SUBCLONAL	1	TRUE	1	0.23	2		583	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0027745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	58	678	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.84	0.72	0.97	0.84	0.72	0.97	CLONAL	1	TRUE	1	0.19	2		678	727	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0027745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	34	537	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.5	0.407	0.605	0.5	0.407	0.605	SUBCLONAL	1	TRUE	1	0.19	2		537	716	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	97	315	1				ENST00000310581	NM_198253.2	-/1132			0.434394278845078	1	FACETS	0.413	0.372	0.456	0.413	0.372	0.456	INDETERMINATE	1	TRUE	0	0.838430703167221	1		316	325	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692901	89692901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786204929	NA	P-0027747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	312	536	2	ENST00000371953.3:c.385G>A	p.Gly129Arg	p.G129R	ENST00000371953	NM_000314.4	129	Gga/Aga	5/9	0.838430703167221	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.838430703167221	1		538	424	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0027748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	103	443	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.65	0.585	0.719	0.65	0.585	0.719	SUBCLONAL	1	TRUE	1	0.65310764128521	2		443	485	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12043154	12043154	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0027748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	69	203	0	ENST00000353533.5:c.1041-2A>C		p.X347_splice	ENST00000353533	NM_003010.3	347			0.473481182927756	1	FACETS	0.445	0.39	0.503	0.445	0.39	0.503	SUBCLONAL	1	TRUE	0	0.65310764128521	1		203	320	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231849	36231850	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	142	492	1	ENST00000300305.3:c.534dup	p.Val179CysfsTer34	p.V179Cfs*34	ENST00000300305		178	-/T	5/8	1	2	FACETS	0.586	0.535	0.64	0.586	0.535	0.64	SUBCLONAL	1	TRUE	1	0.65310764128521	2		493	742	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349243	70349243	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	87	549	0	ENST00000374080.3:c.3655G>C	p.Ala1219Pro	p.A1219P	ENST00000374080		1219	Gcc/Ccc	26/45	1	2	FACETS	0.326	0.288	0.366	0.326	0.288	0.366	SUBCLONAL	1	TRUE	1	0.65310764128521	2		549	818	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440334	52440334	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0001103-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	87	353	0	ENST00000460680.1:c.718A>T	p.Lys240Ter	p.K240*	ENST00000460680	NM_004656.3	240	Aag/Tag	9/17	0.231880551809247	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.231880551809247	1		353	520	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620665	52620665	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001103-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	42	424	1	ENST00000394830.3:c.3088G>T	p.Asp1030Tyr	p.D1030Y	ENST00000394830	NM_018313.4	1030	Gat/Tat	21/30	0.231880551809247	1	FACETS	0.478	0.398	0.567	0.478	0.398	0.567	SUBCLONAL	1	TRUE	0	0.231880551809247	1		425	670	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609965	117609965	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001705-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	169	373	1	ENST00000368508.3:c.6734G>T	p.Gly2245Val	p.G2245V	ENST00000368508	NM_002944.2	2245	gGt/gTt	43/43	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.869171494824119	2		374	378	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	71	474	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.82	0.724	0.921			1	INDETERMINATE	1	TRUE	NA	0.64644086427546	2		474	268	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	18	279	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.164	0.123	0.212	0.164	0.123	0.212	SUBCLONAL	1	TRUE	1	0.64644086427546	2		279	340	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	81	177	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.783	0.696	0.874	0.783	0.696	0.874	SUBCLONAL	1	TRUE	1	0.64644086427546	2		177	320	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038231	30038231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	28	442	0	ENST00000338641.4:c.404C>T	p.Pro135Leu	p.P135L	ENST00000338641	NM_000268.3	135	cCt/cTt	4/16	1	2	FACETS	0.167	0.133	0.206	0.167	0.133	0.206	SUBCLONAL	1	TRUE	1	0.64644086427546	2		442	518	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781509	9781509	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	16	366	0	ENST00000377346.4:c.1819G>A	p.Glu607Lys	p.E607K	ENST00000377346	NM_005026.3	607	Gag/Aag	15/24	0.64644086427546	1	FACETS	0.157	0.116	0.205	0.157	0.116	0.205	SUBCLONAL	1	TRUE	0	0.64644086427546	1		366	214	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543620	29543620	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	41	548	0	ENST00000389048.3:c.1543C>T	p.Gln515Ter	p.Q515*	ENST00000389048	NM_004304.4	515	Caa/Taa	7/29	1	2	FACETS	0.224	0.186	0.266	0.224	0.186	0.266	SUBCLONAL	1	TRUE	1	0.64644086427546	2		548	567	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595851	52595851	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	43	481	0	ENST00000394830.3:c.4064G>A	p.Gly1355Glu	p.G1355E	ENST00000394830	NM_018313.4	1355	gGg/gAg	26/30	NA	2	FACETS	0.228	0.19	0.27			1	INDETERMINATE	1	TRUE	NA	0.64644086427546	2		481	584	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447294	187447294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	41	512	1	ENST00000232014.4:c.899G>A	p.Ser300Asn	p.S300N	ENST00000232014	NM_001130845.1	300	aGc/aAc	5/10	1	2	FACETS	0.266	0.221	0.316	0.266	0.221	0.316	SUBCLONAL	1	TRUE	1	0.64644086427546	2		513	477	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638522	176638522	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	67	584	0	ENST00000439151.2:c.3122A>G	p.Asn1041Ser	p.N1041S	ENST00000439151	NM_022455.4	1041	aAc/aGc	5/23	0.166349642568125	0	FACETS	0.107	0.093	0.123			1	INDETERMINATE	1	TRUE	0	0.64644086427546	0		584	683	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405092	405092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	52	473	1	ENST00000380956.4:c.1174C>T	p.Pro392Ser	p.P392S	ENST00000380956	NM_001195286.1	392	Cca/Tca	8/9	NA	2	FACETS	0.272	0.231	0.317			1	INDETERMINATE	1	TRUE	NA	0.64644086427546	2		474	591	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166452	32166452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	53	602	1	ENST00000375023.3:c.4591C>T	p.Pro1531Ser	p.P1531S	ENST00000375023	NM_004557.3	1531	Cct/Tct	25/30	1	2	FACETS	0.252	0.214	0.293	0.252	0.214	0.293	SUBCLONAL	1	TRUE	1	0.64644086427546	2		603	651	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157519986	157519986	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	44	538	0	ENST00000346085.5:c.4055C>T	p.Pro1352Leu	p.P1352L	ENST00000346085	NM_020732.3	1352	cCc/cTc	17/20	1	2	FACETS	0.212	0.177	0.25	0.212	0.177	0.25	SUBCLONAL	1	TRUE	1	0.64644086427546	2		538	643	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683626	162683626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs529360617	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	35	442	0	ENST00000366898.1:c.343G>A	p.Asp115Asn	p.D115N	ENST00000366898	NM_004562.2	115	Gac/Aac	3/12	1	2	FACETS	0.191	0.156	0.23	0.191	0.156	0.23	SUBCLONAL	1	TRUE	1	0.64644086427546	2		442	568	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415138	116415138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	34	443	0	ENST00000397752.3:c.3232G>A	p.Val1078Met	p.V1078M	ENST00000397752	NM_000245.2	1078	Gtg/Atg	15/21	1	2	FACETS	0.161	0.131	0.195	0.161	0.131	0.195	SUBCLONAL	1	TRUE	1	0.64644086427546	2		443	653	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277118	38277118	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	29	501	0	ENST00000425967.3:c.1310G>A	p.Ser437Asn	p.S437N	ENST00000425967	NM_001174067.1	437	aGt/aAt	10/19	1	2	FACETS	0.179	0.143	0.221	0.179	0.143	0.221	SUBCLONAL	1	TRUE	1	0.64644086427546	2		501	500	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400047	139400047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	28	703	0	ENST00000277541.6:c.4301G>A	p.Gly1434Asp	p.G1434D	ENST00000277541	NM_017617.3	1434	gGt/gAt	25/34	1	2	FACETS	0.192	0.153	0.236	0.192	0.153	0.236	SUBCLONAL	1	TRUE	1	0.64644086427546	2		703	452	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871249	12871249	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	19	187	0	ENST00000228872.4:c.475+1G>A		p.X159_splice	ENST00000228872	NM_004064.3	159			1	2	FACETS	0.248	0.188	0.318	0.248	0.188	0.318	SUBCLONAL	1	TRUE	1	0.64644086427546	2		187	237	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231362	46231362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	45	361	0	ENST00000334344.6:c.1202G>A	p.Arg401Lys	p.R401K	ENST00000334344	NM_152641.2	401	aGa/aAa	10/21	1	2	FACETS	0.223	0.187	0.263	0.223	0.187	0.263	SUBCLONAL	1	TRUE	1	0.64644086427546	2		361	624	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926528	59926528	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	53	573	0	ENST00000259008.2:c.469G>A	p.Glu157Lys	p.E157K	ENST00000259008	NM_032043.2	157	Gag/Aag	5/20	1	2	FACETS	0.205	0.174	0.239	0.205	0.174	0.239	SUBCLONAL	1	TRUE	1	0.64644086427546	2		573	800	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45422953	45422953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	41	335	0	ENST00000262160.6:c.175G>A	p.Asp59Asn	p.D59N	ENST00000262160	NM_005901.5	59	Gat/Aat	2/11	1	2	FACETS	0.236	0.196	0.28	0.236	0.196	0.28	SUBCLONAL	1	TRUE	1	0.64644086427546	2		335	538	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573460	48573460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	23	245	0	ENST00000342988.3:c.44C>T	p.Ala15Val	p.A15V	ENST00000342988	NM_005359.5	15	gCc/gTc	2/12	1	2	FACETS	0.201	0.156	0.253	0.201	0.156	0.253	SUBCLONAL	1	TRUE	1	0.64644086427546	2		245	354	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223021	1223021	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	30	633	0	ENST00000326873.7:c.958G>A	p.Val320Met	p.V320M	ENST00000326873	NM_000455.4	320	Gtg/Atg	8/10	0.333500535860123	1	FACETS	0.135	0.108	0.165	0.135	0.108	0.165	INDETERMINATE	1	TRUE	0	0.64644086427546	1		633	465	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291034	15291034	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	38	817	0	ENST00000263388.2:c.3176G>A	p.Gly1059Glu	p.G1059E	ENST00000263388	NM_000435.2	1059	gGg/gAg	20/33	0.4282336937855	1	FACETS	0.131	0.108	0.157	0.131	0.108	0.157	SUBCLONAL	1	TRUE	0	0.64644086427546	1		817	607	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376428	15376428	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	66	902	0	ENST00000263377.2:c.586G>A	p.Val196Ile	p.V196I	ENST00000263377	NM_058243.2	196	Gta/Ata	5/20	NA	2	FACETS	0.228	0.197	0.262			1	INDETERMINATE	1	TRUE	NA	0.64644086427546	2		902	896	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791757	42791757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568504941	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	136	541	0	ENST00000575354.2:c.643C>T	p.Arg215Trp	p.R215W	ENST00000575354	NM_015125.3	215	Cgg/Tgg	5/20	0.64644086427546	1	FACETS	0.949	0.878	1	0.949	0.878	1	CLONAL	1	TRUE	0	0.64644086427546	1		541	300	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931990	39931990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	46	291	0	ENST00000378444.4:c.2609C>T	p.Thr870Ile	p.T870I	ENST00000378444	NM_001123385.1	870	aCt/aTt	4/15	1	1	FACETS	0.313	0.264	0.365	0.313	0.264	0.365	SUBCLONAL	1	TRUE	0	0.64644086427546	1		291	308	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035968	47035968	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	53	328	0	ENST00000377604.3:c.646G>A	p.Asp216Asn	p.D216N	ENST00000377604	NM_001204468.1	216	Gac/Aac	7/24	1	1	FACETS	0.302	0.259	0.35	0.302	0.259	0.35	SUBCLONAL	1	TRUE	0	0.64644086427546	1		328	367	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190057	123190057	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	56	213	2	ENST00000218089.9:c.1276G>A	p.Val426Ile	p.V426I	ENST00000218089	NM_001042749.1	426	Gta/Ata	14/35	1	1	FACETS	0.329	0.283	0.379	0.329	0.283	0.379	SUBCLONAL	1	TRUE	0	0.64644086427546	1		215	356	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433867	78433870	+	frameshift_variant	Frame_Shift_Del	DEL	CTTT	CTTT	-	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	184	327	0	ENST00000370768.2:c.229_232del	p.Lys77LeufsTer23	p.K77Lfs*23	ENST00000370768	NM_003902.3	77	AAAGtt/tt	3/20	0.64644086427546	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.64644086427546	1		327	385	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182709	38182709	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370623345	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	34	488	0	ENST00000396334.3:c.862G>A	p.Asp288Asn	p.D288N	ENST00000396334	NM_002468.4	288	Gac/Aac	5/5	1	2	FACETS	0.21	0.171	0.253	0.21	0.171	0.253	SUBCLONAL	1	TRUE	1	0.64644086427546	2		488	502	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992187	72992187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1413049341	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	53	582	0	ENST00000268489.5:c.1858C>T	p.His620Tyr	p.H620Y	ENST00000268489	NM_006885.3	620	Cac/Tac	2/10	1	2	FACETS	0.327	0.278	0.379	0.327	0.278	0.379	SUBCLONAL	1	TRUE	1	0.64644086427546	2		582	502	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156735	20156735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	49	143	0	ENST00000379607.5:c.22G>A	p.Gly8Arg	p.G8R	ENST00000379607	NM_001412.3	8	Gga/Aga	2/7	1	1	FACETS	0.409	0.349	0.473	0.409	0.349	0.473	SUBCLONAL	1	TRUE	0	0.64644086427546	1		143	251	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106805	27106805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	57	534	1	ENST00000324856.7:c.6416C>T	p.Pro2139Leu	p.P2139L	ENST00000324856	NM_006015.4	2139	cCc/cTc	20/20	0.64644086427546	1	FACETS	0.322	0.277	0.37	0.322	0.277	0.37	SUBCLONAL	1	TRUE	0	0.64644086427546	1		535	371	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936109	49936109	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	24	524	0	ENST00000296474.3:c.1561C>T	p.Pro521Ser	p.P521S	ENST00000296474	NM_002447.2	521	Cct/Tct	4/20	NA	2	FACETS	0.194	0.152	0.243			1	INDETERMINATE	1	TRUE	NA	0.64644086427546	2		524	382	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967961	93967961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1231037263	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	53	354	0	ENST00000369303.4:c.1966G>A	p.Gly656Arg	p.G656R	ENST00000369303	NM_004440.3	656	Ggg/Agg	11/17	1	2	FACETS	0.207	0.176	0.241	0.207	0.176	0.241	SUBCLONAL	1	TRUE	1	0.64644086427546	2		354	792	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015851	112015851	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	46	382	0	ENST00000368678.4:c.1090C>T	p.Leu364Phe	p.L364F	ENST00000368678		364	Ctt/Ttt	10/13	1	2	FACETS	0.23	0.193	0.27	0.23	0.193	0.27	SUBCLONAL	1	TRUE	1	0.64644086427546	2		382	620	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915819	127915819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	30	317	0	ENST00000373547.4:c.662C>T	p.Thr221Ile	p.T221I	ENST00000373547	NM_002721.4	221	aCa/aTa	6/7	1	2	FACETS	0.197	0.159	0.242	0.197	0.159	0.242	SUBCLONAL	1	TRUE	1	0.64644086427546	2		317	470	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868039	56868039	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	17	260	0	ENST00000308159.5:c.1538-1G>A		p.X513_splice	ENST00000308159	NM_014669.4	513			1	2	FACETS	0.175	0.13	0.228	0.175	0.13	0.228	SUBCLONAL	1	TRUE	1	0.64644086427546	2		260	301	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262260	46262260	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	158	361	0	ENST00000371998.3:c.844A>C	p.Thr282Pro	p.T282P	ENST00000371998		282	Aca/Cca	9/23	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.64644086427546	2		361	472	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46277842	46277842	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	39	372	1	ENST00000371998.3:c.3640G>A	p.Val1214Met	p.V1214M	ENST00000371998		1214	Gtg/Atg	19/23	1	2	FACETS	0.263	0.218	0.314	0.263	0.218	0.314	SUBCLONAL	1	TRUE	1	0.64644086427546	2		373	458	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281155	46281155	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	44	439	0	ENST00000371998.3:c.3952G>A	p.Gly1318Arg	p.G1318R	ENST00000371998		1318	Gga/Aga	21/23	1	2	FACETS	0.265	0.222	0.313	0.265	0.222	0.313	SUBCLONAL	1	TRUE	1	0.64644086427546	2		439	514	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192092	108192092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	54	458	0	ENST00000278616.4:c.6517C>T	p.Leu2173Phe	p.L2173F	ENST00000278616	NM_000051.3	2173	Ctt/Ttt	45/63	1	2	FACETS	0.234	0.199	0.272	0.234	0.199	0.272	SUBCLONAL	1	TRUE	1	0.64644086427546	2		458	715	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859457	57859457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	47	549	0	ENST00000228682.2:c.602G>A	p.Ser201Asn	p.S201N	ENST00000228682	NM_005269.2	201	aGc/aAc	6/12	1	2	FACETS	0.291	0.246	0.342	0.291	0.246	0.342	SUBCLONAL	1	TRUE	1	0.64644086427546	2		549	499	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971375	13971375	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	42	319	0	ENST00000405192.2:c.555-1G>A		p.X185_splice	ENST00000405192	NM_001163147.1	185			1	2	FACETS	0.238	0.198	0.282	0.238	0.198	0.282	SUBCLONAL	1	TRUE	1	0.64644086427546	2		319	546	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092812	27092812	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	50	580	0	ENST00000324856.7:c.2833G>A	p.Gly945Arg	p.G945R	ENST00000324856	NM_006015.4	945	Gga/Aga	9/20	0.64644086427546	1	FACETS	0.281	0.239	0.327	0.281	0.239	0.327	SUBCLONAL	1	TRUE	0	0.64644086427546	1		580	373	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724431	162724431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	43	386	0	ENST00000367921.3:c.203G>A	p.Gly68Glu	p.G68E	ENST00000367921	NM_006182.2	68	gGg/gAg	5/18	0.147220224113737	3	FACETS	0.37	0.309	0.437	0.185	0.154	0.219	INDETERMINATE	1	TRUE	1	0.64644086427546	3		386	476	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948167	71948167	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	46	755	0	ENST00000298229.2:c.2880-1G>A		p.X960_splice	ENST00000298229	NM_001567.3	960			1	2	FACETS	0.217	0.182	0.255	0.217	0.182	0.255	SUBCLONAL	1	TRUE	1	0.64644086427546	2		755	657	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196249	108196249	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs876660017	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	54	399	0	ENST00000278616.4:c.6785C>G	p.Ala2262Gly	p.A2262G	ENST00000278616	NM_000051.3	2262	gCc/gGc	46/63	1	2	FACETS	0.257	0.219	0.299	0.257	0.219	0.299	SUBCLONAL	1	TRUE	1	0.64644086427546	2		399	649	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442480	49442480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	34	532	0	ENST00000301067.7:c.4093G>A	p.Val1365Ile	p.V1365I	ENST00000301067	NM_003482.3	1365	Gtt/Att	13/54	1	2	FACETS	0.169	0.137	0.205	0.169	0.137	0.205	SUBCLONAL	1	TRUE	1	0.64644086427546	2		532	623	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445163	49445163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	44	716	0	ENST00000301067.7:c.2303C>T	p.Pro768Leu	p.P768L	ENST00000301067	NM_003482.3	768	cCa/cTa	10/54	1	2	FACETS	0.207	0.173	0.245	0.207	0.173	0.245	SUBCLONAL	1	TRUE	1	0.64644086427546	2		716	658	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448200	49448200	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	23	466	0	ENST00000301067.7:c.401-1G>A		p.X134_splice	ENST00000301067	NM_003482.3	134			1	2	FACETS	0.166	0.129	0.209	0.166	0.129	0.209	SUBCLONAL	1	TRUE	1	0.64644086427546	2		466	428	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434103	121434103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	30	630	0	ENST00000257555.6:c.994G>A	p.Glu332Lys	p.E332K	ENST00000257555		332	Gaa/Aaa	5/10	1	2	FACETS	0.174	0.14	0.214	0.174	0.14	0.214	SUBCLONAL	1	TRUE	1	0.64644086427546	2		630	532	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549232	21549232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	80	668	0	ENST00000382592.4:c.3044G>A	p.Ser1015Asn	p.S1015N	ENST00000382592	NM_014572.2	1015	aGc/aAc	8/8	1	2	FACETS	0.317	0.279	0.359	0.317	0.279	0.359	SUBCLONAL	1	TRUE	1	0.64644086427546	2		668	780	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590807	95590807	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	36	312	0	ENST00000393063.1:c.1102C>T	p.Leu368Phe	p.L368F	ENST00000393063	NM_030621.3	368	Ctt/Ttt	9/28	1	2	FACETS	0.3	0.247	0.36	0.3	0.247	0.36	SUBCLONAL	1	TRUE	1	0.64644086427546	2		312	371	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900524	3900524	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	68	711	0	ENST00000262367.5:c.572G>A	p.Ser191Asn	p.S191N	ENST00000262367	NM_004380.2	191	aGt/aAt	2/31	1	2	FACETS	0.274	0.238	0.314	0.274	0.238	0.314	SUBCLONAL	1	TRUE	1	0.64644086427546	2		711	767	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900704	3900704	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	36	475	0	ENST00000262367.5:c.392C>T	p.Pro131Leu	p.P131L	ENST00000262367	NM_004380.2	131	cCc/cTc	2/31	1	2	FACETS	0.253	0.207	0.303	0.253	0.207	0.303	SUBCLONAL	1	TRUE	1	0.64644086427546	2		475	441	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634452	23634452	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs515726099	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	23	257	0	ENST00000261584.4:c.2835-1G>A		p.X945_splice	ENST00000261584	NM_024675.3	945			1	2	FACETS	0.199	0.155	0.251	0.199	0.155	0.251	SUBCLONAL	1	TRUE	1	0.64644086427546	2		257	357	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645240	67645240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	47	566	1	ENST00000264010.4:c.505G>A	p.Val169Met	p.V169M	ENST00000264010	NM_006565.3	169	Gtg/Atg	3/12	1	2	FACETS	0.269	0.226	0.316	0.269	0.226	0.316	SUBCLONAL	1	TRUE	1	0.64644086427546	2		567	541	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40371849	40371849	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	84	844	0	ENST00000293328.3:c.562C>T	p.Pro188Ser	p.P188S	ENST00000293328	NM_012448.3	188	Ccg/Tcg	6/19	1	2	FACETS	0.369	0.326	0.416	0.369	0.326	0.416	SUBCLONAL	1	TRUE	1	0.64644086427546	2		844	704	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213601	2213601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568359208	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	32	801	1	ENST00000398665.3:c.1621G>A	p.Glu541Lys	p.E541K	ENST00000398665	NM_032482.2	541	Gag/Aag	17/28	0.333500535860123	1	FACETS	0.114	0.092	0.139	0.114	0.092	0.139	INDETERMINATE	1	TRUE	0	0.64644086427546	1		802	590	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243981	5243981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750397382	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	34	627	0	ENST00000357368.4:c.1501G>A	p.Val501Met	p.V501M	ENST00000357368	NM_002850.3	501	Gtg/Atg	11/38	0.333500535860123	1	FACETS	0.159	0.13	0.193	0.159	0.13	0.193	INDETERMINATE	1	TRUE	0	0.64644086427546	1		627	447	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17389690	17389690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	57	659	0	ENST00000359435.4:c.823G>A	p.Gly275Ser	p.G275S	ENST00000359435	NM_001033549.1	275	Ggt/Agt	9/9	NA	2	FACETS	0.331	0.284	0.383			1	INDETERMINATE	1	TRUE	NA	0.64644086427546	2		659	532	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190656603	190656603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	34	223	3	ENST00000441310.2:c.68G>A	p.Ser23Asn	p.S23N	ENST00000441310	NM_000534.4	23	aGt/aAt	2/13	1	2	FACETS	0.276	0.225	0.333	0.276	0.225	0.333	SUBCLONAL	1	TRUE	1	0.64644086427546	2		226	381	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346756	225346756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	46	400	0	ENST00000264414.4:c.1882G>A	p.Val628Ile	p.V628I	ENST00000264414	NM_003590.4	628	Gtt/Att	14/16	1	2	FACETS	0.256	0.215	0.301	0.256	0.215	0.301	SUBCLONAL	1	TRUE	1	0.64644086427546	2		400	556	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793316	242793316	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	60	710	0	ENST00000334409.5:c.761C>T	p.Pro254Leu	p.P254L	ENST00000334409	NM_005018.2	254	cCt/cTt	5/5	1	2	FACETS	0.334	0.288	0.385	0.334	0.288	0.385	SUBCLONAL	1	TRUE	1	0.64644086427546	2		710	555	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723151	49723151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	57	644	2	ENST00000449682.2:c.1265C>T	p.Ser422Phe	p.S422F	ENST00000449682	NM_020998.3	422	tCc/tTc	11/18	NA	2	FACETS	0.329	0.282	0.38			1	INDETERMINATE	1	TRUE	NA	0.64644086427546	2		646	536	SUCCESS
ATR	545	MSKCC	GRCh37	3	142177813	142177813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	62	254	0	ENST00000350721.4:c.7490G>A	p.Cys2497Tyr	p.C2497Y	ENST00000350721	NM_001184.3	2497	tGt/tAt	44/47	1	2	FACETS	0.46	0.398	0.526	0.46	0.398	0.526	SUBCLONAL	1	TRUE	1	0.64644086427546	2		254	417	SUCCESS
ATR	545	MSKCC	GRCh37	3	142177832	142177832	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs556313656	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	63	303	1	ENST00000350721.4:c.7471G>A	p.Val2491Ile	p.V2491I	ENST00000350721	NM_001184.3	2491	Gta/Ata	44/47	1	2	FACETS	0.374	0.324	0.429	0.374	0.324	0.429	SUBCLONAL	1	TRUE	1	0.64644086427546	2		304	521	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156301	106156301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	55	289	0	ENST00000380013.4:c.1202C>T	p.Pro401Leu	p.P401L	ENST00000380013	NM_001127208.2	401	cCa/cTa	3/11	1	2	FACETS	0.449	0.385	0.518	0.449	0.385	0.518	SUBCLONAL	1	TRUE	1	0.64644086427546	2		289	379	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509993	187509993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	32	404	0	ENST00000441802.2:c.13520G>A	p.Gly4507Asp	p.G4507D	ENST00000441802	NM_005245.3	4507	gGt/gAt	27/27	1	2	FACETS	0.253	0.205	0.306	0.253	0.205	0.306	SUBCLONAL	1	TRUE	1	0.64644086427546	2		404	392	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532663	187532663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	56	373	0	ENST00000441802.2:c.9730C>T	p.Leu3244Phe	p.L3244F	ENST00000441802	NM_005245.3	3244	Ctt/Ttt	14/27	1	2	FACETS	0.347	0.297	0.401	0.347	0.297	0.401	SUBCLONAL	1	TRUE	1	0.64644086427546	2		373	499	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180504	56180504	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	45	284	0	ENST00000399503.3:c.3833G>A	p.Arg1278Lys	p.R1278K	ENST00000399503	NM_005921.1	1278	aGa/aAa	16/20	1	2	FACETS	0.353	0.297	0.415	0.353	0.297	0.415	SUBCLONAL	1	TRUE	1	0.64644086427546	2		284	394	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628452	86628452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	26	166	0	ENST00000274376.6:c.821C>T	p.Pro274Leu	p.P274L	ENST00000274376	NM_002890.2	274	cCa/cTa	3/25	1	2	FACETS	0.261	0.207	0.323	0.261	0.207	0.323	SUBCLONAL	1	TRUE	1	0.64644086427546	2		166	308	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184730	32184730	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	45	595	0	ENST00000375023.3:c.1853G>A	p.Gly618Asp	p.G618D	ENST00000375023	NM_004557.3	618	gGt/gAt	11/30	1	2	FACETS	0.265	0.222	0.312	0.265	0.222	0.312	SUBCLONAL	1	TRUE	1	0.64644086427546	2		595	525	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818783	32818783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	38	589	0	ENST00000354258.4:c.1168G>A	p.Val390Ile	p.V390I	ENST00000354258	NM_000593.5	390	Gtc/Atc	4/11	1	2	FACETS	0.177	0.145	0.212	0.177	0.145	0.212	SUBCLONAL	1	TRUE	1	0.64644086427546	2		589	665	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288363	33288363	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	38	325	0	ENST00000374542.5:c.1045G>A	p.Asp349Asn	p.D349N	ENST00000374542	NM_001141970.1	349	Gac/Aac	4/8	1	2	FACETS	0.285	0.236	0.341	0.285	0.236	0.341	SUBCLONAL	1	TRUE	1	0.64644086427546	2		325	412	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100220	157100220	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	11	100	0	ENST00000346085.5:c.1157G>A	p.Gly386Glu	p.G386E	ENST00000346085	NM_020732.3	386	gGg/gAg	1/20	1	2	FACETS	0.284	0.197	0.39	0.284	0.197	0.39	SUBCLONAL	1	TRUE	1	0.64644086427546	2		100	120	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207417	29207417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	27	434	0	ENST00000240100.2:c.379G>A	p.Val127Met	p.V127M	ENST00000240100	NM_001394.6	127	Gtg/Atg	1/4	1	2	FACETS	0.216	0.172	0.267	0.216	0.172	0.267	SUBCLONAL	1	TRUE	1	0.64644086427546	2		434	386	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293670	137293670	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	38	770	0	ENST00000481739.1:c.221C>T	p.Pro74Leu	p.P74L	ENST00000481739	NM_002957.4	74	cCc/cTc	2/10	1	2	FACETS	0.215	0.177	0.257	0.215	0.177	0.257	SUBCLONAL	1	TRUE	1	0.64644086427546	2		770	547	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401288	139401288	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	40	772	1	ENST00000277541.6:c.3781G>A	p.Gly1261Ser	p.G1261S	ENST00000277541	NM_017617.3	1261	Ggt/Agt	23/34	1	2	FACETS	0.215	0.178	0.257	0.215	0.178	0.257	SUBCLONAL	1	TRUE	1	0.64644086427546	2		773	575	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401341	139401341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1474959824	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	43	672	1	ENST00000277541.6:c.3728C>T	p.Thr1243Ile	p.T1243I	ENST00000277541	NM_017617.3	1243	aCc/aTc	23/34	1	2	FACETS	0.239	0.199	0.283	0.239	0.199	0.283	SUBCLONAL	1	TRUE	1	0.64644086427546	2		673	557	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776883	76776883	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1557041328	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	50	222	1	ENST00000373344.5:c.7069G>A	p.Val2357Ile	p.V2357I	ENST00000373344	NM_000489.3	2357	Gta/Ata	33/35	1	1	FACETS	0.278	0.236	0.323	0.278	0.236	0.323	SUBCLONAL	1	TRUE	0	0.64644086427546	1		223	377	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020182	123020183	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0001882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	19	283	0	ENST00000355640.3:c.671_672del	p.Phe224SerfsTer2	p.F224Sfs*2	ENST00000355640		224	TTt/t	2/7	1	1	FACETS	0.111	0.084	0.143	0.111	0.084	0.143	SUBCLONAL	1	TRUE	0	0.64644086427546	1		283	359	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870952	12870952	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002652-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	69	164	1	ENST00000228872.4:c.179G>A	p.Trp60Ter	p.W60*	ENST00000228872	NM_004064.3	60	tGg/tAg	1/3	1	2	FACETS	0.933	0.817	1	0.933	0.817	1	CLONAL	1	TRUE	1	0.390149507600168	2		165	379	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916934	178916936	+	inframe_deletion	In_Frame_Del	DEL	CCG	CCG	-	rs1553820399	NA	P-0002652-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	104	282	0	ENST00000263967.3:c.321_323del	p.Arg108del	p.R108del	ENST00000263967	NM_006218.2	107	aaCCGt/aat	2/21	0.294108563808923	3	FACETS	1	0.961	1			1	CLONAL	1	TRUE	NA	0.390149507600168	3		282	556	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164595	36164597	+	inframe_deletion	In_Frame_Del	DEL	CGC	CGC	-	novel	NA	P-0002652-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	205	208	0	ENST00000300305.3:c.1278_1280del	p.Arg427del	p.R427del	ENST00000300305		426	ccGCGc/ccc	8/8	0.390149507600168	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.390149507600168	2		208	422	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164607	36164613	+	frameshift_variant	Frame_Shift_Del	DEL	CGCTCGC	CGCTCGC	-	novel	NA	P-0002652-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	189	210	0	ENST00000300305.3:c.1262_1268del	p.Gly421AlafsTer171	p.G421Afs*171	ENST00000300305		421	gGCGAGCGc/gc	8/8	0.390149507600168	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.390149507600168	2		210	439	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002685-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	103	474	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.719487420696748	2		474	247	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0002685-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	100	385	0	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	0.413758569295167	1	FACETS	0.36	0.323	0.4	0.36	0.323	0.4	INDETERMINATE	1	TRUE	0	0.719487420696748	1		385	494	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692911	89692911	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002685-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	267	397	0	ENST00000371953.3:c.395G>C	p.Gly132Ala	p.G132A	ENST00000371953	NM_000314.4	132	gGt/gCt	5/9	0.702107558888001	2	FACETS	0.937	0.898	0.976	0.937	0.898	0.976	CLONAL	2	TRUE	0	0.719487420696748	2		397	396	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550494	29550497	+	frameshift_variant	Frame_Shift_Del	DEL	TAAC	TAAC	-	rs786202782	NA	P-0002685-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	114	328	0	ENST00000356175.3:c.1756_1759del	p.Thr586ValfsTer18	p.T586Vfs*18	ENST00000356175	NM_000267.3	585	tTAACt/tt	16/57	1	2	FACETS	0.852	0.775	0.932	0.852	0.775	0.932	CLONAL	1	TRUE	1	0.719487420696748	2		328	372	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179198	123179198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	18	202	0	ENST00000218089.9:c.647G>A	p.Arg216Gln	p.R216Q	ENST00000218089	NM_001042749.1	216	cGa/cAa	8/35	0.148134430859916	2	FACETS	0.255	0.191	0.33			1	INDETERMINATE	1	TRUE	NA	0.409822691925147	2		202	345	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0003882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	29	336	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.891	0.737	1	0.891	0.737	1	CLONAL	1	TRUE	1	0.748348526607726	2		336	87	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0003882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	9	547	2	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	1	2	FACETS	0.072	0.047	0.105	0.072	0.047	0.105	SUBCLONAL	1	TRUE	1	0.748348526607726	2		549	332	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0003882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	39	509	1	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.748348526607726	2		510	99	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710744	117710744	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1375443218	NA	P-0003882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	25	274	0	ENST00000368508.3:c.1528C>T	p.Leu510Phe	p.L510F	ENST00000368508	NM_002944.2	510	Ctt/Ttt	12/43	0.344102839374137	3	FACETS	0.998	0.806	1	0.499	0.403	0.604	INDETERMINATE	1	TRUE	1	0.748348526607726	3		274	92	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948801	55948801	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	28	307	1	ENST00000263923.4:c.3664C>T	p.Gln1222Ter	p.Q1222*	ENST00000263923	NM_002253.2	1222	Cag/Tag	28/30	0.283560452939777	1	FACETS	0.65	0.54	0.766	0.65	0.54	0.766	INDETERMINATE	1	TRUE	0	0.748348526607726	1		308	72	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118829	115118829	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0003882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	120	343	0	ENST00000257566.3:c.512del	p.Met171ArgfsTer37	p.M171Rfs*37	ENST00000257566	NM_016569.3	171	aTg/ag	2/8	0.528574253221024	3	FACETS	1	0.986	1	0.732	0.671	0.794	CLONAL	1	TRUE	1	0.748348526607726	3		343	301	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223772	53223772	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003882-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	94	632	0	ENST00000375401.3:c.3587G>C	p.Gly1196Ala	p.G1196A	ENST00000375401	NM_004187.3	1196	gGg/gCg	23/26	0.298847047069275	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.748348526607726	0		632	187	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0004146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	316	592	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.492553881202146	1	FACETS	0.827	0.789	0.864	1	0.996	1	CLONAL	2	TRUE	0	0.492553881202146	1		594	585	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0004146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	250	309	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.485429843037783	4	FACETS	0.871	0.822	0.92	0.871	0.822	0.92	CLONAL	3	TRUE	1	0.492553881202146	4		309	580	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0004146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	19	379	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.242	0.183	0.311	0.242	0.183	0.311	SUBCLONAL	1	TRUE	1	0.492553881202146	2		379	319	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0004146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	337	538	3	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.492553881202146	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.492553881202146	3		541	777	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023449	27023449	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	42	570	0	ENST00000324856.7:c.555G>C	p.Gln185His	p.Q185H	ENST00000324856	NM_006015.4	185	caG/caC	1/20	0.137769730905331	4	FACETS	0.341	0.283	0.405	0.17	0.141	0.203	INDETERMINATE	1	TRUE	2	0.492553881202146	4		570	747	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518244	204518244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	40	260	0	ENST00000367182.3:c.907G>A	p.Glu303Lys	p.E303K	ENST00000367182	NM_001278516.1	303	Gag/Aag	11/11	0.477235779781554	5	FACETS	0.357	0.295	0.426	0.089	0.073	0.107	SUBCLONAL	1	TRUE	1	0.492553881202146	5		260	792	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051250	128051250	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	194	413	0	ENST00000285398.2:c.73G>C	p.Asp25His	p.D25H	ENST00000285398	NM_000122.1	25	Gat/Cat	2/15	0.307645295769108	3	FACETS	1	0.991	1	0.734	0.682	0.787	CLONAL	1	TRUE	1	0.492553881202146	3		413	669	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940456	49940456	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs778170442	NA	P-0004146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	309	735	1	ENST00000296474.3:c.587A>G	p.Tyr196Cys	p.Y196C	ENST00000296474	NM_002447.2	196	tAt/tGt	1/20	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.492553881202146	2		736	966	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143352367	143352367	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1241506007	NA	P-0004146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	44	360	0	ENST00000262992.4:c.46C>G	p.Leu16Val	p.L16V	ENST00000262992	NM_001101669.1	16	Ctt/Gtt	2/24	0.492553881202146	3	FACETS	0.26	0.217	0.307	0.13	0.108	0.154	SUBCLONAL	1	TRUE	1	0.492553881202146	3		360	858	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685281	89685281	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1060500116	NA	P-0004146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	23	150	0	ENST00000371953.3:c.176C>G	p.Ser59Ter	p.S59*	ENST00000371953	NM_000314.4	59	tCa/tGa	3/9	0.492553881202146	1	FACETS	0.238	0.185	0.298	0.238	0.185	0.298	SUBCLONAL	1	TRUE	0	0.492553881202146	1		150	296	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712015	89712015	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	rs121909232	NA	P-0004146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	88	118	0	ENST00000371953.3:c.633C>A	p.Cys211Ter	p.C211*	ENST00000371953	NM_000314.4	211	tgC/tgA	6/9	0.492553881202146	1	FACETS	0.792	0.723	0.861	1	0.985	1	SUBCLONAL	2	TRUE	0	0.492553881202146	1		118	170	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143509	108143509	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	95	486	0	ENST00000278616.4:c.3214G>A	p.Glu1072Lys	p.E1072K	ENST00000278616	NM_000051.3	1072	Gaa/Aaa	22/63	0.202009972241842	4	FACETS	0.572	0.508	0.641	0.286	0.254	0.321	INDETERMINATE	1	TRUE	2	0.492553881202146	4		486	1006	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435419	18435419	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	60	353	0	ENST00000266497.5:c.404G>C	p.Gly135Ala	p.G135A	ENST00000266497		135	gGt/gCt	1/31	0.195930901126096	3	FACETS	0.461	0.396	0.531	0.154	0.132	0.177	INDETERMINATE	1	TRUE	0	0.492553881202146	3		353	659	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915168	32915168	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	738	787	0	ENST00000380152.3:c.6676G>C	p.Glu2226Gln	p.E2226Q	ENST00000380152		2226	Gaa/Caa	11/27	0.492553881202146	3	FACETS	0.96	0.932	0.988	0.96	0.932	0.988	CLONAL	3	TRUE	0	0.492553881202146	3		787	1297	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143174	24143174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	42	457	0	ENST00000263121.7:c.406C>T	p.Pro136Ser	p.P136S	ENST00000263121	NM_003073.3	136	Ccc/Tcc	4/9	0.492553881202146	3	FACETS	0.295	0.245	0.35	0.147	0.122	0.175	SUBCLONAL	1	TRUE	1	0.492553881202146	3		457	721	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0004729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	99	256	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.414799902651662	3	FACETS	1	0.959	1	0.571	0.511	0.633	CLONAL	1	TRUE	1	0.414799902651662	3		257	505	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0004729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	151	497	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.224540990990228	5	FACETS	0.891	0.817	0.968	0.594	0.544	0.645	INDETERMINATE	2	TRUE	2	0.414799902651662	5		497	663	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0004729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	236	346	0	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.414799902651662	2	FACETS	0.995	0.936	1	0.995	0.936	1	CLONAL	2	TRUE	0	0.414799902651662	2		346	572	SUCCESS
APC	324	MSKCC	GRCh37	5	112174682	112174682	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs878853438	NA	P-0004729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	76	206	0	ENST00000257430.4:c.3391C>T	p.Gln1131Ter	p.Q1131*	ENST00000257430	NM_000038.5	1131	Caa/Taa	16/16	0.414799902651662	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.414799902651662	1		206	251	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966554	36966554	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1288922202	NA	P-0004729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	352	324	0	ENST00000358127.4:c.772C>A	p.Pro258Thr	p.P258T	ENST00000358127	NM_001280556.1	258	Ccc/Acc	6/10	0.414799902651662	3	FACETS	1	0.983	1			1	CLONAL	3	TRUE	NA	0.414799902651662	3		324	648	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112035	115112035	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	116	399	0	ENST00000257566.3:c.1705G>C	p.Gly569Arg	p.G569R	ENST00000257566	NM_016569.3	569	Gga/Cga	7/8	0.414799902651662	2	FACETS	0.931	0.841	1	0.465	0.42	0.513	CLONAL	1	TRUE	0	0.414799902651662	2		399	601	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340935	70340935	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	101	362	0	ENST00000374080.3:c.668C>A	p.Pro223His	p.P223H	ENST00000374080		223	cCc/cAc	5/45	1	2	FACETS	0.947	0.85	1	0.947	0.85	1	CLONAL	1	TRUE	1	0.414799902651662	2		362	514	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	341	690	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.678473693161425	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.698506961386232	1		690	584	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566711	212566711	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	161	493	0	ENST00000342788.4:c.1470C>G	p.Asn490Lys	p.N490K	ENST00000342788	NM_005235.2	490	aaC/aaG	12/28	1	2	FACETS	0.981	0.907	1	0.981	0.907	1	CLONAL	1	TRUE	1	0.698506961386232	2		493	470	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189442	56189442	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	137	566	0	ENST00000399503.3:c.4474C>T	p.Gln1492Ter	p.Q1492*	ENST00000399503	NM_005921.1	1492	Caa/Taa	20/20	1	2	FACETS	0.817	0.748	0.888	0.817	0.748	0.888	CLONAL	1	TRUE	1	0.698506961386232	2		566	480	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0005152-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	93	336	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.298728024553582	5	FACETS	0.915	0.82	1	0.915	0.82	1	CLONAL	3	TRUE	2	0.24	5		336	384	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0005393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	80	647	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.26420579053121	3	FACETS	0.886	0.784	0.993	0.886	0.784	0.993	CLONAL	2	FALSE	1	0.26420579053121	3		647	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555525857	NA	P-0005393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	35	708	1	ENST00000269305.4:c.596G>A	p.Gly199Glu	p.G199E	ENST00000269305	NM_001126112.2	199	gGa/gAa	6/11	0.156129680653757	1	FACETS	0.801	0.659	0.959	0.801	0.659	0.959	INDETERMINATE	1	FALSE	0	0.26420579053121	1		709	287	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996231	73996231	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	10	308	0	ENST00000318443.5:c.965A>T	p.Asn322Ile	p.N322I	ENST00000318443	NM_001024736.1	322	aAt/aTt	5/10	0.156129680653757	1	FACETS	0.534	0.364	0.746	0.534	0.364	0.746	INDETERMINATE	1	FALSE	0	0.26420579053121	1		308	123	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678391	88678391	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	27	881	1	ENST00000360948.2:c.1145A>T	p.Asn382Ile	p.N382I	ENST00000360948	NM_001012338.2	382	aAc/aTc	9/19	0.156129680653757	1	FACETS	0.49	0.39	0.604	0.49	0.39	0.604	INDETERMINATE	1	FALSE	0	0.26420579053121	1		882	362	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144018	11144018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749001381	NA	P-0005393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	26	680	0	ENST00000358026.2:c.3599G>A	p.Arg1200His	p.R1200H	ENST00000358026	NM_001128849.1	1200	cGt/cAt	26/36	0.117845440636553	0	FACETS	0.467	0.37	0.578			1	INDETERMINATE	1	FALSE	0	0.26420579053121	0		680	310	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70362067	70362067	+	stop_lost	Nonstop_Mutation	SNP	G	G	T	novel	NA	P-0005393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	49	828	0	ENST00000374080.3:c.6533G>T	p.Ter2178LeuextTer18	p.*2178Lext*18	ENST00000374080		2178	tGa/tTa	45/45	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	FALSE	1	0.26420579053121	2		828	365	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0005728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	103	606	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.997	0.898	1	0.997	0.898	1	CLONAL	1	TRUE	1	0.462116290029662	2		606	447	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0005728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	106	379	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.245865810619707	5	FACETS	0.881	0.794	0.971	0.587	0.529	0.647	INDETERMINATE	2	TRUE	2	0.462116290029662	5		379	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0005732-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	736	659	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.929288560046617	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.929288560046617	2		659	769	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845344	156845344	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005732-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	329	601	1	ENST00000524377.1:c.1387G>T	p.Ala463Ser	p.A463S	ENST00000524377	NM_002529.3	463	Gcc/Tcc	12/17	0.894778876990017	4	FACETS	0.931	0.878	0.985	0.31	0.292	0.329	CLONAL	1	TRUE	1	0.929288560046617	4		602	1468	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466816	25466816	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005732-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	321	562	0	ENST00000264709.3:c.1887G>T	p.Glu629Asp	p.E629D	ENST00000264709	NM_175629.2	629	gaG/gaT	16/23	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.929288560046617	2		562	678	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738275	190738275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005732-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	208	410	1	ENST00000441310.2:c.2527C>T	p.Pro843Ser	p.P843S	ENST00000441310	NM_000534.4	843	Cca/Tca	12/13	1	2	FACETS	0.94	0.883	0.999	0.94	0.883	0.999	CLONAL	1	TRUE	1	0.929288560046617	2		411	476	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748573	43748573	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005732-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	458	402	0	ENST00000523873.1:c.527G>A	p.Trp176Ter	p.W176*	ENST00000523873		176	tGg/tAg	6/8	0.929288560046617	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.929288560046617	3		402	714	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304138	91304138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567041193	NA	P-0005732-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	300	554	0	ENST00000355112.3:c.1535G>A	p.Gly512Glu	p.G512E	ENST00000355112	NM_000057.2	512	gGa/gAa	7/22	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.929288560046617	2		554	611	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788615	3788615	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005732-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	567	595	0	ENST00000262367.5:c.4339A>T	p.Thr1447Ser	p.T1447S	ENST00000262367	NM_004380.2	1447	Aca/Tca	26/31	0.929288560046617	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.929288560046617	2		595	600	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788617	3788617	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519884	NA	P-0005732-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	560	583	1	ENST00000262367.5:c.4337G>T	p.Arg1446Leu	p.R1446L	ENST00000262367	NM_004380.2	1446	cGc/cTc	26/31	0.929288560046617	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.929288560046617	2		584	596	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740365	58740365	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs780886952	NA	P-0005732-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	474	418	0	ENST00000305921.3:c.1270G>T	p.Glu424Ter	p.E424*	ENST00000305921	NM_003620.3	424	Gag/Tag	6/6	0.929288560046617	3	FACETS	0.949	0.916	0.982	0.949	0.916	0.982	CLONAL	2	TRUE	1	0.929288560046617	3		418	787	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095922	29095922	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005732-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	260	531	0	ENST00000328354.6:c.912G>T	p.Met304Ile	p.M304I	ENST00000328354	NM_007194.3	304	atG/atT	9/15	1	2	FACETS	0.973	0.92	1	0.973	0.92	1	CLONAL	1	TRUE	1	0.929288560046617	2		531	575	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921460	39921460	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs967564648	NA	P-0005732-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	301	644	0	ENST00000378444.4:c.4360C>T	p.Arg1454Trp	p.R1454W	ENST00000378444	NM_001123385.1	1454	Cgg/Tgg	10/15	1	2	FACETS	0.994	0.944	1	0.994	0.944	1	CLONAL	1	TRUE	1	0.929288560046617	2		644	652	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422458	47422458	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005732-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	317	696	0	ENST00000377045.4:c.92C>A	p.Thr31Lys	p.T31K	ENST00000377045	NM_001654.4	31	aCg/aAg	2/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.929288560046617	2		696	675	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553520	29553520	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060500364	NA	P-0005732-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	473	471	0	ENST00000356175.3:c.2071del	p.Leu691CysfsTer57	p.L691Cfs*57	ENST00000356175	NM_000267.3	690	gCc/gc	18/57	0.929288560046617	3	FACETS	0.919	0.886	0.952	0.919	0.886	0.952	CLONAL	2	TRUE	1	0.929288560046617	3		471	811	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	293	501	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.44127648935082	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.44127648935082	2		501	657	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0005997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	280	379	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.44127648935082	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.44127648935082	1		380	944	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069931	5069931	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0005997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	93	262	0	ENST00000381652.3:c.1520C>G	p.Ser507Ter	p.S507*	ENST00000381652	NM_004972.3	507	tCa/tGa	12/25	0.380669212702603	0	FACETS	0.826	0.745	0.911			1	CLONAL	1	TRUE	0	0.44127648935082	0		262	285	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604836	48604836	+	stop_lost	Nonstop_Mutation	SNP	G	G	T	novel	NA	P-0005997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	114	311	1	ENST00000342988.3:c.1658G>T	p.Ter553LeuextTer40	p.*553Lext*40	ENST00000342988	NM_005359.5	553	tGa/tTa	12/12	0.44127648935082	1	FACETS	0.959	0.87	1	0.959	0.87	1	CLONAL	1	TRUE	0	0.44127648935082	1		312	420	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0006139-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	193	497	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.262908027071864	3	FACETS	1	0.985	1	0.632	0.584	0.681	CLONAL	1	TRUE	1	0.364724575734044	3		497	990	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812583	43812583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006139-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	46	640	1	ENST00000372470.3:c.1286G>A	p.Gly429Glu	p.G429E	ENST00000372470	NM_005373.2	429	gGa/gAa	8/12	1	2	FACETS	0.294	0.246	0.347	0.294	0.246	0.347	SUBCLONAL	1	TRUE	1	0.364724575734044	2		641	858	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226406	133226406	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs756246229	NA	P-0006139-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	42	618	0	ENST00000320574.5:c.3652G>T	p.Val1218Leu	p.V1218L	ENST00000320574	NM_006231.2	1218	Gta/Tta	30/49	1	2	FACETS	0.295	0.245	0.351	0.295	0.245	0.351	SUBCLONAL	1	TRUE	1	0.364724575734044	2		618	780	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306700	41306700	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006139-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	72	543	0	ENST00000373198.4:c.959T>G	p.Ile320Ser	p.I320S	ENST00000373198	NM_133170.3	320	aTc/aGc	7/32	1	2	FACETS	0.506	0.441	0.576	0.506	0.441	0.576	SUBCLONAL	1	TRUE	1	0.364724575734044	2		543	781	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039658	47039659	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006139-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	115	655	0	ENST00000377604.3:c.1111dup	p.Thr371AsnfsTer10	p.T371Nfs*10	ENST00000377604	NM_001204468.1	370	-/A	11/24	0.364724575734044	3	FACETS	0.611	0.549	0.678	0.306	0.274	0.339	SUBCLONAL	1	TRUE	1	0.364724575734044	3		655	1220	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0006631-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	86	273	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.975	0.87	1	0.975	0.87	1	CLONAL	1	TRUE	1	0.485743517627117	2		273	363	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849442	68849442	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006631-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	125	291	1	ENST00000261769.5:c.1345C>T	p.Gln449Ter	p.Q449*	ENST00000261769	NM_004360.3	449	Cag/Tag	10/16	0.484934498939209	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.485743517627117	1		292	357	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0006631-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	120	222	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.485743517627117	2		222	458	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060780	38060797	+	inframe_deletion	In_Frame_Del	DEL	GTTGATGGAGAACGGGTG	GTTGATGGAGAACGGGTG	-	novel	NA	P-0006631-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	170	525	0	ENST00000250448.2:c.1192_1209del	p.His398_Asn403del	p.H398_N403del	ENST00000250448	NM_004496.3	398	CACCCGTTCTCCATCAAC/-	2/2	1	2	FACETS	0.846	0.779	0.916	0.846	0.779	0.916	CLONAL	1	TRUE	1	0.485743517627117	2		525	827	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293291	91293291	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006631-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	79	174	0	ENST00000355112.3:c.793G>C	p.Glu265Gln	p.E265Q	ENST00000355112	NM_000057.2	265	Gaa/Caa	3/22	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.485743517627117	2		174	311	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537180	41537180	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006631-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	136	328	0	ENST00000263253.7:c.2007G>C	p.Met669Ile	p.M669I	ENST00000263253	NM_001429.3	669	atG/atC	10/31	1	2	FACETS	0.964	0.88	1	0.964	0.88	1	CLONAL	1	TRUE	1	0.485743517627117	2		328	581	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191540	10191540	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs5030822	NA	P-0006639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	187	580	0	ENST00000256474.2:c.533T>C	p.Leu178Pro	p.L178P	ENST00000256474	NM_000551.3	178	cTg/cCg	3/3	0.277271765720027	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	0	0.277271765720027	2		580	667	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134741	41134746	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCAT	GGCCAT	A	novel	NA	P-0006639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	89	384	0	ENST00000379561.5:c.882_887delinsT	p.Lys294AsnfsTer10	p.K294Nfs*10	ENST00000379561	NM_002015.3	294	aaATGGCCt/aaTt	2/3	0.277271765720027	4	FACETS	1	0.976	1	0.703	0.625	0.787	CLONAL	1	TRUE	2	0.277271765720027	4		384	583	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0007513-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	240	459	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.248773311965381	3	FACETS	0.816	0.761	0.874	0.816	0.761	0.874	CLONAL	2	FALSE	1	0.248773311965381	3		459	1329	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0007864-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	180	454	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.613856053400406	2		454	541	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0007864-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	201	518	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.612273005693691	4	FACETS	1	0.962	1	0.53	0.491	0.571	CLONAL	1	TRUE	2	0.613856053400406	4		518	997	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0007864-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	122	373	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	0.598445127761888	1	FACETS	0.906	0.832	0.982	0.906	0.832	0.982	CLONAL	1	TRUE	0	0.613856053400406	1		373	304	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0007864-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	213	665	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.612273005693691	4	FACETS	0.893	0.828	0.961	0.447	0.414	0.481	CLONAL	1	TRUE	2	0.613856053400406	4		665	1254	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004270	150004270	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007864-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	151	405	0	ENST00000253339.5:c.1955A>G	p.Lys652Arg	p.K652R	ENST00000253339		652	aAa/aGa	3/7	1	2	FACETS	0.952	0.876	1	0.952	0.876	1	CLONAL	1	TRUE	1	0.613856053400406	2		405	517	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713613	30713613	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007864-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	199	458	0	ENST00000295754.5:c.939del	p.Lys314ArgfsTer10	p.K314Rfs*10	ENST00000295754	NM_003242.5	313	cGg/cg	4/7	0.598445127761888	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.613856053400406	1		458	423	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249092	55249092	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007864-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	222	696	0	ENST00000275493.2:c.2390G>C	p.Cys797Ser	p.C797S	ENST00000275493	NM_005228.3	797	tGc/tCc	20/28	0.612273005693691	4	FACETS	0.879	0.816	0.944	0.439	0.408	0.472	CLONAL	1	TRUE	2	0.613856053400406	4		696	1328	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0008083-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	247	747	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	0.241016410701542	4	FACETS	0.757	0.71	0.805	0.757	0.71	0.805	INDETERMINATE	2	TRUE	2	0.666576306109724	4		747	816	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0008083-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	308	442	1	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.625131227109649	1	FACETS	0.991	0.943	1	0.991	0.943	1	CLONAL	1	TRUE	0	0.666576306109724	1		443	622	SUCCESS
APC	324	MSKCC	GRCh37	5	112164585	112164585	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398123116	NA	P-0008083-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	95	463	0	ENST00000257430.4:c.1659G>A	p.Trp553Ter	p.W553*	ENST00000257430	NM_000038.5	553	tgG/tgA	14/16	0.604707738938225	1	FACETS	0.757	0.686	0.831	0.757	0.686	0.831	SUBCLONAL	1	TRUE	0	0.666576306109724	1		463	251	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045946	26045946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008083-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	203	569	2	ENST00000540144.1:c.308G>T	p.Gly103Val	p.G103V	ENST00000540144	NM_003531.2	103	gGa/gTa	1/1	0.114614863955344	4	FACETS	1	0.989	1	0.662	0.615	0.71	INDETERMINATE	1	TRUE	2	0.666576306109724	4		571	767	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2952986	2952986	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747477589	NA	P-0008083-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	459	766	0	ENST00000396946.4:c.2954C>G	p.Ala985Gly	p.A985G	ENST00000396946	NM_032415.4	985	gCc/gGc	22/25	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.666576306109724	2		766	969	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501331	140501331	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008083-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	107	463	0	ENST00000288602.6:c.741T>A	p.Phe247Leu	p.F247L	ENST00000288602	NM_004333.4	247	ttT/ttA	6/18	1	2	FACETS	0.819	0.741	0.901	0.819	0.741	0.901	CLONAL	1	TRUE	1	0.666576306109724	2		463	392	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920396	114920396	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008083-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	254	627	0	ENST00000543371.1:c.1337A>C	p.Lys446Thr	p.K446T	ENST00000543371	NM_001198531.1	446	aAg/aCg	13/14	0.157247396725735	1	FACETS	0.677	0.637	0.719	0.677	0.637	0.719	INDETERMINATE	1	TRUE	0	0.666576306109724	1		627	750	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052630	42052630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372072518	NA	P-0008083-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	266	633	0	ENST00000219905.7:c.7301G>A	p.Arg2434Gln	p.R2434Q	ENST00000219905	NM_001164273.1	2434	cGg/cAg	20/24	1	2	FACETS	0.932	0.877	0.989	0.932	0.877	0.989	CLONAL	1	TRUE	1	0.666576306109724	2		633	856	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646234	23646234	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs180177103	NA	P-0008083-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	372	766	0	ENST00000261584.4:c.1633G>T	p.Glu545Ter	p.E545*	ENST00000261584	NM_024675.3	545	Gaa/Taa	4/13	0.615033049453155	2	FACETS	0.94	0.904	0.975	0.94	0.904	0.975	CLONAL	2	TRUE	0	0.666576306109724	2		766	594	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581186	48581204	+	frameshift_variant	Frame_Shift_Del	DEL	CATGACTTTGAGGGACAGC	CATGACTTTGAGGGACAGC	-	novel	NA	P-0008083-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	113	506	0	ENST00000342988.3:c.493_511del	p.Asp165ArgfsTer31	p.D165Rfs*31	ENST00000342988	NM_005359.5	164	CATGACTTTGAGGGACAGCca/ca	5/12	0.666576306109724	1	FACETS	0.689	0.628	0.752	0.689	0.628	0.752	SUBCLONAL	1	TRUE	0	0.666576306109724	1		506	328	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930154	68930154	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0008083-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	129	560	0	ENST00000288368.4:c.213+2T>C		p.X71_splice	ENST00000288368	NM_024870.2	71			0.110988153469161	0	FACETS	0.286	0.26	0.311			1	INDETERMINATE	1	TRUE	0	0.666576306109724	0		560	452	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128206802	128206802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008083-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	182	606	0	ENST00000265960.3:c.1421C>T	p.Thr474Ile	p.T474I	ENST00000265960	NM_001006617.1	474	aCc/aTc	11/12	0.625131227109649	1	FACETS	0.943	0.883	1	0.943	0.883	1	CLONAL	1	TRUE	0	0.666576306109724	1		606	386	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584479	52584490	+	inframe_deletion	In_Frame_Del	DEL	CACTGAGTCCTT	CACTGAGTCCTT	-	novel	NA	P-0008083-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	94	634	0	ENST00000394830.3:c.4523_4534del	p.Glu1508_Ser1511del	p.E1508_S1511del	ENST00000394830	NM_018313.4	1508	gAAGGACTCAGTGcg/gcg	29/30	0.666576306109724	1	FACETS	0.381	0.34	0.424	0.381	0.34	0.424	SUBCLONAL	1	TRUE	0	0.666576306109724	1		634	494	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597440	52597466	+	inframe_deletion	In_Frame_Del	DEL	TTTAGCTTCTAGCAACTGGATCTTCTT	TTTAGCTTCTAGCAACTGGATCTTCTT	-	novel	NA	P-0008083-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	87	667	0	ENST00000394830.3:c.3844_3870del	p.Lys1282_Lys1290del	p.K1282_K1290del	ENST00000394830	NM_018313.4	1282	AAGAAGATCCAGTTGCTAGAAGCTAAA/-	25/30	0.666576306109724	1	FACETS	0.398	0.354	0.445	0.398	0.354	0.445	SUBCLONAL	1	TRUE	0	0.666576306109724	1		667	437	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65312393	65312393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008398-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	61	717	0	ENST00000342505.4:c.1926G>A	p.Met642Ile	p.M642I	ENST00000342505	NM_002227.2	642	atG/atA	14/25	0.699363573760973	2	FACETS	0.156	0.134	0.18	0.078	0.067	0.09	SUBCLONAL	1	TRUE	0	0.699363573760973	2		717	1118	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21627796	21627796	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1268138348	NA	P-0008398-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	71	771	0	ENST00000421138.2:c.1334C>T	p.Ser445Leu	p.S445L	ENST00000421138		445	tCa/tTa	12/16	1	2	FACETS	0.183	0.159	0.209	0.183	0.159	0.209	SUBCLONAL	1	TRUE	1	0.699363573760973	2		771	1109	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845757	68845757	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587780784	NA	P-0008398-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	326	437	0	ENST00000261769.5:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000261769	NM_004360.3	335	Cga/Tga	7/16	0.699363573760973	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.699363573760973	1		437	557	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993389	72993389	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008398-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	78	843	0	ENST00000268489.5:c.656C>T	p.Ser219Leu	p.S219L	ENST00000268489	NM_006885.3	219	tCa/tTa	2/10	0.699363573760973	1	FACETS	0.155	0.135	0.176	0.155	0.135	0.176	SUBCLONAL	1	TRUE	0	0.699363573760973	1		843	937	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780677	56780677	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060502588	NA	P-0008398-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	386	667	1	ENST00000337432.4:c.692C>T	p.Ser231Leu	p.S231L	ENST00000337432	NM_058216.2	231	tCa/tTa	4/9	1	2	FACETS	0.953	0.906	1	0.953	0.906	1	CLONAL	1	TRUE	1	0.699363573760973	2		668	1158	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256713	19256713	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008398-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	468	821	0	ENST00000162023.5:c.1000C>A	p.Pro334Thr	p.P334T	ENST00000162023		334	Cct/Act	13/13	1	2	FACETS	0.999	0.955	1	0.999	0.955	1	CLONAL	1	TRUE	1	0.699363573760973	2		821	1340	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259368	89259368	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008398-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	322	627	0	ENST00000336596.2:c.512T>C	p.Val171Ala	p.V171A	ENST00000336596	NM_005233.5	171	gTa/gCa	3/17	1	2	FACETS	0.967	0.916	1	0.967	0.916	1	CLONAL	1	TRUE	1	0.699363573760973	2		627	952	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565858	55565858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008398-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	92	777	2	ENST00000288135.5:c.682G>A	p.Glu228Lys	p.E228K	ENST00000288135	NM_000222.2	228	Gaa/Aaa	4/21	1	2	FACETS	0.204	0.18	0.229	0.204	0.18	0.229	SUBCLONAL	1	TRUE	1	0.699363573760973	2		779	1292	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595556	55595556	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008398-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	64	618	0	ENST00000288135.5:c.2046G>C	p.Leu682Phe	p.L682F	ENST00000288135	NM_000222.2	682	ttG/ttC	14/21	1	2	FACETS	0.23	0.198	0.264	0.23	0.198	0.264	SUBCLONAL	1	TRUE	1	0.699363573760973	2		618	796	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31521249	31521249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008398-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	76	692	0	ENST00000344624.3:c.928G>A	p.Glu310Lys	p.E310K	ENST00000344624		310	Gag/Aag	3/33	1	2	FACETS	0.179	0.156	0.204	0.179	0.156	0.204	SUBCLONAL	1	TRUE	1	0.699363573760973	2		692	1212	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873518	151873518	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008398-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	439	631	0	ENST00000262189.6:c.9020del	p.Gly3007GlufsTer25	p.G3007Efs*25	ENST00000262189	NM_170606.2	3007	gGa/ga	38/59	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.699363573760973	2		631	1145	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878356	151878356	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008398-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	458	667	1	ENST00000262189.6:c.6589C>T	p.Gln2197Ter	p.Q2197*	ENST00000262189	NM_170606.2	2197	Cag/Tag	36/59	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.699363573760973	2		668	1203	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878785	151878785	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008398-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	333	606	0	ENST00000262189.6:c.6160C>G	p.Gln2054Glu	p.Q2054E	ENST00000262189	NM_170606.2	2054	Cag/Gag	36/59	1	2	FACETS	0.959	0.909	1	0.959	0.909	1	CLONAL	1	TRUE	1	0.699363573760973	2		606	993	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0008909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	127	424	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	0.452800971184665	2		424	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578412	+	protein_altering_variant	In_Frame_Del	DEL	GCCTCA	GCCTCA	CCC	novel	NA	P-0008909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	117	278	0	ENST00000269305.4:c.518_523delinsGGG	p.Val173_Arg175delinsGlyGly	p.V173_R175delinsGG	ENST00000269305	NM_001126112.2	173	gTGAGGCgc/gGGGgc	5/11	0.452800971184665	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.452800971184665	2		278	237	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0009399-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	105	385	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	0.438139272408753	4	FACETS	0.967	0.867	1	0.484	0.433	0.537	CLONAL	1	TRUE	2	0.445890522356527	4		385	704	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150022928	150022928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009399-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	173	487	0	ENST00000253339.5:c.335C>T	p.Ala112Val	p.A112V	ENST00000253339		112	gCt/gTt	1/7	0.265921439577058	4	FACETS	0.881	0.814	0.949	0.881	0.814	0.949	INDETERMINATE	2	TRUE	2	0.445890522356527	4		487	637	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835662	68835662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009399-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	129	650	0	ENST00000261769.5:c.253G>T	p.Val85Phe	p.V85F	ENST00000261769	NM_004360.3	85	Gtc/Ttc	3/16	0.1467865494583	5	FACETS	1	0.913	1	0.252	0.228	0.278	INDETERMINATE	1	TRUE	1	0.445890522356527	5		650	957	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579378	7579378	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0009399-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	446	815	0	ENST00000269305.4:c.309C>G	p.Tyr103Ter	p.Y103*	ENST00000269305	NM_001126112.2	103	taC/taG	4/11	0.437363268473513	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.445890522356527	2		815	983	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0009474-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	63	336	1	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.19297657992225	2	FACETS	1	0.953	1	0.614	0.533	0.701	CLONAL	1	TRUE	0	0.257972063439214	2		337	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0009474-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	109	409	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.19297657992225	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	2	TRUE	0	0.257972063439214	2		409	412	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151564	55151564	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009474-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	30	282	0	ENST00000257290.5:c.2350G>C	p.Asp784His	p.D784H	ENST00000257290	NM_006206.4	784	Gat/Cat	17/23	0.253118092870907	1	FACETS	0.653	0.528	0.796	0.653	0.528	0.796	SUBCLONAL	1	TRUE	0	0.257972063439214	1		282	310	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638885	176638885	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009474-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	78	354	0	ENST00000439151.2:c.3485G>A	p.Arg1162His	p.R1162H	ENST00000439151	NM_022455.4	1162	cGt/cAt	5/23	0.179324958403124	3	FACETS	1	0.968	1	0.656	0.578	0.74	CLONAL	1	TRUE	1	0.257972063439214	3		354	520	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973698	15973698	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009474-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	23	206	0	ENST00000268712.3:c.4294C>G	p.Arg1432Gly	p.R1432G	ENST00000268712	NM_006311.3	1432	Cgg/Ggg	31/46	0.19297657992225	2	FACETS	0.74	0.579	0.925	0.37	0.289	0.463	CLONAL	1	TRUE	0	0.257972063439214	2		206	241	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215993	142215993	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009474-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	16	248	0	ENST00000350721.4:c.5600T>A	p.Leu1867His	p.L1867H	ENST00000350721	NM_001184.3	1867	cTt/cAt	33/47	1	2	FACETS	0.4	0.295	0.526	0.4	0.295	0.526	SUBCLONAL	1	TRUE	1	0.257972063439214	2		248	310	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441477	52441477	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0009513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	27	499	0	ENST00000460680.1:c.376-1G>A		p.X126_splice	ENST00000460680	NM_004656.3	126			0.3	1	FACETS	0.385	0.306	0.476	0.385	0.306	0.476	SUBCLONAL	1	FALSE	0	0.3	1		499	397	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136804	55136804	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	44	498	2	ENST00000257290.5:c.1126C>T	p.Arg376Ter	p.R376*	ENST00000257290	NM_006206.4	376	Cga/Tga	8/23	0.0801252394432932	3	FACETS	0.553	0.463	0.653	0.277	0.231	0.327	INDETERMINATE	1	FALSE	1	0.3	3		500	610	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441459	52441476	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	AATCGCATATCCTTTGCT	AATCGCATATCCTTTGCT	-	novel	NA	P-0009513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	27	538	0	ENST00000460680.1:c.376_393del	p.Ser126_Ile131del	p.S126_I131del	ENST00000460680	NM_004656.3	126	AGCAAAGGATATGCGATT/-	6/17	0.3	1	FACETS	0.392	0.312	0.484	0.392	0.312	0.484	SUBCLONAL	1	FALSE	0	0.3	1		538	390	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221313	1221314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs121913321	NA	P-0010403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	69	818	1	ENST00000326873.7:c.842dup	p.Leu282AlafsTer3	p.L282Afs*3	ENST00000326873	NM_000455.4	279	ggc/ggCc	6/10	0.177488477729752	1	FACETS	0.799	0.694	0.913	0.799	0.694	0.913	CLONAL	1	TRUE	0	0.177488477729752	1		819	887	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100999	41100999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1371429276	NA	P-0010403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	85	717	1	ENST00000373198.4:c.1357C>T	p.Arg453Cys	p.R453C	ENST00000373198	NM_133170.3	453	Cgc/Tgc	8/32	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.177488477729752	2		718	851	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602374	10602374	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	113	902	1	ENST00000171111.5:c.1204C>T	p.Gln402Ter	p.Q402*	ENST00000171111	NM_203500.1	402	Cag/Tag	3/6	0.177488477729752	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.177488477729752	1		903	1040	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37876056	37876056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	114	848	0	ENST00000269571.5:c.1915G>A	p.Asp639Asn	p.D639N	ENST00000269571		639	Gac/Aac	16/27	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.177488477729752	2		848	1076	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2193709	2193709	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	86	975	3	ENST00000398665.3:c.515A>T	p.Gln172Leu	p.Q172L	ENST00000398665	NM_032482.2	172	cAg/cTg	6/28	0.177488477729752	1	FACETS	0.907	0.8	1	0.907	0.8	1	CLONAL	1	TRUE	0	0.177488477729752	1		978	974	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660967	227660967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	101	811	0	ENST00000305123.5:c.2488C>T	p.Pro830Ser	p.P830S	ENST00000305123	NM_005544.2	830	Cca/Tca	1/2	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.177488477729752	2		811	947	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662127	227662127	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs745943416	NA	P-0010403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	86	722	1	ENST00000305123.5:c.1328G>T	p.Arg443Leu	p.R443L	ENST00000305123	NM_005544.2	443	cGc/cTc	1/2	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.177488477729752	2		723	951	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662281	227662281	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1438378264	NA	P-0010403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	94	784	0	ENST00000305123.5:c.1174C>G	p.Leu392Val	p.L392V	ENST00000305123	NM_005544.2	392	Ctg/Gtg	1/2	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.177488477729752	2		784	1028	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149245626	149245626	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	95	792	0	ENST00000360632.3:c.902A>G	p.Asn301Ser	p.N301S	ENST00000360632	NM_015472.4	301	aAt/aGt	5/7	1	2	FACETS	0.952	0.846	1	0.952	0.846	1	CLONAL	1	TRUE	1	0.177488477729752	2		792	1124	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860756	151860756	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	75	637	0	ENST00000262189.6:c.9906del	p.Thr3303ProfsTer58	p.T3303Pfs*58	ENST00000262189	NM_170606.2	3302	ccC/cc	43/59	1	2	FACETS	0.993	0.869	1	0.993	0.869	1	CLONAL	1	TRUE	1	0.177488477729752	2		637	851	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110251321	110251321	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	65	614	1	ENST00000374672.4:c.16G>T	p.Gly6Cys	p.G6C	ENST00000374672	NM_004235.4	6	Ggc/Tgc	2/5	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.177488477729752	2		615	707	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010677-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	149	215	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	0.808	0.745	0.873	0.808	0.745	0.873	CLONAL	1	TRUE	1	0.813931707768956	2		215	453	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095824	178095824	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010677-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	299	297	0	ENST00000397062.3:c.1507A>T	p.Arg503Trp	p.R503W	ENST00000397062	NM_006164.4	503	Agg/Tgg	5/5	1	2	FACETS	0.985	0.933	1	0.985	0.933	1	CLONAL	1	TRUE	1	0.813931707768956	2		297	746	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562340	21562340	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs753286419	NA	P-0010677-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	185	217	0	ENST00000382592.4:c.1579A>C	p.Lys527Gln	p.K527Q	ENST00000382592	NM_014572.2	527	Aag/Cag	4/8	1	2	FACETS	0.973	0.908	1	0.973	0.908	1	CLONAL	1	TRUE	1	0.813931707768956	2		217	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0011108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	93	572	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.154432655434624	3	FACETS	1	0.975	1	0.832	0.754	0.911	INDETERMINATE	2	TRUE	0	0.388820939730137	3		572	229	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0011108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	158	501	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.388820939730137	3	FACETS	1	0.97	1	0.729	0.674	0.785	CLONAL	2	TRUE	0	0.388820939730137	3		501	444	SUCCESS
APC	324	MSKCC	GRCh37	5	112116494	112116494	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0011108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	67	299	0	ENST00000257430.4:c.539T>G	p.Leu180Ter	p.L180*	ENST00000257430	NM_000038.5	180	tTa/tGa	6/16	0.302282141823637	3	FACETS	0.792	0.696	0.893	0.528	0.464	0.595	SUBCLONAL	2	TRUE	0	0.388820939730137	3		299	260	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459462	50459462	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	78	370	0	ENST00000331340.3:c.751G>T	p.Glu251Ter	p.E251*	ENST00000331340	NM_006060.4	251	Gaa/Taa	7/8	0.388820939730137	5	FACETS	0.948	0.84	1			1	CLONAL	2	TRUE	NA	0.388820939730137	5		370	335	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342789	87342789	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	77	539	0	ENST00000277120.3:c.1074C>G	p.Asp358Glu	p.D358E	ENST00000277120		358	gaC/gaG	9/19	0.388820939730137	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.388820939730137	1		539	279	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	532715	532715	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753977266	NA	P-0011108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	50	620	1	ENST00000451590.1:c.491G>A	p.Arg164Gln	p.R164Q	ENST00000451590	NM_001130442.1	164	cGg/cAg	5/5	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.388820939730137	2		621	212	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143448	108143448	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1555085973	NA	P-0011108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	45	393	0	ENST00000278616.4:c.3154-1G>A		p.X1052_splice	ENST00000278616	NM_000051.3	1052			NA	2	FACETS	0.737	0.622	0.863			1	INDETERMINATE	1	TRUE	NA	0.388820939730137	2		393	314	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163500	108163500	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	55	413	0	ENST00000278616.4:c.4591C>T	p.Gln1531Ter	p.Q1531*	ENST00000278616	NM_000051.3	1531	Cag/Tag	30/63	NA	2	FACETS	0.855	0.735	0.984			1	INDETERMINATE	1	TRUE	NA	0.388820939730137	2		413	331	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754574	42754574	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768322408	NA	P-0011108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	47	587	1	ENST00000222329.4:c.166G>A	p.Val56Ile	p.V56I	ENST00000222329	NM_006494.2	56	Gtc/Atc	2/4	NA	2	FACETS	1	0.919	1			1	INDETERMINATE	1	TRUE	NA	0.388820939730137	2		588	216	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100094	30100094	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1344627350	NA	P-0011108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	45	642	0	ENST00000331968.5:c.1526A>G	p.Asn509Ser	p.N509S	ENST00000331968	NM_002742.2	509	aAt/aGt	10/18	0.325845862800681	4	FACETS	0.741	0.623	0.87	0.185	0.155	0.218	SUBCLONAL	1	TRUE	0	0.388820939730137	4		642	434	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43699608	43699609	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0011108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	32	593	0	ENST00000382044.4:c.5906_5907del	p.Lys1969IlefsTer2	p.K1969Ifs*2	ENST00000382044	NM_001141980.1	1969	aAA/a	28/28	0.35517861516341	3	FACETS	0.526	0.427	0.637	0.263	0.213	0.319	SUBCLONAL	1	TRUE	1	0.388820939730137	3		593	374	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0012223-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	316	336	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.642046926705761	3	FACETS	0.951	0.904	0.997	0.951	0.904	0.997	CLONAL	2	TRUE	1	0.642046926705761	3		336	684	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562664	29562664	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012223-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	233	402	0	ENST00000356175.3:c.3745del	p.Ser1249LeufsTer17	p.S1249Lfs*17	ENST00000356175	NM_000267.3	1248	gaT/ga	28/57	0.605810343093181	1	FACETS	0.974	0.918	1	0.974	0.918	1	CLONAL	1	TRUE	0	0.642046926705761	1		402	506	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012632-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	104	690	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.871	0.786	0.961	0.871	0.786	0.961	CLONAL	1	TRUE	1	0.5781119501361	2		690	413	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38064155	38064155	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012632-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	85	527	1	ENST00000250448.2:c.23A>T	p.Glu8Val	p.E8V	ENST00000250448	NM_004496.3	8	gAa/gTa	1/2	0.5781119501361	3	FACETS	0.892	0.792	0.997	0.446	0.396	0.499	CLONAL	1	TRUE	1	0.5781119501361	3		528	425	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624292	89624321	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTAGACTTGACCTGTATCCATTTCTGCGG	CTTAGACTTGACCTGTATCCATTTCTGCGG	-	novel	NA	P-0012632-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	54	566	0	ENST00000371953.3:c.68_79+18del		p.X23_splice	ENST00000371953	NM_000314.4	23		1/9	NA	2	FACETS	0.785	0.678	0.9			1	INDETERMINATE	1	TRUE	NA	0.5781119501361	2		566	238	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164858	36164859	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGCGCGGGGAACT	novel	NA	P-0012632-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	93	725	3	ENST00000300305.3:c.1004_1016dup	p.Pro340ValfsTer264	p.P340Vfs*264	ENST00000300305		339	ctg/ctAGTTCCCCGCGCTg	8/8	0.5781119501361	3	FACETS	0.687	0.611	0.767	0.343	0.305	0.384	SUBCLONAL	1	TRUE	1	0.5781119501361	3		728	604	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867178	68867196	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCCTTCTTCTTTAGAATC	TCCCTTCTTCTTTAGAATC	-	novel	NA	P-0012632-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	163	412	0	ENST00000261769.5:c.2440-14_2444del		p.X814_splice	ENST00000261769	NM_004360.3	814		16/16	0.566301195282249	2	FACETS	0.976	0.915	1	0.976	0.915	1	CLONAL	2	TRUE	0	0.5781119501361	2		412	289	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935699	13935699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012632-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	97	463	0	ENST00000405192.2:c.1157G>A	p.Arg386Lys	p.R386K	ENST00000405192	NM_001163147.1	386	aGa/aAa	12/12	0.5781119501361	3	FACETS	0.985	0.884	1	0.493	0.442	0.546	CLONAL	1	TRUE	1	0.5781119501361	3		463	439	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	265	503	2	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	0.995	1	CLONAL	2	TRUE	1	0.260432868193625	2		505	947	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0012912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1250	196	592	2	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	0.260432868193625	2		594	1446	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0012912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	192	322	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.260432868193625	2		322	1042	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604750	48604750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	105	546	0	ENST00000342988.3:c.1572G>T	p.Trp524Cys	p.W524C	ENST00000342988	NM_005359.5	524	tgG/tgT	12/12	1	2	FACETS	0.769	0.687	0.856	0.769	0.687	0.856	SUBCLONAL	1	TRUE	1	0.260432868193625	2		546	1049	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052633	42052633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1378	108	785	1	ENST00000219905.7:c.7304G>A	p.Arg2435Gln	p.R2435Q	ENST00000219905	NM_001164273.1	2435	cGg/cAg	20/24	1	2	FACETS	0.558	0.499	0.622	0.558	0.499	0.622	SUBCLONAL	1	TRUE	1	0.260432868193625	2		786	1486	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273958	10273958	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	154	621	1	ENST00000330684.3:c.311C>T	p.Thr104Met	p.T104M	ENST00000330684	NM_001134407.1	104	aCg/aTg	2/13	1	2	FACETS	0.955	0.871	1	0.955	0.871	1	CLONAL	1	TRUE	1	0.260432868193625	2		622	1239	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484772	57484772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	274	511	0	ENST00000371085.3:c.752G>A	p.Ser251Asn	p.S251N	ENST00000371085	NM_000516.4	251	aGc/aAc	10/13	1	2	FACETS	1	0.96	1	1	0.995	1	CLONAL	2	TRUE	1	0.260432868193625	2		511	1024	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411005	63411005	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	64	655	0	ENST00000330258.3:c.2162T>G	p.Leu721Arg	p.L721R	ENST00000330258	NM_152424.3	721	cTc/cGc	2/2	1	2	FACETS	0.425	0.367	0.489	0.425	0.367	0.489	SUBCLONAL	1	TRUE	1	0.260432868193625	2		655	1156	SUCCESS
APC	324	MSKCC	GRCh37	5	112173912	112173913	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs863225330	NA	P-0012912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	184	349	0	ENST00000257430.4:c.2624dup	p.Arg876AlafsTer36	p.R876Afs*36	ENST00000257430	NM_000038.5	874	tca/tcAa	16/16	1	2	FACETS	0.98	0.907	1	1	0.993	1	CLONAL	2	TRUE	1	0.260432868193625	2		349	721	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0014065-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	166	424	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.944	0.87	1	0.944	0.87	1	CLONAL	1	TRUE	1	0.51023198054268	2		424	689	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143579	108143579	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014065-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	384	322	0	ENST00000278616.4:c.3284G>T	p.Arg1095Ile	p.R1095I	ENST00000278616	NM_000051.3	1095	aGa/aTa	22/63	0.51023198054268	3	FACETS	0.972	0.934	1	0.972	0.934	1	CLONAL	3	TRUE	0	0.51023198054268	3		322	648	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222902	36222902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1246187078	NA	P-0014065-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	308	711	0	ENST00000222270.7:c.5531C>T	p.Pro1844Leu	p.P1844L	ENST00000222270	NM_014727.1	1844	cCa/cTa	27/37	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.51023198054268	2		711	1160	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41562637	41562637	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555910814	NA	P-0014065-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	150	426	0	ENST00000263253.7:c.3841C>T	p.Arg1281Ter	p.R1281*	ENST00000263253	NM_001429.3	1281	Cga/Tga	23/31	1	2	FACETS	0.933	0.856	1	0.933	0.856	1	CLONAL	1	TRUE	1	0.51023198054268	2		426	630	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170016891	170016891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014065-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	207	547	2	ENST00000295797.4:c.1696G>A	p.Asp566Asn	p.D566N	ENST00000295797	NM_002740.5	566	Gat/Aat	17/18	1	2	FACETS	0.997	0.927	1	0.997	0.927	1	CLONAL	1	TRUE	1	0.51023198054268	2		549	814	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729805	41729805	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014065-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	114	263	0	ENST00000242208.4:c.724A>G	p.Ile242Val	p.I242V	ENST00000242208	NM_002192.2	242	Att/Gtt	3/3	0.485124711640604	4	FACETS	1	0.958	1	0.371	0.334	0.409	CLONAL	1	TRUE	1	0.51023198054268	4		263	607	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931775	39931775	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014065-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	193	540	0	ENST00000378444.4:c.2824G>T	p.Asp942Tyr	p.D942Y	ENST00000378444	NM_001123385.1	942	Gat/Tat	4/15	NA	2	FACETS	0.873	0.808	0.939			1	INDETERMINATE	1	TRUE	NA	0.51023198054268	2		540	867	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014263-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	87	633	0	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.233433439841553	2		633	672	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0015094-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	317	551	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.786734546047819	2		551	773	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0015211-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	431	922	1	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.58754133555971	2		923	1430	SUCCESS
AR	367	MSKCC	GRCh37	X	66943552	66943552	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137852578	NA	P-0015211-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	96	269	0	ENST00000374690.3:c.2632A>G	p.Thr878Ala	p.T878A	ENST00000374690	NM_000044.3	878	Act/Gct	8/8	1	1	FACETS	0.522	0.468	0.58	0.522	0.468	0.58	SUBCLONAL	1	TRUE	0	0.58754133555971	1		269	442	SUCCESS
APC	324	MSKCC	GRCh37	5	112111408	112111411	+	frameshift_variant	Frame_Shift_Del	DEL	ATAG	ATAG	-	rs387906231	NA	P-0015211-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	188	418	0	ENST00000257430.4:c.509_512del	p.Asp170ValfsTer4	p.D170Vfs*4	ENST00000257430	NM_000038.5	169	ATAGat/at	5/16	0.58754133555971	1	FACETS	0.978	0.914	1	0.978	0.914	1	CLONAL	1	TRUE	0	0.58754133555971	1		418	462	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0015211-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	118	762	4	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	0.337	0.303	0.373	0.337	0.303	0.373	SUBCLONAL	1	TRUE	1	0.58754133555971	2		766	1192	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0015211-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	308	301	1	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.58754133555971	2		302	1037	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015211-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	230	605	0	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	0.933	0.872	0.996	0.933	0.872	0.996	CLONAL	1	TRUE	1	0.58754133555971	2		605	839	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030692	48030692	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs267608092	NA	P-0015211-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	195	459	0	ENST00000234420.5:c.3312del	p.Phe1104LeufsTer11	p.F1104Lfs*11	ENST00000234420	NM_000179.2	1102	acT/ac	5/10	0.58754133555971	1	FACETS	0.997	0.933	1	0.997	0.933	1	CLONAL	1	TRUE	0	0.58754133555971	1		459	470	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612346	1612346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769011342	NA	P-0015211-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	278	893	0	ENST00000344749.5:c.1673G>A	p.Arg558His	p.R558H	ENST00000344749	NM_001136139.2	558	cGc/cAc	18/19	1	2	FACETS	0.721	0.676	0.768	0.721	0.676	0.768	SUBCLONAL	1	TRUE	1	0.58754133555971	2		893	1312	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163744	72163744	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1248852117	NA	P-0015211-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	322	815	1	ENST00000357731.5:c.614C>T	p.Ala205Val	p.A205V	ENST00000357731	NM_173808.2	205	gCg/gTg	4/7	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.58754133555971	2		816	1083	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830441	72830441	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015211-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	57	367	0	ENST00000268489.5:c.6140del	p.Pro2047LeufsTer54	p.P2047Lfs*54	ENST00000268489	NM_006885.3	2047	cCt/ct	9/10	1	2	FACETS	0.313	0.268	0.363	0.313	0.268	0.363	SUBCLONAL	1	TRUE	1	0.58754133555971	2		367	619	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489845	2489845	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015211-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	367	797	1	ENST00000355716.4:c.242G>A	p.Gly81Asp	p.G81D	ENST00000355716	NM_003820.2	81	gGc/gAc	3/8	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.58754133555971	2		798	1227	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743782	46743782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201788900	NA	P-0015211-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	372	808	2	ENST00000371975.4:c.2072G>A	p.Arg691Gln	p.R691Q	ENST00000371975	NM_003579.3	691	cGg/cAg	18/18	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.58754133555971	2		810	1184	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630476	90630476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015211-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	376	770	2	ENST00000330062.3:c.835G>A	p.Asp279Asn	p.D279N	ENST00000330062	NM_002168.2	279	Gac/Aac	7/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.58754133555971	2		772	1154	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823760	3823760	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376314132	NA	P-0015211-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	240	496	0	ENST00000262367.5:c.2455G>A	p.Val819Met	p.V819M	ENST00000262367	NM_004380.2	819	Gtg/Atg	13/31	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.58754133555971	2		496	767	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374912	45374912	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015211-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	340	730	0	ENST00000262160.6:c.931T>C	p.Phe311Leu	p.F311L	ENST00000262160	NM_005901.5	311	Ttc/Ctc	8/11	1	2	FACETS	0.767	0.731	0.804	1	0.995	1	SUBCLONAL	2	TRUE	1	0.58754133555971	2		730	754	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403245	213403245	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015211-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	231	664	0	ENST00000342788.4:c.10G>A	p.Ala4Thr	p.A4T	ENST00000342788	NM_005235.2	4	Gcg/Acg	1/28	1	2	FACETS	0.964	0.901	1	0.964	0.901	1	CLONAL	1	TRUE	1	0.58754133555971	2		664	816	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725324	49725324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748664213	NA	P-0015211-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	283	575	0	ENST00000449682.2:c.101G>A	p.Arg34His	p.R34H	ENST00000449682	NM_020998.3	34	cGc/cAc	2/18	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.58754133555971	2		575	908	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442507	52442507	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015211-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	281	629	0	ENST00000460680.1:c.238A>G	p.Met80Val	p.M80V	ENST00000460680	NM_004656.3	80	Atg/Gtg	4/17	1	2	FACETS	0.982	0.924	1	0.982	0.924	1	CLONAL	1	TRUE	1	0.58754133555971	2		629	974	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435496	18435497	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015211-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	78	308	0	ENST00000266497.5:c.485dup	p.Asn162LysfsTer2	p.N162Kfs*2	ENST00000266497		161	gaa/gAaa	1/31	1	2	FACETS	0.491	0.432	0.554	0.491	0.432	0.554	SUBCLONAL	1	TRUE	1	0.58754133555971	2		308	541	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965830	18965830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015211-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	104	560	3	ENST00000262803.5:c.1408G>A	p.Asp470Asn	p.D470N	ENST00000262803	NM_002911.3	470	Gac/Aac	10/24	1	2	FACETS	0.41	0.366	0.456	0.41	0.366	0.456	SUBCLONAL	1	TRUE	1	0.58754133555971	2		563	864	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206809	36206816	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTGCGC	CTGTGCGC	-	novel	NA	P-0015992-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	63	340	0	ENST00000300305.3:c.696_703del	p.Arg233HisfsTer25	p.R233Hfs*25	ENST00000300305		232	cgGCGCACAGcc/cgcc	6/8	1	2	FACETS	0.647	0.56	0.74	0.647	0.56	0.74	SUBCLONAL	1	TRUE	1	0.416366162857234	2		340	468	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0017623-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	87	336	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.57762155906191	2		336	269	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0017623-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	129	545	0	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	1	2	FACETS	0.812	0.74	0.888	0.812	0.74	0.888	CLONAL	1	TRUE	1	0.57762155906191	2		545	550	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117311	115117311	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017623-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	97	392	0	ENST00000257566.3:c.863del	p.Lys288ArgfsTer2	p.K288Rfs*2	ENST00000257566	NM_016569.3	288	aAg/ag	4/8	1	2	FACETS	0.842	0.756	0.932	0.842	0.756	0.932	CLONAL	1	TRUE	1	0.57762155906191	2		392	399	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587511	29587511	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017623-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	93	447	0	ENST00000356175.3:c.4494del	p.Gln1499SerfsTer54	p.Q1499Sfs*54	ENST00000356175	NM_000267.3	1498	Ggg/gg	33/57	0.473461261462927	1	FACETS	0.718	0.645	0.794	0.718	0.645	0.794	SUBCLONAL	1	TRUE	0	0.57762155906191	1		447	319	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252972	36252974	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	novel	NA	P-0017623-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	199	417	0	ENST00000300305.3:c.388_390del	p.Val130del	p.V130del	ENST00000300305		130	GTC/-	4/8	0.495975490989465	3	FACETS	0.794	0.741	0.849	0.794	0.741	0.849	SUBCLONAL	2	TRUE	1	0.57762155906191	3		417	559	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174833	56174849	+	frameshift_variant	Frame_Shift_Del	DEL	TACTCCTTGCCACAGTT	TACTCCTTGCCACAGTT	-	novel	NA	P-0017623-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	66	396	0	ENST00000399503.3:c.1994_2010del	p.Thr665SerfsTer26	p.T665Sfs*26	ENST00000399503	NM_005921.1	664	taTACTCCTTGCCACAGTTta/tata	11/20	1	2	FACETS	0.601	0.524	0.684	0.601	0.524	0.684	SUBCLONAL	1	TRUE	1	0.57762155906191	2		396	380	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	410	422	0	ENST00000347630.2:c.399C>A	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttA	6/11	1	2	FACETS	0.937	0.896	0.979	0.937	0.896	0.979	CLONAL	1	TRUE	1	0.93751536342867	2		422	933	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577129	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519986	NA	P-0018068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	1056	538	0	ENST00000269305.4:c.809T>C	p.Phe270Ser	p.F270S	ENST00000269305	NM_001126112.2	270	tTt/tCt	8/11	0.931485193046434	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.93751536342867	2		538	1121	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264271	46264271	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	231	299	0	ENST00000371998.3:c.1318G>T	p.Ala440Ser	p.A440S	ENST00000371998		440	Gct/Tct	11/23	1	2	FACETS	0.913	0.859	0.967	0.913	0.859	0.967	CLONAL	1	TRUE	1	0.93751536342867	2		299	540	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411774	63411774	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	562	340	0	ENST00000330258.3:c.1393C>T	p.Pro465Ser	p.P465S	ENST00000330258	NM_152424.3	465	Ccc/Tcc	2/2	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.93751536342867	1		340	596	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97869405	97869407	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0018068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	476	540	0	ENST00000289081.3:c.1474_1476del	p.Leu492del	p.L492del	ENST00000289081	NM_000136.2	492	CTC/-	14/15	1	2	FACETS	0.936	0.898	0.974	0.936	0.898	0.974	CLONAL	1	TRUE	1	0.93751536342867	2		540	1085	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391511	139391511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751456570	NA	P-0018779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	190	879	1	ENST00000277541.6:c.6680C>T	p.Pro2227Leu	p.P2227L	ENST00000277541	NM_017617.3	2227	cCg/cTg	34/34	0.886913593909312	4	FACETS	0.975	0.903	1	0.488	0.451	0.525	CLONAL	1	TRUE	2	0.886913593909312	4		880	829	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32439195	32439195	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs907964605	NA	P-0018779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	227	397	0	ENST00000332351.3:c.878A>G	p.Asn293Ser	p.N293S	ENST00000332351	NM_024426.4	293	aAt/aGt	4/10	0.886913593909312	3	FACETS	0.933	0.885	0.981			1	CLONAL	2	TRUE	NA	0.886913593909312	3		397	396	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117756	108117756	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587781511	NA	P-0018779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	350	357	0	ENST00000278616.4:c.967A>G	p.Ile323Val	p.I323V	ENST00000278616	NM_000051.3	323	Ata/Gta	8/63	0.886913593909312	5	FACETS	0.973	0.932	1	0.973	0.932	1	CLONAL	3	TRUE	2	0.886913593909312	5		357	630	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39550380	39550380	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	217	337	0	ENST00000262039.4:c.491G>C	p.Ser164Thr	p.S164T	ENST00000262039	NM_002647.2	164	aGt/aCt	4/25	0.516747797311308	4	FACETS	0.86	0.816	0.903	0.86	0.816	0.903	INDETERMINATE	3	TRUE	1	0.886913593909312	4		337	358	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760358	133760358	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064160	NA	P-0018779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	298	580	0	ENST00000318560.5:c.2681G>A	p.Arg894Lys	p.R894K	ENST00000318560	NM_005157.4	894	aGg/aAg	11/11	0.886913593909312	4	FACETS	0.966	0.917	1	0.966	0.917	1	CLONAL	2	TRUE	2	0.886913593909312	4		580	656	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425830	49425830	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	133	416	0	ENST00000301067.7:c.12658C>T	p.Gln4220Ter	p.Q4220*	ENST00000301067	NM_003482.3	4220	Cag/Tag	39/54	0.886913593909312	3	FACETS	1	0.922	1	0.503	0.461	0.547	CLONAL	1	TRUE	1	0.886913593909312	3		416	430	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862076	68862076	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs1385720097	NA	P-0018869-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	45	202	0	ENST00000261769.5:c.2165-1G>T		p.X722_splice	ENST00000261769	NM_004360.3	722			0.452342727881454	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	0	0.452342727881454	1		202	113	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913315	NA	P-0018869-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	8	370	0	ENST00000326873.7:c.580G>A	p.Asp194Asn	p.D194N	ENST00000326873	NM_000455.4	194	Gac/Aac	4/10	1	2	FACETS	0.089	0.056	0.131	0.089	0.056	0.131	SUBCLONAL	1	FALSE	1	0.452342727881454	2		370	399	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880219	37880230	+	protein_altering_variant	In_Frame_Del	DEL	TTGAGGGAAAAC	TTGAGGGAAAAC	GGAAAACAA	novel	NA	P-0018869-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	35	388	2	ENST00000269571.5:c.2263_2274delinsGGAAAACAA	p.Leu755_Asn758delinsGlyLysGln	p.L755_N758delinsGKQ	ENST00000269571		755	TTGAGGGAAAAC/GGAAAACAA	19/27	1	2	FACETS	0.85	0.705	1	0.85	0.705	1	CLONAL	1	FALSE	1	0.452342727881454	2		390	182	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181881	56181881	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018869-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	30	181	0	ENST00000399503.3:c.4105G>T	p.Asp1369Tyr	p.D1369Y	ENST00000399503	NM_005921.1	1369	Gat/Tat	17/20	1	2	FACETS	0.954	0.781	1	0.954	0.781	1	CLONAL	1	FALSE	1	0.452342727881454	2		181	139	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045858	26045858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018869-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	63	292	0	ENST00000540144.1:c.220G>A	p.Glu74Lys	p.E74K	ENST00000540144	NM_003531.2	74	Gaa/Aaa	1/1	0.115505560357606	4	FACETS	1	0.953	1	0.607	0.529	0.692	INDETERMINATE	1	FALSE	2	0.452342727881454	4		292	333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0019607-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	196	572	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.206590514631768	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.206590514631768	1		572	1305	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874031	123874031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1447464550	NA	P-0019607-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	10	60	0	ENST00000330479.4:c.62C>T	p.Ala21Val	p.A21V	ENST00000330479	NM_020382.3	21	gCg/gTg	2/9	1	2	FACETS	0.794	0.54	1	0.794	0.54	1	CLONAL	1	TRUE	1	0.206590514631768	2		60	122	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162722905	162722905	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019607-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	72	623	0	ENST00000367921.3:c.103G>C	p.Gly35Arg	p.G35R	ENST00000367921	NM_006182.2	35	Ggc/Cgc	4/18	1	2	FACETS	0.622	0.542	0.71	0.622	0.542	0.71	SUBCLONAL	1	TRUE	1	0.206590514631768	2		623	1120	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50818262	50818262	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019607-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	42	431	0	ENST00000398568.2:c.1840C>G	p.Leu614Val	p.L614V	ENST00000398568	NM_001042412.1	614	Ctg/Gtg	11/18	1	2	FACETS	0.518	0.431	0.615	0.518	0.431	0.615	SUBCLONAL	1	TRUE	1	0.206590514631768	2		431	785	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028623	12028623	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019607-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	55	402	2	ENST00000353533.5:c.826G>T	p.Asp276Tyr	p.D276Y	ENST00000353533	NM_003010.3	276	Gac/Tac	8/11	0.206590514631768	1	FACETS	0.628	0.536	0.729	0.628	0.536	0.729	SUBCLONAL	1	TRUE	0	0.206590514631768	1		404	760	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880221	37880221	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019607-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1202	78	738	0	ENST00000269571.5:c.2265G>C	p.Leu755Phe	p.L755F	ENST00000269571		755	ttG/ttC	19/27	0.206590514631768	1	FACETS	0.529	0.463	0.601	0.529	0.463	0.601	SUBCLONAL	1	TRUE	0	0.206590514631768	1		738	1280	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412045	116412045	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0019607-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	431	753	0	ENST00000397752.3:c.3028+2T>G		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.192072069878136	2	FACETS	0.946	0.9	0.992	1	0.995	1	CLONAL	3	TRUE	0	0.206590514631768	2		753	1471	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0019852-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	114	518	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.313927226120662	3	FACETS	0.771	0.697	0.849	0.771	0.697	0.849	SUBCLONAL	2	TRUE	1	0.313927226120662	3		518	545	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123837	46123837	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0019852-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	54	136	0	ENST00000334344.6:c.103A>T	p.Lys35Ter	p.K35*	ENST00000334344	NM_152641.2	35	Aaa/Taa	2/21	0.245370226915957	2	FACETS	1	0.909	1	0.539	0.463	0.621	CLONAL	1	TRUE	0	0.313927226120662	2		136	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691039	NA	P-0019852-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	163	287	0	ENST00000269305.4:c.919+1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			NA	2	FACETS	0.877	0.809	0.948			1	INDETERMINATE	2	TRUE	NA	0.313927226120662	2		287	592	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871861	12871861	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019852-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	65	111	0	ENST00000228872.4:c.578del	p.Leu193ProfsTer32	p.L193Pfs*32	ENST00000228872	NM_004064.3	193	cTc/cc	2/3	0.245370226915957	2	FACETS	0.822	0.721	0.928	0.822	0.721	0.928	CLONAL	2	TRUE	0	0.313927226120662	2		111	252	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39537702	39537702	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs770629565	NA	P-0019852-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	23	128	0	ENST00000262039.4:c.236A>G	p.Lys79Arg	p.K79R	ENST00000262039	NM_002647.2	79	aAa/aGa	2/25	0.313927226120662	1	FACETS	0.475	0.371	0.595	0.475	0.371	0.595	SUBCLONAL	1	TRUE	0	0.313927226120662	1		128	260	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0020250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	82	347	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.945827120674285	2		347	168	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0020250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	100	177	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	0.945827120674285	2		177	200	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0020250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	240	416	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.889	0.837	0.941	0.889	0.837	0.941	CLONAL	1	TRUE	1	0.945827120674285	2		416	571	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791794	42791794	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	280	353	0	ENST00000575354.2:c.680A>T	p.Asn227Ile	p.N227I	ENST00000575354	NM_015125.3	227	aAc/aTc	5/20	0.945827120674285	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.945827120674285	1		353	306	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646219	215646219	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	119	161	0	ENST00000260947.4:c.379A>G	p.Lys127Glu	p.K127E	ENST00000260947	NM_000465.2	127	Aaa/Gaa	4/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.945827120674285	2		161	245	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0021060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	30	483	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.976	0.79	1	0.976	0.79	1	CLONAL	1	TRUE	1	0.237421553398073	2		483	259	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943725	9943725	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	21	357	0	ENST00000330684.3:c.1216C>T	p.Leu406Phe	p.L406F	ENST00000330684	NM_001134407.1	406	Ctc/Ttc	5/13	1	2	FACETS	0.565	0.435	0.717	0.565	0.435	0.717	SUBCLONAL	1	TRUE	1	0.237421553398073	2		357	313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574032	7574032	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	48	361	0	ENST00000269305.4:c.995T>A	p.Ile332Asn	p.I332N	ENST00000269305	NM_001126112.2	332	aTc/aAc	10/11	0.237421553398073	1	FACETS	0.998	0.847	1	0.998	0.847	1	CLONAL	1	TRUE	0	0.237421553398073	1		361	357	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949162	151949162	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	38	262	0	ENST00000262189.6:c.1483G>T	p.Glu495Ter	p.E495*	ENST00000262189	NM_170606.2	495	Gag/Tag	11/59	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.237421553398073	2		262	244	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0021095-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	175	379	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.300341314904471	3	FACETS	0.906	0.835	0.981	0.906	0.835	0.981	CLONAL	2	TRUE	1	0.23	3		379	936	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0021095-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	166	611	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	0.204353554987254	2	FACETS	0.86	0.791	0.933	0.86	0.791	0.933	CLONAL	2	TRUE	0	0.23	2		611	839	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928872	44928872	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs755440519	NA	P-0021095-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	88	339	0	ENST00000377967.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000377967	NM_021140.2	658	Cga/Tga	17/29	0.121661149918727	4	FACETS	0.9	0.8	1	0.9	0.8	1	INDETERMINATE	2	TRUE	2	0.23	4		339	523	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490337	29490337	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021095-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	286	433	0	ENST00000356175.3:c.425del	p.Leu142TyrfsTer23	p.L142Yfs*23	ENST00000356175	NM_000267.3	141	gTt/gt	4/57	0.301307064114411	3	FACETS	0.916	0.865	0.967			1	CLONAL	4	TRUE	NA	0.23	3		433	757	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0021112-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	50	302	0	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	1	2	FACETS	0.81	0.685	0.947	0.81	0.685	0.947	CLONAL	1	TRUE	1	0.16	2		302	772	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469829	157469829	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021112-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	59	335	0	ENST00000346085.5:c.2623G>T	p.Gly875Cys	p.G875C	ENST00000346085	NM_020732.3	875	Ggt/Tgt	9/20	1	2	FACETS	0.963	0.827	1	0.963	0.827	1	CLONAL	1	TRUE	1	0.16	2		335	766	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411861	116411889	+	intron_variant	Intron	DEL	ATAGCCGTCTTTAACAAGCTCTTTCTTTC	ATAGCCGTCTTTAACAAGCTCTTTCTTTC	-	novel	NA	P-0021112-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	52	396	0	ENST00000397752.3:c.2888-42_2888-14del		p.*963*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.727	0.617	0.849	0.727	0.617	0.849	SUBCLONAL	1	TRUE	1	0.16	2		396	894	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149245741	149245741	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021112-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	45	223	0	ENST00000360632.3:c.787C>G	p.Arg263Gly	p.R263G	ENST00000360632	NM_015472.4	263	Cga/Gga	5/7	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.16	2		223	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0021328-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	311	322	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.283017485427739	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	FALSE	1	0.283017485427739	3		322	1211	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0021328-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	218	323	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.256152304463984	3	FACETS	0.763	0.708	0.819	0.763	0.708	0.819	SUBCLONAL	2	FALSE	1	0.283017485427739	3		323	1153	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0021328-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	154	122	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.169630823503862	5	FACETS	0.994	0.915	1	0.994	0.915	1	INDETERMINATE	3	FALSE	2	0.283017485427739	5		122	520	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120802531	120802531	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021328-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	214	751	0	ENST00000257552.2:c.295C>G	p.Arg99Gly	p.R99G	ENST00000257552	NM_002442.3	99	Cga/Gga	5/15	0.225215643000889	4	FACETS	1	0.99	1	0.706	0.654	0.759	CLONAL	1	FALSE	2	0.283017485427739	4		751	1375	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519187	103519187	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021328-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	75	511	0	ENST00000355739.4:c.2525A>G	p.Asn842Ser	p.N842S	ENST00000355739	NM_000123.3	842	aAt/aGt	11/15	0.283017485427739	3	FACETS	0.748	0.654	0.849			1	SUBCLONAL	1	FALSE	NA	0.283017485427739	3		511	809	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852472	63852472	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021328-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	91	616	0	ENST00000279873.7:c.3250G>T	p.Gly1084Trp	p.G1084W	ENST00000279873	NM_032199.2	1084	Ggg/Tgg	10/10	0.281210949397865	3	FACETS	0.759	0.673	0.852			1	SUBCLONAL	1	FALSE	NA	0.283017485427739	3		616	967	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38942987	38942987	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021328-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	82	640	0	ENST00000357387.3:c.5000T>G	p.Leu1667Arg	p.L1667R	ENST00000357387	NM_152756.3	1667	cTt/cGt	37/38	0.283017485427739	5	FACETS	0.725	0.637	0.82			1	SUBCLONAL	1	FALSE	NA	0.283017485427739	5		640	1139	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692791	89692791	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021543-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	67	305	0	ENST00000371953.3:c.275A>T	p.Asp92Val	p.D92V	ENST00000371953	NM_000314.4	92	gAc/gTc	5/9	0.233017528902574	1	FACETS	0.975	0.849	1	0.975	0.849	1	CLONAL	1	TRUE	0	0.233017528902574	1		305	521	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115965	8115974	+	frameshift_variant	Frame_Shift_Del	DEL	CATGGTCACC	CATGGTCACC	-	novel	NA	P-0021543-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	54	269	0	ENST00000346208.3:c.1311_1320del	p.Ser437ArgfsTer35	p.S437Rfs*35	ENST00000346208		437	agCATGGTCACC/ag	6/6	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.233017528902574	2		269	385	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575085	64575085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs794728624	NA	P-0021543-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	103	622	0	ENST00000312049.6:c.722G>A	p.Cys241Tyr	p.C241Y	ENST00000312049	NM_130799.2	241	tGt/tAt	4/10	0.233017528902574	1	FACETS	0.958	0.857	1	0.958	0.857	1	CLONAL	1	TRUE	0	0.233017528902574	1		622	815	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920649	96920658	+	frameshift_variant	Frame_Shift_Del	DEL	AAGCGGAGAG	AAGCGGAGAG	-	novel	NA	P-0021543-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	45	427	0	ENST00000258439.3:c.322_331del	p.Leu108SerfsTer13	p.L108Sfs*13	ENST00000258439	NM_001193304.2	108	CTCTCCGCTTtc/tc	3/4	1	2	FACETS	0.595	0.499	0.702	0.595	0.499	0.702	SUBCLONAL	1	TRUE	1	0.233017528902574	2		427	649	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874763	151874763	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021543-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	115	312	0	ENST00000262189.6:c.7775del	p.Asn2592ThrfsTer55	p.N2592Tfs*55	ENST00000262189	NM_170606.2	2592	aAc/ac	38/59	0.0217191888056774	3	FACETS	0.903	0.82	0.989			1	INDETERMINATE	3	TRUE	NA	0.233017528902574	3		312	407	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391086	139391086	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021543-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	62	640	2	ENST00000277541.6:c.7105C>T	p.Pro2369Ser	p.P2369S	ENST00000277541	NM_017617.3	2369	Ccc/Tcc	34/34	0.233017528902574	1	FACETS	0.569	0.49	0.655	0.569	0.49	0.655	SUBCLONAL	1	TRUE	0	0.233017528902574	1		642	826	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0022421-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	258	571	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.487422031270136	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.501402400616978	2		572	513	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022421-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	237	536	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.443570017462144	4	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	2	0.501402400616978	4		536	685	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28601351	28601351	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022421-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	192	565	0	ENST00000253063.3:c.1036G>C	p.Asp346His	p.D346H	ENST00000253063	NM_031459.4	346	Gac/Cac	8/10	0.323262288967197	4	FACETS	0.995	0.926	1	0.995	0.926	1	CLONAL	2	TRUE	2	0.501402400616978	4		565	578	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721228	176721228	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022421-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	138	322	0	ENST00000439151.2:c.6859G>C	p.Asp2287His	p.D2287H	ENST00000439151	NM_022455.4	2287	Gac/Cac	23/23	0.443570017462144	4	FACETS	0.92	0.844	0.999	0.92	0.844	0.999	CLONAL	2	TRUE	2	0.501402400616978	4		322	449	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62325806	62325806	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1182805971	NA	P-0022421-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	43	570	0	ENST00000360203.5:c.3074G>T	p.Gly1025Val	p.G1025V	ENST00000360203	NM_001283009.1	1025	gGc/gTc	31/35	0.323262288967197	4	FACETS	0.453	0.378	0.535	0.226	0.189	0.268	SUBCLONAL	1	TRUE	2	0.501402400616978	4		570	569	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	52	474	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.762	0.649	0.885	1	0.965	1	SUBCLONAL	2	TRUE	1	0.143415542138491	2		474	476	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947827	178947827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	36	344	1	ENST00000263967.3:c.2702G>T	p.Cys901Phe	p.C901F	ENST00000263967	NM_006218.2	901	tGt/tTt	19/21	1	2	FACETS	0.89	0.731	1	0.89	0.731	1	CLONAL	1	TRUE	1	0.143415542138491	2		345	564	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309613	30309613	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	82	656	1	ENST00000307677.4:c.409T>A	p.Trp137Arg	p.W137R	ENST00000307677	NM_138578.1	137	Tgg/Agg	2/3	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.143415542138491	2		657	1081	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633564	69633574	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGCGCCGGG	GCGGCGCCGGG	-	novel	NA	P-0023035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3049	238	337	0	ENST00000334134.2:c.128_138del	p.Pro43GlnfsTer81	p.P43Qfs*81	ENST00000334134	NM_005247.2	43	cCCCGGCGCCGC/c	1/3	0.767417727247761	13	FACETS	0.985	0.914	1			1	CLONAL	1	TRUE	NA	0.767417727247761	13		337	3287	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0023035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	464	656	1	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.767417727247761	1	FACETS	0.987	0.953	1	0.987	0.953	1	CLONAL	1	TRUE	0	0.767417727247761	1		657	755	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46603773	46603773	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023493-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	521	640	0	ENST00000263734.3:c.1130G>C	p.Ser377Thr	p.S377T	ENST00000263734	NM_001430.4	377	aGt/aCt	9/16	0.474326370398329	3	FACETS	0.894	0.858	0.931	0.894	0.858	0.931	CLONAL	2	TRUE	1	0.562712784174145	3		640	1327	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336345	80336345	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023493-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	232	463	0	ENST00000286548.4:c.974A>T	p.Tyr325Phe	p.Y325F	ENST00000286548	NM_002072.3	325	tAc/tTc	7/7	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.562712784174145	2		463	786	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023843-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	42	474	0				ENST00000310581	NM_198253.2	-/1132			0.162066220434938	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		474	126	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0023843-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	61	483	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		483	294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578276	7578312	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGAGGGGCCAGACCTAAGAGCAATCAGTGAGGAATC	AGGAGGGGCCAGACCTAAGAGCAATCAGTGAGGAATC	-	novel	NA	P-0024217-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	91	626	1	ENST00000269305.4:c.560-23_573del		p.X187_splice	ENST00000269305	NM_001126112.2	187		6/11	0.3	1	FACETS	0.459	0.406	0.515	0.459	0.406	0.515	SUBCLONAL	1	TRUE	0	0.35	1		627	935	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762871	40762871	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024217-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	216	592	0	ENST00000392038.2:c.137A>T	p.Asp46Val	p.D46V	ENST00000392038	NM_001626.4	46	gAt/gTt	3/14	0.3	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.35	1		592	1010	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157335	106157336	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0024217-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	163	384	0	ENST00000380013.4:c.2241dup	p.Leu748IlefsTer6	p.L748Ifs*6	ENST00000380013	NM_001127208.2	746	caa/cAaa	3/11	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.35	2		384	908	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646257	23646257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142103232	NA	P-0024809-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	13	479	0	ENST00000261584.4:c.1610C>T	p.Ser537Leu	p.S537L	ENST00000261584	NM_024675.3	537	tCg/tTg	4/13	1	2	FACETS	0.522	0.372	0.705	0.522	0.372	0.705	SUBCLONAL	1	TRUE	1	0.21	2		479	237	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288796	11288796	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	127	509	0	ENST00000361445.4:c.2959G>A	p.Val987Met	p.V987M	ENST00000361445	NM_004958.3	987	Gtg/Atg	19/58	0.208439846103517	5	FACETS	0.87	0.788	0.956	0.58	0.525	0.637	CLONAL	2	TRUE	2	0.25132026174989	5		509	800	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316992	11316992	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	94	298	0	ENST00000361445.4:c.502G>T	p.Ala168Ser	p.A168S	ENST00000361445	NM_004958.3	168	Gct/Tct	4/58	0.208439846103517	5	FACETS	1	0.909	1	0.68	0.607	0.757	CLONAL	2	TRUE	2	0.25132026174989	5		298	505	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573126	41573126	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371065099	NA	P-0024875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	211	777	0	ENST00000263253.7:c.5411C>T	p.Pro1804Leu	p.P1804L	ENST00000263253	NM_001429.3	1804	cCg/cTg	31/31	0.212040009677803	4	FACETS	0.938	0.87	1	0.938	0.87	1	CLONAL	2	TRUE	2	0.25132026174989	4		777	1120	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046765	42046765	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs768068238	NA	P-0024965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	75	560	0	ENST00000219905.7:c.7139C>T	p.Pro2380Leu	p.P2380L	ENST00000219905	NM_001164273.1	2380	cCg/cTg	18/24	1	2	FACETS	0.779	0.681	0.884	0.779	0.681	0.884	SUBCLONAL	1	TRUE	1	0.233399689548582	2		560	825	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646892	37646892	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	144	821	0	ENST00000447079.4:c.2014C>G	p.Pro672Ala	p.P672A	ENST00000447079	NM_015083.1	672	Cct/Gct	3/14	1	2	FACETS	0.957	0.87	1	0.957	0.87	1	CLONAL	1	TRUE	1	0.233399689548582	2		821	1290	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24134006	24134006	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	196	458	0	ENST00000263121.7:c.157C>T	p.Arg53Ter	p.R53*	ENST00000263121	NM_003073.3	53	Cga/Tga	2/9	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.663184283143708	2		458	486	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56878466	56878466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764588936	NA	P-0025138-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	379	444	1	ENST00000308159.5:c.2405G>A	p.Arg802Gln	p.R802Q	ENST00000308159	NM_014669.4	802	cGa/cAa	22/22	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.671798312645396	2		445	1107	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540229	23540230	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCTCC	rs753037741	NA	P-0025138-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	153	406	0	ENST00000380871.4:c.168_173dup	p.Pro62_Glu63dup	p.P62_E63dup	ENST00000380871	NM_006167.3	62	cca/ccGGAGCCa	1/2	0.666554771152841	1	FACETS	0.533	0.49	0.578	0.533	0.49	0.578	SUBCLONAL	1	TRUE	0	0.671798312645396	1		406	567	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041596	47041596	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0025138-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	467	332	0	ENST00000377604.3:c.1821C>G	p.Tyr607Ter	p.Y607*	ENST00000377604	NM_001204468.1	607	taC/taG	17/24	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.671798312645396	1		332	727	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432664	29432664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113994087	NA	P-0025148-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	28	314	0	ENST00000389048.3:c.3824G>A	p.Arg1275Gln	p.R1275Q	ENST00000389048	NM_004304.4	1275	cGa/cAa	25/29	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		314	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0025262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	25	352	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	1	2	FACETS	0.087	0.068	0.109	0.087	0.068	0.109	SUBCLONAL	1	TRUE	1	0.895903240817148	2		352	643	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867546	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGC	GGCGGCGGC	-	rs11466445	NA	P-0025262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	12	20	0	ENST00000374994.4:c.70_78del	p.Ala24_Ala26del	p.A24_A26del	ENST00000374994	NM_004612.2	17	ctGGCGGCGGCg/ctg	1/9	1	2	FACETS	0.595	0.433	0.779	0.595	0.433	0.779	SUBCLONAL	1	TRUE	1	0.895903240817148	2		20	45	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037933	49037934	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	41	367	0	ENST00000267163.4:c.2174dup	p.Thr726AsnfsTer25	p.T726Nfs*25	ENST00000267163	NM_000321.2	725	gta/gTta	21/27	0.895903240817148	1	FACETS	0.155	0.129	0.183	0.155	0.129	0.183	SUBCLONAL	1	TRUE	0	0.895903240817148	1		367	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577017	7577017	+	splice_donor_variant	Splice_Site	SNP	A	A	C	rs1131691016	NA	P-0025262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	242	373	0	ENST00000269305.4:c.919+2T>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.895903240817148	2		373	530	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033823	49033823	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0025262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	157	221	0	ENST00000267163.4:c.1961-1G>A		p.X654_splice	ENST00000267163	NM_000321.2	654			0.895903240817148	1	FACETS	0.953	0.909	0.995	0.953	0.909	0.995	CLONAL	1	TRUE	0	0.895903240817148	1		221	203	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577013	7577042	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTTACCTCGCTTAGTGCTCCCTGGGGGCA	GCTTACCTCGCTTAGTGCTCCCTGGGGGCA	-	novel	NA	P-0025262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	235	361	0	ENST00000269305.4:c.896_919+6del		p.X299_splice	ENST00000269305	NM_001126112.2	299		8/11	1	2	FACETS	0.973	0.917	1	0.973	0.917	1	CLONAL	1	TRUE	1	0.895903240817148	2		361	539	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181929	32181929	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	293	407	1	ENST00000375023.3:c.2125C>T	p.Gln709Ter	p.Q709*	ENST00000375023	NM_004557.3	709	Cag/Tag	13/30	0.895903240817148	3	FACETS	1	0.954	1	0.506	0.477	0.536	CLONAL	1	TRUE	1	0.895903240817148	3		408	935	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	148	483	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	0.27	2		483	955	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	118	424	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.3	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.27	1		424	657	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	115	454	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.819	0.741	0.901	1	0.986	1	CLONAL	2	TRUE	1	0.27	2		456	520	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	72	699	1	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.797	0.696	0.906	0.797	0.696	0.906	CLONAL	1	TRUE	1	0.27	2		700	669	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120031	70120031	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	14	62	0	ENST00000245479.2:c.1037del	p.Pro346ArgfsTer37	p.P346Rfs*37	ENST00000245479	NM_000346.3	345	Ccc/cc	3/3	0.3	1	FACETS	1	0.748	1	1	0.748	1	CLONAL	1	TRUE	0	0.27	1		62	88	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	155	475	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.27	2		475	1020	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391024	89391024	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	107	519	0	ENST00000336596.2:c.1095del	p.Lys365AsnfsTer6	p.K365Nfs*6	ENST00000336596	NM_005233.5	364	Aaa/aa	5/17	1	2	FACETS	0.963	0.863	1	0.963	0.863	1	CLONAL	1	TRUE	1	0.27	2		519	823	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	113	481	0	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	0.901	0.81	0.998	0.901	0.81	0.998	CLONAL	1	TRUE	1	0.27	2		481	929	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118684	11118684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550731833	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	116	638	0	ENST00000358026.2:c.2108C>T	p.Ala703Val	p.A703V	ENST00000358026	NM_001128849.1	703	gCg/gTg	14/36	0.3	1	FACETS	0.927	0.835	1	0.927	0.835	1	CLONAL	1	TRUE	0	0.27	1		638	802	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653796	89653798	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs1554893765	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	68	448	0	ENST00000371953.3:c.97_99del	p.Ile33del	p.I33del	ENST00000371953	NM_000314.4	32	ATT/-	2/9	1	2	FACETS	0.725	0.63	0.827	0.725	0.63	0.827	SUBCLONAL	1	TRUE	1	0.27	2		448	695	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736166	204736166	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	72	415	2	ENST00000302823.3:c.529del	p.Tyr177IlefsTer10	p.Y177Ifs*10	ENST00000302823	NM_005214.4	175	Ttt/tt	3/4	1	2	FACETS	0.705	0.615	0.802	0.705	0.615	0.802	SUBCLONAL	1	TRUE	1	0.27	2		417	757	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459525	50459525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778820674	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	84	399	0	ENST00000331340.3:c.814G>A	p.Ala272Thr	p.A272T	ENST00000331340	NM_006060.4	272	Gcc/Acc	7/8	0.271466646313228	4	FACETS	0.808	0.712	0.911	0.269	0.237	0.304	CLONAL	1	TRUE	1	0.27	4		399	978	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355942	73355942	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	191	694	3	ENST00000377767.4:c.29del	p.Lys10ArgfsTer7	p.K10Rfs*7	ENST00000377767	NM_014953.3	10	aAg/ag	1/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.27	2		697	1258	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	48	538	0	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	0.3	1	FACETS	0.539	0.455	0.631	0.539	0.455	0.631	SUBCLONAL	1	TRUE	0	0.27	1		538	571	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129338	152129338	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1361952517	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	69	436	0	ENST00000206249.3:c.296del	p.Pro99HisfsTer10	p.P99Hfs*10	ENST00000206249	NM_000125.3	97	ttC/tt	1/8	1	2	FACETS	0.991	0.864	1	0.991	0.864	1	CLONAL	1	TRUE	1	0.27	2		436	516	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533939	63533940	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs771001164	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	67	378	1	ENST00000307078.5:c.1214_1215del	p.Glu405GlyfsTer56	p.E405Gfs*56	ENST00000307078	NM_004655.3	405	gAG/g	6/11	0.3	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.27	1		379	318	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827732	72827732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241554729	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	71	494	0	ENST00000268489.5:c.8849G>A	p.Arg2950His	p.R2950H	ENST00000268489	NM_006885.3	2950	cGc/cAc	9/10	0.3	1	FACETS	0.917	0.802	1	0.917	0.802	1	CLONAL	1	TRUE	0	0.27	1		494	496	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101612	27101612	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	132	823	1	ENST00000324856.7:c.4899del	p.Met1634Ter	p.M1634*	ENST00000324856	NM_006015.4	1632	Ccc/cc	18/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.27	2		824	884	SUCCESS
APC	324	MSKCC	GRCh37	5	112177050	112177050	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780599	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	76	561	2	ENST00000257430.4:c.5759G>A	p.Arg1920Gln	p.R1920Q	ENST00000257430	NM_000038.5	1920	cGa/cAa	16/16	1	2	FACETS	0.697	0.61	0.79	0.697	0.61	0.79	SUBCLONAL	1	TRUE	1	0.27	2		563	808	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250948	10250948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1255153711	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	84	592	2	ENST00000340748.4:c.3532C>T	p.Arg1178Trp	p.R1178W	ENST00000340748		1178	Cgg/Tgg	32/40	0.3	1	FACETS	0.828	0.732	0.931	0.828	0.732	0.931	CLONAL	1	TRUE	0	0.27	1		594	650	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272201	15272201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113178142	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	48	550	2	ENST00000263388.2:c.6238C>T	p.Arg2080Trp	p.R2080W	ENST00000263388	NM_000435.2	2080	Cgg/Tgg	33/33	0.3	1	FACETS	0.843	0.715	0.982	0.843	0.715	0.982	CLONAL	1	TRUE	0	0.27	1		552	365	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106042	8106042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	94	510	0	ENST00000346208.3:c.862G>A	p.Gly288Arg	p.G288R	ENST00000346208		288	Ggg/Agg	4/6	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.27	2		510	643	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878077	48878082	+	inframe_deletion	In_Frame_Del	DEL	CCGCCA	CCGCCA	-	novel	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	48	197	0	ENST00000267163.4:c.34_39del	p.Thr12_Ala13del	p.T12_A13del	ENST00000267163	NM_000321.2	10	gCCGCCAcc/gcc	1/27	1	2	FACETS	0.898	0.761	1	0.898	0.761	1	CLONAL	1	TRUE	1	0.27	2		197	396	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631830	90631830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	69	521	1	ENST00000330062.3:c.523C>T	p.His175Tyr	p.H175Y	ENST00000330062	NM_002168.2	175	Cat/Tat	4/11	1	2	FACETS	0.989	0.863	1	0.989	0.863	1	CLONAL	1	TRUE	1	0.27	2		522	517	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344955	118344955	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	44	326	1	ENST00000534358.1:c.3086del	p.Lys1029ArgfsTer65	p.K1029Rfs*65	ENST00000534358	NM_005933.3	1027	ctA/ct	3/36	1	2	FACETS	0.742	0.623	0.874	0.742	0.623	0.874	SUBCLONAL	1	TRUE	1	0.27	2		327	439	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557762	21557762	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1172808550	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	129	620	2	ENST00000382592.4:c.2083G>A	p.Ala695Thr	p.A695T	ENST00000382592	NM_014572.2	695	Gcc/Acc	5/8	0.3	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.27	1		622	745	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	97	875	1	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	0.3	1	FACETS	0.697	0.62	0.778	0.697	0.62	0.778	SUBCLONAL	1	TRUE	0	0.27	1		876	892	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156652	106156652	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	94	446	0	ENST00000380013.4:c.1557del	p.Phe519LeufsTer14	p.F519Lfs*14	ENST00000380013	NM_001127208.2	518	aTt/at	3/11	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.27	2		446	634	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439679	220439679	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372427524	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	92	672	2	ENST00000243786.2:c.532G>A	p.Val178Met	p.V178M	ENST00000243786	NM_002191.3	178	Gtg/Atg	2/2	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.27	2		674	613	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657656	37657656	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	92	602	0	ENST00000447079.4:c.2573G>T	p.Arg858Leu	p.R858L	ENST00000447079	NM_015083.1	858	cGg/cTg	6/14	1	2	FACETS	0.914	0.811	1	0.914	0.811	1	CLONAL	1	TRUE	1	0.27	2		602	746	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413936	139413936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	129	685	1	ENST00000277541.6:c.824G>A	p.Gly275Asp	p.G275D	ENST00000277541	NM_017617.3	275	gGc/gAc	5/34	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.27	2		686	795	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098425	11098425	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	49	444	0	ENST00000358026.2:c.947del	p.Pro316LeufsTer10	p.P316Lfs*10	ENST00000358026	NM_001128849.1	315	Ccc/cc	6/36	0.3	1	FACETS	0.77	0.653	0.897	0.77	0.653	0.897	SUBCLONAL	1	TRUE	0	0.27	1		444	408	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265848	16265848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs908404058	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	99	683	1	ENST00000375759.3:c.10921C>T	p.Arg3641Cys	p.R3641C	ENST00000375759	NM_015001.2	3641	Cgc/Tgc	15/15	1	2	FACETS	0.922	0.823	1	0.922	0.823	1	CLONAL	1	TRUE	1	0.27	2		684	795	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462141	120462141	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1369160674	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	100	619	1	ENST00000256646.2:c.5575A>G	p.Ile1859Val	p.I1859V	ENST00000256646	NM_024408.3	1859	Atc/Gtc	31/34	1	2	FACETS	0.952	0.85	1	0.952	0.85	1	CLONAL	1	TRUE	1	0.27	2		620	778	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570832	226570832	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746522692	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	38	541	3	ENST00000366794.5:c.1064G>A	p.Arg355His	p.R355H	ENST00000366794	NM_001618.3	355	cGt/cAt	8/23	1	2	FACETS	0.372	0.306	0.446	0.372	0.306	0.446	SUBCLONAL	1	TRUE	1	0.27	2		544	757	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852248	63852248	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	124	575	0	ENST00000279873.7:c.3026C>G	p.Ala1009Gly	p.A1009G	ENST00000279873	NM_032199.2	1009	gCg/gGg	10/10	0.290297959383968	4	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.27	4		575	808	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70412276	70412276	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	69	464	1	ENST00000373644.4:c.4386C>A	p.Asn1462Lys	p.N1462K	ENST00000373644	NM_030625.2	1462	aaC/aaA	6/12	1	2	FACETS	0.773	0.673	0.882	0.773	0.673	0.882	SUBCLONAL	1	TRUE	1	0.27	2		465	661	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432249	432249	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	122	464	0	ENST00000399788.2:c.2274del	p.Asp759IlefsTer2	p.D759Ifs*2	ENST00000399788	NM_001042603.1	758	aaA/aa	16/28	NA	2	FACETS	1	0.934	1			1	INDETERMINATE	1	TRUE	NA	0.27	2		464	867	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201523	133201523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370305500	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	121	675	0	ENST00000320574.5:c.6715G>A	p.Ala2239Thr	p.A2239T	ENST00000320574	NM_006231.2	2239	Gcg/Acg	48/49	0.3	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.27	1		675	624	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964206	28964206	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	66	351	0	ENST00000282397.4:c.1696del	p.Met566CysfsTer8	p.M566Cfs*8	ENST00000282397	NM_002019.4	566	Atg/tg	13/30	1	2	FACETS	0.876	0.761	1	0.876	0.761	1	CLONAL	1	TRUE	1	0.27	2		351	558	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054395	42054396	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	60	472	0	ENST00000219905.7:c.7585dup	p.Arg2529LysfsTer9	p.R2529Kfs*9	ENST00000219905	NM_001164273.1	2527	caa/cAaa	22/24	1	2	FACETS	0.778	0.671	0.895	0.778	0.671	0.895	SUBCLONAL	1	TRUE	1	0.27	2		472	571	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43700281	43700281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	117	682	1	ENST00000382044.4:c.5606C>T	p.Pro1869Leu	p.P1869L	ENST00000382044	NM_001141980.1	1869	cCc/cTc	27/28	1	2	FACETS	0.893	0.804	0.987	0.893	0.804	0.987	CLONAL	1	TRUE	1	0.27	2		683	971	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248651	10248651	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1568220903	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	61	478	0	ENST00000340748.4:c.4102C>T	p.Arg1368Ter	p.R1368*	ENST00000340748		1368	Cga/Tga	35/40	0.3	1	FACETS	0.861	0.744	0.987	0.861	0.744	0.987	CLONAL	1	TRUE	0	0.27	1		478	454	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216215	36216215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1309505674	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	67	611	2	ENST00000222270.7:c.3623C>T	p.Ala1208Val	p.A1208V	ENST00000222270	NM_014727.1	1208	gCc/gTc	11/37	0.3	1	FACETS	0.743	0.646	0.848	0.743	0.646	0.848	SUBCLONAL	1	TRUE	0	0.27	1		613	578	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213317	39213317	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	174	720	1	ENST00000402219.2:c.3650G>A	p.Arg1217Gln	p.R1217Q	ENST00000402219	NM_005633.3	1217	cGa/cAa	23/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.27	2		721	1137	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104655	209104655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	99	519	0	ENST00000345146.2:c.923C>T	p.Ala308Val	p.A308V	ENST00000345146	NM_005896.2	308	gCc/gTc	8/10	1	2	FACETS	0.952	0.85	1	0.952	0.85	1	CLONAL	1	TRUE	1	0.27	2		519	770	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742793	39742793	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	81	416	0	ENST00000361337.2:c.1636C>T	p.Arg546Ter	p.R546*	ENST00000361337	NM_003286.2	546	Cga/Tga	15/21	0.3	1	FACETS	0.821	0.724	0.925	0.821	0.724	0.925	CLONAL	1	TRUE	0	0.27	1		416	632	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446201	187446201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375595181	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	126	766	1	ENST00000232014.4:c.1487C>T	p.Thr496Met	p.T496M	ENST00000232014	NM_001130845.1	496	aCg/aTg	6/10	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.27	2		767	905	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1952895	1952895	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	100	610	0	ENST00000382891.5:c.1978C>T	p.Arg660Ter	p.R660*	ENST00000382891	NM_133335.3	660	Cga/Tga	10/22	1	2	FACETS	0.912	0.814	1	0.912	0.814	1	CLONAL	1	TRUE	1	0.27	2		610	812	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157648	106157648	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs369370690	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	54	337	1	ENST00000380013.4:c.2549A>G	p.His850Arg	p.H850R	ENST00000380013	NM_001127208.2	850	cAt/cGt	3/11	1	2	FACETS	0.708	0.604	0.821	0.708	0.604	0.821	SUBCLONAL	1	TRUE	1	0.27	2		338	565	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111624	56111624	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	70	255	0	ENST00000399503.3:c.224A>C	p.Glu75Ala	p.E75A	ENST00000399503	NM_005921.1	75	gAg/gCg	1/20	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.27	2		255	497	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638499	176638499	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	122	624	4	ENST00000439151.2:c.3103del	p.Ser1035GlnfsTer5	p.S1035Qfs*5	ENST00000439151	NM_022455.4	1033	gcT/gc	5/23	0.3	1	FACETS	0.768	0.693	0.847	0.768	0.693	0.847	SUBCLONAL	1	TRUE	0	0.27	1		628	1018	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800519	32800519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376467259	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	181	782	4	ENST00000374899.4:c.1028G>A	p.Arg343His	p.R343H	ENST00000374899	NM_018833.2	343	cGc/cAc	6/12	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.27	2		786	1263	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946435	2946435	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751651073	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	89	673	0	ENST00000396946.4:c.3302G>A	p.Arg1101His	p.R1101H	ENST00000396946	NM_032415.4	1101	cGc/cAc	25/25	0.271466646313228	4	FACETS	0.966	0.855	1	0.322	0.285	0.362	CLONAL	1	TRUE	1	0.27	4		673	867	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856117	151856117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	105	480	2	ENST00000262189.6:c.11501G>A	p.Gly3834Asp	p.G3834D	ENST00000262189	NM_170606.2	3834	gGc/gAc	44/59	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.27	2		482	752	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860577	151860577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	74	509	1	ENST00000262189.6:c.10085C>T	p.Thr3362Ile	p.T3362I	ENST00000262189	NM_170606.2	3362	aCt/aTt	43/59	1	2	FACETS	0.765	0.669	0.868	0.765	0.669	0.868	SUBCLONAL	1	TRUE	1	0.27	2		510	717	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372312	55372313	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	74	638	0	ENST00000297316.4:c.1007dup	p.Pro337SerfsTer28	p.P337Sfs*28	ENST00000297316	NM_022454.3	334	-/C	2/2	1	2	FACETS	0.806	0.705	0.915	0.806	0.705	0.915	CLONAL	1	TRUE	1	0.27	2		638	680	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572621	141572621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748022421	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	49	593	0	ENST00000220592.5:c.449G>A	p.Arg150Gln	p.R150Q	ENST00000220592	NM_012154.3	150	cGg/cAg	4/19	1	2	FACETS	0.637	0.539	0.745	0.637	0.539	0.745	SUBCLONAL	1	TRUE	1	0.27	2		593	570	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737341	145737341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	121	700	1	ENST00000428558.2:c.3346C>T	p.Pro1116Ser	p.P1116S	ENST00000428558	NM_004260.3	1116	Ccg/Tcg	20/22	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.27	2		701	719	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389232	8389232	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025330-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	88	483	0	ENST00000356435.5:c.4386G>T	p.Arg1462Ser	p.R1462S	ENST00000356435		1462	agG/agT	26/35	1	2	FACETS	0.95	0.842	1	0.95	0.842	1	CLONAL	1	TRUE	1	0.27	2		483	686	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602748	10602748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025330-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	53	425	0	ENST00000171111.5:c.830C>T	p.Thr277Met	p.T277M	ENST00000171111	NM_203500.1	277	aCg/aTg	3/6	0.424890170943612	1	FACETS	0.797	0.689	0.911	0.797	0.689	0.911	CLONAL	1	TRUE	0	0.497274042912636	1		425	201	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0025330-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	68	451	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.404030108828784	1	FACETS	0.867	0.765	0.974	0.867	0.765	0.974	CLONAL	1	TRUE	0	0.497274042912636	1		451	237	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36934797	36934797	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025330-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	25	404	0	ENST00000361632.4:c.1536G>T	p.Met512Ile	p.M512I	ENST00000361632		512	atG/atT	11/16	1	2	FACETS	0.591	0.47	0.728	0.591	0.47	0.728	SUBCLONAL	1	TRUE	1	0.497274042912636	2		404	170	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888102	81888102	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025330-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	10	270	1	ENST00000359376.3:c.247G>T	p.Glu83Ter	p.E83*	ENST00000359376	NM_002661.3	83	Gag/Tag	3/33	0.497274042912636	1	FACETS	0.177	0.119	0.248	0.177	0.119	0.248	SUBCLONAL	1	TRUE	0	0.497274042912636	1		271	171	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015126	37015126	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025330-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	32	409	0	ENST00000358127.4:c.278C>G	p.Pro93Arg	p.P93R	ENST00000358127	NM_001280556.1	93	cCc/cGc	3/10	0.150466023584418	0	FACETS	0.322	0.263	0.387			1	INDETERMINATE	1	TRUE	0	0.497274042912636	0		409	201	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615080	100615080	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025330-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	31	302	0	ENST00000308731.7:c.835T>C	p.Tyr279His	p.Y279H	ENST00000308731	NM_000061.2	279	Tat/Cat	9/19	0.497274042912636	1	FACETS	0.732	0.603	0.872	0.732	0.603	0.872	SUBCLONAL	1	TRUE	0	0.497274042912636	1		302	128	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	162	333	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	0.299182403230857	3	FACETS	0.926	0.854	1	0.926	0.854	1	CLONAL	2	TRUE	1	0.34	3		333	602	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	70	690	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.298414068749304	3	FACETS	0.884	0.772	1	0.442	0.386	0.503	CLONAL	1	TRUE	1	0.34	3		690	545	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41021708	41021708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	20	161	0	ENST00000267868.3:c.650C>T	p.Ala217Val	p.A217V	ENST00000267868	NM_002875.4	217	gCa/gTa	8/10	0.299182403230857	3	FACETS	0.406	0.31	0.519	0.203	0.155	0.26	SUBCLONAL	1	TRUE	1	0.34	3		161	339	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23635339	23635339	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	61	295	0	ENST00000261584.4:c.2825G>A	p.Arg942Lys	p.R942K	ENST00000261584	NM_024675.3	942	aGa/aAa	8/13	0.299182403230857	6	FACETS	0.707	0.608	0.814	0.177	0.152	0.204	SUBCLONAL	1	TRUE	2	0.34	6		295	853	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032511	12032514	+	frameshift_variant	Frame_Shift_Del	DEL	AACT	AACT	-	novel	NA	P-0025567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	107	175	1	ENST00000353533.5:c.950_953del	p.Leu317HisfsTer4	p.L317Hfs*4	ENST00000353533	NM_003010.3	316	cAACTa/ca	9/11	0.299182403230857	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.34	2		176	289	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15960969	15960969	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	119	238	1	ENST00000268712.3:c.6251del	p.Ser2084TyrfsTer10	p.S2084Yfs*10	ENST00000268712	NM_006311.3	2084	tCa/ta	40/46	0.299182403230857	2	FACETS	0.907	0.826	0.99	0.907	0.826	0.99	CLONAL	2	TRUE	0	0.34	2		239	386	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0025686-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	144	373	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.212816395328314	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	2	0.286239071359828	4		373	598	SUCCESS
APC	324	MSKCC	GRCh37	5	112163696	112163697	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1131691555	NA	P-0025686-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	77	164	0	ENST00000257430.4:c.1620dup	p.Gln541ThrfsTer19	p.Q541Tfs*19	ENST00000257430	NM_000038.5	540	tta/ttAa	13/16	0.147892993198184	3	FACETS	0.961	0.851	1	0.641	0.567	0.718	INDETERMINATE	2	TRUE	0	0.286239071359828	3		164	320	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306559	163306559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781627921	NA	P-0025686-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	42	319	0	ENST00000271452.3:c.356G>A	p.Arg119Gln	p.R119Q	ENST00000271452	NM_145697.2	119	cGg/cAg	6/14	0.271109322267169	4	FACETS	0.645	0.538	0.765	0.323	0.269	0.383	SUBCLONAL	1	TRUE	2	0.286239071359828	4		319	585	SUCCESS
APC	324	MSKCC	GRCh37	5	112162945	112162946	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0025686-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	21	169	0	ENST00000257430.4:c.1548+2dup		p.X516_splice	ENST00000257430	NM_000038.5	516			0.147892993198184	3	FACETS	0.61	0.47	0.772	0.203	0.156	0.258	INDETERMINATE	1	TRUE	0	0.286239071359828	3		169	275	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564519	55564519	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025686-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	34	311	0	ENST00000288135.5:c.407G>C	p.Cys136Ser	p.C136S	ENST00000288135	NM_000222.2	136	tGt/tCt	3/21	1	2	FACETS	0.489	0.399	0.59	0.489	0.399	0.59	SUBCLONAL	1	TRUE	1	0.286239071359828	2		311	486	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55962496	55962496	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025686-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	21	222	0	ENST00000263923.4:c.2628C>A	p.His876Gln	p.H876Q	ENST00000263923	NM_002253.2	876	caC/caA	19/30	1	2	FACETS	0.451	0.347	0.573	0.451	0.347	0.573	SUBCLONAL	1	TRUE	1	0.286239071359828	2		222	325	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0025713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	91	273	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.94	0.834	1	0.94	0.834	1	CLONAL	1	FALSE	1	0.237572892136096	2		273	815	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0025713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	80	518	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	NA	2	FACETS	0.68	0.597	0.77			1	INDETERMINATE	1	FALSE	NA	0.237572892136096	2		518	990	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233079	69233180	+	inframe_deletion	In_Frame_Del	DEL	ATGAAATGAATCCCCCCCTTCCATCACATTGCAACAGATGTTGGGCCCTTCGTGAGAATTGGCTTCCTGAAGATAAAGGGAAAGATAAAGGGGAAATCTCTG	ATGAAATGAATCCCCCCCTTCCATCACATTGCAACAGATGTTGGGCCCTTCGTGAGAATTGGCTTCCTGAAGATAAAGGGAAAGATAAAGGGGAAATCTCTG	-	novel	NA	P-0025713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	90	430	0	ENST00000462284.1:c.945_1046del	p.Asn315_Glu349delinsLys	p.N315_E349delinsK	ENST00000462284	NM_002392.5	315	aATGAAATGAATCCCCCCCTTCCATCACATTGCAACAGATGTTGGGCCCTTCGTGAGAATTGGCTTCCTGAAGATAAAGGGAAAGATAAAGGGGAAATCTCTGag/aag	11/11	0.205293071816018	2	FACETS	1	0.949	1	0.56	0.497	0.628	CLONAL	1	FALSE	0	0.237572892136096	2		430	676	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0025736-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	142	459	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	1	2	FACETS	0.737	0.671	0.806	0.737	0.671	0.806	SUBCLONAL	1	TRUE	1	0.394463900688878	2		459	977	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341172	8341172	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025736-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	162	457	1	ENST00000356435.5:c.5044G>A	p.Glu1682Lys	p.E1682K	ENST00000356435		1682	Gaa/Aaa	30/35	1	2	FACETS	0.984	0.903	1	0.984	0.903	1	CLONAL	1	TRUE	1	0.394463900688878	2		458	835	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0025796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	97	388	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.832	0.748	0.92	1	0.985	1	CLONAL	2	TRUE	1	0.307506371301375	2		388	379	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0025796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	46	313	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.965	0.817	1	0.965	0.817	1	CLONAL	1	TRUE	1	0.307506371301375	2		313	310	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056314	27056314	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	47	275	0	ENST00000324856.7:c.1312del	p.Ala438ArgfsTer181	p.A438Rfs*181	ENST00000324856	NM_006015.4	437	cGg/cg	2/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.307506371301375	2		275	241	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779755	3779755	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	66	320	0	ENST00000262367.5:c.5293del	p.Gln1765ArgfsTer6	p.Q1765Rfs*6	ENST00000262367	NM_004380.2	1765	Cag/ag	31/31	0.208371285138502	4	FACETS	0.85	0.743	0.965	0.85	0.743	0.965	CLONAL	2	TRUE	2	0.307506371301375	4		320	330	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830285	72830285	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	26	131	0	ENST00000268489.5:c.6296C>A	p.Pro2099Gln	p.P2099Q	ENST00000268489	NM_006885.3	2099	cCg/cAg	9/10	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.307506371301375	2		131	144	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578467	7578467	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	108	470	0	ENST00000269305.4:c.463A>C	p.Thr155Pro	p.T155P	ENST00000269305	NM_001126112.2	155	Acc/Ccc	5/11	0.27983346653347	2	FACETS	0.752	0.679	0.829	0.752	0.679	0.829	SUBCLONAL	2	TRUE	0	0.307506371301375	2		470	467	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0025796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	55	279	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	0.228231779576375	3	FACETS	0.871	0.753	0.996	0.58	0.502	0.664	CLONAL	2	TRUE	0	0.307506371301375	3		279	237	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97934327	97934327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	67	249	1	ENST00000289081.3:c.448C>T	p.Leu150Phe	p.L150F	ENST00000289081	NM_000136.2	150	Ctt/Ttt	5/15	0.208371285138502	4	FACETS	0.916	0.803	1	0.916	0.803	1	CLONAL	2	TRUE	2	0.307506371301375	4		250	311	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030472	47030472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782522553	NA	P-0025796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	82	447	2	ENST00000377604.3:c.247C>T	p.Arg83Trp	p.R83W	ENST00000377604	NM_001204468.1	83	Cgg/Tgg	4/24	0.277108315145772	3	FACETS	1	0.948	1	0.567	0.5	0.637	CLONAL	1	TRUE	1	0.307506371301375	3		449	543	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191469	10191469	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs5030816	NA	P-0025849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	45	435	0	ENST00000256474.2:c.464-2A>G		p.X155_splice	ENST00000256474	NM_000551.3	155			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		435	187	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0025850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	572	528	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.734999279987748	2	FACETS	0.946	0.919	0.972	0.946	0.919	0.972	CLONAL	2	TRUE	0	0.734999279987748	2		528	823	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404911	404911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	175	503	2	ENST00000399788.2:c.4283G>A	p.Arg1428Gln	p.R1428Q	ENST00000399788	NM_001042603.1	1428	cGa/cAa	26/28	1	2	FACETS	0.531	0.489	0.575	0.531	0.489	0.575	SUBCLONAL	1	TRUE	1	0.734999279987748	2		505	897	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060696	38060697	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0025850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	421	831	0	ENST00000250448.2:c.1292_1293del	p.Ser431TyrfsTer126	p.S431Yfs*126	ENST00000250448	NM_004496.3	431	tCT/t	2/2	0.734999279987748	2	FACETS	0.949	0.905	0.994	0.475	0.452	0.497	CLONAL	1	TRUE	0	0.734999279987748	2		831	1207	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061185	38061185	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	172	274	0	ENST00000250448.2:c.804C>G	p.Cys268Trp	p.C268W	ENST00000250448	NM_004496.3	268	tgC/tgG	2/2	0.734999279987748	2	FACETS	1	0.962	1	0.526	0.489	0.564	CLONAL	1	TRUE	0	0.734999279987748	2		274	445	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847382	68847382	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	359	528	0	ENST00000261769.5:c.1307del	p.Leu436Ter	p.L436*	ENST00000261769	NM_004360.3	435	aTt/at	9/16	0.734999279987748	1	FACETS	0.973	0.933	1	0.973	0.933	1	CLONAL	1	TRUE	0	0.734999279987748	1		528	635	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177871	56177875	+	frameshift_variant	Frame_Shift_Del	DEL	AACAG	AACAG	-	novel	NA	P-0025850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	180	361	0	ENST00000399503.3:c.2845_2849del	p.Thr949AlafsTer53	p.T949Afs*53	ENST00000399503	NM_005921.1	948	acAACAGag/acag	14/20	0.607621796263348	1	FACETS	0.78	0.729	0.832	0.78	0.729	0.832	SUBCLONAL	1	TRUE	0	0.734999279987748	1		361	397	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0025852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	240	825	0	ENST00000397752.3:c.3028+1G>C		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.292306279756789	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.292306279756789	1		825	950	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31401640	31401640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561462275	NA	P-0025852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	47	495	1	ENST00000344624.3:c.4024C>T	p.Arg1342Trp	p.R1342W	ENST00000344624		1342	Cgg/Tgg	33/33	0.251319666248279	3	FACETS	0.397	0.334	0.468	0.199	0.167	0.234	SUBCLONAL	1	TRUE	1	0.292306279756789	3		496	928	SUCCESS
BTK	695	MSKCC	GRCh37	X	100614298	100614298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	44	555	0	ENST00000308731.7:c.877del	p.Gln293AsnfsTer3	p.Q293Nfs*3	ENST00000308731	NM_000061.2	293	Caa/aa	10/19	1	2	FACETS	0.343	0.287	0.406	0.343	0.287	0.406	SUBCLONAL	1	TRUE	1	0.292306279756789	2		555	877	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667366	241667366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	114	419	1	ENST00000366560.3:c.1084G>A	p.Glu362Lys	p.E362K	ENST00000366560	NM_000143.3	362	Gaa/Aaa	7/10	0.295864479394861	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.31	2		420	335	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437266	220437266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753111199	NA	P-0025857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	151	837	1	ENST00000243786.2:c.170G>A	p.Arg57Gln	p.R57Q	ENST00000243786	NM_002191.3	57	cGg/cAg	1/2	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.232485514267351	2		838	1030	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	359986	359986	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	210	632	0	ENST00000262320.3:c.1103T>G	p.Leu368Arg	p.L368R	ENST00000262320	NM_003502.3	368	cTa/cGa	4/11	0.232485514267351	5	FACETS	1	0.948	1			1	CLONAL	2	FALSE	NA	0.232485514267351	5		632	1186	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121113	11121113	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	440	665	0	ENST00000358026.2:c.2180G>T	p.Gly727Val	p.G727V	ENST00000358026	NM_001128849.1	727	gGc/gTc	15/36	0.206739224876426	3	FACETS	1	0.986	1			1	CLONAL	3	FALSE	NA	0.232485514267351	3		665	1305	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340422	8340422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376310467	NA	P-0025857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	62	486	0	ENST00000356435.5:c.5174C>T	p.Thr1725Ile	p.T1725I	ENST00000356435		1725	aCt/aTt	31/35	0.22879584083892	1	FACETS	0.709	0.612	0.815	0.709	0.612	0.815	SUBCLONAL	1	FALSE	0	0.232485514267351	1		486	665	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0025858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	84	454	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.852	0.762	0.946	0.852	0.762	0.946	CLONAL	1	TRUE	1	0.709393942912152	2		454	278	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0025858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1991	174	471	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.709393942912152	11	FACETS	0.95	0.87	1			1	CLONAL	1	TRUE	NA	0.709393942912152	11		471	2165	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115722	8115724	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0025858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	125	302	1	ENST00000346208.3:c.1072_1074del	p.Lys358del	p.K358del	ENST00000346208		356	atGAAg/atg	6/6	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.709393942912152	2		303	349	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805104	89805104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778321	NA	P-0025858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	138	334	2	ENST00000389301.3:c.4273C>T	p.Arg1425Cys	p.R1425C	ENST00000389301	NM_000135.2	1425	Cgt/Tgt	43/43	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.709393942912152	2		336	348	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	46	503	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.666	0.559	0.784	0.666	0.559	0.784	SUBCLONAL	1	TRUE	1	0.19	2		505	727	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0025860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	52	313	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.724	0.615	0.844	0.724	0.615	0.844	SUBCLONAL	1	TRUE	1	0.19	2		313	756	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046766	42046766	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0025860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	67	451	1	ENST00000219905.7:c.7139+1G>A		p.X2380_splice	ENST00000219905	NM_001164273.1	2380			1	2	FACETS	0.801	0.695	0.917	0.801	0.695	0.917	CLONAL	1	TRUE	1	0.19	2		452	880	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985802	60985802	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	38	238	0	ENST00000333681.4:c.98G>C	p.Gly33Ala	p.G33A	ENST00000333681		33	gGa/gCa	2/3	1	2	FACETS	0.922	0.762	1	0.922	0.762	1	CLONAL	1	TRUE	1	0.19	2		238	434	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406013	70406013	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	87	563	0	ENST00000373644.4:c.3529del	p.Glu1177LysfsTer15	p.E1177Kfs*15	ENST00000373644	NM_030625.2	1176	tGg/tg	4/12	1	2	FACETS	0.899	0.794	1	0.899	0.794	1	CLONAL	1	TRUE	1	0.19	2		563	1019	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508438	29508438	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1057518360	NA	P-0025860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	46	317	0	ENST00000356175.3:c.587-2A>G		p.X196_splice	ENST00000356175	NM_000267.3	196			1	2	FACETS	0.988	0.832	1	0.988	0.832	1	CLONAL	1	TRUE	1	0.19	2		317	490	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653159	29653159	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	35	269	0	ENST00000356175.3:c.5094A>G	p.Ile1698Met	p.I1698M	ENST00000356175	NM_000267.3	1698	atA/atG	36/57	1	2	FACETS	0.567	0.463	0.684	0.567	0.463	0.684	SUBCLONAL	1	TRUE	1	0.19	2		269	650	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353757	40353757	+	stop_lost	Nonstop_Mutation	SNP	C	C	A	novel	NA	P-0025860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	40	431	0	ENST00000293328.3:c.2363G>T	p.Ter788LeuextTer25	p.*788Lext*25	ENST00000293328	NM_012448.3	788	tGa/tTa	19/19	1	2	FACETS	0.547	0.453	0.652	0.547	0.453	0.652	SUBCLONAL	1	TRUE	1	0.19	2		431	770	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40864369	40864370	+	missense_variant	Missense_Mutation	DNP	CA	CA	AT	novel	NA	P-0025860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	100	578	3	ENST00000428826.2:c.1338_1339delinsAT	p.His446_Gly447delinsGlnCys	p.H446_G447delinsQC	ENST00000428826		446	caTGgc/caATgc	12/21	1	2	FACETS	0.922	0.821	1	0.922	0.821	1	CLONAL	1	TRUE	1	0.19	2		581	1142	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637960	39637960	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	95	512	0	ENST00000262039.4:c.2377G>T	p.Glu793Ter	p.E793*	ENST00000262039	NM_002647.2	793	Gag/Tag	22/25	1	2	FACETS	0.959	0.852	1	0.959	0.852	1	CLONAL	1	TRUE	1	0.19	2		512	1043	SUCCESS
ALK	238	MSKCC	GRCh37	2	29541234	29541235	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0025860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	78	486	2	ENST00000389048.3:c.1582_1583delinsTT	p.Ala528Phe	p.A528F	ENST00000389048	NM_004304.4	528	GCt/TTt	8/29	1	2	FACETS	0.915	0.803	1	0.915	0.803	1	CLONAL	1	TRUE	1	0.19	2		488	897	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43749823	43749823	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0025860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	55	284	0	ENST00000523873.1:c.676A>T	p.Arg226Ter	p.R226*	ENST00000523873		226	Aga/Tga	7/8	1	2	FACETS	0.873	0.746	1	0.873	0.746	1	CLONAL	1	TRUE	1	0.19	2		284	663	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94128986	94128986	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	67	390	0	ENST00000369303.4:c.74G>T	p.Gly25Val	p.G25V	ENST00000369303	NM_004440.3	25	gGg/gTg	1/17	1	2	FACETS	0.969	0.841	1	0.969	0.841	1	CLONAL	1	TRUE	1	0.19	2		390	728	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005209	150005209	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	36	370	1	ENST00000253339.5:c.1016A>T	p.Asn339Ile	p.N339I	ENST00000253339		339	aAc/aTc	3/7	1	2	FACETS	0.598	0.49	0.719	0.598	0.49	0.719	SUBCLONAL	1	TRUE	1	0.19	2		371	634	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222749	53222749	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	91	658	0	ENST00000375401.3:c.4187G>T	p.Arg1396Leu	p.R1396L	ENST00000375401	NM_004187.3	1396	cGg/cTg	25/26	1	2	FACETS	0.928	0.822	1	0.928	0.822	1	CLONAL	1	TRUE	1	0.19	2		658	1032	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410463	63410463	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	67	525	0	ENST00000330258.3:c.2704C>A	p.Leu902Met	p.L902M	ENST00000330258	NM_152424.3	902	Ctg/Atg	2/2	1	2	FACETS	0.805	0.698	0.922	0.805	0.698	0.922	CLONAL	1	TRUE	1	0.19	2		525	876	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410537	63410537	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	80	541	0	ENST00000330258.3:c.2630G>T	p.Gly877Val	p.G877V	ENST00000330258	NM_152424.3	877	gGc/gTc	2/2	1	2	FACETS	0.873	0.766	0.987	0.873	0.766	0.987	CLONAL	1	TRUE	1	0.19	2		541	965	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206815	36206816	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0025944-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	48	566	0	ENST00000300305.3:c.696dup	p.Arg233AlafsTer28	p.R233Afs*28	ENST00000300305		232	-/G	6/8	1	2	FACETS	0.185	0.156	0.217	0.185	0.156	0.217	SUBCLONAL	1	TRUE	1	0.717659619506247	2		566	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0025947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	142	322	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	0.965	0.895	1			1	INDETERMINATE	2	TRUE	NA	0.48094162267723	2		322	306	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0025947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	129	334	2	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.451139512139756	3	FACETS	0.79	0.723	0.86	0.79	0.723	0.86	SUBCLONAL	2	TRUE	1	0.48094162267723	3		336	421	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0025947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	109	322	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	0.346198979187538	5	FACETS	0.938	0.848	1	0.625	0.565	0.688	CLONAL	2	TRUE	2	0.48094162267723	5		322	416	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206647680	206647680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs549538401	NA	P-0025947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	74	346	0	ENST00000367120.3:c.94G>A	p.Gly32Arg	p.G32R	ENST00000367120	NM_014002.3	32	Gga/Aga	4/22	0.48094162267723	4	FACETS	1	0.971	1	0.452	0.399	0.509	CLONAL	1	TRUE	1	0.48094162267723	4		346	336	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396528	30396528	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	19	458	0	ENST00000331968.5:c.191T>A	p.Leu64Gln	p.L64Q	ENST00000331968	NM_002742.2	64	cTg/cAg	1/18	0.451139512139756	3	FACETS	0.308	0.234	0.396	0.154	0.117	0.198	SUBCLONAL	1	TRUE	1	0.48094162267723	3		458	318	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482815	67482815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	208	468	0	ENST00000327367.4:c.1219C>T	p.Leu407Phe	p.L407F	ENST00000327367	NM_005902.3	407	Ctt/Ttt	9/9	0.48094162267723	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.48094162267723	2		468	386	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244068	5244068	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747170106	NA	P-0025947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	179	634	1	ENST00000357368.4:c.1414G>A	p.Val472Met	p.V472M	ENST00000357368	NM_002850.3	472	Gtg/Atg	11/38	0.477498080863715	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.48094162267723	3		635	435	SUCCESS
ALK	238	MSKCC	GRCh37	2	29419706	29419706	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	55	404	0	ENST00000389048.3:c.4094G>T	p.Cys1365Phe	p.C1365F	ENST00000389048	NM_004304.4	1365	tGc/tTc	28/29	0.48094162267723	3	FACETS	0.72	0.618	0.831	0.36	0.309	0.416	SUBCLONAL	1	TRUE	1	0.48094162267723	3		404	394	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468364	89468364	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	61	204	0	ENST00000336596.2:c.1898G>T	p.Gly633Val	p.G633V	ENST00000336596	NM_005233.5	633	gGa/gTa	11/17	0.41066057015693	4	FACETS	0.87	0.761	0.984	0.87	0.761	0.984	CLONAL	2	TRUE	2	0.48094162267723	4		204	216	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186834	142186834	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	19	366	0	ENST00000350721.4:c.6629A>C	p.Lys2210Thr	p.K2210T	ENST00000350721	NM_001184.3	2210	aAg/aCg	39/47	0.41066057015693	4	FACETS	0.325	0.246	0.418	0.163	0.123	0.209	SUBCLONAL	1	TRUE	2	0.48094162267723	4		366	360	SUCCESS
APC	324	MSKCC	GRCh37	5	112173622	112173623	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0025947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	141	270	0	ENST00000257430.4:c.2333dup	p.Asn778LysfsTer10	p.N778Kfs*10	ENST00000257430	NM_000038.5	777	-/A	16/16	0.346198979187538	5	FACETS	0.867	0.799	0.937	0.867	0.799	0.937	CLONAL	3	TRUE	2	0.48094162267723	5		270	388	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15838412	15838412	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	128	193	0	ENST00000307771.7:c.910G>A	p.Val304Met	p.V304M	ENST00000307771	NM_005089.3	304	Gtg/Atg	10/11	0.36097173620345	2	FACETS	1	0.986	1			1	CLONAL	2	TRUE	NA	0.48094162267723	2		193	213	SUCCESS
APC	324	MSKCC	GRCh37	5	112173625	112173625	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	149	269	0	ENST00000257430.4:c.2334T>A	p.Asn778Lys	p.N778K	ENST00000257430	NM_000038.5	778	aaT/aaA	16/16	0.346198979187538	5	FACETS	0.916	0.847	0.987	0.916	0.847	0.987	CLONAL	3	TRUE	2	0.48094162267723	5		269	388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0025950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	536	632	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.48616921651964	4	FACETS	0.981	0.951	1			1	CLONAL	4	TRUE	NA	0.48616921651964	4		632	835	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031883	26031884	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs758780418	NA	P-0025950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	29	146	0	ENST00000244661.2:c.405_406del	p.Arg135SerfsTer12	p.R135Sfs*12	ENST00000244661	NM_003537.3	135	agAGcg/agcg	1/1	0.421427820583205	4	FACETS	0.836	0.676	1	0.279	0.225	0.339	CLONAL	1	TRUE	1	0.48616921651964	4		146	212	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784049	9784051	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0025950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	51	424	0	ENST00000377346.4:c.2620_2622del	p.Glu874del	p.E874del	ENST00000377346	NM_005026.3	873	GAG/-	21/24	0.381789316949705	4	FACETS	0.407	0.345	0.476	0.204	0.172	0.238	SUBCLONAL	1	TRUE	2	0.48616921651964	4		424	766	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911591	114911591	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	38	432	0	ENST00000543371.1:c.1109C>G	p.Ala370Gly	p.A370G	ENST00000543371	NM_001198531.1	370	gCt/gGt	10/14	0.48616921651964	3	FACETS	0.269	0.222	0.323	0.09	0.074	0.108	SUBCLONAL	1	TRUE	0	0.48616921651964	3		432	722	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392694	118392694	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	146	334	0	ENST00000534358.1:c.11726A>G	p.Asn3909Ser	p.N3909S	ENST00000534358	NM_005933.3	3909	aAt/aGt	36/36	0.284140811774556	5	FACETS	0.888	0.814	0.965	0.592	0.542	0.643	INDETERMINATE	2	TRUE	2	0.48616921651964	5		334	585	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851780	134851780	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	54	392	0	ENST00000398015.3:c.1186C>A	p.Leu396Met	p.L396M	ENST00000398015	NM_004441.4	396	Ctg/Atg	5/16	0.381789316949705	4	FACETS	0.555	0.473	0.644	0.277	0.236	0.322	SUBCLONAL	1	TRUE	2	0.48616921651964	4		392	595	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	87	503	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.94	0.833	1	0.94	0.833	1	CLONAL	1	TRUE	1	0.294676443604757	2		505	628	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0025951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	125	530	2	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.294676443604757	1	FACETS	0.923	0.835	1	0.923	0.835	1	CLONAL	1	TRUE	0	0.294676443604757	1		532	784	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41197783	41197783	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs273902776	NA	P-0025951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	61	489	1	ENST00000357654.3:c.5504G>A	p.Arg1835Gln	p.R1835Q	ENST00000357654	NM_007294.3	1835	cGa/cAa	23/23	1	2	FACETS	0.523	0.45	0.603	0.523	0.45	0.603	SUBCLONAL	1	TRUE	1	0.294676443604757	2		490	791	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397740	49397740	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	121	529	0	ENST00000418115.1:c.484A>G	p.Lys162Glu	p.K162E	ENST00000418115	NM_001664.2	162	Aag/Gag	5/5	1	2	FACETS	0.94	0.848	1	0.94	0.848	1	CLONAL	1	TRUE	1	0.294676443604757	2		529	874	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547329	106547329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	94	425	1	ENST00000369096.4:c.566C>T	p.Pro189Leu	p.P189L	ENST00000369096	NM_001198.3	189	cCc/cTc	4/7	0.294676443604757	1	FACETS	0.869	0.774	0.97	0.869	0.774	0.97	CLONAL	1	TRUE	0	0.294676443604757	1		426	626	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223487	53223487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	114	441	2	ENST00000375401.3:c.3872G>A	p.Arg1291His	p.R1291H	ENST00000375401	NM_004187.3	1291	cGc/cAc	23/26	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.294676443604757	2		443	702	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0025956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	93	388	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.138436712671016	4	FACETS	1	0.979	1	0.736	0.655	0.821	INDETERMINATE	1	TRUE	2	0.273766869764127	4		388	588	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0025956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	123	479	0	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.183719604481846	2	FACETS	1	0.984	1	0.731	0.662	0.802	CLONAL	1	TRUE	0	0.273766869764127	2		479	615	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602584	10602584	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	118	471	0	ENST00000171111.5:c.994G>A	p.Gly332Ser	p.G332S	ENST00000171111	NM_203500.1	332	Ggc/Agc	3/6	0.183719604481846	2	FACETS	1	0.98	1	0.672	0.608	0.74	CLONAL	1	TRUE	0	0.273766869764127	2		471	641	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735560	40735560	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	93	349	0	ENST00000373198.4:c.3313G>T	p.Ala1105Ser	p.A1105S	ENST00000373198	NM_133170.3	1105	Gct/Tct	25/32	0.183719604481846	2	FACETS	1	0.979	1	0.721	0.644	0.803	CLONAL	1	TRUE	0	0.273766869764127	2		349	471	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113836	11113836	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0025956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	74	441	0	ENST00000358026.2:c.1943+1G>A		p.X648_splice	ENST00000358026	NM_001128849.1	648			0.183719604481846	2	FACETS	1	0.959	1	0.607	0.534	0.686	CLONAL	1	TRUE	0	0.273766869764127	2		441	445	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755607	39755607	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0025956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	94	371	0	ENST00000288319.7:c.1158C>G	p.Tyr386Ter	p.Y386*	ENST00000288319	NM_182918.3	386	taC/taG	10/10	0.138436712671016	4	FACETS	1	0.98	1	0.749	0.668	0.835	INDETERMINATE	1	TRUE	2	0.273766869764127	4		371	584	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0025957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	295	326	2	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.868013696515931	2		328	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0025957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	384	588	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.868013696515931	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.868013696515931	1		588	488	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870845	12870846	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0025957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	156	151	0	ENST00000228872.4:c.74dup	p.Pro26AlafsTer99	p.P26Afs*99	ENST00000228872	NM_004064.3	24	-/A	1/3	0.868735111897296	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.868013696515931	1		151	196	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863582	68863582	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1060501248	NA	P-0025957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	416	552	0	ENST00000261769.5:c.2324del	p.Gly775AlafsTer8	p.G775Afs*8	ENST00000261769	NM_004360.3	774	aGg/ag	15/16	0.868013696515931	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.868013696515931	1		552	538	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680915	30680915	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	207	542	4	ENST00000376406.3:c.804G>T	p.Arg268Ser	p.R268S	ENST00000376406	NM_014641.2	268	agG/agT	5/15	1	2	FACETS	0.505	0.469	0.543	0.505	0.469	0.543	SUBCLONAL	1	TRUE	1	0.868013696515931	2		546	944	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025972-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	76	474	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.764	0.671	0.864	0.764	0.671	0.864	SUBCLONAL	1	TRUE	1	0.368304277726688	2		474	540	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57567467	57567467	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025972-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	114	428	0	ENST00000316660.6:c.58G>T	p.Glu20Ter	p.E20*	ENST00000316660	NM_021127.2	20	Gag/Tag	1/2	1	2	FACETS	0.986	0.889	1	0.986	0.889	1	CLONAL	1	TRUE	1	0.368304277726688	2		428	628	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045656	26045656	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025972-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	53	269	0	ENST00000540144.1:c.18A>C	p.Gln6His	p.Q6H	ENST00000540144	NM_003531.2	6	caA/caC	1/1	1	2	FACETS	0.682	0.583	0.79	0.682	0.583	0.79	SUBCLONAL	1	TRUE	1	0.368304277726688	2		269	422	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211083	+	missense_variant	Missense_Mutation	ONP	GAGG	GAGG	AAGC	novel	NA	P-0025972-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12569	786	630	1	ENST00000275493.2:c.323_326delinsAAGC	p.Arg108_Gly109delinsLysAla	p.R108_G109delinsKA	ENST00000275493	NM_005228.3	108	aGAGGa/aAAGCa	3/28	0.368304277726688	28	FACETS	0.925	0.887	0.964			1	CLONAL	2	TRUE	NA	0.368304277726688	28		631	13355	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119789	70119789	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	95	574	0	ENST00000245479.2:c.791G>C	p.Arg264Thr	p.R264T	ENST00000245479	NM_000346.3	264	aGa/aCa	3/3	0.409315151382085	3	FACETS	0.421	0.373	0.472	0.21	0.186	0.236	SUBCLONAL	1	TRUE	1	0.422625411642155	3		574	1294	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176132122	176132122	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	142	403	0	ENST00000367669.3:c.645T>G	p.Asn215Lys	p.N215K	ENST00000367669	NM_022457.5	215	aaT/aaG	5/20	1	2	FACETS	0.864	0.788	0.943	0.864	0.788	0.943	CLONAL	1	TRUE	1	0.422625411642155	2		403	778	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374837	118374837	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	52	323	1	ENST00000534358.1:c.8230C>A	p.Pro2744Thr	p.P2744T	ENST00000534358	NM_005933.3	2744	Cca/Aca	27/36	0.414000017561723	1	FACETS	0.477	0.407	0.553	0.477	0.407	0.553	SUBCLONAL	1	TRUE	0	0.422625411642155	1		324	407	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610560	81610560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	41	312	0	ENST00000298171.2:c.2158C>T	p.Gln720Ter	p.Q720*	ENST00000298171	NM_000369.2	720	Cag/Tag	10/10	0.414000017561723	1	FACETS	0.328	0.273	0.389	0.328	0.273	0.389	SUBCLONAL	1	TRUE	0	0.422625411642155	1		312	467	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126084	2126084	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1060504116	NA	P-0026031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	140	673	1	ENST00000219476.3:c.2655C>G	p.Ile885Met	p.I885M	ENST00000219476	NM_000548.3	885	atC/atG	24/42	1	2	FACETS	0.547	0.497	0.6	0.547	0.497	0.6	SUBCLONAL	1	TRUE	1	0.422625411642155	2		674	1211	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761202	59761202	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1296	174	585	0	ENST00000259008.2:c.3205C>T	p.Gln1069Ter	p.Q1069*	ENST00000259008	NM_032043.2	1069	Caa/Taa	20/20	0.233658724527796	6	FACETS	1	0.943	1			1	INDETERMINATE	1	TRUE	NA	0.422625411642155	6		585	1470	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536262	41536262	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0026031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	75	427	0	ENST00000263253.7:c.1878+1G>A		p.X626_splice	ENST00000263253	NM_001429.3	626			1	2	FACETS	0.441	0.386	0.501	0.441	0.386	0.501	SUBCLONAL	1	TRUE	1	0.422625411642155	2		427	804	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22008941	22008941	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	84	472	0	ENST00000276925.6:c.12G>C	p.Glu4Asp	p.E4D	ENST00000276925	NM_004936.3	4	gaG/gaC	1/2	0.422625411642155	1	FACETS	0.434	0.383	0.488	0.434	0.383	0.488	SUBCLONAL	1	TRUE	0	0.422625411642155	1		472	723	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930636	32930637	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCTTTCCA	novel	NA	P-0026032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	76	413	0	ENST00000380152.3:c.7508_7515dup	p.Gln2506SerfsTer21	p.Q2506Sfs*21	ENST00000380152		2503	gtc/gTCTTTCCAtc	15/27	0.486340503660891	1	FACETS	0.528	0.465	0.595	0.528	0.465	0.595	SUBCLONAL	1	TRUE	0	0.493793450576382	1		413	439	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554505	63554505	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1567769335	NA	P-0026032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	79	485	0	ENST00000307078.5:c.234G>A	p.Trp78Ter	p.W78*	ENST00000307078	NM_004655.3	78	tgG/tgA	2/11	0.480871810292122	3	FACETS	0.877	0.774	0.986	0.438	0.387	0.493	CLONAL	1	TRUE	1	0.493793450576382	3		485	455	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204737453	204737453	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	140	518	0	ENST00000302823.3:c.590C>G	p.Thr197Arg	p.T197R	ENST00000302823	NM_005214.4	197	aCa/aGa	4/4	0.192915584002133	3	FACETS	1	0.977	1	0.6	0.549	0.654	INDETERMINATE	1	TRUE	1	0.493793450576382	3		518	589	SUCCESS
AR	367	MSKCC	GRCh37	X	66765090	66765090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1027110412	NA	P-0026032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	28	614	0	ENST00000374690.3:c.102C>G	p.Ile34Met	p.I34M	ENST00000374690	NM_000044.3	34	atC/atG	1/8	1	2	FACETS	0.249	0.199	0.307	0.249	0.199	0.307	SUBCLONAL	1	TRUE	1	0.493793450576382	2		614	455	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0026033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	196	497	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.167700275703608	5	FACETS	0.94	0.87	1	0.94	0.87	1	CLONAL	3	TRUE	2	0.167700275703608	5		497	1037	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0026033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	165	716	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.204387785168531	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.167700275703608	3		716	901	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	86	474	0				ENST00000310581	NM_198253.2	-/1132			0.327798796298623	1	FACETS	0.529	0.476	0.582	0.529	0.476	0.582	INDETERMINATE	1	TRUE	0	0.848042841461145	1		474	221	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916726	178916726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772110575	NA	P-0026034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	15	409	0	ENST00000263967.3:c.113G>A	p.Arg38His	p.R38H	ENST00000263967	NM_006218.2	38	cGt/cAt	2/21	1	2	FACETS	0.087	0.063	0.116	0.087	0.063	0.116	SUBCLONAL	1	TRUE	1	0.848042841461145	2		409	405	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152864479	152864480	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	15	60	0	ENST00000406277.2:c.48_49insT	p.Gly17TrpfsTer39	p.G17Wfs*39	ENST00000406277	NM_152274.4	16	-/T	2/7	0.668077864430608		FACETS		0.667	1				CLONAL	1	TRUE	1	0.848042841461145	3		60	57	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0026036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	360	503	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.633902602800426	3	FACETS	0.949	0.905	0.993	0.949	0.905	0.993	CLONAL	2	TRUE	1	0.633902602800426	3		505	788	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0026036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	591	632	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.618625131590844	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.633902602800426	2		632	903	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226859	2226879	+	inframe_deletion	In_Frame_Del	DEL	GCGGCGTCCTCCGCAGGCGGC	GCGGCGTCCTCCGCAGGCGGC	-	rs748637415	NA	P-0026036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	92	387	0	ENST00000398665.3:c.4353_4373del	p.Gly1452_Ala1458del	p.G1452_A1458del	ENST00000398665	NM_032482.2	1447	GCGGCGTCCTCCGCAGGCGGC/-	27/28	0.633902602800426	1	FACETS	0.529	0.473	0.587	0.529	0.473	0.587	SUBCLONAL	1	TRUE	0	0.633902602800426	1		387	375	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932084	39932085	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1394942244	NA	P-0026036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	224	549	1	ENST00000378444.4:c.2514dup	p.Lys839GlnfsTer5	p.K839Qfs*5	ENST00000378444	NM_001123385.1	838	-/C	4/15	1	2	FACETS	0.899	0.84	0.96	0.899	0.84	0.96	CLONAL	1	TRUE	1	0.633902602800426	2		550	786	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004254	29004254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143093353	NA	P-0026036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	201	296	0	ENST00000282397.4:c.1039G>A	p.Val347Ile	p.V347I	ENST00000282397	NM_002019.4	347	Gta/Ata	8/30	0.310357562103257	3	FACETS	0.752	0.703	0.803	0.752	0.703	0.803	INDETERMINATE	2	TRUE	1	0.633902602800426	3		296	555	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440948	56440948	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	388	452	1	ENST00000407977.2:c.389G>T	p.Gly130Val	p.G130V	ENST00000407977		130	gGt/gTt	4/10	0.618625131590844	2	FACETS	0.961	0.924	0.997	0.961	0.924	0.997	CLONAL	2	TRUE	0	0.633902602800426	2		453	637	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123721	11123721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	205	504	1	ENST00000358026.2:c.2371G>A	p.Ala791Thr	p.A791T	ENST00000358026	NM_001128849.1	791	Gcg/Acg	16/36	0.633902602800426	1	FACETS	0.928	0.87	0.986	0.928	0.87	0.986	CLONAL	1	TRUE	0	0.633902602800426	1		505	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0026038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	495	322	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.59785487996896	2	FACETS	0.948	0.917	0.978	0.948	0.917	0.978	CLONAL	2	TRUE	0	0.681078297876793	2		322	767	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0026038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	272	334	2	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.342127595911176	2	FACETS	1	0.992	1	0.651	0.616	0.687	INDETERMINATE	1	TRUE	0	0.681078297876793	2		336	613	SUCCESS
APC	324	MSKCC	GRCh37	5	112174359	112174359	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	173	203	0	ENST00000257430.4:c.3068del	p.Thr1023AsnfsTer3	p.T1023Nfs*3	ENST00000257430	NM_000038.5	1023	aCa/aa	16/16	0.663643976468093	2	FACETS	0.894	0.843	0.944	0.894	0.843	0.944	CLONAL	2	TRUE	0	0.681078297876793	2		203	284	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578490	7578490	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1453167097	NA	P-0026039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	603	831	0	ENST00000269305.4:c.440T>G	p.Val147Gly	p.V147G	ENST00000269305	NM_001126112.2	147	gTt/gGt	5/11	0.760907572832257	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	FALSE	0	0.763005345097804	2		831	743	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716326	52716326	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	570	485	0	ENST00000322088.6:c.770G>T	p.Trp257Leu	p.W257L	ENST00000322088	NM_014225.5	257	tGg/tTg	6/15	0.634745193795267	5	FACETS	1	0.995	1			1	CLONAL	3	FALSE	NA	0.763005345097804	5		485	919	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626796	14626796	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1327285879	NA	P-0026039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1683	230	524	0	ENST00000254322.2:c.979C>T	p.Pro327Ser	p.P327S	ENST00000254322	NM_006145.1	327	Ccc/Tcc	3/3	0.763005345097804	9	FACETS	1	0.981	1	0.193	0.179	0.208	CLONAL	1	FALSE	3	0.763005345097804	9		524	1913	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593270	67593273	+	frameshift_variant	Frame_Shift_Del	DEL	AAAC	AAAC	-	novel	NA	P-0026039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	169	265	0	ENST00000274335.5:c.2019_2022del	p.Asn673LysfsTer18	p.N673Kfs*18	ENST00000274335		672	atAAAC/at	15/15	0.760907572832257	4	FACETS	0.962	0.895	1			1	CLONAL	2	FALSE	NA	0.763005345097804	4		265	406	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589563	67589591	+	protein_altering_variant	In_Frame_Del	DEL	TGAAGCTGTAGGGAAAAAATTACATGAAT	TGAAGCTGTAGGGAAAAAATTACATGAAT	ATTCA	novel	NA	P-0026039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	34	252	0	ENST00000274335.5:c.1326_1354delinsATTCA	p.Glu443_Tyr452delinsPheAsn	p.E443_Y452delinsFN	ENST00000274335		442	atTGAAGCTGTAGGGAAAAAATTACATGAATat/atATTCAat	10/15	0.760907572832257	4	FACETS	0.657	0.54	0.787			1	SUBCLONAL	1	FALSE	NA	0.763005345097804	4		252	239	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0026055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	977	379	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.793974312557195	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.793974312557195	2		379	1192	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434614	110434614	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781421239	NA	P-0026055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	305	757	1	ENST00000375856.3:c.3787G>A	p.Gly1263Arg	p.G1263R	ENST00000375856	NM_003749.2	1263	Ggg/Agg	1/2	1	2	FACETS	0.568	0.534	0.602	0.568	0.534	0.602	SUBCLONAL	1	TRUE	1	0.793974312557195	2		758	1353	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853257	68853321	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTGGACAGGGAGGATTTTGAGCACGTGAAGAACAGCACGTACACAGCCCTAATCATAGCTACA	AGCTGGACAGGGAGGATTTTGAGCACGTGAAGAACAGCACGTACACAGCCCTAATCATAGCTACA	CGCTTCTTCAGTTATATGGTTACTTCC	novel	NA	P-0026055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	232	640	4	ENST00000261769.5:c.1640_1704delinsCGCTTCTTCAGTTATATGGTTACTTCC	p.Glu547AlafsTer28	p.E547Afs*28	ENST00000261769	NM_004360.3	547	gAGCTGGACAGGGAGGATTTTGAGCACGTGAAGAACAGCACGTACACAGCCCTAATCATAGCTACA/gCGCTTCTTCAGTTATATGGTTACTTCC	11/16	0.793974312557195	1	FACETS	0.788	0.746	0.831	0.788	0.746	0.831	SUBCLONAL	1	TRUE	0	0.793974312557195	1		644	447	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412890	49412890	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	448	718	0	ENST00000418115.1:c.133G>C	p.Asp45His	p.D45H	ENST00000418115	NM_001664.2	45	Gat/Cat	2/5	1	2	FACETS	0.875	0.836	0.916	0.875	0.836	0.916	CLONAL	1	TRUE	1	0.793974312557195	2		718	1289	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190897	185190897	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1357	80	757	1	ENST00000265026.3:c.1778G>T	p.Gly593Val	p.G593V	ENST00000265026	NM_004721.4	593	gGg/gTg	11/14	0.793974312557195	2	FACETS	0.14	0.123	0.159	0.07	0.061	0.08	SUBCLONAL	1	TRUE	0	0.793974312557195	2		758	1437	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111518	56111518	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1292090378	NA	P-0026055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	97	95	0	ENST00000399503.3:c.118G>T	p.Ala40Ser	p.A40S	ENST00000399503	NM_005921.1	40	Gcc/Tcc	1/20	0.39437078954161	1	FACETS	0.982	0.911	1	0.982	0.911	1	INDETERMINATE	1	TRUE	0	0.793974312557195	1		95	150	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0026056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	125	668	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.343463435636586	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	4	FALSE	0	0.429694744442022	4		668	192	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245694	46245694	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	40	520	0	ENST00000334344.6:c.3788T>C	p.Ile1263Thr	p.I1263T	ENST00000334344	NM_152641.2	1263	aTt/aCt	15/21	0.429694744442022	4	FACETS	0.89	0.743	1	0.223	0.185	0.263	CLONAL	1	FALSE	0	0.429694744442022	4		520	299	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105565	30105565	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	53	598	0	ENST00000331968.5:c.1121A>G	p.Glu374Gly	p.E374G	ENST00000331968	NM_002742.2	374	gAg/gGg	7/18	0.429694744442022	6	FACETS	1	0.956	1	0.33	0.282	0.381	CLONAL	1	FALSE	2	0.429694744442022	6		598	348	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386340	31386340	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	45	686	0	ENST00000328111.2:c.1565G>A	p.Trp522Ter	p.W522*	ENST00000328111	NM_006892.3	522	tGg/tAg	15/23	0.429694744442022	10	FACETS	1	0.917	1	0.191	0.16	0.225	CLONAL	1	FALSE	4	0.429694744442022	10		686	496	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0026057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	277	528	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.355573545463528	2	FACETS	1	0.986	1	1	0.997	1	CLONAL	5	TRUE	0	0.355573545463528	2		528	307	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0026057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	217	568	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.355573545463528	1	FACETS	0.836	0.79	0.882	1	0.995	1	CLONAL	3	TRUE	0	0.355573545463528	1		568	400	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0026057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	98	363	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	1	0.967	1	1	0.989	1	CLONAL	2	TRUE	1	0.355573545463528	2		363	241	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540493	187540493	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	64	328	0	ENST00000441802.2:c.7247A>T	p.Asp2416Val	p.D2416V	ENST00000441802	NM_005245.3	2416	gAt/gTt	10/27	1	2	FACETS	0.891	0.785	1	1	0.98	1	CLONAL	2	TRUE	1	0.355573545463528	2		328	202	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0026057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	135	528	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	NA	2	FACETS	1	0.939	1			1	INDETERMINATE	1	TRUE	NA	0.533396911858181	2		528	490	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0026057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	89	568	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.606	0.538	0.677	0.606	0.538	0.677	SUBCLONAL	1	TRUE	1	0.533396911858181	2		568	551	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0026057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	72	363	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.53	0.464	0.601	0.53	0.464	0.601	SUBCLONAL	1	TRUE	1	0.533396911858181	2		363	509	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817765	3817765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746263232	NA	P-0026057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	175	597	1	ENST00000262367.5:c.3206G>A	p.Gly1069Asp	p.G1069D	ENST00000262367	NM_004380.2	1069	gGc/gAc	16/31	1	2	FACETS	0.703	0.648	0.761	0.703	0.648	0.761	SUBCLONAL	1	TRUE	1	0.533396911858181	2		598	933	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540493	187540493	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	93	328	0	ENST00000441802.2:c.7247A>T	p.Asp2416Val	p.D2416V	ENST00000441802	NM_005245.3	2416	gAt/gTt	10/27	0.124497333045444	4	FACETS	0.983	0.876	1	0.491	0.438	0.548	INDETERMINATE	1	TRUE	2	0.533396911858181	4		328	544	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0026059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	73	313	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.278383507616229	1	FACETS	0.391	0.343	0.442	0.391	0.343	0.442	INDETERMINATE	1	TRUE	0	0.581231730770859	1		313	456	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0026059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	182	496	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.522163131136169	1	FACETS	0.989	0.923	1	0.989	0.923	1	CLONAL	1	TRUE	0	0.581231730770859	1		496	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0026059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	186	606	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.571349439653909	1	FACETS	0.95	0.886	1	0.95	0.886	1	CLONAL	1	TRUE	0	0.581231730770859	1		606	478	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186501406	186501406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	112	252	0	ENST00000323963.5:c.7G>A	p.Gly3Ser	p.G3S	ENST00000323963		3	Ggt/Agt	1/11	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.581231730770859	2		252	375	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100301	27100301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	204	670	3	ENST00000324856.7:c.4013C>T	p.Ser1338Phe	p.S1338F	ENST00000324856	NM_006015.4	1338	tCc/tTc	17/20	1	2	FACETS	0.889	0.826	0.953	0.889	0.826	0.953	CLONAL	1	TRUE	1	0.581231730770859	2		673	790	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100430	8100430	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs770601456	NA	P-0026059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	107	817	0	ENST00000346208.3:c.404C>A	p.Pro135Gln	p.P135Q	ENST00000346208		135	cCg/cAg	3/6	0.302691791791699	1	FACETS	0.433	0.389	0.48	0.433	0.389	0.48	INDETERMINATE	1	TRUE	0	0.581231730770859	1		817	603	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427690	72427690	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	126	373	0	ENST00000477973.2:c.800G>T	p.Arg267Leu	p.R267L	ENST00000477973	NM_012234.5	267	cGc/cTc	4/4	1	2	FACETS	0.872	0.794	0.953	0.872	0.794	0.953	CLONAL	1	TRUE	1	0.581231730770859	2		373	497	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005533	150005533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	194	375	0	ENST00000253339.5:c.692G>A	p.Gly231Glu	p.G231E	ENST00000253339		231	gGa/gAa	3/7	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	2	FALSE	NA	0.3	2		375	572	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681762	78681762	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs778786780	NA	P-0026061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	24	725	0	ENST00000306801.3:c.470G>T	p.Arg157Leu	p.R157L	ENST00000306801	NM_020761.2	157	cGg/cTg	4/34	1	2	FACETS	0.349	0.272	0.437	0.349	0.272	0.437	SUBCLONAL	1	FALSE	1	0.3	2		725	459	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004358	150004358	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	221	427	0	ENST00000253339.5:c.1867G>C	p.Asp623His	p.D623H	ENST00000253339		623	Gat/Cat	3/7	NA	2	FACETS	1	0.936	1			1	INDETERMINATE	2	FALSE	NA	0.3	2		427	735	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004424	150004424	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	247	462	0	ENST00000253339.5:c.1801G>C	p.Asp601His	p.D601H	ENST00000253339		601	Gat/Cat	3/7	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	2	FALSE	NA	0.3	2		462	754	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004621	150004621	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	282	532	0	ENST00000253339.5:c.1604G>T	p.Gly535Val	p.G535V	ENST00000253339		535	gGa/gTa	3/7	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	2	FALSE	NA	0.3	2		532	829	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005278	150005278	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	265	426	0	ENST00000253339.5:c.947G>T	p.Gly316Val	p.G316V	ENST00000253339		316	gGa/gTa	3/7	NA	2	FACETS	0.858	0.81	0.908			1	INDETERMINATE	3	FALSE	NA	0.3	2		426	686	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005678	150005678	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	221	383	0	ENST00000253339.5:c.547G>C	p.Glu183Gln	p.E183Q	ENST00000253339		183	Gaa/Caa	3/7	NA	2	FACETS	0.837	0.784	0.89			1	INDETERMINATE	3	FALSE	NA	0.3	2		383	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0026062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	789	711	0	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	0.727705334494674	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.727705334494674	2		711	1039	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	100	474	0				ENST00000310581	NM_198253.2	-/1132			0.201760953677037	3	FACETS	1	0.961	1	0.578	0.517	0.642	INDETERMINATE	1	TRUE	1	0.357377712759169	3		474	571	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0026063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	15	454	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.201760953677037	3	FACETS	0.664	0.488	0.872	0.332	0.244	0.436	INDETERMINATE	1	TRUE	1	0.357377712759169	3		454	149	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0026063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	65	407	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	0.201760953677037	3	FACETS	1	0.933	1	0.557	0.485	0.634	INDETERMINATE	1	TRUE	1	0.357377712759169	3		407	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	99	766	0	ENST00000269305.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	336	Gag/Tag	10/11	1	2	FACETS	0.888	0.794	0.988	0.888	0.794	0.988	CLONAL	1	TRUE	1	0.357377712759169	2		766	624	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121266	29121266	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730881701	NA	P-0026063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	111	826	1	ENST00000328354.6:c.409C>T	p.Arg137Ter	p.R137*	ENST00000328354	NM_007194.3	137	Cga/Tga	3/15	0.24217192177245	3	FACETS	0.817	0.739	0.899	0.545	0.493	0.599	CLONAL	2	TRUE	0	0.357377712759169	3		827	448	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420277	49420277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	117	690	0	ENST00000301067.7:c.15472G>A	p.Glu5158Lys	p.E5158K	ENST00000301067	NM_003482.3	5158	Gag/Aag	48/54	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.357377712759169	2		690	622	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803117	1803117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1330260382	NA	P-0026063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	119	858	0	ENST00000260795.2:c.469G>A	p.Glu157Lys	p.E157K	ENST00000260795		157	Gag/Aag	4/17	0.357377712759169	1	FACETS	0.699	0.631	0.77	0.699	0.631	0.77	SUBCLONAL	1	TRUE	0	0.357377712759169	1		858	783	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491366	2491366	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	128	951	4	ENST00000355716.4:c.409G>T	p.Ala137Ser	p.A137S	ENST00000355716	NM_003820.2	137	Gcg/Tcg	4/8	0.234600781187368	3	FACETS	1	0.914	1			1	CLONAL	1	TRUE	NA	0.357377712759169	3		955	837	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258652	16258652	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	127	594	1	ENST00000375759.3:c.5917G>A	p.Glu1973Lys	p.E1973K	ENST00000375759	NM_015001.2	1973	Gaa/Aaa	11/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.357377712759169	2		595	548	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226305	133226305	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	160	935	0	ENST00000320574.5:c.3753G>T	p.Trp1251Cys	p.W1251C	ENST00000320574	NM_006231.2	1251	tgG/tgT	30/49	1	2	FACETS	0.983	0.901	1	0.983	0.901	1	CLONAL	1	TRUE	1	0.357377712759169	2		935	911	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149176	61149176	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	36	360	0	ENST00000295025.8:c.1366A>G	p.Asn456Asp	p.N456D	ENST00000295025	NM_002908.2	456	Aat/Gat	11/11	1	2	FACETS	0.709	0.586	0.847	0.709	0.586	0.847	SUBCLONAL	1	TRUE	1	0.357377712759169	2		360	284	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570071	212570071	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	42	565	0	ENST00000342788.4:c.1170C>A	p.Asn390Lys	p.N390K	ENST00000342788	NM_005235.2	390	aaC/aaA	10/28	1	2	FACETS	0.936	0.788	1	0.936	0.788	1	CLONAL	1	TRUE	1	0.357377712759169	2		565	251	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22123570	22123570	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	48	648	0	ENST00000215832.6:c.1006G>T	p.Asp336Tyr	p.D336Y	ENST00000215832	NM_002745.4	336	Gat/Tat	8/9	0.24217192177245	3	FACETS	0.684	0.579	0.8	0.228	0.193	0.267	SUBCLONAL	1	TRUE	0	0.357377712759169	3		648	463	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356178	66356178	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	100	577	0	ENST00000273854.3:c.1319A>G	p.Glu440Gly	p.E440G	ENST00000273854	NM_004439.5	440	gAg/gGg	5/18	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.357377712759169	2		577	549	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035238	6035238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1805322	NA	P-0026063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	86	468	1	ENST00000265849.7:c.830C>T	p.Thr277Met	p.T277M	ENST00000265849	NM_000535.5	277	aCg/aTg	8/15	0.357377712759169	2	FACETS	1	0.972	1	0.65	0.579	0.725	CLONAL	1	TRUE	0	0.357377712759169	2		469	370	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917646	151917646	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0026063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	32	898	0	ENST00000262189.6:c.3674C>G	p.Ser1225Ter	p.S1225*	ENST00000262189	NM_170606.2	1225	tCa/tGa	23/59	0.33005181254858	2	FACETS	0.624	0.508	0.754	0.312	0.254	0.377	SUBCLONAL	1	TRUE	0	0.357377712759169	2		898	287	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566080	141566080	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	79	701	0	ENST00000220592.5:c.1184G>C	p.Arg395Pro	p.R395P	ENST00000220592	NM_012154.3	395	cGt/cCt	10/19	0.209590287338202	3	FACETS	0.814	0.716	0.919	0.407	0.358	0.46	INDETERMINATE	1	TRUE	1	0.357377712759169	3		701	640	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412651	139412651	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	268	964	0	ENST00000277541.6:c.1193G>T	p.Cys398Phe	p.C398F	ENST00000277541	NM_017617.3	398	tGc/tTc	7/34	0.357377712759169	1	FACETS	0.858	0.809	0.908	1	0.995	1	CLONAL	2	TRUE	0	0.357377712759169	1		964	718	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294138	1294138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774657340	NA	P-0026064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	791	1040	6	ENST00000310581.5:c.863C>T	p.Ala288Val	p.A288V	ENST00000310581	NM_198253.2	288	gCg/gTg	2/16	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.858193767226654	2		1046	1811	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575362	64575362	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs794728622	NA	P-0026064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	477	582	0	ENST00000312049.6:c.654+1G>T		p.X218_splice	ENST00000312049	NM_130799.2	218			0.858193767226654	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.858193767226654	1		582	598	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119733	108119733	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203855	NA	P-0026064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	43	310	0	ENST00000278616.4:c.1139A>G	p.Tyr380Cys	p.Y380C	ENST00000278616	NM_000051.3	380	tAc/tGc	9/63	0.858193767226654	1	FACETS	0.151	0.126	0.178	0.151	0.126	0.178	SUBCLONAL	1	TRUE	0	0.858193767226654	1		310	380	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861951	57861951	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564218374	NA	P-0026064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	433	539	0	ENST00000228682.2:c.1252C>T	p.Arg418Trp	p.R418W	ENST00000228682	NM_005269.2	418	Cgg/Tgg	10/12	1	2	FACETS	0.965	0.923	1	0.965	0.923	1	CLONAL	1	TRUE	1	0.858193767226654	2		539	1046	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515400	103515400	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1011309306	NA	P-0026064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	38	317	1	ENST00000355739.4:c.1901T>C	p.Ile634Thr	p.I634T	ENST00000355739	NM_000123.3	634	aTt/aCt	8/15	1	2	FACETS	0.119	0.098	0.143	0.119	0.098	0.143	SUBCLONAL	1	TRUE	1	0.858193767226654	2		318	745	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572909	41572909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	553	603	1	ENST00000263253.7:c.5194C>T	p.Arg1732Cys	p.R1732C	ENST00000263253	NM_001429.3	1732	Cgc/Tgc	31/31	0.858193767226654	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.858193767226654	1		604	713	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20488368	20488368	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	45	564	0	ENST00000346618.3:c.1024A>G	p.Thr342Ala	p.T342A	ENST00000346618	NM_001949.4	342	Acc/Gcc	6/7	0.858193767226654	1	FACETS	0.084	0.07	0.1	0.084	0.07	0.1	SUBCLONAL	1	TRUE	0	0.858193767226654	1		564	710	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0026070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	188	379	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	0.582246060860309	2		379	631	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577197	64577197	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	224	746	0	ENST00000312049.6:c.385del	p.Leu129SerfsTer56	p.L129Sfs*56	ENST00000312049	NM_130799.2	129	Ctc/tc	2/10	0.582246060860309	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.582246060860309	3		746	473	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947833	178947833	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	46	368	0	ENST00000263967.3:c.2708G>C	p.Gly903Ala	p.G903A	ENST00000263967	NM_006218.2	903	gGa/gCa	19/21	1	2	FACETS	0.31	0.261	0.365	0.31	0.261	0.365	SUBCLONAL	1	TRUE	1	0.582246060860309	2		368	509	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27172703	27172703	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	32	643	1	ENST00000380036.4:c.718T>A	p.Cys240Ser	p.C240S	ENST00000380036	NM_000459.3	240	Tgc/Agc	5/23	1	2	FACETS	0.189	0.153	0.23	0.189	0.153	0.23	SUBCLONAL	1	TRUE	1	0.582246060860309	2		644	581	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303763	65303763	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	325	596	0	ENST00000342505.4:c.2992C>T	p.Gln998Ter	p.Q998*	ENST00000342505	NM_002227.2	998	Caa/Taa	22/25	0.824177993136149	1	FACETS	0.997	0.96	1	0.997	0.96	1	CLONAL	1	TRUE	0	0.824177993136149	1		596	465	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024647	31024647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	370	651	0	ENST00000375687.4:c.4132C>T	p.Leu1378Phe	p.L1378F	ENST00000375687	NM_015338.5	1378	Ctt/Ttt	13/13	0.214734962846749	3	FACETS	1	0.994	1	0.652	0.62	0.684	INDETERMINATE	1	TRUE	1	0.824177993136149	3		651	972	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949046	151949047	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	1046	592	0	ENST00000262189.6:c.1598dup	p.Glu534GlyfsTer4	p.E534Gfs*4	ENST00000262189	NM_170606.2	533	gtg/gtTg	11/59	0.824177993136149	4	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	1	0.824177993136149	4		592	1461	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942685	48942685	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913301	NA	P-0026073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	212	395	0	ENST00000267163.4:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000267163	NM_000321.2	358	Cga/Tga	11/27	0.722686276923555	3	FACETS	1	0.935	1	0.501	0.467	0.536	CLONAL	1	TRUE	1	0.828250134661044	3		395	722	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578496	7578496	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587782197	NA	P-0026073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	878	813	0	ENST00000269305.4:c.434T>A	p.Leu145Gln	p.L145Q	ENST00000269305	NM_001126112.2	145	cTg/cAg	5/11	0.828250134661044	2	FACETS	0.998	0.981	1	0.998	0.981	1	CLONAL	2	TRUE	0	0.828250134661044	2		813	1062	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947584	48947594	+	frameshift_variant	Frame_Shift_Del	DEL	TCAGCAAGTGA	TCAGCAAGTGA	-	novel	NA	P-0026073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	333	478	0	ENST00000267163.4:c.1174_1184del	p.Ala392ThrfsTer10	p.A392Tfs*10	ENST00000267163	NM_000321.2	391	TCAGCAAGTGAt/t	12/27	0.722686276923555	3	FACETS	1	0.995	1	0.723	0.688	0.759	CLONAL	1	TRUE	1	0.828250134661044	3		478	786	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947602	48947602	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	339	418	0	ENST00000267163.4:c.1189T>G	p.Ser397Ala	p.S397A	ENST00000267163	NM_000321.2	397	Tca/Gca	12/27	0.722686276923555	3	FACETS	0.814	0.776	0.852	0.814	0.776	0.852	CLONAL	2	TRUE	1	0.828250134661044	3		418	711	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485226	8485226	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0026073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	59	443	0	ENST00000356435.5:c.3153+1G>T		p.X1051_splice	ENST00000356435		1051			0.824877644611542	3	FACETS	0.226	0.193	0.261	0.113	0.096	0.131	SUBCLONAL	1	TRUE	1	0.828250134661044	3		443	892	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131895051	131895051	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	165	427	0	ENST00000265335.6:c.205G>T	p.Asp69Tyr	p.D69Y	ENST00000265335		69	Gat/Tat	2/25	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.619901749806344	2		427	492	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845813	151845813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	304	645	4	ENST00000262189.6:c.13199G>A	p.Arg4400Gln	p.R4400Q	ENST00000262189	NM_170606.2	4400	cGg/cAg	52/59	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.619901749806344	2		649	950	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	196	474	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.472079004827963	2		474	644	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0026076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	172	483	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	0.472079004827963	2		483	697	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0026076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	148	454	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.472079004827963	2		454	588	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0026076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	154	361	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.472079004827963	2		361	649	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0026076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	214	483	6	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	0.991	0.922	1	0.991	0.922	1	CLONAL	1	TRUE	1	0.472079004827963	2		489	915	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0026077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	800	503	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.825400368008854	5	FACETS	0.992	0.98	1	0.992	0.98	1	CLONAL	5	TRUE	0	0.830394906340295	5		505	872	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285838	87285838	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	374	658	0	ENST00000277120.3:c.175G>A	p.Glu59Lys	p.E59K	ENST00000277120		59	Gag/Aag	2/19	0.818097480110724	5	FACETS	1	0.953	1	0.668	0.635	0.701	CLONAL	2	TRUE	2	0.830394906340295	5		658	1010	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210438	36210438	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1426611662	NA	P-0026079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	92	525	0	ENST00000222270.7:c.431A>G	p.Gln144Arg	p.Q144R	ENST00000222270	NM_014727.1	144	cAg/cGg	2/37	1	2	FACETS	0.737	0.656	0.824	0.737	0.656	0.824	SUBCLONAL	1	TRUE	1	0.4	2		525	624	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916929	+	inframe_deletion	In_Frame_Del	DEL	CAGTAG	CAGTAG	-	novel	NA	P-0026079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	77	595	0	ENST00000263967.3:c.311_316del	p.Pro104_Gly106delinsArg	p.P104_G106delinsR	ENST00000263967	NM_006218.2	104	cCAGTAGgc/cgc	2/21	1	2	FACETS	0.355	0.31	0.403	0.355	0.31	0.403	SUBCLONAL	1	TRUE	1	0.4	2		595	1086	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467825	66467825	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	56	385	0	ENST00000273854.3:c.444G>C	p.Lys148Asn	p.K148N	ENST00000273854	NM_004439.5	148	aaG/aaC	3/18	1	2	FACETS	0.429	0.367	0.497	0.429	0.367	0.497	SUBCLONAL	1	TRUE	1	0.4	2		385	653	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168532	56168533	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCTCATGATTTCCTGG	novel	NA	P-0026079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	57	309	0	ENST00000399503.3:c.1500_1501insCTGGTCTCATGATTTC	p.Tyr501LeufsTer4	p.Y501Lfs*4	ENST00000399503	NM_005921.1	496	-/TCTCATGATTTCCTGG	8/20	1	2	FACETS	0.442	0.379	0.511	0.442	0.379	0.511	SUBCLONAL	1	TRUE	1	0.4	2		309	645	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	107	474	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.396650625618304	2		474	482	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0026081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	126	483	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.396650625618304	2		483	604	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711889	89711892	+	frameshift_variant	Frame_Shift_Del	DEL	CAGT	CAGT	-	novel	NA	P-0026081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	135	498	0	ENST00000371953.3:c.510_513del	p.Ser170ArgfsTer12	p.S170Rfs*12	ENST00000371953	NM_000314.4	169	ccCAGT/cc	6/9	0.396650625618304	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.396650625618304	1		498	451	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215360	123215360	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	119	457	0	ENST00000218089.9:c.2906C>G	p.Ala969Gly	p.A969G	ENST00000218089	NM_001042749.1	969	gCc/gGc	28/35	0.396650625618304	1	FACETS	0.986	0.895	1	0.986	0.895	1	CLONAL	1	TRUE	0	0.396650625618304	1		457	488	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0026083-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	254	502	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		502	540	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0026097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	14	385	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	0.266	0.192	0.356	0.266	0.192	0.356	SUBCLONAL	1	TRUE	1	0.365766433062048	2		385	288	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0026097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	81	259	0	ENST00000269305.4:c.673-2A>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.306157564152866	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.365766433062048	1		259	331	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215595215	215595215	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587781948	NA	P-0026097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	30	166	1	ENST00000260947.4:c.1921C>T	p.Arg641Ter	p.R641*	ENST00000260947	NM_000465.2	641	Cga/Tga	10/11	0.188253483471207	2	FACETS	0.641	0.518	0.778	0.32	0.259	0.389	INDETERMINATE	1	TRUE	0	0.365766433062048	2		167	256	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879872	44879884	+	frameshift_variant	Frame_Shift_Del	DEL	AGGAGGTGCTTTA	AGGAGGTGCTTTA	-	novel	NA	P-0026097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	55	106	0	ENST00000377967.4:c.461_473del	p.Gln154LeufsTer22	p.Q154Lfs*22	ENST00000377967	NM_021140.2	154	cAGGAGGTGCTTTAt/ct	6/29	0.364915411170692	2	FACETS	1	0.939	1			1	CLONAL	2	TRUE	NA	0.365766433062048	2		106	135	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272308	38272308	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs869320694	NA	P-0026098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	333	325	1	ENST00000425967.3:c.2059A>G	p.Lys687Glu	p.K687E	ENST00000425967	NM_001174067.1	687	Aag/Gag	15/19	0.609286909058395	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.609286909058395	2		326	515	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178942502	178942502	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749840319	NA	P-0026098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	63	175	0	ENST00000263967.3:c.2309G>A	p.Arg770Gln	p.R770Q	ENST00000263967	NM_006218.2	770	cGa/cAa	16/21	0.496979615708265	3	FACETS	0.964	0.841	1	0.482	0.42	0.547	CLONAL	1	TRUE	1	0.609286909058395	3		175	280	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942234	71942234	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0026098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	130	234	0	ENST00000298229.2:c.1497+1G>A		p.X499_splice	ENST00000298229	NM_001567.3	499			1	2	FACETS	0.997	0.912	1	0.997	0.912	1	CLONAL	1	TRUE	1	0.609286909058395	2		234	428	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937339	76937339	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0026098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	75	120	0	ENST00000373344.5:c.3409A>T	p.Arg1137Ter	p.R1137*	ENST00000373344	NM_000489.3	1137	Aga/Tga	9/35	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.609286909058395	1		120	117	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0026099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	38	255	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.189840619151753	3	FACETS	1	0.873	1	0.534	0.442	0.636	CLONAL	1	TRUE	1	0.202096050413696	3		255	388	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0026099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	19	209	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.555	0.42	0.713	0.555	0.42	0.713	SUBCLONAL	1	TRUE	1	0.202096050413696	2		210	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0026099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	97	409	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.184014931997424	2	FACETS	0.853	0.762	0.948	0.853	0.762	0.948	CLONAL	2	TRUE	0	0.202096050413696	2		409	563	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643727	52643728	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0026099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	34	320	0	ENST00000394830.3:c.2168_2169del	p.Ser723TyrfsTer3	p.S723Yfs*3	ENST00000394830	NM_018313.4	723	tCT/t	17/30	0.189840619151753	3	FACETS	0.741	0.605	0.895	0.37	0.302	0.448	SUBCLONAL	1	TRUE	1	0.202096050413696	3		320	500	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197660	106197660	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	47	189	0	ENST00000380013.4:c.5993A>G	p.Tyr1998Cys	p.Y1998C	ENST00000380013	NM_001127208.2	1998	tAc/tGc	11/11	0.184014931997424	2	FACETS	0.973	0.829	1	0.973	0.829	1	CLONAL	2	TRUE	0	0.202096050413696	2		189	239	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332826	153332826	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	61	240	0	ENST00000281708.4:c.130C>T	p.Gln44Ter	p.Q44*	ENST00000281708	NM_033632.3	44	Caa/Taa	2/12	0.184014931997424	2	FACETS	0.855	0.742	0.977	0.855	0.742	0.977	CLONAL	2	TRUE	0	0.202096050413696	2		240	353	SUCCESS
APC	324	MSKCC	GRCh37	5	112128170	112128170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768233232	NA	P-0026099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	29	264	0	ENST00000257430.4:c.673G>A	p.Glu225Lys	p.E225K	ENST00000257430	NM_000038.5	225	Gaa/Aaa	7/16	1	2	FACETS	0.692	0.555	0.847	0.692	0.555	0.847	SUBCLONAL	1	TRUE	1	0.202096050413696	2		264	415	SUCCESS
APC	324	MSKCC	GRCh37	5	112175494	112175500	+	frameshift_variant	Frame_Shift_Del	DEL	TGCCAGC	TGCCAGC	-	novel	NA	P-0026099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	16	159	0	ENST00000257430.4:c.4204_4210del	p.Ala1402ProfsTer11	p.A1402Pfs*11	ENST00000257430	NM_000038.5	1401	atTGCCAGC/at	16/16	1	2	FACETS	0.68	0.503	0.89	0.68	0.503	0.89	SUBCLONAL	1	TRUE	1	0.202096050413696	2		159	233	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	66	282	0	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.268232480387271	2		282	462	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857240	9857240	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	41	254	2	ENST00000330684.3:c.4161C>A	p.Tyr1387Ter	p.Y1387*	ENST00000330684	NM_001134407.1	1387	taC/taA	13/13	1	2	FACETS	0.653	0.544	0.775	0.653	0.544	0.775	SUBCLONAL	1	TRUE	1	0.268232480387271	2		256	468	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458219	12458219	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	37	256	0	ENST00000287820.6:c.836A>G	p.Asp279Gly	p.D279G	ENST00000287820	NM_015869.4	279	gAc/gGc	6/7	1	2	FACETS	0.61	0.503	0.73	0.61	0.503	0.73	SUBCLONAL	1	TRUE	1	0.268232480387271	2		256	452	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964454	70964454	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	36	324	0	ENST00000276594.2:c.1574C>A	p.Ser525Tyr	p.S525Y	ENST00000276594	NM_024504.3	525	tCt/tAt	8/8	1	2	FACETS	0.513	0.421	0.617	0.513	0.421	0.617	SUBCLONAL	1	TRUE	1	0.268232480387271	2		324	523	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0026106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	106	273	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.193202076988494	5	FACETS	0.835	0.753	0.92	0.835	0.753	0.92	CLONAL	3	TRUE	2	0.284087879997679	5		273	425	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098806	178098806	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	92	377	0	ENST00000397062.3:c.239C>G	p.Thr80Arg	p.T80R	ENST00000397062	NM_006164.4	80	aCa/aGa	2/5	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.284087879997679	2		377	522	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711895	89711895	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	29	297	0	ENST00000371953.3:c.513G>C	p.Gln171His	p.Q171H	ENST00000371953	NM_000314.4	171	caG/caC	6/9	1	2	FACETS	0.556	0.447	0.681	0.556	0.447	0.681	SUBCLONAL	1	TRUE	1	0.284087879997679	2		297	367	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0026108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	126	454	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.262511224611624	1	FACETS	0.968	0.876	1	0.968	0.876	1	CLONAL	1	TRUE	0	0.25	1		454	911	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43817960	43817960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752258550	NA	P-0026108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	73	331	1	ENST00000372470.3:c.1639G>A	p.Ala547Thr	p.A547T	ENST00000372470	NM_005373.2	547	Gca/Aca	11/12	1	2	FACETS	0.859	0.751	0.975	0.859	0.751	0.975	CLONAL	1	TRUE	1	0.25	2		332	680	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505474	25505474	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	70	279	0	ENST00000264709.3:c.284A>G	p.Lys95Arg	p.K95R	ENST00000264709	NM_175629.2	95	aAg/aGg	4/23	0.3	8	FACETS	0.863	0.75	0.987			1	CLONAL	1	TRUE	NA	0.25	8		279	1135	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56912094	56912094	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	57	338	0	ENST00000519728.1:c.1322A>C	p.Lys441Thr	p.K441T	ENST00000519728	NM_002350.3	441	aAa/aCa	12/13	1	2	FACETS	0.703	0.602	0.812	0.703	0.602	0.812	SUBCLONAL	1	TRUE	1	0.25	2		338	649	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593605	55593613	+	inframe_deletion	In_Frame_Del	DEL	GAAGGTTGT	GAAGGTTGT	-	novel	NA	P-0026110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	128	288	0	ENST00000288135.5:c.1671_1679del	p.Trp557_Val560delinsCys	p.W557_V560delinsC	ENST00000288135	NM_000222.2	557	tgGAAGGTTGTt/tgt	11/21	1	2	FACETS	0.722	0.659	0.787	0.722	0.659	0.787	SUBCLONAL	1	TRUE	1	0.80034947331788	2		288	443	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0026113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	126	379	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.983	0.897	1	0.983	0.897	1	CLONAL	1	TRUE	1	0.59473913348589	2		379	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0026114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	231	322	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.547953539843477	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.549207587360945	2		322	409	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096951	11096951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138689221	NA	P-0026114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	46	389	1	ENST00000358026.2:c.442G>A	p.Gly148Arg	p.G148R	ENST00000358026	NM_001128849.1	148	Ggg/Agg	4/36	0.549207587360945	3	FACETS	0.283	0.238	0.334	0.094	0.079	0.112	SUBCLONAL	1	TRUE	0	0.549207587360945	3		390	754	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370813	225370813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1206525768	NA	P-0026114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	88	248	1	ENST00000264414.4:c.1066C>T	p.Leu356Phe	p.L356F	ENST00000264414	NM_003590.4	356	Ctc/Ttc	8/16	0.522061833914496	3	FACETS	0.914	0.813	1	0.457	0.406	0.51	CLONAL	1	TRUE	1	0.549207587360945	3		249	447	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259401	89259401	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	99	244	0	ENST00000336596.2:c.545C>T	p.Ala182Val	p.A182V	ENST00000336596	NM_005233.5	182	gCa/gTa	3/17	1	2	FACETS	0.808	0.726	0.895	0.808	0.726	0.895	CLONAL	1	TRUE	1	0.549207587360945	2		244	446	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968196	55968196	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0026114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	67	191	0	ENST00000263923.4:c.2135-1G>T		p.X712_splice	ENST00000263923	NM_002253.2	712			0.549207587360945	5	FACETS	0.726	0.631	0.829			1	SUBCLONAL	1	TRUE	NA	0.549207587360945	5		191	613	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0026136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	67	411	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.921	0.806	1	0.921	0.806	1	CLONAL	1	TRUE	1	0.425237356411869	2		411	342	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0026136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	120	460	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.425237356411869	2		460	432	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122257	2122257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397515241	NA	P-0026136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	78	719	0	ENST00000219476.3:c.2113G>A	p.Val705Met	p.V705M	ENST00000219476	NM_000548.3	705	Gtg/Atg	20/42	NA	2	FACETS	0.828	0.731	0.932			1	INDETERMINATE	1	TRUE	NA	0.425237356411869	2		719	443	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968200	134968200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143309901	NA	P-0026136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	97	607	0	ENST00000398015.3:c.2713C>T	p.Arg905Cys	p.R905C	ENST00000398015	NM_004441.4	905	Cgc/Tgc	15/16	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.425237356411869	2		607	430	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956789	68956789	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	38	868	0	ENST00000288368.4:c.907G>A	p.Glu303Lys	p.E303K	ENST00000288368	NM_024870.2	303	Gag/Aag	8/40	1	2	FACETS	0.261	0.215	0.313	0.261	0.215	0.313	SUBCLONAL	1	TRUE	1	0.425237356411869	2		868	684	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730904	40730904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770182876	NA	P-0026136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	65	713	2	ENST00000373198.4:c.3631G>A	p.Glu1211Lys	p.E1211K	ENST00000373198	NM_133170.3	1211	Gag/Aag	27/32	1	2	FACETS	0.678	0.589	0.773	0.678	0.589	0.773	SUBCLONAL	1	TRUE	1	0.425237356411869	2		715	451	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2137898	2137898	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45483392	NA	P-0026136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	190	847	0	ENST00000219476.3:c.5024C>T	p.Pro1675Leu	p.P1675L	ENST00000219476	NM_000548.3	1675	cCg/cTg	39/42	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.425237356411869	2		847	603	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65323381	65323381	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	141	715	0	ENST00000342505.4:c.1416T>G	p.Phe472Leu	p.F472L	ENST00000342505	NM_002227.2	472	ttT/ttG	10/25	0.236353643077297	2	FACETS	1	0.986	1	0.687	0.63	0.745	INDETERMINATE	1	TRUE	0	0.425237356411869	2		715	483	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920731	96920731	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	36	510	0	ENST00000258439.3:c.249C>G	p.Phe83Leu	p.F83L	ENST00000258439	NM_001193304.2	83	ttC/ttG	3/4	1	2	FACETS	0.425	0.35	0.51	0.425	0.35	0.51	SUBCLONAL	1	TRUE	1	0.425237356411869	2		510	398	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402660	20402660	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	144	577	0	ENST00000346618.3:c.198del	p.Thr67ProfsTer13	p.T67Pfs*13	ENST00000346618	NM_001949.4	66	tCc/tc	1/7	0.425237356411869	3	FACETS	0.765	0.701	0.83	0.765	0.701	0.83	SUBCLONAL	2	TRUE	1	0.425237356411869	3		577	537	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273416	38273416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765629435	NA	P-0026136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	40	1055	1	ENST00000425967.3:c.1919G>A	p.Arg640Gln	p.R640Q	ENST00000425967	NM_001174067.1	640	cGa/cAa	14/19	1	2	FACETS	0.27	0.224	0.322	0.27	0.224	0.322	SUBCLONAL	1	TRUE	1	0.425237356411869	2		1056	696	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572697	141572697	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	34	656	0	ENST00000220592.5:c.373G>C	p.Asp125His	p.D125H	ENST00000220592	NM_012154.3	125	Gat/Cat	4/19	1	2	FACETS	0.351	0.287	0.424	0.351	0.287	0.424	SUBCLONAL	1	TRUE	1	0.425237356411869	2		656	455	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	142	474	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.879	0.812	0.947	0.879	0.812	0.947	CLONAL	1	TRUE	1	0.9154212834777	2		474	353	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946194	13946194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781237791	NA	P-0026137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	82	572	0	ENST00000405192.2:c.902G>A	p.Arg301Gln	p.R301Q	ENST00000405192	NM_001163147.1	301	cGg/cAg	10/12	0.725790330657932	4	FACETS	0.378	0.332	0.427	0.126	0.11	0.143	SUBCLONAL	1	TRUE	1	0.9154212834777	4		572	909	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609902	117609902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781588795	NA	P-0026139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	201	494	0	ENST00000368508.3:c.6797C>T	p.Thr2266Met	p.T2266M	ENST00000368508	NM_002944.2	2266	aCg/aTg	43/43	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.666258248556286	NA		494	418	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0026140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	72	388	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA	2	FACETS	0.997	0.871	1			1	INDETERMINATE	1	TRUE	NA	0.229292112397652	2		388	630	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597401	10597401	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	115	651	0	ENST00000171111.5:c.1802G>T	p.Arg601Leu	p.R601L	ENST00000171111	NM_203500.1	601	cGg/cTg	6/6	0.229292112397652	0	FACETS	1	0.978	1			1	CLONAL	1	TRUE	0	0.229292112397652	0		651	597	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189104	38189104	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0026140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	51	393	0	ENST00000317025.8:c.911-1G>A		p.X304_splice	ENST00000317025	NM_023034.1	304			1	2	FACETS	0.953	0.811	1	0.953	0.811	1	CLONAL	1	TRUE	1	0.229292112397652	2		393	467	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78420988	78420988	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	86	408	0	ENST00000370768.2:c.1732G>T	p.Gly578Ter	p.G578*	ENST00000370768	NM_003902.3	578	Gga/Tga	18/20	0.0929660925956433	3	FACETS	1	0.974	1	0.69	0.611	0.774	INDETERMINATE	1	TRUE	1	0.229292112397652	3		408	606	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913395	28913395	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	95	535	1	ENST00000282397.4:c.2398G>T	p.Asp800Tyr	p.D800Y	ENST00000282397	NM_002019.4	800	Gac/Tac	17/30	0.229292112397652	0	FACETS	1	0.938	1			1	CLONAL	1	TRUE	0	0.229292112397652	0		536	594	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041792	14041792	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	61	397	0	ENST00000311895.7:c.2339C>A	p.Ser780Tyr	p.S780Y	ENST00000311895	NM_005236.2	780	tCc/tAc	11/11	0.157720545804224	1	FACETS	0.871	0.752	1	0.871	0.752	1	CLONAL	1	TRUE	0	0.229292112397652	1		397	541	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964736	15964736	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	73	417	0	ENST00000268712.3:c.5860A>G	p.Ser1954Gly	p.S1954G	ENST00000268712	NM_006311.3	1954	Agt/Ggt	37/46	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.229292112397652	2		417	546	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219335	1219336	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0026140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	107	586	1	ENST00000326873.7:c.387_388delinsTT	p.Met129_Glu130delinsIleTer	p.M129_E130delinsI*	ENST00000326873	NM_000455.4	129	atGGag/atTTag	3/10	0.224792171309162	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.229292112397652	1		587	744	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095947	11095947	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0026140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	73	586	2	ENST00000358026.2:c.223-2A>T		p.X75_splice	ENST00000358026	NM_001128849.1	75			0.229292112397652	0	FACETS	1	0.895	1			1	CLONAL	1	TRUE	0	0.229292112397652	0		588	480	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918796	50918796	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs748904485	NA	P-0026140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	111	612	0	ENST00000440232.2:c.2666G>T	p.Arg889Leu	p.R889L	ENST00000440232	NM_002691.3	889	cGc/cTc	21/27	0.229292112397652	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.229292112397652	1		612	716	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561885	55561885	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	51	309	0	ENST00000288135.5:c.275C>A	p.Thr92Asn	p.T92N	ENST00000288135	NM_000222.2	92	aCc/aAc	2/21	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.229292112397652	2		309	379	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638735	176638735	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	84	580	0	ENST00000439151.2:c.3335G>T	p.Ser1112Ile	p.S1112I	ENST00000439151	NM_022455.4	1112	aGc/aTc	5/23	0.157720545804224	1	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	0	0.229292112397652	1		580	636	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222438	53222438	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1184598695	NA	P-0026140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	112	582	0	ENST00000375401.3:c.4394G>T	p.Arg1465Leu	p.R1465L	ENST00000375401	NM_004187.3	1465	cGg/cTg	26/26	0.229292112397652	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.229292112397652	1		582	749	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411017	63411017	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	77	523	0	ENST00000330258.3:c.2150G>T	p.Cys717Phe	p.C717F	ENST00000330258	NM_152424.3	717	tGc/tTc	2/2	0.229292112397652	1	FACETS	0.976	0.858	1	0.976	0.858	1	CLONAL	1	TRUE	0	0.229292112397652	1		523	609	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349964	15349964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1411701353	NA	P-0026142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	146	522	0	ENST00000263377.2:c.3688G>A	p.Ala1230Thr	p.A1230T	ENST00000263377	NM_058243.2	1230	Gcc/Acc	18/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.634048488027894	2		522	444	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442577	52442578	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0026142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	359	429	0	ENST00000460680.1:c.167_168del	p.Arg56ProfsTer12	p.R56Pfs*12	ENST00000460680	NM_004656.3	56	cGC/c	4/17	0.634048488027894	3	FACETS	1	0.99	1	0.74	0.708	0.772	CLONAL	2	TRUE	0	0.634048488027894	3		429	672	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	33	501	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.855	0.695	1	0.855	0.695	1	CLONAL	1	TRUE	1	0.13	2		501	594	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0026149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	31	313	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.819	1	1	0.819	1	CLONAL	1	TRUE	1	0.13	2		313	470	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711361	114711361	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	16	242	0	ENST00000543371.1:c.376C>T	p.Arg126Ter	p.R126*	ENST00000543371	NM_001198531.1	126	Cga/Tga	3/14	1	2	FACETS	0.981	0.725	1	0.981	0.725	1	CLONAL	1	TRUE	1	0.13	2		242	251	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453138	140453139	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTA	rs727502902	NA	P-0026151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	228	570	0	ENST00000288602.6:c.1794_1796dup	p.Thr599dup	p.T599dup	ENST00000288602	NM_004333.4	599	aca/acTACa	15/18	0.420164667345728	3	FACETS	0.962	0.902	1	0.962	0.902	1	CLONAL	2	TRUE	1	0.444246352898255	3		570	652	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952086	178952086	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	13	540	0	ENST00000263967.3:c.3141T>A	p.His1047Gln	p.H1047Q	ENST00000263967	NM_006218.2	1047	caT/caA	21/21	1	2	FACETS	0.071	0.05	0.097	0.071	0.05	0.097	SUBCLONAL	1	TRUE	1	0.678115703934163	2		540	537	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874713	151874713	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	182	414	1	ENST00000262189.6:c.7825C>T	p.Arg2609Ter	p.R2609*	ENST00000262189	NM_170606.2	2609	Cga/Tga	38/59	1	2	FACETS	0.741	0.686	0.799	0.741	0.686	0.799	SUBCLONAL	1	TRUE	1	0.678115703934163	2		415	724	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148544344	148544344	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	40	680	3	ENST00000320356.2:c.47G>A	p.Arg16Gln	p.R16Q	ENST00000320356	NM_004456.4	16	cGg/cAg	2/20	1	2	FACETS	0.148	0.122	0.177	0.148	0.122	0.177	SUBCLONAL	1	TRUE	1	0.678115703934163	2		683	796	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328452	137328452	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	319	782	0	ENST00000481739.1:c.1381A>T	p.Met461Leu	p.M461L	ENST00000481739	NM_002957.4	461	Atg/Ttg	10/10	1	2	FACETS	0.891	0.842	0.941	0.891	0.842	0.941	CLONAL	1	TRUE	1	0.678115703934163	2		782	1056	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274897	41274897	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	617	485	0	ENST00000349496.5:c.1147T>C	p.Trp383Arg	p.W383R	ENST00000349496	NM_001904.3	383	Tgg/Cgg	8/15	0.734601966120498	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.734601966120498	3		485	1129	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869433	102869433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	313	602	0	ENST00000307046.8:c.208G>A	p.Gly70Ser	p.G70S	ENST00000307046	NM_001111285.1	70	Ggc/Agc	2/4	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.734601966120498	2		602	820	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770075	56770075	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	306	567	0	ENST00000337432.4:c.71G>C	p.Arg24Pro	p.R24P	ENST00000337432	NM_058216.2	24	cGg/cCg	1/9	NA	2	FACETS	0.965	0.913	1			1	INDETERMINATE	1	TRUE	NA	0.734601966120498	2		567	863	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368226	45368226	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	288	505	0	ENST00000262160.6:c.1376del	p.Pro459LeufsTer21	p.P459Lfs*21	ENST00000262160	NM_005901.5	459	cCt/ct	11/11	0.734601966120498	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.734601966120498	1		505	481	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508194	106508194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	136	265	1	ENST00000359195.3:c.188G>A	p.Gly63Asp	p.G63D	ENST00000359195	NM_002649.2	63	gGc/gAc	2/11	1	2	FACETS	0.897	0.823	0.972	0.897	0.823	0.972	CLONAL	1	TRUE	1	0.734601966120498	2		266	413	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409740	139409740	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0026153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	305	544	0	ENST00000277541.6:c.2014+2T>C		p.X672_splice	ENST00000277541	NM_017617.3	672			1	2	FACETS	0.928	0.877	0.98	0.928	0.877	0.98	CLONAL	1	TRUE	1	0.734601966120498	2		544	895	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969399	44969399	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	440	430	0	ENST00000377967.4:c.4081T>C	p.Cys1361Arg	p.C1361R	ENST00000377967	NM_021140.2	1361	Tgt/Cgt	28/29	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.734601966120498	1		430	596	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0026156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	143	347	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.985	0.905	1	0.985	0.905	1	CLONAL	1	TRUE	1	0.638162129468838	2		347	455	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0026156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6713	7691	768	2	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.638162129468838	29	FACETS	1	0.994	1			1	CLONAL	16	TRUE	NA	0.638162129468838	29		770	14404	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969086	93969086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774868013	NA	P-0026156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	117	326	0	ENST00000369303.4:c.1910G>A	p.Arg637His	p.R637H	ENST00000369303	NM_004440.3	637	cGt/cAt	10/17	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.638162129468838	2		326	353	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188100	11188100	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	202	512	0	ENST00000361445.4:c.5994G>T	p.Met1998Ile	p.M1998I	ENST00000361445	NM_004958.3	1998	atG/atT	43/58	1	2	FACETS	0.895	0.833	0.959	0.895	0.833	0.959	CLONAL	1	TRUE	1	0.638162129468838	2		512	707	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0026157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	152	854	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	TRUE	1	0.250661326216365	2		854	817	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057302	30057302	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315496	NA	P-0026157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	84	586	0	ENST00000338641.4:c.784C>T	p.Arg262Ter	p.R262*	ENST00000338641	NM_000268.3	262	Cga/Tga	8/16	0.250661326216365	1	FACETS	0.714	0.63	0.805	0.714	0.63	0.805	SUBCLONAL	1	TRUE	0	0.250661326216365	1		586	821	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438491	52438491	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	106	610	1	ENST00000460680.1:c.1228C>T	p.Gln410Ter	p.Q410*	ENST00000460680	NM_004656.3	410	Cag/Tag	12/17	0.250661326216365	1	FACETS	0.94	0.842	1	0.94	0.842	1	CLONAL	1	TRUE	0	0.250661326216365	1		611	787	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647143	2647143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	66	577	0	ENST00000342085.4:c.1421G>A	p.Arg474Gln	p.R474Q	ENST00000342085	NM_002613.4	474	cGa/cAa	13/14	NA	2	FACETS	0.667	0.577	0.763			1	INDETERMINATE	1	TRUE	NA	0.250661326216365	2		577	790	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	278	474	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.767113762738055	2		474	644	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981252	201981253	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	1124	830	0	ENST00000359651.3:c.332dup	p.Leu112SerfsTer23	p.L112Sfs*23	ENST00000359651		111	cgt/cGgt	2/8	0.767113762738055	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.767113762738055	2		830	1417	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361181	66361181	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	192	396	0	ENST00000273854.3:c.991G>T	p.Glu331Ter	p.E331*	ENST00000273854	NM_004439.5	331	Gaa/Taa	4/18	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.767113762738055	2		396	472	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0026161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	445	495	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.227981660395087	7	FACETS	0.907	0.866	0.95			1	CLONAL	5	TRUE	NA	0.227981660395087	7		495	1351	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333573	70333573	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	112	479	0	ENST00000373644.4:c.1478C>A	p.Ala493Asp	p.A493D	ENST00000373644	NM_030625.2	493	gCt/gAt	2/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.227981660395087	2		479	819	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137183	64137183	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	118	500	0	ENST00000334205.4:c.1615G>T	p.Ala539Ser	p.A539S	ENST00000334205	NM_003942.2	539	Gcc/Tcc	14/17	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.227981660395087	2		500	1000	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858967	57858967	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	181	677	0	ENST00000228682.2:c.463G>T	p.Gly155Cys	p.G155C	ENST00000228682	NM_005269.2	155	Ggt/Tgt	5/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.227981660395087	2		677	1306	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112319	115112319	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762031545	NA	P-0026161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	25	116	0	ENST00000257566.3:c.1421C>T	p.Pro474Leu	p.P474L	ENST00000257566	NM_016569.3	474	cCg/cTg	7/8	1	2	FACETS	0.997	0.79	1	0.997	0.79	1	CLONAL	1	TRUE	1	0.227981660395087	2		116	220	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476369	88476369	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	126	587	0	ENST00000360948.2:c.1763A>C	p.Glu588Ala	p.E588A	ENST00000360948	NM_001012338.2	588	gAg/gCg	15/19	0.219530757785144	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.227981660395087	1		587	907	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857112	9857112	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	91	336	0	ENST00000330684.3:c.4289C>T	p.Pro1430Leu	p.P1430L	ENST00000330684	NM_001134407.1	1430	cCt/cTt	13/13	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.227981660395087	2		336	552	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641693	23641693	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	119	615	0	ENST00000261584.4:c.1782G>T	p.Arg594Ser	p.R594S	ENST00000261584	NM_024675.3	594	agG/agT	5/13	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.227981660395087	2		615	974	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713589	30713589	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	72	399	0	ENST00000295754.5:c.914T>C	p.Leu305Pro	p.L305P	ENST00000295754	NM_003242.5	305	cTc/cCc	4/7	1	2	FACETS	0.781	0.681	0.889	0.781	0.681	0.889	SUBCLONAL	1	TRUE	1	0.227981660395087	2		399	809	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233137	66233137	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	160	466	0	ENST00000273854.3:c.1862G>T	p.Cys621Phe	p.C621F	ENST00000273854	NM_004439.5	621	tGt/tTt	10/18	0.227981660395087	2	FACETS	0.847	0.777	0.919	0.847	0.777	0.919	CLONAL	2	TRUE	0	0.227981660395087	2		466	829	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066435	94066435	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	37	249	0	ENST00000369303.4:c.1324G>A	p.Ala442Thr	p.A442T	ENST00000369303	NM_004440.3	442	Gct/Act	5/17	1	2	FACETS	0.897	0.741	1	0.897	0.741	1	CLONAL	1	TRUE	1	0.227981660395087	2		249	362	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212860	27212860	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	51	678	0	ENST00000380036.4:c.2842G>C	p.Val948Leu	p.V948L	ENST00000380036	NM_000459.3	948	Gtg/Ctg	17/23	0.227981660395087	1	FACETS	0.394	0.334	0.462	0.394	0.334	0.462	SUBCLONAL	1	TRUE	0	0.227981660395087	1		678	1005	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	91	474	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.649	0.579	0.722	0.649	0.579	0.722	SUBCLONAL	1	TRUE	1	0.6695220088075	2		474	419	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874011	123874013	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs780061449	NA	P-0026163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	12	44	0	ENST00000330479.4:c.62_64del	p.Ala21del	p.A21del	ENST00000330479	NM_020382.3	14	gaGGCg/gag	2/9	0.282210356054826	1	FACETS	0.367	0.263	0.488	0.367	0.263	0.488	INDETERMINATE	1	TRUE	0	0.6695220088075	1		44	65	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0026163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	308	475	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.6695220088075	2		475	667	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717715	89717716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587782341	NA	P-0026163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	212	424	0	ENST00000371953.3:c.741dup	p.Pro248ThrfsTer5	p.P248Tfs*5	ENST00000371953	NM_000314.4	247	tta/ttAa	7/9	0.6695220088075	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.6695220088075	1		424	361	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337289	89337289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	178	466	0	ENST00000301030.4:c.7742G>A	p.Arg2581His	p.R2581H	ENST00000301030	NM_001256183.1	2581	cGt/cAt	12/13	1	2	FACETS	0.759	0.701	0.818	0.759	0.701	0.818	SUBCLONAL	1	TRUE	1	0.6695220088075	2		466	701	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46270960	46270962	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0026163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	109	391	0	ENST00000371998.3:c.3088_3090del	p.Leu1030del	p.L1030del	ENST00000371998		1028	ccTCTt/cct	17/23	1	2	FACETS	0.824	0.746	0.905	0.824	0.746	0.905	CLONAL	1	TRUE	1	0.6695220088075	2		391	395	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204927	128204927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	195	731	1	ENST00000341105.2:c.514G>A	p.Gly172Ser	p.G172S	ENST00000341105	NM_032638.4	172	Ggc/Agc	3/6	1	2	FACETS	0.682	0.632	0.734	0.682	0.632	0.734	SUBCLONAL	1	TRUE	1	0.6695220088075	2		732	854	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133791	55133791	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1537	4870	485	0	ENST00000257290.5:c.1004T>C	p.Phe335Ser	p.F335S	ENST00000257290	NM_006206.4	335	tTt/tCt	7/23	0.6695220088075	36	FACETS	1	0.994	1			1	CLONAL	28	TRUE	NA	0.6695220088075	36		485	6407	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932334	39932335	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0026163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	265	818	0	ENST00000378444.4:c.2264dup	p.Tyr755Ter	p.Y755*	ENST00000378444	NM_001123385.1	755	tac/taAc	4/15	1	2	FACETS	0.847	0.795	0.9	0.847	0.795	0.9	CLONAL	1	TRUE	1	0.6695220088075	2		818	935	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176471	123176471	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	190	394	0	ENST00000218089.9:c.442del	p.Met148Ter	p.M148*	ENST00000218089	NM_001042749.1	146	cgA/cg	7/35	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.6695220088075	2		394	522	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254583	46254583	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0026164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	141	340	0	ENST00000334344.6:c.4774-1G>A		p.X1592_splice	ENST00000334344	NM_152641.2	1592			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.476939139686762	2		340	482	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846235	156846235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201564883	NA	P-0026164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	110	564	0	ENST00000524377.1:c.1676G>A	p.Arg559His	p.R559H	ENST00000524377	NM_002529.3	559	cGt/cAt	14/17	0.476939139686762	1	FACETS	0.552	0.497	0.611	0.552	0.497	0.611	SUBCLONAL	1	TRUE	0	0.476939139686762	1		564	636	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61709597	61709597	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	121	310	0	ENST00000401558.2:c.2890C>G	p.Pro964Ala	p.P964A	ENST00000401558	NM_003400.3	964	Cct/Gct	23/25	1	2	FACETS	0.965	0.876	1	0.965	0.876	1	CLONAL	1	TRUE	1	0.476939139686762	2		310	526	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155275	106155275	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	53	338	1	ENST00000380013.4:c.176G>C	p.Ser59Thr	p.S59T	ENST00000380013	NM_001127208.2	59	aGt/aCt	3/11	NA	2	FACETS	0.543	0.464	0.629			1	INDETERMINATE	1	TRUE	NA	0.476939139686762	2		339	409	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	83	474	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.989	0.879	1	0.989	0.879	1	CLONAL	1	TRUE	1	0.453770717313933	2		474	370	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861143	57861143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772799269	NA	P-0026166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	141	474	0	ENST00000228682.2:c.940C>T	p.Arg314Cys	p.R314C	ENST00000228682	NM_005269.2	314	Cgc/Tgc	9/12	1	2	FACETS	0.919	0.84	1	0.919	0.84	1	CLONAL	1	TRUE	1	0.453770717313933	2		474	676	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0026167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	108	504	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.3	2		504	509	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867546	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGC	GGCGGCGGC	-	rs11466445	NA	P-0026168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	12	20	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	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.343757660421787	2		20	49	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600369	10600369	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	380	760	0	ENST00000171111.5:c.1486G>T	p.Glu496Ter	p.E496*	ENST00000171111	NM_203500.1	496	Gag/Tag	4/6	0.343757660421787	2	FACETS	0.928	0.882	0.975	0.928	0.882	0.975	CLONAL	2	TRUE	0	0.343757660421787	2		760	1191	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576183	88576183	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	148	578	0	ENST00000360948.2:c.1490G>T	p.Gly497Val	p.G497V	ENST00000360948	NM_001012338.2	497	gGg/gTg	13/19	0.343757660421787	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.343757660421787	1		578	658	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481412	140481412	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913353	NA	P-0026168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	124	449	0	ENST00000288602.6:c.1396G>C	p.Gly466Arg	p.G466R	ENST00000288602	NM_004333.4	466	Gga/Cga	11/18	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.343757660421787	2		449	670	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606895	43606895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770395347	NA	P-0026168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	193	812	1	ENST00000355710.3:c.1504G>A	p.Val502Ile	p.V502I	ENST00000355710	NM_020975.4	502	Gta/Ata	7/20	1	2	FACETS	0.988	0.913	1	0.988	0.913	1	CLONAL	1	TRUE	1	0.343757660421787	2		813	1136	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156691	2156691	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	150	686	0	ENST00000434045.2:c.231C>G	p.Cys77Trp	p.C77W	ENST00000434045	NM_001127598.1	77	tgC/tgG	3/5	1	2	FACETS	0.871	0.795	0.951	0.871	0.795	0.951	CLONAL	1	TRUE	1	0.343757660421787	2		686	1002	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691123	18691123	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	93	441	0	ENST00000266497.5:c.3234G>T	p.Met1078Ile	p.M1078I	ENST00000266497		1078	atG/atT	23/31	1	2	FACETS	0.995	0.887	1	0.995	0.887	1	CLONAL	1	TRUE	1	0.343757660421787	2		441	544	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244311	46244311	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	96	406	0	ENST00000334344.6:c.2405T>G	p.Phe802Cys	p.F802C	ENST00000334344	NM_152641.2	802	tTt/tGt	15/21	1	2	FACETS	0.841	0.75	0.938	0.841	0.75	0.938	CLONAL	1	TRUE	1	0.343757660421787	2		406	664	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984200	7984203	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ACTC	ACTC	-	novel	NA	P-0026168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	118	495	0	ENST00000319144.4:c.526_527+2del		p.X176_splice	ENST00000319144	NM_001139.2	176		4/15	1	2	FACETS	0.87	0.785	0.96	0.87	0.785	0.96	CLONAL	1	TRUE	1	0.343757660421787	2		495	789	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1206976	1206979	+	frameshift_variant	Frame_Shift_Del	DEL	ATGG	ATGG	-	novel	NA	P-0026168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	303	548	0	ENST00000326873.7:c.65_68del	p.Met22ThrfsTer28	p.M22Tfs*28	ENST00000326873	NM_000455.4	22	ATGGac/ac	1/10	0.343757660421787	2	FACETS	0.972	0.918	1	0.972	0.918	1	CLONAL	2	TRUE	0	0.343757660421787	2		548	907	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47643565	47643565	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	90	449	0	ENST00000233146.2:c.1073A>G	p.Glu358Gly	p.E358G	ENST00000233146	NM_000251.2	358	gAg/gGg	6/16	1	2	FACETS	0.826	0.734	0.924	0.826	0.734	0.924	CLONAL	1	TRUE	1	0.343757660421787	2		449	634	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719484	190719484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777734081	NA	P-0026168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	63	321	0	ENST00000441310.2:c.1486G>A	p.Asp496Asn	p.D496N	ENST00000441310	NM_000534.4	496	Gat/Aat	9/13	1	2	FACETS	0.923	0.802	1	0.923	0.802	1	CLONAL	1	TRUE	1	0.343757660421787	2		321	397	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048758	180048758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754621734	NA	P-0026168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	190	653	1	ENST00000261937.6:c.1804C>T	p.His602Tyr	p.H602Y	ENST00000261937	NM_182925.4	602	Cac/Tac	13/30	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.343757660421787	2		654	1010	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460552	8460552	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	111	407	0	ENST00000356435.5:c.3734C>A	p.Pro1245His	p.P1245H	ENST00000356435		1245	cCt/cAt	22/35	1	2	FACETS	0.912	0.821	1	0.912	0.821	1	CLONAL	1	TRUE	1	0.343757660421787	2		407	708	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0026169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	80	427	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.96	0.845	1	0.96	0.845	1	CLONAL	1	TRUE	1	0.245488341633789	2		428	679	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0026169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	280	409	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.236192806801719	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.245488341633789	2		409	1005	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0026169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	103	532	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.245488341633789	2		532	775	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941101	36941101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1207837094	NA	P-0026169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	103	630	0	ENST00000361632.4:c.238G>A	p.Asp80Asn	p.D80N	ENST00000361632		80	Gat/Aat	3/16	1	2	FACETS	0.962	0.86	1	0.962	0.86	1	CLONAL	1	TRUE	1	0.245488341633789	2		630	872	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0026170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	255	495	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.730636617422721	2	FACETS	0.992	0.952	1	0.992	0.952	1	CLONAL	2	TRUE	0	0.730636617422721	2		495	352	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602800	10602800	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	704	621	1	ENST00000171111.5:c.778C>T	p.Arg260Ter	p.R260*	ENST00000171111	NM_203500.1	260	Cga/Tga	3/6	0.730636617422721	2	FACETS	0.997	0.974	1	0.997	0.974	1	CLONAL	2	TRUE	0	0.730636617422721	2		622	966	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865281	57865282	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0026170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	436	511	2	ENST00000228682.2:c.2758_2759delinsTT	p.Ala920Phe	p.A920F	ENST00000228682	NM_005269.2	920	GCc/TTc	12/12	0.730636617422721	2	FACETS	0.944	0.914	0.974	0.944	0.914	0.974	CLONAL	2	TRUE	0	0.730636617422721	2		513	632	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243728	41243729	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0026170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	273	485	0	ENST00000357654.3:c.3819_3820delinsTT	p.Gln1273_Val1274delinsHisLeu	p.Q1273_V1274delinsHL	ENST00000357654	NM_007294.3	1273	caGGta/caTTta	10/23	0.730636617422721	2	FACETS	0.929	0.891	0.967	0.929	0.891	0.967	CLONAL	2	TRUE	0	0.730636617422721	2		485	402	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162014	22162014	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	337	473	0	ENST00000215832.6:c.241G>C	p.Glu81Gln	p.E81Q	ENST00000215832	NM_002745.4	81	Gag/Cag	2/9	0.730636617422721	2	FACETS	0.915	0.88	0.949	0.915	0.88	0.949	CLONAL	2	TRUE	0	0.730636617422721	2		473	504	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865281	57865281	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	436	509	0	ENST00000228682.2:c.2758G>T	p.Ala920Ser	p.A920S	ENST00000228682	NM_005269.2	920	Gcc/Tcc	12/12	0.730636617422721	2	FACETS	0.944	0.914	0.974	0.944	0.914	0.974	CLONAL	2	TRUE	0	0.730636617422721	2		509	632	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572662	64572662	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	ATG	novel	NA	P-0026170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	401	452	0	ENST00000312049.6:c.1194delinsCAT	p.Gln398HisfsTer48	p.Q398Hfs*48	ENST00000312049	NM_130799.2	398	caG/caCAT	9/10	0.705788652452436	2	FACETS	0.98	0.948	1	0.98	0.948	1	CLONAL	2	TRUE	0	0.730636617422721	2		452	560	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196119	138196119	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	33	313	1	ENST00000237289.4:c.433G>T	p.Glu145Ter	p.E145*	ENST00000237289	NM_001270507.1	145	Gag/Tag	3/9	1	2	FACETS	0.625	0.508	0.758	0.625	0.508	0.758	SUBCLONAL	1	TRUE	1	0.195077928525904	2		314	541	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950807	32950807	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	48	335	0	ENST00000380152.3:c.8636del	p.Asn2879ThrfsTer12	p.N2879Tfs*12	ENST00000380152		2878	gAa/ga	21/27	0.192871696909285	1	FACETS	0.985	0.834	1	0.985	0.834	1	CLONAL	1	TRUE	0	0.195077928525904	1		335	451	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928036	178928037	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGAAAAATGGCTTTGAATCTTTGGCCAGTACCTCATGGATTAGAA	novel	NA	P-0026171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	46	481	0	ENST00000263967.3:c.1316_1360dup	p.Gly439_Glu453dup	p.G439_E453dup	ENST00000263967	NM_006218.2	439	-/GGAAAAATGGCTTTGAATCTTTGGCCAGTACCTCATGGATTAGAA	8/21	1	2	FACETS	0.62	0.52	0.73	0.62	0.52	0.73	SUBCLONAL	1	TRUE	1	0.195077928525904	2		481	761	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936995	48936995	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778842	NA	P-0026173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	254	312	0	ENST00000267163.4:c.763C>T	p.Arg255Ter	p.R255*	ENST00000267163	NM_000321.2	255	Cga/Tga	8/27	0.87911361904248	1	FACETS	0.967	0.93	1	0.967	0.93	1	CLONAL	1	TRUE	0	0.87911361904248	1		312	335	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874011	123874013	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs780061449	NA	P-0026173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	11	44	0	ENST00000330479.4:c.62_64del	p.Ala21del	p.A21del	ENST00000330479	NM_020382.3	14	gaGGCg/gag	2/9	0.520825233956103	3	FACETS	0.222	0.154	0.307	0.111	0.077	0.154	INDETERMINATE	1	TRUE	1	0.87911361904248	3		44	162	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411387	63411387	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	414	483	2	ENST00000330258.3:c.1780C>A	p.His594Asn	p.H594N	ENST00000330258	NM_152424.3	594	Cac/Aac	2/2	1	2	FACETS	0.971	0.928	1	0.971	0.928	1	CLONAL	1	TRUE	1	0.87911361904248	2		485	970	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795034	45795034	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	482	559	0	ENST00000450313.1:c.1594T>G	p.Phe532Val	p.F532V	ENST00000450313	NM_012222.2	532	Ttc/Gtc	16/16	1	2	FACETS	0.98	0.94	1	0.98	0.94	1	CLONAL	1	TRUE	1	0.87911361904248	2		559	1119	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239651	105239651	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	498	610	0	ENST00000349310.3:c.894G>C	p.Glu298Asp	p.E298D	ENST00000349310	NM_001014432.1	298	gaG/gaC	11/15	1	2	FACETS	0.938	0.9	0.976	0.938	0.9	0.976	CLONAL	1	TRUE	1	0.87911361904248	2		610	1208	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576901	7576922	+	frameshift_variant	Frame_Shift_Del	DEL	AGAGGAGCTGGTGTTGTTGGGC	AGAGGAGCTGGTGTTGTTGGGC	-	novel	NA	P-0026173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	463	518	0	ENST00000269305.4:c.924_945del	p.Asn310SerfsTer28	p.N310Sfs*28	ENST00000269305	NM_001126112.2	308	ctGCCCAACAACACCAGCTCCTCT/ct	9/11	0.87911361904248	2	FACETS	0.949	0.927	0.97	0.949	0.927	0.97	CLONAL	2	TRUE	0	0.87911361904248	2		518	555	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687664	29687664	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	726	571	1	ENST00000356175.3:c.8257G>T	p.Ala2753Ser	p.A2753S	ENST00000356175	NM_000267.3	2753	Gcc/Tcc	56/57	0.520825233956103	3	FACETS	0.91	0.883	0.937	0.91	0.883	0.937	INDETERMINATE	2	TRUE	1	0.87911361904248	3		572	1307	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921448	39921448	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	174	425	0	ENST00000378444.4:c.4372G>T	p.Val1458Phe	p.V1458F	ENST00000378444	NM_001123385.1	1458	Gtc/Ttc	10/15	1	2	FACETS	0.415	0.382	0.45	0.415	0.382	0.45	SUBCLONAL	1	TRUE	1	0.87911361904248	2		425	954	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0026174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	223	423	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.319966037360404	2	FACETS	0.851	0.797	0.906	0.851	0.797	0.906	CLONAL	2	TRUE	0	0.406309176831888	2		423	645	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576105	29576105	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555617368	NA	P-0026174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	142	523	0	ENST00000356175.3:c.4078C>T	p.Gln1360Ter	p.Q1360*	ENST00000356175	NM_000267.3	1360	Caa/Taa	30/57	0.319966037360404	2	FACETS	0.927	0.855	1	0.927	0.855	1	CLONAL	2	TRUE	0	0.406309176831888	2		523	377	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724315	52724315	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	61	537	0	ENST00000322088.6:c.1447A>T	p.Ile483Phe	p.I483F	ENST00000322088	NM_014225.5	483	Atc/Ttc	12/15	1	2	FACETS	0.541	0.467	0.622	0.541	0.467	0.622	SUBCLONAL	1	TRUE	1	0.406309176831888	2		537	555	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713548	30713548	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	118	401	0	ENST00000295754.5:c.873G>T	p.Lys291Asn	p.K291N	ENST00000295754	NM_003242.5	291	aaG/aaT	4/7	0.406309176831888	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.406309176831888	1		401	382	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515172	31515172	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	139	688	1	ENST00000344624.3:c.1213G>A	p.Glu405Lys	p.E405K	ENST00000344624		405	Gaa/Aaa	5/33	0.406309176831888	3	FACETS	1	0.939	1	0.519	0.473	0.568	CLONAL	1	TRUE	1	0.406309176831888	3		689	793	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86658451	86658452	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	35	296	0	ENST00000274376.6:c.1421dup	p.Asn474LysfsTer4	p.N474Kfs*4	ENST00000274376	NM_002890.2	472	-/A	10/25	0.406309176831888	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	0	0.406309176831888	1		296	122	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68982092	68982092	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1296181442	NA	P-0026174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	27	772	0	ENST00000288368.4:c.1466T>C	p.Leu489Pro	p.L489P	ENST00000288368	NM_024870.2	489	cTt/cCt	13/40	1	2	FACETS	0.406	0.324	0.501	0.406	0.324	0.501	SUBCLONAL	1	TRUE	1	0.406309176831888	2		772	327	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357730	70357730	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	125	341	0	ENST00000374080.3:c.5981G>T	p.Arg1994Leu	p.R1994L	ENST00000374080		1994	cGg/cTg	41/45	0.204877455172738	0	FACETS	0.578	0.531	0.626			1	INDETERMINATE	2	TRUE	NA	0.406309176831888	0		341	316	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763935	76763935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	76	237	0	ENST00000373344.5:c.7373G>A	p.Gly2458Glu	p.G2458E	ENST00000373344	NM_000489.3	2458	gGa/gAa	35/35	0.204877455172738	0	FACETS	0.572	0.512	0.634			1	INDETERMINATE	2	TRUE	NA	0.406309176831888	0		237	194	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0026175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	127	683	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.199369379445086	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.2	1		683	1004	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363247	40363247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs112099561	NA	P-0026175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	80	383	0	ENST00000397332.2:c.982C>T	p.Arg328Cys	p.R328C	ENST00000397332	NM_001033082.2	328	Cgt/Tgt	3/3	0.3	2	FACETS	1	0.938	1			1	CLONAL	1	TRUE	NA	0.2	2		383	723	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37865580	37865580	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	416	611	0	ENST00000269571.5:c.449A>G	p.Lys150Arg	p.K150R	ENST00000269571		150	aAa/aGa	4/27	0.3	4	FACETS	1	0.968	1			1	CLONAL	4	TRUE	NA	0.2	4		611	1224	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703657	47703657	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	64	407	1	ENST00000233146.2:c.2157G>T	p.Leu719Phe	p.L719F	ENST00000233146	NM_000251.2	719	ttG/ttT	13/16	1	2	FACETS	0.933	0.807	1	0.933	0.807	1	CLONAL	1	TRUE	1	0.2	2		408	686	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468389	89468389	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	42	224	0	ENST00000336596.2:c.1923A>T	p.Lys641Asn	p.K641N	ENST00000336596	NM_005233.5	641	aaA/aaT	11/17	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.2	2		224	344	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942852	68942852	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	62	638	0	ENST00000288368.4:c.664G>A	p.Glu222Lys	p.E222K	ENST00000288368	NM_024870.2	222	Gaa/Aaa	6/40	1	2	FACETS	0.693	0.597	0.798	0.693	0.597	0.798	SUBCLONAL	1	TRUE	1	0.2	2		638	895	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399799	139399799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	63	570	0	ENST00000277541.6:c.4549G>T	p.Asp1517Tyr	p.D1517Y	ENST00000277541	NM_017617.3	1517	Gac/Tac	25/34	1	2	FACETS	0.67	0.578	0.771	0.67	0.578	0.771	SUBCLONAL	1	TRUE	1	0.2	2		570	940	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654857	29654857	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786202112	NA	P-0026176-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	107	246	0	ENST00000356175.3:c.5546G>A	p.Arg1849Gln	p.R1849Q	ENST00000356175	NM_000267.3	1849	cGg/cAg	37/57	0.698688179264193	3	FACETS	0.975	0.88	1	0.487	0.44	0.537	CLONAL	1	TRUE	1	0.698688179264193	3		246	424	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591135	67591136	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0026176-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	185	317	0	ENST00000274335.5:c.1732_1733del	p.Asp578ProfsTer23	p.D578Pfs*23	ENST00000274335		576	acGAga/acga	12/15	1	2	FACETS	0.761	0.715	0.806	1	0.992	1	SUBCLONAL	2	TRUE	1	0.698688179264193	2		317	348	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926872	112926872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507541	NA	P-0026176-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	138	429	0	ENST00000351677.2:c.1492C>T	p.Arg498Trp	p.R498W	ENST00000351677	NM_002834.3	498	Cgg/Tgg	13/16	1	2	FACETS	0.689	0.63	0.751	0.689	0.63	0.751	SUBCLONAL	1	TRUE	1	0.698688179264193	2		429	573	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606678	29606678	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs188859061	NA	P-0026176-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	389	468	0	ENST00000389048.3:c.1202G>A	p.Arg401Gln	p.R401Q	ENST00000389048	NM_004304.4	401	cGa/cAa	5/29	0.698688179264193	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.698688179264193	3		468	716	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528478	29528478	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1567836090	NA	P-0026176-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	318	390	0	ENST00000356175.3:c.1235A>G	p.Asn412Ser	p.N412S	ENST00000356175	NM_000267.3	412	aAt/aGt	11/57	0.698688179264193	3	FACETS	0.942	0.897	0.987	0.942	0.897	0.987	CLONAL	2	TRUE	1	0.698688179264193	3		390	652	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	264	629	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.375283055362354	3	FACETS	0.821	0.77	0.872	0.821	0.77	0.872	CLONAL	2	TRUE	1	0.412382077634484	3		629	941	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026708	6026708	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs63750668	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	281	659	1	ENST00000265849.7:c.1688G>T	p.Arg563Leu	p.R563L	ENST00000265849	NM_000535.5	563	cGa/cTa	11/15	0.375283055362354	3	FACETS	0.787	0.739	0.835	0.787	0.739	0.835	SUBCLONAL	2	TRUE	1	0.412382077634484	3		660	1045	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032069	26032069	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	195	345	0	ENST00000244661.2:c.220G>C	p.Glu74Gln	p.E74Q	ENST00000244661	NM_003537.3	74	Gaa/Caa	1/1	0.380263154008073	2	FACETS	0.936	0.875	0.999	0.936	0.875	0.999	CLONAL	2	TRUE	0	0.412382077634484	2		345	505	SUCCESS
APC	324	MSKCC	GRCh37	5	112175328	112175328	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	143	261	0	ENST00000257430.4:c.4037C>G	p.Ser1346Ter	p.S1346*	ENST00000257430	NM_000038.5	1346	tCa/tGa	16/16	0.343551747931252	2	FACETS	0.799	0.735	0.865	0.799	0.735	0.865	SUBCLONAL	2	TRUE	0	0.412382077634484	2		261	434	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602493	10602493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	199	486	0	ENST00000171111.5:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000171111	NM_203500.1	362	cGg/cAg	3/6	0.380263154008073	2	FACETS	0.932	0.871	0.994	0.932	0.871	0.994	CLONAL	2	TRUE	0	0.412382077634484	2		486	518	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422552	225422552	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	57	310	1	ENST00000264414.4:c.88G>T	p.Val30Leu	p.V30L	ENST00000264414	NM_003590.4	30	Gta/Tta	2/16	0.375283055362354	3	FACETS	0.768	0.661	0.885	0.384	0.33	0.443	SUBCLONAL	1	TRUE	1	0.412382077634484	3		311	434	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207105	1207105	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	305	698	0	ENST00000326873.7:c.193G>T	p.Glu65Ter	p.E65*	ENST00000326873	NM_000455.4	65	Gag/Tag	1/10	0.380263154008073	2	FACETS	0.978	0.927	1	0.978	0.927	1	CLONAL	2	TRUE	0	0.412382077634484	2		698	756	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212522509	212522509	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs532377012	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	84	444	0	ENST00000342788.4:c.1916C>T	p.Thr639Met	p.T639M	ENST00000342788	NM_005235.2	639	aCg/aTg	16/28	0.375283055362354	3	FACETS	0.708	0.625	0.797	0.354	0.312	0.399	SUBCLONAL	1	TRUE	1	0.412382077634484	3		444	694	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396516	30396516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs537554301	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	129	400	0	ENST00000331968.5:c.203C>T	p.Ser68Leu	p.S68L	ENST00000331968	NM_002742.2	68	tCg/tTg	1/18	0.343551747931252	2	FACETS	0.769	0.703	0.836	0.769	0.703	0.836	SUBCLONAL	2	TRUE	0	0.412382077634484	2		400	407	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	140	495	0	ENST00000269305.4:c.375+1G>T		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.375283055362354	3	FACETS	1	0.965	1	0.558	0.509	0.609	CLONAL	1	TRUE	1	0.412382077634484	3		495	734	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082599	16082599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	81	197	0	ENST00000281043.3:c.413G>A	p.Arg138His	p.R138H	ENST00000281043	NM_005378.4	138	cGc/cAc	2/3	0.375283055362354	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	1	0.412382077634484	3		197	209	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199414	11199414	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	262	559	0	ENST00000361445.4:c.5077C>T	p.His1693Tyr	p.H1693Y	ENST00000361445	NM_004958.3	1693	Cac/Tac	36/58	NA	2	FACETS	0.886	0.835	0.938			1	INDETERMINATE	2	TRUE	NA	0.412382077634484	2		559	717	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22413244	22413244	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	20	43	0	ENST00000344548.3:c.371C>G	p.Ser124Cys	p.S124C	ENST00000344548	NM_001039802.1	124	tCt/tGt	6/7	0.380263154008073	2	FACETS	1	0.924	1	0.746	0.59	0.916	CLONAL	1	TRUE	0	0.412382077634484	2		43	65	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462948	120462948	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	200	488	0	ENST00000256646.2:c.5383G>C	p.Glu1795Gln	p.E1795Q	ENST00000256646	NM_024408.3	1795	Gaa/Caa	30/34	0.412382077634484	3	FACETS	1	0.99	1			1	CLONAL	1	TRUE	NA	0.412382077634484	3		488	802	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456773	32456773	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	131	469	3	ENST00000332351.3:c.119G>A	p.Trp40Ter	p.W40*	ENST00000332351	NM_024426.4	40	tGg/tAg	1/10	0.373169572515619	2	FACETS	0.815	0.747	0.884	0.815	0.747	0.884	CLONAL	2	TRUE	0	0.412382077634484	2		472	390	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588819	69588819	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	179	637	1	ENST00000168712.1:c.417G>T	p.Met139Ile	p.M139I	ENST00000168712	NM_002007.2	139	atG/atT	2/3	0.374702425431199	4	FACETS	1	0.988	1	0.685	0.632	0.74	CLONAL	1	TRUE	2	0.412382077634484	4		638	895	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641492	18641492	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	112	550	1	ENST00000266497.5:c.2491G>T	p.Glu831Ter	p.E831*	ENST00000266497		831	Gag/Tag	17/31	0.375283055362354	3	FACETS	0.863	0.777	0.955	0.432	0.388	0.478	CLONAL	1	TRUE	1	0.412382077634484	3		551	759	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435065	110435065	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	210	557	1	ENST00000375856.3:c.3336G>T	p.Glu1112Asp	p.E1112D	ENST00000375856	NM_003749.2	1112	gaG/gaT	1/2	0.380263154008073	2	FACETS	0.918	0.859	0.977	0.918	0.859	0.977	CLONAL	2	TRUE	0	0.412382077634484	2		558	555	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059047	42059047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	179	426	0	ENST00000219905.7:c.8767C>T	p.Pro2923Ser	p.P2923S	ENST00000219905	NM_001164273.1	2923	Cca/Tca	24/24	0.302642038704771	4	FACETS	0.88	0.813	0.948	0.88	0.813	0.948	CLONAL	2	TRUE	2	0.412382077634484	4		426	697	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304415	91304415	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	219	494	0	ENST00000355112.3:c.1812G>T	p.Lys604Asn	p.K604N	ENST00000355112	NM_000057.2	604	aaG/aaT	7/22	0.302642038704771	4	FACETS	0.822	0.765	0.88	0.822	0.765	0.88	CLONAL	2	TRUE	2	0.412382077634484	4		494	913	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098705	2098705	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	126	617	0	ENST00000219476.3:c.89C>T	p.Ser30Phe	p.S30F	ENST00000219476	NM_000548.3	30	tCt/tTt	2/42	1	2	FACETS	0.661	0.598	0.727	0.661	0.598	0.727	SUBCLONAL	1	TRUE	1	0.412382077634484	2		617	925	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108852	2108852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500970	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	96	601	0	ENST00000219476.3:c.953C>T	p.Ser318Phe	p.S318F	ENST00000219476	NM_000548.3	318	tCt/tTt	10/42	1	2	FACETS	0.682	0.608	0.76	0.682	0.608	0.76	SUBCLONAL	1	TRUE	1	0.412382077634484	2		601	683	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827277	72827277	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	137	585	0	ENST00000268489.5:c.9304G>C	p.Asp3102His	p.D3102H	ENST00000268489	NM_006885.3	3102	Gac/Cac	9/10	0.329630388619751	2	FACETS	0.892	0.812	0.975	0.446	0.406	0.488	CLONAL	1	TRUE	0	0.412382077634484	2		585	745	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075208	16075208	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	224	540	0	ENST00000268712.3:c.344C>G	p.Ser115Cys	p.S115C	ENST00000268712	NM_006311.3	115	tCt/tGt	4/46	0.375283055362354	3	FACETS	0.787	0.735	0.842	0.787	0.735	0.842	SUBCLONAL	2	TRUE	1	0.412382077634484	3		540	832	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664473	29664473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	140	621	1	ENST00000356175.3:c.6452C>T	p.Ser2151Leu	p.S2151L	ENST00000356175	NM_000267.3	2151	tCa/tTa	42/57	0.375283055362354	3	FACETS	0.842	0.766	0.922	0.421	0.383	0.461	CLONAL	1	TRUE	1	0.412382077634484	3		622	973	SUCCESS
YES1	7525	MSKCC	GRCh37	18	742956	742956	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	313	574	0	ENST00000314574.4:c.1022A>G	p.Glu341Gly	p.E341G	ENST00000314574	NM_005433.3	341	gAa/gGa	8/12	NA	2	FACETS	0.995	0.944	1			1	INDETERMINATE	2	TRUE	NA	0.412382077634484	2		574	763	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575200	48575200	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	96	397	0	ENST00000342988.3:c.394C>G	p.His132Asp	p.H132D	ENST00000342988	NM_005359.5	132	Cac/Gac	3/12	0.412382077634484	1	FACETS	0.846	0.758	0.938	0.846	0.758	0.938	CLONAL	1	TRUE	0	0.412382077634484	1		397	437	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223132	1223132	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs759473833	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	270	630	0	ENST00000326873.7:c.1069G>C	p.Glu357Gln	p.E357Q	ENST00000326873	NM_000455.4	357	Gag/Cag	8/10	0.380263154008073	2	FACETS	0.908	0.857	0.96	0.908	0.857	0.96	CLONAL	2	TRUE	0	0.412382077634484	2		630	721	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2180711	2180711	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	266	569	1	ENST00000398665.3:c.82-1G>T		p.X28_splice	ENST00000398665	NM_032482.2	28			0.380263154008073	2	FACETS	0.919	0.866	0.972	0.919	0.866	0.972	CLONAL	2	TRUE	0	0.412382077634484	2		570	702	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243960	5243960	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	223	520	0	ENST00000357368.4:c.1522G>T	p.Gly508Cys	p.G508C	ENST00000357368	NM_002850.3	508	Ggc/Tgc	11/38	0.380263154008073	2	FACETS	0.897	0.841	0.954	0.897	0.841	0.954	CLONAL	2	TRUE	0	0.412382077634484	2		520	603	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105503	11105503	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	192	484	0	ENST00000358026.2:c.1420-1G>T		p.X474_splice	ENST00000358026	NM_001128849.1	474			0.380263154008073	2	FACETS	0.807	0.751	0.864	0.807	0.751	0.864	CLONAL	2	TRUE	0	0.412382077634484	2		484	577	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248362	212248362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	76	268	0	ENST00000342788.4:c.3905G>A	p.Arg1302Lys	p.R1302K	ENST00000342788	NM_005235.2	1302	aGa/aAa	28/28	0.375283055362354	3	FACETS	1	0.964	1	0.621	0.548	0.698	CLONAL	1	TRUE	1	0.412382077634484	3		268	358	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440233	220440233	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	137	664	1	ENST00000243786.2:c.1086C>A	p.His362Gln	p.H362Q	ENST00000243786	NM_002191.3	362	caC/caA	2/2	0.375283055362354	3	FACETS	0.966	0.879	1	0.483	0.439	0.529	CLONAL	1	TRUE	1	0.412382077634484	3		665	830	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944527	40944527	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs371433526	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	130	580	0	ENST00000373198.4:c.1975G>T	p.Asp659Tyr	p.D659Y	ENST00000373198	NM_133170.3	659	Gat/Tat	12/32	0.375283055362354	3	FACETS	1	0.961	1	0.553	0.503	0.607	CLONAL	1	TRUE	1	0.412382077634484	3		580	687	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121033	29121033	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555926862	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	314	641	0	ENST00000328354.6:c.524T>C	p.Val175Ala	p.V175A	ENST00000328354	NM_007194.3	175	gTa/gCa	4/15	0.374702425431199	4	FACETS	0.873	0.823	0.924	0.873	0.823	0.924	CLONAL	2	TRUE	2	0.412382077634484	4		641	1232	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582070	189582070	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	247	570	0	ENST00000264731.3:c.629C>A	p.Pro210His	p.P210H	ENST00000264731	NM_003722.4	210	cCc/cAc	5/14	0.374702425431199	4	FACETS	0.896	0.839	0.955	0.896	0.839	0.955	CLONAL	2	TRUE	2	0.412382077634484	4		570	944	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250862	153250862	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	210	547	0	ENST00000281708.4:c.1198G>A	p.Asp400Asn	p.D400N	ENST00000281708	NM_033632.3	400	Gac/Aac	8/12	0.343551747931252	2	FACETS	0.758	0.707	0.81	0.758	0.707	0.81	SUBCLONAL	2	TRUE	0	0.412382077634484	2		547	672	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950435	38950435	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	205	431	0	ENST00000357387.3:c.3515C>G	p.Thr1172Ser	p.T1172S	ENST00000357387	NM_152756.3	1172	aCt/aGt	31/38	0.302642038704771	4	FACETS	0.944	0.878	1	0.944	0.878	1	CLONAL	2	TRUE	2	0.412382077634484	4		431	744	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517466	176517466	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	243	634	2	ENST00000292408.4:c.167G>T	p.Cys56Phe	p.C56F	ENST00000292408	NM_213647.1	56	tGc/tTc	3/18	0.380263154008073	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.412382077634484	2		636	575	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056706	180056706	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	215	539	2	ENST00000261937.6:c.806C>A	p.Pro269Gln	p.P269Q	ENST00000261937	NM_182925.4	269	cCa/cAa	6/30	0.380263154008073	2	FACETS	0.841	0.786	0.897	0.841	0.786	0.897	CLONAL	2	TRUE	0	0.412382077634484	2		541	620	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983286	149983286	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	313	615	0	ENST00000253339.5:c.2972G>T	p.Gly991Val	p.G991V	ENST00000253339		991	gGa/gTa	7/7	0.308917857823573	3	FACETS	0.897	0.847	0.947	0.897	0.847	0.947	CLONAL	2	TRUE	1	0.412382077634484	3		615	1021	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163775	152163775	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	103	531	1	ENST00000206249.3:c.496G>A	p.Ala166Thr	p.A166T	ENST00000206249	NM_000125.3	166	Gcc/Acc	2/8	0.308917857823573	3	FACETS	0.876	0.784	0.973	0.438	0.392	0.487	CLONAL	1	TRUE	1	0.412382077634484	3		532	688	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265452	152265452	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	218	536	0	ENST00000206249.3:c.905A>T	p.Lys302Met	p.K302M	ENST00000206249	NM_000125.3	302	aAg/aTg	4/8	0.308917857823573	3	FACETS	0.884	0.826	0.944	0.884	0.826	0.944	CLONAL	2	TRUE	1	0.412382077634484	3		536	721	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953041	2953041	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	238	627	1	ENST00000396946.4:c.2899C>A	p.Arg967Ser	p.R967S	ENST00000396946	NM_032415.4	967	Cgc/Agc	22/25	0.375283055362354	3	FACETS	0.888	0.832	0.946	0.888	0.832	0.946	CLONAL	2	TRUE	1	0.412382077634484	3		628	784	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467634	50467634	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	98	367	0	ENST00000331340.3:c.869A>G	p.Asp290Gly	p.D290G	ENST00000331340	NM_006060.4	290	gAc/gGc	8/8	0.375283055362354	3	FACETS	1	0.961	1	0.578	0.518	0.642	CLONAL	1	TRUE	1	0.412382077634484	3		367	496	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334963	81334963	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	118	500	1	ENST00000222390.5:c.1864T>A	p.Leu622Met	p.L622M	ENST00000222390	NM_000601.4	622	Ttg/Atg	16/18	0.375283055362354	3	FACETS	0.862	0.777	0.951	0.431	0.388	0.476	CLONAL	1	TRUE	1	0.412382077634484	3		501	801	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508509	106508509	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	90	237	0	ENST00000359195.3:c.503T>A	p.Val168Glu	p.V168E	ENST00000359195	NM_002649.2	168	gTg/gAg	2/11	0.375283055362354	3	FACETS	0.779	0.697	0.864	0.779	0.697	0.864	SUBCLONAL	2	TRUE	1	0.412382077634484	3		237	338	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849873	151849874	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	184	404	0	ENST00000262189.6:c.12442_12443delinsTT	p.Pro4148Leu	p.P4148L	ENST00000262189	NM_170606.2	4148	CCg/TTg	49/59	0.375283055362354	3	FACETS	0.842	0.781	0.905	0.842	0.781	0.905	CLONAL	2	TRUE	1	0.412382077634484	3		404	639	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371682	55371684	+	missense_variant	Missense_Mutation	TNP	GCG	GCG	TGC	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	84	542	1	ENST00000297316.4:c.372_374delinsTGC	p.Arg125Ala	p.R125A	ENST00000297316	NM_022454.3	124	ctGCGc/ctTGCc	2/2	1	2	FACETS	0.813	0.72	0.912	0.813	0.72	0.912	CLONAL	1	TRUE	1	0.412382077634484	2		543	501	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371726	55371726	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	80	437	0	ENST00000297316.4:c.416C>G	p.Pro139Arg	p.P139R	ENST00000297316	NM_022454.3	139	cCg/cGg	2/2	1	2	FACETS	0.951	0.842	1	0.951	0.842	1	CLONAL	1	TRUE	1	0.412382077634484	2		437	408	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981334	68981334	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	152	558	0	ENST00000288368.4:c.1406T>G	p.Phe469Cys	p.F469C	ENST00000288368	NM_024870.2	469	tTt/tGt	12/40	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.412382077634484	2		558	663	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980726	70980726	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	190	641	0	ENST00000276594.2:c.742C>T	p.Gln248Ter	p.Q248*	ENST00000276594	NM_024504.3	248	Caa/Taa	3/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.412382077634484	2		641	817	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040965	47040965	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	123	622	0	ENST00000377604.3:c.1495G>T	p.Ala499Ser	p.A499S	ENST00000377604	NM_001204468.1	499	Gcc/Tcc	14/24	1	2	FACETS	0.751	0.679	0.827	0.751	0.679	0.827	SUBCLONAL	1	TRUE	1	0.412382077634484	2		622	794	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939274	76939274	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1418531949	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	139	689	0	ENST00000373344.5:c.1474G>A	p.Glu492Lys	p.E492K	ENST00000373344	NM_000489.3	492	Gaa/Aaa	9/35	1	2	FACETS	0.712	0.647	0.78	0.712	0.647	0.78	SUBCLONAL	1	TRUE	1	0.412382077634484	2		689	947	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76954118	76954118	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	109	501	0	ENST00000373344.5:c.134-1G>C		p.X45_splice	ENST00000373344	NM_000489.3	45			1	2	FACETS	0.832	0.749	0.921	0.832	0.749	0.921	CLONAL	1	TRUE	1	0.412382077634484	2		501	635	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223726	36223727	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	T	novel	NA	P-0026187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	559	722	0	ENST00000222270.7:c.6276_6277delinsT	p.Ala2093GlnfsTer26	p.A2093Qfs*26	ENST00000222270	NM_014727.1	2092	cgGGca/cgTca	28/37	0.412382077634484	4	FACETS	0.99	0.957	1			1	CLONAL	4	TRUE	NA	0.412382077634484	4		722	967	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797333	45797333	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	104	374	0	ENST00000450313.1:c.1186G>C	p.Gly396Arg	p.G396R	ENST00000450313	NM_012222.2	396	Ggt/Cgt	12/16	0.319649801997729	5	FACETS	0.904	0.818	0.992	0.452	0.409	0.496	INDETERMINATE	2	FALSE	1	0.722388749879626	5		374	332	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649908	88649908	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	55	399	1	ENST00000372037.3:c.157G>T	p.Glu53Ter	p.E53*	ENST00000372037	NM_004329.2	53	Gag/Tag	4/13	0.631157021080657	4	FACETS	0.719	0.617	0.828			1	SUBCLONAL	1	FALSE	NA	0.722388749879626	4		400	365	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0026191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	154	591	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.952	0.874	1	0.952	0.874	1	CLONAL	1	TRUE	1	0.476278724167647	2		591	679	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	92	633	0	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	0.476278724167647	1	FACETS	0.526	0.468	0.587	0.526	0.468	0.587	SUBCLONAL	1	TRUE	0	0.476278724167647	1		633	560	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089499	27089499	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	83	622	1	ENST00000324856.7:c.2457del	p.Asn820MetfsTer13	p.N820Mfs*13	ENST00000324856	NM_006015.4	819	Ccc/cc	8/20	0.248827759631896	1	FACETS	0.473	0.418	0.532	0.473	0.418	0.532	INDETERMINATE	1	TRUE	0	0.476278724167647	1		623	561	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982411	201982411	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	83	629	0	ENST00000359651.3:c.790A>C	p.Lys264Gln	p.K264Q	ENST00000359651		264	Aag/Cag	6/8	1	2	FACETS	0.496	0.438	0.559	0.496	0.438	0.559	SUBCLONAL	1	TRUE	1	0.476278724167647	2		629	702	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115713	8115888	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAGAACAGCTCGTTTAACCCGGCCGCCCTCTCCAGACACATGTCCTCCCTGAGCCACATCTCGCCCTTCAGCCACT	CCTGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAGAACAGCTCGTTTAACCCGGCCGCCCTCTCCAGACACATGTCCTCCCTGAGCCACATCTCGCCCTTCAGCCACT	-	novel	NA	P-0026191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	94	378	0	ENST00000346208.3:c.1061_1236del	p.Leu354GlnfsTer94	p.L354Qfs*94	ENST00000346208		353	ccCCTGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAGAACAGCTCGTTTAACCCGGCCGCCCTCTCCAGACACATGTCCTCCCTGAGCCACATCTCGCCCTTCAGCCACTcc/cccc	6/6	1	2	FACETS	0.972	0.871	1	0.972	0.871	1	CLONAL	1	TRUE	1	0.476278724167647	2		378	406	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457809	69457809	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	46	269	0	ENST00000227507.2:c.209A>C	p.Glu70Ala	p.E70A	ENST00000227507	NM_053056.2	70	gAa/gCa	2/5	0.476278724167647	5	FACETS	0.576	0.484	0.677			1	SUBCLONAL	1	TRUE	NA	0.476278724167647	5		269	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573922	7573977	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCACCTGGAGTGAGCCCTGCTCCCCCCTGGCTCCTTCCCAGCCTGGGCATCCTTG	CTCACCTGGAGTGAGCCCTGCTCCCCCCTGGCTCCTTCCCAGCCTGGGCATCCTTG	-	novel	NA	P-0026191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	130	428	0	ENST00000269305.4:c.1050_1100+5del		p.X350_splice	ENST00000269305	NM_001126112.2	350		10/11	0.476278724167647	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.476278724167647	1		428	411	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721531	49721531	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	66	547	0	ENST00000449682.2:c.2108G>T	p.Arg703Leu	p.R703L	ENST00000449682	NM_020998.3	703	cGc/cTc	18/18	0.476278724167647	1	FACETS	0.506	0.441	0.577	0.506	0.441	0.577	SUBCLONAL	1	TRUE	0	0.476278724167647	1		547	417	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265645	152265645	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0026191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	62	333	0	ENST00000206249.3:c.1096+2T>C		p.X366_splice	ENST00000206249	NM_000125.3	366			0.476278724167647	1	FACETS	0.456	0.395	0.522	0.456	0.395	0.522	SUBCLONAL	1	TRUE	0	0.476278724167647	1		333	435	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685314	89685315	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TG	TG	-	rs1564826836	NA	P-0026192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	162	436	0	ENST00000371953.3:c.209+1_209+2del		p.X70_splice	ENST00000371953	NM_000314.4	70		3/9	0.337643240525277	3	FACETS	1	0.981	1	0.781	0.724	0.84	CLONAL	2	TRUE	0	0.374735314941854	3		436	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0026192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	260	691	0	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.374735314941854	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.374735314941854	2		691	687	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922301	178922301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	203	535	0	ENST00000263967.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000263967	NM_006218.2	357	cGa/cAa	6/21	0.374735314941854	4	FACETS	1	0.96	1	0.697	0.649	0.747	CLONAL	2	TRUE	1	0.374735314941854	4		535	712	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26911754	26911754	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	339	610	0	ENST00000381527.3:c.179C>A	p.Ser60Tyr	p.S60Y	ENST00000381527	NM_001260.1	60	tCt/tAt	2/13	0.374735314941854	6	FACETS	0.951	0.904	0.999	0.761	0.723	0.799	CLONAL	4	TRUE	1	0.374735314941854	6		610	832	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945648	54945648	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	51	257	0	ENST00000312783.6:c.922G>T	p.Glu308Ter	p.E308*	ENST00000312783	NM_198436.1	308	Gag/Tag	9/10	0.374735314941854	6	FACETS	1	0.942	1	0.407	0.347	0.473	CLONAL	1	TRUE	3	0.374735314941854	6		257	390	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990444	81990444	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1471753383	NA	P-0026193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	58	765	1	ENST00000359376.3:c.3715G>A	p.Glu1239Lys	p.E1239K	ENST00000359376	NM_002661.3	1239	Gag/Aag	32/33	0.68386032659607	3	FACETS	0.227	0.194	0.263	0.113	0.097	0.132	SUBCLONAL	1	TRUE	1	0.700776616714829	3		766	985	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579519	7579523	+	frameshift_variant	Frame_Shift_Del	DEL	TTCAG	TTCAG	-	novel	NA	P-0026193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	857	767	0	ENST00000269305.4:c.164_168del	p.Thr55ArgfsTer6	p.T55Rfs*6	ENST00000269305	NM_001126112.2	55	aCTGAA/a	4/11	0.568304822610004	4	FACETS	0.927	0.908	0.945			1	CLONAL	4	TRUE	NA	0.700776616714829	4		767	1122	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324010	31324010	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs41558016	NA	P-0026193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	39	311	0	ENST00000412585.2:c.553G>C	p.Glu185Gln	p.E185Q	ENST00000412585	NM_005514.6	185	Gag/Cag	3/8	0.570042338236418	3	FACETS	0.32	0.265	0.381	0.107	0.088	0.127	SUBCLONAL	1	TRUE	0	0.700776616714829	3		311	470	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0026194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	792	550	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.67333383165222	5	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	2	0.67333383165222	5		550	1479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577529	7577529	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs730882027	NA	P-0026194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	467	564	0	ENST00000269305.4:c.752T>G	p.Ile251Ser	p.I251S	ENST00000269305	NM_001126112.2	251	aTc/aGc	7/11	0.67333383165222	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.67333383165222	2		564	692	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0026196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	123	572	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	0.267279008580621	2		572	681	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	146	483	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.968	0.887	1	0.968	0.887	1	CLONAL	1	TRUE	1	0.502055590061328	2		483	601	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	109	424	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.83	0.749	0.916	0.83	0.749	0.916	CLONAL	1	TRUE	1	0.502055590061328	2		424	523	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	90	419	6	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	1	2	FACETS	0.99	0.886	1	0.99	0.886	1	CLONAL	1	TRUE	1	0.502055590061328	2		425	362	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	229	892	13	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	0.502055590061328	2		905	767	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	131	551	3	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.502055590061328	2		554	471	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	214	568	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	0.502055590061328	3	FACETS	1	0.991	1	0.7	0.652	0.749	CLONAL	1	TRUE	1	0.502055590061328	3		570	762	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	149	662	0	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	0.903	0.828	0.982	0.903	0.828	0.982	CLONAL	1	TRUE	1	0.502055590061328	2		662	657	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	114	528	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.923	0.835	1	0.923	0.835	1	CLONAL	1	TRUE	1	0.502055590061328	2		528	492	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	127	709	4	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.933	0.849	1	0.933	0.849	1	CLONAL	1	TRUE	1	0.502055590061328	2		713	542	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781141	135781141	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs118203585	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	163	679	0	ENST00000298552.3:c.1824del	p.Phe608LeufsTer21	p.F608Lfs*21	ENST00000298552	NM_001162426.1	608	ttT/tt	15/23	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.502055590061328	2		679	624	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161907	47161907	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	26	505	0	ENST00000409792.3:c.4219del	p.Arg1407GlyfsTer5	p.R1407Gfs*5	ENST00000409792	NM_014159.6	1407	Agg/gg	3/21	1	2	FACETS	0.229	0.18	0.284	0.229	0.18	0.284	SUBCLONAL	1	TRUE	1	0.502055590061328	2		505	453	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	135	601	2	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.972	0.888	1	0.972	0.888	1	CLONAL	1	TRUE	1	0.502055590061328	2		603	553	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406317	406318	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	221	729	0	ENST00000399788.2:c.4123dup	p.Cys1375LeufsTer2	p.C1375Lfs*2	ENST00000399788	NM_001042603.1	1375	tgt/tTgt	25/28	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.502055590061328	2		729	801	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953632	32953633	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359732	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	115	527	0	ENST00000380152.3:c.8940dup	p.Glu2981ArgfsTer37	p.E2981Rfs*37	ENST00000380152		2978	tca/tcAa	22/27	1	2	FACETS	0.817	0.738	0.899	0.817	0.738	0.899	CLONAL	1	TRUE	1	0.502055590061328	2		527	561	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446269	187446270	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770320988	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	130	619	0	ENST00000232014.4:c.1418dup	p.Lys474GlufsTer26	p.K474Efs*26	ENST00000232014	NM_001130845.1	473	ccg/ccCg	6/10	1	2	FACETS	0.918	0.836	1	0.918	0.836	1	CLONAL	1	TRUE	1	0.502055590061328	2		619	564	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	68	272	1	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.809	0.708	0.915	0.809	0.708	0.915	CLONAL	1	TRUE	1	0.502055590061328	2		273	335	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554355	81554355	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747687365	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	107	586	0	ENST00000298171.2:c.379del	p.Leu127SerfsTer2	p.L127Sfs*2	ENST00000298171	NM_000369.2	125	ctC/ct	4/10	1	2	FACETS	0.899	0.811	0.992	0.899	0.811	0.992	CLONAL	1	TRUE	1	0.502055590061328	2		586	474	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687471	37687472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs760014508	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	46	408	1	ENST00000447079.4:c.4382dup	p.Thr1463AsnfsTer50	p.T1463Nfs*50	ENST00000447079	NM_015083.1	1459	tgg/tGgg	14/14	1	2	FACETS	0.566	0.478	0.661	0.566	0.478	0.661	SUBCLONAL	1	TRUE	1	0.502055590061328	2		409	324	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245587	41245587	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357522	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	185	744	5	ENST00000357654.3:c.1961del	p.Lys654SerfsTer47	p.K654Sfs*47	ENST00000357654	NM_007294.3	654	aAg/ag	10/23	1	2	FACETS	0.952	0.881	1	0.952	0.881	1	CLONAL	1	TRUE	1	0.502055590061328	2		749	774	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117594	70117594	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	150	519	2	ENST00000245479.2:c.66del	p.Ser23AlafsTer38	p.S23Afs*38	ENST00000245479	NM_000346.3	21	gCc/gc	1/3	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.502055590061328	2		521	525	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434413	140434413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775889922	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	127	582	0	ENST00000288602.6:c.2285C>T	p.Ala762Val	p.A762V	ENST00000288602	NM_004333.4	762	gCg/gTg	18/18	1	2	FACETS	0.886	0.806	0.97	0.886	0.806	0.97	CLONAL	1	TRUE	1	0.502055590061328	2		582	571	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567647	226567647	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	134	588	2	ENST00000366794.5:c.1519del	p.Ser507AlafsTer17	p.S507Afs*17	ENST00000366794	NM_001618.3	507	Agc/gc	10/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.502055590061328	2		590	446	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884908	134884908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202034365	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	125	534	0	ENST00000398015.3:c.1684G>A	p.Val562Ile	p.V562I	ENST00000398015	NM_004441.4	562	Gtc/Atc	8/16	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.502055590061328	2		534	489	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248123	59248123	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs370122841	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	30	100	0	ENST00000371222.2:c.620C>A	p.Pro207Gln	p.P207Q	ENST00000371222	NM_002228.3	207	cCg/cAg	1/1	1	2	FACETS	0.948	0.778	1	0.948	0.778	1	CLONAL	1	TRUE	1	0.502055590061328	2		100	126	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439919	56439919	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	196	585	2	ENST00000407977.2:c.673del	p.Arg225AlafsTer194	p.R225Afs*194	ENST00000407977		225	Cgc/gc	6/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.502055590061328	2		587	623	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21304066	21304066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444326760	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	203	703	2	ENST00000354336.3:c.845G>A	p.Arg282His	p.R282H	ENST00000354336	NM_005207.3	282	cGc/cAc	3/3	1	2	FACETS	0.98	0.911	1	0.98	0.911	1	CLONAL	1	TRUE	1	0.502055590061328	2		705	825	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993731	72993731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	63	423	4	ENST00000268489.5:c.314del	p.Pro105ArgfsTer4	p.P105Rfs*4	ENST00000268489	NM_006885.3	105	cCg/cg	2/10	1	2	FACETS	0.787	0.685	0.895	0.787	0.685	0.895	SUBCLONAL	1	TRUE	1	0.502055590061328	2		427	319	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259043	16259043	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	137	655	0	ENST00000375759.3:c.6313del	p.Ala2105LeufsTer33	p.A2105Lfs*33	ENST00000375759	NM_015001.2	2103	aGg/ag	11/15	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.502055590061328	2		655	506	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	115	639	0	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.82	0.741	0.902	0.82	0.741	0.902	CLONAL	1	TRUE	1	0.502055590061328	2		639	559	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630173	100630173	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141488935	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	38	669	0	ENST00000308731.7:c.100G>A	p.Val34Met	p.V34M	ENST00000308731	NM_000061.2	34	Gtg/Atg	2/19	1	2	FACETS	0.244	0.201	0.292	0.244	0.201	0.292	SUBCLONAL	1	TRUE	1	0.502055590061328	2		669	620	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468282	50468282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	144	657	0	ENST00000331340.3:c.1517C>T	p.Ser506Leu	p.S506L	ENST00000331340	NM_006060.4	506	tCg/tTg	8/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.502055590061328	2		657	505	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242899	142242899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750252420	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	176	683	1	ENST00000350721.4:c.4088C>T	p.Ala1363Val	p.A1363V	ENST00000350721	NM_001184.3	1363	gCg/gTg	22/47	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.502055590061328	2		684	671	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549394	21549394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148935054	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	97	484	1	ENST00000382592.4:c.2882G>A	p.Arg961Gln	p.R961Q	ENST00000382592	NM_014572.2	961	cGg/cAg	8/8	1	2	FACETS	0.959	0.861	1	0.959	0.861	1	CLONAL	1	TRUE	1	0.502055590061328	2		485	403	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466824	57466826	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	100	350	0	ENST00000371085.3:c.46_48del	p.Glu16del	p.E16del	ENST00000371085	NM_000516.4	15	GAG/-	1/13	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.502055590061328	2		350	389	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213243	39213243	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	177	787	1	ENST00000402219.2:c.3724del	p.Ser1242ValfsTer37	p.S1242Vfs*37	ENST00000402219	NM_005633.3	1242	Agt/gt	23/23	0.502055590061328	3	FACETS	0.986	0.909	1	0.493	0.454	0.533	CLONAL	1	TRUE	1	0.502055590061328	3		788	895	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375152	118375152	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	95	474	0	ENST00000534358.1:c.8545C>T	p.Pro2849Ser	p.P2849S	ENST00000534358	NM_005933.3	2849	Cct/Tct	27/36	1	2	FACETS	0.884	0.792	0.981	0.884	0.792	0.981	CLONAL	1	TRUE	1	0.502055590061328	2		474	428	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994829	73994829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751833994	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	33	229	1	ENST00000318443.5:c.313G>A	p.Ala105Thr	p.A105T	ENST00000318443	NM_001024736.1	105	Gca/Aca	3/10	1	2	FACETS	0.674	0.554	0.807	0.674	0.554	0.807	SUBCLONAL	1	TRUE	1	0.502055590061328	2		230	195	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303302	11303304	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	202	767	1	ENST00000361445.4:c.1279_1281del	p.Glu427del	p.E427del	ENST00000361445	NM_004958.3	427	GAG/-	9/58	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.502055590061328	2		768	713	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256232	16256232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749550885	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	173	743	1	ENST00000375759.3:c.3497C>T	p.Thr1166Met	p.T1166M	ENST00000375759	NM_015001.2	1166	aCg/aTg	11/15	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.502055590061328	2		744	682	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743365	162743365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1433720646	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	108	434	0	ENST00000367921.3:c.1835C>T	p.Ala612Val	p.A612V	ENST00000367921	NM_006182.2	612	gCa/gTa	14/18	1	2	FACETS	0.933	0.842	1	0.933	0.842	1	CLONAL	1	TRUE	1	0.502055590061328	2		434	461	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163295914	163295914	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	160	855	1	ENST00000271452.3:c.73G>T	p.Gly25Ter	p.G25*	ENST00000271452	NM_145697.2	25	Gga/Tga	2/14	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.502055590061328	2		856	626	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451480	70451480	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1468649418	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	183	771	0	ENST00000373644.4:c.6320A>G	p.His2107Arg	p.H2107R	ENST00000373644	NM_030625.2	2107	cAt/cGt	12/12	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.502055590061328	2		771	708	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659599	88659599	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	187	657	0	ENST00000372037.3:c.382A>G	p.Asn128Asp	p.N128D	ENST00000372037	NM_004329.2	128	Aat/Gat	6/13	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.502055590061328	2		657	653	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998234	100998234	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	65	358	0	ENST00000325455.5:c.1568T>C	p.Leu523Pro	p.L523P	ENST00000325455	NM_001202474.3	523	cTc/cCc	1/8	1	2	FACETS	0.902	0.789	1	0.902	0.789	1	CLONAL	1	TRUE	1	0.502055590061328	2		358	287	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023182	1023182	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	148	650	0	ENST00000358495.3:c.1073T>C	p.Leu358Ser	p.L358S	ENST00000358495	NM_134424.2	358	tTa/tCa	11/12	NA	2	FACETS	0.959	0.879	1			1	INDETERMINATE	1	TRUE	NA	0.502055590061328	2		650	615	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495660	56495660	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	127	546	1	ENST00000267101.3:c.3850G>A	p.Ala1284Thr	p.A1284T	ENST00000267101	NM_001982.3	1284	Gca/Aca	28/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.502055590061328	2		547	443	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120806011	120806011	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	142	648	1	ENST00000257552.2:c.166del	p.Leu56Ter	p.L56*	ENST00000257552	NM_002442.3	56	Ctg/tg	3/15	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.502055590061328	2		649	554	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240687	133240687	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060500875	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	32	727	0	ENST00000320574.5:c.2609A>G	p.Asn870Ser	p.N870S	ENST00000320574	NM_006231.2	870	aAc/aGc	23/49	1	2	FACETS	0.209	0.169	0.254	0.209	0.169	0.254	SUBCLONAL	1	TRUE	1	0.502055590061328	2		727	611	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435790	110435790	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1446914389	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	10	232	2	ENST00000375856.3:c.2611C>T	p.Arg871Trp	p.R871W	ENST00000375856	NM_003749.2	871	Cgg/Tgg	1/2	1	2	FACETS	0.213	0.144	0.3	0.213	0.144	0.3	SUBCLONAL	1	TRUE	1	0.502055590061328	2		234	187	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437532	110437532	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	126	644	0	ENST00000375856.3:c.869C>T	p.Ala290Val	p.A290V	ENST00000375856	NM_003749.2	290	gCc/gTc	1/2	1	2	FACETS	0.874	0.795	0.958	0.874	0.795	0.958	CLONAL	1	TRUE	1	0.502055590061328	2		644	574	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30133062	30133062	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	91	432	0	ENST00000331968.5:c.539G>A	p.Cys180Tyr	p.C180Y	ENST00000331968	NM_002742.2	180	tGt/tAt	4/18	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.502055590061328	2		432	347	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986898	36986898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	100	314	3	ENST00000354822.5:c.791G>A	p.Gly264Asp	p.G264D	ENST00000354822	NM_001079668.2	264	gGc/gAc	3/3	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.502055590061328	2		317	353	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42002990	42002990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	172	749	0	ENST00000219905.7:c.2527G>A	p.Gly843Ser	p.G843S	ENST00000219905	NM_001164273.1	843	Ggt/Agt	8/24	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.502055590061328	2		749	684	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632600	3632600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771897046	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	33	786	1	ENST00000294008.3:c.5248G>A	p.Ala1750Thr	p.A1750T	ENST00000294008	NM_032444.2	1750	Gcg/Acg	15/15	1	2	FACETS	0.219	0.178	0.266	0.219	0.178	0.266	SUBCLONAL	1	TRUE	1	0.502055590061328	2		787	599	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778167	3778167	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793091	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	133	685	1	ENST00000262367.5:c.6881G>A	p.Arg2294Gln	p.R2294Q	ENST00000262367	NM_004380.2	2294	cGg/cAg	31/31	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.502055590061328	2		686	525	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029286	14029286	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	127	456	0	ENST00000311895.7:c.1500del	p.Lys500AsnfsTer19	p.K500Nfs*19	ENST00000311895	NM_005236.2	499	ggA/gg	8/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.502055590061328	2		456	456	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953241	81953241	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1195957943	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	120	413	1	ENST00000359376.3:c.2211del	p.Glu738SerfsTer12	p.E738Sfs*12	ENST00000359376	NM_002661.3	736	aCc/ac	20/33	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.502055590061328	2		414	420	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357465	89357465	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	161	721	0	ENST00000301030.4:c.353C>T	p.Ala118Val	p.A118V	ENST00000301030	NM_001256183.1	118	gCc/gTc	5/13	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.502055590061328	2		721	577	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15952264	15952264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779213445	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	185	771	0	ENST00000268712.3:c.6431C>T	p.Ser2144Leu	p.S2144L	ENST00000268712	NM_006311.3	2144	tCg/tTg	41/46	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.502055590061328	2		771	703	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489501	40489501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	141	661	0	ENST00000264657.5:c.749C>T	p.Ala250Val	p.A250V	ENST00000264657	NM_139276.2	250	gCc/gTc	8/24	1	2	FACETS	0.879	0.803	0.958	0.879	0.803	0.958	CLONAL	1	TRUE	1	0.502055590061328	2		661	639	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234583	41234583	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	38	587	0	ENST00000357654.3:c.4195A>G	p.Thr1399Ala	p.T1399A	ENST00000357654	NM_007294.3	1399	Acc/Gcc	12/23	1	2	FACETS	0.256	0.211	0.306	0.256	0.211	0.306	SUBCLONAL	1	TRUE	1	0.502055590061328	2		587	592	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58711218	58711218	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	159	613	1	ENST00000305921.3:c.706A>G	p.Met236Val	p.M236V	ENST00000305921	NM_003620.3	236	Atg/Gtg	3/6	1	2	FACETS	0.966	0.888	1	0.966	0.888	1	CLONAL	1	TRUE	1	0.502055590061328	2		614	656	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119773	70119803	+	frameshift_variant	Frame_Shift_Del	DEL	TTGCCAGAGGGGGGCAGACAGCCCCCTATCG	TTGCCAGAGGGGGGCAGACAGCCCCCTATCG	-	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	140	604	0	ENST00000245479.2:c.775_805del	p.Leu259ThrfsTer10	p.L259Tfs*10	ENST00000245479	NM_000346.3	259	TTGCCAGAGGGGGGCAGACAGCCCCCTATCGac/ac	3/3	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.502055590061328	2		604	519	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732278	74732278	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	76	348	0	ENST00000359995.5:c.631A>G	p.Lys211Glu	p.K211E	ENST00000359995	NM_001195427.1	211	Aag/Gag	2/3	1	2	FACETS	0.893	0.789	1	0.893	0.789	1	CLONAL	1	TRUE	1	0.502055590061328	2		348	339	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226433	2226433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	137	737	2	ENST00000398665.3:c.3913G>A	p.Gly1305Arg	p.G1305R	ENST00000398665	NM_032482.2	1305	Gga/Aga	27/28	1	2	FACETS	0.941	0.859	1	0.941	0.859	1	CLONAL	1	TRUE	1	0.502055590061328	2		739	580	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629007	14629007	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	133	596	0	ENST00000254322.2:c.155A>G	p.Tyr52Cys	p.Y52C	ENST00000254322	NM_006145.1	52	tAc/tGc	1/3	1	2	FACETS	0.871	0.794	0.952	0.871	0.794	0.952	CLONAL	1	TRUE	1	0.502055590061328	2		596	608	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300195	15300195	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	174	755	1	ENST00000263388.2:c.1081C>A	p.His361Asn	p.H361N	ENST00000263388	NM_000435.2	361	Cac/Aac	7/33	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.502055590061328	2		756	676	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302570	15302570	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	132	665	1	ENST00000263388.2:c.788C>A	p.Pro263His	p.P263H	ENST00000263388	NM_000435.2	263	cCt/cAt	5/33	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.502055590061328	2		666	522	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387345	17387345	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550805861	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	177	805	0	ENST00000359435.4:c.611C>T	p.Thr204Met	p.T204M	ENST00000359435	NM_001033549.1	204	aCg/aTg	7/9	1	2	FACETS	0.999	0.923	1	0.999	0.923	1	CLONAL	1	TRUE	1	0.502055590061328	2		805	706	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221657	36221657	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	171	801	0	ENST00000222270.7:c.5326T>C	p.Tyr1776His	p.Y1776H	ENST00000222270	NM_014727.1	1776	Tat/Cat	26/37	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.502055590061328	2		801	678	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223319	36223327	+	inframe_deletion	In_Frame_Del	DEL	GAGCTGGCT	GAGCTGGCT	-	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	155	839	0	ENST00000222270.7:c.5869_5877del	p.Glu1957_Ala1959del	p.E1957_A1959del	ENST00000222270	NM_014727.1	1957	GAGCTGGCT/-	28/37	1	2	FACETS	0.941	0.864	1	0.941	0.864	1	CLONAL	1	TRUE	1	0.502055590061328	2		839	656	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967156	25967156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201808592	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	65	378	0	ENST00000435504.4:c.2050G>A	p.Ala684Thr	p.A684T	ENST00000435504		684	Gcc/Acc	13/13	0.502055590061328	3	FACETS	0.912	0.796	1	0.456	0.398	0.519	CLONAL	1	TRUE	1	0.502055590061328	3		378	355	SUCCESS
REL	5966	MSKCC	GRCh37	2	61121628	61121628	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	172	738	0	ENST00000295025.8:c.250T>G	p.Cys84Gly	p.C84G	ENST00000295025	NM_002908.2	84	Tgc/Ggc	3/11	0.502055590061328	3	FACETS	1	0.955	1	0.527	0.485	0.57	CLONAL	1	TRUE	1	0.502055590061328	3		738	814	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145678	61145678	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773764180	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	107	634	0	ENST00000295025.8:c.790C>T	p.Arg264Trp	p.R264W	ENST00000295025	NM_002908.2	264	Cgg/Tgg	7/11	0.502055590061328	3	FACETS	0.657	0.589	0.729	0.328	0.294	0.365	SUBCLONAL	1	TRUE	1	0.502055590061328	3		634	812	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881602	111881602	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	158	690	0	ENST00000393256.3:c.280A>G	p.Ser94Gly	p.S94G	ENST00000393256	NM_006538.4	94	Agt/Ggt	2/4	0.502055590061328	3	FACETS	0.987	0.905	1	0.493	0.452	0.536	CLONAL	1	TRUE	1	0.502055590061328	3		690	798	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617541	158617541	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1398213948	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	129	574	0	ENST00000263640.3:c.1115A>G	p.Asn372Ser	p.N372S	ENST00000263640	NM_001105.4	372	aAc/aGc	9/11	0.502055590061328	3	FACETS	0.973	0.884	1	0.486	0.442	0.533	CLONAL	1	TRUE	1	0.502055590061328	3		574	661	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212289016	212289016	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1391443605	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	69	519	0	ENST00000342788.4:c.2730A>G	p.Ile910Met	p.I910M	ENST00000342788	NM_005235.2	910	atA/atG	23/28	0.502055590061328	3	FACETS	0.628	0.547	0.714	0.314	0.273	0.357	SUBCLONAL	1	TRUE	1	0.502055590061328	3		519	548	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440141	220440141	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	98	714	0	ENST00000243786.2:c.994C>A	p.Pro332Thr	p.P332T	ENST00000243786	NM_002191.3	332	Cca/Aca	2/2	0.502055590061328	3	FACETS	0.694	0.619	0.773	0.347	0.309	0.387	SUBCLONAL	1	TRUE	1	0.502055590061328	3		714	704	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662980	227662980	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1215890148	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	91	629	0	ENST00000305123.5:c.475G>A	p.Ala159Thr	p.A159T	ENST00000305123	NM_005544.2	159	Gca/Aca	1/2	0.502055590061328	3	FACETS	0.675	0.599	0.755	0.337	0.299	0.378	SUBCLONAL	1	TRUE	1	0.502055590061328	3		629	672	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827985	40827985	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	25	505	1	ENST00000373198.4:c.2443A>G	p.Arg815Gly	p.R815G	ENST00000373198	NM_133170.3	815	Agg/Ggg	17/32	0.502055590061328	1	FACETS	0.201	0.158	0.25	0.201	0.158	0.25	SUBCLONAL	1	TRUE	0	0.502055590061328	1		506	372	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979322	40979322	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	120	690	0	ENST00000373198.4:c.1811A>G	p.Asp604Gly	p.D604G	ENST00000373198	NM_133170.3	604	gAc/gGc	11/32	0.502055590061328	1	FACETS	0.58	0.525	0.638	0.58	0.525	0.638	SUBCLONAL	1	TRUE	0	0.502055590061328	1		690	617	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262920	46262920	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	146	673	0	ENST00000371998.3:c.1093T>C	p.Ser365Pro	p.S365P	ENST00000371998		365	Tca/Cca	10/23	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.502055590061328	2		673	565	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633240	12633240	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	164	684	1	ENST00000251849.4:c.1160T>G	p.Phe387Cys	p.F387C	ENST00000251849	NM_002880.3	387	tTc/tGc	11/17	1	2	FACETS	0.977	0.899	1	0.977	0.899	1	CLONAL	1	TRUE	1	0.502055590061328	2		685	669	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72866489	72866489	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	69	517	1	ENST00000325599.8:c.774T>A	p.Asn258Lys	p.N258K	ENST00000325599	NM_018130.2	258	aaT/aaA	7/11	1	2	FACETS	0.639	0.559	0.726	0.639	0.559	0.726	SUBCLONAL	1	TRUE	1	0.502055590061328	2		518	430	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202842	128202842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	116	568	0	ENST00000341105.2:c.878G>A	p.Arg293Gln	p.R293Q	ENST00000341105	NM_032638.4	293	cGg/cAg	4/6	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.502055590061328	2		568	450	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968200	134968200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	23	561	0	ENST00000398015.3:c.2713C>A	p.Arg905Ser	p.R905S	ENST00000398015	NM_004441.4	905	Cgc/Agc	15/16	1	2	FACETS	0.205	0.159	0.258	0.205	0.159	0.258	SUBCLONAL	1	TRUE	1	0.502055590061328	2		561	447	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281829	142281829	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	163	606	0	ENST00000350721.4:c.415C>T	p.Pro139Ser	p.P139S	ENST00000350721	NM_001184.3	139	Cct/Tct	4/47	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.502055590061328	2		606	553	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170015161	170015161	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs866058843	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	151	714	1	ENST00000295797.4:c.1567C>T	p.Arg523Ter	p.R523*	ENST00000295797	NM_002740.5	523	Cga/Tga	16/18	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.502055590061328	2		715	594	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902713	1902713	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	225	776	1	ENST00000382891.5:c.332C>A	p.Pro111His	p.P111H	ENST00000382891	NM_133335.3	111	cCc/cAc	2/22	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.502055590061328	2		777	846	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157282	106157282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	184	653	1	ENST00000380013.4:c.2183C>T	p.Ala728Val	p.A728V	ENST00000380013	NM_001127208.2	728	gCa/gTa	3/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.502055590061328	2		654	661	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332817	153332817	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	159	590	0	ENST00000281708.4:c.139C>T	p.Gln47Ter	p.Q47*	ENST00000281708	NM_033632.3	47	Caa/Taa	2/12	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.502055590061328	2		590	582	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629600	187629600	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	157	649	0	ENST00000441802.2:c.1382del	p.Pro461LeufsTer23	p.P461Lfs*23	ENST00000441802	NM_005245.3	461	cCt/ct	2/27	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.502055590061328	2		649	607	SUCCESS
APC	324	MSKCC	GRCh37	5	112177874	112177878	+	frameshift_variant	Frame_Shift_Del	DEL	TATAA	TATAA	-	rs748823446	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	90	408	0	ENST00000257430.4:c.6583_6587del	p.Tyr2195LysfsTer10	p.Y2195Kfs*10	ENST00000257430	NM_000038.5	2195	TATAAa/a	16/16	1	2	FACETS	0.8	0.714	0.892	0.8	0.714	0.892	SUBCLONAL	1	TRUE	1	0.502055590061328	2		408	448	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056197	26056197	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs548795634	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	110	471	0	ENST00000343677.2:c.460A>G	p.Thr154Ala	p.T154A	ENST00000343677	NM_005319.3	154	Aca/Gca	1/1	1	2	FACETS	0.871	0.786	0.96	0.871	0.786	0.96	CLONAL	1	TRUE	1	0.502055590061328	2		471	503	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056286	26056286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	33	515	0	ENST00000343677.2:c.371G>A	p.Gly124Asp	p.G124D	ENST00000343677	NM_005319.3	124	gGc/gAc	1/1	1	2	FACETS	0.261	0.212	0.316	0.261	0.212	0.316	SUBCLONAL	1	TRUE	1	0.502055590061328	2		515	504	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288863	33288863	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201985154	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	112	447	0	ENST00000374542.5:c.689G>A	p.Arg230His	p.R230H	ENST00000374542	NM_001141970.1	230	cGt/cAt	3/8	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.502055590061328	2		447	432	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963940	2963941	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGA	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	106	756	0	ENST00000396946.4:c.1864_1866dup	p.Ser622dup	p.S622dup	ENST00000396946	NM_032415.4	622	-/TCC	15/25	1	2	FACETS	0.716	0.643	0.792	0.716	0.643	0.792	SUBCLONAL	1	TRUE	1	0.502055590061328	2		756	590	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211142	55211142	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	81	631	0	ENST00000275493.2:c.385A>G	p.Lys129Glu	p.K129E	ENST00000275493	NM_005228.3	129	Aaa/Gaa	3/28	1	2	FACETS	0.558	0.492	0.629	0.558	0.492	0.629	SUBCLONAL	1	TRUE	1	0.502055590061328	2		631	578	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545632	106545632	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	37	673	0	ENST00000359195.3:c.3109A>G	p.Thr1037Ala	p.T1037A	ENST00000359195	NM_002649.2	1037	Aca/Gca	11/11	1	2	FACETS	0.237	0.195	0.285	0.237	0.195	0.285	SUBCLONAL	1	TRUE	1	0.502055590061328	2		673	622	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879429	151879429	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	151	605	0	ENST00000262189.6:c.5516del	p.Thr1839SerfsTer10	p.T1839Sfs*10	ENST00000262189	NM_170606.2	1839	aCg/ag	36/59	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.502055590061328	2		605	512	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009342	69009342	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758520881	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	126	679	1	ENST00000288368.4:c.2459G>A	p.Gly820Asp	p.G820D	ENST00000288368	NM_024870.2	820	gGt/gAt	22/40	0.502055590061328	3	FACETS	0.907	0.823	0.996	0.454	0.411	0.498	CLONAL	1	TRUE	1	0.502055590061328	3		680	692	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317917	8317917	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	130	500	3	ENST00000356435.5:c.5696C>T	p.Ala1899Val	p.A1899V	ENST00000356435		1899	gCc/gTc	35/35	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.502055590061328	2		503	488	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242267	98242267	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	156	648	0	ENST00000331920.6:c.1051A>G	p.Thr351Ala	p.T351A	ENST00000331920	NM_000264.3	351	Act/Gct	7/24	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.502055590061328	2		648	621	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771998	135771998	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	85	442	1	ENST00000298552.3:c.3119G>A	p.Ser1040Asn	p.S1040N	ENST00000298552	NM_001162426.1	1040	aGc/aAc	23/23	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.502055590061328	2		443	291	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20153854	20153854	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	148	580	0	ENST00000379607.5:c.204+2T>C		p.X68_splice	ENST00000379607	NM_001412.3	68			1	2	FACETS	0.999	0.917	1	0.999	0.917	1	CLONAL	1	TRUE	1	0.502055590061328	2		580	590	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412406	63412406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	117	794	0	ENST00000330258.3:c.761C>T	p.Ala254Val	p.A254V	ENST00000330258	NM_152424.3	254	gCc/gTc	2/2	1	2	FACETS	0.862	0.78	0.947	0.862	0.78	0.947	CLONAL	1	TRUE	1	0.502055590061328	2		794	541	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944388	76944388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064795090	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	197	869	0	ENST00000373344.5:c.517G>A	p.Ala173Thr	p.A173T	ENST00000373344	NM_000489.3	173	Gct/Act	7/35	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.502055590061328	2		869	732	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448297	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	T	novel	NA	P-0026197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	141	678	0	ENST00000407977.2:c.349_350delinsA	p.Arg117ThrfsTer41	p.R117Tfs*41	ENST00000407977		117	CGc/Ac	3/10	1	2	FACETS	0.925	0.846	1	0.925	0.846	1	CLONAL	1	TRUE	1	0.502055590061328	2		678	607	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798191	42798191	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	333	632	0	ENST00000575354.2:c.4145C>T	p.Ser1382Leu	p.S1382L	ENST00000575354	NM_015125.3	1382	tCa/tTa	17/20	1	2	FACETS	0.981	0.929	1	0.981	0.929	1	CLONAL	1	TRUE	1	0.709739843652385	2		632	957	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859663	57859663	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	251	489	1	ENST00000228682.2:c.717G>A	p.Trp239Ter	p.W239*	ENST00000228682	NM_005269.2	239	tgG/tgA	7/12	0.709739843652385	1	FACETS	0.933	0.884	0.982	0.933	0.884	0.982	CLONAL	1	TRUE	0	0.709739843652385	1		490	489	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78923242	78923242	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0026198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	248	511	0	ENST00000306801.3:c.3266-1G>A		p.X1089_splice	ENST00000306801	NM_020761.2	1089			0.703669906630251	3	FACETS	0.989	0.926	1	0.495	0.463	0.527	CLONAL	1	TRUE	1	0.709739843652385	3		511	957	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028127	69028127	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	334	709	1	ENST00000288368.4:c.3286G>T	p.Asp1096Tyr	p.D1096Y	ENST00000288368	NM_024870.2	1096	Gat/Tat	26/40	1	2	FACETS	0.937	0.888	0.988	0.937	0.888	0.988	CLONAL	1	TRUE	1	0.709739843652385	2		710	1004	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720825	89720825	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	100	246	0	ENST00000371953.3:c.976G>C	p.Asp326His	p.D326H	ENST00000371953	NM_000314.4	326	Gac/Cac	8/9	0.761421761746335	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.763542997951772	1		246	155	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0026199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	259	586	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.763542997951772	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.763542997951772	1		586	390	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105641	30105641	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1440124618	NA	P-0026199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	177	536	0	ENST00000331968.5:c.1045G>C	p.Asp349His	p.D349H	ENST00000331968	NM_002742.2	349	Gat/Cat	7/18	1	2	FACETS	0.933	0.867	1	0.933	0.867	1	CLONAL	1	TRUE	1	0.763542997951772	2		536	497	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174806	56174806	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0026199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	74	247	0	ENST00000399503.3:c.1966-1G>C		p.X656_splice	ENST00000399503	NM_005921.1	656			0.323073527788609	1	FACETS	0.55	0.489	0.612	0.55	0.489	0.612	INDETERMINATE	1	TRUE	0	0.763542997951772	1		247	218	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939518	76939518	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	92	533	0	ENST00000373344.5:c.1230A>C	p.Glu410Asp	p.E410D	ENST00000373344	NM_000489.3	410	gaA/gaC	9/35	0.507248161797111	1	FACETS	0.495	0.445	0.547	0.495	0.445	0.547	SUBCLONAL	1	TRUE	0	0.763542997951772	1		533	301	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0026201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	103	322	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	FALSE	NA	0.278468318741873	2		322	508	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739894	41739894	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	51	285	1	ENST00000242208.4:c.79G>A	p.Glu27Lys	p.E27K	ENST00000242208	NM_002192.2	27	Gag/Aag	2/3	0.203184888221439	3	FACETS	0.998	0.85	1	0.499	0.425	0.58	CLONAL	1	FALSE	1	0.278468318741873	3		286	418	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456872	32456872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	36	333	0	ENST00000332351.3:c.20C>T	p.Thr7Met	p.T7M	ENST00000332351	NM_024426.4	7	aCg/aTg	1/10	1	2	FACETS	0.758	0.625	0.907	0.758	0.625	0.907	CLONAL	1	FALSE	1	0.278468318741873	2		333	341	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125525184	125525184	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	34	416	0	ENST00000428830.2:c.1400G>A	p.Ser467Asn	p.S467N	ENST00000428830	NM_001114121.2	467	aGc/aAc	13/14	0.278468318741873	1	FACETS	0.371	0.303	0.449	0.371	0.303	0.449	SUBCLONAL	1	FALSE	0	0.278468318741873	1		416	566	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60795959	60795959	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748122615	NA	P-0026201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	40	442	4	ENST00000333681.4:c.619C>T	p.Arg207Trp	p.R207W	ENST00000333681		207	Cgg/Tgg	3/3	1	2	FACETS	0.452	0.374	0.538	0.452	0.374	0.538	SUBCLONAL	1	FALSE	1	0.278468318741873	2		446	636	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99162438	99162438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751521973	NA	P-0026201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	33	296	0	ENST00000074304.5:c.956C>T	p.Ser319Leu	p.S319L	ENST00000074304	NM_001134224.1	319	tCg/tTg	12/26	1	2	FACETS	0.524	0.427	0.635	0.524	0.427	0.635	SUBCLONAL	1	FALSE	1	0.278468318741873	2		296	452	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480499	123480499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	30	179	0	ENST00000371139.4:c.7G>A	p.Ala3Thr	p.A3T	ENST00000371139	NM_001114937.2	3	Gca/Aca	1/4	0.0921744880803068	2	FACETS	0.838	0.678	1			1	INDETERMINATE	1	FALSE	NA	0.278468318741873	2		179	257	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519966	NA	P-0026202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	190	470	0	ENST00000347630.2:c.397T>A	p.Phe133Ile	p.F133I	ENST00000347630	NM_001007230.1	133	Ttc/Atc	6/11	1	2	FACETS	0.903	0.84	0.968	0.903	0.84	0.968	CLONAL	1	TRUE	1	0.711989224824377	2		470	591	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11022869	11022869	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	279	564	0	ENST00000327064.4:c.568G>T	p.Asp190Tyr	p.D190Y	ENST00000327064	NM_199141.1	190	Gat/Tat	5/16	1	2	FACETS	0.861	0.811	0.913	0.861	0.811	0.913	CLONAL	1	TRUE	1	0.711989224824377	2		564	910	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729478	41729478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	59	395	1	ENST00000242208.4:c.1051G>A	p.Glu351Lys	p.E351K	ENST00000242208	NM_002192.2	351	Gag/Aag	3/3	0.3	3	FACETS	1	0.969	1	0.746	0.644	0.856	CLONAL	1	TRUE	1	0.22	3		396	399	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191477	10191478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCTT	novel	NA	P-0026203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	15	330	0	ENST00000256474.2:c.473_474insTTCT	p.Lys159SerfsTer16	p.K159Sfs*16	ENST00000256474	NM_000551.3	157	act/acTCTTt	3/3	0.239299553123178	3	FACETS	0.658	0.482	0.87	0.329	0.241	0.435	SUBCLONAL	1	TRUE	1	0.22	3		330	230	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441334	52441334	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0026203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	19	332	1	ENST00000460680.1:c.438-2A>T		p.X146_splice	ENST00000460680	NM_004656.3	146			0.239299553123178	3	FACETS	0.657	0.498	0.843	0.328	0.249	0.422	SUBCLONAL	1	TRUE	1	0.22	3		333	292	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956946	2956946	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	128	457	0	ENST00000396946.4:c.2681T>G	p.Phe894Cys	p.F894C	ENST00000396946	NM_032415.4	894	tTc/tGc	20/25	0.3	3	FACETS	1	0.96	1	1	0.988	1	CLONAL	3	TRUE	1	0.22	3		457	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	428	489	0	ENST00000269305.4:c.853G>T	p.Glu285Ter	p.E285*	ENST00000269305	NM_001126112.2	285	Gag/Tag	8/11	0.907391522520671	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.908539131091858	1		489	497	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132428	11132428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	425	509	1	ENST00000358026.2:c.2644G>A	p.Glu882Lys	p.E882K	ENST00000358026	NM_001128849.1	882	Gaa/Aaa	19/36	0.464008381578243	1	FACETS	0.709	0.683	0.735	0.709	0.683	0.735	INDETERMINATE	1	TRUE	0	0.908539131091858	1		510	720	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	395	438	0	ENST00000391945.4:c.713A>T	p.Asn238Ile	p.N238I	ENST00000391945	NM_000400.3	238	aAc/aTc	8/23	0.464008381578243	1	FACETS	0.707	0.68	0.734	0.707	0.68	0.734	INDETERMINATE	1	TRUE	0	0.908539131091858	1		438	671	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662475	227662475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	120	303	1	ENST00000305123.5:c.980G>A	p.Arg327His	p.R327H	ENST00000305123	NM_005544.2	327	cGc/cAc	1/2	0.908539131091858	1	FACETS	0.519	0.476	0.561	0.519	0.476	0.561	SUBCLONAL	1	TRUE	0	0.908539131091858	1		304	278	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256822	16256822	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	450	465	0	ENST00000375759.3:c.4087G>C	p.Asp1363His	p.D1363H	ENST00000375759	NM_015001.2	1363	Gat/Cat	11/15	0.456368178346153	1	FACETS	0.746	0.719	0.771	0.746	0.719	0.771	INDETERMINATE	1	TRUE	0	0.908539131091858	1		465	725	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243708883	243708883	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	202	340	0	ENST00000263826.5:c.1180G>C	p.Asp394His	p.D394H	ENST00000263826	NM_005465.4	394	Gat/Cat	11/13	1	2	FACETS	0.942	0.883	1	0.942	0.883	1	CLONAL	1	TRUE	1	0.908539131091858	2		340	472	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421791	49421791	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1555186232	NA	P-0026205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	473	513	0	ENST00000301067.7:c.14515+1G>T		p.X4839_splice	ENST00000301067	NM_003482.3	4839			1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.908539131091858	2		513	1041	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433004	49433004	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1057518149	NA	P-0026205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	429	381	2	ENST00000301067.7:c.8366+1G>A		p.X2789_splice	ENST00000301067	NM_003482.3	2789			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.908539131091858	2		383	917	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42057133	42057133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	476	492	0	ENST00000219905.7:c.7794G>A	p.Met2598Ile	p.M2598I	ENST00000219905	NM_001164273.1	2598	atG/atA	23/24	0.908539131091858	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.908539131091858	1		492	544	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779755	3779755	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	192	399	0	ENST00000262367.5:c.5293C>T	p.Gln1765Ter	p.Q1765*	ENST00000262367	NM_004380.2	1765	Cag/Tag	31/31	0.422065076090737	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.908539131091858	0		399	432	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99185101	99185101	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	285	392	0	ENST00000074304.5:c.2503G>C	p.Glu835Gln	p.E835Q	ENST00000074304	NM_001134224.1	835	Gag/Cag	23/26	1	2	FACETS	0.932	0.883	0.982	0.932	0.883	0.982	CLONAL	1	TRUE	1	0.908539131091858	2		392	673	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72881619	72881619	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	163	333	0	ENST00000325599.8:c.500A>G	p.Asp167Gly	p.D167G	ENST00000325599	NM_018130.2	167	gAt/gGt	5/11	0.908539131091858	1	FACETS	0.47	0.436	0.504	0.47	0.436	0.504	SUBCLONAL	1	TRUE	0	0.908539131091858	1		333	417	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170009723	170009723	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	174	278	0	ENST00000295797.4:c.1285G>T	p.Asp429Tyr	p.D429Y	ENST00000295797	NM_002740.5	429	Gat/Tat	13/18	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.908539131091858	2		278	383	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114301	143114301	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	291	397	0	ENST00000262992.4:c.1120C>G	p.Gln374Glu	p.Q374E	ENST00000262992	NM_001101669.1	374	Cag/Gag	13/24	0.908539131091858	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.908539131091858	1		397	342	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946206	13946206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	254	343	1	ENST00000405192.2:c.890C>T	p.Pro297Leu	p.P297L	ENST00000405192	NM_001163147.1	297	cCa/cTa	10/12	1	2	FACETS	0.89	0.839	0.942	0.89	0.839	0.942	CLONAL	1	TRUE	1	0.908539131091858	2		344	628	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55229203	55229203	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	208	254	0	ENST00000275493.2:c.1510C>T	p.Gln504Ter	p.Q504*	ENST00000275493	NM_005228.3	504	Cag/Tag	13/28	0.908539131091858	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.908539131091858	1		254	245	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069611	69069611	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	179	514	0	ENST00000288368.4:c.4286T>C	p.Phe1429Ser	p.F1429S	ENST00000288368	NM_024870.2	1429	tTt/tCt	35/40	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.908539131091858	2		514	322	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069619	69069619	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	171	511	1	ENST00000288368.4:c.4294C>G	p.Gln1432Glu	p.Q1432E	ENST00000288368	NM_024870.2	1432	Cag/Gag	35/40	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.908539131091858	2		512	327	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0026206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	174	388	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.468890191998496	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.502364823103021	1		388	457	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519920	NA	P-0026206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	93	255	0	ENST00000397062.3:c.85G>T	p.Asp29Tyr	p.D29Y	ENST00000397062	NM_006164.4	29	Gat/Tat	2/5	1	2	FACETS	0.974	0.873	1	0.974	0.873	1	CLONAL	1	TRUE	1	0.502364823103021	2		255	380	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023622	27023622	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1356791422	NA	P-0026206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	11	95	0	ENST00000324856.7:c.728C>T	p.Ala243Val	p.A243V	ENST00000324856	NM_006015.4	243	gCg/gTg	1/20	1	2	FACETS	0.272	0.188	0.376	0.272	0.188	0.376	SUBCLONAL	1	TRUE	1	0.502364823103021	2		95	161	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504500	103504500	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	105	329	0	ENST00000355739.4:c.122del	p.Gly41GlufsTer10	p.G41Efs*10	ENST00000355739	NM_000123.3	41	Gga/ga	2/15	1	2	FACETS	0.886	0.798	0.978	0.886	0.798	0.978	CLONAL	1	TRUE	1	0.502364823103021	2		329	472	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50788313	50788313	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	281	585	0	ENST00000398568.2:c.891G>T	p.Leu297Phe	p.L297F	ENST00000398568	NM_001042412.1	297	ttG/ttT	5/18	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.502364823103021	2		585	976	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207070	1207070	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	131	554	0	ENST00000326873.7:c.158del	p.Asp53AlafsTer11	p.D53Afs*11	ENST00000326873	NM_000455.4	53	gAc/gc	1/10	0.502364823103021	1	FACETS	0.76	0.693	0.829	0.76	0.693	0.829	SUBCLONAL	1	TRUE	0	0.502364823103021	1		554	514	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	33	474	0				ENST00000310581	NM_198253.2	-/1132			0.145134576523141	3	FACETS	1	0.91	1	0.591	0.486	0.707	INDETERMINATE	1	FALSE	1	0.34861080336887	3		474	188	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0026208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	21	483	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.279	0.214	0.355	0.279	0.214	0.355	SUBCLONAL	1	FALSE	1	0.34861080336887	2		483	432	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0026208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	13	396	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	1	2	FACETS	0.189	0.134	0.256	0.189	0.134	0.256	SUBCLONAL	1	FALSE	1	0.34861080336887	2		396	395	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347889	73347889	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	22	324	1	ENST00000377767.4:c.1172C>T	p.Ser391Phe	p.S391F	ENST00000377767	NM_014953.3	391	tCc/tTc	8/21	1	2	FACETS	0.379	0.293	0.478	0.379	0.293	0.478	SUBCLONAL	1	FALSE	1	0.34861080336887	2		325	333	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022180	5022180	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs773146013	NA	P-0026208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	23	463	0	ENST00000381652.3:c.193G>C	p.Glu65Gln	p.E65Q	ENST00000381652	NM_004972.3	65	Gaa/Caa	3/25	1	2	FACETS	0.333	0.259	0.419	0.333	0.259	0.419	SUBCLONAL	1	FALSE	1	0.34861080336887	2		463	396	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	96	474	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.419819848588941	2		474	371	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0026209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	353	592	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.419819848588941	3	FACETS	0.902	0.86	0.944	0.902	0.86	0.944	CLONAL	3	TRUE	0	0.419819848588941	3		594	752	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631839	90631839	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519906	NA	P-0026209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	70	517	0	ENST00000330062.3:c.514A>G	p.Arg172Gly	p.R172G	ENST00000330062	NM_002168.2	172	Agg/Ggg	4/11	1	2	FACETS	0.655	0.572	0.744	0.655	0.572	0.744	SUBCLONAL	1	TRUE	1	0.419819848588941	2		517	509	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63537676	63537676	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0026209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	60	418	0	ENST00000307078.5:c.957-1G>T		p.X319_splice	ENST00000307078	NM_004655.3	319			0.365334337739691	2	FACETS	0.65	0.561	0.745	0.325	0.28	0.373	SUBCLONAL	1	TRUE	0	0.419819848588941	2		418	440	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422929	12422929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773089349	NA	P-0026209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	53	621	1	ENST00000287820.6:c.419G>A	p.Arg140His	p.R140H	ENST00000287820	NM_015869.4	140	cGt/cAt	3/7	0.208770844662261	3	FACETS	0.505	0.43	0.587	0.168	0.143	0.196	INDETERMINATE	1	TRUE	0	0.419819848588941	3		622	605	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	71	501	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.15	2		501	937	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165788	108165788	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0026210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	47	425	0	ENST00000278616.4:c.4909+2T>C		p.X1637_splice	ENST00000278616	NM_000051.3	1637			1	2	FACETS	0.884	0.744	1	0.884	0.744	1	CLONAL	1	TRUE	1	0.15	2		425	709	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973958	55973958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769193899	NA	P-0026210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	65	515	2	ENST00000263923.4:c.1358C>T	p.Pro453Leu	p.P453L	ENST00000263923	NM_002253.2	453	cCg/cTg	10/30	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.15	2		517	831	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993375	72993378	+	frameshift_variant	Frame_Shift_Del	DEL	GCCC	GCCC	-	novel	NA	P-0026210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	36	559	0	ENST00000268489.5:c.667_670del	p.Gly223SerfsTer22	p.G223Sfs*22	ENST00000268489	NM_006885.3	223	GGGCtc/tc	2/10	1	2	FACETS	0.709	0.581	0.853	0.709	0.581	0.853	SUBCLONAL	1	TRUE	1	0.15	2		559	677	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175838	24175839	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0026211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	21	531	0	ENST00000263121.7:c.1067dup	p.Thr357AspfsTer4	p.T357Dfs*4	ENST00000263121	NM_003073.3	356	ctg/cTtg	8/9	0.1772010726658	0	FACETS	0.269	0.207	0.342			1	INDETERMINATE	1	TRUE	0	0.309610472722771	0		531	348	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988741	41988741	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	43	390	0	ENST00000219905.7:c.1533C>A	p.Tyr511Ter	p.Y511*	ENST00000219905	NM_001164273.1	511	taC/taA	3/24	1	2	FACETS	0.955	0.803	1	0.955	0.803	1	CLONAL	1	TRUE	1	0.309610472722771	2		390	291	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220275	55220275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751295137	NA	P-0026212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	10	576	0	ENST00000275493.2:c.665G>A	p.Arg222His	p.R222H	ENST00000275493	NM_005228.3	222	cGc/cAc	6/28	1	2	FACETS	0.211	0.142	0.298	0.211	0.142	0.298	SUBCLONAL	1	TRUE	1	0.19	2		576	500	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882058	36882058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141574393	NA	P-0026212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	28	516	2	ENST00000358127.4:c.955G>A	p.Val319Ile	p.V319I	ENST00000358127	NM_001280556.1	319	Gtc/Atc	8/10	0.234452287133768	0	FACETS	0.517	0.412	0.636			1	SUBCLONAL	1	TRUE	0	0.19	0		518	462	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0026214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	213	547	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	0.944395207570771	1	FACETS	0.847	0.812	0.88	0.847	0.812	0.88	CLONAL	1	TRUE	0	0.944557666539631	1		547	281	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913514	NA	P-0026214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	292	477	0	ENST00000288135.5:c.2466T>A	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaA	17/21	0.944395207570771	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.944557666539631	1		477	317	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796748	135796748	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1564497308	NA	P-0026214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	441	279	0	ENST00000298552.3:c.737+2T>C		p.X246_splice	ENST00000298552	NM_001162426.1	246			0.937751775178476	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.944557666539631	2		279	458	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0026214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	487	547	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	0.3	11	FACETS	1	0.991	1			1	INDETERMINATE	4	TRUE	NA	0.9	11		547	1230	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798850	135798854	+	frameshift_variant	Frame_Shift_Del	DEL	TGTTG	TGTTG	-	novel	NA	P-0026214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	253	266	0	ENST00000298552.3:c.389_393del	p.Thr130ArgfsTer22	p.T130Rfs*22	ENST00000298552	NM_001162426.1	130	aCAACA/a	6/23	0.3	1	FACETS	1	0.993	1	1	0.993	1	INDETERMINATE	1	TRUE	0	0.9	1		266	287	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167447	24167447	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	73	654	0	ENST00000263121.7:c.832del	p.Gln278SerfsTer18	p.Q278Sfs*18	ENST00000263121	NM_003073.3	277	gaC/ga	7/9	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		654	361	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860569	45860569	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs757100147	NA	P-0026218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	23	657	0	ENST00000391945.4:c.1438A>G	p.Thr480Ala	p.T480A	ENST00000391945	NM_000400.3	480	Acc/Gcc	15/23	1	2	FACETS	0.226	0.176	0.284	0.226	0.176	0.284	SUBCLONAL	1	TRUE	1	0.553062889587317	2		657	368	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541724	187541724	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	130	318	0	ENST00000441802.2:c.6016A>G	p.Asn2006Asp	p.N2006D	ENST00000441802	NM_005245.3	2006	Aat/Gat	10/27	0.262475642112078	4	FACETS	0.873	0.799	0.95	0.873	0.799	0.95	INDETERMINATE	2	TRUE	2	0.553062889587317	4		318	418	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218052	108218052	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1064794840	NA	P-0026219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	247	408	0	ENST00000278616.4:c.8631G>C	p.Leu2877Phe	p.L2877F	ENST00000278616	NM_000051.3	2877	ttG/ttC	59/63	0.67191617893862	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.679551965186335	1		408	461	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577576	64577576	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	144	235	0	ENST00000312049.6:c.6del	p.Leu3Ter	p.L3*	ENST00000312049	NM_130799.2	2	ggG/gg	2/10	0.679551965186335	1	FACETS	0.891	0.827	0.956	0.891	0.827	0.956	CLONAL	1	TRUE	0	0.679551965186335	1		235	314	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394796	45394796	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	240	350	0	ENST00000262160.6:c.553G>A	p.Glu185Lys	p.E185K	ENST00000262160	NM_005901.5	185	Gag/Aag	5/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.679551965186335	2		350	655	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384655	31384655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	303	462	0	ENST00000328111.2:c.1357G>A	p.Gly453Arg	p.G453R	ENST00000328111	NM_006892.3	453	Ggg/Agg	13/23	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.679551965186335	2		462	807	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620545	52620545	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	35	452	0	ENST00000394830.3:c.3208G>A	p.Val1070Ile	p.V1070I	ENST00000394830	NM_018313.4	1070	Gtt/Att	21/30	1	2	FACETS	0.165	0.135	0.199	0.165	0.135	0.199	SUBCLONAL	1	TRUE	1	0.975749978498418	2		452	435	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0026221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	560	424	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.926	0.9	0.951	1	0.998	1	CLONAL	2	TRUE	1	0.765601208563866	2		424	790	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0026221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	412	454	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.765601208563866	2		456	763	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0026221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	510	420	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.765601208563866	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.765601208563866	3		420	605	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0026221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	301	568	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.968	0.916	1	0.968	0.916	1	CLONAL	1	TRUE	1	0.765601208563866	2		568	812	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0026221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	333	435	0	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.765601208563866	2		435	790	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0026221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	257	349	8	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	0.977	0.92	1	0.977	0.92	1	CLONAL	1	TRUE	1	0.765601208563866	2		357	687	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032048	26032048	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs756087316	NA	P-0026221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	214	306	0	ENST00000244661.2:c.241A>G	p.Thr81Ala	p.T81A	ENST00000244661	NM_003537.3	81	Acc/Gcc	1/1	1	2	FACETS	0.956	0.894	1	0.956	0.894	1	CLONAL	1	TRUE	1	0.765601208563866	2		306	585	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289908	15289908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257835251	NA	P-0026221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	364	498	2	ENST00000263388.2:c.3646G>A	p.Ala1216Thr	p.A1216T	ENST00000263388	NM_000435.2	1216	Gcg/Acg	22/33	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.765601208563866	2		500	928	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861143	57861143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772799269	NA	P-0026221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	338	474	0	ENST00000228682.2:c.940C>T	p.Arg314Cys	p.R314C	ENST00000228682	NM_005269.2	314	Cgc/Tgc	9/12	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.765601208563866	2		474	879	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133981	38133981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	267	536	0	ENST00000317025.8:c.3905del	p.Asn1302MetfsTer4	p.N1302Mfs*4	ENST00000317025	NM_023034.1	1302	aAt/at	23/24	1	2	FACETS	0.824	0.775	0.875	0.824	0.775	0.875	CLONAL	1	TRUE	1	0.765601208563866	2		536	846	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801064	1801064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs2305178	NA	P-0026221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	387	531	0	ENST00000260795.2:c.193G>A	p.Gly65Arg	p.G65R	ENST00000260795		65	Ggg/Agg	2/17	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.765601208563866	2		531	924	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912140	114912140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	381	478	2	ENST00000543371.1:c.1210C>T	p.Arg404Trp	p.R404W	ENST00000543371	NM_001198531.1	404	Cgg/Tgg	11/14	0.765601208563866	3	FACETS	1	0.983	1	0.36	0.341	0.378	CLONAL	1	TRUE	0	0.765601208563866	3		480	1276	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129351	64129351	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	295	430	3	ENST00000334205.4:c.788del	p.Pro263LeufsTer112	p.P263Lfs*112	ENST00000334205	NM_003942.2	261	ttC/tt	8/17	1	2	FACETS	0.962	0.91	1	0.962	0.91	1	CLONAL	1	TRUE	1	0.765601208563866	2		433	801	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254617	46254617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs922849184	NA	P-0026221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	244	457	0	ENST00000334344.6:c.4807G>A	p.Val1603Met	p.V1603M	ENST00000334344	NM_152641.2	1603	Gtg/Atg	16/21	1	2	FACETS	0.915	0.859	0.971	0.915	0.859	0.971	CLONAL	1	TRUE	1	0.765601208563866	2		457	697	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335837	73335837	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372878316	NA	P-0026221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	204	349	0	ENST00000377767.4:c.2458C>T	p.Arg820Trp	p.R820W	ENST00000377767	NM_014953.3	820	Cgg/Tgg	18/21	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.765601208563866	2		349	533	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830672	72830672	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	342	482	1	ENST00000268489.5:c.5909del	p.Lys1970ArgfsTer27	p.K1970Rfs*27	ENST00000268489	NM_006885.3	1970	aAg/ag	9/10	1	2	FACETS	0.904	0.858	0.952	0.904	0.858	0.952	CLONAL	1	TRUE	1	0.765601208563866	2		483	988	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576120	29576120	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	277	467	0	ENST00000356175.3:c.4093T>C	p.Cys1365Arg	p.C1365R	ENST00000356175	NM_000267.3	1365	Tgc/Cgc	30/57	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.765601208563866	2		467	706	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625614	1625616	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0026221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	296	491	0	ENST00000344749.5:c.458_460del	p.Tyr153del	p.Y153del	ENST00000344749	NM_001136139.2	153	tACTcc/tcc	7/19	1	2	FACETS	0.861	0.813	0.91	0.861	0.813	0.91	CLONAL	1	TRUE	1	0.765601208563866	2		491	898	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794358	242794358	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1304651269	NA	P-0026221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	285	466	0	ENST00000334409.5:c.584C>T	p.Ala195Val	p.A195V	ENST00000334409	NM_005018.2	195	gCc/gTc	3/5	1	2	FACETS	0.981	0.927	1	0.981	0.927	1	CLONAL	1	TRUE	1	0.765601208563866	2		466	759	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595632	55595632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146337870	NA	P-0026221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	137	304	0	ENST00000288135.5:c.2122C>T	p.His708Tyr	p.H708Y	ENST00000288135	NM_000222.2	708	Cat/Tat	14/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.765601208563866	2		304	348	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245396	153245396	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	296	486	0	ENST00000281708.4:c.1795G>A	p.Ala599Thr	p.A599T	ENST00000281708	NM_033632.3	599	Gca/Aca	11/12	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.765601208563866	2		486	706	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80150113	80150113	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	168	505	0	ENST00000265081.6:c.2978C>T	p.Thr993Ile	p.T993I	ENST00000265081	NM_002439.4	993	aCa/aTa	21/24	1	2	FACETS	0.847	0.784	0.912	0.847	0.784	0.912	CLONAL	1	TRUE	1	0.765601208563866	2		505	518	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564671	86564671	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	310	456	2	ENST00000274376.6:c.407del	p.Pro136LeufsTer38	p.P136Lfs*38	ENST00000274376	NM_002890.2	135	Ccc/cc	1/25	1	2	FACETS	0.965	0.914	1	0.965	0.914	1	CLONAL	1	TRUE	1	0.765601208563866	2		458	839	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031903	26031903	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	135	245	0	ENST00000244661.2:c.386G>C	p.Arg129Pro	p.R129P	ENST00000244661	NM_003537.3	129	cGc/cCc	1/1	1	2	FACETS	0.884	0.812	0.958	0.884	0.812	0.958	CLONAL	1	TRUE	1	0.765601208563866	2		245	399	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157488298	157488298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs527731946	NA	P-0026221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	232	336	0	ENST00000346085.5:c.3004G>A	p.Ala1002Thr	p.A1002T	ENST00000346085	NM_020732.3	1002	Gcc/Acc	10/20	1	2	FACETS	0.971	0.912	1	0.971	0.912	1	CLONAL	1	TRUE	1	0.765601208563866	2		336	624	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739585	41739585	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	167	235	0	ENST00000242208.4:c.388G>T	p.Gly130Ter	p.G130*	ENST00000242208	NM_002192.2	130	Gga/Tga	2/3	1	2	FACETS	0.905	0.839	0.973	0.905	0.839	0.973	CLONAL	1	TRUE	1	0.765601208563866	2		235	482	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753187	128753187	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs779123478	NA	P-0026221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	203	356	0	ENST00000377970.2:c.1348C>G	p.Arg450Gly	p.R450G	ENST00000377970	NM_002467.4	450	Cgg/Ggg	3/3	1	2	FACETS	0.927	0.866	0.99	0.927	0.866	0.99	CLONAL	1	TRUE	1	0.765601208563866	2		356	572	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243975	53243975	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	386	570	1	ENST00000375401.3:c.1018C>A	p.Leu340Met	p.L340M	ENST00000375401	NM_004187.3	340	Ctg/Atg	8/26	1	2	FACETS	0.993	0.946	1	0.993	0.946	1	CLONAL	1	TRUE	1	0.765601208563866	2		571	1015	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0026221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	297	483	6	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	0.927	0.876	0.979	0.927	0.876	0.979	CLONAL	1	TRUE	1	0.765601208563866	2		489	837	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874315	76874316	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0026221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	168	513	0	ENST00000373344.5:c.5406dup	p.Arg1803ThrfsTer7	p.R1803Tfs*7	ENST00000373344	NM_000489.3	1802	-/A	21/35	1	2	FACETS	0.758	0.7	0.817	0.758	0.7	0.817	SUBCLONAL	1	TRUE	1	0.765601208563866	2		513	579	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534484	187534484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748020206	NA	P-0026221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	175	274	0	ENST00000441802.2:c.9242C>T	p.Thr3081Met	p.T3081M	ENST00000441802	NM_005245.3	3081	aCg/aTg	13/27	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.765601208563866	2		274	428	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16203172	16203172	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	271	445	1	ENST00000375759.3:c.880A>G	p.Ser294Gly	p.S294G	ENST00000375759	NM_015001.2	294	Agc/Ggc	3/15	1	2	FACETS	0.982	0.926	1	0.982	0.926	1	CLONAL	1	TRUE	1	0.765601208563866	2		446	721	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742073	145742073	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	259	490	0	ENST00000428558.2:c.430G>T	p.Gly144Cys	p.G144C	ENST00000428558	NM_004260.3	144	Ggt/Tgt	5/22	1	2	FACETS	0.706	0.662	0.751	0.706	0.662	0.751	SUBCLONAL	1	TRUE	1	0.765601208563866	2		490	958	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0026221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	543	424	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.985	0.962	1	1	0.998	1	CLONAL	2	TRUE	1	0.800881371933948	2		424	688	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296358	15296358	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	213	866	1	ENST00000263388.2:c.2084del	p.Pro695ArgfsTer165	p.P695Rfs*165	ENST00000263388	NM_000435.2	695	cCg/cg	13/33	1	2	FACETS	0.943	0.883	1	0.943	0.883	1	CLONAL	1	TRUE	1	0.800881371933948	2		867	564	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0026221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	450	420	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.800881371933948	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.800881371933948	3		420	519	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0026221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	273	568	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.419187354485873	1	FACETS	0.776	0.737	0.814	0.776	0.737	0.814	INDETERMINATE	1	TRUE	0	0.800881371933948	1		568	527	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552144	29552144	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	27	317	1	ENST00000356175.3:c.1882del	p.Tyr628ThrfsTer3	p.Y628Tfs*3	ENST00000356175	NM_000267.3	626	cTt/ct	17/57	1	2	FACETS	0.366	0.294	0.448	0.366	0.294	0.448	SUBCLONAL	1	TRUE	1	0.800881371933948	2		318	184	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779211	3779211	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783507	NA	P-0026221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	24	372	2	ENST00000262367.5:c.5837del	p.Pro1946HisfsTer30	p.P1946Hfs*30	ENST00000262367	NM_004380.2	1946	cCa/ca	31/31	1	2	FACETS	0.223	0.175	0.278	0.223	0.175	0.278	SUBCLONAL	1	TRUE	1	0.800881371933948	2		374	269	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0026221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	261	435	0	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.800881371933948	2		435	627	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0026221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	282	709	4	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.894	0.843	0.945	0.894	0.843	0.945	CLONAL	1	TRUE	1	0.800881371933948	2		713	788	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0026221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	168	349	8	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	NA	2	FACETS	0.964	0.896	1			1	INDETERMINATE	1	TRUE	NA	0.800881371933948	2		357	435	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032048	26032048	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs756087316	NA	P-0026221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	187	306	0	ENST00000244661.2:c.241A>G	p.Thr81Ala	p.T81A	ENST00000244661	NM_003537.3	81	Acc/Gcc	1/1	1	2	FACETS	0.943	0.879	1	0.943	0.879	1	CLONAL	1	TRUE	1	0.800881371933948	2		306	495	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289908	15289908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257835251	NA	P-0026221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	271	498	2	ENST00000263388.2:c.3646G>A	p.Ala1216Thr	p.A1216T	ENST00000263388	NM_000435.2	1216	Gcg/Acg	22/33	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.800881371933948	2		500	637	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861143	57861143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772799269	NA	P-0026221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	249	474	0	ENST00000228682.2:c.940C>T	p.Arg314Cys	p.R314C	ENST00000228682	NM_005269.2	314	Cgc/Tgc	9/12	1	2	FACETS	0.946	0.891	1	0.946	0.891	1	CLONAL	1	TRUE	1	0.800881371933948	2		474	657	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	156	696	2	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	0.547	0.502	0.594	0.547	0.502	0.594	SUBCLONAL	1	TRUE	1	0.800881371933948	2		698	712	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133981	38133981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	185	536	0	ENST00000317025.8:c.3905del	p.Asn1302MetfsTer4	p.N1302Mfs*4	ENST00000317025	NM_023034.1	1302	aAt/at	23/24	1	2	FACETS	0.803	0.746	0.862	0.803	0.746	0.862	CLONAL	1	TRUE	1	0.800881371933948	2		536	575	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801064	1801064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs2305178	NA	P-0026221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	290	531	0	ENST00000260795.2:c.193G>A	p.Gly65Arg	p.G65R	ENST00000260795		65	Ggg/Agg	2/17	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.800881371933948	2		531	658	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912140	114912140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	267	478	2	ENST00000543371.1:c.1210C>T	p.Arg404Trp	p.R404W	ENST00000543371	NM_001198531.1	404	Cgg/Tgg	11/14	0.800881371933948	3	FACETS	0.988	0.928	1	0.329	0.309	0.35	CLONAL	1	TRUE	0	0.800881371933948	3		480	945	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129351	64129351	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	254	430	3	ENST00000334205.4:c.788del	p.Pro263LeufsTer112	p.P263Lfs*112	ENST00000334205	NM_003942.2	261	ttC/tt	8/17	1	2	FACETS	0.905	0.851	0.959	0.905	0.851	0.959	CLONAL	1	TRUE	1	0.800881371933948	2		433	701	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254617	46254617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs922849184	NA	P-0026221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	232	457	0	ENST00000334344.6:c.4807G>A	p.Val1603Met	p.V1603M	ENST00000334344	NM_152641.2	1603	Gtg/Atg	16/21	1	2	FACETS	0.995	0.936	1	0.995	0.936	1	CLONAL	1	TRUE	1	0.800881371933948	2		457	582	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335837	73335837	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372878316	NA	P-0026221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	167	349	0	ENST00000377767.4:c.2458C>T	p.Arg820Trp	p.R820W	ENST00000377767	NM_014953.3	820	Cgg/Tgg	18/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.800881371933948	2		349	398	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830672	72830672	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	270	482	1	ENST00000268489.5:c.5909del	p.Lys1970ArgfsTer27	p.K1970Rfs*27	ENST00000268489	NM_006885.3	1970	aAg/ag	9/10	1	2	FACETS	0.969	0.914	1	0.969	0.914	1	CLONAL	1	TRUE	1	0.800881371933948	2		483	696	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576120	29576120	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	179	467	0	ENST00000356175.3:c.4093T>C	p.Cys1365Arg	p.C1365R	ENST00000356175	NM_000267.3	1365	Tgc/Cgc	30/57	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.800881371933948	2		467	444	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625614	1625616	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0026221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	242	491	0	ENST00000344749.5:c.458_460del	p.Tyr153del	p.Y153del	ENST00000344749	NM_001136139.2	153	tACTcc/tcc	7/19	1	2	FACETS	0.903	0.849	0.959	0.903	0.849	0.959	CLONAL	1	TRUE	1	0.800881371933948	2		491	669	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794358	242794358	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1304651269	NA	P-0026221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	247	466	0	ENST00000334409.5:c.584C>T	p.Ala195Val	p.A195V	ENST00000334409	NM_005018.2	195	gCc/gTc	3/5	NA	2	FACETS	0.996	0.939	1			1	INDETERMINATE	1	TRUE	NA	0.800881371933948	2		466	619	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595632	55595632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146337870	NA	P-0026221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	97	304	0	ENST00000288135.5:c.2122C>T	p.His708Tyr	p.H708Y	ENST00000288135	NM_000222.2	708	Cat/Tat	14/21	1	2	FACETS	0.904	0.818	0.992	0.904	0.818	0.992	CLONAL	1	TRUE	1	0.800881371933948	2		304	268	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245396	153245396	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	164	486	0	ENST00000281708.4:c.1795G>A	p.Ala599Thr	p.A599T	ENST00000281708	NM_033632.3	599	Gca/Aca	11/12	1	2	FACETS	0.877	0.812	0.943	0.877	0.812	0.943	CLONAL	1	TRUE	1	0.800881371933948	2		486	467	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80150113	80150113	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	131	505	0	ENST00000265081.6:c.2978C>T	p.Thr993Ile	p.T993I	ENST00000265081	NM_002439.4	993	aCa/aTa	21/24	1	2	FACETS	0.82	0.751	0.89	0.82	0.751	0.89	CLONAL	1	TRUE	1	0.800881371933948	2		505	399	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564671	86564671	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	266	456	2	ENST00000274376.6:c.407del	p.Pro136LeufsTer38	p.P136Lfs*38	ENST00000274376	NM_002890.2	135	Ccc/cc	1/25	1	2	FACETS	0.974	0.919	1	0.974	0.919	1	CLONAL	1	TRUE	1	0.800881371933948	2		458	682	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031903	26031903	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	135	245	0	ENST00000244661.2:c.386G>C	p.Arg129Pro	p.R129P	ENST00000244661	NM_003537.3	129	cGc/cCc	1/1	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.800881371933948	2		245	329	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157488298	157488298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs527731946	NA	P-0026221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	198	336	0	ENST00000346085.5:c.3004G>A	p.Ala1002Thr	p.A1002T	ENST00000346085	NM_020732.3	1002	Gcc/Acc	10/20	1	2	FACETS	0.958	0.895	1	0.958	0.895	1	CLONAL	1	TRUE	1	0.800881371933948	2		336	516	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739585	41739585	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	134	235	0	ENST00000242208.4:c.388G>T	p.Gly130Ter	p.G130*	ENST00000242208	NM_002192.2	130	Gga/Tga	2/3	1	2	FACETS	0.93	0.855	1	0.93	0.855	1	CLONAL	1	TRUE	1	0.800881371933948	2		235	360	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753187	128753187	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs779123478	NA	P-0026221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	140	356	0	ENST00000377970.2:c.1348C>G	p.Arg450Gly	p.R450G	ENST00000377970	NM_002467.4	450	Cgg/Ggg	3/3	1	2	FACETS	0.786	0.721	0.852	0.786	0.721	0.852	SUBCLONAL	1	TRUE	1	0.800881371933948	2		356	445	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243975	53243975	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	210	570	1	ENST00000375401.3:c.1018C>A	p.Leu340Met	p.L340M	ENST00000375401	NM_004187.3	340	Ctg/Atg	8/26	0.419187354485873	1	FACETS	0.491	0.458	0.525	0.491	0.458	0.525	INDETERMINATE	1	TRUE	0	0.800881371933948	1		571	640	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936057	71936058	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs878853122	NA	P-0026221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	17	15	0	ENST00000298229.2:c.35dup	p.Ala13ArgfsTer62	p.A13Rfs*62	ENST00000298229	NM_001567.3	10	ccg/ccGg	1/28	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.800881371933948	2		15	36	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632417	3632417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	76	823	2	ENST00000294008.3:c.5431G>A	p.Ala1811Thr	p.A1811T	ENST00000294008	NM_032444.2	1811	Gcc/Acc	15/15	1	2	FACETS	0.286	0.251	0.324	0.286	0.251	0.324	SUBCLONAL	1	TRUE	1	0.800881371933948	2		825	663	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727176	40727176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	34	639	0	ENST00000373198.4:c.3788C>T	p.Ala1263Val	p.A1263V	ENST00000373198	NM_133170.3	1263	gCc/gTc	28/32	0.419187354485873	1	FACETS	0.079	0.064	0.096	0.079	0.064	0.096	INDETERMINATE	1	TRUE	0	0.800881371933948	1		639	647	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	156	403	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.599871442311734	1	FACETS	0.951	0.882	1	0.951	0.882	1	CLONAL	1	TRUE	0	0.599871442311734	1		403	383	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061240	38061240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	173	449	0	ENST00000250448.2:c.749C>T	p.Ser250Phe	p.S250F	ENST00000250448	NM_004496.3	250	tCc/tTc	2/2	1	2	FACETS	0.978	0.905	1	0.978	0.905	1	CLONAL	1	TRUE	1	0.599871442311734	2		449	590	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	73	225	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.580649904995014	1	FACETS	0.796	0.708	0.887	0.796	0.708	0.887	SUBCLONAL	1	TRUE	0	0.599871442311734	1		225	214	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230523	46230523	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	64	182	0	ENST00000334344.6:c.773-1G>C		p.X258_splice	ENST00000334344	NM_152641.2	258			1	2	FACETS	0.85	0.745	0.961	0.85	0.745	0.961	CLONAL	1	TRUE	1	0.599871442311734	2		182	251	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266713	198266713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776846119	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	117	298	0	ENST00000335508.6:c.2219G>A	p.Gly740Glu	p.G740E	ENST00000335508	NM_012433.2	740	gGa/gAa	15/25	1	2	FACETS	0.998	0.908	1	0.998	0.908	1	CLONAL	1	TRUE	1	0.599871442311734	2		298	391	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518560	204518560	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	70	155	0	ENST00000367182.3:c.1223C>G	p.Ser408Ter	p.S408*	ENST00000367182	NM_001278516.1	408	tCa/tGa	11/11	0.599871442311734	4	FACETS	0.806	0.705	0.915	0.269	0.235	0.305	CLONAL	1	TRUE	1	0.599871442311734	4		155	463	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849442	68849442	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	142	291	1	ENST00000261769.5:c.1345C>T	p.Gln449Ter	p.Q449*	ENST00000261769	NM_004360.3	449	Cag/Tag	10/16	0.599871442311734	1	FACETS	0.934	0.862	1	0.934	0.862	1	CLONAL	1	TRUE	0	0.599871442311734	1		292	355	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665360	138665360	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906920	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	320	644	0	ENST00000330315.3:c.205G>A	p.Glu69Lys	p.E69K	ENST00000330315	NM_023067.3	69	Gag/Aag	1/1	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.599871442311734	2		644	935	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649565	206649565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	164	305	0	ENST00000367120.3:c.400C>T	p.Arg134Cys	p.R134C	ENST00000367120	NM_014002.3	134	Cgc/Tgc	6/22	0.599871442311734	4	FACETS	1	0.954	1	0.352	0.323	0.382	CLONAL	1	TRUE	1	0.599871442311734	4		305	829	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174870	56174870	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	84	215	0	ENST00000399503.3:c.2029C>T	p.Gln677Ter	p.Q677*	ENST00000399503	NM_005921.1	677	Cag/Tag	11/20	0.599871442311734	5	FACETS	0.761	0.672	0.857			1	SUBCLONAL	1	TRUE	NA	0.599871442311734	5		215	699	SUCCESS
AR	367	MSKCC	GRCh37	X	66766450	66766450	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	124	238	0	ENST00000374690.3:c.1462C>G	p.Gln488Glu	p.Q488E	ENST00000374690	NM_000044.3	488	Cag/Gag	1/8	0.599871442311734	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.599871442311734	1		238	265	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174450	11174450	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	182	392	0	ENST00000361445.4:c.7225G>C	p.Glu2409Gln	p.E2409Q	ENST00000361445	NM_004958.3	2409	Gag/Cag	53/58	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.599871442311734	2		392	599	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257246	16257246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	162	349	0	ENST00000375759.3:c.4511C>T	p.Ser1504Leu	p.S1504L	ENST00000375759	NM_015001.2	1504	tCa/tTa	11/15	1	2	FACETS	0.894	0.824	0.967	0.894	0.824	0.967	CLONAL	1	TRUE	1	0.599871442311734	2		349	604	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258220	16258220	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	199	345	0	ENST00000375759.3:c.5485C>T	p.Gln1829Ter	p.Q1829*	ENST00000375759	NM_015001.2	1829	Cag/Tag	11/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.599871442311734	2		345	609	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307241	65307241	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	137	250	0	ENST00000342505.4:c.2447C>T	p.Ser816Leu	p.S816L	ENST00000342505	NM_002227.2	816	tCa/tTa	18/25	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.599871442311734	2		250	403	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648238	206648238	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	102	286	0	ENST00000367120.3:c.259G>C	p.Glu87Gln	p.E87Q	ENST00000367120	NM_014002.3	87	Gag/Cag	5/22	0.599871442311734	4	FACETS	0.795	0.712	0.884	0.265	0.237	0.295	SUBCLONAL	1	TRUE	1	0.599871442311734	4		286	684	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658624	206658624	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	128	317	1	ENST00000367120.3:c.1597C>T	p.Gln533Ter	p.Q533*	ENST00000367120	NM_014002.3	533	Cag/Tag	15/22	0.599871442311734	4	FACETS	0.9	0.816	0.988	0.3	0.272	0.33	CLONAL	1	TRUE	1	0.599871442311734	4		318	759	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666707	206666707	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	151	416	0	ENST00000367120.3:c.2041C>G	p.Leu681Val	p.L681V	ENST00000367120	NM_014002.3	681	Ctc/Gtc	20/22	0.599871442311734	4	FACETS	0.836	0.764	0.912	0.279	0.254	0.304	CLONAL	1	TRUE	1	0.599871442311734	4		416	963	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925373	114925373	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1022989384	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	176	444	0	ENST00000543371.1:c.1451C>G	p.Ser484Cys	p.S484C	ENST00000543371	NM_001198531.1	484	tCt/tGt	14/14	1	2	FACETS	0.903	0.835	0.973	0.903	0.835	0.973	CLONAL	1	TRUE	1	0.599871442311734	2		444	650	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118361966	118361966	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	115	183	0	ENST00000534358.1:c.4752G>C	p.Lys1584Asn	p.K1584N	ENST00000534358	NM_005933.3	1584	aaG/aaC	14/36	0.599871442311734	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.599871442311734	1		183	234	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245580	46245580	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	85	189	0	ENST00000334344.6:c.3674C>G	p.Ala1225Gly	p.A1225G	ENST00000334344	NM_152641.2	1225	gCt/gGt	15/21	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.599871442311734	2		189	274	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033966	49033971	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CCAAGT	CCAAGT	-	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	120	272	0	ENST00000267163.4:c.2103_2106+2del		p.X701_splice	ENST00000267163	NM_000321.2	701		20/27	0.599871442311734	1	FACETS	0.934	0.856	1	0.934	0.856	1	CLONAL	1	TRUE	0	0.599871442311734	1		272	300	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988237	36988237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	156	476	1	ENST00000354822.5:c.416C>T	p.Ser139Phe	p.S139F	ENST00000354822	NM_001079668.2	139	tCt/tTt	2/3	1	2	FACETS	0.919	0.846	0.994	0.919	0.846	0.994	CLONAL	1	TRUE	1	0.599871442311734	2		477	566	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060623	38060623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	324	721	0	ENST00000250448.2:c.1366G>A	p.Glu456Lys	p.E456K	ENST00000250448	NM_004496.3	456	Gag/Aag	2/2	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.599871442311734	2		721	1028	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060883	38060883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	170	378	0	ENST00000250448.2:c.1106C>T	p.Ser369Phe	p.S369F	ENST00000250448	NM_004496.3	369	tCt/tTt	2/2	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.599871442311734	2		378	500	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100464	2100464	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767626323	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	121	309	3	ENST00000219476.3:c.202G>A	p.Ala68Thr	p.A68T	ENST00000219476	NM_000548.3	68	Gca/Aca	3/42	1	2	FACETS	0.893	0.812	0.976	0.893	0.812	0.976	CLONAL	1	TRUE	1	0.599871442311734	2		312	452	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14021925	14021925	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	139	311	0	ENST00000311895.7:c.626del	p.Pro209LeufsTer4	p.P209Lfs*4	ENST00000311895	NM_005236.2	209	Cct/ct	4/11	1	2	FACETS	0.958	0.878	1	0.958	0.878	1	CLONAL	1	TRUE	1	0.599871442311734	2		311	484	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826520	50826520	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	76	201	0	ENST00000398568.2:c.2245C>G	p.Leu749Val	p.L749V	ENST00000398568	NM_001042412.1	749	Ctg/Gtg	15/18	0.599871442311734	1	FACETS	0.959	0.86	1	0.959	0.86	1	CLONAL	1	TRUE	0	0.599871442311734	1		201	185	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842691	68843244	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGAAACAGGATGGCTGAAGGTGACAGAGCCTCTGGATAGAGAACGCATTGCCACATACACTGTAAGTATCTCTTAGAAGCTTGTTGACACCGGGGTAACATCCACCCAGGATTTTTTGGTCAACCCATGCTGGATCCGCAGATCAGAGGCTCTGAACACATGAGGAGCTTAACTTGACACCTCTTGACCTGTTGCTAAGGAGAAGTGATGGGAGAACGTGGGACAGTTTGGGGTTGTTAATTTTTCTCCTTGTCAGGAAGAAAGGAAGGAGAATCCGCATGCATCCTCATACAACCAGGACAAATTTAGACCCAAGATGTCAACCTGTTCTTGGGGCTGGAAGTCCCTGACCTAAAGGAACAGGACAGTGATGATATAAGGGAGCAAAACCCATTTCTTGGGCTTGGCAGCAGCAAGAGCTTAGGAAAACCAAGAGGTCTTTTTTTTTTTTTTTTGAGATAGGGTTTCACTCTGTCACCCAGGCTGGAACCACAACCTCCACTTCCCGGGTTCAAGTGATTCTCCTGCTTCAACCTCCCGAGTAGCTGGATTAT	AGAAACAGGATGGCTGAAGGTGACAGAGCCTCTGGATAGAGAACGCATTGCCACATACACTGTAAGTATCTCTTAGAAGCTTGTTGACACCGGGGTAACATCCACCCAGGATTTTTTGGTCAACCCATGCTGGATCCGCAGATCAGAGGCTCTGAACACATGAGGAGCTTAACTTGACACCTCTTGACCTGTTGCTAAGGAGAAGTGATGGGAGAACGTGGGACAGTTTGGGGTTGTTAATTTTTCTCCTTGTCAGGAAGAAAGGAAGGAGAATCCGCATGCATCCTCATACAACCAGGACAAATTTAGACCCAAGATGTCAACCTGTTCTTGGGGCTGGAAGTCCCTGACCTAAAGGAACAGGACAGTGATGATATAAGGGAGCAAAACCCATTTCTTGGGCTTGGCAGCAGCAAGAGCTTAGGAAAACCAAGAGGTCTTTTTTTTTTTTTTTTGAGATAGGGTTTCACTCTGTCACCCAGGCTGGAACCACAACCTCCACTTCCCGGGTTCAAGTGATTCTCCTGCTTCAACCTCCCGAGTAGCTGGATTAT	-	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	113	397	0	ENST00000261769.5:c.629_687+495del		p.X210_splice	ENST00000261769	NM_004360.3	210		5/16	0.599871442311734	1	FACETS	0.756	0.688	0.826	0.756	0.688	0.826	SUBCLONAL	1	TRUE	0	0.599871442311734	1		397	349	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845691	68845691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	198	423	0	ENST00000261769.5:c.937G>A	p.Asp313Asn	p.D313N	ENST00000261769	NM_004360.3	313	Gac/Aac	7/16	0.599871442311734	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.599871442311734	1		423	449	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831397	89831397	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	171	368	0	ENST00000389301.3:c.2679G>C	p.Trp893Cys	p.W893C	ENST00000389301	NM_000135.2	893	tgG/tgC	28/43	0.599871442311734	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.599871442311734	1		368	368	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17120423	17120423	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	171	372	1	ENST00000285071.4:c.1136G>C	p.Arg379Thr	p.R379T	ENST00000285071	NM_144997.5	379	aGa/aCa	10/14	0.599871442311734	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.599871442311734	1		373	390	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868586	37868586	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	130	344	0	ENST00000269571.5:c.1033C>G	p.Leu345Val	p.L345V	ENST00000269571		345	Ctg/Gtg	9/27	0.599871442311734	3	FACETS	0.968	0.881	1	0.484	0.44	0.53	CLONAL	1	TRUE	1	0.599871442311734	3		344	582	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37871550	37871550	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	194	439	0	ENST00000269571.5:c.1160C>A	p.Ser387Tyr	p.S387Y	ENST00000269571		387	tCc/tAc	10/27	0.599871442311734	3	FACETS	1	0.958	1	0.524	0.486	0.564	CLONAL	1	TRUE	1	0.599871442311734	3		439	802	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879583	37879583	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	202	436	1	ENST00000269571.5:c.1958C>T	p.Ser653Phe	p.S653F	ENST00000269571		653	tCc/tTc	17/27	0.599871442311734	3	FACETS	1	0.976	1	0.556	0.516	0.596	CLONAL	1	TRUE	1	0.599871442311734	3		437	788	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632106	1632106	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138963927	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	202	412	0	ENST00000344749.5:c.229G>A	p.Glu77Lys	p.E77K	ENST00000344749	NM_001136139.2	77	Gag/Aag	5/19	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.599871442311734	2		412	610	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793146	33793146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	133	278	0	ENST00000498907.2:c.175G>A	p.Glu59Lys	p.E59K	ENST00000498907	NM_004364.3	59	Gag/Aag	1/1	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.599871442311734	2		278	427	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223625	36223625	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	263	615	0	ENST00000222270.7:c.6175G>C	p.Glu2059Gln	p.E2059Q	ENST00000222270	NM_014727.1	2059	Gaa/Caa	28/37	0.547412893129621	3	FACETS	1	0.948	1			1	CLONAL	1	TRUE	NA	0.599871442311734	3		615	1125	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519758	29519758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	123	290	0	ENST00000389048.3:c.1813G>A	p.Asp605Asn	p.D605N	ENST00000389048	NM_004304.4	605	Gac/Aac	9/29	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.599871442311734	2		290	396	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495232	212495232	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	154	357	0	ENST00000342788.4:c.2034G>T	p.Lys678Asn	p.K678N	ENST00000342788	NM_005235.2	678	aaG/aaT	17/28	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.599871442311734	2		357	482	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945545	54945545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	259	692	0	ENST00000312783.6:c.1025C>T	p.Ser342Leu	p.S342L	ENST00000312783	NM_198436.1	342	tCa/tTa	9/10	1	2	FACETS	0.859	0.805	0.915	0.859	0.805	0.915	CLONAL	1	TRUE	1	0.599871442311734	2		692	1005	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627341	37627341	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	267	763	0	ENST00000249071.6:c.378C>G	p.Ile126Met	p.I126M	ENST00000249071	NM_002872.4	126	atC/atG	5/7	1	2	FACETS	0.858	0.805	0.912	0.858	0.805	0.912	CLONAL	1	TRUE	1	0.599871442311734	2		763	1038	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183592	10183592	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	238	596	0	ENST00000256474.2:c.61G>A	p.Glu21Lys	p.E21K	ENST00000256474	NM_000551.3	21	Gaa/Aaa	1/3	0.599871442311734	3	FACETS	0.982	0.917	1	0.327	0.305	0.35	CLONAL	1	TRUE	0	0.599871442311734	3		596	1050	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928842	49928842	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	214	481	1	ENST00000296474.3:c.3524C>T	p.Ser1175Leu	p.S1175L	ENST00000296474	NM_002447.2	1175	tCa/tTa	16/20	0.256182617146315	3	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.599871442311734	3		482	876	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49929204	49929204	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	208	454	0	ENST00000296474.3:c.3339C>G	p.Ile1113Met	p.I1113M	ENST00000296474	NM_002447.2	1113	atC/atG	15/20	0.256182617146315	3	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.599871442311734	3		454	737	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155583	106155583	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	98	379	0	ENST00000380013.4:c.484G>T	p.Asp162Tyr	p.D162Y	ENST00000380013	NM_001127208.2	162	Gat/Tat	3/11	1	2	FACETS	0.967	0.871	1	0.967	0.871	1	CLONAL	1	TRUE	1	0.599871442311734	2		379	338	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081562	143081562	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	103	264	0	ENST00000262992.4:c.1512G>A	p.Met504Ile	p.M504I	ENST00000262992	NM_001101669.1	504	atG/atA	15/24	1	2	FACETS	0.859	0.774	0.947	0.859	0.774	0.947	CLONAL	1	TRUE	1	0.599871442311734	2		264	400	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522533	187522533	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	259	302	0	ENST00000441802.2:c.11530C>G	p.Leu3844Val	p.L3844V	ENST00000441802	NM_005245.3	3844	Ctg/Gtg	21/27	0.599871442311734	3	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	1	0.599871442311734	3		302	559	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549674	187549674	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	221	269	0	ENST00000441802.2:c.4567G>A	p.Glu1523Lys	p.E1523K	ENST00000441802	NM_005245.3	1523	Gaa/Aaa	8/27	0.599871442311734	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.599871442311734	3		269	469	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557945	187557945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	187	201	0	ENST00000441802.2:c.3766G>A	p.Glu1256Lys	p.E1256K	ENST00000441802	NM_005245.3	1256	Gag/Aag	5/27	0.599871442311734	3	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	1	0.599871442311734	3		201	404	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197268	26197268	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	124	242	0	ENST00000356476.2:c.211C>G	p.Leu71Val	p.L71V	ENST00000356476		71	Cta/Gta	1/1	1	2	FACETS	0.946	0.862	1	0.946	0.862	1	CLONAL	1	TRUE	1	0.599871442311734	2		242	437	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527577	157527577	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs558541490	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	135	321	0	ENST00000346085.5:c.5302C>G	p.Pro1768Ala	p.P1768A	ENST00000346085	NM_020732.3	1768	Ccg/Gcg	20/20	1	2	FACETS	0.926	0.847	1	0.926	0.847	1	CLONAL	1	TRUE	1	0.599871442311734	2		321	486	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622171	162622171	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	64	182	0	ENST00000366898.1:c.526T>A	p.Leu176Met	p.L176M	ENST00000366898	NM_004562.2	176	Ttg/Atg	4/12	1	2	FACETS	0.979	0.86	1	0.979	0.86	1	CLONAL	1	TRUE	1	0.599871442311734	2		182	218	SUCCESS
MET	4233	MSKCC	GRCh37	7	116417478	116417478	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	95	183	0	ENST00000397752.3:c.3295G>C	p.Asp1099His	p.D1099H	ENST00000397752	NM_000245.2	1099	Gac/Cac	16/21	0.156325855598772	6	FACETS	0.917	0.823	1			1	INDETERMINATE	2	TRUE	NA	0.599871442311734	6		183	380	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423459	116423459	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	122	191	0	ENST00000397752.3:c.3734T>A	p.Leu1245Gln	p.L1245Q	ENST00000397752	NM_000245.2	1245	cTg/cAg	19/21	0.156325855598772	6	FACETS	0.96	0.873	1			1	INDETERMINATE	2	TRUE	NA	0.599871442311734	6		191	466	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476777	140476777	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	126	255	0	ENST00000288602.6:c.1629C>G	p.Ile543Met	p.I543M	ENST00000288602	NM_004333.4	543	atC/atG	13/18	0.599871442311734	2	FACETS	1	0.922	1	0.505	0.461	0.55	CLONAL	1	TRUE	0	0.599871442311734	2		255	416	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133960	38133960	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1225975674	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2017	168	468	0	ENST00000317025.8:c.3926G>A	p.Arg1309Lys	p.R1309K	ENST00000317025	NM_023034.1	1309	aGa/aAa	23/24	0.599871442311734	9	FACETS	0.795	0.727	0.866			1	SUBCLONAL	1	TRUE	NA	0.599871442311734	9		468	2185	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141549512	141549512	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	124	285	0	ENST00000220592.5:c.2076C>G	p.Ile692Met	p.I692M	ENST00000220592	NM_012154.3	692	atC/atG	16/19	0.156325855598772	6	FACETS	0.911	0.829	0.997			1	INDETERMINATE	2	TRUE	NA	0.599871442311734	6		285	499	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141582928	141582928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	196	498	0	ENST00000220592.5:c.319C>T	p.Pro107Ser	p.P107S	ENST00000220592	NM_012154.3	107	Ccg/Tcg	3/19	0.156325855598772	6	FACETS	0.837	0.775	0.9			1	INDETERMINATE	2	TRUE	NA	0.599871442311734	6		498	859	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238436	98238436	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	97	205	1	ENST00000331920.6:c.1608G>T	p.Arg536Ser	p.R536S	ENST00000331920	NM_000264.3	536	agG/agT	12/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.599871442311734	2		206	277	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787810	135787810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs118203450	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	124	261	0	ENST00000298552.3:c.772G>A	p.Glu258Lys	p.E258K	ENST00000298552	NM_001162426.1	258	Gag/Aag	9/23	0.156325855598772	6	FACETS	0.821	0.746	0.899			1	INDETERMINATE	2	TRUE	NA	0.599871442311734	6		261	554	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44920614	44920614	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	121	300	0	ENST00000377967.4:c.1375C>G	p.Pro459Ala	p.P459A	ENST00000377967	NM_021140.2	459	Cca/Gca	14/29	NA	2	FACETS	0.974	0.888	1			1	INDETERMINATE	1	TRUE	NA	0.599871442311734	2		300	414	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44920632	44920632	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	125	323	0	ENST00000377967.4:c.1393C>A	p.His465Asn	p.H465N	ENST00000377967	NM_021140.2	465	Cat/Aat	14/29	NA	2	FACETS	0.954	0.87	1			1	INDETERMINATE	1	TRUE	NA	0.599871442311734	2		323	437	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349532	70349532	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	141	303	0	ENST00000374080.3:c.3694G>C	p.Asp1232His	p.D1232H	ENST00000374080		1232	Gat/Cat	27/45	0.599871442311734	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.599871442311734	1		303	311	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0026226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	68	273	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.76	0.666	0.86	1	0.975	1	SUBCLONAL	2	TRUE	1	0.273627440752747	2		273	327	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155725	56155726	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0026226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	50	198	0	ENST00000399503.3:c.819_820del	p.Arg273SerfsTer27	p.R273Sfs*27	ENST00000399503	NM_005921.1	273	AGa/a	3/20	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.273627440752747	2		198	312	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115440	115115440	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	46	341	0	ENST00000257566.3:c.886A>G	p.Asn296Asp	p.N296D	ENST00000257566	NM_016569.3	296	Aac/Gac	5/8	1	2	FACETS	0.597	0.502	0.702	0.597	0.502	0.702	SUBCLONAL	1	TRUE	1	0.273627440752747	2		341	563	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348810	89348811	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0026226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	201	688	0	ENST00000301030.4:c.4139dup	p.Tyr1380Ter	p.Y1380*	ENST00000301030	NM_001256183.1	1380	tac/taAc	9/13	0.273627440752747	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.273627440752747	1		688	915	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189417	56189418	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0026226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	60	316	0	ENST00000399503.3:c.4451_4452del	p.Val1484GlyfsTer38	p.V1484Gfs*38	ENST00000399503	NM_005921.1	1483	gaTGtg/gatg	20/20	1	2	FACETS	0.931	0.804	1	0.931	0.804	1	CLONAL	1	TRUE	1	0.273627440752747	2		316	471	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918709	44918709	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	46	275	0	ENST00000377967.4:c.1192C>T	p.Gln398Ter	p.Q398*	ENST00000377967	NM_021140.2	398	Cag/Tag	12/29	1	2	FACETS	0.741	0.624	0.869	0.741	0.624	0.869	SUBCLONAL	1	TRUE	1	0.273627440752747	2		275	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578421	7578421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779000871	NA	P-0026227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	9	411	0	ENST00000269305.4:c.509C>T	p.Thr170Met	p.T170M	ENST00000269305	NM_001126112.2	170	aCg/aTg	5/11	0.256174078813465	4	FACETS	0.205	0.135	0.296			1	SUBCLONAL	1	FALSE	NA	0.256174078813465	4		411	430	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913499	NA	P-0026227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	44	160	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	0.98	1	CLONAL	3	FALSE	1	0.256174078813465	2		160	109	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0026227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	322	305	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.256174078813465	4	FACETS	1	0.995	1			1	CLONAL	9	FALSE	NA	0.256174078813465	4		305	338	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938752	76938752	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	43	170	0	ENST00000373344.5:c.1996C>T	p.Arg666Ter	p.R666*	ENST00000373344	NM_000489.3	666	Cga/Tga	9/35	1	1	FACETS	1	0.923	1	1	0.975	1	CLONAL	2	FALSE	0	0.256174078813465	1		170	130	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14015954	14015954	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	49	160	0	ENST00000311895.7:c.274A>G	p.Ile92Val	p.I92V	ENST00000311895	NM_005236.2	92	Atc/Gtc	2/11	1	2	FACETS	0.981	0.853	1	1	0.981	1	CLONAL	3	FALSE	1	0.256174078813465	2		160	130	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576365	67576365	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	17	159	0	ENST00000274335.5:c.644G>A	p.Ser215Asn	p.S215N	ENST00000274335		215	aGc/aAc	5/15	1	2	FACETS	1	0.805	1	1	0.805	1	CLONAL	1	FALSE	1	0.256174078813465	2		159	123	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939948	76939949	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTAGCAATACCATTGGTTGTT	novel	NA	P-0026227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	16	177	0	ENST00000373344.5:c.778_799dup	p.Ile267LysfsTer22	p.I267Kfs*22	ENST00000373344	NM_000489.3	267	att/aAACAACCAATGGTATTGCTACAtt	9/35	1	1	FACETS	0.947	0.708	1	0.947	0.708	1	CLONAL	1	FALSE	0	0.256174078813465	1		177	115	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0026228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	104	154	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	0.997	0.908	1	0.997	0.908	1	CLONAL	1	TRUE	1	0.796166368452338	2		154	262	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115438	115115439	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0026228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	216	361	0	ENST00000257566.3:c.887dup	p.Asn296LysfsTer31	p.N296Kfs*31	ENST00000257566	NM_016569.3	296	aac/aaAc	5/8	0.76625543882505	1	FACETS	0.981	0.933	1	0.981	0.933	1	CLONAL	1	TRUE	0	0.796166368452338	1		361	333	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223458	2223459	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTCT	novel	NA	P-0026228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	129	231	0	ENST00000398665.3:c.3570_3573dup	p.Glu1192LeufsTer2	p.E1192Lfs*2	ENST00000398665	NM_032482.2	1190	ggc/ggCTCTc	25/28	1	2	FACETS	0.994	0.914	1	0.994	0.914	1	CLONAL	1	TRUE	1	0.796166368452338	2		231	326	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100143	30100143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs191202207	NA	P-0026229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	37	355	0	ENST00000331968.5:c.1477G>A	p.Glu493Lys	p.E493K	ENST00000331968	NM_002742.2	493	Gaa/Aaa	10/18	1	2	FACETS	0.892	0.74	1	0.892	0.74	1	CLONAL	1	TRUE	1	0.34	2		355	244	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835903	151835903	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	38	224	0	ENST00000262189.6:c.14621G>C	p.Arg4874Pro	p.R4874P	ENST00000262189	NM_170606.2	4874	cGg/cCg	58/59	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.34	2		224	207	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0026230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	94	258	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	1	2	FACETS	0.791	0.712	0.873	0.791	0.712	0.873	SUBCLONAL	1	TRUE	1	0.766375078455666	2		258	310	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484339	50484339	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	91	266	1	ENST00000394963.4:c.1099C>A	p.Pro367Thr	p.P367T	ENST00000394963	NM_003076.4	367	Cca/Aca	9/13	1	2	FACETS	0.91	0.82	1	0.91	0.82	1	CLONAL	1	TRUE	1	0.766375078455666	2		267	261	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932760	39932797	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGGTGCTGCTACTGTGCTTGGCAGGAGTGGCCGGGG	GCTGGTGCTGCTACTGTGCTTGGCAGGAGTGGCCGGGG	-	novel	NA	P-0026230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	167	505	0	ENST00000378444.4:c.1802_1839del	p.Pro601GlnfsTer31	p.P601Qfs*31	ENST00000378444	NM_001123385.1	601	cCCCCGGCCACTCCTGCCAAGCACAGTAGCAGCACCAGC/c	4/15	0.435297817483665	1	FACETS	0.664	0.617	0.711	0.664	0.617	0.711	INDETERMINATE	1	TRUE	0	0.766375078455666	1		505	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0026233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	259	461	1	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	0.462585918624644	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.488367785564989	2		462	502	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873104	134873104	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202048188	NA	P-0026233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	24	275	0	ENST00000398015.3:c.1408C>T	p.Arg470Trp	p.R470W	ENST00000398015	NM_004441.4	470	Cgg/Tgg	6/16	0.488367785564989	3	FACETS	0.277	0.216	0.347	0.138	0.108	0.174	SUBCLONAL	1	TRUE	1	0.488367785564989	3		275	442	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230818	66230818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs910705978	NA	P-0026233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	46	172	0	ENST00000273854.3:c.2153G>A	p.Arg718His	p.R718H	ENST00000273854	NM_004439.5	718	cGc/cAc	12/18	0.305382759159707	3	FACETS	0.855	0.737	0.979			1	CLONAL	2	TRUE	NA	0.488367785564989	3		172	137	SUCCESS
CALR	811	MSKCC	GRCh37	19	13049956	13049956	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	26	230	0	ENST00000316448.5:c.100A>T	p.Thr34Ser	p.T34S	ENST00000316448	NM_004343.3	34	Act/Tct	2/9	0.488367785564989	3	FACETS	0.392	0.31	0.485	0.196	0.155	0.243	SUBCLONAL	1	TRUE	1	0.488367785564989	3		230	338	SUCCESS
APC	324	MSKCC	GRCh37	5	112175251	112175255	+	frameshift_variant	Frame_Shift_Del	DEL	GAGCG	GAGCG	-	novel	NA	P-0026233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	43	100	0	ENST00000257430.4:c.3960_3964del	p.Glu1322SerfsTer8	p.E1322Sfs*8	ENST00000257430	NM_000038.5	1320	gtGAGCGaa/gtaa	16/16	0.488367785564989	2	FACETS	0.779	0.671	0.891	0.779	0.671	0.891	SUBCLONAL	2	TRUE	0	0.488367785564989	2		100	113	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0026234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	111	366	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.257840738570146	1	FACETS	0.838	0.757	0.924	0.838	0.757	0.924	CLONAL	1	TRUE	0	0.418685824786556	1		366	500	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479795	67479795	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs757106110	NA	P-0026234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	93	270	0	ENST00000327367.4:c.1102C>T	p.Arg368Ter	p.R368*	ENST00000327367	NM_005902.3	368	Cga/Tga	8/9	1	2	FACETS	0.949	0.848	1	0.949	0.848	1	CLONAL	1	TRUE	1	0.418685824786556	2		270	468	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174395	11174395	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1085307113	NA	P-0026234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	104	356	0	ENST00000361445.4:c.7280T>A	p.Leu2427Gln	p.L2427Q	ENST00000361445	NM_004958.3	2427	cTg/cAg	53/58	0.418685824786556	1	FACETS	0.956	0.862	1	0.956	0.862	1	CLONAL	1	TRUE	0	0.418685824786556	1		356	411	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37665992	37665992	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	75	238	0	ENST00000447079.4:c.2644C>T	p.Arg882Trp	p.R882W	ENST00000447079	NM_015083.1	882	Cgg/Tgg	7/14	0.257840738570146	1	FACETS	0.98	0.868	1	0.98	0.868	1	CLONAL	1	TRUE	0	0.418685824786556	1		238	289	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912267	32912267	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587782071	NA	P-0026234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	41	281	0	ENST00000380152.3:c.3775A>C	p.Ser1259Arg	p.S1259R	ENST00000380152		1259	Agt/Cgt	11/27	1	2	FACETS	0.541	0.452	0.64	0.541	0.452	0.64	SUBCLONAL	1	TRUE	1	0.418685824786556	2		281	362	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482833	67482833	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	64	327	0	ENST00000327367.4:c.1237C>T	p.Gln413Ter	p.Q413*	ENST00000327367	NM_005902.3	413	Cag/Tag	9/9	1	2	FACETS	0.703	0.61	0.802	0.703	0.61	0.802	SUBCLONAL	1	TRUE	1	0.418685824786556	2		327	435	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991632	72991632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781454634	NA	P-0026234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	110	306	0	ENST00000268489.5:c.2413C>T	p.Arg805Trp	p.R805W	ENST00000268489	NM_006885.3	805	Cgg/Tgg	2/10	0.257840738570146	1	FACETS	0.989	0.895	1	0.989	0.895	1	CLONAL	1	TRUE	0	0.418685824786556	1		306	420	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374902	45374902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	152	329	0	ENST00000262160.6:c.941G>A	p.Gly314Asp	p.G314D	ENST00000262160	NM_005901.5	314	gGt/gAt	8/11	0.418685824786556	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.418685824786556	1		329	386	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855904	45855904	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773359656	NA	P-0026234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	67	427	2	ENST00000391945.4:c.1906C>T	p.Arg636Trp	p.R636W	ENST00000391945	NM_000400.3	636	Cgg/Tgg	21/23	0.257840738570146	1	FACETS	0.492	0.428	0.561	0.492	0.428	0.561	SUBCLONAL	1	TRUE	0	0.418685824786556	1		429	514	SUCCESS
APC	324	MSKCC	GRCh37	5	112175488	112175488	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	22	155	0	ENST00000257430.4:c.4198del	p.Ser1400ArgfsTer15	p.S1400Rfs*15	ENST00000257430	NM_000038.5	1399	cgT/cg	16/16	0.257840738570146	1	FACETS	0.422	0.328	0.529	0.422	0.328	0.529	SUBCLONAL	1	TRUE	0	0.418685824786556	1		155	197	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0026237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	152	572	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.207041718068972	0	FACETS	0.813	0.754	0.873			1	CLONAL	4	FALSE	0	0.207041718068972	0		572	358	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852481	42852481	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759250613	NA	P-0026237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	123	334	0	ENST00000398585.3:c.605G>A	p.Arg202Lys	p.R202K	ENST00000398585	NM_001135099.1	202	aGg/aAg	6/14	1	2	FACETS	0.85	0.774	0.929	1	0.991	1	CLONAL	3	FALSE	1	0.207041718068972	2		334	466	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832266	72832266	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	99	220	0	ENST00000268489.5:c.4315C>T	p.Arg1439Ter	p.R1439*	ENST00000268489	NM_006885.3	1439	Cga/Tga	9/10	0.207041718068972	0	FACETS	0.832	0.758	0.906			1	CLONAL	4	FALSE	0	0.207041718068972	0		220	228	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456434	29456434	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	139	389	0	ENST00000389048.3:c.2484T>A	p.Phe828Leu	p.F828L	ENST00000389048	NM_004304.4	828	ttT/ttA	14/29	0.182336289578122	1	FACETS	0.845	0.774	0.917	1	0.992	1	CLONAL	3	FALSE	0	0.207041718068972	1		389	475	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0026239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	449	423	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			NA	2	FACETS	0.884	0.851	0.917			1	INDETERMINATE	2	TRUE	NA	0.633141008351077	2		423	802	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919631	28919631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200840674	NA	P-0026239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	336	347	1	ENST00000282397.4:c.2306C>T	p.Ala769Val	p.A769V	ENST00000282397	NM_002019.4	769	gCg/gTg	16/30	0.414683035086325	3	FACETS	0.843	0.801	0.885	0.843	0.801	0.885	CLONAL	2	TRUE	1	0.633141008351077	3		348	829	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40738999	40738999	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	201	271	0	ENST00000373198.4:c.3285A>C	p.Glu1095Asp	p.E1095D	ENST00000373198	NM_133170.3	1095	gaA/gaC	24/32	0.402600468090158	3	FACETS	0.753	0.703	0.804	0.753	0.703	0.804	SUBCLONAL	2	TRUE	1	0.633141008351077	3		271	555	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946316	2946316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759870621	NA	P-0026239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	81	384	0	ENST00000396946.4:c.3421G>A	p.Glu1141Lys	p.E1141K	ENST00000396946	NM_032415.4	1141	Gag/Aag	25/25	0.633141008351077	3	FACETS	0.333	0.292	0.376	0.166	0.146	0.188	SUBCLONAL	1	TRUE	1	0.633141008351077	3		384	1013	SUCCESS
APC	324	MSKCC	GRCh37	5	112173374	112173374	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	20	185	0	ENST00000257430.4:c.2083C>T	p.Gln695Ter	p.Q695*	ENST00000257430	NM_000038.5	695	Cag/Tag	16/16	0.633141008351077	1	FACETS	0.165	0.126	0.211	0.165	0.126	0.211	SUBCLONAL	1	TRUE	0	0.633141008351077	1		185	261	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81557433	81557433	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	47	258	0	ENST00000298171.2:c.413T>G	p.Leu138Arg	p.L138R	ENST00000298171	NM_000369.2	138	cTt/cGt	5/10	0.633141008351077	1	FACETS	0.266	0.224	0.311	0.266	0.224	0.311	SUBCLONAL	1	TRUE	0	0.633141008351077	1		258	382	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680662	88680662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	159	332	0	ENST00000360948.2:c.595C>T	p.Leu199Phe	p.L199F	ENST00000360948	NM_001012338.2	199	Ctc/Ttc	6/19	1	2	FACETS	0.948	0.874	1	0.948	0.874	1	CLONAL	1	TRUE	1	0.633141008351077	2		332	530	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054718	13054718	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs148604761	NA	P-0026239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	54	188	0	ENST00000316448.5:c.1245C>G	p.Asp415Glu	p.D415E	ENST00000316448	NM_004343.3	415	gaC/gaG	9/9	0.592683101581416	2	FACETS	0.455	0.39	0.526	0.227	0.195	0.263	SUBCLONAL	1	TRUE	0	0.633141008351077	2		188	375	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546703	9546703	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	31	165	1	ENST00000353224.5:c.1319T>G	p.Val440Gly	p.V440G	ENST00000353224	NM_177990.2	440	gTc/gGc	5/10	0.402600468090158	3	FACETS	0.369	0.299	0.449	0.185	0.149	0.225	SUBCLONAL	1	TRUE	1	0.633141008351077	3		166	349	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983111	111983111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	166	231	0	ENST00000368678.4:c.1436G>A	p.Gly479Asp	p.G479D	ENST00000368678		479	gGc/gAc	13/13	0.606584589249046	2	FACETS	0.802	0.75	0.854	0.802	0.75	0.854	CLONAL	2	TRUE	0	0.633141008351077	2		231	327	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403296	116403296	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	61	317	0	ENST00000397752.3:c.2557G>A	p.Gly853Ser	p.G853S	ENST00000397752	NM_000245.2	853	Ggc/Agc	11/21	0.352958146095728	5	FACETS	0.432	0.371	0.498			1	INDETERMINATE	1	TRUE	NA	0.633141008351077	5		317	870	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845689	151845689	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	73	328	0	ENST00000262189.6:c.13323G>C	p.Glu4441Asp	p.E4441D	ENST00000262189	NM_170606.2	4441	gaG/gaC	52/59	0.335919810183205	1	FACETS	0.294	0.257	0.334	0.294	0.257	0.334	INDETERMINATE	1	TRUE	0	0.633141008351077	1		328	536	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930138	68930138	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	58	334	0	ENST00000288368.4:c.199G>C	p.Glu67Gln	p.E67Q	ENST00000288368	NM_024870.2	67	Gaa/Caa	2/40	0.23032467963634	4	FACETS	0.447	0.384	0.517	0.224	0.192	0.259	INDETERMINATE	1	TRUE	2	0.633141008351077	4		334	669	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0026241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	521	440	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.840192789894826	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	FALSE	0	0.840192789894826	2		441	581	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0026241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	411	336	1	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.840192789894826	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	FALSE	0	0.840192789894826	2		337	460	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936995	48936995	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778842	NA	P-0026241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	334	312	0	ENST00000267163.4:c.763C>T	p.Arg255Ter	p.R255*	ENST00000267163	NM_000321.2	255	Cga/Tga	8/27	0.840192789894826	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	FALSE	0	0.840192789894826	2		312	383	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101099	27101099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	495	389	0	ENST00000324856.7:c.4381C>T	p.Arg1461Ter	p.R1461*	ENST00000324856	NM_006015.4	1461	Cga/Tga	18/20	0.840192789894826	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	FALSE	0	0.840192789894826	2		389	551	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0026241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	435	395	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	0.840192789894826	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	FALSE	0	0.840192789894826	2		395	489	SUCCESS
APC	324	MSKCC	GRCh37	5	112175912	112175912	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201801	NA	P-0026241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	235	160	0	ENST00000257430.4:c.4621C>T	p.Gln1541Ter	p.Q1541*	ENST00000257430	NM_000038.5	1541	Cag/Tag	16/16	0.840192789894826	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	FALSE	0	0.840192789894826	2		160	259	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528178	29528178	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs864622161	NA	P-0026241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	379	327	2	ENST00000356175.3:c.1185+1G>A		p.X395_splice	ENST00000356175	NM_000267.3	395			0.840192789894826	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	FALSE	0	0.840192789894826	2		329	436	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0026242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	44	347	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.38259413273025	2		347	218	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624296	89624296	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs786201995	NA	P-0026242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	86	307	0	ENST00000371953.3:c.70G>C	p.Asp24His	p.D24H	ENST00000371953	NM_000314.4	24	Gac/Cac	1/9	0.38259413273025	1	FACETS	0.954	0.85	1	0.954	0.85	1	CLONAL	1	TRUE	0	0.38259413273025	1		307	381	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098913	47098913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	66	354	0	ENST00000409792.3:c.6361C>T	p.Arg2121Cys	p.R2121C	ENST00000409792	NM_014159.6	2121	Cgc/Tgc	15/21	1	2	FACETS	0.624	0.542	0.713	0.624	0.542	0.713	SUBCLONAL	1	TRUE	1	0.38259413273025	2		354	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863224683	NA	P-0026242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	121	428	0	ENST00000269305.4:c.388C>T	p.Leu130Phe	p.L130F	ENST00000269305	NM_001126112.2	130	Ctc/Ttc	5/11	0.38259413273025	1	FACETS	0.951	0.863	1	0.951	0.863	1	CLONAL	1	TRUE	0	0.38259413273025	1		428	538	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606436	93606436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201455170	NA	P-0026242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	30	299	0	ENST00000375746.1:c.256G>A	p.Ala86Thr	p.A86T	ENST00000375746	NM_001174167.1	86	Gcc/Acc	2/14	1	2	FACETS	0.361	0.29	0.441	0.361	0.29	0.441	SUBCLONAL	1	TRUE	1	0.38259413273025	2		299	435	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1956908	1956908	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	172	393	0	ENST00000382891.5:c.2359C>T	p.Arg787Cys	p.R787C	ENST00000382891	NM_133335.3	787	Cgc/Tgc	13/22	1	2	FACETS	0.761	0.704	0.82	1	0.99	1	SUBCLONAL	2	TRUE	1	0.38259413273025	2		393	591	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215352	123215353	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0026242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	77	257	0	ENST00000218089.9:c.2898_2899del	p.Glu968SerfsTer15	p.E968Sfs*15	ENST00000218089	NM_001042749.1	966	acAAga/acga	28/35	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.38259413273025	2		257	371	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888208	112888208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	95	314	0	ENST00000351677.2:c.224C>T	p.Ala75Val	p.A75V	ENST00000351677	NM_002834.3	75	gCt/gTt	3/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.38259413273025	2		314	424	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828095	3828095	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	87	367	1	ENST00000262367.5:c.2030G>A	p.Gly677Asp	p.G677D	ENST00000262367	NM_004380.2	677	gGc/gAc	10/31	1	2	FACETS	0.926	0.823	1	0.926	0.823	1	CLONAL	1	TRUE	1	0.38259413273025	2		368	491	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020764	26020764	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1265819917	NA	P-0026242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	33	103	0	ENST00000357647.3:c.47C>T	p.Ala16Val	p.A16V	ENST00000357647	NM_003529.2	16	gCg/gTg	1/1	0.199944355289235	1	FACETS	0.956	0.79	1	0.956	0.79	1	INDETERMINATE	1	TRUE	0	0.38259413273025	1		103	146	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757274881	NA	P-0026245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	336	461	0	ENST00000269305.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	144	Cag/Tag	5/11	0.392952589755247	3	FACETS	0.87	0.83	0.91	0.87	0.83	0.91	CLONAL	3	FALSE	0	0.462078154328476	3		461	686	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436084	51436084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs548300689	NA	P-0026245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	76	221	0	ENST00000262662.1:c.44G>A	p.Arg15Lys	p.R15K	ENST00000262662		15	aGg/aAg	3/4	0.210963869532237	4	FACETS	1	0.956	1	0.592	0.522	0.667	INDETERMINATE	1	FALSE	2	0.462078154328476	4		221	406	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	31	244	0	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	1	2	FACETS	0.456	0.37	0.552	0.456	0.37	0.552	SUBCLONAL	1	TRUE	1	0.499868364182338	2		244	272	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144049	11144051	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0026249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	34	381	0	ENST00000358026.2:c.3634_3636del	p.Glu1212del	p.E1212del	ENST00000358026	NM_001128849.1	1210	gtGGAg/gtg	26/36	0.358328264557399	1	FACETS	0.232	0.189	0.28	0.232	0.189	0.28	SUBCLONAL	1	TRUE	0	0.499868364182338	1		381	440	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851765	134851765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	66	267	0	ENST00000398015.3:c.1171G>A	p.Val391Ile	p.V391I	ENST00000398015	NM_004441.4	391	Gtc/Atc	5/16	1	2	FACETS	0.886	0.776	1	0.886	0.776	1	CLONAL	1	TRUE	1	0.499868364182338	2		267	298	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266833	198266833	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519756	NA	P-0026249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	93	312	0	ENST00000335508.6:c.2099A>C	p.Lys700Thr	p.K700T	ENST00000335508	NM_012433.2	700	aAa/aCa	15/25	1	2	FACETS	0.816	0.729	0.908	0.816	0.729	0.908	CLONAL	1	TRUE	1	0.499868364182338	2		312	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0026250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	239	379	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.321772373615979	3	FACETS	1	0.988	1	0.785	0.741	0.828	CLONAL	2	TRUE	0	0.514759384711802	3		380	496	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794881	242794881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs190602950	NA	P-0026250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	201	363	1	ENST00000334409.5:c.328G>A	p.Val110Met	p.V110M	ENST00000334409	NM_005018.2	110	Gtg/Atg	2/5	0.514759384711802	3	FACETS	0.851	0.794	0.909	0.851	0.794	0.909	CLONAL	2	TRUE	1	0.514759384711802	3		364	577	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412898	49412898	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519954	NA	P-0026250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	299	380	0	ENST00000418115.1:c.125A>G	p.Tyr42Cys	p.Y42C	ENST00000418115	NM_001664.2	42	tAt/tGt	2/5	0.454971127341542	3	FACETS	0.842	0.802	0.883	0.842	0.802	0.883	CLONAL	3	TRUE	0	0.514759384711802	3		380	578	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106649	27106649	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	319	330	0	ENST00000324856.7:c.6260G>A	p.Gly2087Glu	p.G2087E	ENST00000324856	NM_006015.4	2087	gGa/gAa	20/20	0.514759384711802	3	FACETS	0.923	0.882	0.963	0.923	0.882	0.963	CLONAL	3	TRUE	0	0.514759384711802	3		330	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0026252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	258	379	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.310173681188899	5	FACETS	0.968	0.92	1			1	CLONAL	5	TRUE	NA	0.353050194304042	5		380	462	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433373	49433373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771966959	NA	P-0026252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	32	350	0	ENST00000301067.7:c.8074C>T	p.Arg2692Trp	p.R2692W	ENST00000301067	NM_003482.3	2692	Cgg/Tgg	32/54	0.354034686559324	4	FACETS	0.531	0.43	0.645	0.265	0.215	0.323	SUBCLONAL	1	TRUE	2	0.353050194304042	4		350	462	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492806	56492806	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0026252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	370	304	1	ENST00000407977.2:c.133A>T	p.Lys45Ter	p.K45*	ENST00000407977		45	Aaa/Taa	2/10	0.354034686559324	4	FACETS	1	0.992	1	1	0.996	1	CLONAL	5	TRUE	0	0.353050194304042	4		305	518	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138197141	138197141	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	76	121	0	ENST00000237289.4:c.643C>G	p.Leu215Val	p.L215V	ENST00000237289	NM_001270507.1	215	Cta/Gta	5/9	0.353050194304042	7	FACETS	1	0.928	1			1	CLONAL	3	TRUE	NA	0.353050194304042	7		121	255	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534285	534285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894226	NA	P-0026256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	37	349	0	ENST00000451590.1:c.38G>A	p.Gly13Asp	p.G13D	ENST00000451590	NM_001130442.1	13	gGt/gAt	2/5	1	2	FACETS	0.539	0.445	0.643	0.539	0.445	0.643	SUBCLONAL	1	TRUE	1	0.41	2		349	335	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061127	38061197	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGC	TGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGC	-	novel	NA	P-0026256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	67	75	0	ENST00000250448.2:c.792_862del	p.Arg265GlyfsTer4	p.R265Gfs*4	ENST00000250448	NM_004496.3	264	aaGCGCTTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGCGGCGCCAag/aaag	2/2	0.053239182642121	3	FACETS	0.972	0.873	1	1	0.978	1	INDETERMINATE	3	TRUE	1	0.41	3		75	135	SUCCESS
ALK	238	MSKCC	GRCh37	2	29436892	29436892	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	9	334	1	ENST00000389048.3:c.3701C>A	p.Ala1234Asp	p.A1234D	ENST00000389048	NM_004304.4	1234	gCc/gAc	24/29	1	2	FACETS	0.171	0.113	0.246	0.171	0.113	0.246	SUBCLONAL	1	TRUE	1	0.41	2		335	256	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969945	81969945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	206	285	0	ENST00000359376.3:c.3014G>A	p.Cys1005Tyr	p.C1005Y	ENST00000359376	NM_002661.3	1005	tGc/tAc	27/33	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	1	0.279923083577478	2		285	612	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536204	41536204	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	118	355	1	ENST00000263253.7:c.1821C>A	p.Asn607Lys	p.N607K	ENST00000263253	NM_001429.3	607	aaC/aaA	9/31	0.279923083577478	0	FACETS	0.891	0.824	0.959			1	CLONAL	3	TRUE	0	0.279923083577478	0		356	227	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645051	86645052	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTG	novel	NA	P-0026257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	25	171	0	ENST00000274376.6:c.1125_1127dup	p.Val376dup	p.V376dup	ENST00000274376	NM_002890.2	376	ctt/cTTGtt	8/25	1	2	FACETS	1	0.911	1	1	0.96	1	CLONAL	2	TRUE	1	0.279923083577478	2		171	73	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982056	93982056	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	127	260	1	ENST00000369303.4:c.1409A>G	p.Asn470Ser	p.N470S	ENST00000369303	NM_004440.3	470	aAt/aGt	6/17	1	2	FACETS	0.864	0.793	0.938	1	0.992	1	CLONAL	3	TRUE	1	0.279923083577478	2		261	350	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143248	24143256	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGAGAAC	GAAGAGAAC	A	novel	NA	P-0026257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	337	408	0	ENST00000263121.7:c.480_488delinsA	p.Lys161LeufsTer6	p.K161Lfs*6	ENST00000263121	NM_003073.3	160	aaGAAGAGAACc/aaAc	4/9	0.279923083577478	0	FACETS	0.76	0.729	0.792			1	SUBCLONAL	4	TRUE	0	0.279923083577478	0		408	570	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912790	100912790	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026257-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	12	291	1	ENST00000325455.5:c.2532G>A	p.Met844Ile	p.M844I	ENST00000325455	NM_001202474.3	844	atG/atA	7/8	1	2	FACETS	0.959	0.698	1	1	0.93	1	CLONAL	4	TRUE	1	0.135965987911239	2		292	46	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44733190	44733191	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	T	novel	NA	P-0026257-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	12	159	0	ENST00000377967.4:c.182_183delinsT	p.Arg61IlefsTer23	p.R61Ifs*23	ENST00000377967	NM_021140.2	61	aGA/aT	2/29	0.105964152423086	2	FACETS	1	0.745	1			1	CLONAL	5	TRUE	NA	0.135965987911239	2		159	35	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0026259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	53	424	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.909	0.775	1	0.909	0.775	1	CLONAL	1	TRUE	1	0.2	2		424	583	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0026259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	72	336	1	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.881	0.769	1	0.881	0.769	1	CLONAL	1	TRUE	1	0.2	2		337	817	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0026259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	59	485	3	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.775	0.666	0.895	0.775	0.666	0.895	SUBCLONAL	1	TRUE	1	0.2	2		488	761	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0026259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	45	454	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.856	0.719	1	0.856	0.719	1	CLONAL	1	TRUE	1	0.2	2		456	526	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0026259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	68	351	1	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.892	0.775	1	0.892	0.775	1	CLONAL	1	TRUE	1	0.2	2		352	762	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0026259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	57	420	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.911	0.781	1	0.911	0.781	1	CLONAL	1	TRUE	1	0.2	2		420	626	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436026	56436026	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771831816	NA	P-0026259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	38	157	1	ENST00000407977.2:c.1111C>T	p.Arg371Ter	p.R371*	ENST00000407977		371	Cga/Tga	9/10	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.2	2		158	302	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222961	36222961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	65	471	0	ENST00000222270.7:c.5590C>T	p.Arg1864Ter	p.R1864*	ENST00000222270	NM_014727.1	1864	Cga/Tga	27/37	1	2	FACETS	0.895	0.775	1	0.895	0.775	1	CLONAL	1	TRUE	1	0.2	2		471	726	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243915	46243915	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	70	265	0	ENST00000334344.6:c.2009C>A	p.Pro670His	p.P670H	ENST00000334344	NM_152641.2	670	cCt/cAt	15/21	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.2	2		265	607	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534404	63534404	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	61	398	0	ENST00000307078.5:c.1117G>T	p.Glu373Ter	p.E373*	ENST00000307078	NM_004655.3	373	Gag/Tag	5/11	1	2	FACETS	0.82	0.706	0.944	0.82	0.706	0.944	CLONAL	1	TRUE	1	0.2	2		398	744	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355329	15355346	+	inframe_deletion	In_Frame_Del	DEL	GGGGGCTGCTGGGGAGGC	GGGGGCTGCTGGGGAGGC	-	novel	NA	P-0026259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	26	214	0	ENST00000263377.2:c.2277_2294del	p.Gln762_Pro767del	p.Q762_P767del	ENST00000263377	NM_058243.2	759	ccGCCTCCCCAGCAGCCCCCa/cca	13/20	1	2	FACETS	0.855	0.678	1	0.855	0.678	1	CLONAL	1	TRUE	1	0.2	2		214	304	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36208926	36208935	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCGGCG	GGCGGCGGCG	-	novel	NA	P-0026259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	11	16	0	ENST00000222270.7:c.15_24del	p.Gly6ValfsTer37	p.G6Vfs*37	ENST00000222270	NM_014727.1	2	gcGGCGGCGGCG/gc	1/37	1	2	FACETS	1	0.81	1	1	0.909	1	CLONAL	2	TRUE	1	0.2	2		16	46	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535412	66535412	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	32	195	0	ENST00000273854.3:c.49G>A	p.Gly17Ser	p.G17S	ENST00000273854	NM_004439.5	17	Ggc/Agc	1/18	1	2	FACETS	1	0.826	1	1	0.826	1	CLONAL	1	TRUE	1	0.2	2		195	315	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31435934	31435936	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0026259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	54	300	0	ENST00000344624.3:c.2978_2980del	p.Glu993del	p.E993del	ENST00000344624		993	gAAGga/gga	22/33	1	2	FACETS	0.956	0.816	1	0.956	0.816	1	CLONAL	1	TRUE	1	0.2	2		300	565	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197265	26197265	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	37	274	1	ENST00000356476.2:c.214G>A	p.Val72Ile	p.V72I	ENST00000356476		72	Gtc/Atc	1/1	1	2	FACETS	0.734	0.605	0.879	0.734	0.605	0.879	SUBCLONAL	1	TRUE	1	0.2	2		275	504	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152093	55152093	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121908585	NA	P-0026260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	215	384	0	ENST00000257290.5:c.2525A>T	p.Asp842Val	p.D842V	ENST00000257290	NM_006206.4	842	gAc/gTc	18/23	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.820955271117825	2		384	472	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699262	117699262	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	119	242	0	ENST00000369458.3:c.379A>C	p.Thr127Pro	p.T127P	ENST00000369458	NM_024626.3	127	Acc/Ccc	3/6	0.184388221817628	1	FACETS	0.283	0.256	0.311	0.283	0.256	0.311	INDETERMINATE	1	TRUE	0	0.820955271117825	1		242	604	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0026261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	90	454	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.605	0.539	0.676	0.605	0.539	0.676	SUBCLONAL	1	TRUE	1	0.615591318278984	2		454	483	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139157	108139157	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	78	263	1	ENST00000278616.4:c.2659G>A	p.Glu887Lys	p.E887K	ENST00000278616	NM_000051.3	887	Gaa/Aaa	18/63	1	2	FACETS	0.543	0.478	0.611	0.543	0.478	0.611	SUBCLONAL	1	TRUE	1	0.615591318278984	2		264	467	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847399	68847399	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0026261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	84	251	0	ENST00000261769.5:c.1320+1G>A		p.X440_splice	ENST00000261769	NM_004360.3	440			0.376409861224533	1	FACETS	0.472	0.419	0.528	0.472	0.419	0.528	SUBCLONAL	1	TRUE	0	0.615591318278984	1		251	400	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5260818	5260818	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs747842113	NA	P-0026261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	100	383	3	ENST00000357368.4:c.593G>A	p.Arg198Gln	p.R198Q	ENST00000357368	NM_002850.3	198	cGa/cAa	7/38	1	2	FACETS	0.585	0.524	0.65	0.585	0.524	0.65	SUBCLONAL	1	TRUE	1	0.615591318278984	2		386	555	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652272	36652272	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	95	276	0	ENST00000244741.5:c.394G>A	p.Gly132Ser	p.G132S	ENST00000244741	NM_000389.4	132	Ggt/Agt	2/3	1	2	FACETS	0.578	0.516	0.644	0.578	0.516	0.644	SUBCLONAL	1	TRUE	1	0.615591318278984	2		276	534	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227947	123227947	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	81	323	0	ENST00000218089.9:c.3658G>A	p.Glu1220Lys	p.E1220K	ENST00000218089	NM_001042749.1	1220	Gag/Aag	33/35	1	2	FACETS	0.522	0.461	0.587	0.522	0.461	0.587	SUBCLONAL	1	TRUE	1	0.615591318278984	2		323	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0026262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	52	361	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.19	2		361	497	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0026262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	55	388	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	0.19	2		388	404	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0026262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	14	159	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	1	2	FACETS	0.705	0.51	0.94	0.705	0.51	0.94	CLONAL	1	TRUE	1	0.19	2		159	209	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023618	27023618	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	12	214	0	ENST00000324856.7:c.724G>T	p.Gly242Cys	p.G242C	ENST00000324856	NM_006015.4	242	Ggc/Tgc	1/20	1	2	FACETS	0.672	0.473	0.916	0.672	0.473	0.916	SUBCLONAL	1	TRUE	1	0.19	2		214	188	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241868	72241868	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	20	202	0	ENST00000357731.5:c.522C>A	p.His174Gln	p.H174Q	ENST00000357731	NM_173808.2	174	caC/caA	3/7	1	2	FACETS	0.532	0.406	0.68	0.532	0.406	0.68	SUBCLONAL	1	TRUE	1	0.19	2		202	396	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163315477	163315477	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	31	248	0	ENST00000271452.3:c.817G>T	p.Val273Leu	p.V273L	ENST00000271452	NM_145697.2	273	Gtg/Ttg	11/14	1	2	FACETS	0.759	0.613	0.924	0.759	0.613	0.924	CLONAL	1	TRUE	1	0.19	2		248	430	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136254	64136254	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	32	361	0	ENST00000334205.4:c.1413G>T	p.Glu471Asp	p.E471D	ENST00000334205	NM_003942.2	471	gaG/gaT	12/17	1	2	FACETS	0.861	0.7	1	0.861	0.7	1	CLONAL	1	TRUE	1	0.19	2		361	391	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449788	29449788	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	37	446	0	ENST00000389048.3:c.3067G>T	p.Val1023Leu	p.V1023L	ENST00000389048	NM_004304.4	1023	Gtg/Ttg	18/29	1	2	FACETS	0.7	0.577	0.84	0.7	0.577	0.84	SUBCLONAL	1	TRUE	1	0.19	2		446	556	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973965	55973965	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	28	307	0	ENST00000263923.4:c.1351C>G	p.Pro451Ala	p.P451A	ENST00000263923	NM_002253.2	451	Cct/Gct	10/30	1	2	FACETS	0.658	0.525	0.81	0.658	0.525	0.81	SUBCLONAL	1	TRUE	1	0.19	2		307	448	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094907	143094907	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	46	279	0	ENST00000262992.4:c.1237G>C	p.Val413Leu	p.V413L	ENST00000262992	NM_001101669.1	413	Gtt/Ctt	14/24	1	2	FACETS	0.819	0.689	0.963	0.819	0.689	0.963	CLONAL	1	TRUE	1	0.19	2		279	591	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295356	1295356	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0026262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	23	198	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.816	1	1	0.816	1	CLONAL	1	TRUE	1	0.19	2		198	231	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867451	35867451	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	23	211	0	ENST00000303115.3:c.265C>G	p.Gln89Glu	p.Q89E	ENST00000303115	NM_002185.3	89	Caa/Gaa	3/8	0.148668606016312	3	FACETS	0.617	0.48	0.775	0.308	0.24	0.388	SUBCLONAL	1	TRUE	1	0.19	3		211	430	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873750	35873750	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	19	153	0	ENST00000303115.3:c.706G>T	p.Gly236Trp	p.G236W	ENST00000303115	NM_002185.3	236	Ggg/Tgg	5/8	0.148668606016312	3	FACETS	0.666	0.505	0.855	0.333	0.252	0.428	SUBCLONAL	1	TRUE	1	0.19	3		153	329	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566456	139566456	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	34	364	0	ENST00000308874.7:c.715C>A	p.Leu239Ile	p.L239I	ENST00000308874		239	Ctc/Atc	9/10	1	2	FACETS	0.957	0.783	1	0.957	0.783	1	CLONAL	1	TRUE	1	0.19	2		364	374	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889056	76889056	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	30	200	0	ENST00000373344.5:c.4954G>T	p.Glu1652Ter	p.E1652*	ENST00000373344	NM_000489.3	1652	Gag/Tag	18/35	1	2	FACETS	0.766	0.617	0.936	0.766	0.617	0.936	CLONAL	1	TRUE	1	0.19	2		200	412	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0026271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	96	388	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.988	0.879	1	0.988	0.879	1	CLONAL	1	TRUE	1	0.230629315422295	2		388	843	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220415	1220415	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913323	NA	P-0026271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	101	741	0	ENST00000326873.7:c.508C>T	p.Gln170Ter	p.Q170*	ENST00000326873	NM_000455.4	170	Cag/Tag	4/10	0.230629315422295	1	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	0	0.230629315422295	1		741	767	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212519	133212519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371862779	NA	P-0026271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	80	668	3	ENST00000320574.5:c.5770G>A	p.Gly1924Arg	p.G1924R	ENST00000320574	NM_006231.2	1924	Gga/Aga	42/49	1	2	FACETS	0.875	0.769	0.989	0.875	0.769	0.989	CLONAL	1	TRUE	1	0.230629315422295	2		671	793	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610409	10610409	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	90	705	0	ENST00000171111.5:c.301G>A	p.Ala101Thr	p.A101T	ENST00000171111	NM_203500.1	101	Gcc/Acc	2/6	0.230629315422295	1	FACETS	0.958	0.85	1	0.958	0.85	1	CLONAL	1	TRUE	0	0.230629315422295	1		705	721	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0026272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	161	503	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.245356281357895	7	FACETS	0.986	0.918	1	1	0.983	1	CLONAL	6	TRUE	2	0.245356281357895	7		505	358	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0026272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	62	659	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.21915970091465	3	FACETS	0.896	0.786	1	0.896	0.786	1	CLONAL	3	TRUE	0	0.245356281357895	3		659	211	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928065	178928076	+	inframe_deletion	In_Frame_Del	DEL	TACCTCATGGAT	TACCTCATGGAT	-	novel	NA	P-0026272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	66	653	1	ENST00000263967.3:c.1345_1356del	p.Pro449_Leu452del	p.P449_L452del	ENST00000263967	NM_006218.2	448	gTACCTCATGGATta/gta	8/21	0.230176562346296	4	FACETS	0.98	0.862	1	1	0.974	1	CLONAL	3	TRUE	2	0.245356281357895	4		654	228	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535354	187535354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	33	467	2	ENST00000441802.2:c.9220C>T	p.Pro3074Ser	p.P3074S	ENST00000441802	NM_005245.3	3074	Cca/Tca	12/27	0.245356281357895	5	FACETS	1	0.894	1			1	CLONAL	2	TRUE	NA	0.245356281357895	5		469	164	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535413	187535413	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	54	523	1	ENST00000441802.2:c.9161C>T	p.Ser3054Phe	p.S3054F	ENST00000441802	NM_005245.3	3054	tCt/tTt	12/27	0.245356281357895	5	FACETS	0.974	0.844	1			1	CLONAL	3	TRUE	NA	0.245356281357895	5		524	206	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	63	501	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.231161987121346	3	FACETS	1	0.969	1	0.726	0.63	0.829	CLONAL	1	FALSE	1	0.231161987121346	3		501	419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0026273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	17	580	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	0.435	0.324	0.567	0.435	0.324	0.567	SUBCLONAL	1	FALSE	1	0.231161987121346	2		581	338	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480507	57480507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	18	438	0	ENST00000371085.3:c.502G>A	p.Glu168Lys	p.E168K	ENST00000371085	NM_000516.4	168	Gag/Aag	6/13	1	2	FACETS	0.49	0.368	0.633	0.49	0.368	0.633	SUBCLONAL	1	FALSE	1	0.231161987121346	2		438	318	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0026276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	73	606	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.772	0.674	0.879	0.772	0.674	0.879	SUBCLONAL	1	TRUE	1	0.2	2		606	945	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202846	16202846	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	50	554	1	ENST00000375759.3:c.554C>A	p.Ala185Asp	p.A185D	ENST00000375759	NM_015001.2	185	gCt/gAt	3/15	1	2	FACETS	0.651	0.551	0.762	0.651	0.551	0.762	SUBCLONAL	1	TRUE	1	0.2	2		555	768	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0026277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	479	751	0	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	0.286447660267904	4	FACETS	0.915	0.884	0.947	0.915	0.884	0.947	INDETERMINATE	4	TRUE	0	0.488712088343343	4		751	797	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0026277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	152	341	0	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	0.467353497902476	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.488712088343343	2		341	301	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841541	156841541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774654606	NA	P-0026277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	385	717	2	ENST00000524377.1:c.844G>A	p.Val282Ile	p.V282I	ENST00000524377	NM_002529.3	282	Gtc/Atc	7/17	0.437194814984339	4	FACETS	0.952	0.91	0.995	0.952	0.91	0.995	CLONAL	3	TRUE	1	0.488712088343343	4		719	821	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935669	15935669	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	50	458	0	ENST00000268712.3:c.7264C>T	p.Arg2422Ter	p.R2422*	ENST00000268712	NM_006311.3	2422	Cga/Tga	46/46	0.286447660267904	4	FACETS	0.565	0.479	0.66	0.141	0.119	0.165	INDETERMINATE	1	TRUE	0	0.488712088343343	4		458	539	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930087	68930087	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	76	541	0	ENST00000288368.4:c.148T>G	p.Leu50Val	p.L50V	ENST00000288368	NM_024870.2	50	Tta/Gta	2/40	0.470245704822977	3	FACETS	0.75	0.659	0.847	0.25	0.219	0.283	SUBCLONAL	1	TRUE	0	0.488712088343343	3		541	516	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40872450	40872450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766116813	NA	P-0026277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	34	661	0	ENST00000428826.2:c.505G>A	p.Val169Ile	p.V169I	ENST00000428826		169	Gtt/Att	7/21	NA	2	FACETS	0.23	0.187	0.279			1	INDETERMINATE	1	TRUE	NA	0.488712088343343	2		661	604	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120347	70120347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	159	974	0	ENST00000245479.2:c.1349C>T	p.Ser450Phe	p.S450F	ENST00000245479	NM_000346.3	450	tCc/tTc	3/3	0.467922835581297	3	FACETS	0.949	0.871	1	0.475	0.435	0.516	CLONAL	1	TRUE	1	0.488712088343343	3		974	853	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187398	38187398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253076420	NA	P-0026277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	235	484	0	ENST00000317025.8:c.1079G>A	p.Arg360Gln	p.R360Q	ENST00000317025	NM_023034.1	360	cGa/cAa	6/24	0.470245704822977	3	FACETS	0.923	0.875	0.972	0.923	0.875	0.972	CLONAL	3	TRUE	0	0.488712088343343	3		484	432	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958788	55958788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780764266	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	211	622	0	ENST00000263923.4:c.3065G>A	p.Arg1022Gln	p.R1022Q	ENST00000263923	NM_002253.2	1022	cGa/cAa	22/30	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.57	2		622	687	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902622	1902622	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs771287635	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	218	605	1	ENST00000382891.5:c.241G>T	p.Asp81Tyr	p.D81Y	ENST00000382891	NM_133335.3	81	Gat/Tat	2/22	1	2	FACETS	0.908	0.847	0.972	0.908	0.847	0.972	CLONAL	1	TRUE	1	0.57	2		606	842	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155583	106155583	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	143	379	0	ENST00000380013.4:c.484G>T	p.Asp162Tyr	p.D162Y	ENST00000380013	NM_001127208.2	162	Gat/Tat	3/11	1	2	FACETS	0.8	0.732	0.871	0.8	0.732	0.871	SUBCLONAL	1	TRUE	1	0.57	2		379	627	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	168	538	3	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.796	0.733	0.861	0.796	0.733	0.861	SUBCLONAL	1	TRUE	1	0.57	2		541	741	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	170	532	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.925	0.854	0.998	0.925	0.854	0.998	CLONAL	1	TRUE	1	0.57	2		532	645	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15960850	15960850	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	77	294	0	ENST00000268712.3:c.6370C>A	p.Leu2124Ile	p.L2124I	ENST00000268712	NM_006311.3	2124	Ctt/Att	40/46	1	2	FACETS	0.768	0.679	0.862	0.768	0.679	0.862	SUBCLONAL	1	TRUE	1	0.57	2		294	352	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344018	70344018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747113641	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	252	645	0	ENST00000374080.3:c.1754G>A	p.Arg585Gln	p.R585Q	ENST00000374080		585	cGa/cAa	13/45	1	2	FACETS	0.981	0.92	1	0.981	0.92	1	CLONAL	1	TRUE	1	0.57	2		645	901	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026994	71026994	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147756430	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	157	487	1	ENST00000318789.4:c.1333G>A	p.Val445Met	p.V445M	ENST00000318789	NM_032682.5	445	Gtg/Atg	15/21	1	2	FACETS	0.884	0.813	0.958	0.884	0.813	0.958	CLONAL	1	TRUE	1	0.57	2		488	623	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623587	28623587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35602083	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	215	520	0	ENST00000241453.7:c.970G>A	p.Asp324Asn	p.D324N	ENST00000241453	NM_004119.2	324	Gac/Aac	8/24	1	2	FACETS	0.972	0.906	1	0.972	0.906	1	CLONAL	1	TRUE	1	0.57	2		520	776	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	17	439	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	1	2	FACETS	0.083	0.061	0.109	0.083	0.061	0.109	SUBCLONAL	1	TRUE	1	0.57	2		439	718	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151625	55151625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571523023	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	254	651	0	ENST00000257290.5:c.2411G>A	p.Arg804Gln	p.R804Q	ENST00000257290	NM_006206.4	804	cGa/cAa	17/23	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.57	2		651	883	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459166	120459166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113023165	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	210	545	0	ENST00000256646.2:c.6179G>A	p.Arg2060His	p.R2060H	ENST00000256646	NM_024408.3	2060	cGc/cAc	34/34	1	2	FACETS	0.992	0.924	1	0.992	0.924	1	CLONAL	1	TRUE	1	0.57	2		545	743	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	183	464	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.57	2		464	640	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909629	76909629	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs919106518	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	155	588	1	ENST00000373344.5:c.4276C>T	p.Arg1426Ter	p.R1426*	ENST00000373344	NM_000489.3	1426	Cga/Tga	14/35	1	2	FACETS	0.731	0.67	0.794	0.731	0.67	0.794	SUBCLONAL	1	TRUE	1	0.57	2		589	744	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242774	66242774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151302542	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	124	380	0	ENST00000273854.3:c.1798G>A	p.Glu600Lys	p.E600K	ENST00000273854	NM_004439.5	600	Gaa/Aaa	9/18	1	2	FACETS	0.838	0.762	0.918	0.838	0.762	0.918	CLONAL	1	TRUE	1	0.57	2		380	519	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944624	38944624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1377027840	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	191	460	0	ENST00000357387.3:c.4837C>T	p.Arg1613Cys	p.R1613C	ENST00000357387	NM_152756.3	1613	Cgc/Tgc	36/38	1	2	FACETS	0.841	0.779	0.905	0.841	0.779	0.905	CLONAL	1	TRUE	1	0.57	2		460	797	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742679	39742679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	180	430	1	ENST00000361337.2:c.1522C>T	p.Arg508Cys	p.R508C	ENST00000361337	NM_003286.2	508	Cgt/Tgt	15/21	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.57	2		431	617	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039371	47039371	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	216	635	3	ENST00000377604.3:c.994C>T	p.Arg332Cys	p.R332C	ENST00000377604	NM_001204468.1	332	Cgc/Tgc	10/24	1	2	FACETS	0.995	0.928	1	0.995	0.928	1	CLONAL	1	TRUE	1	0.57	2		638	762	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528768	8528768	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	126	338	1	ENST00000356435.5:c.364C>T	p.Pro122Ser	p.P122S	ENST00000356435		122	Ccc/Tcc	4/35	1	2	FACETS	0.927	0.845	1	0.927	0.845	1	CLONAL	1	TRUE	1	0.57	2		339	477	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164577	47164577	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	114	350	0	ENST00000409792.3:c.1549G>T	p.Glu517Ter	p.E517*	ENST00000409792	NM_014159.6	517	Gaa/Taa	3/21	1	2	FACETS	0.862	0.781	0.947	0.862	0.781	0.947	CLONAL	1	TRUE	1	0.57	2		350	464	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706936	117706936	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	205	562	0	ENST00000368508.3:c.2214G>T	p.Glu738Asp	p.E738D	ENST00000368508	NM_002944.2	738	gaG/gaT	15/43	1	2	FACETS	0.932	0.867	0.999	0.932	0.867	0.999	CLONAL	1	TRUE	1	0.57	2		562	772	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845086	128845086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761395599	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	282	692	0	ENST00000249373.3:c.580G>A	p.Glu194Lys	p.E194K	ENST00000249373	NM_005631.4	194	Gaa/Aaa	3/12	1	2	FACETS	0.998	0.939	1	0.998	0.939	1	CLONAL	1	TRUE	1	0.57	2		692	991	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024619	31024619	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	163	482	0	ENST00000375687.4:c.4104G>T	p.Lys1368Asn	p.K1368N	ENST00000375687	NM_015338.5	1368	aaG/aaT	13/13	1	2	FACETS	0.844	0.777	0.913	0.844	0.777	0.913	CLONAL	1	TRUE	1	0.57	2		482	678	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	214	416	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.852	0.793	0.913	0.852	0.793	0.913	CLONAL	1	TRUE	1	0.57	2		416	881	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021785	71021785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs112795301	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	135	330	0	ENST00000318789.4:c.1573C>T	p.Arg525Ter	p.R525*	ENST00000318789	NM_032682.5	525	Cga/Tga	18/21	1	2	FACETS	0.993	0.909	1	0.993	0.909	1	CLONAL	1	TRUE	1	0.57	2		330	477	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922973	44922973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	255	628	1	ENST00000377967.4:c.1834C>T	p.Arg612Ter	p.R612*	ENST00000377967	NM_021140.2	612	Cga/Tga	16/29	1	2	FACETS	0.941	0.882	1	0.941	0.882	1	CLONAL	1	TRUE	1	0.57	2		629	951	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900171	101900171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564161322	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	108	351	0	ENST00000374994.4:c.605C>T	p.Ala202Val	p.A202V	ENST00000374994	NM_004612.2	202	gCg/gTg	4/9	1	2	FACETS	0.808	0.729	0.891	0.808	0.729	0.891	CLONAL	1	TRUE	1	0.57	2		351	469	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922321	178922321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	267	520	0	ENST00000263967.3:c.1090G>A	p.Gly364Arg	p.G364R	ENST00000263967	NM_006218.2	364	Gga/Aga	6/21	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.57	2		520	886	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600447	10600447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	26	687	1	ENST00000171111.5:c.1408C>T	p.Arg470Cys	p.R470C	ENST00000171111	NM_203500.1	470	Cgt/Tgt	4/6	1	2	FACETS	0.106	0.083	0.132	0.106	0.083	0.132	SUBCLONAL	1	TRUE	1	0.57	2		688	862	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259071	153259071	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	99	250	0	ENST00000281708.4:c.744G>T	p.Glu248Asp	p.E248D	ENST00000281708	NM_033632.3	248	gaG/gaT	5/12	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.57	2		250	346	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172385	108172385	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764389018	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	176	481	1	ENST00000278616.4:c.5188C>T	p.Arg1730Ter	p.R1730*	ENST00000278616	NM_000051.3	1730	Cga/Tga	35/63	1	2	FACETS	0.943	0.872	1	0.943	0.872	1	CLONAL	1	TRUE	1	0.57	2		482	655	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845588	63845588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774238244	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	141	343	0	ENST00000279873.7:c.1327C>T	p.Arg443Cys	p.R443C	ENST00000279873	NM_032199.2	443	Cgc/Tgc	9/10	1	2	FACETS	0.89	0.815	0.968	0.89	0.815	0.968	CLONAL	1	TRUE	1	0.57	2		343	556	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371704	89371704	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144947610	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	191	553	0	ENST00000301030.4:c.136G>A	p.Asp46Asn	p.D46N	ENST00000301030	NM_001256183.1	46	Gat/Aat	4/13	1	2	FACETS	0.889	0.824	0.956	0.889	0.824	0.956	CLONAL	1	TRUE	1	0.57	2		553	754	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679547	86679547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	205	380	0	ENST00000274376.6:c.2708G>A	p.Arg903Gln	p.R903Q	ENST00000274376	NM_002890.2	903	cGa/cAa	21/25	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.57	2		380	583	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730859	40730859	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	199	654	0	ENST00000373198.4:c.3676C>T	p.Arg1226Ter	p.R1226*	ENST00000373198	NM_133170.3	1226	Cga/Tga	27/32	1	2	FACETS	0.863	0.801	0.927	0.863	0.801	0.927	CLONAL	1	TRUE	1	0.57	2		654	809	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998898	11998898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	129	307	0	ENST00000353533.5:c.400C>T	p.Arg134Trp	p.R134W	ENST00000353533	NM_003010.3	134	Cgg/Tgg	4/11	1	2	FACETS	0.939	0.857	1	0.939	0.857	1	CLONAL	1	TRUE	1	0.57	2		307	482	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428511	78428511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408536007	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	236	558	1	ENST00000370768.2:c.1288C>T	p.Arg430Cys	p.R430C	ENST00000370768	NM_003902.3	430	Cgt/Tgt	14/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.57	2		559	791	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332915	153332915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200698994	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	115	347	0	ENST00000281708.4:c.41G>A	p.Arg14Gln	p.R14Q	ENST00000281708	NM_033632.3	14	cGa/cAa	2/12	1	2	FACETS	0.844	0.765	0.927	0.844	0.765	0.927	CLONAL	1	TRUE	1	0.57	2		347	478	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517921	187517921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	176	423	0	ENST00000441802.2:c.12773C>T	p.Pro4258Leu	p.P4258L	ENST00000441802	NM_005245.3	4258	cCg/cTg	25/27	1	2	FACETS	0.95	0.879	1	0.95	0.879	1	CLONAL	1	TRUE	1	0.57	2		423	650	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	155	442	1	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.57	2		443	505	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951156	48951156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060503078	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	175	432	0	ENST00000267163.4:c.1318G>A	p.Glu440Lys	p.E440K	ENST00000267163	NM_000321.2	440	Gaa/Aaa	13/27	1	2	FACETS	0.907	0.838	0.978	0.907	0.838	0.978	CLONAL	1	TRUE	1	0.57	2		432	677	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218483	1218483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775595174	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	225	593	1	ENST00000326873.7:c.358G>A	p.Glu120Lys	p.E120K	ENST00000326873	NM_000455.4	120	Gaa/Aaa	2/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.57	2		594	751	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051011	180051011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146167161	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	53	626	4	ENST00000261937.6:c.1472C>T	p.Ala491Val	p.A491V	ENST00000261937	NM_182925.4	491	gCg/gTg	11/30	1	2	FACETS	0.214	0.182	0.25	0.214	0.182	0.25	SUBCLONAL	1	TRUE	1	0.57	2		630	868	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677876	47677876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	208	540	2	ENST00000347630.2:c.989C>T	p.Ser330Leu	p.S330L	ENST00000347630	NM_001007230.1	330	tCg/tTg	11/11	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.57	2		542	718	SUCCESS
AR	367	MSKCC	GRCh37	X	66943532	66943532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143040492	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	128	329	3	ENST00000374690.3:c.2612C>T	p.Ala871Val	p.A871V	ENST00000374690	NM_000044.3	871	gCg/gTg	8/8	1	2	FACETS	0.934	0.852	1	0.934	0.852	1	CLONAL	1	TRUE	1	0.57	2		332	481	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202857	16202857	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1307834195	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	179	489	0	ENST00000375759.3:c.565C>T	p.Arg189Ter	p.R189*	ENST00000375759	NM_015001.2	189	Cga/Tga	3/15	1	2	FACETS	0.896	0.829	0.966	0.896	0.829	0.966	CLONAL	1	TRUE	1	0.57	2		489	701	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494187	140494187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1158980679	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	287	654	2	ENST00000288602.6:c.1061G>A	p.Arg354Gln	p.R354Q	ENST00000288602	NM_004333.4	354	cGa/cAa	8/18	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.57	2		656	989	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161380	55161380	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376544204	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	185	516	1	ENST00000257290.5:c.3211G>A	p.Asp1071Asn	p.D1071N	ENST00000257290	NM_006206.4	1071	Gac/Aac	23/23	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.57	2		517	649	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302627	15302627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768437995	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	258	703	1	ENST00000263388.2:c.731G>A	p.Arg244Gln	p.R244Q	ENST00000263388	NM_000435.2	244	cGa/cAa	5/33	1	2	FACETS	0.914	0.857	0.973	0.914	0.857	0.973	CLONAL	1	TRUE	1	0.57	2		704	990	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587777894	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	205	614	0	ENST00000361445.4:c.6644C>A	p.Ser2215Tyr	p.S2215Y	ENST00000361445	NM_004958.3	2215	tCt/tAt	47/58	1	2	FACETS	0.871	0.809	0.934	0.871	0.809	0.934	CLONAL	1	TRUE	1	0.57	2		614	826	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858600	57858600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756282060	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	218	591	1	ENST00000228682.2:c.338G>A	p.Arg113Gln	p.R113Q	ENST00000228682	NM_005269.2	113	cGa/cAa	4/12	1	2	FACETS	0.982	0.916	1	0.982	0.916	1	CLONAL	1	TRUE	1	0.57	2		592	779	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610357	81610357	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	137	392	0	ENST00000298171.2:c.1955C>A	p.Pro652His	p.P652H	ENST00000298171	NM_000369.2	652	cCt/cAt	10/10	1	2	FACETS	0.857	0.783	0.934	0.857	0.783	0.934	CLONAL	1	TRUE	1	0.57	2		392	561	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446209	29446209	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs774951734	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	116	330	0	ENST00000389048.3:c.3358C>T	p.Arg1120Trp	p.R1120W	ENST00000389048	NM_004304.4	1120	Cgg/Tgg	20/29	1	2	FACETS	0.843	0.764	0.925	0.843	0.764	0.925	CLONAL	1	TRUE	1	0.57	2		330	483	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333864	70333864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528233201	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	149	357	0	ENST00000373644.4:c.1769G>A	p.Arg590Gln	p.R590Q	ENST00000373644	NM_030625.2	590	cGa/cAa	2/12	1	2	FACETS	0.885	0.812	0.96	0.885	0.812	0.96	CLONAL	1	TRUE	1	0.57	2		357	591	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109744	115109744	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	182	570	1	ENST00000257566.3:c.2134G>A	p.Ala712Thr	p.A712T	ENST00000257566	NM_016569.3	712	Gcg/Acg	8/8	1	2	FACETS	0.95	0.88	1	0.95	0.88	1	CLONAL	1	TRUE	1	0.57	2		571	672	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125356	47125356	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	160	424	0	ENST00000409792.3:c.5914G>T	p.Glu1972Ter	p.E1972*	ENST00000409792	NM_014159.6	1972	Gaa/Taa	12/21	1	2	FACETS	0.848	0.78	0.919	0.848	0.78	0.919	CLONAL	1	TRUE	1	0.57	2		424	662	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820303	139820303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774782158	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	182	625	1	ENST00000247668.2:c.1456C>T	p.Arg486Trp	p.R486W	ENST00000247668	NM_021138.3	486	Cgg/Tgg	11/11	1	2	FACETS	0.799	0.739	0.862	0.799	0.739	0.862	SUBCLONAL	1	TRUE	1	0.57	2		626	799	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164893	123164893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	200	462	1	ENST00000218089.9:c.206G>A	p.Arg69Gln	p.R69Q	ENST00000218089	NM_001042749.1	69	cGa/cAa	5/35	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.57	2		463	643	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925441	114925441	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138649767	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	222	518	2	ENST00000543371.1:c.1519G>A	p.Ala507Thr	p.A507T	ENST00000543371	NM_001198531.1	507	Gcc/Acc	14/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.57	2		520	695	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	26	530	0	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	1	2	FACETS	0.109	0.086	0.136	0.109	0.086	0.136	SUBCLONAL	1	TRUE	1	0.57	2		530	836	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765576	41765576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763066660	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	232	675	1	ENST00000301178.4:c.2452G>A	p.Glu818Lys	p.E818K	ENST00000301178	NM_021913.4	818	Gaa/Aaa	20/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.57	2		676	734	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467875	99467875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1469290616	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	169	387	0	ENST00000268035.6:c.2744C>T	p.Ser915Leu	p.S915L	ENST00000268035	NM_000875.3	915	tCg/tTg	13/21	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.57	2		387	571	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760421	133760421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368347512	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	160	513	1	ENST00000318560.5:c.2744C>T	p.Ser915Leu	p.S915L	ENST00000318560	NM_005157.4	915	tCg/tTg	11/11	1	2	FACETS	0.866	0.797	0.938	0.866	0.797	0.938	CLONAL	1	TRUE	1	0.57	2		514	648	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430600	181430600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1372564199	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	95	201	1	ENST00000325404.1:c.452C>T	p.Ala151Val	p.A151V	ENST00000325404	NM_003106.3	151	gCg/gTg	1/1	1	2	FACETS	0.986	0.887	1	0.986	0.887	1	CLONAL	1	TRUE	1	0.57	2		202	338	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939208	76939208	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	262	673	0	ENST00000373344.5:c.1540G>T	p.Asp514Tyr	p.D514Y	ENST00000373344	NM_000489.3	514	Gac/Tac	9/35	1	2	FACETS	0.997	0.936	1	0.997	0.936	1	CLONAL	1	TRUE	1	0.57	2		673	922	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924421	131924421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146370443	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	153	447	0	ENST00000265335.6:c.1094G>A	p.Arg365Gln	p.R365Q	ENST00000265335		365	cGa/cAa	8/25	1	2	FACETS	0.902	0.829	0.978	0.902	0.829	0.978	CLONAL	1	TRUE	1	0.57	2		447	595	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587118	189587118	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	185	392	0	ENST00000264731.3:c.1135C>A	p.Arg379Ser	p.R379S	ENST00000264731	NM_003722.4	379	Cgt/Agt	9/14	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.57	2		392	621	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006828	47006828	+	5_prime_UTR_variant	5'UTR	SNP	G	G	A	rs781795179	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	225	646	1	ENST00000377604.3:c.-53G>A		p.*18*	ENST00000377604	NM_001204468.1	-/852		2/24	1	2	FACETS	0.967	0.903	1	0.967	0.903	1	CLONAL	1	TRUE	1	0.57	2		647	816	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879904	44879904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs912069418	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	229	559	0	ENST00000377967.4:c.493C>T	p.Arg165Ter	p.R165*	ENST00000377967	NM_021140.2	165	Cga/Tga	6/29	1	2	FACETS	0.952	0.889	1	0.952	0.889	1	CLONAL	1	TRUE	1	0.57	2		559	844	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467829	50467829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	110	344	0	ENST00000331340.3:c.1064C>T	p.Ala355Val	p.A355V	ENST00000331340	NM_006060.4	355	gCg/gTg	8/8	1	2	FACETS	0.854	0.772	0.94	0.854	0.772	0.94	CLONAL	1	TRUE	1	0.57	2		344	452	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103525641	103525641	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750643985	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	154	522	0	ENST00000355739.4:c.2912C>T	p.Thr971Met	p.T971M	ENST00000355739	NM_000123.3	971	aCg/aTg	14/15	1	2	FACETS	0.813	0.746	0.882	0.813	0.746	0.882	CLONAL	1	TRUE	1	0.57	2		522	665	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858337	9858337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs560057284	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	109	386	1	ENST00000330684.3:c.3064C>T	p.Arg1022Cys	p.R1022C	ENST00000330684	NM_001134407.1	1022	Cgc/Tgc	13/13	1	2	FACETS	0.863	0.78	0.95	0.863	0.78	0.95	CLONAL	1	TRUE	1	0.57	2		387	443	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993104	72993104	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1469786547	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	275	646	0	ENST00000268489.5:c.941G>A	p.Arg314Gln	p.R314Q	ENST00000268489	NM_006885.3	314	cGg/cAg	2/10	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.57	2		646	965	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048632	180048632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	163	539	1	ENST00000261937.6:c.1930G>A	p.Ala644Thr	p.A644T	ENST00000261937	NM_182925.4	644	Gcg/Acg	13/30	1	2	FACETS	0.898	0.827	0.971	0.898	0.827	0.971	CLONAL	1	TRUE	1	0.57	2		540	637	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750454	57750454	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	193	458	2	ENST00000274289.3:c.2014C>T	p.Arg672Ter	p.R672*	ENST00000274289	NM_006622.3	672	Cga/Tga	14/14	1	2	FACETS	0.958	0.889	1	0.958	0.889	1	CLONAL	1	TRUE	1	0.57	2		460	707	SUCCESS
BLM	641	MSKCC	GRCh37	15	91352484	91352484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1031421025	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	135	420	1	ENST00000355112.3:c.3869C>T	p.Ser1290Leu	p.S1290L	ENST00000355112	NM_000057.2	1290	tCg/tTg	20/22	1	2	FACETS	0.853	0.779	0.931	0.853	0.779	0.931	CLONAL	1	TRUE	1	0.57	2		421	555	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273266	198273266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	179	457	0	ENST00000335508.6:c.944G>A	p.Arg315Gln	p.R315Q	ENST00000335508	NM_012433.2	315	cGa/cAa	8/25	1	2	FACETS	0.926	0.857	0.998	0.926	0.857	0.998	CLONAL	1	TRUE	1	0.57	2		457	678	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367830	15367830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867596343	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	214	687	2	ENST00000263377.2:c.1496C>T	p.Ser499Leu	p.S499L	ENST00000263377	NM_058243.2	499	tCg/tTg	8/20	1	2	FACETS	0.939	0.874	1	0.939	0.874	1	CLONAL	1	TRUE	1	0.57	2		689	800	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670124	86670124	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	179	491	0	ENST00000274376.6:c.1921G>T	p.Glu641Ter	p.E641*	ENST00000274376	NM_002890.2	641	Gag/Tag	14/25	1	2	FACETS	0.971	0.899	1	0.971	0.899	1	CLONAL	1	TRUE	1	0.57	2		491	647	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212495	133212495	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879254168	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	171	447	0	ENST00000320574.5:c.5794C>T	p.Arg1932Cys	p.R1932C	ENST00000320574	NM_006231.2	1932	Cgt/Tgt	42/49	1	2	FACETS	0.963	0.89	1	0.963	0.89	1	CLONAL	1	TRUE	1	0.57	2		447	623	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435111	110435111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	178	416	0	ENST00000375856.3:c.3290G>A	p.Arg1097His	p.R1097H	ENST00000375856	NM_003749.2	1097	cGc/cAc	1/2	1	2	FACETS	0.971	0.899	1	0.971	0.899	1	CLONAL	1	TRUE	1	0.57	2		416	643	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626755	28626755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750445891	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	429	538	0	ENST00000241453.7:c.541G>A	p.Ala181Thr	p.A181T	ENST00000241453	NM_004119.2	181	Gcc/Acc	5/24	1	2	FACETS	0.943	0.906	0.98	1	0.997	1	CLONAL	2	TRUE	1	0.57	2		538	798	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100947	41100947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372070542	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	166	485	2	ENST00000373198.4:c.1409G>A	p.Arg470Gln	p.R470Q	ENST00000373198	NM_133170.3	470	cGa/cAa	8/32	1	2	FACETS	0.847	0.78	0.916	0.847	0.78	0.916	CLONAL	1	TRUE	1	0.57	2		487	688	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549116	21549116	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	142	459	0	ENST00000382592.4:c.3160C>T	p.Arg1054Ter	p.R1054*	ENST00000382592	NM_014572.2	1054	Cga/Tga	8/8	1	2	FACETS	0.724	0.661	0.79	0.724	0.661	0.79	SUBCLONAL	1	TRUE	1	0.57	2		459	688	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938028	76938028	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143413618	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	205	559	1	ENST00000373344.5:c.2720G>A	p.Arg907Gln	p.R907Q	ENST00000373344	NM_000489.3	907	cGa/cAa	9/35	1	2	FACETS	0.941	0.876	1	0.941	0.876	1	CLONAL	1	TRUE	1	0.57	2		560	764	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293799	1293799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs539667998	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	226	647	0	ENST00000310581.5:c.1202C>T	p.Ala401Val	p.A401V	ENST00000310581	NM_198253.2	401	gCg/gTg	2/16	1	2	FACETS	0.997	0.932	1	0.997	0.932	1	CLONAL	1	TRUE	1	0.57	2		647	795	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427369	49427369	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1565779294	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	232	630	0	ENST00000301067.7:c.11119C>T	p.Arg3707Ter	p.R3707*	ENST00000301067	NM_003482.3	3707	Cga/Tga	39/54	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.57	2		630	762	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62309650	62309650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753838163	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	211	554	0	ENST00000360203.5:c.988G>A	p.Asp330Asn	p.D330N	ENST00000360203	NM_001283009.1	330	Gat/Aat	12/35	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.57	2		554	678	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353760	40353760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748370281	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	215	498	0	ENST00000293328.3:c.2360C>T	p.Ser787Leu	p.S787L	ENST00000293328	NM_012448.3	787	tCg/tTg	19/19	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.57	2		498	746	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538912	187538912	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201085583	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	114	395	0	ENST00000441802.2:c.8828C>T	p.Thr2943Met	p.T2943M	ENST00000441802	NM_005245.3	2943	aCg/aTg	10/27	1	2	FACETS	0.818	0.74	0.899	0.818	0.74	0.899	CLONAL	1	TRUE	1	0.57	2		395	489	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58711261	58711261	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571290585	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	281	382	0	ENST00000305921.3:c.749G>A	p.Arg250Gln	p.R250Q	ENST00000305921	NM_003620.3	250	cGa/cAa	3/6	1	2	FACETS	0.967	0.909	1	0.967	0.909	1	CLONAL	1	TRUE	1	0.57	2		382	1020	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795352	39795352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372598575	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	176	564	4	ENST00000288319.7:c.368G>A	p.Arg123His	p.R123H	ENST00000288319	NM_182918.3	123	cGc/cAc	3/10	1	2	FACETS	0.941	0.871	1	0.941	0.871	1	CLONAL	1	TRUE	1	0.57	2		568	656	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164697	47164697	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	158	349	0	ENST00000409792.3:c.1429T>C	p.Ser477Pro	p.S477P	ENST00000409792	NM_014159.6	477	Tcc/Ccc	3/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.57	2		349	530	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879673	151879673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	80	210	2	ENST00000262189.6:c.5272C>T	p.Arg1758Cys	p.R1758C	ENST00000262189	NM_170606.2	1758	Cgt/Tgt	36/59	1	2	FACETS	0.958	0.853	1	0.958	0.853	1	CLONAL	1	TRUE	1	0.57	2		212	293	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158594104	158594104	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554387941	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	165	457	0	ENST00000263640.3:c.1469G>A	p.Arg490His	p.R490H	ENST00000263640	NM_001105.4	490	cGt/cAt	11/11	1	2	FACETS	0.849	0.782	0.918	0.849	0.782	0.918	CLONAL	1	TRUE	1	0.57	2		457	682	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039158	49039158	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	121	342	1	ENST00000267163.4:c.2236G>T	p.Glu746Ter	p.E746*	ENST00000267163	NM_000321.2	746	Gaa/Taa	22/27	1	2	FACETS	0.704	0.638	0.774	0.704	0.638	0.774	SUBCLONAL	1	TRUE	1	0.57	2		343	603	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747912	41747912	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	144	392	0	ENST00000226382.2:c.857C>T	p.Ser286Leu	p.S286L	ENST00000226382	NM_003924.3	286	tCg/tTg	3/3	1	2	FACETS	0.962	0.883	1	0.962	0.883	1	CLONAL	1	TRUE	1	0.57	2		392	525	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43769902	43769902	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	231	530	0	ENST00000382044.4:c.844G>T	p.Glu282Ter	p.E282*	ENST00000382044	NM_001141980.1	282	Gaa/Taa	8/28	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.57	2		530	791	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266570	115266570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	202	629	1	ENST00000438362.2:c.1945C>T	p.Arg649Cys	p.R649C	ENST00000438362	NM_001242891.1	649	Cgc/Tgc	16/20	1	2	FACETS	0.796	0.739	0.856	0.796	0.739	0.856	SUBCLONAL	1	TRUE	1	0.57	2		630	890	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582249	52582249	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	83	185	2	ENST00000394830.3:c.4579C>T	p.Arg1527Ter	p.R1527*	ENST00000394830	NM_018313.4	1527	Cga/Tga	30/30	1	2	FACETS	0.925	0.824	1	0.925	0.824	1	CLONAL	1	TRUE	1	0.57	2		187	315	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16055259	16055259	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	200	506	0	ENST00000268712.3:c.842+1G>A		p.X281_splice	ENST00000268712	NM_006311.3	281			1	2	FACETS	0.858	0.796	0.921	0.858	0.796	0.921	CLONAL	1	TRUE	1	0.57	2		506	818	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508788	148508788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587783625	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	199	415	1	ENST00000320356.2:c.1876G>A	p.Val626Met	p.V626M	ENST00000320356	NM_004456.4	626	Gtg/Atg	16/20	1	2	FACETS	0.986	0.917	1	0.986	0.917	1	CLONAL	1	TRUE	1	0.57	2		416	708	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273878	10273878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	219	570	3	ENST00000330684.3:c.391G>A	p.Ala131Thr	p.A131T	ENST00000330684	NM_001134407.1	131	Gca/Aca	2/13	1	2	FACETS	0.852	0.793	0.912	0.852	0.793	0.912	CLONAL	1	TRUE	1	0.57	2		573	902	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962629	38962629	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	168	460	0	ENST00000357387.3:c.1626G>T	p.Glu542Asp	p.E542D	ENST00000357387	NM_152756.3	542	gaG/gaT	18/38	1	2	FACETS	0.882	0.814	0.953	0.882	0.814	0.953	CLONAL	1	TRUE	1	0.57	2		460	668	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175540	108175540	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	184	425	0	ENST00000278616.4:c.5635C>G	p.Gln1879Glu	p.Q1879E	ENST00000278616	NM_000051.3	1879	Caa/Gaa	37/63	1	2	FACETS	0.865	0.801	0.932	0.865	0.801	0.932	CLONAL	1	TRUE	1	0.57	2		425	746	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845582	72845582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370933867	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	196	566	0	ENST00000268489.5:c.3758G>A	p.Arg1253His	p.R1253H	ENST00000268489	NM_006885.3	1253	cGc/cAc	7/10	1	2	FACETS	0.873	0.81	0.938	0.873	0.81	0.938	CLONAL	1	TRUE	1	0.57	2		566	788	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169092	32169092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs189264181	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	190	641	1	ENST00000375023.3:c.3941C>T	p.Ala1314Val	p.A1314V	ENST00000375023	NM_004557.3	1314	gCc/gTc	22/30	1	2	FACETS	0.916	0.849	0.985	0.916	0.849	0.985	CLONAL	1	TRUE	1	0.57	2		642	728	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637008	93637008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201479078	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	134	501	0	ENST00000375746.1:c.1058C>T	p.Ala353Val	p.A353V	ENST00000375746	NM_001174167.1	353	gCg/gTg	9/14	1	2	FACETS	0.801	0.73	0.875	0.801	0.73	0.875	CLONAL	1	TRUE	1	0.57	2		501	587	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643705	38643705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1345810751	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	149	659	3	ENST00000299084.4:c.1175C>T	p.Ser392Leu	p.S392L	ENST00000299084	NM_152594.2	392	tCg/tTg	7/7	1	2	FACETS	0.617	0.563	0.672	0.617	0.563	0.672	SUBCLONAL	1	TRUE	1	0.57	2		662	848	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625218	69625218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1168737490	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	215	598	3	ENST00000334134.2:c.575G>A	p.Arg192Gln	p.R192Q	ENST00000334134	NM_005247.2	192	cGg/cAg	3/3	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.57	2		601	745	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233666	233666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147014102	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	62	209	0	ENST00000264932.6:c.970G>A	p.Glu324Lys	p.E324K	ENST00000264932	NM_004168.2	324	Gaa/Aaa	8/15	1	2	FACETS	0.892	0.779	1	0.892	0.779	1	CLONAL	1	TRUE	1	0.57	2		209	244	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037210	71037210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748393867	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	123	370	2	ENST00000318789.4:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000318789	NM_032682.5	361	Cgc/Tgc	14/21	1	2	FACETS	0.865	0.786	0.947	0.865	0.786	0.947	CLONAL	1	TRUE	1	0.57	2		372	499	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458579	120458579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147522485	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	160	577	0	ENST00000256646.2:c.6766C>T	p.Arg2256Cys	p.R2256C	ENST00000256646	NM_024408.3	2256	Cgc/Tgc	34/34	1	2	FACETS	0.794	0.73	0.861	0.794	0.73	0.861	SUBCLONAL	1	TRUE	1	0.57	2		577	707	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526547	66526547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	186	392	0	ENST00000358598.2:c.1103G>A	p.Arg368Gln	p.R368Q	ENST00000358598	NM_212471.2	368	cGa/cAa	11/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.57	2		392	567	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967309	134967309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs186851943	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	196	569	2	ENST00000398015.3:c.2648G>A	p.Arg883Gln	p.R883Q	ENST00000398015	NM_004441.4	883	cGg/cAg	14/16	1	2	FACETS	0.907	0.842	0.974	0.907	0.842	0.974	CLONAL	1	TRUE	1	0.57	2		571	758	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261278	115261278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	179	563	0	ENST00000438362.2:c.2443C>T	p.Arg815Cys	p.R815C	ENST00000438362	NM_001242891.1	815	Cgc/Tgc	19/20	1	2	FACETS	0.814	0.751	0.878	0.814	0.751	0.878	CLONAL	1	TRUE	1	0.57	2		563	772	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928852	44928852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750754452	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	125	355	0	ENST00000377967.4:c.1952C>T	p.Ser651Leu	p.S651L	ENST00000377967	NM_021140.2	651	tCg/tTg	17/29	1	2	FACETS	0.863	0.786	0.944	0.863	0.786	0.944	CLONAL	1	TRUE	1	0.57	2		355	508	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350734	89350734	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146294483	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	318	627	0	ENST00000301030.4:c.2216C>T	p.Ser739Leu	p.S739L	ENST00000301030	NM_001256183.1	739	tCg/tTg	9/13	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.57	2		627	1076	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420268	49420268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757664799	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	259	631	1	ENST00000301067.7:c.15481G>A	p.Glu5161Lys	p.E5161K	ENST00000301067	NM_003482.3	5161	Gag/Aag	48/54	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.57	2		632	818	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224725	36224725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372416919	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	290	739	1	ENST00000222270.7:c.7111G>A	p.Asp2371Asn	p.D2371N	ENST00000222270	NM_014727.1	2371	Gat/Aat	30/37	1	2	FACETS	0.964	0.908	1	0.964	0.908	1	CLONAL	1	TRUE	1	0.57	2		740	1055	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066913	30066913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	208	521	3	ENST00000331968.5:c.2218C>T	p.Arg740Trp	p.R740W	ENST00000331968	NM_002742.2	740	Cgg/Tgg	16/18	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.57	2		524	685	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141012	55141012	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501502	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	147	325	0	ENST00000257290.5:c.1658C>T	p.Pro553Leu	p.P553L	ENST00000257290	NM_006206.4	553	cCg/cTg	12/23	1	2	FACETS	0.936	0.859	1	0.936	0.859	1	CLONAL	1	TRUE	1	0.57	2		325	551	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775948	9775948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	221	569	0	ENST00000377346.4:c.412G>A	p.Asp138Asn	p.D138N	ENST00000377346	NM_005026.3	138	Gac/Aac	5/24	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.57	2		569	771	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187089	11187089	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1182513423	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	217	506	0	ENST00000361445.4:c.6329G>A	p.Arg2110Gln	p.R2110Q	ENST00000361445	NM_004958.3	2110	cGa/cAa	45/58	1	2	FACETS	0.964	0.899	1	0.964	0.899	1	CLONAL	1	TRUE	1	0.57	2		506	790	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11193208	11193208	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	229	556	0	ENST00000361445.4:c.5293A>C	p.Asn1765His	p.N1765H	ENST00000361445	NM_004958.3	1765	Aat/Cat	38/58	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.57	2		556	797	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199622	16199622	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	177	500	0	ENST00000375759.3:c.395G>T	p.Arg132Ile	p.R132I	ENST00000375759	NM_015001.2	132	aGa/aTa	2/15	1	2	FACETS	0.858	0.792	0.925	0.858	0.792	0.925	CLONAL	1	TRUE	1	0.57	2		500	724	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16247378	16247378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772371033	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	25	274	0	ENST00000375759.3:c.1649G>A	p.Arg550His	p.R550H	ENST00000375759	NM_015001.2	550	cGc/cAc	9/15	1	2	FACETS	0.189	0.149	0.236	0.189	0.149	0.236	SUBCLONAL	1	TRUE	1	0.57	2		274	463	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255211	16255211	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	212	487	0	ENST00000375759.3:c.2476G>T	p.Gly826Ter	p.G826*	ENST00000375759	NM_015001.2	826	Gga/Tga	11/15	1	2	FACETS	0.965	0.899	1	0.965	0.899	1	CLONAL	1	TRUE	1	0.57	2		487	771	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105688	27105688	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	132	265	1	ENST00000324856.7:c.5299G>T	p.Glu1767Ter	p.E1767*	ENST00000324856	NM_006015.4	1767	Gaa/Taa	20/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.57	2		266	426	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363246	40363246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1337002326	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	174	492	0	ENST00000397332.2:c.983G>A	p.Arg328His	p.R328H	ENST00000397332	NM_001033082.2	328	cGt/cAt	3/3	1	2	FACETS	0.949	0.878	1	0.949	0.878	1	CLONAL	1	TRUE	1	0.57	2		492	643	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363382	40363382	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376493390	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	198	563	0	ENST00000397332.2:c.847G>A	p.Glu283Lys	p.E283K	ENST00000397332	NM_001033082.2	283	Gag/Aag	3/3	1	2	FACETS	0.894	0.83	0.96	0.894	0.83	0.96	CLONAL	1	TRUE	1	0.57	2		563	777	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363564	40363564	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1198444872	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	213	562	1	ENST00000397332.2:c.665G>A	p.Arg222Gln	p.R222Q	ENST00000397332	NM_001033082.2	222	cGa/cAa	3/3	1	2	FACETS	0.933	0.869	0.999	0.933	0.869	0.999	CLONAL	1	TRUE	1	0.57	2		563	801	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748142	72748142	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	146	434	0	ENST00000357731.5:c.36C>A	p.Cys12Ter	p.C12*	ENST00000357731	NM_173808.2	12	tgC/tgA	1/7	1	2	FACETS	0.876	0.803	0.951	0.876	0.803	0.951	CLONAL	1	TRUE	1	0.57	2		434	585	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733583	85733583	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	179	510	1	ENST00000370580.1:c.429C>A	p.Phe143Leu	p.F143L	ENST00000370580	NM_003921.4	143	ttC/ttA	3/3	1	2	FACETS	0.917	0.848	0.988	0.917	0.848	0.988	CLONAL	1	TRUE	1	0.57	2		511	685	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261263	115261263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	194	562	1	ENST00000438362.2:c.2458C>T	p.Arg820Cys	p.R820C	ENST00000438362	NM_001242891.1	820	Cgt/Tgt	19/20	1	2	FACETS	0.859	0.797	0.924	0.859	0.797	0.924	CLONAL	1	TRUE	1	0.57	2		563	792	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261338	115261338	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs558231202	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	36	399	1	ENST00000438362.2:c.2383C>T	p.Arg795Ter	p.R795*	ENST00000438362	NM_001242891.1	795	Cga/Tga	19/20	1	2	FACETS	0.221	0.181	0.266	0.221	0.181	0.266	SUBCLONAL	1	TRUE	1	0.57	2		400	572	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263314	115263314	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	236	550	0	ENST00000438362.2:c.2036C>A	p.Pro679Gln	p.P679Q	ENST00000438362	NM_001242891.1	679	cCa/cAa	17/20	1	2	FACETS	0.925	0.865	0.987	0.925	0.865	0.987	CLONAL	1	TRUE	1	0.57	2		550	895	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275232	115275232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753559097	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	189	453	0	ENST00000438362.2:c.1181G>A	p.Arg394Gln	p.R394Q	ENST00000438362	NM_001242891.1	394	cGa/cAa	10/20	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.57	2		453	655	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956179	175956179	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	187	475	0	ENST00000367669.3:c.2033T>G	p.Phe678Cys	p.F678C	ENST00000367669	NM_022457.5	678	tTt/tGt	18/20	1	2	FACETS	0.844	0.782	0.909	0.844	0.782	0.909	CLONAL	1	TRUE	1	0.57	2		475	777	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204499915	204499915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	214	564	0	ENST00000367182.3:c.257G>A	p.Gly86Glu	p.G86E	ENST00000367182	NM_001278516.1	86	gGa/gAa	4/11	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.57	2		564	743	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245912885	245912885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374803671	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	181	418	1	ENST00000388985.4:c.1267G>A	p.Ala423Thr	p.A423T	ENST00000388985		423	Gcc/Acc	12/12	1	2	FACETS	0.971	0.899	1	0.971	0.899	1	CLONAL	1	TRUE	1	0.57	2		419	654	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246091330	246091330	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	122	395	0	ENST00000388985.4:c.605C>A	p.Ser202Tyr	p.S202Y	ENST00000388985		202	tCt/tAt	7/12	1	2	FACETS	0.755	0.685	0.828	0.755	0.685	0.828	SUBCLONAL	1	TRUE	1	0.57	2		395	567	SUCCESS
RET	5979	MSKCC	GRCh37	10	43613844	43613844	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775711017	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	273	737	0	ENST00000355710.3:c.2308C>T	p.Arg770Ter	p.R770*	ENST00000355710	NM_020975.4	770	Cga/Tga	13/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.57	2		737	912	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406379	70406379	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	249	619	0	ENST00000373644.4:c.3893C>A	p.Pro1298His	p.P1298H	ENST00000373644	NM_030625.2	1298	cCt/cAt	4/12	1	2	FACETS	0.955	0.894	1	0.955	0.894	1	CLONAL	1	TRUE	1	0.57	2		619	915	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88651982	88651982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	80	377	0	ENST00000372037.3:c.329G>A	p.Cys110Tyr	p.C110Y	ENST00000372037	NM_004329.2	110	tGc/tAc	5/13	1	2	FACETS	0.581	0.513	0.654	0.581	0.513	0.654	SUBCLONAL	1	TRUE	1	0.57	2		377	483	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104357021	104357021	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761234425	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	188	443	0	ENST00000369902.3:c.881G>A	p.Gly294Asp	p.G294D	ENST00000369902	NM_016169.3	294	gGc/gAc	7/12	1	2	FACETS	0.982	0.911	1	0.982	0.911	1	CLONAL	1	TRUE	1	0.57	2		443	672	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251980	8251980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	219	626	0	ENST00000335790.3:c.97G>A	p.Asp33Asn	p.D33N	ENST00000335790	NM_002315.2	33	Gac/Aac	2/4	1	2	FACETS	0.857	0.798	0.917	0.857	0.798	0.917	CLONAL	1	TRUE	1	0.57	2		626	897	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741357	17741357	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	242	547	1	ENST00000250003.3:c.28G>A	p.Asp10Asn	p.D10N	ENST00000250003	NM_002478.4	10	Gac/Aac	1/3	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.57	2		548	720	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741514	17741514	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs370665547	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	160	364	0	ENST00000250003.3:c.185A>G	p.His62Arg	p.H62R	ENST00000250003	NM_002478.4	62	cAc/cGc	1/3	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.57	2		364	540	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741567	17741567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	92	161	0	ENST00000250003.3:c.238C>T	p.His80Tyr	p.H80Y	ENST00000250003	NM_002478.4	80	Cat/Tat	1/3	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.57	2		161	246	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741730	17741730	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	211	482	0	ENST00000250003.3:c.401G>A	p.Arg134His	p.R134H	ENST00000250003	NM_002478.4	134	cGc/cAc	1/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.57	2		482	684	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741874	17741874	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	29	56	0	ENST00000250003.3:c.545G>A	p.Gly182Asp	p.G182D	ENST00000250003	NM_002478.4	182	gGc/gAc	1/3	1	2	FACETS	0.848	0.715	0.981	1	0.96	1	CLONAL	2	TRUE	1	0.57	2		56	60	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414273	32414273	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	180	525	0	ENST00000332351.3:c.1278G>T	p.Lys426Asn	p.K426N	ENST00000332351	NM_024426.4	426	aaG/aaT	8/10	1	2	FACETS	0.853	0.789	0.92	0.853	0.789	0.92	CLONAL	1	TRUE	1	0.57	2		525	740	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466027	69466027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771951669	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	158	450	0	ENST00000227507.2:c.865G>A	p.Asp289Asn	p.D289N	ENST00000227507	NM_053056.2	289	Gac/Aac	5/5	1	2	FACETS	0.906	0.834	0.981	0.906	0.834	0.981	CLONAL	1	TRUE	1	0.57	2		450	612	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588190	69588190	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	237	575	0	ENST00000168712.1:c.508G>A	p.Glu170Lys	p.E170K	ENST00000168712	NM_002007.2	170	Gag/Aag	3/3	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.57	2		575	795	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77060319	77060319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	28	322	0	ENST00000356341.3:c.850G>A	p.Val284Met	p.V284M	ENST00000356341	NM_002576.4	284	Gtg/Atg	9/15	1	2	FACETS	0.188	0.15	0.232	0.188	0.15	0.232	SUBCLONAL	1	TRUE	1	0.57	2		322	522	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94906445	94906445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766496091	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	486	617	0	ENST00000536441.1:c.1453C>T	p.Arg485Cys	p.R485C	ENST00000536441	NM_144665.3	485	Cgt/Tgt	10/10	1	2	FACETS	0.942	0.907	0.977	1	0.997	1	CLONAL	2	TRUE	1	0.57	2		617	905	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343767	118343767	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	223	452	1	ENST00000534358.1:c.1893C>A	p.Tyr631Ter	p.Y631*	ENST00000534358	NM_005933.3	631	taC/taA	3/36	1	2	FACETS	0.972	0.907	1	0.972	0.907	1	CLONAL	1	TRUE	1	0.57	2		453	805	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360927	118360927	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	172	495	0	ENST00000534358.1:c.4659C>A	p.Phe1553Leu	p.F1553L	ENST00000534358	NM_005933.3	1553	ttC/ttA	13/36	1	2	FACETS	0.845	0.78	0.913	0.845	0.78	0.913	CLONAL	1	TRUE	1	0.57	2		495	714	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	463282	463282	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	50	628	0	ENST00000399788.2:c.989T>C	p.Val330Ala	p.V330A	ENST00000399788	NM_001042603.1	330	gTg/gCg	8/28	1	2	FACETS	0.204	0.172	0.239	0.204	0.172	0.239	SUBCLONAL	1	TRUE	1	0.57	2		628	859	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699338	18699338	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	95	427	0	ENST00000266497.5:c.3439G>T	p.Asp1147Tyr	p.D1147Y	ENST00000266497		1147	Gac/Tac	24/31	1	2	FACETS	0.485	0.432	0.542	0.485	0.432	0.542	SUBCLONAL	1	TRUE	1	0.57	2		427	687	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636463	21636463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542491982	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	133	518	0	ENST00000421138.2:c.547G>A	p.Glu183Lys	p.E183K	ENST00000421138		183	Gag/Aag	7/16	1	2	FACETS	0.592	0.538	0.649	0.592	0.538	0.649	SUBCLONAL	1	TRUE	1	0.57	2		518	788	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21652495	21652495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201737130	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	242	712	0	ENST00000421138.2:c.10G>A	p.Val4Ile	p.V4I	ENST00000421138		4	Gtt/Att	3/16	1	2	FACETS	0.859	0.803	0.917	0.859	0.803	0.917	CLONAL	1	TRUE	1	0.57	2		712	988	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25368477	25368477	+	intron_variant	Intron	SNP	A	A	C	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	156	412	0	ENST00000311936.3:c.451-5632T>G		p.*151*	ENST00000311936	NM_004985.3	156/189			1	2	FACETS	0.804	0.738	0.872	0.804	0.738	0.872	CLONAL	1	TRUE	1	0.57	2		412	681	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865059	57865059	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771594350	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	209	676	1	ENST00000228682.2:c.2536C>T	p.Pro846Ser	p.P846S	ENST00000228682	NM_005269.2	846	Cct/Tct	12/12	1	2	FACETS	0.824	0.766	0.884	0.824	0.766	0.884	CLONAL	1	TRUE	1	0.57	2		677	890	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112910820	112910820	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	233	459	0	ENST00000351677.2:c.829A>C	p.Asn277His	p.N277H	ENST00000351677	NM_002834.3	277	Aat/Cat	7/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.57	2		459	760	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109704	115109704	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	204	641	0	ENST00000257566.3:c.2174A>C	p.Gln725Pro	p.Q725P	ENST00000257566	NM_016569.3	725	cAg/cCg	8/8	1	2	FACETS	0.886	0.823	0.95	0.886	0.823	0.95	CLONAL	1	TRUE	1	0.57	2		641	808	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109936	115109936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1320834041	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	128	430	0	ENST00000257566.3:c.1942C>T	p.Pro648Ser	p.P648S	ENST00000257566	NM_016569.3	648	Ccg/Tcg	8/8	1	2	FACETS	0.87	0.793	0.951	0.87	0.793	0.951	CLONAL	1	TRUE	1	0.57	2		430	516	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117351	115117351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1234535767	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	184	389	0	ENST00000257566.3:c.823G>A	p.Glu275Lys	p.E275K	ENST00000257566	NM_016569.3	275	Gaa/Aaa	4/8	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.57	2		389	622	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784089	120784089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265704785	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	250	657	1	ENST00000257552.2:c.896C>T	p.Ser299Leu	p.S299L	ENST00000257552	NM_002442.3	299	tCg/tTg	13/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.57	2		658	835	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588594	28588594	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	151	454	0	ENST00000241453.7:c.2854G>T	p.Glu952Ter	p.E952*	ENST00000241453	NM_004119.2	952	Gaa/Taa	23/24	1	2	FACETS	0.824	0.756	0.895	0.824	0.756	0.895	CLONAL	1	TRUE	1	0.57	2		454	643	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610123	28610123	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	215	542	0	ENST00000241453.7:c.1367G>A	p.Gly456Glu	p.G456E	ENST00000241453	NM_004119.2	456	gGa/gAa	11/24	1	2	FACETS	0.873	0.813	0.935	0.873	0.813	0.935	CLONAL	1	TRUE	1	0.57	2		542	864	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906949	32906949	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202373	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	160	374	1	ENST00000380152.3:c.1334C>A	p.Ser445Tyr	p.S445Y	ENST00000380152		445	tCt/tAt	10/27	1	2	FACETS	0.84	0.773	0.91	0.84	0.773	0.91	CLONAL	1	TRUE	1	0.57	2		375	668	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907377	32907377	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	164	385	0	ENST00000380152.3:c.1762A>C	p.Asn588His	p.N588H	ENST00000380152		588	Aat/Cat	10/27	1	2	FACETS	0.916	0.845	0.99	0.916	0.845	0.99	CLONAL	1	TRUE	1	0.57	2		385	628	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912872	32912872	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	164	421	0	ENST00000380152.3:c.4380T>G	p.Phe1460Leu	p.F1460L	ENST00000380152		1460	ttT/ttG	11/27	1	2	FACETS	0.885	0.816	0.957	0.885	0.816	0.957	CLONAL	1	TRUE	1	0.57	2		421	650	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32918713	32918713	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	98	231	1	ENST00000380152.3:c.6860G>T	p.Arg2287Ile	p.R2287I	ENST00000380152		2287	aGa/aTa	12/27	1	2	FACETS	0.945	0.85	1	0.945	0.85	1	CLONAL	1	TRUE	1	0.57	2		232	364	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32921032	32921032	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs431825347	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	165	489	0	ENST00000380152.3:c.7006C>T	p.Arg2336Cys	p.R2336C	ENST00000380152		2336	Cgc/Tgc	13/27	1	2	FACETS	0.949	0.876	1	0.949	0.876	1	CLONAL	1	TRUE	1	0.57	2		489	610	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134998	41134998	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	115	235	0	ENST00000379561.5:c.631-1G>T		p.X211_splice	ENST00000379561	NM_002015.3	211			1	2	FACETS	0.984	0.894	1	0.984	0.894	1	CLONAL	1	TRUE	1	0.57	2		235	410	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527680	103527680	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	121	324	0	ENST00000355739.4:c.2988C>A	p.Phe996Leu	p.F996L	ENST00000355739	NM_000123.3	996	ttC/ttA	15/15	1	2	FACETS	0.789	0.716	0.866	0.789	0.716	0.866	SUBCLONAL	1	TRUE	1	0.57	2		324	538	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527789	103527789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41551412	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	178	479	0	ENST00000355739.4:c.3097G>A	p.Glu1033Lys	p.E1033K	ENST00000355739	NM_000123.3	1033	Gaa/Aaa	15/15	1	2	FACETS	0.903	0.835	0.973	0.903	0.835	0.973	CLONAL	1	TRUE	1	0.57	2		479	692	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435649	110435649	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	137	313	0	ENST00000375856.3:c.2752G>T	p.Glu918Ter	p.E918*	ENST00000375856	NM_003749.2	918	Gag/Tag	1/2	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.57	2		313	412	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331802	68331802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	231	553	0	ENST00000487270.1:c.398G>A	p.Gly133Glu	p.G133E	ENST00000487270	NM_133509.3	133	gGa/gAa	5/11	1	2	FACETS	0.944	0.881	1	0.944	0.881	1	CLONAL	1	TRUE	1	0.57	2		553	859	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95593014	95593014	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	185	499	0	ENST00000393063.1:c.806G>T	p.Arg269Ile	p.R269I	ENST00000393063	NM_030621.3	269	aGa/aTa	8/28	1	2	FACETS	0.759	0.702	0.819	0.759	0.702	0.819	SUBCLONAL	1	TRUE	1	0.57	2		499	855	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241337	105241337	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	198	543	0	ENST00000349310.3:c.571G>A	p.Glu191Lys	p.E191K	ENST00000349310	NM_001014432.1	191	Gag/Aag	8/15	1	2	FACETS	0.972	0.903	1	0.972	0.903	1	CLONAL	1	TRUE	1	0.57	2		543	715	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591593	38591593	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs750777752	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	152	407	0	ENST00000299084.4:c.52C>T	p.Arg18Ter	p.R18*	ENST00000299084	NM_152594.2	18	Cga/Tga	2/7	1	2	FACETS	0.88	0.808	0.955	0.88	0.808	0.955	CLONAL	1	TRUE	1	0.57	2		407	606	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991306	41991306	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	262	606	1	ENST00000219905.7:c.2137G>T	p.Asp713Tyr	p.D713Y	ENST00000219905	NM_001164273.1	713	Gat/Tat	5/24	1	2	FACETS	0.985	0.925	1	0.985	0.925	1	CLONAL	1	TRUE	1	0.57	2		607	933	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032323	42032323	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	199	584	0	ENST00000219905.7:c.4507A>G	p.Met1503Val	p.M1503V	ENST00000219905	NM_001164273.1	1503	Atg/Gtg	14/24	1	2	FACETS	0.853	0.791	0.916	0.853	0.791	0.916	CLONAL	1	TRUE	1	0.57	2		584	819	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042329	42042329	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	226	556	0	ENST00000219905.7:c.6524G>T	p.Arg2175Ile	p.R2175I	ENST00000219905	NM_001164273.1	2175	aGa/aTa	17/24	1	2	FACETS	0.96	0.896	1	0.96	0.896	1	CLONAL	1	TRUE	1	0.57	2		556	826	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42050033	42050033	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs548371365	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	146	371	1	ENST00000219905.7:c.7187G>A	p.Arg2396Gln	p.R2396Q	ENST00000219905	NM_001164273.1	2396	cGa/cAa	19/24	1	2	FACETS	0.862	0.79	0.937	0.862	0.79	0.937	CLONAL	1	TRUE	1	0.57	2		372	594	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701263	43701263	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1157211964	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	143	554	1	ENST00000382044.4:c.5432C>T	p.Ala1811Val	p.A1811V	ENST00000382044	NM_001141980.1	1811	gCg/gTg	26/28	1	2	FACETS	0.619	0.565	0.677	0.619	0.565	0.677	SUBCLONAL	1	TRUE	1	0.57	2		555	810	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43739654	43739654	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	146	305	0	ENST00000382044.4:c.2746G>T	p.Glu916Ter	p.E916*	ENST00000382044	NM_001141980.1	916	Gaa/Taa	13/28	1	2	FACETS	0.987	0.906	1	0.987	0.906	1	CLONAL	1	TRUE	1	0.57	2		305	519	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007713	45007713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148494241	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	169	419	0	ENST00000558401.1:c.160G>A	p.Asp54Asn	p.D54N	ENST00000558401	NM_004048.2	54	Gac/Aac	2/4	1	2	FACETS	0.975	0.901	1	0.975	0.901	1	CLONAL	1	TRUE	1	0.57	2		419	608	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476390	88476390	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	181	461	0	ENST00000360948.2:c.1742C>A	p.Ala581Asp	p.A581D	ENST00000360948	NM_001012338.2	581	gCc/gAc	15/19	1	2	FACETS	0.964	0.893	1	0.964	0.893	1	CLONAL	1	TRUE	1	0.57	2		461	659	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293004	91293004	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1013299710	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	252	576	0	ENST00000355112.3:c.506T>G	p.Phe169Cys	p.F169C	ENST00000355112	NM_000057.2	169	tTt/tGt	3/22	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.57	2		576	833	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304374	91304374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777647725	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	184	476	0	ENST00000355112.3:c.1771C>T	p.Arg591Trp	p.R591W	ENST00000355112	NM_000057.2	591	Cgg/Tgg	7/22	1	2	FACETS	0.888	0.822	0.956	0.888	0.822	0.956	CLONAL	1	TRUE	1	0.57	2		476	727	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310181	91310181	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	197	433	0	ENST00000355112.3:c.2235A>C	p.Glu745Asp	p.E745D	ENST00000355112	NM_000057.2	745	gaA/gaC	10/22	1	2	FACETS	0.893	0.829	0.959	0.893	0.829	0.959	CLONAL	1	TRUE	1	0.57	2		433	774	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456366	99456366	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs143784321	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	185	527	1	ENST00000268035.6:c.1683C>A	p.Asp561Glu	p.D561E	ENST00000268035	NM_000875.3	561	gaC/gaA	8/21	1	2	FACETS	0.966	0.895	1	0.966	0.895	1	CLONAL	1	TRUE	1	0.57	2		528	672	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222251	2222251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771233423	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	219	626	1	ENST00000326181.6:c.535G>A	p.Glu179Lys	p.E179K	ENST00000326181	NM_032271.2	179	Gag/Aag	8/21	1	2	FACETS	0.926	0.863	0.99	0.926	0.863	0.99	CLONAL	1	TRUE	1	0.57	2		627	830	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642845	3642845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776707468	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	232	638	0	ENST00000294008.3:c.2182G>A	p.Ala728Thr	p.A728T	ENST00000294008	NM_032444.2	728	Gct/Act	11/15	1	2	FACETS	0.952	0.89	1	0.952	0.89	1	CLONAL	1	TRUE	1	0.57	2		638	855	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781890	3781890	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	203	636	0	ENST00000262367.5:c.4777A>G	p.Thr1593Ala	p.T1593A	ENST00000262367	NM_004380.2	1593	Acc/Gcc	29/31	1	2	FACETS	0.884	0.821	0.948	0.884	0.821	0.948	CLONAL	1	TRUE	1	0.57	2		636	806	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14026041	14026041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750883282	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	133	362	0	ENST00000311895.7:c.1001C>T	p.Ser334Leu	p.S334L	ENST00000311895	NM_005236.2	334	tCg/tTg	6/11	1	2	FACETS	0.911	0.832	0.993	0.911	0.832	0.993	CLONAL	1	TRUE	1	0.57	2		362	512	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647412	23647412	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	158	485	0	ENST00000261584.4:c.455A>C	p.Lys152Thr	p.K152T	ENST00000261584	NM_024675.3	152	aAg/aCg	4/13	1	2	FACETS	0.779	0.715	0.845	0.779	0.715	0.845	SUBCLONAL	1	TRUE	1	0.57	2		485	712	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129104	30129104	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	152	486	2	ENST00000263025.4:c.662G>A	p.Gly221Asp	p.G221D	ENST00000263025	NM_002746.2	221	gGc/gAc	5/9	1	2	FACETS	0.845	0.776	0.917	0.845	0.776	0.917	CLONAL	1	TRUE	1	0.57	2		488	631	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845491	72845491	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	175	504	0	ENST00000268489.5:c.3849G>T	p.Glu1283Asp	p.E1283D	ENST00000268489	NM_006885.3	1283	gaG/gaT	7/10	1	2	FACETS	0.878	0.811	0.948	0.878	0.811	0.948	CLONAL	1	TRUE	1	0.57	2		504	699	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888183	81888183	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	181	542	0	ENST00000359376.3:c.328A>C	p.Ser110Arg	p.S110R	ENST00000359376	NM_002661.3	110	Agc/Cgc	3/33	1	2	FACETS	0.838	0.775	0.903	0.838	0.775	0.903	CLONAL	1	TRUE	1	0.57	2		542	758	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929510	81929510	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	192	502	1	ENST00000359376.3:c.1171G>T	p.Asp391Tyr	p.D391Y	ENST00000359376	NM_002661.3	391	Gac/Tac	13/33	1	2	FACETS	0.883	0.819	0.949	0.883	0.819	0.949	CLONAL	1	TRUE	1	0.57	2		503	763	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972418	81972418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758678624	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	169	419	1	ENST00000359376.3:c.3211C>T	p.Arg1071Cys	p.R1071C	ENST00000359376	NM_002661.3	1071	Cgc/Tgc	29/33	1	2	FACETS	0.929	0.858	1	0.929	0.858	1	CLONAL	1	TRUE	1	0.57	2		420	638	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805660	89805660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1392502645	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	209	582	1	ENST00000389301.3:c.4048G>A	p.Glu1350Lys	p.E1350K	ENST00000389301	NM_000135.2	1350	Gaa/Aaa	41/43	1	2	FACETS	0.817	0.759	0.876	0.817	0.759	0.876	CLONAL	1	TRUE	1	0.57	2		583	898	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813245	89813245	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	235	564	0	ENST00000389301.3:c.3402C>A	p.Phe1134Leu	p.F1134L	ENST00000389301	NM_000135.2	1134	ttC/ttA	34/43	1	2	FACETS	0.971	0.908	1	0.971	0.908	1	CLONAL	1	TRUE	1	0.57	2		564	849	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965425	15965425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1286197692	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	155	368	0	ENST00000268712.3:c.5381G>A	p.Arg1794Gln	p.R1794Q	ENST00000268712	NM_006311.3	1794	cGa/cAa	36/46	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.57	2		368	503	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122412	17122412	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	184	586	0	ENST00000285071.4:c.983A>C	p.Glu328Ala	p.E328A	ENST00000285071	NM_144997.5	328	gAg/gCg	9/14	1	2	FACETS	0.9	0.834	0.969	0.9	0.834	0.969	CLONAL	1	TRUE	1	0.57	2		586	717	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315405	30315405	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	221	564	0	ENST00000322652.5:c.1090G>T	p.Glu364Ter	p.E364*	ENST00000322652	NM_015355.2	364	Gag/Tag	10/16	1	2	FACETS	0.889	0.829	0.952	0.889	0.829	0.952	CLONAL	1	TRUE	1	0.57	2		564	872	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880254	37880254	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	182	547	0	ENST00000269571.5:c.2298A>C	p.Glu766Asp	p.E766D	ENST00000269571		766	gaA/gaC	19/27	1	2	FACETS	0.829	0.767	0.894	0.829	0.767	0.894	CLONAL	1	TRUE	1	0.57	2		547	770	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223166	41223166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357002	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	232	544	3	ENST00000357654.3:c.4765C>T	p.Arg1589Cys	p.R1589C	ENST00000357654	NM_007294.3	1589	Cgt/Tgt	15/23	1	2	FACETS	0.976	0.912	1	0.976	0.912	1	CLONAL	1	TRUE	1	0.57	2		547	834	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448358	56448358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771597876	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	217	697	2	ENST00000407977.2:c.289G>A	p.Asp97Asn	p.D97N	ENST00000407977		97	Gac/Aac	3/10	1	2	FACETS	0.863	0.804	0.925	0.863	0.804	0.925	CLONAL	1	TRUE	1	0.57	2		699	882	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761418	59761418	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	177	425	0	ENST00000259008.2:c.2989A>G	p.Thr997Ala	p.T997A	ENST00000259008	NM_032043.2	997	Aca/Gca	20/20	1	2	FACETS	0.95	0.879	1	0.95	0.879	1	CLONAL	1	TRUE	1	0.57	2		425	654	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66522028	66522028	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768934933	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	108	334	0	ENST00000358598.2:c.683G>A	p.Arg228Gln	p.R228Q	ENST00000358598	NM_212471.2	228	cGa/cAa	7/11	1	2	FACETS	0.75	0.676	0.828	0.75	0.676	0.828	SUBCLONAL	1	TRUE	1	0.57	2		334	505	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39576681	39576681	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1321481448	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	169	365	0	ENST00000262039.4:c.971C>T	p.Thr324Met	p.T324M	ENST00000262039	NM_002647.2	324	aCg/aTg	9/25	1	2	FACETS	0.911	0.841	0.984	0.911	0.841	0.984	CLONAL	1	TRUE	1	0.57	2		365	651	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39629563	39629563	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	148	400	0	ENST00000262039.4:c.2257A>C	p.Lys753Gln	p.K753Q	ENST00000262039	NM_002647.2	753	Aaa/Caa	21/25	1	2	FACETS	0.842	0.772	0.915	0.842	0.772	0.915	CLONAL	1	TRUE	1	0.57	2		400	617	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39638012	39638012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs893280651	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	210	534	1	ENST00000262039.4:c.2429G>A	p.Arg810Gln	p.R810Q	ENST00000262039	NM_002647.2	810	cGa/cAa	22/25	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.57	2		535	729	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372159	45372159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	151	449	0	ENST00000262160.6:c.1010G>A	p.Arg337His	p.R337H	ENST00000262160	NM_005901.5	337	cGc/cAc	9/11	1	2	FACETS	0.823	0.755	0.893	0.823	0.755	0.893	CLONAL	1	TRUE	1	0.57	2		449	644	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56376743	56376744	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	219	543	0	ENST00000348428.3:c.788dup	p.Asn263LysfsTer2	p.N263Kfs*2	ENST00000348428	NM_006785.3	261	-/A	5/17	1	2	FACETS	0.984	0.918	1	0.984	0.918	1	CLONAL	1	TRUE	1	0.57	2		543	781	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56415017	56415017	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	228	472	1	ENST00000348428.3:c.2418G>T	p.Glu806Asp	p.E806D	ENST00000348428	NM_006785.3	806	gaG/gaT	17/17	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.57	2		473	790	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2185896	2185896	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	251	638	0	ENST00000398665.3:c.168G>T	p.Glu56Asp	p.E56D	ENST00000398665	NM_032482.2	56	gaG/gaT	3/28	1	2	FACETS	0.964	0.903	1	0.964	0.903	1	CLONAL	1	TRUE	1	0.57	2		638	914	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220166	5220166	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	163	506	0	ENST00000357368.4:c.3550-1G>T		p.X1184_splice	ENST00000357368	NM_002850.3	1184			1	2	FACETS	0.998	0.921	1	0.998	0.921	1	CLONAL	1	TRUE	1	0.57	2		506	573	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262187	10262187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368319266	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	178	599	0	ENST00000340748.4:c.2104G>A	p.Asp702Asn	p.D702N	ENST00000340748		702	Gat/Aat	23/40	1	2	FACETS	0.755	0.697	0.816	0.755	0.697	0.816	SUBCLONAL	1	TRUE	1	0.57	2		599	827	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291505	10291505	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	259	556	0	ENST00000340748.4:c.174G>T	p.Lys58Asn	p.K58N	ENST00000340748		58	aaG/aaT	3/40	1	2	FACETS	0.994	0.933	1	0.994	0.933	1	CLONAL	1	TRUE	1	0.57	2		556	914	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376187	15376187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1348283029	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	170	446	0	ENST00000263377.2:c.827C>T	p.Ala276Val	p.A276V	ENST00000263377	NM_058243.2	276	gCg/gTg	5/20	1	2	FACETS	0.988	0.913	1	0.988	0.913	1	CLONAL	1	TRUE	1	0.57	2		446	604	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952544	17952544	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	222	566	1	ENST00000458235.1:c.889G>T	p.Glu297Ter	p.E297*	ENST00000458235	NM_000215.3	297	Gaa/Taa	7/24	1	2	FACETS	0.981	0.916	1	0.981	0.916	1	CLONAL	1	TRUE	1	0.57	2		567	794	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258632	19258632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757401725	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	178	469	1	ENST00000162023.5:c.268C>T	p.Arg90Trp	p.R90W	ENST00000162023		90	Cgg/Tgg	8/13	1	2	FACETS	0.936	0.866	1	0.936	0.866	1	CLONAL	1	TRUE	1	0.57	2		470	667	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792294	33792294	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1439202716	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	185	561	0	ENST00000498907.2:c.1027C>T	p.Arg343Cys	p.R343C	ENST00000498907	NM_004364.3	343	Cgc/Tgc	1/1	1	2	FACETS	0.872	0.808	0.94	0.872	0.808	0.94	CLONAL	1	TRUE	1	0.57	2		561	744	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222821	36222821	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	254	624	0	ENST00000222270.7:c.5450G>T	p.Gly1817Val	p.G1817V	ENST00000222270	NM_014727.1	1817	gGt/gTt	27/37	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.57	2		624	855	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551311	29551311	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	217	721	2	ENST00000389048.3:c.1319C>T	p.Ser440Phe	p.S440F	ENST00000389048	NM_004304.4	440	tCc/tTc	6/29	1	2	FACETS	0.954	0.89	1	0.954	0.89	1	CLONAL	1	TRUE	1	0.57	2		723	798	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222281	39222281	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572955351	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	207	524	0	ENST00000402219.2:c.3329C>T	p.Ser1110Leu	p.S1110L	ENST00000402219	NM_005633.3	1110	tCg/tTg	20/23	1	2	FACETS	0.842	0.782	0.903	0.842	0.782	0.903	CLONAL	1	TRUE	1	0.57	2		524	863	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241979	39241979	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	186	424	0	ENST00000402219.2:c.1867T>A	p.Phe623Ile	p.F623I	ENST00000402219	NM_005633.3	623	Ttt/Att	11/23	1	2	FACETS	0.981	0.91	1	0.981	0.91	1	CLONAL	1	TRUE	1	0.57	2		424	665	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702367	47702367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs549467183	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	157	371	0	ENST00000233146.2:c.1963G>A	p.Val655Ile	p.V655I	ENST00000233146	NM_000251.2	655	Gta/Ata	12/16	1	2	FACETS	0.827	0.76	0.897	0.827	0.76	0.897	CLONAL	1	TRUE	1	0.57	2		371	666	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026124	48026124	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	184	380	1	ENST00000234420.5:c.1002G>T	p.Lys334Asn	p.K334N	ENST00000234420	NM_000179.2	334	aaG/aaT	4/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.57	2		381	604	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033790	48033790	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs267608122	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	149	315	0	ENST00000234420.5:c.4001G>A	p.Arg1334Gln	p.R1334Q	ENST00000234420	NM_000179.2	1334	cGg/cAg	9/10	1	2	FACETS	0.97	0.891	1	0.97	0.891	1	CLONAL	1	TRUE	1	0.57	2		315	539	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719628	190719628	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs751506189	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	85	221	0	ENST00000441310.2:c.1630G>T	p.Asp544Tyr	p.D544Y	ENST00000441310	NM_000534.4	544	Gat/Tat	9/13	1	2	FACETS	0.95	0.848	1	0.95	0.848	1	CLONAL	1	TRUE	1	0.57	2		221	314	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736100	204736100	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	92	306	0	ENST00000302823.3:c.458-1G>T		p.X153_splice	ENST00000302823	NM_005214.4	153			1	2	FACETS	0.811	0.726	0.901	0.811	0.726	0.901	CLONAL	1	TRUE	1	0.57	2		306	398	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209103849	209103849	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	198	505	0	ENST00000345146.2:c.1100T>G	p.Ile367Ser	p.I367S	ENST00000345146	NM_005896.2	367	aTt/aGt	9/10	1	2	FACETS	0.908	0.843	0.975	0.908	0.843	0.975	CLONAL	1	TRUE	1	0.57	2		505	765	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793263	242793263	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754424677	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	222	707	1	ENST00000334409.5:c.814C>T	p.Arg272Trp	p.R272W	ENST00000334409	NM_005018.2	272	Cgg/Tgg	5/5	1	2	FACETS	0.969	0.904	1	0.969	0.904	1	CLONAL	1	TRUE	1	0.57	2		708	804	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793404	242793404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1480910547	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	205	666	1	ENST00000334409.5:c.673G>A	p.Glu225Lys	p.E225K	ENST00000334409	NM_005018.2	225	Gag/Aag	5/5	1	2	FACETS	0.876	0.814	0.94	0.876	0.814	0.94	CLONAL	1	TRUE	1	0.57	2		667	821	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021518	31021518	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1464693264	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	176	506	1	ENST00000375687.4:c.1517G>T	p.Arg506Ile	p.R506I	ENST00000375687	NM_015338.5	506	aGa/aTa	12/13	1	2	FACETS	0.922	0.852	0.994	0.922	0.852	0.994	CLONAL	1	TRUE	1	0.57	2		507	670	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076912	41076912	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	191	576	0	ENST00000373198.4:c.1508A>G	p.Tyr503Cys	p.Y503C	ENST00000373198	NM_133170.3	503	tAc/tGc	9/32	1	2	FACETS	0.957	0.888	1	0.957	0.888	1	CLONAL	1	TRUE	1	0.57	2		576	700	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385176	41385176	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	206	653	0	ENST00000373198.4:c.785T>C	p.Val262Ala	p.V262A	ENST00000373198	NM_133170.3	262	gTc/gCc	6/32	1	2	FACETS	0.914	0.85	0.98	0.914	0.85	0.98	CLONAL	1	TRUE	1	0.57	2		653	791	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264072	46264072	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	165	327	0	ENST00000371998.3:c.1119G>T	p.Gln373His	p.Q373H	ENST00000371998		373	caG/caT	11/23	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.57	2		327	564	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127191	22127191	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	137	494	0	ENST00000215832.6:c.937C>A	p.Leu313Met	p.L313M	ENST00000215832	NM_002745.4	313	Ctg/Atg	7/9	1	2	FACETS	0.629	0.573	0.688	0.629	0.573	0.688	SUBCLONAL	1	TRUE	1	0.57	2		494	764	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41560087	41560087	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	184	440	1	ENST00000263253.7:c.3759G>T	p.Lys1253Asn	p.K1253N	ENST00000263253	NM_001429.3	1253	aaG/aaT	22/31	1	2	FACETS	0.921	0.853	0.991	0.921	0.853	0.991	CLONAL	1	TRUE	1	0.57	2		441	701	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573312	41573312	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763290593	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	280	587	0	ENST00000263253.7:c.5597C>T	p.Pro1866Leu	p.P1866L	ENST00000263253	NM_001429.3	1866	cCg/cTg	31/31	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.57	2		587	933	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574620	41574620	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	235	648	1	ENST00000263253.7:c.6905C>A	p.Ser2302Tyr	p.S2302Y	ENST00000263253	NM_001429.3	2302	tCt/tAt	31/31	1	2	FACETS	0.866	0.809	0.925	0.866	0.809	0.925	CLONAL	1	TRUE	1	0.57	2		649	952	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626661	12626661	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	178	479	0	ENST00000251849.4:c.1628C>T	p.Thr543Met	p.T543M	ENST00000251849	NM_002880.3	543	aCg/aTg	15/17	1	2	FACETS	0.833	0.769	0.899	0.833	0.769	0.899	CLONAL	1	TRUE	1	0.57	2		479	750	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691777	30691777	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	170	511	1	ENST00000295754.5:c.279G>T	p.Glu93Asp	p.E93D	ENST00000295754	NM_003242.5	93	gaG/gaT	3/7	1	2	FACETS	0.82	0.756	0.887	0.82	0.756	0.887	CLONAL	1	TRUE	1	0.57	2		512	727	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181447	38181447	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	116	506	0	ENST00000396334.3:c.460A>G	p.Thr154Ala	p.T154A	ENST00000396334	NM_002468.4	154	Aca/Gca	2/5	1	2	FACETS	0.557	0.502	0.615	0.557	0.502	0.615	SUBCLONAL	1	TRUE	1	0.57	2		506	731	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182053	38182053	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	131	386	0	ENST00000396334.3:c.677A>G	p.Glu226Gly	p.E226G	ENST00000396334	NM_002468.4	226	gAa/gGa	3/5	1	2	FACETS	0.811	0.739	0.886	0.811	0.739	0.886	CLONAL	1	TRUE	1	0.57	2		386	567	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277291	41277291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	179	439	1	ENST00000349496.5:c.1760G>A	p.Arg587Gln	p.R587Q	ENST00000349496	NM_001904.3	587	cGa/cAa	11/15	1	2	FACETS	0.871	0.805	0.939	0.871	0.805	0.939	CLONAL	1	TRUE	1	0.57	2		440	721	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47061272	47061272	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	193	456	0	ENST00000409792.3:c.7409G>T	p.Ser2470Ile	p.S2470I	ENST00000409792	NM_014159.6	2470	aGc/aTc	19/21	1	2	FACETS	0.935	0.868	1	0.935	0.868	1	CLONAL	1	TRUE	1	0.57	2		456	724	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928076	49928076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748976824	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	214	531	0	ENST00000296474.3:c.3652G>A	p.Glu1218Lys	p.E1218K	ENST00000296474	NM_002447.2	1218	Gag/Aag	18/20	1	2	FACETS	0.989	0.922	1	0.989	0.922	1	CLONAL	1	TRUE	1	0.57	2		531	759	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438571	52438571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374620220	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	186	479	1	ENST00000460680.1:c.1148G>A	p.Arg383His	p.R383H	ENST00000460680	NM_004656.3	383	cGc/cAc	12/17	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.57	2		480	634	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442502	52442502	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	213	502	0	ENST00000460680.1:c.243C>A	p.Phe81Leu	p.F81L	ENST00000460680	NM_004656.3	81	ttC/ttA	4/17	1	2	FACETS	0.99	0.923	1	0.99	0.923	1	CLONAL	1	TRUE	1	0.57	2		502	755	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643668	52643668	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	200	436	0	ENST00000394830.3:c.2228C>A	p.Ser743Tyr	p.S743Y	ENST00000394830	NM_018313.4	743	tCt/tAt	17/30	1	2	FACETS	0.946	0.879	1	0.946	0.879	1	CLONAL	1	TRUE	1	0.57	2		436	742	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52676036	52676036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764156634	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	187	513	0	ENST00000394830.3:c.1021C>T	p.Arg341Cys	p.R341C	ENST00000394830	NM_018313.4	341	Cgt/Tgt	11/30	1	2	FACETS	0.893	0.827	0.961	0.893	0.827	0.961	CLONAL	1	TRUE	1	0.57	2		513	735	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71064803	71064803	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	104	324	0	ENST00000318789.4:c.871T>G	p.Leu291Val	p.L291V	ENST00000318789	NM_032682.5	291	Ttg/Gtg	12/21	1	2	FACETS	0.879	0.793	0.97	0.879	0.793	0.97	CLONAL	1	TRUE	1	0.57	2		324	415	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468407	89468407	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs201062946	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	121	317	3	ENST00000336596.2:c.1941G>T	p.Glu647Asp	p.E647D	ENST00000336596	NM_005233.5	647	gaG/gaT	11/17	1	2	FACETS	0.992	0.903	1	0.992	0.903	1	CLONAL	1	TRUE	1	0.57	2		320	428	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480365	89480365	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	116	315	0	ENST00000336596.2:c.2202G>T	p.Met734Ile	p.M734I	ENST00000336596	NM_005233.5	734	atG/atT	13/17	1	2	FACETS	0.971	0.882	1	0.971	0.882	1	CLONAL	1	TRUE	1	0.57	2		315	419	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851847	134851847	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	233	629	0	ENST00000398015.3:c.1253T>C	p.Phe418Ser	p.F418S	ENST00000398015	NM_004441.4	418	tTc/tCc	5/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.57	2		629	780	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374314	138374314	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	176	558	0	ENST00000289153.2:c.3130A>C	p.Lys1044Gln	p.K1044Q	ENST00000289153	NM_006219.2	1044	Aaa/Caa	22/22	1	2	FACETS	0.845	0.78	0.912	0.845	0.78	0.912	CLONAL	1	TRUE	1	0.57	2		558	731	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374319	138374319	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	155	534	0	ENST00000289153.2:c.3125A>C	p.Lys1042Thr	p.K1042T	ENST00000289153	NM_006219.2	1042	aAg/aCg	22/22	1	2	FACETS	0.765	0.702	0.831	0.765	0.702	0.831	SUBCLONAL	1	TRUE	1	0.57	2		534	711	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281396	142281396	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	230	497	0	ENST00000350721.4:c.848T>G	p.Met283Arg	p.M283R	ENST00000350721	NM_001184.3	283	aTg/aGg	4/47	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.57	2		497	807	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191008	185191008	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	311	734	0	ENST00000265026.3:c.1889C>A	p.Ser630Tyr	p.S630Y	ENST00000265026	NM_004721.4	630	tCt/tAt	11/14	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.57	2		734	1020	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806600	1806600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529493162	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	195	701	2	ENST00000260795.2:c.1316G>A	p.Arg439His	p.R439H	ENST00000260795		439	cGc/cAc	9/17	1	2	FACETS	0.84	0.778	0.903	0.84	0.778	0.903	CLONAL	1	TRUE	1	0.57	2		703	815	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957492	1957492	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	219	563	0	ENST00000382891.5:c.2591A>G	p.Asp864Gly	p.D864G	ENST00000382891	NM_133335.3	864	gAc/gGc	14/22	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.57	2		563	761	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133574	55133574	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373948582	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	214	561	1	ENST00000257290.5:c.878G>A	p.Arg293His	p.R293H	ENST00000257290	NM_006206.4	293	cGc/cAc	6/23	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.57	2		562	733	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161294	55161294	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs764265933	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	120	363	2	ENST00000257290.5:c.3125C>T	p.Ser1042Leu	p.S1042L	ENST00000257290	NM_006206.4	1042	tCg/tTg	23/23	1	2	FACETS	0.854	0.775	0.936	0.854	0.775	0.936	CLONAL	1	TRUE	1	0.57	2		365	493	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599295	55599295	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	192	545	1	ENST00000288135.5:c.2421G>T	p.Lys807Asn	p.K807N	ENST00000288135	NM_000222.2	807	aaG/aaT	17/21	1	2	FACETS	0.885	0.821	0.952	0.885	0.821	0.952	CLONAL	1	TRUE	1	0.57	2		546	761	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976728	55976728	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	159	427	0	ENST00000263923.4:c.1097A>C	p.Lys366Thr	p.K366T	ENST00000263923	NM_002253.2	366	aAa/aCa	9/30	1	2	FACETS	0.919	0.846	0.995	0.919	0.846	0.995	CLONAL	1	TRUE	1	0.57	2		427	607	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808294	99808294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	143	336	0	ENST00000280892.6:c.395G>A	p.Arg132Gln	p.R132Q	ENST00000280892	NM_001130678.1	132	cGa/cAa	5/7	1	2	FACETS	0.992	0.91	1	0.992	0.91	1	CLONAL	1	TRUE	1	0.57	2		336	506	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156922	106156922	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	154	387	0	ENST00000380013.4:c.1823A>T	p.Asn608Ile	p.N608I	ENST00000380013	NM_001127208.2	608	aAt/aTt	3/11	1	2	FACETS	0.922	0.848	0.999	0.922	0.848	0.999	CLONAL	1	TRUE	1	0.57	2		387	586	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539339	187539339	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	149	398	0	ENST00000441802.2:c.8401G>T	p.Asp2801Tyr	p.D2801Y	ENST00000441802	NM_005245.3	2801	Gat/Tat	10/27	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.57	2		398	480	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628277	187628277	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	202	536	0	ENST00000441802.2:c.2705G>T	p.Arg902Ile	p.R902I	ENST00000441802	NM_005245.3	902	aGa/aTa	2/27	1	2	FACETS	0.984	0.916	1	0.984	0.916	1	CLONAL	1	TRUE	1	0.57	2		536	720	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628379	187628379	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	198	613	0	ENST00000441802.2:c.2603T>G	p.Phe868Cys	p.F868C	ENST00000441802	NM_005245.3	868	tTt/tGt	2/27	1	2	FACETS	0.856	0.794	0.919	0.856	0.794	0.919	CLONAL	1	TRUE	1	0.57	2		613	812	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31468119	31468119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767966111	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	254	656	0	ENST00000344624.3:c.2293G>A	p.Asp765Asn	p.D765N	ENST00000344624		765	Gat/Aat	15/33	1	2	FACETS	0.907	0.849	0.966	0.907	0.849	0.966	CLONAL	1	TRUE	1	0.57	2		656	983	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31521294	31521294	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs751444046	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	213	523	0	ENST00000344624.3:c.883C>T	p.Arg295Ter	p.R295*	ENST00000344624		295	Cga/Tga	3/33	1	2	FACETS	0.954	0.889	1	0.954	0.889	1	CLONAL	1	TRUE	1	0.57	2		523	783	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871173	35871173	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	115	326	0	ENST00000303115.3:c.395C>A	p.Pro132His	p.P132H	ENST00000303115	NM_002185.3	132	cCt/cAt	4/8	1	2	FACETS	0.785	0.71	0.863	0.785	0.71	0.863	SUBCLONAL	1	TRUE	1	0.57	2		326	514	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875656	35875656	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	162	492	1	ENST00000303115.3:c.843G>T	p.Lys281Asn	p.K281N	ENST00000303115	NM_002185.3	281	aaG/aaT	7/8	1	2	FACETS	0.833	0.767	0.903	0.833	0.767	0.903	CLONAL	1	TRUE	1	0.57	2		493	682	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958874	38958874	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	160	352	0	ENST00000357387.3:c.2238C>A	p.Phe746Leu	p.F746L	ENST00000357387	NM_152756.3	746	ttC/ttA	23/38	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.57	2		352	547	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168531	56168531	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	110	316	0	ENST00000399503.3:c.1487G>T	p.Arg496Ile	p.R496I	ENST00000399503	NM_005921.1	496	aGa/aTa	8/20	1	2	FACETS	0.794	0.717	0.875	0.794	0.717	0.875	SUBCLONAL	1	TRUE	1	0.57	2		316	486	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79968674	79968674	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	150	395	0	ENST00000265081.6:c.1024G>T	p.Glu342Ter	p.E342*	ENST00000265081	NM_002439.4	342	Gaa/Taa	6/24	1	2	FACETS	0.83	0.761	0.902	0.83	0.761	0.902	CLONAL	1	TRUE	1	0.57	2		395	634	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80074543	80074543	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	158	445	1	ENST00000265081.6:c.2323A>T	p.Lys775Ter	p.K775*	ENST00000265081	NM_002439.4	775	Aaa/Taa	17/24	1	2	FACETS	0.808	0.743	0.876	0.808	0.743	0.876	CLONAL	1	TRUE	1	0.57	2		446	686	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86637128	86637128	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	120	322	0	ENST00000274376.6:c.1039G>T	p.Glu347Ter	p.E347*	ENST00000274376	NM_002890.2	347	Gaa/Taa	6/25	1	2	FACETS	0.861	0.782	0.944	0.861	0.782	0.944	CLONAL	1	TRUE	1	0.57	2		322	489	SUCCESS
APC	324	MSKCC	GRCh37	5	112177377	112177377	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	193	327	0	ENST00000257430.4:c.6086C>A	p.Ser2029Tyr	p.S2029Y	ENST00000257430	NM_000038.5	2029	tCt/tAt	16/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.57	2		327	568	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131978011	131978011	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	215	512	0	ENST00000265335.6:c.3894G>T	p.Glu1298Asp	p.E1298D	ENST00000265335		1298	gaG/gaT	25/25	1	2	FACETS	0.878	0.818	0.941	0.878	0.818	0.941	CLONAL	1	TRUE	1	0.57	2		512	859	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176678831	176678831	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	186	406	0	ENST00000439151.2:c.4742T>G	p.Phe1581Cys	p.F1581C	ENST00000439151	NM_022455.4	1581	tTt/tGt	12/23	1	2	FACETS	0.996	0.924	1	0.996	0.924	1	CLONAL	1	TRUE	1	0.57	2		406	655	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709524	176709524	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587784169	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	225	449	1	ENST00000439151.2:c.5951G>A	p.Arg1984Gln	p.R1984Q	ENST00000439151	NM_022455.4	1984	cGa/cAa	19/23	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.57	2		450	725	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180040072	180040072	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	216	642	0	ENST00000261937.6:c.3370T>G	p.Phe1124Val	p.F1124V	ENST00000261937	NM_182925.4	1124	Ttc/Gtc	25/30	1	2	FACETS	0.944	0.88	1	0.944	0.88	1	CLONAL	1	TRUE	1	0.57	2		642	803	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911286	29911286	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs281864758	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	21	152	0	ENST00000376809.5:c.585C>A	p.Tyr195Ter	p.Y195*	ENST00000376809	NM_002116.7	195	taC/taA	3/8	1	2	FACETS	0.412	0.319	0.518	0.412	0.319	0.518	SUBCLONAL	1	TRUE	1	0.57	2		152	179	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166249	32166249	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	192	660	2	ENST00000375023.3:c.4705C>T	p.Pro1569Ser	p.P1569S	ENST00000375023	NM_004557.3	1569	Cct/Tct	26/30	1	2	FACETS	0.864	0.801	0.929	0.864	0.801	0.929	CLONAL	1	TRUE	1	0.57	2		662	780	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172143	32172143	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	247	610	0	ENST00000375023.3:c.2889G>T	p.Gln963His	p.Q963H	ENST00000375023	NM_004557.3	963	caG/caT	19/30	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.57	2		610	855	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180361	32180361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	223	631	0	ENST00000375023.3:c.2570C>T	p.Ser857Phe	p.S857F	ENST00000375023	NM_004557.3	857	tCc/tTc	17/30	1	2	FACETS	0.965	0.9	1	0.965	0.9	1	CLONAL	1	TRUE	1	0.57	2		631	811	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965635	93965635	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	120	562	1	ENST00000369303.4:c.2293C>A	p.Leu765Ile	p.L765I	ENST00000369303	NM_004440.3	765	Ctt/Att	13/17	1	2	FACETS	0.666	0.603	0.733	0.666	0.603	0.733	SUBCLONAL	1	TRUE	1	0.57	2		563	632	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201838	152201838	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	144	476	0	ENST00000206249.3:c.692A>C	p.Lys231Thr	p.K231T	ENST00000206249	NM_000125.3	231	aAa/aCa	3/8	1	2	FACETS	0.714	0.652	0.778	0.714	0.652	0.778	SUBCLONAL	1	TRUE	1	0.57	2		476	708	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963984	2963984	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778150	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	176	557	1	ENST00000396946.4:c.1823G>A	p.Arg608His	p.R608H	ENST00000396946	NM_032415.4	608	cGc/cAc	15/25	1	2	FACETS	0.911	0.842	0.982	0.911	0.842	0.982	CLONAL	1	TRUE	1	0.57	2		558	678	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210105	55210105	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	183	506	0	ENST00000275493.2:c.215G>T	p.Arg72Met	p.R72M	ENST00000275493	NM_005228.3	72	aGg/aTg	2/28	1	2	FACETS	0.904	0.837	0.974	0.904	0.837	0.974	CLONAL	1	TRUE	1	0.57	2		506	710	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398585	116398585	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	186	576	0	ENST00000397752.3:c.2175A>C	p.Lys725Asn	p.K725N	ENST00000397752	NM_000245.2	725	aaA/aaC	9/21	1	2	FACETS	0.849	0.785	0.914	0.849	0.785	0.914	CLONAL	1	TRUE	1	0.57	2		576	769	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411929	116411929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756031094	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	287	693	1	ENST00000397752.3:c.2914G>A	p.Asp972Asn	p.D972N	ENST00000397752	NM_000245.2	972	Gat/Aat	14/21	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.57	2		694	995	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418998	116418998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369838973	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	122	256	0	ENST00000397752.3:c.3509G>A	p.Arg1170Gln	p.R1170Q	ENST00000397752	NM_000245.2	1170	cGa/cAa	17/21	1	2	FACETS	0.975	0.888	1	0.975	0.888	1	CLONAL	1	TRUE	1	0.57	2		256	439	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434495	140434495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	87	431	0	ENST00000288602.6:c.2203C>T	p.Arg735Trp	p.R735W	ENST00000288602	NM_004333.4	735	Cgg/Tgg	18/18	1	2	FACETS	0.602	0.535	0.674	0.602	0.535	0.674	SUBCLONAL	1	TRUE	1	0.57	2		431	507	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525837	148525837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765147666	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	147	362	0	ENST00000320356.2:c.620G>A	p.Arg207Gln	p.R207Q	ENST00000320356	NM_004456.4	207	cGa/cAa	6/20	1	2	FACETS	0.946	0.869	1	0.946	0.869	1	CLONAL	1	TRUE	1	0.57	2		362	545	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845289	151845289	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs917877853	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	143	489	0	ENST00000262189.6:c.13723C>A	p.Leu4575Ile	p.L4575I	ENST00000262189	NM_170606.2	4575	Ctc/Atc	52/59	1	2	FACETS	0.963	0.883	1	0.963	0.883	1	CLONAL	1	TRUE	1	0.57	2		489	521	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860908	151860908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	110	341	2	ENST00000262189.6:c.9754C>T	p.Arg3252Cys	p.R3252C	ENST00000262189	NM_170606.2	3252	Cgt/Tgt	43/59	1	2	FACETS	0.972	0.881	1	0.972	0.881	1	CLONAL	1	TRUE	1	0.57	2		343	397	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189002	38189002	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	234	711	0	ENST00000317025.8:c.1012G>T	p.Glu338Ter	p.E338*	ENST00000317025	NM_023034.1	338	Gaa/Taa	5/24	1	2	FACETS	0.855	0.798	0.914	0.855	0.798	0.914	CLONAL	1	TRUE	1	0.57	2		711	960	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56860222	56860222	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	214	580	0	ENST00000519728.1:c.224A>G	p.Asp75Gly	p.D75G	ENST00000519728	NM_002350.3	75	gAt/gGt	4/13	1	2	FACETS	0.867	0.807	0.929	0.867	0.807	0.929	CLONAL	1	TRUE	1	0.57	2		580	866	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989659	68989659	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	185	589	0	ENST00000288368.4:c.1597A>C	p.Met533Leu	p.M533L	ENST00000288368	NM_024870.2	533	Atg/Ctg	15/40	1	2	FACETS	0.851	0.787	0.916	0.851	0.787	0.916	CLONAL	1	TRUE	1	0.57	2		589	763	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70967581	70967581	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	261	660	0	ENST00000276594.2:c.1442G>A	p.Arg481Gln	p.R481Q	ENST00000276594	NM_024504.3	481	cGa/cAa	7/8	1	2	FACETS	0.989	0.928	1	0.989	0.928	1	CLONAL	1	TRUE	1	0.57	2		660	926	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965489	90965489	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	121	299	0	ENST00000265433.3:c.1828G>T	p.Glu610Ter	p.E610*	ENST00000265433	NM_002485.4	610	Gaa/Taa	11/16	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.57	2		299	423	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982641	90982641	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	138	375	2	ENST00000265433.3:c.847C>T	p.Pro283Ser	p.P283S	ENST00000265433	NM_002485.4	283	Cct/Tct	7/16	1	2	FACETS	0.835	0.763	0.91	0.835	0.763	0.91	CLONAL	1	TRUE	1	0.57	2		377	580	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993724	90993724	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660922	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	167	347	0	ENST00000265433.3:c.199A>G	p.Thr67Ala	p.T67A	ENST00000265433	NM_002485.4	67	Aca/Gca	3/16	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.57	2		347	572	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741646	145741646	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757320755	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	202	568	2	ENST00000428558.2:c.857C>T	p.Ser286Leu	p.S286L	ENST00000428558	NM_004260.3	286	tCg/tTg	5/22	1	2	FACETS	0.959	0.892	1	0.959	0.892	1	CLONAL	1	TRUE	1	0.57	2		570	739	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050791	5050791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	243	564	0	ENST00000381652.3:c.574G>A	p.Glu192Lys	p.E192K	ENST00000381652	NM_004972.3	192	Gaa/Aaa	6/25	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.57	2		564	849	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5064926	5064926	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	127	405	1	ENST00000381652.3:c.1100C>A	p.Ser367Ter	p.S367*	ENST00000381652	NM_004972.3	367	tCa/tAa	9/25	1	2	FACETS	0.685	0.621	0.751	0.685	0.621	0.751	SUBCLONAL	1	TRUE	1	0.57	2		406	651	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5557725	5557725	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	156	433	1	ENST00000397747.3:c.739C>A	p.Leu247Ile	p.L247I	ENST00000397747	NM_025239.3	247	Ctc/Atc	5/7	1	2	FACETS	0.937	0.862	1	0.937	0.862	1	CLONAL	1	TRUE	1	0.57	2		434	584	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331647	8331647	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	159	504	2	ENST00000356435.5:c.5469C>A	p.Phe1823Leu	p.F1823L	ENST00000356435		1823	ttC/ttA	33/35	1	2	FACETS	0.838	0.77	0.908	0.838	0.77	0.908	CLONAL	1	TRUE	1	0.57	2		506	666	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197425	27197425	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	249	686	3	ENST00000380036.4:c.1737G>T	p.Glu579Asp	p.E579D	ENST00000380036	NM_000459.3	579	gaG/gaT	12/23	1	2	FACETS	0.892	0.835	0.951	0.892	0.835	0.951	CLONAL	1	TRUE	1	0.57	2		689	979	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336418	80336418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1236524878	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	68	298	0	ENST00000286548.4:c.901G>A	p.Asp301Asn	p.D301N	ENST00000286548	NM_002072.3	301	Gat/Aat	7/7	1	2	FACETS	0.68	0.595	0.77	0.68	0.595	0.77	SUBCLONAL	1	TRUE	1	0.57	2		298	351	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97873833	97873833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200719554	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	224	608	1	ENST00000289081.3:c.1241C>T	p.Ser414Leu	p.S414L	ENST00000289081	NM_000136.2	414	tCg/tTg	13/15	1	2	FACETS	0.948	0.885	1	0.948	0.885	1	CLONAL	1	TRUE	1	0.57	2		609	829	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772663	135772663	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	173	476	0	ENST00000298552.3:c.2883G>T	p.Glu961Asp	p.E961D	ENST00000298552	NM_001162426.1	961	gaG/gaT	22/23	1	2	FACETS	0.832	0.767	0.898	0.832	0.767	0.898	CLONAL	1	TRUE	1	0.57	2		476	730	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772991	135772991	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	66	149	0	ENST00000298552.3:c.2632G>T	p.Glu878Ter	p.E878*	ENST00000298552	NM_001162426.1	878	Gaa/Taa	21/23	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.57	2		149	211	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139794095	139794095	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	241	575	1	ENST00000247668.2:c.238G>T	p.Glu80Ter	p.E80*	ENST00000247668	NM_021138.3	80	Gaa/Taa	3/11	1	2	FACETS	0.995	0.931	1	0.995	0.931	1	CLONAL	1	TRUE	1	0.57	2		576	850	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913528	39913528	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	246	619	0	ENST00000378444.4:c.4800C>A	p.Phe1600Leu	p.F1600L	ENST00000378444	NM_001123385.1	1600	ttC/ttA	13/15	1	2	FACETS	0.902	0.844	0.962	0.902	0.844	0.962	CLONAL	1	TRUE	1	0.57	2		619	957	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041149	47041149	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs963940626	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	191	540	0	ENST00000377604.3:c.1577C>T	p.Ser526Leu	p.S526L	ENST00000377604	NM_001204468.1	526	tCg/tTg	15/24	1	2	FACETS	0.978	0.908	1	0.978	0.908	1	CLONAL	1	TRUE	1	0.57	2		540	685	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875919	76875919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	212	626	3	ENST00000373344.5:c.5216G>A	p.Arg1739Gln	p.R1739Q	ENST00000373344	NM_000489.3	1739	cGa/cAa	20/35	1	2	FACETS	0.908	0.846	0.973	0.908	0.846	0.973	CLONAL	1	TRUE	1	0.57	2		629	819	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952164	76952164	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	159	466	1	ENST00000373344.5:c.271G>T	p.Glu91Ter	p.E91*	ENST00000373344	NM_000489.3	91	Gaa/Taa	5/35	1	2	FACETS	0.716	0.657	0.778	0.716	0.657	0.778	SUBCLONAL	1	TRUE	1	0.57	2		467	779	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436128	116436128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	145	393	0	ENST00000397752.3:c.4123G>A	p.Ala1375Thr	p.A1375T	ENST00000397752	NM_000245.2	1375	Gct/Act	21/21	1	2	FACETS	0.844	0.773	0.917	0.844	0.773	0.917	CLONAL	1	TRUE	1	0.57	2		393	603	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174395	11174395	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	67	619	0	ENST00000361445.4:c.7280T>G	p.Leu2427Arg	p.L2427R	ENST00000361445	NM_004958.3	2427	cTg/cGg	53/58	0.178824053988253	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		619	731	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	449	935	0	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.329116645258277	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.342882964829765	2		935	1080	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40682049	40682049	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs376078990	NA	P-0026282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	141	600	3	ENST00000249776.8:c.604G>T	p.Asp202Tyr	p.D202Y	ENST00000249776	NM_033286.3	202	Gac/Tac	6/9	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.342882964829765	2		603	744	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967946	93967946	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs758348899	NA	P-0026282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	101	573	0	ENST00000369303.4:c.1981G>T	p.Ala661Ser	p.A661S	ENST00000369303	NM_004440.3	661	Gca/Tca	11/17	1	2	FACETS	0.99	0.887	1	0.99	0.887	1	CLONAL	1	TRUE	1	0.342882964829765	2		573	595	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	146	244	0	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	0.318953939735265	3	FACETS	1	0.97	1	0.563	0.516	0.611	INDETERMINATE	1	TRUE	1	0.578792094230597	3		244	578	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40384097	40384097	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	96	705	0	ENST00000293328.3:c.49C>T	p.Gln17Ter	p.Q17*	ENST00000293328	NM_012448.3	17	Cag/Tag	2/19	0.283658094942618	2	FACETS	0.478	0.426	0.533	0.239	0.213	0.267	INDETERMINATE	1	TRUE	0	0.578792094230597	2		705	694	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182662947	182662947	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	76	463	0	ENST00000292782.4:c.715C>T	p.Leu239Phe	p.L239F	ENST00000292782	NM_020640.2	239	Ctt/Ttt	7/7	0.289024506206452	5	FACETS	0.627	0.549	0.711	0.209	0.183	0.237	INDETERMINATE	1	TRUE	2	0.578792094230597	5		463	783	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349610	89349610	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	127	796	0	ENST00000301030.4:c.3340T>C	p.Tyr1114His	p.Y1114H	ENST00000301030	NM_001256183.1	1114	Tac/Cac	9/13	NA	2	FACETS	1	0.972	1			1	INDETERMINATE	1	TRUE	NA	0.366068213095028	2		796	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	145	322	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.264294782222109	2	FACETS	0.824	0.756	0.894	0.824	0.756	0.894	CLONAL	2	TRUE	0	0.338984689598266	2		322	519	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	44	505	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.416	0.348	0.491	0.416	0.348	0.491	SUBCLONAL	1	TRUE	1	0.338984689598266	2		505	624	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	72	501	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	0.338984689598266	2		501	366	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253974	133253974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61732929	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	112	381	1	ENST00000320574.5:c.776G>A	p.Arg259His	p.R259H	ENST00000320574	NM_006231.2	259	cGc/cAc	8/49	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.338984689598266	2		382	455	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592108	67592108	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1419325070	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	56	202	0	ENST00000274335.5:c.1924C>T	p.Arg642Ter	p.R642*	ENST00000274335		642	Cga/Tga	14/15	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.338984689598266	2		202	294	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482927	140482927	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	60	369	0	ENST00000288602.6:c.1208del	p.Pro403LeufsTer8	p.P403Lfs*8	ENST00000288602	NM_004333.4	403	cCt/ct	10/18	1	2	FACETS	0.863	0.746	0.99	0.863	0.746	0.99	CLONAL	1	TRUE	1	0.338984689598266	2		369	410	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129655	11129655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	95	366	1	ENST00000358026.2:c.2461G>A	p.Glu821Lys	p.E821K	ENST00000358026	NM_001128849.1	821	Gag/Aag	17/36	1	2	FACETS	0.997	0.89	1	0.997	0.89	1	CLONAL	1	TRUE	1	0.338984689598266	2		367	562	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911443	32911443	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359365	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	40	274	0	ENST00000380152.3:c.2957del	p.Asn986IlefsTer5	p.N986Ifs*5	ENST00000380152		984	gAa/ga	11/27	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.338984689598266	2		274	206	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905055	50905055	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	36	279	1	ENST00000440232.2:c.342del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	113	Ggg/gg	4/27	1	2	FACETS	0.464	0.381	0.557	0.464	0.381	0.557	SUBCLONAL	1	TRUE	1	0.338984689598266	2		280	458	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390736	139390736	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	176	518	0	ENST00000277541.6:c.7455del	p.Ser2486ArgfsTer103	p.S2486Rfs*103	ENST00000277541	NM_017617.3	2485	ccC/cc	34/34	0.274921601174206	2	FACETS	0.761	0.704	0.821	0.761	0.704	0.821	SUBCLONAL	2	TRUE	0	0.338984689598266	2		518	682	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517815	187517815	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	24	167	0	ENST00000441802.2:c.12879del	p.His4293GlnfsTer56	p.H4293Qfs*56	ENST00000441802	NM_005245.3	4293	caC/ca	25/27	1	2	FACETS	0.502	0.394	0.626	0.502	0.394	0.626	SUBCLONAL	1	TRUE	1	0.338984689598266	2		167	282	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911074	32911074	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	20	322	0	ENST00000380152.3:c.2588del	p.Asn863IlefsTer11	p.N863Ifs*11	ENST00000380152		861	cAa/ca	11/27	1	2	FACETS	0.518	0.397	0.658	0.518	0.397	0.658	SUBCLONAL	1	TRUE	1	0.338984689598266	2		322	228	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467843	50467843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	71	267	0	ENST00000331340.3:c.1078C>T	p.Arg360Cys	p.R360C	ENST00000331340	NM_006060.4	360	Cgc/Tgc	8/8	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.338984689598266	2		267	408	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306553	41306553	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	52	370	0	ENST00000373198.4:c.1106del	p.Gly369ValfsTer28	p.G369Vfs*28	ENST00000373198	NM_133170.3	369	gGt/gt	7/32	1	2	FACETS	0.647	0.552	0.752	0.647	0.552	0.752	SUBCLONAL	1	TRUE	1	0.338984689598266	2		370	474	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248859	133248859	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149296223	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	62	397	3	ENST00000320574.5:c.1736G>A	p.Arg579His	p.R579H	ENST00000320574	NM_006231.2	579	cGc/cAc	16/49	1	2	FACETS	0.691	0.598	0.793	0.691	0.598	0.793	SUBCLONAL	1	TRUE	1	0.338984689598266	2		400	529	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230914	53230914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	97	182	0	ENST00000375401.3:c.1879C>T	p.Arg627Cys	p.R627C	ENST00000375401	NM_004187.3	627	Cgc/Tgc	14/26	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.338984689598266	1		182	330	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141545628	141545628	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	40	462	0	ENST00000220592.5:c.2210A>G	p.Asp737Gly	p.D737G	ENST00000220592	NM_012154.3	737	gAc/gGc	17/19	0.263180248177165	3	FACETS	0.365	0.302	0.436	0.183	0.151	0.218	SUBCLONAL	1	TRUE	1	0.338984689598266	3		462	756	SUCCESS
MET	4233	MSKCC	GRCh37	7	116413126	116413126	+	intron_variant	Intron	DEL	A	A	-	rs377420134	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	53	394	1	ENST00000397752.3:c.3028+1091del		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.928	0.795	1	0.928	0.795	1	CLONAL	1	TRUE	1	0.338984689598266	2		395	337	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222455	2222455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1251069640	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	66	391	1	ENST00000398665.3:c.3287C>T	p.Thr1096Met	p.T1096M	ENST00000398665	NM_032482.2	1096	aCg/aTg	24/28	1	2	FACETS	0.747	0.65	0.853	0.747	0.65	0.853	SUBCLONAL	1	TRUE	1	0.338984689598266	2		392	521	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347143	347143	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367788267	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	106	500	2	ENST00000262320.3:c.1868C>T	p.Ser623Leu	p.S623L	ENST00000262320	NM_003502.3	623	tCg/tTg	7/11	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.338984689598266	2		502	618	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306549	163306549	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753469318	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	31	289	0	ENST00000271452.3:c.346C>T	p.Arg116Trp	p.R116W	ENST00000271452	NM_145697.2	116	Cgg/Tgg	6/14	1	2	FACETS	1	0.83	1	1	0.83	1	CLONAL	1	TRUE	1	0.338984689598266	2		289	180	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023778	27023778	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	45	317	0	ENST00000324856.7:c.884T>G	p.Leu295Arg	p.L295R	ENST00000324856	NM_006015.4	295	cTc/cGc	1/20	1	2	FACETS	0.578	0.486	0.68	0.578	0.486	0.68	SUBCLONAL	1	TRUE	1	0.338984689598266	2		317	459	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444610	78444612	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	89	253	1	ENST00000370768.2:c.77_79del	p.Gly26del	p.G26del	ENST00000370768	NM_003902.3	26	gGAGtt/gtt	1/20	1	2	FACETS	0.941	0.836	1	0.941	0.836	1	CLONAL	1	TRUE	1	0.338984689598266	2		254	558	SUCCESS
FH	2271	MSKCC	GRCh37	1	241671944	241671944	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781682	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	46	351	0	ENST00000366560.3:c.697C>T	p.Arg233Cys	p.R233C	ENST00000366560	NM_000143.3	233	Cgt/Tgt	5/10	1	2	FACETS	0.72	0.608	0.843	0.72	0.608	0.843	SUBCLONAL	1	TRUE	1	0.338984689598266	2		351	377	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192149	108192149	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	26	297	0	ENST00000278616.4:c.6572+2T>C		p.X2191_splice	ENST00000278616	NM_000051.3	2191			1	2	FACETS	0.377	0.298	0.467	0.377	0.298	0.467	SUBCLONAL	1	TRUE	1	0.338984689598266	2		297	407	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383352	4383352	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	58	432	0	ENST00000261254.3:c.146A>C	p.Lys49Thr	p.K49T	ENST00000261254	NM_001759.3	49	aAg/aCg	1/5	1	2	FACETS	0.57	0.49	0.658	0.57	0.49	0.658	SUBCLONAL	1	TRUE	1	0.338984689598266	2		432	600	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256789	133256789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770323795	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	125	348	2	ENST00000320574.5:c.305C>T	p.Pro102Leu	p.P102L	ENST00000320574	NM_006231.2	102	cCg/cTg	4/49	1	2	FACETS	0.793	0.722	0.866	1	0.987	1	SUBCLONAL	2	TRUE	1	0.338984689598266	2		350	465	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987117	36987117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	44	414	0	ENST00000354822.5:c.572G>A	p.Arg191His	p.R191H	ENST00000354822	NM_001079668.2	191	cGc/cAc	3/3	0.242067539088183	1	FACETS	0.406	0.34	0.479	0.406	0.34	0.479	SUBCLONAL	1	TRUE	0	0.338984689598266	1		414	531	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680751	88680751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201252722	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	133	421	1	ENST00000360948.2:c.506G>A	p.Arg169His	p.R169H	ENST00000360948	NM_001012338.2	169	cGc/cAc	6/19	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.338984689598266	2		422	542	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727515	88727515	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	35	338	0	ENST00000360948.2:c.264G>A	p.Trp88Ter	p.W88*	ENST00000360948	NM_001012338.2	88	tgG/tgA	3/19	1	2	FACETS	0.442	0.362	0.532	0.442	0.362	0.532	SUBCLONAL	1	TRUE	1	0.338984689598266	2		338	467	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121604	2121604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746677177	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	86	407	1	ENST00000219476.3:c.1933G>A	p.Val645Ile	p.V645I	ENST00000219476	NM_000548.3	645	Gtc/Atc	18/42	1	2	FACETS	0.846	0.749	0.949	0.846	0.749	0.949	CLONAL	1	TRUE	1	0.338984689598266	2		408	600	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020477	14020477	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145402255	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	40	307	0	ENST00000311895.7:c.448C>T	p.Arg150Cys	p.R150C	ENST00000311895	NM_005236.2	150	Cgc/Tgc	3/11	1	2	FACETS	0.659	0.549	0.781	0.659	0.549	0.781	SUBCLONAL	1	TRUE	1	0.338984689598266	2		307	358	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832571	72832571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764024381	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	37	218	0	ENST00000268489.5:c.4010G>A	p.Ser1337Asn	p.S1337N	ENST00000268489	NM_006885.3	1337	aGc/aAc	9/10	1	2	FACETS	0.689	0.569	0.821	0.689	0.569	0.821	SUBCLONAL	1	TRUE	1	0.338984689598266	2		218	317	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512359	38512359	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	97	273	0	ENST00000254066.5:c.1270A>C	p.Ser424Arg	p.S424R	ENST00000254066	NM_000964.3	424	Agc/Cgc	9/9	0.264294782222109	2	FACETS	0.788	0.709	0.871	0.788	0.709	0.871	SUBCLONAL	2	TRUE	0	0.338984689598266	2		273	363	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395793	45395793	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1404495202	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	36	204	0	ENST00000262160.6:c.341G>A	p.Arg114His	p.R114H	ENST00000262160	NM_005901.5	114	cGt/cAt	4/11	1	2	FACETS	0.889	0.736	1	0.889	0.736	1	CLONAL	1	TRUE	1	0.338984689598266	2		204	239	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207609	2207609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	107	492	4	ENST00000398665.3:c.893C>T	p.Pro298Leu	p.P298L	ENST00000398665	NM_032482.2	298	cCc/cTc	11/28	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.338984689598266	2		496	569	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7174672	7174672	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759347211	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	92	382	0	ENST00000302850.5:c.1045G>A	p.Asp349Asn	p.D349N	ENST00000302850	NM_000208.2	349	Gac/Aac	4/22	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.338984689598266	2		382	543	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249229	10249229	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766051225	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	45	315	1	ENST00000340748.4:c.3953C>T	p.Ala1318Val	p.A1318V	ENST00000340748		1318	gCg/gTg	34/40	1	2	FACETS	0.562	0.473	0.662	0.562	0.473	0.662	SUBCLONAL	1	TRUE	1	0.338984689598266	2		316	472	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097602	11097602	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs757327891	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	85	479	0	ENST00000358026.2:c.782C>A	p.Pro261His	p.P261H	ENST00000358026	NM_001128849.1	261	cCt/cAt	5/36	1	2	FACETS	0.912	0.808	1	0.912	0.808	1	CLONAL	1	TRUE	1	0.338984689598266	2		479	550	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130370	11130370	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	97	445	1	ENST00000358026.2:c.2609T>A	p.Leu870His	p.L870H	ENST00000358026	NM_001128849.1	870	cTc/cAc	18/36	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.338984689598266	2		446	559	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966799	18966799	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1427738876	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	103	542	1	ENST00000262803.5:c.1610C>T	p.Thr537Met	p.T537M	ENST00000262803	NM_002911.3	537	aCg/aTg	12/24	1	2	FACETS	0.947	0.848	1	0.947	0.848	1	CLONAL	1	TRUE	1	0.338984689598266	2		543	642	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753821	42753821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755151370	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	129	572	0	ENST00000222329.4:c.443C>T	p.Thr148Met	p.T148M	ENST00000222329	NM_006494.2	148	aCg/aTg	4/4	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.338984689598266	2		572	753	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009121	27009126	+	inframe_deletion	In_Frame_Del	DEL	CCCGAC	CCCGAC	-	novel	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	51	140	0	ENST00000335756.4:c.66_71del	p.Thr23_Pro24del	p.T23_P24del	ENST00000335756	NM_001809.3	19	agCCCGACc/agc	1/5	0.338984689598266	1	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	0	0.338984689598266	1		140	237	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657036	47657037	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	66	299	0	ENST00000233146.2:c.1235dup	p.Asn412LysfsTer5	p.N412Kfs*5	ENST00000233146	NM_000251.2	411	ata/atAa	7/16	0.338984689598266	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.338984689598266	1		299	287	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156098	99156098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs541626439	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	132	334	0	ENST00000074304.5:c.778C>T	p.Arg260Trp	p.R260W	ENST00000074304	NM_001134224.1	260	Cgg/Tgg	10/26	0.338984689598266	3	FACETS	0.799	0.728	0.873			1	SUBCLONAL	2	TRUE	NA	0.338984689598266	3		334	570	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728832	190728833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	30	304	0	ENST00000441310.2:c.2224dup	p.Thr742AsnfsTer10	p.T742Nfs*10	ENST00000441310	NM_000534.4	740	-/A	10/13	1	2	FACETS	0.694	0.562	0.843	0.694	0.562	0.843	SUBCLONAL	1	TRUE	1	0.338984689598266	2		304	255	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572366	41572366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	53	374	2	ENST00000263253.7:c.4895C>T	p.Thr1632Met	p.T1632M	ENST00000263253	NM_001429.3	1632	aCg/aTg	30/31	1	2	FACETS	0.671	0.573	0.778	0.671	0.573	0.778	SUBCLONAL	1	TRUE	1	0.338984689598266	2		376	466	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31511154	31511154	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367768426	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	85	372	2	ENST00000344624.3:c.1420G>A	p.Asp474Asn	p.D474N	ENST00000344624		474	Gat/Aat	6/33	1	2	FACETS	0.825	0.73	0.926	0.825	0.73	0.926	CLONAL	1	TRUE	1	0.338984689598266	2		374	608	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903745	41903745	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764155094	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	162	408	2	ENST00000372991.4:c.812G>A	p.Arg271Gln	p.R271Q	ENST00000372991	NM_001760.3	271	cGg/cAg	5/5	0.263180248177165	3	FACETS	0.904	0.833	0.978	0.904	0.833	0.978	CLONAL	2	TRUE	1	0.338984689598266	3		410	618	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521860	157521860	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746412839	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	32	314	0	ENST00000346085.5:c.4132G>A	p.Gly1378Ser	p.G1378S	ENST00000346085	NM_020732.3	1378	Ggc/Agc	18/20	1	2	FACETS	0.441	0.358	0.535	0.441	0.358	0.535	SUBCLONAL	1	TRUE	1	0.338984689598266	2		314	428	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730014	41730014	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	57	355	0	ENST00000242208.4:c.515C>A	p.Thr172Asn	p.T172N	ENST00000242208	NM_002192.2	172	aCc/aAc	3/3	1	2	FACETS	0.693	0.596	0.8	0.693	0.596	0.8	SUBCLONAL	1	TRUE	1	0.338984689598266	2		355	485	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189058	38189058	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	48	398	0	ENST00000317025.8:c.956G>T	p.Arg319Met	p.R319M	ENST00000317025	NM_023034.1	319	aGg/aTg	5/24	1	2	FACETS	0.554	0.468	0.649	0.554	0.468	0.649	SUBCLONAL	1	TRUE	1	0.338984689598266	2		398	511	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089865	5089865	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0026285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	57	200	0	ENST00000381652.3:c.2761+2T>C		p.X921_splice	ENST00000381652	NM_004972.3	921			0.274921601174206	2	FACETS	0.837	0.729	0.95	0.837	0.729	0.95	CLONAL	2	TRUE	0	0.338984689598266	2		200	201	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022430	12022431	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	48	415	0	ENST00000396373.4:c.537dup	p.His180AlafsTer16	p.H180Afs*16	ENST00000396373	NM_001987.4	179	ttg/ttGg	5/8	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		415	609	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593607	55593608	+	protein_altering_variant	In_Frame_Ins	INS	-	-	TCC	novel	NA	P-0026287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	162	321	0	ENST00000288135.5:c.1673_1674insTCC	p.Lys558delinsAsnPro	p.K558delinsNP	ENST00000288135	NM_000222.2	558	aag/aaTCCg	11/21	0.820407456919832	4	FACETS	0.895	0.831	0.96	0.895	0.831	0.96	CLONAL	2	TRUE	2	0.833837660293627	4		321	398	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164360	47164360	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	127	204	0	ENST00000409792.3:c.1766del	p.Ser589IlefsTer12	p.S589Ifs*12	ENST00000409792	NM_014159.6	589	aGt/at	3/21	0.833837660293627	3	FACETS	0.93	0.864	0.996	0.93	0.864	0.996	CLONAL	2	TRUE	1	0.833837660293627	3		204	232	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0026289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	33	334	2	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.123249151164987	3	FACETS	0.914	0.745	1	0.457	0.372	0.553	CLONAL	1	TRUE	1	0.2	3		336	397	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205781	108205781	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	29	264	0	ENST00000278616.4:c.8096C>T	p.Pro2699Leu	p.P2699L	ENST00000278616	NM_000051.3	2699	cCa/cTa	55/63	1	2	FACETS	0.817	0.656	0.999	0.817	0.656	0.999	CLONAL	1	TRUE	1	0.2	2		264	355	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602293	10602293	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	83	346	0	ENST00000171111.5:c.1285G>T	p.Gly429Cys	p.G429C	ENST00000171111	NM_203500.1	429	Ggc/Tgc	3/6	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.2	2		346	746	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074036	8074036	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	23	223	0	ENST00000377482.5:c.623A>T	p.Asn208Ile	p.N208I	ENST00000377482	NM_018948.3	208	aAc/aTc	4/4	1	2	FACETS	0.635	0.495	0.798	0.635	0.495	0.798	SUBCLONAL	1	TRUE	1	0.2	2		223	362	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631132	69631132	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	45	354	0	ENST00000334134.2:c.280G>T	p.Gly94Trp	p.G94W	ENST00000334134	NM_005247.2	94	Ggg/Tgg	2/3	1	2	FACETS	0.622	0.522	0.734	0.622	0.522	0.734	SUBCLONAL	1	TRUE	1	0.2	2		354	723	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37882851	37882851	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	64	362	2	ENST00000269571.5:c.2909G>T	p.Arg970Leu	p.R970L	ENST00000269571		970	cGg/cTg	24/27	0.123249151164987	3	FACETS	0.868	0.75	0.996	0.434	0.375	0.498	CLONAL	1	TRUE	1	0.2	3		364	811	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147573	47147573	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	21	205	0	ENST00000409792.3:c.4753G>T	p.Asp1585Tyr	p.D1585Y	ENST00000409792	NM_014159.6	1585	Gat/Tat	6/21	1	2	FACETS	0.502	0.386	0.639	0.502	0.386	0.639	SUBCLONAL	1	TRUE	1	0.2	2		205	418	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259025	89259025	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	14	84	0	ENST00000336596.2:c.169G>C	p.Gly57Arg	p.G57R	ENST00000336596	NM_005233.5	57	Ggt/Cgt	3/17	1	2	FACETS	0.765	0.554	1	0.765	0.554	1	CLONAL	1	TRUE	1	0.2	2		84	183	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401621	401621	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780902340	NA	P-0026289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	49	295	2	ENST00000380956.4:c.943G>A	p.Val315Met	p.V315M	ENST00000380956	NM_001195286.1	315	Gtg/Atg	7/9	0.3	3	FACETS	0.865	0.732	1	0.433	0.366	0.506	CLONAL	1	TRUE	1	0.2	3		297	623	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197091	26197091	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	84	218	0	ENST00000356476.2:c.388C>A	p.Arg130Ser	p.R130S	ENST00000356476		130	Cgc/Agc	1/1	0.3	3	FACETS	0.752	0.665	0.846	0.752	0.665	0.846	SUBCLONAL	2	TRUE	1	0.2	3		218	614	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392062	81392062	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	18	173	0	ENST00000222390.5:c.215A>T	p.Asn72Ile	p.N72I	ENST00000222390	NM_000601.4	72	aAt/aTt	2/18	1	2	FACETS	0.627	0.472	0.81	0.627	0.472	0.81	SUBCLONAL	1	TRUE	1	0.2	2		173	287	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521352	8521352	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	43	252	0	ENST00000356435.5:c.886C>A	p.Gln296Lys	p.Q296K	ENST00000356435		296	Cag/Aag	9/35	1	2	FACETS	0.863	0.722	1	0.863	0.722	1	CLONAL	1	TRUE	1	0.2	2		252	498	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0026291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	50	177	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.879	0.763	1	0.879	0.763	1	CLONAL	1	TRUE	1	0.789640635007675	2		177	144	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106916	27106917	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0026291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	52	259	0	ENST00000324856.7:c.6527_6528del	p.Gln2176ArgfsTer48	p.Q2176Rfs*48	ENST00000324856	NM_006015.4	2176	cAG/c	20/20	1	2	FACETS	0.392	0.335	0.454	0.392	0.335	0.454	SUBCLONAL	1	TRUE	1	0.789640635007675	2		259	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579383	7579383	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	551	430	0	ENST00000269305.4:c.304del	p.Thr102ProfsTer21	p.T102Pfs*21	ENST00000269305	NM_001126112.2	102	Acc/cc	4/11	0.789640635007675	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.789640635007675	2		430	676	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854978	76854979	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	184	226	0	ENST00000373344.5:c.5857_5858insT	p.Glu1953ValfsTer4	p.E1953Vfs*4	ENST00000373344	NM_000489.3	1953	gaa/gTaa	25/35	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.789640635007675	1		226	250	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854894	76854895	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0026291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	14	179	0	ENST00000373344.5:c.5941_5942del	p.Leu1981LysfsTer6	p.L1981Kfs*6	ENST00000373344	NM_000489.3	1981	TTa/a	25/35	1	1	FACETS	0.1	0.072	0.134	0.1	0.072	0.134	SUBCLONAL	1	TRUE	0	0.789640635007675	1		179	215	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0026292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	192	497	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.314209727191368	3	FACETS	0.972	0.903	1	0.972	0.903	1	CLONAL	2	TRUE	1	0.355107372334966	3		497	655	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576433	67576433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	43	319	0	ENST00000274335.5:c.712C>T	p.Leu238Phe	p.L238F	ENST00000274335		238	Ctt/Ttt	5/15	0.355107372334966	3	FACETS	0.519	0.433	0.613	0.259	0.216	0.307	SUBCLONAL	1	TRUE	1	0.355107372334966	3		319	550	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039401	47039401	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	139	333	0	ENST00000377604.3:c.1025del	p.Asn342ThrfsTer143	p.N342Tfs*143	ENST00000377604	NM_001204468.1	342	Aac/ac	10/24	0.314209727191368	3	FACETS	0.886	0.812	0.964	0.886	0.812	0.964	CLONAL	2	TRUE	1	0.355107372334966	3		333	520	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0026293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	419	497	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.71829581453063	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.731435088560847	3		497	689	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175942	176175942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs964768927	NA	P-0026293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	40	55	0	ENST00000367669.3:c.173C>T	p.Ser58Leu	p.S58L	ENST00000367669	NM_022457.5	58	tCg/tTg	1/20	0.39257948860728	3	FACETS	1	0.96	1	0.718	0.615	0.825	INDETERMINATE	1	TRUE	1	0.731435088560847	3		55	104	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721024	176721024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	64	285	2	ENST00000439151.2:c.6655C>T	p.Arg2219Cys	p.R2219C	ENST00000439151	NM_022455.4	2219	Cgt/Tgt	23/23	0.71829581453063	3	FACETS	0.462	0.401	0.529	0.231	0.2	0.265	SUBCLONAL	1	TRUE	1	0.731435088560847	3		287	517	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834148	156834148	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs758965412	NA	P-0026293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1452	80	444	0	ENST00000524377.1:c.215A>G	p.Tyr72Cys	p.Y72C	ENST00000524377	NM_002529.3	72	tAc/tGc	2/17	0.731435088560847	6	FACETS	0.352	0.308	0.399	0.07	0.061	0.08	SUBCLONAL	1	TRUE	1	0.731435088560847	6		444	1532	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924319	11924319	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0026293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	87	122	0	ENST00000353533.5:c.115+1G>T		p.X39_splice	ENST00000353533	NM_003010.3	39			0.712630962736689	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.731435088560847	1		122	137	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241659	55241659	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	419	383	0	ENST00000275493.2:c.2107C>G	p.Leu703Val	p.L703V	ENST00000275493	NM_005228.3	703	Ctc/Gtc	18/28	0.71829581453063	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.731435088560847	3		383	723	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0026295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	20	497	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.239	0.182	0.307	0.239	0.182	0.307	SUBCLONAL	1	TRUE	1	0.27	2		497	620	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985881	60985881	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	43	284	1	ENST00000333681.4:c.19A>T	p.Thr7Ser	p.T7S	ENST00000333681		7	Aca/Tca	2/3	1	2	FACETS	0.642	0.537	0.759	0.642	0.537	0.759	SUBCLONAL	1	TRUE	1	0.27	2		285	496	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	85	501	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.300141899918666	3	FACETS	1	0.9	1	1	0.9	1	CLONAL	2	TRUE	1	0.31	3		501	314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0026296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	112	406	0	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	0.300141899918666	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.31	1		406	479	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167577	NA	P-0026296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	67	182	0	ENST00000257430.4:c.4463del	p.Leu1488TyrfsTer19	p.L1488Yfs*19	ENST00000257430	NM_000038.5	1487	acT/ac	16/16	0.300141899918666	3	FACETS	1	0.955	1	0.781	0.69	0.877	CLONAL	2	TRUE	0	0.31	3		182	213	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858477	57858477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760192848	NA	P-0026296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	141	302	0	ENST00000228682.2:c.215G>A	p.Arg72Gln	p.R72Q	ENST00000228682	NM_005269.2	72	cGg/cAg	4/12	0.300141899918666	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.31	3		302	440	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117788	70117788	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	125	366	0	ENST00000245479.2:c.256T>C	p.Trp86Arg	p.W86R	ENST00000245479	NM_000346.3	86	Tgg/Cgg	1/3	0.300141899918666	3	FACETS	1	0.916	1	1	0.916	1	CLONAL	2	TRUE	1	0.31	3		366	463	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119913	70119914	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0026296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	61	313	0	ENST00000245479.2:c.917_918dup	p.Pro307CysfsTer77	p.P307Cfs*77	ENST00000245479	NM_000346.3	305	-/GT	3/3	0.300141899918666	3	FACETS	1	0.882	1	0.511	0.442	0.586	CLONAL	1	TRUE	1	0.31	3		313	445	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120337	70120338	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACTCC	novel	NA	P-0026296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	257	655	0	ENST00000245479.2:c.1341_1345dup	p.Ser449ThrfsTer23	p.S449Tfs*23	ENST00000245479	NM_000346.3	447	aac/aACTCCac	3/3	0.300141899918666	3	FACETS	0.916	0.858	0.976	0.916	0.858	0.976	CLONAL	2	TRUE	1	0.31	3		655	1045	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512365	149512365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375484098	NA	P-0026296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	272	366	0	ENST00000261799.4:c.1075G>A	p.Asp359Asn	p.D359N	ENST00000261799	NM_002609.3	359	Gac/Aac	7/23	0.300141899918666	3	FACETS	0.895	0.849	0.942	1	0.99	1	CLONAL	4	TRUE	0	0.31	3		366	566	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378351	225378351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	100	178	0	ENST00000264414.4:c.544G>A	p.Ala182Thr	p.A182T	ENST00000264414	NM_003590.4	182	Gca/Aca	5/16	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.733822532449766	2		178	248	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876343	35876343	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200570812	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	172	296	0	ENST00000303115.3:c.1135G>A	p.Ala379Thr	p.A379T	ENST00000303115	NM_002185.3	379	Gcc/Acc	8/8	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.733822532449766	2		296	447	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	169	416	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.802	0.742	0.865	0.802	0.742	0.865	CLONAL	1	TRUE	1	0.733822532449766	2		416	574	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58711261	58711261	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571290585	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	178	382	0	ENST00000305921.3:c.749G>A	p.Arg250Gln	p.R250Q	ENST00000305921	NM_003620.3	250	cGa/cAa	3/6	1	2	FACETS	0.88	0.817	0.946	0.88	0.817	0.946	CLONAL	1	TRUE	1	0.733822532449766	2		382	551	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212088	5212088	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	174	417	0	ENST00000357368.4:c.4943C>T	p.Ala1648Val	p.A1648V	ENST00000357368	NM_002850.3	1648	gCc/gTc	32/38	1	2	FACETS	0.853	0.79	0.917	0.853	0.79	0.917	CLONAL	1	TRUE	1	0.733822532449766	2		417	556	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144150	11144150	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502060	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	202	379	0	ENST00000358026.2:c.3731G>A	p.Arg1244His	p.R1244H	ENST00000358026	NM_001128849.1	1244	cGc/cAc	26/36	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.733822532449766	2		379	550	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	198	413	0	ENST00000269305.4:c.859G>T	p.Glu287Ter	p.E287*	ENST00000269305	NM_001126112.2	287	Gag/Tag	8/11	1	2	FACETS	0.895	0.834	0.957	0.895	0.834	0.957	CLONAL	1	TRUE	1	0.733822532449766	2		413	603	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994790	73994790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs562558740	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	154	393	1	ENST00000318443.5:c.274C>T	p.Arg92Cys	p.R92C	ENST00000318443	NM_001024736.1	92	Cgc/Tgc	3/10	0.700271663806496	2	FACETS	0.889	0.82	0.96	0.445	0.41	0.48	CLONAL	1	TRUE	0	0.733822532449766	2		394	472	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293767	1293767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34094720	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	237	456	0	ENST00000310581.5:c.1234C>T	p.His412Tyr	p.H412Y	ENST00000310581	NM_198253.2	412	Cac/Tac	2/16	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.733822532449766	2		456	633	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788617	3788617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519884	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	153	291	0	ENST00000262367.5:c.4337G>A	p.Arg1446His	p.R1446H	ENST00000262367	NM_004380.2	1446	cGc/cAc	26/31	1	2	FACETS	0.931	0.859	1	0.931	0.859	1	CLONAL	1	TRUE	1	0.733822532449766	2		291	448	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	141	475	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.933	0.858	1	0.933	0.858	1	CLONAL	1	TRUE	1	0.733822532449766	2		475	412	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015293	128015293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770995913	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	127	259	0	ENST00000285398.2:c.2228G>A	p.Arg743His	p.R743H	ENST00000285398	NM_000122.1	743	cGc/cAc	15/15	1	2	FACETS	0.975	0.894	1	0.975	0.894	1	CLONAL	1	TRUE	1	0.733822532449766	2		259	355	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022652	12022652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200525003	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	164	281	0	ENST00000396373.4:c.758C>T	p.Pro253Leu	p.P253L	ENST00000396373	NM_001987.4	253	cCg/cTg	5/8	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.733822532449766	2		281	432	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047283	77047283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs972319037	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	137	302	0	ENST00000356341.3:c.1261C>T	p.Arg421Trp	p.R421W	ENST00000356341	NM_002576.4	421	Cgg/Tgg	13/15	1	2	FACETS	0.948	0.871	1	0.948	0.871	1	CLONAL	1	TRUE	1	0.733822532449766	2		302	394	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012603	36012603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	171	311	1	ENST00000358208.4:c.47G>A	p.Arg16His	p.R16H	ENST00000358208		16	cGc/cAc	2/12	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.733822532449766	2		312	451	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121076	11121076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1131691371	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	176	395	0	ENST00000358026.2:c.2143G>A	p.Asp715Asn	p.D715N	ENST00000358026	NM_001128849.1	715	Gat/Aat	15/36	1	2	FACETS	0.898	0.833	0.965	0.898	0.833	0.965	CLONAL	1	TRUE	1	0.733822532449766	2		395	534	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170814993	170814993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	85	268	0	ENST00000296930.5:c.41C>T	p.Pro14Leu	p.P14L	ENST00000296930	NM_002520.6	14	cCc/cTc	1/11	1	2	FACETS	0.822	0.735	0.911	0.822	0.735	0.911	CLONAL	1	TRUE	1	0.733822532449766	2		268	282	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144113	11144113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	223	419	1	ENST00000358026.2:c.3694G>A	p.Gly1232Ser	p.G1232S	ENST00000358026	NM_001128849.1	1232	Ggc/Agc	26/36	1	2	FACETS	0.948	0.888	1	0.948	0.888	1	CLONAL	1	TRUE	1	0.733822532449766	2		420	641	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650778	48650778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104894809	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	176	508	0	ENST00000376670.3:c.647G>A	p.Arg216Gln	p.R216Q	ENST00000376670	NM_002049.3	216	cGg/cAg	4/6	1	2	FACETS	0.977	0.908	1	0.977	0.908	1	CLONAL	1	TRUE	1	0.733822532449766	2		508	491	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749500	41749500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	165	429	1	ENST00000226382.2:c.295C>T	p.Arg99Trp	p.R99W	ENST00000226382	NM_003924.3	99	Cgg/Tgg	2/3	1	2	FACETS	0.92	0.851	0.99	0.92	0.851	0.99	CLONAL	1	TRUE	1	0.733822532449766	2		430	489	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254929	16254929	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs751475729	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	154	324	0	ENST00000375759.3:c.2194C>T	p.Arg732Ter	p.R732*	ENST00000375759	NM_015001.2	732	Cga/Tga	11/15	1	2	FACETS	0.853	0.787	0.922	0.853	0.787	0.922	CLONAL	1	TRUE	1	0.733822532449766	2		324	492	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247618	123247618	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1466101220	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	131	239	1	ENST00000358487.5:c.1873C>T	p.Arg625Ter	p.R625*	ENST00000358487	NM_000141.4	625	Cga/Tga	14/18	1	2	FACETS	0.888	0.814	0.965	0.888	0.814	0.965	CLONAL	1	TRUE	1	0.733822532449766	2		240	402	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919203	178919203	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	94	228	0	ENST00000263967.3:c.688C>T	p.Arg230Ter	p.R230*	ENST00000263967	NM_006218.2	230	Cga/Tga	4/21	1	2	FACETS	0.843	0.759	0.93	0.843	0.759	0.93	CLONAL	1	TRUE	1	0.733822532449766	2		228	304	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953730	48953730	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs3092891	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	104	153	0	ENST00000267163.4:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000267163	NM_000321.2	445	Cga/Tga	14/27	1	2	FACETS	0.954	0.866	1	0.954	0.866	1	CLONAL	1	TRUE	1	0.733822532449766	2		153	297	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725078	49725078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	225	427	0	ENST00000449682.2:c.266G>A	p.Ser89Asn	p.S89N	ENST00000449682	NM_020998.3	89	aGc/aAc	3/18	1	2	FACETS	0.973	0.912	1	0.973	0.912	1	CLONAL	1	TRUE	1	0.733822532449766	2		427	630	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921567	178921567	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553821144	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	91	180	0	ENST00000263967.3:c.1049A>G	p.Asp350Gly	p.D350G	ENST00000263967	NM_006218.2	350	gAc/gGc	5/21	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.733822532449766	2		180	248	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76931785	76931785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	137	309	0	ENST00000373344.5:c.3745G>A	p.Ala1249Thr	p.A1249T	ENST00000373344	NM_000489.3	1249	Gcc/Acc	10/35	1	2	FACETS	0.837	0.768	0.909	0.837	0.768	0.909	CLONAL	1	TRUE	1	0.733822532449766	2		309	446	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133308	30133308	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	163	353	2	ENST00000263025.4:c.190C>T	p.Arg64Cys	p.R64C	ENST00000263025	NM_002746.2	64	Cgc/Tgc	2/9	1	2	FACETS	0.926	0.857	0.996	0.926	0.857	0.996	CLONAL	1	TRUE	1	0.733822532449766	2		355	480	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741928	17741928	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	93	159	0	ENST00000250003.3:c.599C>A	p.Ser200Tyr	p.S200Y	ENST00000250003	NM_002478.4	200	tCc/tAc	1/3	1	2	FACETS	0.942	0.85	1	0.942	0.85	1	CLONAL	1	TRUE	1	0.733822532449766	2		159	269	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530162	63530162	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777885192	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	188	283	0	ENST00000307078.5:c.2273C>T	p.Ala758Val	p.A758V	ENST00000307078	NM_004655.3	758	gCg/gTg	10/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.733822532449766	2		283	450	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208051	5208051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1477222866	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	127	299	0	ENST00000357368.4:c.5660C>T	p.Thr1887Met	p.T1887M	ENST00000357368	NM_002850.3	1887	aCg/aTg	37/38	1	2	FACETS	0.946	0.866	1	0.946	0.866	1	CLONAL	1	TRUE	1	0.733822532449766	2		299	366	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944961	31944961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1441610501	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	160	318	2	ENST00000340398.3:c.140C>T	p.Ala47Val	p.A47V	ENST00000340398	NM_001013699.2	47	gCg/gTg	1/1	1	2	FACETS	0.982	0.909	1	0.982	0.909	1	CLONAL	1	TRUE	1	0.733822532449766	2		320	444	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972013	55972013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	134	304	0	ENST00000263923.4:c.1631C>T	p.Ser544Phe	p.S544F	ENST00000263923	NM_002253.2	544	tCc/tTc	12/30	1	2	FACETS	0.929	0.853	1	0.929	0.853	1	CLONAL	1	TRUE	1	0.733822532449766	2		304	393	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145645	11145645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	237	419	0	ENST00000358026.2:c.4007G>A	p.Arg1336His	p.R1336H	ENST00000358026	NM_001128849.1	1336	cGc/cAc	29/36	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.733822532449766	2		419	615	SUCCESS
RET	5979	MSKCC	GRCh37	10	43602002	43602002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754859905	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	209	488	1	ENST00000355710.3:c.1046C>T	p.Ala349Val	p.A349V	ENST00000355710	NM_020975.4	349	gCg/gTg	5/20	1	2	FACETS	0.937	0.875	1	0.937	0.875	1	CLONAL	1	TRUE	1	0.733822532449766	2		489	608	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244223	5244223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199851847	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	178	408	1	ENST00000357368.4:c.1259G>A	p.Arg420His	p.R420H	ENST00000357368	NM_002850.3	420	cGc/cAc	11/38	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.733822532449766	2		409	472	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871205	35871205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372676633	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	118	268	0	ENST00000303115.3:c.427G>A	p.Ala143Thr	p.A143T	ENST00000303115	NM_002185.3	143	Gcc/Acc	4/8	1	2	FACETS	0.748	0.68	0.819	0.748	0.68	0.819	SUBCLONAL	1	TRUE	1	0.733822532449766	2		268	430	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557908	187557908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113970444	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	146	289	0	ENST00000441802.2:c.3803G>A	p.Arg1268Gln	p.R1268Q	ENST00000441802	NM_005245.3	1268	cGg/cAg	5/27	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.733822532449766	2		289	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912664	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	193	384	1	ENST00000269305.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000269305	NM_001126112.2	337	cGc/cAc	10/11	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.733822532449766	2		385	519	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390606	139390606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1052013977	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	234	554	1	ENST00000277541.6:c.7585G>A	p.Val2529Ile	p.V2529I	ENST00000277541	NM_017617.3	2529	Gtc/Atc	34/34	1	2	FACETS	0.956	0.897	1	0.956	0.897	1	CLONAL	1	TRUE	1	0.733822532449766	2		555	667	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447384	187447384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780987785	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	198	333	0	ENST00000232014.4:c.809G>A	p.Arg270Gln	p.R270Q	ENST00000232014	NM_001130845.1	270	cGa/cAa	5/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.733822532449766	2		333	534	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575491	64575491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376872829	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	201	339	2	ENST00000312049.6:c.526G>A	p.Ala176Thr	p.A176T	ENST00000312049	NM_130799.2	176	Gcc/Acc	3/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.733822532449766	2		341	520	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735456	204735456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376038796	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	126	243	0	ENST00000302823.3:c.257C>T	p.Ala86Val	p.A86V	ENST00000302823	NM_005214.4	86	gCg/gTg	2/4	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.733822532449766	2		243	312	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891287	101891287	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757374917	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	173	383	0	ENST00000374994.4:c.248C>T	p.Pro83Leu	p.P83L	ENST00000374994	NM_004612.2	83	cCg/cTg	2/9	1	2	FACETS	0.832	0.77	0.895	0.832	0.77	0.895	CLONAL	1	TRUE	1	0.733822532449766	2		383	567	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730125	41730125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142519810	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	74	218	0	ENST00000242208.4:c.404C>T	p.Thr135Met	p.T135M	ENST00000242208	NM_002192.2	135	aCg/aTg	3/3	1	2	FACETS	0.767	0.68	0.858	0.767	0.68	0.858	SUBCLONAL	1	TRUE	1	0.733822532449766	2		218	263	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779578	3779578	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	280	596	0	ENST00000262367.5:c.5470G>A	p.Ala1824Thr	p.A1824T	ENST00000262367	NM_004380.2	1824	Gcc/Acc	31/31	1	2	FACETS	0.985	0.929	1	0.985	0.929	1	CLONAL	1	TRUE	1	0.733822532449766	2		596	775	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106327	27106327	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780084398	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	172	380	0	ENST00000324856.7:c.5938C>T	p.Arg1980Cys	p.R1980C	ENST00000324856	NM_006015.4	1980	Cgc/Tgc	20/20	1	2	FACETS	0.963	0.893	1	0.963	0.893	1	CLONAL	1	TRUE	1	0.733822532449766	2		380	487	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738094	145738094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561220929	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	216	573	2	ENST00000428558.2:c.2816C>T	p.Ala939Val	p.A939V	ENST00000428558	NM_004260.3	939	gCg/gTg	17/22	1	2	FACETS	0.861	0.804	0.919	0.861	0.804	0.919	CLONAL	1	TRUE	1	0.733822532449766	2		575	684	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861822	57861822	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	175	413	0	ENST00000228682.2:c.1123G>T	p.Asp375Tyr	p.D375Y	ENST00000228682	NM_005269.2	375	Gat/Tat	10/12	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.733822532449766	2		413	470	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630236	100630236	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs128620187	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	127	259	1	ENST00000308731.7:c.37C>T	p.Arg13Ter	p.R13*	ENST00000308731	NM_000061.2	13	Cga/Tga	2/19	1	2	FACETS	0.883	0.808	0.96	0.883	0.808	0.96	CLONAL	1	TRUE	1	0.733822532449766	2		260	392	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860787	45860787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760834335	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	150	365	1	ENST00000391945.4:c.1322C>T	p.Ser441Leu	p.S441L	ENST00000391945	NM_000400.3	441	tCg/tTg	14/23	1	2	FACETS	0.987	0.912	1	0.987	0.912	1	CLONAL	1	TRUE	1	0.733822532449766	2		366	414	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277885	41277885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1168206875	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	130	211	0	ENST00000349496.5:c.1849G>A	p.Val617Ile	p.V617I	ENST00000349496	NM_001904.3	617	Gtc/Atc	12/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.733822532449766	2		211	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578421	7578421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779000871	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	172	411	0	ENST00000269305.4:c.509C>T	p.Thr170Met	p.T170M	ENST00000269305	NM_001126112.2	170	aCg/aTg	5/11	1	2	FACETS	0.969	0.899	1	0.969	0.899	1	CLONAL	1	TRUE	1	0.733822532449766	2		411	484	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231774	36231774	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1569061768	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	231	430	0	ENST00000300305.3:c.610C>T	p.Arg204Ter	p.R204*	ENST00000300305		204	Cga/Tga	5/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.733822532449766	2		430	592	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820836	3820836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747877878	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	270	561	2	ENST00000262367.5:c.2615C>T	p.Thr872Met	p.T872M	ENST00000262367	NM_004380.2	872	aCg/aTg	14/31	1	2	FACETS	0.954	0.899	1	0.954	0.899	1	CLONAL	1	TRUE	1	0.733822532449766	2		563	771	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919548	78919548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769436510	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	147	263	0	ENST00000306801.3:c.3107C>T	p.Pro1036Leu	p.P1036L	ENST00000306801	NM_020761.2	1036	cCg/cTg	26/34	1	2	FACETS	0.968	0.893	1	0.968	0.893	1	CLONAL	1	TRUE	1	0.733822532449766	2		263	414	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276310	15276310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369768722	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	205	418	3	ENST00000263388.2:c.5684G>A	p.Arg1895His	p.R1895H	ENST00000263388	NM_000435.2	1895	cGc/cAc	31/33	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.733822532449766	2		421	538	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138145	64138145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757839757	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	199	439	1	ENST00000334205.4:c.2068G>A	p.Val690Met	p.V690M	ENST00000334205	NM_003942.2	690	Gtg/Atg	16/17	1	2	FACETS	0.983	0.917	1	0.983	0.917	1	CLONAL	1	TRUE	1	0.733822532449766	2		440	552	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107008	27107008	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	28	258	1	ENST00000324856.7:c.6619C>T	p.Gln2207Ter	p.Q2207*	ENST00000324856	NM_006015.4	2207	Cag/Tag	20/20	1	2	FACETS	0.178	0.142	0.22	0.178	0.142	0.22	SUBCLONAL	1	TRUE	1	0.733822532449766	2		259	428	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542357	187542357	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs769432838	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	84	215	1	ENST00000441802.2:c.5383C>T	p.Arg1795Ter	p.R1795*	ENST00000441802	NM_005245.3	1795	Cga/Tga	10/27	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.733822532449766	2		216	227	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495736	56495736	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747453114	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	139	293	0	ENST00000267101.3:c.3926G>A	p.Arg1309His	p.R1309H	ENST00000267101	NM_001982.3	1309	cGc/cAc	28/28	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.733822532449766	2		293	348	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430798	47430798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776912006	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	249	429	1	ENST00000377045.4:c.1763G>A	p.Arg588His	p.R588H	ENST00000377045	NM_001654.4	588	cGc/cAc	16/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.733822532449766	2		430	620	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828129	243828129	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	143	307	0	ENST00000263826.5:c.229C>A	p.Leu77Ile	p.L77I	ENST00000263826	NM_005465.4	77	Ctc/Atc	3/13	0.733822532449766	3	FACETS	0.898	0.822	0.977	0.449	0.411	0.489	CLONAL	1	TRUE	1	0.733822532449766	3		307	593	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277225	41277225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760837728	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	109	184	0	ENST00000349496.5:c.1694G>A	p.Arg565His	p.R565H	ENST00000349496	NM_001904.3	565	cGc/cAc	11/15	1	2	FACETS	0.977	0.89	1	0.977	0.89	1	CLONAL	1	TRUE	1	0.733822532449766	2		184	304	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493772	56493772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370221639	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	195	373	0	ENST00000267101.3:c.3088G>A	p.Ala1030Thr	p.A1030T	ENST00000267101	NM_001982.3	1030	Gcc/Acc	25/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.733822532449766	2		373	471	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612244	1612244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1325068914	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	161	299	0	ENST00000344749.5:c.1775C>T	p.Ala592Val	p.A592V	ENST00000344749	NM_001136139.2	592	gCc/gTc	18/19	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.733822532449766	2		299	427	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231238	98231238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1366288601	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	184	404	0	ENST00000331920.6:c.2045G>A	p.Arg682His	p.R682H	ENST00000331920	NM_000264.3	682	cGc/cAc	14/24	1	2	FACETS	0.865	0.803	0.928	0.865	0.803	0.928	CLONAL	1	TRUE	1	0.733822532449766	2		404	580	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368254	31368254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751741367	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	176	337	0	ENST00000328111.2:c.125G>A	p.Arg42His	p.R42H	ENST00000328111	NM_006892.3	42	cGc/cAc	2/23	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.733822532449766	2		337	437	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027661	48027661	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	100	174	0	ENST00000234420.5:c.2539G>T	p.Glu847Ter	p.E847*	ENST00000234420	NM_000179.2	847	Gaa/Taa	4/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.733822532449766	2		174	239	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628841	187628841	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200579335	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	176	374	2	ENST00000441802.2:c.2141C>T	p.Pro714Leu	p.P714L	ENST00000441802	NM_005245.3	714	cCg/cTg	2/27	1	2	FACETS	0.852	0.79	0.916	0.852	0.79	0.916	CLONAL	1	TRUE	1	0.733822532449766	2		376	563	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288785	33288785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765273333	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	115	229	0	ENST00000374542.5:c.767G>A	p.Arg256His	p.R256H	ENST00000374542	NM_001141970.1	256	cGc/cAc	3/8	1	2	FACETS	0.922	0.84	1	0.922	0.84	1	CLONAL	1	TRUE	1	0.733822532449766	2		229	340	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310916	123310916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	175	319	0	ENST00000358487.5:c.512C>T	p.Ala171Val	p.A171V	ENST00000358487	NM_000141.4	171	gCg/gTg	5/18	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.733822532449766	2		319	471	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914815	32914815	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35029074	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	123	300	0	ENST00000380152.3:c.6323G>A	p.Arg2108His	p.R2108H	ENST00000380152		2108	cGt/cAt	11/27	1	2	FACETS	0.808	0.737	0.881	0.808	0.737	0.881	CLONAL	1	TRUE	1	0.733822532449766	2		300	415	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856283	111856283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1420086510	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	17	21	1	ENST00000341259.2:c.334G>A	p.Ala112Thr	p.A112T	ENST00000341259	NM_005475.2	112	Gcc/Acc	2/8	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.733822532449766	2		22	36	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153601	108153601	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	78	97	0	ENST00000278616.4:c.3741C>A	p.Phe1247Leu	p.F1247L	ENST00000278616	NM_000051.3	1247	ttC/ttA	25/63	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.733822532449766	2		97	199	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288474	21288474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749456958	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	188	348	0	ENST00000354336.3:c.719C>T	p.Ala240Val	p.A240V	ENST00000354336	NM_005207.3	240	gCg/gTg	2/3	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.733822532449766	2		348	500	SUCCESS
APC	324	MSKCC	GRCh37	5	112176873	112176873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	141	244	0	ENST00000257430.4:c.5582C>T	p.Ser1861Phe	p.S1861F	ENST00000257430	NM_000038.5	1861	tCt/tTt	16/16	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.733822532449766	2		244	384	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933872	39933872	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1274186244	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	233	454	2	ENST00000378444.4:c.727C>T	p.Arg243Cys	p.R243C	ENST00000378444	NM_001123385.1	243	Cgc/Tgc	4/15	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.733822532449766	2		456	632	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347553	118347553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555037629	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	142	252	0	ENST00000534358.1:c.3190C>T	p.Arg1064Ter	p.R1064*	ENST00000534358	NM_005933.3	1064	Cga/Tga	4/36	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.733822532449766	2		252	383	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875634	35875634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	154	281	0	ENST00000303115.3:c.821C>T	p.Pro274Leu	p.P274L	ENST00000303115	NM_002185.3	274	cCc/cTc	7/8	1	2	FACETS	0.978	0.904	1	0.978	0.904	1	CLONAL	1	TRUE	1	0.733822532449766	2		281	429	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961688	41961688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	121	302	1	ENST00000219905.7:c.596G>A	p.Arg199His	p.R199H	ENST00000219905	NM_001164273.1	199	cGt/cAt	2/24	0.700271663806496	2	FACETS	0.861	0.786	0.939	0.431	0.393	0.47	CLONAL	1	TRUE	0	0.733822532449766	2		303	383	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456597	32456597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	45	65	0	ENST00000332351.3:c.295G>A	p.Ala99Thr	p.A99T	ENST00000332351	NM_024426.4	99	Gcg/Acg	1/10	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.733822532449766	2		65	122	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720857	89720857	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	158	268	0	ENST00000371953.3:c.1008C>A	p.Tyr336Ter	p.Y336*	ENST00000371953	NM_000314.4	336	taC/taA	8/9	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.733822532449766	2		268	378	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456365	32456365	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	209	455	1	ENST00000332351.3:c.527G>A	p.Arg176His	p.R176H	ENST00000332351	NM_024426.4	176	cGc/cAc	1/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.733822532449766	2		456	556	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228979	36228979	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555734923	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	175	612	3	ENST00000222270.7:c.7759C>T	p.Arg2587Ter	p.R2587*	ENST00000222270	NM_014727.1	2587	Cga/Tga	36/37	1	2	FACETS	0.91	0.844	0.978	0.91	0.844	0.978	CLONAL	1	TRUE	1	0.733822532449766	2		615	524	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509138	106509138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753981231	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	155	325	2	ENST00000359195.3:c.1132G>A	p.Asp378Asn	p.D378N	ENST00000359195	NM_002649.2	378	Gac/Aac	2/11	1	2	FACETS	0.943	0.871	1	0.943	0.871	1	CLONAL	1	TRUE	1	0.733822532449766	2		327	448	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36024634	36024634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867236697	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	233	474	4	ENST00000358208.4:c.623G>A	p.Arg208His	p.R208H	ENST00000358208		208	cGc/cAc	6/12	1	2	FACETS	0.982	0.921	1	0.982	0.921	1	CLONAL	1	TRUE	1	0.733822532449766	2		478	647	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399216	139399216	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs566680728	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	185	381	0	ENST00000277541.6:c.4927G>A	p.Ala1643Thr	p.A1643T	ENST00000277541	NM_017617.3	1643	Gcc/Acc	26/34	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.733822532449766	2		381	472	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793286	242793286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757334336	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	168	474	0	ENST00000334409.5:c.791G>A	p.Arg264His	p.R264H	ENST00000334409	NM_005018.2	264	cGc/cAc	5/5	1	2	FACETS	0.908	0.841	0.977	0.908	0.841	0.977	CLONAL	1	TRUE	1	0.733822532449766	2		474	504	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47672741	47672741	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs557339938	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	156	362	1	ENST00000233146.2:c.1331G>A	p.Arg444His	p.R444H	ENST00000233146	NM_000251.2	444	cGt/cAt	8/16	1	2	FACETS	0.924	0.854	0.996	0.924	0.854	0.996	CLONAL	1	TRUE	1	0.733822532449766	2		363	460	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512332	149512332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200684708	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	143	285	0	ENST00000261799.4:c.1108C>T	p.Arg370Cys	p.R370C	ENST00000261799	NM_002609.3	370	Cgc/Tgc	7/23	1	2	FACETS	0.932	0.858	1	0.932	0.858	1	CLONAL	1	TRUE	1	0.733822532449766	2		285	418	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149516600	149516600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144923639	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	174	420	1	ENST00000261799.4:c.11C>T	p.Pro4Leu	p.P4L	ENST00000261799	NM_002609.3	4	cCg/cTg	2/23	1	2	FACETS	0.88	0.816	0.946	0.88	0.816	0.946	CLONAL	1	TRUE	1	0.733822532449766	2		421	539	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631362	117631362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150262256	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	128	245	0	ENST00000368508.3:c.6316G>A	p.Ala2106Thr	p.A2106T	ENST00000368508	NM_002944.2	2106	Gcc/Acc	40/43	1	2	FACETS	0.906	0.83	0.985	0.906	0.83	0.985	CLONAL	1	TRUE	1	0.733822532449766	2		245	385	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498444	89498444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	96	234	0	ENST00000336596.2:c.2416G>A	p.Asp806Asn	p.D806N	ENST00000336596	NM_005233.5	806	Gat/Aat	14/17	1	2	FACETS	0.833	0.751	0.919	0.833	0.751	0.919	CLONAL	1	TRUE	1	0.733822532449766	2		234	314	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245539	16245539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1471081719	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	120	327	0	ENST00000375759.3:c.1514G>A	p.Arg505His	p.R505H	ENST00000375759	NM_015001.2	505	cGc/cAc	7/15	1	2	FACETS	0.768	0.699	0.839	0.768	0.699	0.839	SUBCLONAL	1	TRUE	1	0.733822532449766	2		327	426	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086209	16086209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	162	269	0	ENST00000281043.3:c.1385G>A	p.Arg462Gln	p.R462Q	ENST00000281043	NM_005378.4	462	cGg/cAg	3/3	1	2	FACETS	0.973	0.901	1	0.973	0.901	1	CLONAL	1	TRUE	1	0.733822532449766	2		269	454	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430729	47430729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	176	355	0	ENST00000377045.4:c.1694C>T	p.Ala565Val	p.A565V	ENST00000377045	NM_001654.4	565	gCc/gTc	16/16	1	2	FACETS	0.995	0.925	1	0.995	0.925	1	CLONAL	1	TRUE	1	0.733822532449766	2		355	482	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808010	3808010	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	131	263	0	ENST00000262367.5:c.3409A>G	p.Thr1137Ala	p.T1137A	ENST00000262367	NM_004380.2	1137	Acc/Gcc	18/31	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.733822532449766	2		263	355	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62294213	62294213	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750794827	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	198	414	0	ENST00000360203.5:c.509G>A	p.Arg170His	p.R170H	ENST00000360203	NM_001283009.1	170	cGc/cAc	6/35	1	2	FACETS	0.947	0.883	1	0.947	0.883	1	CLONAL	1	TRUE	1	0.733822532449766	2		414	570	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843243	128843243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173715127	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	158	416	0	ENST00000249373.3:c.350G>A	p.Arg117His	p.R117H	ENST00000249373	NM_005631.4	117	cGc/cAc	2/12	1	2	FACETS	0.839	0.774	0.906	0.839	0.774	0.906	CLONAL	1	TRUE	1	0.733822532449766	2		416	513	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94923009	94923009	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	176	327	0	ENST00000536441.1:c.459A>C	p.Lys153Asn	p.K153N	ENST00000536441	NM_144665.3	153	aaA/aaC	4/10	1	2	FACETS	0.956	0.887	1	0.956	0.887	1	CLONAL	1	TRUE	1	0.733822532449766	2		327	502	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515239	31515239	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1478716580	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	240	465	0	ENST00000344624.3:c.1146G>T	p.Lys382Asn	p.K382N	ENST00000344624		382	aaG/aaT	5/33	1	2	FACETS	0.985	0.925	1	0.985	0.925	1	CLONAL	1	TRUE	1	0.733822532449766	2		465	664	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739584	145739584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772515188	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	219	449	0	ENST00000428558.2:c.1867C>T	p.Arg623Cys	p.R623C	ENST00000428558	NM_004260.3	623	Cgc/Tgc	11/22	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.733822532449766	2		449	578	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790066	40790066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1357627666	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	191	405	3	ENST00000373198.4:c.2665C>T	p.Arg889Trp	p.R889W	ENST00000373198	NM_133170.3	889	Cgg/Tgg	18/32	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.733822532449766	2		408	486	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970924	70970924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1277239045	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	152	357	2	ENST00000276594.2:c.1337G>A	p.Arg446Gln	p.R446Q	ENST00000276594	NM_024504.3	446	cGg/cAg	6/8	1	2	FACETS	0.83	0.765	0.898	0.83	0.765	0.898	CLONAL	1	TRUE	1	0.733822532449766	2		359	499	SUCCESS
AR	367	MSKCC	GRCh37	X	66765382	66765382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770661499	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	175	400	0	ENST00000374690.3:c.394G>A	p.Val132Ile	p.V132I	ENST00000374690	NM_000044.3	132	Gtc/Atc	1/8	1	2	FACETS	0.992	0.921	1	0.992	0.921	1	CLONAL	1	TRUE	1	0.733822532449766	2		400	481	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599948	10599948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs111830952	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	194	445	1	ENST00000171111.5:c.1628C>T	p.Thr543Met	p.T543M	ENST00000171111	NM_203500.1	543	aCg/aTg	5/6	1	2	FACETS	0.97	0.905	1	0.97	0.905	1	CLONAL	1	TRUE	1	0.733822532449766	2		446	545	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281699	49281699	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	269	472	0	ENST00000282018.3:c.746T>C	p.Ile249Thr	p.I249T	ENST00000282018	NM_020377.2	249	aTc/aCc	1/1	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.733822532449766	2		472	700	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428252	33428252	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372038369	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	121	252	2	ENST00000345365.6:c.871C>T	p.Arg291Cys	p.R291C	ENST00000345365	NM_002878.3	291	Cgc/Tgc	9/10	1	2	FACETS	0.929	0.849	1	0.929	0.849	1	CLONAL	1	TRUE	1	0.733822532449766	2		254	355	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251560	251560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1042170	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	172	376	0	ENST00000264932.6:c.1771G>A	p.Ala591Thr	p.A591T	ENST00000264932	NM_004168.2	591	Gcg/Acg	13/15	1	2	FACETS	0.959	0.89	1	0.959	0.89	1	CLONAL	1	TRUE	1	0.733822532449766	2		376	489	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491347	2491347	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	210	443	0	ENST00000355716.4:c.390G>T	p.Gln130His	p.Q130H	ENST00000355716	NM_003820.2	130	caG/caT	4/8	1	2	FACETS	0.935	0.874	0.998	0.935	0.874	0.998	CLONAL	1	TRUE	1	0.733822532449766	2		443	612	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199369	16199369	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	124	233	0	ENST00000375759.3:c.142G>A	p.Ala48Thr	p.A48T	ENST00000375759	NM_015001.2	48	Gct/Act	2/15	1	2	FACETS	0.901	0.824	0.981	0.901	0.824	0.981	CLONAL	1	TRUE	1	0.733822532449766	2		233	375	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254764	16254764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	215	407	0	ENST00000375759.3:c.2029C>T	p.Pro677Ser	p.P677S	ENST00000375759	NM_015001.2	677	Cct/Tct	11/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.733822532449766	2		407	541	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262717	16262717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139094823	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	166	241	1	ENST00000375759.3:c.9982G>A	p.Ala3328Thr	p.A3328T	ENST00000375759	NM_015001.2	3328	Gct/Act	11/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.733822532449766	2		242	406	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265301	16265301	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	136	369	0	ENST00000375759.3:c.10793C>A	p.Ala3598Asp	p.A3598D	ENST00000375759	NM_015001.2	3598	gCc/gAc	14/15	1	2	FACETS	0.818	0.75	0.889	0.818	0.75	0.889	CLONAL	1	TRUE	1	0.733822532449766	2		369	453	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023522	27023522	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	212	378	0	ENST00000324856.7:c.628C>A	p.His210Asn	p.H210N	ENST00000324856	NM_006015.4	210	Cac/Aac	1/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.733822532449766	2		378	503	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105815	27105815	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	136	299	0	ENST00000324856.7:c.5426T>G	p.Phe1809Cys	p.F1809C	ENST00000324856	NM_006015.4	1809	tTt/tGt	20/20	1	2	FACETS	0.958	0.88	1	0.958	0.88	1	CLONAL	1	TRUE	1	0.733822532449766	2		299	387	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106047	27106047	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	129	296	1	ENST00000324856.7:c.5658G>T	p.Glu1886Asp	p.E1886D	ENST00000324856	NM_006015.4	1886	gaG/gaT	20/20	1	2	FACETS	0.93	0.852	1	0.93	0.852	1	CLONAL	1	TRUE	1	0.733822532449766	2		297	378	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106133	27106133	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	155	310	0	ENST00000324856.7:c.5744T>C	p.Leu1915Ser	p.L1915S	ENST00000324856	NM_006015.4	1915	tTg/tCg	20/20	1	2	FACETS	0.967	0.894	1	0.967	0.894	1	CLONAL	1	TRUE	1	0.733822532449766	2		310	437	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932085	36932085	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	166	294	0	ENST00000361632.4:c.2384G>T	p.Ser795Ile	p.S795I	ENST00000361632		795	aGc/aTc	16/16	1	2	FACETS	0.997	0.924	1	0.997	0.924	1	CLONAL	1	TRUE	1	0.733822532449766	2		294	454	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932327	36932327	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	183	433	0	ENST00000361632.4:c.2142C>A	p.Ser714Arg	p.S714R	ENST00000361632		714	agC/agA	16/16	1	2	FACETS	0.948	0.882	1	0.948	0.882	1	CLONAL	1	TRUE	1	0.733822532449766	2		433	526	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935334	36935334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	206	406	0	ENST00000361632.4:c.1393C>A	p.Leu465Met	p.L465M	ENST00000361632		465	Ctg/Atg	10/16	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.733822532449766	2		406	516	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939205	36939205	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	184	421	0	ENST00000361632.4:c.504G>T	p.Gln168His	p.Q168H	ENST00000361632		168	caG/caT	5/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.733822532449766	2		421	491	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805223	43805223	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	212	408	0	ENST00000372470.3:c.673A>G	p.Thr225Ala	p.T225A	ENST00000372470	NM_005373.2	225	Acc/Gcc	4/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.733822532449766	2		408	548	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46512241	46512241	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	138	324	0	ENST00000262741.5:c.998A>G	p.Lys333Arg	p.K333R	ENST00000262741	NM_003629.3	333	aAg/aGg	8/10	1	2	FACETS	0.861	0.79	0.934	0.861	0.79	0.934	CLONAL	1	TRUE	1	0.733822532449766	2		324	437	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531852	46531852	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	99	132	0	ENST00000262741.5:c.496-1G>T		p.X166_splice	ENST00000262741	NM_003629.3	166			1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.733822532449766	2		132	262	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301888	65301888	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	103	171	0	ENST00000342505.4:c.3151G>T	p.Glu1051Ter	p.E1051*	ENST00000342505	NM_002227.2	1051	Gaa/Taa	23/25	1	2	FACETS	0.877	0.794	0.963	0.877	0.794	0.963	CLONAL	1	TRUE	1	0.733822532449766	2		171	320	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115272983	115272983	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	176	439	0	ENST00000438362.2:c.1390G>T	p.Val464Phe	p.V464F	ENST00000438362	NM_001242891.1	464	Gtt/Ttt	12/20	1	2	FACETS	0.789	0.73	0.849	0.789	0.73	0.849	SUBCLONAL	1	TRUE	1	0.733822532449766	2		439	608	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276614	115276614	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	161	328	0	ENST00000438362.2:c.845G>T	p.Arg282Ile	p.R282I	ENST00000438362	NM_001242891.1	282	aGa/aTa	8/20	1	2	FACETS	0.982	0.909	1	0.982	0.909	1	CLONAL	1	TRUE	1	0.733822532449766	2		328	447	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166058	118166058	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	120	264	0	ENST00000369448.3:c.568T>G	p.Ser190Ala	p.S190A	ENST00000369448	NM_017709.3	190	Tct/Gct	2/2	1	2	FACETS	0.921	0.841	1	0.921	0.841	1	CLONAL	1	TRUE	1	0.733822532449766	2		264	355	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458982	120458982	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	189	404	0	ENST00000256646.2:c.6363G>T	p.Lys2121Asn	p.K2121N	ENST00000256646	NM_024408.3	2121	aaG/aaT	34/34	1	2	FACETS	0.989	0.921	1	0.989	0.921	1	CLONAL	1	TRUE	1	0.733822532449766	2		404	521	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466455	120466455	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	197	359	0	ENST00000256646.2:c.4664C>A	p.Pro1555His	p.P1555H	ENST00000256646	NM_024408.3	1555	cCt/cAt	26/34	1	2	FACETS	0.983	0.918	1	0.983	0.918	1	CLONAL	1	TRUE	1	0.733822532449766	2		359	546	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843599	156843599	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770090356	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	236	413	2	ENST00000524377.1:c.1025G>A	p.Arg342Gln	p.R342Q	ENST00000524377	NM_002529.3	342	cGg/cAg	8/17	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.733822532449766	2		415	592	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851379	156851379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	173	399	0	ENST00000524377.1:c.2336C>T	p.Ala779Val	p.A779V	ENST00000524377	NM_002529.3	779	gCc/gTc	17/17	1	2	FACETS	0.941	0.873	1	0.941	0.873	1	CLONAL	1	TRUE	1	0.733822532449766	2		399	501	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743329	162743329	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1266317724	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	133	228	0	ENST00000367921.3:c.1799A>G	p.Asn600Ser	p.N600S	ENST00000367921	NM_006182.2	600	aAc/aGc	14/18	1	2	FACETS	0.964	0.885	1	0.964	0.885	1	CLONAL	1	TRUE	1	0.733822532449766	2		228	376	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746072	162746072	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757948884	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	129	229	0	ENST00000367921.3:c.2195G>A	p.Ser732Asn	p.S732N	ENST00000367921	NM_006182.2	732	aGc/aAc	16/18	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.733822532449766	2		229	351	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749905	162749905	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	143	260	0	ENST00000367921.3:c.2437T>C	p.Tyr813His	p.Y813H	ENST00000367921	NM_006182.2	813	Tac/Cac	18/18	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.733822532449766	2		260	382	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162750032	162750032	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	115	231	0	ENST00000367921.3:c.2564A>G	p.Glu855Gly	p.E855G	ENST00000367921	NM_006182.2	855	gAg/gGg	18/18	1	2	FACETS	0.97	0.886	1	0.97	0.886	1	CLONAL	1	TRUE	1	0.733822532449766	2		231	323	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104562	193104562	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	303	305	0	ENST00000367435.3:c.349G>T	p.Gly117Cys	p.G117C	ENST00000367435	NM_024529.4	117	Ggt/Tgt	4/17	0.733822532449766	3	FACETS	0.918	0.873	0.962	0.918	0.873	0.962	CLONAL	2	TRUE	1	0.733822532449766	3		305	615	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649665	206649665	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	199	341	0	ENST00000367120.3:c.500A>G	p.Asp167Gly	p.D167G	ENST00000367120	NM_014002.3	167	gAt/gGt	6/22	0.733822532449766	3	FACETS	1	0.968	1	0.535	0.497	0.574	CLONAL	1	TRUE	1	0.733822532449766	3		341	693	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650023	206650023	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	123	253	1	ENST00000367120.3:c.543T>A	p.His181Gln	p.H181Q	ENST00000367120	NM_014002.3	181	caT/caA	7/22	0.733822532449766	3	FACETS	0.941	0.856	1	0.47	0.428	0.515	CLONAL	1	TRUE	1	0.733822532449766	3		254	487	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612893	228612893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1358711210	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	148	245	0	ENST00000366696.1:c.134G>A	p.Gly45Asp	p.G45D	ENST00000366696	NM_003493.2	45	gGc/gAc	1/1	0.733822532449766	3	FACETS	1	0.974	1	0.57	0.524	0.617	CLONAL	1	TRUE	1	0.733822532449766	3		245	484	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663773	241663773	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	299	328	0	ENST00000366560.3:c.1354T>C	p.Ser452Pro	p.S452P	ENST00000366560	NM_000143.3	452	Tct/Cct	9/10	0.733822532449766	3	FACETS	0.915	0.87	0.959	0.915	0.87	0.959	CLONAL	2	TRUE	1	0.733822532449766	3		328	609	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619222	43619222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	142	320	0	ENST00000355710.3:c.2905C>T	p.Arg969Trp	p.R969W	ENST00000355710	NM_020975.4	969	Cgg/Tgg	17/20	1	2	FACETS	0.958	0.882	1	0.958	0.882	1	CLONAL	1	TRUE	1	0.733822532449766	2		320	404	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333132	70333132	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	204	401	0	ENST00000373644.4:c.1037A>G	p.Gln346Arg	p.Q346R	ENST00000373644	NM_030625.2	346	cAa/cGa	2/12	1	2	FACETS	0.998	0.933	1	0.998	0.933	1	CLONAL	1	TRUE	1	0.733822532449766	2		401	557	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70441190	70441190	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	156	387	1	ENST00000373644.4:c.4859C>T	p.Ala1620Val	p.A1620V	ENST00000373644	NM_030625.2	1620	gCt/gTt	9/12	1	2	FACETS	0.835	0.77	0.902	0.835	0.77	0.902	CLONAL	1	TRUE	1	0.733822532449766	2		388	509	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451407	70451407	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	185	341	0	ENST00000373644.4:c.6247C>T	p.Gln2083Ter	p.Q2083*	ENST00000373644	NM_030625.2	2083	Caa/Taa	12/12	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.733822532449766	2		341	499	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123246939	123246939	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	156	303	0	ENST00000358487.5:c.1987-1G>T		p.X663_splice	ENST00000358487	NM_000141.4	663			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.733822532449766	2		303	383	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138835	64138835	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	186	382	0	ENST00000334205.4:c.2202G>T	p.Lys734Asn	p.K734N	ENST00000334205	NM_003942.2	734	aaG/aaT	17/17	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.733822532449766	2		382	491	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138840	64138840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761347218	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	186	364	0	ENST00000334205.4:c.2207G>A	p.Arg736Gln	p.R736Q	ENST00000334205	NM_003942.2	736	cGg/cAg	17/17	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.733822532449766	2		364	479	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572181	64572181	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	152	228	0	ENST00000312049.6:c.1458G>T	p.Glu486Asp	p.E486D	ENST00000312049	NM_130799.2	486	gaG/gaT	10/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.733822532449766	2		228	359	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462845	69462845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1404273153	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	229	444	1	ENST00000227507.2:c.658C>T	p.Pro220Ser	p.P220S	ENST00000227507	NM_053056.2	220	Ccc/Tcc	4/5	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.733822532449766	2		445	602	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462909	69462909	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	201	309	0	ENST00000227507.2:c.722C>A	p.Pro241Gln	p.P241Q	ENST00000227507	NM_053056.2	241	cCg/cAg	4/5	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.733822532449766	2		309	468	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625236	69625236	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	188	414	0	ENST00000334134.2:c.557G>T	p.Arg186Met	p.R186M	ENST00000334134	NM_005247.2	186	aGg/aTg	3/3	1	2	FACETS	0.922	0.857	0.987	0.922	0.857	0.987	CLONAL	1	TRUE	1	0.733822532449766	2		414	556	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940537	71940537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	207	385	0	ENST00000298229.2:c.688G>A	p.Glu230Lys	p.E230K	ENST00000298229	NM_001567.3	230	Gag/Aag	6/28	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.733822532449766	2		385	548	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940993	71940993	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	247	435	0	ENST00000298229.2:c.869G>T	p.Ser290Ile	p.S290I	ENST00000298229	NM_001567.3	290	aGc/aTc	8/28	1	2	FACETS	0.958	0.9	1	0.958	0.9	1	CLONAL	1	TRUE	1	0.733822532449766	2		435	703	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941936	71941936	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	200	420	0	ENST00000298229.2:c.1295del	p.Asn432ThrfsTer11	p.N432Tfs*11	ENST00000298229	NM_001567.3	432	Aac/ac	11/28	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.733822532449766	2		420	521	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942084	71942084	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	265	456	0	ENST00000298229.2:c.1348G>T	p.Gly450Cys	p.G450C	ENST00000298229	NM_001567.3	450	Ggt/Tgt	12/28	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.733822532449766	2		456	715	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942624	71942624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	201	452	1	ENST00000298229.2:c.1580C>T	p.Thr527Met	p.T527M	ENST00000298229	NM_001567.3	527	aCg/aTg	13/28	1	2	FACETS	0.98	0.915	1	0.98	0.915	1	CLONAL	1	TRUE	1	0.733822532449766	2		453	559	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948508	71948508	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	225	497	0	ENST00000298229.2:c.3220G>T	p.Gly1074Trp	p.G1074W	ENST00000298229	NM_001567.3	1074	Ggg/Tgg	26/28	1	2	FACETS	0.949	0.889	1	0.949	0.889	1	CLONAL	1	TRUE	1	0.733822532449766	2		497	646	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194193	94194193	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	124	227	0	ENST00000323929.3:c.1235T>C	p.Ile412Thr	p.I412T	ENST00000323929	NM_005591.3	412	aTc/aCc	12/20	1	2	FACETS	0.966	0.884	1	0.966	0.884	1	CLONAL	1	TRUE	1	0.733822532449766	2		227	350	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204870	94204870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	127	277	0	ENST00000323929.3:c.715G>A	p.Asp239Asn	p.D239N	ENST00000323929	NM_005591.3	239	Gat/Aat	8/20	1	2	FACETS	0.842	0.77	0.917	0.842	0.77	0.917	CLONAL	1	TRUE	1	0.733822532449766	2		277	411	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998565	100998565	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	205	389	1	ENST00000325455.5:c.1237G>T	p.Ala413Ser	p.A413S	ENST00000325455	NM_001202474.3	413	Gcc/Tcc	1/8	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.733822532449766	2		390	534	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190748	108190748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	159	271	0	ENST00000278616.4:c.6415G>A	p.Glu2139Lys	p.E2139K	ENST00000278616	NM_000051.3	2139	Gaa/Aaa	44/63	1	2	FACETS	0.877	0.81	0.946	0.877	0.81	0.946	CLONAL	1	TRUE	1	0.733822532449766	2		271	494	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235896	108235896	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786203721	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	133	247	1	ENST00000278616.4:c.8938C>A	p.Leu2980Ile	p.L2980I	ENST00000278616	NM_000051.3	2980	Ctt/Att	62/63	1	2	FACETS	0.934	0.858	1	0.934	0.858	1	CLONAL	1	TRUE	1	0.733822532449766	2		248	388	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348681	118348681	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	89	144	0	ENST00000534358.1:c.3335-1G>T		p.X1112_splice	ENST00000534358	NM_005933.3	1112			1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.733822532449766	2		144	230	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514435	125514435	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	95	277	0	ENST00000428830.2:c.1130T>C	p.Met377Thr	p.M377T	ENST00000428830	NM_001114121.2	377	aTg/aCg	11/14	1	2	FACETS	0.74	0.665	0.818	0.74	0.665	0.818	SUBCLONAL	1	TRUE	1	0.733822532449766	2		277	350	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416751	416751	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	82	170	0	ENST00000399788.2:c.3799G>T	p.Asp1267Tyr	p.D1267Y	ENST00000399788	NM_001042603.1	1267	Gat/Tat	23/28	1	2	FACETS	0.916	0.82	1	0.916	0.82	1	CLONAL	1	TRUE	1	0.733822532449766	2		170	244	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006463	12006463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	224	404	1	ENST00000396373.4:c.431C>T	p.Pro144Leu	p.P144L	ENST00000396373	NM_001987.4	144	cCg/cTg	4/8	1	2	FACETS	0.998	0.935	1	0.998	0.935	1	CLONAL	1	TRUE	1	0.733822532449766	2		405	612	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446852	18446852	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs766981923	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	119	210	0	ENST00000266497.5:c.937G>T	p.Asp313Tyr	p.D313Y	ENST00000266497		313	Gat/Tat	4/31	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.733822532449766	2		210	303	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21643203	21643203	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	249	484	0	ENST00000421138.2:c.324G>T	p.Glu108Asp	p.E108D	ENST00000421138		108	gaG/gaT	5/16	1	2	FACETS	0.902	0.847	0.959	0.902	0.847	0.959	CLONAL	1	TRUE	1	0.733822532449766	2		484	752	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49430997	49430997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	130	284	0	ENST00000301067.7:c.10142C>T	p.Pro3381Leu	p.P3381L	ENST00000301067	NM_003482.3	3381	cCc/cTc	34/54	1	2	FACETS	0.998	0.917	1	0.998	0.917	1	CLONAL	1	TRUE	1	0.733822532449766	2		284	355	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433620	49433620	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555191740	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	271	521	1	ENST00000301067.7:c.7933C>T	p.Arg2645Ter	p.R2645*	ENST00000301067	NM_003482.3	2645	Cga/Tga	31/54	1	2	FACETS	0.958	0.903	1	0.958	0.903	1	CLONAL	1	TRUE	1	0.733822532449766	2		522	771	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438643	49438643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370897971	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	206	400	0	ENST00000301067.7:c.4847G>A	p.Gly1616Glu	p.G1616E	ENST00000301067	NM_003482.3	1616	gGa/gAa	19/54	1	2	FACETS	0.994	0.929	1	0.994	0.929	1	CLONAL	1	TRUE	1	0.733822532449766	2		400	565	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69203052	69203052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	163	309	0	ENST00000462284.1:c.79G>A	p.Ala27Thr	p.A27T	ENST00000462284	NM_002392.5	27	Gct/Act	2/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.733822532449766	2		309	423	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111886089	111886089	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs766652046	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	146	290	0	ENST00000341259.2:c.1711C>T	p.Gln571Ter	p.Q571*	ENST00000341259	NM_005475.2	571	Cag/Tag	8/8	1	2	FACETS	0.913	0.841	0.987	0.913	0.841	0.987	CLONAL	1	TRUE	1	0.733822532449766	2		290	436	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120785294	120785294	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767743668	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	164	344	0	ENST00000257552.2:c.814C>T	p.Pro272Ser	p.P272S	ENST00000257552	NM_002442.3	272	Cca/Tca	12/15	1	2	FACETS	0.959	0.889	1	0.959	0.889	1	CLONAL	1	TRUE	1	0.733822532449766	2		344	466	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201565	133201565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765125852	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	133	352	0	ENST00000320574.5:c.6673C>T	p.Arg2225Cys	p.R2225C	ENST00000320574	NM_006231.2	2225	Cgc/Tgc	48/49	NA	2	FACETS	0.829	0.76	0.902			1	INDETERMINATE	1	TRUE	NA	0.733822532449766	2		352	437	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249426	133249426	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	90	226	0	ENST00000320574.5:c.1474-1G>T		p.X492_splice	ENST00000320574	NM_006231.2	492			NA	2	FACETS	1	0.926	1			1	INDETERMINATE	1	TRUE	NA	0.733822532449766	2		226	238	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252328	133252328	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	144	293	0	ENST00000320574.5:c.1099T>G	p.Phe367Val	p.F367V	ENST00000320574	NM_006231.2	367	Ttt/Gtt	11/49	NA	2	FACETS	0.986	0.909	1			1	INDETERMINATE	1	TRUE	NA	0.733822532449766	2		293	398	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597589	28597589	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	189	449	0	ENST00000241453.7:c.2316A>C	p.Lys772Asn	p.K772N	ENST00000241453	NM_004119.2	772	aaA/aaC	19/24	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.733822532449766	2		449	514	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900240	32900240	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	107	222	0	ENST00000380152.3:c.428C>A	p.Pro143His	p.P143H	ENST00000380152		143	cCt/cAt	5/27	1	2	FACETS	0.863	0.783	0.946	0.863	0.783	0.946	CLONAL	1	TRUE	1	0.733822532449766	2		222	338	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913665	32913665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786204275	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	113	265	0	ENST00000380152.3:c.5173G>A	p.Ala1725Thr	p.A1725T	ENST00000380152		1725	Gct/Act	11/27	1	2	FACETS	0.922	0.84	1	0.922	0.84	1	CLONAL	1	TRUE	1	0.733822532449766	2		265	334	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936799	32936799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	122	272	0	ENST00000380152.3:c.7945C>A	p.Pro2649Thr	p.P2649T	ENST00000380152		2649	Cca/Aca	17/27	1	2	FACETS	0.984	0.901	1	0.984	0.901	1	CLONAL	1	TRUE	1	0.733822532449766	2		272	338	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950810	32950810	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	132	221	0	ENST00000380152.3:c.8636A>G	p.Asn2879Ser	p.N2879S	ENST00000380152		2879	aAc/aGc	21/27	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.733822532449766	2		221	342	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972571	32972571	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	163	315	0	ENST00000380152.3:c.9921A>C	p.Lys3307Asn	p.K3307N	ENST00000380152		3307	aaA/aaC	27/27	1	2	FACETS	0.914	0.846	0.984	0.914	0.846	0.984	CLONAL	1	TRUE	1	0.733822532449766	2		315	486	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934264	48934264	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	121	285	0	ENST00000267163.4:c.718+1G>T		p.X240_splice	ENST00000267163	NM_000321.2	240			1	2	FACETS	0.896	0.818	0.976	0.896	0.818	0.976	CLONAL	1	TRUE	1	0.733822532449766	2		285	368	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037934	49037934	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	140	322	0	ENST00000267163.4:c.2174T>C	p.Val725Ala	p.V725A	ENST00000267163	NM_000321.2	725	gTa/gCa	21/27	1	2	FACETS	0.917	0.843	0.993	0.917	0.843	0.993	CLONAL	1	TRUE	1	0.733822532449766	2		322	416	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435436	110435436	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	217	425	0	ENST00000375856.3:c.2965C>A	p.Pro989Thr	p.P989T	ENST00000375856	NM_003749.2	989	Cct/Act	1/2	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.733822532449766	2		425	572	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436654	110436654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1200592095	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	245	520	1	ENST00000375856.3:c.1747C>T	p.Arg583Trp	p.R583W	ENST00000375856	NM_003749.2	583	Cgg/Tgg	1/2	1	2	FACETS	0.975	0.916	1	0.975	0.916	1	CLONAL	1	TRUE	1	0.733822532449766	2		521	685	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436947	110436947	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	73	159	0	ENST00000375856.3:c.1454G>T	p.Ser485Ile	p.S485I	ENST00000375856	NM_003749.2	485	aGc/aTc	1/2	1	2	FACETS	0.843	0.748	0.942	0.843	0.748	0.942	CLONAL	1	TRUE	1	0.733822532449766	2		159	236	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132946	30132946	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	174	331	0	ENST00000331968.5:c.655T>G	p.Ser219Ala	p.S219A	ENST00000331968	NM_002742.2	219	Tct/Gct	4/18	1	2	FACETS	0.902	0.836	0.969	0.902	0.836	0.969	CLONAL	1	TRUE	1	0.733822532449766	2		331	526	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988463	36988463	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs201631950	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	205	304	0	ENST00000354822.5:c.190C>A	p.Leu64Ile	p.L64I	ENST00000354822	NM_001079668.2	64	Ctc/Atc	2/3	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.733822532449766	2		304	454	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81574778	81574778	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1186709643	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	143	290	0	ENST00000298171.2:c.674A>G	p.Tyr225Cys	p.Y225C	ENST00000298171	NM_000369.2	225	tAc/tGc	8/10	1	2	FACETS	0.845	0.777	0.916	0.845	0.777	0.916	CLONAL	1	TRUE	1	0.733822532449766	2		290	461	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606120	81606120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1279981655	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	203	397	0	ENST00000298171.2:c.790C>A	p.Pro264Thr	p.P264T	ENST00000298171	NM_000369.2	264	Cca/Aca	9/10	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.733822532449766	2		397	547	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022974	33022974	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	114	288	0	ENST00000300177.4:c.83G>A	p.Gly28Glu	p.G28E	ENST00000300177	NM_001191322.1	28	gGg/gAg	2/2	0.700271663806496	2	FACETS	0.868	0.79	0.949	0.434	0.395	0.475	CLONAL	1	TRUE	0	0.733822532449766	2		288	358	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035287	42035287	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	177	336	1	ENST00000219905.7:c.5129T>C	p.Val1710Ala	p.V1710A	ENST00000219905	NM_001164273.1	1710	gTg/gCg	15/24	0.700271663806496	2	FACETS	1	0.961	1	0.523	0.487	0.56	CLONAL	1	TRUE	0	0.733822532449766	2		337	461	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054497	42054497	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	165	341	0	ENST00000219905.7:c.7681A>T	p.Met2561Leu	p.M2561L	ENST00000219905	NM_001164273.1	2561	Atg/Ttg	22/24	0.700271663806496	2	FACETS	0.993	0.92	1	0.496	0.46	0.533	CLONAL	1	TRUE	0	0.733822532449766	2		341	453	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43766946	43766946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	100	239	0	ENST00000382044.4:c.1105G>A	p.Ala369Thr	p.A369T	ENST00000382044	NM_001141980.1	369	Gct/Act	10/28	0.700271663806496	2	FACETS	0.897	0.811	0.985	0.448	0.405	0.493	CLONAL	1	TRUE	0	0.733822532449766	2		239	304	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477188	67477188	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	171	266	0	ENST00000327367.4:c.995G>A	p.Cys332Tyr	p.C332Y	ENST00000327367	NM_005902.3	332	tGc/tAc	7/9	0.700271663806496	2	FACETS	1	0.978	1	0.56	0.521	0.6	CLONAL	1	TRUE	0	0.733822532449766	2		266	416	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354413	354413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150141520	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	179	381	0	ENST00000262320.3:c.1145G>A	p.Arg382His	p.R382H	ENST00000262320	NM_003502.3	382	cGc/cAc	5/11	1	2	FACETS	0.957	0.889	1	0.957	0.889	1	CLONAL	1	TRUE	1	0.733822532449766	2		381	510	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094692	2094692	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1314362714	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	217	426	0	ENST00000219066.1:c.488G>A	p.Ser163Asn	p.S163N	ENST00000219066	NM_002528.5	163	aGc/aAc	3/6	1	2	FACETS	0.917	0.857	0.978	0.917	0.857	0.978	CLONAL	1	TRUE	1	0.733822532449766	2		426	645	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126499	2126499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397515046	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	206	371	0	ENST00000219476.3:c.2750G>A	p.Arg917Gln	p.R917Q	ENST00000219476	NM_000548.3	917	cGg/cAg	25/42	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.733822532449766	2		371	527	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138115	2138115	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45517394	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	208	443	0	ENST00000219476.3:c.5135C>T	p.Ala1712Val	p.A1712V	ENST00000219476	NM_000548.3	1712	gCc/gTc	40/42	1	2	FACETS	0.931	0.869	0.994	0.931	0.869	0.994	CLONAL	1	TRUE	1	0.733822532449766	2		443	609	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213991	2213991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758738357	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	184	360	2	ENST00000326181.6:c.70G>A	p.Val24Ile	p.V24I	ENST00000326181	NM_032271.2	24	Gtc/Atc	2/21	1	2	FACETS	0.968	0.901	1	0.968	0.901	1	CLONAL	1	TRUE	1	0.733822532449766	2		362	518	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223810	2223810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	203	438	0	ENST00000326181.6:c.1108G>A	p.Ala370Thr	p.A370T	ENST00000326181	NM_032271.2	370	Gcg/Acg	12/21	1	2	FACETS	0.888	0.828	0.949	0.888	0.828	0.949	CLONAL	1	TRUE	1	0.733822532449766	2		438	623	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225338	2225338	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	228	445	0	ENST00000326181.6:c.1423A>G	p.Ile475Val	p.I475V	ENST00000326181	NM_032271.2	475	Atc/Gtc	16/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.733822532449766	2		445	596	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636771	2636771	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	187	342	1	ENST00000342085.4:c.1220G>T	p.Arg407Met	p.R407M	ENST00000342085	NM_002613.4	407	aGg/aTg	11/14	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.733822532449766	2		343	479	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633258	3633258	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	231	599	0	ENST00000294008.3:c.4993C>T	p.Pro1665Ser	p.P1665S	ENST00000294008	NM_032444.2	1665	Ccc/Tcc	14/15	1	2	FACETS	0.945	0.886	1	0.945	0.886	1	CLONAL	1	TRUE	1	0.733822532449766	2		599	666	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923431	9923431	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	145	426	0	ENST00000330684.3:c.1856T>C	p.Val619Ala	p.V619A	ENST00000330684	NM_001134407.1	619	gTc/gCc	9/13	1	2	FACETS	0.839	0.771	0.909	0.839	0.771	0.909	CLONAL	1	TRUE	1	0.733822532449766	2		426	471	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349302	11349302	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	157	359	2	ENST00000332029.2:c.34G>A	p.Ala12Thr	p.A12T	ENST00000332029	NM_003745.1	12	Gca/Aca	2/2	1	2	FACETS	0.834	0.769	0.901	0.834	0.769	0.901	CLONAL	1	TRUE	1	0.733822532449766	2		361	513	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14028108	14028108	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs199505105	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	204	473	0	ENST00000311895.7:c.1162T>G	p.Leu388Val	p.L388V	ENST00000311895	NM_005236.2	388	Tta/Gta	7/11	1	2	FACETS	0.931	0.869	0.995	0.931	0.869	0.995	CLONAL	1	TRUE	1	0.733822532449766	2		473	597	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785726	50785726	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	182	381	0	ENST00000398568.2:c.716A>C	p.Lys239Thr	p.K239T	ENST00000398568	NM_001042412.1	239	aAg/aCg	4/18	1	2	FACETS	0.936	0.87	1	0.936	0.87	1	CLONAL	1	TRUE	1	0.733822532449766	2		381	530	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56867177	56867177	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	195	346	0	ENST00000308159.5:c.1396C>A	p.Leu466Met	p.L466M	ENST00000308159	NM_014669.4	466	Ctg/Atg	13/22	1	2	FACETS	0.979	0.913	1	0.979	0.913	1	CLONAL	1	TRUE	1	0.733822532449766	2		346	543	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822199	72822199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781682309	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	196	449	0	ENST00000268489.5:c.9976G>A	p.Ala3326Thr	p.A3326T	ENST00000268489	NM_006885.3	3326	Gcc/Acc	10/10	1	2	FACETS	0.945	0.881	1	0.945	0.881	1	CLONAL	1	TRUE	1	0.733822532449766	2		449	565	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991395	72991395	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148618101	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	198	448	1	ENST00000268489.5:c.2650G>A	p.Ala884Thr	p.A884T	ENST00000268489	NM_006885.3	884	Gcc/Acc	2/10	1	2	FACETS	0.962	0.897	1	0.962	0.897	1	CLONAL	1	TRUE	1	0.733822532449766	2		449	561	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341503	89341503	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	149	390	0	ENST00000301030.4:c.7567C>T	p.Arg2523Trp	p.R2523W	ENST00000301030	NM_001256183.1	2523	Cgg/Tgg	10/13	1	2	FACETS	0.896	0.826	0.969	0.896	0.826	0.969	CLONAL	1	TRUE	1	0.733822532449766	2		390	453	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346291	89346291	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758225743	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	62	209	1	ENST00000301030.4:c.6659C>T	p.Ala2220Val	p.A2220V	ENST00000301030	NM_001256183.1	2220	gCg/gTg	9/13	1	2	FACETS	0.809	0.709	0.913	0.809	0.709	0.913	CLONAL	1	TRUE	1	0.733822532449766	2		210	209	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348595	89348595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	208	541	0	ENST00000301030.4:c.4355C>T	p.Ala1452Val	p.A1452V	ENST00000301030	NM_001256183.1	1452	gCc/gTc	9/13	1	2	FACETS	0.913	0.852	0.975	0.913	0.852	0.975	CLONAL	1	TRUE	1	0.733822532449766	2		541	621	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351763	89351763	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145699896	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	264	546	1	ENST00000301030.4:c.1187C>T	p.Thr396Met	p.T396M	ENST00000301030	NM_001256183.1	396	aCg/aTg	9/13	1	2	FACETS	0.988	0.931	1	0.988	0.931	1	CLONAL	1	TRUE	1	0.733822532449766	2		547	728	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89874721	89874721	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	236	434	0	ENST00000389301.3:c.577C>A	p.Leu193Met	p.L193M	ENST00000389301	NM_000135.2	193	Ctg/Atg	6/43	1	2	FACETS	0.939	0.881	0.998	0.939	0.881	0.998	CLONAL	1	TRUE	1	0.733822532449766	2		434	685	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578277	7578277	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587778718	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	217	397	0	ENST00000269305.4:c.572C>A	p.Pro191His	p.P191H	ENST00000269305	NM_001126112.2	191	cCt/cAt	6/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.733822532449766	2		397	513	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976980	7976980	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	178	370	0	ENST00000319144.4:c.1750G>T	p.Gly584Cys	p.G584C	ENST00000319144	NM_001139.2	584	Ggc/Tgc	13/15	1	2	FACETS	0.99	0.921	1	0.99	0.921	1	CLONAL	1	TRUE	1	0.733822532449766	2		370	490	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990615	7990615	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs143526675	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	122	271	0	ENST00000319144.4:c.146C>T	p.Ala49Val	p.A49V	ENST00000319144	NM_001139.2	49	gCg/gTg	1/15	1	2	FACETS	0.87	0.795	0.949	0.87	0.795	0.949	CLONAL	1	TRUE	1	0.733822532449766	2		271	382	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108559	8108559	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	194	435	0	ENST00000585124.1:c.836A>C	p.Asn279Thr	p.N279T	ENST00000585124	NM_004217.3	279	aAc/aCc	8/9	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.733822532449766	2		435	526	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17124919	17124919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775085512	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	148	334	0	ENST00000285071.4:c.803G>A	p.Arg268Gln	p.R268Q	ENST00000285071	NM_144997.5	268	cGg/cAg	8/14	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.733822532449766	2		334	391	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546096	29546096	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	177	337	0	ENST00000356175.3:c.1601C>A	p.Pro534His	p.P534H	ENST00000356175	NM_000267.3	534	cCt/cAt	14/57	1	2	FACETS	0.912	0.846	0.979	0.912	0.846	0.979	CLONAL	1	TRUE	1	0.733822532449766	2		337	529	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33446632	33446632	+	start_lost	Translation_Start_Site	SNP	T	T	C	rs561425038	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	138	318	0	ENST00000345365.6:c.1A>G	p.Met1?	p.M1?	ENST00000345365	NM_002878.3	1	Atg/Gtg	1/10	1	2	FACETS	0.9	0.827	0.975	0.9	0.827	0.975	CLONAL	1	TRUE	1	0.733822532449766	2		318	418	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883983	37883983	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	223	384	1	ENST00000269571.5:c.3454C>T	p.Pro1152Ser	p.P1152S	ENST00000269571		1152	Ccc/Tcc	27/27	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.733822532449766	2		385	495	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780639	56780639	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	185	348	0	ENST00000337432.4:c.654G>T	p.Glu218Asp	p.E218D	ENST00000337432	NM_058216.2	218	gaG/gaT	4/9	1	2	FACETS	0.983	0.915	1	0.983	0.915	1	CLONAL	1	TRUE	1	0.733822532449766	2		348	513	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58725369	58725369	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	176	370	0	ENST00000305921.3:c.943G>A	p.Gly315Arg	p.G315R	ENST00000305921	NM_003620.3	315	Gga/Aga	4/6	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.733822532449766	2		370	459	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526105	63526105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs527766429	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	206	337	0	ENST00000307078.5:c.2521C>T	p.Arg841Trp	p.R841W	ENST00000307078	NM_004655.3	841	Cgg/Tgg	11/11	1	2	FACETS	0.961	0.898	1	0.961	0.898	1	CLONAL	1	TRUE	1	0.733822532449766	2		337	584	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526219	63526219	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	165	285	0	ENST00000307078.5:c.2407T>C	p.Tyr803His	p.Y803H	ENST00000307078	NM_004655.3	803	Tat/Cat	11/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.733822532449766	2		285	396	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511581	66511581	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757185291	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	124	264	0	ENST00000358598.2:c.41G>A	p.Ser14Asn	p.S14N	ENST00000358598	NM_212471.2	14	aGc/aAc	2/11	1	2	FACETS	0.974	0.892	1	0.974	0.892	1	CLONAL	1	TRUE	1	0.733822532449766	2		264	347	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526082	66526082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	147	278	0	ENST00000358598.2:c.913C>T	p.Arg305Cys	p.R305C	ENST00000358598	NM_212471.2	305	Cgt/Tgt	10/11	1	2	FACETS	0.987	0.911	1	0.987	0.911	1	CLONAL	1	TRUE	1	0.733822532449766	2		278	406	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117684	70117684	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs969167599	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	211	432	0	ENST00000245479.2:c.152A>G	p.Asn51Ser	p.N51S	ENST00000245479	NM_000346.3	51	aAc/aGc	1/3	1	2	FACETS	0.988	0.924	1	0.988	0.924	1	CLONAL	1	TRUE	1	0.733822532449766	2		432	582	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897382	78897382	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	175	359	1	ENST00000306801.3:c.2717C>A	p.Pro906Gln	p.P906Q	ENST00000306801	NM_020761.2	906	cCg/cAg	23/34	1	2	FACETS	0.91	0.844	0.978	0.91	0.844	0.978	CLONAL	1	TRUE	1	0.733822532449766	2		360	524	SUCCESS
YES1	7525	MSKCC	GRCh37	18	751704	751704	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs368508541	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	121	282	0	ENST00000314574.4:c.371+1G>A		p.X124_splice	ENST00000314574	NM_005433.3	124			1	2	FACETS	0.798	0.727	0.872	0.798	0.727	0.872	SUBCLONAL	1	TRUE	1	0.733822532449766	2		282	413	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39550371	39550371	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	125	298	0	ENST00000262039.4:c.482G>A	p.Gly161Asp	p.G161D	ENST00000262039	NM_002647.2	161	gGc/gAc	4/25	1	2	FACETS	0.852	0.778	0.928	0.852	0.778	0.928	CLONAL	1	TRUE	1	0.733822532449766	2		298	400	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617657	39617657	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	90	218	0	ENST00000262039.4:c.1841G>A	p.Ser614Asn	p.S614N	ENST00000262039	NM_002647.2	614	aGt/aAt	17/25	1	2	FACETS	0.892	0.802	0.985	0.892	0.802	0.985	CLONAL	1	TRUE	1	0.733822532449766	2		218	275	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207072	1207072	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	223	497	0	ENST00000326873.7:c.160C>A	p.Leu54Met	p.L54M	ENST00000326873	NM_000455.4	54	Ctg/Atg	1/10	1	2	FACETS	0.987	0.925	1	0.987	0.925	1	CLONAL	1	TRUE	1	0.733822532449766	2		497	616	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2199928	2199928	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372248188	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	185	445	1	ENST00000398665.3:c.697G>A	p.Ala233Thr	p.A233T	ENST00000398665	NM_032482.2	233	Gcc/Acc	8/28	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.733822532449766	2		446	504	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207668	2207668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	177	367	0	ENST00000398665.3:c.952G>A	p.Asp318Asn	p.D318N	ENST00000398665	NM_032482.2	318	Gac/Aac	11/28	1	2	FACETS	0.94	0.873	1	0.94	0.873	1	CLONAL	1	TRUE	1	0.733822532449766	2		367	513	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099303	4099303	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	184	455	0	ENST00000262948.5:c.815C>T	p.Ala272Val	p.A272V	ENST00000262948	NM_030662.3	272	gCc/gTc	7/11	1	2	FACETS	0.908	0.844	0.974	0.908	0.844	0.974	CLONAL	1	TRUE	1	0.733822532449766	2		455	552	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214574	5214574	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1205787412	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	157	339	0	ENST00000357368.4:c.4492C>T	p.Arg1498Trp	p.R1498W	ENST00000357368	NM_002850.3	1498	Cgg/Tgg	29/38	1	2	FACETS	0.962	0.889	1	0.962	0.889	1	CLONAL	1	TRUE	1	0.733822532449766	2		339	445	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246438	10246438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	173	466	0	ENST00000340748.4:c.4699G>A	p.Gly1567Ser	p.G1567S	ENST00000340748		1567	Ggc/Agc	38/40	1	2	FACETS	0.832	0.77	0.895	0.832	0.77	0.895	CLONAL	1	TRUE	1	0.733822532449766	2		466	567	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248654	10248654	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	133	289	0	ENST00000340748.4:c.4099G>T	p.Val1367Leu	p.V1367L	ENST00000340748		1367	Gtg/Ttg	35/40	1	2	FACETS	0.915	0.84	0.993	0.915	0.84	0.993	CLONAL	1	TRUE	1	0.733822532449766	2		289	396	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097158	11097158	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	166	405	0	ENST00000358026.2:c.649A>G	p.Met217Val	p.M217V	ENST00000358026	NM_001128849.1	217	Atg/Gtg	4/36	1	2	FACETS	0.88	0.814	0.948	0.88	0.814	0.948	CLONAL	1	TRUE	1	0.733822532449766	2		405	514	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101977	11101977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1374559246	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	197	399	0	ENST00000358026.2:c.1397G>A	p.Arg466His	p.R466H	ENST00000358026	NM_001128849.1	466	cGc/cAc	8/36	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.733822532449766	2		399	522	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141422	11141422	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	213	335	0	ENST00000358026.2:c.3399G>T	p.Glu1133Asp	p.E1133D	ENST00000358026	NM_001128849.1	1133	gaG/gaT	25/36	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.733822532449766	2		335	538	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285167	15285167	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs940480447	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	281	539	2	ENST00000263388.2:c.4448G>A	p.Arg1483His	p.R1483H	ENST00000263388	NM_000435.2	1483	cGc/cAc	25/33	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.733822532449766	2		541	741	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302865	15302865	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	196	539	0	ENST00000263388.2:c.585G>T	p.Glu195Asp	p.E195D	ENST00000263388	NM_000435.2	195	gaG/gaT	4/33	1	2	FACETS	0.901	0.839	0.964	0.901	0.839	0.964	CLONAL	1	TRUE	1	0.733822532449766	2		539	593	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366389	15366389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs577973488	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	79	205	0	ENST00000263377.2:c.1766C>T	p.Ala589Val	p.A589V	ENST00000263377	NM_058243.2	589	gCg/gTg	10/20	1	2	FACETS	0.882	0.788	0.981	0.882	0.788	0.981	CLONAL	1	TRUE	1	0.733822532449766	2		205	244	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945726	17945726	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	185	392	0	ENST00000458235.1:c.2134G>T	p.Gly712Cys	p.G712C	ENST00000458235	NM_000215.3	712	Ggc/Tgc	16/24	1	2	FACETS	0.939	0.873	1	0.939	0.873	1	CLONAL	1	TRUE	1	0.733822532449766	2		392	537	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954613	17954613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	223	509	0	ENST00000458235.1:c.281G>A	p.Ser94Asn	p.S94N	ENST00000458235	NM_000215.3	94	aGc/aAc	3/24	1	2	FACETS	0.924	0.865	0.984	0.924	0.865	0.984	CLONAL	1	TRUE	1	0.733822532449766	2		509	658	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976909	18976909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	164	389	0	ENST00000262803.5:c.3294C>A	p.Asp1098Glu	p.D1098E	ENST00000262803	NM_002911.3	1098	gaC/gaA	23/24	1	2	FACETS	0.914	0.846	0.984	0.914	0.846	0.984	CLONAL	1	TRUE	1	0.733822532449766	2		389	489	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976943	18976943	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	157	394	0	ENST00000262803.5:c.3328G>A	p.Gly1110Ser	p.G1110S	ENST00000262803	NM_002911.3	1110	Ggc/Agc	23/24	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.733822532449766	2		394	422	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256641	19256641	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	143	401	0	ENST00000162023.5:c.1072C>T	p.Arg358Cys	p.R358C	ENST00000162023		358	Cgc/Tgc	13/13	1	2	FACETS	0.944	0.869	1	0.944	0.869	1	CLONAL	1	TRUE	1	0.733822532449766	2		401	413	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212371	36212371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753909605	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	186	401	1	ENST00000222270.7:c.2122G>A	p.Ala708Thr	p.A708T	ENST00000222270	NM_014727.1	708	Gcc/Acc	3/37	1	2	FACETS	0.953	0.887	1	0.953	0.887	1	CLONAL	1	TRUE	1	0.733822532449766	2		402	532	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223009	36223009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	250	493	0	ENST00000222270.7:c.5638G>A	p.Val1880Ile	p.V1880I	ENST00000222270	NM_014727.1	1880	Gtc/Atc	27/37	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.733822532449766	2		493	640	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224588	36224588	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	208	503	0	ENST00000222270.7:c.7049+1G>A		p.X2350_splice	ENST00000222270	NM_014727.1	2350			1	2	FACETS	0.971	0.907	1	0.971	0.907	1	CLONAL	1	TRUE	1	0.733822532449766	2		503	584	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40743884	40743884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	148	297	0	ENST00000392038.2:c.823G>A	p.Asp275Asn	p.D275N	ENST00000392038	NM_001626.4	275	Gac/Aac	9/14	1	2	FACETS	0.913	0.841	0.986	0.913	0.841	0.986	CLONAL	1	TRUE	1	0.733822532449766	2		297	442	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383069	42383069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1263805787	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	99	234	0	ENST00000221972.3:c.89G>A	p.Cys30Tyr	p.C30Y	ENST00000221972	NM_021601.3	30	tGc/tAc	2/5	1	2	FACETS	0.964	0.873	1	0.964	0.873	1	CLONAL	1	TRUE	1	0.733822532449766	2		234	280	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752786	42752786	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762382429	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	214	452	1	ENST00000222329.4:c.1478G>A	p.Arg493His	p.R493H	ENST00000222329	NM_006494.2	493	cGc/cAc	4/4	1	2	FACETS	0.872	0.814	0.931	0.872	0.814	0.931	CLONAL	1	TRUE	1	0.733822532449766	2		453	669	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868157	45868157	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	188	522	0	ENST00000391945.4:c.533A>C	p.Asp178Ala	p.D178A	ENST00000391945	NM_000400.3	178	gAt/gCt	7/23	1	2	FACETS	0.846	0.786	0.907	0.846	0.786	0.907	CLONAL	1	TRUE	1	0.733822532449766	2		522	606	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872377	45872377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	202	405	0	ENST00000391945.4:c.134G>A	p.Gly45Asp	p.G45D	ENST00000391945	NM_000400.3	45	gGc/gAc	3/23	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.733822532449766	2		405	525	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905041	50905041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs577686721	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	113	271	0	ENST00000440232.2:c.323C>T	p.Ala108Val	p.A108V	ENST00000440232	NM_002691.3	108	gCg/gTg	4/27	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.733822532449766	2		271	267	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50916693	50916693	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	166	345	0	ENST00000440232.2:c.2165G>A	p.Gly722Glu	p.G722E	ENST00000440232	NM_002691.3	722	gGg/gAg	18/27	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.733822532449766	2		345	414	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52693428	52693428	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	191	423	2	ENST00000322088.6:c.78+1G>A		p.X26_splice	ENST00000322088	NM_014225.5	26			1	2	FACETS	0.858	0.797	0.919	0.858	0.797	0.919	CLONAL	1	TRUE	1	0.733822532449766	2		425	607	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52705233	52705233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs949208712	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	131	312	0	ENST00000322088.6:c.115G>A	p.Ala39Thr	p.A39T	ENST00000322088	NM_014225.5	39	Gcc/Acc	2/15	1	2	FACETS	0.828	0.758	0.901	0.828	0.758	0.901	CLONAL	1	TRUE	1	0.733822532449766	2		312	431	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716036	52716036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749905469	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	192	432	0	ENST00000322088.6:c.601G>A	p.Val201Ile	p.V201I	ENST00000322088	NM_014225.5	201	Gtc/Atc	5/15	1	2	FACETS	0.98	0.914	1	0.98	0.914	1	CLONAL	1	TRUE	1	0.733822532449766	2		432	534	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716069	52716069	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	198	473	0	ENST00000322088.6:c.634C>A	p.Leu212Met	p.L212M	ENST00000322088	NM_014225.5	212	Ctg/Atg	5/15	1	2	FACETS	0.988	0.923	1	0.988	0.923	1	CLONAL	1	TRUE	1	0.733822532449766	2		473	546	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52725363	52725363	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	132	233	1	ENST00000322088.6:c.1530G>T	p.Glu510Asp	p.E510D	ENST00000322088	NM_014225.5	510	gaG/gaT	13/15	1	2	FACETS	0.972	0.893	1	0.972	0.893	1	CLONAL	1	TRUE	1	0.733822532449766	2		234	370	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52725461	52725461	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	173	384	0	ENST00000322088.6:c.1628C>A	p.Ser543Tyr	p.S543Y	ENST00000322088	NM_014225.5	543	tCt/tAt	13/15	1	2	FACETS	0.972	0.903	1	0.972	0.903	1	CLONAL	1	TRUE	1	0.733822532449766	2		384	485	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469587	25469587	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	172	441	0	ENST00000264709.3:c.1181A>G	p.Asp394Gly	p.D394G	ENST00000264709	NM_175629.2	394	gAc/gGc	10/23	1	2	FACETS	0.81	0.749	0.872	0.81	0.749	0.872	CLONAL	1	TRUE	1	0.733822532449766	2		441	579	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964989	25964989	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746010291	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	122	257	1	ENST00000435504.4:c.4217C>T	p.Ala1406Val	p.A1406V	ENST00000435504		1406	gCc/gTc	13/13	1	2	FACETS	0.896	0.819	0.976	0.896	0.819	0.976	CLONAL	1	TRUE	1	0.733822532449766	2		258	371	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973187	25973187	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	113	225	0	ENST00000435504.4:c.1238C>A	p.Pro413His	p.P413H	ENST00000435504		413	cCt/cAt	12/13	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.733822532449766	2		225	305	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443646	29443646	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	200	390	0	ENST00000389048.3:c.3571C>T	p.Pro1191Ser	p.P1191S	ENST00000389048	NM_004304.4	1191	Ccc/Tcc	23/29	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.733822532449766	2		390	511	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519846	29519846	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	162	363	0	ENST00000389048.3:c.1725G>T	p.Lys575Asn	p.K575N	ENST00000389048	NM_004304.4	575	aaG/aaT	9/29	1	2	FACETS	0.928	0.858	0.999	0.928	0.858	0.999	CLONAL	1	TRUE	1	0.733822532449766	2		363	476	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39294807	39294807	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1442738935	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	163	342	1	ENST00000402219.2:c.175C>A	p.Leu59Ile	p.L59I	ENST00000402219	NM_005633.3	59	Cta/Ata	2/23	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.733822532449766	2		343	433	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574157	46574157	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	204	393	0	ENST00000263734.3:c.172C>T	p.Arg58Ter	p.R58*	ENST00000263734	NM_001430.4	58	Cga/Tga	2/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.733822532449766	2		393	535	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026414	48026414	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	136	273	0	ENST00000234420.5:c.1292A>C	p.Lys431Thr	p.K431T	ENST00000234420	NM_000179.2	431	aAa/aCa	4/10	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.733822532449766	2		273	364	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026572	48026572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782706	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	122	248	0	ENST00000234420.5:c.1450G>A	p.Glu484Lys	p.E484K	ENST00000234420	NM_000179.2	484	Gaa/Aaa	4/10	1	2	FACETS	0.978	0.895	1	0.978	0.895	1	CLONAL	1	TRUE	1	0.733822532449766	2		248	340	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99162453	99162453	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	121	235	0	ENST00000074304.5:c.971G>T	p.Ser324Ile	p.S324I	ENST00000074304	NM_001134224.1	324	aGt/aTt	12/26	1	2	FACETS	0.934	0.854	1	0.934	0.854	1	CLONAL	1	TRUE	1	0.733822532449766	2		235	353	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99185114	99185114	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	127	235	0	ENST00000074304.5:c.2516A>G	p.Glu839Gly	p.E839G	ENST00000074304	NM_001134224.1	839	gAa/gGa	23/26	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.733822532449766	2		235	331	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189332	99189332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	168	293	0	ENST00000074304.5:c.2588G>A	p.Gly863Asp	p.G863D	ENST00000074304	NM_001134224.1	863	gGt/gAt	24/26	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.733822532449766	2		293	450	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038135	128038135	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753633161	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	155	282	0	ENST00000285398.2:c.1415G>A	p.Arg472His	p.R472H	ENST00000285398	NM_000122.1	472	cGc/cAc	9/15	1	2	FACETS	0.982	0.909	1	0.982	0.909	1	CLONAL	1	TRUE	1	0.733822532449766	2		282	430	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872714	136872714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1275022868	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	121	289	0	ENST00000241393.3:c.784G>A	p.Asp262Asn	p.D262N	ENST00000241393	NM_003467.2	262	Gac/Aac	2/2	1	2	FACETS	0.899	0.821	0.979	0.899	0.821	0.979	CLONAL	1	TRUE	1	0.733822532449766	2		289	367	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095539	178095539	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	105	212	0	ENST00000397062.3:c.1792A>G	p.Lys598Glu	p.K598E	ENST00000397062	NM_006164.4	598	Aag/Gag	5/5	1	2	FACETS	0.96	0.872	1	0.96	0.872	1	CLONAL	1	TRUE	1	0.733822532449766	2		212	298	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190656635	190656635	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	114	227	3	ENST00000441310.2:c.100G>T	p.Asp34Tyr	p.D34Y	ENST00000441310	NM_000534.4	34	Gat/Tat	2/13	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.733822532449766	2		230	297	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660559	190660559	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	122	251	0	ENST00000441310.2:c.197C>T	p.Ala66Val	p.A66V	ENST00000441310	NM_000534.4	66	gCa/gTa	3/13	1	2	FACETS	0.942	0.861	1	0.942	0.861	1	CLONAL	1	TRUE	1	0.733822532449766	2		251	353	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660669	190660669	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	130	252	0	ENST00000441310.2:c.307A>G	p.Ile103Val	p.I103V	ENST00000441310	NM_000534.4	103	Ata/Gta	3/13	1	2	FACETS	0.958	0.879	1	0.958	0.879	1	CLONAL	1	TRUE	1	0.733822532449766	2		252	370	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732536	190732536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	114	216	0	ENST00000441310.2:c.2354G>A	p.Gly785Glu	p.G785E	ENST00000441310	NM_000534.4	785	gGa/gAa	11/13	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.733822532449766	2		216	306	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149587	202149587	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	122	265	0	ENST00000358485.4:c.1028A>G	p.His343Arg	p.H343R	ENST00000358485	NM_001080125.1	343	cAc/cGc	8/9	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.733822532449766	2		265	328	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989579	212989579	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	118	167	0	ENST00000342788.4:c.132G>T	p.Gln44His	p.Q44H	ENST00000342788	NM_005235.2	44	caG/caT	2/28	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.733822532449766	2		167	312	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346651	225346651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	150	296	0	ENST00000264414.4:c.1987G>A	p.Asp663Asn	p.D663N	ENST00000264414	NM_003590.4	663	Gat/Aat	14/16	1	2	FACETS	0.964	0.89	1	0.964	0.89	1	CLONAL	1	TRUE	1	0.733822532449766	2		296	424	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242800974	242800974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769034572	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	159	397	1	ENST00000334409.5:c.17C>T	p.Ala6Val	p.A6V	ENST00000334409	NM_005018.2	6	gCg/gTg	1/5	1	2	FACETS	0.865	0.799	0.933	0.865	0.799	0.933	CLONAL	1	TRUE	1	0.733822532449766	2		398	501	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31020692	31020692	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	125	283	0	ENST00000375687.4:c.989C>A	p.Thr330Asn	p.T330N	ENST00000375687	NM_015338.5	330	aCt/aAt	11/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.733822532449766	2		283	296	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021181	31021181	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs534065676	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	219	353	2	ENST00000375687.4:c.1180C>T	p.Arg394Cys	p.R394C	ENST00000375687	NM_015338.5	394	Cgt/Tgt	12/13	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.733822532449766	2		355	587	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024768	31024768	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	175	319	0	ENST00000375687.4:c.4253G>T	p.Gly1418Val	p.G1418V	ENST00000375687	NM_015338.5	1418	gGg/gTg	13/13	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.733822532449766	2		319	425	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376760	31376760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754201724	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	157	410	0	ENST00000328111.2:c.755G>A	p.Arg252Gln	p.R252Q	ENST00000328111	NM_006892.3	252	cGa/cAa	7/23	1	2	FACETS	0.905	0.836	0.975	0.905	0.836	0.975	CLONAL	1	TRUE	1	0.733822532449766	2		410	473	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39721152	39721152	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	201	343	0	ENST00000361337.2:c.655T>G	p.Phe219Val	p.F219V	ENST00000361337	NM_003286.2	219	Ttc/Gtc	9/21	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.733822532449766	2		343	529	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39729934	39729934	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1287698565	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	171	355	0	ENST00000361337.2:c.1249A>G	p.Thr417Ala	p.T417A	ENST00000361337	NM_003286.2	417	Aca/Gca	13/21	1	2	FACETS	0.947	0.879	1	0.947	0.879	1	CLONAL	1	TRUE	1	0.733822532449766	2		355	492	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790071	40790071	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	167	425	0	ENST00000373198.4:c.2660C>T	p.Ala887Val	p.A887V	ENST00000373198	NM_133170.3	887	gCc/gTc	18/32	1	2	FACETS	0.925	0.857	0.995	0.925	0.857	0.995	CLONAL	1	TRUE	1	0.733822532449766	2		425	492	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62317222	62317222	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	177	358	0	ENST00000360203.5:c.1345C>T	p.Arg449Ter	p.R449*	ENST00000360203	NM_001283009.1	449	Cga/Tga	16/35	1	2	FACETS	0.979	0.909	1	0.979	0.909	1	CLONAL	1	TRUE	1	0.733822532449766	2		358	493	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62323135	62323135	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	222	459	0	ENST00000360203.5:c.2597G>T	p.Arg866Met	p.R866M	ENST00000360203	NM_001283009.1	866	aGg/aTg	28/35	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.733822532449766	2		459	562	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755623	39755623	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	173	329	0	ENST00000288319.7:c.1142T>G	p.Val381Gly	p.V381G	ENST00000288319	NM_182918.3	381	gTc/gGc	10/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.733822532449766	2		329	444	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655419	45655419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1181740577	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	208	470	1	ENST00000407780.3:c.433G>A	p.Ala145Thr	p.A145T	ENST00000407780	NM_001283052.1	145	Gcc/Acc	4/7	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.733822532449766	2		471	542	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288246	21288246	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200712124	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	169	413	2	ENST00000354336.3:c.491G>A	p.Arg164Gln	p.R164Q	ENST00000354336	NM_005207.3	164	cGg/cAg	2/3	1	2	FACETS	0.931	0.862	1	0.931	0.862	1	CLONAL	1	TRUE	1	0.733822532449766	2		415	495	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035186	30035186	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	149	308	0	ENST00000338641.4:c.348T>G	p.His116Gln	p.H116Q	ENST00000338641	NM_000268.3	116	caT/caG	3/16	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.733822532449766	2		308	397	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574545	41574545	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	204	437	0	ENST00000263253.7:c.6830C>A	p.Pro2277His	p.P2277H	ENST00000263253	NM_001429.3	2277	cCc/cAc	31/31	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.733822532449766	2		437	525	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475528	12475528	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	146	347	0	ENST00000287820.6:c.1402A>G	p.Thr468Ala	p.T468A	ENST00000287820	NM_015869.4	468	Aca/Gca	7/7	1	2	FACETS	0.869	0.799	0.94	0.869	0.799	0.94	CLONAL	1	TRUE	1	0.733822532449766	2		347	458	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686388	30686388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	89	239	0	ENST00000295754.5:c.244G>A	p.Glu82Lys	p.E82K	ENST00000295754	NM_003242.5	82	Gaa/Aaa	2/7	1	2	FACETS	0.793	0.711	0.878	0.793	0.711	0.878	SUBCLONAL	1	TRUE	1	0.733822532449766	2		239	306	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713298	30713298	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	166	248	0	ENST00000295754.5:c.623A>C	p.Lys208Thr	p.K208T	ENST00000295754	NM_003242.5	208	aAg/aCg	4/7	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.733822532449766	2		248	398	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713801	30713801	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755967723	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	162	309	0	ENST00000295754.5:c.1126G>A	p.Val376Met	p.V376M	ENST00000295754	NM_003242.5	376	Gtg/Atg	4/7	1	2	FACETS	0.99	0.917	1	0.99	0.917	1	CLONAL	1	TRUE	1	0.733822532449766	2		309	446	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275751	41275751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	149	335	0	ENST00000349496.5:c.1646G>A	p.Arg549His	p.R549H	ENST00000349496	NM_001904.3	549	cGc/cAc	10/15	1	2	FACETS	0.871	0.803	0.942	0.871	0.803	0.942	CLONAL	1	TRUE	1	0.733822532449766	2		335	466	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280637	41280637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753246841	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	164	366	0	ENST00000349496.5:c.2150G>A	p.Arg717His	p.R717H	ENST00000349496	NM_001904.3	717	cGt/cAt	15/15	1	2	FACETS	0.896	0.829	0.965	0.896	0.829	0.965	CLONAL	1	TRUE	1	0.733822532449766	2		366	499	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125328	47125328	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs189529024	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	132	230	0	ENST00000409792.3:c.5942A>G	p.Gln1981Arg	p.Q1981R	ENST00000409792	NM_014159.6	1981	cAa/cGa	12/21	1	2	FACETS	0.915	0.84	0.993	0.915	0.84	0.993	CLONAL	1	TRUE	1	0.733822532449766	2		230	393	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163098	47163098	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	100	248	0	ENST00000409792.3:c.3028G>T	p.Glu1010Ter	p.E1010*	ENST00000409792	NM_014159.6	1010	Gaa/Taa	3/21	1	2	FACETS	0.984	0.892	1	0.984	0.892	1	CLONAL	1	TRUE	1	0.733822532449766	2		248	277	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936050	49936050	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs747000944	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	225	434	0	ENST00000296474.3:c.1620G>T	p.Trp540Cys	p.W540C	ENST00000296474	NM_002447.2	540	tgG/tgT	4/20	1	2	FACETS	0.932	0.873	0.992	0.932	0.873	0.992	CLONAL	1	TRUE	1	0.733822532449766	2		434	658	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440346	52440346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1559589762	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	191	327	0	ENST00000460680.1:c.706G>A	p.Asp236Asn	p.D236N	ENST00000460680	NM_004656.3	236	Gac/Aac	9/17	1	2	FACETS	0.988	0.921	1	0.988	0.921	1	CLONAL	1	TRUE	1	0.733822532449766	2		327	527	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443582	52443582	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	157	313	0	ENST00000460680.1:c.110G>T	p.Ser37Ile	p.S37I	ENST00000460680	NM_004656.3	37	aGc/aTc	3/17	1	2	FACETS	0.899	0.83	0.969	0.899	0.83	0.969	CLONAL	1	TRUE	1	0.733822532449766	2		313	476	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651348	52651348	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	147	342	0	ENST00000394830.3:c.1748A>C	p.Glu583Ala	p.E583A	ENST00000394830	NM_018313.4	583	gAa/gCa	15/30	1	2	FACETS	0.97	0.895	1	0.97	0.895	1	CLONAL	1	TRUE	1	0.733822532449766	2		342	413	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498508	89498508	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	90	212	0	ENST00000336596.2:c.2480A>T	p.Glu827Val	p.E827V	ENST00000336596	NM_005233.5	827	gAg/gTg	14/17	1	2	FACETS	0.929	0.837	1	0.929	0.837	1	CLONAL	1	TRUE	1	0.733822532449766	2		212	264	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670437	134670437	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	128	315	0	ENST00000398015.3:c.348G>T	p.Glu116Asp	p.E116D	ENST00000398015	NM_004441.4	116	gaG/gaT	3/16	1	2	FACETS	0.964	0.884	1	0.964	0.884	1	CLONAL	1	TRUE	1	0.733822532449766	2		315	362	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898780	134898780	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	94	298	0	ENST00000398015.3:c.1838A>G	p.Glu613Gly	p.E613G	ENST00000398015	NM_004441.4	613	gAg/gGg	10/16	1	2	FACETS	0.871	0.785	0.961	0.871	0.785	0.961	CLONAL	1	TRUE	1	0.733822532449766	2		298	294	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911432	134911432	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	123	359	0	ENST00000398015.3:c.1897G>A	p.Val633Met	p.V633M	ENST00000398015	NM_004441.4	633	Gtg/Atg	11/16	1	2	FACETS	0.767	0.699	0.838	0.767	0.699	0.838	SUBCLONAL	1	TRUE	1	0.733822532449766	2		359	437	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413742	138413742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769082299	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	103	240	2	ENST00000289153.2:c.1778C>T	p.Ala593Val	p.A593V	ENST00000289153	NM_006219.2	593	gCg/gTg	12/22	1	2	FACETS	0.942	0.855	1	0.942	0.855	1	CLONAL	1	TRUE	1	0.733822532449766	2		242	298	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138423310	138423310	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	182	359	0	ENST00000289153.2:c.1556C>A	p.Ala519Glu	p.A519E	ENST00000289153	NM_006219.2	519	gCa/gAa	10/22	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.733822532449766	2		359	478	SUCCESS
ATR	545	MSKCC	GRCh37	3	142171992	142171992	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	162	387	0	ENST00000350721.4:c.7739C>A	p.Thr2580Asn	p.T2580N	ENST00000350721	NM_001184.3	2580	aCt/aAt	46/47	1	2	FACETS	0.866	0.8	0.933	0.866	0.8	0.933	CLONAL	1	TRUE	1	0.733822532449766	2		387	510	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279152	142279152	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	185	321	0	ENST00000350721.4:c.1494A>C	p.Gln498His	p.Q498H	ENST00000350721	NM_001184.3	498	caA/caC	6/47	1	2	FACETS	0.979	0.911	1	0.979	0.911	1	CLONAL	1	TRUE	1	0.733822532449766	2		321	515	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281651	142281651	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759878676	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	147	308	0	ENST00000350721.4:c.593G>A	p.Ser198Asn	p.S198N	ENST00000350721	NM_001184.3	198	aGt/aAt	4/47	1	2	FACETS	0.965	0.891	1	0.965	0.891	1	CLONAL	1	TRUE	1	0.733822532449766	2		308	415	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430591	181430591	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754275280	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	152	267	0	ENST00000325404.1:c.443G>A	p.Gly148Asp	p.G148D	ENST00000325404	NM_003106.3	148	gGc/gAc	1/1	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.733822532449766	2		267	413	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430869	181430869	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	271	526	1	ENST00000325404.1:c.721G>T	p.Gly241Cys	p.G241C	ENST00000325404	NM_003106.3	241	Ggt/Tgt	1/1	1	2	FACETS	0.968	0.912	1	0.968	0.912	1	CLONAL	1	TRUE	1	0.733822532449766	2		527	763	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146718	185146718	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	177	419	0	ENST00000265026.3:c.349A>G	p.Lys117Glu	p.K117E	ENST00000265026	NM_004721.4	117	Aag/Gag	2/14	1	2	FACETS	0.907	0.842	0.974	0.907	0.842	0.974	CLONAL	1	TRUE	1	0.733822532449766	2		419	532	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607189	189607189	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1362748295	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	200	470	0	ENST00000264731.3:c.1568A>C	p.Gln523Pro	p.Q523P	ENST00000264731	NM_003722.4	523	cAg/cCg	12/14	1	2	FACETS	0.94	0.877	1	0.94	0.877	1	CLONAL	1	TRUE	1	0.733822532449766	2		470	580	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920295	1920295	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	199	416	1	ENST00000382891.5:c.1355G>T	p.Arg452Met	p.R452M	ENST00000382891	NM_133335.3	452	aGg/aTg	5/22	1	2	FACETS	0.981	0.915	1	0.981	0.915	1	CLONAL	1	TRUE	1	0.733822532449766	2		417	553	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957835	1957835	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388626156	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	212	407	0	ENST00000382891.5:c.2801C>T	p.Ala934Val	p.A934V	ENST00000382891	NM_133335.3	934	gCg/gTg	15/22	1	2	FACETS	0.935	0.874	0.997	0.935	0.874	0.997	CLONAL	1	TRUE	1	0.733822532449766	2		407	618	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138639	55138639	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	163	315	0	ENST00000257290.5:c.1316G>A	p.Gly439Asp	p.G439D	ENST00000257290	NM_006206.4	439	gGc/gAc	9/23	1	2	FACETS	0.966	0.895	1	0.966	0.895	1	CLONAL	1	TRUE	1	0.733822532449766	2		315	460	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144627	55144627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	120	249	0	ENST00000257290.5:c.2101C>T	p.Pro701Ser	p.P701S	ENST00000257290	NM_006206.4	701	Cca/Tca	15/23	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.733822532449766	2		249	326	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561755	55561755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759250095	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	96	243	0	ENST00000288135.5:c.145C>T	p.Arg49Cys	p.R49C	ENST00000288135	NM_000222.2	49	Cgc/Tgc	2/21	1	2	FACETS	0.852	0.768	0.939	0.852	0.768	0.939	CLONAL	1	TRUE	1	0.733822532449766	2		243	307	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594075	55594075	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1560418178	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	113	235	0	ENST00000288135.5:c.1861G>A	p.Ala621Thr	p.A621T	ENST00000288135	NM_000222.2	621	Gct/Act	12/21	1	2	FACETS	0.898	0.817	0.981	0.898	0.817	0.981	CLONAL	1	TRUE	1	0.733822532449766	2		235	343	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602770	55602770	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	101	199	0	ENST00000288135.5:c.2591C>A	p.Ser864Tyr	p.S864Y	ENST00000288135	NM_000222.2	864	tCt/tAt	18/21	1	2	FACETS	0.842	0.761	0.926	0.842	0.761	0.926	CLONAL	1	TRUE	1	0.733822532449766	2		199	327	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197721	66197721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs74487329	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	129	258	0	ENST00000273854.3:c.2978C>T	p.Ser993Leu	p.S993L	ENST00000273854	NM_004439.5	993	tCa/tTa	17/18	1	2	FACETS	0.837	0.766	0.911	0.837	0.766	0.911	CLONAL	1	TRUE	1	0.733822532449766	2		258	420	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230797	66230797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	114	266	0	ENST00000273854.3:c.2174C>T	p.Ala725Val	p.A725V	ENST00000273854	NM_004439.5	725	gCa/gTa	12/18	1	2	FACETS	0.888	0.808	0.97	0.888	0.808	0.97	CLONAL	1	TRUE	1	0.733822532449766	2		266	350	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280125	66280125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	96	196	0	ENST00000273854.3:c.1564G>A	p.Glu522Lys	p.E522K	ENST00000273854	NM_004439.5	522	Gag/Aag	7/18	1	2	FACETS	0.852	0.768	0.939	0.852	0.768	0.939	CLONAL	1	TRUE	1	0.733822532449766	2		196	307	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535333	66535333	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	194	427	1	ENST00000273854.3:c.128G>A	p.Cys43Tyr	p.C43Y	ENST00000273854	NM_004439.5	43	tGc/tAc	1/18	1	2	FACETS	0.871	0.811	0.933	0.871	0.811	0.933	CLONAL	1	TRUE	1	0.733822532449766	2		428	607	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99809104	99809104	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	90	239	0	ENST00000280892.6:c.282-1G>A		p.X94_splice	ENST00000280892	NM_001130678.1	94			1	2	FACETS	0.807	0.724	0.893	0.807	0.724	0.893	CLONAL	1	TRUE	1	0.733822532449766	2		239	304	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164848	106164848	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	142	330	0	ENST00000380013.4:c.3716C>A	p.Ser1239Tyr	p.S1239Y	ENST00000380013	NM_001127208.2	1239	tCt/tAt	6/11	1	2	FACETS	0.913	0.84	0.988	0.913	0.84	0.988	CLONAL	1	TRUE	1	0.733822532449766	2		330	424	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197216	106197216	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	105	182	1	ENST00000380013.4:c.5549G>T	p.Ser1850Ile	p.S1850I	ENST00000380013	NM_001127208.2	1850	aGc/aTc	11/11	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.733822532449766	2		183	284	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081657	143081657	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	150	231	1	ENST00000262992.4:c.1417C>A	p.Leu473Ile	p.L473I	ENST00000262992	NM_001101669.1	473	Ctc/Atc	15/24	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.733822532449766	2		232	395	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538232	187538232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1310860834	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	198	406	0	ENST00000441802.2:c.9002G>A	p.Gly3001Asp	p.G3001D	ENST00000441802	NM_005245.3	3001	gGc/gAc	11/27	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.733822532449766	2		406	535	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584619	187584619	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	145	340	0	ENST00000441802.2:c.3414G>T	p.Gln1138His	p.Q1138H	ENST00000441802	NM_005245.3	1138	caG/caT	3/27	1	2	FACETS	0.878	0.808	0.95	0.878	0.808	0.95	CLONAL	1	TRUE	1	0.733822532449766	2		340	450	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628551	187628551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765982067	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	238	445	0	ENST00000441802.2:c.2431G>A	p.Val811Met	p.V811M	ENST00000441802	NM_005245.3	811	Gtg/Atg	2/27	1	2	FACETS	0.932	0.874	0.991	0.932	0.874	0.991	CLONAL	1	TRUE	1	0.733822532449766	2		445	696	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628574	187628574	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	231	452	1	ENST00000441802.2:c.2408C>A	p.Ala803Asp	p.A803D	ENST00000441802	NM_005245.3	803	gCt/gAt	2/27	1	2	FACETS	0.984	0.923	1	0.984	0.923	1	CLONAL	1	TRUE	1	0.733822532449766	2		453	640	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282710	1282710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	183	363	0	ENST00000310581.5:c.1603C>T	p.Arg535Cys	p.R535C	ENST00000310581	NM_198253.2	535	Cgt/Tgt	3/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.733822532449766	2		363	470	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294123	1294123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1309920442	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	237	530	1	ENST00000310581.5:c.878G>A	p.Arg293His	p.R293H	ENST00000310581	NM_198253.2	293	cGc/cAc	2/16	1	2	FACETS	0.951	0.893	1	0.951	0.893	1	CLONAL	1	TRUE	1	0.733822532449766	2		531	679	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31464386	31464386	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	247	442	0	ENST00000344624.3:c.2531G>A	p.Ser844Asn	p.S844N	ENST00000344624		844	aGc/aAc	17/33	1	2	FACETS	0.895	0.84	0.951	0.895	0.84	0.951	CLONAL	1	TRUE	1	0.733822532449766	2		442	752	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31466354	31466354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376262500	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	227	410	1	ENST00000344624.3:c.2401C>T	p.Arg801Cys	p.R801C	ENST00000344624		801	Cgc/Tgc	16/33	1	2	FACETS	0.902	0.844	0.961	0.902	0.844	0.961	CLONAL	1	TRUE	1	0.733822532449766	2		411	686	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515115	31515115	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	168	405	0	ENST00000344624.3:c.1270A>G	p.Ser424Gly	p.S424G	ENST00000344624		424	Agt/Ggt	5/33	1	2	FACETS	0.894	0.828	0.962	0.894	0.828	0.962	CLONAL	1	TRUE	1	0.733822532449766	2		405	512	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177771	56177771	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	122	222	0	ENST00000399503.3:c.2744T>G	p.Leu915Ter	p.L915*	ENST00000399503	NM_005921.1	915	tTa/tGa	14/20	1	2	FACETS	0.978	0.895	1	0.978	0.895	1	CLONAL	1	TRUE	1	0.733822532449766	2		222	340	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591109	67591109	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	146	240	0	ENST00000274335.5:c.1702C>T	p.Pro568Ser	p.P568S	ENST00000274335		568	Cca/Tca	12/15	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.733822532449766	2		240	392	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79952342	79952342	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1456712758	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	147	329	0	ENST00000265081.6:c.350G>A	p.Gly117Asp	p.G117D	ENST00000265081	NM_002439.4	117	gGc/gAc	2/24	1	2	FACETS	0.792	0.728	0.858	0.792	0.728	0.858	SUBCLONAL	1	TRUE	1	0.733822532449766	2		329	506	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970948	79970948	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	246	411	0	ENST00000265081.6:c.1173+1G>T		p.X391_splice	ENST00000265081	NM_002439.4	391			1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.733822532449766	2		411	651	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86682664	86682664	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	83	163	0	ENST00000274376.6:c.2869A>G	p.Asn957Asp	p.N957D	ENST00000274376	NM_002890.2	957	Aat/Gat	23/25	1	2	FACETS	0.877	0.785	0.972	0.877	0.785	0.972	CLONAL	1	TRUE	1	0.733822532449766	2		163	258	SUCCESS
APC	324	MSKCC	GRCh37	5	112177591	112177591	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	92	253	0	ENST00000257430.4:c.6300T>G	p.Asp2100Glu	p.D2100E	ENST00000257430	NM_000038.5	2100	gaT/gaG	16/16	1	2	FACETS	0.85	0.765	0.939	0.85	0.765	0.939	CLONAL	1	TRUE	1	0.733822532449766	2		253	295	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441342	149441342	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	198	368	0	ENST00000286301.3:c.1697C>A	p.Pro566His	p.P566H	ENST00000286301	NM_005211.3	566	cCc/cAc	12/22	1	2	FACETS	0.988	0.923	1	0.988	0.923	1	CLONAL	1	TRUE	1	0.733822532449766	2		368	546	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522584	176522584	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	189	413	0	ENST00000292408.4:c.1681T>G	p.Phe561Val	p.F561V	ENST00000292408	NM_213647.1	561	Ttc/Gtc	13/18	1	2	FACETS	0.945	0.88	1	0.945	0.88	1	CLONAL	1	TRUE	1	0.733822532449766	2		413	545	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030390	180030390	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	164	417	0	ENST00000261937.6:c.3894C>A	p.Ser1298Arg	p.S1298R	ENST00000261937	NM_182925.4	1298	agC/agA	30/30	1	2	FACETS	0.894	0.827	0.963	0.894	0.827	0.963	CLONAL	1	TRUE	1	0.733822532449766	2		417	500	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481629	20481629	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	79	202	0	ENST00000346618.3:c.698A>G	p.Lys233Arg	p.K233R	ENST00000346618	NM_001949.4	233	aAg/aGg	3/7	1	2	FACETS	0.758	0.674	0.846	0.758	0.674	0.846	SUBCLONAL	1	TRUE	1	0.733822532449766	2		202	284	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778262	27778262	+	stop_lost	Nonstop_Mutation	SNP	A	A	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	135	235	0	ENST00000369163.2:c.411A>T	p.Ter137CysextTer6	p.*137Cext*6	ENST00000369163	NM_003536.2	137	tgA/tgT	1/1	1	2	FACETS	0.946	0.869	1	0.946	0.869	1	CLONAL	1	TRUE	1	0.733822532449766	2		235	389	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910691	29910691	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	243	678	0	ENST00000376809.5:c.231G>T	p.Glu77Asp	p.E77D	ENST00000376809	NM_002116.7	77	gaG/gaT	2/8	1	2	FACETS	0.793	0.743	0.845	0.793	0.743	0.845	SUBCLONAL	1	TRUE	1	0.733822532449766	2		678	835	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670441	30670441	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	138	280	0	ENST00000376406.3:c.5992-1G>T		p.X1998_splice	ENST00000376406	NM_014641.2	1998			1	2	FACETS	0.957	0.88	1	0.957	0.88	1	CLONAL	1	TRUE	1	0.733822532449766	2		280	393	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671580	30671580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	181	410	1	ENST00000376406.3:c.5380G>A	p.Ala1794Thr	p.A1794T	ENST00000376406	NM_014641.2	1794	Gca/Aca	10/15	1	2	FACETS	0.934	0.868	1	0.934	0.868	1	CLONAL	1	TRUE	1	0.733822532449766	2		411	528	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672050	30672050	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	202	440	0	ENST00000376406.3:c.4910C>T	p.Ala1637Val	p.A1637V	ENST00000376406	NM_014641.2	1637	gCc/gTc	10/15	1	2	FACETS	0.962	0.899	1	0.962	0.899	1	CLONAL	1	TRUE	1	0.733822532449766	2		440	572	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681702	30681702	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1045903416	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	138	293	0	ENST00000376406.3:c.395G>A	p.Arg132His	p.R132H	ENST00000376406	NM_014641.2	132	cGc/cAc	3/15	1	2	FACETS	0.924	0.849	1	0.924	0.849	1	CLONAL	1	TRUE	1	0.733822532449766	2		293	407	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940432	31940432	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	169	421	1	ENST00000375333.2:c.465G>T	p.Gln155His	p.Q155H	ENST00000375333	NM_032454.1	155	caG/caT	3/8	1	2	FACETS	0.839	0.776	0.904	0.839	0.776	0.904	CLONAL	1	TRUE	1	0.733822532449766	2		422	549	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940482	31940482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1179080235	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	228	416	0	ENST00000375333.2:c.515G>A	p.Arg172Lys	p.R172K	ENST00000375333	NM_032454.1	172	aGg/aAg	3/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.733822532449766	2		416	588	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948227	31948227	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	120	278	0	ENST00000375333.2:c.816-1G>T		p.X272_splice	ENST00000375333	NM_032454.1	272			1	2	FACETS	0.861	0.785	0.939	0.861	0.785	0.939	CLONAL	1	TRUE	1	0.733822532449766	2		278	380	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165092	32165092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1463590184	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	199	346	0	ENST00000375023.3:c.5036C>T	p.Ala1679Val	p.A1679V	ENST00000375023	NM_004557.3	1679	gCt/gTt	27/30	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.733822532449766	2		346	520	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185808	32185808	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	187	403	0	ENST00000375023.3:c.1588G>A	p.Asp530Asn	p.D530N	ENST00000375023	NM_004557.3	530	Gac/Aac	9/30	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.733822532449766	2		403	461	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816896	32816896	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1159721335	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	134	297	0	ENST00000354258.4:c.1429-1G>T		p.X477_splice	ENST00000354258	NM_000593.5	477			1	2	FACETS	0.913	0.838	0.99	0.913	0.838	0.99	CLONAL	1	TRUE	1	0.733822532449766	2		297	400	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818162	32818162	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	218	418	1	ENST00000354258.4:c.1363C>T	p.Gln455Ter	p.Q455*	ENST00000354258	NM_000593.5	455	Caa/Taa	5/11	1	2	FACETS	0.923	0.863	0.984	0.923	0.863	0.984	CLONAL	1	TRUE	1	0.733822532449766	2		419	644	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820165	32820165	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	146	368	0	ENST00000354258.4:c.893G>T	p.Ser298Ile	p.S298I	ENST00000354258	NM_000593.5	298	aGt/aTt	2/11	1	2	FACETS	0.896	0.825	0.969	0.896	0.825	0.969	CLONAL	1	TRUE	1	0.733822532449766	2		368	444	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287515	33287515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	180	364	0	ENST00000374542.5:c.1582G>A	p.Val528Met	p.V528M	ENST00000374542	NM_001141970.1	528	Gtg/Atg	6/8	1	2	FACETS	0.94	0.873	1	0.94	0.873	1	CLONAL	1	TRUE	1	0.733822532449766	2		364	522	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140787	37140787	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1183187519	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	139	262	2	ENST00000373509.5:c.623G>T	p.Ser208Ile	p.S208I	ENST00000373509	NM_002648.3	208	aGc/aTc	5/6	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.733822532449766	2		264	370	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066669	94066669	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	167	311	0	ENST00000369303.4:c.1090A>G	p.Thr364Ala	p.T364A	ENST00000369303	NM_004440.3	364	Acc/Gcc	5/17	1	2	FACETS	0.954	0.884	1	0.954	0.884	1	CLONAL	1	TRUE	1	0.733822532449766	2		311	477	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120297	94120297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	85	143	0	ENST00000369303.4:c.754G>A	p.Ala252Thr	p.A252T	ENST00000369303	NM_004440.3	252	Gca/Aca	3/17	1	2	FACETS	0.973	0.875	1	0.973	0.875	1	CLONAL	1	TRUE	1	0.733822532449766	2		143	238	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109311950	109311950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1261981726	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	210	402	0	ENST00000436639.2:c.1322C>T	p.Ala441Val	p.A441V	ENST00000436639	NM_014454.2	441	gCt/gTt	8/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.733822532449766	2		402	521	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709026	117709026	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	187	351	0	ENST00000368508.3:c.1931A>C	p.Lys644Thr	p.K644T	ENST00000368508	NM_002944.2	644	aAa/aCa	13/43	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.733822532449766	2		351	473	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983373	149983373	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	123	275	0	ENST00000253339.5:c.2885T>C	p.Val962Ala	p.V962A	ENST00000253339		962	gTt/gCt	7/7	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.733822532449766	2		275	332	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001335	150001335	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	161	326	0	ENST00000253339.5:c.2269C>A	p.Leu757Met	p.L757M	ENST00000253339		757	Ctg/Atg	4/7	1	2	FACETS	0.982	0.909	1	0.982	0.909	1	CLONAL	1	TRUE	1	0.733822532449766	2		326	447	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004595	150004595	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	197	411	0	ENST00000253339.5:c.1630C>A	p.Pro544Thr	p.P544T	ENST00000253339		544	Cca/Aca	3/7	1	2	FACETS	0.991	0.924	1	0.991	0.924	1	CLONAL	1	TRUE	1	0.733822532449766	2		411	542	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099610	157099610	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	44	56	0	ENST00000346085.5:c.547G>T	p.Gly183Cys	p.G183C	ENST00000346085	NM_020732.3	183	Ggc/Tgc	1/20	1	2	FACETS	0.952	0.818	1	0.952	0.818	1	CLONAL	1	TRUE	1	0.733822532449766	2		56	126	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042116	6042116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881916	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	67	109	0	ENST00000265849.7:c.505C>T	p.Arg169Cys	p.R169C	ENST00000265849	NM_000535.5	169	Cgc/Tgc	5/15	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.733822532449766	2		109	168	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441629	6441629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	192	398	0	ENST00000356142.4:c.476C>T	p.Pro159Leu	p.P159L	ENST00000356142	NM_018890.3	159	cCg/cTg	6/7	1	2	FACETS	0.976	0.91	1	0.976	0.91	1	CLONAL	1	TRUE	1	0.733822532449766	2		398	536	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975457	13975457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	99	206	0	ENST00000405192.2:c.430C>T	p.Pro144Ser	p.P144S	ENST00000405192	NM_001163147.1	144	Cca/Tca	7/12	1	2	FACETS	0.851	0.769	0.937	0.851	0.769	0.937	CLONAL	1	TRUE	1	0.733822532449766	2		206	317	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221761	55221761	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	211	371	0	ENST00000275493.2:c.805C>A	p.Leu269Ile	p.L269I	ENST00000275493	NM_005228.3	269	Ctc/Atc	7/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.733822532449766	2		371	534	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508409	106508409	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	86	150	0	ENST00000359195.3:c.403A>G	p.Ile135Val	p.I135V	ENST00000359195	NM_002649.2	135	Atc/Gtc	2/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.733822532449766	2		150	211	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509484	106509484	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	217	343	0	ENST00000359195.3:c.1478A>G	p.Asp493Gly	p.D493G	ENST00000359195	NM_002649.2	493	gAc/gGc	2/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.733822532449766	2		343	550	SUCCESS
MET	4233	MSKCC	GRCh37	7	116413350	116413350	+	intron_variant	Intron	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	318	610	0	ENST00000397752.3:c.3028+1307G>A		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.733822532449766	2		610	825	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128849189	128849189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17710891	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	186	367	0	ENST00000249373.3:c.1417G>A	p.Asp473Asn	p.D473N	ENST00000249373	NM_005631.4	473	Gac/Aac	8/12	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.733822532449766	2		367	489	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851955	128851955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	224	457	1	ENST00000249373.3:c.2027G>A	p.Arg676Lys	p.R676K	ENST00000249373	NM_005631.4	676	aGg/aAg	12/12	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.733822532449766	2		458	563	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846039	151846039	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	131	225	0	ENST00000262189.6:c.12973C>A	p.Leu4325Met	p.L4325M	ENST00000262189	NM_170606.2	4325	Ctg/Atg	52/59	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.733822532449766	2		225	343	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860837	151860837	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	133	250	0	ENST00000262189.6:c.9825G>A	p.Met3275Ile	p.M3275I	ENST00000262189	NM_170606.2	3275	atG/atA	43/59	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.733822532449766	2		250	348	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133352	38133352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1271164016	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	150	261	0	ENST00000317025.8:c.4121C>T	p.Ala1374Val	p.A1374V	ENST00000317025	NM_023034.1	1374	gCt/gTt	24/24	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.733822532449766	2		261	394	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978600	70978600	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	184	384	0	ENST00000276594.2:c.1053G>T	p.Glu351Asp	p.E351D	ENST00000276594	NM_024504.3	351	gaG/gaT	5/8	1	2	FACETS	0.972	0.904	1	0.972	0.904	1	CLONAL	1	TRUE	1	0.733822532449766	2		384	516	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868966	117868966	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	118	264	0	ENST00000297338.2:c.733C>A	p.Pro245Thr	p.P245T	ENST00000297338	NM_006265.2	245	Ccc/Acc	7/14	1	2	FACETS	0.851	0.775	0.929	0.851	0.775	0.929	CLONAL	1	TRUE	1	0.733822532449766	2		264	378	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141569604	141569604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	122	247	0	ENST00000220592.5:c.680C>T	p.Ala227Val	p.A227V	ENST00000220592	NM_012154.3	227	gCa/gTa	6/19	1	2	FACETS	0.908	0.83	0.989	0.908	0.83	0.989	CLONAL	1	TRUE	1	0.733822532449766	2		247	366	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595218	141595218	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	188	340	1	ENST00000220592.5:c.215G>A	p.Arg72Lys	p.R72K	ENST00000220592	NM_012154.3	72	aGg/aAg	2/19	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.733822532449766	2		341	510	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080541	5080541	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs199661171	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	83	150	0	ENST00000381652.3:c.2292A>C	p.Gln764His	p.Q764H	ENST00000381652	NM_004972.3	764	caA/caC	18/25	1	2	FACETS	0.931	0.835	1	0.931	0.835	1	CLONAL	1	TRUE	1	0.733822532449766	2		150	243	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8338930	8338930	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1380382010	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	127	259	0	ENST00000356435.5:c.5371G>T	p.Asp1791Tyr	p.D1791Y	ENST00000356435		1791	Gat/Tat	32/35	1	2	FACETS	0.978	0.897	1	0.978	0.897	1	CLONAL	1	TRUE	1	0.733822532449766	2		259	354	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180244	27180244	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1564080006	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	159	332	0	ENST00000380036.4:c.908A>G	p.His303Arg	p.H303R	ENST00000380036	NM_000459.3	303	cAc/cGc	7/23	1	2	FACETS	0.91	0.841	0.981	0.91	0.841	0.981	CLONAL	1	TRUE	1	0.733822532449766	2		332	476	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002653	37002653	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	148	300	0	ENST00000358127.4:c.596G>T	p.Arg199Ile	p.R199I	ENST00000358127	NM_001280556.1	199	aGa/aTa	5/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.733822532449766	2		300	364	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37006526	37006526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	102	205	0	ENST00000358127.4:c.419G>A	p.Arg140Gln	p.R140Q	ENST00000358127	NM_001280556.1	140	cGg/cAg	4/10	1	2	FACETS	0.815	0.737	0.897	0.815	0.737	0.897	CLONAL	1	TRUE	1	0.733822532449766	2		205	341	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020790	37020790	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	166	305	0	ENST00000358127.4:c.55G>T	p.Gly19Ter	p.G19*	ENST00000358127	NM_001280556.1	19	Gga/Tga	2/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.733822532449766	2		305	424	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342722	87342722	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	147	363	0	ENST00000277120.3:c.1007T>G	p.Val336Gly	p.V336G	ENST00000277120		336	gTt/gGt	9/19	1	2	FACETS	0.842	0.774	0.911	0.842	0.774	0.911	CLONAL	1	TRUE	1	0.733822532449766	2		363	476	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209585	98209585	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536440590	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	167	346	1	ENST00000331920.6:c.3953C>T	p.Pro1318Leu	p.P1318L	ENST00000331920	NM_000264.3	1318	cCg/cTg	23/24	1	2	FACETS	0.966	0.896	1	0.966	0.896	1	CLONAL	1	TRUE	1	0.733822532449766	2		347	471	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220348	98220348	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	111	259	0	ENST00000331920.6:c.3115A>C	p.Thr1039Pro	p.T1039P	ENST00000331920	NM_000264.3	1039	Aca/Cca	18/24	1	2	FACETS	0.906	0.824	0.99	0.906	0.824	0.99	CLONAL	1	TRUE	1	0.733822532449766	2		259	334	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242737	98242737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	147	308	0	ENST00000331920.6:c.880C>T	p.Arg294Cys	p.R294C	ENST00000331920	NM_000264.3	294	Cgc/Tgc	6/24	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.733822532449766	2		308	391	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891254	101891254	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	145	315	0	ENST00000374994.4:c.215T>C	p.Ile72Thr	p.I72T	ENST00000374994	NM_004612.2	72	aTa/aCa	2/9	1	2	FACETS	0.888	0.817	0.961	0.888	0.817	0.961	CLONAL	1	TRUE	1	0.733822532449766	2		315	445	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894964	101894964	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	97	186	0	ENST00000374994.4:c.517G>T	p.Glu173Ter	p.E173*	ENST00000374994	NM_004612.2	173	Gag/Tag	3/9	1	2	FACETS	0.921	0.833	1	0.921	0.833	1	CLONAL	1	TRUE	1	0.733822532449766	2		186	287	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907023	101907023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	96	193	0	ENST00000374994.4:c.983C>T	p.Ala328Val	p.A328V	ENST00000374994	NM_004612.2	328	gCc/gTc	6/9	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.733822532449766	2		193	249	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250311	110250311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753267332	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	234	482	2	ENST00000374672.4:c.364G>A	p.Ala122Thr	p.A122T	ENST00000374672	NM_004235.4	122	Gcc/Acc	3/5	1	2	FACETS	0.987	0.927	1	0.987	0.927	1	CLONAL	1	TRUE	1	0.733822532449766	2		484	646	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771986	135771986	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	94	219	0	ENST00000298552.3:c.3131A>T	p.Glu1044Val	p.E1044V	ENST00000298552	NM_001162426.1	1044	gAg/gTg	23/23	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.733822532449766	2		219	248	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137321022	137321022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	204	473	0	ENST00000481739.1:c.979G>A	p.Ala327Thr	p.A327T	ENST00000481739	NM_002957.4	327	Gcc/Acc	7/10	1	2	FACETS	0.995	0.929	1	0.995	0.929	1	CLONAL	1	TRUE	1	0.733822532449766	2		473	559	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391608	139391608	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376422513	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	228	496	0	ENST00000277541.6:c.6583G>A	p.Gly2195Ser	p.G2195S	ENST00000277541	NM_017617.3	2195	Ggc/Agc	34/34	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.733822532449766	2		496	587	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391992	139391992	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	154	348	0	ENST00000277541.6:c.6199C>A	p.Leu2067Met	p.L2067M	ENST00000277541	NM_017617.3	2067	Ctg/Atg	34/34	1	2	FACETS	0.992	0.918	1	0.992	0.918	1	CLONAL	1	TRUE	1	0.733822532449766	2		348	423	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400206	139400206	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752551426	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	186	403	0	ENST00000277541.6:c.4142C>T	p.Pro1381Leu	p.P1381L	ENST00000277541	NM_017617.3	1381	cCc/cTc	25/34	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.733822532449766	2		403	483	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400299	139400299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150343794	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	227	404	2	ENST00000277541.6:c.4049G>A	p.Arg1350His	p.R1350H	ENST00000277541	NM_017617.3	1350	cGt/cAt	25/34	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.733822532449766	2		406	520	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139563116	139563116	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	148	342	0	ENST00000308874.7:c.188G>A	p.Ser63Asn	p.S63N	ENST00000308874		63	aGc/aAc	4/10	1	2	FACETS	0.945	0.871	1	0.945	0.871	1	CLONAL	1	TRUE	1	0.733822532449766	2		342	427	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916542	39916542	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	196	401	0	ENST00000378444.4:c.4461T>G	p.Ile1487Met	p.I1487M	ENST00000378444	NM_001123385.1	1487	atT/atG	11/15	1	2	FACETS	0.937	0.874	1	0.937	0.874	1	CLONAL	1	TRUE	1	0.733822532449766	2		401	570	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921574	39921574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	201	348	0	ENST00000378444.4:c.4246C>T	p.Pro1416Ser	p.P1416S	ENST00000378444	NM_001123385.1	1416	Cca/Tca	10/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.733822532449766	2		348	519	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224571	53224571	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	240	430	1	ENST00000375401.3:c.3142C>A	p.Leu1048Met	p.L1048M	ENST00000375401	NM_004187.3	1048	Ctg/Atg	21/26	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.733822532449766	2		431	601	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239882	53239882	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	150	310	0	ENST00000375401.3:c.1559G>T	p.Ser520Ile	p.S520I	ENST00000375401	NM_004187.3	520	aGt/aTt	11/26	1	2	FACETS	0.931	0.859	1	0.931	0.859	1	CLONAL	1	TRUE	1	0.733822532449766	2		310	439	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240770	53240770	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	213	413	0	ENST00000375401.3:c.1310C>A	p.Thr437Asn	p.T437N	ENST00000375401	NM_004187.3	437	aCt/aAt	10/26	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.733822532449766	2		413	580	SUCCESS
AR	367	MSKCC	GRCh37	X	66766027	66766027	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	264	547	1	ENST00000374690.3:c.1039C>A	p.Leu347Ile	p.L347I	ENST00000374690	NM_000044.3	347	Ctc/Atc	1/8	1	2	FACETS	0.982	0.925	1	0.982	0.925	1	CLONAL	1	TRUE	1	0.733822532449766	2		548	733	SUCCESS
AR	367	MSKCC	GRCh37	X	66863187	66863187	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	158	322	0	ENST00000374690.3:c.1706G>T	p.Gly569Val	p.G569V	ENST00000374690	NM_000044.3	569	gGg/gTg	2/8	1	2	FACETS	0.974	0.901	1	0.974	0.901	1	CLONAL	1	TRUE	1	0.733822532449766	2		322	442	SUCCESS
AR	367	MSKCC	GRCh37	X	66863211	66863211	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	148	303	1	ENST00000374690.3:c.1730G>A	p.Cys577Tyr	p.C577Y	ENST00000374690	NM_000044.3	577	tGt/tAt	2/8	1	2	FACETS	0.911	0.839	0.984	0.911	0.839	0.984	CLONAL	1	TRUE	1	0.733822532449766	2		304	443	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338681	70338681	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	152	389	0	ENST00000374080.3:c.77C>A	p.Pro26His	p.P26H	ENST00000374080		26	cCt/cAt	1/45	1	2	FACETS	0.908	0.838	0.981	0.908	0.838	0.981	CLONAL	1	TRUE	1	0.733822532449766	2		389	456	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340917	70340917	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	170	368	0	ENST00000374080.3:c.650C>A	p.Ser217Tyr	p.S217Y	ENST00000374080		217	tCc/tAc	5/45	1	2	FACETS	0.936	0.868	1	0.936	0.868	1	CLONAL	1	TRUE	1	0.733822532449766	2		368	495	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342197	70342197	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	86	246	0	ENST00000374080.3:c.1248+1G>A		p.X416_splice	ENST00000374080		416			1	2	FACETS	0.696	0.621	0.774	0.696	0.621	0.774	SUBCLONAL	1	TRUE	1	0.733822532449766	2		246	337	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342400	70342400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	190	400	3	ENST00000374080.3:c.1291C>T	p.Arg431Trp	p.R431W	ENST00000374080		431	Cgg/Tgg	9/45	1	2	FACETS	0.963	0.897	1	0.963	0.897	1	CLONAL	1	TRUE	1	0.733822532449766	2		403	538	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939957	76939957	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	185	363	0	ENST00000373344.5:c.791A>G	p.Tyr264Cys	p.Y264C	ENST00000373344	NM_000489.3	264	tAt/tGt	9/35	1	2	FACETS	0.948	0.882	1	0.948	0.882	1	CLONAL	1	TRUE	1	0.733822532449766	2		363	532	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613644	100613644	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	186	337	2	ENST00000308731.7:c.935C>T	p.Ala312Val	p.A312V	ENST00000308731	NM_000061.2	312	gCt/gTt	11/19	1	2	FACETS	0.982	0.915	1	0.982	0.915	1	CLONAL	1	TRUE	1	0.733822532449766	2		339	516	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020144	123020144	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	259	430	0	ENST00000355640.3:c.632A>G	p.Glu211Gly	p.E211G	ENST00000355640		211	gAa/gGa	2/7	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.733822532449766	2		430	604	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123505215	123505215	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	85	290	0	ENST00000371139.4:c.361C>A	p.Pro121Thr	p.P121T	ENST00000371139	NM_001114937.2	121	Cct/Act	4/4	1	2	FACETS	0.81	0.725	0.899	0.81	0.725	0.899	CLONAL	1	TRUE	1	0.733822532449766	2		290	286	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860040	152860040	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	127	360	0	ENST00000406277.2:c.388C>A	p.Leu130Met	p.L130M	ENST00000406277	NM_152274.4	130	Ctg/Atg	5/7	1		FACETS		0.749	0.894				CLONAL	1	TRUE	1	0.733822532449766	2		360	422	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435303	110435303	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1260159870	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	78	126	0	ENST00000375856.3:c.3098C>T	p.Pro1033Leu	p.P1033L	ENST00000375856	NM_003749.2	1033	cCa/cTa	1/2	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.733822532449766	2		126	199	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1036330	1036333	+	missense_variant	Missense_Mutation	ONP	CGTC	CGTC	TGTA	novel	NA	P-0026297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	128	324	0	ENST00000358495.3:c.445_448delinsTACA	p.Asp149_Gly150delinsTyrArg	p.D149_G150delinsYR	ENST00000358495	NM_134424.2	149	GACGgg/TACAgg	6/12	1	2	FACETS	0.839	0.767	0.913	0.839	0.767	0.913	CLONAL	1	TRUE	1	0.733822532449766	2		324	416	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0026298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	29	496	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.995	0.805	1	0.995	0.805	1	CLONAL	1	FALSE	1	0.308510739383524	2		496	189	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805051	43805051	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	74	330	0	ENST00000372470.3:c.501C>A	p.Tyr167Ter	p.Y167*	ENST00000372470	NM_005373.2	167	taC/taA	4/12	0.308510739383524	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	0	0.308510739383524	1		330	320	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244710	46244710	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	23	320	0	ENST00000334344.6:c.2804A>G	p.Gln935Arg	p.Q935R	ENST00000334344	NM_152641.2	935	cAa/cGa	15/21	0.308510739383524	0	FACETS	0.889	0.704	1			1	CLONAL	1	FALSE	0	0.308510739383524	0		320	116	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968931	15968931	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	25	283	0	ENST00000268712.3:c.4819G>C	p.Glu1607Gln	p.E1607Q	ENST00000268712	NM_006311.3	1607	Gag/Cag	33/46	1	2	FACETS	0.806	0.639	0.996	0.806	0.639	0.996	CLONAL	1	FALSE	1	0.308510739383524	2		283	201	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610075	10610096	+	frameshift_variant	Frame_Shift_Del	DEL	CCAAAATGCATGTAGATGTACT	CCAAAATGCATGTAGATGTACT	-	novel	NA	P-0026298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	197	362	0	ENST00000171111.5:c.614_635del	p.Glu205GlyfsTer18	p.E205Gfs*18	ENST00000171111	NM_203500.1	205	gAGTACATCTACATGCATTTTGGg/gg	2/6	0.254382109788574	3	FACETS	0.918	0.857	0.981	0.918	0.857	0.981	CLONAL	3	FALSE	0	0.308510739383524	3		362	535	SUCCESS
FH	2271	MSKCC	GRCh37	1	241676946	241676946	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	173	254	0	ENST00000366560.3:c.335T>C	p.Leu112Pro	p.L112P	ENST00000366560	NM_000143.3	112	cTt/cCt	3/10	0.569560204325538	2	FACETS	0.977	0.918	1	0.977	0.918	1	CLONAL	2	TRUE	0	0.569560204325538	2		254	311	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0026316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	78	301	1	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	0.709	0.627	0.796	0.709	0.627	0.796	SUBCLONAL	1	TRUE	1	0.589509586181822	2		302	373	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0026316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	70	162	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.589509586181822	1	FACETS	0.896	0.797	0.997	0.896	0.797	0.997	CLONAL	1	TRUE	0	0.589509586181822	1		162	187	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435069	49435073	+	frameshift_variant	Frame_Shift_Del	DEL	TGAGG	TGAGG	-	novel	NA	P-0026316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	219	343	0	ENST00000301067.7:c.6480_6484del	p.Phe2160LeufsTer40	p.F2160Lfs*40	ENST00000301067	NM_003482.3	2160	ttCCTCAag/ttag	31/54	0.589509586181822	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.589509586181822	3		343	465	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830100	72830101	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0026316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	101	300	0	ENST00000268489.5:c.6480dup	p.Arg2161AlafsTer5	p.R2161Afs*5	ENST00000268489	NM_006885.3	2160	-/G	9/10	1	2	FACETS	0.848	0.764	0.937	0.848	0.764	0.937	CLONAL	1	TRUE	1	0.589509586181822	2		300	404	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933965	39933966	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0026316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	20	240	0	ENST00000378444.4:c.633_634insG	p.Lys212GlufsTer89	p.K212Efs*89	ENST00000378444	NM_001123385.1	211	-/G	4/15	1	1	FACETS	0.158	0.12	0.202	0.158	0.12	0.202	SUBCLONAL	1	TRUE	0	0.589509586181822	1		240	303	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	154	442	1	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.266858542014217	4	FACETS	0.86	0.79	0.934	0.86	0.79	0.934	CLONAL	2	TRUE	2	0.370700270995077	4		443	662	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	167	471	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.266858542014217	4	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	2	0.370700270995077	4		472	599	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	227	319	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	0.370700270995077	3	FACETS	1	0.98	1	1	0.994	1	CLONAL	3	TRUE	1	0.370700270995077	3		319	447	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250867	153250867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	414	279	0	ENST00000281708.4:c.1193C>T	p.Ser398Phe	p.S398F	ENST00000281708	NM_033632.3	398	tCt/tTt	8/12	0.370700270995077	14	FACETS	1	0.979	1			1	CLONAL	11	TRUE	NA	0.370700270995077	14		279	641	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973495	15973495	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	30	163	0	ENST00000268712.3:c.4497G>A	p.Met1499Ile	p.M1499I	ENST00000268712	NM_006311.3	1499	atG/atA	31/46	0.266858542014217	4	FACETS	1	0.859	1	0.536	0.435	0.649	CLONAL	1	TRUE	2	0.370700270995077	4		163	207	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253817	153253817	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	67	300	0	ENST00000281708.4:c.916C>T	p.Gln306Ter	p.Q306*	ENST00000281708	NM_033632.3	306	Cag/Tag	6/12	0.370700270995077	14	FACETS	0.874	0.759	0.998			1	CLONAL	2	TRUE	NA	0.370700270995077	14		300	667	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057853	27057853	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	148	462	1	ENST00000324856.7:c.1561C>T	p.Gln521Ter	p.Q521*	ENST00000324856	NM_006015.4	521	Cag/Tag	3/20	0.318068401234251	3	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	1	0.370700270995077	3		463	458	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276442	115276442	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	77	433	0	ENST00000438362.2:c.886C>T	p.Gln296Ter	p.Q296*	ENST00000438362	NM_001242891.1	296	Caa/Taa	9/20	0.266858542014217	4	FACETS	0.818	0.724	0.918	0.818	0.724	0.918	CLONAL	2	TRUE	2	0.370700270995077	4		433	348	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843624	3843624	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	81	221	0	ENST00000262367.5:c.979C>T	p.Gln327Ter	p.Q327*	ENST00000262367	NM_004380.2	327	Cag/Tag	4/31	0.370700270995077	3	FACETS	0.945	0.843	1	0.945	0.843	1	CLONAL	2	TRUE	1	0.370700270995077	3		221	274	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023163	33023163	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1216397987	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	89	336	0	ENST00000300177.4:c.272G>A	p.Arg91Gln	p.R91Q	ENST00000300177	NM_001191322.1	91	cGa/cAa	2/2	0.370700270995077	6	FACETS	0.905	0.806	1	0.452	0.403	0.505	CLONAL	2	TRUE	2	0.370700270995077	6		336	462	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831471	89831471	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1286812517	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	79	358	0	ENST00000389301.3:c.2605C>T	p.Gln869Ter	p.Q869*	ENST00000389301	NM_000135.2	869	Cag/Tag	28/43	0.318068401234251	3	FACETS	1	0.977	1	0.736	0.653	0.825	CLONAL	1	TRUE	1	0.370700270995077	3		358	343	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120496253	120496253	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	98	352	0	ENST00000256646.2:c.2278G>A	p.Glu760Lys	p.E760K	ENST00000256646	NM_024408.3	760	Gaa/Aaa	14/34	0.266858542014217	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.370700270995077	4		352	323	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838426	156838426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	122	482	2	ENST00000524377.1:c.704C>T	p.Ser235Leu	p.S235L	ENST00000524377	NM_002529.3	235	tCa/tTa	6/17	0.266858542014217	4	FACETS	0.871	0.791	0.954	0.871	0.791	0.954	CLONAL	2	TRUE	2	0.370700270995077	4		484	518	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939507	71939507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373971775	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	215	552	0	ENST00000298229.2:c.362G>A	p.Arg121Gln	p.R121Q	ENST00000298229	NM_001567.3	121	cGa/cAa	3/28	0.318068401234251	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.370700270995077	3		552	585	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156272	119156272	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	48	248	0	ENST00000264033.4:c.1937C>T	p.Ser646Phe	p.S646F	ENST00000264033	NM_005188.3	646	tCc/tTc	11/16	0.318068401234251	3	FACETS	1	0.942	1	0.611	0.521	0.709	CLONAL	1	TRUE	1	0.370700270995077	3		248	251	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447007	49447007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	111	273	0	ENST00000301067.7:c.937C>T	p.His313Tyr	p.H313Y	ENST00000301067	NM_003482.3	313	Cac/Tac	7/54	0.318068401234251	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.370700270995077	3		273	284	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349366	73349366	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	39	291	0	ENST00000377767.4:c.970G>C	p.Glu324Gln	p.E324Q	ENST00000377767	NM_014953.3	324	Gaa/Caa	6/21	0.370700270995077	3	FACETS	1	0.852	1	0.511	0.426	0.604	CLONAL	1	TRUE	1	0.370700270995077	3		291	244	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988387	36988387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1488542462	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	34	84	0	ENST00000354822.5:c.266G>A	p.Gly89Glu	p.G89E	ENST00000354822	NM_001079668.2	89	gGg/gAg	2/3	0.370700270995077	3	FACETS	1	0.951	1	0.75	0.622	0.888	CLONAL	1	TRUE	1	0.370700270995077	3		84	145	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991070	41991070	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	30	309	0	ENST00000219905.7:c.2023G>C	p.Asp675His	p.D675H	ENST00000219905	NM_001164273.1	675	Gac/Cac	4/24	0.370700270995077	6	FACETS	0.736	0.593	0.898	0.184	0.148	0.225	SUBCLONAL	1	TRUE	2	0.370700270995077	6		309	383	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629038	14629038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1490195444	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	61	263	0	ENST00000254322.2:c.124G>A	p.Glu42Lys	p.E42K	ENST00000254322	NM_006145.1	42	Gag/Aag	1/3	NA	2	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.370700270995077	2		263	243	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872189	45872189	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	126	383	0	ENST00000391945.4:c.245A>G	p.Lys82Arg	p.K82R	ENST00000391945	NM_000400.3	82	aAg/aGg	4/23	0.321778828796696	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.370700270995077	2		383	297	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42840456	42840456	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	79	304	0	ENST00000398585.3:c.1292C>T	p.Ser431Leu	p.S431L	ENST00000398585	NM_001135099.1	431	tCa/tTa	12/14	0.266858542014217	4	FACETS	0.852	0.755	0.954	0.852	0.755	0.954	CLONAL	2	TRUE	2	0.370700270995077	4		304	343	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158225	47158225	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	22	245	0	ENST00000409792.3:c.4474C>G	p.Arg1492Gly	p.R1492G	ENST00000409792	NM_014159.6	1492	Cga/Gga	4/21	0.266858542014217	4	FACETS	0.552	0.428	0.695	0.276	0.214	0.348	SUBCLONAL	1	TRUE	2	0.370700270995077	4		245	295	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094889	143094889	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	35	363	0	ENST00000262992.4:c.1255C>G	p.Gln419Glu	p.Q419E	ENST00000262992	NM_001101669.1	419	Caa/Gaa	14/24	0.370700270995077	6	FACETS	0.751	0.615	0.903			1	CLONAL	1	TRUE	NA	0.370700270995077	6		363	438	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630695	187630756	+	frameshift_variant	Frame_Shift_Del	DEL	AGAAAGCAAAAGTCTCCGAGAATGTACTCTTCAGCTTTGAACAGGTTTTCACTGTCTCCGGA	AGAAAGCAAAAGTCTCCGAGAATGTACTCTTCAGCTTTGAACAGGTTTTCACTGTCTCCGGA	-	novel	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	66	379	0	ENST00000441802.2:c.226_287del	p.Ser76LysfsTer13	p.S76Kfs*13	ENST00000441802	NM_005245.3	76	TCCGGAGACAGTGAAAACCTGTTCAAAGCTGAAGAGTACATTCTCGGAGACTTTTGCTTTCTa/a	2/27	0.370700270995077	3	FACETS	1	0.948	1	0.585	0.51	0.664	CLONAL	1	TRUE	1	0.370700270995077	3		379	361	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931372	131931372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	103	284	0	ENST00000265335.6:c.2077G>A	p.Glu693Lys	p.E693K	ENST00000265335		693	Gag/Aag	13/25	0.266858542014217	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.370700270995077	4		284	342	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771139	161771139	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	52	332	0	ENST00000366898.1:c.1390G>A	p.Asp464Asn	p.D464N	ENST00000366898	NM_004562.2	464	Gac/Aac	12/12	1	2	FACETS	0.948	0.812	1	0.948	0.812	1	CLONAL	1	TRUE	1	0.370700270995077	2		332	296	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221753	55221753	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	64	383	0	ENST00000275493.2:c.797C>T	p.Pro266Leu	p.P266L	ENST00000275493	NM_005228.3	266	cCa/cTa	7/28	0.266858542014217	4	FACETS	1	0.872	1	0.502	0.436	0.574	CLONAL	1	TRUE	2	0.370700270995077	4		383	471	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411975	116411975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910937816	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	161	480	0	ENST00000397752.3:c.2960G>A	p.Arg987Gln	p.R987Q	ENST00000397752	NM_000245.2	987	cGa/cAa	14/21	0.266858542014217	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.370700270995077	4		480	502	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172201	38172201	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	39	306	0	ENST00000317025.8:c.2206C>T	p.Pro736Ser	p.P736S	ENST00000317025	NM_023034.1	736	Cct/Tct	12/24	NA	2	FACETS	0.866	0.723	1			1	INDETERMINATE	1	TRUE	NA	0.370700270995077	2		306	243	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38194841	38194841	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	62	381	0	ENST00000317025.8:c.892A>T	p.Thr298Ser	p.T298S	ENST00000317025	NM_023034.1	298	Act/Tct	4/24	NA	2	FACETS	1	0.873	1			1	INDETERMINATE	1	TRUE	NA	0.370700270995077	2		381	333	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759978	133759985	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGGAGA	AGGGGAGA	-	novel	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	130	514	0	ENST00000318560.5:c.2302_2309del	p.Gly768GlnfsTer3	p.G768Qfs*3	ENST00000318560	NM_005157.4	767	gcAGGGGAGAac/gcac	11/11	0.318068401234251	3	FACETS	0.813	0.742	0.888	0.813	0.742	0.888	CLONAL	2	TRUE	1	0.370700270995077	3		514	511	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15809130	15809130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	95	189	0	ENST00000307771.7:c.115G>A	p.Asp39Asn	p.D39N	ENST00000307771	NM_005089.3	39	Gac/Aac	2/11	0.28134167308627	2	FACETS	0.904	0.827	0.981			1	CLONAL	3	TRUE	NA	0.370700270995077	2		189	189	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870265	44870265	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	85	163	0	ENST00000377967.4:c.443+1G>A		p.X148_splice	ENST00000377967	NM_021140.2	148			0.28134167308627	2	FACETS	0.986	0.901	1			1	CLONAL	3	TRUE	NA	0.370700270995077	2		163	155	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045172	47045172	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	66	226	0	ENST00000377604.3:c.2413G>C	p.Glu805Gln	p.E805Q	ENST00000377604	NM_001204468.1	805	Gag/Cag	21/24	0.28134167308627	2	FACETS	1	0.959	1			1	CLONAL	1	TRUE	NA	0.370700270995077	2		226	288	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272264	15272264	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	30	333	0	ENST00000263388.2:c.6175G>C	p.Gly2059Arg	p.G2059R	ENST00000263388	NM_000435.2	2059	Ggg/Cgg	33/33	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.370700270995077	NA		333	328	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983251	149983254	+	missense_variant	Missense_Mutation	ONP	CATC	CATC	TATT	novel	NA	P-0026324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	41	389	0	ENST00000253339.5:c.3004_3007delinsAATA	p.Asp1002_Glu1003delinsAsnLys	p.D1002_E1003delinsNK	ENST00000253339		1002	GATGaa/AATAaa	7/7	1	2	FACETS	0.881	0.739	1	0.881	0.739	1	CLONAL	1	TRUE	1	0.370700270995077	2		389	251	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0026326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	210	854	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.449893849629954	2		854	631	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	68	474	0				ENST00000310581	NM_198253.2	-/1132			0.235770995102079	3	FACETS	1	0.967	1	0.817	0.731	0.905	INDETERMINATE	2	TRUE	0	0.449893849629954	3		474	151	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444317	50444317	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	89	256	1	ENST00000331340.3:c.247C>T	p.Arg83Ter	p.R83*	ENST00000331340	NM_006060.4	83	Cga/Tga	4/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.449893849629954	2		257	315	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259262	89259262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770780950	NA	P-0026326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	34	240	0	ENST00000336596.2:c.406C>T	p.Arg136Ter	p.R136*	ENST00000336596	NM_005233.5	136	Cga/Tga	3/17	0.208816642657365	2	FACETS	0.496	0.406	0.596	0.248	0.203	0.298	INDETERMINATE	1	TRUE	0	0.449893849629954	2		240	305	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245411	153245411	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	110	411	0	ENST00000281708.4:c.1780C>T	p.Leu594Phe	p.L594F	ENST00000281708	NM_033632.3	594	Ctt/Ttt	11/12	0.254519990090536	1	FACETS	0.842	0.761	0.927	0.842	0.761	0.927	INDETERMINATE	1	TRUE	0	0.449893849629954	1		411	450	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243979	41243979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755209182	NA	P-0026326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	127	425	0	ENST00000357654.3:c.3569C>T	p.Pro1190Leu	p.P1190L	ENST00000357654	NM_007294.3	1190	cCt/cTt	10/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.449893849629954	2		425	480	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014170	70014170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769488988	NA	P-0026326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	63	454	1	ENST00000394351.3:c.1031C>T	p.Thr344Met	p.T344M	ENST00000394351	NM_000248.3	344	aCg/aTg	9/9	0.208816642657365	2	FACETS	0.473	0.409	0.543	0.237	0.204	0.272	INDETERMINATE	1	TRUE	0	0.449893849629954	2		455	592	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435049	49435050	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0026326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	60	342	0	ENST00000301067.7:c.6503_6504delinsTT	p.Pro2168Leu	p.P2168L	ENST00000301067	NM_003482.3	2168	cCC/cTT	31/54	0.113858735173793	0	FACETS	0.511	0.444	0.583			1	INDETERMINATE	1	TRUE	0	0.449893849629954	0		342	287	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438592	49438593	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGATTTCC	novel	NA	P-0026326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	50	425	11	ENST00000301067.7:c.4897_4898insGGAAATCG	p.Asp1633GlyfsTer92	p.D1633Gfs*92	ENST00000301067	NM_003482.3	1633	gat/gGGAAATCGat	19/54	0.113858735173793	0	FACETS	0.314	0.267	0.366			1	INDETERMINATE	1	TRUE	0	0.449893849629954	0		436	389	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445809	49445809	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772559303	NA	P-0026326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	94	654	1	ENST00000301067.7:c.1657C>T	p.Pro553Ser	p.P553S	ENST00000301067	NM_003482.3	553	Cct/Tct	10/54	0.113858735173793	0	FACETS	0.34	0.302	0.38			1	INDETERMINATE	1	TRUE	0	0.449893849629954	0		655	677	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123880969	123880970	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0026326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	47	206	0	ENST00000330479.4:c.587_588delinsTT	p.Ala196Val	p.A196V	ENST00000330479	NM_020382.3	196	gCC/gTT	5/9	0.113858735173793	0	FACETS	0.445	0.379	0.518			1	INDETERMINATE	1	TRUE	0	0.449893849629954	0		206	258	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28971138	28971138	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	74	285	0	ENST00000282397.4:c.1619A>G	p.Lys540Arg	p.K540R	ENST00000282397	NM_002019.4	540	aAa/aGa	12/30	1	2	FACETS	0.954	0.841	1	0.954	0.841	1	CLONAL	1	TRUE	1	0.449893849629954	2		285	345	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40874903	40874903	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	92	472	0	ENST00000428826.2:c.397C>T	p.Pro133Ser	p.P133S	ENST00000428826		133	Ccc/Tcc	6/21	1	2	FACETS	0.77	0.686	0.859	0.77	0.686	0.859	SUBCLONAL	1	TRUE	1	0.449893849629954	2		472	531	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086124	16086124	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	100	335	0	ENST00000281043.3:c.1300C>T	p.Gln434Ter	p.Q434*	ENST00000281043	NM_005378.4	434	Cag/Tag	3/3	1	2	FACETS	0.99	0.889	1	0.99	0.889	1	CLONAL	1	TRUE	1	0.449893849629954	2		335	449	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400169	41400169	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	75	364	0	ENST00000373198.4:c.590G>A	p.Arg197Gln	p.R197Q	ENST00000373198	NM_133170.3	197	cGa/cAa	5/32	1	2	FACETS	0.819	0.721	0.923	0.819	0.721	0.923	CLONAL	1	TRUE	1	0.449893849629954	2		364	407	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972936	55972936	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	80	361	0	ENST00000263923.4:c.1454G>A	p.Trp485Ter	p.W485*	ENST00000263923	NM_002253.2	485	tGg/tAg	11/30	0.254519990090536	1	FACETS	0.641	0.567	0.72	0.641	0.567	0.72	INDETERMINATE	1	TRUE	0	0.449893849629954	1		361	430	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183092	32183092	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	138	578	0	ENST00000375023.3:c.1932A>T	p.Lys644Asn	p.K644N	ENST00000375023	NM_004557.3	644	aaA/aaT	12/30	0.317517941559499	4	FACETS	1	0.948	1	0.353	0.321	0.387	CLONAL	1	TRUE	1	0.449893849629954	4		578	839	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981789	70981789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs889703632	NA	P-0026326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	50	470	0	ENST00000276594.2:c.307C>T	p.Pro103Ser	p.P103S	ENST00000276594	NM_024504.3	103	Cca/Tca	2/8	0.404451193621157	3	FACETS	0.443	0.375	0.517	0.221	0.187	0.259	SUBCLONAL	1	TRUE	1	0.449893849629954	3		470	615	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636815	8636815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	139	304	1	ENST00000356435.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000356435		32	Gat/Aat	2/35	0.202134469034075	1	FACETS	1	0.979	1	1	0.979	1	INDETERMINATE	1	TRUE	0	0.449893849629954	1		305	401	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0026327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	91	480	2	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.172907685384697	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	FALSE	0	0.212922396221365	2		482	404	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161466	2161466	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	28	470	0	ENST00000434045.2:c.61C>G	p.Gln21Glu	p.Q21E	ENST00000434045	NM_001127598.1	21	Caa/Gaa	2/5	0.202783289581866	3	FACETS	0.752	0.601	0.924	0.251	0.2	0.308	CLONAL	1	FALSE	0	0.212922396221365	3		470	387	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562436	21562436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	17	195	0	ENST00000382592.4:c.1483G>A	p.Gly495Ser	p.G495S	ENST00000382592	NM_014572.2	495	Ggc/Agc	4/8	0.212922396221365	4	FACETS	1	0.839	1	0.583	0.438	0.754	CLONAL	1	FALSE	2	0.212922396221365	4		195	166	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653271	29653271	+	splice_donor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0026327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	61	181	0	ENST00000356175.3:c.5205+1del		p.X1735_splice	ENST00000356175	NM_000267.3	1735			0.172907685384697	2	FACETS	0.841	0.735	0.953	1	0.96	1	CLONAL	3	FALSE	0	0.212922396221365	2		181	227	SUCCESS
AXL	558	MSKCC	GRCh37	19	41736920	41736920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	41	462	0	ENST00000301178.4:c.635G>A	p.Gly212Glu	p.G212E	ENST00000301178	NM_021913.4	212	gGg/gAg	5/20	0.212922396221365	3	FACETS	0.895	0.746	1	0.448	0.373	0.531	CLONAL	1	FALSE	1	0.212922396221365	3		462	476	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702303	47702303	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	158	425	0	ENST00000233146.2:c.1899A>G	p.Ile633Met	p.I633M	ENST00000233146	NM_000251.2	633	atA/atG	12/16	0.212922396221365	5	FACETS	0.938	0.865	1	0.938	0.865	1	CLONAL	4	FALSE	1	0.212922396221365	5		425	522	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0026328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	370	323	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.469077366062433	6	FACETS	1	0.957	1			1	CLONAL	4	FALSE	NA	0.469077366062433	6		323	763	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0026328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	346	354	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.469077366062433	4	FACETS	0.994	0.955	1	0.994	0.955	1	CLONAL	4	FALSE	0	0.469077366062433	4		354	545	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517201	NA	P-0026328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	200	372	0	ENST00000263967.3:c.1637A>C	p.Gln546Pro	p.Q546P	ENST00000263967	NM_006218.2	546	cAg/cCg	10/21	0.469077366062433	5	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	FALSE	2	0.469077366062433	5		372	434	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30095744	30095744	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	23	324	1	ENST00000331968.5:c.1744C>T	p.Gln582Ter	p.Q582*	ENST00000331968	NM_002742.2	582	Cag/Tag	12/18	0.16453823222031	6	FACETS	0.644	0.503	0.808	0.215	0.167	0.27	INDETERMINATE	1	FALSE	3	0.469077366062433	6		325	295	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793381	242793381	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	126	519	0	ENST00000334409.5:c.696G>C	p.Glu232Asp	p.E232D	ENST00000334409	NM_005018.2	232	gaG/gaC	5/5	0.448713484329249	3	FACETS	0.93	0.843	1	0.465	0.421	0.511	CLONAL	1	FALSE	1	0.469077366062433	3		519	713	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267331	198267331	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	201	321	2	ENST00000335508.6:c.2026G>A	p.Gly676Ser	p.G676S	ENST00000335508	NM_012433.2	676	Ggc/Agc	14/25	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.742519772814685	2		323	497	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140746	55140746	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	220	330	0	ENST00000257290.5:c.1607T>A	p.Val536Glu	p.V536E	ENST00000257290	NM_006206.4	536	gTg/gAg	11/23	1	2	FACETS	0.981	0.919	1	0.981	0.919	1	CLONAL	1	TRUE	1	0.742519772814685	2		330	604	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	90	474	0				ENST00000310581	NM_198253.2	-/1132			0.630407790200975	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.630407790200975	3		474	153	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033823	49033823	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0026331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	124	221	0	ENST00000267163.4:c.1961-1G>A		p.X654_splice	ENST00000267163	NM_000321.2	654			0.596615104881976	2	FACETS	0.988	0.923	1	0.988	0.923	1	CLONAL	2	TRUE	0	0.630407790200975	2		221	199	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0026331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	274	379	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.611993192637077	3	FACETS	0.88	0.841	0.918	0.88	0.841	0.918	CLONAL	3	TRUE	0	0.630407790200975	3		380	433	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022899	33022899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868208266	NA	P-0026331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	36	202	1	ENST00000300177.4:c.8G>A	p.Arg3His	p.R3H	ENST00000300177	NM_001191322.1	3	cGc/cAc	2/2	0.163707361488527	2	FACETS	0.457	0.378	0.544	0.228	0.189	0.272	INDETERMINATE	1	TRUE	0	0.630407790200975	2		203	250	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711889	89711892	+	frameshift_variant	Frame_Shift_Del	DEL	CAGT	CAGT	-	novel	NA	P-0026331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	202	498	0	ENST00000371953.3:c.510_513del	p.Ser170ArgfsTer12	p.S170Rfs*12	ENST00000371953	NM_000314.4	169	ccCAGT/cc	6/9	0.629596914158026	2	FACETS	0.965	0.914	1	0.965	0.914	1	CLONAL	2	TRUE	0	0.630407790200975	2		498	332	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533257	29533262	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GTCCGC	GTCCGC	-	novel	NA	P-0026331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	78	201	0	ENST00000356175.3:c.1261-1_1265del		p.X421_splice	ENST00000356175	NM_000267.3	421		12/57	0.630407790200975	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.630407790200975	1		201	140	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224282	98224282	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	rs878853852	NA	P-0026331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	17	121	0	ENST00000331920.6:c.2561-2A>T		p.X854_splice	ENST00000331920	NM_000264.3	854			1	2	FACETS	0.372	0.279	0.48	0.372	0.279	0.48	SUBCLONAL	1	TRUE	1	0.630407790200975	2		121	145	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026331-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	262	474	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.973	1	1	0.995	1	CLONAL	2	FALSE	1	0.341663879099044	2		474	726	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033823	49033823	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0026331-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	91	221	0	ENST00000267163.4:c.1961-1G>A		p.X654_splice	ENST00000267163	NM_000321.2	654			0.251796837110568	2	FACETS	0.77	0.69	0.854	0.77	0.69	0.854	SUBCLONAL	2	FALSE	0	0.341663879099044	2		221	346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0026331-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	404	379	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.341663879099044	2	FACETS	0.989	0.941	1	0.989	0.941	1	CLONAL	2	FALSE	0	0.341663879099044	2		380	1196	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022899	33022899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868208266	NA	P-0026331-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	9	202	1	ENST00000300177.4:c.8G>A	p.Arg3His	p.R3H	ENST00000300177	NM_001191322.1	3	cGc/cAc	2/2	0.182092784258428	2	FACETS	0.088	0.057	0.127	0.044	0.028	0.064	INDETERMINATE	1	FALSE	0	0.341663879099044	2		203	601	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711889	89711892	+	frameshift_variant	Frame_Shift_Del	DEL	CAGT	CAGT	-	novel	NA	P-0026331-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	61	498	0	ENST00000371953.3:c.510_513del	p.Ser170ArgfsTer12	p.S170Rfs*12	ENST00000371953	NM_000314.4	169	ccCAGT/cc	6/9	0.283684931151706	2	FACETS	0.819	0.717	0.927	0.819	0.717	0.927	CLONAL	2	FALSE	0	0.341663879099044	2		498	218	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533257	29533262	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GTCCGC	GTCCGC	-	novel	NA	P-0026331-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	63	201	0	ENST00000356175.3:c.1261-1_1265del		p.X421_splice	ENST00000356175	NM_000267.3	421		12/57	0.341663879099044	2	FACETS	1	0.968	1	0.685	0.599	0.778	CLONAL	1	FALSE	0	0.341663879099044	2		201	269	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593647	55593648	+	inframe_insertion	In_Frame_Ins	INS	-	-	GACCCAACACAACTTCCT	novel	NA	P-0026342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	175	296	0	ENST00000288135.5:c.1714_1731dup	p.Asp572_Pro577dup	p.D572_P577dup	ENST00000288135	NM_000222.2	572	-/GACCCAACACAACTTCCT	11/21	1	2	FACETS	0.741	0.688	0.796	0.741	0.688	0.796	SUBCLONAL	1	TRUE	1	0.89586134388922	2		296	527	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0026343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	277	441	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.777392016296004	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.803479746870739	1		441	380	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593604	55593609	+	inframe_deletion	In_Frame_Del	DEL	GGAAGG	GGAAGG	-	novel	NA	P-0026343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	153	269	0	ENST00000288135.5:c.1670_1675del	p.Trp557_Val559delinsPhe	p.W557_V559delinsF	ENST00000288135	NM_000222.2	557	tGGAAGGtt/ttt	11/21	1	2	FACETS	0.896	0.828	0.966	0.896	0.828	0.966	CLONAL	1	TRUE	1	0.803479746870739	2		269	425	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193121522	193121522	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	19	207	0	ENST00000367435.3:c.920T>G	p.Phe307Cys	p.F307C	ENST00000367435	NM_024529.4	307	tTc/tGc	10/17	0.774409807199111	2	FACETS	0.253	0.193	0.323	0.126	0.096	0.162	SUBCLONAL	1	TRUE	0	0.803479746870739	2		207	187	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600573	43600573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	13	283	0	ENST00000355710.3:c.799G>A	p.Asp267Asn	p.D267N	ENST00000355710	NM_020975.4	267	Gac/Aac	4/20	0.803479746870739	1	FACETS	0.118	0.084	0.159	0.118	0.084	0.159	SUBCLONAL	1	TRUE	0	0.803479746870739	1		283	164	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	123	474	0				ENST00000310581	NM_198253.2	-/1132			0.762268754579823	3	FACETS	0.923	0.873	0.969	0.923	0.873	0.969	CLONAL	3	TRUE	0	0.762268754579823	3		474	161	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579433	7579433	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1064793279	NA	P-0026344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	252	298	2	ENST00000269305.4:c.254del	p.Pro85LeufsTer38	p.P85Lfs*38	ENST00000269305	NM_001126112.2	85	cCt/ct	4/11	0.647949513991963	2	FACETS	0.87	0.832	0.907	0.87	0.832	0.907	CLONAL	2	TRUE	0	0.762268754579823	2		300	380	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425047	49425047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778628310	NA	P-0026344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	146	366	0	ENST00000301067.7:c.13441G>A	p.Glu4481Lys	p.E4481K	ENST00000301067	NM_003482.3	4481	Gag/Aag	39/54	0.762268754579823	3	FACETS	0.915	0.839	0.994	0.458	0.419	0.497	CLONAL	1	TRUE	1	0.762268754579823	3		366	578	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149517	61149517	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	105	231	0	ENST00000295025.8:c.1707del	p.Cys569TrpfsTer6	p.C569Wfs*6	ENST00000295025	NM_002908.2	569	tgT/tg	11/11	0.762268754579823	3	FACETS	1	0.95	1	0.539	0.488	0.592	CLONAL	1	TRUE	1	0.762268754579823	3		231	353	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927976	178927981	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	ACACTG	ACACTG	-	novel	NA	P-0026344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	70	147	0	ENST00000263967.3:c.1254_1259del	p.Glu418_Cys420delinsAsp	p.E418_C420delinsD	ENST00000263967	NM_006218.2	418	gaACACTGt/gat	8/21	0.73583888254569	4	FACETS	0.813	0.722	0.907	0.813	0.722	0.907	CLONAL	2	TRUE	2	0.762268754579823	4		147	199	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629347	187629361	+	inframe_deletion	In_Frame_Del	DEL	CAAGCCCCAGTCTGA	CAAGCCCCAGTCTGA	-	novel	NA	P-0026344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	367	327	0	ENST00000441802.2:c.1621_1635del	p.Ser541_Leu545del	p.S541_L545del	ENST00000441802	NM_005245.3	541	TCAGACTGGGGCTTG/-	2/27	0.762268754579823	3	FACETS	0.848	0.818	0.876	0.848	0.818	0.876	CLONAL	3	TRUE	0	0.762268754579823	3		327	523	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	13	474	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		474	61	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0026346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	188	347	0				ENST00000310581	NM_198253.2	-/1132			0.723172641129421	6	FACETS	0.969	0.914	1	0.969	0.914	1	CLONAL	4	TRUE	2	0.723172641129421	6		347	328	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0026346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	97	454	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.68924089758864	3	FACETS	1	0.948	1	0.542	0.488	0.598	CLONAL	1	TRUE	1	0.723172641129421	3		454	337	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0026346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	86	181	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.68924089758864	3	FACETS	1	0.893	1	0.5	0.446	0.556	CLONAL	1	TRUE	1	0.723172641129421	3		181	324	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971000	21971000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	328	209	0	ENST00000304494.5:c.358G>T	p.Glu120Ter	p.E120*	ENST00000304494	NM_000077.4	120	Gag/Tag	2/3	0.723172641129421	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.723172641129421	3		209	383	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412282	139412282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	476	390	1	ENST00000277541.6:c.1363G>A	p.Glu455Lys	p.E455K	ENST00000277541	NM_017617.3	455	Gag/Aag	8/34	0.723172641129421	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	0	0.723172641129421	3		391	595	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0026346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	219	238	1	ENST00000269305.4:c.559+1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.723172641129421	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.723172641129421	2		239	289	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243776981	243776981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	117	420	0	ENST00000263826.5:c.688G>A	p.Gly230Arg	p.G230R	ENST00000263826	NM_005465.4	230	Ggg/Agg	7/13	1	2	FACETS	0.863	0.786	0.942	0.863	0.786	0.942	CLONAL	1	TRUE	1	0.723172641129421	2		420	375	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917590	94917590	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	77	308	0	ENST00000536441.1:c.931C>A	p.His311Asn	p.H311N	ENST00000536441	NM_144665.3	311	Cat/Aat	6/10	0.723172641129421	2	FACETS	0.777	0.69	0.868	0.389	0.345	0.434	SUBCLONAL	1	TRUE	0	0.723172641129421	2		308	274	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873823	35873823	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	46	107	0	ENST00000216797.5:c.28G>C	p.Glu10Gln	p.E10Q	ENST00000216797	NM_020529.2	10	Gag/Cag	1/6	0.723172641129421	2	FACETS	1	0.891	1	0.517	0.447	0.59	CLONAL	1	TRUE	0	0.723172641129421	2		107	123	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271304	1271304	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	132	375	0	ENST00000310581.5:c.2398G>C	p.Glu800Gln	p.E800Q	ENST00000310581	NM_198253.2	800	Gag/Cag	8/16	0.723172641129421	6	FACETS	0.948	0.86	1	0.237	0.215	0.261	CLONAL	1	TRUE	2	0.723172641129421	6		375	942	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090751	5090751	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	116	171	0	ENST00000381652.3:c.2899C>G	p.Leu967Val	p.L967V	ENST00000381652	NM_004972.3	967	Ctt/Gtt	22/25	0.723172641129421	3	FACETS	0.962	0.888	1	0.641	0.592	0.691	CLONAL	2	TRUE	0	0.723172641129421	3		171	227	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0026347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	213	322	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.82133094473151	2		322	518	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0026347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	108	177	0	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	0.82133094473151	2		177	229	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845369	76845372	+	frameshift_variant	Frame_Shift_Del	DEL	TCAA	TCAA	-	novel	NA	P-0026347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	39	278	0	ENST00000373344.5:c.6149_6152del	p.Ile2050LysfsTer6	p.I2050Kfs*6	ENST00000373344	NM_000489.3	2050	aTTGAa/aa	27/35	0.143624245166431	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.82133094473151	0		278	322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578234	7578234	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs786202222	NA	P-0026347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	232	392	0	ENST00000269305.4:c.615T>A	p.Tyr205Ter	p.Y205*	ENST00000269305	NM_001126112.2	205	taT/taA	6/11	1	2	FACETS	0.943	0.886	1	0.943	0.886	1	CLONAL	1	TRUE	1	0.82133094473151	2		392	599	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907697	76907697	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	149	309	0	ENST00000373344.5:c.4464del	p.Lys1488AsnfsTer2	p.K1488Nfs*2	ENST00000373344	NM_000489.3	1488	aaA/aa	15/35	0.143624245166431	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.82133094473151	0		309	483	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449388	31449388	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	112	233	0	ENST00000344624.3:c.2821G>C	p.Gly941Arg	p.G941R	ENST00000344624		941	Ggg/Cgg	19/33	0.365663405193202	0	FACETS	0.8	0.743	0.855			1	SUBCLONAL	2	TRUE	0	0.433547259568921	0		233	183	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732909	44732909	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	14	248	0	ENST00000377967.4:c.112T>A	p.Ser38Thr	p.S38T	ENST00000377967	NM_021140.2	38	Tcc/Acc	1/29	0.380136938608532	1	FACETS	0.229	0.165	0.306	0.229	0.165	0.306	SUBCLONAL	1	TRUE	0	0.433547259568921	1		248	221	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594258	55594258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913523	NA	P-0026349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	223	236	0	ENST00000288135.5:c.1961T>C	p.Val654Ala	p.V654A	ENST00000288135	NM_000222.2	654	gTg/gCg	13/21	0.927113681876259	2	FACETS	0.988	0.93	1	0.494	0.465	0.523	CLONAL	1	TRUE	0	0.927113681876259	2		236	487	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593615	+	inframe_deletion	In_Frame_Del	DEL	AGTGGAAGGTTGTTG	AGTGGAAGGTTGTTG	-	novel	NA	P-0026349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	297	245	0	ENST00000288135.5:c.1669_1683del	p.Trp557_Glu561del	p.W557_E561del	ENST00000288135	NM_000222.2	556	cAGTGGAAGGTTGTTGag/cag	11/21	0.927113681876259	2	FACETS	0.986	0.964	1	0.986	0.964	1	CLONAL	2	TRUE	0	0.927113681876259	2		245	325	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	91	474	0				ENST00000310581	NM_198253.2	-/1132			0.657870393657181	3	FACETS	0.901	0.819	0.985	0.901	0.819	0.985	CLONAL	2	TRUE	1	0.661949585789296	3		474	203	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841505	156841505	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145222195	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	323	454	1	ENST00000524377.1:c.808G>A	p.Asp270Asn	p.D270N	ENST00000524377	NM_002529.3	270	Gat/Aat	7/17	0.302892823983844	5	FACETS	1	0.983	1	0.724	0.686	0.763	INDETERMINATE	2	TRUE	2	0.661949585789296	5		455	895	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117717422	117717422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	178	224	1	ENST00000368508.3:c.785C>T	p.Ser262Phe	p.S262F	ENST00000368508	NM_002944.2	262	tCt/tTt	8/43	0.333839431151813	5	FACETS	1	0.965	1	0.709	0.659	0.76	INDETERMINATE	2	TRUE	2	0.661949585789296	5		225	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578541	7578541	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	626	471	1	ENST00000269305.4:c.389T>G	p.Leu130Arg	p.L130R	ENST00000269305	NM_001126112.2	130	cTc/cGc	5/11	0.660172591589361	3	FACETS	0.972	0.948	0.996	0.972	0.948	0.996	CLONAL	3	TRUE	0	0.661949585789296	3		472	863	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664894	29664894	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1567617727	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	233	217	0	ENST00000356175.3:c.6637C>T	p.Gln2213Ter	p.Q2213*	ENST00000356175	NM_000267.3	2213	Caa/Taa	43/57	0.594931893914286	3	FACETS	0.913	0.872	0.953	0.913	0.872	0.953	CLONAL	3	TRUE	0	0.661949585789296	3		217	342	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120377	94120377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	107	182	0	ENST00000369303.4:c.674C>T	p.Ser225Phe	p.S225F	ENST00000369303	NM_004440.3	225	tCc/tTc	3/17	0.333839431151813	5	FACETS	0.973	0.883	1	0.649	0.589	0.711	INDETERMINATE	2	TRUE	2	0.661949585789296	5		182	331	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925411	114925411	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	143	340	0	ENST00000543371.1:c.1489C>T	p.Pro497Ser	p.P497S	ENST00000543371	NM_001198531.1	497	Ccg/Tcg	14/14	0.506882649119677	3	FACETS	0.943	0.863	1	0.471	0.431	0.513	CLONAL	1	TRUE	1	0.661949585789296	3		340	610	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298138	123298138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780846065	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	154	377	0	ENST00000358487.5:c.716C>T	p.Ser239Phe	p.S239F	ENST00000358487	NM_000141.4	239	tCc/tTc	6/18	0.657870393657181	3	FACETS	1	0.95	1	0.522	0.48	0.566	CLONAL	1	TRUE	1	0.661949585789296	3		377	593	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503099	125503099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140276570	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	110	215	0	ENST00000428830.2:c.466C>T	p.Arg156Trp	p.R156W	ENST00000428830	NM_001114121.2	156	Cgg/Tgg	6/14	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.661949585789296	2		215	312	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076945	41076945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767453141	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	325	289	0	ENST00000373198.4:c.1475C>T	p.Ser492Phe	p.S492F	ENST00000373198	NM_133170.3	492	tCc/tTc	9/32	0.588600318770579	5	FACETS	0.939	0.893	0.984	0.939	0.893	0.984	CLONAL	3	TRUE	2	0.661949585789296	5		289	695	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971167	21971167	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	152	238	0	ENST00000304494.5:c.191T>C	p.Leu64Pro	p.L64P	ENST00000304494	NM_000077.4	64	cTg/cCg	2/3	0.652452201498706	2	FACETS	0.915	0.859	0.97	0.915	0.859	0.97	CLONAL	2	TRUE	0	0.661949585789296	2		238	251	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622131	43622131	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	150	335	0	ENST00000355710.3:c.3148C>T	p.Arg1050Ter	p.R1050*	ENST00000355710	NM_020975.4	1050	Cga/Tga	19/20	0.506882649119677	3	FACETS	1	0.921	1	0.502	0.46	0.545	CLONAL	1	TRUE	1	0.661949585789296	3		335	601	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223358	36223358	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	202	485	0	ENST00000222270.7:c.5908C>T	p.Pro1970Ser	p.P1970S	ENST00000222270	NM_014727.1	1970	Cct/Tct	28/37	0.661949585789296	3	FACETS	0.878	0.815	0.944	0.439	0.407	0.472	CLONAL	1	TRUE	1	0.661949585789296	3		485	925	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41542772	41542772	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200624197	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	120	316	0	ENST00000263253.7:c.2083C>T	p.Arg695Cys	p.R695C	ENST00000263253	NM_001429.3	695	Cgt/Tgt	11/31	0.591489936451045	4	FACETS	0.809	0.731	0.891	0.404	0.365	0.446	CLONAL	1	TRUE	2	0.661949585789296	4		316	745	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120270	94120270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	105	147	0	ENST00000369303.4:c.781G>A	p.Gly261Arg	p.G261R	ENST00000369303	NM_004440.3	261	Gga/Aga	3/17	0.333839431151813	5	FACETS	1	0.956	1	0.724	0.658	0.792	INDETERMINATE	2	TRUE	2	0.661949585789296	5		147	291	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566839	212566839	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	163	182	0	ENST00000342788.4:c.1342C>T	p.Gln448Ter	p.Q448*	ENST00000342788	NM_005235.2	448	Cag/Tag	12/28	0.591489936451045	4	FACETS	0.89	0.824	0.957	0.89	0.824	0.957	CLONAL	2	TRUE	2	0.661949585789296	4		182	460	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120508139	120508139	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	239	270	0	ENST00000256646.2:c.1618C>T	p.Pro540Ser	p.P540S	ENST00000256646	NM_024408.3	540	Ccg/Tcg	10/34	0.661949585789296	4	FACETS	0.9	0.845	0.955	0.9	0.845	0.955	CLONAL	2	TRUE	2	0.661949585789296	4		270	667	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212088	5212088	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	179	417	0	ENST00000357368.4:c.4943C>T	p.Ala1648Val	p.A1648V	ENST00000357368	NM_002850.3	1648	gCc/gTc	32/38	0.333839431151813	5	FACETS	1	0.988	1	0.459	0.424	0.495	INDETERMINATE	1	TRUE	2	0.661949585789296	5		417	783	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778959	9778959	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	298	321	0	ENST00000377346.4:c.1228A>C	p.Lys410Gln	p.K410Q	ENST00000377346	NM_005026.3	410	Aag/Cag	9/24	0.661949585789296	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.661949585789296	4		321	681	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343150	118343150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	103	227	0	ENST00000534358.1:c.1276C>T	p.Arg426Trp	p.R426W	ENST00000534358	NM_005933.3	426	Cgg/Tgg	3/36	1	2	FACETS	0.894	0.808	0.983	0.894	0.808	0.983	CLONAL	1	TRUE	1	0.661949585789296	2		227	348	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149235	119149235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756530482	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	120	332	1	ENST00000264033.4:c.1243G>A	p.Gly415Ser	p.G415S	ENST00000264033	NM_005188.3	415	Ggc/Agc	9/16	1	2	FACETS	0.991	0.904	1	0.991	0.904	1	CLONAL	1	TRUE	1	0.661949585789296	2		333	366	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443676	49443676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1208909878	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	350	340	1	ENST00000301067.7:c.3695C>T	p.Pro1232Leu	p.P1232L	ENST00000301067	NM_003482.3	1232	cCg/cTg	11/54	0.661949585789296	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.661949585789296	2		341	500	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21553867	21553867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	352	385	0	ENST00000382592.4:c.2735C>T	p.Pro912Leu	p.P912L	ENST00000382592	NM_014572.2	912	cCc/cTc	7/8	0.643349791179455	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.661949585789296	3		385	652	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912235	32912235	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	257	358	0	ENST00000380152.3:c.3743G>A	p.Ser1248Asn	p.S1248N	ENST00000380152		1248	aGt/aAt	11/27	0.643349791179455	3	FACETS	0.903	0.854	0.953	0.903	0.854	0.953	CLONAL	2	TRUE	1	0.661949585789296	3		358	572	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914203	32914203	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs876658494	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	229	255	0	ENST00000380152.3:c.5711T>A	p.Leu1904His	p.L1904H	ENST00000380152		1904	cTt/cAt	11/27	0.643349791179455	3	FACETS	0.949	0.895	1	0.949	0.895	1	CLONAL	2	TRUE	1	0.661949585789296	3		255	485	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43771698	43771698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767165113	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	188	390	0	ENST00000382044.4:c.685G>A	p.Glu229Lys	p.E229K	ENST00000382044	NM_001141980.1	229	Gaa/Aaa	7/28	0.298156463773731	4	FACETS	1	0.99	1	0.716	0.665	0.769	INDETERMINATE	1	TRUE	2	0.661949585789296	4		390	659	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472594	88472594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	98	205	0	ENST00000360948.2:c.1961C>T	p.Ser654Phe	p.S654F	ENST00000360948	NM_001012338.2	654	tCc/tTc	16/19	0.298156463773731	4	FACETS	1	0.974	1	0.634	0.57	0.701	INDETERMINATE	1	TRUE	2	0.661949585789296	4		205	388	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251043	99251043	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	256	336	0	ENST00000268035.6:c.347C>T	p.Ala116Val	p.A116V	ENST00000268035	NM_000875.3	116	gCc/gTc	2/21	0.298156463773731	4	FACETS	1	0.988	1	1	0.988	1	INDETERMINATE	2	TRUE	2	0.661949585789296	4		336	554	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900815	3900815	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs979410323	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	108	262	0	ENST00000262367.5:c.281C>T	p.Pro94Leu	p.P94L	ENST00000262367	NM_004380.2	94	cCc/cTc	2/31	0.661949585789296	3	FACETS	1	0.904	1	0.5	0.452	0.551	CLONAL	1	TRUE	1	0.661949585789296	3		262	434	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845478	72845478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	179	258	0	ENST00000268489.5:c.3862A>T	p.Thr1288Ser	p.T1288S	ENST00000268489	NM_006885.3	1288	Acg/Tcg	7/10	0.661949585789296	3	FACETS	0.876	0.818	0.934	0.876	0.818	0.934	CLONAL	2	TRUE	1	0.661949585789296	3		258	411	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990375	81990375	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs770521320	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	284	351	0	ENST00000359376.3:c.3646C>A	p.Leu1216Met	p.L1216M	ENST00000359376	NM_002661.3	1216	Ctg/Atg	32/33	0.661949585789296	3	FACETS	0.917	0.869	0.964	0.917	0.869	0.964	CLONAL	2	TRUE	1	0.661949585789296	3		351	623	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346447	89346448	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	133	356	1	ENST00000301030.4:c.6502_6503delinsTT	p.Pro2168Leu	p.P2168L	ENST00000301030	NM_001256183.1	2168	CCa/TTa	9/13	0.661949585789296	3	FACETS	0.848	0.772	0.927	0.424	0.386	0.464	CLONAL	1	TRUE	1	0.661949585789296	3		357	631	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55704641	55704641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	400	407	0	ENST00000284073.2:c.704C>T	p.Pro235Leu	p.P235L	ENST00000284073	NM_138962.2	235	cCa/cTa	10/14	0.591489936451045	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	2	0.661949585789296	4		407	973	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117549	70117550	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	102	279	2	ENST00000245479.2:c.17_18delinsTT	p.Pro6Leu	p.P6L	ENST00000245479	NM_000346.3	6	cCC/cTT	1/3	0.591489936451045	4	FACETS	0.784	0.702	0.871	0.392	0.351	0.436	SUBCLONAL	1	TRUE	2	0.661949585789296	4		281	653	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78831612	78831612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	118	310	0	ENST00000306801.3:c.1421C>T	p.Pro474Leu	p.P474L	ENST00000306801	NM_020761.2	474	cCc/cTc	13/34	0.591489936451045	4	FACETS	0.894	0.808	0.984	0.447	0.404	0.492	CLONAL	1	TRUE	2	0.661949585789296	4		310	663	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223550	36223550	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	186	430	0	ENST00000222270.7:c.6100del	p.Tyr2034ThrfsTer6	p.Y2034Tfs*6	ENST00000222270	NM_014727.1	2034	Tac/ac	28/37	0.661949585789296	3	FACETS	0.903	0.835	0.974	0.452	0.417	0.487	CLONAL	1	TRUE	1	0.661949585789296	3		430	828	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40742183	40742183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140987550	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	388	407	0	ENST00000392038.2:c.941C>T	p.Pro314Leu	p.P314L	ENST00000392038	NM_001626.4	314	cCg/cTg	10/14	0.661949585789296	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.661949585789296	3		407	750	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727961	41727961	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	224	265	1	ENST00000301178.4:c.586G>A	p.Gly196Arg	p.G196R	ENST00000301178	NM_021913.4	196	Ggg/Agg	4/20	0.661949585789296	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.661949585789296	3		266	435	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158595040	158595040	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	212	244	0	ENST00000263640.3:c.1307C>T	p.Pro436Leu	p.P436L	ENST00000263640	NM_001105.4	436	cCc/cTc	10/11	0.591489936451045	4	FACETS	0.984	0.922	1	0.984	0.922	1	CLONAL	2	TRUE	2	0.661949585789296	4		244	541	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662089	227662089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	255	332	1	ENST00000305123.5:c.1366G>A	p.Ala456Thr	p.A456T	ENST00000305123	NM_005544.2	456	Gcc/Acc	1/2	0.591489936451045	4	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	2	0.661949585789296	4		333	640	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794458	242794458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749368245	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	356	438	0	ENST00000334409.5:c.484C>T	p.Pro162Ser	p.P162S	ENST00000334409	NM_005018.2	162	Cca/Tca	3/5	0.507854308096891	4	FACETS	1	0.952	1			1	CLONAL	2	TRUE	NA	0.661949585789296	4		438	893	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523294	9523295	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	215	342	1	ENST00000353224.5:c.1942_1943delinsTT	p.Pro648Phe	p.P648F	ENST00000353224	NM_177990.2	648	CCc/TTc	9/10	0.302892823983844	5	FACETS	0.996	0.931	1	0.664	0.62	0.708	INDETERMINATE	2	TRUE	2	0.661949585789296	5		343	650	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546559	9546559	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs958970085	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	229	298	1	ENST00000353224.5:c.1463G>A	p.Arg488Gln	p.R488Q	ENST00000353224	NM_177990.2	488	cGa/cAa	5/10	0.302892823983844	5	FACETS	1	0.984	1	0.761	0.714	0.808	INDETERMINATE	2	TRUE	2	0.661949585789296	5		299	604	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561448	9561448	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	211	293	1	ENST00000353224.5:c.334G>A	p.Ala112Thr	p.A112T	ENST00000353224	NM_177990.2	112	Gcc/Acc	4/10	0.302892823983844	5	FACETS	1	0.963	1	0.695	0.65	0.742	INDETERMINATE	2	TRUE	2	0.661949585789296	5		294	609	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100956	41100956	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	231	309	1	ENST00000373198.4:c.1400C>T	p.Pro467Leu	p.P467L	ENST00000373198	NM_133170.3	467	cCc/cTc	8/32	0.588600318770579	5	FACETS	0.977	0.915	1	0.651	0.61	0.694	CLONAL	2	TRUE	2	0.661949585789296	5		310	712	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121057	29121057	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	223	462	0	ENST00000328354.6:c.500G>C	p.Gly167Ala	p.G167A	ENST00000328354	NM_007194.3	167	gGa/gCa	4/15	0.591489936451045	4	FACETS	1	0.978	1	0.558	0.52	0.598	CLONAL	1	TRUE	2	0.661949585789296	4		462	1003	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026853	71026853	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	103	191	0	ENST00000318789.4:c.1369G>A	p.Glu457Lys	p.E457K	ENST00000318789	NM_032682.5	457	Gaa/Aaa	16/21	0.172949665056298	3	FACETS	0.784	0.714	0.857	0.523	0.476	0.571	INDETERMINATE	2	TRUE	0	0.661949585789296	3		191	264	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911427	134911427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	63	327	0	ENST00000398015.3:c.1892G>A	p.Gly631Glu	p.G631E	ENST00000398015	NM_004441.4	631	gGa/gAa	11/16	0.172949665056298	3	FACETS	0.593	0.515	0.678	0.198	0.171	0.226	INDETERMINATE	1	TRUE	0	0.661949585789296	3		327	427	SUCCESS
ATR	545	MSKCC	GRCh37	3	142212099	142212099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	138	353	0	ENST00000350721.4:c.5953C>T	p.Pro1985Ser	p.P1985S	ENST00000350721	NM_001184.3	1985	Cct/Tct	35/47	0.367406858792767	3	FACETS	0.984	0.899	1	0.492	0.449	0.536	INDETERMINATE	1	TRUE	1	0.661949585789296	3		353	564	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916935	178916940	+	inframe_deletion	In_Frame_Del	DEL	CGTGAA	CGTGAA	-	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	117	298	0	ENST00000263967.3:c.322_327del	p.Arg108_Glu109del	p.R108_E109del	ENST00000263967	NM_006218.2	108	CGTGAA/-	2/21	0.367406858792767	3	FACETS	1	0.941	1	0.524	0.475	0.574	INDETERMINATE	1	TRUE	1	0.661949585789296	3		298	449	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921578	178921578	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	51	171	0	ENST00000263967.3:c.1059+1G>A		p.X353_splice	ENST00000263967	NM_006218.2	353			0.367406858792767	3	FACETS	0.688	0.589	0.796	0.344	0.294	0.398	INDETERMINATE	1	TRUE	1	0.661949585789296	3		171	298	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955621	55955622	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	195	254	1	ENST00000263923.4:c.3323_3324delinsTA	p.Gly1108Val	p.G1108V	ENST00000263923	NM_002253.2	1108	gGG/gTA	25/30	0.657870393657181	3	FACETS	0.947	0.889	1	0.947	0.889	1	CLONAL	2	TRUE	1	0.661949585789296	3		255	414	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984903	55984903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	221	284	1	ENST00000263923.4:c.226G>A	p.Val76Met	p.V76M	ENST00000263923	NM_002253.2	76	Gtg/Atg	3/30	0.657870393657181	3	FACETS	0.952	0.896	1	0.952	0.896	1	CLONAL	2	TRUE	1	0.661949585789296	3		285	467	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036943	180036943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	308	413	0	ENST00000261937.6:c.3769G>A	p.Glu1257Lys	p.E1257K	ENST00000261937	NM_182925.4	1257	Gaa/Aaa	28/30	0.657870393657181	3	FACETS	0.945	0.899	0.992	0.945	0.899	0.992	CLONAL	2	TRUE	1	0.661949585789296	3		413	655	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180313	32180313	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	251	386	1	ENST00000375023.3:c.2618G>A	p.Gly873Glu	p.G873E	ENST00000375023	NM_004557.3	873	gGa/gAa	17/30	0.333839431151813	5	FACETS	0.975	0.916	1	0.65	0.61	0.691	INDETERMINATE	2	TRUE	2	0.661949585789296	5		387	775	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683984	117683984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	208	281	0	ENST00000368508.3:c.3163G>A	p.Gly1055Arg	p.G1055R	ENST00000368508	NM_002944.2	1055	Gga/Aga	21/43	0.333839431151813	5	FACETS	0.95	0.886	1	0.634	0.591	0.677	INDETERMINATE	2	TRUE	2	0.661949585789296	5		281	659	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511333	157511333	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs149389876	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	175	186	0	ENST00000346085.5:c.3851G>T	p.Gly1284Val	p.G1284V	ENST00000346085	NM_020732.3	1284	gGa/gTa	15/20	0.333839431151813	5	FACETS	0.844	0.787	0.902	0.844	0.787	0.902	INDETERMINATE	3	TRUE	2	0.661949585789296	5		186	416	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528496	157528496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149978361	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	190	279	0	ENST00000346085.5:c.6221C>T	p.Ser2074Leu	p.S2074L	ENST00000346085	NM_020732.3	2074	tCg/tTg	20/20	0.333839431151813	5	FACETS	0.939	0.873	1	0.626	0.582	0.672	INDETERMINATE	2	TRUE	2	0.661949585789296	5		279	609	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683798	162683798	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	139	171	0	ENST00000366898.1:c.172-1G>A		p.X58_splice	ENST00000366898	NM_004562.2	58			0.333839431151813	5	FACETS	1	0.982	1	0.813	0.751	0.877	INDETERMINATE	2	TRUE	2	0.661949585789296	5		171	343	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974215	2974216	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	287	394	1	ENST00000396946.4:c.1389_1390delinsAA	p.Asp464Asn	p.D464N	ENST00000396946	NM_032415.4	463	ggGGat/ggAAat	10/25	0.591489936451045	4	FACETS	0.911	0.86	0.962	0.911	0.86	0.962	CLONAL	2	TRUE	2	0.661949585789296	4		395	791	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223547	55223547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	348	333	0	ENST00000275493.2:c.914G>A	p.Gly305Asp	p.G305D	ENST00000275493	NM_005228.3	305	gGc/gAc	8/28	0.591489936451045	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	2	0.661949585789296	4		333	776	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508928	106508928	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196800615	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	218	234	0	ENST00000359195.3:c.922G>A	p.Asp308Asn	p.D308N	ENST00000359195	NM_002649.2	308	Gac/Aac	2/11	0.661949585789296	4	FACETS	0.986	0.925	1	0.986	0.925	1	CLONAL	2	TRUE	2	0.661949585789296	4		234	555	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397798	116397798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	314	364	0	ENST00000397752.3:c.2072C>T	p.Ser691Leu	p.S691L	ENST00000397752	NM_000245.2	691	tCa/tTa	8/21	0.661949585789296	4	FACETS	0.97	0.919	1	0.97	0.919	1	CLONAL	2	TRUE	2	0.661949585789296	4		364	813	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829322	128829323	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	267	350	0	ENST00000249373.3:c.330_331delinsAA	p.Gly111Ser	p.G111S	ENST00000249373	NM_005631.4	110	tcGGgc/tcAAgc	1/12	0.661949585789296	4	FACETS	0.956	0.902	1	0.956	0.902	1	CLONAL	2	TRUE	2	0.661949585789296	4		350	701	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538885	23538885	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	124	242	0	ENST00000380871.4:c.554C>T	p.Ser185Phe	p.S185F	ENST00000380871	NM_006167.3	185	tCc/tTc	2/2	0.661949585789296	3	FACETS	1	0.966	1	0.56	0.51	0.612	CLONAL	1	TRUE	1	0.661949585789296	3		242	445	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539122	23539122	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	116	228	0	ENST00000380871.4:c.317C>T	p.Ser106Phe	p.S106F	ENST00000380871	NM_006167.3	106	tCt/tTt	2/2	0.661949585789296	3	FACETS	0.966	0.875	1	0.483	0.437	0.53	CLONAL	1	TRUE	1	0.661949585789296	3		228	483	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968167	68968167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1054156818	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	364	404	0	ENST00000288368.4:c.1196G>A	p.Arg399Gln	p.R399Q	ENST00000288368	NM_024870.2	399	cGa/cAa	10/40	0.661949585789296	3	FACETS	0.971	0.927	1	0.971	0.927	1	CLONAL	2	TRUE	1	0.661949585789296	3		404	754	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046299	69046299	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	68	161	0	ENST00000288368.4:c.3772G>A	p.Glu1258Lys	p.E1258K	ENST00000288368	NM_024870.2	1258	Gag/Aag	32/40	0.661949585789296	3	FACETS	0.871	0.764	0.985	0.435	0.382	0.493	CLONAL	1	TRUE	1	0.661949585789296	3		161	314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0026351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	57	322	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.242754726582996	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.242754726582996	1		322	356	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457243	25457243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377577594	NA	P-0026351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	21	281	1	ENST00000264709.3:c.2644C>T	p.Arg882Cys	p.R882C	ENST00000264709	NM_175629.2	882	Cgc/Tgc	23/23	1	2	FACETS	0.321	0.246	0.409	0.321	0.246	0.409	SUBCLONAL	1	TRUE	1	0.242754726582996	2		282	539	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218623	98218623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778629	NA	P-0026351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	37	247	1	ENST00000331920.6:c.3241G>A	p.Val1081Met	p.V1081M	ENST00000331920	NM_000264.3	1081	Gtg/Atg	19/24	0.242754726582996	1	FACETS	0.652	0.538	0.779	0.652	0.538	0.779	SUBCLONAL	1	TRUE	0	0.242754726582996	1		248	411	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030384	49030384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554834063	NA	P-0026351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	35	253	0	ENST00000267163.4:c.1859C>T	p.Thr620Met	p.T620M	ENST00000267163	NM_000321.2	620	aCg/aTg	19/27	0.242754726582996	1	FACETS	0.732	0.601	0.879	0.732	0.601	0.879	SUBCLONAL	1	TRUE	0	0.242754726582996	1		253	346	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136247	202136247	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	50	246	0	ENST00000358485.4:c.491T>A	p.Leu164His	p.L164H	ENST00000358485	NM_001080125.1	164	cTc/cAc	3/9	1	2	FACETS	0.94	0.799	1	0.94	0.799	1	CLONAL	1	TRUE	1	0.242754726582996	2		246	438	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820829	36820829	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777336899	NA	P-0026351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	25	207	0	ENST00000373129.3:c.548G>A	p.Arg183His	p.R183H	ENST00000373129	NM_032017.1	183	cGc/cAc	6/12	1	2	FACETS	0.555	0.437	0.691	0.555	0.437	0.691	SUBCLONAL	1	TRUE	1	0.242754726582996	2		207	371	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226539	41226539	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs80358189	NA	P-0026351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	37	228	0	ENST00000357654.3:c.4485-1G>A		p.X1495_splice	ENST00000357654	NM_007294.3	1495			0.242754726582996	1	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	0	0.242754726582996	1		228	233	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0026353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	47	528	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.928	0.785	1	0.928	0.785	1	CLONAL	1	TRUE	1	0.25	2		528	405	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714131	43714131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs949246182	NA	P-0026353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	86	458	0	ENST00000382044.4:c.4022C>T	p.Pro1341Leu	p.P1341L	ENST00000382044	NM_001141980.1	1341	cCa/cTa	19/28	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.25	2		458	626	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61724108	61724109	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0026353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	41	263	0	ENST00000401558.2:c.793_794del	p.Leu265GlufsTer5	p.L265Efs*5	ENST00000401558	NM_003400.3	265	CTg/g	10/25	1	2	FACETS	0.794	0.662	0.94	0.794	0.662	0.94	CLONAL	1	TRUE	1	0.25	2		263	413	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	40	474	0				ENST00000310581	NM_198253.2	-/1132			0.574298322221085	5	FACETS	0.821	0.693	0.958	0.547	0.462	0.639	CLONAL	2	TRUE	2	0.574298322221085	5		474	158	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381516	81381516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	52	200	1	ENST00000222390.5:c.545G>A	p.Gly182Glu	p.G182E	ENST00000222390	NM_000601.4	182	gGg/gAg	5/18	0.574298322221085	3	FACETS	0.883	0.758	1	0.441	0.379	0.509	CLONAL	1	TRUE	1	0.574298322221085	3		201	264	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0026354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	134	208	0	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	0.310220243158567	6	FACETS	1	0.922	1	1	0.922	1	INDETERMINATE	3	TRUE	3	0.574298322221085	6		208	334	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566827	212566827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202247795	NA	P-0026354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	61	213	0	ENST00000342788.4:c.1354G>A	p.Glu452Lys	p.E452K	ENST00000342788	NM_005235.2	452	Gaa/Aaa	12/28	0.574298322221085	3	FACETS	1	0.92	1	0.538	0.469	0.612	CLONAL	1	TRUE	1	0.574298322221085	3		213	254	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032793	30032794	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0026354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	135	212	0	ENST00000338641.4:c.168_169delinsTT	p.Arg57Ter	p.R57*	ENST00000338641	NM_000268.3	56	ctCCga/ctTTga	2/16	0.574298322221085	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.574298322221085	2		212	226	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310941	123310941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	70	213	0	ENST00000358487.5:c.487G>A	p.Glu163Lys	p.E163K	ENST00000358487	NM_000141.4	163	Gaa/Aaa	5/18	1	2	FACETS	0.949	0.837	1	0.949	0.837	1	CLONAL	1	TRUE	1	0.574298322221085	2		213	257	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8497265	8497265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1270795879	NA	P-0026354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	56	286	0	ENST00000356435.5:c.2326G>A	p.Glu776Lys	p.E776K	ENST00000356435		776	Gaa/Aaa	15/35	0.574298322221085	3	FACETS	0.884	0.763	1	0.442	0.381	0.507	CLONAL	1	TRUE	1	0.574298322221085	3		286	284	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676137	29676137	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0026354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	111	182	0	ENST00000356175.3:c.7127-1G>A		p.X2376_splice	ENST00000356175	NM_000267.3	2376			0.310220243158567	6	FACETS	0.854	0.778	0.933	0.854	0.778	0.933	INDETERMINATE	3	TRUE	3	0.574298322221085	6		182	324	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280672	115280672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	687	302	0	ENST00000438362.2:c.359C>T	p.Ser120Leu	p.S120L	ENST00000438362	NM_001242891.1	120	tCa/tTa	4/20	0.574298322221085	20	FACETS	1	0.984	1			1	CLONAL	8	TRUE	NA	0.574298322221085	20		302	1783	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518613	204518613	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	104	214	0	ENST00000367182.3:c.1276A>C	p.Asn426His	p.N426H	ENST00000367182	NM_001278516.1	426	Aac/Cac	11/11	0.574298322221085	6	FACETS	0.819	0.737	0.905			1	CLONAL	2	TRUE	NA	0.574298322221085	6		214	475	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18649067	18649067	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	225	279	0	ENST00000266497.5:c.2742A>T	p.Lys914Asn	p.K914N	ENST00000266497		914	aaA/aaT	19/31	0.574298322221085	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	1	0.574298322221085	4		279	381	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916241	9916241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	148	294	0	ENST00000330684.3:c.2048G>A	p.Gly683Glu	p.G683E	ENST00000330684	NM_001134407.1	683	gGg/gAg	10/13	0.574298322221085	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	1	0.574298322221085	3		294	320	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33430290	33430290	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	221	371	0	ENST00000345365.6:c.721C>T	p.Leu241Phe	p.L241F	ENST00000345365	NM_002878.3	241	Ctt/Ttt	8/10	0.310220243158567	6	FACETS	0.959	0.899	1	0.959	0.899	1	INDETERMINATE	3	TRUE	3	0.574298322221085	6		371	575	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793224	33793224	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	22	24	0	ENST00000498907.2:c.97T>A	p.Phe33Ile	p.F33I	ENST00000498907	NM_004364.3	33	Ttt/Att	1/1	0.574298322221085	3	FACETS	1	0.89	1	1	0.89	1	CLONAL	2	TRUE	1	0.574298322221085	3		24	44	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212083	36212083	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	118	406	0	ENST00000222270.7:c.1834A>G	p.Thr612Ala	p.T612A	ENST00000222270	NM_014727.1	612	Acc/Gcc	3/37	0.574298322221085	3	FACETS	1	0.938	1	0.523	0.474	0.574	CLONAL	1	TRUE	1	0.574298322221085	3		406	506	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250154	39250154	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	120	418	0	ENST00000402219.2:c.1415A>C	p.Lys472Thr	p.K472T	ENST00000402219	NM_005633.3	472	aAa/aCa	10/23	0.574298322221085	3	FACETS	1	0.925	1	0.511	0.464	0.561	CLONAL	1	TRUE	1	0.574298322221085	3		418	526	SUCCESS
APC	324	MSKCC	GRCh37	5	112174881	112174881	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	124	215	0	ENST00000257430.4:c.3590T>C	p.Phe1197Ser	p.F1197S	ENST00000257430	NM_000038.5	1197	tTc/tCc	16/16	0.574298322221085	5	FACETS	0.943	0.869	1	0.943	0.869	1	CLONAL	3	TRUE	2	0.574298322221085	5		215	284	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168984	32168984	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	133	402	0	ENST00000375023.3:c.4049A>T	p.Lys1350Met	p.K1350M	ENST00000375023	NM_004557.3	1350	aAg/aTg	22/30	0.574298322221085	6	FACETS	1	0.957	1	0.273	0.247	0.3	CLONAL	1	TRUE	2	0.574298322221085	6		402	912	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964501	93964502	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0026354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	50	227	0	ENST00000369303.4:c.2395_2396delinsTT	p.Pro799Leu	p.P799L	ENST00000369303	NM_004440.3	799	CCa/TTa	14/17	1	2	FACETS	0.907	0.781	1	0.907	0.781	1	CLONAL	1	TRUE	1	0.574298322221085	2		227	192	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729683	41729683	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	67	317	0	ENST00000242208.4:c.846T>G	p.Asp282Glu	p.D282E	ENST00000242208	NM_002192.2	282	gaT/gaG	3/3	0.565608635144978	4	FACETS	0.93	0.812	1	0.465	0.406	0.529	CLONAL	1	TRUE	2	0.574298322221085	4		317	395	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002692	37002693	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0026354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	170	275	1	ENST00000358127.4:c.556_557delinsAA	p.Gly186Asn	p.G186N	ENST00000358127	NM_001280556.1	186	GGc/AAc	5/10	0.574298322221085	3	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	1	0.574298322221085	3		276	378	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832553	72832569	+	frameshift_variant	Frame_Shift_Del	DEL	TCTCCGCTTTGCTCTGT	TCTCCGCTTTGCTCTGT	C	novel	NA	P-0026354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	41	205	0	ENST00000268489.5:c.4012_4028delinsG	p.Thr1338ValfsTer2	p.T1338Vfs*2	ENST00000268489	NM_006885.3	1338	ACAGAGCAAAGCGGAGAt/Gt	9/10	0.574298322221085	3	FACETS	0.729	0.612	0.858	0.365	0.306	0.429	SUBCLONAL	1	TRUE	1	0.574298322221085	3		205	252	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696689	47696689	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519972	NA	P-0026355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	124	311	0	ENST00000347630.2:c.259T>A	p.Tyr87Asn	p.Y87N	ENST00000347630	NM_001007230.1	87	Tac/Aac	5/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.653198952932678	2		311	354	SUCCESS
BLM	641	MSKCC	GRCh37	15	91341543	91341543	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1352520577	NA	P-0026355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	103	348	0	ENST00000355112.3:c.3334A>C	p.Asn1112His	p.N1112H	ENST00000355112	NM_000057.2	1112	Aat/Cat	17/22	1	2	FACETS	0.919	0.831	1	0.919	0.831	1	CLONAL	1	TRUE	1	0.653198952932678	2		348	343	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	69	474	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.67720023146742	2		474	185	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307265	118307265	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	11	63	0	ENST00000534358.1:c.38C>T	p.Pro13Leu	p.P13L	ENST00000534358	NM_005933.3	13	cCc/cTc	1/36	0.510232370905909	1	FACETS	0.398	0.282	0.534	0.398	0.282	0.534	SUBCLONAL	1	TRUE	0	0.67720023146742	1		63	54	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118370117	118370117	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	51	202	0	ENST00000534358.1:c.6061A>C	p.Asn2021His	p.N2021H	ENST00000534358	NM_005933.3	2021	Aat/Cat	23/36	0.510232370905909	1	FACETS	0.727	0.634	0.824	0.727	0.634	0.824	SUBCLONAL	1	TRUE	0	0.67720023146742	1		202	137	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290241	15290241	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	135	512	0	ENST00000263388.2:c.3394del	p.Gln1132SerfsTer140	p.Q1132Sfs*140	ENST00000263388	NM_000435.2	1132	Cag/ag	21/33	1	2	FACETS	0.982	0.901	1	0.982	0.901	1	CLONAL	1	TRUE	1	0.67720023146742	2		512	406	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217324	11217335	+	inframe_deletion	In_Frame_Del	DEL	TCTCATACCAGG	TCTCATACCAGG	-	novel	NA	P-0026358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	24	325	0	ENST00000361445.4:c.4343_4354del	p.Thr1448_Glu1451del	p.T1448_E1451del	ENST00000361445	NM_004958.3	1448	aCCTGGTATGAGAaa/aaa	30/58	1	2	FACETS	0.283	0.222	0.353	0.283	0.222	0.353	SUBCLONAL	1	TRUE	1	0.576519469447063	2		325	294	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891205	151891205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776685589	NA	P-0026358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	77	254	0	ENST00000262189.6:c.4549G>A	p.Gly1517Arg	p.G1517R	ENST00000262189	NM_170606.2	1517	Gga/Aga	31/59	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.576519469447063	2		254	237	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0026359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	220	503	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.290365812118465	7	FACETS	1	0.959	1	1	0.993	1	CLONAL	8	FALSE	1	0.290365812118465	7		505	325	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0026359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	78	122	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.290365812118465	6	FACETS	0.99	0.9	1	1	0.971	1	CLONAL	6	FALSE	1	0.290365812118465	6		122	143	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866439	56866439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	99	265	1	ENST00000519728.1:c.686C>T	p.Pro229Leu	p.P229L	ENST00000519728	NM_002350.3	229	cCc/cTc	8/13	1	2	FACETS	1	0.971	1	1	0.991	1	CLONAL	3	FALSE	1	0.290365812118465	2		266	199	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0026360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	16	454	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.220522336450728	3	FACETS	0.671	0.496	0.879	0.336	0.248	0.44	SUBCLONAL	1	TRUE	1	0.219533890388306	3		454	241	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528489	29528489	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764079291	NA	P-0026360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	55	308	0	ENST00000356175.3:c.1246C>T	p.Arg416Ter	p.R416*	ENST00000356175	NM_000267.3	416	Cga/Tga	11/57	0.169666210074253	2	FACETS	1	0.965	1	0.724	0.622	0.834	CLONAL	1	TRUE	0	0.219533890388306	2		308	346	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907792	76907792	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	12	188	0	ENST00000373344.5:c.4369G>T	p.Glu1457Ter	p.E1457*	ENST00000373344	NM_000489.3	1457	Gag/Tag	15/35	1	2	FACETS	0.473	0.332	0.647	0.473	0.332	0.647	SUBCLONAL	1	TRUE	1	0.219533890388306	2		188	231	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019660	123019660	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	23	305	0	ENST00000355640.3:c.148G>T	p.Ala50Ser	p.A50S	ENST00000355640		50	Gca/Tca	2/7	1	2	FACETS	0.467	0.363	0.587	0.467	0.363	0.587	SUBCLONAL	1	TRUE	1	0.219533890388306	2		305	449	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609921	117609921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	196	277	0	ENST00000368508.3:c.6778C>T	p.Pro2260Ser	p.P2260S	ENST00000368508	NM_002944.2	2260	Cca/Tca	43/43	0.454656546604793	1	FACETS	0.674	0.637	0.71	0.674	0.637	0.71	INDETERMINATE	1	TRUE	0	0.941613926256681	1		277	327	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938233	76938233	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0026362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	254	319	0	ENST00000373344.5:c.2515A>T	p.Lys839Ter	p.K839*	ENST00000373344	NM_000489.3	839	Aaa/Taa	9/35	0.358937026846304	1	FACETS	0.652	0.62	0.683	0.652	0.62	0.683	INDETERMINATE	1	TRUE	0	0.941613926256681	1		319	438	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0026363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	104	388	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.43478155335017	3	FACETS	1	0.982	1	0.728	0.657	0.802	CLONAL	1	TRUE	1	0.43478155335017	3		388	400	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003496	42003496	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	21	285	0	ENST00000219905.7:c.3033C>A	p.Tyr1011Ter	p.Y1011*	ENST00000219905	NM_001164273.1	1011	taC/taA	8/24	1	2	FACETS	0.288	0.222	0.366	0.288	0.222	0.366	SUBCLONAL	1	TRUE	1	0.43478155335017	2		285	335	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039842	47039846	+	frameshift_variant	Frame_Shift_Del	DEL	TCGCA	TCGCA	-	novel	NA	P-0026363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	50	374	0	ENST00000377604.3:c.1187_1191del	p.Arg396GlnfsTer45	p.R396Qfs*45	ENST00000377604	NM_001204468.1	395	agTCGCAtc/agtc	12/24	1	2	FACETS	0.439	0.372	0.512	0.439	0.372	0.512	SUBCLONAL	1	TRUE	1	0.43478155335017	2		374	524	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	92	501	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.993	0.89	1	0.993	0.89	1	CLONAL	1	TRUE	1	0.513244165180746	2		501	361	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436026	56436026	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771831816	NA	P-0026364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	162	157	1	ENST00000407977.2:c.1111C>T	p.Arg371Ter	p.R371*	ENST00000407977		371	Cga/Tga	9/10	0.513244165180746	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.513244165180746	2		158	310	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984414	201984414	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	193	383	0	ENST00000359651.3:c.1079G>T	p.Gly360Val	p.G360V	ENST00000359651		360	gGc/gTc	8/8	0.482201761448177	3	FACETS	1	0.977	1	0.567	0.525	0.61	CLONAL	1	TRUE	1	0.513244165180746	3		383	834	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218036	108218036	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	70	264	0	ENST00000278616.4:c.8615A>T	p.His2872Leu	p.H2872L	ENST00000278616	NM_000051.3	2872	cAt/cTt	59/63	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.513244165180746	2		264	248	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691943	30691943	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	174	214	0	ENST00000295754.5:c.445T>A	p.Phe149Ile	p.F149I	ENST00000295754	NM_003242.5	149	Ttc/Atc	3/7	0.513244165180746	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.513244165180746	2		214	319	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044594	47044595	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	209	224	0	ENST00000377604.3:c.2091_2092insA	p.Glu698ArgfsTer22	p.E698Rfs*22	ENST00000377604	NM_001204468.1	697	-/A	18/24	1	1	FACETS	0.778	0.734	0.822	1	0.993	1	SUBCLONAL	2	TRUE	0	0.513244165180746	1		224	389	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222635	69222635	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	138	610	0	ENST00000462284.1:c.608T>C	p.Leu203Pro	p.L203P	ENST00000462284	NM_002392.5	203	cTg/cCg	8/11	0.501426745291118	4	FACETS	0.929	0.845	1	0.464	0.422	0.509	CLONAL	1	TRUE	2	0.527925448935498	4		610	860	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191529	10191529	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	166	483	0	ENST00000256474.2:c.523del	p.Tyr175ThrfsTer27	p.Y175Tfs*27	ENST00000256474	NM_000551.3	174	aaT/aa	3/3	0.527925448935498	2	FACETS	0.834	0.777	0.892	0.834	0.777	0.892	CLONAL	2	TRUE	0	0.527925448935498	2		483	377	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584834	52584834	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0026365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	117	544	0	ENST00000394830.3:c.4289-1G>A		p.X1430_splice	ENST00000394830	NM_018313.4	1430			NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.527925448935498	2		544	305	SUCCESS
BTK	695	MSKCC	GRCh37	X	100612505	100612505	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	178	233	0	ENST00000308731.7:c.1169T>C	p.Leu390Pro	p.L390P	ENST00000308731	NM_000061.2	390	cTg/cCg	13/19	0.406336668779748	2	FACETS	1	0.99	1			1	CLONAL	2	TRUE	NA	0.527925448935498	2		233	272	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0026366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	91	298	1	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	0.141306605486521	3	FACETS	0.928	0.833	1	0.619	0.555	0.686	INDETERMINATE	2	TRUE	0	0.350039905988593	3		299	329	SUCCESS
APC	324	MSKCC	GRCh37	5	112128185	112128185	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779805	NA	P-0026366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	105	416	1	ENST00000257430.4:c.688C>T	p.Arg230Cys	p.R230C	ENST00000257430	NM_000038.5	230	Cgt/Tgt	7/16	0.322416334546327	3	FACETS	0.958	0.858	1	0.479	0.429	0.532	CLONAL	1	TRUE	1	0.350039905988593	3		417	736	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285863	46285863	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	207	379	0	ENST00000334344.6:c.5131C>T	p.Gln1711Ter	p.Q1711*	ENST00000334344	NM_152641.2	1711	Cag/Tag	18/21	0.350039905988593	2	FACETS	0.895	0.834	0.957	0.895	0.834	0.957	CLONAL	2	TRUE	0	0.350039905988593	2		379	661	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446463	49446463	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	147	332	0	ENST00000301067.7:c.1142C>T	p.Pro381Leu	p.P381L	ENST00000301067	NM_003482.3	381	cCc/cTc	9/54	0.350039905988593	2	FACETS	0.963	0.888	1	0.963	0.888	1	CLONAL	2	TRUE	0	0.350039905988593	2		332	436	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223283	2223283	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	112	524	1	ENST00000326181.6:c.895C>T	p.His299Tyr	p.H299Y	ENST00000326181	NM_032271.2	299	Cac/Tac	10/21	0.244580696065106	4	FACETS	0.977	0.878	1	0.489	0.439	0.541	CLONAL	1	TRUE	2	0.350039905988593	4		525	884	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222976	5222976	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	269	382	1	ENST00000357368.4:c.2827G>A	p.Ala943Thr	p.A943T	ENST00000357368	NM_002850.3	943	Gcc/Acc	18/38	0.350039905988593	5	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	2	0.350039905988593	5		383	709	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755738	39755738	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	134	376	1	ENST00000288319.7:c.1027G>A	p.Asp343Asn	p.D343N	ENST00000288319	NM_182918.3	343	Gat/Aat	10/10	0.244580696065106	4	FACETS	0.874	0.797	0.955	0.874	0.797	0.955	CLONAL	2	TRUE	2	0.350039905988593	4		377	591	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916794	178916794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	63	456	0	ENST00000263967.3:c.181C>T	p.Leu61Phe	p.L61F	ENST00000263967	NM_006218.2	61	Ctt/Ttt	2/21	0.244580696065106	4	FACETS	0.654	0.565	0.751	0.327	0.282	0.376	SUBCLONAL	1	TRUE	2	0.350039905988593	4		456	743	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86637110	86637110	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	60	267	0	ENST00000274376.6:c.1021C>T	p.Arg341Trp	p.R341W	ENST00000274376	NM_002890.2	341	Cgg/Tgg	6/25	0.322416334546327	3	FACETS	0.909	0.785	1	0.455	0.392	0.522	CLONAL	1	TRUE	1	0.350039905988593	3		267	443	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131895034	131895034	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854789	NA	P-0026366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	82	291	1	ENST00000265335.6:c.188G>A	p.Gly63Glu	p.G63E	ENST00000265335		63	gGa/gAa	2/25	0.322416334546327	3	FACETS	0.936	0.827	1	0.468	0.413	0.527	CLONAL	1	TRUE	1	0.350039905988593	3		292	588	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930121	68930121	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	103	384	0	ENST00000288368.4:c.182T>C	p.Val61Ala	p.V61A	ENST00000288368	NM_024870.2	61	gTt/gCt	2/40	0.244580696065106	4	FACETS	0.865	0.773	0.964	0.433	0.386	0.482	CLONAL	1	TRUE	2	0.350039905988593	4		384	918	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937786	76937786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	113	453	0	ENST00000373344.5:c.2962G>A	p.Gly988Arg	p.G988R	ENST00000373344	NM_000489.3	988	Gga/Aga	9/35	0.141306605486521	3	FACETS	0.942	0.848	1	0.314	0.282	0.348	INDETERMINATE	1	TRUE	0	0.350039905988593	3		453	805	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	130	474	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.964	0.884	1	1	0.99	1	CLONAL	2	TRUE	1	0.342156382162581	2		474	394	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270593	98270595	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	rs756897237	NA	P-0026367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	10	56	0	ENST00000331920.6:c.49_51del	p.Gly17del	p.G17del	ENST00000331920	NM_000264.3	17	GGC/-	1/24	1	2	FACETS	0.541	0.369	0.754	0.541	0.369	0.754	SUBCLONAL	1	TRUE	1	0.342156382162581	2		56	108	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307414	118307416	+	inframe_deletion	In_Frame_Del	DEL	GCG	GCG	-	rs781936420	NA	P-0026367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	11	53	0	ENST00000534358.1:c.200_202del	p.Ala67del	p.A67del	ENST00000534358	NM_005933.3	63	GCG/-	1/36	1	2	FACETS	1	0.77	1	1	0.77	1	CLONAL	1	TRUE	1	0.342156382162581	2		53	58	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497902	25497902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1311728146	NA	P-0026367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	116	645	2	ENST00000264709.3:c.547C>T	p.Arg183Trp	p.R183W	ENST00000264709	NM_175629.2	183	Cgg/Tgg	6/23	0.342156382162581	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.342156382162581	1		647	480	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183205	56183205	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	51	339	0	ENST00000399503.3:c.4115G>A	p.Gly1372Asp	p.G1372D	ENST00000399503	NM_005921.1	1372	gGt/gAt	18/20	1	2	FACETS	0.413	0.351	0.481	0.413	0.351	0.481	SUBCLONAL	1	TRUE	1	0.5	2		339	494	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38942434	38942434	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201229460	NA	P-0026368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	92	411	0	ENST00000357387.3:c.5099C>T	p.Pro1700Leu	p.P1700L	ENST00000357387	NM_152756.3	1700	cCt/cTt	38/38	1	2	FACETS	0.538	0.478	0.602	0.538	0.478	0.602	SUBCLONAL	1	TRUE	1	0.5	2		411	684	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552837	106552837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1399614609	NA	P-0026369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	145	559	1	ENST00000369096.4:c.802C>T	p.Arg268Cys	p.R268C	ENST00000369096	NM_001198.3	268	Cgt/Tgt	5/7	0.187280560771838	3	FACETS	1	0.97	1	0.563	0.516	0.612	INDETERMINATE	1	TRUE	1	0.57847292679144	3		560	574	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0026370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	170	518	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.234954742516563	3	FACETS	1	0.988	1	0.696	0.642	0.751	INDETERMINATE	1	TRUE	1	0.452545173596927	3		518	662	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0026370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	99	338	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.452545173596927	1	FACETS	0.795	0.714	0.879	0.795	0.714	0.879	SUBCLONAL	1	TRUE	0	0.452545173596927	1		338	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0026370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	97	522	1	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.452545173596927	1	FACETS	0.844	0.758	0.934	0.844	0.758	0.934	CLONAL	1	TRUE	0	0.452545173596927	1		523	393	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729814	41729814	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	74	297	0	ENST00000242208.4:c.715G>T	p.Asp239Tyr	p.D239Y	ENST00000242208	NM_002192.2	239	Gac/Tac	3/3	0.234954742516563	3	FACETS	0.988	0.869	1	0.494	0.434	0.557	INDETERMINATE	1	TRUE	1	0.452545173596927	3		297	406	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560514	65560514	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	112	355	0	ENST00000358664.4:c.83A>G	p.His28Arg	p.H28R	ENST00000358664	NM_002382.4	28	cAt/cGt	3/5	1	2	FACETS	0.932	0.841	1	0.932	0.841	1	CLONAL	1	TRUE	1	0.420847825816557	2		355	571	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240786	55240786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756870976	NA	P-0026373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	25	569	2	ENST00000275493.2:c.2030G>A	p.Arg677His	p.R677H	ENST00000275493	NM_005228.3	677	cGc/cAc	17/28	1	2	FACETS	0.168	0.131	0.21	0.168	0.131	0.21	SUBCLONAL	1	TRUE	1	0.420847825816557	2		571	708	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092823	27092823	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0026373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	151	543	0	ENST00000324856.7:c.2844T>G	p.Tyr948Ter	p.Y948*	ENST00000324856	NM_006015.4	948	taT/taG	9/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.420847825816557	2		543	616	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845593	63845593	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	88	337	1	ENST00000279873.7:c.1332del	p.Lys445AsnfsTer34	p.K445Nfs*34	ENST00000279873	NM_032199.2	444	atC/at	9/10	1	2	FACETS	0.862	0.767	0.964	0.862	0.767	0.964	CLONAL	1	TRUE	1	0.420847825816557	2		338	485	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653789	89653789	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0026373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	206	341	0	ENST00000371953.3:c.87T>G	p.Tyr29Ter	p.Y29*	ENST00000371953	NM_000314.4	29	taT/taG	2/9	0.40847169951726	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.420847825816557	2		341	434	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247361	153247362	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATCTCGA	novel	NA	P-0026373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	83	315	0	ENST00000281708.4:c.1434_1440dup	p.Ala481SerfsTer6	p.A481Sfs*6	ENST00000281708	NM_033632.3	480	-/TCGAGAT	10/12	1	2	FACETS	0.818	0.725	0.918	0.818	0.725	0.918	CLONAL	1	TRUE	1	0.420847825816557	2		315	482	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	188	474	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.68	2		474	471	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0026375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	226	661	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	1	2	FACETS	0.824	0.769	0.88	0.824	0.769	0.88	CLONAL	1	TRUE	1	0.68	2		661	807	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780667	56780667	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	249	525	0	ENST00000337432.4:c.682G>C	p.Asp228His	p.D228H	ENST00000337432	NM_058216.2	228	Gat/Cat	4/9	1	2	FACETS	0.77	0.721	0.821	0.77	0.721	0.821	SUBCLONAL	1	TRUE	1	0.68	2		525	951	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0026376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	22	472	0	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	0.604048210996758	1	FACETS	0.08	0.062	0.102	0.08	0.062	0.102	SUBCLONAL	1	TRUE	0	0.604048210996758	1		472	632	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0026376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	276	388	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.132328035428443	5	FACETS	1	0.986	1	0.571	0.539	0.605	INDETERMINATE	2	TRUE	1	0.604048210996758	5		388	762	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578179	7578179	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	350	623	0	ENST00000269305.4:c.670G>T	p.Glu224Ter	p.E224*	ENST00000269305	NM_001126112.2	224	Gag/Tag	6/11	0.443601238097895	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.604048210996758	1		623	748	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220706	1220706	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555738475	NA	P-0026376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	170	464	0	ENST00000326873.7:c.727del	p.Val243SerfsTer44	p.V243Sfs*44	ENST00000326873	NM_000455.4	242	Ggg/gg	5/10	0.604048210996758	1	FACETS	0.8	0.742	0.86	0.8	0.742	0.86	SUBCLONAL	1	TRUE	0	0.604048210996758	1		464	491	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356385	66356385	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	166	380	0	ENST00000273854.3:c.1112C>G	p.Thr371Ser	p.T371S	ENST00000273854	NM_004439.5	371	aCt/aGt	5/18	0.276541856805012	1	FACETS	0.674	0.623	0.727	0.674	0.623	0.727	INDETERMINATE	1	TRUE	0	0.604048210996758	1		380	569	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510141	187510141	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	116	392	0	ENST00000441802.2:c.13372C>A	p.Gln4458Lys	p.Q4458K	ENST00000441802	NM_005245.3	4458	Cag/Aag	27/27	0.276541856805012	1	FACETS	0.404	0.364	0.445	0.404	0.364	0.445	INDETERMINATE	1	TRUE	0	0.604048210996758	1		392	664	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922249	39922249	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	156	341	0	ENST00000378444.4:c.3923A>T	p.Gln1308Leu	p.Q1308L	ENST00000378444	NM_001123385.1	1308	cAg/cTg	9/15	1	2	FACETS	0.903	0.831	0.977	0.903	0.831	0.977	CLONAL	1	TRUE	1	0.604048210996758	2		341	572	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148931	119148931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs985412813	NA	P-0026385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	31	534	0	ENST00000264033.4:c.1151G>A	p.Cys384Tyr	p.C384Y	ENST00000264033	NM_005188.3	384	tGt/tAt	8/16	1	2	FACETS	0.302	0.243	0.369	0.302	0.243	0.369	SUBCLONAL	1	TRUE	1	0.368526750686563	2		534	557	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035159	30035159	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	132	552	0	ENST00000338641.4:c.322del	p.Glu108SerfsTer15	p.E108Sfs*15	ENST00000338641	NM_000268.3	107	gaG/ga	3/16	0.368526750686563	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.368526750686563	1		552	470	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893363	32893363	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398122741	NA	P-0026387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	409	575	0	ENST00000380152.3:c.217C>T	p.Gln73Ter	p.Q73*	ENST00000380152		73	Cag/Tag	3/27	0.548695281527603	2	FACETS	0.916	0.879	0.953	0.916	0.879	0.953	CLONAL	2	TRUE	0	0.570190385048029	2		575	783	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793244	242793244	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs773969430	NA	P-0026387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	300	703	1	ENST00000334409.5:c.833G>T	p.Arg278Met	p.R278M	ENST00000334409	NM_005018.2	278	aGg/aTg	5/5	0.570190385048029	3	FACETS	1	0.983	1	0.554	0.521	0.588	CLONAL	1	TRUE	1	0.570190385048029	3		704	1220	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0026388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	326	388	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.369185401052492	4	FACETS	1	0.979	1			1	INDETERMINATE	2	TRUE	NA	0.823938904406415	4		388	688	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0026388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	451	632	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.823938904406415	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.823938904406415	1		632	644	SUCCESS
APC	324	MSKCC	GRCh37	5	112175897	112175897	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	61	318	2	ENST00000257430.4:c.4606G>T	p.Glu1536Ter	p.E1536*	ENST00000257430	NM_000038.5	1536	Gaa/Taa	16/16	0.823938904406415	1	FACETS	0.799	0.718	0.878	0.799	0.718	0.878	SUBCLONAL	1	TRUE	0	0.823938904406415	1		320	109	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411411	63411411	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	297	631	1	ENST00000330258.3:c.1756C>T	p.Arg586Ter	p.R586*	ENST00000330258	NM_152424.3	586	Cga/Tga	2/2	0.61869999495988	1	FACETS	0.782	0.746	0.818	0.782	0.746	0.818	SUBCLONAL	1	TRUE	0	0.823938904406415	1		632	542	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729775	41729775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	172	335	1	ENST00000242208.4:c.754G>A	p.Ala252Thr	p.A252T	ENST00000242208	NM_002192.2	252	Gcc/Acc	3/3	0.475569206519511	6	FACETS	0.854	0.789	0.922	0.427	0.394	0.461	INDETERMINATE	2	TRUE	2	0.823938904406415	6		336	647	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962914	2962914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147823569	NA	P-0026388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1351	153	797	1	ENST00000396946.4:c.1994C>T	p.Ser665Leu	p.S665L	ENST00000396946	NM_032415.4	665	tCg/tTg	16/25	0.475569206519511	6	FACETS	0.654	0.596	0.715	0.163	0.149	0.179	INDETERMINATE	1	TRUE	2	0.823938904406415	6		798	1504	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201847	67201848	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0026388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	251	639	0	ENST00000312629.5:c.1048dup	p.Gln350ProfsTer10	p.Q350Pfs*10	ENST00000312629	NM_003952.2	349	-/C		0.226190385820734	1	FACETS	0.475	0.446	0.505	0.475	0.446	0.505	INDETERMINATE	1	TRUE	0	0.823938904406415	1		639	754	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368280	45368280	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	275	522	0	ENST00000262160.6:c.1322A>C	p.His441Pro	p.H441P	ENST00000262160	NM_005901.5	441	cAt/cCt	11/11	0.823938904406415	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.823938904406415	1		522	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0026389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	610	751	0	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	0.36188496091091	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.36188496091091	3		751	1195	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21553909	21553911	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0026389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	113	442	0	ENST00000382592.4:c.2691_2693del	p.Trp897_Ser898delinsCys	p.W897_S898delinsC	ENST00000382592	NM_014572.2	897	tgGAGt/tgt	7/8	1	2	FACETS	0.82	0.738	0.906	0.82	0.738	0.906	CLONAL	1	TRUE	1	0.36188496091091	2		442	762	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995197	15995197	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	134	549	0	ENST00000268712.3:c.2996G>A	p.Ser999Asn	p.S999N	ENST00000268712	NM_006311.3	999	aGt/aAt	22/46	0.36188496091091	2	FACETS	0.962	0.875	1	0.481	0.437	0.527	CLONAL	1	TRUE	0	0.36188496091091	2		549	770	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244217	5244217	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	157	556	0	ENST00000357368.4:c.1265G>T	p.Gly422Val	p.G422V	ENST00000357368	NM_002850.3	422	gGc/gTc	11/38	0.36188496091091	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.36188496091091	1		556	686	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748914	41748914	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	115	493	1	ENST00000301178.4:c.1439G>T	p.Arg480Leu	p.R480L	ENST00000301178	NM_021913.4	480	cGt/cTt	11/20	0.360050815751722	3	FACETS	0.833	0.75	0.921	0.417	0.375	0.461	CLONAL	1	TRUE	1	0.36188496091091	3		494	901	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352288	70352288	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	154	318	0	ENST00000374080.3:c.4315G>T	p.Val1439Phe	p.V1439F	ENST00000374080		1439	Gtc/Ttc	31/45	0.316053686391476	2	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.36188496091091	2		318	648	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512257	120512257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	141	597	1	ENST00000256646.2:c.985G>A	p.Gly329Ser	p.G329S	ENST00000256646	NM_024408.3	329	Ggc/Agc	6/34	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.250925199143874	2		598	841	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	176	501	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.301005937620338	4	FACETS	0.813	0.751	0.878	0.813	0.751	0.878	CLONAL	2	TRUE	2	0.404117110607879	4		501	752	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0026391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	218	695	3	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.288977281895636	2	FACETS	0.815	0.762	0.869	0.815	0.762	0.869	CLONAL	2	TRUE	0	0.404117110607879	2		698	662	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420109	49420109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123728	NA	P-0026391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	77	665	0	ENST00000301067.7:c.15640C>T	p.Arg5214Cys	p.R5214C	ENST00000301067	NM_003482.3	5214	Cgc/Tgc	48/54	NA	2	FACETS	0.723	0.636	0.816			1	INDETERMINATE	1	TRUE	NA	0.404117110607879	2		665	527	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114259	115114259	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	84	596	1	ENST00000257566.3:c.958C>A	p.Gln320Lys	p.Q320K	ENST00000257566	NM_016569.3	320	Cag/Aag	6/8	0.310777579541218	2	FACETS	0.733	0.649	0.823	0.367	0.324	0.412	SUBCLONAL	1	TRUE	0	0.404117110607879	2		597	567	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041864	42041865	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0026391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	68	650	0	ENST00000219905.7:c.6061_6062del	p.Leu2021GlufsTer2	p.L2021Efs*2	ENST00000219905	NM_001164273.1	2020	aCT/a	17/24	0.309450718877592	3	FACETS	0.615	0.534	0.702	0.307	0.267	0.351	SUBCLONAL	1	TRUE	1	0.404117110607879	3		650	658	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096166	178096166	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	55	448	0	ENST00000397062.3:c.1165A>G	p.Lys389Glu	p.K389E	ENST00000397062	NM_006164.4	389	Aaa/Gaa	5/5	0.301005937620338	4	FACETS	0.525	0.448	0.609	0.262	0.224	0.305	SUBCLONAL	1	TRUE	2	0.404117110607879	4		448	728	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0026392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	391	322	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.69081183808565	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.69081183808565	1		322	710	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0026392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	316	550	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.953	0.901	1	0.953	0.901	1	CLONAL	1	TRUE	1	0.69081183808565	2		550	960	SUCCESS
APC	324	MSKCC	GRCh37	5	112175248	112175249	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0026392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	289	295	1	ENST00000257430.4:c.3959_3960del	p.Val1320GlufsTer11	p.V1320Efs*11	ENST00000257430	NM_000038.5	1319	ccTGtg/cctg	16/16	0.663091276336658	2	FACETS	0.881	0.842	0.919	0.881	0.842	0.919	CLONAL	2	TRUE	0	0.69081183808565	2		296	475	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041197	112041197	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759104731	NA	P-0026392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	161	411	0	ENST00000368678.4:c.58G>A	p.Gly20Ser	p.G20S	ENST00000368678		20	Ggc/Agc	3/13	0.330729612207683	1	FACETS	0.405	0.372	0.439	0.405	0.372	0.439	INDETERMINATE	1	TRUE	0	0.69081183808565	1		411	754	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289720	15289720	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369213011	NA	P-0026392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	458	706	0	ENST00000263388.2:c.3751G>A	p.Glu1251Lys	p.E1251K	ENST00000263388	NM_000435.2	1251	Gag/Aag	23/33	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.69081183808565	2		706	1241	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943628	9943628	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	106	482	0	ENST00000330684.3:c.1313A>C	p.Lys438Thr	p.K438T	ENST00000330684	NM_001134407.1	438	aAg/aCg	5/13	1	2	FACETS	0.335	0.299	0.372	0.335	0.299	0.372	SUBCLONAL	1	TRUE	1	0.69081183808565	2		482	917	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050753	5050753	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	135	523	0	ENST00000381652.3:c.536T>A	p.Leu179His	p.L179H	ENST00000381652	NM_004972.3	179	cTt/cAt	6/25	0.158915492746383	1	FACETS	0.314	0.285	0.344	0.314	0.285	0.344	INDETERMINATE	1	TRUE	0	0.69081183808565	1		523	816	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0026393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	106	373	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.39372754064315	4	FACETS	1	0.955	1	0.558	0.501	0.619	CLONAL	1	TRUE	2	0.39372754064315	4		373	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579361	7579361	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1064796722	NA	P-0026393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	431	710	1	ENST00000269305.4:c.326T>G	p.Phe109Cys	p.F109C	ENST00000269305	NM_001126112.2	109	tTc/tGc	4/11	0.39372754064315	2	FACETS	0.855	0.82	0.889	1	0.995	1	CLONAL	3	TRUE	0	0.39372754064315	2		711	854	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560382	95560382	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	176	557	0	ENST00000393063.1:c.5207G>T	p.Arg1736Leu	p.R1736L	ENST00000393063	NM_030621.3	1736	cGg/cTg	25/28	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.39372754064315	2		557	783	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476406	88476406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1395756451	NA	P-0026393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	192	389	0	ENST00000360948.2:c.1726G>A	p.Asp576Asn	p.D576N	ENST00000360948	NM_001012338.2	576	Gat/Aat	15/19	0.310564237356143	3	FACETS	0.883	0.82	0.948	0.883	0.82	0.948	CLONAL	2	TRUE	1	0.39372754064315	3		389	661	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576098	29576098	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1135402852	NA	P-0026393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	194	560	1	ENST00000356175.3:c.4076del	p.Pro1359LeufsTer26	p.P1359Lfs*26	ENST00000356175	NM_000267.3	1357	ttC/tt	30/57	0.39372754064315	6	FACETS	1	0.974	1	0.739	0.685	0.794	CLONAL	2	TRUE	3	0.39372754064315	6		561	795	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484353	120484353	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1553196495	NA	P-0026393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	82	457	0	ENST00000256646.2:c.2777G>C	p.Cys926Ser	p.C926S	ENST00000256646	NM_024408.3	926	tGt/tCt	18/34	0.39223761636556	4	FACETS	1	0.929	1	0.357	0.315	0.402	CLONAL	1	TRUE	1	0.39372754064315	4		457	542	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891093	112891093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	143	577	2	ENST00000351677.2:c.427C>T	p.His143Tyr	p.H143Y	ENST00000351677	NM_002834.3	143	Cac/Tac	4/16	0.39372754064315	3	FACETS	1	0.97	1	0.57	0.521	0.623	CLONAL	1	TRUE	1	0.39372754064315	3		579	762	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515076	103515076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	256	314	0	ENST00000355739.4:c.1577C>T	p.Ser526Phe	p.S526F	ENST00000355739	NM_000123.3	526	tCt/tTt	8/15	0.39372754064315	5	FACETS	0.968	0.911	1	0.968	0.911	1	CLONAL	3	TRUE	2	0.39372754064315	5		314	712	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871995	45871995	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	239	458	0	ENST00000391945.4:c.253G>T	p.Glu85Ter	p.E85*	ENST00000391945	NM_000400.3	85	Gaa/Taa	5/23	0.39372754064315	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	1	0.39372754064315	3		458	718	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877373	40877373	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1230	290	551	0	ENST00000373198.4:c.2323del	p.Met775CysfsTer9	p.M775Cfs*9	ENST00000373198	NM_133170.3	775	Atg/tg	15/32	0.39372754064315	7	FACETS	0.962	0.902	1	0.385	0.361	0.409	CLONAL	2	TRUE	2	0.39372754064315	7		551	1520	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505528	157505528	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	85	352	0	ENST00000346085.5:c.3509G>T	p.Gly1170Val	p.G1170V	ENST00000346085	NM_020732.3	1170	gGg/gTg	13/20	0.39372754064315	4	FACETS	1	0.906	1	0.342	0.303	0.385	CLONAL	1	TRUE	1	0.39372754064315	4		352	586	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388074	81388075	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	111	549	1	ENST00000222390.5:c.300dup	p.Phe101LeufsTer3	p.F101Lfs*3	ENST00000222390	NM_000601.4	100	-/C	3/18	0.39372754064315	2	FACETS	0.972	0.887	1	0.972	0.887	1	CLONAL	2	TRUE	0	0.39372754064315	2		550	290	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180379	38180379	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	145	693	2	ENST00000396334.3:c.228del	p.Gln76HisfsTer24	p.Q76Hfs*24	ENST00000396334	NM_002468.4	76	cAa/ca	1/5	0.39372754064315	3	FACETS	1	0.914	1	0.501	0.457	0.547	CLONAL	1	TRUE	1	0.39372754064315	3		695	880	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0026393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	250	373	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	1	2	FACETS	0.487	0.455	0.52	0.487	0.455	0.52	SUBCLONAL	1	TRUE	1	0.90988199931656	2		373	1128	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579361	7579361	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1064796722	NA	P-0026393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	706	710	1	ENST00000269305.4:c.326T>G	p.Phe109Cys	p.F109C	ENST00000269305	NM_001126112.2	109	tTc/tGc	4/11	0.90988199931656	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.90988199931656	1		711	826	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560382	95560382	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	540	557	0	ENST00000393063.1:c.5207G>T	p.Arg1736Leu	p.R1736L	ENST00000393063	NM_030621.3	1736	cGg/cTg	25/28	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.90988199931656	2		557	1147	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476406	88476406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1395756451	NA	P-0026393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	423	389	0	ENST00000360948.2:c.1726G>A	p.Asp576Asn	p.D576N	ENST00000360948	NM_001012338.2	576	Gat/Aat	15/19	0.445038940932799	1	FACETS	0.758	0.731	0.784	0.758	0.731	0.784	INDETERMINATE	1	TRUE	0	0.90988199931656	1		389	669	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576098	29576098	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1135402852	NA	P-0026393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	482	560	1	ENST00000356175.3:c.4076del	p.Pro1359LeufsTer26	p.P1359Lfs*26	ENST00000356175	NM_000267.3	1357	ttC/tt	30/57	0.291407434065669	5	FACETS	0.878	0.839	0.917			1	INDETERMINATE	2	TRUE	NA	0.90988199931656	5		561	1427	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484353	120484353	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1553196495	NA	P-0026393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	176	457	0	ENST00000256646.2:c.2777G>C	p.Cys926Ser	p.C926S	ENST00000256646	NM_024408.3	926	tGt/tCt	18/34	0.458090654932109	2	FACETS	0.492	0.454	0.532	0.246	0.227	0.266	INDETERMINATE	1	TRUE	0	0.90988199931656	2		457	786	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891093	112891093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	481	577	2	ENST00000351677.2:c.427C>T	p.His143Tyr	p.H143Y	ENST00000351677	NM_002834.3	143	Cac/Tac	4/16	1	2	FACETS	0.889	0.852	0.927	0.889	0.852	0.927	CLONAL	1	TRUE	1	0.90988199931656	2		579	1189	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515076	103515076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	398	314	0	ENST00000355739.4:c.1577C>T	p.Ser526Phe	p.S526F	ENST00000355739	NM_000123.3	526	tCt/tTt	8/15	0.526207225402382	3	FACETS	0.918	0.882	0.954	0.918	0.882	0.954	INDETERMINATE	2	TRUE	1	0.90988199931656	3		314	693	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871995	45871995	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	472	458	0	ENST00000391945.4:c.253G>T	p.Glu85Ter	p.E85*	ENST00000391945	NM_000400.3	85	Gaa/Taa	5/23	1	2	FACETS	0.966	0.926	1	0.966	0.926	1	CLONAL	1	TRUE	1	0.90988199931656	2		458	1074	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877373	40877373	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	80	551	0	ENST00000373198.4:c.2323del	p.Met775CysfsTer9	p.M775Cfs*9	ENST00000373198	NM_133170.3	775	Atg/tg	15/32	0.763056097672649	2	FACETS	0.142	0.124	0.161	0.071	0.062	0.081	SUBCLONAL	1	TRUE	0	0.90988199931656	2		551	1241	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505528	157505528	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	277	352	0	ENST00000346085.5:c.3509G>T	p.Gly1170Val	p.G1170V	ENST00000346085	NM_020732.3	1170	gGg/gTg	13/20	0.322147288753176	1	FACETS	0.621	0.59	0.652	0.621	0.59	0.652	INDETERMINATE	1	TRUE	0	0.90988199931656	1		352	534	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388074	81388075	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	423	549	1	ENST00000222390.5:c.300dup	p.Phe101LeufsTer3	p.F101Lfs*3	ENST00000222390	NM_000601.4	100	-/C	3/18	0.90988199931656	1	FACETS	0.926	0.9	0.952	0.926	0.9	0.952	CLONAL	1	TRUE	0	0.90988199931656	1		550	547	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0026394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	102	334	2	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.159596917467703	2	FACETS	0.883	0.792	0.979	0.883	0.792	0.979	CLONAL	2	TRUE	0	0.20565544057453	2		336	562	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0026394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	128	430	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.20565544057453	5	FACETS	1	0.96	1	0.738	0.669	0.81	CLONAL	2	TRUE	2	0.20565544057453	5		430	736	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0026394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	74	529	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.159596917467703	2	FACETS	1	0.968	1	0.671	0.589	0.76	CLONAL	1	TRUE	0	0.20565544057453	2		529	536	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245506	153245506	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	32	463	0	ENST00000281708.4:c.1685C>A	p.Ser562Ter	p.S562*	ENST00000281708	NM_033632.3	562	tCa/tAa	11/12	1	2	FACETS	0.529	0.428	0.644	0.529	0.428	0.644	SUBCLONAL	1	TRUE	1	0.20565544057453	2		463	588	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2111996	2111996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374936223	NA	P-0026394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	34	443	0	ENST00000219476.3:c.1244C>T	p.Ala415Val	p.A415V	ENST00000219476	NM_000548.3	415	gCg/gTg	12/42	0.20565544057453	3	FACETS	0.565	0.461	0.684	0.283	0.23	0.342	SUBCLONAL	1	TRUE	1	0.20565544057453	3		443	645	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244148	153244148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	64	444	2	ENST00000281708.4:c.2009G>A	p.Gly670Glu	p.G670E	ENST00000281708	NM_033632.3	670	gGa/gAa	12/12	1	2	FACETS	0.963	0.834	1	0.963	0.834	1	CLONAL	1	TRUE	1	0.20565544057453	2		446	646	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339205	65339205	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	29	374	0	ENST00000342505.4:c.331T>C	p.Phe111Leu	p.F111L	ENST00000342505	NM_002227.2	111	Ttc/Ctc	5/25	1	2	FACETS	0.618	0.496	0.758	0.618	0.496	0.758	SUBCLONAL	1	TRUE	1	0.20565544057453	2		374	456	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467484	66467484	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	32	318	0	ENST00000273854.3:c.785G>T	p.Cys262Phe	p.C262F	ENST00000273854	NM_004439.5	262	tGt/tTt	3/18	1	2	FACETS	0.761	0.618	0.923	0.761	0.618	0.923	CLONAL	1	TRUE	1	0.20565544057453	2		318	409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0026395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	427	595	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.399838993100774	0	FACETS	0.64	0.617	0.662			1	SUBCLONAL	3	FALSE	0	0.399838993100774	0		595	668	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495704	72495704	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	511	448	1	ENST00000477973.2:c.368A>G	p.Asn123Ser	p.N123S	ENST00000477973	NM_012234.5	123	aAc/aGc	1/4	NA	2	FACETS	0.987	0.954	1			1	INDETERMINATE	3	FALSE	NA	0.399838993100774	2		449	863	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0026396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	244	323	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	0.426718956418328	2		323	1033	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936093	178936093	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913275	NA	P-0026396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	89	543	1	ENST00000263967.3:c.1635G>T	p.Glu545Asp	p.E545D	ENST00000263967	NM_006218.2	545	gaG/gaT	10/21	1	2	FACETS	0.942	0.839	1	0.942	0.839	1	CLONAL	1	TRUE	1	0.426718956418328	2		544	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578206	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs886039484	NA	P-0026396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	461	658	0	ENST00000269305.4:c.643A>G	p.Ser215Gly	p.S215G	ENST00000269305	NM_001126112.2	215	Agt/Ggt	6/11	0.397334437578195	2	FACETS	0.936	0.896	0.977	0.936	0.896	0.977	CLONAL	2	TRUE	0	0.426718956418328	2		658	1154	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645739	215645739	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	58	487	0	ENST00000260947.4:c.859G>C	p.Glu287Gln	p.E287Q	ENST00000260947	NM_000465.2	287	Gag/Cag	4/11	1	2	FACETS	0.326	0.279	0.377	0.326	0.279	0.377	SUBCLONAL	1	TRUE	1	0.426718956418328	2		487	835	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211883	36211883	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202218975	NA	P-0026396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1376	75	787	1	ENST00000222270.7:c.1634G>A	p.Arg545Gln	p.R545Q	ENST00000222270	NM_014727.1	545	cGa/cAa	3/37	1	2	FACETS	0.242	0.211	0.276	0.242	0.211	0.276	SUBCLONAL	1	TRUE	1	0.426718956418328	2		788	1451	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280688	115280688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	72	474	0	ENST00000438362.2:c.343G>A	p.Val115Ile	p.V115I	ENST00000438362	NM_001242891.1	115	Gtt/Att	4/20	0.235478643146341	1	FACETS	0.403	0.352	0.459	0.403	0.352	0.459	INDETERMINATE	1	TRUE	0	0.426718956418328	1		474	658	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680493	241680493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	71	556	0	ENST00000366560.3:c.256G>A	p.Glu86Lys	p.E86K	ENST00000366560	NM_000143.3	86	Gaa/Aaa	2/10	0.427385830617196	3	FACETS	0.412	0.359	0.471	0.206	0.179	0.236	SUBCLONAL	1	TRUE	1	0.426718956418328	3		556	979	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533569	533569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1170748930	NA	P-0026396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	176	676	1	ENST00000451590.1:c.334G>A	p.Val112Met	p.V112M	ENST00000451590	NM_001130442.1	112	Gtg/Atg	4/5	1	2	FACETS	0.765	0.703	0.828	0.765	0.703	0.828	SUBCLONAL	1	TRUE	1	0.426718956418328	2		677	1079	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350074	89350074	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs755666999	NA	P-0026396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	82	682	0	ENST00000301030.4:c.2876A>G	p.Lys959Arg	p.K959R	ENST00000301030	NM_001256183.1	959	aAg/aGg	9/13	1	2	FACETS	0.344	0.302	0.389	0.344	0.302	0.389	SUBCLONAL	1	TRUE	1	0.426718956418328	2		682	1117	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075149	16075149	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	95	388	0	ENST00000268712.3:c.403G>T	p.Glu135Ter	p.E135*	ENST00000268712	NM_006311.3	135	Gaa/Taa	4/46	0.139136913646687	5	FACETS	1	0.908	1			1	INDETERMINATE	1	TRUE	NA	0.426718956418328	5		388	715	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257983	19257983	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1576	279	774	0	ENST00000162023.5:c.403C>T	p.Pro135Ser	p.P135S	ENST00000162023		135	Cct/Tct	9/13	0.25349196773182	6	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.426718956418328	6		774	1855	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47643551	47643551	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	134	555	0	ENST00000233146.2:c.1059G>C	p.Lys353Asn	p.K353N	ENST00000233146	NM_000251.2	353	aaG/aaC	6/16	1	2	FACETS	0.932	0.848	1	0.932	0.848	1	CLONAL	1	TRUE	1	0.426718956418328	2		555	674	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37628020	37628020	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	198	637	0	ENST00000249071.6:c.240C>G	p.Ile80Met	p.I80M	ENST00000249071	NM_002872.4	80	atC/atG	4/7	1	2	FACETS	0.911	0.843	0.981	0.911	0.843	0.981	CLONAL	1	TRUE	1	0.426718956418328	2		637	1019	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099283	157099283	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554247230	NA	P-0026396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	132	428	0	ENST00000346085.5:c.220G>T	p.Glu74Ter	p.E74*	ENST00000346085	NM_020732.3	74	Gaa/Taa	1/20	1	2	FACETS	0.933	0.849	1	0.933	0.849	1	CLONAL	1	TRUE	1	0.426718956418328	2		428	663	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040962	47040962	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782623757	NA	P-0026396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	62	636	2	ENST00000377604.3:c.1492C>T	p.Arg498Cys	p.R498C	ENST00000377604	NM_001204468.1	498	Cgc/Tgc	14/24	1	2	FACETS	0.254	0.219	0.294	0.254	0.219	0.294	SUBCLONAL	1	TRUE	1	0.426718956418328	2		638	1142	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0026397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	36	273	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.48	0.392	0.578	0.48	0.392	0.578	SUBCLONAL	1	TRUE	1	0.15	2		273	1001	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	40	501	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.603	0.499	0.719	0.603	0.499	0.719	SUBCLONAL	1	TRUE	1	0.15	2		501	885	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717769	89717770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	55	449	2	ENST00000371953.3:c.800dup	p.Asp268GlyfsTer30	p.D268Gfs*30	ENST00000371953	NM_000314.4	265	cta/ctAa	7/9	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.15	2		451	722	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023310	27023365	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCGGCCGCCTTGCCGCCCCCAGCCTACGGCTTCGGGCAACCCTACGGCCGGAGC	CCGCGGCCGCCTTGCCGCCCCCAGCCTACGGCTTCGGGCAACCCTACGGCCGGAGC	-	novel	NA	P-0026397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	22	303	1	ENST00000324856.7:c.419_474del	p.Ala140ValfsTer241	p.A140Vfs*241	ENST00000324856	NM_006015.4	139	gCCGCGGCCGCCTTGCCGCCCCCAGCCTACGGCTTCGGGCAACCCTACGGCCGGAGC/g	1/20	1	2	FACETS	0.762	0.59	0.962	0.762	0.59	0.962	CLONAL	1	TRUE	1	0.15	2		304	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0026398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	268	652	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.371893239542338	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	0	0.371893239542338	1		653	877	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563192	21563192	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	118	793	0	ENST00000382592.4:c.727G>C	p.Gly243Arg	p.G243R	ENST00000382592	NM_014572.2	243	Ggg/Cgg	4/8	0.222797070057866	1	FACETS	0.671	0.605	0.74	0.671	0.605	0.74	INDETERMINATE	1	FALSE	0	0.371893239542338	1		793	770	SUCCESS
APC	324	MSKCC	GRCh37	5	112175057	112175057	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs77056664	NA	P-0026398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	113	303	0	ENST00000257430.4:c.3766C>T	p.Gln1256Ter	p.Q1256*	ENST00000257430	NM_000038.5	1256	Caa/Taa	16/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.371893239542338	2		303	507	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975444	13975444	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	258	511	0	ENST00000405192.2:c.443T>C	p.Leu148Pro	p.L148P	ENST00000405192	NM_001163147.1	148	cTg/cCg	7/12	0.227723443979497	3	FACETS	0.996	0.936	1	0.996	0.936	1	CLONAL	2	FALSE	1	0.371893239542338	3		511	826	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729609	41729609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	288	613	1	ENST00000242208.4:c.920G>A	p.Arg307Gln	p.R307Q	ENST00000242208	NM_002192.2	307	cGg/cAg	3/3	0.227723443979497	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	FALSE	1	0.371893239542338	3		614	882	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	162	775	0	ENST00000347630.2:c.397T>C	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	Ttc/Ctc	6/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.317037108770027	2		775	969	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821485	32821485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757941717	NA	P-0026399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	97	762	1	ENST00000354258.4:c.109C>T	p.Arg37Trp	p.R37W	ENST00000354258	NM_000593.5	37	Cgg/Tgg	1/11	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.317037108770027	2		763	591	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950724	79950725	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCGCAGCGC	rs1554066076	NA	P-0026400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	23	256	7	ENST00000265081.6:c.181_189dup	p.Ala61_Pro63dup	p.A61_P63dup	ENST00000265081	NM_002439.4	61	gcc/gCCGCAGCGCcc	1/24	0.908657841595506	2	FACETS	0.335	0.264	0.416	0.168	0.132	0.208	SUBCLONAL	1	FALSE	0	0.908657841595506	2		263	151	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933156	39933159	+	frameshift_variant	Frame_Shift_Del	DEL	CTCA	CTCA	-	novel	NA	P-0026400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	506	671	0	ENST00000378444.4:c.1440_1443del	p.Ser480ArgfsTer47	p.S480Rfs*47	ENST00000378444	NM_001123385.1	480	agTGAG/ag	4/15	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	FALSE	NA	0.908657841595506	2		671	1088	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752989	128752989	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	121	549	0	ENST00000377970.2:c.1150G>C	p.Glu384Gln	p.E384Q	ENST00000377970	NM_002467.4	384	Gag/Cag	3/3	1	2	FACETS	0.461	0.415	0.509	0.461	0.415	0.509	SUBCLONAL	1	TRUE	1	0.447741703185982	2		549	1173	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0026405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	40	322	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.7	0.58	0.835	0.7	0.58	0.835	SUBCLONAL	1	TRUE	1	0.14	2		322	816	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0026405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	61	537	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.14	2		537	843	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980527	1980527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760185069	NA	P-0026405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	49	698	0	ENST00000382891.5:c.3989C>T	p.Ala1330Val	p.A1330V	ENST00000382891	NM_133335.3	1330	gCg/gTg	22/22	1	2	FACETS	0.838	0.708	0.983	0.838	0.708	0.983	CLONAL	1	TRUE	1	0.14	2		698	835	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	TGCGT	novel	NA	P-0026407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	289	677	0	ENST00000269305.4:c.848delinsACGCA	p.Arg283HisfsTer24	p.R283Hfs*24	ENST00000269305	NM_001126112.2	283	cGc/cACGCAc	8/11	0.580801628040849	1	FACETS	0.986	0.933	1	0.986	0.933	1	CLONAL	1	TRUE	0	0.580801628040849	1		677	716	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0026409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	300	454	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.77	2		454	769	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952117	178952117	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	318	522	0	ENST00000263967.3:c.3172A>C	p.Ile1058Leu	p.I1058L	ENST00000263967	NM_006218.2	1058	Atc/Ctc	21/21	1	2	FACETS	0.975	0.924	1	0.975	0.924	1	CLONAL	1	TRUE	1	0.77	2		522	847	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0026409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	143	339	4	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.761	0.699	0.826	0.761	0.699	0.826	SUBCLONAL	1	TRUE	1	0.77	2		343	488	SUCCESS
AR	367	MSKCC	GRCh37	X	66943543	66943543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852581	NA	P-0026409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	310	275	0	ENST00000374690.3:c.2623C>T	p.His875Tyr	p.H875Y	ENST00000374690	NM_000044.3	875	Cat/Tat	8/8	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.77	1		275	427	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717661	89717675	+	inframe_deletion	In_Frame_Del	DEL	CAGGACCCACACGAC	CAGGACCCACACGAC	-	novel	NA	P-0026409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	242	754	0	ENST00000371953.3:c.686_700del	p.Ser229_Arg234delinsTrp	p.S229_R234delinsW	ENST00000371953	NM_000314.4	229	tCAGGACCCACACGACgg/tgg	7/9	0.748141039530906	1	FACETS	0.784	0.741	0.827	0.784	0.741	0.827	SUBCLONAL	1	TRUE	0	0.77	1		754	493	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508499	106508499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752602335	NA	P-0026410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	31	230	0	ENST00000359195.3:c.493G>A	p.Val165Ile	p.V165I	ENST00000359195	NM_002649.2	165	Gtc/Atc	2/11	0.220532022222086	3	FACETS	0.811	0.656	0.986	0.405	0.328	0.493	CLONAL	1	TRUE	1	0.220532022222086	3		230	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579321	7579322	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs587780067	NA	P-0026410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	225	535	0	ENST00000269305.4:c.365_366del	p.Val122AspfsTer26	p.V122Dfs*26	ENST00000269305	NM_001126112.2	122	gTG/g	4/11	0.220532022222086	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.220532022222086	3		535	997	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86637111	86637111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759265277	NA	P-0026410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	67	405	0	ENST00000274376.6:c.1022G>A	p.Arg341Gln	p.R341Q	ENST00000274376	NM_002890.2	341	cGg/cAg	6/25	0.208674436660006	2	FACETS	0.942	0.818	1	0.471	0.409	0.538	CLONAL	1	TRUE	0	0.220532022222086	2		405	645	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292740	91292740	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1292	117	672	0	ENST00000355112.3:c.242C>A	p.Thr81Lys	p.T81K	ENST00000355112	NM_000057.2	81	aCa/aAa	3/22	0.148646623841003	4	FACETS	0.919	0.826	1	0.46	0.413	0.509	CLONAL	1	TRUE	2	0.220532022222086	4		672	1409	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858369	9858369	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1163766811	NA	P-0026410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	67	496	0	ENST00000330684.3:c.3032G>A	p.Arg1011Gln	p.R1011Q	ENST00000330684	NM_001134407.1	1011	cGg/cAg	13/13	0.220532022222086	3	FACETS	0.88	0.763	1	0.44	0.381	0.503	CLONAL	1	TRUE	1	0.220532022222086	3		496	767	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735532	40735532	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	99	621	0	ENST00000373198.4:c.3341T>G	p.Ile1114Ser	p.I1114S	ENST00000373198	NM_133170.3	1114	aTt/aGt	25/32	0.148646623841003	4	FACETS	0.989	0.881	1	0.495	0.44	0.553	CLONAL	1	TRUE	2	0.220532022222086	4		621	1108	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55229273	55229273	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150477666	NA	P-0026410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1218	113	690	0	ENST00000275493.2:c.1580G>A	p.Arg527Gln	p.R527Q	ENST00000275493	NM_005228.3	527	cGg/cAg	13/28	0.220532022222086	5	FACETS	1	0.916	1	0.342	0.306	0.379	CLONAL	1	TRUE	2	0.220532022222086	5		690	1331	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874011	123874013	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs780061449	NA	P-0026421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	16	44	0	ENST00000330479.4:c.62_64del	p.Ala21del	p.A21del	ENST00000330479	NM_020382.3	14	gaGGCg/gag	2/9	0.478941880112182	4	FACETS	0.361	0.267	0.473	0.18	0.133	0.237	SUBCLONAL	1	TRUE	2	0.55309515525419	4		44	249	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577569	7577569	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519981	NA	P-0026421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	485	636	0	ENST00000269305.4:c.712T>C	p.Cys238Arg	p.C238R	ENST00000269305	NM_001126112.2	238	Tgt/Cgt	7/11	0.55309515525419	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.55309515525419	2		636	784	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217380	123217380	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	220	521	0	ENST00000218089.9:c.3034C>T	p.Arg1012Ter	p.R1012*	ENST00000218089	NM_001042749.1	1012	Cga/Tga	29/35	0.55309515525419	2	FACETS	1	0.963	1	0.523	0.488	0.559	CLONAL	1	TRUE	0	0.55309515525419	2		521	760	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726698	88726698	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375475747	NA	P-0026421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	315	478	2	ENST00000360948.2:c.346C>T	p.Arg116Trp	p.R116W	ENST00000360948	NM_001012338.2	116	Cgg/Tgg	4/19	0.54150626435224	3	FACETS	0.782	0.739	0.825	0.782	0.739	0.825	SUBCLONAL	2	TRUE	1	0.55309515525419	3		480	930	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972621	76972621	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	85	561	0	ENST00000373344.5:c.120G>A	p.Met40Ile	p.M40I	ENST00000373344	NM_000489.3	40	atG/atA	2/35	0.55309515525419	2	FACETS	0.375	0.331	0.423	0.188	0.165	0.212	SUBCLONAL	1	TRUE	0	0.55309515525419	2		561	819	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993398	72993398	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200201291	NA	P-0026421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	257	726	0	ENST00000268489.5:c.647C>T	p.Pro216Leu	p.P216L	ENST00000268489	NM_006885.3	216	cCg/cTg	2/10	0.55309515525419	3	FACETS	1	0.937	1	0.501	0.468	0.534	CLONAL	1	TRUE	1	0.55309515525419	3		726	1185	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981854	101981854	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	313	745	0	ENST00000282441.5:c.275C>T	p.Pro92Leu	p.P92L	ENST00000282441	NM_001130145.2	92	cCc/cTc	1/9	NA	2	FACETS	0.904	0.852	0.957			1	INDETERMINATE	1	TRUE	NA	0.55309515525419	2		745	1252	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95596500	95596500	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	308	366	1	ENST00000393063.1:c.468G>T	p.Leu156Phe	p.L156F	ENST00000393063	NM_030621.3	156	ttG/ttT	6/28	0.468572076032094	4	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.55309515525419	4		367	708	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778369	3778369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	102	490	0	ENST00000262367.5:c.6679G>A	p.Gly2227Arg	p.G2227R	ENST00000262367	NM_004380.2	2227	Ggg/Agg	31/31	0.3797839687385	4	FACETS	0.684	0.611	0.761	0.342	0.305	0.381	SUBCLONAL	1	TRUE	2	0.55309515525419	4		490	838	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216602	7216602	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	367	479	0	ENST00000380728.2:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000380728		245	Cag/Tag	9/11	0.55309515525419	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.55309515525419	2		479	584	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144180	11144180	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	78	653	0	ENST00000358026.2:c.3761A>C	p.Glu1254Ala	p.E1254A	ENST00000358026	NM_001128849.1	1254	gAg/gCg	26/36	0.24233745469731	5	FACETS	0.465	0.407	0.528	0.155	0.135	0.176	INDETERMINATE	1	TRUE	2	0.55309515525419	5		653	1110	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250090	39250090	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	238	623	0	ENST00000402219.2:c.1479G>T	p.Lys493Asn	p.K493N	ENST00000402219	NM_005633.3	493	aaG/aaT	10/23	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.55309515525419	2		623	808	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674266	117674266	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	155	656	0	ENST00000368508.3:c.4208A>G	p.Asp1403Gly	p.D1403G	ENST00000368508	NM_002944.2	1403	gAc/gGc	26/43	0.478941880112182	4	FACETS	0.683	0.623	0.745	0.341	0.311	0.373	SUBCLONAL	1	TRUE	2	0.55309515525419	4		656	1275	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917702	151917702	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	49	246	0	ENST00000262189.6:c.3618G>C	p.Leu1206Phe	p.L1206F	ENST00000262189	NM_170606.2	1206	ttG/ttC	23/59	0.455087592674872	1	FACETS	0.613	0.526	0.707	0.613	0.526	0.707	SUBCLONAL	1	TRUE	0	0.55309515525419	1		246	209	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128419946	128419946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1432	84	623	0	ENST00000265960.3:c.482C>A	p.Ser161Tyr	p.S161Y	ENST00000265960	NM_001006617.1	161	tCc/tAc	4/12	0.55309515525419	4	FACETS	0.311	0.273	0.352	0.156	0.136	0.176	SUBCLONAL	1	TRUE	2	0.55309515525419	4		623	1516	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0026422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	86	295	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	1	2	FACETS	0.849	0.756	0.948	0.849	0.756	0.948	CLONAL	1	TRUE	1	0.505148213104345	2		295	401	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1555525585	NA	P-0026422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	127	463	0	ENST00000269305.4:c.673-2A>G		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.505148213104345	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.505148213104345	1		463	355	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243944	5243944	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	109	549	1	ENST00000357368.4:c.1538C>T	p.Ser513Leu	p.S513L	ENST00000357368	NM_002850.3	513	tCg/tTg	11/38	1	2	FACETS	0.914	0.826	1	0.914	0.826	1	CLONAL	1	TRUE	1	0.505148213104345	2		550	472	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306574	41306575	+	missense_variant	Missense_Mutation	DNP	AG	AG	CA	novel	NA	P-0026422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	151	646	2	ENST00000373198.4:c.1084_1085delinsTG	p.Leu362Cys	p.L362C	ENST00000373198	NM_133170.3	362	CTc/TGc	7/32	0.33200475985646	5	FACETS	1	0.914	1	0.334	0.304	0.364	CLONAL	1	TRUE	2	0.505148213104345	5		648	1050	SUCCESS
APC	324	MSKCC	GRCh37	5	112170727	112170728	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTA	novel	NA	P-0026422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	86	573	0	ENST00000257430.4:c.1824_1827dup	p.Asp610CysfsTer25	p.D610Cfs*25	ENST00000257430	NM_000038.5	608	gct/gcTGTAt	15/16	1	2	FACETS	0.709	0.63	0.794	0.709	0.63	0.794	SUBCLONAL	1	TRUE	1	0.505148213104345	2		573	480	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420606	49420606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886041404	NA	P-0026423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	307	629	0	ENST00000301067.7:c.15143G>A	p.Arg5048His	p.R5048H	ENST00000301067	NM_003482.3	5048	cGt/cAt	48/54	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.563387736164162	2		629	1074	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251635	212251635	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1211840752	NA	P-0026424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	115	455	2	ENST00000342788.4:c.3424C>T	p.Arg1142Ter	p.R1142*	ENST00000342788	NM_005235.2	1142	Cga/Tga	27/28	0.296763376819932	3	FACETS	0.915	0.825	1	0.458	0.412	0.506	CLONAL	1	TRUE	1	0.401222351353909	3		457	752	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380183	25380183	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	165	444	0	ENST00000311936.3:c.275A>T	p.Asp92Val	p.D92V	ENST00000311936	NM_004985.3	92	gAt/gTt	3/5	0.401222351353909	6	FACETS	0.802	0.737	0.871	0.401	0.368	0.436	CLONAL	2	TRUE	2	0.401222351353909	6		444	924	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0026425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	469	571	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.674135868206651	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.674135868206651	1		572	899	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238356	98238356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	61	559	0	ENST00000331920.6:c.1688C>T	p.Ala563Val	p.A563V	ENST00000331920	NM_000264.3	563	gCg/gTg	12/24	0.331284216615668	2	FACETS	0.235	0.202	0.271	0.118	0.101	0.136	INDETERMINATE	1	TRUE	0	0.674135868206651	2		559	769	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738292	190738293	+	missense_variant	Missense_Mutation	DNP	AG	AG	TT	novel	NA	P-0026425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	62	473	0	ENST00000441310.2:c.2544_2545delinsTT	p.Asp849Tyr	p.D849Y	ENST00000441310	NM_000534.4	848	gcAGat/gcTTat	12/13	0.389245333382436	3	FACETS	0.303	0.261	0.349	0.101	0.087	0.117	INDETERMINATE	1	TRUE	0	0.674135868206651	3		473	811	SUCCESS
APC	324	MSKCC	GRCh37	5	112174891	112174891	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	265	397	0	ENST00000257430.4:c.3601del	p.Ser1201HisfsTer64	p.S1201Hfs*64	ENST00000257430	NM_000038.5	1200	agT/ag	16/16	0.561619581627855	2	FACETS	0.912	0.87	0.953	0.912	0.87	0.953	CLONAL	2	TRUE	0	0.674135868206651	2		397	431	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771151	161771151	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	149	743	0	ENST00000366898.1:c.1378G>T	p.Asp460Tyr	p.D460Y	ENST00000366898	NM_004562.2	460	Gac/Tac	12/12	0.605263994672988	3	FACETS	0.523	0.477	0.572	0.262	0.238	0.286	SUBCLONAL	1	TRUE	1	0.674135868206651	3		743	1130	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106519968	106519968	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	89	291	0	ENST00000359195.3:c.2400del	p.Lys800AsnfsTer4	p.K800Nfs*4	ENST00000359195	NM_002649.2	799	gAa/ga	6/11	0.605263994672988	3	FACETS	0.829	0.739	0.924	0.414	0.369	0.462	CLONAL	1	TRUE	1	0.674135868206651	3		291	426	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0026426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	18	509	1	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.239063405665991	1	FACETS	0.164	0.122	0.213	0.164	0.122	0.213	SUBCLONAL	1	TRUE	0	0.239063405665991	1		510	810	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0026426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	193	649	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.239063405665991	2		649	1194	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733140	74733140	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	45	699	2	ENST00000359995.5:c.103G>C	p.Glu35Gln	p.E35Q	ENST00000359995	NM_001195427.1	35	Gag/Cag	1/3	0.239063405665991	3	FACETS	0.513	0.43	0.606	0.257	0.215	0.303	SUBCLONAL	1	TRUE	1	0.239063405665991	3		701	821	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872029	37872029	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	55	810	0	ENST00000269571.5:c.1350C>G	p.Ile450Met	p.I450M	ENST00000269571		450	atC/atG	12/27	0.239063405665991	3	FACETS	0.481	0.41	0.559	0.24	0.205	0.28	SUBCLONAL	1	TRUE	1	0.239063405665991	3		810	1071	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188868	32188868	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	52	663	0	ENST00000375023.3:c.686C>T	p.Pro229Leu	p.P229L	ENST00000375023	NM_004557.3	229	cCa/cTa	4/30	0.198919435933108	2	FACETS	0.56	0.475	0.653	0.28	0.237	0.327	SUBCLONAL	1	TRUE	0	0.239063405665991	2		663	777	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0026427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	788	340	1	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	2	TRUE	NA	0.704718431474511	2		341	1118	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954189	48954191	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0026427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	88	339	0	ENST00000267163.4:c.1396_1398del	p.Glu466del	p.E466del	ENST00000267163	NM_000321.2	464	GAA/-	15/27	0.707898186804214	1	FACETS	0.644	0.58	0.711	0.644	0.58	0.711	SUBCLONAL	1	TRUE	0	0.704718431474511	1		339	251	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619281	37619281	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0026427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	1945	527	0	ENST00000447079.4:c.957C>G	p.Tyr319Ter	p.Y319*	ENST00000447079	NM_015083.1	319	taC/taG	1/14	0.704718431474511	6	FACETS	1	0.997	1			1	CLONAL	6	TRUE	NA	0.704718431474511	6		527	2173	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220469	133220469	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	438	691	0	ENST00000320574.5:c.4244A>C	p.Asn1415Thr	p.N1415T	ENST00000320574	NM_006231.2	1415	aAc/aCc	33/49	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.704718431474511	2		691	1189	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664723	138664723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762185841	NA	P-0026427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1322	163	350	1	ENST00000330315.3:c.842C>T	p.Pro281Leu	p.P281L	ENST00000330315	NM_023067.3	281	cCg/cTg	1/1	0.704718431474511	8	FACETS	0.97	0.887	1			1	CLONAL	1	TRUE	NA	0.704718431474511	8		351	1485	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430815	78430815	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	297	651	0	ENST00000370768.2:c.574A>C	p.Ile192Leu	p.I192L	ENST00000370768	NM_003902.3	192	Att/Ctt	8/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.594729288252909	2		651	982	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430823	78430823	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	300	655	0	ENST00000370768.2:c.566A>C	p.Glu189Ala	p.E189A	ENST00000370768	NM_003902.3	189	gAa/gCa	8/20	1	2	FACETS	0.998	0.941	1	0.998	0.941	1	CLONAL	1	TRUE	1	0.594729288252909	2		655	1011	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981549	201981549	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	729	853	1	ENST00000359651.3:c.463G>A	p.Asp155Asn	p.D155N	ENST00000359651		155	Gac/Aac	3/8	0.594729288252909	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.594729288252909	3		854	1564	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934264	48934264	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0026428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	203	519	0	ENST00000267163.4:c.718+1G>A		p.X240_splice	ENST00000267163	NM_000321.2	240			0.592616627800108	1	FACETS	0.967	0.906	1	0.967	0.906	1	CLONAL	1	TRUE	0	0.594729288252909	1		519	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0026428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	424	826	0	ENST00000269305.4:c.376-1G>C		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.592616627800108	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.594729288252909	1		826	951	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796498	42796530	+	inframe_deletion	In_Frame_Del	DEL	ACCAGCCCTGCGTCCAGCCAGGCTGGAACAGTC	ACCAGCCCTGCGTCCAGCCAGGCTGGAACAGTC	-	novel	NA	P-0026428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	352	820	2	ENST00000575354.2:c.3058_3090del	p.Pro1021_Ser1031del	p.P1021_S1031del	ENST00000575354	NM_015125.3	1019	ACCAGCCCTGCGTCCAGCCAGGCTGGAACAGTC/-	13/20	0.594729288252909	1	FACETS	0.983	0.936	1	0.983	0.936	1	CLONAL	1	TRUE	0	0.594729288252909	1		822	846	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662662	227662662	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1412312472	NA	P-0026428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	259	633	1	ENST00000305123.5:c.793C>T	p.Arg265Cys	p.R265C	ENST00000305123	NM_005544.2	265	Cgc/Tgc	1/2	1	2	FACETS	0.956	0.897	1	0.956	0.897	1	CLONAL	1	TRUE	1	0.594729288252909	2		634	911	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928069	178928083	+	inframe_deletion	In_Frame_Del	DEL	TCATGGATTAGAAGA	TCATGGATTAGAAGA	-	novel	NA	P-0026428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	403	628	0	ENST00000263967.3:c.1348_1362del	p.His450_Asp454del	p.H450_D454del	ENST00000263967	NM_006218.2	449	ccTCATGGATTAGAAGAt/cct	8/21	0.594729288252909	2	FACETS	0.782	0.748	0.817	0.782	0.748	0.817	SUBCLONAL	2	TRUE	0	0.594729288252909	2		628	866	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444317	50444317	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	409	256	1	ENST00000331340.3:c.247C>T	p.Arg83Ter	p.R83*	ENST00000331340	NM_006060.4	83	Cga/Tga	4/8	0.594729288252909	3	FACETS	0.99	0.947	1			1	CLONAL	2	TRUE	NA	0.594729288252909	3		257	901	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0026430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	443	610	2	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.688169693916339	2	FACETS	0.979	0.947	1	0.979	0.947	1	CLONAL	2	TRUE	0	0.690825791220017	2		612	655	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974695	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691187	NA	P-0026430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	373	434	0	ENST00000304494.5:c.132del	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	taC/ta	1/3	0.688169693916339	2	FACETS	0.959	0.924	0.993	0.959	0.924	0.993	CLONAL	2	TRUE	0	0.690825791220017	2		434	563	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260876	16260876	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780166942	NA	P-0026430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	159	491	0	ENST00000375759.3:c.8141C>T	p.Thr2714Met	p.T2714M	ENST00000375759	NM_015001.2	2714	aCg/aTg	11/15	0.287742000567926	5	FACETS	1	0.986	1	0.446	0.41	0.484	INDETERMINATE	1	TRUE	2	0.690825791220017	5		491	700	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641544	23641544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs875989794	NA	P-0026430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	529	620	0	ENST00000261584.4:c.1931G>A	p.Gly644Glu	p.G644E	ENST00000261584	NM_024675.3	644	gGa/gAa	5/13	0.690825791220017	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.690825791220017	3		620	1030	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49399952	49399952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	243	617	0	ENST00000418115.1:c.385C>T	p.Arg129Trp	p.R129W	ENST00000418115	NM_001664.2	129	Cgg/Tgg	4/5	0.688402369091527	2	FACETS	0.921	0.864	0.979	0.46	0.432	0.49	CLONAL	1	TRUE	0	0.690825791220017	2		617	764	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0026431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	564	720	0	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	0.850039218381831	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.850039218381831	1		720	760	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325171	39325171	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1041991009	NA	P-0026431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	345	666	0	ENST00000373001.3:c.148G>T	p.Gly50Cys	p.G50C	ENST00000373001	NM_022157.3	50	Ggt/Tgt	1/7	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.850039218381831	2		666	738	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937081	48937081	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0026431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	378	329	1	ENST00000267163.4:c.849T>A	p.Cys283Ter	p.C283*	ENST00000267163	NM_000321.2	283	tgT/tgA	8/27	0.850039218381831	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.850039218381831	1		330	470	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796554	42796554	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	395	703	0	ENST00000575354.2:c.3111del	p.Val1038Ter	p.V1038*	ENST00000575354	NM_015125.3	1037	tcT/tc	13/20	0.850039218381831	3	FACETS	0.902	0.856	0.949	0.451	0.428	0.475	CLONAL	1	TRUE	1	0.850039218381831	3		703	1468	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0026436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	12	347	0				ENST00000310581	NM_198253.2	-/1132			0.268945656364372	0	FACETS	0.725	0.541	0.92			1	CLONAL	3	FALSE	0	0.268945656364372	0		347	30	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917496	178917496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	35	436	0	ENST00000263967.3:c.371C>T	p.Pro124Leu	p.P124L	ENST00000263967	NM_006218.2	124	cCa/cTa	3/21	0.119295965724027	3	FACETS	1	0.905	1	1	0.905	1	INDETERMINATE	2	FALSE	1	0.268945656364372	3		436	131	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591032	67591042	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGAAGATTG	GAAGAAGATTG	-	novel	NA	P-0026436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	25	407	0	ENST00000274335.5:c.1633_1643del	p.Asp548AlafsTer4	p.D548Afs*4	ENST00000274335		542	aGAAGAAGATTG/a	12/15	0.141605642403881	4	FACETS	1	0.845	1			1	INDETERMINATE	2	FALSE	NA	0.268945656364372	4		407	111	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626683	100626683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	33	613	0	ENST00000308731.7:c.247G>A	p.Gly83Ser	p.G83S	ENST00000308731	NM_000061.2	83	Ggt/Agt	4/19	0.262832112345187	0	FACETS	0.997	0.838	1			1	CLONAL	2	FALSE	0	0.268945656364372	0		613	90	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	99	505	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.237	0.211	0.266	0.237	0.211	0.266	SUBCLONAL	1	TRUE	1	0.714624809483678	2		505	1167	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	30	652	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.071	0.057	0.088	0.071	0.057	0.088	SUBCLONAL	1	TRUE	1	0.714624809483678	2		653	1175	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860053	57860053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200444628	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	404	877	4	ENST00000228682.2:c.793C>T	p.Arg265Trp	p.R265W	ENST00000228682	NM_005269.2	265	Cgg/Tgg	8/12	1	2	FACETS	0.874	0.832	0.918	0.874	0.832	0.918	CLONAL	1	TRUE	1	0.714624809483678	2		881	1293	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	222	435	0	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	1	2	FACETS	0.618	0.575	0.662	0.618	0.575	0.662	SUBCLONAL	1	TRUE	1	0.714624809483678	2		435	1006	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	56	440	2	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.173	0.147	0.201	0.173	0.147	0.201	SUBCLONAL	1	TRUE	1	0.714624809483678	2		442	908	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165653	118165653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763834209	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	65	478	0	ENST00000369448.3:c.163G>A	p.Val55Ile	p.V55I	ENST00000369448	NM_017709.3	55	Gtc/Atc	2/2	1	2	FACETS	0.246	0.213	0.282	0.246	0.213	0.282	SUBCLONAL	1	TRUE	1	0.714624809483678	2		478	739	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791320	42791320	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754556504	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	97	768	3	ENST00000575354.2:c.380C>T	p.Thr127Met	p.T127M	ENST00000575354	NM_015125.3	127	aCg/aTg	3/20	1	2	FACETS	0.247	0.219	0.276	0.247	0.219	0.276	SUBCLONAL	1	TRUE	1	0.714624809483678	2		771	1101	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	95	475	2	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.353	0.314	0.394	0.353	0.314	0.394	SUBCLONAL	1	TRUE	1	0.714624809483678	2		477	754	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119796	17119796	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148257120	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	71	708	0	ENST00000285071.4:c.1198G>A	p.Val400Ile	p.V400I	ENST00000285071	NM_144997.5	400	Gtc/Atc	11/14	1	2	FACETS	0.173	0.15	0.198	0.173	0.15	0.198	SUBCLONAL	1	TRUE	1	0.714624809483678	2		708	1147	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874316	76874316	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	244	730	0	ENST00000373344.5:c.5406del	p.Lys1802AsnfsTer10	p.K1802Nfs*10	ENST00000373344	NM_000489.3	1802	aaA/aa	21/35	1	2	FACETS	0.752	0.704	0.802	0.752	0.704	0.802	SUBCLONAL	1	TRUE	1	0.714624809483678	2		730	908	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1223	94	883	0	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.2	0.177	0.224	0.2	0.177	0.224	SUBCLONAL	1	TRUE	1	0.714624809483678	2		883	1317	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264348	46264348	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	80	505	1	ENST00000371998.3:c.1400del	p.Pro467HisfsTer15	p.P467Hfs*15	ENST00000371998		465	agC/ag	11/23	1	2	FACETS	0.268	0.235	0.303	0.268	0.235	0.303	SUBCLONAL	1	TRUE	1	0.714624809483678	2		506	835	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941430	71941430	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755089930	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	98	764	1	ENST00000298229.2:c.1115G>A	p.Arg372His	p.R372H	ENST00000298229	NM_001567.3	372	cGt/cAt	10/28	1	2	FACETS	0.218	0.194	0.245	0.218	0.194	0.245	SUBCLONAL	1	TRUE	1	0.714624809483678	2		765	1256	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514781	44514781	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	79	570	0	ENST00000291552.4:c.466C>T	p.Arg156Cys	p.R156C	ENST00000291552	NM_006758.2	156	Cgt/Tgt	6/8	1	2	FACETS	0.234	0.205	0.265	0.234	0.205	0.265	SUBCLONAL	1	TRUE	1	0.714624809483678	2		570	946	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	111	857	3	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.249	0.223	0.277	0.249	0.223	0.277	SUBCLONAL	1	TRUE	1	0.714624809483678	2		860	1249	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224124	36224124	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	91	652	0	ENST00000222270.7:c.6678del	p.Thr2227ArgfsTer34	p.T2227Rfs*34	ENST00000222270	NM_014727.1	2225	tCc/tc	28/37	1	2	FACETS	0.26	0.23	0.293	0.26	0.23	0.293	SUBCLONAL	1	TRUE	1	0.714624809483678	2		652	978	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435199	49435199	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	218	451	1	ENST00000301067.7:c.6354del	p.Ala2119LeufsTer25	p.A2119Lfs*25	ENST00000301067	NM_003482.3	2118	ccC/cc	31/54	1	2	FACETS	0.883	0.825	0.942	0.883	0.825	0.942	CLONAL	1	TRUE	1	0.714624809483678	2		452	691	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059207	27059207	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	104	606	0	ENST00000324856.7:c.1848del	p.Ser617GlnfsTer2	p.S617Qfs*2	ENST00000324856	NM_006015.4	615	gCc/gc	4/20	1	2	FACETS	0.313	0.28	0.349	0.313	0.28	0.349	SUBCLONAL	1	TRUE	1	0.714624809483678	2		606	929	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906394	50906394	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556862476	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	325	774	1	ENST00000440232.2:c.1055G>A	p.Arg352His	p.R352H	ENST00000440232	NM_002691.3	352	cGc/cAc	9/27	1	2	FACETS	0.859	0.812	0.907	0.859	0.812	0.907	CLONAL	1	TRUE	1	0.714624809483678	2		775	1059	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210893	36210893	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	84	696	2	ENST00000222270.7:c.649del	p.Arg217GlyfsTer22	p.R217Gfs*22	ENST00000222270	NM_014727.1	215	aCc/ac	3/37	1	2	FACETS	0.214	0.188	0.242	0.214	0.188	0.242	SUBCLONAL	1	TRUE	1	0.714624809483678	2		698	1098	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741528	17741528	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	61	455	0	ENST00000250003.3:c.199G>A	p.Ala67Thr	p.A67T	ENST00000250003	NM_002478.4	67	Gcg/Acg	1/3	1	2	FACETS	0.227	0.195	0.261	0.227	0.195	0.261	SUBCLONAL	1	TRUE	1	0.714624809483678	2		455	753	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419118	419118	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	33	355	0	ENST00000399788.2:c.3229del	p.Arg1077GlyfsTer17	p.R1077Gfs*17	ENST00000399788	NM_001042603.1	1077	Cgg/gg	22/28	1	2	FACETS	0.157	0.127	0.191	0.157	0.127	0.191	SUBCLONAL	1	TRUE	1	0.714624809483678	2		355	587	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066817	30066817	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	48	675	0	ENST00000331968.5:c.2314A>G	p.Ile772Val	p.I772V	ENST00000331968	NM_002742.2	772	Atc/Gtc	16/18	1	2	FACETS	0.145	0.122	0.171	0.145	0.122	0.171	SUBCLONAL	1	TRUE	1	0.714624809483678	2		675	925	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061594	38061594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	67	182	0	ENST00000250448.2:c.395C>T	p.Ala132Val	p.A132V	ENST00000250448	NM_004496.3	132	gCc/gTc	2/2	1	2	FACETS	0.539	0.471	0.611	0.539	0.471	0.611	SUBCLONAL	1	TRUE	1	0.714624809483678	2		182	348	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274043	10274043	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1236030143	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	134	813	3	ENST00000330684.3:c.226C>T	p.Arg76Cys	p.R76C	ENST00000330684	NM_001134407.1	76	Cgc/Tgc	2/13	1	2	FACETS	0.306	0.277	0.337	0.306	0.277	0.337	SUBCLONAL	1	TRUE	1	0.714624809483678	2		816	1225	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614793	23614793	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	69	513	1	ENST00000261584.4:c.3548A>G	p.Tyr1183Cys	p.Y1183C	ENST00000261584	NM_024675.3	1183	tAc/tGc	13/13	1	2	FACETS	0.23	0.199	0.263	0.23	0.199	0.263	SUBCLONAL	1	TRUE	1	0.714624809483678	2		514	840	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937701	17937701	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	67	518	0	ENST00000458235.1:c.3226C>A	p.Leu1076Met	p.L1076M	ENST00000458235	NM_000215.3	1076	Ctg/Atg	24/24	1	2	FACETS	0.204	0.177	0.235	0.204	0.177	0.235	SUBCLONAL	1	TRUE	1	0.714624809483678	2		518	917	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792348	33792348	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781549846	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	63	762	2	ENST00000498907.2:c.973C>T	p.Arg325Cys	p.R325C	ENST00000498907	NM_004364.3	325	Cgc/Tgc	1/1	1	2	FACETS	0.164	0.141	0.189	0.164	0.141	0.189	SUBCLONAL	1	TRUE	1	0.714624809483678	2		764	1076	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905736	50905736	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571623032	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	119	808	0	ENST00000440232.2:c.784G>A	p.Gly262Ser	p.G262S	ENST00000440232	NM_002691.3	262	Ggc/Agc	7/27	1	2	FACETS	0.288	0.259	0.319	0.288	0.259	0.319	SUBCLONAL	1	TRUE	1	0.714624809483678	2		808	1156	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158595029	158595029	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs745343863	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	60	552	0	ENST00000263640.3:c.1318A>G	p.Ser440Gly	p.S440G	ENST00000263640	NM_001105.4	440	Agt/Ggt	10/11	1	2	FACETS	0.192	0.165	0.222	0.192	0.165	0.222	SUBCLONAL	1	TRUE	1	0.714624809483678	2		552	873	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661972	227661972	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	115	622	0	ENST00000305123.5:c.1483A>G	p.Thr495Ala	p.T495A	ENST00000305123	NM_005544.2	495	Acc/Gcc	1/2	1	2	FACETS	0.299	0.269	0.332	0.299	0.269	0.332	SUBCLONAL	1	TRUE	1	0.714624809483678	2		622	1075	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574665	41574665	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	114	837	6	ENST00000263253.7:c.6950G>T	p.Arg2317Leu	p.R2317L	ENST00000263253	NM_001429.3	2317	cGg/cTg	31/31	1	2	FACETS	0.253	0.227	0.281	0.253	0.227	0.281	SUBCLONAL	1	TRUE	1	0.714624809483678	2		843	1262	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37038115	37038115	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs63751094	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	144	279	0	ENST00000231790.2:c.122A>T	p.Asp41Val	p.D41V	ENST00000231790	NM_000249.3	41	gAt/gTt	2/19	0.714624809483678	1	FACETS	0.852	0.791	0.913	0.852	0.791	0.913	CLONAL	1	TRUE	0	0.714624809483678	1		279	304	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629115	187629115	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	221	653	0	ENST00000441802.2:c.1867del	p.Val623TyrfsTer4	p.V623Yfs*4	ENST00000441802	NM_005245.3	623	Gta/ta	2/27	1	2	FACETS	0.559	0.52	0.6	0.559	0.52	0.6	SUBCLONAL	1	TRUE	1	0.714624809483678	2		653	1106	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294361	1294361	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	468	538	0	ENST00000310581.5:c.640del	p.Leu214TrpfsTer137	p.L214Wfs*137	ENST00000310581	NM_198253.2	214	Ctg/tg	2/16	0.714624809483678	4	FACETS	0.829	0.792	0.866	0.552	0.528	0.577	CLONAL	2	TRUE	1	0.714624809483678	4		538	1355	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468044	50468044	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	226	548	0	ENST00000331340.3:c.1279T>A	p.Ser427Thr	p.S427T	ENST00000331340	NM_006060.4	427	Tcg/Acg	8/8	1	2	FACETS	0.781	0.729	0.834	0.781	0.729	0.834	SUBCLONAL	1	TRUE	1	0.714624809483678	2		548	810	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981408	70981408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs958196847	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1242	758	776	0	ENST00000276594.2:c.688C>T	p.Pro230Ser	p.P230S	ENST00000276594	NM_024504.3	230	Cca/Tca	2/8	0.714624809483678	4	FACETS	0.909	0.878	0.941	0.606	0.585	0.627	CLONAL	2	TRUE	1	0.714624809483678	4		776	2000	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300812	137300812	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	79	702	0	ENST00000481739.1:c.457G>A	p.Glu153Lys	p.E153K	ENST00000481739	NM_002957.4	153	Gag/Aag	4/10	1	2	FACETS	0.195	0.171	0.222	0.195	0.171	0.222	SUBCLONAL	1	TRUE	1	0.714624809483678	2		702	1132	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412700	139412700	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	373	815	0	ENST00000277541.6:c.1144A>G	p.Asn382Asp	p.N382D	ENST00000277541	NM_017617.3	382	Aac/Gac	7/34	1	2	FACETS	0.867	0.823	0.912	0.867	0.823	0.912	CLONAL	1	TRUE	1	0.714624809483678	2		815	1204	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0026441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	237	347	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.802390534582068	2		347	532	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692830	89692830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782343	NA	P-0026441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	106	167	1	ENST00000371953.3:c.314G>A	p.Cys105Tyr	p.C105Y	ENST00000371953	NM_000314.4	105	tGt/tAt	5/9	0.802390534582068	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.802390534582068	1		168	152	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954205	48954206	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CATTCAAA	novel	NA	P-0026441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	139	322	0	ENST00000267163.4:c.1407_1414dup	p.Asn472ThrfsTer9	p.N472Tfs*9	ENST00000267163	NM_000321.2	469	tcc/tcCATTCAAAc	15/27	0.802390534582068	1	FACETS	0.619	0.572	0.667	0.619	0.572	0.667	SUBCLONAL	1	TRUE	0	0.802390534582068	1		322	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	411	627	1	ENST00000269305.4:c.701del	p.Tyr234SerfsTer13	p.Y234Sfs*13	ENST00000269305	NM_001126112.2	234	tAc/tc	7/11	0.77400327617245	1	FACETS	0.989	0.955	1	0.989	0.955	1	CLONAL	1	TRUE	0	0.802390534582068	1		628	620	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325623	87325623	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs76950094	NA	P-0026442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	233	578	1	ENST00000277120.3:c.500C>A	p.Ser167Tyr	p.S167Y	ENST00000277120		167	tCc/tAc	6/19	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.720670137270147	2		579	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578175	7578175	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0026442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	401	807	0	ENST00000269305.4:c.672+2T>G		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.67672109653176	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.720670137270147	1		807	632	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243045	105243046	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTGCAGGCAGCGGATGATGAAGGTGTTGGGCCGGGGCCG	novel	NA	P-0026442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	195	775	3	ENST00000349310.3:c.199_237dup	p.Arg67_Gln79dup	p.R67_Q79dup	ENST00000349310	NM_001014432.1	67	-/CGGCCCCGGCCCAACACCTTCATCATCCGCTGCCTGCAG	5/15	1	2	FACETS	0.493	0.456	0.532	0.493	0.456	0.532	SUBCLONAL	1	TRUE	1	0.720670137270147	2		778	1097	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753697	42753698	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs1555750816	NA	P-0026442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	1080	866	1	ENST00000222329.4:c.566_567del	p.Cys189Ter	p.C189*	ENST00000222329	NM_006494.2	189	tGT/t	4/4	0.703662139678814	3	FACETS	0.993	0.976	1	0.993	0.976	1	CLONAL	3	TRUE	0	0.720670137270147	3		867	1368	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0026443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	20	379	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.291985062738225	1	FACETS	0.557	0.433	0.696	0.557	0.433	0.696	INDETERMINATE	1	TRUE	0	0.520818380152514	1		379	102	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604502	43604502	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	24	688	0	ENST00000355710.3:c.1087T>G	p.Ser363Ala	p.S363A	ENST00000355710	NM_020975.4	363	Tcc/Gcc	6/20	0.246382094583959	1	FACETS	0.37	0.292	0.459	0.37	0.292	0.459	INDETERMINATE	1	TRUE	0	0.520818380152514	1		688	184	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632419	3632419	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs757727147	NA	P-0026443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	25	792	0	ENST00000294008.3:c.5429C>G	p.Thr1810Ser	p.T1810S	ENST00000294008	NM_032444.2	1810	aCt/aGt	15/15	0.520818380152514	3	FACETS	0.467	0.369	0.579	0.234	0.184	0.29	SUBCLONAL	1	TRUE	1	0.520818380152514	3		792	259	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225674	26225674	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	30	593	0	ENST00000360408.1:c.292G>A	p.Glu98Lys	p.E98K	ENST00000360408	NM_003532.2	98	Gag/Aag	1/1	0.387379233613947	5	FACETS	0.987	0.801	1	0.329	0.267	0.398	CLONAL	1	TRUE	2	0.520818380152514	5		593	208	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0026446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	182	714	1	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.637649792657406	2	FACETS	0.956	0.904	1	0.956	0.904	1	CLONAL	2	TRUE	0	0.65905413309696	2		715	289	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527610	29527612	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TAA	TAA	-	novel	NA	P-0026446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	110	447	0	ENST00000356175.3:c.1059_1061del	p.Lys354del	p.K354del	ENST00000356175	NM_000267.3	353	ctTAAg/ctg	9/57	0.637649792657406	2	FACETS	0.959	0.892	1	0.959	0.892	1	CLONAL	2	TRUE	0	0.65905413309696	2		447	174	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0026447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	663	688	1	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	0.730481560455058	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.730481560455058	3		689	801	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916928	178916939	+	inframe_deletion	In_Frame_Del	DEL	AGGCAACCGTGA	AGGCAACCGTGA	-	novel	NA	P-0026447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	140	535	0	ENST00000263967.3:c.317_328del	p.Gly106_Glu109del	p.G106_E109del	ENST00000263967	NM_006218.2	105	gtAGGCAACCGTGAa/gta	2/21	0.730481560455058	3	FACETS	0.783	0.715	0.855	0.392	0.357	0.428	SUBCLONAL	1	TRUE	1	0.730481560455058	3		535	668	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720813	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0026447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	98	264	0	ENST00000371953.3:c.967_968del	p.Asn323Ter	p.N323*	ENST00000371953	NM_000314.4	321	acAAaa/acaa	8/9	0.723785969445591	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.730481560455058	1		264	170	SUCCESS
APC	324	MSKCC	GRCh37	5	112175888	112175895	+	frameshift_variant	Frame_Shift_Del	DEL	AATGGGAA	AATGGGAA	-	novel	NA	P-0026447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	213	326	0	ENST00000257430.4:c.4597_4604del	p.Asn1533Ter	p.N1533*	ENST00000257430	NM_000038.5	1533	AATGGGAAt/t	16/16	0.730481560455058	2	FACETS	0.959	0.916	1	0.959	0.916	1	CLONAL	2	TRUE	0	0.730481560455058	2		326	304	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240995	53240995	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	213	285	0	ENST00000375401.3:c.1216G>A	p.Ala406Thr	p.A406T	ENST00000375401	NM_004187.3	406	Gct/Act	9/26	0.730481560455058	3	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.730481560455058	3		285	703	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0026448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	120	339	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.533120024329461	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.533120024329461	1		339	299	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604790	48604790	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1568211615	NA	P-0026448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	182	500	0	ENST00000342988.3:c.1612G>T	p.Glu538Ter	p.E538*	ENST00000342988	NM_005359.5	538	Gaa/Taa	12/12	0.528889550282505	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.533120024329461	1		500	477	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473728	67473728	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	264	720	0	ENST00000327367.4:c.808T>A	p.Cys270Ser	p.C270S	ENST00000327367	NM_005902.3	270	Tgc/Agc	6/9	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.533120024329461	2		720	889	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667657	29667657	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	156	475	0	ENST00000356175.3:c.6993del	p.Asn2331LysfsTer44	p.N2331Kfs*44	ENST00000356175	NM_000267.3	2331	aaT/aa	46/57	0.533120024329461	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.533120024329461	1		475	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578259	7578259	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1567551903	NA	P-0026449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	206	784	0	ENST00000269305.4:c.590T>A	p.Val197Glu	p.V197E	ENST00000269305	NM_001126112.2	197	gTg/gAg	6/11	0.245186540610844	3	FACETS	0.864	0.805	0.925	0.864	0.805	0.925	CLONAL	3	TRUE	0	0.258705609827498	3		784	694	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947593	48947593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753350745	NA	P-0026449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	122	660	1	ENST00000267163.4:c.1180G>A	p.Asp394Asn	p.D394N	ENST00000267163	NM_000321.2	394	Gat/Aat	12/27	0.258705609827498	6	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.258705609827498	6		661	1000	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	44	425	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.4	0.334	0.473	0.4	0.334	0.473	SUBCLONAL	1	TRUE	1	0.33	2		426	667	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	319	424	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.98	0.927	1	1	0.996	1	CLONAL	2	TRUE	1	0.33	2		424	986	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	68	454	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.67	0.583	0.764	0.67	0.583	0.764	SUBCLONAL	1	TRUE	1	0.33	2		454	615	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	71	501	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.723	0.631	0.822	0.723	0.631	0.822	SUBCLONAL	1	TRUE	1	0.33	2		501	595	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	126	475	2	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.88	0.796	0.968	0.88	0.796	0.968	CLONAL	1	TRUE	1	0.33	2		477	868	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228979	36228979	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555734923	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	163	612	3	ENST00000222270.7:c.7759C>T	p.Arg2587Ter	p.R2587*	ENST00000222270	NM_014727.1	2587	Cga/Tga	36/37	1	2	FACETS	0.91	0.834	0.989	0.91	0.834	0.989	CLONAL	1	TRUE	1	0.33	2		615	1086	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	170	627	9	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.33	2		636	997	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085728	16085728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144939456	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	169	609	0	ENST00000281043.3:c.904C>T	p.Arg302Cys	p.R302C	ENST00000281043	NM_005378.4	302	Cgt/Tgt	3/3	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.33	2		609	1004	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	61	512	2	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	1	2	FACETS	0.741	0.64	0.85	0.741	0.64	0.85	SUBCLONAL	1	TRUE	1	0.33	2		514	499	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101054	27101054	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	172	694	1	ENST00000324856.7:c.4336C>T	p.Arg1446Ter	p.R1446*	ENST00000324856	NM_006015.4	1446	Cga/Tga	18/20	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.33	2		695	1037	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692916	89692918	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	rs1554898152	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	80	623	0	ENST00000371953.3:c.402_404del	p.Met134del	p.M134del	ENST00000371953	NM_000314.4	134	ATG/-	5/9	1	2	FACETS	0.753	0.663	0.849	0.753	0.663	0.849	SUBCLONAL	1	TRUE	1	0.33	2		623	644	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106910	11106910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	196	693	2	ENST00000358026.2:c.1615C>T	p.Arg539Cys	p.R539C	ENST00000358026	NM_001128849.1	539	Cgc/Tgc	10/36	1	2	FACETS	0.997	0.921	1	0.997	0.921	1	CLONAL	1	TRUE	1	0.33	2		695	1192	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772951	135772951	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs118203724	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	86	421	0	ENST00000298552.3:c.2672del	p.Asn891ThrfsTer40	p.N891Tfs*40	ENST00000298552	NM_001162426.1	891	aAc/ac	21/23	1	2	FACETS	0.769	0.68	0.864	0.769	0.68	0.864	SUBCLONAL	1	TRUE	1	0.33	2		421	678	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913253	39913253	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	45	610	0	ENST00000378444.4:c.4862del	p.Pro1621GlnfsTer53	p.P1621Qfs*53	ENST00000378444	NM_001123385.1	1621	cCa/ca	14/15	1	2	FACETS	0.308	0.258	0.364	0.308	0.258	0.364	SUBCLONAL	1	TRUE	1	0.33	2		610	886	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602748	10602748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	204	425	0	ENST00000171111.5:c.830C>T	p.Thr277Met	p.T277M	ENST00000171111	NM_203500.1	277	aCg/aTg	3/6	1	2	FACETS	0.947	0.876	1	0.947	0.876	1	CLONAL	1	TRUE	1	0.33	2		425	1306	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098363	11098363	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	184	611	0	ENST00000358026.2:c.885del	p.Thr296ArgfsTer7	p.T296Rfs*7	ENST00000358026	NM_001128849.1	294	gCc/gc	6/36	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.33	2		611	933	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086032	16086032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777508469	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	178	599	0	ENST00000281043.3:c.1208C>T	p.Thr403Met	p.T403M	ENST00000281043	NM_005378.4	403	aCg/aTg	3/3	1	2	FACETS	0.946	0.871	1	0.946	0.871	1	CLONAL	1	TRUE	1	0.33	2		599	1140	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984024	7984024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	103	479	1	ENST00000319144.4:c.602G>A	p.Arg201His	p.R201H	ENST00000319144	NM_001139.2	201	cGc/cAc	5/15	1	2	FACETS	0.798	0.714	0.888	0.798	0.714	0.888	SUBCLONAL	1	TRUE	1	0.33	2		480	782	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602341	10602341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1178941219	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	195	770	2	ENST00000171111.5:c.1237C>T	p.Arg413Cys	p.R413C	ENST00000171111	NM_203500.1	413	Cgt/Tgt	3/6	1	2	FACETS	0.98	0.905	1	0.98	0.905	1	CLONAL	1	TRUE	1	0.33	2		772	1206	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098392	11098392	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	152	576	0	ENST00000358026.2:c.914del	p.Pro305ArgfsTer21	p.P305Rfs*21	ENST00000358026	NM_001128849.1	304	Ccc/cc	6/36	1	2	FACETS	0.964	0.881	1	0.964	0.881	1	CLONAL	1	TRUE	1	0.33	2		576	956	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127731	64127731	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1455628289	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	152	608	1	ENST00000334205.4:c.224G>A	p.Arg75His	p.R75H	ENST00000334205	NM_003942.2	75	cGc/cAc	3/17	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.33	2		609	813	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257950	16257950	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	143	554	2	ENST00000375759.3:c.5218del	p.Ala1740ProfsTer10	p.A1740Pfs*10	ENST00000375759	NM_015001.2	1739	Ggg/gg	11/15	1	2	FACETS	0.875	0.797	0.958	0.875	0.797	0.958	CLONAL	1	TRUE	1	0.33	2		556	990	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12653479	12653479	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	143	495	0	ENST00000251849.4:c.290C>T	p.Ala97Val	p.A97V	ENST00000251849	NM_002880.3	97	gCa/gTa	3/17	1	2	FACETS	0.908	0.828	0.993	0.908	0.828	0.993	CLONAL	1	TRUE	1	0.33	2		495	954	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52621447	52621447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	120	605	0	ENST00000394830.3:c.2970del	p.Glu991LysfsTer17	p.E991Kfs*17	ENST00000394830	NM_018313.4	990	aaA/aa	20/30	1	2	FACETS	0.916	0.827	1	0.916	0.827	1	CLONAL	1	TRUE	1	0.33	2		605	794	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466362	120466362	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	141	541	0	ENST00000256646.2:c.4757A>G	p.Glu1586Gly	p.E1586G	ENST00000256646	NM_024408.3	1586	gAa/gGa	26/34	1	2	FACETS	0.999	0.911	1	0.999	0.911	1	CLONAL	1	TRUE	1	0.33	2		541	855	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94963994	94963994	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1228129466	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	112	299	1	ENST00000536441.1:c.31G>A	p.Ala11Thr	p.A11T	ENST00000536441	NM_144665.3	11	Gcc/Acc	1/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.33	2		300	458	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650740	67650740	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1185134308	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	198	715	0	ENST00000264010.4:c.1045A>G	p.Lys349Glu	p.K349E	ENST00000264010	NM_006565.3	349	Aag/Gag	5/12	1	2	FACETS	0.933	0.862	1	0.933	0.862	1	CLONAL	1	TRUE	1	0.33	2		715	1286	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40469209	40469209	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	108	511	0	ENST00000264657.5:c.2135G>A	p.Cys712Tyr	p.C712Y	ENST00000264657	NM_139276.2	712	tGt/tAt	22/24	1	2	FACETS	0.73	0.654	0.81	0.73	0.654	0.81	SUBCLONAL	1	TRUE	1	0.33	2		511	897	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220869	36220869	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1336661633	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	38	181	0	ENST00000222270.7:c.4919G>A	p.Arg1640His	p.R1640H	ENST00000222270	NM_014727.1	1640	cGc/cAc	23/37	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.33	2		181	220	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855820	45855820	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	180	756	0	ENST00000391945.4:c.1990G>A	p.Val664Met	p.V664M	ENST00000391945	NM_000400.3	664	Gtg/Atg	21/23	1	2	FACETS	0.868	0.798	0.94	0.868	0.798	0.94	CLONAL	1	TRUE	1	0.33	2		756	1257	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143231	24143231	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1458920579	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	188	761	0	ENST00000263121.7:c.463C>T	p.Arg155Cys	p.R155C	ENST00000263121	NM_003073.3	155	Cgc/Tgc	4/9	1	2	FACETS	0.922	0.85	0.997	0.922	0.85	0.997	CLONAL	1	TRUE	1	0.33	2		761	1236	SUCCESS
ATR	545	MSKCC	GRCh37	3	142204071	142204071	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	107	689	0	ENST00000350721.4:c.6132G>T	p.Lys2044Asn	p.K2044N	ENST00000350721	NM_001184.3	2044	aaG/aaT	36/47	1	2	FACETS	0.839	0.752	0.931	0.839	0.752	0.931	CLONAL	1	TRUE	1	0.33	2		689	773	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502672	149502672	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770635073	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	152	589	0	ENST00000261799.4:c.2116G>A	p.Asp706Asn	p.D706N	ENST00000261799	NM_002609.3	706	Gac/Aac	15/23	1	2	FACETS	0.939	0.858	1	0.939	0.858	1	CLONAL	1	TRUE	1	0.33	2		589	981	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522539	176522539	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	155	640	0	ENST00000292408.4:c.1636C>A	p.Leu546Met	p.L546M	ENST00000292408	NM_213647.1	546	Ctg/Atg	13/18	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.33	2		640	886	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176718968	176718968	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	96	314	0	ENST00000439151.2:c.6273del	p.Thr2092ArgfsTer58	p.T2092Rfs*58	ENST00000439151	NM_022455.4	2091	gCc/gc	22/23	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.33	2		314	517	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64290050	64290050	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs546134768	NA	P-0026456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	88	527	2	ENST00000370651.3:c.493G>A	p.Gly165Ser	p.G165S	ENST00000370651	NM_003463.4	165	Ggt/Agt	6/6	1	2	FACETS	0.698	0.618	0.784	0.698	0.618	0.784	SUBCLONAL	1	TRUE	1	0.33	2		529	764	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0026457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	222	483	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.912	0.854	0.97	0.912	0.854	0.97	CLONAL	1	TRUE	1	0.810440712621336	2		483	601	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123691	11123691	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	192	661	2	ENST00000358026.2:c.2341A>G	p.Met781Val	p.M781V	ENST00000358026	NM_001128849.1	781	Atg/Gtg	16/36	0.500137319655013	1	FACETS	0.438	0.407	0.47	0.438	0.407	0.47	SUBCLONAL	1	TRUE	0	0.810440712621336	1		663	643	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0026458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	276	411	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.512134752722577	2		411	763	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0026458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	375	564	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.512134752722577	2		564	983	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220622	1220622	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690923	NA	P-0026458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	441	640	1	ENST00000326873.7:c.640C>T	p.Gln214Ter	p.Q214*	ENST00000326873	NM_000455.4	214	Cag/Tag	5/10	0.512134752722577	1	FACETS	0.834	0.803	0.865	1	0.997	1	CLONAL	2	TRUE	0	0.512134752722577	1		641	768	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098380	11098380	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	384	582	0	ENST00000358026.2:c.898C>T	p.Gln300Ter	p.Q300*	ENST00000358026	NM_001128849.1	300	Cag/Tag	6/36	0.512134752722577	1	FACETS	0.881	0.847	0.915	1	0.997	1	CLONAL	2	TRUE	0	0.512134752722577	1		582	633	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281634	15281634	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	460	812	4	ENST00000263388.2:c.4739C>T	p.Ser1580Leu	p.S1580L	ENST00000263388	NM_000435.2	1580	tCg/tTg	26/33	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	1	TRUE	NA	0.512134752722577	2		816	1261	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2202697	2202697	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0026458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	392	657	0	ENST00000398665.3:c.708-2A>T		p.X236_splice	ENST00000398665	NM_032482.2	236			0.512134752722577	1	FACETS	0.793	0.761	0.825	1	0.996	1	SUBCLONAL	2	TRUE	0	0.512134752722577	1		657	718	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610422	10610422	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	443	718	0	ENST00000171111.5:c.288C>G	p.His96Gln	p.H96Q	ENST00000171111	NM_203500.1	96	caC/caG	2/6	0.512134752722577	1	FACETS	0.86	0.829	0.891	1	0.997	1	CLONAL	2	TRUE	0	0.512134752722577	1		718	748	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821553	32821553	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	435	733	0	ENST00000354258.4:c.41G>C	p.Trp14Ser	p.W14S	ENST00000354258	NM_000593.5	14	tGg/tCg	1/11	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.512134752722577	2		733	1269	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0026459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	477	714	1	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.557817518118666	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.557817518118666	2		715	844	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50916770	50916770	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	192	643	0	ENST00000440232.2:c.2242A>G	p.Ser748Gly	p.S748G	ENST00000440232	NM_002691.3	748	Agt/Ggt	18/27	0.534074581726344	4	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.557817518118666	4		643	925	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233111	46233111	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0026459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	93	273	0	ENST00000334344.6:c.1331-1G>C		p.X444_splice	ENST00000334344	NM_152641.2	444			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.557817518118666	2		273	273	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778664	3778664	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	193	716	0	ENST00000262367.5:c.6384A>T	p.Gln2128His	p.Q2128H	ENST00000262367	NM_004380.2	2128	caA/caT	31/31	0.19778099673392	5	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.557817518118666	5		716	856	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967746	90967746	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0026459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	137	310	0	ENST00000265433.3:c.1162A>T	p.Lys388Ter	p.K388*	ENST00000265433	NM_002485.4	388	Aaa/Taa	10/16	0.557817518118666	10	FACETS	0.937	0.852	1	0.234	0.213	0.257	CLONAL	2	TRUE	2	0.557817518118666	10		310	847	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796587	42796610	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CGGCCCCGCCTTCGTGCAGCCCCT	CGGCCCCGCCTTCGTGCAGCCCCT	GTGAG	novel	NA	P-0026459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	173	665	0	ENST00000575354.2:c.3144_3167delinsGTGAG	p.Ser1048ArgfsTer2	p.S1048Rfs*2	ENST00000575354	NM_015125.3	1048	agCGGCCCCGCCTTCGTGCAGCCCCTg/agGTGAGg	13/20	0.19778099673392	5	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.557817518118666	5		665	886	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	102	474	0				ENST00000310581	NM_198253.2	-/1132			0.306026556408715	3	FACETS	1	0.978	1	0.671	0.603	0.742	CLONAL	1	TRUE	1	0.40137145023149	3		474	455	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACAACCCCC	rs397517115	NA	P-0026460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	288	539	0	ENST00000275493.2:c.2311_2319dup	p.Asn771_His773dup	p.N771_H773dup	ENST00000275493	NM_005228.3	771	gac/gACAACCCCCac	20/28	0.40137145023149	5	FACETS	1	0.989	1	0.808	0.761	0.855	CLONAL	2	TRUE	2	0.40137145023149	5		539	949	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131232	17131232	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	217	743	1	ENST00000285071.4:c.220C>A	p.Pro74Thr	p.P74T	ENST00000285071	NM_144997.5	74	Ccg/Acg	4/14	0.309158196088477	4	FACETS	0.788	0.733	0.844	0.788	0.733	0.844	SUBCLONAL	2	TRUE	2	0.40137145023149	4		744	962	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11210220	11210220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	193	633	0	ENST00000361445.4:c.4533G>T	p.Lys1511Asn	p.K1511N	ENST00000361445	NM_004958.3	1511	aaG/aaT	31/58	0.306026556408715	3	FACETS	0.769	0.713	0.826	0.769	0.713	0.826	SUBCLONAL	2	TRUE	1	0.40137145023149	3		633	751	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023588	27023642	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTCCCCGAGAGGTGGCACTCCGGGCTCCGGCGCGGCGGCGGCTGCCGGCTCCA	AGCTCCCCGAGAGGTGGCACTCCGGGCTCCGGCGCGGCGGCGGCTGCCGGCTCCA	-	novel	NA	P-0026460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	144	410	0	ENST00000324856.7:c.697_751del	p.Ser233ArgfsTer112	p.S233Rfs*112	ENST00000324856	NM_006015.4	232	AGCTCCCCGAGAGGTGGCACTCCGGGCTCCGGCGCGGCGGCGGCTGCCGGCTCCAag/ag	1/20	0.306026556408715	3	FACETS	0.819	0.751	0.889	0.819	0.751	0.889	CLONAL	2	TRUE	1	0.40137145023149	3		410	526	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092946	27092946	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0026460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	118	377	0	ENST00000324856.7:c.2879-2A>T		p.X960_splice	ENST00000324856	NM_006015.4	960			0.306026556408715	3	FACETS	0.905	0.824	0.989	0.905	0.824	0.989	CLONAL	2	TRUE	1	0.40137145023149	3		377	390	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40856633	40856633	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	167	580	0	ENST00000428826.2:c.2004C>G	p.Phe668Leu	p.F668L	ENST00000428826		668	ttC/ttG	18/21	0.309158196088477	4	FACETS	1	0.988	1	0.729	0.67	0.79	CLONAL	1	TRUE	2	0.40137145023149	4		580	800	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86681165	86681165	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	149	411	0	ENST00000274376.6:c.2806T>C	p.Ser936Pro	p.S936P	ENST00000274376	NM_002890.2	936	Tct/Cct	22/25	0.306026556408715	3	FACETS	0.94	0.866	1	0.94	0.866	1	CLONAL	2	TRUE	1	0.40137145023149	3		411	474	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692791	89692796	+	inframe_deletion	In_Frame_Del	DEL	ACCATA	ACCATA	-	novel	NA	P-0026461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	164	418	0	ENST00000371953.3:c.278_283del	p.His93_Asn94del	p.H93_N94del	ENST00000371953	NM_000314.4	92	gACCATAac/gac	5/9	0.504823217493045	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.504823217493045	1		418	450	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220369	1220388	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGGTACTTCTGTCAGCTGA	CAGGTACTTCTGTCAGCTGA	-	novel	NA	P-0026461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	116	530	0	ENST00000326873.7:c.465-3_481del		p.X155_splice	ENST00000326873	NM_000455.4	155		4/10	0.504823217493045	1	FACETS	0.816	0.741	0.894	0.816	0.741	0.894	CLONAL	1	TRUE	0	0.504823217493045	1		530	421	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224384	36224384	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	250	831	1	ENST00000222270.7:c.6934C>T	p.Gln2312Ter	p.Q2312*	ENST00000222270	NM_014727.1	2312	Cag/Tag	28/37	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.504823217493045	2		832	919	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253911	NA	P-0026464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	122	617	0	ENST00000269305.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000269305	NM_001126112.2	180	Gag/Aag	5/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.217381884760942	2		617	872	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACT	novel	NA	P-0026464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	101	533	0	ENST00000275493.2:c.2310_2311insTAC	p.Asp770_Asn771insTyr	p.D770_N771insY	ENST00000275493	NM_005228.3	770	gac/gACTac	20/28	0.135777681992675	4	FACETS	1	0.909	1	0.511	0.455	0.57	CLONAL	1	TRUE	2	0.217381884760942	4		533	1107	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40871161	40871161	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	133	583	0	ENST00000428826.2:c.729G>A	p.Met243Ile	p.M243I	ENST00000428826		243	atG/atA	8/21	0.594759082640127	3	FACETS	0.875	0.797	0.957	0.438	0.398	0.479	CLONAL	1	TRUE	1	0.594759082640127	3		583	663	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43772163	43772163	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	65	647	1	ENST00000382044.4:c.552G>T	p.Gln184His	p.Q184H	ENST00000382044	NM_001141980.1	184	caG/caT	6/28	0.366910977202367	1	FACETS	0.129	0.111	0.148	0.129	0.111	0.148	INDETERMINATE	1	TRUE	0	0.683649605930939	1		648	971	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0026470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	34	424	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.741	0.603	0.897	0.741	0.603	0.897	SUBCLONAL	1	TRUE	1	0.13	2		424	706	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782664	NA	P-0026471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	593	673	0	ENST00000269305.4:c.711G>C	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atC	7/11	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.76689166822938	2		673	763	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725019	47725019	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs762488821	NA	P-0026471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1293	284	696	4	ENST00000449228.1:c.725del	p.Gly242AlafsTer48	p.G242Afs*48	ENST00000449228	NM_001127240.2	242	gGc/gc	4/4	0.643395923372228	4	FACETS	0.83	0.778	0.884	0.415	0.389	0.442	CLONAL	1	TRUE	2	0.76689166822938	4		700	1577	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22417957	22417957	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	103	179	0	ENST00000344548.3:c.523G>T	p.Ala175Ser	p.A175S	ENST00000344548	NM_001039802.1	175	Gct/Tct	7/7	0.676839984842672	3	FACETS	1	0.968	1	0.581	0.526	0.637	CLONAL	1	TRUE	1	0.76689166822938	3		179	320	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218087	108218087	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	214	477	0	ENST00000278616.4:c.8666A>T	p.Asp2889Val	p.D2889V	ENST00000278616	NM_000051.3	2889	gAt/gTt	59/63	0.76689166822938	3	FACETS	0.926	0.873	0.978	0.926	0.873	0.978	CLONAL	2	TRUE	1	0.76689166822938	3		477	417	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858914	57858914	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	604	737	0	ENST00000228682.2:c.410C>G	p.Ala137Gly	p.A137G	ENST00000228682	NM_005269.2	137	gCc/gGc	5/12	0.744280259256446	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.76689166822938	3		737	1085	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954215	48954215	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1555286573	NA	P-0026471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	213	296	0	ENST00000267163.4:c.1419del	p.Phe473LeufsTer5	p.F473Lfs*5	ENST00000267163	NM_000321.2	472	aaT/aa	15/27	0.76689166822938	2	FACETS	0.917	0.875	0.957	0.917	0.875	0.957	CLONAL	2	TRUE	0	0.76689166822938	2		296	303	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640593	3640594	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0026471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	384	818	0	ENST00000294008.3:c.3045dup	p.Leu1016AlafsTer78	p.L1016Afs*78	ENST00000294008	NM_032444.2	1015	-/G	12/15	0.76689166822938	3	FACETS	0.979	0.929	1	0.49	0.464	0.515	CLONAL	1	TRUE	1	0.76689166822938	3		818	1415	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857367	68857367	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0026471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	269	663	1	ENST00000261769.5:c.2002A>T	p.Lys668Ter	p.K668*	ENST00000261769	NM_004360.3	668	Aag/Tag	13/16	0.76689166822938	3	FACETS	1	0.943	1	0.502	0.471	0.533	CLONAL	1	TRUE	1	0.76689166822938	3		664	967	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900369	3900370	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	C	novel	NA	P-0026471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	502	629	0	ENST00000262367.5:c.726_727delinsG	p.Leu243Ter	p.L243*	ENST00000262367	NM_004380.2	242	acCCta/acGta	2/31	0.76689166822938	3	FACETS	0.951	0.916	0.986	0.951	0.916	0.986	CLONAL	2	TRUE	1	0.76689166822938	3		629	952	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948801	55948801	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	66	307	1	ENST00000263923.4:c.3664C>T	p.Gln1222Ter	p.Q1222*	ENST00000263923	NM_002253.2	1222	Cag/Tag	28/30	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.48139988759996	2		308	273	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344774	65344774	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	91	460	2	ENST00000342505.4:c.263G>A	p.Trp88Ter	p.W88*	ENST00000342505	NM_002227.2	88	tGg/tAg	4/25	0.445688797766841	1	FACETS	0.932	0.837	1	0.932	0.837	1	CLONAL	1	TRUE	0	0.48139988759996	1		462	308	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155779	119155779	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	102	646	0	ENST00000264033.4:c.1532C>T	p.Ser511Leu	p.S511L	ENST00000264033	NM_005188.3	511	tCa/tTa	10/16	0.47451956226713	1	FACETS	0.922	0.833	1	0.922	0.833	1	CLONAL	1	TRUE	0	0.48139988759996	1		646	349	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896403	28896403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	80	398	0	ENST00000282397.4:c.3047G>A	p.Arg1016Lys	p.R1016K	ENST00000282397	NM_002019.4	1016	aGa/aAa	22/30	0.47451956226713	1	FACETS	0.914	0.815	1	0.914	0.815	1	CLONAL	1	TRUE	0	0.48139988759996	1		398	276	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941654	48941654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776534331	NA	P-0026472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	56	266	0	ENST00000267163.4:c.964G>A	p.Glu322Lys	p.E322K	ENST00000267163	NM_000321.2	322	Gaa/Aaa	10/27	0.47451956226713	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.48139988759996	1		266	161	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571448	95571448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373412959	NA	P-0026472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	64	334	0	ENST00000393063.1:c.3229G>A	p.Asp1077Asn	p.D1077N	ENST00000393063	NM_030621.3	1077	Gat/Aat	21/28	1	2	FACETS	0.974	0.852	1	0.974	0.852	1	CLONAL	1	TRUE	1	0.48139988759996	2		334	273	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799155	88799155	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	77	500	0	ENST00000360948.2:c.230C>T	p.Ser77Leu	p.S77L	ENST00000360948	NM_001012338.2	77	tCa/tTa	2/19	1	2	FACETS	0.814	0.719	0.915	0.814	0.719	0.915	CLONAL	1	TRUE	1	0.48139988759996	2		500	393	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639021	3639021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769950582	NA	P-0026472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	93	530	1	ENST00000294008.3:c.4618G>A	p.Glu1540Lys	p.E1540K	ENST00000294008	NM_032444.2	1540	Gaa/Aaa	12/15	1	2	FACETS	0.909	0.813	1	0.909	0.813	1	CLONAL	1	TRUE	1	0.48139988759996	2		531	425	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509666	29509666	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	92	581	0	ENST00000356175.3:c.871G>T	p.Glu291Ter	p.E291*	ENST00000356175	NM_000267.3	291	Gaa/Taa	8/57	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.48139988759996	2		581	363	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763458	59763458	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	95	549	0	ENST00000259008.2:c.2644G>C	p.Ala882Pro	p.A882P	ENST00000259008	NM_032043.2	882	Gct/Cct	19/20	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.48139988759996	2		549	361	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591825	48591825	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	78	436	0	ENST00000342988.3:c.988G>C	p.Glu330Gln	p.E330Q	ENST00000342988	NM_005359.5	330	Gaa/Caa	9/12	0.48139988759996	1	FACETS	0.984	0.877	1	0.984	0.877	1	CLONAL	1	TRUE	0	0.48139988759996	1		436	250	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591865	48591865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	21	491	1	ENST00000342988.3:c.1028C>T	p.Ser343Leu	p.S343L	ENST00000342988	NM_005359.5	343	tCa/tTa	9/12	0.48139988759996	1	FACETS	0.216	0.166	0.275	0.216	0.166	0.275	SUBCLONAL	1	TRUE	0	0.48139988759996	1		492	306	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223087	1223087	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	134	679	0	ENST00000326873.7:c.1024G>T	p.Glu342Ter	p.E342*	ENST00000326873	NM_000455.4	342	Gag/Tag	8/10	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.48139988759996	2		679	531	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615783	1615783	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1347340570	NA	P-0026472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	96	620	0	ENST00000344749.5:c.1488G>C	p.Glu496Asp	p.E496D	ENST00000344749	NM_001136139.2	496	gaG/gaC	17/19	1	2	FACETS	0.819	0.733	0.91	0.819	0.733	0.91	CLONAL	1	TRUE	1	0.48139988759996	2		620	487	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597373	10597373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	144	692	0	ENST00000171111.5:c.1830G>A	p.Met610Ile	p.M610I	ENST00000171111	NM_203500.1	610	atG/atA	6/6	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.48139988759996	2		692	553	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272134	18272134	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	16	66	0	ENST00000222254.8:c.644C>T	p.Pro215Leu	p.P215L	ENST00000222254	NM_005027.3	215	cCg/cTg	6/16	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.48139988759996	2		66	55	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733274	40733274	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	92	596	0	ENST00000373198.4:c.3532C>G	p.Leu1178Val	p.L1178V	ENST00000373198	NM_133170.3	1178	Ctc/Gtc	26/32	0.48139988759996	10	FACETS	0.927	0.821	1			1	CLONAL	1	TRUE	NA	0.48139988759996	10		596	1206	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191563	10191563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367545984	NA	P-0026472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	100	519	0	ENST00000256474.2:c.556G>A	p.Glu186Lys	p.E186K	ENST00000256474	NM_000551.3	186	Gaa/Aaa	3/3	0.48139988759996	2	FACETS	0.953	0.856	1	0.476	0.428	0.527	CLONAL	1	TRUE	0	0.48139988759996	2		519	436	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645786	12645786	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	140	465	0	ENST00000251849.4:c.683C>T	p.Ser228Phe	p.S228F	ENST00000251849	NM_002880.3	228	tCt/tTt	7/17	0.48139988759996	2	FACETS	0.929	0.86	0.999	0.929	0.86	0.999	CLONAL	2	TRUE	0	0.48139988759996	2		465	313	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541457	187541457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	89	500	1	ENST00000441802.2:c.6283G>A	p.Glu2095Lys	p.E2095K	ENST00000441802	NM_005245.3	2095	Gag/Aag	10/27	1	2	FACETS	0.86	0.766	0.959	0.86	0.766	0.959	CLONAL	1	TRUE	1	0.48139988759996	2		501	430	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39074433	39074433	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	80	486	1	ENST00000357387.3:c.47G>A	p.Arg16Gln	p.R16Q	ENST00000357387	NM_152756.3	16	cGa/cAa	1/38	1	2	FACETS	0.87	0.771	0.975	0.87	0.771	0.975	CLONAL	1	TRUE	1	0.48139988759996	2		487	382	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961069	79961069	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	100	527	0	ENST00000265081.6:c.466C>G	p.Leu156Val	p.L156V	ENST00000265081	NM_002439.4	156	Ctg/Gtg	3/24	1	2	FACETS	0.994	0.894	1	0.994	0.894	1	CLONAL	1	TRUE	1	0.48139988759996	2		527	418	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853329	151853329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	77	449	0	ENST00000262189.6:c.11773G>A	p.Glu3925Lys	p.E3925K	ENST00000262189	NM_170606.2	3925	Gaa/Aaa	45/59	0.48139988759996	3	FACETS	0.863	0.76	0.972	0.431	0.38	0.486	CLONAL	1	TRUE	1	0.48139988759996	3		449	460	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002860	69002860	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	79	348	0	ENST00000288368.4:c.2160C>G	p.Ile720Met	p.I720M	ENST00000288368	NM_024870.2	720	atC/atG	20/40	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.48139988759996	2		348	320	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127920583	127920583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754347046	NA	P-0026472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	119	579	1	ENST00000373547.4:c.316C>T	p.Arg106Cys	p.R106C	ENST00000373547	NM_002721.4	106	Cgt/Tgt	4/7	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.48139988759996	2		580	468	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410556	63410556	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	110	643	1	ENST00000330258.3:c.2611C>T	p.Arg871Ter	p.R871*	ENST00000330258	NM_152424.3	871	Cga/Tga	2/2	1	2	FACETS	0.962	0.869	1	0.962	0.869	1	CLONAL	1	TRUE	1	0.48139988759996	2		644	475	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0026473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	343	571	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.528005397943552	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.528005397943552	1		572	903	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	224	501	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	0.528005397943552	2		501	831	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0026473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	238	322	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	0.194401724508491	2	FACETS	1	0.992	1	0.68	0.638	0.722	INDETERMINATE	1	TRUE	0	0.528005397943552	2		322	663	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0026473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	122	410	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.194401724508491	2	FACETS	0.64	0.579	0.704	0.32	0.289	0.352	INDETERMINATE	1	TRUE	0	0.528005397943552	2		410	722	SUCCESS
APC	324	MSKCC	GRCh37	5	112154771	112154771	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1314843920	NA	P-0026473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	160	458	3	ENST00000257430.4:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000257430	NM_000038.5	348	Cga/Tga	10/16	0.194401724508491	2	FACETS	0.719	0.659	0.781	0.359	0.329	0.391	INDETERMINATE	1	TRUE	0	0.528005397943552	2		461	843	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038756	47038756	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	128	634	1	ENST00000377604.3:c.763C>T	p.Gln255Ter	p.Q255*	ENST00000377604	NM_001204468.1	255	Cag/Tag	9/24	0.353283782605196	1	FACETS	0.373	0.337	0.41	0.373	0.337	0.41	SUBCLONAL	1	TRUE	0	0.528005397943552	1		635	957	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692802	89692802	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	150	290	0	ENST00000371953.3:c.286C>A	p.Pro96Thr	p.P96T	ENST00000371953	NM_000314.4	96	Cca/Aca	5/9	0.528005397943552	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.528005397943552	1		290	398	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479807	67479807	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	113	533	1	ENST00000327367.4:c.1114A>T	p.Ile372Phe	p.I372F	ENST00000327367	NM_005902.3	372	Atc/Ttc	8/9	NA	2	FACETS	0.584	0.526	0.646			1	INDETERMINATE	1	TRUE	NA	0.528005397943552	2		534	733	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522720	67522721	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0026473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	214	305	1	ENST00000274335.5:c.218dup	p.Tyr73Ter	p.Y73*	ENST00000274335		73	tac/tAac	1/15	0.274648346131978	1	FACETS	1	0.991	1	1	0.991	1	INDETERMINATE	1	TRUE	0	0.528005397943552	1		306	454	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063389	67063389	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0026475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	331	476	2	ENST00000412916.2:c.78+1G>A		p.X26_splice	ENST00000412916		26			0.924586598050638	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.924586598050638	1		478	377	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115722	8115723	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	288	517	0	ENST00000346208.3:c.1070dup	p.Lys358GlufsTer13	p.K358Efs*13	ENST00000346208		356	-/A	6/6	1	2	FACETS	0.873	0.826	0.92	0.873	0.826	0.92	CLONAL	1	TRUE	1	0.924586598050638	2		517	714	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933833	39933833	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	288	796	1	ENST00000378444.4:c.766C>T	p.His256Tyr	p.H256Y	ENST00000378444	NM_001123385.1	256	Cac/Tac	4/15	0.493667310601512	1	FACETS	0.367	0.346	0.389	0.367	0.346	0.389	INDETERMINATE	1	TRUE	0	0.924586598050638	1		797	912	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934574	NA	P-0026476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	203	684	0	ENST00000269305.4:c.844C>G	p.Arg282Gly	p.R282G	ENST00000269305	NM_001126112.2	282	Cgg/Ggg	8/11	0.414749031773934	1	FACETS	0.942	0.875	1	0.942	0.875	1	CLONAL	1	TRUE	0	0.414749031773934	1		684	824	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158464	26158464	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs916752202	NA	P-0026476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	174	621	0	ENST00000289316.2:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000289316	NM_138720.2	23	Cag/Tag	1/2	0.414749031773934	1	FACETS	0.984	0.909	1	0.984	0.909	1	CLONAL	1	TRUE	0	0.414749031773934	1		621	676	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468219	120468219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1395144495	NA	P-0026476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	116	664	0	ENST00000256646.2:c.4220C>T	p.Ser1407Leu	p.S1407L	ENST00000256646	NM_024408.3	1407	tCg/tTg	25/34	0.202885818613849	1	FACETS	0.582	0.524	0.643	0.582	0.524	0.643	INDETERMINATE	1	TRUE	0	0.414749031773934	1		664	762	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262275	115262275	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	186	594	0	ENST00000438362.2:c.2279G>T	p.Gly760Val	p.G760V	ENST00000438362	NM_001242891.1	760	gGa/gTa	18/20	0.202885818613849	1	FACETS	0.959	0.888	1	0.959	0.888	1	INDETERMINATE	1	TRUE	0	0.414749031773934	1		594	741	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230646	46230646	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	141	463	2	ENST00000334344.6:c.895G>T	p.Glu299Ter	p.E299*	ENST00000334344	NM_152641.2	299	Gag/Tag	8/21	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.414749031773934	2		465	669	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422666	49422666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	197	720	1	ENST00000301067.7:c.14327del	p.Lys4776ArgfsTer21	p.K4776Rfs*21	ENST00000301067	NM_003482.3	4776	aAg/ag	45/54	1	2	FACETS	0.925	0.856	0.997	0.925	0.856	0.997	CLONAL	1	TRUE	1	0.414749031773934	2		721	1027	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112884188	112884188	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	184	597	0	ENST00000351677.2:c.123C>G	p.Phe41Leu	p.F41L	ENST00000351677	NM_002834.3	41	ttC/ttG	2/16	0.401059275459285	1	FACETS	0.978	0.906	1	0.978	0.906	1	CLONAL	1	TRUE	0	0.414749031773934	1		597	719	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825430	134825430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	169	523	2	ENST00000398015.3:c.946G>A	p.Glu316Lys	p.E316K	ENST00000398015	NM_004441.4	316	Gaa/Aaa	4/16	0.414749031773934	3	FACETS	1	0.967	1	0.548	0.504	0.595	CLONAL	1	TRUE	1	0.414749031773934	3		525	897	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20483135	20483135	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1320278537	NA	P-0026476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	134	430	0	ENST00000346618.3:c.868G>C	p.Asp290His	p.D290H	ENST00000346618	NM_001949.4	290	Gat/Cat	4/7	0.414749031773934	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.414749031773934	1		430	494	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683595	162683595	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	118	461	0	ENST00000366898.1:c.374C>A	p.Thr125Asn	p.T125N	ENST00000366898	NM_004562.2	125	aCt/aAt	3/12	0.414749031773934	1	FACETS	0.942	0.854	1	0.942	0.854	1	CLONAL	1	TRUE	0	0.414749031773934	1		461	479	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034436	123034436	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs770431804	NA	P-0026476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	53	591	0	ENST00000355640.3:c.1193A>G	p.Gln398Arg	p.Q398R	ENST00000355640		398	cAg/cGg	6/7	0.173785688343739	3	FACETS	0.403	0.343	0.47			1	INDETERMINATE	1	TRUE	NA	0.414749031773934	3		591	765	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152864447	152864447	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	34	176	0	ENST00000406277.2:c.79C>G	p.Arg27Gly	p.R27G	ENST00000406277	NM_152274.4	27	Cga/Gga	3/7	NA		FACETS		NA	1				INDETERMINATE	NA	TRUE	NA	0.414749031773934	NA		176	193	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0026477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	143	591	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.863	0.786	0.945	0.863	0.786	0.945	CLONAL	1	TRUE	1	0.318506067483411	2		591	1040	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0026477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	252	326	2	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.231435364125118	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.318506067483411	3		328	783	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0026478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	162	388	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.144932505282537	3	FACETS	1	0.943	1	1	0.943	1	INDETERMINATE	2	TRUE	1	0.356277347357482	3		388	523	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618899	37618899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759887608	NA	P-0026478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	119	677	1	ENST00000447079.4:c.575C>T	p.Ser192Phe	p.S192F	ENST00000447079	NM_015083.1	192	tCt/tTt	1/14	0.208248640179057	1	FACETS	0.44	0.396	0.487	0.44	0.396	0.487	INDETERMINATE	1	TRUE	0	0.356277347357482	1		678	1247	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087939	27087940	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAATCAA	novel	NA	P-0026478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	195	677	0	ENST00000324856.7:c.2227_2233dup	p.Ser745ThrfsTer74	p.S745Tfs*74	ENST00000324856	NM_006015.4	742	-/CAATCAA	6/20	0.208248640179057	1	FACETS	0.876	0.81	0.944	0.876	0.81	0.944	INDETERMINATE	1	TRUE	0	0.356277347357482	1		677	1027	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106285	27106331	+	frameshift_variant	Frame_Shift_Del	DEL	CCACTGTGTACCCTTCTGGACTGGCAGGATTCTCTTGCCAAGCGCTG	CCACTGTGTACCCTTCTGGACTGGCAGGATTCTCTTGCCAAGCGCTG	-	novel	NA	P-0026478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	79	676	0	ENST00000324856.7:c.5897_5943del	p.Pro1966ArgfsTer17	p.P1966Rfs*17	ENST00000324856	NM_006015.4	1966	CCACTGTGTACCCTTCTGGACTGGCAGGATTCTCTTGCCAAGCGCTGc/c	20/20	0.208248640179057	1	FACETS	0.359	0.315	0.407	0.359	0.315	0.407	INDETERMINATE	1	TRUE	0	0.356277347357482	1		676	1015	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216546	108216546	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs529296539	NA	P-0026478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	81	421	1	ENST00000278616.4:c.8495G>T	p.Arg2832Leu	p.R2832L	ENST00000278616	NM_000051.3	2832	cGt/cTt	58/63	0.356277347357482	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.356277347357482	1		422	292	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569750	95569750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	82	305	0	ENST00000393063.1:c.3983C>T	p.Thr1328Ile	p.T1328I	ENST00000393063	NM_030621.3	1328	aCc/aTc	22/28	1	2	FACETS	0.892	0.789	1	0.892	0.789	1	CLONAL	1	TRUE	1	0.356277347357482	2		305	516	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223817	2223817	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	253	747	0	ENST00000326181.6:c.1115T>G	p.Leu372Arg	p.L372R	ENST00000326181	NM_032271.2	372	cTg/cGg	12/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.356277347357482	2		747	1310	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106194031	106194031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777027345	NA	P-0026478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	130	406	0	ENST00000380013.4:c.4493G>A	p.Arg1498His	p.R1498H	ENST00000380013	NM_001127208.2	1498	cGt/cAt	10/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.356277347357482	2		406	694	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	58	501	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.305	0.261	0.352	0.305	0.261	0.352	SUBCLONAL	1	TRUE	1	0.534996396437812	2		501	712	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	109	460	3	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	NA	3	FACETS	0.709	0.637	0.786			1	INDETERMINATE	1	TRUE	NA	0.534996396437812	3		463	728	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088788	27088788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	135	519	0	ENST00000324856.7:c.2402del	p.Gly801ValfsTer32	p.G801Vfs*32	ENST00000324856	NM_006015.4	799	caG/ca	7/20	1	2	FACETS	0.609	0.553	0.667	0.609	0.553	0.667	SUBCLONAL	1	TRUE	1	0.534996396437812	2		519	829	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	108	440	2	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.541	0.486	0.6	0.541	0.486	0.6	SUBCLONAL	1	TRUE	1	0.534996396437812	2		442	746	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	81	277	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.57	0.503	0.642	0.57	0.503	0.642	SUBCLONAL	1	TRUE	1	0.534996396437812	2		277	531	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	77	333	1	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	1	2	FACETS	0.535	0.47	0.604	0.535	0.47	0.604	SUBCLONAL	1	TRUE	1	0.534996396437812	2		334	538	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	69	417	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.334	0.29	0.382	0.334	0.29	0.382	SUBCLONAL	1	TRUE	1	0.534996396437812	2		417	772	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007834	45007834	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	66	455	0	ENST00000558401.1:c.285del	p.Asp96MetfsTer7	p.D96Mfs*7	ENST00000558401	NM_004048.2	94	gAa/ga	2/4	1	2	FACETS	0.299	0.259	0.343	0.299	0.259	0.343	SUBCLONAL	1	TRUE	1	0.534996396437812	2		455	824	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	27	146	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	0.367	0.293	0.452	0.367	0.293	0.452	SUBCLONAL	1	TRUE	1	0.534996396437812	2		146	275	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	255	689	2	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	1	2	FACETS	0.785	0.734	0.838	0.785	0.734	0.838	SUBCLONAL	1	TRUE	1	0.534996396437812	2		691	1214	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	199	699	1	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.669	0.619	0.721	0.669	0.619	0.721	SUBCLONAL	1	TRUE	1	0.534996396437812	2		700	1112	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022443	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	rs750318549	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	59	232	0	ENST00000375687.4:c.1933_1934del	p.Gly645TrpfsTer12	p.G645Wfs*12	ENST00000375687	NM_015338.5	643	GGg/g	13/13	NA	2	FACETS	0.675	0.584	0.772			1	INDETERMINATE	1	TRUE	NA	0.534996396437812	2		232	327	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354008	15354008	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	39	193	3	ENST00000263377.2:c.2872del	p.Leu958CysfsTer110	p.L958Cfs*110	ENST00000263377	NM_058243.2	958	Ctg/tg	14/20	1	2	FACETS	0.451	0.375	0.536	0.451	0.375	0.536	SUBCLONAL	1	TRUE	1	0.534996396437812	2		196	323	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724626	162724626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879065950	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	128	435	0	ENST00000367921.3:c.398G>A	p.Arg133Gln	p.R133Q	ENST00000367921	NM_006182.2	133	cGg/cAg	5/18	1	2	FACETS	0.657	0.596	0.721	0.657	0.596	0.721	SUBCLONAL	1	TRUE	1	0.534996396437812	2		435	728	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023769	27023769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	66	415	0	ENST00000324856.7:c.879del	p.Thr294ProfsTer69	p.T294Pfs*69	ENST00000324856	NM_006015.4	292	aCc/ac	1/20	1	2	FACETS	0.38	0.33	0.435	0.38	0.33	0.435	SUBCLONAL	1	TRUE	1	0.534996396437812	2		415	649	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852118	63852118	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	159	548	0	ENST00000279873.7:c.2901del	p.Lys967AsnfsTer15	p.K967Nfs*15	ENST00000279873	NM_032199.2	966	Aaa/aa	10/10	1	2	FACETS	0.682	0.626	0.742	0.682	0.626	0.742	SUBCLONAL	1	TRUE	1	0.534996396437812	2		548	871	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964077	28964077	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1565998842	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	41	439	0	ENST00000282397.4:c.1825del	p.Met609TrpfsTer16	p.M609Wfs*16	ENST00000282397	NM_002019.4	609	Atg/tg	13/30	1	2	FACETS	0.208	0.173	0.248	0.208	0.173	0.248	SUBCLONAL	1	TRUE	1	0.534996396437812	2		439	736	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781141	135781141	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs118203585	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	137	679	0	ENST00000298552.3:c.1824del	p.Phe608LeufsTer21	p.F608Lfs*21	ENST00000298552	NM_001162426.1	608	ttT/tt	15/23	1	2	FACETS	0.589	0.535	0.645	0.589	0.535	0.645	SUBCLONAL	1	TRUE	1	0.534996396437812	2		679	870	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690848	89690848	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1224040268	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	36	351	0	ENST00000371953.3:c.253+2T>C		p.X85_splice	ENST00000371953	NM_000314.4	85			1	2	FACETS	0.261	0.214	0.314	0.261	0.214	0.314	SUBCLONAL	1	TRUE	1	0.534996396437812	2		351	515	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149634	202149635	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	114	466	0	ENST00000358485.4:c.1077dup	p.Leu360ThrfsTer6	p.L360Tfs*6	ENST00000358485	NM_001080125.1	359	caa/cAaa	8/9	1	2	FACETS	0.598	0.538	0.66	0.598	0.538	0.66	SUBCLONAL	1	TRUE	1	0.534996396437812	2		466	713	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120031	70120031	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	34	62	0	ENST00000245479.2:c.1037del	p.Pro346ArgfsTer37	p.P346Rfs*37	ENST00000245479	NM_000346.3	345	Ccc/cc	3/3	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.534996396437812	2		62	123	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750681	128750681	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756091827	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	165	547	0	ENST00000377970.2:c.218C>T	p.Thr73Ile	p.T73I	ENST00000377970	NM_002467.4	73	aCc/aTc	2/3	1	2	FACETS	0.796	0.732	0.862	0.796	0.732	0.862	SUBCLONAL	1	TRUE	1	0.534996396437812	2		547	775	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412266	139412266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776258761	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	247	679	0	ENST00000277541.6:c.1379C>T	p.Pro460Leu	p.P460L	ENST00000277541	NM_017617.3	460	cCg/cTg	8/34	1	2	FACETS	0.712	0.665	0.762	0.712	0.665	0.762	SUBCLONAL	1	TRUE	1	0.534996396437812	2		679	1296	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212403	5212403	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs558410776	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	169	685	3	ENST00000357368.4:c.4714C>T	p.Arg1572Trp	p.R1572W	ENST00000357368	NM_002850.3	1572	Cgg/Tgg	31/38	1	2	FACETS	0.579	0.531	0.629	0.579	0.531	0.629	SUBCLONAL	1	TRUE	1	0.534996396437812	2		688	1091	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156729	106156729	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1440692352	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	199	400	1	ENST00000380013.4:c.1630C>T	p.Arg544Ter	p.R544*	ENST00000380013	NM_001127208.2	544	Cga/Tga	3/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.534996396437812	2		401	729	SUCCESS
ATR	545	MSKCC	GRCh37	3	142204114	142204114	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755650081	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	57	521	1	ENST00000350721.4:c.6089C>T	p.Ala2030Val	p.A2030V	ENST00000350721	NM_001184.3	2030	gCg/gTg	36/47	1	2	FACETS	0.295	0.252	0.341	0.295	0.252	0.341	SUBCLONAL	1	TRUE	1	0.534996396437812	2		522	723	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830204	72830204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752051101	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	79	381	0	ENST00000268489.5:c.6377C>T	p.Ala2126Val	p.A2126V	ENST00000268489	NM_006885.3	2126	gCg/gTg	9/10	1	2	FACETS	0.548	0.483	0.618	0.548	0.483	0.618	SUBCLONAL	1	TRUE	1	0.534996396437812	2		381	539	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270726	10270726	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	157	491	2	ENST00000340748.4:c.1009del	p.Met337TrpfsTer8	p.M337Wfs*8	ENST00000340748		337	Atg/tg	14/40	1	2	FACETS	0.668	0.612	0.726	0.668	0.612	0.726	SUBCLONAL	1	TRUE	1	0.534996396437812	2		493	879	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522741	67522741	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	61	332	2	ENST00000274335.5:c.244del	p.Ile82SerfsTer32	p.I82Sfs*32	ENST00000274335		80	Aaa/aa	1/15	1	2	FACETS	0.446	0.385	0.512	0.446	0.385	0.512	SUBCLONAL	1	TRUE	1	0.534996396437812	2		334	511	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	62	414	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	0.327	0.282	0.376	0.327	0.282	0.376	SUBCLONAL	1	TRUE	1	0.534996396437812	2		414	709	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	195	666	2	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	1	2	FACETS	0.605	0.559	0.654	0.605	0.559	0.654	SUBCLONAL	1	TRUE	1	0.534996396437812	2		668	1204	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800902	120800903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs748469666	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	324	645	4	ENST00000257552.2:c.345dup	p.Leu116AlafsTer15	p.L116Afs*15	ENST00000257552	NM_002442.3	115	-/G	6/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.534996396437812	2		649	1175	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434972	110434973	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	198	662	2	ENST00000375856.3:c.3428dup	p.Arg1144ProfsTer181	p.R1144Pfs*181	ENST00000375856	NM_003749.2	1143	ggc/ggGc	1/2	1	2	FACETS	0.641	0.593	0.692	0.641	0.593	0.692	SUBCLONAL	1	TRUE	1	0.534996396437812	2		664	1154	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37680930	37680930	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	46	343	0	ENST00000447079.4:c.3103del	p.His1035ThrfsTer22	p.H1035Tfs*22	ENST00000447079	NM_015083.1	1033	ctC/ct	12/14	1	2	FACETS	0.319	0.268	0.375	0.319	0.268	0.375	SUBCLONAL	1	TRUE	1	0.534996396437812	2		343	539	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573966	7573966	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs752142489	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	95	643	0	ENST00000269305.4:c.1061A>G	p.Gln354Arg	p.Q354R	ENST00000269305	NM_001126112.2	354	cAg/cGg	10/11	1	2	FACETS	0.334	0.296	0.374	0.334	0.296	0.374	SUBCLONAL	1	TRUE	1	0.534996396437812	2		643	1063	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214728	36214728	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	77	402	1	ENST00000222270.7:c.3159del	p.Arg1055GlyfsTer127	p.R1055Gfs*127	ENST00000222270	NM_014727.1	1052	Ggg/gg	8/37	1	2	FACETS	0.482	0.423	0.545	0.482	0.423	0.545	SUBCLONAL	1	TRUE	1	0.534996396437812	2		403	597	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030582	47030582	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs868917893	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	165	311	4	ENST00000377604.3:c.357G>T	p.Glu119Asp	p.E119D	ENST00000377604	NM_001204468.1	119	gaG/gaT	4/24	1	1	FACETS	0.891	0.824	0.96	0.891	0.824	0.96	CLONAL	1	TRUE	0	0.534996396437812	1		315	507	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620657	52620657	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	92	393	0	ENST00000394830.3:c.3096del	p.Phe1032LeufsTer102	p.F1032Lfs*102	ENST00000394830	NM_018313.4	1032	ttT/tt	21/30	0.534996396437812	2	FACETS	0.437	0.388	0.49	0.219	0.194	0.245	SUBCLONAL	1	TRUE	0	0.534996396437812	2		393	787	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717719	89717720	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs780264945	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	133	404	0	ENST00000371953.3:c.750_751del	p.Cys250TrpfsTer2	p.C250Wfs*2	ENST00000371953	NM_000314.4	248	ccTGtg/cctg	7/9	1	2	FACETS	0.717	0.653	0.785	0.717	0.653	0.785	SUBCLONAL	1	TRUE	1	0.534996396437812	2		404	693	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778549	3778549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	203	597	0	ENST00000262367.5:c.6499del	p.Gln2167ArgfsTer5	p.Q2167Rfs*5	ENST00000262367	NM_004380.2	2167	Cag/ag	31/31	1	2	FACETS	0.744	0.69	0.801	0.744	0.69	0.801	SUBCLONAL	1	TRUE	1	0.534996396437812	2		597	1020	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998275	100998275	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	52	226	0	ENST00000325455.5:c.1527del	p.Ala510ArgfsTer36	p.A510Rfs*36	ENST00000325455	NM_001202474.3	509	ccC/cc	1/8	1	2	FACETS	0.613	0.525	0.709	0.613	0.525	0.709	SUBCLONAL	1	TRUE	1	0.534996396437812	2		226	317	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602745	10602745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1040740503	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1173	92	663	2	ENST00000171111.5:c.833C>T	p.Pro278Leu	p.P278L	ENST00000171111	NM_203500.1	278	cCg/cTg	3/6	1	2	FACETS	0.272	0.24	0.306	0.272	0.24	0.306	SUBCLONAL	1	TRUE	1	0.534996396437812	2		665	1265	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294297	11294297	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	163	524	0	ENST00000361445.4:c.2234G>T	p.Gly745Val	p.G745V	ENST00000361445	NM_004958.3	745	gGg/gTg	14/58	1	2	FACETS	0.747	0.686	0.81	0.747	0.686	0.81	SUBCLONAL	1	TRUE	1	0.534996396437812	2		524	816	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885719	23885719	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	158	546	0	ENST00000374561.5:c.199G>C	p.Val67Leu	p.V67L	ENST00000374561	NM_002167.4	67	Gtg/Ctg	1/3	1	2	FACETS	0.625	0.572	0.68	0.625	0.572	0.68	SUBCLONAL	1	TRUE	1	0.534996396437812	2		546	945	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256455	115256455	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	143	484	0	ENST00000369535.4:c.256A>G	p.Asn86Asp	p.N86D	ENST00000369535	NM_002524.4	86	Aat/Gat	3/7	1	2	FACETS	0.719	0.657	0.785	0.719	0.657	0.785	SUBCLONAL	1	TRUE	1	0.534996396437812	2		484	743	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458973	120458973	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	97	622	0	ENST00000256646.2:c.6372G>T	p.Lys2124Asn	p.K2124N	ENST00000256646	NM_024408.3	2124	aaG/aaT	34/34	1	2	FACETS	0.394	0.351	0.441	0.394	0.351	0.441	SUBCLONAL	1	TRUE	1	0.534996396437812	2		622	920	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054993	176054993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	113	615	0	ENST00000367669.3:c.1060G>A	p.Ala354Thr	p.A354T	ENST00000367669	NM_022457.5	354	Gca/Aca	10/20	1	2	FACETS	0.501	0.45	0.555	0.501	0.45	0.555	SUBCLONAL	1	TRUE	1	0.534996396437812	2		615	843	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727061	243727061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	77	477	0	ENST00000263826.5:c.909G>A	p.Met303Ile	p.M303I	ENST00000263826	NM_005465.4	303	atG/atA	9/13	1	2	FACETS	0.435	0.382	0.493	0.435	0.382	0.493	SUBCLONAL	1	TRUE	1	0.534996396437812	2		477	661	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852409	63852409	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	210	509	0	ENST00000279873.7:c.3191del	p.Gly1064AlafsTer43	p.G1064Afs*43	ENST00000279873	NM_032199.2	1063	Ggg/gg	10/10	1	2	FACETS	0.917	0.853	0.983	0.917	0.853	0.983	CLONAL	1	TRUE	1	0.534996396437812	2		509	856	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405601	70405601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1312926475	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	194	504	0	ENST00000373644.4:c.3115C>T	p.Pro1039Ser	p.P1039S	ENST00000373644	NM_030625.2	1039	Cca/Tca	4/12	1	2	FACETS	0.916	0.849	0.985	0.916	0.849	0.985	CLONAL	1	TRUE	1	0.534996396437812	2		504	792	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129438	64129438	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	198	671	3	ENST00000334205.4:c.874del	p.Ala292HisfsTer83	p.A292Hfs*83	ENST00000334205	NM_003942.2	290	caG/ca	8/17	1	2	FACETS	0.687	0.636	0.741	0.687	0.636	0.741	SUBCLONAL	1	TRUE	1	0.534996396437812	2		674	1077	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201754	102201754	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	30	434	0	ENST00000263464.3:c.1106A>G	p.Asp369Gly	p.D369G	ENST00000263464	NM_001165.4	369	gAc/gGc	6/9	1	2	FACETS	0.2	0.161	0.245	0.2	0.161	0.245	SUBCLONAL	1	TRUE	1	0.534996396437812	2		434	560	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431249	49431249	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	58	500	0	ENST00000301067.7:c.9890T>C	p.Leu3297Ser	p.L3297S	ENST00000301067	NM_003482.3	3297	tTg/tCg	34/54	1	2	FACETS	0.274	0.234	0.317	0.274	0.234	0.317	SUBCLONAL	1	TRUE	1	0.534996396437812	2		500	792	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28897047	28897047	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	44	418	3	ENST00000282397.4:c.2833del	p.Met945TrpfsTer13	p.M945Wfs*13	ENST00000282397	NM_002019.4	945	Atg/tg	21/30	1	2	FACETS	0.223	0.186	0.264	0.223	0.186	0.264	SUBCLONAL	1	TRUE	1	0.534996396437812	2		421	737	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007719	45007720	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	195	373	2	ENST00000558401.1:c.168dup	p.Val57SerfsTer2	p.V57Sfs*2	ENST00000558401	NM_004048.2	56	gaa/gAaa	2/4	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.534996396437812	2		375	659	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73991987	73991987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770116040	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	53	511	0	ENST00000318443.5:c.7C>T	p.Arg3Cys	p.R3C	ENST00000318443	NM_001024736.1	3	Cgt/Tgt	2/10	0.291251655836663	2	FACETS	0.209	0.177	0.244	0.105	0.088	0.122	INDETERMINATE	1	TRUE	0	0.534996396437812	2		511	948	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647641	3647641	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	187	640	0	ENST00000294008.3:c.1422G>T	p.Gln474His	p.Q474H	ENST00000294008	NM_032444.2	474	caG/caT	7/15	1	2	FACETS	0.579	0.534	0.627	0.579	0.534	0.627	SUBCLONAL	1	TRUE	1	0.534996396437812	2		640	1207	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853329	68853329	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs886041161	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	49	515	0	ENST00000261769.5:c.1711+1G>A		p.X571_splice	ENST00000261769	NM_004360.3	571			1	2	FACETS	0.23	0.194	0.27	0.23	0.194	0.27	SUBCLONAL	1	TRUE	1	0.534996396437812	2		515	795	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867346	68867347	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	258	449	0	ENST00000261769.5:c.2597dup	p.Asn867GlnfsTer8	p.N867Qfs*8	ENST00000261769	NM_004360.3	865	tgg/tGgg	16/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.534996396437812	2		449	888	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881619	37881619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375135008	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	190	613	1	ENST00000269571.5:c.2689C>T	p.Arg897Trp	p.R897W	ENST00000269571		897	Cgg/Tgg	22/27	1	2	FACETS	0.65	0.6	0.702	0.65	0.6	0.702	SUBCLONAL	1	TRUE	1	0.534996396437812	2		614	1092	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40364151	40364151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	53	265	0	ENST00000293328.3:c.1531C>T	p.Leu511Phe	p.L511F	ENST00000293328	NM_012448.3	511	Ctc/Ttc	13/19	1	2	FACETS	0.48	0.41	0.556	0.48	0.41	0.556	SUBCLONAL	1	TRUE	1	0.534996396437812	2		265	413	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40864314	40864314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	50	468	0	ENST00000428826.2:c.1394G>A	p.Cys465Tyr	p.C465Y	ENST00000428826		465	tGc/tAc	12/21	1	2	FACETS	0.224	0.189	0.263	0.224	0.189	0.263	SUBCLONAL	1	TRUE	1	0.534996396437812	2		468	834	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243466	41243466	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs763596987	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	162	567	0	ENST00000357654.3:c.4082T>C	p.Met1361Thr	p.M1361T	ENST00000357654	NM_007294.3	1361	aTg/aCg	10/23	1	2	FACETS	0.608	0.557	0.661	0.608	0.557	0.661	SUBCLONAL	1	TRUE	1	0.534996396437812	2		567	996	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774173	56774173	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1192165096	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	180	501	0	ENST00000337432.4:c.524C>T	p.Ala175Val	p.A175V	ENST00000337432	NM_058216.2	175	gCc/gTc	3/9	1	2	FACETS	0.903	0.835	0.974	0.903	0.835	0.974	CLONAL	1	TRUE	1	0.534996396437812	2		501	745	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677989	58677989	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	65	224	0	ENST00000305921.3:c.214G>A	p.Ala72Thr	p.A72T	ENST00000305921	NM_003620.3	72	Gcc/Acc	1/6	1	2	FACETS	0.759	0.663	0.862	0.759	0.663	0.862	SUBCLONAL	1	TRUE	1	0.534996396437812	2		224	320	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39647427	39647427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	75	495	1	ENST00000262039.4:c.2599G>A	p.Val867Ile	p.V867I	ENST00000262039	NM_002647.2	867	Gtc/Atc	24/25	1	2	FACETS	0.333	0.291	0.378	0.333	0.291	0.378	SUBCLONAL	1	TRUE	1	0.534996396437812	2		496	843	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223024	1223024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	166	612	0	ENST00000326873.7:c.961C>T	p.Pro321Ser	p.P321S	ENST00000326873	NM_000455.4	321	Ccc/Tcc	8/10	1	2	FACETS	0.587	0.538	0.638	0.587	0.538	0.638	SUBCLONAL	1	TRUE	1	0.534996396437812	2		612	1057	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117481	4117481	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142271248	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	177	360	0	ENST00000262948.5:c.239C>T	p.Ala80Val	p.A80V	ENST00000262948	NM_030662.3	80	gCg/gTg	2/11	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.534996396437812	2		360	659	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231341	5231341	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	46	559	0	ENST00000357368.4:c.2135T>C	p.Val712Ala	p.V712A	ENST00000357368	NM_002850.3	712	gTc/gCc	14/38	1	2	FACETS	0.191	0.16	0.226	0.191	0.16	0.226	SUBCLONAL	1	TRUE	1	0.534996396437812	2		559	899	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349778	15349778	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199833114	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	166	596	1	ENST00000263377.2:c.3796G>A	p.Glu1266Lys	p.E1266K	ENST00000263377	NM_058243.2	1266	Gag/Aag	19/20	1	2	FACETS	0.684	0.628	0.742	0.684	0.628	0.742	SUBCLONAL	1	TRUE	1	0.534996396437812	2		597	907	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905182	50905182	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	223	707	0	ENST00000440232.2:c.463+1G>A		p.X155_splice	ENST00000440232	NM_002691.3	155			1	2	FACETS	0.717	0.667	0.77	0.717	0.667	0.77	SUBCLONAL	1	TRUE	1	0.534996396437812	2		707	1162	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250173	39250173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	71	666	0	ENST00000402219.2:c.1396G>A	p.Gly466Ser	p.G466S	ENST00000402219	NM_005633.3	466	Ggc/Agc	10/23	1	2	FACETS	0.292	0.254	0.334	0.292	0.254	0.334	SUBCLONAL	1	TRUE	1	0.534996396437812	2		666	908	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46583903	46583903	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	161	573	1	ENST00000263734.3:c.410C>A	p.Pro137His	p.P137H	ENST00000263734	NM_001430.4	137	cCc/cAc	4/16	1	2	FACETS	0.677	0.621	0.736	0.677	0.621	0.736	SUBCLONAL	1	TRUE	1	0.534996396437812	2		574	889	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385209	41385209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	53	587	0	ENST00000373198.4:c.752C>T	p.Thr251Ile	p.T251I	ENST00000373198	NM_133170.3	251	aCa/aTa	6/32	1	2	FACETS	0.215	0.182	0.251	0.215	0.182	0.251	SUBCLONAL	1	TRUE	1	0.534996396437812	2		587	923	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281255	46281255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	136	433	0	ENST00000371998.3:c.4052C>A	p.Pro1351Gln	p.P1351Q	ENST00000371998		1351	cCg/cAg	21/23	1	2	FACETS	0.716	0.652	0.783	0.716	0.652	0.783	SUBCLONAL	1	TRUE	1	0.534996396437812	2		433	710	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655328	45655328	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776339033	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1227	120	750	0	ENST00000407780.3:c.524C>T	p.Thr175Met	p.T175M	ENST00000407780	NM_001283052.1	175	aCg/aTg	4/7	1	2	FACETS	0.333	0.299	0.369	0.333	0.299	0.369	SUBCLONAL	1	TRUE	1	0.534996396437812	2		750	1347	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732946	30732946	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	48	265	0	ENST00000295754.5:c.1559G>A	p.Cys520Tyr	p.C520Y	ENST00000295754	NM_003242.5	520	tGc/tAc	7/7	0.534996396437812	2	FACETS	0.313	0.264	0.367	0.157	0.132	0.184	SUBCLONAL	1	TRUE	0	0.534996396437812	2		265	573	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37061907	37061907	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	364	409	0	ENST00000231790.2:c.991G>T	p.Glu331Ter	p.E331*	ENST00000231790	NM_000249.3	331	Gag/Tag	11/19	0.534996396437812	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.534996396437812	2		409	647	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265882	41266241	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAG	CTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAG	-	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	10	25	0	ENST00000349496.5:c.14-132_241del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.534996396437812	2	FACETS	1	0.844	1	0.668	0.479	0.874	CLONAL	1	TRUE	0	0.534996396437812	2		25	28	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267044	41267044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	54	412	0	ENST00000349496.5:c.715G>A	p.Ala239Thr	p.A239T	ENST00000349496	NM_001904.3	239	Gcc/Acc	5/15	0.534996396437812	2	FACETS	0.324	0.276	0.376	0.162	0.138	0.188	SUBCLONAL	1	TRUE	0	0.534996396437812	2		412	623	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119545639	119545639	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	119	339	0	ENST00000316626.5:c.1298C>T	p.Thr433Ile	p.T433I	ENST00000316626		433	aCc/aTc	12/12	1	2	FACETS	0.649	0.587	0.715	0.649	0.587	0.715	SUBCLONAL	1	TRUE	1	0.534996396437812	2		339	685	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188297	142188297	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	121	494	0	ENST00000350721.4:c.6434T>C	p.Leu2145Ser	p.L2145S	ENST00000350721	NM_001184.3	2145	tTg/tCg	38/47	1	2	FACETS	0.739	0.669	0.812	0.739	0.669	0.812	SUBCLONAL	1	TRUE	1	0.534996396437812	2		494	612	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268428	142268431	+	frameshift_variant	Frame_Shift_Del	DEL	TTAA	TTAA	-	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	193	458	0	ENST00000350721.4:c.3061_3064del	p.Leu1021MetfsTer8	p.L1021Mfs*8	ENST00000350721	NM_001184.3	1021	TTAAat/at	15/47	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.534996396437812	2		458	711	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981462	55981462	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs545112274	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	42	453	0	ENST00000263923.4:c.475G>C	p.Val159Leu	p.V159L	ENST00000263923	NM_002253.2	159	Gtg/Ctg	4/30	1	2	FACETS	0.24	0.199	0.285	0.24	0.199	0.285	SUBCLONAL	1	TRUE	1	0.534996396437812	2		453	655	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332916	153332916	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1362274408	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	44	361	0	ENST00000281708.4:c.40C>T	p.Arg14Ter	p.R14*	ENST00000281708	NM_033632.3	14	Cga/Tga	2/12	1	2	FACETS	0.263	0.22	0.311	0.263	0.22	0.311	SUBCLONAL	1	TRUE	1	0.534996396437812	2		361	626	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629828	187629828	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	298	647	1	ENST00000441802.2:c.1154C>A	p.Pro385His	p.P385H	ENST00000441802	NM_005245.3	385	cCt/cAt	2/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.534996396437812	2		648	1027	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161222	56161222	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	107	466	4	ENST00000399503.3:c.1091G>T	p.Arg364Leu	p.R364L	ENST00000399503	NM_005921.1	364	cGg/cTg	5/20	1	2	FACETS	0.556	0.498	0.616	0.556	0.498	0.616	SUBCLONAL	1	TRUE	1	0.534996396437812	2		470	720	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518025	176518025	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775590700	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	209	634	0	ENST00000292408.4:c.523G>A	p.Ala175Thr	p.A175T	ENST00000292408	NM_213647.1	175	Gca/Aca	5/18	1	2	FACETS	0.719	0.667	0.774	0.719	0.667	0.774	SUBCLONAL	1	TRUE	1	0.534996396437812	2		634	1086	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20486919	20486919	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs376318599	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	77	329	0	ENST00000346618.3:c.885-1C>T		p.X295_splice	ENST00000346618	NM_001949.4	295			1	2	FACETS	0.612	0.539	0.691	0.612	0.539	0.691	SUBCLONAL	1	TRUE	1	0.534996396437812	2		329	470	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163855	32163855	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	54	450	0	ENST00000375023.3:c.5371del	p.Ala1791GlnfsTer11	p.A1791Qfs*11	ENST00000375023	NM_004557.3	1791	Gca/ca	30/30	1	2	FACETS	0.282	0.24	0.328	0.282	0.24	0.328	SUBCLONAL	1	TRUE	1	0.534996396437812	2		450	715	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181578	32181578	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	215	632	0	ENST00000375023.3:c.2207G>T	p.Gly736Val	p.G736V	ENST00000375023	NM_004557.3	736	gGg/gTg	14/30	1	2	FACETS	0.755	0.702	0.811	0.755	0.702	0.811	SUBCLONAL	1	TRUE	1	0.534996396437812	2		632	1064	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026806	6026806	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	27	212	0	ENST00000265849.7:c.1590G>T	p.Gln530His	p.Q530H	ENST00000265849	NM_000535.5	530	caG/caT	11/15	1	2	FACETS	0.258	0.205	0.319	0.258	0.205	0.319	SUBCLONAL	1	TRUE	1	0.534996396437812	2		212	391	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508553	106508553	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	75	300	0	ENST00000359195.3:c.547C>A	p.Pro183Thr	p.P183T	ENST00000359195	NM_002649.2	183	Ccg/Acg	2/11	1	2	FACETS	0.663	0.583	0.748	0.663	0.583	0.748	SUBCLONAL	1	TRUE	1	0.534996396437812	2		300	423	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860135	151860135	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	111	450	1	ENST00000262189.6:c.10527G>T	p.Gln3509His	p.Q3509H	ENST00000262189	NM_170606.2	3509	caG/caT	43/59	1	2	FACETS	0.592	0.532	0.655	0.592	0.532	0.655	SUBCLONAL	1	TRUE	1	0.534996396437812	2		451	701	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021821	69021821	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	170	606	0	ENST00000288368.4:c.3109C>G	p.Leu1037Val	p.L1037V	ENST00000288368	NM_024870.2	1037	Ctg/Gtg	25/40	1	2	FACETS	0.672	0.618	0.728	0.672	0.618	0.728	SUBCLONAL	1	TRUE	1	0.534996396437812	2		606	946	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028026	69028026	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775893443	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	73	519	0	ENST00000288368.4:c.3185G>A	p.Arg1062His	p.R1062H	ENST00000288368	NM_024870.2	1062	cGt/cAt	26/40	1	2	FACETS	0.392	0.342	0.446	0.392	0.342	0.446	SUBCLONAL	1	TRUE	1	0.534996396437812	2		519	696	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430544	80430544	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	112	551	0	ENST00000286548.4:c.464A>G	p.Asp155Gly	p.D155G	ENST00000286548	NM_002072.3	155	gAc/gGc	3/7	1	2	FACETS	0.582	0.524	0.644	0.582	0.524	0.644	SUBCLONAL	1	TRUE	1	0.534996396437812	2		551	719	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209369	98209369	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	51	524	0	ENST00000331920.6:c.4169G>T	p.Gly1390Val	p.G1390V	ENST00000331920	NM_000264.3	1390	gGg/gTg	23/24	1	2	FACETS	0.269	0.228	0.315	0.269	0.228	0.315	SUBCLONAL	1	TRUE	1	0.534996396437812	2		524	708	SUCCESS
AR	367	MSKCC	GRCh37	X	66905911	66905911	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	22	237	0	ENST00000374690.3:c.1832del	p.Asn611IlefsTer15	p.N611Ifs*15	ENST00000374690	NM_000044.3	610	Aaa/aa	3/8	1	1	FACETS	0.176	0.136	0.223	0.176	0.136	0.223	SUBCLONAL	1	TRUE	0	0.534996396437812	1		237	342	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183764	10183764	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs5030804	NA	P-0026483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	294	676	0	ENST00000256474.2:c.233A>G	p.Asn78Ser	p.N78S	ENST00000256474	NM_000551.3	78	aAt/aGt	1/3	0.665891452171195	1	FACETS	0.878	0.832	0.924	0.878	0.832	0.924	CLONAL	1	TRUE	0	0.665891452171195	1		676	671	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11177096	11177096	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	84	555	0	ENST00000361445.4:c.6981G>C	p.Met2327Ile	p.M2327I	ENST00000361445	NM_004958.3	2327	atG/atC	50/58	1	2	FACETS	0.684	0.608	0.763	0.684	0.608	0.763	SUBCLONAL	1	TRUE	1	0.665891452171195	2		555	369	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643921	52643921	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	84	393	0	ENST00000394830.3:c.1975C>T	p.Gln659Ter	p.Q659*	ENST00000394830	NM_018313.4	659	Cag/Tag	17/30	0.665891452171195	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.665891452171195	1		393	155	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542155	187542155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	86	394	0	ENST00000441802.2:c.5585C>A	p.Ala1862Glu	p.A1862E	ENST00000441802	NM_005245.3	1862	gCa/gAa	10/27	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.665891452171195	2		394	255	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0026484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	255	471	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.408479246204939	2	FACETS	0.867	0.816	0.919	0.867	0.816	0.919	CLONAL	2	TRUE	0	0.408479246204939	2		472	720	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0026484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	102	611	5	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	0.356865091626957	3	FACETS	0.922	0.826	1	0.461	0.413	0.513	CLONAL	1	TRUE	1	0.408479246204939	3		616	652	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916706	178916706	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	25	380	0	ENST00000263967.3:c.93A>G	p.Ile31Met	p.I31M	ENST00000263967	NM_006218.2	31	atA/atG	2/21	0.408479246204939	5	FACETS	0.606	0.477	0.753	0.202	0.159	0.251	SUBCLONAL	1	TRUE	2	0.408479246204939	5		380	326	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0026484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	122	361	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	0.346496016767741	4	FACETS	0.882	0.802	0.965	0.882	0.802	0.965	CLONAL	2	TRUE	2	0.408479246204939	4		361	477	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739374	145739374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776218553	NA	P-0026484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	153	733	3	ENST00000428558.2:c.1996G>A	p.Gly666Arg	p.G666R	ENST00000428558	NM_004260.3	666	Ggg/Agg	12/22	0.244081202393978	4	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.408479246204939	4		736	894	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771827	135771827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs118203750	NA	P-0026484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	126	710	2	ENST00000298552.3:c.3290G>A	p.Arg1097His	p.R1097H	ENST00000298552	NM_001162426.1	1097	cGt/cAt	23/23	0.408479246204939	2	FACETS	1	0.95	1	0.534	0.485	0.585	CLONAL	1	TRUE	0	0.408479246204939	2		712	578	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11181367	11181367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	117	652	0	ENST00000361445.4:c.6869C>T	p.Ala2290Val	p.A2290V	ENST00000361445	NM_004958.3	2290	gCc/gTc	49/58	0.356865091626957	3	FACETS	0.937	0.846	1	0.469	0.423	0.517	CLONAL	1	TRUE	1	0.408479246204939	3		652	736	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798993	45798993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553129892	NA	P-0026484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	183	688	0	ENST00000450313.1:c.352G>A	p.Glu118Lys	p.E118K	ENST00000450313	NM_012222.2	118	Gaa/Aaa	4/16	0.408479246204939	6	FACETS	0.804	0.741	0.869			1	CLONAL	2	TRUE	NA	0.408479246204939	6		688	1013	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120479979	120479979	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	123	676	0	ENST00000256646.2:c.3448C>T	p.Leu1150Phe	p.L1150F	ENST00000256646	NM_024408.3	1150	Ctc/Ttc	21/34	0.408479246204939	6	FACETS	1	0.914	1			1	CLONAL	1	TRUE	NA	0.408479246204939	6		676	1080	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041927	14041927	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765253522	NA	P-0026484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	74	320	1	ENST00000311895.7:c.2474C>T	p.Ala825Val	p.A825V	ENST00000311895	NM_005236.2	825	gCg/gTg	11/11	0.346496016767741	4	FACETS	1	0.963	1	0.625	0.55	0.706	CLONAL	1	TRUE	2	0.408479246204939	4		321	408	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983221	7983221	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	105	598	0	ENST00000319144.4:c.793G>C	p.Gly265Arg	p.G265R	ENST00000319144	NM_001139.2	265	Ggg/Cgg	7/15	0.408479246204939	2	FACETS	0.966	0.869	1	0.483	0.434	0.535	CLONAL	1	TRUE	0	0.408479246204939	2		598	532	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619253	37619253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs964263389	NA	P-0026484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1999	188	382	0	ENST00000447079.4:c.929C>T	p.Ser310Leu	p.S310L	ENST00000447079	NM_015083.1	310	tCg/tTg	1/14	0.408479246204939	26	FACETS	1	0.983	1			1	CLONAL	2	TRUE	NA	0.408479246204939	26		382	2187	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222272	2222272	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0026484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	297	785	0	ENST00000398665.3:c.3104C>G	p.Ser1035Ter	p.S1035*	ENST00000398665	NM_032482.2	1035	tCa/tGa	24/28	0.408479246204939	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.408479246204939	2		785	719	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094975	11094975	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	125	746	0	ENST00000358026.2:c.148C>G	p.Pro50Ala	p.P50A	ENST00000358026	NM_001128849.1	50	Ccc/Gcc	2/36	0.338230483244048	5	FACETS	0.945	0.854	1			1	CLONAL	1	TRUE	NA	0.408479246204939	5		746	1044	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170431	11170431	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	177	545	0	ENST00000358026.2:c.4734C>G	p.Ile1578Met	p.I1578M	ENST00000358026	NM_001128849.1	1578	atC/atG	34/36	0.338230483244048	5	FACETS	0.791	0.73	0.856			1	SUBCLONAL	2	TRUE	NA	0.408479246204939	5		545	883	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266796	18266796	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768075445	NA	P-0026484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	86	619	0	ENST00000222254.8:c.107C>T	p.Ala36Val	p.A36V	ENST00000222254	NM_005027.3	36	gCg/gTg	2/16	0.356865091626957	3	FACETS	0.664	0.587	0.746	0.332	0.293	0.373	SUBCLONAL	1	TRUE	1	0.408479246204939	3		619	764	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39294835	39294835	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	34	471	0	ENST00000402219.2:c.147A>C	p.Glu49Asp	p.E49D	ENST00000402219	NM_005633.3	49	gaA/gaC	2/23	0.356865091626957	3	FACETS	0.432	0.353	0.522	0.216	0.176	0.261	SUBCLONAL	1	TRUE	1	0.408479246204939	3		471	464	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39294861	39294861	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	26	477	1	ENST00000402219.2:c.121A>G	p.Asn41Asp	p.N41D	ENST00000402219	NM_005633.3	41	Aat/Gat	2/23	0.356865091626957	3	FACETS	0.355	0.28	0.44	0.177	0.14	0.22	SUBCLONAL	1	TRUE	1	0.408479246204939	3		478	432	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39294866	39294871	+	frameshift_variant	Frame_Shift_Del	DEL	TCGAGA	TCGAGA	ACGAG	novel	NA	P-0026484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	27	471	2	ENST00000402219.2:c.111_116delinsCTCGT	p.Leu38SerfsTer14	p.L38Sfs*14	ENST00000402219	NM_005633.3	37	acTCTCGAg/acCTCGTg	2/23	0.356865091626957	3	FACETS	0.371	0.295	0.459	0.186	0.147	0.23	SUBCLONAL	1	TRUE	1	0.408479246204939	3		473	429	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268749	46268749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1410071299	NA	P-0026484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	199	638	0	ENST00000371998.3:c.3034G>A	p.Asp1012Asn	p.D1012N	ENST00000371998		1012	Gat/Aat	16/23	0.356865091626957	3	FACETS	0.855	0.795	0.917	0.855	0.795	0.917	CLONAL	2	TRUE	1	0.408479246204939	3		638	686	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37091976	37091976	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs587778978	NA	P-0026484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	142	351	0	ENST00000231790.2:c.2104-1G>A		p.X702_splice	ENST00000231790	NM_000249.3	702			0.408479246204939	2	FACETS	0.99	0.915	1	0.99	0.915	1	CLONAL	2	TRUE	0	0.408479246204939	2		351	351	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916948	178916948	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	40	356	0	ENST00000263967.3:c.335T>C	p.Ile112Thr	p.I112T	ENST00000263967	NM_006218.2	112	aTc/aCc	2/21	0.408479246204939	5	FACETS	0.802	0.667	0.951	0.267	0.222	0.317	CLONAL	1	TRUE	2	0.408479246204939	5		356	394	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180040054	180040054	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	169	804	2	ENST00000261937.6:c.3388G>T	p.Asp1130Tyr	p.D1130Y	ENST00000261937	NM_182925.4	1130	Gac/Tac	25/30	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.408479246204939	2		806	731	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056551	26056551	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1393266086	NA	P-0026484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	34	222	0	ENST00000343677.2:c.106T>C	p.Ser36Pro	p.S36P	ENST00000343677	NM_005319.3	36	Tct/Cct	1/1	0.408479246204939	8	FACETS	0.901	0.737	1			1	CLONAL	1	TRUE	NA	0.408479246204939	8		222	411	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864407	162864407	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	107	592	4	ENST00000366898.1:c.106del	p.Val36PhefsTer8	p.V36Ffs*8	ENST00000366898	NM_004562.2	36	Gtt/tt	2/12	0.407695164262467	4	FACETS	0.962	0.863	1	0.481	0.431	0.534	CLONAL	1	TRUE	2	0.408479246204939	4		596	767	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764146326	NA	P-0026485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	204	720	1	ENST00000269305.4:c.841G>T	p.Asp281Tyr	p.D281Y	ENST00000269305	NM_001126112.2	281	Gac/Tac	8/11	0.426799338843867	6	FACETS	1	0.933	1			1	INDETERMINATE	1	FALSE	NA	0.722090638035236	6		721	1368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	756	668	0	ENST00000269305.4:c.517del	p.Val173Ter	p.V173*	ENST00000269305	NM_001126112.2	173	Gtg/tg	5/11	0.426799338843867	6	FACETS	0.908	0.885	0.931			1	INDETERMINATE	5	FALSE	NA	0.722090638035236	6		668	1127	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786205228	NA	P-0026485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	575	520	1	ENST00000322088.6:c.536C>T	p.Pro179Leu	p.P179L	ENST00000322088	NM_014225.5	179	cCc/cTc	5/15	0.60305534831084	3	FACETS	1	0.987	1			1	CLONAL	3	FALSE	NA	0.722090638035236	3		521	712	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511619	46511619	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	36	551	0	ENST00000262741.5:c.1158C>G	p.Ser386Arg	p.S386R	ENST00000262741	NM_003629.3	386	agC/agG	9/10	0.681285161183764	3	FACETS	0.229	0.187	0.275	0.114	0.093	0.138	SUBCLONAL	1	FALSE	1	0.722090638035236	3		551	593	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519036	103519036	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	88	487	0	ENST00000355739.4:c.2374G>C	p.Ala792Pro	p.A792P	ENST00000355739	NM_000123.3	792	Gcg/Ccg	11/15	0.669416687854441	3	FACETS	0.618	0.549	0.691	0.309	0.274	0.346	SUBCLONAL	1	FALSE	1	0.722090638035236	3		487	537	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426910	49426910	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	226	524	0	ENST00000301067.7:c.11578C>T	p.Gln3860Ter	p.Q3860*	ENST00000301067	NM_003482.3	3860	Cag/Tag	39/54	1	2	FACETS	0.944	0.88	1	0.944	0.88	1	CLONAL	1	TRUE	1	0.548725841994778	2		524	873	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0026487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	174	420	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.519981904258665	3	FACETS	0.87	0.817	0.923	0.87	0.817	0.923	CLONAL	3	TRUE	0	0.519981904258665	3		420	323	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0026487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	162	568	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.519981904258665	2		568	591	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098954	178098954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553488015	NA	P-0026487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	91	240	0	ENST00000397062.3:c.91G>A	p.Gly31Arg	p.G31R	ENST00000397062	NM_006164.4	31	Gga/Aga	2/5	0.519981904258665	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.519981904258665	2		240	165	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226467	1226469	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs1064794167	NA	P-0026487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	59	826	0	ENST00000326873.7:c.1127_1129del	p.Glu376del	p.E376del	ENST00000326873	NM_000455.4	375	GAG/-	9/10	1	2	FACETS	0.263	0.225	0.304	0.263	0.225	0.304	SUBCLONAL	1	TRUE	1	0.519981904258665	2		826	863	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591135	67591143	+	inframe_deletion	In_Frame_Del	DEL	GAGAGACCA	GAGAGACCA	-	novel	NA	P-0026487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	14	335	0	ENST00000274335.5:c.1728_1736del	p.Arg577_Gln579del	p.R577_Q579del	ENST00000274335		576	acGAGAGACCAa/aca	12/15	1	2	FACETS	0.357	0.259	0.474	0.357	0.259	0.474	SUBCLONAL	1	TRUE	1	0.519981904258665	2		335	151	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591259	67591303	+	inframe_deletion	In_Frame_Del	DEL	AAAAAGGTGTTCGGCAAAAGAAGTTGAACGAGTGGTTGGGCAATG	AAAAAGGTGTTCGGCAAAAGAAGTTGAACGAGTGGTTGGGCAATG	-	novel	NA	P-0026487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	18	397	0	ENST00000274335.5:c.1761_1805del	p.Lys587_Glu601del	p.K587_E601del	ENST00000274335		586	cAAAAAGGTGTTCGGCAAAAGAAGTTGAACGAGTGGTTGGGCAATGaa/caa	13/15	1	2	FACETS	0.312	0.235	0.402	0.312	0.235	0.402	SUBCLONAL	1	TRUE	1	0.519981904258665	2		397	222	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098944	178098944	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	365	414	1	ENST00000397062.3:c.101G>T	p.Arg34Leu	p.R34L	ENST00000397062	NM_006164.4	34	cGa/cTa	2/5	0.4417624834063	6	FACETS	1	0.979	1			1	CLONAL	5	TRUE	NA	0.4417624834063	6		415	605	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356248	66356248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202046693	NA	P-0026491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	149	787	2	ENST00000273854.3:c.1249C>T	p.Arg417Trp	p.R417W	ENST00000273854	NM_004439.5	417	Cgg/Tgg	5/18	0.4417624834063	3	FACETS	0.927	0.847	1	0.309	0.282	0.337	CLONAL	1	TRUE	0	0.4417624834063	3		789	888	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31429602	31429602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370990538	NA	P-0026491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	81	866	1	ENST00000344624.3:c.3196C>T	p.Arg1066Cys	p.R1066C	ENST00000344624		1066	Cgc/Tgc	24/33	0.364517141890865	3	FACETS	0.73	0.644	0.823	0.365	0.322	0.412	SUBCLONAL	1	TRUE	1	0.4417624834063	3		867	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577555	7577568	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGGAACTGTTAC	GCAGGAACTGTTAC	-	novel	NA	P-0026491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	389	888	2	ENST00000269305.4:c.713_726del	p.Cys238TyrfsTer21	p.C238Yfs*21	ENST00000269305	NM_001126112.2	238	tGTAACAGTTCCTGC/t	7/11	0.4417624834063	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.4417624834063	2		890	832	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056094	26056094	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs375462135	NA	P-0026491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	107	545	0	ENST00000343677.2:c.563G>C	p.Ser188Thr	p.S188T	ENST00000343677	NM_005319.3	188	aGt/aCt	1/1	1	2	FACETS	0.917	0.826	1	0.917	0.826	1	CLONAL	1	TRUE	1	0.4417624834063	2		545	528	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940500	76940500	+	splice_acceptor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0026492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	183	396	0	ENST00000373344.5:c.595-2del		p.X199_splice	ENST00000373344	NM_000489.3	199			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		396	451	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657656	37657656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	345	525	1	ENST00000447079.4:c.2573G>A	p.Arg858Gln	p.R858Q	ENST00000447079	NM_015083.1	858	cGg/cAg	6/14	0.787381974740712	2	FACETS	0.955	0.923	0.985	0.955	0.923	0.985	CLONAL	2	TRUE	0	0.787381974740712	2		526	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577082	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0026493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	659	753	0	ENST00000269305.4:c.856dup	p.Glu286GlyfsTer20	p.E286Gfs*20	ENST00000269305	NM_001126112.2	286	gaa/gGaa	8/11	0.761796010065968	2	FACETS	0.916	0.893	0.938	0.916	0.893	0.938	CLONAL	2	TRUE	0	0.787381974740712	2		753	914	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320308	30320308	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	173	401	0	ENST00000322652.5:c.1249G>A	p.Asp417Asn	p.D417N	ENST00000322652	NM_015355.2	417	Gat/Aat	11/16	0.787381974740712	2	FACETS	0.933	0.867	1	0.466	0.433	0.501	CLONAL	1	TRUE	0	0.787381974740712	2		401	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0026495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	579	403	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.441212175914646	3	FACETS	0.971	0.938	1			1	CLONAL	3	TRUE	NA	0.441212175914646	3		403	1100	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430559	78430559	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	196	401	0	ENST00000370768.2:c.731T>G	p.Val244Gly	p.V244G	ENST00000370768	NM_003902.3	244	gTt/gGt	9/20	0.441212175914646	3	FACETS	0.869	0.809	0.931	0.869	0.809	0.931	CLONAL	2	TRUE	1	0.441212175914646	3		401	624	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223634	36223634	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	320	911	1	ENST00000222270.7:c.6184G>A	p.Asp2062Asn	p.D2062N	ENST00000222270	NM_014727.1	2062	Gac/Aac	28/37	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.441212175914646	2		912	1205	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0026496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	202	379	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.192033314933235	4	FACETS	1	0.981	1	1	0.981	1	INDETERMINATE	2	TRUE	2	0.510100669477248	4		379	531	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0026496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	108	373	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	0.170276349347195	4	FACETS	0.969	0.88	1	0.969	0.88	1	INDETERMINATE	2	TRUE	2	0.510100669477248	4		373	330	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466027	69466035	+	inframe_deletion	In_Frame_Del	DEL	GACGTGCGG	GACGTGCGG	-	novel	NA	P-0026496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	245	852	0	ENST00000227507.2:c.871_879del	p.Arg291_Val293del	p.R291_V293del	ENST00000227507	NM_053056.2	289	GACGTGCGG/-	5/5	0.373958256006406	3	FACETS	1	0.99	1			1	CLONAL	2	TRUE	NA	0.510100669477248	3		852	497	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443666	49443667	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0026496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	299	626	0	ENST00000301067.7:c.3704dup	p.Gly1236TrpfsTer14	p.G1236Wfs*14	ENST00000301067	NM_003482.3	1235	ggt/ggGt	11/54	0.378176522527713	6	FACETS	0.947	0.9	0.994	0.947	0.9	0.994	CLONAL	4	TRUE	2	0.510100669477248	6		626	625	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380338	14380339	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCCCACGCC	novel	NA	P-0026496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	53	430	0	ENST00000256196.4:c.70_78dup	p.Gly24_Gly26dup	p.G24_G26dup	ENST00000256196		24	-/GGCGTGGGC	1/6	0.50313680184936	4	FACETS	0.96	0.823	1	0.32	0.274	0.37	CLONAL	1	TRUE	1	0.510100669477248	4		430	327	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89851273	89851273	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143083764	NA	P-0026496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	126	581	0	ENST00000389301.3:c.1459C>T	p.Arg487Trp	p.R487W	ENST00000389301	NM_000135.2	487	Cgg/Tgg	15/43	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.510100669477248	2		581	368	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099469	27099469	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	202	442	0	ENST00000324856.7:c.3706del	p.Met1236Ter	p.M1236*	ENST00000324856	NM_006015.4	1236	Atg/tg	14/20	0.510100669477248	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	3	TRUE	0	0.510100669477248	3		442	323	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431705	49431705	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	187	717	0	ENST00000301067.7:c.9434del	p.Pro3145LeufsTer10	p.P3145Lfs*10	ENST00000301067	NM_003482.3	3145	cCt/ct	34/54	0.378176522527713	6	FACETS	1	0.981	1	0.582	0.54	0.625	CLONAL	2	TRUE	2	0.510100669477248	6		717	636	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696708	47696708	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	139	448	0	ENST00000347630.2:c.240C>A	p.Ser80Arg	p.S80R	ENST00000347630	NM_001007230.1	80	agC/agA	5/11	0.192033314933235	4	FACETS	1	0.938	1	1	0.938	1	INDETERMINATE	2	TRUE	2	0.510100669477248	4		448	402	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4097294	4097294	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	135	742	0	ENST00000262948.5:c.967G>T	p.Asp323Tyr	p.D323Y	ENST00000262948	NM_030662.3	323	Gac/Tac	8/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.510100669477248	2		742	398	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221514	36221514	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	150	711	0	ENST00000222270.7:c.5273A>G	p.Tyr1758Cys	p.Y1758C	ENST00000222270	NM_014727.1	1758	tAc/tGc	25/37	1	2	FACETS	0.752	0.695	0.81	1	0.989	1	SUBCLONAL	2	TRUE	1	0.510100669477248	2		711	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0026498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	373	379	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.609734587134724	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.614887571037401	1		380	776	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147577	47147579	+	inframe_deletion	In_Frame_Del	DEL	TAC	TAC	-	novel	NA	P-0026498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	182	463	0	ENST00000409792.3:c.4747_4749del	p.Val1583del	p.V1583del	ENST00000409792	NM_014159.6	1583	GTA/-	6/21	0.614887571037401	1	FACETS	0.921	0.859	0.984	0.921	0.859	0.984	CLONAL	1	TRUE	0	0.614887571037401	1		463	445	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440835	52440855	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGCCCTTACCCTGCAGTGGC	GGGCCCTTACCCTGCAGTGGC	-	novel	NA	P-0026498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	229	533	0	ENST00000460680.1:c.649_659+10del		p.X217_splice	ENST00000460680	NM_004656.3	217		8/17	0.614887571037401	1	FACETS	0.916	0.861	0.972	0.916	0.861	0.972	CLONAL	1	TRUE	0	0.614887571037401	1		533	563	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0026499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	500	483	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.679859335304197	3	FACETS	0.914	0.878	0.95	0.914	0.878	0.95	CLONAL	2	TRUE	1	0.679859335304197	3		483	1078	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871182	12871182	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1328655695	NA	P-0026499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	328	298	1	ENST00000228872.4:c.410del	p.Pro137ArgfsTer8	p.P137Rfs*8	ENST00000228872	NM_004064.3	137	Ccg/cg	1/3	0.679859335304197	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.679859335304197	3		299	642	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467763	50467763	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	295	651	0	ENST00000331340.3:c.998C>T	p.Thr333Met	p.T333M	ENST00000331340	NM_006060.4	333	aCg/aTg	8/8	0.677144042083781	3	FACETS	1	0.951	1	0.506	0.476	0.536	CLONAL	1	TRUE	1	0.679859335304197	3		651	1150	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385239	41385239	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377294483	NA	P-0026499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	621	591	0	ENST00000373198.4:c.722G>A	p.Arg241His	p.R241H	ENST00000373198	NM_133170.3	241	cGt/cAt	6/32	0.670061076290881	4	FACETS	0.978	0.942	1	0.978	0.942	1	CLONAL	2	TRUE	2	0.679859335304197	4		591	1569	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244107	5244107	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1258	418	843	1	ENST00000357368.4:c.1375G>A	p.Gly459Ser	p.G459S	ENST00000357368	NM_002850.3	459	Ggc/Agc	11/38	0.679859335304197	3	FACETS	0.983	0.934	1	0.492	0.467	0.517	CLONAL	1	TRUE	1	0.679859335304197	3		844	1676	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435095	49435095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	302	652	0	ENST00000301067.7:c.6458C>T	p.Pro2153Leu	p.P2153L	ENST00000301067	NM_003482.3	2153	cCt/cTt	31/54	0.679859335304197	2	FACETS	0.933	0.881	0.986	0.467	0.44	0.493	CLONAL	1	TRUE	0	0.679859335304197	2		652	952	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223063	41223063	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	367	704	0	ENST00000357654.3:c.4868C>A	p.Ala1623Asp	p.A1623D	ENST00000357654	NM_007294.3	1623	gCt/gAt	15/23	0.679859335304197	2	FACETS	1	0.972	1	0.516	0.49	0.542	CLONAL	1	TRUE	0	0.679859335304197	2		704	1046	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440722	56440722	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	599	607	0	ENST00000407977.2:c.496G>T	p.Gly166Cys	p.G166C	ENST00000407977		166	Ggt/Tgt	5/10	0.679859335304197	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.679859335304197	2		607	866	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113807	11113807	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587778680	NA	P-0026499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	410	720	0	ENST00000358026.2:c.1915C>G	p.Leu639Val	p.L639V	ENST00000358026	NM_001128849.1	639	Ctg/Gtg	12/36	0.679859335304197	3	FACETS	1	0.982	1	0.535	0.508	0.562	CLONAL	1	TRUE	1	0.679859335304197	3		720	1510	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312909	30312909	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	233	466	0	ENST00000262643.3:c.712A>G	p.Lys238Glu	p.K238E	ENST00000262643	NM_001238.2	238	Aag/Gag	9/12	0.679859335304197	3	FACETS	0.961	0.897	1	0.48	0.448	0.514	CLONAL	1	TRUE	1	0.679859335304197	3		466	956	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876455	35876455	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	280	595	0	ENST00000303115.3:c.1247C>A	p.Pro416His	p.P416H	ENST00000303115	NM_002185.3	416	cCc/cAc	8/8	1	2	FACETS	0.956	0.9	1	0.956	0.9	1	CLONAL	1	TRUE	1	0.679859335304197	2		595	862	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721235	176721235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318451897	NA	P-0026499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	185	424	0	ENST00000439151.2:c.6866G>A	p.Arg2289Lys	p.R2289K	ENST00000439151	NM_022455.4	2289	aGg/aAg	23/23	1	2	FACETS	0.9	0.835	0.966	0.9	0.835	0.966	CLONAL	1	TRUE	1	0.679859335304197	2		424	605	SUCCESS
AR	367	MSKCC	GRCh37	X	66941680	66941680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137852572	NA	P-0026499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	236	252	1	ENST00000374690.3:c.2324G>A	p.Arg775His	p.R775H	ENST00000374690	NM_000044.3	775	cGc/cAc	6/8	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.679859335304197	1		253	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573995	7573996	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCT	novel	NA	P-0026499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	684	789	0	ENST00000269305.4:c.1031_1032insAGCC	p.Asn345AlafsTer3	p.N345Afs*3	ENST00000269305	NM_001126112.2	344	ctg/ctAGCCg	10/11	0.679859335304197	2	FACETS	0.903	0.877	0.929	0.903	0.877	0.929	CLONAL	2	TRUE	0	0.679859335304197	2		789	1114	SUCCESS
ATM	472	MSKCC	GRCh37	11	108213949	108213949	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs761625350	NA	P-0026500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	113	281	0	ENST00000278616.4:c.8269G>A	p.Val2757Met	p.V2757M	ENST00000278616	NM_000051.3	2757	Gtg/Atg	57/63	0.483698033361845	1	FACETS	0.928	0.844	1	0.928	0.844	1	CLONAL	1	TRUE	0	0.501241792216209	1		281	364	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	126	483	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.237599971545518	3	FACETS	1	0.909	1	1	0.909	1	CLONAL	2	TRUE	1	0.21	3		483	662	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	76	424	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.93	0.815	1	0.93	0.815	1	CLONAL	1	TRUE	1	0.21	2		424	778	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	56	385	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	1	2	FACETS	0.913	0.782	1	0.913	0.782	1	CLONAL	1	TRUE	1	0.21	2		385	584	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769886672	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	64	318	1	ENST00000405192.2:c.414dup	p.Thr139HisfsTer24	p.T139Hfs*24	ENST00000405192	NM_001163147.1	138	-/C	7/12	0.237599971545518	3	FACETS	0.78	0.677	0.89	0.78	0.677	0.89	SUBCLONAL	2	TRUE	1	0.21	3		319	432	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955165	17955165	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752820429	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	81	791	1	ENST00000458235.1:c.62C>T	p.Thr21Met	p.T21M	ENST00000458235	NM_000215.3	21	aCg/aTg	2/24	1	2	FACETS	0.731	0.642	0.826	0.731	0.642	0.826	SUBCLONAL	1	TRUE	1	0.21	2		792	1056	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	65	460	3	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	1	2	FACETS	0.909	0.788	1	0.909	0.788	1	CLONAL	1	TRUE	1	0.21	2		463	681	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088788	27088788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	67	519	0	ENST00000324856.7:c.2402del	p.Gly801ValfsTer32	p.G801Vfs*32	ENST00000324856	NM_006015.4	799	caG/ca	7/20	1	2	FACETS	0.958	0.832	1	0.958	0.832	1	CLONAL	1	TRUE	1	0.21	2		519	666	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	64	522	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.936	0.81	1	0.936	0.81	1	CLONAL	1	TRUE	1	0.21	2		522	651	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352608	68352608	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61755649	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	44	358	0	ENST00000487270.1:c.475C>T	p.Arg159Cys	p.R159C	ENST00000487270	NM_133509.3	159	Cgt/Tgt	6/11	1	2	FACETS	0.794	0.665	0.936	0.794	0.665	0.936	CLONAL	1	TRUE	1	0.21	2		358	528	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740623	58740624	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs763475304	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	65	619	3	ENST00000305921.3:c.1535dup	p.Asn512LysfsTer16	p.N512Kfs*16	ENST00000305921	NM_003620.3	510	caa/cAaa	6/6	1	2	FACETS	0.762	0.66	0.874	0.762	0.66	0.874	SUBCLONAL	1	TRUE	1	0.21	2		622	812	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375459	40375459	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	87	629	0	ENST00000293328.3:c.491del	p.Lys164SerfsTer17	p.K164Sfs*17	ENST00000293328	NM_012448.3	164	aAg/ag	5/19	1	2	FACETS	0.798	0.705	0.899	0.798	0.705	0.899	SUBCLONAL	1	TRUE	1	0.21	2		629	1038	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513282	44513287	+	inframe_deletion	In_Frame_Del	DEL	CCACCG	CCACCG	-	rs745888281	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	71	785	1	ENST00000291552.4:c.648_653del	p.Gly222_Gly223del	p.G222_G223del	ENST00000291552	NM_006758.2	216	ggCGGTGGt/ggt	8/8	1	2	FACETS	0.597	0.519	0.681	0.597	0.519	0.681	SUBCLONAL	1	TRUE	1	0.21	2		786	1133	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437230	220437230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs960266462	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	120	832	3	ENST00000243786.2:c.134C>T	p.Ala45Val	p.A45V	ENST00000243786	NM_002191.3	45	gCg/gTg	1/2	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.21	2		835	1077	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007901	45007901	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	38	320	0	ENST00000558401.1:c.346+2T>C		p.X116_splice	ENST00000558401	NM_004048.2	116			1	2	FACETS	0.674	0.556	0.806	0.674	0.556	0.806	SUBCLONAL	1	TRUE	1	0.21	2		320	537	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920173	76920173	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	45	543	4	ENST00000373344.5:c.3904del	p.Arg1302GlufsTer44	p.R1302Efs*44	ENST00000373344	NM_000489.3	1302	Aga/ga	11/35	1	2	FACETS	0.574	0.481	0.677	0.574	0.481	0.677	SUBCLONAL	1	TRUE	1	0.21	2		547	747	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2185874	2185874	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1378442482	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	134	777	0	ENST00000398665.3:c.146C>T	p.Pro49Leu	p.P49L	ENST00000398665	NM_032482.2	49	cCg/cTg	3/28	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.21	2		777	1213	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72866457	72866457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375075276	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	48	411	0	ENST00000325599.8:c.806G>A	p.Arg269His	p.R269H	ENST00000325599	NM_018130.2	269	cGt/cAt	7/11	1	2	FACETS	0.842	0.711	0.986	0.842	0.711	0.986	CLONAL	1	TRUE	1	0.21	2		411	543	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742888	17742888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749457890	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	94	708	1	ENST00000250003.3:c.796G>A	p.Ala266Thr	p.A266T	ENST00000250003	NM_002478.4	266	Gcg/Acg	3/3	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.21	2		709	864	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276756	15276756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143617599	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	72	701	2	ENST00000263388.2:c.5509C>T	p.Arg1837Cys	p.R1837C	ENST00000263388	NM_000435.2	1837	Cgt/Tgt	30/33	1	2	FACETS	0.687	0.599	0.783	0.687	0.599	0.783	SUBCLONAL	1	TRUE	1	0.21	2		703	998	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440643	56440643	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	88	537	1	ENST00000407977.2:c.575del	p.Pro192ArgfsTer11	p.P192Rfs*11	ENST00000407977		192	cCg/cg	5/10	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.21	2		538	795	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106917	27106917	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	61	437	0	ENST00000324856.7:c.6532del	p.Asp2178ThrfsTer22	p.D2178Tfs*22	ENST00000324856	NM_006015.4	2176	caG/ca	20/20	1	2	FACETS	0.904	0.779	1	0.904	0.779	1	CLONAL	1	TRUE	1	0.21	2		437	643	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563349	21563349	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	101	924	0	ENST00000382592.4:c.570del	p.Tyr191ThrfsTer49	p.Y191Tfs*49	ENST00000382592	NM_014572.2	190	ccC/cc	4/8	1	2	FACETS	0.79	0.704	0.883	0.79	0.704	0.883	SUBCLONAL	1	TRUE	1	0.21	2		924	1217	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512401	38512401	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1441911200	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	79	612	1	ENST00000254066.5:c.1312G>C	p.Ala438Pro	p.A438P	ENST00000254066	NM_000964.3	438	Gcc/Ccc	9/9	1	2	FACETS	0.99	0.87	1	0.99	0.87	1	CLONAL	1	TRUE	1	0.21	2		613	760	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246445	105246445	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	89	608	0	ENST00000349310.3:c.155T>G	p.Leu52Arg	p.L52R	ENST00000349310	NM_001014432.1	52	cTc/cGc	4/15	1	2	FACETS	0.925	0.819	1	0.925	0.819	1	CLONAL	1	TRUE	1	0.21	2		608	916	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582147	52582147	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1436814738	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	73	387	0	ENST00000394830.3:c.4681C>T	p.Arg1561Cys	p.R1561C	ENST00000394830	NM_018313.4	1561	Cgc/Tgc	30/30	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.21	2		387	694	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681120	117681120	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs748436511	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	64	513	0	ENST00000368508.3:c.3500del	p.Leu1167Ter	p.L1167*	ENST00000368508	NM_002944.2	1167	tTa/ta	23/43	1	2	FACETS	0.908	0.786	1	0.908	0.786	1	CLONAL	1	TRUE	1	0.21	2		513	671	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222730	5222731	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs756013055	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	73	656	1	ENST00000357368.4:c.3072dup	p.Val1025ArgfsTer34	p.V1025Rfs*34	ENST00000357368	NM_002850.3	1024	-/C	18/38	1	2	FACETS	0.885	0.772	1	0.885	0.772	1	CLONAL	1	TRUE	1	0.21	2		657	786	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998128	169998128	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs753143066	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	89	765	8	ENST00000295797.4:c.826del	p.Thr276GlnfsTer7	p.T276Qfs*7	ENST00000295797	NM_002740.5	273	ttA/tt	9/18	1	2	FACETS	0.878	0.777	0.987	0.878	0.777	0.987	CLONAL	1	TRUE	1	0.21	2		773	965	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391358	84391358	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1560574509	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	74	543	0	ENST00000321945.7:c.474del	p.Gly159AspfsTer8	p.G159Dfs*8	ENST00000321945	NM_139076.2	158	aaA/aa	5/9	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.21	2		543	645	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527931	103527931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs4150388	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	30	342	0	ENST00000355739.4:c.3239G>A	p.Gly1080Glu	p.G1080E	ENST00000355739	NM_000123.3	1080	gGa/gAa	15/15	1	2	FACETS	0.5	0.401	0.611	0.5	0.401	0.611	SUBCLONAL	1	TRUE	1	0.21	2		342	572	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418346	139418346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532574807	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	113	874	0	ENST00000277541.6:c.226G>A	p.Val76Met	p.V76M	ENST00000277541	NM_017617.3	76	Gtg/Atg	3/34	1	2	FACETS	0.963	0.865	1	0.963	0.865	1	CLONAL	1	TRUE	1	0.21	2		874	1117	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780873	9780873	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	106	837	1	ENST00000377346.4:c.1595G>T	p.Trp532Leu	p.W532L	ENST00000377346	NM_005026.3	532	tGg/tTg	13/24	1	2	FACETS	0.984	0.88	1	0.984	0.88	1	CLONAL	1	TRUE	1	0.21	2		838	1026	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462033	120462033	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753822819	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	79	572	2	ENST00000256646.2:c.5683C>T	p.Arg1895Cys	p.R1895C	ENST00000256646	NM_024408.3	1895	Cgt/Tgt	31/34	1	2	FACETS	0.995	0.875	1	0.995	0.875	1	CLONAL	1	TRUE	1	0.21	2		574	756	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551904	150551904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	38	365	1	ENST00000369026.2:c.103C>T	p.Leu35Phe	p.L35F	ENST00000369026	NM_021960.4	35	Ctt/Ttt	1/3	1	2	FACETS	0.739	0.61	0.882	0.739	0.61	0.882	SUBCLONAL	1	TRUE	1	0.21	2		366	490	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380331	14380331	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	56	406	0	ENST00000256196.4:c.86C>T	p.Ala29Val	p.A29V	ENST00000256196		29	gCg/gTg	1/6	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.21	2		406	496	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741475	17741475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769475374	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	94	765	0	ENST00000250003.3:c.146G>A	p.Arg49His	p.R49H	ENST00000250003	NM_002478.4	49	cGc/cAc	1/3	1	2	FACETS	0.815	0.723	0.914	0.815	0.723	0.914	CLONAL	1	TRUE	1	0.21	2		765	1098	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61213502	61213502	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778585796	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	67	508	0	ENST00000301761.2:c.460C>T	p.Arg154Cys	p.R154C	ENST00000301761	NM_017841.2	154	Cgt/Tgt	4/4	1	2	FACETS	0.789	0.684	0.902	0.789	0.684	0.902	CLONAL	1	TRUE	1	0.21	2		508	809	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151826	108151826	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	52	503	0	ENST00000278616.4:c.3507A>C	p.Glu1169Asp	p.E1169D	ENST00000278616	NM_000051.3	1169	gaA/gaC	24/63	1	2	FACETS	0.677	0.576	0.79	0.677	0.576	0.79	SUBCLONAL	1	TRUE	1	0.21	2		503	731	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173730	108173730	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	59	381	0	ENST00000278616.4:c.5470C>A	p.Leu1824Ile	p.L1824I	ENST00000278616	NM_000051.3	1824	Ctt/Att	36/63	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.21	2		381	459	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201015	108201015	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768461085	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	34	407	0	ENST00000278616.4:c.7382G>A	p.Arg2461His	p.R2461H	ENST00000278616	NM_000051.3	2461	cGc/cAc	50/63	1	2	FACETS	0.5	0.408	0.605	0.5	0.408	0.605	SUBCLONAL	1	TRUE	1	0.21	2		407	647	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434142	49434142	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	119	806	0	ENST00000301067.7:c.7411del	p.Arg2471AspfsTer14	p.R2471Dfs*14	ENST00000301067	NM_003482.3	2471	Cga/ga	31/54	0.189973301291059	3	FACETS	1	0.969	1	0.592	0.533	0.654	CLONAL	1	TRUE	1	0.21	3		806	1058	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434354	49434354	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	82	761	0	ENST00000301067.7:c.7199del	p.Pro2400LeufsTer26	p.P2400Lfs*26	ENST00000301067	NM_003482.3	2400	cCt/ct	31/54	0.189973301291059	3	FACETS	0.858	0.754	0.969	0.429	0.377	0.485	CLONAL	1	TRUE	1	0.21	3		761	1006	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549059	21549059	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	43	301	0	ENST00000382592.4:c.3217A>C	p.Ser1073Arg	p.S1073R	ENST00000382592	NM_014572.2	1073	Agc/Cgc	8/8	1	2	FACETS	0.968	0.811	1	0.968	0.811	1	CLONAL	1	TRUE	1	0.21	2		301	423	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29007975	29007975	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	28	259	0	ENST00000282397.4:c.794C>A	p.Thr265Asn	p.T265N	ENST00000282397	NM_002019.4	265	aCc/aAc	6/30	1	2	FACETS	0.672	0.537	0.826	0.672	0.537	0.826	SUBCLONAL	1	TRUE	1	0.21	2		259	397	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506194	103506194	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	54	502	0	ENST00000355739.4:c.352G>T	p.Ala118Ser	p.A118S	ENST00000355739	NM_000123.3	118	Gcc/Tcc	3/15	1	2	FACETS	0.66	0.562	0.768	0.66	0.562	0.768	SUBCLONAL	1	TRUE	1	0.21	2		502	779	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40998474	40998474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	76	666	0	ENST00000267868.3:c.325C>T	p.Leu109Phe	p.L109F	ENST00000267868	NM_002875.4	109	Ctt/Ttt	4/10	1	2	FACETS	0.833	0.729	0.945	0.833	0.729	0.945	CLONAL	1	TRUE	1	0.21	2		666	869	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66777436	66777436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555420656	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	81	652	0	ENST00000307102.5:c.802G>A	p.Ala268Thr	p.A268T	ENST00000307102	NM_002755.3	268	Gcc/Acc	7/11	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.21	2		652	770	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420270	88420270	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	59	500	0	ENST00000360948.2:c.2416T>C	p.Cys806Arg	p.C806R	ENST00000360948	NM_001012338.2	806	Tgc/Cgc	19/19	1	2	FACETS	0.767	0.658	0.885	0.767	0.658	0.885	SUBCLONAL	1	TRUE	1	0.21	2		500	733	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339440	339440	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	45	591	0	ENST00000262320.3:c.2462G>T	p.Arg821Ile	p.R821I	ENST00000262320	NM_003502.3	821	aGa/aTa	10/11	1	2	FACETS	0.48	0.402	0.568	0.48	0.402	0.568	SUBCLONAL	1	TRUE	1	0.21	2		591	892	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127615	2127615	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	101	696	2	ENST00000219476.3:c.2859del	p.Lys954AsnfsTer4	p.K954Nfs*4	ENST00000219476	NM_000548.3	952	Ccc/cc	26/42	1	2	FACETS	0.972	0.867	1	0.972	0.867	1	CLONAL	1	TRUE	1	0.21	2		698	990	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779754	3779755	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	76	531	0	ENST00000262367.5:c.5293dup	p.Gln1765ProfsTer201	p.Q1765Pfs*201	ENST00000262367	NM_004380.2	1765	cag/cCag	31/31	1	2	FACETS	0.901	0.789	1	0.901	0.789	1	CLONAL	1	TRUE	1	0.21	2		531	803	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489474	40489474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	81	490	0	ENST00000264657.5:c.776G>A	p.Cys259Tyr	p.C259Y	ENST00000264657	NM_139276.2	259	tGc/tAc	8/24	1	2	FACETS	0.906	0.797	1	0.906	0.797	1	CLONAL	1	TRUE	1	0.21	2		490	851	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40857166	40857166	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	61	391	0	ENST00000428826.2:c.1875G>T	p.Trp625Cys	p.W625C	ENST00000428826		625	tgG/tgT	17/21	1	2	FACETS	0.939	0.809	1	0.939	0.809	1	CLONAL	1	TRUE	1	0.21	2		391	619	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58725429	58725429	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	50	524	0	ENST00000305921.3:c.1008del	p.Lys336AsnfsTer3	p.K336Nfs*3	ENST00000305921	NM_003620.3	335	Aaa/aa	4/6	1	2	FACETS	0.687	0.582	0.803	0.687	0.582	0.803	SUBCLONAL	1	TRUE	1	0.21	2		524	693	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220643	1220643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782546	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	108	773	0	ENST00000326873.7:c.661C>T	p.Pro221Ser	p.P221S	ENST00000326873	NM_000455.4	221	Ccg/Tcg	5/10	0.3	2	FACETS	0.97	0.869	1			1	CLONAL	1	TRUE	NA	0.21	2		773	1060	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295806	15295806	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	117	913	1	ENST00000263388.2:c.2321C>A	p.Pro774His	p.P774H	ENST00000263388	NM_000435.2	774	cCc/cAc	15/33	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.21	2		914	1003	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950344	17950344	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	118	751	1	ENST00000458235.1:c.1383del	p.Leu462CysfsTer3	p.L462Cfs*3	ENST00000458235	NM_000215.3	461	ggG/gg	10/24	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.21	2		752	992	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228599	36228599	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	99	836	0	ENST00000222270.7:c.7613C>G	p.Ala2538Gly	p.A2538G	ENST00000222270	NM_014727.1	2538	gCc/gGc	34/37	1	2	FACETS	0.885	0.788	0.989	0.885	0.788	0.989	CLONAL	1	TRUE	1	0.21	2		836	1065	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551306	29551306	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	94	719	0	ENST00000389048.3:c.1324A>G	p.Thr442Ala	p.T442A	ENST00000389048	NM_004304.4	442	Act/Gct	6/29	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.21	2		719	863	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118904	61118904	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	50	497	1	ENST00000295025.8:c.97G>T	p.Gly33Cys	p.G33C	ENST00000295025	NM_002908.2	33	Ggc/Tgc	2/11	1	2	FACETS	0.621	0.525	0.726	0.621	0.525	0.726	SUBCLONAL	1	TRUE	1	0.21	2		498	767	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193492	99193492	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	88	666	0	ENST00000074304.5:c.2687A>C	p.Lys896Thr	p.K896T	ENST00000074304	NM_001134224.1	896	aAg/aCg	25/26	1	2	FACETS	0.856	0.757	0.963	0.856	0.757	0.963	CLONAL	1	TRUE	1	0.21	2		666	979	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131495	202131495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	43	452	0	ENST00000358485.4:c.463G>A	p.Ala155Thr	p.A155T	ENST00000358485	NM_001080125.1	155	Gct/Act	2/9	1	2	FACETS	0.627	0.524	0.742	0.627	0.524	0.742	SUBCLONAL	1	TRUE	1	0.21	2		452	653	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660795	227660795	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	92	516	0	ENST00000305123.5:c.2660C>A	p.Pro887His	p.P887H	ENST00000305123	NM_005544.2	887	cCt/cAt	1/2	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.21	2		516	683	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164773	36164773	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	59	778	0	ENST00000300305.3:c.1102A>G	p.Met368Val	p.M368V	ENST00000300305		368	Atg/Gtg	8/8	1	2	FACETS	0.598	0.513	0.692	0.598	0.513	0.692	SUBCLONAL	1	TRUE	1	0.21	2		778	939	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755423	39755423	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	41	516	3	ENST00000288319.7:c.1342G>A	p.Ala448Thr	p.A448T	ENST00000288319	NM_182918.3	448	Gcc/Acc	10/10	1	2	FACETS	0.592	0.492	0.703	0.592	0.492	0.703	SUBCLONAL	1	TRUE	1	0.21	2		519	660	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24129436	24129436	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs763994045	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	36	405	0	ENST00000263121.7:c.80T>C	p.Met27Thr	p.M27T	ENST00000263121	NM_003073.3	27	aTg/aCg	1/9	1	2	FACETS	0.585	0.48	0.703	0.585	0.48	0.703	SUBCLONAL	1	TRUE	1	0.21	2		405	586	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247354	71247354	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs374060287	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	50	393	0	ENST00000318789.4:c.179A>G	p.Gln60Arg	p.Q60R	ENST00000318789	NM_032682.5	60	cAg/cGg	6/21	1	2	FACETS	0.737	0.624	0.861	0.737	0.624	0.861	SUBCLONAL	1	TRUE	1	0.21	2		393	646	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84388678	84388679	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	37	368	0	ENST00000321945.7:c.609dup	p.Glu204Ter	p.E204*	ENST00000321945	NM_139076.2	203	-/T	7/9	1	2	FACETS	0.716	0.59	0.858	0.716	0.59	0.858	SUBCLONAL	1	TRUE	1	0.21	2		368	492	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247382	153247383	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	31	246	0	ENST00000281708.4:c.1419_1420del	p.Arg473SerfsTer3	p.R473Sfs*3	ENST00000281708	NM_033632.3	473	agAGtt/agtt	10/12	1	2	FACETS	0.623	0.503	0.759	0.623	0.503	0.759	SUBCLONAL	1	TRUE	1	0.21	2		246	474	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509935	187509935	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	29	355	0	ENST00000441802.2:c.13578C>A	p.His4526Gln	p.H4526Q	ENST00000441802	NM_005245.3	4526	caC/caA	27/27	1	2	FACETS	0.536	0.429	0.658	0.536	0.429	0.658	SUBCLONAL	1	TRUE	1	0.21	2		355	515	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032186	26032186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	29	251	0	ENST00000244661.2:c.103G>A	p.Gly35Ser	p.G35S	ENST00000244661	NM_003537.3	35	Ggc/Agc	1/1	1	2	FACETS	0.927	0.746	1	0.927	0.746	1	CLONAL	1	TRUE	1	0.21	2		251	298	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415640	152415640	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	74	586	0	ENST00000206249.3:c.1490T>C	p.Leu497Pro	p.L497P	ENST00000206249	NM_000125.3	497	cTg/cCg	7/8	1	2	FACETS	0.837	0.731	0.951	0.837	0.731	0.951	CLONAL	1	TRUE	1	0.21	2		586	842	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525000	157525000	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	43	329	0	ENST00000346085.5:c.4895T>A	p.Val1632Asp	p.V1632D	ENST00000346085	NM_020732.3	1632	gTt/gAt	19/20	1	2	FACETS	0.811	0.678	0.958	0.811	0.678	0.958	CLONAL	1	TRUE	1	0.21	2		329	505	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020429	69020429	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	77	616	0	ENST00000288368.4:c.2801G>A	p.Cys934Tyr	p.C934Y	ENST00000288368	NM_024870.2	934	tGc/tAc	24/40	1	2	FACETS	0.871	0.763	0.987	0.871	0.763	0.987	CLONAL	1	TRUE	1	0.21	2		616	842	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021739	69021739	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	105	559	0	ENST00000288368.4:c.3027T>A	p.His1009Gln	p.H1009Q	ENST00000288368	NM_024870.2	1009	caT/caA	25/40	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.21	2		559	778	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033193	69033193	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	44	570	1	ENST00000288368.4:c.3637del	p.Arg1213GlyfsTer31	p.R1213Gfs*31	ENST00000288368	NM_024870.2	1211	ccA/cc	30/40	1	2	FACETS	0.548	0.459	0.649	0.548	0.459	0.649	SUBCLONAL	1	TRUE	1	0.21	2		571	764	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742085	145742085	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	66	667	0	ENST00000428558.2:c.418C>A	p.Pro140Thr	p.P140T	ENST00000428558	NM_004260.3	140	Cca/Aca	5/22	1	2	FACETS	0.71	0.615	0.814	0.71	0.615	0.814	SUBCLONAL	1	TRUE	1	0.21	2		667	885	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197554	27197554	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	50	579	0	ENST00000380036.4:c.1870del	p.Glu624AsnfsTer33	p.E624Nfs*33	ENST00000380036	NM_000459.3	622	caG/ca	12/23	1	2	FACETS	0.644	0.545	0.753	0.644	0.545	0.753	SUBCLONAL	1	TRUE	1	0.21	2		579	740	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231383	98231383	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764218645	NA	P-0026501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	66	699	0	ENST00000331920.6:c.1900C>T	p.His634Tyr	p.H634Y	ENST00000331920	NM_000264.3	634	Cac/Tac	14/24	1	2	FACETS	0.74	0.641	0.848	0.74	0.641	0.848	SUBCLONAL	1	TRUE	1	0.21	2		699	849	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578466	7578466	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786202752	NA	P-0026504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	407	972	0	ENST00000269305.4:c.464C>A	p.Thr155Asn	p.T155N	ENST00000269305	NM_001126112.2	155	aCc/aAc	5/11	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	2	TRUE	NA	0.547571776889939	2		972	712	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104352349	104352349	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	22	527	0	ENST00000369902.3:c.465C>G	p.Phe155Leu	p.F155L	ENST00000369902	NM_016169.3	155	ttC/ttG	4/12	0.549368507134009	2	FACETS	0.186	0.143	0.235	0.093	0.071	0.118	SUBCLONAL	1	TRUE	0	0.547571776889939	2		527	433	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245615	41245615	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	357	659	1	ENST00000357654.3:c.1933del	p.Ser645LeufsTer6	p.S645Lfs*6	ENST00000357654	NM_007294.3	645	Tct/ct	10/23	0.438647058344199	3	FACETS	1	0.992	1			1	CLONAL	3	TRUE	NA	0.547571776889939	3		660	504	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939271	76939271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1041529012	NA	P-0026504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	82	768	1	ENST00000373344.5:c.1477C>T	p.His493Tyr	p.H493Y	ENST00000373344	NM_000489.3	493	Cat/Tat	9/35	0.549368507134009	5	FACETS	0.813	0.717	0.916	0.271	0.239	0.306	CLONAL	1	TRUE	2	0.547571776889939	5		769	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0026508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	262	592	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.681735043549443	1	FACETS	0.94	0.891	0.989	0.94	0.891	0.989	CLONAL	1	TRUE	0	0.681735043549443	1		594	539	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764146326	NA	P-0026508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	190	720	1	ENST00000269305.4:c.841G>T	p.Asp281Tyr	p.D281Y	ENST00000269305	NM_001126112.2	281	Gac/Tac	8/11	0.681735043549443	1	FACETS	0.597	0.555	0.641	0.597	0.555	0.641	SUBCLONAL	1	TRUE	0	0.681735043549443	1		721	615	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557630	95557630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	294	508	0	ENST00000393063.1:c.5437G>A	p.Glu1813Lys	p.E1813K	ENST00000393063	NM_030621.3	1813	Gag/Aag	26/28	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.681735043549443	2		508	614	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274090	10274090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758117698	NA	P-0026508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	51	720	1	ENST00000330684.3:c.179C>T	p.Ala60Val	p.A60V	ENST00000330684	NM_001134407.1	60	gCg/gTg	2/13	1	2	FACETS	0.212	0.179	0.247	0.212	0.179	0.247	SUBCLONAL	1	TRUE	1	0.681735043549443	2		721	707	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619169	43619169	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	291	644	0	ENST00000355710.3:c.2852C>G	p.Pro951Arg	p.P951R	ENST00000355710	NM_020975.4	951	cCc/cGc	17/20	0.34106763551687	1	FACETS	0.826	0.783	0.87	0.826	0.783	0.87	INDETERMINATE	1	TRUE	0	0.681735043549443	1		644	681	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557628	95557629	+	missense_variant	Missense_Mutation	DNP	CT	CT	AC	novel	NA	P-0026508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	235	497	1	ENST00000393063.1:c.5438_5439delinsGT	p.Glu1813Gly	p.E1813G	ENST00000393063	NM_030621.3	1813	gAG/gGT	26/28	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.681735043549443	2		498	591	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45873798	45873798	+	start_lost	Translation_Start_Site	SNP	T	T	C	rs757252017	NA	P-0026508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	310	562	0	ENST00000391945.4:c.1A>G	p.Met1?	p.M1?	ENST00000391945	NM_000400.3	1	Atg/Gtg	1/23	0.277582496929696	3	FACETS	0.947	0.901	0.993	0.947	0.901	0.993	INDETERMINATE	2	TRUE	1	0.681735043549443	3		562	644	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586386	189586386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113993967	NA	P-0026510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	127	357	0	ENST00000264731.3:c.1010G>A	p.Arg337Gln	p.R337Q	ENST00000264731	NM_003722.4	337	cGa/cAa	8/14	0.291640915013696	5	FACETS	0.893	0.81	0.98	0.595	0.54	0.653	CLONAL	2	TRUE	2	0.291640915013696	5		357	701	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579468	7579469	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0026510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	136	630	1	ENST00000269305.4:c.218_219del	p.Val73GlyfsTer75	p.V73Gfs*75	ENST00000269305	NM_001126112.2	73	gTG/g	4/11	0.291640915013696	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.291640915013696	1		631	614	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396214	139396214	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	112	687	0	ENST00000277541.6:c.5624A>G	p.Asn1875Ser	p.N1875S	ENST00000277541	NM_017617.3	1875	aAt/aGt	30/34	0.246567253184033	1	FACETS	0.939	0.845	1	0.939	0.845	1	CLONAL	1	TRUE	0	0.291640915013696	1		687	699	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223844	53223844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	331	915	0	ENST00000375401.3:c.3515C>T	p.Pro1172Leu	p.P1172L	ENST00000375401	NM_004187.3	1172	cCc/cTc	23/26	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.291640915013696	2		915	966	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	180	501	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.861	0.795	0.93	1	0.992	1	CLONAL	2	TRUE	1	0.25	2		501	836	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0026511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	273	640	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.141144965344208	3	FACETS	0.834	0.784	0.886			1	INDETERMINATE	3	TRUE	NA	0.25	3		640	982	SUCCESS
APC	324	MSKCC	GRCh37	5	112176063	112176064	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	64	399	0	ENST00000257430.4:c.4778dup	p.Pro1594AlafsTer38	p.P1594Afs*38	ENST00000257430	NM_000038.5	1591	gca/gcAa	16/16	0.255924445367927	3	FACETS	0.803	0.695	0.921	0.402	0.347	0.461	CLONAL	1	TRUE	1	0.25	3		399	717	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30103628	30103628	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763394987	NA	P-0026511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	67	585	0	ENST00000331968.5:c.1310C>T	p.Thr437Met	p.T437M	ENST00000331968	NM_002742.2	437	aCg/aTg	8/18	1	2	FACETS	0.558	0.484	0.64	0.558	0.484	0.64	SUBCLONAL	1	TRUE	1	0.25	2		585	960	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612867	228612867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	70	590	0	ENST00000366696.1:c.160C>T	p.Arg54Cys	p.R54C	ENST00000366696	NM_003493.2	54	Cgc/Tgc	1/1	1	2	FACETS	0.655	0.57	0.747	0.655	0.57	0.747	SUBCLONAL	1	TRUE	1	0.25	2		590	855	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600591	43600591	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	73	603	0	ENST00000355710.3:c.817C>G	p.Pro273Ala	p.P273A	ENST00000355710	NM_020975.4	273	Ccc/Gcc	4/20	1	2	FACETS	0.614	0.536	0.699	0.614	0.536	0.699	SUBCLONAL	1	TRUE	1	0.25	2		603	951	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741678	17741678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	113	538	2	ENST00000250003.3:c.349C>T	p.Arg117Cys	p.R117C	ENST00000250003	NM_002478.4	117	Cgc/Tgc	1/3	0.2308520083686	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.25	1		540	735	SUCCESS
APC	324	MSKCC	GRCh37	5	112111413	112111414	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	68	338	0	ENST00000257430.4:c.511dup	p.Ser171LysfsTer6	p.S171Kfs*6	ENST00000257430	NM_000038.5	170	-/A	5/16	0.255924445367927	3	FACETS	0.904	0.786	1	0.452	0.393	0.516	CLONAL	1	TRUE	1	0.25	3		338	677	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030335	180030335	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	54	747	1	ENST00000261937.6:c.3949G>T	p.Gly1317Trp	p.G1317W	ENST00000261937	NM_182925.4	1317	Ggg/Tgg	30/30	0.3	1	FACETS	0.398	0.339	0.464	0.398	0.339	0.464	SUBCLONAL	1	TRUE	0	0.25	1		748	949	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0026513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	300	454	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.320042887428394	6	FACETS	0.996	0.944	1	0.996	0.944	1	INDETERMINATE	3	TRUE	3	0.628286274451377	6		454	721	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0026513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	196	279	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.320042887428394	6	FACETS	1	0.978	1	1	0.978	1	INDETERMINATE	3	TRUE	3	0.628286274451377	6		279	429	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684357	29684363	+	frameshift_variant	Frame_Shift_Del	DEL	GTGTTGT	GTGTTGT	-	novel	NA	P-0026513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	109	596	0	ENST00000356175.3:c.7879_7885del	p.Val2627PhefsTer29	p.V2627Ffs*29	ENST00000356175	NM_000267.3	2626	aGTGTTGTg/ag	53/57	0.609138349432742	1	FACETS	0.755	0.687	0.826	0.755	0.687	0.826	SUBCLONAL	1	TRUE	0	0.628286274451377	1		596	315	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732984	74732984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1859	111	461	1	ENST00000359995.5:c.259G>A	p.Val87Met	p.V87M	ENST00000359995	NM_001195427.1	87	Gtg/Atg	1/3	0.628286274451377	14	FACETS	0.856	0.765	0.952			1	CLONAL	1	TRUE	NA	0.628286274451377	14		462	1970	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948166	55948166	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	141	662	1	ENST00000263923.4:c.3805C>A	p.Leu1269Met	p.L1269M	ENST00000263923	NM_002253.2	1269	Ctg/Atg	29/30	0.320042887428394	6	FACETS	1	0.966	1	0.373	0.34	0.409	INDETERMINATE	1	TRUE	3	0.628286274451377	6		663	904	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187558044	187558044	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	71	230	0	ENST00000441802.2:c.3667C>G	p.Pro1223Ala	p.P1223A	ENST00000441802	NM_005245.3	1223	Ccc/Gcc	5/27	1	2	FACETS	0.814	0.719	0.913	0.814	0.719	0.913	CLONAL	1	TRUE	1	0.687000529494137	2		230	254	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891140	151891140	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	35	431	0	ENST00000262189.6:c.4614G>C	p.Leu1538Phe	p.L1538F	ENST00000262189	NM_170606.2	1538	ttG/ttC	31/59	1	2	FACETS	0.169	0.138	0.204	0.169	0.138	0.204	SUBCLONAL	1	TRUE	1	0.687000529494137	2		431	604	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	27	379	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	1	2	FACETS	0.795	0.634	0.978	0.795	0.634	0.978	CLONAL	1	FALSE	1	0.235064562674806	2		379	289	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022388	31022388	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs868446207	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	15	205	0	ENST00000375687.4:c.1873C>T	p.Arg625Ter	p.R625*	ENST00000375687	NM_015338.5	625	Cga/Tga	13/13	1	2	FACETS	0.938	0.691	1	0.938	0.691	1	CLONAL	1	FALSE	1	0.235064562674806	2		205	136	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642495	117642495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs9489124	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	29	517	0	ENST00000368508.3:c.5704G>A	p.Glu1902Lys	p.E1902K	ENST00000368508	NM_002944.2	1902	Gaa/Aaa	35/43	1	2	FACETS	0.504	0.403	0.618	0.504	0.403	0.618	SUBCLONAL	1	FALSE	1	0.235064562674806	2		517	490	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870379	155870379	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	24	418	0	ENST00000368323.3:c.460C>T	p.Arg154Ter	p.R154*	ENST00000368323	NM_006912.5	154	Cga/Tga	6/6	1	2	FACETS	0.65	0.51	0.812	0.65	0.51	0.812	SUBCLONAL	1	FALSE	1	0.235064562674806	2		418	314	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955086	93955086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	18	378	1	ENST00000369303.4:c.2812G>A	p.Glu938Lys	p.E938K	ENST00000369303	NM_004440.3	938	Gaa/Aaa	16/17	1	2	FACETS	0.669	0.505	0.862	0.669	0.505	0.862	SUBCLONAL	1	FALSE	1	0.235064562674806	2		379	229	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971027	21971028	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	48	418	1	ENST00000304494.5:c.330_331delinsAA	p.Trp110_Gly111delinsTer	p.W110_G111delins*	ENST00000304494	NM_000077.4	110	tgGGgc/tgAAgc	2/3	0.235064562674806	3	FACETS	1	0.862	1	1	0.862	1	CLONAL	2	FALSE	1	0.235064562674806	3		419	226	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097020	11097020	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	28	704	0	ENST00000358026.2:c.511C>T	p.Pro171Ser	p.P171S	ENST00000358026	NM_001128849.1	171	Cca/Tca	4/36	0.235064562674806	1	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	FALSE	0	0.235064562674806	1		704	200	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135385	30135385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	55	374	0	ENST00000331968.5:c.433C>T	p.Arg145Cys	p.R145C	ENST00000331968	NM_002742.2	145	Cgt/Tgt	3/18	1	2	FACETS	0.936	0.801	1	0.936	0.801	1	CLONAL	1	FALSE	1	0.235064562674806	2		374	500	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31511181	31511181	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	34	620	0	ENST00000344624.3:c.1393C>T	p.Pro465Ser	p.P465S	ENST00000344624		465	Ccg/Tcg	6/33	1	2	FACETS	0.537	0.438	0.648	0.537	0.438	0.648	SUBCLONAL	1	FALSE	1	0.235064562674806	2		620	539	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28631516	28631516	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs560052209	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	13	346	0	ENST00000241453.7:c.452A>G	p.Asn151Ser	p.N151S	ENST00000241453	NM_004119.2	151	aAt/aGt	4/24	0.235064562674806	1	FACETS	0.478	0.341	0.645	0.478	0.341	0.645	SUBCLONAL	1	FALSE	0	0.235064562674806	1		346	204	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057740	27057740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	32	787	0	ENST00000324856.7:c.1448C>T	p.Pro483Leu	p.P483L	ENST00000324856	NM_006015.4	483	cCa/cTa	3/20	1	2	FACETS	0.541	0.439	0.658	0.541	0.439	0.658	SUBCLONAL	1	FALSE	1	0.235064562674806	2		787	503	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097752	27097752	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	41	450	0	ENST00000324856.7:c.3341C>T	p.Pro1114Leu	p.P1114L	ENST00000324856	NM_006015.4	1114	cCc/cTc	12/20	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	FALSE	1	0.235064562674806	2		450	342	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120509077	120509077	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	33	419	0	ENST00000256646.2:c.1489G>A	p.Glu497Lys	p.E497K	ENST00000256646	NM_024408.3	497	Gaa/Aaa	9/34	0.181391310864232	3	FACETS	0.779	0.634	0.941	0.389	0.317	0.471	CLONAL	1	FALSE	1	0.235064562674806	3		419	403	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153522	108153522	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	17	357	0	ENST00000278616.4:c.3662G>A	p.Trp1221Ter	p.W1221*	ENST00000278616	NM_000051.3	1221	tGg/tAg	25/63	1	2	FACETS	0.499	0.372	0.649	0.499	0.372	0.649	SUBCLONAL	1	FALSE	1	0.235064562674806	2		357	290	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871127	12871127	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	17	269	0	ENST00000228872.4:c.355del	p.Ile119LeufsTer26	p.I119Lfs*26	ENST00000228872	NM_004064.3	118	ttA/tt	1/3	NA	2	FACETS	0.742	0.555	0.961			1	INDETERMINATE	1	FALSE	NA	0.235064562674806	2		269	195	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628738	21628738	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1387446307	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	32	331	0	ENST00000421138.2:c.970C>T	p.Gln324Ter	p.Q324*	ENST00000421138		324	Cag/Tag	10/16	1	2	FACETS	0.825	0.671	0.998	0.825	0.671	0.998	CLONAL	1	FALSE	1	0.235064562674806	2		331	330	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712865	43712865	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	40	567	0	ENST00000382044.4:c.4319C>T	p.Ser1440Phe	p.S1440F	ENST00000382044	NM_001141980.1	1440	tCc/tTc	21/28	0.235064562674806	1	FACETS	0.692	0.575	0.822	0.692	0.575	0.822	SUBCLONAL	1	FALSE	0	0.235064562674806	1		567	434	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748255	43748255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	21	640	0	ENST00000382044.4:c.2551C>T	p.Leu851Phe	p.L851F	ENST00000382044	NM_001141980.1	851	Ctt/Ttt	12/28	0.235064562674806	1	FACETS	0.45	0.346	0.572	0.45	0.346	0.572	SUBCLONAL	1	FALSE	0	0.235064562674806	1		640	350	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984845	9984845	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	22	414	0	ENST00000330684.3:c.1120A>G	p.Lys374Glu	p.K374E	ENST00000330684	NM_001134407.1	374	Aag/Gag	4/13	1	2	FACETS	0.507	0.393	0.641	0.507	0.393	0.641	SUBCLONAL	1	FALSE	1	0.235064562674806	2		414	369	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842340	68842340	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	26	369	0	ENST00000261769.5:c.401G>A	p.Gly134Glu	p.G134E	ENST00000261769	NM_004360.3	134	gGa/gAa	4/16	1	2	FACETS	0.885	0.703	1	0.885	0.703	1	CLONAL	1	FALSE	1	0.235064562674806	2		369	250	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577031	7577032	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	27	533	0	ENST00000269305.4:c.906dup	p.Ser303GlufsTer3	p.S303Efs*3	ENST00000269305	NM_001126112.2	302	-/G	8/11	1	2	FACETS	0.7	0.558	0.863	0.7	0.558	0.863	SUBCLONAL	1	FALSE	1	0.235064562674806	2		533	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578384	+	frameshift_variant	Frame_Shift_Del	DEL	GAG	GAG	AA	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	17	499	1	ENST00000269305.4:c.546_548delinsTT	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	182	tgCTCa/tgTTa	5/11	1	2	FACETS	0.738	0.553	0.956	0.738	0.553	0.956	CLONAL	1	FALSE	1	0.235064562674806	2		500	196	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33430506	33430507	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	36	612	1	ENST00000345365.6:c.633_634delinsAA	p.Val212Ile	p.V212I	ENST00000345365	NM_002878.3	211	gtGGtt/gtAAtt	7/10	1	2	FACETS	0.77	0.633	0.922	0.77	0.633	0.922	CLONAL	1	FALSE	1	0.235064562674806	2		613	398	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78933952	78933953	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	29	597	2	ENST00000306801.3:c.3552_3553delinsTT	p.Leu1185Phe	p.L1185F	ENST00000306801	NM_020761.2	1184	ggCCtc/ggTTtc	30/34	1	2	FACETS	1	0.839	1	1	0.839	1	CLONAL	1	FALSE	1	0.235064562674806	2		599	236	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632372	1632372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	32	711	0	ENST00000344749.5:c.178G>A	p.Gly60Ser	p.G60S	ENST00000344749	NM_001136139.2	60	Ggc/Agc	4/19	0.235064562674806	1	FACETS	1	0.84	1	1	0.84	1	CLONAL	1	FALSE	0	0.235064562674806	1		711	233	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094895	11094895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	23	621	0	ENST00000358026.2:c.68C>T	p.Ser23Phe	p.S23F	ENST00000358026	NM_001128849.1	23	tCc/tTc	2/36	0.235064562674806	1	FACETS	0.863	0.677	1	0.863	0.677	1	CLONAL	1	FALSE	0	0.235064562674806	1		621	200	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224156	36224156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs986786657	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	14	610	0	ENST00000222270.7:c.6706C>T	p.Pro2236Ser	p.P2236S	ENST00000222270	NM_014727.1	2236	Cca/Tca	28/37	0.235064562674806	1	FACETS	0.494	0.357	0.658	0.494	0.357	0.658	SUBCLONAL	1	FALSE	0	0.235064562674806	1		610	213	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463254	25463254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	19	490	0	ENST00000264709.3:c.2239G>A	p.Asp747Asn	p.D747N	ENST00000264709	NM_175629.2	747	Gat/Aat	19/23	1	2	FACETS	0.504	0.382	0.647	0.504	0.382	0.647	SUBCLONAL	1	FALSE	1	0.235064562674806	2		490	321	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551293	29551293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	27	599	3	ENST00000389048.3:c.1337G>A	p.Gly446Glu	p.G446E	ENST00000389048	NM_004304.4	446	gGg/gAg	6/29	1	2	FACETS	0.692	0.551	0.853	0.692	0.551	0.853	SUBCLONAL	1	FALSE	1	0.235064562674806	2		602	332	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630496	47630496	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587779102	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	26	601	0	ENST00000233146.2:c.166G>A	p.Glu56Lys	p.E56K	ENST00000233146	NM_000251.2	56	Gag/Aag	1/16	1	2	FACETS	0.698	0.553	0.863	0.698	0.553	0.863	SUBCLONAL	1	FALSE	1	0.235064562674806	2		601	317	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262931	46262932	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	16	352	0	ENST00000371998.3:c.1104_1105delinsTT	p.Leu369Phe	p.L369F	ENST00000371998		368	ttCCtt/ttTTtt	10/23	1	2	FACETS	0.452	0.334	0.594	0.452	0.334	0.594	SUBCLONAL	1	FALSE	1	0.235064562674806	2		352	301	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400060	49400060	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	12	367	0	ENST00000418115.1:c.278-1G>A		p.X93_splice	ENST00000418115	NM_001664.2	93			1	2	FACETS	0.489	0.343	0.667	0.489	0.343	0.667	SUBCLONAL	1	FALSE	1	0.235064562674806	2		367	209	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52685796	52685796	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	13	389	1	ENST00000394830.3:c.676G>A	p.Glu226Lys	p.E226K	ENST00000394830	NM_018313.4	226	Gag/Aag	7/30	1	2	FACETS	0.507	0.362	0.685	0.507	0.362	0.685	SUBCLONAL	1	FALSE	1	0.235064562674806	2		390	218	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133770	55133770	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs878854835	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	24	484	0	ENST00000257290.5:c.983A>G	p.Asn328Ser	p.N328S	ENST00000257290	NM_006206.4	328	aAc/aGc	7/23	1	2	FACETS	0.537	0.421	0.672	0.537	0.421	0.672	SUBCLONAL	1	FALSE	1	0.235064562674806	2		484	380	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467646	66467646	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1000620204	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	23	310	0	ENST00000273854.3:c.623A>G	p.Lys208Arg	p.K208R	ENST00000273854	NM_004439.5	208	aAg/aGg	3/18	1	2	FACETS	0.691	0.54	0.866	0.691	0.54	0.866	SUBCLONAL	1	FALSE	1	0.235064562674806	2		310	283	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159054	143159054	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561571731	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	24	325	0	ENST00000262992.4:c.799G>A	p.Glu267Lys	p.E267K	ENST00000262992	NM_001101669.1	267	Gaa/Aaa	10/24	1	2	FACETS	0.659	0.517	0.822	0.659	0.517	0.822	SUBCLONAL	1	FALSE	1	0.235064562674806	2		325	310	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294636	1294636	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	10	507	1	ENST00000310581.5:c.365A>T	p.Tyr122Phe	p.Y122F	ENST00000310581	NM_198253.2	122	tAc/tTc	2/16	1	2	FACETS	0.599	0.407	0.839	0.599	0.407	0.839	SUBCLONAL	1	FALSE	1	0.235064562674806	2		508	142	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31424550	31424551	+	missense_variant	Missense_Mutation	DNP	GG	GG	CA	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	46	690	0	ENST00000344624.3:c.3244_3245delinsTG	p.Pro1082Cys	p.P1082C	ENST00000344624		1082	CCt/TGt	25/33	1	2	FACETS	0.623	0.524	0.733	0.623	0.524	0.733	SUBCLONAL	1	FALSE	1	0.235064562674806	2		690	628	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056500	26056500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	10	170	0	ENST00000343677.2:c.157G>A	p.Glu53Lys	p.E53K	ENST00000343677	NM_005319.3	53	Gag/Aag	1/1	0.235064562674806	6	FACETS	0.658	0.446	0.925			1	SUBCLONAL	1	FALSE	NA	0.235064562674806	6		170	190	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188218	32188219	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	14	568	1	ENST00000375023.3:c.1122_1123delinsAA	p.Gly375Ser	p.G375S	ENST00000375023	NM_004557.3	374	gtGGgc/gtAAgc	6/30	1	2	FACETS	0.476	0.344	0.637	0.476	0.344	0.637	SUBCLONAL	1	FALSE	1	0.235064562674806	2		569	250	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955048	93955048	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	22	263	1	ENST00000369303.4:c.2850T>A	p.Asn950Lys	p.N950K	ENST00000369303	NM_004440.3	950	aaT/aaA	16/17	1	2	FACETS	1	0.84	1	1	0.84	1	CLONAL	1	FALSE	1	0.235064562674806	2		264	171	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536287	106536287	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	36	377	0	ENST00000369096.4:c.254G>A	p.Arg85Lys	p.R85K	ENST00000369096	NM_001198.3	85	aGg/aAg	2/7	1	2	FACETS	0.648	0.532	0.777	0.648	0.532	0.777	SUBCLONAL	1	FALSE	1	0.235064562674806	2		377	473	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686306	117686306	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751947980	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	24	311	0	ENST00000368508.3:c.3035C>T	p.Ala1012Val	p.A1012V	ENST00000368508	NM_002944.2	1012	gCc/gTc	20/43	1	2	FACETS	0.697	0.547	0.869	0.697	0.547	0.869	SUBCLONAL	1	FALSE	1	0.235064562674806	2		311	293	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686887	117686888	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	16	353	1	ENST00000368508.3:c.2829_2830delinsTT	p.Pro944Ser	p.P944S	ENST00000368508	NM_002944.2	943	acCCct/acTTct	19/43	1	2	FACETS	0.474	0.35	0.623	0.474	0.35	0.623	SUBCLONAL	1	FALSE	1	0.235064562674806	2		354	287	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525005	157525005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	27	250	1	ENST00000346085.5:c.4900C>T	p.Pro1634Ser	p.P1634S	ENST00000346085	NM_020732.3	1634	Cct/Tct	19/20	1	2	FACETS	0.945	0.756	1	0.945	0.756	1	CLONAL	1	FALSE	1	0.235064562674806	2		251	243	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058569	69058569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	53	600	0	ENST00000288368.4:c.4213C>T	p.Pro1405Ser	p.P1405S	ENST00000288368	NM_024870.2	1405	Cct/Tct	34/40	1	2	FACETS	0.749	0.638	0.871	0.749	0.638	0.871	SUBCLONAL	1	FALSE	1	0.235064562674806	2		600	602	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76777797	76777797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	27	316	0	ENST00000373344.5:c.6919C>T	p.Pro2307Ser	p.P2307S	ENST00000373344	NM_000489.3	2307	Cct/Tct	32/35	1	1	FACETS	0.885	0.708	1	0.885	0.708	1	CLONAL	1	FALSE	0	0.235064562674806	1		316	229	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912096	76912096	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	32	216	0	ENST00000373344.5:c.4168A>T	p.Ser1390Cys	p.S1390C	ENST00000373344	NM_000489.3	1390	Agt/Tgt	13/35	1	1	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	FALSE	0	0.235064562674806	1		216	218	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746132	162746132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1374086542	NA	P-0026525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	43	223	0	ENST00000367921.3:c.2255G>A	p.Arg752His	p.R752H	ENST00000367921	NM_006182.2	752	cGc/cAc	16/18	0.252024135522451	3	FACETS	0.679	0.567	0.802	0.339	0.283	0.401	SUBCLONAL	1	TRUE	1	0.267542608156915	3		223	537	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0026525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	168	649	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.232891190333601	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.267542608156915	1		649	852	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865888	56865888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755863852	NA	P-0026525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	70	317	1	ENST00000308159.5:c.1220C>T	p.Ala407Val	p.A407V	ENST00000308159	NM_014669.4	407	gCg/gTg	11/22	1	2	FACETS	0.789	0.688	0.899	0.789	0.688	0.899	SUBCLONAL	1	TRUE	1	0.267542608156915	2		318	663	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621011	1621011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs963433488	NA	P-0026525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1310	208	759	0	ENST00000344749.5:c.1049C>T	p.Ser350Leu	p.S350L	ENST00000344749	NM_001136139.2	350	tCg/tTg	13/19	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.267542608156915	2		759	1518	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662856	227662856	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	122	546	0	ENST00000305123.5:c.599A>C	p.Glu200Ala	p.E200A	ENST00000305123	NM_005544.2	200	gAg/gCg	1/2	1	2	FACETS	0.9	0.812	0.993	0.9	0.812	0.993	CLONAL	1	TRUE	1	0.267542608156915	2		546	1013	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	563	474	0				ENST00000310581	NM_198253.2	-/1132			0.52034968204253	7	FACETS	0.932	0.899	0.964	1	0.995	1	CLONAL	5	TRUE	3	0.52034968204253	7		474	1069	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	137	471	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.447547160008329	5	FACETS	0.907	0.824	0.994	0.181	0.164	0.199	CLONAL	1	TRUE	0	0.52034968204253	5		472	1034	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	32	407	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	0.353143141085198	4	FACETS	0.364	0.295	0.442	0.182	0.147	0.221	SUBCLONAL	1	TRUE	2	0.52034968204253	4		407	514	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	136	560	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.52034968204253	5	FACETS	0.748	0.678	0.822	0.249	0.226	0.274	SUBCLONAL	1	TRUE	2	0.52034968204253	5		560	1244	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912660	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	678	565	0	ENST00000269305.4:c.839G>T	p.Arg280Ile	p.R280I	ENST00000269305	NM_001126112.2	280	aGa/aTa	8/11	0.447547160008329	5	FACETS	0.912	0.887	0.936	0.912	0.887	0.936	CLONAL	5	TRUE	0	0.52034968204253	5		565	1018	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059260	27059260	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	308	527	0	ENST00000324856.7:c.1897C>T	p.Gln633Ter	p.Q633*	ENST00000324856	NM_006015.4	633	Cag/Tag	4/20	0.481580422940615	5	FACETS	1	0.99	1			1	CLONAL	2	TRUE	NA	0.52034968204253	5		527	881	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031885	26031885	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	39	188	0	ENST00000244661.2:c.404G>C	p.Arg135Thr	p.R135T	ENST00000244661	NM_003537.3	135	aGa/aCa	1/1	0.307574915716675	5	FACETS	1	0.833	1	0.333	0.277	0.395	INDETERMINATE	1	TRUE	2	0.52034968204253	5		188	267	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915952	127915952	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs865855853	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	77	382	0	ENST00000373547.4:c.529C>T	p.Arg177Ter	p.R177*	ENST00000373547	NM_002721.4	177	Cga/Tga	6/7	0.45931853747149	5	FACETS	0.718	0.63	0.813	0.239	0.21	0.271	SUBCLONAL	1	TRUE	2	0.52034968204253	5		382	734	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651906	36651906	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	104	430	0	ENST00000244741.5:c.28C>T	p.Gln10Ter	p.Q10*	ENST00000244741	NM_000389.4	10	Cag/Tag	2/3	0.307574915716675	5	FACETS	0.791	0.707	0.88	0.264	0.235	0.294	INDETERMINATE	1	TRUE	2	0.52034968204253	5		430	900	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860053	57860053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200444628	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	78	877	4	ENST00000228682.2:c.793C>T	p.Arg265Trp	p.R265W	ENST00000228682	NM_005269.2	265	Cgg/Tgg	8/12	0.45931853747149	5	FACETS	0.426	0.372	0.483	0.142	0.124	0.161	SUBCLONAL	1	TRUE	2	0.52034968204253	5		881	1254	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184055	123184055	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	23	173	0	ENST00000218089.9:c.913C>T	p.Arg305Ter	p.R305*	ENST00000218089	NM_001042749.1	305	Cga/Tga	11/35	0.302618157967201	2	FACETS	0.315	0.245	0.394			1	INDETERMINATE	1	TRUE	NA	0.52034968204253	2		173	281	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856356	45856356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	519	663	0	ENST00000391945.4:c.1816G>A	p.Glu606Lys	p.E606K	ENST00000391945	NM_000400.3	606	Gag/Aag	19/23	0.307574915716675	5	FACETS	1	0.993	1	1	0.993	1	INDETERMINATE	3	TRUE	2	0.52034968204253	5		663	1048	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902622	1902622	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs771287635	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	67	605	1	ENST00000382891.5:c.241G>T	p.Asp81Tyr	p.D81Y	ENST00000382891	NM_133335.3	81	Gat/Tat	2/22	0.52034968204253	3	FACETS	0.339	0.294	0.389	0.113	0.098	0.13	SUBCLONAL	1	TRUE	0	0.52034968204253	3		606	957	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199408	11199408	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	72	431	0	ENST00000361445.4:c.5083C>G	p.Gln1695Glu	p.Q1695E	ENST00000361445	NM_004958.3	1695	Cag/Gag	36/58	0.45931853747149	5	FACETS	0.54	0.47	0.615	0.18	0.156	0.205	SUBCLONAL	1	TRUE	2	0.52034968204253	5		431	913	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255328	16255328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	103	521	0	ENST00000375759.3:c.2593G>A	p.Glu865Lys	p.E865K	ENST00000375759	NM_015001.2	865	Gag/Aag	11/15	0.45931853747149	5	FACETS	0.661	0.59	0.736	0.22	0.196	0.246	SUBCLONAL	1	TRUE	2	0.52034968204253	5		521	1067	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106700	27106700	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	131	448	1	ENST00000324856.7:c.6312del	p.Thr2105ProfsTer30	p.T2105Pfs*30	ENST00000324856	NM_006015.4	2104	tCc/tc	20/20	0.481580422940615	5	FACETS	0.889	0.806	0.978			1	CLONAL	1	TRUE	NA	0.52034968204253	5		449	1008	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796910	45796910	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	237	477	0	ENST00000450313.1:c.1420C>G	p.Arg474Gly	p.R474G	ENST00000450313	NM_012222.2	474	Cgc/Ggc	14/16	0.52034968204253	7	FACETS	1	0.992	1			1	CLONAL	1	TRUE	NA	0.52034968204253	7		477	1412	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248679	59248679	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1580	252	696	2	ENST00000371222.2:c.64G>T	p.Glu22Ter	p.E22*	ENST00000371222	NM_002228.3	22	Gag/Tag	1/1	0.52034968204253	7	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.52034968204253	7		698	1832	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263326	115263326	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	66	519	0	ENST00000438362.2:c.2024G>A	p.Gly675Asp	p.G675D	ENST00000438362	NM_001242891.1	675	gGt/gAt	17/20	0.353143141085198	4	FACETS	0.452	0.391	0.518	0.226	0.195	0.259	SUBCLONAL	1	TRUE	2	0.52034968204253	4		519	853	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533539	533539	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	57	675	0	ENST00000451590.1:c.364G>T	p.Ala122Ser	p.A122S	ENST00000451590	NM_001130442.1	122	Gca/Tca	4/5	0.52034968204253	3	FACETS	0.248	0.211	0.288			1	SUBCLONAL	1	TRUE	NA	0.52034968204253	3		675	1115	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64126723	64126723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1160458687	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	89	450	0	ENST00000334205.4:c.16G>A	p.Asp6Asn	p.D6N	ENST00000334205	NM_003942.2	6	Gac/Aac	1/17	0.141070351911955	5	FACETS	0.95	0.843	1			1	INDETERMINATE	1	TRUE	NA	0.52034968204253	5		450	641	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335792	73335792	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	87	218	0	ENST00000377767.4:c.2503C>T	p.His835Tyr	p.H835Y	ENST00000377767	NM_014953.3	835	Cat/Tat	18/21	0.52034968204253	5	FACETS	1	0.937	1	0.362	0.32	0.405	CLONAL	1	TRUE	2	0.52034968204253	5		218	549	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95584011	95584011	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	36	364	1	ENST00000393063.1:c.1457A>G	p.Lys486Arg	p.K486R	ENST00000393063	NM_030621.3	486	aAg/aGg	10/28	0.45931853747149	5	FACETS	0.387	0.317	0.465	0.129	0.105	0.155	SUBCLONAL	1	TRUE	2	0.52034968204253	5		365	637	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005564	42005564	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	64	462	0	ENST00000219905.7:c.3300G>C	p.Gln1100His	p.Q1100H	ENST00000219905	NM_001164273.1	1100	caG/caC	9/24	0.492062179202937	3	FACETS	0.438	0.379	0.503	0.146	0.126	0.168	SUBCLONAL	1	TRUE	0	0.52034968204253	3		462	707	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727414	66727414	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	48	320	0	ENST00000307102.5:c.130G>C	p.Glu44Gln	p.E44Q	ENST00000307102	NM_002755.3	44	Gag/Cag	2/11	0.492062179202937	3	FACETS	0.452	0.382	0.53	0.151	0.127	0.177	SUBCLONAL	1	TRUE	0	0.52034968204253	3		320	514	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843501	3843501	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	123	433	0	ENST00000262367.5:c.1102C>T	p.Gln368Ter	p.Q368*	ENST00000262367	NM_004380.2	368	Cag/Tag	4/31	0.37783565066366	3	FACETS	0.97	0.88	1	0.485	0.44	0.533	CLONAL	1	TRUE	1	0.52034968204253	3		433	614	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347299	89347299	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	123	552	0	ENST00000301030.4:c.5651C>G	p.Ser1884Ter	p.S1884*	ENST00000301030	NM_001256183.1	1884	tCa/tGa	9/13	0.413662527592481	3	FACETS	0.679	0.614	0.749	0.34	0.307	0.375	SUBCLONAL	1	TRUE	1	0.52034968204253	3		552	877	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877180	89877180	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs774448881	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	129	501	0	ENST00000389301.3:c.457C>G	p.Gln153Glu	p.Q153E	ENST00000389301	NM_000135.2	153	Cag/Gag	5/43	0.413662527592481	3	FACETS	0.957	0.87	1	0.478	0.435	0.524	CLONAL	1	TRUE	1	0.52034968204253	3		501	653	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577069	7577069	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs55819519	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	72	548	1	ENST00000269305.4:c.869G>T	p.Arg290Leu	p.R290L	ENST00000269305	NM_001126112.2	290	cGc/cTc	8/11	0.447547160008329	5	FACETS	0.488	0.425	0.556	0.098	0.085	0.112	SUBCLONAL	1	TRUE	0	0.52034968204253	5		549	1010	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883195	37883195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	325	546	1	ENST00000269571.5:c.3098C>T	p.Pro1033Leu	p.P1033L	ENST00000269571		1033	cCa/cTa	25/27	0.52034968204253	5	FACETS	0.844	0.797	0.893	0.563	0.531	0.596	CLONAL	2	TRUE	2	0.52034968204253	5		547	1317	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191113	2191113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	90	549	2	ENST00000398665.3:c.367G>A	p.Glu123Lys	p.E123K	ENST00000398665	NM_032482.2	123	Gag/Aag	5/28	0.37783565066366	3	FACETS	0.5	0.443	0.561	0.25	0.221	0.281	SUBCLONAL	1	TRUE	1	0.52034968204253	3		551	872	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219748	36219748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1335	98	714	0	ENST00000222270.7:c.4645G>A	p.Glu1549Lys	p.E1549K	ENST00000222270	NM_014727.1	1549	Gag/Aag	20/37	0.309309407149474	6	FACETS	0.536	0.477	0.601	0.134	0.119	0.151	INDETERMINATE	1	TRUE	2	0.52034968204253	6		714	1433	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161816	47161816	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	38	324	0	ENST00000409792.3:c.4310C>T	p.Ser1437Leu	p.S1437L	ENST00000409792	NM_014159.6	1437	tCa/tTa	3/21	0.473732916452264	5	FACETS	0.451	0.372	0.539	0.15	0.124	0.18	SUBCLONAL	1	TRUE	2	0.52034968204253	5		324	577	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598140	52598140	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	70	471	0	ENST00000394830.3:c.3726G>C	p.Gln1242His	p.Q1242H	ENST00000394830	NM_018313.4	1242	caG/caC	24/30	0.473732916452264	5	FACETS	0.531	0.462	0.606	0.177	0.154	0.202	SUBCLONAL	1	TRUE	2	0.52034968204253	5		471	902	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155267	185155267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	138	370	0	ENST00000265026.3:c.508G>A	p.Glu170Lys	p.E170K	ENST00000265026	NM_004721.4	170	Gag/Aag	3/14	0.309309407149474	6	FACETS	1	0.985	1	0.356	0.324	0.389	INDETERMINATE	1	TRUE	2	0.52034968204253	6		370	761	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383798	84383798	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	114	415	0	ENST00000321945.7:c.1054G>C	p.Asp352His	p.D352H	ENST00000321945	NM_139076.2	352	Gat/Cat	9/9	0.52034968204253	3	FACETS	0.874	0.788	0.964	0.291	0.262	0.322	CLONAL	1	TRUE	0	0.52034968204253	3		415	632	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562169	176562169	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	50	518	0	ENST00000439151.2:c.65T>G	p.Leu22Ter	p.L22*	ENST00000439151	NM_022455.4	22	tTa/tGa	2/23	0.52034968204253	3	FACETS	0.357	0.302	0.418	0.119	0.1	0.14	SUBCLONAL	1	TRUE	0	0.52034968204253	3		518	678	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176684035	176684035	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	85	615	0	ENST00000439151.2:c.4849G>A	p.Glu1617Lys	p.E1617K	ENST00000439151	NM_022455.4	1617	Gaa/Aaa	13/23	0.52034968204253	3	FACETS	0.469	0.414	0.529	0.156	0.138	0.177	SUBCLONAL	1	TRUE	0	0.52034968204253	3		615	877	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439667	140439667	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	34	296	0	ENST00000288602.6:c.2072G>C	p.Arg691Thr	p.R691T	ENST00000288602	NM_004333.4	691	aGa/aCa	17/18	0.307574915716675	5	FACETS	0.525	0.429	0.634	0.175	0.143	0.212	INDETERMINATE	1	TRUE	2	0.52034968204253	5		296	443	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38186967	38186967	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	52	602	0	ENST00000317025.8:c.1510G>C	p.Glu504Gln	p.E504Q	ENST00000317025	NM_023034.1	504	Gaa/Caa	6/24	0.28132757347952	3	FACETS	0.314	0.266	0.367	0.157	0.133	0.184	INDETERMINATE	1	TRUE	1	0.52034968204253	3		602	802	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187067	38187067	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	45	547	0	ENST00000317025.8:c.1410G>C	p.Trp470Cys	p.W470C	ENST00000317025	NM_023034.1	470	tgG/tgC	6/24	0.28132757347952	3	FACETS	0.278	0.232	0.328	0.139	0.116	0.164	INDETERMINATE	1	TRUE	1	0.52034968204253	3		547	785	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187096	38187096	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1215165385	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	54	546	0	ENST00000317025.8:c.1381G>A	p.Glu461Lys	p.E461K	ENST00000317025	NM_023034.1	461	Gaa/Aaa	6/24	0.28132757347952	3	FACETS	0.34	0.289	0.395	0.17	0.144	0.198	INDETERMINATE	1	TRUE	1	0.52034968204253	3		546	770	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187349	38187349	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	31	403	0	ENST00000317025.8:c.1128G>C	p.Glu376Asp	p.E376D	ENST00000317025	NM_023034.1	376	gaG/gaC	6/24	0.28132757347952	3	FACETS	0.28	0.226	0.342	0.14	0.113	0.171	INDETERMINATE	1	TRUE	1	0.52034968204253	3		403	536	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127916204	127916241	+	frameshift_variant	Frame_Shift_Del	DEL	TCAAAAACTTTGGTACAGTATCTCCAGGCATTAGCATT	TCAAAAACTTTGGTACAGTATCTCCAGGCATTAGCATT	-	novel	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	35	391	0	ENST00000373547.4:c.403_440del	p.Asn135HisfsTer10	p.N135Hfs*10	ENST00000373547	NM_002721.4	135	AATGCTAATGCCTGGAGATACTGTACCAAAGTTTTTGAc/c	5/7	0.45931853747149	5	FACETS	0.365	0.298	0.441	0.122	0.099	0.147	SUBCLONAL	1	TRUE	2	0.52034968204253	5		391	656	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911475	39911475	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	71	266	0	ENST00000378444.4:c.5155G>C	p.Glu1719Gln	p.E1719Q	ENST00000378444	NM_001123385.1	1719	Gaa/Caa	15/15	0.52034968204253	2	FACETS	0.505	0.441	0.574			1	SUBCLONAL	1	TRUE	NA	0.52034968204253	2		266	540	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038717	47038717	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0026526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	60	256	0	ENST00000377604.3:c.725-1G>C		p.X242_splice	ENST00000377604	NM_001204468.1	242			0.52034968204253	2	FACETS	0.34	0.292	0.392			1	SUBCLONAL	1	TRUE	NA	0.52034968204253	2		256	679	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692899	89692899	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	162	391	0	ENST00000371953.3:c.383A>C	p.Lys128Thr	p.K128T	ENST00000371953	NM_000314.4	128	aAg/aCg	5/9	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.749829602056163	2		391	431	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180526	94180526	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	77	351	1	ENST00000323929.3:c.1642A>T	p.Ile548Leu	p.I548L	ENST00000323929	NM_005591.3	548	Ata/Tta	15/20	0.749829602056163	3	FACETS	0.348	0.305	0.395	0.174	0.152	0.198	SUBCLONAL	1	TRUE	1	0.749829602056163	3		352	811	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344053	118344055	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs1555036383	NA	P-0026527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	132	299	1	ENST00000534358.1:c.2184_2186del	p.Ser729del	p.S729del	ENST00000534358	NM_005933.3	727	TCT/-	3/36	0.749829602056163	3	FACETS	0.91	0.83	0.993			1	CLONAL	1	TRUE	NA	0.749829602056163	3		300	532	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445040	49445040	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	616	458	1	ENST00000301067.7:c.2426A>T	p.Gln809Leu	p.Q809L	ENST00000301067	NM_003482.3	809	cAg/cTg	10/54	0.716627492713567	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.749829602056163	4		459	1364	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606091	81606091	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	279	555	0	ENST00000298171.2:c.761C>A	p.Ala254Glu	p.A254E	ENST00000298171	NM_000369.2	254	gCa/gAa	9/10	0.749829602056163	3	FACETS	0.966	0.908	1	0.483	0.454	0.513	CLONAL	1	TRUE	1	0.749829602056163	3		555	1059	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578466	7578467	+	missense_variant	Missense_Mutation	DNP	GT	GT	AA	novel	NA	P-0026527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	864	787	0	ENST00000269305.4:c.463_464delinsTT	p.Thr155Phe	p.T155F	ENST00000269305	NM_001126112.2	155	ACc/TTc	5/11	0.749829602056163	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.749829602056163	2		787	1081	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966235	25966235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1355243165	NA	P-0026527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	256	449	0	ENST00000435504.4:c.2971G>A	p.Gly991Arg	p.G991R	ENST00000435504		991	Gga/Aga	13/13	0.749829602056163	3	FACETS	0.86	0.805	0.916	0.43	0.402	0.458	CLONAL	1	TRUE	1	0.749829602056163	3		449	1092	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187558002	187558002	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	143	311	0	ENST00000441802.2:c.3709G>T	p.Asp1237Tyr	p.D1237Y	ENST00000441802	NM_005245.3	1237	Gat/Tat	5/27	0.749829602056163	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.749829602056163	1		311	220	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79968560	79968560	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	338	375	0	ENST00000265081.6:c.910G>C	p.Val304Leu	p.V304L	ENST00000265081	NM_002439.4	304	Gtg/Ctg	6/24	0.749829602056163	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.749829602056163	2		375	446	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140449109	140449109	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0026527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	266	517	0	ENST00000288602.6:c.1970C>G	p.Ser657Ter	p.S657*	ENST00000288602	NM_004333.4	657	tCa/tGa	16/18	0.749829602056163	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.749829602056163	2		517	348	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424650	47424650	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0026527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	580	558	2	ENST00000377045.4:c.459-1G>T		p.X153_splice	ENST00000377045	NM_001654.4	153			0.628988876650384	4	FACETS	0.901	0.866	0.936	0.901	0.866	0.936	CLONAL	2	TRUE	2	0.749829602056163	4		560	1502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0026528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	276	361	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	0.170541834369498	3	FACETS	1	0.973	1			1	CLONAL	3	FALSE	NA	0.170541834369498	3		361	1101	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362576	118362576	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	92	415	0	ENST00000534358.1:c.4937C>G	p.Ser1646Cys	p.S1646C	ENST00000534358	NM_005933.3	1646	tCt/tGt	15/36	0.170541834369498	2	FACETS	0.898	0.799	1	0.898	0.799	1	CLONAL	2	FALSE	0	0.170541834369498	2		415	601	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395624	45395625	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGAG	novel	NA	P-0026528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	46	389	0	ENST00000262160.6:c.509_510insCTCA	p.Glu171SerfsTer2	p.E171Sfs*2	ENST00000262160	NM_005901.5	170	gtt/gtCTCAt	4/11	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	FALSE	1	0.170541834369498	2		389	528	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148726	20148727	+	splice_acceptor_variant	Splice_Site	DNP	CT	CT	AA	novel	NA	P-0026528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	44	388	0	ENST00000379607.5:c.338-2_338-1delinsTT		p.X113_splice	ENST00000379607	NM_001412.3	113			0.170541834369498	1	FACETS	0.788	0.66	0.93	0.788	0.66	0.93	CLONAL	1	FALSE	0	0.170541834369498	1		388	599	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0026530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	55	606	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.215470903881982	1	FACETS	0.992	0.85	1	0.992	0.85	1	CLONAL	1	TRUE	0	0.215470903881982	1		606	459	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17371376	17371376	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	40	301	0	ENST00000375499.3:c.80G>T	p.Arg27Leu	p.R27L	ENST00000375499	NM_003000.2	27	cGa/cTa	2/8	1	2	FACETS	0.811	0.674	0.963	0.811	0.674	0.963	CLONAL	1	TRUE	1	0.215470903881982	2		301	458	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821643	72821645	+	inframe_deletion	In_Frame_Del	DEL	CCG	CCG	-	rs762513291	NA	P-0026530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	13	96	1	ENST00000268489.5:c.10530_10532del	p.Gly3512del	p.G3512del	ENST00000268489	NM_006885.3	3510	ggCGGt/ggt	10/10	1	2	FACETS	0.804	0.576	1	0.804	0.576	1	CLONAL	1	TRUE	1	0.215470903881982	2		97	150	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44520605	44520605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	34	350	1	ENST00000291552.4:c.157C>T	p.Arg53Cys	p.R53C	ENST00000291552	NM_006758.2	53	Cgt/Tgt	3/8	1	2	FACETS	0.622	0.508	0.752	0.622	0.508	0.752	SUBCLONAL	1	TRUE	1	0.215470903881982	2		351	507	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0026530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	73	313	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.215470903881982	2		313	482	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0026532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	63	379	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.24	2		379	392	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100175	27100176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0026532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	35	406	0	ENST00000324856.7:c.3977dup	p.Gln1327AlafsTer11	p.Q1327Afs*11	ENST00000324856	NM_006015.4	1324	tac/taCc	16/20	1	2	FACETS	0.895	0.735	1	0.895	0.735	1	CLONAL	1	TRUE	1	0.24	2		406	326	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0026532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	36	363	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.24	2		363	289	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0026532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	35	354	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.288932245808013	3	FACETS	1	0.91	1	0.59	0.485	0.706	CLONAL	1	TRUE	1	0.24	3		354	277	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692768	89692768	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0026532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	55	355	0	ENST00000371953.3:c.254-2A>C		p.X85_splice	ENST00000371953	NM_000314.4	85			0.288932245808013	3	FACETS	1	0.961	1	0.686	0.589	0.791	CLONAL	1	TRUE	1	0.24	3		355	374	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624265	89624275	+	frameshift_variant	Frame_Shift_Del	DEL	AAGGAGATATC	AAGGAGATATC	-	novel	NA	P-0026532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	88	288	0	ENST00000371953.3:c.42_52del	p.Arg15GlyfsTer25	p.R15Gfs*25	ENST00000371953	NM_000314.4	13	aaAAGGAGATATCaa/aaaa	1/9	0.288932245808013	3	FACETS	0.938	0.841	1	1	0.979	1	CLONAL	3	TRUE	1	0.24	3		288	292	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222823	36222823	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	72	858	0	ENST00000222270.7:c.5452G>A	p.Glu1818Lys	p.E1818K	ENST00000222270	NM_014727.1	1818	Gag/Aag	27/37	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.24	2		858	571	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0026534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	31	215	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.249	0.201	0.302	0.249	0.201	0.302	SUBCLONAL	1	TRUE	1	0.694863371276206	2		215	359	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035328	42035329	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0026534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	45	413	0	ENST00000219905.7:c.5173_5174del	p.Ser1725ArgfsTer3	p.S1725Rfs*3	ENST00000219905	NM_001164273.1	1724	CTc/c	15/24	1	2	FACETS	0.212	0.178	0.25	0.212	0.178	0.25	SUBCLONAL	1	TRUE	1	0.694863371276206	2		413	611	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922109	39922109	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs780712297	NA	P-0026534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	40	346	0	ENST00000378444.4:c.4063G>T	p.Glu1355Ter	p.E1355*	ENST00000378444	NM_001123385.1	1355	Gag/Tag	9/15	1	1	FACETS	0.11	0.091	0.131	0.11	0.091	0.131	SUBCLONAL	1	TRUE	0	0.694863371276206	1		346	684	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564083	139564083	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs574267042	NA	P-0026535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	73	648	2	ENST00000308874.7:c.223C>T	p.Arg75Cys	p.R75C	ENST00000308874		75	Cgc/Tgc	5/10	0.162776687741388	1	FACETS	0.946	0.826	1	0.946	0.826	1	CLONAL	1	TRUE	0	0.17	1		650	831	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954327	48954328	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0026535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	54	289	0	ENST00000267163.4:c.1450_1451del	p.Met484ValfsTer8	p.M484Vfs*8	ENST00000267163	NM_000321.2	483	cAT/c	16/27	0.162776687741388	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.17	1		289	475	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174458	11174458	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	76	543	0	ENST00000361445.4:c.7217T>G	p.Val2406Gly	p.V2406G	ENST00000361445	NM_004958.3	2406	gTg/gGg	53/58	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.17	2		543	877	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579385	7579391	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTGGG	TTCTGGG	-	novel	NA	P-0026535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	70	703	0	ENST00000269305.4:c.296_302del	p.Ser99Ter	p.S99*	ENST00000269305	NM_001126112.2	99	tCCCAGAAa/ta	4/11	1	2	FACETS	0.894	0.778	1	0.894	0.778	1	CLONAL	1	TRUE	1	0.17	2		703	921	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468483	89468483	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	45	361	1	ENST00000336596.2:c.2017A>T	p.Ile673Phe	p.I673F	ENST00000336596	NM_005233.5	673	Att/Ttt	11/17	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.17	2		362	469	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690801	89690805	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGTTG	AGTTG	T	novel	NA	P-0026535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	31	278	0	ENST00000371953.3:c.210-2_212delinsT		p.X70_splice	ENST00000371953	NM_000314.4	70		4/9	0.162776687741388	1	FACETS	1	0.826	1	1	0.826	1	CLONAL	1	TRUE	0	0.17	1		278	327	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0026536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	88	454	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.250780670183757	3	FACETS	1	0.972	1	0.434	0.386	0.486	CLONAL	1	TRUE	0	0.305882725110719	3		454	509	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0026536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	122	388	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.793	0.72	0.869	1	0.987	1	SUBCLONAL	2	TRUE	1	0.305882725110719	2		388	503	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955550	48955550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913304	NA	P-0026536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	84	420	1	ENST00000267163.4:c.1666C>T	p.Arg556Ter	p.R556*	ENST00000267163	NM_000321.2	556	Cga/Tga	17/27	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.305882725110719	2		421	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786201059	NA	P-0026536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	144	667	0	ENST00000269305.4:c.856G>C	p.Glu286Gln	p.E286Q	ENST00000269305	NM_001126112.2	286	Gaa/Caa	8/11	0.305882725110719	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.305882725110719	1		667	700	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423587	88423587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1366437707	NA	P-0026536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	107	540	0	ENST00000360948.2:c.2248G>A	p.Glu750Lys	p.E750K	ENST00000360948	NM_001012338.2	750	Gag/Aag	18/19	0.269396103883074	2	FACETS	0.821	0.742	0.904	0.821	0.742	0.904	CLONAL	2	TRUE	0	0.305882725110719	2		540	426	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003746	45003746	+	start_lost	Translation_Start_Site	SNP	T	T	G	rs1057519879	NA	P-0026536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	64	385	0	ENST00000558401.1:c.2T>G	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	aTg/aGg	1/4	0.269396103883074	2	FACETS	1	0.932	1	0.556	0.484	0.634	CLONAL	1	TRUE	0	0.305882725110719	2		385	376	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067041	143067041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	80	410	0	ENST00000262992.4:c.1672G>A	p.Gly558Arg	p.G558R	ENST00000262992	NM_001101669.1	558	Gga/Aga	16/24	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.305882725110719	2		410	369	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28601511	28601511	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	113	662	0	ENST00000253063.3:c.1196G>T	p.Cys399Phe	p.C399F	ENST00000253063	NM_031459.4	399	tGc/tTc	8/10	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.305882725110719	2		662	715	SUCCESS
EED	8726	MSKCC	GRCh37	11	85956350	85956350	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	85	291	0	ENST00000263360.6:c.79G>A	p.Glu27Lys	p.E27K	ENST00000263360	NM_003797.3	27	Gag/Aag	1/12	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.305882725110719	2		291	397	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544631	65544631	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	88	463	0	ENST00000358664.4:c.295G>C	p.Val99Leu	p.V99L	ENST00000358664	NM_002382.4	99	Gtc/Ctc	4/5	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.305882725110719	2		463	406	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223531	2223532	+	missense_variant	Missense_Mutation	DNP	CC	CC	GT	novel	NA	P-0026536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	116	751	3	ENST00000326181.6:c.1062_1063delinsGT	p.Phe354_Arg355delinsLeuTrp	p.F354_R355delinsLW	ENST00000326181	NM_032271.2	354	ttCCgg/ttGTgg	11/21	0.305882725110719	3	FACETS	1	0.963	1	0.569	0.513	0.629	CLONAL	1	TRUE	1	0.305882725110719	3		754	768	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639706	3639706	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs374311917	NA	P-0026536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	168	919	0	ENST00000294008.3:c.3933C>G	p.Ile1311Met	p.I1311M	ENST00000294008	NM_032444.2	1311	atC/atG	12/15	0.305882725110719	3	FACETS	1	0.974	1	0.574	0.526	0.623	CLONAL	1	TRUE	1	0.305882725110719	3		919	1104	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639878	3639878	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750580998	NA	P-0026536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	101	655	1	ENST00000294008.3:c.3761C>T	p.Ser1254Leu	p.S1254L	ENST00000294008	NM_032444.2	1254	tCg/tTg	12/15	0.305882725110719	3	FACETS	1	0.962	1	0.581	0.52	0.646	CLONAL	1	TRUE	1	0.305882725110719	3		656	655	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17117130	17117130	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs879255683	NA	P-0026536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	96	509	1	ENST00000285071.4:c.1579C>T	p.Arg527Ter	p.R527*	ENST00000285071	NM_144997.5	527	Cga/Tga	14/14	0.305882725110719	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.305882725110719	1		510	503	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508758	29508758	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	87	485	0	ENST00000356175.3:c.685G>T	p.Asp229Tyr	p.D229Y	ENST00000356175	NM_000267.3	229	Gat/Tat	7/57	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.305882725110719	2		485	555	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349205	15349205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	129	541	1	ENST00000263377.2:c.4072G>A	p.Glu1358Lys	p.E1358K	ENST00000263377	NM_058243.2	1358	Gaa/Aaa	20/20	1	2	FACETS	0.772	0.703	0.844	1	0.987	1	SUBCLONAL	2	TRUE	1	0.305882725110719	2		542	546	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285837	39285837	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	104	553	0	ENST00000402219.2:c.322G>C	p.Glu108Gln	p.E108Q	ENST00000402219	NM_005633.3	108	Gaa/Caa	3/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.305882725110719	2		553	519	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907638	111907638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	28	305	0	ENST00000393256.3:c.412G>A	p.Glu138Lys	p.E138K	ENST00000393256	NM_006538.4	138	Gaa/Aaa	3/4	1	2	FACETS	0.448	0.357	0.551	0.448	0.357	0.551	SUBCLONAL	1	TRUE	1	0.305882725110719	2		305	409	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62316898	62316898	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375916694	NA	P-0026536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	142	522	1	ENST00000360203.5:c.1214C>T	p.Ser405Phe	p.S405F	ENST00000360203	NM_001283009.1	405	tCc/tTc	15/35	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.305882725110719	2		523	683	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540569	187540569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	34	279	0	ENST00000441802.2:c.7171G>A	p.Glu2391Lys	p.E2391K	ENST00000441802	NM_005245.3	2391	Gaa/Aaa	10/27	1	2	FACETS	0.643	0.526	0.773	0.643	0.526	0.773	SUBCLONAL	1	TRUE	1	0.305882725110719	2		279	346	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500823	149500823	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	107	618	0	ENST00000261799.4:c.2407C>G	p.Leu803Val	p.L803V	ENST00000261799	NM_002609.3	803	Ctc/Gtc	17/23	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.305882725110719	2		618	589	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528718	157528718	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	83	456	0	ENST00000346085.5:c.6443C>G	p.Ala2148Gly	p.A2148G	ENST00000346085	NM_020732.3	2148	gCc/gGc	20/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.305882725110719	2		456	475	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039871	47039872	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0026536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	142	354	0	ENST00000377604.3:c.1215dup	p.Ala406CysfsTer37	p.A406Cfs*37	ENST00000377604	NM_001204468.1	405	act/acTt	12/24	0.0747459690348693	2	FACETS	1	0.981	1			1	INDETERMINATE	2	TRUE	NA	0.305882725110719	2		354	383	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223532	2223532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	114	751	0	ENST00000326181.6:c.1063C>T	p.Arg355Trp	p.R355W	ENST00000326181	NM_032271.2	355	Cgg/Tgg	11/21	0.305882725110719	3	FACETS	1	0.958	1	0.559	0.504	0.619	CLONAL	1	TRUE	1	0.305882725110719	3		751	768	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0026538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	320	538	0	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	0.624118762620628	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.624118762620628	1		538	627	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868209	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0026538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	1202	514	0	ENST00000269571.5:c.929_930delinsAT	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCC/tAT	8/27	0.624118762620628	7	FACETS	1	0.996	1			1	CLONAL	5	TRUE	NA	0.624118762620628	7		514	1855	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211862	36211862	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	110	743	1	ENST00000222270.7:c.1613G>A	p.Arg538His	p.R538H	ENST00000222270	NM_014727.1	538	cGt/cAt	3/37	1	2	FACETS	0.307	0.275	0.342	0.307	0.275	0.342	SUBCLONAL	1	TRUE	1	0.624118762620628	2		744	1147	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564620	86564620	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0026538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	248	516	0	ENST00000274376.6:c.352A>T	p.Lys118Ter	p.K118*	ENST00000274376	NM_002890.2	118	Aaa/Taa	1/25	0.335418770947919	1	FACETS	0.808	0.759	0.857	0.808	0.759	0.857	INDETERMINATE	1	TRUE	0	0.624118762620628	1		516	677	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645069	86645069	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	55	210	0	ENST00000274376.6:c.1142del	p.Asn381IlefsTer30	p.N381Ifs*30	ENST00000274376	NM_002890.2	381	Aat/at	8/25	0.335418770947919	1	FACETS	0.493	0.426	0.565	0.493	0.426	0.565	INDETERMINATE	1	TRUE	0	0.624118762620628	1		210	246	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0026539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	244	379	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	0.778481332357042	2		379	602	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0026539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	354	495	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	0.638093304803256	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.778481332357042	3		495	605	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637574	176637574	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774810620	NA	P-0026539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	169	457	0	ENST00000439151.2:c.2174C>T	p.Thr725Met	p.T725M	ENST00000439151	NM_022455.4	725	aCg/aTg	5/23	1	2	FACETS	0.884	0.82	0.95	0.884	0.82	0.95	CLONAL	1	TRUE	1	0.778481332357042	2		457	491	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023255	27023260	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGGC	CCCGGC	GG	novel	NA	P-0026539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	110	271	2	ENST00000324856.7:c.361_366delinsGG	p.Pro121GlyfsTer110	p.P121Gfs*110	ENST00000324856	NM_006015.4	121	CCCGGC/GG	1/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.778481332357042	2		273	226	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105963	27105966	+	frameshift_variant	Frame_Shift_Del	DEL	CTTC	CTTC	-	novel	NA	P-0026539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	174	415	0	ENST00000324856.7:c.5574_5577del	p.His1858GlnfsTer24	p.H1858Qfs*24	ENST00000324856	NM_006015.4	1858	caCTTC/ca	20/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.778481332357042	2		415	422	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891728	28891728	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	161	494	0	ENST00000282397.4:c.3293C>A	p.Ser1098Tyr	p.S1098Y	ENST00000282397	NM_002019.4	1098	tCt/tAt	25/30	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.778481332357042	2		494	409	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78858812	78858812	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	239	531	0	ENST00000306801.3:c.1847G>T	p.Arg616Leu	p.R616L	ENST00000306801	NM_020761.2	616	cGc/cTc	17/34	0.401775755579173	3	FACETS	0.907	0.859	0.956	0.907	0.859	0.956	INDETERMINATE	2	TRUE	1	0.778481332357042	3		531	470	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860728	151860728	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	168	384	0	ENST00000262189.6:c.9934C>T	p.Gln3312Ter	p.Q3312*	ENST00000262189	NM_170606.2	3312	Cag/Tag	43/59	0.778481332357042	2	FACETS	0.963	0.894	1	0.482	0.447	0.517	CLONAL	1	TRUE	0	0.778481332357042	2		384	448	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205052	38205052	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0026539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	263	567	0	ENST00000317025.8:c.638C>G	p.Ser213Ter	p.S213*	ENST00000317025	NM_023034.1	213	tCa/tGa	2/24	1	2	FACETS	0.937	0.883	0.992	0.937	0.883	0.992	CLONAL	1	TRUE	1	0.778481332357042	2		567	721	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0026540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	209	379	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.516496495309826	4	FACETS	0.959	0.899	1	0.959	0.899	1	CLONAL	2	TRUE	2	0.714190528864653	4		379	523	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610171	10610171	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	132	614	0	ENST00000171111.5:c.539A>T	p.Asp180Val	p.D180V	ENST00000171111	NM_203500.1	180	gAc/gTc	2/6	0.163892989407931	1	FACETS	0.527	0.482	0.574	0.527	0.482	0.574	INDETERMINATE	1	TRUE	0	0.714190528864653	1		614	451	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174909	56174909	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	83	295	0	ENST00000399503.3:c.2070del	p.Lys690AsnfsTer35	p.K690Nfs*35	ENST00000399503	NM_005921.1	690	Aaa/aa	11/20	0.714190528864653	4	FACETS	0.828	0.734	0.929	0.276	0.244	0.31	CLONAL	1	TRUE	1	0.714190528864653	4		295	481	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178245	56178246	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	208	246	0	ENST00000399503.3:c.3221dup	p.Asp1075ArgfsTer6	p.D1075Rfs*6	ENST00000399503	NM_005921.1	1073	cag/caGg	14/20	0.714190528864653	4	FACETS	0.869	0.82	0.917	0.869	0.82	0.917	CLONAL	3	TRUE	1	0.714190528864653	4		246	383	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878175	151878175	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	229	443	0	ENST00000262189.6:c.6770del	p.Arg2257GlnfsTer10	p.R2257Qfs*10	ENST00000262189	NM_170606.2	2257	cGa/ca	36/59	0.516496495309826	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.714190528864653	4		443	524	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	191	474	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		474	626	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052520	42052520	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0026543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	154	259	0	ENST00000219905.7:c.7192-1G>C		p.X2398_splice	ENST00000219905	NM_001164273.1	2398			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		259	400	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528490	29528490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343309278	NA	P-0026544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	46	438	0	ENST00000356175.3:c.1247G>A	p.Arg416Gln	p.R416Q	ENST00000356175	NM_000267.3	416	cGa/cAa	11/57	0.195099106782363	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.21729115161729	1		438	256	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207203	1207203	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1131690950	NA	P-0026544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	129	574	0	ENST00000326873.7:c.290+1G>A		p.X97_splice	ENST00000326873	NM_000455.4	97			0.21729115161729	0	FACETS	0.95	0.874	1			1	CLONAL	3	TRUE	0	0.21729115161729	0		574	326	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	42	312	0	ENST00000263967.3:c.1034A>G	p.Asn345Ser	p.N345S	ENST00000263967	NM_006218.2	345	aAt/aGt	5/21	0.21729115161729	3	FACETS	0.835	0.708	0.972	1	0.942	1	CLONAL	3	TRUE	1	0.21729115161729	3		312	171	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694575	176694575	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	29	320	0	ENST00000439151.2:c.5159T>C	p.Leu1720Pro	p.L1720P	ENST00000439151	NM_022455.4	1720	cTg/cCg	15/23	0.165841564709766	3	FACETS	1	0.912	1	1	0.912	1	CLONAL	2	TRUE	1	0.21729115161729	3		320	122	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577519	7577527	+	inframe_deletion	In_Frame_Del	DEL	GATGGTGAG	GATGGTGAG	-	novel	NA	P-0026548-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	185	627	0	ENST00000269305.4:c.754_762del	p.Leu252_Ile254del	p.L252_I254del	ENST00000269305	NM_001126112.2	252	CTCACCATC/-	7/11	0.315299288948952	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.315299288948952	1		627	939	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104389902	104389902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765358771	NA	P-0026548-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	78	479	0	ENST00000369902.3:c.1445C>T	p.Pro482Leu	p.P482L	ENST00000369902	NM_016169.3	482	cCg/cTg	12/12	1	2	FACETS	0.648	0.568	0.733	0.648	0.568	0.733	SUBCLONAL	1	TRUE	1	0.315299288948952	2		479	764	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683191	88683191	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0026548-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	44	177	0	ENST00000372037.3:c.1401C>G	p.Tyr467Ter	p.Y467*	ENST00000372037	NM_004329.2	467	taC/taG	12/13	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.315299288948952	2		177	233	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448297	56448298	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0026548-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	158	590	0	ENST00000407977.2:c.348_349dup	p.Arg117ProfsTer42	p.R117Pfs*42	ENST00000407977		117	cgc/cCCgc	3/10	0.315299288948952	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.315299288948952	1		590	841	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191010	2191010	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0026548-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	103	355	0	ENST00000398665.3:c.265-1G>A		p.X89_splice	ENST00000398665	NM_032482.2	89			1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.315299288948952	2		355	440	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0026557-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	140	540	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.682834352709694	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.682834352709694	1		540	257	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0026557-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	254	482	1	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.626991580647781	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.682834352709694	2		483	368	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0026557-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	73	477	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.207853285406582	1	FACETS	0.447	0.394	0.503	0.447	0.394	0.503	INDETERMINATE	1	TRUE	0	0.682834352709694	1		477	315	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206943197	206943197	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026557-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	51	430	0	ENST00000423557.1:c.421C>A	p.Gln141Lys	p.Q141K	ENST00000423557	NM_000572.2	141	Cag/Aag	4/5	1	2	FACETS	0.332	0.282	0.386	0.332	0.282	0.386	SUBCLONAL	1	TRUE	1	0.682834352709694	2		430	450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0026609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	272	440	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.376367357642096	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.376367357642096	1		441	1024	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069326	30069327	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	242	816	2	ENST00000338641.4:c.1191_1192insA	p.Leu398ThrfsTer9	p.L398Tfs*9	ENST00000338641	NM_000268.3	397	-/A	12/16	0.376367357642096	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.376367357642096	1		818	1003	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0026611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	316	409	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.526526640126258	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.536968027482172	1		409	841	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450636	70450636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	307	499	1	ENST00000373644.4:c.5476G>A	p.Asp1826Asn	p.D1826N	ENST00000373644	NM_030625.2	1826	Gac/Aac	12/12	0.524719656913256	2	FACETS	0.838	0.796	0.881	0.838	0.796	0.881	CLONAL	2	TRUE	0	0.536968027482172	2		500	682	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829101	72829101	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	89	541	1	ENST00000268489.5:c.7480T>A	p.Leu2494Ile	p.L2494I	ENST00000268489	NM_006885.3	2494	Tta/Ata	9/10	0.118463275868386	4	FACETS	0.797	0.708	0.893	0.399	0.354	0.447	INDETERMINATE	1	TRUE	2	0.536968027482172	4		542	639	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012245	152012245	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	473	407	0	ENST00000262189.6:c.568C>T	p.Arg190Ter	p.R190*	ENST00000262189	NM_170606.2	190	Cga/Tga	4/59	0.536968027482172	4	FACETS	0.937	0.901	0.974	0.937	0.901	0.974	CLONAL	3	TRUE	1	0.536968027482172	4		407	963	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0026612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	89	177	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	0.549479438231784	2		177	263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0026612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	312	379	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.549479438231784	2		380	1008	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0026613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	159	503	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.427236466216106	2		505	723	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0026613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	161	475	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.427236466216106	2		475	743	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578204	7578204	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520001	NA	P-0026613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	247	871	0	ENST00000269305.4:c.645T>G	p.Ser215Arg	p.S215R	ENST00000269305	NM_001126112.2	215	agT/agG	6/11	0.427236466216106	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.427236466216106	1		871	849	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729162	66729162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519732	NA	P-0026613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	208	813	1	ENST00000307102.5:c.370C>T	p.Pro124Ser	p.P124S	ENST00000307102	NM_002755.3	124	Ccg/Tcg	3/11	1	2	FACETS	0.924	0.857	0.993	0.924	0.857	0.993	CLONAL	1	TRUE	1	0.427236466216106	2		814	1054	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100954	27100955	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCA	novel	NA	P-0026613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	195	755	0	ENST00000324856.7:c.4243_4246dup	p.Gln1416ProfsTer30	p.Q1416Pfs*30	ENST00000324856	NM_006015.4	1412	-/GCCA	18/20	1	2	FACETS	0.869	0.803	0.936	0.869	0.803	0.936	CLONAL	1	TRUE	1	0.427236466216106	2		755	1051	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039235	49039235	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0026613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	181	658	1	ENST00000267163.4:c.2313T>A	p.Tyr771Ter	p.Y771*	ENST00000267163	NM_000321.2	771	taT/taA	22/27	0.427236466216106	1	FACETS	0.961	0.89	1	0.961	0.89	1	CLONAL	1	TRUE	0	0.427236466216106	1		659	693	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591900	48591914	+	inframe_deletion	In_Frame_Del	DEL	GACCCTTCTGGAGGA	GACCCTTCTGGAGGA	-	novel	NA	P-0026613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	107	613	0	ENST00000342988.3:c.1065_1079del	p.Pro356_Asp360del	p.P356_D360del	ENST00000342988	NM_005359.5	355	GACCCTTCTGGAGGA/-	9/12	0.427236466216106	1	FACETS	0.821	0.74	0.905	0.821	0.74	0.905	CLONAL	1	TRUE	0	0.427236466216106	1		613	480	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923743	131923743	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	127	583	0	ENST00000265335.6:c.1014del	p.Leu339SerfsTer32	p.L339Sfs*32	ENST00000265335		338	cTt/ct	7/25	1	2	FACETS	0.97	0.881	1	0.97	0.881	1	CLONAL	1	TRUE	1	0.427236466216106	2		583	613	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0026614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	566	379	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.734848233467422	3	FACETS	0.987	0.953	1	0.987	0.953	1	CLONAL	2	TRUE	1	0.734848233467422	3		379	1067	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	822	799	2	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.734848233467422	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.734848233467422	2		801	1096	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971324	13971324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752431857	NA	P-0026614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	283	563	0	ENST00000405192.2:c.605C>T	p.Thr202Met	p.T202M	ENST00000405192	NM_001163147.1	202	aCg/aTg	8/12	0.734848233467422	4	FACETS	0.998	0.936	1	0.499	0.468	0.531	CLONAL	1	TRUE	2	0.734848233467422	4		563	1339	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0026615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	18	454	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.249345121386907	3	FACETS	0.533	0.401	0.689	0.266	0.2	0.345	SUBCLONAL	1	TRUE	1	0.249264188309939	3		454	305	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45805924	45805924	+	start_lost	Translation_Start_Site	SNP	C	C	T	rs757906591	NA	P-0026615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	44	584	0	ENST00000450313.1:c.3G>A	p.Met1?	p.M1?	ENST00000450313	NM_012222.2	1	atG/atA	1/16	1	2	FACETS	0.592	0.496	0.699	0.592	0.496	0.699	SUBCLONAL	1	TRUE	1	0.249264188309939	2		584	596	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915576	131915576	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	19	303	0	ENST00000265335.6:c.574C>G	p.Leu192Val	p.L192V	ENST00000265335		192	Ctt/Gtt	5/25	1	2	FACETS	0.729	0.556	0.932	0.729	0.556	0.932	CLONAL	1	TRUE	1	0.249264188309939	2		303	209	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139794907	139794907	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	39	474	1	ENST00000247668.2:c.301G>A	p.Glu101Lys	p.E101K	ENST00000247668	NM_021138.3	101	Gag/Aag	4/11	0.231712681140851	3	FACETS	0.601	0.497	0.717	0.3	0.248	0.359	SUBCLONAL	1	TRUE	1	0.249264188309939	3		475	586	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0026616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	167	831	0	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	0.347653205224605	1	FACETS	0.917	0.843	0.994	0.917	0.843	0.994	CLONAL	1	TRUE	0	0.347653205224605	1		831	866	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	150	923	0	ENST00000397752.3:c.3028G>C	p.Asp1010His	p.D1010H	ENST00000397752	NM_000245.2	1010	Gat/Cat	14/21	0.347653205224605	1	FACETS	0.839	0.767	0.914	0.839	0.767	0.914	CLONAL	1	TRUE	0	0.347653205224605	1		923	850	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974695	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691187	NA	P-0026616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	79	434	0	ENST00000304494.5:c.132del	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	taC/ta	1/3	0.347653205224605	1	FACETS	0.849	0.75	0.955	0.849	0.75	0.955	CLONAL	1	TRUE	0	0.347653205224605	1		434	442	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480479	120480479	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0026616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	70	391	0	ENST00000256646.2:c.3337+1G>T		p.X1113_splice	ENST00000256646	NM_024408.3	1113			1	2	FACETS	0.825	0.721	0.937	0.825	0.721	0.937	CLONAL	1	TRUE	1	0.347653205224605	2		391	488	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246670	46246671	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0026616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	44	233	1	ENST00000334344.6:c.4764_4765delinsTT	p.Val1589Phe	p.V1589F	ENST00000334344	NM_152641.2	1588	gtGGtc/gtTTtc	15/21	1	2	FACETS	0.885	0.747	1	0.885	0.747	1	CLONAL	1	TRUE	1	0.347653205224605	2		234	286	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561303	9561303	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	87	504	0	ENST00000353224.5:c.479A>T	p.Tyr160Phe	p.Y160F	ENST00000353224	NM_177990.2	160	tAt/tTt	4/10	1	2	FACETS	0.818	0.725	0.917	0.818	0.725	0.917	CLONAL	1	TRUE	1	0.347653205224605	2		504	612	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492868	56492868	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	269	443	0	ENST00000407977.2:c.71G>T	p.Gly24Val	p.G24V	ENST00000407977		24	gGc/gTc	2/10	0.463060496211196	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.500335955401626	4		443	785	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171473	123171473	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	118	259	0	ENST00000218089.9:c.385G>A	p.Gly129Arg	p.G129R	ENST00000218089	NM_001042749.1	129	Gga/Aga	6/35	0.398041150548645	2	FACETS	0.873	0.816	0.928			1	CLONAL	3	TRUE	NA	0.500335955401626	2		259	180	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0026623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	427	406	0	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	0.425239259214373	2	FACETS	0.855	0.818	0.893	0.855	0.818	0.893	CLONAL	2	TRUE	0	0.49674421957798	2		406	1005	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657369	29657369	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	307	520	0	ENST00000356175.3:c.5602G>T	p.Glu1868Ter	p.E1868*	ENST00000356175	NM_000267.3	1868	Gag/Tag	38/57	0.425239259214373	2	FACETS	0.774	0.733	0.816	0.774	0.733	0.816	SUBCLONAL	2	TRUE	0	0.49674421957798	2		520	798	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271785	15271795	+	frameshift_variant	Frame_Shift_Del	DEL	GCCATGTCCTG	GCCATGTCCTG	-	novel	NA	P-0026623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	434	912	1	ENST00000263388.2:c.6644_6654del	p.Pro2215ArgfsTer23	p.P2215Rfs*23	ENST00000263388	NM_000435.2	2215	cCAGGACATGGC/c	33/33	0.425239259214373	2	FACETS	0.783	0.748	0.818	0.783	0.748	0.818	SUBCLONAL	2	TRUE	0	0.49674421957798	2		913	1116	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	309	501	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.580809033594384	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.580809033594384	3		501	590	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47087991	47087991	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	241	479	0	ENST00000409792.3:c.7084C>T	p.Gln2362Ter	p.Q2362*	ENST00000409792	NM_014159.6	2362	Cag/Tag	16/21	0.580809033594384	3	FACETS	0.999	0.942	1	0.999	0.942	1	CLONAL	2	TRUE	1	0.580809033594384	3		479	536	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919638	28919638	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	303	552	0	ENST00000282397.4:c.2299G>T	p.Val767Leu	p.V767L	ENST00000282397	NM_002019.4	767	Gtg/Ttg	16/30	0.579524239629144	3	FACETS	0.837	0.799	0.875	0.837	0.799	0.875	CLONAL	3	TRUE	0	0.580809033594384	3		552	536	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420080	41420080	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	152	301	0	ENST00000373198.4:c.241G>T	p.Gly81Trp	p.G81W	ENST00000373198	NM_133170.3	81	Ggg/Tgg	3/32	0.357517851254715	5	FACETS	1	0.983	1	0.814	0.753	0.876	CLONAL	2	TRUE	2	0.580809033594384	5		301	401	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164086	108164086	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1064793390	NA	P-0026624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	112	206	0	ENST00000278616.4:c.4661del	p.Asn1554ThrfsTer9	p.N1554Tfs*9	ENST00000278616	NM_000051.3	1553	gAa/ga	31/63	0.580809033594384	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	0	0.580809033594384	2		206	191	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593492	48593492	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	167	340	0	ENST00000342988.3:c.1243G>C	p.Asp415His	p.D415H	ENST00000342988	NM_005359.5	415	Gac/Cac	10/12	0.580809033594384	3	FACETS	0.974	0.907	1	0.974	0.907	1	CLONAL	2	TRUE	1	0.580809033594384	3		340	381	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149453025	149453025	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	202	429	0	ENST00000286301.3:c.921G>T	p.Gln307His	p.Q307H	ENST00000286301	NM_005211.3	307	caG/caT	7/22	0.494076592287798	4	FACETS	0.971	0.907	1	0.971	0.907	1	CLONAL	2	TRUE	2	0.580809033594384	4		429	566	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759821	133759821	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	245	551	1	ENST00000318560.5:c.2144G>T	p.Arg715Leu	p.R715L	ENST00000318560	NM_005157.4	715	cGc/cTc	11/11	0.580809033594384	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.580809033594384	3		552	505	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040613	47040613	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0026624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	156	377	0	ENST00000377604.3:c.1249-1G>T		p.X417_splice	ENST00000377604	NM_001204468.1	417			0.268211932314947	5	FACETS	1	0.975	1	0.753	0.696	0.811	INDETERMINATE	2	TRUE	2	0.580809033594384	5		377	445	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0026625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	25	463	1	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.123	0.096	0.154	0.123	0.096	0.154	SUBCLONAL	1	TRUE	1	0.666215482688022	2		464	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782177	NA	P-0026625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1241	29	781	0	ENST00000269305.4:c.644G>A	p.Ser215Asn	p.S215N	ENST00000269305	NM_001126112.2	215	aGt/aAt	6/11	1	2	FACETS	0.069	0.054	0.085	0.069	0.054	0.085	SUBCLONAL	1	TRUE	1	0.666215482688022	2		781	1270	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849309	89849309	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	822	643	0	ENST00000389301.3:c.1584G>T	p.Met528Ile	p.M528I	ENST00000389301	NM_000135.2	528	atG/atT	17/43	0.614910509868071	5	FACETS	0.957	0.928	0.986	0.957	0.928	0.986	CLONAL	3	TRUE	2	0.666215482688022	5		643	1719	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251942	8251942	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	86	793	0	ENST00000335790.3:c.135C>G	p.His45Gln	p.H45Q	ENST00000335790	NM_002315.2	45	caC/caG	2/4	0.417200147031506	3	FACETS	0.618	0.546	0.695	0.309	0.273	0.348	SUBCLONAL	1	TRUE	1	0.417200147031506	3		793	806	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89869693	89869695	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	rs555210441	NA	P-0026629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	56	597	0	ENST00000389301.3:c.764_766del	p.Arg255del	p.R255del	ENST00000389301	NM_000135.2	255	aGAAct/act	8/43	0.417200147031506	2	FACETS	0.338	0.288	0.392	0.169	0.144	0.196	SUBCLONAL	1	TRUE	0	0.417200147031506	2		597	795	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	239	512	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.417200147031506	2	FACETS	0.96	0.903	1	0.96	0.903	1	CLONAL	2	TRUE	0	0.417200147031506	2		512	597	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41558784	41558784	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0026629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	270	438	1	ENST00000263253.7:c.3728+1G>T		p.X1243_splice	ENST00000263253	NM_001429.3	1243			0.411472404626768	3	FACETS	1	0.99	1	0.813	0.769	0.859	CLONAL	2	TRUE	0	0.417200147031506	3		439	641	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0026630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	347	790	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.441580006008388	2	FACETS	0.907	0.864	0.951	0.907	0.864	0.951	CLONAL	2	TRUE	0	0.486555009675958	2		790	786	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725507	162725507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773159664	NA	P-0026630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	84	530	0	ENST00000367921.3:c.619G>A	p.Gly207Ser	p.G207S	ENST00000367921	NM_006182.2	207	Ggt/Agt	7/18	0.486823868675841	3	FACETS	0.531	0.468	0.598	0.265	0.234	0.299	SUBCLONAL	1	TRUE	1	0.486555009675958	3		530	809	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485389	57485389	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	66	275	0	ENST00000371085.3:c.971C>T	p.Ala324Val	p.A324V	ENST00000371085	NM_000516.4	324	gCt/gTt	12/13	0.486823868675841	4	FACETS	0.761	0.661	0.869	0.254	0.22	0.29	SUBCLONAL	1	TRUE	1	0.486555009675958	4		275	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0026632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	314	409	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.377635329022195	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.386380473205141	2		409	779	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973658	15973658	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1429469964	NA	P-0026635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	281	375	1	ENST00000268712.3:c.4334G>A	p.Arg1445His	p.R1445H	ENST00000268712	NM_006311.3	1445	cGt/cAt	31/46	1	2	FACETS	0.968	0.916	1	0.968	0.916	1	CLONAL	1	TRUE	1	0.885309821674154	2		376	656	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719494	61719494	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	391	434	0	ENST00000401558.2:c.1689G>T	p.Lys563Asn	p.K563N	ENST00000401558	NM_003400.3	563	aaG/aaT	15/25	1	2	FACETS	0.935	0.892	0.978	0.935	0.892	0.978	CLONAL	1	TRUE	1	0.885309821674154	2		434	945	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012636	36012636	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	281	379	0	ENST00000358208.4:c.80C>A	p.Ala27Asp	p.A27D	ENST00000358208		27	gCt/gAt	2/12	0.885309821674154	3	FACETS	0.972	0.915	1	0.486	0.457	0.516	CLONAL	1	TRUE	1	0.885309821674154	3		379	942	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0026647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	320	388	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.269747176033942	3	FACETS	0.949	0.895	1	0.949	0.895	1	CLONAL	2	TRUE	1	0.269747176033942	3		388	1418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0026647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	265	874	0	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.203375864653472	2	FACETS	0.836	0.783	0.891	0.836	0.783	0.891	CLONAL	2	TRUE	0	0.269747176033942	2		874	1175	SUCCESS
APC	324	MSKCC	GRCh37	5	112175621	112175621	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	173	604	0	ENST00000257430.4:c.4330C>T	p.Gln1444Ter	p.Q1444*	ENST00000257430	NM_000038.5	1444	Caa/Taa	16/16	0.203375864653472	2	FACETS	0.778	0.717	0.842	0.778	0.717	0.842	SUBCLONAL	2	TRUE	0	0.269747176033942	2		604	824	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106894	27106894	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	100	664	0	ENST00000324856.7:c.6505G>T	p.Val2169Leu	p.V2169L	ENST00000324856	NM_006015.4	2169	Gta/Tta	20/20	0.214245571799105	3	FACETS	0.782	0.697	0.873	0.391	0.348	0.437	SUBCLONAL	1	TRUE	1	0.269747176033942	3		664	1076	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243778422	243778422	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	169	773	0	ENST00000263826.5:c.603G>T	p.Lys201Asn	p.K201N	ENST00000263826	NM_005465.4	201	aaG/aaT	6/13	0.214245571799105	3	FACETS	1	0.985	1	0.665	0.611	0.722	CLONAL	1	TRUE	1	0.269747176033942	3		773	1069	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77034327	77034327	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	259	860	0	ENST00000356341.3:c.1630A>G	p.Asn544Asp	p.N544D	ENST00000356341	NM_002576.4	544	Aat/Gat	15/15	0.214245571799105	3	FACETS	0.803	0.751	0.857	0.803	0.751	0.857	CLONAL	2	TRUE	1	0.269747176033942	3		860	1357	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114820	108114820	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1169	89	772	1	ENST00000278616.4:c.637T>C	p.Phe213Leu	p.F213L	ENST00000278616	NM_000051.3	213	Ttt/Ctt	6/63	0.214245571799105	3	FACETS	0.595	0.526	0.67	0.298	0.263	0.335	SUBCLONAL	1	TRUE	1	0.269747176033942	3		773	1258	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198432	108198432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144497088	NA	P-0026647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	202	830	1	ENST00000278616.4:c.7036G>A	p.Ala2346Thr	p.A2346T	ENST00000278616	NM_000051.3	2346	Gca/Aca	48/63	0.214245571799105	3	FACETS	1	0.99	1	0.728	0.673	0.784	CLONAL	1	TRUE	1	0.269747176033942	3		831	1168	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865708	57865708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1230	134	954	1	ENST00000228682.2:c.3185C>T	p.Pro1062Leu	p.P1062L	ENST00000228682	NM_005269.2	1062	cCt/cTt	12/12	1	2	FACETS	0.728	0.66	0.801	0.728	0.66	0.801	SUBCLONAL	1	TRUE	1	0.269747176033942	2		955	1364	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885568	111885568	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1238	223	846	0	ENST00000341259.2:c.1345G>T	p.Glu449Ter	p.E449*	ENST00000341259	NM_005475.2	449	Gag/Tag	7/8	0.269747176033942	4	FACETS	1	0.99	1	0.718	0.667	0.772	CLONAL	1	TRUE	2	0.269747176033942	4		846	1461	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48921961	48921961	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	182	703	0	ENST00000267163.4:c.501G>T	p.Arg167Ser	p.R167S	ENST00000267163	NM_000321.2	167	agG/agT	5/27	0.269747176033942	2	FACETS	0.774	0.714	0.835	0.774	0.714	0.835	SUBCLONAL	2	TRUE	0	0.269747176033942	2		703	872	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561471	9561471	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	60	674	0	ENST00000353224.5:c.311G>T	p.Ser104Ile	p.S104I	ENST00000353224	NM_177990.2	104	aGc/aTc	4/10	NA	2	FACETS	0.416	0.357	0.481			1	INDETERMINATE	1	TRUE	NA	0.269747176033942	2		674	1069	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843242	128843242	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	117	851	0	ENST00000249373.3:c.349C>A	p.Arg117Ser	p.R117S	ENST00000249373	NM_005631.4	117	Cgc/Agc	2/12	0.214245571799105	3	FACETS	0.778	0.699	0.861	0.389	0.349	0.431	SUBCLONAL	1	TRUE	1	0.269747176033942	3		851	1266	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974762	21974763	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	98	286	0	ENST00000304494.5:c.64dup	p.Arg22ProfsTer22	p.R22Pfs*22	ENST00000304494	NM_000077.4	22	cgg/cCgg	1/3	0.210184526526459	2	FACETS	0.828	0.743	0.917	0.828	0.743	0.917	CLONAL	2	TRUE	0	0.269747176033942	2		286	439	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242481	+	inframe_deletion	In_Frame_Del	DEL	AATTAAGAGAAGCAA	AATTAAGAGAAGCAA	-	rs121913425	NA	P-0026650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	88	599	0	ENST00000275493.2:c.2237_2251del	p.Glu746_Thr751delinsAla	p.E746_T751delinsA	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAAca/gca	19/28	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.21	2		599	823	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105643	30105643	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1365483457	NA	P-0026650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	135	725	0	ENST00000331968.5:c.1043A>G	p.Asn348Ser	p.N348S	ENST00000331968	NM_002742.2	348	aAt/aGt	7/18	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.21	2		725	1253	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372129	45372129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	62	600	0	ENST00000262160.6:c.1040C>T	p.Ala347Val	p.A347V	ENST00000262160	NM_005901.5	347	gCt/gTt	9/11	1	2	FACETS	0.531	0.457	0.613	0.531	0.457	0.613	SUBCLONAL	1	TRUE	1	0.21	2		600	1111	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	66	474	0				ENST00000310581	NM_198253.2	-/1132			0.579987905045065	1	FACETS	0.539	0.48	0.599	0.539	0.48	0.599	SUBCLONAL	1	TRUE	0	0.892267210332621	1		474	152	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807889	1807889	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs78311289	NA	P-0026651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	179	711	0	ENST00000260795.2:c.1948A>G	p.Lys650Glu	p.K650E	ENST00000260795		650	Aag/Gag	13/17	NA	2	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.892267210332621	2		711	388	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851601	134851601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs961044599	NA	P-0026651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	124	648	0	ENST00000398015.3:c.1007C>T	p.Thr336Met	p.T336M	ENST00000398015	NM_004441.4	336	aCg/aTg	5/16	1	2	FACETS	0.949	0.873	1	0.949	0.873	1	CLONAL	1	TRUE	1	0.892267210332621	2		648	293	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061275	38061276	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	182	743	0	ENST00000250448.2:c.713dup	p.Lys240GlnfsTer53	p.K240Qfs*53	ENST00000250448	NM_004496.3	238	ccg/ccCg	2/2	1	2	FACETS	0.831	0.773	0.889	0.831	0.773	0.889	CLONAL	1	TRUE	1	0.892267210332621	2		743	491	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942803	15942803	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749499082	NA	P-0026651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	49	683	0	ENST00000268712.3:c.6899C>T	p.Ser2300Leu	p.S2300L	ENST00000268712	NM_006311.3	2300	tCa/tTa	44/46	1	2	FACETS	0.235	0.199	0.275	0.235	0.199	0.275	SUBCLONAL	1	TRUE	1	0.892267210332621	2		683	467	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572423	41572429	+	frameshift_variant	Frame_Shift_Del	DEL	CCATGTG	CCATGTG	-	novel	NA	P-0026651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	37	809	0	ENST00000263253.7:c.4953_4959del	p.Met1652CysfsTer55	p.M1652Cfs*55	ENST00000263253	NM_001429.3	1651	aCCATGTGc/ac	30/31	1	2	FACETS	0.194	0.159	0.232	0.194	0.159	0.232	SUBCLONAL	1	TRUE	1	0.892267210332621	2		809	428	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956194	55956194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs922679946	NA	P-0026651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	49	659	1	ENST00000263923.4:c.3121G>A	p.Val1041Met	p.V1041M	ENST00000263923	NM_002253.2	1041	Gtg/Atg	23/30	0.579987905045065	1	FACETS	0.12	0.101	0.14	0.12	0.101	0.14	SUBCLONAL	1	TRUE	0	0.892267210332621	1		660	508	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813525	32813525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1323308777	NA	P-0026651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	27	515	0	ENST00000354258.4:c.2258C>T	p.Ser753Phe	p.S753F	ENST00000354258	NM_000593.5	753	tCc/tTc	11/11	1	2	FACETS	0.203	0.162	0.25	0.203	0.162	0.25	SUBCLONAL	1	TRUE	1	0.892267210332621	2		515	298	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0026652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	583	580	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	0.759531346905256	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.759531346905256	3		580	1038	SUCCESS
ATR	545	MSKCC	GRCh37	3	142286917	142286917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	490	433	0	ENST00000350721.4:c.139G>A	p.Asp47Asn	p.D47N	ENST00000350721	NM_001184.3	47	Gat/Aat	2/47	0.759531346905256	4	FACETS	0.936	0.897	0.975	0.936	0.897	0.975	CLONAL	2	TRUE	2	0.759531346905256	4		433	1213	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0026653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	1428	273	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.447101996047919	8	FACETS	1	0.988	1			1	CLONAL	7	TRUE	NA	0.447101996047919	8		273	2119	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0026653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	517	632	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.408568804130618	2	FACETS	0.933	0.896	0.971	0.933	0.896	0.971	CLONAL	2	TRUE	0	0.447101996047919	2		632	1239	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205217	46205217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	117	412	0	ENST00000334344.6:c.301G>A	p.Glu101Lys	p.E101K	ENST00000334344	NM_152641.2	101	Gag/Aag	4/21	0.22053703773189	1	FACETS	0.487	0.438	0.538	0.487	0.438	0.538	INDETERMINATE	1	TRUE	0	0.447101996047919	1		412	835	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030410	49030410	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	133	488	0	ENST00000267163.4:c.1885G>T	p.Glu629Ter	p.E629*	ENST00000267163	NM_000321.2	629	Gag/Tag	19/27	0.329951463705936	0	FACETS	0.42	0.381	0.46			1	SUBCLONAL	1	TRUE	0	0.447101996047919	0		488	784	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945054	31945054	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	129	570	0	ENST00000340398.3:c.47C>A	p.Ala16Asp	p.A16D	ENST00000340398	NM_001013699.2	16	gCc/gAc	1/1	0.22053703773189	1	FACETS	0.428	0.387	0.472	0.428	0.387	0.472	INDETERMINATE	1	TRUE	0	0.447101996047919	1		570	1046	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744007	41744007	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	298	618	0	ENST00000301178.4:c.942C>A	p.Ser314Arg	p.S314R	ENST00000301178	NM_021913.4	314	agC/agA	7/20	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.447101996047919	2		618	1179	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	384	474	0				ENST00000310581	NM_198253.2	-/1132			0.478154662116164	4	FACETS	0.921	0.881	0.961			1	CLONAL	3	TRUE	NA	0.550106039356146	4		474	783	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	425	489	0	ENST00000269305.4:c.853G>T	p.Glu285Ter	p.E285*	ENST00000269305	NM_001126112.2	285	Gag/Tag	8/11	0.550106039356146	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.550106039356146	1		489	923	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346338	73346338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	267	593	1	ENST00000377767.4:c.1462G>A	p.Asp488Asn	p.D488N	ENST00000377767	NM_014953.3	488	Gat/Aat	10/21	0.278465784360099	1	FACETS	1	0.978	1	1	0.978	1	INDETERMINATE	1	TRUE	0	0.550106039356146	1		594	658	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220666	1220666	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	290	713	0	ENST00000326873.7:c.685del	p.Asp229ThrfsTer58	p.D229Tfs*58	ENST00000326873	NM_000455.4	228	ctG/ct	5/10	0.550106039356146	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.550106039356146	1		713	723	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863395	57863395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775171324	NA	P-0026654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	254	683	3	ENST00000228682.2:c.1490G>A	p.Arg497His	p.R497H	ENST00000228682	NM_005269.2	497	cGc/cAc	11/12	0.213444608821643	2	FACETS	1	0.986	1	0.579	0.544	0.616	INDETERMINATE	1	TRUE	0	0.550106039356146	2		686	797	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845473	128845473	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758800465	NA	P-0026654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	266	688	1	ENST00000249373.3:c.770G>A	p.Arg257Gln	p.R257Q	ENST00000249373	NM_005631.4	257	cGg/cAg	4/12	1	2	FACETS	0.971	0.911	1	0.971	0.911	1	CLONAL	1	TRUE	1	0.550106039356146	2		689	996	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115260837	115260837	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	81	508	0	ENST00000438362.2:c.2488G>T	p.Gly830Trp	p.G830W	ENST00000438362	NM_001242891.1	830	Ggg/Tgg	20/20	0.278465784360099	1	FACETS	0.332	0.292	0.375	0.332	0.292	0.375	INDETERMINATE	1	TRUE	0	0.550106039356146	1		508	643	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742464	17742464	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs768887479	NA	P-0026654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	278	548	0	ENST00000250003.3:c.646C>A	p.Pro216Thr	p.P216T	ENST00000250003	NM_002478.4	216	Ccc/Acc	2/3	0.550106039356146	2	FACETS	0.803	0.761	0.846	0.803	0.761	0.846	CLONAL	2	TRUE	0	0.550106039356146	2		548	629	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041713	14041713	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	240	579	0	ENST00000311895.7:c.2260C>A	p.Arg754Ser	p.R754S	ENST00000311895	NM_005236.2	754	Cgt/Agt	11/11	0.550106039356146	1	FACETS	0.961	0.903	1	0.961	0.903	1	CLONAL	1	TRUE	0	0.550106039356146	1		579	658	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602357	10602380	+	inframe_deletion	In_Frame_Del	DEL	GGCGCAGGGCGACCACTGATTGGT	GGCGCAGGGCGACCACTGATTGGT	-	novel	NA	P-0026654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	311	775	0	ENST00000171111.5:c.1198_1221del	p.Thr400_Ala407del	p.T400_A407del	ENST00000171111	NM_203500.1	400	ACCAATCAGTGGTCGCCCTGCGCC/-	3/6	0.550106039356146	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.550106039356146	1		775	754	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379901	17379901	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0026654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	281	774	0	ENST00000359435.4:c.285+1G>C		p.X95_splice	ENST00000359435	NM_001033549.1	95			0.550106039356146	1	FACETS	0.824	0.776	0.873	0.824	0.776	0.873	CLONAL	1	TRUE	0	0.550106039356146	1		774	899	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719356	190719356	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	65	431	0	ENST00000441310.2:c.1358A>T	p.Tyr453Phe	p.Y453F	ENST00000441310	NM_000534.4	453	tAt/tTt	9/13	0.278465784360099	1	FACETS	0.325	0.282	0.372	0.325	0.282	0.372	INDETERMINATE	1	TRUE	0	0.550106039356146	1		431	527	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39744080	39744080	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0026654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	187	438	0	ENST00000361337.2:c.1707+1G>T		p.X569_splice	ENST00000361337	NM_003286.2	569			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.550106039356146	2		438	640	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101032	41101033	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0026654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	165	653	1	ENST00000373198.4:c.1323_1324delinsAA	p.Gln442Lys	p.Q442K	ENST00000373198	NM_133170.3	441	atCCag/atAAag	8/32	1	2	FACETS	0.789	0.726	0.855	0.789	0.726	0.855	SUBCLONAL	1	TRUE	1	0.550106039356146	2		654	760	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095844	29095844	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs9625537	NA	P-0026654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	223	609	0	ENST00000328354.6:c.990G>T	p.Gln330His	p.Q330H	ENST00000328354	NM_007194.3	330	caG/caT	9/15	0.550106039356146	1	FACETS	0.971	0.911	1	0.971	0.911	1	CLONAL	1	TRUE	0	0.550106039356146	1		609	605	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566576	41566576	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0026654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	90	361	0	ENST00000263253.7:c.4452+1G>A		p.X1484_splice	ENST00000263253	NM_001429.3	1484			0.550106039356146	1	FACETS	0.532	0.474	0.593	0.532	0.474	0.593	SUBCLONAL	1	TRUE	0	0.550106039356146	1		361	446	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205155	128205155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	239	587	1	ENST00000341105.2:c.286C>A	p.Pro96Thr	p.P96T	ENST00000341105	NM_032638.4	96	Ccc/Acc	3/6	0.550106039356146	1	FACETS	0.949	0.891	1	0.949	0.891	1	CLONAL	1	TRUE	0	0.550106039356146	1		588	664	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981108	55981108	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	228	616	0	ENST00000263923.4:c.591G>T	p.Met197Ile	p.M197I	ENST00000263923	NM_002253.2	197	atG/atT	5/30	0.550106039356146	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.550106039356146	1		616	537	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149506136	149506136	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	246	668	0	ENST00000261799.4:c.1621C>A	p.Leu541Met	p.L541M	ENST00000261799	NM_002609.3	541	Ctg/Atg	11/23	0.550106039356146	1	FACETS	0.981	0.923	1	0.981	0.923	1	CLONAL	1	TRUE	0	0.550106039356146	1		668	661	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819716	170819716	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	37	116	0	ENST00000296930.5:c.355G>T	p.Val119Leu	p.V119L	ENST00000296930	NM_002520.6	119	Gtg/Ttg	5/11	0.550106039356146	1	FACETS	0.947	0.803	1	0.947	0.803	1	CLONAL	1	TRUE	0	0.550106039356146	1		116	103	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455159	50455159	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1386107897	NA	P-0026654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	145	432	0	ENST00000331340.3:c.706C>A	p.Leu236Met	p.L236M	ENST00000331340	NM_006060.4	236	Ctg/Atg	6/8	1	2	FACETS	0.966	0.886	1	0.966	0.886	1	CLONAL	1	TRUE	1	0.550106039356146	2		432	546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0026654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	187	659	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.213988552950646	5	FACETS	0.982	0.917	1	0.982	0.917	1	CLONAL	5	TRUE	0	0.213988552950646	5		659	470	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538366	9538366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	44	384	0	ENST00000353224.5:c.1632G>T	p.Gln544His	p.Q544H	ENST00000353224	NM_177990.2	544	caG/caT	7/10	0.15777184245414	4	FACETS	0.935	0.789	1	0.623	0.526	0.729	CLONAL	2	TRUE	1	0.213988552950646	4		384	267	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395520	116395520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774945178	NA	P-0026654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	160	483	0	ENST00000397752.3:c.1813C>T	p.Leu605Phe	p.L605F	ENST00000397752	NM_000245.2	605	Ctt/Ttt	6/21	0.213988552950646	11	FACETS	1	0.968	1			1	CLONAL	4	TRUE	NA	0.213988552950646	11		483	665	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625278	69625278	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	27	748	0	ENST00000334134.2:c.515C>A	p.Thr172Lys	p.T172K	ENST00000334134	NM_005247.2	172	aCa/aAa	3/3	NA	2	FACETS	1	0.909	1			1	INDETERMINATE	1	TRUE	NA	0.213988552950646	2		748	200	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385207	4385207	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	58	506	0	ENST00000261254.3:c.232C>A	p.Pro78Thr	p.P78T	ENST00000261254	NM_001759.3	78	Cct/Act	2/5	0.107249784806069	3	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.213988552950646	3		506	401	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246146	46246146	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0026654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	92	447	0	ENST00000334344.6:c.4240A>T	p.Arg1414Ter	p.R1414*	ENST00000334344	NM_152641.2	1414	Aga/Tga	15/21	0.213988552950646	6	FACETS	1	0.895	1	1	0.895	1	CLONAL	3	TRUE	3	0.213988552950646	6		447	409	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484151	50484151	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs575681571	NA	P-0026654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	91	597	0	ENST00000394963.4:c.1001G>A	p.Arg334Gln	p.R334Q	ENST00000394963	NM_003076.4	334	cGg/cAg	8/13	0.213988552950646	6	FACETS	0.929	0.829	1	0.929	0.829	1	CLONAL	3	TRUE	3	0.213988552950646	6		597	436	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110108	115110108	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0026654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	21	913	1	ENST00000257566.3:c.1771-1G>A		p.X591_splice	ENST00000257566	NM_016569.3	591			0.214732174838153	1	FACETS	0.48	0.369	0.61	0.48	0.369	0.61	SUBCLONAL	1	TRUE	0	0.213988552950646	1		914	365	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112455	115112455	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	31	637	0	ENST00000257566.3:c.1285G>T	p.Asp429Tyr	p.D429Y	ENST00000257566	NM_016569.3	429	Gac/Tac	7/8	0.214732174838153	1	FACETS	1	0.818	1	1	0.818	1	CLONAL	1	TRUE	0	0.213988552950646	1		637	257	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988847	41988847	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0026654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	113	581	0	ENST00000219905.7:c.1639A>T	p.Lys547Ter	p.K547*	ENST00000219905	NM_001164273.1	547	Aaa/Taa	3/24	0.214732174838153	2	FACETS	0.959	0.872	1	1	0.984	1	CLONAL	3	TRUE	0	0.213988552950646	2		581	367	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81973597	81973597	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	50	697	1	ENST00000359376.3:c.3414A>T	p.Glu1138Asp	p.E1138D	ENST00000359376	NM_002661.3	1138	gaA/gaT	30/33	0.214732174838153	2	FACETS	0.811	0.693	0.939	0.811	0.693	0.939	CLONAL	2	TRUE	0	0.213988552950646	2		698	288	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541478	29541499	+	frameshift_variant	Frame_Shift_Del	DEL	TTTAAAGAAAAAGTAACAAGCC	TTTAAAGAAAAAGTAACAAGCC	-	novel	NA	P-0026654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	30	224	0	ENST00000356175.3:c.1404_1425del	p.Phe468LeufsTer23	p.F468Lfs*23	ENST00000356175	NM_000267.3	468	TTTAAAGAAAAAGTAACAAGCCtt/tt	13/57	0.214732174838153	3	FACETS	0.853	0.694	1	0.853	0.694	1	CLONAL	2	TRUE	1	0.213988552950646	3		224	182	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110622	4110622	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	71	648	0	ENST00000262948.5:c.335G>T	p.Arg112Leu	p.R112L	ENST00000262948	NM_030662.3	112	cGg/cTg	3/11	0.214732174838153	1	FACETS	0.89	0.782	1	1	0.98	1	CLONAL	2	TRUE	0	0.213988552950646	1		648	333	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727161	40727161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	46	637	1	ENST00000373198.4:c.3803C>T	p.Thr1268Ile	p.T1268I	ENST00000373198	NM_133170.3	1268	aCc/aTc	28/32	0.214732174838153	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.213988552950646	1		638	282	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462393	89462393	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	69	640	0	ENST00000336596.2:c.1865C>A	p.Ser622Tyr	p.S622Y	ENST00000336596	NM_005233.5	622	tCc/tAc	10/17	0.213988552950646	5	FACETS	0.793	0.692	0.903	0.793	0.692	0.903	CLONAL	2	TRUE	3	0.213988552950646	5		640	537	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920377	134920377	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	45	562	1	ENST00000398015.3:c.2192G>T	p.Gly731Val	p.G731V	ENST00000398015	NM_004441.4	731	gGc/gTc	12/16	0.214732174838153	0	FACETS	0.664	0.562	0.774			1	SUBCLONAL	2	TRUE	0	0.213988552950646	0		563	249	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968588	55968588	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	150	616	0	ENST00000263923.4:c.2075G>T	p.Gly692Val	p.G692V	ENST00000263923	NM_002253.2	692	gGg/gTg	14/30	0.15777184245414	4	FACETS	1	0.936	1	1	0.936	1	CLONAL	3	TRUE	1	0.213988552950646	4		616	555	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161744	56161744	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1406908752	NA	P-0026654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	113	595	0	ENST00000399503.3:c.1241G>T	p.Arg414Leu	p.R414L	ENST00000399503	NM_005921.1	414	cGc/cTc	6/20	0.213988552950646	6	FACETS	0.931	0.841	1			1	CLONAL	3	TRUE	NA	0.213988552950646	6		595	540	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181526	32181526	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	25	703	0	ENST00000375023.3:c.2259C>A	p.Cys753Ter	p.C753*	ENST00000375023	NM_004557.3	753	tgC/tgA	14/30	0.214732174838153	3	FACETS	0.709	0.558	0.882	0.354	0.279	0.441	SUBCLONAL	1	TRUE	1	0.213988552950646	3		703	365	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750737	128750737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	47	567	1	ENST00000377970.2:c.274G>A	p.Val92Ile	p.V92I	ENST00000377970	NM_002467.4	92	Gtc/Atc	2/3	0.213988552950646	7	FACETS	1	0.957	1	0.238	0.201	0.279	CLONAL	1	TRUE	1	0.213988552950646	7		568	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0026654-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	231	945	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.262149941316232	3	FACETS	1	0.98	1	0.737	0.691	0.785	CLONAL	2	TRUE	0	0.369204933302353	3		945	670	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610123	10610123	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026654-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	210	734	0	ENST00000171111.5:c.587G>T	p.Cys196Phe	p.C196F	ENST00000171111	NM_203500.1	196	tGt/tTt	2/6	0.369204933302353	2	FACETS	0.962	0.9	1	0.962	0.9	1	CLONAL	2	TRUE	0	0.369204933302353	2		734	591	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019401	42019401	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026654-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	210	508	1	ENST00000219905.7:c.3454C>T	p.Gln1152Ter	p.Q1152*	ENST00000219905	NM_001164273.1	1152	Cag/Tag	10/24	0.310784661812154	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.369204933302353	2		509	533	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217317	11217317	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026654-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	106	736	0	ENST00000361445.4:c.4361A>G	p.His1454Arg	p.H1454R	ENST00000361445	NM_004958.3	1454	cAc/cGc	30/58	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.369204933302353	2		736	498	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956203	175956203	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026654-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	150	467	0	ENST00000367669.3:c.2009G>T	p.Gly670Val	p.G670V	ENST00000367669	NM_022457.5	670	gGa/gTa	18/20	0.299177232231822	4	FACETS	0.979	0.9	1	0.979	0.9	1	CLONAL	2	TRUE	2	0.369204933302353	4		467	568	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245243	46245243	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026654-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	103	462	0	ENST00000334344.6:c.3337G>T	p.Gly1113Trp	p.G1113W	ENST00000334344	NM_152641.2	1113	Ggg/Tgg	15/21	0.267204160258068	4	FACETS	0.853	0.767	0.942			1	CLONAL	2	TRUE	NA	0.369204933302353	4		462	448	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30095689	30095689	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0026654-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	199	646	0	ENST00000331968.5:c.1798+1G>T		p.X600_splice	ENST00000331968	NM_002742.2	600			0.204058964832786	4	FACETS	1	0.971	1			1	INDETERMINATE	2	TRUE	NA	0.369204933302353	4		646	682	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934900	9934900	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026654-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	100	554	0	ENST00000330684.3:c.1390C>A	p.Leu464Met	p.L464M	ENST00000330684	NM_001134407.1	464	Ctg/Atg	6/13	0.318987468477975	2	FACETS	0.769	0.694	0.848	0.769	0.694	0.848	SUBCLONAL	2	TRUE	0	0.369204933302353	2		554	352	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512393	38512393	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026654-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	132	614	0	ENST00000254066.5:c.1304G>T	p.Gly435Val	p.G435V	ENST00000254066	NM_000964.3	435	gGt/gTt	9/9	0.34517891443021	3	FACETS	0.945	0.865	1	0.945	0.865	1	CLONAL	2	TRUE	1	0.369204933302353	3		614	448	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954670	17954670	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026654-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	184	833	0	ENST00000458235.1:c.224C>G	p.Thr75Arg	p.T75R	ENST00000458235	NM_000215.3	75	aCg/aGg	3/24	0.369204933302353	2	FACETS	0.861	0.799	0.924	0.861	0.799	0.924	CLONAL	2	TRUE	0	0.369204933302353	2		833	579	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162332	47162332	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026654-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	32	347	0	ENST00000409792.3:c.3794A>T	p.Glu1265Val	p.E1265V	ENST00000409792	NM_014159.6	1265	gAa/gTa	3/21	0.198366155598839	3	FACETS	0.567	0.461	0.687	0.284	0.23	0.344	INDETERMINATE	1	TRUE	1	0.369204933302353	3		347	362	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391097	89391097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1339518966	NA	P-0026654-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	171	680	0	ENST00000336596.2:c.1163G>T	p.Gly388Val	p.G388V	ENST00000336596	NM_005233.5	388	gGa/gTa	5/17	0.34517891443021	3	FACETS	0.829	0.765	0.895	0.829	0.765	0.895	CLONAL	2	TRUE	1	0.369204933302353	3		680	662	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55124951	55124951	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs759019262	NA	P-0026654-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	170	789	0	ENST00000257290.5:c.16C>G	p.Pro6Ala	p.P6A	ENST00000257290	NM_006206.4	6	Ccg/Gcg	2/23	0.306799192076245	2	FACETS	1	0.988	1	0.688	0.635	0.743	CLONAL	1	TRUE	0	0.369204933302353	2		789	669	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55987322	55987322	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026654-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	113	512	0	ENST00000263923.4:c.103A>C	p.Ser35Arg	p.S35R	ENST00000263923	NM_002253.2	35	Agc/Cgc	2/30	0.348611588495009	4	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.369204933302353	4		512	679	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356296	66356296	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026654-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	38	545	0	ENST00000273854.3:c.1201C>A	p.His401Asn	p.H401N	ENST00000273854	NM_004439.5	401	Cat/Aat	5/18	0.198366155598839	3	FACETS	0.513	0.424	0.613	0.257	0.212	0.307	INDETERMINATE	1	TRUE	1	0.369204933302353	3		545	475	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846411	128846411	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026654-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	112	552	0	ENST00000249373.3:c.1247G>T	p.Gly416Val	p.G416V	ENST00000249373	NM_005631.4	416	gGc/gTc	6/12	0.369204933302353	5	FACETS	1	0.916	1	0.676	0.611	0.743	CLONAL	2	TRUE	2	0.369204933302353	5		552	465	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27213497	27213497	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026654-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	104	522	0	ENST00000380036.4:c.2893C>A	p.Leu965Met	p.L965M	ENST00000380036	NM_000459.3	965	Ctg/Atg	18/23	0.256811696788961	3	FACETS	0.76	0.685	0.839	0.76	0.685	0.839	SUBCLONAL	2	TRUE	1	0.369204933302353	3		522	439	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0026655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	416	706	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.82585288377922	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.82585288377922	2		706	478	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796795	135796795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1322586198	NA	P-0026655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	16	483	0	ENST00000298552.3:c.692C>T	p.Pro231Leu	p.P231L	ENST00000298552	NM_001162426.1	231	cCg/cTg	8/23	0.82585288377922	3	FACETS	0.187	0.138	0.247	0.094	0.069	0.124	SUBCLONAL	1	TRUE	1	0.82585288377922	3		483	292	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738814	145738814	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750304658	NA	P-0026655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1508	245	697	0	ENST00000428558.2:c.2251C>T	p.Arg751Trp	p.R751W	ENST00000428558	NM_004260.3	751	Cgg/Tgg	14/22	0.82585288377922	6	FACETS	0.898	0.836	0.962	0.18	0.167	0.193	CLONAL	1	TRUE	1	0.82585288377922	6		697	1753	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120132	70120133	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0026655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	265	184	0	ENST00000245479.2:c.1137_1138dup	p.His380ArgfsTer4	p.H380Rfs*4	ENST00000245479	NM_000346.3	378	-/GC	3/3	0.82585288377922	4	FACETS	0.918	0.889	0.945	0.918	0.889	0.945	CLONAL	4	TRUE	0	0.82585288377922	4		184	319	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606899	43606899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1226167606	NA	P-0026655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	537	773	1	ENST00000355710.3:c.1508C>T	p.Thr503Ile	p.T503I	ENST00000355710	NM_020975.4	503	aCa/aTa	7/20	0.82585288377922	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.82585288377922	3		774	886	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959366	26959366	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1418353379	NA	P-0026655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	278	387	0	ENST00000381527.3:c.533G>A	p.Arg178Gln	p.R178Q	ENST00000381527	NM_001260.1	178	cGa/cAa	6/13	0.82585288377922	5	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	TRUE	2	0.82585288377922	5		387	486	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45422934	45422934	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	211	495	0	ENST00000262160.6:c.194T>C	p.Ile65Thr	p.I65T	ENST00000262160	NM_005901.5	65	aTc/aCc	2/11	0.82585288377922	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.82585288377922	2		495	250	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575206	48575206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	18	427	0	ENST00000342988.3:c.400G>A	p.Glu134Lys	p.E134K	ENST00000342988	NM_005359.5	134	Gaa/Aaa	3/12	0.82585288377922	2	FACETS	0.19	0.143	0.245	0.095	0.071	0.123	SUBCLONAL	1	TRUE	0	0.82585288377922	2		427	230	SUCCESS
APC	324	MSKCC	GRCh37	5	112174403	112174629	+	frameshift_variant	Frame_Shift_Del	DEL	TCTGGAAGGCAAAGTCCTTCACAGAATGAAAGATGGGCAAGACCCAAACACATAATAGAAGATGAAATAAAACAAAGTGAGCAAAGACAATCAAGGAATCAAAGTACAACTTATCCTGTTTATACTGAGAGCACTGATGATAAACACCTCAAGTTCCAACCACATTTTGGACAGCAGGAATGTGTTTCTCCATACAGGTCACGGGGAGCCAATGGTTCAGAAACAAA	TCTGGAAGGCAAAGTCCTTCACAGAATGAAAGATGGGCAAGACCCAAACACATAATAGAAGATGAAATAAAACAAAGTGAGCAAAGACAATCAAGGAATCAAAGTACAACTTATCCTGTTTATACTGAGAGCACTGATGATAAACACCTCAAGTTCCAACCACATTTTGGACAGCAGGAATGTGTTTCTCCATACAGGTCACGGGGAGCCAATGGTTCAGAAACAAA	-	novel	NA	P-0026655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	133	389	0	ENST00000257430.4:c.3114_3340del	p.Gly1039SerfsTer4	p.G1039Sfs*4	ENST00000257430	NM_000038.5	1038	TCTGGAAGGCAAAGTCCTTCACAGAATGAAAGATGGGCAAGACCCAAACACATAATAGAAGATGAAATAAAACAAAGTGAGCAAAGACAATCAAGGAATCAAAGTACAACTTATCCTGTTTATACTGAGAGCACTGATGATAAACACCTCAAGTTCCAACCACATTTTGGACAGCAGGAATGTGTTTCTCCATACAGGTCACGGGGAGCCAATGGTTCAGAAACAAAt/t	16/16	0.82585288377922	2	FACETS	0.953	0.906	0.996	0.953	0.906	0.996	CLONAL	2	TRUE	0	0.82585288377922	2		389	169	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0026657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	218	379	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.580564599895945	3	FACETS	1	0.988	1	0.637	0.594	0.681	CLONAL	1	TRUE	1	0.580564599895945	3		379	761	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0026657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	585	589	0	ENST00000269305.4:c.673-1G>C		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.177007545578135	3	FACETS	0.903	0.875	0.931			1	INDETERMINATE	3	TRUE	NA	0.580564599895945	3		589	960	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259123	16259123	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1940	183	748	0	ENST00000375759.3:c.6388G>C	p.Glu2130Gln	p.E2130Q	ENST00000375759	NM_015001.2	2130	Gag/Cag	11/15	0.580564599895945	5	FACETS	0.556	0.51	0.603	0.185	0.17	0.201	SUBCLONAL	1	TRUE	2	0.580564599895945	5		748	2123	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247804	59247804	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1194	421	750	0	ENST00000371222.2:c.939G>T	p.Met313Ile	p.M313I	ENST00000371222	NM_002228.3	313	atG/atT	1/1	0.341488287702657	4	FACETS	1	0.995	1	0.355	0.337	0.373	INDETERMINATE	1	TRUE	0	0.580564599895945	4		750	1615	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719934	18719934	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1296146485	NA	P-0026657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	303	669	0	ENST00000266497.5:c.3831C>G	p.Phe1277Leu	p.F1277L	ENST00000266497		1277	ttC/ttG	27/31	0.342200253046648	3	FACETS	1	0.989	1	0.401	0.378	0.425	INDETERMINATE	1	TRUE	0	0.580564599895945	3		669	1119	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039441	49039441	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	381	642	0	ENST00000267163.4:c.2426T>G	p.Leu809Arg	p.L809R	ENST00000267163	NM_000321.2	809	cTg/cGg	23/27	0.414626484076266	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.580564599895945	1		642	772	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122730	7122730	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1619	404	749	0	ENST00000302850.5:c.3424G>A	p.Glu1142Lys	p.E1142K	ENST00000302850	NM_000208.2	1142	Gag/Aag	19/22	0.580564599895945	4	FACETS	1	0.984	1	0.544	0.515	0.573	CLONAL	1	TRUE	2	0.580564599895945	4		749	2023	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190742112	190742112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	203	677	1	ENST00000441310.2:c.2749C>T	p.His917Tyr	p.H917Y	ENST00000441310	NM_000534.4	917	Cat/Tat	13/13	0.187854292812862	3	FACETS	0.966	0.896	1	0.483	0.448	0.519	INDETERMINATE	1	TRUE	1	0.580564599895945	3		678	934	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963866	2963866	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0026657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	280	624	0	ENST00000396946.4:c.1940+1G>C		p.X647_splice	ENST00000396946	NM_032415.4	647			0.57346065407798	4	FACETS	1	0.981	1	0.557	0.522	0.593	CLONAL	1	TRUE	2	0.580564599895945	4		624	1368	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593588	55593605	+	inframe_deletion	In_Frame_Del	DEL	ATGTATGAAGTACAGTGG	ATGTATGAAGTACAGTGG	-	novel	NA	P-0026664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	62	218	0	ENST00000288135.5:c.1655_1672del	p.Met552_Trp557del	p.M552_W557del	ENST00000288135	NM_000222.2	552	ATGTATGAAGTACAGTGG/-	11/21	1	2	FACETS	0.705	0.617	0.799	0.705	0.617	0.799	SUBCLONAL	1	TRUE	1	0.744767384792385	2		218	236	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	87	474	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.56	2		474	308	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0026665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	53	483	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	0.56	2		483	176	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218089	108218089	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587779874	NA	P-0026665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	10	228	0	ENST00000278616.4:c.8668C>G	p.Leu2890Val	p.L2890V	ENST00000278616	NM_000051.3	2890	Cta/Gta	59/63	1	2	FACETS	0.331	0.225	0.461	0.331	0.225	0.461	SUBCLONAL	1	TRUE	1	0.56	2		228	108	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202231	108202231	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	18	283	0	ENST00000278616.4:c.7576A>G	p.Arg2526Gly	p.R2526G	ENST00000278616	NM_000051.3	2526	Aga/Gga	51/63	1	2	FACETS	0.39	0.295	0.5	0.39	0.295	0.5	SUBCLONAL	1	TRUE	1	0.56	2		283	165	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0026666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	198	364	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.393111590710414	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	0	0.393111590710414	3		364	365	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955538	48955538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913303	NA	P-0026666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	122	238	0	ENST00000267163.4:c.1654C>T	p.Arg552Ter	p.R552*	ENST00000267163	NM_000321.2	552	Cga/Tga	17/27	0.390501654066677	2	FACETS	0.952	0.872	1	0.952	0.872	1	CLONAL	2	TRUE	0	0.393111590710414	2		238	326	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928834	49928834	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs878910700	NA	P-0026666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	89	361	2	ENST00000296474.3:c.3532C>T	p.Arg1178Trp	p.R1178W	ENST00000296474	NM_002447.2	1178	Cgg/Tgg	16/20	0.370082823797724	3	FACETS	1	0.975	1	0.672	0.6	0.749	CLONAL	1	TRUE	1	0.393111590710414	3		363	403	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0026667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	164	503	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.210437825469597	4	FACETS	0.886	0.821	0.953	0.886	0.821	0.953	CLONAL	4	TRUE	0	0.25172297777064	4		505	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0026667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	165	592	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.227783615084201	3	FACETS	1	0.973	1	0.75	0.691	0.811	CLONAL	2	TRUE	0	0.25172297777064	3		594	656	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14317380	14317380	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	69	260	1	ENST00000256196.4:c.130G>T	p.Asp44Tyr	p.D44Y	ENST00000256196		44	Gat/Tat	2/6	0.218673058427953	2	FACETS	0.876	0.769	0.989	0.876	0.769	0.989	CLONAL	2	TRUE	0	0.25172297777064	2		261	313	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793385	242793385	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750496363	NA	P-0026667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	72	442	0	ENST00000334409.5:c.692G>A	p.Arg231Gln	p.R231Q	ENST00000334409	NM_005018.2	231	cGa/cAa	5/5	0.159656693482036	4	FACETS	1	0.942	1	0.569	0.497	0.647	CLONAL	1	TRUE	2	0.25172297777064	4		442	629	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280142	66280142	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	42	199	0	ENST00000273854.3:c.1547C>G	p.Thr516Arg	p.T516R	ENST00000273854	NM_004439.5	516	aCg/aGg	7/18	0.218673058427953	2	FACETS	0.897	0.759	1	0.897	0.759	1	CLONAL	2	TRUE	0	0.25172297777064	2		199	186	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0026668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	387	592	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.924174464064278	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.924174464064278	1		594	421	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911797	32911797	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	224	289	0	ENST00000380152.3:c.3305A>T	p.Asn1102Ile	p.N1102I	ENST00000380152		1102	aAt/aTt	11/27	0.439713160949747	5	FACETS	1	0.989	1	0.431	0.402	0.462	INDETERMINATE	1	TRUE	2	0.924174464064278	5		289	894	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881489	48881490	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGAGAGAGCTTGGTTAACTTGGGAGAAAGTTTCATCTGTG	novel	NA	P-0026668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	142	217	2	ENST00000267163.4:c.214_254dup	p.Asp85GlufsTer6	p.D85Efs*6	ENST00000267163	NM_000321.2	71	aga/aGAGAGAGAGCTTGGTTAACTTGGGAGAAAGTTTCATCTGTGga	2/27	0.565597521208574	1	FACETS	0.42	0.386	0.454	0.42	0.386	0.454	SUBCLONAL	1	TRUE	0	0.924174464064278	1		219	394	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647544	23647544	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	266	296	2	ENST00000261584.4:c.323A>T	p.Asn108Ile	p.N108I	ENST00000261584	NM_024675.3	108	aAc/aTc	4/13	1	2	FACETS	0.966	0.914	1	0.966	0.914	1	CLONAL	1	TRUE	1	0.924174464064278	2		298	596	SUCCESS
APC	324	MSKCC	GRCh37	5	112173784	112173784	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	127	178	2	ENST00000257430.4:c.2493del	p.Leu831PhefsTer11	p.L831Ffs*11	ENST00000257430	NM_000038.5	831	ttA/tt	16/16	0.924174464064278	1	FACETS	0.942	0.896	0.983	0.942	0.896	0.983	CLONAL	1	TRUE	0	0.924174464064278	1		180	157	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371798	116371798	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	203	270	0	ENST00000397752.3:c.1277G>T	p.Arg426Leu	p.R426L	ENST00000397752	NM_000245.2	426	cGc/cTc	3/21	1	2	FACETS	0.891	0.835	0.948	0.891	0.835	0.948	CLONAL	1	TRUE	1	0.924174464064278	2		270	493	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0026669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	121	707	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	0.943	0.853	1	0.943	0.853	1	CLONAL	1	TRUE	1	0.380371695789576	2		707	675	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271364	18271364	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	129	304	0	ENST00000222254.8:c.406G>T	p.Glu136Ter	p.E136*	ENST00000222254	NM_005027.3	136	Gaa/Taa	3/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.380371695789576	2		304	578	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573130	41573130	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	137	390	1	ENST00000263253.7:c.5415C>A	p.Phe1805Leu	p.F1805L	ENST00000263253	NM_001429.3	1805	ttC/ttA	31/31	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.380371695789576	2		391	676	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117755	70117755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	68	345	0	ENST00000245479.2:c.223G>A	p.Glu75Lys	p.E75K	ENST00000245479	NM_000346.3	75	Gag/Aag	1/3	0.378113071460101	14	FACETS	1	0.909	1	0.097	0.083	0.111	CLONAL	1	TRUE	3	0.378113071460101	14		345	1107	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115889	8115926	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGCCACATGCTGACCACGCCCACGCCGATGCACCCG	CCAGCCACATGCTGACCACGCCCACGCCGATGCACCCG	-	novel	NA	P-0026670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	135	271	0	ENST00000346208.3:c.1238_1275del	p.Ser413IlefsTer81	p.S413Ifs*81	ENST00000346208		412	tCCAGCCACATGCTGACCACGCCCACGCCGATGCACCCG/t	6/6	0.378113071460101	3	FACETS	0.82	0.749	0.893	0.82	0.749	0.893	CLONAL	2	TRUE	1	0.378113071460101	3		271	518	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39708819	39708819	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1325065963	NA	P-0026670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	29	110	2	ENST00000361337.2:c.430G>A	p.Asp144Asn	p.D144N	ENST00000361337	NM_003286.2	144	Gat/Aat	6/21	0.378113071460101	5	FACETS	0.865	0.696	1	0.288	0.232	0.352	CLONAL	1	TRUE	2	0.378113071460101	5		112	278	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243058	105243059	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATGATGAAGGTGTTGGGCCGGGGCCGCTCCGTCTTC	novel	NA	P-0026671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	142	357	1	ENST00000349310.3:c.189_224dup	p.Met63_Ile74dup	p.M63_I74dup	ENST00000349310	NM_001014432.1	63	atc/atGAAGACGGAGCGGCCCCGGCCCAACACCTTCATCATc	5/15	0.441888032756432	1	FACETS	0.305	0.278	0.333	0.305	0.278	0.333	INDETERMINATE	1	TRUE	0	0.825003389183901	1		358	663	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272308	38272308	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs869320694	NA	P-0026671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	111	325	1	ENST00000425967.3:c.2059A>G	p.Lys687Glu	p.K687E	ENST00000425967	NM_001174067.1	687	Aag/Gag	15/19	0.825003389183901	1	FACETS	0.393	0.356	0.432	0.393	0.356	0.432	SUBCLONAL	1	TRUE	0	0.825003389183901	1		326	402	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515307	31515307	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0026671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	38	319	0	ENST00000344624.3:c.1078A>T	p.Lys360Ter	p.K360*	ENST00000344624		360	Aag/Tag	5/33	1	2	FACETS	0.374	0.311	0.444	0.374	0.311	0.444	SUBCLONAL	1	TRUE	1	0.825003389183901	2		319	246	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257106	198257106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	10	467	2	ENST00000335508.6:c.3836C>T	p.Ala1279Val	p.A1279V	ENST00000335508	NM_012433.2	1279	gCt/gTt	25/25	1	2	FACETS	0.317	0.215	0.446	0.317	0.215	0.446	SUBCLONAL	1	TRUE	1	0.32	2		469	197	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0026671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	44	502	1	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	0.32	2		503	216	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243058	105243059	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATGATGAAGGTGTTGGGCCGGGGCCGCTCCGTCTTC	novel	NA	P-0026671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	30	357	1	ENST00000349310.3:c.189_224dup	p.Met63_Ile74dup	p.M63_I74dup	ENST00000349310	NM_001014432.1	63	atc/atGAAGACGGAGCGGCCCCGGCCCAACACCTTCATCATc	5/15	1	2	FACETS	0.864	0.701	1	0.864	0.701	1	CLONAL	1	TRUE	1	0.32	2		358	217	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116116	67116117	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	36	276	0	ENST00000412916.2:c.401dup	p.Glu135GlyfsTer10	p.E135Gfs*10	ENST00000412916		134	cag/cAag	5/6	0.199708481930802	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.32	1		276	128	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0026672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	289	592	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.635184843739129	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.635184843739129	2		594	450	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819212	3819212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	155	358	1	ENST00000262367.5:c.3023C>T	p.Pro1008Leu	p.P1008L	ENST00000262367	NM_004380.2	1008	cCc/cTc	15/31	0.635184843739129	4	FACETS	1	0.979	1	0.299	0.274	0.325	CLONAL	1	TRUE	0	0.635184843739129	4		359	667	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471066	8471066	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1462367917	NA	P-0026672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	15	210	0	ENST00000356435.5:c.3433G>C	p.Val1145Leu	p.V1145L	ENST00000356435		1145	Gtg/Ctg	20/35	0.635184843739129	2	FACETS	0.18	0.131	0.239	0.09	0.065	0.12	SUBCLONAL	1	TRUE	0	0.635184843739129	2		210	262	SUCCESS
APC	324	MSKCC	GRCh37	5	112175524	112175524	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	176	245	0	ENST00000257430.4:c.4233del	p.Ser1411ArgfsTer4	p.S1411Rfs*4	ENST00000257430	NM_000038.5	1411	agT/ag	16/16	0.301023087342332	4	FACETS	0.931	0.867	0.996	0.931	0.867	0.996	INDETERMINATE	2	TRUE	2	0.741103983354598	4		245	444	SUCCESS
APC	324	MSKCC	GRCh37	5	112157650	112157650	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1060503333	NA	P-0026674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	256	289	0	ENST00000257430.4:c.1370C>A	p.Ser457Ter	p.S457*	ENST00000257430	NM_000038.5	457	tCa/tAa	11/16	0.301023087342332	4	FACETS	0.996	0.94	1	0.996	0.94	1	INDETERMINATE	2	TRUE	2	0.741103983354598	4		289	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576911	7576912	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0026674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	479	381	0	ENST00000269305.4:c.934_935del	p.Thr312GlnfsTer24	p.T312Qfs*24	ENST00000269305	NM_001126112.2	312	ACc/c	9/11	0.741103983354598	2	FACETS	0.99	0.961	1	0.99	0.961	1	CLONAL	2	TRUE	0	0.741103983354598	2		381	653	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138729528	NA	P-0026675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	769	383	4	ENST00000269305.4:c.523C>G	p.Arg175Gly	p.R175G	ENST00000269305	NM_001126112.2	175	Cgc/Ggc	5/11	0.950725968054884	2	FACETS	0.992	0.981	1	0.992	0.981	1	CLONAL	2	TRUE	0	0.950725968054884	2		387	815	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955540	48955541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	275	309	0	ENST00000267163.4:c.1656_1657insG	p.Cys553ValfsTer2	p.C553Vfs*2	ENST00000267163	NM_000321.2	552	-/G	17/27	0.950725968054884	1	FACETS	0.998	0.975	1	0.998	0.975	1	CLONAL	1	TRUE	0	0.950725968054884	1		309	304	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748819	43748819	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	100	526	0	ENST00000382044.4:c.1987G>C	p.Gly663Arg	p.G663R	ENST00000382044	NM_001141980.1	663	Ggg/Cgg	12/28	0.950725968054884	1	FACETS	0.254	0.228	0.282	0.254	0.228	0.282	SUBCLONAL	1	TRUE	0	0.950725968054884	1		526	434	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374428	81374428	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	123	305	0	ENST00000222390.5:c.634A>G	p.Met212Val	p.M212V	ENST00000222390	NM_000601.4	212	Atg/Gtg	6/18	0.477292019983763	1	FACETS	0.286	0.26	0.313	0.286	0.26	0.313	INDETERMINATE	1	TRUE	0	0.950725968054884	1		305	475	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646961	37646961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	86	419	0	ENST00000447079.4:c.2083C>T	p.Gln695Ter	p.Q695*	ENST00000447079	NM_015083.1	695	Cag/Tag	3/14	1	2	FACETS	0.558	0.493	0.627	0.558	0.493	0.627	SUBCLONAL	1	TRUE	1	0.434140560133773	2		419	710	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657611	37657612	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AATGGAAGGATTGG	novel	NA	P-0026676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	64	397	0	ENST00000447079.4:c.2532_2545dup	p.Tyr849TrpfsTer24	p.Y849Wfs*24	ENST00000447079	NM_015083.1	843	cta/ctAATGGAAGGATTGGa	6/14	1	2	FACETS	0.541	0.469	0.619	0.541	0.469	0.619	SUBCLONAL	1	TRUE	1	0.434140560133773	2		397	545	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0026680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	96	518	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.241889869414546	3	FACETS	1	0.98	1	0.741	0.662	0.826	CLONAL	1	TRUE	1	0.241889869414546	3		518	600	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717733	89717733	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1554825235	NA	P-0026680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	51	246	0	ENST00000371953.3:c.758T>A	p.Ile253Asn	p.I253N	ENST00000371953	NM_000314.4	253	aTc/aAc	7/9	0.241889869414546	1	FACETS	0.913	0.778	1	0.913	0.778	1	CLONAL	1	TRUE	0	0.241889869414546	1		246	406	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031883	26031884	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs758780418	NA	P-0026680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	20	146	0	ENST00000244661.2:c.405_406del	p.Arg135SerfsTer12	p.R135Sfs*12	ENST00000244661	NM_003537.3	135	agAGcg/agcg	1/1	1	2	FACETS	0.866	0.665	1	0.866	0.665	1	CLONAL	1	TRUE	1	0.241889869414546	2		146	191	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427614	49427614	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	49	296	0	ENST00000301067.7:c.10874C>T	p.Pro3625Leu	p.P3625L	ENST00000301067	NM_003482.3	3625	cCc/cTc	39/54	1	2	FACETS	0.869	0.737	1	0.869	0.737	1	CLONAL	1	TRUE	1	0.241889869414546	2		296	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574029	7574029	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	49	335	0	ENST00000269305.4:c.998G>C	p.Arg333Pro	p.R333P	ENST00000269305	NM_001126112.2	333	cGt/cCt	10/11	0.241889869414546	1	FACETS	0.702	0.595	0.821	0.702	0.595	0.821	SUBCLONAL	1	TRUE	0	0.241889869414546	1		335	507	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78519487	78519487	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	66	314	0	ENST00000306801.3:c.58G>C	p.Asp20His	p.D20H	ENST00000306801	NM_020761.2	20	Gat/Cat	1/34	1	2	FACETS	0.858	0.745	0.981	0.858	0.745	0.981	CLONAL	1	TRUE	1	0.241889869414546	2		314	636	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0026682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	28	629	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		629	450	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344741	65344741	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	29	187	0	ENST00000342505.4:c.296A>G	p.Asp99Gly	p.D99G	ENST00000342505	NM_002227.2	99	gAc/gGc	4/25	1	2	FACETS	0.275	0.22	0.337	0.275	0.22	0.337	SUBCLONAL	1	TRUE	1	0.545141402964147	2		187	387	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636701	176636701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	104	258	0	ENST00000439151.2:c.1301C>T	p.Pro434Leu	p.P434L	ENST00000439151	NM_022455.4	434	cCc/cTc	5/23	1	2	FACETS	0.922	0.831	1	0.922	0.831	1	CLONAL	1	TRUE	1	0.545141402964147	2		258	414	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0026685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	212	503	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.730556713386219	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.739276753288303	3		505	387	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692941	89692941	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	230	325	0	ENST00000371953.3:c.428del	p.Gly143AlafsTer4	p.G143Afs*4	ENST00000371953	NM_000314.4	142	cGg/cg	5/9	0.730556713386219	3	FACETS	0.996	0.942	1	0.996	0.942	1	CLONAL	2	TRUE	1	0.739276753288303	3		325	428	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720822	89720822	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1554825602	NA	P-0026685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	87	134	0	ENST00000371953.3:c.973del	p.Asp326ThrfsTer18	p.D326Tfs*18	ENST00000371953	NM_000314.4	325	Ctt/tt	8/9	0.730556713386219	3	FACETS	1	0.974	1	0.64	0.575	0.706	CLONAL	1	TRUE	1	0.739276753288303	3		134	252	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480583	123480583	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	152	387	0	ENST00000371139.4:c.91del	p.Leu31Ter	p.L31*	ENST00000371139	NM_001114937.2	31	Ctg/tg	1/4	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.739276753288303	2		387	390	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0026687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	189	503	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.291794333724266	3	FACETS	0.843	0.778	0.911	1	0.985	1	CLONAL	3	TRUE	1	0.14	3		505	1142	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0026687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1502	119	945	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.14	2		945	1621	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032767	48032768	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1057517764	NA	P-0026687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	45	389	0	ENST00000234420.5:c.3573dup	p.Val1192CysfsTer2	p.V1192Cfs*2	ENST00000234420	NM_000179.2	1189	-/T	7/10	1	2	FACETS	0.995	0.835	1	0.995	0.835	1	CLONAL	1	TRUE	1	0.14	2		389	646	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231437	46231437	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	54	603	1	ENST00000334344.6:c.1277C>T	p.Thr426Met	p.T426M	ENST00000334344	NM_152641.2	426	aCg/aTg	10/21	0.291794333724266	3	FACETS	0.871	0.741	1	0.435	0.37	0.507	CLONAL	1	TRUE	1	0.14	3		604	948	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274159	10274159	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	73	525	0	ENST00000330684.3:c.110C>T	p.Ala37Val	p.A37V	ENST00000330684	NM_001134407.1	37	gCg/gTg	2/13	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.14	2		525	834	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287446	46287446	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs774801990	NA	P-0026687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	56	568	0	ENST00000334344.6:c.5305C>T	p.Arg1769Ter	p.R1769*	ENST00000334344	NM_152641.2	1769	Cga/Tga	20/21	NA	2	FACETS	0.805	0.687	0.934			1	INDETERMINATE	1	TRUE	NA	0.14	2		568	994	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945648	206945648	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs570050304	NA	P-0026687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1222	90	708	0	ENST00000423557.1:c.133C>T	p.Arg45Ter	p.R45*	ENST00000423557	NM_000572.2	45	Cga/Tga	1/5	1	2	FACETS	0.98	0.866	1	0.98	0.866	1	CLONAL	1	TRUE	1	0.14	2		708	1312	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026106	71026106	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759521321	NA	P-0026687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	56	556	1	ENST00000318789.4:c.1516G>A	p.Ala506Thr	p.A506T	ENST00000318789	NM_032682.5	506	Gcg/Acg	17/21	1	2	FACETS	0.795	0.679	0.923	0.795	0.679	0.923	CLONAL	1	TRUE	1	0.14	2		557	1006	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169166	119169166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140725852	NA	P-0026687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	84	640	0	ENST00000264033.4:c.2350G>A	p.Val784Met	p.V784M	ENST00000264033	NM_005188.3	784	Gtg/Atg	15/16	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.14	2		640	1098	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416736	416736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748802448	NA	P-0026687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	139	367	0	ENST00000399788.2:c.3814G>A	p.Ala1272Thr	p.A1272T	ENST00000399788	NM_001042603.1	1272	Gcc/Acc	23/28	0.291794333724266	3	FACETS	0.927	0.845	1	1	0.984	1	CLONAL	3	TRUE	1	0.14	3		367	764	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431474	121431474	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1225	71	854	0	ENST00000257555.6:c.678G>T	p.Lys226Asn	p.K226N	ENST00000257555		226	aaG/aaT	3/10	NA	2	FACETS	0.783	0.68	0.894			1	INDETERMINATE	1	TRUE	NA	0.14	2		854	1296	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355016	73355016	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	58	530	0	ENST00000377767.4:c.354G>T	p.Lys118Asn	p.K118N	ENST00000377767	NM_014953.3	118	aaG/aaT	2/21	1	2	FACETS	0.935	0.801	1	0.935	0.801	1	CLONAL	1	TRUE	1	0.14	2		530	886	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671731	67671731	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1385636609	NA	P-0026687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	137	758	1	ENST00000264010.4:c.2140G>A	p.Gly714Arg	p.G714R	ENST00000264010	NM_006565.3	714	Gga/Aga	12/12	1	2	FACETS	0.783	0.711	0.86	1	0.987	1	SUBCLONAL	2	TRUE	1	0.14	2		759	1249	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184478	7184478	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	88	742	0	ENST00000302850.5:c.823T>C	p.Phe275Leu	p.F275L	ENST00000302850	NM_000208.2	275	Ttc/Ctc	3/22	0.155928274993367	1	FACETS	0.932	0.823	1	0.932	0.823	1	CLONAL	1	TRUE	0	0.14	1		742	1255	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62320861	62320861	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766112578	NA	P-0026687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	67	768	0	ENST00000360203.5:c.1885G>A	p.Glu629Lys	p.E629K	ENST00000360203	NM_001283009.1	629	Gag/Aag	23/35	1	2	FACETS	0.809	0.7	0.928	0.809	0.7	0.928	CLONAL	1	TRUE	1	0.14	2		768	1183	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205741	128205741	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	95	655	0	ENST00000341105.2:c.134T>C	p.Val45Ala	p.V45A	ENST00000341105	NM_032638.4	45	gTg/gCg	2/6	0.186919463121989	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.14	1		655	1157	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226017	226017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759827541	NA	P-0026687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	26	132	0	ENST00000264932.6:c.476C>T	p.Pro159Leu	p.P159L	ENST00000264932	NM_004168.2	159	cCg/cTg	5/15	1	2	FACETS	0.804	0.64	0.99	1	0.939	1	CLONAL	2	TRUE	1	0.14	2		132	231	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815713	32815713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1168560265	NA	P-0026687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1477	86	726	0	ENST00000354258.4:c.1903C>T	p.Arg635Cys	p.R635C	ENST00000354258	NM_000593.5	635	Cgc/Tgc	8/11	0.171429308168717	4	FACETS	0.896	0.789	1	0.448	0.394	0.506	CLONAL	1	TRUE	2	0.14	4		726	1563	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0026688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	94	503	2	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	0.261911100406992	2		505	651	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602763	10602763	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs774469695	NA	P-0026688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	168	717	0	ENST00000171111.5:c.815G>T	p.Arg272Leu	p.R272L	ENST00000171111	NM_203500.1	272	cGc/cTc	3/6	0.261911100406992	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.261911100406992	1		717	888	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22417972	22417972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	25	129	0	ENST00000344548.3:c.538C>T	p.Pro180Ser	p.P180S	ENST00000344548	NM_001039802.1	180	Cca/Tca	7/7	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.261911100406992	2		129	173	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945357	71945357	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	186	748	0	ENST00000298229.2:c.2245G>T	p.Glu749Ter	p.E749*	ENST00000298229	NM_001567.3	749	Gag/Tag	20/28	0.230192482212776	2	FACETS	1	0.99	1	0.745	0.688	0.805	CLONAL	1	TRUE	0	0.261911100406992	2		748	953	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226469	133226469	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	64	393	0	ENST00000320574.5:c.3589A>G	p.Met1197Val	p.M1197V	ENST00000320574	NM_006231.2	1197	Atg/Gtg	30/49	1	2	FACETS	0.91	0.789	1	0.91	0.789	1	CLONAL	1	TRUE	1	0.261911100406992	2		393	537	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919688	28919689	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0026688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	55	380	1	ENST00000282397.4:c.2249-1_2249delinsTT		p.X750_splice	ENST00000282397	NM_002019.4	750		16/30	1	2	FACETS	0.847	0.725	0.98	0.847	0.725	0.98	CLONAL	1	TRUE	1	0.261911100406992	2		381	496	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778802	3778802	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	98	713	2	ENST00000262367.5:c.6246G>T	p.Gln2082His	p.Q2082H	ENST00000262367	NM_004380.2	2082	caG/caT	31/31	1	2	FACETS	0.882	0.786	0.985	0.882	0.786	0.985	CLONAL	1	TRUE	1	0.261911100406992	2		715	848	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39870295	39870295	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	61	394	0	ENST00000288319.7:c.10A>G	p.Thr4Ala	p.T4A	ENST00000288319	NM_182918.3	4	Act/Gct	1/10	1	2	FACETS	0.838	0.723	0.962	0.838	0.723	0.962	CLONAL	1	TRUE	1	0.261911100406992	2		394	556	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928394	69928394	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	59	433	0	ENST00000352241.4:c.214G>T	p.Glu72Ter	p.E72*	ENST00000352241	NM_198159.2	72	Gag/Tag	2/10	1	2	FACETS	0.866	0.746	0.997	0.866	0.746	0.997	CLONAL	1	TRUE	1	0.261911100406992	2		433	520	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888750	76888750	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	68	559	0	ENST00000373344.5:c.5079G>T	p.Arg1693Ser	p.R1693S	ENST00000373344	NM_000489.3	1693	agG/agT	19/35	1	2	FACETS	0.811	0.706	0.926	0.811	0.706	0.926	CLONAL	1	TRUE	1	0.261911100406992	2		559	640	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938103	76938106	+	frameshift_variant	Frame_Shift_Del	DEL	TTTC	TTTC	-	novel	NA	P-0026688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	88	624	1	ENST00000373344.5:c.2642_2645del	p.Arg881AsnfsTer23	p.R881Nfs*23	ENST00000373344	NM_000489.3	881	aGAAAa/aa	9/35	1	2	FACETS	0.912	0.808	1	0.912	0.808	1	CLONAL	1	TRUE	1	0.261911100406992	2		625	737	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165782	108165783	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	A	novel	NA	P-0026688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	128	474	0	ENST00000278616.4:c.4905_4906delinsA	p.Gln1636ArgfsTer10	p.Q1636Rfs*10	ENST00000278616	NM_000051.3	1635	tcTCag/tcAag	32/63	0.230192482212776	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	0	0.261911100406992	2		474	469	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533630	63533631	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	A	novel	NA	P-0026688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	138	646	0	ENST00000307078.5:c.1523_1524delinsT	p.Lys508IlefsTer181	p.K508Ifs*181	ENST00000307078	NM_004655.3	508	aAG/aT	6/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.261911100406992	2		646	769	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0026689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	424	706	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.470795621382515	2	FACETS	0.802	0.767	0.836	0.802	0.767	0.836	CLONAL	2	TRUE	0	0.556237499074398	2		706	951	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191385	185191385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	141	606	1	ENST00000265026.3:c.2266G>A	p.Asp756Asn	p.D756N	ENST00000265026	NM_004721.4	756	Gac/Aac	11/14	0.477583235212356	2	FACETS	0.559	0.509	0.612	0.279	0.254	0.306	SUBCLONAL	1	TRUE	0	0.556237499074398	2		607	907	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0026689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	675	604	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.556237499074398	5	FACETS	0.966	0.937	0.995			1	CLONAL	4	TRUE	NA	0.556237499074398	5		604	1152	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242494	55242494	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	641	534	0	ENST00000275493.2:c.2264C>G	p.Ala755Gly	p.A755G	ENST00000275493	NM_005228.3	755	gCc/gGc	19/28	0.556237499074398	5	FACETS	1	0.986	1			1	CLONAL	4	TRUE	NA	0.556237499074398	5		534	1030	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176666819	176666819	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	115	549	0	ENST00000439151.2:c.4255G>C	p.Asp1419His	p.D1419H	ENST00000439151	NM_022455.4	1419	Gac/Cac	8/23	0.212564296197814	5	FACETS	0.601	0.539	0.666	0.2	0.179	0.222	INDETERMINATE	1	TRUE	2	0.556237499074398	5		549	1263	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218654	98218654	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	108	476	0	ENST00000331920.6:c.3210G>A	p.Met1070Ile	p.M1070I	ENST00000331920	NM_000264.3	1070	atG/atA	19/24	0.550715975405858	1	FACETS	0.464	0.417	0.514	0.464	0.417	0.514	SUBCLONAL	1	TRUE	0	0.556237499074398	1		476	604	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378351	225378351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	85	178	0	ENST00000264414.4:c.544G>A	p.Ala182Thr	p.A182T	ENST00000264414	NM_003590.4	182	Gca/Aca	5/16	0.174718865228129	2	FACETS	0.447	0.395	0.503	0.223	0.197	0.252	INDETERMINATE	1	TRUE	0	0.556237499074398	2		178	684	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876343	35876343	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200570812	NA	P-0026689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	217	296	0	ENST00000303115.3:c.1135G>A	p.Ala379Thr	p.A379T	ENST00000303115	NM_002185.3	379	Gcc/Acc	8/8	0.212564296197814	5	FACETS	0.763	0.71	0.818	0.509	0.473	0.545	INDETERMINATE	2	TRUE	2	0.556237499074398	5		296	938	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288928	11288928	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1481	78	525	0	ENST00000361445.4:c.2827C>G	p.Leu943Val	p.L943V	ENST00000361445	NM_004958.3	943	Ctg/Gtg	19/58	0.556237499074398	5	FACETS	0.33	0.288	0.375	0.082	0.072	0.094	SUBCLONAL	1	TRUE	1	0.556237499074398	5		525	1559	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736388	85736388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs949558985	NA	P-0026689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	186	437	0	ENST00000370580.1:c.259C>T	p.Arg87Trp	p.R87W	ENST00000370580	NM_003921.4	87	Cgg/Tgg	2/3	0.256137319045023	4	FACETS	1	0.953	1	0.522	0.482	0.564	INDETERMINATE	1	TRUE	2	0.556237499074398	4		437	996	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117297	7117297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145697152	NA	P-0026689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	59	695	1	ENST00000302850.5:c.3919G>A	p.Glu1307Lys	p.E1307K	ENST00000302850	NM_000208.2	1307	Gag/Aag	22/22	0.198414874177906	3	FACETS	0.238	0.203	0.275	0.079	0.067	0.092	INDETERMINATE	1	TRUE	0	0.556237499074398	3		696	1141	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260290	10260290	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	66	584	0	ENST00000340748.4:c.2377C>G	p.His793Asp	p.H793D	ENST00000340748		793	Cac/Gac	25/40	0.198414874177906	3	FACETS	0.333	0.288	0.381	0.111	0.096	0.127	INDETERMINATE	1	TRUE	0	0.556237499074398	3		584	912	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762872	40762872	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	87	661	0	ENST00000392038.2:c.136G>C	p.Asp46His	p.D46H	ENST00000392038	NM_001626.4	46	Gat/Cat	3/14	0.439200228788525	3	FACETS	0.358	0.316	0.404	0.179	0.158	0.202	SUBCLONAL	1	TRUE	1	0.556237499074398	3		661	1116	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0026690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	487	388	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.3	9	FACETS	0.978	0.941	1			1	CLONAL	9	TRUE	NA	0.2	9		388	941	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579592	7579592	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0026690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	89	600	0	ENST00000269305.4:c.97-2A>T		p.X33_splice	ENST00000269305	NM_001126112.2	33			1	2	FACETS	0.837	0.74	0.941	0.837	0.74	0.941	CLONAL	1	TRUE	1	0.2	2		600	1063	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85742010	85742010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1496	85	678	0	ENST00000370580.1:c.26C>T	p.Thr9Ile	p.T9I	ENST00000370580	NM_003921.4	9	aCc/aTc	1/3	1	2	FACETS	0.538	0.473	0.608	0.538	0.473	0.608	SUBCLONAL	1	TRUE	1	0.2	2		678	1581	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998887	100998887	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	120	662	1	ENST00000325455.5:c.915C>A	p.His305Gln	p.H305Q	ENST00000325455	NM_001202474.3	305	caC/caA	1/8	1	2	FACETS	0.975	0.878	1	0.975	0.878	1	CLONAL	1	TRUE	1	0.2	2		663	1231	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934155	48934155	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	14	377	2	ENST00000267163.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000267163	NM_000321.2	204	Gaa/Taa	7/27	1	2	FACETS	0.619	0.448	0.827	0.619	0.448	0.827	SUBCLONAL	1	TRUE	1	0.2	2		379	226	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046617	30046617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149150061	NA	P-0026690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	73	615	1	ENST00000331968.5:c.2566G>A	p.Gly856Arg	p.G856R	ENST00000331968	NM_002742.2	856	Ggg/Agg	18/18	1	2	FACETS	0.817	0.713	0.929	0.817	0.713	0.929	CLONAL	1	TRUE	1	0.2	2		616	894	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423660	88423660	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0026690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	42	359	2	ENST00000360948.2:c.2176-1G>T		p.X726_splice	ENST00000360948	NM_001012338.2	726			1	2	FACETS	0.665	0.554	0.788	0.665	0.554	0.788	SUBCLONAL	1	TRUE	1	0.2	2		361	632	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56857677	56857677	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	97	609	0	ENST00000308159.5:c.713C>A	p.Ala238Glu	p.A238E	ENST00000308159	NM_014669.4	238	gCa/gAa	8/22	1	2	FACETS	0.779	0.692	0.872	0.779	0.692	0.872	SUBCLONAL	1	TRUE	1	0.2	2		609	1245	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39573237	39573238	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0026690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	21	469	1	ENST00000262039.4:c.718_719delinsCT	p.Gly240Leu	p.G240L	ENST00000262039	NM_002647.2	240	GGt/CTt	7/25	1	2	FACETS	0.631	0.485	0.8	0.631	0.485	0.8	SUBCLONAL	1	TRUE	1	0.2	2		470	333	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602319	10602320	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0026690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1399	162	698	0	ENST00000171111.5:c.1258dup	p.Val420GlyfsTer25	p.V420Gfs*25	ENST00000171111	NM_203500.1	420	gtc/gGtc	3/6	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.2	2		698	1561	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714377	40714377	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	53	556	1	ENST00000373198.4:c.4020C>A	p.Asn1340Lys	p.N1340K	ENST00000373198	NM_133170.3	1340	aaC/aaA	29/32	0.118458695608062	3	FACETS	0.558	0.474	0.651	0.279	0.237	0.326	INDETERMINATE	1	TRUE	1	0.2	3		557	1045	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524834	187524834	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	88	655	0	ENST00000441802.2:c.10846G>T	p.Val3616Leu	p.V3616L	ENST00000441802	NM_005245.3	3616	Gta/Tta	19/27	1	2	FACETS	0.81	0.716	0.912	0.81	0.716	0.912	CLONAL	1	TRUE	1	0.2	2		655	1086	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050750	5050750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	39	642	1	ENST00000381652.3:c.533G>A	p.Cys178Tyr	p.C178Y	ENST00000381652	NM_004972.3	178	tGt/tAt	6/25	1	2	FACETS	0.682	0.564	0.813	0.682	0.564	0.813	SUBCLONAL	1	TRUE	1	0.2	2		643	572	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0026691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	200	459	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.21166032202512	4	FACETS	1	0.989	1	0.699	0.646	0.755	CLONAL	1	TRUE	2	0.278144699770543	4		459	1314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578177	7578177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs267605076	NA	P-0026691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	267	629	0	ENST00000269305.4:c.672G>T	p.Glu224Asp	p.E224D	ENST00000269305	NM_001126112.2	224	gaG/gaT	6/11	0.23104278620275	2	FACETS	0.863	0.809	0.919	0.863	0.809	0.919	CLONAL	2	TRUE	0	0.278144699770543	2		629	1112	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646376	23646377	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0026691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1229	290	505	0	ENST00000261584.4:c.1490dup	p.Asn497LysfsTer2	p.N497Kfs*2	ENST00000261584	NM_024675.3	497	aat/aaAt	4/13	0.278144699770543	6	FACETS	1	0.974	1			1	CLONAL	2	TRUE	NA	0.278144699770543	6		505	1519	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853800	59853800	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	248	537	0	ENST00000259008.2:c.2059G>C	p.Val687Leu	p.V687L	ENST00000259008	NM_032043.2	687	Gtg/Ctg	14/20	0.21166032202512	4	FACETS	0.906	0.846	0.968	0.906	0.846	0.968	CLONAL	2	TRUE	2	0.278144699770543	4		537	1258	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350927	89350927	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1334	83	944	0	ENST00000301030.4:c.2023G>C	p.Glu675Gln	p.E675Q	ENST00000301030	NM_001256183.1	675	Gag/Cag	9/13	1	2	FACETS	0.375	0.329	0.424	0.375	0.329	0.424	SUBCLONAL	1	TRUE	1	0.312569241230831	2		944	1417	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170519	11170519	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1235280916	NA	P-0026693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	76	699	0	ENST00000358026.2:c.4822G>A	p.Glu1608Lys	p.E1608K	ENST00000358026	NM_001128849.1	1608	Gag/Aag	34/36	1	2	FACETS	0.451	0.394	0.512	0.451	0.394	0.512	SUBCLONAL	1	TRUE	1	0.312569241230831	2		699	1079	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170531	11170531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	72	701	0	ENST00000358026.2:c.4834G>A	p.Glu1612Lys	p.E1612K	ENST00000358026	NM_001128849.1	1612	Gag/Aag	34/36	1	2	FACETS	0.451	0.393	0.515	0.451	0.393	0.515	SUBCLONAL	1	TRUE	1	0.312569241230831	2		701	1021	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170528	11170528	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568564823	NA	P-0026693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	70	705	1	ENST00000358026.2:c.4831G>A	p.Glu1611Lys	p.E1611K	ENST00000358026	NM_001128849.1	1611	Gaa/Aaa	34/36	1	2	FACETS	0.434	0.377	0.496	0.434	0.377	0.496	SUBCLONAL	1	TRUE	1	0.312569241230831	2		706	1032	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0026694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	322	424	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.0896019364154433	5	FACETS	1	0.952	1			1	INDETERMINATE	2	TRUE	NA	0.466233810278136	5		424	1164	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579585	7579585	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	219	637	2	ENST00000269305.4:c.102del	p.Leu35CysfsTer9	p.L35Cfs*9	ENST00000269305	NM_001126112.2	34	ccC/cc	4/11	0.447476782022209	1	FACETS	0.936	0.873	1	0.936	0.873	1	CLONAL	1	TRUE	0	0.466233810278136	1		639	770	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746132	162746132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1374086542	NA	P-0026694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	246	223	0	ENST00000367921.3:c.2255G>A	p.Arg752His	p.R752H	ENST00000367921	NM_006182.2	752	cGc/cAc	16/18	0.466233810278136	3	FACETS	0.922	0.866	0.978	0.922	0.866	0.978	CLONAL	2	TRUE	1	0.466233810278136	3		223	706	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600427	43600427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	155	553	4	ENST00000355710.3:c.653C>T	p.Pro218Leu	p.P218L	ENST00000355710	NM_020975.4	218	cCg/cTg	4/20	1	2	FACETS	0.961	0.882	1	0.961	0.882	1	CLONAL	1	TRUE	1	0.466233810278136	2		557	692	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0026695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	431	518	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.714185214865656	3	FACETS	0.79	0.755	0.824	0.79	0.755	0.824	SUBCLONAL	2	TRUE	1	0.744645992480849	3		518	1006	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0026695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	411	410	1	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.677712628847079	2	FACETS	0.858	0.828	0.889	0.858	0.828	0.889	CLONAL	2	TRUE	0	0.744645992480849	2		411	643	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	26	474	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	0.45	0.356	0.558	0.45	0.356	0.558	SUBCLONAL	1	TRUE	0	0.27	1		474	370	SUCCESS
AR	367	MSKCC	GRCh37	X	66766196	66766196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772490323	NA	P-0026696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	32	410	0	ENST00000374690.3:c.1208C>T	p.Ala403Val	p.A403V	ENST00000374690	NM_000044.3	403	gCg/gTg	1/8	0.3	1	FACETS	0.659	0.536	0.797	0.659	0.536	0.797	SUBCLONAL	1	TRUE	0	0.27	1		410	311	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0026697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	49	388	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.145671206873851	1	FACETS	0.995	0.842	1	0.995	0.842	1	CLONAL	1	TRUE	0	0.145671206873851	1		388	627	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714227	43714227	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	51	753	2	ENST00000382044.4:c.3926C>T	p.Ser1309Phe	p.S1309F	ENST00000382044	NM_001141980.1	1309	tCc/tTc	19/28	1	2	FACETS	0.836	0.708	0.976	0.836	0.708	0.976	CLONAL	1	TRUE	1	0.145671206873851	2		755	838	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003775	45003775	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs104894481	NA	P-0026697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	36	425	0	ENST00000558401.1:c.31G>C	p.Ala11Pro	p.A11P	ENST00000558401	NM_004048.2	11	Gcg/Ccg	1/4	1	2	FACETS	0.751	0.616	0.904	0.751	0.616	0.904	CLONAL	1	TRUE	1	0.145671206873851	2		425	658	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420309	88420309	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs878997142	NA	P-0026697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	38	516	1	ENST00000360948.2:c.2377C>T	p.Arg793Ter	p.R793*	ENST00000360948	NM_001012338.2	793	Cga/Tga	19/19	1	2	FACETS	0.705	0.581	0.844	0.705	0.581	0.844	SUBCLONAL	1	TRUE	1	0.145671206873851	2		517	740	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341349	89341349	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	70	474	0	ENST00000301030.4:c.7586C>T	p.Ser2529Phe	p.S2529F	ENST00000301030	NM_001256183.1	2529	tCc/tTc	11/13	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.145671206873851	2		474	680	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211611	5211611	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	33	389	0	ENST00000357368.4:c.5224G>C	p.Asp1742His	p.D1742H	ENST00000357368	NM_002850.3	1742	Gat/Cat	33/38	1	2	FACETS	0.748	0.607	0.907	0.748	0.607	0.907	CLONAL	1	TRUE	1	0.145671206873851	2		389	606	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215574	36215574	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1386551503	NA	P-0026697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	97	748	3	ENST00000222270.7:c.3371C>T	p.Pro1124Leu	p.P1124L	ENST00000222270	NM_014727.1	1124	cCc/cTc	9/37	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.145671206873851	2		751	994	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796325	42796325	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1135401825	NA	P-0026697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	83	749	1	ENST00000575354.2:c.2974C>T	p.Gln992Ter	p.Q992*	ENST00000575354	NM_015125.3	992	Cag/Tag	12/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.145671206873851	2		750	900	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528617	89528617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	44	379	0	ENST00000336596.2:c.2917G>A	p.Glu973Lys	p.E973K	ENST00000336596	NM_005233.5	973	Gaa/Aaa	17/17	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.145671206873851	2		379	552	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396221	139396222	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0026697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	71	674	1	ENST00000277541.6:c.5616_5617delinsTT	p.Met1872_Asp1873delinsIleTyr	p.M1872_D1873delinsIY	ENST00000277541	NM_017617.3	1872	atGGac/atTTac	30/34	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.145671206873851	2		675	879	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7978925	7978925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397514532	NA	P-0026698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	204	513	0	ENST00000319144.4:c.1642C>T	p.Arg548Trp	p.R548W	ENST00000319144	NM_001139.2	548	Cgg/Tgg	12/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.648507069801607	2		513	582	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56857674	56857674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144804729	NA	P-0026698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	287	626	1	ENST00000308159.5:c.710C>T	p.Pro237Leu	p.P237L	ENST00000308159	NM_014669.4	237	cCg/cTg	8/22	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.648507069801607	2		627	829	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877859	151877860	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	450	452	0	ENST00000262189.6:c.7085dup	p.Gly2363ArgfsTer4	p.G2363Rfs*4	ENST00000262189	NM_170606.2	2362	tca/tcCa	36/59	0.648507069801607	3	FACETS	0.978	0.938	1	0.978	0.938	1	CLONAL	2	TRUE	1	0.648507069801607	3		452	940	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0026699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	614	503	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.729063553470442	3	FACETS	0.973	0.941	1	0.973	0.941	1	CLONAL	2	TRUE	1	0.736719269710228	3		505	1172	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699324	18699324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369934938	NA	P-0026699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	609	474	1	ENST00000266497.5:c.3425G>A	p.Arg1142His	p.R1142H	ENST00000266497		1142	cGt/cAt	24/31	0.729063553470442	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.736719269710228	3		475	1104	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959432	26959432	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	319	544	0	ENST00000381527.3:c.599G>A	p.Arg200Gln	p.R200Q	ENST00000381527	NM_001260.1	200	cGa/cAa	6/13	0.729063553470442	3	FACETS	0.946	0.892	1	0.473	0.446	0.501	CLONAL	1	TRUE	1	0.736719269710228	3		544	1253	SUCCESS
APC	324	MSKCC	GRCh37	5	112175411	112175412	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	202	341	0	ENST00000257430.4:c.4122dup	p.His1375ThrfsTer11	p.H1375Tfs*11	ENST00000257430	NM_000038.5	1374	gaa/gAaa	16/16	0.736719269710228	1	FACETS	0.992	0.938	1	0.992	0.938	1	CLONAL	1	TRUE	0	0.736719269710228	1		341	349	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0026701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	211	388	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.555768918270017	3	FACETS	0.931	0.873	0.99	0.931	0.873	0.99	CLONAL	2	TRUE	1	0.555768918270017	3		388	521	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165852	118165852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1191996445	NA	P-0026701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	308	470	0	ENST00000369448.3:c.362C>T	p.Pro121Leu	p.P121L	ENST00000369448	NM_017709.3	121	cCa/cTa	2/2	0.553204935133459	2	FACETS	0.939	0.895	0.983	0.939	0.895	0.983	CLONAL	2	TRUE	0	0.555768918270017	2		470	590	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858503	57858503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753380800	NA	P-0026701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	239	709	1	ENST00000228682.2:c.241C>T	p.Arg81Trp	p.R81W	ENST00000228682	NM_005269.2	81	Cgg/Tgg	4/12	0.555768918270017	3	FACETS	0.95	0.886	1	0.475	0.443	0.508	CLONAL	1	TRUE	1	0.555768918270017	3		710	1157	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953728	48953728	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1555286503	NA	P-0026701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	222	315	0	ENST00000267163.4:c.1333-2A>G		p.X445_splice	ENST00000267163	NM_000321.2	445			0.555768918270017	2	FACETS	0.933	0.882	0.985	0.933	0.882	0.985	CLONAL	2	TRUE	0	0.555768918270017	2		315	428	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220706	1220706	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs878853992	NA	P-0026701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	370	596	0	ENST00000326873.7:c.724G>T	p.Gly242Trp	p.G242W	ENST00000326873	NM_000455.4	242	Ggg/Tgg	5/10	0.555768918270017	2	FACETS	0.898	0.859	0.938	0.898	0.859	0.938	CLONAL	2	TRUE	0	0.555768918270017	2		596	741	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602618	10602621	+	frameshift_variant	Frame_Shift_Del	DEL	CCGG	CCGG	-	novel	NA	P-0026701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	378	645	0	ENST00000171111.5:c.957_960del	p.Cys319TrpfsTer8	p.C319Wfs*8	ENST00000171111	NM_203500.1	319	tgCCGG/tg	3/6	0.555768918270017	2	FACETS	0.853	0.815	0.891	0.853	0.815	0.891	CLONAL	2	TRUE	0	0.555768918270017	2		645	797	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61722714	61722714	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	134	498	0	ENST00000401558.2:c.923A>G	p.Tyr308Cys	p.Y308C	ENST00000401558	NM_003400.3	308	tAc/tGc	11/25	0.398496217887011	3	FACETS	0.935	0.852	1	0.468	0.426	0.511	CLONAL	1	TRUE	1	0.555768918270017	3		498	659	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041582	47041582	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	190	399	3	ENST00000377604.3:c.1807C>T	p.Gln603Ter	p.Q603*	ENST00000377604	NM_001204468.1	603	Cag/Tag	17/24	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.555768918270017	1		402	366	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429999	78429999	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	257	489	0	ENST00000370768.2:c.880A>G	p.Asn294Asp	p.N294D	ENST00000370768	NM_003902.3	294	Aat/Gat	11/20	0.278196766740416	2	FACETS	1	0.994	1	0.737	0.697	0.778	INDETERMINATE	1	TRUE	0	0.609621162175226	2		489	572	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186775	108186775	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	465	640	0	ENST00000278616.4:c.6133G>C	p.Ala2045Pro	p.A2045P	ENST00000278616	NM_000051.3	2045	Gcc/Ccc	42/63	0.301762187126451	4	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.609621162175226	4		640	1140	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752756	128752756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766292378	NA	P-0026706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	35	334	0	ENST00000377970.2:c.917C>T	p.Pro306Leu	p.P306L	ENST00000377970	NM_002467.4	306	cCt/cTt	3/3	0.609621162175226	4	FACETS	0.266	0.217	0.322			1	SUBCLONAL	1	TRUE	NA	0.609621162175226	4		334	694	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0026708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	416	606	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.365699702339802	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.365699702339802	2		606	928	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075152	16075152	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	132	441	0	ENST00000268712.3:c.400C>G	p.Pro134Ala	p.P134A	ENST00000268712	NM_006311.3	134	Cca/Gca	4/46	0.364361541311111	3	FACETS	0.964	0.875	1	0.482	0.437	0.529	CLONAL	1	TRUE	1	0.365699702339802	3		441	886	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794882	242794882	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	317	702	0	ENST00000334409.5:c.327C>A	p.Ser109Arg	p.S109R	ENST00000334409	NM_005018.2	109	agC/agA	2/5	0.354148119464708	4	FACETS	0.952	0.898	1	0.952	0.898	1	CLONAL	2	TRUE	2	0.365699702339802	4		702	1244	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207037	1207037	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	328	680	0	ENST00000326873.7:c.127del	p.Ala43ProfsTer8	p.A43Pfs*8	ENST00000326873	NM_000455.4	42	cGg/cg	1/10	0.365699702339802	2	FACETS	0.977	0.926	1	0.977	0.926	1	CLONAL	2	TRUE	0	0.365699702339802	2		680	918	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602473	10602473	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	302	565	1	ENST00000171111.5:c.1105G>T	p.Val369Leu	p.V369L	ENST00000171111	NM_203500.1	369	Gtg/Ttg	3/6	0.365699702339802	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.365699702339802	2		566	808	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36945080	36945080	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	184	667	0	ENST00000361632.4:c.18C>A	p.Asn6Lys	p.N6K	ENST00000361632		6	aaC/aaA	2/16	0.365699702339802	2	FACETS	0.994	0.917	1	0.497	0.458	0.537	CLONAL	1	TRUE	0	0.365699702339802	2		667	1012	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169139	119169139	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	165	588	2	ENST00000264033.4:c.2323G>T	p.Asp775Tyr	p.D775Y	ENST00000264033	NM_005188.3	775	Gat/Tat	15/16	0.364361541311111	3	FACETS	1	0.97	1	0.558	0.512	0.606	CLONAL	1	TRUE	1	0.365699702339802	3		590	956	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122482	17122482	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	137	671	0	ENST00000285071.4:c.913G>C	p.Glu305Gln	p.E305Q	ENST00000285071	NM_144997.5	305	Gaa/Caa	9/14	0.364361541311111	3	FACETS	0.716	0.65	0.787	0.358	0.325	0.394	SUBCLONAL	1	TRUE	1	0.365699702339802	3		671	1237	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920012	1920012	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	170	652	0	ENST00000382891.5:c.1072C>G	p.Gln358Glu	p.Q358E	ENST00000382891	NM_133335.3	358	Caa/Gaa	5/22	0.364361541311111	3	FACETS	0.902	0.828	0.98	0.451	0.414	0.49	CLONAL	1	TRUE	1	0.365699702339802	3		652	1219	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637232	176637232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1424984701	NA	P-0026708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1216	187	675	2	ENST00000439151.2:c.1832G>A	p.Arg611Gln	p.R611Q	ENST00000439151	NM_022455.4	611	cGa/cAa	5/23	0.354148119464708	4	FACETS	0.996	0.917	1	0.498	0.458	0.539	CLONAL	1	TRUE	2	0.365699702339802	4		677	1403	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0026710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	109	333	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	1	2	FACETS	0.725	0.65	0.806	0.725	0.65	0.806	SUBCLONAL	1	TRUE	1	0.293154241355281	2		333	1025	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646198	3646198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774683778	NA	P-0026710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	181	618	0	ENST00000294008.3:c.1880C>T	p.Pro627Leu	p.P627L	ENST00000294008	NM_032444.2	627	cCg/cTg	8/15	1	2	FACETS	0.961	0.884	1	0.961	0.884	1	CLONAL	1	TRUE	1	0.293154241355281	2		618	1285	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371900	55371900	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	45	272	0	ENST00000297316.4:c.590C>T	p.Pro197Leu	p.P197L	ENST00000297316	NM_022454.3	197	cCg/cTg	2/2	0.293154241355281	3	FACETS	0.449	0.376	0.53	0.224	0.188	0.265	SUBCLONAL	1	TRUE	1	0.293154241355281	3		272	784	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	118	474	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.971	0.876	1	0.971	0.876	1	CLONAL	1	TRUE	1	0.313764080368289	2		474	775	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161483	2161483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	163	689	0	ENST00000434045.2:c.44C>T	p.Thr15Ile	p.T15I	ENST00000434045	NM_001127598.1	15	aCc/aTc	2/5	1	2	FACETS	0.896	0.82	0.975	0.896	0.82	0.975	CLONAL	1	TRUE	1	0.313764080368289	2		689	1160	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183758	10183761	+	missense_variant	Missense_Mutation	ONP	TCTG	TCTG	CTTT	novel	NA	P-0026711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	127	618	1	ENST00000256474.2:c.227_230delinsCTTT	p.Phe76_Cys77delinsSerPhe	p.F76_C77delinsSF	ENST00000256474	NM_000551.3	76	tTCTGc/tCTTTc	1/3	0.313764080368289	1	FACETS	0.76	0.688	0.836	0.76	0.688	0.836	SUBCLONAL	1	TRUE	0	0.313764080368289	1		619	898	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0026717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	110	503	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.3	4	FACETS	1	0.948	1			1	CLONAL	3	TRUE	NA	0.16	4		505	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0026717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	75	592	2	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	0.16	2		594	706	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106151	27106151	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	67	511	0	ENST00000324856.7:c.5763del	p.Leu1922Ter	p.L1922*	ENST00000324856	NM_006015.4	1921	aCc/ac	20/20	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.16	2		511	714	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749260	43749260	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs751008850	NA	P-0026717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	27	563	0	ENST00000382044.4:c.1546G>T	p.Asp516Tyr	p.D516Y	ENST00000382044	NM_001141980.1	516	Gat/Tat	12/28	1	2	FACETS	0.706	0.561	0.873	0.706	0.561	0.873	SUBCLONAL	1	TRUE	1	0.16	2		563	478	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0026722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	54	388	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.932	0.795	1	0.932	0.795	1	CLONAL	1	TRUE	1	0.18	2		388	644	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143324179	143324179	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	41	349	0	ENST00000262992.4:c.284G>T	p.Gly95Val	p.G95V	ENST00000262992	NM_001101669.1	95	gGt/gTt	5/24	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.18	2		349	390	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	178	474	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.702510110262503	2		474	401	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651883	36651883	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0026723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	176	493	0	ENST00000244741.5:c.5C>G	p.Ser2Ter	p.S2*	ENST00000244741	NM_000389.4	2	tCa/tGa	2/3	1	2	FACETS	0.724	0.669	0.781	0.724	0.669	0.781	SUBCLONAL	1	TRUE	1	0.702510110262503	2		493	692	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796214	45796214	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	47	562	0	ENST00000450313.1:c.1492C>T	p.Gln498Ter	p.Q498*	ENST00000450313	NM_012222.2	498	Cag/Tag	15/16	1	2	FACETS	0.153	0.128	0.181	0.153	0.128	0.181	SUBCLONAL	1	TRUE	1	0.702510110262503	2		562	874	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041722	29041722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	42	424	0	ENST00000282397.4:c.97G>A	p.Glu33Lys	p.E33K	ENST00000282397	NM_002019.4	33	Gaa/Aaa	2/30	1	2	FACETS	0.169	0.14	0.201	0.169	0.14	0.201	SUBCLONAL	1	TRUE	1	0.702510110262503	2		424	707	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15978952	15978952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	46	521	0	ENST00000268712.3:c.3566G>A	p.Arg1189Lys	p.R1189K	ENST00000268712	NM_006311.3	1189	aGa/aAa	27/46	0.702510110262503	1	FACETS	0.179	0.15	0.21	0.179	0.15	0.21	SUBCLONAL	1	TRUE	0	0.702510110262503	1		521	475	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015081	27015081	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	41	548	0	ENST00000335756.4:c.183G>C	p.Leu61Phe	p.L61F	ENST00000335756	NM_001809.3	61	ttG/ttC	2/5	1	2	FACETS	0.156	0.129	0.186	0.156	0.129	0.186	SUBCLONAL	1	TRUE	1	0.702510110262503	2		548	750	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12632358	12632358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764496629	NA	P-0026723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	55	567	1	ENST00000251849.4:c.1309G>A	p.Glu437Lys	p.E437K	ENST00000251849	NM_002880.3	437	Gag/Aag	12/17	1	2	FACETS	0.165	0.14	0.192	0.165	0.14	0.192	SUBCLONAL	1	TRUE	1	0.702510110262503	2		568	950	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651973	36651984	+	frameshift_variant	Frame_Shift_Del	DEL	GCGACTGTGATG	GCGACTGTGATG	CAGT	novel	NA	P-0026723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	127	588	3	ENST00000244741.5:c.95_106delinsCAGT	p.Arg32ProfsTer13	p.R32Pfs*13	ENST00000244741	NM_000389.4	32	cGCGACTGTGATGcg/cCAGTcg	2/3	1	2	FACETS	0.367	0.332	0.404	0.367	0.332	0.404	SUBCLONAL	1	TRUE	1	0.702510110262503	2		591	985	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509078	106509078	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs62001903	NA	P-0026723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	91	501	0	ENST00000359195.3:c.1072G>A	p.Asp358Asn	p.D358N	ENST00000359195	NM_002649.2	358	Gac/Aac	2/11	1	2	FACETS	0.347	0.308	0.389	0.347	0.308	0.389	SUBCLONAL	1	TRUE	1	0.702510110262503	2		501	747	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0026724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	39	322	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.52	0.429	0.622	0.52	0.429	0.622	SUBCLONAL	1	TRUE	1	0.14	2		322	1072	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100414	157100414	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1438676618	NA	P-0026724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	11	41	0	ENST00000346085.5:c.1351T>C	p.Ser451Pro	p.S451P	ENST00000346085	NM_020732.3	451	Tcg/Ccg	1/20	1	2	FACETS	0.786	0.548	1	1	0.865	1	CLONAL	2	TRUE	1	0.14	2		41	100	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097270	11097270	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0026724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	72	581	0	ENST00000358026.2:c.760+1G>A		p.X254_splice	ENST00000358026	NM_001128849.1	254			1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.14	2		581	1005	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692893	89692893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1114167656	NA	P-0026725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	67	376	1	ENST00000371953.3:c.377C>T	p.Ala126Val	p.A126V	ENST00000371953	NM_000314.4	126	gCt/gTt	5/9	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.17	2		377	695	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032088	48032088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376799914	NA	P-0026725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	38	369	0	ENST00000234420.5:c.3478G>A	p.Val1160Ile	p.V1160I	ENST00000234420	NM_000179.2	1160	Gtc/Atc	6/10	1	2	FACETS	0.594	0.489	0.711	0.594	0.489	0.711	SUBCLONAL	1	TRUE	1	0.17	2		369	753	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578204	7578216	+	frameshift_variant	Frame_Shift_Del	DEL	ACTATGTCGAAAA	ACTATGTCGAAAA	-	novel	NA	P-0026725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	104	811	0	ENST00000269305.4:c.633_645del	p.Phe212TrpfsTer31	p.F212Wfs*31	ENST00000269305	NM_001126112.2	211	acTTTTCGACATAGT/ac	6/11	1	2	FACETS	0.998	0.891	1	0.998	0.891	1	CLONAL	1	TRUE	1	0.17	2		811	1226	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589612	67589613	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAAGTC	novel	NA	P-0026725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	55	378	0	ENST00000274335.5:c.1376_1381dup	p.Ser460_Arg461insGlnSer	p.S460_R461insQS	ENST00000274335		459	aaa/aAAAGTCaa	10/15	1	2	FACETS	0.9	0.769	1	0.9	0.769	1	CLONAL	1	TRUE	1	0.17	2		378	719	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0026727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	112	379	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.859	0.771	0.952	0.859	0.771	0.952	CLONAL	1	TRUE	1	0.26	2		379	1003	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115416	115115416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	152	653	5	ENST00000257566.3:c.910C>T	p.Arg304Trp	p.R304W	ENST00000257566	NM_016569.3	304	Cgg/Tgg	5/8	1	2	FACETS	0.905	0.825	0.989	0.905	0.825	0.989	CLONAL	1	TRUE	1	0.26	2		658	1292	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857482	68857482	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	130	606	0	ENST00000261769.5:c.2119del	p.Ile707PhefsTer15	p.I707Ffs*15	ENST00000261769	NM_004360.3	706	cAa/ca	13/16	0.292257621977588	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.26	1		606	857	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164508	47164508	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs201756643	NA	P-0026728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	223	392	0	ENST00000409792.3:c.1618C>T	p.Arg540Ter	p.R540*	ENST00000409792	NM_014159.6	540	Cga/Tga	3/21	1	2	FACETS	0.872	0.815	0.93	0.872	0.815	0.93	CLONAL	1	TRUE	1	0.719234640667789	2		392	711	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578401	7578402	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCA	novel	NA	P-0026729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	718	650	15	ENST00000269305.4:c.526_528dup	p.Cys176dup	p.C176dup	ENST00000269305	NM_001126112.2	176	-/TGC	5/11	0.874999614391426	2	FACETS	0.972	0.955	0.989	0.972	0.955	0.989	CLONAL	2	TRUE	0	0.874999614391426	2		665	844	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164769	36164769	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755073984	NA	P-0026729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	393	741	14	ENST00000300305.3:c.1106C>T	p.Ser369Leu	p.S369L	ENST00000300305		369	tCg/tTg	8/8	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.874999614391426	2		755	776	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876449	35876449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2229232	NA	P-0026729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	648	669	24	ENST00000303115.3:c.1241C>T	p.Thr414Met	p.T414M	ENST00000303115	NM_002185.3	414	aCg/aTg	8/8	0.874999614391426	4	FACETS	0.973	0.939	1	0.973	0.939	1	CLONAL	2	TRUE	2	0.874999614391426	4		693	1427	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054810	5054810	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	511	538	5	ENST00000381652.3:c.862A>T	p.Ile288Phe	p.I288F	ENST00000381652	NM_004972.3	288	Att/Ttt	7/25	0.874999614391426	6	FACETS	0.992	0.949	1			1	CLONAL	2	TRUE	NA	0.874999614391426	6		543	1619	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44920585	44920585	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	209	520	2	ENST00000377967.4:c.1346G>T	p.Trp449Leu	p.W449L	ENST00000377967	NM_021140.2	449	tGg/tTg	14/29	0.874999614391426	3	FACETS	0.917	0.854	0.982	0.458	0.427	0.491	CLONAL	1	TRUE	1	0.874999614391426	3		522	749	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0026730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	323	502	1	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			0.488176013294625	3	FACETS	0.811	0.769	0.853	0.811	0.769	0.853	CLONAL	2	TRUE	1	0.627435328724919	3		503	834	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281770	49281770	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs935458798	NA	P-0026730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	222	711	0	ENST00000282018.3:c.817A>G	p.Thr273Ala	p.T273A	ENST00000282018	NM_020377.2	273	Aca/Gca	1/1	1	2	FACETS	0.696	0.648	0.746	0.696	0.648	0.746	SUBCLONAL	1	TRUE	1	0.627435328724919	2		711	1017	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063372	67063372	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	172	509	0	ENST00000412916.2:c.62T>C	p.Leu21Pro	p.L21P	ENST00000412916		21	cTg/cCg	1/6	0.533560408364017	1	FACETS	0.627	0.58	0.676	0.627	0.58	0.676	SUBCLONAL	1	TRUE	0	0.627435328724919	1		509	600	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021716	31021722	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TCCGGGT	TCCGGGT	-	novel	NA	P-0026730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	216	531	0	ENST00000375687.4:c.1715_1719+2del		p.X572_splice	ENST00000375687	NM_015338.5	572		12/13	1	2	FACETS	0.832	0.775	0.89	0.832	0.775	0.89	CLONAL	1	TRUE	1	0.627435328724919	2		531	828	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123040912	123040912	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	52	507	1	ENST00000355640.3:c.1375G>A	p.Ala459Thr	p.A459T	ENST00000355640		459	Gct/Act	7/7	1	2	FACETS	0.27	0.229	0.315	0.27	0.229	0.315	SUBCLONAL	1	TRUE	1	0.627435328724919	2		508	614	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242481	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAGCAA	TTAAGAGAAGCAA	C	rs397509368	NA	P-0026732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	52	590	0	ENST00000275493.2:c.2239_2251delinsC	p.Leu747_Thr751delinsPro	p.L747_T751delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGCAAca/Cca	19/28	1	2	FACETS	0.872	0.74	1	0.872	0.74	1	CLONAL	1	TRUE	1	0.14	2		590	852	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0026734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	41	483	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.98	0.815	1	0.98	0.815	1	CLONAL	1	TRUE	1	0.12	2		483	697	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715724	30715724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782979	NA	P-0026734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	29	394	0	ENST00000295754.5:c.1382G>A	p.Cys461Tyr	p.C461Y	ENST00000295754	NM_003242.5	461	tGt/tAt	5/7	1	2	FACETS	0.992	0.795	1	0.992	0.795	1	CLONAL	1	TRUE	1	0.12	2		394	487	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38064160	38064160	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	199	658	0	ENST00000250448.2:c.18G>C	p.Lys6Asn	p.K6N	ENST00000250448	NM_004496.3	6	aaG/aaC	1/2	1	2	FACETS	0.847	0.785	0.912	0.847	0.785	0.912	CLONAL	1	TRUE	1	0.485937275175556	2		658	967	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578493	7578493	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1206165503	NA	P-0026751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	17	822	0	ENST00000269305.4:c.437G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tGg/tAg	5/11	1	2	FACETS	0.758	0.567	0.982	0.758	0.567	0.982	CLONAL	1	TRUE	1	0.22	2		822	204	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279976	18279976	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	13	587	0	ENST00000222254.8:c.2059G>A	p.Gly687Arg	p.G687R	ENST00000222254	NM_005027.3	687	Ggg/Agg	16/16	1	2	FACETS	0.591	0.422	0.796	0.591	0.422	0.796	SUBCLONAL	1	TRUE	1	0.22	2		587	200	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061191	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	92	339	0	ENST00000250448.2:c.798C>G	p.Phe266Leu	p.F266L	ENST00000250448	NM_004496.3	266	ttC/ttG	2/2	1	2	FACETS	0.954	0.852	1	0.954	0.852	1	CLONAL	1	TRUE	1	0.422961999976326	2		339	456	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376152	118376152	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs770458074	NA	P-0026752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	129	537	0	ENST00000534358.1:c.9545A>G	p.Asn3182Ser	p.N3182S	ENST00000534358	NM_005933.3	3182	aAt/aGt	27/36	1	2	FACETS	0.898	0.816	0.985	0.898	0.816	0.985	CLONAL	1	TRUE	1	0.422961999976326	2		537	679	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0026753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	218	503	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.478756115376496	2	FACETS	0.902	0.847	0.957	0.902	0.847	0.957	CLONAL	2	TRUE	0	0.478756115376496	2		505	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0026753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	322	632	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.478756115376496	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.478756115376496	1		632	811	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968259	2968259	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	616	770	2	ENST00000396946.4:c.1727G>A	p.Arg576His	p.R576H	ENST00000396946	NM_032415.4	576	cGc/cAc	13/25	0.478756115376496	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.478756115376496	3		772	1455	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278106	41278106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	133	383	0	ENST00000349496.5:c.1982G>A	p.Arg661Gln	p.R661Q	ENST00000349496	NM_001904.3	661	cGa/cAa	13/15	0.478756115376496	1	FACETS	0.95	0.869	1	0.95	0.869	1	CLONAL	1	TRUE	0	0.478756115376496	1		383	445	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806171	1806171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542210035	NA	P-0026753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	138	738	1	ENST00000260795.2:c.1190G>A	p.Arg397His	p.R397H	ENST00000260795		397	cGc/cAc	8/17	1	2	FACETS	0.616	0.56	0.675	0.616	0.56	0.675	SUBCLONAL	1	TRUE	1	0.478756115376496	2		739	936	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429273	78429286	+	frameshift_variant	Frame_Shift_Del	DEL	AATCCAGTTTTCCC	AATCCAGTTTTCCC	-	novel	NA	P-0026753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	37	498	0	ENST00000370768.2:c.1156_1169del	p.Gly386AsnfsTer7	p.G386Nfs*7	ENST00000370768	NM_003902.3	386	GGGAAAACTGGATTa/a	13/20	1	2	FACETS	0.245	0.201	0.294	0.245	0.201	0.294	SUBCLONAL	1	TRUE	1	0.478756115376496	2		498	632	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42851204	42851204	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	64	413	0	ENST00000398585.3:c.689A>T	p.Asn230Ile	p.N230I	ENST00000398585	NM_001135099.1	230	aAt/aTt	7/14	0.174756804923139	2	FACETS	0.489	0.423	0.56	0.244	0.211	0.28	INDETERMINATE	1	TRUE	0	0.478756115376496	2		413	547	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266092	41266097	+	inframe_deletion	In_Frame_Del	DEL	ACCTGG	ACCTGG	-	novel	NA	P-0026753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	126	302	0	ENST00000349496.5:c.91_96del	p.Leu31_Asp32del	p.L31_D32del	ENST00000349496	NM_001904.3	30	tACCTGGac/tac	3/15	0.478756115376496	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.478756115376496	1		302	376	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009278	69009278	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	114	476	0	ENST00000288368.4:c.2395G>C	p.Ala799Pro	p.A799P	ENST00000288368	NM_024870.2	799	Gcc/Ccc	22/40	0.325312885188166	3	FACETS	0.958	0.865	1	0.479	0.432	0.528	CLONAL	1	TRUE	1	0.478756115376496	3		476	616	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654718	29654718	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs370858405	NA	P-0026756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	113	415	0	ENST00000356175.3:c.5407A>G	p.Ile1803Val	p.I1803V	ENST00000356175	NM_000267.3	1803	Atc/Gtc	37/57	0.533351897625611	3	FACETS	0.958	0.865	1	0.479	0.432	0.528	CLONAL	1	TRUE	1	0.533351897625611	3		415	560	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934975	49934976	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CGGAGGTGCCGTCTACC	novel	NA	P-0026756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	102	656	0	ENST00000296474.3:c.2007_2023dup	p.Val675GlyfsTer2	p.V675Gfs*2	ENST00000296474	NM_002447.2	675	gtg/gGGTAGACGGCACCTCCGtg	6/20	0.533351897625611	3	FACETS	0.465	0.415	0.519	0.233	0.207	0.26	SUBCLONAL	1	TRUE	1	0.533351897625611	3		656	1041	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935967	49935967	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	180	658	0	ENST00000296474.3:c.1703C>A	p.Pro568Gln	p.P568Q	ENST00000296474	NM_002447.2	568	cCa/cAa	4/20	0.533351897625611	3	FACETS	0.872	0.804	0.944	0.436	0.402	0.472	CLONAL	1	TRUE	1	0.533351897625611	3		658	980	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720987	176720987	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	137	510	0	ENST00000439151.2:c.6618C>G	p.Asp2206Glu	p.D2206E	ENST00000439151	NM_022455.4	2206	gaC/gaG	23/23	1	2	FACETS	0.922	0.843	1	0.922	0.843	1	CLONAL	1	TRUE	1	0.533351897625611	2		510	557	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839780	27839780	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	108	576	0	ENST00000328488.2:c.314T>C	p.Phe105Ser	p.F105S	ENST00000328488	NM_003533.2	105	tTt/tCt	1/1	0.46221616677351	3	FACETS	0.728	0.653	0.806	0.364	0.326	0.403	SUBCLONAL	1	TRUE	1	0.533351897625611	3		576	705	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577518	7577518	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519995	NA	P-0026758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	317	648	0	ENST00000269305.4:c.763A>T	p.Ile255Phe	p.I255F	ENST00000269305	NM_001126112.2	255	Atc/Ttc	7/11	0.266561623400998	2	FACETS	0.906	0.855	0.958	0.906	0.855	0.958	CLONAL	2	TRUE	0	0.310981142086097	2		648	1125	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651322	45651322	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	124	487	0	ENST00000407780.3:c.703G>C	p.Asp235His	p.D235H	ENST00000407780	NM_001283052.1	235	Gac/Cac	5/7	0.25644991381923	4	FACETS	0.884	0.797	0.975	0.442	0.398	0.488	CLONAL	1	TRUE	2	0.310981142086097	4		487	1183	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158584	26158584	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	104	471	0	ENST00000289316.2:c.187A>T	p.Met63Leu	p.M63L	ENST00000289316	NM_138720.2	63	Atg/Ttg	1/2	0.310981142086097	3	FACETS	0.818	0.731	0.91	0.409	0.365	0.455	CLONAL	1	TRUE	1	0.310981142086097	3		471	945	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119691	108119692	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0026759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	59	274	0	ENST00000278616.4:c.1098_1099del	p.Gln368IlefsTer10	p.Q368Ifs*10	ENST00000278616	NM_000051.3	366	aTT/a	9/63	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.327096626959475	2		274	283	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216406	36216406	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	181	901	0	ENST00000222270.7:c.3671del	p.Pro1224HisfsTer131	p.P1224Hfs*131	ENST00000222270	NM_014727.1	1223	gaC/ga	12/37	1	2	FACETS	0.931	0.857	1	0.931	0.857	1	CLONAL	1	TRUE	1	0.327096626959475	2		901	1189	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595854	52595854	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	175	636	0	ENST00000394830.3:c.4061del	p.Phe1354SerfsTer26	p.F1354Sfs*26	ENST00000394830	NM_018313.4	1354	tTc/tc	26/30	0.327096626959475	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.327096626959475	1		636	779	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0026760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	209	807	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.398301507782968	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.398301507782968	1		807	737	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770576	40770576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	45	488	0	ENST00000373198.4:c.2806C>T	p.Arg936Ter	p.R936*	ENST00000373198	NM_133170.3	936	Cga/Tga	19/32	0.398301507782968	3	FACETS	0.425	0.357	0.502	0.213	0.178	0.251	SUBCLONAL	1	TRUE	1	0.398301507782968	3		488	637	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166103	118166103	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	73	408	0	ENST00000369448.3:c.613C>G	p.His205Asp	p.H205D	ENST00000369448	NM_017709.3	205	Cac/Gac	2/2	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.398301507782968	2		408	344	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004603	16004603	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	171	468	1	ENST00000268712.3:c.2651G>C	p.Ser884Thr	p.S884T	ENST00000268712	NM_006311.3	884	aGc/aCc	20/46	0.398301507782968	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.398301507782968	1		469	584	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970955	21970979	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCAGCCGCGCGCAGGTACCGTGC	CCGCAGCCGCGCGCAGGTACCGTGC	GCG	novel	NA	P-0026760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	233	637	4	ENST00000304494.5:c.379_403delinsCGC	p.Ala127ArgfsTer12	p.A127Rfs*12	ENST00000304494	NM_000077.4	127	GCACGGTACCTGCGCGCGGCTGCGGgg/CGCgg	2/3	0.398301507782968	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.398301507782968	1		641	688	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	12	215	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	0.244075013680665	3	FACETS	0.186	0.129	0.256	0.093	0.064	0.128	SUBCLONAL	1	TRUE	1	0.253084568088763	3		215	575	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405954	49405954	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	300	618	0	ENST00000418115.1:c.184G>A	p.Gly62Arg	p.G62R	ENST00000418115	NM_001664.2	62	Ggg/Agg	3/5	0.253084568088763	5	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	2	0.253084568088763	5		618	1031	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070608	67070608	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	90	225	0	ENST00000412916.2:c.232C>T	p.Arg78Ter	p.R78*	ENST00000412916		78	Cga/Tga	3/6	1	2	FACETS	0.865	0.772	0.963	1	0.984	1	CLONAL	2	TRUE	1	0.253084568088763	2		225	411	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115806	8115809	+	frameshift_variant	Frame_Shift_Del	DEL	CTTC	CTTC	-	novel	NA	P-0026763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	170	575	0	ENST00000346208.3:c.1153_1156del	p.Phe385ProfsTer18	p.F385Pfs*18	ENST00000346208		384	gaCTTC/ga	6/6	0.244075013680665	3	FACETS	0.914	0.841	0.989	0.914	0.841	0.989	CLONAL	2	TRUE	1	0.253084568088763	3		575	828	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844202	68844202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	191	629	0	ENST00000261769.5:c.790C>T	p.Gln264Ter	p.Q264*	ENST00000261769	NM_004360.3	264	Cag/Tag	6/16	0.253084568088763	1	FACETS	0.957	0.888	1	1	0.993	1	CLONAL	2	TRUE	0	0.253084568088763	1		629	689	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519998	NA	P-0026764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	119	561	0	ENST00000269305.4:c.581T>C	p.Leu194Pro	p.L194P	ENST00000269305	NM_001126112.2	194	cTt/cCt	6/11	0.395597411242404	3	FACETS	0.894	0.826	0.963	0.894	0.826	0.963	CLONAL	3	TRUE	0	0.460656374701175	3		561	237	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952073	178952073	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519937	NA	P-0026764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	86	342	0	ENST00000263967.3:c.3128T>C	p.Met1043Thr	p.M1043T	ENST00000263967	NM_006218.2	1043	aTg/aCg	21/21	0.195845396455658	3	FACETS	1	0.93	1	0.693	0.625	0.763	INDETERMINATE	2	TRUE	0	0.460656374701175	3		342	221	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165557	47165557	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs563907746	NA	P-0026764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	72	405	0	ENST00000409792.3:c.569C>T	p.Pro190Leu	p.P190L	ENST00000409792	NM_014159.6	190	cCg/cTg	3/21	0.460656374701175	3	FACETS	1	0.949	1	0.574	0.505	0.647	CLONAL	1	TRUE	1	0.460656374701175	3		405	335	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845839	72845839	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	153	514	0	ENST00000268489.5:c.3628C>T	p.Arg1210Ter	p.R1210*	ENST00000268489	NM_006885.3	1210	Cga/Tga	6/10	0.460656374701175	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.460656374701175	2		514	285	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627369	14627369	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	109	658	0	ENST00000254322.2:c.701A>G	p.Asp234Gly	p.D234G	ENST00000254322	NM_006145.1	234	gAt/gGt	2/3	0.460656374701175	3	FACETS	1	0.956	1	0.555	0.5	0.612	CLONAL	1	TRUE	1	0.460656374701175	3		658	525	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268824	98268824	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	25	374	0	ENST00000331920.6:c.259T>A	p.Leu87Ile	p.L87I	ENST00000331920	NM_000264.3	87	Tta/Ata	2/24	0.460656374701175	2	FACETS	0.305	0.24	0.379	0.152	0.12	0.19	SUBCLONAL	1	TRUE	0	0.460656374701175	2		374	356	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0026766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	383	273	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.639225332523737	5	FACETS	0.954	0.912	0.997	0.954	0.912	0.997	CLONAL	3	TRUE	2	0.639225332523737	5		273	820	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177874	56177875	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0026766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	241	305	0	ENST00000399503.3:c.2849_2850del	p.Glu950AlafsTer53	p.E950Afs*53	ENST00000399503	NM_005921.1	949	acAGag/acag	14/20	0.639225332523737	3	FACETS	0.895	0.843	0.947	0.895	0.843	0.947	CLONAL	2	TRUE	1	0.639225332523737	3		305	556	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180586	56180588	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	rs1357146419	NA	P-0026766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	177	293	0	ENST00000399503.3:c.3918_3920del	p.Ile1307del	p.I1307del	ENST00000399503	NM_005921.1	1305	aaCATc/aac	16/20	0.639225332523737	3	FACETS	1	0.964	1	0.535	0.494	0.577	CLONAL	1	TRUE	1	0.639225332523737	3		293	683	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879598	151879598	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	160	205	0	ENST00000262189.6:c.5347C>T	p.Gln1783Ter	p.Q1783*	ENST00000262189	NM_170606.2	1783	Cag/Tag	36/59	0.621636330498994	4	FACETS	0.977	0.906	1	0.977	0.906	1	CLONAL	2	TRUE	2	0.639225332523737	4		205	420	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022344	26022344	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	177	355	0	ENST00000435504.4:c.313C>T	p.Gln105Ter	p.Q105*	ENST00000435504		105	Cag/Tag	5/13	0.578727844973152	1	FACETS	0.836	0.793	0.877	1	0.994	1	CLONAL	2	TRUE	0	0.578727844973152	1		355	260	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842666	68842666	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs146777134	NA	P-0026768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	96	536	0	ENST00000261769.5:c.602C>A	p.Pro201His	p.P201H	ENST00000261769	NM_004360.3	201	cCt/cAt	5/16	1	2	FACETS	0.544	0.485	0.606	0.544	0.485	0.606	SUBCLONAL	1	TRUE	1	0.578727844973152	2		536	610	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955915	55955933	+	frameshift_variant	Frame_Shift_Del	DEL	TGTACACTCTGTCAAAAAT	TGTACACTCTGTCAAAAAT	-	novel	NA	P-0026768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	238	396	0	ENST00000263923.4:c.3229_3247del	p.Ile1077GlnfsTer19	p.I1077Qfs*19	ENST00000263923	NM_002253.2	1077	ATTTTTGACAGAGTGTACAca/ca	24/30	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.578727844973152	2		396	606	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891116	151891116	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	161	299	0	ENST00000262189.6:c.4638G>T	p.Gln1546His	p.Q1546H	ENST00000262189	NM_170606.2	1546	caG/caT	31/59	0.442961121036469	1	FACETS	0.955	0.886	1	0.955	0.886	1	CLONAL	1	TRUE	0	0.578727844973152	1		299	414	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412396	63412404	+	frameshift_variant	Frame_Shift_Del	DEL	ATCTTTACA	ATCTTTACA	TTTTTCT	novel	NA	P-0026768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	297	292	2	ENST00000330258.3:c.763_771delinsAGAAAAA	p.Cys255ArgfsTer22	p.C255Rfs*22	ENST00000330258	NM_152424.3	255	TGTAAAGAT/AGAAAAA	2/2	1	1	FACETS	0.967	0.936	0.997	1	0.997	1	CLONAL	2	TRUE	0	0.578727844973152	1		294	377	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974792	21974792	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs141798398	NA	P-0026769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	135	91	0	ENST00000304494.5:c.35C>A	p.Ser12Ter	p.S12*	ENST00000304494	NM_000077.4	12	tCg/tAg	1/3	0.658908659652421	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	3	FALSE	0	0.708967241392493	3		91	169	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577530	7577530	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	692	520	0	ENST00000269305.4:c.751A>T	p.Ile251Phe	p.I251F	ENST00000269305	NM_001126112.2	251	Atc/Ttc	7/11	0.656583616920172	3	FACETS	0.965	0.943	0.987	0.965	0.943	0.987	CLONAL	3	FALSE	0	0.708967241392493	3		520	913	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93607788	93607789	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1433438204	NA	P-0026769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	101	383	0	ENST00000375746.1:c.496dup	p.Met166AsnfsTer14	p.M166Nfs*14	ENST00000375746	NM_001174167.1	164	gaa/gAaa	3/14	0.594412375912451	4	FACETS	0.656	0.586	0.73	0.219	0.195	0.244	SUBCLONAL	1	FALSE	1	0.708967241392493	4		383	742	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30676081	30676081	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	330	341	0	ENST00000376406.3:c.2275G>T	p.Glu759Ter	p.E759*	ENST00000376406	NM_014641.2	759	Gag/Tag	8/15	0.362415379231707	3	FACETS	1	0.993	1	0.787	0.755	0.819	INDETERMINATE	2	FALSE	0	0.708967241392493	3		341	534	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499687	8499687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	179	374	0	ENST00000356435.5:c.2282G>A	p.Gly761Asp	p.G761D	ENST00000356435		761	gGc/gAc	14/35	0.662892999785378	2	FACETS	1	0.986	1	0.605	0.565	0.646	CLONAL	1	FALSE	0	0.708967241392493	2		374	417	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261718	16261718	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	54	417	0	ENST00000375759.3:c.8983C>T	p.Pro2995Ser	p.P2995S	ENST00000375759	NM_015001.2	2995	Cct/Tct	11/15	1	2	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	TRUE	1	0.15	2		417	720	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717701	89717712	+	inframe_deletion	In_Frame_Del	DEL	GTTCCCTCAGCC	GTTCCCTCAGCC	-	novel	NA	P-0026780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	67	347	0	ENST00000371953.3:c.729_740del	p.Phe243_Pro246del	p.F243_P246del	ENST00000371953	NM_000314.4	242	gaGTTCCCTCAGCCg/gag	7/9	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.15	2		347	708	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78599530	78599530	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	53	425	4	ENST00000306801.3:c.202G>T	p.Val68Phe	p.V68F	ENST00000306801	NM_020761.2	68	Gtt/Ttt	2/34	1	2	FACETS	0.78	0.663	0.909	0.78	0.663	0.909	CLONAL	1	TRUE	1	0.15	2		429	906	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754599	57754599	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	32	338	0	ENST00000274289.3:c.448G>C	p.Glu150Gln	p.E150Q	ENST00000274289	NM_006622.3	150	Gag/Cag	3/14	1	2	FACETS	0.734	0.595	0.893	0.734	0.595	0.893	SUBCLONAL	1	TRUE	1	0.15	2		338	581	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649709	48649709	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	56	633	0	ENST00000376670.3:c.193G>A	p.Asp65Asn	p.D65N	ENST00000376670	NM_002049.3	65	Gac/Aac	2/6	1	2	FACETS	0.826	0.706	0.958	0.826	0.706	0.958	CLONAL	1	TRUE	1	0.15	2		633	904	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	233	474	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.887	0.834	0.941	0.887	0.834	0.941	CLONAL	1	TRUE	1	0.890103952609386	2		474	590	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981298	201981309	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGACCTCAGTG	GAGACCTCAGTG	-	novel	NA	P-0026783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	266	445	0	ENST00000359651.3:c.377_385+3del		p.X126_splice	ENST00000359651		126		2/8	1	2	FACETS	0.832	0.785	0.881	0.832	0.785	0.881	CLONAL	1	TRUE	1	0.890103952609386	2		445	718	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651921	36651937	+	frameshift_variant	Frame_Shift_Del	DEL	AGCAAGGCCTGCCGCCG	AGCAAGGCCTGCCGCCG	-	novel	NA	P-0026783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	619	411	0	ENST00000244741.5:c.43_59del	p.Ser15ProfsTer15	p.S15Pfs*15	ENST00000244741	NM_000389.4	15	AGCAAGGCCTGCCGCCGc/c	2/3	0.88766757168045	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.890103952609386	2		411	667	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665270	117665270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	138	248	0	ENST00000368508.3:c.4477G>A	p.Glu1493Lys	p.E1493K	ENST00000368508	NM_002944.2	1493	Gaa/Aaa	27/43	0.88766757168045	2	FACETS	0.781	0.718	0.846	0.391	0.359	0.423	SUBCLONAL	1	TRUE	0	0.890103952609386	2		248	397	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	407	485	3	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.662863497999431	2		488	1020	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	231	568	2	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	0.959	1	CLONAL	1	TRUE	1	0.662863497999431	2		570	677	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	47	661	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	1	2	FACETS	0.151	0.126	0.178	0.151	0.126	0.178	SUBCLONAL	1	TRUE	1	0.662863497999431	2		661	942	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	234	575	15	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.949	0.889	1	0.949	0.889	1	CLONAL	1	TRUE	1	0.662863497999431	2		590	744	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	763	472	0	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	1	2	FACETS	0.919	0.907	0.931	1	0.999	1	CLONAL	3	TRUE	1	0.662863497999431	2		472	835	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281197	15281197	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	89	689	0	ENST00000263388.2:c.5059G>A	p.Ala1687Thr	p.A1687T	ENST00000263388	NM_000435.2	1687	Gcc/Acc	27/33	1	2	FACETS	0.282	0.249	0.317	0.282	0.249	0.317	SUBCLONAL	1	TRUE	1	0.662863497999431	2		689	953	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	54	676	1	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	1	2	FACETS	0.154	0.131	0.18	0.154	0.131	0.18	SUBCLONAL	1	TRUE	1	0.662863497999431	2		677	1057	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	291	454	1	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.662863497999431	2		455	633	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578463	7578463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371524413	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	194	705	0	ENST00000269305.4:c.467G>A	p.Arg156His	p.R156H	ENST00000269305	NM_001126112.2	156	cGc/cAc	5/11	1	2	FACETS	0.594	0.55	0.641	0.594	0.55	0.641	SUBCLONAL	1	TRUE	1	0.662863497999431	2		705	985	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	48	605	0	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	1	2	FACETS	0.167	0.14	0.197	0.167	0.14	0.197	SUBCLONAL	1	TRUE	1	0.662863497999431	2		605	867	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	210	582	0	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	0.828	0.771	0.887	0.828	0.771	0.887	CLONAL	1	TRUE	1	0.662863497999431	2		582	765	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	86	196	2	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.662863497999431	2		198	206	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	263	662	0	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.662863497999431	2		662	599	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341230	341230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756690670	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	335	696	0	ENST00000262320.3:c.2254G>A	p.Val752Met	p.V752M	ENST00000262320	NM_003502.3	752	Gtg/Atg	9/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.662863497999431	2		696	973	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807363	3807364	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	271	347	0	ENST00000262367.5:c.3623dup	p.Gln1209ThrfsTer25	p.Q1209Tfs*25	ENST00000262367	NM_004380.2	1208	cca/ccCa	19/31	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.662863497999431	2		347	612	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245586	41245587	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs80357522	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	74	517	2	ENST00000357654.3:c.1961dup	p.Tyr655ValfsTer18	p.Y655Vfs*18	ENST00000357654	NM_007294.3	654	aag/aaAg	10/23	1	2	FACETS	0.305	0.266	0.346	0.305	0.266	0.346	SUBCLONAL	1	TRUE	1	0.662863497999431	2		519	733	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280142	66280142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1327931544	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	95	245	1	ENST00000273854.3:c.1547C>T	p.Thr516Met	p.T516M	ENST00000273854	NM_004439.5	516	aCg/aTg	7/18	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.662863497999431	2		246	271	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95595941	95595941	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749484792	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	195	403	0	ENST00000393063.1:c.602G>A	p.Arg201His	p.R201H	ENST00000393063	NM_030621.3	201	cGc/cAc	7/28	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.662863497999431	2		403	450	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427588	72427588	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	136	209	0	ENST00000477973.2:c.902G>A	p.Arg301His	p.R301H	ENST00000477973	NM_012234.5	301	cGt/cAt	4/4	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.662863497999431	2		209	290	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209298	133209298	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060500809	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	332	645	0	ENST00000320574.5:c.6088del	p.Ala2030ProfsTer18	p.A2030Pfs*18	ENST00000320574	NM_006231.2	2030	Gcc/cc	44/49	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.662863497999431	2		645	783	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154241	2154242	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755455183	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	77	590	4	ENST00000434045.2:c.686dup	p.Glu230ArgfsTer50	p.E230Rfs*50	ENST00000434045	NM_001127598.1	229	cca/ccCa	5/5	1	2	FACETS	0.265	0.232	0.301	0.265	0.232	0.301	SUBCLONAL	1	TRUE	1	0.662863497999431	2		594	876	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641388	18641389	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1229278001	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	87	198	0	ENST00000266497.5:c.2393dup	p.Asn798LysfsTer5	p.N798Kfs*5	ENST00000266497		796	cta/ctAa	17/31	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.662863497999431	2		198	215	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656969	47656969	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779075	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	198	359	0	ENST00000233146.2:c.1165C>T	p.Arg389Ter	p.R389*	ENST00000233146	NM_000251.2	389	Cga/Tga	7/16	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.662863497999431	2		359	441	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67646013	67646014	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs1470210640	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	167	404	2	ENST00000264010.4:c.950_951del	p.Thr317ArgfsTer91	p.T317Rfs*91	ENST00000264010	NM_006565.3	314	aAC/a	4/12	1	2	FACETS	0.872	0.805	0.94	0.872	0.805	0.94	CLONAL	1	TRUE	1	0.662863497999431	2		406	578	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038451	180038451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370304760	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	330	701	0	ENST00000261937.6:c.3566G>A	p.Arg1189His	p.R1189H	ENST00000261937	NM_182925.4	1189	cGc/cAc	27/30	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.662863497999431	2		701	871	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444318	50444318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1427077431	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	166	312	1	ENST00000331340.3:c.248G>A	p.Arg83Gln	p.R83Q	ENST00000331340	NM_006060.4	83	cGa/cAa	4/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.662863497999431	2		313	385	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043973	180043973	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149033942	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	319	568	1	ENST00000261937.6:c.3023C>T	p.Pro1008Leu	p.P1008L	ENST00000261937	NM_182925.4	1008	cCg/cTg	22/30	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.662863497999431	2		569	709	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	414	922	1	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.662863497999431	2		923	960	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836855	151836855	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	254	430	2	ENST00000262189.6:c.14365C>T	p.Arg4789Ter	p.R4789*	ENST00000262189	NM_170606.2	4789	Cga/Tga	56/59	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.662863497999431	2		432	586	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433374	138433374	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746292811	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	183	440	0	ENST00000289153.2:c.1238C>T	p.Thr413Met	p.T413M	ENST00000289153	NM_006219.2	413	aCg/aTg	7/22	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.662863497999431	2		440	450	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	383	505	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.662863497999431	2		505	956	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864217	57864218	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1469076238	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	52	376	0	ENST00000228682.2:c.1700dup	p.Gly568TrpfsTer74	p.G568Wfs*74	ENST00000228682	NM_005269.2	565	ttc/ttCc	12/12	1	2	FACETS	0.275	0.233	0.32	0.275	0.233	0.32	SUBCLONAL	1	TRUE	1	0.662863497999431	2		376	571	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643296	38643296	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1331443136	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	41	396	1	ENST00000299084.4:c.766C>T	p.Arg256Cys	p.R256C	ENST00000299084	NM_152594.2	256	Cgt/Tgt	7/7	1	2	FACETS	0.241	0.2	0.286	0.241	0.2	0.286	SUBCLONAL	1	TRUE	1	0.662863497999431	2		397	513	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505430	25505431	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1446314200	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	201	419	0	ENST00000264709.3:c.327dup	p.Gln110AlafsTer14	p.Q110Afs*14	ENST00000264709	NM_175629.2	109	-/G	4/23	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.662863497999431	2		419	479	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821381	72821382	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	154	431	0	ENST00000268489.5:c.10793dup	p.Pro3599SerfsTer67	p.P3599Sfs*67	ENST00000268489	NM_006885.3	3598	cct/ccCt	10/10	1	2	FACETS	0.908	0.836	0.981	0.908	0.836	0.981	CLONAL	1	TRUE	1	0.662863497999431	2		431	512	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14028124	14028124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	183	429	0	ENST00000311895.7:c.1178C>T	p.Ala393Val	p.A393V	ENST00000311895	NM_005236.2	393	gCa/gTa	7/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.662863497999431	2		429	436	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109315691	109315692	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	192	443	0	ENST00000436639.2:c.1093dup	p.Arg365LysfsTer11	p.R365Kfs*11	ENST00000436639	NM_014454.2	365	aga/aAga	6/10	1	2	FACETS	0.943	0.877	1	0.943	0.877	1	CLONAL	1	TRUE	1	0.662863497999431	2		443	614	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226090	2226090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316961587	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	62	695	0	ENST00000326181.6:c.1787C>T	p.Thr596Met	p.T596M	ENST00000326181	NM_032271.2	596	aCg/aTg	19/21	1	2	FACETS	0.189	0.162	0.218	0.189	0.162	0.218	SUBCLONAL	1	TRUE	1	0.662863497999431	2		695	992	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8252045	8252045	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	75	508	0	ENST00000335790.3:c.32C>A	p.Pro11Gln	p.P11Q	ENST00000335790	NM_002315.2	11	cCg/cAg	2/4	1	2	FACETS	0.347	0.303	0.393	0.347	0.303	0.393	SUBCLONAL	1	TRUE	1	0.662863497999431	2		508	653	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448408	49448408	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs797045661	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	318	516	1	ENST00000301067.7:c.303del	p.Ser102AlafsTer28	p.S102Afs*28	ENST00000301067	NM_003482.3	101	ggG/gg	3/54	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.662863497999431	2		517	750	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891121	112891121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507521	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	315	556	0	ENST00000351677.2:c.455G>A	p.Arg152His	p.R152H	ENST00000351677	NM_002834.3	152	cGc/cAc	4/16	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.662863497999431	2		556	765	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563104	21563104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	264	617	0	ENST00000382592.4:c.815G>A	p.Ser272Asn	p.S272N	ENST00000382592	NM_014572.2	272	aGc/aAc	4/8	1	2	FACETS	0.915	0.859	0.971	0.915	0.859	0.971	CLONAL	1	TRUE	1	0.662863497999431	2		617	871	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239770	41239770	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	376	669	3	ENST00000379561.5:c.580G>A	p.Val194Met	p.V194M	ENST00000379561	NM_002015.3	194	Gtg/Atg	1/3	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.662863497999431	2		672	1042	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870487	40870487	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770125478	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	39	412	0	ENST00000428826.2:c.916G>A	p.Asp306Asn	p.D306N	ENST00000428826		306	Gac/Aac	9/21	1	2	FACETS	0.156	0.129	0.187	0.156	0.129	0.187	SUBCLONAL	1	TRUE	1	0.662863497999431	2		412	754	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118596	11118596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	197	385	0	ENST00000358026.2:c.2020C>T	p.Pro674Ser	p.P674S	ENST00000358026	NM_001128849.1	674	Ccg/Tcg	14/36	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.662863497999431	2		385	542	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152098	11152098	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1290442223	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	48	533	0	ENST00000358026.2:c.4382G>A	p.Arg1461His	p.R1461H	ENST00000358026	NM_001128849.1	1461	cGc/cAc	31/36	1	2	FACETS	0.176	0.148	0.207	0.176	0.148	0.207	SUBCLONAL	1	TRUE	1	0.662863497999431	2		533	822	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212524	36212524	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	220	740	1	ENST00000222270.7:c.2275C>T	p.Gln759Ter	p.Q759*	ENST00000222270	NM_014727.1	759	Cag/Tag	3/37	1	2	FACETS	0.602	0.559	0.646	0.602	0.559	0.646	SUBCLONAL	1	TRUE	1	0.662863497999431	2		741	1103	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221467	36221470	+	frameshift_variant	Frame_Shift_Del	DEL	TCTG	TCTG	-	novel	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	335	664	0	ENST00000222270.7:c.5230_5233del	p.Ser1744IlefsTer150	p.S1744Ifs*150	ENST00000222270	NM_014727.1	1742	acTCTG/ac	25/37	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.662863497999431	2		664	1001	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62323163	62323165	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs1555812473	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	286	475	0	ENST00000360203.5:c.2630_2632del	p.Lys877del	p.K877del	ENST00000360203	NM_001283009.1	875	agGAAg/agg	28/35	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.662863497999431	2		475	638	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803165	1803165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1031160906	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	506	712	1	ENST00000260795.2:c.517C>T	p.Arg173Cys	p.R173C	ENST00000260795		173	Cgc/Tgc	4/17	1	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	1	0.662863497999431	2		713	1051	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1919941	1919941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	88	611	3	ENST00000382891.5:c.1001G>A	p.Ser334Asn	p.S334N	ENST00000382891	NM_133335.3	334	aGc/aAc	5/22	1	2	FACETS	0.345	0.305	0.387	0.345	0.305	0.387	SUBCLONAL	1	TRUE	1	0.662863497999431	2		614	770	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271234	153271234	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	103	304	0	ENST00000281708.4:c.544del	p.Ser182LeufsTer57	p.S182Lfs*57	ENST00000281708	NM_033632.3	182	Tct/ct	3/12	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.662863497999431	2		304	267	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524815	187524815	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778212581	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	292	512	3	ENST00000441802.2:c.10865C>T	p.Thr3622Met	p.T3622M	ENST00000441802	NM_005245.3	3622	aCg/aTg	19/27	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.662863497999431	2		515	620	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294346	1294346	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	255	579	0	ENST00000310581.5:c.655C>A	p.Pro219Thr	p.P219T	ENST00000310581	NM_198253.2	219	Ccg/Acg	2/16	1	2	FACETS	0.962	0.903	1	0.962	0.903	1	CLONAL	1	TRUE	1	0.662863497999431	2		579	800	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947490	38947490	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	24	254	0	ENST00000357387.3:c.4190C>A	p.Pro1397His	p.P1397H	ENST00000357387	NM_152756.3	1397	cCt/cAt	32/38	1	2	FACETS	0.193	0.151	0.242	0.193	0.151	0.242	SUBCLONAL	1	TRUE	1	0.662863497999431	2		254	375	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522559	176522559	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	221	586	0	ENST00000292408.4:c.1656C>G	p.Cys552Trp	p.C552W	ENST00000292408	NM_213647.1	552	tgC/tgG	13/18	1	2	FACETS	0.873	0.815	0.932	0.873	0.815	0.932	CLONAL	1	TRUE	1	0.662863497999431	2		586	764	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171591	32171591	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	253	623	0	ENST00000375023.3:c.3187G>A	p.Ala1063Thr	p.A1063T	ENST00000375023	NM_004557.3	1063	Gcc/Acc	20/30	1	2	FACETS	0.967	0.909	1	0.967	0.909	1	CLONAL	1	TRUE	1	0.662863497999431	2		623	789	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652144	36652145	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	303	576	0	ENST00000244741.5:c.269dup	p.Gly91ArgfsTer38	p.G91Rfs*38	ENST00000244741	NM_000389.4	89	ttg/ttGg	2/3	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.662863497999431	2		576	730	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528427	157528427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	266	454	0	ENST00000346085.5:c.6152G>A	p.Gly2051Asp	p.G2051D	ENST00000346085	NM_020732.3	2051	gGc/gAc	20/20	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.662863497999431	2		454	588	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572597	141572597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376660302	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	311	528	1	ENST00000220592.5:c.473C>T	p.Thr158Met	p.T158M	ENST00000220592	NM_012154.3	158	aCg/aTg	4/19	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.662863497999431	2		529	742	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738636	145738637	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	239	580	0	ENST00000428558.2:c.2427dup	p.Gln810AlafsTer74	p.Q810Afs*74	ENST00000428558	NM_004260.3	809	-/G	15/22	1	2	FACETS	0.929	0.871	0.989	0.929	0.871	0.989	CLONAL	1	TRUE	1	0.662863497999431	2		580	776	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27228299	27228299	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759970580	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	220	402	2	ENST00000380036.4:c.3296G>A	p.Arg1099Gln	p.R1099Q	ENST00000380036	NM_000459.3	1099	cGa/cAa	22/23	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.662863497999431	2		404	551	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395101	139395101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777423973	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	298	555	0	ENST00000277541.6:c.5837G>A	p.Arg1946His	p.R1946H	ENST00000277541	NM_017617.3	1946	cGc/cAc	31/34	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.662863497999431	2		555	808	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400020	139400020	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750010764	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	55	664	0	ENST00000277541.6:c.4328C>T	p.Pro1443Leu	p.P1443L	ENST00000277541	NM_017617.3	1443	cCg/cTg	25/34	1	2	FACETS	0.211	0.179	0.245	0.211	0.179	0.245	SUBCLONAL	1	TRUE	1	0.662863497999431	2		664	788	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354666	70354666	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs727503868	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	47	564	1	ENST00000374080.3:c.4831C>T	p.Arg1611Cys	p.R1611C	ENST00000374080		1611	Cgt/Tgt	35/45	1	2	FACETS	0.159	0.134	0.188	0.159	0.134	0.188	SUBCLONAL	1	TRUE	1	0.662863497999431	2		565	890	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108330	8108330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768656332	NA	P-0026784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	102	553	0	ENST00000585124.1:c.894G>A	p.Met298Ile	p.M298I	ENST00000585124	NM_004217.3	298	atG/atA	9/9	1	2	FACETS	0.372	0.332	0.414	0.372	0.332	0.414	SUBCLONAL	1	TRUE	1	0.662863497999431	2		553	828	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0026785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	57	610	2	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	1	2	FACETS	0.249	0.213	0.288	0.249	0.213	0.288	SUBCLONAL	1	TRUE	1	0.748118311423902	2		612	612	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115975	8115976	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0026785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	77	250	0	ENST00000346208.3:c.1323dup	p.Met442HisfsTer65	p.M442Hfs*65	ENST00000346208		441	gcc/gCcc	6/6	1	2	FACETS	0.73	0.648	0.816	0.73	0.648	0.816	SUBCLONAL	1	TRUE	1	0.748118311423902	2		250	282	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966765	18966765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	109	717	1	ENST00000262803.5:c.1576G>A	p.Ala526Thr	p.A526T	ENST00000262803	NM_002911.3	526	Gcc/Acc	12/24	1	2	FACETS	0.356	0.319	0.395	0.356	0.319	0.395	SUBCLONAL	1	TRUE	1	0.748118311423902	2		718	819	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199489	11199489	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	94	320	0	ENST00000361445.4:c.5002C>G	p.Leu1668Val	p.L1668V	ENST00000361445	NM_004958.3	1668	Ctt/Gtt	36/58	0.10197837629619	6	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.748118311423902	6		320	524	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510787	120510787	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	134	388	0	ENST00000256646.2:c.1177A>C	p.Asn393His	p.N393H	ENST00000256646	NM_024408.3	393	Aac/Cac	7/34	1	2	FACETS	0.784	0.718	0.852	0.784	0.718	0.852	SUBCLONAL	1	TRUE	1	0.748118311423902	2		388	457	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549403	5549403	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	465	552	0	ENST00000397747.3:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000397747	NM_025239.3	144	Cag/Tag	4/7	0.685945973122592	3	FACETS	0.963	0.926	1			1	CLONAL	2	TRUE	NA	0.748118311423902	3		552	887	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0026786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	104	309	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	1	2	FACETS	0.737	0.663	0.816	0.737	0.663	0.816	SUBCLONAL	1	TRUE	1	0.541342956297254	2		309	521	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721550	176721550	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	163	434	0	ENST00000439151.2:c.7181T>C	p.Ile2394Thr	p.I2394T	ENST00000439151	NM_022455.4	2394	aTt/aCt	23/23	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.541342956297254	2		434	574	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	169	474	0				ENST00000310581	NM_198253.2	-/1132			0.34533330990824	3	FACETS	1	0.966	1	0.547	0.502	0.594	CLONAL	1	TRUE	1	0.370243447461904	3		474	989	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0026787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	167	483	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	0.370243447461904	2		483	804	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054241	30054241	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0026787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	199	382	0	ENST00000338641.4:c.663C>G	p.Tyr221Ter	p.Y221*	ENST00000338641	NM_000268.3	221	taC/taG	7/16	0.370243447461904	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.370243447461904	1		382	731	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	112	501	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.87	0.782	0.962	0.87	0.782	0.962	CLONAL	1	TRUE	1	0.32	2		501	805	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0026790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	99	373	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.30599551406321	3	FACETS	0.847	0.756	0.945	0.424	0.378	0.473	CLONAL	1	TRUE	1	0.32	3		373	847	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097621	27097622	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	69	386	0	ENST00000324856.7:c.3216dup	p.Trp1073MetfsTer32	p.W1073Mfs*32	ENST00000324856	NM_006015.4	1070	-/A	12/20	1	2	FACETS	0.506	0.439	0.578	0.506	0.439	0.578	SUBCLONAL	1	TRUE	1	0.32	2		386	853	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691039	NA	P-0026790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	165	433	0	ENST00000269305.4:c.919+1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.356552146370367	2	FACETS	1	0.953	1			1	CLONAL	1	TRUE	NA	0.32	2		433	978	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562441	21562441	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1176877473	NA	P-0026790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	49	151	0	ENST00000382592.4:c.1478C>T	p.Ala493Val	p.A493V	ENST00000382592	NM_014572.2	493	gCg/gTg	4/8	0.356552146370367	5	FACETS	0.757	0.64	0.885			1	SUBCLONAL	1	TRUE	NA	0.32	5		151	599	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028614	12028614	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	106	159	0	ENST00000353533.5:c.817G>C	p.Glu273Gln	p.E273Q	ENST00000353533	NM_003010.3	273	Gaa/Caa	8/11	0.356552146370367	3	FACETS	1	0.911	1	0.509	0.456	0.565	CLONAL	1	TRUE	1	0.32	3		159	755	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028644	12028645	+	missense_variant	Missense_Mutation	DNP	GG	GG	CA	novel	NA	P-0026790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	126	191	0	ENST00000353533.5:c.847_848delinsCA	p.Gly283Gln	p.G283Q	ENST00000353533	NM_003010.3	283	GGa/CAa	8/11	0.356552146370367	3	FACETS	0.954	0.862	1	0.477	0.431	0.525	CLONAL	1	TRUE	1	0.32	3		191	958	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0026791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	249	652	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.49862633289346	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.49862633289346	1		653	709	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0026791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	267	670	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	0.49862633289346	3	FACETS	0.931	0.871	0.993	0.466	0.435	0.497	CLONAL	1	TRUE	1	0.49862633289346	3		670	1437	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256219	123256219	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	10962	400	0	ENST00000358487.5:c.1690G>C	p.Val564Leu	p.V564L	ENST00000358487	NM_000141.4	564	Gtt/Ctt	13/18	0.49862633289346	56	FACETS	1	0.999	1			1	CLONAL	56	TRUE	NA	0.49862633289346	56		400	11280	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435968	49435968	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	249	689	0	ENST00000301067.7:c.6013C>T	p.Arg2005Cys	p.R2005C	ENST00000301067	NM_003482.3	2005	Cgc/Tgc	28/54	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.49862633289346	2		689	974	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0026792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	154	388	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.245656916533767	4	FACETS	1	0.959	1	0.714	0.655	0.775	CLONAL	2	TRUE	1	0.271591265325517	4		388	673	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371005	55371005	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	79	598	2	ENST00000297316.4:c.307G>T	p.Gly103Cys	p.G103C	ENST00000297316	NM_022454.3	103	Ggc/Tgc	1/2	1	2	FACETS	0.742	0.652	0.839	0.742	0.652	0.839	SUBCLONAL	1	TRUE	1	0.271591265325517	2		600	784	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0026792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	266	703	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	1	2	FACETS	0.829	0.776	0.883	1	0.994	1	CLONAL	2	TRUE	1	0.271591265325517	2		703	1182	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416218	416218	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs368037236	NA	P-0026792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	141	470	0	ENST00000399788.2:c.3968G>T	p.Arg1323Leu	p.R1323L	ENST00000399788	NM_001042603.1	1323	cGg/cTg	24/28	0.10300439201992	3	FACETS	0.855	0.78	0.932			1	INDETERMINATE	2	TRUE	NA	0.271591265325517	3		470	690	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683689	162683689	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs770930242	NA	P-0026792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	95	502	0	ENST00000366898.1:c.280G>T	p.Gly94Cys	p.G94C	ENST00000366898	NM_004562.2	94	Ggc/Tgc	3/12	1	2	FACETS	0.763	0.678	0.854	0.763	0.678	0.854	SUBCLONAL	1	TRUE	1	0.271591265325517	2		502	917	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949100	71949100	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	76	493	1	ENST00000298229.2:c.3567G>T	p.Gln1189His	p.Q1189H	ENST00000298229	NM_001567.3	1189	caG/caT	27/28	1	2	FACETS	0.678	0.594	0.77	0.678	0.594	0.77	SUBCLONAL	1	TRUE	1	0.271591265325517	2		494	825	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729734	162729734	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	84	507	0	ENST00000367921.3:c.820G>A	p.Glu274Lys	p.E274K	ENST00000367921	NM_006182.2	274	Gaa/Aaa	8/18	1	2	FACETS	0.692	0.61	0.78	0.692	0.61	0.78	SUBCLONAL	1	TRUE	1	0.271591265325517	2		507	894	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246515	46246515	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0026792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	71	266	0	ENST00000334344.6:c.4609A>T	p.Arg1537Ter	p.R1537*	ENST00000334344	NM_152641.2	1537	Aga/Tga	15/21	0.194194125995156	2	FACETS	1	0.96	1	0.621	0.544	0.703	CLONAL	1	TRUE	0	0.271591265325517	2		266	421	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865671	57865671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	202	727	1	ENST00000228682.2:c.3148G>A	p.Val1050Met	p.V1050M	ENST00000228682	NM_005269.2	1050	Gtg/Atg	12/12	0.194194125995156	2	FACETS	1	0.988	1	0.665	0.616	0.717	CLONAL	1	TRUE	0	0.271591265325517	2		728	1118	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557423	95557423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	59	420	0	ENST00000393063.1:c.5551C>T	p.Arg1851Cys	p.R1851C	ENST00000393063	NM_030621.3	1851	Cgt/Tgt	27/28	1	2	FACETS	0.753	0.648	0.868	0.753	0.648	0.868	SUBCLONAL	1	TRUE	1	0.271591265325517	2		420	577	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784635	43784635	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	79	571	0	ENST00000382044.4:c.39G>T	p.Leu13Phe	p.L13F	ENST00000382044	NM_001141980.1	13	ttG/ttT	2/28	1	2	FACETS	0.786	0.691	0.889	0.786	0.691	0.889	SUBCLONAL	1	TRUE	1	0.271591265325517	2		571	740	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774218	66774218	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0026792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	67	749	0	ENST00000307102.5:c.693+1G>A		p.X231_splice	ENST00000307102	NM_002755.3	231			1	2	FACETS	0.512	0.444	0.587	0.512	0.444	0.587	SUBCLONAL	1	TRUE	1	0.271591265325517	2		749	963	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476307	88476307	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	84	668	0	ENST00000360948.2:c.1825G>C	p.Asp609His	p.D609H	ENST00000360948	NM_001012338.2	609	Gat/Cat	15/19	1	2	FACETS	0.713	0.629	0.804	0.713	0.629	0.804	SUBCLONAL	1	TRUE	1	0.271591265325517	2		668	867	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191155	2191155	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	140	705	0	ENST00000398665.3:c.412del	p.Glu138ArgfsTer10	p.E138Rfs*10	ENST00000398665	NM_032482.2	137	Ggg/gg	5/28	0.271591265325517	1	FACETS	0.801	0.728	0.877	0.801	0.728	0.877	CLONAL	1	TRUE	0	0.271591265325517	1		705	1113	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735452	204735452	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	35	387	0	ENST00000302823.3:c.253T>G	p.Cys85Gly	p.C85G	ENST00000302823	NM_005214.4	85	Tgt/Ggt	2/4	1	2	FACETS	0.391	0.319	0.472	0.391	0.319	0.472	SUBCLONAL	1	TRUE	1	0.271591265325517	2		387	659	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225400313	225400313	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs886055696	NA	P-0026792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	25	302	0	ENST00000264414.4:c.310A>T	p.Thr104Ser	p.T104S	ENST00000264414	NM_003590.4	104	Acg/Tcg	3/16	1	2	FACETS	0.385	0.303	0.48	0.385	0.303	0.48	SUBCLONAL	1	TRUE	1	0.271591265325517	2		302	478	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561052	9561052	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs760823835	NA	P-0026792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	51	276	1	ENST00000353224.5:c.730G>T	p.Gly244Trp	p.G244W	ENST00000353224	NM_177990.2	244	Ggg/Tgg	4/10	1	2	FACETS	0.855	0.728	0.995	0.855	0.728	0.995	CLONAL	1	TRUE	1	0.271591265325517	2		277	439	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651274	45651274	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201791685	NA	P-0026792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	105	582	1	ENST00000407780.3:c.751G>A	p.Glu251Lys	p.E251K	ENST00000407780	NM_001283052.1	251	Gag/Aag	5/7	0.271591265325517	1	FACETS	0.706	0.631	0.785	0.706	0.631	0.785	SUBCLONAL	1	TRUE	0	0.271591265325517	1		583	947	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204743	128204743	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	53	773	0	ENST00000341105.2:c.698T>A	p.Leu233Gln	p.L233Q	ENST00000341105	NM_032638.4	233	cTa/cAa	3/6	1	2	FACETS	0.372	0.316	0.434	0.372	0.316	0.434	SUBCLONAL	1	TRUE	1	0.271591265325517	2		773	1050	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374339	81374339	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	38	357	0	ENST00000222390.5:c.723C>G	p.His241Gln	p.H241Q	ENST00000222390	NM_000601.4	241	caC/caG	6/18	1	2	FACETS	0.565	0.467	0.675	0.565	0.467	0.675	SUBCLONAL	1	TRUE	1	0.271591265325517	2		357	495	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509396	106509396	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	72	506	0	ENST00000359195.3:c.1390G>T	p.Val464Leu	p.V464L	ENST00000359195	NM_002649.2	464	Gtg/Ttg	2/11	1	2	FACETS	0.578	0.504	0.659	0.578	0.504	0.659	SUBCLONAL	1	TRUE	1	0.271591265325517	2		506	917	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934319	68934319	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	76	697	1	ENST00000288368.4:c.385G>T	p.Ala129Ser	p.A129S	ENST00000288368	NM_024870.2	129	Gca/Tca	4/40	1	2	FACETS	0.597	0.523	0.678	0.597	0.523	0.678	SUBCLONAL	1	TRUE	1	0.271591265325517	2		698	937	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0026794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	171	540	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.325742153943462	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.325742153943462	1		540	869	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770576	40770576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	245	488	0	ENST00000373198.4:c.2806C>T	p.Arg936Ter	p.R936*	ENST00000373198	NM_133170.3	936	Cga/Tga	19/32	0.325742153943462	3	FACETS	0.958	0.897	1	0.958	0.897	1	CLONAL	2	TRUE	1	0.325742153943462	3		488	913	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0026794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	214	414	1	ENST00000311936.3:c.34_35delinsCT	p.Gly12Leu	p.G12L	ENST00000311936	NM_004985.3	12	GGt/CTt	2/5	0.297801743775158	3	FACETS	0.885	0.824	0.948	0.885	0.824	0.948	CLONAL	2	TRUE	1	0.325742153943462	3		415	863	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998972	100998972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	116	497	1	ENST00000325455.5:c.830C>T	p.Ala277Val	p.A277V	ENST00000325455	NM_001202474.3	277	gCg/gTg	1/8	1	2	FACETS	0.842	0.758	0.93	0.842	0.758	0.93	CLONAL	1	TRUE	1	0.325742153943462	2		498	846	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0026796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	182	885	1	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.295912546332299	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.28	1		886	1077	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0026796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	77	388	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.835	0.733	0.944	0.835	0.733	0.944	CLONAL	1	TRUE	1	0.28	2		388	659	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0026796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	65	357	1	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.28	2		358	439	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984812	55984812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781436993	NA	P-0026796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	124	563	1	ENST00000263923.4:c.317G>A	p.Arg106Gln	p.R106Q	ENST00000263923	NM_002253.2	106	cGg/cAg	3/30	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.28	2		564	772	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573666	48573666	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0026796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	21	334	2	ENST00000342988.3:c.249+1G>T		p.X83_splice	ENST00000342988	NM_005359.5	83			0.295912546332299	1	FACETS	0.336	0.258	0.427	0.336	0.258	0.427	SUBCLONAL	1	TRUE	0	0.28	1		336	384	SUCCESS
APC	324	MSKCC	GRCh37	5	112176008	112176033	+	frameshift_variant	Frame_Shift_Del	DEL	GAAATACTAGAAGAATGTATTATTTC	GAAATACTAGAAGAATGTATTATTTC	A	novel	NA	P-0026796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	42	274	0	ENST00000257430.4:c.4717_4742delinsA	p.Glu1573MetfsTer69	p.E1573Mfs*69	ENST00000257430	NM_000038.5	1573	GAAATACTAGAAGAATGTATTATTTCt/At	16/16	1	2	FACETS	0.792	0.662	0.934	0.792	0.662	0.934	CLONAL	1	TRUE	1	0.28	2		274	379	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967089	18967089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334288478	NA	P-0026797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	240	610	1	ENST00000262803.5:c.1804G>A	p.Ala602Thr	p.A602T	ENST00000262803	NM_002911.3	602	Gca/Aca	13/24	0.41609580262524	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.41609580262524	3		611	641	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054920	176054920	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759451215	NA	P-0026797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	71	399	5	ENST00000367669.3:c.1133G>A	p.Arg378His	p.R378H	ENST00000367669	NM_022457.5	378	cGt/cAt	10/20	0.41609580262524	5	FACETS	0.893	0.779	1	0.298	0.259	0.339	CLONAL	1	TRUE	2	0.41609580262524	5		404	621	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115852	8115853	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs1085307641	NA	P-0026797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	203	550	0	ENST00000346208.3:c.1198_1199del	p.Met400ValfsTer106	p.M400Vfs*106	ENST00000346208		400	ATg/g	6/6	0.38477012311493	4	FACETS	0.958	0.892	1	0.958	0.892	1	CLONAL	2	TRUE	2	0.41609580262524	4		550	721	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554277	106554277	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	42	394	0	ENST00000369096.4:c.1805C>G	p.Pro602Arg	p.P602R	ENST00000369096	NM_001198.3	602	cCt/cGt	6/7	0.41609580262524	3	FACETS	0.546	0.456	0.645	0.273	0.228	0.323	SUBCLONAL	1	TRUE	1	0.41609580262524	3		394	447	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416665	121416665	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	196	702	2	ENST00000257555.6:c.94G>T	p.Glu32Ter	p.E32*	ENST00000257555		32	Gag/Tag	1/10	1	2	FACETS	0.947	0.882	1	0.947	0.882	1	CLONAL	1	TRUE	1	0.66	2		704	627	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431437	121431437	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	215	651	0	ENST00000257555.6:c.641T>A	p.Leu214Gln	p.L214Q	ENST00000257555		214	cTg/cAg	3/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.66	2		651	600	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348491	70348491	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	139	464	0	ENST00000374080.3:c.3398C>A	p.Ala1133Asp	p.A1133D	ENST00000374080		1133	gCc/gAc	24/45	1	2	FACETS	0.885	0.811	0.961	0.885	0.811	0.961	CLONAL	1	TRUE	1	0.66	2		464	476	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416665	121416665	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026798-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	258	702	2	ENST00000257555.6:c.94G>T	p.Glu32Ter	p.E32*	ENST00000257555		32	Gag/Tag	1/10	1	2	FACETS	0.903	0.848	0.958	0.903	0.848	0.958	CLONAL	1	TRUE	1	0.72	2		704	794	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431437	121431437	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026798-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	313	651	0	ENST00000257555.6:c.641T>A	p.Leu214Gln	p.L214Q	ENST00000257555		214	cTg/cAg	3/10	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.72	2		651	867	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348491	70348491	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026798-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	224	464	0	ENST00000374080.3:c.3398C>A	p.Ala1133Asp	p.A1133D	ENST00000374080		1133	gCc/gAc	24/45	1	2	FACETS	0.957	0.896	1	0.957	0.896	1	CLONAL	1	TRUE	1	0.72	2		464	650	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0026799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	235	322	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.751375892304332	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.751375892304332	1		322	363	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0026799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	795	255	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.751375892304332	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	4	TRUE	0	0.751375892304332	4		255	912	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	246	196	0	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	0.733205526348102	2	FACETS	0.995	0.956	1	0.995	0.956	1	CLONAL	2	TRUE	0	0.751375892304332	2		196	329	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188164	11188164	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587777893	NA	P-0026799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	242	421	0	ENST00000361445.4:c.5930C>A	p.Thr1977Lys	p.T1977K	ENST00000361445	NM_004958.3	1977	aCa/aAa	43/58	1	2	FACETS	0.979	0.92	1	0.979	0.92	1	CLONAL	1	TRUE	1	0.751375892304332	2		421	658	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014356	70014356	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1018390529	NA	P-0026799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	213	478	0	ENST00000394351.3:c.1217G>A	p.Arg406Gln	p.R406Q	ENST00000394351	NM_000248.3	406	cGg/cAg	9/9	1	2	FACETS	0.947	0.885	1	0.947	0.885	1	CLONAL	1	TRUE	1	0.751375892304332	2		478	599	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0026800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	284	528	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.2464028765894	5	FACETS	0.861	0.813	0.909	0.861	0.813	0.909	INDETERMINATE	3	TRUE	2	0.513775294283093	5		528	758	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0026800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	411	652	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	2	TRUE	NA	0.513775294283093	2		652	760	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	46	447	1	ENST00000346208.3:c.1220_1221insA	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcAg	6/6	1	2	FACETS	0.952	0.811	1	0.952	0.811	1	CLONAL	1	TRUE	1	0.447256549228075	2		448	216	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0026801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	41	530	2	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.447256549228075	1	FACETS	0.823	0.695	0.96	0.823	0.695	0.96	CLONAL	1	TRUE	0	0.447256549228075	1		532	173	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939442	71939443	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCCT	novel	NA	P-0026801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	70	665	0	ENST00000298229.2:c.299_303dup	p.Tyr102AlafsTer18	p.Y102Afs*18	ENST00000298229	NM_001567.3	99	-/GGCCT	3/28	0.447256549228075	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.447256549228075	1		665	187	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192639	94192639	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	42	504	0	ENST00000323929.3:c.1435G>C	p.Glu479Gln	p.E479Q	ENST00000323929	NM_005591.3	479	Gaa/Caa	13/20	0.313825310401897	0	FACETS	0.57	0.483	0.665			1	SUBCLONAL	1	TRUE	0	0.447256549228075	0		504	182	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492625	56492625	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	42	457	0	ENST00000267101.3:c.2775G>C	p.Glu925Asp	p.E925D	ENST00000267101	NM_001982.3	925	gaG/gaC	23/28	0.447256549228075	3	FACETS	0.711	0.596	0.838	0.356	0.298	0.419	SUBCLONAL	1	TRUE	1	0.447256549228075	3		457	323	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0026802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	268	339	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.817239105608552	1	FACETS	0.926	0.885	0.966	0.926	0.885	0.966	CLONAL	1	TRUE	0	0.817239105608552	1		339	419	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0026802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	443	537	1	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.817239105608552	1	FACETS	0.997	0.965	1	0.997	0.965	1	CLONAL	1	TRUE	0	0.817239105608552	1		538	643	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589589	67589591	+	inframe_deletion	In_Frame_Del	DEL	AAT	AAT	-	novel	NA	P-0026802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	357	386	0	ENST00000274335.5:c.1353_1355del	p.Glu451_Tyr452delinsAsp	p.E451_Y452delinsD	ENST00000274335		451	gAATat/gat	10/15	0.817239105608552	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.817239105608552	1		386	511	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041074	42041074	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	569	631	3	ENST00000219905.7:c.5452C>T	p.Arg1818Ter	p.R1818*	ENST00000219905	NM_001164273.1	1818	Cga/Tga	16/24	0.817239105608552	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.817239105608552	1		634	805	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645318	67645318	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	220	535	3	ENST00000264010.4:c.583C>A	p.Pro195Thr	p.P195T	ENST00000264010	NM_006565.3	195	Cca/Aca	3/12	1	2	FACETS	0.436	0.405	0.468	0.436	0.405	0.468	SUBCLONAL	1	TRUE	1	0.817239105608552	2		538	1235	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740402	58740403	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	501	625	0	ENST00000305921.3:c.1307_1308insG	p.Ile436MetfsTer7	p.I436Mfs*7	ENST00000305921	NM_003620.3	436	ata/atGa	6/6	0.817239105608552	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.817239105608552	1		625	691	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550586	29550586	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1567845945	NA	P-0026804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	160	282	0	ENST00000356175.3:c.1845+1G>A		p.X615_splice	ENST00000356175	NM_000267.3	615			0.220596865097809	6	FACETS	1	0.974	1	0.745	0.689	0.802	INDETERMINATE	2	TRUE	3	0.80139144318698	6		282	465	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864630	56864630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210415750	NA	P-0026804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	262	687	0	ENST00000519728.1:c.593G>A	p.Arg198Gln	p.R198Q	ENST00000519728	NM_002350.3	198	cGa/cAa	7/13	0.80139144318698	3	FACETS	0.947	0.889	1	0.474	0.444	0.504	CLONAL	1	TRUE	1	0.80139144318698	3		687	967	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294911	1294911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1561215067	NA	P-0026804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	305	130	0	ENST00000310581.5:c.194C>T	p.Pro65Leu	p.P65L	ENST00000310581	NM_198253.2	65	cCc/cTc	1/16	0.80139144318698	12	FACETS	0.926	0.874	0.979			1	CLONAL	4	TRUE	NA	0.80139144318698	12		130	1029	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968095	68968095	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	310	509	0	ENST00000288368.4:c.1124G>T	p.Trp375Leu	p.W375L	ENST00000288368	NM_024870.2	375	tGg/tTg	10/40	0.80139144318698	3	FACETS	0.897	0.855	0.939	0.897	0.855	0.939	CLONAL	2	TRUE	1	0.80139144318698	3		509	604	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295348	1295348	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0026804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2352	316	484	1				ENST00000310581	NM_198253.2	-/1132			0.80139144318698	12	FACETS	1	0.993	1			1	CLONAL	1	TRUE	NA	0.80139144318698	12		485	2668	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	218	501	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.98	0.914	1	0.98	0.914	1	CLONAL	1	TRUE	1	0.581065159448953	2		501	766	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0026805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	228	427	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.581065159448953	2		428	684	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0026805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	502	707	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.581065159448953	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.581065159448953	2		707	834	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0026805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	115	285	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.581065159448953	2		285	386	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0026805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	185	209	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.946	0.877	1	0.946	0.877	1	CLONAL	1	TRUE	1	0.581065159448953	2		210	673	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607597	43607597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs545625150	NA	P-0026805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	262	837	2	ENST00000355710.3:c.1573C>T	p.Arg525Trp	p.R525W	ENST00000355710	NM_020975.4	525	Cgg/Tgg	8/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.581065159448953	2		839	882	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206581	108206581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	137	461	0	ENST00000278616.4:c.8161G>A	p.Asp2721Asn	p.D2721N	ENST00000278616	NM_000051.3	2721	Gac/Aac	56/63	1	2	FACETS	0.807	0.737	0.88	0.807	0.737	0.88	CLONAL	1	TRUE	1	0.581065159448953	2		461	584	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223194	36223194	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746724776	NA	P-0026805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	308	998	1	ENST00000222270.7:c.5744G>A	p.Arg1915His	p.R1915H	ENST00000222270	NM_014727.1	1915	cGt/cAt	28/37	1	2	FACETS	0.983	0.928	1	0.983	0.928	1	CLONAL	1	TRUE	1	0.581065159448953	2		999	1078	SUCCESS
REL	5966	MSKCC	GRCh37	2	61144066	61144067	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0026805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	245	678	0	ENST00000295025.8:c.452_453del	p.Cys151PhefsTer7	p.C151Ffs*7	ENST00000295025	NM_002908.2	150	cTG/c	5/11	1	2	FACETS	0.978	0.916	1	0.978	0.916	1	CLONAL	1	TRUE	1	0.581065159448953	2		678	862	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934312	49934312	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	161	586	0	ENST00000296474.3:c.2195G>A	p.Gly732Glu	p.G732E	ENST00000296474	NM_002447.2	732	gGg/gAg	8/20	1	2	FACETS	0.81	0.745	0.878	0.81	0.745	0.878	CLONAL	1	TRUE	1	0.581065159448953	2		586	684	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038508	47038508	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781804786	NA	P-0026805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	202	689	0	ENST00000377604.3:c.670G>A	p.Val224Ile	p.V224I	ENST00000377604	NM_001204468.1	224	Gtc/Atc	8/24	1	2	FACETS	0.942	0.876	1	0.942	0.876	1	CLONAL	1	TRUE	1	0.581065159448953	2		689	738	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0026806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	338	592	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.555445569707361	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.555445569707361	1		594	860	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0026807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	13	279	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.427	0.303	0.579	0.427	0.303	0.579	SUBCLONAL	1	TRUE	1	0.15	2		279	406	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0026807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	33	256	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.698	0.567	0.847	0.698	0.567	0.847	SUBCLONAL	1	TRUE	1	0.15	2		257	630	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720876	89720876	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs786201041	NA	P-0026807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	47	291	0	ENST00000371953.3:c.1026+1G>C		p.X342_splice	ENST00000371953	NM_000314.4	342			1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.15	2		291	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0026808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	581	572	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.785293144396797	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.785293144396797	2		572	708	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021583	31021583	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs746873290	NA	P-0026808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	638	461	0	ENST00000375687.4:c.1582G>T	p.Glu528Ter	p.E528*	ENST00000375687	NM_015338.5	528	Gag/Tag	12/13	0.656582390465172	5	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	2	0.785293144396797	5		461	1141	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176618930	176618930	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	260	537	0	ENST00000439151.2:c.973G>C	p.Asp325His	p.D325H	ENST00000439151	NM_022455.4	325	Gat/Cat	3/23	0.785293144396797	3	FACETS	0.732	0.685	0.781			1	SUBCLONAL	1	TRUE	NA	0.785293144396797	3		537	1260	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176618995	176618995	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	217	486	0	ENST00000439151.2:c.1038G>T	p.Leu346Phe	p.L346F	ENST00000439151	NM_022455.4	346	ttG/ttT	3/23	0.785293144396797	3	FACETS	0.694	0.645	0.745			1	SUBCLONAL	1	TRUE	NA	0.785293144396797	3		486	1109	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163648	32163648	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs764118051	NA	P-0026808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	135	452	0	ENST00000375023.3:c.5578C>A	p.Arg1860Ser	p.R1860S	ENST00000375023	NM_004557.3	1860	Cgc/Agc	30/30	0.656582390465172	5	FACETS	0.877	0.797	0.961	0.292	0.265	0.321	CLONAL	1	TRUE	2	0.785293144396797	5		452	854	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061334	38061334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	190	744	0	ENST00000250448.2:c.655C>T	p.Arg219Cys	p.R219C	ENST00000250448	NM_004496.3	219	Cgc/Tgc	2/2	1	2	FACETS	0.753	0.695	0.813	1	0.99	1	SUBCLONAL	2	TRUE	1	0.234056829411584	2		744	1078	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0026813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	82	340	1	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.226215002204894	2		341	638	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593405	48593405	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	68	378	0	ENST00000342988.3:c.1156G>C	p.Gly386Arg	p.G386R	ENST00000342988	NM_005359.5	386	Ggt/Cgt	10/12	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.226215002204894	2		378	497	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983120	201983121	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	105	655	0	ENST00000359651.3:c.970dup	p.Met324AsnfsTer147	p.M324Nfs*147	ENST00000359651		323	-/A	7/8	0.226215002204894	2	FACETS	1	0.956	1	0.564	0.505	0.627	CLONAL	1	TRUE	0	0.226215002204894	2		655	823	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50490711	50490711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	79	605	0	ENST00000394963.4:c.1348G>A	p.Gly450Ser	p.G450S	ENST00000394963	NM_003076.4	450	Ggt/Agt	11/13	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.226215002204894	2		605	682	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569715	41569715	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	62	460	0	ENST00000263253.7:c.4706A>G	p.Lys1569Arg	p.K1569R	ENST00000263253	NM_001429.3	1569	aAg/aGg	29/31	1	2	FACETS	0.852	0.736	0.979	0.852	0.736	0.979	CLONAL	1	TRUE	1	0.226215002204894	2		460	643	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162779	47162779	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	29	418	0	ENST00000409792.3:c.3347A>C	p.Lys1116Thr	p.K1116T	ENST00000409792	NM_014159.6	1116	aAa/aCa	3/21	1	2	FACETS	0.53	0.424	0.65	0.53	0.424	0.65	SUBCLONAL	1	TRUE	1	0.226215002204894	2		418	484	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0026814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	50	424	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.506	0.429	0.592	0.506	0.429	0.592	SUBCLONAL	1	TRUE	1	0.289260981475938	2		424	683	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023905	27023905	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	27	175	0	ENST00000324856.7:c.1011G>A	p.Trp337Ter	p.W337*	ENST00000324856	NM_006015.4	337	tgG/tgA	1/20	0.251376474975236	1	FACETS	0.76	0.609	0.931	0.76	0.609	0.931	CLONAL	1	TRUE	0	0.289260981475938	1		175	210	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880957	134880957	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770406411	NA	P-0026814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	53	511	0	ENST00000398015.3:c.1520G>A	p.Arg507His	p.R507H	ENST00000398015	NM_004441.4	507	cGt/cAt	7/16	1	2	FACETS	0.586	0.499	0.682	0.586	0.499	0.682	SUBCLONAL	1	TRUE	1	0.289260981475938	2		511	625	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070871	30070871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs74315503	NA	P-0026814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	78	657	1	ENST00000338641.4:c.1387G>A	p.Glu463Lys	p.E463K	ENST00000338641	NM_000268.3	463	Gag/Aag	13/16	1	2	FACETS	0.71	0.623	0.803	0.71	0.623	0.803	SUBCLONAL	1	TRUE	1	0.289260981475938	2		658	760	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448536	49448536	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0026814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	65	474	0	ENST00000301067.7:c.177-2A>C		p.X59_splice	ENST00000301067	NM_003482.3	59			1	2	FACETS	0.759	0.658	0.868	0.759	0.658	0.868	SUBCLONAL	1	TRUE	1	0.289260981475938	2		474	592	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639873	3639873	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	65	678	0	ENST00000294008.3:c.3766C>G	p.Leu1256Val	p.L1256V	ENST00000294008	NM_032444.2	1256	Ctg/Gtg	12/15	1	2	FACETS	0.635	0.55	0.727	0.635	0.55	0.727	SUBCLONAL	1	TRUE	1	0.289260981475938	2		678	708	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63553963	63553963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239640498	NA	P-0026814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	100	439	0	ENST00000307078.5:c.776C>T	p.Ala259Val	p.A259V	ENST00000307078	NM_004655.3	259	gCg/gTg	2/11	0.286068153991999	3	FACETS	1	0.975	1	0.653	0.584	0.726	CLONAL	1	TRUE	1	0.289260981475938	3		439	606	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967174	25967174	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376019147	NA	P-0026814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	36	271	0	ENST00000435504.4:c.2032G>A	p.Ala678Thr	p.A678T	ENST00000435504		678	Gcc/Acc	13/13	1	2	FACETS	0.761	0.627	0.91	0.761	0.627	0.91	CLONAL	1	TRUE	1	0.289260981475938	2		271	327	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095896	29095896	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1039682955	NA	P-0026814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	73	617	0	ENST00000328354.6:c.938T>C	p.Val313Ala	p.V313A	ENST00000328354	NM_007194.3	313	gTg/gCg	9/15	1	2	FACETS	0.579	0.505	0.659	0.579	0.505	0.659	SUBCLONAL	1	TRUE	1	0.289260981475938	2		617	872	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55603372	55603372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	42	427	0	ENST00000288135.5:c.2728G>A	p.Asp910Asn	p.D910N	ENST00000288135	NM_000222.2	910	Gat/Aat	20/21	1	2	FACETS	0.575	0.48	0.681	0.575	0.48	0.681	SUBCLONAL	1	TRUE	1	0.289260981475938	2		427	505	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970913	55970913	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	72	510	0	ENST00000263923.4:c.1884G>T	p.Glu628Asp	p.E628D	ENST00000263923	NM_002253.2	628	gaG/gaT	13/30	1	2	FACETS	0.769	0.672	0.874	0.769	0.672	0.874	SUBCLONAL	1	TRUE	1	0.289260981475938	2		510	647	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31511237	31511238	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0026814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	91	750	0	ENST00000344624.3:c.1336_1337del	p.Asp446GlnfsTer3	p.D446Qfs*3	ENST00000344624		446	GAc/c	6/33	1	2	FACETS	0.671	0.595	0.753	0.671	0.595	0.753	SUBCLONAL	1	TRUE	1	0.289260981475938	2		750	937	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443695	29443695	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs863225281	NA	P-0121542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	175	520	3	ENST00000389048.3:c.3522C>A	p.Phe1174Leu	p.F1174L	ENST00000389048	NM_004304.4	1174	ttC/ttA	23/29	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	NA	1	0.58613108629535	2		523	575	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707683	176707683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587784154	NA	P-0121542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	109	386	0	ENST00000439151.2:c.5740C>T	p.Arg1914Cys	p.R1914C	ENST00000439151	NM_022455.4	1914	Cgc/Tgc	18/23	1	2	FACETS	0.656	0.591	0.725	0.656	0.591	0.725	SUBCLONAL	1	NA	1	0.58613108629535	2		386	567	SUCCESS
APC	324	MSKCC	GRCh37	5	112176044	112176044	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0121542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	136	285	0	ENST00000257430.4:c.4753A>G	p.Thr1585Ala	p.T1585A	ENST00000257430	NM_000038.5	1585	Aca/Gca	16/16	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	NA	1	0.58613108629535	2		285	460	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375702	118375702	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	378	545	2	ENST00000534358.1:c.9095C>A	p.Pro3032His	p.P3032H	ENST00000534358	NM_005933.3	3032	cCt/cAt	27/36	1	2	FACETS	0.962	0.917	1	0.962	0.917	1	CLONAL	1	TRUE	1	0.831508480622182	2		547	945	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385165	41385165	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	423	657	0	ENST00000373198.4:c.796C>A	p.Arg266Ser	p.R266S	ENST00000373198	NM_133170.3	266	Cgc/Agc	6/32	1	2	FACETS	0.975	0.932	1	0.975	0.932	1	CLONAL	1	TRUE	1	0.831508480622182	2		657	1043	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288945	33288945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746835251	NA	P-0026818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	266	354	0	ENST00000374542.5:c.607C>T	p.Arg203Trp	p.R203W	ENST00000374542	NM_001141970.1	203	Cgg/Tgg	3/8	1	2	FACETS	0.99	0.935	1	0.99	0.935	1	CLONAL	1	TRUE	1	0.831508480622182	2		354	646	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0026829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	82	454	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.859	0.764	0.959	1	0.987	1	CLONAL	3	FALSE	1	0.190024921569348	2		454	335	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	118	541	2	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	0.904	0.821	0.99	1	0.991	1	CLONAL	3	FALSE	1	0.190024921569348	2		543	458	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106058	8106058	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	188	560	0	ENST00000346208.3:c.878T>A	p.Met293Lys	p.M293K	ENST00000346208		293	aTg/aAg	4/6	0.161737273957138	3	FACETS	1	0.981	1	1	0.992	1	CLONAL	3	FALSE	1	0.190024921569348	3		560	621	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692926	89692926	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	30	521	0	ENST00000371953.3:c.410C>G	p.Ala137Gly	p.A137G	ENST00000371953	NM_000314.4	137	gCa/gGa	5/9	0.161737273957138	3	FACETS	0.9	0.726	1	0.45	0.363	0.549	CLONAL	1	FALSE	1	0.190024921569348	3		521	384	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356173	66356173	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	40	553	0	ENST00000273854.3:c.1324G>C	p.Glu442Gln	p.E442Q	ENST00000273854	NM_004439.5	442	Gag/Cag	5/18	1	2	FACETS	0.803	0.667	0.956	0.803	0.667	0.956	CLONAL	1	FALSE	1	0.190024921569348	2		553	524	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891445	76891445	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0026829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	34	436	0	ENST00000373344.5:c.4660A>T	p.Arg1554Ter	p.R1554*	ENST00000373344	NM_000489.3	1554	Aga/Tga	16/35	0.155444461660604	0	FACETS	1	0.923	1			1	CLONAL	1	FALSE	0	0.190024921569348	0		436	233	SUCCESS
AR	367	MSKCC	GRCh37	X	66905872	66905872	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137852569	NA	P-0026841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	51	381	0	ENST00000374690.3:c.1789G>A	p.Ala597Thr	p.A597T	ENST00000374690	NM_000044.3	597	Gcc/Acc	3/8	0.219685847019712	1	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	0	0.219685847019712	1		381	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0026841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	249	614	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.219685847019712	6	FACETS	1	0.982	1	1	0.982	1	CLONAL	4	TRUE	2	0.219685847019712	6		614	733	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938326	76938326	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	137	519	0	ENST00000373344.5:c.2422C>T	p.Arg808Ter	p.R808*	ENST00000373344	NM_000489.3	808	Cga/Tga	9/35	0.219685847019712	1	FACETS	0.949	0.867	1	1	0.99	1	CLONAL	2	TRUE	0	0.219685847019712	1		519	585	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47088102	47088102	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	59	380	0	ENST00000409792.3:c.6973C>A	p.Gln2325Lys	p.Q2325K	ENST00000409792	NM_014159.6	2325	Cag/Aag	16/21	0.219685847019712	5	FACETS	1	0.949	1	0.41	0.352	0.472	CLONAL	1	TRUE	2	0.219685847019712	5		380	581	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059350	42059354	+	missense_variant	Missense_Mutation	ONP	GTTGG	GTTGG	CTGGT	novel	NA	P-0026841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	44	452	0	ENST00000219905.7:c.9070_9074delinsCTGGT	p.Val3024_Gly3025delinsLeuVal	p.V3024_G3025delinsLV	ENST00000219905	NM_001164273.1	3024	GTTGGa/CTGGTa	24/24	0.219685847019712	1	FACETS	0.825	0.693	0.972	0.825	0.693	0.972	CLONAL	1	TRUE	0	0.219685847019712	1		452	432	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	327	501	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.576241329572638	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.576241329572638	2		501	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587781702	NA	P-0026842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	207	517	0	ENST00000269305.4:c.920-1G>C		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.511495023538892	1	FACETS	0.945	0.885	1	0.945	0.885	1	CLONAL	1	TRUE	0	0.576241329572638	1		517	541	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908787	101908787	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	141	316	0	ENST00000374994.4:c.1151T>G	p.Leu384Arg	p.L384R	ENST00000374994	NM_004612.2	384	cTc/cGc	7/9	0.576241329572638	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.576241329572638	1		316	302	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183725	10183725	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs5030826	NA	P-0026843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	39	580	0	ENST00000256474.2:c.194C>A	p.Ser65Ter	p.S65*	ENST00000256474	NM_000551.3	65	tCg/tAg	1/3	NA	2	FACETS	1	0.943	1			1	INDETERMINATE	1	TRUE	NA	0.441347629678503	2		580	138	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772204	68772204	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	27	533	0	ENST00000261769.5:c.53C>A	p.Ser18Tyr	p.S18Y	ENST00000261769	NM_004360.3	18	tCc/tAc	2/16	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.441347629678503	2		533	105	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584498	52584498	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	13	455	0	ENST00000394830.3:c.4515del	p.Lys1505AsnfsTer42	p.K1505Nfs*42	ENST00000394830	NM_018313.4	1505	aaA/aa	29/30	0.386368726258277	1	FACETS	0.765	0.582	0.955	1	0.902	1	CLONAL	2	TRUE	0	0.441347629678503	1		455	30	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0026844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	194	351	1	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.835	0.775	0.898	0.835	0.775	0.898	CLONAL	1	TRUE	1	0.615292054444064	2		352	755	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0026844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	623	647	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.401922864823077	4	FACETS	0.861	0.831	0.89			1	CLONAL	3	TRUE	NA	0.615292054444064	4		647	1267	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846065	68846065	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	295	660	1	ENST00000261769.5:c.1036C>T	p.Gln346Ter	p.Q346*	ENST00000261769	NM_004360.3	346	Caa/Taa	8/16	0.615292054444064	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.615292054444064	1		661	645	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942705	44942705	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	121	321	0	ENST00000377967.4:c.3285G>T	p.Lys1095Asn	p.K1095N	ENST00000377967	NM_021140.2	1095	aaG/aaT	23/29	1	2	FACETS	0.768	0.697	0.842	0.768	0.697	0.842	SUBCLONAL	1	TRUE	1	0.615292054444064	2		321	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579366	7579366	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs770776262	NA	P-0026845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	19	642	2	ENST00000269305.4:c.321C>A	p.Tyr107Ter	p.Y107*	ENST00000269305	NM_001126112.2	107	taC/taA	4/11	0.691244612001372	1	FACETS	0.045	0.033	0.058	0.045	0.033	0.058	SUBCLONAL	1	TRUE	0	0.691244612001372	1		644	806	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913517	NA	P-0026845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	232	428	0	ENST00000288135.5:c.1676T>G	p.Val559Gly	p.V559G	ENST00000288135	NM_000222.2	559	gTt/gGt	11/21	1	2	FACETS	0.912	0.854	0.972	0.912	0.854	0.972	CLONAL	1	TRUE	1	0.691244612001372	2		428	736	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148882	119148882	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	129	285	0	ENST00000264033.4:c.1102T>A	p.Tyr368Asn	p.Y368N	ENST00000264033	NM_005188.3	368	Tat/Aat	8/16	1	2	FACETS	0.626	0.57	0.685	0.626	0.57	0.685	SUBCLONAL	1	TRUE	1	0.691244612001372	2		285	596	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0026848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	35	475	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.95	0.777	1	0.95	0.777	1	CLONAL	1	TRUE	1	0.12	2		475	614	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913351	NA	P-0026848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	24	391	0	ENST00000288602.6:c.1397G>T	p.Gly466Val	p.G466V	ENST00000288602	NM_004333.4	466	gGa/gTa	11/18	1	2	FACETS	0.714	0.558	0.895	0.714	0.558	0.895	SUBCLONAL	1	TRUE	1	0.12	2		391	560	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0026848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	20	334	2	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.464	0.353	0.596	0.464	0.353	0.596	SUBCLONAL	1	TRUE	1	0.12	2		336	718	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192084	108192084	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	48	465	0	ENST00000278616.4:c.6509del	p.Tyr2170PhefsTer65	p.Y2170Ffs*65	ENST00000278616	NM_000051.3	2170	tAt/tt	45/63	1	2	FACETS	0.986	0.832	1	0.986	0.832	1	CLONAL	1	TRUE	1	0.12	2		465	811	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578193	7578193	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	51	790	0	ENST00000269305.4:c.656C>G	p.Pro219Arg	p.P219R	ENST00000269305	NM_001126112.2	219	cCc/cGc	6/11	1	2	FACETS	0.902	0.765	1	0.902	0.765	1	CLONAL	1	TRUE	1	0.16	2		790	707	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305469	65305469	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	34	422	1	ENST00000342505.4:c.2659G>T	p.Gly887Trp	p.G887W	ENST00000342505	NM_002227.2	887	Ggg/Tgg	20/25	1	2	FACETS	0.889	0.726	1	0.889	0.726	1	CLONAL	1	TRUE	1	0.16	2		423	478	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178711	108178711	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	29	336	0	ENST00000278616.4:c.5762G>C	p.Arg1921Thr	p.R1921T	ENST00000278616	NM_000051.3	1921	aGa/aCa	38/63	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.16	2		336	326	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628464	187628464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	46	741	0	ENST00000441802.2:c.2518G>A	p.Glu840Lys	p.E840K	ENST00000441802	NM_005245.3	840	Gaa/Aaa	2/27	1	2	FACETS	0.778	0.654	0.916	0.778	0.654	0.916	CLONAL	1	TRUE	1	0.16	2		741	739	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438641	49438641	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759226682	NA	P-0026851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	367	620	0	ENST00000301067.7:c.4849C>T	p.Arg1617Trp	p.R1617W	ENST00000301067	NM_003482.3	1617	Cgg/Tgg	19/54	0.815691740002495	3	FACETS	0.966	0.916	1	0.483	0.458	0.509	CLONAL	1	TRUE	1	0.815691740002495	3		620	1311	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885293	111885293	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	317	486	0	ENST00000341259.2:c.1181G>C	p.Ser394Thr	p.S394T	ENST00000341259	NM_005475.2	394	aGc/aCc	6/8	0.352204592026501	6	FACETS	1	0.994	1	0.364	0.343	0.386	INDETERMINATE	1	TRUE	2	0.815691740002495	6		486	1405	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0026851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	867	528	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.741963151226582	3	FACETS	0.984	0.968	0.999			1	CLONAL	3	TRUE	NA	0.815691740002495	3		528	1014	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789673	3789673	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1340848193	NA	P-0026851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	414	584	0	ENST00000262367.5:c.4186C>G	p.Leu1396Val	p.L1396V	ENST00000262367	NM_004380.2	1396	Ctg/Gtg	25/31	0.472843890882872	3	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.815691740002495	3		584	1367	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0026851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	393	634	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.815691740002495	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.815691740002495	1		634	567	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268359	198268359	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	327	526	0	ENST00000335508.6:c.1669G>C	p.Asp557His	p.D557H	ENST00000335508	NM_012433.2	557	Gat/Cat	12/25	1	2	FACETS	0.961	0.912	1	0.961	0.912	1	CLONAL	1	TRUE	1	0.815691740002495	2		526	834	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169953118	169953118	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	435	457	0	ENST00000295797.4:c.202A>G	p.Met68Val	p.M68V	ENST00000295797	NM_002740.5	68	Atg/Gtg	2/18	0.444620498287801	4	FACETS	0.828	0.791	0.866	0.828	0.791	0.866	INDETERMINATE	2	TRUE	2	0.815691740002495	4		457	1169	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936097	178936097	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	329	541	0	ENST00000263967.3:c.1639G>C	p.Glu547Gln	p.E547Q	ENST00000263967	NM_006218.2	547	Gag/Cag	10/21	0.444620498287801	4	FACETS	1	0.988	1	0.582	0.55	0.616	INDETERMINATE	1	TRUE	2	0.815691740002495	4		541	1258	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673696	30673696	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	346	547	0	ENST00000376406.3:c.3264A>T	p.Glu1088Asp	p.E1088D	ENST00000376406	NM_014641.2	1088	gaA/gaT	10/15	0.815691740002495	2	FACETS	0.985	0.937	1	0.493	0.468	0.517	CLONAL	1	TRUE	0	0.815691740002495	2		547	861	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681838	30681838	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	364	585	0	ENST00000376406.3:c.259C>G	p.Pro87Ala	p.P87A	ENST00000376406	NM_014641.2	87	Cct/Gct	3/15	0.815691740002495	2	FACETS	0.973	0.926	1	0.487	0.463	0.511	CLONAL	1	TRUE	0	0.815691740002495	2		585	917	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750579	128751408	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTGCGACGAGGAGGAGAACTTCTACCAGCAGCAGCAGCAGAGCGAGCTGCAGCCCCCGGCGCCCAGCGAGGATATCTGGAAGAAATTCGAGCTGCTGCCCACCCCGCCCCTGTCCCCTAGCCGCCGCTCCGGGCTCTGCTCGCCCTCCTACGTTGCGGTCACACCCTTCTCCCTTCGGGGAGACAACGACGGCGGTGGCGGGAGCTTCTCCACGGCCGACCAGCTGGAGATGGTGACCGAGCTGCTGGGAGGAGACATGGTGAACCAGAGTTTCATCTGCGACCCGGACGACGAGACCTTCATCAAAAACATCATCATCCAGGACTGTATGTGGAGCGGCTTCTCGGCCGCCGCCAAGCTCGTCTCAGAGAAGCTGGCCTCCTACCAGGCTGCGCGCAAAGACAGCGGCAGCCCGAACCCCGCCCGCGGCCACAGCGTCTGCTCCACCTCCAGCTTGTACCTGCAGGATCTGAGCGCCGCCGCCTCAGAGTGCATCGACCCCTCGGTGGTCTTCCCCTACCCTCTCAACGACAGCAGCTCGCCCAAGTCCTGCGCCTCGCAAGACTCCAGCGCCTTCTCTCCGTCCTCGGATTCTCTGCTCTCCTCGACGGAGTCCTCCCCGCAGGGCAGCCCCGAGCCCCTGGTGCTCCATGAGGAGACACCGCCCACCACCAGCAGCGACTCTGGTAAGCGAAGCCCGCCCAGGCCTGTCAAAAGTGGGCGGCTGGATACCTTTCCCATTTTCATTGGCAGCTTATTTAACGGGCCACTCTTATTAGGAAGGAGAGATAGCAGATCTGGAGAGATTTGGGAGCTCATCACCTCTGAA	ACTGCGACGAGGAGGAGAACTTCTACCAGCAGCAGCAGCAGAGCGAGCTGCAGCCCCCGGCGCCCAGCGAGGATATCTGGAAGAAATTCGAGCTGCTGCCCACCCCGCCCCTGTCCCCTAGCCGCCGCTCCGGGCTCTGCTCGCCCTCCTACGTTGCGGTCACACCCTTCTCCCTTCGGGGAGACAACGACGGCGGTGGCGGGAGCTTCTCCACGGCCGACCAGCTGGAGATGGTGACCGAGCTGCTGGGAGGAGACATGGTGAACCAGAGTTTCATCTGCGACCCGGACGACGAGACCTTCATCAAAAACATCATCATCCAGGACTGTATGTGGAGCGGCTTCTCGGCCGCCGCCAAGCTCGTCTCAGAGAAGCTGGCCTCCTACCAGGCTGCGCGCAAAGACAGCGGCAGCCCGAACCCCGCCCGCGGCCACAGCGTCTGCTCCACCTCCAGCTTGTACCTGCAGGATCTGAGCGCCGCCGCCTCAGAGTGCATCGACCCCTCGGTGGTCTTCCCCTACCCTCTCAACGACAGCAGCTCGCCCAAGTCCTGCGCCTCGCAAGACTCCAGCGCCTTCTCTCCGTCCTCGGATTCTCTGCTCTCCTCGACGGAGTCCTCCCCGCAGGGCAGCCCCGAGCCCCTGGTGCTCCATGAGGAGACACCGCCCACCACCAGCAGCGACTCTGGTAAGCGAAGCCCGCCCAGGCCTGTCAAAAGTGGGCGGCTGGATACCTTTCCCATTTTCATTGGCAGCTTATTTAACGGGCCACTCTTATTAGGAAGGAGAGATAGCAGATCTGGAGAGATTTGGGAGCTCATCACCTCTGAA	-	novel	NA	P-0026851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1931	307	596	0	ENST00000377970.2:c.118_802+145del		p.X40_splice	ENST00000377970	NM_002467.4	40		2/3	0.733117484571252	5	FACETS	0.748	0.702	0.796			1	SUBCLONAL	1	TRUE	NA	0.815691740002495	5		596	2238	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0026853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	80	181	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.613654199020277	1	FACETS	0.878	0.788	0.969	0.878	0.788	0.969	CLONAL	1	TRUE	0	0.61560774355175	1		181	205	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0026853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	115	550	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.988	0.899	1	0.988	0.899	1	CLONAL	1	TRUE	1	0.61560774355175	2		550	378	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221229	1221229	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	139	652	0	ENST00000326873.7:c.752G>T	p.Gly251Val	p.G251V	ENST00000326873	NM_000455.4	251	gGt/gTt	6/10	0.613654199020277	1	FACETS	0.968	0.895	1	0.968	0.895	1	CLONAL	1	TRUE	0	0.61560774355175	1		652	323	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435431	18435431	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	100	318	0	ENST00000266497.5:c.417del	p.Arg140AspfsTer5	p.R140Dfs*5	ENST00000266497		139	tCc/tc	1/31	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.61560774355175	2		318	279	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602551	10602551	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	142	622	0	ENST00000171111.5:c.1027del	p.Glu343ArgfsTer57	p.E343Rfs*57	ENST00000171111	NM_203500.1	343	Gag/ag	3/6	0.613654199020277	1	FACETS	0.977	0.904	1	0.977	0.904	1	CLONAL	1	TRUE	0	0.61560774355175	1		622	327	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713814	30713814	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	104	624	0	ENST00000295754.5:c.1139T>G	p.Leu380Arg	p.L380R	ENST00000295754	NM_003242.5	380	cTc/cGc	4/7	0.613654199020277	1	FACETS	0.91	0.829	0.992	0.91	0.829	0.992	CLONAL	1	TRUE	0	0.61560774355175	1		624	257	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682371	52682371	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	17	332	0	ENST00000394830.3:c.802C>T	p.Gln268Ter	p.Q268*	ENST00000394830	NM_018313.4	268	Caa/Taa	8/30	0.613654199020277	1	FACETS	0.199	0.149	0.258	0.199	0.149	0.258	SUBCLONAL	1	TRUE	0	0.61560774355175	1		332	192	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608279	100608279	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	131	721	0	ENST00000308731.7:c.1811G>T	p.Ser604Ile	p.S604I	ENST00000308731	NM_000061.2	604	aGt/aTt	18/19	0.121517975521054	1	FACETS	0.668	0.611	0.727	0.668	0.611	0.727	INDETERMINATE	1	TRUE	0	0.61560774355175	1		721	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0026856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	450	572	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.334120524544343	3	FACETS	0.854	0.819	0.889			1	CLONAL	3	TRUE	NA	0.445462333404509	3		572	964	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609834	81609834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1236978415	NA	P-0026856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	197	333	1	ENST00000298171.2:c.1432C>T	p.His478Tyr	p.H478Y	ENST00000298171	NM_000369.2	478	Cac/Tac	10/10	0.445462333404509	3	FACETS	0.923	0.86	0.987	0.615	0.573	0.658	CLONAL	2	TRUE	0	0.445462333404509	3		334	586	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170759	11170759	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	272	736	0	ENST00000358026.2:c.4903G>C	p.Glu1635Gln	p.E1635Q	ENST00000358026	NM_001128849.1	1635	Gag/Cag	35/36	0.445462333404509	2	FACETS	1	0.987	1	0.588	0.552	0.625	CLONAL	1	TRUE	0	0.445462333404509	2		736	1039	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468480	89468480	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	98	421	0	ENST00000336596.2:c.2014A>C	p.Ser672Arg	p.S672R	ENST00000336596	NM_005233.5	672	Agc/Cgc	11/17	0.445462333404509	2	FACETS	0.623	0.556	0.695	0.312	0.278	0.348	SUBCLONAL	1	TRUE	0	0.445462333404509	2		421	706	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878029	151878029	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs369563648	NA	P-0026856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	121	358	0	ENST00000262189.6:c.6916C>G	p.Pro2306Ala	p.P2306A	ENST00000262189	NM_170606.2	2306	Cca/Gca	36/59	0.445462333404509	3	FACETS	0.882	0.797	0.971	0.441	0.398	0.486	CLONAL	1	TRUE	1	0.445462333404509	3		358	753	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884882	151884882	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	197	469	0	ENST00000262189.6:c.4711C>G	p.His1571Asp	p.H1571D	ENST00000262189	NM_170606.2	1571	Cat/Gat	32/59	0.445462333404509	3	FACETS	1	0.955	1	0.521	0.482	0.562	CLONAL	1	TRUE	1	0.445462333404509	3		469	1037	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0026857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	158	854	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.113591484805384	4	FACETS	0.939	0.864	1	0.939	0.864	1	INDETERMINATE	2	TRUE	2	0.362827183700299	4		854	632	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266112	41266112	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913228	NA	P-0026857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	111	351	0	ENST00000349496.5:c.109T>G	p.Ser37Ala	p.S37A	ENST00000349496	NM_001904.3	37	Tct/Gct	3/15	0.191750139503874	4	FACETS	0.916	0.829	1	0.916	0.829	1	INDETERMINATE	2	TRUE	2	0.362827183700299	4		351	455	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0026858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	613	606	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.655876446933173	2	FACETS	0.989	0.96	1	0.989	0.96	1	CLONAL	2	TRUE	0	0.655876446933173	2		606	945	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584513	48584514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs377767334	NA	P-0026858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	266	396	0	ENST00000342988.3:c.692dup	p.Ser232GlnfsTer3	p.S232Qfs*3	ENST00000342988	NM_005359.5	229	ctg/ctGg	6/12	0.655876446933173	1	FACETS	0.988	0.936	1	0.988	0.936	1	CLONAL	1	TRUE	0	0.655876446933173	1		396	552	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120041	70120042	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	63	76	0	ENST00000245479.2:c.1044dup	p.Pro349AlafsTer229	p.P349Afs*229	ENST00000245479	NM_000346.3	348	cag/caGg	3/3	NA	2	FACETS	1	0.881	1			1	INDETERMINATE	1	TRUE	NA	0.655876446933173	2		76	192	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061211	38061240	+	inframe_deletion	In_Frame_Del	DEL	AGTAGCAGCCGTTCTCGAACATGTTGCCGG	AGTAGCAGCCGTTCTCGAACATGTTGCCGG	-	novel	NA	P-0026861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	244	516	0	ENST00000250448.2:c.749_778del	p.Ser250_Tyr259del	p.S250_Y259del	ENST00000250448	NM_004496.3	250	tCCGGCAACATGTTCGAGAACGGCTGCTACTtg/ttg	2/2	1	2	FACETS	0.984	0.923	1	0.984	0.923	1	CLONAL	1	TRUE	1	0.65	2		516	763	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914670	32914670	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	69	585	1	ENST00000380152.3:c.6178A>G	p.Thr2060Ala	p.T2060A	ENST00000380152		2060	Aca/Gca	11/27	1	2	FACETS	0.223	0.194	0.256	0.223	0.194	0.256	SUBCLONAL	1	TRUE	1	0.65	2		586	950	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589560	67589583	+	inframe_deletion	In_Frame_Del	DEL	TATTGAAGCTGTAGGGAAAAAATT	TATTGAAGCTGTAGGGAAAAAATT	-	novel	NA	P-0026861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	87	345	0	ENST00000274335.5:c.1323_1346del	p.Asn441_Leu449delinsLys	p.N441_L449delinsK	ENST00000274335		441	aaTATTGAAGCTGTAGGGAAAAAATTa/aaa	10/15	0.714053801044699	1	FACETS	0.478	0.426	0.533	0.478	0.426	0.533	SUBCLONAL	1	TRUE	0	0.65	1		345	378	SUCCESS
APC	324	MSKCC	GRCh37	5	112175883	112175884	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0026861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	171	321	0	ENST00000257430.4:c.4593dup	p.Asp1532Ter	p.D1532*	ENST00000257430	NM_000038.5	1531	aat/aaTt	16/16	0.714053801044699	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.65	1		321	328	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866612	117866614	+	inframe_deletion	In_Frame_Del	DEL	AAT	AAT	-	novel	NA	P-0026861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	300	591	0	ENST00000297338.2:c.1031_1033del	p.Tyr344del	p.Y344del	ENST00000297338	NM_006265.2	344	tATTca/tca	9/14	0.751153579721621	3	FACETS	0.975	0.918	1	0.488	0.459	0.517	CLONAL	1	TRUE	1	0.65	3		591	1254	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222564	69222564	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3039	212	435	0	ENST00000462284.1:c.537T>A	p.Asp179Glu	p.D179E	ENST00000462284	NM_002392.5	179	gaT/gaA	8/11	0.3	28	FACETS	0.978	0.903	1			1	CLONAL	2	TRUE	NA	0.5	28		435	3251	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670615	134670615	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781004053	NA	P-0026863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	81	702	1	ENST00000398015.3:c.526G>A	p.Ala176Thr	p.A176T	ENST00000398015	NM_004441.4	176	Gct/Act	3/16	0.297138658806613	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.29	1		703	434	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508769	29508769	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	146	574	0	ENST00000356175.3:c.699del	p.Lys233AsnfsTer48	p.K233Nfs*48	ENST00000356175	NM_000267.3	232	acA/ac	7/57	0.0567944598862868	3	FACETS	1	0.987	1	0.742	0.678	0.809	INDETERMINATE	1	TRUE	1	0.29	3		574	777	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654492	29654527	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCACCCCGTCACCACCACTTTCCAGGTTGGTTCTAC	TCACCCCGTCACCACCACTTTCCAGGTTGGTTCTAC	AT	novel	NA	P-0026863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	30	302	2	ENST00000356175.3:c.5206-25_5216delinsAT		p.X1736_splice	ENST00000356175	NM_000267.3	1736		37/57	0.0567944598862868	3	FACETS	0.511	0.411	0.624	0.255	0.205	0.312	INDETERMINATE	1	TRUE	1	0.29	3		304	464	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0026864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	112	440	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.18	2		441	1193	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46240637	46240637	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0026864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	48	247	0	ENST00000334344.6:c.1499-2A>C		p.X500_splice	ENST00000334344	NM_152641.2	500			1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.18	2		247	495	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245755	46245755	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	54	406	0	ENST00000334344.6:c.3851del	p.Lys1284ArgfsTer11	p.K1284Rfs*11	ENST00000334344	NM_152641.2	1283	acA/ac	15/21	1	2	FACETS	0.676	0.575	0.786	0.676	0.575	0.786	SUBCLONAL	1	TRUE	1	0.18	2		406	888	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061634	38061634	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764371648	NA	P-0026864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	26	288	0	ENST00000250448.2:c.355C>T	p.Gln119Ter	p.Q119*	ENST00000250448	NM_004496.3	119	Cag/Tag	2/2	1	2	FACETS	0.58	0.458	0.72	0.58	0.458	0.72	SUBCLONAL	1	TRUE	1	0.18	2		288	498	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56862939	56862939	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	54	344	0	ENST00000308159.5:c.845A>C	p.Gln282Pro	p.Q282P	ENST00000308159	NM_014669.4	282	cAg/cCg	9/22	1	2	FACETS	0.82	0.699	0.953	0.82	0.699	0.953	CLONAL	1	TRUE	1	0.18	2		344	732	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0026867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	200	503	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.317116616276809	3	FACETS	0.821	0.764	0.881	0.821	0.764	0.881	CLONAL	2	TRUE	1	0.416034461289996	3		505	707	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0026867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	404	885	1	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	NA	2	FACETS	0.984	0.939	1			1	INDETERMINATE	2	TRUE	NA	0.416034461289996	2		886	987	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0026867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	113	352	1	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.979	0.884	1	0.979	0.884	1	CLONAL	1	TRUE	1	0.416034461289996	2		353	555	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397187	397187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	145	385	1	ENST00000380956.4:c.572C>T	p.Pro191Leu	p.P191L	ENST00000380956	NM_001195286.1	191	cCg/cTg	5/9	1	2	FACETS	0.964	0.881	1	0.964	0.881	1	CLONAL	1	TRUE	1	0.416034461289996	2		386	723	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718801	190718802	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0026867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	63	256	0	ENST00000441310.2:c.961_962del	p.Asn321Ter	p.N321*	ENST00000441310	NM_000534.4	320	cAA/c	8/13	1	2	FACETS	0.793	0.689	0.905	0.793	0.689	0.905	CLONAL	1	TRUE	1	0.416034461289996	2		256	382	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	185	474	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.708753665739235	2		474	464	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579369	7579369	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555526581	NA	P-0026869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	637	810	0	ENST00000269305.4:c.318C>G	p.Ser106Arg	p.S106R	ENST00000269305	NM_001126112.2	106	agC/agG	4/11	0.694374605431203	2	FACETS	0.953	0.927	0.979	0.953	0.927	0.979	CLONAL	2	TRUE	0	0.708753665739235	2		810	943	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936983	48936983	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690863	NA	P-0026869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	208	612	0	ENST00000267163.4:c.751C>T	p.Arg251Ter	p.R251*	ENST00000267163	NM_000321.2	251	Cga/Tga	8/27	0.609692421163849	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.708753665739235	2		612	293	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032794	30032794	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121434259	NA	P-0026869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	115	517	0	ENST00000338641.4:c.169C>T	p.Arg57Ter	p.R57*	ENST00000338641	NM_000268.3	57	Cga/Tga	2/16	0.708753665739235	1	FACETS	0.428	0.387	0.47	0.428	0.387	0.47	SUBCLONAL	1	TRUE	0	0.708753665739235	1		517	490	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253377	226253377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	86	300	0	ENST00000366813.1:c.149G>A	p.Arg50His	p.R50H	ENST00000366813		50	cGt/cAt	2/3	1	2	FACETS	0.87	0.779	0.964	0.87	0.779	0.964	CLONAL	1	TRUE	1	0.708753665739235	2		300	279	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023789	27023792	+	frameshift_variant	Frame_Shift_Del	DEL	CTCA	CTCA	-	novel	NA	P-0026869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	259	556	0	ENST00000324856.7:c.896_899del	p.Leu299ArgfsTer63	p.L299Rfs*63	ENST00000324856	NM_006015.4	299	CTCAcg/cg	1/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.708753665739235	2		556	699	SUCCESS
APC	324	MSKCC	GRCh37	5	112162833	112162834	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0026869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	91	528	0	ENST00000257430.4:c.1438dup	p.Gln480ProfsTer5	p.Q480Pfs*5	ENST00000257430	NM_000038.5	479	-/C	12/16	0.708753665739235	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.708753665739235	1		528	153	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222991	53222991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	202	818	0	ENST00000375401.3:c.4081G>A	p.Glu1361Lys	p.E1361K	ENST00000375401	NM_004187.3	1361	Gag/Aag	24/26	NA	2	FACETS	0.728	0.676	0.781			1	INDETERMINATE	1	TRUE	NA	0.708753665739235	2		818	783	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17349132	17349132	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs146800605	NA	P-0026871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	647	546	0	ENST00000375499.3:c.736A>G	p.Ile246Val	p.I246V	ENST00000375499	NM_003000.2	246	Atc/Gtc	7/8	0.730483562017882	3	FACETS	0.931	0.911	0.951	0.931	0.911	0.951	CLONAL	3	TRUE	0	0.793937311872056	3		546	815	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138058	64138058	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	495	642	0	ENST00000334205.4:c.1981A>C	p.Lys661Gln	p.K661Q	ENST00000334205	NM_003942.2	661	Aag/Cag	16/17	0.710513731007331	3	FACETS	0.933	0.898	0.967	0.933	0.898	0.967	CLONAL	2	TRUE	1	0.793937311872056	3		642	934	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418601	49418601	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	53	451	2	ENST00000301067.7:c.15913G>T	p.Ala5305Ser	p.A5305S	ENST00000301067	NM_003482.3	5305	Gct/Tct	49/54	0.792105241880929	3	FACETS	0.253	0.215	0.295	0.127	0.107	0.148	SUBCLONAL	1	TRUE	1	0.793937311872056	3		453	736	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896455	28896455	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	72	549	0	ENST00000282397.4:c.2995C>G	p.Leu999Val	p.L999V	ENST00000282397	NM_002019.4	999	Ctg/Gtg	22/30	0.788059852844959	3	FACETS	0.309	0.27	0.353	0.155	0.135	0.177	SUBCLONAL	1	TRUE	1	0.793937311872056	3		549	819	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911683	32911683	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs864622609	NA	P-0026871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	359	446	1	ENST00000380152.3:c.3191C>A	p.Ser1064Ter	p.S1064*	ENST00000380152		1064	tCa/tAa	11/27	0.113720882625692	1	FACETS	1	0.977	1	1	0.977	1	INDETERMINATE	1	TRUE	0	0.793937311872056	1		447	535	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061228	38061228	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	444	595	2	ENST00000250448.2:c.761del	p.Phe254SerfsTer67	p.F254Sfs*67	ENST00000250448	NM_004496.3	254	tTc/tc	2/2	0.656772008419447	4	FACETS	0.904	0.864	0.944	0.904	0.864	0.944	CLONAL	2	TRUE	2	0.793937311872056	4		597	1110	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0026871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	435	610	2	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	1	2	FACETS	0.815	0.787	0.843	1	0.997	1	CLONAL	2	TRUE	1	0.793937311872056	2		612	672	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627555	37627591	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTGTTAAAGATTTGAAAGCACAGGGAACAAGAGAC	TCTTGTTAAAGATTTGAAAGCACAGGGAACAAGAGAC	-	novel	NA	P-0026871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	189	613	0	ENST00000447079.4:c.1473_1509del	p.Val492AsnfsTer3	p.V492Nfs*3	ENST00000447079	NM_015083.1	490	caTCTTGTTAAAGATTTGAAAGCACAGGGAACAAGAGAC/ca	2/14	0.788059852844959	3	FACETS	0.701	0.648	0.756	0.35	0.324	0.378	SUBCLONAL	1	TRUE	1	0.793937311872056	3		613	949	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1650217	1650217	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	87	672	0	ENST00000344749.5:c.31G>C	p.Gly11Arg	p.G11R	ENST00000344749	NM_001136139.2	11	Ggc/Cgc	2/19	1	2	FACETS	0.263	0.232	0.296	0.263	0.232	0.296	SUBCLONAL	1	TRUE	1	0.793937311872056	2		672	834	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026539	48026539	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1060502924	NA	P-0026871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	321	449	0	ENST00000234420.5:c.1417C>G	p.Leu473Val	p.L473V	ENST00000234420	NM_000179.2	473	Ctg/Gtg	4/10	0.57085162905092	3	FACETS	0.84	0.8	0.881			1	CLONAL	2	TRUE	NA	0.793937311872056	3		449	672	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207468	29207468	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	302	411	0	ENST00000240100.2:c.328G>C	p.Glu110Gln	p.E110Q	ENST00000240100	NM_001394.6	110	Gag/Cag	1/4	0.793937311872056	3	FACETS	1	0.993	1			1	CLONAL	1	TRUE	NA	0.793937311872056	3		411	778	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0026874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	47	347	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.863	0.727	1	0.863	0.727	1	CLONAL	1	TRUE	1	0.17	2		347	641	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0026874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	46	525	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.811	0.682	0.955	0.811	0.682	0.955	CLONAL	1	TRUE	1	0.17	2		525	667	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0026874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	80	711	1	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.17	2		712	903	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651931	36651932	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0026874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	63	525	0	ENST00000244741.5:c.55dup	p.Arg19ProfsTer17	p.R19Pfs*17	ENST00000244741	NM_000389.4	18	tgc/tgCc	2/3	1	2	FACETS	0.968	0.836	1	0.968	0.836	1	CLONAL	1	TRUE	1	0.17	2		525	766	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797342	135797343	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	44	387	0	ENST00000298552.3:c.526dup	p.Tyr176LeufsTer42	p.Y176Lfs*42	ENST00000298552	NM_001162426.1	176	tat/tTat	7/23	1	2	FACETS	0.91	0.762	1	0.91	0.762	1	CLONAL	1	TRUE	1	0.17	2		387	569	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487554	38487554	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	143	560	0	ENST00000254066.5:c.89del	p.Pro30LeufsTer12	p.P30Lfs*12	ENST00000254066	NM_000964.3	28	ttC/tt	2/9	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.443534527378428	2		560	634	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	98	483	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.443534527378428	3	FACETS	0.924	0.827	1	0.462	0.413	0.514	CLONAL	1	TRUE	1	0.443534527378428	3		483	584	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	106	273	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	0.443534527378428	2		273	466	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	97	425	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.835	0.747	0.928	0.835	0.747	0.928	CLONAL	1	TRUE	1	0.443534527378428	2		426	524	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	302	424	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.982	1	1	0.996	1	CLONAL	2	TRUE	1	0.443534527378428	2		424	638	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296358	15296358	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	154	866	1	ENST00000263388.2:c.2084del	p.Pro695ArgfsTer165	p.P695Rfs*165	ENST00000263388	NM_000435.2	695	cCg/cg	13/33	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.443534527378428	2		867	619	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910866	32910866	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1484798037	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	103	492	0	ENST00000380152.3:c.2374T>C	p.Tyr792His	p.Y792H	ENST00000380152		792	Tac/Cac	11/27	1	2	FACETS	0.954	0.857	1	0.954	0.857	1	CLONAL	1	TRUE	1	0.443534527378428	2		492	487	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10283797	10283797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771381056	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	165	577	0	ENST00000340748.4:c.689G>A	p.Arg230His	p.R230H	ENST00000340748		230	cGc/cAc	8/40	0.443534527378428	2	FACETS	1	0.923	1	0.501	0.461	0.543	CLONAL	1	TRUE	0	0.443534527378428	2		577	742	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	102	336	1	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.782	0.701	0.868	0.782	0.701	0.868	SUBCLONAL	1	TRUE	1	0.443534527378428	2		337	588	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	167	576	0	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.443534527378428	2		576	748	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80646042	80646042	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	70	310	0	ENST00000286548.4:c.110G>A	p.Arg37His	p.R37H	ENST00000286548	NM_002072.3	37	cGc/cAc	1/7	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.443534527378428	2		310	291	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	150	485	3	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.836	0.765	0.911	0.836	0.765	0.911	CLONAL	1	TRUE	1	0.443534527378428	2		488	809	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	144	592	4	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	1	2	FACETS	0.959	0.877	1	0.959	0.877	1	CLONAL	1	TRUE	1	0.443534527378428	2		596	677	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	96	435	3	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.898	0.804	0.998	0.898	0.804	0.998	CLONAL	1	TRUE	1	0.443534527378428	2		438	482	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347983	347983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760961378	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	159	648	5	ENST00000262320.3:c.1523del	p.Gly508ValfsTer197	p.G508Vfs*197	ENST00000262320	NM_003502.3	508	gGt/gt	6/11	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.443534527378428	2		653	707	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	130	419	6	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.443534527378428	2		425	488	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012656	36012656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1288993928	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	76	242	0	ENST00000358208.4:c.100G>A	p.Ala34Thr	p.A34T	ENST00000358208		34	Gcc/Acc	2/12	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.443534527378428	2		242	281	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020769	37020769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	140	545	2	ENST00000358127.4:c.76del	p.Val26PhefsTer3	p.V26Ffs*3	ENST00000358127	NM_001280556.1	26	Gtt/tt	2/10	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.443534527378428	2		547	628	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619309	37619309	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	106	430	0	ENST00000447079.4:c.985C>T	p.Arg329Ter	p.R329*	ENST00000447079	NM_015083.1	329	Cga/Tga	1/14	1	2	FACETS	0.97	0.873	1	0.97	0.873	1	CLONAL	1	TRUE	1	0.443534527378428	2		430	493	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612818	228612818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143639671	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	148	527	0	ENST00000366696.1:c.209G>A	p.Arg70Gln	p.R70Q	ENST00000366696	NM_003493.2	70	cGg/cAg	1/1	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.443534527378428	2		527	631	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983042	111983042	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	181	585	3	ENST00000368678.4:c.1505del	p.Lys502ArgfsTer53	p.K502Rfs*53	ENST00000368678		502	aAg/ag	13/13	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.443534527378428	2		588	707	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533517	63533517	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555577625	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	151	535	4	ENST00000307078.5:c.1637del	p.Gly546AlafsTer143	p.G546Afs*143	ENST00000307078	NM_004655.3	546	gGc/gc	6/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.443534527378428	2		539	657	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383228	42383228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782110924	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	180	584	1	ENST00000221972.3:c.248C>T	p.Pro83Leu	p.P83L	ENST00000221972	NM_021601.3	83	cCg/cTg	2/5	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.443534527378428	2		585	659	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538941	187538941	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs113224498	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	129	463	0	ENST00000441802.2:c.8799del	p.Gly2934ValfsTer3	p.G2934Vfs*3	ENST00000441802	NM_005245.3	2933	caA/ca	10/27	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.443534527378428	2		463	510	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71161712	71161712	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	114	397	0	ENST00000318789.4:c.257G>A	p.Arg86Lys	p.R86K	ENST00000318789	NM_032682.5	86	aGg/aAg	7/21	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.443534527378428	2		397	513	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	125	454	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.992	0.902	1	0.992	0.902	1	CLONAL	1	TRUE	1	0.443534527378428	2		456	568	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	291	892	13	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.923	0.874	0.972	1	0.995	1	CLONAL	2	TRUE	1	0.443534527378428	2		905	711	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324892	31324892	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs765875917	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	35	238	0	ENST00000412585.2:c.44del	p.Ala15GlyfsTer5	p.A15Gfs*5	ENST00000412585	NM_005514.6	15	gCg/gg	1/8	0.443534527378428	1	FACETS	0.646	0.535	0.768	0.646	0.535	0.768	SUBCLONAL	1	TRUE	0	0.443534527378428	1		238	190	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	120	521	6	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	0.443534527378428	3	FACETS	0.864	0.781	0.952	0.432	0.39	0.476	CLONAL	1	TRUE	1	0.443534527378428	3		527	765	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204992	128204992	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	120	562	0	ENST00000341105.2:c.449del	p.Gly150GlufsTer68	p.G150Efs*68	ENST00000341105	NM_032638.4	150	gGa/ga	3/6	1	2	FACETS	0.977	0.885	1	0.977	0.885	1	CLONAL	1	TRUE	1	0.443534527378428	2		562	554	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214871	36214871	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	62	677	0	ENST00000222270.7:c.3302del	p.Pro1101LeufsTer81	p.P1101Lfs*81	ENST00000222270	NM_014727.1	1099	ggC/gg	8/37	1	2	FACETS	0.378	0.326	0.435	0.378	0.326	0.435	SUBCLONAL	1	TRUE	1	0.443534527378428	2		677	740	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431874	49431874	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	163	584	2	ENST00000301067.7:c.9265del	p.Val3089TrpfsTer30	p.V3089Wfs*30	ENST00000301067	NM_003482.3	3089	Gtg/tg	34/54	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.443534527378428	2		586	628	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39214651	39214651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	120	619	0	ENST00000402219.2:c.3473G>A	p.Arg1158Gln	p.R1158Q	ENST00000402219	NM_005633.3	1158	cGa/cAa	22/23	1	2	FACETS	0.742	0.671	0.818	0.742	0.671	0.818	SUBCLONAL	1	TRUE	1	0.443534527378428	2		619	729	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	143	551	3	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.443534527378428	2		554	513	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427282	49427282	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	120	428	0	ENST00000301067.7:c.11206C>T	p.Gln3736Ter	p.Q3736*	ENST00000301067	NM_003482.3	3736	Cag/Tag	39/54	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.443534527378428	2		428	488	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792249	33792249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	143	477	0	ENST00000498907.2:c.1072G>A	p.Ala358Thr	p.A358T	ENST00000498907	NM_004364.3	358	Gcg/Acg	1/1	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.443534527378428	2		477	538	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535355	66535355	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	158	594	1	ENST00000273854.3:c.106C>T	p.Arg36Ter	p.R36*	ENST00000273854	NM_004439.5	36	Cga/Tga	1/18	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.443534527378428	2		595	629	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164464	36164464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	77	325	0	ENST00000300305.3:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000300305		471	Cgc/Tgc	8/8	1	2	FACETS	0.954	0.843	1	0.954	0.843	1	CLONAL	1	TRUE	1	0.443534527378428	2		325	364	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056328	27056328	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1350278856	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	125	385	0	ENST00000324856.7:c.1324A>G	p.Met442Val	p.M442V	ENST00000324856	NM_006015.4	442	Atg/Gtg	2/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.443534527378428	2		385	494	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363211	40363211	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1177671093	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	38	473	0	ENST00000397332.2:c.1018A>G	p.Thr340Ala	p.T340A	ENST00000397332	NM_001033082.2	340	Acc/Gcc	3/3	1	2	FACETS	0.285	0.235	0.341	0.285	0.235	0.341	SUBCLONAL	1	TRUE	1	0.443534527378428	2		473	601	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658408	206658408	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	121	506	0	ENST00000367120.3:c.1502C>T	p.Thr501Ile	p.T501I	ENST00000367120	NM_014002.3	501	aCt/aTt	14/22	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.443534527378428	2		506	534	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457989	69457989	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1131439	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	92	465	0	ENST00000227507.2:c.389A>G	p.Asn130Ser	p.N130S	ENST00000227507	NM_053056.2	130	aAc/aGc	2/5	1	2	FACETS	0.988	0.883	1	0.988	0.883	1	CLONAL	1	TRUE	1	0.443534527378428	2		465	420	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518521	69518521	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	139	526	0	ENST00000294312.3:c.124A>G	p.Ile42Val	p.I42V	ENST00000294312	NM_005117.2	42	Atc/Gtc	1/3	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.443534527378428	2		526	479	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941276	71941276	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	185	604	1	ENST00000298229.2:c.1051G>A	p.Asp351Asn	p.D351N	ENST00000298229	NM_001567.3	351	Gac/Aac	9/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.443534527378428	2		605	688	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943302	71943302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1175303291	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	148	619	0	ENST00000298229.2:c.1634G>A	p.Gly545Asp	p.G545D	ENST00000298229	NM_001567.3	545	gGc/gAc	14/28	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.443534527378428	2		619	626	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435130	18435130	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	88	435	0	ENST00000266497.5:c.115G>T	p.Gly39Cys	p.G39C	ENST00000266497		39	Ggt/Tgt	1/31	0.443534527378428	3	FACETS	0.845	0.75	0.946	0.422	0.375	0.473	CLONAL	1	TRUE	1	0.443534527378428	3		435	574	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428388	49428388	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	199	679	0	ENST00000301067.7:c.10417C>A	p.His3473Asn	p.H3473N	ENST00000301067	NM_003482.3	3473	Cat/Aat	36/54	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.443534527378428	2		679	838	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28599019	28599019	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	118	538	0	ENST00000241453.7:c.2269G>T	p.Gly757Trp	p.G757W	ENST00000241453	NM_004119.2	757	Ggg/Tgg	18/24	1	2	FACETS	0.955	0.865	1	0.955	0.865	1	CLONAL	1	TRUE	1	0.443534527378428	2		538	557	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457675	67457675	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	146	653	0	ENST00000327367.4:c.488del	p.Asn163ThrfsTer23	p.N163Tfs*23	ENST00000327367	NM_005902.3	162	gAa/ga	3/9	1	2	FACETS	0.945	0.864	1	0.945	0.864	1	CLONAL	1	TRUE	1	0.443534527378428	2		653	697	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434767	99434767	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	147	521	0	ENST00000268035.6:c.854T>A	p.Ile285Asn	p.I285N	ENST00000268035	NM_000875.3	285	aTc/aAc	3/21	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.443534527378428	2		521	653	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900297	3900297	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	158	526	1	ENST00000262367.5:c.798+1G>A		p.X266_splice	ENST00000262367	NM_004380.2	266			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.443534527378428	2		527	598	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273980	10273980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	189	666	3	ENST00000330684.3:c.289G>A	p.Gly97Ser	p.G97S	ENST00000330684	NM_001134407.1	97	Ggc/Agc	2/13	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.443534527378428	2		669	747	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346882	89346882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753973951	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	66	257	0	ENST00000301030.4:c.6068C>T	p.Ala2023Val	p.A2023V	ENST00000301030	NM_001256183.1	2023	gCc/gTc	9/13	1	2	FACETS	0.995	0.872	1	0.995	0.872	1	CLONAL	1	TRUE	1	0.443534527378428	2		257	299	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348998	89348998	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	195	648	0	ENST00000301030.4:c.3952A>G	p.Thr1318Ala	p.T1318A	ENST00000301030	NM_001256183.1	1318	Act/Gct	9/13	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.443534527378428	2		648	836	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024389	16024389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778685775	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	111	306	0	ENST00000268712.3:c.1829C>T	p.Pro610Leu	p.P610L	ENST00000268712	NM_006311.3	610	cCt/cTt	16/46	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.443534527378428	2		306	481	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554308	29554308	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	162	634	2	ENST00000356175.3:c.2324A>G	p.Glu775Gly	p.E775G	ENST00000356175	NM_000267.3	775	gAg/gGg	19/57	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.443534527378428	2		636	707	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667608	29667608	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	150	619	0	ENST00000356175.3:c.6944C>T	p.Ala2315Val	p.A2315V	ENST00000356175	NM_000267.3	2315	gCa/gTa	46/57	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.443534527378428	2		619	664	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646889	37646889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	194	679	0	ENST00000447079.4:c.2011C>T	p.Leu671Phe	p.L671F	ENST00000447079	NM_015083.1	671	Ctc/Ttc	3/14	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.443534527378428	2		679	777	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511646	38511646	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	134	561	0	ENST00000254066.5:c.1144A>G	p.Thr382Ala	p.T382A	ENST00000254066	NM_000964.3	382	Act/Gct	8/9	1	2	FACETS	0.952	0.867	1	0.952	0.867	1	CLONAL	1	TRUE	1	0.443534527378428	2		561	635	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244967	41244967	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	155	642	0	ENST00000357654.3:c.2581T>C	p.Phe861Leu	p.F861L	ENST00000357654	NM_007294.3	861	Ttc/Ctc	10/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.443534527378428	2		642	627	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526140	63526140	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1285654850	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	176	641	2	ENST00000307078.5:c.2486C>T	p.Pro829Leu	p.P829L	ENST00000307078	NM_004655.3	829	cCg/cTg	11/11	1	2	FACETS	0.979	0.903	1	0.979	0.903	1	CLONAL	1	TRUE	1	0.443534527378428	2		643	811	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145716	11145718	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs148514235	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	154	681	7	ENST00000358026.2:c.4090_4092del	p.Glu1364del	p.E1364del	ENST00000358026	NM_001128849.1	1360	GAG/-	29/36	1	2	FACETS	0.977	0.896	1	0.977	0.896	1	CLONAL	1	TRUE	1	0.443534527378428	2		688	711	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375316	15375316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200264318	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	179	602	0	ENST00000263377.2:c.1111G>A	p.Ala371Thr	p.A371T	ENST00000263377	NM_058243.2	371	Gcc/Acc	6/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.443534527378428	2		602	672	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273229	18273229	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	200	588	0	ENST00000222254.8:c.1022A>G	p.Asn341Ser	p.N341S	ENST00000222254	NM_005027.3	341	aAc/aGc	9/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.443534527378428	2		588	786	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40746010	40746010	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	146	608	0	ENST00000392038.2:c.581T>C	p.Val194Ala	p.V194A	ENST00000392038	NM_001626.4	194	gTc/gCc	7/14	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.443534527378428	2		608	588	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136301	202136301	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	135	647	0	ENST00000358485.4:c.545T>G	p.Leu182Arg	p.L182R	ENST00000358485	NM_001080125.1	182	cTt/cGt	3/9	1	2	FACETS	0.976	0.889	1	0.976	0.889	1	CLONAL	1	TRUE	1	0.443534527378428	2		647	624	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161751	47161751	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	69	318	0	ENST00000409792.3:c.4375C>T	p.Arg1459Ter	p.R1459*	ENST00000409792	NM_014159.6	1459	Cga/Tga	3/21	1	2	FACETS	0.724	0.632	0.821	0.724	0.632	0.821	SUBCLONAL	1	TRUE	1	0.443534527378428	2		318	430	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69986988	69986988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs994568417	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	143	502	0	ENST00000394351.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000394351	NM_000248.3	17	Gaa/Aaa	2/9	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.443534527378428	2		502	585	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413703	138413704	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	121	436	0	ENST00000289153.2:c.1816dup	p.Ala606GlyfsTer27	p.A606Gfs*27	ENST00000289153	NM_006219.2	606	gcc/gGcc	12/22	1	2	FACETS	0.957	0.868	1	0.957	0.868	1	CLONAL	1	TRUE	1	0.443534527378428	2		436	570	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502228	186502230	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs759276609	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	77	336	0	ENST00000323963.5:c.40_42del	p.Gly14del	p.G14del	ENST00000323963		13	GGC/-	2/11	1	2	FACETS	0.886	0.782	0.996	0.886	0.782	0.996	CLONAL	1	TRUE	1	0.443534527378428	2		336	392	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803231	1803231	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	149	620	0	ENST00000260795.2:c.583T>C	p.Phe195Leu	p.F195L	ENST00000260795		195	Ttc/Ctc	4/17	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.443534527378428	2		620	652	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807485	1807485	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	138	583	0	ENST00000260795.2:c.1654T>C	p.Tyr552His	p.Y552H	ENST00000260795		552	Tac/Cac	12/17	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.443534527378428	2		583	541	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948190	55948190	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	133	524	0	ENST00000263923.4:c.3781G>A	p.Gly1261Ser	p.G1261S	ENST00000263923	NM_002253.2	1261	Ggt/Agt	29/30	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.443534527378428	2		524	532	SUCCESS
APC	324	MSKCC	GRCh37	5	112178449	112178449	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	85	484	0	ENST00000257430.4:c.7158G>T	p.Lys2386Asn	p.K2386N	ENST00000257430	NM_000038.5	2386	aaG/aaT	16/16	1	2	FACETS	0.8	0.71	0.896	0.8	0.71	0.896	SUBCLONAL	1	TRUE	1	0.443534527378428	2		484	479	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323989	31323989	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	82	175	0	ENST00000412585.2:c.574C>A	p.Leu192Ile	p.L192I	ENST00000412585	NM_005514.6	192	Ctc/Atc	3/8	0.443534527378428	1	FACETS	0.817	0.74	0.896	1	0.984	1	CLONAL	2	TRUE	0	0.443534527378428	1		175	176	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816451	32816451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760636031	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	156	708	0	ENST00000354258.4:c.1724G>A	p.Arg575His	p.R575H	ENST00000354258	NM_000593.5	575	cGc/cAc	7/11	1	2	FACETS	0.872	0.799	0.948	0.872	0.799	0.948	CLONAL	1	TRUE	1	0.443534527378428	2		708	807	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793888	89793888	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	121	364	0	ENST00000336032.3:c.961del	p.Thr321ArgfsTer16	p.T321Rfs*16	ENST00000336032	NM_006813.2	319	ttA/tt	2/2	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.443534527378428	2		364	509	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983151	111983151	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	96	304	0	ENST00000368678.4:c.1397-1G>T		p.X466_splice	ENST00000368678		466			1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.443534527378428	2		304	417	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192429	138192429	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199876928	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	99	341	0	ENST00000237289.4:c.65G>A	p.Arg22Gln	p.R22Q	ENST00000237289	NM_001270507.1	22	cGg/cAg	2/9	1	2	FACETS	0.936	0.839	1	0.936	0.839	1	CLONAL	1	TRUE	1	0.443534527378428	2		341	477	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099886	157099886	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1282168193	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	119	587	3	ENST00000346085.5:c.826del	p.Ala276ProfsTer93	p.A276Pfs*93	ENST00000346085	NM_020732.3	275	Ggg/gg	1/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.443534527378428	2		590	476	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392054	81392054	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	93	451	0	ENST00000222390.5:c.223A>G	p.Thr75Ala	p.T75A	ENST00000222390	NM_000601.4	75	Act/Gct	2/18	0.443534527378428	3	FACETS	0.94	0.838	1	0.47	0.419	0.524	CLONAL	1	TRUE	1	0.443534527378428	3		451	545	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877850	151877853	+	frameshift_variant	Frame_Shift_Del	DEL	AGTT	AGTT	-	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	87	378	0	ENST00000262189.6:c.7092_7095del	p.Thr2365IlefsTer6	p.T2365Ifs*6	ENST00000262189	NM_170606.2	2364	gtAACT/gt	36/59	0.443534527378428	3	FACETS	0.925	0.822	1	0.463	0.411	0.518	CLONAL	1	TRUE	1	0.443534527378428	3		378	518	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942745	68942745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781270008	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	107	434	0	ENST00000288368.4:c.557G>A	p.Arg186Gln	p.R186Q	ENST00000288368	NM_024870.2	186	cGg/cAg	6/40	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.443534527378428	2		434	453	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859930	117859930	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1363929252	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	62	264	2	ENST00000297338.2:c.1705C>T	p.Arg569Cys	p.R569C	ENST00000297338	NM_006265.2	569	Cgt/Tgt	14/14	1	2	FACETS	0.77	0.669	0.879	0.77	0.669	0.879	SUBCLONAL	1	TRUE	1	0.443534527378428	2		266	363	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089718	5089718	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	98	337	0	ENST00000381652.3:c.2616G>T	p.Gln872His	p.Q872H	ENST00000381652	NM_004972.3	872	caG/caT	20/25	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.443534527378428	2		337	395	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123120	5123120	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs772889316	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	80	438	0	ENST00000381652.3:c.3176C>T	p.Ala1059Val	p.A1059V	ENST00000381652	NM_004972.3	1059	gCg/gTg	23/25	1	2	FACETS	0.811	0.717	0.911	0.811	0.717	0.911	CLONAL	1	TRUE	1	0.443534527378428	2		438	445	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570245	87570245	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	98	366	1	ENST00000277120.3:c.1985C>T	p.Thr662Met	p.T662M	ENST00000277120		662	aCg/aTg	17/19	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.443534527378428	2		367	408	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93629479	93629479	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	83	354	0	ENST00000375746.1:c.913A>G	p.Lys305Glu	p.K305E	ENST00000375746	NM_001174167.1	305	Aag/Gag	7/14	1	2	FACETS	0.856	0.759	0.959	0.856	0.759	0.959	CLONAL	1	TRUE	1	0.443534527378428	2		354	437	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93657853	93657853	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	146	479	0	ENST00000375746.1:c.1879C>T	p.Arg627Cys	p.R627C	ENST00000375746	NM_001174167.1	627	Cgc/Tgc	14/14	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.443534527378428	2		479	620	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128419964	128419964	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	134	666	0	ENST00000265960.3:c.464A>G	p.Asn155Ser	p.N155S	ENST00000265960	NM_001006617.1	155	aAc/aGc	4/12	1	2	FACETS	0.93	0.847	1	0.93	0.847	1	CLONAL	1	TRUE	1	0.443534527378428	2		666	650	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412242	139412242	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	125	643	0	ENST00000277541.6:c.1403T>C	p.Leu468Pro	p.L468P	ENST00000277541	NM_017617.3	468	cTg/cCg	8/34	1	2	FACETS	0.822	0.745	0.902	0.822	0.745	0.902	CLONAL	1	TRUE	1	0.443534527378428	2		643	686	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931787	39931788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	172	267	0	ENST00000378444.4:c.2811dup	p.Thr938HisfsTer8	p.T938Hfs*8	ENST00000378444	NM_001123385.1	937	-/C	4/15	1	1	FACETS	0.838	0.784	0.893	1	0.992	1	CLONAL	2	TRUE	0	0.443534527378428	1		267	360	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427508	49427509	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	A	novel	NA	P-0026875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	134	533	1	ENST00000301067.7:c.10979_10980delinsT	p.Gly3660ValfsTer89	p.G3660Vfs*89	ENST00000301067	NM_003482.3	3660	gGG/gT	39/54	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.443534527378428	2		534	583	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204511930	204511930	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2328	452	266	0	ENST00000367182.3:c.530A>T	p.Asn177Ile	p.N177I	ENST00000367182	NM_001278516.1	177	aAt/aTt	8/11	0.622062433625534	16	FACETS	0.933	0.886	0.981			1	CLONAL	3	TRUE	NA	0.622062433625534	16		266	2780	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115869	8115873	+	frameshift_variant	Frame_Shift_Del	DEL	CATCT	CATCT	-	novel	NA	P-0026876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	202	608	0	ENST00000346208.3:c.1216_1220del	p.Ile406AlafsTer99	p.I406Afs*99	ENST00000346208		405	caCATCTcg/cacg	6/6	1	2	FACETS	0.772	0.717	0.829	0.772	0.717	0.829	SUBCLONAL	1	TRUE	1	0.622062433625534	2		608	841	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492748	50492765	+	inframe_deletion	In_Frame_Del	DEL	GAATTAGAGCAAGCCCTG	GAATTAGAGCAAGCCCTG	-	novel	NA	P-0026876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	226	520	0	ENST00000394963.4:c.1514_1531del	p.Glu505_Leu510del	p.E505_L510del	ENST00000394963	NM_003076.4	505	GAATTAGAGCAAGCCCTG/-	13/13	1	2	FACETS	0.926	0.865	0.988	0.926	0.865	0.988	CLONAL	1	TRUE	1	0.622062433625534	2		520	785	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089777	27089777	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0026877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	214	488	0	ENST00000324856.7:c.2732+1G>T		p.X911_splice	ENST00000324856	NM_006015.4	911			0.701701763724663	3	FACETS	0.847	0.796	0.898	0.847	0.796	0.898	CLONAL	2	TRUE	1	0.737225775673895	3		488	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578191	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs530941076	NA	P-0026877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	340	718	0	ENST00000269305.4:c.658T>C	p.Tyr220His	p.Y220H	ENST00000269305	NM_001126112.2	220	Tat/Cat	6/11	0.626737658169599	2	FACETS	0.877	0.843	0.91	0.877	0.843	0.91	CLONAL	2	TRUE	0	0.737225775673895	2		718	526	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958788	55958788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780764266	NA	P-0026877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	205	622	0	ENST00000263923.4:c.3065G>A	p.Arg1022Gln	p.R1022Q	ENST00000263923	NM_002253.2	1022	cGa/cAa	22/30	0.490730193595555	3	FACETS	1	0.992	1	0.742	0.694	0.79	CLONAL	1	TRUE	1	0.737225775673895	3		622	513	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710633	114710634	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0026877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	291	529	0	ENST00000543371.1:c.118_119insT	p.Asp40ValfsTer4	p.D40Vfs*4	ENST00000543371	NM_001198531.1	40	gat/gTat	1/14	0.567745819973898	3	FACETS	0.881	0.837	0.926	0.881	0.837	0.926	CLONAL	2	TRUE	1	0.737225775673895	3		529	613	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118948	70118949	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0026877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	336	689	0	ENST00000245479.2:c.521_522dup	p.Gln175ThrfsTer9	p.Q175Tfs*9	ENST00000245479	NM_000346.3	174	tac/tACac	2/3	0.646490229306761	3	FACETS	0.829	0.789	0.87	0.829	0.789	0.87	CLONAL	2	TRUE	1	0.737225775673895	3		689	752	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593505	48593505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	189	292	0	ENST00000342988.3:c.1256G>A	p.Gly419Glu	p.G419E	ENST00000342988	NM_005359.5	419	gGg/gAg	10/12	0.626737658169599	2	FACETS	0.843	0.798	0.888	0.843	0.798	0.888	CLONAL	2	TRUE	0	0.737225775673895	2		292	304	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089008	37089008	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs267607852	NA	P-0026877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	133	266	1	ENST00000231790.2:c.1732-2A>T		p.X578_splice	ENST00000231790	NM_000249.3	578			0.646490229306761	3	FACETS	0.826	0.763	0.889	0.826	0.763	0.889	CLONAL	2	TRUE	1	0.737225775673895	3		267	299	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233081	66233081	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	186	357	0	ENST00000273854.3:c.1918G>T	p.Gly640Trp	p.G640W	ENST00000273854	NM_004439.5	640	Ggg/Tgg	10/18	0.490730193595555	3	FACETS	0.818	0.765	0.872	0.818	0.765	0.872	CLONAL	2	TRUE	1	0.737225775673895	3		357	422	SUCCESS
APC	324	MSKCC	GRCh37	5	112174223	112174223	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	126	491	1	ENST00000257430.4:c.2932C>T	p.Gln978Ter	p.Q978*	ENST00000257430	NM_000038.5	978	Caa/Taa	16/16	1	2	FACETS	0.96	0.88	1	0.96	0.88	1	CLONAL	1	TRUE	1	0.737225775673895	2		492	356	SUCCESS
APC	324	MSKCC	GRCh37	5	112175220	112175221	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0026877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	58	311	0	ENST00000257430.4:c.3929_3930insTT	p.Lys1310AsnfsTer2	p.K1310Nfs*2	ENST00000257430	NM_000038.5	1310	aag/aaTTg	16/16	1	2	FACETS	0.715	0.623	0.813	0.715	0.623	0.813	SUBCLONAL	1	TRUE	1	0.737225775673895	2		311	220	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982031	70982031	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	135	690	0	ENST00000276594.2:c.65G>A	p.Ser22Asn	p.S22N	ENST00000276594	NM_024504.3	22	aGc/aAc	2/8	0.452567025278636	4	FACETS	0.752	0.683	0.824	0.376	0.341	0.412	SUBCLONAL	1	TRUE	2	0.737225775673895	4		690	846	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0000081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	193	336	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.645355282681854	2		336	587	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178400	56178401	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0000081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	67	232	0	ENST00000399503.3:c.3373_3374insGT	p.Asn1125SerfsTer24	p.N1125Sfs*24	ENST00000399503	NM_005921.1	1125	aat/aGTat	14/20	0.330269727140414	2	FACETS	0.506	0.442	0.576	0.253	0.221	0.288	INDETERMINATE	1	TRUE	0	0.645355282681854	2		232	410	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183240	56183241	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0000081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	291	411	1	ENST00000399503.3:c.4151dup	p.Arg1385LysfsTer35	p.R1385Kfs*35	ENST00000399503	NM_005921.1	1384	cta/cTta	18/20	0.330269727140414	2	FACETS	1	0.994	1	0.721	0.685	0.758	INDETERMINATE	1	TRUE	0	0.645355282681854	2		412	625	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0000081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	218	635	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.330269727140414	2	FACETS	0.758	0.706	0.812	0.379	0.353	0.406	INDETERMINATE	1	TRUE	0	0.645355282681854	2		635	891	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194194	94194194	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	74	336	0	ENST00000323929.3:c.1234A>T	p.Ile412Phe	p.I412F	ENST00000323929	NM_005591.3	412	Atc/Ttc	12/20	1	2	FACETS	0.433	0.379	0.49	0.433	0.379	0.49	SUBCLONAL	1	TRUE	1	0.645355282681854	2		336	530	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436548	110436548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1401	193	806	3	ENST00000375856.3:c.1853C>T	p.Ala618Val	p.A618V	ENST00000375856	NM_003749.2	618	gCg/gTg	1/2	0.645355282681854	3	FACETS	0.496	0.457	0.537	0.248	0.228	0.269	SUBCLONAL	1	TRUE	1	0.645355282681854	3		809	1594	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624293	89624293	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs876661244	NA	P-0000104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	125	953	0	ENST00000371953.3:c.67T>G	p.Leu23Val	p.L23V	ENST00000371953	NM_000314.4	23	Tta/Gta	1/9	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.280940579803801	2		953	797	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692887	89692887	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	63	653	0	ENST00000371953.3:c.371G>C	p.Cys124Ser	p.C124S	ENST00000371953	NM_000314.4	124	tGt/tCt	5/9	1	2	FACETS	0.988	0.857	1	0.988	0.857	1	CLONAL	1	TRUE	1	0.280940579803801	2		653	454	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061240	38061240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	108	1227	0	ENST00000250448.2:c.749C>T	p.Ser250Phe	p.S250F	ENST00000250448	NM_004496.3	250	tCc/tTc	2/2	0.220500295468948	1	FACETS	0.848	0.761	0.941	0.848	0.761	0.941	CLONAL	1	TRUE	0	0.280940579803801	1		1227	779	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845682	68845682	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	133	1331	1	ENST00000261769.5:c.928G>T	p.Glu310Ter	p.E310*	ENST00000261769	NM_004360.3	310	Gag/Tag	7/16	0.280940579803801	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.280940579803801	1		1332	779	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344075	118344076	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	78	574	0	ENST00000534358.1:c.2206dup	p.Arg736LysfsTer7	p.R736Kfs*7	ENST00000534358	NM_005933.3	734	aga/agAa	3/36	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.280940579803801	2		574	532	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845349	156845349	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	84	1111	0	ENST00000524377.1:c.1392G>A	p.Met464Ile	p.M464I	ENST00000524377	NM_002529.3	464	atG/atA	12/17	0.251036279425422	1	FACETS	0.578	0.509	0.651	0.578	0.509	0.651	SUBCLONAL	1	TRUE	0	0.280940579803801	1		1111	890	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097794	8097794	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	61	1286	0	ENST00000346208.3:c.176A>G	p.His59Arg	p.H59R	ENST00000346208		59	cAc/cGc	2/6	0.216803193753051	3	FACETS	0.513	0.441	0.592	0.257	0.22	0.296	SUBCLONAL	1	TRUE	1	0.280940579803801	3		1286	965	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28897002	28897002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554058758	NA	P-0000104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	47	1040	4	ENST00000282397.4:c.2878G>A	p.Val960Ile	p.V960I	ENST00000282397	NM_002019.4	960	Gtc/Atc	21/30	1	2	FACETS	0.445	0.374	0.523	0.445	0.374	0.523	SUBCLONAL	1	TRUE	1	0.280940579803801	2		1044	752	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099235	4099235	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	59	1041	0	ENST00000262948.5:c.883T>G	p.Ser295Ala	p.S295A	ENST00000262948	NM_030662.3	295	Tcg/Gcg	7/11	1	2	FACETS	0.542	0.465	0.626	0.542	0.465	0.626	SUBCLONAL	1	TRUE	1	0.280940579803801	2		1041	775	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374375	31374375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1341617203	NA	P-0000104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	110	971	1	ENST00000328111.2:c.374G>A	p.Arg125Gln	p.R125Q	ENST00000328111	NM_006892.3	125	cGa/cAa	5/23	1	2	FACETS	0.927	0.832	1	0.927	0.832	1	CLONAL	1	TRUE	1	0.280940579803801	2		972	845	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133517	55133517	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	111	1140	0	ENST00000257290.5:c.821C>A	p.Thr274Asn	p.T274N	ENST00000257290	NM_006206.4	274	aCt/aAt	6/23	1	2	FACETS	0.933	0.838	1	0.933	0.838	1	CLONAL	1	TRUE	1	0.280940579803801	2		1140	847	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599320	55599320	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913506	NA	P-0000246-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	178	569	0	ENST00000288135.5:c.2446G>C	p.Asp816His	p.D816H	ENST00000288135	NM_000222.2	816	Gac/Cac	17/21	0.243371865436933	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.243371865436933	2		569	623	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235853	108235853	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200899512	NA	P-0000246-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	53	555	0	ENST00000278616.4:c.8895G>T	p.Leu2965Phe	p.L2965F	ENST00000278616	NM_000051.3	2965	ttG/ttT	62/63	0.194121579290998	2	FACETS	0.728	0.621	0.847	0.364	0.31	0.424	SUBCLONAL	1	TRUE	0	0.243371865436933	2		555	598	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398262	25398262	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913538	NA	P-0000246-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	71	621	0	ENST00000311936.3:c.57G>C	p.Leu19Phe	p.L19F	ENST00000311936	NM_004985.3	19	ttG/ttC	2/5	0.195606685558152	3	FACETS	0.837	0.729	0.953	0.418	0.364	0.477	CLONAL	1	TRUE	1	0.243371865436933	3		621	782	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259507	16259507	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000246-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	49	474	1	ENST00000375759.3:c.6772C>A	p.Pro2258Thr	p.P2258T	ENST00000375759	NM_015001.2	2258	Cct/Act	11/15	1	2	FACETS	0.685	0.579	0.801	0.685	0.579	0.801	SUBCLONAL	1	TRUE	1	0.243371865436933	2		475	588	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421653	49421653	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000246-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	81	654	0	ENST00000301067.7:c.14576A>T	p.Gln4859Leu	p.Q4859L	ENST00000301067	NM_003482.3	4859	cAg/cTg	47/54	0.195606685558152	3	FACETS	0.806	0.709	0.911	0.403	0.354	0.456	CLONAL	1	TRUE	1	0.243371865436933	3		654	926	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041842	42041842	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779273324	NA	P-0000246-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	78	657	1	ENST00000219905.7:c.6037G>A	p.Gly2013Arg	p.G2013R	ENST00000219905	NM_001164273.1	2013	Gga/Aga	17/24	0.195606685558152	3	FACETS	0.825	0.724	0.935	0.413	0.362	0.468	CLONAL	1	TRUE	1	0.243371865436933	3		658	871	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652129	3652129	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000246-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	88	833	2	ENST00000294008.3:c.940C>A	p.His314Asn	p.H314N	ENST00000294008	NM_032444.2	314	Cat/Aat	4/15	0.195606685558152	3	FACETS	0.794	0.702	0.894	0.397	0.351	0.447	SUBCLONAL	1	TRUE	1	0.243371865436933	3		835	1021	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900707	3900707	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1333746955	NA	P-0000246-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	79	476	1	ENST00000262367.5:c.389C>A	p.Ala130Asp	p.A130D	ENST00000262367	NM_004380.2	130	gCc/gAc	2/31	0.195606685558152	3	FACETS	1	0.96	1	0.608	0.535	0.686	CLONAL	1	TRUE	1	0.243371865436933	3		477	599	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830442	72830442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000246-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	25	305	0	ENST00000268489.5:c.6139C>T	p.Pro2047Ser	p.P2047S	ENST00000268489	NM_006885.3	2047	Cct/Tct	9/10	0.195606685558152	3	FACETS	0.599	0.471	0.745	0.299	0.235	0.373	SUBCLONAL	1	TRUE	1	0.243371865436933	3		305	385	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728683	190728683	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000246-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	85	561	0	ENST00000441310.2:c.2071A>T	p.Ser691Cys	p.S691C	ENST00000441310	NM_000534.4	691	Agt/Tgt	10/13	0.195606685558152	3	FACETS	0.965	0.852	1	0.482	0.426	0.543	CLONAL	1	TRUE	1	0.243371865436933	3		561	812	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871163	35871163	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs756821231	NA	P-0000246-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	45	289	0	ENST00000303115.3:c.385C>A	p.Pro129Thr	p.P129T	ENST00000303115	NM_002185.3	129	Cct/Act	4/8	0.195606685558152	3	FACETS	0.914	0.768	1	0.457	0.384	0.537	CLONAL	1	TRUE	1	0.243371865436933	3		289	454	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0000489-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	289	577	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	0.57918015459833	2		577	960	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000489-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	378	598	0	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.57918015459833	2		598	1277	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0000690-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	724	376	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.749801364735841	4	FACETS	0.979	0.961	0.996	0.979	0.961	0.996	CLONAL	4	TRUE	0	0.749801364735841	4		376	863	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0000690-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	484	581	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.704080966896087	2	FACETS	0.931	0.903	0.959	0.931	0.903	0.959	CLONAL	2	TRUE	0	0.749801364735841	2		581	693	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448571	89448571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000690-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	644	688	0	ENST00000336596.2:c.1535G>A	p.Arg512Gln	p.R512Q	ENST00000336596	NM_005233.5	512	cGa/cAa	7/17	0.665713522305835	3	FACETS	0.902	0.88	0.923	0.902	0.88	0.923	CLONAL	3	TRUE	0	0.749801364735841	3		688	873	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031855	10031855	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000690-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	254	663	0	ENST00000330684.3:c.968A>G	p.Gln323Arg	p.Q323R	ENST00000330684	NM_001134407.1	323	cAg/cGg	3/13	0.72517470545843	4	FACETS	0.927	0.866	0.99			1	CLONAL	1	TRUE	NA	0.749801364735841	4		663	1279	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354786	40354786	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000690-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	202	609	0	ENST00000293328.3:c.2118A>C	p.Gln706His	p.Q706H	ENST00000293328	NM_012448.3	706	caA/caC	17/19	0.607502111266805	4	FACETS	0.921	0.853	0.991	0.46	0.426	0.496	CLONAL	1	TRUE	2	0.749801364735841	4		609	1024	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223935	36223940	+	inframe_deletion	In_Frame_Del	DEL	CATTTG	CATTTG	-	novel	NA	P-0000690-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	577	914	0	ENST00000222270.7:c.6486_6491del	p.Phe2163_Ala2164del	p.F2163_A2164del	ENST00000222270	NM_014727.1	2162	aCATTTGcc/acc	28/37	0.586478452133897	4	FACETS	0.868	0.834	0.902	0.868	0.834	0.902	CLONAL	2	TRUE	2	0.749801364735841	4		914	1552	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46588135	46588138	+	frameshift_variant	Frame_Shift_Del	DEL	ATCC	ATCC	-	novel	NA	P-0000690-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	285	825	0	ENST00000263734.3:c.686_689del	p.Ile229SerfsTer16	p.I229Sfs*16	ENST00000263734	NM_001430.4	229	ATCCag/ag	6/16	0.749801364735841	3	FACETS	0.88	0.827	0.935	0.44	0.413	0.468	CLONAL	1	TRUE	1	0.749801364735841	3		825	1188	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620677	52620680	+	missense_variant	Missense_Mutation	ONP	AGTT	AGTT	CGTG	novel	NA	P-0000690-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	189	382	0	ENST00000394830.3:c.3073_3076delinsCACG	p.Asn1025_Phe1026delinsHisVal	p.N1025_F1026delinsHV	ENST00000394830	NM_018313.4	1025	AACTtc/CACGtc	21/30	0.665713522305835	3	FACETS	1	0.989	1	0.449	0.418	0.48	CLONAL	1	TRUE	0	0.749801364735841	3		382	515	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0000713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	99	326	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.867	0.778	0.962	0.867	0.778	0.962	CLONAL	1	TRUE	1	0.467736665698851	2		326	488	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736461	85736461	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	208	334	0	ENST00000370580.1:c.186A>T	p.Arg62Ser	p.R62S	ENST00000370580	NM_003921.4	62	agA/agT	2/3	1	2	FACETS	0.966	0.897	1	0.966	0.897	1	CLONAL	1	TRUE	1	0.467736665698851	2		334	921	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466330	120466330	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	117	366	0	ENST00000256646.2:c.4789T>G	p.Ser1597Ala	p.S1597A	ENST00000256646	NM_024408.3	1597	Tca/Gca	26/34	1	2	FACETS	0.581	0.523	0.642	0.581	0.523	0.642	SUBCLONAL	1	TRUE	1	0.467736665698851	2		366	861	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631839	+	missense_variant	Missense_Mutation	DNP	CT	CT	AC	novel	NA	P-0000713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	92	412	0	ENST00000330062.3:c.514_515delinsGT	p.Arg172Val	p.R172V	ENST00000330062	NM_002168.2	172	AGg/GTg	4/11	0.412802199346729	3	FACETS	0.44	0.39	0.494	0.22	0.195	0.247	SUBCLONAL	1	TRUE	1	0.467736665698851	3		412	1103	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54956605	54956605	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	139	412	0	ENST00000312783.6:c.589T>A	p.Tyr197Asn	p.Y197N	ENST00000312783	NM_198436.1	197	Tat/Aat	7/10	1	2	FACETS	0.6	0.546	0.658	0.6	0.546	0.658	SUBCLONAL	1	TRUE	1	0.467736665698851	2		412	990	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937202	76937203	+	missense_variant	Missense_Mutation	DNP	CT	CT	AC	novel	NA	P-0000713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	108	459	0	ENST00000373344.5:c.3545_3546delinsGT	p.Lys1182Ser	p.K1182S	ENST00000373344	NM_000489.3	1182	aAG/aGT	9/35	1	2	FACETS	0.413	0.369	0.459	0.413	0.369	0.459	SUBCLONAL	1	TRUE	1	0.467736665698851	2		459	1119	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0000749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	235	749	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.530925001755883	1	FACETS	0.291	0.272	0.312	0.291	0.272	0.312	INDETERMINATE	1	TRUE	0	0.89082661087058	1		750	1004	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0000749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	349	388	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.530925001755883	1	FACETS	0.836	0.805	0.866	0.836	0.805	0.866	INDETERMINATE	1	TRUE	0	0.89082661087058	1		388	520	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0000749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	114	260	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.46086265103038	1	FACETS	0.364	0.33	0.399	0.364	0.33	0.399	INDETERMINATE	1	TRUE	0	0.89082661087058	1		260	390	SUCCESS
APC	324	MSKCC	GRCh37	5	112154694	112154694	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	123	320	0	ENST00000257430.4:c.965T>G	p.Leu322Arg	p.L322R	ENST00000257430	NM_000038.5	322	cTt/cGt	10/16	0.46086265103038	1	FACETS	0.306	0.278	0.335	0.306	0.278	0.335	INDETERMINATE	1	TRUE	0	0.89082661087058	1		320	501	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888758	76888758	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	620	334	0	ENST00000373344.5:c.5071C>T	p.Gln1691Ter	p.Q1691*	ENST00000373344	NM_000489.3	1691	Caa/Taa	19/35	1	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.89082661087058	1		334	664	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783968	50783968	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	419	630	1	ENST00000398568.2:c.359G>A	p.Ser120Asn	p.S120N	ENST00000398568	NM_001042412.1	120	aGt/aAt	3/18	0.4759975259758	1	FACETS	0.599	0.574	0.624	0.599	0.574	0.624	INDETERMINATE	1	TRUE	0	0.89082661087058	1		631	871	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	135	297	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.853818027682204	2		297	309	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0000818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	304	578	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.853818027682204	1	FACETS	0.94	0.905	0.975	0.94	0.905	0.975	CLONAL	1	TRUE	0	0.853818027682204	1		578	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0000818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	1003	628	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.853818027682204	2	FACETS	0.992	0.977	1	0.992	0.977	1	CLONAL	2	TRUE	0	0.853818027682204	2		628	1184	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954222	48954222	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0000818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	208	299	0	ENST00000267163.4:c.1421+2T>A		p.X474_splice	ENST00000267163	NM_000321.2	474			0.853818027682204	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.853818027682204	1		299	274	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0000847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	82	1151	1	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.320647216084531	1	FACETS	0.333	0.292	0.377	0.333	0.292	0.377	SUBCLONAL	1	TRUE	0	0.352434099929845	1		1152	1152	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061208	38061208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	150	682	0	ENST00000250448.2:c.781C>T	p.Arg261Cys	p.R261C	ENST00000250448	NM_004496.3	261	Cgc/Tgc	2/2	1	2	FACETS	0.906	0.827	0.988	0.906	0.827	0.988	CLONAL	1	TRUE	1	0.352434099929845	2		682	940	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578505	7578506	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0000847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	202	1165	0	ENST00000269305.4:c.424_425del	p.Pro142CysfsTer6	p.P142Cfs*6	ENST00000269305	NM_001126112.2	142	CCt/t	5/11	0.320647216084531	1	FACETS	0.882	0.817	0.949	0.882	0.817	0.949	CLONAL	1	TRUE	0	0.352434099929845	1		1165	1071	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0000894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	1207	650	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.367162980813432	10	FACETS	0.979	0.958	0.998	0.979	0.958	0.998	CLONAL	9	TRUE	1	0.367162980813432	10		650	1843	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223550	55223550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	1431	740	1	ENST00000275493.2:c.917C>T	p.Ser306Leu	p.S306L	ENST00000275493	NM_005228.3	306	tCg/tTg	8/28	0.367162980813432	10	FACETS	0.961	0.944	0.977	1	0.997	1	CLONAL	10	TRUE	1	0.367162980813432	10		741	2003	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259551	55259551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	1145	687	0	ENST00000275493.2:c.2609A>G	p.His870Arg	p.H870R	ENST00000275493	NM_005228.3	870	cAt/cGt	21/28	0.367162980813432	10	FACETS	0.961	0.941	0.981	0.961	0.941	0.981	CLONAL	9	TRUE	1	0.367162980813432	10		687	1780	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572002	64572002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779413959	NA	P-0000894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	194	1024	2	ENST00000312049.6:c.1637C>T	p.Pro546Leu	p.P546L	ENST00000312049	NM_130799.2	546	cCg/cTg	10/10	0.28814531028171	3	FACETS	1	0.966	1	0.36	0.332	0.389	CLONAL	1	TRUE	0	0.367162980813432	3		1026	1158	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244452	46244452	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs980692773	NA	P-0000894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	100	674	0	ENST00000334344.6:c.2546C>T	p.Ala849Val	p.A849V	ENST00000334344	NM_152641.2	849	gCa/gTa	15/21	0.338154146601787	3	FACETS	0.743	0.663	0.828	0.248	0.221	0.276	SUBCLONAL	1	TRUE	0	0.367162980813432	3		674	868	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314925	1314925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2189	1051	593	0	ENST00000400841.2:c.736C>T	p.Leu246Phe	p.L246F	ENST00000400841		246	Ctc/Ttc	6/6	0.367162980813432	4	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.367162980813432	4		593	3240	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0000928-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	334	628	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.543490327272689	2	FACETS	0.892	0.861	0.923	1	0.996	1	CLONAL	3	TRUE	0	0.534322936804317	2		628	467	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0000928-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	215	435	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.534322936804317	2		435	552	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720741	89720741	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs371387815	NA	P-0000928-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	28	203	1	ENST00000371953.3:c.892C>T	p.Gln298Ter	p.Q298*	ENST00000371953	NM_000314.4	298	Caa/Taa	8/9	0.543490327272689	1	FACETS	0.686	0.559	0.824	0.686	0.559	0.824	SUBCLONAL	1	TRUE	0	0.534322936804317	1		204	112	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265024	46265024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1172968588	NA	P-0000928-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	163	564	0	ENST00000371998.3:c.1894C>T	p.Arg632Trp	p.R632W	ENST00000371998		632	Cgg/Tgg	12/23	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.534322936804317	2		564	515	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169953080	169953080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000928-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	171	645	1	ENST00000295797.4:c.164G>A	p.Arg55Gln	p.R55Q	ENST00000295797	NM_002740.5	55	cGa/cAa	2/18	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.534322936804317	2		646	428	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300537	11300537	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001037-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1516	163	814	0	ENST00000361445.4:c.1609G>A	p.Asp537Asn	p.D537N	ENST00000361445	NM_004958.3	537	Gat/Aat	11/58	0.285065692523189	5	FACETS	0.972	0.889	1			1	CLONAL	1	TRUE	NA	0.285065692523189	5		814	1679	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213872	66213872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772452750	NA	P-0001037-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	108	478	0	ENST00000273854.3:c.2558G>A	p.Arg853Gln	p.R853Q	ENST00000273854	NM_004439.5	853	cGa/cAa	15/18	1	2	FACETS	0.953	0.855	1	0.953	0.855	1	CLONAL	1	TRUE	1	0.285065692523189	2		478	795	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294327	1294327	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001037-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1630	99	503	0	ENST00000310581.5:c.674G>A	p.Gly225Glu	p.G225E	ENST00000310581	NM_198253.2	225	gGg/gAg	2/16	0.285065692523189	13	FACETS	1	0.913	1			1	CLONAL	1	TRUE	NA	0.285065692523189	13		503	1729	SUCCESS
APC	324	MSKCC	GRCh37	5	112177049	112177049	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001037-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	120	599	1	ENST00000257430.4:c.5758C>T	p.Arg1920Ter	p.R1920*	ENST00000257430	NM_000038.5	1920	Cga/Tga	16/16	0.285065692523189	3	FACETS	0.97	0.874	1	0.485	0.437	0.536	CLONAL	1	TRUE	1	0.285065692523189	3		600	992	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001037-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	3630	665	0	ENST00000397752.3:c.3028G>C	p.Asp1010His	p.D1010H	ENST00000397752	NM_000245.2	1010	Gat/Cat	14/21	0.285065692523189	24	FACETS	0.999	0.991	1			1	CLONAL	24	TRUE	NA	0.285065692523189	24		665	4392	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110251451	110251451	+	start_lost,splice_region_variant	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0001037-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	127	621	1	ENST00000374672.4:c.3G>A	p.Met1?	p.M1?	ENST00000374672	NM_004235.4	1	atG/atA	1/5	0.285065692523189	3	FACETS	1	0.935	1			1	CLONAL	1	TRUE	NA	0.285065692523189	3		622	977	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118368773	118368773	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001037-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	102	357	0	ENST00000534358.1:c.5787C>G	p.Ile1929Met	p.I1929M	ENST00000534358	NM_005933.3	1929	atC/atG	21/36	0.285065692523189	3	FACETS	1	0.955	1	0.562	0.502	0.625	CLONAL	1	TRUE	1	0.285065692523189	3		357	728	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560263	95560263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001037-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	80	336	0	ENST00000393063.1:c.5326C>T	p.Gln1776Ter	p.Q1776*	ENST00000393063	NM_030621.3	1776	Cag/Tag	25/28	0.285065692523189	3	FACETS	0.892	0.785	1	0.446	0.392	0.504	CLONAL	1	TRUE	1	0.285065692523189	3		336	719	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073841	8073841	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138692060	NA	P-0001037-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	57	241	0	ENST00000377482.5:c.818C>T	p.Ser273Phe	p.S273F	ENST00000377482	NM_018948.3	273	tCt/tTt	4/4	0.285065692523189	5	FACETS	0.902	0.773	1			1	CLONAL	1	TRUE	NA	0.285065692523189	5		241	633	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873760	35873760	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001037-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	126	612	0	ENST00000216797.5:c.91G>T	p.Asp31Tyr	p.D31Y	ENST00000216797	NM_020529.2	31	Gac/Tac	1/6	0.285065692523189	3	FACETS	1	0.924	1	0.513	0.463	0.565	CLONAL	1	TRUE	1	0.285065692523189	3		612	985	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0001054-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	565	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.625253798337321	5	FACETS	0.922	0.889	0.956			1	CLONAL	3	TRUE	NA	0.748607859996332	5		493	1158	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0001054-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	731	708	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.748607859996332	6	FACETS	1	0.974	1			1	CLONAL	3	TRUE	NA	0.748607859996332	6		708	1613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912655	NA	P-0001054-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	618	572	0	ENST00000269305.4:c.725G>C	p.Cys242Ser	p.C242S	ENST00000269305	NM_001126112.2	242	tGc/tCc	7/11	0.748607859996332	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.748607859996332	3		572	734	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591891	48591891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912581	NA	P-0001054-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	315	413	2	ENST00000342988.3:c.1054G>A	p.Gly352Arg	p.G352R	ENST00000342988	NM_005359.5	352	Gga/Aga	9/12	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	2	TRUE	NA	0.748607859996332	2		415	413	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260328	10260328	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148987580	NA	P-0001054-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	272	404	0	ENST00000340748.4:c.2339C>T	p.Thr780Met	p.T780M	ENST00000340748		780	aCg/aTg	25/40	0.748607859996332	4	FACETS	0.94	0.888	0.993	0.47	0.444	0.497	CLONAL	2	TRUE	0	0.748607859996332	4		404	676	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920227	76920227	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001054-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	162	443	0	ENST00000373344.5:c.3850C>A	p.Leu1284Ile	p.L1284I	ENST00000373344	NM_000489.3	1284	Ctt/Att	11/35	0.748607859996332	3	FACETS	0.946	0.871	1	0.473	0.435	0.512	CLONAL	1	TRUE	1	0.748607859996332	3		443	629	SUCCESS
APC	324	MSKCC	GRCh37	5	112175765	112175774	+	frameshift_variant	Frame_Shift_Del	DEL	GCCACGGAAA	GCCACGGAAA	-	novel	NA	P-0001054-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	214	256	0	ENST00000257430.4:c.4475_4484del	p.Ala1492ValfsTer12	p.A1492Vfs*12	ENST00000257430	NM_000038.5	1492	GCCACGGAAAgt/gt	16/16	NA	2	FACETS	0.95	0.907	0.99			1	INDETERMINATE	2	TRUE	NA	0.748607859996332	2		256	301	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399521	139399521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001054-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1291	259	825	0	ENST00000277541.6:c.4622G>A	p.Ser1541Asn	p.S1541N	ENST00000277541	NM_017617.3	1541	aGc/aAc	26/34	0.748607859996332	5	FACETS	0.948	0.885	1	0.316	0.295	0.338	CLONAL	1	TRUE	2	0.748607859996332	5		825	1550	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458578	120458578	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001054-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	171	432	1	ENST00000256646.2:c.6767G>T	p.Arg2256Leu	p.R2256L	ENST00000256646	NM_024408.3	2256	cGc/cTc	34/34	0.743498402813082	2	FACETS	0.987	0.916	1	0.493	0.458	0.529	CLONAL	1	TRUE	0	0.748607859996332	2		433	463	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589681	69589681	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001054-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	56	153	0	ENST00000168712.1:c.172C>G	p.Leu58Val	p.L58V	ENST00000168712	NM_002007.2	58	Ctg/Gtg	1/3	1	2	FACETS	0.959	0.84	1	0.959	0.84	1	CLONAL	1	TRUE	1	0.748607859996332	2		153	156	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239423	105239424	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0001054-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	164	581	0	ENST00000349310.3:c.963_964delinsTT	p.Glu322Ter	p.E322*	ENST00000349310	NM_001014432.1	321	ctGGag/ctTTag	12/15	0.690536668233975	5	FACETS	0.843	0.772	0.916			1	CLONAL	1	TRUE	NA	0.748607859996332	5		581	1104	SUCCESS
YES1	7525	MSKCC	GRCh37	18	732881	732882	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0001054-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2469	174	626	1	ENST00000314574.4:c.1375_1376delinsTT	p.Gly459Leu	p.G459L	ENST00000314574	NM_005433.3	459	GGa/TTa	11/12	0.748607859996332	10	FACETS	0.703	0.643	0.765			1	SUBCLONAL	1	TRUE	NA	0.748607859996332	10		627	2643	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247406	71247408	+	frameshift_variant	Frame_Shift_Del	DEL	CCG	CCG	AA	novel	NA	P-0001054-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	93	511	2	ENST00000318789.4:c.125_127delinsTT	p.Pro42LeufsTer40	p.P42Lfs*40	ENST00000318789	NM_032682.5	42	cCGGcc/cTTcc	6/21	0.683100241106061	4	FACETS	0.595	0.529	0.666			1	SUBCLONAL	1	TRUE	NA	0.748607859996332	4		513	730	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480496	89480496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001054-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	66	289	0	ENST00000336596.2:c.2333C>T	p.Ala778Val	p.A778V	ENST00000336596	NM_005233.5	778	gCt/gTt	13/17	0.683100241106061	4	FACETS	0.719	0.626	0.818			1	SUBCLONAL	1	TRUE	NA	0.748607859996332	4		289	429	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372282	55372282	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001054-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	236	837	0	ENST00000297316.4:c.972G>C	p.Gln324His	p.Q324H	ENST00000297316	NM_022454.3	324	caG/caC	2/2	0.748607859996332	5	FACETS	0.962	0.896	1	0.321	0.298	0.344	CLONAL	1	TRUE	2	0.748607859996332	5		837	1391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001242-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	203	356	0	ENST00000269305.4:c.736del	p.Met246Ter	p.M246*	ENST00000269305	NM_001126112.2	246	Atg/tg	7/11	0.470861486559625	1	FACETS	0.878	0.819	0.938	0.878	0.819	0.938	CLONAL	1	TRUE	0	0.543349767924695	1		356	620	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670327	134670327	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373140258	NA	P-0001242-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	118	273	0	ENST00000398015.3:c.238C>T	p.Arg80Trp	p.R80W	ENST00000398015	NM_004441.4	80	Cgg/Tgg	3/16	0.533655228886333	3	FACETS	0.628	0.566	0.694	0.314	0.283	0.347	SUBCLONAL	1	TRUE	1	0.543349767924695	3		273	879	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752631	42752631	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001242-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	65	291	1	ENST00000222329.4:c.1633del	p.His545ThrfsTer54	p.H545Tfs*54	ENST00000222329	NM_006494.2	545	Cac/ac	4/4	NA	2	FACETS	0.431	0.374	0.493			1	INDETERMINATE	1	TRUE	NA	0.543349767924695	2		292	555	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0001243-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1396	263	664	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.402863533572035	4	FACETS	1	0.978	1	0.368	0.343	0.393	CLONAL	1	TRUE	1	0.402863533572035	4		665	1659	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242478	55242478	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913229	NA	P-0001243-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1271	624	801	0	ENST00000275493.2:c.2248G>C	p.Ala750Pro	p.A750P	ENST00000275493	NM_005228.3	750	Gca/Cca	19/28	0.402863533572035	4	FACETS	1	0.993	1	0.764	0.735	0.795	CLONAL	2	TRUE	1	0.402863533572035	4		801	1895	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63816919	63816919	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001243-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	188	325	0	ENST00000279873.7:c.890A>G	p.Asn297Ser	p.N297S	ENST00000279873	NM_032199.2	297	aAc/aGc	6/10	0.233178204879315	2	FACETS	1	0.99	1	0.709	0.658	0.762	INDETERMINATE	1	TRUE	0	0.402863533572035	2		325	658	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222741	53222741	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001243-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1630	266	925	0	ENST00000375401.3:c.4195T>A	p.Leu1399Met	p.L1399M	ENST00000375401	NM_004187.3	1399	Ttg/Atg	25/26	1	2	FACETS	0.696	0.65	0.744	0.696	0.65	0.744	SUBCLONAL	1	TRUE	1	0.402863533572035	2		925	1896	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0001243-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1339	604	394	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	0.402863533572035	4	FACETS	1	0.989	1	0.722	0.693	0.751	CLONAL	2	TRUE	1	0.402863533572035	4		394	1943	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149290731	149290731	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1183739240	NA	P-0001243-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	174	619	0	ENST00000360632.3:c.488T>C	p.Leu163Pro	p.L163P	ENST00000360632	NM_015472.4	163	cTg/cCg	3/7	0.154624409284163	2	FACETS	0.654	0.601	0.711	0.327	0.3	0.356	INDETERMINATE	1	TRUE	0	0.402863533572035	2		619	1320	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149290739	149290739	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001243-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	161	586	0	ENST00000360632.3:c.480T>G	p.Asn160Lys	p.N160K	ENST00000360632	NM_015472.4	160	aaT/aaG	3/7	0.154624409284163	2	FACETS	0.65	0.595	0.708	0.325	0.297	0.354	INDETERMINATE	1	TRUE	0	0.402863533572035	2		586	1229	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149290743	149290743	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs376585599	NA	P-0001243-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	155	566	0	ENST00000360632.3:c.476T>C	p.Met159Thr	p.M159T	ENST00000360632	NM_015472.4	159	aTg/aCg	3/7	0.154624409284163	2	FACETS	0.649	0.593	0.708	0.324	0.296	0.354	INDETERMINATE	1	TRUE	0	0.402863533572035	2		566	1186	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90996767	90996768	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0001243-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	236	387	1	ENST00000265433.3:c.22_23delinsAA	p.Ala8Lys	p.A8K	ENST00000265433	NM_002485.4	8	GCg/AAg	1/16	0.235680436163488	3	FACETS	0.767	0.716	0.819	0.767	0.716	0.819	INDETERMINATE	2	TRUE	1	0.402863533572035	3		388	918	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117799	108117799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202160435	NA	P-0001313-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	687	619	0	ENST00000278616.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000278616	NM_000051.3	337	cGt/cAt	8/63	0.792775115186885	2	FACETS	0.977	0.956	0.998	0.977	0.956	0.998	CLONAL	2	TRUE	0	0.796019857572272	2		619	883	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134975	2134975	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001313-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	541	976	2	ENST00000219476.3:c.4517A>G	p.His1506Arg	p.H1506R	ENST00000219476	NM_000548.3	1506	cAt/cGt	35/42	0.796019857572272	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.796019857572272	1		978	796	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945263	54945263	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0001313-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	244	494	0	ENST00000312783.6:c.1163C>G	p.Ser388Ter	p.S388*	ENST00000312783	NM_198436.1	388	tCa/tGa	10/10	1	2	FACETS	0.948	0.891	1	0.948	0.891	1	CLONAL	1	TRUE	1	0.796019857572272	2		494	647	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0001313-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	350	690	5	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	0.796019857572272	1	FACETS	0.914	0.877	0.951	0.914	0.877	0.951	CLONAL	1	TRUE	0	0.796019857572272	1		695	579	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448301	56448301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001313-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	220	895	0	ENST00000407977.2:c.346C>T	p.Pro116Ser	p.P116S	ENST00000407977		116	Ccc/Tcc	3/10	0.406599954469476	1	FACETS	0.36	0.335	0.386	0.36	0.335	0.386	INDETERMINATE	1	TRUE	0	0.796019857572272	1		895	924	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66518943	66518943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001313-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	136	676	0	ENST00000358598.2:c.224C>T	p.Thr75Ile	p.T75I	ENST00000358598	NM_212471.2	75	aCa/aTa	3/11	0.406599954469476	1	FACETS	0.313	0.285	0.342	0.313	0.285	0.342	INDETERMINATE	1	TRUE	0	0.796019857572272	1		676	658	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781233	135781233	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001313-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	171	705	0	ENST00000298552.3:c.1732A>T	p.Thr578Ser	p.T578S	ENST00000298552	NM_001162426.1	578	Acc/Tcc	15/23	0.406599954469476	1	FACETS	0.356	0.328	0.385	0.356	0.328	0.385	INDETERMINATE	1	TRUE	0	0.796019857572272	1		705	727	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222562	69222562	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001372-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	97	617	0	ENST00000462284.1:c.535G>T	p.Asp179Tyr	p.D179Y	ENST00000462284	NM_002392.5	179	Gat/Tat	8/11	0.453715999279836	5	FACETS	0.903	0.811	0.999	0.602	0.54	0.666	CLONAL	2	TRUE	2	0.453715999279836	5		617	398	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108765	2108765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755631210	NA	P-0001372-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	244	826	2	ENST00000219476.3:c.866C>T	p.Ala289Val	p.A289V	ENST00000219476	NM_000548.3	289	gCg/gTg	10/42	0.453715999279836	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	3	TRUE	1	0.453715999279836	4		828	510	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349200	70349200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001372-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	135	823	0	ENST00000374080.3:c.3612C>A	p.Asp1204Glu	p.D1204E	ENST00000374080		1204	gaC/gaA	26/45	0.453715999279836	3	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	1	0.453715999279836	3		823	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577146	7577147	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0001372-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	116	813	2	ENST00000269305.4:c.791dup	p.Leu265ThrfsTer7	p.L265Tfs*7	ENST00000269305	NM_001126112.2	264	cta/ctTa	8/11	0.453715999279836	2	FACETS	0.861	0.788	0.935	0.861	0.788	0.935	CLONAL	2	TRUE	0	0.453715999279836	2		815	297	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435931	49435931	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001372-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	75	1071	0	ENST00000301067.7:c.6050C>G	p.Thr2017Ser	p.T2017S	ENST00000301067	NM_003482.3	2017	aCc/aGc	28/54	NA	2	FACETS	1	0.902	1			1	INDETERMINATE	1	TRUE	NA	0.453715999279836	2		1071	323	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495658	56495658	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001372-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	80	720	0	ENST00000267101.3:c.3848C>A	p.Pro1283Gln	p.P1283Q	ENST00000267101	NM_001982.3	1283	cCa/cAa	28/28	0.453715999279836	5	FACETS	1	0.952	1	0.385	0.34	0.434	CLONAL	1	TRUE	2	0.453715999279836	5		720	513	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435927	110435927	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001372-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	64	842	0	ENST00000375856.3:c.2474T>C	p.Leu825Pro	p.L825P	ENST00000375856	NM_003749.2	825	cTc/cCc	1/2	0.375638259333304	3	FACETS	1	0.953	1	0.401	0.35	0.455	CLONAL	1	TRUE	0	0.453715999279836	3		842	288	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15978851	15978851	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001372-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	73	627	0	ENST00000268712.3:c.3667G>T	p.Asp1223Tyr	p.D1223Y	ENST00000268712	NM_006311.3	1223	Gat/Tat	27/46	0.453715999279836	2	FACETS	1	0.947	1	0.565	0.499	0.634	CLONAL	1	TRUE	0	0.453715999279836	2		627	285	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619222	1619222	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001372-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	79	1009	0	ENST00000344749.5:c.1338C>A	p.Ser446Arg	p.S446R	ENST00000344749	NM_001136139.2	446	agC/agA	16/19	0.453715999279836	3	FACETS	1	0.949	1	0.378	0.334	0.424	CLONAL	1	TRUE	0	0.453715999279836	3		1009	377	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211999	36212014	+	frameshift_variant	Frame_Shift_Del	DEL	CCACGTGCCCCAACTC	CCACGTGCCCCAACTC	-	novel	NA	P-0001372-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	47	1264	0	ENST00000222270.7:c.1751_1766del	p.Pro584LeufsTer16	p.P584Lfs*16	ENST00000222270	NM_014727.1	584	CCACGTGCCCCAACTCct/ct	3/37	0.453715999279836	3	FACETS	0.551	0.465	0.646	0.276	0.232	0.323	SUBCLONAL	1	TRUE	1	0.453715999279836	3		1264	461	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262397	39262397	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001372-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	82	1032	1	ENST00000402219.2:c.1030C>A	p.Leu344Met	p.L344M	ENST00000402219	NM_005633.3	344	Ctg/Atg	8/23	0.453715999279836	4	FACETS	0.98	0.866	1	0.245	0.216	0.276	CLONAL	1	TRUE	0	0.453715999279836	4		1033	536	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690287	47690287	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001372-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	148	753	0	ENST00000233146.2:c.1504G>C	p.Asp502His	p.D502H	ENST00000233146	NM_000251.2	502	Gat/Cat	9/16	0.453715999279836	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.453715999279836	2		753	306	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812159	212812159	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001372-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	57	434	1	ENST00000342788.4:c.417G>T	p.Leu139Phe	p.L139F	ENST00000342788	NM_005235.2	139	ttG/ttT	3/28	0.453715999279836	4	FACETS	0.966	0.832	1	0.242	0.208	0.278	CLONAL	1	TRUE	0	0.453715999279836	4		435	378	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659848	227659848	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001372-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	55	577	3	ENST00000305123.5:c.3607C>A	p.Pro1203Thr	p.P1203T	ENST00000305123	NM_005544.2	1203	Cca/Aca	1/2	0.453715999279836	4	FACETS	0.993	0.853	1	0.248	0.213	0.286	CLONAL	1	TRUE	0	0.453715999279836	4		580	355	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980900	40980900	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001372-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	70	657	0	ENST00000373198.4:c.1586T>C	p.Leu529Pro	p.L529P	ENST00000373198	NM_133170.3	529	cTg/cCg	10/32	0.313342219385276	5	FACETS	1	0.959	1	0.412	0.36	0.467	CLONAL	1	TRUE	2	0.453715999279836	5		657	420	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445089	89445089	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001372-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	45	657	0	ENST00000336596.2:c.1409A>T	p.Tyr470Phe	p.Y470F	ENST00000336596	NM_005233.5	470	tAc/tTc	6/17	0.453715999279836	3	FACETS	0.724	0.611	0.848	0.362	0.305	0.424	SUBCLONAL	1	TRUE	1	0.453715999279836	3		657	336	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541612	187541612	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001372-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	58	505	0	ENST00000441802.2:c.6128A>G	p.Gln2043Arg	p.Q2043R	ENST00000441802	NM_005245.3	2043	cAg/cGg	10/27	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.453715999279836	2		505	223	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875096	151875096	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0001372-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	71	105	0	ENST00000262189.6:c.7443-1G>T		p.X2481_splice	ENST00000262189	NM_170606.2	2481			0.453715999279836	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	4	TRUE	0	0.453715999279836	4		105	106	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978556	70978556	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001372-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	169	880	0	ENST00000276594.2:c.1097A>G	p.Tyr366Cys	p.Y366C	ENST00000276594	NM_024504.3	366	tAt/tGt	5/8	0.439360806379908	5	FACETS	1	0.964	1	0.536	0.495	0.578	CLONAL	2	TRUE	1	0.453715999279836	5		880	584	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412234	139412234	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001372-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	62	875	1	ENST00000277541.6:c.1411A>T	p.Ile471Phe	p.I471F	ENST00000277541	NM_017617.3	471	Att/Ttt	8/34	0.453715999279836	3	FACETS	0.869	0.754	0.992	0.29	0.251	0.331	CLONAL	1	TRUE	0	0.453715999279836	3		876	386	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166014	118166014	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001490-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	145	426	0	ENST00000369448.3:c.524G>A	p.Arg175His	p.R175H	ENST00000369448	NM_017709.3	175	cGt/cAt	2/2	1	2	FACETS	0.909	0.831	0.991	0.909	0.831	0.991	CLONAL	1	TRUE	1	0.451065262197794	2		426	707	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0001490-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	407	665	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.451065262197794	3	FACETS	0.944	0.9	0.99	0.944	0.9	0.99	CLONAL	2	TRUE	1	0.451065262197794	3		665	1171	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495462	56495462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001490-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	172	650	0	ENST00000267101.3:c.3652G>A	p.Glu1218Lys	p.E1218K	ENST00000267101	NM_001982.3	1218	Gag/Aag	28/28	1	2	FACETS	0.723	0.664	0.784	0.723	0.664	0.784	SUBCLONAL	1	TRUE	1	0.451065262197794	2		650	1055	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001366	29001366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779189056	NA	P-0001490-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	260	397	0	ENST00000282397.4:c.1366G>A	p.Ala456Thr	p.A456T	ENST00000282397	NM_002019.4	456	Gca/Aca	10/30	0.451065262197794	5	FACETS	0.983	0.922	1	0.655	0.614	0.697	CLONAL	2	TRUE	2	0.451065262197794	5		397	983	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821437	72821437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371324694	NA	P-0001490-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	552	682	0	ENST00000268489.5:c.10738G>A	p.Asp3580Asn	p.D3580N	ENST00000268489	NM_006885.3	3580	Gat/Aat	10/10	0.451065262197794	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.451065262197794	3		682	1318	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519998	NA	P-0001490-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	492	686	1	ENST00000269305.4:c.581T>A	p.Leu194His	p.L194H	ENST00000269305	NM_001126112.2	194	cTt/cAt	6/11	0.451065262197794	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.451065262197794	2		687	1068	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131408	202131408	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001490-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	154	578	0	ENST00000358485.4:c.376T>G	p.Phe126Val	p.F126V	ENST00000358485	NM_001080125.1	126	Ttc/Gtc	2/9	0.451065262197794	2	FACETS	0.74	0.677	0.806	0.37	0.338	0.403	SUBCLONAL	1	TRUE	0	0.451065262197794	2		578	923	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0001490-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	251	425	3	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	0.234904787672584	5	FACETS	0.959	0.898	1	0.639	0.598	0.681	INDETERMINATE	2	TRUE	2	0.451065262197794	5		428	973	SUCCESS
APC	324	MSKCC	GRCh37	5	112175524	112175524	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001490-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	251	367	0	ENST00000257430.4:c.4233del	p.Ser1411ArgfsTer4	p.S1411Rfs*4	ENST00000257430	NM_000038.5	1411	agT/ag	16/16	0.234904787672584	5	FACETS	1	0.972	1	0.708	0.664	0.754	INDETERMINATE	2	TRUE	2	0.451065262197794	5		367	878	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371941	55371941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001490-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	123	531	1	ENST00000297316.4:c.631G>A	p.Ala211Thr	p.A211T	ENST00000297316	NM_022454.3	211	Gcg/Acg	2/2	0.451065262197794	3	FACETS	0.593	0.534	0.654	0.296	0.267	0.327	SUBCLONAL	1	TRUE	1	0.451065262197794	3		532	1128	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499786	8499786	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs141698449	NA	P-0001490-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	88	581	0	ENST00000356435.5:c.2183T>G	p.Val728Gly	p.V728G	ENST00000356435		728	gTt/gGt	14/35	1	2	FACETS	0.429	0.379	0.482	0.429	0.379	0.482	SUBCLONAL	1	TRUE	1	0.451065262197794	2		581	910	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001632-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	213	472	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.428700260474408	2	FACETS	1	0.97	1	0.539	0.501	0.578	CLONAL	1	TRUE	0	0.433550924592053	2		472	912	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835596	68835596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587783047	NA	P-0001632-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	373	384	1	ENST00000261769.5:c.187C>T	p.Arg63Ter	p.R63*	ENST00000261769	NM_004360.3	63	Cga/Tga	3/16	0.433550924592053	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.433550924592053	2		385	847	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940994	71940995	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0001632-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	227	489	0	ENST00000298229.2:c.871_872del	p.Ser291HisfsTer12	p.S291Hfs*12	ENST00000298229	NM_001567.3	290	agCTcc/agcc	8/28	0.433550924592053	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.433550924592053	1		489	811	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856304	111856304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001632-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	31	48	0	ENST00000341259.2:c.355C>T	p.Arg119Cys	p.R119C	ENST00000341259	NM_005475.2	119	Cgc/Tgc	2/8	NA	2	FACETS	1	0.891	1			1	INDETERMINATE	1	TRUE	NA	0.433550924592053	2		48	128	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941717	48941717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001632-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	134	263	0	ENST00000267163.4:c.1027C>T	p.Leu343Phe	p.L343F	ENST00000267163	NM_000321.2	343	Ctt/Ttt	10/27	0.433550924592053	1	FACETS	0.994	0.909	1	0.994	0.909	1	CLONAL	1	TRUE	0	0.433550924592053	1		263	487	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151893024	151893024	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0001632-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	211	422	0	ENST00000262189.6:c.4346C>G	p.Ser1449Ter	p.S1449*	ENST00000262189	NM_170606.2	1449	tCa/tGa	28/59	NA	2	FACETS	1	0.947	1			1	INDETERMINATE	1	TRUE	NA	0.433550924592053	2		422	952	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938713	76938713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001632-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	226	448	1	ENST00000373344.5:c.2035G>A	p.Glu679Lys	p.E679K	ENST00000373344	NM_000489.3	679	Gaa/Aaa	9/35	0.433550924592053	3	FACETS	0.984	0.915	1	0.492	0.457	0.528	CLONAL	1	TRUE	1	0.433550924592053	3		449	1289	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0001639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	92	522	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.687120158667572	3	FACETS	0.606	0.539	0.677	0.303	0.269	0.339	SUBCLONAL	1	TRUE	1	0.687120158667572	3		522	594	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0001639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	256	673	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.687120158667572	2		673	719	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0001733-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	215	699	2	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.247456762601922	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.17	2		701	1023	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875627	35875627	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369971728	NA	P-0001733-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	44	467	0	ENST00000303115.3:c.814G>A	p.Val272Ile	p.V272I	ENST00000303115	NM_002185.3	272	Gta/Ata	7/8	0.148942394866322	2	FACETS	0.722	0.604	0.853	0.361	0.302	0.427	SUBCLONAL	1	TRUE	0	0.17	2		467	717	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509006	106509006	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201525740	NA	P-0001733-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	41	429	0	ENST00000359195.3:c.1000G>A	p.Gly334Ser	p.G334S	ENST00000359195	NM_002649.2	334	Ggc/Agc	2/11	0.247456762601922	2	FACETS	0.914	0.76	1	0.457	0.38	0.542	CLONAL	1	TRUE	0	0.17	2		429	528	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31369176	31369176	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760640013	NA	P-0001733-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	129	521	2	ENST00000328111.2:c.160C>T	p.Arg54Ter	p.R54*	ENST00000328111	NM_006892.3	54	Cga/Tga	3/23	0.199592457760124	4	FACETS	0.904	0.819	0.994	0.904	0.819	0.994	CLONAL	2	TRUE	2	0.17	4		523	982	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649843	88649843	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001733-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	31	412	0	ENST00000372037.3:c.92A>G	p.His31Arg	p.H31R	ENST00000372037	NM_004329.2	31	cAt/cGt	4/13	1	2	FACETS	0.654	0.527	0.797	0.654	0.527	0.797	SUBCLONAL	1	TRUE	1	0.17	2		412	558	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987124	36987124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1433487495	NA	P-0001733-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	54	742	4	ENST00000354822.5:c.565G>A	p.Ala189Thr	p.A189T	ENST00000354822	NM_001079668.2	189	Gcg/Acg	3/3	0.207183698374825	2	FACETS	0.828	0.706	0.963	0.414	0.353	0.482	CLONAL	1	TRUE	0	0.17	2		746	767	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723120	52723120	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	T	novel	NA	P-0001733-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	20	229	0	ENST00000322088.6:c.1302+3G>T		p.X434_splice	ENST00000322088	NM_014225.5	434			0.30474627241267	3	FACETS	0.922	0.706	1	0.461	0.353	0.587	CLONAL	1	TRUE	1	0.17	3		229	277	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121025	29121026	+	stop_gained	Nonsense_Mutation	DNP	CT	CT	AC	novel	NA	P-0001733-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	45	695	1	ENST00000328354.6:c.531_532delinsGT	p.Gly178Ter	p.G178*	ENST00000328354	NM_007194.3	177	aaAGga/aaGTga	4/15	0.1939208029168	3	FACETS	0.67	0.561	0.791	0.223	0.187	0.264	SUBCLONAL	1	TRUE	0	0.17	3		696	857	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891659	28891659	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001855-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	63	584	1	ENST00000282397.4:c.3362C>A	p.Ala1121Asp	p.A1121D	ENST00000282397	NM_002019.4	1121	gCt/gAt	25/30	1	2	FACETS	0.551	0.474	0.634	0.551	0.474	0.634	SUBCLONAL	1	TRUE	1	0.184858200175982	2		585	1238	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212149	5212149	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1377011238	NA	P-0001855-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	81	701	1	ENST00000357368.4:c.4882C>T	p.Arg1628Cys	p.R1628C	ENST00000357368	NM_002850.3	1628	Cgc/Tgc	32/38	1	2	FACETS	0.69	0.606	0.781	0.69	0.606	0.781	SUBCLONAL	1	TRUE	1	0.184858200175982	2		702	1270	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045000	47045000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556782020	NA	P-0001855-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	112	287	0	ENST00000377604.3:c.2326C>T	p.Arg776Trp	p.R776W	ENST00000377604	NM_001204468.1	776	Cgg/Tgg	20/24	1	1	FACETS	0.786	0.707	0.868	1	0.985	1	SUBCLONAL	2	TRUE	0	0.184858200175982	1		287	700	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577525	7577525	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001855-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	117	479	3	ENST00000269305.4:c.756del	p.Thr253ProfsTer92	p.T253Pfs*92	ENST00000269305	NM_001126112.2	252	ctC/ct	7/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.184858200175982	2		482	1033	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578468	7578469	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0001855-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1273	30	648	3	ENST00000269305.4:c.461_462delinsTT	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGC/gTT	5/11	1	2	FACETS	0.249	0.199	0.306	0.249	0.199	0.306	SUBCLONAL	1	TRUE	1	0.184858200175982	2		651	1303	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604789	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0001855-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	55	391	0	ENST00000342988.3:c.1610_1611del	p.Asp537GlyfsTer39	p.D537Gfs*39	ENST00000342988	NM_005359.5	537	gAC/g	12/12	1	2	FACETS	0.703	0.6	0.817	0.703	0.6	0.817	SUBCLONAL	1	TRUE	1	0.184858200175982	2		391	846	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715661	30715669	+	inframe_deletion	In_Frame_Del	DEL	AGTCCTTCA	AGTCCTTCA	-	novel	NA	P-0001855-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	57	265	0	ENST00000295754.5:c.1321_1329del	p.Ser441_Lys443del	p.S441_K443del	ENST00000295754	NM_003242.5	440	gAGTCCTTCAag/gag	5/7	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.184858200175982	2		265	509	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0002095-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	349	722	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	0.724383663787532	2		722	945	SUCCESS
APC	324	MSKCC	GRCh37	5	112175751	112175752	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1114167577	NA	P-0002095-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	212	344	0	ENST00000257430.4:c.4463dup	p.Leu1488PhefsTer26	p.L1488Ffs*26	ENST00000257430	NM_000038.5	1487	act/acTt	16/16	1	2	FACETS	0.906	0.846	0.967	0.906	0.846	0.967	CLONAL	1	TRUE	1	0.724383663787532	2		344	646	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457371	67457373	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0002095-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	404	590	0	ENST00000327367.4:c.349_351del	p.Lys117del	p.K117del	ENST00000327367	NM_005902.3	115	atGAAg/atg	2/9	1	2	FACETS	0.949	0.904	0.995	0.949	0.904	0.995	CLONAL	1	TRUE	1	0.724383663787532	2		590	1175	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976100	18976100	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs750432625	NA	P-0002095-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	397	656	2	ENST00000262803.5:c.2860C>T	p.Arg954Trp	p.R954W	ENST00000262803	NM_002911.3	954	Cgg/Tgg	21/24	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.724383663787532	2		658	1076	SUCCESS
APC	324	MSKCC	GRCh37	5	112174475	112174476	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0002095-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	259	342	0	ENST00000257430.4:c.3187dup	p.Ser1063LysfsTer2	p.S1063Kfs*2	ENST00000257430	NM_000038.5	1062	caa/cAaa	16/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.724383663787532	2		342	692	SUCCESS
APC	324	MSKCC	GRCh37	5	112176212	112176226	+	inframe_deletion	In_Frame_Del	DEL	GTGTATTGTGTTGAA	GTGTATTGTGTTGAA	-	novel	NA	P-0002095-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	283	399	0	ENST00000257430.4:c.4922_4936del	p.Val1641_Glu1645del	p.V1641_E1645del	ENST00000257430	NM_000038.5	1641	GTGTATTGTGTTGAA/-	16/16	1	2	FACETS	0.829	0.78	0.878	0.829	0.78	0.878	CLONAL	1	TRUE	1	0.724383663787532	2		399	943	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539104	23539104	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002095-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	294	523	0	ENST00000380871.4:c.335C>T	p.Ala112Val	p.A112V	ENST00000380871	NM_006167.3	112	gCc/gTc	2/2	1	2	FACETS	0.959	0.906	1	0.959	0.906	1	CLONAL	1	TRUE	1	0.724383663787532	2		523	846	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200221	123200221	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002095-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	359	507	0	ENST00000218089.9:c.2200C>A	p.Leu734Met	p.L734M	ENST00000218089	NM_001042749.1	734	Ctg/Atg	23/35	1	2	FACETS	0.944	0.896	0.992	0.944	0.896	0.992	CLONAL	1	TRUE	1	0.724383663787532	2		507	1050	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0002101-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	92	456	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	1	2	FACETS	0.743	0.66	0.832	0.743	0.66	0.832	SUBCLONAL	1	TRUE	1	0.34	2		456	728	SUCCESS
AR	367	MSKCC	GRCh37	X	66943552	66943552	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137852578	NA	P-0002101-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1328	28	233	0	ENST00000374690.3:c.2632A>G	p.Thr878Ala	p.T878A	ENST00000374690	NM_000044.3	878	Act/Gct	8/8	0.3	12	FACETS	0.328	0.26	0.406			1	SUBCLONAL	1	TRUE	NA	0.34	12		233	1356	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896361	151896362	+	splice_donor_variant,intron_variant	Splice_Site	DNP	TA	TA	AG	novel	NA	P-0002101-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	85	377	0	ENST00000262189.6:c.4273+2_4273+3delinsCT		p.X1425_splice	ENST00000262189	NM_170606.2	1425			0.247315682044887	3	FACETS	1	0.928	1			1	CLONAL	1	TRUE	NA	0.34	3		377	550	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0002281-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	100	797	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.941	0.84	1	0.941	0.84	1	CLONAL	1	TRUE	1	0.242510512171532	2		798	876	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097304	178097304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763097686	NA	P-0002281-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	74	335	1	ENST00000397062.3:c.410C>T	p.Ser137Leu	p.S137L	ENST00000397062	NM_006164.4	137	tCg/tTg	4/5	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.242510512171532	2		336	573	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247846	59247847	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002281-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	157	814	0	ENST00000371222.2:c.896dup	p.Asn299LysfsTer11	p.N299Kfs*11	ENST00000371222	NM_002228.3	299	aac/aaAc	1/1	0.238061856769683	1	FACETS	0.963	0.88	1	0.963	0.88	1	CLONAL	1	TRUE	0	0.242510512171532	1		814	1182	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063316	67063338	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCGTCGTGCCCGACCAGAGAA	GCGCGTCGTGCCCGACCAGAGAA	-	novel	NA	P-0002281-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	39	283	1	ENST00000412916.2:c.8_30del	p.Arg3GlnfsTer9	p.R3Qfs*9	ENST00000412916		2	ccGCGCGTCGTGCCCGACCAGAGAAgc/ccgc	1/6	0.242510512171532	1	FACETS	0.87	0.723	1	0.87	0.723	1	CLONAL	1	TRUE	0	0.242510512171532	1		284	325	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881024	37881024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002281-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	107	761	1	ENST00000269571.5:c.2353C>T	p.Leu785Phe	p.L785F	ENST00000269571		785	Ctt/Ttt	20/27	1	2	FACETS	0.82	0.734	0.912	0.82	0.734	0.912	CLONAL	1	TRUE	1	0.242510512171532	2		762	1076	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038621	14038621	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002281-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	78	512	0	ENST00000311895.7:c.1946G>C	p.Arg649Thr	p.R649T	ENST00000311895	NM_005236.2	649	aGa/aCa	10/11	0.242510512171532	3	FACETS	0.821	0.72	0.931	0.411	0.36	0.466	CLONAL	1	TRUE	1	0.242510512171532	3		512	878	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128017000	128017000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374262917	NA	P-0002281-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	119	581	0	ENST00000285398.2:c.2089G>A	p.Glu697Lys	p.E697K	ENST00000285398	NM_000122.1	697	Gag/Aag	14/15	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.242510512171532	2		581	918	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030973	36030973	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002281-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	81	417	0	ENST00000358208.4:c.1252G>C	p.Glu418Gln	p.E418Q	ENST00000358208		418	Gag/Cag	10/12	1	2	FACETS	0.979	0.863	1	0.979	0.863	1	CLONAL	1	TRUE	1	0.242510512171532	2		417	682	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22153373	22153373	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002281-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	117	579	0	ENST00000215832.6:c.537T>A	p.Asp179Glu	p.D179E	ENST00000215832	NM_002745.4	179	gaT/gaA	4/9	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.242510512171532	2		579	879	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138382809	138382809	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002281-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	103	514	0	ENST00000289153.2:c.2735C>G	p.Ser912Cys	p.S912C	ENST00000289153	NM_006219.2	912	tCt/tGt	19/22	0.238061856769683	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.242510512171532	1		514	711	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239881	98239881	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002281-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	87	533	0	ENST00000331920.6:c.1451G>C	p.Gly484Ala	p.G484A	ENST00000331920	NM_000264.3	484	gGa/gCa	10/24	1	2	FACETS	0.932	0.824	1	0.932	0.824	1	CLONAL	1	TRUE	1	0.242510512171532	2		533	770	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0002431-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	89	464	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.207638943438708	1	FACETS	0.962	0.852	1	0.962	0.852	1	CLONAL	1	TRUE	0	0.207638943438708	1		464	799	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589576	69589576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002431-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	94	309	2	ENST00000168712.1:c.277G>A	p.Gly93Ser	p.G93S	ENST00000168712	NM_002007.2	93	Ggc/Agc	1/3	0.197559017939338	2	FACETS	0.974	0.87	1	0.974	0.87	1	CLONAL	2	TRUE	0	0.207638943438708	2		311	465	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0002622-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	479	843	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.529166793139317	3	FACETS	0.986	0.954	1			1	CLONAL	3	TRUE	NA	0.569129861528105	3		843	731	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070594	67070594	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002622-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	138	372	1	ENST00000412916.2:c.218G>A	p.Trp73Ter	p.W73*	ENST00000412916		73	tGg/tAg	3/6	0.569129861528105	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.569129861528105	1		373	347	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654689	29654690	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0002622-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	159	434	0	ENST00000356175.3:c.5380dup	p.Gln1794ProfsTer4	p.Q1794Pfs*4	ENST00000356175	NM_000267.3	1793	cac/caCc	37/57	0.565312368553544	1	FACETS	0.909	0.841	0.977	0.909	0.841	0.977	CLONAL	1	TRUE	0	0.569129861528105	1		434	440	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577041	7577137	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCTCGTGGTGAGGCTCCCCTTTCTTGCGGAGATTCTCTTCCTCTGTGCGCCGGTCTCTCCCAGGACAGGCACAAACACGCACCTCAAAGCTGTTC	CAGCTCGTGGTGAGGCTCCCCTTTCTTGCGGAGATTCTCTTCCTCTGTGCGCCGGTCTCTCCCAGGACAGGCACAAACACGCACCTCAAAGCTGTTC	-	novel	NA	P-0002622-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	108	633	0	ENST00000269305.4:c.801_897del	p.Asn268ProfsTer45	p.N268Pfs*45	ENST00000269305	NM_001126112.2	267	cgGAACAGCTTTGAGGTGCGTGTTTGTGCCTGTCCTGGGAGAGACCGGCGCACAGAGGAAGAGAATCTCCGCAAGAAAGGGGAGCCTCACCACGAGCTG/cg	8/11	0.565312368553544	1	FACETS	0.569	0.513	0.628	0.569	0.513	0.628	SUBCLONAL	1	TRUE	0	0.569129861528105	1		633	477	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226170	2226170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1394758490	NA	P-0002622-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	277	658	0	ENST00000326181.6:c.1867C>T	p.Arg623Trp	p.R623W	ENST00000326181	NM_032271.2	623	Cgg/Tgg	19/21	0.569129861528105	3	FACETS	1	0.98	1	0.549	0.515	0.584	CLONAL	1	TRUE	1	0.569129861528105	3		658	1139	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0002622-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	168	455	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.84	0.774	0.908	0.84	0.774	0.908	CLONAL	1	TRUE	1	0.569129861528105	2		455	703	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845349	156845349	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1278248260	NA	P-0002622-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	278	690	0	ENST00000524377.1:c.1392G>T	p.Met464Ile	p.M464I	ENST00000524377	NM_002529.3	464	atG/atT	12/17	0.569129861528105	3	FACETS	1	0.962	1	0.517	0.485	0.55	CLONAL	1	TRUE	1	0.569129861528105	3		690	1214	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857590	9857590	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002622-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	62	383	0	ENST00000330684.3:c.3811T>C	p.Trp1271Arg	p.W1271R	ENST00000330684	NM_001134407.1	1271	Tgg/Cgg	13/13	0.569129861528105	3	FACETS	0.487	0.42	0.559	0.243	0.21	0.28	SUBCLONAL	1	TRUE	1	0.569129861528105	3		383	575	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917707	151917707	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0002622-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	52	214	0	ENST00000262189.6:c.3613A>T	p.Lys1205Ter	p.K1205*	ENST00000262189	NM_170606.2	1205	Aaa/Taa	23/59	1	2	FACETS	0.669	0.574	0.772	0.669	0.574	0.772	SUBCLONAL	1	TRUE	1	0.569129861528105	2		214	273	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793284	139793284	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002622-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	130	747	0	ENST00000247668.2:c.92A>C	p.Lys31Thr	p.K31T	ENST00000247668	NM_021138.3	31	aAg/aCg	2/11	1	2	FACETS	0.508	0.46	0.558	0.508	0.46	0.558	SUBCLONAL	1	TRUE	1	0.569129861528105	2		747	900	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0002687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	160	522	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.564430276991089	2		522	564	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0002687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	794	760	1	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	0.564430276991089	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	TRUE	0	0.564430276991089	3		761	1202	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339230	70339230	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs199469667	NA	P-0002687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	322	808	0	ENST00000374080.3:c.107T>G	p.Leu36Arg	p.L36R	ENST00000374080		36	cTg/cGg	2/45	0.564430276991089	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.564430276991089	1		808	810	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489560	40489577	+	inframe_deletion	In_Frame_Del	DEL	GTACTCCATCGCTGACAA	GTACTCCATCGCTGACAA	-	novel	NA	P-0002687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1325	248	774	1	ENST00000264657.5:c.673_690del	p.Leu225_Tyr230del	p.L225_Y230del	ENST00000264657	NM_139276.2	225	TTGTCAGCGATGGAGTAC/-	8/24	0.564430276991089	4	FACETS	0.874	0.815	0.936	0.437	0.407	0.468	CLONAL	1	TRUE	2	0.564430276991089	4		775	1573	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045879	26045879	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	181	494	0	ENST00000540144.1:c.241A>G	p.Thr81Ala	p.T81A	ENST00000540144	NM_003531.2	81	Acc/Gcc	1/1	0.564430276991089	2	FACETS	0.924	0.855	0.995	0.462	0.427	0.498	CLONAL	1	TRUE	0	0.564430276991089	2		494	694	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207783	29207783	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	267	661	0	ENST00000240100.2:c.13G>C	p.Glu5Gln	p.E5Q	ENST00000240100	NM_001394.6	5	Gag/Cag	1/4	0.564430276991089	3	FACETS	1	0.939	1	0.501	0.469	0.534	CLONAL	1	TRUE	1	0.564430276991089	3		661	1210	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0002841-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	131	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	0.348550755255723	2		336	701	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002841-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	164	472	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.348550755255723	2		472	869	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002841-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	119	548	0	ENST00000263967.3:c.333G>T	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaT	2/21	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.348550755255723	2		548	658	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458591	120458591	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002841-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	130	540	0	ENST00000256646.2:c.6754G>A	p.Asp2252Asn	p.D2252N	ENST00000256646	NM_024408.3	2252	Gat/Aat	34/34	0.256289494696072	4	FACETS	0.94	0.851	1	0.47	0.425	0.517	CLONAL	1	TRUE	2	0.348550755255723	4		540	1070	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463227	25463227	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002841-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	151	584	0	ENST00000264709.3:c.2266G>C	p.Glu756Gln	p.E756Q	ENST00000264709	NM_175629.2	756	Gag/Cag	19/23	1	2	FACETS	0.884	0.808	0.964	0.884	0.808	0.964	CLONAL	1	TRUE	1	0.348550755255723	2		584	980	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88651921	88651921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002841-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	147	533	0	ENST00000372037.3:c.268G>A	p.Asp90Asn	p.D90N	ENST00000372037	NM_004329.2	90	Gac/Aac	5/13	1	2	FACETS	0.878	0.801	0.959	0.878	0.801	0.959	CLONAL	1	TRUE	1	0.348550755255723	2		533	961	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534316	534316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002841-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	123	414	0	ENST00000451590.1:c.7G>A	p.Glu3Lys	p.E3K	ENST00000451590	NM_001130442.1	3	Gaa/Aaa	2/5	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.348550755255723	2		414	664	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213538	2213538	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002841-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	172	643	0	ENST00000398665.3:c.1558G>A	p.Glu520Lys	p.E520K	ENST00000398665	NM_032482.2	520	Gag/Aag	17/28	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.348550755255723	2		643	878	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533763	533763	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0002841-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	158	592	0	ENST00000451590.1:c.290+3G>A		p.X97_splice	ENST00000451590	NM_001130442.1	97			1	2	FACETS	0.993	0.91	1	0.993	0.91	1	CLONAL	1	TRUE	1	0.348550755255723	2		592	913	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213003	39213003	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002841-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	231	770	0	ENST00000402219.2:c.3964G>C	p.Asp1322His	p.D1322H	ENST00000402219	NM_005633.3	1322	Gat/Cat	23/23	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.348550755255723	2		770	1262	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55945935	55946136	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	CCTCTTCCAGGATATGCCTAGAAGACTGGCTCCCTGCAGTCCGAGGTCCTTTTTCTGTTGTCGAAATGAAAATCAAATGCGGCTACTTCCTGCTGGTGGAAAGAACAACACTTGAAAATCTGAGCAGCACCTCTCATGTGATGTCCAGGAGTTGGGGGTGTGGATGCTTCCTTTTAAACAGGAGGAGAGCTCAGTGTGGTCC	CCTCTTCCAGGATATGCCTAGAAGACTGGCTCCCTGCAGTCCGAGGTCCTTTTTCTGTTGTCGAAATGAAAATCAAATGCGGCTACTTCCTGCTGGTGGAAAGAACAACACTTGAAAATCTGAGCAGCACCTCTCATGTGATGTCCAGGAGTTGGGGGTGTGGATGCTTCCTTTTAAACAGGAGGAGAGCTCAGTGTGGTCC	-	novel	NA	P-0002841-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6	53	9	0	ENST00000263923.4:c.4043_*173del		p.*1348*	ENST00000263923	NM_002253.2	1348		30/30	0.311756533250767	3	FACETS	1	0.949	1			1	CLONAL	6	TRUE	NA	0.348550755255723	3		9	59	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946319	55946336	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCACCATTCCACTGCAG	GGCACCATTCCACTGCAG	AT	novel	NA	P-0002841-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	70	165	1	ENST00000263923.4:c.3849-6_3860delinsAT		p.X1283_splice	ENST00000263923	NM_002253.2	1283		30/30	0.311756533250767	3	FACETS	1	0.952	1			1	CLONAL	1	TRUE	NA	0.348550755255723	3		166	400	SUCCESS
STAG3L2	442582	MSKCC	GRCh37	7	74114618	74114618	+	intron_variant,non_coding_transcript_variant	Intron	SNP	G	G	T	novel	NA	P-0002841-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	119	396	1	ENST00000380775.3:n.1219-2192C>A		p.*407*	ENST00000380775		139/998			0.311756533250767	3	FACETS	1	0.926	1			1	CLONAL	1	TRUE	NA	0.348550755255723	3		397	778	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0002880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	197	396	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	0.916	0.849	0.987	0.916	0.849	0.987	CLONAL	1	TRUE	1	0.446909860337088	2		396	962	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188164	11188164	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	148	373	0	ENST00000361445.4:c.5930C>G	p.Thr1977Arg	p.T1977R	ENST00000361445	NM_004958.3	1977	aCa/aGa	43/58	0.335470631919524	3	FACETS	0.965	0.881	1	0.482	0.44	0.526	CLONAL	1	TRUE	1	0.446909860337088	3		373	840	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0002940-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	129	376	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.577741385196355	2		376	435	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028875	47028875	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002940-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	154	368	0	ENST00000377604.3:c.179C>A	p.Ser60Ter	p.S60*	ENST00000377604	NM_001204468.1	60	tCa/tAa	3/24	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.577741385196355	1		368	253	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170002328	170002328	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002940-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	93	215	0	ENST00000295797.4:c.1147A>C	p.Asn383His	p.N383H	ENST00000295797	NM_002740.5	383	Aat/Cat	12/18	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.577741385196355	2		215	239	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157454272	157454272	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	276	467	0	ENST00000346085.5:c.2482A>T	p.Ile828Phe	p.I828F	ENST00000346085	NM_020732.3	828	Atc/Ttc	8/20	0.632095752532895	1	FACETS	0.909	0.86	0.959	0.909	0.86	0.959	CLONAL	1	TRUE	0	0.632095752532895	1		467	657	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848525	151848525	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0002974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	176	435	0	ENST00000262189.6:c.12666+2T>A		p.X4222_splice	ENST00000262189	NM_170606.2	4222			1	2	FACETS	0.688	0.634	0.743	0.688	0.634	0.743	SUBCLONAL	1	TRUE	1	0.632095752532895	2		435	810	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750684	128750684	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002978-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	308	530	0	ENST00000377970.2:c.221C>A	p.Pro74Gln	p.P74Q	ENST00000377970	NM_002467.4	74	cCg/cAg	2/3	0.513615611890126	3	FACETS	0.933	0.883	0.983	0.933	0.883	0.983	CLONAL	2	TRUE	1	0.513615611890126	3		530	808	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878081	48878112	+	frameshift_variant	Frame_Shift_Del	DEL	CACCGCCGCCGCTGCCGCCGCGGAACCCCCGG	CACCGCCGCCGCTGCCGCCGCGGAACCCCCGG	-	novel	NA	P-0002978-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	168	244	0	ENST00000267163.4:c.45_76del	p.Ala17ProfsTer3	p.A17Pfs*3	ENST00000267163	NM_000321.2	11	gcCACCGCCGCCGCTGCCGCCGCGGAACCCCCGGca/gcca	1/27	0.501783826727359	1	FACETS	0.894	0.827	0.963	0.894	0.827	0.963	CLONAL	1	TRUE	0	0.513615611890126	1		244	544	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750684	128750684	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002978-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	1148	530	0	ENST00000377970.2:c.221C>A	p.Pro74Gln	p.P74Q	ENST00000377970	NM_002467.4	74	cCg/cAg	2/3	0.591154276140487	6	FACETS	0.989	0.969	1	0.989	0.969	1	CLONAL	5	TRUE	1	0.591154276140487	6		530	1714	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878081	48878112	+	frameshift_variant	Frame_Shift_Del	DEL	CACCGCCGCCGCTGCCGCCGCGGAACCCCCGG	CACCGCCGCCGCTGCCGCCGCGGAACCCCCGG	-	novel	NA	P-0002978-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	335	244	0	ENST00000267163.4:c.45_76del	p.Ala17ProfsTer3	p.A17Pfs*3	ENST00000267163	NM_000321.2	11	gcCACCGCCGCCGCTGCCGCCGCGGAACCCCCGGca/gcca	1/27	0.589578952315308	2	FACETS	0.967	0.926	1	0.967	0.926	1	CLONAL	2	TRUE	0	0.591154276140487	2		244	586	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0002982-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	101	943	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.153257850641782	3	FACETS	0.816	0.729	0.909	0.816	0.729	0.909	CLONAL	2	TRUE	1	0.16	3		943	835	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557310	187557310	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002982-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	63	856	0	ENST00000441802.2:c.4052C>A	p.Pro1351Gln	p.P1351Q	ENST00000441802	NM_005245.3	1351	cCg/cAg	6/27	1	2	FACETS	0.919	0.793	1	0.919	0.793	1	CLONAL	1	TRUE	1	0.16	2		856	857	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0002995-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	358	602	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.223380203393626	3	FACETS	0.932	0.884	0.982			1	CLONAL	3	TRUE	NA	0.245863553988141	3		604	1169	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567317	226567317	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002995-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	78	425	0	ENST00000366794.5:c.1569G>C	p.Met523Ile	p.M523I	ENST00000366794	NM_001618.3	523	atG/atC	11/23	0.188568560473337	4	FACETS	0.912	0.8	1	0.304	0.266	0.345	CLONAL	1	TRUE	1	0.245863553988141	4		425	867	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470950	25470950	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002995-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	109	517	1	ENST00000264709.3:c.811G>A	p.Asp271Asn	p.D271N	ENST00000264709	NM_175629.2	271	Gac/Aac	7/23	0.245863553988141	5	FACETS	1	0.972	1	0.414	0.371	0.459	CLONAL	1	TRUE	2	0.245863553988141	5		518	978	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965690	25965690	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002995-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	88	582	0	ENST00000435504.4:c.3516G>C	p.Glu1172Asp	p.E1172D	ENST00000435504		1172	gaG/gaC	13/13	0.245863553988141	5	FACETS	0.831	0.734	0.936	0.277	0.244	0.312	CLONAL	1	TRUE	2	0.245863553988141	5		582	1179	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702205	47702205	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002995-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	63	471	0	ENST00000233146.2:c.1801C>G	p.Gln601Glu	p.Q601E	ENST00000233146	NM_000251.2	601	Cag/Gag	12/16	0.245863553988141	5	FACETS	0.762	0.658	0.877	0.254	0.219	0.293	SUBCLONAL	1	TRUE	2	0.245863553988141	5		471	920	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033771	48033771	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002995-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	62	282	0	ENST00000234420.5:c.3982C>A	p.Gln1328Lys	p.Q1328K	ENST00000234420	NM_000179.2	1328	Cag/Aag	9/10	0.245863553988141	5	FACETS	0.972	0.839	1	0.324	0.279	0.373	CLONAL	1	TRUE	2	0.245863553988141	5		282	710	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665015	138665015	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002995-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	24	133	0	ENST00000330315.3:c.550G>C	p.Asp184His	p.D184H	ENST00000330315	NM_023067.3	184	Gac/Cac	1/1	0.245863553988141	3	FACETS	0.83	0.653	1	0.415	0.326	0.517	CLONAL	1	TRUE	1	0.245863553988141	3		133	264	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645036	86645036	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002995-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	54	276	0	ENST00000274376.6:c.1108C>G	p.Gln370Glu	p.Q370E	ENST00000274376	NM_002890.2	370	Caa/Gaa	8/25	0.188568560473337	4	FACETS	1	0.879	1	0.344	0.294	0.399	CLONAL	1	TRUE	1	0.245863553988141	4		276	530	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056399	180056399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002995-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	58	387	1	ENST00000261937.6:c.845G>A	p.Arg282Gln	p.R282Q	ENST00000261937	NM_182925.4	282	cGa/cAa	7/30	0.188568560473337	4	FACETS	0.856	0.734	0.988	0.285	0.244	0.33	CLONAL	1	TRUE	1	0.245863553988141	4		388	687	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158417	26158417	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs368384735	NA	P-0002995-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1467	133	805	0	ENST00000289316.2:c.20C>G	p.Ser7Cys	p.S7C	ENST00000289316	NM_138720.2	7	tCt/tGt	1/2	0.245863553988141	4	FACETS	0.842	0.762	0.928	0.281	0.254	0.31	CLONAL	1	TRUE	1	0.245863553988141	4		805	1600	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277102	38277102	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002995-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1265	106	485	0	ENST00000425967.3:c.1326G>C	p.Gln442His	p.Q442H	ENST00000425967	NM_001174067.1	442	caG/caC	10/19	0.245863553988141	8	FACETS	1	0.946	1			1	CLONAL	1	TRUE	NA	0.245863553988141	8		485	1371	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250386	110250386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752786911	NA	P-0002995-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	88	596	0	ENST00000374672.4:c.289G>A	p.Glu97Lys	p.E97K	ENST00000374672	NM_004235.4	97	Gag/Aag	3/5	0.244825606578528	2	FACETS	0.855	0.757	0.961	0.428	0.378	0.481	CLONAL	1	TRUE	0	0.245863553988141	2		596	837	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88672017	88672017	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1131691185	NA	P-0002995-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	88	470	0	ENST00000372037.3:c.551C>G	p.Ser184Ter	p.S184*	ENST00000372037	NM_004329.2	184	tCa/tGa	8/13	0.245863553988141	3	FACETS	0.892	0.789	1	0.446	0.394	0.502	CLONAL	1	TRUE	1	0.245863553988141	3		470	901	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795082	42795082	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002995-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1549	106	681	0	ENST00000575354.2:c.2162C>G	p.Ser721Cys	p.S721C	ENST00000575354	NM_015125.3	721	tCc/tGc	10/20	0.245863553988141	6	FACETS	0.777	0.694	0.867	0.259	0.231	0.289	SUBCLONAL	1	TRUE	3	0.245863553988141	6		681	1655	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223756	53223756	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002995-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	133	785	0	ENST00000375401.3:c.3603G>C	p.Gln1201His	p.Q1201H	ENST00000375401	NM_004187.3	1201	caG/caC	23/26	0.244825606578528	2	FACETS	0.976	0.884	1	0.488	0.442	0.536	CLONAL	1	TRUE	0	0.245863553988141	2		785	1109	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117311	115117311	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002995-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	139	366	0	ENST00000257566.3:c.863del	p.Lys288ArgfsTer2	p.K288Rfs*2	ENST00000257566	NM_016569.3	288	aAg/ag	4/8	0.228813909863786	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	1	0.245863553988141	3		366	603	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855965	68856011	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCCCCATACCAGAACCTCGAACTATATTCTTCTGTGAGAGGAATC	CGCCCCCATACCAGAACCTCGAACTATATTCTTCTGTGAGAGGAATC	-	novel	NA	P-0002995-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	260	592	1	ENST00000261769.5:c.1774_1820del	p.Ala592LysfsTer9	p.A592Kfs*9	ENST00000261769	NM_004360.3	591	aaCGCCCCCATACCAGAACCTCGAACTATATTCTTCTGTGAGAGGAATCca/aaca	12/16	0.236383112964681	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.245863553988141	2		593	959	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112438	115112438	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1423724888	NA	P-0003150-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	382	946	0	ENST00000257566.3:c.1302C>G	p.Asp434Glu	p.D434E	ENST00000257566	NM_016569.3	434	gaC/gaG	7/8	1	2	FACETS	0.882	0.838	0.926	0.882	0.838	0.926	CLONAL	1	TRUE	1	0.749357913347637	2		946	1156	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984265	7984265	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003150-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	407	851	0	ENST00000319144.4:c.464G>T	p.Ser155Ile	p.S155I	ENST00000319144	NM_001139.2	155	aGc/aTc	4/15	0.749357913347637	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.749357913347637	1		851	671	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003170-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	143	297	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.859	0.785	0.936	0.859	0.785	0.936	CLONAL	1	TRUE	1	0.509015252392308	2		297	654	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0003170-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2282	5728	654	4	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.509015252392308	37	FACETS	0.994	0.985	1			1	CLONAL	28	TRUE	NA	0.509015252392308	37		658	8010	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164648	47164648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757035494	NA	P-0003170-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	104	396	0	ENST00000409792.3:c.1478G>A	p.Arg493Gln	p.R493Q	ENST00000409792	NM_014159.6	493	cGg/cAg	3/21	1	2	FACETS	0.925	0.833	1	0.925	0.833	1	CLONAL	1	TRUE	1	0.509015252392308	2		396	442	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003195-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	239	830	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.641982861463686	5	FACETS	1	0.988	1	0.422	0.393	0.451	CLONAL	1	FALSE	2	0.732573095364173	5		830	1083	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410051	139410051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61755997	NA	P-0003195-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	631	691	5	ENST00000277541.6:c.1787C>T	p.Thr596Met	p.T596M	ENST00000277541	NM_017617.3	596	aCg/aTg	11/34	0.409765159770153	5	FACETS	0.953	0.921	0.985	0.953	0.921	0.985	INDETERMINATE	3	FALSE	2	0.732573095364173	5		696	1265	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106910	11106910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003195-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	223	733	1	ENST00000358026.2:c.1615C>T	p.Arg539Cys	p.R539C	ENST00000358026	NM_001128849.1	539	Cgc/Tgc	10/36	0.735057212538341	3	FACETS	0.838	0.78	0.897	0.419	0.39	0.449	CLONAL	1	FALSE	1	0.732573095364173	3		734	993	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911686	32911686	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs397507657	NA	P-0003195-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	624	554	0	ENST00000380152.3:c.3195del	p.Asn1066IlefsTer11	p.N1066Ifs*11	ENST00000380152		1065	aTt/at	11/27	0.716052877233896	3	FACETS	1	0.989	1			1	CLONAL	3	FALSE	NA	0.732573095364173	3		554	763	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16097831	16097837	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTGTT	CTTTGTT	-	novel	NA	P-0003195-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	366	543	0	ENST00000268712.3:c.47_53del	p.Glu16ValfsTer33	p.E16Vfs*33	ENST00000268712	NM_006311.3	16	gAACAAAGt/gt	2/46	0.735057212538341	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	FALSE	0	0.732573095364173	2		543	490	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115221	8115874	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCCAGGTAGAAGAGAGGCAACCGAAAGTTACTCAGTAGAACAGTACAGTCCTCATTTCTTCAAGGCAGACAGCCTTAACCACCTAGAGGCTGATGGCCTGGGGAGTACTTTTCAAGTTCTGAAGCAGATTTGTCAAAGTAGCCAAAATGGCATTTCCCTCCTGAAGATTCTTCACTACCTCGATTCTTATGAAATAGTCTAAGGAAGTTCTAAAGAAATAAGACAAGTGAATTCTATTTTCGTTACCAGAGAAATACAATCGTACTAGACGGGGCTGTAATCTGGTAACTGTATGTATTTTAGTTCTTCAGTCCCTGGGAAGGAGACAGGAGAAGGTGGGAGGGAGGAAGGGGCCAGCTGAAATGGAAACAGATCCCTGATCCGGGGCGGTCAGTGGAACCCTTCTTGGTGTGCGAGAGCCTGTGCATTTCAGAGGCAGCAAAAAAGTAAAAAAAAAAAAAAAAAATTGATCTTTGTTTAGATTAACAGACCCCTGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAGAACAGCTCGTTTAACCCGGCCGCCCTCTCCAGACACATGTCCTCCCTGAGCCACATCTC	GCCAGGTAGAAGAGAGGCAACCGAAAGTTACTCAGTAGAACAGTACAGTCCTCATTTCTTCAAGGCAGACAGCCTTAACCACCTAGAGGCTGATGGCCTGGGGAGTACTTTTCAAGTTCTGAAGCAGATTTGTCAAAGTAGCCAAAATGGCATTTCCCTCCTGAAGATTCTTCACTACCTCGATTCTTATGAAATAGTCTAAGGAAGTTCTAAAGAAATAAGACAAGTGAATTCTATTTTCGTTACCAGAGAAATACAATCGTACTAGACGGGGCTGTAATCTGGTAACTGTATGTATTTTAGTTCTTCAGTCCCTGGGAAGGAGACAGGAGAAGGTGGGAGGGAGGAAGGGGCCAGCTGAAATGGAAACAGATCCCTGATCCGGGGCGGTCAGTGGAACCCTTCTTGGTGTGCGAGAGCCTGTGCATTTCAGAGGCAGCAAAAAAGTAAAAAAAAAAAAAAAAAATTGATCTTTGTTTAGATTAACAGACCCCTGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAGAACAGCTCGTTTAACCCGGCCGCCCTCTCCAGACACATGTCCTCCCTGAGCCACATCTC	-	novel	NA	P-0003195-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	0	90	0	0	ENST00000346208.3:c.1048-478_1223del		p.X350_splice	ENST00000346208		350		6/6	0.735057212538341	5	FACETS		NA	1			1	NA	6	FALSE	NA	0.732573095364173	5		0	90	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158611	26158611	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003195-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	127	368	0	ENST00000289316.2:c.214G>C	p.Glu72Gln	p.E72Q	ENST00000289316	NM_138720.2	72	Gag/Cag	1/2	0.735057212538341	3	FACETS	1	0.971	1	0.572	0.523	0.623	CLONAL	1	FALSE	1	0.732573095364173	3		368	414	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003223-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	352	376	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.766759359578252	2		376	821	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912359	97912359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554302947	NA	P-0003223-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	296	528	0	ENST00000289081.3:c.532G>A	p.Glu178Lys	p.E178K	ENST00000289081	NM_000136.2	178	Gag/Aag	7/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.766759359578252	2		528	722	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857481	68857481	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003223-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	339	686	0	ENST00000261769.5:c.2116C>T	p.Gln706Ter	p.Q706*	ENST00000261769	NM_004360.3	706	Caa/Taa	13/16	0.766759359578252	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.766759359578252	1		686	545	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043412	6043412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1243546223	NA	P-0003223-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	18	64	0	ENST00000265849.7:c.262C>T	p.His88Tyr	p.H88Y	ENST00000265849	NM_000535.5	88	Cac/Tac	4/15	1	2	FACETS	0.594	0.458	0.747	0.594	0.458	0.747	SUBCLONAL	1	TRUE	1	0.766759359578252	2		64	79	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484597	57484597	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs137854533	NA	P-0003329-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	46	437	0	ENST00000371085.3:c.681G>T	p.Gln227His	p.Q227H	ENST00000371085	NM_000516.4	227	caG/caT	9/13	1	2	FACETS	0.515	0.432	0.608	0.515	0.432	0.608	SUBCLONAL	1	TRUE	1	0.21	2		437	850	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270138	66270138	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003329-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	67	630	0	ENST00000273854.3:c.1744G>A	p.Gly582Arg	p.G582R	ENST00000273854	NM_004439.5	582	Gga/Aga	8/18	1	2	FACETS	0.537	0.465	0.616	0.537	0.465	0.616	SUBCLONAL	1	TRUE	1	0.21	2		630	1188	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023858	27023858	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003329-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	22	230	0	ENST00000324856.7:c.964G>T	p.Asp322Tyr	p.D322Y	ENST00000324856	NM_006015.4	322	Gac/Tac	1/20	1	2	FACETS	0.525	0.406	0.664	0.525	0.406	0.664	SUBCLONAL	1	TRUE	1	0.21	2		230	399	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852473	63852473	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003329-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	61	580	0	ENST00000279873.7:c.3251G>A	p.Gly1084Glu	p.G1084E	ENST00000279873	NM_032199.2	1084	gGg/gAg	10/10	1	2	FACETS	0.629	0.541	0.725	0.629	0.541	0.725	SUBCLONAL	1	TRUE	1	0.21	2		580	924	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846326	156846326	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003329-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1274	58	682	0	ENST00000524377.1:c.1767T>G	p.Phe589Leu	p.F589L	ENST00000524377	NM_002529.3	589	ttT/ttG	14/17	1	2	FACETS	0.415	0.354	0.481	0.415	0.354	0.481	SUBCLONAL	1	TRUE	1	0.21	2		682	1332	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0003357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	29	510	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	1	2	FACETS	0.348	0.278	0.43	0.348	0.278	0.43	SUBCLONAL	1	TRUE	1	0.14	2		510	1189	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371785	55371785	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	23	205	0	ENST00000297316.4:c.475C>A	p.Leu159Met	p.L159M	ENST00000297316	NM_022454.3	159	Ctg/Atg	2/2	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.14	2		205	293	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0003544-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	528	722	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.814590394688205	2	FACETS	0.994	0.971	1	0.994	0.971	1	CLONAL	2	TRUE	0	0.814590394688205	2		722	652	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146667	185146667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003544-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	151	402	1	ENST00000265026.3:c.298G>A	p.Gly100Arg	p.G100R	ENST00000265026	NM_004721.4	100	Ggg/Agg	2/14	1	2	FACETS	0.519	0.475	0.565	0.519	0.475	0.565	SUBCLONAL	1	TRUE	1	0.814590394688205	2		403	714	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423360	116423360	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003544-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	101	213	0	ENST00000397752.3:c.3635T>G	p.Leu1212Arg	p.L1212R	ENST00000397752	NM_000245.2	1212	cTg/cGg	19/21	0.814590394688205	3	FACETS	0.556	0.497	0.618	0.278	0.248	0.309	SUBCLONAL	1	TRUE	1	0.814590394688205	3		213	628	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0003573-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	160	664	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.51736474824017	3	FACETS	0.817	0.749	0.888	0.408	0.374	0.444	CLONAL	1	TRUE	1	0.51736474824017	3		665	953	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0003573-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	368	396	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.51736474824017	3	FACETS	0.874	0.831	0.918	0.874	0.831	0.918	CLONAL	2	TRUE	1	0.51736474824017	3		396	1024	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0003573-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	105	638	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.839	0.755	0.926	0.839	0.755	0.926	CLONAL	1	TRUE	1	0.51736474824017	2		638	484	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201856	152201856	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003573-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	153	681	0	ENST00000206249.3:c.710G>A	p.Cys237Tyr	p.C237Y	ENST00000206249	NM_000125.3	237	tGc/tAc	3/8	0.412094291188242	1	FACETS	0.897	0.826	0.969	0.897	0.826	0.969	CLONAL	1	TRUE	0	0.51736474824017	1		681	489	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030398	49030398	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003573-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	79	776	0	ENST00000267163.4:c.1873A>G	p.Thr625Ala	p.T625A	ENST00000267163	NM_000321.2	625	Act/Gct	19/27	1	2	FACETS	0.407	0.358	0.461	0.407	0.358	0.461	SUBCLONAL	1	TRUE	1	0.51736474824017	2		776	750	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3113463	3113463	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003573-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	150	768	0	ENST00000078429.4:c.457C>G	p.Leu153Val	p.L153V	ENST00000078429	NM_002067.2	153	Ctc/Gtc	3/7	1	2	FACETS	0.826	0.757	0.898	0.826	0.757	0.898	CLONAL	1	TRUE	1	0.51736474824017	2		768	702	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226354	41226354	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs80356906	NA	P-0003573-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	169	828	0	ENST00000357654.3:c.4669G>C	p.Asp1557His	p.D1557H	ENST00000357654	NM_007294.3	1557	Gat/Cat	14/23	1	2	FACETS	0.707	0.65	0.767	0.707	0.65	0.767	SUBCLONAL	1	TRUE	1	0.51736474824017	2		828	924	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004211	150004212	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	TACCCGCATCATTTCATTCTCTAATTGTTTTTTACGATGTAGACGCTGCTGATGAGATTTGAG	novel	NA	P-0003573-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	27	530	0	ENST00000253339.5:c.1951_2010+3dup		p.X651_splice	ENST00000253339		651			0.412094291188242	1	FACETS	0.144	0.114	0.179	0.144	0.114	0.179	SUBCLONAL	1	TRUE	0	0.51736474824017	1		530	536	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0003580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	473	514	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.342094447009072	5	FACETS	0.926	0.889	0.963			1	INDETERMINATE	3	TRUE	NA	0.684061791318433	5		514	1009	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602493	10602493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	147	496	0	ENST00000171111.5:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000171111	NM_203500.1	362	cGg/cAg	3/6	0.684061791318433	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.684061791318433	1		496	271	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256532	115256532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267606920	NA	P-0003580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	269	774	1	ENST00000369535.4:c.179G>A	p.Gly60Glu	p.G60E	ENST00000369535	NM_002524.4	60	gGa/gAa	3/7	0.120186608236071	4	FACETS	0.871	0.821	0.923	0.871	0.821	0.923	INDETERMINATE	2	TRUE	2	0.684061791318433	4		775	760	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40467798	40467798	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	132	509	0	ENST00000264657.5:c.2278G>T	p.Glu760Ter	p.E760*	ENST00000264657	NM_139276.2	760	Gag/Tag	24/24	1	2	FACETS	0.841	0.769	0.915	0.841	0.769	0.915	CLONAL	1	TRUE	1	0.684061791318433	2		509	459	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604656	48604656	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	278	397	0	ENST00000342988.3:c.1478A>G	p.Asp493Gly	p.D493G	ENST00000342988	NM_005359.5	493	gAt/gGt	12/12	0.503469377319805	4	FACETS	0.891	0.857	0.924	1	0.993	1	CLONAL	4	TRUE	1	0.684061791318433	4		397	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577557	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGG	novel	NA	P-0003580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	399	600	0	ENST00000269305.4:c.722_724dup	p.Ser241dup	p.S241dup	ENST00000269305	NM_001126112.2	241	tgc/tCCTgc	7/11	NA	2	FACETS	0.989	0.955	1			1	INDETERMINATE	2	TRUE	NA	0.684061791318433	2		600	590	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551935	150551946	+	inframe_deletion	In_Frame_Del	DEL	GCCGGCCCCCAA	GCCGGCCCCCAA	-	rs779327179	NA	P-0003580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	52	500	0	ENST00000369026.2:c.61_72del	p.Leu21_Gly24del	p.L21_G24del	ENST00000369026	NM_021960.4	21	TTGGGGGCCGGC/-	1/3	0.503469377319805	4	FACETS	0.408	0.347	0.476	0.136	0.115	0.159	SUBCLONAL	1	TRUE	1	0.684061791318433	4		500	627	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169151	32169151	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	182	665	1	ENST00000375023.3:c.3882del	p.Ser1296ProfsTer8	p.S1296Pfs*8	ENST00000375023	NM_004557.3	1294	ggG/gg	22/30	0.21854372570096	2	FACETS	1	0.986	1	0.613	0.572	0.655	INDETERMINATE	1	TRUE	0	0.684061791318433	2		666	434	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003581-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	418	612	0	ENST00000206249.3:c.1607T>A	p.Leu536His	p.L536H	ENST00000206249	NM_000125.3	536	cTc/cAc	8/8	0.360958773953048	6	FACETS	0.878	0.837	0.919	0.659	0.628	0.69	CLONAL	3	TRUE	2	0.575777350351182	6		612	1186	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677925	58677948	+	inframe_deletion	In_Frame_Del	DEL	TCCGCGGCCGTCGCCGGCCGCCCT	TCCGCGGCCGTCGCCGGCCGCCCT	-	novel	NA	P-0003581-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	164	451	1	ENST00000305921.3:c.153_176del	p.Arg52_Pro59del	p.R52_P59del	ENST00000305921	NM_003620.3	50	ccTCCGCGGCCGTCGCCGGCCGCCCTt/cct	1/6	0.497563093985769	6	FACETS	0.94	0.866	1	0.47	0.433	0.508	CLONAL	2	TRUE	2	0.575777350351182	6		452	652	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111471	8111472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0003581-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	223	768	0	ENST00000346208.3:c.958dup	p.Cys320LeufsTer32	p.C320Lfs*32	ENST00000346208		319	-/T	5/6	0.575777350351182	3	FACETS	0.943	0.878	1	0.471	0.439	0.506	CLONAL	1	TRUE	1	0.575777350351182	3		768	1058	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151932962	151932962	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003581-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4	21	2	0	ENST00000262189.6:c.2709del	p.Arg904GlufsTer9	p.R904Efs*9	ENST00000262189	NM_170606.2	903	ggG/gg	16/59	0.573765814595419	3	FACETS	0.939	0.829	1	1	0.961	1	CLONAL	4	TRUE	1	0.575777350351182	3		2	25	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115922	8115923	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCG	novel	NA	P-0003581-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	137	603	0	ENST00000346208.3:c.1271_1274dup	p.Ser426AlafsTer82	p.S426Afs*82	ENST00000346208		423	cac/caCCCGc	6/6	0.575777350351182	3	FACETS	0.812	0.739	0.888	0.406	0.369	0.444	CLONAL	1	TRUE	1	0.575777350351182	3		603	755	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526125	63526125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199838262	NA	P-0003581-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1403	255	1015	1	ENST00000307078.5:c.2501G>A	p.Arg834Gln	p.R834Q	ENST00000307078	NM_004655.3	834	cGg/cAg	11/11	0.497563093985769	6	FACETS	1	0.982	1	0.287	0.268	0.308	CLONAL	1	TRUE	2	0.575777350351182	6		1016	1658	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003581-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	202	612	0	ENST00000206249.3:c.1607T>A	p.Leu536His	p.L536H	ENST00000206249	NM_000125.3	536	cTc/cAc	8/8	0.341017414684126	5	FACETS	1	0.984	1	0.795	0.739	0.852	CLONAL	2	TRUE	2	0.341017414684126	5		612	751	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677925	58677948	+	inframe_deletion	In_Frame_Del	DEL	TCCGCGGCCGTCGCCGGCCGCCCT	TCCGCGGCCGTCGCCGGCCGCCCT	-	novel	NA	P-0003581-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	44	451	1	ENST00000305921.3:c.153_176del	p.Arg52_Pro59del	p.R52_P59del	ENST00000305921	NM_003620.3	50	ccTCCGCGGCCGTCGCCGGCCGCCCTt/cct	1/6	0.187820795773208	5	FACETS	0.905	0.76	1	0.302	0.253	0.355	INDETERMINATE	1	TRUE	2	0.341017414684126	5		452	431	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111471	8111472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0003581-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	58	768	0	ENST00000346208.3:c.958dup	p.Cys320LeufsTer32	p.C320Lfs*32	ENST00000346208		319	-/T	5/6	0.338241059944497	3	FACETS	0.6	0.515	0.693	0.3	0.257	0.347	SUBCLONAL	1	TRUE	1	0.341017414684126	3		768	664	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115922	8115923	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCG	novel	NA	P-0003581-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	56	603	0	ENST00000346208.3:c.1271_1274dup	p.Ser426AlafsTer82	p.S426Afs*82	ENST00000346208		423	cac/caCCCGc	6/6	0.338241059944497	3	FACETS	0.788	0.676	0.91	0.394	0.338	0.455	CLONAL	1	TRUE	1	0.341017414684126	3		603	488	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526125	63526125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199838262	NA	P-0003581-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	114	1015	1	ENST00000307078.5:c.2501G>A	p.Arg834Gln	p.R834Q	ENST00000307078	NM_004655.3	834	cGg/cAg	11/11	0.187820795773208	5	FACETS	1	0.936	1	0.352	0.316	0.39	INDETERMINATE	1	TRUE	2	0.341017414684126	5		1016	957	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0003616-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	183	358	0	ENST00000374080.3:c.3670C>T	p.Leu1224Phe	p.L1224F	ENST00000374080		1224	Ctc/Ttc	26/45	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.635771204133597	1		358	296	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430562	80430562	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003616-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	181	422	0	ENST00000286548.4:c.446G>A	p.Arg149Gln	p.R149Q	ENST00000286548	NM_002072.3	149	cGa/cAa	3/7	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.635771204133597	2		422	521	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759985	63759985	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003616-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	119	301	0	ENST00000279873.7:c.638T>C	p.Ile213Thr	p.I213T	ENST00000279873	NM_032199.2	213	aTt/aCt	4/10	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.635771204133597	2		301	365	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266111	+	inframe_deletion	In_Frame_Del	DEL	TCTGGAATCCAT	TCTGGAATCCAT	-	novel	NA	P-0003616-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	99	319	0	ENST00000349496.5:c.102_113del	p.Ile35_Gly38del	p.I35_G38del	ENST00000349496	NM_001904.3	33	TCTGGAATCCAT/-	3/15	1	2	FACETS	0.916	0.826	1	0.916	0.826	1	CLONAL	1	TRUE	1	0.635771204133597	2		319	340	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891549	76891549	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0003616-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	140	226	1	ENST00000373344.5:c.4558-2A>T		p.X1520_splice	ENST00000373344	NM_000489.3	1520			1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.635771204133597	1		227	245	SUCCESS
ATR	545	MSKCC	GRCh37	3	142211980	142212001	+	frameshift_variant	Frame_Shift_Del	DEL	TTTTTTCATAATTGCATTGCTT	TTTTTTCATAATTGCATTGCTT	-	novel	NA	P-0003697-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	85	427	0	ENST00000350721.4:c.6051_6072del	p.Glu2017AspfsTer5	p.E2017Dfs*5	ENST00000350721	NM_001184.3	2017	gaAAGCAATGCAATTATGAAAAAA/ga	35/47	1	2	FACETS	0.298	0.263	0.335	0.298	0.263	0.335	SUBCLONAL	1	TRUE	1	0.963443203114772	2		427	592	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003866-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	246	577	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	0.770811201778183	2		577	614	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870839	12870840	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0003866-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	109	151	0	ENST00000228872.4:c.67dup	p.His23ProfsTer102	p.H23Pfs*102	ENST00000228872	NM_004064.3	22	-/C	1/3	0.770811201778183	1	FACETS	0.96	0.891	1	0.96	0.891	1	CLONAL	1	TRUE	0	0.770811201778183	1		151	181	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003866-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	252	460	0	ENST00000206249.3:c.1609T>C	p.Tyr537His	p.Y537H	ENST00000206249	NM_000125.3	537	Tat/Cat	8/8	0.770811201778183	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.770811201778183	1		460	375	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0003892-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	153	665	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.251536891601894	3	FACETS	1	0.983	1	0.436	0.398	0.475	CLONAL	1	TRUE	0	0.251536891601894	3		665	1048	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003892-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	134	444	1	ENST00000342988.3:c.1610A>T	p.Asp537Val	p.D537V	ENST00000342988	NM_005359.5	537	gAc/gTc	12/12	0.251536891601894	2	FACETS	0.854	0.778	0.933	0.854	0.778	0.933	CLONAL	2	TRUE	0	0.251536891601894	2		445	624	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0003892-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	121	444	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.183540970254567	3	FACETS	0.762	0.689	0.838	0.762	0.689	0.838	SUBCLONAL	2	TRUE	1	0.251536891601894	3		444	711	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668619	52668619	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003892-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	61	417	1	ENST00000394830.3:c.1300C>T	p.Arg434Ter	p.R434*	ENST00000394830	NM_018313.4	434	Cga/Tga	12/30	0.251536891601894	1	FACETS	0.752	0.649	0.864	0.752	0.649	0.864	SUBCLONAL	1	TRUE	0	0.251536891601894	1		418	564	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450646	70450646	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003892-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	74	590	0	ENST00000373644.4:c.5486A>T	p.Lys1829Ile	p.K1829I	ENST00000373644	NM_030625.2	1829	aAa/aTa	12/12	1	2	FACETS	0.689	0.602	0.783	0.689	0.602	0.783	SUBCLONAL	1	TRUE	1	0.251536891601894	2		590	854	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215582	5215582	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003892-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	60	449	1	ENST00000357368.4:c.4121C>T	p.Pro1374Leu	p.P1374L	ENST00000357368	NM_002850.3	1374	cCc/cTc	27/38	0.167613755902014	2	FACETS	0.649	0.558	0.748	0.325	0.279	0.374	SUBCLONAL	1	TRUE	0	0.251536891601894	2		450	735	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31472334	31472334	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003892-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	57	446	0	ENST00000344624.3:c.2077G>A	p.Gly693Arg	p.G693R	ENST00000344624		693	Gga/Aga	14/33	1	2	FACETS	0.676	0.58	0.782	0.676	0.58	0.782	SUBCLONAL	1	TRUE	1	0.251536891601894	2		446	670	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69011943	69011943	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003892-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	59	720	0	ENST00000288368.4:c.2580T>G	p.Asp860Glu	p.D860E	ENST00000288368	NM_024870.2	860	gaT/gaG	23/40	0.18955813388723	1	FACETS	0.44	0.377	0.508	0.44	0.377	0.508	SUBCLONAL	1	TRUE	0	0.251536891601894	1		720	933	SUCCESS
AR	367	MSKCC	GRCh37	X	66765246	66765246	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003892-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	43	387	0	ENST00000374690.3:c.258G>T	p.Gln86His	p.Q86H	ENST00000374690	NM_000044.3	86	caG/caT	1/8	0.251536891601894	1	FACETS	0.604	0.505	0.713	0.604	0.505	0.713	SUBCLONAL	1	TRUE	0	0.251536891601894	1		387	495	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004023-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	208	472	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.705830708791122	2	FACETS	0.769	0.726	0.812	0.769	0.726	0.812	SUBCLONAL	2	TRUE	0	0.705830708791122	2		472	383	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0004123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	138	628	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.2	2		628	927	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0004123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	76	664	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.176959630239437	4	FACETS	0.933	0.816	1	0.466	0.408	0.53	CLONAL	1	TRUE	2	0.2	4		665	978	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0004123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	95	396	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.176959630239437	4	FACETS	1	0.954	1	0.57	0.506	0.638	CLONAL	1	TRUE	2	0.2	4		396	1000	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921555	178921555	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	53	287	0	ENST00000263967.3:c.1037T>A	p.Val346Glu	p.V346E	ENST00000263967	NM_006218.2	346	gTa/gAa	5/21	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.2	2		287	527	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560422	95560422	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	192	965	0	ENST00000393063.1:c.5167G>T	p.Asp1723Tyr	p.D1723Y	ENST00000393063	NM_030621.3	1723	Gac/Tac	25/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		965	817	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490550	56490550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757680970	NA	P-0004163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	179	803	0	ENST00000267101.3:c.2194G>A	p.Gly732Ser	p.G732S	ENST00000267101	NM_001982.3	732	Ggt/Agt	19/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		803	920	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135804241	135804241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	162	640	0	ENST00000298552.3:c.19G>A	p.Val7Ile	p.V7I	ENST00000298552	NM_001162426.1	7	Gtc/Atc	3/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		640	644	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288749	33288749	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	325	335	0	ENST00000374542.5:c.803A>G	p.Asn268Ser	p.N268S	ENST00000374542	NM_001141970.1	268	aAc/aGc	3/8	0.865924777138414	1	FACETS	0.974	0.941	1	0.974	0.941	1	CLONAL	1	TRUE	0	0.865924777138414	1		335	437	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778800	76778800	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	318	333	0	ENST00000373344.5:c.6779A>G	p.His2260Arg	p.H2260R	ENST00000373344	NM_000489.3	2260	cAc/cGc	31/35	0.859118215082241	0	FACETS		NA	1			1	NA	1	TRUE	NA	0.865924777138414	0		333	439	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573786	64573786	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1114167541	NA	P-0004185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	499	551	0	ENST00000312049.6:c.967del	p.Tyr323ThrfsTer45	p.Y323Tfs*45	ENST00000312049	NM_130799.2	323	Tac/ac	7/10	0.865924777138414	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.865924777138414	1		551	648	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108877	2108877	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	C	rs1131692179	NA	P-0004185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	464	499	0	ENST00000219476.3:c.975+3A>C		p.X325_splice	ENST00000219476	NM_000548.3	325			0.865924777138414	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.865924777138414	1		499	593	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398262	25398262	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913538	NA	P-0004226-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	296	621	0	ENST00000311936.3:c.57G>C	p.Leu19Phe	p.L19F	ENST00000311936	NM_004985.3	19	ttG/ttC	2/5	1	2	FACETS	0.898	0.849	0.948	0.898	0.849	0.948	CLONAL	1	TRUE	1	0.807206698527804	2		621	817	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004226-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	148	297	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.807206698527804	2		297	337	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0004226-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	305	514	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.917	0.868	0.967	0.917	0.868	0.967	CLONAL	1	TRUE	1	0.807206698527804	2		514	824	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158626	26158626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772836222	NA	P-0004226-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	117	188	1	ENST00000289316.2:c.229G>A	p.Glu77Lys	p.E77K	ENST00000289316	NM_138720.2	77	Gag/Aag	1/2	1	2	FACETS	0.833	0.76	0.908	0.833	0.76	0.908	CLONAL	1	TRUE	1	0.807206698527804	2		189	348	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645693	12645693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397516827	NA	P-0004226-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	161	245	0	ENST00000251849.4:c.776C>T	p.Ser259Phe	p.S259F	ENST00000251849	NM_002880.3	259	tCc/tTc	7/17	1	2	FACETS	0.95	0.881	1	0.95	0.881	1	CLONAL	1	TRUE	1	0.807206698527804	2		245	420	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230772	46230772	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004226-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	131	283	0	ENST00000334344.6:c.1021G>C	p.Glu341Gln	p.E341Q	ENST00000334344	NM_152641.2	341	Gag/Cag	8/21	1	2	FACETS	0.856	0.786	0.929	0.856	0.786	0.929	CLONAL	1	TRUE	1	0.807206698527804	2		283	379	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588849	69588849	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004226-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	255	550	0	ENST00000168712.1:c.387C>A	p.Phe129Leu	p.F129L	ENST00000168712	NM_002007.2	129	ttC/ttA	2/3	0.790798042066882	4	FACETS	0.903	0.844	0.964	0.301	0.281	0.322	CLONAL	1	TRUE	1	0.807206698527804	4		550	1265	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0004288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	590	397	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	NA	2	FACETS	0.903	0.877	0.929			1	INDETERMINATE	3	TRUE	NA	0.489823817957021	2		397	889	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913499	NA	P-0004288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	158	243	0	ENST00000345146.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000345146	NM_005896.2	132	Cgt/Ggt	4/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.489823817957021	2		243	507	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881488	48881489	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0004288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	146	250	1	ENST00000267163.4:c.219_220dup	p.Ala74GlufsTer4	p.A74Efs*4	ENST00000267163	NM_000321.2	70	-/AG	2/27	0.489823817957021	1	FACETS	0.867	0.796	0.941	0.867	0.796	0.941	CLONAL	1	TRUE	0	0.489823817957021	1		251	519	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061341	38061341	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	169	507	0	ENST00000250448.2:c.648C>A	p.Asn216Lys	p.N216K	ENST00000250448	NM_004496.3	216	aaC/aaA	2/2	1	2	FACETS	0.809	0.744	0.876	0.809	0.744	0.876	CLONAL	1	TRUE	1	0.489823817957021	2		507	853	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524590	187524590	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1560924328	NA	P-0004288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	135	507	0	ENST00000441802.2:c.11090T>C	p.Phe3697Ser	p.F3697S	ENST00000441802	NM_005245.3	3697	tTt/tCt	19/27	1	2	FACETS	0.501	0.454	0.55	0.501	0.454	0.55	SUBCLONAL	1	TRUE	1	0.489823817957021	2		507	1101	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005020	150005020	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	90	308	0	ENST00000253339.5:c.1205del	p.Asn402MetfsTer8	p.N402Mfs*8	ENST00000253339		402	aAt/at	3/7	0.701266677040717	1	FACETS	0.397	0.354	0.442	0.397	0.354	0.442	SUBCLONAL	1	TRUE	0	0.701266677040717	1		308	420	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203629	108203629	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0004308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	139	172	1	ENST00000278616.4:c.7927+2T>A		p.X2643_splice	ENST00000278616	NM_000051.3	2643			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.701266677040717	2		173	373	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0004314-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	151	336	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.215152746739714	5	FACETS	1	0.986	1	0.479	0.437	0.523	CLONAL	1	TRUE	2	0.263381869894726	5		336	1114	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004314-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	178	472	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.224938046524262	4	FACETS	0.781	0.719	0.846	0.781	0.719	0.846	SUBCLONAL	2	TRUE	2	0.263381869894726	4		472	1093	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434825	99434825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398752572	NA	P-0004314-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	74	479	0	ENST00000268035.6:c.912G>A	p.Met304Ile	p.M304I	ENST00000268035	NM_000875.3	304	atG/atA	3/21	0.212248746423219	4	FACETS	0.843	0.737	0.958	0.281	0.245	0.32	CLONAL	1	TRUE	1	0.263381869894726	4		479	842	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112449	115112450	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004314-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	217	681	0	ENST00000257566.3:c.1290dup	p.Ala431SerfsTer8	p.A431Sfs*8	ENST00000257566	NM_016569.3	430	-/A	7/8	0.263381869894726	5	FACETS	0.94	0.872	1	0.94	0.872	1	CLONAL	2	TRUE	3	0.263381869894726	5		681	1223	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248589	59248590	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCAC	novel	NA	P-0004314-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	111	893	0	ENST00000371222.2:c.153_154insGTGGG	p.His52ValfsTer30	p.H52Vfs*30	ENST00000371222	NM_002228.3	51	-/GTGGG	1/1	0.263381869894726	3	FACETS	0.741	0.664	0.823	0.371	0.332	0.412	SUBCLONAL	1	TRUE	1	0.263381869894726	3		893	1287	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750460	57750461	+	stop_gained	Nonsense_Mutation	DNP	TT	TT	AA	novel	NA	P-0004314-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	74	642	1	ENST00000274289.3:c.2007_2008inv	p.Leu669_Lys670delinsPheTer	p.L669_K670delinsF*	ENST00000274289	NM_006622.3	669	ttAAaa/ttTTaa	14/14	0.215152746739714	5	FACETS	0.631	0.55	0.719	0.21	0.183	0.24	SUBCLONAL	1	TRUE	2	0.263381869894726	5		643	1242	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115731	8115732	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004314-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1215	108	835	0	ENST00000346208.3:c.1079dup	p.Ile361HisfsTer10	p.I361Hfs*10	ENST00000346208		359	-/G	6/6	0.263381869894726	3	FACETS	0.702	0.627	0.781	0.351	0.313	0.391	SUBCLONAL	1	TRUE	1	0.263381869894726	3		835	1323	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112641	115112641	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0004314-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1579	403	1027	0	ENST00000257566.3:c.1100-1G>A		p.X367_splice	ENST00000257566	NM_016569.3	367			0.263381869894726	5	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	3	0.263381869894726	5		1027	1982	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	126	775	1	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.841	0.766	0.919	0.841	0.766	0.919	CLONAL	1	TRUE	1	0.615380889348864	2		776	487	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	55	859	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.445	0.381	0.513	0.445	0.381	0.513	SUBCLONAL	1	TRUE	1	0.615380889348864	2		859	402	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520465	176520465	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61737768	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	78	1352	1	ENST00000292408.4:c.1310G>A	p.Arg437His	p.R437H	ENST00000292408	NM_213647.1	437	cGt/cAt	10/18	0.271351988722077	1	FACETS	0.341	0.3	0.385	0.341	0.3	0.385	INDETERMINATE	1	TRUE	0	0.615380889348864	1		1353	514	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252086	133252086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778572159	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	143	887	0	ENST00000320574.5:c.1124G>A	p.Arg375Gln	p.R375Q	ENST00000320574	NM_006231.2	375	cGg/cAg	12/49	0.271351988722077	1	FACETS	0.675	0.619	0.731	0.675	0.619	0.731	INDETERMINATE	1	TRUE	0	0.615380889348864	1		887	477	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	106	776	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	0.826	0.746	0.91	0.826	0.746	0.91	CLONAL	1	TRUE	1	0.615380889348864	2		776	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	68	848	2	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	0.515164409152092	1	FACETS	0.484	0.424	0.548	0.484	0.424	0.548	SUBCLONAL	1	TRUE	0	0.615380889348864	1		850	316	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	94	760	4	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.615380889348864	2		764	293	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163503	32163505	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	75	846	0	ENST00000375023.3:c.5721_5723del	p.Gly1908del	p.G1908del	ENST00000375023	NM_004557.3	1907	ggAGGc/ggc	30/30	1	2	FACETS	0.741	0.654	0.832	0.741	0.654	0.832	SUBCLONAL	1	TRUE	1	0.615380889348864	2		846	329	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061412	38061412	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1310740071	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	138	881	0	ENST00000250448.2:c.577C>G	p.Leu193Val	p.L193V	ENST00000250448	NM_004496.3	193	Ctg/Gtg	2/2	1	2	FACETS	0.988	0.906	1	0.988	0.906	1	CLONAL	1	TRUE	1	0.615380889348864	2		881	454	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046958	128046958	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs772883177	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	182	970	1	ENST00000285398.2:c.777A>T	p.Glu259Asp	p.E259D	ENST00000285398	NM_000122.1	259	gaA/gaT	6/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.615380889348864	2		971	549	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733513	85733513	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs387906350	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	61	777	2	ENST00000370580.1:c.499del	p.Ser167LeufsTer6	p.S167Lfs*6	ENST00000370580	NM_003921.4	167	Tct/ct	3/3	1	2	FACETS	0.446	0.385	0.511	0.446	0.385	0.511	SUBCLONAL	1	TRUE	1	0.615380889348864	2		779	445	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155721	56155722	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	31	590	0	ENST00000399503.3:c.816_817del	p.Arg273SerfsTer27	p.R273Sfs*27	ENST00000399503	NM_005921.1	271	agAAaa/agaa	3/20	1	2	FACETS	0.285	0.231	0.347	0.285	0.231	0.347	SUBCLONAL	1	TRUE	1	0.615380889348864	2		590	353	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928373	69928373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770693882	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	43	587	1	ENST00000352241.4:c.193C>T	p.Arg65Cys	p.R65C	ENST00000352241	NM_198159.2	65	Cgt/Tgt	2/10	1	2	FACETS	0.485	0.408	0.57	0.485	0.408	0.57	SUBCLONAL	1	TRUE	1	0.615380889348864	2		588	288	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966159	25966159	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747070149	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	145	931	0	ENST00000435504.4:c.3047C>T	p.Thr1016Met	p.T1016M	ENST00000435504		1016	aCg/aTg	13/13	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.615380889348864	2		931	450	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217557	142217557	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1268253442	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	73	861	3	ENST00000350721.4:c.5440del	p.Arg1814GlufsTer10	p.R1814Efs*10	ENST00000350721	NM_001184.3	1814	Aga/ga	32/47	1	2	FACETS	0.465	0.407	0.527	0.465	0.407	0.527	SUBCLONAL	1	TRUE	1	0.615380889348864	2		864	510	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099253	4099255	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs763469132	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	144	1195	0	ENST00000262948.5:c.863_865del	p.Glu288del	p.E288del	ENST00000262948	NM_030662.3	288	gAAGga/gga	7/11	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.615380889348864	2		1195	459	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748502	162748502	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1218815846	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	77	549	0	ENST00000367921.3:c.2416C>T	p.Arg806Ter	p.R806*	ENST00000367921	NM_006182.2	806	Cga/Tga	17/18	1	2	FACETS	0.863	0.766	0.965	0.863	0.766	0.965	CLONAL	1	TRUE	1	0.615380889348864	2		549	290	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274018	10274018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1354238435	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	80	1184	0	ENST00000330684.3:c.251C>T	p.Thr84Met	p.T84M	ENST00000330684	NM_001134407.1	84	aCg/aTg	2/13	1	2	FACETS	0.562	0.496	0.631	0.562	0.496	0.631	SUBCLONAL	1	TRUE	1	0.615380889348864	2		1184	463	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119447	193119447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762716583	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	70	609	0	ENST00000367435.3:c.842G>A	p.Arg281His	p.R281H	ENST00000367435	NM_024529.4	281	cGc/cAc	9/17	1	2	FACETS	0.567	0.497	0.643	0.567	0.497	0.643	SUBCLONAL	1	TRUE	1	0.615380889348864	2		609	401	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650845	37650845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	107	1117	1	ENST00000447079.4:c.2317C>T	p.Arg773Cys	p.R773C	ENST00000447079	NM_015083.1	773	Cgt/Tgt	5/14	1	2	FACETS	0.546	0.49	0.605	0.546	0.49	0.605	SUBCLONAL	1	TRUE	1	0.615380889348864	2		1118	637	SUCCESS
RET	5979	MSKCC	GRCh37	10	43598017	43598017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1210452561	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	80	1066	2	ENST00000355710.3:c.565C>T	p.Arg189Cys	p.R189C	ENST00000355710	NM_020975.4	189	Cgc/Tgc	3/20	1	2	FACETS	0.603	0.533	0.678	0.603	0.533	0.678	SUBCLONAL	1	TRUE	1	0.615380889348864	2		1068	431	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825519	50825519	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	50	813	4	ENST00000398568.2:c.2156del	p.Asn719MetfsTer13	p.N719Mfs*13	ENST00000398568	NM_001042412.1	717	gAa/ga	14/18	1	2	FACETS	0.371	0.315	0.432	0.371	0.315	0.432	SUBCLONAL	1	TRUE	1	0.615380889348864	2		817	438	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240767	55240767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770193776	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	61	1215	1	ENST00000275493.2:c.2011C>T	p.Arg671Cys	p.R671C	ENST00000275493	NM_005228.3	671	Cgc/Tgc	17/28	1	2	FACETS	0.386	0.333	0.443	0.386	0.333	0.443	SUBCLONAL	1	TRUE	1	0.615380889348864	2		1216	514	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141545617	141545617	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	73	1356	0	ENST00000220592.5:c.2221A>G	p.Thr741Ala	p.T741A	ENST00000220592	NM_012154.3	741	Acc/Gcc	17/19	1	2	FACETS	0.379	0.331	0.43	0.379	0.331	0.43	SUBCLONAL	1	TRUE	1	0.615380889348864	2		1356	626	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387390	17387390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200016717	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	51	1230	1	ENST00000359435.4:c.656G>A	p.Arg219His	p.R219H	ENST00000359435	NM_001033549.1	219	cGt/cAt	7/9	1	2	FACETS	0.297	0.252	0.346	0.297	0.252	0.346	SUBCLONAL	1	TRUE	1	0.615380889348864	2		1231	559	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226576366	226576366	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	127	1011	1	ENST00000366794.5:c.708del	p.Ala237ProfsTer2	p.A237Pfs*2	ENST00000366794	NM_001618.3	236	aaA/aa	5/23	1	2	FACETS	0.895	0.817	0.977	0.895	0.817	0.977	CLONAL	1	TRUE	1	0.615380889348864	2		1012	461	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280136	142280136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369434236	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	107	936	0	ENST00000350721.4:c.1298G>A	p.Arg433His	p.R433H	ENST00000350721	NM_001184.3	433	cGt/cAt	5/47	1	2	FACETS	0.577	0.518	0.638	0.577	0.518	0.638	SUBCLONAL	1	TRUE	1	0.615380889348864	2		936	603	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794469	42794469	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	58	1205	3	ENST00000575354.2:c.1553del	p.Pro518ArgfsTer5	p.P518Rfs*5	ENST00000575354	NM_015125.3	517	Ccc/cc	10/20	1	2	FACETS	0.335	0.287	0.386	0.335	0.287	0.386	SUBCLONAL	1	TRUE	1	0.615380889348864	2		1208	563	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109313997	109313997	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772956928	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	63	673	1	ENST00000436639.2:c.1226G>A	p.Arg409His	p.R409H	ENST00000436639	NM_014454.2	409	cGt/cAt	7/10	1	2	FACETS	0.569	0.494	0.649	0.569	0.494	0.649	SUBCLONAL	1	TRUE	1	0.615380889348864	2		674	360	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184567	11184567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	82	947	1	ENST00000361445.4:c.6650G>A	p.Arg2217Gln	p.R2217Q	ENST00000361445	NM_004958.3	2217	cGg/cAg	47/58	1	2	FACETS	0.534	0.472	0.6	0.534	0.472	0.6	SUBCLONAL	1	TRUE	1	0.615380889348864	2		948	499	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937866	36937866	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	85	1355	0	ENST00000361632.4:c.970A>G	p.Ser324Gly	p.S324G	ENST00000361632		324	Agc/Ggc	7/16	1	2	FACETS	0.531	0.471	0.596	0.531	0.471	0.596	SUBCLONAL	1	TRUE	1	0.615380889348864	2		1355	520	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136031	64136031	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	76	1058	3	ENST00000334205.4:c.1292G>A	p.Arg431His	p.R431H	ENST00000334205	NM_003942.2	431	cGc/cAc	11/17	1	2	FACETS	0.592	0.522	0.667	0.592	0.522	0.667	SUBCLONAL	1	TRUE	1	0.615380889348864	2		1061	417	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149290	119149290	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140627020	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	32	887	0	ENST00000264033.4:c.1298C>T	p.Pro433Leu	p.P433L	ENST00000264033	NM_005188.3	433	cCg/cTg	9/16	1	2	FACETS	0.21	0.17	0.255	0.21	0.17	0.255	SUBCLONAL	1	TRUE	1	0.615380889348864	2		887	496	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427983	49427983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866777837	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	78	943	1	ENST00000301067.7:c.10607G>A	p.Arg3536His	p.R3536H	ENST00000301067	NM_003482.3	3536	cGc/cAc	38/54	1	2	FACETS	0.543	0.478	0.611	0.543	0.478	0.611	SUBCLONAL	1	TRUE	1	0.615380889348864	2		944	467	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435063	49435063	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	32	755	0	ENST00000301067.7:c.6490C>A	p.Pro2164Thr	p.P2164T	ENST00000301067	NM_003482.3	2164	Cca/Aca	31/54	1	2	FACETS	0.319	0.259	0.386	0.319	0.259	0.386	SUBCLONAL	1	TRUE	1	0.615380889348864	2		755	326	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856595	111856595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1454335466	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	37	369	1	ENST00000341259.2:c.646C>T	p.Arg216Cys	p.R216C	ENST00000341259	NM_005475.2	216	Cgc/Tgc	2/8	1	2	FACETS	0.699	0.584	0.824	0.699	0.584	0.824	SUBCLONAL	1	TRUE	1	0.615380889348864	2		370	172	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95579448	95579448	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	52	568	0	ENST00000393063.1:c.2021C>A	p.Pro674His	p.P674H	ENST00000393063	NM_030621.3	674	cCt/cAt	13/28	1	2	FACETS	0.506	0.433	0.585	0.506	0.433	0.585	SUBCLONAL	1	TRUE	1	0.615380889348864	2		568	334	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021365	42021365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs984878518	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	109	576	0	ENST00000219905.7:c.3661C>T	p.Arg1221Trp	p.R1221W	ENST00000219905	NM_001164273.1	1221	Cgg/Tgg	11/24	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.615380889348864	2		576	296	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632584	3632584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372921011	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	27	1166	3	ENST00000294008.3:c.5264C>T	p.Ala1755Val	p.A1755V	ENST00000294008	NM_032444.2	1755	gCg/gTg	15/15	1	2	FACETS	0.178	0.141	0.221	0.178	0.141	0.221	SUBCLONAL	1	TRUE	1	0.615380889348864	2		1169	492	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892147	9892147	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	52	787	0	ENST00000330684.3:c.2343del	p.Gln781HisfsTer27	p.Q781Hfs*27	ENST00000330684	NM_001134407.1	781	caG/ca	11/13	1	2	FACETS	0.425	0.362	0.493	0.425	0.362	0.493	SUBCLONAL	1	TRUE	1	0.615380889348864	2		787	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578199	7578199	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	62	1035	1	ENST00000269305.4:c.650T>C	p.Val217Ala	p.V217A	ENST00000269305	NM_001126112.2	217	gTg/gCg	6/11	0.515164409152092	1	FACETS	0.379	0.329	0.433	0.379	0.329	0.433	SUBCLONAL	1	TRUE	0	0.615380889348864	1		1036	368	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024413	16024413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749634427	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	35	550	2	ENST00000268712.3:c.1805C>T	p.Ala602Val	p.A602V	ENST00000268712	NM_006311.3	602	gCg/gTg	16/46	1	2	FACETS	0.395	0.325	0.473	0.395	0.325	0.473	SUBCLONAL	1	TRUE	1	0.615380889348864	2		552	288	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16097814	16097814	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	87	910	0	ENST00000268712.3:c.70T>G	p.Ser24Ala	p.S24A	ENST00000268712	NM_006311.3	24	Tct/Gct	2/46	1	2	FACETS	0.468	0.415	0.525	0.468	0.415	0.525	SUBCLONAL	1	TRUE	1	0.615380889348864	2		910	604	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099324	4099324	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1377552828	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	32	1259	0	ENST00000262948.5:c.794A>G	p.Tyr265Cys	p.Y265C	ENST00000262948	NM_030662.3	265	tAc/tGc	7/11	1	2	FACETS	0.202	0.164	0.246	0.202	0.164	0.246	SUBCLONAL	1	TRUE	1	0.615380889348864	2		1259	514	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610129	10610129	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	29	1060	0	ENST00000171111.5:c.581T>C	p.Ile194Thr	p.I194T	ENST00000171111	NM_203500.1	194	aTt/aCt	2/6	1	2	FACETS	0.178	0.142	0.219	0.178	0.142	0.219	SUBCLONAL	1	TRUE	1	0.615380889348864	2		1060	530	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215632	36215632	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	50	898	0	ENST00000222270.7:c.3429G>T	p.Lys1143Asn	p.K1143N	ENST00000222270	NM_014727.1	1143	aaG/aaT	9/37	1	2	FACETS	0.432	0.368	0.503	0.432	0.368	0.503	SUBCLONAL	1	TRUE	1	0.615380889348864	2		898	376	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905061	50905061	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs754917939	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	48	853	1	ENST00000440232.2:c.343C>G	p.Pro115Ala	p.P115A	ENST00000440232	NM_002691.3	115	Ccc/Gcc	4/27	1	2	FACETS	0.462	0.392	0.538	0.462	0.392	0.538	SUBCLONAL	1	TRUE	1	0.615380889348864	2		854	338	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920514	50920514	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	44	816	0	ENST00000440232.2:c.3206T>C	p.Val1069Ala	p.V1069A	ENST00000440232	NM_002691.3	1069	gTc/gCc	26/27	1	2	FACETS	0.451	0.38	0.529	0.451	0.38	0.529	SUBCLONAL	1	TRUE	1	0.615380889348864	2		816	317	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416263	29416263	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	71	823	0	ENST00000389048.3:c.4690G>T	p.Ala1564Ser	p.A1564S	ENST00000389048	NM_004304.4	1564	Gcc/Tcc	29/29	1	2	FACETS	0.543	0.476	0.615	0.543	0.476	0.615	SUBCLONAL	1	TRUE	1	0.615380889348864	2		823	425	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574083	46574083	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	63	1126	0	ENST00000263734.3:c.98T>C	p.Val33Ala	p.V33A	ENST00000263734	NM_001430.4	33	gTg/gCg	2/16	0.615380889348864	1	FACETS	0.416	0.361	0.474	0.416	0.361	0.474	SUBCLONAL	1	TRUE	0	0.615380889348864	1		1126	341	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026788	48026788	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060502895	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	17	697	0	ENST00000234420.5:c.1666T>C	p.Tyr556His	p.Y556H	ENST00000234420	NM_000179.2	556	Tat/Cat	4/10	0.615380889348864	1	FACETS	0.131	0.097	0.171	0.131	0.097	0.171	SUBCLONAL	1	TRUE	0	0.615380889348864	1		697	292	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61709534	61709534	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	24	631	2	ENST00000401558.2:c.2953G>A	p.Ala985Thr	p.A985T	ENST00000401558	NM_003400.3	985	Gcc/Acc	23/25	1	2	FACETS	0.202	0.158	0.252	0.202	0.158	0.252	SUBCLONAL	1	TRUE	1	0.615380889348864	2		633	387	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61725896	61725896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	92	841	0	ENST00000401558.2:c.671C>T	p.Ala224Val	p.A224V	ENST00000401558	NM_003400.3	224	gCa/gTa	9/25	1	2	FACETS	0.535	0.476	0.597	0.535	0.476	0.597	SUBCLONAL	1	TRUE	1	0.615380889348864	2		841	559	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156077	99156077	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs966111733	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	63	913	1	ENST00000074304.5:c.757G>A	p.Val253Met	p.V253M	ENST00000074304	NM_001134224.1	253	Gtg/Atg	10/26	1	2	FACETS	0.484	0.42	0.553	0.484	0.42	0.553	SUBCLONAL	1	TRUE	1	0.615380889348864	2		914	423	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99181121	99181121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749167994	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	78	910	1	ENST00000074304.5:c.2062G>A	p.Gly688Ser	p.G688S	ENST00000074304	NM_001134224.1	688	Ggc/Agc	20/26	1	2	FACETS	0.513	0.452	0.578	0.513	0.452	0.578	SUBCLONAL	1	TRUE	1	0.615380889348864	2		911	494	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99185035	99185035	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	19	580	0	ENST00000074304.5:c.2437T>C	p.Phe813Leu	p.F813L	ENST00000074304	NM_001134224.1	813	Ttt/Ctt	23/26	1	2	FACETS	0.189	0.143	0.243	0.189	0.143	0.243	SUBCLONAL	1	TRUE	1	0.615380889348864	2		580	327	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046269	128046269	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	65	810	0	ENST00000285398.2:c.994C>T	p.Arg332Cys	p.R332C	ENST00000285398	NM_000122.1	332	Cgt/Tgt	7/15	1	2	FACETS	0.486	0.422	0.554	0.486	0.422	0.554	SUBCLONAL	1	TRUE	1	0.615380889348864	2		810	435	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225400301	225400301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	50	516	0	ENST00000264414.4:c.322G>A	p.Ala108Thr	p.A108T	ENST00000264414	NM_003590.4	108	Gct/Act	3/16	1	2	FACETS	0.45	0.383	0.523	0.45	0.383	0.523	SUBCLONAL	1	TRUE	1	0.615380889348864	2		516	361	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281255	46281255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781251226	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	112	654	0	ENST00000371998.3:c.4052C>T	p.Pro1351Leu	p.P1351L	ENST00000371998		1351	cCg/cTg	21/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.615380889348864	2		654	311	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42851147	42851147	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1306263181	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	120	918	0	ENST00000398585.3:c.746T>C	p.Leu249Pro	p.L249P	ENST00000398585	NM_001135099.1	249	cTg/cCg	7/14	1	2	FACETS	0.647	0.586	0.711	0.647	0.586	0.711	SUBCLONAL	1	TRUE	1	0.615380889348864	2		918	603	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806162	1806162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747694886	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	71	1338	7	ENST00000260795.2:c.1181C>T	p.Thr394Met	p.T394M	ENST00000260795		394	aCg/aTg	8/17	1	2	FACETS	0.473	0.413	0.537	0.473	0.413	0.537	SUBCLONAL	1	TRUE	1	0.615380889348864	2		1345	488	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984792	55984792	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437960932	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	69	766	1	ENST00000263923.4:c.337G>A	p.Val113Ile	p.V113I	ENST00000263923	NM_002253.2	113	Gtc/Atc	3/30	1	2	FACETS	0.496	0.433	0.564	0.496	0.433	0.564	SUBCLONAL	1	TRUE	1	0.615380889348864	2		767	452	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161662	56161662	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	100	671	0	ENST00000399503.3:c.1159A>C	p.Ser387Arg	p.S387R	ENST00000399503	NM_005921.1	387	Agt/Cgt	6/20	1	2	FACETS	0.81	0.729	0.895	0.81	0.729	0.895	CLONAL	1	TRUE	1	0.615380889348864	2		671	401	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751606	57751606	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	12	379	0	ENST00000274289.3:c.1385G>A	p.Cys462Tyr	p.C462Y	ENST00000274289	NM_006622.3	462	tGc/tAc	11/14	1	2	FACETS	0.187	0.131	0.255	0.187	0.131	0.255	SUBCLONAL	1	TRUE	1	0.615380889348864	2		379	209	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449812	149449812	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	99	1238	1	ENST00000286301.3:c.1252T>A	p.Leu418Met	p.L418M	ENST00000286301	NM_005211.3	418	Ttg/Atg	9/22	0.271351988722077	1	FACETS	0.439	0.393	0.488	0.439	0.393	0.488	INDETERMINATE	1	TRUE	0	0.615380889348864	1		1239	507	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149450136	149450136	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	92	1207	0	ENST00000286301.3:c.1083-2A>G		p.X361_splice	ENST00000286301	NM_005211.3	361			0.271351988722077	1	FACETS	0.411	0.366	0.458	0.411	0.366	0.458	INDETERMINATE	1	TRUE	0	0.615380889348864	1		1207	504	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858455	27858455	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	75	652	1	ENST00000359303.2:c.116C>T	p.Pro39Leu	p.P39L	ENST00000359303	NM_003535.2	39	cCc/cTc	1/1	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.615380889348864	2		653	240	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793767	89793767	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	66	735	0	ENST00000336032.3:c.836A>G	p.Tyr279Cys	p.Y279C	ENST00000336032	NM_006813.2	279	tAt/tGt	2/2	1	2	FACETS	0.491	0.427	0.559	0.491	0.427	0.559	SUBCLONAL	1	TRUE	1	0.615380889348864	2		735	437	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553313	106553313	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	108	738	0	ENST00000369096.4:c.1278C>A	p.Ser426Arg	p.S426R	ENST00000369096	NM_001198.3	426	agC/agA	5/7	1	2	FACETS	0.978	0.886	1	0.978	0.886	1	CLONAL	1	TRUE	1	0.615380889348864	2		738	359	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975519	13975519	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	21	367	0	ENST00000405192.2:c.368C>G	p.Ala123Gly	p.A123G	ENST00000405192	NM_001163147.1	123	gCc/gGc	7/12	1	2	FACETS	0.32	0.247	0.405	0.32	0.247	0.405	SUBCLONAL	1	TRUE	1	0.615380889348864	2		367	213	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884406	151884406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	76	596	1	ENST00000262189.6:c.4949C>T	p.Thr1650Ile	p.T1650I	ENST00000262189	NM_170606.2	1650	aCt/aTt	33/59	1	2	FACETS	0.632	0.557	0.711	0.632	0.557	0.711	SUBCLONAL	1	TRUE	1	0.615380889348864	2		597	391	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371911	55371911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1310843210	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	75	686	2	ENST00000297316.4:c.601G>A	p.Gly201Ser	p.G201S	ENST00000297316	NM_022454.3	201	Ggc/Agc	2/2	1	2	FACETS	0.821	0.726	0.92	0.821	0.726	0.92	CLONAL	1	TRUE	1	0.615380889348864	2		688	297	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413945	139413945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	88	1238	1	ENST00000277541.6:c.815G>A	p.Cys272Tyr	p.C272Y	ENST00000277541	NM_017617.3	272	tGt/tAt	5/34	0.615380889348864	1	FACETS	0.442	0.393	0.494	0.442	0.393	0.494	SUBCLONAL	1	TRUE	0	0.615380889348864	1		1239	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0004401-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	583	840	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.380685817269076	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.380685817269076	2		842	1525	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964925	55964925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149745504	NA	P-0004401-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	87	451	0	ENST00000263923.4:c.2312C>T	p.Thr771Met	p.T771M	ENST00000263923	NM_002253.2	771	aCg/aTg	16/30	0.380685817269076	1	FACETS	0.45	0.397	0.506	0.45	0.397	0.506	SUBCLONAL	1	TRUE	0	0.380685817269076	1		451	823	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161326467	161326467	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004401-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1699	157	833	0	ENST00000367975.2:c.242G>A	p.Gly81Glu	p.G81E	ENST00000367975	NM_003001.3	81	gGg/gAg	5/6	0.126634241178454	3	FACETS	0.529	0.482	0.578	0.176	0.16	0.193	INDETERMINATE	1	TRUE	0	0.380685817269076	3		833	1856	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406361	70406361	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004401-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	332	779	1	ENST00000373644.4:c.3875C>A	p.Ala1292Asp	p.A1292D	ENST00000373644	NM_030625.2	1292	gCc/gAc	4/12	0.173157368185807	2	FACETS	1	0.992	1	0.655	0.619	0.693	INDETERMINATE	1	TRUE	0	0.380685817269076	2		780	1331	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50483727	50483727	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200921207	NA	P-0004401-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	101	454	2	ENST00000394963.4:c.832G>A	p.Val278Met	p.V278M	ENST00000394963	NM_003076.4	278	Gtg/Atg	7/13	1	2	FACETS	0.519	0.463	0.579	0.519	0.463	0.579	SUBCLONAL	1	TRUE	1	0.380685817269076	2		456	1022	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81574787	81574787	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004401-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	275	419	0	ENST00000298171.2:c.683C>A	p.Pro228Gln	p.P228Q	ENST00000298171	NM_000369.2	228	cCa/cAa	8/10	1	2	FACETS	0.784	0.738	0.832	1	0.994	1	SUBCLONAL	2	TRUE	1	0.380685817269076	2		419	921	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916139	9916140	+	missense_variant	Missense_Mutation	DNP	AA	AA	GT	novel	NA	P-0004401-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	77	461	0	ENST00000330684.3:c.2149_2150delinsAC	p.Leu717Thr	p.L717T	ENST00000330684	NM_001134407.1	717	TTg/ACg	10/13	1	2	FACETS	0.436	0.382	0.495	0.436	0.382	0.495	SUBCLONAL	1	TRUE	1	0.380685817269076	2		461	927	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671694	67671694	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004401-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	90	487	0	ENST00000264010.4:c.2103A>T	p.Glu701Asp	p.E701D	ENST00000264010	NM_006565.3	701	gaA/gaT	12/12	0.126634241178454	3	FACETS	0.561	0.497	0.63	0.187	0.165	0.21	INDETERMINATE	1	TRUE	0	0.380685817269076	3		487	1003	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456508	29456508	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004401-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	234	658	1	ENST00000389048.3:c.2410G>T	p.Glu804Ter	p.E804*	ENST00000389048	NM_004304.4	804	Gaa/Taa	14/29	0.359971172108934	2	FACETS	1	0.966	1	0.529	0.492	0.566	CLONAL	1	TRUE	0	0.380685817269076	2		659	1163	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46603869	46603869	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004401-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	50	452	0	ENST00000263734.3:c.1226A>G	p.Asp409Gly	p.D409G	ENST00000263734	NM_001430.4	409	gAc/gGc	9/16	0.359971172108934	2	FACETS	0.279	0.235	0.327	0.139	0.117	0.164	SUBCLONAL	1	TRUE	0	0.380685817269076	2		452	943	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332576	153332576	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004401-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	67	332	0	ENST00000281708.4:c.380A>G	p.Gln127Arg	p.Q127R	ENST00000281708	NM_033632.3	127	cAg/cGg	2/12	0.359971172108934	2	FACETS	0.576	0.501	0.658	0.288	0.25	0.329	SUBCLONAL	1	TRUE	0	0.380685817269076	2		332	611	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589537	67589563	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GATCAAGTTGTCAAAGAAGATAATATT	GATCAAGTTGTCAAAGAAGATAATATT	-	novel	NA	P-0004401-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	64	262	0	ENST00000274335.5:c.1302_1328del	p.Asp434_Ile442del	p.D434_I442del	ENST00000274335		434	GATCAAGTTGTCAAAGAAGATAATATT/-	10/15	0.380685817269076	1	FACETS	0.76	0.662	0.866	0.76	0.662	0.866	SUBCLONAL	1	TRUE	0	0.380685817269076	1		262	358	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194583	29194583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004401-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	113	729	0	ENST00000240100.2:c.1145C>T	p.Pro382Leu	p.P382L	ENST00000240100	NM_001394.6	382	cCc/cTc	4/4	0.380685817269076	1	FACETS	0.5	0.449	0.554	0.5	0.449	0.554	SUBCLONAL	1	TRUE	0	0.380685817269076	1		729	962	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916140	9916140	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004401-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	77	461	0	ENST00000330684.3:c.2149T>A	p.Leu717Met	p.L717M	ENST00000330684	NM_001134407.1	717	Ttg/Atg	10/13	1	2	FACETS	0.436	0.382	0.495	0.436	0.382	0.495	SUBCLONAL	1	TRUE	1	0.380685817269076	2		461	927	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916139	9916139	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004401-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	77	460	0	ENST00000330684.3:c.2150T>C	p.Leu717Ser	p.L717S	ENST00000330684	NM_001134407.1	717	tTg/tCg	10/13	1	2	FACETS	0.439	0.385	0.498	0.439	0.385	0.498	SUBCLONAL	1	TRUE	1	0.380685817269076	2		460	921	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990481	69990481	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs201247895	NA	P-0004728-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	122	403	0	ENST00000394351.3:c.440C>T	p.Thr147Met	p.T147M	ENST00000394351	NM_000248.3	147	aCg/aTg	4/9	0.552608761987673	3	FACETS	0.948	0.86	1			1	CLONAL	1	TRUE	NA	0.591152508526288	3		403	564	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146644	55146644	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004728-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	230	802	0	ENST00000257290.5:c.2318T>C	p.Met773Thr	p.M773T	ENST00000257290	NM_006206.4	773	aTg/aCg	16/23	0.53821481221754	4	FACETS	0.973	0.906	1			1	CLONAL	1	TRUE	NA	0.591152508526288	4		802	1272	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115900	8115901	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004835-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	467	377	0	ENST00000346208.3:c.1247dup	p.Thr417AspfsTer90	p.T417Dfs*90	ENST00000346208		416	ctg/cTtg	6/6	0.807150158412141	5	FACETS	0.981	0.938	1	0.654	0.625	0.683	CLONAL	2	TRUE	2	0.805046918168719	5		377	1306	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609812	81609812	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004835-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	63	249	0	ENST00000298171.2:c.1410C>G	p.Ile470Met	p.I470M	ENST00000298171	NM_000369.2	470	atC/atG	10/10	0.807150158412141	5	FACETS	0.373	0.322	0.429	0.124	0.107	0.143	SUBCLONAL	1	TRUE	2	0.805046918168719	5		249	926	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494334	2494334	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005038-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	163	1089	0	ENST00000355716.4:c.725A>G	p.Gln242Arg	p.Q242R	ENST00000355716	NM_003820.2	242	cAg/cGg	7/8	0.352664491795717	1	FACETS	0.744	0.682	0.809	0.744	0.682	0.809	SUBCLONAL	1	FALSE	0	0.356387383421841	1		1089	1010	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310503	65310503	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005038-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	235	779	0	ENST00000342505.4:c.2185A>T	p.Ser729Cys	p.S729C	ENST00000342505	NM_002227.2	729	Agt/Tgt	16/25	0.352664491795717	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	FALSE	0	0.356387383421841	1		779	729	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575153	64575153	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0005038-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	165	517	0	ENST00000312049.6:c.655-1G>A		p.X219_splice	ENST00000312049	NM_130799.2	219			1	2	FACETS	0.779	0.719	0.842	1	0.99	1	SUBCLONAL	2	FALSE	1	0.356387383421841	2		517	594	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474026	29474026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147858673	NA	P-0005038-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	383	1037	2	ENST00000389048.3:c.2149G>A	p.Glu717Lys	p.E717K	ENST00000389048	NM_004304.4	717	Gag/Aag	12/29	1	2	FACETS	0.945	0.899	0.992	1	0.996	1	CLONAL	2	FALSE	1	0.356387383421841	2		1039	1137	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0005065-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	874	581	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.546149246413645	7	FACETS	0.993	0.975	1			1	CLONAL	7	TRUE	NA	0.546149246413645	7		581	1089	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518464	204518464	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777416962	NA	P-0005065-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	178	579	0	ENST00000367182.3:c.1127C>T	p.Ala376Val	p.A376V	ENST00000367182	NM_001278516.1	376	gCg/gTg	11/11	0.546149246413645	8	FACETS	0.913	0.841	0.987			1	CLONAL	2	TRUE	NA	0.546149246413645	8		579	942	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244137	153244137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140856583	NA	P-0005065-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	180	711	4	ENST00000281708.4:c.2020C>T	p.Arg674Trp	p.R674W	ENST00000281708	NM_033632.3	674	Cgg/Tgg	12/12	0.554103842134774	3	FACETS	1	0.988	1	0.673	0.624	0.725	CLONAL	1	TRUE	1	0.546149246413645	3		715	623	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940111	49940111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005065-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	62	691	0	ENST00000296474.3:c.932C>A	p.Ala311Asp	p.A311D	ENST00000296474	NM_002447.2	311	gCc/gAc	1/20	NA	2	FACETS	0.505	0.437	0.578			1	INDETERMINATE	1	TRUE	NA	0.546149246413645	2		691	450	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851908	63851908	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005065-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	109	826	0	ENST00000279873.7:c.2686G>T	p.Ala896Ser	p.A896S	ENST00000279873	NM_032199.2	896	Gca/Tca	10/10	0.546149246413645	5	FACETS	0.754	0.676	0.837			1	SUBCLONAL	1	TRUE	NA	0.546149246413645	5		826	963	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127994	64127994	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005065-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	96	902	0	ENST00000334205.4:c.392A>G	p.Gln131Arg	p.Q131R	ENST00000334205	NM_003942.2	131	cAg/cGg	4/17	0.432128924262422	4	FACETS	0.695	0.619	0.776	0.348	0.309	0.388	SUBCLONAL	1	TRUE	2	0.546149246413645	4		902	782	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869492	102869492	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005065-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	69	713	0	ENST00000307046.8:c.149C>G	p.Pro50Arg	p.P50R	ENST00000307046	NM_001111285.1	50	cCg/cGg	2/4	0.546149246413645	5	FACETS	0.491	0.426	0.561			1	SUBCLONAL	1	TRUE	NA	0.546149246413645	5		713	936	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636138	87636174	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTCTCATCCTATCTTTGATCTCCATCCAGGTGATAGA	GTCTCATCCTATCTTTGATCTCCATCCAGGTGATAGA	-	novel	NA	P-0005065-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	35	263	0	ENST00000277120.3:c.2332-27_2341del		p.X778_splice	ENST00000277120		778		19/19	0.144364873480395	3	FACETS	0.989	0.821	1	0.494	0.41	0.586	INDETERMINATE	1	TRUE	1	0.546149246413645	3		263	165	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140507763	140507763	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005065-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	89	645	0	ENST00000288602.6:c.708C>G	p.Asn236Lys	p.N236K	ENST00000288602	NM_004333.4	236	aaC/aaG	5/18	0.546149246413645	8	FACETS	0.71	0.627	0.798	0.142	0.125	0.16	SUBCLONAL	1	TRUE	3	0.546149246413645	8		645	1212	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43806163	43806163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005065-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	66	635	1	ENST00000372470.3:c.959C>T	p.Ala320Val	p.A320V	ENST00000372470	NM_005373.2	320	gCa/gTa	6/12	0.372485899068777	5	FACETS	0.709	0.615	0.811			1	SUBCLONAL	1	TRUE	NA	0.546149246413645	5		636	620	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39772512	39772512	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005065-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	71	712	0	ENST00000288319.7:c.729A>T	p.Arg243Ser	p.R243S	ENST00000288319	NM_182918.3	243	agA/agT	6/10	0.546149246413645	6	FACETS	0.507	0.441	0.579			1	SUBCLONAL	1	TRUE	NA	0.546149246413645	6		712	1072	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138409841	138409841	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0005065-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	146	647	0	ENST00000289153.2:c.2036+1G>C		p.X679_splice	ENST00000289153	NM_006219.2	679			NA	2	FACETS	0.95	0.871	1			1	INDETERMINATE	1	TRUE	NA	0.546149246413645	2		647	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578250	7578250	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1131691011	NA	P-0005188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	813	765	0	ENST00000269305.4:c.599del	p.Asn200IlefsTer47	p.N200Ifs*47	ENST00000269305	NM_001126112.2	200	aAt/at	6/11	0.647433106506132	2	FACETS	0.935	0.91	0.96	0.935	0.91	0.96	CLONAL	2	TRUE	0	0.647433106506132	2		765	1343	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685303	89685304	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0005188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	524	373	0	ENST00000371953.3:c.202_203dup	p.Asn69ThrfsTer31	p.N69Tfs*31	ENST00000371953	NM_000314.4	66	-/AT	3/9	0.647433106506132	2	FACETS	0.918	0.887	0.948	0.918	0.887	0.948	CLONAL	2	TRUE	0	0.647433106506132	2		373	882	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56878465	56878465	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	331	515	0	ENST00000308159.5:c.2404C>T	p.Arg802Ter	p.R802*	ENST00000308159	NM_014669.4	802	Cga/Tga	22/22	1	2	FACETS	0.933	0.883	0.984	0.933	0.883	0.984	CLONAL	1	TRUE	1	0.647433106506132	2		515	1096	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408906	41408906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	266	472	1	ENST00000373198.4:c.520C>T	p.Pro174Ser	p.P174S	ENST00000373198	NM_133170.3	174	Cct/Tct	4/32	0.647433106506132	2	FACETS	0.899	0.845	0.955	0.45	0.422	0.478	CLONAL	1	TRUE	0	0.647433106506132	2		473	914	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	620	1054	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.511392846819613	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.511392846819613	2		1054	1178	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953587	32953587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886040798	NA	P-0005205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1380	207	1065	0	ENST00000380152.3:c.8888C>T	p.Ser2963Leu	p.S2963L	ENST00000380152		2963	tCa/tTa	22/27	0.46517525395696	4	FACETS	0.771	0.713	0.832			1	SUBCLONAL	1	TRUE	NA	0.511392846819613	4		1065	1587	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953632	32953632	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs80359144	NA	P-0005205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	99	738	2	ENST00000380152.3:c.8933C>A	p.Ser2978Ter	p.S2978*	ENST00000380152		2978	tCa/tAa	22/27	0.46517525395696	4	FACETS	0.508	0.452	0.568			1	SUBCLONAL	1	TRUE	NA	0.511392846819613	4		740	1152	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913351	NA	P-0121548-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	19	713	0	ENST00000288602.6:c.1397G>A	p.Gly466Glu	p.G466E	ENST00000288602	NM_004333.4	466	gGa/gAa	11/18	0.66246577036244	3	FACETS	0.106	0.08	0.137	0.035	0.026	0.046	SUBCLONAL	1	NA	0	0.66246577036244	3		713	719	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432664	29432664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113994087	NA	P-0121548-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	211	607	1	ENST00000389048.3:c.3824G>A	p.Arg1275Gln	p.R1275Q	ENST00000389048	NM_004304.4	1275	cGa/cAa	25/29	0.645940318464626	4	FACETS	1	0.989	1	0.439	0.408	0.471	CLONAL	1	NA	1	0.66246577036244	4		608	804	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245201	41245201	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0121548-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	202	776	0	ENST00000357654.3:c.2347A>C	p.Ile783Leu	p.I783L	ENST00000357654	NM_007294.3	783	Atc/Ctc	10/23	0.406101408089419	5	FACETS	1	0.979	1	0.383	0.355	0.413	CLONAL	1	NA	2	0.66246577036244	5		776	1057	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940000	76940000	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1311466929	NA	P-0121548-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	187	359	3	ENST00000373344.5:c.748C>T	p.Arg250Ter	p.R250*	ENST00000373344	NM_000489.3	250	Cga/Tga	9/35	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	NA	0	0.66246577036244	1		362	321	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156677	2156677	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0121548-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	73	650	0	ENST00000434045.2:c.245A>C	p.Tyr82Ser	p.Y82S	ENST00000434045	NM_001127598.1	82	tAc/tCc	3/5	0.66246577036244	3	FACETS	0.544	0.477	0.617	0.181	0.159	0.206	SUBCLONAL	1	NA	0	0.66246577036244	3		650	539	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433541	49433541	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121548-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	185	862	1	ENST00000301067.7:c.8012G>T	p.Gly2671Val	p.G2671V	ENST00000301067	NM_003482.3	2671	gGc/gTc	31/54	0.66246577036244	3	FACETS	1	0.97	1	0.545	0.505	0.586	CLONAL	1	NA	1	0.66246577036244	3		863	682	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944265	81944265	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121548-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	27	731	0	ENST00000359376.3:c.1874C>A	p.Ala625Asp	p.A625D	ENST00000359376	NM_002661.3	625	gCc/gAc	18/33	1	2	FACETS	0.182	0.144	0.225	0.182	0.144	0.225	SUBCLONAL	1	NA	1	0.66246577036244	2		731	448	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1959670	1959670	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0121548-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	100	407	0	ENST00000382891.5:c.2892A>T	p.Glu964Asp	p.E964D	ENST00000382891	NM_133335.3	964	gaA/gaT	16/22	0.635931520351729	2	FACETS	0.977	0.884	1	0.489	0.442	0.537	CLONAL	1	NA	0	0.66246577036244	2		407	309	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279449	1279449	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0121548-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	121	921	0	ENST00000310581.5:c.2087G>C	p.Arg696Pro	p.R696P	ENST00000310581	NM_198253.2	696	cGt/cCt	5/16	0.264013740002611	3	FACETS	0.961	0.873	1			1	INDETERMINATE	1	NA	NA	0.66246577036244	3		921	506	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821552	32821552	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1161132915	NA	P-0121548-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	80	800	0	ENST00000354258.4:c.42G>A	p.Trp14Ter	p.W14*	ENST00000354258	NM_000593.5	14	tgG/tgA	1/11	0.361334939117416	6	FACETS	0.735	0.646	0.83	0.245	0.215	0.277	INDETERMINATE	1	NA	3	0.66246577036244	6		800	764	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432664	29432664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113994087	NA	P-0121533-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	335	607	1	ENST00000389048.3:c.3824G>A	p.Arg1275Gln	p.R1275Q	ENST00000389048	NM_004304.4	1275	cGa/cAa	25/29	0.49335517207176	4	FACETS	1	0.992	1	0.422	0.399	0.445	INDETERMINATE	1	NA	1	0.952066441256482	4		608	1086	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042083	14042083	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121533-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	211	378	0	ENST00000311895.7:c.2630C>A	p.Ala877Glu	p.A877E	ENST00000311895	NM_005236.2	877	gCa/gAa	11/11	1	2	FACETS	0.927	0.871	0.984	0.927	0.871	0.984	CLONAL	1	NA	1	0.952066441256482	2		378	478	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989510	7989510	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0121533-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	309	561	0	ENST00000319144.4:c.176A>T	p.Gln59Leu	p.Q59L	ENST00000319144	NM_001139.2	59	cAg/cTg	2/15	1	2	FACETS	0.941	0.894	0.988	0.941	0.894	0.988	CLONAL	1	NA	1	0.952066441256482	2		561	690	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682407	52682407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776146971	NA	P-0121533-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	263	439	0	ENST00000394830.3:c.766G>A	p.Ala256Thr	p.A256T	ENST00000394830	NM_018313.4	256	Gca/Aca	8/30	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	NA	1	0.952066441256482	2		439	547	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005349-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	87	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.985	0.87	1	0.985	0.87	1	CLONAL	1	TRUE	1	0.183867364599353	2		493	961	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577497	7577497	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0005349-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	81	509	0	ENST00000269305.4:c.782+2T>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.16960584650509	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.183867364599353	1		509	727	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0121458-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	486	649	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.732139365096056	5	FACETS	0.961	0.919	1	0.64	0.612	0.669	CLONAL	2	NA	2	0.732139365096056	5		649	1450	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007156	62007156	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121458-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1281	197	487	0	ENST00000392795.3:c.526G>T	p.Val176Leu	p.V176L	ENST00000392795	NM_001039933.1	176	Gtg/Ttg	4/6	0.732139365096056	8	FACETS	1	0.979	1	0.233	0.214	0.252	CLONAL	1	NA	3	0.732139365096056	8		487	1478	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075406	8075406	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121458-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	39	348	0	ENST00000377482.5:c.164G>T	p.Ser55Ile	p.S55I	ENST00000377482	NM_018948.3	55	aGt/aTt	3/4	0.72146762640899	3	FACETS	0.297	0.246	0.354	0.149	0.123	0.177	SUBCLONAL	1	NA	1	0.732139365096056	3		348	490	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627772	37627772	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005445-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	531	695	0	ENST00000447079.4:c.1687C>T	p.Gln563Ter	p.Q563*	ENST00000447079	NM_015083.1	563	Caa/Taa	2/14	1	2	FACETS	0.981	0.943	1	0.981	0.943	1	CLONAL	1	TRUE	1	0.852986567246781	2		695	1269	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618549	37618550	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005445-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	460	555	0	ENST00000447079.4:c.226dup	p.Ile76AsnfsTer4	p.I76Nfs*4	ENST00000447079	NM_015083.1	75	-/A	1/14	1	2	FACETS	0.968	0.927	1	0.968	0.927	1	CLONAL	1	TRUE	1	0.852986567246781	2		555	1114	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876964	151876980	+	frameshift_variant	Frame_Shift_Del	DEL	TAGGGTCCACGCTGATC	TAGGGTCCACGCTGATC	-	novel	NA	P-0005445-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	246	418	0	ENST00000262189.6:c.7381_7397del	p.Asp2461SerfsTer3	p.D2461Sfs*3	ENST00000262189	NM_170606.2	2461	GATCAGCGTGGACCCTAt/t	37/59	0.427545062444208	5	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.852986567246781	5		418	1211	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0005464-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	64	650	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.3	1	FACETS	0.721	0.622	0.829	0.721	0.622	0.829	SUBCLONAL	1	TRUE	0	0.16	1		650	1021	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0005464-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	112	428	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.16	2		428	1195	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252969	36252977	+	inframe_deletion	In_Frame_Del	DEL	AGTGACCAG	AGTGACCAG	-	novel	NA	P-0005464-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	79	472	0	ENST00000300305.3:c.385_393del	p.Leu129_Thr131del	p.L129_T131del	ENST00000300305		129	CTGGTCACT/-	4/8	1	2	FACETS	0.914	0.802	1	0.914	0.802	1	CLONAL	1	TRUE	1	0.16	2		472	1080	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	172	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.158115417034417	2	FACETS	0.839	0.773	0.909	1	0.984	1	CLONAL	3	TRUE	0	0.158115417034417	2		493	864	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846291	156846291	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760764097	NA	P-0005518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	63	864	0	ENST00000524377.1:c.1732G>A	p.Val578Ile	p.V578I	ENST00000524377	NM_002529.3	578	Gtc/Atc	14/17	0.158115417034417	2	FACETS	0.766	0.66	0.882	0.383	0.33	0.441	SUBCLONAL	1	TRUE	0	0.158115417034417	2		864	1040	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467144	25467144	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	57	676	0	ENST00000264709.3:c.1731G>C	p.Lys577Asn	p.K577N	ENST00000264709	NM_175629.2	577	aaG/aaC	15/23	0.129135645332874	2	FACETS	0.87	0.744	1	0.435	0.372	0.504	CLONAL	1	TRUE	0	0.158115417034417	2		676	829	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578281	7578281	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660254	NA	P-0005518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	99	449	0	ENST00000269305.4:c.568C>A	p.Pro190Thr	p.P190T	ENST00000269305	NM_001126112.2	190	Cct/Act	6/11	0.129135645332874	2	FACETS	0.806	0.719	0.898	0.806	0.719	0.898	CLONAL	2	TRUE	0	0.158115417034417	2		449	777	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827922	40827922	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	40	667	0	ENST00000373198.4:c.2506G>T	p.Asp836Tyr	p.D836Y	ENST00000373198	NM_133170.3	836	Gat/Tat	17/32	0.142013768340747	3	FACETS	0.75	0.621	0.894	0.375	0.31	0.447	SUBCLONAL	1	TRUE	1	0.158115417034417	3		667	728	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475632	40475632	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	45	588	0	ENST00000264657.5:c.1612A>C	p.Asn538His	p.N538H	ENST00000264657	NM_139276.2	538	Aat/Cat	18/24	0.129135645332874	2	FACETS	0.917	0.769	1	0.458	0.384	0.54	CLONAL	1	TRUE	0	0.158115417034417	2		588	621	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946385	2946385	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	63	1025	5	ENST00000396946.4:c.3352G>A	p.Ala1118Thr	p.A1118T	ENST00000396946	NM_032415.4	1118	Gcc/Acc	25/25	0.142013768340747	3	FACETS	0.697	0.601	0.803	0.349	0.3	0.402	SUBCLONAL	1	TRUE	1	0.158115417034417	3		1030	1233	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0005551-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	30	722	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.519	0.416	0.636	0.519	0.416	0.636	SUBCLONAL	1	TRUE	1	0.14	2		722	826	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220370	1220370	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0005551-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	71	848	1	ENST00000326873.7:c.465-2A>T		p.X155_splice	ENST00000326873	NM_000455.4	155			0.3	2	FACETS	1	0.903	1			1	CLONAL	1	TRUE	NA	0.14	2		849	971	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs11575997	NA	P-0005551-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	29	321	0	ENST00000269305.4:c.993+1G>T		p.X331_splice	ENST00000269305	NM_001126112.2	331			1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.14	2		321	347	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096987	11096987	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005551-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1427	95	1532	1	ENST00000358026.2:c.478C>T	p.Gln160Ter	p.Q160*	ENST00000358026	NM_001128849.1	160	Cag/Tag	4/36	1	2	FACETS	0.892	0.791	1	0.892	0.791	1	CLONAL	1	TRUE	1	0.14	2		1533	1522	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444590	187444590	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005551-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	45	678	0	ENST00000232014.4:c.1637A>G	p.Tyr546Cys	p.Y546C	ENST00000232014	NM_001130845.1	546	tAc/tGc	7/10	1	2	FACETS	0.801	0.671	0.945	0.801	0.671	0.945	CLONAL	1	TRUE	1	0.14	2		678	803	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522703	176522703	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005551-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	84	1236	2	ENST00000292408.4:c.1800G>T	p.Met600Ile	p.M600I	ENST00000292408	NM_213647.1	600	atG/atT	13/18	1	2	FACETS	0.98	0.863	1	0.98	0.863	1	CLONAL	1	TRUE	1	0.14	2		1238	1224	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039519	180039519	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1426017403	NA	P-0005551-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1519	108	1537	0	ENST00000261937.6:c.3524G>T	p.Gly1175Val	p.G1175V	ENST00000261937	NM_182925.4	1175	gGc/gTc	26/30	1	2	FACETS	0.948	0.847	1	0.948	0.847	1	CLONAL	1	TRUE	1	0.14	2		1537	1627	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309813	65309813	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0121532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	119	551	0	ENST00000342505.4:c.2337T>G	p.Phe779Leu	p.F779L	ENST00000342505	NM_002227.2	779	ttT/ttG	17/25	0.28686247929628	3	FACETS	1	0.957	1	0.555	0.501	0.613	CLONAL	1	NA	1	0.28686247929628	3		551	854	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0005772-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	1738	577	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.730760008294965	6	FACETS	0.973	0.958	0.988	0.973	0.958	0.988	CLONAL	5	TRUE	1	0.730760008294965	6		577	2407	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0005772-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	325	408	2	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	1	2	FACETS	0.989	0.938	1	0.989	0.938	1	CLONAL	1	TRUE	1	0.730760008294965	2		410	899	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907712	111907712	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0005772-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	197	297	0	ENST00000393256.3:c.486C>G	p.Tyr162Ter	p.Y162*	ENST00000393256	NM_006538.4	162	taC/taG	3/4	1	2	FACETS	0.954	0.89	1	0.954	0.89	1	CLONAL	1	TRUE	1	0.730760008294965	2		297	565	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645088	86645088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005772-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	232	346	0	ENST00000274376.6:c.1160C>T	p.Ser387Leu	p.S387L	ENST00000274376	NM_002890.2	387	tCa/tTa	8/25	1	2	FACETS	0.898	0.841	0.956	0.898	0.841	0.956	CLONAL	1	TRUE	1	0.730760008294965	2		346	707	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119998	70119998	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005772-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	122	132	0	ENST00000245479.2:c.1000G>A	p.Val334Met	p.V334M	ENST00000245479	NM_000346.3	334	Gtg/Atg	3/3	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.730760008294965	2		132	285	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191158	2191158	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005772-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	509	579	2	ENST00000398665.3:c.412G>T	p.Glu138Ter	p.E138*	ENST00000398665	NM_032482.2	138	Gag/Tag	5/28	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.730760008294965	2		581	1286	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43772110	43772110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756804341	NA	P-0005772-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	503	635	0	ENST00000382044.4:c.605C>T	p.Ser202Leu	p.S202L	ENST00000382044	NM_001141980.1	202	tCa/tTa	6/28	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.730760008294965	2		635	1332	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474395	40474395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005772-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	66	392	0	ENST00000264657.5:c.2006C>T	p.Pro669Leu	p.P669L	ENST00000264657	NM_139276.2	669	cCa/cTa	21/24	1	2	FACETS	0.182	0.157	0.209	0.182	0.157	0.209	SUBCLONAL	1	TRUE	1	0.730760008294965	2		392	992	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	232	297	0				ENST00000310581	NM_198253.2	-/1132			0.26006539496715	4	FACETS	0.951	0.89	1	0.951	0.89	1	INDETERMINATE	2	TRUE	2	0.47394835239097	4		297	759	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0006008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	313	1023	1	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	0.47394835239097	2		1024	1222	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149917	202149917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	1442	1168	3	ENST00000358485.4:c.1358C>T	p.Pro453Leu	p.P453L	ENST00000358485	NM_001080125.1	453	cCg/cTg	8/9	0.47394835239097	7	FACETS	0.924	0.905	0.942			1	CLONAL	6	TRUE	NA	0.47394835239097	7		1171	2399	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518842	187518842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773654248	NA	P-0006008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	161	945	1	ENST00000441802.2:c.12362G>A	p.Gly4121Glu	p.G4121E	ENST00000441802	NM_005245.3	4121	gGa/gAa	24/27	1	2	FACETS	0.834	0.765	0.905	0.834	0.765	0.905	CLONAL	1	TRUE	1	0.47394835239097	2		946	815	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518091	8518091	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs970315764	NA	P-0006008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	84	813	0	ENST00000356435.5:c.1300A>G	p.Ile434Val	p.I434V	ENST00000356435		434	Att/Gtt	10/35	0.47394835239097	3	FACETS	0.471	0.415	0.532	0.157	0.138	0.178	SUBCLONAL	1	TRUE	0	0.47394835239097	3		813	930	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578262	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs483352697	NA	P-0006008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	193	1168	0	ENST00000269305.4:c.587G>T	p.Arg196Leu	p.R196L	ENST00000269305	NM_001126112.2	196	cGa/cTa	6/11	1	2	FACETS	0.75	0.693	0.809	0.75	0.693	0.809	SUBCLONAL	1	TRUE	1	0.47394835239097	2		1168	1086	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243598	41243598	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	297	1280	0	ENST00000357654.3:c.3950del	p.Leu1317Ter	p.L1317*	ENST00000357654	NM_007294.3	1317	tTg/tg	10/23	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.47394835239097	2		1280	1136	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218908	193218908	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	294	755	0	ENST00000367435.3:c.1467del	p.Gln490ArgfsTer5	p.Q490Rfs*5	ENST00000367435	NM_024529.4	489	gTt/gt	16/17	0.47394835239097	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.47394835239097	3		755	744	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098816	178098816	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1424	401	1335	3	ENST00000397062.3:c.229G>T	p.Asp77Tyr	p.D77Y	ENST00000397062	NM_006164.4	77	Gat/Tat	2/5	0.250242822496615	6	FACETS	0.903	0.856	0.951			1	INDETERMINATE	2	TRUE	NA	0.47394835239097	6		1338	1825	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170002371	170002371	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	236	636	0	ENST00000295797.4:c.1190A>C	p.Tyr397Ser	p.Y397S	ENST00000295797	NM_002740.5	397	tAc/tCc	12/18	0.260501586680389	3	FACETS	0.981	0.921	1	0.981	0.921	1	INDETERMINATE	2	TRUE	1	0.47394835239097	3		636	628	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32790078	32790078	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	121	613	0	ENST00000374899.4:c.1950C>G	p.Phe650Leu	p.F650L	ENST00000374899	NM_018833.2	650	ttC/ttG	12/12	0.462255344823136	2	FACETS	0.829	0.751	0.911	0.414	0.375	0.456	CLONAL	1	TRUE	0	0.47394835239097	2		613	616	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876995	151876995	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	266	878	0	ENST00000262189.6:c.7366G>T	p.Ala2456Ser	p.A2456S	ENST00000262189	NM_170606.2	2456	Gct/Tct	37/59	0.22555696321906	4	FACETS	0.864	0.812	0.919	0.864	0.812	0.919	INDETERMINATE	2	TRUE	2	0.47394835239097	4		878	957	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246324	53246324	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0006008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	265	532	0	ENST00000375401.3:c.657+1G>A		p.X219_splice	ENST00000375401	NM_004187.3	219			1	1	FACETS	0.858	0.815	0.901	1	0.995	1	CLONAL	2	TRUE	0	0.47394835239097	1		532	497	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	253	297	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.411643872118858	2		297	513	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0006064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	453	943	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.411643872118858	3	FACETS	0.96	0.916	1	0.96	0.916	1	CLONAL	2	TRUE	1	0.411643872118858	3		943	1382	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039133	49039133	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0006064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	111	254	0	ENST00000267163.4:c.2212-1G>C		p.X738_splice	ENST00000267163	NM_000321.2	738			0.411643872118858	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	0	0.411643872118858	1		254	428	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845466	128845466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	548	819	0	ENST00000249373.3:c.763G>A	p.Asp255Asn	p.D255N	ENST00000249373	NM_005631.4	255	Gac/Aac	4/12	0.411643872118858	3	FACETS	0.955	0.915	0.995	0.955	0.915	0.995	CLONAL	2	TRUE	1	0.411643872118858	3		819	1681	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205238	46205238	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	206	576	1	ENST00000334344.6:c.322G>T	p.Glu108Ter	p.E108*	ENST00000334344	NM_152641.2	108	Gag/Tag	4/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.411643872118858	2		577	967	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46727055	46727055	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	155	430	1	ENST00000371975.4:c.889G>A	p.Glu297Lys	p.E297K	ENST00000371975	NM_003579.3	297	Gag/Aag	8/18	1	2	FACETS	0.91	0.833	0.989	0.91	0.833	0.989	CLONAL	1	TRUE	1	0.411643872118858	2		431	828	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325932	65325932	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	203	504	0	ENST00000342505.4:c.1190C>G	p.Ser397Cys	p.S397C	ENST00000342505	NM_002227.2	397	tCt/tGt	9/25	1	2	FACETS	0.953	0.883	1	0.953	0.883	1	CLONAL	1	TRUE	1	0.411643872118858	2		504	1035	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422652	49422652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	274	768	0	ENST00000301067.7:c.14341G>A	p.Glu4781Lys	p.E4781K	ENST00000301067	NM_003482.3	4781	Gag/Aag	45/54	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.411643872118858	2		768	1316	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782214	56782214	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	142	436	0	ENST00000308159.5:c.55G>C	p.Glu19Gln	p.E19Q	ENST00000308159	NM_014669.4	19	Gag/Cag	2/22	1	2	FACETS	0.89	0.812	0.972	0.89	0.812	0.972	CLONAL	1	TRUE	1	0.411643872118858	2		436	775	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673730	37673730	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	301	725	0	ENST00000447079.4:c.2884G>C	p.Asp962His	p.D962H	ENST00000447079	NM_015083.1	962	Gat/Cat	10/14	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.411643872118858	2		725	1392	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120192	70120192	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	230	605	1	ENST00000245479.2:c.1194G>C	p.Lys398Asn	p.K398N	ENST00000245479	NM_000346.3	398	aaG/aaC	3/3	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.411643872118858	2		606	1077	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209103921	209103921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	182	523	0	ENST00000345146.2:c.1028G>A	p.Arg343Lys	p.R343K	ENST00000345146	NM_005896.2	343	aGa/aAa	9/10	0.411394680199237	2	FACETS	0.926	0.854	1	0.463	0.427	0.501	CLONAL	1	TRUE	0	0.411643872118858	2		523	955	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30956859	30956859	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	249	616	1	ENST00000375687.4:c.185C>G	p.Ser62Cys	p.S62C	ENST00000375687	NM_015338.5	62	tCc/tGc	4/13	0.396659480379554	3	FACETS	1	0.964	1	0.525	0.489	0.561	CLONAL	1	TRUE	1	0.411643872118858	3		617	1390	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264982	46264982	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	190	588	0	ENST00000371998.3:c.1852C>G	p.His618Asp	p.H618D	ENST00000371998		618	Cat/Gat	12/23	0.396659480379554	3	FACETS	0.894	0.825	0.966	0.447	0.412	0.483	CLONAL	1	TRUE	1	0.411643872118858	3		588	1245	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696169	52696169	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	349	842	0	ENST00000394830.3:c.508C>G	p.Gln170Glu	p.Q170E	ENST00000394830	NM_018313.4	170	Cag/Gag	5/30	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.411643872118858	2		842	1519	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231731	66231731	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388138471	NA	P-0006064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	167	525	0	ENST00000273854.3:c.1969G>A	p.Glu657Lys	p.E657K	ENST00000273854	NM_004439.5	657	Gag/Aag	11/18	1	2	FACETS	0.987	0.908	1	0.987	0.908	1	CLONAL	1	TRUE	1	0.411643872118858	2		525	822	SUCCESS
APC	324	MSKCC	GRCh37	5	112175999	112175999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1267672358	NA	P-0006064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	158	397	0	ENST00000257430.4:c.4708G>A	p.Asp1570Asn	p.D1570N	ENST00000257430	NM_000038.5	1570	Gat/Aat	16/16	1	2	FACETS	0.926	0.849	1	0.926	0.849	1	CLONAL	1	TRUE	1	0.411643872118858	2		397	829	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433633	149433633	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	novel	NA	P-0006064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	211	699	0	ENST00000286301.3:c.2918G>C	p.Ter973SerextTer43	p.*973Sext*43	ENST00000286301	NM_005211.3	973	tGa/tCa	22/22	1	2	FACETS	0.895	0.83	0.962	0.895	0.83	0.962	CLONAL	1	TRUE	1	0.411643872118858	2		699	1146	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209256	98209256	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	284	802	0	ENST00000331920.6:c.4282G>C	p.Glu1428Gln	p.E1428Q	ENST00000331920	NM_000264.3	1428	Gaa/Caa	23/24	1	2	FACETS	0.966	0.906	1	0.966	0.906	1	CLONAL	1	TRUE	1	0.411643872118858	2		802	1428	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	280	463	0	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	0.457340380819003	3	FACETS	1	0.991	1	0.631	0.594	0.669	CLONAL	1	FALSE	1	0.652827446072332	3		463	901	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111524	8111525	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0006169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	152	601	0	ENST00000346208.3:c.1011dup	p.Cys338LeufsTer14	p.C338Lfs*14	ENST00000346208		337	gtc/gtCc	5/6	0.302102357436491	4	FACETS	0.684	0.624	0.747			1	INDETERMINATE	1	FALSE	NA	0.652827446072332	4		601	1125	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46597593	46597593	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	137	476	0	ENST00000262741.5:c.32A>G	p.Asp11Gly	p.D11G	ENST00000262741	NM_003629.3	11	gAt/gGt	1/10	0.401086108151263	3	FACETS	0.692	0.63	0.758			1	SUBCLONAL	1	FALSE	NA	0.652827446072332	3		476	804	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508190	106508190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	89	173	0	ENST00000359195.3:c.184G>A	p.Ala62Thr	p.A62T	ENST00000359195	NM_002649.2	62	Gcc/Acc	2/11	0.277961380635726	5	FACETS	0.805	0.721	0.894	0.537	0.48	0.596	INDETERMINATE	2	FALSE	2	0.652827446072332	5		173	335	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752752	42752752	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	184	761	0	ENST00000222329.4:c.1512T>G	p.Phe504Leu	p.F504L	ENST00000222329	NM_006494.2	504	ttT/ttG	4/4	0.652827446072332	3	FACETS	0.561	0.517	0.608	0.281	0.258	0.304	SUBCLONAL	1	FALSE	1	0.652827446072332	3		761	1332	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38137094	38137094	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1351115556	NA	P-0006169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1274	172	664	0	ENST00000317025.8:c.3724C>T	p.Arg1242Ter	p.R1242*	ENST00000317025	NM_023034.1	1242	Cga/Tga	21/24	0.279258547132589	6	FACETS	0.84	0.771	0.913	0.21	0.192	0.229	INDETERMINATE	1	FALSE	2	0.652827446072332	6		664	1446	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0006227-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	738	843	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.283432557280594	13	FACETS	1	0.977	1			1	CLONAL	12	TRUE	NA	0.283432557280594	13		843	1107	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0006227-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	92	631	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.283432557280594	1	FACETS	0.988	0.88	1	0.988	0.88	1	CLONAL	1	TRUE	0	0.283432557280594	1		631	564	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0006227-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	47	693	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	1	2	FACETS	0.428	0.36	0.504	0.428	0.36	0.504	SUBCLONAL	1	TRUE	1	0.283432557280594	2		693	774	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862208	68862208	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0006227-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	48	421	1	ENST00000261769.5:c.2295+1G>A		p.X765_splice	ENST00000261769	NM_004360.3	765			0.283432557280594	1	FACETS	0.699	0.592	0.816	0.699	0.592	0.816	SUBCLONAL	1	TRUE	0	0.283432557280594	1		422	416	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15836709	15836709	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0006227-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	62	397	0	ENST00000307771.7:c.772-1G>C		p.X258_splice	ENST00000307771	NM_005089.3	258			1	2	FACETS	0.766	0.662	0.879	0.766	0.662	0.879	SUBCLONAL	1	TRUE	1	0.283432557280594	2		397	571	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612358	1612358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770576452	NA	P-0006227-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	67	574	1	ENST00000344749.5:c.1661G>A	p.Arg554Gln	p.R554Q	ENST00000344749	NM_001136139.2	554	cGg/cAg	18/19	0.193299037429467	1	FACETS	0.703	0.611	0.803	0.703	0.611	0.803	SUBCLONAL	1	TRUE	0	0.283432557280594	1		575	577	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270037	198270037	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006227-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	35	533	0	ENST00000335508.6:c.1399T>A	p.Leu467Ile	p.L467I	ENST00000335508	NM_012433.2	467	Tta/Ata	10/25	1	2	FACETS	0.419	0.343	0.506	0.419	0.343	0.506	SUBCLONAL	1	TRUE	1	0.283432557280594	2		533	589	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591019	67591021	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs397514046	NA	P-0006227-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	19	281	0	ENST00000274335.5:c.1615_1617del	p.Ile539del	p.I539del	ENST00000274335		538	ATT/-	12/15	1	2	FACETS	0.41	0.311	0.527	0.41	0.311	0.527	SUBCLONAL	1	TRUE	1	0.283432557280594	2		281	327	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112100	115112101	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	C	novel	NA	P-0006227-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	62	681	0	ENST00000257566.3:c.1639_1640delinsG	p.Ser547ValfsTer85	p.S547Vfs*85	ENST00000257566	NM_016569.3	547	TCt/Gt	7/8	0.193299037429467	1	FACETS	0.665	0.574	0.763	0.665	0.574	0.763	SUBCLONAL	1	TRUE	0	0.283432557280594	1		681	565	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006283-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	41	830	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.165943846728401	2	FACETS	0.617	0.512	0.734	0.308	0.256	0.367	SUBCLONAL	1	FALSE	0	0.165943846728401	2		830	801	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99160428	99160428	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006283-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	66	727	0	ENST00000074304.5:c.907C>G	p.Leu303Val	p.L303V	ENST00000074304	NM_001134224.1	303	Ctc/Gtc	11/26	0.0838572090080296	4	FACETS	0.802	0.693	0.92	0.401	0.346	0.46	INDETERMINATE	1	FALSE	2	0.165943846728401	4		727	1157	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024477	16024477	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1183742719	NA	P-0006283-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	43	358	0	ENST00000268712.3:c.1741C>A	p.Arg581Ser	p.R581S	ENST00000268712	NM_006311.3	581	Cgt/Agt	16/46	1	2	FACETS	0.767	0.64	0.908	0.767	0.64	0.908	CLONAL	1	FALSE	1	0.165943846728401	2		358	676	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845341	42845341	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006283-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	74	672	1	ENST00000398585.3:c.921G>T	p.Gln307His	p.Q307H	ENST00000398585	NM_001135099.1	307	caG/caT	9/14	0.165943846728401	1	FACETS	0.857	0.749	0.975	0.857	0.749	0.975	CLONAL	1	FALSE	0	0.165943846728401	1		673	954	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180317	27180317	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006283-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	60	448	0	ENST00000380036.4:c.981A>C	p.Gln327His	p.Q327H	ENST00000380036	NM_000459.3	327	caA/caC	7/23	1	2	FACETS	0.927	0.797	1	0.927	0.797	1	CLONAL	1	FALSE	1	0.165943846728401	2		448	780	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923160	48923160	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776789	NA	P-0006369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	213	326	0	ENST00000267163.4:c.607+1G>A		p.X203_splice	ENST00000267163	NM_000321.2	203			0.684195605867049	2	FACETS	0.917	0.872	0.961	0.917	0.872	0.961	CLONAL	2	TRUE	0	0.703757997014092	2		326	330	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15818059	15818059	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	193	292	0	ENST00000307771.7:c.186G>C	p.Lys62Asn	p.K62N	ENST00000307771	NM_005089.3	62	aaG/aaC	3/11	0.552208186084708	2	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.703757997014092	2		292	408	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803500	32803500	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	242	668	0	ENST00000374899.4:c.659G>C	p.Arg220Pro	p.R220P	ENST00000374899	NM_018833.2	220	cGa/cCa	4/12	0.344744067659566	3	FACETS	1	0.981	1	0.373	0.349	0.398	INDETERMINATE	1	TRUE	0	0.703757997014092	3		668	830	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087503	27087503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006376-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	379	674	1	ENST00000324856.7:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000324856	NM_006015.4	693	Cga/Tga	5/20	0.685238584565668	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.685238584565668	1		675	706	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881002	37881003	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCTCCCCA	rs397516982	NA	P-0006376-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	500	650	0	ENST00000269571.5:c.2332_2340dup	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	-/GGCTCCCCA	20/27	0.226953857637259	2	FACETS	1	0.995	1	0.632	0.607	0.658	INDETERMINATE	1	TRUE	0	0.685238584565668	2		650	1154	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562734	29562734	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006376-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	250	505	0	ENST00000356175.3:c.3814C>T	p.Gln1272Ter	p.Q1272*	ENST00000356175	NM_000267.3	1272	Cag/Tag	28/57	1	2	FACETS	0.783	0.733	0.834	0.783	0.733	0.834	SUBCLONAL	1	TRUE	1	0.685238584565668	2		505	932	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508508	29508509	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0006376-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	366	665	0	ENST00000356175.3:c.654+2dup		p.X218_splice	ENST00000356175	NM_000267.3	218			1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.685238584565668	2		665	962	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88677065	88677065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765530074	NA	P-0006376-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	367	554	2	ENST00000372037.3:c.850C>T	p.Arg284Cys	p.R284C	ENST00000372037	NM_004329.2	284	Cgc/Tgc	9/13	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.685238584565668	2		556	965	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	95	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.878	0.78	0.982	0.878	0.78	0.982	CLONAL	1	TRUE	1	0.238631223095531	2		493	907	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0006417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	47	1085	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.425	0.357	0.501	0.425	0.357	0.501	SUBCLONAL	1	TRUE	1	0.238631223095531	2		1085	926	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022423	12022423	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1361	102	958	0	ENST00000396373.4:c.529G>T	p.Glu177Ter	p.E177*	ENST00000396373	NM_001987.4	177	Gaa/Taa	5/8	1	2	FACETS	0.584	0.52	0.653	0.584	0.52	0.653	SUBCLONAL	1	TRUE	1	0.238631223095531	2		958	1463	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446137	49446137	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1205	65	976	0	ENST00000301067.7:c.1329del	p.Pro444LeufsTer486	p.P444Lfs*486	ENST00000301067	NM_003482.3	443	ccA/cc	10/54	1	2	FACETS	0.429	0.37	0.493	0.429	0.37	0.493	SUBCLONAL	1	TRUE	1	0.238631223095531	2		976	1270	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111855990	111855990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201886863	NA	P-0006417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	78	674	1	ENST00000341259.2:c.41C>T	p.Ala14Val	p.A14V	ENST00000341259	NM_005475.2	14	gCg/gTg	2/8	0.238631223095531	1	FACETS	0.614	0.538	0.696	0.614	0.538	0.696	SUBCLONAL	1	TRUE	0	0.238631223095531	1		675	938	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246233	41246233	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064794098	NA	P-0006417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	50	570	1	ENST00000357654.3:c.1315G>A	p.Ala439Thr	p.A439T	ENST00000357654	NM_007294.3	439	Gct/Act	10/23	1	2	FACETS	0.488	0.413	0.572	0.488	0.413	0.572	SUBCLONAL	1	TRUE	1	0.238631223095531	2		571	858	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448270	56448270	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0006417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	85	568	0	ENST00000407977.2:c.375+2T>C		p.X125_splice	ENST00000407977		125			1	2	FACETS	0.906	0.8	1	0.906	0.8	1	CLONAL	1	TRUE	1	0.238631223095531	2		568	786	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206693	36206710	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CATCTGGTACTTACCCTG	CATCTGGTACTTACCCTG	-	novel	NA	P-0006417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	89	741	0	ENST00000300305.3:c.802_805+14del		p.X268_splice	ENST00000300305		268		6/8	1	2	FACETS	0.751	0.664	0.844	0.751	0.664	0.844	SUBCLONAL	1	TRUE	1	0.238631223095531	2		741	993	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797232	32797232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1247287824	NA	P-0006417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	85	872	2	ENST00000374899.4:c.1877G>A	p.Arg626Gln	p.R626Q	ENST00000374899	NM_018833.2	626	cGg/cAg	11/12	1	2	FACETS	0.593	0.522	0.669	0.593	0.522	0.669	SUBCLONAL	1	TRUE	1	0.238631223095531	2		874	1201	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090570	5090570	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	73	484	0	ENST00000381652.3:c.2886G>C	p.Lys962Asn	p.K962N	ENST00000381652	NM_004972.3	962	aaG/aaC	21/25	0.238631223095531	1	FACETS	0.825	0.722	0.937	0.825	0.722	0.937	CLONAL	1	TRUE	0	0.238631223095531	1		484	653	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0006439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1215	482	336	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.592056130946598	6	FACETS	1	0.98	1	0.524	0.5	0.548	CLONAL	2	FALSE	2	0.592056130946598	6		336	1697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0006439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	336	464	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.363463420783686	3	FACETS	1	0.99	1	0.6	0.567	0.634	CLONAL	1	FALSE	1	0.592056130946598	3		464	1225	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578552	7578552	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	629	898	0	ENST00000269305.4:c.378C>A	p.Tyr126Ter	p.Y126*	ENST00000269305	NM_001126112.2	126	taC/taA	5/11	0.363463420783686	3	FACETS	0.785	0.756	0.816	0.785	0.756	0.816	SUBCLONAL	2	FALSE	1	0.592056130946598	3		898	1753	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846267	156846267	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	171	762	2	ENST00000524377.1:c.1708C>T	p.Gln570Ter	p.Q570*	ENST00000524377	NM_002529.3	570	Cag/Tag	14/17	0.528116490047601	3	FACETS	0.538	0.493	0.585	0.269	0.246	0.293	SUBCLONAL	1	FALSE	1	0.592056130946598	3		764	1391	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681033	117681033	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	117	621	0	ENST00000368508.3:c.3587del	p.Gly1196AspfsTer47	p.G1196Dfs*47	ENST00000368508	NM_002944.2	1196	gGa/ga	23/43	0.322207318185906	3	FACETS	0.447	0.401	0.495	0.149	0.133	0.165	INDETERMINATE	1	FALSE	0	0.592056130946598	3		621	1147	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226595603	226595603	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	166	699	0	ENST00000366794.5:c.28C>G	p.Arg10Gly	p.R10G	ENST00000366794	NM_001618.3	10	Cga/Gga	1/23	0.503879312697297	3	FACETS	0.548	0.502	0.597	0.274	0.251	0.299	SUBCLONAL	1	FALSE	1	0.592056130946598	3		699	1325	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422373	225422373	+	splice_region_variant,intron_variant	Splice_Region	SNP	T	T	A	novel	NA	P-0006439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	276	479	0	ENST00000264414.4:c.264+3A>T		p.X88_splice	ENST00000264414	NM_003590.4	88			0.361369582305969	2	FACETS	1	0.991	1	0.627	0.591	0.663	CLONAL	1	FALSE	0	0.592056130946598	2		479	744	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977907	134977907	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs766596954	NA	P-0006439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1485	153	639	0	ENST00000398015.3:c.2900A>G	p.Asn967Ser	p.N967S	ENST00000398015	NM_004441.4	967	aAc/aGc	16/16	0.592056130946598	4	FACETS	0.502	0.458	0.55	0.251	0.229	0.275	SUBCLONAL	1	FALSE	2	0.592056130946598	4		639	1638	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839872	27839872	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	107	448	0	ENST00000328488.2:c.222G>T	p.Glu74Asp	p.E74D	ENST00000328488	NM_003533.2	74	gaG/gaT	1/1	0.291661771482303	4	FACETS	0.586	0.525	0.651	0.293	0.262	0.326	INDETERMINATE	1	FALSE	2	0.592056130946598	4		448	982	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935527	13935527	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	67	327	0	ENST00000405192.2:c.1329C>A	p.Cys443Ter	p.C443*	ENST00000405192	NM_001163147.1	443	tgC/tgA	12/12	0.524275988994628	5	FACETS	0.521	0.452	0.596	0.174	0.15	0.199	SUBCLONAL	1	FALSE	2	0.592056130946598	5		327	820	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436143	116436143	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	84	368	0	ENST00000397752.3:c.4138G>C	p.Asp1380His	p.D1380H	ENST00000397752	NM_000245.2	1380	Gac/Cac	21/21	0.592056130946598	3	FACETS	0.507	0.448	0.571	0.254	0.224	0.286	SUBCLONAL	1	FALSE	1	0.592056130946598	3		368	725	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009413	69009413	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	139	587	1	ENST00000288368.4:c.2530G>T	p.Gly844Cys	p.G844C	ENST00000288368	NM_024870.2	844	Ggt/Tgt	22/40	0.326633067588989	4	FACETS	0.639	0.58	0.701	0.16	0.145	0.176	INDETERMINATE	1	FALSE	0	0.592056130946598	4		588	1170	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0006505-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	164	361	2	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		363	535	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833934	44833935	+	stop_gained	Nonsense_Mutation	INS	-	-	AGG	novel	NA	P-0006505-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	218	344	0	ENST00000377967.4:c.359_360insGGA	p.Tyr120delinsTer	p.Y120delins*	ENST00000377967	NM_021140.2	120	tac/tAGGac	4/29	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		344	419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0006634-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	191	746	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.384486904258882	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.423402821259898	1		747	695	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0006634-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	127	418	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.942	0.855	1	0.942	0.855	1	CLONAL	1	TRUE	1	0.423402821259898	2		418	637	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043449	180043449	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1460237997	NA	P-0006634-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	188	798	0	ENST00000261937.6:c.3137C>T	p.Ser1046Leu	p.S1046L	ENST00000261937	NM_182925.4	1046	tCg/tTg	23/30	1	2	FACETS	0.962	0.889	1	0.962	0.889	1	CLONAL	1	TRUE	1	0.423402821259898	2		798	923	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748533	43748533	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006634-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	182	592	0	ENST00000523873.1:c.487T>C	p.Trp163Arg	p.W163R	ENST00000523873		163	Tgg/Cgg	6/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.423402821259898	2		592	782	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332895	152332895	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0006634-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	121	512	0	ENST00000206249.3:c.1201A>T	p.Lys401Ter	p.K401*	ENST00000206249	NM_000125.3	401	Aag/Tag	5/8	1	2	FACETS	0.903	0.818	0.992	0.903	0.818	0.992	CLONAL	1	TRUE	1	0.423402821259898	2		512	633	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243885	46243885	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0006634-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	149	479	0	ENST00000334344.6:c.1979C>G	p.Ser660Ter	p.S660*	ENST00000334344	NM_152641.2	660	tCa/tGa	15/21	0.405474831318172	3	FACETS	0.959	0.876	1	0.48	0.438	0.523	CLONAL	1	TRUE	1	0.423402821259898	3		479	889	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245592	46245592	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0006634-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	247	427	0	ENST00000334344.6:c.3686C>G	p.Ser1229Ter	p.S1229*	ENST00000334344	NM_152641.2	1229	tCa/tGa	15/21	0.405474831318172	3	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	1	0.423402821259898	3		427	703	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604777	48605475	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	CCAGCTCCTAGACGAAGTACTTCATACCATGCCGATTGCAGACCCACAACCTTTAGACTGAGGTCTTTTACCGTTGGGGCCCTTAACCTTATCAGGATGGTGGACTACAAAATACAATCCTGTTTATAATCTGAAGATATATTTCACTTTTGTTCTGCTTTATCTTTTCATAAAGGGTTGAAAATGTGTTTGCTGCCTTGCTCCTAGCAGACAGAAACTGGATTAAAACAATTTTTTTTTTCCTCTTCAGAACTTGTCAGGCATGGCTCAGAGCTTGAAGATTAGGAGAAACACATTCTTATTAATTCTTCACCTGTTATGTATGAAGGAATCATTCCAGTGCTAGAAAATTTAGCCCTTTAAAACGTCTTAGAGCCTTTTATCTGCAGAACATCGATATGTATATCATTCTACAGAATAATCCAGTATTGCTGATTTTAAAGGCAGAGAAGTTCTCAAAGTTAATTCACCTATGTTATTTTGTGTACAAGTTGTTATTGTTGAACATACTTCAAAAATAATGTGCCATGTGGGTGAGTTAATTTTACCAAGAGTAACTTTACTCTGTGTTTAAAAAGTAAGTTAATAATGTATTGTAATCTTTCATCCAAAATATTTTTTGCAAGTTATATTAGTGAAGATGGTTTCAATTCAGATTGTCTTGCAACTTCAGTTTTATTTTTGCCAAGGCAAAAAACT	CCAGCTCCTAGACGAAGTACTTCATACCATGCCGATTGCAGACCCACAACCTTTAGACTGAGGTCTTTTACCGTTGGGGCCCTTAACCTTATCAGGATGGTGGACTACAAAATACAATCCTGTTTATAATCTGAAGATATATTTCACTTTTGTTCTGCTTTATCTTTTCATAAAGGGTTGAAAATGTGTTTGCTGCCTTGCTCCTAGCAGACAGAAACTGGATTAAAACAATTTTTTTTTTCCTCTTCAGAACTTGTCAGGCATGGCTCAGAGCTTGAAGATTAGGAGAAACACATTCTTATTAATTCTTCACCTGTTATGTATGAAGGAATCATTCCAGTGCTAGAAAATTTAGCCCTTTAAAACGTCTTAGAGCCTTTTATCTGCAGAACATCGATATGTATATCATTCTACAGAATAATCCAGTATTGCTGATTTTAAAGGCAGAGAAGTTCTCAAAGTTAATTCACCTATGTTATTTTGTGTACAAGTTGTTATTGTTGAACATACTTCAAAAATAATGTGCCATGTGGGTGAGTTAATTTTACCAAGAGTAACTTTACTCTGTGTTTAAAAAGTAAGTTAATAATGTATTGTAATCTTTCATCCAAAATATTTTTTGCAAGTTATATTAGTGAAGATGGTTTCAATTCAGATTGTCTTGCAACTTCAGTTTTATTTTTGCCAAGGCAAAAAACT	-	novel	NA	P-0006634-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	96	560	0	ENST00000342988.3:c.1600_*639del		p.*534*	ENST00000342988	NM_005359.5	533		12/12	0.384486904258882	1	FACETS	0.673	0.602	0.749	0.673	0.602	0.749	SUBCLONAL	1	TRUE	0	0.423402821259898	1		560	531	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0006634-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	294	656	0	ENST00000311936.3:c.34_35delinsAT	p.Gly12Ile	p.G12I	ENST00000311936	NM_004985.3	12	GGt/ATt	2/5	0.405474831318172	3	FACETS	0.778	0.732	0.824	0.778	0.732	0.824	SUBCLONAL	2	TRUE	1	0.423402821259898	3		656	1082	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212045	94212045	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	T	novel	NA	P-0006634-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	115	438	0	ENST00000323929.3:c.403-3T>A		p.X135_splice	ENST00000323929	NM_005591.3	135			1	2	FACETS	0.846	0.764	0.933	0.846	0.764	0.933	CLONAL	1	TRUE	1	0.423402821259898	2		438	642	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	367	722	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.526664713908116	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.526664713908116	3		722	867	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578504	7578540	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTG	AGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTG	-	novel	NA	P-0006691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	526	949	0	ENST00000269305.4:c.390_426del	p.Asn131CysfsTer27	p.N131Cfs*27	ENST00000269305	NM_001126112.2	130	ctCAACAAGATGTTTTGCCAACTGGCCAAGACCTGCCCT/ct	5/11	0.526664713908116	2	FACETS	0.899	0.865	0.933	0.899	0.865	0.933	CLONAL	2	TRUE	0	0.526664713908116	2		949	1111	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573622	48573622	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	25	383	0	ENST00000342988.3:c.206del	p.Ser69IlefsTer25	p.S69Ifs*25	ENST00000342988	NM_005359.5	69	aGt/at	2/12	0.526664713908116	1	FACETS	0.171	0.134	0.213	0.171	0.134	0.213	SUBCLONAL	1	TRUE	0	0.526664713908116	1		383	410	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584822	48584822	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	93	339	0	ENST00000342988.3:c.901del	p.Tyr301ThrfsTer35	p.Y301Tfs*35	ENST00000342988	NM_005359.5	300	caT/ca	7/12	0.526664713908116	1	FACETS	0.761	0.683	0.842	0.761	0.683	0.842	SUBCLONAL	1	TRUE	0	0.526664713908116	1		339	342	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0006721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	258	749	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.315800508954655	2	FACETS	0.982	0.922	1	0.982	0.922	1	CLONAL	2	TRUE	0	0.317838546589277	2		750	827	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775569	39775569	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	170	659	0	ENST00000288319.7:c.451G>C	p.Gly151Arg	p.G151R	ENST00000288319	NM_182918.3	151	Ggc/Cgc	4/10	0.315800508954655	2	FACETS	0.972	0.9	1	0.972	0.9	1	CLONAL	2	TRUE	0	0.317838546589277	2		659	550	SUCCESS
APC	324	MSKCC	GRCh37	5	112175498	112175498	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	117	423	0	ENST00000257430.4:c.4207del	p.Ser1403AlafsTer12	p.S1403Afs*12	ENST00000257430	NM_000038.5	1403	Agc/gc	16/16	0.315800508954655	2	FACETS	0.916	0.833	1	0.916	0.833	1	CLONAL	2	TRUE	0	0.317838546589277	2		423	402	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101271	4101271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776316565	NA	P-0006721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	100	863	0	ENST00000262948.5:c.536G>A	p.Arg179Gln	p.R179Q	ENST00000262948	NM_030662.3	179	cGg/cAg	5/11	0.317838546589277	3	FACETS	0.95	0.848	1	0.317	0.282	0.353	CLONAL	1	TRUE	0	0.317838546589277	3		863	768	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0006803-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1312	81	749	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.159	0.139	0.181	0.159	0.139	0.181	SUBCLONAL	1	TRUE	1	0.731315452495182	2		750	1393	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732285	74732285	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006803-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	156	442	0	ENST00000359995.5:c.624T>G	p.Ser208Arg	p.S208R	ENST00000359995	NM_001195427.1	208	agT/agG	2/3	1	2	FACETS	0.965	0.892	1	0.965	0.892	1	CLONAL	1	TRUE	1	0.731315452495182	2		442	442	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211069	36211069	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006803-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	510	1911	0	ENST00000222270.7:c.820C>G	p.Pro274Ala	p.P274A	ENST00000222270	NM_014727.1	274	Cca/Gca	3/37	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.731315452495182	2		1911	1338	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133173	38133173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006803-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	408	1325	0	ENST00000317025.8:c.4300G>A	p.Glu1434Lys	p.E1434K	ENST00000317025	NM_023034.1	1434	Gaa/Aaa	24/24	1	2	FACETS	0.912	0.869	0.957	0.912	0.869	0.957	CLONAL	1	TRUE	1	0.731315452495182	2		1325	1223	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599904	10599904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006950-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	326	838	0	ENST00000171111.5:c.1672G>A	p.Gly558Arg	p.G558R	ENST00000171111	NM_203500.1	558	Ggg/Agg	5/6	0.399584761217172	2	FACETS	0.944	0.896	0.994	0.944	0.896	0.994	CLONAL	2	TRUE	0	0.4	2		838	863	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422367	47422367	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0006950-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	93	470	0	ENST00000377045.4:c.1A>G	p.Met1?	p.M1?	ENST00000377045	NM_001654.4	1	Atg/Gtg	2/16	1	2	FACETS	0.934	0.833	1	0.934	0.833	1	CLONAL	1	TRUE	1	0.4	2		470	498	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0007080-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	100	650	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.21	2		650	902	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266490	55266490	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007080-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	64	827	0	ENST00000275493.2:c.2782G>C	p.Glu928Gln	p.E928Q	ENST00000275493	NM_005228.3	928	Gag/Cag	23/28	1	2	FACETS	0.79	0.683	0.906	0.79	0.683	0.906	CLONAL	1	TRUE	1	0.21	2		827	772	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0007082-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	220	577	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.274340818894338	3	FACETS	0.993	0.925	1	0.993	0.925	1	CLONAL	2	TRUE	1	0.29	3		577	875	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0007082-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	162	493	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.286224143909448	4	FACETS	1	0.985	1	0.679	0.622	0.738	CLONAL	1	TRUE	2	0.29	4		493	1062	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652129	36652129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34916193	NA	P-0007082-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	79	556	0	ENST00000244741.5:c.251G>A	p.Arg84Gln	p.R84Q	ENST00000244741	NM_000389.4	84	cGa/cAa	2/3	0.302151237204602	3	FACETS	0.623	0.547	0.706	0.312	0.273	0.353	SUBCLONAL	1	TRUE	1	0.29	3		556	1001	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222934	5222934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768350891	NA	P-0007082-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	94	695	0	ENST00000357368.4:c.2869G>A	p.Glu957Lys	p.E957K	ENST00000357368	NM_002850.3	957	Gag/Aag	18/38	1	2	FACETS	0.68	0.603	0.761	0.68	0.603	0.761	SUBCLONAL	1	TRUE	1	0.29	2		695	954	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857875	9857875	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007082-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	89	519	0	ENST00000330684.3:c.3526G>A	p.Glu1176Lys	p.E1176K	ENST00000330684	NM_001134407.1	1176	Gag/Aag	13/13	0.302151237204602	4	FACETS	0.881	0.78	0.989	0.294	0.26	0.33	CLONAL	1	TRUE	1	0.29	4		519	899	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164126	47164127	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007082-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	75	297	0	ENST00000409792.3:c.1999dup	p.Cys667LeufsTer16	p.C667Lfs*16	ENST00000409792	NM_014159.6	667	tgt/tTgt	3/21	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.29	2		297	499	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0007083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	497	592	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.501388745577242	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	4	TRUE	0	0.501388745577242	4		592	722	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1023835002	NA	P-0007083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	144	314	0	ENST00000558401.1:c.1A>G	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Gtg	1/4	0.501388745577242	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.501388745577242	1		314	317	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579533	7579533	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	175	730	0	ENST00000269305.4:c.154C>T	p.Gln52Ter	p.Q52*	ENST00000269305	NM_001126112.2	52	Caa/Taa	4/11	0.501388745577242	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.501388745577242	1		730	466	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133883	55133883	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	112	345	0	ENST00000257290.5:c.1096G>C	p.Asp366His	p.D366H	ENST00000257290	NM_006206.4	366	Gat/Cat	7/23	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.501388745577242	2		345	353	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972633	25972633	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	181	355	0	ENST00000435504.4:c.1792C>T	p.Gln598Ter	p.Q598*	ENST00000435504		598	Cag/Tag	12/13	0.501388745577242	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.501388745577242	2		355	352	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52663002	52663002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	104	371	0	ENST00000394830.3:c.1351G>A	p.Asp451Asn	p.D451N	ENST00000394830	NM_018313.4	451	Gat/Aat	13/30	0.501388745577242	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.501388745577242	1		371	300	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81399233	81399233	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	312	625	0	ENST00000222390.5:c.55C>T	p.Leu19Phe	p.L19F	ENST00000222390	NM_000601.4	19	Ctc/Ttc	1/18	0.501388745577242	4	FACETS	0.993	0.939	1	0.993	0.939	1	CLONAL	2	TRUE	2	0.501388745577242	4		625	941	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220464	133220464	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	148	566	0	ENST00000320574.5:c.4249G>T	p.Glu1417Ter	p.E1417*	ENST00000320574	NM_006231.2	1417	Gag/Tag	33/49	0.501388745577242	3	FACETS	1	0.969	1	0.373	0.342	0.406	CLONAL	1	TRUE	0	0.501388745577242	3		566	659	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252685	133252685	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149029910	NA	P-0007083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	98	539	1	ENST00000320574.5:c.1015G>A	p.Asp339Asn	p.D339N	ENST00000320574	NM_006231.2	339	Gat/Aat	10/49	0.501388745577242	3	FACETS	0.781	0.698	0.869	0.26	0.232	0.29	SUBCLONAL	1	TRUE	0	0.501388745577242	3		540	626	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619027	37619027	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	282	573	0	ENST00000447079.4:c.703G>C	p.Asp235His	p.D235H	ENST00000447079	NM_015083.1	235	Gat/Cat	1/14	0.501388745577242	3	FACETS	0.985	0.931	1	0.985	0.931	1	CLONAL	2	TRUE	1	0.501388745577242	3		573	714	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022766	31022766	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs6058693	NA	P-0007083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	612	501	0	ENST00000375687.4:c.2251G>T	p.Val751Phe	p.V751F	ENST00000375687	NM_015338.5	751	Gtt/Ttt	13/13	0.501388745577242	5	FACETS	1	0.994	1			1	CLONAL	5	TRUE	NA	0.501388745577242	5		501	811	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28903809	28903809	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	120	586	1	ENST00000282397.4:c.2650del	p.His884ThrfsTer6	p.H884Tfs*6	ENST00000282397	NM_002019.4	884	Cac/ac	19/30	0.501388745577242	2	FACETS	0.926	0.84	1	0.463	0.42	0.508	CLONAL	1	TRUE	0	0.501388745577242	2		587	517	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007770	45007787	+	inframe_deletion	In_Frame_Del	DEL	GACTTGTCTTTCAGCAAG	GACTTGTCTTTCAGCAAG	-	novel	NA	P-0007083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	193	314	0	ENST00000558401.1:c.221_238del	p.Leu74_Asp79del	p.L74_D79del	ENST00000558401	NM_004048.2	73	GACTTGTCTTTCAGCAAG/-	2/4	NA	2	FACETS	0.908	0.851	0.965			1	INDETERMINATE	2	TRUE	NA	0.501388745577242	2		314	424	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646388	3646388	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	177	632	1	ENST00000294008.3:c.1690A>G	p.Met564Val	p.M564V	ENST00000294008	NM_032444.2	564	Atg/Gtg	8/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.501388745577242	2		633	597	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874283	151874283	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	207	309	2	ENST00000262189.6:c.8255G>T	p.Gly2752Val	p.G2752V	ENST00000262189	NM_170606.2	2752	gGa/gTa	38/59	0.501388745577242	4	FACETS	1	0.984	1			1	CLONAL	2	TRUE	NA	0.501388745577242	4		311	535	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38148103	38148105	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0007083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	91	735	0	ENST00000317025.8:c.3006_3008del	p.Phe1003del	p.F1003del	ENST00000317025	NM_023034.1	1002	ttCTTt/ttt	17/24	1	2	FACETS	0.544	0.483	0.609	0.544	0.483	0.609	SUBCLONAL	1	TRUE	1	0.501388745577242	2		735	667	SUCCESS
AR	367	MSKCC	GRCh37	X	66943552	66943552	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137852578	NA	P-0007137-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	131	233	0	ENST00000374690.3:c.2632A>G	p.Thr878Ala	p.T878A	ENST00000374690	NM_000044.3	878	Act/Gct	8/8	1	1	FACETS	0.86	0.792	0.929	1	0.99	1	CLONAL	2	TRUE	0	0.378849384290193	1		233	326	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0007137-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	164	358	0	ENST00000374080.3:c.3670C>T	p.Leu1224Phe	p.L1224F	ENST00000374080		1224	Ctc/Ttc	26/45	1	1	FACETS	0.904	0.841	0.968	1	0.992	1	CLONAL	2	TRUE	0	0.378849384290193	1		358	388	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255092	16255093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007137-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	148	540	4	ENST00000375759.3:c.2363dup	p.Asn788LysfsTer2	p.N788Kfs*2	ENST00000375759	NM_015001.2	786	aca/acAa	11/15	1	2	FACETS	0.974	0.891	1	0.974	0.891	1	CLONAL	1	TRUE	1	0.378849384290193	2		544	802	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139648	202139648	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007137-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	114	411	0	ENST00000358485.4:c.809C>G	p.Ser270Cys	p.S270C	ENST00000358485	NM_001080125.1	270	tCt/tGt	6/9	1	2	FACETS	0.852	0.768	0.941	0.852	0.768	0.941	CLONAL	1	TRUE	1	0.378849384290193	2		411	706	SUCCESS
AR	367	MSKCC	GRCh37	X	66905879	66905879	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007137-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	25	203	0	ENST00000374690.3:c.1796G>C	p.Arg599Thr	p.R599T	ENST00000374690	NM_000044.3	599	aGa/aCa	3/8	1	1	FACETS	0.305	0.24	0.379	0.305	0.24	0.379	SUBCLONAL	1	TRUE	0	0.378849384290193	1		203	351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576913	7576913	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567546373	NA	P-0007307-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	78	514	0	ENST00000269305.4:c.933del	p.Asn311LysfsTer34	p.N311Kfs*34	ENST00000269305	NM_001126112.2	311	aaC/aa	9/11	1	2	FACETS	0.642	0.565	0.726	0.642	0.565	0.726	SUBCLONAL	1	TRUE	1	0.38	2		514	639	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0007415-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	199	435	0				ENST00000310581	NM_198253.2	-/1132			0.32463595518333	6	FACETS	1	0.99	1	0.477	0.442	0.514	INDETERMINATE	1	TRUE	3	0.761983210487822	6		435	921	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0007415-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	439	943	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.32463595518333	6	FACETS	0.899	0.86	0.939	0.899	0.86	0.939	INDETERMINATE	3	TRUE	3	0.761983210487822	6		943	1078	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0007415-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	908	733	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	0.761983210487822	2	FACETS	0.982	0.962	1	0.982	0.962	1	CLONAL	2	TRUE	0	0.761983210487822	2		733	1213	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916852	48916852	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0007415-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	115	586	0	ENST00000267163.4:c.380+2T>C		p.X127_splice	ENST00000267163	NM_000321.2	127			0.761983210487822	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.761983210487822	1		586	185	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0007415-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	201	435	0				ENST00000310581	NM_198253.2	-/1132			0.537327250390665	4	FACETS	0.987	0.914	1			1	CLONAL	1	TRUE	NA	0.674736389758219	4		435	1011	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0007415-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	444	943	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.674736389758219	4	FACETS	0.945	0.903	0.987	0.945	0.903	0.987	CLONAL	2	TRUE	2	0.674736389758219	4		943	1166	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0007415-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	579	733	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	0.674736389758219	2	FACETS	0.938	0.909	0.966	0.938	0.909	0.966	CLONAL	2	TRUE	0	0.674736389758219	2		733	915	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916852	48916852	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0007415-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	116	586	0	ENST00000267163.4:c.380+2T>C		p.X127_splice	ENST00000267163	NM_000321.2	127			0.671937686559251	1	FACETS	0.85	0.78	0.921	0.85	0.78	0.921	CLONAL	1	TRUE	0	0.674736389758219	1		586	268	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945028	151945028	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007415-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	28	232	0	ENST00000262189.6:c.2491A>G	p.Thr831Ala	p.T831A	ENST00000262189	NM_170606.2	831	Act/Gct	14/59	0.674736389758219	4	FACETS	0.517	0.414	0.633	0.258	0.207	0.317	SUBCLONAL	1	TRUE	2	0.674736389758219	4		232	269	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751958	57751958	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007415-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	157	627	0	ENST00000274289.3:c.1279G>A	p.Val427Ile	p.V427I	ENST00000274289	NM_006622.3	427	Gtt/Att	10/14	0.674736389758219	4	FACETS	0.769	0.703	0.837	0.384	0.351	0.419	SUBCLONAL	1	TRUE	2	0.674736389758219	4		627	1014	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0007415-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	149	435	0				ENST00000310581	NM_198253.2	-/1132			0.360476081593283	4	FACETS	0.892	0.815	0.973			1	CLONAL	1	TRUE	NA	0.567166824091591	4		435	923	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0007415-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	398	943	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.56718682817328	4	FACETS	0.953	0.907	0.999	0.953	0.907	0.999	CLONAL	2	TRUE	2	0.567166824091591	4		943	1154	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0007415-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	455	733	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	0.567166824091591	2	FACETS	0.97	0.934	1	0.97	0.934	1	CLONAL	2	TRUE	0	0.567166824091591	2		733	827	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916852	48916852	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0007415-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	162	586	0	ENST00000267163.4:c.380+2T>C		p.X127_splice	ENST00000267163	NM_000321.2	127			0.551105606322656	1	FACETS	0.965	0.895	1	0.965	0.895	1	CLONAL	1	TRUE	0	0.567166824091591	1		586	424	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945028	151945028	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007415-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	28	232	0	ENST00000262189.6:c.2491A>G	p.Thr831Ala	p.T831A	ENST00000262189	NM_170606.2	831	Act/Gct	14/59	0.56718682817328	4	FACETS	0.469	0.375	0.576	0.234	0.187	0.288	SUBCLONAL	1	TRUE	2	0.567166824091591	4		232	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0007508-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	344	1002	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.738102125906268	1	FACETS	0.974	0.933	1	0.974	0.933	1	CLONAL	1	TRUE	0	0.746657802922551	1		1003	593	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0007508-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	1640	650	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.746657802922551	7	FACETS	0.956	0.941	0.97	0.956	0.941	0.97	CLONAL	6	TRUE	1	0.746657802922551	7		650	2196	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0007508-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1833	257	664	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.746657802922551	7	FACETS	0.944	0.88	1	0.157	0.146	0.169	CLONAL	1	TRUE	1	0.746657802922551	7		665	2090	SUCCESS
APC	324	MSKCC	GRCh37	5	112175809	112175809	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007508-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	155	223	0	ENST00000257430.4:c.4518del	p.Ser1507ValfsTer3	p.S1507Vfs*3	ENST00000257430	NM_000038.5	1506	ctG/ct	16/16	0.726558673436653	1	FACETS	0.957	0.896	1	0.957	0.896	1	CLONAL	1	TRUE	0	0.746657802922551	1		223	272	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465566	8465566	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007508-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	148	457	0	ENST00000356435.5:c.3614T>A	p.Leu1205Gln	p.L1205Q	ENST00000356435		1205	cTg/cAg	21/35	0.61540485208601	3	FACETS	0.513	0.467	0.56	0.171	0.155	0.187	SUBCLONAL	1	TRUE	0	0.746657802922551	3		457	1062	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593387	48593387	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0007630-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	319	255	0	ENST00000342988.3:c.1140-2A>T		p.X380_splice	ENST00000342988	NM_005359.5	380			0.795653513180588	2	FACETS	0.983	0.952	1	0.983	0.952	1	CLONAL	2	TRUE	0	0.801336210268812	2		255	405	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102067	27102067	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0007630-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	49	479	0	ENST00000324856.7:c.4994-1G>A		p.X1665_splice	ENST00000324856	NM_006015.4	1665			0.795653513180588	2	FACETS	0.138	0.116	0.162	0.069	0.058	0.081	SUBCLONAL	1	TRUE	0	0.801336210268812	2		479	887	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843689	156843689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007630-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1313	463	847	0	ENST00000524377.1:c.1115C>T	p.Ala372Val	p.A372V	ENST00000524377	NM_002529.3	372	gCc/gTc	8/17	0.801336210268812	3	FACETS	0.911	0.868	0.955	0.456	0.434	0.478	CLONAL	1	TRUE	1	0.801336210268812	3		847	1776	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188147	108188148	+	stop_gained	Nonsense_Mutation	DNP	AG	AG	GT	novel	NA	P-0007630-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	283	485	0	ENST00000278616.4:c.6246_6247delinsGT	p.Gly2083Ter	p.G2083*	ENST00000278616	NM_000051.3	2082	aaAGga/aaGTga	43/63	0.801336210268812	2	FACETS	0.839	0.791	0.888	0.419	0.395	0.444	CLONAL	1	TRUE	0	0.801336210268812	2		485	842	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272246	15272246	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007630-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	96	408	1	ENST00000263388.2:c.6193A>T	p.Arg2065Trp	p.R2065W	ENST00000263388	NM_000435.2	2065	Agg/Tgg	33/33	0.801336210268812	3	FACETS	0.356	0.316	0.398	0.178	0.158	0.199	SUBCLONAL	1	TRUE	1	0.801336210268812	3		409	944	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18958610	18958610	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007630-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1325	157	717	0	ENST00000262803.5:c.429G>C	p.Trp143Cys	p.W143C	ENST00000262803	NM_002911.3	143	tgG/tgC	3/24	0.801336210268812	3	FACETS	0.37	0.338	0.405	0.185	0.169	0.203	SUBCLONAL	1	TRUE	1	0.801336210268812	3		717	1482	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76919008	76919008	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007630-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	66	366	0	ENST00000373344.5:c.3983C>G	p.Ser1328Cys	p.S1328C	ENST00000373344	NM_000489.3	1328	tCt/tGt	12/35	0.795653513180588	2	FACETS	0.239	0.207	0.273	0.119	0.103	0.137	SUBCLONAL	1	TRUE	0	0.801336210268812	2		366	690	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0007659-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	550	493	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.87932110059792	4	FACETS	0.97	0.942	0.998	0.97	0.942	0.998	CLONAL	3	TRUE	1	0.87932110059792	4		493	808	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0007659-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	294	668	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.87932110059792	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.87932110059792	1		669	373	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223695	36223695	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007659-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2215	165	884	0	ENST00000222270.7:c.6245G>T	p.Gly2082Val	p.G2082V	ENST00000222270	NM_014727.1	2082	gGc/gTc	28/37	0.87932110059792	6	FACETS	0.435	0.397	0.475			1	SUBCLONAL	1	TRUE	NA	0.87932110059792	6		884	2380	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6048647	6048647	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1554309080	NA	P-0007659-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	251	674	0	ENST00000265849.7:c.4G>C	p.Glu2Gln	p.E2Q	ENST00000265849	NM_000535.5	2	Gag/Cag	1/15	0.87932110059792	4	FACETS	0.975	0.912	1	0.325	0.304	0.347	CLONAL	1	TRUE	1	0.87932110059792	4		674	1100	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246447	53246447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782726212	NA	P-0007677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	429	436	0	ENST00000375401.3:c.535C>T	p.Arg179Cys	p.R179C	ENST00000375401	NM_004187.3	179	Cgt/Tgt	5/26	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.675065595737671	1		436	642	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0007788-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	253	396	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.400012487165647	3	FACETS	1	0.969	1	1	0.993	1	CLONAL	3	TRUE	1	0.12	3		396	1401	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0007788-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	12	202	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.342	0.239	0.471	0.342	0.239	0.471	SUBCLONAL	1	TRUE	1	0.12	2		202	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577562	7577563	+	missense_variant	Missense_Mutation	DNP	CT	CT	AA	novel	NA	P-0007788-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	63	625	0	ENST00000269305.4:c.718_719delinsTT	p.Ser240Phe	p.S240F	ENST00000269305	NM_001126112.2	240	AGt/TTt	7/11	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.12	2		625	931	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0007895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	488	1365	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.310481524524277	3	FACETS	1	0.994	1	0.804	0.771	0.838	CLONAL	2	TRUE	0	0.413795949802982	3		1365	1180	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514758	103514758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143667470	NA	P-0007895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	27	336	1	ENST00000355739.4:c.1259G>A	p.Arg420His	p.R420H	ENST00000355739	NM_000123.3	420	cGt/cAt	8/15	0.376979496258602	3	FACETS	0.408	0.324	0.504	0.204	0.162	0.252	SUBCLONAL	1	TRUE	1	0.413795949802982	3		337	386	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201692	66201692	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753118521	NA	P-0007895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	34	669	0	ENST00000273854.3:c.2810G>A	p.Arg937His	p.R937H	ENST00000273854	NM_004439.5	937	cGt/cAt	16/18	0.221803862706133	2	FACETS	0.299	0.244	0.362	0.15	0.122	0.181	INDETERMINATE	1	TRUE	0	0.413795949802982	2		669	549	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058474	69058474	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	26	340	1	ENST00000288368.4:c.4118G>T	p.Ser1373Ile	p.S1373I	ENST00000288368	NM_024870.2	1373	aGt/aTt	34/40	0.180281558283342	3	FACETS	0.435	0.344	0.538	0.145	0.114	0.18	INDETERMINATE	1	TRUE	0	0.413795949802982	3		341	349	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007898-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	143	722	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.783	0.714	0.856	0.783	0.714	0.856	SUBCLONAL	1	TRUE	1	0.398584132310415	2		722	916	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0007898-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	170	867	8	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.356151584053565	1	FACETS	0.969	0.894	1	0.969	0.894	1	CLONAL	1	TRUE	0	0.398584132310415	1		875	705	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243668559	243668559	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007898-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	111	438	0	ENST00000263826.5:c.1432C>T	p.Arg478Ter	p.R478*	ENST00000263826	NM_005465.4	478	Cga/Tga	13/13	1	2	FACETS	0.812	0.731	0.898	0.812	0.731	0.898	CLONAL	1	TRUE	1	0.398584132310415	2		438	686	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48586246	48586247	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007898-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	177	517	0	ENST00000342988.3:c.917dup	p.Asn306LysfsTer2	p.N306Kfs*2	ENST00000342988	NM_005359.5	305	-/A	8/12	0.356151584053565	1	FACETS	0.973	0.899	1	0.973	0.899	1	CLONAL	1	TRUE	0	0.398584132310415	1		517	731	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880169	151880169	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007898-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	326	509	1	ENST00000262189.6:c.5155C>T	p.Gln1719Ter	p.Q1719*	ENST00000262189	NM_170606.2	1719	Cag/Tag	35/59	0.391279668571269	3	FACETS	0.966	0.914	1	0.966	0.914	1	CLONAL	2	TRUE	1	0.398584132310415	3		510	1015	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431257	49431267	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCTGGGCAG	GGCCTGGGCAG	-	novel	NA	P-0007898-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	122	390	0	ENST00000301067.7:c.9872_9882del	p.Pro3291HisfsTer6	p.P3291Hfs*6	ENST00000301067	NM_003482.3	3291	cCTGCCCAGGCC/c	34/54	1	2	FACETS	0.908	0.822	0.999	0.908	0.822	0.999	CLONAL	1	TRUE	1	0.398584132310415	2		390	674	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0008024-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	514	376	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.901730236885469	2	FACETS	1	0.984	1	0.52	0.5	0.54	CLONAL	1	TRUE	0	0.901730236885469	2		376	1096	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115873	8115874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0008024-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	617	725	0	ENST00000346208.3:c.1220dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tCcg	6/6	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.901730236885469	2		725	1306	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426305	49426305	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs775432028	NA	P-0008024-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	1564	1163	2	ENST00000301067.7:c.12183A>C	p.Glu4061Asp	p.E4061D	ENST00000301067	NM_003482.3	4061	gaA/gaC	39/54	0.609764786347536	3	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.901730236885469	3		1165	2473	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609442	81609442	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008024-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	504	665	0	ENST00000298171.2:c.1040A>T	p.His347Leu	p.H347L	ENST00000298171	NM_000369.2	347	cAt/cTt	10/10	1	2	FACETS	0.951	0.913	0.99	0.951	0.913	0.99	CLONAL	1	TRUE	1	0.901730236885469	2		665	1175	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934162	48934162	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0008024-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	322	388	0	ENST00000267163.4:c.617T>A	p.Leu206Ter	p.L206*	ENST00000267163	NM_000321.2	206	tTa/tAa	7/27	0.900991164557829	1	FACETS	0.973	0.943	1	0.973	0.943	1	CLONAL	1	TRUE	0	0.901730236885469	1		388	403	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047952	180047952	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008024-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1386	618	952	2	ENST00000261937.6:c.2223G>T	p.Glu741Asp	p.E741D	ENST00000261937	NM_182925.4	741	gaG/gaT	15/30	0.831139878214054	3	FACETS	0.992	0.953	1	0.496	0.476	0.516	CLONAL	1	TRUE	1	0.901730236885469	3		954	2004	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939016	76939023	+	frameshift_variant	Frame_Shift_Del	DEL	TTTTTGAT	TTTTTGAT	-	novel	NA	P-0008024-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	431	651	0	ENST00000373344.5:c.1725_1732del	p.Lys575AsnfsTer4	p.K575Nfs*4	ENST00000373344	NM_000489.3	575	aaATCAAAAAct/aact	9/35	0.900991164557829	1	FACETS	0.932	0.906	0.958	0.932	0.906	0.958	CLONAL	1	TRUE	0	0.901730236885469	1		651	563	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0008238-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	159	722	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.205561395940859	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.205561395940859	3		722	788	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0008238-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	248	1002	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	NA	2	FACETS	0.996	0.93	1			1	INDETERMINATE	2	TRUE	NA	0.205561395940859	2		1003	1211	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979623	55979623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764358120	NA	P-0008238-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	67	771	0	ENST00000263923.4:c.824G>A	p.Arg275Gln	p.R275Q	ENST00000263923	NM_002253.2	275	cGa/cAa	7/30	NA	2	FACETS	0.804	0.697	0.92			1	INDETERMINATE	1	TRUE	NA	0.205561395940859	2		771	811	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0008334-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	612	577	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.754719558905148	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.778764573132853	3		577	1046	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008334-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	1118	365	0	ENST00000206249.3:c.1610A>G	p.Tyr537Cys	p.Y537C	ENST00000206249	NM_000125.3	537	tAt/tGt	8/8	0.270696156304578	6	FACETS	1	0.997	1			1	INDETERMINATE	4	TRUE	NA	0.778764573132853	6		365	1639	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459277	120459277	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs761872871	NA	P-0008334-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	302	314	0	ENST00000256646.2:c.6068A>G	p.Tyr2023Cys	p.Y2023C	ENST00000256646	NM_024408.3	2023	tAt/tGt	34/34	0.754719558905148	3	FACETS	0.927	0.873	0.982	0.463	0.436	0.491	CLONAL	1	TRUE	1	0.778764573132853	3		314	1163	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984739	11984739	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008334-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	222	272	0	ENST00000353533.5:c.285G>A	p.Trp95Ter	p.W95*	ENST00000353533	NM_003010.3	95	tgG/tgA	3/11	0.778764573132853	1	FACETS	0.978	0.93	1	0.978	0.93	1	CLONAL	1	TRUE	0	0.778764573132853	1		272	356	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453380	40453380	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008334-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	394	517	0	ENST00000345506.4:c.1077G>T	p.Lys359Asn	p.K359N	ENST00000345506	NM_003152.3	359	aaG/aaT	10/20	1	2	FACETS	0.927	0.883	0.972	0.927	0.883	0.972	CLONAL	1	TRUE	1	0.778764573132853	2		517	1091	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755515	39755515	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008334-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	234	272	0	ENST00000288319.7:c.1250A>T	p.Tyr417Phe	p.Y417F	ENST00000288319	NM_182918.3	417	tAc/tTc	10/10	1	2	FACETS	0.948	0.89	1	0.948	0.89	1	CLONAL	1	TRUE	1	0.778764573132853	2		272	634	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662606	117662606	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008334-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	52	361	0	ENST00000368508.3:c.4859T>G	p.Leu1620Arg	p.L1620R	ENST00000368508	NM_002944.2	1620	cTc/cGc	29/43	0.778764573132853	1	FACETS	0.154	0.131	0.179	0.154	0.131	0.179	SUBCLONAL	1	TRUE	0	0.778764573132853	1		361	530	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0008346-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	164	843	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.995	0.913	1	0.995	0.913	1	CLONAL	1	TRUE	1	0.32	2		843	1030	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884952	111884952	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1281832778	NA	P-0008346-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	67	907	0	ENST00000341259.2:c.950T>C	p.Met317Thr	p.M317T	ENST00000341259	NM_005475.2	317	aTg/aCg	5/8	1	2	FACETS	0.415	0.359	0.476	0.415	0.359	0.476	SUBCLONAL	1	TRUE	1	0.32	2		907	1009	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061137	38061161	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCCCGCTTCCGCTCCCGCCCCCG	GCCCCCGCTTCCGCTCCCGCCCCCG	-	novel	NA	P-0008346-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	38	199	0	ENST00000250448.2:c.828_852del	p.Gly277AlafsTer36	p.G277Afs*36	ENST00000250448	NM_004496.3	276	ggCGGGGGCGGGAGCGGAAGCGGGGGC/gg	2/2	1	2	FACETS	0.784	0.651	0.931	0.784	0.651	0.931	CLONAL	1	TRUE	1	0.32	2		199	303	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954334	48954335	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	rs587778832	NA	P-0008346-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	46	612	0	ENST00000267163.4:c.1456_1457del	p.Leu486IlefsTer6	p.L486Ifs*6	ENST00000267163	NM_000321.2	485	tcTTta/tcta	16/27	1	2	FACETS	0.365	0.306	0.431	0.365	0.306	0.431	SUBCLONAL	1	TRUE	1	0.32	2		612	787	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004609	16004609	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008346-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	60	631	0	ENST00000268712.3:c.2645del	p.Thr882SerfsTer27	p.T882Sfs*27	ENST00000268712	NM_006311.3	882	aCg/ag	20/46	1	2	FACETS	0.458	0.393	0.528	0.458	0.393	0.528	SUBCLONAL	1	TRUE	1	0.32	2		631	819	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579403	7579410	+	frameshift_variant	Frame_Shift_Del	DEL	GATGACAG	GATGACAG	-	novel	NA	P-0008346-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	87	972	0	ENST00000269305.4:c.277_284del	p.Leu93PhefsTer53	p.L93Ffs*53	ENST00000269305	NM_001126112.2	93	CTGTCATCt/t	4/11	1	2	FACETS	0.445	0.392	0.502	0.445	0.392	0.502	SUBCLONAL	1	TRUE	1	0.32	2		972	1222	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954309	48954309	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008548-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	250	349	0	ENST00000267163.4:c.1430T>G	p.Leu477Arg	p.L477R	ENST00000267163	NM_000321.2	477	cTg/cGg	16/27	0.598707492198995	1	FACETS	0.966	0.91	1	0.966	0.91	1	CLONAL	1	TRUE	0	0.598707492198995	1		349	606	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593640	55593660	+	inframe_deletion	In_Frame_Del	DEL	TTTACATAGACCCAACACAAC	TTTACATAGACCCAACACAAC	-	novel	NA	P-0008548-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	651	503	0	ENST00000288135.5:c.1708_1728del	p.Tyr570_Leu576del	p.Y570_L576del	ENST00000288135	NM_000222.2	569	gTTTACATAGACCCAACACAACtt/gtt	11/21	0.532726880478676	3	FACETS	0.878	0.846	0.91	0.878	0.846	0.91	CLONAL	2	TRUE	1	0.598707492198995	3		503	1609	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120546244	120546244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008548-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	330	534	1	ENST00000229340.5:c.80G>A	p.Arg27His	p.R27H	ENST00000229340	NM_006861.6	27	cGt/cAt	2/6	0.245933053452092	2	FACETS	0.756	0.713	0.8	0.378	0.356	0.4	INDETERMINATE	1	TRUE	0	0.598707492198995	2		535	1458	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599332	55599332	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519710	NA	P-0008548-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	378	445	0	ENST00000288135.5:c.2458G>C	p.Asp820His	p.D820H	ENST00000288135	NM_000222.2	820	Gat/Cat	17/21	0.532726880478676	3	FACETS	1	0.986	1	0.553	0.524	0.583	CLONAL	1	TRUE	1	0.598707492198995	3		445	1484	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0008599-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	19	617	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.170405783714489	4	FACETS	0.325	0.246	0.42	0.163	0.123	0.21	SUBCLONAL	1	TRUE	2	0.261703235834365	4		617	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0008599-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	109	1156	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.223019091122573	1	FACETS	0.813	0.73	0.903	0.813	0.73	0.903	CLONAL	1	TRUE	0	0.261703235834365	1		1156	890	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501595	149501595	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008599-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	91	593	1	ENST00000261799.4:c.2192C>A	p.Ser731Tyr	p.S731Y	ENST00000261799	NM_002609.3	731	tCc/tAc	16/23	0.154672235411258	5	FACETS	1	0.979	1	0.372	0.33	0.416	INDETERMINATE	1	TRUE	1	0.261703235834365	5		594	651	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0008645-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	57	396	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.0939888884904656	3	FACETS	1	0.916	1	0.552	0.472	0.64	CLONAL	1	TRUE	1	0.1	3		396	1084	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0008645-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	40	727	1	ENST00000269305.4:c.920-2A>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			NA	2	FACETS	1	0.877	1			1	INDETERMINATE	1	TRUE	NA	0.1	2		728	746	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879531	151879531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008645-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	36	466	1	ENST00000262189.6:c.5414G>A	p.Gly1805Glu	p.G1805E	ENST00000262189	NM_170606.2	1805	gGg/gAg	36/59	0.0939888884904656	3	FACETS	1	0.924	1	0.629	0.516	0.756	CLONAL	1	TRUE	1	0.1	3		467	601	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10274026	10274026	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs765923835	NA	P-0008695-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	67	827	0	ENST00000340748.4:c.854A>G	p.Lys285Arg	p.K285R	ENST00000340748		285	aAg/aGg	11/40	1	2	FACETS	0.52	0.45	0.596	0.52	0.45	0.596	SUBCLONAL	1	TRUE	1	0.252768073636472	2		827	1020	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302630	15302630	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1349602672	NA	P-0008695-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	79	954	0	ENST00000263388.2:c.728A>G	p.His243Arg	p.H243R	ENST00000263388	NM_000435.2	243	cAc/cGc	5/33	1	2	FACETS	0.535	0.469	0.606	0.535	0.469	0.606	SUBCLONAL	1	TRUE	1	0.252768073636472	2		954	1169	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0008839-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	372	616	1	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.283018937131095	3	FACETS	1	0.965	1			1	CLONAL	3	TRUE	NA	0.283018937131095	3		617	983	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604314	189604314	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008839-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	88	357	0	ENST00000264731.3:c.1481C>A	p.Thr494Asn	p.T494N	ENST00000264731	NM_003722.4	494	aCc/aAc	11/14	0.283018937131095	2	FACETS	0.908	0.805	1	0.454	0.402	0.509	CLONAL	1	TRUE	0	0.283018937131095	2		357	685	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331681	8331681	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008839-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	72	316	0	ENST00000356435.5:c.5435G>T	p.Gly1812Val	p.G1812V	ENST00000356435		1812	gGa/gTa	33/35	1	2	FACETS	0.955	0.835	1	0.955	0.835	1	CLONAL	1	TRUE	1	0.283018937131095	2		316	533	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0008849-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	452	617	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.34653591026508	9	FACETS	1	0.969	1	0.725	0.694	0.757	CLONAL	5	TRUE	2	0.34653591026508	9		617	1137	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242494	55242494	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008849-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	447	515	0	ENST00000275493.2:c.2264C>G	p.Ala755Gly	p.A755G	ENST00000275493	NM_005228.3	755	gCc/gGc	19/28	0.34653591026508	9	FACETS	1	0.985	1	0.758	0.725	0.791	CLONAL	5	TRUE	2	0.34653591026508	9		515	1076	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204513718	204513718	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008849-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	21	205	0	ENST00000367182.3:c.728A>T	p.Glu243Val	p.E243V	ENST00000367182	NM_001278516.1	243	gAg/gTg	9/11	0.300612570604545	2	FACETS	0.381	0.293	0.484	0.191	0.146	0.242	SUBCLONAL	1	TRUE	0	0.34653591026508	2		205	318	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348996	70348996	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008849-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	241	634	0	ENST00000374080.3:c.3508C>G	p.Arg1170Gly	p.R1170G	ENST00000374080		1170	Cgg/Ggg	25/45	0.34653591026508	2	FACETS	0.941	0.883	1	0.941	0.883	1	CLONAL	2	TRUE	0	0.34653591026508	2		634	739	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577132	7577132	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008849-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	268	667	0	ENST00000269305.4:c.806del	p.Ser269ThrfsTer76	p.S269Tfs*76	ENST00000269305	NM_001126112.2	269	aGc/ac	8/11	0.300612570604545	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.34653591026508	2		667	695	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437596	52437597	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0008849-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	82	434	0	ENST00000460680.1:c.1564_1565del	p.Pro522CysfsTer14	p.P522Cfs*14	ENST00000460680	NM_004656.3	522	CCt/t	13/17	0.273483672304287	2	FACETS	1	0.976	1	0.702	0.624	0.784	CLONAL	1	TRUE	0	0.34653591026508	2		434	337	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299806	15299806	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008849-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	23	478	0	ENST00000263388.2:c.1372A>G	p.Met458Val	p.M458V	ENST00000263388	NM_000435.2	458	Atg/Gtg	8/33	1	2	FACETS	0.302	0.235	0.381	0.302	0.235	0.381	SUBCLONAL	1	TRUE	1	0.34653591026508	2		478	439	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958127	2958127	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs769192567	NA	P-0008849-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	82	479	0	ENST00000396946.4:c.2605C>T	p.Arg869Trp	p.R869W	ENST00000396946	NM_032415.4	869	Cgg/Tgg	19/25	0.34653591026508	3	FACETS	1	0.952	1	0.572	0.506	0.643	CLONAL	1	TRUE	1	0.34653591026508	3		479	485	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0008978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1322	368	664	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.360407748123878	5	FACETS	1	0.993	1	0.449	0.424	0.474	INDETERMINATE	1	TRUE	2	0.628182082933225	5		665	1690	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0008978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1230	578	396	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.360407748123878	5	FACETS	0.988	0.948	1	0.659	0.632	0.686	INDETERMINATE	2	TRUE	2	0.628182082933225	5		396	1808	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0008978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	879	1023	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.628182082933225	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.628182082933225	2		1024	1389	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976922	18976922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	146	621	1	ENST00000262803.5:c.3307G>A	p.Gly1103Arg	p.G1103R	ENST00000262803	NM_002911.3	1103	Gga/Aga	23/24	1	2	FACETS	0.475	0.433	0.52	0.475	0.433	0.52	SUBCLONAL	1	TRUE	1	0.628182082933225	2		622	978	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0009056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	657	668	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.751603115301428	2		669	857	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640608	3640608	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2149	226	964	1	ENST00000294008.3:c.3031G>T	p.Val1011Phe	p.V1011F	ENST00000294008	NM_032444.2	1011	Gtc/Ttc	12/15	0.730434809633768	5	FACETS	0.539	0.499	0.58	0.18	0.166	0.194	SUBCLONAL	1	TRUE	2	0.751603115301428	5		965	2375	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391488	84391488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	180	390	0	ENST00000321945.7:c.344G>A	p.Arg115Lys	p.R115K	ENST00000321945	NM_139076.2	115	aGg/aAg	5/9	0.389310404504499	2	FACETS	0.889	0.825	0.954	0.444	0.412	0.477	INDETERMINATE	1	TRUE	0	0.751603115301428	2		390	539	SUCCESS
APC	324	MSKCC	GRCh37	5	112175903	112176111	+	frameshift_variant	Frame_Shift_Del	DEL	GAATCAGAGCAGCCTAAAGAATCAAATGAAAACCAAGAGAAAGAGGCAGAAAAAACTATTGATTCTGAAAAGGACCTATTAGATGATTCAGATGATGATGATATTGAAATACTAGAAGAATGTATTATTTCTGCCATGCCAACAAAGTCATCACGTAAAGCAAAAAAGCCAGCCCAGACTGCTTCAAAATTACCTCCACCTGTGGCAAG	GAATCAGAGCAGCCTAAAGAATCAAATGAAAACCAAGAGAAAGAGGCAGAAAAAACTATTGATTCTGAAAAGGACCTATTAGATGATTCAGATGATGATGATATTGAAATACTAGAAGAATGTATTATTTCTGCCATGCCAACAAAGTCATCACGTAAAGCAAAAAAGCCAGCCCAGACTGCTTCAAAATTACCTCCACCTGTGGCAAG	-	novel	NA	P-0009056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	256	379	0	ENST00000257430.4:c.4615_4823del	p.Ser1539ThrfsTer23	p.S1539Tfs*23	ENST00000257430	NM_000038.5	1538	GAATCAGAGCAGCCTAAAGAATCAAATGAAAACCAAGAGAAAGAGGCAGAAAAAACTATTGATTCTGAAAAGGACCTATTAGATGATTCAGATGATGATGATATTGAAATACTAGAAGAATGTATTATTTCTGCCATGCCAACAAAGTCATCACGTAAAGCAAAAAAGCCAGCCCAGACTGCTTCAAAATTACCTCCACCTGTGGCAAGg/g	16/16	0.751603115301428	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.751603115301428	1		379	375	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553534	106553534	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	62	325	0	ENST00000369096.4:c.1499G>T	p.Gly500Val	p.G500V	ENST00000369096	NM_001198.3	500	gGg/gTg	5/7	1	2	FACETS	0.432	0.374	0.494	0.432	0.374	0.494	SUBCLONAL	1	TRUE	1	0.751603115301428	2		325	382	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554386	141554386	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1864	193	863	1	ENST00000220592.5:c.1765C>A	p.Gln589Lys	p.Q589K	ENST00000220592	NM_012154.3	589	Cag/Aag	14/19	0.581244250846334	6	FACETS	0.625	0.575	0.677	0.156	0.143	0.17	SUBCLONAL	1	TRUE	2	0.751603115301428	6		864	2057	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273884	18273884	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201531496	NA	P-0009247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	99	507	1	ENST00000222254.8:c.1217G>A	p.Arg406His	p.R406H	ENST00000222254	NM_005027.3	406	cGc/cAc	10/16	0.706488823557203	2	FACETS	0.374	0.333	0.417	0.187	0.166	0.209	SUBCLONAL	1	TRUE	0	0.735808898867312	2		508	720	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0009247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	479	478	0	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	0.735808898867312	2	FACETS	0.966	0.937	0.994	0.966	0.937	0.994	CLONAL	2	TRUE	0	0.735808898867312	2		478	674	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11291409	11291409	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	130	474	0	ENST00000361445.4:c.2597A>G	p.Glu866Gly	p.E866G	ENST00000361445	NM_004958.3	866	gAg/gGg	17/58	0.269614968399892	3	FACETS	0.522	0.473	0.574	0.261	0.236	0.287	INDETERMINATE	1	TRUE	1	0.735808898867312	3		474	926	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256315	16256316	+	missense_variant	Missense_Mutation	DNP	AG	AG	TT	novel	NA	P-0009247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	139	541	1	ENST00000375759.3:c.3580_3581delinsTT	p.Ser1194Phe	p.S1194F	ENST00000375759	NM_015001.2	1194	AGt/TTt	11/15	1	2	FACETS	0.444	0.404	0.487	0.444	0.404	0.487	SUBCLONAL	1	TRUE	1	0.735808898867312	2		542	850	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720761	89720761	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	19	158	0	ENST00000371953.3:c.912C>A	p.Cys304Ter	p.C304*	ENST00000371953	NM_000314.4	304	tgC/tgA	8/9	0.735808898867312	2	FACETS	0.568	0.439	0.712	0.284	0.219	0.356	SUBCLONAL	1	TRUE	0	0.735808898867312	2		158	91	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3824654	3824655	+	missense_variant	Missense_Mutation	DNP	CT	CT	AA	novel	NA	P-0009247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	80	358	1	ENST00000262367.5:c.2198_2199delinsTT	p.Gln733Leu	p.Q733L	ENST00000262367	NM_004380.2	733	cAG/cTT	12/31	0.387929638832375	4	FACETS	0.418	0.367	0.473	0.209	0.183	0.237	INDETERMINATE	1	TRUE	2	0.735808898867312	4		359	903	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862125	68862125	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	179	443	1	ENST00000261769.5:c.2213A>T	p.Lys738Ile	p.K738I	ENST00000261769	NM_004360.3	738	aAa/aTa	14/16	0.387929638832375	4	FACETS	0.841	0.775	0.91	0.421	0.387	0.455	INDETERMINATE	1	TRUE	2	0.735808898867312	4		444	1004	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032737	30032737	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	A	novel	NA	P-0009247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	256	200	0	ENST00000338641.4:c.115-3C>A		p.X39_splice	ENST00000338641	NM_000268.3	39			0.735808898867312	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.735808898867312	2		200	336	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582332	119582332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	55	277	0	ENST00000316626.5:c.1069C>T	p.Arg357Trp	p.R357W	ENST00000316626		357	Cgg/Tgg	10/12	0.735808898867312	3	FACETS	0.387	0.331	0.449	0.129	0.11	0.15	SUBCLONAL	1	TRUE	0	0.735808898867312	3		277	528	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658408	117658408	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0009247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	520	502	0	ENST00000368508.3:c.5175T>G	p.Tyr1725Ter	p.Y1725*	ENST00000368508	NM_002944.2	1725	taT/taG	31/43	0.569650759239466	2	FACETS	0.908	0.881	0.936	0.908	0.881	0.936	CLONAL	2	TRUE	0	0.735808898867312	2		502	778	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965467	68965467	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	150	527	0	ENST00000288368.4:c.1079G>C	p.Arg360Thr	p.R360T	ENST00000288368	NM_024870.2	360	aGa/aCa	9/40	0.735808898867312	3	FACETS	0.498	0.454	0.544	0.166	0.151	0.182	SUBCLONAL	1	TRUE	0	0.735808898867312	3		527	1121	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060929	38060931	+	missense_variant	Missense_Mutation	TNP	AGG	AGG	GGT	novel	NA	P-0009247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	58	278	0	ENST00000250448.2:c.1058_1060delinsACC	p.Ala353_Ser354delinsAspPro	p.A353_S354delinsDP	ENST00000250448	NM_004496.3	353	gCCTcc/gACCcc	2/2	0.735808898867312	2	FACETS	0.39	0.336	0.449	0.195	0.168	0.225	SUBCLONAL	1	TRUE	0	0.735808898867312	2		278	404	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0009293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	22	522	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.371	0.286	0.47	0.371	0.286	0.47	SUBCLONAL	1	TRUE	1	0.21	2		522	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577084	7577084	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121912667	NA	P-0009293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	74	682	1	ENST00000269305.4:c.854A>T	p.Glu285Val	p.E285V	ENST00000269305	NM_001126112.2	285	gAg/gTg	8/11	1	2	FACETS	0.679	0.593	0.773	0.679	0.593	0.773	SUBCLONAL	1	TRUE	1	0.21	2		683	1038	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435246	110435246	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	84	473	0	ENST00000375856.3:c.3155C>T	p.Thr1052Ile	p.T1052I	ENST00000375856	NM_003749.2	1052	aCc/aTc	1/2	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.21	2		473	642	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164240	47164240	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	78	502	0	ENST00000409792.3:c.1886A>T	p.Lys629Met	p.K629M	ENST00000409792	NM_014159.6	629	aAg/aTg	3/21	1	2	FACETS	0.985	0.865	1	0.985	0.865	1	CLONAL	1	TRUE	1	0.21	2		502	754	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156130	106156130	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	51	475	0	ENST00000380013.4:c.1031C>A	p.Thr344Lys	p.T344K	ENST00000380013	NM_001127208.2	344	aCa/aAa	3/11	1	2	FACETS	0.575	0.488	0.673	0.575	0.488	0.673	SUBCLONAL	1	TRUE	1	0.21	2		475	844	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157600	106157600	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	56	577	0	ENST00000380013.4:c.2501G>C	p.Cys834Ser	p.C834S	ENST00000380013	NM_001127208.2	834	tGt/tCt	3/11	1	2	FACETS	0.619	0.529	0.718	0.619	0.529	0.718	SUBCLONAL	1	TRUE	1	0.21	2		577	862	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535351	187535351	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	45	604	0	ENST00000441802.2:c.9223G>T	p.Asp3075Tyr	p.D3075Y	ENST00000441802	NM_005245.3	3075	Gac/Tac	12/27	1	2	FACETS	0.505	0.423	0.597	0.505	0.423	0.597	SUBCLONAL	1	TRUE	1	0.21	2		604	848	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453149	140453149	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913361	NA	P-0009293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	69	652	0	ENST00000288602.6:c.1786G>C	p.Gly596Arg	p.G596R	ENST00000288602	NM_004333.4	596	Ggt/Cgt	15/18	1	2	FACETS	0.704	0.612	0.805	0.704	0.612	0.805	SUBCLONAL	1	TRUE	1	0.21	2		652	933	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471044	8471044	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	102	637	1	ENST00000356435.5:c.3455G>T	p.Gly1152Val	p.G1152V	ENST00000356435		1152	gGg/gTg	20/35	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.21	2		638	869	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548914	29548914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	39	477	0	ENST00000356175.3:c.1688C>T	p.Pro563Leu	p.P563L	ENST00000356175	NM_000267.3	563	cCt/cTt	15/57	0.163032105494467	3	FACETS	0.596	0.492	0.712	0.298	0.246	0.356	SUBCLONAL	1	TRUE	1	0.21	3		477	689	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661899	29661899	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	72	632	0	ENST00000356175.3:c.5793G>C	p.Trp1931Cys	p.W1931C	ENST00000356175	NM_000267.3	1931	tgG/tgC	39/57	0.163032105494467	3	FACETS	0.776	0.676	0.884	0.388	0.338	0.442	SUBCLONAL	1	TRUE	1	0.21	3		632	977	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868185	37868185	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	142	573	0	ENST00000269571.5:c.906C>G	p.Asn302Lys	p.N302K	ENST00000269571		302	aaC/aaG	8/27	0.163032105494467	3	FACETS	1	0.98	1	0.638	0.58	0.699	CLONAL	1	TRUE	1	0.21	3		573	1172	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760959	59760959	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	88	722	0	ENST00000259008.2:c.3448G>T	p.Ala1150Ser	p.A1150S	ENST00000259008	NM_032043.2	1150	Gct/Tct	20/20	0.163032105494467	3	FACETS	0.809	0.714	0.91	0.404	0.357	0.455	CLONAL	1	TRUE	1	0.21	3		722	1145	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719044	52719044	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	52	453	0	ENST00000322088.6:c.820G>T	p.Val274Leu	p.V274L	ENST00000322088	NM_014225.5	274	Gtg/Ttg	7/15	1	2	FACETS	0.618	0.524	0.72	0.618	0.524	0.72	SUBCLONAL	1	TRUE	1	0.21	2		453	802	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795341	39795341	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	71	422	0	ENST00000288319.7:c.379G>C	p.Val127Leu	p.V127L	ENST00000288319	NM_182918.3	127	Gtg/Ctg	3/10	1	2	FACETS	0.893	0.779	1	0.893	0.779	1	CLONAL	1	TRUE	1	0.21	2		422	757	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387689	17387689	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	97	534	0	ENST00000359435.4:c.757G>T	p.Glu253Ter	p.E253*	ENST00000359435	NM_001033549.1	253	Gag/Tag	8/9	1	2	FACETS	0.939	0.835	1	0.939	0.835	1	CLONAL	1	TRUE	1	0.21	2		534	984	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961315	1961315	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	61	687	1	ENST00000382891.5:c.3103A>T	p.Arg1035Trp	p.R1035W	ENST00000382891	NM_133335.3	1035	Agg/Tgg	17/22	1	2	FACETS	0.479	0.411	0.553	0.479	0.411	0.553	SUBCLONAL	1	TRUE	1	0.21	2		688	1214	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0009306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	55	326	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	FALSE	1	0.169986718156224	2		326	558	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39214636	39214636	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	99	753	0	ENST00000402219.2:c.3488C>G	p.Pro1163Arg	p.P1163R	ENST00000402219	NM_005633.3	1163	cCa/cGa	22/23	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.169986718156224	2		753	960	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819350	3819350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs905975793	NA	P-0009358-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	253	680	0	ENST00000262367.5:c.2885C>T	p.Ser962Phe	p.S962F	ENST00000262367	NM_004380.2	962	tCc/tTc	15/31	1	2	FACETS	0.864	0.809	0.92	0.864	0.809	0.92	CLONAL	1	TRUE	1	0.588185739162436	2		680	996	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791018	42791018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs914662436	NA	P-0009358-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	189	488	0	ENST00000575354.2:c.163C>T	p.Pro55Ser	p.P55S	ENST00000575354	NM_015125.3	55	Ccg/Tcg	2/20	1	2	FACETS	0.959	0.89	1	0.959	0.89	1	CLONAL	1	TRUE	1	0.588185739162436	2		488	670	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612250	189612250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749906547	NA	P-0009358-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	483	531	0	ENST00000264731.3:c.2002C>T	p.Arg668Cys	p.R668C	ENST00000264731	NM_003722.4	668	Cgc/Tgc	14/14	0.495329468357405	4	FACETS	1	0.995	1	0.828	0.795	0.861	CLONAL	2	TRUE	1	0.588185739162436	4		531	1050	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0009406-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	361	336	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.254403675996091	4	FACETS	0.924	0.879	0.971	1	0.994	1	CLONAL	3	TRUE	2	0.362828099624692	4		336	978	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181413	185181413	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009406-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	168	696	0	ENST00000265026.3:c.1354G>C	p.Glu452Gln	p.E452Q	ENST00000265026	NM_004721.4	452	Gaa/Caa	8/14	0.254403675996091	4	FACETS	1	0.972	1	0.565	0.518	0.614	CLONAL	1	TRUE	2	0.362828099624692	4		696	1117	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181440	185181440	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009406-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	154	693	0	ENST00000265026.3:c.1381G>C	p.Glu461Gln	p.E461Q	ENST00000265026	NM_004721.4	461	Gag/Cag	8/14	0.254403675996091	4	FACETS	1	0.953	1	0.532	0.486	0.58	CLONAL	1	TRUE	2	0.362828099624692	4		693	1088	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405802	70405802	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009406-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	104	845	0	ENST00000373644.4:c.3316A>G	p.Ser1106Gly	p.S1106G	ENST00000373644	NM_030625.2	1106	Agc/Ggc	4/12	0.348901479677663	1	FACETS	0.536	0.479	0.596	0.536	0.479	0.596	SUBCLONAL	1	TRUE	0	0.362828099624692	1		845	876	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102056760	102056760	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009406-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	116	506	0	ENST00000282441.5:c.700G>C	p.Asp234His	p.D234H	ENST00000282441	NM_001130145.2	234	Gat/Cat	4/9	0.362828099624692	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.362828099624692	1		506	460	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188181	108188181	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009406-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	140	590	2	ENST00000278616.4:c.6280G>A	p.Glu2094Lys	p.E2094K	ENST00000278616	NM_000051.3	2094	Gaa/Aaa	43/63	0.362828099624692	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.362828099624692	1		592	576	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188190	108188190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009406-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	134	557	0	ENST00000278616.4:c.6289G>A	p.Glu2097Lys	p.E2097K	ENST00000278616	NM_000051.3	2097	Gaa/Aaa	43/63	0.362828099624692	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.362828099624692	1		557	557	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923137	48923137	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009406-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	95	431	0	ENST00000267163.4:c.585G>A	p.Trp195Ter	p.W195*	ENST00000267163	NM_000321.2	195	tgG/tgA	6/27	0.362828099624692	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.362828099624692	1		431	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0009406-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	265	623	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.362828099624692	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.362828099624692	1		623	1119	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544137	18544137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009406-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	97	728	0	ENST00000266497.5:c.1954G>A	p.Glu652Lys	p.E652K	ENST00000266497		652	Gag/Aag	13/31	0.210175745491168	2	FACETS	0.617	0.549	0.689	0.308	0.274	0.345	INDETERMINATE	1	TRUE	0	0.362828099624692	2		728	867	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244823	46244828	+	inframe_deletion	In_Frame_Del	DEL	TCACCA	TCACCA	-	novel	NA	P-0009406-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	101	1026	0	ENST00000334344.6:c.2922_2927del	p.Ser975_Pro976del	p.S975_P976del	ENST00000334344	NM_152641.2	973	TCACCA/-	15/21	0.329352258669065	2	FACETS	0.461	0.411	0.515	0.231	0.205	0.258	SUBCLONAL	1	TRUE	0	0.362828099624692	2		1026	1207	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874913	151874919	+	frameshift_variant	Frame_Shift_Del	DEL	GAAAAAT	GAAAAAT	AAAAAA	novel	NA	P-0009406-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	161	489	2	ENST00000262189.6:c.7619_7625delinsTTTTTT	p.His2540LeufsTer22	p.H2540Lfs*22	ENST00000262189	NM_170606.2	2540	cATTTTTCa/cTTTTTTa	38/59	0.329352258669065	2	FACETS	0.751	0.692	0.812	0.751	0.692	0.812	SUBCLONAL	2	TRUE	0	0.362828099624692	2		491	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578498	7578499	+	missense_variant	Missense_Mutation	DNP	CT	CT	GG	novel	NA	P-0009450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	508	1033	1	ENST00000269305.4:c.431_432delinsCC	p.Gln144Pro	p.Q144P	ENST00000269305	NM_001126112.2	144	cAG/cCC	5/11	0.363459281597921	3	FACETS	1	0.994	1	0.781	0.75	0.812	CLONAL	2	TRUE	0	0.460515737479768	3		1034	1159	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48921906	48921975	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TATGACTTCTAAATTACGAAAAAATGTTAAAAAGTCATAATGTTTTTCTTTTCAGGACATGTGAACTTAT	TATGACTTCTAAATTACGAAAAAATGTTAAAAAGTCATAATGTTTTTCTTTTCAGGACATGTGAACTTAT	-	novel	NA	P-0009450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	169	361	0	ENST00000267163.4:c.501-55_515del		p.X167_splice	ENST00000267163	NM_000321.2	167		5/27	0.438941298139535	2	FACETS	0.801	0.744	0.86	0.801	0.744	0.86	CLONAL	2	TRUE	0	0.460515737479768	2		361	458	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602323	10602323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	117	721	0	ENST00000171111.5:c.1255G>A	p.Gly419Arg	p.G419R	ENST00000171111	NM_203500.1	419	Ggg/Agg	3/6	0.462164469008929	1	FACETS	0.505	0.455	0.557	0.505	0.455	0.557	SUBCLONAL	1	TRUE	0	0.460515737479768	1		721	775	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012564	36012565	+	missense_variant	Missense_Mutation	DNP	GC	GC	AG	novel	NA	P-0009450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	83	578	3	ENST00000358208.4:c.8_9delinsAG	p.Ser3Lys	p.S3K	ENST00000358208		3	aGC/aAG	2/12	0.462164469008929	3	FACETS	0.478	0.421	0.539	0.239	0.21	0.27	SUBCLONAL	1	TRUE	1	0.460515737479768	3		581	928	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	93	297	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.838	0.75	0.931	0.838	0.75	0.931	CLONAL	1	TRUE	1	0.550628124483522	2		297	403	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717609	89717609	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs876661024	NA	P-0009451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	191	291	0	ENST00000371953.3:c.635-1G>T		p.X212_splice	ENST00000371953	NM_000314.4	212			0.550628124483522	1	FACETS	0.958	0.893	1	0.958	0.893	1	CLONAL	1	TRUE	0	0.550628124483522	1		291	525	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944391	76944391	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	296	241	0	ENST00000373344.5:c.514A>T	p.Thr172Ser	p.T172S	ENST00000373344	NM_000489.3	172	Act/Tct	7/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.550628124483522	1		241	581	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046512	30046512	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	229	341	0	ENST00000331968.5:c.2671C>T	p.His891Tyr	p.H891Y	ENST00000331968	NM_002742.2	891	Cac/Tac	18/18	1	2	FACETS	0.872	0.813	0.932	0.872	0.813	0.932	CLONAL	1	TRUE	1	0.550628124483522	2		341	954	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023161	31023162	+	missense_variant	Missense_Mutation	DNP	AG	AG	TA	novel	NA	P-0009451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	129	540	0	ENST00000375687.4:c.2646_2647delinsTA	p.Gln882_Glu883delinsHisLys	p.Q882_E883delinsHK	ENST00000375687	NM_015338.5	882	caAGaa/caTAaa	13/13	1	2	FACETS	0.442	0.4	0.487	0.442	0.4	0.487	SUBCLONAL	1	TRUE	1	0.550628124483522	2		540	1059	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001381	29001381	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009463-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	16	328	0	ENST00000282397.4:c.1351A>C	p.Ile451Leu	p.I451L	ENST00000282397	NM_002019.4	451	Atc/Ctc	10/30	1	2	FACETS	0.401	0.296	0.526	0.401	0.296	0.526	SUBCLONAL	1	TRUE	1	0.285147869256266	2		328	280	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128230365	128230365	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009463-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	45	613	0	ENST00000265960.3:c.1231A>G	p.Ile411Val	p.I411V	ENST00000265960	NM_001006617.1	411	Ata/Gta	10/12	1	2	FACETS	0.757	0.637	0.889	0.757	0.637	0.889	SUBCLONAL	1	TRUE	1	0.285147869256266	2		613	417	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	704	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.427508390816638	8	FACETS	0.993	0.97	1			1	CLONAL	8	FALSE	NA	0.427508390816638	8		493	946	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0009488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	195	631	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	1	2	FACETS	0.859	0.801	0.918	1	0.993	1	CLONAL	2	FALSE	1	0.427508390816638	2		631	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0009488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	193	616	1	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	1	2	FACETS	0.77	0.717	0.825	1	0.992	1	SUBCLONAL	2	FALSE	1	0.427508390816638	2		617	586	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713883	30713883	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143095746	NA	P-0009488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	180	501	2	ENST00000295754.5:c.1208G>A	p.Arg403His	p.R403H	ENST00000295754	NM_003242.5	403	cGt/cAt	4/7	1	2	FACETS	0.866	0.806	0.928	1	0.992	1	CLONAL	2	FALSE	1	0.427508390816638	2		503	486	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394941	394941	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753842732	NA	P-0009488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	184	516	0	ENST00000380956.4:c.337C>T	p.Arg113Trp	p.R113W	ENST00000380956	NM_001195286.1	113	Cgg/Tgg	3/9	1	2	FACETS	0.832	0.775	0.892	1	0.992	1	CLONAL	2	FALSE	1	0.427508390816638	2		516	517	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604797	48604797	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	181	394	0	ENST00000342988.3:c.1619T>A	p.Leu540His	p.L540H	ENST00000342988	NM_005359.5	540	cTt/cAt	12/12	0.427508390816638	0	FACETS	0.881	0.835	0.926			1	CLONAL	2	FALSE	0	0.427508390816638	0		394	275	SUCCESS
APC	324	MSKCC	GRCh37	5	112174505	112174505	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	CGTACAAC	novel	NA	P-0009488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	59	413	0	ENST00000257430.4:c.3214delinsCGTACAAC	p.Ser1072ArgfsTer11	p.S1072Rfs*11	ENST00000257430	NM_000038.5	1072	Agt/CGTACAACgt	16/16	0.427508390816638	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	0	0.427508390816638	1		413	182	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296361	15296361	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	97	816	0	ENST00000263388.2:c.2081C>A	p.Pro694His	p.P694H	ENST00000263388	NM_000435.2	694	cCc/cAc	13/33	1	2	FACETS	0.871	0.775	0.973	0.871	0.775	0.973	CLONAL	1	TRUE	1	0.25	2		816	891	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0009640-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	82	446	2	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.583939266886301	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.594669049822719	1		448	170	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589608	67589771	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGAAAAAAGTCGAGAATATGATAGATTATATGAAGAATATACCCGCACATCCCAGGTGAGTTTTCTATGAAAATCAGATTAAAAAATAAGAGTTCTAAACTTTTAAAGACTAACATGGAAAAAAGAATTTAAAAGGTTGAGTTTTTACGAATGAGGTGGGGGTG	AGAAAAAAGTCGAGAATATGATAGATTATATGAAGAATATACCCGCACATCCCAGGTGAGTTTTCTATGAAAATCAGATTAAAAAATAAGAGTTCTAAACTTTTAAAGACTAACATGGAAAAAAGAATTTAAAAGGTTGAGTTTTTACGAATGAGGTGGGGGTG	-	novel	NA	P-0009640-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	20	261	0	ENST00000274335.5:c.1374_1425+112del		p.X458_splice	ENST00000274335		458		10/15	0.592824304661613	1	FACETS	0.418	0.324	0.525	0.418	0.324	0.525	SUBCLONAL	1	TRUE	0	0.594669049822719	1		261	113	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0009745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	76	202	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.808	0.713	0.907	0.808	0.713	0.907	CLONAL	1	TRUE	1	0.530213483443234	2		202	355	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0009745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	17	375	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.109	0.081	0.144	0.109	0.081	0.144	SUBCLONAL	1	TRUE	1	0.530213483443234	2		375	586	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912660	NA	P-0009753-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	62	984	0	ENST00000269305.4:c.839G>T	p.Arg280Ile	p.R280I	ENST00000269305	NM_001126112.2	280	aGa/aTa	8/11	1	2	FACETS	0.715	0.617	0.822	0.715	0.617	0.822	SUBCLONAL	1	TRUE	1	0.23	2		984	754	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753210	42753210	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009753-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	43	1027	0	ENST00000222329.4:c.1054C>A	p.Pro352Thr	p.P352T	ENST00000222329	NM_006494.2	352	Ccc/Acc	4/4	NA	2	FACETS	0.521	0.435	0.618			1	INDETERMINATE	1	TRUE	NA	0.23	2		1027	717	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958441	90958441	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009753-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	50	553	0	ENST00000265433.3:c.1997A>C	p.Asn666Thr	p.N666T	ENST00000265433	NM_002485.4	666	aAc/aCc	13/16	0.3	4	FACETS	0.633	0.535	0.741	0.316	0.267	0.371	SUBCLONAL	1	TRUE	2	0.23	4		553	845	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0009861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	130	396	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	0.762	0.69	0.837	0.762	0.69	0.837	SUBCLONAL	1	TRUE	1	0.369841705366548	2		396	923	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0009861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	74	498	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	1	2	FACETS	0.481	0.42	0.547	0.481	0.42	0.547	SUBCLONAL	1	TRUE	1	0.369841705366548	2		498	832	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0009927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	248	373	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.891	0.834	0.949	0.891	0.834	0.949	CLONAL	1	TRUE	1	0.595947416138104	2		373	934	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727455	66727455	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs869025608	NA	P-0009927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	226	298	0	ENST00000307102.5:c.171G>T	p.Lys57Asn	p.K57N	ENST00000307102	NM_002755.3	57	aaG/aaT	2/11	1	2	FACETS	0.919	0.858	0.982	0.919	0.858	0.982	CLONAL	1	TRUE	1	0.595947416138104	2		298	825	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44921977	44921977	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	343	545	0	ENST00000377967.4:c.1511T>C	p.Leu504Ser	p.L504S	ENST00000377967	NM_021140.2	504	tTa/tCa	15/29	1	2	FACETS	0.948	0.897	1	0.948	0.897	1	CLONAL	1	TRUE	1	0.595947416138104	2		545	1214	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0010021-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	38	464	0	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	0.973	1	CLONAL	2	TRUE	1	0.242565393650114	2		464	129	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0010021-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	17	565	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.242182744322391	1	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	0	0.242565393650114	1		565	87	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0010021-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	22	567	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.242565393650114	0	FACETS	0.763	0.615	0.92			1	CLONAL	3	TRUE	0	0.242565393650114	0		567	60	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374301	138374301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1170276441	NA	P-0010021-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	35	638	0	ENST00000289153.2:c.3143C>T	p.Ala1048Val	p.A1048V	ENST00000289153	NM_006219.2	1048	gCg/gTg	22/22	1	2	FACETS	1	0.912	1	1	0.969	1	CLONAL	2	TRUE	1	0.242565393650114	2		638	126	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696461	47696461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010021-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	51	583	0	ENST00000347630.2:c.362G>A	p.Arg121Gln	p.R121Q	ENST00000347630	NM_001007230.1	121	cGg/cAg	6/11	0.242565393650114	2	FACETS	0.973	0.857	1	1	0.979	1	CLONAL	4	TRUE	0	0.242565393650114	2		583	108	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023882	27023883	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	TA	novel	NA	P-0010021-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	13	271	2	ENST00000324856.7:c.988_989delinsTA	p.Ala330Ter	p.A330*	ENST00000324856	NM_006015.4	330	GCg/TAg	1/20	0.147810507636235	3	FACETS	0.835	0.607	1	0.835	0.607	1	CLONAL	2	TRUE	1	0.242565393650114	3		273	72	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690802	89690802	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1114167621	NA	P-0010021-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	34	407	0	ENST00000371953.3:c.210-1G>A		p.X70_splice	ENST00000371953	NM_000314.4	70			0.242182744322391	1	FACETS	1	0.855	1	1	0.966	1	CLONAL	2	TRUE	0	0.242565393650114	1		407	120	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658295	18658295	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs577345777	NA	P-0010021-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	25	635	0	ENST00000266497.5:c.3100C>T	p.Arg1034Cys	p.R1034C	ENST00000266497		1034	Cgt/Tgt	22/31	1	2	FACETS	0.848	0.688	1	1	0.961	1	CLONAL	3	TRUE	1	0.242565393650114	2		635	81	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106543583	106543583	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010021-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	14	383	0	ENST00000369096.4:c.385A>G	p.Asn129Asp	p.N129D	ENST00000369096	NM_001198.3	129	Aac/Gac	3/7	0.147810507636235	3	FACETS	0.78	0.573	1	0.78	0.573	1	CLONAL	2	TRUE	1	0.242565393650114	3		383	83	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0010130-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	355	493	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	0.734417628668334	2		493	945	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0010130-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	325	780	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.734417628668334	1	FACETS	0.899	0.858	0.94	0.899	0.858	0.94	CLONAL	1	TRUE	0	0.734417628668334	1		780	623	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145430	58145430	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894340	NA	P-0010130-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	244	315	1	ENST00000257904.6:c.71G>T	p.Arg24Leu	p.R24L	ENST00000257904	NM_000075.3	24	cGt/cTt	2/8	1	2	FACETS	0.904	0.848	0.961	0.904	0.848	0.961	CLONAL	1	TRUE	1	0.734417628668334	2		316	735	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72842091	72842091	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010130-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	246	340	0	ENST00000325599.8:c.1157A>G	p.Tyr386Cys	p.Y386C	ENST00000325599	NM_018130.2	386	tAc/tGc	10/11	1	2	FACETS	0.928	0.871	0.985	0.928	0.871	0.985	CLONAL	1	TRUE	1	0.734417628668334	2		340	722	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168743	32168743	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010130-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	888	656	2	ENST00000375023.3:c.4180C>A	p.Pro1394Thr	p.P1394T	ENST00000375023	NM_004557.3	1394	Cct/Act	23/30	0.72633286717029	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.734417628668334	2		658	1191	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469983	157469983	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010130-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	243	369	0	ENST00000346085.5:c.2777A>T	p.Gln926Leu	p.Q926L	ENST00000346085	NM_020732.3	926	cAg/cTg	9/20	1	2	FACETS	0.945	0.888	1	0.945	0.888	1	CLONAL	1	TRUE	1	0.734417628668334	2		369	700	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456696	32456696	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1392405207	NA	P-0010130-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	271	343	0	ENST00000332351.3:c.196C>A	p.Pro66Thr	p.P66T	ENST00000332351	NM_024426.4	66	Ccg/Acg	1/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.734417628668334	2		343	675	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662454	67662454	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010130-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	319	504	0	ENST00000264010.4:c.1700G>C	p.Arg567Pro	p.R567P	ENST00000264010	NM_006565.3	567	cGg/cCg	9/12	0.734417628668334	3	FACETS	0.847	0.798	0.897			1	CLONAL	1	TRUE	NA	0.734417628668334	3		504	1402	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991365	72991365	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010130-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	384	537	0	ENST00000268489.5:c.2680G>T	p.Asp894Tyr	p.D894Y	ENST00000268489	NM_006885.3	894	Gat/Tat	2/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.734417628668334	2		537	1027	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511517	38511517	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1416311365	NA	P-0010130-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	238	347	0	ENST00000254066.5:c.1015C>T	p.Arg339Cys	p.R339C	ENST00000254066	NM_000964.3	339	Cgc/Tgc	8/9	1	2	FACETS	0.942	0.884	1	0.942	0.884	1	CLONAL	1	TRUE	1	0.734417628668334	2		347	688	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2214500	2214500	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010130-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	388	529	0	ENST00000398665.3:c.1828G>T	p.Asp610Tyr	p.D610Y	ENST00000398665	NM_032482.2	610	Gac/Tac	19/28	1	2	FACETS	0.99	0.943	1	0.99	0.943	1	CLONAL	1	TRUE	1	0.734417628668334	2		529	1067	SUCCESS
AR	367	MSKCC	GRCh37	X	66766439	66766439	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010130-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	184	269	0	ENST00000374690.3:c.1451C>A	p.Thr484Asn	p.T484N	ENST00000374690	NM_000044.3	484	aCt/aAt	1/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.734417628668334	2		269	449	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76777855	76777855	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010130-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	309	539	0	ENST00000373344.5:c.6861G>T	p.Met2287Ile	p.M2287I	ENST00000373344	NM_000489.3	2287	atG/atT	32/35	1	2	FACETS	0.847	0.8	0.895	0.847	0.8	0.895	CLONAL	1	TRUE	1	0.734417628668334	2		539	993	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872017	35872019	+	inframe_deletion	In_Frame_Del	DEL	ACG	ACG	-	novel	NA	P-0010130-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	261	351	0	ENST00000216797.5:c.594_596del	p.Ile198_Val199delinsMet	p.I198_V199delinsM	ENST00000216797	NM_020529.2	198	atCGTg/atg	4/6	0.734417628668334	3	FACETS	0.74	0.692	0.789	0.37	0.346	0.395	SUBCLONAL	1	TRUE	1	0.734417628668334	3		351	1314	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030513	47030513	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010130-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	409	649	0	ENST00000377604.3:c.292del	p.Arg98GlufsTer36	p.R98Efs*36	ENST00000377604	NM_001204468.1	96	ttC/tt	4/24	1	2	FACETS	0.965	0.92	1	0.965	0.92	1	CLONAL	1	TRUE	1	0.734417628668334	2		649	1154	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797912	45797912	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010130-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	374	520	0	ENST00000450313.1:c.859G>T	p.Ala287Ser	p.A287S	ENST00000450313	NM_012222.2	287	Gcc/Tcc	10/16	NA	2	FACETS	0.978	0.931	1			1	INDETERMINATE	1	TRUE	NA	0.734417628668334	2		520	1041	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624426	21624426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010130-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	372	567	0	ENST00000421138.2:c.1603C>T	p.Pro535Ser	p.P535S	ENST00000421138		535	Ccc/Tcc	14/16	1	2	FACETS	0.932	0.886	0.979	0.932	0.886	0.979	CLONAL	1	TRUE	1	0.734417628668334	2		567	1087	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865761	57865761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010130-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	348	504	0	ENST00000228682.2:c.3238C>T	p.Pro1080Ser	p.P1080S	ENST00000228682	NM_005269.2	1080	Ccc/Tcc	12/12	1	2	FACETS	0.837	0.793	0.882	0.837	0.793	0.882	CLONAL	1	TRUE	1	0.734417628668334	2		504	1132	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879747	123879747	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010130-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	79	120	0	ENST00000330479.4:c.443C>G	p.Thr148Ser	p.T148S	ENST00000330479	NM_020382.3	148	aCc/aGc	4/9	1	2	FACETS	0.987	0.884	1	0.987	0.884	1	CLONAL	1	TRUE	1	0.734417628668334	2		120	218	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944557	32944557	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80359075	NA	P-0010130-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	264	496	0	ENST00000380152.3:c.8350C>T	p.Arg2784Trp	p.R2784W	ENST00000380152		2784	Cgg/Tgg	19/27	0.734417628668334	1	FACETS	0.892	0.847	0.937	0.892	0.847	0.937	CLONAL	1	TRUE	0	0.734417628668334	1		496	510	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881534	111881534	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770692189	NA	P-0010130-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	328	499	0	ENST00000393256.3:c.212G>A	p.Gly71Asp	p.G71D	ENST00000393256	NM_006538.4	71	gGc/gAc	2/4	1	2	FACETS	0.974	0.923	1	0.974	0.923	1	CLONAL	1	TRUE	1	0.734417628668334	2		499	917	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143226641	143226660	+	frameshift_variant	Frame_Shift_Del	DEL	GACTTCAGCAGCTCTCCCAC	GACTTCAGCAGCTCTCCCAC	-	novel	NA	P-0010130-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	134	446	0	ENST00000262992.4:c.454_473del	p.Val152LysfsTer32	p.V152Kfs*32	ENST00000262992	NM_001101669.1	152	GTGGGAGAGCTGCTGAAGTCa/a	7/24	0.734417628668334	3	FACETS	0.467	0.423	0.513	0.234	0.211	0.257	SUBCLONAL	1	TRUE	1	0.734417628668334	3		446	1068	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39074240	39074240	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010130-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	279	394	0	ENST00000357387.3:c.70G>C	p.Glu24Gln	p.E24Q	ENST00000357387	NM_152756.3	24	Gag/Cag	2/38	0.734417628668334	3	FACETS	1	0.94	1	0.5	0.47	0.531	CLONAL	1	TRUE	1	0.734417628668334	3		394	1039	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549606	5549606	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0010130-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1217	312	419	0	ENST00000397747.3:c.631+2T>C		p.X211_splice	ENST00000397747	NM_025239.3	211			0.431436544453731	5	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.734417628668334	5		419	1529	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010326-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	94	489	0	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	0.298118939398906	5	FACETS	1	0.901	1			1	CLONAL	1	TRUE	NA	0.41	5		489	731	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523505	106523505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010326-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	24	302	0	ENST00000359195.3:c.2657C>T	p.Thr886Met	p.T886M	ENST00000359195	NM_002649.2	886	aCg/aTg	8/11	0.298118939398906	3	FACETS	0.296	0.232	0.371	0.148	0.116	0.186	SUBCLONAL	1	TRUE	1	0.41	3		302	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0010326-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	217	560	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.298118939398906	2	FACETS	0.911	0.853	0.97	0.911	0.853	0.97	CLONAL	2	TRUE	0	0.41	2		560	581	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0010458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	120	376	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.557626560521126	2		376	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0010458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	206	602	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.557626560521126	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.557626560521126	1		604	468	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958311	11958311	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	T	novel	NA	P-0010458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	89	468	0	ENST00000353533.5:c.218+3G>T		p.X73_splice	ENST00000353533	NM_003010.3	73			0.557626560521126	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.557626560521126	1		468	198	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274911	41274911	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010507-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	130	630	0	ENST00000349496.5:c.1161T>G	p.Asn387Lys	p.N387K	ENST00000349496	NM_001904.3	387	aaT/aaG	8/15	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.317562194813484	2		630	761	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098566	11098566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776534924	NA	P-0010507-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	155	787	4	ENST00000358026.2:c.1084G>A	p.Asp362Asn	p.D362N	ENST00000358026	NM_001128849.1	362	Gac/Aac	6/36	0.294758438327255	4	FACETS	1	0.929	1			1	CLONAL	1	TRUE	NA	0.317562194813484	4		791	1262	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0010528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	254	840	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.236104392461404	3	FACETS	1	0.981	1	0.728	0.685	0.771	INDETERMINATE	2	TRUE	0	0.428024696715651	3		842	660	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201059	NA	P-0010528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	104	560	2	ENST00000269305.4:c.856G>T	p.Glu286Ter	p.E286*	ENST00000269305	NM_001126112.2	286	Gaa/Taa	8/11	0.236104392461404	3	FACETS	0.964	0.865	1	0.321	0.288	0.357	INDETERMINATE	1	TRUE	0	0.428024696715651	3		562	612	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576831	212576831	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	100	477	0	ENST00000342788.4:c.1068C>G	p.Phe356Leu	p.F356L	ENST00000342788	NM_005235.2	356	ttC/ttG	9/28	0.431036139086483	3	FACETS	0.728	0.65	0.811	0.364	0.325	0.406	SUBCLONAL	1	TRUE	1	0.428024696715651	3		477	779	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673055	30673055	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	103	481	0	ENST00000376406.3:c.3905C>A	p.Thr1302Asn	p.T1302N	ENST00000376406	NM_014641.2	1302	aCc/aAc	10/15	0.428024696715651	7	FACETS	0.982	0.877	1	0.164	0.146	0.183	CLONAL	1	TRUE	1	0.428024696715651	7		481	1015	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235883	133235883	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	44	291	0	ENST00000320574.5:c.3273G>C	p.Glu1091Asp	p.E1091D	ENST00000320574	NM_006231.2	1091	gaG/gaC	26/49	0.217042799664884	2	FACETS	0.819	0.692	0.957	0.41	0.346	0.479	INDETERMINATE	1	TRUE	0	0.428024696715651	2		291	251	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937130	76937132	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs782162142	NA	P-0010528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	72	469	0	ENST00000373344.5:c.3616_3618del	p.Ser1206del	p.S1206del	ENST00000373344	NM_000489.3	1206	TCT/-	9/35	NA	2	FACETS	0.557	0.487	0.633			1	INDETERMINATE	1	TRUE	NA	0.428024696715651	2		469	604	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665704	86665704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010533-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	32	365	0	ENST00000274376.6:c.1685C>T	p.Pro562Leu	p.P562L	ENST00000274376	NM_002890.2	562	cCa/cTa	12/25	1	2	FACETS	0.848	0.686	1	0.848	0.686	1	CLONAL	1	TRUE	1	0.12	2		365	629	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873802	35873802	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	96	643	0	ENST00000216797.5:c.49C>G	p.Arg17Gly	p.R17G	ENST00000216797	NM_020529.2	17	Cgc/Ggc	1/6	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.45107633801333	2		643	383	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441182	52441239	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTGCCTACCATGGTCAATGGGGTAGACCTTCAGCCCATCCAGCTCAAAGAGCCGGCCT	GTGCCTACCATGGTCAATGGGGTAGACCTTCAGCCCATCCAGCTCAAAGAGCCGGCCT	-	novel	NA	P-0010679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	66	295	0	ENST00000460680.1:c.531_580+8del		p.X177_splice	ENST00000460680	NM_004656.3	177		7/17	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.45107633801333	2		295	238	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439286	52439286	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	125	825	0	ENST00000460680.1:c.956del	p.Ser319TyrfsTer16	p.S319Yfs*16	ENST00000460680	NM_004656.3	319	tCa/ta	11/17	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.45107633801333	2		825	491	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219127	94219127	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	72	756	0	ENST00000323929.3:c.277del	p.Ile93PhefsTer17	p.I93Ffs*17	ENST00000323929	NM_005591.3	93	Att/tt	4/20	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.45107633801333	2		756	316	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057231	30057231	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	110	704	0	ENST00000338641.4:c.715del	p.Leu239TrpfsTer12	p.L239Wfs*12	ENST00000338641	NM_000268.3	238	gCc/gc	8/16	0.45107633801333	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.45107633801333	1		704	367	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974332	18974332	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	124	863	0	ENST00000262803.5:c.2686A>C	p.Lys896Gln	p.K896Q	ENST00000262803	NM_002911.3	896	Aag/Cag	19/24	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.45107633801333	2		863	517	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630242	100630242	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	99	314	3	ENST00000308731.7:c.31C>A	p.Leu11Met	p.L11M	ENST00000308731	NM_000061.2	11	Ctg/Atg	2/19	0.140390306292961	0	FACETS	0.655	0.601	0.708			1	INDETERMINATE	2	TRUE	NA	0.45107633801333	0		317	184	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812340	212812340	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	155	436	0	ENST00000342788.4:c.236C>A	p.Ser79Tyr	p.S79Y	ENST00000342788	NM_005235.2	79	tCt/tAt	3/28	0.811051534632855	3	FACETS	1	0.965	1	0.54	0.498	0.583	CLONAL	1	FALSE	1	0.814446066900127	3		436	496	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754633	42754633	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs111300456	NA	P-0010796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	227	811	0	ENST00000222329.4:c.107T>C	p.Leu36Pro	p.L36P	ENST00000222329	NM_006494.2	36	cTg/cCg	2/4	0.776722617424712	3	FACETS	0.905	0.844	0.967	0.452	0.422	0.484	CLONAL	1	FALSE	1	0.814446066900127	3		811	867	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	43	297	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.95	1			1	INDETERMINATE	1	TRUE	NA	0.257670032574715	2		297	248	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439692	51439692	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1363868066	NA	P-0010802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	68	335	0	ENST00000262662.1:c.257T>C	p.Leu86Ser	p.L86S	ENST00000262662		86	tTa/tCa	4/4	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.257670032574715	2		335	486	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527725	103527725	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	78	431	0	ENST00000355739.4:c.3033G>T	p.Lys1011Asn	p.K1011N	ENST00000355739	NM_000123.3	1011	aaG/aaT	15/15	1	2	FACETS	0.881	0.774	0.996	0.881	0.774	0.996	CLONAL	1	TRUE	1	0.257670032574715	2		431	687	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412045	116412045	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0010983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	615	599	0	ENST00000397752.3:c.3028+2T>C		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.439481645894314	3	FACETS	0.862	0.833	0.891	0.862	0.833	0.891	CLONAL	3	TRUE	0	0.498782805645646	3		599	1192	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40458409	40458409	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	245	424	0	ENST00000345506.4:c.1624A>G	p.Ser542Gly	p.S542G	ENST00000345506	NM_003152.3	542	Agc/Ggc	14/20	0.155338562545752	5	FACETS	1	0.984	1			1	INDETERMINATE	4	TRUE	NA	0.498782805645646	5		424	399	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932041	36932041	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	131	776	0	ENST00000361632.4:c.2428G>T	p.Asp810Tyr	p.D810Y	ENST00000361632		810	Gac/Tac	16/16	0.357732449682903	3	FACETS	0.821	0.746	0.901			1	CLONAL	1	TRUE	NA	0.498782805645646	3		776	799	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042599	42042599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	109	766	0	ENST00000219905.7:c.6794G>A	p.Arg2265Lys	p.R2265K	ENST00000219905	NM_001164273.1	2265	aGa/aAa	17/24	1	2	FACETS	0.653	0.587	0.723	0.653	0.587	0.723	SUBCLONAL	1	TRUE	1	0.498782805645646	2		766	669	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0010995-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	309	628	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.410696252346718	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.414801614180635	2		628	738	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625251	69625251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782147248	NA	P-0010995-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	145	659	1	ENST00000334134.2:c.542G>A	p.Arg181His	p.R181H	ENST00000334134	NM_005247.2	181	cGc/cAc	3/3	0.40790801457675	3	FACETS	1	0.916	1	0.502	0.458	0.548	CLONAL	1	TRUE	1	0.414801614180635	3		660	841	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249020	55249022	+	missense_variant	Missense_Mutation	TNP	ACG	ACG	TCA	novel	NA	P-0010995-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	275	407	0	ENST00000275493.2:c.2318_2320delinsTCA	p.His773_Val774delinsLeuMet	p.H773_V774delinsLM	ENST00000275493	NM_005228.3	773	cACGtg/cTCAtg	20/28	0.414801614180635	4	FACETS	0.971	0.919	1	0.971	0.919	1	CLONAL	3	TRUE	1	0.414801614180635	4		407	644	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294753	1294753	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010995-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	53	431	0	ENST00000310581.5:c.248G>T	p.Arg83Leu	p.R83L	ENST00000310581	NM_198253.2	83	cGa/cTa	2/16	0.373114592249246	4	FACETS	0.483	0.411	0.562	0.241	0.205	0.281	SUBCLONAL	1	TRUE	2	0.414801614180635	4		431	749	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115728	8115729	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0011015-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	40	626	0	ENST00000346208.3:c.1075_1076dup	p.Gly360LysfsTer45	p.G360Kfs*45	ENST00000346208		358	-/GA	6/6	0.167969491474663	2	FACETS	0.438	0.365	0.518	0.219	0.182	0.259	INDETERMINATE	1	TRUE	0	0.600515260024333	2		626	304	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0011100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	98	664	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.212722481369558	3	FACETS	0.522	0.465	0.584	0.261	0.232	0.292	INDETERMINATE	1	TRUE	1	0.420459532514303	3		665	1080	SUCCESS
APC	324	MSKCC	GRCh37	5	112175621	112175621	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	195	534	0	ENST00000257430.4:c.4330C>T	p.Gln1444Ter	p.Q1444*	ENST00000257430	NM_000038.5	1444	Caa/Taa	16/16	0.420459532514303	1	FACETS	0.974	0.904	1	0.974	0.904	1	CLONAL	1	TRUE	0	0.420459532514303	1		534	752	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242481	+	inframe_deletion	In_Frame_Del	DEL	AATTAAGAGAAGCAA	AATTAAGAGAAGCAA	-	rs121913425	NA	P-0011100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	187	654	0	ENST00000275493.2:c.2237_2251del	p.Glu746_Thr751delinsAla	p.E746_T751delinsA	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAAca/gca	19/28	0.212722481369558	3	FACETS	0.837	0.771	0.906	0.419	0.385	0.453	INDETERMINATE	1	TRUE	1	0.420459532514303	3		654	1286	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073393	8073393	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	140	527	0	ENST00000377482.5:c.1266A>C	p.Gln422His	p.Q422H	ENST00000377482	NM_018948.3	422	caA/caC	4/4	1	2	FACETS	0.665	0.605	0.729	0.665	0.605	0.729	SUBCLONAL	1	TRUE	1	0.420459532514303	2		527	1001	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073415	8073415	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	127	528	0	ENST00000377482.5:c.1244A>C	p.Glu415Ala	p.E415A	ENST00000377482	NM_018948.3	415	gAa/gCa	4/4	1	2	FACETS	0.615	0.556	0.677	0.615	0.556	0.677	SUBCLONAL	1	TRUE	1	0.420459532514303	2		528	982	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073434	8073434	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0011100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	99	505	0	ENST00000377482.5:c.1225A>T	p.Lys409Ter	p.K409*	ENST00000377482	NM_018948.3	409	Aaa/Taa	4/4	1	2	FACETS	0.511	0.455	0.57	0.511	0.455	0.57	SUBCLONAL	1	TRUE	1	0.420459532514303	2		505	922	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541586	187541586	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	158	426	0	ENST00000441802.2:c.6154G>A	p.Glu2052Lys	p.E2052K	ENST00000441802	NM_005245.3	2052	Gaa/Aaa	10/27	0.420459532514303	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.420459532514303	1		426	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519988	NA	P-0011113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	877	748	2	ENST00000269305.4:c.808T>C	p.Phe270Leu	p.F270L	ENST00000269305	NM_001126112.2	270	Ttt/Ctt	8/11	0.611253090514537	4	FACETS	0.974	0.954	0.994			1	CLONAL	4	TRUE	NA	0.634905019645041	4		750	1159	SUCCESS
CBL	867	MSKCC	GRCh37	11	119145566	119145566	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	352	430	0	ENST00000264033.4:c.772T>C	p.Trp258Arg	p.W258R	ENST00000264033	NM_005188.3	258	Tgg/Cgg	5/16	0.63761717911619	4	FACETS	1	0.993	1	0.831	0.793	0.869	CLONAL	2	TRUE	1	0.634905019645041	4		430	727	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984357	201984357	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1410	124	674	2	ENST00000359651.3:c.1022T>C	p.Ile341Thr	p.I341T	ENST00000359651		341	aTc/aCc	8/8	0.359217698744285	5	FACETS	0.497	0.448	0.55	0.099	0.089	0.11	INDETERMINATE	1	TRUE	0	0.634905019645041	5		676	1534	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941403	71941403	+	splice_region_variant,intron_variant	Splice_Region	SNP	T	T	C	novel	NA	P-0011113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	593	582	0	ENST00000298229.2:c.1091-3T>C		p.X364_splice	ENST00000298229	NM_001567.3	364			0.634905019645041	6	FACETS	1	0.984	1			1	CLONAL	3	TRUE	NA	0.634905019645041	6		582	1364	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59820400	59820400	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	125	592	1	ENST00000259008.2:c.2353C>A	p.Pro785Thr	p.P785T	ENST00000259008	NM_032043.2	785	Cct/Act	16/20	0.63761717911619	4	FACETS	0.788	0.713	0.867	0.197	0.178	0.217	SUBCLONAL	1	TRUE	0	0.634905019645041	4		593	817	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0011142-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	127	665	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.165173327787921	2	FACETS	1	0.977	1	0.623	0.565	0.684	INDETERMINATE	1	TRUE	0	0.278156719145871	2		665	733	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0011142-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	233	634	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	0.0777733443411281	3	FACETS	0.942	0.879	1			1	INDETERMINATE	2	TRUE	NA	0.278156719145871	3		634	1013	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672219	86672219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194205020	NA	P-0011142-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	45	403	1	ENST00000274376.6:c.2021G>A	p.Arg674His	p.R674H	ENST00000274376	NM_002890.2	674	cGc/cAc	16/25	1	2	FACETS	0.761	0.641	0.894	0.761	0.641	0.894	SUBCLONAL	1	TRUE	1	0.278156719145871	2		404	425	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466558	120466558	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011142-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	192	554	1	ENST00000256646.2:c.4561G>T	p.Gly1521Trp	p.G1521W	ENST00000256646	NM_024408.3	1521	Ggg/Tgg	26/34	0.278156719145871	5	FACETS	1	0.982	1	0.79	0.731	0.85	CLONAL	2	TRUE	2	0.278156719145871	5		555	826	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47607041	47607041	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011142-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	171	751	0	ENST00000263735.4:c.791T>C	p.Leu264Pro	p.L264P	ENST00000263735	NM_002354.2	264	cTa/cCa	7/9	0.196341023190203	2	FACETS	0.802	0.739	0.867	0.802	0.739	0.867	CLONAL	2	TRUE	0	0.278156719145871	2		751	767	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390201	89390201	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1167543166	NA	P-0011142-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	36	396	0	ENST00000336596.2:c.950C>A	p.Pro317His	p.P317H	ENST00000336596	NM_005233.5	317	cCt/cAt	4/17	0.196341023190203	2	FACETS	0.627	0.515	0.751	0.313	0.257	0.376	SUBCLONAL	1	TRUE	0	0.278156719145871	2		396	413	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968212	134968212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011142-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	81	585	0	ENST00000398015.3:c.2725G>A	p.Asp909Asn	p.D909N	ENST00000398015	NM_004441.4	909	Gac/Aac	15/16	0.196341023190203	2	FACETS	0.799	0.703	0.901	0.399	0.351	0.451	CLONAL	1	TRUE	0	0.278156719145871	2		585	729	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968311	2968311	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011142-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	82	801	0	ENST00000396946.4:c.1675A>T	p.Ser559Cys	p.S559C	ENST00000396946	NM_032415.4	559	Agc/Tgc	13/25	0.278156719145871	3	FACETS	0.621	0.546	0.702	0.311	0.273	0.351	SUBCLONAL	1	TRUE	1	0.278156719145871	3		801	1081	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220509	133220509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767191767	NA	P-0011142-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	57	760	0	ENST00000320574.5:c.4204G>A	p.Val1402Met	p.V1402M	ENST00000320574	NM_006231.2	1402	Gtg/Atg	33/49	0.188621241093945	3	FACETS	0.547	0.468	0.634	0.274	0.234	0.317	SUBCLONAL	1	TRUE	1	0.278156719145871	3		760	853	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15378289	15378289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011142-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	105	755	1	ENST00000263377.2:c.497C>T	p.Thr166Ile	p.T166I	ENST00000263377	NM_058243.2	166	aCa/aTa	4/20	0.165173327787921	2	FACETS	0.957	0.857	1	0.478	0.428	0.532	INDETERMINATE	1	TRUE	0	0.278156719145871	2		756	789	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022481	31022481	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765459479	NA	P-0011142-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	21	269	0	ENST00000375687.4:c.1966G>A	p.Asp656Asn	p.D656N	ENST00000375687	NM_015338.5	656	Gat/Aat	13/13	0.188621241093945	3	FACETS	0.534	0.411	0.678	0.267	0.205	0.339	SUBCLONAL	1	TRUE	1	0.278156719145871	3		269	322	SUCCESS
AR	367	MSKCC	GRCh37	X	66765427	66765427	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011142-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	24	352	0	ENST00000374690.3:c.439C>G	p.Gln147Glu	p.Q147E	ENST00000374690	NM_000044.3	147	Cag/Gag	1/8	0.215956205906886	2	FACETS	0.487	0.382	0.609			1	SUBCLONAL	1	TRUE	NA	0.278156719145871	2		352	354	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411605	63411606	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0011142-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	79	485	0	ENST00000330258.3:c.1561_1562delinsTT	p.Gly521Leu	p.G521L	ENST00000330258	NM_152424.3	521	GGa/TTa	2/2	1	1	FACETS	0.935	0.824	1	0.935	0.824	1	CLONAL	1	TRUE	0	0.278156719145871	1		485	523	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317917	8317917	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011142-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	32	547	0	ENST00000356435.5:c.5696C>A	p.Ala1899Asp	p.A1899D	ENST00000356435		1899	gCc/gAc	35/35	1	2	FACETS	0.364	0.294	0.443	0.364	0.294	0.443	SUBCLONAL	1	TRUE	1	0.278156719145871	2		547	632	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425634	49425634	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs893293173	NA	P-0011142-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	150	750	0	ENST00000301067.7:c.12854G>T	p.Gly4285Val	p.G4285V	ENST00000301067	NM_003482.3	4285	gGc/gTc	39/54	0.188621241093945	3	FACETS	0.854	0.782	0.929	0.854	0.782	0.929	CLONAL	2	TRUE	1	0.278156719145871	3		750	719	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046590	30046590	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011142-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	37	648	0	ENST00000331968.5:c.2593G>A	p.Asp865Asn	p.D865N	ENST00000331968	NM_002742.2	865	Gat/Aat	18/18	NA	2	FACETS	0.375	0.308	0.45			1	INDETERMINATE	1	TRUE	NA	0.278156719145871	2		648	710	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274556	198274556	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011142-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	37	587	1	ENST00000335508.6:c.842A>T	p.His281Leu	p.H281L	ENST00000335508	NM_012433.2	281	cAt/cTt	7/25	0.196341023190203	2	FACETS	0.366	0.301	0.44	0.183	0.15	0.22	SUBCLONAL	1	TRUE	0	0.278156719145871	2		588	727	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023118	31023118	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011142-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	43	630	0	ENST00000375687.4:c.2603T>A	p.Leu868His	p.L868H	ENST00000375687	NM_015338.5	868	cTt/cAt	13/13	0.188621241093945	3	FACETS	0.486	0.406	0.576	0.243	0.203	0.288	SUBCLONAL	1	TRUE	1	0.278156719145871	3		630	724	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739108	40739108	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011142-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	91	705	0	ENST00000373198.4:c.3176G>C	p.Arg1059Pro	p.R1059P	ENST00000373198	NM_133170.3	1059	cGg/cCg	24/32	0.188621241093945	3	FACETS	0.912	0.809	1	0.456	0.404	0.511	CLONAL	1	TRUE	1	0.278156719145871	3		705	817	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534484	187534484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748020206	NA	P-0011142-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	36	422	0	ENST00000441802.2:c.9242C>T	p.Thr3081Met	p.T3081M	ENST00000441802	NM_005245.3	3081	aCg/aTg	13/27	1	2	FACETS	0.558	0.458	0.67	0.558	0.458	0.67	SUBCLONAL	1	TRUE	1	0.278156719145871	2		422	464	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521857	157521857	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011142-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	28	453	0	ENST00000346085.5:c.4129G>T	p.Asp1377Tyr	p.D1377Y	ENST00000346085	NM_020732.3	1377	Gac/Tac	18/20	1	2	FACETS	0.366	0.292	0.451	0.366	0.292	0.451	SUBCLONAL	1	TRUE	1	0.278156719145871	2		453	550	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931890	68931890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011142-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	89	811	0	ENST00000288368.4:c.320C>T	p.Thr107Ile	p.T107I	ENST00000288368	NM_024870.2	107	aCc/aTc	3/40	0.188621241093945	3	FACETS	0.744	0.658	0.836	0.372	0.329	0.418	SUBCLONAL	1	TRUE	1	0.278156719145871	3		811	980	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376047	8376047	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011142-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	29	462	0	ENST00000356435.5:c.4550C>G	p.Thr1517Ser	p.T1517S	ENST00000356435		1517	aCc/aGc	28/35	1	2	FACETS	0.371	0.297	0.456	0.371	0.297	0.456	SUBCLONAL	1	TRUE	1	0.278156719145871	2		462	562	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528773	8528773	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011142-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	25	403	0	ENST00000356435.5:c.359A>C	p.Gln120Pro	p.Q120P	ENST00000356435		120	cAa/cCa	4/35	1	2	FACETS	0.392	0.308	0.488	0.392	0.308	0.488	SUBCLONAL	1	TRUE	1	0.278156719145871	2		403	459	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158002	27158002	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011142-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	109	810	0	ENST00000380036.4:c.226C>A	p.Gln76Lys	p.Q76K	ENST00000380036	NM_000459.3	76	Caa/Aaa	2/23	1	2	FACETS	0.828	0.742	0.919	0.828	0.742	0.919	CLONAL	1	TRUE	1	0.278156719145871	2		810	947	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602637	10602637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777523734	NA	P-0011198-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	214	599	0	ENST00000171111.5:c.941C>T	p.Thr314Met	p.T314M	ENST00000171111	NM_203500.1	314	aCg/aTg	3/6	1	2	FACETS	0.702	0.651	0.753	0.702	0.651	0.753	SUBCLONAL	1	TRUE	1	0.566490291690299	2		599	1077	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443613	29443613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519783	NA	P-0011203-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	95	873	0	ENST00000389048.3:c.3604G>A	p.Gly1202Arg	p.G1202R	ENST00000389048	NM_004304.4	1202	Gga/Aga	23/29	0.165882846107894	3	FACETS	1	0.968	1	0.625	0.555	0.7	CLONAL	1	TRUE	1	0.16	3		873	1026	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609778	81609778	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762578626	NA	P-0011203-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	50	479	1	ENST00000298171.2:c.1376C>T	p.Ala459Val	p.A459V	ENST00000298171	NM_000369.2	459	gCg/gTg	10/10	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.16	2		480	562	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061105	38061174	+	frameshift_variant	Frame_Shift_Del	DEL	TTGCGGCTCTCAGGGCCGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCG	TTGCGGCTCTCAGGGCCGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCG	-	novel	NA	P-0011203-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	44	53	0	ENST00000250448.2:c.815_884del	p.Pro272ArgfsTer26	p.P272Rfs*26	ENST00000250448	NM_004496.3	272	cCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGCGGCGCCAAGGGCGGCCCTGAGAGCCGCAAg/cg	2/2	1	2	FACETS	0.902	0.776	1	1	0.981	1	CLONAL	5	TRUE	1	0.16	2		53	122	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0011243-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	735	454	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.351029139968087	6	FACETS	0.979	0.946	1	0.979	0.946	1	CLONAL	4	TRUE	2	0.351029139968087	6		454	1820	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8252051	8252051	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011243-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	222	348	0	ENST00000335790.3:c.26G>T	p.Gly9Val	p.G9V	ENST00000335790	NM_002315.2	9	gGc/gTc	2/4	0.351029139968088	3	FACETS	0.939	0.876	1	0.939	0.876	1	CLONAL	2	TRUE	1	0.351029139968087	3		348	792	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610247	10610247	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011243-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	365	690	1	ENST00000171111.5:c.463G>T	p.Val155Phe	p.V155F	ENST00000171111	NM_203500.1	155	Gtc/Ttc	2/6	0.351029139968087	2	FACETS	0.98	0.931	1	0.98	0.931	1	CLONAL	2	TRUE	0	0.351029139968087	2		691	1061	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81557479	81557479	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011243-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	291	491	0	ENST00000298171.2:c.459C>A	p.Phe153Leu	p.F153L	ENST00000298171	NM_000369.2	153	ttC/ttA	5/10	0.351029139968087	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.351029139968087	2		491	821	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099454	27099454	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011243-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	250	387	0	ENST00000324856.7:c.3691G>T	p.Asp1231Tyr	p.D1231Y	ENST00000324856	NM_006015.4	1231	Gat/Tat	14/20	1	2	FACETS	0.874	0.82	0.929	1	0.994	1	CLONAL	2	TRUE	1	0.351029139968087	2		387	815	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998843	100998843	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs774235489	NA	P-0011243-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	361	630	1	ENST00000325455.5:c.959C>A	p.Thr320Asn	p.T320N	ENST00000325455	NM_001202474.3	320	aCt/aAt	1/8	0.351029139968088	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	1	0.351029139968087	3		631	1203	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28599073	28599073	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011243-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	289	472	0	ENST00000241453.7:c.2215G>T	p.Gly739Cys	p.G739C	ENST00000241453	NM_004119.2	739	Ggt/Tgt	18/24	0.351029139968087	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.351029139968087	2		472	769	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828666	72828666	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011243-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	319	508	0	ENST00000268489.5:c.7915C>T	p.Gln2639Ter	p.Q2639*	ENST00000268489	NM_006885.3	2639	Cag/Tag	9/10	0.351029139968088	3	FACETS	0.967	0.913	1	0.967	0.913	1	CLONAL	2	TRUE	1	0.351029139968087	3		508	1105	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219321	1219321	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0011243-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	269	461	0	ENST00000326873.7:c.375-2A>C		p.X125_splice	ENST00000326873	NM_000455.4	125			NA	2	FACETS	0.979	0.922	1			1	INDETERMINATE	2	TRUE	NA	0.351029139968087	2		461	783	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286284	66286284	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0011243-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	170	243	0	ENST00000273854.3:c.1403-1G>T		p.X468_splice	ENST00000273854	NM_004439.5	468			0.326347830056203	4	FACETS	0.977	0.901	1	0.977	0.901	1	CLONAL	2	TRUE	2	0.351029139968087	4		243	670	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0011311-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	79	943	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.792	0.694	0.897	0.792	0.694	0.897	SUBCLONAL	1	TRUE	1	0.2	2		943	998	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958190	2958190	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753952757	NA	P-0011311-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	110	594	1	ENST00000396946.4:c.2542C>T	p.Arg848Cys	p.R848C	ENST00000396946	NM_032415.4	848	Cgc/Tgc	19/25	1	2	FACETS	0.993	0.89	1	0.993	0.89	1	CLONAL	1	TRUE	1	0.2	2		595	1108	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446110	70446110	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	G	novel	NA	P-0011311-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	56	356	0	ENST00000373644.4:c.5053-3C>G		p.X1685_splice	ENST00000373644	NM_030625.2	1685			1	2	FACETS	0.799	0.683	0.925	0.799	0.683	0.925	CLONAL	1	TRUE	1	0.2	2		356	701	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211475	46211477	+	frameshift_variant	Frame_Shift_Del	DEL	GCT	GCT	CC	novel	NA	P-0011311-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	26	228	0	ENST00000334344.6:c.441_443delinsCC	p.Leu148ArgfsTer67	p.L148Rfs*67	ENST00000334344	NM_152641.2	147	ggGCTg/ggCCg	5/21	1	2	FACETS	0.516	0.408	0.641	0.516	0.408	0.641	SUBCLONAL	1	TRUE	1	0.2	2		228	504	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614537	38614538	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1555391053	NA	P-0011311-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	150	626	0	ENST00000299084.4:c.304dup	p.Thr102AsnfsTer7	p.T102Nfs*7	ENST00000299084	NM_152594.2	101	-/A	3/7	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.2	2		626	1174	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346897	89346897	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011311-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	45	209	0	ENST00000301030.4:c.6053del	p.Pro2018LeufsTer69	p.P2018Lfs*69	ENST00000301030	NM_001256183.1	2018	cCt/ct	9/13	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.2	2		209	444	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526429	66526429	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011311-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	171	386	0	ENST00000358598.2:c.985C>G	p.Leu329Val	p.L329V	ENST00000358598	NM_212471.2	329	Cta/Gta	11/11	0.186055633586441	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	1	0.2	3		386	897	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164620	47164623	+	frameshift_variant	Frame_Shift_Del	DEL	TAAG	TAAG	-	novel	NA	P-0011311-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	50	303	0	ENST00000409792.3:c.1503_1506del	p.Tyr501Ter	p.Y501*	ENST00000409792	NM_014159.6	501	taCTTA/ta	3/21	1	2	FACETS	0.906	0.768	1	0.906	0.768	1	CLONAL	1	TRUE	1	0.2	2		303	552	SUCCESS
APC	324	MSKCC	GRCh37	5	112154829	112154829	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1554080012	NA	P-0011311-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	198	597	0	ENST00000257430.4:c.1100C>G	p.Ser367Cys	p.S367C	ENST00000257430	NM_000038.5	367	tCt/tGt	10/16	0.186055633586441	3	FACETS	0.915	0.846	0.987	0.915	0.846	0.987	CLONAL	2	TRUE	1	0.2	3		597	1190	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001124	150001124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011311-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	85	505	0	ENST00000253339.5:c.2480G>A	p.Arg827Lys	p.R827K	ENST00000253339		827	aGa/aAa	4/7	0.293935784671457	1	FACETS	0.896	0.791	1	0.896	0.791	1	CLONAL	1	TRUE	0	0.2	1		505	854	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974238	2974238	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011311-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1204	115	743	0	ENST00000396946.4:c.1367C>A	p.Thr456Asn	p.T456N	ENST00000396946	NM_032415.4	456	aCc/aAc	10/25	1	2	FACETS	0.872	0.783	0.967	0.872	0.783	0.967	CLONAL	1	TRUE	1	0.2	2		743	1319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0011537-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	491	634	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	0.641490698953964	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.641490698953964	1		634	1025	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412187	63412187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011537-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	516	441	0	ENST00000330258.3:c.980G>A	p.Gly327Asp	p.G327D	ENST00000330258	NM_152424.3	327	gGt/gAt	2/2	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.641490698953964	1		441	859	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015676	112015676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011537-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	140	417	0	ENST00000368678.4:c.1166G>A	p.Arg389Gln	p.R389Q	ENST00000368678		389	cGa/cAa	11/13	0.35441402932901	1	FACETS	0.363	0.33	0.397	0.363	0.33	0.397	INDETERMINATE	1	TRUE	0	0.641490698953964	1		417	817	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1253913	1253913	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011537-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1606	203	503	2	ENST00000310581.5:c.3329C>A	p.Thr1110Lys	p.T1110K	ENST00000310581	NM_198253.2	1110	aCg/aAg	16/16	0.620768702175253	3	FACETS	0.462	0.426	0.499	0.231	0.213	0.25	SUBCLONAL	1	TRUE	1	0.641490698953964	3		505	1809	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0011566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	237	326	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.469535066636395	2	FACETS	0.87	0.819	0.922	0.87	0.819	0.922	CLONAL	2	TRUE	0	0.469535066636395	2		326	580	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434595	NA	P-0011566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	227	491	1	ENST00000369535.4:c.37G>A	p.Gly13Ser	p.G13S	ENST00000369535	NM_002524.4	13	Ggt/Agt	2/7	1	2	FACETS	0.974	0.907	1	0.974	0.907	1	CLONAL	1	TRUE	1	0.469535066636395	2		492	993	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023205	27023221	+	frameshift_variant	Frame_Shift_Del	DEL	ACGGGAACGCGGGCCCT	ACGGGAACGCGGGCCCT	-	novel	NA	P-0011566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	74	217	0	ENST00000324856.7:c.312_328del	p.Asn104LysfsTer7	p.N104Kfs*7	ENST00000324856	NM_006015.4	104	aACGGGAACGCGGGCCCT/a	1/20	0.452665789227019	1	FACETS	0.807	0.713	0.905	0.807	0.713	0.905	CLONAL	1	TRUE	0	0.469535066636395	1		217	299	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	283	297	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.838	0.792	0.883			1	INDETERMINATE	2	TRUE	NA	0.491055381060817	2		297	688	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0012057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	783	650	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.491055381060817	4	FACETS	0.902	0.877	0.927	0.902	0.877	0.927	CLONAL	4	TRUE	0	0.491055381060817	4		650	1318	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663346	227663346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024227751	NA	P-0012057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	100	230	0	ENST00000305123.5:c.109G>A	p.Glu37Lys	p.E37K	ENST00000305123	NM_005544.2	37	Gag/Aag	1/2	0.376970604337967	3	FACETS	0.826	0.739	0.918	0.413	0.369	0.459	CLONAL	1	TRUE	1	0.491055381060817	3		230	614	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519991	NA	P-0012057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	317	396	0	ENST00000269305.4:c.536A>C	p.His179Pro	p.H179P	ENST00000269305	NM_001126112.2	179	cAt/cCt	5/11	0.389029238024934	2	FACETS	0.769	0.729	0.81	0.769	0.729	0.81	SUBCLONAL	2	TRUE	0	0.491055381060817	2		396	839	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650617	18650617	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	108	327	1	ENST00000266497.5:c.2828G>T	p.Trp943Leu	p.W943L	ENST00000266497		943	tGg/tTg	20/31	0.391487734014649	3	FACETS	0.719	0.645	0.797	0.24	0.215	0.266	SUBCLONAL	1	TRUE	0	0.491055381060817	3		328	762	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902287	50902287	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0012057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	254	668	0	ENST00000440232.2:c.179C>G	p.Ser60Ter	p.S60*	ENST00000440232	NM_002691.3	60	tCa/tGa	2/27	1	2	FACETS	0.793	0.741	0.847	0.793	0.741	0.847	SUBCLONAL	1	TRUE	1	0.491055381060817	2		668	1304	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918247	50918247	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs868847470	NA	P-0012057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	178	436	0	ENST00000440232.2:c.2564G>T	p.Arg855Leu	p.R855L	ENST00000440232	NM_002691.3	855	cGa/cTa	20/27	1	2	FACETS	0.911	0.841	0.983	0.911	0.841	0.983	CLONAL	1	TRUE	1	0.491055381060817	2		436	796	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274662	198274662	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	173	348	1	ENST00000335508.6:c.736G>T	p.Gly246Ter	p.G246*	ENST00000335508	NM_012433.2	246	Gga/Tga	7/25	0.376970604337967	3	FACETS	0.958	0.882	1	0.479	0.441	0.519	CLONAL	1	TRUE	1	0.491055381060817	3		349	916	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458614	12458614	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	264	312	1	ENST00000287820.6:c.1231G>A	p.Asp411Asn	p.D411N	ENST00000287820	NM_015869.4	411	Gac/Aac	6/7	0.377995043332682	3	FACETS	0.826	0.777	0.876	0.826	0.777	0.876	CLONAL	2	TRUE	1	0.491055381060817	3		313	811	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72873584	72873584	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	74	253	0	ENST00000325599.8:c.718G>T	p.Ala240Ser	p.A240S	ENST00000325599	NM_018130.2	240	Gct/Tct	6/11	0.377995043332682	3	FACETS	0.606	0.531	0.688	0.303	0.265	0.344	SUBCLONAL	1	TRUE	1	0.491055381060817	3		253	619	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066699	94066699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	114	327	0	ENST00000369303.4:c.1060C>T	p.Pro354Ser	p.P354S	ENST00000369303	NM_004440.3	354	Cct/Tct	5/17	NA	2	FACETS	0.556	0.5	0.615			1	INDETERMINATE	1	TRUE	NA	0.491055381060817	2		327	835	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012057-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	158	297	0				ENST00000310581	NM_198253.2	-/1132			0.321299510254573	3	FACETS	0.755	0.694	0.818	0.755	0.694	0.818	SUBCLONAL	2	TRUE	1	0.390303889460047	3		297	641	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0012057-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	641	650	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.360995781068172	4	FACETS	0.96	0.929	0.991	1	0.998	1	CLONAL	4	TRUE	2	0.390303889460047	4		650	1189	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663346	227663346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024227751	NA	P-0012057-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	62	230	0	ENST00000305123.5:c.109G>A	p.Glu37Lys	p.E37K	ENST00000305123	NM_005544.2	37	Gag/Aag	1/2	0.321299510254573	3	FACETS	0.747	0.646	0.857	0.374	0.323	0.429	SUBCLONAL	1	TRUE	1	0.390303889460047	3		230	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519991	NA	P-0012057-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	187	396	0	ENST00000269305.4:c.536A>C	p.His179Pro	p.H179P	ENST00000269305	NM_001126112.2	179	cAt/cCt	5/11	0.273834066014869	2	FACETS	0.832	0.773	0.892	0.832	0.773	0.892	CLONAL	2	TRUE	0	0.390303889460047	2		396	576	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902287	50902287	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0012057-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	149	668	0	ENST00000440232.2:c.179C>G	p.Ser60Ter	p.S60*	ENST00000440232	NM_002691.3	60	tCa/tGa	2/27	1	2	FACETS	0.689	0.628	0.753	0.689	0.628	0.753	SUBCLONAL	1	TRUE	1	0.390303889460047	2		668	1108	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918247	50918247	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs868847470	NA	P-0012057-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	107	436	0	ENST00000440232.2:c.2564G>T	p.Arg855Leu	p.R855L	ENST00000440232	NM_002691.3	855	cGa/cTa	20/27	1	2	FACETS	0.873	0.785	0.967	0.873	0.785	0.967	CLONAL	1	TRUE	1	0.390303889460047	2		436	628	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274662	198274662	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012057-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	101	348	1	ENST00000335508.6:c.736G>T	p.Gly246Ter	p.G246*	ENST00000335508	NM_012433.2	246	Gga/Tga	7/25	0.321299510254573	3	FACETS	0.786	0.702	0.875	0.393	0.351	0.438	SUBCLONAL	1	TRUE	1	0.390303889460047	3		349	787	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458614	12458614	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012057-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	176	312	1	ENST00000287820.6:c.1231G>A	p.Asp411Asn	p.D411N	ENST00000287820	NM_015869.4	411	Gac/Aac	6/7	0.278654223196007	3	FACETS	0.838	0.775	0.903	0.838	0.775	0.903	CLONAL	2	TRUE	1	0.390303889460047	3		313	643	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72873584	72873584	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012057-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	45	253	0	ENST00000325599.8:c.718G>T	p.Ala240Ser	p.A240S	ENST00000325599	NM_018130.2	240	Gct/Tct	6/11	0.278654223196007	3	FACETS	0.628	0.528	0.738	0.314	0.264	0.369	SUBCLONAL	1	TRUE	1	0.390303889460047	3		253	439	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066699	94066699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012057-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	85	327	0	ENST00000369303.4:c.1060C>T	p.Pro354Ser	p.P354S	ENST00000369303	NM_004440.3	354	Cct/Tct	5/17	0.278654223196007	3	FACETS	0.759	0.671	0.853	0.379	0.335	0.427	SUBCLONAL	1	TRUE	1	0.390303889460047	3		327	686	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591104	67591115	+	inframe_deletion	In_Frame_Del	DEL	TTAAACCAGACC	TTAAACCAGACC	-	novel	NA	P-0012109-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	204	421	0	ENST00000274335.5:c.1700_1711del	p.Lys567_Leu570del	p.K567_L570del	ENST00000274335		566	aTTAAACCAGACCtt/att	12/15	0.764672076275934	3	FACETS	0.902	0.838	0.968	0.451	0.419	0.484	CLONAL	1	TRUE	1	0.768329998466544	3		421	815	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578213	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012109-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	1030	820	1	ENST00000269305.4:c.636dup	p.Arg213SerfsTer3	p.R213Sfs*3	ENST00000269305	NM_001126112.2	212	-/T	6/11	0.768329998466544	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.768329998466544	2		821	1335	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838333	156838333	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012109-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1267	472	889	1	ENST00000524377.1:c.611C>G	p.Ser204Trp	p.S204W	ENST00000524377	NM_002529.3	204	tCg/tGg	6/17	0.764672076275934	3	FACETS	0.978	0.933	1	0.489	0.466	0.512	CLONAL	1	TRUE	1	0.768329998466544	3		890	1739	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084177	47084177	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012109-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	219	445	0	ENST00000409792.3:c.7112T>A	p.Val2371Glu	p.V2371E	ENST00000409792	NM_014159.6	2371	gTg/gAg	17/21	0.693051230124397	4	FACETS	0.861	0.8	0.924	0.287	0.266	0.308	CLONAL	1	TRUE	1	0.768329998466544	4		445	1171	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690821	89690821	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0012109-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	211	435	1	ENST00000371953.3:c.228T>A	p.Tyr76Ter	p.Y76*	ENST00000371953	NM_000314.4	76	taT/taA	4/9	0.768329998466544	1	FACETS	0.995	0.944	1	0.995	0.944	1	CLONAL	1	TRUE	0	0.768329998466544	1		436	340	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0012181-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	208	401	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.499171021373232	4	FACETS	0.905	0.844	0.968	0.905	0.844	0.968	CLONAL	2	FALSE	2	0.526772800349539	4		401	666	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696644	47696644	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519964	NA	P-0012181-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	262	576	0	ENST00000347630.2:c.304T>G	p.Phe102Val	p.F102V	ENST00000347630	NM_001007230.1	102	Ttc/Gtc	5/11	0.499171021373232	4	FACETS	0.829	0.778	0.881	0.829	0.778	0.881	CLONAL	2	FALSE	2	0.526772800349539	4		576	916	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172490	108172490	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012181-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	186	442	0	ENST00000278616.4:c.5293C>T	p.Gln1765Ter	p.Q1765*	ENST00000278616	NM_000051.3	1765	Cag/Tag	35/63	0.493486986315903	4	FACETS	0.829	0.769	0.891			1	CLONAL	2	FALSE	NA	0.526772800349539	4		442	650	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731532	47731532	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012181-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	45	69	0	ENST00000449228.1:c.260del	p.Pro87LeufsTer142	p.P87Lfs*142	ENST00000449228	NM_001127240.2	87	cCt/ct	2/4	0.509699515997717	3	FACETS	0.87	0.751	0.995	0.87	0.751	0.995	CLONAL	2	FALSE	1	0.526772800349539	3		69	124	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439146	52439146	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012181-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	361	682	0	ENST00000460680.1:c.1096T>G	p.Tyr366Asp	p.Y366D	ENST00000460680	NM_004656.3	366	Tat/Gat	11/17	0.499171021373232	4	FACETS	0.912	0.865	0.96	0.912	0.865	0.96	CLONAL	2	FALSE	2	0.526772800349539	4		682	1147	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0012223-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	571	188	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.654598738521172	3	FACETS	0.946	0.911	0.98	0.946	0.911	0.98	CLONAL	2	TRUE	1	0.654598738521172	3		188	1224	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562664	29562664	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012223-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	386	536	0	ENST00000356175.3:c.3745del	p.Ser1249LeufsTer17	p.S1249Lfs*17	ENST00000356175	NM_000267.3	1248	gaT/ga	28/57	0.654598738521172	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.654598738521172	1		536	721	SUCCESS
AXL	558	MSKCC	GRCh37	19	41737177	41737177	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012257-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	118	505	0	ENST00000301178.4:c.757T>A	p.Tyr253Asn	p.Y253N	ENST00000301178	NM_021913.4	253	Tac/Aac	6/20	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.16	2		505	1023	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101044	41101044	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012257-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	37	340	0	ENST00000373198.4:c.1312G>T	p.Glu438Ter	p.E438*	ENST00000373198	NM_133170.3	438	Gag/Tag	8/32	0.250586471809281	1	FACETS	0.719	0.591	0.862	0.719	0.591	0.862	SUBCLONAL	1	TRUE	0	0.16	1		340	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	169	885	1	ENST00000269305.4:c.880del	p.Glu294SerfsTer51	p.E294Sfs*51	ENST00000269305	NM_001126112.2	294	Gag/ag	8/11	0.226864618501366	2	FACETS	1	0.986	1	0.676	0.622	0.733	CLONAL	1	TRUE	0	0.29	2		886	862	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380276	+	missense_variant	Missense_Mutation	DNP	TT	TT	CA	novel	NA	P-0012289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	358	889	3	ENST00000311936.3:c.182_183delinsTG	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAA/cTG	3/5	0.267445563140595	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.29	2		892	1199	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728765	39728765	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	174	819	0	ENST00000361337.2:c.1045A>G	p.Arg349Gly	p.R349G	ENST00000361337	NM_003286.2	349	Agg/Ggg	12/21	0.116021640258371	3	FACETS	1	0.988	1	0.705	0.649	0.764	INDETERMINATE	1	TRUE	1	0.29	3		819	974	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0012393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	58	577	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.284342640647639	3	FACETS	0.909	0.782	1	0.455	0.391	0.524	CLONAL	1	FALSE	1	0.3	3		577	489	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0012393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1501	68	664	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.3	9	FACETS	0.592	0.513	0.679	0.074	0.064	0.085	SUBCLONAL	1	FALSE	1	0.3	9		665	1569	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0012393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	690	396	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.3	9	FACETS	1	0.989	1	0.912	0.884	0.941	CLONAL	7	FALSE	1	0.3	9		396	1292	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	124	297	0				ENST00000310581	NM_198253.2	-/1132			0.282252554069142	2	FACETS	0.841	0.767	0.918	0.841	0.767	0.918	CLONAL	2	TRUE	0	0.346746989853278	2		297	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0012451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	447	437	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	3	TRUE	NA	0.346746989853278	2		437	798	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0012451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	495	695	1	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.346746989853278	3	FACETS	1	0.98	1	1	0.998	1	CLONAL	4	TRUE	1	0.346746989853278	3		696	820	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845086	128845086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761395599	NA	P-0012451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	82	1034	1	ENST00000249373.3:c.580G>A	p.Glu194Lys	p.E194K	ENST00000249373	NM_005631.4	194	Gaa/Aaa	3/12	0.238778044437706	5	FACETS	0.599	0.526	0.678	0.2	0.175	0.226	SUBCLONAL	1	TRUE	2	0.346746989853278	5		1035	1200	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0012451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	188	705	0	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			NA	2	FACETS	0.933	0.868	1			1	INDETERMINATE	2	TRUE	NA	0.346746989853278	2		705	581	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649915	88649915	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	94	603	0	ENST00000372037.3:c.165del	p.Leu56CysfsTer4	p.L56Cfs*4	ENST00000372037	NM_004329.2	55	aCc/ac	4/13	0.253772211495687	0	FACETS	0.652	0.582	0.727			1	SUBCLONAL	1	TRUE	0	0.346746989853278	0		603	543	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289869	15289869	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	99	1029	0	ENST00000263388.2:c.3685G>A	p.Gly1229Ser	p.G1229S	ENST00000263388	NM_000435.2	1229	Ggt/Agt	22/33	1	2	FACETS	0.662	0.591	0.739	0.662	0.591	0.739	SUBCLONAL	1	TRUE	1	0.346746989853278	2		1029	862	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090581	71090581	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	54	656	0	ENST00000318789.4:c.767C>G	p.Thr256Arg	p.T256R	ENST00000318789	NM_032682.5	256	aCg/aGg	11/21	0.346746989853278	3	FACETS	0.482	0.41	0.56	0.241	0.205	0.28	SUBCLONAL	1	TRUE	1	0.346746989853278	3		656	759	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518197	187518197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376106855	NA	P-0012451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	125	439	0	ENST00000441802.2:c.12497C>T	p.Ala4166Val	p.A4166V	ENST00000441802	NM_005245.3	4166	gCg/gTg	25/27	NA	2	FACETS	0.769	0.7	0.84			1	INDETERMINATE	2	TRUE	NA	0.346746989853278	2		439	469	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564653	86564653	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	77	997	0	ENST00000274376.6:c.387del	p.Pro130GlnfsTer44	p.P130Qfs*44	ENST00000274376	NM_002890.2	129	Ggg/gg	1/25	0.238778044437706	5	FACETS	0.623	0.545	0.707	0.208	0.181	0.236	SUBCLONAL	1	TRUE	2	0.346746989853278	5		997	1084	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0012459-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1429	384	1167	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	0.77336940976794	5	FACETS	1	0.988	1	0.38	0.36	0.401	CLONAL	1	TRUE	2	0.838190228908874	5		1167	1813	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435311	18435311	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012459-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	427	839	1	ENST00000266497.5:c.296A>T	p.His99Leu	p.H99L	ENST00000266497		99	cAt/cTt	1/31	0.80834375352142	4	FACETS	0.953	0.911	0.994	0.953	0.911	0.994	CLONAL	2	TRUE	2	0.838190228908874	4		840	983	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991140	41991141	+	splice_donor_variant	Splice_Site	DEL	GT	GT	-	novel	NA	P-0012459-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	551	1255	0	ENST00000219905.7:c.2092+1_2092+2del		p.X698_splice	ENST00000219905	NM_001164273.1	698			0.838190228908874	2	FACETS	0.942	0.919	0.964	0.942	0.919	0.964	CLONAL	2	TRUE	0	0.838190228908874	2		1255	698	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0012473-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	311	733	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	1	2	FACETS	0.964	0.912	1	0.964	0.912	1	CLONAL	1	TRUE	1	0.722052727403749	2		733	894	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339266	70339286	+	inframe_deletion	In_Frame_Del	DEL	AGCCTGCTGTCTCTGGGGATG	AGCCTGCTGTCTCTGGGGATG	-	novel	NA	P-0012473-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	271	612	0	ENST00000374080.3:c.146_166del	p.Pro49_Glu55del	p.P49_E55del	ENST00000374080		48	cAGCCTGCTGTCTCTGGGGATGag/cag	2/45	1	2	FACETS	0.821	0.772	0.872	0.821	0.772	0.872	CLONAL	1	TRUE	1	0.722052727403749	2		612	914	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551688	150551692	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCC	GCGCC	-	novel	NA	P-0012473-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	148	372	0	ENST00000369026.2:c.315_319del	p.Pro107Ter	p.P107*	ENST00000369026	NM_021960.4	105	gcGGCGCcg/gccg	1/3	0.722052727403749	3	FACETS	0.977	0.897	1	0.489	0.448	0.53	CLONAL	1	TRUE	1	0.722052727403749	3		372	571	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0012476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	44	644	0	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.3	1	FACETS	0.901	0.757	1	0.901	0.757	1	CLONAL	1	TRUE	0	0.23	1		644	376	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141502	11141502	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	46	818	1	ENST00000358026.2:c.3479G>T	p.Gly1160Val	p.G1160V	ENST00000358026	NM_001128849.1	1160	gGg/gTg	25/36	0.3	1	FACETS	0.77	0.649	0.903	0.77	0.649	0.903	CLONAL	1	TRUE	0	0.23	1		819	460	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094376	27094377	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0012476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	61	712	1	ENST00000324856.7:c.3084_3085delinsCT	p.Ala1029Ser	p.A1029S	ENST00000324856	NM_006015.4	1028	ctGGcc/ctCTcc	11/20	1	2	FACETS	0.887	0.765	1	0.887	0.765	1	CLONAL	1	TRUE	1	0.23	2		713	598	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163315581	163315581	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	138	726	0	ENST00000271452.3:c.921G>T	p.Arg307Ser	p.R307S	ENST00000271452	NM_145697.2	307	agG/agT	11/14	0.3	3	FACETS	1	0.965	1	0.564	0.511	0.619	CLONAL	1	TRUE	1	0.23	3		726	1187	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607607	43607607	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	42	915	0	ENST00000355710.3:c.1583G>C	p.Cys528Ser	p.C528S	ENST00000355710	NM_020975.4	528	tGt/tCt	8/20	1	2	FACETS	0.632	0.527	0.749	0.632	0.527	0.749	SUBCLONAL	1	TRUE	1	0.23	2		915	578	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999621	100999621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	118	1176	0	ENST00000325455.5:c.181C>T	p.Pro61Ser	p.P61S	ENST00000325455	NM_001202474.3	61	Cct/Tct	1/8	0.284604107447097	3	FACETS	1	0.982	1	0.71	0.64	0.783	CLONAL	1	TRUE	1	0.23	3		1176	806	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141818	108141818	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	119	790	0	ENST00000278616.4:c.2866G>T	p.Gly956Ter	p.G956*	ENST00000278616	NM_000051.3	956	Gga/Tga	19/63	0.284604107447097	3	FACETS	1	0.97	1	0.599	0.54	0.662	CLONAL	1	TRUE	1	0.23	3		790	963	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120546261	120546261	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	43	846	0	ENST00000229340.5:c.63G>C	p.Lys21Asn	p.K21N	ENST00000229340	NM_006861.6	21	aaG/aaC	2/6	1	2	FACETS	0.637	0.532	0.753	0.637	0.532	0.753	SUBCLONAL	1	TRUE	1	0.23	2		846	587	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650279	12650279	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	81	798	0	ENST00000251849.4:c.567C>G	p.Asn189Lys	p.N189K	ENST00000251849	NM_002880.3	189	aaC/aaG	5/17	1	2	FACETS	0.695	0.611	0.786	0.695	0.611	0.786	SUBCLONAL	1	TRUE	1	0.23	2		798	1013	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035242	6035242	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	65	689	0	ENST00000265849.7:c.826T>G	p.Cys276Gly	p.C276G	ENST00000265849	NM_000535.5	276	Tgc/Ggc	8/15	1	2	FACETS	0.757	0.655	0.867	0.757	0.655	0.867	SUBCLONAL	1	TRUE	1	0.23	2		689	747	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540214	23540214	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	47	520	1	ENST00000380871.4:c.189G>T	p.Glu63Asp	p.E63D	ENST00000380871	NM_006167.3	63	gaG/gaT	1/2	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.23	2		521	332	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032555	47032555	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	27	740	0	ENST00000377604.3:c.461T>G	p.Val154Gly	p.V154G	ENST00000377604	NM_001204468.1	154	gTg/gGg	5/24	1	2	FACETS	0.496	0.394	0.614	0.496	0.394	0.614	SUBCLONAL	1	TRUE	1	0.23	2		740	473	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs104886003	NA	P-0012548-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	52	765	0	ENST00000263967.3:c.1633G>C	p.Glu545Gln	p.E545Q	ENST00000263967	NM_006218.2	545	Gag/Cag	10/21	1	2	FACETS	0.347	0.294	0.405	0.347	0.294	0.405	SUBCLONAL	1	TRUE	1	0.338908925125027	2		765	885	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750639	128750639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775522201	NA	P-0012548-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	46	542	0	ENST00000377970.2:c.176C>T	p.Ala59Val	p.A59V	ENST00000377970	NM_002467.4	59	gCg/gTg	2/3	1	2	FACETS	0.406	0.341	0.478	0.406	0.341	0.478	SUBCLONAL	1	TRUE	1	0.338908925125027	2		542	669	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900863	3900863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012548-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	68	620	0	ENST00000262367.5:c.233G>A	p.Ser78Asn	p.S78N	ENST00000262367	NM_004380.2	78	aGc/aAc	2/31	1	2	FACETS	0.451	0.391	0.516	0.451	0.391	0.516	SUBCLONAL	1	TRUE	1	0.338908925125027	2		620	890	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574004	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAACATCTCGAAGCGCTCACGCCCAC	novel	NA	P-0012548-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	62	810	1	ENST00000269305.4:c.998_1023dup	p.Arg342ValfsTer12	p.R342Vfs*12	ENST00000269305	NM_001126112.2	341	-/GTGGGCGTGAGCGCTTCGAGATGTTC	10/11	1	2	FACETS	0.32	0.275	0.369	0.32	0.275	0.369	SUBCLONAL	1	TRUE	1	0.338908925125027	2		811	1144	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245480	153245480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012548-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	54	661	0	ENST00000281708.4:c.1711G>A	p.Gly571Arg	p.G571R	ENST00000281708	NM_033632.3	571	Ggg/Agg	11/12	1	2	FACETS	0.354	0.301	0.412	0.354	0.301	0.412	SUBCLONAL	1	TRUE	1	0.338908925125027	2		661	900	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630740	187630740	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012548-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	68	629	0	ENST00000441802.2:c.242del	p.Asn81ThrfsTer16	p.N81Tfs*16	ENST00000441802	NM_005245.3	81	aAc/ac	2/27	1	2	FACETS	0.376	0.326	0.431	0.376	0.326	0.431	SUBCLONAL	1	TRUE	1	0.338908925125027	2		629	1066	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591277	67591278	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0012548-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	43	428	0	ENST00000274335.5:c.1776_1777del	p.Lys593ValfsTer8	p.K593Vfs*8	ENST00000274335		592	aAG/a	13/15	1	2	FACETS	0.355	0.296	0.421	0.355	0.296	0.421	SUBCLONAL	1	TRUE	1	0.338908925125027	2		428	714	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578513	7578513	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012552-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	490	1295	0	ENST00000269305.4:c.417G>C	p.Lys139Asn	p.K139N	ENST00000269305	NM_001126112.2	139	aaG/aaC	5/11	0.48358136769649	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.48358136769649	2		1295	951	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577500	64577500	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs953827589	NA	P-0012552-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	45	834	0	ENST00000312049.6:c.82G>C	p.Gly28Arg	p.G28R	ENST00000312049	NM_130799.2	28	Ggc/Cgc	2/10	0.479215925665575	3	FACETS	0.308	0.258	0.364	0.154	0.129	0.182	SUBCLONAL	1	TRUE	1	0.48358136769649	3		834	750	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512471	38512471	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012552-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	127	1326	0	ENST00000254066.5:c.1382C>G	p.Ser461Cys	p.S461C	ENST00000254066	NM_000964.3	461	tCc/tGc	9/9	0.48358136769649	2	FACETS	0.521	0.471	0.573	0.26	0.235	0.287	SUBCLONAL	1	TRUE	0	0.48358136769649	2		1326	1009	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888189	112888189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507511	NA	P-0012629-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	177	684	5	ENST00000351677.2:c.205G>A	p.Glu69Lys	p.E69K	ENST00000351677	NM_002834.3	69	Gag/Aag	3/16	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.463647263283213	2		689	742	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs869320707	NA	P-0012629-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	164	883	1	ENST00000397752.3:c.3028+1G>T		p.X1010_splice	ENST00000397752	NM_000245.2	1010			1	2	FACETS	0.651	0.597	0.708	0.651	0.597	0.708	SUBCLONAL	1	TRUE	1	0.463647263283213	2		884	1086	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92247520	92247520	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012629-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	33	284	0	ENST00000265734.4:c.700G>T	p.Val234Leu	p.V234L	ENST00000265734	NM_001259.6	234	Gtg/Ttg	7/8	1	2	FACETS	0.473	0.386	0.57	0.473	0.386	0.57	SUBCLONAL	1	TRUE	1	0.463647263283213	2		284	301	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149251	119149251	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012629-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	15	615	2	ENST00000264033.4:c.1259G>T	p.Arg420Leu	p.R420L	ENST00000264033	NM_005188.3	420	cGa/cTa	9/16	1	2	FACETS	0.089	0.064	0.119	0.089	0.064	0.119	SUBCLONAL	1	TRUE	1	0.463647263283213	2		617	728	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031928	10031928	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012629-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	59	535	0	ENST00000330684.3:c.895C>G	p.Leu299Val	p.L299V	ENST00000330684	NM_001134407.1	299	Cta/Gta	3/13	1	2	FACETS	0.414	0.356	0.477	0.414	0.356	0.477	SUBCLONAL	1	TRUE	1	0.463647263283213	2		535	615	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39251221	39251221	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012629-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	156	763	4	ENST00000402219.2:c.1132A>T	p.Thr378Ser	p.T378S	ENST00000402219	NM_005633.3	378	Aca/Tca	9/23	1	2	FACETS	0.867	0.795	0.942	0.867	0.795	0.942	CLONAL	1	TRUE	1	0.463647263283213	2		767	776	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162475146	162475146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012629-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	37	584	0	ENST00000366898.1:c.595C>T	p.Pro199Ser	p.P199S	ENST00000366898	NM_004562.2	199	Cca/Tca	5/12	1	2	FACETS	0.225	0.185	0.271	0.225	0.185	0.271	SUBCLONAL	1	TRUE	1	0.463647263283213	2		584	709	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0012651-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	322	749	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	2	TRUE	NA	0.532506971545339	2		750	598	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953785	48953785	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0012651-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	60	200	0	ENST00000267163.4:c.1388C>G	p.Ser463Ter	p.S463*	ENST00000267163	NM_000321.2	463	tCa/tGa	14/27	0.532506971545339	1	FACETS	0.924	0.811	1	0.924	0.811	1	CLONAL	1	TRUE	0	0.532506971545339	1		200	179	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11210214	11210222	+	inframe_deletion	In_Frame_Del	DEL	GGCCATCTT	GGCCATCTT	-	novel	NA	P-0012651-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	107	390	0	ENST00000361445.4:c.4531_4539del	p.Lys1511_Ala1513del	p.K1511_A1513del	ENST00000361445	NM_004958.3	1511	AAGATGGCC/-	31/58	0.47379057719054	3	FACETS	0.876	0.788	0.969			1	CLONAL	1	TRUE	NA	0.532506971545339	3		390	581	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650880	37650880	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012651-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	176	538	0	ENST00000447079.4:c.2353del	p.Ser785ValfsTer5	p.S785Vfs*5	ENST00000447079	NM_015083.1	784	cgA/cg	5/14	0.532506971545339	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.532506971545339	1		538	417	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799688	72799688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012651-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	80	408	0	ENST00000325599.8:c.1481C>T	p.Pro494Leu	p.P494L	ENST00000325599	NM_018130.2	494	cCc/cTc	11/11	0.532506971545339	3	FACETS	0.703	0.62	0.792			1	SUBCLONAL	1	TRUE	NA	0.532506971545339	3		408	541	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878985	151878985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012651-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	93	358	0	ENST00000262189.6:c.5960C>T	p.Ser1987Phe	p.S1987F	ENST00000262189	NM_170606.2	1987	tCt/tTt	36/59	0.532506971545339	7	FACETS	0.942	0.837	1			1	CLONAL	1	TRUE	NA	0.532506971545339	7		358	864	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879285	151879285	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012651-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	81	314	0	ENST00000262189.6:c.5660C>T	p.Ser1887Phe	p.S1887F	ENST00000262189	NM_170606.2	1887	tCt/tTt	36/59	0.532506971545339	7	FACETS	0.953	0.839	1			1	CLONAL	1	TRUE	NA	0.532506971545339	7		314	744	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0012675-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	418	358	0	ENST00000374080.3:c.3670C>T	p.Leu1224Phe	p.L1224F	ENST00000374080		1224	Ctc/Ttc	26/45	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.785663447674563	1		358	492	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853077	151853077	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012675-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	637	490	0	ENST00000262189.6:c.11878C>T	p.Arg3960Ter	p.R3960*	ENST00000262189	NM_170606.2	3960	Cga/Tga	46/59	0.785663447674563	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.785663447674563	3		490	1072	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012716-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	44	722	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.3	5	FACETS	0.926	0.793	1	1	0.945	1	CLONAL	4	TRUE	2	0.23	5		722	139	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0012750-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	163	843	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.172201515213938	3	FACETS	1	0.951	1	1	0.99	1	CLONAL	3	TRUE	1	0.172201515213938	3		843	656	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100584	67100584	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0012750-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	92	282	0	ENST00000412916.2:c.283-1G>A		p.X95_splice	ENST00000412916		95			NA	2	FACETS	1	0.962	1			1	INDETERMINATE	2	TRUE	NA	0.172201515213938	2		282	456	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916743	48916744	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012825-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	534	280	0	ENST00000267163.4:c.274dup	p.Ile92AsnfsTer18	p.I92Nfs*18	ENST00000267163	NM_000321.2	91	-/A	3/27	0.596820253916936	3	FACETS	0.902	0.873	0.93	0.902	0.873	0.93	CLONAL	3	TRUE	0	0.596820253916936	3		280	859	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0012829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	77	577	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.929	0.815	1	0.929	0.815	1	CLONAL	1	TRUE	1	0.24	2		577	691	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0012829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	17	366	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.444	0.331	0.579	0.444	0.331	0.579	SUBCLONAL	1	TRUE	1	0.24	2		366	319	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941003	71941004	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0012829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	79	531	0	ENST00000298229.2:c.884dup	p.Ala296SerfsTer8	p.A296Sfs*8	ENST00000298229	NM_001567.3	293	-/C	8/28	1	2	FACETS	0.871	0.765	0.984	0.871	0.765	0.984	CLONAL	1	TRUE	1	0.24	2		531	756	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576846	7576882	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTAGTACCTGAAGGGTGAAATATTCTCCATCCAGTGG	TTAGTACCTGAAGGGTGAAATATTCTCCATCCAGTGG	-	novel	NA	P-0012829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	25	285	0	ENST00000269305.4:c.964_993+7del		p.X322_splice	ENST00000269305	NM_001126112.2	322		9/11	1	2	FACETS	0.521	0.41	0.649	0.521	0.41	0.649	SUBCLONAL	1	TRUE	1	0.24	2		285	400	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41542754	41542754	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	68	318	0	ENST00000263253.7:c.2065C>A	p.Pro689Thr	p.P689T	ENST00000263253	NM_001429.3	689	Cct/Act	11/31	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.24	2		318	556	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0012834-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	315	428	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	NA	2	FACETS	0.923	0.878	0.967			1	INDETERMINATE	2	TRUE	NA	0.514214758807567	2		428	664	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104377055	104377055	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012834-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	98	301	0	ENST00000369902.3:c.1166T>C	p.Leu389Pro	p.L389P	ENST00000369902	NM_016169.3	389	cTc/cCc	10/12	0.444548217758384	4	FACETS	0.868	0.775	0.967	0.434	0.387	0.484	CLONAL	1	TRUE	2	0.514214758807567	4		301	665	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054524	13054524	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0012834-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	111	245	0	ENST00000316448.5:c.1054-3C>T		p.X352_splice	ENST00000316448	NM_004343.3	352			0.514214758807567	6	FACETS	0.938	0.842	1	0.234	0.21	0.26	CLONAL	1	TRUE	2	0.514214758807567	6		245	934	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352751	70352752	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0012834-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	217	318	0	ENST00000374080.3:c.4473_4474dup	p.Gln1492ArgfsTer21	p.Q1492Rfs*21	ENST00000374080		1491	ggg/ggGCg	32/45	0.505643673611564	2	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.514214758807567	2		318	674	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0012850-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	106	664	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.856036471308781	6	FACETS	0.798	0.715	0.886	0.266	0.238	0.296	SUBCLONAL	1	TRUE	3	0.856036471308781	6		665	842	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0012850-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	320	493	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.856036471308781	6	FACETS	1	0.992	1	0.815	0.773	0.858	CLONAL	2	TRUE	3	0.856036471308781	6		493	829	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233408	69233408	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012850-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1907	302	544	0	ENST00000462284.1:c.1273A>C	p.Thr425Pro	p.T425P	ENST00000462284	NM_002392.5	425	Acc/Ccc	11/11	0.856036471308781	20	FACETS	0.927	0.869	0.987			1	CLONAL	3	TRUE	NA	0.856036471308781	20		544	2209	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281768	49281768	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148425155	NA	P-0012850-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	410	776	0	ENST00000282018.3:c.815C>T	p.Thr272Met	p.T272M	ENST00000282018	NM_020377.2	272	aCg/aTg	1/1	0.823254626685163	2	FACETS	0.97	0.945	0.993	0.97	0.945	0.993	CLONAL	2	TRUE	0	0.856036471308781	2		776	494	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967180	134967180	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012850-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	62	486	0	ENST00000398015.3:c.2519A>T	p.Asp840Val	p.D840V	ENST00000398015	NM_004441.4	840	gAc/gTc	14/16	0.856036471308781	3	FACETS	0.366	0.316	0.42	0.183	0.158	0.21	SUBCLONAL	1	TRUE	1	0.856036471308781	3		486	565	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012870-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	59	297	0				ENST00000310581	NM_198253.2	-/1132			0.19968351559342	5	FACETS	1	0.881	1	0.681	0.588	0.781	CLONAL	2	TRUE	2	0.19968351559342	5		297	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012870-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	120	596	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.19968351559342	2		596	928	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739100	40739100	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1158638222	NA	P-0012870-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	92	604	0	ENST00000373198.4:c.3184C>T	p.Arg1062Cys	p.R1062C	ENST00000373198	NM_133170.3	1062	Cgc/Tgc	24/32	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.19968351559342	2		604	650	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845378	89845378	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012870-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	59	862	0	ENST00000389301.3:c.1749C>G	p.Phe583Leu	p.F583L	ENST00000389301	NM_000135.2	583	ttC/ttG	19/43	1	2	FACETS	0.535	0.458	0.619	0.535	0.458	0.619	SUBCLONAL	1	TRUE	1	0.19968351559342	2		862	1105	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106151	27106173	+	frameshift_variant	Frame_Shift_Del	DEL	CCTTGACCGAGGATGGAGCTAAG	CCTTGACCGAGGATGGAGCTAAG	-	novel	NA	P-0012870-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	58	552	0	ENST00000324856.7:c.5762_5784del	p.Thr1921LysfsTer16	p.T1921Kfs*16	ENST00000324856	NM_006015.4	1921	aCCTTGACCGAGGATGGAGCTAAG/a	20/20	1	2	FACETS	0.719	0.616	0.831	0.719	0.616	0.831	SUBCLONAL	1	TRUE	1	0.19968351559342	2		552	808	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435649	18435649	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012870-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	40	374	0	ENST00000266497.5:c.634C>G	p.Leu212Val	p.L212V	ENST00000266497		212	Ctt/Gtt	1/31	1	2	FACETS	0.816	0.678	0.97	0.816	0.678	0.97	CLONAL	1	TRUE	1	0.19968351559342	2		374	491	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830457	72830457	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012870-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	36	422	0	ENST00000268489.5:c.6124C>A	p.Pro2042Thr	p.P2042T	ENST00000268489	NM_006885.3	2042	Cct/Act	9/10	1	2	FACETS	0.77	0.633	0.925	0.77	0.633	0.925	CLONAL	1	TRUE	1	0.19968351559342	2		422	468	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217298	7217298	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012870-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	74	545	0	ENST00000380728.2:c.407G>A	p.Gly136Glu	p.G136E	ENST00000380728		136	gGa/gAa	6/11	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.19968351559342	2		545	633	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217911	7217911	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012870-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	96	473	0	ENST00000380728.2:c.100G>T	p.Glu34Ter	p.E34*	ENST00000380728		34	Gaa/Taa	3/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.19968351559342	2		473	669	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131373	17131373	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs779449668	NA	P-0012870-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	86	694	2	ENST00000285071.4:c.79G>T	p.Ala27Ser	p.A27S	ENST00000285071	NM_144997.5	27	Gcc/Tcc	4/14	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.19968351559342	2		696	696	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409998	63409998	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012870-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	114	242	0	ENST00000330258.3:c.3169G>A	p.Glu1057Lys	p.E1057K	ENST00000330258	NM_152424.3	1057	Gag/Aag	2/2	1	1	FACETS	1	0.957	1	1	0.992	1	CLONAL	3	TRUE	0	0.19968351559342	1		242	317	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012870-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	88	297	0				ENST00000310581	NM_198253.2	-/1132			0.198539370260273	6	FACETS	1	0.977	1	0.365	0.322	0.41	CLONAL	1	TRUE	2	0.198539370260273	6		297	849	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012870-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	115	596	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	1	2	FACETS	0.995	0.899	1	1	0.989	1	CLONAL	2	TRUE	1	0.198539370260273	2		596	582	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739100	40739100	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1158638222	NA	P-0012870-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	112	604	0	ENST00000373198.4:c.3184C>T	p.Arg1062Cys	p.R1062C	ENST00000373198	NM_133170.3	1062	Cgc/Tgc	24/32	0.163524948095608	3	FACETS	0.924	0.832	1	0.924	0.832	1	CLONAL	2	TRUE	1	0.198539370260273	3		604	671	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845378	89845378	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012870-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	61	862	0	ENST00000389301.3:c.1749C>G	p.Phe583Leu	p.F583L	ENST00000389301	NM_000135.2	583	ttC/ttG	19/43	1	2	FACETS	0.717	0.617	0.826	0.717	0.617	0.826	SUBCLONAL	1	TRUE	1	0.198539370260273	2		862	857	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106151	27106173	+	frameshift_variant	Frame_Shift_Del	DEL	CCTTGACCGAGGATGGAGCTAAG	CCTTGACCGAGGATGGAGCTAAG	-	novel	NA	P-0012870-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	43	552	0	ENST00000324856.7:c.5762_5784del	p.Thr1921LysfsTer16	p.T1921Kfs*16	ENST00000324856	NM_006015.4	1921	aCCTTGACCGAGGATGGAGCTAAG/a	20/20	1	2	FACETS	0.788	0.658	0.931	0.788	0.658	0.931	CLONAL	1	TRUE	1	0.198539370260273	2		552	550	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435649	18435649	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012870-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	26	374	0	ENST00000266497.5:c.634C>G	p.Leu212Val	p.L212V	ENST00000266497		212	Ctt/Gtt	1/31	1	2	FACETS	0.794	0.629	0.982	0.794	0.629	0.982	CLONAL	1	TRUE	1	0.198539370260273	2		374	330	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830457	72830457	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012870-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	38	422	0	ENST00000268489.5:c.6124C>A	p.Pro2042Thr	p.P2042T	ENST00000268489	NM_006885.3	2042	Cct/Act	9/10	1	2	FACETS	0.95	0.786	1	0.95	0.786	1	CLONAL	1	TRUE	1	0.198539370260273	2		422	403	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217298	7217298	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012870-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	79	545	0	ENST00000380728.2:c.407G>A	p.Gly136Glu	p.G136E	ENST00000380728		136	gGa/gAa	6/11	1	2	FACETS	0.876	0.774	0.986	1	0.981	1	CLONAL	2	TRUE	1	0.198539370260273	2		545	454	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217911	7217911	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012870-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	71	473	0	ENST00000380728.2:c.100G>T	p.Glu34Ter	p.E34*	ENST00000380728		34	Gaa/Taa	3/11	1	2	FACETS	0.815	0.714	0.923	1	0.977	1	CLONAL	2	TRUE	1	0.198539370260273	2		473	439	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131373	17131373	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs779449668	NA	P-0012870-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	90	694	2	ENST00000285071.4:c.79G>T	p.Ala27Ser	p.A27S	ENST00000285071	NM_144997.5	27	Gcc/Tcc	4/14	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.198539370260273	2		696	640	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409998	63409998	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012870-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	144	242	0	ENST00000330258.3:c.3169G>A	p.Glu1057Lys	p.E1057K	ENST00000330258	NM_152424.3	1057	Gag/Aag	2/2	0.198539370260273	4	FACETS	1	0.969	1			1	CLONAL	5	TRUE	NA	0.198539370260273	4		242	320	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164717	47164717	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0012870-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	27	396	0	ENST00000409792.3:c.1409C>G	p.Ser470Ter	p.S470*	ENST00000409792	NM_014159.6	470	tCa/tGa	3/21	1	2	FACETS	0.687	0.546	0.848	0.687	0.546	0.848	SUBCLONAL	1	TRUE	1	0.198539370260273	2		396	396	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0012979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	289	577	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.359396635583406	4	FACETS	0.995	0.939	1	0.995	0.939	1	CLONAL	2	TRUE	2	0.493427543707211	4		577	879	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	176	297	0				ENST00000310581	NM_198253.2	-/1132			0.359396635583406	4	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	2	0.493427543707211	4		297	521	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462123	120462123	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	184	769	0	ENST00000256646.2:c.5593C>T	p.Gln1865Ter	p.Q1865*	ENST00000256646	NM_024408.3	1865	Cag/Tag	31/34	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.493427543707211	2		769	688	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508728	148508728	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs267601395	NA	P-0012979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	425	714	0	ENST00000320356.2:c.1936T>C	p.Tyr646His	p.Y646H	ENST00000320356	NM_004456.4	646	Tac/Cac	16/20	0.471733825751214	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	TRUE	1	0.493427543707211	4		714	849	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747342068	NA	P-0012979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	496	1235	0	ENST00000269305.4:c.394A>G	p.Lys132Glu	p.K132E	ENST00000269305	NM_001126112.2	132	Aag/Gag	5/11	0.493427543707211	3	FACETS	0.932	0.892	0.972	0.932	0.892	0.972	CLONAL	2	TRUE	1	0.493427543707211	3		1235	1345	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257447	16257447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	292	743	0	ENST00000375759.3:c.4712G>A	p.Ser1571Asn	p.S1571N	ENST00000375759	NM_015001.2	1571	aGc/aAc	11/15	0.47030607435057	4	FACETS	0.928	0.875	0.983	0.928	0.875	0.983	CLONAL	2	TRUE	2	0.493427543707211	4		743	952	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982502	25982502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	151	413	0	ENST00000435504.4:c.788G>A	p.Arg263Lys	p.R263K	ENST00000435504		263	aGa/aAa	9/13	0.420289767803437	4	FACETS	0.968	0.892	1	0.968	0.892	1	CLONAL	2	TRUE	2	0.493427543707211	4		413	472	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12632405	12632405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	342	904	1	ENST00000251849.4:c.1262C>T	p.Thr421Ile	p.T421I	ENST00000251849	NM_002880.3	421	aCc/aTc	12/17	0.47030607435057	4	FACETS	0.819	0.774	0.864	0.819	0.774	0.864	CLONAL	2	TRUE	2	0.493427543707211	4		905	1264	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167695	185167695	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	200	607	1	ENST00000265026.3:c.1018G>A	p.Gly340Arg	p.G340R	ENST00000265026	NM_004721.4	340	Gga/Aga	6/14	0.359396635583406	4	FACETS	0.835	0.776	0.895	0.835	0.776	0.895	CLONAL	2	TRUE	2	0.493427543707211	4		608	725	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557992	187557992	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	165	458	0	ENST00000441802.2:c.3719A>G	p.Asp1240Gly	p.D1240G	ENST00000441802	NM_005245.3	1240	gAc/gGc	5/27	0.479255158026703	3	FACETS	0.988	0.917	1	0.988	0.917	1	CLONAL	2	TRUE	1	0.493427543707211	3		458	422	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584747	187584747	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1358297166	NA	P-0012979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	128	506	1	ENST00000441802.2:c.3286C>T	p.Arg1096Ter	p.R1096*	ENST00000441802	NM_005245.3	1096	Cga/Tga	3/27	0.479255158026703	3	FACETS	1	0.975	1	0.6	0.546	0.656	CLONAL	1	TRUE	1	0.493427543707211	3		507	539	SUCCESS
APC	324	MSKCC	GRCh37	5	112174899	112174899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141444802	NA	P-0012979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	179	473	0	ENST00000257430.4:c.3608G>A	p.Gly1203Glu	p.G1203E	ENST00000257430	NM_000038.5	1203	gGa/gAa	16/16	0.47030607435057	4	FACETS	0.888	0.823	0.955	0.888	0.823	0.955	CLONAL	2	TRUE	2	0.493427543707211	4		473	610	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545815	106545815	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs370598588	NA	P-0012979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	195	491	0	ENST00000359195.3:c.3292G>C	p.Glu1098Gln	p.E1098Q	ENST00000359195	NM_002649.2	1098	Gag/Cag	11/11	0.479255158026703	3	FACETS	0.964	0.9	1	0.964	0.9	1	CLONAL	2	TRUE	1	0.493427543707211	3		491	511	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494241	140494241	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	757	1208	0	ENST00000288602.6:c.1007C>T	p.Pro336Leu	p.P336L	ENST00000288602	NM_004333.4	336	cCt/cTt	8/18	0.471733825751214	4	FACETS	0.966	0.936	0.996	0.966	0.936	0.996	CLONAL	3	TRUE	1	0.493427543707211	4		1208	1581	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994260	21994260	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	301	800	0	ENST00000579755.1:c.71T>A	p.Val24Glu	p.V24E	ENST00000579755		24	gTg/gAg	1/3	NA		FACETS		0.94	1				INDETERMINATE	2	TRUE	NA	0.493427543707211	2		800	617	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606727	43606727	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs115423919	NA	P-0012979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	181	945	0	ENST00000355710.3:c.1336G>A	p.Gly446Ser	p.G446S	ENST00000355710	NM_020975.4	446	Ggt/Agt	7/20	0.479255158026703	3	FACETS	0.967	0.892	1	0.483	0.446	0.523	CLONAL	1	TRUE	1	0.493427543707211	3		945	946	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195794	102195794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	191	466	0	ENST00000263464.3:c.554C>T	p.Ser185Leu	p.S185L	ENST00000263464	NM_001165.4	185	tCg/tTg	2/9	0.493427543707211	3	FACETS	0.935	0.872	1	0.935	0.872	1	CLONAL	2	TRUE	1	0.493427543707211	3		466	516	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231439	46231439	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	218	575	0	ENST00000334344.6:c.1279G>T	p.Glu427Ter	p.E427*	ENST00000334344	NM_152641.2	427	Gaa/Taa	10/21	0.445406767912359	4	FACETS	0.881	0.822	0.941			1	CLONAL	2	TRUE	NA	0.493427543707211	4		575	749	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245000	46245000	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	376	925	0	ENST00000334344.6:c.3094C>T	p.Gln1032Ter	p.Q1032*	ENST00000334344	NM_152641.2	1032	Cag/Tag	15/21	0.445406767912359	4	FACETS	1	0.964	1			1	CLONAL	2	TRUE	NA	0.493427543707211	4		925	1118	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358521	67358521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	170	408	0	ENST00000327367.4:c.29C>T	p.Pro10Leu	p.P10L	ENST00000327367	NM_005902.3	10	cCg/cTg	1/9	0.493427543707211	2	FACETS	0.984	0.92	1	0.984	0.92	1	CLONAL	2	TRUE	0	0.493427543707211	2		408	350	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554546	63554546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	250	612	2	ENST00000307078.5:c.193C>T	p.Pro65Ser	p.P65S	ENST00000307078	NM_004655.3	65	Ccg/Tcg	2/11	0.47030607435057	4	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	2	0.493427543707211	4		614	755	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300168	15300168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	400	925	0	ENST00000263388.2:c.1108C>T	p.Pro370Ser	p.P370S	ENST00000263388	NM_000435.2	370	Ccg/Tcg	7/33	0.493427543707211	3	FACETS	0.945	0.9	0.989	0.945	0.9	0.989	CLONAL	2	TRUE	1	0.493427543707211	3		925	1070	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164524	36164524	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	176	532	1	ENST00000300305.3:c.1351G>A	p.Asp451Asn	p.D451N	ENST00000300305		451	Gac/Aac	8/8	0.359396635583406	4	FACETS	0.88	0.815	0.948	0.88	0.815	0.948	CLONAL	2	TRUE	2	0.493427543707211	4		533	605	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627345	37627345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1179	590	1393	0	ENST00000249071.6:c.374C>T	p.Thr125Ile	p.T125I	ENST00000249071	NM_002872.4	125	aCc/aTc	5/7	0.47030607435057	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.493427543707211	4		1393	1769	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412303	139412304	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	545	952	3	ENST00000277541.6:c.1341_1342delinsTT	p.Arg448Ter	p.R448*	ENST00000277541	NM_017617.3	447	ccCCga/ccTTga	8/34	0.493427543707211	3	FACETS	0.997	0.964	1	0.997	0.964	1	CLONAL	3	TRUE	0	0.493427543707211	3		955	921	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417362	139417363	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AT	novel	NA	P-0012979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	347	811	2	ENST00000277541.6:c.681_682delinsAT	p.Cys227_Gln228delinsTer	p.C227_Q228delins*	ENST00000277541	NM_017617.3	227	tgCCag/tgATag	4/34	0.493427543707211	3	FACETS	0.92	0.873	0.967	0.613	0.582	0.645	CLONAL	2	TRUE	0	0.493427543707211	3		813	953	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436589	110436590	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	331	984	3	ENST00000375856.3:c.1811_1812delinsTT	p.Thr604Ile	p.T604I	ENST00000375856	NM_003749.2	604	aCC/aTT	1/2	0.493427543707211	2	FACETS	0.925	0.881	0.97	0.925	0.881	0.97	CLONAL	2	TRUE	0	0.493427543707211	2		987	725	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37628034	37628034	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	319	647	0	ENST00000249071.6:c.226G>A	p.Asp76Asn	p.D76N	ENST00000249071	NM_002872.4	76	Gac/Aac	4/7	0.47030607435057	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.493427543707211	4		647	881	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599270	28599270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	453	1109	0	ENST00000253063.3:c.716G>A	p.Ser239Asn	p.S239N	ENST00000253063	NM_031459.4	239	aGc/aAc	5/10	0.47030607435057	4	FACETS	0.953	0.909	0.997	0.953	0.909	0.997	CLONAL	2	TRUE	2	0.493427543707211	4		1109	1439	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372530	118372531	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0012979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	323	871	1	ENST00000534358.1:c.6463_6464delinsTT	p.Pro2155Leu	p.P2155L	ENST00000534358	NM_005933.3	2155	CCa/TTa	26/36	0.493427543707211	2	FACETS	0.954	0.908	1	0.954	0.908	1	CLONAL	2	TRUE	0	0.493427543707211	2		872	686	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1555525367	NA	P-0012979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	157	790	0	ENST00000269305.4:c.783-1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.493427543707211	3	FACETS	0.942	0.864	1	0.471	0.432	0.512	CLONAL	1	TRUE	1	0.493427543707211	3		790	842	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11032429	11032429	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	214	957	0	ENST00000327064.4:c.1823G>A	p.Ser608Asn	p.S608N	ENST00000327064	NM_199141.1	608	aGc/aAc	16/16	0.493427543707211	3	FACETS	0.995	0.924	1	0.497	0.462	0.534	CLONAL	1	TRUE	1	0.493427543707211	3		957	1087	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356419	66356419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	31	469	0	ENST00000273854.3:c.1078G>A	p.Ala360Thr	p.A360T	ENST00000273854	NM_004439.5	360	Gct/Act	5/18	0.479255158026703	3	FACETS	0.308	0.248	0.375	0.154	0.124	0.188	SUBCLONAL	1	TRUE	1	0.493427543707211	3		469	509	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820821	32820821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1251434507	NA	P-0012979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	407	944	0	ENST00000354258.4:c.773C>T	p.Ser258Phe	p.S258F	ENST00000354258	NM_000593.5	258	tCt/tTt	1/11	0.47030607435057	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.493427543707211	4		944	1145	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133308	38133308	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	275	720	1	ENST00000317025.8:c.4165C>T	p.His1389Tyr	p.H1389Y	ENST00000317025	NM_023034.1	1389	Cat/Tat	24/24	0.47030607435057	4	FACETS	0.91	0.856	0.965	0.91	0.856	0.965	CLONAL	2	TRUE	2	0.493427543707211	4		721	915	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0013059-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	901	336	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.872835054100827	3	FACETS	0.958	0.934	0.983	0.958	0.934	0.983	CLONAL	2	TRUE	1	0.872835054100827	3		336	1547	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519998	NA	P-0013059-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	538	597	0	ENST00000269305.4:c.581T>C	p.Leu194Pro	p.L194P	ENST00000269305	NM_001126112.2	194	cTt/cCt	6/11	0.872835054100827	1	FACETS	0.993	0.967	1	0.993	0.967	1	CLONAL	1	TRUE	0	0.872835054100827	1		597	700	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013074-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	150	297	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.873	0.806	0.94	0.873	0.806	0.94	CLONAL	1	TRUE	1	0.857359776801196	2		297	401	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684326	29684326	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201367	NA	P-0013074-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	275	527	2	ENST00000356175.3:c.7846C>T	p.Arg2616Ter	p.R2616*	ENST00000356175	NM_000267.3	2616	Cga/Tga	53/57	0.844477558927249	1	FACETS	0.942	0.905	0.978	0.942	0.905	0.978	CLONAL	1	TRUE	0	0.857359776801196	1		529	389	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397142	397142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs999945656	NA	P-0013074-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	190	491	1	ENST00000380956.4:c.527G>A	p.Arg176Gln	p.R176Q	ENST00000380956	NM_001195286.1	176	cGa/cAa	5/9	1	2	FACETS	0.97	0.906	1	0.97	0.906	1	CLONAL	1	TRUE	1	0.857359776801196	2		492	457	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888163	112888163	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397507509	NA	P-0013074-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	367	761	1	ENST00000351677.2:c.179G>T	p.Gly60Val	p.G60V	ENST00000351677	NM_002834.3	60	gGt/gTt	3/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.857359776801196	2		762	833	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0013112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	88	361	2	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	0.459	0.408	0.513	0.459	0.408	0.513	SUBCLONAL	1	TRUE	1	0.805095125803297	2		363	476	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	255	444	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	0.805095125803297	2		444	582	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913294	NA	P-0013112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	317	731	0	ENST00000371953.3:c.518G>C	p.Arg173Pro	p.R173P	ENST00000371953	NM_000314.4	173	cGc/cCc	6/9	0.452727871416032	2	FACETS	1	0.983	1	0.537	0.51	0.565	INDETERMINATE	1	TRUE	0	0.805095125803297	2		731	733	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0013112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	136	423	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.412	0.374	0.451	0.412	0.374	0.451	SUBCLONAL	1	TRUE	1	0.805095125803297	2		423	821	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	106	297	5	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	1	2	FACETS	0.575	0.518	0.634	0.575	0.518	0.634	SUBCLONAL	1	TRUE	1	0.805095125803297	2		302	458	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0013112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	210	846	7	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	0.439	0.407	0.473	0.439	0.407	0.473	SUBCLONAL	1	TRUE	1	0.805095125803297	2		853	1188	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066557	94066557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	139	563	0	ENST00000369303.4:c.1202C>T	p.Thr401Ile	p.T401I	ENST00000369303	NM_004440.3	401	aCt/aTt	5/17	1	2	FACETS	0.498	0.454	0.544	0.498	0.454	0.544	SUBCLONAL	1	TRUE	1	0.805095125803297	2		563	693	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088681	27088682	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0013112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	288	1031	0	ENST00000324856.7:c.2296dup	p.Gln766ProfsTer51	p.Q766Pfs*51	ENST00000324856	NM_006015.4	764	tcc/tCcc	7/20	1	2	FACETS	0.511	0.479	0.543	0.511	0.479	0.543	SUBCLONAL	1	TRUE	1	0.805095125803297	2		1031	1401	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023093	27023093	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	26	63	0	ENST00000324856.7:c.199C>T	p.Gln67Ter	p.Q67*	ENST00000324856	NM_006015.4	67	Cag/Tag	1/20	1	2	FACETS	0.778	0.634	0.932	0.778	0.634	0.932	CLONAL	1	TRUE	1	0.805095125803297	2		63	83	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831378	72831378	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	77	266	0	ENST00000268489.5:c.5203del	p.Gln1735AsnfsTer32	p.Q1735Nfs*32	ENST00000268489	NM_006885.3	1735	Caa/aa	9/10	1	2	FACETS	0.621	0.55	0.696	0.621	0.55	0.696	SUBCLONAL	1	TRUE	1	0.805095125803297	2		266	308	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1241	320	1239	13	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.509	0.479	0.54	0.509	0.479	0.54	SUBCLONAL	1	TRUE	1	0.805095125803297	2		1252	1561	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0013112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	203	856	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.476	0.441	0.513	0.476	0.441	0.513	SUBCLONAL	1	TRUE	1	0.805095125803297	2		859	1059	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445500	49445500	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs886042284	NA	P-0013112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	237	1020	2	ENST00000301067.7:c.1966del	p.Leu656CysfsTer274	p.L656Cfs*274	ENST00000301067	NM_003482.3	656	Ctg/tg	10/54	1	2	FACETS	0.541	0.505	0.579	0.541	0.505	0.579	SUBCLONAL	1	TRUE	1	0.805095125803297	2		1022	1088	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615053	43615053	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	195	771	1	ENST00000355710.3:c.2467G>T	p.Gly823Trp	p.G823W	ENST00000355710	NM_020975.4	823	Ggg/Tgg	14/20	1	2	FACETS	0.537	0.497	0.578	0.537	0.497	0.578	SUBCLONAL	1	TRUE	1	0.805095125803297	2		772	902	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917642	94917644	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs757169940	NA	P-0013112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	163	960	0	ENST00000536441.1:c.877_879del	p.Glu293del	p.E293del	ENST00000536441	NM_144665.3	293	GAG/-	6/10	1	2	FACETS	0.425	0.39	0.462	0.425	0.39	0.462	SUBCLONAL	1	TRUE	1	0.805095125803297	2		960	952	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374497	118374498	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	128	492	0	ENST00000534358.1:c.7896dup	p.Gly2633TrpfsTer13	p.G2633Wfs*13	ENST00000534358	NM_005933.3	2630	-/T	27/36	1	2	FACETS	0.497	0.451	0.545	0.497	0.451	0.545	SUBCLONAL	1	TRUE	1	0.805095125803297	2		492	640	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434052	49434052	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	182	717	0	ENST00000301067.7:c.7501G>A	p.Gly2501Arg	p.G2501R	ENST00000301067	NM_003482.3	2501	Ggg/Agg	31/54	1	2	FACETS	0.511	0.472	0.552	0.511	0.472	0.552	SUBCLONAL	1	TRUE	1	0.805095125803297	2		717	884	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441824	49441824	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	186	782	0	ENST00000301067.7:c.4160G>C	p.Gly1387Ala	p.G1387A	ENST00000301067	NM_003482.3	1387	gGc/gCc	14/54	1	2	FACETS	0.395	0.364	0.427	0.395	0.364	0.427	SUBCLONAL	1	TRUE	1	0.805095125803297	2		782	1170	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134013	41134013	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	117	415	0	ENST00000379561.5:c.1615del	p.Leu539CysfsTer5	p.L539Cfs*5	ENST00000379561	NM_002015.3	539	Ctg/tg	2/3	1	2	FACETS	0.511	0.462	0.562	0.511	0.462	0.562	SUBCLONAL	1	TRUE	1	0.805095125803297	2		415	569	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2137932	2137932	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	212	863	1	ENST00000219476.3:c.5058G>T	p.Gln1686His	p.Q1686H	ENST00000219476	NM_000548.3	1686	caG/caT	39/42	1	2	FACETS	0.497	0.461	0.534	0.497	0.461	0.534	SUBCLONAL	1	TRUE	1	0.805095125803297	2		864	1059	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641198	3641198	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1299	312	1346	0	ENST00000294008.3:c.2441A>T	p.Asn814Ile	p.N814I	ENST00000294008	NM_032444.2	814	aAt/aTt	12/15	1	2	FACETS	0.481	0.452	0.511	0.481	0.452	0.511	SUBCLONAL	1	TRUE	1	0.805095125803297	2		1346	1611	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752342	55752342	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs893101427	NA	P-0013112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	203	898	0	ENST00000284073.2:c.800C>T	p.Pro267Leu	p.P267L	ENST00000284073	NM_138962.2	267	cCg/cTg	12/14	1	2	FACETS	0.437	0.404	0.471	0.437	0.404	0.471	SUBCLONAL	1	TRUE	1	0.805095125803297	2		898	1154	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119767	70119767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	252	906	2	ENST00000245479.2:c.769C>T	p.Arg257Cys	p.R257C	ENST00000245479	NM_000346.3	257	Cgc/Tgc	3/3	1	2	FACETS	0.556	0.52	0.593	0.556	0.52	0.593	SUBCLONAL	1	TRUE	1	0.805095125803297	2		908	1126	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212196	36212206	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTCAGTTTA	CCCTCAGTTTA	-	novel	NA	P-0013112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	182	875	0	ENST00000222270.7:c.1950_1960del	p.Gln651LysfsTer21	p.Q651Kfs*21	ENST00000222270	NM_014727.1	649	gcCCCTCAGTTTAcc/gccc	3/37	1	2	FACETS	0.435	0.4	0.47	0.435	0.4	0.47	SUBCLONAL	1	TRUE	1	0.805095125803297	2		875	1040	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547850	41547850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	118	623	0	ENST00000263253.7:c.2831C>T	p.Ala944Val	p.A944V	ENST00000263253	NM_001429.3	944	gCt/gTt	15/31	1	2	FACETS	0.388	0.35	0.428	0.388	0.35	0.428	SUBCLONAL	1	TRUE	1	0.805095125803297	2		623	755	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205004	128205004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	138	551	0	ENST00000341105.2:c.437del	p.Gly146ValfsTer72	p.G146Vfs*72	ENST00000341105	NM_032638.4	146	gGt/gt	3/6	1	2	FACETS	0.473	0.431	0.517	0.473	0.431	0.517	SUBCLONAL	1	TRUE	1	0.805095125803297	2		551	725	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592119	67592120	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0013112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	107	344	0	ENST00000274335.5:c.1937_1938del	p.Phe646SerfsTer7	p.F646Sfs*7	ENST00000274335		645	acTTtt/actt	14/15	1	2	FACETS	0.515	0.464	0.569	0.515	0.464	0.569	SUBCLONAL	1	TRUE	1	0.805095125803297	2		344	516	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92247445	92247445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772153440	NA	P-0013112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	29	438	1	ENST00000265734.4:c.775G>A	p.Ala259Thr	p.A259T	ENST00000265734	NM_001259.6	259	Gcc/Acc	7/8	1	2	FACETS	0.127	0.101	0.156	0.127	0.101	0.156	SUBCLONAL	1	TRUE	1	0.805095125803297	2		439	568	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273543	38273543	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	155	559	1	ENST00000425967.3:c.1792G>T	p.Gly598Cys	p.G598C	ENST00000425967	NM_001174067.1	598	Ggc/Tgc	14/19	0.463218333559384	3	FACETS	0.642	0.588	0.699	0.321	0.294	0.35	INDETERMINATE	1	TRUE	1	0.805095125803297	3		560	841	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370781	55370782	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0013112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	197	327	0	ENST00000297316.4:c.86_87dup	p.Cys30ProfsTer8	p.C30Pfs*8	ENST00000297316	NM_022454.3	28	ggc/ggCCc	1/2	0.463218333559384	3	FACETS	1	0.987	1	0.616	0.575	0.659	INDETERMINATE	1	TRUE	1	0.805095125803297	3		327	557	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650836	93650836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	117	457	1	ENST00000375746.1:c.1762G>A	p.Gly588Arg	p.G588R	ENST00000375746	NM_001174167.1	588	Gga/Aga	13/14	1	2	FACETS	0.524	0.474	0.576	0.524	0.474	0.576	SUBCLONAL	1	TRUE	1	0.805095125803297	2		458	555	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226063	53226063	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782148639	NA	P-0013112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	214	923	0	ENST00000375401.3:c.2786G>A	p.Arg929Gln	p.R929Q	ENST00000375401	NM_004187.3	929	cGa/cAa	19/26	1	2	FACETS	0.509	0.473	0.547	0.509	0.473	0.547	SUBCLONAL	1	TRUE	1	0.805095125803297	2		923	1044	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0013115-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	226	376	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.277579977161028	4	FACETS	0.955	0.89	1	0.955	0.89	1	CLONAL	2	TRUE	2	0.316101586793349	4		376	985	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0013115-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	380	986	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	0.237277188267099	2	FACETS	0.9	0.854	0.947	0.9	0.854	0.947	CLONAL	2	TRUE	0	0.316101586793349	2		986	1335	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0013115-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	323	831	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	0.831	0.784	0.879	1	0.995	1	CLONAL	2	TRUE	1	0.316101586793349	2		831	1230	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151293	202151293	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013115-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	306	860	0	ENST00000358485.4:c.1593A>C	p.Lys531Asn	p.K531N	ENST00000358485	NM_001080125.1	531	aaA/aaC	9/9	0.265471130022686	2	FACETS	0.819	0.772	0.868	0.819	0.772	0.868	CLONAL	2	TRUE	0	0.316101586793349	2		860	1182	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112430	115112431	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0013115-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	261	795	0	ENST00000257566.3:c.1309dup	p.His437ProfsTer2	p.H437Pfs*2	ENST00000257566	NM_016569.3	437	cat/cCat	7/8	1	2	FACETS	0.768	0.72	0.818	1	0.993	1	SUBCLONAL	2	TRUE	1	0.316101586793349	2		795	1075	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456563	29456563	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0013115-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	189	670	0	ENST00000389048.3:c.2356-1G>A		p.X786_splice	ENST00000389048	NM_004304.4	786			0.151788294536043	5	FACETS	0.86	0.794	0.928	0.573	0.529	0.619	INDETERMINATE	2	TRUE	2	0.316101586793349	5		670	1025	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117799	108117799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202160435	NA	P-0013143-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	113	619	0	ENST00000278616.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000278616	NM_000051.3	337	cGt/cAt	8/63	0.294080737396663	3	FACETS	0.938	0.843	1	0.469	0.421	0.52	CLONAL	1	TRUE	1	0.294080737396663	3		619	940	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0013143-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	24	188	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.287	0.224	0.361	0.287	0.224	0.361	SUBCLONAL	1	TRUE	1	0.294080737396663	2		188	568	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242448	55242449	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTCCCGTCGCTATCAAGG	novel	NA	P-0013143-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	200	668	0	ENST00000275493.2:c.2219_2236dup	p.Lys745_Glu746insValProValAlaIleLys	p.K745_E746insVPVAIK	ENST00000275493	NM_005228.3	740	att/aTTCCCGTCGCTATCAAGGtt	19/28	0.294080737396663	4	FACETS	1	0.99	1	0.725	0.67	0.782	CLONAL	1	TRUE	2	0.294080737396663	4		668	1214	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955100	55955100	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013143-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	71	610	0	ENST00000263923.4:c.3445C>T	p.Gln1149Ter	p.Q1149*	ENST00000263923	NM_002253.2	1149	Cag/Tag	26/30	0.294080737396663	2	FACETS	0.597	0.52	0.68	0.298	0.26	0.34	SUBCLONAL	1	TRUE	0	0.294080737396663	2		610	809	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0013162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	159	394	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	0.295100219725113	4	FACETS	1	0.961	1	0.363	0.332	0.396	CLONAL	1	TRUE	1	0.29	4		394	1298	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439907	49439907	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	58	362	0	ENST00000301067.7:c.4634A>G	p.Gln1545Arg	p.Q1545R	ENST00000301067	NM_003482.3	1545	cAg/cGg	17/54	1	2	FACETS	0.522	0.447	0.603	0.522	0.447	0.603	SUBCLONAL	1	TRUE	1	0.29	2		362	767	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991086	41991086	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	92	341	0	ENST00000219905.7:c.2039A>C	p.Asp680Ala	p.D680A	ENST00000219905	NM_001164273.1	680	gAt/gCt	4/24	0.202980861428385	2	FACETS	0.673	0.597	0.755	0.336	0.298	0.378	SUBCLONAL	1	TRUE	0	0.29	2		341	943	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224590	36224590	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	T	novel	NA	P-0013162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	89	420	2	ENST00000222270.7:c.7049+3G>T		p.X2350_splice	ENST00000222270	NM_014727.1	2350			0.295100219725113	2	FACETS	0.857	0.76	0.961	0.429	0.38	0.481	CLONAL	1	TRUE	0	0.29	2		422	716	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431563	6431563	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1554263624	NA	P-0013162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	37	83	0	ENST00000356142.4:c.116A>G	p.Asn39Ser	p.N39S	ENST00000356142	NM_018890.3	39	aAt/aGt	3/7	0.295100219725113	4	FACETS	1	0.945	1	0.463	0.384	0.55	CLONAL	1	TRUE	1	0.29	4		83	237	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0013182-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	167	1210	2	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.289504553248924	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.31	1		1212	798	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381485	81381485	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1213509732	NA	P-0013182-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	46	553	2	ENST00000222390.5:c.576C>A	p.Ser192Arg	p.S192R	ENST00000222390	NM_000601.4	192	agC/agA	5/18	1	2	FACETS	0.59	0.497	0.693	0.59	0.497	0.693	SUBCLONAL	1	TRUE	1	0.31	2		555	503	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289710	15289710	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013182-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	295	1159	0	ENST00000263388.2:c.3761C>A	p.Pro1254Gln	p.P1254Q	ENST00000263388	NM_000435.2	1254	cCa/cAa	23/33	0.233359261759444	4	FACETS	1	0.985	1	0.756	0.711	0.801	CLONAL	2	TRUE	1	0.31	4		1159	1100	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314932	1314932	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013182-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	161	891	0	ENST00000400841.2:c.729G>T	p.Met243Ile	p.M243I	ENST00000400841		243	atG/atT	6/6	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.31	2		891	797	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469614	25469614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775677376	NA	P-0013182-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	48	1020	3	ENST00000264709.3:c.1154C>T	p.Pro385Leu	p.P385L	ENST00000264709	NM_175629.2	385	cCg/cTg	10/23	1	2	FACETS	0.428	0.361	0.502	0.428	0.361	0.502	SUBCLONAL	1	TRUE	1	0.31	2		1023	724	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260397	16260399	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0013185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	139	377	0	ENST00000375759.3:c.7665_7667del	p.Thr2556del	p.T2556del	ENST00000375759	NM_015001.2	2554	gtCACc/gtc	11/15	0.247344636232156	3	FACETS	0.95	0.867	1	0.95	0.867	1	CLONAL	2	FALSE	1	0.247344636232156	3		377	665	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298149	123298149	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	100	549	0	ENST00000358487.5:c.705T>A	p.Asn235Lys	p.N235K	ENST00000358487	NM_000141.4	235	aaT/aaA	6/18	0.229822076617702	3	FACETS	1	0.971	1	0.417	0.372	0.464	CLONAL	1	FALSE	0	0.247344636232156	3		549	727	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250909	153251075	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATCACATGATCATCATGTCCTTTCAGCACCTATAAGAAAGATGTGCAGATTAGAAATATGTTAATTAAATTATGTTCTTTAAAATACTGGTGAAGAGAAAAATGAAGGCATAAACAGGAACAGTAATTTGTAGTCTATCTCTAGAATTTAAATTTATATAAAGCATT	ATCACATGATCATCATGTCCTTTCAGCACCTATAAGAAAGATGTGCAGATTAGAAATATGTTAATTAAATTATGTTCTTTAAAATACTGGTGAAGAGAAAAATGAAGGCATAAACAGGAACAGTAATTTGTAGTCTATCTCTAGAATTTAAATTTATATAAAGCATT	-	novel	NA	P-0013185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	69	363	0	ENST00000281708.4:c.1123-138_1151del		p.X375_splice	ENST00000281708	NM_033632.3	375		8/12	0.247344636232156	5	FACETS	1	0.965	1			1	CLONAL	1	FALSE	NA	0.247344636232156	5		363	576	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721066	176721066	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1294159848	NA	P-0013185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	106	299	0	ENST00000439151.2:c.6697A>G	p.Ser2233Gly	p.S2233G	ENST00000439151	NM_022455.4	2233	Agc/Ggc	23/23	0.137933103129361	4	FACETS	0.85	0.763	0.941	0.85	0.763	0.941	INDETERMINATE	2	FALSE	2	0.247344636232156	4		299	629	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545569	106545569	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs765208119	NA	P-0013185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	64	313	0	ENST00000359195.3:c.3046G>C	p.Ala1016Pro	p.A1016P	ENST00000359195	NM_002649.2	1016	Gct/Cct	11/11	0.247344636232156	6	FACETS	1	0.916	1	0.27	0.233	0.31	CLONAL	1	FALSE	2	0.247344636232156	6		313	716	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802667	139802667	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	88	282	0	ENST00000247668.2:c.512del	p.Cys171SerfsTer5	p.C171Sfs*5	ENST00000247668	NM_021138.3	171	tGc/tc	5/11	0.247344636232156	5	FACETS	0.874	0.776	0.978	0.583	0.517	0.652	CLONAL	2	FALSE	2	0.247344636232156	5		282	558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579310	7579310	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1555526469	NA	P-0013185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	225	391	0	ENST00000269305.4:c.375+2T>C		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.247344636232156	5	FACETS	1	0.977	1	0.822	0.768	0.877	CLONAL	3	FALSE	1	0.247344636232156	5		391	759	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013196-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	41	297	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		297	729	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013219-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	204	472	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.657241146531542	2	FACETS	0.884	0.823	0.947	0.442	0.411	0.474	CLONAL	1	TRUE	0	0.657241146531542	2		472	702	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0013219-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	786	812	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.657241146531542	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	0	0.657241146531542	3		813	1046	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110035	115110035	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs763473739	NA	P-0013219-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	321	860	0	ENST00000257566.3:c.1843T>G	p.Ser615Ala	p.S615A	ENST00000257566	NM_016569.3	615	Tcc/Gcc	8/8	0.657241146531542	3	FACETS	0.899	0.847	0.952	0.449	0.423	0.476	CLONAL	1	TRUE	1	0.657241146531542	3		860	1444	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609721	28609721	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013219-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	588	694	0	ENST00000241453.7:c.1508T>G	p.Met503Arg	p.M503R	ENST00000241453	NM_004119.2	503	aTg/aGg	12/24	0.657241146531542	2	FACETS	0.961	0.932	0.99	0.961	0.932	0.99	CLONAL	2	TRUE	0	0.657241146531542	2		694	931	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624289	89624290	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GACTT	novel	NA	P-0013219-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	357	515	0	ENST00000371953.3:c.64_68dup	p.Asp24ThrfsTer2	p.D24Tfs*2	ENST00000371953	NM_000314.4	21	-/GACTT	1/9	0.657241146531542	2	FACETS	0.831	0.795	0.866	0.831	0.795	0.866	CLONAL	2	TRUE	0	0.657241146531542	2		515	654	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944012	71944012	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs777831045	NA	P-0013219-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	563	683	0	ENST00000298229.2:c.1945C>T	p.Arg649Ter	p.R649*	ENST00000298229	NM_001567.3	649	Cga/Tga	16/28	0.657241146531542	2	FACETS	0.978	0.948	1	0.978	0.948	1	CLONAL	2	TRUE	0	0.657241146531542	2		683	876	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859492	151859492	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013219-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	168	464	0	ENST00000262189.6:c.11170G>T	p.Glu3724Ter	p.E3724*	ENST00000262189	NM_170606.2	3724	Gag/Tag	43/59	0.657241146531542	3	FACETS	0.839	0.772	0.908	0.419	0.386	0.454	CLONAL	1	TRUE	1	0.657241146531542	3		464	810	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864630	56864630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210415750	NA	P-0013219-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1558	291	739	2	ENST00000519728.1:c.593G>A	p.Arg198Gln	p.R198Q	ENST00000519728	NM_002350.3	198	cGa/cAa	7/13	0.525820998062989	6	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.657241146531542	6		741	1849	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0013223-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	166	942	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	0.959	0.88	1	0.959	0.88	1	CLONAL	1	TRUE	1	0.33114933672687	2		942	1045	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041395	42041396	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013223-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	138	786	0	ENST00000219905.7:c.5591dup	p.Met1864IlefsTer29	p.M1864Ifs*29	ENST00000219905	NM_001164273.1	1864	atg/aTtg	17/24	1	2	FACETS	0.965	0.878	1	0.965	0.878	1	CLONAL	1	TRUE	1	0.33114933672687	2		786	864	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0013243-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	174	260	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.868	0.807	0.93	0.868	0.807	0.93	CLONAL	1	TRUE	1	0.873398834697129	2		260	459	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0013243-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	273	435	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.873398834697129	2		435	569	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968322	2968323	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs762770988	NA	P-0013243-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	81	702	4	ENST00000396946.4:c.1663dup	p.Arg555ProfsTer38	p.R555Pfs*38	ENST00000396946	NM_032415.4	555	cgg/cCgg	13/25	1	2	FACETS	0.241	0.212	0.273	0.241	0.212	0.273	SUBCLONAL	1	TRUE	1	0.873398834697129	2		706	769	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577526	7577526	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121912653	NA	P-0013243-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	84	698	0	ENST00000269305.4:c.755T>C	p.Leu252Pro	p.L252P	ENST00000269305	NM_001126112.2	252	cTc/cCc	7/11	1	2	FACETS	0.247	0.218	0.278	0.247	0.218	0.278	SUBCLONAL	1	TRUE	1	0.873398834697129	2		698	779	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30103715	30103715	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013243-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	326	593	0	ENST00000331968.5:c.1223G>T	p.Arg408Met	p.R408M	ENST00000331968	NM_002742.2	408	aGg/aTg	8/18	1	2	FACETS	0.943	0.895	0.99	0.943	0.895	0.99	CLONAL	1	TRUE	1	0.873398834697129	2		593	792	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260178	149260178	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013243-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	77	628	0	ENST00000360632.3:c.715A>G	p.Arg239Gly	p.R239G	ENST00000360632	NM_015472.4	239	Aga/Gga	4/7	1	2	FACETS	0.273	0.239	0.309	0.273	0.239	0.309	SUBCLONAL	1	TRUE	1	0.873398834697129	2		628	646	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401837	139401837	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013243-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1269	79	938	1	ENST00000277541.6:c.3563T>C	p.Leu1188Pro	p.L1188P	ENST00000277541	NM_017617.3	1188	cTc/cCc	22/34	0.873398834697129	3	FACETS	0.193	0.169	0.219	0.096	0.084	0.11	SUBCLONAL	1	TRUE	1	0.873398834697129	3		939	1348	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412619	139412619	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013243-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	635	691	0	ENST00000277541.6:c.1225T>A	p.Cys409Ser	p.C409S	ENST00000277541	NM_017617.3	409	Tgc/Agc	7/34	0.873398834697129	3	FACETS	0.93	0.901	0.959	0.93	0.901	0.959	CLONAL	2	TRUE	1	0.873398834697129	3		691	1123	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0013265-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	259	462	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.278596437006129	3	FACETS	0.876	0.823	0.93			1	CLONAL	3	TRUE	NA	0.278596437006129	3		462	806	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599252	55599252	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013265-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	102	525	0	ENST00000288135.5:c.2378T>C	p.Leu793Ser	p.L793S	ENST00000288135	NM_000222.2	793	tTg/tCg	17/21	0.278596437006129	2	FACETS	1	0.97	1	0.613	0.55	0.681	CLONAL	1	TRUE	0	0.278596437006129	2		525	597	SUCCESS
ATR	545	MSKCC	GRCh37	3	142297507	142297507	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013265-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1181	83	580	0	ENST00000350721.4:c.40G>T	p.Ala14Ser	p.A14S	ENST00000350721	NM_001184.3	14	Gcc/Tcc	1/47	0.278596437006129	8	FACETS	0.865	0.761	0.978			1	CLONAL	1	TRUE	NA	0.278596437006129	8		580	1264	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968641	55968641	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs139644107	NA	P-0013265-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	112	687	0	ENST00000263923.4:c.2022G>C	p.Glu674Asp	p.E674D	ENST00000263923	NM_002253.2	674	gaG/gaC	14/30	0.278596437006129	2	FACETS	0.906	0.815	1	0.453	0.407	0.502	CLONAL	1	TRUE	0	0.278596437006129	2		687	887	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986592	36986592	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013265-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	84	476	0	ENST00000354822.5:c.1097G>A	p.Ser366Asn	p.S366N	ENST00000354822	NM_001079668.2	366	aGc/aAc	3/3	0.211988628263853	3	FACETS	0.936	0.826	1	0.468	0.413	0.527	CLONAL	1	TRUE	1	0.278596437006129	3		476	734	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16021210	16021210	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0013265-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	50	377	0	ENST00000268712.3:c.2047A>T	p.Lys683Ter	p.K683*	ENST00000268712	NM_006311.3	683	Aaa/Taa	18/46	0.236870119620277	2	FACETS	0.863	0.734	1	0.431	0.367	0.502	CLONAL	1	TRUE	0	0.278596437006129	2		377	416	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851802	134851802	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013265-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	94	815	0	ENST00000398015.3:c.1209del	p.Phe404LeufsTer44	p.F404Lfs*44	ENST00000398015	NM_004441.4	403	aCc/ac	5/16	0.244645791044605	4	FACETS	0.697	0.618	0.782			1	SUBCLONAL	1	TRUE	NA	0.278596437006129	4		815	1238	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413744	138413749	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CTGAAG	CTGAAG	-	novel	NA	P-0013265-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	60	505	0	ENST00000289153.2:c.1771_1776del	p.Leu591_Gln592del	p.L591_Q592del	ENST00000289153	NM_006219.2	591	CTTCAG/-	12/22	0.278596437006129	8	FACETS	0.795	0.682	0.918			1	CLONAL	1	TRUE	NA	0.278596437006129	8		505	995	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724531	112724531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013265-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	78	667	1	ENST00000369452.4:c.415C>T	p.Pro139Ser	p.P139S	ENST00000369452	NM_007373.3	139	Cca/Tca	2/9	0.236870119620277	2	FACETS	0.785	0.69	0.888	0.393	0.345	0.444	SUBCLONAL	1	TRUE	0	0.278596437006129	2		668	713	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64286877	64286877	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs779426223	NA	P-0013265-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	58	592	0	ENST00000370651.3:c.92A>G	p.Asn31Ser	p.N31S	ENST00000370651	NM_003463.4	31	aAc/aGc	2/6	0.278596437006129	3	FACETS	0.581	0.498	0.672			1	SUBCLONAL	1	TRUE	NA	0.278596437006129	3		592	816	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848029	151848029	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013265-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	63	534	0	ENST00000262189.6:c.12730A>C	p.Ile4244Leu	p.I4244L	ENST00000262189	NM_170606.2	4244	Att/Ctt	51/59	0.264996974244785	3	FACETS	0.708	0.611	0.813	0.354	0.305	0.407	SUBCLONAL	1	TRUE	1	0.278596437006129	3		534	728	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490261	29490290	+	inframe_deletion	In_Frame_Del	DEL	GAAATCTGCCATTTTCTTCACACCTGTCGT	GAAATCTGCCATTTTCTTCACACCTGTCGT	-	novel	NA	P-0013280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	49	667	0	ENST00000356175.3:c.349_378del	p.Ile117_Glu126del	p.I117_E126del	ENST00000356175	NM_000267.3	116	GAAATCTGCCATTTTCTTCACACCTGTCGT/-	4/57	0.227692563393645	2	FACETS	0.866	0.738	1	0.433	0.369	0.502	INDETERMINATE	1	FALSE	0	0.386408261130891	2		667	293	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578499	7578510	+	inframe_deletion	In_Frame_Del	DEL	TGCACAGGGCAG	TGCACAGGGCAG	-	novel	NA	P-0013280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	158	1124	0	ENST00000269305.4:c.420_431del	p.Cys141_Gln144del	p.C141_Q144del	ENST00000269305	NM_001126112.2	140	acCTGCCCTGTGCAg/acg	5/11	0.227692563393645	2	FACETS	1	0.985	1	0.651	0.599	0.705	INDETERMINATE	1	FALSE	0	0.386408261130891	2		1124	628	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973212	25973227	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTTTTCTTTACTTT	GGGTTTTCTTTACTTT	-	novel	NA	P-0013280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	35	451	0	ENST00000435504.4:c.1198_1213del	p.Lys400GlnfsTer18	p.K400Qfs*18	ENST00000435504		400	AAAGTAAAGAAAACCCca/ca	12/13	0.207169127569074	4	FACETS	0.86	0.708	1	0.287	0.236	0.344	INDETERMINATE	1	FALSE	1	0.386408261130891	4		451	292	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965476	68965476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751712561	NA	P-0013280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	57	838	1	ENST00000288368.4:c.1088G>A	p.Arg363Gln	p.R363Q	ENST00000288368	NM_024870.2	363	cGg/cAg	9/40	0.157642894956188	2	FACETS	0.73	0.629	0.841	0.365	0.314	0.421	INDETERMINATE	1	FALSE	0	0.386408261130891	2		839	404	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0013290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1261	523	943	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.671396557938781	6	FACETS	1	0.973	1	0.511	0.489	0.534	CLONAL	2	FALSE	2	0.671396557938781	6		943	1784	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578281	7578281	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660254	NA	P-0013290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	732	449	0	ENST00000269305.4:c.568C>A	p.Pro190Thr	p.P190T	ENST00000269305	NM_001126112.2	190	Cct/Act	6/11	0.671396557938781	3	FACETS	0.956	0.933	0.978	0.956	0.933	0.978	CLONAL	3	FALSE	0	0.671396557938781	3		449	1016	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419986	41419986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372989163	NA	P-0013290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	586	353	2	ENST00000373198.4:c.335G>A	p.Arg112His	p.R112H	ENST00000373198	NM_133170.3	112	cGt/cAt	3/32	0.659107070704359	5	FACETS	0.932	0.899	0.966	0.932	0.899	0.966	CLONAL	3	FALSE	2	0.671396557938781	5		355	1253	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16203094	16203094	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	188	372	0	ENST00000375759.3:c.802T>G	p.Ser268Ala	p.S268A	ENST00000375759	NM_015001.2	268	Tcc/Gcc	3/15	0.671396557938781	3	FACETS	0.792	0.731	0.854	0.396	0.365	0.427	SUBCLONAL	1	FALSE	1	0.671396557938781	3		372	945	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337663	73337663	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	156	307	0	ENST00000377767.4:c.2053C>G	p.His685Asp	p.H685D	ENST00000377767	NM_014953.3	685	Cat/Gat	16/21	0.659107070704359	5	FACETS	0.887	0.811	0.966	0.296	0.27	0.322	CLONAL	1	FALSE	2	0.671396557938781	5		307	1052	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448387	56448387	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	660	482	0	ENST00000407977.2:c.260del	p.Pro87ArgfsTer71	p.P87Rfs*71	ENST00000407977		87	cCg/cg	3/10	0.671396557938781	3	FACETS	0.904	0.88	0.928	0.904	0.88	0.928	CLONAL	3	FALSE	0	0.671396557938781	3		482	968	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250399	10250399	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755492225	NA	P-0013290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1479	364	352	0	ENST00000340748.4:c.3853C>T	p.Arg1285Cys	p.R1285C	ENST00000340748		1285	Cgc/Tgc	33/40	0.671396557938781	9	FACETS	0.985	0.931	1	0.328	0.31	0.347	CLONAL	2	FALSE	3	0.671396557938781	9		352	1843	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728699	39728699	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	90	302	0	ENST00000361337.2:c.979A>C	p.Ile327Leu	p.I327L	ENST00000361337	NM_003286.2	327	Atc/Ctc	12/21	0.659107070704359	5	FACETS	0.568	0.502	0.637	0.189	0.167	0.213	SUBCLONAL	1	FALSE	2	0.671396557938781	5		302	948	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93973626	93973626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	215	370	0	ENST00000369303.4:c.1750G>A	p.Gly584Ser	p.G584S	ENST00000369303	NM_004440.3	584	Ggt/Agt	9/17	0.576988609068344	4	FACETS	0.974	0.905	1	0.487	0.452	0.523	CLONAL	1	FALSE	2	0.671396557938781	4		370	1099	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140487343	140487345	+	splice_region_variant,intron_variant	Splice_Region	DEL	CTT	CTT	-	novel	NA	P-0013290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	1188	654	0	ENST00000288602.6:c.1177+3_1177+5del		p.X393_splice	ENST00000288602	NM_004333.4	393			0.671396557938781	6	FACETS	0.895	0.873	0.917	0.895	0.873	0.917	CLONAL	4	FALSE	2	0.671396557938781	6		654	2316	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259949	16259949	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013301-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	161	605	0	ENST00000375759.3:c.7214T>G	p.Ile2405Ser	p.I2405S	ENST00000375759	NM_015001.2	2405	aTt/aGt	11/15	NA	2	FACETS	0.626	0.576	0.678			1	INDETERMINATE	1	TRUE	NA	0.757540919574025	2		605	679	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220439	1220439	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0013301-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	588	717	0	ENST00000326873.7:c.532A>T	p.Lys178Ter	p.K178*	ENST00000326873	NM_000455.4	178	Aag/Tag	4/10	0.757540919574025	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.757540919574025	1		717	851	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610574	10610610	+	frameshift_variant	Frame_Shift_Del	DEL	GGGAGGGCGTCACCTCCGCCTTGCACTCAGTGGAGGC	GGGAGGGCGTCACCTCCGCCTTGCACTCAGTGGAGGC	-	novel	NA	P-0013301-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	297	555	0	ENST00000171111.5:c.100_136del	p.Ala34SerfsTer22	p.A34Sfs*22	ENST00000171111	NM_203500.1	34	GCCTCCACTGAGTGCAAGGCGGAGGTGACGCCCTCCCag/ag	2/6	0.757540919574025	1	FACETS	0.923	0.88	0.965	0.923	0.88	0.965	CLONAL	1	TRUE	0	0.757540919574025	1		555	528	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751220	57751220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013301-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	21	251	0	ENST00000274289.3:c.1647G>T	p.Glu549Asp	p.E549D	ENST00000274289	NM_006622.3	549	gaG/gaT	12/14	1	2	FACETS	0.153	0.117	0.194	0.153	0.117	0.194	SUBCLONAL	1	TRUE	1	0.757540919574025	2		251	363	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339127	116339127	+	splice_region_variant,5_prime_UTR_variant	Splice_Region	SNP	A	A	T	novel	NA	P-0013301-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	22	136	0	ENST00000397752.3:c.-12A>T		p.X4_splice	ENST00000397752	NM_000245.2	4		2/21	1	2	FACETS	0.22	0.17	0.277	0.22	0.17	0.277	SUBCLONAL	1	TRUE	1	0.757540919574025	2		136	264	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0013341-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	83	376	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.31449020206187	3	FACETS	1	0.929	1	0.536	0.473	0.602	CLONAL	1	TRUE	1	0.31449020206187	3		376	570	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013341-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	133	297	0				ENST00000310581	NM_198253.2	-/1132			0.31449020206187	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	TRUE	0	0.31449020206187	3		297	287	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0013341-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	300	943	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.31449020206187	5	FACETS	0.98	0.925	1	0.98	0.925	1	CLONAL	3	TRUE	2	0.31449020206187	5		943	955	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873660	35873660	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs201559094	NA	P-0013341-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	41	513	0	ENST00000303115.3:c.616C>T	p.Arg206Ter	p.R206*	ENST00000303115	NM_002185.3	206	Cga/Tga	5/8	0.303310221678147	4	FACETS	0.556	0.462	0.661			1	SUBCLONAL	1	TRUE	NA	0.31449020206187	4		513	616	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524329	148524329	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013341-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	231	608	1	ENST00000320356.2:c.655C>T	p.Pro219Ser	p.P219S	ENST00000320356	NM_004456.4	219	Cct/Tct	7/20	0.31449020206187	5	FACETS	0.958	0.897	1	0.958	0.897	1	CLONAL	3	TRUE	2	0.31449020206187	5		609	752	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733635	85733635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1320962678	NA	P-0013341-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	93	578	2	ENST00000370580.1:c.377C>T	p.Pro126Leu	p.P126L	ENST00000370580	NM_003921.4	126	cCa/cTa	3/3	0.3131900017416	2	FACETS	1	0.949	1	0.555	0.495	0.619	CLONAL	1	TRUE	0	0.31449020206187	2		580	533	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849897	156849897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013341-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	251	865	2	ENST00000524377.1:c.2153G>A	p.Trp718Ter	p.W718*	ENST00000524377	NM_002529.3	718	tGg/tAg	16/17	0.306935674069172	4	FACETS	0.952	0.89	1	0.952	0.89	1	CLONAL	2	TRUE	2	0.31449020206187	4		867	1102	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267156	41267156	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013341-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	67	400	1	ENST00000349496.5:c.740C>T	p.Pro247Leu	p.P247L	ENST00000349496	NM_001904.3	247	cCa/cTa	6/15	0.31449020206187	3	FACETS	0.965	0.84	1	0.482	0.42	0.55	CLONAL	1	TRUE	1	0.31449020206187	3		401	511	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89478294	89478294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013341-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	179	557	0	ENST00000336596.2:c.2113G>A	p.Gly705Ser	p.G705S	ENST00000336596	NM_005233.5	705	Ggt/Agt	12/17	0.31449020206187	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.31449020206187	3		557	630	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961023	55961023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868853292	NA	P-0013341-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	127	720	1	ENST00000263923.4:c.2917G>A	p.Ala973Thr	p.A973T	ENST00000263923	NM_002253.2	973	Gcc/Acc	21/30	0.31449020206187	3	FACETS	1	0.926	1	0.514	0.465	0.565	CLONAL	1	TRUE	1	0.31449020206187	3		721	910	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722272	176722272	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013341-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	88	566	1	ENST00000439151.2:c.7903G>A	p.Gly2635Arg	p.G2635R	ENST00000439151	NM_022455.4	2635	Ggg/Agg	23/23	1	2	FACETS	0.883	0.783	0.989	0.883	0.783	0.989	CLONAL	1	TRUE	1	0.31449020206187	2		567	634	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052998	180052998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867280522	NA	P-0013341-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	141	1057	1	ENST00000261937.6:c.1292C>T	p.Ser431Phe	p.S431F	ENST00000261937	NM_182925.4	431	tCc/tTc	10/30	1	2	FACETS	0.96	0.874	1	0.96	0.874	1	CLONAL	1	TRUE	1	0.31449020206187	2		1058	934	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977657	2977657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013341-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	261	828	0	ENST00000396946.4:c.1027G>A	p.Glu343Lys	p.E343K	ENST00000396946	NM_032415.4	343	Gag/Aag	8/25	0.31449020206187	5	FACETS	1	0.976	1	0.722	0.676	0.769	CLONAL	2	TRUE	2	0.31449020206187	5		828	1128	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530108	63530108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013341-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	119	796	2	ENST00000307078.5:c.2327C>T	p.Pro776Leu	p.P776L	ENST00000307078	NM_004655.3	776	cCa/cTa	10/11	0.31449020206187	3	FACETS	0.97	0.875	1	0.485	0.437	0.536	CLONAL	1	TRUE	1	0.31449020206187	3		798	903	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106952	11106952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013341-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	126	1015	1	ENST00000358026.2:c.1657C>T	p.Leu553Phe	p.L553F	ENST00000358026	NM_001128849.1	553	Ctc/Ttc	10/36	0.306935674069172	4	FACETS	0.853	0.77	0.941	0.426	0.385	0.471	CLONAL	1	TRUE	2	0.31449020206187	4		1016	1235	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246443	53246443	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013341-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	128	348	0	ENST00000375401.3:c.539C>T	p.Pro180Leu	p.P180L	ENST00000375401	NM_004187.3	180	cCa/cTa	5/26	0.28920303362581	2	FACETS	0.864	0.788	0.943			1	CLONAL	2	TRUE	NA	0.31449020206187	2		348	471	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981779	201981779	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013341-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	97	822	0	ENST00000359651.3:c.490C>T	p.Pro164Ser	p.P164S	ENST00000359651		164	Ccc/Tcc	4/8	0.269953828691468	5	FACETS	0.822	0.731	0.92	0.274	0.243	0.307	CLONAL	1	TRUE	2	0.31449020206187	5		822	1104	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948724	71948724	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757498981	NA	P-0013341-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	115	741	1	ENST00000298229.2:c.3436C>T	p.Leu1146Phe	p.L1146F	ENST00000298229	NM_001567.3	1146	Ctc/Ttc	26/28	0.31449020206187	3	FACETS	0.981	0.883	1	0.49	0.441	0.542	CLONAL	1	TRUE	1	0.31449020206187	3		742	863	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133242010	133242011	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0013341-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	203	771	5	ENST00000320574.5:c.2345_2346delinsAT	p.Ala782Asp	p.A782D	ENST00000320574	NM_006231.2	782	gCC/gAT	21/49	0.31449020206187	3	FACETS	0.872	0.809	0.936	0.872	0.809	0.936	CLONAL	2	TRUE	1	0.31449020206187	3		776	857	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194643	29194643	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013341-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	129	931	0	ENST00000240100.2:c.1085C>T	p.Ser362Leu	p.S362L	ENST00000240100	NM_001394.6	362	tCg/tTg	4/4	0.306935674069172	4	FACETS	0.968	0.876	1	0.484	0.438	0.533	CLONAL	1	TRUE	2	0.31449020206187	4		931	1114	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56879412	56879412	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013341-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	56	773	0	ENST00000519728.1:c.929C>T	p.Thr310Ile	p.T310I	ENST00000519728	NM_002350.3	310	aCc/aTc	9/13	0.306935674069172	4	FACETS	0.423	0.361	0.492	0.212	0.18	0.246	SUBCLONAL	1	TRUE	2	0.31449020206187	4		773	1106	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013544-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	243	297	0				ENST00000310581	NM_198253.2	-/1132			0.387018349706238	3	FACETS	0.855	0.807	0.903	0.855	0.807	0.903	INDETERMINATE	2	TRUE	1	0.744263758921685	3		297	524	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602719	55602719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752695117	NA	P-0013544-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	2779	415	0	ENST00000288135.5:c.2540C>T	p.Thr847Met	p.T847M	ENST00000288135	NM_000222.2	847	aCg/aTg	18/21	0.744263758921685	13	FACETS	0.978	0.969	0.987			1	CLONAL	12	TRUE	NA	0.744263758921685	13		415	3241	SUCCESS
REL	5966	MSKCC	GRCh37	2	61144084	61144084	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013544-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	66	523	0	ENST00000295025.8:c.467T>C	p.Leu156Pro	p.L156P	ENST00000295025	NM_002908.2	156	cTc/cCc	5/11	0.279463775793587	3	FACETS	0.223	0.192	0.256	0.074	0.064	0.086	INDETERMINATE	1	TRUE	0	0.744263758921685	3		523	1092	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755449	39755449	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013544-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	352	325	0	ENST00000288319.7:c.1316C>T	p.Pro439Leu	p.P439L	ENST00000288319	NM_182918.3	439	cCc/cTc	10/10	0.72472585668312	2	FACETS	0.957	0.924	0.99	0.957	0.924	0.99	CLONAL	2	TRUE	0	0.744263758921685	2		325	494	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522240	157522240	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013544-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1261	212	461	0	ENST00000346085.5:c.4512G>C	p.Gln1504His	p.Q1504H	ENST00000346085	NM_020732.3	1504	caG/caC	18/20	0.408067419311774	6	FACETS	0.962	0.891	1			1	INDETERMINATE	1	TRUE	NA	0.744263758921685	6		461	1473	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013603-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	94	297	0				ENST00000310581	NM_198253.2	-/1132			0.280847090056483	1	FACETS	0.753	0.675	0.834	0.753	0.675	0.834	INDETERMINATE	1	TRUE	0	0.506578760797031	1		297	368	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888199	112888199	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121918454	NA	P-0013603-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	50	648	0	ENST00000351677.2:c.215C>G	p.Ala72Gly	p.A72G	ENST00000351677	NM_002834.3	72	gCc/gGc	3/16	1	2	FACETS	0.327	0.277	0.382	0.327	0.277	0.382	SUBCLONAL	1	TRUE	1	0.506578760797031	2		648	604	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653842	89653842	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057518425	NA	P-0013603-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	175	552	0	ENST00000371953.3:c.140G>A	p.Arg47Lys	p.R47K	ENST00000371953	NM_000314.4	47	aGg/aAg	2/9	0.506578760797031	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.506578760797031	1		552	482	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557277	29557277	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs1060500273	NA	P-0013603-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	209	419	0	ENST00000356175.3:c.2991-1G>C		p.X997_splice	ENST00000356175	NM_000267.3	997			0.506578760797031	2	FACETS	0.953	0.897	1	0.953	0.897	1	CLONAL	2	TRUE	0	0.506578760797031	2		419	433	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321380	65321403	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGCTATTCGGGAAATGACCAGAAA	TGCTATTCGGGAAATGACCAGAAA	-	novel	NA	P-0013603-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	34	559	0	ENST00000342505.4:c.1459-22_1460del		p.X487_splice	ENST00000342505	NM_002227.2	487		11/25	1	2	FACETS	0.265	0.216	0.321	0.265	0.216	0.321	SUBCLONAL	1	TRUE	1	0.506578760797031	2		559	506	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219883	133219883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013603-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	145	764	0	ENST00000320574.5:c.4478C>T	p.Ala1493Val	p.A1493V	ENST00000320574	NM_006231.2	1493	gCa/gTa	35/49	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.506578760797031	2		764	572	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037187	71037187	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013603-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	162	547	0	ENST00000318789.4:c.1104C>A	p.His368Gln	p.H368Q	ENST00000318789	NM_032682.5	368	caC/caA	14/21	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.506578760797031	2		547	609	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99809068	99809068	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013603-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	77	754	0	ENST00000280892.6:c.317T>G	p.Met106Arg	p.M106R	ENST00000280892	NM_001130678.1	106	aTg/aGg	4/7	1	2	FACETS	0.388	0.34	0.44	0.388	0.34	0.44	SUBCLONAL	1	TRUE	1	0.506578760797031	2		754	783	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831465	72831465	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013865-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	529	833	1	ENST00000268489.5:c.5116del	p.Glu1706SerfsTer13	p.E1706Sfs*13	ENST00000268489	NM_006885.3	1706	Gag/ag	9/10	0.83881098734891	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.842761187796831	1		834	712	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143161	24143161	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013884-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	39	762	0	ENST00000263121.7:c.393G>C	p.Trp131Cys	p.W131C	ENST00000263121	NM_003073.3	131	tgG/tgC	4/9	0.513596152953169	5	FACETS	0.922	0.824	1	1	0.973	1	CLONAL	5	FALSE	2	0.571042668207477	5		762	55	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0013956-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	159	435	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.967	0.89	1	0.967	0.89	1	CLONAL	1	TRUE	1	0.522835897841834	2		435	629	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0013956-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	174	544	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.522835897841834	3	FACETS	0.899	0.828	0.973	0.449	0.414	0.487	CLONAL	1	TRUE	1	0.522835897841834	3		544	934	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947540	48947540	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0013956-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	194	591	0	ENST00000267163.4:c.1128-1G>C		p.X376_splice	ENST00000267163	NM_000321.2	376			0.522835897841834	1	FACETS	0.901	0.839	0.966	0.901	0.839	0.966	CLONAL	1	TRUE	0	0.522835897841834	1		591	608	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362164	40362195	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GACATAAGAAGGGAGGGGCACTCACGAGAATC	GACATAAGAAGGGAGGGGCACTCACGAGAATC	-	novel	NA	P-0013956-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	102	310	0	ENST00000293328.3:c.1900_1906+25del		p.X634_splice	ENST00000293328	NM_012448.3	634		15/19	1	2	FACETS	0.787	0.707	0.871	0.787	0.707	0.871	SUBCLONAL	1	TRUE	1	0.522835897841834	2		310	496	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905494	50905494	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013956-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	563	705	0	ENST00000440232.2:c.622C>T	p.Pro208Ser	p.P208S	ENST00000440232	NM_002691.3	208	Ccg/Tcg	6/27	0.504764239211905	2	FACETS	0.975	0.941	1	0.975	0.941	1	CLONAL	2	TRUE	0	0.522835897841834	2		705	1104	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014325	70014325	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013956-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	261	608	0	ENST00000394351.3:c.1186G>C	p.Val396Leu	p.V396L	ENST00000394351	NM_000248.3	396	Gtg/Ctg	9/9	1	2	FACETS	0.973	0.912	1	0.973	0.912	1	CLONAL	1	TRUE	1	0.522835897841834	2		608	1026	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37865621	37865621	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013956-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	252	716	0	ENST00000269571.5:c.490C>G	p.Gln164Glu	p.Q164E	ENST00000269571		164	Cag/Gag	4/27	1	2	FACETS	0.856	0.801	0.913	0.856	0.801	0.913	CLONAL	1	TRUE	1	0.522835897841834	2		716	1126	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0014004-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	452	464	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.692192055248671	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.692192055248671	2		464	616	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95583961	95583961	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014004-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	32	301	1	ENST00000393063.1:c.1507G>A	p.Glu503Lys	p.E503K	ENST00000393063	NM_030621.3	503	Gag/Aag	10/28	0.644406143710512	4	FACETS	0.281	0.227	0.342	0.14	0.113	0.171	SUBCLONAL	1	TRUE	2	0.692192055248671	4		302	557	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945543	54945543	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs774552788	NA	P-0014004-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1462	648	1228	1	ENST00000312783.6:c.1027C>T	p.Arg343Trp	p.R343W	ENST00000312783	NM_198436.1	343	Cgg/Tgg	9/10	0.692192055248671	6	FACETS	1	0.987	1			1	CLONAL	2	TRUE	NA	0.692192055248671	6		1229	2110	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274923	142274923	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014004-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	347	747	0	ENST00000350721.4:c.2137C>T	p.Gln713Ter	p.Q713*	ENST00000350721	NM_001184.3	713	Caa/Taa	10/47	0.692192055248671	3	FACETS	0.952	0.908	0.995	0.952	0.908	0.995	CLONAL	2	TRUE	1	0.692192055248671	3		747	709	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683565	162683565	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014004-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	85	667	0	ENST00000366898.1:c.404del	p.Gly135GlufsTer42	p.G135Efs*42	ENST00000366898	NM_004562.2	135	gGa/ga	3/12	0.370281392387105	5	FACETS	0.781	0.691	0.877	0.26	0.23	0.293	INDETERMINATE	1	TRUE	2	0.692192055248671	5		667	641	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549430	5549430	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014004-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	487	866	0	ENST00000397747.3:c.457G>C	p.Val153Leu	p.V153L	ENST00000397747	NM_025239.3	153	Gta/Cta	4/7	0.692192055248671	3	FACETS	0.963	0.926	1	0.963	0.926	1	CLONAL	2	TRUE	1	0.692192055248671	3		866	983	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0014004-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	712	464	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.876545870417502	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	FALSE	0	0.876545870417502	2		464	797	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945543	54945543	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs774552788	NA	P-0014004-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1671	928	1228	1	ENST00000312783.6:c.1027C>T	p.Arg343Trp	p.R343W	ENST00000312783	NM_198436.1	343	Cgg/Tgg	9/10	0.861839766601596	5	FACETS	0.943	0.913	0.973			1	CLONAL	2	FALSE	NA	0.876545870417502	5		1229	2599	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274923	142274923	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014004-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	640	747	0	ENST00000350721.4:c.2137C>T	p.Gln713Ter	p.Q713*	ENST00000350721	NM_001184.3	713	Caa/Taa	10/47	0.876545870417502	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	FALSE	1	0.876545870417502	3		747	1047	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683565	162683565	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014004-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	257	667	0	ENST00000366898.1:c.404del	p.Gly135GlufsTer42	p.G135Efs*42	ENST00000366898	NM_004562.2	135	gGa/ga	3/12	0.876545870417502	3	FACETS	1	0.978	1	0.542	0.509	0.575	CLONAL	1	FALSE	1	0.876545870417502	3		667	778	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549430	5549430	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014004-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	727	866	0	ENST00000397747.3:c.457G>C	p.Val153Leu	p.V153L	ENST00000397747	NM_025239.3	153	Gta/Cta	4/7	0.876545870417502	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	FALSE	1	0.876545870417502	3		866	1185	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0014047-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	191	435	0				ENST00000310581	NM_198253.2	-/1132			0.205002948136124	1	FACETS	1	0.978	1	1	0.978	1	INDETERMINATE	1	TRUE	0	0.408768595783068	1		435	657	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778779	9778780	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0014047-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	275	744	2	ENST00000377346.4:c.1048_1049delinsAA	p.Gly350Asn	p.G350N	ENST00000377346	NM_005026.3	350	GGc/AAc	9/24	0.360811566822185	2	FACETS	0.928	0.876	0.981	0.928	0.876	0.981	CLONAL	2	TRUE	0	0.408768595783068	2		746	725	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0014047-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	435	899	1	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.360811566822185	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.408768595783068	2		900	1047	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813397	102813397	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014047-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	145	728	0	ENST00000307046.8:c.292C>G	p.Arg98Gly	p.R98G	ENST00000307046	NM_001111285.1	98	Cgg/Ggg	3/4	1	2	FACETS	0.985	0.901	1	0.985	0.901	1	CLONAL	1	TRUE	1	0.408768595783068	2		728	720	SUCCESS
BLM	641	MSKCC	GRCh37	15	91352431	91352432	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	T	novel	NA	P-0014047-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	237	596	1	ENST00000355112.3:c.3816_3817delinsT	p.Glu1272AspfsTer7	p.E1272Dfs*7	ENST00000355112	NM_000057.2	1272	gaAAaa/gaTaa	20/22	0.306050635153754	3	FACETS	0.9	0.843	0.958	0.9	0.843	0.958	CLONAL	2	TRUE	1	0.408768595783068	3		597	776	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641214	3641214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs546657275	NA	P-0014047-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	248	1333	1	ENST00000294008.3:c.2425G>A	p.Glu809Lys	p.E809K	ENST00000294008	NM_032444.2	809	Gaa/Aaa	12/15	1	2	FACETS	0.868	0.81	0.928	0.868	0.81	0.928	CLONAL	1	TRUE	1	0.408768595783068	2		1334	1398	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644471	3644471	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1183210458	NA	P-0014047-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	240	1186	0	ENST00000294008.3:c.2143C>T	p.Pro715Ser	p.P715S	ENST00000294008	NM_032444.2	715	Ccg/Tcg	10/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.408768595783068	2		1186	1130	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872829	37872829	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014047-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	189	970	0	ENST00000269571.5:c.1708C>T	p.Gln570Ter	p.Q570*	ENST00000269571		570	Cag/Tag	14/27	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.408768595783068	2		970	810	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394730	45394730	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014047-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	94	706	0	ENST00000262160.6:c.619C>T	p.Pro207Ser	p.P207S	ENST00000262160	NM_005901.5	207	Cca/Tca	5/11	1	2	FACETS	0.638	0.567	0.713	0.638	0.567	0.713	SUBCLONAL	1	TRUE	1	0.408768595783068	2		706	721	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099351	4099351	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014047-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	138	1165	1	ENST00000262948.5:c.767C>T	p.Ser256Phe	p.S256F	ENST00000262948	NM_030662.3	256	tCc/tTc	7/11	0.191454763281582	2	FACETS	0.595	0.54	0.653	0.298	0.27	0.327	INDETERMINATE	1	TRUE	0	0.408768595783068	2		1166	1134	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366278	15366279	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0014047-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	207	803	3	ENST00000263377.2:c.1876_1877delinsTT	p.Pro626Phe	p.P626F	ENST00000263377	NM_058243.2	626	CCc/TTc	10/20	0.191454763281582	2	FACETS	1	0.989	1	0.672	0.625	0.72	INDETERMINATE	1	TRUE	0	0.408768595783068	2		806	754	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443592	29443592	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs769449619	NA	P-0014047-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	231	822	0	ENST00000389048.3:c.3625C>T	p.Arg1209Ter	p.R1209*	ENST00000389048	NM_004304.4	1209	Cga/Tga	23/29	0.205002948136124	1	FACETS	1	0.975	1	1	0.975	1	INDETERMINATE	1	TRUE	0	0.408768595783068	1		822	829	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281963	39281963	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	rs397517174	NA	P-0014047-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	61	337	0	ENST00000402219.2:c.512T>G	p.Val171Gly	p.V171G	ENST00000402219	NM_005633.3	171	gTa/gGa	5/23	0.205002948136124	1	FACETS	0.924	0.806	1	0.924	0.806	1	INDETERMINATE	1	TRUE	0	0.408768595783068	1		337	257	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546788	9546788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772481025	NA	P-0014047-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	171	448	0	ENST00000353224.5:c.1234C>T	p.Pro412Ser	p.P412S	ENST00000353224	NM_177990.2	412	Ccg/Tcg	5/10	0.402212998676838	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.408768595783068	3		448	475	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131930595	131930595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014047-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	49	487	0	ENST00000265335.6:c.1828C>T	p.His610Tyr	p.H610Y	ENST00000265335		610	Cat/Tat	12/25	0.205002948136124	1	FACETS	0.372	0.315	0.435	0.372	0.315	0.435	INDETERMINATE	1	TRUE	0	0.408768595783068	1		487	513	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30676114	30676114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014047-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	129	433	1	ENST00000376406.3:c.2242G>A	p.Glu748Lys	p.E748K	ENST00000376406	NM_014641.2	748	Gag/Aag	8/15	0.185669278694845	3	FACETS	1	0.985	1	0.721	0.657	0.788	INDETERMINATE	1	TRUE	1	0.408768595783068	3		434	527	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805731	32805731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014047-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	199	790	0	ENST00000374899.4:c.280G>A	p.Val94Ile	p.V94I	ENST00000374899	NM_018833.2	94	Gtc/Atc	2/12	0.185669278694845	3	FACETS	1	0.988	1	0.67	0.621	0.721	INDETERMINATE	1	TRUE	1	0.408768595783068	3		790	875	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549499	5549499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014047-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	197	1007	1	ENST00000397747.3:c.526G>A	p.Val176Ile	p.V176I	ENST00000397747	NM_025239.3	176	Gtc/Atc	4/7	0.408768595783068	1	FACETS	0.846	0.783	0.91	0.846	0.783	0.91	CLONAL	1	TRUE	0	0.408768595783068	1		1008	907	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521405	8521405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014047-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	192	1005	0	ENST00000356435.5:c.833C>T	p.Pro278Leu	p.P278L	ENST00000356435		278	cCt/cTt	9/35	0.408768595783068	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.408768595783068	1		1005	737	SUCCESS
AR	367	MSKCC	GRCh37	X	66905921	66905921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014047-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	158	806	1	ENST00000374690.3:c.1838C>T	p.Pro613Leu	p.P613L	ENST00000374690	NM_000044.3	613	cCa/cTa	3/8	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.408768595783068	2		807	757	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855277	76855277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014047-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	87	654	0	ENST00000373344.5:c.5710G>A	p.Glu1904Lys	p.E1904K	ENST00000373344	NM_000489.3	1904	Gaa/Aaa	24/35	1	2	FACETS	0.889	0.79	0.994	0.889	0.79	0.994	CLONAL	1	TRUE	1	0.408768595783068	2		654	479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0014067-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	380	480	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.398529324897813	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.399914311735827	2		480	939	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168682	32168682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs935064991	NA	P-0014067-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	195	603	1	ENST00000375023.3:c.4241C>T	p.Ala1414Val	p.A1414V	ENST00000375023	NM_004557.3	1414	gCg/gTg	23/30	0.399914311735827	3	FACETS	0.985	0.91	1	0.493	0.455	0.532	CLONAL	1	TRUE	1	0.399914311735827	3		604	1188	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118379891	118379891	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014067-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	131	301	0	ENST00000534358.1:c.10876C>G	p.Pro3626Ala	p.P3626A	ENST00000534358	NM_005933.3	3626	Cca/Gca	29/36	NA	2	FACETS	0.851	0.773	0.933			1	INDETERMINATE	1	TRUE	NA	0.399914311735827	2		301	770	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81558939	81558939	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014067-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	123	436	0	ENST00000298171.2:c.532G>C	p.Glu178Gln	p.E178Q	ENST00000298171	NM_000369.2	178	Gaa/Caa	6/10	0.374171222970062	3	FACETS	0.752	0.679	0.829			1	SUBCLONAL	1	TRUE	NA	0.399914311735827	3		436	982	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980478	70980478	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014067-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1937	191	647	0	ENST00000276594.2:c.899C>T	p.Ser300Phe	p.S300F	ENST00000276594	NM_024504.3	300	tCt/tTt	4/8	0.399914311735827	6	FACETS	0.808	0.743	0.876	0.202	0.185	0.219	CLONAL	1	TRUE	2	0.399914311735827	6		647	2128	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0014096-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	620	668	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.468143622673079	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.468143622673079	2		669	1233	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856658	111856658	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014096-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	648	630	0	ENST00000341259.2:c.709C>A	p.Leu237Met	p.L237M	ENST00000341259	NM_005475.2	237	Ctg/Atg	2/8	0.468143622673079	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.468143622673079	2		630	1293	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242279	98242279	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1060502279	NA	P-0014096-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	503	656	2	ENST00000331920.6:c.1039G>T	p.Val347Phe	p.V347F	ENST00000331920	NM_000264.3	347	Gtc/Ttc	7/24	0.288098816412257	4	FACETS	0.937	0.896	0.979	0.937	0.896	0.979	CLONAL	2	TRUE	2	0.468143622673079	4		658	1683	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410498	139410520	+	frameshift_variant	Frame_Shift_Del	DEL	GTGCTGGCACACTCGTCCACATC	GTGCTGGCACACTCGTCCACATC	-	novel	NA	P-0014096-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	543	871	0	ENST00000277541.6:c.1582_1604del	p.Asp528ProfsTer34	p.D528Pfs*34	ENST00000277541	NM_017617.3	528	GATGTGGACGAGTGTGCCAGCACc/c	10/34	0.468143622673079	2	FACETS	0.808	0.775	0.841	0.808	0.775	0.841	CLONAL	2	TRUE	0	0.468143622673079	2		871	1436	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951122	48951128	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	GAAATTT	GAAATTT	TGTATAGGATACATCTTTAAA	novel	NA	P-0014096-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	100	370	0	ENST00000267163.4:c.1284_1290delinsTGTATAGGATACATCTTTAAA	p.Glu428AspfsTer3	p.E428Dfs*3	ENST00000267163	NM_000321.2	428	gaGAAATTT/gaTGTATAGGATACATCTTTAAA	13/27	0.468143622673079	2	FACETS	1	0.963	1	0.574	0.517	0.634	CLONAL	1	TRUE	0	0.468143622673079	2		370	372	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044602	47044602	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014096-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1644	215	894	0	ENST00000377604.3:c.2099A>C	p.Lys700Thr	p.K700T	ENST00000377604	NM_001204468.1	700	aAg/aCg	18/24	0.236242385000124	2	FACETS	0.494	0.457	0.533	0.247	0.228	0.267	INDETERMINATE	1	TRUE	0	0.468143622673079	2		894	1859	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0014129-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	94	557	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	NA	2	FACETS	0.741	0.658	0.831			1	INDETERMINATE	1	FALSE	NA	0.226005864411624	2		557	1122	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563077	21563077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014129-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	71	540	0	ENST00000382592.4:c.842C>T	p.Pro281Leu	p.P281L	ENST00000382592	NM_014572.2	281	cCg/cTg	4/8	1	2	FACETS	0.603	0.525	0.688	0.603	0.525	0.688	SUBCLONAL	1	FALSE	1	0.226005864411624	2		540	1042	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723122	49723122	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014129-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	62	448	0	ENST00000449682.2:c.1294T>G	p.Phe432Val	p.F432V	ENST00000449682	NM_020998.3	432	Ttc/Gtc	11/18	1	2	FACETS	0.514	0.442	0.593	0.514	0.442	0.593	SUBCLONAL	1	FALSE	1	0.226005864411624	2		448	1067	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0014220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	164	435	0				ENST00000310581	NM_198253.2	-/1132			0.365134996206221	1	FACETS	0.983	0.908	1	0.983	0.908	1	CLONAL	1	FALSE	0	0.464098170153987	1		435	552	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245513	16245513	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	244	747	4	ENST00000375759.3:c.1488G>T	p.Met496Ile	p.M496I	ENST00000375759	NM_015001.2	496	atG/atT	7/15	0.365134996206221	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	0	0.464098170153987	1		751	772	SUCCESS
CBL	867	MSKCC	GRCh37	11	119146841	119146841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	147	482	2	ENST00000264033.4:c.1004G>A	p.Gly335Asp	p.G335D	ENST00000264033	NM_005188.3	335	gGc/gAc	6/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.464098170153987	2		484	539	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488757	212488757	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	170	696	0	ENST00000342788.4:c.2092T>G	p.Leu698Val	p.L698V	ENST00000342788	NM_005235.2	698	Tta/Gta	18/28	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.464098170153987	2		696	698	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710607	40710607	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	199	866	0	ENST00000373198.4:c.4244A>G	p.Glu1415Gly	p.E1415G	ENST00000373198	NM_133170.3	1415	gAg/gGg	31/32	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.464098170153987	2		866	809	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589605	67589616	+	inframe_deletion	In_Frame_Del	DEL	TCAAGAAAAAAG	TCAAGAAAAAAG	-	novel	NA	P-0014220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	133	581	0	ENST00000274335.5:c.1370_1381del	p.Gln457_Ser460del	p.Q457_S460del	ENST00000274335		456	ttTCAAGAAAAAAGt/ttt	10/15	0.177869776844186	3	FACETS	1	0.953	1	0.537	0.488	0.587	INDETERMINATE	1	FALSE	1	0.464098170153987	3		581	658	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77054897	77054901	+	frameshift_variant	Frame_Shift_Del	DEL	TTTTC	TTTTC	-	novel	NA	P-0014220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	49	601	0	ENST00000356341.3:c.961_965del	p.Glu321GlnfsTer17	p.E321Qfs*17	ENST00000356341	NM_002576.4	321	GAAAAc/c	10/15	1	2	FACETS	0.341	0.288	0.399	0.341	0.288	0.399	SUBCLONAL	1	FALSE	1	0.464098170153987	2		601	619	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39644744	39644744	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	38	749	0	ENST00000262039.4:c.2473G>A	p.Asp825Asn	p.D825N	ENST00000262039	NM_002647.2	825	Gat/Aat	23/25	0.177869776844186	3	FACETS	0.281	0.231	0.336	0.14	0.115	0.168	INDETERMINATE	1	FALSE	1	0.464098170153987	3		749	719	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864466	57864466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367789336	NA	P-0014223-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	198	640	0	ENST00000228682.2:c.1943G>A	p.Arg648His	p.R648H	ENST00000228682	NM_005269.2	648	cGt/cAt	12/12	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.521083051713326	2		640	719	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249016	55249017	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCCACG	rs397517114	NA	P-0014223-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	323	552	0	ENST00000275493.2:c.2315_2320dup	p.His773_Val774insAlaHis	p.H773_V774insAH	ENST00000275493	NM_005228.3	772	ccc/cCCCACGcc	20/28	0.521850132065876	3	FACETS	0.928	0.88	0.977	0.928	0.88	0.977	CLONAL	2	TRUE	1	0.521083051713326	3		552	842	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864466	57864466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367789336	NA	P-0014223-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	134	640	0	ENST00000228682.2:c.1943G>A	p.Arg648His	p.R648H	ENST00000228682	NM_005269.2	648	cGt/cAt	12/12	0.197397890965528	3	FACETS	1	0.985	1	0.715	0.652	0.782	INDETERMINATE	1	TRUE	1	0.357965765649263	3		640	617	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249016	55249017	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCCACG	rs397517114	NA	P-0014223-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	220	552	0	ENST00000275493.2:c.2315_2320dup	p.His773_Val774insAlaHis	p.H773_V774insAH	ENST00000275493	NM_005228.3	772	ccc/cCCCACGcc	20/28	0.357965765649263	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.357965765649263	3		552	669	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197443	106197443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1452689450	NA	P-0014254-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	73	366	1	ENST00000380013.4:c.5776C>T	p.Arg1926Cys	p.R1926C	ENST00000380013	NM_001127208.2	1926	Cgt/Tgt	11/11	0.409886483681461	3	FACETS	0.392	0.342	0.447	0.196	0.171	0.224	SUBCLONAL	1	FALSE	1	0.409886483681461	3		367	1094	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0014262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	39	522	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.631	0.523	0.751	0.631	0.523	0.751	SUBCLONAL	1	TRUE	1	0.287444872477312	2		522	430	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0014262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	155	617	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.243503823266265	4	FACETS	0.784	0.718	0.854	0.523	0.479	0.569	SUBCLONAL	2	TRUE	1	0.287444872477312	4		617	885	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs17849781	NA	P-0014262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	168	847	0	ENST00000269305.4:c.832C>A	p.Pro278Thr	p.P278T	ENST00000269305	NM_001126112.2	278	Cct/Act	8/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.287444872477312	2		847	994	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023042	48023042	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs63749873	NA	P-0014262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	25	318	0	ENST00000234420.5:c.467C>G	p.Ser156Ter	p.S156*	ENST00000234420	NM_000179.2	156	tCa/tGa	3/10	1	2	FACETS	0.368	0.289	0.459	0.368	0.289	0.459	SUBCLONAL	1	TRUE	1	0.287444872477312	2		318	473	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033962	48033962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	41	486	1	ENST00000234420.5:c.4046C>T	p.Ala1349Val	p.A1349V	ENST00000234420	NM_000179.2	1349	gCt/gTt	10/10	1	2	FACETS	0.542	0.451	0.644	0.542	0.451	0.644	SUBCLONAL	1	TRUE	1	0.287444872477312	2		487	526	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212252715	212252715	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	rs1285745508	NA	P-0014262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	27	263	0	ENST00000342788.4:c.3138T>G	p.Ser1046Arg	p.S1046R	ENST00000342788	NM_005235.2	1046	agT/agG	26/28	1	2	FACETS	0.556	0.442	0.685	0.556	0.442	0.685	SUBCLONAL	1	TRUE	1	0.287444872477312	2		263	338	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542201	187542201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs189523191	NA	P-0014305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	136	364	0	ENST00000441802.2:c.5539G>A	p.Val1847Ile	p.V1847I	ENST00000441802	NM_005245.3	1847	Gtc/Atc	10/27	0.487097989717536	1	FACETS	0.262	0.238	0.286	0.262	0.238	0.286	INDETERMINATE	1	TRUE	0	0.911883052824616	1		364	620	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599321	55599321	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913507	NA	P-0014305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2752	227	450	0	ENST00000288135.5:c.2447A>T	p.Asp816Val	p.D816V	ENST00000288135	NM_000222.2	816	gAc/gTc	17/21	0.911883052824616	6	FACETS	0.472	0.437	0.509			1	SUBCLONAL	1	TRUE	NA	0.911883052824616	6		450	2979	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829066	128829066	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs41304185	NA	P-0014305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	14	15	1	ENST00000249373.3:c.74A>G	p.Asp25Gly	p.D25G	ENST00000249373	NM_005631.4	25	gAc/gGc	1/12	0.683174293036553	1	FACETS	0.557	0.431	0.685	0.557	0.431	0.685	SUBCLONAL	1	TRUE	0	0.911883052824616	1		16	30	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610148	43610148	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1564496551	NA	P-0014305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	487	514	0	ENST00000355710.3:c.2100G>A	p.Met700Ile	p.M700I	ENST00000355710	NM_020975.4	700	atG/atA	11/20	0.911883052824616	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.911883052824616	1		514	562	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944205	71944205	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1227965351	NA	P-0014305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	187	472	0	ENST00000298229.2:c.2038G>A	p.Gly680Arg	p.G680R	ENST00000298229	NM_001567.3	680	Ggg/Agg	17/28	NA	2	FACETS	0.413	0.382	0.447			1	INDETERMINATE	1	TRUE	NA	0.911883052824616	2		472	992	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18478017	18478017	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0014305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	294	605	1	ENST00000266497.5:c.1257C>G	p.Tyr419Ter	p.Y419*	ENST00000266497		419	taC/taG	7/31	1	2	FACETS	0.458	0.43	0.487	0.458	0.43	0.487	SUBCLONAL	1	TRUE	1	0.911883052824616	2		606	1409	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431050	181431050	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1270775176	NA	P-0014305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	269	528	1	ENST00000325404.1:c.902G>A	p.Gly301Asp	p.G301D	ENST00000325404	NM_003106.3	301	gGc/gAc	1/1	0.487097989717536	1	FACETS	0.385	0.362	0.408	0.385	0.362	0.408	INDETERMINATE	1	TRUE	0	0.911883052824616	1		529	834	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301110	65301110	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774820863	NA	P-0014305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	123	244	1	ENST00000342505.4:c.3338G>A	p.Arg1113His	p.R1113H	ENST00000342505	NM_002227.2	1113	cGc/cAc	24/25	0.487097989717536	1	FACETS	0.349	0.318	0.382	0.349	0.318	0.382	INDETERMINATE	1	TRUE	0	0.911883052824616	1		245	420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577091	7577091	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149633775	NA	P-0014305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1334	37	623	0	ENST00000269305.4:c.847C>G	p.Arg283Gly	p.R283G	ENST00000269305	NM_001126112.2	283	Cgc/Ggc	8/11	1	2	FACETS	0.059	0.048	0.072	0.059	0.048	0.072	SUBCLONAL	1	TRUE	1	0.911883052824616	2		623	1371	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0014306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	72	1085	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.79	0.689	0.898	0.79	0.689	0.898	SUBCLONAL	1	TRUE	1	0.254690652737484	2		1085	716	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916926	+	inframe_deletion	In_Frame_Del	DEL	CAG	CAG	-	novel	NA	P-0014306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	120	403	0	ENST00000263967.3:c.311_313del	p.Pro104_Val105delinsLeu	p.P104_V105delinsL	ENST00000263967	NM_006218.2	104	cCAGta/cta	2/21	0.239746072561889	4	FACETS	0.858	0.776	0.944	0.858	0.776	0.944	CLONAL	2	TRUE	2	0.254690652737484	4		403	689	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346832	89346832	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772993940	NA	P-0014306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	26	209	0	ENST00000301030.4:c.6118G>A	p.Gly2040Arg	p.G2040R	ENST00000301030	NM_001256183.1	2040	Gga/Aga	9/13	0.254690652737484	1	FACETS	0.799	0.636	0.984	0.799	0.636	0.984	CLONAL	1	TRUE	0	0.254690652737484	1		209	223	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197160	26197160	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	53	311	1	ENST00000356476.2:c.319G>T	p.Asp107Tyr	p.D107Y	ENST00000356476		107	Gac/Tac	1/1	0.254690652737484	7	FACETS	0.918	0.781	1	0.23	0.195	0.268	CLONAL	1	TRUE	3	0.254690652737484	7		312	742	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511598	38511598	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014333-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	243	549	1	ENST00000254066.5:c.1096C>T	p.Arg366Trp	p.R366W	ENST00000254066	NM_000964.3	366	Cgg/Tgg	8/9	0.147229272352416	5	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.551547482708541	5		550	1104	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602688	55602688	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014333-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	123	308	0	ENST00000288135.5:c.2509G>C	p.Ala837Pro	p.A837P	ENST00000288135	NM_000222.2	837	Gca/Cca	18/21	0.551547482708541	3	FACETS	0.922	0.836	1	0.461	0.418	0.506	CLONAL	1	TRUE	1	0.551547482708541	3		308	617	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700279	117700279	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014333-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	509	637	0	ENST00000368508.3:c.2540G>T	p.Trp847Leu	p.W847L	ENST00000368508	NM_002944.2	847	tGg/tTg	17/43	0.551547482708541	2	FACETS	0.987	0.952	1	0.987	0.952	1	CLONAL	2	TRUE	0	0.551547482708541	2		637	935	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0014372-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	148	635	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	1	2	FACETS	0.647	0.591	0.706	0.647	0.591	0.706	SUBCLONAL	1	TRUE	1	0.516137600928198	2		635	886	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061313	38061313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1204900727	NA	P-0014372-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	200	740	2	ENST00000250448.2:c.676G>A	p.Asp226Asn	p.D226N	ENST00000250448	NM_004496.3	226	Gac/Aac	2/2	1	2	FACETS	0.893	0.828	0.96	0.893	0.828	0.96	CLONAL	1	TRUE	1	0.516137600928198	2		742	868	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847393	68847393	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014372-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	194	684	0	ENST00000261769.5:c.1315del	p.Ala439GlnfsTer16	p.A439Qfs*16	ENST00000261769	NM_004360.3	439	Gca/ca	9/16	0.516137600928198	1	FACETS	0.907	0.844	0.972	0.907	0.844	0.972	CLONAL	1	TRUE	0	0.516137600928198	1		684	615	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030223	180030223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200835339	NA	P-0014372-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	189	644	2	ENST00000261937.6:c.4061G>A	p.Arg1354His	p.R1354H	ENST00000261937	NM_182925.4	1354	cGc/cAc	30/30	1	2	FACETS	0.937	0.867	1	0.937	0.867	1	CLONAL	1	TRUE	1	0.516137600928198	2		646	782	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0014430-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	155	946	2	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.288818088420188	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.292189184365821	1		948	855	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098944	178098944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014430-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	11	546	1	ENST00000397062.3:c.101G>A	p.Arg34Gln	p.R34Q	ENST00000397062	NM_006164.4	34	cGa/cAa	2/5	0.292189184365821	3	FACETS	0.163	0.112	0.228	0.082	0.056	0.114	SUBCLONAL	1	TRUE	1	0.292189184365821	3		547	529	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182641	38182641	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs387907272	NA	P-0014430-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	21	787	0	ENST00000396334.3:c.794T>C	p.Leu265Pro	p.L265P	ENST00000396334	NM_002468.4	265	cTg/cCg	5/5	0.292189184365821	1	FACETS	0.369	0.283	0.468	0.369	0.283	0.468	SUBCLONAL	1	TRUE	0	0.292189184365821	1		787	333	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266498	198266498	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014430-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	121	608	0	ENST00000335508.6:c.2338C>G	p.Pro780Ala	p.P780A	ENST00000335508	NM_012433.2	780	Cct/Gct	16/25	0.292189184365821	3	FACETS	0.899	0.816	0.986	0.899	0.816	0.986	CLONAL	2	TRUE	1	0.292189184365821	3		608	528	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447084	187447084	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1394202381	NA	P-0014430-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	314	880	0	ENST00000232014.4:c.1109C>A	p.Pro370His	p.P370H	ENST00000232014	NM_001130845.1	370	cCc/cAc	5/10	0.292189184365821	4	FACETS	0.849	0.802	0.898	0.849	0.802	0.898	CLONAL	3	TRUE	1	0.292189184365821	4		880	1090	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628266	187628266	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014430-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	96	828	1	ENST00000441802.2:c.2716C>T	p.Gln906Ter	p.Q906*	ENST00000441802	NM_005245.3	906	Cag/Tag	2/27	0.288818088420188	1	FACETS	0.895	0.798	0.997	0.895	0.798	0.997	CLONAL	1	TRUE	0	0.292189184365821	1		829	627	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0014453-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	100	644	0	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.281821463627426	1	FACETS	0.886	0.792	0.986	0.886	0.792	0.986	CLONAL	1	TRUE	0	0.281821463627426	1		644	688	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121913370	NA	P-0014453-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	52	287	0	ENST00000288602.6:c.1742A>G	p.Asn581Ser	p.N581S	ENST00000288602	NM_004333.4	581	aAt/aGt	15/18	1	2	FACETS	0.734	0.625	0.853	0.734	0.625	0.853	SUBCLONAL	1	TRUE	1	0.281821463627426	2		287	503	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600408	10600408	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014453-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	131	729	1	ENST00000171111.5:c.1447C>A	p.Arg483Ser	p.R483S	ENST00000171111	NM_203500.1	483	Cgc/Agc	4/6	0.281821463627426	1	FACETS	0.855	0.775	0.939	0.855	0.775	0.939	CLONAL	1	TRUE	0	0.281821463627426	1		730	934	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147241	61147241	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014453-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	94	435	0	ENST00000295025.8:c.919C>G	p.His307Asp	p.H307D	ENST00000295025	NM_002908.2	307	Cac/Gac	8/11	1	2	FACETS	0.725	0.644	0.812	0.725	0.644	0.812	SUBCLONAL	1	TRUE	1	0.281821463627426	2		435	920	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951955	178951955	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014453-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	104	456	0	ENST00000263967.3:c.3010A>G	p.Met1004Val	p.M1004V	ENST00000263967	NM_006218.2	1004	Atg/Gtg	21/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.281821463627426	2		456	672	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040706	47040706	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014453-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	130	402	0	ENST00000377604.3:c.1342del	p.Gln448ArgfsTer37	p.Q448Rfs*37	ENST00000377604	NM_001204468.1	447	agC/ag	13/24	1	1	FACETS	0.788	0.719	0.86	1	0.987	1	SUBCLONAL	2	TRUE	0	0.281821463627426	1		402	503	SUCCESS
AR	367	MSKCC	GRCh37	X	66941796	66941796	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014499-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	113	316	0	ENST00000374690.3:c.2440T>G	p.Phe814Val	p.F814V	ENST00000374690	NM_000044.3	814	Ttc/Gtc	6/8	0.304618900931987	2	FACETS	1	0.974	1			1	CLONAL	1	TRUE	NA	0.31	2		316	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0014499-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1206	543	1071	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.295068121287427	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.31	2		1071	1749	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008546	70008546	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014499-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	129	526	0	ENST00000394351.3:c.833A>C	p.Asn278Thr	p.N278T	ENST00000394351	NM_000248.3	278	aAc/aCc	8/9	0.295068121287427	2	FACETS	0.923	0.836	1	0.461	0.418	0.507	CLONAL	1	TRUE	0	0.31	2		526	902	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	88	297	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.867	0.773	0.965	0.867	0.773	0.965	CLONAL	1	TRUE	1	0.540115188426245	2		297	376	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915455	112915455	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121918463	NA	P-0014677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	238	706	0	ENST00000351677.2:c.854T>C	p.Phe285Ser	p.F285S	ENST00000351677	NM_002834.3	285	tTt/tCt	8/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.540115188426245	2		706	816	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720802	89720807	+	inframe_deletion	In_Frame_Del	DEL	TTACTT	TTACTT	-	novel	NA	P-0014677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	150	342	0	ENST00000371953.3:c.954_959del	p.Leu320_Thr321del	p.L320_T321del	ENST00000371953	NM_000314.4	318	cTTACTTta/cta	8/9	0.540115188426245	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.540115188426245	1		342	382	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591255	67591255	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	172	707	0	ENST00000274335.5:c.1753A>C	p.Thr585Pro	p.T585P	ENST00000274335		585	Act/Cct	13/15	0.216899962021295	3	FACETS	0.868	0.799	0.94	0.434	0.399	0.47	INDETERMINATE	1	TRUE	1	0.540115188426245	3		707	932	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0014703-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	448	780	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.431766298813817	3	FACETS	0.89	0.855	0.924	0.89	0.855	0.924	CLONAL	3	TRUE	0	0.49783524768017	3		780	842	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653805	89653805	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659443	NA	P-0014703-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	214	389	0	ENST00000371953.3:c.103A>G	p.Met35Val	p.M35V	ENST00000371953	NM_000314.4	35	Atg/Gtg	2/9	0.446713826997581	2	FACETS	0.841	0.789	0.894	0.841	0.789	0.894	CLONAL	2	TRUE	0	0.49783524768017	2		389	511	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027248	49027248	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0014703-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	378	379	1	ENST00000267163.4:c.1814+1G>A		p.X605_splice	ENST00000267163	NM_000321.2	605			0.452156282015306	3	FACETS	0.939	0.901	0.977	0.939	0.901	0.977	CLONAL	3	TRUE	0	0.49783524768017	3		380	673	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111191	193111191	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014703-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	42	291	0	ENST00000367435.3:c.724G>T	p.Gly242Ter	p.G242*	ENST00000367435	NM_024529.4	242	Gga/Tga	7/17	0.49783524768017	4	FACETS	0.466	0.389	0.552	0.233	0.194	0.276	SUBCLONAL	1	TRUE	2	0.49783524768017	4		291	542	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443871	18443871	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014703-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	147	432	0	ENST00000266497.5:c.844C>G	p.Leu282Val	p.L282V	ENST00000266497		282	Ctc/Gtc	3/31	0.49783524768017	3	FACETS	0.929	0.849	1	0.464	0.424	0.507	CLONAL	1	TRUE	1	0.49783524768017	3		432	794	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73343000	73343000	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1413258245	NA	P-0014703-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	160	393	0	ENST00000377767.4:c.1806G>T	p.Met602Ile	p.M602I	ENST00000377767	NM_014953.3	602	atG/atT	14/21	0.452156282015306	3	FACETS	1	0.971	1	0.374	0.343	0.405	CLONAL	1	TRUE	0	0.49783524768017	3		393	716	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523328	9523328	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014703-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	73	404	0	ENST00000353224.5:c.1909A>T	p.Ile637Phe	p.I637F	ENST00000353224	NM_177990.2	637	Att/Ttt	9/10	0.49783524768017	5	FACETS	0.54	0.471	0.615	0.18	0.157	0.205	SUBCLONAL	1	TRUE	2	0.49783524768017	5		404	949	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970996	55970996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014703-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	74	430	0	ENST00000263923.4:c.1801C>T	p.Pro601Ser	p.P601S	ENST00000263923	NM_002253.2	601	Cct/Tct	13/30	0.23959528890021	4	FACETS	0.535	0.467	0.608	0.134	0.116	0.152	INDETERMINATE	1	TRUE	0	0.49783524768017	4		430	833	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873585	35873585	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014703-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	264	201	0	ENST00000303115.3:c.541G>T	p.Val181Leu	p.V181L	ENST00000303115	NM_002185.3	181	Gtg/Ttg	5/8	0.49783524768017	6	FACETS	1	0.967	1	1	0.967	1	CLONAL	3	TRUE	3	0.49783524768017	6		201	681	SUCCESS
APC	324	MSKCC	GRCh37	5	112176482	112176482	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014703-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	202	333	0	ENST00000257430.4:c.5191G>C	p.Ala1731Pro	p.A1731P	ENST00000257430	NM_000038.5	1731	Gct/Cct	16/16	0.446713826997581	2	FACETS	0.858	0.804	0.912	0.858	0.804	0.912	CLONAL	2	TRUE	0	0.49783524768017	2		333	473	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724416	117724416	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014703-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	84	444	0	ENST00000368508.3:c.463G>T	p.Val155Phe	p.V155F	ENST00000368508	NM_002944.2	155	Gtc/Ttc	6/43	0.482855610706103	3	FACETS	0.539	0.475	0.607	0.18	0.158	0.203	SUBCLONAL	1	TRUE	0	0.49783524768017	3		444	782	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786500	135786501	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0014703-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	275	366	1	ENST00000298552.3:c.1030-1_1030delinsTT		p.X344_splice	ENST00000298552	NM_001162426.1	344		11/23	0.431766298813817	3	FACETS	1	0.989	1	0.774	0.734	0.815	CLONAL	2	TRUE	0	0.49783524768017	3		367	594	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412256	139412256	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014703-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	432	505	0	ENST00000277541.6:c.1389del	p.Asn463LysfsTer168	p.N463Kfs*168	ENST00000277541	NM_017617.3	463	aaC/aa	8/34	0.431766298813817	3	FACETS	0.834	0.8	0.868	0.834	0.8	0.868	CLONAL	3	TRUE	0	0.49783524768017	3		505	866	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937134	76937134	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014703-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	46	382	0	ENST00000373344.5:c.3614C>G	p.Ser1205Cys	p.S1205C	ENST00000373344	NM_000489.3	1205	tCt/tGt	9/35	0.267400927533088	2	FACETS	0.363	0.305	0.427	0.182	0.152	0.214	INDETERMINATE	1	TRUE	0	0.49783524768017	2		382	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0014796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	207	547	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.893100180254409	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.893100180254409	1		547	244	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913233	NA	P-0014796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	942	681	0	ENST00000451590.1:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000451590	NM_001130442.1	61	cAg/cTg	3/5	NA	2	FACETS	1	0.998	1			1	INDETERMINATE	2	TRUE	NA	0.893100180254409	2		681	977	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446204	187446204	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	217	625	0	ENST00000232014.4:c.1484C>T	p.Pro495Leu	p.P495L	ENST00000232014	NM_001130845.1	495	cCc/cTc	6/10	0.432928175605661	1	FACETS	0.437	0.409	0.466	0.437	0.409	0.466	INDETERMINATE	1	TRUE	0	0.893100180254409	1		625	615	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0014817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	194	592	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.1996965688908	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		592	1155	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633658	69633658	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	32	92	0	ENST00000334134.2:c.44G>T	p.Gly15Val	p.G15V	ENST00000334134	NM_005247.2	15	gGc/gTc	1/3	0.1996965688908	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		92	99	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578209	28578209	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	104	678	1	ENST00000241453.7:c.2962G>A	p.Ala988Thr	p.A988T	ENST00000241453	NM_004119.2	988	Gct/Act	24/24	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		679	1207	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988250	36988250	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	342	733	0	ENST00000354822.5:c.403A>T	p.Arg135Trp	p.R135W	ENST00000354822	NM_001079668.2	135	Agg/Tgg	2/3	0.353311830487056	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		733	1381	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391075	89391075	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1237	169	825	0	ENST00000336596.2:c.1141C>G	p.Arg381Gly	p.R381G	ENST00000336596	NM_005233.5	381	Cgc/Ggc	5/17	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		825	1406	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099815	157099815	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	139	749	0	ENST00000346085.5:c.752G>A	p.Cys251Tyr	p.C251Y	ENST00000346085	NM_020732.3	251	tGc/tAc	1/20	0.1996965688908	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		749	1162	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038779	47038779	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	230	766	0	ENST00000377604.3:c.787del	p.Arg263GlyfsTer3	p.R263Gfs*3	ENST00000377604	NM_001204468.1	262	ggC/gg	9/24	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		766	1190	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0014822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	141	689	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.22	2		689	951	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0014822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	30	249	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	0.781	0.63	0.953	0.781	0.63	0.953	CLONAL	1	TRUE	1	0.22	2		249	349	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4123815	4123815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	38	342	0	ENST00000262948.5:c.58G>A	p.Glu20Lys	p.E20K	ENST00000262948	NM_030662.3	20	Gag/Aag	1/11	1	2	FACETS	0.74	0.611	0.883	0.74	0.611	0.883	SUBCLONAL	1	TRUE	1	0.22	2		342	467	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259208	16259208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144493499	NA	P-0014822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	29	478	2	ENST00000375759.3:c.6473C>T	p.Pro2158Leu	p.P2158L	ENST00000375759	NM_015001.2	2158	cCg/cTg	11/15	1	2	FACETS	0.467	0.373	0.573	0.467	0.373	0.573	SUBCLONAL	1	TRUE	1	0.22	2		480	565	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011229	12011240	+	splice_region_variant,intron_variant	Splice_Region	DEL	AAGTACCTGGTC	AAGTACCTGGTC	-	novel	NA	P-0014822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	27	325	0	ENST00000353533.5:c.633+3_633+14del		p.X211_splice	ENST00000353533	NM_003010.3	211			1	2	FACETS	0.703	0.56	0.867	0.703	0.56	0.867	SUBCLONAL	1	TRUE	1	0.22	2		325	349	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84384669	84384669	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	42	570	1	ENST00000321945.7:c.774A>T	p.Arg258Ser	p.R258S	ENST00000321945	NM_139076.2	258	agA/agT	8/9	1	2	FACETS	0.458	0.381	0.544	0.458	0.381	0.544	SUBCLONAL	1	TRUE	1	0.22	2		571	834	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0014899-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	193	943	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	0.603656335774565	2		943	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0014899-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	603	1023	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.603656335774565	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.603656335774565	1		1024	1080	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052636	42052636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1054243525	NA	P-0014899-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	243	856	3	ENST00000219905.7:c.7307G>A	p.Arg2436His	p.R2436H	ENST00000219905	NM_001164273.1	2436	cGt/cAt	20/24	1	2	FACETS	0.994	0.931	1	0.994	0.931	1	CLONAL	1	TRUE	1	0.603656335774565	2		859	810	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041097	42041098	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0014899-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	233	875	0	ENST00000219905.7:c.5476_5477dup	p.Leu1826PhefsTer13	p.L1826Ffs*13	ENST00000219905	NM_001164273.1	1825	-/TT	16/24	1	2	FACETS	0.87	0.813	0.929	0.87	0.813	0.929	CLONAL	1	TRUE	1	0.603656335774565	2		875	887	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008476	70008476	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057517966	NA	P-0014899-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	128	457	0	ENST00000394351.3:c.763C>T	p.Arg255Ter	p.R255*	ENST00000394351	NM_000248.3	255	Cga/Tga	8/9	0.369619539100148	1	FACETS	0.359	0.325	0.395	0.359	0.325	0.395	SUBCLONAL	1	TRUE	0	0.603656335774565	1		457	825	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376446	118376446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014899-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	200	797	0	ENST00000534358.1:c.9839C>T	p.Ser3280Leu	p.S3280L	ENST00000534358	NM_005933.3	3280	tCa/tTa	27/36	0.369619539100148	1	FACETS	0.799	0.745	0.854	0.799	0.745	0.854	SUBCLONAL	1	TRUE	0	0.603656335774565	1		797	579	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0014899-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	326	943	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.304754733513602	1	FACETS	0.906	0.859	0.953	0.906	0.859	0.953	INDETERMINATE	1	TRUE	0	0.586787709149306	1		943	867	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0014899-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	643	1023	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.568214363317171	2	FACETS	0.945	0.916	0.975	0.945	0.916	0.975	CLONAL	2	TRUE	0	0.586787709149306	2		1024	1159	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052636	42052636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1054243525	NA	P-0014899-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	295	856	3	ENST00000219905.7:c.7307G>A	p.Arg2436His	p.R2436H	ENST00000219905	NM_001164273.1	2436	cGt/cAt	20/24	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.586787709149306	2		859	979	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041097	42041098	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0014899-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	305	875	0	ENST00000219905.7:c.5476_5477dup	p.Leu1826PhefsTer13	p.L1826Ffs*13	ENST00000219905	NM_001164273.1	1825	-/TT	16/24	1	2	FACETS	0.902	0.85	0.956	0.902	0.85	0.956	CLONAL	1	TRUE	1	0.586787709149306	2		875	1152	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376446	118376446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014899-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	338	797	0	ENST00000534358.1:c.9839C>T	p.Ser3280Leu	p.S3280L	ENST00000534358	NM_005933.3	3280	tCa/tTa	27/36	0.304754733513602	1	FACETS	0.83	0.787	0.874	0.83	0.787	0.874	INDETERMINATE	1	TRUE	0	0.586787709149306	1		797	981	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0014945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	297	464	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.717734890562804	1	FACETS	0.891	0.851	0.93	0.891	0.851	0.93	CLONAL	1	TRUE	0	0.795172478696937	1		464	505	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251907	153251907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	225	386	0	ENST00000281708.4:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000281708	NM_033632.3	367	Cga/Tga	7/12	1	2	FACETS	0.863	0.808	0.919	0.863	0.808	0.919	CLONAL	1	TRUE	1	0.795172478696937	2		386	656	SUCCESS
APC	324	MSKCC	GRCh37	5	112174922	112174923	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTCT	novel	NA	P-0014945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	158	319	0	ENST00000257430.4:c.3633_3637dup	p.Ser1213CysfsTer54	p.S1213Cfs*54	ENST00000257430	NM_000038.5	1211	atg/aTGTCTtg	16/16	1	2	FACETS	0.747	0.689	0.807	0.747	0.689	0.807	SUBCLONAL	1	TRUE	1	0.795172478696937	2		319	532	SUCCESS
APC	324	MSKCC	GRCh37	5	112176021	112176021	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	238	376	0	ENST00000257430.4:c.4731del	p.Glu1577AspfsTer73	p.E1577Dfs*73	ENST00000257430	NM_000038.5	1577	gAa/ga	16/16	1	2	FACETS	0.989	0.931	1	0.989	0.931	1	CLONAL	1	TRUE	1	0.795172478696937	2		376	605	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0014983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	746	592	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.373600556518914	4	FACETS	0.912	0.884	0.94	0.912	0.884	0.94	CLONAL	4	TRUE	0	0.385462493221012	4		592	1470	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023006	27023006	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	16	62	0	ENST00000324856.7:c.112G>T	p.Glu38Ter	p.E38*	ENST00000324856	NM_006015.4	38	Gag/Tag	1/20	0.171059221376364	2	FACETS	0.589	0.438	0.765	0.294	0.219	0.383	INDETERMINATE	1	TRUE	0	0.385462493221012	2		62	141	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68758650	68758650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	194	368	0	ENST00000487270.1:c.806C>T	p.Ser269Phe	p.S269F	ENST00000487270	NM_133509.3	269	tCt/tTt	8/11	0.323544648405774	4	FACETS	1	0.961	1			1	CLONAL	1	TRUE	NA	0.385462493221012	4		368	1310	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498474	89498474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	132	341	0	ENST00000336596.2:c.2446G>A	p.Glu816Lys	p.E816K	ENST00000336596	NM_005233.5	816	Gag/Aag	14/17	0.256617623684584	1	FACETS	0.789	0.717	0.864	0.789	0.717	0.864	SUBCLONAL	1	TRUE	0	0.385462493221012	1		341	701	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964338	55964338	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	183	447	0	ENST00000263923.4:c.2475C>A	p.Ser825Arg	p.S825R	ENST00000263923	NM_002253.2	825	agC/agA	17/30	1	2	FACETS	0.84	0.774	0.909	0.84	0.774	0.909	CLONAL	1	TRUE	1	0.385462493221012	2		447	1130	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392170	81392170	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	46	178	0	ENST00000222390.5:c.107G>C	p.Arg36Thr	p.R36T	ENST00000222390	NM_000601.4	36	aGa/aCa	2/18	0.221495676351839	3	FACETS	0.501	0.421	0.589	0.167	0.14	0.197	INDETERMINATE	1	TRUE	0	0.385462493221012	3		178	568	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836846	151836846	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1339	116	494	0	ENST00000262189.6:c.14374G>A	p.Glu4792Lys	p.E4792K	ENST00000262189	NM_170606.2	4792	Gag/Aag	56/59	0.221495676351839	3	FACETS	0.493	0.443	0.547	0.164	0.147	0.183	INDETERMINATE	1	TRUE	0	0.385462493221012	3		494	1455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572990	7572991	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	A	novel	NA	P-0014983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	184	380	1	ENST00000269305.4:c.1118_1119delinsT	p.Lys373MetfsTer49	p.K373Mfs*49	ENST00000269305	NM_001126112.2	373	aAG/aT	11/11	0.351877458397039	1	FACETS	0.972	0.899	1	0.972	0.899	1	CLONAL	1	TRUE	0	0.385462493221012	1		381	793	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176153824	176153824	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014984-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	100	237	0	ENST00000367669.3:c.412A>T	p.Ile138Phe	p.I138F	ENST00000367669	NM_022457.5	138	Atc/Ttc	2/20	0.833593666790248	3	FACETS	0.571	0.511	0.635	0.286	0.255	0.318	SUBCLONAL	1	TRUE	1	0.875362877524879	3		237	575	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196805	123196806	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0014984-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	412	217	0	ENST00000218089.9:c.1692_1693del	p.Glu565AlafsTer22	p.E565Afs*22	ENST00000218089	NM_001042749.1	564	acTGag/acag	18/35	0.830670459623862	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.875362877524879	2		217	439	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	66	297	0				ENST00000310581	NM_198253.2	-/1132			0.378771266210845	1	FACETS	0.569	0.496	0.648	0.569	0.496	0.648	SUBCLONAL	1	TRUE	0	0.425550051270253	1		297	429	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0015007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	147	943	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.911	0.833	0.993	0.911	0.833	0.993	CLONAL	1	TRUE	1	0.425550051270253	2		943	758	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161330	55161330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	183	800	0	ENST00000257290.5:c.3161C>T	p.Ser1054Phe	p.S1054F	ENST00000257290	NM_006206.4	1054	tCc/tTc	23/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.425550051270253	2		800	787	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851426	156851426	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	175	1084	0	ENST00000524377.1:c.2383C>A	p.Leu795Met	p.L795M	ENST00000524377	NM_002529.3	795	Ctg/Atg	17/17	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.425550051270253	2		1084	778	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624273	89624274	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	119	619	0	ENST00000371953.3:c.48dup	p.Gln17SerfsTer27	p.Q17Sfs*27	ENST00000371953	NM_000314.4	16	tat/taTt	1/9	0.425550051270253	1	FACETS	0.891	0.809	0.977	0.891	0.809	0.977	CLONAL	1	TRUE	0	0.425550051270253	1		619	494	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416895	416895	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	99	591	0	ENST00000399788.2:c.3655C>T	p.Arg1219Ter	p.R1219*	ENST00000399788	NM_001042603.1	1219	Cga/Tga	23/28	NA	2	FACETS	0.863	0.773	0.959			1	INDETERMINATE	1	TRUE	NA	0.425550051270253	2		591	539	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434057	49434057	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	119	820	1	ENST00000301067.7:c.7496C>T	p.Pro2499Leu	p.P2499L	ENST00000301067	NM_003482.3	2499	cCc/cTc	31/54	0.183800736388139	3	FACETS	1	0.92	1	0.51	0.461	0.562	INDETERMINATE	1	TRUE	1	0.425550051270253	3		821	665	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184333	7184333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	140	774	0	ENST00000302850.5:c.968C>T	p.Ser323Phe	p.S323F	ENST00000302850	NM_000208.2	323	tCc/tTc	3/22	1	2	FACETS	0.883	0.805	0.965	0.883	0.805	0.965	CLONAL	1	TRUE	1	0.425550051270253	2		774	745	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0015061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	222	396	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.394539507614667	4	FACETS	1	0.991	1	0.727	0.676	0.779	CLONAL	1	TRUE	2	0.394539507614667	4		396	1080	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902197	151902197	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs138119145	NA	P-0015061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	48	623	0	ENST00000262189.6:c.3955G>C	p.Asp1319His	p.D1319H	ENST00000262189	NM_170606.2	1319	Gat/Cat	25/59	0.339190263139457	3	FACETS	0.349	0.294	0.41	0.174	0.147	0.205	SUBCLONAL	1	TRUE	1	0.394539507614667	3		623	835	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725119	47725119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1544	125	853	0	ENST00000449228.1:c.625C>T	p.His209Tyr	p.H209Y	ENST00000449228	NM_001127240.2	209	Cat/Tat	4/4	0.11138104339284	5	FACETS	0.604	0.545	0.668			1	INDETERMINATE	1	TRUE	NA	0.394539507614667	5		853	1669	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919214	48919214	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0015061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	57	97	0	ENST00000267163.4:c.381-2A>G		p.X127_splice	ENST00000267163	NM_000321.2	127			0.291893081143316	2	FACETS	0.892	0.782	1	0.892	0.782	1	CLONAL	2	TRUE	0	0.394539507614667	2		97	162	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95577712	95577714	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs1566782237	NA	P-0015061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	144	338	0	ENST00000393063.1:c.2196_2198del	p.Glu733del	p.E733del	ENST00000393063	NM_030621.3	732	gaAGAg/gag	15/28	0.339190263139457	3	FACETS	1	0.987	1	0.73	0.668	0.794	CLONAL	1	TRUE	1	0.394539507614667	3		338	599	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793115	42793115	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1446	231	760	0	ENST00000575354.2:c.1007G>T	p.Cys336Phe	p.C336F	ENST00000575354	NM_015125.3	336	tGt/tTt	7/20	0.11138104339284	5	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.394539507614667	5		760	1677	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982045	70982045	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1584	222	720	0	ENST00000276594.2:c.51C>A	p.Tyr17Ter	p.Y17*	ENST00000276594	NM_024504.3	17	taC/taA	2/8	0.375837911686399	4	FACETS	0.869	0.806	0.935	0.29	0.268	0.312	CLONAL	1	TRUE	1	0.394539507614667	4		720	1806	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	94	297	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.969	0.877	1	0.969	0.877	1	CLONAL	1	TRUE	1	0.788559459317151	2		297	246	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0015062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	174	480	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	1	2	FACETS	0.998	0.929	1	0.998	0.929	1	CLONAL	1	TRUE	1	0.788559459317151	2		480	442	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519896	NA	P-0015062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	9	404	1	ENST00000281708.4:c.1514G>A	p.Arg505His	p.R505H	ENST00000281708	NM_033632.3	505	cGc/cAc	10/12	1	2	FACETS	0.057	0.037	0.083	0.057	0.037	0.083	SUBCLONAL	1	TRUE	1	0.788559459317151	2		405	400	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799060	42799060	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	59	951	0	ENST00000575354.2:c.4544G>A	p.Arg1515His	p.R1515H	ENST00000575354	NM_015125.3	1515	cGc/cAc	20/20	0.788559459317151	1	FACETS	0.178	0.153	0.205	0.178	0.153	0.205	SUBCLONAL	1	TRUE	0	0.788559459317151	1		951	509	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791328	42791328	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	75	645	0	ENST00000575354.2:c.388G>T	p.Glu130Ter	p.E130*	ENST00000575354	NM_015125.3	130	Gag/Tag	3/20	0.788559459317151	1	FACETS	0.273	0.24	0.308	0.273	0.24	0.308	SUBCLONAL	1	TRUE	0	0.788559459317151	1		645	422	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796237	42796237	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	60	528	0	ENST00000575354.2:c.2887-1G>A		p.X963_splice	ENST00000575354	NM_015125.3	963			0.788559459317151	1	FACETS	0.338	0.293	0.385	0.338	0.293	0.385	SUBCLONAL	1	TRUE	0	0.788559459317151	1		528	273	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102198842	102198842	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	33	519	0	ENST00000263464.3:c.1013A>T	p.Tyr338Phe	p.Y338F	ENST00000263464	NM_001165.4	338	tAc/tTc	4/9	0.551812441424489	1	FACETS	0.209	0.17	0.253	0.209	0.17	0.253	SUBCLONAL	1	TRUE	0	0.551812441424489	1		519	415	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244937	41244937	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	59	571	1	ENST00000357654.3:c.2611C>T	p.Pro871Ser	p.P871S	ENST00000357654	NM_007294.3	871	Ccg/Tcg	10/23	1	2	FACETS	0.224	0.192	0.259	0.224	0.192	0.259	SUBCLONAL	1	TRUE	1	0.551812441424489	2		572	955	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244945	41244945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	61	577	0	ENST00000357654.3:c.2603C>T	p.Ser868Leu	p.S868L	ENST00000357654	NM_007294.3	868	tCa/tTa	10/23	1	2	FACETS	0.227	0.195	0.262	0.227	0.195	0.262	SUBCLONAL	1	TRUE	1	0.551812441424489	2		577	975	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244957	41244957	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357003	NA	P-0015063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	64	607	1	ENST00000357654.3:c.2591C>T	p.Ser864Leu	p.S864L	ENST00000357654	NM_007294.3	864	tCa/tTa	10/23	1	2	FACETS	0.234	0.202	0.269	0.234	0.202	0.269	SUBCLONAL	1	TRUE	1	0.551812441424489	2		608	992	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564822	41564822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	227	540	0	ENST00000263253.7:c.4123G>A	p.Gly1375Ser	p.G1375S	ENST00000263253	NM_001429.3	1375	Ggc/Agc	25/31	1	2	FACETS	0.906	0.845	0.969	0.906	0.845	0.969	CLONAL	1	TRUE	1	0.551812441424489	2		540	908	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	307	472	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.858526308869523	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.858526308869523	1		472	397	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564822	41564822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	312	540	0	ENST00000263253.7:c.4123G>A	p.Gly1375Ser	p.G1375S	ENST00000263253	NM_001429.3	1375	Ggc/Agc	25/31	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.858526308869523	2		540	682	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236203	108236203	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121434219	NA	P-0015063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	341	611	0	ENST00000278616.4:c.9139C>T	p.Arg3047Ter	p.R3047*	ENST00000278616	NM_000051.3	3047	Cga/Tga	63/63	0.858526308869523	1	FACETS	0.959	0.925	0.991	0.959	0.925	0.991	CLONAL	1	TRUE	0	0.858526308869523	1		611	473	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957471	175957471	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	264	464	0	ENST00000367669.3:c.1925A>G	p.Glu642Gly	p.E642G	ENST00000367669	NM_022457.5	642	gAa/gGa	17/20	0.858526308869523	4	FACETS	0.885	0.828	0.943	0.295	0.276	0.315	CLONAL	1	TRUE	1	0.858526308869523	4		464	1292	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0015066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	368	703	0	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	0.78958655187431	1	FACETS	0.835	0.801	0.868	0.835	0.801	0.868	CLONAL	1	TRUE	0	0.825659745850988	1		703	627	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914236	32914236	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs4987117	NA	P-0015066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	169	396	0	ENST00000380152.3:c.5744C>T	p.Thr1915Met	p.T1915M	ENST00000380152		1915	aCg/aTg	11/27	1	2	FACETS	0.864	0.801	0.928	0.864	0.801	0.928	CLONAL	1	TRUE	1	0.825659745850988	2		396	474	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115929	8115929	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	284	454	0	ENST00000346208.3:c.1275del	p.Ser426ProfsTer49	p.S426Pfs*49	ENST00000346208		425	ccA/cc	6/6	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.825659745850988	2		454	681	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572282	64572282	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	390	788	0	ENST00000312049.6:c.1357C>T	p.Gln453Ter	p.Q453*	ENST00000312049	NM_130799.2	453	Cag/Tag	10/10	0.825659745850988	1	FACETS	0.931	0.897	0.963	0.931	0.897	0.963	CLONAL	1	TRUE	0	0.825659745850988	1		788	596	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151871215	151871230	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CCTGCTCATCACCATT	CCTGCTCATCACCATT	-	novel	NA	P-0015066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	290	423	0	ENST00000262189.6:c.9360_9374+1del		p.X3120_splice	ENST00000262189	NM_170606.2	3120		39/59	0.784193634974139	3	FACETS	1	0.994	1	0.75	0.71	0.789	CLONAL	1	TRUE	1	0.825659745850988	3		423	662	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0015076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	20	336	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.145317922560435	4	FACETS	0.832	0.641	1			1	INDETERMINATE	1	TRUE	NA	0.458466439699956	4		336	153	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28934577	NA	P-0015076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	34	525	0	ENST00000269305.4:c.770T>C	p.Leu257Pro	p.L257P	ENST00000269305	NM_001126112.2	257	cTg/cCg	7/11	0.315813885722922	4	FACETS	1	0.945	1	0.702	0.582	0.833	CLONAL	1	TRUE	2	0.458466439699956	4		525	154	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727443	66727443	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519908	NA	P-0015076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	10	473	0	ENST00000307102.5:c.159T>G	p.Phe53Leu	p.F53L	ENST00000307102	NM_002755.3	53	ttT/ttG	2/11	0.310091458738896	6	FACETS	0.54	0.366	0.756			1	SUBCLONAL	1	TRUE	NA	0.458466439699956	6		473	155	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380346	14380346	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	21	360	1	ENST00000256196.4:c.71G>T	p.Gly24Val	p.G24V	ENST00000256196		24	gGc/gTc	1/6	0.187994936695294	3	FACETS	0.834	0.65	1	0.417	0.325	0.522	INDETERMINATE	1	TRUE	1	0.458466439699956	3		361	135	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200773	128200774	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTTCTGGCGGC	novel	NA	P-0015076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	11	487	0	ENST00000341105.2:c.1021_1031dup	p.Ala345ProfsTer46	p.A345Pfs*46	ENST00000341105	NM_032638.4	344	aga/agGCCGCCAGAAGa	5/6	NA	2	FACETS	0.444	0.309	0.609			1	INDETERMINATE	1	TRUE	NA	0.458466439699956	2		487	108	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372470	55372470	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	42	1079	0	ENST00000297316.4:c.1160A>G	p.Asn387Ser	p.N387S	ENST00000297316	NM_022454.3	387	aAt/aGt	2/2	1	2	FACETS	0.98	0.829	1	0.98	0.829	1	CLONAL	1	TRUE	1	0.458466439699956	2		1079	187	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101765	71101765	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	12	209	0	ENST00000318789.4:c.433G>T	p.Glu145Ter	p.E145*	ENST00000318789	NM_032682.5	145	Gag/Tag	9/21	0.309952953857526	5	FACETS	0.581	0.41	0.79	0.194	0.136	0.264	SUBCLONAL	1	TRUE	2	0.458466439699956	5		209	152	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	747	722	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.591234395959405	5	FACETS	0.971	0.947	0.995			1	CLONAL	4	TRUE	NA	0.737699212961549	5		722	1098	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831226	3831226	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398406959	NA	P-0015078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	168	347	0	ENST00000262367.5:c.1655C>T	p.Pro552Leu	p.P552L	ENST00000262367	NM_004380.2	552	cCg/cTg	7/31	0.687942672287466	3	FACETS	1	0.967	1	0.541	0.5	0.584	CLONAL	1	TRUE	1	0.737699212961549	3		347	576	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224493	108224493	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs748192003	NA	P-0015078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	159	169	0	ENST00000278616.4:c.8672G>A	p.Gly2891Asp	p.G2891D	ENST00000278616	NM_000051.3	2891	gGt/gAt	60/63	0.737699212961549	2	FACETS	0.967	0.917	1	0.967	0.917	1	CLONAL	2	TRUE	0	0.737699212961549	2		169	223	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087965	27087965	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0015078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	209	539	2	ENST00000324856.7:c.2251+1G>T		p.X751_splice	ENST00000324856	NM_006015.4	751			NA	2	FACETS	0.949	0.887	1			1	INDETERMINATE	1	TRUE	NA	0.737699212961549	2		541	597	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281502	49281502	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	175	495	0	ENST00000282018.3:c.549T>A	p.Ser183Arg	p.S183R	ENST00000282018	NM_020377.2	183	agT/agA	1/1	0.737699212961549	3	FACETS	1	0.945	1	0.513	0.474	0.553	CLONAL	1	TRUE	1	0.737699212961549	3		495	633	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209108313	209108313	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	121	344	0	ENST00000345146.2:c.536C>A	p.Ala179Asp	p.A179D	ENST00000345146	NM_005896.2	179	gCc/gAc	6/10	0.737699212961549	3	FACETS	0.895	0.812	0.98	0.447	0.406	0.49	CLONAL	1	TRUE	1	0.737699212961549	3		344	502	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198275	185198275	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	192	424	0	ENST00000265026.3:c.2757G>T	p.Gln919His	p.Q919H	ENST00000265026	NM_004721.4	919	caG/caT	13/14	0.737699212961549	3	FACETS	1	0.965	1	0.531	0.493	0.57	CLONAL	1	TRUE	1	0.737699212961549	3		424	671	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163255	32163255	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	1003	988	0	ENST00000375023.3:c.5971C>T	p.Gln1991Ter	p.Q1991*	ENST00000375023	NM_004557.3	1991	Caa/Taa	30/30	0.730409810739086	4	FACETS	0.981	0.958	1	0.981	0.958	1	CLONAL	3	TRUE	1	0.737699212961549	4		988	1605	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879144	151879144	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	1151	494	1	ENST00000262189.6:c.5801G>T	p.Arg1934Met	p.R1934M	ENST00000262189	NM_170606.2	1934	aGg/aTg	36/59	0.737699212961549	6	FACETS	1	0.99	1	1	0.99	1	CLONAL	6	TRUE	0	0.737699212961549	6		495	1285	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015079-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	42	493	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		493	554	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0015079-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	37	577	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		577	447	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100368	27100368	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015079-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	34	796	0	ENST00000324856.7:c.4081del	p.Met1361CysfsTer120	p.M1361Cfs*120	ENST00000324856	NM_006015.4	1360	acA/ac	17/20	0.154091564068706	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		796	548	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0015081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	409	399	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.639963105568651	3	FACETS	1	0.995	1	0.817	0.787	0.846	CLONAL	2	TRUE	0	0.694059721027073	3		399	648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0015081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	187	566	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.673476351373624	2	FACETS	0.904	0.856	0.952	0.904	0.856	0.952	CLONAL	2	TRUE	0	0.694059721027073	2		566	298	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459760	149459760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	85	512	0	ENST00000286301.3:c.447G>A	p.Met149Ile	p.M149I	ENST00000286301	NM_005211.3	149	atG/atA	4/22	0.702979488037238	1	FACETS	0.711	0.64	0.784	0.711	0.64	0.784	SUBCLONAL	1	TRUE	0	0.694059721027073	1		512	225	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814616	43814616	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	272	570	0	ENST00000372470.3:c.1411C>G	p.Gln471Glu	p.Q471E	ENST00000372470	NM_005373.2	471	Caa/Gaa	9/12	0.688283667388583	2	FACETS	0.995	0.954	1	0.995	0.954	1	CLONAL	2	TRUE	0	0.694059721027073	2		570	394	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736468	85736468	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0015081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	103	280	0	ENST00000370580.1:c.179C>G	p.Ser60Ter	p.S60*	ENST00000370580	NM_003921.4	60	tCa/tGa	2/3	0.688283667388583	2	FACETS	0.601	0.54	0.665	0.3	0.27	0.333	SUBCLONAL	1	TRUE	0	0.694059721027073	2		280	494	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456273	32456273	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	33	801	2	ENST00000332351.3:c.619G>A	p.Glu207Lys	p.E207K	ENST00000332351	NM_024426.4	207	Gag/Aag	1/10	0.702979488037238	1	FACETS	0.289	0.237	0.347	0.289	0.237	0.347	SUBCLONAL	1	TRUE	0	0.694059721027073	1		803	215	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871001	12871001	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	228	349	2	ENST00000228872.4:c.228G>T	p.Trp76Cys	p.W76C	ENST00000228872	NM_004064.3	76	tgG/tgT	1/3	0.702979488037238	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.694059721027073	1		351	323	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448320	49448320	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	59	535	0	ENST00000301067.7:c.391G>T	p.Glu131Ter	p.E131*	ENST00000301067	NM_003482.3	131	Gaa/Taa	3/54	0.427091092988298	1	FACETS	0.36	0.312	0.412	0.36	0.312	0.412	SUBCLONAL	1	TRUE	0	0.694059721027073	1		535	308	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109974	115109974	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	41	887	0	ENST00000257566.3:c.1904G>C	p.Arg635Pro	p.R635P	ENST00000257566	NM_016569.3	635	cGc/cCc	8/8	0.33648657049716	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.694059721027073	0		887	254	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563179	21563179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753049071	NA	P-0015081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	63	766	2	ENST00000382592.4:c.740C>T	p.Pro247Leu	p.P247L	ENST00000382592	NM_014572.2	247	cCg/cTg	4/8	0.469579310407919	1	FACETS	0.386	0.336	0.439	0.386	0.336	0.439	SUBCLONAL	1	TRUE	0	0.694059721027073	1		768	307	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81558915	81558915	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	155	493	0	ENST00000298171.2:c.508A>G	p.Asn170Asp	p.N170D	ENST00000298171	NM_000369.2	170	Aat/Gat	6/10	0.493902402332498	1	FACETS	0.909	0.846	0.971	0.909	0.846	0.971	CLONAL	1	TRUE	0	0.694059721027073	1		493	321	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349862	89349862	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	51	889	0	ENST00000301030.4:c.3088G>C	p.Glu1030Gln	p.E1030Q	ENST00000301030	NM_001256183.1	1030	Gag/Cag	9/13	0.398944822622504	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.694059721027073	0		889	269	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321692	30321692	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs137920170	NA	P-0015081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	172	588	0	ENST00000322652.5:c.1547G>T	p.Arg516Leu	p.R516L	ENST00000322652	NM_015355.2	516	cGc/cTc	13/16	0.486717461013606	3	FACETS	0.958	0.884	1			1	CLONAL	1	TRUE	NA	0.694059721027073	3		588	697	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602856	10602856	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	133	819	0	ENST00000171111.5:c.722G>T	p.Cys241Phe	p.C241F	ENST00000171111	NM_203500.1	241	tGc/tTc	3/6	0.702979488037238	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.694059721027073	1		819	239	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793430	42793430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144065857	NA	P-0015081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	45	454	1	ENST00000575354.2:c.1232C>T	p.Ala411Val	p.A411V	ENST00000575354	NM_015125.3	411	gCg/gTg	8/20	0.371955689832183	3	FACETS	0.517	0.436	0.606	0.258	0.218	0.303	INDETERMINATE	1	TRUE	1	0.694059721027073	3		455	338	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965835	25965846	+	inframe_deletion	In_Frame_Del	DEL	TAGTGCCCTGCC	TAGTGCCCTGCC	-	novel	NA	P-0015081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	176	477	0	ENST00000435504.4:c.3360_3371del	p.Met1120_Tyr1124delinsIle	p.M1120_Y1124delinsI	ENST00000435504		1120	atGGCAGGGCACTAc/atc	13/13	0.486717461013606	3	FACETS	0.852	0.795	0.909			1	CLONAL	2	TRUE	NA	0.694059721027073	3		477	401	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41558740	41558740	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	50	387	0	ENST00000263253.7:c.3685G>C	p.Glu1229Gln	p.E1229Q	ENST00000263253	NM_001429.3	1229	Gaa/Caa	21/31	0.673476351373624	2	FACETS	0.387	0.329	0.45	0.194	0.164	0.225	SUBCLONAL	1	TRUE	0	0.694059721027073	2		387	372	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445091	89445091	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	46	620	3	ENST00000336596.2:c.1411G>A	p.Glu471Lys	p.E471K	ENST00000336596	NM_005233.5	471	Gag/Aag	6/17	0.471939375593625	0	FACETS		NA	1			1	NA	1	TRUE	0	0.694059721027073	0		623	194	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467617	66467617	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	98	359	0	ENST00000273854.3:c.652G>C	p.Gly218Arg	p.G218R	ENST00000273854	NM_004439.5	218	Ggt/Cgt	3/18	1	2	FACETS	0.872	0.786	0.96	0.872	0.786	0.96	CLONAL	1	TRUE	1	0.694059721027073	2		359	324	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820000	32820000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs36229525	NA	P-0015081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	57	558	0	ENST00000354258.4:c.910G>A	p.Val304Met	p.V304M	ENST00000354258	NM_000593.5	304	Gtg/Atg	3/11	0.420933626683235	4	FACETS	0.461	0.395	0.533	0.23	0.197	0.267	SUBCLONAL	1	TRUE	2	0.694059721027073	4		558	604	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141557689	141557689	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	90	628	0	ENST00000220592.5:c.1626G>T	p.Met542Ile	p.M542I	ENST00000220592	NM_012154.3	542	atG/atT	13/19	0.517506779385384	1	FACETS	0.637	0.573	0.702	0.637	0.573	0.702	SUBCLONAL	1	TRUE	0	0.694059721027073	1		628	266	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786395	135786395	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	75	460	0	ENST00000298552.3:c.1135A>G	p.Thr379Ala	p.T379A	ENST00000298552	NM_001162426.1	379	Aca/Gca	11/23	0.702979488037238	1	FACETS	0.899	0.81	0.988	0.899	0.81	0.988	CLONAL	1	TRUE	0	0.694059721027073	1		460	157	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401858	139401858	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766409196	NA	P-0015081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	101	647	0	ENST00000277541.6:c.3542C>T	p.Ser1181Phe	p.S1181F	ENST00000277541	NM_017617.3	1181	tCt/tTt	22/34	0.702979488037238	1	FACETS	0.905	0.828	0.982	0.905	0.828	0.982	CLONAL	1	TRUE	0	0.694059721027073	1		647	210	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814797	139814797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144427288	NA	P-0015081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	103	641	0	ENST00000247668.2:c.790G>A	p.Ala264Thr	p.A264T	ENST00000247668	NM_021138.3	264	Gcg/Acg	8/11	0.702979488037238	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.694059721027073	1		641	187	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424249	47424249	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	71	581	0	ENST00000377045.4:c.254A>T	p.Glu85Val	p.E85V	ENST00000377045	NM_001654.4	85	gAg/gTg	4/16	0.62167398663821	1	FACETS	0.365	0.32	0.413	0.365	0.32	0.413	SUBCLONAL	1	TRUE	0	0.694059721027073	1		581	366	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428972	47428972	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	61	663	0	ENST00000377045.4:c.1335C>G	p.Ile445Met	p.I445M	ENST00000377045	NM_001654.4	445	atC/atG	13/16	0.62167398663821	1	FACETS	0.368	0.319	0.42	0.368	0.319	0.42	SUBCLONAL	1	TRUE	0	0.694059721027073	1		663	312	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223424	53223424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs971564188	NA	P-0015081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	47	660	0	ENST00000375401.3:c.3935G>A	p.Arg1312His	p.R1312H	ENST00000375401	NM_004187.3	1312	cGc/cAc	23/26	0.62167398663821	1	FACETS	0.324	0.275	0.377	0.324	0.275	0.377	SUBCLONAL	1	TRUE	0	0.694059721027073	1		660	273	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0015084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	222	376	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.171292769186294	4	FACETS	0.886	0.825	0.949	0.886	0.825	0.949	INDETERMINATE	2	TRUE	2	0.358262813109649	4		376	950	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539018	187539018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374444088	NA	P-0015084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	116	385	1	ENST00000441802.2:c.8722G>A	p.Val2908Ile	p.V2908I	ENST00000441802	NM_005245.3	2908	Gtc/Atc	10/27	1	2	FACETS	0.993	0.897	1	0.993	0.897	1	CLONAL	1	TRUE	1	0.358262813109649	2		386	652	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0015086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	21	260	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.661	0.514	0.828	0.661	0.514	0.828	SUBCLONAL	1	TRUE	1	0.43247240304182	2		260	147	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0015086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	89	435	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.994	0.887	1	0.994	0.887	1	CLONAL	1	TRUE	1	0.43247240304182	2		435	414	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437173	220437173	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746580263	NA	P-0015086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	50	715	1	ENST00000243786.2:c.77G>A	p.Arg26Gln	p.R26Q	ENST00000243786	NM_002191.3	26	cGg/cAg	1/2	1	2	FACETS	0.282	0.239	0.331	0.282	0.239	0.331	SUBCLONAL	1	TRUE	1	0.43247240304182	2		716	819	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0015092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	185	797	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.796	0.734	0.86	1	0.991	1	SUBCLONAL	2	TRUE	1	0.222751474513543	2		798	1044	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617177	100617177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555978785	NA	P-0015092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	72	809	0	ENST00000308731.7:c.572C>T	p.Thr191Met	p.T191M	ENST00000308731	NM_000061.2	191	aCg/aTg	7/19	0.184357234958143	3	FACETS	0.7	0.61	0.798	0.35	0.305	0.399	SUBCLONAL	1	TRUE	1	0.222751474513543	3		809	1026	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0015093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	66	260	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.598	0.521	0.679	0.598	0.521	0.679	SUBCLONAL	1	TRUE	1	0.585880807923751	2		260	377	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423474	116423474	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913245	NA	P-0015096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	207	693	0	ENST00000397752.3:c.3749T>C	p.Met1250Thr	p.M1250T	ENST00000397752	NM_000245.2	1250	aTg/aCg	19/21	1	2	FACETS	0.855	0.799	0.912	0.855	0.799	0.912	CLONAL	1	TRUE	1	0.833180311651218	2		693	581	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66679737	66679737	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	332	732	1	ENST00000307102.5:c.52T>A	p.Ser18Thr	p.S18T	ENST00000307102	NM_002755.3	18	Tct/Act	1/11	1	2	FACETS	0.994	0.944	1	0.994	0.944	1	CLONAL	1	TRUE	1	0.833180311651218	2		733	802	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47600677	47600677	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	261	974	0	ENST00000263735.4:c.152T>C	p.Val51Ala	p.V51A	ENST00000263735	NM_002354.2	51	gTt/gCt	2/9	1	2	FACETS	0.887	0.836	0.94	0.887	0.836	0.94	CLONAL	1	TRUE	1	0.833180311651218	2		974	706	SUCCESS
APC	324	MSKCC	GRCh37	5	112103010	112103010	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	270	736	0	ENST00000257430.4:c.345G>T	p.Met115Ile	p.M115I	ENST00000257430	NM_000038.5	115	atG/atT	4/16	1	2	FACETS	0.999	0.944	1	0.999	0.944	1	CLONAL	1	TRUE	1	0.833180311651218	2		736	649	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0015097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	44	336	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.20585891993004	3	FACETS	0.901	0.755	1	0.45	0.377	0.532	CLONAL	1	TRUE	1	0.19	3		336	563	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	50	830	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.20585891993004	3	FACETS	0.892	0.756	1	0.446	0.378	0.521	CLONAL	1	TRUE	1	0.19	3		830	646	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0015097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	72	850	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.20585891993004	3	FACETS	1	0.943	1	0.573	0.5	0.652	CLONAL	1	TRUE	1	0.19	3		850	724	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46740336	46740336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754074702	NA	P-0015097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	34	810	0	ENST00000371975.4:c.1816C>T	p.Arg606Trp	p.R606W	ENST00000371975	NM_003579.3	606	Cgg/Tgg	16/18	1	2	FACETS	0.543	0.442	0.657	0.543	0.442	0.657	SUBCLONAL	1	TRUE	1	0.19	2		810	659	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645920	67645920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567609067	NA	P-0015097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	58	918	1	ENST00000264010.4:c.848G>A	p.Arg283His	p.R283H	ENST00000264010	NM_006565.3	283	cGt/cAt	4/12	1	2	FACETS	0.814	0.698	0.941	0.814	0.698	0.941	CLONAL	1	TRUE	1	0.19	2		919	750	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939859	49939859	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766244325	NA	P-0015097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	65	1069	2	ENST00000296474.3:c.1184G>A	p.Arg395Gln	p.R395Q	ENST00000296474	NM_002447.2	395	cGg/cAg	1/20	0.20585891993004	3	FACETS	0.922	0.797	1	0.461	0.398	0.529	CLONAL	1	TRUE	1	0.19	3		1071	813	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168654	56168655	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0015097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	35	459	0	ENST00000399503.3:c.1509dup	p.Glu504ArgfsTer37	p.E504Rfs*37	ENST00000399503	NM_005921.1	503	cac/caCc	9/20	0.20585891993004	3	FACETS	0.731	0.598	0.881	0.365	0.299	0.441	SUBCLONAL	1	TRUE	1	0.19	3		459	552	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853290	151853290	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	49	599	0	ENST00000262189.6:c.11812G>A	p.Val3938Ile	p.V3938I	ENST00000262189	NM_170606.2	3938	Gtt/Att	45/59	1	2	FACETS	0.929	0.787	1	0.929	0.787	1	CLONAL	1	TRUE	1	0.19	2		599	555	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412596	139412596	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	58	741	0	ENST00000277541.6:c.1248C>G	p.Cys416Trp	p.C416W	ENST00000277541	NM_017617.3	416	tgC/tgG	7/34	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.19	2		741	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0015098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	516	1002	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.258202108103024	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	0	0.334487695680916	3		1003	1172	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	212	681	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	0.334487695680916	3	FACETS	0.861	0.801	0.923	0.861	0.801	0.923	CLONAL	2	TRUE	1	0.334487695680916	3		681	859	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934292	49934292	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	137	877	0	ENST00000296474.3:c.2215C>T	p.Pro739Ser	p.P739S	ENST00000296474	NM_002447.2	739	Ccc/Tcc	8/20	0.326019359932098	4	FACETS	0.957	0.869	1	0.319	0.289	0.351	CLONAL	1	TRUE	1	0.334487695680916	4		877	1142	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782177	NA	P-0015099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	672	972	0	ENST00000269305.4:c.644G>C	p.Ser215Thr	p.S215T	ENST00000269305	NM_001126112.2	215	aGt/aCt	6/11	0.602003791984271	2	FACETS	0.994	0.965	1	0.994	0.965	1	CLONAL	2	TRUE	0	0.602003791984271	2		972	1123	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1316	515	676	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	0.486658514213163	4	FACETS	1	0.996	1	0.748	0.715	0.782	CLONAL	1	TRUE	2	0.602003791984271	4		676	1831	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653849	89653859	+	frameshift_variant	Frame_Shift_Del	DEL	TATTGATGATG	TATTGATGATG	-	novel	NA	P-0015099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	174	529	0	ENST00000371953.3:c.149_159del	p.Ile50SerfsTer9	p.I50Sfs*9	ENST00000371953	NM_000314.4	49	aaTATTGATGATGta/aata	2/9	0.602003791984271	1	FACETS	0.908	0.845	0.972	0.908	0.845	0.972	CLONAL	1	TRUE	0	0.602003791984271	1		529	445	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437350	110437350	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	161	164	0	ENST00000375856.3:c.1051C>G	p.Pro351Ala	p.P351A	ENST00000375856	NM_003749.2	351	Ccg/Gcg	1/2	0.602003791984271	6	FACETS	0.851	0.787	0.915	0.638	0.59	0.687	CLONAL	3	TRUE	2	0.602003791984271	6		164	462	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396959	396959	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1239	335	819	1	ENST00000262320.3:c.67C>A	p.Pro23Thr	p.P23T	ENST00000262320	NM_003502.3	23	Ccc/Acc	2/11	0.561337591698483	4	FACETS	1	0.986	1	0.566	0.534	0.6	CLONAL	1	TRUE	2	0.602003791984271	4		820	1574	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042320	16042320	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0015099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	360	440	0	ENST00000268712.3:c.1352+2T>C		p.X451_splice	ENST00000268712	NM_006311.3	451			0.602003791984271	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.602003791984271	2		440	561	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249826	39249826	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	199	602	0	ENST00000402219.2:c.1743C>G	p.Asp581Glu	p.D581E	ENST00000402219	NM_005633.3	581	gaC/gaG	10/23	0.602003791984271	2	FACETS	0.904	0.84	0.97	0.452	0.42	0.485	CLONAL	1	TRUE	0	0.602003791984271	2		602	731	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46587864	46587864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1402203251	NA	P-0015099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	97	646	0	ENST00000263734.3:c.542G>A	p.Arg181His	p.R181H	ENST00000263734	NM_001430.4	181	cGt/cAt	5/16	0.602003791984271	3	FACETS	0.395	0.351	0.442	0.197	0.175	0.221	SUBCLONAL	1	TRUE	1	0.602003791984271	3		646	1062	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672836	86672836	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	152	417	0	ENST00000274376.6:c.2323G>C	p.Asp775His	p.D775H	ENST00000274376	NM_002890.2	775	Gac/Cac	17/25	0.602003791984271	3	FACETS	1	0.974	1	0.571	0.525	0.619	CLONAL	1	TRUE	1	0.602003791984271	3		417	575	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953040	2953040	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141751925	NA	P-0015099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	310	967	1	ENST00000396946.4:c.2900G>A	p.Arg967His	p.R967H	ENST00000396946	NM_032415.4	967	cGc/cAc	22/25	0.602003791984271	3	FACETS	1	0.949	1	0.504	0.474	0.535	CLONAL	1	TRUE	1	0.602003791984271	3		968	1329	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965472	68965472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200682883	NA	P-0015100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	275	897	1	ENST00000288368.4:c.1084C>T	p.Arg362Trp	p.R362W	ENST00000288368	NM_024870.2	362	Cgg/Tgg	9/40	0.602029734094496	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		898	916	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0015101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	204	435	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.837	0.784	0.889	1	0.993	1	CLONAL	2	TRUE	1	0.517757087156537	2		435	471	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932891	39932892	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0015101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	242	604	0	ENST00000378444.4:c.1706_1707dup	p.Ala570ProfsTer20	p.A570Pfs*20	ENST00000378444	NM_001123385.1	569	-/CC	4/15	1	2	FACETS	0.798	0.751	0.845	1	0.994	1	SUBCLONAL	2	TRUE	1	0.517757087156537	2		604	586	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937549	76937549	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	42	599	0	ENST00000373344.5:c.3199T>C	p.Ser1067Pro	p.S1067P	ENST00000373344	NM_000489.3	1067	Tca/Cca	9/35	1	2	FACETS	0.426	0.356	0.503	0.426	0.356	0.503	SUBCLONAL	1	TRUE	1	0.517757087156537	2		599	381	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696450	47696450	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	228	715	0	ENST00000347630.2:c.373T>G	p.Phe125Val	p.F125V	ENST00000347630	NM_001007230.1	125	Ttt/Gtt	6/11	1	2	FACETS	0.862	0.805	0.92	0.862	0.805	0.92	CLONAL	1	TRUE	1	0.630051378400351	2		715	840	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061247	38061247	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	692	952	2	ENST00000250448.2:c.742C>A	p.Pro248Thr	p.P248T	ENST00000250448	NM_004496.3	248	Ccg/Acg	2/2	0.62808108063659	3	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.630051378400351	3		954	1389	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832200	72832200	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	197	645	0	ENST00000268489.5:c.4381del	p.Gln1461AsnfsTer27	p.Q1461Nfs*27	ENST00000268489	NM_006885.3	1461	Caa/aa	9/10	1	2	FACETS	0.967	0.899	1	0.967	0.899	1	CLONAL	1	TRUE	1	0.630051378400351	2		645	647	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545952	41545954	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	rs770125372	NA	P-0015102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	321	1085	0	ENST00000263253.7:c.2573_2575del	p.Thr858del	p.T858del	ENST00000263253	NM_001429.3	856	gCAAca/gca	14/31	1	2	FACETS	0.848	0.8	0.896	0.848	0.8	0.896	CLONAL	1	TRUE	1	0.630051378400351	2		1085	1202	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0015103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	139	800	0	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.274516205900764	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.274516205900764	1		800	819	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057961	27057961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	112	825	1	ENST00000324856.7:c.1669C>T	p.Gln557Ter	p.Q557*	ENST00000324856	NM_006015.4	557	Cag/Tag	3/20	0.274516205900764	1	FACETS	0.844	0.759	0.935	0.844	0.759	0.935	CLONAL	1	TRUE	0	0.274516205900764	1		826	834	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281778	39281778	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519963	NA	P-0015103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	46	529	0	ENST00000402219.2:c.697A>T	p.Asn233Tyr	p.N233Y	ENST00000402219	NM_005633.3	233	Aat/Tat	5/23	1	2	FACETS	0.787	0.663	0.922	0.787	0.663	0.922	CLONAL	1	TRUE	1	0.274516205900764	2		529	426	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11227568	11227568	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	50	494	0	ENST00000361445.4:c.4260T>G	p.Asn1420Lys	p.N1420K	ENST00000361445	NM_004958.3	1420	aaT/aaG	29/58	0.396824380275546	0	FACETS	0.578	0.494	0.668			1	SUBCLONAL	1	TRUE	0	0.396824380275546	0		494	263	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191468	10191468	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	G	novel	NA	P-0015104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	61	459	0	ENST00000256474.2:c.464-3C>G		p.X155_splice	ENST00000256474	NM_000551.3	155			0.396824380275546	1	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	0	0.396824380275546	1		459	246	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443644	52444342	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	GCAGTAGGGAAGGACAGCCCCTGATGAGTGAGGGCGCAGGGGTGGGCCGCCACAGCCCCGGTCCGGCAGGGAGAAAAGGCTCTTACCGAAATCTTCCACGAGCAGGGTGAAGAGGCCTGGGTGGGGCGACAAGAGGAGGGGGTGATGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCCTCCTCACCTGGGTCGCTCTCCAGCTCCAGCCAGCCCTTATTCATCTTCCCGCGGGGCGGCCCCTCAGCGCCATGTCCAGGCCCTCCCTCCCCACCGCTGCCCCCACCGGGAGCCCCCACCGCCCCCGGGGCCCCTCAGTCCCACACACAGACAACGGGCCCAGTCGCGTCACCCGCCCGCGCCGGCGGCAGACGTCACCAAGGCGCGACGGCCCTGCTCCGCCTCTGGGCTCGTCTTCCGCCTGTCGGACAGCAGATGCGGGCATGCGCTCGAAGGCGAACGCGCACGCGCGGAGGGACGGGGGCGAAGGGGAGGGACGGGGGCGAAGGGGAGGGGCGGGGCGGGACGGGACGGGGGCGAAGGGGAGGGGCGGGGCGGGACGGGGGCGAAGGGGAGGGTCGGGACGAGGCGGGCGAAGGGAAGAGGGGGTCCGGGCGATGCTGAGCGCTGAGGCTCGAGAGGAGGGGCGGGACGGGCAGTACTAGGCCCGGG	GCAGTAGGGAAGGACAGCCCCTGATGAGTGAGGGCGCAGGGGTGGGCCGCCACAGCCCCGGTCCGGCAGGGAGAAAAGGCTCTTACCGAAATCTTCCACGAGCAGGGTGAAGAGGCCTGGGTGGGGCGACAAGAGGAGGGGGTGATGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCCTCCTCACCTGGGTCGCTCTCCAGCTCCAGCCAGCCCTTATTCATCTTCCCGCGGGGCGGCCCCTCAGCGCCATGTCCAGGCCCTCCCTCCCCACCGCTGCCCCCACCGGGAGCCCCCACCGCCCCCGGGGCCCCTCAGTCCCACACACAGACAACGGGCCCAGTCGCGTCACCCGCCCGCGCCGGCGGCAGACGTCACCAAGGCGCGACGGCCCTGCTCCGCCTCTGGGCTCGTCTTCCGCCTGTCGGACAGCAGATGCGGGCATGCGCTCGAAGGCGAACGCGCACGCGCGGAGGGACGGGGGCGAAGGGGAGGGACGGGGGCGAAGGGGAGGGGCGGGGCGGGACGGGACGGGGGCGAAGGGGAGGGGCGGGGCGGGACGGGGGCGAAGGGGAGGGTCGGGACGAGGCGGGCGAAGGGAAGAGGGGGTCCGGGCGATGCTGAGCGCTGAGGCTCGAGAGGAGGGGCGGGACGGGCAGTACTAGGCCCGGG	-	novel	NA	P-0015104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	40	640	0	ENST00000460680.1:c.-448_68-20del		p.X150_splice	ENST00000460680	NM_004656.3	150		1-2/17	0.396824380275546	1	FACETS	0.52	0.433	0.615	0.52	0.433	0.615	SUBCLONAL	1	TRUE	0	0.396824380275546	1		640	311	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520060	106520060	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	49	490	0	ENST00000359195.3:c.2488A>C	p.Ile830Leu	p.I830L	ENST00000359195	NM_002649.2	830	Att/Ctt	6/11	1	2	FACETS	0.784	0.667	0.911	0.784	0.667	0.911	CLONAL	1	TRUE	1	0.396824380275546	2		490	315	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696713	47696713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	143	585	0	ENST00000347630.2:c.235G>A	p.Glu79Lys	p.E79K	ENST00000347630	NM_001007230.1	79	Gaa/Aaa	5/11	0.363389946829674	4	FACETS	0.959	0.879	1	0.639	0.586	0.695	CLONAL	2	FALSE	1	0.37098785543731	4		585	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578445	7578445	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587780069	NA	P-0015105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	86	870	1	ENST00000269305.4:c.485T>G	p.Ile162Ser	p.I162S	ENST00000269305	NM_001126112.2	162	aTc/aGc	5/11	0.37098785543731	1	FACETS	0.841	0.747	0.94	0.841	0.747	0.94	CLONAL	1	FALSE	0	0.37098785543731	1		871	449	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279674	123279674	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	30	359	0	ENST00000358487.5:c.758C>T	p.Pro253Leu	p.P253L	ENST00000358487	NM_000141.4	253	cCt/cTt	7/18	1	2	FACETS	0.599	0.484	0.728	0.599	0.484	0.728	SUBCLONAL	1	FALSE	1	0.37098785543731	2		359	270	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	326	297	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.971	0.92	1	0.971	0.92	1	CLONAL	1	TRUE	1	0.737915919055346	2		297	910	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510207	187510207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	479	659	0	ENST00000441802.2:c.13306C>T	p.Pro4436Ser	p.P4436S	ENST00000441802	NM_005245.3	4436	Cct/Tct	27/27	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.737915919055346	2		659	1280	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0015106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	945	757	1	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.688300910454053	5	FACETS	0.92	0.898	0.941	0.92	0.898	0.941	CLONAL	4	TRUE	1	0.737915919055346	5		758	1467	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993546	72993546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	441	630	0	ENST00000268489.5:c.499C>T	p.Pro167Ser	p.P167S	ENST00000268489	NM_006885.3	167	Ccc/Tcc	2/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.737915919055346	2		630	1137	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262739	16262739	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	232	370	1	ENST00000375759.3:c.10004C>T	p.Ser3335Phe	p.S3335F	ENST00000375759	NM_015001.2	3335	tCc/tTc	11/15	1	2	FACETS	0.929	0.871	0.988	0.929	0.871	0.988	CLONAL	1	TRUE	1	0.737915919055346	2		371	677	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087940	27087940	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	590	908	2	ENST00000324856.7:c.2227C>T	p.Gln743Ter	p.Q743*	ENST00000324856	NM_006015.4	743	Caa/Taa	6/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.737915919055346	2		910	1554	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097754	27097754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	407	734	3	ENST00000324856.7:c.3343C>T	p.Pro1115Ser	p.P1115S	ENST00000324856	NM_006015.4	1115	Cca/Tca	12/20	1	2	FACETS	0.885	0.842	0.928	0.885	0.842	0.928	CLONAL	1	TRUE	1	0.737915919055346	2		737	1247	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163295954	163295954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766669864	NA	P-0015106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	300	908	1	ENST00000271452.3:c.113C>T	p.Pro38Leu	p.P38L	ENST00000271452	NM_145697.2	38	cCa/cTa	2/14	1	2	FACETS	0.982	0.929	1	0.982	0.929	1	CLONAL	1	TRUE	1	0.737915919055346	2		909	828	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129437	64129438	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	517	933	0	ENST00000334205.4:c.874dup	p.Ala292GlyfsTer78	p.A292Gfs*78	ENST00000334205	NM_003942.2	290	cag/caGg	8/17	1	2	FACETS	0.919	0.881	0.959	0.919	0.881	0.959	CLONAL	1	TRUE	1	0.737915919055346	2		933	1524	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434445	49434445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1028524252	NA	P-0015106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	552	918	1	ENST00000301067.7:c.7108C>T	p.Arg2370Cys	p.R2370C	ENST00000301067	NM_003482.3	2370	Cgc/Tgc	31/54	1	2	FACETS	0.942	0.904	0.981	0.942	0.904	0.981	CLONAL	1	TRUE	1	0.737915919055346	2		919	1588	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134653	2134653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752693719	NA	P-0015106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	552	869	0	ENST00000219476.3:c.4430G>A	p.Arg1477Lys	p.R1477K	ENST00000219476	NM_000548.3	1477	aGg/aAg	34/42	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.737915919055346	2		869	1496	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031873	10031873	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	344	624	0	ENST00000330684.3:c.950A>C	p.Lys317Thr	p.K317T	ENST00000330684	NM_001134407.1	317	aAg/aCg	3/13	1	2	FACETS	0.849	0.804	0.895	0.849	0.804	0.895	CLONAL	1	TRUE	1	0.737915919055346	2		624	1098	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662307	67662308	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	299	572	0	ENST00000264010.4:c.1553_1554delinsTT	p.Thr518Ile	p.T518I	ENST00000264010	NM_006565.3	518	aCC/aTT	9/12	1	2	FACETS	0.905	0.855	0.957	0.905	0.855	0.957	CLONAL	1	TRUE	1	0.737915919055346	2		572	895	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350791	15350791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	735	919	1	ENST00000263377.2:c.3212C>T	p.Pro1071Leu	p.P1071L	ENST00000263377	NM_058243.2	1071	cCc/cTc	15/20	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.737915919055346	2		920	1754	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218158	36218158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1311138959	NA	P-0015106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	264	467	1	ENST00000222270.7:c.4105G>A	p.Glu1369Lys	p.E1369K	ENST00000222270	NM_014727.1	1369	Gag/Aag	15/37	1	2	FACETS	0.938	0.883	0.994	0.938	0.883	0.994	CLONAL	1	TRUE	1	0.737915919055346	2		468	763	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082336	16082336	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	517	1037	0	ENST00000281043.3:c.150G>A	p.Trp50Ter	p.W50*	ENST00000281043	NM_005378.4	50	tgG/tgA	2/3	1	2	FACETS	0.921	0.882	0.961	0.921	0.882	0.961	CLONAL	1	TRUE	1	0.737915919055346	2		1037	1521	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025939	48025939	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587779948	NA	P-0015106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	328	528	0	ENST00000234420.5:c.817G>A	p.Gly273Arg	p.G273R	ENST00000234420	NM_000179.2	273	Gga/Aga	4/10	1	2	FACETS	0.95	0.9	1	0.95	0.9	1	CLONAL	1	TRUE	1	0.737915919055346	2		528	936	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881510	111881510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376019476	NA	P-0015106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	400	630	0	ENST00000393256.3:c.188C>T	p.Pro63Leu	p.P63L	ENST00000393256	NM_006538.4	63	cCg/cTg	2/4	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.737915919055346	2		630	960	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41521946	41521946	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550476180	NA	P-0015106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	476	891	1	ENST00000263253.7:c.808C>T	p.Leu270Phe	p.L270F	ENST00000263253	NM_001429.3	270	Ctt/Ttt	3/31	1	2	FACETS	0.952	0.911	0.994	0.952	0.911	0.994	CLONAL	1	TRUE	1	0.737915919055346	2		892	1355	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293799	1293799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs539667998	NA	P-0015106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	537	954	3	ENST00000310581.5:c.1202C>T	p.Ala401Val	p.A401V	ENST00000310581	NM_198253.2	401	gCg/gTg	2/16	1	2	FACETS	0.963	0.923	1	0.963	0.923	1	CLONAL	1	TRUE	1	0.737915919055346	2		957	1512	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673271	30673271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1204	454	653	0	ENST00000376406.3:c.3689G>A	p.Gly1230Glu	p.G1230E	ENST00000376406	NM_014641.2	1230	gGa/gAa	10/15	0.712395931681878	3	FACETS	1	0.966	1	0.508	0.484	0.533	CLONAL	1	TRUE	1	0.737915919055346	3		653	1658	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109311846	109311846	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0015106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	332	715	0	ENST00000436639.2:c.1424+2T>C		p.X475_splice	ENST00000436639	NM_014454.2	475			1	2	FACETS	0.958	0.908	1	0.958	0.908	1	CLONAL	1	TRUE	1	0.737915919055346	2		715	939	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467934	50467934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	324	517	2	ENST00000331340.3:c.1169C>T	p.Pro390Leu	p.P390L	ENST00000331340	NM_006060.4	390	cCg/cTg	8/8	1	2	FACETS	0.976	0.925	1	0.976	0.925	1	CLONAL	1	TRUE	1	0.737915919055346	2		519	900	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964488	70964488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	510	879	2	ENST00000276594.2:c.1540G>A	p.Glu514Lys	p.E514K	ENST00000276594	NM_024504.3	514	Gag/Aag	8/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.737915919055346	2		881	1287	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650802	93650802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	40	499	0	ENST00000375746.1:c.1728G>A	p.Met576Ile	p.M576I	ENST00000375746	NM_001174167.1	576	atG/atA	13/14	0.737915919055346	1	FACETS	0.163	0.135	0.193	0.163	0.135	0.193	SUBCLONAL	1	TRUE	0	0.737915919055346	1		499	421	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437669	52437669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	299	977	0	ENST00000460680.1:c.1492G>A	p.Glu498Lys	p.E498K	ENST00000460680	NM_004656.3	498	Gag/Aag	13/17	0.654700845307265	1	FACETS	0.965	0.916	1	0.965	0.916	1	CLONAL	1	TRUE	0	0.654700845307265	1		977	637	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257229	16257229	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	171	946	0	ENST00000375759.3:c.4494G>C	p.Lys1498Asn	p.K1498N	ENST00000375759	NM_015001.2	1498	aaG/aaC	11/15	1	2	FACETS	0.769	0.71	0.831	0.769	0.71	0.831	SUBCLONAL	1	TRUE	1	0.654700845307265	2		946	679	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427906	49427906	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	310	1065	0	ENST00000301067.7:c.10684G>T	p.Glu3562Ter	p.E3562*	ENST00000301067	NM_003482.3	3562	Gag/Tag	38/54	1	2	FACETS	0.966	0.913	1	0.966	0.913	1	CLONAL	1	TRUE	1	0.654700845307265	2		1065	980	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441789	49441789	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	344	1085	3	ENST00000301067.7:c.4195C>T	p.Gln1399Ter	p.Q1399*	ENST00000301067	NM_003482.3	1399	Cag/Tag	14/54	1	2	FACETS	0.963	0.913	1	0.963	0.913	1	CLONAL	1	TRUE	1	0.654700845307265	2		1088	1091	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715959	52715959	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0015107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	179	840	0	ENST00000322088.6:c.524C>G	p.Ser175Ter	p.S175*	ENST00000322088	NM_014225.5	175	tCa/tGa	5/15	1	2	FACETS	0.693	0.64	0.748	0.693	0.64	0.748	SUBCLONAL	1	TRUE	1	0.654700845307265	2		840	789	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436815	52436815	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	310	1116	0	ENST00000460680.1:c.1963G>C	p.Glu655Gln	p.E655Q	ENST00000460680	NM_004656.3	655	Gag/Cag	15/17	0.654700845307265	1	FACETS	0.877	0.833	0.922	0.877	0.833	0.922	CLONAL	1	TRUE	0	0.654700845307265	1		1116	726	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437169	52437171	+	frameshift_variant	Frame_Shift_Del	DEL	CTC	CTC	TA	novel	NA	P-0015107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	224	1031	1	ENST00000460680.1:c.1873_1875delinsTA	p.Glu625Ter	p.E625*	ENST00000460680	NM_004656.3	625	GAG/TA	14/17	0.654700845307265	1	FACETS	0.834	0.783	0.885	0.834	0.783	0.885	CLONAL	1	TRUE	0	0.654700845307265	1		1032	552	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549788	187549788	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	182	774	0	ENST00000441802.2:c.4453G>A	p.Glu1485Lys	p.E1485K	ENST00000441802	NM_005245.3	1485	Gag/Aag	8/27	0.647946165817132	1	FACETS	0.635	0.589	0.682	0.635	0.589	0.682	SUBCLONAL	1	TRUE	0	0.654700845307265	1		774	589	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818230	32818230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147332077	NA	P-0015107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	296	1024	0	ENST00000354258.4:c.1295C>T	p.Ser432Leu	p.S432L	ENST00000354258	NM_000593.5	432	tCg/tTg	5/11	1	2	FACETS	0.912	0.86	0.966	0.912	0.86	0.966	CLONAL	1	TRUE	1	0.654700845307265	2		1024	991	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169582	27169582	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	318	1176	1	ENST00000380036.4:c.583G>A	p.Gly195Arg	p.G195R	ENST00000380036	NM_000459.3	195	Gga/Aga	4/23	1	2	FACETS	0.962	0.909	1	0.962	0.909	1	CLONAL	1	TRUE	1	0.654700845307265	2		1177	1010	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413166	139413166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564200310	NA	P-0015107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	878	1366	2	ENST00000277541.6:c.976G>A	p.Gly326Ser	p.G326S	ENST00000277541	NM_017617.3	326	Ggc/Agc	6/34	0.581192765596748	3	FACETS	0.952	0.924	0.98	0.952	0.924	0.98	CLONAL	2	TRUE	1	0.654700845307265	3		1368	1870	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	150	722	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.318344280990204	2		722	879	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577501	7577501	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	rs1427471466	NA	P-0015108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	123	945	1	ENST00000269305.4:c.780del	p.Ser261ValfsTer84	p.S261Vfs*84	ENST00000269305	NM_001126112.2	260	tcC/tc	7/11	0.318344280990204	1	FACETS	0.893	0.808	0.982	0.893	0.808	0.982	CLONAL	1	TRUE	0	0.318344280990204	1		946	728	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016558	12016558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	64	601	1	ENST00000353533.5:c.694C>T	p.Pro232Ser	p.P232S	ENST00000353533	NM_003010.3	232	Cct/Tct	7/11	0.318344280990204	1	FACETS	0.792	0.688	0.904	0.792	0.688	0.904	CLONAL	1	TRUE	0	0.318344280990204	1		602	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0015109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	649	902	1	ENST00000269305.4:c.97-1G>A		p.X33_splice	ENST00000269305	NM_001126112.2	33			NA	2	FACETS	0.993	0.979	1			1	INDETERMINATE	2	TRUE	NA	0.925307232558383	2		903	706	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875920	76875920	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	440	442	1	ENST00000373344.5:c.5215C>T	p.Arg1739Ter	p.R1739*	ENST00000373344	NM_000489.3	1739	Cga/Tga	20/35	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.925307232558383	1		443	468	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114801	108114810	+	frameshift_variant	Frame_Shift_Del	DEL	TTCCAAATTT	TTCCAAATTT	-	novel	NA	P-0015110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	321	821	0	ENST00000278616.4:c.620_629del	p.Ser207TrpfsTer20	p.S207Wfs*20	ENST00000278616	NM_000051.3	206	aaTTCCAAATTT/aa	6/63	0.630495896618841	4	FACETS	0.893	0.846	0.94	0.893	0.846	0.94	CLONAL	2	TRUE	2	0.711029121054497	4		821	865	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0015112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	149	577	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	0.3	2		577	782	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0015112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	89	592	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.243232219723426	1	FACETS	0.578	0.512	0.65	0.578	0.512	0.65	SUBCLONAL	1	TRUE	0	0.3	1		592	872	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044550	47044550	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	217	1273	1	ENST00000377604.3:c.2047G>T	p.Glu683Ter	p.E683*	ENST00000377604	NM_001204468.1	683	Gag/Tag	18/24	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.3	2		1274	1300	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187560904	187560904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758878500	NA	P-0015112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	128	686	1	ENST00000441802.2:c.3614G>A	p.Arg1205Gln	p.R1205Q	ENST00000441802	NM_005245.3	1205	cGa/cAa	4/27	1	2	FACETS	0.942	0.853	1	0.942	0.853	1	CLONAL	1	TRUE	1	0.3	2		687	906	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163617	47163618	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACAT	novel	NA	P-0015112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	87	599	0	ENST00000409792.3:c.2505_2508dup	p.Asp837MetfsTer2	p.D837Mfs*2	ENST00000409792	NM_014159.6	836	-/ATGT	3/21	1	2	FACETS	0.976	0.866	1	0.976	0.866	1	CLONAL	1	TRUE	1	0.3	2		599	594	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165333	47165333	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	78	518	0	ENST00000409792.3:c.793del	p.Glu265AsnfsTer3	p.E265Nfs*3	ENST00000409792	NM_014159.6	265	Gaa/aa	3/21	1	2	FACETS	0.877	0.771	0.99	0.877	0.771	0.99	CLONAL	1	TRUE	1	0.3	2		518	593	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524631	187524631	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	182	1061	2	ENST00000441802.2:c.11049G>T	p.Leu3683Phe	p.L3683F	ENST00000441802	NM_005245.3	3683	ttG/ttT	19/27	1	2	FACETS	0.911	0.838	0.987	0.911	0.838	0.987	CLONAL	1	TRUE	1	0.3	2		1063	1332	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535442	187535442	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	99	645	0	ENST00000441802.2:c.9132G>C	p.Gln3044His	p.Q3044H	ENST00000441802	NM_005245.3	3044	caG/caC	12/27	1	2	FACETS	0.898	0.802	1	0.898	0.802	1	CLONAL	1	TRUE	1	0.3	2		645	735	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120456	94120456	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	116	710	0	ENST00000369303.4:c.595A>G	p.Lys199Glu	p.K199E	ENST00000369303	NM_004440.3	199	Aaa/Gaa	3/17	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.3	2		710	766	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356438	70356438	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	167	1172	1	ENST00000374080.3:c.5333G>T	p.Ser1778Ile	p.S1778I	ENST00000374080		1778	aGt/aTt	37/45	1	2	FACETS	0.849	0.778	0.924	0.849	0.778	0.924	CLONAL	1	TRUE	1	0.3	2		1173	1311	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0015113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	169	638	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.995	0.915	1	0.995	0.915	1	CLONAL	1	TRUE	1	0.397860381317981	2		638	854	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052636	42052636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1054243525	NA	P-0015113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	248	856	3	ENST00000219905.7:c.7307G>A	p.Arg2436His	p.R2436H	ENST00000219905	NM_001164273.1	2436	cGt/cAt	20/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.397860381317981	2		859	1179	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0015113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	185	358	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.968	0.893	1	0.968	0.893	1	CLONAL	1	TRUE	1	0.397860381317981	2		358	961	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717715	89717716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587782341	NA	P-0015113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	224	840	2	ENST00000371953.3:c.741dup	p.Pro248ThrfsTer5	p.P248Tfs*5	ENST00000371953	NM_000314.4	247	tta/ttAa	7/9	0.376971592485395	3	FACETS	1	0.953	1	0.517	0.48	0.555	CLONAL	1	TRUE	1	0.397860381317981	3		842	1306	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222925	5222925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749356058	NA	P-0015113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	272	1099	5	ENST00000357368.4:c.2878G>A	p.Gly960Arg	p.G960R	ENST00000357368	NM_002850.3	960	Ggg/Agg	18/38	1	2	FACETS	0.992	0.929	1	0.992	0.929	1	CLONAL	1	TRUE	1	0.397860381317981	2		1104	1378	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624242	89624242	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	172	343	0	ENST00000371953.3:c.16A>G	p.Lys6Glu	p.K6E	ENST00000371953	NM_000314.4	6	Aaa/Gaa	1/9	0.376971592485395	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	1	0.397860381317981	3		343	506	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087911	27087911	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	600	1210	0	ENST00000324856.7:c.2198del	p.Ser733TrpfsTer9	p.S733Wfs*9	ENST00000324856	NM_006015.4	733	tCg/tg	6/20	0.397549969192513	2	FACETS	0.91	0.875	0.946	0.91	0.875	0.946	CLONAL	2	TRUE	0	0.397860381317981	2		1210	1657	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913294	NA	P-0015113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	393	902	3	ENST00000371953.3:c.518G>T	p.Arg173Leu	p.R173L	ENST00000371953	NM_000314.4	173	cGc/cTc	6/9	0.376971592485395	3	FACETS	0.93	0.884	0.977	0.93	0.884	0.977	CLONAL	2	TRUE	1	0.397860381317981	3		905	1273	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447416	49447416	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	242	998	2	ENST00000301067.7:c.682C>A	p.Arg228Ser	p.R228S	ENST00000301067	NM_003482.3	228	Cgc/Agc	6/54	1	2	FACETS	0.902	0.841	0.966	0.902	0.841	0.966	CLONAL	1	TRUE	1	0.397860381317981	2		1000	1348	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645309	67645310	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	231	1013	2	ENST00000264010.4:c.579dup	p.Asp194ArgfsTer36	p.D194Rfs*36	ENST00000264010	NM_006565.3	192	caa/cAaa	3/12	1	2	FACETS	0.87	0.809	0.933	0.87	0.809	0.933	CLONAL	1	TRUE	1	0.397860381317981	2		1015	1335	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589637	67589859	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATGAAGAATATACCCGCACATCCCAGGTGAGTTTTCTATGAAAATCAGATTAAAAAATAAGAGTTCTAAACTTTTAAAGACTAACATGGAAAAAAGAATTTAAAAGGTTGAGTTTTTACGAATGAGGTGGGGGTGAGAGCATTTATTTGTGAATCATTGTTGATTATTCTAGTGTAATATCTCTAAAGCTTTAAACCAAAAATTTTAAGTATCAGAATAATAA	ATGAAGAATATACCCGCACATCCCAGGTGAGTTTTCTATGAAAATCAGATTAAAAAATAAGAGTTCTAAACTTTTAAAGACTAACATGGAAAAAAGAATTTAAAAGGTTGAGTTTTTACGAATGAGGTGGGGGTGAGAGCATTTATTTGTGAATCATTGTTGATTATTCTAGTGTAATATCTCTAAAGCTTTAAACCAAAAATTTTAAGTATCAGAATAATAA	-	novel	NA	P-0015113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	43	606	0	ENST00000274335.5:c.1402_1425+199del		p.X468_splice	ENST00000274335		468		10/15	1	2	FACETS	0.331	0.276	0.392	0.331	0.276	0.392	SUBCLONAL	1	TRUE	1	0.397860381317981	2		606	653	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591105	+	inframe_deletion	In_Frame_Del	DEL	AACAGCATT	AACAGCATT	-	novel	NA	P-0015113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	146	676	1	ENST00000274335.5:c.1692_1700del	p.Asn564_Ile566del	p.N564_I566del	ENST00000274335		564	AACAGCATT/-	12/15	1	2	FACETS	0.886	0.809	0.967	0.886	0.809	0.967	CLONAL	1	TRUE	1	0.397860381317981	2		677	828	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149447846	149447846	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1221	307	1288	2	ENST00000286301.3:c.1558G>C	p.Val520Leu	p.V520L	ENST00000286301	NM_005211.3	520	Gtc/Ctc	11/22	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.397860381317981	2		1290	1528	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0015114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	241	649	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.3	4	FACETS	0.965	0.903	1	0.965	0.903	1	CLONAL	3	TRUE	1	0.23	4		649	890	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589765	69589765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	29	290	2	ENST00000168712.1:c.88G>A	p.Ala30Thr	p.A30T	ENST00000168712	NM_002007.2	30	Gcc/Acc	1/3	1	2	FACETS	0.704	0.566	0.862	0.704	0.566	0.862	SUBCLONAL	1	TRUE	1	0.23	2		292	358	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434793	99434793	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201529410	NA	P-0015114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	183	990	1	ENST00000268035.6:c.880G>A	p.Glu294Lys	p.E294K	ENST00000268035	NM_000875.3	294	Gag/Aag	3/21	0.213699674177384	3	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	1	0.23	3		991	887	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119873	70119874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0015114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	115	1558	0	ENST00000245479.2:c.876dup	p.Glu293ArgfsTer3	p.E293Rfs*3	ENST00000245479	NM_000346.3	292	aac/aaCc	3/3	1	2	FACETS	0.892	0.802	0.988	0.892	0.802	0.988	CLONAL	1	TRUE	1	0.23	2		1558	1121	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223032	5223032	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370088739	NA	P-0015114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	226	1403	1	ENST00000357368.4:c.2771C>T	p.Pro924Leu	p.P924L	ENST00000357368	NM_002850.3	924	cCg/cTg	18/38	0.213699674177384	3	FACETS	0.939	0.873	1	0.939	0.873	1	CLONAL	2	TRUE	1	0.23	3		1404	1167	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25459802	25459802	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	novel	NA	P-0015114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	200	1028	0	ENST00000264709.3:c.2478+3C>T		p.X826_splice	ENST00000264709	NM_175629.2	826			0.171742468185833	3	FACETS	0.99	0.918	1	0.99	0.918	1	CLONAL	2	TRUE	1	0.23	3		1028	979	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	42	607	0	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	1	2	FACETS	0.857	0.717	1	0.857	0.717	1	CLONAL	1	TRUE	1	0.23	2		607	426	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852242	128852242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140172891	NA	P-0015114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	115	1582	1	ENST00000249373.3:c.2314C>T	p.Arg772Cys	p.R772C	ENST00000249373	NM_005631.4	772	Cgc/Tgc	12/12	0.129476265924597	5	FACETS	1	0.94	1	0.355	0.319	0.394	INDETERMINATE	1	TRUE	2	0.23	5		1583	1262	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589607	67589609	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0015115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	215	304	0	ENST00000274335.5:c.1372_1374del	p.Glu458del	p.E458del	ENST00000274335		457	cAAGaa/caa	10/15	0.149980815009215	3	FACETS	1	0.988	1	0.631	0.588	0.676	INDETERMINATE	1	TRUE	1	0.53	3		304	813	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0015115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	112	615	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.881	0.796	0.969	0.881	0.796	0.969	CLONAL	1	TRUE	1	0.53	2		615	480	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881392	37881392	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	185	1332	0	ENST00000269571.5:c.2584A>G	p.Thr862Ala	p.T862A	ENST00000269571		862	Aca/Gca	21/27	1	2	FACETS	0.99	0.917	1	0.99	0.917	1	CLONAL	1	TRUE	1	0.53	2		1332	705	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105565	27105565	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	139	833	0	ENST00000324856.7:c.5176G>T	p.Glu1726Ter	p.E1726*	ENST00000324856	NM_006015.4	1726	Gag/Tag	20/20	1	2	FACETS	0.949	0.868	1	0.949	0.868	1	CLONAL	1	TRUE	1	0.53	2		833	553	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692929	89692929	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1554898159	NA	P-0015115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	199	1012	0	ENST00000371953.3:c.413A>G	p.Tyr138Cys	p.Y138C	ENST00000371953	NM_000314.4	138	tAt/tGt	5/9	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.53	2		1012	751	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174411	11174411	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	217	1245	0	ENST00000361445.4:c.7264G>C	p.Val2422Leu	p.V2422L	ENST00000361445	NM_004958.3	2422	Gtc/Ctc	53/58	0.3	1	FACETS	0.866	0.809	0.925	0.866	0.809	0.925	INDETERMINATE	1	TRUE	0	0.53	1		1245	695	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720754	89720755	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0015115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	16	358	0	ENST00000371953.3:c.906dup	p.Ile303HisfsTer9	p.I303Hfs*9	ENST00000371953	NM_000314.4	302	agc/agCc	8/9	1	2	FACETS	0.285	0.211	0.373	0.285	0.211	0.373	SUBCLONAL	1	TRUE	1	0.53	2		358	212	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662278	67662289	+	frameshift_variant	Frame_Shift_Del	DEL	GCACATGATCAT	GCACATGATCAT	AG	novel	NA	P-0015115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	61	659	2	ENST00000264010.4:c.1524_1535delinsAG	p.His509GlyfsTer72	p.H509Gfs*72	ENST00000264010	NM_006565.3	508	agGCACATGATCATg/agAGg	9/12	1	2	FACETS	0.604	0.523	0.691	0.604	0.523	0.691	SUBCLONAL	1	TRUE	1	0.53	2		661	381	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008485	70008485	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	221	990	0	ENST00000394351.3:c.772C>T	p.Gln258Ter	p.Q258*	ENST00000394351	NM_000248.3	258	Caa/Taa	8/9	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.53	2		990	815	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402522	139402522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1336014812	NA	P-0015115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	131	1235	3	ENST00000277541.6:c.3395G>A	p.Arg1132His	p.R1132H	ENST00000277541	NM_017617.3	1132	cGc/cAc	21/34	0.3	1	FACETS	0.724	0.661	0.789	0.724	0.661	0.789	INDETERMINATE	1	TRUE	0	0.53	1		1238	502	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	370	676	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	0.580144550562051	3	FACETS	1	0.995	1	0.722	0.686	0.758	CLONAL	1	TRUE	1	0.661631245757486	3		676	1031	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100189	27100189	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	163	404	1	ENST00000324856.7:c.3985C>T	p.Gln1329Ter	p.Q1329*	ENST00000324856	NM_006015.4	1329	Cag/Tag	16/20	1	2	FACETS	0.797	0.735	0.862	0.797	0.735	0.862	SUBCLONAL	1	TRUE	1	0.661631245757486	2		405	618	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239876	41239876	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	196	471	0	ENST00000379561.5:c.474C>G	p.Asn158Lys	p.N158K	ENST00000379561	NM_002015.3	158	aaC/aaG	1/3	0.543756478998357	2	FACETS	0.865	0.804	0.928	0.432	0.402	0.464	CLONAL	1	TRUE	0	0.661631245757486	2		471	685	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0015116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	360	439	0	ENST00000269305.4:c.673-2A>C		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.514085475170373	2	FACETS	0.772	0.738	0.806	0.772	0.738	0.806	SUBCLONAL	2	TRUE	0	0.661631245757486	2		439	705	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876518	59876518	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs779237423	NA	P-0015116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1527	113	452	0	ENST00000259008.2:c.1283A>C	p.Asn428Thr	p.N428T	ENST00000259008	NM_032043.2	428	aAt/aCt	9/20	0.661631245757486	6	FACETS	0.484	0.433	0.538	0.121	0.108	0.135	SUBCLONAL	1	TRUE	2	0.661631245757486	6		452	1640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577575	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587782289	NA	P-0015117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	467	511	0	ENST00000269305.4:c.706T>G	p.Tyr236Asp	p.Y236D	ENST00000269305	NM_001126112.2	236	Tac/Gac	7/11	0.853198500194166	1	FACETS	0.993	0.965	1	0.993	0.965	1	CLONAL	1	TRUE	0	0.853198500194166	1		511	632	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472592	88472592	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	292	367	0	ENST00000360948.2:c.1963C>A	p.Gln655Lys	p.Q655K	ENST00000360948	NM_001012338.2	655	Caa/Aaa	16/19	0.853198500194166	1	FACETS	0.962	0.925	0.997	0.962	0.925	0.997	CLONAL	1	TRUE	0	0.853198500194166	1		367	408	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584533	189584533	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	38	458	0	ENST00000264731.3:c.829G>C	p.Glu277Gln	p.E277Q	ENST00000264731	NM_003722.4	277	Gaa/Caa	6/14	0.853198500194166	1	FACETS	0.089	0.073	0.107	0.089	0.073	0.107	SUBCLONAL	1	TRUE	0	0.853198500194166	1		458	572	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0015118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	358	428	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	0.938	0.892	0.986	0.938	0.892	0.986	CLONAL	1	TRUE	1	0.784189085356622	2		428	973	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs775623976	NA	P-0015118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	291	297	0	ENST00000335508.6:c.1873C>G	p.Arg625Gly	p.R625G	ENST00000335508	NM_012433.2	625	Cgt/Ggt	14/25	1	2	FACETS	0.911	0.86	0.962	0.911	0.86	0.962	CLONAL	1	TRUE	1	0.784189085356622	2		297	815	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0015119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	20	376	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.398509842943304	4	FACETS	0.152	0.115	0.195	0.051	0.038	0.065	SUBCLONAL	1	TRUE	1	0.398509842943304	4		376	924	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0015119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	334	510	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.398509842943304	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.398509842943304	1		510	1116	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0015119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	92	730	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.363136820365738	1	FACETS	0.683	0.609	0.763	0.683	0.609	0.763	SUBCLONAL	1	TRUE	0	0.398509842943304	1		730	541	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0015119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	154	367	1	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.398509842943304	1	FACETS	0.9	0.825	0.977	0.9	0.825	0.977	CLONAL	1	TRUE	0	0.398509842943304	1		368	688	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	14	296	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	0.398509842943304	1	FACETS	0.106	0.076	0.143	0.106	0.076	0.143	SUBCLONAL	1	TRUE	0	0.398509842943304	1		296	529	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951053	48951053	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs587778831	NA	P-0015119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	83	167	0	ENST00000267163.4:c.1216-1G>A		p.X406_splice	ENST00000267163	NM_000321.2	406			0.398509842943304	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.398509842943304	1		167	324	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777978	27777978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	44	219	0	ENST00000369163.2:c.127C>T	p.Arg43Trp	p.R43W	ENST00000369163	NM_003536.2	43	Cgg/Tgg	1/1	0.267993470003652	3	FACETS	0.466	0.39	0.55	0.233	0.195	0.275	SUBCLONAL	1	TRUE	1	0.398509842943304	3		219	568	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618717	37618738	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAAGCCAAGAAGTCTCCAGC	AAAAAGCCAAGAAGTCTCCAGC	-	novel	NA	P-0015119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	166	439	0	ENST00000447079.4:c.395_416del	p.Lys132SerfsTer5	p.K132Sfs*5	ENST00000447079	NM_015083.1	131	gaAAAAAGCCAAGAAGTCTCCAGC/ga	1/14	1	2	FACETS	0.796	0.731	0.865	0.796	0.731	0.865	SUBCLONAL	1	TRUE	1	0.398509842943304	2		439	1046	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867041	45867042	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	92	434	0	ENST00000391945.4:c.1077dup	p.Gly360ArgfsTer18	p.G360Rfs*18	ENST00000391945	NM_000400.3	359	-/C	11/23	0.398509842943304	3	FACETS	0.444	0.393	0.499	0.222	0.196	0.25	SUBCLONAL	1	TRUE	1	0.398509842943304	3		434	1248	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464485	25464510	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCACCATGCCCACCGTGATGGAGT	CCGCACCATGCCCACCGTGATGGAGT	-	novel	NA	P-0015119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	119	433	0	ENST00000264709.3:c.2003_2028del	p.Asp668AlafsTer36	p.D668Afs*36	ENST00000264709	NM_175629.2	668	gACTCCATCACGGTGGGCATGGTGCGG/g	17/23	1	2	FACETS	0.633	0.57	0.699	0.633	0.57	0.699	SUBCLONAL	1	TRUE	1	0.398509842943304	2		433	944	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433543	138433543	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1205885222	NA	P-0015119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	123	328	0	ENST00000289153.2:c.1069C>G	p.Leu357Val	p.L357V	ENST00000289153	NM_006219.2	357	Ctt/Gtt	7/22	0.398509842943304	4	FACETS	1	0.946	1	0.356	0.322	0.392	CLONAL	1	TRUE	1	0.398509842943304	4		328	808	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047888	180047888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	246	629	2	ENST00000261937.6:c.2287G>A	p.Val763Met	p.V763M	ENST00000261937	NM_182925.4	763	Gtg/Atg	15/30	1	2	FACETS	0.99	0.924	1	0.99	0.924	1	CLONAL	1	TRUE	1	0.398509842943304	2		631	1247	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790803	89790803	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	169	567	0	ENST00000336032.3:c.190G>C	p.Asp64His	p.D64H	ENST00000336032	NM_006813.2	64	Gat/Cat	1/2	1	2	FACETS	0.693	0.636	0.753	0.693	0.636	0.753	SUBCLONAL	1	TRUE	1	0.398509842943304	2		567	1224	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194826	29194826	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	214	655	0	ENST00000240100.2:c.902T>C	p.Val301Ala	p.V301A	ENST00000240100	NM_001394.6	301	gTg/gCg	4/4	0.245692781601293	1	FACETS	0.666	0.618	0.717	0.666	0.618	0.717	SUBCLONAL	1	TRUE	0	0.398509842943304	1		655	1291	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992683	68992683	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	92	422	0	ENST00000288368.4:c.1648G>C	p.Glu550Gln	p.E550Q	ENST00000288368	NM_024870.2	550	Gaa/Caa	16/40	1	2	FACETS	0.703	0.625	0.786	0.703	0.625	0.786	SUBCLONAL	1	TRUE	1	0.398509842943304	2		422	657	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0015120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	129	514	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.872	0.79	0.958	0.872	0.79	0.958	CLONAL	1	TRUE	1	0.320341730938941	2		514	924	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577569	7577569	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519981	NA	P-0015120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	207	515	0	ENST00000269305.4:c.712T>G	p.Cys238Gly	p.C238G	ENST00000269305	NM_001126112.2	238	Tgt/Ggt	7/11	0.291418204683134	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.320341730938941	1		515	1073	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575054	48575054	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1555685142	NA	P-0015120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	106	301	0	ENST00000342988.3:c.250-2A>G		p.X84_splice	ENST00000342988	NM_005359.5	84			0.302989125197645	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.320341730938941	1		301	543	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467972	66467972	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0015120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	98	315	0	ENST00000273854.3:c.297C>G	p.Tyr99Ter	p.Y99*	ENST00000273854	NM_004439.5	99	taC/taG	3/18	1	2	FACETS	0.898	0.802	1	0.898	0.802	1	CLONAL	1	TRUE	1	0.320341730938941	2		315	681	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	307	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.236413870418667	5	FACETS	1	0.972	1	0.699	0.66	0.74	INDETERMINATE	2	TRUE	2	0.483913753198614	5		493	1044	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0015121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	157	1023	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.44759583979427	3	FACETS	0.718	0.656	0.782	0.359	0.328	0.391	SUBCLONAL	1	TRUE	1	0.483913753198614	3		1024	1123	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	390	737	0	ENST00000269305.4:c.166del	p.Glu56LysfsTer67	p.E56Kfs*67	ENST00000269305	NM_001126112.2	56	Gaa/aa	4/11	0.44759583979427	3	FACETS	0.922	0.877	0.966	0.922	0.877	0.966	CLONAL	2	TRUE	1	0.483913753198614	3		737	1086	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0015121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	138	254	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	0.452956433438464	2	FACETS	0.799	0.736	0.863	0.799	0.736	0.863	SUBCLONAL	2	TRUE	0	0.483913753198614	2		254	357	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455082	50455082	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs869312883	NA	P-0015121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	236	390	0	ENST00000331340.3:c.629A>G	p.Tyr210Cys	p.Y210C	ENST00000331340	NM_006060.4	210	tAt/tGt	6/8	0.236413870418667	5	FACETS	0.956	0.894	1	0.638	0.596	0.681	INDETERMINATE	2	TRUE	2	0.483913753198614	5		390	880	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0015122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	121	435	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.778	0.705	0.856	0.778	0.705	0.856	SUBCLONAL	1	TRUE	1	0.476894092808572	2		435	652	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481806	56481806	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	438	442	0	ENST00000267101.3:c.734C>T	p.Ala245Val	p.A245V	ENST00000267101	NM_001982.3	245	gCc/gTc	7/28	0.463473866761482	2	FACETS	0.949	0.909	0.989	0.949	0.909	0.989	CLONAL	2	TRUE	0	0.476894092808572	2		442	968	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873721	35873721	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	217	494	0	ENST00000216797.5:c.130C>T	p.Gln44Ter	p.Q44*	ENST00000216797	NM_020529.2	44	Cag/Tag	1/6	1	2	FACETS	0.883	0.821	0.947	0.883	0.821	0.947	CLONAL	1	TRUE	1	0.476894092808572	2		494	1031	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943712	9943712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	185	470	0	ENST00000330684.3:c.1229C>T	p.Thr410Ile	p.T410I	ENST00000330684	NM_001134407.1	410	aCc/aTc	5/13	1	2	FACETS	0.888	0.82	0.958	0.888	0.82	0.958	CLONAL	1	TRUE	1	0.476894092808572	2		470	874	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647182	23647182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	214	500	1	ENST00000261584.4:c.685C>T	p.Pro229Ser	p.P229S	ENST00000261584	NM_024675.3	229	Cca/Tca	4/13	1	2	FACETS	0.817	0.758	0.877	0.817	0.758	0.877	CLONAL	1	TRUE	1	0.476894092808572	2		501	1099	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942924	15942924	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	198	369	0	ENST00000268712.3:c.6778A>T	p.Asn2260Tyr	p.N2260Y	ENST00000268712	NM_006311.3	2260	Aat/Tat	44/46	0.476726164797473	1	FACETS	0.925	0.86	0.991	0.925	0.86	0.991	CLONAL	1	TRUE	0	0.476894092808572	1		369	684	SUCCESS
ALK	238	MSKCC	GRCh37	2	29420436	29420436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	190	447	0	ENST00000389048.3:c.4045G>A	p.Asp1349Asn	p.D1349N	ENST00000389048	NM_004304.4	1349	Gac/Aac	27/29	1	2	FACETS	0.833	0.77	0.898	0.833	0.77	0.898	CLONAL	1	TRUE	1	0.476894092808572	2		447	957	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752817	57752817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	310	257	0	ENST00000274289.3:c.1111C>T	p.Leu371Phe	p.L371F	ENST00000274289	NM_006622.3	371	Ctt/Ttt	8/14	0.220581675483094	3	FACETS	0.966	0.915	1			1	INDETERMINATE	2	TRUE	NA	0.476894092808572	3		257	833	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956765	68956765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374334623	NA	P-0015122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	270	520	0	ENST00000288368.4:c.883C>T	p.Leu295Phe	p.L295F	ENST00000288368	NM_024870.2	295	Ctt/Ttt	8/40	0.183872206722291	1	FACETS	0.699	0.655	0.744	0.699	0.655	0.744	INDETERMINATE	1	TRUE	0	0.476894092808572	1		520	1234	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005858	69005858	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776078625	NA	P-0015122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	148	343	0	ENST00000288368.4:c.2269G>A	p.Val757Ile	p.V757I	ENST00000288368	NM_024870.2	757	Gtt/Att	21/40	0.183872206722291	1	FACETS	0.655	0.599	0.713	0.655	0.599	0.713	INDETERMINATE	1	TRUE	0	0.476894092808572	1		343	722	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054712	5054712	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	112	306	0	ENST00000381652.3:c.764T>C	p.Leu255Pro	p.L255P	ENST00000381652	NM_004972.3	255	cTt/cCt	7/25	1	2	FACETS	0.755	0.681	0.834	0.755	0.681	0.834	SUBCLONAL	1	TRUE	1	0.476894092808572	2		306	622	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453133	140453136	+	missense_variant	Missense_Mutation	ONP	TTCA	TTCA	ATTT	novel	NA	P-0015122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	245	377	1	ENST00000288602.6:c.1799_1802delinsAAAT	p.Val600_Lys601delinsGluIle	p.V600_K601delinsEI	ENST00000288602	NM_004333.4	600	gTGAAa/gAAATa	15/18	0.446676255257553	2	FACETS	1	0.993	1	0.749	0.704	0.795	CLONAL	1	TRUE	0	0.476894092808572	2		378	686	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0015123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	118	514	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	0.204890247055629	2		514	1057	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0015123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	123	812	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.204890247055629	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.204890247055629	1		813	1034	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372033	55372033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	129	579	0	ENST00000297316.4:c.723G>A	p.Met241Ile	p.M241I	ENST00000297316	NM_022454.3	241	atG/atA	2/2	0.204890247055629	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.204890247055629	1		579	927	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0015124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	141	336	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.93153246361114	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	0	0.93153246361114	1		336	149	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0015124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	165	401	0	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.930344937788565	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	0	0.93153246361114	1		401	178	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37048502	37048502	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	263	412	0	ENST00000231790.2:c.401A>T	p.Lys134Ile	p.K134I	ENST00000231790	NM_000249.3	134	aAa/aTa	5/19	0.739796005802485	1	FACETS	0.935	0.889	0.981	0.935	0.889	0.981	CLONAL	1	TRUE	0	0.739796005802485	1		412	479	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760928	133760928	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1414848177	NA	P-0015126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	524	700	6	ENST00000318560.5:c.3251G>A	p.Arg1084Gln	p.R1084Q	ENST00000318560	NM_005157.4	1084	cGa/cAa	11/11	1	2	FACETS	0.995	0.954	1	0.995	0.954	1	CLONAL	1	TRUE	1	0.739796005802485	2		706	1424	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0015128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	371	943	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.613475707151352	2	FACETS	0.88	0.848	0.912	0.88	0.848	0.912	CLONAL	2	TRUE	0	0.748786083220675	2		943	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0015128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	487	602	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.720889751773365	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.748786083220675	1		604	755	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65312338	65312338	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	392	462	0	ENST00000342505.4:c.1981G>T	p.Val661Leu	p.V661L	ENST00000342505	NM_002227.2	661	Gtg/Ttg	14/25	0.748786083220675	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.748786083220675	1		462	647	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0015129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	760	650	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.217011328594714	8	FACETS	0.964	0.933	0.995	0.964	0.933	0.995	CLONAL	7	TRUE	1	0.217011328594714	8		650	1714	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0015129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	183	623	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	1	2	FACETS	0.848	0.782	0.916	1	0.991	1	CLONAL	2	TRUE	1	0.217011328594714	2		623	995	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0015130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	101	336	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.24136096273238	3	FACETS	1	0.975	1	0.654	0.585	0.728	CLONAL	1	FALSE	1	0.241200555248375	3		336	717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0015130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	71	749	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.767	0.668	0.873	0.767	0.668	0.873	SUBCLONAL	1	FALSE	1	0.241200555248375	2		750	768	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505471	25505471	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771499883	NA	P-0015130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	45	477	0	ENST00000264709.3:c.287G>A	p.Arg96Gln	p.R96Q	ENST00000264709	NM_175629.2	96	cGg/cAg	4/23	NA	2	FACETS	0.712	0.598	0.838			1	INDETERMINATE	1	FALSE	NA	0.241200555248375	2		477	524	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715979	52715979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786205227	NA	P-0015130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	65	496	1	ENST00000322088.6:c.544C>T	p.Arg182Trp	p.R182W	ENST00000322088	NM_014225.5	182	Cgg/Tgg	5/15	0.180624647006632	1	FACETS	0.915	0.794	1	0.915	0.794	1	CLONAL	1	FALSE	0	0.241200555248375	1		497	518	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332357	70332357	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	46	491	1	ENST00000373644.4:c.262G>C	p.Glu88Gln	p.E88Q	ENST00000373644	NM_030625.2	88	Gag/Cag	2/12	0.139274762596726	3	FACETS	0.611	0.513	0.719			1	INDETERMINATE	1	FALSE	NA	0.241200555248375	3		492	700	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6048636	6048636	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	28	443	0	ENST00000265849.7:c.15G>C	p.Glu5Asp	p.E5D	ENST00000265849	NM_000535.5	5	gaG/gaC	1/15	0.241200555248375	1	FACETS	0.371	0.296	0.458	0.371	0.296	0.458	SUBCLONAL	1	FALSE	0	0.241200555248375	1		443	550	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923117	48923117	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	71	317	0	ENST00000267163.4:c.566del	p.Leu189TrpfsTer3	p.L189Wfs*3	ENST00000267163	NM_000321.2	189	Ttg/tg	6/27	0.240713758445793	0	FACETS	0.899	0.805	0.996			1	CLONAL	3	FALSE	0	0.240713758445793	0		317	166	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923126	48923126	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	75	331	0	ENST00000267163.4:c.574A>G	p.Lys192Glu	p.K192E	ENST00000267163	NM_000321.2	192	Aaa/Gaa	6/27	0.240713758445793	0	FACETS	0.962	0.866	1			1	CLONAL	3	FALSE	0	0.240713758445793	0		331	164	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641575	23641575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	47	546	0	ENST00000261584.4:c.1900C>T	p.Pro634Ser	p.P634S	ENST00000261584	NM_024675.3	634	Cca/Tca	5/13	0.121784975874696	5	FACETS	1	0.915	1	0.376	0.317	0.441	INDETERMINATE	1	FALSE	2	0.240713758445793	5		546	471	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752996	42752996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	90	607	0	ENST00000222329.4:c.1268C>T	p.Pro423Leu	p.P423L	ENST00000222329	NM_006494.2	423	cCa/cTa	4/4	0.0649223549265614	4	FACETS	0.88	0.779	0.989			1	INDETERMINATE	1	FALSE	NA	0.240713758445793	4		607	1054	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38971990	38971990	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	20	458	0	ENST00000357387.3:c.961A>G	p.Met321Val	p.M321V	ENST00000357387	NM_152756.3	321	Atg/Gtg	11/38	0.172725661631583	5	FACETS	0.616	0.471	0.787	0.205	0.157	0.263	SUBCLONAL	1	FALSE	2	0.240713758445793	5		458	367	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589607	67589609	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0015135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	80	304	0	ENST00000274335.5:c.1372_1374del	p.Glu458del	p.E458del	ENST00000274335		457	cAAGaa/caa	10/15	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.21	2		304	702	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0015135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	46	303	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	0.672	0.565	0.791	0.672	0.565	0.791	SUBCLONAL	1	TRUE	1	0.21	2		303	652	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692980	89692980	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1060500126	NA	P-0015135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	101	393	0	ENST00000371953.3:c.464A>G	p.Tyr155Cys	p.Y155C	ENST00000371953	NM_000314.4	155	tAt/tGt	5/9	0.22567882348173	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.21	2		393	446	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458255	120458256	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0015135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	58	515	0	ENST00000256646.2:c.7088_7089dup	p.Gln2364GlyfsTer3	p.Q2364Gfs*3	ENST00000256646	NM_024408.3	2363	-/GG	34/34	1	2	FACETS	0.478	0.409	0.554	0.478	0.409	0.554	SUBCLONAL	1	TRUE	1	0.21	2		515	1155	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418337	139418337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761439288	NA	P-0015135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	201	679	0	ENST00000277541.6:c.235C>T	p.Arg79Cys	p.R79C	ENST00000277541	NM_017617.3	79	Cgc/Tgc	3/34	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.21	2		679	1291	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0015136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	23	202	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.253132350914783	3	FACETS	0.657	0.515	0.819	0.329	0.257	0.41	INDETERMINATE	1	TRUE	1	0.437357345674569	3		202	195	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210907	133210907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	156	509	0	ENST00000320574.5:c.5869G>A	p.Glu1957Lys	p.E1957K	ENST00000320574	NM_006231.2	1957	Gag/Aag	43/49	1	2	FACETS	0.568	0.519	0.62	0.568	0.519	0.62	SUBCLONAL	1	TRUE	1	0.437357345674569	2		509	1255	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922341	178922341	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	132	431	0	ENST00000263967.3:c.1110T>G	p.Asn370Lys	p.N370K	ENST00000263967	NM_006218.2	370	aaT/aaG	6/21	0.253132350914783	3	FACETS	1	0.975	1	0.597	0.544	0.653	INDETERMINATE	1	TRUE	1	0.437357345674569	3		431	616	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0015139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	174	336	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.218392934992369	4	FACETS	1	0.958	1	1	0.958	1	INDETERMINATE	2	TRUE	2	0.373232133420868	4		336	609	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0015139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	710	581	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.223562999236769	4	FACETS	0.969	0.939	0.999	0.969	0.939	0.999	INDETERMINATE	4	TRUE	0	0.373232133420868	4		581	1348	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	169	485	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	NA	2	FACETS	1	0.962	1			1	INDETERMINATE	1	TRUE	NA	0.373232133420868	2		485	843	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712016	89712019	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTA	AGTA	-	novel	NA	P-0015139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	31	148	0	ENST00000371953.3:c.634+3_634+6del		p.X212_splice	ENST00000371953	NM_000314.4	212		6/9	0.157160158126953	5	FACETS	1	0.937	1	0.464	0.379	0.559	INDETERMINATE	1	TRUE	2	0.373232133420868	5		148	186	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591038	67591038	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	73	243	0	ENST00000274335.5:c.1631G>A	p.Arg544Lys	p.R544K	ENST00000274335		544	aGa/aAa	12/15	0.373232133420868	2	FACETS	1	0.963	1	0.621	0.548	0.698	CLONAL	1	TRUE	0	0.373232133420868	2		243	315	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519390	176519390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs550870047	NA	P-0015139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	329	461	1	ENST00000292408.4:c.796G>A	p.Asp266Asn	p.D266N	ENST00000292408	NM_213647.1	266	Gac/Aac	7/18	0.373232133420868	5	FACETS	1	0.991	1	0.807	0.763	0.852	CLONAL	2	TRUE	2	0.373232133420868	5		462	1136	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509930	106509930	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	76	423	0	ENST00000359195.3:c.1924G>C	p.Ala642Pro	p.A642P	ENST00000359195	NM_002649.2	642	Gcc/Ccc	2/11	0.373232133420868	2	FACETS	0.656	0.575	0.742	0.328	0.287	0.371	SUBCLONAL	1	TRUE	0	0.373232133420868	2		423	621	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0015140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	157	867	8	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.504	0.461	0.548	0.504	0.461	0.548	SUBCLONAL	1	TRUE	1	0.727505808633301	2		875	857	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0015140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	88	249	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.717954322242946	1	FACETS	0.814	0.74	0.89	0.814	0.74	0.89	CLONAL	1	TRUE	0	0.727505808633301	1		249	189	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398279	25398279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894365	NA	P-0015140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	301	445	1	ENST00000311936.3:c.40G>A	p.Val14Ile	p.V14I	ENST00000311936	NM_004985.3	14	Gta/Ata	2/5	1	2	FACETS	0.928	0.876	0.98	0.928	0.876	0.98	CLONAL	1	TRUE	1	0.727505808633301	2		446	892	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164721	47164721	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	201	310	0	ENST00000409792.3:c.1405T>C	p.Tyr469His	p.Y469H	ENST00000409792	NM_014159.6	469	Tac/Cac	3/21	0.717954322242946	1	FACETS	0.985	0.93	1	0.985	0.93	1	CLONAL	1	TRUE	0	0.727505808633301	1		310	357	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105622	11105622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	105	606	0	ENST00000358026.2:c.1538G>A	p.Arg513Gln	p.R513Q	ENST00000358026	NM_001128849.1	513	cGg/cAg	9/36	1	2	FACETS	0.273	0.244	0.304	0.273	0.244	0.304	SUBCLONAL	1	TRUE	1	0.727505808633301	2		606	1057	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868176	45868176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559154781	NA	P-0015140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	396	643	0	ENST00000391945.4:c.514G>A	p.Ala172Thr	p.A172T	ENST00000391945	NM_000400.3	172	Gct/Act	7/23	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.727505808633301	2		643	1087	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119796	17119796	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148257120	NA	P-0015140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	348	555	0	ENST00000285071.4:c.1198G>A	p.Val400Ile	p.V400I	ENST00000285071	NM_144997.5	400	Gtc/Atc	11/14	1	2	FACETS	0.958	0.909	1	0.958	0.909	1	CLONAL	1	TRUE	1	0.727505808633301	2		555	999	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351950	70351950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223696	NA	P-0015140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	216	551	2	ENST00000374080.3:c.4147G>A	p.Ala1383Thr	p.A1383T	ENST00000374080		1383	Gcc/Acc	30/45	0.727505808633301	1	FACETS	0.585	0.547	0.624	0.585	0.547	0.624	SUBCLONAL	1	TRUE	0	0.727505808633301	1		553	646	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187173	11187173	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	312	446	0	ENST00000361445.4:c.6245A>T	p.Gln2082Leu	p.Q2082L	ENST00000361445	NM_004958.3	2082	cAa/cTa	45/58	0.717954322242946	1	FACETS	0.943	0.899	0.986	0.943	0.899	0.986	CLONAL	1	TRUE	0	0.727505808633301	1		446	579	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465301	120465301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758689134	NA	P-0015140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	240	309	14	ENST00000256646.2:c.4960G>A	p.Ala1654Thr	p.A1654T	ENST00000256646	NM_024408.3	1654	Gcc/Acc	27/34	0.717954322242946	1	FACETS	0.999	0.949	1	0.999	0.949	1	CLONAL	1	TRUE	0	0.727505808633301	1		323	420	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681327	88681327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780107	NA	P-0015140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	159	253	1	ENST00000372037.3:c.1217G>A	p.Arg406His	p.R406H	ENST00000372037	NM_004329.2	406	cGc/cAc	11/13	0.717954322242946	1	FACETS	0.983	0.921	1	0.983	0.921	1	CLONAL	1	TRUE	0	0.727505808633301	1		254	283	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573165	64573165	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1114167471	NA	P-0015140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	343	477	0	ENST00000312049.6:c.1127T>C	p.Leu376Pro	p.L376P	ENST00000312049	NM_130799.2	376	cTg/cCg	8/10	0.717954322242946	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.727505808633301	1		477	592	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3799632	3799632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267606752	NA	P-0015140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	249	401	1	ENST00000262367.5:c.3832G>A	p.Glu1278Lys	p.E1278K	ENST00000262367	NM_004380.2	1278	Gaa/Aaa	21/31	0.717954322242946	1	FACETS	0.891	0.844	0.938	0.891	0.844	0.938	CLONAL	1	TRUE	0	0.727505808633301	1		402	489	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010455	48010455	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	285	418	0	ENST00000234420.5:c.83C>A	p.Ser28Ter	p.S28*	ENST00000234420	NM_000179.2	28	tCa/tAa	1/10	0.717954322242946	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.727505808633301	1		418	498	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125245	47125245	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	263	314	0	ENST00000409792.3:c.6025G>C	p.Ala2009Pro	p.A2009P	ENST00000409792	NM_014159.6	2009	Gcc/Ccc	12/21	0.717954322242946	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.727505808633301	1		314	454	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287859	33287859	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	381	457	0	ENST00000374542.5:c.1394del	p.Glu465GlyfsTer63	p.E465Gfs*63	ENST00000374542	NM_001141970.1	465	gAg/gg	5/8	0.727505808633301	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.727505808633301	1		457	657	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64289969	64289969	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	211	302	0	ENST00000370651.3:c.412C>T	p.Arg138Cys	p.R138C	ENST00000370651	NM_003463.4	138	Cgt/Tgt	6/6	0.727505808633301	1	FACETS	0.946	0.894	0.999	0.946	0.894	0.999	CLONAL	1	TRUE	0	0.727505808633301	1		302	390	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300845	137300845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	129	600	3	ENST00000481739.1:c.490C>T	p.Arg164Cys	p.R164C	ENST00000481739	NM_002957.4	164	Cgc/Tgc	4/10	1	2	FACETS	0.32	0.29	0.353	0.32	0.29	0.353	SUBCLONAL	1	TRUE	1	0.727505808633301	2		603	1107	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233732	233734	+	missense_variant	Missense_Mutation	TNP	TCC	TCC	CCG	novel	NA	P-0015140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	135	395	0	ENST00000264932.6:c.1036_1038delinsCCG	p.Ser346Pro	p.S346P	ENST00000264932	NM_004168.2	346	TCC/CCG	8/15	1	2	FACETS	0.536	0.488	0.587	0.536	0.488	0.587	SUBCLONAL	1	TRUE	1	0.727505808633301	2		395	692	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412045	116412045	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0015141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	1007	599	0	ENST00000397752.3:c.3028+2T>C		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.3	7	FACETS	0.988	0.963	1			1	CLONAL	7	TRUE	NA	0.28	7		599	1768	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076745	72076745	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	140	459	0	ENST00000357731.5:c.752C>A	p.Pro251Gln	p.P251Q	ENST00000357731	NM_173808.2	251	cCg/cAg	5/7	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.28	2		459	915	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449929	29449929	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	193	779	1	ENST00000389048.3:c.2926C>A	p.His976Asn	p.H976N	ENST00000389048	NM_004304.4	976	Cac/Aac	18/29	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.28	2		780	1253	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757400	40757400	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0015141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	113	535	0	ENST00000373198.4:c.2898C>G	p.Tyr966Ter	p.Y966*	ENST00000373198	NM_133170.3	966	taC/taG	20/32	1	2	FACETS	0.924	0.83	1	0.924	0.83	1	CLONAL	1	TRUE	1	0.28	2		535	874	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69032495	69032506	+	frameshift_variant	Frame_Shift_Del	DEL	ATCTCACTCCAG	ATCTCACTCCAG	T	novel	NA	P-0015141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	89	572	0	ENST00000288368.4:c.3569_3580delinsT	p.Tyr1190LeufsTer48	p.Y1190Lfs*48	ENST00000288368	NM_024870.2	1190	tATCTCACTCCAGgc/tTgc	29/40	0.279394124869957	3	FACETS	0.721	0.638	0.811	0.361	0.319	0.406	SUBCLONAL	1	TRUE	1	0.28	3		572	1005	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0015142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	35	435	0				ENST00000310581	NM_198253.2	-/1132			0.0808572337521752	0	FACETS	0.619	0.507	0.745			1	INDETERMINATE	1	TRUE	0	0.19	0		435	482	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945092	38945092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769767383	NA	P-0015142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	19	387	0	ENST00000357387.3:c.4712C>T	p.Ser1571Leu	p.S1571L	ENST00000357387	NM_152756.3	1571	tCg/tTg	35/38	0.0808572337521752	0	FACETS	0.733	0.558	0.938			1	INDETERMINATE	1	TRUE	0	0.19	0		387	221	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844777	156844777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56320207	NA	P-0015142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	32	426	2	ENST00000524377.1:c.1331G>A	p.Arg444Gln	p.R444Q	ENST00000524377	NM_002529.3	444	cGg/cAg	11/17	1	2	FACETS	0.686	0.556	0.833	0.686	0.556	0.833	SUBCLONAL	1	TRUE	1	0.19	2		428	491	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412380	139412381	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	34	392	2	ENST00000277541.6:c.1264_1265delinsTT	p.Pro422Phe	p.P422F	ENST00000277541	NM_017617.3	422	CCc/TTc	8/34	1	2	FACETS	0.726	0.592	0.876	0.726	0.592	0.876	SUBCLONAL	1	TRUE	1	0.19	2		394	493	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756572	756572	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	17	366	0	ENST00000314574.4:c.256C>T	p.Pro86Ser	p.P86S	ENST00000314574	NM_005433.3	86	Cct/Tct	2/12	1	2	FACETS	0.918	0.687	1	0.918	0.687	1	CLONAL	1	TRUE	1	0.19	2		366	195	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758315	41758315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	39	542	0	ENST00000301178.4:c.1771G>A	p.Glu591Lys	p.E591K	ENST00000301178	NM_021913.4	591	Gaa/Aaa	15/20	0.0808572337521752	3	FACETS	0.981	0.814	1	0.491	0.407	0.585	INDETERMINATE	1	TRUE	1	0.19	3		542	458	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573281	55573281	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	10	274	0	ENST00000288135.5:c.943A>G	p.Ile315Val	p.I315V	ENST00000288135	NM_000222.2	315	Atc/Gtc	6/21	0.0808572337521752	0	FACETS	0.782	0.534	1			1	INDETERMINATE	1	TRUE	0	0.19	0		274	109	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032191	26032207	+	frameshift_variant	Frame_Shift_Del	DEL	GTAGCCGGCGCGCTCTT	GTAGCCGGCGCGCTCTT	-	novel	NA	P-0015142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	18	148	0	ENST00000244661.2:c.82_98del	p.Lys28ArgfsTer65	p.K28Rfs*65	ENST00000244661	NM_003537.3	28	AAGAGCGCGCCGGCTACc/c	1/1	0.521817127184788	4	FACETS	0.82	0.618	1	0.41	0.309	0.53	CLONAL	1	TRUE	2	0.19	4		148	275	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477843	140477853	+	protein_altering_variant	In_Frame_Del	DEL	CTGTCACATTC	CTGTCACATTC	AG	novel	NA	P-0015142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	85	425	2	ENST00000288602.6:c.1455_1465delinsCT	p.Leu485_Ala489delinsPheSer	p.L485_A489delinsFS	ENST00000288602	NM_004333.4	485	ttGAATGTGACAGca/ttCTca	12/18	0.844064186935268	3	FACETS	1	0.959	1	1	0.984	1	CLONAL	3	TRUE	1	0.19	3		427	285	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0015145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	127	255	0	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS	0.542	0.494	0.593	0.542	0.494	0.593	SUBCLONAL	1	TRUE	1	0.910929791924225	2		255	514	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218084	108218084	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs760955058	NA	P-0015145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	233	280	0	ENST00000278616.4:c.8663T>C	p.Ile2888Thr	p.I2888T	ENST00000278616	NM_000051.3	2888	aTa/aCa	59/63	1	2	FACETS	0.912	0.858	0.966	0.912	0.858	0.966	CLONAL	1	TRUE	1	0.910929791924225	2		280	561	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593603	55593614	+	inframe_deletion	In_Frame_Del	DEL	TGGAAGGTTGTT	TGGAAGGTTGTT	-	novel	NA	P-0015145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	219	312	0	ENST00000288135.5:c.1669_1680del	p.Trp557_Val560del	p.W557_V560del	ENST00000288135	NM_000222.2	557	TGGAAGGTTGTT/-	11/21	1	2	FACETS	0.815	0.764	0.867	0.815	0.764	0.867	CLONAL	1	TRUE	1	0.910929791924225	2		312	590	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023818	27023818	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	37	427	0	ENST00000324856.7:c.924C>A	p.Tyr308Ter	p.Y308*	ENST00000324856	NM_006015.4	308	taC/taA	1/20	1	2	FACETS	0.599	0.492	0.719	0.599	0.492	0.719	SUBCLONAL	1	TRUE	1	0.17	2		427	727	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982913	201982970	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGGGGACACCTGGATGGCAAACTGATGGAGGCTGGCCTTGCAGCGCCCAGAGGCACC	GAGGGGACACCTGGATGGCAAACTGATGGAGGCTGGCCTTGCAGCGCCCAGAGGCACC	-	novel	NA	P-0015147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	57	317	0	ENST00000359651.3:c.806-44_819del		p.X269_splice	ENST00000359651		269		7/8	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.17	2		317	609	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202225	108202225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	53	500	0	ENST00000278616.4:c.7570G>A	p.Ala2524Thr	p.A2524T	ENST00000278616	NM_000051.3	2524	Gct/Act	51/63	1	2	FACETS	0.726	0.617	0.846	0.726	0.617	0.846	SUBCLONAL	1	TRUE	1	0.17	2		500	859	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56363690	56363690	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	53	437	0	ENST00000348428.3:c.469C>T	p.Gln157Ter	p.Q157*	ENST00000348428	NM_006785.3	157	Caa/Taa	3/17	1	2	FACETS	0.694	0.59	0.808	0.694	0.59	0.808	SUBCLONAL	1	TRUE	1	0.17	2		437	899	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945620	151945632	+	frameshift_variant	Frame_Shift_Del	DEL	TTCAGAAGACATT	TTCAGAAGACATT	-	novel	NA	P-0015147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	44	480	0	ENST00000262189.6:c.1887_1899del	p.Met630Ter	p.M630*	ENST00000262189	NM_170606.2	629	aaAATGTCTTCTGAA/aa	14/59	1	2	FACETS	0.588	0.491	0.696	0.588	0.491	0.696	SUBCLONAL	1	TRUE	1	0.17	2		480	880	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0015148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	472	424	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.439995726447415	3	FACETS	0.902	0.867	0.937	0.902	0.867	0.937	CLONAL	3	TRUE	0	0.453680162357491	3		424	943	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056206	26056206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1486283762	NA	P-0015148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	370	321	0	ENST00000343677.2:c.451G>A	p.Ala151Thr	p.A151T	ENST00000343677	NM_005319.3	151	Gct/Act	1/1	0.442180445304589	4	FACETS	0.965	0.921	1	0.965	0.921	1	CLONAL	3	TRUE	1	0.453680162357491	4		321	819	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745476	162745476	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	255	285	0	ENST00000367921.3:c.1891C>G	p.Arg631Gly	p.R631G	ENST00000367921	NM_006182.2	631	Cgg/Ggg	15/18	0.453680162357491	8	FACETS	1	0.987	1	0.479	0.448	0.511	CLONAL	2	TRUE	3	0.453680162357491	8		285	1108	SUCCESS
CBL	867	MSKCC	GRCh37	11	119146812	119146812	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	287	392	0	ENST00000264033.4:c.975C>G	p.Phe325Leu	p.F325L	ENST00000264033	NM_005188.3	325	ttC/ttG	6/16	0.454232517626888	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.453680162357491	3		392	759	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0015149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	119	456	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.23	2		456	1006	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439913	56439914	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0015149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	100	439	0	ENST00000407977.2:c.678_679del	p.His226GlnfsTer32	p.H226Qfs*32	ENST00000407977		226	caCAgc/cagc	6/10	1	2	FACETS	0.979	0.874	1	0.979	0.874	1	CLONAL	1	TRUE	1	0.23	2		439	888	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0015150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	231	329	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	0.51643215494744	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	FALSE	2	0.788346749134809	4		329	502	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913250	NA	P-0015150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	417	315	0	ENST00000369535.4:c.34G>T	p.Gly12Cys	p.G12C	ENST00000369535	NM_002524.4	12	Ggt/Tgt	2/7	0.788346749134809	5	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	FALSE	2	0.788346749134809	5		315	723	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022250	31022250	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	201	248	0	ENST00000375687.4:c.1735A>T	p.Ile579Phe	p.I579F	ENST00000375687	NM_015338.5	579	Atc/Ttc	13/13	0.564414727273021	4	FACETS	0.87	0.813	0.928	0.87	0.813	0.928	CLONAL	2	FALSE	2	0.788346749134809	4		248	524	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041680	47041680	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	602	546	0	ENST00000377604.3:c.1905G>C	p.Glu635Asp	p.E635D	ENST00000377604	NM_001204468.1	635	gaG/gaC	17/24	0.556439411278752	3	FACETS	0.971	0.94	1	0.971	0.94	1	CLONAL	2	FALSE	1	0.788346749134809	3		546	1096	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65569055	65569055	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0015151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	369	375	0	ENST00000358664.4:c.3G>A	p.Met1?	p.M1?	ENST00000358664	NM_002382.4	1	atG/atA	1/5	0.632327472645135	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.632327472645135	2		375	575	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309899	65309899	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0015151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	275	237	0	ENST00000342505.4:c.2252-1G>A		p.X751_splice	ENST00000342505	NM_002227.2	751			NA	2	FACETS	1	0.972	1			1	INDETERMINATE	2	TRUE	NA	0.632327472645135	2		237	426	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410605	32410605	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	novel	NA	P-0015151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	278	299	0	ENST00000332351.3:c.1553G>C	p.Ter518SerextTer22	p.*518Sext*22	ENST00000332351	NM_024426.4	518	tGa/tCa	10/10	0.529740972368855	4	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	2	0.632327472645135	4		299	716	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231458	46231458	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	226	287	1	ENST00000334344.6:c.1298G>C	p.Cys433Ser	p.C433S	ENST00000334344	NM_152641.2	433	tGc/tCc	10/21	0.631918117383387	4	FACETS	0.857	0.802	0.913	0.857	0.802	0.913	CLONAL	2	TRUE	2	0.632327472645135	4		288	681	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913895	32914593	+	inframe_deletion	In_Frame_Del	DEL	ACAAACTGTAAATGAAGATATTTGCGTTGAGGAACTTGTGACTAGCTCTTCACCCTGCAAAAATAAAAATGCAGCCATTAAATTGTCCATATCTAATAGTAATAATTTTGAGGTAGGGCCACCTGCATTTAGGATAGCCAGTGGTAAAATCGTTTGTGTTTCACATGAAACAATTAAAAAAGTGAAAGACATATTTACAGACAGTTTCAGTAAAGTAATTAAGGAAAACAACGAGAATAAATCAAAAATTTGCCAAACGAAAATTATGGCAGGTTGTTACGAGGCATTGGATGATTCAGAGGATATTCTTCATAACTCTCTAGATAATGATGAATGTAGCACGCATTCACATAAGGTTTTTGCTGACATTCAGAGTGAAGAAATTTTACAACATAACCAAAATATGTCTGGATTGGAGAAAGTTTCTAAAATATCACCTTGTGATGTTAGTTTGGAAACTTCAGATATATGTAAATGTAGTATAGGGAAGCTTCATAAGTCAGTCTCATCTGCAAATACTTGTGGGATTTTTAGCACAGCAAGTGGAAAATCTGTCCAGGTATCAGATGCTTCATTACAAAACGCAAGACAAGTGTTTTCTGAAATAGAAGATAGTACCAAGCAAGTCTTTTCCAAAGTATTGTTTAAAAGTAACGAACATTCAGACCAGCTCACAAGAGAAGAAAATACTGCTATACG	ACAAACTGTAAATGAAGATATTTGCGTTGAGGAACTTGTGACTAGCTCTTCACCCTGCAAAAATAAAAATGCAGCCATTAAATTGTCCATATCTAATAGTAATAATTTTGAGGTAGGGCCACCTGCATTTAGGATAGCCAGTGGTAAAATCGTTTGTGTTTCACATGAAACAATTAAAAAAGTGAAAGACATATTTACAGACAGTTTCAGTAAAGTAATTAAGGAAAACAACGAGAATAAATCAAAAATTTGCCAAACGAAAATTATGGCAGGTTGTTACGAGGCATTGGATGATTCAGAGGATATTCTTCATAACTCTCTAGATAATGATGAATGTAGCACGCATTCACATAAGGTTTTTGCTGACATTCAGAGTGAAGAAATTTTACAACATAACCAAAATATGTCTGGATTGGAGAAAGTTTCTAAAATATCACCTTGTGATGTTAGTTTGGAAACTTCAGATATATGTAAATGTAGTATAGGGAAGCTTCATAAGTCAGTCTCATCTGCAAATACTTGTGGGATTTTTAGCACAGCAAGTGGAAAATCTGTCCAGGTATCAGATGCTTCATTACAAAACGCAAGACAAGTGTTTTCTGAAATAGAAGATAGTACCAAGCAAGTCTTTTCCAAAGTATTGTTTAAAAGTAACGAACATTCAGACCAGCTCACAAGAGAAGAAAATACTGCTATACG	-	novel	NA	P-0015151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	277	402	0	ENST00000380152.3:c.5403_6101del	p.Gln1802_Arg2034del	p.Q1802_R2034del	ENST00000380152		1801	ccACAAACTGTAAATGAAGATATTTGCGTTGAGGAACTTGTGACTAGCTCTTCACCCTGCAAAAATAAAAATGCAGCCATTAAATTGTCCATATCTAATAGTAATAATTTTGAGGTAGGGCCACCTGCATTTAGGATAGCCAGTGGTAAAATCGTTTGTGTTTCACATGAAACAATTAAAAAAGTGAAAGACATATTTACAGACAGTTTCAGTAAAGTAATTAAGGAAAACAACGAGAATAAATCAAAAATTTGCCAAACGAAAATTATGGCAGGTTGTTACGAGGCATTGGATGATTCAGAGGATATTCTTCATAACTCTCTAGATAATGATGAATGTAGCACGCATTCACATAAGGTTTTTGCTGACATTCAGAGTGAAGAAATTTTACAACATAACCAAAATATGTCTGGATTGGAGAAAGTTTCTAAAATATCACCTTGTGATGTTAGTTTGGAAACTTCAGATATATGTAAATGTAGTATAGGGAAGCTTCATAAGTCAGTCTCATCTGCAAATACTTGTGGGATTTTTAGCACAGCAAGTGGAAAATCTGTCCAGGTATCAGATGCTTCATTACAAAACGCAAGACAAGTGTTTTCTGAAATAGAAGATAGTACCAAGCAAGTCTTTTCCAAAGTATTGTTTAAAAGTAACGAACATTCAGACCAGCTCACAAGAGAAGAAAATACTGCTATACGt/cct	11/27	0.632005479117803	2	FACETS	0.901	0.859	0.943	0.901	0.859	0.943	CLONAL	2	TRUE	0	0.632327472645135	2		402	486	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098840	178098840	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	437	414	0	ENST00000397062.3:c.205G>C	p.Ala69Pro	p.A69P	ENST00000397062	NM_006164.4	69	Gcc/Ccc	2/5	0.632327472645135	6	FACETS	0.873	0.834	0.913			1	CLONAL	3	TRUE	NA	0.632327472645135	6		414	1195	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589515	67589641	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAATTTATTTTAATCTTTCTAGGATCAAGTTGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACACTCAGTTTCAAGAAAAAAGTCGAGAATATGATAGATTATATGAA	GAATTTATTTTAATCTTTCTAGGATCAAGTTGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACACTCAGTTTCAAGAAAAAAGTCGAGAATATGATAGATTATATGAA	-	novel	NA	P-0015151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	55	128	0	ENST00000274335.5:c.1300-18_1408del		p.X434_splice	ENST00000274335		434		10/15	0.632327472645135	2	FACETS	0.763	0.676	0.851	0.763	0.676	0.851	SUBCLONAL	2	TRUE	0	0.632327472645135	2		128	114	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149498378	149498378	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	158	469	0	ENST00000261799.4:c.2836G>C	p.Glu946Gln	p.E946Q	ENST00000261799	NM_002609.3	946	Gag/Cag	21/23	0.612911171370169	4	FACETS	0.664	0.607	0.724	0.166	0.151	0.181	SUBCLONAL	1	TRUE	0	0.632327472645135	4		469	1229	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066477	94066477	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	232	300	0	ENST00000369303.4:c.1282C>G	p.Gln428Glu	p.Q428E	ENST00000369303	NM_004440.3	428	Cag/Gag	5/17	0.388483579071545	5	FACETS	1	0.972	1	0.709	0.665	0.755	CLONAL	2	TRUE	2	0.632327472645135	5		300	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0015152-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	399	464	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.523652632605804	2	FACETS	0.946	0.906	0.985	0.946	0.906	0.985	CLONAL	2	TRUE	0	0.537545821980277	2		464	785	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977984	131977984	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015152-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	222	410	0	ENST00000265335.6:c.3867T>G	p.Ile1289Met	p.I1289M	ENST00000265335		1289	atT/atG	25/25	0.290724444171348	5	FACETS	1	0.988	1	0.825	0.773	0.877	INDETERMINATE	2	TRUE	2	0.537545821980277	5		410	603	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604716	48604716	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	38	366	0	ENST00000342988.3:c.1538A>G	p.Tyr513Cys	p.Y513C	ENST00000342988	NM_005359.5	513	tAc/tGc	12/12	1	2	FACETS	0.101	0.083	0.122	0.101	0.083	0.122	SUBCLONAL	1	TRUE	1	1.14	2		366	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0015154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	56	749	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.593	0.506	0.689	0.593	0.506	0.689	SUBCLONAL	1	TRUE	1	0.15	2		750	1259	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932171	39932171	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555918056	NA	P-0015154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	116	243	0	ENST00000378444.4:c.2428C>T	p.Arg810Ter	p.R810*	ENST00000378444	NM_001123385.1	810	Cga/Tga	4/15	1	1	FACETS	1	0.932	1	1	0.989	1	CLONAL	2	TRUE	0	0.15	1		243	687	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576112	29576112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540108477	NA	P-0015154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	49	358	0	ENST00000356175.3:c.4085G>A	p.Arg1362Gln	p.R1362Q	ENST00000356175	NM_000267.3	1362	cGa/cAa	30/57	1	2	FACETS	0.7	0.59	0.82	0.7	0.59	0.82	SUBCLONAL	1	TRUE	1	0.15	2		358	934	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156719	20156719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	21	155	1	ENST00000379607.5:c.38G>A	p.Arg13His	p.R13H	ENST00000379607	NM_001412.3	13	cGc/cAc	2/7	1	1	FACETS	0.635	0.488	0.807	0.635	0.488	0.807	SUBCLONAL	1	TRUE	0	0.15	1		156	408	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440643	56440643	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	54	417	0	ENST00000407977.2:c.575del	p.Pro192ArgfsTer11	p.P192Rfs*11	ENST00000407977		192	cCg/cg	5/10	1	2	FACETS	0.714	0.608	0.832	0.714	0.608	0.832	SUBCLONAL	1	TRUE	1	0.15	2		417	1008	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143119	30143119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745712273	NA	P-0015154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	54	505	0	ENST00000389048.3:c.407G>A	p.Arg136Gln	p.R136Q	ENST00000389048	NM_004304.4	136	cGg/cAg	1/29	1	2	FACETS	0.707	0.602	0.823	0.707	0.602	0.823	SUBCLONAL	1	TRUE	1	0.15	2		505	1018	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518216	187518216	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	30	218	0	ENST00000441802.2:c.12478C>T	p.Arg4160Cys	p.R4160C	ENST00000441802	NM_005245.3	4160	Cgt/Tgt	25/27	1	2	FACETS	0.765	0.615	0.935	0.765	0.615	0.935	CLONAL	1	TRUE	1	0.15	2		218	523	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512313	149512313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1442264858	NA	P-0015154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	37	234	1	ENST00000261799.4:c.1127G>A	p.Arg376Gln	p.R376Q	ENST00000261799	NM_002609.3	376	cGg/cAg	7/23	1	2	FACETS	0.768	0.632	0.922	0.768	0.632	0.922	CLONAL	1	TRUE	1	0.15	2		235	642	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967900	93967900	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	53	386	1	ENST00000369303.4:c.2027G>T	p.Arg676Met	p.R676M	ENST00000369303	NM_004440.3	676	aGg/aTg	11/17	1	2	FACETS	0.683	0.581	0.797	0.683	0.581	0.797	SUBCLONAL	1	TRUE	1	0.15	2		387	1034	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239931	53239931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	48	251	2	ENST00000375401.3:c.1510G>A	p.Val504Met	p.V504M	ENST00000375401	NM_004187.3	504	Gtg/Atg	11/26	1	1	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	0	0.15	1		253	589	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061212	38061235	+	inframe_deletion	In_Frame_Del	DEL	GTAGCAGCCGTTCTCGAACATGTT	GTAGCAGCCGTTCTCGAACATGTT	-	novel	NA	P-0015155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	89	388	0	ENST00000250448.2:c.754_777del	p.Asn252_Tyr259del	p.N252_Y259del	ENST00000250448	NM_004496.3	252	AACATGTTCGAGAACGGCTGCTAC/-	2/2	1	2	FACETS	0.72	0.639	0.807	0.72	0.639	0.807	SUBCLONAL	1	TRUE	1	0.361925326460369	2		388	683	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117784	70117784	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1555629022	NA	P-0015155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	54	431	0	ENST00000245479.2:c.252C>G	p.Tyr84Ter	p.Y84*	ENST00000245479	NM_000346.3	84	taC/taG	1/3	1	2	FACETS	0.338	0.288	0.393	0.338	0.288	0.393	SUBCLONAL	1	TRUE	1	0.361925326460369	2		431	883	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0015156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	109	943	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	0.452830016373471	2		943	462	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130180	2130180	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45451497	NA	P-0015157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	263	405	0	ENST00000219476.3:c.3412C>T	p.Arg1138Ter	p.R1138*	ENST00000219476	NM_000548.3	1138	Cga/Tga	30/42	1	2	FACETS	0.511	0.479	0.544	0.511	0.479	0.544	SUBCLONAL	1	TRUE	1	1.07	2		405	962	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122854	2122854	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs45517220	NA	P-0015157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	264	364	0	ENST00000219476.3:c.2225C>G	p.Ser742Ter	p.S742*	ENST00000219476	NM_000548.3	742	tCa/tGa	21/42	1	2	FACETS	0.561	0.527	0.596	0.561	0.527	0.596	SUBCLONAL	1	TRUE	1	1.07	2		364	879	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145611	11145611	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	284	450	0	ENST00000358026.2:c.3973C>T	p.Arg1325Cys	p.R1325C	ENST00000358026	NM_001128849.1	1325	Cgc/Tgc	29/36	1	2	FACETS	0.554	0.521	0.587	0.554	0.521	0.587	SUBCLONAL	1	TRUE	1	1.07	2		450	959	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	151	722	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.230045268187422	3	FACETS	1	0.92	1	1	0.92	1	CLONAL	2	TRUE	1	0.230045268187422	3		722	729	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0015175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	15	129	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	1	2	FACETS	0.852	0.627	1	0.852	0.627	1	CLONAL	1	TRUE	1	0.230045268187422	2		129	153	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0015175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	118	1023	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.230045268187422	1	FACETS	0.971	0.875	1	0.971	0.875	1	CLONAL	1	TRUE	0	0.230045268187422	1		1024	935	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0015175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	66	389	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.230045268187422	2		389	525	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591895	48591895	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs377767346	NA	P-0015175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	78	520	0	ENST00000342988.3:c.1058A>G	p.Tyr353Cys	p.Y353C	ENST00000342988	NM_005359.5	353	tAc/tGc	9/12	0.230045268187422	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.230045268187422	1		520	547	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073616	8073616	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760980466	NA	P-0015175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	41	360	0	ENST00000377482.5:c.1043C>T	p.Pro348Leu	p.P348L	ENST00000377482	NM_018948.3	348	cCg/cTg	4/4	NA	2	FACETS	0.758	0.632	0.899			1	INDETERMINATE	1	TRUE	NA	0.230045268187422	2		360	470	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128299	30128299	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	93	788	0	ENST00000263025.4:c.933A>C	p.Leu311Phe	p.L311F	ENST00000263025	NM_002746.2	311	ttA/ttC	7/9	0.230045268187422	3	FACETS	0.828	0.734	0.928	0.414	0.367	0.464	CLONAL	1	TRUE	1	0.230045268187422	3		788	1089	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554725	63554725	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	57	378	0	ENST00000307078.5:c.14T>C	p.Met5Thr	p.M5T	ENST00000307078	NM_004655.3	5	aTg/aCg	2/11	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.230045268187422	2		378	462	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11015679	11015679	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	96	573	1	ENST00000327064.4:c.273C>A	p.Ser91Arg	p.S91R	ENST00000327064	NM_199141.1	91	agC/agA	2/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.230045268187422	2		574	752	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52692207	52692218	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCACTTACCACT	TCACTTACCACT	-	novel	NA	P-0015176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	55	342	0	ENST00000394830.3:c.642_645+8del		p.X214_splice	ENST00000394830	NM_018313.4	214		6/30	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		342	161	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	76	297	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.937	0.825	1	1	0.982	1	CLONAL	2	TRUE	1	0.194569443455283	2		297	417	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0015177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	316	649	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.194569443455283	5	FACETS	0.911	0.859	0.963	0.911	0.859	0.963	CLONAL	4	TRUE	1	0.194569443455283	5		649	1152	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044595	47044595	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	96	525	1	ENST00000377604.3:c.2092G>T	p.Glu698Ter	p.E698*	ENST00000377604	NM_001204468.1	698	Gag/Tag	18/24	0.0502510176456665	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.194569443455283	2		526	681	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171455	123171455	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	98	333	0	ENST00000218089.9:c.367C>T	p.Gln123Ter	p.Q123*	ENST00000218089	NM_001042749.1	123	Cag/Tag	6/35	0.0502510176456665	2	FACETS	0.917	0.821	1			1	INDETERMINATE	2	TRUE	NA	0.194569443455283	2		333	549	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945036	151945036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771250133	NA	P-0015177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	69	610	0	ENST00000262189.6:c.2483C>T	p.Pro828Leu	p.P828L	ENST00000262189	NM_170606.2	828	cCa/cTa	14/59	0.118362233627071	3	FACETS	0.727	0.631	0.832	0.364	0.315	0.416	SUBCLONAL	1	TRUE	1	0.194569443455283	3		610	1070	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120374	70120374	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1416	148	1276	0	ENST00000245479.2:c.1376G>C	p.Gly459Ala	p.G459A	ENST00000245479	NM_000346.3	459	gGc/gCc	3/3	1	2	FACETS	0.973	0.885	1	0.973	0.885	1	CLONAL	1	TRUE	1	0.194569443455283	2		1276	1564	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39567860	39567860	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	43	298	0	ENST00000262039.4:c.616G>T	p.Glu206Ter	p.E206*	ENST00000262039	NM_002647.2	206	Gag/Tag	5/25	0.157229873668105	3	FACETS	0.896	0.75	1	0.448	0.375	0.53	CLONAL	1	TRUE	1	0.194569443455283	3		298	541	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739108	40739109	+	missense_variant	Missense_Mutation	DNP	CG	CG	AA	novel	NA	P-0015177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	70	599	2	ENST00000373198.4:c.3175_3176delinsTT	p.Arg1059Leu	p.R1059L	ENST00000373198	NM_133170.3	1059	CGg/TTg	24/32	1	2	FACETS	0.882	0.767	1	0.882	0.767	1	CLONAL	1	TRUE	1	0.194569443455283	2		601	816	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119666165	119666165	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	62	541	0	ENST00000316626.5:c.316C>G	p.His106Asp	p.H106D	ENST00000316626		106	Cac/Gac	3/12	1	2	FACETS	0.803	0.692	0.923	0.803	0.692	0.923	CLONAL	1	TRUE	1	0.194569443455283	2		541	794	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523493	106523493	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	60	401	0	ENST00000359195.3:c.2645T>A	p.Val882Glu	p.V882E	ENST00000359195	NM_002649.2	882	gTg/gAg	8/11	0.118362233627071	3	FACETS	1	0.934	1	0.573	0.493	0.659	CLONAL	1	TRUE	1	0.194569443455283	3		401	591	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0015179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	315	515	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	0.451909452346744	1	FACETS	0.644	0.614	0.673	0.644	0.614	0.673	INDETERMINATE	1	TRUE	0	0.910715304481712	1		515	585	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0015179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15026	1160	702	2	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.910715304481712	18	FACETS	1	0.997	1			1	CLONAL	1	TRUE	NA	0.910715304481712	18		704	16186	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39725902	39725902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1349958802	NA	P-0015179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	118	432	0	ENST00000361337.2:c.773C>T	p.Thr258Met	p.T258M	ENST00000361337	NM_003286.2	258	aCg/aTg	10/21	0.88993813049927	3	FACETS	0.346	0.311	0.383	0.173	0.155	0.192	SUBCLONAL	1	TRUE	1	0.910715304481712	3		432	1089	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120708	115120708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs902279692	NA	P-0015179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	193	719	0	ENST00000257566.3:c.298G>A	p.Glu100Lys	p.E100K	ENST00000257566	NM_016569.3	100	Gag/Aag	1/8	1	2	FACETS	0.438	0.405	0.472	0.438	0.405	0.472	SUBCLONAL	1	TRUE	1	0.910715304481712	2		719	968	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40491420	40491420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	356	514	0	ENST00000264657.5:c.380G>A	p.Gly127Asp	p.G127D	ENST00000264657	NM_139276.2	127	gGc/gAc	5/24	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.910715304481712	2		514	777	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177996	56177996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377424271	NA	P-0015179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	345	408	0	ENST00000399503.3:c.2969C>T	p.Thr990Ile	p.T990I	ENST00000399503	NM_005921.1	990	aCc/aTc	14/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.910715304481712	2		408	755	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	56	722	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.621	0.532	0.718	0.621	0.532	0.718	SUBCLONAL	1	FALSE	1	0.333547398035289	2		722	541	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0015180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	80	624	1	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	FALSE	1	0.333547398035289	2		625	449	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256105	133256105	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375213599	NA	P-0015180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	70	495	0	ENST00000320574.5:c.556G>A	p.Ala186Thr	p.A186T	ENST00000320574	NM_006231.2	186	Gcg/Acg	6/49	0.30835837260649	1	FACETS	0.702	0.614	0.798	0.702	0.614	0.798	SUBCLONAL	1	FALSE	0	0.333547398035289	1		495	498	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949986	44949986	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	46	261	0	ENST00000377967.4:c.3755C>A	p.Ala1252Glu	p.A1252E	ENST00000377967	NM_021140.2	1252	gCa/gAa	26/29	1	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	0	0.333547398035289	1		261	174	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523644	41523645	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs36068041	NA	P-0015181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	31	744	0	ENST00000263253.7:c.1063dup	p.Glu355GlyfsTer56	p.E355Gfs*56	ENST00000263253	NM_001429.3	354	cgg/cGgg	4/31	1	2	FACETS	0.233	0.188	0.283	0.233	0.188	0.283	SUBCLONAL	1	TRUE	1	0.840982429127369	2		744	317	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0015182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	183	434	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.789765287868237	2	FACETS	0.927	0.863	0.992	0.463	0.431	0.496	CLONAL	1	TRUE	0	0.789765287868237	2		434	500	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266134	41266136	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs587776850	NA	P-0015182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	220	344	0	ENST00000349496.5:c.133_135del	p.Ser45del	p.S45del	ENST00000349496	NM_001904.3	44	cCTTct/cct	3/15	0.789765287868237	2	FACETS	1	0.966	1	0.522	0.49	0.554	CLONAL	1	TRUE	0	0.789765287868237	2		344	534	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900268	101900270	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs863223830	NA	P-0015182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	176	484	0	ENST00000374994.4:c.705_707del	p.Ser236del	p.S236del	ENST00000374994	NM_004612.2	234	ttCTCc/ttc	4/9	0.789765287868237	1	FACETS	0.585	0.544	0.627	0.585	0.544	0.627	SUBCLONAL	1	TRUE	0	0.789765287868237	1		484	461	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156718	20156719	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0015182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	272	268	2	ENST00000379607.5:c.38_39delinsTT	p.Arg13Leu	p.R13L	ENST00000379607	NM_001412.3	13	cGC/cTT	2/7	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.789765287868237	1		270	349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0015184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	351	1074	1	ENST00000269305.4:c.376-1G>T		p.X126_splice	ENST00000269305	NM_001126112.2	126			1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.516983227736213	2		1075	938	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38318617	38318617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	184	649	5	ENST00000425967.3:c.8C>T	p.Ala3Val	p.A3V	ENST00000425967	NM_001174067.1	3	gCa/gTa	2/19	1	2	FACETS	0.899	0.831	0.969	0.899	0.831	0.969	CLONAL	1	TRUE	1	0.516983227736213	2		654	792	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0015185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	430	464	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.734500049569786	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.734500049569786	2		464	550	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420337	49420337	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	213	589	0	ENST00000301067.7:c.15412A>T	p.Ile5138Phe	p.I5138F	ENST00000301067	NM_003482.3	5138	Atc/Ttc	48/54	0.734500049569786	4	FACETS	0.893	0.829	0.96	0.447	0.414	0.48	CLONAL	1	TRUE	2	0.734500049569786	4		589	1126	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0015186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	98	435	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.350283672767313	2		435	499	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0015186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	121	843	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.350283672767313	2		843	684	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260699	16260699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	141	1191	0	ENST00000375759.3:c.7964C>T	p.Thr2655Ile	p.T2655I	ENST00000375759	NM_015001.2	2655	aCt/aTt	11/15	1	2	FACETS	0.89	0.81	0.973	0.89	0.81	0.973	CLONAL	1	TRUE	1	0.350283672767313	2		1191	905	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246518371	246518371	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	105	463	0	ENST00000388985.4:c.190C>T	p.Gln64Ter	p.Q64*	ENST00000388985		64	Cag/Tag	2/12	0.332999914555593	3	FACETS	0.809	0.724	0.899	0.404	0.362	0.45	CLONAL	1	TRUE	1	0.350283672767313	3		463	871	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421078	49421078	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	124	543	1	ENST00000301067.7:c.14671C>T	p.Gln4891Ter	p.Q4891*	ENST00000301067	NM_003482.3	4891	Cag/Tag	48/54	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.350283672767313	2		544	700	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30103666	30103666	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1434071220	NA	P-0015186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	126	1096	0	ENST00000331968.5:c.1272G>A	p.Met424Ile	p.M424I	ENST00000331968	NM_002742.2	424	atG/atA	8/18	1	2	FACETS	0.886	0.802	0.974	0.886	0.802	0.974	CLONAL	1	TRUE	1	0.350283672767313	2		1096	812	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117645	70117645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	184	1110	0	ENST00000245479.2:c.113G>A	p.Gly38Asp	p.G38D	ENST00000245479	NM_000346.3	38	gGc/gAc	1/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.350283672767313	2		1110	943	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637434	47637434	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs763459034	NA	P-0015186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	131	1011	0	ENST00000233146.2:c.568C>G	p.Leu190Val	p.L190V	ENST00000233146	NM_000251.2	190	Ctc/Gtc	3/16	1	2	FACETS	0.942	0.855	1	0.942	0.855	1	CLONAL	1	TRUE	1	0.350283672767313	2		1011	794	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0015186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	175	1367	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.350283672767313	2		1367	861	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198260931	198260931	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	133	1360	0	ENST00000335508.6:c.3388C>G	p.Pro1130Ala	p.P1130A	ENST00000335508	NM_012433.2	1130	Cct/Gct	23/25	1	2	FACETS	0.904	0.821	0.991	0.904	0.821	0.991	CLONAL	1	TRUE	1	0.350283672767313	2		1360	840	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661755	227661755	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	137	871	0	ENST00000305123.5:c.1700G>C	p.Arg567Pro	p.R567P	ENST00000305123	NM_005544.2	567	cGa/cCa	1/2	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.350283672767313	2		871	750	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0015186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	161	816	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.875	0.808	0.945	1	0.991	1	CLONAL	2	TRUE	1	0.350283672767313	2		816	525	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015602	112015602	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	137	979	0	ENST00000368678.4:c.1240G>C	p.Asp414His	p.D414H	ENST00000368678		414	Gac/Cac	11/13	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.350283672767313	2		979	682	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918581	44918585	+	frameshift_variant	Frame_Shift_Del	DEL	GGATG	GGATG	-	novel	NA	P-0015186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	122	1047	1	ENST00000377967.4:c.1065_1069del	p.Trp355Ter	p.W355*	ENST00000377967	NM_021140.2	355	tGGATG/t	12/29	1	2	FACETS	0.917	0.829	1	0.917	0.829	1	CLONAL	1	TRUE	1	0.350283672767313	2		1048	760	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0015186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	263	435	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.949	0.896	1	0.949	0.896	1	CLONAL	1	TRUE	1	0.866251506511958	2		435	640	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0015186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	226	843	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.842	0.789	0.895	0.842	0.789	0.895	CLONAL	1	TRUE	1	0.866251506511958	2		843	620	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260699	16260699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	349	1191	0	ENST00000375759.3:c.7964C>T	p.Thr2655Ile	p.T2655I	ENST00000375759	NM_015001.2	2655	aCt/aTt	11/15	1	2	FACETS	0.976	0.929	1	0.976	0.929	1	CLONAL	1	TRUE	1	0.866251506511958	2		1191	826	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421078	49421078	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	153	543	1	ENST00000301067.7:c.14671C>T	p.Gln4891Ter	p.Q4891*	ENST00000301067	NM_003482.3	4891	Cag/Tag	48/54	1	2	FACETS	0.794	0.733	0.856	0.794	0.733	0.856	SUBCLONAL	1	TRUE	1	0.866251506511958	2		544	445	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30103666	30103666	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1434071220	NA	P-0015186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	264	1096	0	ENST00000331968.5:c.1272G>A	p.Met424Ile	p.M424I	ENST00000331968	NM_002742.2	424	atG/atA	8/18	1	2	FACETS	0.924	0.872	0.976	0.924	0.872	0.976	CLONAL	1	TRUE	1	0.866251506511958	2		1096	660	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117645	70117645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	316	1110	0	ENST00000245479.2:c.113G>A	p.Gly38Asp	p.G38D	ENST00000245479	NM_000346.3	38	gGc/gAc	1/3	1	2	FACETS	0.969	0.92	1	0.969	0.92	1	CLONAL	1	TRUE	1	0.866251506511958	2		1110	753	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637434	47637434	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs763459034	NA	P-0015186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	227	1011	0	ENST00000233146.2:c.568C>G	p.Leu190Val	p.L190V	ENST00000233146	NM_000251.2	190	Ctc/Gtc	3/16	1	2	FACETS	0.905	0.85	0.961	0.905	0.85	0.961	CLONAL	1	TRUE	1	0.866251506511958	2		1011	579	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0015186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	152	1367	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	1	2	FACETS	0.435	0.398	0.474	0.435	0.398	0.474	SUBCLONAL	1	TRUE	1	0.866251506511958	2		1367	806	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198260931	198260931	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	291	1360	0	ENST00000335508.6:c.3388C>G	p.Pro1130Ala	p.P1130A	ENST00000335508	NM_012433.2	1130	Cct/Gct	23/25	1	2	FACETS	0.934	0.884	0.985	0.934	0.884	0.985	CLONAL	1	TRUE	1	0.866251506511958	2		1360	719	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661755	227661755	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	180	871	0	ENST00000305123.5:c.1700G>C	p.Arg567Pro	p.R567P	ENST00000305123	NM_005544.2	567	cGa/cCa	1/2	1	2	FACETS	0.86	0.801	0.921	0.86	0.801	0.921	CLONAL	1	TRUE	1	0.866251506511958	2		871	483	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0015186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	342	816	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.992	0.967	1	1	0.997	1	CLONAL	2	TRUE	1	0.866251506511958	2		816	398	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015602	112015602	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	276	979	0	ENST00000368678.4:c.1240G>C	p.Asp414His	p.D414H	ENST00000368678		414	Gac/Cac	11/13	1	2	FACETS	0.905	0.855	0.956	0.905	0.855	0.956	CLONAL	1	TRUE	1	0.866251506511958	2		979	704	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918581	44918585	+	frameshift_variant	Frame_Shift_Del	DEL	GGATG	GGATG	-	novel	NA	P-0015186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	242	1047	1	ENST00000377967.4:c.1065_1069del	p.Trp355Ter	p.W355*	ENST00000377967	NM_021140.2	355	tGGATG/t	12/29	1	2	FACETS	0.848	0.797	0.9	0.848	0.797	0.9	CLONAL	1	TRUE	1	0.866251506511958	2		1048	659	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102874100	102874100	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	54	430	0	ENST00000307046.8:c.60G>C	p.Leu20Phe	p.L20F	ENST00000307046	NM_001111285.1	20	ttG/ttC	1/4	1	2	FACETS	0.789	0.674	0.916	0.789	0.674	0.916	CLONAL	1	TRUE	1	0.24	2		430	570	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50820824	50820824	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	139	493	2	ENST00000398568.2:c.1999G>T	p.Glu667Ter	p.E667*	ENST00000398568	NM_001042412.1	667	Gag/Tag	12/18	0.540933111657759	1	FACETS	0.835	0.766	0.906	0.835	0.766	0.906	CLONAL	1	TRUE	0	0.540933111657759	1		495	449	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161821	47161821	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs970305479	NA	P-0015188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	112	344	0	ENST00000409792.3:c.4305G>T	p.Glu1435Asp	p.E1435D	ENST00000409792	NM_014159.6	1435	gaG/gaT	3/21	1	2	FACETS	0.798	0.721	0.879	0.798	0.721	0.879	SUBCLONAL	1	TRUE	1	0.540933111657759	2		344	519	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0015189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	370	464	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.790477807488745	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.790477807488745	1		464	555	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729734	162729734	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	376	486	0	ENST00000367921.3:c.820G>T	p.Glu274Ter	p.E274*	ENST00000367921	NM_006182.2	274	Gaa/Taa	8/18	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.790477807488745	2		486	924	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582897	95582897	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	313	306	0	ENST00000393063.1:c.1645T>C	p.Ser549Pro	p.S549P	ENST00000393063	NM_030621.3	549	Tct/Cct	11/28	0.325978514107439	1	FACETS	1	0.993	1	1	0.993	1	INDETERMINATE	1	TRUE	0	0.790477807488745	1		306	419	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510706	38510706	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	244	404	0	ENST00000254066.5:c.960G>T	p.Glu320Asp	p.E320D	ENST00000254066	NM_000964.3	320	gaG/gaT	7/9	0.790477807488745	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.790477807488745	1		404	373	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401469	401469	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	112	241	0	ENST00000380956.4:c.791A>T	p.Lys264Met	p.K264M	ENST00000380956	NM_001195286.1	264	aAg/aTg	7/9	0.764926316590591	1	FACETS	0.952	0.886	1	0.952	0.886	1	CLONAL	1	TRUE	0	0.790477807488745	1		241	180	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959168	2959168	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1296	347	530	0	ENST00000396946.4:c.2348A>G	p.Asn783Ser	p.N783S	ENST00000396946	NM_032415.4	783	aAc/aGc	18/25	0.790477807488745	4	FACETS	0.957	0.903	1	0.319	0.301	0.338	CLONAL	1	TRUE	1	0.790477807488745	4		530	1643	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0015190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	113	525	2	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	0.471798383260893	3	FACETS	0.952	0.858	1	0.476	0.429	0.525	CLONAL	1	TRUE	1	0.471798383260893	3		527	622	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0015190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	182	400	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.471798383260893	2	FACETS	0.897	0.838	0.957	0.897	0.838	0.957	CLONAL	2	TRUE	0	0.471798383260893	2		401	430	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248675	59248676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	600	821	0	ENST00000371222.2:c.67dup	p.Ser23LysfsTer8	p.S23Kfs*8	ENST00000371222	NM_002228.3	23	agc/aAgc	1/1	0.471798383260893	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.471798383260893	2		821	1220	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0015190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	349	483	0	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.471798383260893	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.471798383260893	2		483	707	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576914	7576914	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	127	616	0	ENST00000269305.4:c.932del	p.Asn311ThrfsTer34	p.N311Tfs*34	ENST00000269305	NM_001126112.2	311	aAc/ac	9/11	0.262239754101132	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.262239754101132	1		616	728	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321292	1321292	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	35	510	0	ENST00000400841.2:c.463C>T	p.Pro155Ser	p.P155S	ENST00000400841		155	Ccc/Tcc	4/6	0.219476113019016	3	FACETS	0.433	0.354	0.523			1	SUBCLONAL	1	TRUE	NA	0.262239754101132	3		510	697	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0015192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	14	188	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.642841534892541	3	FACETS	0.177	0.127	0.237	0.088	0.063	0.119	SUBCLONAL	1	TRUE	1	0.642841534892541	3		188	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0015192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	700	547	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.642841534892541	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.642841534892541	2		547	892	SUCCESS
AR	367	MSKCC	GRCh37	X	66765239	66765239	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	42	333	0	ENST00000374690.3:c.251C>A	p.Pro84His	p.P84H	ENST00000374690	NM_000044.3	84	cCc/cAc	1/8	0.329833747915971	5	FACETS	0.334	0.278	0.397	0.111	0.092	0.133	INDETERMINATE	1	TRUE	2	0.642841534892541	5		333	768	SUCCESS
AR	367	MSKCC	GRCh37	X	66765666	66765667	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1368	772	913	0	ENST00000374690.3:c.683dup	p.Thr229HisfsTer6	p.T229Hfs*6	ENST00000374690	NM_000044.3	226	-/G	1/8	0.329833747915971	5	FACETS	1	0.993	1	0.735	0.71	0.76	INDETERMINATE	2	TRUE	2	0.642841534892541	5		913	2140	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909922	100909922	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	52	490	0	ENST00000325455.5:c.2727G>C	p.Met909Ile	p.M909I	ENST00000325455	NM_001202474.3	909	atG/atC	8/8	0.642841534892541	3	FACETS	0.563	0.48	0.652	0.281	0.24	0.326	SUBCLONAL	1	TRUE	1	0.642841534892541	3		490	380	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102056857	102056857	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	217	476	0	ENST00000282441.5:c.797G>A	p.Arg266His	p.R266H	ENST00000282441	NM_001130145.2	266	cGt/cAt	4/9	0.642841534892541	3	FACETS	0.875	0.821	0.928	0.875	0.821	0.928	CLONAL	2	TRUE	1	0.642841534892541	3		476	510	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489093	56489093	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1200363001	NA	P-0015192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	272	487	0	ENST00000267101.3:c.1912G>T	p.Gly638Cys	p.G638C	ENST00000267101	NM_001982.3	638	Ggc/Tgc	16/28	0.642841534892541	3	FACETS	1	0.988	1	0.592	0.557	0.629	CLONAL	1	TRUE	1	0.642841534892541	3		487	944	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039385	49039385	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs794727372	NA	P-0015192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	535	723	0	ENST00000267163.4:c.2370C>A	p.Tyr790Ter	p.Y790*	ENST00000267163	NM_000321.2	790	taC/taA	23/27	0.642841534892541	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.642841534892541	2		723	766	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1627369	1627369	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1296	262	593	0	ENST00000344749.5:c.355G>T	p.Gly119Cys	p.G119C	ENST00000344749	NM_001136139.2	119	Ggc/Tgc	6/19	0.642841534892541	3	FACETS	0.691	0.646	0.739	0.346	0.323	0.37	SUBCLONAL	1	TRUE	1	0.642841534892541	3		593	1558	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876319	35876319	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	418	438	0	ENST00000303115.3:c.1111G>T	p.Ala371Ser	p.A371S	ENST00000303115	NM_002185.3	371	Gct/Tct	8/8	0.329833747915971	5	FACETS	0.84	0.802	0.877	0.84	0.802	0.877	INDETERMINATE	3	TRUE	2	0.642841534892541	5		438	1014	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948275	31948275	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	689	647	0	ENST00000375333.2:c.863G>T	p.Trp288Leu	p.W288L	ENST00000375333	NM_032454.1	288	tGg/tTg	6/8	0.547841643911405	5	FACETS	1	0.993	1	0.746	0.719	0.773	CLONAL	2	TRUE	2	0.642841534892541	5		647	1882	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993637	90993637	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	93	438	0	ENST00000265433.3:c.286G>C	p.Gly96Arg	p.G96R	ENST00000265433	NM_002485.4	96	Ggt/Cgt	3/16	1	2	FACETS	0.74	0.663	0.821	0.74	0.663	0.821	SUBCLONAL	1	TRUE	1	0.642841534892541	2		438	391	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402421	139402421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754815022	NA	P-0015192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	846	748	1	ENST00000277541.6:c.3496G>A	p.Gly1166Ser	p.G1166S	ENST00000277541	NM_017617.3	1166	Ggc/Agc	21/34	0.542498619618943	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	1	0.642841534892541	3		749	1616	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245315	53245315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	612	687	0	ENST00000375401.3:c.722C>T	p.Ala241Val	p.A241V	ENST00000375401	NM_004187.3	241	gCa/gTa	6/26	0.329833747915971	5	FACETS	1	0.994	1	0.78	0.75	0.809	INDETERMINATE	2	TRUE	2	0.642841534892541	5		687	1599	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	84	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.91	0.804	1	0.91	0.804	1	CLONAL	1	TRUE	1	0.273882671297509	2		493	674	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101195	27101195	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	100	644	0	ENST00000324856.7:c.4477C>T	p.Gln1493Ter	p.Q1493*	ENST00000324856	NM_006015.4	1493	Cag/Tag	18/20	0.273882671297509	1	FACETS	0.925	0.827	1	0.925	0.827	1	CLONAL	1	TRUE	0	0.273882671297509	1		644	681	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44896898	44896898	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0015193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	133	586	0	ENST00000377967.4:c.620-2A>G		p.X207_splice	ENST00000377967	NM_021140.2	207			0.273882671297509	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.273882671297509	1		586	751	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	213	297	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.867841685551267	2		297	437	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519938	NA	P-0015194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	173	314	0	ENST00000263967.3:c.1034A>C	p.Asn345Thr	p.N345T	ENST00000263967	NM_006218.2	345	aAt/aCt	5/21	1	2	FACETS	0.923	0.859	0.988	0.923	0.859	0.988	CLONAL	1	TRUE	1	0.867841685551267	2		314	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0015195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	147	749	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.205071406892559	2		750	1026	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663157	227663157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs570775459	NA	P-0015195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	111	531	1	ENST00000305123.5:c.298G>A	p.Glu100Lys	p.E100K	ENST00000305123	NM_005544.2	100	Gag/Aag	1/2	0.205071406892559	6	FACETS	0.751	0.674	0.833			1	SUBCLONAL	2	TRUE	NA	0.205071406892559	6		532	1016	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774795	73774795	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1526	335	745	0	ENST00000254810.4:c.292G>A	p.Glu98Lys	p.E98K	ENST00000254810	NM_005324.3	98	Gaa/Aaa	4/4	0.205071406892559	5	FACETS	1	0.987	1	0.765	0.721	0.811	CLONAL	2	TRUE	2	0.205071406892559	5		745	1861	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373325	118373325	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	43	454	0	ENST00000534358.1:c.6718G>C	p.Glu2240Gln	p.E2240Q	ENST00000534358	NM_005933.3	2240	Gaa/Caa	27/36	0.205071406892559	3	FACETS	0.605	0.505	0.717	0.202	0.168	0.239	SUBCLONAL	1	TRUE	0	0.205071406892559	3		454	764	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041045	29041045	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	22	291	0	ENST00000282397.4:c.383T>C	p.Ile128Thr	p.I128T	ENST00000282397	NM_002019.4	128	aTt/aCt	3/30	0.205071406892559	3	FACETS	0.566	0.438	0.715	0.189	0.146	0.239	SUBCLONAL	1	TRUE	0	0.205071406892559	3		291	418	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054719	13054719	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	22	271	0	ENST00000316448.5:c.1246G>T	p.Glu416Ter	p.E416*	ENST00000316448	NM_004343.3	416	Gag/Tag	9/9	0.205071406892559	3	FACETS	0.57	0.441	0.721	0.19	0.147	0.241	SUBCLONAL	1	TRUE	0	0.205071406892559	3		271	415	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678763	52678763	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	179	453	0	ENST00000394830.3:c.856G>T	p.Glu286Ter	p.E286*	ENST00000394830	NM_018313.4	286	Gaa/Taa	9/30	0.205071406892559	3	FACETS	0.939	0.869	1	0.939	0.869	1	CLONAL	3	TRUE	0	0.205071406892559	3		453	683	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056213	26056213	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs568647778	NA	P-0015195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	145	344	0	ENST00000343677.2:c.444G>T	p.Lys148Asn	p.K148N	ENST00000343677	NM_005319.3	148	aaG/aaT	1/1	0.205071406892559	7	FACETS	1	0.975	1	0.592	0.54	0.647	CLONAL	2	TRUE	3	0.205071406892559	7		344	903	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187990	32187990	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1395	96	665	0	ENST00000375023.3:c.1231C>G	p.Pro411Ala	p.P411A	ENST00000375023	NM_004557.3	411	Ccc/Gcc	7/30	0.205071406892559	7	FACETS	0.95	0.843	1	0.237	0.21	0.267	CLONAL	1	TRUE	3	0.205071406892559	7		665	1491	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604598	55604598	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	138	562	0	ENST00000288135.5:c.2806T>G	p.Tyr936Asp	p.Y936D	ENST00000288135	NM_000222.2	936	Tac/Gac	21/21	0.456243860632117	5	FACETS	0.781	0.708	0.857	0.26	0.236	0.286	SUBCLONAL	1	TRUE	2	0.456243860632117	5		562	1305	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981949	70981949	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	85	904	2	ENST00000276594.2:c.147C>A	p.Asp49Glu	p.D49E	ENST00000276594	NM_024504.3	49	gaC/gaA	2/8	0.441676829763952	3	FACETS	0.4	0.353	0.452	0.2	0.176	0.226	SUBCLONAL	1	TRUE	1	0.456243860632117	3		906	1143	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243482	41243482	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	70	536	0	ENST00000357654.3:c.4066C>G	p.Gln1356Glu	p.Q1356E	ENST00000357654	NM_007294.3	1356	Caa/Gaa	10/23	0.344223685813898	5	FACETS	1	0.928	1	0.547	0.477	0.622	CLONAL	1	TRUE	3	0.344223685813898	5		536	564	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133208987	133208987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1285938402	NA	P-0015197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	110	600	1	ENST00000320574.5:c.6244G>A	p.Glu2082Lys	p.E2082K	ENST00000320574	NM_006231.2	2082	Gag/Aag	45/49	0.240944252678581	4	FACETS	0.954	0.856	1	0.318	0.285	0.353	CLONAL	1	TRUE	1	0.344223685813898	4		601	901	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091782	29091782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373073383	NA	P-0015197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	119	595	2	ENST00000328354.6:c.1175C>T	p.Ala392Val	p.A392V	ENST00000328354	NM_007194.3	392	gCg/gTg	11/15	0.344223685813898	3	FACETS	0.938	0.846	1	0.469	0.423	0.518	CLONAL	1	TRUE	1	0.344223685813898	3		597	864	SUCCESS
ATR	545	MSKCC	GRCh37	3	142171975	142171975	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	35	538	0	ENST00000350721.4:c.7756G>A	p.Glu2586Lys	p.E2586K	ENST00000350721	NM_001184.3	2586	Gaa/Aaa	46/47	0.344223685813898	3	FACETS	0.611	0.501	0.734	0.306	0.25	0.367	SUBCLONAL	1	TRUE	1	0.344223685813898	3		538	390	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549445	5549445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141466336	NA	P-0015197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	128	670	0	ENST00000397747.3:c.472G>A	p.Val158Ile	p.V158I	ENST00000397747	NM_025239.3	158	Gtc/Atc	4/7	NA	2	FACETS	0.915	0.829	1			1	INDETERMINATE	1	TRUE	NA	0.344223685813898	2		670	813	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579717	7579717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs922736614	NA	P-0015198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	368	761	1	ENST00000269305.4:c.79C>T	p.Pro27Ser	p.P27S	ENST00000269305	NM_001126112.2	27	Cct/Tct	3/11	0.800985940722477	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.800985940722477	1		762	551	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644821	67644821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	247	477	0	ENST00000264010.4:c.86G>A	p.Arg29Gln	p.R29Q	ENST00000264010	NM_006565.3	29	cGg/cAg	3/12	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.800985940722477	2		477	612	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	240	297	0				ENST00000310581	NM_198253.2	-/1132			0.362864595707455	5	FACETS	1	0.989	1	0.829	0.779	0.88	CLONAL	2	TRUE	2	0.516853176404134	5		297	663	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361148	70361149	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAC	novel	NA	P-0015199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	58	334	22	ENST00000374080.3:c.6338_6339insCCA	p.Gln2112_Gln2113insHis	p.Q2112_Q2113insH	ENST00000374080		2112	-/CAC	43/45	0.438719106597439	2	FACETS	0.279	0.239	0.324			1	SUBCLONAL	1	TRUE	NA	0.516853176404134	2		356	803	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45873425	45873425	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	409	610	0	ENST00000391945.4:c.71A>G	p.Tyr24Cys	p.Y24C	ENST00000391945	NM_000400.3	24	tAc/tGc	2/23	0.381955842009691	4	FACETS	0.886	0.843	0.93	0.886	0.843	0.93	CLONAL	2	TRUE	2	0.516853176404134	4		610	1355	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436239	110436239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771355031	NA	P-0015199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	87	292	2	ENST00000375856.3:c.2162C>T	p.Pro721Leu	p.P721L	ENST00000375856	NM_003749.2	721	cCg/cTg	1/2	0.319608800046927	6	FACETS	0.878	0.776	0.986	0.293	0.258	0.329	CLONAL	1	TRUE	3	0.516853176404134	6		294	780	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467631	50467631	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	133	409	0	ENST00000331340.3:c.866C>A	p.Ser289Tyr	p.S289Y	ENST00000331340	NM_006060.4	289	tCc/tAc	8/8	0.491719095828211	3	FACETS	0.943	0.858	1	0.471	0.429	0.516	CLONAL	1	TRUE	1	0.516853176404134	3		409	687	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999781	100999781	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1188	174	607	0	ENST00000325455.5:c.21G>T	p.Lys7Asn	p.K7N	ENST00000325455	NM_001202474.3	7	aaG/aaT	1/8	0.516853176404134	4	FACETS	0.75	0.688	0.814	0.25	0.229	0.272	SUBCLONAL	1	TRUE	1	0.516853176404134	4		607	1362	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106939	27106960	+	frameshift_variant	Frame_Shift_Del	DEL	GCCATTGCAGTGCAGAAGGGCA	GCCATTGCAGTGCAGAAGGGCA	-	novel	NA	P-0015199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	244	372	0	ENST00000324856.7:c.6551_6572del	p.Ala2184ValfsTer9	p.A2184Vfs*9	ENST00000324856	NM_006015.4	2184	GCCATTGCAGTGCAGAAGGGCAgt/gt	20/20	0.489024196332826	3	FACETS	0.887	0.833	0.941	0.887	0.833	0.941	CLONAL	2	TRUE	1	0.516853176404134	3		372	670	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439577	51439577	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	221	323	1	ENST00000262662.1:c.142G>T	p.Gly48Ter	p.G48*	ENST00000262662		48	Gga/Tga	4/4	0.489024196332826	3	FACETS	0.947	0.889	1	0.947	0.889	1	CLONAL	2	TRUE	1	0.516853176404134	3		324	568	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70442635	70442635	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	176	516	0	ENST00000373644.4:c.4957A>G	p.Lys1653Glu	p.K1653E	ENST00000373644	NM_030625.2	1653	Aag/Gag	10/12	0.491719095828211	3	FACETS	0.951	0.877	1	0.476	0.438	0.515	CLONAL	1	TRUE	1	0.516853176404134	3		516	901	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142462	119142462	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	494	493	1	ENST00000264033.4:c.461T>C	p.Leu154Pro	p.L154P	ENST00000264033	NM_005188.3	154	cTg/cCg	3/16	0.516853176404134	4	FACETS	0.963	0.926	1	0.963	0.926	1	CLONAL	3	TRUE	1	0.516853176404134	4		494	1004	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433304	49433304	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	362	530	0	ENST00000301067.7:c.8143G>T	p.Gly2715Trp	p.G2715W	ENST00000301067	NM_003482.3	2715	Ggg/Tgg	32/54	0.491719095828211	3	FACETS	0.925	0.88	0.971	0.925	0.88	0.971	CLONAL	2	TRUE	1	0.516853176404134	3		530	953	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589780	28589780	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	366	518	0	ENST00000241453.7:c.2600T>C	p.Ile867Thr	p.I867T	ENST00000241453	NM_004119.2	867	aTt/aCt	21/24	0.319608800046927	6	FACETS	1	0.976	1	0.701	0.664	0.739	CLONAL	2	TRUE	3	0.516853176404134	6		518	1369	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047519	49047519	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1131690908	NA	P-0015199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	223	371	0	ENST00000267163.4:c.2513C>G	p.Ser838Ter	p.S838*	ENST00000267163	NM_000321.2	838	tCa/tGa	24/27	0.276702261968225	3	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.516853176404134	3		371	470	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022892	33022892	+	start_lost,splice_region_variant	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0015199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	111	283	0	ENST00000300177.4:c.1A>G	p.Met1?	p.M1?	ENST00000300177	NM_001191322.1	1	Atg/Gtg	2/2	1	2	FACETS	0.985	0.892	1	0.985	0.892	1	CLONAL	1	TRUE	1	0.516853176404134	2		283	436	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991327	41991327	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0015199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	222	587	0	ENST00000219905.7:c.2158A>T	p.Lys720Ter	p.K720*	ENST00000219905	NM_001164273.1	720	Aag/Tag	5/24	1	2	FACETS	0.978	0.912	1	0.978	0.912	1	CLONAL	1	TRUE	1	0.516853176404134	2		587	878	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587781702	NA	P-0015199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	849	572	0	ENST00000269305.4:c.920-1G>C		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.471121433036196	4	FACETS	0.996	0.972	1	0.996	0.972	1	CLONAL	4	TRUE	0	0.516853176404134	4		572	1251	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78921083	78921083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755012671	NA	P-0015199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	197	651	1	ENST00000306801.3:c.3197G>A	p.Arg1066Gln	p.R1066Q	ENST00000306801	NM_020761.2	1066	cGg/cAg	27/34	0.491719095828211	3	FACETS	0.807	0.746	0.871	0.404	0.373	0.436	CLONAL	1	TRUE	1	0.516853176404134	3		652	1188	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376212	15376212	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs551722840	NA	P-0015199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	170	499	1	ENST00000263377.2:c.802G>T	p.Val268Leu	p.V268L	ENST00000263377	NM_058243.2	268	Gta/Tta	5/20	0.491719095828211	3	FACETS	0.928	0.854	1	0.464	0.427	0.503	CLONAL	1	TRUE	1	0.516853176404134	3		500	892	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968177	18968177	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	372	553	1	ENST00000262803.5:c.2017A>G	p.Lys673Glu	p.K673E	ENST00000262803	NM_002911.3	673	Aag/Gag	15/24	0.491719095828211	3	FACETS	0.936	0.891	0.981	0.936	0.891	0.981	CLONAL	2	TRUE	1	0.516853176404134	3		554	968	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091750	29091750	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	171	437	1	ENST00000328354.6:c.1207G>A	p.Gly403Arg	p.G403R	ENST00000328354	NM_007194.3	403	Ggg/Agg	11/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.516853176404134	2		438	614	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97897747	97897747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	155	421	0	ENST00000289081.3:c.724C>T	p.Leu242Phe	p.L242F	ENST00000289081	NM_000136.2	242	Ctc/Ttc	8/15	0.49545715086533	3	FACETS	0.856	0.783	0.931	0.428	0.391	0.466	CLONAL	1	TRUE	1	0.516853176404134	3		421	882	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035973	47035973	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	565	415	1	ENST00000377604.3:c.651G>A	p.Trp217Ter	p.W217*	ENST00000377604	NM_001204468.1	217	tgG/tgA	7/24	0.438719106597439	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.516853176404134	2		416	875	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0015200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	176	635	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	1	2	FACETS	0.996	0.921	1	0.996	0.921	1	CLONAL	1	TRUE	1	0.529594046389639	2		635	667	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431939	49431939	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	207	816	1	ENST00000301067.7:c.9200A>T	p.Asn3067Ile	p.N3067I	ENST00000301067	NM_003482.3	3067	aAt/aTt	34/54	1	2	FACETS	0.97	0.902	1	0.97	0.902	1	CLONAL	1	TRUE	1	0.529594046389639	2		817	806	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0015201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	429	636	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.803279855024393	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.803279855024393	1		636	605	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254678	16254679	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0015201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	356	615	1	ENST00000375759.3:c.1943_1944delinsTT	p.Arg648Leu	p.R648L	ENST00000375759	NM_015001.2	648	cGG/cTT	11/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.803279855024393	2		616	867	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636080	28636080	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1483557529	NA	P-0015201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	764	673	0	ENST00000241453.7:c.292C>A	p.Pro98Thr	p.P98T	ENST00000241453	NM_004119.2	98	Cca/Aca	3/24	0.803279855024393	2	FACETS	0.991	0.971	1	0.991	0.971	1	CLONAL	2	TRUE	0	0.803279855024393	2		673	960	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916735	48916735	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	231	342	0	ENST00000267163.4:c.265G>T	p.Gly89Ter	p.G89*	ENST00000267163	NM_000321.2	89	Gga/Tga	3/27	0.803279855024393	2	FACETS	0.934	0.896	0.969	0.934	0.896	0.969	CLONAL	2	TRUE	0	0.803279855024393	2		342	308	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7132306	7132306	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs753474375	NA	P-0015201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	285	484	0	ENST00000302850.5:c.2705G>T	p.Arg902Leu	p.R902L	ENST00000302850	NM_000208.2	902	cGc/cTc	14/22	1	2	FACETS	0.965	0.913	1	0.965	0.913	1	CLONAL	1	TRUE	1	0.803279855024393	2		484	735	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266774	18266774	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	382	365	0	ENST00000222254.8:c.85G>T	p.Asp29Tyr	p.D29Y	ENST00000222254	NM_005027.3	29	Gac/Tac	2/16	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.803279855024393	2		365	823	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197161	26197161	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	255	464	0	ENST00000356476.2:c.318G>C	p.Glu106Asp	p.E106D	ENST00000356476		106	gaG/gaC	1/1	1	2	FACETS	0.932	0.878	0.988	0.932	0.878	0.988	CLONAL	1	TRUE	1	0.803279855024393	2		464	681	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396312	139396322	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCCGGTGGT	CTGCCGGTGGT	-	novel	NA	P-0015201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	483	841	0	ENST00000277541.6:c.5516_5526del	p.Asp1839ValfsTer10	p.D1839Vfs*10	ENST00000277541	NM_017617.3	1839	gACCACCGGCAG/g	30/34	1	2	FACETS	0.901	0.862	0.94	0.901	0.862	0.94	CLONAL	1	TRUE	1	0.803279855024393	2		841	1335	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412266	139412266	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	550	828	0	ENST00000277541.6:c.1379del	p.Pro460ArgfsTer171	p.P460Rfs*171	ENST00000277541	NM_017617.3	460	cCg/cg	8/34	1	2	FACETS	0.949	0.911	0.987	0.949	0.911	0.987	CLONAL	1	TRUE	1	0.803279855024393	2		828	1443	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932902	39932902	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	392	536	0	ENST00000378444.4:c.1697G>T	p.Arg566Leu	p.R566L	ENST00000378444	NM_001123385.1	566	cGc/cTc	4/15	0.14585636261117	4	FACETS	0.965	0.921	1	0.965	0.921	1	INDETERMINATE	2	TRUE	2	0.803279855024393	4		536	912	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504029	123504029	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	166	332	0	ENST00000371139.4:c.205G>T	p.Ala69Ser	p.A69S	ENST00000371139	NM_001114937.2	69	Gca/Tca	3/4	0.14585636261117	4	FACETS	0.78	0.722	0.838	0.78	0.722	0.838	INDETERMINATE	2	TRUE	2	0.803279855024393	4		332	478	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0015202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	560	840	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.467566014415904	2	FACETS	0.893	0.865	0.921	1	0.997	1	CLONAL	3	TRUE	0	0.467566014415904	2		842	894	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830754	3830754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	101	338	0	ENST00000262367.5:c.1802G>A	p.Arg601Gln	p.R601Q	ENST00000262367	NM_004380.2	601	cGg/cAg	8/31	0.38892845907876	3	FACETS	1	0.979	1	0.454	0.409	0.502	CLONAL	1	TRUE	0	0.467566014415904	3		338	391	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557547	21557547	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	114	572	0	ENST00000382592.4:c.2298C>G	p.His766Gln	p.H766Q	ENST00000382592	NM_014572.2	766	caC/caG	5/8	0.368411837692537	3	FACETS	1	0.914	1	0.338	0.305	0.372	CLONAL	1	TRUE	0	0.467566014415904	3		572	594	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467800	66467800	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	12	289	0	ENST00000273854.3:c.469G>C	p.Glu157Gln	p.E157Q	ENST00000273854	NM_004439.5	157	Gag/Cag	3/18	0.266470998721156	3	FACETS	0.265	0.186	0.363	0.132	0.093	0.182	INDETERMINATE	1	TRUE	1	0.467566014415904	3		289	239	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467874	66467874	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	84	291	0	ENST00000273854.3:c.395T>G	p.Phe132Cys	p.F132C	ENST00000273854	NM_004439.5	132	tTt/tGt	3/18	0.266470998721156	3	FACETS	0.815	0.729	0.904	0.815	0.729	0.904	INDETERMINATE	2	TRUE	1	0.467566014415904	3		291	272	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31451743	31451743	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	86	275	0	ENST00000344624.3:c.2579C>T	p.Ala860Val	p.A860V	ENST00000344624		860	gCa/gTa	18/33	0.3401358602143	3	FACETS	0.938	0.843	1	0.938	0.843	1	CLONAL	2	TRUE	1	0.467566014415904	3		275	242	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672359	86672359	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	14	321	0	ENST00000274376.6:c.2161G>T	p.Glu721Ter	p.E721*	ENST00000274376	NM_002890.2	721	Gaa/Taa	16/25	0.243140736430507	0	FACETS	0.142	0.102	0.19			1	INDETERMINATE	1	TRUE	0	0.467566014415904	0		321	225	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046507	69046507	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	43	486	0	ENST00000288368.4:c.3980A>C	p.Asn1327Thr	p.N1327T	ENST00000288368	NM_024870.2	1327	aAc/aCc	32/40	0.467566014415904	3	FACETS	0.427	0.357	0.505	0.214	0.178	0.253	SUBCLONAL	1	TRUE	1	0.467566014415904	3		486	531	SUCCESS
AR	367	MSKCC	GRCh37	X	66905953	66905953	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	21	252	1	ENST00000374690.3:c.1870G>A	p.Gly624Arg	p.G624R	ENST00000374690	NM_000044.3	624	Ggg/Agg	3/8	0.467566014415904	2	FACETS	0.336	0.259	0.426			1	SUBCLONAL	1	TRUE	NA	0.467566014415904	2		253	267	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	13	297	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.754	0.538	1	0.754	0.538	1	CLONAL	1	TRUE	1	0.15	2		297	230	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15827398	15827398	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	13	229	1	ENST00000307771.7:c.514T>A	p.Cys172Ser	p.C172S	ENST00000307771	NM_005089.3	172	Tgt/Agt	7/11	1	1	FACETS	0.826	0.59	1	0.826	0.59	1	CLONAL	1	TRUE	0	0.15	1		230	194	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266112	41266112	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913228	NA	P-0015203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	20	291	0	ENST00000349496.5:c.109T>C	p.Ser37Pro	p.S37P	ENST00000349496	NM_001904.3	37	Tct/Cct	3/15	1	2	FACETS	0.794	0.607	1	0.794	0.607	1	CLONAL	1	TRUE	1	0.15	2		291	336	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855831	45855831	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747646421	NA	P-0015203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	32	608	0	ENST00000391945.4:c.1979C>T	p.Ala660Val	p.A660V	ENST00000391945	NM_000400.3	660	gCg/gTg	21/23	1	2	FACETS	0.805	0.652	0.978	0.805	0.652	0.978	CLONAL	1	TRUE	1	0.15	2		608	530	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114905804	114905804	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	43	551	0	ENST00000543371.1:c.823G>T	p.Gly275Ter	p.G275*	ENST00000543371	NM_001198531.1	275	Gga/Tga	8/14	1	2	FACETS	0.968	0.809	1	0.968	0.809	1	CLONAL	1	TRUE	1	0.15	2		551	592	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446438	49446438	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0015203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	50	424	0	ENST00000301067.7:c.1167C>G	p.Tyr389Ter	p.Y389*	ENST00000301067	NM_003482.3	389	taC/taG	9/54	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.15	2		424	483	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789707	3789707	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	25	490	0	ENST00000262367.5:c.4152A>T	p.Glu1384Asp	p.E1384D	ENST00000262367	NM_004380.2	1384	gaA/gaT	25/31	1	2	FACETS	0.703	0.553	0.877	0.703	0.553	0.877	SUBCLONAL	1	TRUE	1	0.15	2		490	474	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466829	57466829	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	31	393	1	ENST00000371085.3:c.48G>T	p.Glu16Asp	p.E16D	ENST00000371085	NM_000516.4	16	gaG/gaT	1/13	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.15	2		394	278	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128419974	128419974	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	30	550	2	ENST00000265960.3:c.454C>A	p.Gln152Lys	p.Q152K	ENST00000265960	NM_001006617.1	152	Cag/Aag	4/12	1	2	FACETS	0.67	0.538	0.82	0.67	0.538	0.82	SUBCLONAL	1	TRUE	1	0.15	2		552	597	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939807	76939807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	24	230	0	ENST00000373344.5:c.941G>A	p.Arg314Lys	p.R314K	ENST00000373344	NM_000489.3	314	aGa/aAa	9/35	1	1	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	0	0.15	1		230	258	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578412	7578412	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519747	NA	P-0015204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	161	684	0	ENST00000269305.4:c.518T>G	p.Val173Gly	p.V173G	ENST00000269305	NM_001126112.2	173	gTg/gGg	5/11	0.337104738044087	2	FACETS	0.844	0.779	0.911	0.844	0.779	0.911	CLONAL	2	TRUE	0	0.351274035254367	2		684	543	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383268	4383268	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	32	475	0	ENST00000261254.3:c.62T>A	p.Leu21His	p.L21H	ENST00000261254	NM_001759.3	21	cTc/cAc	1/5	0.351274035254367	4	FACETS	0.425	0.344	0.517			1	SUBCLONAL	1	TRUE	NA	0.351274035254367	4		475	579	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500294	99500294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	129	587	0	ENST00000268035.6:c.3727G>A	p.Glu1243Lys	p.E1243K	ENST00000268035	NM_000875.3	1243	Gaa/Aaa	21/21	0.351274035254367	3	FACETS	0.764	0.696	0.836	0.509	0.464	0.557	SUBCLONAL	2	TRUE	0	0.351274035254367	3		587	565	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39237798	39237798	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	62	468	0	ENST00000402219.2:c.2437G>C	p.Asp813His	p.D813H	ENST00000402219	NM_005633.3	813	Gac/Cac	15/23	0.319303275915814	5	FACETS	0.689	0.594	0.793	0.138	0.118	0.159	SUBCLONAL	1	TRUE	0	0.351274035254367	5		468	782	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754904	57754905	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	50	305	0	ENST00000274289.3:c.285dup	p.Cys96MetfsTer10	p.C96Mfs*10	ENST00000274289	NM_006622.3	95	-/A	2/14	0.340174310754304	4	FACETS	0.772	0.656	0.901	0.386	0.328	0.451	CLONAL	1	TRUE	2	0.351274035254367	4		305	498	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845479	151845479	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	157	618	0	ENST00000262189.6:c.13533T>G	p.Ile4511Met	p.I4511M	ENST00000262189	NM_170606.2	4511	atT/atG	52/59	0.351274035254367	3	FACETS	0.756	0.694	0.82			1	SUBCLONAL	2	TRUE	NA	0.351274035254367	3		618	695	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0015206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1169	64	577	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.577	0.497	0.664	0.577	0.497	0.664	SUBCLONAL	1	TRUE	1	0.18	2		577	1233	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696689	47696689	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519972	NA	P-0015206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	58	637	0	ENST00000347630.2:c.259T>A	p.Tyr87Asn	p.Y87N	ENST00000347630	NM_001007230.1	87	Tac/Aac	5/11	1	2	FACETS	0.597	0.511	0.692	0.597	0.511	0.692	SUBCLONAL	1	TRUE	1	0.18	2		637	1079	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533099	63533099	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	66	642	1	ENST00000307078.5:c.1795G>T	p.Ala599Ser	p.A599S	ENST00000307078	NM_004655.3	599	Gcc/Tcc	7/11	1	2	FACETS	0.811	0.702	0.93	0.811	0.702	0.93	CLONAL	1	TRUE	1	0.18	2		643	904	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325622	87325622	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	50	561	0	ENST00000277120.3:c.499T>C	p.Ser167Pro	p.S167P	ENST00000277120		167	Tcc/Ccc	6/19	1	2	FACETS	0.624	0.528	0.731	0.624	0.528	0.731	SUBCLONAL	1	TRUE	1	0.18	2		561	890	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929401	44929407	+	frameshift_variant	Frame_Shift_Del	DEL	AGCAGAC	AGCAGAC	-	novel	NA	P-0015206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	64	456	0	ENST00000377967.4:c.2502_2508del	p.Gln835ProfsTer30	p.Q835Pfs*30	ENST00000377967	NM_021140.2	834	gAGCAGACa/ga	17/29	1	1	FACETS	0.839	0.726	0.963	0.839	0.726	0.963	CLONAL	1	TRUE	0	0.18	1		456	771	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55569989	55569989	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	247	440	0	ENST00000288135.5:c.856G>C	p.Gly286Arg	p.G286R	ENST00000288135	NM_000222.2	286	Gga/Cga	5/21	0.234641020510859	1	FACETS	1	0.987	1	1	0.987	1	INDETERMINATE	1	TRUE	0	0.599876985343888	1		440	508	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624288	89624288	+	frameshift_variant	Frame_Shift_Ins	INS	T	T	GGATG	novel	NA	P-0015207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	150	476	0	ENST00000371953.3:c.62delinsGGATG	p.Phe21TrpfsTer24	p.F21Wfs*24	ENST00000371953	NM_000314.4	21	tTc/tGGATGc	1/9	0.494995689174037	1	FACETS	0.778	0.717	0.84	0.778	0.717	0.84	SUBCLONAL	1	TRUE	0	0.599876985343888	1		476	450	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	157	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.558561386721054	3	FACETS	0.823	0.761	0.886	0.823	0.761	0.886	CLONAL	2	TRUE	1	0.558561386721054	3		493	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0015208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	339	749	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.521304128913469	2	FACETS	0.917	0.875	0.958	0.917	0.875	0.958	CLONAL	2	TRUE	0	0.558561386721054	2		750	662	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0015208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	144	699	1	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.145118455918582	6	FACETS	1	0.935	1	0.681	0.625	0.74	INDETERMINATE	2	TRUE	3	0.558561386721054	6		700	534	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81991588	81991589	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	98	342	0	ENST00000359376.3:c.3785dup	p.Phe1263ValfsTer11	p.F1263Vfs*11	ENST00000359376	NM_002661.3	1261	-/A	33/33	0.131208362222128	4	FACETS	0.839	0.757	0.924	0.839	0.757	0.924	INDETERMINATE	2	TRUE	2	0.558561386721054	4		342	326	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47596676	47596676	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	75	292	0	ENST00000263735.4:c.32T>G	p.Leu11Arg	p.L11R	ENST00000263735	NM_002354.2	11	cTt/cGt	1/9	0.558561386721054	3	FACETS	0.85	0.749	0.958	0.425	0.374	0.479	CLONAL	1	TRUE	1	0.558561386721054	3		292	404	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043464	180043464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	212	634	0	ENST00000261937.6:c.3122G>A	p.Arg1041Gln	p.R1041Q	ENST00000261937	NM_182925.4	1041	cGg/cAg	23/30	0.145118455918582	6	FACETS	1	0.986	1	0.8	0.746	0.854	INDETERMINATE	2	TRUE	3	0.558561386721054	6		634	670	SUCCESS
APC	324	MSKCC	GRCh37	5	112170714	112170715	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	T	novel	NA	P-0015208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	156	502	0	ENST00000257430.4:c.1810_1811delinsT	p.Ala604LeufsTer6	p.A604Lfs*6	ENST00000257430	NM_000038.5	604	GCt/Tt	15/16	0.145118455918582	6	FACETS	0.844	0.78	0.91	0.844	0.78	0.91	INDETERMINATE	3	TRUE	3	0.558561386721054	6		502	467	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0015209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	146	404	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.555971915700202	2		404	496	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125525140	125525140	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	200	538	0	ENST00000428830.2:c.1356G>C	p.Lys452Asn	p.K452N	ENST00000428830	NM_001114121.2	452	aaG/aaC	13/14	1	2	FACETS	0.938	0.871	1	0.938	0.871	1	CLONAL	1	TRUE	1	0.555971915700202	2		538	767	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541116	187541121	+	inframe_deletion	In_Frame_Del	DEL	GCTGTT	GCTGTT	-	novel	NA	P-0015209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	114	358	0	ENST00000441802.2:c.6619_6624del	p.Asn2207_Ser2208del	p.N2207_S2208del	ENST00000441802	NM_005245.3	2207	AACAGC/-	10/27	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.555971915700202	2		358	396	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0015211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	379	775	1	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.997	0.947	1	0.997	0.947	1	CLONAL	1	TRUE	1	0.604260560954124	2		776	1258	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0015211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	234	673	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	0.865	0.808	0.924	0.865	0.808	0.924	CLONAL	1	TRUE	1	0.604260560954124	2		673	895	SUCCESS
APC	324	MSKCC	GRCh37	5	112111408	112111411	+	frameshift_variant	Frame_Shift_Del	DEL	ATAG	ATAG	-	rs387906231	NA	P-0015211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	142	411	0	ENST00000257430.4:c.509_512del	p.Asp170ValfsTer4	p.D170Vfs*4	ENST00000257430	NM_000038.5	169	ATAGat/at	5/16	0.585113246489996	1	FACETS	0.818	0.753	0.884	0.818	0.753	0.884	CLONAL	1	TRUE	0	0.604260560954124	1		411	401	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	172	461	4	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	0.909	0.841	0.981	0.909	0.841	0.981	CLONAL	1	TRUE	1	0.604260560954124	2		465	626	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030692	48030692	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs267608092	NA	P-0015211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	176	406	1	ENST00000234420.5:c.3312del	p.Phe1104LeufsTer11	p.F1104Lfs*11	ENST00000234420	NM_000179.2	1102	acT/ac	5/10	0.604260560954124	1	FACETS	0.912	0.849	0.975	0.912	0.849	0.975	CLONAL	1	TRUE	0	0.604260560954124	1		407	446	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163744	72163744	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1248852117	NA	P-0015211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	282	770	0	ENST00000357731.5:c.614C>T	p.Ala205Val	p.A205V	ENST00000357731	NM_173808.2	205	gCg/gTg	4/7	1	2	FACETS	0.976	0.919	1	0.976	0.919	1	CLONAL	1	TRUE	1	0.604260560954124	2		770	956	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489845	2489845	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	283	740	1	ENST00000355716.4:c.242G>A	p.Gly81Asp	p.G81D	ENST00000355716	NM_003820.2	81	gGc/gAc	3/8	1	2	FACETS	0.924	0.869	0.98	0.924	0.869	0.98	CLONAL	1	TRUE	1	0.604260560954124	2		741	1014	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743782	46743782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201788900	NA	P-0015211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	270	683	1	ENST00000371975.4:c.2072G>A	p.Arg691Gln	p.R691Q	ENST00000371975	NM_003579.3	691	cGg/cAg	18/18	1	2	FACETS	0.994	0.935	1	0.994	0.935	1	CLONAL	1	TRUE	1	0.604260560954124	2		684	899	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630476	90630476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	285	691	1	ENST00000330062.3:c.835G>A	p.Asp279Asn	p.D279N	ENST00000330062	NM_002168.2	279	Gac/Aac	7/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.604260560954124	2		692	923	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823760	3823760	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376314132	NA	P-0015211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	157	359	1	ENST00000262367.5:c.2455G>A	p.Val819Met	p.V819M	ENST00000262367	NM_004380.2	819	Gtg/Atg	13/31	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.604260560954124	2		360	517	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374912	45374912	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	283	621	0	ENST00000262160.6:c.931T>C	p.Phe311Leu	p.F311L	ENST00000262160	NM_005901.5	311	Ttc/Ctc	8/11	1	2	FACETS	0.753	0.714	0.792	1	0.994	1	SUBCLONAL	2	TRUE	1	0.604260560954124	2		621	622	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403245	213403245	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	211	604	0	ENST00000342788.4:c.10G>A	p.Ala4Thr	p.A4T	ENST00000342788	NM_005235.2	4	Gcg/Acg	1/28	1	2	FACETS	0.883	0.822	0.946	0.883	0.822	0.946	CLONAL	1	TRUE	1	0.604260560954124	2		604	791	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725324	49725324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748664213	NA	P-0015211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	278	577	0	ENST00000449682.2:c.101G>A	p.Arg34His	p.R34H	ENST00000449682	NM_020998.3	34	cGc/cAc	2/18	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.604260560954124	2		577	782	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442507	52442507	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	295	643	0	ENST00000460680.1:c.238A>G	p.Met80Val	p.M80V	ENST00000460680	NM_004656.3	80	Atg/Gtg	4/17	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.604260560954124	2		643	969	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156926	89156928	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs1257815746	NA	P-0015211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	100	579	0	ENST00000336596.2:c.30_32del	p.Leu11del	p.L11del	ENST00000336596	NM_005233.5	10	CTT/-	1/17	1	2	FACETS	0.406	0.362	0.453	0.406	0.362	0.453	SUBCLONAL	1	TRUE	1	0.604260560954124	2		579	815	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953041	2953041	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149857605	NA	P-0015211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	262	864	0	ENST00000396946.4:c.2899C>T	p.Arg967Cys	p.R967C	ENST00000396946	NM_032415.4	967	Cgc/Tgc	22/25	0.604260560954124	3	FACETS	0.825	0.771	0.88	0.412	0.385	0.44	CLONAL	1	TRUE	1	0.604260560954124	3		864	1369	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0015212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	69	551	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.345575258688352	4	FACETS	0.57	0.495	0.651	0.285	0.247	0.326	SUBCLONAL	1	TRUE	2	0.355817459835334	4		551	923	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0015212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	61	587	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	0.3601297903969	3	FACETS	0.656	0.565	0.754	0.328	0.282	0.377	SUBCLONAL	1	TRUE	1	0.355817459835334	3		587	616	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221131	5221131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201447856	NA	P-0015212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	33	617	1	ENST00000357368.4:c.3335C>T	p.Thr1112Met	p.T1112M	ENST00000357368	NM_002850.3	1112	aCg/aTg	20/38	0.356814806573734	1	FACETS	0.384	0.313	0.464	0.384	0.313	0.464	SUBCLONAL	1	TRUE	0	0.355817459835334	1		618	397	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691945	30691945	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	57	300	0	ENST00000295754.5:c.447C>A	p.Phe149Leu	p.F149L	ENST00000295754	NM_003242.5	149	ttC/ttA	3/7	0.275769164845433	4	FACETS	0.627	0.537	0.725	0.313	0.268	0.363	SUBCLONAL	1	TRUE	2	0.355817459835334	4		300	693	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971042	21971055	+	frameshift_variant	Frame_Shift_Del	DEL	CGTCCAGCCGCGCC	CGTCCAGCCGCGCC	-	novel	NA	P-0015212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	86	311	0	ENST00000304494.5:c.303_316del	p.Leu104CysfsTer11	p.L104Cfs*11	ENST00000304494	NM_000077.4	101	ggGGCGCGGCTGGACGtg/ggtg	2/3	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.355817459835334	2		311	474	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0015213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	57	454	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.648	0.554	0.752	0.648	0.554	0.752	SUBCLONAL	1	TRUE	1	0.18	2		454	977	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559101	29559101	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202023	NA	P-0015213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	24	92	1	ENST00000356175.3:c.3208C>T	p.Gln1070Ter	p.Q1070*	ENST00000356175	NM_000267.3	1070	Cag/Tag	25/57	1	2	FACETS	0.92	0.722	1	0.92	0.722	1	CLONAL	1	TRUE	1	0.18	2		93	290	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220698	1220698	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	118	755	0	ENST00000326873.7:c.716G>T	p.Trp239Leu	p.W239L	ENST00000326873	NM_000455.4	239	tGg/tTg	5/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.18	2		755	1108	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610500	10610501	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0015213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	54	579	0	ENST00000171111.5:c.209_210delinsCT	p.Leu70Pro	p.L70P	ENST00000171111	NM_203500.1	70	cTG/cCT	2/6	1	2	FACETS	0.639	0.544	0.744	0.639	0.544	0.744	SUBCLONAL	1	TRUE	1	0.18	2		579	939	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422501	225422501	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0015213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	90	394	0	ENST00000264414.4:c.139A>T	p.Lys47Ter	p.K47*	ENST00000264414	NM_003590.4	47	Aag/Tag	2/16	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.18	2		394	921	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274910	41274910	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	57	348	0	ENST00000349496.5:c.1160A>G	p.Asn387Ser	p.N387S	ENST00000349496	NM_001904.3	387	aAt/aGt	8/15	1	2	FACETS	0.806	0.69	0.933	0.806	0.69	0.933	CLONAL	1	TRUE	1	0.18	2		348	786	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437351	52437587	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGACACTTTGTGGTCACTTGGCCACTTCCCTCCTCCCTCCTGGGTGCACCAAGTGGCCAGTGAGCCAGTCCAAGGCCCACCTGTCAGCGCCAGGGGACTCAGCACCCCATCCTCAGCCAGGTGCAGCAGGCCTGTGCTGATGACAGGACCCAGATCACGGACAGCACGGTTGTAGCGTATGCAGTCAACACGCAGCAGGCTGTCATCCTCTCCAAAAAGCACCTTGGAGATGTGGG	AGGACACTTTGTGGTCACTTGGCCACTTCCCTCCTCCCTCCTGGGTGCACCAAGTGGCCAGTGAGCCAGTCCAAGGCCCACCTGTCAGCGCCAGGGGACTCAGCACCCCATCCTCAGCCAGGTGCAGCAGGCCTGTGCTGATGACAGGACCCAGATCACGGACAGCACGGTTGTAGCGTATGCAGTCAACACGCAGCAGGCTGTCATCCTCTCCAAAAAGCACCTTGGAGATGTGGG	-	novel	NA	P-0015213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	60	298	0	ENST00000460680.1:c.1574_1730-37del		p.X525_splice	ENST00000460680	NM_004656.3	525		13/17	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.18	2		298	576	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242872	142242872	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0015213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	64	500	2	ENST00000350721.4:c.4115C>G	p.Ser1372Ter	p.S1372*	ENST00000350721	NM_001184.3	1372	tCa/tGa	22/47	1	2	FACETS	0.66	0.569	0.759	0.66	0.569	0.759	SUBCLONAL	1	TRUE	1	0.18	2		502	1078	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	276	722	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.429623135173175	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.429623135173175	3		722	739	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100956	41100956	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	101	436	2	ENST00000373198.4:c.1400C>A	p.Pro467His	p.P467H	ENST00000373198	NM_133170.3	467	cCc/cAc	8/32	0.321106038381126	3	FACETS	0.917	0.821	1			1	CLONAL	1	TRUE	NA	0.429623135173175	3		438	623	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs149840192	NA	P-0015214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	45	618	3	ENST00000275493.2:c.866C>A	p.Ala289Asp	p.A289D	ENST00000275493	NM_005228.3	289	gCc/gAc	7/28	0.214062848869083	5	FACETS	0.343	0.287	0.406	0.114	0.095	0.136	INDETERMINATE	1	TRUE	2	0.429623135173175	5		621	1003	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578463	7578463	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371524413	NA	P-0015214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	356	832	0	ENST00000269305.4:c.467G>C	p.Arg156Pro	p.R156P	ENST00000269305	NM_001126112.2	156	cGc/cCc	5/11	0.320726914283638	3	FACETS	1	0.993	1	0.831	0.791	0.87	CLONAL	2	TRUE	0	0.429623135173175	3		832	808	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541523	187541523	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	248	354	0	ENST00000441802.2:c.6217G>T	p.Asp2073Tyr	p.D2073Y	ENST00000441802	NM_005245.3	2073	Gac/Tac	10/27	0.383387096184933	3	FACETS	1	0.99	1	0.826	0.779	0.873	CLONAL	2	TRUE	0	0.429623135173175	3		354	566	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383489	31383489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1203334353	NA	P-0015214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	61	499	0	ENST00000328111.2:c.1286G>A	p.Ser429Asn	p.S429N	ENST00000328111	NM_006892.3	429	aGc/aAc	12/23	0.429623135173175	4	FACETS	0.463	0.398	0.534	0.154	0.132	0.178	SUBCLONAL	1	TRUE	1	0.429623135173175	4		499	877	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237660	16237660	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	50	455	0	ENST00000375759.3:c.1107G>T	p.Gln369His	p.Q369H	ENST00000375759	NM_015001.2	369	caG/caT	5/15	0.262162883047296	3	FACETS	0.372	0.314	0.435	0.124	0.104	0.145	SUBCLONAL	1	TRUE	0	0.429623135173175	3		455	761	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400916	72400916	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	46	311	0	ENST00000357731.5:c.255del	p.Trp85CysfsTer12	p.W85Cfs*12	ENST00000357731	NM_173808.2	85	tgG/tg	2/7	0.262162883047296	3	FACETS	0.54	0.454	0.634	0.18	0.151	0.212	SUBCLONAL	1	TRUE	0	0.429623135173175	3		311	482	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135709	64135709	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	218	542	1	ENST00000334205.4:c.1177G>T	p.Val393Leu	p.V393L	ENST00000334205	NM_003942.2	393	Gtg/Ttg	10/17	0.420477525861378	3	FACETS	0.854	0.797	0.912	0.854	0.797	0.912	CLONAL	2	TRUE	1	0.429623135173175	3		543	722	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4388073	4388073	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	23	241	1	ENST00000261254.3:c.559C>A	p.Leu187Met	p.L187M	ENST00000261254	NM_001759.3	187	Ctg/Atg	3/5	0.429623135173175	3	FACETS	0.367	0.286	0.462	0.184	0.143	0.231	SUBCLONAL	1	TRUE	1	0.429623135173175	3		242	354	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434700	49434700	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs771287738	NA	P-0015214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	73	745	0	ENST00000301067.7:c.6853C>G	p.Leu2285Val	p.L2285V	ENST00000301067	NM_003482.3	2285	Cta/Gta	31/54	0.2092430305774	3	FACETS	0.538	0.469	0.611			1	INDETERMINATE	1	TRUE	NA	0.429623135173175	3		745	768	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354453	91354453	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	77	299	1	ENST00000355112.3:c.3893G>T	p.Gly1298Val	p.G1298V	ENST00000355112	NM_000057.2	1298	gGg/gTg	21/22	1	2	FACETS	0.892	0.787	1	0.892	0.787	1	CLONAL	1	TRUE	1	0.429623135173175	2		300	402	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991473	72991473	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	449	619	1	ENST00000268489.5:c.2572G>T	p.Glu858Ter	p.E858*	ENST00000268489	NM_006885.3	858	Gag/Tag	2/10	0.398572055800249	4	FACETS	0.949	0.908	0.989	1	0.996	1	CLONAL	3	TRUE	2	0.429623135173175	4		620	1050	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40876390	40876390	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	70	604	1	ENST00000428826.2:c.299G>A	p.Arg100Lys	p.R100K	ENST00000428826		100	aGg/aAg	5/21	0.214062848869083	5	FACETS	0.562	0.488	0.641	0.187	0.162	0.214	INDETERMINATE	1	TRUE	2	0.429623135173175	5		605	954	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533868	63533868	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	205	446	0	ENST00000307078.5:c.1286G>T	p.Gly429Val	p.G429V	ENST00000307078	NM_004655.3	429	gGc/gTc	6/11	0.214062848869083	5	FACETS	0.868	0.81	0.927	0.868	0.81	0.927	INDETERMINATE	3	TRUE	2	0.429623135173175	5		446	603	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17386615	17386615	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	342	785	2	ENST00000359435.4:c.550G>T	p.Glu184Ter	p.E184*	ENST00000359435	NM_001033549.1	184	Gaa/Taa	6/9	0.429623135173175	2	FACETS	0.942	0.896	0.989	0.942	0.896	0.989	CLONAL	2	TRUE	0	0.429623135173175	2		787	845	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748590	40748590	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	149	486	0	ENST00000392038.2:c.292G>T	p.Glu98Ter	p.E98*	ENST00000392038	NM_001626.4	98	Gag/Tag	5/14	0.420477525861378	3	FACETS	1	0.986	1	0.691	0.633	0.75	CLONAL	1	TRUE	1	0.429623135173175	3		486	610	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394118	31394118	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	281	360	0	ENST00000328111.2:c.2405G>T	p.Cys802Phe	p.C802F	ENST00000328111	NM_006892.3	802	tGc/tTc	22/23	0.429623135173175	4	FACETS	0.86	0.812	0.908	0.86	0.812	0.908	CLONAL	3	TRUE	1	0.429623135173175	4		360	725	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39763592	39763592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	40	336	0	ENST00000288319.7:c.860G>T	p.Arg287Leu	p.R287L	ENST00000288319	NM_182918.3	287	cGt/cTt	8/10	0.383387096184933	3	FACETS	0.339	0.28	0.404	0.113	0.093	0.135	SUBCLONAL	1	TRUE	0	0.429623135173175	3		336	668	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523644	41523645	+	missense_variant	Missense_Mutation	DNP	CG	CG	TT	novel	NA	P-0015214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	266	675	0	ENST00000263253.7:c.1060_1061delinsTT	p.Arg354Leu	p.R354L	ENST00000263253	NM_001429.3	354	CGg/TTg	4/31	0.429623135173175	2	FACETS	0.972	0.918	1	0.972	0.918	1	CLONAL	2	TRUE	0	0.429623135173175	2		675	637	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41562613	41562613	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	54	325	0	ENST00000263253.7:c.3817G>T	p.Asp1273Tyr	p.D1273Y	ENST00000263253	NM_001429.3	1273	Gat/Tat	23/31	0.429623135173175	2	FACETS	0.413	0.353	0.48	0.207	0.176	0.24	SUBCLONAL	1	TRUE	0	0.429623135173175	2		325	608	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928972	49928972	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	70	623	0	ENST00000296474.3:c.3394G>T	p.Gly1132Trp	p.G1132W	ENST00000296474	NM_002447.2	1132	Ggg/Tgg	16/20	1	2	FACETS	0.606	0.529	0.689	0.606	0.529	0.689	SUBCLONAL	1	TRUE	1	0.429623135173175	2		623	538	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987111	69987111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	50	426	0	ENST00000394351.3:c.172G>T	p.Gly58Cys	p.G58C	ENST00000394351	NM_000248.3	58	Ggc/Tgc	2/9	1	2	FACETS	0.506	0.43	0.59	0.506	0.43	0.59	SUBCLONAL	1	TRUE	1	0.429623135173175	2		426	460	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584501	189584501	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	156	337	0	ENST00000264731.3:c.797G>T	p.Arg266Leu	p.R266L	ENST00000264731	NM_003722.4	266	cGa/cTa	6/14	0.389598898032487	3	FACETS	0.925	0.854	0.998	0.925	0.854	0.998	CLONAL	2	TRUE	1	0.429623135173175	3		337	477	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188946	32188946	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	434	615	0	ENST00000375023.3:c.608G>T	p.Gly203Val	p.G203V	ENST00000375023	NM_004557.3	203	gGa/gTa	4/30	0.429623135173175	3	FACETS	0.912	0.875	0.95	1	0.996	1	CLONAL	3	TRUE	1	0.429623135173175	3		615	897	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829192	128829192	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	133	360	0	ENST00000249373.3:c.200C>A	p.Ala67Asp	p.A67D	ENST00000249373	NM_005631.4	67	gCt/gAt	1/12	0.214062848869083	5	FACETS	0.935	0.859	1	0.935	0.859	1	INDETERMINATE	3	TRUE	2	0.429623135173175	5		360	363	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227699	53227699	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	179	530	0	ENST00000375401.3:c.2489T>C	p.Leu830Pro	p.L830P	ENST00000375401	NM_004187.3	830	cTg/cCg	17/26	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.429623135173175	2		530	683	SUCCESS
AR	367	MSKCC	GRCh37	X	66765238	66765238	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	21	320	0	ENST00000374690.3:c.250C>A	p.Pro84Thr	p.P84T	ENST00000374690	NM_000044.3	84	Ccc/Acc	1/8	0.429623135173175	1	FACETS	0.293	0.226	0.371	0.293	0.226	0.371	SUBCLONAL	1	TRUE	0	0.429623135173175	1		320	262	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231248	98231248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771882746	NA	P-0015215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	220	530	4	ENST00000331920.6:c.2035G>A	p.Ala679Thr	p.A679T	ENST00000331920	NM_000264.3	679	Gct/Act	14/24	0.477674543698068	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.519280990802901	1		534	612	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	283	297	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.857074367322128	2		297	658	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs149840192	NA	P-0015216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	27923	618	3	ENST00000275493.2:c.866C>A	p.Ala289Asp	p.A289D	ENST00000275493	NM_005228.3	289	gCc/gAc	7/28	0.857074367322128	26	FACETS	0.992	0.991	0.994			1	CLONAL	26	TRUE	NA	0.857074367322128	26		621	28504	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508257	106508257	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766854286	NA	P-0015216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	141	253	1	ENST00000359195.3:c.251C>T	p.Ala84Val	p.A84V	ENST00000359195	NM_002649.2	84	gCg/gTg	2/11	0.823842840009203	3	FACETS	0.929	0.852	1	0.464	0.426	0.505	CLONAL	1	TRUE	1	0.857074367322128	3		254	506	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711910	89711910	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0015216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	260	396	0	ENST00000371953.3:c.528T>A	p.Tyr176Ter	p.Y176*	ENST00000371953	NM_000314.4	176	taT/taA	6/9	0.857074367322128	1	FACETS	0.945	0.906	0.982	0.945	0.906	0.982	CLONAL	1	TRUE	0	0.857074367322128	1		396	367	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	250	493	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	0.66311007536612	2		493	745	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0015219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	291	509	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	0.66311007536612	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.66311007536612	1		509	554	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212540	36212540	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144673174	NA	P-0015219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1283	93	799	2	ENST00000222270.7:c.2291C>T	p.Pro764Leu	p.P764L	ENST00000222270	NM_014727.1	764	cCg/cTg	3/37	1	2	FACETS	0.204	0.18	0.229	0.204	0.18	0.229	SUBCLONAL	1	TRUE	1	0.66311007536612	2		801	1376	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212546	36212546	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1304	88	830	0	ENST00000222270.7:c.2297C>T	p.Pro766Leu	p.P766L	ENST00000222270	NM_014727.1	766	cCa/cTa	3/37	1	2	FACETS	0.191	0.168	0.215	0.191	0.168	0.215	SUBCLONAL	1	TRUE	1	0.66311007536612	2		830	1392	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214897	36214897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754957565	NA	P-0015219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1261	76	817	0	ENST00000222270.7:c.3323C>T	p.Pro1108Leu	p.P1108L	ENST00000222270	NM_014727.1	1108	cCc/cTc	8/37	1	2	FACETS	0.171	0.149	0.195	0.171	0.149	0.195	SUBCLONAL	1	TRUE	1	0.66311007536612	2		817	1337	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929300	44929301	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0015219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	391	831	0	ENST00000377967.4:c.2400_2401del	p.Asn801Ter	p.N801*	ENST00000377967	NM_021140.2	800	gtCAat/gtat	17/29	0.66311007536612	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.66311007536612	1		831	784	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611866	100611867	+	stop_gained	Nonsense_Mutation	DNP	CA	CA	AT	novel	NA	P-0015219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	236	729	3	ENST00000308731.7:c.1254_1255delinsAT	p.Tyr418_Gly419delinsTer	p.Y418_G419delins*	ENST00000308731	NM_000061.2	418	taTGgg/taATgg	14/19	0.355176959300826	3	FACETS	0.755	0.703	0.808	0.377	0.351	0.404	INDETERMINATE	1	TRUE	1	0.66311007536612	3		732	1256	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0015220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1355	531	577	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.757907467955901	NA		577	1886	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504056	123504056	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1362460627	NA	P-0015220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	138	234	1	ENST00000371139.4:c.232C>T	p.Arg78Trp	p.R78W	ENST00000371139	NM_001114937.2	78	Cgg/Tgg	3/4	0.584784080023759	4	FACETS	0.921	0.84	1	0.461	0.42	0.503	CLONAL	1	TRUE	2	0.757907467955901	4		235	695	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934576	NA	P-0015220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	975	601	0	ENST00000269305.4:c.818G>C	p.Arg273Pro	p.R273P	ENST00000269305	NM_001126112.2	273	cGt/cCt	8/11	0.757907467955901	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.757907467955901	2		601	1261	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881429	48881429	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	169	111	0	ENST00000267163.4:c.151G>T	p.Glu51Ter	p.E51*	ENST00000267163	NM_000321.2	51	Gaa/Taa	2/27	0.757907467955901	2	FACETS	0.987	0.94	1	0.987	0.94	1	CLONAL	2	TRUE	0	0.757907467955901	2		111	226	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257453	19257453	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2324	558	790	1	ENST00000162023.5:c.680G>T	p.Ser227Ile	p.S227I	ENST00000162023		227	aGc/aTc	11/13	0.666561589088736	4	FACETS	0.898	0.858	0.939	0.449	0.429	0.47	CLONAL	1	TRUE	2	0.757907467955901	4		791	2882	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876449	35876449	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	703	507	0	ENST00000303115.3:c.1241C>A	p.Thr414Lys	p.T414K	ENST00000303115	NM_002185.3	414	aCg/aAg	8/8	0.722924477280003	4	FACETS	0.955	0.922	0.988	0.955	0.922	0.988	CLONAL	2	TRUE	2	0.757907467955901	4		507	1708	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056352	26056352	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	155	184	0	ENST00000343677.2:c.305C>G	p.Ser102Cys	p.S102C	ENST00000343677	NM_005319.3	102	tCt/tGt	1/1	0.757907467955901	4	FACETS	0.838	0.767	0.912			1	CLONAL	1	TRUE	NA	0.757907467955901	4		184	858	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129052	152129052	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	758	483	0	ENST00000206249.3:c.5C>A	p.Thr2Asn	p.T2N	ENST00000206249	NM_000125.3	2	aCc/aAc	1/8	0.722924477280003	4	FACETS	0.961	0.929	0.993	0.961	0.929	0.993	CLONAL	2	TRUE	2	0.757907467955901	4		483	1829	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404640	8404640	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1263318118	NA	P-0015220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	227	190	0	ENST00000356435.5:c.4107G>T	p.Gln1369His	p.Q1369H	ENST00000356435		1369	caG/caT	25/35	0.757907467955901	2	FACETS	0.954	0.913	0.993	0.954	0.913	0.993	CLONAL	2	TRUE	0	0.757907467955901	2		190	314	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195666	123195666	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1434323354	NA	P-0015220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	379	391	0	ENST00000218089.9:c.1580G>T	p.Cys527Phe	p.C527F	ENST00000218089	NM_001042749.1	527	tGt/tTt	17/35	0.584784080023759	4	FACETS	0.817	0.777	0.858	0.817	0.777	0.858	CLONAL	2	TRUE	2	0.757907467955901	4		391	1076	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0015221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	473	840	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.321357152263238	2	FACETS	0.924	0.882	0.966	0.924	0.882	0.966	CLONAL	2	TRUE	0	0.346620207960983	2		842	1477	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128201212	128201212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374025668	NA	P-0015221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	105	563	0	ENST00000265960.3:c.1523G>A	p.Arg508His	p.R508H	ENST00000265960	NM_001006617.1	508	cGt/cAt	12/12	0.189110477897898	2	FACETS	0.533	0.476	0.594	0.266	0.238	0.297	INDETERMINATE	1	TRUE	0	0.346620207960983	2		563	1137	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294444	1294444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1736	102	743	1	ENST00000310581.5:c.557C>T	p.Pro186Leu	p.P186L	ENST00000310581	NM_198253.2	186	cCc/cTc	2/16	0.346620207960983	5	FACETS	0.487	0.433	0.544	0.122	0.108	0.136	SUBCLONAL	1	TRUE	1	0.346620207960983	5		744	1838	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	200	722	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.302760397824465	2	FACETS	0.869	0.809	0.931	0.869	0.809	0.931	CLONAL	2	TRUE	0	0.346575337200076	2		722	664	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0015222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	207	644	0	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.346575337200076	1	FACETS	0.992	0.92	1	0.992	0.92	1	CLONAL	1	TRUE	0	0.346575337200076	1		644	996	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0015222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	275	453	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	0.302760397824465	2	FACETS	0.823	0.774	0.874	0.823	0.774	0.874	CLONAL	2	TRUE	0	0.346575337200076	2		453	964	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602923	10602923	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	363	847	0	ENST00000171111.5:c.655G>T	p.Glu219Ter	p.E219*	ENST00000171111	NM_203500.1	219	Gag/Tag	3/6	0.346575337200076	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.346575337200076	1		847	1378	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400815	72400815	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	30	320	0	ENST00000357731.5:c.356C>G	p.Ser119Cys	p.S119C	ENST00000357731	NM_173808.2	119	tCt/tGt	2/7	0.346575337200076	1	FACETS	0.314	0.252	0.384	0.314	0.252	0.384	SUBCLONAL	1	TRUE	0	0.346575337200076	1		320	456	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763410	41763410	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	230	522	0	ENST00000301178.4:c.2209G>C	p.Val737Leu	p.V737L	ENST00000301178	NM_021913.4	737	Gtg/Ctg	19/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.346575337200076	2		522	990	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980434	55980434	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0015222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	56	236	0	ENST00000263923.4:c.659-2A>G		p.X220_splice	ENST00000263923	NM_002253.2	220			0.273158431437787	1	FACETS	0.714	0.614	0.823	0.714	0.614	0.823	SUBCLONAL	1	TRUE	0	0.346575337200076	1		236	374	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515146	148515146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	119	339	0	ENST00000320356.2:c.1063C>T	p.Pro355Ser	p.P355S	ENST00000320356	NM_004456.4	355	Cca/Tca	10/20	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.346575337200076	2		339	639	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500865	8500865	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	149	439	0	ENST00000356435.5:c.2017C>G	p.Leu673Val	p.L673V	ENST00000356435		673	Ctt/Gtt	13/35	0.346575337200076	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.346575337200076	1		439	663	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559090	29559090	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1223905930	NA	P-0015226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	41	40	0	ENST00000356175.3:c.3198-1G>A		p.X1066_splice	ENST00000356175	NM_000267.3	1066			0.175139152308223	3	FACETS	0.909	0.773	1	1	0.969	1	CLONAL	4	TRUE	1	0.175139152308223	3		40	140	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560382	95560382	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	56	394	0	ENST00000393063.1:c.5207G>T	p.Arg1736Leu	p.R1736L	ENST00000393063	NM_030621.3	1736	cGg/cTg	25/28	1	2	FACETS	0.789	0.674	0.914	0.789	0.674	0.914	CLONAL	1	TRUE	1	0.175139152308223	2		394	811	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944864	31944864	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs768711923	NA	P-0015226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	124	519	0	ENST00000340398.3:c.237C>A	p.Asn79Lys	p.N79K	ENST00000340398	NM_001013699.2	79	aaC/aaA	1/1	0.175139152308223	4	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.175139152308223	4		519	1234	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577567	7577569	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0015226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	132	473	0	ENST00000269305.4:c.712_714del	p.Cys238del	p.C238del	ENST00000269305	NM_001126112.2	238	TGT/-	7/11	NA	2	FACETS	0.773	0.701	0.849			1	INDETERMINATE	2	TRUE	NA	0.175139152308223	2		473	975	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576091	29576091	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1131691087	NA	P-0015226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	152	538	0	ENST00000356175.3:c.4064C>G	p.Ser1355Ter	p.S1355*	ENST00000356175	NM_000267.3	1355	tCa/tGa	30/57	0.175139152308223	3	FACETS	0.791	0.721	0.863	0.791	0.721	0.863	SUBCLONAL	2	TRUE	1	0.175139152308223	3		538	1194	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467898	50467898	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	47	426	0	ENST00000331340.3:c.1133A>G	p.Lys378Arg	p.K378R	ENST00000331340	NM_006060.4	378	aAg/aGg	8/8	0.155289767237649	2	FACETS	0.704	0.593	0.828	0.352	0.296	0.414	SUBCLONAL	1	TRUE	0	0.175139152308223	2		426	762	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965913	90965913	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730881851	NA	P-0015226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	58	153	0	ENST00000265433.3:c.1404G>T	p.Arg468Ser	p.R468S	ENST00000265433	NM_002485.4	468	agG/agT	11/16	0.175139152308223	4	FACETS	1	0.935	1	0.763	0.659	0.875	CLONAL	2	TRUE	1	0.175139152308223	4		153	340	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0015227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	34	336	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.112796768124907	3	FACETS	0.376	0.306	0.455	0.188	0.153	0.228	INDETERMINATE	1	TRUE	1	0.365104250901331	3		336	586	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191488	10191488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs5030818	NA	P-0015227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	118	354	0	ENST00000256474.2:c.481C>T	p.Arg161Ter	p.R161*	ENST00000256474	NM_000551.3	161	Cga/Tga	3/3	0.365104250901331	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.365104250901331	1		354	487	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122754	108122754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	31	566	0	ENST00000278616.4:c.1798C>T	p.His600Tyr	p.H600Y	ENST00000278616	NM_000051.3	600	Cac/Tac	11/63	0.22833149498975	2	FACETS	0.311	0.252	0.377	0.155	0.126	0.189	INDETERMINATE	1	TRUE	0	0.707330467566333	2		566	282	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	54	297	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.618	0.527	0.717	0.618	0.527	0.717	SUBCLONAL	1	TRUE	1	0.306716771668872	2		297	570	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508508	29508509	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0015230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	68	665	0	ENST00000356175.3:c.654+2dup		p.X218_splice	ENST00000356175	NM_000267.3	218			1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.306716771668872	2		665	392	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78426147	78426147	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	64	538	1	ENST00000370768.2:c.1378C>T	p.His460Tyr	p.H460Y	ENST00000370768	NM_003902.3	460	Cat/Tat	15/20	1	2	FACETS	0.948	0.824	1	0.948	0.824	1	CLONAL	1	TRUE	1	0.306716771668872	2		539	440	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888156	112888156	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs397507505	NA	P-0015230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	36	903	0	ENST00000351677.2:c.172A>T	p.Asn58Tyr	p.N58Y	ENST00000351677	NM_002834.3	58	Aac/Tac	3/16	1	2	FACETS	0.35	0.287	0.421	0.35	0.287	0.421	SUBCLONAL	1	TRUE	1	0.306716771668872	2		903	671	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437276	52437276	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	179	834	0	ENST00000460680.1:c.1768C>G	p.Gln590Glu	p.Q590E	ENST00000460680	NM_004656.3	590	Caa/Gaa	14/17	NA	2	FACETS	0.444	0.409	0.48			1	INDETERMINATE	1	TRUE	NA	0.814610231173967	2		834	990	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088756	27088756	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	326	940	1	ENST00000324856.7:c.2365C>T	p.Gln789Ter	p.Q789*	ENST00000324856	NM_006015.4	789	Cag/Tag	7/20	0.677713141310091	1	FACETS	0.983	0.937	1	0.983	0.937	1	CLONAL	1	TRUE	0	0.677713141310091	1		941	647	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646417	23646417	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	330	790	1	ENST00000261584.4:c.1450T>A	p.Leu484Ile	p.L484I	ENST00000261584	NM_024675.3	484	Tta/Ata	4/13	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.677713141310091	2		791	883	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84397829	84397829	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1288629338	NA	P-0015232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	259	616	0	ENST00000321945.7:c.182T>C	p.Ile61Thr	p.I61T	ENST00000321945	NM_139076.2	61	aTt/aCt	3/9	0.677713141310091	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.677713141310091	1		616	481	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	17	297	0				ENST00000310581	NM_198253.2	-/1132			0.510226114620407	1	FACETS	0.776	0.624	0.925	1	0.93	1	CLONAL	2	TRUE	0	0.510226114620407	1		297	32	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0015233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	37	715	3	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	0.510226114620407	4	FACETS	0.782	0.657	0.917	0.782	0.657	0.917	CLONAL	2	TRUE	2	0.510226114620407	4		718	140	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0015233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	87	1091	0	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	0.478735165675499	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	0	0.510226114620407	2		1091	168	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727483	66727483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504317	NA	P-0015233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	42	660	0	ENST00000307102.5:c.199G>A	p.Asp67Asn	p.D67N	ENST00000307102	NM_002755.3	67	Gac/Aac	2/11	0.478735165675499	2	FACETS	0.925	0.803	1	0.925	0.803	1	CLONAL	2	TRUE	0	0.510226114620407	2		660	89	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720845	89720845	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	39	464	0	ENST00000371953.3:c.996A>C	p.Lys332Asn	p.K332N	ENST00000371953	NM_000314.4	332	aaA/aaC	8/9	0.273676064756832	1	FACETS	0.633	0.531	0.743	0.633	0.531	0.743	INDETERMINATE	1	TRUE	0	0.510226114620407	1		464	180	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491675	56491675	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	53	645	0	ENST00000267101.3:c.2567C>G	p.Ala856Gly	p.A856G	ENST00000267101	NM_001982.3	856	gCt/gGt	21/28	0.510226114620407	4	FACETS	0.857	0.743	0.978	0.857	0.743	0.978	CLONAL	2	TRUE	2	0.510226114620407	4		645	183	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396755	396756	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0015233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	49	698	0	ENST00000262320.3:c.270_271del	p.Ser91ProfsTer4	p.S91Pfs*4	ENST00000262320	NM_003502.3	90	caTTcc/cacc	2/11	0.510226114620407	1	FACETS	0.894	0.799	0.986	1	0.979	1	CLONAL	2	TRUE	0	0.510226114620407	1		698	80	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577157	7577157	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0015233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	26	687	1	ENST00000269305.4:c.783-2A>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.510226114620407	1	FACETS	0.791	0.641	0.953	0.791	0.641	0.953	CLONAL	1	TRUE	0	0.510226114620407	1		688	96	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859828	151859829	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTTCTTC	novel	NA	P-0015233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	15	402	0	ENST00000262189.6:c.10827_10833dup	p.Arg3612GlufsTer5	p.R3612Efs*5	ENST00000262189	NM_170606.2	3611	-/GAAGAAA	43/59	1	2	FACETS	0.878	0.658	1	0.878	0.658	1	CLONAL	1	TRUE	1	0.510226114620407	2		402	67	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032598	47032598	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0015233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	19	698	0	ENST00000377604.3:c.502+2T>G		p.X168_splice	ENST00000377604	NM_001204468.1	168			0.510226114620407	1	FACETS	0.853	0.669	1	0.853	0.669	1	CLONAL	1	TRUE	0	0.510226114620407	1		698	65	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	494	722	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.76718847527224	3	FACETS	0.958	0.923	0.993	0.958	0.923	0.993	CLONAL	2	TRUE	1	0.76718847527224	3		722	930	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0015235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	171	522	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.879	0.815	0.945	0.879	0.815	0.945	CLONAL	1	TRUE	1	0.76718847527224	2		522	507	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865657	57865657	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	469	1112	0	ENST00000228682.2:c.3134C>A	p.Thr1045Asn	p.T1045N	ENST00000228682	NM_005269.2	1045	aCt/aAt	12/12	0.76718847527224	3	FACETS	1	0.988	1	0.547	0.522	0.572	CLONAL	1	TRUE	1	0.76718847527224	3		1112	1547	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	80	722	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.834	0.735	0.941	0.834	0.735	0.941	CLONAL	1	TRUE	1	0.292761395276349	2		722	655	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235935	108235935	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770641163	NA	P-0015236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	54	223	1	ENST00000278616.4:c.8977C>T	p.Arg2993Ter	p.R2993*	ENST00000278616	NM_000051.3	2993	Cga/Tga	62/63	0.291083599288518	3	FACETS	0.856	0.732	0.992	0.428	0.366	0.496	CLONAL	1	TRUE	1	0.292761395276349	3		224	494	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106279	27106280	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	105	419	0	ENST00000324856.7:c.5891dup	p.Thr1965AspfsTer34	p.T1965Dfs*34	ENST00000324856	NM_006015.4	1964	gag/gAag	20/20	0.292761395276349	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.292761395276349	1		419	569	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120218	70120218	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	101	464	0	ENST00000245479.2:c.1220del	p.Tyr407SerfsTer63	p.Y407Sfs*63	ENST00000245479	NM_000346.3	407	tAc/tc	3/3	1	2	FACETS	0.996	0.891	1	0.996	0.891	1	CLONAL	1	TRUE	1	0.292761395276349	2		464	693	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015236-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	186	722	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.270919157572852	3	FACETS	0.947	0.877	1	0.947	0.877	1	CLONAL	2	FALSE	1	0.3	3		722	753	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235935	108235935	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770641163	NA	P-0015236-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	136	223	1	ENST00000278616.4:c.8977C>T	p.Arg2993Ter	p.R2993*	ENST00000278616	NM_000051.3	2993	Cga/Tga	62/63	0.3	3	FACETS	0.924	0.844	1	0.924	0.844	1	CLONAL	2	FALSE	1	0.3	3		224	564	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106279	27106280	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015236-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	267	419	0	ENST00000324856.7:c.5891dup	p.Thr1965AspfsTer34	p.T1965Dfs*34	ENST00000324856	NM_006015.4	1964	gag/gAag	20/20	NA	2	FACETS	1	0.941	1			1	INDETERMINATE	2	FALSE	NA	0.3	2		419	889	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120218	70120218	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015236-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	280	464	0	ENST00000245479.2:c.1220del	p.Tyr407SerfsTer63	p.Y407Sfs*63	ENST00000245479	NM_000346.3	407	tAc/tc	3/3	0.276042868197366	4	FACETS	0.987	0.927	1	0.987	0.927	1	CLONAL	2	FALSE	2	0.3	4		464	1229	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729775	41729775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015236-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	41	186	1	ENST00000242208.4:c.754G>A	p.Ala252Thr	p.A252T	ENST00000242208	NM_002192.2	252	Gcc/Acc	3/3	0.233899045860912	4	FACETS	0.643	0.535	0.763	0.321	0.267	0.382	SUBCLONAL	1	FALSE	2	0.3	4		187	553	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	544	859	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.894	0.865	0.923	1	0.998	1	CLONAL	2	TRUE	1	0.660617677775282	2		859	921	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	401	1023	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.660617677775282	2		1024	1156	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	128	813	3	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	0.391986347281024	1	FACETS	0.39	0.354	0.427	0.39	0.354	0.427	INDETERMINATE	1	TRUE	0	0.660617677775282	1		816	666	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	179	668	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	0.660617677775282	2	FACETS	0.978	0.908	1	0.489	0.454	0.525	CLONAL	1	TRUE	0	0.660617677775282	2		668	554	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	123	689	3	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	0.391986347281024	1	FACETS	0.443	0.402	0.486	0.443	0.402	0.486	INDETERMINATE	1	TRUE	0	0.660617677775282	1		692	563	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	236	617	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	0.660617677775282	2	FACETS	1	0.983	1	0.563	0.529	0.598	CLONAL	1	TRUE	0	0.660617677775282	2		617	634	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	262	599	2	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	0.391986347281024	1	FACETS	1	0.973	1	1	0.973	1	INDETERMINATE	1	TRUE	0	0.660617677775282	1		601	511	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	281	842	5	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.803	0.755	0.853	0.803	0.755	0.853	CLONAL	1	TRUE	1	0.660617677775282	2		847	1059	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931452	131931452	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507178	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	383	626	22	ENST00000265335.6:c.2165del	p.Lys722ArgfsTer14	p.K722Rfs*14	ENST00000265335		719	ctA/ct	13/25	1	2	FACETS	0.853	0.818	0.887	1	0.997	1	CLONAL	2	TRUE	1	0.660617677775282	2		648	680	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	365	695	21	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	0.316213524692391	2	FACETS	0.751	0.717	0.784	0.751	0.717	0.784	INDETERMINATE	2	TRUE	0	0.660617677775282	2		716	736	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	260	588	11	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.660617677775282	2		599	717	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661664	227661664	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs761880048	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	277	572	10	ENST00000305123.5:c.1791del	p.His598ThrfsTer38	p.H598Tfs*38	ENST00000305123	NM_005544.2	597	ggG/gg	1/2	0.331969353126767	2	FACETS	1	0.994	1	0.698	0.661	0.734	INDETERMINATE	1	TRUE	0	0.660617677775282	2		582	601	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272447	15272447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201105335	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	248	1249	4	ENST00000263388.2:c.5992C>T	p.Arg1998Cys	p.R1998C	ENST00000263388	NM_000435.2	1998	Cgt/Tgt	33/33	0.369208254048639	1	FACETS	0.398	0.371	0.425	0.398	0.371	0.425	INDETERMINATE	1	TRUE	0	0.660617677775282	1		1253	1264	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	174	934	9	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	0.391986347281024	1	FACETS	0.424	0.39	0.458	0.424	0.39	0.458	INDETERMINATE	1	TRUE	0	0.660617677775282	1		943	833	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11264661	11264661	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	146	797	2	ENST00000361445.4:c.3901C>T	p.Arg1301Cys	p.R1301C	ENST00000361445	NM_004958.3	1301	Cgc/Tgc	26/58	0.369208254048639	1	FACETS	0.423	0.387	0.461	0.423	0.387	0.461	INDETERMINATE	1	TRUE	0	0.660617677775282	1		799	699	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760024	133760024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	330	1125	5	ENST00000318560.5:c.2352del	p.Arg785GlyfsTer3	p.R785Gfs*3	ENST00000318560	NM_005157.4	783	Ccc/cc	11/11	0.391986347281024	1	FACETS	0.71	0.673	0.748	0.71	0.673	0.748	INDETERMINATE	1	TRUE	0	0.660617677775282	1		1130	942	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245024	133245024	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs752846614	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	176	981	6	ENST00000320574.5:c.2091del	p.Leu698CysfsTer94	p.L698Cfs*94	ENST00000320574	NM_006231.2	697	ccC/cc	19/49	1	2	FACETS	0.497	0.457	0.538	0.497	0.457	0.538	SUBCLONAL	1	TRUE	1	0.660617677775282	2		987	1073	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345768	152345769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs759063323	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	156	465	0	ENST00000359321.1:c.801dup	p.His268ThrfsTer11	p.H268Tfs*11	ENST00000359321	NM_005431.1	267	-/A	3/3	1	2	FACETS	0.862	0.794	0.932	0.862	0.794	0.932	CLONAL	1	TRUE	1	0.660617677775282	2		465	548	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202351	138202351	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	134	818	0	ENST00000237289.4:c.2274del	p.Lys759SerfsTer57	p.K759Sfs*57	ENST00000237289	NM_001270507.1	756	gaC/ga	9/9	0.410566435461666	1	FACETS	0.368	0.334	0.403	0.368	0.334	0.403	SUBCLONAL	1	TRUE	0	0.660617677775282	1		818	739	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	340	856	1	ENST00000311936.3:c.180_181delinsAA	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggAAaa	3/5	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.660617677775282	2		857	832	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955112	17955112	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755706305	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	312	949	8	ENST00000458235.1:c.115del	p.Gln39SerfsTer108	p.Q39Sfs*108	ENST00000458235	NM_000215.3	39	Cag/ag	2/24	0.369208254048639	1	FACETS	0.787	0.746	0.829	0.787	0.746	0.829	INDETERMINATE	1	TRUE	0	0.660617677775282	1		957	804	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001524	150001524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	191	821	2	ENST00000253339.5:c.2080C>T	p.Arg694Cys	p.R694C	ENST00000253339		694	Cgt/Tgt	4/7	0.410566435461666	1	FACETS	0.688	0.64	0.736	0.688	0.64	0.736	SUBCLONAL	1	TRUE	0	0.660617677775282	1		823	563	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	298	1055	9	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.891	0.84	0.943	0.891	0.84	0.943	CLONAL	1	TRUE	1	0.660617677775282	2		1064	1013	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514810	44514810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	141	716	2	ENST00000291552.4:c.437C>T	p.Pro146Leu	p.P146L	ENST00000291552	NM_006758.2	146	cCc/cTc	6/8	1	2	FACETS	0.499	0.454	0.545	0.499	0.454	0.545	SUBCLONAL	1	TRUE	1	0.660617677775282	2		718	856	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598900	28598900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753794131	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	351	982	0	ENST00000253063.3:c.460G>A	p.Glu154Lys	p.E154K	ENST00000253063	NM_031459.4	154	Gag/Aag	4/10	0.369208254048639	1	FACETS	0.795	0.756	0.835	0.795	0.756	0.835	INDETERMINATE	1	TRUE	0	0.660617677775282	1		982	895	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248438	59248438	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	245	618	0	ENST00000371222.2:c.305A>C	p.Asn102Thr	p.N102T	ENST00000371222	NM_002228.3	102	aAc/aCc	1/1	0.369208254048639	1	FACETS	0.796	0.749	0.844	0.796	0.749	0.844	INDETERMINATE	1	TRUE	0	0.660617677775282	1		618	624	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567685	226567685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	216	675	1	ENST00000366794.5:c.1481C>T	p.Ala494Val	p.A494V	ENST00000366794	NM_001618.3	494	gCc/gTc	10/23	1	2	FACETS	0.929	0.867	0.992	0.929	0.867	0.992	CLONAL	1	TRUE	1	0.660617677775282	2		676	704	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63810688	63810688	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	192	538	0	ENST00000279873.7:c.775C>A	p.Pro259Thr	p.P259T	ENST00000279873	NM_032199.2	259	Cca/Aca	5/10	1	2	FACETS	0.964	0.897	1	0.964	0.897	1	CLONAL	1	TRUE	1	0.660617677775282	2		538	603	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446306	70446306	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	145	819	0	ENST00000373644.4:c.5246A>G	p.Gln1749Arg	p.Q1749R	ENST00000373644	NM_030625.2	1749	cAg/cGg	11/12	1	2	FACETS	0.437	0.398	0.478	0.437	0.398	0.478	SUBCLONAL	1	TRUE	1	0.660617677775282	2		819	1004	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588877	69588877	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1179344852	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	261	792	3	ENST00000168712.1:c.359C>T	p.Pro120Leu	p.P120L	ENST00000168712	NM_002007.2	120	cCc/cTc	2/3	1	2	FACETS	0.957	0.899	1	0.957	0.899	1	CLONAL	1	TRUE	1	0.660617677775282	2		795	826	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589732	69589732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217041826	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	95	239	0	ENST00000168712.1:c.121G>A	p.Ala41Thr	p.A41T	ENST00000168712	NM_002007.2	41	Gcc/Acc	1/3	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.660617677775282	2		239	267	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999142	100999142	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	327	883	2	ENST00000325455.5:c.660G>T	p.Glu220Asp	p.E220D	ENST00000325455	NM_001202474.3	220	gaG/gaT	1/8	0.391986347281024	1	FACETS	0.859	0.816	0.902	0.859	0.816	0.902	INDETERMINATE	1	TRUE	0	0.660617677775282	1		885	772	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981871	101981871	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	199	1102	0	ENST00000282441.5:c.292C>T	p.Pro98Ser	p.P98S	ENST00000282441	NM_001130145.2	98	Ccg/Tcg	1/9	0.391986347281024	1	FACETS	0.447	0.414	0.481	0.447	0.414	0.481	INDETERMINATE	1	TRUE	0	0.660617677775282	1		1102	902	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426576	49426578	+	inframe_deletion	In_Frame_Del	DEL	TGC	TGC	-	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	138	813	0	ENST00000301067.7:c.11910_11912del	p.Gln3974del	p.Q3974del	ENST00000301067	NM_003482.3	3970	caGCAa/caa	39/54	1	2	FACETS	0.422	0.383	0.462	0.422	0.383	0.462	SUBCLONAL	1	TRUE	1	0.660617677775282	2		813	991	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562043	21562043	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs770191896	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	225	1297	6	ENST00000382592.4:c.1876C>T	p.Gln626Ter	p.Q626*	ENST00000382592	NM_014572.2	626	Cag/Tag	4/8	1	2	FACETS	0.599	0.557	0.642	0.599	0.557	0.642	SUBCLONAL	1	TRUE	1	0.660617677775282	2		1303	1138	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528078	103528078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368829739	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	247	621	0	ENST00000355739.4:c.3386C>T	p.Ser1129Leu	p.S1129L	ENST00000355739	NM_000123.3	1129	tCg/tTg	15/15	0.660617677775282	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.660617677775282	1		621	468	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95599668	95599668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367797765	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	162	569	3	ENST00000393063.1:c.128C>T	p.Thr43Met	p.T43M	ENST00000393063	NM_030621.3	43	aCg/aTg	3/28	1	2	FACETS	0.952	0.88	1	0.952	0.88	1	CLONAL	1	TRUE	1	0.660617677775282	2		572	515	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578193	7578193	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	348	1113	0	ENST00000269305.4:c.656C>A	p.Pro219His	p.P219H	ENST00000269305	NM_001126112.2	219	cCc/cAc	6/11	1	2	FACETS	0.907	0.859	0.956	0.907	0.859	0.956	CLONAL	1	TRUE	1	0.660617677775282	2		1113	1162	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980013	7980013	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764862348	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	290	951	2	ENST00000319144.4:c.1324C>T	p.Arg442Trp	p.R442W	ENST00000319144	NM_001139.2	442	Cgg/Tgg	10/15	1	2	FACETS	0.914	0.861	0.967	0.914	0.861	0.967	CLONAL	1	TRUE	1	0.660617677775282	2		953	961	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804391	46804391	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	176	630	0	ENST00000290295.7:c.616C>T	p.His206Tyr	p.H206Y	ENST00000290295	NM_006361.5	206	Cac/Tac	2/2	1	2	FACETS	0.903	0.836	0.972	0.903	0.836	0.972	CLONAL	1	TRUE	1	0.660617677775282	2		630	590	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435355	56435357	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	145	919	0	ENST00000407977.2:c.1780_1782del	p.Pro594del	p.P594del	ENST00000407977		594	CCT/-	9/10	1	2	FACETS	0.5	0.456	0.546	0.5	0.456	0.546	SUBCLONAL	1	TRUE	1	0.660617677775282	2		919	878	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119096	70119096	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	122	487	0	ENST00000245479.2:c.672del	p.Gly225AlafsTer28	p.G225Afs*28	ENST00000245479	NM_000346.3	223	tCc/tc	2/3	1	2	FACETS	0.788	0.716	0.862	0.788	0.716	0.862	SUBCLONAL	1	TRUE	1	0.660617677775282	2		487	469	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39600670	39600670	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	44	382	0	ENST00000262039.4:c.1484+1G>A		p.X495_splice	ENST00000262039	NM_002647.2	495			0.416937334623346	1	FACETS	0.328	0.277	0.384	0.328	0.277	0.384	SUBCLONAL	1	TRUE	0	0.660617677775282	1		382	272	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226454	2226454	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	191	1054	0	ENST00000398665.3:c.3934C>A	p.Pro1312Thr	p.P1312T	ENST00000398665	NM_032482.2	1312	Cct/Act	27/28	0.369208254048639	1	FACETS	0.387	0.357	0.418	0.387	0.357	0.418	INDETERMINATE	1	TRUE	0	0.660617677775282	1		1054	1001	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141412	11141412	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	147	770	3	ENST00000358026.2:c.3389C>T	p.Thr1130Met	p.T1130M	ENST00000358026	NM_001128849.1	1130	aCg/aTg	25/36	0.369208254048639	1	FACETS	0.37	0.338	0.403	0.37	0.338	0.403	INDETERMINATE	1	TRUE	0	0.660617677775282	1		773	806	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967089	18967089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334288478	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	194	936	1	ENST00000262803.5:c.1804G>A	p.Ala602Thr	p.A602T	ENST00000262803	NM_002911.3	602	Gca/Aca	13/24	0.369208254048639	1	FACETS	0.467	0.433	0.503	0.467	0.433	0.503	INDETERMINATE	1	TRUE	0	0.660617677775282	1		937	842	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264348	46264348	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	105	671	0	ENST00000371998.3:c.1400del	p.Pro467HisfsTer15	p.P467Hfs*15	ENST00000371998		465	agC/ag	11/23	1	2	FACETS	0.509	0.457	0.565	0.509	0.457	0.565	SUBCLONAL	1	TRUE	1	0.660617677775282	2		671	624	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553172	41553172	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	68	548	0	ENST00000263253.7:c.3262-1G>A		p.X1088_splice	ENST00000263253	NM_001429.3	1088			0.391986347281024	1	FACETS	0.377	0.329	0.427	0.377	0.329	0.427	INDETERMINATE	1	TRUE	0	0.660617677775282	1		548	366	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933695	49933695	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	377	1078	0	ENST00000296474.3:c.2582C>T	p.Pro861Leu	p.P861L	ENST00000296474	NM_002447.2	861	cCc/cTc	10/20	0.391986347281024	1	FACETS	0.841	0.802	0.881	0.841	0.802	0.881	INDETERMINATE	1	TRUE	0	0.660617677775282	1		1078	909	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610608	52610608	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	122	828	0	ENST00000394830.3:c.3565G>T	p.Glu1189Ter	p.E1189*	ENST00000394830	NM_018313.4	1189	Gaa/Taa	23/30	0.391986347281024	1	FACETS	0.391	0.354	0.43	0.391	0.354	0.43	INDETERMINATE	1	TRUE	0	0.660617677775282	1		828	632	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138384031	138384031	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	115	729	0	ENST00000289153.2:c.2519G>A	p.Gly840Asp	p.G840D	ENST00000289153	NM_006219.2	840	gGc/gAc	18/22	0.391986347281024	1	FACETS	0.398	0.359	0.439	0.398	0.359	0.439	INDETERMINATE	1	TRUE	0	0.660617677775282	1		729	586	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38978703	38978703	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745378144	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	170	687	0	ENST00000357387.3:c.803C>T	p.Thr268Ile	p.T268I	ENST00000357387	NM_152756.3	268	aCa/aTa	9/38	1	2	FACETS	0.877	0.811	0.945	0.877	0.811	0.945	CLONAL	1	TRUE	1	0.660617677775282	2		687	587	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636997	176636997	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	141	936	2	ENST00000439151.2:c.1597C>A	p.Leu533Ile	p.L533I	ENST00000439151	NM_022455.4	533	Ctt/Att	5/23	0.391986347281024	1	FACETS	0.384	0.35	0.42	0.384	0.35	0.42	INDETERMINATE	1	TRUE	0	0.660617677775282	1		938	744	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680418	30680418	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	239	747	0	ENST00000376406.3:c.1301A>G	p.Asp434Gly	p.D434G	ENST00000376406	NM_014641.2	434	gAc/gGc	5/15	0.410566435461666	1	FACETS	0.764	0.718	0.811	0.764	0.718	0.811	SUBCLONAL	1	TRUE	0	0.660617677775282	1		747	634	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876974	151876974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750213944	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	186	687	2	ENST00000262189.6:c.7387C>T	p.Arg2463Cys	p.R2463C	ENST00000262189	NM_170606.2	2463	Cgt/Tgt	37/59	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.660617677775282	2		689	551	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891145	151891145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	222	803	1	ENST00000262189.6:c.4609C>T	p.Pro1537Ser	p.P1537S	ENST00000262189	NM_170606.2	1537	Cca/Tca	31/59	1	2	FACETS	0.879	0.82	0.938	0.879	0.82	0.938	CLONAL	1	TRUE	1	0.660617677775282	2		804	765	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900029	151900029	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	130	637	0	ENST00000262189.6:c.4082C>T	p.Ala1361Val	p.A1361V	ENST00000262189	NM_170606.2	1361	gCc/gTc	26/59	1	2	FACETS	0.871	0.796	0.948	0.871	0.796	0.948	CLONAL	1	TRUE	1	0.660617677775282	2		637	452	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370754	55370754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	127	751	0	ENST00000297316.4:c.56C>T	p.Ala19Val	p.A19V	ENST00000297316	NM_022454.3	19	gCg/gTg	1/2	0.660617677775282	3	FACETS	0.52	0.471	0.573	0.26	0.235	0.287	SUBCLONAL	1	TRUE	1	0.660617677775282	3		751	983	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372202	55372202	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	146	652	1	ENST00000297316.4:c.892G>T	p.Gly298Cys	p.G298C	ENST00000297316	NM_022454.3	298	Ggc/Tgc	2/2	0.660617677775282	3	FACETS	0.671	0.612	0.733	0.336	0.306	0.367	SUBCLONAL	1	TRUE	1	0.660617677775282	3		653	876	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636345	87636345	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	215	894	0	ENST00000277120.3:c.2510T>C	p.Leu837Pro	p.L837P	ENST00000277120		837	cTa/cCa	19/19	0.391986347281024	1	FACETS	0.693	0.648	0.739	0.693	0.648	0.739	INDETERMINATE	1	TRUE	0	0.660617677775282	1		894	629	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0015238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	133	260	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.953	0.877	1	0.953	0.877	1	CLONAL	1	TRUE	1	0.828489832240533	2		260	337	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	152	297	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.927	0.857	0.997	0.927	0.857	0.997	CLONAL	1	TRUE	1	0.828489832240533	2		297	396	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793495	42793499	+	frameshift_variant	Frame_Shift_Del	DEL	GACAT	GACAT	-	novel	NA	P-0015238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	241	723	0	ENST00000575354.2:c.1300_1304del	p.Met434GlufsTer2	p.M434Efs*2	ENST00000575354	NM_015125.3	433	GACATg/g	8/20	0.828489832240533	1	FACETS	0.688	0.651	0.726	0.688	0.651	0.726	SUBCLONAL	1	TRUE	0	0.828489832240533	1		723	495	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796885	42796887	+	frameshift_variant	Frame_Shift_Del	DEL	CCC	CCC	T	novel	NA	P-0015238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	105	820	1	ENST00000575354.2:c.3343_3345delinsT	p.Pro1115SerfsTer35	p.P1115Sfs*35	ENST00000575354	NM_015125.3	1115	CCC/T	14/20	0.828489832240533	1	FACETS	0.283	0.254	0.313	0.283	0.254	0.313	SUBCLONAL	1	TRUE	0	0.828489832240533	1		821	525	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0015239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	150	455	1	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.339111844138169	0	FACETS	0.919	0.856	0.983			1	CLONAL	2	FALSE	0	0.349271334825678	0		456	304	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871830	35871835	+	inframe_deletion	In_Frame_Del	DEL	CCACTG	CCACTG	-	novel	NA	P-0015239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	132	769	0	ENST00000216797.5:c.671_676del	p.Ala224_Val225del	p.A224_V225del	ENST00000216797	NM_020529.2	224	gCAGTGGac/gac	5/6	NA	2	FACETS	1	0.938	1			1	INDETERMINATE	1	FALSE	NA	0.349271334825678	2		769	726	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213242	39213243	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1558454973	NA	P-0015239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	135	1199	3	ENST00000402219.2:c.3724dup	p.Ser1242LysfsTer2	p.S1242Kfs*2	ENST00000402219	NM_005633.3	1242	agt/aAgt	23/23	1	2	FACETS	0.837	0.76	0.917	0.837	0.76	0.917	CLONAL	1	FALSE	1	0.349271334825678	2		1202	924	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	252	489	0	ENST00000397062.3:c.92G>A	p.Gly31Glu	p.G31E	ENST00000397062	NM_006164.4	31	gGa/gAa	2/5	0.705101922628618	3	FACETS	0.957	0.907	1	0.957	0.907	1	CLONAL	2	TRUE	1	0.705101922628618	3		489	505	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692893	89692893	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	348	605	0	ENST00000371953.3:c.377C>A	p.Ala126Asp	p.A126D	ENST00000371953	NM_000314.4	126	gCt/gAt	5/9	0.705101922628618	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.705101922628618	2		605	481	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs17849781	NA	P-0015240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	891	961	0	ENST00000269305.4:c.832C>G	p.Pro278Ala	p.P278A	ENST00000269305	NM_001126112.2	278	Cct/Gct	8/11	0.705101922628618	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	0	0.705101922628618	3		961	1140	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741455	39741455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	217	704	1	ENST00000361337.2:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000361337	NM_003286.2	448	Cgg/Tgg	14/21	0.705101922628618	6	FACETS	1	0.972	1	0.274	0.254	0.295	CLONAL	1	TRUE	2	0.705101922628618	6		705	1355	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs730881677	NA	P-0015240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	447	643	1	ENST00000304494.5:c.151-1G>T		p.X51_splice	ENST00000304494	NM_000077.4	51			0.691355997736053	3	FACETS	0.951	0.923	0.978	0.951	0.923	0.978	CLONAL	3	TRUE	0	0.705101922628618	3		644	601	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163313578	163313578	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	111	517	0	ENST00000271452.3:c.725C>G	p.Thr242Arg	p.T242R	ENST00000271452	NM_145697.2	242	aCa/aGa	10/14	0.687232056309447	4	FACETS	0.728	0.655	0.806	0.243	0.218	0.269	SUBCLONAL	1	TRUE	1	0.705101922628618	4		517	737	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233138	46233138	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	138	449	0	ENST00000334344.6:c.1357G>C	p.Asp453His	p.D453H	ENST00000334344	NM_152641.2	453	Gat/Cat	11/21	0.705101922628618	3	FACETS	0.881	0.805	0.96	0.44	0.402	0.48	CLONAL	1	TRUE	1	0.705101922628618	3		449	601	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416099	49416099	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	523	720	0	ENST00000301067.7:c.16376A>T	p.His5459Leu	p.H5459L	ENST00000301067	NM_003482.3	5459	cAt/cTt	52/54	0.705101922628618	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.705101922628618	3		720	994	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748219	43748219	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0015240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	266	1037	0	ENST00000382044.4:c.2587A>T	p.Lys863Ter	p.K863*	ENST00000382044	NM_001141980.1	863	Aaa/Taa	12/28	0.705101922628618	3	FACETS	0.99	0.929	1	0.495	0.464	0.527	CLONAL	1	TRUE	1	0.705101922628618	3		1037	1031	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934308	81934308	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	494	851	0	ENST00000359376.3:c.1285C>A	p.Leu429Met	p.L429M	ENST00000359376	NM_002661.3	429	Ctg/Atg	14/33	0.676056438321941	4	FACETS	0.953	0.914	0.993	0.953	0.914	0.993	CLONAL	2	TRUE	2	0.705101922628618	4		851	1253	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110129	8110130	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs745673717	NA	P-0015240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	236	778	1	ENST00000585124.1:c.475dup	p.Arg159ProfsTer15	p.R159Pfs*15	ENST00000585124	NM_004217.3	159	cgc/cCgc	6/9	0.705101922628618	3	FACETS	1	0.958	1	0.344	0.321	0.367	CLONAL	1	TRUE	0	0.705101922628618	3		779	877	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39623721	39623721	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	186	638	0	ENST00000262039.4:c.2128A>T	p.Ser710Cys	p.S710C	ENST00000262039	NM_002647.2	710	Agt/Tgt	20/25	1	2	FACETS	0.914	0.85	0.981	0.914	0.85	0.981	CLONAL	1	TRUE	1	0.705101922628618	2		638	577	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2193686	2193686	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0015240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	156	863	1	ENST00000398665.3:c.494-2A>T		p.X165_splice	ENST00000398665	NM_032482.2	165			0.230397895893625	2	FACETS	0.666	0.612	0.723	0.333	0.306	0.362	INDETERMINATE	1	TRUE	0	0.705101922628618	2		864	664	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354080	15354080	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	48	748	1	ENST00000263377.2:c.2800C>T	p.Gln934Ter	p.Q934*	ENST00000263377	NM_058243.2	934	Cag/Tag	14/20	0.268300148213673	3	FACETS	0.261	0.22	0.307	0.131	0.11	0.154	INDETERMINATE	1	TRUE	1	0.705101922628618	3		749	705	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098762	47098762	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	487	910	0	ENST00000409792.3:c.6512A>T	p.Tyr2171Phe	p.Y2171F	ENST00000409792	NM_014159.6	2171	tAt/tTt	15/21	0.705101922628618	2	FACETS	0.921	0.891	0.95	0.921	0.891	0.95	CLONAL	2	TRUE	0	0.705101922628618	2		910	750	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884872	134884872	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	1065	685	3	ENST00000398015.3:c.1648G>T	p.Val550Phe	p.V550F	ENST00000398015	NM_004441.4	550	Gtc/Ttc	8/16	0.705101922628618	7	FACETS	0.995	0.973	1	0.995	0.973	1	CLONAL	5	TRUE	2	0.705101922628618	7		688	1677	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242724	66242724	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	171	710	0	ENST00000273854.3:c.1848C>A	p.Ser616Arg	p.S616R	ENST00000273854	NM_004439.5	616	agC/agA	9/18	0.705101922628618	2	FACETS	0.892	0.826	0.959	0.446	0.413	0.48	CLONAL	1	TRUE	0	0.705101922628618	2		710	544	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172960	38172960	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	275	973	0	ENST00000317025.8:c.2089A>G	p.Met697Val	p.M697V	ENST00000317025	NM_023034.1	697	Atg/Gtg	11/24	0.705101922628618	3	FACETS	1	0.951	1	0.507	0.476	0.539	CLONAL	1	TRUE	1	0.705101922628618	3		973	1040	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918522	44918522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	325	256	0	ENST00000377967.4:c.1005G>A	p.Met335Ile	p.M335I	ENST00000377967	NM_021140.2	335	atG/atA	12/29	0.513498909054454	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.705101922628618	2		256	401	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714672	52714672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	119	825	4	ENST00000322088.6:c.430C>T	p.Arg144Cys	p.R144C	ENST00000322088	NM_014225.5	144	Cgc/Tgc	4/15	0.186554524112268	0	FACETS	0.515	0.467	0.566			1	INDETERMINATE	1	TRUE	0	0.469485338636953	0		829	522	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	216	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.884	0.824	0.946	0.884	0.824	0.946	CLONAL	1	TRUE	1	0.609094506730238	2		493	802	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0015244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	197	730	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.609094506730238	1	FACETS	0.947	0.886	1	0.947	0.886	1	CLONAL	1	TRUE	0	0.609094506730238	1		730	475	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175951	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1392778905	NA	P-0015244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	126	517	1	ENST00000257430.4:c.4660G>T	p.Glu1554Ter	p.E1554*	ENST00000257430	NM_000038.5	1554	Gaa/Taa	16/16	0.609094506730238	1	FACETS	0.829	0.76	0.9	0.829	0.76	0.9	CLONAL	1	TRUE	0	0.609094506730238	1		518	347	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711876	89711876	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	167	332	0	ENST00000371953.3:c.494G>A	p.Gly165Glu	p.G165E	ENST00000371953	NM_000314.4	165	gGa/gAa	6/9	0.609094506730238	1	FACETS	0.902	0.838	0.966	0.902	0.838	0.966	CLONAL	1	TRUE	0	0.609094506730238	1		332	423	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662086	227662086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs896026781	NA	P-0015244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	256	863	1	ENST00000305123.5:c.1369C>T	p.Arg457Cys	p.R457C	ENST00000305123	NM_005544.2	457	Cgc/Tgc	1/2	1	2	FACETS	0.966	0.907	1	0.966	0.907	1	CLONAL	1	TRUE	1	0.609094506730238	2		864	870	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186783	11186785	+	missense_variant	Missense_Mutation	TNP	GGC	GGC	TGG	novel	NA	P-0015244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	213	886	1	ENST00000361445.4:c.6420_6422delinsCCA	p.Pro2141Gln	p.P2141Q	ENST00000361445	NM_004958.3	2140	gtGCCa/gtCCAa	46/58	0.609094506730238	1	FACETS	0.824	0.771	0.879	0.824	0.771	0.879	CLONAL	1	TRUE	0	0.609094506730238	1		887	590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0015245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	171	791	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.375558902265954	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.375558902265954	1		791	683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0015246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	136	840	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.289355986431221	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.289355986431221	1		842	674	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333715	70333715	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	62	625	0	ENST00000373644.4:c.1620A>C	p.Lys540Asn	p.K540N	ENST00000373644	NM_030625.2	540	aaA/aaC	2/12	0.0946582158964484	3	FACETS	1	0.933	1	0.564	0.488	0.645	INDETERMINATE	1	TRUE	1	0.289355986431221	3		625	435	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224428	53224428	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	119	735	0	ENST00000375401.3:c.3285C>A	p.Cys1095Ter	p.C1095*	ENST00000375401	NM_004187.3	1095	tgC/tgA	21/26	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.289355986431221	2		735	622	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	233	297	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.766135883704982	2		297	574	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000102	30000102	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	352	909	0	ENST00000338641.4:c.114+1G>A		p.X38_splice	ENST00000338641	NM_000268.3	38			0.766135883704982	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.766135883704982	1		909	557	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023426	27023426	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	100	659	0	ENST00000324856.7:c.532A>G	p.Ser178Gly	p.S178G	ENST00000324856	NM_006015.4	178	Agc/Ggc	1/20	NA	2	FACETS	0.307	0.274	0.343			1	INDETERMINATE	1	TRUE	NA	0.766135883704982	2		659	850	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822028	72822048	+	inframe_deletion	In_Frame_Del	DEL	GTTGCCGCTGCTGCTGCTGCT	GTTGCCGCTGCTGCTGCTGCT	-	novel	NA	P-0015247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	195	355	0	ENST00000268489.5:c.10127_10147del	p.Gln3376_Gln3382del	p.Q3376_Q3382del	ENST00000268489	NM_006885.3	3376	cAGCAGCAGCAGCAGCGGCAACta/cta	10/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.766135883704982	2		355	451	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281526	15281526	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	413	908	2	ENST00000263388.2:c.4847C>A	p.Ala1616Glu	p.A1616E	ENST00000263388	NM_000435.2	1616	gCg/gAg	26/33	1	2	FACETS	0.984	0.938	1	0.984	0.938	1	CLONAL	1	TRUE	1	0.766135883704982	2		910	1096	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288547	15288547	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	42	102	0	ENST00000263388.2:c.4192G>C	p.Asp1398His	p.D1398H	ENST00000263388	NM_000435.2	1398	Gac/Cac	24/33	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.766135883704982	2		102	105	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306529	41306529	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	219	645	0	ENST00000373198.4:c.1130T>C	p.Leu377Pro	p.L377P	ENST00000373198	NM_133170.3	377	cTc/cCc	7/32	1	2	FACETS	0.878	0.821	0.936	0.878	0.821	0.936	CLONAL	1	TRUE	1	0.766135883704982	2		645	651	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164583	36164623	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCAGGATGCGCGGCGGCGAGCGCTCGCCGCCCACCAT	GGCGGCAGGATGCGCGGCGGCGAGCGCTCGCCGCCCACCAT	-	novel	NA	P-0015247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	379	674	0	ENST00000300305.3:c.1252_1292del	p.Met418LeufsTer168	p.M418Lfs*168	ENST00000300305		418	ATGGTGGGCGGCGAGCGCTCGCCGCCGCGCATCCTGCCGCCc/c	8/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.766135883704982	2		674	938	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268353	142268353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	64	592	0	ENST00000350721.4:c.3139G>A	p.Asp1047Asn	p.D1047N	ENST00000350721	NM_001184.3	1047	Gat/Aat	15/47	NA	2	FACETS	0.247	0.213	0.283			1	INDETERMINATE	1	TRUE	NA	0.766135883704982	2		592	677	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505130	149505130	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	393	775	0	ENST00000261799.4:c.1685A>G	p.Tyr562Cys	p.Y562C	ENST00000261799	NM_002609.3	562	tAc/tGc	12/23	0.766135883704982	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.766135883704982	1		775	588	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5535043	5535043	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	195	477	0	ENST00000397747.3:c.354A>C	p.Lys118Asn	p.K118N	ENST00000397747	NM_025239.3	118	aaA/aaC	3/7	0.766135883704982	1	FACETS	0.984	0.932	1	0.984	0.932	1	CLONAL	1	TRUE	0	0.766135883704982	1		477	319	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0015248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	134	943	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		943	668	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650826	48650826	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	100	1289	0	ENST00000376670.3:c.695A>C	p.His232Pro	p.H232P	ENST00000376670	NM_002049.3	232	cAc/cCc	4/6	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		1289	872	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579849	7579849	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	416	1028	0	ENST00000269305.4:c.64C>G	p.Leu22Val	p.L22V	ENST00000269305	NM_001126112.2	22	Cta/Gta	2/11	NA	2	FACETS	0.987	0.945	1			1	INDETERMINATE	2	TRUE	NA	0.491982752832736	2		1028	857	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839737	42839737	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	294	981	0	ENST00000398585.3:c.1502G>C	p.Gly501Ala	p.G501A	ENST00000398585	NM_001135099.1	501	gGc/gCc	13/14	0.237956301809672	4	FACETS	0.761	0.716	0.807	0.761	0.716	0.807	INDETERMINATE	2	TRUE	2	0.491982752832736	4		981	1172	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2218111	2218111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	329	1094	0	ENST00000326181.6:c.173G>A	p.Arg58Lys	p.R58K	ENST00000326181	NM_032271.2	58	aGg/aAg	4/21	0.473417745876935	3	FACETS	1	0.985	1	0.564	0.532	0.597	CLONAL	1	TRUE	1	0.484334769625809	3		1094	1496	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888108	81888108	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	44	783	0	ENST00000359376.3:c.253G>C	p.Ala85Pro	p.A85P	ENST00000359376	NM_002661.3	85	Gca/Cca	3/33	0.484334769625809	1	FACETS	0.225	0.188	0.266	0.225	0.188	0.266	SUBCLONAL	1	TRUE	0	0.484334769625809	1		783	611	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520008	NA	P-0015250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	282	931	0	ENST00000269305.4:c.613T>G	p.Tyr205Asp	p.Y205D	ENST00000269305	NM_001126112.2	205	Tat/Gat	6/11	0.484334769625809	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.484334769625809	1		931	677	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982806	7982806	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	302	1056	4	ENST00000319144.4:c.979G>A	p.Val327Met	p.V327M	ENST00000319144	NM_001139.2	327	Gtg/Atg	8/15	0.484334769625809	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.484334769625809	1		1060	751	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754086	42754086	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs886041001	NA	P-0015250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	165	755	0	ENST00000222329.4:c.266A>G	p.Tyr89Cys	p.Y89C	ENST00000222329	NM_006494.2	89	tAt/tGt	3/4	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.484334769625809	2		755	652	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099439	157099439	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs911746269	NA	P-0015250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	94	507	3	ENST00000346085.5:c.376C>T	p.Gln126Ter	p.Q126*	ENST00000346085	NM_020732.3	126	Cag/Tag	1/20	1	2	FACETS	0.749	0.669	0.834	0.749	0.669	0.834	SUBCLONAL	1	TRUE	1	0.484334769625809	2		510	518	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151933019	151933019	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0015250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	14	130	0	ENST00000262189.6:c.2653-1G>A		p.X885_splice	ENST00000262189	NM_170606.2	885			0.484334769625809	1	FACETS	0.337	0.245	0.446	0.337	0.245	0.446	SUBCLONAL	1	TRUE	0	0.484334769625809	1		130	130	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0015251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	319	867	8	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.508161094642337	2	FACETS	0.918	0.875	0.961	0.918	0.875	0.961	CLONAL	2	TRUE	0	0.5454926374555	2		875	637	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156051	99156051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776096061	NA	P-0015251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	397	861	2	ENST00000074304.5:c.731G>A	p.Arg244Gln	p.R244Q	ENST00000074304	NM_001134224.1	244	cGg/cAg	10/26	0.5454926374555	3	FACETS	0.995	0.95	1	0.995	0.95	1	CLONAL	2	TRUE	1	0.5454926374555	3		863	931	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163795	72163795	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	256	822	0	ENST00000357731.5:c.563T>C	p.Leu188Ser	p.L188S	ENST00000357731	NM_173808.2	188	tTg/tCg	4/7	0.302511426095502	3	FACETS	1	0.989	1	0.772	0.731	0.813	INDETERMINATE	2	TRUE	0	0.5454926374555	3		822	516	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748059	72748059	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	348	872	0	ENST00000357731.5:c.119T>C	p.Phe40Ser	p.F40S	ENST00000357731	NM_173808.2	40	tTc/tCc	1/7	0.302511426095502	3	FACETS	1	0.993	1	0.804	0.769	0.84	INDETERMINATE	2	TRUE	0	0.5454926374555	3		872	673	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736387	85736387	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	274	608	0	ENST00000370580.1:c.260G>C	p.Arg87Pro	p.R87P	ENST00000370580	NM_003921.4	87	cGg/cCg	2/3	0.302511426095502	3	FACETS	1	0.975	1	0.7	0.663	0.737	INDETERMINATE	2	TRUE	0	0.5454926374555	3		608	609	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530157	212530157	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	121	640	0	ENST00000342788.4:c.1762A>C	p.Asn588His	p.N588H	ENST00000342788	NM_005235.2	588	Aac/Cac	15/28	0.337618326713141	3	FACETS	1	0.96	1	0.551	0.5	0.605	CLONAL	1	TRUE	1	0.5454926374555	3		640	512	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812207	212812207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	161	606	0	ENST00000342788.4:c.369C>A	p.Tyr123Ter	p.Y123*	ENST00000342788	NM_005235.2	123	taC/taA	3/28	0.337618326713141	3	FACETS	0.757	0.7	0.816	0.757	0.7	0.816	SUBCLONAL	2	TRUE	1	0.5454926374555	3		606	496	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467931	66467931	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	120	668	0	ENST00000273854.3:c.338T>C	p.Leu113Pro	p.L113P	ENST00000273854	NM_004439.5	113	cTt/cCt	3/18	1	2	FACETS	0.917	0.833	1	0.917	0.833	1	CLONAL	1	TRUE	1	0.5454926374555	2		668	480	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198347	138198347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776397709	NA	P-0015251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	300	641	0	ENST00000237289.4:c.940G>A	p.Val314Ile	p.V314I	ENST00000237289	NM_001270507.1	314	Gtc/Atc	6/9	0.263683821105076	5	FACETS	0.871	0.825	0.918	0.871	0.825	0.918	INDETERMINATE	3	TRUE	2	0.5454926374555	5		641	765	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021760	69021760	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	437	1031	0	ENST00000288368.4:c.3048A>C	p.Lys1016Asn	p.K1016N	ENST00000288368	NM_024870.2	1016	aaA/aaC	25/40	0.263683821105076	5	FACETS	1	0.993	1	0.805	0.768	0.841	INDETERMINATE	2	TRUE	2	0.5454926374555	5		1031	1207	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118354982	118354982	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	153	719	0	ENST00000534358.1:c.4171C>A	p.Gln1391Lys	p.Q1391K	ENST00000534358	NM_005933.3	1391	Caa/Aaa	9/36	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.459286298994281	2		719	662	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143176	24143177	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	188	797	0	ENST00000263121.7:c.410dup	p.Asn137LysfsTer33	p.N137Kfs*33	ENST00000263121	NM_003073.3	136	-/A	4/9	0.459286298994281	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.459286298994281	1		797	575	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	81	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.738	0.65	0.832	0.738	0.65	0.832	SUBCLONAL	1	TRUE	1	0.346256196792666	2		493	634	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956129	175956129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1209327714	NA	P-0015256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	51	778	0	ENST00000367669.3:c.2083G>A	p.Asp695Asn	p.D695N	ENST00000367669	NM_022457.5	695	Gat/Aat	18/20	0.346256196792666	3	FACETS	0.381	0.323	0.446	0.191	0.161	0.223	SUBCLONAL	1	TRUE	1	0.346256196792666	3		778	906	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923650	72923650	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	62	728	0	ENST00000268489.5:c.3428G>T	p.Arg1143Met	p.R1143M	ENST00000268489	NM_006885.3	1143	aGg/aTg	4/10	1	2	FACETS	0.656	0.567	0.752	0.656	0.567	0.752	SUBCLONAL	1	TRUE	1	0.346256196792666	2		728	546	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221340	1221340	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0015256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	92	754	0	ENST00000326873.7:c.862+1G>C		p.X288_splice	ENST00000326873	NM_000455.4	288			0.205743924588651	2	FACETS	1	0.91	1	0.512	0.456	0.571	INDETERMINATE	1	TRUE	0	0.346256196792666	2		754	519	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610129	10610132	+	frameshift_variant	Frame_Shift_Del	DEL	ATCT	ATCT	-	novel	NA	P-0015256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	113	932	0	ENST00000171111.5:c.578_581del	p.Gln193LeufsTer36	p.Q193Lfs*36	ENST00000171111	NM_203500.1	193	cAGATt/ct	2/6	0.205743924588651	2	FACETS	0.811	0.729	0.897	0.405	0.364	0.449	INDETERMINATE	1	TRUE	0	0.346256196792666	2		932	805	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266605	198266605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	33	587	2	ENST00000335508.6:c.2231C>T	p.Ala744Val	p.A744V	ENST00000335508	NM_012433.2	744	gCt/gTt	16/25	1	2	FACETS	0.322	0.261	0.391	0.322	0.261	0.391	SUBCLONAL	1	TRUE	1	0.346256196792666	2		589	592	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143326475	143326475	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	26	510	0	ENST00000262992.4:c.139T>C	p.Cys47Arg	p.C47R	ENST00000262992	NM_001101669.1	47	Tgc/Cgc	4/24	1	2	FACETS	0.365	0.289	0.453	0.365	0.289	0.453	SUBCLONAL	1	TRUE	1	0.346256196792666	2		510	411	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518150	187518150	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	59	712	0	ENST00000441802.2:c.12544G>T	p.Gly4182Ter	p.G4182*	ENST00000441802	NM_005245.3	4182	Gga/Tga	25/27	1	2	FACETS	0.53	0.455	0.611	0.53	0.455	0.611	SUBCLONAL	1	TRUE	1	0.346256196792666	2		712	643	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518174	187518174	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	53	612	0	ENST00000441802.2:c.12520C>G	p.Pro4174Ala	p.P4174A	ENST00000441802	NM_005245.3	4174	Ccg/Gcg	25/27	1	2	FACETS	0.607	0.518	0.705	0.607	0.518	0.705	SUBCLONAL	1	TRUE	1	0.346256196792666	2		612	504	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341130	8341130	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	54	813	0	ENST00000356435.5:c.5086G>T	p.Gly1696Ter	p.G1696*	ENST00000356435		1696	Gga/Tga	30/35	1	2	FACETS	0.518	0.442	0.601	0.518	0.442	0.601	SUBCLONAL	1	TRUE	1	0.346256196792666	2		813	602	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0015258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	467	1105	2	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.769113292329957	1	FACETS	0.954	0.923	0.986	0.954	0.923	0.986	CLONAL	1	TRUE	0	0.805945034878844	1		1107	725	SUCCESS
AR	367	MSKCC	GRCh37	X	66765072	66765072	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	374	1084	0	ENST00000374690.3:c.84G>C	p.Gln28His	p.Q28H	ENST00000374690	NM_000044.3	28	caG/caC	1/8	1	2	FACETS	0.94	0.895	0.986	0.94	0.895	0.986	CLONAL	1	TRUE	1	0.805945034878844	2		1084	987	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920582	96920582	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782203	NA	P-0015258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	170	542	0	ENST00000258439.3:c.398A>G	p.His133Arg	p.H133R	ENST00000258439	NM_001193304.2	133	cAt/cGt	3/4	1	2	FACETS	0.854	0.792	0.918	0.854	0.792	0.918	CLONAL	1	TRUE	1	0.805945034878844	2		542	494	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944353	76944354	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0015258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	359	903	0	ENST00000373344.5:c.551_552del	p.Asp184ValfsTer4	p.D184Vfs*4	ENST00000373344	NM_000489.3	184	gAT/g	7/35	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.805945034878844	2		903	884	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	52	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.196821377626881	3	FACETS	0.915	0.788	1	0.61	0.525	0.701	CLONAL	2	TRUE	0	0.284710156730529	3		493	228	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0015259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	19	366	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.284710156730529	5	FACETS	0.962	0.743	1			1	CLONAL	2	TRUE	NA	0.284710156730529	5		366	99	SUCCESS
ATM	472	MSKCC	GRCh37	11	108214045	108214045	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0015259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	52	534	0	ENST00000278616.4:c.8365A>T	p.Lys2789Ter	p.K2789*	ENST00000278616	NM_000051.3	2789	Aaa/Taa	57/63	0.284710156730529	3	FACETS	1	0.944	1	0.786	0.681	0.897	CLONAL	2	TRUE	0	0.284710156730529	3		534	177	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594258	55594258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913523	NA	P-0015260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	193	721	0	ENST00000288135.5:c.1961T>C	p.Val654Ala	p.V654A	ENST00000288135	NM_000222.2	654	gTg/gCg	13/21	0.551218204921551	1	FACETS	0.954	0.889	1	0.954	0.889	1	CLONAL	1	TRUE	0	0.551218204921551	1		721	532	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420938	49420941	+	frameshift_variant	Frame_Shift_Del	DEL	GGGA	GGGA	-	novel	NA	P-0015260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	164	720	2	ENST00000301067.7:c.14808_14811del	p.Thr4938AsnfsTer56	p.T4938Nfs*56	ENST00000301067	NM_003482.3	4936	ctTCCC/ct	48/54	1	2	FACETS	0.865	0.796	0.936	0.865	0.796	0.936	CLONAL	1	TRUE	1	0.551218204921551	2		722	688	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593621	55593660	+	protein_altering_variant	In_Frame_Del	DEL	ATAAATGGAAACAATTATGTTTACATAGACCCAACACAAC	ATAAATGGAAACAATTATGTTTACATAGACCCAACACAAC	T	novel	NA	P-0015260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	165	678	0	ENST00000288135.5:c.1687_1726delinsT	p.Ile563_Leu576delinsPhe	p.I563_L576delinsF	ENST00000288135	NM_000222.2	563	ATAAATGGAAACAATTATGTTTACATAGACCCAACACAACtt/Ttt	11/21	0.551218204921551	1	FACETS	0.927	0.859	0.996	0.927	0.859	0.996	CLONAL	1	TRUE	0	0.551218204921551	1		678	468	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	137	297	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		297	502	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0015263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	358	616	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.396699444126011	3	FACETS	0.91	0.874	0.946	1	0.994	1	CLONAL	4	TRUE	0	0.396699444126011	3		617	594	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913351	NA	P-0015263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	233	713	0	ENST00000288602.6:c.1397G>A	p.Gly466Glu	p.G466E	ENST00000288602	NM_004333.4	466	gGa/gAa	11/18	0.396699444126011	6	FACETS	0.978	0.916	1	0.734	0.687	0.781	CLONAL	3	TRUE	2	0.396699444126011	6		713	718	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0015263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	95	699	1	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.396699444126011	3	FACETS	0.78	0.694	0.871	0.26	0.231	0.291	SUBCLONAL	1	TRUE	0	0.396699444126011	3		700	736	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0015263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	718	1322	2	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.396699444126011	1	FACETS	0.933	0.909	0.956	1	0.998	1	CLONAL	3	TRUE	0	0.396699444126011	1		1324	1037	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398254	25398254	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs727503110	NA	P-0015263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	259	890	0	ENST00000311936.3:c.65A>T	p.Gln22Leu	p.Q22L	ENST00000311936	NM_004985.3	22	cAg/cTg	2/5	0.261065082161544	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.396699444126011	3		890	636	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59937157	59937157	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs372581879	NA	P-0015263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	100	585	0	ENST00000259008.2:c.205G>A	p.Gly69Arg	p.G69R	ENST00000259008	NM_032043.2	69	Ggg/Agg	3/20	0.239567281357004	4	FACETS	1	0.978	1	0.68	0.609	0.754	CLONAL	1	TRUE	2	0.396699444126011	4		585	518	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045898	180045898	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1453695178	NA	P-0015263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	68	682	0	ENST00000261937.6:c.2873G>C	p.Gly958Ala	p.G958A	ENST00000261937	NM_182925.4	958	gGa/gCa	21/30	0.369956347614401	4	FACETS	0.676	0.588	0.772	0.169	0.147	0.193	SUBCLONAL	1	TRUE	0	0.396699444126011	4		682	708	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971177	21971177	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913382	NA	P-0015264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	235	579	0	ENST00000304494.5:c.181G>T	p.Glu61Ter	p.E61*	ENST00000304494	NM_000077.4	61	Gag/Tag	2/3	1	2	FACETS	0.914	0.856	0.972	0.914	0.856	0.972	CLONAL	1	TRUE	1	0.712485035204226	2		579	722	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624296	89624296	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs786201995	NA	P-0015264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	292	753	0	ENST00000371953.3:c.70G>C	p.Asp24His	p.D24H	ENST00000371953	NM_000314.4	24	Gac/Cac	1/9	0.673567619692677	1	FACETS	0.919	0.874	0.964	0.919	0.874	0.964	CLONAL	1	TRUE	0	0.712485035204226	1		753	574	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799281	42799281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	300	617	2	ENST00000575354.2:c.4765G>A	p.Glu1589Lys	p.E1589K	ENST00000575354	NM_015125.3	1589	Gag/Aag	20/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.712485035204226	2		619	818	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164508	47164508	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs201756643	NA	P-0015264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	212	527	0	ENST00000409792.3:c.1618C>T	p.Arg540Ter	p.R540*	ENST00000409792	NM_014159.6	540	Cga/Tga	3/21	1	2	FACETS	0.839	0.783	0.897	0.839	0.783	0.897	CLONAL	1	TRUE	1	0.712485035204226	2		527	709	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923034	44923034	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	424	458	2	ENST00000377967.4:c.1895G>A	p.Trp632Ter	p.W632*	ENST00000377967	NM_021140.2	632	tGg/tAg	16/29	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.712485035204226	1		460	601	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028835	47028835	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782587193	NA	P-0015264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	439	465	0	ENST00000377604.3:c.139G>A	p.Glu47Lys	p.E47K	ENST00000377604	NM_001204468.1	47	Gag/Aag	3/24	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.712485035204226	1		465	604	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	39	722	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		722	658	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0015268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	182	423	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.846	0.78	0.914	0.846	0.78	0.914	CLONAL	1	TRUE	1	0.456929834951952	2		423	942	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023485	27023486	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0015268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	240	765	0	ENST00000324856.7:c.595dup	p.Gln199ProfsTer201	p.Q199Pfs*201	ENST00000324856	NM_006015.4	197	-/C	1/20	0.456929834951952	1	FACETS	0.865	0.809	0.923	0.865	0.809	0.923	CLONAL	1	TRUE	0	0.456929834951952	1		765	937	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696598	47696598	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	355	379	0	ENST00000347630.2:c.350T>C	p.Met117Thr	p.M117T	ENST00000347630	NM_001007230.1	117	aTg/aCg	5/11	0.456929834951952	2	FACETS	0.991	0.945	1	0.991	0.945	1	CLONAL	2	TRUE	0	0.456929834951952	2		379	784	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776361	76776361	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	163	555	0	ENST00000373344.5:c.7105G>C	p.Val2369Leu	p.V2369L	ENST00000373344	NM_000489.3	2369	Gta/Cta	34/35	1	2	FACETS	0.748	0.686	0.813	0.748	0.686	0.813	SUBCLONAL	1	TRUE	1	0.456929834951952	2		555	954	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577101	7577101	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	627	681	0	ENST00000269305.4:c.837del	p.Arg280GlufsTer65	p.R280Efs*65	ENST00000269305	NM_001126112.2	279	ggG/gg	8/11	0.555931874028028	3	FACETS	0.849	0.822	0.876	0.849	0.822	0.876	CLONAL	3	TRUE	0	0.555931874028028	3		681	1132	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300599	11300599	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	254	421	0	ENST00000361445.4:c.1547C>A	p.Ala516Asp	p.A516D	ENST00000361445	NM_004958.3	516	gCc/gAc	11/58	0.48020387553415	5	FACETS	0.932	0.874	0.992	0.466	0.437	0.496	CLONAL	2	TRUE	1	0.555931874028028	5		421	899	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462024	120462024	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	265	418	0	ENST00000256646.2:c.5692G>T	p.Asp1898Tyr	p.D1898Y	ENST00000256646	NM_024408.3	1898	Gat/Tat	31/34	0.375757537717734	6	FACETS	1	0.976	1	0.719	0.675	0.764	CLONAL	2	TRUE	3	0.555931874028028	6		418	934	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953749	48953749	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	108	263	0	ENST00000267163.4:c.1352G>C	p.Arg451Pro	p.R451P	ENST00000267163	NM_000321.2	451	cGc/cCc	14/27	0.534657603726761	2	FACETS	0.816	0.748	0.885	0.816	0.748	0.885	CLONAL	2	TRUE	0	0.555931874028028	2		263	238	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435483	110435483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	497	812	1	ENST00000375856.3:c.2918C>T	p.Ser973Phe	p.S973F	ENST00000375856	NM_003749.2	973	tCt/tTt	1/2	0.534657603726761	2	FACETS	0.924	0.889	0.958	0.924	0.889	0.958	CLONAL	2	TRUE	0	0.555931874028028	2		813	968	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281180	46281180	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	306	486	0	ENST00000371998.3:c.3977G>A	p.Gly1326Asp	p.G1326D	ENST00000371998		1326	gGt/gAt	21/23	0.555931874028028	4	FACETS	0.915	0.864	0.966	0.915	0.864	0.966	CLONAL	2	TRUE	2	0.555931874028028	4		486	936	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339280	116339280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374050750	NA	P-0015269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	221	355	0	ENST00000397752.3:c.142G>A	p.Ala48Thr	p.A48T	ENST00000397752	NM_000245.2	48	Gcg/Acg	2/21	0.555931874028028	3	FACETS	0.973	0.915	1	0.973	0.915	1	CLONAL	2	TRUE	1	0.555931874028028	3		355	522	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76954118	76954118	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0015269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	111	275	0	ENST00000373344.5:c.134-1G>A		p.X45_splice	ENST00000373344	NM_000489.3	45			0.52796761385789	3	FACETS	0.865	0.789	0.943	0.865	0.789	0.943	CLONAL	2	TRUE	1	0.555931874028028	3		275	295	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0015273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	34	577	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.102	0.083	0.125	0.102	0.083	0.125	SUBCLONAL	1	TRUE	1	0.614486860709039	2		577	1080	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711876	89711876	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	13	332	0	ENST00000371953.3:c.494G>A	p.Gly165Glu	p.G165E	ENST00000371953	NM_000314.4	165	gGa/gAa	6/9	0.597903952693149	1	FACETS	0.062	0.044	0.085	0.062	0.044	0.085	SUBCLONAL	1	TRUE	0	0.614486860709039	1		332	469	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919734	50919734	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878854545	NA	P-0015273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	331	652	1	ENST00000440232.2:c.2902C>T	p.Arg968Cys	p.R968C	ENST00000440232	NM_002691.3	968	Cgc/Tgc	23/27	0.531522264752997	3	FACETS	1	0.963	1	0.513	0.484	0.543	CLONAL	1	TRUE	1	0.614486860709039	3		653	1372	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667473	241667473	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553341037	NA	P-0015273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	31	241	0	ENST00000366560.3:c.977G>A	p.Gly326Glu	p.G326E	ENST00000366560	NM_000143.3	326	gGa/gAa	7/10	1	2	FACETS	0.184	0.148	0.224	0.184	0.148	0.224	SUBCLONAL	1	TRUE	1	0.614486860709039	2		241	549	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717637	89717637	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1221700050	NA	P-0015273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	47	355	0	ENST00000371953.3:c.662A>G	p.Lys221Arg	p.K221R	ENST00000371953	NM_000314.4	221	aAg/aGg	7/9	0.597903952693149	1	FACETS	0.189	0.159	0.222	0.189	0.159	0.222	SUBCLONAL	1	TRUE	0	0.614486860709039	1		355	561	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061115	38061115	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	80	215	0	ENST00000250448.2:c.874G>T	p.Glu292Ter	p.E292*	ENST00000250448	NM_004496.3	292	Gag/Tag	2/2	1	2	FACETS	0.799	0.709	0.893	0.799	0.709	0.893	SUBCLONAL	1	TRUE	1	0.614486860709039	2		215	326	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31495482	31495482	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	C	novel	NA	P-0015273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	199	418	0	ENST00000344624.3:c.1669-3C>G		p.X557_splice	ENST00000344624		557			1	2	FACETS	0.691	0.64	0.743	0.691	0.64	0.743	SUBCLONAL	1	TRUE	1	0.614486860709039	2		418	938	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	1053	592	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.353462380765045	9	FACETS	1	0.986	1			1	CLONAL	9	TRUE	NA	0.353462380765045	9		592	1470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	238	566	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.353462380765045	2	FACETS	0.909	0.852	0.967	0.909	0.852	0.967	CLONAL	2	TRUE	0	0.353462380765045	2		566	741	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052726	42052726	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	115	345	0	ENST00000219905.7:c.7397G>C	p.Arg2466Pro	p.R2466P	ENST00000219905	NM_001164273.1	2466	cGa/cCa	20/24	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.353462380765045	2		345	527	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721189	176721189	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	223	322	0	ENST00000439151.2:c.6820C>T	p.Gln2274Ter	p.Q2274*	ENST00000439151	NM_022455.4	2274	Cag/Tag	23/23	0.347286622442624	4	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.353462380765045	4		322	694	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699277	117699277	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	183	361	0	ENST00000369458.3:c.364C>A	p.Leu122Ile	p.L122I	ENST00000369458	NM_024626.3	122	Ctc/Atc	3/6	0.34595804588173	3	FACETS	0.923	0.855	0.993	0.923	0.855	0.993	CLONAL	2	TRUE	1	0.353462380765045	3		361	660	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468378	120468378	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	300	570	0	ENST00000256646.2:c.4061G>T	p.Gly1354Val	p.G1354V	ENST00000256646	NM_024408.3	1354	gGg/gTg	25/34	0.34595804588173	3	FACETS	0.97	0.914	1	0.97	0.914	1	CLONAL	2	TRUE	1	0.353462380765045	3		570	1030	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834522	156834522	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	326	664	0	ENST00000524377.1:c.290C>A	p.Thr97Asn	p.T97N	ENST00000524377	NM_002529.3	97	aCc/aAc	3/17	0.353462380765045	5	FACETS	0.996	0.939	1	0.664	0.626	0.703	CLONAL	2	TRUE	2	0.353462380765045	5		664	1417	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176132092	176132092	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1381146238	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	247	491	0	ENST00000367669.3:c.675G>T	p.Trp225Cys	p.W225C	ENST00000367669	NM_022457.5	225	tgG/tgT	5/20	0.353462380765045	5	FACETS	1	0.954	1	0.683	0.639	0.729	CLONAL	2	TRUE	2	0.353462380765045	5		491	1043	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100612	8100612	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	227	616	0	ENST00000346208.3:c.586C>A	p.Leu196Met	p.L196M	ENST00000346208		196	Ctg/Atg	3/6	0.34595804588173	3	FACETS	1	0.991	1	0.712	0.663	0.763	CLONAL	1	TRUE	1	0.353462380765045	3		616	1061	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63662166	63662166	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	104	276	0	ENST00000279873.7:c.270T>G	p.His90Gln	p.H90Q	ENST00000279873	NM_032199.2	90	caT/caG	2/10	0.34595804588173	3	FACETS	1	0.96	1	0.569	0.511	0.631	CLONAL	1	TRUE	1	0.353462380765045	3		276	608	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865725	57865726	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	268	600	0	ENST00000228682.2:c.3206dup	p.Ser1070GlnfsTer36	p.S1070Qfs*36	ENST00000228682	NM_005269.2	1068	cgg/cGgg	12/12	0.353462380765045	3	FACETS	0.862	0.809	0.917	0.575	0.539	0.611	CLONAL	2	TRUE	0	0.353462380765045	3		600	1035	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865761	57865761	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	135	578	2	ENST00000228682.2:c.3243del	p.Asn1082ThrfsTer7	p.N1082Tfs*7	ENST00000228682	NM_005269.2	1080	Ccc/cc	12/12	0.353462380765045	3	FACETS	0.915	0.831	1	0.305	0.277	0.335	CLONAL	1	TRUE	0	0.353462380765045	3		580	982	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900640	32900640	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	138	283	0	ENST00000380152.3:c.521G>T	p.Arg174Leu	p.R174L	ENST00000380152		174	cGt/cTt	7/27	0.353462380765045	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.353462380765045	2		283	367	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42002891	42002891	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	47	203	1	ENST00000219905.7:c.2428G>T	p.Gly810Ter	p.G810*	ENST00000219905	NM_001164273.1	810	Gga/Tga	8/24	1	2	FACETS	0.808	0.685	0.943	0.808	0.685	0.943	CLONAL	1	TRUE	1	0.353462380765045	2		204	329	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705535	43705535	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	T	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	166	469	0	ENST00000382044.4:c.5090-3C>A		p.X1697_splice	ENST00000382044	NM_001141980.1	1697			1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.353462380765045	2		469	897	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679760	88679760	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	126	617	0	ENST00000360948.2:c.703G>T	p.Gly235Ter	p.G235*	ENST00000360948	NM_001012338.2	235	Gga/Tga	7/19	1	2	FACETS	0.861	0.78	0.947	0.861	0.78	0.947	CLONAL	1	TRUE	1	0.353462380765045	2		617	828	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467906	99467906	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	101	248	0	ENST00000268035.6:c.2775G>T	p.Gln925His	p.Q925H	ENST00000268035	NM_000875.3	925	caG/caT	13/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.353462380765045	2		248	404	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14015960	14015960	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	183	242	0	ENST00000311895.7:c.280A>G	p.Ser94Gly	p.S94G	ENST00000311895	NM_005236.2	94	Agc/Ggc	2/11	0.262550073106159	4	FACETS	1	0.98	1			1	CLONAL	2	TRUE	NA	0.353462380765045	4		242	606	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832193	72832193	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	185	376	0	ENST00000268489.5:c.4388T>C	p.Leu1463Pro	p.L1463P	ENST00000268489	NM_006885.3	1463	cTt/cCt	9/10	0.34595804588173	3	FACETS	0.952	0.883	1	0.952	0.883	1	CLONAL	2	TRUE	1	0.353462380765045	3		376	647	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355391	15355391	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	261	510	0	ENST00000263377.2:c.2232G>C	p.Gln744His	p.Q744H	ENST00000263377	NM_058243.2	744	caG/caC	13/20	0.353462380765045	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.353462380765045	3		510	844	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952520	17952520	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	280	594	0	ENST00000458235.1:c.913C>A	p.Gln305Lys	p.Q305K	ENST00000458235	NM_000215.3	305	Cag/Aag	7/24	0.353462380765045	3	FACETS	0.881	0.828	0.935	0.881	0.828	0.935	CLONAL	2	TRUE	1	0.353462380765045	3		594	1058	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25461999	25461999	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	179	426	0	ENST00000264709.3:c.2408G>T	p.Arg803Met	p.R803M	ENST00000264709	NM_175629.2	803	aGg/aTg	20/23	0.19165791650151	4	FACETS	0.89	0.822	0.96	0.89	0.822	0.96	INDETERMINATE	2	TRUE	2	0.353462380765045	4		426	770	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593408	215593408	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	82	213	0	ENST00000260947.4:c.2326G>T	p.Asp776Tyr	p.D776Y	ENST00000260947	NM_000465.2	776	Gac/Tac	11/11	0.19165791650151	4	FACETS	0.951	0.847	1	0.951	0.847	1	INDETERMINATE	2	TRUE	2	0.353462380765045	4		213	330	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306782	41306783	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	65	266	0	ENST00000373198.4:c.876dup	p.Ala293CysfsTer54	p.A293Cfs*54	ENST00000373198	NM_133170.3	292	-/T	7/32	0.34595804588173	3	FACETS	0.921	0.8	1	0.46	0.4	0.526	CLONAL	1	TRUE	1	0.353462380765045	3		266	470	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434207	12434208	+	missense_variant	Missense_Mutation	DNP	AC	AC	GT	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	136	448	1	ENST00000287820.6:c.575_576inv	p.Tyr192Cys	p.Y192C	ENST00000287820	NM_015869.4	192	tAC/tGT	4/7	0.292640614723203	3	FACETS	1	0.961	1			1	CLONAL	1	TRUE	NA	0.353462380765045	3		449	822	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114861	73114861	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	63	86	0	ENST00000356692.5:c.1242G>T	p.Met414Ile	p.M414I	ENST00000356692		414	atG/atT	9/9	0.290634495223698	4	FACETS	0.846	0.746	0.952	1	0.964	1	CLONAL	3	TRUE	2	0.353462380765045	4		86	190	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231776	66231776	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	132	264	0	ENST00000273854.3:c.1925-1G>T		p.X642_splice	ENST00000273854	NM_004439.5	642			0.34595804588173	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.353462380765045	3		264	374	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294386	1294386	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1369	176	630	1	ENST00000310581.5:c.615T>A	p.His205Gln	p.H205Q	ENST00000310581	NM_198253.2	205	caT/caA	2/16	0.353462380765045	6	FACETS	1	0.967	1	0.275	0.252	0.299	CLONAL	1	TRUE	2	0.353462380765045	6		631	1545	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80109413	80109413	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	172	380	0	ENST00000265081.6:c.2666A>T	p.Glu889Val	p.E889V	ENST00000265081	NM_002439.4	889	gAg/gTg	20/24	0.353462380765045	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.353462380765045	2		380	451	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058706	180058706	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	390	784	0	ENST00000261937.6:c.131G>T	p.Gly44Val	p.G44V	ENST00000261937	NM_182925.4	44	gGt/gTt	2/30	0.347286622442624	4	FACETS	0.935	0.887	0.985			1	CLONAL	2	TRUE	NA	0.353462380765045	4		784	1597	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490591	20490591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	204	467	0	ENST00000346618.3:c.1328G>A	p.Gly443Asp	p.G443D	ENST00000346618	NM_001949.4	443	gGc/gAc	7/7	0.290634495223698	4	FACETS	0.895	0.831	0.961	0.895	0.831	0.961	CLONAL	2	TRUE	2	0.353462380765045	4		467	873	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015659	112015659	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	218	426	1	ENST00000368678.4:c.1183G>T	p.Val395Leu	p.V395L	ENST00000368678		395	Gtg/Ttg	11/13	0.353462380765045	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.353462380765045	2		427	611	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523502	106523502	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	72	296	0	ENST00000359195.3:c.2654C>G	p.Ala885Gly	p.A885G	ENST00000359195	NM_002649.2	885	gCc/gGc	8/11	0.34595804588173	3	FACETS	0.898	0.786	1	0.449	0.393	0.509	CLONAL	1	TRUE	1	0.353462380765045	3		296	534	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5535038	5535038	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	166	261	0	ENST00000397747.3:c.349C>A	p.Leu117Met	p.L117M	ENST00000397747	NM_025239.3	117	Ctg/Atg	3/7	0.353462380765045	8	FACETS	1	0.971	1	0.373	0.343	0.405	CLONAL	2	TRUE	2	0.353462380765045	8		261	864	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202866	27202866	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	271	480	1	ENST00000380036.4:c.1958C>A	p.Ser653Tyr	p.S653Y	ENST00000380036	NM_000459.3	653	tCc/tAc	13/23	0.262550073106159	4	FACETS	0.98	0.92	1			1	CLONAL	2	TRUE	NA	0.353462380765045	4		481	1059	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321299	1321299	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	232	515	0	ENST00000400841.2:c.456C>A	p.Tyr152Ter	p.Y152*	ENST00000400841		152	taC/taA	4/6	0.353462380765045	3	FACETS	0.972	0.909	1	0.972	0.909	1	CLONAL	2	TRUE	1	0.353462380765045	3		515	795	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038735	47038735	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	150	590	0	ENST00000377604.3:c.742C>A	p.Pro248Thr	p.P248T	ENST00000377604	NM_001204468.1	248	Ccc/Acc	9/24	0.353462380765045	3	FACETS	1	0.915	1	0.501	0.457	0.547	CLONAL	1	TRUE	1	0.353462380765045	3		590	997	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045006	47045006	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	173	711	0	ENST00000377604.3:c.2332C>T	p.Gln778Ter	p.Q778*	ENST00000377604	NM_001204468.1	778	Cag/Tag	20/24	0.353462380765045	3	FACETS	0.977	0.898	1	0.489	0.449	0.53	CLONAL	1	TRUE	1	0.353462380765045	3		711	1179	SUCCESS
AR	367	MSKCC	GRCh37	X	66766123	66766124	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	219	534	1	ENST00000374690.3:c.1135_1136insG	p.Pro379ArgfsTer123	p.P379Rfs*123	ENST00000374690	NM_000044.3	379	ccg/cGcg	1/8	0.241009430309085	4	FACETS	0.88	0.819	0.943	0.88	0.819	0.943	CLONAL	2	TRUE	2	0.353462380765045	4		535	953	SUCCESS
AR	367	MSKCC	GRCh37	X	66863220	66863220	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	169	425	0	ENST00000374690.3:c.1739G>C	p.Cys580Ser	p.C580S	ENST00000374690	NM_000044.3	580	tGc/tCc	2/8	0.241009430309085	4	FACETS	0.756	0.695	0.819	0.756	0.695	0.819	SUBCLONAL	2	TRUE	2	0.353462380765045	4		425	856	SUCCESS
AR	367	MSKCC	GRCh37	X	66931281	66931281	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	196	402	0	ENST00000374690.3:c.1923G>T	p.Gln641His	p.Q641H	ENST00000374690	NM_000044.3	641	caG/caT	4/8	0.241009430309085	4	FACETS	0.976	0.906	1	0.976	0.906	1	CLONAL	2	TRUE	2	0.353462380765045	4		402	769	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123499674	123499674	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	190	463	2	ENST00000371139.4:c.201G>T	p.Glu67Asp	p.E67D	ENST00000371139	NM_001114937.2	67	gaG/gaT	2/4	0.241009430309085	4	FACETS	0.859	0.795	0.925	0.859	0.795	0.925	CLONAL	2	TRUE	2	0.353462380765045	4		465	847	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861634	152861634	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	225	505	2	ENST00000406277.2:c.118G>T	p.Gly40Trp	p.G40W	ENST00000406277	NM_152274.4	40	Ggg/Tgg	4/7	0.353462380765045		FACETS		0.719	0.826				SUBCLONAL	2	TRUE	NA	0.353462380765045	3		507	971	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687422	117687422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	28	266	0	ENST00000368508.3:c.2629G>A	p.Ala877Thr	p.A877T	ENST00000368508	NM_002944.2	877	Gcc/Acc	18/43	1	2	FACETS	0.346	0.276	0.427	0.346	0.276	0.427	SUBCLONAL	1	TRUE	1	0.3	2		266	539	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923188	39923188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	21	196	0	ENST00000378444.4:c.3520G>A	p.Glu1174Lys	p.E1174K	ENST00000378444	NM_001123385.1	1174	Gaa/Aaa	8/15	0.134464278764432	2	FACETS	0.519	0.4	0.657			1	INDETERMINATE	1	TRUE	NA	0.3	2		196	270	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121438947	121438947	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	173	804	0	ENST00000257555.6:c.1848C>G	p.Ser616Arg	p.S616R	ENST00000257555		616	agC/agG	10/10	0.176518841416109	2	FACETS	1	0.98	1	0.599	0.551	0.649	INDETERMINATE	1	TRUE	0	0.3	2		804	963	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579522	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0015276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	159	639	0	ENST00000269305.4:c.165_166del	p.Glu56ArgfsTer6	p.E56Rfs*6	ENST00000269305	NM_001126112.2	55	acTGaa/acaa	4/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.3	2		639	767	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660148	227660148	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	96	530	0	ENST00000305123.5:c.3307A>T	p.Thr1103Ser	p.T1103S	ENST00000305123	NM_005544.2	1103	Act/Tct	1/2	1	2	FACETS	0.891	0.794	0.995	0.891	0.794	0.995	CLONAL	1	TRUE	1	0.3	2		530	718	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687422	117687422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015276-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	45	266	0	ENST00000368508.3:c.2629G>A	p.Ala877Thr	p.A877T	ENST00000368508	NM_002944.2	877	Gcc/Acc	18/43	1	2	FACETS	0.454	0.381	0.536	0.454	0.381	0.536	SUBCLONAL	1	TRUE	1	0.278322605323625	2		266	712	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121438947	121438947	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015276-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1263	208	804	0	ENST00000257555.6:c.1848C>G	p.Ser616Arg	p.S616R	ENST00000257555		616	agC/agG	10/10	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.278322605323625	2		804	1471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579522	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0015276-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	245	639	0	ENST00000269305.4:c.165_166del	p.Glu56ArgfsTer6	p.E56Rfs*6	ENST00000269305	NM_001126112.2	55	acTGaa/acaa	4/11	0.278322605323625	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.278322605323625	1		639	1283	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660148	227660148	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015276-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	144	530	0	ENST00000305123.5:c.3307A>T	p.Thr1103Ser	p.T1103S	ENST00000305123	NM_005544.2	1103	Act/Tct	1/2	1	2	FACETS	0.91	0.828	0.996	0.91	0.828	0.996	CLONAL	1	TRUE	1	0.278322605323625	2		530	1137	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521367	8521367	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015276-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	69	470	0	ENST00000356435.5:c.871C>A	p.Leu291Met	p.L291M	ENST00000356435		291	Ctg/Atg	9/35	1	2	FACETS	0.497	0.431	0.568	0.497	0.431	0.568	SUBCLONAL	1	TRUE	1	0.278322605323625	2		470	998	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248093	110248093	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015276-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	81	385	0	ENST00000374672.4:c.1379A>C	p.Lys460Thr	p.K460T	ENST00000374672	NM_004235.4	460	aAa/aCa	5/5	1	2	FACETS	0.633	0.557	0.716	0.633	0.557	0.716	SUBCLONAL	1	TRUE	1	0.278322605323625	2		385	919	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916798	48916798	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	37	399	0	ENST00000267163.4:c.328C>G	p.Leu110Val	p.L110V	ENST00000267163	NM_000321.2	110	Cta/Gta	3/27	0.448477840136687	1	FACETS	0.332	0.274	0.398	0.332	0.274	0.398	SUBCLONAL	1	TRUE	0	0.448477840136687	1		399	385	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836626	89836627	+	missense_variant	Missense_Mutation	DNP	CC	CC	GT	novel	NA	P-0015277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	72	681	0	ENST00000389301.3:c.2263_2264delinsAC	p.Gly755Thr	p.G755T	ENST00000389301	NM_000135.2	755	GGa/ACa	25/43	0.448477840136687	1	FACETS	0.912	0.806	1	0.912	0.806	1	CLONAL	1	TRUE	0	0.448477840136687	1		681	273	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950301	15950302	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	167	620	0	ENST00000268712.3:c.6642dup	p.Lys2215Ter	p.K2215*	ENST00000268712	NM_006311.3	2214	-/T	42/46	0.448477840136687	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.448477840136687	1		620	502	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0015278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	18	376	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.229	0.172	0.298	0.229	0.172	0.298	SUBCLONAL	1	FALSE	1	0.290087364586911	2		376	541	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0015278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	43	326	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.885	0.743	1	0.885	0.743	1	CLONAL	1	FALSE	1	0.290087364586911	2		326	335	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593609	55593611	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	rs121913685	NA	P-0015279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	426	308	0	ENST00000288135.5:c.1679_1681del	p.Val560del	p.V560del	ENST00000288135	NM_000222.2	559	GTT/-	11/21	1	2	FACETS	0.962	0.92	1	0.962	0.92	1	CLONAL	1	TRUE	1	0.88069845783028	2		308	1006	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	293	297	0				ENST00000310581	NM_198253.2	-/1132			0.288352129067741	4	FACETS	0.815	0.767	0.864			1	CLONAL	2	TRUE	NA	0.478819146320483	4		297	1111	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17117084	17117084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	606	453	0	ENST00000285071.4:c.1625C>T	p.Ser542Phe	p.S542F	ENST00000285071	NM_144997.5	542	tCc/tTc	14/14	0.230067006194968	3	FACETS	0.862	0.832	0.892			1	INDETERMINATE	3	TRUE	NA	0.478819146320483	3		453	1213	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980903	40980903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs906977293	NA	P-0015281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	262	273	0	ENST00000373198.4:c.1583C>T	p.Ser528Leu	p.S528L	ENST00000373198	NM_133170.3	528	tCg/tTg	10/32	0.230067006194968	3	FACETS	0.831	0.781	0.882			1	INDETERMINATE	2	TRUE	NA	0.478819146320483	3		273	816	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577142	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	534	527	0	ENST00000269305.4:c.796_797delinsAA	p.Gly266Lys	p.G266K	ENST00000269305	NM_001126112.2	266	GGa/AAa	8/11	0.477329874581995	2	FACETS	0.953	0.917	0.99	0.953	0.917	0.99	CLONAL	2	TRUE	0	0.478819146320483	2		527	1170	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434122	12434122	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1170672782	NA	P-0015281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	46	286	1	ENST00000287820.6:c.490C>T	p.Arg164Trp	p.R164W	ENST00000287820	NM_015869.4	164	Cgg/Tgg	4/7	0.470427564788697	3	FACETS	0.591	0.498	0.693	0.295	0.249	0.347	SUBCLONAL	1	TRUE	1	0.478819146320483	3		287	403	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187123	11187123	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	249	512	0	ENST00000361445.4:c.6295C>T	p.Gln2099Ter	p.Q2099*	ENST00000361445	NM_004958.3	2099	Caa/Taa	45/58	0.470427564788697	3	FACETS	0.931	0.868	0.995	0.465	0.434	0.498	CLONAL	1	TRUE	1	0.478819146320483	3		512	1385	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699417	117699417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	230	503	0	ENST00000369458.3:c.224G>A	p.Gly75Asp	p.G75D	ENST00000369458	NM_024626.3	75	gGt/gAt	3/6	0.37594501991484	3	FACETS	1	0.94	1			1	CLONAL	1	TRUE	NA	0.478819146320483	3		503	1178	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417954	32417954	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0015281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	181	307	0	ENST00000332351.3:c.1099-1G>A		p.X367_splice	ENST00000332351	NM_024426.4	367			1	2	FACETS	0.976	0.902	1	0.976	0.902	1	CLONAL	1	TRUE	1	0.478819146320483	2		307	775	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998826	100998826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	225	610	0	ENST00000325455.5:c.976G>A	p.Asp326Asn	p.D326N	ENST00000325455	NM_001202474.3	326	Gac/Aac	1/8	1	2	FACETS	0.851	0.792	0.912	0.851	0.792	0.912	CLONAL	1	TRUE	1	0.478819146320483	2		610	1104	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562186	21562186	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1407	518	923	0	ENST00000382592.4:c.1733T>C	p.Val578Ala	p.V578A	ENST00000382592	NM_014572.2	578	gTt/gCt	4/8	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.478819146320483	2		923	1925	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964014	28964014	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	77	255	0	ENST00000282397.4:c.1888G>A	p.Asp630Asn	p.D630N	ENST00000282397	NM_002019.4	630	Gat/Aat	13/30	1	2	FACETS	0.879	0.777	0.987	0.879	0.777	0.987	CLONAL	1	TRUE	1	0.478819146320483	2		255	366	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830868	72830868	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	181	387	0	ENST00000268489.5:c.5713C>T	p.Pro1905Ser	p.P1905S	ENST00000268489	NM_006885.3	1905	Ccg/Tcg	9/10	1	2	FACETS	0.845	0.779	0.913	0.845	0.779	0.913	CLONAL	1	TRUE	1	0.478819146320483	2		387	895	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559658	29559837	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTTAGCTTTCTAGTTGATACGGCCTTCACTATGTAAAGGTCAGTCTTTTTATTTCTCAGATACTTCACATTATTTATGAACCTTTTGAATGACTGCAGTGAAGTTGAAGATGAAAGTGCGCAAACAGGTGGCAGGAAACGTGGCATGTCTCGGAGGCTGGCATCACTGAGGCACTGTAC	GGTTAGCTTTCTAGTTGATACGGCCTTCACTATGTAAAGGTCAGTCTTTTTATTTCTCAGATACTTCACATTATTTATGAACCTTTTGAATGACTGCAGTGAAGTTGAAGATGAAAGTGCGCAAACAGGTGGCAGGAAACGTGGCATGTCTCGGAGGCTGGCATCACTGAGGCACTGTAC	-	novel	NA	P-0015281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	92	34	0	ENST00000356175.3:c.3315-57_3437del		p.X1105_splice	ENST00000356175	NM_000267.3	1105		26/57	0.477329874581995	2	FACETS	0.922	0.854	0.986	1	0.986	1	CLONAL	3	TRUE	0	0.478819146320483	2		34	139	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217780	2217780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1292	316	600	0	ENST00000398665.3:c.2554G>A	p.Glu852Lys	p.E852K	ENST00000398665	NM_032482.2	852	Gag/Aag	22/28	0.439499074752254	3	FACETS	1	0.955	1	0.509	0.478	0.54	CLONAL	1	TRUE	1	0.478819146320483	3		600	1608	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296382	15296382	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	725	717	0	ENST00000263388.2:c.2060C>T	p.Ser687Phe	p.S687F	ENST00000263388	NM_000435.2	687	tCc/tTc	13/33	0.439499074752254	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.478819146320483	3		717	1851	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082601	16082601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	85	191	0	ENST00000281043.3:c.415G>A	p.Gly139Arg	p.G139R	ENST00000281043	NM_005378.4	139	Ggg/Agg	2/3	1	2	FACETS	0.676	0.599	0.758	0.676	0.599	0.758	SUBCLONAL	1	TRUE	1	0.478819146320483	2		191	525	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470477	25470477	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	325	635	0	ENST00000264709.3:c.997G>C	p.Asp333His	p.D333H	ENST00000264709	NM_175629.2	333	Gac/Cac	8/23	1	2	FACETS	0.977	0.921	1	0.977	0.921	1	CLONAL	1	TRUE	1	0.478819146320483	2		635	1390	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024516	31024516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	456	423	0	ENST00000375687.4:c.4001C>T	p.Pro1334Leu	p.P1334L	ENST00000375687	NM_015338.5	1334	cCc/cTc	13/13	0.412639817544267	4	FACETS	0.946	0.902	0.99	0.946	0.902	0.99	CLONAL	2	TRUE	2	0.478819146320483	4		423	1489	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527596	41527596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	490	400	0	ENST00000263253.7:c.1487C>T	p.Pro496Leu	p.P496L	ENST00000263253	NM_001429.3	496	cCt/cTt	6/31	0.439499074752254	3	FACETS	0.957	0.917	0.998	0.957	0.917	0.998	CLONAL	2	TRUE	1	0.478819146320483	3		400	1325	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665465	138665465	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	247	589	0	ENST00000330315.3:c.100C>T	p.Pro34Ser	p.P34S	ENST00000330315	NM_023067.3	34	Cca/Tca	1/1	0.470427564788697	3	FACETS	1	0.946	1	0.508	0.474	0.543	CLONAL	1	TRUE	1	0.478819146320483	3		589	1259	SUCCESS
ATR	545	MSKCC	GRCh37	3	142203992	142203992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	125	347	0	ENST00000350721.4:c.6211C>T	p.His2071Tyr	p.H2071Y	ENST00000350721	NM_001184.3	2071	Cat/Tat	36/47	0.470427564788697	3	FACETS	0.986	0.895	1	0.493	0.447	0.542	CLONAL	1	TRUE	1	0.478819146320483	3		347	656	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557327	187557327	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	172	500	1	ENST00000441802.2:c.4035G>A	p.Trp1345Ter	p.W1345*	ENST00000441802	NM_005245.3	1345	tgG/tgA	6/27	1	2	FACETS	0.945	0.872	1	0.945	0.872	1	CLONAL	1	TRUE	1	0.478819146320483	2		501	760	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557813	187557813	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	153	358	0	ENST00000441802.2:c.3898T>A	p.Phe1300Ile	p.F1300I	ENST00000441802	NM_005245.3	1300	Ttt/Att	5/27	1	2	FACETS	0.886	0.813	0.963	0.886	0.813	0.963	CLONAL	1	TRUE	1	0.478819146320483	2		358	721	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670948	30670948	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536243116	NA	P-0015281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1364	686	519	0	ENST00000376406.3:c.5798G>A	p.Arg1933Gln	p.R1933Q	ENST00000376406	NM_014641.2	1933	cGg/cAg	12/15	0.478819146320483	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.478819146320483	4		519	2050	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199867	138199867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	363	333	0	ENST00000237289.4:c.1285G>A	p.Gly429Arg	p.G429R	ENST00000237289	NM_001270507.1	429	Ggg/Agg	7/9	0.478819146320483	3	FACETS	0.943	0.897	0.991	0.943	0.897	0.991	CLONAL	2	TRUE	1	0.478819146320483	3		333	996	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878409	151878409	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	171	492	0	ENST00000262189.6:c.6536A>G	p.Gln2179Arg	p.Q2179R	ENST00000262189	NM_170606.2	2179	cAa/cGa	36/59	0.470427564788697	3	FACETS	0.726	0.667	0.789	0.363	0.333	0.395	SUBCLONAL	1	TRUE	1	0.478819146320483	3		492	1219	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222439	53222439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781851693	NA	P-0015281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	386	376	2	ENST00000375401.3:c.4393C>T	p.Arg1465Trp	p.R1465W	ENST00000375401	NM_004187.3	1465	Cgg/Tgg	26/26	1	1	FACETS	0.809	0.774	0.843	1	0.996	1	CLONAL	2	TRUE	0	0.478819146320483	1		378	758	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197039	123197039	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	311	205	0	ENST00000218089.9:c.1805C>T	p.Thr602Ile	p.T602I	ENST00000218089	NM_001042749.1	602	aCt/aTt	19/35	0.478819146320483	2	FACETS	0.945	0.909	0.981			1	CLONAL	3	TRUE	NA	0.478819146320483	2		205	458	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239899	105239899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768606668	NA	P-0015281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	251	447	1	ENST00000349310.3:c.721C>T	p.Arg241Trp	p.R241W	ENST00000349310	NM_001014432.1	241	Cgg/Tgg	10/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.478819146320483	2		448	985	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830587	72830589	+	frameshift_variant	Frame_Shift_Ins	INS	TAA	TAA	AAAT	novel	NA	P-0015281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	187	465	0	ENST00000268489.5:c.5992_5994delinsATTT	p.Leu1998IlefsTer2	p.L1998Ifs*2	ENST00000268489	NM_006885.3	1998	TTA/ATTT	9/10	1	2	FACETS	0.922	0.853	0.994	0.922	0.853	0.994	CLONAL	1	TRUE	1	0.478819146320483	2		465	847	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144114	11144114	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	186	702	0	ENST00000358026.2:c.3695G>A	p.Gly1232Asp	p.G1232D	ENST00000358026	NM_001128849.1	1232	gGc/gAc	26/36	1	2	FACETS	0.997	0.919	1	0.997	0.919	1	CLONAL	1	FALSE	1	0.3195448143792	2		702	1168	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183755	10183757	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs5030648	NA	P-0015282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	112	710	0	ENST00000256474.2:c.227_229del	p.Phe76del	p.F76del	ENST00000256474	NM_000551.3	75	aTCTtc/atc	1/3	0.156365594834977	1	FACETS	0.739	0.665	0.818	0.739	0.665	0.818	INDETERMINATE	1	FALSE	0	0.3195448143792	1		710	797	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692960	89692960	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	59	506	0	ENST00000371953.3:c.444del	p.Gln149LysfsTer4	p.Q149Kfs*4	ENST00000371953	NM_000314.4	148	gcA/gc	5/9	0.298241162643869	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	FALSE	0	0.3195448143792	1		506	275	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95596401	95596401	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	37	299	0	ENST00000393063.1:c.567del	p.Met190Ter	p.M190*	ENST00000393063	NM_030621.3	189	atT/at	6/28	0.156365594834977	1	FACETS	0.7	0.58	0.833	0.7	0.58	0.833	INDETERMINATE	1	FALSE	0	0.3195448143792	1		299	278	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082626	16082626	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	32	136	0	ENST00000281043.3:c.440C>G	p.Ala147Gly	p.A147G	ENST00000281043	NM_005378.4	147	gCc/gGc	2/3	1	2	FACETS	0.764	0.623	0.922	0.764	0.623	0.922	CLONAL	1	FALSE	1	0.3195448143792	2		136	262	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163376	47163377	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	19	312	0	ENST00000409792.3:c.2749dup	p.Ser917LysfsTer18	p.S917Kfs*18	ENST00000409792	NM_014159.6	917	agt/aAgt	3/21	0.156365594834977	1	FACETS	0.719	0.551	0.912	0.719	0.551	0.912	INDETERMINATE	1	FALSE	0	0.3195448143792	1		312	139	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099209	157099209	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	110	526	0	ENST00000346085.5:c.146C>G	p.Ser49Cys	p.S49C	ENST00000346085	NM_020732.3	49	tCt/tGt	1/20	1	2	FACETS	0.864	0.776	0.957	0.864	0.776	0.957	CLONAL	1	FALSE	1	0.3195448143792	2		526	797	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0015283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	369	336	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.385800953410972	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.385800953410972	4		336	1273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578453	7578453	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	558	691	1	ENST00000269305.4:c.477del	p.Met160TrpfsTer10	p.M160Wfs*10	ENST00000269305	NM_001126112.2	159	gcC/gc	5/11	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.385800953410972	2		692	1345	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332618	70332618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	161	523	0	ENST00000373644.4:c.523G>A	p.Val175Ile	p.V175I	ENST00000373644	NM_030625.2	175	Gta/Ata	2/12	1	2	FACETS	0.841	0.771	0.915	0.841	0.771	0.915	CLONAL	1	TRUE	1	0.385800953410972	2		523	992	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860384	151860396	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCAAAGCTCTT	CTGCAAAGCTCTT	-	novel	NA	P-0015283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	198	480	0	ENST00000262189.6:c.10266_10278del	p.Gln3422HisfsTer16	p.Q3422Hfs*16	ENST00000262189	NM_170606.2	3422	caAAGAGCTTTGCAG/ca	43/59	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.385800953410972	2		480	975	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285855	87285855	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	176	476	0	ENST00000277120.3:c.192T>A	p.Asp64Glu	p.D64E	ENST00000277120		64	gaT/gaA	2/19	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.385800953410972	2		476	865	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695979	117695979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757275063	NA	P-0015284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	21	432	0	ENST00000369458.3:c.458C>T	p.Pro153Leu	p.P153L	ENST00000369458	NM_024626.3	153	cCg/cTg	4/6	0.341263695360088	4	FACETS	1	0.864	1	0.581	0.452	0.728	CLONAL	1	TRUE	2	0.341263695360088	4		432	142	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647016	23647016	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	12	580	0	ENST00000261584.4:c.851del	p.Thr284IlefsTer4	p.T284Ifs*4	ENST00000261584	NM_024675.3	284	aCt/at	4/13	NA	2	FACETS	0.397	0.28	0.541			1	INDETERMINATE	1	TRUE	NA	0.341263695360088	2		580	177	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971000	21971000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	1408	609	0	ENST00000304494.5:c.358G>T	p.Glu120Ter	p.E120*	ENST00000304494	NM_000077.4	120	Gag/Tag	2/3	0.968672706409018	3	FACETS	0.963	0.955	0.971	0.963	0.955	0.971	CLONAL	3	TRUE	0	0.968672706409018	3		609	1493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578467	7578467	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	1032	663	0	ENST00000269305.4:c.463A>C	p.Thr155Pro	p.T155P	ENST00000269305	NM_001126112.2	155	Acc/Ccc	5/11	NA	2	FACETS	0.938	0.927	0.948			1	INDETERMINATE	2	TRUE	NA	0.968672706409018	2		663	1136	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873195	71873195	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1557515843	NA	P-0015285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	269	392	0	ENST00000357731.5:c.999G>T	p.Trp333Cys	p.W333C	ENST00000357731	NM_173808.2	333	tgG/tgT	7/7	0.839750919867501	3	FACETS	0.932	0.876	0.988	0.466	0.438	0.494	CLONAL	1	TRUE	1	0.968672706409018	3		392	885	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115267920	115267920	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	699	498	0	ENST00000438362.2:c.1813G>T	p.Gly605Trp	p.G605W	ENST00000438362	NM_001242891.1	605	Ggg/Tgg	15/20	0.839750919867501	3	FACETS	0.919	0.893	0.946	0.919	0.893	0.946	CLONAL	2	TRUE	1	0.968672706409018	3		498	1165	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156848913	156848913	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	2755	536	0	ENST00000524377.1:c.1806-1G>A		p.X602_splice	ENST00000524377	NM_002529.3	602			0.968672706409018	8	FACETS	1	0.998	1			1	CLONAL	6	TRUE	NA	0.968672706409018	8		536	3547	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849068	156849068	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	3883	749	0	ENST00000524377.1:c.1960C>A	p.Arg654Ser	p.R654S	ENST00000524377	NM_002529.3	654	Cgc/Agc	15/17	0.968672706409018	8	FACETS	1	0.999	1			1	CLONAL	6	TRUE	NA	0.968672706409018	8		749	4952	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716067	243716067	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	273	436	0	ENST00000263826.5:c.1127T>C	p.Leu376Ser	p.L376S	ENST00000263826	NM_005465.4	376	tTg/tCg	10/13	0.539081804854121	4	FACETS	1	0.982	1	0.371	0.348	0.394	INDETERMINATE	1	TRUE	1	0.968672706409018	4		436	997	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263369	123263369	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	505	374	0	ENST00000358487.5:c.1374del	p.Met459CysfsTer23	p.M459Cfs*23	ENST00000358487	NM_000141.4	458	ccC/cc	10/18	0.341383957106669	6	FACETS	0.883	0.848	0.918	0.883	0.848	0.918	INDETERMINATE	3	TRUE	3	0.968672706409018	6		374	1156	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456746	32456746	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	704	533	0	ENST00000332351.3:c.146G>T	p.Ser49Ile	p.S49I	ENST00000332351	NM_024426.4	49	aGc/aTc	1/10	0.69635054564166	3	FACETS	0.954	0.927	0.98	0.954	0.927	0.98	CLONAL	2	TRUE	1	0.968672706409018	3		533	1131	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575101	64575101	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	423	508	0	ENST00000312049.6:c.706G>A	p.Val236Met	p.V236M	ENST00000312049	NM_130799.2	236	Gtg/Atg	4/10	0.69635054564166	3	FACETS	1	0.97	1	0.511	0.487	0.536	CLONAL	1	TRUE	1	0.968672706409018	3		508	1268	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022891	12022891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	863	577	0	ENST00000396373.4:c.997G>T	p.Gly333Trp	p.G333W	ENST00000396373	NM_001987.4	333	Ggg/Tgg	5/8	0.740482045107304	3	FACETS	1	0.979	1			1	CLONAL	2	TRUE	NA	0.968672706409018	3		577	1318	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433768	49433768	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	1130	745	0	ENST00000301067.7:c.7785del	p.Ser2597AlafsTer94	p.S2597Afs*94	ENST00000301067	NM_003482.3	2595	ggG/gg	31/54	0.968672706409018	3	FACETS	0.961	0.94	0.982	0.961	0.94	0.982	CLONAL	2	TRUE	1	0.968672706409018	3		745	1801	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861895	57861895	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	356	495	2	ENST00000228682.2:c.1196G>T	p.Gly399Val	p.G399V	ENST00000228682	NM_005269.2	399	gGg/gTg	10/12	0.968672706409018	3	FACETS	0.852	0.807	0.899	0.426	0.403	0.45	CLONAL	1	TRUE	1	0.968672706409018	3		497	1280	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865728	57865728	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	1091	689	0	ENST00000228682.2:c.3205G>T	p.Gly1069Cys	p.G1069C	ENST00000228682	NM_005269.2	1069	Ggc/Tgc	12/12	0.968672706409018	3	FACETS	0.98	0.958	1	0.98	0.958	1	CLONAL	2	TRUE	1	0.968672706409018	3		689	1706	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303888	91303888	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	684	399	0	ENST00000355112.3:c.1285A>G	p.Arg429Gly	p.R429G	ENST00000355112	NM_000057.2	429	Aga/Gga	7/22	0.929282275213127	2	FACETS	0.953	0.94	0.965	0.953	0.94	0.965	CLONAL	2	TRUE	0	0.968672706409018	2		399	741	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830519	72830519	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	418	526	1	ENST00000268489.5:c.6062A>G	p.Gln2021Arg	p.Q2021R	ENST00000268489	NM_006885.3	2021	cAg/cGg	9/10	0.839750919867501	3	FACETS	0.938	0.893	0.984	0.469	0.446	0.492	CLONAL	1	TRUE	1	0.968672706409018	3		527	1365	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984615	72984615	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	989	650	0	ENST00000268489.5:c.2969G>T	p.Arg990Leu	p.R990L	ENST00000268489	NM_006885.3	990	cGc/cTc	3/10	0.839750919867501	3	FACETS	0.914	0.892	0.936	0.914	0.892	0.936	CLONAL	2	TRUE	1	0.968672706409018	3		650	1658	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40872305	40872305	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs773742282	NA	P-0015285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	840	516	0	ENST00000428826.2:c.650G>T	p.Arg217Leu	p.R217L	ENST00000428826		217	cGa/cTa	7/21	0.968672706409018	3	FACETS	0.933	0.909	0.957	0.933	0.909	0.957	CLONAL	2	TRUE	1	0.968672706409018	3		516	1379	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435162	56435162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	389	570	0	ENST00000407977.2:c.1975G>A	p.Gly659Ser	p.G659S	ENST00000407977		659	Ggt/Agt	9/10	0.968672706409018	3	FACETS	0.976	0.928	1	0.488	0.464	0.513	CLONAL	1	TRUE	1	0.968672706409018	3		570	1221	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120209	70120209	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	463	602	0	ENST00000245479.2:c.1211C>A	p.Pro404His	p.P404H	ENST00000245479	NM_000346.3	404	cCc/cAc	3/3	0.968672706409018	3	FACETS	0.935	0.893	0.979	0.468	0.446	0.49	CLONAL	1	TRUE	1	0.968672706409018	3		602	1517	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169039	11169040	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	TT	novel	NA	P-0015285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	809	607	1	ENST00000358026.2:c.4629_4629+1delinsTT		p.X1543_splice	ENST00000358026	NM_001128849.1	1543		32/36	0.929282275213127	2	FACETS	0.945	0.932	0.956	0.945	0.932	0.956	CLONAL	2	TRUE	0	0.968672706409018	2		608	884	SUCCESS
ALK	238	MSKCC	GRCh37	2	29473998	29473998	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	665	634	0	ENST00000389048.3:c.2177G>T	p.Trp726Leu	p.W726L	ENST00000389048	NM_004304.4	726	tGg/tTg	12/29	0.341383957106669	6	FACETS	1	0.993	1	0.747	0.72	0.775	INDETERMINATE	2	TRUE	3	0.968672706409018	6		634	1799	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268720	41268720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	357	252	0	ENST00000349496.5:c.958G>A	p.Gly320Arg	p.G320R	ENST00000349496	NM_001904.3	320	Gga/Aga	7/15	0.920968519259078	2	FACETS	0.955	0.937	0.971	0.955	0.937	0.971	CLONAL	2	TRUE	0	0.968672706409018	2		252	386	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146751	185146751	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	766	572	1	ENST00000265026.3:c.382G>T	p.Gly128Cys	p.G128C	ENST00000265026	NM_004721.4	128	Ggt/Tgt	2/14	0.786051836089367	4	FACETS	0.885	0.856	0.913	0.885	0.856	0.913	CLONAL	2	TRUE	2	0.968672706409018	4		573	1760	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247301	153247301	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	335	373	0	ENST00000281708.4:c.1501G>T	p.Val501Phe	p.V501F	ENST00000281708	NM_033632.3	501	Gtt/Ttt	10/12	0.220025876638247	3	FACETS	1	0.995	1	0.73	0.696	0.765	INDETERMINATE	1	TRUE	1	0.968672706409018	3		373	703	SUCCESS
APC	324	MSKCC	GRCh37	5	112175926	112175926	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	319	221	0	ENST00000257430.4:c.4637del	p.Asn1546MetfsTer19	p.N1546Mfs*19	ENST00000257430	NM_000038.5	1545	tcA/tc	16/16	0.920968519259078	2	FACETS	0.89	0.867	0.911	0.89	0.867	0.911	CLONAL	2	TRUE	0	0.968672706409018	2		221	370	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686752	117686752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	695	351	0	ENST00000368508.3:c.2965C>T	p.His989Tyr	p.H989Y	ENST00000368508	NM_002944.2	989	Cat/Tat	19/43	0.909252735474123	3	FACETS	0.952	0.94	0.963	0.952	0.94	0.963	CLONAL	3	TRUE	0	0.968672706409018	3		351	746	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771175	161771175	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	478	548	0	ENST00000366898.1:c.1354G>T	p.Glu452Ter	p.E452*	ENST00000366898	NM_004562.2	452	Gag/Tag	12/12	0.909252735474123	3	FACETS	1	0.994	1	0.4	0.383	0.417	CLONAL	1	TRUE	0	0.968672706409018	3		548	1221	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392114	81392114	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	207	313	0	ENST00000222390.5:c.163C>A	p.Pro55Thr	p.P55T	ENST00000222390	NM_000601.4	55	Cca/Aca	2/18	0.968672706409018	3	FACETS	0.922	0.859	0.986	0.307	0.286	0.329	CLONAL	1	TRUE	0	0.968672706409018	3		313	688	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392191	81392191	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	T	novel	NA	P-0015285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	102	138	0	ENST00000222390.5:c.89-3T>A		p.X30_splice	ENST00000222390	NM_000601.4	30			0.968672706409018	3	FACETS	0.939	0.849	1	0.313	0.283	0.344	CLONAL	1	TRUE	0	0.968672706409018	3		138	333	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829105	128829105	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	183	45	1	ENST00000249373.3:c.113G>T	p.Gly38Val	p.G38V	ENST00000249373	NM_005631.4	38	gGg/gTg	1/12	0.968672706409018	3	FACETS	1	0.989	1	0.757	0.722	0.79	CLONAL	2	TRUE	0	0.968672706409018	3		46	247	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880210	151880210	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	263	317	0	ENST00000262189.6:c.5114G>C	p.Arg1705Pro	p.R1705P	ENST00000262189	NM_170606.2	1705	cGc/cCc	35/59	0.968672706409018	3	FACETS	0.851	0.799	0.905	0.284	0.266	0.302	CLONAL	1	TRUE	0	0.968672706409018	3		317	947	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020564	69020564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	614	337	0	ENST00000288368.4:c.2936A>T	p.Gln979Leu	p.Q979L	ENST00000288368	NM_024870.2	979	cAa/cTa	24/40	0.908094758622731	3	FACETS	0.968	0.956	0.978	0.968	0.956	0.978	CLONAL	3	TRUE	0	0.968672706409018	3		337	648	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249918	110249918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750429416	NA	P-0015285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	633	442	0	ENST00000374672.4:c.757G>A	p.Gly253Ser	p.G253S	ENST00000374672	NM_004235.4	253	Ggc/Agc	3/5	0.931193270107732	2	FACETS	0.964	0.951	0.975	0.964	0.951	0.975	CLONAL	2	TRUE	0	0.968672706409018	2		442	678	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610154	10610154	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	290	694	0	ENST00000171111.5:c.556G>T	p.Gly186Cys	p.G186C	ENST00000171111	NM_203500.1	186	Ggc/Tgc	2/6	0.218116309381707	2	FACETS	0.993	0.933	1	0.993	0.933	1	CLONAL	2	TRUE	0	0.218116309381707	2		694	1339	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868282	37868282	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	635	530	0	ENST00000269571.5:c.1003A>T	p.Ser335Cys	p.S335C	ENST00000269571		335	Agc/Tgc	8/27	0.218116309381707	7	FACETS	1	0.989	1			1	CLONAL	5	TRUE	NA	0.218116309381707	7		530	1683	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78938087	78938089	+	inframe_deletion	In_Frame_Del	DEL	ACT	ACT	-	novel	NA	P-0015286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1428	226	682	0	ENST00000306801.3:c.3970_3972del	p.Tyr1324del	p.Y1324del	ENST00000306801	NM_020761.2	1322	gACTac/gac	34/34	0.218116309381707	5	FACETS	0.831	0.772	0.894	0.554	0.514	0.596	CLONAL	2	TRUE	2	0.218116309381707	5		682	1654	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221920	1221948	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GACAGGCTCCTCGCCGGCTTCTCCTCAGG	GACAGGCTCCTCGCCGGCTTCTCCTCAGG	-	novel	NA	P-0015286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	207	592	1	ENST00000326873.7:c.863-26_865del		p.X288_splice	ENST00000326873	NM_000455.4	288		7/10	0.218116309381707	2	FACETS	0.884	0.819	0.95	0.884	0.819	0.95	CLONAL	2	TRUE	0	0.218116309381707	2		593	1074	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2202713	2202713	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	213	601	0	ENST00000398665.3:c.722A>C	p.Asn241Thr	p.N241T	ENST00000398665	NM_032482.2	241	aAt/aCt	9/28	0.218116309381707	2	FACETS	0.868	0.806	0.933	0.868	0.806	0.933	CLONAL	2	TRUE	0	0.218116309381707	2		601	1125	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2202720	2202733	+	frameshift_variant	Frame_Shift_Del	DEL	TGCCTTTGGTCCTG	TGCCTTTGGTCCTG	-	novel	NA	P-0015286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	223	605	0	ENST00000398665.3:c.729_742del	p.Phe243LeufsTer35	p.F243Lfs*35	ENST00000398665	NM_032482.2	243	ttTGCCTTTGGTCCTGag/ttag	9/28	0.218116309381707	2	FACETS	0.899	0.836	0.964	0.899	0.836	0.964	CLONAL	2	TRUE	0	0.218116309381707	2		605	1137	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129645	11129645	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	282	680	0	ENST00000358026.2:c.2451C>A	p.Asn817Lys	p.N817K	ENST00000358026	NM_001128849.1	817	aaC/aaA	17/36	0.218116309381707	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.218116309381707	2		680	1174	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971137	21971137	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	104	482	0	ENST00000304494.5:c.221A>G	p.Asp74Gly	p.D74G	ENST00000304494	NM_000077.4	74	gAc/gGc	2/3	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.218116309381707	2		482	685	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494319	2494319	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	304	985	0	ENST00000355716.4:c.710T>C	p.Val237Ala	p.V237A	ENST00000355716	NM_003820.2	237	gTg/gCg	7/8	1	2	FACETS	0.808	0.761	0.856	0.808	0.761	0.856	CLONAL	1	TRUE	1	0.63	2		985	1195	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9787025	9787025	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	61	717	0	ENST00000377346.4:c.3056T>G	p.Phe1019Cys	p.F1019C	ENST00000377346	NM_005026.3	1019	tTt/tGt	24/24	1	2	FACETS	0.169	0.145	0.196	0.169	0.145	0.196	SUBCLONAL	1	TRUE	1	0.63	2		717	1145	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11177124	11177124	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	243	632	1	ENST00000361445.4:c.6953C>T	p.Thr2318Ile	p.T2318I	ENST00000361445	NM_004958.3	2318	aCc/aTc	50/58	1	2	FACETS	0.917	0.859	0.977	0.917	0.859	0.977	CLONAL	1	TRUE	1	0.63	2		633	841	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11264621	11264621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	197	526	1	ENST00000361445.4:c.3941C>T	p.Ala1314Val	p.A1314V	ENST00000361445	NM_004958.3	1314	gCc/gTc	26/58	1	2	FACETS	0.949	0.883	1	0.949	0.883	1	CLONAL	1	TRUE	1	0.63	2		527	659	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237602	16237602	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	139	407	1	ENST00000375759.3:c.1049G>T	p.Ser350Ile	p.S350I	ENST00000375759	NM_015001.2	350	aGc/aTc	5/15	1	2	FACETS	0.893	0.818	0.971	0.893	0.818	0.971	CLONAL	1	TRUE	1	0.63	2		408	494	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258029	16258029	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	40	552	0	ENST00000375759.3:c.5294A>G	p.Lys1765Arg	p.K1765R	ENST00000375759	NM_015001.2	1765	aAg/aGg	11/15	1	2	FACETS	0.161	0.133	0.192	0.161	0.133	0.192	SUBCLONAL	1	TRUE	1	0.63	2		552	790	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258641	16258641	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1319518361	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	51	629	0	ENST00000375759.3:c.5906A>G	p.Lys1969Arg	p.K1969R	ENST00000375759	NM_015001.2	1969	aAg/aGg	11/15	1	2	FACETS	0.179	0.151	0.209	0.179	0.151	0.209	SUBCLONAL	1	TRUE	1	0.63	2		629	905	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263853	16263853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777908524	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	236	766	0	ENST00000375759.3:c.10222C>T	p.Pro3408Ser	p.P3408S	ENST00000375759	NM_015001.2	3408	Cct/Tct	12/15	1	2	FACETS	0.748	0.699	0.8	0.748	0.699	0.8	SUBCLONAL	1	TRUE	1	0.63	2		766	1001	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099056	27099056	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	421	846	2	ENST00000324856.7:c.3472G>T	p.Gly1158Ter	p.G1158*	ENST00000324856	NM_006015.4	1158	Gga/Tga	13/20	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.63	2		848	1162	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39318113	39318113	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	207	771	0	ENST00000373001.3:c.689G>A	p.Ser230Asn	p.S230N	ENST00000373001	NM_022157.3	230	aGt/aAt	4/7	1	2	FACETS	0.703	0.652	0.755	0.703	0.652	0.755	SUBCLONAL	1	TRUE	1	0.63	2		771	935	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363208	40363208	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	240	552	0	ENST00000397332.2:c.1021C>A	p.Leu341Met	p.L341M	ENST00000397332	NM_001033082.2	341	Ctg/Atg	3/3	1	2	FACETS	0.993	0.931	1	0.993	0.931	1	CLONAL	1	TRUE	1	0.63	2		552	767	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363274	40363274	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	54	672	0	ENST00000397332.2:c.955C>A	p.Leu319Met	p.L319M	ENST00000397332	NM_001033082.2	319	Ctg/Atg	3/3	1	2	FACETS	0.194	0.165	0.226	0.194	0.165	0.226	SUBCLONAL	1	TRUE	1	0.63	2		672	885	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818382	43818382	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	293	776	1	ENST00000372470.3:c.1847G>A	p.Cys616Tyr	p.C616Y	ENST00000372470	NM_005373.2	616	tGc/tAc	12/12	1	2	FACETS	0.876	0.825	0.928	0.876	0.825	0.928	CLONAL	1	TRUE	1	0.63	2		777	1062	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46715711	46715711	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs751720515	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	76	766	0	ENST00000371975.4:c.130C>T	p.Gln44Ter	p.Q44*	ENST00000371975	NM_003579.3	44	Cag/Tag	3/18	1	2	FACETS	0.231	0.202	0.263	0.231	0.202	0.263	SUBCLONAL	1	TRUE	1	0.63	2		766	1043	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46724379	46724379	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	311	651	0	ENST00000371975.4:c.232T>A	p.Leu78Met	p.L78M	ENST00000371975	NM_003579.3	78	Ttg/Atg	4/18	1	2	FACETS	0.987	0.933	1	0.987	0.933	1	CLONAL	1	TRUE	1	0.63	2		651	1000	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748145	72748145	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	225	465	0	ENST00000357731.5:c.33T>A	p.Cys11Ter	p.C11*	ENST00000357731	NM_173808.2	11	tgT/tgA	1/7	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.63	2		465	692	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466309	120466309	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	205	624	0	ENST00000256646.2:c.4810A>G	p.Arg1604Gly	p.R1604G	ENST00000256646	NM_024408.3	1604	Agg/Ggg	26/34	1	2	FACETS	0.781	0.726	0.838	0.781	0.726	0.838	SUBCLONAL	1	TRUE	1	0.63	2		624	833	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120509025	120509025	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs34308573	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	327	705	0	ENST00000256646.2:c.1541A>T	p.Asn514Ile	p.N514I	ENST00000256646	NM_024408.3	514	aAt/aTt	9/34	1	2	FACETS	0.919	0.869	0.971	0.919	0.869	0.971	CLONAL	1	TRUE	1	0.63	2		705	1129	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838002	156838002	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	77	1062	2	ENST00000524377.1:c.535G>A	p.Gly179Arg	p.G179R	ENST00000524377	NM_002529.3	179	Ggg/Agg	5/17	1	2	FACETS	0.209	0.182	0.237	0.209	0.182	0.237	SUBCLONAL	1	TRUE	1	0.63	2		1064	1172	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162735809	162735809	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	70	625	0	ENST00000367921.3:c.1118A>G	p.Asn373Ser	p.N373S	ENST00000367921	NM_006182.2	373	aAc/aGc	10/18	1	2	FACETS	0.254	0.22	0.29	0.254	0.22	0.29	SUBCLONAL	1	TRUE	1	0.63	2		625	876	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518500	204518500	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	189	376	0	ENST00000367182.3:c.1163C>A	p.Pro388His	p.P388H	ENST00000367182	NM_001278516.1	388	cCc/cAc	11/11	1	2	FACETS	0.99	0.92	1	0.99	0.92	1	CLONAL	1	TRUE	1	0.63	2		376	606	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727022	243727022	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	160	430	0	ENST00000263826.5:c.948G>T	p.Glu316Asp	p.E316D	ENST00000263826	NM_005465.4	316	gaG/gaT	9/13	1	2	FACETS	0.953	0.879	1	0.953	0.879	1	CLONAL	1	TRUE	1	0.63	2		430	533	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115859	8115859	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	330	711	0	ENST00000346208.3:c.1205C>A	p.Ser402Tyr	p.S402Y	ENST00000346208		402	tCc/tAc	6/6	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.63	2		711	908	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406238	70406238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	244	830	1	ENST00000373644.4:c.3752C>T	p.Ala1251Val	p.A1251V	ENST00000373644	NM_030625.2	1251	gCa/gTa	4/12	1	2	FACETS	0.912	0.855	0.972	0.912	0.855	0.972	CLONAL	1	TRUE	1	0.63	2		831	849	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	212	626	1	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	0.953	0.889	1	0.953	0.889	1	CLONAL	1	TRUE	1	0.63	2		627	706	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154354	2154354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	261	968	2	ENST00000434045.2:c.574G>A	p.Ala192Thr	p.A192T	ENST00000434045	NM_001127598.1	192	Gcc/Acc	5/5	1	2	FACETS	0.737	0.69	0.785	0.737	0.69	0.785	SUBCLONAL	1	TRUE	1	0.63	2		970	1125	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741751	17741751	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	371	847	0	ENST00000250003.3:c.422A>C	p.Asn141Thr	p.N141T	ENST00000250003	NM_002478.4	141	aAc/aCc	1/3	1	2	FACETS	0.971	0.921	1	0.971	0.921	1	CLONAL	1	TRUE	1	0.63	2		847	1213	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741867	17741867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	23	228	0	ENST00000250003.3:c.538G>A	p.Ala180Thr	p.A180T	ENST00000250003	NM_002478.4	180	Gcg/Acg	1/3	1	2	FACETS	0.279	0.217	0.349	0.279	0.217	0.349	SUBCLONAL	1	TRUE	1	0.63	2		228	262	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128009	64128009	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	266	962	1	ENST00000334205.4:c.407C>A	p.Ala136Asp	p.A136D	ENST00000334205	NM_003942.2	136	gCt/gAt	4/17	1	2	FACETS	0.702	0.657	0.748	0.702	0.657	0.748	SUBCLONAL	1	TRUE	1	0.63	2		963	1203	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196460	67196460	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	232	682	1	ENST00000312629.5:c.86G>A	p.Cys29Tyr	p.C29Y	ENST00000312629	NM_003952.2	29	tGt/tAt	2/15	1	2	FACETS	0.806	0.752	0.861	0.806	0.752	0.861	CLONAL	1	TRUE	1	0.63	2		683	914	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94201047	94201047	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	134	370	0	ENST00000323929.3:c.1030C>A	p.Leu344Ile	p.L344I	ENST00000323929	NM_005591.3	344	Ctt/Att	10/20	1	2	FACETS	0.792	0.723	0.864	0.792	0.723	0.864	SUBCLONAL	1	TRUE	1	0.63	2		370	537	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101985014	101985014	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758900950	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	286	639	1	ENST00000282441.5:c.461C>T	p.Thr154Ile	p.T154I	ENST00000282441	NM_001130145.2	154	aCa/aTa	2/9	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.63	2		640	818	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106556	108106556	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	151	356	0	ENST00000278616.4:c.491G>T	p.Trp164Leu	p.W164L	ENST00000278616	NM_000051.3	164	tGg/tTg	5/63	1	2	FACETS	0.929	0.855	1	0.929	0.855	1	CLONAL	1	TRUE	1	0.63	2		356	516	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143447	108143447	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs730881357	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	168	490	0	ENST00000278616.4:c.3154-2A>G		p.X1052_splice	ENST00000278616	NM_000051.3	1052			1	2	FACETS	0.995	0.921	1	0.995	0.921	1	CLONAL	1	TRUE	1	0.63	2		490	536	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153534	108153534	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	146	415	0	ENST00000278616.4:c.3674A>G	p.Gln1225Arg	p.Q1225R	ENST00000278616	NM_000051.3	1225	cAa/cGa	25/63	1	2	FACETS	0.784	0.719	0.852	0.784	0.719	0.852	SUBCLONAL	1	TRUE	1	0.63	2		415	591	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164163	108164164	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs864622164	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	130	344	0	ENST00000278616.4:c.4741dup	p.Ile1581AsnfsTer5	p.I1581Nfs*5	ENST00000278616	NM_000051.3	1579	caa/cAaa	31/63	1	2	FACETS	0.849	0.775	0.926	0.849	0.775	0.926	CLONAL	1	TRUE	1	0.63	2		344	486	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236064	108236064	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	38	551	0	ENST00000278616.4:c.9000G>T	p.Gln3000His	p.Q3000H	ENST00000278616	NM_000051.3	3000	caG/caT	63/63	1	2	FACETS	0.168	0.138	0.202	0.168	0.138	0.202	SUBCLONAL	1	TRUE	1	0.63	2		551	718	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111959601	111959601	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs750688879	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	67	751	0	ENST00000375549.3:c.180G>T	p.Lys60Asn	p.K60N	ENST00000375549	NM_003002.3	60	aaG/aaT	3/4	1	2	FACETS	0.203	0.176	0.233	0.203	0.176	0.233	SUBCLONAL	1	TRUE	1	0.63	2		751	1046	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343356	118343356	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	187	371	2	ENST00000534358.1:c.1482G>T	p.Glu494Asp	p.E494D	ENST00000534358	NM_005933.3	494	gaG/gaT	3/36	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.63	2		373	569	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362022	118362022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	114	356	0	ENST00000534358.1:c.4808C>T	p.Ser1603Leu	p.S1603L	ENST00000534358	NM_005933.3	1603	tCa/tTa	14/36	1	2	FACETS	0.704	0.637	0.775	0.704	0.637	0.775	SUBCLONAL	1	TRUE	1	0.63	2		356	514	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375905	118375905	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	273	584	0	ENST00000534358.1:c.9298G>A	p.Gly3100Arg	p.G3100R	ENST00000534358	NM_005933.3	3100	Gga/Aga	27/36	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.63	2		584	773	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375961	118375961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	223	586	1	ENST00000534358.1:c.9354G>A	p.Met3118Ile	p.M3118I	ENST00000534358	NM_005933.3	3118	atG/atA	27/36	1	2	FACETS	0.921	0.86	0.983	0.921	0.86	0.983	CLONAL	1	TRUE	1	0.63	2		587	769	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376347	118376350	+	missense_variant	Missense_Mutation	ONP	CCCC	CCCC	TCCT	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	240	664	0	ENST00000534358.1:c.9740_9743delinsTCCT	p.Ala3247_Pro3248delinsValLeu	p.A3247_P3248delinsVL	ENST00000534358	NM_005933.3	3247	gCCCCt/gTCCTt	27/36	1	2	FACETS	0.857	0.802	0.914	0.857	0.802	0.914	CLONAL	1	TRUE	1	0.63	2		664	889	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628447	21628447	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	208	764	0	ENST00000421138.2:c.1171A>T	p.Met391Leu	p.M391L	ENST00000421138		391	Atg/Ttg	11/16	1	2	FACETS	0.876	0.815	0.938	0.876	0.815	0.938	CLONAL	1	TRUE	1	0.63	2		764	754	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs770248150	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	205	534	0	ENST00000311936.3:c.351A>T	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaT	4/5	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.63	2		534	648	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427656	49427656	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	40	539	0	ENST00000301067.7:c.10832A>T	p.Gln3611Leu	p.Q3611L	ENST00000301067	NM_003482.3	3611	cAa/cTa	39/54	1	2	FACETS	0.178	0.147	0.212	0.178	0.147	0.212	SUBCLONAL	1	TRUE	1	0.63	2		539	714	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438088	49438088	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	335	717	0	ENST00000301067.7:c.5084-1G>T		p.X1695_splice	ENST00000301067	NM_003482.3	1695			1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.63	2		717	927	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443908	49443908	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	317	882	3	ENST00000301067.7:c.3463C>A	p.Leu1155Met	p.L1155M	ENST00000301067	NM_003482.3	1155	Ctg/Atg	11/54	1	2	FACETS	0.864	0.815	0.914	0.864	0.815	0.914	CLONAL	1	TRUE	1	0.63	2		885	1165	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479207	50479207	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	257	744	0	ENST00000394963.4:c.55T>C	p.Ser19Pro	p.S19P	ENST00000394963	NM_003076.4	19	Tca/Cca	1/13	1	2	FACETS	0.985	0.925	1	0.985	0.925	1	CLONAL	1	TRUE	1	0.63	2		744	828	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484063	50484063	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	389	820	0	ENST00000394963.4:c.913C>A	p.Leu305Met	p.L305M	ENST00000394963	NM_003076.4	305	Ctg/Atg	8/13	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.63	2		820	1159	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859414	57859414	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	241	631	0	ENST00000228682.2:c.559G>A	p.Val187Ile	p.V187I	ENST00000228682	NM_005269.2	187	Gtt/Att	6/12	1	2	FACETS	0.953	0.893	1	0.953	0.893	1	CLONAL	1	TRUE	1	0.63	2		631	803	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859638	57859638	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	269	692	0	ENST00000228682.2:c.692C>A	p.Ser231Tyr	p.S231Y	ENST00000228682	NM_005269.2	231	tCt/tAt	7/12	1	2	FACETS	0.922	0.867	0.979	0.922	0.867	0.979	CLONAL	1	TRUE	1	0.63	2		692	926	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69230480	69230480	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	182	574	0	ENST00000462284.1:c.869G>A	p.Gly290Glu	p.G290E	ENST00000462284	NM_002392.5	290	gGg/gAg	10/11	1	2	FACETS	0.85	0.787	0.915	0.85	0.787	0.915	CLONAL	1	TRUE	1	0.63	2		574	680	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884997	111884997	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	312	878	0	ENST00000341259.2:c.998del	p.Gly333AlafsTer40	p.G333Afs*40	ENST00000341259	NM_005475.2	332	aGg/ag	5/8	1	2	FACETS	0.967	0.914	1	0.967	0.914	1	CLONAL	1	TRUE	1	0.63	2		878	1024	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435315	121435315	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	227	808	0	ENST00000257555.6:c.1348A>G	p.Asn450Asp	p.N450D	ENST00000257555		450	Aac/Gac	7/10	1	2	FACETS	0.593	0.551	0.636	0.593	0.551	0.636	SUBCLONAL	1	TRUE	1	0.63	2		808	1216	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435468	121435468	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs371807951	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	678	1044	0	ENST00000257555.6:c.1501G>A	p.Ala501Thr	p.A501T	ENST00000257555		501	Gcc/Acc	7/10	1	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	1	0.63	2		1044	1475	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557703	21557703	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	330	762	0	ENST00000382592.4:c.2142G>T	p.Lys714Asn	p.K714N	ENST00000382592	NM_014572.2	714	aaG/aaT	5/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.63	2		762	1005	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562307	21562307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532409148	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	336	830	1	ENST00000382592.4:c.1612G>A	p.Ala538Thr	p.A538T	ENST00000382592	NM_014572.2	538	Gca/Aca	4/8	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.63	2		831	1063	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28599018	28599018	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	234	601	3	ENST00000241453.7:c.2270G>T	p.Gly757Val	p.G757V	ENST00000241453	NM_004119.2	757	gGg/gTg	18/24	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.63	2		604	716	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911073	32911074	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359335	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	175	565	1	ENST00000380152.3:c.2588dup	p.Asn863LysfsTer18	p.N863Kfs*18	ENST00000380152		861	caa/cAaa	11/27	1	2	FACETS	0.747	0.689	0.806	0.747	0.689	0.806	SUBCLONAL	1	TRUE	1	0.63	2		566	744	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953652	32953652	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	158	372	0	ENST00000380152.3:c.8953G>T	p.Val2985Phe	p.V2985F	ENST00000380152		2985	Gtt/Ttt	22/27	1	2	FACETS	0.966	0.892	1	0.966	0.892	1	CLONAL	1	TRUE	1	0.63	2		372	519	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972483	32972483	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	305	855	0	ENST00000380152.3:c.9833C>A	p.Pro3278His	p.P3278H	ENST00000380152		3278	cCt/cAt	27/27	1	2	FACETS	0.954	0.9	1	0.954	0.9	1	CLONAL	1	TRUE	1	0.63	2		855	1015	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134420	41134420	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	199	600	0	ENST00000379561.5:c.1208C>A	p.Pro403Gln	p.P403Q	ENST00000379561	NM_002015.3	403	cCg/cAg	2/3	1	2	FACETS	0.763	0.708	0.82	0.763	0.708	0.82	SUBCLONAL	1	TRUE	1	0.63	2		600	828	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134937	41134937	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	105	349	0	ENST00000379561.5:c.691A>G	p.Thr231Ala	p.T231A	ENST00000379561	NM_002015.3	231	Act/Gct	2/3	1	2	FACETS	0.616	0.554	0.682	0.616	0.554	0.682	SUBCLONAL	1	TRUE	1	0.63	2		349	541	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039378	49039378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	76	871	0	ENST00000267163.4:c.2363G>A	p.Ser788Asn	p.S788N	ENST00000267163	NM_000321.2	788	aGc/aAc	23/27	1	2	FACETS	0.215	0.188	0.245	0.215	0.188	0.245	SUBCLONAL	1	TRUE	1	0.63	2		871	1122	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346401	73346401	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs143362001	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	126	356	1	ENST00000377767.4:c.1399C>T	p.Arg467Ter	p.R467*	ENST00000377767	NM_014953.3	467	Cga/Tga	10/21	1	2	FACETS	0.969	0.885	1	0.969	0.885	1	CLONAL	1	TRUE	1	0.63	2		357	413	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524605	103524606	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	149	431	0	ENST00000355739.4:c.2739dup	p.Val914SerfsTer16	p.V914Sfs*16	ENST00000355739	NM_000123.3	912	-/A	13/15	1	2	FACETS	0.854	0.784	0.926	0.854	0.784	0.926	CLONAL	1	TRUE	1	0.63	2		431	554	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132984	30132984	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	259	728	0	ENST00000331968.5:c.617del	p.Asn206ThrfsTer58	p.N206Tfs*58	ENST00000331968	NM_002742.2	206	aAc/ac	4/18	1	2	FACETS	0.904	0.848	0.961	0.904	0.848	0.961	CLONAL	1	TRUE	1	0.63	2		728	910	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873659	35873659	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	236	565	0	ENST00000216797.5:c.192G>T	p.Glu64Asp	p.E64D	ENST00000216797	NM_020529.2	64	gaG/gaT	1/6	1	2	FACETS	0.999	0.936	1	0.999	0.936	1	CLONAL	1	TRUE	1	0.63	2		565	750	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68301881	68301881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	170	594	0	ENST00000487270.1:c.283C>T	p.His95Tyr	p.H95Y	ENST00000487270	NM_133509.3	95	Cat/Tat	4/11	1	2	FACETS	0.634	0.583	0.687	0.634	0.583	0.687	SUBCLONAL	1	TRUE	1	0.63	2		594	851	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	69061312	69061313	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	24	104	0	ENST00000487270.1:c.1153dup	p.Ter385LeufsTer15	p.*385Lfs*15	ENST00000487270	NM_133509.3	383	att/aTtt	11/11	1	2	FACETS	1	0.832	1	1	0.832	1	CLONAL	1	TRUE	1	0.63	2		104	74	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562395	95562395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	197	467	0	ENST00000393063.1:c.4862G>A	p.Cys1621Tyr	p.C1621Y	ENST00000393063	NM_030621.3	1621	tGt/tAt	24/28	1	2	FACETS	0.859	0.798	0.922	0.859	0.798	0.922	CLONAL	1	TRUE	1	0.63	2		467	728	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590944	95590944	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	147	330	0	ENST00000393063.1:c.965C>A	p.Ala322Asp	p.A322D	ENST00000393063	NM_030621.3	322	gCt/gAt	9/28	1	2	FACETS	0.995	0.916	1	0.995	0.916	1	CLONAL	1	TRUE	1	0.63	2		330	469	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241497	105241497	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	67	868	2	ENST00000349310.3:c.483C>A	p.Phe161Leu	p.F161L	ENST00000349310	NM_001014432.1	161	ttC/ttA	7/15	1	2	FACETS	0.186	0.161	0.214	0.186	0.161	0.214	SUBCLONAL	1	TRUE	1	0.63	2		870	1143	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591611	38591611	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121434313	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	64	591	2	ENST00000299084.4:c.70C>T	p.Arg24Ter	p.R24*	ENST00000299084	NM_152594.2	24	Cga/Tga	2/7	1	2	FACETS	0.245	0.211	0.282	0.245	0.211	0.282	SUBCLONAL	1	TRUE	1	0.63	2		593	829	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38632044	38632044	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs553832516	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	294	825	1	ENST00000299084.4:c.530C>T	p.Pro177Leu	p.P177L	ENST00000299084	NM_152594.2	177	cCc/cTc	5/7	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.63	2		826	838	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988372	41988372	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	217	684	0	ENST00000219905.7:c.1164T>G	p.Asp388Glu	p.D388E	ENST00000219905	NM_001164273.1	388	gaT/gaG	3/24	1	2	FACETS	0.751	0.699	0.805	0.751	0.699	0.805	SUBCLONAL	1	TRUE	1	0.63	2		684	917	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041649	42041649	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	240	690	0	ENST00000219905.7:c.5844G>T	p.Gln1948His	p.Q1948H	ENST00000219905	NM_001164273.1	1948	caG/caT	17/24	1	2	FACETS	0.877	0.82	0.935	0.877	0.82	0.935	CLONAL	1	TRUE	1	0.63	2		690	869	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058600	42058600	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	124	396	0	ENST00000219905.7:c.8320T>C	p.Ser2774Pro	p.S2774P	ENST00000219905	NM_001164273.1	2774	Tca/Cca	24/24	1	2	FACETS	0.92	0.839	1	0.92	0.839	1	CLONAL	1	TRUE	1	0.63	2		396	428	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707827	43707827	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	288	899	0	ENST00000382044.4:c.5054C>T	p.Ala1685Val	p.A1685V	ENST00000382044	NM_001141980.1	1685	gCc/gTc	23/28	1	2	FACETS	0.755	0.709	0.802	0.755	0.709	0.802	SUBCLONAL	1	TRUE	1	0.63	2		899	1211	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713329	43713329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	402	1213	1	ENST00000382044.4:c.4144G>A	p.Glu1382Lys	p.E1382K	ENST00000382044	NM_001141980.1	1382	Gag/Aag	20/28	1	2	FACETS	0.881	0.837	0.926	0.881	0.837	0.926	CLONAL	1	TRUE	1	0.63	2		1214	1449	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43738591	43738591	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	233	543	1	ENST00000382044.4:c.3034C>A	p.Leu1012Met	p.L1012M	ENST00000382044	NM_001141980.1	1012	Ctg/Atg	14/28	1	2	FACETS	0.958	0.897	1	0.958	0.897	1	CLONAL	1	TRUE	1	0.63	2		544	772	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	338136	338136	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	299	736	0	ENST00000262320.3:c.2575del	p.Glu859ArgfsTer79	p.E859Rfs*79	ENST00000262320	NM_003502.3	859	Gag/ag	11/11	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.63	2		736	948	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348100	348100	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	290	909	0	ENST00000262320.3:c.1406G>T	p.Ser469Ile	p.S469I	ENST00000262320	NM_003502.3	469	aGc/aTc	6/11	1	2	FACETS	0.798	0.751	0.847	0.798	0.751	0.847	SUBCLONAL	1	TRUE	1	0.63	2		909	1153	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348206	348206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	413	1011	1	ENST00000262320.3:c.1300C>T	p.Pro434Ser	p.P434S	ENST00000262320	NM_003502.3	434	Ccg/Tcg	6/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.63	2		1012	1163	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396234	396234	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	287	691	3	ENST00000262320.3:c.792del	p.Gly265GlufsTer149	p.G265Efs*149	ENST00000262320	NM_003502.3	264	ccC/cc	2/11	1	2	FACETS	0.904	0.851	0.958	0.904	0.851	0.958	CLONAL	1	TRUE	1	0.63	2		694	1008	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2093617	2093617	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	391	1013	0	ENST00000219066.1:c.660G>T	p.Lys220Asn	p.K220N	ENST00000219066	NM_002528.5	220	aaG/aaT	4/6	1	2	FACETS	0.983	0.934	1	0.983	0.934	1	CLONAL	1	TRUE	1	0.63	2		1013	1263	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135297	2135297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1332979299	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	282	862	7	ENST00000219476.3:c.4636G>A	p.Ala1546Thr	p.A1546T	ENST00000219476	NM_000548.3	1546	Gcc/Acc	36/42	1	2	FACETS	0.819	0.77	0.87	0.819	0.77	0.87	CLONAL	1	TRUE	1	0.63	2		869	1093	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226345	2226345	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	353	987	0	ENST00000326181.6:c.1958G>T	p.Arg653Leu	p.R653L	ENST00000326181	NM_032271.2	653	cGg/cTg	20/21	1	2	FACETS	0.885	0.838	0.933	0.885	0.838	0.933	CLONAL	1	TRUE	1	0.63	2		987	1266	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778567	3778567	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1030655029	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	294	744	0	ENST00000262367.5:c.6481A>G	p.Met2161Val	p.M2161V	ENST00000262367	NM_004380.2	2161	Atg/Gtg	31/31	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.63	2		744	888	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858601	9858601	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	199	482	0	ENST00000330684.3:c.2800A>G	p.Met934Val	p.M934V	ENST00000330684	NM_001134407.1	934	Atg/Gtg	13/13	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.63	2		482	632	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041771	14041771	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	185	492	0	ENST00000311895.7:c.2318G>T	p.Gly773Val	p.G773V	ENST00000311895	NM_005236.2	773	gGt/gTt	11/11	1	2	FACETS	0.739	0.683	0.796	0.739	0.683	0.796	SUBCLONAL	1	TRUE	1	0.63	2		492	795	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56866246	56866246	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	232	453	0	ENST00000308159.5:c.1291C>A	p.Pro431Thr	p.P431T	ENST00000308159	NM_014669.4	431	Cca/Aca	12/22	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.63	2		453	728	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645450	67645450	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	59	500	1	ENST00000264010.4:c.715G>T	p.Glu239Ter	p.E239*	ENST00000264010	NM_006565.3	239	Gag/Tag	3/12	1	2	FACETS	0.25	0.214	0.289	0.25	0.214	0.289	SUBCLONAL	1	TRUE	1	0.63	2		501	749	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821567	72821567	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	105	306	1	ENST00000268489.5:c.10608C>A	p.Ser3536Arg	p.S3536R	ENST00000268489	NM_006885.3	3536	agC/agA	10/10	1	2	FACETS	0.751	0.677	0.828	0.751	0.677	0.828	SUBCLONAL	1	TRUE	1	0.63	2		307	444	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827898	72827898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	354	700	2	ENST00000268489.5:c.8683G>A	p.Val2895Ile	p.V2895I	ENST00000268489	NM_006885.3	2895	Gtc/Atc	9/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.63	2		702	1020	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993731	72993731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	200	522	1	ENST00000268489.5:c.314del	p.Pro105ArgfsTer4	p.P105Rfs*4	ENST00000268489	NM_006885.3	105	cCg/cg	2/10	1	2	FACETS	0.959	0.893	1	0.959	0.893	1	CLONAL	1	TRUE	1	0.63	2		523	662	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993849	72993849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758323451	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	206	485	0	ENST00000268489.5:c.196G>A	p.Ala66Thr	p.A66T	ENST00000268489	NM_006885.3	66	Gcg/Acg	2/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.63	2		485	602	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347359	89347359	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	316	983	1	ENST00000301030.4:c.5591C>A	p.Ala1864Asp	p.A1864D	ENST00000301030	NM_001256183.1	1864	gCt/gAt	9/13	1	2	FACETS	0.795	0.749	0.842	0.795	0.749	0.842	SUBCLONAL	1	TRUE	1	0.63	2		984	1262	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347440	89347440	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	333	830	1	ENST00000301030.4:c.5510del	p.Pro1837ArgfsTer126	p.P1837Rfs*126	ENST00000301030	NM_001256183.1	1837	cCg/cg	9/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.63	2		831	1010	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89809258	89809258	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	370	714	0	ENST00000389301.3:c.3715del	p.Glu1239LysfsTer8	p.E1239Kfs*8	ENST00000389301	NM_000135.2	1239	Gaa/aa	37/43	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.63	2		714	1165	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816208	89816208	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	343	767	0	ENST00000389301.3:c.3169C>T	p.Gln1057Ter	p.Q1057*	ENST00000389301	NM_000135.2	1057	Cag/Tag	32/43	1	2	FACETS	0.953	0.902	1	0.953	0.902	1	CLONAL	1	TRUE	1	0.63	2		767	1143	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216380	7216380	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	215	769	2	ENST00000380728.2:c.868del	p.Gln290SerfsTer55	p.Q290Sfs*55	ENST00000380728		290	Cag/ag	10/11	1	2	FACETS	0.651	0.605	0.699	0.651	0.605	0.699	SUBCLONAL	1	TRUE	1	0.63	2		771	1048	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578218	7578218	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060501198	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	239	1003	0	ENST00000269305.4:c.631A>G	p.Thr211Ala	p.T211A	ENST00000269305	NM_001126112.2	211	Act/Gct	6/11	1	2	FACETS	0.599	0.558	0.642	0.599	0.558	0.642	SUBCLONAL	1	TRUE	1	0.63	2		1003	1266	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964792	15964792	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	340	677	0	ENST00000268712.3:c.5804T>C	p.Val1935Ala	p.V1935A	ENST00000268712	NM_006311.3	1935	gTg/gCg	37/46	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.63	2		677	1065	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325943	30325943	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	207	582	1	ENST00000322652.5:c.2141A>G	p.Glu714Gly	p.E714G	ENST00000322652	NM_015355.2	714	gAa/gGa	16/16	1	2	FACETS	0.952	0.888	1	0.952	0.888	1	CLONAL	1	TRUE	1	0.63	2		583	690	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687245	37687246	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	260	586	0	ENST00000447079.4:c.4153dup	p.Glu1385GlyfsTer40	p.E1385Gfs*40	ENST00000447079	NM_015083.1	1383	-/G	14/14	1	2	FACETS	0.936	0.879	0.994	0.936	0.879	0.994	CLONAL	1	TRUE	1	0.63	2		586	882	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687373	37687373	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	253	649	1	ENST00000447079.4:c.4277G>T	p.Ser1426Ile	p.S1426I	ENST00000447079	NM_015083.1	1426	aGc/aTc	14/14	1	2	FACETS	0.994	0.933	1	0.994	0.933	1	CLONAL	1	TRUE	1	0.63	2		650	808	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687469	37687469	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs752380133	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	164	409	0	ENST00000447079.4:c.4373A>G	p.His1458Arg	p.H1458R	ENST00000447079	NM_015083.1	1458	cAc/cGc	14/14	1	2	FACETS	0.887	0.818	0.958	0.887	0.818	0.958	CLONAL	1	TRUE	1	0.63	2		409	587	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884023	37884023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	74	902	0	ENST00000269571.5:c.3494C>T	p.Ala1165Val	p.A1165V	ENST00000269571		1165	gCc/gTc	27/27	1	2	FACETS	0.222	0.193	0.253	0.222	0.193	0.253	SUBCLONAL	1	TRUE	1	0.63	2		902	1060	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370287	40370287	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	182	887	0	ENST00000293328.3:c.1051A>G	p.Thr351Ala	p.T351A	ENST00000293328	NM_012448.3	351	Act/Gct	9/19	1	2	FACETS	0.545	0.502	0.59	0.545	0.502	0.59	SUBCLONAL	1	TRUE	1	0.63	2		887	1060	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244243	41244243	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs80356900	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	255	753	0	ENST00000357654.3:c.3305A>G	p.Asn1102Ser	p.N1102S	ENST00000357654	NM_007294.3	1102	aAt/aGt	10/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.63	2		753	765	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246661	41246661	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	234	539	0	ENST00000357654.3:c.887G>T	p.Arg296Ile	p.R296I	ENST00000357654	NM_007294.3	296	aGa/aTa	10/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.63	2		539	703	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55754347	55754347	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	270	781	1	ENST00000284073.2:c.946-1G>T		p.X316_splice	ENST00000284073	NM_138962.2	316			1	2	FACETS	0.834	0.783	0.886	0.834	0.783	0.886	CLONAL	1	TRUE	1	0.63	2		782	1028	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436026	56436026	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771831816	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	128	347	1	ENST00000407977.2:c.1111C>T	p.Arg371Ter	p.R371*	ENST00000407977		371	Cga/Tga	9/10	1	2	FACETS	0.891	0.813	0.972	0.891	0.813	0.972	CLONAL	1	TRUE	1	0.63	2		348	456	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56787305	56787305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1283065191	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	280	702	1	ENST00000337432.4:c.791G>A	p.Gly264Asp	p.G264D	ENST00000337432	NM_058216.2	264	gGc/gAc	5/9	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.63	2		703	851	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56811557	56811557	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	184	576	0	ENST00000337432.4:c.1105T>C	p.Ser369Pro	p.S369P	ENST00000337432	NM_058216.2	369	Tca/Cca	9/9	1	2	FACETS	0.702	0.649	0.757	0.702	0.649	0.757	SUBCLONAL	1	TRUE	1	0.63	2		576	832	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678122	58678122	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	358	784	1	ENST00000305921.3:c.347C>T	p.Ala116Val	p.A116V	ENST00000305921	NM_003620.3	116	gCc/gTc	1/6	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.63	2		785	1006	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732318	74732318	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	210	330	0	ENST00000359995.5:c.591G>T	p.Lys197Asn	p.K197N	ENST00000359995	NM_001195427.1	197	aaG/aaT	2/3	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.63	2		330	624	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207175	1207175	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	384	1003	0	ENST00000326873.7:c.263T>C	p.Ile88Thr	p.I88T	ENST00000326873	NM_000455.4	88	aTc/aCc	1/10	1	2	FACETS	0.936	0.889	0.984	0.936	0.889	0.984	CLONAL	1	TRUE	1	0.63	2		1003	1302	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219373	1219373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568705518	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	332	871	0	ENST00000326873.7:c.425G>A	p.Ser142Asn	p.S142N	ENST00000326873	NM_000455.4	142	aGc/aAc	3/10	1	2	FACETS	0.895	0.846	0.945	0.895	0.846	0.945	CLONAL	1	TRUE	1	0.63	2		871	1178	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221232	1221232	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	315	893	0	ENST00000326873.7:c.755T>C	p.Leu252Pro	p.L252P	ENST00000326873	NM_000455.4	252	cTg/cCg	6/10	1	2	FACETS	0.779	0.734	0.825	0.779	0.734	0.825	SUBCLONAL	1	TRUE	1	0.63	2		893	1284	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622396	1622396	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs935082974	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	236	941	3	ENST00000344749.5:c.568G>T	p.Gly190Cys	p.G190C	ENST00000344749	NM_001136139.2	190	Ggt/Tgt	9/19	1	2	FACETS	0.66	0.615	0.706	0.66	0.615	0.706	SUBCLONAL	1	TRUE	1	0.63	2		944	1135	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222530	2222530	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760394488	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	260	1029	1	ENST00000398665.3:c.3362C>T	p.Ser1121Leu	p.S1121L	ENST00000398665	NM_032482.2	1121	tCg/tTg	24/28	1	2	FACETS	0.617	0.577	0.659	0.617	0.577	0.659	SUBCLONAL	1	TRUE	1	0.63	2		1030	1337	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101061	4101061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	134	434	0	ENST00000262948.5:c.661G>A	p.Asp221Asn	p.D221N	ENST00000262948	NM_030662.3	221	Gac/Aac	6/11	1	2	FACETS	0.795	0.726	0.867	0.795	0.726	0.867	SUBCLONAL	1	TRUE	1	0.63	2		434	535	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117531	4117531	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	202	367	0	ENST00000262948.5:c.189G>T	p.Lys63Asn	p.K63N	ENST00000262948	NM_030662.3	63	aaG/aaT	2/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.63	2		367	517	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245926	5245926	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	391	1050	1	ENST00000357368.4:c.849G>T	p.Glu283Asp	p.E283D	ENST00000357368	NM_002850.3	283	gaG/gaT	10/38	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.63	2		1051	1228	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251469	10251469	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	244	730	0	ENST00000340748.4:c.3463T>G	p.Phe1155Val	p.F1155V	ENST00000340748		1155	Ttc/Gtc	31/40	1	2	FACETS	0.717	0.669	0.765	0.717	0.669	0.765	SUBCLONAL	1	TRUE	1	0.63	2		730	1081	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11018751	11018751	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	350	990	1	ENST00000327064.4:c.386del	p.Gly129AlafsTer34	p.G129Afs*34	ENST00000327064	NM_199141.1	128	cGg/cg	3/16	1	2	FACETS	0.774	0.731	0.817	0.774	0.731	0.817	SUBCLONAL	1	TRUE	1	0.63	2		991	1436	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031764	11031764	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	83	1059	0	ENST00000327064.4:c.1576A>G	p.Ser526Gly	p.S526G	ENST00000327064	NM_199141.1	526	Agt/Ggt	14/16	1	2	FACETS	0.21	0.185	0.238	0.21	0.185	0.238	SUBCLONAL	1	TRUE	1	0.63	2		1059	1253	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11032084	11032084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	345	869	1	ENST00000327064.4:c.1649G>A	p.Arg550Gln	p.R550Q	ENST00000327064	NM_199141.1	550	cGg/cAg	15/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.63	2		870	1077	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096864	11096864	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	432	1086	1	ENST00000358026.2:c.356-1G>T		p.X119_splice	ENST00000358026	NM_001128849.1	119			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.63	2		1087	1284	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107214	11107214	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	96	663	0	ENST00000358026.2:c.1806T>A	p.Asp602Glu	p.D602E	ENST00000358026	NM_001128849.1	602	gaT/gaA	11/36	1	2	FACETS	0.291	0.258	0.326	0.291	0.258	0.326	SUBCLONAL	1	TRUE	1	0.63	2		663	1047	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136097	11136097	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	293	766	0	ENST00000358026.2:c.3082-1G>A		p.X1028_splice	ENST00000358026	NM_001128849.1	1028			1	2	FACETS	0.962	0.907	1	0.962	0.907	1	CLONAL	1	TRUE	1	0.63	2		766	967	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050241	13050241	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	232	447	1	ENST00000316448.5:c.194-1G>T		p.X65_splice	ENST00000316448	NM_004343.3	65			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.63	2		448	671	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272288	15272288	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1307486231	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	251	976	1	ENST00000263388.2:c.6151C>T	p.Pro2051Ser	p.P2051S	ENST00000263388	NM_000435.2	2051	Cct/Tct	33/33	1	2	FACETS	0.781	0.731	0.833	0.781	0.731	0.833	SUBCLONAL	1	TRUE	1	0.63	2		977	1020	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281236	15281236	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs868385844	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	379	1117	0	ENST00000263388.2:c.5020C>A	p.Leu1674Ile	p.L1674I	ENST00000263388	NM_000435.2	1674	Ctc/Atc	27/33	1	2	FACETS	0.991	0.941	1	0.991	0.941	1	CLONAL	1	TRUE	1	0.63	2		1117	1214	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291842	15291842	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	93	982	2	ENST00000263388.2:c.2924del	p.Gly975AlafsTer297	p.G975Afs*297	ENST00000263388	NM_000435.2	975	gGc/gc	18/33	1	2	FACETS	0.274	0.243	0.308	0.274	0.243	0.308	SUBCLONAL	1	TRUE	1	0.63	2		984	1076	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299950	15299950	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	200	866	0	ENST00000263388.2:c.1228A>G	p.Asn410Asp	p.N410D	ENST00000263388	NM_000435.2	410	Aac/Gac	8/33	1	2	FACETS	0.596	0.552	0.642	0.596	0.552	0.642	SUBCLONAL	1	TRUE	1	0.63	2		866	1065	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349605	15349605	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	355	1054	2	ENST00000263377.2:c.3969G>T	p.Gln1323His	p.Q1323H	ENST00000263377	NM_058243.2	1323	caG/caT	19/20	1	2	FACETS	0.962	0.912	1	0.962	0.912	1	CLONAL	1	TRUE	1	0.63	2		1056	1171	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15378281	15378281	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	55	649	0	ENST00000263377.2:c.505A>G	p.Thr169Ala	p.T169A	ENST00000263377	NM_058243.2	169	Acc/Gcc	4/20	1	2	FACETS	0.186	0.158	0.216	0.186	0.158	0.216	SUBCLONAL	1	TRUE	1	0.63	2		649	939	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216408	36216408	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	323	1060	0	ENST00000222270.7:c.3671C>A	p.Pro1224Gln	p.P1224Q	ENST00000222270	NM_014727.1	1224	cCa/cAa	12/37	1	2	FACETS	0.778	0.734	0.823	0.778	0.734	0.823	SUBCLONAL	1	TRUE	1	0.63	2		1060	1318	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741933	40741933	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	319	1059	4	ENST00000392038.2:c.1039C>A	p.Arg347Ser	p.R347S	ENST00000392038	NM_001626.4	347	Cgc/Agc	11/14	1	2	FACETS	0.733	0.691	0.777	0.733	0.691	0.777	SUBCLONAL	1	TRUE	1	0.63	2		1063	1381	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754647	41754647	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	285	747	0	ENST00000301178.4:c.1634-1G>T		p.X545_splice	ENST00000301178	NM_021913.4	545			1	2	FACETS	0.963	0.907	1	0.963	0.907	1	CLONAL	1	TRUE	1	0.63	2		747	940	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793999	42793999	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	497	863	0	ENST00000575354.2:c.1361-1G>A		p.X454_splice	ENST00000575354	NM_015125.3	454			1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.63	2		863	1288	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860910	45860910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	156	948	0	ENST00000391945.4:c.1285G>A	p.Ala429Thr	p.A429T	ENST00000391945	NM_000400.3	429	Gcc/Acc	13/23	1	2	FACETS	0.395	0.36	0.431	0.395	0.36	0.431	SUBCLONAL	1	TRUE	1	0.63	2		948	1255	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902239	50902239	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	380	1196	0	ENST00000440232.2:c.131T>C	p.Met44Thr	p.M44T	ENST00000440232	NM_002691.3	44	aTg/aCg	2/27	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.63	2		1196	1205	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909452	50909452	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	355	844	0	ENST00000440232.2:c.1256C>A	p.Pro419His	p.P419H	ENST00000440232	NM_002691.3	419	cCt/cAt	11/27	1	2	FACETS	0.958	0.908	1	0.958	0.908	1	CLONAL	1	TRUE	1	0.63	2		844	1177	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909694	50909694	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1052471	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	325	1025	0	ENST00000440232.2:c.1414T>C	p.Tyr472His	p.Y472H	ENST00000440232	NM_002691.3	472	Tac/Cac	12/27	1	2	FACETS	0.831	0.785	0.879	0.831	0.785	0.879	CLONAL	1	TRUE	1	0.63	2		1025	1241	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909713	50909713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397514632	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	443	1036	2	ENST00000440232.2:c.1433G>A	p.Ser478Asn	p.S478N	ENST00000440232	NM_002691.3	478	aGc/aAc	12/27	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.63	2		1038	1296	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965362	25965362	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs775732218	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	295	851	1	ENST00000435504.4:c.3844A>T	p.Ile1282Phe	p.I1282F	ENST00000435504		1282	Atc/Ttc	13/13	1	2	FACETS	0.952	0.897	1	0.952	0.897	1	CLONAL	1	TRUE	1	0.63	2		852	984	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972809	25972809	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	41	488	0	ENST00000435504.4:c.1616A>G	p.Lys539Arg	p.K539R	ENST00000435504		539	aAg/aGg	12/13	1	2	FACETS	0.181	0.15	0.215	0.181	0.15	0.215	SUBCLONAL	1	TRUE	1	0.63	2		488	720	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143363	30143363	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1268569052	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	273	945	0	ENST00000389048.3:c.163G>A	p.Ala55Thr	p.A55T	ENST00000389048	NM_004304.4	55	Gca/Aca	1/29	1	2	FACETS	0.821	0.771	0.872	0.821	0.771	0.872	CLONAL	1	TRUE	1	0.63	2		945	1056	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285929	39285930	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	167	541	0	ENST00000402219.2:c.229dup	p.Ser77LysfsTer7	p.S77Kfs*7	ENST00000402219	NM_005633.3	77	agt/aAgt	3/23	1	2	FACETS	0.813	0.75	0.879	0.813	0.75	0.879	CLONAL	1	TRUE	1	0.63	2		541	652	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46611790	46611790	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	250	599	0	ENST00000263734.3:c.2604G>T	p.Gln868His	p.Q868H	ENST00000263734	NM_001430.4	868	caG/caT	16/16	1	2	FACETS	0.995	0.933	1	0.995	0.933	1	CLONAL	1	TRUE	1	0.63	2		599	798	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702166	47702166	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	142	347	0	ENST00000233146.2:c.1762T>C	p.Tyr588His	p.Y588H	ENST00000233146	NM_000251.2	588	Tat/Cat	12/16	1	2	FACETS	0.945	0.868	1	0.945	0.868	1	CLONAL	1	TRUE	1	0.63	2		347	477	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027815	48027815	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	203	434	0	ENST00000234420.5:c.2693C>A	p.Pro898His	p.P898H	ENST00000234420	NM_000179.2	898	cCt/cAt	4/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.63	2		434	556	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145630	61145630	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755123146	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	305	686	1	ENST00000295025.8:c.742C>T	p.Pro248Ser	p.P248S	ENST00000295025	NM_002908.2	248	Cca/Tca	7/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.63	2		687	947	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881570	111881570	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	301	760	2	ENST00000393256.3:c.248T>C	p.Met83Thr	p.M83T	ENST00000393256	NM_006538.4	83	aTg/aCg	2/4	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.63	2		762	951	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128036914	128036914	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	212	668	0	ENST00000285398.2:c.1565A>T	p.Tyr522Phe	p.Y522F	ENST00000285398	NM_000122.1	522	tAt/tTt	10/15	1	2	FACETS	0.747	0.695	0.801	0.747	0.695	0.801	SUBCLONAL	1	TRUE	1	0.63	2		668	901	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096178	178096178	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	194	478	0	ENST00000397062.3:c.1153C>T	p.Pro385Ser	p.P385S	ENST00000397062	NM_006164.4	385	Cct/Tct	5/5	1	2	FACETS	0.935	0.869	1	0.935	0.869	1	CLONAL	1	TRUE	1	0.63	2		478	659	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098837	178098837	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	322	768	0	ENST00000397062.3:c.208T>C	p.Phe70Leu	p.F70L	ENST00000397062	NM_006164.4	70	Ttt/Ctt	2/5	1	2	FACETS	0.942	0.89	0.995	0.942	0.89	0.995	CLONAL	1	TRUE	1	0.63	2		768	1085	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682831	190682831	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	177	577	0	ENST00000441310.2:c.512del	p.Lys171ArgfsTer7	p.K171Rfs*7	ENST00000441310	NM_000534.4	169	atA/at	5/13	1	2	FACETS	0.731	0.675	0.789	0.731	0.675	0.789	SUBCLONAL	1	TRUE	1	0.63	2		577	769	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265046	198265046	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	214	413	0	ENST00000335508.6:c.2831C>A	p.Ser944Tyr	p.S944Y	ENST00000335508	NM_012433.2	944	tCt/tAt	19/25	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.63	2		413	649	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735377	204735377	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	135	298	0	ENST00000302823.3:c.178T>C	p.Tyr60His	p.Y60H	ENST00000302823	NM_005214.4	60	Tat/Cat	2/4	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.63	2		298	421	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543856	212543856	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	288	570	1	ENST00000342788.4:c.1543C>T	p.Pro515Ser	p.P515S	ENST00000342788	NM_005235.2	515	Cct/Tct	13/28	1	2	FACETS	0.998	0.941	1	0.998	0.941	1	CLONAL	1	TRUE	1	0.63	2		571	916	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439464	220439464	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	32	502	1	ENST00000243786.2:c.317C>A	p.Ala106Asp	p.A106D	ENST00000243786	NM_002191.3	106	gCt/gAt	2/2	1	2	FACETS	0.185	0.15	0.225	0.185	0.15	0.225	SUBCLONAL	1	TRUE	1	0.63	2		503	549	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439700	220439701	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	318	854	0	ENST00000243786.2:c.562_563dup	p.Leu189CysfsTer2	p.L189Cfs*2	ENST00000243786	NM_002191.3	185	gct/gCTct	2/2	1	2	FACETS	0.968	0.915	1	0.968	0.915	1	CLONAL	1	TRUE	1	0.63	2		854	1043	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662467	227662467	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1416721377	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	223	561	0	ENST00000305123.5:c.988A>G	p.Ser330Gly	p.S330G	ENST00000305123	NM_005544.2	330	Agt/Ggt	1/2	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.63	2		561	690	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383265	31383265	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	119	662	0	ENST00000328111.2:c.1177T>C	p.Cys393Arg	p.C393R	ENST00000328111	NM_006892.3	393	Tgc/Cgc	11/23	1	2	FACETS	0.367	0.331	0.406	0.367	0.331	0.406	SUBCLONAL	1	TRUE	1	0.63	2		662	1028	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979275	40979275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867428378	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	255	607	0	ENST00000373198.4:c.1858C>T	p.Pro620Ser	p.P620S	ENST00000373198	NM_133170.3	620	Cct/Tct	11/32	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.63	2		607	777	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62311299	62311299	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs201938707	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	124	344	1	ENST00000360203.5:c.1135C>T	p.Arg379Cys	p.R379C	ENST00000360203	NM_001283009.1	379	Cgt/Tgt	13/35	1	2	FACETS	0.869	0.792	0.949	0.869	0.792	0.949	CLONAL	1	TRUE	1	0.63	2		345	453	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775557	39775557	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs552037654	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	277	675	2	ENST00000288319.7:c.463G>A	p.Val155Ile	p.V155I	ENST00000288319	NM_182918.3	155	Gtc/Atc	4/10	1	2	FACETS	0.961	0.904	1	0.961	0.904	1	CLONAL	1	TRUE	1	0.63	2		677	915	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288098	21288098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	48	504	0	ENST00000354336.3:c.343G>A	p.Ala115Thr	p.A115T	ENST00000354336	NM_005207.3	115	Gca/Aca	2/3	1	2	FACETS	0.235	0.198	0.276	0.235	0.198	0.276	SUBCLONAL	1	TRUE	1	0.63	2		504	649	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127186	22127186	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	239	647	0	ENST00000215832.6:c.942G>T	p.Glu314Asp	p.E314D	ENST00000215832	NM_002745.4	314	gaG/gaT	7/9	1	2	FACETS	0.92	0.861	0.98	0.92	0.861	0.98	CLONAL	1	TRUE	1	0.63	2		647	825	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513608	41513608	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs533349187	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	210	757	2	ENST00000263253.7:c.512C>T	p.Ala171Val	p.A171V	ENST00000263253	NM_001429.3	171	gCg/gTg	2/31	1	2	FACETS	0.733	0.681	0.786	0.733	0.681	0.786	SUBCLONAL	1	TRUE	1	0.63	2		759	910	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574679	41574679	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	412	1045	2	ENST00000263253.7:c.6970del	p.His2324ThrfsTer29	p.H2324Tfs*29	ENST00000263253	NM_001429.3	2322	Ccc/cc	31/31	1	2	FACETS	0.986	0.938	1	0.986	0.938	1	CLONAL	1	TRUE	1	0.63	2		1047	1327	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183563	10183563	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	336	981	0	ENST00000256474.2:c.32C>T	p.Ala11Val	p.A11V	ENST00000256474	NM_000551.3	11	gCc/gTc	1/3	1	2	FACETS	0.992	0.939	1	0.992	0.939	1	CLONAL	1	TRUE	1	0.63	2		981	1075	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191522	10191522	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	221	516	1	ENST00000256474.2:c.515C>A	p.Pro172His	p.P172H	ENST00000256474	NM_000551.3	172	cCt/cAt	3/3	1	2	FACETS	0.776	0.723	0.831	0.776	0.723	0.831	SUBCLONAL	1	TRUE	1	0.63	2		517	904	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37045891	37045891	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	45	517	0	ENST00000231790.2:c.307-1G>T		p.X103_splice	ENST00000231790	NM_000249.3	103			1	2	FACETS	0.213	0.178	0.252	0.213	0.178	0.252	SUBCLONAL	1	TRUE	1	0.63	2		517	670	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266826	41266826	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	151	377	1	ENST00000349496.5:c.497T>C	p.Val166Ala	p.V166A	ENST00000349496	NM_001904.3	166	gTg/gCg	5/15	1	2	FACETS	0.965	0.888	1	0.965	0.888	1	CLONAL	1	TRUE	1	0.63	2		378	497	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275054	41275054	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	110	386	0	ENST00000349496.5:c.1220A>G	p.Gln407Arg	p.Q407R	ENST00000349496	NM_001904.3	407	cAg/cGg	9/15	1	2	FACETS	0.741	0.67	0.816	0.741	0.67	0.816	SUBCLONAL	1	TRUE	1	0.63	2		386	471	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162515	47162515	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	139	322	0	ENST00000409792.3:c.3611T>G	p.Ile1204Ser	p.I1204S	ENST00000409792	NM_014159.6	1204	aTt/aGt	3/21	1	2	FACETS	0.829	0.759	0.902	0.829	0.759	0.902	CLONAL	1	TRUE	1	0.63	2		322	532	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933437	49933438	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	216	889	0	ENST00000296474.3:c.2752dup	p.Leu918ProfsTer21	p.L918Pfs*21	ENST00000296474	NM_002447.2	918	ctg/cCtg	11/20	1	2	FACETS	0.775	0.721	0.83	0.775	0.721	0.83	SUBCLONAL	1	TRUE	1	0.63	2		889	885	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935551	49935551	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	373	885	1	ENST00000296474.3:c.1813G>T	p.Gly605Ter	p.G605*	ENST00000296474	NM_002447.2	605	Gga/Tga	5/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.63	2		886	1129	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928307	69928307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	209	423	0	ENST00000352241.4:c.127G>A	p.Ala43Thr	p.A43T	ENST00000352241	NM_198159.2	43	Gcc/Acc	2/10	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.63	2		423	644	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026194	71026194	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	160	319	0	ENST00000318789.4:c.1429-1G>T		p.X477_splice	ENST00000318789	NM_032682.5	477			1	2	FACETS	0.929	0.857	1	0.929	0.857	1	CLONAL	1	TRUE	1	0.63	2		319	547	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090528	71090528	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	156	407	0	ENST00000318789.4:c.820C>T	p.His274Tyr	p.H274Y	ENST00000318789	NM_032682.5	274	Cat/Tat	11/21	1	2	FACETS	0.9	0.829	0.974	0.9	0.829	0.974	CLONAL	1	TRUE	1	0.63	2		407	550	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427611	72427611	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	130	342	0	ENST00000477973.2:c.879G>T	p.Glu293Asp	p.E293D	ENST00000477973	NM_012234.5	293	gaG/gaT	4/4	1	2	FACETS	0.749	0.682	0.818	0.749	0.682	0.818	SUBCLONAL	1	TRUE	1	0.63	2		342	551	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428207	72428207	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	201	528	0	ENST00000477973.2:c.685A>G	p.Thr229Ala	p.T229A	ENST00000477973	NM_012234.5	229	Aca/Gca	3/4	1	2	FACETS	0.905	0.842	0.97	0.905	0.842	0.97	CLONAL	1	TRUE	1	0.63	2		528	705	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259191	89259191	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	30	444	0	ENST00000336596.2:c.338del	p.Leu113Ter	p.L113*	ENST00000336596	NM_005233.5	112	gTt/gt	3/17	1	2	FACETS	0.185	0.148	0.226	0.185	0.148	0.226	SUBCLONAL	1	TRUE	1	0.63	2		444	516	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390110	89390110	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	137	429	0	ENST00000336596.2:c.859T>C	p.Cys287Arg	p.C287R	ENST00000336596	NM_005233.5	287	Tgt/Cgt	4/17	1	2	FACETS	0.698	0.637	0.762	0.698	0.637	0.762	SUBCLONAL	1	TRUE	1	0.63	2		429	623	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204842	128204842	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs768767517	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	87	1119	1	ENST00000341105.2:c.599del	p.Gly200ValfsTer18	p.G200Vfs*18	ENST00000341105	NM_032638.4	200	gGt/gt	3/6	1	2	FACETS	0.223	0.196	0.252	0.223	0.196	0.252	SUBCLONAL	1	TRUE	1	0.63	2		1120	1238	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920490	134920490	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	298	666	0	ENST00000398015.3:c.2305C>A	p.Leu769Ile	p.L769I	ENST00000398015	NM_004441.4	769	Ctc/Atc	12/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.63	2		666	931	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138375045	138375045	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369600257	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	231	706	2	ENST00000289153.2:c.3014C>T	p.Ala1005Val	p.A1005V	ENST00000289153	NM_006219.2	1005	gCg/gTg	21/22	1	2	FACETS	0.74	0.69	0.791	0.74	0.69	0.791	SUBCLONAL	1	TRUE	1	0.63	2		708	991	SUCCESS
ATR	545	MSKCC	GRCh37	3	142185186	142185186	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs758772379	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	125	633	0	ENST00000350721.4:c.6877A>G	p.Ile2293Val	p.I2293V	ENST00000350721	NM_001184.3	2293	Att/Gtt	40/47	1	2	FACETS	0.719	0.653	0.787	0.719	0.653	0.787	SUBCLONAL	1	TRUE	1	0.63	2		633	552	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281210	142281210	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	239	575	1	ENST00000350721.4:c.1034C>A	p.Ala345Asp	p.A345D	ENST00000350721	NM_001184.3	345	gCt/gAt	4/47	1	2	FACETS	0.983	0.921	1	0.983	0.921	1	CLONAL	1	TRUE	1	0.63	2		576	772	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919159	178919159	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	106	335	0	ENST00000263967.3:c.644G>A	p.Cys215Tyr	p.C215Y	ENST00000263967	NM_006218.2	215	tGt/tAt	4/21	1	2	FACETS	0.713	0.642	0.787	0.713	0.642	0.787	SUBCLONAL	1	TRUE	1	0.63	2		335	472	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430596	181430596	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	197	784	1	ENST00000325404.1:c.448G>T	p.Gly150Cys	p.G150C	ENST00000325404	NM_003106.3	150	Ggc/Tgc	1/1	1	2	FACETS	0.912	0.848	0.978	0.912	0.848	0.978	CLONAL	1	TRUE	1	0.63	2		785	686	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430868	181430868	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	303	1094	1	ENST00000325404.1:c.720G>T	p.Met240Ile	p.M240I	ENST00000325404	NM_003106.3	240	atG/atT	1/1	1	2	FACETS	0.863	0.813	0.914	0.863	0.813	0.914	CLONAL	1	TRUE	1	0.63	2		1095	1115	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505332	186505332	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	153	421	0	ENST00000323963.5:c.958C>T	p.Arg320Trp	p.R320W	ENST00000323963		320	Cgg/Tgg	9/11	1	2	FACETS	0.858	0.789	0.93	0.858	0.789	0.93	CLONAL	1	TRUE	1	0.63	2		421	566	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447562	187447562	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	62	652	1	ENST00000232014.4:c.631G>T	p.Glu211Ter	p.E211*	ENST00000232014	NM_001130845.1	211	Gag/Tag	5/10	1	2	FACETS	0.255	0.219	0.293	0.255	0.219	0.293	SUBCLONAL	1	TRUE	1	0.63	2		653	773	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902658	1902658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761663126	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	330	908	0	ENST00000382891.5:c.277G>A	p.Ala93Thr	p.A93T	ENST00000382891	NM_133335.3	93	Gca/Aca	2/22	1	2	FACETS	0.749	0.707	0.793	0.749	0.707	0.793	SUBCLONAL	1	TRUE	1	0.63	2		908	1398	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593594	55593594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	159	485	0	ENST00000288135.5:c.1660G>A	p.Glu554Lys	p.E554K	ENST00000288135	NM_000222.2	554	Gaa/Aaa	11/21	1	2	FACETS	0.96	0.885	1	0.96	0.885	1	CLONAL	1	TRUE	1	0.63	2		485	526	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968595	55968595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199504669	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	308	697	0	ENST00000263923.4:c.2068G>A	p.Ala690Thr	p.A690T	ENST00000263923	NM_002253.2	690	Gca/Aca	14/30	1	2	FACETS	0.974	0.92	1	0.974	0.92	1	CLONAL	1	TRUE	1	0.63	2		697	1004	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467610	66467610	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	169	463	0	ENST00000273854.3:c.659G>A	p.Cys220Tyr	p.C220Y	ENST00000273854	NM_004439.5	220	tGc/tAc	3/18	1	2	FACETS	0.888	0.821	0.958	0.888	0.821	0.958	CLONAL	1	TRUE	1	0.63	2		463	604	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467644	66467644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202165566	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	161	436	0	ENST00000273854.3:c.625G>A	p.Gly209Arg	p.G209R	ENST00000273854	NM_004439.5	209	Gga/Aga	3/18	1	2	FACETS	0.9	0.83	0.972	0.9	0.83	0.972	CLONAL	1	TRUE	1	0.63	2		436	568	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535290	66535290	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	298	966	0	ENST00000273854.3:c.171del	p.Ser58AlafsTer4	p.S58Afs*4	ENST00000273854	NM_004439.5	57	ccC/cc	1/18	1	2	FACETS	0.965	0.911	1	0.965	0.911	1	CLONAL	1	TRUE	1	0.63	2		966	980	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157276	106157276	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	283	648	0	ENST00000380013.4:c.2177A>G	p.Gln726Arg	p.Q726R	ENST00000380013	NM_001127208.2	726	cAg/cGg	3/11	1	2	FACETS	0.994	0.936	1	0.994	0.936	1	CLONAL	1	TRUE	1	0.63	2		648	904	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106182949	106182949	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	163	539	0	ENST00000380013.4:c.3988T>A	p.Ser1330Thr	p.S1330T	ENST00000380013	NM_001127208.2	1330	Tcc/Acc	8/11	1	2	FACETS	0.903	0.833	0.975	0.903	0.833	0.975	CLONAL	1	TRUE	1	0.63	2		539	573	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245454	153245454	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	275	676	0	ENST00000281708.4:c.1737del	p.His580ThrfsTer4	p.H580Tfs*4	ENST00000281708	NM_033632.3	579	ggG/gg	11/12	1	2	FACETS	0.99	0.932	1	0.99	0.932	1	CLONAL	1	TRUE	1	0.63	2		676	882	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247264	153247264	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	206	595	1	ENST00000281708.4:c.1538G>T	p.Arg513Met	p.R513M	ENST00000281708	NM_033632.3	513	aGg/aTg	10/12	1	2	FACETS	0.738	0.685	0.793	0.738	0.685	0.793	SUBCLONAL	1	TRUE	1	0.63	2		596	886	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527336	187527336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559793732	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	299	484	1	ENST00000441802.2:c.10238C>T	p.Ser3413Phe	p.S3413F	ENST00000441802	NM_005245.3	3413	tCt/tTt	17/27	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.63	2		485	912	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534472	187534473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs749145480	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	200	481	0	ENST00000441802.2:c.9253dup	p.Leu3085ProfsTer2	p.L3085Pfs*2	ENST00000441802	NM_005245.3	3085	ctt/cCtt	13/27	1	2	FACETS	0.835	0.776	0.897	0.835	0.776	0.897	CLONAL	1	TRUE	1	0.63	2		481	760	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540583	187540583	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	208	432	0	ENST00000441802.2:c.7157A>T	p.Asn2386Ile	p.N2386I	ENST00000441802	NM_005245.3	2386	aAt/aTt	10/27	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.63	2		432	660	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39003661	39003661	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	150	467	1	ENST00000357387.3:c.259del	p.Cys87ValfsTer4	p.C87Vfs*4	ENST00000357387	NM_152756.3	87	Tgt/gt	4/38	1	2	FACETS	0.883	0.812	0.957	0.883	0.812	0.957	CLONAL	1	TRUE	1	0.63	2		468	539	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170982	56170982	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	116	290	0	ENST00000399503.3:c.1810G>T	p.Gly604Ter	p.G604*	ENST00000399503	NM_005921.1	604	Gga/Tga	10/20	1	2	FACETS	0.918	0.835	1	0.918	0.835	1	CLONAL	1	TRUE	1	0.63	2		290	401	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176603	56176603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	36	479	2	ENST00000399503.3:c.2153C>T	p.Ala718Val	p.A718V	ENST00000399503	NM_005921.1	718	gCa/gTa	12/20	1	2	FACETS	0.16	0.131	0.193	0.16	0.131	0.193	SUBCLONAL	1	TRUE	1	0.63	2		481	713	SUCCESS
APC	324	MSKCC	GRCh37	5	112116577	112116577	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854583	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	179	573	0	ENST00000257430.4:c.622C>T	p.Gln208Ter	p.Q208*	ENST00000257430	NM_000038.5	208	Cag/Tag	6/16	1	2	FACETS	0.944	0.875	1	0.944	0.875	1	CLONAL	1	TRUE	1	0.63	2		573	602	SUCCESS
APC	324	MSKCC	GRCh37	5	112154676	112154676	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659673	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	120	382	0	ENST00000257430.4:c.947A>G	p.Tyr316Cys	p.Y316C	ENST00000257430	NM_000038.5	316	tAt/tGt	10/16	1	2	FACETS	0.75	0.681	0.822	0.75	0.681	0.822	SUBCLONAL	1	TRUE	1	0.63	2		382	508	SUCCESS
APC	324	MSKCC	GRCh37	5	112170647	112170647	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	118	359	0	ENST00000257430.4:c.1744-1G>A		p.X582_splice	ENST00000257430	NM_000038.5	582			1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.63	2		359	369	SUCCESS
APC	324	MSKCC	GRCh37	5	112176170	112176171	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	246	608	0	ENST00000257430.4:c.4883dup	p.His1629AlafsTer3	p.H1629Afs*3	ENST00000257430	NM_000038.5	1627	caa/cAaa	16/16	1	2	FACETS	0.919	0.861	0.978	0.919	0.861	0.978	CLONAL	1	TRUE	1	0.63	2		608	850	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131930736	131930736	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	128	373	0	ENST00000265335.6:c.1969G>T	p.Ala657Ser	p.A657S	ENST00000265335		657	Gcc/Tcc	12/25	1	2	FACETS	0.893	0.815	0.974	0.893	0.815	0.974	CLONAL	1	TRUE	1	0.63	2		373	455	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819968	170819968	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	195	438	0	ENST00000296930.5:c.510G>T	p.Glu170Asp	p.E170D	ENST00000296930	NM_002520.6	170	gaG/gaT	6/11	1	2	FACETS	0.987	0.919	1	0.987	0.919	1	CLONAL	1	TRUE	1	0.63	2		438	627	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517816	176517816	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1562067334	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	235	749	0	ENST00000292408.4:c.430del	p.Gln144SerfsTer67	p.Q144Sfs*67	ENST00000292408	NM_213647.1	142	taC/ta	4/18	1	2	FACETS	0.713	0.665	0.762	0.713	0.665	0.762	SUBCLONAL	1	TRUE	1	0.63	2		749	1047	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721043	176721043	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	218	475	0	ENST00000439151.2:c.6674C>T	p.Pro2225Leu	p.P2225L	ENST00000439151	NM_022455.4	2225	cCa/cTa	23/23	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.63	2		475	649	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057648	180057648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	336	939	1	ENST00000261937.6:c.307G>A	p.Ala103Thr	p.A103T	ENST00000261937	NM_182925.4	103	Gcc/Acc	3/30	1	2	FACETS	0.902	0.853	0.952	0.902	0.853	0.952	CLONAL	1	TRUE	1	0.63	2		940	1182	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20486941	20486941	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	203	418	0	ENST00000346618.3:c.906A>C	p.Gln302His	p.Q302H	ENST00000346618	NM_001949.4	302	caA/caC	5/7	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.63	2		418	568	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26046024	26046024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	118	333	0	ENST00000540144.1:c.386G>A	p.Arg129His	p.R129H	ENST00000540144	NM_003531.2	129	cGt/cAt	1/1	1	2	FACETS	0.714	0.647	0.784	0.714	0.647	0.784	SUBCLONAL	1	TRUE	1	0.63	2		333	525	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056436	26056436	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs748991637	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	111	250	0	ENST00000343677.2:c.221A>G	p.Glu74Gly	p.E74G	ENST00000343677	NM_005319.3	74	gAg/gGg	1/1	1	2	FACETS	0.885	0.803	0.971	0.885	0.803	0.971	CLONAL	1	TRUE	1	0.63	2		250	398	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910398	29910398	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	264	637	2	ENST00000376809.5:c.68G>A	p.Trp23Ter	p.W23*	ENST00000376809	NM_002116.7	23	tGg/tAg	1/8	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.63	2		639	750	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673051	30673051	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	316	821	0	ENST00000376406.3:c.3909del	p.Lys1304SerfsTer57	p.K1304Sfs*57	ENST00000376406	NM_014641.2	1303	ccC/cc	10/15	1	2	FACETS	0.946	0.894	1	0.946	0.894	1	CLONAL	1	TRUE	1	0.63	2		821	1060	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169044	32169044	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	245	841	0	ENST00000375023.3:c.3989G>T	p.Arg1330Met	p.R1330M	ENST00000375023	NM_004557.3	1330	aGg/aTg	22/30	1	2	FACETS	0.757	0.707	0.807	0.757	0.707	0.807	SUBCLONAL	1	TRUE	1	0.63	2		841	1028	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180367	32180367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1382129029	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	296	808	1	ENST00000375023.3:c.2564G>A	p.Arg855His	p.R855H	ENST00000375023	NM_004557.3	855	cGc/cAc	17/30	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.63	2		809	935	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797248	32797248	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	82	971	0	ENST00000374899.4:c.1861C>A	p.Leu621Ile	p.L621I	ENST00000374899	NM_018833.2	621	Ctt/Att	11/12	1	2	FACETS	0.202	0.177	0.229	0.202	0.177	0.229	SUBCLONAL	1	TRUE	1	0.63	2		971	1290	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32814934	32814934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	337	826	0	ENST00000354258.4:c.2131G>A	p.Val711Met	p.V711M	ENST00000354258	NM_000593.5	711	Gtg/Atg	10/11	1	2	FACETS	0.956	0.905	1	0.956	0.905	1	CLONAL	1	TRUE	1	0.63	2		826	1119	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793759	89793759	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	54	509	0	ENST00000336032.3:c.828G>T	p.Lys276Asn	p.K276N	ENST00000336032	NM_006813.2	276	aaG/aaT	2/2	1	2	FACETS	0.219	0.187	0.256	0.219	0.187	0.256	SUBCLONAL	1	TRUE	1	0.63	2		509	781	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647519	117647519	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	200	597	0	ENST00000368508.3:c.5425G>T	p.Gly1809Ter	p.G1809*	ENST00000368508	NM_002944.2	1809	Gga/Tga	33/43	1	2	FACETS	0.989	0.921	1	0.989	0.921	1	CLONAL	1	TRUE	1	0.63	2		597	642	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714484	117714484	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1360638449	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	137	362	0	ENST00000368508.3:c.1165G>A	p.Val389Ile	p.V389I	ENST00000368508	NM_002944.2	389	Gta/Ata	11/43	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.63	2		362	412	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192429	138192429	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	124	387	1	ENST00000237289.4:c.65G>T	p.Arg22Leu	p.R22L	ENST00000237289	NM_001270507.1	22	cGg/cTg	2/9	1	2	FACETS	0.789	0.718	0.863	0.789	0.718	0.863	SUBCLONAL	1	TRUE	1	0.63	2		388	499	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192530	138192530	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	234	572	0	ENST00000237289.4:c.169del	p.Cys57ValfsTer39	p.C57Vfs*39	ENST00000237289	NM_001270507.1	56	Ttt/tt	2/9	1	2	FACETS	0.918	0.859	0.979	0.918	0.859	0.979	CLONAL	1	TRUE	1	0.63	2		572	809	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099599	157099599	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1279864049	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	37	134	0	ENST00000346085.5:c.536T>C	p.Leu179Pro	p.L179P	ENST00000346085	NM_020732.3	179	cTg/cCg	1/20	1	2	FACETS	0.625	0.521	0.738	0.625	0.521	0.738	SUBCLONAL	1	TRUE	1	0.63	2		134	188	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099602	157099602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	73	131	1	ENST00000346085.5:c.539G>A	p.Ser180Asn	p.S180N	ENST00000346085	NM_020732.3	180	aGc/aAc	1/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.63	2		132	196	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521942	157521942	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	54	595	0	ENST00000346085.5:c.4214A>G	p.Asn1405Ser	p.N1405S	ENST00000346085	NM_020732.3	1405	aAc/aGc	18/20	1	2	FACETS	0.233	0.198	0.271	0.233	0.198	0.271	SUBCLONAL	1	TRUE	1	0.63	2		595	735	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528039	157528039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	260	582	0	ENST00000346085.5:c.5764G>A	p.Glu1922Lys	p.E1922K	ENST00000346085	NM_020732.3	1922	Gag/Aag	20/20	1	2	FACETS	0.97	0.911	1	0.97	0.911	1	CLONAL	1	TRUE	1	0.63	2		582	851	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6439761	6439761	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	48	557	0	ENST00000356142.4:c.287T>G	p.Val96Gly	p.V96G	ENST00000356142	NM_018890.3	96	gTg/gGg	5/7	1	2	FACETS	0.185	0.156	0.218	0.185	0.156	0.218	SUBCLONAL	1	TRUE	1	0.63	2		557	822	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268009	55268009	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	229	586	0	ENST00000275493.2:c.2849G>T	p.Cys950Phe	p.C950F	ENST00000275493	NM_005228.3	950	tGc/tTc	24/28	1	2	FACETS	0.912	0.853	0.973	0.912	0.853	0.973	CLONAL	1	TRUE	1	0.63	2		586	797	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509469	106509469	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	279	754	0	ENST00000359195.3:c.1463C>A	p.Ser488Tyr	p.S488Y	ENST00000359195	NM_002649.2	488	tCt/tAt	2/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.63	2		754	871	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526692	106526692	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	206	535	0	ENST00000359195.3:c.2985G>A	p.Met995Ile	p.M995I	ENST00000359195	NM_002649.2	995	atG/atA	10/11	1	2	FACETS	0.937	0.873	1	0.937	0.873	1	CLONAL	1	TRUE	1	0.63	2		535	698	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339192	116339192	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	164	366	0	ENST00000397752.3:c.54G>T	p.Leu18Phe	p.L18F	ENST00000397752	NM_000245.2	18	ttG/ttT	2/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.63	2		366	503	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395482	116395482	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	51	527	1	ENST00000397752.3:c.1775G>T	p.Arg592Met	p.R592M	ENST00000397752	NM_000245.2	592	aGg/aTg	6/21	1	2	FACETS	0.273	0.232	0.319	0.273	0.232	0.319	SUBCLONAL	1	TRUE	1	0.63	2		528	592	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829255	128829255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1327220746	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	310	936	0	ENST00000249373.3:c.263C>T	p.Thr88Ile	p.T88I	ENST00000249373	NM_005631.4	88	aCc/aTc	1/12	1	2	FACETS	0.913	0.861	0.966	0.913	0.861	0.966	CLONAL	1	TRUE	1	0.63	2		936	1078	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843236	128843237	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1248200595	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	297	772	0	ENST00000249373.3:c.349dup	p.Arg117ProfsTer19	p.R117Pfs*19	ENST00000249373	NM_005631.4	115	gcc/gCcc	2/12	1	2	FACETS	0.97	0.915	1	0.97	0.915	1	CLONAL	1	TRUE	1	0.63	2		772	972	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843374	128843374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772755154	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	280	684	0	ENST00000249373.3:c.481C>T	p.Arg161Trp	p.R161W	ENST00000249373	NM_005631.4	161	Cgg/Tgg	2/12	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.63	2		684	861	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481439	140481439	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	248	626	0	ENST00000288602.6:c.1369A>G	p.Ile457Val	p.I457V	ENST00000288602	NM_004333.4	457	Att/Gtt	11/18	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.63	2		626	732	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848667	151848667	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	20	282	0	ENST00000262189.6:c.12527-1G>T		p.X4176_splice	ENST00000262189	NM_170606.2	4176			1	2	FACETS	0.173	0.131	0.221	0.173	0.131	0.221	SUBCLONAL	1	TRUE	1	0.63	2		282	368	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859851	151859851	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	106	317	0	ENST00000262189.6:c.10811del	p.Lys3604ArgfsTer26	p.K3604Rfs*26	ENST00000262189	NM_170606.2	3604	aAg/ag	43/59	1	2	FACETS	0.801	0.723	0.883	0.801	0.723	0.883	CLONAL	1	TRUE	1	0.63	2		317	420	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151871220	151871220	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	200	459	0	ENST00000262189.6:c.9370A>C	p.Ser3124Arg	p.S3124R	ENST00000262189	NM_170606.2	3124	Agc/Cgc	39/59	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.63	2		459	621	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879054	151879054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	228	646	1	ENST00000262189.6:c.5891C>T	p.Ala1964Val	p.A1964V	ENST00000262189	NM_170606.2	1964	gCa/gTa	36/59	1	2	FACETS	0.954	0.892	1	0.954	0.892	1	CLONAL	1	TRUE	1	0.63	2		647	759	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879445	151879445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	186	509	0	ENST00000262189.6:c.5500C>T	p.Pro1834Ser	p.P1834S	ENST00000262189	NM_170606.2	1834	Cca/Tca	36/59	1	2	FACETS	0.867	0.804	0.932	0.867	0.804	0.932	CLONAL	1	TRUE	1	0.63	2		509	681	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151919086	151919086	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	136	417	0	ENST00000262189.6:c.3499G>T	p.Asp1167Tyr	p.D1167Y	ENST00000262189	NM_170606.2	1167	Gac/Tac	22/59	1	2	FACETS	0.741	0.676	0.808	0.741	0.676	0.808	SUBCLONAL	1	TRUE	1	0.63	2		417	583	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945017	151945017	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	23	163	0	ENST00000262189.6:c.2502A>T	p.Lys834Asn	p.K834N	ENST00000262189	NM_170606.2	834	aaA/aaT	14/59	1	2	FACETS	0.245	0.191	0.307	0.245	0.191	0.307	SUBCLONAL	1	TRUE	1	0.63	2		163	298	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38148065	38148065	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	384	970	2	ENST00000317025.8:c.3046G>T	p.Val1016Leu	p.V1016L	ENST00000317025	NM_023034.1	1016	Gtg/Ttg	17/24	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.63	2		972	1176	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162276	38162276	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	174	427	0	ENST00000317025.8:c.2441-1G>T		p.X814_splice	ENST00000317025	NM_023034.1	814			1	2	FACETS	0.973	0.901	1	0.973	0.901	1	CLONAL	1	TRUE	1	0.63	2		427	568	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271223	38271223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	300	811	0	ENST00000425967.3:c.2485C>T	p.His829Tyr	p.H829Y	ENST00000425967	NM_001174067.1	829	Cat/Tat	19/19	1	2	FACETS	0.974	0.919	1	0.974	0.919	1	CLONAL	1	TRUE	1	0.63	2		811	978	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922496	56922496	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	161	502	0	ENST00000519728.1:c.1366C>A	p.Leu456Met	p.L456M	ENST00000519728	NM_002350.3	456	Ctg/Atg	13/13	1	2	FACETS	0.743	0.683	0.805	0.743	0.683	0.805	SUBCLONAL	1	TRUE	1	0.63	2		502	688	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931866	68931866	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	202	881	0	ENST00000288368.4:c.296C>A	p.Pro99His	p.P99H	ENST00000288368	NM_024870.2	99	cCt/cAt	3/40	1	2	FACETS	0.686	0.636	0.738	0.686	0.636	0.738	SUBCLONAL	1	TRUE	1	0.63	2		881	935	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942855	68942855	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	301	860	2	ENST00000288368.4:c.667G>T	p.Val223Phe	p.V223F	ENST00000288368	NM_024870.2	223	Gtt/Ttt	6/40	1	2	FACETS	0.969	0.914	1	0.969	0.914	1	CLONAL	1	TRUE	1	0.63	2		862	986	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69050712	69050713	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	134	538	0	ENST00000288368.4:c.4051dup	p.Tyr1351LeufsTer3	p.Y1351Lfs*3	ENST00000288368	NM_024870.2	1349	-/T	33/40	1	2	FACETS	0.725	0.661	0.791	0.725	0.661	0.791	SUBCLONAL	1	TRUE	1	0.63	2		538	587	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866576	117866576	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	45	642	2	ENST00000297338.2:c.1069A>T	p.Thr357Ser	p.T357S	ENST00000297338	NM_006265.2	357	Acc/Tcc	9/14	1	2	FACETS	0.188	0.157	0.222	0.188	0.157	0.222	SUBCLONAL	1	TRUE	1	0.63	2		644	760	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750811	128750811	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758629773	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	290	694	0	ENST00000377970.2:c.348G>A	p.Met116Ile	p.M116I	ENST00000377970	NM_002467.4	116	atG/atA	2/3	1	2	FACETS	0.983	0.926	1	0.983	0.926	1	CLONAL	1	TRUE	1	0.63	2		694	937	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740373	145740373	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1277433427	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	416	1069	0	ENST00000428558.2:c.1567A>G	p.Ser523Gly	p.S523G	ENST00000428558	NM_004260.3	523	Agc/Ggc	9/22	1	2	FACETS	0.946	0.9	0.993	0.946	0.9	0.993	CLONAL	1	TRUE	1	0.63	2		1069	1396	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741442	145741442	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1264	78	1112	0	ENST00000428558.2:c.1061T>C	p.Val354Ala	p.V354A	ENST00000428558	NM_004260.3	354	gTa/gCa	5/22	1	2	FACETS	0.185	0.161	0.21	0.185	0.161	0.21	SUBCLONAL	1	TRUE	1	0.63	2		1112	1342	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484326	8484326	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs780209225	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	214	599	0	ENST00000356435.5:c.3206A>G	p.Gln1069Arg	p.Q1069R	ENST00000356435		1069	cAg/cGg	19/35	1	2	FACETS	0.841	0.783	0.9	0.841	0.783	0.9	CLONAL	1	TRUE	1	0.63	2		599	808	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169492	27169492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	182	545	0	ENST00000380036.4:c.493G>A	p.Val165Met	p.V165M	ENST00000380036	NM_000459.3	165	Gtg/Atg	4/23	1	2	FACETS	0.893	0.827	0.961	0.893	0.827	0.961	CLONAL	1	TRUE	1	0.63	2		545	647	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206664	27206664	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	283	648	1	ENST00000380036.4:c.2449C>A	p.Pro817Thr	p.P817T	ENST00000380036	NM_000459.3	817	Cca/Aca	15/23	1	2	FACETS	0.948	0.892	1	0.948	0.892	1	CLONAL	1	TRUE	1	0.63	2		649	948	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97888853	97888853	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1354711465	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	230	713	0	ENST00000289081.3:c.854C>T	p.Ala285Val	p.A285V	ENST00000289081	NM_000136.2	285	gCc/gTc	9/15	1	2	FACETS	0.773	0.722	0.827	0.773	0.722	0.827	SUBCLONAL	1	TRUE	1	0.63	2		713	944	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250046	110250046	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	162	698	2	ENST00000374672.4:c.629C>A	p.Pro210Gln	p.P210Q	ENST00000374672	NM_004235.4	210	cCg/cAg	3/5	1	2	FACETS	0.764	0.703	0.827	0.764	0.703	0.827	SUBCLONAL	1	TRUE	1	0.63	2		700	673	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738240	133738240	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	338	676	0	ENST00000318560.5:c.640C>T	p.His214Tyr	p.H214Y	ENST00000318560	NM_005157.4	214	Cat/Tat	4/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.63	2		676	1024	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760165	133760165	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	260	699	0	ENST00000318560.5:c.2488C>A	p.Leu830Ile	p.L830I	ENST00000318560	NM_005157.4	830	Ctc/Atc	11/11	1	2	FACETS	0.977	0.918	1	0.977	0.918	1	CLONAL	1	TRUE	1	0.63	2		699	845	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771768	135771768	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	78	937	0	ENST00000298552.3:c.3349C>A	p.Leu1117Ile	p.L1117I	ENST00000298552	NM_001162426.1	1117	Cta/Ata	23/23	1	2	FACETS	0.219	0.191	0.249	0.219	0.191	0.249	SUBCLONAL	1	TRUE	1	0.63	2		937	1132	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772893	135772894	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	242	727	0	ENST00000298552.3:c.2729dup	p.Leu910PhefsTer40	p.L910Ffs*40	ENST00000298552	NM_001162426.1	910	ttg/ttTg	21/23	1	2	FACETS	0.752	0.703	0.803	0.752	0.703	0.803	SUBCLONAL	1	TRUE	1	0.63	2		727	1021	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772943	135772943	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	160	509	0	ENST00000298552.3:c.2680C>A	p.His894Asn	p.H894N	ENST00000298552	NM_001162426.1	894	Cat/Aat	21/23	1	2	FACETS	0.726	0.667	0.787	0.726	0.667	0.787	SUBCLONAL	1	TRUE	1	0.63	2		509	700	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779070	135779070	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	164	450	0	ENST00000298552.3:c.2176G>T	p.Ala726Ser	p.A726S	ENST00000298552	NM_001162426.1	726	Gca/Tca	17/23	1	2	FACETS	0.75	0.691	0.812	0.75	0.691	0.812	SUBCLONAL	1	TRUE	1	0.63	2		450	694	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135804249	135804249	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	172	390	0	ENST00000298552.3:c.11A>G	p.Gln4Arg	p.Q4R	ENST00000298552	NM_001162426.1	4	cAa/cGa	3/23	1	2	FACETS	0.963	0.891	1	0.963	0.891	1	CLONAL	1	TRUE	1	0.63	2		390	567	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328377	137328377	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	366	933	2	ENST00000481739.1:c.1306C>A	p.Leu436Ile	p.L436I	ENST00000481739	NM_002957.4	436	Ctc/Atc	10/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.63	2		935	1146	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396482	139396482	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	353	932	0	ENST00000277541.6:c.5443del	p.Asp1815ThrfsTer72	p.D1815Tfs*72	ENST00000277541	NM_017617.3	1815	Gac/ac	29/34	1	2	FACETS	0.953	0.903	1	0.953	0.903	1	CLONAL	1	TRUE	1	0.63	2		932	1176	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402523	139402523	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769854763	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	381	754	0	ENST00000277541.6:c.3394C>T	p.Arg1132Cys	p.R1132C	ENST00000277541	NM_017617.3	1132	Cgc/Tgc	21/34	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.63	2		754	1140	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413948	139413948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	414	967	0	ENST00000277541.6:c.812C>T	p.Ala271Val	p.A271V	ENST00000277541	NM_017617.3	271	gCc/gTc	5/34	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.63	2		967	1297	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15838410	15838410	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	227	289	0	ENST00000307771.7:c.908C>A	p.Pro303His	p.P303H	ENST00000307771	NM_005089.3	303	cCc/cAc	10/11	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.63	1		289	377	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15840932	15840932	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	18	219	0	ENST00000307771.7:c.1016T>G	p.Phe339Cys	p.F339C	ENST00000307771	NM_005089.3	339	tTc/tGc	11/11	1	1	FACETS	0.154	0.116	0.199	0.154	0.116	0.199	SUBCLONAL	1	TRUE	0	0.63	1		219	254	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20150318	20150318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	163	295	0	ENST00000379607.5:c.319G>A	p.Gly107Ser	p.G107S	ENST00000379607	NM_001412.3	107	Ggc/Agc	5/7	1	1	FACETS	0.821	0.761	0.881	0.821	0.761	0.881	CLONAL	1	TRUE	0	0.63	1		295	432	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922277	39922277	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	192	196	0	ENST00000378444.4:c.3895A>G	p.Thr1299Ala	p.T1299A	ENST00000378444	NM_001123385.1	1299	Acc/Gcc	9/15	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.63	1		196	312	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247467	53247467	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	271	279	0	ENST00000375401.3:c.342T>A	p.Ser114Arg	p.S114R	ENST00000375401	NM_004187.3	114	agT/agA	3/26	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.63	1		279	422	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344881	70344881	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	281	419	0	ENST00000374080.3:c.2111C>A	p.Pro704Gln	p.P704Q	ENST00000374080		704	cCa/cAa	15/45	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.63	1		419	437	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347301	70347301	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	170	280	0	ENST00000374080.3:c.2965T>C	p.Phe989Leu	p.F989L	ENST00000374080		989	Ttt/Ctt	21/45	1	1	FACETS	0.955	0.891	1	0.955	0.891	1	CLONAL	1	TRUE	0	0.63	1		280	387	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356444	70356444	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	429	484	0	ENST00000374080.3:c.5339A>G	p.Glu1780Gly	p.E1780G	ENST00000374080		1780	gAg/gGg	37/45	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.63	1		484	660	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918951	76918951	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	281	338	0	ENST00000373344.5:c.4040T>C	p.Val1347Ala	p.V1347A	ENST00000373344	NM_000489.3	1347	gTg/gCg	12/35	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.63	1		338	446	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	63	297	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.866	0.749	0.993	0.866	0.749	0.993	CLONAL	1	TRUE	1	0.232075651070725	2		297	627	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556119	29556120	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0015290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	21	191	0	ENST00000356175.3:c.2487_2488insTT	p.Asp830LeufsTer12	p.D830Lfs*12	ENST00000356175	NM_000267.3	829	tct/tcTTt	21/57	1	2	FACETS	0.854	0.66	1	0.854	0.66	1	CLONAL	1	TRUE	1	0.232075651070725	2		191	212	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670026	29670026	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0015290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	72	412	0	ENST00000356175.3:c.7000-1G>C		p.X2334_splice	ENST00000356175	NM_000267.3	2334			1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.232075651070725	2		412	524	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589582	67589583	+	inframe_insertion	In_Frame_Ins	INS	-	-	TACATGAATATAACACTCAGTTTCAAGAAAAAAGTCGAGAATATG	novel	NA	P-0015290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	30	510	0	ENST00000274335.5:c.1346_1390dup	p.Tyr463_Asp464insValHisGluTyrAsnThrGlnPheGlnGluLysSerArgGluTyr	p.Y463_D464insVHEYNTQFQEKSREY	ENST00000274335		449	tta/tTACATGAATATAACACTCAGTTTCAAGAAAAAAGTCGAGAATATGta	10/15	1	2	FACETS	0.54	0.434	0.66	0.54	0.434	0.66	SUBCLONAL	1	TRUE	1	0.232075651070725	2		510	479	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096161	2096161	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	49	965	0	ENST00000219066.1:c.346G>A	p.Glu116Lys	p.E116K	ENST00000219066	NM_002528.5	116	Gag/Aag	2/6	1	2	FACETS	0.849	0.719	0.993	0.849	0.719	0.993	CLONAL	1	TRUE	1	0.2	2		965	577	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865224	57865224	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	258	1040	0	ENST00000228682.2:c.2701T>A	p.Tyr901Asn	p.Y901N	ENST00000228682	NM_005269.2	901	Tat/Aat	12/12	NA	2	FACETS	1	0.955	1			1	INDETERMINATE	1	TRUE	NA	0.496624790960052	2		1040	1016	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286764	212286765	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0015294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	88	762	1	ENST00000342788.4:c.2931_2932delinsTT	p.Met977_Ala978delinsIleSer	p.M977_A978delinsIS	ENST00000342788	NM_005235.2	977	atGGct/atTTct	24/28	0.468763932737087	1	FACETS	0.418	0.37	0.468	0.418	0.37	0.468	SUBCLONAL	1	TRUE	0	0.496624790960052	1		763	638	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023161	150023206	+	frameshift_variant	Frame_Shift_Del	DEL	AATTTCTTGTAACATTTGCCGGCTACTGACAGTATAGTTACTGGCA	AATTTCTTGTAACATTTGCCGGCTACTGACAGTATAGTTACTGGCA	-	novel	NA	P-0015294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	255	916	0	ENST00000253339.5:c.57_102del	p.Ala20GlyfsTer20	p.A20Gfs*20	ENST00000253339		19	ccTGCCAGTAACTATACTGTCAGTAGCCGGCAAATGTTACAAGAAATT/cc	1/7	0.496624790960052	2	FACETS	0.784	0.739	0.83	0.784	0.739	0.83	SUBCLONAL	2	TRUE	0	0.496624790960052	2		916	655	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960210	151960210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761700904	NA	P-0015294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	116	289	0	ENST00000262189.6:c.1190C>T	p.Ser397Leu	p.S397L	ENST00000262189	NM_170606.2	397	tCg/tTg	9/59	0.496624790960052	3	FACETS	0.831	0.757	0.907	0.831	0.757	0.907	CLONAL	2	TRUE	1	0.496624790960052	3		289	351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579363	7579363	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	TTT	novel	NA	P-0015294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	314	1105	0	ENST00000269305.4:c.324delinsAAA	p.Phe109AsnfsTer15	p.F109Nfs*15	ENST00000269305	NM_001126112.2	108	ggT/ggAAA	4/11	0.359795654610534	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.496624790960052	1		1105	838	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0015295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	33	577	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.258	0.21	0.313	0.258	0.21	0.313	SUBCLONAL	1	FALSE	1	0.564642798655963	2		577	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0015295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	351	867	8	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.564642798655963	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	FALSE	0	0.564642798655963	1		875	725	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0015295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	175	699	1	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.295386576972432	1	FACETS	0.639	0.59	0.69	0.639	0.59	0.69	INDETERMINATE	1	FALSE	0	0.564642798655963	1		700	696	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0015295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	58	739	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.295386576972432	1	FACETS	0.387	0.334	0.445	0.387	0.334	0.445	INDETERMINATE	1	FALSE	0	0.564642798655963	1		739	381	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509436	106509436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200175951	NA	P-0015295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	56	880	2	ENST00000359195.3:c.1430G>A	p.Arg477His	p.R477H	ENST00000359195	NM_002649.2	477	cGt/cAt	2/11	0.232024660484975	3	FACETS	0.229	0.195	0.266	0.114	0.097	0.133	INDETERMINATE	1	FALSE	1	0.564642798655963	3		882	1113	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4388085	4388085	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	24	437	0	ENST00000261254.3:c.571G>C	p.Asp191His	p.D191H	ENST00000261254	NM_001759.3	191	Gac/Cac	3/5	1	2	FACETS	0.179	0.14	0.225	0.179	0.14	0.225	SUBCLONAL	1	FALSE	1	0.564642798655963	2		437	474	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250238	133250238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150032060	NA	P-0015295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	310	975	1	ENST00000320574.5:c.1282G>A	p.Ala428Thr	p.A428T	ENST00000320574	NM_006231.2	428	Gcc/Acc	13/49	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.564642798655963	2		976	1027	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562905	21562906	+	stop_gained	Nonsense_Mutation	DNP	GA	GA	TT	novel	NA	P-0015295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	423	1004	1	ENST00000382592.4:c.1013_1014delinsAA	p.Phe338Ter	p.F338*	ENST00000382592	NM_014572.2	338	tTC/tAA	4/8	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	FALSE	1	0.564642798655963	2		1005	1212	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24133968	24133968	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	258	646	2	ENST00000263121.7:c.119G>A	p.Arg40Gln	p.R40Q	ENST00000263121	NM_003073.3	40	cGa/cAa	2/9	0.33408488571175	1	FACETS	1	0.962	1	1	0.962	1	INDETERMINATE	1	FALSE	0	0.564642798655963	1		648	640	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245467	153245480	+	frameshift_variant	Frame_Shift_Del	DEL	TGAATGCAATTCCC	TGAATGCAATTCCC	-	novel	NA	P-0015295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	138	907	0	ENST00000281708.4:c.1711_1724del	p.Gly571HisfsTer29	p.G571Hfs*29	ENST00000281708	NM_033632.3	571	GGGAATTGCATTCAc/c	11/12	0.360643285822513	1	FACETS	0.618	0.564	0.673	0.618	0.564	0.673	SUBCLONAL	1	FALSE	0	0.564642798655963	1		907	568	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965600	93965600	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	38	885	0	ENST00000369303.4:c.2328T>G	p.Asp776Glu	p.D776E	ENST00000369303	NM_004440.3	776	gaT/gaG	13/17	1	2	FACETS	0.193	0.158	0.231	0.193	0.158	0.231	SUBCLONAL	1	FALSE	1	0.564642798655963	2		885	699	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101910062	101910062	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	84	417	0	ENST00000374994.4:c.1382G>C	p.Cys461Ser	p.C461S	ENST00000374994	NM_004612.2	461	tGt/tCt	8/9	1	2	FACETS	0.969	0.865	1	0.969	0.865	1	CLONAL	1	FALSE	1	0.564642798655963	2		417	307	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5207955	5207955	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1412878073	NA	P-0015296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	457	1027	2	ENST00000357368.4:c.5756G>A	p.Arg1919Gln	p.R1919Q	ENST00000357368	NM_002850.3	1919	cGg/cAg	37/38	0.421470992769101	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.431043703115657	2		1029	1060	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539090	187539090	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	69	743	1	ENST00000441802.2:c.8650C>T	p.Gln2884Ter	p.Q2884*	ENST00000441802	NM_005245.3	2884	Cag/Tag	10/27	0.322376330276615	0	FACETS	0.316	0.275	0.36			1	SUBCLONAL	1	TRUE	0	0.431043703115657	0		744	576	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599874	10599874	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	410	947	0	ENST00000171111.5:c.1702G>T	p.Val568Phe	p.V568F	ENST00000171111	NM_203500.1	568	Gtc/Ttc	5/6	0.421470992769101	2	FACETS	0.929	0.887	0.971	0.929	0.887	0.971	CLONAL	2	TRUE	0	0.431043703115657	2		947	1024	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180832	106180832	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	287	501	0	ENST00000380013.4:c.3860T>C	p.Phe1287Ser	p.F1287S	ENST00000380013	NM_001127208.2	1287	tTt/tCt	7/11	0.427375816729599	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.431043703115657	2		501	623	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729819	41729819	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	34	472	0	ENST00000242208.4:c.710C>A	p.Ser237Tyr	p.S237Y	ENST00000242208	NM_002192.2	237	tCc/tAc	3/3	0.431172883543183	4	FACETS	0.351	0.286	0.425	0.176	0.143	0.213	SUBCLONAL	1	TRUE	2	0.431043703115657	4		472	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	421	1020	0	ENST00000269305.4:c.469G>C	p.Val157Leu	p.V157L	ENST00000269305	NM_001126112.2	157	Gtc/Ctc	5/11	0.33061166933006	2	FACETS	0.931	0.889	0.973	0.931	0.889	0.973	CLONAL	2	TRUE	0	0.431043703115657	2		1020	1049	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625170	69625170	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	362	874	2	ENST00000334134.2:c.623C>A	p.Pro208His	p.P208H	ENST00000334134	NM_005247.2	208	cCc/cAc	3/3	0.411633769268594	3	FACETS	0.994	0.944	1	0.994	0.944	1	CLONAL	2	TRUE	1	0.431043703115657	3		876	1027	SUCCESS
EED	8726	MSKCC	GRCh37	11	85968629	85968629	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	127	565	0	ENST00000263360.6:c.625G>T	p.Val209Leu	p.V209L	ENST00000263360	NM_003797.3	209	Gta/Tta	6/12	0.411633769268594	3	FACETS	0.827	0.749	0.91	0.414	0.374	0.455	CLONAL	1	TRUE	1	0.431043703115657	3		565	866	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675099	40675099	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	226	1106	0	ENST00000249776.8:c.63G>T	p.Glu21Asp	p.E21D	ENST00000249776	NM_033286.3	21	gaG/gaT	1/9	0.253873295110705	1	FACETS	0.775	0.721	0.83	0.775	0.721	0.83	INDETERMINATE	1	TRUE	0	0.431043703115657	1		1106	1062	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961661	41961661	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	130	673	2	ENST00000219905.7:c.569G>T	p.Gly190Val	p.G190V	ENST00000219905	NM_001164273.1	190	gGg/gTg	2/24	0.253873295110705	1	FACETS	0.752	0.684	0.824	0.752	0.684	0.824	INDETERMINATE	1	TRUE	0	0.431043703115657	1		675	629	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041815	14041815	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	265	674	0	ENST00000311895.7:c.2362C>G	p.Leu788Val	p.L788V	ENST00000311895	NM_005236.2	788	Ctc/Gtc	11/11	0.431172883543183	4	FACETS	0.905	0.85	0.962			1	CLONAL	2	TRUE	NA	0.431043703115657	4		674	972	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961041	15961041	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	132	484	0	ENST00000268712.3:c.6179C>T	p.Thr2060Ile	p.T2060I	ENST00000268712	NM_006311.3	2060	aCa/aTa	40/46	0.33061166933006	2	FACETS	1	0.926	1	0.51	0.464	0.557	CLONAL	1	TRUE	0	0.431043703115657	2		484	601	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096964	11096964	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	418	941	0	ENST00000358026.2:c.458del	p.Pro153ArgfsTer150	p.P153Rfs*150	ENST00000358026	NM_001128849.1	152	gCc/gc	4/36	0.421470992769101	2	FACETS	0.999	0.955	1	0.999	0.955	1	CLONAL	2	TRUE	0	0.431043703115657	2		941	971	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727935	41727935	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	2411	764	0	ENST00000301178.4:c.560G>T	p.Gly187Val	p.G187V	ENST00000301178	NM_021913.4	187	gGc/gTc	4/20	0.431043703115657	14	FACETS	0.991	0.981	1			1	CLONAL	14	TRUE	NA	0.431043703115657	14		764	2892	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082832	16082832	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	23	70	0	ENST00000281043.3:c.646G>A	p.Gly216Ser	p.G216S	ENST00000281043	NM_005378.4	216	Ggc/Agc	2/3	0.234585477559458	3	FACETS	0.754	0.603	0.92	0.754	0.603	0.92	INDETERMINATE	2	TRUE	1	0.431043703115657	3		70	86	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306566	41306566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	147	871	0	ENST00000373198.4:c.1093C>T	p.Pro365Ser	p.P365S	ENST00000373198	NM_133170.3	365	Cca/Tca	7/32	0.234585477559458	3	FACETS	0.995	0.909	1	0.498	0.454	0.543	INDETERMINATE	1	TRUE	1	0.431043703115657	3		871	833	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627378	37627378	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	260	1131	2	ENST00000249071.6:c.341G>A	p.Gly114Asp	p.G114D	ENST00000249071	NM_002872.4	114	gGc/gAc	5/7	0.411633769268594	3	FACETS	1	0.97	1	0.531	0.496	0.567	CLONAL	1	TRUE	1	0.431043703115657	3		1133	1381	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598165	55598165	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	206	527	0	ENST00000288135.5:c.2361+1G>A		p.X787_splice	ENST00000288135	NM_000222.2	787			0.357740147594586	2	FACETS	0.943	0.883	1	0.943	0.883	1	CLONAL	2	TRUE	0	0.431043703115657	2		527	507	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201821	66201821	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	211	715	1	ENST00000273854.3:c.2681G>T	p.Gly894Val	p.G894V	ENST00000273854	NM_004439.5	894	gGc/gTc	16/18	0.357740147594586	2	FACETS	0.783	0.732	0.836	0.783	0.732	0.836	SUBCLONAL	2	TRUE	0	0.431043703115657	2		716	625	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056406	180056406	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	136	620	1	ENST00000261937.6:c.838C>A	p.Pro280Thr	p.P280T	ENST00000261937	NM_182925.4	280	Ccc/Acc	7/30	0.421470992769101	2	FACETS	0.989	0.902	1	0.495	0.451	0.54	CLONAL	1	TRUE	0	0.431043703115657	2		621	638	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197234	26197234	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	227	478	0	ENST00000356476.2:c.245A>T	p.Asp82Val	p.D82V	ENST00000356476		82	gAt/gTt	1/1	0.431172883543183	4	FACETS	0.93	0.869	0.993	0.93	0.869	0.993	CLONAL	2	TRUE	2	0.431043703115657	4		478	810	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138197234	138197234	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	116	574	0	ENST00000237289.4:c.736T>C	p.Tyr246His	p.Y246H	ENST00000237289	NM_001270507.1	246	Tac/Cac	5/9	0.421470992769101	2	FACETS	0.818	0.738	0.902	0.409	0.369	0.451	CLONAL	1	TRUE	0	0.431043703115657	2		574	658	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016354	150016354	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	146	567	3	ENST00000253339.5:c.352A>T	p.Met118Leu	p.M118L	ENST00000253339		118	Atg/Ttg	2/7	0.421470992769101	2	FACETS	0.972	0.889	1	0.486	0.444	0.529	CLONAL	1	TRUE	0	0.431043703115657	2		570	697	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	45	297	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.488703686321235	2		297	150	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468173	50468173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	14	719	2	ENST00000331340.3:c.1408C>T	p.Leu470Phe	p.L470F	ENST00000331340	NM_006060.4	470	Ctc/Ttc	8/8	0.488703686321235	3	FACETS	0.859	0.631	1	0.429	0.315	0.562	CLONAL	1	TRUE	1	0.488703686321235	3		721	83	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	265	780	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.208169061673431	2	FACETS	1	0.993	1	0.749	0.703	0.796	INDETERMINATE	1	TRUE	0	0.36	2		780	983	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812121	43812121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	159	418	0	ENST00000372470.3:c.986C>T	p.Pro329Leu	p.P329L	ENST00000372470	NM_005373.2	329	cCc/cTc	7/12	0.113404686190611	4	FACETS	0.839	0.771	0.91	0.839	0.771	0.91	INDETERMINATE	2	TRUE	2	0.36	4		418	716	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497663	120497663	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	69	300	0	ENST00000256646.2:c.2219G>C	p.Gly740Ala	p.G740A	ENST00000256646	NM_024408.3	740	gGa/gCa	13/34	0.113404686190611	4	FACETS	0.902	0.786	1	0.451	0.393	0.514	INDETERMINATE	1	TRUE	2	0.36	4		300	578	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843479	156843479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	165	510	0	ENST00000524377.1:c.905C>T	p.Pro302Leu	p.P302L	ENST00000524377	NM_002529.3	302	cCc/cTc	8/17	0.21919641792625	4	FACETS	1	0.984	1	0.647	0.593	0.702	CLONAL	1	TRUE	2	0.36	4		510	964	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845960	156845960	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	324	888	0	ENST00000524377.1:c.1590C>A	p.His530Gln	p.H530Q	ENST00000524377	NM_002529.3	530	caC/caA	13/17	0.21919641792625	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.36	4		888	1130	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246518364	246518364	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	108	515	0	ENST00000388985.4:c.197G>T	p.Arg66Leu	p.R66L	ENST00000388985		66	cGc/cTc	2/12	0.21919641792625	4	FACETS	0.921	0.826	1	0.46	0.413	0.511	CLONAL	1	TRUE	2	0.36	4		515	886	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115837	8115838	+	missense_variant	Missense_Mutation	DNP	GC	GC	TG	novel	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	230	732	1	ENST00000346208.3:c.1183_1184delinsTG	p.Ala395Cys	p.A395C	ENST00000346208		395	GCc/TGc	6/6	0.113404686190611	4	FACETS	0.77	0.717	0.824	0.77	0.717	0.824	INDETERMINATE	2	TRUE	2	0.36	4		733	1129	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332684	70332684	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	157	665	0	ENST00000373644.4:c.589G>C	p.Glu197Gln	p.E197Q	ENST00000373644	NM_030625.2	197	Gag/Cag	2/12	0.113404686190611	4	FACETS	1	0.984	1	0.651	0.596	0.708	INDETERMINATE	1	TRUE	2	0.36	4		665	911	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70441172	70441172	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs140933489	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	90	675	0	ENST00000373644.4:c.4841A>G	p.Asp1614Gly	p.D1614G	ENST00000373644	NM_030625.2	1614	gAt/gGt	9/12	0.113404686190611	4	FACETS	0.971	0.862	1	0.486	0.431	0.544	INDETERMINATE	1	TRUE	2	0.36	4		675	700	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94201004	94201004	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	55	432	0	ENST00000323929.3:c.1073C>T	p.Pro358Leu	p.P358L	ENST00000323929	NM_005591.3	358	cCa/cTa	10/20	0.113404686190611	4	FACETS	0.772	0.661	0.894	0.386	0.33	0.447	INDETERMINATE	1	TRUE	2	0.36	4		432	538	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865092	57865093	+	frameshift_variant	Frame_Shift_Ins	INS	CC	CC	TCT	novel	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	308	989	0	ENST00000228682.2:c.2569_2570delinsTCT	p.Pro857SerfsTer15	p.P857Sfs*15	ENST00000228682	NM_005269.2	857	CCc/TCTc	12/12	0.21919641792625	4	FACETS	0.82	0.772	0.87	0.82	0.772	0.87	CLONAL	2	TRUE	2	0.36	4		989	1419	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438394	110438394	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	38	106	0	ENST00000375856.3:c.7A>T	p.Ser3Cys	p.S3C	ENST00000375856	NM_003749.2	3	Agc/Tgc	1/2	0.21919641792625	4	FACETS	0.806	0.675	0.949	0.806	0.675	0.949	CLONAL	2	TRUE	2	0.36	4		106	178	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961436	41961438	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	TAG	TAG	AA	novel	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	171	415	1	ENST00000219905.7:c.344_346delinsAA	p.Leu115Ter	p.L115*	ENST00000219905	NM_001164273.1	115	tTAGat/tAAat	2/24	0.299076552340995	2	FACETS	0.776	0.717	0.837	0.776	0.717	0.837	SUBCLONAL	2	TRUE	0	0.36	2		416	612	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	368	462	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.299076552340995	2	FACETS	0.985	0.936	1	0.985	0.936	1	CLONAL	2	TRUE	0	0.36	2		462	1038	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	364667	364667	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	214	748	0	ENST00000262320.3:c.895G>C	p.Glu299Gln	p.E299Q	ENST00000262320	NM_003502.3	299	Gag/Cag	3/11	0.113404686190611	4	FACETS	0.778	0.723	0.835	0.778	0.723	0.835	INDETERMINATE	2	TRUE	2	0.36	4		748	1039	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663394	29663394	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	136	655	0	ENST00000356175.3:c.5987C>G	p.Thr1996Ser	p.T1996S	ENST00000356175	NM_000267.3	1996	aCc/aGc	40/57	0.258050081892422	4	FACETS	1	0.98	1	0.635	0.578	0.695	CLONAL	1	TRUE	2	0.36	4		655	809	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29701105	29701105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771006452	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	208	487	0	ENST00000356175.3:c.8389G>A	p.Ala2797Thr	p.A2797T	ENST00000356175	NM_000267.3	2797	Gca/Aca	57/57	0.258050081892422	4	FACETS	1	0.99	1	0.705	0.653	0.758	CLONAL	1	TRUE	2	0.36	4		487	1115	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118996	70118996	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1257	258	1043	0	ENST00000245479.2:c.568G>T	p.Glu190Ter	p.E190*	ENST00000245479	NM_000346.3	190	Gag/Tag	2/3	0.299076552340995	6	FACETS	0.814	0.76	0.869	0.407	0.38	0.435	CLONAL	2	TRUE	2	0.36	6		1043	1515	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207184	1207184	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	429	1004	0	ENST00000326873.7:c.272G>T	p.Gly91Val	p.G91V	ENST00000326873	NM_000455.4	91	gGg/gTg	1/10	0.259676944695983	2	FACETS	0.856	0.815	0.897	0.856	0.815	0.897	CLONAL	2	TRUE	0	0.36	2		1004	1392	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122679	7122679	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	137	897	0	ENST00000302850.5:c.3475G>T	p.Asp1159Tyr	p.D1159Y	ENST00000302850	NM_000208.2	1159	Gac/Tac	19/22	0.299076552340995	1	FACETS	0.691	0.628	0.757	0.691	0.628	0.757	SUBCLONAL	1	TRUE	0	0.36	1		897	903	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965365	25965365	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	249	694	1	ENST00000435504.4:c.3841G>T	p.Ala1281Ser	p.A1281S	ENST00000435504		1281	Gca/Tca	13/13	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.36	2		695	1059	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794941	242794942	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	108	905	0	ENST00000334409.5:c.267dup	p.Gly90ArgfsTer16	p.G90Rfs*16	ENST00000334409	NM_005018.2	89	-/C	2/5	1	2	FACETS	0.566	0.507	0.629	0.566	0.507	0.629	SUBCLONAL	1	TRUE	1	0.36	2		905	1060	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944463	40944463	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	154	539	0	ENST00000373198.4:c.2039C>A	p.Thr680Lys	p.T680K	ENST00000373198	NM_133170.3	680	aCa/aAa	12/32	1	2	FACETS	0.956	0.875	1	0.956	0.875	1	CLONAL	1	TRUE	1	0.36	2		539	895	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561876	55561876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	169	366	0	ENST00000288135.5:c.266C>T	p.Ala89Val	p.A89V	ENST00000288135	NM_000222.2	89	gCc/gTc	2/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.36	2		366	727	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539894	187539894	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	81	355	0	ENST00000441802.2:c.7846G>C	p.Val2616Leu	p.V2616L	ENST00000441802	NM_005245.3	2616	Gtt/Ctt	10/27	0.299076552340995	1	FACETS	0.722	0.638	0.812	0.722	0.638	0.812	SUBCLONAL	1	TRUE	0	0.36	1		355	511	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111758	56111758	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	20	35	0	ENST00000399503.3:c.358G>C	p.Gly120Arg	p.G120R	ENST00000399503	NM_005921.1	120	Ggc/Cgc	1/20	0.299076552340995	4	FACETS	0.994	0.781	1	0.994	0.781	1	CLONAL	2	TRUE	2	0.36	4		35	76	SUCCESS
APC	324	MSKCC	GRCh37	5	112174793	112174793	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	97	342	0	ENST00000257430.4:c.3502G>T	p.Glu1168Ter	p.E1168*	ENST00000257430	NM_000038.5	1168	Gaa/Taa	16/16	0.208169061673431	2	FACETS	1	0.976	1	0.654	0.587	0.724	INDETERMINATE	1	TRUE	0	0.36	2		342	412	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401537	401537	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	144	464	0	ENST00000380956.4:c.859C>A	p.Leu287Met	p.L287M	ENST00000380956	NM_001195286.1	287	Ctg/Atg	7/9	0.17185945016846	3	FACETS	1	0.975	1			1	INDETERMINATE	1	TRUE	NA	0.36	3		464	801	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184836	32184836	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	169	503	1	ENST00000375023.3:c.1747G>T	p.Gly583Trp	p.G583W	ENST00000375023	NM_004557.3	583	Ggg/Tgg	11/30	0.0597313272477327	3	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.36	3		504	773	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138630	37138630	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	318	457	0	ENST00000373509.5:c.164G>T	p.Gly55Val	p.G55V	ENST00000373509	NM_002648.3	55	gGc/gTc	2/6	0.257563153801449	4	FACETS	0.872	0.822	0.924	0.872	0.822	0.924	CLONAL	2	TRUE	2	0.36	4		457	1377	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553213	106553213	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	115	527	0	ENST00000369096.4:c.1178C>A	p.Ala393Glu	p.A393E	ENST00000369096	NM_001198.3	393	gCa/gAa	5/7	0.212142072346628	3	FACETS	0.763	0.686	0.845	0.382	0.343	0.423	INDETERMINATE	1	TRUE	1	0.36	3		527	988	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494190	140494190	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	302	820	0	ENST00000288602.6:c.1058A>C	p.His353Pro	p.H353P	ENST00000288602	NM_004333.4	353	cAt/cCt	8/18	0.200914142586704	3	FACETS	0.816	0.768	0.865	0.816	0.768	0.865	INDETERMINATE	2	TRUE	1	0.36	3		820	1213	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030882	69030882	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	T	novel	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	99	553	0	ENST00000288368.4:c.3421+3G>T		p.X1141_splice	ENST00000288368	NM_024870.2	1141			1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.36	2		553	522	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090454	5090454	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	54	366	0	ENST00000381652.3:c.2770A>T	p.Asn924Tyr	p.N924Y	ENST00000381652	NM_004972.3	924	Aat/Tat	21/25	0.212142072346628	3	FACETS	1	0.912	1	0.543	0.466	0.626	INDETERMINATE	1	TRUE	1	0.36	3		366	326	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507338	8507338	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	80	383	0	ENST00000356435.5:c.1640A>G	p.Tyr547Cys	p.Y547C	ENST00000356435		547	tAt/tGt	11/35	0.212142072346628	3	FACETS	0.938	0.827	1	0.469	0.413	0.529	INDETERMINATE	1	TRUE	1	0.36	3		383	559	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115838	8115838	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	230	1067	0	ENST00000346208.3:c.1184C>G	p.Ala395Gly	p.A395G	ENST00000346208		395	gCc/gGc	6/6	0.113404686190611	4	FACETS	0.77	0.717	0.825	0.77	0.717	0.825	INDETERMINATE	2	TRUE	2	0.36	4		1067	1128	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29579965	29579966	+	intron_variant	Intron	DEL	CA	CA	T	novel	NA	P-0015300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	70	443	0	ENST00000356175.3:c.4110+3828_4110+3829delinsT		p.*1370*	ENST00000356175	NM_000267.3	1374/2839			0.258050081892422	4	FACETS	0.944	0.824	1	0.472	0.412	0.537	CLONAL	1	TRUE	2	0.36	4		443	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	121	780	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.369485554085116	1	FACETS	0.836	0.757	0.919	0.836	0.757	0.919	CLONAL	1	TRUE	0	0.369485554085116	1		780	639	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812121	43812121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	101	418	0	ENST00000372470.3:c.986C>T	p.Pro329Leu	p.P329L	ENST00000372470	NM_005373.2	329	cCc/cTc	7/12	0.226088159386063	3	FACETS	0.751	0.676	0.831	0.751	0.676	0.831	SUBCLONAL	2	TRUE	1	0.369485554085116	3		418	431	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497663	120497663	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	45	300	0	ENST00000256646.2:c.2219G>C	p.Gly740Ala	p.G740A	ENST00000256646	NM_024408.3	740	gGa/gCa	13/34	1	2	FACETS	0.768	0.649	0.899	0.768	0.649	0.899	SUBCLONAL	1	TRUE	1	0.369485554085116	2		300	317	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843479	156843479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	94	510	0	ENST00000524377.1:c.905C>T	p.Pro302Leu	p.P302L	ENST00000524377	NM_002529.3	302	cCc/cTc	8/17	0.263529294445734	3	FACETS	0.952	0.848	1	0.476	0.424	0.532	CLONAL	1	TRUE	1	0.369485554085116	3		510	633	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845960	156845960	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	207	888	0	ENST00000524377.1:c.1590C>A	p.His530Gln	p.H530Q	ENST00000524377	NM_002529.3	530	caC/caA	13/17	0.263529294445734	3	FACETS	1	0.991	1	0.742	0.689	0.796	CLONAL	1	TRUE	1	0.369485554085116	3		888	895	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246518364	246518364	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	65	515	0	ENST00000388985.4:c.197G>T	p.Arg66Leu	p.R66L	ENST00000388985		66	cGc/cTc	2/12	0.263529294445734	3	FACETS	0.671	0.582	0.768	0.336	0.291	0.384	SUBCLONAL	1	TRUE	1	0.369485554085116	3		515	621	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115837	8115838	+	missense_variant	Missense_Mutation	DNP	GC	GC	TG	novel	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	59	732	1	ENST00000346208.3:c.1183_1184delinsTG	p.Ala395Cys	p.A395C	ENST00000346208		395	GCc/TGc	6/6	1	2	FACETS	0.501	0.431	0.578	0.501	0.431	0.578	SUBCLONAL	1	TRUE	1	0.369485554085116	2		733	637	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332684	70332684	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	56	665	0	ENST00000373644.4:c.589G>C	p.Glu197Gln	p.E197Q	ENST00000373644	NM_030625.2	197	Gag/Cag	2/12	1	2	FACETS	0.525	0.45	0.608	0.525	0.45	0.608	SUBCLONAL	1	TRUE	1	0.369485554085116	2		665	577	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70441172	70441172	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs140933489	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	75	675	0	ENST00000373644.4:c.4841A>G	p.Asp1614Gly	p.D1614G	ENST00000373644	NM_030625.2	1614	gAt/gGt	9/12	1	2	FACETS	0.846	0.743	0.955	0.846	0.743	0.955	CLONAL	1	TRUE	1	0.369485554085116	2		675	480	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94201004	94201004	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	47	432	0	ENST00000323929.3:c.1073C>T	p.Pro358Leu	p.P358L	ENST00000323929	NM_005591.3	358	cCa/cTa	10/20	1	2	FACETS	0.644	0.545	0.753	0.644	0.545	0.753	SUBCLONAL	1	TRUE	1	0.369485554085116	2		432	395	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865092	57865093	+	frameshift_variant	Frame_Shift_Ins	INS	CC	CC	TCT	novel	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	152	989	0	ENST00000228682.2:c.2569_2570delinsTCT	p.Pro857SerfsTer15	p.P857Sfs*15	ENST00000228682	NM_005269.2	857	CCc/TCTc	12/12	1	2	FACETS	0.859	0.785	0.936	0.859	0.785	0.936	CLONAL	1	TRUE	1	0.369485554085116	2		989	958	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961436	41961438	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	TAG	TAG	AA	novel	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	89	415	1	ENST00000219905.7:c.344_346delinsAA	p.Leu115Ter	p.L115*	ENST00000219905	NM_001164273.1	115	tTAGat/tAAat	2/24	0.288087093418877	2	FACETS	1	0.978	1	0.706	0.632	0.784	CLONAL	1	TRUE	0	0.369485554085116	2		416	341	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	98	462	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.288087093418877	2	FACETS	1	0.98	1	0.698	0.628	0.772	CLONAL	1	TRUE	0	0.369485554085116	2		462	380	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	364667	364667	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	114	748	0	ENST00000262320.3:c.895G>C	p.Glu299Gln	p.E299Q	ENST00000262320	NM_003502.3	299	Gag/Cag	3/11	1	2	FACETS	0.846	0.763	0.935	0.846	0.763	0.935	CLONAL	1	TRUE	1	0.369485554085116	2		748	729	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663394	29663394	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	96	655	0	ENST00000356175.3:c.5987C>G	p.Thr1996Ser	p.T1996S	ENST00000356175	NM_000267.3	1996	aCc/aGc	40/57	0.263529294445734	3	FACETS	1	0.903	1	0.506	0.452	0.564	CLONAL	1	TRUE	1	0.369485554085116	3		655	608	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29701105	29701105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771006452	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	90	487	0	ENST00000356175.3:c.8389G>A	p.Ala2797Thr	p.A2797T	ENST00000356175	NM_000267.3	2797	Gca/Aca	57/57	0.263529294445734	3	FACETS	1	0.925	1	0.526	0.467	0.588	CLONAL	1	TRUE	1	0.369485554085116	3		487	549	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118996	70118996	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	159	1043	0	ENST00000245479.2:c.568G>T	p.Glu190Ter	p.E190*	ENST00000245479	NM_000346.3	190	Gag/Tag	2/3	0.263529294445734	3	FACETS	0.827	0.756	0.901	0.413	0.378	0.451	CLONAL	1	TRUE	1	0.369485554085116	3		1043	1233	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207184	1207184	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	318	1004	0	ENST00000326873.7:c.272G>T	p.Gly91Val	p.G91V	ENST00000326873	NM_000455.4	91	gGg/gTg	1/10	0.369485554085116	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.369485554085116	1		1004	1043	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122679	7122679	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	125	897	0	ENST00000302850.5:c.3475G>T	p.Asp1159Tyr	p.D1159Y	ENST00000302850	NM_000208.2	1159	Gac/Tac	19/22	0.369485554085116	1	FACETS	0.69	0.625	0.759	0.69	0.625	0.759	SUBCLONAL	1	TRUE	0	0.369485554085116	1		897	799	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965365	25965365	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	118	694	1	ENST00000435504.4:c.3841G>T	p.Ala1281Ser	p.A1281S	ENST00000435504		1281	Gca/Tca	13/13	1	2	FACETS	0.939	0.849	1	0.939	0.849	1	CLONAL	1	TRUE	1	0.369485554085116	2		695	680	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794941	242794942	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	115	905	0	ENST00000334409.5:c.267dup	p.Gly90ArgfsTer16	p.G90Rfs*16	ENST00000334409	NM_005018.2	89	-/C	2/5	1	2	FACETS	0.732	0.659	0.81	0.732	0.659	0.81	SUBCLONAL	1	TRUE	1	0.369485554085116	2		905	850	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944463	40944463	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	66	539	0	ENST00000373198.4:c.2039C>A	p.Thr680Lys	p.T680K	ENST00000373198	NM_133170.3	680	aCa/aAa	12/32	1	2	FACETS	0.667	0.579	0.761	0.667	0.579	0.761	SUBCLONAL	1	TRUE	1	0.369485554085116	2		539	536	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561876	55561876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	92	366	0	ENST00000288135.5:c.266C>T	p.Ala89Val	p.A89V	ENST00000288135	NM_000222.2	89	gCc/gTc	2/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.369485554085116	2		366	414	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539894	187539894	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	32	355	0	ENST00000441802.2:c.7846G>C	p.Val2616Leu	p.V2616L	ENST00000441802	NM_005245.3	2616	Gtt/Ctt	10/27	0.369485554085116	1	FACETS	0.547	0.446	0.66	0.547	0.446	0.66	SUBCLONAL	1	TRUE	0	0.369485554085116	1		355	258	SUCCESS
APC	324	MSKCC	GRCh37	5	112174793	112174793	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	29	342	0	ENST00000257430.4:c.3502G>T	p.Glu1168Ter	p.E1168*	ENST00000257430	NM_000038.5	1168	Gaa/Taa	16/16	0.369485554085116	1	FACETS	0.435	0.35	0.532	0.435	0.35	0.532	SUBCLONAL	1	TRUE	0	0.369485554085116	1		342	294	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401537	401537	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	69	464	0	ENST00000380956.4:c.859C>A	p.Leu287Met	p.L287M	ENST00000380956	NM_001195286.1	287	Ctg/Atg	7/9	1	2	FACETS	0.79	0.689	0.897	0.79	0.689	0.897	SUBCLONAL	1	TRUE	1	0.369485554085116	2		464	473	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184836	32184836	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	74	503	1	ENST00000375023.3:c.1747G>T	p.Gly583Trp	p.G583W	ENST00000375023	NM_004557.3	583	Ggg/Tgg	11/30	1	2	FACETS	0.94	0.827	1	0.94	0.827	1	CLONAL	1	TRUE	1	0.369485554085116	2		504	426	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138630	37138630	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	96	457	0	ENST00000373509.5:c.164G>T	p.Gly55Val	p.G55V	ENST00000373509	NM_002648.3	55	gGc/gTc	2/6	1	2	FACETS	0.846	0.755	0.943	0.846	0.755	0.943	CLONAL	1	TRUE	1	0.369485554085116	2		457	614	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553213	106553213	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	78	527	0	ENST00000369096.4:c.1178C>A	p.Ala393Glu	p.A393E	ENST00000369096	NM_001198.3	393	gCa/gAa	5/7	1	2	FACETS	0.801	0.705	0.904	0.801	0.705	0.904	CLONAL	1	TRUE	1	0.369485554085116	2		527	527	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494190	140494190	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	139	820	0	ENST00000288602.6:c.1058A>C	p.His353Pro	p.H353P	ENST00000288602	NM_004333.4	353	cAt/cCt	8/18	1	2	FACETS	0.891	0.812	0.975	0.891	0.812	0.975	CLONAL	1	TRUE	1	0.369485554085116	2		820	844	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090454	5090454	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	25	366	0	ENST00000381652.3:c.2770A>T	p.Asn924Tyr	p.N924Y	ENST00000381652	NM_004972.3	924	Aat/Tat	21/25	1	2	FACETS	0.629	0.499	0.778	0.629	0.499	0.778	SUBCLONAL	1	TRUE	1	0.369485554085116	2		366	215	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507338	8507338	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	50	383	0	ENST00000356435.5:c.1640A>G	p.Tyr547Cys	p.Y547C	ENST00000356435		547	tAt/tGt	11/35	1	2	FACETS	0.78	0.664	0.906	0.78	0.664	0.906	CLONAL	1	TRUE	1	0.369485554085116	2		383	347	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29579965	29579966	+	intron_variant	Intron	DEL	CA	CA	T	novel	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	63	443	0	ENST00000356175.3:c.4110+3828_4110+3829delinsT		p.*1370*	ENST00000356175	NM_000267.3	1374/2839			0.263529294445734	3	FACETS	1	0.944	1	0.582	0.506	0.663	CLONAL	1	TRUE	1	0.369485554085116	3		443	347	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259409	16259409	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	37	349	0	ENST00000375759.3:c.6674A>G	p.Asp2225Gly	p.D2225G	ENST00000375759	NM_015001.2	2225	gAc/gGc	11/15	0.226088159386063	3	FACETS	0.561	0.462	0.671	0.28	0.231	0.336	SUBCLONAL	1	TRUE	1	0.369485554085116	3		349	423	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352521	89352521	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	55	592	0	ENST00000301030.4:c.818T>G	p.Val273Gly	p.V273G	ENST00000301030	NM_001256183.1	273	gTg/gGg	8/13	1	2	FACETS	0.427	0.365	0.496	0.427	0.365	0.496	SUBCLONAL	1	TRUE	1	0.369485554085116	2		592	697	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139787	55139787	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	41	551	1	ENST00000257290.5:c.1448C>A	p.Thr483Asn	p.T483N	ENST00000257290	NM_006206.4	483	aCc/aAc	10/23	1	2	FACETS	0.351	0.292	0.418	0.351	0.292	0.418	SUBCLONAL	1	TRUE	1	0.369485554085116	2		552	632	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143352375	143352376	+	missense_variant	Missense_Mutation	DNP	TG	TG	CT	novel	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	43	727	0	ENST00000262992.4:c.37_38delinsAG	p.Gln13Arg	p.Q13R	ENST00000262992	NM_001101669.1	13	CAg/AGg	2/24	0.183074998330506	4	FACETS	0.403	0.336	0.478			1	INDETERMINATE	1	TRUE	NA	0.369485554085116	4		727	790	SUCCESS
AR	367	MSKCC	GRCh37	X	66941712	66941712	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	55	657	1	ENST00000374690.3:c.2356G>T	p.Val786Phe	p.V786F	ENST00000374690	NM_000044.3	786	Gtc/Ttc	6/8	0.369485554085116	1	FACETS	0.401	0.342	0.464	0.401	0.342	0.464	SUBCLONAL	1	TRUE	0	0.369485554085116	1		658	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0015301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	312	812	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.520628958563493	2	FACETS	0.975	0.93	1	0.975	0.93	1	CLONAL	2	TRUE	0	0.539379305073564	2		813	593	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394684	394684	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758258839	NA	P-0015301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	123	882	0	ENST00000399788.2:c.5011C>T	p.Pro1671Ser	p.P1671S	ENST00000399788	NM_001042603.1	1671	Cca/Tca	28/28	0.539379305073564	7	FACETS	0.842	0.759	0.93	0.168	0.151	0.186	CLONAL	1	TRUE	2	0.539379305073564	7		882	1272	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942749	15942749	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0015302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	45	569	0	ENST00000268712.3:c.6953C>G	p.Ser2318Ter	p.S2318*	ENST00000268712	NM_006311.3	2318	tCa/tGa	44/46	0.192308031457575	3	FACETS	0.881	0.74	1	0.294	0.246	0.346	CLONAL	1	FALSE	0	0.192308031457575	3		569	582	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106003	8106003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	59	567	1	ENST00000346208.3:c.823C>T	p.Arg275Trp	p.R275W	ENST00000346208		275	Cgg/Tgg	4/6	NA	2	FACETS	1	0.95	1			1	INDETERMINATE	1	FALSE	NA	0.192308031457575	2		568	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0015302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	309	914	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.192308031457575	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	FALSE	0	0.192308031457575	3		914	1016	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0015303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	230	336	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.704440233291463	2		336	644	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0015303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	408	861	2	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.704440233291463	2		863	1103	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438542	52438542	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	373	889	0	ENST00000460680.1:c.1177C>T	p.Gln393Ter	p.Q393*	ENST00000460680	NM_004656.3	393	Cag/Tag	12/17	0.704440233291463	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.704440233291463	1		889	649	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817720	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	249	604	1	ENST00000262367.5:c.3250dup	p.Ile1084AsnfsTer3	p.I1084Nfs*3	ENST00000262367	NM_004380.2	1084	atc/aAtc		1	2	FACETS	0.933	0.876	0.991	0.933	0.876	0.991	CLONAL	1	TRUE	1	0.704440233291463	2		605	758	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266079	41266079	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	230	528	0	ENST00000349496.5:c.76C>T	p.Gln26Ter	p.Q26*	ENST00000349496	NM_001904.3	26	Cag/Tag	3/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.704440233291463	2		528	600	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950099	44950099	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	220	709	0	ENST00000377967.4:c.3868G>T	p.Glu1290Ter	p.E1290*	ENST00000377967	NM_021140.2	1290	Gaa/Taa	26/29	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.704440233291463	2		709	577	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	116	297	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.551378155964063	2		297	399	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351208	89351208	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	196	441	0	ENST00000301030.4:c.1742C>G	p.Ser581Cys	p.S581C	ENST00000301030	NM_001256183.1	581	tCt/tGt	9/13	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.551378155964063	2		441	697	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245515	41245515	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555590634	NA	P-0015310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	223	753	3	ENST00000357654.3:c.2033C>T	p.Ala678Val	p.A678V	ENST00000357654	NM_007294.3	678	gCc/gTc	10/23	1	2	FACETS	0.946	0.882	1	0.946	0.882	1	CLONAL	1	TRUE	1	0.551378155964063	2		756	855	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015312-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	261	722	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.523299303019805	2	FACETS	0.986	0.935	1	0.986	0.935	1	CLONAL	2	TRUE	0	0.523299303019805	2		722	506	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213546	36213546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1280247669	NA	P-0015312-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	228	1029	3	ENST00000222270.7:c.2648G>A	p.Arg883Gln	p.R883Q	ENST00000222270	NM_014727.1	883	cGg/cAg	5/37	0.281871519456854	1	FACETS	0.871	0.814	0.928	0.871	0.814	0.928	INDETERMINATE	1	TRUE	0	0.523299303019805	1		1032	739	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0015321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	160	342	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.776	0.713	0.843	0.776	0.713	0.843	SUBCLONAL	1	TRUE	1	0.531798387794273	2		342	775	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527666	103527666	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs373426451	NA	P-0015324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	44	325	0	ENST00000355739.4:c.2974C>T	p.Arg992Ter	p.R992*	ENST00000355739	NM_000123.3	992	Cga/Tga	15/15	1	2	FACETS	0.366	0.307	0.432	0.366	0.307	0.432	SUBCLONAL	1	TRUE	1	0.51	2		325	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0015325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	363	726	0	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	0.318142783359185	5	FACETS	0.925	0.88	0.97			1	CLONAL	4	TRUE	NA	0.318142783359185	5		726	911	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	198	548	0	ENST00000263967.3:c.333G>T	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaT	2/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.716307428166716	2		548	520	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0015326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	242	592	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.716307428166716	1	FACETS	0.979	0.928	1	0.979	0.928	1	CLONAL	1	TRUE	0	0.716307428166716	1		592	443	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457910	69457910	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs753115532	NA	P-0015326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	440	604	0	ENST00000227507.2:c.310G>T	p.Ala104Ser	p.A104S	ENST00000227507	NM_053056.2	104	Gcc/Tcc	2/5	0.423137897695485	1	FACETS	0.833	0.798	0.867	0.833	0.798	0.867	INDETERMINATE	1	TRUE	0	0.716307428166716	1		604	947	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962570	100962570	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	269	575	0	ENST00000325455.5:c.1827C>A	p.Cys609Ter	p.C609*	ENST00000325455	NM_001202474.3	609	tgC/tgA	3/8	0.39080102284694	1	FACETS	0.661	0.623	0.7	0.661	0.623	0.7	INDETERMINATE	1	TRUE	0	0.716307428166716	1		575	729	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998862	100998862	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	252	790	0	ENST00000325455.5:c.940G>T	p.Ala314Ser	p.A314S	ENST00000325455	NM_001202474.3	314	Gcc/Tcc	1/8	0.39080102284694	1	FACETS	0.412	0.385	0.44	0.412	0.385	0.44	INDETERMINATE	1	TRUE	0	0.716307428166716	1		790	1096	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919283	48919283	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0015326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	250	370	0	ENST00000267163.4:c.448A>T	p.Arg150Ter	p.R150*	ENST00000267163	NM_000321.2	150	Aga/Tga	4/27	0.678576046167	2	FACETS	0.948	0.907	0.988	0.948	0.907	0.988	CLONAL	2	TRUE	0	0.716307428166716	2		370	368	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422130	81422130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	365	523	0	ENST00000298171.2:c.106G>A	p.Asp36Asn	p.D36N	ENST00000298171	NM_000369.2	36	Gac/Aac	1/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.716307428166716	2		523	1015	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934578	NA	P-0015326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	410	636	0	ENST00000269305.4:c.524G>T	p.Arg175Leu	p.R175L	ENST00000269305	NM_001126112.2	175	cGc/cTc	5/11	0.716307428166716	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.716307428166716	1		636	682	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388038	81388038	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	194	669	0	ENST00000222390.5:c.337G>T	p.Gly113Cys	p.G113C	ENST00000222390	NM_000601.4	113	Ggc/Tgc	3/18	1	2	FACETS	0.91	0.847	0.975	0.91	0.847	0.975	CLONAL	1	TRUE	1	0.716307428166716	2		669	595	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502190	157502190	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs387907144	NA	P-0015327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	90	491	1	ENST00000346085.5:c.3223C>T	p.Arg1075Ter	p.R1075*	ENST00000346085	NM_020732.3	1075	Cga/Tga	12/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.256043263681465	2		492	550	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	127	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.989	0.897	1	0.989	0.897	1	CLONAL	1	TRUE	1	0.376075651638679	2		493	683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0015328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	216	747	1	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	0.376075651638679	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.376075651638679	1		748	924	SUCCESS
APC	324	MSKCC	GRCh37	5	112157623	112157625	+	inframe_deletion	In_Frame_Del	DEL	CTG	CTG	-	novel	NA	P-0015328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	110	574	0	ENST00000257430.4:c.1346_1348del	p.Ala449del	p.A449del	ENST00000257430	NM_000038.5	448	cCTGct/cct	11/16	0.376075651638679	1	FACETS	0.845	0.762	0.933	0.845	0.762	0.933	CLONAL	1	TRUE	0	0.376075651638679	1		574	562	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891537	151891537	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	115	552	0	ENST00000262189.6:c.4495del	p.Met1499TrpfsTer64	p.M1499Wfs*64	ENST00000262189	NM_170606.2	1499	Atg/tg	29/59	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.376075651638679	2		552	581	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	236	297	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.474171545331361	2		297	908	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445091	89445091	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	182	620	3	ENST00000336596.2:c.1411G>A	p.Glu471Lys	p.E471K	ENST00000336596	NM_005233.5	471	Gag/Aag	6/17	1	2	FACETS	0.866	0.8	0.936	0.866	0.8	0.936	CLONAL	1	TRUE	1	0.474171545331361	2		623	886	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0015329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	283	641	3	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.474171545331361	1	FACETS	0.971	0.914	1	0.971	0.914	1	CLONAL	1	TRUE	0	0.474171545331361	1		644	938	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105526	27105527	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	173	567	0	ENST00000324856.7:c.5138dup	p.Glu1714ArgfsTer13	p.E1714Rfs*13	ENST00000324856	NM_006015.4	1713	cta/cTta	20/20	0.231317506524464	1	FACETS	0.793	0.732	0.856	0.793	0.732	0.856	INDETERMINATE	1	TRUE	0	0.474171545331361	1		567	702	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262206	115262206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769519003	NA	P-0015329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	123	589	0	ENST00000438362.2:c.2348G>A	p.Arg783Gln	p.R783Q	ENST00000438362	NM_001242891.1	783	cGa/cAa	18/20	0.231317506524464	1	FACETS	0.41	0.37	0.452	0.41	0.37	0.452	INDETERMINATE	1	TRUE	0	0.474171545331361	1		589	965	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030378	49030378	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0015329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	185	565	0	ENST00000267163.4:c.1853C>G	p.Ser618Ter	p.S618*	ENST00000267163	NM_000321.2	618	tCa/tGa	19/27	0.474171545331361	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.474171545331361	1		565	551	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650671	67650671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	282	614	0	ENST00000264010.4:c.976G>A	p.Asp326Asn	p.D326N	ENST00000264010	NM_006565.3	326	Gac/Aac	5/12	0.474171545331361	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.474171545331361	1		614	906	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772199	68772199	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	310	754	0	ENST00000261769.5:c.49-1G>A		p.X17_splice	ENST00000261769	NM_004360.3	17			0.474171545331361	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.474171545331361	1		754	980	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627640	37627640	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	336	929	0	ENST00000447079.4:c.1555G>C	p.Glu519Gln	p.E519Q	ENST00000447079	NM_015083.1	519	Gaa/Caa	2/14	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.474171545331361	2		929	1386	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229543	5229543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	151	248	0	ENST00000357368.4:c.2308G>A	p.Gly770Arg	p.G770R	ENST00000357368	NM_002850.3	770	Ggg/Agg	15/38	0.474171545331361	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.474171545331361	1		248	471	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259037	89259037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1487544308	NA	P-0015329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	99	326	0	ENST00000336596.2:c.181C>T	p.His61Tyr	p.H61Y	ENST00000336596	NM_005233.5	61	Cat/Tat	3/17	1	2	FACETS	0.951	0.854	1	0.951	0.854	1	CLONAL	1	TRUE	1	0.474171545331361	2		326	439	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592076	67592076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs515726149	NA	P-0015329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	178	481	0	ENST00000274335.5:c.1892G>A	p.Arg631Gln	p.R631Q	ENST00000274335		631	cGa/cAa	14/15	0.474171545331361	1	FACETS	0.918	0.85	0.988	0.918	0.85	0.988	CLONAL	1	TRUE	0	0.474171545331361	1		481	624	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157454193	157454193	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	296	693	0	ENST00000346085.5:c.2403G>C	p.Gln801His	p.Q801H	ENST00000346085	NM_020732.3	801	caG/caC	8/20	0.474171545331361	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.474171545331361	1		693	913	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92244495	92244495	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	154	417	0	ENST00000265734.4:c.940C>A	p.Leu314Met	p.L314M	ENST00000265734	NM_001259.6	314	Ctg/Atg	8/8	1	2	FACETS	0.87	0.797	0.945	0.87	0.797	0.945	CLONAL	1	TRUE	1	0.474171545331361	2		417	747	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371854	55371854	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	136	283	0	ENST00000297316.4:c.544C>T	p.Gln182Ter	p.Q182*	ENST00000297316	NM_022454.3	182	Cag/Tag	2/2	1	2	FACETS	0.898	0.819	0.98	0.898	0.819	0.98	CLONAL	1	TRUE	1	0.474171545331361	2		283	639	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27218780	27218780	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	284	737	0	ENST00000380036.4:c.3068C>G	p.Ser1023Cys	p.S1023C	ENST00000380036	NM_000459.3	1023	tCc/tGc	20/23	NA	2	FACETS	0.983	0.923	1			1	INDETERMINATE	1	TRUE	NA	0.474171545331361	2		737	1219	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240455	98240455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	202	540	0	ENST00000331920.6:c.1229G>A	p.Ser410Asn	p.S410N	ENST00000331920	NM_000264.3	410	aGt/aAt	9/24	1	2	FACETS	0.992	0.921	1	0.992	0.921	1	CLONAL	1	TRUE	1	0.474171545331361	2		540	859	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0015331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	365	407	0	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	0.4088930068944	2	FACETS	0.991	0.946	1	0.991	0.946	1	CLONAL	2	TRUE	0	0.482324021248675	2		407	764	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011144	12011144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	158	458	0	ENST00000353533.5:c.551C>T	p.Ser184Leu	p.S184L	ENST00000353533	NM_003010.3	184	tCg/tTg	5/11	0.4088930068944	2	FACETS	0.767	0.71	0.825	0.767	0.71	0.825	SUBCLONAL	2	TRUE	0	0.482324021248675	2		458	427	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111110	193111110	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	124	474	0	ENST00000367435.3:c.643G>T	p.Asp215Tyr	p.D215Y	ENST00000367435	NM_024529.4	215	Gat/Tat	7/17	0.413602196669836	3	FACETS	1	0.979	1	0.422	0.384	0.462	CLONAL	1	TRUE	0	0.482324021248675	3		474	504	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912693	100912693	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	35	559	0	ENST00000325455.5:c.2629C>T	p.Leu877Phe	p.L877F	ENST00000325455	NM_001202474.3	877	Ctt/Ttt	7/8	0.437283496893938	2	FACETS	0.293	0.239	0.353	0.146	0.119	0.177	SUBCLONAL	1	TRUE	0	0.482324021248675	2		559	496	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437980	49437980	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	A	novel	NA	P-0015331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	93	512	0	ENST00000301067.7:c.5188+3G>T		p.X1730_splice	ENST00000301067	NM_003482.3	1730			0.127044717287701	6	FACETS	1	0.922	1			1	INDETERMINATE	1	TRUE	NA	0.482324021248675	6		512	724	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354402	354402	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	430	773	2	ENST00000262320.3:c.1156C>T	p.Gln386Ter	p.Q386*	ENST00000262320	NM_003502.3	386	Cag/Tag	5/11	NA	2	FACETS	1	0.961	1			1	INDETERMINATE	2	TRUE	NA	0.482324021248675	2		775	889	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72833971	72833971	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	236	636	0	ENST00000268489.5:c.3922G>A	p.Asp1308Asn	p.D1308N	ENST00000268489	NM_006885.3	1308	Gat/Aat	8/10	0.200824863282379	4	FACETS	0.897	0.839	0.956	0.897	0.839	0.956	INDETERMINATE	2	TRUE	2	0.482324021248675	4		636	809	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325820	30325820	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0015331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	176	421	0	ENST00000322652.5:c.2018C>G	p.Ser673Ter	p.S673*	ENST00000322652	NM_015355.2	673	tCa/tGa	16/16	0.371631275373871	4	FACETS	0.852	0.788	0.918	0.852	0.788	0.918	CLONAL	2	TRUE	2	0.482324021248675	4		421	635	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025887	48025887	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1558659230	NA	P-0015331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	61	528	0	ENST00000234420.5:c.765G>C	p.Glu255Asp	p.E255D	ENST00000234420	NM_000179.2	255	gaG/gaC	4/10	0.200824863282379	4	FACETS	0.47	0.405	0.542	0.235	0.202	0.271	INDETERMINATE	1	TRUE	2	0.482324021248675	4		528	797	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026947	48026947	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1426910114	NA	P-0015331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	50	438	0	ENST00000234420.5:c.1825C>G	p.Leu609Val	p.L609V	ENST00000234420	NM_000179.2	609	Cta/Gta	4/10	0.200824863282379	4	FACETS	0.52	0.441	0.607	0.26	0.22	0.304	INDETERMINATE	1	TRUE	2	0.482324021248675	4		438	591	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426696	212426696	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	129	687	0	ENST00000342788.4:c.2419T>A	p.Tyr807Asn	p.Y807N	ENST00000342788	NM_005235.2	807	Tat/Aat	20/28	1	2	FACETS	0.701	0.636	0.769	0.701	0.636	0.769	SUBCLONAL	1	TRUE	1	0.482324021248675	2		687	763	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368143	31368143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201455430	NA	P-0015331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	247	664	0	ENST00000328111.2:c.14C>T	p.Thr5Ile	p.T5I	ENST00000328111	NM_006892.3	5	aCc/aTc	2/23	0.228384954396749	5	FACETS	0.945	0.885	1	0.63	0.59	0.672	INDETERMINATE	2	TRUE	2	0.482324021248675	5		664	934	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564712	55564712	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs772105682	NA	P-0015331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	47	566	0	ENST00000288135.5:c.600C>A	p.Phe200Leu	p.F200L	ENST00000288135	NM_000222.2	200	ttC/ttA	3/21	0.428330905846492	2	FACETS	0.284	0.239	0.334	0.142	0.119	0.167	SUBCLONAL	1	TRUE	0	0.482324021248675	2		566	687	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31504677	31504678	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATGCTGTGC	novel	NA	P-0015331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	609	779	0	ENST00000344624.3:c.1644_1652dup	p.Ser550_Ile551insMetHisSer	p.S550_I551insMHS	ENST00000344624		551	att/atGCACAGCATt	8/33	0.482324021248675	6	FACETS	1	0.978	1			1	CLONAL	3	TRUE	NA	0.482324021248675	6		779	1617	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526541	31526541	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1330	195	835	1	ENST00000344624.3:c.499C>G	p.Gln167Glu	p.Q167E	ENST00000344624		167	Cag/Gag	2/33	0.482324021248675	6	FACETS	1	0.951	1			1	CLONAL	1	TRUE	NA	0.482324021248675	6		836	1525	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961034	79961034	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	99	714	0	ENST00000265081.6:c.431C>G	p.Ser144Cys	p.S144C	ENST00000265081	NM_002439.4	144	tCt/tGt	3/24	0.4088930068944	2	FACETS	0.625	0.558	0.695	0.312	0.279	0.348	SUBCLONAL	1	TRUE	0	0.482324021248675	2		714	657	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139156	37139156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772592158	NA	P-0015331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	87	472	0	ENST00000373509.5:c.496C>T	p.Arg166Cys	p.R166C	ENST00000373509	NM_002648.3	166	Cgc/Tgc	4/6	0.467041388811402	4	FACETS	0.666	0.589	0.749	0.333	0.294	0.375	SUBCLONAL	1	TRUE	2	0.482324021248675	4		472	803	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138197157	138197157	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0015331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	183	421	0	ENST00000237289.4:c.659C>G	p.Ser220Ter	p.S220*	ENST00000237289	NM_001270507.1	220	tCa/tGa	5/9	0.310224925707785	5	FACETS	0.997	0.924	1	0.399	0.369	0.429	CLONAL	2	TRUE	0	0.482324021248675	5		421	656	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227905	55227905	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	106	555	0	ENST00000275493.2:c.1372G>A	p.Asp458Asn	p.D458N	ENST00000275493	NM_005228.3	458	Gat/Aat	12/28	NA	2	FACETS	0.689	0.619	0.763			1	INDETERMINATE	1	TRUE	NA	0.482324021248675	2		555	638	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020555	69020555	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	85	571	0	ENST00000288368.4:c.2927C>G	p.Ser976Cys	p.S976C	ENST00000288368	NM_024870.2	976	tCt/tGt	24/40	0.163567605918818	4	FACETS	0.835	0.738	0.937	0.417	0.369	0.469	INDETERMINATE	1	TRUE	2	0.482324021248675	4		571	626	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0015332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	75	358	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	0.274282803834466	2		358	385	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0015332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	145	563	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	0.209875601832903	3	FACETS	0.867	0.793	0.945	0.867	0.793	0.945	CLONAL	2	TRUE	1	0.274282803834466	3		563	693	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137797	64137797	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	120	802	3	ENST00000334205.4:c.1898T>A	p.Phe633Tyr	p.F633Y	ENST00000334205	NM_003942.2	633	tTc/tAc	15/17	1	2	FACETS	0.941	0.849	1	0.941	0.849	1	CLONAL	1	TRUE	1	0.274282803834466	2		805	930	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041022	42041022	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	252	637	1	ENST00000219905.7:c.5400del	p.Leu1800PhefsTer38	p.L1800Ffs*38	ENST00000219905	NM_001164273.1	1800	ttA/tt	16/24	0.186549129498385	2	FACETS	0.868	0.816	0.92	1	0.991	1	CLONAL	3	TRUE	0	0.274282803834466	2		638	706	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351086	89351086	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	112	543	0	ENST00000301030.4:c.1864C>A	p.Leu622Met	p.L622M	ENST00000301030	NM_001256183.1	622	Ctg/Atg	9/13	1	2	FACETS	0.759	0.685	0.836	1	0.984	1	SUBCLONAL	2	TRUE	1	0.274282803834466	2		543	538	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155384	47155384	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	161	460	0	ENST00000409792.3:c.4697C>A	p.Ala1566Asp	p.A1566D	ENST00000409792	NM_014159.6	1566	gCt/gAt	5/21	0.0740690827848942	3	FACETS	1	0.983	1	1	0.983	1	INDETERMINATE	2	TRUE	1	0.274282803834466	3		460	543	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989717	15989717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777268103	NA	P-0015333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	52	312	0	ENST00000268712.3:c.3056C>T	p.Pro1019Leu	p.P1019L	ENST00000268712	NM_006311.3	1019	cCt/cTt	23/46	1	2	FACETS	0.45	0.383	0.522	0.45	0.383	0.522	SUBCLONAL	1	TRUE	1	0.510458172767723	2		312	453	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460527	149460527	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139635308	NA	P-0015333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	55	633	0	ENST00000286301.3:c.110C>T	p.Thr37Met	p.T37M	ENST00000286301	NM_005211.3	37	aCg/aTg	3/22	1	2	FACETS	0.273	0.232	0.317	0.273	0.232	0.317	SUBCLONAL	1	TRUE	1	0.510458172767723	2		633	790	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	597	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.595019509015977	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	1	0.595019509015977	4		493	1050	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156955	89156956	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	256	603	0	ENST00000336596.2:c.61dup	p.Glu21GlyfsTer9	p.E21Gfs*9	ENST00000336596	NM_005233.5	19	-/G	1/17	0.254446520824096	3	FACETS	0.791	0.744	0.838	0.791	0.744	0.838	INDETERMINATE	2	TRUE	1	0.595019509015977	3		603	706	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916636	178916636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	74	417	0	ENST00000263967.3:c.23G>A	p.Gly8Asp	p.G8D	ENST00000263967	NM_006218.2	8	gGt/gAt	2/21	0.254446520824096	3	FACETS	0.685	0.602	0.775	0.343	0.301	0.388	INDETERMINATE	1	TRUE	1	0.595019509015977	3		417	471	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593615	+	inframe_deletion	In_Frame_Del	DEL	AGTGGAAGGTTGTTG	AGTGGAAGGTTGTTG	-	novel	NA	P-0015335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	185	541	0	ENST00000288135.5:c.1669_1683del	p.Trp557_Glu561del	p.W557_E561del	ENST00000288135	NM_000222.2	556	cAGTGGAAGGTTGTTGag/cag	11/21	1	2	FACETS	0.647	0.599	0.696	0.647	0.599	0.696	SUBCLONAL	1	TRUE	1	0.813476976585055	2		541	703	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030467	49030486	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TCACTGTTTTATAAAAAAGG	TCACTGTTTTATAAAAAAGG	-	novel	NA	P-0015337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	305	512	0	ENST00000267163.4:c.1943_1960+2del		p.X648_splice	ENST00000267163	NM_000321.2	648		19/27	0.937926647941728	1	FACETS	0.951	0.926	0.975	0.951	0.926	0.975	CLONAL	1	TRUE	0	0.950546839676417	1		512	354	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095012	11095012	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	662	996	1	ENST00000358026.2:c.185G>T	p.Gly62Val	p.G62V	ENST00000358026	NM_001128849.1	62	gGa/gTa	2/36	0.950546839676417	1	FACETS	0.525	0.507	0.543	0.525	0.507	0.543	SUBCLONAL	1	TRUE	0	0.950546839676417	1		997	1393	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095026	11095026	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	647	1014	0	ENST00000358026.2:c.199G>A	p.Asp67Asn	p.D67N	ENST00000358026	NM_001128849.1	67	Gac/Aac	2/36	0.950546839676417	1	FACETS	0.524	0.506	0.543	0.524	0.506	0.543	SUBCLONAL	1	TRUE	0	0.950546839676417	1		1014	1362	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106934	11106934	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	677	883	0	ENST00000358026.2:c.1639G>C	p.Asp547His	p.D547H	ENST00000358026	NM_001128849.1	547	Gac/Cac	10/36	1	2	FACETS	0.992	0.959	1	0.992	0.959	1	CLONAL	1	TRUE	1	0.950546839676417	2		883	1436	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107189	11107189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750891894	NA	P-0015337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	485	624	0	ENST00000358026.2:c.1781G>A	p.Gly594Glu	p.G594E	ENST00000358026	NM_001128849.1	594	gGa/gAa	11/36	1	2	FACETS	0.955	0.917	0.994	0.955	0.917	0.994	CLONAL	1	TRUE	1	0.950546839676417	2		624	1068	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814273	76814278	+	inframe_deletion	In_Frame_Del	DEL	ATTCCT	ATTCCT	-	novel	NA	P-0015337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	392	548	0	ENST00000373344.5:c.6366_6371del	p.Gly2123_Ile2124del	p.G2123_I2124del	ENST00000373344	NM_000489.3	2122	ctAGGAATt/ctt	29/35	0.640649397956505	1	FACETS	0.717	0.691	0.742	0.717	0.691	0.742	SUBCLONAL	1	TRUE	0	0.950546839676417	1		548	604	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468501	89468501	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202059523	NA	P-0015339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	59	468	1	ENST00000336596.2:c.2035C>T	p.His679Tyr	p.H679Y	ENST00000336596	NM_005233.5	679	Cac/Tac	11/17	1	2	FACETS	0.577	0.496	0.665	0.577	0.496	0.665	SUBCLONAL	1	TRUE	1	0.34021414898309	2		469	601	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459558	50459558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	137	375	0	ENST00000331340.3:c.847C>T	p.Leu283Phe	p.L283F	ENST00000331340	NM_006060.4	283	Ctt/Ttt	7/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.34021414898309	2		375	632	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145629	11145629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	137	675	3	ENST00000358026.2:c.3991C>T	p.Pro1331Ser	p.P1331S	ENST00000358026	NM_001128849.1	1331	Ccc/Tcc	29/36	0.117489333946447	4	FACETS	1	0.957	1			1	INDETERMINATE	1	TRUE	NA	0.34021414898309	4		678	990	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615143	43615143	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	72	721	0	ENST00000355710.3:c.2557T>A	p.Ser853Thr	p.S853T	ENST00000355710	NM_020975.4	853	Tca/Aca	14/20	1	2	FACETS	0.544	0.474	0.619	0.544	0.474	0.619	SUBCLONAL	1	TRUE	1	0.34021414898309	2		721	778	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640525	3640526	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	128	724	1	ENST00000294008.3:c.3113_3114delinsAA	p.Gly1038Glu	p.G1038E	ENST00000294008	NM_032444.2	1038	gGG/gAA	12/15	0.117489333946447	4	FACETS	1	0.938	1			1	INDETERMINATE	1	TRUE	NA	0.34021414898309	4		725	963	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50784021	50784021	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	103	670	0	ENST00000398568.2:c.412G>A	p.Gly138Arg	p.G138R	ENST00000398568	NM_001042412.1	138	Ggg/Agg	3/18	1	2	FACETS	0.748	0.669	0.833	0.748	0.669	0.833	SUBCLONAL	1	TRUE	1	0.34021414898309	2		670	809	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55334501	55334501	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0015339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	226	413	0	ENST00000284073.2:c.103+2T>A		p.X35_splice	ENST00000284073	NM_138962.2	35			0.309802278350057	3	FACETS	0.908	0.852	0.964	1	0.991	1	CLONAL	3	TRUE	1	0.34021414898309	3		413	571	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867585	78867585	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	112	648	0	ENST00000306801.3:c.2321A>T	p.Asn774Ile	p.N774I	ENST00000306801	NM_020761.2	774	aAt/aTt	20/34	0.34021414898309	6	FACETS	0.823	0.738	0.914	0.137	0.123	0.153	CLONAL	1	TRUE	0	0.34021414898309	6		648	1344	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710534	40710534	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	81	607	0	ENST00000373198.4:c.4317G>A	p.Met1439Ile	p.M1439I	ENST00000373198	NM_133170.3	1439	atG/atA	31/32	0.34021414898309	1	FACETS	0.627	0.553	0.707	0.627	0.553	0.707	SUBCLONAL	1	TRUE	0	0.34021414898309	1		607	630	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752821	128752821	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	65	338	1	ENST00000377970.2:c.982C>T	p.Pro328Ser	p.P328S	ENST00000377970	NM_002467.4	328	Ccc/Tcc	3/3	0.289115353115598	3	FACETS	0.865	0.751	0.988	0.432	0.375	0.494	CLONAL	1	TRUE	1	0.34021414898309	3		339	517	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952070	76952070	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	182	233	0	ENST00000373344.5:c.365del	p.Pro122GlnfsTer5	p.P122Qfs*5	ENST00000373344	NM_000489.3	122	cCa/ca	5/35	0.228966357040033	2	FACETS	1	0.983	1			1	CLONAL	2	TRUE	NA	0.34021414898309	2		233	456	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80057396	80057396	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	114	508	0	ENST00000265081.6:c.1795G>A	p.Glu599Lys	p.E599K	ENST00000265081	NM_002439.4	599	Gaa/Aaa	13/24	0.169334566464819	5	FACETS	1	0.962	1	0.382	0.343	0.423	INDETERMINATE	1	TRUE	2	0.34021414898309	5		508	884	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195619	102195619	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758535139	NA	P-0015339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	161	505	0	ENST00000263464.3:c.379G>A	p.Gly127Ser	p.G127S	ENST00000263464	NM_001165.4	127	Ggt/Agt	2/9	0.34021414898309	6	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.34021414898309	6		505	1381	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685300	89685300	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs878853936	NA	P-0015340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	111	369	0	ENST00000371953.3:c.195C>A	p.Tyr65Ter	p.Y65*	ENST00000371953	NM_000314.4	65	taC/taA	3/9	0.580423947157332	1	FACETS	0.887	0.809	0.968	0.887	0.809	0.968	CLONAL	1	TRUE	0	0.580423947157332	1		369	306	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577330	64577333	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	rs587776841	NA	P-0015340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	191	678	0	ENST00000312049.6:c.249_252del	p.Ile85SerfsTer33	p.I85Sfs*33	ENST00000312049	NM_130799.2	83	ctGTCT/ct	2/10	0.580423947157332	1	FACETS	0.881	0.821	0.943	0.881	0.821	0.943	CLONAL	1	TRUE	0	0.580423947157332	1		678	530	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286530	33286530	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	216	556	0	ENST00000374542.5:c.2213A>T	p.Asp738Val	p.D738V	ENST00000374542	NM_001141970.1	738	gAc/gTc	8/8	0.555497211219036	1	FACETS	0.959	0.899	1	0.959	0.899	1	CLONAL	1	TRUE	0	0.580423947157332	1		556	551	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	364679	364679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373147968	NA	P-0015340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	101	698	0	ENST00000262320.3:c.883G>A	p.Gly295Arg	p.G295R	ENST00000262320	NM_003502.3	295	Gga/Aga	3/11	0.580423947157332	1	FACETS	0.472	0.423	0.524	0.472	0.423	0.524	SUBCLONAL	1	TRUE	0	0.580423947157332	1		698	523	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183762	10183771	+	frameshift_variant	Frame_Shift_Del	DEL	CAATCGCAGT	CAATCGCAGT	-	novel	NA	P-0015342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	182	722	0	ENST00000256474.2:c.232_241del	p.Asn78ArgfsTer78	p.N78Rfs*78	ENST00000256474	NM_000551.3	77	tgCAATCGCAGT/tg	1/3	0.493605549139157	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	0	0.493605549139157	1		722	539	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30664735	30664735	+	intron_variant	Intron	SNP	T	T	A	novel	NA	P-0015342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	67	561	1	ENST00000295754.5:c.94+16266T>A		p.*32*	ENST00000295754	NM_003242.5	47/592			0.493605549139157	1	FACETS	0.766	0.673	0.864	0.766	0.673	0.864	SUBCLONAL	1	FALSE	0	0.493605549139157	1		562	267	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668721	52668721	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	68	630	0	ENST00000394830.3:c.1198del	p.Gln400LysfsTer4	p.Q400Kfs*4	ENST00000394830	NM_018313.4	400	Caa/aa	12/30	0.493605549139157	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	0	0.493605549139157	1		630	159	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0015343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	145	840	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.24	2		842	1012	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931463	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622007	NA	P-0015345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	475	364	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	0.76972065450868	1		364	602	SUCCESS
AR	367	MSKCC	GRCh37	X	66943543	66943543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852581	NA	P-0015345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	286	280	7	ENST00000374690.3:c.2623C>T	p.His875Tyr	p.H875Y	ENST00000374690	NM_000044.3	875	Cat/Tat	8/8	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.76972065450868	1		287	375	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830064	72830064	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	417	692	0	ENST00000268489.5:c.6517G>T	p.Glu2173Ter	p.E2173*	ENST00000268489	NM_006885.3	2173	Gag/Tag	9/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.76972065450868	2		692	1068	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372161	55372161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200451706	NA	P-0015345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	156	666	0	ENST00000297316.4:c.851C>T	p.Pro284Leu	p.P284L	ENST00000297316	NM_022454.3	284	cCg/cTg	2/2	1	2	FACETS	0.427	0.391	0.465	0.427	0.391	0.465	SUBCLONAL	1	TRUE	1	0.76972065450868	2		666	949	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929273	44929288	+	frameshift_variant	Frame_Shift_Del	DEL	TGTGGGTACTGGAACC	TGTGGGTACTGGAACC	-	novel	NA	P-0015345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	448	444	0	ENST00000377967.4:c.2377_2392del	p.Gly793ThrfsTer69	p.G793Tfs*69	ENST00000377967	NM_021140.2	791	aaTGTGGGTACTGGAACC/aa	17/29	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.76972065450868	1		444	662	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0015346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	30	435	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.574	0.464	0.699	0.574	0.464	0.699	SUBCLONAL	1	TRUE	1	0.363972106743799	2		435	287	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934575	NA	P-0015346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	116	667	0	ENST00000269305.4:c.733G>C	p.Gly245Arg	p.G245R	ENST00000269305	NM_001126112.2	245	Ggc/Cgc	7/11	0.363972106743799	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.363972106743799	1		667	403	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951171	48951171	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587778846	NA	P-0015346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	68	502	0	ENST00000267163.4:c.1332+1G>A		p.X444_splice	ENST00000267163	NM_000321.2	444			0.363972106743799	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.363972106743799	1		502	275	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	189	297	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.944	0.878	1	0.944	0.878	1	CLONAL	1	TRUE	1	0.663757435908024	2		297	603	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264387	30264387	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	72	452	0	ENST00000322652.5:c.123del	p.Gly42AlafsTer30	p.G42Afs*30	ENST00000322652	NM_015355.2	41	tCc/tc	1/16	0.587166518631727	1	FACETS	0.283	0.247	0.321	0.283	0.247	0.321	SUBCLONAL	1	TRUE	0	0.663757435908024	1		452	513	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641212	23641212	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1060502794	NA	P-0015347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	325	658	0	ENST00000261584.4:c.2263T>C	p.Cys755Arg	p.C755R	ENST00000261584	NM_024675.3	755	Tgc/Cgc	5/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.663757435908024	2		658	956	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654787	29654787	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	215	408	0	ENST00000356175.3:c.5477del	p.Pro1826GlnfsTer16	p.P1826Qfs*16	ENST00000356175	NM_000267.3	1826	Cca/ca	37/57	0.587166518631727	1	FACETS	0.599	0.559	0.641	0.599	0.559	0.641	SUBCLONAL	1	TRUE	0	0.663757435908024	1		408	722	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662487	227662487	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	213	418	0	ENST00000305123.5:c.968C>T	p.Ser323Phe	p.S323F	ENST00000305123	NM_005544.2	323	tCc/tTc	1/2	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.663757435908024	2		418	632	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250047	53250047	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	339	702	0	ENST00000375401.3:c.202C>G	p.Arg68Gly	p.R68G	ENST00000375401	NM_004187.3	68	Cga/Gga	2/26	0.31600027333108	1	FACETS	0.661	0.626	0.696	0.661	0.626	0.696	INDETERMINATE	1	TRUE	0	0.663757435908024	1		702	1033	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0015348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	552	592	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.363746021917462	6	FACETS	1	0.986	1	1	0.986	1	CLONAL	4	TRUE	2	0.363746021917462	6		592	1248	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544630	65544630	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0015348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	211	471	0	ENST00000358664.4:c.295+1G>T		p.X99_splice	ENST00000358664	NM_002382.4	99			0.363746021917462	3	FACETS	1	0.973	1			1	CLONAL	2	TRUE	NA	0.363746021917462	3		471	636	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731136	162731136	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	230	609	2	ENST00000367921.3:c.991G>T	p.Ala331Ser	p.A331S	ENST00000367921	NM_006182.2	331	Gct/Tct	9/18	0.363746021917462	5	FACETS	0.984	0.918	1	0.656	0.612	0.702	CLONAL	2	TRUE	2	0.363746021917462	5		611	993	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163309268	163309268	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0015348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	299	486	1	ENST00000271452.3:c.606+1G>T		p.X202_splice	ENST00000271452	NM_145697.2	202			0.363746021917462	5	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	TRUE	2	0.363746021917462	5		487	820	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675391	241675391	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057521425	NA	P-0015348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	160	469	1	ENST00000366560.3:c.431G>T	p.Gly144Val	p.G144V	ENST00000366560	NM_000143.3	144	gGa/gTa	4/10	0.363746021917462	5	FACETS	0.792	0.727	0.861	0.528	0.484	0.574	SUBCLONAL	2	TRUE	2	0.363746021917462	5		470	858	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250217	133250217	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	262	588	0	ENST00000320574.5:c.1303G>T	p.Asp435Tyr	p.D435Y	ENST00000320574	NM_006231.2	435	Gat/Tat	13/49	0.356993065882818	2	FACETS	0.951	0.896	1	0.951	0.896	1	CLONAL	2	TRUE	0	0.363746021917462	2		588	757	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872359	35872359	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	125	567	0	ENST00000216797.5:c.544A>C	p.Asn182His	p.N182H	ENST00000216797	NM_020529.2	182	Aat/Cat	3/6	0.363746021917462	6	FACETS	1	0.905	1			1	CLONAL	1	TRUE	NA	0.363746021917462	6		567	1185	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0015348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	239	526	2	ENST00000269305.4:c.673-2A>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			NA	2	FACETS	0.969	0.91	1			1	INDETERMINATE	2	TRUE	NA	0.363746021917462	2		528	678	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166845	32166845	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	268	854	0	ENST00000375023.3:c.4393C>A	p.Leu1465Ile	p.L1465I	ENST00000375023	NM_004557.3	1465	Ctt/Att	24/30	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.363746021917462	2		854	983	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987294	2987294	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	250	598	0	ENST00000396946.4:c.135C>A	p.Tyr45Ter	p.Y45*	ENST00000396946	NM_032415.4	45	taC/taA	3/25	0.363746021917462	5	FACETS	0.925	0.864	0.987			1	CLONAL	2	TRUE	NA	0.363746021917462	5		598	1149	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069040	5069040	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	66	350	1	ENST00000381652.3:c.1345T>C	p.Tyr449His	p.Y449H	ENST00000381652	NM_004972.3	449	Tat/Cat	11/25	0.347498663409753	2	FACETS	0.894	0.779	1	0.447	0.389	0.509	CLONAL	1	TRUE	0	0.363746021917462	2		351	406	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805589	46805589	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	247	839	0	ENST00000290295.7:c.367C>G	p.Arg123Gly	p.R123G	ENST00000290295	NM_006361.5	123	Cgc/Ggc	1/2	0.31383715160741	4	FACETS	0.82	0.766	0.875	0.82	0.766	0.875	CLONAL	2	TRUE	2	0.363746021917462	4		839	1130	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846011	151846011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs183426496	NA	P-0015349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	80	566	0	ENST00000262189.6:c.13001G>A	p.Arg4334Gln	p.R4334Q	ENST00000262189	NM_170606.2	4334	cGg/cAg	52/59	0.313917804544484	3	FACETS	0.737	0.648	0.833	0.369	0.324	0.417	SUBCLONAL	1	TRUE	1	0.313917804544484	3		566	800	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105824	27105851	+	frameshift_variant	Frame_Shift_Del	DEL	TTCCAGTAAAGATCGTACAGAAGAATGA	TTCCAGTAAAGATCGTACAGAAGAATGA	-	novel	NA	P-0015349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	84	661	0	ENST00000324856.7:c.5436_5463del	p.Pro1813HisfsTer61	p.P1813Hfs*61	ENST00000324856	NM_006015.4	1812	cTTCCAGTAAAGATCGTACAGAAGAATGAt/ct	20/20	0.30220202800017	2	FACETS	0.661	0.583	0.744	0.33	0.291	0.372	SUBCLONAL	1	TRUE	0	0.313917804544484	2		661	810	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115862	8115863	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1619	375	728	0	ENST00000346208.3:c.1209dup	p.Ser404GlufsTer103	p.S404Efs*103	ENST00000346208		403	ctg/ctGg	6/6	0.313917804544484	5	FACETS	0.881	0.833	0.931			1	CLONAL	2	TRUE	NA	0.313917804544484	5		728	1994	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056224	26056224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs945973136	NA	P-0015349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	89	478	0	ENST00000343677.2:c.433G>A	p.Ala145Thr	p.A145T	ENST00000343677	NM_005319.3	145	Gca/Aca	1/1	0.289387259055317	4	FACETS	0.953	0.844	1	0.476	0.422	0.535	CLONAL	1	TRUE	2	0.313917804544484	4		478	782	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0015350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	174	493	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.263836105574719	4	FACETS	0.97	0.898	1			1	CLONAL	3	TRUE	NA	0.263836105574719	4		493	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0015350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	50	498	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	1	2	FACETS	0.955	0.812	1	0.955	0.812	1	CLONAL	1	TRUE	1	0.263836105574719	2		498	397	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111478	8111479	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0015351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	146	404	0	ENST00000346208.3:c.966dup	p.Thr323HisfsTer29	p.T323Hfs*29	ENST00000346208		322	acc/aCcc	5/6	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.453513775320399	2		404	572	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871039	12871040	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0015351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	34	225	1	ENST00000228872.4:c.267_268del	p.Tyr89Ter	p.Y89*	ENST00000228872	NM_004064.3	89	tAC/t	1/3	1	2	FACETS	0.42	0.343	0.506	0.42	0.343	0.506	SUBCLONAL	1	TRUE	1	0.453513775320399	2		226	357	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880984	37880985	+	inframe_insertion	In_Frame_Ins	INS	-	-	TACGTGATGGCT	rs397516977	NA	P-0015352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	119	468	0	ENST00000269571.5:c.2314_2325dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/TACGTGATGGCT	20/27	1	2	FACETS	0.838	0.757	0.925	0.838	0.757	0.925	CLONAL	1	FALSE	1	0.345346302247427	2		468	822	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424162	49424163	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0015352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	60	410	0	ENST00000301067.7:c.13899_13900delinsTT	p.Val4634Leu	p.V4634L	ENST00000301067	NM_003482.3	4633	tcGGtg/tcTTtg	42/54	1	2	FACETS	0.497	0.428	0.573	0.497	0.428	0.573	SUBCLONAL	1	FALSE	1	0.345346302247427	2		410	699	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877422	40877422	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	109	422	0	ENST00000373198.4:c.2274G>T	p.Lys758Asn	p.K758N	ENST00000373198	NM_133170.3	758	aaG/aaT	15/32	0.217226969976985	3	FACETS	0.815	0.731	0.905	0.408	0.365	0.453	CLONAL	1	FALSE	1	0.345346302247427	3		422	908	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891299	101891299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	65	569	1	ENST00000374994.4:c.260C>T	p.Ala87Val	p.A87V	ENST00000374994	NM_004612.2	87	gCa/gTa	2/9	1	2	FACETS	0.415	0.359	0.476	0.415	0.359	0.476	SUBCLONAL	1	FALSE	1	0.345346302247427	2		570	907	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372022	55372022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	390	254	2	ENST00000297316.4:c.712G>A	p.Ala238Thr	p.A238T	ENST00000297316	NM_022454.3	238	Gcc/Acc	2/2	0.561755961106742	14	FACETS	0.917	0.871	0.964			1	CLONAL	5	TRUE	NA	0.561755961106742	14		256	1323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882005	NA	P-0015353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	455	440	0	ENST00000269305.4:c.713G>C	p.Cys238Ser	p.C238S	ENST00000269305	NM_001126112.2	238	tGt/tCt	7/11	0.276559332486301	6	FACETS	0.932	0.905	0.959			1	INDETERMINATE	6	TRUE	NA	0.561755961106742	6		440	615	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274794	123274794	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913478	NA	P-0015353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	202	476	2	ENST00000358487.5:c.1124A>G	p.Tyr375Cys	p.Y375C	ENST00000358487	NM_000141.4	375	tAc/tGc	9/18	0.561755961106742	2	FACETS	0.951	0.897	1	0.951	0.897	1	CLONAL	2	TRUE	0	0.561755961106742	2		478	378	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0015355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	44	188	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.713	0.598	0.84	0.713	0.598	0.84	SUBCLONAL	1	TRUE	1	0.276097651571183	2		188	447	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226549222	226549222	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	29	246	1	ENST00000366794.5:c.2984C>A	p.Ala995Asp	p.A995D	ENST00000366794	NM_001618.3	995	gCt/gAt	23/23	0.276097651571183	4	FACETS	0.469	0.376	0.577	0.156	0.125	0.193	SUBCLONAL	1	TRUE	1	0.276097651571183	4		247	571	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484165	50484165	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	32	289	0	ENST00000394963.4:c.1015T>C	p.Cys339Arg	p.C339R	ENST00000394963	NM_003076.4	339	Tgt/Cgt	8/13	0.183817721201578	2	FACETS	0.444	0.36	0.54	0.222	0.18	0.27	SUBCLONAL	1	TRUE	0	0.276097651571183	2		289	522	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847307	68847307	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	82	328	0	ENST00000261769.5:c.1229del	p.Glu410GlyfsTer7	p.E410Gfs*7	ENST00000261769	NM_004360.3	410	gAg/gg	9/16	0.276097651571183	1	FACETS	0.992	0.877	1	0.992	0.877	1	CLONAL	1	TRUE	0	0.276097651571183	1		328	516	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118767	115118768	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	92	341	0	ENST00000257566.3:c.573dup	p.Ala192ArgfsTer35	p.A192Rfs*35	ENST00000257566	NM_016569.3	191	-/C	2/8	1	2	FACETS	0.926	0.827	1	0.926	0.827	1	CLONAL	1	TRUE	1	0.449465505232008	2		341	442	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631837	90631837	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	177	356	0	ENST00000330062.3:c.516G>T	p.Arg172Ser	p.R172S	ENST00000330062	NM_002168.2	172	agG/agT	4/11	0.177208326272876	1	FACETS	0.923	0.855	0.992	1	0.992	1	CLONAL	2	TRUE	0	0.285893448295934	1		356	575	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919735	50919735	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	222	520	1	ENST00000440232.2:c.2903G>A	p.Arg968His	p.R968H	ENST00000440232	NM_002691.3	968	cGc/cAc	23/27	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.285893448295934	2		521	672	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793188	33793188	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	25	102	0	ENST00000498907.2:c.133C>A	p.Pro45Thr	p.P45T	ENST00000498907	NM_004364.3	45	Cca/Aca	1/1	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.285893448295934	2		102	159	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539821	187539821	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1265407568	NA	P-0015357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	120	268	0	ENST00000441802.2:c.7919A>G	p.Glu2640Gly	p.E2640G	ENST00000441802	NM_005245.3	2640	gAa/gGa	10/27	1	2	FACETS	0.933	0.848	1	1	0.989	1	CLONAL	2	TRUE	1	0.285893448295934	2		268	450	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206941983	206941983	+	stop_lost	Nonstop_Mutation	SNP	A	A	T	novel	NA	P-0015358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	20	179	0	ENST00000423557.1:c.535T>A	p.Ter179ArgextTer8	p.*179Rext*8	ENST00000423557	NM_000572.2	179	Tga/Aga	5/5	1	2	FACETS	0.791	0.605	1	0.791	0.605	1	CLONAL	1	TRUE	1	0.18	2		179	281	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533857	533857	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs771774973	NA	P-0015358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	35	393	0	ENST00000451590.1:c.199A>G	p.Met67Val	p.M67V	ENST00000451590	NM_001130442.1	67	Atg/Gtg	3/5	1	2	FACETS	0.775	0.634	0.933	0.775	0.634	0.933	CLONAL	1	TRUE	1	0.18	2		393	502	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999210	100999210	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	37	285	0	ENST00000325455.5:c.592C>A	p.Pro198Thr	p.P198T	ENST00000325455	NM_001202474.3	198	Ccg/Acg	1/8	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.18	2		285	359	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50481183	50481183	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs767607029	NA	P-0015358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	31	295	0	ENST00000394963.4:c.569T>C	p.Phe190Ser	p.F190S	ENST00000394963	NM_003076.4	190	tTc/tCc	5/13	1	2	FACETS	0.679	0.549	0.828	0.679	0.549	0.828	SUBCLONAL	1	TRUE	1	0.18	2		295	507	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570152	95570152	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	29	237	1	ENST00000393063.1:c.3581G>T	p.Arg1194Ile	p.R1194I	ENST00000393063	NM_030621.3	1194	aGa/aTa	22/28	1	2	FACETS	0.985	0.792	1	0.985	0.792	1	CLONAL	1	TRUE	1	0.18	2		238	327	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221282	1221282	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0015358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	35	401	0	ENST00000326873.7:c.805A>T	p.Lys269Ter	p.K269*	ENST00000326873	NM_000455.4	269	Aag/Tag	6/10	1	2	FACETS	0.824	0.675	0.991	0.824	0.675	0.991	CLONAL	1	TRUE	1	0.18	2		401	472	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221496	36221496	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	113	413	0	ENST00000222270.7:c.5255G>T	p.Arg1752Leu	p.R1752L	ENST00000222270	NM_014727.1	1752	cGg/cTg	25/37	0.3	3	FACETS	1	0.963	1			1	CLONAL	2	TRUE	NA	0.18	3		413	602	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389227	31389227	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	30	281	0	ENST00000328111.2:c.2140C>A	p.Leu714Met	p.L714M	ENST00000328111	NM_006892.3	714	Ctg/Atg	19/23	1	2	FACETS	0.794	0.639	0.969	0.794	0.639	0.969	CLONAL	1	TRUE	1	0.18	2		281	420	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730031	41730031	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1374218408	NA	P-0015358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	36	279	0	ENST00000242208.4:c.498G>T	p.Arg166Ser	p.R166S	ENST00000242208	NM_002192.2	166	agG/agT	3/3	0.242111859229369	3	FACETS	1	0.883	1	0.549	0.452	0.658	CLONAL	1	TRUE	1	0.18	3		279	397	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140454007	140454007	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	24	207	0	ENST00000288602.6:c.1721A>T	p.His574Leu	p.H574L	ENST00000288602	NM_004333.4	574	cAc/cTc	14/18	1	2	FACETS	0.913	0.717	1	0.913	0.717	1	CLONAL	1	TRUE	1	0.18	2		207	292	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005919	69005919	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	68	363	1	ENST00000288368.4:c.2330G>A	p.Gly777Glu	p.G777E	ENST00000288368	NM_024870.2	777	gGa/gAa	21/40	1	2	FACETS	0.805	0.703	0.916	1	0.976	1	CLONAL	2	TRUE	1	0.18	2		364	469	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760054	133760054	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	33	391	0	ENST00000318560.5:c.2377G>T	p.Ala793Ser	p.A793S	ENST00000318560	NM_005157.4	793	Gct/Tct	11/11	1	2	FACETS	0.861	0.701	1	0.861	0.701	1	CLONAL	1	TRUE	1	0.18	2		391	426	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70362030	70362030	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	42	480	0	ENST00000374080.3:c.6496C>A	p.Gln2166Lys	p.Q2166K	ENST00000374080		2166	Cag/Aag	45/45	1	2	FACETS	0.904	0.755	1	0.904	0.755	1	CLONAL	1	TRUE	1	0.18	2		480	516	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0015359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	191	396	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.440747876478734	4	FACETS	1	0.958	1	0.693	0.646	0.741	CLONAL	2	TRUE	1	0.520276352247348	4		396	537	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068378	26068378	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	220	364	1	ENST00000435504.4:c.112A>T	p.Ile38Phe	p.I38F	ENST00000435504		38	Atc/Ttc	2/13	0.453892082149799	3	FACETS	0.81	0.757	0.863	0.81	0.757	0.863	CLONAL	2	TRUE	1	0.520276352247348	3		365	658	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356262	70356297	+	inframe_deletion	In_Frame_Del	DEL	GCAGCAGCGGTTGCTGCTCTACCACACACACCTGAG	GCAGCAGCGGTTGCTGCTCTACCACACACACCTGAG	-	novel	NA	P-0015359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	143	318	0	ENST00000374080.3:c.5159_5194del	p.Gln1720_Arg1731del	p.Q1720_R1731del	ENST00000374080		1719	gaGCAGCAGCGGTTGCTGCTCTACCACACACACCTGAGg/gag	37/45	0.462373626362712	2	FACETS	1	0.988	1	0.716	0.66	0.773	CLONAL	1	TRUE	0	0.520276352247348	2		318	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579697	7579697	+	splice_region_variant,intron_variant	Splice_Region	SNP	T	T	A	novel	NA	P-0015359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	146	310	0	ENST00000269305.4:c.96+3A>T		p.X32_splice	ENST00000269305	NM_001126112.2	32			NA	2	FACETS	0.795	0.736	0.855			1	INDETERMINATE	2	TRUE	NA	0.520276352247348	2		310	353	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0015360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	17	375	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.188	0.139	0.245	0.188	0.139	0.245	SUBCLONAL	1	TRUE	1	0.405421074184914	2		375	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0015360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	34	567	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	1	2	FACETS	0.253	0.205	0.306	0.253	0.205	0.306	SUBCLONAL	1	TRUE	1	0.405421074184914	2		567	664	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436097	56436097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	62	372	0	ENST00000407977.2:c.1040G>A	p.Gly347Asp	p.G347D	ENST00000407977		347	gGc/gAc	9/10	1	2	FACETS	0.525	0.453	0.602	0.525	0.453	0.602	SUBCLONAL	1	TRUE	1	0.405421074184914	2		372	583	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615692	1615692	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	36	502	0	ENST00000344749.5:c.1579del	p.Arg527GlyfsTer16	p.R527Gfs*16	ENST00000344749	NM_001136139.2	527	Cgg/gg	17/19	1	2	FACETS	0.293	0.24	0.352	0.293	0.24	0.352	SUBCLONAL	1	TRUE	1	0.405421074184914	2		502	607	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936098	71936098	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	10	111	0	ENST00000298229.2:c.70C>T	p.Arg24Cys	p.R24C	ENST00000298229	NM_001567.3	24	Cgc/Tgc	1/28	1	2	FACETS	0.422	0.287	0.588	0.422	0.287	0.588	SUBCLONAL	1	TRUE	1	0.405421074184914	2		111	117	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120872	115120872	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	18	295	0	ENST00000257566.3:c.134C>A	p.Thr45Lys	p.T45K	ENST00000257566	NM_016569.3	45	aCg/aAg	1/8	1	2	FACETS	0.277	0.208	0.358	0.277	0.208	0.358	SUBCLONAL	1	TRUE	1	0.405421074184914	2		295	321	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610256	10610256	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	55	588	0	ENST00000171111.5:c.454G>T	p.Val152Phe	p.V152F	ENST00000171111	NM_203500.1	152	Gtc/Ttc	2/6	1	2	FACETS	0.372	0.318	0.432	0.372	0.318	0.432	SUBCLONAL	1	TRUE	1	0.405421074184914	2		588	729	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390216	89390216	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	28	291	0	ENST00000336596.2:c.965G>C	p.Cys322Ser	p.C322S	ENST00000336596	NM_005233.5	322	tGt/tCt	4/17	1	2	FACETS	0.319	0.254	0.393	0.319	0.254	0.393	SUBCLONAL	1	TRUE	1	0.405421074184914	2		291	433	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129287	152129287	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	34	444	1	ENST00000206249.3:c.240C>A	p.Tyr80Ter	p.Y80*	ENST00000206249	NM_000125.3	80	taC/taA	1/8	1	2	FACETS	0.325	0.265	0.393	0.325	0.265	0.393	SUBCLONAL	1	TRUE	1	0.405421074184914	2		445	516	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0015360-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	28	375	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.366	0.291	0.452	0.366	0.291	0.452	SUBCLONAL	1	FALSE	1	0.222370365231104	2		375	688	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0015360-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	88	567	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	1	2	FACETS	0.734	0.649	0.826	0.734	0.649	0.826	SUBCLONAL	1	FALSE	1	0.222370365231104	2		567	1078	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436097	56436097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015360-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	80	372	0	ENST00000407977.2:c.1040G>A	p.Gly347Asp	p.G347D	ENST00000407977		347	gGc/gAc	9/10	1	2	FACETS	0.995	0.876	1	0.995	0.876	1	CLONAL	1	FALSE	1	0.222370365231104	2		372	723	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615692	1615692	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015360-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	80	502	0	ENST00000344749.5:c.1579del	p.Arg527GlyfsTer16	p.R527Gfs*16	ENST00000344749	NM_001136139.2	527	Cgg/gg	17/19	1	2	FACETS	0.84	0.738	0.949	0.84	0.738	0.949	CLONAL	1	FALSE	1	0.222370365231104	2		502	857	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936098	71936098	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015360-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	19	111	0	ENST00000298229.2:c.70C>T	p.Arg24Cys	p.R24C	ENST00000298229	NM_001567.3	24	Cgc/Tgc	1/28	1	2	FACETS	1	0.785	1	1	0.785	1	CLONAL	1	FALSE	1	0.222370365231104	2		111	166	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120872	115120872	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015360-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	40	295	0	ENST00000257566.3:c.134C>A	p.Thr45Lys	p.T45K	ENST00000257566	NM_016569.3	45	aCg/aAg	1/8	1	2	FACETS	0.796	0.662	0.945	0.796	0.662	0.945	CLONAL	1	FALSE	1	0.222370365231104	2		295	452	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610256	10610256	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015360-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	85	588	0	ENST00000171111.5:c.454G>T	p.Val152Phe	p.V152F	ENST00000171111	NM_203500.1	152	Gtc/Ttc	2/6	1	2	FACETS	0.704	0.62	0.794	0.704	0.62	0.794	SUBCLONAL	1	FALSE	1	0.222370365231104	2		588	1086	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390216	89390216	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015360-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	34	291	0	ENST00000336596.2:c.965G>C	p.Cys322Ser	p.C322S	ENST00000336596	NM_005233.5	322	tGt/tCt	4/17	1	2	FACETS	0.603	0.492	0.728	0.603	0.492	0.728	SUBCLONAL	1	FALSE	1	0.222370365231104	2		291	507	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129287	152129287	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015360-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	37	444	1	ENST00000206249.3:c.240C>A	p.Tyr80Ter	p.Y80*	ENST00000206249	NM_000125.3	80	taC/taA	1/8	1	2	FACETS	0.572	0.47	0.686	0.572	0.47	0.686	SUBCLONAL	1	FALSE	1	0.222370365231104	2		445	582	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981088	201981089	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015360-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	55	371	0	ENST00000359651.3:c.169dup	p.Ala57GlyfsTer35	p.A57Gfs*35	ENST00000359651		56	aag/aaGg	2/8	1	2	FACETS	0.663	0.566	0.77	0.663	0.566	0.77	SUBCLONAL	1	FALSE	1	0.222370365231104	2		371	746	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711957	89711957	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015360-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	46	449	0	ENST00000371953.3:c.575C>A	p.Ala192Glu	p.A192E	ENST00000371953	NM_000314.4	192	gCa/gAa	6/9	1	2	FACETS	0.526	0.441	0.619	0.526	0.441	0.619	SUBCLONAL	1	FALSE	1	0.222370365231104	2		449	787	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233390	69233390	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015360-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	40	379	0	ENST00000462284.1:c.1255G>C	p.Glu419Gln	p.E419Q	ENST00000462284	NM_002392.5	419	Gag/Cag	11/11	1	2	FACETS	0.505	0.418	0.602	0.505	0.418	0.602	SUBCLONAL	1	FALSE	1	0.222370365231104	2		379	713	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992468	72992468	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1309605420	NA	P-0015360-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	99	611	4	ENST00000268489.5:c.1577C>T	p.Ser526Leu	p.S526L	ENST00000268489	NM_006885.3	526	tCa/tTa	2/10	1	2	FACETS	0.706	0.628	0.789	0.706	0.628	0.789	SUBCLONAL	1	FALSE	1	0.222370365231104	2		615	1262	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346786	225346786	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015360-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	41	331	1	ENST00000264414.4:c.1852C>T	p.Gln618Ter	p.Q618*	ENST00000264414	NM_003590.4	618	Caa/Taa	14/16	1	2	FACETS	0.62	0.515	0.736	0.62	0.515	0.736	SUBCLONAL	1	FALSE	1	0.222370365231104	2		332	595	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324665	31324665	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0015360-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	29	276	0	ENST00000412585.2:c.143C>G	p.Ser48Ter	p.S48*	ENST00000412585	NM_005514.6	48	tCa/tGa	2/8	1	2	FACETS	0.557	0.447	0.684	0.557	0.447	0.684	SUBCLONAL	1	FALSE	1	0.222370365231104	2		276	468	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967875	93967875	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015360-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	90	616	0	ENST00000369303.4:c.2052C>A	p.Ser684Arg	p.S684R	ENST00000369303	NM_004440.3	684	agC/agA	11/17	1	2	FACETS	0.703	0.622	0.791	0.703	0.622	0.791	SUBCLONAL	1	FALSE	1	0.222370365231104	2		616	1151	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0015361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	129	396	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	0.626	0.566	0.688	0.626	0.566	0.688	SUBCLONAL	1	TRUE	1	0.417437673511248	2		396	988	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	117	722	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.853	0.773	0.935	0.853	0.773	0.935	CLONAL	1	FALSE	1	0.575357481403826	2		722	477	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0015362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	96	425	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.575357481403826	1	FACETS	0.982	0.891	1	0.982	0.891	1	CLONAL	1	FALSE	0	0.575357481403826	1		425	242	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0015363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	433	650	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.357586612694215	4	FACETS	0.966	0.928	1	0.966	0.928	1	CLONAL	4	TRUE	0	0.374340052656237	4		650	823	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0015363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	146	445	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.275663103778576	2	FACETS	1	0.982	1	0.638	0.585	0.694	CLONAL	1	TRUE	0	0.374340052656237	2		445	611	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259554	55259554	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs397517134	NA	P-0015363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	403	346	0	ENST00000275493.2:c.2612C>G	p.Ala871Gly	p.A871G	ENST00000275493	NM_005228.3	871	gCa/gGa	21/28	0.357586612694215	4	FACETS	0.968	0.929	1	0.968	0.929	1	CLONAL	4	TRUE	0	0.374340052656237	4		346	764	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573496	48573496	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	128	289	0	ENST00000342988.3:c.80G>A	p.Arg27Lys	p.R27K	ENST00000342988	NM_005359.5	27	aGa/aAa	2/12	0.254527407298435	2	FACETS	1	0.986	1	0.732	0.668	0.799	CLONAL	1	TRUE	0	0.374340052656237	2		289	467	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573504	48573504	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	116	299	0	ENST00000342988.3:c.88G>A	p.Gly30Arg	p.G30R	ENST00000342988	NM_005359.5	30	Gga/Aga	2/12	0.254527407298435	2	FACETS	1	0.982	1	0.683	0.619	0.749	CLONAL	1	TRUE	0	0.374340052656237	2		299	454	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575071	48575071	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	145	329	0	ENST00000342988.3:c.265G>C	p.Gly89Arg	p.G89R	ENST00000342988	NM_005359.5	89	Gga/Cga	3/12	0.254527407298435	2	FACETS	1	0.988	1	0.745	0.684	0.808	CLONAL	1	TRUE	0	0.374340052656237	2		329	520	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931791	68931791	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	215	370	0	ENST00000288368.4:c.221T>A	p.Phe74Tyr	p.F74Y	ENST00000288368	NM_024870.2	74	tTc/tAc	3/40	0.344324174623074	2	FACETS	0.915	0.855	0.975	0.915	0.855	0.975	CLONAL	2	TRUE	0	0.374340052656237	2		370	628	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965675	90965675	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	36	282	0	ENST00000265433.3:c.1642A>T	p.Asn548Tyr	p.N548Y	ENST00000265433	NM_002485.4	548	Aat/Tat	11/16	0.374340052656237	3	FACETS	0.401	0.328	0.482	0.134	0.109	0.161	SUBCLONAL	1	TRUE	0	0.374340052656237	3		282	570	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	87	493	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	0.939	1	CLONAL	1	TRUE	1	0.387813669125879	2		493	415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0015366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	239	749	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.265706625353908	2	FACETS	0.808	0.757	0.86	0.808	0.757	0.86	CLONAL	2	TRUE	0	0.387813669125879	2		750	763	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983066	201983066	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	374	585	3	ENST00000359651.3:c.916del	p.Leu306CysfsTer19	p.L306Cfs*19	ENST00000359651		305	ttC/tt	7/8	0.387813669125879	3	FACETS	0.882	0.841	0.923	0.882	0.841	0.923	CLONAL	3	TRUE	0	0.387813669125879	3		588	870	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118660	11118660	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755519197	NA	P-0015366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	144	535	1	ENST00000358026.2:c.2084G>A	p.Ser695Asn	p.S695N	ENST00000358026	NM_001128849.1	695	aGc/aAc	14/36	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.387813669125879	2		536	715	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629075	187629075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	47	462	0	ENST00000441802.2:c.1907C>T	p.Ala636Val	p.A636V	ENST00000441802	NM_005245.3	636	gCa/gTa	2/27	0.281531479130161	2	FACETS	0.526	0.444	0.616	0.263	0.222	0.308	SUBCLONAL	1	TRUE	0	0.387813669125879	2		462	461	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878620	151878620	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	37	427	0	ENST00000262189.6:c.6325T>G	p.Phe2109Val	p.F2109V	ENST00000262189	NM_170606.2	2109	Ttt/Gtt	36/59	0.279884672456593	3	FACETS	0.45	0.371	0.539	0.225	0.185	0.27	SUBCLONAL	1	TRUE	1	0.387813669125879	3		427	506	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133529	55133529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	174	419	0	ENST00000257290.5:c.833C>T	p.Pro278Leu	p.P278L	ENST00000257290	NM_006206.4	278	cCc/cTc	6/23	1	2	FACETS	0.921	0.854	0.99	0.921	0.854	0.99	CLONAL	1	TRUE	1	0.69068759306921	2		419	547	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249015	55249016	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCCCACGTG	novel	NA	P-0015367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10610	3560	359	1	ENST00000275493.2:c.2314_2322dup	p.Pro772_Val774dup	p.P772_V774dup	ENST00000275493	NM_005228.3	772	-/CCCCACGTG	20/28	0.69068759306921	38	FACETS	0.977	0.96	0.994			1	CLONAL	10	TRUE	NA	0.69068759306921	38		360	14170	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0015368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	135	376	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.808	0.737	0.882	0.808	0.737	0.882	CLONAL	1	TRUE	1	0.539085323981718	2		376	620	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0015368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	121	585	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.521442609018399	1	FACETS	0.62	0.562	0.68	0.62	0.562	0.68	SUBCLONAL	1	TRUE	0	0.539085323981718	1		585	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577069	7577069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55819519	NA	P-0015368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	62	581	2	ENST00000269305.4:c.869G>A	p.Arg290His	p.R290H	ENST00000269305	NM_001126112.2	290	cGc/cAc	8/11	0.521442609018399	1	FACETS	0.231	0.199	0.266	0.231	0.199	0.266	SUBCLONAL	1	TRUE	0	0.539085323981718	1		583	727	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220382	1220382	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	188	417	0	ENST00000326873.7:c.475C>T	p.Gln159Ter	p.Q159*	ENST00000326873	NM_000455.4	159	Cag/Tag	4/10	0.539085323981718	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.539085323981718	1		417	449	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677792	47677792	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	138	517	1	ENST00000347630.2:c.1073C>T	p.Ser358Leu	p.S358L	ENST00000347630	NM_001007230.1	358	tCa/tTa	11/11	1	2	FACETS	0.69	0.629	0.754	0.69	0.629	0.754	SUBCLONAL	1	TRUE	1	0.539085323981718	2		518	742	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499363	89499363	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1317589623	NA	P-0015368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	173	346	0	ENST00000336596.2:c.2538del	p.Met847TrpfsTer10	p.M847Wfs*10	ENST00000336596	NM_005233.5	845	Ccc/cc	15/17	NA	2	FACETS	1	0.931	1			1	INDETERMINATE	1	TRUE	NA	0.539085323981718	2		346	637	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550782	150550782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs934123900	NA	P-0015368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	93	406	0	ENST00000369026.2:c.874G>A	p.Glu292Lys	p.E292K	ENST00000369026	NM_021960.4	292	Gaa/Aaa	2/3	0.292214215562854	4	FACETS	0.54	0.479	0.606			1	INDETERMINATE	1	TRUE	NA	0.539085323981718	4		406	983	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143171	30143171	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	99	343	0	ENST00000389048.3:c.355G>T	p.Glu119Ter	p.E119*	ENST00000389048	NM_004304.4	119	Gag/Tag	1/29	1	2	FACETS	0.732	0.656	0.812	0.732	0.656	0.812	SUBCLONAL	1	TRUE	1	0.539085323981718	2		343	502	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115729	8115729	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	203	453	0	ENST00000346208.3:c.1075G>T	p.Glu359Ter	p.E359*	ENST00000346208		359	Gaa/Taa	6/6	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.539085323981718	2		453	746	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748020	72748020	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	141	581	1	ENST00000357731.5:c.158G>A	p.Gly53Glu	p.G53E	ENST00000357731	NM_173808.2	53	gGg/gAg	1/7	1	2	FACETS	0.627	0.571	0.686	0.627	0.571	0.686	SUBCLONAL	1	TRUE	1	0.539085323981718	2		582	834	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196791	108196791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039471	NA	P-0015368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	101	260	0	ENST00000278616.4:c.6814G>A	p.Glu2272Lys	p.E2272K	ENST00000278616	NM_000051.3	2272	Gaa/Aaa	47/63	0.461351351722652	1	FACETS	0.707	0.637	0.78	0.707	0.637	0.78	SUBCLONAL	1	TRUE	0	0.539085323981718	1		260	387	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431596	49431596	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	126	487	0	ENST00000301067.7:c.9543G>C	p.Glu3181Asp	p.E3181D	ENST00000301067	NM_003482.3	3181	gaG/gaC	34/54	1	2	FACETS	0.667	0.605	0.732	0.667	0.605	0.732	SUBCLONAL	1	TRUE	1	0.539085323981718	2		487	701	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557669	95557669	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	81	647	0	ENST00000393063.1:c.5398G>C	p.Glu1800Gln	p.E1800Q	ENST00000393063	NM_030621.3	1800	Gag/Cag	26/28	1	2	FACETS	0.362	0.319	0.41	0.362	0.319	0.41	SUBCLONAL	1	TRUE	1	0.539085323981718	2		647	829	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310153	91310153	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs781008303	NA	P-0015368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	167	344	0	ENST00000355112.3:c.2207A>G	p.Tyr736Cys	p.Y736C	ENST00000355112	NM_000057.2	736	tAt/tGt	10/22	NA	2	FACETS	0.917	0.845	0.991			1	INDETERMINATE	1	TRUE	NA	0.539085323981718	2		344	676	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632389	1632389	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	159	634	0	ENST00000344749.5:c.161C>T	p.Pro54Leu	p.P54L	ENST00000344749	NM_001136139.2	54	cCc/cTc	4/19	0.539085323981718	1	FACETS	0.801	0.739	0.865	0.801	0.739	0.865	CLONAL	1	TRUE	0	0.539085323981718	1		634	538	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2193688	2193688	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	211	537	0	ENST00000398665.3:c.494G>A	p.Gly165Asp	p.G165D	ENST00000398665	NM_032482.2	165	gGt/gAt	6/28	0.539085323981718	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.539085323981718	1		537	570	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602832	10602832	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	253	747	0	ENST00000171111.5:c.746G>T	p.Cys249Phe	p.C249F	ENST00000171111	NM_203500.1	249	tGc/tTc	3/6	0.539085323981718	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.539085323981718	1		747	670	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123739	11123739	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	207	553	1	ENST00000358026.2:c.2389A>T	p.Met797Leu	p.M797L	ENST00000358026	NM_001128849.1	797	Atg/Ttg	16/36	0.539085323981718	1	FACETS	0.951	0.888	1	0.951	0.888	1	CLONAL	1	TRUE	0	0.539085323981718	1		554	590	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613161	52613161	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	59	577	0	ENST00000394830.3:c.3367T>G	p.Phe1123Val	p.F1123V	ENST00000394830	NM_018313.4	1123	Ttt/Gtt	22/30	0.358093394147207	1	FACETS	0.2	0.171	0.231	0.2	0.171	0.231	SUBCLONAL	1	TRUE	0	0.539085323981718	1		577	799	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620498	52620498	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	184	500	0	ENST00000394830.3:c.3255G>C	p.Glu1085Asp	p.E1085D	ENST00000394830	NM_018313.4	1085	gaG/gaC	21/30	0.358093394147207	1	FACETS	0.674	0.624	0.726	0.674	0.624	0.726	SUBCLONAL	1	TRUE	0	0.539085323981718	1		500	740	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86658365	86658365	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0015368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	63	189	0	ENST00000274376.6:c.1333-3C>T		p.X445_splice	ENST00000274376	NM_002890.2	445			1	2	FACETS	0.612	0.531	0.698	0.612	0.531	0.698	SUBCLONAL	1	TRUE	1	0.539085323981718	2		189	382	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514997	148514997	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	148	436	0	ENST00000320356.2:c.1212G>C	p.Glu404Asp	p.E404D	ENST00000320356	NM_004456.4	404	gaG/gaC	10/20	0.377924533712329	1	FACETS	0.57	0.521	0.62	0.57	0.521	0.62	SUBCLONAL	1	TRUE	0	0.539085323981718	1		436	704	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515130	148515130	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	106	378	0	ENST00000320356.2:c.1079G>C	p.Arg360Thr	p.R360T	ENST00000320356	NM_004456.4	360	aGa/aCa	10/20	0.377924533712329	1	FACETS	0.559	0.503	0.618	0.559	0.503	0.618	SUBCLONAL	1	TRUE	0	0.539085323981718	1		378	514	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069054	5069054	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	105	301	0	ENST00000381652.3:c.1359G>C	p.Leu453Phe	p.L453F	ENST00000381652	NM_004972.3	453	ttG/ttC	11/25	0.539085323981718	1	FACETS	0.63	0.567	0.695	0.63	0.567	0.695	SUBCLONAL	1	TRUE	0	0.539085323981718	1		301	452	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	52	297	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.868	0.749	0.996	0.868	0.749	0.996	CLONAL	1	TRUE	1	0.559682266144367	2		297	214	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196022	138196022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	71	141	0	ENST00000237289.4:c.336G>A	p.Met112Ile	p.M112I	ENST00000237289	NM_001270507.1	112	atG/atA	3/9	1	2	FACETS	0.957	0.845	1	0.957	0.845	1	CLONAL	1	TRUE	1	0.559682266144367	2		141	265	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032794	30032794	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121434259	NA	P-0015370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	111	280	0	ENST00000338641.4:c.169C>T	p.Arg57Ter	p.R57*	ENST00000338641	NM_000268.3	57	Cga/Tga	2/16	0.47018659574499	2	FACETS	0.752	0.688	0.818	0.752	0.688	0.818	SUBCLONAL	2	TRUE	0	0.544581050475456	2		280	271	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0015371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	18	342	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.99	0.751	1	0.99	0.751	1	CLONAL	1	TRUE	1	0.249166445144673	2		342	146	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0015371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	16	407	0	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	0.177839392891854	1	FACETS	0.565	0.419	0.739	0.565	0.419	0.739	SUBCLONAL	1	TRUE	0	0.249166445144673	1		407	199	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0015371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	35	477	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.249166445144673	2	FACETS	1	0.935	1	0.656	0.542	0.782	CLONAL	1	TRUE	0	0.249166445144673	2		477	214	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120493349	120493349	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	30	368	0	ENST00000256646.2:c.2477C>T	p.Thr826Ile	p.T826I	ENST00000256646	NM_024408.3	826	aCa/aTa	15/34	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.249166445144673	2		368	212	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774133	66774133	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	8	598	0	ENST00000307102.5:c.609G>T	p.Glu203Asp	p.E203D	ENST00000307102	NM_002755.3	203	gaG/gaT	6/11	1	2	FACETS	0.26	0.167	0.381	0.26	0.167	0.381	SUBCLONAL	1	TRUE	1	0.249166445144673	2		598	247	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246853	10246853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316848811	NA	P-0015371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	37	478	1	ENST00000340748.4:c.4552G>A	p.Glu1518Lys	p.E1518K	ENST00000340748		1518	Gag/Aag	37/40	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.249166445144673	2		479	286	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27217699	27217699	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	20	419	0	ENST00000380036.4:c.3005T>G	p.Val1002Gly	p.V1002G	ENST00000380036	NM_000459.3	1002	gTg/gGg	19/23	1	2	FACETS	0.754	0.578	0.957	0.754	0.578	0.957	CLONAL	1	TRUE	1	0.249166445144673	2		419	213	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015371-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	36	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.842	1	1	0.842	1	CLONAL	1	TRUE	1	0.442750596225613	2		493	161	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0015371-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	30	487	1	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	0.442750596225613	1	FACETS	0.699	0.571	0.84	0.699	0.571	0.84	SUBCLONAL	1	TRUE	0	0.442750596225613	1		488	151	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604665	48604665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660045	NA	P-0015371-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	38	237	0	ENST00000342988.3:c.1487G>A	p.Arg496His	p.R496H	ENST00000342988	NM_005359.5	496	cGt/cAt	12/12	0.442750596225613	1	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	0	0.442750596225613	1		237	130	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968260	134968260	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015371-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	36	490	0	ENST00000398015.3:c.2773A>C	p.Met925Leu	p.M925L	ENST00000398015	NM_004441.4	925	Atg/Ctg	15/16	1	2	FACETS	0.786	0.652	0.933	0.786	0.652	0.933	CLONAL	1	TRUE	1	0.442750596225613	2		490	207	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155230	106155230	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015371-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	38	295	0	ENST00000380013.4:c.131C>G	p.Ala44Gly	p.A44G	ENST00000380013	NM_001127208.2	44	gCt/gGt	3/11	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.442750596225613	2		295	144	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030478	49030478	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0015372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	177	259	0	ENST00000267163.4:c.1953T>G	p.Tyr651Ter	p.Y651*	ENST00000267163	NM_000321.2	651	taT/taG	19/27	0.619980255625535	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.635182272544348	2		259	254	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577088	7577088	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1204379654	NA	P-0015372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	339	457	0	ENST00000269305.4:c.850A>T	p.Thr284Ser	p.T284S	ENST00000269305	NM_001126112.2	284	Aca/Tca	8/11	0.635182272544348	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.635182272544348	2		457	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577091	7577092	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	341	463	0	ENST00000269305.4:c.846_847insA	p.Arg283ThrfsTer23	p.R283Tfs*23	ENST00000269305	NM_001126112.2	282	-/A	8/11	0.635182272544348	2	FACETS	0.998	0.959	1	0.998	0.959	1	CLONAL	2	TRUE	0	0.635182272544348	2		463	538	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874290	76874309	+	frameshift_variant	Frame_Shift_Del	DEL	AACATCTCATAGAGAATGTG	AACATCTCATAGAGAATGTG	-	novel	NA	P-0015372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	129	411	0	ENST00000373344.5:c.5413_5432del	p.His1805SerfsTer49	p.H1805Sfs*49	ENST00000373344	NM_000489.3	1805	CACATTCTCTATGAGATGTTa/a	21/35	0.538186133218493	2	FACETS	0.945	0.882	1	0.945	0.882	1	CLONAL	2	TRUE	0	0.635182272544348	2		411	215	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	52	297	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.321067608372833	2		297	316	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0015377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	40	132	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.887	0.741	1	0.887	0.741	1	CLONAL	1	TRUE	1	0.321067608372833	2		132	281	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857396	9857396	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	83	191	0	ENST00000330684.3:c.4005A>T	p.Lys1335Asn	p.K1335N	ENST00000330684	NM_001134407.1	1335	aaA/aaT	13/13	1	2	FACETS	0.983	0.87	1	0.983	0.87	1	CLONAL	1	TRUE	1	0.321067608372833	2		191	526	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162098	22162098	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	73	184	0	ENST00000215832.6:c.157A>G	p.Ile53Val	p.I53V	ENST00000215832	NM_002745.4	53	Atc/Gtc	2/9	0.321067608372833	1	FACETS	0.911	0.8	1	0.911	0.8	1	CLONAL	1	TRUE	0	0.321067608372833	1		184	419	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574431	41574431	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs775274711	NA	P-0015377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	90	235	0	ENST00000263253.7:c.6716T>C	p.Met2239Thr	p.M2239T	ENST00000263253	NM_001429.3	2239	aTg/aCg	31/31	0.321067608372833	1	FACETS	0.989	0.881	1	0.989	0.881	1	CLONAL	1	TRUE	0	0.321067608372833	1		235	476	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69012053	69012053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	56	258	0	ENST00000288368.4:c.2690G>A	p.Cys897Tyr	p.C897Y	ENST00000288368	NM_024870.2	897	tGt/tAt	23/40	1	2	FACETS	0.666	0.571	0.77	0.666	0.571	0.77	SUBCLONAL	1	TRUE	1	0.321067608372833	2		258	524	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115952	8115953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0015378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	54	333	0	ENST00000346208.3:c.1300dup	p.His434ProfsTer73	p.H434Pfs*73	ENST00000346208		433	cac/caCc	6/6	1	2	FACETS	0.545	0.466	0.631	0.545	0.466	0.631	SUBCLONAL	1	TRUE	1	0.445046983742558	2		333	445	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041026	112041026	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746134687	NA	P-0015378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	112	376	0	ENST00000368678.4:c.229C>T	p.Arg77Cys	p.R77C	ENST00000368678		77	Cgt/Tgt	3/13	0.403595358297564	1	FACETS	0.938	0.85	1	0.938	0.85	1	CLONAL	1	TRUE	0	0.445046983742558	1		376	417	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0015382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	55	336	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.762	0.652	0.881	0.762	0.652	0.881	SUBCLONAL	1	TRUE	1	0.294181863338775	2		336	491	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849637	68849637	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	69	602	1	ENST00000261769.5:c.1540G>T	p.Asp514Tyr	p.D514Y	ENST00000261769	NM_004360.3	514	Gac/Tac	10/16	0.294181863338775	1	FACETS	0.617	0.537	0.704	0.617	0.537	0.704	SUBCLONAL	1	TRUE	0	0.294181863338775	1		603	648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0015384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	71	749	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA	2	FACETS	0.666	0.58	0.759			1	INDETERMINATE	1	TRUE	NA	0.26	2		750	820	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0015384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	21	365	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	0.349	0.268	0.444	0.349	0.268	0.444	SUBCLONAL	1	TRUE	1	0.26	2		365	463	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0015384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	109	468	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.26	2		468	830	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760696	59760706	+	frameshift_variant	Frame_Shift_Del	DEL	AGATGGTTTAA	AGATGGTTTAA	-	novel	NA	P-0015384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	51	456	0	ENST00000259008.2:c.3701_3711del	p.Phe1234SerfsTer5	p.F1234Sfs*5	ENST00000259008	NM_032043.2	1234	tTTAAACCATCT/t	20/20	1	2	FACETS	0.529	0.449	0.618	0.529	0.449	0.618	SUBCLONAL	1	TRUE	1	0.26	2		456	741	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575168	48575168	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0015384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	23	293	0	ENST00000342988.3:c.362T>G	p.Leu121Ter	p.L121*	ENST00000342988	NM_005359.5	121	tTa/tGa	3/12	1	2	FACETS	0.394	0.306	0.496	0.394	0.306	0.496	SUBCLONAL	1	TRUE	1	0.26	2		293	449	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0015388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	192	635	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.246702335662447	4	FACETS	1	0.977	1	0.757	0.7	0.815	CLONAL	2	TRUE	1	0.246702335662447	4		635	855	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129655	11129655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	174	630	1	ENST00000358026.2:c.2461G>A	p.Glu821Lys	p.E821K	ENST00000358026	NM_001128849.1	821	Gag/Aag	17/36	0.164886586498744	4	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	2	0.246702335662447	4		631	862	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138623	11138623	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	131	466	0	ENST00000358026.2:c.3379G>C	p.Asp1127His	p.D1127H	ENST00000358026	NM_001128849.1	1127	Gat/Cat	24/36	0.164886586498744	4	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	2	0.246702335662447	4		466	626	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873834	35873834	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	80	254	0	ENST00000216797.5:c.17A>T	p.Glu6Val	p.E6V	ENST00000216797	NM_020529.2	6	gAg/gTg	1/6	0.246702335662447	4	FACETS	0.963	0.857	1	1	0.978	1	CLONAL	3	TRUE	2	0.246702335662447	4		254	280	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982469	25982469	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	135	320	0	ENST00000435504.4:c.821del	p.Pro274ArgfsTer13	p.P274Rfs*13	ENST00000435504		274	cCg/cg	9/13	0.246702335662447	4	FACETS	0.88	0.804	0.958	0.88	0.804	0.958	CLONAL	3	TRUE	1	0.246702335662447	4		320	517	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0015391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	255	577	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.964	0.904	1	0.964	0.904	1	CLONAL	1	TRUE	1	0.566984323898912	2		577	933	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750684	128750684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1294281543	NA	P-0015391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	209	415	2	ENST00000377970.2:c.221C>T	p.Pro74Leu	p.P74L	ENST00000377970	NM_002467.4	74	cCg/cTg	2/3	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.566984323898912	2		417	673	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483345	120483345	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	212	442	2	ENST00000256646.2:c.3016A>G	p.Ile1006Val	p.I1006V	ENST00000256646	NM_024408.3	1006	Att/Gtt	19/34	1	2	FACETS	0.993	0.926	1	0.993	0.926	1	CLONAL	1	TRUE	1	0.566984323898912	2		444	753	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190320	32190320	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377458854	NA	P-0015391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	185	409	0	ENST00000375023.3:c.419G>A	p.Arg140His	p.R140H	ENST00000375023	NM_004557.3	140	cGc/cAc	3/30	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.566984323898912	2		409	579	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0015392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	79	376	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.24	2		376	589	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	53	297	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.882	0.752	1	0.882	0.752	1	CLONAL	1	TRUE	1	0.24	2		297	501	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991346	72991346	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	60	377	0	ENST00000268489.5:c.2699C>G	p.Ala900Gly	p.A900G	ENST00000268489	NM_006885.3	900	gCc/gGc	2/10	1	2	FACETS	0.737	0.635	0.85	0.737	0.635	0.85	SUBCLONAL	1	TRUE	1	0.24	2		377	678	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346120	152346120	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs371453207	NA	P-0015392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	96	411	0	ENST00000359321.1:c.450C>G	p.Ser150Arg	p.S150R	ENST00000359321	NM_005431.1	150	agC/agG	3/3	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.24	2		411	756	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750692	128750692	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	70	373	0	ENST00000377970.2:c.229T>C	p.Ser77Pro	p.S77P	ENST00000377970	NM_002467.4	77	Tcc/Ccc	2/3	1	2	FACETS	0.831	0.724	0.947	0.831	0.724	0.947	CLONAL	1	TRUE	1	0.24	2		373	702	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589583	67589601	+	protein_altering_variant	In_Frame_Del	DEL	TACATGAATATAACACTCA	TACATGAATATAACACTCA	C	novel	NA	P-0015392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	26	230	0	ENST00000274335.5:c.1346_1364delinsC	p.Leu449_Gln455delinsSer	p.L449_Q455delinsS	ENST00000274335		449	tTACATGAATATAACACTCAg/tCg	10/15	1	2	FACETS	0.496	0.392	0.615	0.496	0.392	0.615	SUBCLONAL	1	TRUE	1	0.24	2		230	437	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272308	38272308	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs869320694	NA	P-0015393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	158	529	0	ENST00000425967.3:c.2059A>G	p.Lys687Glu	p.K687E	ENST00000425967	NM_001174067.1	687	Aag/Gag	15/19	0.537245469408498	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	FALSE	2	0.537245469408498	4		529	378	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184338	7184338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	163	583	0	ENST00000302850.5:c.963G>A	p.Met321Ile	p.M321I	ENST00000302850	NM_000208.2	321	atG/atA	3/22	0.537245469408498	3	FACETS	1	0.984	1	0.782	0.731	0.834	CLONAL	2	FALSE	0	0.537245469408498	3		583	328	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38186952	38186952	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	128	757	0	ENST00000317025.8:c.1525C>G	p.Leu509Val	p.L509V	ENST00000317025	NM_023034.1	509	Ctt/Gtt	6/24	0.537245469408498	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	FALSE	2	0.537245469408498	4		757	316	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889109	76889109	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3	76	266	0	ENST00000373344.5:c.4901G>C	p.Trp1634Ser	p.W1634S	ENST00000373344	NM_000489.3	1634	tGg/tCg	18/35	0.500699755694073	2	FACETS		NA	1			1	NA	4	FALSE	NA	0.537245469408498	2		266	79	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575511	64575527	+	frameshift_variant	Frame_Shift_Del	DEL	CCCAGGGCCTGGCAGGC	CCCAGGGCCTGGCAGGC	-	novel	NA	P-0015400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	120	525	1	ENST00000312049.6:c.490_506del	p.Ala164SerfsTer10	p.A164Sfs*10	ENST00000312049	NM_130799.2	164	GCCTGCCAGGCCCTGGGt/t	3/10	0.405548832041663	2	FACETS	0.86	0.786	0.936	0.86	0.786	0.936	CLONAL	2	TRUE	0	0.405548832041663	2		526	344	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131607	2131607	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	154	564	0	ENST00000219476.3:c.3622T>A	p.Trp1208Arg	p.W1208R	ENST00000219476	NM_000548.3	1208	Tgg/Agg	31/42	0.405548832041663	2	FACETS	0.844	0.787	0.9	1	0.987	1	CLONAL	3	TRUE	0	0.405548832041663	2		564	300	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288510	33288510	+	splice_region_variant,intron_variant	Splice_Region	SNP	T	T	G	novel	NA	P-0015400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	107	366	0	ENST00000374542.5:c.1039+3A>C		p.X347_splice	ENST00000374542	NM_001141970.1	347			0.405548832041663	2	FACETS	0.931	0.86	1	1	0.986	1	CLONAL	3	TRUE	0	0.405548832041663	2		366	189	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	110	297	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	0.668	0.606	0.732	0.668	0.606	0.732	INDETERMINATE	1	TRUE	0	0.63	1		297	358	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933762	39933763	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0015401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	219	464	0	ENST00000378444.4:c.836_837del	p.Leu279ArgfsTer21	p.L279Rfs*21	ENST00000378444	NM_001123385.1	279	cTC/c	4/15	0.3	1	FACETS	0.785	0.735	0.835	0.785	0.735	0.835	INDETERMINATE	1	TRUE	0	0.63	1		464	607	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0015403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	27	400	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.297187072535063	4	FACETS	0.33	0.262	0.409	0.165	0.131	0.205	SUBCLONAL	1	TRUE	2	0.440200040822626	4		401	535	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991961	72991961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1262542686	NA	P-0015403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	23	488	1	ENST00000268489.5:c.2084C>T	p.Pro695Leu	p.P695L	ENST00000268489	NM_006885.3	695	cCg/cTg	2/10	1	2	FACETS	0.294	0.228	0.369	0.294	0.228	0.369	SUBCLONAL	1	TRUE	1	0.440200040822626	2		489	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0015403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	18	508	0	ENST00000269305.4:c.673-1G>C		p.X225_splice	ENST00000269305	NM_001126112.2	225			1	2	FACETS	0.248	0.186	0.321	0.248	0.186	0.321	SUBCLONAL	1	TRUE	1	0.440200040822626	2		508	330	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129710	47129710	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	20	485	0	ENST00000409792.3:c.5170G>T	p.Glu1724Ter	p.E1724*	ENST00000409792	NM_014159.6	1724	Gaa/Taa	10/21	0.0996445525032037	4	FACETS	0.349	0.266	0.446	0.174	0.133	0.223	INDETERMINATE	1	TRUE	2	0.440200040822626	4		485	375	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139465	47139465	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs774671060	NA	P-0015403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	29	577	0	ENST00000409792.3:c.5122C>T	p.Arg1708Ter	p.R1708*	ENST00000409792	NM_014159.6	1708	Cga/Tga	9/21	0.0996445525032037	4	FACETS	0.362	0.29	0.445	0.181	0.145	0.223	INDETERMINATE	1	TRUE	2	0.440200040822626	4		577	524	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	179	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.372190902394874	2	FACETS	0.892	0.829	0.956	0.892	0.829	0.956	CLONAL	2	TRUE	0	0.399864008103709	2		493	502	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164505	47164505	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	150	292	0	ENST00000409792.3:c.1621C>T	p.Arg541Ter	p.R541*	ENST00000409792	NM_014159.6	541	Cga/Tga	3/21	0.399864008103709	3	FACETS	0.886	0.815	0.959	0.591	0.543	0.64	CLONAL	2	TRUE	0	0.399864008103709	3		292	508	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741413	145741413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144637135	NA	P-0015404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	153	674	0	ENST00000428558.2:c.1090G>A	p.Val364Met	p.V364M	ENST00000428558	NM_004260.3	364	Gtg/Atg	5/22	0.390193007768362	4	FACETS	0.811	0.74	0.886	0.405	0.37	0.443	CLONAL	1	TRUE	2	0.399864008103709	4		674	1321	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245051	53245051	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	335	261	0	ENST00000375401.3:c.889G>T	p.Glu297Ter	p.E297*	ENST00000375401	NM_004187.3	297	Gag/Tag	7/26	0.331594581649151	2	FACETS	1	0.974	1			1	CLONAL	3	TRUE	NA	0.399864008103709	2		261	547	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174901	11174901	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	127	608	1	ENST00000361445.4:c.7133G>T	p.Arg2378Ile	p.R2378I	ENST00000361445	NM_004958.3	2378	aGa/aTa	52/58	0.353634363487689	4	FACETS	0.926	0.838	1	0.463	0.419	0.51	CLONAL	1	TRUE	2	0.399864008103709	4		609	960	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741639	17741639	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	94	307	0	ENST00000250003.3:c.310A>C	p.Lys104Gln	p.K104Q	ENST00000250003	NM_002478.4	104	Aag/Cag	1/3	0.353634363487689	4	FACETS	1	0.925	1	0.524	0.467	0.585	CLONAL	1	TRUE	2	0.399864008103709	4		307	628	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456265	32456265	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	321	661	1	ENST00000332351.3:c.627G>T	p.Gln209His	p.Q209H	ENST00000332351	NM_024426.4	209	caG/caT	1/10	0.353634363487689	4	FACETS	0.939	0.886	0.993	0.939	0.886	0.993	CLONAL	2	TRUE	2	0.399864008103709	4		662	1197	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456585	32456585	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	45	78	0	ENST00000332351.3:c.307G>T	p.Ala103Ser	p.A103S	ENST00000332351	NM_024426.4	103	Gcg/Tcg	1/10	0.353634363487689	4	FACETS	0.829	0.706	0.961	0.829	0.706	0.961	CLONAL	2	TRUE	2	0.399864008103709	4		78	190	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948545	71948545	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	295	633	0	ENST00000298229.2:c.3257G>T	p.Arg1086Leu	p.R1086L	ENST00000298229	NM_001567.3	1086	cGt/cTt	26/28	0.353634363487689	4	FACETS	0.913	0.86	0.968	0.913	0.86	0.968	CLONAL	2	TRUE	2	0.399864008103709	4		633	1131	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21629887	21629887	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1307316955	NA	P-0015404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	181	598	0	ENST00000421138.2:c.907G>T	p.Asp303Tyr	p.D303Y	ENST00000421138		303	Gat/Tat	9/16	0.372190902394874	2	FACETS	0.969	0.903	1	0.969	0.903	1	CLONAL	2	TRUE	0	0.399864008103709	2		598	467	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781326	3781326	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1297	143	654	1	ENST00000262367.5:c.5039C>G	p.Ser1680Cys	p.S1680C	ENST00000262367	NM_004380.2	1680	tCc/tGc	30/31	0.399864008103709	5	FACETS	0.795	0.722	0.871	0.265	0.24	0.291	SUBCLONAL	1	TRUE	2	0.399864008103709	5		655	1440	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128072	30128072	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1309	159	652	0	ENST00000263025.4:c.1057G>C	p.Asp353His	p.D353H	ENST00000263025	NM_002746.2	353	Gat/Cat	8/9	0.399864008103709	5	FACETS	0.867	0.792	0.946			1	CLONAL	1	TRUE	NA	0.399864008103709	5		652	1468	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791575	42791575	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1254676708	NA	P-0015404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	134	486	0	ENST00000575354.2:c.556G>A	p.Glu186Lys	p.E186K	ENST00000575354	NM_015125.3	186	Gag/Aag	4/20	0.353634363487689	4	FACETS	1	0.915	1	0.504	0.457	0.553	CLONAL	1	TRUE	2	0.399864008103709	4		486	931	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881462	111881462	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs199602272	NA	P-0015404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	98	418	0	ENST00000393256.3:c.140A>G	p.Asn47Ser	p.N47S	ENST00000393256	NM_006538.4	47	aAt/aGt	2/4	0.390193007768362	4	FACETS	0.922	0.823	1	0.461	0.411	0.514	CLONAL	1	TRUE	2	0.399864008103709	4		418	744	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098852	178098852	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	108	562	0	ENST00000397062.3:c.193G>T	p.Glu65Ter	p.E65*	ENST00000397062	NM_006164.4	65	Gag/Tag	2/5	0.390193007768362	4	FACETS	0.797	0.714	0.885	0.398	0.357	0.443	SUBCLONAL	1	TRUE	2	0.399864008103709	4		562	949	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561118	9561118	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	132	306	0	ENST00000353224.5:c.664G>T	p.Ala222Ser	p.A222S	ENST00000353224	NM_177990.2	222	Gcc/Tcc	4/10	0.353634363487689	4	FACETS	0.897	0.819	0.979	0.897	0.819	0.979	CLONAL	2	TRUE	2	0.399864008103709	4		306	515	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112029188	112029188	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	214	549	0	ENST00000368678.4:c.380C>A	p.Thr127Asn	p.T127N	ENST00000368678		127	aCt/aAt	5/13	0.399864008103709	3	FACETS	0.751	0.699	0.805			1	SUBCLONAL	2	TRUE	NA	0.399864008103709	3		549	855	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527402	137527402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	63	366	1	ENST00000367739.4:c.244C>T	p.His82Tyr	p.H82Y	ENST00000367739	NM_000416.2	82	Cat/Tat	3/7	0.390193007768362	4	FACETS	0.835	0.723	0.957	0.418	0.361	0.479	CLONAL	1	TRUE	2	0.399864008103709	4		367	528	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150478	157150478	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	197	388	0	ENST00000346085.5:c.1660G>T	p.Gly554Cys	p.G554C	ENST00000346085	NM_020732.3	554	Ggc/Tgc	2/20	0.390193007768362	4	FACETS	0.898	0.834	0.964	0.898	0.834	0.964	CLONAL	2	TRUE	2	0.399864008103709	4		388	768	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979445	2979445	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	104	610	0	ENST00000396946.4:c.802G>C	p.Glu268Gln	p.E268Q	ENST00000396946	NM_032415.4	268	Gaa/Caa	6/25	0.390193007768362	4	FACETS	0.73	0.653	0.813	0.365	0.326	0.407	SUBCLONAL	1	TRUE	2	0.399864008103709	4		610	997	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336664	81336665	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	53	341	0	ENST00000222390.5:c.1557_1558insA	p.Gly520ArgfsTer26	p.G520Rfs*26	ENST00000222390	NM_000601.4	519	-/A	14/18	0.398866069697183	3	FACETS	0.835	0.714	0.966	0.417	0.357	0.483	CLONAL	1	TRUE	1	0.399864008103709	3		341	381	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151932963	151932963	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2	24	7	0	ENST00000262189.6:c.2708G>T	p.Gly903Val	p.G903V	ENST00000262189	NM_170606.2	903	gGg/gTg	16/59	0.398866069697183	3	FACETS	0.923	0.846	0.971	1	0.97	1	CLONAL	6	TRUE	1	0.399864008103709	3		7	26	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981722	70981722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	303	750	1	ENST00000276594.2:c.374G>A	p.Ser125Asn	p.S125N	ENST00000276594	NM_024504.3	125	aGc/aAc	2/8	0.390193007768362	4	FACETS	0.869	0.818	0.921	0.869	0.818	0.921	CLONAL	2	TRUE	2	0.399864008103709	4		751	1221	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5073697	5073697	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs1370719342	NA	P-0015404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	159	232	1	ENST00000381652.3:c.1777-1G>T		p.X593_splice	ENST00000381652	NM_004972.3	593			0.384647453822812	4	FACETS	0.93	0.863	0.998	0.93	0.863	0.998	CLONAL	3	TRUE	1	0.399864008103709	4		233	399	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376714	8376714	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	141	463	1	ENST00000356435.5:c.4399C>A	p.Gln1467Lys	p.Q1467K	ENST00000356435		1467	Cag/Aag	27/35	0.384647453822812	4	FACETS	1	0.98	1	0.418	0.38	0.457	CLONAL	1	TRUE	1	0.399864008103709	4		464	788	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399926	139399927	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0015404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	310	767	2	ENST00000277541.6:c.4421_4422delinsCT	p.Trp1474Ser	p.W1474S	ENST00000277541	NM_017617.3	1474	tGG/tCT	25/34	0.200847019073386	4	FACETS	0.945	0.892	1	0.945	0.892	1	INDETERMINATE	2	TRUE	2	0.399864008103709	4		769	1148	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802670	139802670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	161	370	0	ENST00000247668.2:c.515G>A	p.Gly172Glu	p.G172E	ENST00000247668	NM_021138.3	172	gGa/gAa	5/11	0.200847019073386	4	FACETS	0.873	0.803	0.944	0.873	0.803	0.944	INDETERMINATE	2	TRUE	2	0.399864008103709	4		370	646	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317466	1317466	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	374	675	0	ENST00000400841.2:c.599C>A	p.Pro200Gln	p.P200Q	ENST00000400841		200	cCa/cAa	5/6	0.331594581649151	2	FACETS	0.78	0.741	0.82			1	SUBCLONAL	2	TRUE	NA	0.399864008103709	2		675	1199	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0015406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	44	465	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	1	2	FACETS	0.905	0.762	1	0.905	0.762	1	CLONAL	1	TRUE	1	0.284358884724347	2		465	342	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577561	7577561	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs764342812	NA	P-0015406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	79	488	0	ENST00000269305.4:c.720T>G	p.Ser240Arg	p.S240R	ENST00000269305	NM_001126112.2	240	agT/agG	7/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.284358884724347	2		488	480	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061249	38061249	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	77	646	0	ENST00000250448.2:c.740A>G	p.His247Arg	p.H247R	ENST00000250448	NM_004496.3	247	cAc/cGc	2/2	1	2	FACETS	0.892	0.784	1	0.892	0.784	1	CLONAL	1	TRUE	1	0.284358884724347	2		646	607	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559208	29559208	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs767805288	NA	P-0015406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	24	355	0	ENST00000356175.3:c.3314+1G>A		p.X1105_splice	ENST00000356175	NM_000267.3	1105			1	2	FACETS	0.561	0.44	0.7	0.561	0.44	0.7	SUBCLONAL	1	TRUE	1	0.284358884724347	2		355	301	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667586	29667598	+	frameshift_variant	Frame_Shift_Del	DEL	AACTTGTATTCAG	AACTTGTATTCAG	-	novel	NA	P-0015406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	74	664	0	ENST00000356175.3:c.6922_6934del	p.Asn2308GlnfsTer13	p.N2308Qfs*13	ENST00000356175	NM_000267.3	2308	AACTTGTATTCAGca/ca	46/57	1	2	FACETS	0.905	0.793	1	0.905	0.793	1	CLONAL	1	TRUE	1	0.284358884724347	2		664	575	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0015408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	189	336	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.269735394934474	3	FACETS	0.816	0.754	0.88	0.816	0.754	0.88	CLONAL	2	TRUE	1	0.269735394934474	3		336	975	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764146326	NA	P-0015408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	71	652	0	ENST00000269305.4:c.841G>A	p.Asp281Asn	p.D281N	ENST00000269305	NM_001126112.2	281	Gac/Aac	8/11	0.269735394934474	1	FACETS	0.869	0.76	0.987	0.869	0.76	0.987	CLONAL	1	TRUE	0	0.269735394934474	1		652	524	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0015408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	77	337	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	0.269735394934474	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.269735394934474	1		337	452	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013690	12013690	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0015408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	117	344	0	ENST00000353533.5:c.634-2A>T		p.X212_splice	ENST00000353533	NM_003010.3	212			0.269735394934474	1	FACETS	0.998	0.9	1	0.998	0.9	1	CLONAL	1	TRUE	0	0.269735394934474	1		344	752	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503769	186503769	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	232	381	0	ENST00000323963.5:c.446A>G	p.Gln149Arg	p.Q149R	ENST00000323963		149	cAg/cGg	5/11	0.269735394934474	5	FACETS	1	0.965	1			1	CLONAL	2	TRUE	NA	0.269735394934474	5		381	1145	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93607827	93607827	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	31	457	1	ENST00000375746.1:c.529G>T	p.Glu177Ter	p.E177*	ENST00000375746	NM_001174167.1	177	Gaa/Taa	3/14	1	2	FACETS	0.512	0.414	0.623	0.512	0.414	0.623	SUBCLONAL	1	TRUE	1	0.269735394934474	2		458	449	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	47	775	1	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	0.237158579837551	5	FACETS	0.926	0.781	1			1	CLONAL	1	FALSE	NA	0.237158579837551	5		776	580	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	59	462	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	1	2	FACETS	0.829	0.719	0.948	1	0.974	1	CLONAL	2	FALSE	1	0.237158579837551	2		462	300	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490980	56490980	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs931676601	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	95	549	0	ENST00000267101.3:c.2426A>G	p.Gln809Arg	p.Q809R	ENST00000267101	NM_001982.3	809	cAg/cGg	20/28	0.176077421580553	4	FACETS	0.93	0.83	1	0.93	0.83	1	CLONAL	2	FALSE	2	0.237158579837551	4		549	533	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131205	17131205	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs757060348	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	50	651	0	ENST00000285071.4:c.247G>A	p.Glu83Lys	p.E83K	ENST00000285071	NM_144997.5	83	Gag/Aag	4/14	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.237158579837551	2		651	325	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	44	581	2	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.992	0.834	1	0.992	0.834	1	CLONAL	1	FALSE	1	0.237158579837551	2		583	374	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779129	135779129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	23	373	0	ENST00000298552.3:c.2117G>A	p.Arg706His	p.R706H	ENST00000298552	NM_001162426.1	706	cGt/cAt	17/23	1	2	FACETS	0.579	0.451	0.727	0.579	0.451	0.727	SUBCLONAL	1	FALSE	1	0.237158579837551	2		373	335	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639588	47639588	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63749897	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	33	430	2	ENST00000233146.2:c.687del	p.Ala230LeufsTer16	p.A230Lfs*16	ENST00000233146	NM_000251.2	227	agA/ag	4/16	0.232065320119974	3	FACETS	0.837	0.682	1	0.279	0.227	0.337	CLONAL	1	FALSE	0	0.237158579837551	3		432	372	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435136	110435136	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs780127725	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	47	644	0	ENST00000375856.3:c.3265G>C	p.Ala1089Pro	p.A1089P	ENST00000375856	NM_003749.2	1089	Gcc/Ccc	1/2	0.176077421580553	4	FACETS	1	0.93	1	0.592	0.5	0.693	CLONAL	1	FALSE	2	0.237158579837551	4		644	414	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088659	27088659	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	74	706	0	ENST00000324856.7:c.2272del	p.Gln758ArgfsTer75	p.Q758Rfs*75	ENST00000324856	NM_006015.4	756	aaC/aa	7/20	0.176077421580553	4	FACETS	1	0.952	1	0.59	0.517	0.67	CLONAL	1	FALSE	2	0.237158579837551	4		706	654	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107136	27107137	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	47	415	0	ENST00000324856.7:c.6749_6750del	p.Glu2250ValfsTer27	p.E2250Vfs*27	ENST00000324856	NM_006015.4	2249	tcAGag/tcag	20/20	0.176077421580553	4	FACETS	1	0.875	1	0.521	0.439	0.61	CLONAL	1	FALSE	2	0.237158579837551	4		415	471	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856592	111856592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1268789091	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	12	121	2	ENST00000341259.2:c.643G>A	p.Ala215Thr	p.A215T	ENST00000341259	NM_005475.2	215	Gca/Aca	2/8	0.176077421580553	4	FACETS	0.754	0.538	1	0.754	0.538	1	CLONAL	2	FALSE	2	0.237158579837551	4		123	83	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871044	12871044	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	55	261	0	ENST00000228872.4:c.275del	p.Pro92ArgfsTer27	p.P92Rfs*27	ENST00000228872	NM_004064.3	91	Ccc/cc	1/3	0.237158579837551	5	FACETS	1	0.882	1	0.345	0.295	0.4	CLONAL	1	FALSE	2	0.237158579837551	5		261	607	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803483	32803483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536291251	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	67	694	1	ENST00000374899.4:c.676C>T	p.Arg226Trp	p.R226W	ENST00000374899	NM_018833.2	226	Cgg/Tgg	4/12	0.148894757506023	3	FACETS	0.952	0.827	1	0.317	0.275	0.363	CLONAL	1	FALSE	0	0.237158579837551	3		695	664	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733375	85733377	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs587776637	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	59	501	0	ENST00000370580.1:c.635_637del	p.Glu212del	p.E212del	ENST00000370580	NM_003921.4	212	gAAGga/gga	3/3	0.176077421580553	4	FACETS	1	0.892	1	0.522	0.449	0.601	CLONAL	1	FALSE	2	0.237158579837551	4		501	590	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981111	201981111	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	156	582	0	ENST00000359651.3:c.193del	p.Gln65SerfsTer90	p.Q65Sfs*90	ENST00000359651		64	Ccc/cc	2/8	0.120211625890576	3	FACETS	1	0.927	1	1	0.927	1	INDETERMINATE	2	FALSE	1	0.237158579837551	3		582	728	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982387	201982387	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	252	741	1	ENST00000359651.3:c.766G>T	p.Glu256Ter	p.E256*	ENST00000359651		256	Gag/Tag	6/8	0.120211625890576	3	FACETS	0.921	0.864	0.98	1	0.992	1	INDETERMINATE	3	FALSE	1	0.237158579837551	3		742	860	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201089	108201089	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779865	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	37	321	0	ENST00000278616.4:c.7456C>T	p.Arg2486Ter	p.R2486*	ENST00000278616	NM_000051.3	2486	Cga/Tga	50/63	0.176077421580553	4	FACETS	0.946	0.781	1	0.473	0.39	0.566	CLONAL	1	FALSE	2	0.237158579837551	4		321	408	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342685	118342685	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	28	265	0	ENST00000534358.1:c.811A>T	p.Lys271Ter	p.K271*	ENST00000534358	NM_005933.3	271	Aaa/Taa	3/36	0.176077421580553	4	FACETS	1	0.863	1	0.549	0.44	0.672	CLONAL	1	FALSE	2	0.237158579837551	4		265	266	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377230	118377230	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	52	399	0	ENST00000534358.1:c.10627del	p.Thr3543ProfsTer8	p.T3543Pfs*8	ENST00000534358	NM_005933.3	3541	ccA/cc	27/36	0.176077421580553	4	FACETS	1	0.955	1	0.665	0.567	0.771	CLONAL	1	FALSE	2	0.237158579837551	4		399	408	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006467	12006467	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	38	640	1	ENST00000396373.4:c.435G>T	p.Glu145Asp	p.E145D	ENST00000396373	NM_001987.4	145	gaG/gaT	4/8	0.237158579837551	4	FACETS	0.596	0.491	0.714			1	SUBCLONAL	1	FALSE	NA	0.237158579837551	4		641	665	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859457	57859457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	31	507	1	ENST00000228682.2:c.602G>A	p.Ser201Asn	p.S201N	ENST00000228682	NM_005269.2	201	aGc/aAc	6/12	0.176077421580553	4	FACETS	0.853	0.691	1	0.427	0.345	0.519	CLONAL	1	FALSE	2	0.237158579837551	4		508	379	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28908249	28908249	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	38	483	1	ENST00000282397.4:c.2506G>T	p.Gly836Trp	p.G836W	ENST00000282397	NM_002019.4	836	Ggg/Tgg	18/30	0.237158579837551	1	FACETS	0.6	0.495	0.716	0.6	0.495	0.716	SUBCLONAL	1	FALSE	0	0.237158579837551	1		484	471	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337636	73337636	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	34	213	0	ENST00000377767.4:c.2080C>A	p.Pro694Thr	p.P694T	ENST00000377767	NM_014953.3	694	Cca/Aca	16/21	0.176077421580553	4	FACETS	1	0.838	1	0.513	0.419	0.617	CLONAL	1	FALSE	2	0.237158579837551	4		213	346	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435724	110435724	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	27	353	0	ENST00000375856.3:c.2677C>A	p.Leu893Met	p.L893M	ENST00000375856	NM_003749.2	893	Ctg/Atg	1/2	0.176077421580553	4	FACETS	1	0.927	1	0.697	0.559	0.853	CLONAL	1	FALSE	2	0.237158579837551	4		353	202	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122925	2122925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150672640	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	51	697	2	ENST00000219476.3:c.2296G>A	p.Val766Met	p.V766M	ENST00000219476	NM_000548.3	766	Gtg/Atg	21/42	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	FALSE	1	0.237158579837551	2		699	387	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637631	23637631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45476495	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	27	656	1	ENST00000261584.4:c.2674G>A	p.Glu892Lys	p.E892K	ENST00000261584	NM_024675.3	892	Gaa/Aaa	7/13	1	2	FACETS	0.511	0.406	0.631	0.511	0.406	0.631	SUBCLONAL	1	FALSE	1	0.237158579837551	2		657	446	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902172	50902172	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	23	559	0	ENST00000440232.2:c.64C>A	p.Leu22Ile	p.L22I	ENST00000440232	NM_002691.3	22	Ctc/Atc	2/27	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.237158579837551	NA		559	290	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52725368	52725368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	20	399	0	ENST00000322088.6:c.1535G>A	p.Cys512Tyr	p.C512Y	ENST00000322088	NM_014225.5	512	tGt/tAt	13/15	0.237158579837551	0	FACETS	0.532	0.407	0.676			1	SUBCLONAL	1	FALSE	0	0.237158579837551	0		399	242	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994394	25994394	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs565110158	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	43	316	0	ENST00000435504.4:c.419C>A	p.Pro140Gln	p.P140Q	ENST00000435504		140	cCg/cAg	6/13	0.169547900134719	2	FACETS	1	0.862	1	0.515	0.432	0.606	CLONAL	1	FALSE	0	0.237158579837551	2		316	352	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656936	47656936	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	92	319	0	ENST00000233146.2:c.1132G>T	p.Glu378Ter	p.E378*	ENST00000233146	NM_000251.2	378	Gaa/Taa	7/16	0.232065320119974	3	FACETS	0.836	0.75	0.926	0.836	0.75	0.926	CLONAL	3	FALSE	0	0.237158579837551	3		319	346	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439698	220439698	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	42	618	0	ENST00000243786.2:c.551C>G	p.Ser184Cys	p.S184C	ENST00000243786	NM_002191.3	184	tCt/tGt	2/2	0.225116560607642	4	FACETS	1	0.937	1	0.631	0.529	0.745	CLONAL	1	FALSE	2	0.237158579837551	4		618	347	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346615	225346615	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	62	311	0	ENST00000264414.4:c.2023C>G	p.Gln675Glu	p.Q675E	ENST00000264414	NM_003590.4	675	Caa/Gaa	14/16	0.225116560607642	4	FACETS	1	0.961	1	0.663	0.573	0.76	CLONAL	1	FALSE	2	0.237158579837551	4		311	488	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264823	46264823	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	36	464	0	ENST00000371998.3:c.1693C>G	p.Gln565Glu	p.Q565E	ENST00000371998		565	Cag/Gag	12/23	0.237158579837551	1	FACETS	0.752	0.619	0.9	0.752	0.619	0.9	SUBCLONAL	1	FALSE	0	0.237158579837551	1		464	356	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747856	41747856	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	21	520	0	ENST00000226382.2:c.913A>G	p.Lys305Glu	p.K305E	ENST00000226382	NM_003924.3	305	Aaa/Gaa	3/3	1	2	FACETS	0.649	0.5	0.821	0.649	0.5	0.821	SUBCLONAL	1	FALSE	1	0.237158579837551	2		520	273	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217136	66217136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1376354548	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	74	462	0	ENST00000273854.3:c.2479G>A	p.Asp827Asn	p.D827N	ENST00000273854	NM_004439.5	827	Gat/Aat	14/18	0.225116560607642	4	FACETS	1	0.96	1	0.622	0.544	0.705	CLONAL	1	FALSE	2	0.237158579837551	4		462	621	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539148	187539148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	37	373	0	ENST00000441802.2:c.8592G>A	p.Met2864Ile	p.M2864I	ENST00000441802	NM_005245.3	2864	atG/atA	10/27	0.225116560607642	4	FACETS	0.917	0.756	1	0.458	0.378	0.548	CLONAL	1	FALSE	2	0.237158579837551	4		373	421	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540958	187540958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs189912205	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	30	247	1	ENST00000441802.2:c.6782C>T	p.Thr2261Met	p.T2261M	ENST00000441802	NM_005245.3	2261	aCg/aTg	10/27	0.225116560607642	4	FACETS	0.966	0.78	1	0.483	0.39	0.588	CLONAL	1	FALSE	2	0.237158579837551	4		248	324	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803536	32803536	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	52	560	0	ENST00000374899.4:c.623G>A	p.Gly208Asp	p.G208D	ENST00000374899	NM_018833.2	208	gGc/gAc	4/12	0.148894757506023	3	FACETS	0.913	0.778	1	0.304	0.259	0.354	CLONAL	1	FALSE	0	0.237158579837551	3		560	537	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109315704	109315704	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	103	675	1	ENST00000436639.2:c.1081G>T	p.Glu361Ter	p.E361*	ENST00000436639	NM_014454.2	361	Gaa/Taa	6/10	0.176077421580553	4	FACETS	0.902	0.809	1	0.902	0.809	1	CLONAL	2	FALSE	2	0.237158579837551	4		676	596	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207450	29207450	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	43	302	1	ENST00000240100.2:c.346G>T	p.Glu116Ter	p.E116*	ENST00000240100	NM_001394.6	116	Gag/Tag	1/4	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.237158579837551	2		303	282	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5078341	5078342	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	34	340	0	ENST00000381652.3:c.2033dup	p.Asn678LysfsTer21	p.N678Kfs*21	ENST00000381652	NM_004972.3	676	-/A	16/25	1	2	FACETS	0.79	0.646	0.951	0.79	0.646	0.951	CLONAL	1	FALSE	1	0.237158579837551	2		340	363	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0015411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	56	363	2	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	0.65	0.56	0.748	0.65	0.56	0.748	SUBCLONAL	1	TRUE	1	0.523395056955462	2		365	329	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0015411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	74	437	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.451963428860646	1	FACETS	0.756	0.67	0.848	0.756	0.67	0.848	SUBCLONAL	1	TRUE	0	0.523395056955462	1		437	276	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916929	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519931	NA	P-0015411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	54	393	0	ENST00000263967.3:c.316G>C	p.Gly106Arg	p.G106R	ENST00000263967	NM_006218.2	106	Ggc/Cgc	2/21	1	2	FACETS	0.893	0.772	1	0.893	0.772	1	CLONAL	1	TRUE	1	0.523395056955462	2		393	231	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967270	134967270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374549505	NA	P-0015411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	71	490	0	ENST00000398015.3:c.2609G>A	p.Arg870Gln	p.R870Q	ENST00000398015	NM_004441.4	870	cGg/cAg	14/16	1	2	FACETS	0.754	0.662	0.851	0.754	0.662	0.851	SUBCLONAL	1	TRUE	1	0.523395056955462	2		490	360	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944259	81944259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	133	480	0	ENST00000359376.3:c.1868G>A	p.Arg623His	p.R623H	ENST00000359376	NM_002661.3	623	cGc/cAc	18/33	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.523395056955462	2		480	442	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508260	106508260	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	56	233	0	ENST00000359195.3:c.254C>T	p.Ala85Val	p.A85V	ENST00000359195	NM_002649.2	85	gCg/gTg	2/11	0.511180310531165	2	FACETS	0.911	0.789	1	0.455	0.394	0.52	CLONAL	1	TRUE	0	0.523395056955462	2		233	235	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247496	71247496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1202112901	NA	P-0015411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	92	420	1	ENST00000318789.4:c.37G>A	p.Gly13Ser	p.G13S	ENST00000318789	NM_032682.5	13	Ggt/Agt	6/21	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.523395056955462	2		421	344	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63816897	63816897	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	39	215	0	ENST00000279873.7:c.868G>T	p.Ala290Ser	p.A290S	ENST00000279873	NM_032199.2	290	Gcc/Tcc	6/10	1	2	FACETS	0.866	0.728	1	0.866	0.728	1	CLONAL	1	TRUE	1	0.523395056955462	2		215	172	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346979	89346979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs565960089	NA	P-0015411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	58	262	0	ENST00000301030.4:c.5971C>T	p.Pro1991Ser	p.P1991S	ENST00000301030	NM_001256183.1	1991	Cca/Tca	9/13	1	2	FACETS	0.852	0.74	0.973	0.852	0.74	0.973	CLONAL	1	TRUE	1	0.523395056955462	2		262	260	SUCCESS
APC	324	MSKCC	GRCh37	5	112175458	112175464	+	frameshift_variant	Frame_Shift_Del	DEL	TGTCAGT	TGTCAGT	-	novel	NA	P-0015411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	96	275	0	ENST00000257430.4:c.4168_4174del	p.Val1390HisfsTer23	p.V1390Hfs*23	ENST00000257430	NM_000038.5	1389	tcTGTCAGT/tc	16/16	0.471136138542952	2	FACETS	0.815	0.741	0.89	0.815	0.741	0.89	CLONAL	2	TRUE	0	0.523395056955462	2		275	225	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0015412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	667	749	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.595128487493498	2	FACETS	0.993	0.963	1	0.993	0.963	1	CLONAL	2	TRUE	0	0.595128487493498	2		750	1129	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255020	16255020	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747601086	NA	P-0015412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	307	414	0	ENST00000375759.3:c.2285G>A	p.Arg762Gln	p.R762Q	ENST00000375759	NM_015001.2	762	cGg/cAg	11/15	0.442267261084616	3	FACETS	0.88	0.834	0.926	0.88	0.834	0.926	CLONAL	2	TRUE	1	0.595128487493498	3		414	761	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177700	56177700	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	252	391	0	ENST00000399503.3:c.2673C>A	p.Asn891Lys	p.N891K	ENST00000399503	NM_005921.1	891	aaC/aaA	14/20	0.519450669320266	2	FACETS	0.886	0.84	0.931	0.886	0.84	0.931	CLONAL	2	TRUE	0	0.595128487493498	2		391	478	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969923	161969923	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	222	539	2	ENST00000366898.1:c.1046A>T	p.Lys349Ile	p.K349I	ENST00000366898	NM_004562.2	349	aAa/aTa	9/12	0.436115009011302	3	FACETS	0.995	0.926	1			1	CLONAL	1	TRUE	NA	0.595128487493498	3		541	973	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0015413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	751	650	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.601671289158463	5	FACETS	0.937	0.907	0.968	0.937	0.907	0.968	CLONAL	3	TRUE	2	0.601671289158463	5		650	1689	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578463	7578463	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371524413	NA	P-0015413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	348	832	0	ENST00000269305.4:c.467G>C	p.Arg156Pro	p.R156P	ENST00000269305	NM_001126112.2	156	cGc/cCc	5/11	1	2	FACETS	0.937	0.887	0.988	0.937	0.887	0.988	CLONAL	1	TRUE	1	0.601671289158463	2		832	1235	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0015413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	265	641	3	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	1	2	FACETS	0.929	0.872	0.987	0.929	0.872	0.987	CLONAL	1	TRUE	1	0.601671289158463	2		644	948	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680482	30680482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	464	500	0	ENST00000376406.3:c.1237G>A	p.Ala413Thr	p.A413T	ENST00000376406	NM_014641.2	413	Gcg/Acg	5/15	0.601671289158463	3	FACETS	0.973	0.933	1	0.973	0.933	1	CLONAL	2	TRUE	1	0.601671289158463	3		500	1031	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426366	49426366	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1414	439	935	0	ENST00000301067.7:c.12122C>T	p.Pro4041Leu	p.P4041L	ENST00000301067	NM_003482.3	4041	cCc/cTc	39/54	0.178775021437658	5	FACETS	1	0.996	1			1	INDETERMINATE	1	TRUE	NA	0.601671289158463	5		935	1853	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443502	49443502	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751561975	NA	P-0015413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	195	423	0	ENST00000301067.7:c.3869G>A	p.Arg1290Gln	p.R1290Q	ENST00000301067	NM_003482.3	1290	cGg/cAg	11/54	0.178775021437658	5	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.601671289158463	5		423	917	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482366	56482366	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	191	627	0	ENST00000267101.3:c.914G>C	p.Cys305Ser	p.C305S	ENST00000267101	NM_001982.3	305	tGt/tCt	8/28	0.601429417906271	2	FACETS	0.802	0.743	0.863	0.401	0.371	0.432	CLONAL	1	TRUE	0	0.601671289158463	2		627	792	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678499	88678499	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	212	507	1	ENST00000360948.2:c.1037A>T	p.Lys346Met	p.K346M	ENST00000360948	NM_001012338.2	346	aAg/aTg	9/19	1	2	FACETS	0.954	0.889	1	0.954	0.889	1	CLONAL	1	TRUE	1	0.601671289158463	2		508	739	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109315704	109315704	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	132	675	1	ENST00000436639.2:c.1081G>T	p.Glu361Ter	p.E361*	ENST00000436639	NM_014454.2	361	Gaa/Taa	6/10	0.509396648151021	2	FACETS	0.512	0.464	0.563	0.256	0.232	0.282	SUBCLONAL	1	TRUE	0	0.562635358208133	2		676	916	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	90	455	2	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	0.518952343676198	3	FACETS	0.489	0.433	0.549	0.163	0.144	0.183	SUBCLONAL	1	TRUE	0	0.562635358208133	3		457	838	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518111	8518111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	325	420	2	ENST00000356435.5:c.1280G>A	p.Arg427Gln	p.R427Q	ENST00000356435		427	cGa/cAa	10/35	0.490629024884745	2	FACETS	0.865	0.824	0.906	0.865	0.824	0.906	CLONAL	2	TRUE	0	0.562635358208133	2		422	668	SUCCESS
APC	324	MSKCC	GRCh37	5	112173949	112173949	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	86	429	0	ENST00000257430.4:c.2658G>C	p.Gln886His	p.Q886H	ENST00000257430	NM_000038.5	886	caG/caC	16/16	0.373462579100172	3	FACETS	0.49	0.432	0.551	0.245	0.216	0.276	SUBCLONAL	1	TRUE	1	0.562635358208133	3		429	800	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531788	46531788	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	87	477	0	ENST00000262741.5:c.559C>T	p.Gln187Ter	p.Q187*	ENST00000262741	NM_003629.3	187	Cag/Tag	5/10	0.333314051311451	1	FACETS	0.377	0.334	0.423	0.377	0.334	0.423	INDETERMINATE	1	TRUE	0	0.562635358208133	1		477	589	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444604	78444604	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	322	453	0	ENST00000370768.2:c.85G>T	p.Asp29Tyr	p.D29Y	ENST00000370768	NM_003902.3	29	Gac/Tac	1/20	0.387262967837085	3	FACETS	0.763	0.722	0.805	0.763	0.722	0.805	SUBCLONAL	2	TRUE	1	0.562635358208133	3		453	961	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458600	120458600	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	139	574	0	ENST00000256646.2:c.6745G>T	p.Val2249Phe	p.V2249F	ENST00000256646	NM_024408.3	2249	Gtc/Ttc	34/34	0.387262967837085	3	FACETS	0.558	0.507	0.612	0.279	0.253	0.306	SUBCLONAL	1	TRUE	1	0.562635358208133	3		574	1134	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120469223	120469223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	145	528	0	ENST00000256646.2:c.3904G>A	p.Glu1302Lys	p.E1302K	ENST00000256646	NM_024408.3	1302	Gaa/Aaa	24/34	0.387262967837085	3	FACETS	0.592	0.539	0.648	0.296	0.269	0.324	SUBCLONAL	1	TRUE	1	0.562635358208133	3		528	1116	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451167	70451167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	405	590	0	ENST00000373644.4:c.6007G>A	p.Asp2003Asn	p.D2003N	ENST00000373644	NM_030625.2	2003	Gat/Aat	12/12	0.254608414159426	2	FACETS	1	0.995	1	0.684	0.653	0.716	INDETERMINATE	1	TRUE	0	0.562635358208133	2		590	1052	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248579	8248579	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	174	697	1	ENST00000335790.3:c.308G>T	p.Arg103Leu	p.R103L	ENST00000335790	NM_002315.2	103	cGg/cTg	3/4	0.517543026013272	2	FACETS	0.601	0.553	0.652	0.301	0.276	0.326	SUBCLONAL	1	TRUE	0	0.562635358208133	2		698	1029	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443932	49443932	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768785463	NA	P-0015414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1385	163	721	0	ENST00000301067.7:c.3439G>A	p.Glu1147Lys	p.E1147K	ENST00000301067	NM_003482.3	1147	Gaa/Aaa	11/54	0.534662608925381	3	FACETS	0.48	0.438	0.523	0.16	0.146	0.175	SUBCLONAL	1	TRUE	0	0.562635358208133	3		721	1548	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448533	49448533	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	112	480	0	ENST00000301067.7:c.178G>A	p.Gly60Arg	p.G60R	ENST00000301067	NM_003482.3	60	Ggg/Agg	3/54	0.534662608925381	3	FACETS	0.487	0.437	0.54	0.162	0.145	0.18	SUBCLONAL	1	TRUE	0	0.562635358208133	3		480	1048	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109813	115109813	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1571	173	772	2	ENST00000257566.3:c.2065G>T	p.Gly689Cys	p.G689C	ENST00000257566	NM_016569.3	689	Ggc/Tgc	8/8	0.534662608925381	3	FACETS	0.452	0.414	0.492	0.151	0.138	0.164	SUBCLONAL	1	TRUE	0	0.562635358208133	3		774	1744	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109923	115109923	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1525	172	754	0	ENST00000257566.3:c.1955G>T	p.Gly652Val	p.G652V	ENST00000257566	NM_016569.3	652	gGc/gTc	8/8	0.534662608925381	3	FACETS	0.462	0.423	0.502	0.154	0.141	0.168	SUBCLONAL	1	TRUE	0	0.562635358208133	3		754	1697	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120900	115120900	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	99	522	1	ENST00000257566.3:c.106C>A	p.His36Asn	p.H36N	ENST00000257566	NM_016569.3	36	Cac/Aac	1/8	0.534662608925381	3	FACETS	0.419	0.373	0.468	0.14	0.124	0.156	SUBCLONAL	1	TRUE	0	0.562635358208133	3		523	1076	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514615	103514615	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	181	374	0	ENST00000355739.4:c.1116G>T	p.Arg372Ser	p.R372S	ENST00000355739	NM_000123.3	372	agG/agT	8/15	0.544803481940278	1	FACETS	0.957	0.891	1	0.957	0.891	1	CLONAL	1	TRUE	0	0.562635358208133	1		374	483	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576193	88576193	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1305656648	NA	P-0015414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	138	517	0	ENST00000360948.2:c.1480C>G	p.Leu494Val	p.L494V	ENST00000360948	NM_001012338.2	494	Ctg/Gtg	13/19	0.509396648151021	2	FACETS	0.542	0.493	0.594	0.271	0.246	0.297	SUBCLONAL	1	TRUE	0	0.562635358208133	2		517	905	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347132	347132	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1289	245	901	1	ENST00000262320.3:c.1879G>T	p.Glu627Ter	p.E627*	ENST00000262320	NM_003502.3	627	Gag/Tag	7/11	0.560215280714281	2	FACETS	0.568	0.529	0.608	0.284	0.264	0.304	SUBCLONAL	1	TRUE	0	0.562635358208133	2		902	1534	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972460	81972460	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	231	620	0	ENST00000359376.3:c.3253G>C	p.Val1085Leu	p.V1085L	ENST00000359376	NM_002661.3	1085	Gta/Cta	29/33	0.518952343676198	3	FACETS	0.986	0.919	1	0.329	0.306	0.352	CLONAL	1	TRUE	0	0.562635358208133	3		620	1067	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990420	81990420	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	447	659	0	ENST00000359376.3:c.3691C>A	p.Leu1231Met	p.L1231M	ENST00000359376	NM_002661.3	1231	Ctg/Atg	32/33	0.518952343676198	3	FACETS	0.798	0.762	0.835	0.532	0.508	0.557	SUBCLONAL	2	TRUE	0	0.562635358208133	3		659	1275	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0015414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	511	539	0	ENST00000269305.4:c.375+1del		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.538477575517454	2	FACETS	0.952	0.918	0.986	0.952	0.918	0.986	CLONAL	2	TRUE	0	0.562635358208133	2		539	954	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868255	37868255	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1250	148	611	0	ENST00000269571.5:c.976G>C	p.Asp326His	p.D326H	ENST00000269571		326	Gat/Cat	8/27	0.373462579100172	3	FACETS	0.482	0.439	0.528	0.241	0.219	0.264	SUBCLONAL	1	TRUE	1	0.562635358208133	3		611	1398	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533718	63533718	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	122	436	0	ENST00000307078.5:c.1436C>G	p.Ser479Cys	p.S479C	ENST00000307078	NM_004655.3	479	tCc/tGc	6/11	0.373462579100172	3	FACETS	0.603	0.544	0.665	0.301	0.272	0.333	SUBCLONAL	1	TRUE	1	0.562635358208133	3		436	922	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599996	10599997	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0015414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	584	825	1	ENST00000171111.5:c.1579_1580delinsTA	p.Gly527Tyr	p.G527Y	ENST00000171111	NM_203500.1	527	GGt/TAt	5/6	0.509396648151021	2	FACETS	0.824	0.794	0.854	0.824	0.794	0.854	CLONAL	2	TRUE	0	0.562635358208133	2		826	1260	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288654	198288654	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	145	615	0	ENST00000335508.6:c.73C>G	p.Leu25Val	p.L25V	ENST00000335508	NM_012433.2	25	Ctt/Gtt	2/25	0.560215280714281	2	FACETS	0.46	0.419	0.504	0.23	0.209	0.252	SUBCLONAL	1	TRUE	0	0.562635358208133	2		615	1120	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259223	36259223	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	189	652	0	ENST00000300305.3:c.268G>T	p.Val90Leu	p.V90L	ENST00000300305		90	Gtg/Ttg	3/8	0.281549345431971	2	FACETS	0.515	0.474	0.557	0.257	0.237	0.279	INDETERMINATE	1	TRUE	0	0.562635358208133	2		652	1305	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524711	187524711	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	452	725	0	ENST00000441802.2:c.10969G>T	p.Gly3657Cys	p.G3657C	ENST00000441802	NM_005245.3	3657	Ggt/Tgt	19/27	0.173248330843086	5	FACETS	0.947	0.903	0.992			1	INDETERMINATE	2	TRUE	NA	0.562635358208133	5		725	1564	SUCCESS
APC	324	MSKCC	GRCh37	5	112173481	112173481	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	78	368	0	ENST00000257430.4:c.2190G>T	p.Met730Ile	p.M730I	ENST00000257430	NM_000038.5	730	atG/atT	16/16	0.373462579100172	3	FACETS	0.502	0.441	0.568	0.251	0.22	0.284	SUBCLONAL	1	TRUE	1	0.562635358208133	3		368	708	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149447876	149447876	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	397	710	2	ENST00000286301.3:c.1528C>A	p.Pro510Thr	p.P510T	ENST00000286301	NM_005211.3	510	Ccg/Acg	11/22	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.562635358208133	2		712	1331	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508526	106508526	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	313	225	0	ENST00000359195.3:c.520G>T	p.Glu174Ter	p.E174*	ENST00000359195	NM_002649.2	174	Gag/Tag	2/11	0.526533634861983	4	FACETS	0.849	0.807	0.891	1	0.993	1	CLONAL	3	TRUE	2	0.562635358208133	4		225	683	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309036	137309036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779808577	NA	P-0015414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1381	186	865	2	ENST00000481739.1:c.643C>T	p.Arg215Trp	p.R215W	ENST00000481739	NM_002957.4	215	Cgg/Tgg	5/10	0.281549345431971	2	FACETS	0.422	0.388	0.457	0.211	0.194	0.229	INDETERMINATE	1	TRUE	0	0.562635358208133	2		867	1567	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400172	139400173	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	177	740	0	ENST00000277541.6:c.4175dup	p.Gly1394ArgfsTer11	p.G1394Rfs*11	ENST00000277541	NM_017617.3	1392	ctg/ctTg	25/34	0.281549345431971	2	FACETS	0.47	0.431	0.51	0.235	0.215	0.255	INDETERMINATE	1	TRUE	0	0.562635358208133	2		740	1340	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942027	44942027	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	79	173	0	ENST00000377967.4:c.3277G>T	p.Asp1093Tyr	p.D1093Y	ENST00000377967	NM_021140.2	1093	Gac/Tac	22/29	0.420989251393452	0	FACETS	0.65	0.584	0.717			1	SUBCLONAL	1	TRUE	NA	0.562635358208133	0		173	189	SUCCESS
AR	367	MSKCC	GRCh37	X	66765229	66765229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	72	140	0	ENST00000374690.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000374690	NM_000044.3	81	Gag/Aag	1/8	1	1	FACETS	0.721	0.638	0.809	0.721	0.638	0.809	SUBCLONAL	1	TRUE	0	0.562635358208133	1		140	255	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	54	722	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.698	0.594	0.813	0.698	0.594	0.813	SUBCLONAL	1	TRUE	1	0.16	2		722	967	SUCCESS
APC	324	MSKCC	GRCh37	5	112175171	112175171	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085373	NA	P-0015417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	38	264	0	ENST00000257430.4:c.3880C>T	p.Gln1294Ter	p.Q1294*	ENST00000257430	NM_000038.5	1294	Cag/Tag	16/16	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.16	2		264	415	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120131	70120132	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0015417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	29	215	0	ENST00000245479.2:c.1134_1135dup	p.Ala379GlyfsTer5	p.A379Gfs*5	ENST00000245479	NM_000346.3	378	cag/caGGg	3/3	1	2	FACETS	1	0.806	1	1	0.806	1	CLONAL	1	TRUE	1	0.16	2		215	361	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0015423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	119	435	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.587	0.53	0.647	0.587	0.53	0.647	SUBCLONAL	1	TRUE	1	0.577536933622882	2		435	702	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653807	89653807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554893782	NA	P-0015423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	172	393	2	ENST00000371953.3:c.105G>A	p.Met35Ile	p.M35I	ENST00000371953	NM_000314.4	35	atG/atA	2/9	0.577536933622882	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.577536933622882	1		395	374	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805588	46805588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201428095	NA	P-0015423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	248	685	0	ENST00000290295.7:c.368G>A	p.Arg123His	p.R123H	ENST00000290295	NM_006361.5	123	cGc/cAc	1/2	1	2	FACETS	0.81	0.758	0.865	0.81	0.758	0.865	CLONAL	1	TRUE	1	0.577536933622882	2		685	1060	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606562	93606562	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	204	465	0	ENST00000375746.1:c.382A>G	p.Ile128Val	p.I128V	ENST00000375746	NM_001174167.1	128	Atc/Gtc	2/14	1	2	FACETS	0.818	0.759	0.878	0.818	0.759	0.878	CLONAL	1	TRUE	1	0.577536933622882	2		465	864	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	138	297	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.837	0.765	0.913	0.837	0.765	0.913	CLONAL	1	TRUE	1	0.541181925764842	2		297	609	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557401	29557401	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0015424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	83	181	0	ENST00000356175.3:c.3113+1G>C		p.X1038_splice	ENST00000356175	NM_000267.3	1038			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.541181925764842	2		181	236	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735457	40735457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775419119	NA	P-0015424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	217	712	2	ENST00000373198.4:c.3416G>A	p.Arg1139Gln	p.R1139Q	ENST00000373198	NM_133170.3	1139	cGg/cAg	25/32	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.541181925764842	2		714	793	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350109	81350109	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	181	487	0	ENST00000222390.5:c.1223C>A	p.Ser408Tyr	p.S408Y	ENST00000222390	NM_000601.4	408	tCt/tAt	10/18	0.541181925764842	3	FACETS	0.897	0.827	0.969	0.448	0.413	0.485	CLONAL	1	TRUE	1	0.541181925764842	3		487	948	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	159	297	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.423989598400193	2		297	534	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100117	157100119	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs797045268	NA	P-0015426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	16	37	0	ENST00000346085.5:c.1069_1071del	p.Gly357del	p.G357del	ENST00000346085	NM_020732.3	352	GGC/-	1/20	1	2	FACETS	0.49	0.364	0.638	0.49	0.364	0.638	SUBCLONAL	1	TRUE	1	0.423989598400193	2		37	154	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396699	30396699	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs572057574	NA	P-0015426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	19	5	0	ENST00000331968.5:c.20T>C	p.Leu7Pro	p.L7P	ENST00000331968	NM_002742.2	7	cTg/cCg	1/18	1	2	FACETS	1	0.91	1	1	0.953	1	CLONAL	2	TRUE	1	0.423989598400193	2		5	36	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579592	+	splice_acceptor_variant	Splice_Site	DNP	CT	CT	AA	novel	NA	P-0015426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	184	466	1	ENST00000269305.4:c.97-2_97-1delinsTT		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.423989598400193	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.423989598400193	1		467	530	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015426-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	312	297	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		297	1248	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579592	+	splice_acceptor_variant	Splice_Site	DNP	CT	CT	AA	novel	NA	P-0015426-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	355	466	1	ENST00000269305.4:c.97-2_97-1delinsTT		p.X33_splice	ENST00000269305	NM_001126112.2	33			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		467	927	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015426-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	86	297	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.344917355541077	2		297	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579592	+	splice_acceptor_variant	Splice_Site	DNP	CT	CT	AA	novel	NA	P-0015426-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	159	466	1	ENST00000269305.4:c.97-2_97-1delinsTT		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.344917355541077	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.344917355541077	1		467	625	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485943	40485943	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015426-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1246	97	596	0	ENST00000264657.5:c.922A>G	p.Arg308Gly	p.R308G	ENST00000264657	NM_139276.2	308	Aga/Gga	9/24	1	2	FACETS	0.419	0.372	0.469	0.419	0.372	0.469	SUBCLONAL	1	TRUE	1	0.344917355541077	2		596	1343	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0015429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	483	1085	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.994	0.951	1	0.994	0.951	1	CLONAL	1	TRUE	1	0.714990084335804	2		1085	1359	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115427	115115427	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	337	774	0	ENST00000257566.3:c.899C>G	p.Ala300Gly	p.A300G	ENST00000257566	NM_016569.3	300	gCa/gGa	5/8	1	2	FACETS	0.907	0.859	0.956	0.907	0.859	0.956	CLONAL	1	TRUE	1	0.714990084335804	2		774	1039	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120804	115120805	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	231	696	0	ENST00000257566.3:c.201dup	p.Leu68IlefsTer43	p.L68Ifs*43	ENST00000257566	NM_016569.3	67	-/A	1/8	1	2	FACETS	0.964	0.904	1	0.964	0.904	1	CLONAL	1	TRUE	1	0.714990084335804	2		696	670	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148544272	148544272	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0015429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	84	528	0	ENST00000320356.2:c.117+2T>C		p.X39_splice	ENST00000320356	NM_004456.4	39			1	2	FACETS	0.37	0.327	0.416	0.37	0.327	0.416	SUBCLONAL	1	TRUE	1	0.714990084335804	2		528	635	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591132	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	rs1057519842	NA	P-0015430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	479	259	0	ENST00000274335.5:c.1727_1729del	p.Thr576del	p.T576del	ENST00000274335		575	aaGACg/aag	12/15	0.811278277624342	2	FACETS	0.945	0.919	0.969	0.945	0.919	0.969	CLONAL	2	TRUE	0	0.811278277624342	2		259	625	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121912666	NA	P-0015430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	652	605	0	ENST00000269305.4:c.659A>C	p.Tyr220Ser	p.Y220S	ENST00000269305	NM_001126112.2	220	tAt/tCt	6/11	0.811278277624342	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.811278277624342	1		605	940	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348896	11348896	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	76	339	0	ENST00000332029.2:c.440T>G	p.Leu147Arg	p.L147R	ENST00000332029	NM_003745.1	147	cTc/cGc	2/2	0.396670995800787	1	FACETS	0.179	0.157	0.203	0.179	0.157	0.203	INDETERMINATE	1	TRUE	0	0.811278277624342	1		339	621	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354425	40354430	+	inframe_deletion	In_Frame_Del	DEL	TGGCGC	TGGCGC	-	novel	NA	P-0015430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1991	157	673	0	ENST00000293328.3:c.2165_2170del	p.Ser722_Ala723del	p.S722_A723del	ENST00000293328	NM_012448.3	722	aGCGCCAcg/acg	18/19	0.22790590329987	4	FACETS	0.326	0.297	0.357			1	INDETERMINATE	1	TRUE	NA	0.811278277624342	4		673	2148	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602639	10602639	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2174	116	488	0	ENST00000171111.5:c.939del	p.Thr314ArgfsTer3	p.T314Rfs*3	ENST00000171111	NM_203500.1	313	ccC/cc	3/6	0.408889600607956	5	FACETS	0.277	0.248	0.308			1	INDETERMINATE	1	TRUE	NA	0.811278277624342	5		488	2290	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469845	157469896	+	frameshift_variant	Frame_Shift_Del	DEL	ACCAGATGCATGGACAAGGGCCAAGCCAGCCATGTGGTGCTGTGCCCCTGGG	ACCAGATGCATGGACAAGGGCCAAGCCAGCCATGTGGTGCTGTGCCCCTGGG	-	novel	NA	P-0015430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	155	497	0	ENST00000346085.5:c.2641_2692del	p.Gln881GlufsTer16	p.Q881Efs*16	ENST00000346085	NM_020732.3	880	aACCAGATGCATGGACAAGGGCCAAGCCAGCCATGTGGTGCTGTGCCCCTGGGa/aa	9/20	1	2	FACETS	0.341	0.311	0.372	0.341	0.311	0.372	SUBCLONAL	1	TRUE	1	0.811278277624342	2		497	1120	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469821	157469831	+	frameshift_variant	Frame_Shift_Ins	INS	CCGGTATGGGT	CCGGTATGGGT	ACAGCACCACATGGCTGGCTTGGCCCTTGTCCATGC	novel	NA	P-0015430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	214	511	0	ENST00000346085.5:c.2615_2625delinsACAGCACCACATGGCTGGCTTGGCCCTTGTCCATGC	p.Pro872HisfsTer78	p.P872Hfs*78	ENST00000346085	NM_020732.3	872	cCCGGTATGGGT/cACAGCACCACATGGCTGGCTTGGCCCTTGTCCATGC	9/20	1	2	FACETS	0.448	0.415	0.482	0.448	0.415	0.482	SUBCLONAL	1	TRUE	1	0.811278277624342	2		511	1178	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	67	152	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.452981805254926	2		152	249	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	9	128	1	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	2	FACETS	0.346	0.23	0.491	0.346	0.23	0.491	SUBCLONAL	1	TRUE	1	0.452981805254926	2		129	115	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	101	268	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.452981805254926	2		268	412	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	87	454	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.452981805254926	2		454	380	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	53	305	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	1	2	FACETS	0.711	0.61	0.821	0.711	0.61	0.821	SUBCLONAL	1	TRUE	1	0.452981805254926	2		305	329	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100425	8100425	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	108	398	0	ENST00000346208.3:c.404del	p.Pro135ArgfsTer60	p.P135Rfs*60	ENST00000346208		133	taC/ta	3/6	1	2	FACETS	0.912	0.822	1	0.912	0.822	1	CLONAL	1	TRUE	1	0.452981805254926	2		398	523	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	91	363	2	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	0.97	0.867	1	0.97	0.867	1	CLONAL	1	TRUE	1	0.452981805254926	2		365	414	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236087	108236087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781894	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	8	235	0	ENST00000278616.4:c.9023G>A	p.Arg3008His	p.R3008H	ENST00000278616	NM_000051.3	3008	cGt/cAt	63/63	0.452981805254926	2	FACETS	0.089	0.057	0.132	0.045	0.028	0.066	SUBCLONAL	1	TRUE	0	0.452981805254926	2		235	396	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	94	305	0	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	0.97	0.868	1	0.97	0.868	1	CLONAL	1	TRUE	1	0.452981805254926	2		305	428	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335040	81335040	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751819844	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	73	216	0	ENST00000222390.5:c.1787C>T	p.Thr596Met	p.T596M	ENST00000222390	NM_000601.4	596	aCg/aTg	16/18	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.452981805254926	2		216	318	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149818	202149819	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	65	301	0	ENST00000358485.4:c.1264dup	p.Asp422GlyfsTer2	p.D422Gfs*2	ENST00000358485	NM_001080125.1	420	cag/caGg	8/9	1	2	FACETS	0.736	0.641	0.838	0.736	0.641	0.838	SUBCLONAL	1	TRUE	1	0.452981805254926	2		301	390	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	82	219	10	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.452981805254926	2		229	350	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119758	70119758	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	147	320	0	ENST00000245479.2:c.760C>T	p.Arg254Ter	p.R254*	ENST00000245479	NM_000346.3	254	Cga/Tga	3/3	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.452981805254926	2		320	525	SUCCESS
APC	324	MSKCC	GRCh37	5	112178033	112178033	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs773874693	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	33	223	0	ENST00000257430.4:c.6747del	p.Gly2250AlafsTer29	p.G2250Afs*29	ENST00000257430	NM_000038.5	2248	Aaa/aa	16/16	1	2	FACETS	0.472	0.385	0.569	0.472	0.385	0.569	SUBCLONAL	1	TRUE	1	0.452981805254926	2		223	309	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020823	112020823	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	25	267	0	ENST00000368678.4:c.748A>G	p.Thr250Ala	p.T250A	ENST00000368678		250	Acc/Gcc	8/13	1	2	FACETS	0.256	0.201	0.319	0.256	0.201	0.319	SUBCLONAL	1	TRUE	1	0.452981805254926	2		267	432	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910708	29910708	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	31	417	0	ENST00000376809.5:c.248A>G	p.Tyr83Cys	p.Y83C	ENST00000376809	NM_002116.7	83	tAt/tGt	2/8	1	2	FACETS	0.34	0.274	0.413	0.34	0.274	0.413	SUBCLONAL	1	TRUE	1	0.452981805254926	2		417	403	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76919038	76919038	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	35	150	0	ENST00000373344.5:c.3953del	p.Asn1318IlefsTer28	p.N1318Ifs*28	ENST00000373344	NM_000489.3	1318	aAt/at	12/35	1	2	FACETS	0.818	0.677	0.972	0.818	0.677	0.972	CLONAL	1	TRUE	1	0.452981805254926	2		150	189	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270529	98270530	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs751977093	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	35	163	2	ENST00000331920.6:c.114dup	p.Leu39AlafsTer51	p.L39Afs*51	ENST00000331920	NM_000264.3	38	-/G	1/24	1	2	FACETS	0.611	0.503	0.73	0.611	0.503	0.73	SUBCLONAL	1	TRUE	1	0.452981805254926	2		165	253	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041695	14041695	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	17	230	1	ENST00000311895.7:c.2242A>G	p.Met748Val	p.M748V	ENST00000311895	NM_005236.2	748	Atg/Gtg	11/11	1	2	FACETS	0.227	0.169	0.296	0.227	0.169	0.296	SUBCLONAL	1	TRUE	1	0.452981805254926	2		231	331	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324892	31324892	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs765875917	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	46	78	0	ENST00000412585.2:c.44del	p.Ala15GlyfsTer5	p.A15Gfs*5	ENST00000412585	NM_005514.6	15	gCg/gg	1/8	1	2	FACETS	0.861	0.746	0.979	1	0.972	1	CLONAL	2	TRUE	1	0.452981805254926	2		78	118	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	57	775	1	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.421	0.361	0.487	0.421	0.361	0.487	SUBCLONAL	1	TRUE	1	0.452981805254926	2		776	598	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937355	32937355	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507952	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	68	224	0	ENST00000380152.3:c.8021del	p.Lys2674ArgfsTer2	p.K2674Rfs*2	ENST00000380152		2672	atA/at	18/27	1	2	FACETS	0.935	0.82	1	0.935	0.82	1	CLONAL	1	TRUE	1	0.452981805254926	2		224	321	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300040	137300040	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	143	386	1	ENST00000481739.1:c.331del	p.Leu111TrpfsTer57	p.L111Wfs*57	ENST00000481739	NM_002957.4	109	Ccc/cc	3/10	1	2	FACETS	0.93	0.85	1	0.93	0.85	1	CLONAL	1	TRUE	1	0.452981805254926	2		387	679	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	86	331	0	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	0.452981805254926	2	FACETS	0.73	0.648	0.818	0.365	0.324	0.409	SUBCLONAL	1	TRUE	0	0.452981805254926	2		331	520	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169741	11169741	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1228569453	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	98	294	0	ENST00000361445.4:c.7412C>T	p.Thr2471Met	p.T2471M	ENST00000361445	NM_004958.3	2471	aCg/aTg	55/58	1	2	FACETS	0.879	0.788	0.976	0.879	0.788	0.976	CLONAL	1	TRUE	1	0.452981805254926	2		294	492	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427027	49427027	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	20	255	0	ENST00000301067.7:c.11461del	p.Gln3821ArgfsTer9	p.Q3821Rfs*9	ENST00000301067	NM_003482.3	3821	Cag/ag	39/54	1	2	FACETS	0.32	0.245	0.408	0.32	0.245	0.408	SUBCLONAL	1	TRUE	1	0.452981805254926	2		255	276	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31468079	31468079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	117	313	1	ENST00000344624.3:c.2333G>A	p.Arg778His	p.R778H	ENST00000344624		778	cGc/cAc	15/33	1	2	FACETS	0.897	0.811	0.987	0.897	0.811	0.987	CLONAL	1	TRUE	1	0.452981805254926	2		314	576	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883774	37883774	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	126	395	1	ENST00000269571.5:c.3391del	p.Leu1131Ter	p.L1131*	ENST00000269571		1129	gCc/gc	26/27	1	2	FACETS	0.882	0.8	0.967	0.882	0.8	0.967	CLONAL	1	TRUE	1	0.452981805254926	2		396	631	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796223	45796223	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781668	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	106	304	1	ENST00000450313.1:c.1483C>T	p.Arg495Cys	p.R495C	ENST00000450313	NM_012222.2	495	Cgt/Tgt	15/16	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.452981805254926	2		305	438	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927401	245927401	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs151331887	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	43	287	0	ENST00000388985.4:c.1127T>C	p.Val376Ala	p.V376A	ENST00000388985		376	gTt/gCt	11/12	1	2	FACETS	0.436	0.365	0.515	0.436	0.365	0.515	SUBCLONAL	1	TRUE	1	0.452981805254926	2		287	435	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333815	70333815	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	76	214	0	ENST00000373644.4:c.1720T>A	p.Ser574Thr	p.S574T	ENST00000373644	NM_030625.2	574	Tct/Act	2/12	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.452981805254926	2		214	330	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518082	69518082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	119	358	0	ENST00000294312.3:c.283G>A	p.Val95Met	p.V95M	ENST00000294312	NM_005117.2	95	Gtg/Atg	2/3	1	2	FACETS	0.969	0.879	1	0.969	0.879	1	CLONAL	1	TRUE	1	0.452981805254926	2		358	542	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307507	118307512	+	inframe_deletion	In_Frame_Del	DEL	TCGTCA	TCGTCA	-	novel	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	76	271	0	ENST00000534358.1:c.285_290del	p.Ser97_Ser98del	p.S97_S98del	ENST00000534358	NM_005933.3	94	TCGTCA/-	1/36	0.452981805254926	2	FACETS	0.768	0.676	0.866	0.384	0.338	0.433	SUBCLONAL	1	TRUE	0	0.452981805254926	2		271	437	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562976	21562976	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	112	292	0	ENST00000382592.4:c.943C>T	p.His315Tyr	p.H315Y	ENST00000382592	NM_014572.2	315	Cac/Tac	4/8	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.452981805254926	2		292	459	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827811	72827811	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	31	289	0	ENST00000268489.5:c.8770T>A	p.Cys2924Ser	p.C2924S	ENST00000268489	NM_006885.3	2924	Tgc/Agc	9/10	1	2	FACETS	0.386	0.312	0.469	0.386	0.312	0.469	SUBCLONAL	1	TRUE	1	0.452981805254926	2		289	355	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819740	81819740	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1231997442	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	86	289	1	ENST00000359376.3:c.146C>T	p.Thr49Met	p.T49M	ENST00000359376	NM_002661.3	49	aCg/aTg	2/33	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.452981805254926	2		290	368	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483053	29483055	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	103	310	0	ENST00000356175.3:c.117_119del	p.Asn39del	p.N39del	ENST00000356175	NM_000267.3	38	cACAac/cac	2/57	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.452981805254926	2		310	447	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119696	70119696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	103	343	0	ENST00000245479.2:c.698G>A	p.Gly233Asp	p.G233D	ENST00000245479	NM_000346.3	233	gGc/gAc	3/3	1	2	FACETS	0.796	0.715	0.883	0.796	0.715	0.883	SUBCLONAL	1	TRUE	1	0.452981805254926	2		343	571	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221450	36221450	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	160	393	0	ENST00000222270.7:c.5209A>T	p.Ile1737Phe	p.I1737F	ENST00000222270	NM_014727.1	1737	Att/Ttt	25/37	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.452981805254926	2		393	616	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744483	41744483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755240418	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	108	436	0	ENST00000301178.4:c.1103G>A	p.Arg368Gln	p.R368Q	ENST00000301178	NM_021913.4	368	cGg/cAg	8/20	1	2	FACETS	0.9	0.811	0.993	0.9	0.811	0.993	CLONAL	1	TRUE	1	0.452981805254926	2		436	530	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791776	42791776	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	114	370	0	ENST00000575354.2:c.662G>A	p.Arg221His	p.R221H	ENST00000575354	NM_015125.3	221	cGt/cAt	5/20	1	2	FACETS	0.946	0.855	1	0.946	0.855	1	CLONAL	1	TRUE	1	0.452981805254926	2		370	532	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796717	42796717	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	98	233	0	ENST00000575354.2:c.3176-1G>C		p.X1059_splice	ENST00000575354	NM_015125.3	1059			1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.452981805254926	2		233	432	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905536	50905536	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	116	408	0	ENST00000440232.2:c.664C>A	p.Pro222Thr	p.P222T	ENST00000440232	NM_002691.3	222	Ccg/Acg	6/27	1	2	FACETS	0.994	0.901	1	0.994	0.901	1	CLONAL	1	TRUE	1	0.452981805254926	2		408	515	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25462047	25462047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1202038704	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	77	309	0	ENST00000264709.3:c.2360C>T	p.Ala787Val	p.A787V	ENST00000264709	NM_175629.2	787	gCt/gTt	20/23	1	2	FACETS	0.73	0.643	0.822	0.73	0.643	0.822	SUBCLONAL	1	TRUE	1	0.452981805254926	2		309	466	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267418	198267418	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	24	250	0	ENST00000335508.6:c.1939T>C	p.Phe647Leu	p.F647L	ENST00000335508	NM_012433.2	647	Ttc/Ctc	14/25	1	2	FACETS	0.28	0.219	0.351	0.28	0.219	0.351	SUBCLONAL	1	TRUE	1	0.452981805254926	2		250	378	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266000	41266175	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGG	CTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGG	-	novel	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	78	81	0	ENST00000349496.5:c.14-17_172del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.452981805254926	2	FACETS	0.897	0.821	0.971	1	0.981	1	CLONAL	3	TRUE	0	0.452981805254926	2		81	128	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933492	49933492	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56091918	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	149	485	0	ENST00000296474.3:c.2698G>A	p.Val900Met	p.V900M	ENST00000296474	NM_002447.2	900	Gtg/Atg	11/20	0.452981805254926	2	FACETS	1	0.957	1	0.534	0.49	0.58	CLONAL	1	TRUE	0	0.452981805254926	2		485	616	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807549	1807549	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	45	378	0	ENST00000260795.2:c.1718C>A	p.Pro573Gln	p.P573Q	ENST00000260795		573	cCg/cAg	12/17	1	2	FACETS	0.359	0.301	0.423	0.359	0.301	0.423	SUBCLONAL	1	TRUE	1	0.452981805254926	2		378	553	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31472219	31472219	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	50	407	0	ENST00000344624.3:c.2192A>C	p.Gln731Pro	p.Q731P	ENST00000344624		731	cAg/cCg	14/33	1	2	FACETS	0.396	0.336	0.463	0.396	0.336	0.463	SUBCLONAL	1	TRUE	1	0.452981805254926	2		407	557	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460560	149460560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1188913271	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	74	351	1	ENST00000286301.3:c.77G>A	p.Ser26Asn	p.S26N	ENST00000286301	NM_005211.3	26	aGt/aAt	3/22	1	2	FACETS	0.661	0.58	0.748	0.661	0.58	0.748	SUBCLONAL	1	TRUE	1	0.452981805254926	2		352	494	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513239	149513239	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs34586048	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	87	332	1	ENST00000261799.4:c.844G>A	p.Glu282Lys	p.E282K	ENST00000261799	NM_002609.3	282	Gag/Aag	6/23	1	2	FACETS	0.816	0.725	0.912	0.816	0.725	0.912	CLONAL	1	TRUE	1	0.452981805254926	2		333	471	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803023	32803023	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs761765914	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	161	306	0	ENST00000374899.4:c.853A>G	p.Met285Val	p.M285V	ENST00000374899	NM_018833.2	285	Atg/Gtg	5/12	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.452981805254926	2		306	512	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359017	81359017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	54	262	0	ENST00000222390.5:c.944G>A	p.Gly315Asp	p.G315D	ENST00000222390	NM_000601.4	315	gGc/gAc	8/18	1	2	FACETS	0.714	0.613	0.823	0.714	0.613	0.823	SUBCLONAL	1	TRUE	1	0.452981805254926	2		262	334	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843813	151843813	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	60	201	0	ENST00000262189.6:c.13902G>T	p.Trp4634Cys	p.W4634C	ENST00000262189	NM_170606.2	4634	tgG/tgT	53/59	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.452981805254926	2		201	236	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372313	55372313	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	39	289	0	ENST00000297316.4:c.1007del	p.Pro336LeufsTer51	p.P336Lfs*51	ENST00000297316	NM_022454.3	335	Ccc/cc	2/2	1	2	FACETS	0.399	0.33	0.475	0.399	0.33	0.475	SUBCLONAL	1	TRUE	1	0.452981805254926	2		289	432	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268792	98268793	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	101	270	0	ENST00000331920.6:c.290dup	p.Asn97LysfsTer43	p.N97Kfs*43	ENST00000331920	NM_000264.3	97	aac/aaAc	2/24	1	2	FACETS	0.887	0.796	0.982	0.887	0.796	0.982	CLONAL	1	TRUE	1	0.452981805254926	2		270	503	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966745	44966745	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	52	379	0	ENST00000377967.4:c.3972del	p.Glu1325LysfsTer31	p.E1325Kfs*31	ENST00000377967	NM_021140.2	1323	acA/ac	27/29	1	2	FACETS	0.469	0.399	0.545	0.469	0.399	0.545	SUBCLONAL	1	TRUE	1	0.452981805254926	2		379	490	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0026119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	44	722	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.901	0.756	1	0.901	0.756	1	CLONAL	1	TRUE	1	0.220555733588915	2		722	443	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100465	2100465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	63	260	0	ENST00000219476.3:c.203C>T	p.Ala68Val	p.A68V	ENST00000219476	NM_000548.3	68	gCa/gTa	3/42	0.220674246899287	3	FACETS	1	0.919	1	0.544	0.47	0.624	CLONAL	1	TRUE	1	0.220555733588915	3		260	583	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0026122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	93	722	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	0.929	0.83	1			1	INDETERMINATE	1	TRUE	NA	0.454026117770406	2		722	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0026122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	211	1002	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.454026117770406	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.454026117770406	1		1003	568	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0026122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	34	127	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	1	2	FACETS	0.792	0.654	0.945	0.792	0.654	0.945	CLONAL	1	TRUE	1	0.454026117770406	2		127	189	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0026122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	97	616	1	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	0.454026117770406	2		617	327	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515198	106515198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146675267	NA	P-0026122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	114	234	0	ENST00000359195.3:c.2341G>A	p.Glu781Lys	p.E781K	ENST00000359195	NM_002649.2	781	Gaa/Aaa	5/11	0.454026117770406	3	FACETS	1	0.93	1	0.519	0.468	0.572	CLONAL	1	TRUE	1	0.454026117770406	3		234	594	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	124	493	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.404210056314667	3	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	1	0.404210056314667	3		493	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0026123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	150	791	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.404210056314667	2	FACETS	0.952	0.88	1	0.952	0.88	1	CLONAL	2	TRUE	0	0.404210056314667	2		791	390	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0026123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	31	129	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	0.404210056314667	2	FACETS	0.892	0.745	1	0.892	0.745	1	CLONAL	2	TRUE	0	0.404210056314667	2		129	86	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577531	7577531	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567549203	NA	P-0026125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	31	350	1	ENST00000269305.4:c.750del	p.Ile251SerfsTer94	p.I251Sfs*94	ENST00000269305	NM_001126112.2	250	ccC/cc	7/11	1	2	FACETS	0.954	0.773	1	0.954	0.773	1	CLONAL	1	TRUE	1	0.2	2		351	325	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215410	5215410	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	22	253	0	ENST00000357368.4:c.4208G>C	p.Gly1403Ala	p.G1403A	ENST00000357368	NM_002850.3	1403	gGa/gCa	28/38	1	2	FACETS	0.873	0.678	1	0.873	0.678	1	CLONAL	1	TRUE	1	0.2	2		253	252	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735470	40735470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761910971	NA	P-0026200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	233	477	0	ENST00000373198.4:c.3403G>A	p.Val1135Met	p.V1135M	ENST00000373198	NM_133170.3	1135	Gtg/Atg	25/32	0.273274732839577	1	FACETS	0.698	0.653	0.744	0.698	0.653	0.744	INDETERMINATE	1	TRUE	0	0.606021966017883	1		477	768	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591104	67591115	+	inframe_deletion	In_Frame_Del	DEL	TTAAACCAGACC	TTAAACCAGACC	-	novel	NA	P-0026200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	37	421	0	ENST00000274335.5:c.1700_1711del	p.Lys567_Leu570del	p.K567_L570del	ENST00000274335		566	aTTAAACCAGACCtt/att	12/15	0.329277385853195	1	FACETS	0.226	0.187	0.271	0.226	0.187	0.271	INDETERMINATE	1	TRUE	0	0.606021966017883	1		421	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs786201057	NA	P-0026200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	210	389	3	ENST00000269305.4:c.374C>A	p.Thr125Lys	p.T125K	ENST00000269305	NM_001126112.2	125	aCg/aAg	4/11	0.600858882812308	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.606021966017883	1		392	466	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100151	27100151	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	181	353	1	ENST00000324856.7:c.3947C>A	p.Ser1316Ter	p.S1316*	ENST00000324856	NM_006015.4	1316	tCg/tAg	16/20	1	2	FACETS	0.824	0.762	0.888	0.824	0.762	0.888	CLONAL	1	TRUE	1	0.606021966017883	2		354	725	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725050	89725051	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTA	novel	NA	P-0026200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	52	168	0	ENST00000371953.3:c.1034_1037dup	p.Phe347ValfsTer15	p.F347Vfs*15	ENST00000371953	NM_000314.4	345	ctg/cTGTAtg	9/9	0.606021966017883	1	FACETS	0.886	0.774	1	0.886	0.774	1	CLONAL	1	TRUE	0	0.606021966017883	1		168	135	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828914	72828918	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCT	GCGCT	-	novel	NA	P-0026200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	177	426	0	ENST00000268489.5:c.7663_7667del	p.Ser2555AlafsTer22	p.S2555Afs*22	ENST00000268489	NM_006885.3	2555	AGCGCg/g	9/10	0.600858882812308	1	FACETS	0.75	0.696	0.805	0.75	0.696	0.805	SUBCLONAL	1	TRUE	0	0.606021966017883	1		426	543	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113708	11113708	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	281	409	0	ENST00000358026.2:c.1816C>G	p.Leu606Val	p.L606V	ENST00000358026	NM_001128849.1	606	Ctg/Gtg	12/36	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.606021966017883	2		409	866	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590986	67590986	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	61	178	0	ENST00000274335.5:c.1580del	p.Asn527IlefsTer5	p.N527Ifs*5	ENST00000274335		527	Aat/at	12/15	0.329277385853195	1	FACETS	0.691	0.606	0.781	0.691	0.606	0.781	INDETERMINATE	1	TRUE	0	0.606021966017883	1		178	203	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0026204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	184	722	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.285933888107001	1	FACETS	0.835	0.774	0.897	0.835	0.774	0.897	INDETERMINATE	1	TRUE	0	0.515418851921211	1		722	635	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0026204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	220	494	1	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.515418851921211	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.515418851921211	1		495	536	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575671	48575671	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0026204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	125	487	0	ENST00000342988.3:c.431C>G	p.Ser144Ter	p.S144*	ENST00000342988	NM_005359.5	144	tCa/tGa	4/12	0.515418851921211	1	FACETS	0.72	0.655	0.788	0.72	0.655	0.788	SUBCLONAL	1	TRUE	0	0.515418851921211	1		487	500	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267878	7267878	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	35	348	0	ENST00000302850.5:c.130C>G	p.Leu44Val	p.L44V	ENST00000302850	NM_000208.2	44	Ctc/Gtc	2/22	0.515418851921211	1	FACETS	0.215	0.176	0.259	0.215	0.176	0.259	SUBCLONAL	1	TRUE	0	0.515418851921211	1		348	469	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40739780	40739780	+	stop_lost	Nonstop_Mutation	SNP	C	C	A	novel	NA	P-0026204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1852	251	512	0	ENST00000392038.2:c.1445G>T	p.Ter482LeuextTer101	p.*482Lext*101	ENST00000392038	NM_001626.4	482	tGa/tTa	14/14	0.515418851921211	5	FACETS	0.821	0.765	0.88			1	CLONAL	1	TRUE	NA	0.515418851921211	5		512	2103	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0015431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	151	605	1	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	0.3	2		606	976	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029454	16029454	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446800502	NA	P-0015431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	128	209	0	ENST00000268712.3:c.1576G>A	p.Glu526Lys	p.E526K	ENST00000268712	NM_006311.3	526	Gaa/Aaa	15/46	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.3	2		209	765	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243472	46243472	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	127	340	0	ENST00000334344.6:c.1825C>T	p.Gln609Ter	p.Q609*	ENST00000334344	NM_152641.2	609	Cag/Tag	14/21	1	2	FACETS	0.897	0.812	0.987	0.897	0.812	0.987	CLONAL	1	TRUE	1	0.3	2		340	944	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602584	10602584	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1208201314	NA	P-0015431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	131	300	0	ENST00000171111.5:c.994G>T	p.Gly332Cys	p.G332C	ENST00000171111	NM_203500.1	332	Ggc/Tgc	3/6	0.304805106510435	1	FACETS	0.897	0.814	0.984	0.897	0.814	0.984	CLONAL	1	TRUE	0	0.3	1		300	828	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207675	102207675	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	85	177	0	ENST00000263464.3:c.1657G>A	p.Glu553Lys	p.E553K	ENST00000263464	NM_001165.4	553	Gaa/Aaa	9/9	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.3	2		177	565	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220368	1220379	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCAGGTACTTCT	GCAGGTACTTCT	-	novel	NA	P-0015431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	69	362	0	ENST00000326873.7:c.465-3_473del		p.X155_splice	ENST00000326873	NM_000455.4	155		4/10	0.304805106510435	1	FACETS	0.738	0.643	0.839	0.738	0.643	0.839	SUBCLONAL	1	TRUE	0	0.3	1		362	530	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170011239	170011239	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	167	390	0	ENST00000295797.4:c.1360G>C	p.Asp454His	p.D454H	ENST00000295797	NM_002740.5	454	Gat/Cat	14/18	1	2	FACETS	0.895	0.82	0.973	0.895	0.82	0.973	CLONAL	1	TRUE	1	0.3	2		390	1244	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247344	153247344	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	124	285	0	ENST00000281708.4:c.1458G>A	p.Trp486Ter	p.W486*	ENST00000281708	NM_033632.3	486	tgG/tgA	10/12	1	2	FACETS	0.856	0.773	0.943	0.856	0.773	0.943	CLONAL	1	TRUE	1	0.3	2		285	966	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249373	153249373	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	105	280	0	ENST00000281708.4:c.1405C>G	p.Leu469Val	p.L469V	ENST00000281708	NM_033632.3	469	Ctt/Gtt	9/12	1	2	FACETS	0.759	0.679	0.844	0.759	0.679	0.844	SUBCLONAL	1	TRUE	1	0.3	2		280	922	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576837	67576837	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	G	rs1276212806	NA	P-0015431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	74	178	0	ENST00000274335.5:c.916+3A>G		p.X306_splice	ENST00000274335		306			1	2	FACETS	0.754	0.66	0.856	0.754	0.66	0.856	SUBCLONAL	1	TRUE	1	0.3	2		178	654	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097611	27097612	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	237	410	0	ENST00000324856.7:c.3200_3201insG	p.Asn1068GlnfsTer37	p.N1068Qfs*37	ENST00000324856	NM_006015.4	1067	gtc/gtGc	12/20	0.611751902170689	1	FACETS	0.779	0.731	0.829	0.779	0.731	0.829	SUBCLONAL	1	TRUE	0	0.611751902170689	1		410	690	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912646	32912646	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs886038101	NA	P-0015432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	138	373	0	ENST00000380152.3:c.4154C>G	p.Ser1385Ter	p.S1385*	ENST00000380152		1385	tCa/tGa	11/27	0.584146084791159	1	FACETS	0.717	0.658	0.777	0.717	0.658	0.777	SUBCLONAL	1	TRUE	0	0.611751902170689	1		373	437	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420338	88420338	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	227	409	0	ENST00000360948.2:c.2348T>A	p.Ile783Asn	p.I783N	ENST00000360948	NM_001012338.2	783	aTt/aAt	19/19	1	2	FACETS	0.792	0.738	0.847	0.792	0.738	0.847	SUBCLONAL	1	TRUE	1	0.611751902170689	2		409	937	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090535	71090572	+	frameshift_variant	Frame_Shift_Del	DEL	CATTATTAAGGAGGTCTTGGAAGGTGCAGAGGAGGAGA	CATTATTAAGGAGGTCTTGGAAGGTGCAGAGGAGGAGA	-	novel	NA	P-0015432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	148	283	0	ENST00000318789.4:c.776_813del	p.Val259GlufsTer23	p.V259Efs*23	ENST00000318789	NM_032682.5	259	gTCTCCTCCTCTGCACCTTCCAAGACCTCCTTAATAATG/g	11/21	0.466780219135579	1	FACETS	0.706	0.649	0.764	0.706	0.649	0.764	SUBCLONAL	1	TRUE	0	0.611751902170689	1		283	476	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56854531	56854531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	142	415	1	ENST00000519728.1:c.113C>T	p.Ser38Phe	p.S38F	ENST00000519728	NM_002350.3	38	tCc/tTc	2/13	0.611751902170689	4	FACETS	0.665	0.605	0.729	0.222	0.201	0.243	SUBCLONAL	1	TRUE	1	0.611751902170689	4		416	1125	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931925	39931925	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	441	635	0	ENST00000378444.4:c.2674del	p.Leu892Ter	p.L892*	ENST00000378444	NM_001123385.1	892	Cta/ta	4/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.611751902170689	2		635	1391	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089521	27089525	+	frameshift_variant	Frame_Shift_Ins	INS	CAGGC	CAGGC	GAGTTT	novel	NA	P-0015433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	50	380	0	ENST00000324856.7:c.2477_2481delinsGAGTTT	p.Ala826GlyfsTer46	p.A826Gfs*46	ENST00000324856	NM_006015.4	826	gCAGGC/gGAGTTT	8/20	1	2	FACETS	0.337	0.286	0.393	0.337	0.286	0.393	SUBCLONAL	1	TRUE	1	0.596407936177049	2		380	498	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0015436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	165	605	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.314760079161479	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.314760079161479	1		606	752	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223541	53223541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	97	285	0	ENST00000375401.3:c.3818C>T	p.Pro1273Leu	p.P1273L	ENST00000375401	NM_004187.3	1273	cCc/cTc	23/26	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.314760079161479	2		285	585	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143566	108143566	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	83	260	0	ENST00000278616.4:c.3271G>T	p.Glu1091Ter	p.E1091*	ENST00000278616	NM_000051.3	1091	Gag/Tag	22/63	1	2	FACETS	0.942	0.833	1	0.942	0.833	1	CLONAL	1	TRUE	1	0.314760079161479	2		260	560	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198462	108198462	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876658517	NA	P-0015436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	82	284	0	ENST00000278616.4:c.7066A>T	p.Ile2356Phe	p.I2356F	ENST00000278616	NM_000051.3	2356	Atc/Ttc	48/63	1	2	FACETS	0.711	0.626	0.802	0.711	0.626	0.802	SUBCLONAL	1	TRUE	1	0.314760079161479	2		284	733	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219345	1219345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	201	499	0	ENST00000326873.7:c.397del	p.Val133CysfsTer28	p.V133Cfs*28	ENST00000326873	NM_000455.4	133	Gtg/tg	3/10	0.314760079161479	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.314760079161479	1		499	1017	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521690	89521690	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	52	321	0	ENST00000336596.2:c.2767G>C	p.Val923Leu	p.V923L	ENST00000336596	NM_005233.5	923	Gtc/Ctc	16/17	1	2	FACETS	0.431	0.366	0.503	0.431	0.366	0.503	SUBCLONAL	1	TRUE	1	0.314760079161479	2		321	767	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953092	2953092	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	156	463	0	ENST00000396946.4:c.2848C>A	p.Pro950Thr	p.P950T	ENST00000396946	NM_032415.4	950	Cct/Act	22/25	1	2	FACETS	0.952	0.871	1	0.952	0.871	1	CLONAL	1	TRUE	1	0.314760079161479	2		463	1041	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039816	47039816	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0015436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	224	602	0	ENST00000377604.3:c.1161-2A>T		p.X387_splice	ENST00000377604	NM_001204468.1	387			1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.314760079161479	2		602	1208	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361745	70361745	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	183	520	0	ENST00000374080.3:c.6421G>T	p.Gly2141Trp	p.G2141W	ENST00000374080		2141	Ggg/Tgg	44/45	1	2	FACETS	0.936	0.862	1	0.936	0.862	1	CLONAL	1	TRUE	1	0.314760079161479	2		520	1242	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934530	9934530	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	119	418	1	ENST00000330684.3:c.1625G>T	p.Gly542Val	p.G542V	ENST00000330684	NM_001134407.1	542	gGc/gTc	7/13	0.190786492396997	3	FACETS	1	0.967	1	0.582	0.525	0.643	CLONAL	1	TRUE	1	0.26	3		419	888	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218415	1218416	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	TT	novel	NA	P-0015440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	133	451	2	ENST00000326873.7:c.291-1_291delinsTT		p.X97_splice	ENST00000326873	NM_000455.4	97		2/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.26	2		453	818	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281303	46281303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	48	214	0	ENST00000371998.3:c.4100C>T	p.Ser1367Leu	p.S1367L	ENST00000371998		1367	tCa/tTa	21/23	1	2	FACETS	0.666	0.563	0.781	0.666	0.563	0.781	SUBCLONAL	1	TRUE	1	0.26	2		214	554	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319693	62319693	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	87	614	0	ENST00000360203.5:c.1676T>G	p.Phe559Cys	p.F559C	ENST00000360203	NM_001283009.1	559	tTc/tGc	20/35	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.26	NA		614	1029	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390146	89390146	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	44	328	1	ENST00000336596.2:c.895G>T	p.Asp299Tyr	p.D299Y	ENST00000336596	NM_005233.5	299	Gat/Tat	4/17	1	2	FACETS	0.582	0.487	0.686	0.582	0.487	0.686	SUBCLONAL	1	TRUE	1	0.26	2		329	582	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250525	110250525	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	53	355	0	ENST00000374672.4:c.150C>G	p.His50Gln	p.H50Q	ENST00000374672	NM_004235.4	50	caC/caG	3/5	1	2	FACETS	0.668	0.569	0.777	0.668	0.569	0.777	SUBCLONAL	1	TRUE	1	0.26	2		355	610	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725047	89725047	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1554826022	NA	P-0015442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	48	251	0	ENST00000371953.3:c.1030A>T	p.Lys344Ter	p.K344*	ENST00000371953	NM_000314.4	344	Aag/Tag	9/9	0.44625907208592	1	FACETS	0.679	0.579	0.787	0.679	0.579	0.787	SUBCLONAL	1	TRUE	0	0.44625907208592	1		251	246	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691022	NA	P-0015442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	502	708	1	ENST00000269305.4:c.1024del	p.Arg342GlufsTer3	p.R342Efs*3	ENST00000269305	NM_001126112.2	342	Cga/ga	10/11	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.44625907208592	2		709	1034	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098953	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	93	339	0	ENST00000397062.3:c.92G>C	p.Gly31Ala	p.G31A	ENST00000397062	NM_006164.4	31	gGa/gCa	2/5	1	2	FACETS	0.922	0.824	1	0.922	0.824	1	CLONAL	1	TRUE	1	0.44625907208592	2		339	452	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015335	176015335	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	87	338	0	ENST00000367669.3:c.1403C>A	p.Thr468Asn	p.T468N	ENST00000367669	NM_022457.5	468	aCc/aAc	12/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.44625907208592	2		338	323	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624252	89624252	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	36	257	0	ENST00000371953.3:c.26T>A	p.Val9Asp	p.V9D	ENST00000371953	NM_000314.4	9	gTt/gAt	1/9	0.44625907208592	1	FACETS	0.432	0.357	0.516	0.432	0.357	0.516	SUBCLONAL	1	TRUE	0	0.44625907208592	1		257	290	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218273	133218273	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	212	594	0	ENST00000320574.5:c.5338G>T	p.Ala1780Ser	p.A1780S	ENST00000320574	NM_006231.2	1780	Gcc/Tcc	39/49	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.44625907208592	2		594	930	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578251	28578251	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	65	466	0	ENST00000241453.7:c.2920C>G	p.Pro974Ala	p.P974A	ENST00000241453	NM_004119.2	974	Cct/Gct	24/24	0.44625907208592	1	FACETS	0.323	0.279	0.37	0.323	0.279	0.37	SUBCLONAL	1	TRUE	0	0.44625907208592	1		466	701	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916734	48916734	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0015442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	77	310	0	ENST00000267163.4:c.266del		p.X89_splice	ENST00000267163	NM_000321.2	89			0.44625907208592	1	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	0	0.44625907208592	1		310	261	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212289021	212289021	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	120	406	0	ENST00000342788.4:c.2725A>T	p.Thr909Ser	p.T909S	ENST00000342788	NM_005235.2	909	Act/Tct	23/28	0.44625907208592	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.44625907208592	1		406	380	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0015443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	641	663	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.186284287546098	3	FACETS	1	0.982	1			1	INDETERMINATE	3	TRUE	NA	0.322425992698596	3		663	1497	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745623	162745623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs572243397	NA	P-0015443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	53	359	0	ENST00000367921.3:c.2038C>T	p.Arg680Cys	p.R680C	ENST00000367921	NM_006182.2	680	Cgc/Tgc	15/18	1	2	FACETS	0.437	0.371	0.508	0.437	0.371	0.508	SUBCLONAL	1	TRUE	1	0.322425992698596	2		359	753	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443793	49443833	+	frameshift_variant	Frame_Shift_Del	DEL	GCCACCGGTGCACGTGGCTCTTCCTGTTCTTCACATGGTGA	GCCACCGGTGCACGTGGCTCTTCCTGTTCTTCACATGGTGA	-	novel	NA	P-0015443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	182	637	0	ENST00000301067.7:c.3538_3578del	p.Ser1180ProfsTer13	p.S1180Pfs*13	ENST00000301067	NM_003482.3	1180	TCACCATGTGAAGAACAGGAAGAGCCACGTGCACCGGTGGCc/c	11/54	0.318422751929398	2	FACETS	0.945	0.87	1	0.472	0.435	0.512	CLONAL	1	TRUE	0	0.322425992698596	2		637	1195	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268337	142268337	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	61	303	0	ENST00000350721.4:c.3155C>T	p.Ala1052Val	p.A1052V	ENST00000350721	NM_001184.3	1052	gCc/gTc	15/47	1	2	FACETS	0.835	0.722	0.957	0.835	0.722	0.957	CLONAL	1	TRUE	1	0.322425992698596	2		303	453	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068113	94068113	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	91	238	0	ENST00000369303.4:c.849C>A	p.Phe283Leu	p.F283L	ENST00000369303	NM_004440.3	283	ttC/ttA	4/17	0.318422751929398	2	FACETS	1	0.913	1	0.515	0.458	0.575	CLONAL	1	TRUE	0	0.322425992698596	2		238	548	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038207	30038207	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0015444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	68	312	0	ENST00000338641.4:c.380T>G	p.Leu127Ter	p.L127*	ENST00000338641	NM_000268.3	127	tTa/tGa	4/16	0.445114907009071	1	FACETS	0.639	0.558	0.724	0.639	0.558	0.724	SUBCLONAL	1	TRUE	0	0.445114907009071	1		312	372	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038183	30038200	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTTTCAGGTAAAGAAGC	CCTTTCAGGTAAAGAAGC	-	novel	NA	P-0015444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	65	283	0	ENST00000338641.4:c.364-8_373del		p.X122_splice	ENST00000338641	NM_000268.3	122		4/16	0.445114907009071	1	FACETS	0.694	0.606	0.789	0.694	0.606	0.789	SUBCLONAL	1	TRUE	0	0.445114907009071	1		283	327	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176684129	176684129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	33	370	1	ENST00000439151.2:c.4943C>T	p.Pro1648Leu	p.P1648L	ENST00000439151	NM_022455.4	1648	cCa/cTa	13/23	1	2	FACETS	0.254	0.206	0.308	0.254	0.206	0.308	SUBCLONAL	1	TRUE	1	0.445114907009071	2		371	584	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357051	70357051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	183	600	1	ENST00000374080.3:c.5566G>A	p.Asp1856Asn	p.D1856N	ENST00000374080		1856	Gac/Aac	39/45	1	2	FACETS	0.965	0.892	1	0.965	0.892	1	CLONAL	1	TRUE	1	0.445114907009071	2		601	852	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0015445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	220	947	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.27408638568341	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.27408638568341	2		949	687	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775669	9775669	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	42	636	0	ENST00000377346.4:c.212C>G	p.Thr71Ser	p.T71S	ENST00000377346	NM_005026.3	71	aCc/aGc	4/24	0.172932918112376	4	FACETS	0.475	0.395	0.564	0.238	0.197	0.282	SUBCLONAL	1	TRUE	2	0.27408638568341	4		636	822	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505012	186505012	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	101	353	0	ENST00000323963.5:c.868A>G	p.Thr290Ala	p.T290A	ENST00000323963		290	Act/Gct	8/11	0.232101324511266	3	FACETS	1	0.981	1	0.742	0.665	0.823	CLONAL	1	TRUE	1	0.27408638568341	3		353	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0015446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	125	444	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.874	0.79	0.963	0.874	0.79	0.963	CLONAL	1	TRUE	1	0.3	2		444	953	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0015446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	95	636	1	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.3	2		637	613	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911143	40911143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370795038	NA	P-0015446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	64	497	2	ENST00000373198.4:c.2162G>A	p.Arg721His	p.R721H	ENST00000373198	NM_133170.3	721	cGt/cAt	13/32	1	2	FACETS	0.752	0.652	0.861	0.752	0.652	0.861	SUBCLONAL	1	TRUE	1	0.3	2		499	567	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693009	89693009	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0015446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	54	365	0	ENST00000371953.3:c.492+1G>C		p.X164_splice	ENST00000371953	NM_000314.4	164			1	2	FACETS	0.885	0.758	1	0.885	0.758	1	CLONAL	1	TRUE	1	0.3	2		365	407	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591247	67591247	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0015446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	95	399	0	ENST00000274335.5:c.1746-1G>C		p.X582_splice	ENST00000274335		582			1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.3	2		399	622	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088759	27088759	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	130	593	0	ENST00000324856.7:c.2368del	p.Gln790ArgfsTer43	p.Q790Rfs*43	ENST00000324856	NM_006015.4	790	Cag/ag	7/20	1	2	FACETS	0.893	0.809	0.982	0.893	0.809	0.982	CLONAL	1	TRUE	1	0.3	2		593	970	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310935	123310935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1171095092	NA	P-0015446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	38	331	0	ENST00000358487.5:c.493C>T	p.Arg165Trp	p.R165W	ENST00000358487	NM_000141.4	165	Cgg/Tgg	5/18	1	2	FACETS	0.449	0.371	0.537	0.449	0.371	0.537	SUBCLONAL	1	TRUE	1	0.3	2		331	564	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961363	41961363	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	58	358	0	ENST00000219905.7:c.271C>T	p.Arg91Ter	p.R91*	ENST00000219905	NM_001164273.1	91	Cga/Tga	2/24	1	2	FACETS	0.85	0.732	0.978	0.85	0.732	0.978	CLONAL	1	TRUE	1	0.3	2		358	455	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548899	29548899	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	70	527	0	ENST00000356175.3:c.1673T>A	p.Ile558Asn	p.I558N	ENST00000356175	NM_000267.3	558	aTt/aAt	15/57	1	2	FACETS	0.661	0.576	0.753	0.661	0.576	0.753	SUBCLONAL	1	TRUE	1	0.3	2		527	706	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212320	36212320	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	135	649	0	ENST00000222270.7:c.2072del	p.Pro691LeufsTer37	p.P691Lfs*37	ENST00000222270	NM_014727.1	691	Cct/ct	3/37	1	2	FACETS	0.906	0.823	0.994	0.906	0.823	0.994	CLONAL	1	TRUE	1	0.3	2		649	993	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591077	67591077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	68	274	0	ENST00000274335.5:c.1670G>A	p.Arg557Gln	p.R557Q	ENST00000274335		557	cGa/cAa	12/15	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.3	2		274	431	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922300	39922300	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	78	269	0	ENST00000378444.4:c.3872C>A	p.Pro1291Gln	p.P1291Q	ENST00000378444	NM_001123385.1	1291	cCg/cAg	9/15	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.3	2		269	473	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152093	55152093	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121908585	NA	P-0015447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	168	402	0	ENST00000257290.5:c.2525A>T	p.Asp842Val	p.D842V	ENST00000257290	NM_006206.4	842	gAc/gTc	18/23	1	2	FACETS	0.907	0.835	0.982	0.907	0.835	0.982	CLONAL	1	TRUE	1	0.472120045200158	2		402	785	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0015448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	81	670	1	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.485	0.426	0.55	0.485	0.426	0.55	SUBCLONAL	1	TRUE	1	0.286704002693121	2		671	1164	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520006	NA	P-0015448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	190	753	0	ENST00000269305.4:c.821T>C	p.Val274Ala	p.V274A	ENST00000269305	NM_001126112.2	274	gTt/gCt	8/11	0.236651656857657	0	FACETS	1	0.968	1			1	CLONAL	1	TRUE	0	0.286704002693121	0		753	873	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021081	31021111	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTGCAGGCTGGGTTTGACCAAAGAAGAGTCA	TTGCAGGCTGGGTTTGACCAAAGAAGAGTCA	-	novel	NA	P-0015448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	82	437	0	ENST00000375687.4:c.1086_1116del		p.X362_splice	ENST00000375687	NM_015338.5	362		12/13	1	2	FACETS	0.839	0.74	0.945	0.839	0.74	0.945	CLONAL	1	TRUE	1	0.286704002693121	2		437	682	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0015450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	140	457	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.380870170293285	2		457	724	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781475	3781475	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0015451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	126	271	0	ENST00000262367.5:c.4891-1G>A		p.X1631_splice	ENST00000262367	NM_004380.2	1631			1	2	FACETS	0.949	0.869	1	0.949	0.869	1	CLONAL	1	TRUE	1	0.717834452126376	2		271	370	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217875	7217875	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	281	534	0	ENST00000380728.2:c.136G>A	p.Glu46Lys	p.E46K	ENST00000380728		46	Gaa/Aaa	3/11	1	2	FACETS	0.974	0.919	1	0.974	0.919	1	CLONAL	1	TRUE	1	0.717834452126376	2		534	804	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107038	11107038	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	216	359	0	ENST00000358026.2:c.1743G>C	p.Lys581Asn	p.K581N	ENST00000358026	NM_001128849.1	581	aaG/aaC	10/36	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.717834452126376	2		359	550	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973137	25973137	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	41	392	0	ENST00000435504.4:c.1288G>C	p.Glu430Gln	p.E430Q	ENST00000435504		430	Gag/Cag	12/13	0.644655305449398	3	FACETS	0.203	0.168	0.242			1	SUBCLONAL	1	TRUE	NA	0.717834452126376	3		392	764	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346708	225346708	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	145	367	0	ENST00000264414.4:c.1930C>G	p.Leu644Val	p.L644V	ENST00000264414	NM_003590.4	644	Ctt/Gtt	14/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.717834452126376	2		367	383	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0015451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	642	541	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.717834452126376	4	FACETS	0.986	0.957	1	1	0.998	1	CLONAL	3	TRUE	2	0.717834452126376	4		541	1039	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356248	66356248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202046693	NA	P-0015451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	324	512	0	ENST00000273854.3:c.1249C>T	p.Arg417Trp	p.R417W	ENST00000273854	NM_004439.5	417	Cgg/Tgg	5/18	0.712044287921947	3	FACETS	1	0.981	1	0.54	0.51	0.571	CLONAL	1	TRUE	1	0.717834452126376	3		512	1136	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539207	187539208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0015451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	218	363	0	ENST00000441802.2:c.8531_8532dup	p.Met2845LeufsTer29	p.M2845Lfs*29	ENST00000441802	NM_005245.3	2844	-/TT	10/27	0.712044287921947	3	FACETS	1	0.961	1	0.522	0.486	0.558	CLONAL	1	TRUE	1	0.717834452126376	3		363	791	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949801	151949801	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0015451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	126	266	0	ENST00000262189.6:c.1300-1G>A		p.X434_splice	ENST00000262189	NM_170606.2	434			0.717834452126376	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.717834452126376	1		266	209	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157860	27157860	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	43	542	0	ENST00000380036.4:c.84G>C	p.Leu28Phe	p.L28F	ENST00000380036	NM_000459.3	28	ttG/ttC	2/23	1	2	FACETS	0.171	0.142	0.202	0.171	0.142	0.202	SUBCLONAL	1	TRUE	1	0.717834452126376	2		542	702	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578433	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555526101	NA	P-0015452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	44	681	0	ENST00000269305.4:c.497C>G	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	166	tCa/tGa	5/11	1	2	FACETS	0.772	0.653	0.9	1	0.962	1	SUBCLONAL	2	FALSE	1	0.252248934574975	2		681	226	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170817081	170817081	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	11	425	0	ENST00000296930.5:c.85T>G	p.Tyr29Asp	p.Y29D	ENST00000296930	NM_002520.6	29	Tat/Gat	2/11	0.194313003349225	1	FACETS	0.811	0.566	1	0.811	0.566	1	CLONAL	1	FALSE	0	0.252248934574975	1		425	94	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170827907	170827909	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	rs761817600	NA	P-0015452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	13	714	0	ENST00000296930.5:c.652_654del	p.Ser218del	p.S218del	ENST00000296930	NM_002520.6	216	cCATca/cca	8/11	0.194313003349225	1	FACETS	0.472	0.337	0.635	0.472	0.337	0.635	SUBCLONAL	1	FALSE	0	0.252248934574975	1		714	191	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443862	18443862	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	11	504	3	ENST00000266497.5:c.835C>A	p.Pro279Thr	p.P279T	ENST00000266497		279	Ccg/Acg	3/31	1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	FALSE	1	0.252248934574975	2		507	68	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70967594	70967594	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	10	633	0	ENST00000276594.2:c.1429A>C	p.Asn477His	p.N477H	ENST00000276594	NM_024504.3	477	Aac/Cac	7/8	1	2	FACETS	1	0.782	1	1	0.782	1	CLONAL	1	FALSE	1	0.252248934574975	2		633	67	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	130	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.647754851364063	2		248	343	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223304	2223304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	304	603	0	ENST00000326181.6:c.916G>A	p.Ala306Thr	p.A306T	ENST00000326181	NM_032271.2	306	Gcc/Acc	10/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.647754851364063	2		603	902	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0015456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	20	414	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.136	0.103	0.175	0.136	0.103	0.175	SUBCLONAL	1	TRUE	1	0.452502999300421	2		414	650	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0015456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	275	835	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.452502999300421	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.452502999300421	1		836	760	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971029	21971029	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519852	NA	P-0015456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	141	399	1	ENST00000304494.5:c.329G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tGg/tAg	2/3	0.452502999300421	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.452502999300421	1		400	365	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900288	101900288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111854391	NA	P-0015456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	153	689	0	ENST00000374994.4:c.722C>T	p.Ser241Leu	p.S241L	ENST00000374994	NM_004612.2	241	tCg/tTg	4/9	0.452502999300421	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.452502999300421	1		689	519	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0015456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	178	754	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.992	0.916	1	0.992	0.916	1	CLONAL	1	TRUE	1	0.452502999300421	2		755	793	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542671	187542671	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779808082	NA	P-0015456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	78	759	1	ENST00000441802.2:c.5069C>T	p.Thr1690Ile	p.T1690I	ENST00000441802	NM_005245.3	1690	aCa/aTa	10/27	1	2	FACETS	0.575	0.505	0.649	0.575	0.505	0.649	SUBCLONAL	1	TRUE	1	0.452502999300421	2		760	600	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442770	99442770	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	242	778	0	ENST00000268035.6:c.1167G>C	p.Lys389Asn	p.K389N	ENST00000268035	NM_000875.3	389	aaG/aaC	5/21	0.0903843209697823	6	FACETS	0.859	0.802	0.916			1	INDETERMINATE	2	TRUE	NA	0.641736361816392	6		778	1003	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579440	7579440	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	223	650	0	ENST00000269305.4:c.247G>C	p.Ala83Pro	p.A83P	ENST00000269305	NM_001126112.2	83	Gcg/Ccg	4/11	0.641736361816392	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.641736361816392	1		650	470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579561	7579577	+	frameshift_variant	Frame_Shift_Del	DEL	ATCATCCATTGCTTGGG	ATCATCCATTGCTTGGG	-	novel	NA	P-0015457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	214	784	0	ENST00000269305.4:c.110_126del	p.Ser37PhefsTer9	p.S37Ffs*9	ENST00000269305	NM_001126112.2	37	tCCCAAGCAATGGATGAT/t	4/11	0.641736361816392	1	FACETS	0.928	0.872	0.985	0.928	0.872	0.985	CLONAL	1	TRUE	0	0.641736361816392	1		784	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	58	629	0	ENST00000269305.4:c.772G>C	p.Glu258Gln	p.E258Q	ENST00000269305	NM_001126112.2	258	Gaa/Caa	7/11	1	2	FACETS	0.976	0.84	1	0.976	0.84	1	CLONAL	1	TRUE	1	0.24	2		629	495	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220717	1220717	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs587782018	NA	P-0015459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	107	618	0	ENST00000326873.7:c.734+1G>C		p.X245_splice	ENST00000326873	NM_000455.4	245			0.154041570079454	2	FACETS	0.777	0.696	0.863	0.777	0.696	0.863	SUBCLONAL	2	TRUE	0	0.15	2		618	918	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439875	51439875	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs762054057	NA	P-0015459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	49	455	0	ENST00000262662.1:c.440A>G	p.Tyr147Cys	p.Y147C	ENST00000262662		147	tAt/tGt	4/4	1	2	FACETS	0.972	0.822	1	0.972	0.822	1	CLONAL	1	TRUE	1	0.15	2		455	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577107	7577118	+	inframe_deletion	In_Frame_Del	DEL	ACAGGCACAAAC	ACAGGCACAAAC	-	novel	NA	P-0015459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1305	219	889	0	ENST00000269305.4:c.820_831del	p.Val274_Cys277del	p.V274_C277del	ENST00000269305	NM_001126112.2	274	GTTTGTGCCTGT/-	8/11	1	2	FACETS	0.958	0.888	1	1	0.993	1	CLONAL	2	TRUE	1	0.15	2		889	1524	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45854892	45854892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1516	131	1048	1	ENST00000391945.4:c.2278C>T	p.Leu760Phe	p.L760F	ENST00000391945	NM_000400.3	760	Ctc/Ttc	23/23	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.15	2		1049	1647	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480526	57480526	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	113	508	0	ENST00000371085.3:c.521G>C	p.Cys174Ser	p.C174S	ENST00000371085	NM_000516.4	174	tGt/tCt	6/13	0.13997274062273	3	FACETS	0.918	0.826	1	0.918	0.826	1	CLONAL	2	TRUE	1	0.15	3		508	882	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205019	128205019	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	105	722	0	ENST00000341105.2:c.422A>C	p.Tyr141Ser	p.Y141S	ENST00000341105	NM_032638.4	141	tAc/tCc	3/6	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.15	2		722	951	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	52	248	0				ENST00000310581	NM_198253.2	-/1132			0.357747452264491	1	FACETS	0.61	0.529	0.694	0.61	0.529	0.694	INDETERMINATE	1	TRUE	0	0.684350639605935	1		248	164	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0015460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	94	339	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.947	0.854	1	0.947	0.854	1	CLONAL	1	TRUE	1	0.684350639605935	2		339	290	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022297	31022297	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs755974145	NA	P-0015461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	265	452	0	ENST00000375687.4:c.1782C>A	p.Cys594Ter	p.C594*	ENST00000375687	NM_015338.5	594	tgC/tgA	13/13	0.418188010396266	4	FACETS	0.996	0.943	1			1	CLONAL	3	FALSE	NA	0.450517073232263	4		452	571	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988555	36988555	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	227	936	1	ENST00000354822.5:c.98T>G	p.Met33Arg	p.M33R	ENST00000354822	NM_001079668.2	33	aTg/aGg	2/3	1	2	FACETS	1	0.979	1	1	0.995	1	CLONAL	2	FALSE	1	0.450517073232263	2		937	467	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831260	3831260	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	366	462	3	ENST00000262367.5:c.1621C>T	p.Gln541Ter	p.Q541*	ENST00000262367	NM_004380.2	541	Cag/Tag	7/31	0.463829671721424	4	FACETS	0.926	0.883	0.97	1	0.995	1	CLONAL	3	FALSE	2	0.450517073232263	4		465	848	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738225	133738225	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	308	498	0	ENST00000318560.5:c.625C>A	p.Leu209Ile	p.L209I	ENST00000318560	NM_005157.4	209	Ctc/Atc	4/11	0.258605464079218	3	FACETS	1	0.985	1			1	INDETERMINATE	2	FALSE	NA	0.450517073232263	3		498	759	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0015462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	85	704	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.3	3	FACETS	0.788	0.698	0.883			1	SUBCLONAL	2	TRUE	NA	0.23	3		705	523	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0015462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	41	489	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.242893451687552	1	FACETS	0.86	0.718	1	0.86	0.718	1	CLONAL	1	TRUE	0	0.23	1		489	367	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0015462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	71	583	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.891	1	1	0.983	1	CLONAL	2	TRUE	1	0.23	2		583	305	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466845	25466845	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	77	502	0	ENST00000264709.3:c.1858C>T	p.Pro620Ser	p.P620S	ENST00000264709	NM_175629.2	620	Cca/Tca	16/23	0.3	2	FACETS	1	0.96	1			1	CLONAL	1	TRUE	NA	0.23	2		502	549	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120511	94120511	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	18	403	0	ENST00000369303.4:c.540G>T	p.Lys180Asn	p.K180N	ENST00000369303	NM_004440.3	180	aaG/aaT	3/17	0.192969880848568	3	FACETS	0.559	0.421	0.723	0.28	0.21	0.362	SUBCLONAL	1	TRUE	1	0.23	3		403	312	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	57	248	0				ENST00000310581	NM_198253.2	-/1132			0.264926630427758	0	FACETS	0.879	0.794	0.96			1	CLONAL	4	FALSE	0	0.264926630427758	0		248	90	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0015463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	152	704	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.264926630427758	3	FACETS	1	0.943	1	1	0.99	1	CLONAL	3	FALSE	1	0.264926630427758	3		705	423	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0015463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	79	644	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	0.994	0.883	1	1	0.984	1	CLONAL	2	FALSE	1	0.264926630427758	2		644	300	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482926	140482927	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs777474487	NA	P-0015463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	129	466	5	ENST00000288602.6:c.1208dup	p.Ala404CysfsTer9	p.A404Cfs*9	ENST00000288602	NM_004333.4	403	cct/ccCt	10/18	0.264926630427758	3	FACETS	0.903	0.827	0.982	1	0.984	1	CLONAL	3	FALSE	1	0.264926630427758	3		471	407	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138252	2138252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45517409	NA	P-0015463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	34	632	0	ENST00000219476.3:c.5185C>T	p.Arg1729Cys	p.R1729C	ENST00000219476	NM_000548.3	1729	Cgc/Tgc	41/42	0.264926630427758	0	FACETS	0.575	0.471	0.692			1	SUBCLONAL	1	FALSE	0	0.264926630427758	0		632	328	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883794	37883794	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs746595697	NA	P-0015463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	175	562	0	ENST00000269571.5:c.3406C>T	p.Gln1136Ter	p.Q1136*	ENST00000269571		1136	Cag/Tag	26/27	1	2	FACETS	0.968	0.9	1	1	0.994	1	CLONAL	3	FALSE	1	0.264926630427758	2		562	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs863224499	NA	P-0015465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	345	890	0	ENST00000269305.4:c.672+1G>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.304968203818404	2	FACETS	0.951	0.9	1	0.951	0.9	1	CLONAL	2	TRUE	0	0.304968203818404	2		890	1190	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937017	36937035	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGCCAGCCCCCTTTACCT	CTGCCAGCCCCCTTTACCT	-	novel	NA	P-0015465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	117	361	0	ENST00000361632.4:c.1284_1285+17del		p.X428_splice	ENST00000361632		428		9/16	0.284957459417227	3	FACETS	0.947	0.859	1	0.947	0.859	1	CLONAL	2	TRUE	1	0.304968203818404	3		361	467	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607580	43607580	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	212	824	0	ENST00000355710.3:c.1556G>T	p.Cys519Phe	p.C519F	ENST00000355710	NM_020975.4	519	tGt/tTt	8/20	0.244393588718683	3	FACETS	1	0.991	1	0.747	0.694	0.803	CLONAL	1	TRUE	1	0.304968203818404	3		824	1072	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95579434	95579434	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1224940599	NA	P-0015465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	72	365	0	ENST00000393063.1:c.2035A>G	p.Ile679Val	p.I679V	ENST00000393063	NM_030621.3	679	Att/Gtt	13/28	0.284957459417227	3	FACETS	0.919	0.804	1	0.46	0.402	0.522	CLONAL	1	TRUE	1	0.304968203818404	3		365	592	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50815215	50815215	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	111	619	2	ENST00000398568.2:c.1568G>A	p.Cys523Tyr	p.C523Y	ENST00000398568	NM_001042412.1	523	tGt/tAt	9/18	0.207104078889942	4	FACETS	1	0.9	1	0.501	0.45	0.556	CLONAL	1	TRUE	2	0.304968203818404	4		621	948	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122374	17122374	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770396757	NA	P-0015465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	174	531	0	ENST00000285071.4:c.1021C>T	p.Arg341Trp	p.R341W	ENST00000285071	NM_144997.5	341	Cgg/Tgg	9/14	0.304968203818404	2	FACETS	0.926	0.857	0.998	0.926	0.857	0.998	CLONAL	2	TRUE	0	0.304968203818404	2		531	616	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10274011	10274011	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1469	144	826	0	ENST00000340748.4:c.869C>G	p.Pro290Arg	p.P290R	ENST00000340748		290	cCc/cGc	11/40	0.304968203818404	5	FACETS	0.853	0.775	0.936			1	CLONAL	1	TRUE	NA	0.304968203818404	5		826	1613	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273092	198273092	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0015465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	110	536	0	ENST00000335508.6:c.1117+1G>T		p.X373_splice	ENST00000335508	NM_012433.2	373			0.304968203818404	5	FACETS	1	0.965	1			1	CLONAL	1	TRUE	NA	0.304968203818404	5		536	899	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610499	215610499	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369756202	NA	P-0015465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	167	520	0	ENST00000260947.4:c.1757G>A	p.Ser586Asn	p.S586N	ENST00000260947	NM_000465.2	586	aGt/aAt	8/11	0.207104078889942	4	FACETS	0.91	0.838	0.986	0.91	0.838	0.986	CLONAL	2	TRUE	2	0.304968203818404	4		520	785	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574887	41574887	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1247	184	809	0	ENST00000263253.7:c.7172C>G	p.Thr2391Arg	p.T2391R	ENST00000263253	NM_001429.3	2391	aCg/aGg	31/31	0.303339473867242	4	FACETS	1	0.968	1	0.275	0.253	0.298	CLONAL	1	TRUE	0	0.304968203818404	4		809	1431	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965722	93965722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	76	447	0	ENST00000369303.4:c.2206G>A	p.Val736Ile	p.V736I	ENST00000369303	NM_004440.3	736	Gta/Ata	13/17	0.207104078889942	4	FACETS	1	0.953	1	0.587	0.515	0.664	CLONAL	1	TRUE	2	0.304968203818404	4		447	554	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785961	135785961	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	146	600	0	ENST00000298552.3:c.1260G>C	p.Arg420Ser	p.R420S	ENST00000298552	NM_001162426.1	420	agG/agC	12/23	0.304968203818404	5	FACETS	1	0.968	1	0.284	0.258	0.311	CLONAL	1	TRUE	1	0.304968203818404	5		600	1229	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0015466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1527	1585	982	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	0.532491795558476	19	FACETS	0.961	0.941	0.981			1	CLONAL	11	TRUE	NA	0.532491795558476	19		982	3112	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172385	108172385	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764389018	NA	P-0015466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	236	722	0	ENST00000278616.4:c.5188C>T	p.Arg1730Ter	p.R1730*	ENST00000278616	NM_000051.3	1730	Cga/Tga	35/63	0.532491795558476	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.532491795558476	2		722	409	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793372	18793372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	101	732	1	ENST00000266497.5:c.4069G>A	p.Asp1357Asn	p.D1357N	ENST00000266497		1357	Gat/Aat	30/31	0.532491795558476	3	FACETS	0.944	0.847	1	0.315	0.282	0.349	CLONAL	1	TRUE	0	0.532491795558476	3		733	509	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589304	28589304	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	116	695	0	ENST00000241453.7:c.2743A>G	p.Thr915Ala	p.T915A	ENST00000241453	NM_004119.2	915	Aca/Gca	22/24	0.532491795558476	4	FACETS	1	0.929	1	0.345	0.311	0.381	CLONAL	1	TRUE	1	0.532491795558476	4		695	645	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29068962	29068962	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	73	310	1	ENST00000282397.4:c.19A>T	p.Thr7Ser	p.T7S	ENST00000282397	NM_002019.4	7	Acc/Tcc	1/30	0.532491795558476	4	FACETS	1	0.962	1	0.413	0.364	0.466	CLONAL	1	TRUE	1	0.532491795558476	4		311	339	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858118	40858118	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	99	1355	3	ENST00000428826.2:c.1746C>G	p.Asp582Glu	p.D582E	ENST00000428826		582	gaC/gaG	16/21	0.532491795558476	3	FACETS	0.511	0.455	0.57	0.255	0.227	0.285	SUBCLONAL	1	TRUE	1	0.532491795558476	3		1358	922	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346252	152346252	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	60	1140	0	ENST00000359321.1:c.318A>T	p.Glu106Asp	p.E106D	ENST00000359321	NM_005431.1	106	gaA/gaT	3/3	0.303406252506917	3	FACETS	0.408	0.351	0.471	0.136	0.117	0.157	INDETERMINATE	1	TRUE	0	0.532491795558476	3		1140	699	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211749	5211749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759153530	NA	P-0015468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	215	562	2	ENST00000357368.4:c.5086C>T	p.Arg1696Cys	p.R1696C	ENST00000357368	NM_002850.3	1696	Cgc/Tgc	33/38	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.51718784037768	2		564	770	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425298	49425304	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGGTA	CCAGGTA	-	novel	NA	P-0015468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	192	596	0	ENST00000301067.7:c.13184_13190del	p.Val4395GlyfsTer6	p.V4395Gfs*6	ENST00000301067	NM_003482.3	4395	gTACCTGGg/gg	39/54	1	2	FACETS	0.952	0.882	1	0.952	0.882	1	CLONAL	1	TRUE	1	0.51718784037768	2		596	780	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349373	89349386	+	frameshift_variant	Frame_Shift_Del	DEL	CGTCGGCAGCCCCT	CGTCGGCAGCCCCT	-	novel	NA	P-0015468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	209	681	0	ENST00000301030.4:c.3564_3577del	p.Ala1190GlufsTer9	p.A1190Efs*9	ENST00000301030	NM_001256183.1	1188	cgAGGGGCTGCCGACGcg/cgcg	9/13	NA	2	FACETS	0.792	0.735	0.851			1	INDETERMINATE	1	TRUE	NA	0.51718784037768	2		681	1020	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579363	7579364	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0015468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	225	627	0	ENST00000269305.4:c.323dup	p.Arg110ProfsTer39	p.R110Pfs*39	ENST00000269305	NM_001126112.2	108	ggt/ggGt	4/11	0.509844060854653	1	FACETS	0.95	0.889	1	0.95	0.889	1	CLONAL	1	TRUE	0	0.51718784037768	1		627	679	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664601	29664601	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1060500345	NA	P-0015468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	319	371	0	ENST00000356175.3:c.6579+1G>T		p.X2193_splice	ENST00000356175	NM_000267.3	2193			0.51718784037768	2	FACETS	0.988	0.942	1	0.988	0.942	1	CLONAL	2	TRUE	0	0.51718784037768	2		371	624	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757429	40757429	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	191	523	0	ENST00000373198.4:c.2869C>G	p.Pro957Ala	p.P957A	ENST00000373198	NM_133170.3	957	Ccg/Gcg	20/32	0.51718784037768	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.51718784037768	1		523	537	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519643	137519643	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	128	279	0	ENST00000367739.4:c.995C>G	p.Pro332Arg	p.P332R	ENST00000367739	NM_000416.2	332	cCa/cGa	7/7	0.332718688907136	4	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.51718784037768	4		279	571	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864416	151864416	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	124	345	0	ENST00000262189.6:c.9565C>T	p.Gln3189Ter	p.Q3189*	ENST00000262189	NM_170606.2	3189	Cag/Tag	42/59	1	2	FACETS	0.948	0.862	1	0.948	0.862	1	CLONAL	1	TRUE	1	0.51718784037768	2		345	506	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879274	151879274	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	152	364	0	ENST00000262189.6:c.5671C>A	p.Pro1891Thr	p.P1891T	ENST00000262189	NM_170606.2	1891	Cca/Aca	36/59	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.51718784037768	2		364	556	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0015470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	141	358	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.171087690368523	4	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	2	0.199483818689651	4		358	781	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458536	12458536	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs780238349	NA	P-0015471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	164	443	1	ENST00000287820.6:c.1153C>T	p.Arg385Ter	p.R385*	ENST00000287820	NM_015869.4	385	Cga/Tga	6/7	0.523146206511017	4	FACETS	1	0.941	1	0.515	0.473	0.559	CLONAL	1	TRUE	2	0.523146206511017	4		444	927	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5462875	5462875	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	73	164	0	ENST00000381577.3:c.436C>T	p.Pro146Ser	p.P146S	ENST00000381577	NM_014143.3	146	Cca/Tca	4/7	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.523146206511017	2		164	279	SUCCESS
APC	324	MSKCC	GRCh37	5	112174043	112174043	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	277	332	1	ENST00000257430.4:c.2752G>T	p.Glu918Ter	p.E918*	ENST00000257430	NM_000038.5	918	Gag/Tag	16/16	0.335149537950369	4	FACETS	0.944	0.891	0.999	0.944	0.891	0.999	CLONAL	3	TRUE	1	0.335149537950369	4		333	779	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646393	23646393	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	210	491	0	ENST00000261584.4:c.1474G>T	p.Gly492Trp	p.G492W	ENST00000261584	NM_024675.3	492	Ggg/Tgg	4/13	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.335149537950369	2		491	877	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508473	106508473	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370328855	NA	P-0015472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	42	192	1	ENST00000359195.3:c.467C>T	p.Ala156Val	p.A156V	ENST00000359195	NM_002649.2	156	gCg/gTg	2/11	0.29080023852807	3	FACETS	0.846	0.708	0.997	0.282	0.236	0.333	CLONAL	1	TRUE	0	0.335149537950369	3		193	346	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468281	120468282	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0015472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	171	472	0	ENST00000256646.2:c.4157_4158delinsTT	p.Gly1386Val	p.G1386V	ENST00000256646	NM_024408.3	1386	gGG/gTT	25/34	0.335149537950369	3	FACETS	1	0.988	1	0.718	0.661	0.777	CLONAL	1	TRUE	1	0.335149537950369	3		472	830	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111017	193111017	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	327	234	0	ENST00000367435.3:c.550G>C	p.Ala184Pro	p.A184P	ENST00000367435	NM_024529.4	184	Gca/Cca	7/17	0.335149537950369	5	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	TRUE	2	0.335149537950369	5		234	949	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226590011	226590011	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	487	549	0	ENST00000366794.5:c.190A>T	p.Ile64Phe	p.I64F	ENST00000366794	NM_001618.3	64	Atc/Ttc	2/23	0.335149537950369	5	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	2	0.335149537950369	5		549	1325	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998510	100998510	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	247	492	0	ENST00000325455.5:c.1292C>A	p.Pro431Gln	p.P431Q	ENST00000325455	NM_001202474.3	431	cCa/cAa	1/8	0.335149537950369	4	FACETS	0.922	0.862	0.984	0.922	0.862	0.984	CLONAL	2	TRUE	2	0.335149537950369	4		492	1067	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107968	30107968	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	227	485	0	ENST00000331968.5:c.839G>T	p.Arg280Leu	p.R280L	ENST00000331968	NM_002742.2	280	cGg/cTg	5/18	0.267187141611117	4	FACETS	1	0.989	1	0.664	0.617	0.713	CLONAL	1	TRUE	2	0.335149537950369	4		485	1362	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845591	72845591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	136	525	1	ENST00000268489.5:c.3749C>T	p.Pro1250Leu	p.P1250L	ENST00000268489	NM_006885.3	1250	cCc/cTc	7/10	1	2	FACETS	0.864	0.785	0.948	0.864	0.785	0.948	CLONAL	1	TRUE	1	0.335149537950369	2		526	939	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0015472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	183	514	1	ENST00000269305.4:c.560-1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.335149537950369	1	FACETS	0.755	0.7	0.811	1	0.991	1	SUBCLONAL	2	TRUE	0	0.335149537950369	1		515	602	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554291	29554304	+	frameshift_variant	Frame_Shift_Del	DEL	CACTGCAGGAAACA	CACTGCAGGAAACA	-	novel	NA	P-0015472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	225	486	0	ENST00000356175.3:c.2308_2321del	p.Thr770Ter	p.T770*	ENST00000356175	NM_000267.3	769	ccCACTGCAGGAAACAct/ccct	19/57	0.151805132242264	4	FACETS	1	0.99	1	0.685	0.636	0.735	INDETERMINATE	1	TRUE	2	0.335149537950369	4		486	1309	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554309	29554309	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	326	518	0	ENST00000356175.3:c.2325G>T	p.Glu775Asp	p.E775D	ENST00000356175	NM_000267.3	775	gaG/gaT	19/57	0.151805132242264	4	FACETS	0.899	0.848	0.952	0.899	0.848	0.952	INDETERMINATE	2	TRUE	2	0.335149537950369	4		518	1444	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618400	37618400	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	85	354	0	ENST00000447079.4:c.76G>T	p.Gly26Ter	p.G26*	ENST00000447079	NM_015083.1	26	Gga/Tga	1/14	0.151805132242264	4	FACETS	0.852	0.752	0.959	0.426	0.376	0.48	INDETERMINATE	1	TRUE	2	0.335149537950369	4		354	795	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101030	4101030	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730880511	NA	P-0015472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	68	396	0	ENST00000262948.5:c.692G>T	p.Arg231Leu	p.R231L	ENST00000262948	NM_030662.3	231	cGc/cTc	6/11	0.335149537950369	1	FACETS	0.682	0.595	0.777	0.682	0.595	0.777	SUBCLONAL	1	TRUE	0	0.335149537950369	1		396	495	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355565	15355565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	224	509	0	ENST00000263377.2:c.2167C>T	p.Pro723Ser	p.P723S	ENST00000263377	NM_058243.2	723	Ccg/Tcg	12/20	0.311104030919234	2	FACETS	0.862	0.805	0.921	0.862	0.805	0.921	CLONAL	2	TRUE	0	0.335149537950369	2		509	775	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375450	15375450	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	98	512	0	ENST00000263377.2:c.977G>T	p.Arg326Leu	p.R326L	ENST00000263377	NM_058243.2	326	cGg/cTg	6/20	0.311104030919234	2	FACETS	0.639	0.569	0.714	0.32	0.284	0.357	SUBCLONAL	1	TRUE	0	0.335149537950369	2		512	915	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471001	25471001	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	144	471	0	ENST00000264709.3:c.760G>T	p.Ala254Ser	p.A254S	ENST00000264709	NM_175629.2	254	Gca/Tca	7/23	0.200991959773539	3	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.335149537950369	3		471	674	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519809	29519809	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	114	510	0	ENST00000389048.3:c.1762G>T	p.Glu588Ter	p.E588*	ENST00000389048	NM_004304.4	588	Gaa/Taa	9/29	NA	2	FACETS	0.717	0.644	0.794			1	INDETERMINATE	1	TRUE	NA	0.335149537950369	2		510	949	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286769	212286769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs563587222	NA	P-0015472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	300	408	0	ENST00000342788.4:c.2927G>A	p.Arg976Lys	p.R976K	ENST00000342788	NM_005235.2	976	aGg/aAg	24/28	0.250917307708159	3	FACETS	0.898	0.845	0.952	0.898	0.845	0.952	CLONAL	2	TRUE	1	0.335149537950369	3		408	1164	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439509	220439509	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	151	434	0	ENST00000243786.2:c.362C>G	p.Thr121Arg	p.T121R	ENST00000243786	NM_002191.3	121	aCa/aGa	2/2	0.250917307708159	3	FACETS	0.804	0.738	0.874	0.804	0.738	0.874	CLONAL	2	TRUE	1	0.335149537950369	3		434	654	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546669	9546669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	136	321	0	ENST00000353224.5:c.1353C>A	p.Asn451Lys	p.N451K	ENST00000353224	NM_177990.2	451	aaC/aaA	5/10	0.234738418526065	3	FACETS	1	0.985	1	0.701	0.639	0.766	CLONAL	1	TRUE	1	0.335149537950369	3		321	676	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643916	52643916	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	110	439	0	ENST00000394830.3:c.1980G>C	p.Gln660His	p.Q660H	ENST00000394830	NM_018313.4	660	caG/caC	17/30	0.335149537950369	2	FACETS	0.812	0.73	0.9	0.406	0.365	0.45	CLONAL	1	TRUE	0	0.335149537950369	2		439	808	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664910	138664910	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	56	313	0	ENST00000330315.3:c.655C>G	p.Gln219Glu	p.Q219E	ENST00000330315	NM_023067.3	219	Cag/Gag	1/1	0.335149537950369	2	FACETS	0.861	0.741	0.992	0.431	0.37	0.496	CLONAL	1	TRUE	0	0.335149537950369	2		313	388	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629442	187629442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	192	561	0	ENST00000441802.2:c.1540C>T	p.His514Tyr	p.H514Y	ENST00000441802	NM_005245.3	514	Cat/Tat	2/27	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.335149537950369	2		561	1106	SUCCESS
APC	324	MSKCC	GRCh37	5	112176902	112176902	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs538571038	NA	P-0015472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	313	369	1	ENST00000257430.4:c.5611G>T	p.Asp1871Tyr	p.D1871Y	ENST00000257430	NM_000038.5	1871	Gat/Tat	16/16	0.335149537950369	4	FACETS	0.92	0.87	0.97	0.92	0.87	0.97	CLONAL	3	TRUE	1	0.335149537950369	4		370	904	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449626	149449626	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	69	454	0	ENST00000286301.3:c.1320G>T	p.Arg440Ser	p.R440S	ENST00000286301	NM_005211.3	440	agG/agT	10/22	0.311104030919234	2	FACETS	0.632	0.551	0.721	0.316	0.275	0.361	SUBCLONAL	1	TRUE	0	0.335149537950369	2		454	651	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6038812	6038812	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	426	595	0	ENST00000265849.7:c.632G>C	p.Arg211Pro	p.R211P	ENST00000265849	NM_000535.5	211	cGa/cCa	6/15	0.311104030919234	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.335149537950369	2		595	1093	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509802	106509802	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	408	536	1	ENST00000359195.3:c.1796G>C	p.Gly599Ala	p.G599A	ENST00000359195	NM_002649.2	599	gGa/gCa	2/11	0.29080023852807	3	FACETS	1	0.981	1	0.706	0.671	0.741	CLONAL	2	TRUE	0	0.335149537950369	3		537	1343	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931786	68931786	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	169	360	0	ENST00000288368.4:c.216G>T	p.Met72Ile	p.M72I	ENST00000288368	NM_024870.2	72	atG/atT	3/40	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.335149537950369	2		360	889	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566022	141566022	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1564084030	NA	P-0015472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	58	371	1	ENST00000220592.5:c.1242G>T	p.Gln414His	p.Q414H	ENST00000220592	NM_012154.3	414	caG/caT	10/19	1	2	FACETS	0.714	0.614	0.822	0.714	0.614	0.822	SUBCLONAL	1	TRUE	1	0.335149537950369	2		372	485	SUCCESS
AR	367	MSKCC	GRCh37	X	66766439	66766439	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	48	273	0	ENST00000374690.3:c.1451C>G	p.Thr484Ser	p.T484S	ENST00000374690	NM_000044.3	484	aCt/aGt	1/8	0.304394630481817	4	FACETS	0.727	0.615	0.851			1	SUBCLONAL	1	TRUE	NA	0.335149537950369	4		273	526	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229236	123229236	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	174	351	0	ENST00000218089.9:c.3720C>A	p.Asn1240Lys	p.N1240K	ENST00000218089	NM_001042749.1	1240	aaC/aaA	34/35	0.267187141611117	4	FACETS	1	0.978	1	0.589	0.541	0.64	CLONAL	1	TRUE	2	0.335149537950369	4		351	1176	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860046	152860046	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0015472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	208	469	0	ENST00000406277.2:c.382A>T	p.Arg128Ter	p.R128*	ENST00000406277	NM_152274.4	128	Aga/Tga	5/7	0.267187141611117		FACETS		0.852	0.984				CLONAL	2	TRUE	2	0.335149537950369	4		469	904	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0015473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	242	399	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.0866034953938906	3	FACETS	0.929	0.869	0.991			1	INDETERMINATE	3	TRUE	NA	0.202778163998969	3		399	943	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	135	234	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.171501470941432	2	FACETS	1	0.983	1	0.691	0.627	0.758	CLONAL	1	TRUE	0	0.202778163998969	2		234	964	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088699	27088699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1355	89	349	0	ENST00000324856.7:c.2308G>A	p.Ala770Thr	p.A770T	ENST00000324856	NM_006015.4	770	Gcc/Acc	7/20	1	2	FACETS	0.608	0.537	0.685	0.608	0.537	0.685	SUBCLONAL	1	TRUE	1	0.202778163998969	2		349	1444	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047495	49047495	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0015473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	41	142	0	ENST00000267163.4:c.2490-1G>C		p.X830_splice	ENST00000267163	NM_000321.2	830			0.171501470941432	2	FACETS	0.893	0.744	1	0.446	0.372	0.529	CLONAL	1	TRUE	0	0.202778163998969	2		142	453	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778355	3778355	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	129	239	0	ENST00000262367.5:c.6693C>A	p.Phe2231Leu	p.F2231L	ENST00000262367	NM_004380.2	2231	ttC/ttA	31/31	0.125888651472588	3	FACETS	0.793	0.718	0.871	0.793	0.718	0.871	SUBCLONAL	2	TRUE	1	0.202778163998969	3		239	884	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100610	67100610	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	90	228	0	ENST00000412916.2:c.308T>G	p.Leu103Arg	p.L103R	ENST00000412916		103	cTg/cGg	4/6	0.171501470941432	2	FACETS	1	0.923	1	0.527	0.467	0.592	CLONAL	1	TRUE	0	0.202778163998969	2		228	842	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772310	68772311	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	154	255	0	ENST00000261769.5:c.160dup	p.Arg54LysfsTer5	p.R54Kfs*5	ENST00000261769	NM_004360.3	53	-/A	2/16	0.171501470941432	2	FACETS	0.77	0.704	0.839	0.77	0.704	0.839	SUBCLONAL	2	TRUE	0	0.202778163998969	2		255	986	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732530	74732530	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	35	58	0	ENST00000359995.5:c.379C>T	p.Arg127Cys	p.R127C	ENST00000359995	NM_001195427.1	127	Cgc/Tgc	2/3	0.171501470941432	2	FACETS	0.894	0.74	1	0.894	0.74	1	CLONAL	2	TRUE	0	0.202778163998969	2		58	193	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444668	187444668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	96	146	0	ENST00000232014.4:c.1559G>A	p.Cys520Tyr	p.C520Y	ENST00000232014	NM_001130845.1	520	tGc/tAc	7/10	0.202778163998969	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.202778163998969	1		146	602	SUCCESS
APC	324	MSKCC	GRCh37	5	112179431	112179431	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs864622205	NA	P-0015474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	97	255	0	ENST00000257430.4:c.8140C>T	p.Arg2714Cys	p.R2714C	ENST00000257430	NM_000038.5	2714	Cgt/Tgt	16/16	0.530030536575987	1	FACETS	0.857	0.773	0.944	0.857	0.773	0.944	CLONAL	1	TRUE	0	0.530030536575987	1		255	314	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0015474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	68	178	0	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	0.530030536575987	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.530030536575987	1		178	164	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335141	65335141	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	212	322	0	ENST00000342505.4:c.500T>C	p.Val167Ala	p.V167A	ENST00000342505	NM_002227.2	167	gTg/gCg	6/25	0.401144968444925	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.530030536575987	1		322	509	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0015475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	63	235	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.755	0.653	0.866	0.755	0.653	0.866	SUBCLONAL	1	TRUE	1	0.272697008204574	2		235	612	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0015478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	91	414	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	0.26	2		414	602	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0015478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	62	442	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.84	0.726	0.964	0.84	0.726	0.964	CLONAL	1	TRUE	1	0.26	2		442	568	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0015478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	34	515	3	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.454	0.37	0.549	0.454	0.37	0.549	SUBCLONAL	1	TRUE	1	0.26	2		518	576	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249457	153249457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	57	514	1	ENST00000281708.4:c.1321C>T	p.Arg441Trp	p.R441W	ENST00000281708	NM_033632.3	441	Cgg/Tgg	9/12	1	2	FACETS	0.642	0.55	0.743	0.642	0.55	0.743	SUBCLONAL	1	TRUE	1	0.26	2		515	683	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100871	27100871	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	137	485	1	ENST00000324856.7:c.4153G>T	p.Glu1385Ter	p.E1385*	ENST00000324856	NM_006015.4	1385	Gaa/Taa	18/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.26	2		486	882	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653833	89653833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1085308042	NA	P-0015478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	44	429	0	ENST00000371953.3:c.131G>A	p.Gly44Asp	p.G44D	ENST00000371953	NM_000314.4	44	gGc/gAc	2/9	1	2	FACETS	0.582	0.487	0.686	0.582	0.487	0.686	SUBCLONAL	1	TRUE	1	0.26	2		429	582	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211003	36211003	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1342	128	743	1	ENST00000222270.7:c.758del	p.Pro253HisfsTer7	p.P253Hfs*7	ENST00000222270	NM_014727.1	252	Ccc/cc	3/37	1	2	FACETS	0.67	0.605	0.739	0.67	0.605	0.739	SUBCLONAL	1	TRUE	1	0.26	2		744	1470	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59924478	59924478	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	42	220	0	ENST00000259008.2:c.611C>A	p.Ser204Tyr	p.S204Y	ENST00000259008	NM_032043.2	204	tCc/tAc	6/20	1	2	FACETS	0.871	0.729	1	0.871	0.729	1	CLONAL	1	TRUE	1	0.267250369580804	2		220	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0015481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	143	727	0	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.15999826317825	2		727	1262	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919724	50919724	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	87	632	0	ENST00000440232.2:c.2892G>T	p.Lys964Asn	p.K964N	ENST00000440232	NM_002691.3	964	aaG/aaT	23/27	NA	2	FACETS	0.928	0.819	1			1	INDETERMINATE	1	TRUE	NA	0.15999826317825	2		632	1172	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684345	29684345	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0015491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	165	290	0	ENST00000356175.3:c.7865T>G	p.Leu2622Ter	p.L2622*	ENST00000356175	NM_000267.3	2622	tTa/tGa	53/57	0.532794433392594	2	FACETS	0.899	0.828	0.973	0.449	0.414	0.487	CLONAL	1	TRUE	0	0.532794433392594	2		290	689	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264110	46264110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	97	203	0	ENST00000371998.3:c.1157G>A	p.Gly386Glu	p.G386E	ENST00000371998		386	gGg/gAg	11/23	0.183566529729176	5	FACETS	1	0.947	1			1	INDETERMINATE	1	TRUE	NA	0.532794433392594	5		203	596	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749383	41749383	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	112	172	0	ENST00000226382.2:c.412A>G	p.Thr138Ala	p.T138A	ENST00000226382	NM_003924.3	138	Aca/Gca	2/3	0.183566529729176	5	FACETS	1	0.91	1			1	INDETERMINATE	1	TRUE	NA	0.532794433392594	5		172	747	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336346	80336346	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	129	271	0	ENST00000286548.4:c.973T>C	p.Tyr325His	p.Y325H	ENST00000286548	NM_002072.3	325	Tac/Cac	7/7	1	2	FACETS	0.799	0.727	0.875	0.799	0.727	0.875	SUBCLONAL	1	TRUE	1	0.532794433392594	2		271	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0015492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	118	796	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.901	0.812	0.995	0.901	0.812	0.995	CLONAL	1	TRUE	1	0.311084018565517	2		796	842	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0015492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	15	276	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.311084018565517	1	FACETS	0.393	0.288	0.519	0.393	0.288	0.519	SUBCLONAL	1	TRUE	0	0.311084018565517	1		276	207	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102196028	102196028	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	34	169	0	ENST00000263464.3:c.788T>G	p.Phe263Cys	p.F263C	ENST00000263464	NM_001165.4	263	tTt/tGt	2/9	1	2	FACETS	0.677	0.554	0.814	0.677	0.554	0.814	SUBCLONAL	1	TRUE	1	0.311084018565517	2		169	323	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392851	118392851	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	50	372	0	ENST00000534358.1:c.11883C>G	p.Asn3961Lys	p.N3961K	ENST00000534358	NM_005933.3	3961	aaC/aaG	36/36	1	2	FACETS	0.494	0.418	0.577	0.494	0.418	0.577	SUBCLONAL	1	TRUE	1	0.311084018565517	2		372	651	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2137939	2137939	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137854315	NA	P-0015492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	101	462	0	ENST00000219476.3:c.5065A>G	p.Lys1689Glu	p.K1689E	ENST00000219476	NM_000548.3	1689	Aaa/Gaa	39/42	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.311084018565517	2		462	616	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220652	1220653	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	97	599	0	ENST00000326873.7:c.672dup	p.Ala225CysfsTer41	p.A225Cfs*41	ENST00000326873	NM_000455.4	224	att/aTtt	5/10	0.279735102115858	1	FACETS	0.693	0.618	0.773	0.693	0.618	0.773	SUBCLONAL	1	TRUE	0	0.311084018565517	1		599	760	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162475122	162475122	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0015492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	62	328	0	ENST00000366898.1:c.618+1G>T		p.X206_splice	ENST00000366898	NM_004562.2	206			1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.311084018565517	2		328	372	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0015493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	106	348	0	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	1	2	FACETS	0.812	0.729	0.899	1	0.984	1	CLONAL	2	TRUE	1	0.2	2		348	653	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190320	32190320	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377458854	NA	P-0015493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	53	290	0	ENST00000375023.3:c.419G>A	p.Arg140His	p.R140H	ENST00000375023	NM_004557.3	140	cGc/cAc	3/30	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.2	2		290	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0015494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	141	812	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.604872315945292	1	FACETS	0.94	0.868	1	0.94	0.868	1	CLONAL	1	TRUE	0	0.604872315945292	1		812	346	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419958	152419958	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	1227	333	0	ENST00000206249.3:c.1645C>G	p.Leu549Val	p.L549V	ENST00000206249	NM_000125.3	549	Cta/Gta	8/8	NA	2	FACETS	0.845	0.83	0.859			1	INDETERMINATE	3	TRUE	NA	0.604872315945292	2		333	1601	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012391	152012391	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs757111455	NA	P-0015494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	62	189	0	ENST00000262189.6:c.422A>G	p.Glu141Gly	p.E141G	ENST00000262189	NM_170606.2	141	gAa/gGa	4/59	0.339270249630823	1	FACETS	0.603	0.528	0.683	0.603	0.528	0.683	INDETERMINATE	1	TRUE	0	0.604872315945292	1		189	237	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188279	10188280	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0015495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	218	440	0	ENST00000256474.2:c.422_423del	p.Asn141SerfsTer2	p.N141Sfs*2	ENST00000256474	NM_000551.3	141	aAT/a	2/3	0.425823092933235	1	FACETS	0.904	0.842	0.969	0.904	0.842	0.969	CLONAL	1	TRUE	0	0.425823092933235	1		440	891	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155459	47155459	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	33	315	0	ENST00000409792.3:c.4622A>C	p.Asn1541Thr	p.N1541T	ENST00000409792	NM_014159.6	1541	aAt/aCt	5/21	0.425823092933235	1	FACETS	0.244	0.198	0.296	0.244	0.198	0.296	SUBCLONAL	1	TRUE	0	0.425823092933235	1		315	500	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651402	52651402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	131	395	0	ENST00000394830.3:c.1694C>T	p.Pro565Leu	p.P565L	ENST00000394830	NM_018313.4	565	cCa/cTa	15/30	0.425823092933235	1	FACETS	0.907	0.827	0.99	0.907	0.827	0.99	CLONAL	1	TRUE	0	0.425823092933235	1		395	534	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	100	507	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		507	807	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0015497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	88	425	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		425	690	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929353	44929353	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	40	252	0	ENST00000377967.4:c.2453C>A	p.Ser818Ter	p.S818*	ENST00000377967	NM_021140.2	818	tCa/tAa	17/29	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		252	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0015498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	260	835	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	1	2	FACETS	0.824	0.775	0.873	0.824	0.775	0.873	CLONAL	1	TRUE	1	0.834149002648006	2		836	757	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0015498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	188	279	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.924	0.862	0.987	0.924	0.862	0.987	CLONAL	1	TRUE	1	0.834149002648006	2		279	488	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0015498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	904	493	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.834149002648006	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.834149002648006	2		493	1064	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243859016	243859016	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs397514606	NA	P-0015498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	281	192	0	ENST00000263826.5:c.49G>A	p.Glu17Lys	p.E17K	ENST00000263826	NM_005465.4	17	Gaa/Aaa	2/13	0.658236883203352	3	FACETS	0.784	0.743	0.825	0.784	0.743	0.825	SUBCLONAL	2	TRUE	1	0.834149002648006	3		192	609	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431588	49431588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1305161243	NA	P-0015498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	296	429	1	ENST00000301067.7:c.9551C>T	p.Ser3184Phe	p.S3184F	ENST00000301067	NM_003482.3	3184	tCc/tTc	34/54	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.834149002648006	2		430	703	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0015498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	173	371	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.875	0.813	0.939	0.875	0.813	0.939	CLONAL	1	TRUE	1	0.834149002648006	2		371	474	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453146	140453146	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913369	NA	P-0015498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	345	368	0	ENST00000288602.6:c.1789C>G	p.Leu597Val	p.L597V	ENST00000288602	NM_004333.4	597	Cta/Gta	15/18	1	2	FACETS	0.909	0.863	0.955	0.909	0.863	0.955	CLONAL	1	TRUE	1	0.834149002648006	2		368	910	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106733	27106734	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0015498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	54	409	0	ENST00000324856.7:c.6347_6348del	p.Arg2116ThrfsTer33	p.R2116Tfs*33	ENST00000324856	NM_006015.4	2115	cAG/c	20/20	0.834149002648006	2	FACETS	0.149	0.127	0.174	0.075	0.063	0.087	SUBCLONAL	1	TRUE	0	0.834149002648006	2		409	867	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165882	118165882	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774747996	NA	P-0015498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	248	252	0	ENST00000369448.3:c.392C>T	p.Pro131Leu	p.P131L	ENST00000369448	NM_017709.3	131	cCa/cTa	2/2	0.834149002648006	2	FACETS	0.975	0.919	1	0.487	0.459	0.516	CLONAL	1	TRUE	0	0.834149002648006	2		252	610	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444307	49444307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	496	760	0	ENST00000301067.7:c.3064C>T	p.Pro1022Ser	p.P1022S	ENST00000301067	NM_003482.3	1022	Cct/Tct	11/54	1	2	FACETS	0.944	0.905	0.983	0.944	0.905	0.983	CLONAL	1	TRUE	1	0.834149002648006	2		760	1260	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434944	110434946	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0015498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1355	209	774	0	ENST00000375856.3:c.3455_3457del	p.Phe1152del	p.F1152del	ENST00000375856	NM_003749.2	1152	tTCTcc/tcc	1/2	1	2	FACETS	0.32	0.296	0.346	0.32	0.296	0.346	SUBCLONAL	1	TRUE	1	0.834149002648006	2		774	1564	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961891	41961891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	174	214	0	ENST00000219905.7:c.799C>T	p.Pro267Ser	p.P267S	ENST00000219905	NM_001164273.1	267	Ccc/Tcc	2/24	1	2	FACETS	0.895	0.832	0.96	0.895	0.832	0.96	CLONAL	1	TRUE	1	0.834149002648006	2		214	466	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441322	149441322	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376280561	NA	P-0015498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	345	505	0	ENST00000286301.3:c.1717G>A	p.Glu573Lys	p.E573K	ENST00000286301	NM_005211.3	573	Gag/Aag	12/22	1	2	FACETS	0.882	0.837	0.927	0.882	0.837	0.927	CLONAL	1	TRUE	1	0.834149002648006	2		505	938	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839886	27839886	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1027454605	NA	P-0015498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1212	177	338	0	ENST00000328488.2:c.208C>T	p.Arg70Cys	p.R70C	ENST00000328488	NM_003533.2	70	Cgc/Tgc	1/1	0.834149002648006	3	FACETS	0.433	0.398	0.47			1	SUBCLONAL	1	TRUE	NA	0.834149002648006	3		338	1389	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839921	27839921	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1316	203	394	0	ENST00000328488.2:c.173C>A	p.Ser58Ter	p.S58*	ENST00000328488	NM_003533.2	58	tCg/tAg	1/1	0.834149002648006	3	FACETS	0.454	0.419	0.49			1	SUBCLONAL	1	TRUE	NA	0.834149002648006	3		394	1519	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100378	157100378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1271667149	NA	P-0015498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	158	185	2	ENST00000346085.5:c.1315G>A	p.Glu439Lys	p.E439K	ENST00000346085	NM_020732.3	439	Gag/Aag	1/20	0.834149002648006	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.834149002648006	1		187	209	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900244	101900246	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs863223829	NA	P-0015498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	39	299	0	ENST00000374994.4:c.683_685del	p.Glu228del	p.E228del	ENST00000374994	NM_004612.2	226	ggAGAa/gga	4/9	0.834149002648006	1	FACETS	0.14	0.116	0.167	0.14	0.116	0.167	SUBCLONAL	1	TRUE	0	0.834149002648006	1		299	389	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779172	135779172	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203631	NA	P-0015498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	64	281	2	ENST00000298552.3:c.2074C>T	p.Arg692Ter	p.R692*	ENST00000298552	NM_001162426.1	692	Cga/Tga	17/23	0.834149002648006	1	FACETS	0.204	0.177	0.233	0.204	0.177	0.233	SUBCLONAL	1	TRUE	0	0.834149002648006	1		283	439	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798809	135798810	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs118203383	NA	P-0015498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	23	264	0	ENST00000298552.3:c.433_434del	p.Gln145ValfsTer8	p.Q145Vfs*8	ENST00000298552	NM_001162426.1	145	CAg/g	6/23	0.834149002648006	1	FACETS	0.081	0.063	0.102	0.081	0.063	0.102	SUBCLONAL	1	TRUE	0	0.834149002648006	1		264	396	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0015499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	151	414	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.354100731391991	4	FACETS	1	0.975	1	1	0.991	1	CLONAL	3	FALSE	2	0.354100731391991	4		414	346	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0015499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	45	138	1	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	0.354100731391991	4	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	FALSE	2	0.354100731391991	4		139	144	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047310	77047310	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	49	248	0	ENST00000356341.3:c.1234G>C	p.Ala412Pro	p.A412P	ENST00000356341	NM_002576.4	412	Gca/Cca	13/15	0.280542906722265	3	FACETS	0.81	0.695	0.933			1	CLONAL	2	FALSE	NA	0.354100731391991	3		248	201	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161919	47161919	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	68	275	0	ENST00000409792.3:c.4207C>T	p.Pro1403Ser	p.P1403S	ENST00000409792	NM_014159.6	1403	Cct/Tct	3/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.158955625990317	2		275	646	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	129	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.71350325776061	2		248	339	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0015501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	116	470	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.847	0.77	0.926	0.847	0.77	0.926	CLONAL	1	TRUE	1	0.71350325776061	2		470	384	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0015501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	207	475	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.71350325776061	2		475	544	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440404	49440404	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	245	489	0	ENST00000301067.7:c.4406G>A	p.Trp1469Ter	p.W1469*	ENST00000301067	NM_003482.3	1469	tGg/tAg	15/54	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.71350325776061	2		489	665	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174872	11174872	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	132	393	0	ENST00000361445.4:c.7162G>C	p.Glu2388Gln	p.E2388Q	ENST00000361445	NM_004958.3	2388	Gag/Cag	52/58	0.327796081450903	3	FACETS	0.749	0.682	0.82	0.375	0.341	0.41	INDETERMINATE	1	TRUE	1	0.71350325776061	3		393	670	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111452	8111452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	168	343	0	ENST00000346208.3:c.938C>T	p.Ala313Val	p.A313V	ENST00000346208		313	gCa/gTa	5/6	0.325600243610879	6	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.71350325776061	6		343	960	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68290327	68290327	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	148	316	0	ENST00000487270.1:c.67C>G	p.Gln23Glu	p.Q23E	ENST00000487270	NM_133509.3	23	Cag/Gag	2/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.71350325776061	NA		316	272	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645138	67645138	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	193	441	1	ENST00000264010.4:c.403C>T	p.Gln135Ter	p.Q135*	ENST00000264010	NM_006565.3	135	Cag/Tag	3/12	1	2	FACETS	0.958	0.892	1	0.958	0.892	1	CLONAL	1	TRUE	1	0.71350325776061	2		442	565	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998946	11998946	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	26	208	0	ENST00000353533.5:c.448G>C	p.Asp150His	p.D150H	ENST00000353533	NM_003010.3	150	Gat/Cat	4/11	0.664157458864738	1	FACETS	0.178	0.141	0.22	0.178	0.141	0.22	SUBCLONAL	1	TRUE	0	0.71350325776061	1		208	263	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265432	46265432	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	28	232	0	ENST00000371998.3:c.2302C>G	p.Gln768Glu	p.Q768E	ENST00000371998		768	Cag/Gag	12/23	0.680514102212835	3	FACETS	0.192	0.152	0.236	0.096	0.076	0.118	SUBCLONAL	1	TRUE	1	0.71350325776061	3		232	556	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890251	72890251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200658486	NA	P-0015501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	43	344	0	ENST00000325599.8:c.431C>T	p.Pro144Leu	p.P144L	ENST00000325599	NM_018130.2	144	cCg/cTg	4/11	1	2	FACETS	0.201	0.167	0.238	0.201	0.167	0.238	SUBCLONAL	1	TRUE	1	0.71350325776061	2		344	601	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259444	89259444	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	59	317	0	ENST00000336596.2:c.588A>C	p.Arg196Ser	p.R196S	ENST00000336596	NM_005233.5	196	agA/agC	3/17	1	2	FACETS	0.337	0.29	0.388	0.337	0.29	0.388	SUBCLONAL	1	TRUE	1	0.71350325776061	2		317	491	SUCCESS
APC	324	MSKCC	GRCh37	5	112173962	112173962	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	121	256	0	ENST00000257430.4:c.2671A>C	p.Met891Leu	p.M891L	ENST00000257430	NM_000038.5	891	Atg/Ctg	16/16	0.664157458864738	1	FACETS	0.856	0.789	0.923	0.856	0.789	0.923	CLONAL	1	TRUE	0	0.71350325776061	1		256	255	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696618	176696618	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	46	159	0	ENST00000439151.2:c.5319G>C	p.Glu1773Asp	p.E1773D	ENST00000439151	NM_022455.4	1773	gaG/gaC	16/23	0.664157458864738	1	FACETS	0.553	0.475	0.635	0.553	0.475	0.635	SUBCLONAL	1	TRUE	0	0.71350325776061	1		159	150	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331961	81331961	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	49	205	0	ENST00000222390.5:c.2123G>C	p.Arg708Pro	p.R708P	ENST00000222390	NM_000601.4	708	cGa/cCa	18/18	1	2	FACETS	0.485	0.414	0.563	0.485	0.414	0.563	SUBCLONAL	1	TRUE	1	0.71350325776061	2		205	283	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509603	106509603	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	139	405	0	ENST00000359195.3:c.1597C>G	p.Gln533Glu	p.Q533E	ENST00000359195	NM_002649.2	533	Cag/Gag	2/11	1	2	FACETS	0.906	0.832	0.982	0.906	0.832	0.982	CLONAL	1	TRUE	1	0.71350325776061	2		405	430	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615724	100615724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375531341	NA	P-0015501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	196	212	1	ENST00000308731.7:c.608C>T	p.Pro203Leu	p.P203L	ENST00000308731	NM_000061.2	203	cCg/cTg	8/19	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.71350325776061	1		213	284	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651932	36651934	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CCG	CCG	A	novel	NA	P-0015501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	170	354	0	ENST00000244741.5:c.54_56delinsA	p.Cys18Ter	p.C18*	ENST00000244741	NM_000389.4	18	tgCCGc/tgAc	2/3	1	2	FACETS	0.942	0.873	1	0.942	0.873	1	CLONAL	1	TRUE	1	0.71350325776061	2		354	506	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0015510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	445	332	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.425393598145344	5	FACETS	1	0.986	1	1	0.996	1	CLONAL	5	TRUE	1	0.425393598145344	5		332	662	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057519990	NA	P-0015510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	544	367	12	ENST00000269305.4:c.796G>T	p.Gly266Ter	p.G266*	ENST00000269305	NM_001126112.2	266	Gga/Tga	8/11	0.385406479172648	1	FACETS	0.992	0.957	1	1	0.998	1	CLONAL	2	TRUE	0	0.425393598145344	1		379	1015	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579536	7579536	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567556930	NA	P-0015510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	261	560	0	ENST00000269305.4:c.151G>T	p.Glu51Ter	p.E51*	ENST00000269305	NM_001126112.2	51	Gaa/Taa	4/11	0.385406479172648	1	FACETS	0.959	0.9	1	0.959	0.9	1	CLONAL	1	TRUE	0	0.425393598145344	1		560	1007	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477794	140477794	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	106	323	0	ENST00000288602.6:c.1514T>A	p.Leu505His	p.L505H	ENST00000288602	NM_004333.4	505	cTc/cAc	12/18	0.425393598145344	5	FACETS	0.842	0.758	0.929	0.421	0.379	0.465	CLONAL	2	TRUE	1	0.425393598145344	5		323	485	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513462	149513462	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	846	427	0	ENST00000261799.4:c.741G>T	p.Trp247Cys	p.W247C	ENST00000261799	NM_002609.3	247	tgG/tgT	5/23	0.425393598145344	2	FACETS	0.982	0.965	0.998	1	0.999	1	CLONAL	4	TRUE	0	0.425393598145344	2		427	1013	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100873	27100874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	544	361	0	ENST00000324856.7:c.4159dup	p.Glu1387GlyfsTer58	p.E1387Gfs*58	ENST00000324856	NM_006015.4	1385	-/G	18/20	0.425308768668672	2	FACETS	0.904	0.874	0.934	1	0.997	1	CLONAL	3	TRUE	0	0.425393598145344	2		361	943	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333002	70333002	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	400	559	0	ENST00000373644.4:c.907A>T	p.Asn303Tyr	p.N303Y	ENST00000373644	NM_030625.2	303	Aat/Tat	2/12	0.425393598145344	1	FACETS	0.96	0.92	1	1	0.997	1	CLONAL	2	TRUE	0	0.425393598145344	1		559	771	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514506	125514506	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	149	274	1	ENST00000428830.2:c.1201G>T	p.Gly401Cys	p.G401C	ENST00000428830	NM_001114121.2	401	Ggc/Tgc	11/14	0.229857109617186	3	FACETS	0.788	0.724	0.854			1	INDETERMINATE	2	TRUE	NA	0.425393598145344	3		275	539	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114257	115114257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	144	381	0	ENST00000257566.3:c.960G>C	p.Gln320His	p.Q320H	ENST00000257566	NM_016569.3	320	caG/caC	6/8	1	2	FACETS	0.844	0.77	0.921	0.844	0.77	0.921	CLONAL	1	TRUE	1	0.425393598145344	2		381	802	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609474	81609474	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	135	331	0	ENST00000298171.2:c.1072G>C	p.Glu358Gln	p.E358Q	ENST00000298171	NM_000369.2	358	Gaa/Caa	10/10	0.425393598145344	3	FACETS	1	0.916	1	0.504	0.458	0.552	CLONAL	1	TRUE	1	0.425393598145344	3		331	764	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39550347	39550347	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	122	361	0	ENST00000262039.4:c.458G>T	p.Gly153Val	p.G153V	ENST00000262039	NM_002647.2	153	gGa/gTa	4/25	0.404155099531615	1	FACETS	0.892	0.811	0.978	0.892	0.811	0.978	CLONAL	1	TRUE	0	0.425393598145344	1		361	506	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877393	40877393	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	448	419	0	ENST00000373198.4:c.2303G>T	p.Gly768Val	p.G768V	ENST00000373198	NM_133170.3	768	gGc/gTc	15/32	1	2	FACETS	0.996	0.954	1	1	0.997	1	CLONAL	2	TRUE	1	0.425393598145344	2		419	1057	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1258745	1258745	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	434	447	0	ENST00000310581.5:c.3000C>A	p.Asn1000Lys	p.N1000K	ENST00000310581	NM_198253.2	1000	aaC/aaA	13/16	1	2	FACETS	0.958	0.916	1	1	0.997	1	CLONAL	2	TRUE	1	0.425393598145344	2		447	1065	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177083	56177083	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	81	193	1	ENST00000399503.3:c.2353G>A	p.Glu785Lys	p.E785K	ENST00000399503	NM_005921.1	785	Gag/Aag	13/20	0.377154451634564	0	FACETS		NA	1			1	NA	3	TRUE	0	0.425393598145344	0		194	112	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538948	23538948	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	212	401	1	ENST00000380871.4:c.491C>A	p.Thr164Lys	p.T164K	ENST00000380871	NM_006167.3	164	aCg/aAg	2/2	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.425393598145344	2		402	952	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8339040	8339040	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	284	296	0	ENST00000356435.5:c.5261G>C	p.Cys1754Ser	p.C1754S	ENST00000356435		1754	tGt/tCt	32/35	0.425393598145344	3	FACETS	0.969	0.921	1	1	0.994	1	CLONAL	3	TRUE	1	0.425393598145344	3		296	557	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484342	8484342	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	239	346	1	ENST00000356435.5:c.3190G>T	p.Asp1064Tyr	p.D1064Y	ENST00000356435		1064	Gat/Tat	19/35	0.425393598145344	3	FACETS	0.96	0.9	1	0.96	0.9	1	CLONAL	2	TRUE	1	0.425393598145344	3		347	710	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229398	98229398	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	81	156	0	ENST00000331920.6:c.2560G>A	p.Gly854Arg	p.G854R	ENST00000331920	NM_000264.3	854	Gga/Aga	15/24	0.425393598145344	3	FACETS	1	0.904	1	0.512	0.453	0.575	CLONAL	1	TRUE	1	0.425393598145344	3		156	451	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393576	139393576	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	266	463	1	ENST00000277541.6:c.6070G>T	p.Val2024Leu	p.V2024L	ENST00000277541	NM_017617.3	2024	Gta/Tta	32/34	0.148804005158237	3	FACETS	1	0.984	1	0.382	0.357	0.408	INDETERMINATE	1	TRUE	0	0.425393598145344	3		464	1323	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343457	70343457	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	372	377	0	ENST00000374080.3:c.1631C>A	p.Ser544Ter	p.S544*	ENST00000374080		544	tCa/tAa	12/45	1	2	FACETS	0.966	0.921	1	1	0.996	1	CLONAL	2	TRUE	1	0.425393598145344	2		377	905	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940463	76940463	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	97	465	0	ENST00000373344.5:c.630C>A	p.Ser210Arg	p.S210R	ENST00000373344	NM_000489.3	210	agC/agA	8/35	0.425393598145344	5	FACETS	1	0.946	1	0.366	0.326	0.408	CLONAL	1	TRUE	2	0.425393598145344	5		465	681	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339726	70339727	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AG	AG	T	novel	NA	P-0015510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	370	459	0	ENST00000374080.3:c.395_396delinsT	p.Lys132MetfsTer15	p.K132Mfs*15	ENST00000374080		132	aAG/aT	3/45	1	2	FACETS	0.823	0.782	0.864	1	0.996	1	CLONAL	2	TRUE	1	0.425393598145344	2		459	1057	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0015511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	597	704	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.843266936926323	5	FACETS	0.98	0.947	1	0.98	0.947	1	CLONAL	3	TRUE	2	0.843266936926323	5		705	1091	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0015511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	323	583	0				ENST00000310581	NM_198253.2	-/1132			0.33366145829213	5	FACETS	0.981	0.947	1			1	INDETERMINATE	4	TRUE	NA	0.843266936926323	5		583	442	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0015511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	352	519	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.842199340016151	5	FACETS	0.931	0.883	0.979			1	CLONAL	2	TRUE	NA	0.843266936926323	5		519	1016	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0015511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	572	290	1	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.843266936926323	4	FACETS	1	0.995	1	1	0.995	1	CLONAL	4	TRUE	0	0.843266936926323	4		291	613	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0015511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	126	342	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.767652265521585	4	FACETS	0.951	0.865	1	0.476	0.432	0.521	CLONAL	1	TRUE	2	0.843266936926323	4		342	579	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587118	189587118	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761885185	NA	P-0015511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	300	234	0	ENST00000264731.3:c.1135C>T	p.Arg379Cys	p.R379C	ENST00000264731	NM_003722.4	379	Cgt/Tgt	9/14	0.828846874097703	4	FACETS	0.989	0.939	1	0.989	0.939	1	CLONAL	2	TRUE	2	0.843266936926323	4		234	663	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0015511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	173	467	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	0.943	0.878	1	0.943	0.878	1	CLONAL	1	TRUE	1	0.843266936926323	2		467	435	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561352	9561352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773981325	NA	P-0015511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	290	265	0	ENST00000353224.5:c.430G>A	p.Glu144Lys	p.E144K	ENST00000353224	NM_177990.2	144	Gaa/Aaa	4/10	0.828846874097703	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.843266936926323	4		265	588	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729535	41729535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	309	336	0	ENST00000242208.4:c.994G>A	p.Asp332Asn	p.D332N	ENST00000242208	NM_002192.2	332	Gac/Aac	3/3	0.842199340016151	5	FACETS	0.983	0.931	1			1	CLONAL	2	TRUE	NA	0.843266936926323	5		336	844	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971187	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	572	300	1	ENST00000304494.5:c.171_172delinsTT	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	57	gcCCga/gcTTga	2/3	0.843266936926323				0.995	1				CLONAL	4	TRUE	0	0.843266936926323	4		301	613	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445902	49445902	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	636	707	0	ENST00000301067.7:c.1564C>T	p.Pro522Ser	p.P522S	ENST00000301067	NM_003482.3	522	Cca/Tca	10/54	0.843266936926323	3	FACETS	0.988	0.958	1	0.988	0.958	1	CLONAL	2	TRUE	1	0.843266936926323	3		707	1085	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61749764	61749764	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	518	243	0	ENST00000401558.2:c.283C>T	p.Pro95Ser	p.P95S	ENST00000401558	NM_003400.3	95	Cca/Tca	4/25	0.783964650222309	4	FACETS	0.952	0.922	0.981	0.952	0.922	0.981	CLONAL	3	TRUE	1	0.843266936926323	4		243	793	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645336	215645336	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	159	277	0	ENST00000260947.4:c.1262C>T	p.Ala421Val	p.A421V	ENST00000260947	NM_000465.2	421	gCt/gTt	4/11	0.843266936926323	4	FACETS	0.96	0.882	1	0.32	0.294	0.347	CLONAL	1	TRUE	1	0.843266936926323	4		277	724	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031164	36031164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	269	389	0	ENST00000358208.4:c.1283C>T	p.Pro428Leu	p.P428L	ENST00000358208		428	cCc/cTc	11/12	0.60623319590168	4	FACETS	0.95	0.898	1	0.95	0.898	1	CLONAL	2	TRUE	2	0.843266936926323	4		389	619	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405920	49405920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	419	419	0	ENST00000418115.1:c.218C>T	p.Ser73Phe	p.S73F	ENST00000418115	NM_001664.2	73	tCc/tTc	3/5	0.767652265521585	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	2	0.843266936926323	4		419	912	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0015513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	51	704	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.507455539497426	4	FACETS	1	0.916	1	1	0.916	1	CLONAL	3	TRUE	1	0.507455539497426	4		705	97	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950860	32950860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373203204	NA	P-0015513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	23	377	1	ENST00000380152.3:c.8686C>T	p.Arg2896Cys	p.R2896C	ENST00000380152		2896	Cgt/Tgt	21/27	0.507455539497426	3	FACETS	0.924	0.772	1	0.924	0.772	1	CLONAL	3	TRUE	0	0.507455539497426	3		378	41	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0015513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	55	529	0	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	0.320077090426206	5	FACETS	1	0.944	1	0.771	0.673	0.874	CLONAL	2	TRUE	2	0.507455539497426	5		529	165	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330469	65330469	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0015513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	29	251	0	ENST00000342505.4:c.1176+1del		p.X392_splice	ENST00000342505	NM_002227.2	392			0.392135273966607	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	0	0.507455539497426	2		251	49	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777800	3777813	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGGGGGTGTTCA	GCTGGGGGTGTTCA	-	novel	NA	P-0015513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	10	638	0	ENST00000262367.5:c.7235_7248del	p.Leu2412GlnfsTer30	p.L2412Qfs*30	ENST00000262367	NM_004380.2	2412	cTGAACACCCCCAGC/c	31/31	0.369931321644362	3	FACETS	0.61	0.418	0.844	0.305	0.209	0.422	SUBCLONAL	1	TRUE	1	0.507455539497426	3		638	81	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198096	185198096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	18	320	0	ENST00000265026.3:c.2578G>A	p.Glu860Lys	p.E860K	ENST00000265026	NM_004721.4	860	Gag/Aag	13/14	0.232915281014074	2	FACETS	0.806	0.639	0.981	0.806	0.639	0.981	INDETERMINATE	2	TRUE	0	0.507455539497426	2		320	44	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0015514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	375	796	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.594827584169342	1	FACETS	0.921	0.878	0.964	0.921	0.878	0.964	CLONAL	1	TRUE	0	0.62925945457689	1		796	887	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223144	5223144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1007529586	NA	P-0015514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	363	565	0	ENST00000357368.4:c.2659G>A	p.Glu887Lys	p.E887K	ENST00000357368	NM_002850.3	887	Gag/Aag	18/38	0.62925945457689	1	FACETS	0.997	0.951	1	0.997	0.951	1	CLONAL	1	TRUE	0	0.62925945457689	1		565	793	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	235	248	0				ENST00000310581	NM_198253.2	-/1132			0.426336777931292	4	FACETS	0.903	0.847	0.96	0.903	0.847	0.96	CLONAL	2	TRUE	2	0.602974488647573	4		248	692	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0015515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	451	287	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.577892730278749	3	FACETS	0.969	0.937	0.999	0.969	0.937	0.999	CLONAL	3	TRUE	0	0.602974488647573	3		287	670	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540164	187540164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1401234994	NA	P-0015515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	279	248	0	ENST00000441802.2:c.7576C>T	p.His2526Tyr	p.H2526Y	ENST00000441802	NM_005245.3	2526	Cac/Tac	10/27	0.276602772316315	4	FACETS	0.957	0.903	1			1	INDETERMINATE	2	TRUE	NA	0.602974488647573	4		248	775	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325832	30325832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	27	227	0	ENST00000322652.5:c.2030C>T	p.Ala677Val	p.A677V	ENST00000322652	NM_015355.2	677	gCt/gTt	16/16	1	2	FACETS	0.221	0.175	0.273	0.221	0.175	0.273	SUBCLONAL	1	TRUE	1	0.602974488647573	2		227	406	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627349	14627349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	140	331	0	ENST00000254322.2:c.721G>A	p.Asp241Asn	p.D241N	ENST00000254322	NM_006145.1	241	Gac/Aac	2/3	0.582267511402818	3	FACETS	0.528	0.48	0.579	0.264	0.24	0.29	SUBCLONAL	1	TRUE	1	0.602974488647573	3		331	1144	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183868	10183868	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs5030810	NA	P-0015515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	363	266	0	ENST00000256474.2:c.337C>T	p.Arg113Ter	p.R113*	ENST00000256474	NM_000551.3	113	Cga/Tga	1/3	0.602974488647573	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.602974488647573	2		266	593	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251885	153251885	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	25	163	0	ENST00000281708.4:c.1121A>T	p.Lys374Met	p.K374M	ENST00000281708	NM_033632.3	374	aAg/aTg	7/12	0.170560514293872	4	FACETS	0.288	0.226	0.359	0.144	0.113	0.18	INDETERMINATE	1	TRUE	2	0.602974488647573	4		163	462	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542192	187542192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748091046	NA	P-0015515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	235	187	0	ENST00000441802.2:c.5548C>T	p.His1850Tyr	p.H1850Y	ENST00000441802	NM_005245.3	1850	Cat/Tat	10/27	0.276602772316315	4	FACETS	1	0.978	1			1	INDETERMINATE	2	TRUE	NA	0.602974488647573	4		187	578	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549677	187549677	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	211	188	0	ENST00000441802.2:c.4564C>G	p.His1522Asp	p.H1522D	ENST00000441802	NM_005245.3	1522	Cat/Gat	8/27	0.276602772316315	4	FACETS	1	0.966	1			1	INDETERMINATE	2	TRUE	NA	0.602974488647573	4		188	536	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549691	187549691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	209	186	0	ENST00000441802.2:c.4550C>T	p.Ser1517Phe	p.S1517F	ENST00000441802	NM_005245.3	1517	tCt/tTt	8/27	0.276602772316315	4	FACETS	1	0.942	1			1	INDETERMINATE	2	TRUE	NA	0.602974488647573	4		186	552	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519426	176519426	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	222	391	1	ENST00000292408.4:c.832C>T	p.Gln278Ter	p.Q278*	ENST00000292408	NM_213647.1	278	Cag/Tag	7/18	1	2	FACETS	0.939	0.877	1	0.939	0.877	1	CLONAL	1	TRUE	1	0.602974488647573	2		392	784	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931688	39931688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	335	165	0	ENST00000378444.4:c.2911G>A	p.Gly971Ser	p.G971S	ENST00000378444	NM_001123385.1	971	Ggt/Agt	4/15	0.276602772316315	2	FACETS	1	0.982	1			1	INDETERMINATE	2	TRUE	NA	0.602974488647573	2		165	534	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098497	11098497	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	392	336	0	ENST00000358026.2:c.1017del	p.Ala340ArgfsTer71	p.A340Rfs*71	ENST00000358026	NM_001128849.1	339	Ccc/cc	6/36	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.79	2		336	915	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134294	11134309	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	AGTTGCCCGAAAAGGT	AGTTGCCCGAAAAGGT	-	novel	NA	P-0015516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	330	344	0	ENST00000358026.2:c.2960_2973+2del		p.X987_splice	ENST00000358026	NM_001128849.1	987		20/36	1	2	FACETS	0.976	0.926	1	0.976	0.926	1	CLONAL	1	TRUE	1	0.79	2		344	856	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577505	7577505	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs745425759	NA	P-0015517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	193	483	0	ENST00000269305.4:c.776A>T	p.Asp259Val	p.D259V	ENST00000269305	NM_001126112.2	259	gAc/gTc	7/11	0.33832649967856	2	FACETS	0.856	0.796	0.917	0.856	0.796	0.917	CLONAL	2	TRUE	0	0.373355430653567	2		483	604	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992052	72992052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	279	443	0	ENST00000268489.5:c.1993C>T	p.Arg665Cys	p.R665C	ENST00000268489	NM_006885.3	665	Cgt/Tgt	2/10	1	2	FACETS	0.86	0.816	0.905	1	0.996	1	CLONAL	3	TRUE	1	0.373355430653567	2		443	579	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993961	72993961	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	391	585	0	ENST00000268489.5:c.84C>A	p.Asn28Lys	p.N28K	ENST00000268489	NM_006885.3	28	aaC/aaA	2/10	1	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	1	0.373355430653567	2		585	894	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0015518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	888	536	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.597826349772954	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	4	TRUE	0	0.597826349772954	4		536	1172	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578493	7578500	+	frameshift_variant	Frame_Shift_Del	DEL	CACAGCTG	CACAGCTG	-	novel	NA	P-0015518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	647	584	0	ENST00000269305.4:c.430_437del	p.Gln144GlyfsTer2	p.Q144Gfs*2	ENST00000269305	NM_001126112.2	144	CAGCTGTGg/g	5/11	0.597826349772954	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.597826349772954	2		584	984	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609011	43609011	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	303	316	0	ENST00000355710.3:c.1767C>A	p.Ser589Arg	p.S589R	ENST00000355710	NM_020975.4	589	agC/agA	10/20	0.597826349772954	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.597826349772954	3		316	649	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99482514	99482514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777966016	NA	P-0015518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	197	363	0	ENST00000268035.6:c.3382G>A	p.Ala1128Thr	p.A1128T	ENST00000268035	NM_000875.3	1128	Gcc/Acc	18/21	0.597826349772954	3	FACETS	0.905	0.838	0.974	0.452	0.419	0.487	CLONAL	1	TRUE	1	0.597826349772954	3		363	946	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533721	63533721	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	285	262	0	ENST00000307078.5:c.1433del	p.His478ProfsTer29	p.H478Pfs*29	ENST00000307078	NM_004655.3	478	cAc/cc	6/11	0.597826349772954	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.597826349772954	2		262	443	SUCCESS
ALK	238	MSKCC	GRCh37	2	29436932	29436932	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	145	267	0	ENST00000389048.3:c.3661C>A	p.Leu1221Met	p.L1221M	ENST00000389048	NM_004304.4	1221	Ctg/Atg	24/29	0.597826349772954	3	FACETS	0.968	0.886	1	0.484	0.443	0.527	CLONAL	1	TRUE	1	0.597826349772954	3		267	651	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864658	68864658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1418006656	NA	P-0015518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	100	123	0	ENST00000288368.4:c.29G>A	p.Arg10His	p.R10H	ENST00000288368	NM_024870.2	10	cGc/cAc	1/40	0.597826349772954	3	FACETS	1	0.971	1	0.607	0.547	0.669	CLONAL	1	TRUE	1	0.597826349772954	3		123	358	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047527	49047527	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587778850	NA	P-0015519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	97	171	0	ENST00000267163.4:c.2520+1G>T		p.X840_splice	ENST00000267163	NM_000321.2	840			0.915045886976791	1	FACETS	0.865	0.809	0.917	0.865	0.809	0.917	CLONAL	1	TRUE	0	0.915133592509116	1		171	133	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593630	+	inframe_deletion	In_Frame_Del	DEL	TTGTTGAGGAGATAAATGGAA	TTGTTGAGGAGATAAATGGAA	-	novel	NA	P-0015519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	225	323	0	ENST00000288135.5:c.1676_1696del	p.Val559_Asn566delinsAsp	p.V559_N566delinsD	ENST00000288135	NM_000222.2	559	gTTGTTGAGGAGATAAATGGAAac/gac	11/21	1	2	FACETS	0.839	0.787	0.892	0.839	0.787	0.892	CLONAL	1	TRUE	1	0.915133592509116	2		323	586	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305249	39305249	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	505	350	0	ENST00000373001.3:c.1176T>A	p.Asn392Lys	p.N392K	ENST00000373001	NM_022157.3	392	aaT/aaA	7/7	0.905530541623479	1	FACETS	0.969	0.946	0.99	0.969	0.946	0.99	CLONAL	1	TRUE	0	0.915133592509116	1		350	618	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251637	212251637	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	365	267	0	ENST00000342788.4:c.3422C>A	p.Pro1141Gln	p.P1141Q	ENST00000342788	NM_005235.2	1141	cCa/cAa	27/28	0.911123024173512	2	FACETS	0.962	0.918	1	0.481	0.459	0.504	CLONAL	1	TRUE	0	0.915133592509116	2		267	829	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0015520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	130	429	0	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	0.369058649324093	1	FACETS	0.97	0.883	1	0.97	0.883	1	CLONAL	1	TRUE	0	0.369058649324093	1		429	592	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974907	15974907	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	33	282	0	ENST00000268712.3:c.3968C>G	p.Pro1323Arg	p.P1323R	ENST00000268712	NM_006311.3	1323	cCt/cGt	30/46	0.132383518028931	3	FACETS	0.389	0.316	0.472	0.13	0.105	0.158	INDETERMINATE	1	TRUE	0	0.369058649324093	3		282	544	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371838	55371838	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	21	138	0	ENST00000297316.4:c.528G>A	p.Met176Ile	p.M176I	ENST00000297316	NM_022454.3	176	atG/atA	2/2	1	2	FACETS	0.59	0.456	0.743	0.59	0.456	0.743	SUBCLONAL	1	TRUE	1	0.369058649324093	2		138	193	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0015522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	522	605	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.466476449050775	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.497465403524403	2		606	980	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	172	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.497465403524403	2		248	536	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341268	89341268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	84	199	2	ENST00000301030.4:c.7667C>T	p.Thr2556Met	p.T2556M	ENST00000301030	NM_001256183.1	2556	aCg/aTg	11/13	1	2	FACETS	0.851	0.756	0.951	0.851	0.756	0.951	CLONAL	1	TRUE	1	0.497465403524403	2		201	397	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748544	40748544	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	210	441	1	ENST00000392038.2:c.338G>T	p.Arg113Leu	p.R113L	ENST00000392038	NM_001626.4	113	cGg/cTg	5/14	1	2	FACETS	0.956	0.889	1	0.956	0.889	1	CLONAL	1	TRUE	1	0.497465403524403	2		442	883	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710583	40710583	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	185	421	0	ENST00000373198.4:c.4268T>G	p.Ile1423Ser	p.I1423S	ENST00000373198	NM_133170.3	1423	aTt/aGt	31/32	0.454070336160122	4	FACETS	0.81	0.746	0.877			1	CLONAL	1	TRUE	NA	0.497465403524403	4		421	1375	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0015524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	174	286	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.479253984416598	4	FACETS	0.976	0.905	1	0.651	0.603	0.7	CLONAL	2	TRUE	1	0.479253984416598	4		286	550	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0015524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	311	557	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	0.479253984416598	5	FACETS	0.909	0.861	0.958			1	CLONAL	3	TRUE	NA	0.479253984416598	5		557	818	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281200	15281200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	366	817	1	ENST00000263388.2:c.5056G>T	p.Val1686Leu	p.V1686L	ENST00000263388	NM_000435.2	1686	Gtg/Ttg	27/33	0.479253984416598	6	FACETS	1	0.99	1	0.587	0.557	0.619	CLONAL	2	TRUE	2	0.479253984416598	6		818	1273	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546603	9546603	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	99	445	0	ENST00000353224.5:c.1419A>C	p.Lys473Asn	p.K473N	ENST00000353224	NM_177990.2	473	aaA/aaC	5/10	0.402501539458606	4	FACETS	1	0.917	1			1	CLONAL	1	TRUE	NA	0.479253984416598	4		445	594	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965878	90965878	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0015524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	61	266	0	ENST00000265433.3:c.1439C>G	p.Ser480Ter	p.S480*	ENST00000265433	NM_002485.4	480	tCa/tGa	11/16	0.479253984416598	6	FACETS	1	0.914	1	0.269	0.232	0.309	CLONAL	1	TRUE	2	0.479253984416598	6		266	463	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0015525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	29	197	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.948	0.76	1	0.948	0.76	1	CLONAL	1	TRUE	1	0.15	2		197	408	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916929	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519931	NA	P-0015525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	35	425	0	ENST00000263967.3:c.316G>C	p.Gly106Arg	p.G106R	ENST00000263967	NM_006218.2	106	Ggc/Cgc	2/21	1	2	FACETS	0.673	0.55	0.813	0.673	0.55	0.813	SUBCLONAL	1	TRUE	1	0.15	2		425	693	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1615	116	850	1	ENST00000269305.4:c.403del	p.Cys135AlafsTer35	p.C135Afs*35	ENST00000269305	NM_001126112.2	135	Tgc/gc	5/11	1	2	FACETS	0.894	0.802	0.991	0.894	0.802	0.991	CLONAL	1	TRUE	1	0.15	2		851	1731	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023724	27023740	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGCCCCTCCGCGGCC	GCGGCCCCTCCGCGGCC	-	novel	NA	P-0015525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	83	487	0	ENST00000324856.7:c.831_847del	p.Gly278ArgfsTer116	p.G278Rfs*116	ENST00000324856	NM_006015.4	277	gGCGGCCCCTCCGCGGCC/g	1/20	1	2	FACETS	0.986	0.868	1	0.986	0.868	1	CLONAL	1	TRUE	1	0.15	2		487	1122	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087932	27087932	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1231	87	625	0	ENST00000324856.7:c.2220del	p.Met741Ter	p.M741*	ENST00000324856	NM_006015.4	740	tCc/tc	6/20	1	2	FACETS	0.88	0.776	0.992	0.88	0.776	0.992	CLONAL	1	TRUE	1	0.15	2		625	1318	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0015527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	86	339	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.975	0.873	1	0.975	0.873	1	CLONAL	1	TRUE	1	0.612655695158582	2		339	288	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs967461896	NA	P-0015527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	896	368	0	ENST00000269305.4:c.526T>C	p.Cys176Arg	p.C176R	ENST00000269305	NM_001126112.2	176	Tgc/Cgc	5/11	0.612655695158582	3	FACETS	0.885	0.87	0.9			1	CLONAL	4	TRUE	NA	0.612655695158582	3		368	1079	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610059	81610059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908872	NA	P-0015527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	178	235	1	ENST00000298171.2:c.1657G>A	p.Ala553Thr	p.A553T	ENST00000298171	NM_000369.2	553	Gcc/Acc	10/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.612655695158582	2		236	517	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874271	76874271	+	splice_region_variant,intron_variant	Splice_Region	SNP	T	T	C	novel	NA	P-0015527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	121	252	0	ENST00000373344.5:c.5448+3A>G		p.X1816_splice	ENST00000373344	NM_000489.3	1816			0.384152765366098	1	FACETS	0.818	0.748	0.889	0.818	0.748	0.889	CLONAL	1	TRUE	0	0.612655695158582	1		252	335	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	50	414	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.954	0.808	1	0.954	0.808	1	CLONAL	1	TRUE	1	0.13	2		414	806	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0015528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	54	677	3	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.856	0.729	0.997	0.856	0.729	0.997	CLONAL	1	TRUE	1	0.13	2		680	970	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231335	5231335	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769069932	NA	P-0015528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	36	505	1	ENST00000357368.4:c.2141G>A	p.Arg714His	p.R714H	ENST00000357368	NM_002850.3	714	cGc/cAc	14/38	1	2	FACETS	0.819	0.672	0.986	0.819	0.672	0.986	CLONAL	1	TRUE	1	0.13	2		506	676	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236087	108236087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781894	NA	P-0015528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	31	399	2	ENST00000278616.4:c.9023G>A	p.Arg3008His	p.R3008H	ENST00000278616	NM_000051.3	3008	cGt/cAt	63/63	1	2	FACETS	0.619	0.498	0.756	0.619	0.498	0.756	SUBCLONAL	1	TRUE	1	0.13	2		401	771	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0015529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	109	605	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.9	0.808	0.999	0.9	0.808	0.999	CLONAL	1	TRUE	1	0.273592554954182	2		606	885	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112760241	112760241	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	110	326	1	ENST00000369452.4:c.910G>T	p.Ala304Ser	p.A304S	ENST00000369452	NM_007373.3	304	Gca/Tca	4/9	1	2	FACETS	0.866	0.777	0.96	0.866	0.777	0.96	CLONAL	1	TRUE	1	0.273592554954182	2		327	929	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220505	1220505	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	102	431	0	ENST00000326873.7:c.597+1G>A		p.X199_splice	ENST00000326873	NM_000455.4	199			0.273592554954182	1	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	0	0.273592554954182	1		431	637	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610239	10610252	+	protein_altering_variant	In_Frame_Del	DEL	GTTCATGACGTGGA	GTTCATGACGTGGA	AC	novel	NA	P-0015529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	119	513	2	ENST00000171111.5:c.458_471delinsGT	p.Leu153_Asn157delinsArg	p.L153_N157delinsR	ENST00000171111	NM_203500.1	153	cTCCACGTCATGAAC/cGT	2/6	0.273592554954182	1	FACETS	0.841	0.758	0.928	0.841	0.758	0.928	CLONAL	1	TRUE	0	0.273592554954182	1		515	893	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796483	42796483	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs751173226	NA	P-0015529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	132	586	2	ENST00000575354.2:c.3040G>T	p.Ala1014Ser	p.A1014S	ENST00000575354	NM_015125.3	1014	Gcg/Tcg	13/20	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.273592554954182	2		588	911	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379354	225379355	+	missense_variant	Missense_Mutation	DNP	CT	CT	GG	novel	NA	P-0015529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	103	478	0	ENST00000264414.4:c.513_514delinsCC	p.Arg171_Glu172delinsSerGln	p.R171_E172delinsSQ	ENST00000264414	NM_003590.4	171	agAGag/agCCag	4/16	1	2	FACETS	0.632	0.564	0.705	0.632	0.564	0.705	SUBCLONAL	1	TRUE	1	0.273592554954182	2		478	1191	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345744	152345744	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	35	137	0	ENST00000359321.1:c.826G>T	p.Gly276Trp	p.G276W	ENST00000359321	NM_005431.1	276	Ggg/Tgg	3/3	1	2	FACETS	0.62	0.508	0.745	0.62	0.508	0.745	SUBCLONAL	1	TRUE	1	0.273592554954182	2		137	413	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	250	248	0				ENST00000310581	NM_198253.2	-/1132			0.387441893850193	3	FACETS	0.988	0.937	1	0.988	0.937	1	CLONAL	3	TRUE	0	0.430532084070484	3		248	476	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0015530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	247	704	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.419359206061587	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.430532084070484	4		705	744	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435155	56435155	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	192	546	0	ENST00000407977.2:c.1982C>T	p.Ser661Phe	p.S661F	ENST00000407977		661	tCc/tTc	9/10	0.430532084070484	4	FACETS	0.83	0.769	0.892	0.553	0.513	0.595	CLONAL	2	TRUE	1	0.430532084070484	4		546	769	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915886	127915886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	174	504	0	ENST00000373547.4:c.595C>T	p.Pro199Ser	p.P199S	ENST00000373547	NM_002721.4	199	Cct/Tct	6/7	0.430532084070484	2	FACETS	1	0.987	1	0.67	0.62	0.722	CLONAL	1	TRUE	0	0.430532084070484	2		504	603	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650593	18650593	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs757819469	NA	P-0015530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	128	387	1	ENST00000266497.5:c.2804T>C	p.Leu935Pro	p.L935P	ENST00000266497		935	cTt/cCt	20/31	0.396848266478043	3	FACETS	0.772	0.704	0.842	0.772	0.704	0.842	SUBCLONAL	2	TRUE	1	0.430532084070484	3		388	468	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28644733	28644733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	110	346	1	ENST00000241453.7:c.60G>A	p.Met20Ile	p.M20I	ENST00000241453	NM_004119.2	20	atG/atA	2/24	0.182919949142622	5	FACETS	0.962	0.87	1	0.641	0.58	0.706	INDETERMINATE	2	TRUE	2	0.430532084070484	5		347	437	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728574	190728574	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	372	512	0	ENST00000441310.2:c.1962A>G	p.Ile654Met	p.I654M	ENST00000441310	NM_000534.4	654	atA/atG	10/13	0.430532084070484	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.430532084070484	3		512	856	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73995320	73995320	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	37	109	0	ENST00000318443.5:c.626G>T	p.Arg209Leu	p.R209L	ENST00000318443	NM_001024736.1	209	cGg/cTg	4/10	1	2	FACETS	0.595	0.496	0.704	0.595	0.496	0.704	SUBCLONAL	1	TRUE	1	0.634439180663907	2		109	196	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	344	589	1	ENST00000269305.4:c.461del	p.Gly154AlafsTer16	p.G154Afs*16	ENST00000269305	NM_001126112.2	154	gGc/gc	5/11	0.634439180663907	1	FACETS	0.872	0.829	0.916	0.872	0.829	0.916	CLONAL	1	TRUE	0	0.634439180663907	1		590	849	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212361	5212361	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	308	505	2	ENST00000357368.4:c.4756G>T	p.Val1586Leu	p.V1586L	ENST00000357368	NM_002850.3	1586	Gtg/Ttg	31/38	0.634439180663907	1	FACETS	0.841	0.797	0.886	0.841	0.797	0.886	CLONAL	1	TRUE	0	0.634439180663907	1		507	788	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99850077	99850077	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	393	534	0	ENST00000280892.6:c.47T>C	p.Met16Thr	p.M16T	ENST00000280892	NM_001130678.1	16	aTg/aCg	1/7	0.634439180663907	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.634439180663907	1		534	819	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197400	26197400	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	128	174	0	ENST00000356476.2:c.79C>T	p.Arg27Ter	p.R27*	ENST00000356476		27	Cga/Tga	1/1	0.580610997961604	2	FACETS	1	0.964	1	0.547	0.501	0.594	CLONAL	1	TRUE	0	0.634439180663907	2		174	369	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860647	151860647	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	224	347	0	ENST00000262189.6:c.10015A>T	p.Ser3339Cys	p.S3339C	ENST00000262189	NM_170606.2	3339	Agt/Tgt	43/59	1	2	FACETS	0.989	0.925	1	0.989	0.925	1	CLONAL	1	TRUE	1	0.634439180663907	2		347	714	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0015534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	32	442	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.265	0.214	0.322	0.265	0.214	0.322	SUBCLONAL	1	TRUE	1	0.44	2		442	549	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0015534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	126	563	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.455	0.41	0.502	0.455	0.41	0.502	SUBCLONAL	1	TRUE	1	0.44	2		564	1260	SUCCESS
APC	324	MSKCC	GRCh37	5	112170862	112170862	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1060503318	NA	P-0015534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	40	290	0	ENST00000257430.4:c.1958G>A	p.Arg653Lys	p.R653K	ENST00000257430	NM_000038.5	653	aGg/aAg	15/16	1	2	FACETS	0.398	0.33	0.473	0.398	0.33	0.473	SUBCLONAL	1	TRUE	1	0.44	2		290	457	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099968	27099968	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	60	403	0	ENST00000324856.7:c.3847G>A	p.Gly1283Ser	p.G1283S	ENST00000324856	NM_006015.4	1283	Ggt/Agt	15/20	1	2	FACETS	0.255	0.219	0.295	0.255	0.219	0.295	SUBCLONAL	1	TRUE	1	0.44	2		403	1068	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	133	704	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.952	0.865	1	0.952	0.865	1	CLONAL	1	TRUE	1	0.339798696819993	2		705	822	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	105	320	3	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.339798696819993	2		323	558	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	297	668	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.988	0.933	1	1	0.996	1	CLONAL	2	TRUE	1	0.339798696819993	2		671	885	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	36	312	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.536	0.441	0.643	0.536	0.441	0.643	SUBCLONAL	1	TRUE	1	0.339798696819993	2		312	395	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100171	157100172	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	11	83	0	ENST00000346085.5:c.1114dup	p.Arg372ProfsTer163	p.R372Pfs*163	ENST00000346085	NM_020732.3	370	tcc/tCcc	1/20	1	2	FACETS	0.502	0.348	0.69	0.502	0.348	0.69	SUBCLONAL	1	TRUE	1	0.339798696819993	2		83	129	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743932	41743933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs778012871	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	154	1037	3	ENST00000301178.4:c.874dup	p.His292ProfsTer47	p.H292Pfs*47	ENST00000301178	NM_021913.4	289	-/C	7/20	1	2	FACETS	0.897	0.82	0.978	0.897	0.82	0.978	CLONAL	1	TRUE	1	0.339798696819993	2		1040	1010	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240314	5240314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777007079	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	68	927	1	ENST00000357368.4:c.1600G>A	p.Glu534Lys	p.E534K	ENST00000357368	NM_002850.3	534	Gag/Aag	12/38	1	2	FACETS	0.425	0.369	0.487	0.425	0.369	0.487	SUBCLONAL	1	TRUE	1	0.339798696819993	2		928	941	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	55	335	3	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	1	2	FACETS	0.909	0.781	1	0.909	0.781	1	CLONAL	1	TRUE	1	0.339798696819993	2		338	356	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308382	15308383	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs749829137	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	126	895	0	ENST00000263388.2:c.125dup	p.Cys43LeufsTer32	p.C43Lfs*32	ENST00000263388	NM_000435.2	42	cct/ccCt	2/33	1	2	FACETS	0.839	0.759	0.923	0.839	0.759	0.923	CLONAL	1	TRUE	1	0.339798696819993	2		895	884	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279325	18279325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	138	674	1	ENST00000222254.8:c.1777G>A	p.Glu593Lys	p.E593K	ENST00000222254	NM_005027.3	593	Gag/Aag	14/16	1	2	FACETS	0.925	0.842	1	0.925	0.842	1	CLONAL	1	TRUE	1	0.339798696819993	2		675	878	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	134	510	0	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.339798696819993	2		510	768	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968260	2968260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	198	886	1	ENST00000396946.4:c.1726C>T	p.Arg576Cys	p.R576C	ENST00000396946	NM_032415.4	576	Cgc/Tgc	13/25	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.339798696819993	2		887	1023	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	76	621	2	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	0.240292806963581	3	FACETS	0.692	0.606	0.785	0.346	0.303	0.393	SUBCLONAL	1	TRUE	1	0.339798696819993	3		623	756	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687471	37687472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs760014508	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	132	449	3	ENST00000447079.4:c.4382dup	p.Thr1463AsnfsTer50	p.T1463Nfs*50	ENST00000447079	NM_015083.1	1459	tgg/tGgg	14/14	1	2	FACETS	0.844	0.772	0.919	1	0.989	1	CLONAL	2	TRUE	1	0.339798696819993	2		452	460	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245587	41245587	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357522	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	184	867	3	ENST00000357654.3:c.1961del	p.Lys654SerfsTer47	p.K654Sfs*47	ENST00000357654	NM_007294.3	654	aAg/ag	10/23	1	2	FACETS	0.957	0.882	1	0.957	0.882	1	CLONAL	1	TRUE	1	0.339798696819993	2		870	1132	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376726	31376726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867559860	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	92	445	0	ENST00000328111.2:c.721G>A	p.Ala241Thr	p.A241T	ENST00000328111	NM_006892.3	241	Gcc/Acc	7/23	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.339798696819993	2		445	534	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806180	1806181	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760502257	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	132	869	3	ENST00000260795.2:c.1206dup	p.Lys403GlnfsTer93	p.K403Qfs*93	ENST00000260795		400	agc/agCc	8/17	1	2	FACETS	0.736	0.667	0.809	0.736	0.667	0.809	SUBCLONAL	1	TRUE	1	0.339798696819993	2		872	1055	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713896	30713899	+	frameshift_variant	Frame_Shift_Del	DEL	TCTG	TCTG	-	novel	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	114	639	0	ENST00000295754.5:c.1226_1229del	p.Ser409TrpfsTer21	p.S409Wfs*21	ENST00000295754	NM_003242.5	407	acTCTG/ac	4/7	1	2	FACETS	0.918	0.827	1	0.918	0.827	1	CLONAL	1	TRUE	1	0.339798696819993	2		639	731	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154404	2154404	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs868243135	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	213	960	0	ENST00000434045.2:c.524G>A	p.Trp175Ter	p.W175*	ENST00000434045	NM_001127598.1	175	tGg/tAg	5/5	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.339798696819993	2		960	992	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014295	70014295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756044021	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	151	752	1	ENST00000394351.3:c.1156G>A	p.Val386Ile	p.V386I	ENST00000394351	NM_000248.3	386	Gtc/Atc	9/9	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.339798696819993	2		753	865	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023376	27023376	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1427038078	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	20	237	0	ENST00000324856.7:c.482T>C	p.Val161Ala	p.V161A	ENST00000324856	NM_006015.4	161	gTc/gCc	1/20	1	2	FACETS	0.441	0.337	0.562	0.441	0.337	0.562	SUBCLONAL	1	TRUE	1	0.339798696819993	2		237	267	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622415	1622415	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	129	735	0	ENST00000344749.5:c.550-1G>T		p.X184_splice	ENST00000344749	NM_001136139.2	184			1	2	FACETS	0.939	0.851	1	0.939	0.851	1	CLONAL	1	TRUE	1	0.339798696819993	2		735	809	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836879	151836879	+	splice_region_variant,intron_variant	Splice_Region	DEL	A	A	-	rs369965395	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	140	573	3	ENST00000262189.6:c.14344-3del		p.X4782_splice	ENST00000262189	NM_170606.2	4782			1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.339798696819993	2		576	818	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911141	29911141	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	33	410	0	ENST00000376809.5:c.440A>G	p.Tyr147Cys	p.Y147C	ENST00000376809	NM_002116.7	147	tAc/tGc	3/8	1	2	FACETS	0.457	0.372	0.553	0.457	0.372	0.553	SUBCLONAL	1	TRUE	1	0.339798696819993	2		410	425	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	204	892	7	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	0.339798696819993	2		899	1196	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	147	785	5	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.879	0.802	0.96	0.879	0.802	0.96	CLONAL	1	TRUE	1	0.339798696819993	2		790	984	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795090	45795090	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	106	559	0	ENST00000450313.1:c.1538T>C	p.Val513Ala	p.V513A	ENST00000450313	NM_012222.2	513	gTg/gCg	16/16	1	2	FACETS	0.898	0.805	0.995	0.898	0.805	0.995	CLONAL	1	TRUE	1	0.339798696819993	2		559	695	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852298	63852298	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs752506951	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	132	676	1	ENST00000279873.7:c.3076A>G	p.Lys1026Glu	p.K1026E	ENST00000279873	NM_032199.2	1026	Aaa/Gaa	10/10	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.339798696819993	2		677	730	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998685	100998685	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	224	897	0	ENST00000325455.5:c.1117G>A	p.Ala373Thr	p.A373T	ENST00000325455	NM_001202474.3	373	Gcg/Acg	1/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.339798696819993	2		897	1021	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244140	46244140	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	49	570	0	ENST00000334344.6:c.2234A>G	p.Gln745Arg	p.Q745R	ENST00000334344	NM_152641.2	745	cAg/cGg	15/21	1	2	FACETS	0.434	0.366	0.508	0.434	0.366	0.508	SUBCLONAL	1	TRUE	1	0.339798696819993	2		570	665	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426774	49426774	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1334139538	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	41	435	6	ENST00000301067.7:c.11714A>T	p.Gln3905Leu	p.Q3905L	ENST00000301067	NM_003482.3	3905	cAg/cTg	39/54	1	2	FACETS	0.45	0.374	0.535	0.45	0.374	0.535	SUBCLONAL	1	TRUE	1	0.339798696819993	2		441	536	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68292277	68292277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	115	414	0	ENST00000487270.1:c.181G>A	p.Ala61Thr	p.A61T	ENST00000487270	NM_133509.3	61	Gcc/Acc	3/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.339798696819993	2		414	563	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052611	42052611	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	116	541	0	ENST00000219905.7:c.7282C>T	p.His2428Tyr	p.H2428Y	ENST00000219905	NM_001164273.1	2428	Cac/Tac	20/24	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.339798696819993	2		541	680	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708596	43708596	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	129	689	1	ENST00000382044.4:c.4700G>T	p.Arg1567Met	p.R1567M	ENST00000382044	NM_001141980.1	1567	aGg/aTg	22/28	1	2	FACETS	0.93	0.844	1	0.93	0.844	1	CLONAL	1	TRUE	1	0.339798696819993	2		690	816	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627339	37627339	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	177	858	2	ENST00000447079.4:c.1254G>T	p.Lys418Asn	p.K418N	ENST00000447079	NM_015083.1	418	aaG/aaT	2/14	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.339798696819993	2		860	938	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627745	37627745	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	160	938	0	ENST00000447079.4:c.1660T>A	p.Leu554Met	p.L554M	ENST00000447079	NM_015083.1	554	Ttg/Atg	2/14	1	2	FACETS	0.958	0.878	1	0.958	0.878	1	CLONAL	1	TRUE	1	0.339798696819993	2		938	983	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37882063	37882064	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	144	642	0	ENST00000269571.5:c.2835dup	p.Ile946HisfsTer5	p.I946Hfs*5	ENST00000269571		943	-/C	23/27	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.339798696819993	2		642	827	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40371789	40371789	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	44	195	0	ENST00000293328.3:c.622C>T	p.Gln208Ter	p.Q208*	ENST00000293328	NM_012448.3	208	Cag/Tag	6/19	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.339798696819993	2		195	194	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40478132	40478132	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	139	594	1	ENST00000264657.5:c.1365+2T>C		p.X455_splice	ENST00000264657	NM_139276.2	455			1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.339798696819993	2		595	767	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774731	73774731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	46	176	0	ENST00000254810.4:c.356C>T	p.Thr119Ile	p.T119I	ENST00000254810	NM_005324.3	119	aCc/aTc	4/4	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.339798696819993	2		176	242	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78617550	78617550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	106	475	0	ENST00000306801.3:c.288G>T	p.Gln96His	p.Q96H	ENST00000306801	NM_020761.2	96	caG/caT	3/34	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.339798696819993	2		475	586	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262102	10262102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	170	771	3	ENST00000340748.4:c.2189G>A	p.Arg730His	p.R730H	ENST00000340748		730	cGc/cAc	23/40	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.339798696819993	2		774	865	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113837	11113837	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	117	581	1	ENST00000358026.2:c.1943+2T>C		p.X648_splice	ENST00000358026	NM_001128849.1	648			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.339798696819993	2		582	635	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303035	15303035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777257132	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	181	961	0	ENST00000263388.2:c.415G>A	p.Asp139Asn	p.D139N	ENST00000263388	NM_000435.2	139	Gat/Aat	4/33	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.339798696819993	2		961	914	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955064	17955064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749334592	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	186	865	0	ENST00000458235.1:c.163G>A	p.Val55Met	p.V55M	ENST00000458235	NM_000215.3	55	Gtg/Atg	2/24	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.339798696819993	2		865	938	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136247	202136247	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	112	609	0	ENST00000358485.4:c.491T>A	p.Leu164His	p.L164H	ENST00000358485	NM_001080125.1	164	cTc/cAc	3/9	1	2	FACETS	0.824	0.741	0.912	0.824	0.741	0.912	CLONAL	1	TRUE	1	0.339798696819993	2		609	800	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659953	227659954	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	156	860	0	ENST00000305123.5:c.3501_3502del	p.Cys1167TrpfsTer11	p.C1167Wfs*11	ENST00000305123	NM_005544.2	1167	tgTGgg/tggg	1/2	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.339798696819993	2		860	870	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662572	227662572	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	105	515	0	ENST00000305123.5:c.883A>G	p.Ser295Gly	p.S295G	ENST00000305123	NM_005544.2	295	Agc/Ggc	1/2	1	2	FACETS	0.979	0.879	1	0.979	0.879	1	CLONAL	1	TRUE	1	0.339798696819993	2		515	631	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264262	46264262	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	80	454	0	ENST00000371998.3:c.1309A>G	p.Ser437Gly	p.S437G	ENST00000371998		437	Agt/Ggt	11/23	1	2	FACETS	0.923	0.815	1	0.923	0.815	1	CLONAL	1	TRUE	1	0.339798696819993	2		454	510	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967255	134967255	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	129	669	1	ENST00000398015.3:c.2594G>T	p.Arg865Leu	p.R865L	ENST00000398015	NM_004441.4	865	cGg/cTg	14/16	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.339798696819993	2		670	750	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158392	106158392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	81	373	1	ENST00000380013.4:c.3293C>T	p.Ala1098Val	p.A1098V	ENST00000380013	NM_001127208.2	1098	gCt/gTt	3/11	1	2	FACETS	0.894	0.79	1	0.894	0.79	1	CLONAL	1	TRUE	1	0.339798696819993	2		374	533	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524650	187524650	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	185	862	0	ENST00000441802.2:c.11030A>G	p.Asp3677Gly	p.D3677G	ENST00000441802	NM_005245.3	3677	gAc/gGc	19/27	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.339798696819993	2		862	1038	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80040392	80040392	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776668872	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	129	608	0	ENST00000265081.6:c.1721G>A	p.Arg574Gln	p.R574Q	ENST00000265081	NM_002439.4	574	cGg/cAg	12/24	1	2	FACETS	0.867	0.785	0.952	0.867	0.785	0.952	CLONAL	1	TRUE	1	0.339798696819993	2		608	876	SUCCESS
APC	324	MSKCC	GRCh37	5	112177307	112177307	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	117	554	3	ENST00000257430.4:c.6016G>T	p.Gly2006Cys	p.G2006C	ENST00000257430	NM_000038.5	2006	Ggc/Tgc	16/16	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.339798696819993	2		557	653	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927072	131927072	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	96	581	0	ENST00000265335.6:c.1609C>T	p.Gln537Ter	p.Q537*	ENST00000265335		537	Caa/Taa	10/25	1	2	FACETS	0.847	0.755	0.945	0.847	0.755	0.945	CLONAL	1	TRUE	1	0.339798696819993	2		581	667	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056125	26056125	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs762529657	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	121	515	0	ENST00000343677.2:c.532A>G	p.Lys178Glu	p.K178E	ENST00000343677	NM_005319.3	178	Aag/Gag	1/1	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.339798696819993	2		515	705	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561474	141561474	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772070879	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	234	589	0	ENST00000220592.5:c.1331C>T	p.Thr444Met	p.T444M	ENST00000220592	NM_012154.3	444	aCg/aTg	11/19	0.339798696819993	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.339798696819993	3		589	781	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249756	110249756	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs781022969	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	131	823	0	ENST00000374672.4:c.919C>A	p.Leu307Met	p.L307M	ENST00000374672	NM_004235.4	307	Ctg/Atg	3/5	0.240292806963581	3	FACETS	0.979	0.888	1	0.49	0.444	0.538	CLONAL	1	TRUE	1	0.339798696819993	3		823	921	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801087	135801087	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs118203357	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	111	577	0	ENST00000298552.3:c.250G>A	p.Ala84Thr	p.A84T	ENST00000298552	NM_001162426.1	84	Gcc/Acc	5/23	0.240292806963581	3	FACETS	0.98	0.881	1	0.49	0.44	0.543	CLONAL	1	TRUE	1	0.339798696819993	3		577	780	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841177	15841177	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	102	531	0	ENST00000307771.7:c.1261C>T	p.Arg421Ter	p.R421*	ENST00000307771	NM_005089.3	421	Cga/Tga	11/11	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.339798696819993	2		531	591	SUCCESS
AR	367	MSKCC	GRCh37	X	66765097	66765097	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	117	709	1	ENST00000374690.3:c.109C>A	p.Pro37Thr	p.P37T	ENST00000374690	NM_000044.3	37	Ccg/Acg	1/8	1	2	FACETS	0.906	0.817	1	0.906	0.817	1	CLONAL	1	TRUE	1	0.339798696819993	2		710	760	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3114979	3114991	+	frameshift_variant	Frame_Shift_Del	DEL	TACCTGCCCACCC	TACCTGCCCACCC	GACGTGCA	novel	NA	P-0015536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	178	778	2	ENST00000078429.4:c.514_526delinsGACGTGCA	p.Tyr172AspfsTer48	p.Y172Dfs*48	ENST00000078429	NM_002067.2	172	TACCTGCCCACCCag/GACGTGCAag	4/7	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.339798696819993	2		780	978	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554919	106554919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368754839	NA	P-0015538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	52	455	1	ENST00000369096.4:c.2036G>A	p.Arg679His	p.R679H	ENST00000369096	NM_001198.3	679	cGt/cAt	7/7	0.827568825706059	3	FACETS	0.241	0.204	0.281	0.12	0.102	0.141	SUBCLONAL	1	TRUE	1	0.836438367487479	3		456	733	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837925	156837925	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	833	756	0	ENST00000524377.1:c.458C>G	p.Ser153Cys	p.S153C	ENST00000524377	NM_002529.3	153	tCt/tGt	5/17	0.827568825706059	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.836438367487479	3		756	1365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578229	+	inframe_deletion	In_Frame_Del	DEL	CACTATGTCGAAAAGTGTTTCTGTCAT	CACTATGTCGAAAAGTGTTTCTGTCAT	-	novel	NA	P-0015538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	786	780	1	ENST00000269305.4:c.620_646del	p.Asp207_Ser215del	p.D207_S215del	ENST00000269305	NM_001126112.2	207	gATGACAGAAACACTTTTCGACATAGTGtg/gtg	6/11	0.836438367487479	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.836438367487479	2		781	892	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212615	36212615	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1895	165	836	0	ENST00000222270.7:c.2366A>G	p.Glu789Gly	p.E789G	ENST00000222270	NM_014727.1	789	gAg/gGg	3/37	0.639180013191458	5	FACETS	0.432	0.394	0.471	0.144	0.131	0.157	SUBCLONAL	1	TRUE	2	0.836438367487479	5		836	2060	SUCCESS
AXL	558	MSKCC	GRCh37	19	41759565	41759565	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1416	331	785	2	ENST00000301178.4:c.1988T>C	p.Leu663Pro	p.L663P	ENST00000301178	NM_021913.4	663	cTg/cCg	17/20	0.639180013191458	5	FACETS	1	0.959	1	0.34	0.32	0.361	CLONAL	1	TRUE	2	0.836438367487479	5		787	1747	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572464	41572464	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201883596	NA	P-0015538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	82	707	0	ENST00000263253.7:c.4993C>T	p.Arg1665Cys	p.R1665C	ENST00000263253	NM_001429.3	1665	Cgc/Tgc	30/31	0.454148760742239	3	FACETS	0.244	0.214	0.276			1	INDETERMINATE	1	TRUE	NA	0.836438367487479	3		707	1139	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665410	117665410	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	236	262	0	ENST00000368508.3:c.4337C>G	p.Ser1446Cys	p.S1446C	ENST00000368508	NM_002944.2	1446	tCt/tGt	27/43	0.827568825706059	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.836438367487479	3		262	372	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046328	69046328	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	482	455	0	ENST00000288368.4:c.3801C>G	p.Phe1267Leu	p.F1267L	ENST00000288368	NM_024870.2	1267	ttC/ttG	32/40	0.836438367487479	5	FACETS	0.89	0.856	0.925	0.89	0.856	0.925	CLONAL	3	TRUE	2	0.836438367487479	5		455	973	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046476	69046476	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	741	664	0	ENST00000288368.4:c.3949C>G	p.Leu1317Val	p.L1317V	ENST00000288368	NM_024870.2	1317	Ctt/Gtt	32/40	0.836438367487479	5	FACETS	0.954	0.925	0.983	0.954	0.925	0.983	CLONAL	3	TRUE	2	0.836438367487479	5		664	1396	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0015540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	85	583	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.409531269784026	2		583	394	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711874	89711874	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs786204862	NA	P-0015540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	128	334	1	ENST00000371953.3:c.493-1G>A		p.X165_splice	ENST00000371953	NM_000314.4	165			0.409531269784026	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.409531269784026	1		335	493	SUCCESS
MET	4233	MSKCC	GRCh37	7	116419001	116419001	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	48	215	0	ENST00000397752.3:c.3512A>G	p.Asn1171Ser	p.N1171S	ENST00000397752	NM_000245.2	1171	aAt/aGt	17/21	0.400478998107783	3	FACETS	0.782	0.664	0.912	0.391	0.332	0.456	CLONAL	1	TRUE	1	0.409531269784026	3		215	361	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	40	507	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.666	0.552	0.794	0.666	0.552	0.794	SUBCLONAL	1	TRUE	1	0.16	2		507	751	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577555	7577556	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGGAA	novel	NA	P-0015541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	53	513	0	ENST00000269305.4:c.720_725dup	p.Ser241_Cys242dup	p.S241_C242dup	ENST00000269305	NM_001126112.2	241	tgc/tgTTCCTGc	7/11	1	2	FACETS	0.822	0.699	0.957	0.822	0.699	0.957	CLONAL	1	TRUE	1	0.16	2		513	806	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164902	106164902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs937035385	NA	P-0015542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	117	357	0	ENST00000380013.4:c.3770C>T	p.Thr1257Met	p.T1257M	ENST00000380013	NM_001127208.2	1257	aCg/aTg	6/11	0.767747664103778	3	FACETS	0.661	0.597	0.728	0.33	0.298	0.364	SUBCLONAL	1	TRUE	1	0.755592560463341	3		357	646	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248486	59248486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	369	497	0	ENST00000371222.2:c.257G>A	p.Gly86Glu	p.G86E	ENST00000371222	NM_002228.3	86	gGg/gAg	1/1	0.504383553164391	5	FACETS	1	0.993	1	0.868	0.842	0.894	CLONAL	4	TRUE	0	0.755592560463341	5		497	480	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518608	204518608	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	231	415	0	ENST00000367182.3:c.1271C>A	p.Thr424Lys	p.T424K	ENST00000367182	NM_001278516.1	424	aCa/aAa	11/11	0.275589069132015	4	FACETS	0.937	0.89	0.982	0.703	0.668	0.737	INDETERMINATE	3	TRUE	0	0.755592560463341	4		415	382	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821520	72821520	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	58	581	0	ENST00000268489.5:c.10655T>C	p.Leu3552Ser	p.L3552S	ENST00000268489	NM_006885.3	3552	tTg/tCg	10/10	0.580152941181376	3	FACETS	0.567	0.489	0.651	0.189	0.163	0.217	SUBCLONAL	1	TRUE	0	0.755592560463341	3		581	373	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348119	89348119	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	48	699	0	ENST00000301030.4:c.4831C>G	p.Leu1611Val	p.L1611V	ENST00000301030	NM_001256183.1	1611	Ctg/Gtg	9/13	0.767747664103778	3	FACETS	0.456	0.386	0.532	0.152	0.128	0.178	SUBCLONAL	1	TRUE	0	0.755592560463341	3		699	384	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357185	89357185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777070083	NA	P-0015542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	37	645	0	ENST00000301030.4:c.449C>T	p.Thr150Met	p.T150M	ENST00000301030	NM_001256183.1	150	aCg/aTg	6/13	0.767747664103778	3	FACETS	0.308	0.254	0.369	0.103	0.084	0.123	SUBCLONAL	1	TRUE	0	0.755592560463341	3		645	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578543	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCA	novel	NA	P-0015542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	768	1021	0	ENST00000269305.4:c.384_387dup	p.Leu130CysfsTer20	p.L130Cfs*20	ENST00000269305	NM_001126112.2	129	-/TGCC	5/11	0.767747664103778	4	FACETS	0.951	0.933	0.969	0.951	0.933	0.969	CLONAL	4	TRUE	0	0.755592560463341	4		1021	938	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435478	56435478	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	121	508	0	ENST00000407977.2:c.1659C>G	p.His553Gln	p.H553Q	ENST00000407977		553	caC/caG	9/10	0.767747664103778	3	FACETS	1	0.975	1	0.396	0.362	0.432	CLONAL	1	TRUE	0	0.755592560463341	3		508	371	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119734	70119734	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	206	746	0	ENST00000245479.2:c.736C>A	p.Gln246Lys	p.Q246K	ENST00000245479	NM_000346.3	246	Cag/Aag	3/3	0.767747664103778	3	FACETS	1	0.99	1	0.444	0.415	0.474	CLONAL	1	TRUE	0	0.755592560463341	3		746	564	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10267171	10267171	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	55	554	0	ENST00000340748.4:c.1247A>G	p.His416Arg	p.H416R	ENST00000340748		416	cAc/cGc	17/40	0.700044268240553	5	FACETS	0.407	0.347	0.472	0.136	0.115	0.158	SUBCLONAL	1	TRUE	2	0.755592560463341	5		554	764	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798714	42798755	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	GCCGCTGCTGCAGCCTTGCCATGCTGCCTGTGCCCTGCACAG	GCCGCTGCTGCAGCCTTGCCATGCTGCCTGTGCCCTGCACAG	-	novel	NA	P-0015542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	116	296	0	ENST00000575354.2:c.4328-41_4328del		p.X1443_splice	ENST00000575354	NM_015125.3	1443			0.231156199415798	5	FACETS	0.952	0.891	1			1	INDETERMINATE	4	TRUE	NA	0.755592560463341	5		296	172	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478772	57478772	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	873	422	1	ENST00000371085.3:c.358G>T	p.Ala120Ser	p.A120S	ENST00000371085	NM_000516.4	120	Gcc/Tcc	5/13	0.680332488102589	5	FACETS	1	0.998	1			1	CLONAL	5	TRUE	NA	0.755592560463341	5		423	935	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62322234	62322283	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCAGGGGGCTGCTGGCCGCCCTGGAGCACAGCGAACAGCGGGCGGGGA	GCCCAGGGGGCTGCTGGCCGCCCTGGAGCACAGCGAACAGCGGGCGGGGA	-	novel	NA	P-0015542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	84	827	0	ENST00000360203.5:c.2494_2543del	p.Arg832TrpfsTer16	p.R832Wfs*16	ENST00000360203	NM_001283009.1	830	agGCCCAGGGGGCTGCTGGCCGCCCTGGAGCACAGCGAACAGCGGGCGGGGAgc/aggc	27/35	0.680332488102589	5	FACETS	0.457	0.403	0.516			1	SUBCLONAL	1	TRUE	NA	0.755592560463341	5		827	1037	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42851211	42851211	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0015542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	49	373	0	ENST00000398585.3:c.684-2A>T		p.X228_splice	ENST00000398585	NM_001135099.1	228			0.484819873102273	0	FACETS		NA	1			1	NA	1	TRUE	0	0.755592560463341	0		373	114	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224592	224592	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	67	617	0	ENST00000264932.6:c.268G>A	p.Val90Ile	p.V90I	ENST00000264932	NM_004168.2	90	Gtt/Att	3/15	0.680332488102589	5	FACETS	0.562	0.488	0.643			1	SUBCLONAL	1	TRUE	NA	0.755592560463341	5		617	673	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708988	117708988	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	240	538	0	ENST00000368508.3:c.1969C>G	p.Pro657Ala	p.P657A	ENST00000368508	NM_002944.2	657	Cca/Gca	13/43	0.416856973382755	2	FACETS	1	0.986	1	0.573	0.54	0.607	INDETERMINATE	1	TRUE	0	0.755592560463341	2		538	554	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0015543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	388	414	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.612159424729116	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.612159424729116	3		414	770	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118737	115118738	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	436	511	0	ENST00000257566.3:c.603_604insA	p.Val202SerfsTer25	p.V202Sfs*25	ENST00000257566	NM_016569.3	201	-/A	2/8	0.554819826973836	3	FACETS	0.973	0.932	1	0.973	0.932	1	CLONAL	2	TRUE	1	0.612159424729116	3		511	956	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162494	47162494	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	147	329	0	ENST00000409792.3:c.3632A>T	p.Asp1211Val	p.D1211V	ENST00000409792	NM_014159.6	1211	gAt/gTt	3/21	1	2	FACETS	0.945	0.869	1	0.945	0.869	1	CLONAL	1	TRUE	1	0.612159424729116	2		329	508	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65323345	65323345	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1471834988	NA	P-0015546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	257	305	0	ENST00000342505.4:c.1452G>T	p.Lys484Asn	p.K484N	ENST00000342505	NM_002227.2	484	aaG/aaT	10/25	1	2	FACETS	0.899	0.848	0.951	0.899	0.848	0.951	CLONAL	1	TRUE	1	0.876790835073526	2		305	652	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406723	70406723	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs536548153	NA	P-0015546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	355	370	0	ENST00000373644.4:c.4237A>G	p.Ile1413Val	p.I1413V	ENST00000373644	NM_030625.2	1413	Ata/Gta	4/12	0.876790835073526	1	FACETS	0.995	0.965	1	0.995	0.965	1	CLONAL	1	TRUE	0	0.876790835073526	1		370	457	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32449571	32449571	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	473	440	0	ENST00000332351.3:c.803A>T	p.Tyr268Phe	p.Y268F	ENST00000332351	NM_024426.4	268	tAt/tTt	3/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.876790835073526	2		440	1046	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462867	69462867	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	455	449	0	ENST00000227507.2:c.680A>G	p.Tyr227Cys	p.Y227C	ENST00000227507	NM_053056.2	227	tAc/tGc	4/5	1	2	FACETS	0.921	0.881	0.961	0.921	0.881	0.961	CLONAL	1	TRUE	1	0.876790835073526	2		449	1127	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462875	69462875	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	442	458	0	ENST00000227507.2:c.688A>G	p.Thr230Ala	p.T230A	ENST00000227507	NM_053056.2	230	Aca/Gca	4/5	1	2	FACETS	0.907	0.867	0.947	0.907	0.867	0.947	CLONAL	1	TRUE	1	0.876790835073526	2		458	1112	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939543	71939543	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0015546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	620	488	0	ENST00000298229.2:c.397+1G>C		p.X133_splice	ENST00000298229	NM_001567.3	133			1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.876790835073526	2		488	1409	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123888138	123888138	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	233	247	0	ENST00000330479.4:c.616A>C	p.Ile206Leu	p.I206L	ENST00000330479	NM_020382.3	206	Ata/Cta	6/9	1	2	FACETS	0.997	0.939	1	0.997	0.939	1	CLONAL	1	TRUE	1	0.876790835073526	2		247	533	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251742	212251742	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	199	208	0	ENST00000342788.4:c.3317G>T	p.Cys1106Phe	p.C1106F	ENST00000342788	NM_005235.2	1106	tGc/tTc	27/28	1	2	FACETS	0.844	0.788	0.901	0.844	0.788	0.901	CLONAL	1	TRUE	1	0.876790835073526	2		208	538	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143044447	143044447	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	165	275	0	ENST00000262992.4:c.2015A>G	p.Tyr672Cys	p.Y672C	ENST00000262992	NM_001101669.1	672	tAc/tGc	18/24	1	2	FACETS	0.973	0.905	1	0.973	0.905	1	CLONAL	1	TRUE	1	0.876790835073526	2		275	387	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150479	157150479	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	318	308	1	ENST00000346085.5:c.1661G>A	p.Gly554Asp	p.G554D	ENST00000346085	NM_020732.3	554	gGc/gAc	2/20	0.477074487754596	1	FACETS	0.674	0.643	0.706	0.674	0.643	0.706	INDETERMINATE	1	TRUE	0	0.876790835073526	1		309	604	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523600	106523600	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	195	330	0	ENST00000359195.3:c.2752G>A	p.Glu918Lys	p.E918K	ENST00000359195	NM_002649.2	918	Gaa/Aaa	8/11	0.796277405567258	3	FACETS	0.744	0.689	0.801			1	SUBCLONAL	1	TRUE	NA	0.876790835073526	3		330	860	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396479	139396479	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	497	483	0	ENST00000277541.6:c.5446G>T	p.Glu1816Ter	p.E1816*	ENST00000277541	NM_017617.3	1816	Gag/Tag	29/34	0.876790835073526	1	FACETS	0.99	0.964	1	0.99	0.964	1	CLONAL	1	TRUE	0	0.876790835073526	1		483	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577068	7577069	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	T	novel	NA	P-0015546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	1024	461	0	ENST00000269305.4:c.869_870delinsA	p.Arg290GlnfsTer55	p.R290Qfs*55	ENST00000269305	NM_001126112.2	290	cGC/cA	8/11	0.876790835073526	2	FACETS	0.98	0.965	0.993	0.98	0.965	0.993	CLONAL	2	TRUE	0	0.876790835073526	2		461	1192	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0015547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	53	410	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.239239530975731	1	FACETS	0.138	0.117	0.16	0.138	0.117	0.16	INDETERMINATE	1	TRUE	0	0.94	1		410	434	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0015547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	14	410	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.410822098233403	1	FACETS	0.088	0.063	0.119	0.088	0.063	0.119	SUBCLONAL	1	FALSE	0	0.413663162515779	1		410	609	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972512	81972512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1263457484	NA	P-0015547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	56	366	0	ENST00000359376.3:c.3305C>T	p.Thr1102Met	p.T1102M	ENST00000359376	NM_002661.3	1102	aCg/aTg	29/33	1	2	FACETS	0.243	0.207	0.282	0.243	0.207	0.282	SUBCLONAL	1	FALSE	1	0.413663162515779	2		366	1116	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	369	248	0				ENST00000310581	NM_198253.2	-/1132			0.576212655660769	3	FACETS	0.982	0.946	1	0.982	0.946	1	CLONAL	3	TRUE	0	0.580410670348354	3		248	557	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427111	49427111	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	124	428	0	ENST00000301067.7:c.11377C>T	p.Gln3793Ter	p.Q3793*	ENST00000301067	NM_003482.3	3793	Caa/Taa	39/54	1	2	FACETS	0.994	0.906	1	0.994	0.906	1	CLONAL	1	TRUE	1	0.580410670348354	2		428	430	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425644	49425644	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057517992	NA	P-0015549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	210	621	3	ENST00000301067.7:c.12844C>T	p.Arg4282Ter	p.R4282*	ENST00000301067	NM_003482.3	4282	Cga/Tga	39/54	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.580410670348354	2		624	702	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878287	151878287	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	432	608	0	ENST00000262189.6:c.6658C>T	p.Gln2220Ter	p.Q2220*	ENST00000262189	NM_170606.2	2220	Cag/Tag	36/59	0.580406222131055	2	FACETS	0.926	0.89	0.962	0.926	0.89	0.962	CLONAL	2	TRUE	0	0.580410670348354	2		608	804	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456352	32456352	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	333	819	2	ENST00000332351.3:c.540C>A	p.Phe180Leu	p.F180L	ENST00000332351	NM_024426.4	180	ttC/ttA	1/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.580410670348354	2		821	1039	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628612	21628612	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs1326657671	NA	P-0015549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	155	471	0	ENST00000421138.2:c.1096C>T	p.Gln366Ter	p.Q366*	ENST00000421138		366	Cag/Tag	10/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.580410670348354	2		471	481	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823866	3823866	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	251	645	0	ENST00000262367.5:c.2349G>A	p.Met783Ile	p.M783I	ENST00000262367	NM_004380.2	783	atG/atA	13/31	1	2	FACETS	0.999	0.936	1	0.999	0.936	1	CLONAL	1	TRUE	1	0.580410670348354	2		645	866	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11114057	11114057	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060502104	NA	P-0015549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	243	543	0	ENST00000358026.2:c.1985C>T	p.Ser662Leu	p.S662L	ENST00000358026	NM_001128849.1	662	tCa/tTa	13/36	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.580410670348354	2		543	808	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182052	38182052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1190702008	NA	P-0015549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	186	421	0	ENST00000396334.3:c.676G>A	p.Glu226Lys	p.E226K	ENST00000396334	NM_002468.4	226	Gaa/Aaa	3/5	0.580410670348354	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.580410670348354	1		421	439	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38978710	38978710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	255	519	0	ENST00000357387.3:c.796C>T	p.Pro266Ser	p.P266S	ENST00000357387	NM_152756.3	266	Cca/Tca	9/38	0.580406222131055	2	FACETS	0.829	0.785	0.874	0.829	0.785	0.874	CLONAL	2	TRUE	0	0.580410670348354	2		519	530	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955507	90955507	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	162	536	0	ENST00000265433.3:c.2158G>C	p.Glu720Gln	p.E720Q	ENST00000265433	NM_002485.4	720	Gaa/Caa	14/16	1	2	FACETS	0.921	0.849	0.996	0.921	0.849	0.996	CLONAL	1	TRUE	1	0.580410670348354	2		536	606	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751242	128751242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	150	344	0	ENST00000377970.2:c.779C>T	p.Pro260Leu	p.P260L	ENST00000377970	NM_002467.4	260	cCg/cTg	2/3	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.580410670348354	2		344	477	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27213572	27213572	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	208	607	0	ENST00000380036.4:c.2968G>C	p.Glu990Gln	p.E990Q	ENST00000380036	NM_000459.3	990	Gag/Cag	18/23	1	2	FACETS	0.954	0.889	1	0.954	0.889	1	CLONAL	1	TRUE	1	0.580410670348354	2		607	751	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212137	98212137	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	249	419	0	ENST00000331920.6:c.3535G>C	p.Gly1179Arg	p.G1179R	ENST00000331920	NM_000264.3	1179	Gga/Cga	21/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.580410670348354	2		419	756	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930311	39930311	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	310	687	0	ENST00000378444.4:c.3153G>C	p.Trp1051Cys	p.W1051C	ENST00000378444	NM_001123385.1	1051	tgG/tgC	6/15	1	2	FACETS	0.978	0.923	1	0.978	0.923	1	CLONAL	1	TRUE	1	0.580410670348354	2		687	1092	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849567	68849570	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	novel	NA	P-0015551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	223	733	0	ENST00000261769.5:c.1471_1474del	p.Lys491GlufsTer30	p.K491Efs*30	ENST00000261769	NM_004360.3	490	gaAAAG/ga	10/16	0.431706131092902	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.431706131092902	1		733	708	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952378	38952378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368396509	NA	P-0015551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	27	320	0	ENST00000357387.3:c.3047C>T	p.Ser1016Leu	p.S1016L	ENST00000357387	NM_152756.3	1016	tCa/tTa	30/38	1	2	FACETS	0.301	0.239	0.372	0.301	0.239	0.372	SUBCLONAL	1	TRUE	1	0.431706131092902	2		320	416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578476	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTGCCGGGCGG	GGGTGCCGGGCGG	-	rs876659215	NA	P-0015553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	434	903	0	ENST00000269305.4:c.454_466del	p.Pro152AlafsTer14	p.P152Afs*14	ENST00000269305	NM_001126112.2	152	CCGCCCGGCACCCgc/gc	5/11	0.56890241053438	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.564046718633208	2		903	714	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088659	27088659	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	253	988	3	ENST00000324856.7:c.2272del	p.Gln758ArgfsTer75	p.Q758Rfs*75	ENST00000324856	NM_006015.4	756	aaC/aa	7/20	0.137655909892507	3	FACETS	1	0.992	1	0.706	0.662	0.75	INDETERMINATE	1	TRUE	1	0.564046718633208	3		991	815	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108079	30108079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754654624	NA	P-0015553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	466	750	0	ENST00000331968.5:c.728G>A	p.Arg243Gln	p.R243Q	ENST00000331968	NM_002742.2	243	cGa/cAa	5/18	0.56890241053438	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.564046718633208	2		750	700	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606158	81606158	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	111	610	0	ENST00000298171.2:c.828C>A	p.Asp276Glu	p.D276E	ENST00000298171	NM_000369.2	276	gaC/gaA	9/10	0.56890241053438	2	FACETS	0.867	0.784	0.953	0.433	0.392	0.477	CLONAL	1	TRUE	0	0.564046718633208	2		610	454	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678626	88678626	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	37	341	0	ENST00000360948.2:c.910C>G	p.Pro304Ala	p.P304A	ENST00000360948	NM_001012338.2	304	Ccc/Gcc	9/19	NA	2	FACETS	0.556	0.461	0.66			1	INDETERMINATE	1	TRUE	NA	0.564046718633208	2		341	236	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843386	3843386	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0015553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	74	265	0	ENST00000262367.5:c.1216+1G>A		p.X406_splice	ENST00000262367	NM_004380.2	406			0.136857592417223	4	FACETS	1	0.963	1	0.31	0.273	0.349	INDETERMINATE	1	TRUE	0	0.564046718633208	4		265	331	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143345	30143345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	265	804	0	ENST00000389048.3:c.181C>T	p.Pro61Ser	p.P61S	ENST00000389048	NM_004304.4	61	Ccc/Tcc	1/29	NA	2	FACETS	0.881	0.836	0.927			1	INDETERMINATE	2	TRUE	NA	0.564046718633208	2		804	533	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587179	212587179	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	146	615	0	ENST00000342788.4:c.822A>C	p.Gln274His	p.Q274H	ENST00000342788	NM_005235.2	274	caA/caC	7/28	0.56890241053438	3	FACETS	1	0.933	1	0.511	0.468	0.557	CLONAL	1	TRUE	1	0.564046718633208	3		615	649	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103689	47103689	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	304	438	0	ENST00000409792.3:c.6257C>A	p.Ser2086Tyr	p.S2086Y	ENST00000409792	NM_014159.6	2086	tCt/tAt	14/21	0.56890241053438	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.564046718633208	2		438	513	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499712	8499712	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	152	631	0	ENST00000356435.5:c.2257A>G	p.Arg753Gly	p.R753G	ENST00000356435		753	Agg/Ggg	14/35	0.56890241053438	3	FACETS	1	0.97	1	0.373	0.342	0.405	CLONAL	1	TRUE	0	0.564046718633208	3		631	617	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	19	507	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.652	0.497	0.834	0.652	0.497	0.834	SUBCLONAL	1	TRUE	1	0.28	2		507	208	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	51	414	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	0.921	0.788	1			1	INDETERMINATE	1	TRUE	NA	0.381902588124355	2		414	290	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602662	10602662	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1457377196	NA	P-0015556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	158	665	0	ENST00000171111.5:c.916G>T	p.Glu306Ter	p.E306*	ENST00000171111	NM_203500.1	306	Gag/Tag	3/6	1	2	FACETS	0.796	0.728	0.866	0.796	0.728	0.866	SUBCLONAL	1	TRUE	1	0.381902588124355	2		665	1040	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503787	186503789	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs1560084666	NA	P-0015556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	135	497	4	ENST00000323963.5:c.470_472del	p.Val157del	p.V157del	ENST00000323963		155	aTTGtt/att	5/11	0.187926576850992	3	FACETS	1	0.978	1	0.615	0.56	0.673	INDETERMINATE	1	TRUE	1	0.381902588124355	3		501	684	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056429	26056429	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	49	256	0	ENST00000343677.2:c.228del	p.Asn76LysfsTer13	p.N76Kfs*13	ENST00000343677	NM_005319.3	76	aaC/aa	1/1	1	2	FACETS	0.618	0.525	0.721	0.618	0.525	0.721	SUBCLONAL	1	TRUE	1	0.381902588124355	2		256	415	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023100	150023100	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	92	549	1	ENST00000253339.5:c.163A>T	p.Ser55Cys	p.S55C	ENST00000253339		55	Agt/Tgt	1/7	1	2	FACETS	0.706	0.628	0.79	0.706	0.628	0.79	SUBCLONAL	1	TRUE	1	0.381902588124355	2		550	682	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0015557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1538	242	860	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.395028929146701	3	FACETS	0.824	0.767	0.884	0.412	0.383	0.442	CLONAL	1	TRUE	1	0.395028929146701	3		861	1780	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579321	7579322	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs587780067	NA	P-0015557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	374	573	0	ENST00000269305.4:c.365_366del	p.Val122AspfsTer26	p.V122Dfs*26	ENST00000269305	NM_001126112.2	122	gTG/g	4/11	0.395028929146701	3	FACETS	0.939	0.892	0.988	0.939	0.892	0.988	CLONAL	2	TRUE	1	0.395028929146701	3		573	1207	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023558	27023558	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1293494045	NA	P-0015557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	132	593	0	ENST00000324856.7:c.664T>C	p.Tyr222His	p.Y222H	ENST00000324856	NM_006015.4	222	Tac/Cac	1/20	0.174302511537495	1	FACETS	0.621	0.564	0.682	0.621	0.564	0.682	INDETERMINATE	1	TRUE	0	0.395028929146701	1		593	863	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982989	201982989	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	1142	850	0	ENST00000359651.3:c.838C>G	p.Arg280Gly	p.R280G	ENST00000359651		280	Cgg/Ggg	7/8	0.395028929146701	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.395028929146701	3		850	2050	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298741	46298741	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	62	454	0	ENST00000334344.6:c.5388C>G	p.Asn1796Lys	p.N1796K	ENST00000334344	NM_152641.2	1796	aaC/aaG	21/21	1	2	FACETS	0.43	0.371	0.495	0.43	0.371	0.495	SUBCLONAL	1	TRUE	1	0.395028929146701	2		454	730	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574363	95574363	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	40	374	0	ENST00000393063.1:c.2504G>C	p.Gly835Ala	p.G835A	ENST00000393063	NM_030621.3	835	gGt/gCt	17/28	1	2	FACETS	0.274	0.227	0.327	0.274	0.227	0.327	SUBCLONAL	1	TRUE	1	0.395028929146701	2		374	738	SUCCESS
ATR	545	MSKCC	GRCh37	3	142238551	142238551	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	34	307	0	ENST00000350721.4:c.4342G>C	p.Glu1448Gln	p.E1448Q	ENST00000350721	NM_001184.3	1448	Gag/Cag	24/47	1	2	FACETS	0.266	0.217	0.323	0.266	0.217	0.323	SUBCLONAL	1	TRUE	1	0.395028929146701	2		307	646	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0015558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	70	860	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.809	0.703	0.925	0.809	0.703	0.925	CLONAL	1	TRUE	1	0.14	2		861	1236	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374324	81374324	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	33	252	0	ENST00000222390.5:c.738G>C	p.Leu246Phe	p.L246F	ENST00000222390	NM_000601.4	246	ttG/ttC	6/18	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.14	2		252	399	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752842	128752842	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	29	318	0	ENST00000377970.2:c.1003C>G	p.Pro335Ala	p.P335A	ENST00000377970	NM_002467.4	335	Cct/Gct	3/3	0.172833126648116	3	FACETS	0.785	0.628	0.963	0.392	0.314	0.482	CLONAL	1	TRUE	1	0.14	3		318	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691039	NA	P-0015559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	168	554	0	ENST00000269305.4:c.919+1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		554	555	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	279	248	0				ENST00000310581	NM_198253.2	-/1132			0.42437166407771	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.609356726675975	3		248	527	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0015560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	97	470	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	NA	2	FACETS	0.8	0.718	0.885			1	INDETERMINATE	1	TRUE	NA	0.609356726675975	2		470	398	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0015560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	138	475	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.537	0.489	0.588	0.537	0.489	0.588	SUBCLONAL	1	TRUE	1	0.609356726675975	2		475	843	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0015560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	47	194	1	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.728	0.621	0.842	0.728	0.621	0.842	SUBCLONAL	1	TRUE	1	0.609356726675975	2		195	212	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032069	26032069	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	123	360	0	ENST00000244661.2:c.220G>C	p.Glu74Gln	p.E74Q	ENST00000244661	NM_003537.3	74	Gaa/Caa	1/1	0.42437166407771	3	FACETS	1	0.93	1	0.513	0.466	0.562	CLONAL	1	TRUE	1	0.609356726675975	3		360	513	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101468	27101468	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	52	766	0	ENST00000324856.7:c.4750C>T	p.Gln1584Ter	p.Q1584*	ENST00000324856	NM_006015.4	1584	Cag/Tag	18/20	0.242508653316251	1	FACETS	0.141	0.119	0.165	0.141	0.119	0.165	INDETERMINATE	1	TRUE	0	0.609356726675975	1		766	842	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508565	106508565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	42	313	0	ENST00000359195.3:c.559G>A	p.Glu187Lys	p.E187K	ENST00000359195	NM_002649.2	187	Gag/Aag	2/11	1	2	FACETS	0.46	0.385	0.541	0.46	0.385	0.541	SUBCLONAL	1	TRUE	1	0.609356726675975	2		313	300	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989385	7989385	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200663524	NA	P-0015560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	126	711	1	ENST00000319144.4:c.301G>A	p.Ala101Thr	p.A101T	ENST00000319144	NM_001139.2	101	Gcc/Acc	2/15	1	2	FACETS	0.534	0.484	0.587	0.534	0.484	0.587	SUBCLONAL	1	TRUE	1	0.609356726675975	2		712	774	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152567	56152567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375239979	NA	P-0015560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	72	321	0	ENST00000399503.3:c.623G>A	p.Arg208Gln	p.R208Q	ENST00000399503	NM_005921.1	208	cGa/cAa	2/20	1	2	FACETS	0.559	0.49	0.632	0.559	0.49	0.632	SUBCLONAL	1	TRUE	1	0.609356726675975	2		321	423	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812270	43812270	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	113	545	0	ENST00000372470.3:c.1135C>G	p.Leu379Val	p.L379V	ENST00000372470	NM_005373.2	379	Ctg/Gtg	7/12	0.242508653316251	1	FACETS	0.416	0.375	0.459	0.416	0.375	0.459	INDETERMINATE	1	TRUE	0	0.609356726675975	1		545	620	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981828	201981829	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0015560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	346	777	0	ENST00000359651.3:c.542_543dup	p.Gly182ProfsTer73	p.G182Pfs*73	ENST00000359651		180	cac/caCCc	4/8	0.351576900778436	2	FACETS	1	0.995	1	0.712	0.677	0.746	INDETERMINATE	1	TRUE	0	0.609356726675975	2		777	798	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415628	49415628	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	134	354	0	ENST00000301067.7:c.16549G>C	p.Glu5517Gln	p.E5517Q	ENST00000301067	NM_003482.3	5517	Gag/Cag	54/54	1	2	FACETS	0.916	0.838	0.997	0.916	0.838	0.997	CLONAL	1	TRUE	1	0.609356726675975	2		354	480	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367942	15367942	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	131	727	2	ENST00000263377.2:c.1384G>A	p.Glu462Lys	p.E462K	ENST00000263377	NM_058243.2	462	Gag/Aag	8/20	1	2	FACETS	0.501	0.454	0.55	0.501	0.454	0.55	SUBCLONAL	1	TRUE	1	0.609356726675975	2		729	858	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729829	47729829	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs893049418	NA	P-0015560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	81	670	0	ENST00000449228.1:c.560G>C	p.Arg187Pro	p.R187P	ENST00000449228	NM_001127240.2	187	cGa/cCa	3/4	1	2	FACETS	0.325	0.285	0.367	0.325	0.285	0.367	SUBCLONAL	1	TRUE	1	0.609356726675975	2		670	819	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129689	47129689	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	109	583	0	ENST00000409792.3:c.5191G>C	p.Asp1731His	p.D1731H	ENST00000409792	NM_014159.6	1731	Gat/Cat	10/21	0.42437166407771	3	FACETS	0.492	0.441	0.547	0.246	0.22	0.274	SUBCLONAL	1	TRUE	1	0.609356726675975	3		583	948	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163479	47163479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269748231	NA	P-0015560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	236	321	0	ENST00000409792.3:c.2647C>T	p.Leu883Phe	p.L883F	ENST00000409792	NM_014159.6	883	Ctt/Ttt	3/21	0.42437166407771	3	FACETS	0.871	0.82	0.923	0.871	0.82	0.923	CLONAL	2	TRUE	1	0.609356726675975	3		321	580	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197086	106197086	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	33	321	0	ENST00000380013.4:c.5419G>C	p.Asp1807His	p.D1807H	ENST00000380013	NM_001127208.2	1807	Gat/Cat	11/11	1	2	FACETS	0.26	0.211	0.314	0.26	0.211	0.314	SUBCLONAL	1	TRUE	1	0.609356726675975	2		321	417	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159098	143159098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1321044670	NA	P-0015560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	205	502	0	ENST00000262992.4:c.755G>A	p.Arg252Gln	p.R252Q	ENST00000262992	NM_001101669.1	252	cGa/cAa	10/24	1	2	FACETS	0.889	0.827	0.953	0.889	0.827	0.953	CLONAL	1	TRUE	1	0.609356726675975	2		502	757	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402576	20402576	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	38	299	0	ENST00000346618.3:c.113T>A	p.Leu38Gln	p.L38Q	ENST00000346618	NM_001949.4	38	cTg/cAg	1/7	0.42437166407771	3	FACETS	0.406	0.336	0.484	0.203	0.168	0.242	SUBCLONAL	1	TRUE	1	0.609356726675975	3		299	401	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289023	33289023	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	66	572	0	ENST00000374542.5:c.529C>T	p.Gln177Ter	p.Q177*	ENST00000374542	NM_001141970.1	177	Cag/Tag	3/8	1	2	FACETS	0.277	0.24	0.318	0.277	0.24	0.318	SUBCLONAL	1	TRUE	1	0.609356726675975	2		572	782	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651994	36651995	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	208	607	0	ENST00000244741.5:c.119dup	p.Cys41LeufsTer7	p.C41Lfs*7	ENST00000244741	NM_000389.4	39	gcg/gcGg	2/3	0.115283420282943	6	FACETS	0.842	0.783	0.904			1	INDETERMINATE	2	TRUE	NA	0.609356726675975	6		607	899	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652025	36652025	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	423	666	0	ENST00000244741.5:c.147G>T	p.Trp49Cys	p.W49C	ENST00000244741	NM_000389.4	49	tgG/tgT	2/3	0.115283420282943	6	FACETS	1	0.982	1			1	INDETERMINATE	3	TRUE	NA	0.609356726675975	6		666	979	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024205	112024205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	57	303	0	ENST00000368678.4:c.580G>A	p.Asp194Asn	p.D194N	ENST00000368678		194	Gat/Aat	7/13	0.609356726675975	1	FACETS	0.334	0.287	0.384	0.334	0.287	0.384	SUBCLONAL	1	TRUE	0	0.609356726675975	1		303	390	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137320982	137320982	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	260	852	0	ENST00000481739.1:c.939C>G	p.Phe313Leu	p.F313L	ENST00000481739	NM_002957.4	313	ttC/ttG	7/10	0.609356726675975	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.609356726675975	1		852	577	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0015561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	282	399	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.368823431015907	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.368823431015907	2		399	694	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280804	41280804	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	92	274	0	ENST00000349496.5:c.2317C>T	p.Gln773Ter	p.Q773*	ENST00000349496	NM_001904.3	773	Cag/Tag	15/15	0.368823431015907	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.368823431015907	1		274	368	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042745	42042745	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	149	446	0	ENST00000219905.7:c.6940G>T	p.Asp2314Tyr	p.D2314Y	ENST00000219905	NM_001164273.1	2314	Gat/Tat	17/24	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.368823431015907	2		446	740	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831316	89831316	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	158	480	0	ENST00000389301.3:c.2760G>C	p.Leu920Phe	p.L920F	ENST00000389301	NM_000135.2	920	ttG/ttC	28/43	0.368823431015907	2	FACETS	1	0.952	1	0.527	0.483	0.573	CLONAL	1	TRUE	0	0.368823431015907	2		480	813	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217806	7217806	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0015561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	213	639	0	ENST00000380728.2:c.204+1G>C		p.X68_splice	ENST00000380728		68			0.368823431015907	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.368823431015907	1		639	872	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054837	5054837	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	144	439	0	ENST00000381652.3:c.889C>T	p.Gln297Ter	p.Q297*	ENST00000381652	NM_004972.3	297	Cag/Tag	7/25	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.368823431015907	2		439	762	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593613	55593613	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913521	NA	P-0015562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	82	426	0	ENST00000288135.5:c.1679T>A	p.Val560Asp	p.V560D	ENST00000288135	NM_000222.2	560	gTt/gAt	11/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.242113039871615	2		426	507	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593613	55593613	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913521	NA	P-0015562-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	126	426	0	ENST00000288135.5:c.1679T>A	p.Val560Asp	p.V560D	ENST00000288135	NM_000222.2	560	gTt/gAt	11/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.822620560716214	2		426	270	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0015563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	273	475	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.77794824050573	4	FACETS	1	0.978	1	0.706	0.669	0.744	CLONAL	2	TRUE	1	0.77794824050573	4		475	589	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720709	89720709	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs863224909	NA	P-0015563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	218	175	0	ENST00000371953.3:c.860C>G	p.Ser287Ter	p.S287*	ENST00000371953	NM_000314.4	287	tCa/tGa	8/9	0.77794824050573	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.77794824050573	3		175	246	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0015565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	222	541	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	0.519471888604805	2		541	819	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	50	355	0	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	0.519471888604805	2	FACETS	0.289	0.245	0.339	0.145	0.122	0.17	SUBCLONAL	1	TRUE	0	0.519471888604805	2		355	665	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604796	48604798	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0015565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	45	559	0	ENST00000342988.3:c.1619_1621del	p.Leu540del	p.L540del	ENST00000342988	NM_005359.5	540	CTT/-	12/12	0.519008418285666	1	FACETS	0.25	0.209	0.294	0.25	0.209	0.294	SUBCLONAL	1	TRUE	0	0.519471888604805	1		559	514	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528489	29528489	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764079291	NA	P-0015565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	391	830	0	ENST00000356175.3:c.1246C>T	p.Arg416Ter	p.R416*	ENST00000356175	NM_000267.3	416	Cga/Tga	11/57	0.519471888604805	2	FACETS	0.893	0.854	0.932	0.893	0.854	0.932	CLONAL	2	TRUE	0	0.519471888604805	2		830	843	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248409	59248409	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1184098204	NA	P-0015565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	135	407	0	ENST00000371222.2:c.334G>C	p.Glu112Gln	p.E112Q	ENST00000371222	NM_002228.3	112	Gag/Cag	1/1	1	2	FACETS	0.979	0.894	1	0.979	0.894	1	CLONAL	1	TRUE	1	0.519471888604805	2		407	531	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300363	11300363	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	122	425	0	ENST00000361445.4:c.1783G>C	p.Glu595Gln	p.E595Q	ENST00000361445	NM_004958.3	595	Gaa/Caa	11/58	1	2	FACETS	0.905	0.822	0.992	0.905	0.822	0.992	CLONAL	1	TRUE	1	0.519471888604805	2		425	519	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643647	38643647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	212	620	1	ENST00000299084.4:c.1117G>A	p.Glu373Lys	p.E373K	ENST00000299084	NM_152594.2	373	Gag/Aag	7/7	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.519471888604805	2		621	787	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845638	68845673	+	inframe_deletion	In_Frame_Del	DEL	CCTACAATGCCGCCATCGCTTACACCATCCTCAGCC	CCTACAATGCCGCCATCGCTTACACCATCCTCAGCC	-	novel	NA	P-0015565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	358	929	0	ENST00000261769.5:c.884_919del	p.Thr295_Gln307delinsLys	p.T295_Q307delinsK	ENST00000261769	NM_004360.3	295	aCCTACAATGCCGCCATCGCTTACACCATCCTCAGCCaa/aaa	7/16	0.519471888604805	2	FACETS	0.808	0.769	0.847	0.808	0.769	0.847	CLONAL	2	TRUE	0	0.519471888604805	2		929	853	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217683	7217683	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	356	599	0	ENST00000380728.2:c.244G>T	p.Glu82Ter	p.E82*	ENST00000380728		82	Gag/Tag	4/11	0.519471888604805	2	FACETS	0.945	0.903	0.988	0.945	0.903	0.988	CLONAL	2	TRUE	0	0.519471888604805	2		599	725	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016634	12016634	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	319	452	0	ENST00000353533.5:c.770C>G	p.Ser257Cys	p.S257C	ENST00000353533	NM_003010.3	257	tCt/tGt	7/11	0.519471888604805	2	FACETS	0.978	0.932	1	0.978	0.932	1	CLONAL	2	TRUE	0	0.519471888604805	2		452	628	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797279	42797279	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs979283584	NA	P-0015565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	278	869	0	ENST00000575354.2:c.3641G>A	p.Arg1214Gln	p.R1214Q	ENST00000575354	NM_015125.3	1214	cGa/cAa	15/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.519471888604805	2		869	1044	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990420	69990420	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	153	508	0	ENST00000394351.3:c.379G>C	p.Glu127Gln	p.E127Q	ENST00000394351	NM_000248.3	127	Gaa/Caa	4/9	1	2	FACETS	0.881	0.808	0.956	0.881	0.808	0.956	CLONAL	1	TRUE	1	0.519471888604805	2		508	669	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967167	134967167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	153	427	1	ENST00000398015.3:c.2506G>A	p.Ala836Thr	p.A836T	ENST00000398015	NM_004441.4	836	Gcc/Acc	14/16	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.519471888604805	2		428	556	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155793	106155793	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	201	518	0	ENST00000380013.4:c.694C>A	p.Gln232Lys	p.Q232K	ENST00000380013	NM_001127208.2	232	Caa/Aaa	3/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.519471888604805	2		518	693	SUCCESS
APC	324	MSKCC	GRCh37	5	112175091	112175091	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	66	232	0	ENST00000257430.4:c.3800C>G	p.Thr1267Ser	p.T1267S	ENST00000257430	NM_000038.5	1267	aCt/aGt	16/16	0.5208438893447	3	FACETS	0.81	0.707	0.922	0.405	0.353	0.461	CLONAL	1	TRUE	1	0.519471888604805	3		232	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0015566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	547	790	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.564083410724532	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	FALSE	0	0.564083410724532	2		792	943	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0015566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	157	259	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.564083410724532	3	FACETS	0.967	0.898	1	0.967	0.898	1	CLONAL	2	FALSE	1	0.564083410724532	3		259	369	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958789	55958789	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	323	649	0	ENST00000263923.4:c.3064C>T	p.Arg1022Ter	p.R1022*	ENST00000263923	NM_002253.2	1022	Cga/Tga	22/30	0.266165557246727	4	FACETS	0.88	0.832	0.928	0.88	0.832	0.928	INDETERMINATE	2	FALSE	2	0.564083410724532	4		649	1018	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450139	32450139	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	188	580	0	ENST00000332351.3:c.673A>G	p.Thr225Ala	p.T225A	ENST00000332351	NM_024426.4	225	Acg/Gcg	2/10	0.564083410724532	3	FACETS	1	0.963	1	0.355	0.328	0.382	CLONAL	1	FALSE	0	0.564083410724532	3		580	803	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046524	30046524	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	90	556	0	ENST00000331968.5:c.2659C>G	p.Pro887Ala	p.P887A	ENST00000331968	NM_002742.2	887	Cca/Gca	18/18	0.352398126348538	3	FACETS	0.567	0.503	0.636	0.284	0.251	0.318	SUBCLONAL	1	FALSE	1	0.564083410724532	3		556	721	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944554	40944554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775796300	NA	P-0015566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	1056	587	0	ENST00000373198.4:c.1948G>A	p.Val650Met	p.V650M	ENST00000373198	NM_133170.3	650	Gtg/Atg	12/32	0.564083410724532	7	FACETS	0.989	0.968	1	0.989	0.968	1	CLONAL	6	FALSE	1	0.564083410724532	7		587	1521	SUCCESS
APC	324	MSKCC	GRCh37	5	112173306	112173316	+	frameshift_variant	Frame_Shift_Del	DEL	ATAGTTTGACA	ATAGTTTGACA	-	novel	NA	P-0015566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	90	288	0	ENST00000257430.4:c.2020_2030del	p.Leu674GlnfsTer2	p.L674Qfs*2	ENST00000257430	NM_000038.5	672	cATAGTTTGACA/c	16/16	0.564083410724532	3	FACETS	0.905	0.807	1	0.453	0.403	0.505	CLONAL	1	FALSE	1	0.564083410724532	3		288	452	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871060	12871070	+	frameshift_variant	Frame_Shift_Del	DEL	AAGGTGCCTGC	AAGGTGCCTGC	-	novel	NA	P-0015568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	112	320	0	ENST00000228872.4:c.295_305del	p.Cys99GlyfsTer22	p.C99Gfs*22	ENST00000228872	NM_004064.3	96	aAAGGTGCCTGC/a	1/3	0.71595706293224	5	FACETS	1	0.953	1	0.366	0.33	0.405	CLONAL	1	TRUE	2	0.58	5		320	657	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115854	8115855	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0015568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	74	735	0	ENST00000346208.3:c.1200_1201insC	p.Ser401LeufsTer106	p.S401Lfs*106	ENST00000346208		400	-/C	6/6	0.797262400298844	4	FACETS	0.886	0.778	1	0.443	0.389	0.501	CLONAL	1	TRUE	2	0.58	4		735	455	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575562	64575588	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AATTTGGTGCCTGTGGAAGGGGGAGGT	AATTTGGTGCCTGTGGAAGGGGGAGGT	-	novel	NA	P-0015568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	12	498	0	ENST00000312049.6:c.446-17_455del		p.X149_splice	ENST00000312049	NM_130799.2	149		3/10	0.393443416754654	8	FACETS	0.537	0.378	0.734			1	SUBCLONAL	1	TRUE	NA	0.58	8		498	211	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871060	12871070	+	frameshift_variant	Frame_Shift_Del	DEL	AAGGTGCCTGC	AAGGTGCCTGC	-	novel	NA	P-0015568-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	378	320	0	ENST00000228872.4:c.295_305del	p.Cys99GlyfsTer22	p.C99Gfs*22	ENST00000228872	NM_004064.3	96	aAAGGTGCCTGC/a	1/3	0.842038249895884	2	FACETS	0.872	0.844	0.898	0.872	0.844	0.898	CLONAL	2	TRUE	0	0.860546432532288	2		320	504	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115854	8115855	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0015568-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	468	735	0	ENST00000346208.3:c.1200_1201insC	p.Ser401LeufsTer106	p.S401Lfs*106	ENST00000346208		400	-/C	6/6	1	2	FACETS	0.87	0.832	0.908	0.87	0.832	0.908	CLONAL	1	TRUE	1	0.860546432532288	2		735	1250	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575562	64575588	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AATTTGGTGCCTGTGGAAGGGGGAGGT	AATTTGGTGCCTGTGGAAGGGGGAGGT	-	novel	NA	P-0015568-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	254	498	0	ENST00000312049.6:c.446-17_455del		p.X149_splice	ENST00000312049	NM_130799.2	149		3/10	0.860586393105687	1	FACETS	0.837	0.798	0.874	0.837	0.798	0.874	CLONAL	1	TRUE	0	0.860546432532288	1		498	402	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713616	30713616	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015568-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	320	465	0	ENST00000295754.5:c.941A>G	p.Lys314Arg	p.K314R	ENST00000295754	NM_003242.5	314	aAg/aGg	4/7	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.860546432532288	2		465	704	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419893	152419901	+	inframe_deletion	In_Frame_Del	DEL	GCATGAAGT	GCATGAAGT	-	novel	NA	P-0015568-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1734	611	484	0	ENST00000206249.3:c.1583_1591del	p.Met528_Cys530del	p.M528_C530del	ENST00000206249	NM_000125.3	527	aGCATGAAGTgc/agc	8/8	0.860586393105687	5	FACETS	1	0.996	1			1	CLONAL	1	TRUE	NA	0.860546432532288	5		484	2345	SUCCESS
AR	367	MSKCC	GRCh37	X	66931330	66931330	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015568-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	448	669	0	ENST00000374690.3:c.1972C>T	p.Gln658Ter	p.Q658*	ENST00000374690	NM_000044.3	658	Cag/Tag	4/8	NA	2	FACETS	0.961	0.92	1			1	INDETERMINATE	1	TRUE	NA	0.860546432532288	2		669	1083	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0015569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	221	474	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.413249712072629	2		474	862	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914004	32914004	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	58	533	0	ENST00000380152.3:c.5512G>C	p.Glu1838Gln	p.E1838Q	ENST00000380152		1838	Gag/Cag	11/27	1	2	FACETS	0.321	0.275	0.371	0.321	0.275	0.371	SUBCLONAL	1	TRUE	1	0.413249712072629	2		533	875	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	49	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.578	0.488	0.677	0.578	0.488	0.677	SUBCLONAL	1	TRUE	1	0.23	2		248	737	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0015571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	70	568	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	1	2	FACETS	0.735	0.64	0.839	0.735	0.64	0.839	SUBCLONAL	1	TRUE	1	0.23	2		568	828	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030434	49030434	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778833	NA	P-0015571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	68	486	1	ENST00000267163.4:c.1909C>T	p.Gln637Ter	p.Q637*	ENST00000267163	NM_000321.2	637	Cag/Tag	19/27	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.23	2		487	484	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212885	27212885	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	112	529	0	ENST00000380036.4:c.2867G>A	p.Ser956Asn	p.S956N	ENST00000380036	NM_000459.3	956	aGc/aAc	17/23	1	2	FACETS	0.909	0.816	1	0.909	0.816	1	CLONAL	1	TRUE	1	0.23	2		529	1071	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615626	100615626	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	59	565	0	ENST00000308731.7:c.706C>G	p.Arg236Gly	p.R236G	ENST00000308731	NM_000061.2	236	Cgg/Ggg	8/19	1	2	FACETS	0.564	0.484	0.652	0.564	0.484	0.652	SUBCLONAL	1	TRUE	1	0.23	2		565	910	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	195	583	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.961	1			1	INDETERMINATE	1	TRUE	NA	0.642553939256289	2		583	580	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	259	568	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.642553939256289	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.642553939256289	1		568	511	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	54	346	0	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	0.642553939256289	1	FACETS	0.251	0.214	0.291	0.251	0.214	0.291	SUBCLONAL	1	TRUE	0	0.642553939256289	1		346	455	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94129038	94129038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746638787	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	230	408	0	ENST00000369303.4:c.22C>T	p.Pro8Ser	p.P8S	ENST00000369303	NM_004440.3	8	Cct/Tct	1/17	1	2	FACETS	0.937	0.876	0.999	0.937	0.876	0.999	CLONAL	1	TRUE	1	0.642553939256289	2		408	764	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261038	16261038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144525015	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	244	511	1	ENST00000375759.3:c.8303C>T	p.Ala2768Val	p.A2768V	ENST00000375759	NM_015001.2	2768	gCg/gTg	11/15	0.626667476378177	3	FACETS	1	0.95	1			1	CLONAL	1	TRUE	NA	0.642553939256289	3		512	985	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055910	180055910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	249	631	0	ENST00000261937.6:c.1075G>A	p.Ala359Thr	p.A359T	ENST00000261937	NM_182925.4	359	Gca/Aca	8/30	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.642553939256289	2		631	763	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197354	106197354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	238	450	0	ENST00000380013.4:c.5687G>A	p.Arg1896Lys	p.R1896K	ENST00000380013	NM_001127208.2	1896	aGg/aAg	11/11	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.642553939256289	2		450	740	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955394	48955394	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886043247	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	190	230	0	ENST00000267163.4:c.1510C>T	p.Gln504Ter	p.Q504*	ENST00000267163	NM_000321.2	504	Cag/Tag	17/27	0.642553939256289	1	FACETS	0.956	0.895	1	0.956	0.895	1	CLONAL	1	TRUE	0	0.642553939256289	1		230	420	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415825	49415825	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	148	318	2	ENST00000301067.7:c.16521+1G>A		p.X5507_splice	ENST00000301067	NM_003482.3	5507			1	2	FACETS	0.964	0.887	1	0.964	0.887	1	CLONAL	1	TRUE	1	0.642553939256289	2		320	478	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206942010	206942010	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1011475317	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	404	415	0	ENST00000423557.1:c.508G>A	p.Ala170Thr	p.A170T	ENST00000423557	NM_000572.2	170	Gcc/Acc	5/5	0.642553939256289	3	FACETS	0.964	0.922	1	0.964	0.922	1	CLONAL	2	TRUE	1	0.642553939256289	3		415	862	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446112	70446112	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	202	404	0	ENST00000373644.4:c.5053-1G>A		p.X1685_splice	ENST00000373644	NM_030625.2	1685			0.642553939256289	1	FACETS	0.961	0.902	1	0.961	0.902	1	CLONAL	1	TRUE	0	0.642553939256289	1		404	444	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720811	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1327134140	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	179	372	0	ENST00000371953.3:c.962del	p.Thr321LysfsTer23	p.T321Kfs*23	ENST00000371953	NM_000314.4	321	aCa/aa	8/9	0.642553939256289	1	FACETS	0.846	0.788	0.905	0.846	0.788	0.905	CLONAL	1	TRUE	0	0.642553939256289	1		372	447	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498157	498157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	239	507	0	ENST00000399788.2:c.101G>A	p.Ser34Asn	p.S34N	ENST00000399788	NM_001042603.1	34	aGc/aAc	1/28	NA	2	FACETS	0.948	0.888	1			1	INDETERMINATE	1	TRUE	NA	0.642553939256289	2		507	785	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244256	46244256	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	271	410	0	ENST00000334344.6:c.2350C>T	p.Pro784Ser	p.P784S	ENST00000334344	NM_152641.2	784	Cct/Tct	15/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.642553939256289	2		410	796	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426333	49426333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1327956137	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	403	953	0	ENST00000301067.7:c.12155G>A	p.Gly4052Glu	p.G4052E	ENST00000301067	NM_003482.3	4052	gGa/gAa	39/54	1	2	FACETS	0.997	0.949	1	0.997	0.949	1	CLONAL	1	TRUE	1	0.642553939256289	2		953	1258	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440549	49440549	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	391	890	0	ENST00000301067.7:c.4261G>A	p.Gly1421Ser	p.G1421S	ENST00000301067	NM_003482.3	1421	Ggc/Agc	15/54	1	2	FACETS	0.978	0.929	1	0.978	0.929	1	CLONAL	1	TRUE	1	0.642553939256289	2		890	1245	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495432	56495432	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	300	736	0	ENST00000267101.3:c.3622C>T	p.Pro1208Ser	p.P1208S	ENST00000267101	NM_001982.3	1208	Cca/Tca	28/28	1	2	FACETS	0.963	0.908	1	0.963	0.908	1	CLONAL	1	TRUE	1	0.642553939256289	2		736	970	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355927	73355927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	334	699	2	ENST00000377767.4:c.44G>A	p.Gly15Asp	p.G15D	ENST00000377767	NM_014953.3	15	gGc/gAc	1/21	0.642553939256289	1	FACETS	0.997	0.95	1	0.997	0.95	1	CLONAL	1	TRUE	0	0.642553939256289	1		701	708	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005625	42005625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779311505	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	278	544	0	ENST00000219905.7:c.3361G>A	p.Glu1121Lys	p.E1121K	ENST00000219905	NM_001164273.1	1121	Gag/Aag	9/24	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.642553939256289	2		544	819	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134343	2134344	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs137854289	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	65	824	0	ENST00000219476.3:c.4123_4124del	p.Ser1375LeufsTer38	p.S1375Lfs*38	ENST00000219476	NM_000548.3	1374	CTc/c	34/42	0.521452979877882	1	FACETS	0.186	0.16	0.213	0.186	0.16	0.213	SUBCLONAL	1	TRUE	0	0.642553939256289	1		824	739	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3645694	3645694	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	243	679	0	ENST00000294008.3:c.1925G>A	p.Gly642Glu	p.G642E	ENST00000294008	NM_032444.2	642	gGg/gAg	9/15	0.521452979877882	1	FACETS	0.766	0.72	0.813	0.766	0.72	0.813	SUBCLONAL	1	TRUE	0	0.642553939256289	1		679	670	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826539	50826539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1315227790	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	138	337	1	ENST00000398568.2:c.2264G>A	p.Arg755Gln	p.R755Q	ENST00000398568	NM_001042412.1	755	cGa/cAa	15/18	0.349492435426153	1	FACETS	0.422	0.384	0.461	0.422	0.384	0.461	INDETERMINATE	1	TRUE	0	0.642553939256289	1		338	691	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993695	72993695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	244	580	0	ENST00000268489.5:c.350G>A	p.Gly117Asp	p.G117D	ENST00000268489	NM_006885.3	117	gGt/gAt	2/10	0.349492435426153	1	FACETS	0.849	0.8	0.899	0.849	0.8	0.899	INDETERMINATE	1	TRUE	0	0.642553939256289	1		580	607	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858413	89858413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754491008	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	336	857	0	ENST00000389301.3:c.1147G>A	p.Glu383Lys	p.E383K	ENST00000389301	NM_000135.2	383	Gag/Aag	13/43	0.467232443467791	1	FACETS	0.772	0.732	0.812	0.772	0.732	0.812	SUBCLONAL	1	TRUE	0	0.642553939256289	1		857	920	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8111076	8111076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201438176	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	98	785	3	ENST00000585124.1:c.131G>A	p.Arg44His	p.R44H	ENST00000585124	NM_004217.3	44	cGc/cAc	3/9	1	2	FACETS	0.282	0.251	0.316	0.282	0.251	0.316	SUBCLONAL	1	TRUE	1	0.642553939256289	2		788	1080	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654698	29654698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	192	418	0	ENST00000356175.3:c.5387G>A	p.Cys1796Tyr	p.C1796Y	ENST00000356175	NM_000267.3	1796	tGt/tAt	37/57	1	2	FACETS	0.867	0.805	0.931	0.867	0.805	0.931	CLONAL	1	TRUE	1	0.642553939256289	2		418	689	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33446607	33446607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	261	607	0	ENST00000345365.6:c.26G>A	p.Cys9Tyr	p.C9Y	ENST00000345365	NM_002878.3	9	tGc/tAc	1/10	1	2	FACETS	0.98	0.921	1	0.98	0.921	1	CLONAL	1	TRUE	1	0.642553939256289	2		607	829	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246293	41246293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876658873	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	356	643	1	ENST00000357654.3:c.1255G>A	p.Val419Ile	p.V419I	ENST00000357654	NM_007294.3	419	Gta/Ata	10/23	1	2	FACETS	0.975	0.925	1	0.975	0.925	1	CLONAL	1	TRUE	1	0.642553939256289	2		644	1136	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533063	63533063	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	220	628	0	ENST00000307078.5:c.1831G>A	p.Glu611Lys	p.E611K	ENST00000307078	NM_004655.3	611	Gag/Aag	7/11	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.642553939256289	2		628	678	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533954	63533954	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	141	301	0	ENST00000307078.5:c.1201-1G>A		p.X401_splice	ENST00000307078	NM_004655.3	401			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.642553939256289	2		301	417	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857722	78857722	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	262	706	0	ENST00000306801.3:c.1792G>A	p.Asp598Asn	p.D598N	ENST00000306801	NM_020761.2	598	Gac/Aac	16/34	1	2	FACETS	0.961	0.903	1	0.961	0.903	1	CLONAL	1	TRUE	1	0.642553939256289	2		706	849	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274316	5274316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	324	776	0	ENST00000357368.4:c.131G>A	p.Gly44Asp	p.G44D	ENST00000357368	NM_002850.3	44	gGc/gAc	3/38	0.214720359899373	0	FACETS	0.403	0.382	0.425			1	INDETERMINATE	1	TRUE	0	0.642553939256289	0		776	894	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170513	11170513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	294	827	0	ENST00000358026.2:c.4816G>A	p.Glu1606Lys	p.E1606K	ENST00000358026	NM_001128849.1	1606	Gag/Aag	34/36	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.642553939256289	2		827	889	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220895	36220895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	97	240	0	ENST00000222270.7:c.4945G>A	p.Ala1649Thr	p.A1649T	ENST00000222270	NM_014727.1	1649	Gcc/Acc	23/37	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.642553939256289	2		240	286	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455315	29455315	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1311699420	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	149	361	0	ENST00000389048.3:c.2488-1G>A		p.X830_splice	ENST00000389048	NM_004304.4	830			1	2	FACETS	0.918	0.845	0.994	0.918	0.845	0.994	CLONAL	1	TRUE	1	0.642553939256289	2		361	505	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46611648	46611648	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	313	673	0	ENST00000263734.3:c.2462G>A	p.Gly821Asp	p.G821D	ENST00000263734	NM_001430.4	821	gGc/gAc	16/16	1	2	FACETS	0.973	0.92	1	0.973	0.92	1	CLONAL	1	TRUE	1	0.642553939256289	2		673	1001	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145682	61145682	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	316	540	0	ENST00000295025.8:c.794G>A	p.Arg265Lys	p.R265K	ENST00000295025	NM_002908.2	265	aGa/aAa	7/11	NA	2	FACETS	0.922	0.871	0.974			1	INDETERMINATE	1	TRUE	NA	0.642553939256289	2		540	1067	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99185039	99185039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	215	479	2	ENST00000074304.5:c.2441G>A	p.Gly814Asp	p.G814D	ENST00000074304	NM_001134224.1	814	gGc/gAc	23/26	1	2	FACETS	0.877	0.818	0.938	0.877	0.818	0.938	CLONAL	1	TRUE	1	0.642553939256289	2		481	763	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662857	227662857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	316	615	0	ENST00000305123.5:c.598G>A	p.Glu200Lys	p.E200K	ENST00000305123	NM_005544.2	200	Gag/Aag	1/2	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.642553939256289	2		615	958	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62305314	62305314	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	366	941	1	ENST00000360203.5:c.787G>A	p.Ala263Thr	p.A263T	ENST00000360203	NM_001283009.1	263	Gca/Aca	10/35	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.642553939256289	2		942	1031	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513306	44513306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	319	771	3	ENST00000291552.4:c.629G>A	p.Gly210Asp	p.G210D	ENST00000291552	NM_006758.2	210	gGt/gAt	8/8	0.642553939256289	3	FACETS	0.953	0.898	1	0.476	0.449	0.505	CLONAL	1	TRUE	1	0.642553939256289	3		774	1377	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573923	41573923	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	283	712	0	ENST00000263253.7:c.6208G>A	p.Val2070Met	p.V2070M	ENST00000263253	NM_001429.3	2070	Gtg/Atg	31/31	0.642553939256289	1	FACETS	0.985	0.934	1	0.985	0.934	1	CLONAL	1	TRUE	0	0.642553939256289	1		712	607	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935955	49935955	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1559479162	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	266	667	0	ENST00000296474.3:c.1715C>T	p.Thr572Ile	p.T572I	ENST00000296474	NM_002447.2	572	aCt/aTt	4/20	0.642553939256289	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.642553939256289	1		667	525	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144565	55144565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	278	494	0	ENST00000257290.5:c.2039G>A	p.Gly680Glu	p.G680E	ENST00000257290	NM_006206.4	680	gGa/gAa	15/23	1	2	FACETS	0.999	0.941	1	0.999	0.941	1	CLONAL	1	TRUE	1	0.642553939256289	2		494	866	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245486	153245486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	291	560	0	ENST00000281708.4:c.1705G>A	p.Glu569Lys	p.E569K	ENST00000281708	NM_033632.3	569	Gag/Aag	11/12	1	2	FACETS	0.926	0.873	0.981	0.926	0.873	0.981	CLONAL	1	TRUE	1	0.642553939256289	2		560	978	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527252	187527252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	261	479	0	ENST00000441802.2:c.10322C>T	p.Ser3441Phe	p.S3441F	ENST00000441802	NM_005245.3	3441	tCc/tTc	17/27	NA	2	FACETS	0.985	0.926	1			1	INDETERMINATE	1	TRUE	NA	0.642553939256289	2		479	825	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751415	57751415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140637834	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	217	369	1	ENST00000274289.3:c.1576G>A	p.Gly526Ser	p.G526S	ENST00000274289	NM_006622.3	526	Ggt/Agt	11/14	1	2	FACETS	0.937	0.875	1	0.937	0.875	1	CLONAL	1	TRUE	1	0.642553939256289	2		370	721	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048243	180048243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	332	962	1	ENST00000261937.6:c.2030C>T	p.Ala677Val	p.A677V	ENST00000261937	NM_182925.4	677	gCc/gTc	14/30	1	2	FACETS	0.943	0.892	0.995	0.943	0.892	0.995	CLONAL	1	TRUE	1	0.642553939256289	2		963	1096	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166311	32166311	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755096040	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	57	753	2	ENST00000375023.3:c.4643C>T	p.Thr1548Met	p.T1548M	ENST00000375023	NM_004557.3	1548	aCg/aTg	26/30	1	2	FACETS	0.182	0.155	0.211	0.182	0.155	0.211	SUBCLONAL	1	TRUE	1	0.642553939256289	2		755	977	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169120	32169120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	275	666	0	ENST00000375023.3:c.3913C>T	p.Pro1305Ser	p.P1305S	ENST00000375023	NM_004557.3	1305	Ccc/Tcc	22/30	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.642553939256289	2		666	831	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527428	137527428	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	176	290	0	ENST00000367739.4:c.218G>A	p.Trp73Ter	p.W73*	ENST00000367739	NM_000416.2	73	tGg/tAg	3/7	1	2	FACETS	0.959	0.889	1	0.959	0.889	1	CLONAL	1	TRUE	1	0.642553939256289	2		290	571	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2964000	2964000	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	202	606	0	ENST00000396946.4:c.1808-1G>A		p.X603_splice	ENST00000396946	NM_032415.4	603			NA	2	FACETS	0.743	0.69	0.798			1	INDETERMINATE	1	TRUE	NA	0.642553939256289	2		606	846	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223624	55223624	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	179	474	0	ENST00000275493.2:c.991G>A	p.Gly331Arg	p.G331R	ENST00000275493	NM_005228.3	331	Ggg/Agg	8/28	0.642553939256289	3	FACETS	0.924	0.853	0.997	0.462	0.426	0.499	CLONAL	1	TRUE	1	0.642553939256289	3		474	797	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896468	151896468	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	267	427	0	ENST00000262189.6:c.4169G>A	p.Gly1390Glu	p.G1390E	ENST00000262189	NM_170606.2	1390	gGa/gAa	27/59	0.642553939256289	3	FACETS	0.939	0.88	1	0.47	0.44	0.5	CLONAL	1	TRUE	1	0.642553939256289	3		427	1169	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080345	5080345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	172	313	0	ENST00000381652.3:c.2248G>A	p.Gly750Arg	p.G750R	ENST00000381652	NM_004972.3	750	Gga/Aga	17/25	1	2	FACETS	0.775	0.715	0.837	0.775	0.715	0.837	SUBCLONAL	1	TRUE	1	0.642553939256289	2		313	691	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080379	5080379	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	130	258	0	ENST00000381652.3:c.2282G>A	p.Arg761Lys	p.R761K	ENST00000381652	NM_004972.3	761	aGa/aAa	17/25	1	2	FACETS	0.755	0.688	0.825	0.755	0.688	0.825	SUBCLONAL	1	TRUE	1	0.642553939256289	2		258	536	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396539	139396539	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1216304049	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	272	666	0	ENST00000277541.6:c.5386C>T	p.Pro1796Ser	p.P1796S	ENST00000277541	NM_017617.3	1796	Ccc/Tcc	29/34	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.642553939256289	2		666	761	SUCCESS
AR	367	MSKCC	GRCh37	X	66942710	66942710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	368	409	0	ENST00000374690.3:c.2491C>T	p.Leu831Phe	p.L831F	ENST00000374690	NM_000044.3	831	Ctt/Ttt	7/8	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.642553939256289	1		409	604	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944393	76944393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	422	294	0	ENST00000373344.5:c.512G>A	p.Cys171Tyr	p.C171Y	ENST00000373344	NM_000489.3	171	tGc/tAc	7/35	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.642553939256289	1		294	632	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220486	123220486	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0015573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	365	327	0	ENST00000218089.9:c.3143T>A	p.Leu1048Ter	p.L1048*	ENST00000218089	NM_001042749.1	1048	tTg/tAg	30/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.642553939256289	1		327	567	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534285	534285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894226	NA	P-0015575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	522	491	0	ENST00000451590.1:c.38G>T	p.Gly13Val	p.G13V	ENST00000451590	NM_001130442.1	13	gGt/gTt	2/5	0.460949015818665	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.460949015818665	3		491	1329	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593630	55593630	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519705	NA	P-0015575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	162	468	0	ENST00000288135.5:c.1696A>G	p.Asn566Asp	p.N566D	ENST00000288135	NM_000222.2	566	Aac/Gac	11/21	1	2	FACETS	0.984	0.905	1	0.984	0.905	1	CLONAL	1	TRUE	1	0.460949015818665	2		468	714	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247533	53247533	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	269	548	0	ENST00000375401.3:c.276C>G	p.Phe92Leu	p.F92L	ENST00000375401	NM_004187.3	92	ttC/ttG	3/26	1	2	FACETS	0.957	0.896	1	0.957	0.896	1	CLONAL	1	TRUE	1	0.460949015818665	2		548	1220	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380283	25380283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913528	NA	P-0015576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	101	466	0	ENST00000311936.3:c.175G>A	p.Ala59Thr	p.A59T	ENST00000311936	NM_004985.3	59	Gca/Aca	3/5	1	2	FACETS	0.969	0.864	1	0.969	0.864	1	CLONAL	1	TRUE	1	0.17	2		466	1226	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988276	41988277	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	75	420	0	ENST00000219905.7:c.1069dup	p.Ile357AsnfsTer6	p.I357Nfs*6	ENST00000219905	NM_001164273.1	356	-/A	3/24	0.157691476276411	1	FACETS	0.729	0.637	0.829	0.729	0.637	0.829	SUBCLONAL	1	TRUE	0	0.17	1		420	1107	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602611	10602611	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	90	548	0	ENST00000171111.5:c.967A>G	p.Lys323Glu	p.K323E	ENST00000171111	NM_203500.1	323	Aag/Gag	3/6	0.157691476276411	1	FACETS	0.917	0.811	1	0.917	0.811	1	CLONAL	1	TRUE	0	0.17	1		548	1057	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095626	178095626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750553272	NA	P-0015577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	201	419	0	ENST00000397062.3:c.1705C>T	p.Arg569Cys	p.R569C	ENST00000397062	NM_006164.4	569	Cgt/Tgt	5/5	1	2	FACETS	0.894	0.832	0.958	0.894	0.832	0.958	CLONAL	1	TRUE	1	0.63148664029512	2		419	712	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267491	198267491	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763149798	NA	P-0015577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	225	337	0	ENST00000335508.6:c.1866G>T	p.Glu622Asp	p.E622D	ENST00000335508	NM_012433.2	622	gaG/gaT	14/25	1	2	FACETS	0.861	0.803	0.92	0.861	0.803	0.92	CLONAL	1	TRUE	1	0.63148664029512	2		337	828	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207203	1207203	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0015578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	168	514	0	ENST00000326873.7:c.290+1G>T		p.X97_splice	ENST00000326873	NM_000455.4	97			0.231378774855592	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.231378774855592	1		514	1026	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371409680	NA	P-0015578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	221	433	0	ENST00000269305.4:c.848G>C	p.Arg283Pro	p.R283P	ENST00000269305	NM_001126112.2	283	cGc/cCc	8/11	0.180595922876034	2	FACETS	0.762	0.707	0.818	0.762	0.707	0.818	SUBCLONAL	2	TRUE	0	0.231378774855592	2		433	1254	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874261	155874261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352822	NA	P-0015578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1409	83	435	1	ENST00000368323.3:c.270G>A	p.Met90Ile	p.M90I	ENST00000368323	NM_006912.5	90	atG/atA	5/6	0.228726886629267	3	FACETS	0.536	0.471	0.607	0.268	0.235	0.304	SUBCLONAL	1	TRUE	1	0.231378774855592	3		436	1492	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729154	66729154	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519731	NA	P-0015578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	142	450	0	ENST00000307102.5:c.362G>C	p.Cys121Ser	p.C121S	ENST00000307102	NM_002755.3	121	tGc/tCc	3/11	1	2	FACETS	0.999	0.908	1	0.999	0.908	1	CLONAL	1	TRUE	1	0.231378774855592	2		450	1229	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294234	11294234	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1154	103	509	0	ENST00000361445.4:c.2297G>T	p.Arg766Leu	p.R766L	ENST00000361445	NM_004958.3	766	cGa/cTa	14/58	NA	2	FACETS	0.708	0.632	0.79			1	INDETERMINATE	1	TRUE	NA	0.231378774855592	2		509	1257	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145614	11145614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1482864360	NA	P-0015578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	53	468	0	ENST00000358026.2:c.3976G>A	p.Glu1326Lys	p.E1326K	ENST00000358026	NM_001128849.1	1326	Gag/Aag	29/36	0.231378774855592	1	FACETS	0.416	0.353	0.485	0.416	0.353	0.485	SUBCLONAL	1	TRUE	0	0.231378774855592	1		468	975	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140154	50140154	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1374610832	NA	P-0015578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	169	408	0	ENST00000246792.3:c.271G>A	p.Gly91Arg	p.G91R	ENST00000246792	NM_006270.3	91	Ggg/Agg	3/6	0.231378774855592	1	FACETS	0.763	0.702	0.826	1	0.989	1	SUBCLONAL	2	TRUE	0	0.231378774855592	1		408	847	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119666168	119666168	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	77	332	0	ENST00000316626.5:c.313G>T	p.Asp105Tyr	p.D105Y	ENST00000316626		105	Gat/Tat	3/12	0.180595922876034	2	FACETS	0.801	0.702	0.908	0.4	0.351	0.454	CLONAL	1	TRUE	0	0.231378774855592	2		332	831	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670672	134670672	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0015578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	108	399	0	ENST00000398015.3:c.583A>T	p.Lys195Ter	p.K195*	ENST00000398015	NM_004441.4	195	Aag/Tag	3/16	0.180595922876034	2	FACETS	0.88	0.788	0.978	0.44	0.394	0.489	CLONAL	1	TRUE	0	0.231378774855592	2		399	1061	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254616	1254616	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	280	311	0	ENST00000310581.5:c.3162G>T	p.Met1054Ile	p.M1054I	ENST00000310581	NM_198253.2	1054	atG/atT	15/16	0.231378774855592	6	FACETS	1	0.967	1	1	0.967	1	CLONAL	3	TRUE	3	0.231378774855592	6		311	1131	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729691	41729691	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	103	372	0	ENST00000242208.4:c.838G>T	p.Gly280Ter	p.G280*	ENST00000242208	NM_002192.2	280	Gga/Tga	3/3	0.161146177174464	4	FACETS	1	0.958	1	0.381	0.34	0.425	CLONAL	1	TRUE	1	0.231378774855592	4		372	958	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250428	10250428	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	147	493	0	ENST00000340748.4:c.3824A>G	p.Lys1275Arg	p.K1275R	ENST00000340748		1275	aAg/aGg	33/40	1	2	FACETS	0.785	0.717	0.856	0.785	0.717	0.856	SUBCLONAL	1	TRUE	1	0.460821160940021	2		493	813	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230856	53230856	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	185	592	0	ENST00000375401.3:c.1937A>C	p.Glu646Ala	p.E646A	ENST00000375401	NM_004187.3	646	gAg/gCg	14/26	0.460821160940021	1	FACETS	0.792	0.733	0.854	0.792	0.733	0.854	SUBCLONAL	1	TRUE	0	0.460821160940021	1		592	780	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272361	38272361	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015579-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	29	524	0	ENST00000425967.3:c.2006A>G	p.Lys669Arg	p.K669R	ENST00000425967	NM_001174067.1	669	aAg/aGg	15/19	0.234141849907934	1	FACETS	0.497	0.414	0.582	0.497	0.414	0.582	INDETERMINATE	1	TRUE	0	0.895418094905368	1		524	72	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240681	53240681	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015579-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	35	566	0	ENST00000375401.3:c.1399G>T	p.Glu467Ter	p.E467*	ENST00000375401	NM_004187.3	467	Gag/Tag	10/26	0.895418094905368	1	FACETS	0.939	0.841	1	0.939	0.841	1	CLONAL	1	TRUE	0	0.895418094905368	1		566	46	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404552	70404552	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	217	449	0	ENST00000373644.4:c.2066C>G	p.Pro689Arg	p.P689R	ENST00000373644	NM_030625.2	689	cCa/cGa	4/12	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.378992989444335	2		449	1095	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448414	49448414	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	223	541	0	ENST00000301067.7:c.297del	p.Ser102AlafsTer28	p.S102Afs*28	ENST00000301067	NM_003482.3	99	ccT/cc	3/54	NA	2	FACETS	1	0.933	1			1	INDETERMINATE	1	TRUE	NA	0.378992989444335	2		541	1173	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0015582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	104	235	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.352858913032586	2		235	560	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063717	+	splice_donor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0015582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	45	269	0	ENST00000412916.2:c.165+1del		p.X55_splice	ENST00000412916		55			0.352858913032586	1	FACETS	0.89	0.755	1	0.89	0.755	1	CLONAL	1	TRUE	0	0.352858913032586	1		269	236	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870993	12870994	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0015582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	73	349	0	ENST00000228872.4:c.221dup	p.Tyr74Ter	p.Y74*	ENST00000228872	NM_004064.3	74	tac/tAac	1/3	1	2	FACETS	0.784	0.687	0.888	0.784	0.687	0.888	SUBCLONAL	1	TRUE	1	0.352858913032586	2		349	528	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110064	115110070	+	frameshift_variant	Frame_Shift_Del	DEL	TAGGGGT	TAGGGGT	-	novel	NA	P-0015582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	158	747	0	ENST00000257566.3:c.1808_1814del	p.Tyr603SerfsTer27	p.Y603Sfs*27	ENST00000257566	NM_016569.3	603	tACCCCTAc/tc	8/8	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.352858913032586	2		747	888	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120639	115120639	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	179	743	0	ENST00000257566.3:c.367A>G	p.Met123Val	p.M123V	ENST00000257566	NM_016569.3	123	Atg/Gtg	1/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.352858913032586	2		743	902	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853179	68853187	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCAGATATC	TCAGATATC	-	novel	NA	P-0015582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	97	378	0	ENST00000261769.5:c.1566-4_1570del		p.X522_splice	ENST00000261769	NM_004360.3	522		11/16	0.352858913032586	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.352858913032586	1		378	421	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0015583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	119	541	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	0.26	2		541	784	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945696	17945696	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3213409	NA	P-0015583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1336	164	529	0	ENST00000458235.1:c.2164G>A	p.Val722Ile	p.V722I	ENST00000458235	NM_000215.3	722	Gtc/Atc	16/24	1	2	FACETS	0.841	0.769	0.916	0.841	0.769	0.916	CLONAL	1	TRUE	1	0.26	2		529	1500	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527461	29527461	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786203950	NA	P-0015583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	55	292	0	ENST00000356175.3:c.910C>T	p.Arg304Ter	p.R304*	ENST00000356175	NM_000267.3	304	Cga/Tga	9/57	1	2	FACETS	0.746	0.638	0.864	0.746	0.638	0.864	SUBCLONAL	1	TRUE	1	0.26	2		292	567	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685271	89685271	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	26	160	0	ENST00000371953.3:c.166T>G	p.Phe56Val	p.F56V	ENST00000371953	NM_000314.4	56	Ttt/Gtt	3/9	1	2	FACETS	0.784	0.623	0.967	0.784	0.623	0.967	CLONAL	1	TRUE	1	0.26	2		160	255	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845609	63845612	+	frameshift_variant	Frame_Shift_Del	DEL	AAAA	AAAA	-	novel	NA	P-0015583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	77	279	0	ENST00000279873.7:c.1348_1351del	p.Lys450AlafsTer28	p.K450Afs*28	ENST00000279873	NM_032199.2	450	AAAAgc/gc	9/10	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.26	2		279	579	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692826	89692826	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	34	163	2	ENST00000371953.3:c.313del	p.Cys105ValfsTer8	p.C105Vfs*8	ENST00000371953	NM_000314.4	104	Ttt/tt	5/9	1	2	FACETS	0.899	0.737	1	0.899	0.737	1	CLONAL	1	TRUE	1	0.26	2		165	291	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725050	89725073	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTACTTCACAAAAACAGTAGAG	CTGTACTTCACAAAAACAGTAGAG	TT	novel	NA	P-0015583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	15	171	2	ENST00000371953.3:c.1033_1056delinsTT	p.Tyr346SerfsTer13	p.Y346Sfs*13	ENST00000371953	NM_000314.4	345	CTGTACTTCACAAAAACAGTAGAG/TT	9/9	1	2	FACETS	0.475	0.347	0.628	0.475	0.347	0.628	SUBCLONAL	1	TRUE	1	0.26	2		173	243	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576115	29576116	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0015583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	70	441	0	ENST00000356175.3:c.4093_4094del	p.Cys1365ProfsTer8	p.C1365Pfs*8	ENST00000356175	NM_000267.3	1363	aGT/a	30/57	1	2	FACETS	0.636	0.553	0.725	0.636	0.553	0.725	SUBCLONAL	1	TRUE	1	0.26	2		441	847	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176684087	176684087	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	114	509	1	ENST00000439151.2:c.4901G>A	p.Arg1634Gln	p.R1634Q	ENST00000439151	NM_022455.4	1634	cGg/cAg	13/23	1	2	FACETS	0.76	0.682	0.842	0.76	0.682	0.842	SUBCLONAL	1	TRUE	1	0.26	2		510	1154	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100213	157100253	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCGGGGCCGCGAGCCTCAGCAAGGCGGCCGCCGGCTC	GGCGGCGGGGCCGCGAGCCTCAGCAAGGCGGCCGCCGGCTC	-	novel	NA	P-0015583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	68	53	0	ENST00000346085.5:c.1160_1200del	p.Ala387GlyfsTer134	p.A387Gfs*134	ENST00000346085	NM_020732.3	384	GGCGGCGGGGCCGCGAGCCTCAGCAAGGCGGCCGCCGGCTCg/g	1/20	1	2	FACETS	1	0.916	1	1	0.983	1	CLONAL	2	TRUE	1	0.26	2		53	249	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511155	148511155	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	134	348	0	ENST00000320356.2:c.1747C>T	p.Arg583Ter	p.R583*	ENST00000320356	NM_004456.4	583	Cga/Tga	15/20	1	2	FACETS	0.97	0.879	1	0.97	0.879	1	CLONAL	1	TRUE	1	0.26	2		348	1063	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0015584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	165	583	0				ENST00000310581	NM_198253.2	-/1132			0.274242791345118	1	FACETS	0.913	0.839	0.989	0.913	0.839	0.989	CLONAL	1	TRUE	0	0.365292565372986	1		583	809	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578529	7578529	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	301	586	0	ENST00000269305.4:c.401T>C	p.Phe134Ser	p.F134S	ENST00000269305	NM_001126112.2	134	tTt/tCt	5/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.365292565372986	2		586	1500	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55154983	55154983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1185214354	NA	P-0015584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	180	378	0	ENST00000257290.5:c.2692G>A	p.Gly898Ser	p.G898S	ENST00000257290	NM_006206.4	898	Ggc/Agc	20/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.365292565372986	2		378	839	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176710894	176710894	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	195	445	0	ENST00000439151.2:c.6116G>A	p.Arg2039His	p.R2039H	ENST00000439151	NM_022455.4	2039	cGt/cAt	20/23	0.231120611984133	1	FACETS	0.997	0.924	1	0.997	0.924	1	CLONAL	1	TRUE	0	0.365292565372986	1		445	875	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0015584-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	81	583	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.272545067837393	2		583	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578529	7578529	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015584-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	163	586	0	ENST00000269305.4:c.401T>C	p.Phe134Ser	p.F134S	ENST00000269305	NM_001126112.2	134	tTt/tCt	5/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.272545067837393	2		586	1094	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55154983	55154983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1185214354	NA	P-0015584-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	111	378	0	ENST00000257290.5:c.2692G>A	p.Gly898Ser	p.G898S	ENST00000257290	NM_006206.4	898	Ggc/Agc	20/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.272545067837393	2		378	667	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176710894	176710894	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015584-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	109	445	0	ENST00000439151.2:c.6116G>A	p.Arg2039His	p.R2039H	ENST00000439151	NM_022455.4	2039	cGt/cAt	20/23	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.272545067837393	2		445	709	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0015585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	55	251	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.135486807350605	3	FACETS	0.974	0.834	1	0.487	0.417	0.563	INDETERMINATE	1	TRUE	1	0.28	3		251	460	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0015585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	134	618	2	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	TRUE	1	0.28	2		620	857	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0015585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	94	431	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	1	2	FACETS	0.861	0.765	0.963	0.861	0.765	0.963	CLONAL	1	TRUE	1	0.28	2		431	780	SUCCESS
FH	2271	MSKCC	GRCh37	1	241669381	241669381	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	124	387	0	ENST00000366560.3:c.826G>T	p.Gly276Cys	p.G276C	ENST00000366560	NM_000143.3	276	Ggc/Tgc	6/10	0.135486807350605	3	FACETS	1	0.969	1	0.584	0.528	0.643	INDETERMINATE	1	TRUE	1	0.28	3		387	865	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0015586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	507	399	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.623804090882095	2	FACETS	0.969	0.937	1	0.969	0.937	1	CLONAL	2	TRUE	0	0.637225738206364	2		399	821	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0015586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	253	356	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.637225738206364	2		356	734	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0015587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	161	356	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.884	0.814	0.957	0.884	0.814	0.957	CLONAL	1	TRUE	1	0.563838430066202	2		356	646	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061137	38061185	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCG	GCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCG	-	novel	NA	P-0015587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	107	181	0	ENST00000250448.2:c.804_852del	p.Cys268Ter	p.C268*	ENST00000250448	NM_004496.3	268	tgCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGC/tg	2/2	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.563838430066202	2		181	334	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098954	178098954	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	124	247	0	ENST00000397062.3:c.91G>C	p.Gly31Arg	p.G31R	ENST00000397062	NM_006164.4	31	Gga/Cga	2/5	1	2	FACETS	0.982	0.895	1	0.982	0.895	1	CLONAL	1	TRUE	1	0.563838430066202	2		247	448	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157470015	157470015	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1442559706	NA	P-0015587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	151	320	0	ENST00000346085.5:c.2809A>G	p.Thr937Ala	p.T937A	ENST00000346085	NM_020732.3	937	Act/Gct	9/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.563838430066202	2		320	516	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0015589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	722	586	1	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	0.790277928886859	4	FACETS	0.943	0.911	0.974	0.943	0.911	0.974	CLONAL	2	TRUE	2	0.861396859746247	4		587	1655	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0015592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	313	605	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.344325614157353	3	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.480248116619712	3		606	670	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	156	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.480248116619712	2		248	634	SUCCESS
CBL	867	MSKCC	GRCh37	11	119145615	119145615	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	145	294	0	ENST00000264033.4:c.821A>T	p.Tyr274Phe	p.Y274F	ENST00000264033	NM_005188.3	274	tAt/tTt	5/16	0.239661514697042	1	FACETS	0.791	0.725	0.86	0.791	0.725	0.86	INDETERMINATE	1	TRUE	0	0.480248116619712	1		294	580	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561040	9561040	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	98	194	0	ENST00000353224.5:c.742G>A	p.Glu248Lys	p.E248K	ENST00000353224	NM_177990.2	248	Gag/Aag	4/10	1	2	FACETS	0.841	0.754	0.934	0.841	0.754	0.934	CLONAL	1	TRUE	1	0.480248116619712	2		194	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0015593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	147	563	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.277961107999921	2	FACETS	0.796	0.726	0.87	0.398	0.363	0.435	SUBCLONAL	1	TRUE	0	0.359412077096086	2		564	1027	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411902	116411902	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	518	562	1	ENST00000397752.3:c.2888-1G>A		p.X963_splice	ENST00000397752	NM_000245.2	963			0.359412077096086	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.359412077096086	2		563	1294	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341313	89341313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773189154	NA	P-0015593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	109	180	0	ENST00000301030.4:c.7622C>T	p.Ala2541Val	p.A2541V	ENST00000301030	NM_001256183.1	2541	gCg/gTg	11/13	0.359412077096086	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.359412077096086	1		180	338	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39657720	39657720	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	89	376	0	ENST00000361337.2:c.13C>G	p.His5Asp	p.H5D	ENST00000361337	NM_003286.2	5	Cac/Gac	1/21	1	2	FACETS	0.721	0.639	0.808	0.721	0.639	0.808	SUBCLONAL	1	TRUE	1	0.359412077096086	2		376	687	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934004	39934004	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	61	521	1	ENST00000378444.4:c.595G>A	p.Ala199Thr	p.A199T	ENST00000378444	NM_001123385.1	199	Gcc/Acc	4/15	0.138839195815251	0	FACETS	0.234	0.201	0.27			1	INDETERMINATE	1	TRUE	0	0.359412077096086	0		522	929	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	21	507	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.3	1	FACETS	0.053	0.04	0.067	0.053	0.04	0.067	INDETERMINATE	1	TRUE	0	0.84	1		507	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0015594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	36	467	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.081	0.066	0.098	0.081	0.066	0.098	SUBCLONAL	1	TRUE	1	0.84	2		468	1060	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575152	48575152	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	23	239	0	ENST00000342988.3:c.346C>T	p.Gln116Ter	p.Q116*	ENST00000342988	NM_005359.5	116	Cag/Tag	3/12	1	2	FACETS	0.132	0.103	0.167	0.132	0.103	0.167	SUBCLONAL	1	TRUE	1	0.84	2		239	414	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726869	61726869	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	177	331	0	ENST00000401558.2:c.569A>T	p.Lys190Ile	p.K190I	ENST00000401558	NM_003400.3	190	aAa/aTa	7/25	0.766078776660987	3	FACETS	0.908	0.839	0.979	0.454	0.419	0.49	CLONAL	1	TRUE	1	0.766078776660987	3		331	704	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380442	31380442	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	408	335	0	ENST00000328111.2:c.932T>C	p.Val311Ala	p.V311A	ENST00000328111	NM_006892.3	311	gTg/gCg	9/23	0.766078776660987	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	2	0.766078776660987	4		335	915	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833909	44833909	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0015595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	31	322	0	ENST00000377967.4:c.335-2A>T		p.X112_splice	ENST00000377967	NM_021140.2	112			1	2	FACETS	0.147	0.118	0.18	0.147	0.118	0.18	SUBCLONAL	1	TRUE	1	0.766078776660987	2		322	551	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636712	2636712	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	98	431	0	ENST00000342085.4:c.1161G>C	p.Gln387His	p.Q387H	ENST00000342085	NM_002613.4	387	caG/caC	11/14	1	2	FACETS	0.769	0.688	0.854	0.769	0.688	0.854	SUBCLONAL	1	TRUE	1	0.482901222136225	2		431	528	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845292	42845294	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0015597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	84	543	0	ENST00000398585.3:c.968_970del	p.Ile323del	p.I323del	ENST00000398585	NM_001135099.1	323	aTCAcc/acc	9/14	0.482901222136225	1	FACETS	0.492	0.436	0.553	0.492	0.436	0.553	SUBCLONAL	1	TRUE	0	0.482901222136225	1		543	536	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374288	138374288	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	37	473	0	ENST00000289153.2:c.3156C>G	p.Ser1052Arg	p.S1052R	ENST00000289153	NM_006219.2	1052	agC/agG	22/22	1	2	FACETS	0.231	0.189	0.277	0.231	0.189	0.277	SUBCLONAL	1	TRUE	1	0.482901222136225	2		473	664	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	135	414	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.728	0.666	0.792	0.728	0.666	0.792	SUBCLONAL	1	TRUE	1	0.752287406605095	2		414	493	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593405	48593405	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519962	NA	P-0015599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	95	301	0	ENST00000342988.3:c.1156G>A	p.Gly386Ser	p.G386S	ENST00000342988	NM_005359.5	386	Ggt/Agt	10/12	1	2	FACETS	0.702	0.63	0.776	0.702	0.63	0.776	SUBCLONAL	1	TRUE	1	0.752287406605095	2		301	360	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023048	27023091	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGCCGCCGGGCAGGAAAGCGAGGGCCCCGCCGTGGGGCCGCC	GCAGCCGCCGGGCAGGAAAGCGAGGGCCCCGCCGTGGGGCCGCC	-	novel	NA	P-0015599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	37	104	0	ENST00000324856.7:c.162_205del	p.Gln56LysfsTer40	p.Q56Kfs*40	ENST00000324856	NM_006015.4	52	GCAGCCGCCGGGCAGGAAAGCGAGGGCCCCGCCGTGGGGCCGCCg/g	1/20	1	2	FACETS	0.403	0.334	0.479	0.403	0.334	0.479	SUBCLONAL	1	TRUE	1	0.752287406605095	2		104	244	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560463	95560463	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555366979	NA	P-0015599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	215	462	0	ENST00000393063.1:c.5126A>G	p.Asp1709Gly	p.D1709G	ENST00000393063	NM_030621.3	1709	gAt/gGt	25/28	0.538413852760367	1	FACETS	0.569	0.532	0.607	0.569	0.532	0.607	SUBCLONAL	1	TRUE	0	0.752287406605095	1		462	627	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727961	78727961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	128	352	0	ENST00000306801.3:c.806C>T	p.Thr269Ile	p.T269I	ENST00000306801	NM_020761.2	269	aCc/aTc	6/34	1	2	FACETS	0.485	0.44	0.532	0.485	0.44	0.532	SUBCLONAL	1	TRUE	1	0.752287406605095	2		352	702	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212450	5212450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196839847	NA	P-0015599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	301	555	0	ENST00000357368.4:c.4667C>T	p.Pro1556Leu	p.P1556L	ENST00000357368	NM_002850.3	1556	cCg/cTg	31/38	1	2	FACETS	0.72	0.678	0.762	0.72	0.678	0.762	SUBCLONAL	1	TRUE	1	0.752287406605095	2		555	1112	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	206	414	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.655589627008716	4	FACETS	0.887	0.83	0.946	0.887	0.83	0.946	CLONAL	2	TRUE	2	0.749340215960879	4		414	542	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0015600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	93	371	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	1	2	FACETS	0.893	0.805	0.984	0.893	0.805	0.984	CLONAL	1	TRUE	1	0.749340215960879	2		371	278	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221313	1221314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs121913321	NA	P-0015600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	955	665	0	ENST00000326873.7:c.842dup	p.Leu282AlafsTer3	p.L282Afs*3	ENST00000326873	NM_000455.4	279	ggc/ggCc	6/10	0.749340215960879	2	FACETS	0.986	0.966	1	0.986	0.966	1	CLONAL	2	TRUE	0	0.749340215960879	2		665	1293	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573869	7574003	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCTTTCCAACCTAGGAAGGCAGGGGAGTAGGGCCAGGAAGGGGCTGAGGTCACTCACCTGGAGTGAGCCCTGCTCCCCCCTGGCTCCTTCCCAGCCTGGGCATCCTTGAGTTCCAAGGCCTCATTCAGCTCTCG	GGCTTTCCAACCTAGGAAGGCAGGGGAGTAGGGCCAGGAAGGGGCTGAGGTCACTCACCTGGAGTGAGCCCTGCTCCCCCCTGGCTCCTTCCCAGCCTGGGCATCCTTGAGTTCCAAGGCCTCATTCAGCTCTCG	-	novel	NA	P-0015600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	400	173	0	ENST00000269305.4:c.1024_1100+58del		p.X342_splice	ENST00000269305	NM_001126112.2	342		10/11	0.749340215960879	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.749340215960879	3		173	462	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095891	29095891	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	238	535	0	ENST00000328354.6:c.943G>T	p.Gly315Trp	p.G315W	ENST00000328354	NM_007194.3	315	Ggg/Tgg	9/15	1	2	FACETS	0.994	0.934	1	0.994	0.934	1	CLONAL	1	TRUE	1	0.749340215960879	2		535	639	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs869320707	NA	P-0015601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	141	736	1	ENST00000397752.3:c.3028+1G>T		p.X1010_splice	ENST00000397752	NM_000245.2	1010			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		737	1134	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670325	134670325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	223	288	1	ENST00000398015.3:c.236G>A	p.Arg79Gln	p.R79Q	ENST00000398015	NM_004441.4	79	cGg/cAg	3/16	0.183870604627352	2	FACETS	0.826	0.773	0.88	0.826	0.773	0.88	INDETERMINATE	2	TRUE	0	0.40359028154719	2		289	669	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115729	8115730	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	149	293	0	ENST00000346208.3:c.1077dup	p.Gly360ArgfsTer11	p.G360Rfs*11	ENST00000346208		359	gaa/gAaa	6/6	1	2	FACETS	0.92	0.841	1	0.92	0.841	1	CLONAL	1	TRUE	1	0.40359028154719	2		293	803	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100668	67100687	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCTGTCTGGAGTTTGATG	GGGCTGTCTGGAGTTTGATG	-	novel	NA	P-0015602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	230	397	0	ENST00000412916.2:c.366_385del	p.Met122IlefsTer16	p.M122Ifs*16	ENST00000412916		122	atGGGCTGTCTGGAGTTTGATGag/atag	4/6	0.40359028154719	2	FACETS	1	0.992	1	0.729	0.681	0.777	CLONAL	1	TRUE	0	0.40359028154719	2		397	782	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663437	67663438	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0015602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	192	187	0	ENST00000264010.4:c.1837+2dup		p.X613_splice	ENST00000264010	NM_006565.3	613			0.40359028154719	2	FACETS	0.965	0.901	1	0.965	0.901	1	CLONAL	2	TRUE	0	0.40359028154719	2		187	493	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266508	198266508	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	116	262	0	ENST00000335508.6:c.2328A>T	p.Glu776Asp	p.E776D	ENST00000335508	NM_012433.2	776	gaA/gaT	16/25	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.40359028154719	2		262	489	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	107	248	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.902	0.82	0.986			1	INDETERMINATE	1	TRUE	NA	0.788206433722487	2		248	301	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720720	89720721	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs786204905	NA	P-0015603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	26	98	0	ENST00000371953.3:c.875dup	p.Asn292LysfsTer6	p.N292Kfs*6	ENST00000371953	NM_000314.4	291	gaa/gAaa	8/9	0.788206433722487	1	FACETS	0.597	0.491	0.707	0.597	0.491	0.707	SUBCLONAL	1	TRUE	0	0.788206433722487	1		98	67	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489901	2489901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	129	387	1	ENST00000355716.4:c.298G>A	p.Asp100Asn	p.D100N	ENST00000355716	NM_003820.2	100	Gac/Aac	3/8	NA	2	FACETS	0.8	0.732	0.87			1	INDETERMINATE	1	TRUE	NA	0.788206433722487	2		388	409	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211061	55211061	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9474	891	449	0	ENST00000275493.2:c.304G>C	p.Glu102Gln	p.E102Q	ENST00000275493	NM_005228.3	102	Gaa/Caa	3/28	0.788206433722487	30	FACETS	0.875	0.842	0.909	0.088	0.084	0.091	CLONAL	3	TRUE	0	0.788206433722487	30		449	10365	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650795	93650795	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0015603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	103	239	0	ENST00000375746.1:c.1723-2A>G		p.X575_splice	ENST00000375746	NM_001174167.1	575			1	2	FACETS	0.957	0.87	1	0.957	0.87	1	CLONAL	1	TRUE	1	0.788206433722487	2		239	273	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207162	1207162	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs137853076	NA	P-0015604-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	414	765	0	ENST00000326873.7:c.250A>T	p.Lys84Ter	p.K84*	ENST00000326873	NM_000455.4	84	Aag/Tag	1/10	0.597960038492265	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.597960038492265	1		765	818	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610293	10610293	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015604-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	405	834	1	ENST00000171111.5:c.417del	p.Phe139LeufsTer18	p.F139Lfs*18	ENST00000171111	NM_203500.1	139	ttC/tt	2/6	0.597960038492265	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.597960038492265	1		835	857	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0015609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	390	664	0	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	2	TRUE	NA	0.579762787208973	2		664	670	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21272490	21272490	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	367	789	0	ENST00000354336.3:c.268A>G	p.Ile90Val	p.I90V	ENST00000354336	NM_005207.3	90	Atc/Gtc	1/3	0.388902850361135	4	FACETS	0.947	0.9	0.995	0.947	0.9	0.995	CLONAL	2	TRUE	2	0.579762787208973	4		789	1056	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939172	76939172	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	213	615	0	ENST00000373344.5:c.1576G>T	p.Glu526Ter	p.E526*	ENST00000373344	NM_000489.3	526	Gaa/Taa	9/35	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.579762787208973	2		615	530	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432766	432766	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	106	413	0	ENST00000399788.2:c.2150G>T	p.Arg717Ile	p.R717I	ENST00000399788	NM_001042603.1	717	aGa/aTa	15/28	0.655357264134667	3	FACETS	0.703	0.633	0.776			1	SUBCLONAL	1	TRUE	NA	0.935786832672362	3		413	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577611	7577611	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	C	novel	NA	P-0015611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	337	391	0	ENST00000269305.4:c.673-3T>G		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.919754093825501	2	FACETS	0.973	0.953	0.991	0.973	0.953	0.991	CLONAL	2	TRUE	0	0.935786832672362	2		391	370	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27217750	27217750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	188	526	3	ENST00000380036.4:c.3056G>T	p.Ser1019Ile	p.S1019I	ENST00000380036	NM_000459.3	1019	aGt/aTt	19/23	NA	2	FACETS	0.957	0.895	1			1	INDETERMINATE	1	TRUE	NA	0.935786832672362	2		529	420	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0015612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	404	583	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	FALSE	NA	0.802361180746625	2		583	917	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643768	52643768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	515	539	3	ENST00000394830.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000394830	NM_018313.4	710	Cga/Tga	17/30	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.802361180746625	2		542	1193	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32918761	32918762	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	252	294	1	ENST00000380152.3:c.6908_6909delinsTT	p.Ser2303Phe	p.S2303F	ENST00000380152		2303	tCC/tTT	12/27	1	2	FACETS	0.95	0.895	1	0.95	0.895	1	CLONAL	1	FALSE	1	0.802361180746625	2		295	661	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0015612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	601	844	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.802361180746625	2		844	1478	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2492097	2492097	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs772088410	NA	P-0015612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	525	567	1	ENST00000355716.4:c.500del	p.Pro167ArgfsTer23	p.P167Rfs*23	ENST00000355716	NM_003820.2	165	tgC/tg	5/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.802361180746625	2		568	1229	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335127	65335127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334600636	NA	P-0015612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	429	480	0	ENST00000342505.4:c.514C>T	p.Pro172Ser	p.P172S	ENST00000342505	NM_002227.2	172	Cct/Tct	6/25	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.802361180746625	2		480	1047	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276376	115276377	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	375	463	1	ENST00000438362.2:c.951_952delinsTT	p.Pro318Ser	p.P318S	ENST00000438362	NM_001242891.1	317	atCCca/atTTca	9/20	1	2	FACETS	0.91	0.866	0.955	0.91	0.866	0.955	CLONAL	1	FALSE	1	0.802361180746625	2		464	1027	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982138	201982139	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	475	593	1	ENST00000359651.3:c.662_663delinsTT	p.Pro221Leu	p.P221L	ENST00000359651		221	cCC/cTT	5/8	1	2	FACETS	0.965	0.924	1	0.965	0.924	1	CLONAL	1	FALSE	1	0.802361180746625	2		594	1227	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14303170	14303170	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	453	409	1	ENST00000256196.4:c.505C>T	p.His169Tyr	p.H169Y	ENST00000256196		169	Cat/Tat	5/6	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.802361180746625	2		410	1020	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242098	105242098	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	490	484	1	ENST00000349310.3:c.326G>A	p.Gly109Asp	p.G109D	ENST00000349310	NM_001014432.1	109	gGc/gAc	6/15	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.802361180746625	2		485	1136	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992668	72992669	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	347	378	0	ENST00000268489.5:c.1376_1377delinsTT	p.Ala459Val	p.A459V	ENST00000268489	NM_006885.3	459	gCC/gTT	2/10	0.802361180746625	4	FACETS	1	0.958	1	0.339	0.32	0.359	CLONAL	1	FALSE	1	0.802361180746625	4		378	1533	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39593447	39593447	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	253	233	0	ENST00000262039.4:c.1212A>T	p.Lys404Asn	p.K404N	ENST00000262039	NM_002647.2	404	aaA/aaT	11/25	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.802361180746625	2		233	562	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15365046	15365046	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200802400	NA	P-0015612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	2125	526	1	ENST00000263377.2:c.2075C>T	p.Ser692Phe	p.S692F	ENST00000263377	NM_058243.2	692	tCc/tTc	11/20	0.802361180746625	4	FACETS	1	0.999	1	1	0.999	1	CLONAL	4	FALSE	0	0.802361180746625	4		527	2292	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211138	36211138	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	2062	780	0	ENST00000222270.7:c.889C>T	p.Arg297Ter	p.R297*	ENST00000222270	NM_014727.1	297	Cga/Tga	3/37	0.802361180746625	3	FACETS	1	0.999	1	1	0.999	1	CLONAL	3	FALSE	0	0.802361180746625	3		780	2253	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225343024	225343047	+	inframe_deletion	In_Frame_Del	DEL	CTTTCCTCTCTGGGTCGGATTCAC	CTTTCCTCTCTGGGTCGGATTCAC	-	novel	NA	P-0015612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	260	572	2	ENST00000264414.4:c.2045_2068del	p.Gly682_Lys689del	p.G682_K689del	ENST00000264414	NM_003590.4	682	gGTGAATCCGACCCAGAGAGGAAAGaa/gaa	15/16	1	2	FACETS	0.654	0.613	0.696	0.654	0.613	0.696	SUBCLONAL	1	FALSE	1	0.802361180746625	2		574	991	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961321	54961321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs2230743	NA	P-0015612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	453	475	0	ENST00000312783.6:c.311C>T	p.Ser104Leu	p.S104L	ENST00000312783	NM_198436.1	104	tCg/tTg	4/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.802361180746625	2		475	1062	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275237	142275237	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749652394	NA	P-0015612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	381	332	0	ENST00000350721.4:c.2066C>T	p.Pro689Leu	p.P689L	ENST00000350721	NM_001184.3	689	cCc/cTc	9/47	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.802361180746625	2		332	858	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747967	41747967	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758728895	NA	P-0015612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	158	171	0	ENST00000226382.2:c.802G>A	p.Gly268Ser	p.G268S	ENST00000226382	NM_003924.3	268	Ggc/Agc	3/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.802361180746625	2		171	362	SUCCESS
APC	324	MSKCC	GRCh37	5	112178106	112178106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	330	286	0	ENST00000257430.4:c.6815G>A	p.Arg2272Lys	p.R2272K	ENST00000257430	NM_000038.5	2272	aGa/aAa	16/16	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.802361180746625	2		286	752	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681073	117681073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	507	550	0	ENST00000368508.3:c.3547G>A	p.Val1183Ile	p.V1183I	ENST00000368508	NM_002944.2	1183	Gtt/Att	23/43	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.802361180746625	2		550	1258	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450394	50450394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	264	317	0	ENST00000331340.3:c.578G>A	p.Arg193Lys	p.R193K	ENST00000331340	NM_006060.4	193	aGg/aAg	5/8	0.802361180746625	4	FACETS	0.929	0.869	0.99	0.31	0.289	0.33	CLONAL	1	FALSE	1	0.802361180746625	4		317	1277	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922665	56922665	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	463	467	0	ENST00000519728.1:c.1535C>A	p.Pro512His	p.P512H	ENST00000519728	NM_002350.3	512	cCt/cAt	13/13	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.802361180746625	2		467	1081	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933403	39933403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	436	486	0	ENST00000378444.4:c.1196G>A	p.Gly399Glu	p.G399E	ENST00000378444	NM_001123385.1	399	gGg/gAg	4/15	NA	2	FACETS	0.996	0.952	1			1	INDETERMINATE	1	FALSE	NA	0.802361180746625	2		486	1091	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637711	52637713	+	stop_gained	Nonsense_Mutation	TNP	GAA	GAA	AAT	novel	NA	P-0015612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	326	428	1	ENST00000394830.3:c.2603_2605delinsATT	p.Leu868_Gln869delinsHisTer	p.L868_Q869delinsH*	ENST00000394830	NM_018313.4	868	cTTCag/cATTag	18/30	1	2	FACETS	0.992	0.942	1	0.992	0.942	1	CLONAL	1	FALSE	1	0.802361180746625	2		429	819	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0015613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	158	339	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.962	0.886	1	0.962	0.886	1	CLONAL	1	TRUE	1	0.556553732318251	2		339	590	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188533	11188533	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	63	397	0	ENST00000361445.4:c.5888A>G	p.Asp1963Gly	p.D1963G	ENST00000361445	NM_004958.3	1963	gAc/gGc	42/58	NA	2	FACETS	0.284	0.245	0.326			1	INDETERMINATE	1	TRUE	NA	0.556553732318251	2		397	798	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230695	46230695	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	175	304	0	ENST00000334344.6:c.944T>C	p.Phe315Ser	p.F315S	ENST00000334344	NM_152641.2	315	tTc/tCc	8/21	1	2	FACETS	0.876	0.809	0.945	0.876	0.809	0.945	CLONAL	1	TRUE	1	0.556553732318251	2		304	718	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953550	32953550	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	223	511	0	ENST00000380152.3:c.8851G>C	p.Ala2951Pro	p.A2951P	ENST00000380152		2951	Gcc/Ccc	22/27	1	2	FACETS	0.839	0.782	0.898	0.839	0.782	0.898	CLONAL	1	TRUE	1	0.556553732318251	2		511	955	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996132	73996132	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	226	634	0	ENST00000318443.5:c.866A>G	p.Asp289Gly	p.D289G	ENST00000318443	NM_001024736.1	289	gAc/gGc	5/10	1	2	FACETS	0.866	0.807	0.926	0.866	0.807	0.926	CLONAL	1	TRUE	1	0.556553732318251	2		634	938	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577529	7577529	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs730882027	NA	P-0015613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	478	429	0	ENST00000269305.4:c.752T>G	p.Ile251Ser	p.I251S	ENST00000269305	NM_001126112.2	251	aTc/aGc	7/11	0.556553732318251	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.556553732318251	2		429	825	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967273	134967273	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	208	454	0	ENST00000398015.3:c.2612T>G	p.Phe871Cys	p.F871C	ENST00000398015	NM_004441.4	871	tTt/tGt	14/16	1	2	FACETS	0.768	0.713	0.825	0.768	0.713	0.825	SUBCLONAL	1	TRUE	1	0.556553732318251	2		454	973	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197366	106197366	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	162	322	0	ENST00000380013.4:c.5699T>C	p.Val1900Ala	p.V1900A	ENST00000380013	NM_001127208.2	1900	gTc/gCc	11/11	1	2	FACETS	0.779	0.716	0.845	0.779	0.716	0.845	SUBCLONAL	1	TRUE	1	0.556553732318251	2		322	747	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197382	106197382	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	154	306	0	ENST00000380013.4:c.5715G>C	p.Lys1905Asn	p.K1905N	ENST00000380013	NM_001127208.2	1905	aaG/aaC	11/11	1	2	FACETS	0.734	0.673	0.798	0.734	0.673	0.798	SUBCLONAL	1	TRUE	1	0.556553732318251	2		306	754	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447429	12447429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs573789959	NA	P-0015614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	158	586	0	ENST00000287820.6:c.668C>T	p.Ala223Val	p.A223V	ENST00000287820	NM_015869.4	223	gCg/gTg	5/7	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.250292306351124	2		586	1226	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713588	52713588	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0015614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	80	448	0	ENST00000394830.3:c.138+2T>C		p.X46_splice	ENST00000394830	NM_018313.4	46			1	2	FACETS	0.599	0.525	0.678	0.599	0.525	0.678	SUBCLONAL	1	TRUE	1	0.250292306351124	2		448	1068	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0015615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	19	475	0	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	1	2	FACETS	0.512	0.389	0.656	0.512	0.389	0.656	SUBCLONAL	1	TRUE	1	0.27	2		475	275	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484597	57484597	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs137854533	NA	P-0015615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	8	415	1	ENST00000371085.3:c.681G>T	p.Gln227His	p.Q227H	ENST00000371085	NM_000516.4	227	caG/caT	9/13	0.3	3	FACETS	0.17	0.109	0.251			1	SUBCLONAL	1	TRUE	NA	0.27	3		416	395	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434587	49434588	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	53	592	0	ENST00000301067.7:c.6965dup	p.Thr2323AspfsTer3	p.T2323Dfs*3	ENST00000301067	NM_003482.3	2322	aag/aaAg	31/54	0.267349092999795	4	FACETS	1	0.962	1	0.706	0.605	0.816	CLONAL	1	TRUE	2	0.27	4		592	353	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253828	30253828	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768665664	NA	P-0015616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	379	570	4	ENST00000307677.4:c.626G>A	p.Arg209His	p.R209H	ENST00000307677	NM_138578.1	209	cGc/cAc	3/3	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.674116298240674	2		574	1063	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814318	76814318	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0015616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	165	197	0	ENST00000373344.5:c.6327-1G>A		p.X2109_splice	ENST00000373344	NM_000489.3	2109			1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.674116298240674	1		197	240	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0015617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	280	583	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.793869150818983	2		583	675	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791797	42791797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	46	703	1	ENST00000575354.2:c.683G>A	p.Arg228Gln	p.R228Q	ENST00000575354	NM_015125.3	228	cGg/cAg	5/20	0.793869150818983	1	FACETS	0.116	0.097	0.136	0.116	0.097	0.136	SUBCLONAL	1	TRUE	0	0.793869150818983	1		704	605	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796882	42796883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761345552	NA	P-0015617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	46	863	0	ENST00000575354.2:c.3347dup	p.Ser1117LysfsTer34	p.S1117Kfs*34	ENST00000575354	NM_015125.3	1114	gcc/gCcc	14/20	0.793869150818983	1	FACETS	0.096	0.08	0.113	0.096	0.08	0.113	SUBCLONAL	1	TRUE	0	0.793869150818983	1		863	728	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913503	NA	P-0015617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	307	545	0	ENST00000330062.3:c.515G>T	p.Arg172Met	p.R172M	ENST00000330062	NM_002168.2	172	aGg/aTg	4/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.793869150818983	2		545	727	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134255	11134255	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	441	738	0	ENST00000358026.2:c.2921C>T	p.Pro974Leu	p.P974L	ENST00000358026	NM_001128849.1	974	cCc/cTc	20/36	0.184018585285236	3	FACETS	1	0.995	1	0.655	0.625	0.685	INDETERMINATE	1	TRUE	1	0.793869150818983	3		738	1185	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780289	9780289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201282174	NA	P-0015617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	35	473	0	ENST00000377346.4:c.1459G>A	p.Ala487Thr	p.A487T	ENST00000377346	NM_005026.3	487	Gcc/Acc	11/24	0.65717072020664	1	FACETS	0.13	0.106	0.157	0.13	0.106	0.157	SUBCLONAL	1	TRUE	0	0.793869150818983	1		473	408	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794725	42794737	+	frameshift_variant	Frame_Shift_Del	DEL	GACCCGAAAGTGT	GACCCGAAAGTGT	CTTTC	novel	NA	P-0015617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	33	654	4	ENST00000575354.2:c.1805_1817delinsCTTTC	p.Arg602ThrfsTer85	p.R602Tfs*85	ENST00000575354	NM_015125.3	602	aGACCCGAAAGTGTg/aCTTTCg	10/20	0.793869150818983	1	FACETS	0.085	0.069	0.104	0.085	0.069	0.104	SUBCLONAL	1	TRUE	0	0.793869150818983	1		658	588	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796516	42796516	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	326	827	2	ENST00000575354.2:c.3073C>T	p.Gln1025Ter	p.Q1025*	ENST00000575354	NM_015125.3	1025	Cag/Tag	13/20	0.793869150818983	1	FACETS	0.593	0.563	0.624	0.593	0.563	0.624	SUBCLONAL	1	TRUE	0	0.793869150818983	1		829	835	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630154	100630154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555980875	NA	P-0015617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	12	545	0	ENST00000308731.7:c.119A>G	p.Tyr40Cys	p.Y40C	ENST00000308731	NM_000061.2	40	tAt/tGt	2/19	0.448264028153003	1	FACETS	0.078	0.054	0.107	0.078	0.054	0.107	INDETERMINATE	1	TRUE	0	0.793869150818983	1		545	234	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934576	NA	P-0015618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	330	701	0	ENST00000269305.4:c.818G>C	p.Arg273Pro	p.R273P	ENST00000269305	NM_001126112.2	273	cGt/cCt	8/11	0.698252343879621	1	FACETS	0.963	0.919	1	0.963	0.919	1	CLONAL	1	TRUE	0	0.698252343879621	1		701	639	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948288	71948296	+	inframe_deletion	In_Frame_Del	DEL	GCCACCCTC	GCCACCCTC	-	novel	NA	P-0015618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1354	526	867	0	ENST00000298229.2:c.3003_3011del	p.Pro1002_Pro1004del	p.P1002_P1004del	ENST00000298229	NM_001567.3	1000	gaGCCACCCTCg/gag	26/28	0.197246656976841	4	FACETS	1	0.996	1	0.68	0.651	0.711	INDETERMINATE	1	TRUE	2	0.698252343879621	4		867	1880	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	443503	443503	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	407	648	0	ENST00000399788.2:c.1394G>T	p.Gly465Val	p.G465V	ENST00000399788	NM_001042603.1	465	gGt/gTt	11/28	0.355661169388388	1	FACETS	0.808	0.772	0.844	0.808	0.772	0.844	INDETERMINATE	1	TRUE	0	0.698252343879621	1		648	939	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2132484	2132484	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	548	691	2	ENST00000219476.3:c.3862C>T	p.His1288Tyr	p.H1288Y	ENST00000219476	NM_000548.3	1288	Cac/Tac	32/42	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.698252343879621	2		693	1295	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17120454	17120454	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	445	701	0	ENST00000285071.4:c.1105C>T	p.Leu369Phe	p.L369F	ENST00000285071	NM_144997.5	369	Ctc/Ttc	10/14	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.698252343879621	2		701	1043	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566718	212566718	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762812065	NA	P-0015618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	122	297	0	ENST00000342788.4:c.1463G>A	p.Arg488Gln	p.R488Q	ENST00000342788	NM_005235.2	488	cGg/cAg	12/28	0.342102823474268	1	FACETS	0.361	0.327	0.397	0.361	0.327	0.397	INDETERMINATE	1	TRUE	0	0.698252343879621	1		297	630	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42848507	42848521	+	frameshift_variant	Frame_Shift_Del	DEL	TACAGCGTAAAGAAA	TACAGCGTAAAGAAA	AAAG	novel	NA	P-0015618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	258	617	3	ENST00000398585.3:c.821_835delinsCTTT	p.Val274AlafsTer63	p.V274Afs*63	ENST00000398585	NM_001135099.1	274	gTTTCTTTACGCTGTAta/gCTTTta	8/14	1	2	FACETS	0.717	0.672	0.764	0.717	0.672	0.764	SUBCLONAL	1	TRUE	1	0.698252343879621	2		620	1030	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0015625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	264	754	1	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	0.686307665180801	2		755	742	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0015625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	197	312	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.686307665180801	2		312	499	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0015625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	215	386	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.686307665180801	2		386	544	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572555	95572555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	105	248	1	ENST00000393063.1:c.2810G>A	p.Arg937His	p.R937H	ENST00000393063	NM_030621.3	937	cGc/cAc	19/28	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.686307665180801	2		249	301	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690832	89690836	+	frameshift_variant	Frame_Shift_Del	DEL	AATTT	AATTT	-	novel	NA	P-0015625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	176	326	0	ENST00000371953.3:c.243_247del	p.Phe81LeufsTer9	p.F81Lfs*9	ENST00000371953	NM_000314.4	80	aAATTT/a	4/9	1	2	FACETS	0.957	0.888	1	0.957	0.888	1	CLONAL	1	TRUE	1	0.686307665180801	2		326	536	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221694	36221694	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs773061649	NA	P-0015625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	421	904	0	ENST00000222270.7:c.5363C>G	p.Pro1788Arg	p.P1788R	ENST00000222270	NM_014727.1	1788	cCg/cGg	26/37	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.686307665180801	2		904	1021	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591147	67591148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	337	342	0	ENST00000274335.5:c.1742dup	p.Leu581PhefsTer21	p.L581Ffs*21	ENST00000274335		580	-/T	12/15	0.686307665180801	3	FACETS	0.964	0.92	1	0.964	0.92	1	CLONAL	2	TRUE	1	0.686307665180801	3		342	684	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	216	636	1	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.66	2		637	617	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	13	342	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.079	0.055	0.107	0.079	0.055	0.107	SUBCLONAL	1	TRUE	1	0.66	2		342	501	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28644733	28644733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	38	346	1	ENST00000241453.7:c.60G>A	p.Met20Ile	p.M20I	ENST00000241453	NM_004119.2	20	atG/atA	2/24	1	2	FACETS	0.259	0.214	0.309	0.259	0.214	0.309	SUBCLONAL	1	TRUE	1	0.66	2		347	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	114	563	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.286	0.256	0.317	0.286	0.256	0.317	SUBCLONAL	1	TRUE	1	0.66	2		564	1209	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	21	868	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.069	0.052	0.089	0.069	0.052	0.089	SUBCLONAL	1	TRUE	1	0.66	2		868	922	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	25	564	1	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	0.096	0.075	0.121	0.096	0.075	0.121	SUBCLONAL	1	TRUE	1	0.66	2		565	786	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	243	583	1	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	1	2	FACETS	0.915	0.857	0.974	0.915	0.857	0.974	CLONAL	1	TRUE	1	0.66	2		584	805	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856015	45856015	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144511865	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	62	706	0	ENST00000391945.4:c.1891C>T	p.Arg631Cys	p.R631C	ENST00000391945	NM_000400.3	631	Cgc/Tgc	20/23	1	2	FACETS	0.219	0.189	0.253	0.219	0.189	0.253	SUBCLONAL	1	TRUE	1	0.66	2		706	856	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518099	8518099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764400127	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	321	414	1	ENST00000356435.5:c.1292C>T	p.Ser431Leu	p.S431L	ENST00000356435		431	tCg/tTg	10/35	1	2	FACETS	0.983	0.943	1	1	0.997	1	CLONAL	2	TRUE	1	0.66	2		415	495	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777792	3777792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200566758	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	418	1004	2	ENST00000262367.5:c.7256C>T	p.Ala2419Val	p.A2419V	ENST00000262367	NM_004380.2	2419	gCg/gTg	31/31	1	2	FACETS	0.992	0.945	1	0.992	0.945	1	CLONAL	1	TRUE	1	0.66	2		1006	1277	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716212	52716212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555791268	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	202	385	0	ENST00000322088.6:c.656C>T	p.Ser219Leu	p.S219L	ENST00000322088	NM_014225.5	219	tCg/tTg	6/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.66	2		385	536	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188397	142188397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1169255490	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	31	396	0	ENST00000350721.4:c.6334C>T	p.Arg2112Cys	p.R2112C	ENST00000350721	NM_001184.3	2112	Cgt/Tgt	38/47	1	2	FACETS	0.198	0.159	0.241	0.198	0.159	0.241	SUBCLONAL	1	TRUE	1	0.66	2		396	475	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1485978447	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	205	452	0	ENST00000324856.7:c.5164C>T	p.Arg1722Ter	p.R1722*	ENST00000324856	NM_006015.4	1722	Cga/Tga	20/20	1	2	FACETS	0.936	0.872	1	0.936	0.872	1	CLONAL	1	TRUE	1	0.66	2		452	664	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	255	657	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.953	0.895	1	0.953	0.895	1	CLONAL	1	TRUE	1	0.66	2		657	811	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222993	5222993	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762510209	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	208	837	1	ENST00000357368.4:c.2810C>T	p.Ala937Val	p.A937V	ENST00000357368	NM_002850.3	937	gCg/gTg	18/38	1	2	FACETS	0.769	0.715	0.824	0.769	0.715	0.824	SUBCLONAL	1	TRUE	1	0.66	2		838	820	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589808	28589808	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568745490	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	219	591	0	ENST00000241453.7:c.2572G>A	p.Glu858Lys	p.E858K	ENST00000241453	NM_004119.2	858	Gaa/Aaa	21/24	1	2	FACETS	0.923	0.862	0.985	0.923	0.862	0.985	CLONAL	1	TRUE	1	0.66	2		591	719	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487277	56487277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035001455	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	263	634	0	ENST00000267101.3:c.1423C>T	p.Arg475Trp	p.R475W	ENST00000267101	NM_001982.3	475	Cgg/Tgg	12/28	1	2	FACETS	0.928	0.872	0.985	0.928	0.872	0.985	CLONAL	1	TRUE	1	0.66	2		634	859	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922301	178922301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	207	420	0	ENST00000263967.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000263967	NM_006218.2	357	cGa/cAa	6/21	1	2	FACETS	0.983	0.917	1	0.983	0.917	1	CLONAL	1	TRUE	1	0.66	2		420	638	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	174	483	0	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	1	2	FACETS	0.943	0.874	1	0.943	0.874	1	CLONAL	1	TRUE	1	0.66	2		483	559	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	148	399	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.946	0.871	1	0.946	0.871	1	CLONAL	1	TRUE	1	0.66	2		399	474	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959144	28959144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767259336	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	156	344	0	ENST00000282397.4:c.1994G>A	p.Arg665Gln	p.R665Q	ENST00000282397	NM_002019.4	665	cGa/cAa	14/30	1	2	FACETS	0.961	0.887	1	0.961	0.887	1	CLONAL	1	TRUE	1	0.66	2		344	492	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685308	89685308	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876660634	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	110	263	0	ENST00000371953.3:c.203A>G	p.Tyr68Cys	p.Y68C	ENST00000371953	NM_000314.4	68	tAc/tGc	3/9	1	2	FACETS	0.79	0.715	0.868	0.79	0.715	0.868	SUBCLONAL	1	TRUE	1	0.66	2		263	422	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041074	42041074	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	300	699	0	ENST00000219905.7:c.5452C>T	p.Arg1818Ter	p.R1818*	ENST00000219905	NM_001164273.1	1818	Cga/Tga	16/24	1	2	FACETS	0.953	0.899	1	0.953	0.899	1	CLONAL	1	TRUE	1	0.66	2		699	954	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	307	284	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	1	0.964	1	1	0.996	1	CLONAL	2	TRUE	1	0.66	2		284	463	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850704	63850705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	202	404	0	ENST00000279873.7:c.1489dup	p.Ile497AsnfsTer31	p.I497Nfs*31	ENST00000279873	NM_032199.2	494	-/A	10/10	1	2	FACETS	0.89	0.828	0.953	0.89	0.828	0.953	CLONAL	1	TRUE	1	0.66	2		404	688	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441970	40441970	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1406350203	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	44	747	2	ENST00000345506.4:c.215C>T	p.Ala72Val	p.A72V	ENST00000345506	NM_003152.3	72	gCg/gTg	4/20	1	2	FACETS	0.159	0.132	0.188	0.159	0.132	0.188	SUBCLONAL	1	TRUE	1	0.66	2		749	840	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637690	52637690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239654517	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	246	399	0	ENST00000394830.3:c.2626C>T	p.Arg876Cys	p.R876C	ENST00000394830	NM_018313.4	876	Cgt/Tgt	18/30	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.66	2		399	707	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291828	15291828	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376187165	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	317	861	3	ENST00000263388.2:c.2938G>A	p.Ala980Thr	p.A980T	ENST00000263388	NM_000435.2	980	Gcc/Acc	18/33	1	2	FACETS	0.978	0.925	1	0.978	0.925	1	CLONAL	1	TRUE	1	0.66	2		864	982	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468024	50468024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	28	449	0	ENST00000331340.3:c.1259C>T	p.Pro420Leu	p.P420L	ENST00000331340	NM_006060.4	420	cCg/cTg	8/8	1	2	FACETS	0.155	0.123	0.191	0.155	0.123	0.191	SUBCLONAL	1	TRUE	1	0.66	2		449	549	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543826	212543826	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775988789	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	59	555	0	ENST00000342788.4:c.1573C>T	p.Arg525Cys	p.R525C	ENST00000342788	NM_005235.2	525	Cgc/Tgc	13/28	1	2	FACETS	0.23	0.197	0.266	0.23	0.197	0.266	SUBCLONAL	1	TRUE	1	0.66	2		555	776	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950648	38950648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776074870	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	12	370	0	ENST00000357387.3:c.3302C>T	p.Ser1101Leu	p.S1101L	ENST00000357387	NM_152756.3	1101	tCg/tTg	31/38	1	2	FACETS	0.091	0.063	0.125	0.091	0.063	0.125	SUBCLONAL	1	TRUE	1	0.66	2		370	399	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674233	86674233	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1463885690	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	176	418	0	ENST00000274376.6:c.2365C>T	p.Arg789Ter	p.R789*	ENST00000274376	NM_002890.2	789	Cga/Tga	18/25	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.66	2		418	493	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692802	89692802	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123320	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	46	411	0	ENST00000371953.3:c.286C>T	p.Pro96Ser	p.P96S	ENST00000371953	NM_000314.4	96	Cca/Tca	5/9	1	2	FACETS	0.293	0.247	0.345	0.293	0.247	0.345	SUBCLONAL	1	TRUE	1	0.66	2		411	475	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	283	601	2	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.66	2		603	821	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39570433	39570433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747825815	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	82	135	0	ENST00000262039.4:c.629G>A	p.Arg210Gln	p.R210Q	ENST00000262039	NM_002647.2	210	cGa/cAa	6/25	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.66	2		135	190	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254839	16254839	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	61	565	0	ENST00000375759.3:c.2104C>T	p.Arg702Ter	p.R702*	ENST00000375759	NM_015001.2	702	Cga/Tga	11/15	1	2	FACETS	0.203	0.174	0.235	0.203	0.174	0.235	SUBCLONAL	1	TRUE	1	0.66	2		565	910	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976165	7976165	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	199	656	0	ENST00000319144.4:c.2030G>A	p.Arg677His	p.R677H	ENST00000319144	NM_001139.2	677	cGc/cAc	15/15	1	2	FACETS	0.665	0.616	0.715	0.665	0.616	0.715	SUBCLONAL	1	TRUE	1	0.66	2		656	907	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539690	187539690	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs748166431	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	163	381	0	ENST00000441802.2:c.8050G>T	p.Glu2684Ter	p.E2684*	ENST00000441802	NM_005245.3	2684	Gaa/Taa	10/27	1	2	FACETS	0.996	0.921	1	0.996	0.921	1	CLONAL	1	TRUE	1	0.66	2		381	496	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456962	149456962	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764483518	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	37	498	1	ENST00000286301.3:c.766C>T	p.Arg256Cys	p.R256C	ENST00000286301	NM_005211.3	256	Cgt/Tgt	6/22	1	2	FACETS	0.179	0.146	0.215	0.179	0.146	0.215	SUBCLONAL	1	TRUE	1	0.66	2		499	628	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155749	106155749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	125	419	0	ENST00000380013.4:c.650C>T	p.Ser217Phe	p.S217F	ENST00000380013	NM_001127208.2	217	tCc/tTc	3/11	1	2	FACETS	0.652	0.592	0.715	0.652	0.592	0.715	SUBCLONAL	1	TRUE	1	0.66	2		419	581	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830931	72830931	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	189	365	0	ENST00000268489.5:c.5650G>T	p.Glu1884Ter	p.E1884*	ENST00000268489	NM_006885.3	1884	Gaa/Taa	9/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.66	2		365	464	SUCCESS
ATR	545	MSKCC	GRCh37	3	142234346	142234346	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	169	409	1	ENST00000350721.4:c.4394C>A	p.Ser1465Tyr	p.S1465Y	ENST00000350721	NM_001184.3	1465	tCt/tAt	25/47	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.66	2		410	506	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506185	148506185	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747933788	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	269	567	1	ENST00000320356.2:c.2173G>A	p.Glu725Lys	p.E725K	ENST00000320356	NM_004456.4	725	Gaa/Aaa	19/20	1	2	FACETS	0.917	0.862	0.973	0.917	0.862	0.973	CLONAL	1	TRUE	1	0.66	2		568	889	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633825	86633825	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	154	357	1	ENST00000274376.6:c.934G>T	p.Glu312Ter	p.E312*	ENST00000274376	NM_002890.2	312	Gaa/Taa	5/25	1	2	FACETS	0.993	0.916	1	0.993	0.916	1	CLONAL	1	TRUE	1	0.66	2		358	470	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159099	143159099	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1332432216	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	203	536	2	ENST00000262992.4:c.754C>T	p.Arg252Ter	p.R252*	ENST00000262992	NM_001101669.1	252	Cga/Tga	10/24	1	2	FACETS	0.983	0.916	1	0.983	0.916	1	CLONAL	1	TRUE	1	0.66	2		538	626	SUCCESS
APC	324	MSKCC	GRCh37	5	112178781	112178781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141010008	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	199	495	0	ENST00000257430.4:c.7490C>T	p.Ser2497Leu	p.S2497L	ENST00000257430	NM_000038.5	2497	tCg/tTg	16/16	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.66	2		495	603	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421355	12421355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777334819	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	369	895	0	ENST00000287820.6:c.235G>A	p.Glu79Lys	p.E79K	ENST00000287820	NM_015869.4	79	Gaa/Aaa	2/7	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.66	2		895	1092	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778917	9778917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774975013	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	197	681	0	ENST00000377346.4:c.1186G>A	p.Ala396Thr	p.A396T	ENST00000377346	NM_005026.3	396	Gcc/Acc	9/24	1	2	FACETS	0.652	0.604	0.702	0.652	0.604	0.702	SUBCLONAL	1	TRUE	1	0.66	2		681	916	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184568	11184568	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	239	575	0	ENST00000361445.4:c.6649C>T	p.Arg2217Trp	p.R2217W	ENST00000361445	NM_004958.3	2217	Cgg/Tgg	47/58	1	2	FACETS	0.876	0.82	0.933	0.876	0.82	0.933	CLONAL	1	TRUE	1	0.66	2		575	827	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258070	16258070	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140024761	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	47	457	0	ENST00000375759.3:c.5335G>A	p.Ala1779Thr	p.A1779T	ENST00000375759	NM_015001.2	1779	Gcc/Acc	11/15	1	2	FACETS	0.264	0.222	0.31	0.264	0.222	0.31	SUBCLONAL	1	TRUE	1	0.66	2		457	540	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321242	65321242	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761801070	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	192	558	4	ENST00000342505.4:c.1598C>T	p.Thr533Met	p.T533M	ENST00000342505	NM_002227.2	533	aCg/aTg	11/25	1	2	FACETS	0.867	0.805	0.931	0.867	0.805	0.931	CLONAL	1	TRUE	1	0.66	2		562	671	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466386	120466386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751299682	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	164	530	0	ENST00000256646.2:c.4733G>A	p.Arg1578His	p.R1578H	ENST00000256646	NM_024408.3	1578	cGc/cAc	26/34	1	2	FACETS	0.652	0.6	0.707	0.652	0.6	0.707	SUBCLONAL	1	TRUE	1	0.66	2		530	762	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120496169	120496169	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	235	523	0	ENST00000256646.2:c.2362A>G	p.Lys788Glu	p.K788E	ENST00000256646	NM_024408.3	788	Aaa/Gaa	14/34	1	2	FACETS	0.92	0.861	0.98	0.92	0.861	0.98	CLONAL	1	TRUE	1	0.66	2		523	774	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874167	155874167	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	60	684	3	ENST00000368323.3:c.364C>T	p.Arg122Ter	p.R122*	ENST00000368323	NM_006912.5	122	Cga/Tga	5/6	1	2	FACETS	0.166	0.142	0.192	0.166	0.142	0.192	SUBCLONAL	1	TRUE	1	0.66	2		687	1096	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226574031	226574031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201975538	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	36	337	0	ENST00000366794.5:c.830C>T	p.Ser277Leu	p.S277L	ENST00000366794	NM_001618.3	277	tCg/tTg	6/23	1	2	FACETS	0.233	0.191	0.28	0.233	0.191	0.28	SUBCLONAL	1	TRUE	1	0.66	2		337	468	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246078935	246078935	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	49	444	0	ENST00000388985.4:c.710T>A	p.Ile237Asn	p.I237N	ENST00000388985		237	aTc/aAc	8/12	1	2	FACETS	0.234	0.197	0.274	0.234	0.197	0.274	SUBCLONAL	1	TRUE	1	0.66	2		444	635	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149280	119149280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs991981291	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	179	630	2	ENST00000264033.4:c.1288G>A	p.Val430Met	p.V430M	ENST00000264033	NM_005188.3	430	Gtg/Atg	9/16	1	2	FACETS	0.588	0.542	0.636	0.588	0.542	0.636	SUBCLONAL	1	TRUE	1	0.66	2		632	923	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419075	419075	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	212	482	0	ENST00000399788.2:c.3272A>C	p.Lys1091Thr	p.K1091T	ENST00000399788	NM_001042603.1	1091	aAa/aCa	22/28	1	2	FACETS	0.909	0.847	0.971	0.909	0.847	0.971	CLONAL	1	TRUE	1	0.66	2		482	707	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	422358	422358	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs371715765	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	32	389	1	ENST00000399788.2:c.2900C>T	p.Pro967Leu	p.P967L	ENST00000399788	NM_001042603.1	967	cCg/cTg	20/28	1	2	FACETS	0.208	0.168	0.253	0.208	0.168	0.253	SUBCLONAL	1	TRUE	1	0.66	2		390	466	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	443476	443476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	282	610	1	ENST00000399788.2:c.1421G>A	p.Gly474Glu	p.G474E	ENST00000399788	NM_001042603.1	474	gGa/gAa	11/28	1	2	FACETS	0.995	0.938	1	0.995	0.938	1	CLONAL	1	TRUE	1	0.66	2		611	859	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246557	46246557	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161560614	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	104	196	0	ENST00000334344.6:c.4651G>A	p.Ala1551Thr	p.A1551T	ENST00000334344	NM_152641.2	1551	Gca/Aca	15/21	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.66	2		196	303	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443497	49443497	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762841102	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	197	443	0	ENST00000301067.7:c.3874C>T	p.Arg1292Cys	p.R1292C	ENST00000301067	NM_003482.3	1292	Cgc/Tgc	11/54	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.66	2		443	594	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588695	28588695	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	124	350	1	ENST00000241453.7:c.2754-1G>T		p.X918_splice	ENST00000241453	NM_004119.2	918			1	2	FACETS	0.899	0.82	0.98	0.899	0.82	0.98	CLONAL	1	TRUE	1	0.66	2		351	418	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914641	32914641	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs767873595	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	215	539	0	ENST00000380152.3:c.6149T>C	p.Val2050Ala	p.V2050A	ENST00000380152		2050	gTa/gCa	11/27	1	2	FACETS	0.968	0.904	1	0.968	0.904	1	CLONAL	1	TRUE	1	0.66	2		539	673	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609979	81609979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	94	292	0	ENST00000298171.2:c.1577C>T	p.Ala526Val	p.A526V	ENST00000298171	NM_000369.2	526	gCc/gTc	10/10	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.66	2		292	269	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582846	95582846	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	21	268	0	ENST00000393063.1:c.1696A>G	p.Thr566Ala	p.T566A	ENST00000393063	NM_030621.3	566	Aca/Gca	11/28	1	2	FACETS	0.153	0.117	0.195	0.153	0.117	0.195	SUBCLONAL	1	TRUE	1	0.66	2		268	416	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643320	38643320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	116	445	0	ENST00000299084.4:c.790C>T	p.Pro264Ser	p.P264S	ENST00000299084	NM_152594.2	264	Cct/Tct	7/7	1	2	FACETS	0.605	0.547	0.666	0.605	0.547	0.666	SUBCLONAL	1	TRUE	1	0.66	2		445	581	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643619	38643619	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs140225135	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	38	528	0	ENST00000299084.4:c.1089A>G	p.Ile363Met	p.I363M	ENST00000299084	NM_152594.2	363	atA/atG	7/7	1	2	FACETS	0.181	0.149	0.217	0.181	0.149	0.217	SUBCLONAL	1	TRUE	1	0.66	2		528	636	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41001250	41001250	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	288	556	0	ENST00000267868.3:c.371A>C	p.Glu124Ala	p.E124A	ENST00000267868	NM_002875.4	124	gAa/gCa	5/10	1	2	FACETS	0.994	0.938	1	0.994	0.938	1	CLONAL	1	TRUE	1	0.66	2		556	878	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961459	41961459	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	176	433	0	ENST00000219905.7:c.367C>A	p.Leu123Ile	p.L123I	ENST00000219905	NM_001164273.1	123	Ctt/Att	2/24	1	2	FACETS	0.937	0.869	1	0.937	0.869	1	CLONAL	1	TRUE	1	0.66	2		433	569	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042593	42042593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	185	476	0	ENST00000219905.7:c.6788G>A	p.Ser2263Asn	p.S2263N	ENST00000219905	NM_001164273.1	2263	aGc/aAc	17/24	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.66	2		476	535	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801726	3801726	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs587783483	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	49	425	0	ENST00000262367.5:c.3779+1G>A		p.X1260_splice	ENST00000262367	NM_004380.2	1260			1	2	FACETS	0.235	0.198	0.275	0.235	0.198	0.275	SUBCLONAL	1	TRUE	1	0.66	2		425	632	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953115	81953115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1336595726	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	63	283	0	ENST00000359376.3:c.2081G>A	p.Arg694His	p.R694H	ENST00000359376	NM_002661.3	694	cGc/cAc	20/33	1	2	FACETS	0.441	0.382	0.504	0.441	0.382	0.504	SUBCLONAL	1	TRUE	1	0.66	2		283	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577111	7577111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	311	857	0	ENST00000269305.4:c.827C>T	p.Ala276Val	p.A276V	ENST00000269305	NM_001126112.2	276	gCc/gTc	8/11	1	2	FACETS	0.774	0.73	0.82	0.774	0.73	0.82	SUBCLONAL	1	TRUE	1	0.66	2		857	1217	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8111118	8111118	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780771169	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	209	784	1	ENST00000585124.1:c.89G>A	p.Arg30Gln	p.R30Q	ENST00000585124	NM_004217.3	30	cGg/cAg	3/9	1	2	FACETS	0.699	0.649	0.75	0.699	0.649	0.75	SUBCLONAL	1	TRUE	1	0.66	2		785	906	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984693	11984693	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	128	319	0	ENST00000353533.5:c.239G>A	p.Ser80Asn	p.S80N	ENST00000353533	NM_003010.3	80	aGc/aAc	3/11	1	2	FACETS	0.9	0.822	0.98	0.9	0.822	0.98	CLONAL	1	TRUE	1	0.66	2		319	431	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942779	15942779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202234006	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	302	633	1	ENST00000268712.3:c.6923G>A	p.Arg2308Gln	p.R2308Q	ENST00000268712	NM_006311.3	2308	cGa/cAa	44/46	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.66	2		634	810	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873597	37873597	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	88	734	1	ENST00000269571.5:c.1762G>A	p.Ala588Thr	p.A588T	ENST00000269571		588	Gcc/Acc	15/27	1	2	FACETS	0.252	0.222	0.284	0.252	0.222	0.284	SUBCLONAL	1	TRUE	1	0.66	2		735	1059	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47684730	47684730	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	183	535	2	ENST00000347630.2:c.719G>A	p.Arg240Gln	p.R240Q	ENST00000347630	NM_001007230.1	240	cGa/cAa	9/11	1	2	FACETS	0.992	0.922	1	0.992	0.922	1	CLONAL	1	TRUE	1	0.66	2		537	559	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55335665	55335665	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	350	739	0	ENST00000284073.2:c.220A>C	p.Ser74Arg	p.S74R	ENST00000284073	NM_138962.2	74	Agt/Cgt	4/14	1	2	FACETS	0.943	0.893	0.993	0.943	0.893	0.993	CLONAL	1	TRUE	1	0.66	2		739	1125	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492900	56492900	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	21	254	0	ENST00000407977.2:c.39G>A	p.Trp13Ter	p.W13*	ENST00000407977		13	tgG/tgA	2/10	1	2	FACETS	0.203	0.156	0.257	0.203	0.156	0.257	SUBCLONAL	1	TRUE	1	0.66	2		254	314	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533850	63533850	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	119	546	0	ENST00000307078.5:c.1304C>T	p.Pro435Leu	p.P435L	ENST00000307078	NM_004655.3	435	cCg/cTg	6/11	1	2	FACETS	0.58	0.524	0.638	0.58	0.524	0.638	SUBCLONAL	1	TRUE	1	0.66	2		546	622	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78854267	78854267	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	42	574	0	ENST00000306801.3:c.1562T>C	p.Val521Ala	p.V521A	ENST00000306801	NM_020761.2	521	gTc/gCc	14/34	1	2	FACETS	0.165	0.137	0.197	0.165	0.137	0.197	SUBCLONAL	1	TRUE	1	0.66	2		574	770	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115015	3115015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	209	844	1	ENST00000078429.4:c.550G>A	p.Val184Met	p.V184M	ENST00000078429	NM_002067.2	184	Gtg/Atg	4/7	1	2	FACETS	0.589	0.546	0.633	0.589	0.546	0.633	SUBCLONAL	1	TRUE	1	0.66	2		845	1075	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134269	11134269	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	199	637	1	ENST00000358026.2:c.2935C>T	p.Arg979Ter	p.R979*	ENST00000358026	NM_001128849.1	979	Cga/Tga	20/36	1	2	FACETS	0.607	0.562	0.653	0.607	0.562	0.653	SUBCLONAL	1	TRUE	1	0.66	2		638	994	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950322	17950322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	310	887	0	ENST00000458235.1:c.1405G>A	p.Val469Met	p.V469M	ENST00000458235	NM_000215.3	469	Gtg/Atg	10/24	1	2	FACETS	0.932	0.88	0.985	0.932	0.88	0.985	CLONAL	1	TRUE	1	0.66	2		887	1008	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228011	36228011	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	273	707	0	ENST00000222270.7:c.7397G>A	p.Gly2466Asp	p.G2466D	ENST00000222270	NM_014727.1	2466	gGc/gAc	33/37	1	2	FACETS	0.978	0.921	1	0.978	0.921	1	CLONAL	1	TRUE	1	0.66	2		707	846	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741000	40741000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	307	798	1	ENST00000392038.2:c.1318G>A	p.Asp440Asn	p.D440N	ENST00000392038	NM_001626.4	440	Gat/Aat	13/14	1	2	FACETS	0.897	0.847	0.949	0.897	0.847	0.949	CLONAL	1	TRUE	1	0.66	2		799	1037	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082460	16082460	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	341	843	1	ENST00000281043.3:c.274G>A	p.Ala92Thr	p.A92T	ENST00000281043	NM_005378.4	92	Gcc/Acc	2/3	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.66	2		844	937	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143096	30143096	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	184	836	0	ENST00000389048.3:c.430G>A	p.Glu144Lys	p.E144K	ENST00000389048	NM_004304.4	144	Gag/Aag	1/29	1	2	FACETS	0.599	0.553	0.647	0.599	0.553	0.647	SUBCLONAL	1	TRUE	1	0.66	2		836	931	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47710056	47710056	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	143	302	0	ENST00000233146.2:c.2773G>T	p.Glu925Ter	p.E925*	ENST00000233146	NM_000251.2	925	Gaa/Taa	16/16	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.66	2		302	410	SUCCESS
REL	5966	MSKCC	GRCh37	2	61121667	61121667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs955883570	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	190	545	0	ENST00000295025.8:c.289C>T	p.Arg97Cys	p.R97C	ENST00000295025	NM_002908.2	97	Cgc/Tgc	3/11	1	2	FACETS	0.89	0.826	0.955	0.89	0.826	0.955	CLONAL	1	TRUE	1	0.66	2		545	647	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726907	61726907	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	215	508	0	ENST00000401558.2:c.531A>C	p.Glu177Asp	p.E177D	ENST00000401558	NM_003400.3	177	gaA/gaC	7/25	1	2	FACETS	0.958	0.895	1	0.958	0.895	1	CLONAL	1	TRUE	1	0.66	2		508	680	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128018835	128018835	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	273	586	0	ENST00000285398.2:c.2033G>T	p.Arg678Ile	p.R678I	ENST00000285398	NM_000122.1	678	aGa/aTa	13/15	1	2	FACETS	0.987	0.93	1	0.987	0.93	1	CLONAL	1	TRUE	1	0.66	2		586	838	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038147	128038147	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144012336	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	43	474	1	ENST00000285398.2:c.1403C>T	p.Ala468Val	p.A468V	ENST00000285398	NM_000122.1	468	gCg/gTg	9/15	1	2	FACETS	0.179	0.149	0.212	0.179	0.149	0.212	SUBCLONAL	1	TRUE	1	0.66	2		475	728	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096729	178096729	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	24	240	0	ENST00000397062.3:c.602A>G	p.Asn201Ser	p.N201S	ENST00000397062	NM_006164.4	201	aAt/aGt	5/5	1	2	FACETS	0.193	0.151	0.242	0.193	0.151	0.242	SUBCLONAL	1	TRUE	1	0.66	2		240	377	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257104	198257104	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs759773104	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	245	540	0	ENST00000335508.6:c.3838C>G	p.Leu1280Val	p.L1280V	ENST00000335508	NM_012433.2	1280	Ctc/Gtc	25/25	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.66	2		540	716	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663333	227663333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747512782	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	160	389	0	ENST00000305123.5:c.122C>T	p.Pro41Leu	p.P41L	ENST00000305123	NM_005544.2	41	cCg/cTg	1/2	1	2	FACETS	0.954	0.881	1	0.954	0.881	1	CLONAL	1	TRUE	1	0.66	2		389	508	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39706263	39706263	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	129	239	0	ENST00000361337.2:c.321A>C	p.Glu107Asp	p.E107D	ENST00000361337	NM_003286.2	107	gaA/gaC	5/21	1	2	FACETS	0.99	0.906	1	0.99	0.906	1	CLONAL	1	TRUE	1	0.66	2		239	395	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728847	39728847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	173	435	0	ENST00000361337.2:c.1127G>A	p.Arg376Gln	p.R376Q	ENST00000361337	NM_003286.2	376	cGa/cAa	12/21	1	2	FACETS	0.901	0.834	0.97	0.901	0.834	0.97	CLONAL	1	TRUE	1	0.66	2		435	582	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733274	40733274	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	243	593	1	ENST00000373198.4:c.3532C>T	p.Leu1178Phe	p.L1178F	ENST00000373198	NM_133170.3	1178	Ctc/Ttc	26/32	0.3	1	FACETS	0.726	0.682	0.77	0.726	0.682	0.77	INDETERMINATE	1	TRUE	0	0.66	1		594	680	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306793	41306793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	101	269	0	ENST00000373198.4:c.866C>T	p.Pro289Leu	p.P289L	ENST00000373198	NM_133170.3	289	cCc/cTc	7/32	0.3	1	FACETS	0.649	0.587	0.713	0.649	0.587	0.713	INDETERMINATE	1	TRUE	0	0.66	1		269	316	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574025	41574025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375274986	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	126	501	0	ENST00000263253.7:c.6310C>T	p.Pro2104Ser	p.P2104S	ENST00000263253	NM_001429.3	2104	Cct/Tct	31/31	1	2	FACETS	0.712	0.648	0.78	0.712	0.648	0.78	SUBCLONAL	1	TRUE	1	0.66	2		501	536	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12629121	12629121	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	191	354	0	ENST00000251849.4:c.1386G>T	p.Lys462Asn	p.K462N	ENST00000251849	NM_002880.3	462	aaG/aaT	13/17	1	2	FACETS	0.996	0.927	1	0.996	0.927	1	CLONAL	1	TRUE	1	0.66	2		354	581	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280137	142280137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs986166179	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	216	523	0	ENST00000350721.4:c.1297C>T	p.Arg433Cys	p.R433C	ENST00000350721	NM_001184.3	433	Cgt/Tgt	5/47	1	2	FACETS	0.939	0.877	1	0.939	0.877	1	CLONAL	1	TRUE	1	0.66	2		523	697	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1918681	1918681	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1033486520	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	262	533	0	ENST00000382891.5:c.844G>A	p.Val282Ile	p.V282I	ENST00000382891	NM_133335.3	282	Gta/Ata	4/22	1	2	FACETS	0.875	0.822	0.93	0.875	0.822	0.93	CLONAL	1	TRUE	1	0.66	2		533	907	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1952854	1952854	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	292	713	0	ENST00000382891.5:c.1937A>G	p.Glu646Gly	p.E646G	ENST00000382891	NM_133335.3	646	gAa/gGa	10/22	1	2	FACETS	0.98	0.924	1	0.98	0.924	1	CLONAL	1	TRUE	1	0.66	2		713	903	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230755	66230755	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	100	386	0	ENST00000273854.3:c.2216T>G	p.Leu739Ter	p.L739*	ENST00000273854	NM_004439.5	739	tTa/tGa	12/18	1	2	FACETS	0.842	0.759	0.928	0.842	0.759	0.928	CLONAL	1	TRUE	1	0.66	2		386	360	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190845	106190845	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	190	498	0	ENST00000380013.4:c.4123T>G	p.Leu1375Val	p.L1375V	ENST00000380013	NM_001127208.2	1375	Ttg/Gtg	9/11	1	2	FACETS	0.795	0.737	0.855	0.795	0.737	0.855	SUBCLONAL	1	TRUE	1	0.66	2		498	724	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114277	143114277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs76891221	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	125	436	0	ENST00000262992.4:c.1144C>T	p.Arg382Trp	p.R382W	ENST00000262992	NM_001101669.1	382	Cgg/Tgg	13/24	1	2	FACETS	0.811	0.739	0.886	0.811	0.739	0.886	CLONAL	1	TRUE	1	0.66	2		436	467	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519169	187519169	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	199	631	1	ENST00000441802.2:c.12214G>T	p.Gly4072Ter	p.G4072*	ENST00000441802	NM_005245.3	4072	Gga/Tga	23/27	1	2	FACETS	0.651	0.603	0.701	0.651	0.603	0.701	SUBCLONAL	1	TRUE	1	0.66	2		632	926	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183276	56183276	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	242	474	0	ENST00000399503.3:c.4186G>A	p.Ala1396Thr	p.A1396T	ENST00000399503	NM_005921.1	1396	Gca/Aca	18/20	1	2	FACETS	0.9	0.843	0.958	0.9	0.843	0.958	CLONAL	1	TRUE	1	0.66	2		474	815	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679577	86679577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	222	462	0	ENST00000274376.6:c.2738G>A	p.Arg913Gln	p.R913Q	ENST00000274376	NM_002890.2	913	cGg/cAg	21/25	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.66	2		462	672	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636964	176636964	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	46	660	0	ENST00000439151.2:c.1564A>G	p.Lys522Glu	p.K522E	ENST00000439151	NM_022455.4	522	Aaa/Gaa	5/23	1	2	FACETS	0.155	0.13	0.183	0.155	0.13	0.183	SUBCLONAL	1	TRUE	1	0.66	2		660	899	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109315802	109315802	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	257	584	0	ENST00000436639.2:c.983C>A	p.Ser328Tyr	p.S328Y	ENST00000436639	NM_014454.2	328	tCt/tAt	6/10	1	2	FACETS	0.953	0.895	1	0.953	0.895	1	CLONAL	1	TRUE	1	0.66	2		584	817	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662700	117662700	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	188	395	0	ENST00000368508.3:c.4765G>T	p.Glu1589Ter	p.E1589*	ENST00000368508	NM_002944.2	1589	Gaa/Taa	29/43	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.66	2		395	523	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663630	117663630	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	220	440	0	ENST00000368508.3:c.4602T>A	p.Asn1534Lys	p.N1534K	ENST00000368508	NM_002944.2	1534	aaT/aaA	28/43	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.66	2		440	584	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117684001	117684001	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	198	430	0	ENST00000368508.3:c.3146T>C	p.Ile1049Thr	p.I1049T	ENST00000368508	NM_002944.2	1049	aTa/aCa	21/43	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.66	2		430	570	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138201339	138201339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	209	481	1	ENST00000237289.4:c.2038G>A	p.Glu680Lys	p.E680K	ENST00000237289	NM_001270507.1	680	Gaa/Aaa	8/9	1	2	FACETS	0.937	0.874	1	0.937	0.874	1	CLONAL	1	TRUE	1	0.66	2		482	676	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979480	2979480	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	297	644	0	ENST00000396946.4:c.767A>G	p.Asp256Gly	p.D256G	ENST00000396946	NM_032415.4	256	gAc/gGc	6/25	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.66	2		644	866	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984061	2984061	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	151	414	1	ENST00000396946.4:c.469C>T	p.Arg157Trp	p.R157W	ENST00000396946	NM_032415.4	157	Cgg/Tgg	5/25	1	2	FACETS	0.868	0.799	0.94	0.868	0.799	0.94	CLONAL	1	TRUE	1	0.66	2		415	527	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374362	81374362	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1224184344	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	158	387	0	ENST00000222390.5:c.700C>T	p.Arg234Cys	p.R234C	ENST00000222390	NM_000601.4	234	Cgc/Tgc	6/18	1	2	FACETS	0.903	0.833	0.976	0.903	0.833	0.976	CLONAL	1	TRUE	1	0.66	2		387	530	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509661	106509661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1182076194	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	230	612	0	ENST00000359195.3:c.1655G>A	p.Arg552His	p.R552H	ENST00000359195	NM_002649.2	552	cGc/cAc	2/11	1	2	FACETS	0.951	0.89	1	0.951	0.89	1	CLONAL	1	TRUE	1	0.66	2		612	733	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852216	128852216	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167098287	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	71	863	0	ENST00000249373.3:c.2288G>A	p.Arg763Gln	p.R763Q	ENST00000249373	NM_005631.4	763	cGa/cAa	12/12	1	2	FACETS	0.224	0.195	0.256	0.224	0.195	0.256	SUBCLONAL	1	TRUE	1	0.66	2		863	961	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878446	151878446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367881455	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	59	639	1	ENST00000262189.6:c.6499C>T	p.Arg2167Trp	p.R2167W	ENST00000262189	NM_170606.2	2167	Cgg/Tgg	36/59	1	2	FACETS	0.179	0.153	0.208	0.179	0.153	0.208	SUBCLONAL	1	TRUE	1	0.66	2		640	997	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56910960	56910960	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	212	670	1	ENST00000519728.1:c.1106G>A	p.Arg369Gln	p.R369Q	ENST00000519728	NM_002350.3	369	cGa/cAa	11/13	1	2	FACETS	0.649	0.603	0.697	0.649	0.603	0.697	SUBCLONAL	1	TRUE	1	0.66	2		671	990	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069580	69069580	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	206	562	0	ENST00000288368.4:c.4255T>C	p.Tyr1419His	p.Y1419H	ENST00000288368	NM_024870.2	1419	Tat/Cat	35/40	1	2	FACETS	0.959	0.894	1	0.959	0.894	1	CLONAL	1	TRUE	1	0.66	2		562	651	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572568	141572568	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	49	513	0	ENST00000220592.5:c.502C>T	p.His168Tyr	p.H168Y	ENST00000220592	NM_012154.3	168	Cac/Tac	4/19	1	2	FACETS	0.228	0.193	0.267	0.228	0.193	0.267	SUBCLONAL	1	TRUE	1	0.66	2		513	651	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409497	80409497	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	283	645	0	ENST00000286548.4:c.617T>C	p.Val206Ala	p.V206A	ENST00000286548	NM_002072.3	206	gTa/gCa	5/7	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.66	2		645	853	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128420050	128420050	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	222	689	0	ENST00000265960.3:c.378A>C	p.Lys126Asn	p.K126N	ENST00000265960	NM_001006617.1	126	aaA/aaC	4/12	1	2	FACETS	0.933	0.872	0.996	0.933	0.872	0.996	CLONAL	1	TRUE	1	0.66	2		689	721	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750269	133750269	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	199	465	0	ENST00000318560.5:c.1100G>A	p.Arg367Gln	p.R367Q	ENST00000318560	NM_005157.4	367	cGa/cAa	7/11	1	2	FACETS	0.941	0.876	1	0.941	0.876	1	CLONAL	1	TRUE	1	0.66	2		465	641	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928873	44928873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376210390	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	41	425	0	ENST00000377967.4:c.1973G>A	p.Arg658Gln	p.R658Q	ENST00000377967	NM_021140.2	658	cGa/cAa	17/29	0.3	2	FACETS	0.205	0.17	0.244			1	INDETERMINATE	1	TRUE	NA	0.66	2		425	607	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430353	47430353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773486607	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	77	812	1	ENST00000377045.4:c.1628G>A	p.Arg543Gln	p.R543Q	ENST00000377045	NM_001654.4	543	cGg/cAg	15/16	1	2	FACETS	0.247	0.216	0.28	0.247	0.216	0.28	SUBCLONAL	1	TRUE	1	0.66	2		813	945	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650810	48650810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	64	967	1	ENST00000376670.3:c.679G>A	p.Ala227Thr	p.A227T	ENST00000376670	NM_002049.3	227	Gcc/Acc	4/6	1	2	FACETS	0.171	0.147	0.197	0.171	0.147	0.197	SUBCLONAL	1	TRUE	1	0.66	2		968	1133	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245264	53245264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782773030	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	255	625	1	ENST00000375401.3:c.773G>A	p.Arg258Gln	p.R258Q	ENST00000375401	NM_004187.3	258	cGg/cAg	6/26	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.66	2		626	749	SUCCESS
AR	367	MSKCC	GRCh37	X	66765929	66765929	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	294	800	0	ENST00000374690.3:c.941G>T	p.Gly314Val	p.G314V	ENST00000374690	NM_000044.3	314	gGa/gTa	1/8	1	2	FACETS	0.968	0.914	1	0.968	0.914	1	CLONAL	1	TRUE	1	0.66	2		800	920	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344062	70344062	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	239	871	0	ENST00000374080.3:c.1798T>C	p.Phe600Leu	p.F600L	ENST00000374080		600	Ttc/Ctc	13/45	1	2	FACETS	0.677	0.632	0.724	0.677	0.632	0.724	SUBCLONAL	1	TRUE	1	0.66	2		871	1070	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0015627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	132	467	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	0.237052905185478	1	FACETS	0.732	0.665	0.803	0.732	0.665	0.803	SUBCLONAL	1	TRUE	0	0.365334765787429	1		467	807	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942124	71942124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1179	127	915	0	ENST00000298229.2:c.1388C>T	p.Pro463Leu	p.P463L	ENST00000298229	NM_001567.3	463	cCc/cTc	12/28	0.237052905185478	1	FACETS	0.435	0.393	0.48	0.435	0.393	0.48	SUBCLONAL	1	TRUE	0	0.365334765787429	1		915	1306	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40874888	40874888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	196	752	0	ENST00000428826.2:c.412G>A	p.Glu138Lys	p.E138K	ENST00000428826		138	Gaa/Aaa	6/21	1	2	FACETS	0.907	0.838	0.979	0.907	0.838	0.979	CLONAL	1	TRUE	1	0.365334765787429	2		752	1183	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099406	157099426	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAGCAA	CAGCAGCAGCAGCAGCAGCAA	-	rs762617219	NA	P-0015628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	68	385	0	ENST00000346085.5:c.363_383del	p.Gln125_Gln131del	p.Q125_Q131del	ENST00000346085	NM_020732.3	115	CAGCAGCAGCAGCAGCAGCAA/-	1/20	0.342153184045065	3	FACETS	0.308	0.267	0.352	0.103	0.089	0.118	INDETERMINATE	1	TRUE	0	0.76294917453858	3		385	800	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs786203436	NA	P-0015628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	528	831	0	ENST00000269305.4:c.487T>A	p.Tyr163Asn	p.Y163N	ENST00000269305	NM_001126112.2	163	Tac/Aac	5/11	0.704975959506123	1	FACETS	0.99	0.957	1	0.99	0.957	1	CLONAL	1	TRUE	0	0.76294917453858	1		831	865	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513182	106513182	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	53	254	2	ENST00000359195.3:c.2089del	p.Trp697GlyfsTer3	p.W697Gfs*3	ENST00000359195	NM_002649.2	696	Ttt/tt	4/11	0.418985558881287	1	FACETS	0.193	0.164	0.224	0.193	0.164	0.224	INDETERMINATE	1	TRUE	0	0.76294917453858	1		256	446	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513200	106513200	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	61	282	0	ENST00000359195.3:c.2104G>C	p.Glu702Gln	p.E702Q	ENST00000359195	NM_002649.2	702	Gag/Cag	4/11	0.418985558881287	1	FACETS	0.206	0.178	0.237	0.206	0.178	0.237	INDETERMINATE	1	TRUE	0	0.76294917453858	1		282	479	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918842	76918905	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTTTACATTCAGAATTAAAACATCTTACCCTTTCTTCTGTTTCTGCCTTTGACTTCTTTATGC	TCTTTACATTCAGAATTAAAACATCTTACCCTTTCTTCTGTTTCTGCCTTTGACTTCTTTATGC	-	novel	NA	P-0015628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	109	161	0	ENST00000373344.5:c.4086_4120+29del		p.X1362_splice	ENST00000373344	NM_000489.3	1362		12/35	0.76294917453858	2	FACETS	0.636	0.575	0.701			1	SUBCLONAL	1	TRUE	NA	0.76294917453858	2		161	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0015629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	739	847	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.372137041391597	4	FACETS	0.984	0.957	1	1	0.997	1	CLONAL	4	TRUE	1	0.456042115657657	4		847	1199	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971153	21971154	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0015629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	210	590	0	ENST00000304494.5:c.204_205delinsTT	p.Glu69Ter	p.E69*	ENST00000304494	NM_000077.4	68	gcGGag/gcTTag	2/3	0.414208197650371	2	FACETS	0.894	0.838	0.951	0.894	0.838	0.951	CLONAL	2	TRUE	0	0.456042115657657	2		590	515	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257210	16257210	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	165	589	0	ENST00000375759.3:c.4475C>G	p.Ser1492Cys	p.S1492C	ENST00000375759	NM_015001.2	1492	tCc/tGc	11/15	0.374599820544822	2	FACETS	0.797	0.739	0.856	0.797	0.739	0.856	SUBCLONAL	2	TRUE	0	0.456042115657657	2		589	454	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057991	27057991	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	286	688	0	ENST00000324856.7:c.1699C>T	p.Gln567Ter	p.Q567*	ENST00000324856	NM_006015.4	567	Cag/Tag	3/20	0.374599820544822	2	FACETS	0.957	0.907	1	0.957	0.907	1	CLONAL	2	TRUE	0	0.456042115657657	2		688	655	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127755	64127755	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	395	673	0	ENST00000334205.4:c.248G>C	p.Arg83Pro	p.R83P	ENST00000334205	NM_003942.2	83	cGc/cCc	3/17	0.456042115657657	4	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.456042115657657	4		673	1013	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046729	42046729	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	290	724	0	ENST00000219905.7:c.7103A>G	p.Lys2368Arg	p.K2368R	ENST00000219905	NM_001164273.1	2368	aAg/aGg	18/24	0.414208197650371	2	FACETS	0.98	0.929	1	0.98	0.929	1	CLONAL	2	TRUE	0	0.456042115657657	2		724	649	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812236	212812236	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	130	432	0	ENST00000342788.4:c.340C>G	p.Arg114Gly	p.R114G	ENST00000342788	NM_005235.2	114	Cga/Gga	3/28	0.29964329714297	5	FACETS	0.923	0.842	1	0.615	0.561	0.672	CLONAL	2	TRUE	2	0.456042115657657	5		432	520	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0015630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	191	414	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.322941940255113	3	FACETS	0.892	0.827	0.96	0.892	0.827	0.96	CLONAL	2	TRUE	1	0.32524964314146	3		414	765	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	105	510	0	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	0.32524964314146	1	FACETS	0.854	0.767	0.947	0.854	0.767	0.947	CLONAL	1	TRUE	0	0.32524964314146	1		510	633	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363418	40363418	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	157	594	0	ENST00000397332.2:c.811G>C	p.Asp271His	p.D271H	ENST00000397332	NM_001033082.2	271	Gat/Cat	3/3	1	2	FACETS	0.969	0.887	1	0.969	0.887	1	CLONAL	1	TRUE	1	0.32524964314146	2		594	996	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955555	55955555	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0015630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	125	511	0	ENST00000263923.4:c.3390T>G	p.Tyr1130Ter	p.Y1130*	ENST00000263923	NM_002253.2	1130	taT/taG	25/30	1	2	FACETS	0.942	0.853	1	0.942	0.853	1	CLONAL	1	TRUE	1	0.32524964314146	2		511	816	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347553	118347553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555037629	NA	P-0015631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	34	532	1	ENST00000534358.1:c.3190C>T	p.Arg1064Ter	p.R1064*	ENST00000534358	NM_005933.3	1064	Cga/Tga	4/36	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.345000965794057	NA		533	132	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs869320707	NA	P-0015632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	188	736	1	ENST00000397752.3:c.3028+1G>T		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.200702734788194	3	FACETS	1	0.99	1	0.745	0.687	0.807	CLONAL	1	TRUE	1	0.21	3		737	1327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782620	NA	P-0015632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1401	153	1019	0	ENST00000269305.4:c.427G>A	p.Val143Met	p.V143M	ENST00000269305	NM_001126112.2	143	Gtg/Atg	5/11	1	2	FACETS	0.938	0.855	1	0.938	0.855	1	CLONAL	1	TRUE	1	0.21	2		1019	1554	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041591	42041591	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	86	626	0	ENST00000219905.7:c.5786A>T	p.Gln1929Leu	p.Q1929L	ENST00000219905	NM_001164273.1	1929	cAg/cTg	17/24	1	2	FACETS	0.818	0.722	0.922	0.818	0.722	0.922	CLONAL	1	TRUE	1	0.21	2		626	1001	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761012	59761012	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	78	500	0	ENST00000259008.2:c.3395T>A	p.Phe1132Tyr	p.F1132Y	ENST00000259008	NM_032043.2	1132	tTt/tAt	20/20	1	2	FACETS	0.893	0.783	1	0.893	0.783	1	CLONAL	1	TRUE	1	0.21	2		500	832	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951153	17951153	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	T	novel	NA	P-0015632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	98	632	0	ENST00000458235.1:c.1143-3C>A		p.X381_splice	ENST00000458235	NM_000215.3	381			1	2	FACETS	0.9	0.801	1	0.9	0.801	1	CLONAL	1	TRUE	1	0.21	2		632	1037	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982029	93982029	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	28	328	0	ENST00000369303.4:c.1436A>T	p.Lys479Met	p.K479M	ENST00000369303	NM_004440.3	479	aAg/aTg	6/17	1	2	FACETS	0.476	0.379	0.587	0.476	0.379	0.587	SUBCLONAL	1	TRUE	1	0.21	2		328	560	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395570	116395570	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1013431413	NA	P-0015632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	44	377	0	ENST00000397752.3:c.1862+1G>A		p.X621_splice	ENST00000397752	NM_000245.2	621			0.200702734788194	3	FACETS	0.602	0.503	0.712	0.301	0.251	0.356	SUBCLONAL	1	TRUE	1	0.21	3		377	769	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0015633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	56	278	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.894	0.765	1	0.894	0.765	1	CLONAL	1	TRUE	1	0.18	2		278	696	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916947	178916947	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	62	382	0	ENST00000263967.3:c.334A>T	p.Ile112Phe	p.I112F	ENST00000263967	NM_006218.2	112	Atc/Ttc	2/21	1	2	FACETS	0.961	0.829	1	0.961	0.829	1	CLONAL	1	TRUE	1	0.18	2		382	717	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520274	176520274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1562071377	NA	P-0015633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	148	643	5	ENST00000292408.4:c.1193G>A	p.Arg398Gln	p.R398Q	ENST00000292408	NM_213647.1	398	cGg/cAg	9/18	0.163315492995733	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	1	0.18	3		648	856	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63700142	63700142	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	41	227	0	ENST00000279873.7:c.477C>A	p.Asp159Glu	p.D159E	ENST00000279873	NM_032199.2	159	gaC/gaA	3/10	1	2	FACETS	1	0.838	1	1	0.838	1	CLONAL	1	TRUE	1	0.18	2		227	453	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070577	67070577	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	44	277	0	ENST00000412916.2:c.201G>T	p.Gln67His	p.Q67H	ENST00000412916		67	caG/caT	3/6	0.207267008112889	1	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	0	0.18	1		277	420	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184102	56184102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	81	477	0	ENST00000399503.3:c.4307G>A	p.Gly1436Asp	p.G1436D	ENST00000399503	NM_005921.1	1436	gGc/gAc	19/20	0.246205800426712	3	FACETS	1	0.928	1	0.54	0.474	0.61	CLONAL	1	TRUE	1	0.18	3		477	909	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860719	151860719	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	118	435	0	ENST00000262189.6:c.9943C>T	p.Gln3315Ter	p.Q3315*	ENST00000262189	NM_170606.2	3315	Cag/Tag	43/59	0.163315492995733	3	FACETS	0.97	0.875	1	0.97	0.875	1	CLONAL	2	TRUE	1	0.18	3		435	737	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878331	151878331	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	78	522	1	ENST00000262189.6:c.6614A>C	p.His2205Pro	p.H2205P	ENST00000262189	NM_170606.2	2205	cAt/cCt	36/59	0.163315492995733	3	FACETS	1	0.928	1	0.542	0.475	0.614	CLONAL	1	TRUE	1	0.18	3		523	872	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370320	40370320	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs760876362	NA	P-0015634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	183	960	0	ENST00000293328.3:c.1018C>G	p.Gln340Glu	p.Q340E	ENST00000293328	NM_012448.3	340	Cag/Gag	9/19	1	2	FACETS	0.497	0.459	0.537	0.497	0.459	0.537	SUBCLONAL	1	TRUE	1	0.79084001854357	2		960	931	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458444	120458457	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGCTCCCGAGGG	AGGGCTCCCGAGGG	-	novel	NA	P-0015634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	104	593	0	ENST00000256646.2:c.6888_6901del	p.Pro2297AlafsTer11	p.P2297Afs*11	ENST00000256646	NM_024408.3	2296	acCCCTCGGGAGCCCTtg/actg	34/34	1	2	FACETS	0.457	0.41	0.506	0.457	0.41	0.506	SUBCLONAL	1	TRUE	1	0.79084001854357	2		593	576	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518452	69518452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	102	443	1	ENST00000294312.3:c.193G>A	p.Asp65Asn	p.D65N	ENST00000294312	NM_005117.2	65	Gac/Aac	1/3	1	2	FACETS	0.53	0.476	0.586	0.53	0.476	0.586	SUBCLONAL	1	TRUE	1	0.79084001854357	2		444	487	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940790	71940790	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	168	797	0	ENST00000298229.2:c.837G>C	p.Gln279His	p.Q279H	ENST00000298229	NM_001567.3	279	caG/caC	7/28	1	2	FACETS	0.528	0.486	0.572	0.528	0.486	0.572	SUBCLONAL	1	TRUE	1	0.79084001854357	2		797	804	SUCCESS
EED	8726	MSKCC	GRCh37	11	85977174	85977174	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	134	461	0	ENST00000263360.6:c.776C>G	p.Ser259Cys	p.S259C	ENST00000263360	NM_003797.3	259	tCt/tGt	8/12	0.10295690573247	6	FACETS	1	0.975	1			1	INDETERMINATE	1	TRUE	NA	0.79084001854357	6		461	726	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343496	118343496	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	114	580	0	ENST00000534358.1:c.1622G>C	p.Arg541Thr	p.R541T	ENST00000534358	NM_005933.3	541	aGa/aCa	3/36	0.10295690573247	6	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.79084001854357	6		580	683	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642836	3642836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760941208	NA	P-0015634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	63	893	0	ENST00000294008.3:c.2191G>A	p.Asp731Asn	p.D731N	ENST00000294008	NM_032444.2	731	Gac/Aac	11/15	1	2	FACETS	0.152	0.131	0.176	0.152	0.131	0.176	SUBCLONAL	1	TRUE	1	0.79084001854357	2		893	1045	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844190	68844190	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	203	884	0	ENST00000261769.5:c.778C>A	p.Pro260Thr	p.P260T	ENST00000261769	NM_004360.3	260	Ccc/Acc	6/16	0.492439901496189	1	FACETS	0.396	0.368	0.425	0.396	0.368	0.425	SUBCLONAL	1	TRUE	0	0.79084001854357	1		884	784	SUCCESS
YES1	7525	MSKCC	GRCh37	18	751756	751756	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	106	637	0	ENST00000314574.4:c.320C>T	p.Thr107Ile	p.T107I	ENST00000314574	NM_005433.3	107	aCa/aTa	3/12	1	2	FACETS	0.323	0.289	0.359	0.323	0.289	0.359	SUBCLONAL	1	TRUE	1	0.79084001854357	2		637	831	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630376	47630376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	198	736	0	ENST00000233146.2:c.46G>A	p.Glu16Lys	p.E16K	ENST00000233146	NM_000251.2	16	Gag/Aag	1/16	1	2	FACETS	0.635	0.59	0.683	0.635	0.59	0.683	SUBCLONAL	1	TRUE	1	0.79084001854357	2		736	788	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685297	86685297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	66	235	0	ENST00000274376.6:c.3013C>T	p.His1005Tyr	p.H1005Y	ENST00000274376	NM_002890.2	1005	Cat/Tat	24/25	1	2	FACETS	0.501	0.438	0.569	0.501	0.438	0.569	SUBCLONAL	1	TRUE	1	0.79084001854357	2		235	333	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190801	32190801	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	213	954	0	ENST00000375023.3:c.136C>G	p.Leu46Val	p.L46V	ENST00000375023	NM_004557.3	46	Ctg/Gtg	2/30	1	2	FACETS	0.516	0.479	0.554	0.516	0.479	0.554	SUBCLONAL	1	TRUE	1	0.79084001854357	2		954	1044	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964367	93964367	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	97	542	0	ENST00000369303.4:c.2530G>C	p.Asp844His	p.D844H	ENST00000369303	NM_004440.3	844	Gat/Cat	14/17	1	2	FACETS	0.513	0.459	0.57	0.513	0.459	0.57	SUBCLONAL	1	TRUE	1	0.79084001854357	2		542	478	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845469	151845469	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1431082369	NA	P-0015634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	70	715	0	ENST00000262189.6:c.13543G>A	p.Glu4515Lys	p.E4515K	ENST00000262189	NM_170606.2	4515	Gaa/Aaa	52/59	1	2	FACETS	0.191	0.166	0.218	0.191	0.166	0.218	SUBCLONAL	1	TRUE	1	0.79084001854357	2		715	927	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874644	151874644	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	130	443	0	ENST00000262189.6:c.7894C>G	p.Gln2632Glu	p.Q2632E	ENST00000262189	NM_170606.2	2632	Caa/Gaa	38/59	1	2	FACETS	0.565	0.514	0.618	0.565	0.514	0.618	SUBCLONAL	1	TRUE	1	0.79084001854357	2		443	582	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740396	145740396	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1260540483	NA	P-0015634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	51	1026	0	ENST00000428558.2:c.1544C>T	p.Pro515Leu	p.P515L	ENST00000428558	NM_004260.3	515	cCa/cTa	9/22	1	2	FACETS	0.134	0.113	0.157	0.134	0.113	0.157	SUBCLONAL	1	TRUE	1	0.79084001854357	2		1026	962	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570195	87570195	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0015634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	47	275	2	ENST00000277120.3:c.1938-3C>T		p.X646_splice	ENST00000277120		646			1	2	FACETS	0.524	0.446	0.607	0.524	0.446	0.607	SUBCLONAL	1	TRUE	1	0.79084001854357	2		277	227	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218668	98218668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	114	544	0	ENST00000331920.6:c.3196G>A	p.Glu1066Lys	p.E1066K	ENST00000331920	NM_000264.3	1066	Gag/Aag	19/24	1	2	FACETS	0.535	0.483	0.589	0.535	0.483	0.589	SUBCLONAL	1	TRUE	1	0.79084001854357	2		544	539	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44935946	44935953	+	frameshift_variant	Frame_Shift_Del	DEL	CTAGGTAA	CTAGGTAA	-	novel	NA	P-0015634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	95	391	0	ENST00000377967.4:c.2707_2714del	p.Leu903LysfsTer5	p.L903Kfs*5	ENST00000377967	NM_021140.2	903	CTAGGTAAa/a	18/29	1	2	FACETS	0.545	0.488	0.605	0.545	0.488	0.605	SUBCLONAL	1	TRUE	1	0.79084001854357	2		391	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0015635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	221	947	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.381302158216458	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.381302158216458	1		949	746	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281070	49281070	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs754945976	NA	P-0015635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	144	518	0	ENST00000282018.3:c.117A>T	p.Glu39Asp	p.E39D	ENST00000282018	NM_020377.2	39	gaA/gaT	1/1	0.381302158216458	3	FACETS	0.887	0.808	0.97	0.296	0.269	0.324	CLONAL	1	TRUE	0	0.381302158216458	3		518	1014	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138570	11138598	+	frameshift_variant	Frame_Shift_Del	DEL	TGACCATCATGGAAGATTACTTTGCGTAT	TGACCATCATGGAAGATTACTTTGCGTAT	-	novel	NA	P-0015635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	109	596	0	ENST00000358026.2:c.3326_3354del	p.Met1109ThrfsTer4	p.M1109Tfs*4	ENST00000358026	NM_001128849.1	1109	aTGACCATCATGGAAGATTACTTTGCGTAT/a	24/36	0.381302158216458	1	FACETS	0.566	0.508	0.627	0.566	0.508	0.627	SUBCLONAL	1	TRUE	0	0.381302158216458	1		596	818	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0015636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	24	754	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.226568002171243	2		755	182	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279760	46279760	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	33	545	0	ENST00000371998.3:c.3686G>T	p.Arg1229Leu	p.R1229L	ENST00000371998		1229	cGc/cTc	20/23	1	2	FACETS	0.928	0.758	1	0.928	0.758	1	CLONAL	1	TRUE	1	0.226568002171243	2		545	314	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440925	52440925	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1430317959	NA	P-0015636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	39	564	0	ENST00000460680.1:c.581-2A>G		p.X194_splice	ENST00000460680	NM_004656.3	194			1	2	FACETS	0.984	0.817	1	0.984	0.817	1	CLONAL	1	TRUE	1	0.226568002171243	2		564	350	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992335	72992335	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	132	1021	0	ENST00000268489.5:c.1710A>C	p.Leu570Phe	p.L570F	ENST00000268489	NM_006885.3	570	ttA/ttC	2/10	0.124171806634012	5	FACETS	1	0.973	1	0.297	0.27	0.327	INDETERMINATE	1	TRUE	1	0.398849629159746	5		1021	889	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913492	NA	P-0015638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	294	628	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	0.797993629680417	2		628	729	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913492	NA	P-0015638-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	268	628	0	ENST00000286548.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000286548	NM_002072.3	209	cAa/cTa	5/7	1	2	FACETS	0.935	0.881	0.991	0.935	0.881	0.991	CLONAL	1	TRUE	1	0.721623840097475	2		628	794	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292753	62292753	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768524684	NA	P-0015639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	252	529	0	ENST00000360203.5:c.205G>A	p.Ala69Thr	p.A69T	ENST00000360203	NM_001283009.1	69	Gcc/Acc	3/35	1	2	FACETS	0.848	0.798	0.898	0.848	0.798	0.898	CLONAL	1	TRUE	1	0.909000056776896	2		529	654	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921566	178921566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793349	NA	P-0015640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	79	321	0	ENST00000263967.3:c.1048G>A	p.Asp350Asn	p.D350N	ENST00000263967	NM_006218.2	350	Gac/Aac	5/21	1	2	FACETS	0.947	0.836	1	0.947	0.836	1	CLONAL	1	TRUE	1	0.348137970538471	2		321	479	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	112	463	0	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.348137970538471	2		463	629	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115947	8115948	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0015640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	85	360	0	ENST00000346208.3:c.1294_1295dup	p.His434ThrfsTer42	p.H434Tfs*42	ENST00000346208		431	-/CC	6/6	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.348137970538471	2		360	459	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28883002	28883002	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	150	741	1	ENST00000282397.4:c.3698C>A	p.Pro1233Gln	p.P1233Q	ENST00000282397	NM_002019.4	1233	cCg/cAg	28/30	0.289082272205679	0	FACETS	1	0.95	1			1	CLONAL	1	TRUE	0	0.410623893699192	0		742	415	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447561	12447561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	233	704	0	ENST00000287820.6:c.800G>A	p.Gly267Glu	p.G267E	ENST00000287820	NM_015869.4	267	gGa/gAa	5/7	0.410623893699192	3	FACETS	0.774	0.723	0.826	0.516	0.482	0.551	SUBCLONAL	2	TRUE	0	0.410623893699192	3		704	884	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984812	55984812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781436993	NA	P-0015641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	74	665	1	ENST00000263923.4:c.317G>A	p.Arg106Gln	p.R106Q	ENST00000263923	NM_002253.2	106	cGg/cAg	3/30	0.147035251484223	3	FACETS	0.786	0.689	0.89	0.262	0.229	0.297	INDETERMINATE	1	TRUE	0	0.410623893699192	3		666	553	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907782	76907796	+	inframe_deletion	In_Frame_Del	DEL	TCCTCCTCCTCCTCC	TCCTCCTCCTCCTCC	-	novel	NA	P-0015641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	49	206	0	ENST00000373344.5:c.4365_4379del	p.Glu1460_Glu1464del	p.E1460_E1464del	ENST00000373344	NM_000489.3	1455	gaGGAGGAGGAGGAGGAa/gaa	15/35	1	1	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	0	0.410623893699192	1		206	187	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0015642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	318	456	1	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.10493186915595	4	FACETS	1	0.987	1			1	INDETERMINATE	2	TRUE	NA	0.470917996510791	4		457	879	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064794618	NA	P-0015642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	200	918	0	ENST00000269305.4:c.159G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgG/tgA	4/11	0.470917996510791	1	FACETS	0.842	0.782	0.904	0.842	0.782	0.904	CLONAL	1	TRUE	0	0.470917996510791	1		918	771	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057665	27057665	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	127	839	0	ENST00000324856.7:c.1373G>T	p.Gly458Val	p.G458V	ENST00000324856	NM_006015.4	458	gGc/gTc	3/20	1	2	FACETS	0.583	0.528	0.642	0.583	0.528	0.642	SUBCLONAL	1	TRUE	1	0.470917996510791	2		839	925	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871848	35871848	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	118	584	0	ENST00000216797.5:c.658G>A	p.Ala220Thr	p.A220T	ENST00000216797	NM_020529.2	220	Gcc/Acc	5/6	1	2	FACETS	0.618	0.557	0.682	0.618	0.557	0.682	SUBCLONAL	1	TRUE	1	0.470917996510791	2		584	811	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492867	56492870	+	frameshift_variant	Frame_Shift_Del	DEL	GCCT	GCCT	-	novel	NA	P-0015642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	97	432	0	ENST00000407977.2:c.69_72del	p.Gly24LeufsTer26	p.G24Lfs*26	ENST00000407977		23	gcAGGC/gc	2/10	0.470917996510791	1	FACETS	0.785	0.705	0.87	0.785	0.705	0.87	SUBCLONAL	1	TRUE	0	0.470917996510791	1		432	401	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575063	48575063	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	134	401	0	ENST00000342988.3:c.257G>T	p.Gly86Val	p.G86V	ENST00000342988	NM_005359.5	86	gGt/gTt	3/12	0.470917996510791	1	FACETS	0.881	0.805	0.959	0.881	0.805	0.959	CLONAL	1	TRUE	0	0.470917996510791	1		401	494	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641068	117641068	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0015642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	179	636	0	ENST00000368508.3:c.5903T>G	p.Leu1968Ter	p.L1968*	ENST00000368508	NM_002944.2	1968	tTa/tGa	36/43	1	2	FACETS	0.977	0.903	1	0.977	0.903	1	CLONAL	1	TRUE	1	0.470917996510791	2		636	778	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0015645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	12	515	3	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.059	0.041	0.082	0.059	0.041	0.082	SUBCLONAL	1	TRUE	1	0.698296171792668	2		518	580	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0015645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	361	910	2	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	0.821	0.778	0.865	0.821	0.778	0.865	CLONAL	1	TRUE	1	0.698296171792668	2		912	1259	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1976641	1976641	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	385	833	2	ENST00000382891.5:c.3424C>A	p.His1142Asn	p.H1142N	ENST00000382891	NM_133335.3	1142	Cac/Aac	19/22	NA	2	FACETS	0.879	0.835	0.924			1	INDETERMINATE	1	TRUE	NA	0.698296171792668	2		835	1254	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057519990	NA	P-0015647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	581	367	12	ENST00000269305.4:c.796G>T	p.Gly266Ter	p.G266*	ENST00000269305	NM_001126112.2	266	Gga/Tga	8/11	0.811199713399031	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.811199713399031	1		379	774	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0015647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	102	410	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.811199713399031	1	FACETS	0.804	0.74	0.867	0.804	0.74	0.867	CLONAL	1	TRUE	0	0.811199713399031	1		410	186	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445025	89445025	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	454	486	7	ENST00000336596.2:c.1345T>A	p.Ser449Thr	p.S449T	ENST00000336596	NM_005233.5	449	Tcc/Acc	6/17	0.70744250910263	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.811199713399031	1		493	593	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591865	48591865	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	TTG	novel	NA	P-0015647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	177	329	0	ENST00000342988.3:c.1028delinsTTG	p.Ser343PhefsTer42	p.S343Ffs*42	ENST00000342988	NM_005359.5	343	tCa/tTTGa	9/12	0.811199713399031	1	FACETS	0.888	0.838	0.938	0.888	0.838	0.938	CLONAL	1	TRUE	0	0.811199713399031	1		329	292	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs1202793339	NA	P-0015651-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	264	721	0	ENST00000269305.4:c.560-1G>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.305792013573878	1	FACETS	1	0.99	1	1	0.99	1	INDETERMINATE	1	TRUE	0	0.650468770844346	1		721	470	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856181	111856181	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015651-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	191	480	0	ENST00000341259.2:c.232G>T	p.Glu78Ter	p.E78*	ENST00000341259	NM_005475.2	78	Gag/Tag	2/8	0.650468770844346	1	FACETS	0.957	0.897	1	0.957	0.897	1	CLONAL	1	TRUE	0	0.650468770844346	1		480	414	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505608	186505608	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015651-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	204	525	0	ENST00000323963.5:c.1016T>G	p.Val339Gly	p.V339G	ENST00000323963		339	gTg/gGg	10/11	0.650468770844346	3	FACETS	0.786	0.729	0.846			1	SUBCLONAL	1	TRUE	NA	0.650468770844346	3		525	1057	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178055	56178086	+	frameshift_variant	Frame_Shift_Del	DEL	ATTCCCTGCAGAATACCTTCTGCATCTCCTCA	ATTCCCTGCAGAATACCTTCTGCATCTCCTCA	-	novel	NA	P-0015651-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	46	591	0	ENST00000399503.3:c.3029_3060del	p.Ile1010AsnfsTer15	p.I1010Nfs*15	ENST00000399503	NM_005921.1	1010	ATTCCCTGCAGAATACCTTCTGCATCTCCTCAa/a	14/20	0.650468770844346	1	FACETS	0.218	0.184	0.256	0.218	0.184	0.256	SUBCLONAL	1	TRUE	0	0.650468770844346	1		591	437	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163608	32163608	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748829728	NA	P-0015651-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	211	571	1	ENST00000375023.3:c.5618G>A	p.Gly1873Asp	p.G1873D	ENST00000375023	NM_004557.3	1873	gGc/gAc	30/30	0.28486109000712	4	FACETS	0.833	0.777	0.889	0.833	0.777	0.889	INDETERMINATE	2	TRUE	2	0.650468770844346	4		572	643	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045479	47045480	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015651-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	113	778	0	ENST00000377604.3:c.2446_2447insT	p.Asp816ValfsTer5	p.D816Vfs*5	ENST00000377604	NM_001204468.1	816	gac/gTac	22/24	0.440280455681942	1	FACETS	0.314	0.283	0.348	0.314	0.283	0.348	SUBCLONAL	1	TRUE	0	0.650468770844346	1		778	746	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	222	248	0				ENST00000310581	NM_198253.2	-/1132			0.365855557502858	3	FACETS	0.993	0.933	1	0.993	0.933	1	CLONAL	2	TRUE	1	0.513392600440458	3		248	547	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894228	NA	P-0015661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	293	462	0	ENST00000451590.1:c.37G>C	p.Gly13Arg	p.G13R	ENST00000451590	NM_001130442.1	13	Ggt/Cgt	2/5	0.513392600440458	2	FACETS	0.906	0.86	0.952	0.906	0.86	0.952	CLONAL	2	TRUE	0	0.513392600440458	2		462	630	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489534	56489534	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	302	684	0	ENST00000267101.3:c.1999C>A	p.Arg667Ser	p.R667S	ENST00000267101	NM_001982.3	667	Cgt/Agt	17/28	0.415773396526972	4	FACETS	0.967	0.913	1	0.967	0.913	1	CLONAL	2	TRUE	2	0.513392600440458	4		684	921	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97873816	97873817	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs765551897	NA	P-0015661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	141	821	0	ENST00000289081.3:c.1257dup	p.Thr420HisfsTer15	p.T420Hfs*15	ENST00000289081	NM_000136.2	419	-/C	13/15	0.510740220642771	3	FACETS	0.772	0.703	0.845	0.257	0.234	0.282	SUBCLONAL	1	TRUE	0	0.513392600440458	3		821	894	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224574	123224581	+	frameshift_variant	Frame_Shift_Del	DEL	CCAATGCA	CCAATGCA	-	novel	NA	P-0015661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	151	397	0	ENST00000218089.9:c.3427_3434del	p.Pro1143AspfsTer2	p.P1143Dfs*2	ENST00000218089	NM_001042749.1	1143	CCAATGCAg/g	31/35	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.513392600440458	1		397	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0015666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	51	947	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.154742104436276	4	FACETS	1	0.948	1	1	0.948	1	INDETERMINATE	2	TRUE	2	0.403836709876371	4		949	148	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0015666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	41	339	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.222225495797796	3	FACETS	1	0.922	1	1	0.922	1	INDETERMINATE	2	TRUE	1	0.403836709876371	3		339	109	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559092	29559092	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	10	74	0	ENST00000356175.3:c.3199G>T	p.Asp1067Tyr	p.D1067Y	ENST00000356175	NM_000267.3	1067	Gat/Tat	25/57	0.154742104436276	4	FACETS	1	0.822	1	0.656	0.455	0.894	INDETERMINATE	1	TRUE	2	0.403836709876371	4		74	53	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530338	187530338	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs202039105	NA	P-0015666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	21	272	0	ENST00000441802.2:c.10205C>T	p.Thr3402Met	p.T3402M	ENST00000441802	NM_005245.3	3402	aCg/aTg	16/27	0.222225495797796	3	FACETS	0.992	0.813	1	1	0.938	1	INDETERMINATE	3	TRUE	1	0.403836709876371	3		272	42	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940024	76940024	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0015666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	20	294	0	ENST00000373344.5:c.724A>T	p.Lys242Ter	p.K242*	ENST00000373344	NM_000489.3	242	Aaa/Taa	9/35	1	1	FACETS	0.823	0.662	0.991	1	0.938	1	CLONAL	2	TRUE	0	0.403836709876371	1		294	48	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0015667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	295	605	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.494441360177449	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.494441360177449	3		606	711	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602581	10602581	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	388	508	0	ENST00000171111.5:c.997G>T	p.Gly333Cys	p.G333C	ENST00000171111	NM_203500.1	333	Ggc/Tgc	3/6	0.494441360177449	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.494441360177449	2		508	768	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979471	55979471	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	111	315	0	ENST00000263923.4:c.976G>T	p.Glu326Ter	p.E326*	ENST00000263923	NM_002253.2	326	Gaa/Taa	7/30	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.494441360177449	2		315	448	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432153	49432153	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	233	586	0	ENST00000301067.7:c.8986G>T	p.Asp2996Tyr	p.D2996Y	ENST00000301067	NM_003482.3	2996	Gat/Tat	34/54	0.494441360177449	3	FACETS	1	0.969	1	0.534	0.498	0.572	CLONAL	1	TRUE	1	0.494441360177449	3		586	1100	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120535162	120535162	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	109	355	0	ENST00000229340.5:c.493A>T	p.Thr165Ser	p.T165S	ENST00000229340	NM_006861.6	165	Acg/Tcg	6/6	0.494441360177449	3	FACETS	0.934	0.841	1	0.467	0.42	0.516	CLONAL	1	TRUE	1	0.494441360177449	3		355	589	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805940	46805940	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	190	258	0	ENST00000290295.7:c.16T>A	p.Tyr6Asn	p.Y6N	ENST00000290295	NM_006361.5	6	Tat/Aat	1/2	0.494441360177449	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.494441360177449	3		258	443	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207014	1207023	+	frameshift_variant	Frame_Shift_Del	DEL	CATCTACCAG	CATCTACCAG	-	novel	NA	P-0015667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	300	567	0	ENST00000326873.7:c.103_112del	p.Ile35ArgfsTer13	p.I35Rfs*13	ENST00000326873	NM_000455.4	34	gtCATCTACCAG/gt	1/10	0.494441360177449	2	FACETS	0.842	0.798	0.886	0.842	0.798	0.886	CLONAL	2	TRUE	0	0.494441360177449	2		567	721	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733234	40733234	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	171	522	0	ENST00000373198.4:c.3572C>G	p.Ser1191Cys	p.S1191C	ENST00000373198	NM_133170.3	1191	tCc/tGc	26/32	0.494441360177449	3	FACETS	0.954	0.878	1	0.477	0.439	0.517	CLONAL	1	TRUE	1	0.494441360177449	3		522	904	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	75	414	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.211531180280558	3	FACETS	0.828	0.726	0.939			1	CLONAL	1	TRUE	NA	0.324892589489979	3		414	648	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092802	27092802	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	104	864	0	ENST00000324856.7:c.2823del	p.Asn942ThrfsTer26	p.N942Tfs*26	ENST00000324856	NM_006015.4	941	atC/at	9/20	1	2	FACETS	0.825	0.739	0.917	0.825	0.739	0.917	CLONAL	1	TRUE	1	0.324892589489979	2		864	776	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520008	NA	P-0015668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	73	898	0	ENST00000269305.4:c.613T>C	p.Tyr205His	p.Y205H	ENST00000269305	NM_001126112.2	205	Tat/Cat	6/11	0.324892589489979	1	FACETS	0.701	0.614	0.794	0.701	0.614	0.794	SUBCLONAL	1	TRUE	0	0.324892589489979	1		898	537	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30099996	30099996	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	65	582	0	ENST00000331968.5:c.1624C>G	p.Pro542Ala	p.P542A	ENST00000331968	NM_002742.2	542	Ccc/Gcc	10/18	0.239877890593445	1	FACETS	0.584	0.506	0.668	0.584	0.506	0.668	SUBCLONAL	1	TRUE	0	0.324892589489979	1		582	574	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094699	2094699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781629683	NA	P-0015668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	99	845	0	ENST00000219066.1:c.481G>A	p.Val161Met	p.V161M	ENST00000219066	NM_002528.5	161	Gtg/Atg	3/6	0.324892589489979	1	FACETS	0.852	0.762	0.947	0.852	0.762	0.947	CLONAL	1	TRUE	0	0.324892589489979	1		845	599	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2225438	2225457	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AACCTTGGAAAATGGTGAGT	AACCTTGGAAAATGGTGAGT	-	novel	NA	P-0015668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	34	657	0	ENST00000398665.3:c.3651_3661+9del		p.X1217_splice	ENST00000398665	NM_032482.2	1217		26/28	0.152170026152508	0	FACETS	0.275	0.224	0.333			1	INDETERMINATE	1	TRUE	0	0.324892589489979	0		657	513	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293694	1293695	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0015668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	57	906	4	ENST00000310581.5:c.1306_1307delinsTT	p.Ala436Leu	p.A436L	ENST00000310581	NM_198253.2	436	GCg/TTg	2/16	0.239877890593445	1	FACETS	0.555	0.476	0.64	0.555	0.476	0.64	SUBCLONAL	1	TRUE	0	0.324892589489979	1		910	530	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679274	29679274	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	133	339	0	ENST00000356175.3:c.7395-1G>A		p.X2465_splice	ENST00000356175	NM_000267.3	2465			0.631871938566043	2	FACETS	0.893	0.834	0.951	0.893	0.834	0.951	CLONAL	2	TRUE	0	0.664870007950491	2		339	224	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0015669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	202	596	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.664870007950491	4	FACETS	0.816	0.761	0.872			1	CLONAL	2	TRUE	NA	0.664870007950491	4		596	620	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692768	89692768	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0015669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	213	487	0	ENST00000371953.3:c.254-2A>C		p.X85_splice	ENST00000371953	NM_000314.4	85			0.614848775343493	2	FACETS	0.787	0.743	0.831	0.787	0.743	0.831	SUBCLONAL	2	TRUE	0	0.664870007950491	2		487	407	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287204	33287204	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1562719507	NA	P-0015669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	477	533	0	ENST00000374542.5:c.1893del	p.Lys631AsnfsTer14	p.K631Nfs*14	ENST00000374542	NM_001141970.1	631	aaA/aa	6/8	0.189024727100883	6	FACETS	0.983	0.947	1			1	INDETERMINATE	4	TRUE	NA	0.664870007950491	6		533	850	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0015670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	286	670	1	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.552156556059964	3	FACETS	1	0.975	1	0.536	0.503	0.569	CLONAL	1	TRUE	1	0.57101737521348	3		671	1202	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0015670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	462	655	2	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.553525370734856	4	FACETS	0.942	0.9	0.985	0.942	0.9	0.985	CLONAL	2	TRUE	2	0.57101737521348	4		657	1349	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107236	193107236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	223	277	1	ENST00000367435.3:c.445G>A	p.Asp149Asn	p.D149N	ENST00000367435	NM_024529.4	149	Gat/Aat	6/17	0.425584500386352	6	FACETS	1	0.965	1	0.701	0.654	0.749	CLONAL	2	TRUE	3	0.57101737521348	6		278	796	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692839	89692839	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	170	161	0	ENST00000371953.3:c.323T>G	p.Leu108Arg	p.L108R	ENST00000371953	NM_000314.4	108	cTt/cGt	5/9	NA	2	FACETS	0.989	0.929	1			1	INDETERMINATE	2	TRUE	NA	0.57101737521348	2		161	301	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801743	3801743	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1179176334	NA	P-0015670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	324	340	0	ENST00000262367.5:c.3763C>T	p.Pro1255Ser	p.P1255S	ENST00000262367	NM_004380.2	1255	Cct/Tct	20/31	0.553525370734856	4	FACETS	0.947	0.897	0.998	0.947	0.897	0.998	CLONAL	2	TRUE	2	0.57101737521348	4		340	941	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2208935	2208935	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	536	387	0	ENST00000398665.3:c.965T>C	p.Leu322Pro	p.L322P	ENST00000398665	NM_032482.2	322	cTt/cCt	12/28	0.57101737521348	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	0	0.57101737521348	3		387	797	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10287988	10287988	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	213	495	0	ENST00000340748.4:c.501C>G	p.Ile167Met	p.I167M	ENST00000340748		167	atC/atG	5/40	0.57101737521348	3	FACETS	0.896	0.832	0.963	0.299	0.277	0.321	CLONAL	1	TRUE	0	0.57101737521348	3		495	1070	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419884	152419884	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2238	742	359	0	ENST00000206249.3:c.1571A>T	p.His524Leu	p.H524L	ENST00000206249	NM_000125.3	524	cAt/cTt	8/8	0.57101737521348	12	FACETS	1	0.993	1			1	CLONAL	3	TRUE	NA	0.57101737521348	12		359	2980	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854883	76854883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	432	489	0	ENST00000373344.5:c.5953G>A	p.Glu1985Lys	p.E1985K	ENST00000373344	NM_000489.3	1985	Gaa/Aaa	25/35	0.553525370734856	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	2	0.57101737521348	4		489	1173	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	78	248	0				ENST00000310581	NM_198253.2	-/1132			0.269612772472206	1	FACETS	0.673	0.595	0.757	0.673	0.595	0.757	INDETERMINATE	1	TRUE	0	0.458879641910523	1		248	389	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841000	15841000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754101239	NA	P-0015671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	152	527	1	ENST00000307771.7:c.1084G>A	p.Glu362Lys	p.E362K	ENST00000307771	NM_005089.3	362	Gaa/Aaa	11/11	1	2	FACETS	0.93	0.853	1	0.93	0.853	1	CLONAL	1	TRUE	1	0.458879641910523	2		528	712	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941626	48941675	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAAGGTTGAAAATCTTTCTAAACGATACGAAGAAATTTATCTTAAAAATA	CAAGGTTGAAAATCTTTCTAAACGATACGAAGAAATTTATCTTAAAAATA	-	novel	NA	P-0015671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	29	193	0	ENST00000267163.4:c.940-4_985del		p.X314_splice	ENST00000267163	NM_000321.2	314		10/27	1	2	FACETS	0.419	0.336	0.511	0.419	0.336	0.511	SUBCLONAL	1	TRUE	1	0.458879641910523	2		193	302	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032582	47032582	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1350195233	NA	P-0015671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	158	455	0	ENST00000377604.3:c.488G>A	p.Arg163Gln	p.R163Q	ENST00000377604	NM_001204468.1	163	cGg/cAg	5/24	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.458879641910523	2		455	636	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	193	507	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.311815540597347	3	FACETS	0.802	0.743	0.864	0.802	0.743	0.864	CLONAL	2	TRUE	1	0.311815540597347	3		507	892	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0015672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	215	329	0	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.311815540597347	2		329	973	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383319	4383319	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	107	381	0	ENST00000261254.3:c.113T>G	p.Leu38Arg	p.L38R	ENST00000261254	NM_001759.3	38	cTt/cGt	1/5	0.311815540597347	3	FACETS	0.761	0.681	0.847	0.381	0.34	0.424	SUBCLONAL	1	TRUE	1	0.311815540597347	3		381	1042	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972533	32972533	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs80359247	NA	P-0015672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	203	325	0	ENST00000380152.3:c.9883C>T	p.Gln3295Ter	p.Q3295*	ENST00000380152		3295	Cag/Tag	27/27	0.217809434674311	2	FACETS	0.769	0.714	0.825	0.769	0.714	0.825	SUBCLONAL	2	TRUE	0	0.311815540597347	2		325	847	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386579	81386579	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	173	318	1	ENST00000222390.5:c.408C>A	p.Tyr136Ter	p.Y136*	ENST00000222390	NM_000601.4	136	taC/taA	4/18	0.581405097279553	3	FACETS	1	0.935	1	0.508	0.468	0.549	CLONAL	1	TRUE	1	0.582581491060923	3		319	755	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939371	36939371	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	174	379	0	ENST00000361632.4:c.479G>C	p.Ser160Thr	p.S160T	ENST00000361632		160	aGt/aCt	4/16	0.582510361326888	5	FACETS	1	0.954	1	0.351	0.323	0.381	CLONAL	1	TRUE	2	0.582581491060923	5		379	1062	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416731	121416743	+	frameshift_variant	Frame_Shift_Del	DEL	CGAGGGGAGCTGG	CGAGGGGAGCTGG	-	novel	NA	P-0015674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	330	603	0	ENST00000257555.6:c.161_173del	p.Arg54LeufsTer97	p.R54Lfs*97	ENST00000257555		54	CGAGGGGAGCTGGct/ct	1/10	0.581405097279553	3	FACETS	1	0.984	1	0.555	0.524	0.587	CLONAL	1	TRUE	1	0.582581491060923	3		603	1317	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650909	37650909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1639	239	443	1	ENST00000447079.4:c.2381C>A	p.Thr794Lys	p.T794K	ENST00000447079	NM_015083.1	794	aCa/aAa	5/14	0.582581491060923	6	FACETS	0.946	0.88	1			1	CLONAL	1	TRUE	NA	0.582581491060923	6		444	1878	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256250	41256251	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs80357604	NA	P-0015674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	124	250	0	ENST00000357654.3:c.329dup	p.Glu111GlyfsTer3	p.E111Gfs*3	ENST00000357654	NM_007294.3	110	aag/aaAg	6/23	0.582581491060923	6	FACETS	0.831	0.75	0.917	0.166	0.15	0.184	CLONAL	1	TRUE	1	0.582581491060923	6		250	1109	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256279	41256279	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs80358116	NA	P-0015674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	471	144	0	ENST00000357654.3:c.302-1G>C		p.X101_splice	ENST00000357654	NM_007294.3	101			0.582581491060923	6	FACETS	0.979	0.947	1	0.979	0.947	1	CLONAL	5	TRUE	1	0.582581491060923	6		144	715	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514515	41514515	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	657	397	0	ENST00000373198.4:c.146C>A	p.Thr49Asn	p.T49N	ENST00000373198	NM_133170.3	49	aCc/aAc	2/32	0.582581491060923	6	FACETS	0.997	0.961	1	0.498	0.48	0.517	CLONAL	3	TRUE	0	0.582581491060923	6		397	1633	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890340	72890340	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	156	267	0	ENST00000325599.8:c.342G>T	p.Glu114Asp	p.E114D	ENST00000325599	NM_018130.2	114	gaG/gaT	4/11	0.58138973805838	2	FACETS	0.977	0.9	1	0.489	0.45	0.529	CLONAL	1	TRUE	0	0.582581491060923	2		267	548	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156333	106156333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778934527	NA	P-0015674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	77	238	0	ENST00000380013.4:c.1234C>T	p.Leu412Phe	p.L412F	ENST00000380013	NM_001127208.2	412	Ctt/Ttt	3/11	0.581405097279553	3	FACETS	0.667	0.587	0.752	0.333	0.293	0.376	SUBCLONAL	1	TRUE	1	0.582581491060923	3		238	512	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072580	5072591	+	inframe_deletion	In_Frame_Del	DEL	AAGTTCTTTTAA	AAGTTCTTTTAA	-	novel	NA	P-0015674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	153	264	0	ENST00000381652.3:c.1737_1748del	p.Leu580_Leu583del	p.L580_L583del	ENST00000381652	NM_004972.3	577	gAAGTTCTTTTAAaa/gaa	13/25	0.582510361326888	1	FACETS	0.856	0.79	0.923	0.856	0.79	0.923	CLONAL	1	TRUE	0	0.582581491060923	1		264	435	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209315	98209315	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	204	456	0	ENST00000331920.6:c.4223T>G	p.Leu1408Arg	p.L1408R	ENST00000331920	NM_000264.3	1408	cTg/cGg	23/24	NA	2	FACETS	0.855	0.795	0.918			1	INDETERMINATE	1	TRUE	NA	0.582581491060923	2		456	819	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	127	414	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.982	0.889	1	0.982	0.889	1	CLONAL	1	TRUE	1	0.272159305411292	2		414	950	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579307	7579320	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGACCGTGCAAGT	CTGACCGTGCAAGT	-	novel	NA	P-0015675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	120	209	0	ENST00000269305.4:c.367_375+5del		p.X123_splice	ENST00000269305	NM_001126112.2	123		4/11	0.272159305411292	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.272159305411292	1		209	565	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965963	18965963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	145	391	0	ENST00000262803.5:c.1456C>T	p.Pro486Ser	p.P486S	ENST00000262803	NM_002911.3	486	Cca/Tca	11/24	0.272159305411292	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.272159305411292	1		391	841	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155322	185155322	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779365471	NA	P-0015675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	176	241	0	ENST00000265026.3:c.563G>A	p.Arg188Gln	p.R188Q	ENST00000265026	NM_004721.4	188	cGg/cAg	3/14	0.240842146062067	3	FACETS	0.897	0.827	0.969	0.897	0.827	0.969	CLONAL	2	TRUE	1	0.272159305411292	3		241	819	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	70	248	0				ENST00000310581	NM_198253.2	-/1132			0.298177392486321	1	FACETS	0.286	0.249	0.325	0.286	0.249	0.325	INDETERMINATE	1	TRUE	0	0.549582902618291	1		248	647	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0015676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	399	235	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.54656744986767	3	FACETS	0.856	0.821	0.89	0.856	0.821	0.89	CLONAL	3	TRUE	0	0.549582902618291	3		235	721	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916746	48916746	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1555282772	NA	P-0015676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	132	183	0	ENST00000267163.4:c.276T>G	p.Ile92Met	p.I92M	ENST00000267163	NM_000321.2	92	atT/atG	3/27	1	2	FACETS	0.814	0.742	0.89	0.814	0.742	0.89	CLONAL	1	TRUE	1	0.549582902618291	2		183	590	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36208925	36208926	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCGGCGGCG	novel	NA	P-0015676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	12	28	0	ENST00000222270.7:c.15_24dup	p.Ser9GlyfsTer110	p.S9Gfs*110	ENST00000222270	NM_014727.1	2	gcg/gcGGCGGCGGCGg	1/37	0.335106337146468	5	FACETS	0.905	0.645	1			1	CLONAL	1	TRUE	NA	0.549582902618291	5		28	88	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	67	507	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.358	0.31	0.41	0.358	0.31	0.41	SUBCLONAL	1	TRUE	1	0.47	2		507	796	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986975	36986975	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	73	395	0	ENST00000354822.5:c.714G>T	p.Trp238Cys	p.W238C	ENST00000354822	NM_001079668.2	238	tgG/tgT	3/3	1	2	FACETS	0.362	0.315	0.412	0.362	0.315	0.412	SUBCLONAL	1	TRUE	1	0.47	2		395	859	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717769	89717770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	186	203	0	ENST00000371953.3:c.800dup	p.Asp268GlyfsTer30	p.D268Gfs*30	ENST00000371953	NM_000314.4	265	cta/ctAa	7/9	0.921985395084903	1	FACETS	0.902	0.864	0.939	0.902	0.864	0.939	CLONAL	1	TRUE	0	0.921985395084903	1		203	241	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662691	117662691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368206665	NA	P-0015679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	326	268	0	ENST00000368508.3:c.4774C>T	p.Arg1592Cys	p.R1592C	ENST00000368508	NM_002944.2	1592	Cgt/Tgt	29/43	0.921985395084903	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.921985395084903	1		268	353	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0015679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	973	329	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.921985395084903	4	FACETS	0.954	0.933	0.974	0.954	0.933	0.974	CLONAL	3	TRUE	1	0.921985395084903	4		329	1418	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562798	95562799	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1131691197	NA	P-0015679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	268	253	1	ENST00000393063.1:c.4458dup	p.Ser1487IlefsTer5	p.S1487Ifs*5	ENST00000393063	NM_030621.3	1486	-/A	24/28	1	2	FACETS	0.91	0.86	0.96	0.91	0.86	0.96	CLONAL	1	TRUE	1	0.921985395084903	2		254	639	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168513	56168513	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	199	166	0	ENST00000399503.3:c.1469T>A	p.Leu490His	p.L490H	ENST00000399503	NM_005921.1	490	cTt/cAt	8/20	1	2	FACETS	0.959	0.899	1	0.959	0.899	1	CLONAL	1	TRUE	1	0.921985395084903	2		166	450	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956729	68956729	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	436	379	0	ENST00000288368.4:c.847A>G	p.Lys283Glu	p.K283E	ENST00000288368	NM_024870.2	283	Aag/Gag	8/40	1	2	FACETS	0.976	0.935	1	0.976	0.935	1	CLONAL	1	TRUE	1	0.921985395084903	2		379	969	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0015680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	414	586	1	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	0.98	0.937	1	0.98	0.937	1	CLONAL	1	TRUE	1	0.918760760605089	2		587	920	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156713	20156713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	331	190	0	ENST00000379607.5:c.44G>A	p.Gly15Asp	p.G15D	ENST00000379607	NM_001412.3	15	gGt/gAt	2/7	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.918760760605089	1		190	361	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820577	44820577	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	37	356	0	ENST00000377967.4:c.274G>T	p.Glu92Ter	p.E92*	ENST00000377967	NM_021140.2	92	Gag/Tag	3/29	0.184852055695577	4	FACETS	1	0.943	1			1	INDETERMINATE	1	TRUE	NA	0.408094746567419	4		356	190	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579470	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	44	436	1	ENST00000269305.4:c.217del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	73	Gtg/tg	4/11	0.136583641564452	5	FACETS	1	0.925	1	0.568	0.485	0.656	INDETERMINATE	2	TRUE	1	0.408094746567419	5		437	153	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001407	29001407	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	114	221	0	ENST00000282397.4:c.1325C>T	p.Ala442Val	p.A442V	ENST00000282397	NM_002019.4	442	gCt/gTt	10/30	0.152544687113936	1	FACETS	0.928	0.84	1	1	0.988	1	CLONAL	2	TRUE	0	0.22	1		221	497	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	28	507	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	0.392	0.318	0.253	0.392	SUBCLONAL	1	TRUE	1	0.27	2		507	653	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0015683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	31	790	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.243	0.196	0.298	0.243	0.196	0.298	SUBCLONAL	1	TRUE	1	0.27	2		792	944	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	58	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.21313254344427	2		248	491	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560085	29560085	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	70	424	0	ENST00000356175.3:c.3562C>T	p.Gln1188Ter	p.Q1188*	ENST00000356175	NM_000267.3	1188	Caa/Taa	27/57	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.21313254344427	2		424	471	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588834	29588834	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555619041	NA	P-0015684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	71	547	0	ENST00000356175.3:c.4621del	p.Asn1542ThrfsTer11	p.N1542Tfs*11	ENST00000356175	NM_000267.3	1540	agC/ag	34/57	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.21313254344427	2		547	492	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72893529	72893529	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	105	873	0	ENST00000325599.8:c.189del	p.Ser64ProfsTer25	p.S64Pfs*25	ENST00000325599	NM_018130.2	63	ggG/gg	2/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.21313254344427	2		873	821	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509049	106509049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1281619231	NA	P-0015684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	79	672	0	ENST00000359195.3:c.1043G>A	p.Ser348Asn	p.S348N	ENST00000359195	NM_002649.2	348	aGt/aAt	2/11	0.21313254344427	3	FACETS	1	0.96	1	0.609	0.536	0.689	CLONAL	1	TRUE	1	0.21313254344427	3		672	673	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0015685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	157	399	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.302015610143778	2	FACETS	0.935	0.862	1	0.935	0.862	1	CLONAL	2	TRUE	0	0.319364913617677	2		399	526	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259199	36259199	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1569084170	NA	P-0015685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	139	705	0	ENST00000300305.3:c.292del	p.Leu98SerfsTer24	p.L98Sfs*24	ENST00000300305		98	Ctc/tc	3/8	0.31129666960328	3	FACETS	1	0.953	1	0.537	0.488	0.588	CLONAL	1	TRUE	1	0.319364913617677	3		705	940	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855944	68855944	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	108	552	0	ENST00000261769.5:c.1753del	p.Leu585CysfsTer4	p.L585Cfs*4	ENST00000261769	NM_004360.3	584	atC/at	12/16	0.319364913617677	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.319364913617677	1		552	488	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	686	248	0				ENST00000310581	NM_198253.2	-/1132			0.864147833229948	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.89642188413037	3		248	1096	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263932	104263948	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCCCCCGGCCCCACC	GCGCCCCCGGCCCCACC	-	novel	NA	P-0015687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	205	152	0	ENST00000369902.3:c.37_53del	p.Thr13TrpfsTer29	p.T13Wfs*29	ENST00000369902	NM_016169.3	8	gGCGCCCCCGGCCCCACC/g	1/12	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.89642188413037	2		152	369	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274346	5274346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	297	472	0	ENST00000357368.4:c.101G>A	p.Arg34Lys	p.R34K	ENST00000357368	NM_002850.3	34	aGg/aAg	3/38	1	2	FACETS	0.941	0.892	0.991	0.941	0.892	0.991	CLONAL	1	TRUE	1	0.89642188413037	2		472	704	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877423	40877423	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	374	546	0	ENST00000373198.4:c.2273A>C	p.Lys758Thr	p.K758T	ENST00000373198	NM_133170.3	758	aAg/aCg	15/32	0.874736938149775	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.89642188413037	1		546	460	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941664	48941687	+	frameshift_variant	Frame_Shift_Del	DEL	ATCTTAAAAATAAAGATCTAGATG	ATCTTAAAAATAAAGATCTAGATG	C	novel	NA	P-0015687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	180	253	0	ENST00000267163.4:c.974_997delinsC	p.Tyr325SerfsTer8	p.Y325Sfs*8	ENST00000267163	NM_000321.2	325	tATCTTAAAAATAAAGATCTAGATGca/tCca	10/27	0.874736938149775	1	FACETS	0.963	0.922	1	0.963	0.922	1	CLONAL	1	TRUE	0	0.89642188413037	1		253	230	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0015688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	221	771	2	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	1	2	FACETS	1	0.963	1	1	0.994	1	CLONAL	2	TRUE	1	0.259189421967908	2		773	814	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097801	27097801	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	100	365	0	ENST00000324856.7:c.3391del	p.Gln1131SerfsTer30	p.Q1131Sfs*30	ENST00000324856	NM_006015.4	1130	atC/at	12/20	0.355152902580621	1	FACETS	0.358	0.321	0.397	0.358	0.321	0.397	INDETERMINATE	1	TRUE	0	0.722973916444977	1		365	493	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450808	70450808	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	195	394	0	ENST00000373644.4:c.5648T>G	p.Met1883Arg	p.M1883R	ENST00000373644	NM_030625.2	1883	aTg/aGg	12/12	1	2	FACETS	0.965	0.9	1	0.965	0.9	1	CLONAL	1	TRUE	1	0.722973916444977	2		394	559	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59924533	59924533	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730881624	NA	P-0015689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1282	77	454	0	ENST00000259008.2:c.556A>G	p.Lys186Glu	p.K186E	ENST00000259008	NM_032043.2	186	Aaa/Gaa	6/20	0.722973916444977	7	FACETS	0.44	0.385	0.5			1	SUBCLONAL	1	TRUE	NA	0.722973916444977	7		454	1359	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430352	47430352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	389	795	3	ENST00000377045.4:c.1627C>T	p.Arg543Trp	p.R543W	ENST00000377045	NM_001654.4	543	Cgg/Tgg	15/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.722973916444977	2		798	1024	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437363	110437373	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGTCGGTGC	GCTGTCGGTGC	A	novel	NA	P-0015689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	59	201	0	ENST00000375856.3:c.1028_1038delinsT	p.Arg343LeufsTer45	p.R343Lfs*45	ENST00000375856	NM_003749.2	343	cGCACCGACAGC/cT	1/2	0.421074592838967	1	FACETS	0.389	0.337	0.444	0.389	0.337	0.444	INDETERMINATE	1	TRUE	0	0.722973916444977	1		201	268	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0015691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	91	467	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.281324313487347	2		467	600	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	104	414	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	0.281324313487347	2		414	501	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0015691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	25	312	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.281262813212237	2	FACETS	0.819	0.649	1	0.41	0.324	0.506	CLONAL	1	TRUE	0	0.281324313487347	2		312	217	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0015691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	78	437	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.813	0.714	0.919	0.813	0.714	0.919	CLONAL	1	TRUE	1	0.281324313487347	2		437	682	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0015691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	216	638	3	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.281324313487347	2		641	1172	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	196	664	2	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.281324313487347	2		666	1116	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671654	67671655	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	43	447	1	ENST00000264010.4:c.2070dup	p.Glu691ArgfsTer5	p.E691Rfs*5	ENST00000264010	NM_006565.3	688	gta/gtAa	12/12	1	2	FACETS	0.426	0.356	0.505	0.426	0.356	0.505	SUBCLONAL	1	TRUE	1	0.281324313487347	2		448	717	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294088	1294088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1373	301	865	1	ENST00000310581.5:c.913G>A	p.Ala305Thr	p.A305T	ENST00000310581	NM_198253.2	305	Gcg/Acg	2/16	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.281324313487347	2		866	1674	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752729	128752731	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs1203089442	NA	P-0015691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	36	207	0	ENST00000377970.2:c.892_894del	p.Ser298del	p.S298del	ENST00000377970	NM_002467.4	297	cCTTct/cct	3/3	1	2	FACETS	0.665	0.547	0.796	0.665	0.547	0.796	SUBCLONAL	1	TRUE	1	0.281324313487347	2		207	385	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29090060	29090060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121908706	NA	P-0015691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	27	208	0	ENST00000328354.6:c.1421G>A	p.Arg474His	p.R474H	ENST00000328354	NM_007194.3	474	cGt/cAt	13/15	1	2	FACETS	0.433	0.344	0.535	0.433	0.344	0.535	SUBCLONAL	1	TRUE	1	0.281324313487347	2		208	443	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100944	27100944	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	76	501	0	ENST00000324856.7:c.4226A>G	p.Gln1409Arg	p.Q1409R	ENST00000324856	NM_006015.4	1409	cAg/cGg	18/20	1	2	FACETS	0.67	0.587	0.76	0.67	0.587	0.76	SUBCLONAL	1	TRUE	1	0.281324313487347	2		501	806	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736254	243736254	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	45	418	0	ENST00000263826.5:c.793G>T	p.Gly265Ter	p.G265*	ENST00000263826	NM_005465.4	265	Gga/Tga	8/13	1	2	FACETS	0.577	0.485	0.68	0.577	0.485	0.68	SUBCLONAL	1	TRUE	1	0.281324313487347	2		418	554	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138473	2138473	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	108	720	1	ENST00000219476.3:c.5286C>A	p.Asn1762Lys	p.N1762K	ENST00000219476	NM_000548.3	1762	aaC/aaA	42/42	1	2	FACETS	0.661	0.591	0.735	0.661	0.591	0.735	SUBCLONAL	1	TRUE	1	0.281324313487347	2		721	1162	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119966	70120018	+	frameshift_variant	Frame_Shift_Del	DEL	GCACCGCGGCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAG	GCACCGCGGCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAG	-	novel	NA	P-0015691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	42	275	0	ENST00000245479.2:c.970_1022del	p.Thr324AlafsTer236	p.T324Afs*236	ENST00000245479	NM_000346.3	323	aGCACCGCGGCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAG/a	3/3	1	2	FACETS	0.619	0.517	0.733	0.619	0.517	0.733	SUBCLONAL	1	TRUE	1	0.281324313487347	2		275	482	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15378230	15378230	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	103	412	0	ENST00000263377.2:c.556A>G	p.Thr186Ala	p.T186A	ENST00000263377	NM_058243.2	186	Aca/Gca	4/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.281324313487347	2		412	611	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215965	36215966	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	219	698	1	ENST00000222270.7:c.3506dup	p.His1169GlnfsTer8	p.H1169Qfs*8	ENST00000222270	NM_014727.1	1169	cac/cAac	10/37	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.281324313487347	2		699	1336	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339242	116339242	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	25	356	0	ENST00000397752.3:c.104T>C	p.Met35Thr	p.M35T	ENST00000397752	NM_000245.2	35	aTg/aCg	2/21	1	2	FACETS	0.361	0.284	0.451	0.361	0.284	0.451	SUBCLONAL	1	TRUE	1	0.281324313487347	2		356	492	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030433	47030433	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	198	603	0	ENST00000377604.3:c.208T>C	p.Tyr70His	p.Y70H	ENST00000377604	NM_001204468.1	70	Tac/Cac	4/24	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.281324313487347	2		603	1220	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0015692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	904	920	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.467532304314129	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.467532304314129	3		920	1567	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	532668	532668	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	526	987	0	ENST00000451590.1:c.538G>C	p.Gly180Arg	p.G180R	ENST00000451590	NM_001130442.1	180	Ggc/Cgc	5/5	0.443113749747876	2	FACETS	0.972	0.935	1	0.972	0.935	1	CLONAL	2	TRUE	0	0.467532304314129	2		987	1157	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951052	48951052	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0015692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	88	223	1	ENST00000267163.4:c.1216-2A>T		p.X406_splice	ENST00000267163	NM_000321.2	406			0.443113749747876	2	FACETS	0.759	0.683	0.837	0.759	0.683	0.837	SUBCLONAL	2	TRUE	0	0.467532304314129	2		224	248	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984370	72984370	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0015692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	260	396	0	ENST00000268489.5:c.3214A>T	p.Lys1072Ter	p.K1072*	ENST00000268489	NM_006885.3	1072	Aag/Tag	3/10	0.448878286054686	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.467532304314129	2		396	527	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117163	7117163	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	164	711	0	ENST00000302850.5:c.4053C>G	p.Phe1351Leu	p.F1351L	ENST00000302850	NM_000208.2	1351	ttC/ttG	22/22	0.448878286054686	2	FACETS	0.765	0.702	0.831	0.383	0.351	0.416	SUBCLONAL	1	TRUE	0	0.467532304314129	2		711	917	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99160381	99160381	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	159	567	0	ENST00000074304.5:c.860G>C	p.Trp287Ser	p.W287S	ENST00000074304	NM_001134224.1	287	tGg/tCg	11/26	0.375761413933347	3	FACETS	0.916	0.84	0.996	0.458	0.42	0.498	CLONAL	1	TRUE	1	0.467532304314129	3		567	916	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268371	142268371	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	161	428	0	ENST00000350721.4:c.3121G>T	p.Val1041Phe	p.V1041F	ENST00000350721	NM_001184.3	1041	Gtc/Ttc	15/47	0.284369730652323	4	FACETS	0.837	0.771	0.905	0.837	0.771	0.905	CLONAL	2	TRUE	2	0.467532304314129	4		428	604	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652068	36652068	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	457	922	1	ENST00000244741.5:c.190G>T	p.Ala64Ser	p.A64S	ENST00000244741	NM_000389.4	64	Gcc/Tcc	2/3	0.46138252772684	2	FACETS	0.96	0.921	1	0.96	0.921	1	CLONAL	2	TRUE	0	0.467532304314129	2		923	1018	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395228	139395228	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	537	885	0	ENST00000277541.6:c.5710del	p.Glu1904ArgfsTer77	p.E1904Rfs*77	ENST00000277541	NM_017617.3	1904	Gag/ag	31/34	0.443113749747876	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.467532304314129	2		885	1134	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	93	248	0				ENST00000310581	NM_198253.2	-/1132			0.169171763286256	3	FACETS	1	0.975	1	0.685	0.608	0.768	CLONAL	1	TRUE	1	0.169171763286256	3		248	870	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579386	7579386	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0015693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	198	724	0	ENST00000269305.4:c.301A>T	p.Lys101Ter	p.K101*	ENST00000269305	NM_001126112.2	101	Aaa/Taa	4/11	0.169171763286256	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.169171763286256	2		724	1090	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067836	30067836	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315499	NA	P-0015693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	99	320	0	ENST00000338641.4:c.1021C>T	p.Arg341Ter	p.R341*	ENST00000338641	NM_000268.3	341	Cga/Tga	11/16	0.169171763286256	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.169171763286256	2		320	515	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0015695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	203	670	1	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.420693707566631	2		671	878	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0015695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	235	414	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.39744195079642	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.420693707566631	3		414	654	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0015697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	26	279	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.774	0.612	0.96	0.774	0.612	0.96	CLONAL	1	TRUE	1	0.14	2		279	480	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913255	NA	P-0015697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	115	578	0	ENST00000369535.4:c.183A>C	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caC	3/7	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.14	2		578	1222	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280616	115280616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437302046	NA	P-0015697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	115	581	0	ENST00000438362.2:c.415G>A	p.Glu139Lys	p.E139K	ENST00000438362	NM_001242891.1	139	Gaa/Aaa	4/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.14	2		581	1193	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685307	89685307	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123317	NA	P-0015697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	46	274	0	ENST00000371953.3:c.202T>C	p.Tyr68His	p.Y68H	ENST00000371953	NM_000314.4	68	Tac/Cac	3/9	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.14	2		274	557	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230691	46230691	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	26	340	0	ENST00000334344.6:c.940C>G	p.Arg314Gly	p.R314G	ENST00000334344	NM_152641.2	314	Cgt/Ggt	8/21	1	2	FACETS	0.606	0.478	0.753	0.606	0.478	0.753	SUBCLONAL	1	TRUE	1	0.14	2		340	613	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120795636	120795636	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	55	446	0	ENST00000257552.2:c.517G>A	p.Glu173Lys	p.E173K	ENST00000257552	NM_002442.3	173	Gaa/Aaa	8/15	1	2	FACETS	0.928	0.791	1	0.928	0.791	1	CLONAL	1	TRUE	1	0.14	2		446	847	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685527	29685527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786203669	NA	P-0015697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	42	397	0	ENST00000356175.3:c.7937C>T	p.Thr2646Ile	p.T2646I	ENST00000356175	NM_000267.3	2646	aCc/aTc	54/57	1	2	FACETS	0.754	0.627	0.895	0.754	0.627	0.895	SUBCLONAL	1	TRUE	1	0.14	2		397	796	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618899	37618899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759887608	NA	P-0015697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1214	68	658	0	ENST00000447079.4:c.575C>T	p.Ser192Phe	p.S192F	ENST00000447079	NM_015083.1	192	tCt/tTt	1/14	1	2	FACETS	0.758	0.657	0.868	0.758	0.657	0.868	SUBCLONAL	1	TRUE	1	0.14	2		658	1282	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533519	63533538	+	frameshift_variant	Frame_Shift_Del	DEL	CCCAGGGCAGAAGCAGTGCA	CCCAGGGCAGAAGCAGTGCA	-	novel	NA	P-0015697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	49	523	0	ENST00000307078.5:c.1616_1635del	p.Val539GlyfsTer82	p.V539Gfs*82	ENST00000307078	NM_004655.3	539	gTGCACTGCTTCTGCCCTGGG/g	6/11	1	2	FACETS	0.726	0.613	0.852	0.726	0.613	0.852	SUBCLONAL	1	TRUE	1	0.14	2		523	964	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7152765	7152765	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1360	92	733	0	ENST00000302850.5:c.2203T>C	p.Tyr735His	p.Y735H	ENST00000302850	NM_000208.2	735	Tac/Cac	10/22	1	2	FACETS	0.905	0.801	1	0.905	0.801	1	CLONAL	1	TRUE	1	0.14	2		733	1452	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184490	7184490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs537134904	NA	P-0015697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	65	598	0	ENST00000302850.5:c.811C>T	p.Pro271Ser	p.P271S	ENST00000302850	NM_000208.2	271	Ccg/Tcg	3/22	1	2	FACETS	0.863	0.746	0.991	0.863	0.746	0.991	CLONAL	1	TRUE	1	0.14	2		598	1076	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560934	9560934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	30	322	0	ENST00000353224.5:c.848G>A	p.Arg283Gln	p.R283Q	ENST00000353224	NM_177990.2	283	cGg/cAg	4/10	1	2	FACETS	0.768	0.617	0.94	0.768	0.617	0.94	CLONAL	1	TRUE	1	0.14	2		322	558	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31483732	31483732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	34	292	1	ENST00000344624.3:c.2000C>T	p.Pro667Leu	p.P667L	ENST00000344624		667	cCt/cTt	13/33	1	2	FACETS	0.781	0.636	0.944	0.781	0.636	0.944	CLONAL	1	TRUE	1	0.14	2		293	622	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982137	93982137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	29	298	0	ENST00000369303.4:c.1328C>T	p.Pro443Leu	p.P443L	ENST00000369303	NM_004440.3	443	cCc/cTc	6/17	1	2	FACETS	0.755	0.604	0.927	0.755	0.604	0.927	CLONAL	1	TRUE	1	0.14	2		298	549	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641087	117641087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	50	509	0	ENST00000368508.3:c.5884G>A	p.Gly1962Arg	p.G1962R	ENST00000368508	NM_002944.2	1962	Gga/Aga	36/43	1	2	FACETS	0.746	0.631	0.874	0.746	0.631	0.874	SUBCLONAL	1	TRUE	1	0.14	2		509	957	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367234	50367234	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	27	329	0	ENST00000331340.3:c.41G>A	p.Gly14Glu	p.G14E	ENST00000331340	NM_006060.4	14	gGg/gAg	3/8	1	2	FACETS	0.75	0.596	0.928	0.75	0.596	0.928	CLONAL	1	TRUE	1	0.14	2		329	514	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506444	148506444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	30	371	1	ENST00000320356.2:c.2068C>T	p.Arg690Cys	p.R690C	ENST00000320356	NM_004456.4	690	Cgt/Tgt	18/20	1	2	FACETS	0.566	0.454	0.694	0.566	0.454	0.694	SUBCLONAL	1	TRUE	1	0.14	2		372	757	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879370	151879370	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	52	412	0	ENST00000262189.6:c.5575C>T	p.Pro1859Ser	p.P1859S	ENST00000262189	NM_170606.2	1859	Cca/Tca	36/59	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.14	2		412	729	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930094	68930094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	48	431	0	ENST00000288368.4:c.155G>A	p.Arg52Lys	p.R52K	ENST00000288368	NM_024870.2	52	aGa/aAa	2/40	1	2	FACETS	0.75	0.632	0.881	0.75	0.632	0.881	SUBCLONAL	1	TRUE	1	0.14	2		431	914	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528767	8528767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752353348	NA	P-0015697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	80	305	1	ENST00000356435.5:c.365C>T	p.Pro122Leu	p.P122L	ENST00000356435		122	cCc/cTc	4/35	1	2	FACETS	0.929	0.819	1	1	0.982	1	CLONAL	2	TRUE	1	0.14	2		306	615	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938127	76938127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782339652	NA	P-0015697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	62	544	2	ENST00000373344.5:c.2621G>A	p.Gly874Glu	p.G874E	ENST00000373344	NM_000489.3	874	gGa/gAa	9/35	1	2	FACETS	0.793	0.682	0.914	0.793	0.682	0.914	CLONAL	1	TRUE	1	0.14	2		546	1117	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575550	64575550	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs794728648	NA	P-0015698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	467	398	0	ENST00000312049.6:c.467G>T	p.Gly156Val	p.G156V	ENST00000312049	NM_130799.2	156	gGt/gTt	3/10	0.784984974634891	1	FACETS	0.962	0.93	0.993	0.962	0.93	0.993	CLONAL	1	TRUE	0	0.803479752255466	1		398	723	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2115499	2115526	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTCCTGGCCTTCTCTTCAAAGGTGATGG	GTCCTGGCCTTCTCTTCAAAGGTGATGG	TCA	novel	NA	P-0015698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	300	558	2	ENST00000219476.3:c.1600-21_1606delinsTCA		p.X534_splice	ENST00000219476	NM_000548.3	534		16/42	0.784984974634891	1	FACETS	0.722	0.686	0.757	0.722	0.686	0.757	SUBCLONAL	1	TRUE	0	0.803479752255466	1		560	619	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286815	33286815	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	510	387	0	ENST00000374542.5:c.2122C>T	p.Gln708Ter	p.Q708*	ENST00000374542	NM_001141970.1	708	Caa/Taa	7/8	0.784984974634891	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.803479752255466	1		387	754	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	462	668	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.958	0.921	0.995	1	0.997	1	CLONAL	2	TRUE	1	0.538110858676879	2		671	896	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	117	892	7	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.931	0.845	1	0.931	0.845	1	CLONAL	1	TRUE	1	0.538110858676879	2		899	467	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	42	385	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	0.538110858676879	1	FACETS	0.528	0.445	0.618	0.528	0.445	0.618	SUBCLONAL	1	TRUE	0	0.538110858676879	1		385	216	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164772	106164772	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761811530	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	54	354	0	ENST00000380013.4:c.3640C>T	p.Arg1214Trp	p.R1214W	ENST00000380013	NM_001127208.2	1214	Cgg/Tgg	6/11	1	2	FACETS	0.325	0.277	0.377	0.325	0.277	0.377	SUBCLONAL	1	TRUE	1	0.538110858676879	2		354	618	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154293	2154293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61732764	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	305	1038	0	ENST00000434045.2:c.635G>A	p.Arg212His	p.R212H	ENST00000434045	NM_001127598.1	212	cGt/cAt	5/5	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.538110858676879	2		1038	1115	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664989	138664989	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	181	473	0	ENST00000330315.3:c.576del	p.Lys193SerfsTer78	p.K193Sfs*78	ENST00000330315	NM_023067.3	192	ccC/cc	1/1	1	2	FACETS	0.982	0.909	1	0.982	0.909	1	CLONAL	1	TRUE	1	0.538110858676879	2		473	685	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420204	49420204	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	250	721	0	ENST00000301067.7:c.15545del	p.Gly5182AlafsTer61	p.G5182Afs*61	ENST00000301067	NM_003482.3	5182	gGc/gc	48/54	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.538110858676879	2		721	929	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	343	851	3	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.946	0.894	0.999	0.946	0.894	0.999	CLONAL	1	TRUE	1	0.538110858676879	2		854	1348	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183339	56183339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	36	457	0	ENST00000399503.3:c.4249G>A	p.Ala1417Thr	p.A1417T	ENST00000399503	NM_005921.1	1417	Gca/Aca	18/20	1	2	FACETS	0.631	0.523	0.75	0.631	0.523	0.75	SUBCLONAL	1	TRUE	1	0.538110858676879	2		457	212	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509081	106509081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs187257485	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	93	613	0	ENST00000359195.3:c.1075C>T	p.Arg359Cys	p.R359C	ENST00000359195	NM_002649.2	359	Cgc/Tgc	2/11	1	2	FACETS	0.45	0.4	0.504	0.45	0.4	0.504	SUBCLONAL	1	TRUE	1	0.538110858676879	2		613	768	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030591	48030591	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	26	472	0	ENST00000234420.5:c.3209del	p.Gly1070ValfsTer9	p.G1070Vfs*9	ENST00000234420	NM_000179.2	1069	Ggg/gg	5/10	1	2	FACETS	0.243	0.192	0.301	0.243	0.192	0.301	SUBCLONAL	1	TRUE	1	0.538110858676879	2		472	398	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	125	509	0	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	0.12244645694458	4	FACETS	0.752	0.685	0.822	0.752	0.685	0.822	INDETERMINATE	2	TRUE	2	0.538110858676879	4		509	475	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030692	48030692	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs267608092	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	66	416	1	ENST00000234420.5:c.3312del	p.Phe1104LeufsTer11	p.F1104Lfs*11	ENST00000234420	NM_000179.2	1102	acT/ac	5/10	1	2	FACETS	0.852	0.746	0.964	0.852	0.746	0.964	CLONAL	1	TRUE	1	0.538110858676879	2		417	288	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781302	3781302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781364836	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	376	1062	1	ENST00000262367.5:c.5063C>T	p.Thr1688Met	p.T1688M	ENST00000262367	NM_004380.2	1688	aCg/aTg	30/31	0.12244645694458	4	FACETS	1	0.995	1	0.726	0.688	0.765	INDETERMINATE	1	TRUE	2	0.538110858676879	4		1063	1481	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272336	15272337	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs771517374	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	486	1127	5	ENST00000263388.2:c.6102dup	p.Gly2035ArgfsTer60	p.G2035Rfs*60	ENST00000263388	NM_000435.2	2034	-/C	33/33	0.159502617881789	4	FACETS	0.993	0.95	1	0.993	0.95	1	INDETERMINATE	2	TRUE	2	0.538110858676879	4		1132	1399	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187558039	187558039	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	14	294	0	ENST00000441802.2:c.3672del	p.Lys1225AsnfsTer9	p.K1225Nfs*9	ENST00000441802	NM_005245.3	1224	ccC/cc	5/27	1	2	FACETS	0.38	0.276	0.503	0.38	0.276	0.503	SUBCLONAL	1	TRUE	1	0.538110858676879	2		294	137	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394066	31394066	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	79	606	0	ENST00000328111.2:c.2357del	p.Asn786ThrfsTer8	p.N786Tfs*8	ENST00000328111	NM_006892.3	785	Aaa/aa	22/23	0.538110858676879	3	FACETS	0.681	0.6	0.768	0.341	0.3	0.384	SUBCLONAL	1	TRUE	1	0.538110858676879	3		606	547	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119765	70119766	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	251	854	1	ENST00000245479.2:c.770_771dup	p.Pro258AlafsTer22	p.P258Afs*22	ENST00000245479	NM_000346.3	256	ggg/ggGCg	3/3	1	2	FACETS	0.913	0.854	0.973	0.913	0.854	0.973	CLONAL	1	TRUE	1	0.538110858676879	2		855	1022	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631575	119631575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	39	594	1	ENST00000316626.5:c.691G>A	p.Ala231Thr	p.A231T	ENST00000316626		231	Gcc/Acc	6/12	1	2	FACETS	0.564	0.47	0.667	0.564	0.47	0.667	SUBCLONAL	1	TRUE	1	0.538110858676879	2		595	257	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578541	7578541	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1131691013	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	352	891	0	ENST00000269305.4:c.389T>C	p.Leu130Pro	p.L130P	ENST00000269305	NM_001126112.2	130	cTc/cCc	5/11	0.538110858676879	1	FACETS	0.987	0.937	1	0.987	0.937	1	CLONAL	1	TRUE	0	0.538110858676879	1		891	969	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681463	30681463	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	79	596	0	ENST00000376406.3:c.549del	p.Lys183AsnfsTer9	p.K183Nfs*9	ENST00000376406	NM_014641.2	183	aaA/aa	4/15	0.414700617809863	2	FACETS	0.798	0.718	0.879	0.798	0.718	0.879	SUBCLONAL	2	TRUE	0	0.538110858676879	2		596	184	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811605	102811605	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1565968684	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	128	633	3	ENST00000307046.8:c.579del	p.Gly194GlufsTer8	p.G194Efs*8	ENST00000307046	NM_001111285.1	193	aaA/aa	4/4	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.538110858676879	2		636	455	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822586	72822586	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	161	507	8	ENST00000268489.5:c.9589del	p.Gln3197SerfsTer44	p.Q3197Sfs*44	ENST00000268489	NM_006885.3	3197	Cag/ag	10/10	0.12244645694458	4	FACETS	1	0.988	1	0.733	0.675	0.793	INDETERMINATE	1	TRUE	2	0.538110858676879	4		515	628	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796328	42796328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	340	1015	0	ENST00000575354.2:c.2977C>T	p.Pro993Ser	p.P993S	ENST00000575354	NM_015125.3	993	Cct/Tct	12/20	0.159502617881789	4	FACETS	1	0.994	1	0.734	0.694	0.775	INDETERMINATE	1	TRUE	2	0.538110858676879	4		1015	1324	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	101	904	1	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	0.414700617809863	2	FACETS	0.414	0.37	0.462	0.207	0.185	0.231	SUBCLONAL	1	TRUE	0	0.538110858676879	2		905	906	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136210	64136210	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	94	948	0	ENST00000334205.4:c.1369C>A	p.Leu457Met	p.L457M	ENST00000334205	NM_003942.2	457	Ctg/Atg	12/17	1	2	FACETS	0.288	0.255	0.324	0.288	0.255	0.324	SUBCLONAL	1	TRUE	1	0.538110858676879	2		948	1212	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939828	71939828	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	102	910	1	ENST00000298229.2:c.459del	p.Thr154LeufsTer25	p.T154Lfs*25	ENST00000298229	NM_001567.3	152	gCc/gc	4/28	1	2	FACETS	0.305	0.271	0.34	0.305	0.271	0.34	SUBCLONAL	1	TRUE	1	0.538110858676879	2		911	1245	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431700	431700	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	63	738	0	ENST00000399788.2:c.2309C>A	p.Ala770Asp	p.A770D	ENST00000399788	NM_001042603.1	770	gCt/gAt	17/28	NA	2	FACETS	0.796	0.695	0.905			1	INDETERMINATE	1	TRUE	NA	0.538110858676879	2		738	294	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038929	12038929	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	117	558	0	ENST00000396373.4:c.1222A>T	p.Arg408Trp	p.R408W	ENST00000396373	NM_001987.4	408	Agg/Tgg	7/8	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.538110858676879	2		558	420	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800847	18800847	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs778955705	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	21	502	0	ENST00000266497.5:c.4223T>C	p.Val1408Ala	p.V1408A	ENST00000266497		1408	gTc/gCc	31/31	1	2	FACETS	0.356	0.275	0.45	0.356	0.275	0.45	SUBCLONAL	1	TRUE	1	0.538110858676879	2		502	219	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123895	46123895	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	78	428	1	ENST00000334344.6:c.161T>A	p.Val54Asp	p.V54D	ENST00000334344	NM_152641.2	54	gTc/gAc	2/21	1	2	FACETS	0.719	0.635	0.809	0.719	0.635	0.809	SUBCLONAL	1	TRUE	1	0.538110858676879	2		429	403	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425349	49425349	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756684775	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	51	828	0	ENST00000301067.7:c.13139del	p.Pro4380GlnfsTer4	p.P4380Qfs*4	ENST00000301067	NM_003482.3	4380	cCa/ca	39/54	1	2	FACETS	0.232	0.196	0.271	0.232	0.196	0.271	SUBCLONAL	1	TRUE	1	0.538110858676879	2		828	818	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437076	121437076	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	245	706	0	ENST00000257555.6:c.1507T>C	p.Tyr503His	p.Y503H	ENST00000257555		503	Tac/Cac	8/10	0.513948856279756	3	FACETS	1	0.972	1	0.537	0.502	0.574	CLONAL	1	TRUE	1	0.538110858676879	3		706	1076	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226103	133226103	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	188	654	0	ENST00000320574.5:c.3796-2A>G		p.X1266_splice	ENST00000320574	NM_006231.2	1266			0.513948856279756	3	FACETS	1	0.973	1	0.553	0.512	0.596	CLONAL	1	TRUE	1	0.538110858676879	3		654	802	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133242038	133242038	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	219	735	0	ENST00000320574.5:c.2320-2A>G		p.X774_splice	ENST00000320574	NM_006231.2	774			0.513948856279756	3	FACETS	0.838	0.779	0.901	0.419	0.389	0.451	CLONAL	1	TRUE	1	0.538110858676879	3		735	1232	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640041	3640041	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	119	951	0	ENST00000294008.3:c.3598G>T	p.Asp1200Tyr	p.D1200Y	ENST00000294008	NM_032444.2	1200	Gat/Tat	12/15	0.12244645694458	4	FACETS	0.934	0.844	1	0.467	0.422	0.515	INDETERMINATE	1	TRUE	2	0.538110858676879	4		951	728	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778468	3778468	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766744145	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	191	1033	1	ENST00000262367.5:c.6580C>T	p.Arg2194Trp	p.R2194W	ENST00000262367	NM_004380.2	2194	Cgg/Tgg	31/31	0.12244645694458	4	FACETS	1	0.984	1	0.619	0.573	0.667	INDETERMINATE	1	TRUE	2	0.538110858676879	4		1034	882	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778884	3778884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	144	561	0	ENST00000262367.5:c.6164G>A	p.Ser2055Asn	p.S2055N	ENST00000262367	NM_004380.2	2055	aGc/aAc	31/31	0.12244645694458	4	FACETS	1	0.986	1	0.708	0.649	0.77	INDETERMINATE	1	TRUE	2	0.538110858676879	4		561	581	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829718	72829718	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	45	848	0	ENST00000268489.5:c.6863T>C	p.Val2288Ala	p.V2288A	ENST00000268489	NM_006885.3	2288	gTg/gCg	9/10	0.12244645694458	4	FACETS	0.402	0.337	0.474	0.201	0.168	0.237	INDETERMINATE	1	TRUE	2	0.538110858676879	4		848	640	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81962231	81962231	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	97	532	0	ENST00000359376.3:c.2581+2T>C		p.X861_splice	ENST00000359376	NM_002661.3	861			0.12244645694458	4	FACETS	1	0.981	1	0.726	0.652	0.803	INDETERMINATE	1	TRUE	2	0.538110858676879	4		532	382	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29563007	29563007	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	63	559	2	ENST00000356175.3:c.3942G>T	p.Trp1314Cys	p.W1314C	ENST00000356175	NM_000267.3	1314	tgG/tgT	29/57	1	2	FACETS	0.851	0.744	0.966	0.851	0.744	0.966	CLONAL	1	TRUE	1	0.538110858676879	2		561	275	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245333	41245333	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs56329598	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	79	783	0	ENST00000357654.3:c.2215A>T	p.Lys739Ter	p.K739*	ENST00000357654	NM_007294.3	739	Aaa/Taa	10/23	1	2	FACETS	0.787	0.697	0.883	0.787	0.697	0.883	SUBCLONAL	1	TRUE	1	0.538110858676879	2		783	373	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603028	48603028	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	95	321	0	ENST00000342988.3:c.1329T>G	p.Cys443Trp	p.C443W	ENST00000342988	NM_005359.5	443	tgT/tgG	11/12	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.538110858676879	2		321	328	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3120996	3120996	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs919502623	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	64	598	0	ENST00000078429.4:c.899G>A	p.Arg300Gln	p.R300Q	ENST00000078429	NM_002067.2	300	cGg/cAg	7/7	0.159502617881789	4	FACETS	0.424	0.366	0.487	0.212	0.183	0.244	INDETERMINATE	1	TRUE	2	0.538110858676879	4		598	863	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138569	11138569	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	166	851	0	ENST00000358026.2:c.3325A>G	p.Met1109Val	p.M1109V	ENST00000358026	NM_001128849.1	1109	Atg/Gtg	24/36	0.159502617881789	4	FACETS	1	0.987	1	0.694	0.639	0.75	INDETERMINATE	1	TRUE	2	0.538110858676879	4		851	684	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961642	18961642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	177	537	1	ENST00000262803.5:c.775G>A	p.Ala259Thr	p.A259T	ENST00000262803	NM_002911.3	259	Gca/Aca	5/24	0.159502617881789	4	FACETS	1	0.978	1	0.581	0.535	0.628	INDETERMINATE	1	TRUE	2	0.538110858676879	4		538	871	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912142	50912142	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	322	975	0	ENST00000440232.2:c.1876A>G	p.Thr626Ala	p.T626A	ENST00000440232	NM_002691.3	626	Act/Gct	15/27	0.159502617881789	4	FACETS	0.793	0.749	0.839	0.793	0.749	0.839	INDETERMINATE	2	TRUE	2	0.538110858676879	4		975	1160	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47600610	47600611	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	72	459	0	ENST00000263735.4:c.87_88del	p.Cys29Ter	p.C29*	ENST00000263735	NM_002354.2	29	TGt/t	2/9	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.538110858676879	2		459	211	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023424	31023424	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	111	504	0	ENST00000375687.4:c.2909G>A	p.Ser970Asn	p.S970N	ENST00000375687	NM_015338.5	970	aGc/aAc	13/13	0.538110858676879	3	FACETS	0.977	0.882	1	0.488	0.441	0.539	CLONAL	1	TRUE	1	0.538110858676879	3		504	536	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727179	40727179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	387	603	0	ENST00000373198.4:c.3785C>T	p.Pro1262Leu	p.P1262L	ENST00000373198	NM_133170.3	1262	cCt/cTt	28/32	0.538110858676879	3	FACETS	0.898	0.856	0.941	0.898	0.856	0.941	CLONAL	2	TRUE	1	0.538110858676879	3		603	1016	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306617	41306617	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	208	779	0	ENST00000373198.4:c.1042T>C	p.Trp348Arg	p.W348R	ENST00000373198	NM_133170.3	348	Tgg/Cgg	7/32	0.538110858676879	3	FACETS	1	0.968	1	0.536	0.498	0.576	CLONAL	1	TRUE	1	0.538110858676879	3		779	915	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321432	62321432	+	splice_region_variant,intron_variant	Splice_Region	DEL	C	C	-	rs755965232	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	234	648	4	ENST00000360203.5:c.2142-3del		p.X714_splice	ENST00000360203	NM_001283009.1	714			0.538110858676879	3	FACETS	1	0.976	1	0.549	0.512	0.587	CLONAL	1	TRUE	1	0.538110858676879	3		652	1005	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326475	62326475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1455366888	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	769	1099	1	ENST00000360203.5:c.3400G>A	p.Asp1134Asn	p.D1134N	ENST00000360203	NM_001283009.1	1134	Gac/Aac	33/35	0.538110858676879	3	FACETS	0.982	0.95	1	0.982	0.95	1	CLONAL	2	TRUE	1	0.538110858676879	3		1100	1846	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130707	29130707	+	start_lost	Translation_Start_Site	SNP	C	C	T	rs786203977	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	112	390	1	ENST00000328354.6:c.3G>A	p.Met1?	p.M1?	ENST00000328354	NM_007194.3	1	atG/atA	2/15	1	2	FACETS	0.819	0.74	0.902	0.819	0.74	0.902	CLONAL	1	TRUE	1	0.538110858676879	2		391	508	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180367	38180367	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1227037938	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	235	881	0	ENST00000396334.3:c.215T>C	p.Leu72Ser	p.L72S	ENST00000396334	NM_002468.4	72	tTg/tCg	1/5	1	2	FACETS	0.97	0.907	1	0.97	0.907	1	CLONAL	1	TRUE	1	0.538110858676879	2		881	900	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162765	47162765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1336548478	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	39	420	0	ENST00000409792.3:c.3361G>A	p.Ala1121Thr	p.A1121T	ENST00000409792	NM_014159.6	1121	Gca/Aca	3/21	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.538110858676879	2		420	134	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026840	71026840	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	23	322	0	ENST00000318789.4:c.1382A>G	p.Asn461Ser	p.N461S	ENST00000318789	NM_032682.5	461	aAc/aGc	16/21	1	2	FACETS	0.743	0.589	0.916	0.743	0.589	0.916	CLONAL	1	TRUE	1	0.538110858676879	2		322	115	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851675	134851675	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	143	481	0	ENST00000398015.3:c.1085del	p.Lys362SerfsTer25	p.K362Sfs*25	ENST00000398015	NM_004441.4	361	Aaa/aa	5/16	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.538110858676879	2		481	503	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807204	1807204	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	144	838	0	ENST00000260795.2:c.1534+1G>A		p.X512_splice	ENST00000260795		512			1	2	FACETS	0.74	0.676	0.807	0.74	0.676	0.807	SUBCLONAL	1	TRUE	1	0.538110858676879	2		838	723	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599315	55599315	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	88	620	0	ENST00000288135.5:c.2441C>A	p.Ala814Asp	p.A814D	ENST00000288135	NM_000222.2	814	gCc/gAc	17/21	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.538110858676879	2		620	304	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524392	187524392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	177	494	0	ENST00000441802.2:c.11288G>A	p.Ser3763Asn	p.S3763N	ENST00000441802	NM_005245.3	3763	aGc/aAc	19/27	1	2	FACETS	0.942	0.871	1	0.942	0.871	1	CLONAL	1	TRUE	1	0.538110858676879	2		494	698	SUCCESS
APC	324	MSKCC	GRCh37	5	112177650	112177650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	16	350	0	ENST00000257430.4:c.6359C>T	p.Ala2120Val	p.A2120V	ENST00000257430	NM_000038.5	2120	gCt/gTt	16/16	1	2	FACETS	0.342	0.253	0.446	0.342	0.253	0.446	SUBCLONAL	1	TRUE	1	0.538110858676879	2		350	174	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439387	149439387	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	203	781	1	ENST00000286301.3:c.2008G>T	p.Asp670Tyr	p.D670Y	ENST00000286301	NM_005211.3	670	Gac/Tac	15/22	1	2	FACETS	0.898	0.834	0.964	0.898	0.834	0.964	CLONAL	1	TRUE	1	0.538110858676879	2		782	840	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149452928	149452928	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	54	734	3	ENST00000286301.3:c.1018G>T	p.Gly340Ter	p.G340*	ENST00000286301	NM_005211.3	340	Gga/Tga	7/22	1	2	FACETS	0.261	0.222	0.303	0.261	0.222	0.303	SUBCLONAL	1	TRUE	1	0.538110858676879	2		737	770	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038457	180038457	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	127	868	0	ENST00000261937.6:c.3560C>G	p.Ala1187Gly	p.A1187G	ENST00000261937	NM_182925.4	1187	gCc/gGc	27/30	1	2	FACETS	0.366	0.33	0.403	0.366	0.33	0.403	SUBCLONAL	1	TRUE	1	0.538110858676879	2		868	1291	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004423	150004423	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	23	542	0	ENST00000253339.5:c.1802A>G	p.Asp601Gly	p.D601G	ENST00000253339		601	gAt/gGt	3/7	1	2	FACETS	0.347	0.271	0.435	0.347	0.271	0.435	SUBCLONAL	1	TRUE	1	0.538110858676879	2		542	246	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268932	55268932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	141	931	1	ENST00000275493.2:c.2998G>A	p.Ala1000Thr	p.A1000T	ENST00000275493	NM_005228.3	1000	Gcc/Acc	25/28	1	2	FACETS	0.702	0.641	0.767	0.702	0.641	0.767	SUBCLONAL	1	TRUE	1	0.538110858676879	2		932	746	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151893021	151893021	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	10	427	0	ENST00000262189.6:c.4349A>G	p.Asp1450Gly	p.D1450G	ENST00000262189	NM_170606.2	1450	gAt/gGt	28/59	1	2	FACETS	0.198	0.134	0.278	0.198	0.134	0.278	SUBCLONAL	1	TRUE	1	0.538110858676879	2		427	188	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0015700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	196	581	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.296297744052247	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.32016076416199	1		582	987	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0015700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	78	345	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	0.296297744052247	1	FACETS	0.787	0.693	0.887	0.787	0.693	0.887	SUBCLONAL	1	TRUE	0	0.32016076416199	1		345	520	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248552	10248552	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1323856557	NA	P-0015700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	186	774	2	ENST00000340748.4:c.4201C>T	p.Arg1401Trp	p.R1401W	ENST00000340748		1401	Cgg/Tgg	35/40	1	2	FACETS	0.884	0.814	0.956	0.884	0.814	0.956	CLONAL	1	TRUE	1	0.32016076416199	2		776	1315	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731065	162731065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747307320	NA	P-0015700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	142	508	0	ENST00000367921.3:c.920G>A	p.Arg307His	p.R307H	ENST00000367921	NM_006182.2	307	cGc/cAc	9/18	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.32016076416199	2		508	883	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	186	414	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.889	0.82	0.961	0.889	0.82	0.961	CLONAL	1	TRUE	1	0.382791262220315	2		414	1093	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0015701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	276	563	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.346338404507639	1	FACETS	0.931	0.873	0.99	0.931	0.873	0.99	CLONAL	1	TRUE	0	0.382791262220315	1		564	1253	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579317	7579317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	101	531	0	ENST00000269305.4:c.370del	p.Cys124AlafsTer46	p.C124Afs*46	ENST00000269305	NM_001126112.2	124	Tgc/gc	4/11	0.372323186833018	1	FACETS	0.706	0.632	0.785	0.706	0.632	0.785	SUBCLONAL	1	TRUE	0	0.372323186833018	1		531	625	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0015703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	143	425	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.232055827390591	3	FACETS	0.842	0.771	0.915	0.842	0.771	0.915	CLONAL	2	TRUE	1	0.34389471791755	3		425	579	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	133	414	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.113558119145436	4	FACETS	1	0.983	1	0.679	0.617	0.744	INDETERMINATE	1	TRUE	2	0.34389471791755	4		414	765	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0015703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	52	280	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.722	0.616	0.837	0.722	0.616	0.837	SUBCLONAL	1	TRUE	1	0.34389471791755	2		280	419	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7120689	7120689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568426700	NA	P-0015703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	55	698	1	ENST00000302850.5:c.3601C>T	p.Arg1201Trp	p.R1201W	ENST00000302850	NM_000208.2	1201	Cgg/Tgg	20/22	1	2	FACETS	0.382	0.325	0.444	0.382	0.325	0.444	SUBCLONAL	1	TRUE	1	0.34389471791755	2		699	838	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972088	55972088	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	74	328	0	ENST00000263923.4:c.1556T>A	p.Ile519Asn	p.I519N	ENST00000263923	NM_002253.2	519	aTc/aAc	12/30	1	2	FACETS	0.906	0.796	1	0.906	0.796	1	CLONAL	1	TRUE	1	0.34389471791755	2		328	475	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047894	180047894	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	91	711	3	ENST00000261937.6:c.2281G>A	p.Ala761Thr	p.A761T	ENST00000261937	NM_182925.4	761	Gcc/Acc	15/30	1	2	FACETS	0.621	0.551	0.697	0.621	0.551	0.697	SUBCLONAL	1	TRUE	1	0.34389471791755	2		714	852	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0015704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	117	549	0	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	0.728566803715984	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	0	0.728566803715984	1		549	194	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003779	45003779	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	185	455	0	ENST00000558401.1:c.35T>C	p.Leu12Pro	p.L12P	ENST00000558401	NM_004048.2	12	cTa/cCa	1/4	0.718816201461917	2	FACETS	1	0.992	1	0.717	0.674	0.761	CLONAL	1	FALSE	0	0.728566803715984	2		455	354	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615595	43615595	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	93	540	0	ENST00000355710.3:c.2674G>C	p.Asp892His	p.D892H	ENST00000355710	NM_020975.4	892	Gat/Cat	15/20	NA	2	FACETS	0.978	0.883	1			1	INDETERMINATE	1	FALSE	NA	0.728566803715984	2		540	261	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219226	94219226	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	82	540	0	ENST00000323929.3:c.178G>T	p.Asp60Tyr	p.D60Y	ENST00000323929	NM_005591.3	60	Gat/Tat	4/20	1	2	FACETS	0.992	0.89	1	0.992	0.89	1	CLONAL	1	FALSE	1	0.728566803715984	2		540	227	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431762	49431762	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs772418918	NA	P-0015704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	100	599	1	ENST00000301067.7:c.9377G>T	p.Gly3126Val	p.G3126V	ENST00000301067	NM_003482.3	3126	gGa/gTa	34/54	1	2	FACETS	0.9	0.814	0.989	0.9	0.814	0.989	CLONAL	1	FALSE	1	0.728566803715984	2		600	305	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109788	115109788	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	98	947	0	ENST00000257566.3:c.2090C>A	p.Ser697Tyr	p.S697Y	ENST00000257566	NM_016569.3	697	tCc/tAc	8/8	0.681952989957108	3	FACETS	0.889	0.798	0.984	0.444	0.399	0.492	CLONAL	1	FALSE	1	0.728566803715984	3		947	413	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541714	120541714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750190278	NA	P-0015704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	93	585	0	ENST00000229340.5:c.143G>A	p.Arg48Gln	p.R48Q	ENST00000229340	NM_006861.6	48	cGg/cAg	3/6	0.681952989957108	3	FACETS	0.854	0.764	0.948	0.427	0.382	0.474	CLONAL	1	FALSE	1	0.728566803715984	3		585	408	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923119	48923119	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	49	309	0	ENST00000267163.4:c.568del	p.Val190CysfsTer2	p.V190Cfs*2	ENST00000267163	NM_000321.2	189	ttG/tt	6/27	1	2	FACETS	0.83	0.716	0.95	0.83	0.716	0.95	CLONAL	1	FALSE	1	0.728566803715984	2		309	162	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954187	48954187	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1555286568	NA	P-0015704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	50	286	0	ENST00000267163.4:c.1390-2A>G		p.X464_splice	ENST00000267163	NM_000321.2	464			1	2	FACETS	0.903	0.782	1	0.903	0.782	1	CLONAL	1	FALSE	1	0.728566803715984	2		286	152	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312768	91312768	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	217	481	0	ENST00000355112.3:c.2507G>A	p.Arg836Lys	p.R836K	ENST00000355112	NM_000057.2	836	aGg/aAg	12/22	0.718816201461917	2	FACETS	0.967	0.924	1	0.967	0.924	1	CLONAL	2	FALSE	0	0.728566803715984	2		481	308	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512331	38512331	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	127	831	3	ENST00000254066.5:c.1243del	p.Glu415ArgfsTer9	p.E415Rfs*9	ENST00000254066	NM_000964.3	414	ttG/tt	9/9	0.199324985829467	1	FACETS	0.658	0.604	0.713	0.658	0.604	0.713	INDETERMINATE	1	FALSE	0	0.728566803715984	1		834	337	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78831699	78831699	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	65	669	0	ENST00000306801.3:c.1508G>T	p.Ser503Ile	p.S503I	ENST00000306801	NM_020761.2	503	aGc/aTc	13/34	0.728566803715984	3	FACETS	0.566	0.492	0.646	0.283	0.246	0.323	SUBCLONAL	1	FALSE	1	0.728566803715984	3		669	430	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39613789	39613789	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0015704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	59	341	1	ENST00000262039.4:c.1708-1G>T		p.X570_splice	ENST00000262039	NM_002647.2	570			1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	FALSE	1	0.728566803715984	2		342	152	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276719	15276719	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	100	721	0	ENST00000263388.2:c.5546A>G	p.Tyr1849Cys	p.Y1849C	ENST00000263388	NM_000435.2	1849	tAt/tGt	30/33	0.331468082658319	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.728566803715984	0		721	273	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266730	18266730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756943808	NA	P-0015704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	205	791	0	ENST00000222254.8:c.41C>T	p.Pro14Leu	p.P14L	ENST00000222254	NM_005027.3	14	cCg/cTg	2/16	0.202714329714986	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.728566803715984	0		791	496	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730772	40730772	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	99	480	3	ENST00000373198.4:c.3763C>A	p.Leu1255Met	p.L1255M	ENST00000373198	NM_133170.3	1255	Ctg/Atg	27/32	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	FALSE	1	0.728566803715984	2		483	255	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264635	46264635	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	56	183	0	ENST00000371998.3:c.1505G>T	p.Gly502Val	p.G502V	ENST00000371998		502	gGt/gTt	12/23	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	FALSE	1	0.728566803715984	2		183	139	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045777	143045777	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs142403292	NA	P-0015704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	115	506	0	ENST00000262992.4:c.1857G>T	p.Met619Ile	p.M619I	ENST00000262992	NM_001101669.1	619	atG/atT	17/24	0.728566803715984	1	FACETS	0.998	0.926	1	0.998	0.926	1	CLONAL	1	FALSE	0	0.728566803715984	1		506	201	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532650	187532650	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	105	511	0	ENST00000441802.2:c.9743A>T	p.Glu3248Val	p.E3248V	ENST00000441802	NM_005245.3	3248	gAa/gTa	14/27	0.728566803715984	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	0	0.728566803715984	1		511	157	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793524	89793524	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	65	392	0	ENST00000336032.3:c.593A>G	p.Gln198Arg	p.Q198R	ENST00000336032	NM_006813.2	198	cAg/cGg	2/2	0.235390676179346	4	FACETS	1	0.963	1	0.635	0.557	0.716	INDETERMINATE	1	FALSE	2	0.728566803715984	4		392	243	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513231	106513232	+	missense_variant	Missense_Mutation	DNP	GG	GG	TC	novel	NA	P-0015704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	42	295	0	ENST00000359195.3:c.2135_2136delinsTC	p.Arg712Ile	p.R712I	ENST00000359195	NM_002649.2	712	aGG/aTC	4/11	0.157511632315093	4	FACETS	1	0.923	1	0.576	0.488	0.671	INDETERMINATE	1	FALSE	2	0.728566803715984	4		295	173	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845224	128845224	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	70	397	2	ENST00000249373.3:c.718G>T	p.Val240Phe	p.V240F	ENST00000249373	NM_005631.4	240	Gtc/Ttc	3/12	1	2	FACETS	0.811	0.717	0.909	0.811	0.717	0.909	CLONAL	1	FALSE	1	0.728566803715984	2		399	237	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945044	151945044	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764420905	NA	P-0015704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	26	898	1	ENST00000262189.6:c.2475G>T	p.Met825Ile	p.M825I	ENST00000262189	NM_170606.2	825	atG/atT	14/59	1	2	FACETS	0.226	0.179	0.28	0.226	0.179	0.28	SUBCLONAL	1	FALSE	1	0.728566803715984	2		899	316	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457268	5457268	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	81	336	0	ENST00000381577.3:c.242A>G	p.Tyr81Cys	p.Y81C	ENST00000381577	NM_014143.3	81	tAc/tGc	3/7	0.116872773065881	4	FACETS	0.839	0.752	0.929	0.839	0.752	0.929	INDETERMINATE	2	FALSE	2	0.728566803715984	4		336	229	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404560	8404560	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	57	304	0	ENST00000356435.5:c.4187G>C	p.Arg1396Pro	p.R1396P	ENST00000356435		1396	cGg/cCg	25/35	0.116872773065881	4	FACETS	0.796	0.696	0.899	0.796	0.696	0.899	INDETERMINATE	2	FALSE	2	0.728566803715984	4		304	170	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436603	8436603	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	67	529	0	ENST00000356435.5:c.4075C>A	p.Gln1359Lys	p.Q1359K	ENST00000356435		1359	Cag/Aag	24/35	0.116872773065881	4	FACETS	0.952	0.847	1	0.952	0.847	1	INDETERMINATE	2	FALSE	2	0.728566803715984	4		529	167	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426708	47426708	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	110	707	0	ENST00000377045.4:c.953C>G	p.Thr318Arg	p.T318R	ENST00000377045	NM_001654.4	318	aCg/aGg	10/16	0.202714329714986	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.728566803715984	0		707	357	SUCCESS
AR	367	MSKCC	GRCh37	X	66766168	66766168	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1304379417	NA	P-0015704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	57	454	0	ENST00000374690.3:c.1180G>T	p.Asp394Tyr	p.D394Y	ENST00000374690	NM_000044.3	394	Gac/Tac	1/8	0.202714329714986	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.728566803715984	0		454	200	SUCCESS
AR	367	MSKCC	GRCh37	X	66766174	66766175	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0015704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	54	438	1	ENST00000374690.3:c.1186_1187delinsTT	p.Gly396Phe	p.G396F	ENST00000374690	NM_000044.3	396	GGc/TTc	1/8	0.202714329714986	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.728566803715984	0		439	186	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340963	70340963	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	76	674	0	ENST00000374080.3:c.696G>T	p.Gln232His	p.Q232H	ENST00000374080		232	caG/caT	5/45	0.202714329714986	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.728566803715984	0		674	296	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348506	70348506	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	75	524	3	ENST00000374080.3:c.3413G>T	p.Arg1138Leu	p.R1138L	ENST00000374080		1138	cGg/cTg	24/45	0.202714329714986	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.728566803715984	0		527	309	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613403	100613403	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	75	542	1	ENST00000308731.7:c.997C>T	p.His333Tyr	p.H333Y	ENST00000308731	NM_000061.2	333	Cat/Tat	12/19	0.356072498185428	1	FACETS	0.559	0.497	0.624	0.559	0.497	0.624	INDETERMINATE	1	FALSE	0	0.728566803715984	1		543	234	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205146	123205146	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	23	444	0	ENST00000218089.9:c.2506G>C	p.Glu836Gln	p.E836Q	ENST00000218089	NM_001042749.1	836	Gaa/Caa	25/35	0.356072498185428	1	FACETS	0.295	0.233	0.365	0.295	0.233	0.365	INDETERMINATE	1	FALSE	0	0.728566803715984	1		444	136	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	256	414	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.527008042367515	6	FACETS	1	0.985	1	0.844	0.797	0.892	CLONAL	3	TRUE	2	0.527008042367515	6		414	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577123	7577123	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876660333	NA	P-0015705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	210	762	1	ENST00000269305.4:c.815T>A	p.Val272Glu	p.V272E	ENST00000269305	NM_001126112.2	272	gTg/gAg	8/11	0.517572959229392	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.527008042367515	2		763	372	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573649	48573649	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0015705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	51	430	0	ENST00000342988.3:c.233T>A	p.Leu78Ter	p.L78*	ENST00000342988	NM_005359.5	78	tTg/tAg	2/12	0.492936180024634	1	FACETS	0.75	0.647	0.86	0.75	0.647	0.86	SUBCLONAL	1	TRUE	0	0.527008042367515	1		430	190	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216446	2216446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1230982104	NA	P-0015705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	81	695	0	ENST00000398665.3:c.2090C>T	p.Thr697Ile	p.T697I	ENST00000398665	NM_032482.2	697	aCc/aTc	20/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.527008042367515	2		695	226	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281488	15281488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	67	699	0	ENST00000263388.2:c.4885G>A	p.Val1629Met	p.V1629M	ENST00000263388	NM_000435.2	1629	Gtg/Atg	26/33	1	2	FACETS	0.989	0.87	1	0.989	0.87	1	CLONAL	1	TRUE	1	0.527008042367515	2		699	257	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212302	36212302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779172651	NA	P-0015705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	85	718	1	ENST00000222270.7:c.2053G>A	p.Asp685Asn	p.D685N	ENST00000222270	NM_014727.1	685	Gat/Aat	3/37	0.528631586993414	4	FACETS	1	0.9	1			1	CLONAL	1	TRUE	NA	0.527008042367515	4		719	485	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221301	1221301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555738685	NA	P-0015707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	88	735	0	ENST00000326873.7:c.824C>T	p.Pro275Leu	p.P275L	ENST00000326873	NM_000455.4	275	cCg/cTg	6/10	NA	2	FACETS	0.537	0.475	0.603			1	INDETERMINATE	1	TRUE	NA	0.388573557542276	2		735	844	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209351	98209351	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	30	582	2	ENST00000331920.6:c.4187G>T	p.Gly1396Val	p.G1396V	ENST00000331920	NM_000264.3	1396	gGa/gTa	23/24	1	2	FACETS	0.272	0.219	0.334	0.272	0.219	0.334	SUBCLONAL	1	TRUE	1	0.388573557542276	2		584	567	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0015708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	31	541	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.598	0.482	0.731	0.598	0.482	0.731	SUBCLONAL	1	TRUE	1	0.12	2		541	864	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520006	NA	P-0015708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1316	66	924	0	ENST00000269305.4:c.821T>G	p.Val274Gly	p.V274G	ENST00000269305	NM_001126112.2	274	gTt/gGt	8/11	1	2	FACETS	0.796	0.688	0.914	0.796	0.688	0.914	CLONAL	1	TRUE	1	0.12	2		924	1382	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0015709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	328	581	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.646554234746539	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.646554234746539	1		582	580	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0015709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	81	574	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.399663501073058	1	FACETS	0.287	0.253	0.323	0.287	0.253	0.323	SUBCLONAL	1	TRUE	0	0.646554234746539	1		574	591	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420037	152420037	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0015709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	246	428	0	ENST00000206249.3:c.1724C>G	p.Ser575Ter	p.S575*	ENST00000206249	NM_000125.3	575	tCa/tGa	8/8	0.44191958644041	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.646554234746539	1		428	501	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	270	482	0	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	0.663173936305333	1	FACETS	0.601	0.565	0.638	0.601	0.565	0.638	SUBCLONAL	1	TRUE	0	0.663173936305333	1		482	906	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10264991	10264991	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	133	275	0	ENST00000340748.4:c.1949G>T	p.Arg650Leu	p.R650L	ENST00000340748		650	cGc/cTc	21/40	NA	2	FACETS	0.601	0.547	0.658			1	INDETERMINATE	1	TRUE	NA	0.663173936305333	2		275	667	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752651	128752653	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs761021550	NA	P-0015710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	74	274	0	ENST00000377970.2:c.816_818del	p.Glu272del	p.E272del	ENST00000377970	NM_002467.4	271	cAAGaa/caa	3/3	0.410305176954661	5	FACETS	0.456	0.398	0.519	0.091	0.079	0.104	SUBCLONAL	1	TRUE	0	0.663173936305333	5		274	976	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881392	37881392	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	1162	820	0	ENST00000269571.5:c.2584A>G	p.Thr862Ala	p.T862A	ENST00000269571		862	Aca/Gca	21/27	0.616890062757119	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.627630712505214	3		820	1586	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577563	7577565	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0015711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	494	622	1	ENST00000269305.4:c.716_718del	p.Asn239del	p.N239del	ENST00000269305	NM_001126112.2	239	aACAgt/agt	7/11	0.627630712505214	2	FACETS	0.933	0.9	0.965	0.933	0.9	0.965	CLONAL	2	TRUE	0	0.627630712505214	2		623	844	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38504619	38504619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1240210247	NA	P-0015711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	294	673	4	ENST00000254066.5:c.230C>T	p.Ser77Leu	p.S77L	ENST00000254066	NM_000964.3	77	tCg/tTg	3/9	0.616890062757119	3	FACETS	0.932	0.876	0.99	0.311	0.292	0.33	CLONAL	1	TRUE	0	0.627630712505214	3		677	1320	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687122	176687122	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	228	575	1	ENST00000439151.2:c.5099G>T	p.Arg1700Leu	p.R1700L	ENST00000439151	NM_022455.4	1700	cGa/cTa	14/23	0.602385912863183	1	FACETS	0.948	0.892	1	0.948	0.892	1	CLONAL	1	TRUE	0	0.627630712505214	1		576	526	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212851	27212851	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760084463	NA	P-0015711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	615	756	0	ENST00000380036.4:c.2833G>A	p.Ala945Thr	p.A945T	ENST00000380036	NM_000459.3	945	Gct/Act	17/23	0.627630712505214	2	FACETS	0.97	0.941	0.999	0.97	0.941	0.999	CLONAL	2	TRUE	0	0.627630712505214	2		756	1010	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0015712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	143	339	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.972	0.897	1	0.972	0.897	1	CLONAL	1	TRUE	1	0.786892331383407	2		339	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0015712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	978	730	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.786892331383407	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.786892331383407	2		730	1173	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937959	76937960	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0015712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	304	293	0	ENST00000373344.5:c.2788_2789del	p.Ser930PhefsTer7	p.S930Ffs*7	ENST00000373344	NM_000489.3	930	AGt/t	9/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.786892331383407	1		293	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0015713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	381	860	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.502043046313267	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.502043046313267	1		861	1082	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0015714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	131	536	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.946	0.861	1	0.946	0.861	1	CLONAL	1	TRUE	1	0.416261020015149	2		536	665	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193121548	193121548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	88	336	1	ENST00000367435.3:c.946C>T	p.His316Tyr	p.H316Y	ENST00000367435	NM_024529.4	316	Cat/Tat	10/17	1	2	FACETS	0.957	0.852	1	0.957	0.852	1	CLONAL	1	TRUE	1	0.416261020015149	2		337	442	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267435	7267435	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	73	381	1	ENST00000302850.5:c.573G>T	p.Lys191Asn	p.K191N	ENST00000302850	NM_000208.2	191	aaG/aaT	2/22	1	2	FACETS	0.897	0.789	1	0.897	0.789	1	CLONAL	1	TRUE	1	0.416261020015149	2		382	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0015716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	11	693	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.281011451154282	3	FACETS	0.604	0.416	0.839	0.302	0.208	0.42	SUBCLONAL	1	TRUE	1	0.12	3		693	322	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	36	181	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	0.3	2	FACETS	1	0.892	1	1	0.958	1	CLONAL	3	TRUE	0	0.12	2		181	182	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486842	56486842	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	18	402	0	ENST00000267101.3:c.1256G>C	p.Gly419Ala	p.G419A	ENST00000267101	NM_001982.3	419	gGa/gCa	11/28	0.281011451154282	4	FACETS	1	0.889	1	0.686	0.517	0.884	CLONAL	1	TRUE	2	0.12	4		402	245	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955217	17955217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	29	890	0	ENST00000458235.1:c.10C>T	p.Pro4Ser	p.P4S	ENST00000458235	NM_000215.3	4	Cca/Tca	2/24	0.281011451154282	4	FACETS	0.962	0.77	1	0.481	0.385	0.591	CLONAL	1	TRUE	2	0.12	4		890	563	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256389	46256389	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	21	605	0	ENST00000371998.3:c.617A>G	p.Asp206Gly	p.D206G	ENST00000371998		206	gAt/gGt	7/23	0.179170234137766	3	FACETS	1	0.858	1	0.583	0.449	0.74	CLONAL	1	TRUE	1	0.12	3		605	318	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651931	36651932	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0015716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	21	464	0	ENST00000244741.5:c.54_55dup	p.Arg19ProfsTer13	p.R19Pfs*13	ENST00000244741	NM_000389.4	18	tgc/tgCCc	2/3	0.281011451154282	4	FACETS	0.942	0.724	1	0.471	0.362	0.599	CLONAL	1	TRUE	2	0.12	4		464	416	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020215	123020215	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764285899	NA	P-0015716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	23	353	0	ENST00000355640.3:c.703C>G	p.Leu235Val	p.L235V	ENST00000355640		235	Ctt/Gtt	2/7	0.3	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	2	TRUE	0	0.12	2		353	157	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0015718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	441	583	0				ENST00000310581	NM_198253.2	-/1132			0.612895373550641	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.612895373550641	3		583	911	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344760	65344760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768706312	NA	P-0015718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	188	539	0	ENST00000342505.4:c.277C>T	p.Arg93Cys	p.R93C	ENST00000342505	NM_002227.2	93	Cgc/Tgc	4/25	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.612895373550641	2		539	565	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0015718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	247	657	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	0.612895373550641	2		657	746	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711875	89711875	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	rs587782603	NA	P-0015718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	203	593	1	ENST00000371953.3:c.493G>T	p.Gly165Ter	p.G165*	ENST00000371953	NM_000314.4	165	Gga/Tga	6/9	0.612895373550641	2	FACETS	0.898	0.847	0.948	0.898	0.847	0.948	CLONAL	2	TRUE	0	0.612895373550641	2		594	369	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446470	49446470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1168216865	NA	P-0015718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	183	595	2	ENST00000301067.7:c.1135G>A	p.Asp379Asn	p.D379N	ENST00000301067	NM_003482.3	379	Gat/Aat	9/54	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.612895373550641	2		597	558	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219315	133219315	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	180	638	0	ENST00000320574.5:c.4729G>A	p.Glu1577Lys	p.E1577K	ENST00000320574	NM_006231.2	1577	Gag/Aag	37/49	1	2	FACETS	0.96	0.89	1	0.96	0.89	1	CLONAL	1	TRUE	1	0.612895373550641	2		638	612	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563108	21563108	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	281	1068	0	ENST00000382592.4:c.811C>G	p.Arg271Gly	p.R271G	ENST00000382592	NM_014572.2	271	Cgc/Ggc	4/8	1	2	FACETS	0.931	0.876	0.987	0.931	0.876	0.987	CLONAL	1	TRUE	1	0.612895373550641	2		1068	985	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592720	28592720	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	175	718	0	ENST00000241453.7:c.2425C>A	p.His809Asn	p.H809N	ENST00000241453	NM_004119.2	809	Cac/Aac	20/24	1	2	FACETS	0.831	0.768	0.897	0.831	0.768	0.897	CLONAL	1	TRUE	1	0.612895373550641	2		718	687	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972298	32972298	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs1555289898	NA	P-0015718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	93	404	0	ENST00000380152.3:c.9649-1G>C		p.X3217_splice	ENST00000380152		3217			1	2	FACETS	0.954	0.858	1	0.954	0.858	1	CLONAL	1	TRUE	1	0.612895373550641	2		404	318	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0015718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	177	719	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.612895373550641	1	FACETS	0.726	0.673	0.78	0.726	0.673	0.78	SUBCLONAL	1	TRUE	0	0.612895373550641	1		720	552	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29662020	29662020	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	112	582	0	ENST00000356175.3:c.5914C>T	p.Gln1972Ter	p.Q1972*	ENST00000356175	NM_000267.3	1972	Caa/Taa	39/57	1	2	FACETS	0.896	0.812	0.983	0.896	0.812	0.983	CLONAL	1	TRUE	1	0.612895373550641	2		582	408	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740417	58740417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770633028	NA	P-0015718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	200	784	2	ENST00000305921.3:c.1322G>A	p.Arg441His	p.R441H	ENST00000305921	NM_003620.3	441	cGt/cAt	6/6	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.612895373550641	2		786	629	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120025	70120025	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	58	180	0	ENST00000245479.2:c.1027C>G	p.Pro343Ala	p.P343A	ENST00000245479	NM_000346.3	343	Ccg/Gcg	3/3	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.612895373550641	2		180	171	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466790	25466790	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253868717	NA	P-0015718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	526	772	0	ENST00000264709.3:c.1913C>T	p.Ser638Phe	p.S638F	ENST00000264709	NM_175629.2	638	tCt/tTt	16/23	0.612895373550641	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.612895373550641	2		772	835	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519902	29519902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200364883	NA	P-0015718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	433	740	0	ENST00000389048.3:c.1669C>T	p.Arg557Cys	p.R557C	ENST00000389048	NM_004304.4	557	Cgt/Tgt	9/29	0.612895373550641	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.612895373550641	2		740	676	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634733	158634734	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	88	410	4	ENST00000263640.3:c.452_453delinsAA	p.Arg151Lys	p.R151K	ENST00000263640	NM_001105.4	151	aGG/aAA	5/11	0.218154074900526	3	FACETS	0.693	0.616	0.776	0.231	0.205	0.259	INDETERMINATE	1	TRUE	0	0.612895373550641	3		414	541	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488721	212488721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	120	679	0	ENST00000342788.4:c.2128C>T	p.Leu710Phe	p.L710F	ENST00000342788	NM_005235.2	710	Ctt/Ttt	18/28	0.218154074900526	3	FACETS	0.645	0.582	0.711	0.215	0.194	0.237	INDETERMINATE	1	TRUE	0	0.612895373550641	3		679	793	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543829	212543829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771154734	NA	P-0015718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	145	628	0	ENST00000342788.4:c.1570C>T	p.Arg524Cys	p.R524C	ENST00000342788	NM_005235.2	524	Cgc/Tgc	13/28	0.218154074900526	3	FACETS	0.718	0.655	0.784	0.239	0.218	0.262	INDETERMINATE	1	TRUE	0	0.612895373550641	3		628	861	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593411	215593411	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553612005	NA	P-0015718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	146	314	0	ENST00000260947.4:c.2323C>T	p.Leu775Phe	p.L775F	ENST00000260947	NM_000465.2	775	Ctt/Ttt	11/11	0.218154074900526	3	FACETS	1	0.96	1	0.699	0.65	0.748	INDETERMINATE	2	TRUE	0	0.612895373550641	3		314	297	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546620	9546620	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764351685	NA	P-0015718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	190	633	0	ENST00000353224.5:c.1402G>A	p.Glu468Lys	p.E468K	ENST00000353224	NM_177990.2	468	Gag/Aag	5/10	0.612895373550641	3	FACETS	0.978	0.906	1	0.489	0.453	0.527	CLONAL	1	TRUE	1	0.612895373550641	3		633	828	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730938	40730938	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0015718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	134	457	0	ENST00000373198.4:c.3598-1G>A		p.X1200_splice	ENST00000373198	NM_133170.3	1200			0.612895373550641	3	FACETS	0.93	0.848	1	0.465	0.424	0.508	CLONAL	1	TRUE	1	0.612895373550641	3		457	614	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324274	62324275	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	561	1098	2	ENST00000360203.5:c.2769_2770delinsAA	p.Gly924Ser	p.G924S	ENST00000360203	NM_001283009.1	923	aaGGgt/aaAAgt	29/35	0.487233451522746	4	FACETS	0.904	0.867	0.941	0.904	0.867	0.941	CLONAL	2	TRUE	2	0.612895373550641	4		1100	1633	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447607	187447607	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	198	852	0	ENST00000232014.4:c.586T>A	p.Ser196Thr	p.S196T	ENST00000232014	NM_001130845.1	196	Tcc/Acc	5/10	1	2	FACETS	0.881	0.819	0.946	0.881	0.819	0.946	CLONAL	1	TRUE	1	0.612895373550641	2		852	733	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455558	189455558	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	168	711	1	ENST00000264731.3:c.92G>A	p.Trp31Ter	p.W31*	ENST00000264731	NM_003722.4	31	tGg/tAg	2/14	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.612895373550641	2		712	532	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627950	187627950	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	230	863	0	ENST00000441802.2:c.3032C>T	p.Ser1011Phe	p.S1011F	ENST00000441802	NM_005245.3	1011	tCt/tTt	2/27	1	2	FACETS	0.999	0.935	1	0.999	0.935	1	CLONAL	1	TRUE	1	0.612895373550641	2		863	751	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435634	149435634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	275	801	1	ENST00000286301.3:c.2509G>A	p.Asp837Asn	p.D837N	ENST00000286301	NM_005211.3	837	Gac/Aac	19/22	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.612895373550641	2		802	867	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137524714	137524716	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs587776858	NA	P-0015718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	119	641	0	ENST00000367739.4:c.653_655del	p.Glu218del	p.E218del	ENST00000367739	NM_000416.2	218	gAAGga/gga	5/7	0.612895373550641	1	FACETS	0.634	0.576	0.693	0.634	0.576	0.693	SUBCLONAL	1	TRUE	0	0.612895373550641	1		641	425	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030479	49030479	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	122	802	0	ENST00000267163.4:c.1959del	p.Val654CysfsTer4	p.V654Cfs*4	ENST00000267163	NM_000321.2	652	Aaa/aa	19/27	0.571514756100891	2	FACETS	0.905	0.837	0.972	0.905	0.837	0.972	CLONAL	2	TRUE	0	0.571514756100891	2		802	236	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0015719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	194	1007	0	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.571514756100891	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.571514756100891	2		1007	329	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274124	10274124	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1413736970	NA	P-0015719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	180	1240	2	ENST00000330684.3:c.145C>A	p.Arg49Ser	p.R49S	ENST00000330684	NM_001134407.1	49	Cgc/Agc	2/13	0.553158292058017	2	FACETS	0.952	0.894	1	0.952	0.894	1	CLONAL	2	TRUE	0	0.571514756100891	2		1242	331	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78599580	78599580	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	96	766	1	ENST00000306801.3:c.253del	p.Glu85AsnfsTer117	p.E85Nfs*117	ENST00000306801	NM_020761.2	84	ttG/tt	2/34	0.571514756100891	2	FACETS	0.965	0.868	1	0.483	0.434	0.534	CLONAL	1	TRUE	0	0.571514756100891	2		767	348	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259631	89259631	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	41	694	1	ENST00000336596.2:c.775T>A	p.Cys259Ser	p.C259S	ENST00000336596	NM_005233.5	259	Tgc/Agc	3/17	0.5713584620198	1	FACETS	0.712	0.604	0.826	0.712	0.604	0.826	SUBCLONAL	1	TRUE	0	0.571514756100891	1		695	144	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233072	66233072	+	splice_region_variant,intron_variant	Splice_Region	SNP	T	T	A	novel	NA	P-0015719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	38	830	0	ENST00000273854.3:c.1924+3A>T		p.X642_splice	ENST00000273854	NM_004439.5	642			0.571514756100891	1	FACETS	0.905	0.77	1	0.905	0.77	1	CLONAL	1	TRUE	0	0.571514756100891	1		830	105	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534266	187534266	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs759492838	NA	P-0015719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	251	689	0	ENST00000441802.2:c.9460G>T	p.Ala3154Ser	p.A3154S	ENST00000441802	NM_005245.3	3154	Gca/Tca	13/27	0.500347029716168	4	FACETS	0.99	0.939	1			1	CLONAL	3	TRUE	NA	0.571514756100891	4		689	465	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048703	180048703	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	114	1329	1	ENST00000261937.6:c.1859T>C	p.Leu620Pro	p.L620P	ENST00000261937	NM_182925.4	620	cTg/cCg	13/30	0.56303329990944	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.571514756100891	1		1330	244	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250359	110250359	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	27	1990	0	ENST00000374672.4:c.316G>C	p.Asp106His	p.D106H	ENST00000374672	NM_004235.4	106	Gac/Cac	3/5	0.5713584620198	1	FACETS	0.146	0.116	0.181	0.146	0.116	0.181	SUBCLONAL	1	TRUE	0	0.571514756100891	1		1990	462	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559090	29559090	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0015719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	16	184	0	ENST00000356175.3:c.3198-1G>C		p.X1066_splice	ENST00000356175	NM_000267.3	1066			0.56303329990944	1	FACETS	0.975	0.759	1	0.975	0.759	1	CLONAL	1	TRUE	0	0.571514756100891	1		184	41	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288463	15288463	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	200	485	0	ENST00000263388.2:c.4276C>T	p.Arg1426Trp	p.R1426W	ENST00000263388	NM_000435.2	1426	Cgg/Tgg	24/33	0.079663250220097	0	FACETS		NA	1			1	NA	NA	TRUE	0	NA	0		485	489	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0015721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	570	467	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.795272720379957	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.797501214783182	2		468	674	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087458	27087458	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	600	755	1	ENST00000324856.7:c.2032C>T	p.Gln678Ter	p.Q678*	ENST00000324856	NM_006015.4	678	Cag/Tag	5/20	0.797501214783182	2	FACETS	0.985	0.962	1	0.985	0.962	1	CLONAL	2	TRUE	0	0.797501214783182	2		756	764	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251907	153251907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	53	477	0	ENST00000281708.4:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000281708	NM_033632.3	367	Cga/Tga	7/12	0.272606372935002	5	FACETS	1	0.967	1	0.292	0.252	0.334	INDETERMINATE	1	TRUE	0	0.797501214783182	5		477	200	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250284	39250284	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	295	1009	0	ENST00000402219.2:c.1285A>G	p.Ile429Val	p.I429V	ENST00000402219	NM_005633.3	429	Att/Gtt	10/23	0.797501214783182	3	FACETS	0.958	0.913	1	0.958	0.913	1	CLONAL	2	TRUE	1	0.797501214783182	3		1009	540	SUCCESS
APC	324	MSKCC	GRCh37	5	112173540	112173541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATCT	novel	NA	P-0015721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	63	381	0	ENST00000257430.4:c.2250_2253dup	p.Leu752IlefsTer5	p.L752Ifs*5	ENST00000257430	NM_000038.5	750	cca/ccATCTa	16/16	0.795272720379957	2	FACETS	0.806	0.733	0.876	0.806	0.733	0.876	CLONAL	2	TRUE	0	0.797501214783182	2		381	98	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	116	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.841	0.76	0.928	0.841	0.76	0.928	CLONAL	1	TRUE	1	0.411521826161548	2		248	670	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347763	347763	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1292652536	NA	P-0015722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	205	655	2	ENST00000262320.3:c.1743T>A	p.Ser581Arg	p.S581R	ENST00000262320	NM_003502.3	581	agT/agA	6/11	1	2	FACETS	0.994	0.922	1	0.994	0.922	1	CLONAL	1	TRUE	1	0.411521826161548	2		657	1002	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140754	55140754	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs866516451	NA	P-0015722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	251	508	0	ENST00000257290.5:c.1615A>G	p.Ile539Val	p.I539V	ENST00000257290	NM_006206.4	539	Atc/Gtc	11/23	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.411521826161548	2		508	1168	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938587	76938598	+	inframe_deletion	In_Frame_Del	DEL	GCTTAGATTTTG	GCTTAGATTTTG	-	novel	NA	P-0015722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	104	416	0	ENST00000373344.5:c.2150_2161del	p.Pro717_Lys720del	p.P717_K720del	ENST00000373344	NM_000489.3	717	cCAAAATCTAAGCaa/caa	9/35	NA	2	FACETS	0.499	0.446	0.556			1	INDETERMINATE	1	TRUE	NA	0.411521826161548	2		416	1012	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136799	2136799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137854153	NA	P-0015723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	687	959	4	ENST00000219476.3:c.4916G>A	p.Arg1639His	p.R1639H	ENST00000219476	NM_000548.3	1639	cGc/cAc	38/42	0.636705303352285	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.636705303352285	1		963	1301	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578281	7578281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	402	702	0	ENST00000269305.4:c.568C>T	p.Pro190Ser	p.P190S	ENST00000269305	NM_001126112.2	190	Cct/Tct	6/11	0.625856710422942	1	FACETS	0.996	0.953	1	0.996	0.953	1	CLONAL	1	TRUE	0	0.636705303352285	1		702	864	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339002	225339002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	36	490	3	ENST00000264414.4:c.2267G>A	p.Arg756Gln	p.R756Q	ENST00000264414	NM_003590.4	756	cGa/cAa	16/16	0.636705303352285	1	FACETS	0.108	0.088	0.13	0.108	0.088	0.13	SUBCLONAL	1	TRUE	0	0.636705303352285	1		493	717	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246363	46246363	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	249	357	0	ENST00000334344.6:c.4457T>C	p.Val1486Ala	p.V1486A	ENST00000334344	NM_152641.2	1486	gTt/gCt	15/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.636705303352285	2		357	735	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487589	56487589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	366	525	0	ENST00000267101.3:c.1522G>A	p.Gly508Arg	p.G508R	ENST00000267101	NM_001982.3	508	Gga/Aga	13/28	1	2	FACETS	0.995	0.945	1	0.995	0.945	1	CLONAL	1	TRUE	1	0.636705303352285	2		525	1155	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1266640	1266640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372868296	NA	P-0015723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	363	554	0	ENST00000310581.5:c.2593C>T	p.Arg865Cys	p.R865C	ENST00000310581	NM_198253.2	865	Cgt/Tgt	10/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.636705303352285	2		554	1114	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64289181	64289181	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	698	541	0	ENST00000370651.3:c.349C>G	p.Leu117Val	p.L117V	ENST00000370651	NM_003463.4	117	Cta/Gta	5/6	0.636705303352285	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.636705303352285	1		541	1089	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552789	106552789	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	464	823	0	ENST00000369096.4:c.754G>C	p.Glu252Gln	p.E252Q	ENST00000369096	NM_001198.3	252	Gaa/Caa	5/7	0.636705303352285	1	FACETS	0.889	0.851	0.926	0.889	0.851	0.926	CLONAL	1	TRUE	0	0.636705303352285	1		823	1118	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814186	76814186	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	242	437	0	ENST00000373344.5:c.6458G>T	p.Arg2153Leu	p.R2153L	ENST00000373344	NM_000489.3	2153	cGc/cTc	29/35	0.636705303352285	1	FACETS	0.989	0.934	1	0.989	0.934	1	CLONAL	1	TRUE	0	0.636705303352285	1		437	524	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047888	180047888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	80	1002	0	ENST00000261937.6:c.2287G>A	p.Val763Met	p.V763M	ENST00000261937	NM_182925.4	763	Gtg/Atg	15/30	0.366460506191437	3	FACETS	0.944	0.833	1	0.472	0.416	0.532	CLONAL	1	FALSE	1	0.366460506191437	3		1002	547	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	1162	507	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.231696400348962	8	FACETS	1	0.982	1	1	0.998	1	CLONAL	10	TRUE	1	0.231696400348962	8		507	1696	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0015727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	455	677	3	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.441683451002783	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.441683451002783	3		680	1166	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120527	70120527	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0015727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	900	827	0	ENST00000245479.2:c.1529G>C	p.Ter510SerextTer49	p.*510Sext*49	ENST00000245479	NM_000346.3	510	tGa/tCa	3/3	0.441683451002783	4	FACETS	0.995	0.966	1	0.995	0.966	1	CLONAL	3	TRUE	1	0.441683451002783	4		827	1968	SUCCESS
APC	324	MSKCC	GRCh37	5	112175419	112175419	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0015727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	155	216	0	ENST00000257430.4:c.4128T>A	p.Tyr1376Ter	p.Y1376*	ENST00000257430	NM_000038.5	1376	taT/taA	16/16	0.441683451002783	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.441683451002783	2		216	331	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196143	108196143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564652222	NA	P-0015727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	120	524	0	ENST00000278616.4:c.6679C>T	p.Arg2227Cys	p.R2227C	ENST00000278616	NM_000051.3	2227	Cgc/Tgc	46/63	1	2	FACETS	0.929	0.841	1	0.929	0.841	1	CLONAL	1	TRUE	1	0.441683451002783	2		524	585	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731139	162731139	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	155	416	0	ENST00000367921.3:c.994C>T	p.Arg332Trp	p.R332W	ENST00000367921	NM_006182.2	332	Cgg/Tgg	9/18	1	2	FACETS	0.973	0.893	1	0.973	0.893	1	CLONAL	1	TRUE	1	0.441683451002783	2		416	721	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2202758	2202758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1197029182	NA	P-0015727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	211	536	0	ENST00000398665.3:c.767G>A	p.Arg256Gln	p.R256Q	ENST00000398665	NM_032482.2	256	cGg/cAg	9/28	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.441683451002783	2		536	861	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212056	5212056	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1314953096	NA	P-0015727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	167	499	2	ENST00000357368.4:c.4975C>T	p.Arg1659Cys	p.R1659C	ENST00000357368	NM_002850.3	1659	Cgc/Tgc	32/38	1	2	FACETS	0.985	0.906	1	0.985	0.906	1	CLONAL	1	TRUE	1	0.441683451002783	2		501	768	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101744	71101744	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	53	237	0	ENST00000318789.4:c.454del	p.Glu152AsnfsTer54	p.E152Nfs*54	ENST00000318789	NM_032682.5	152	Gaa/aa	9/21	1	2	FACETS	0.8	0.687	0.922	0.8	0.687	0.922	CLONAL	1	TRUE	1	0.441683451002783	2		237	300	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922306	178922306	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	90	398	0	ENST00000263967.3:c.1075G>C	p.Gly359Arg	p.G359R	ENST00000263967	NM_006218.2	359	Ggt/Cgt	6/21	1	2	FACETS	0.846	0.753	0.943	0.846	0.753	0.943	CLONAL	1	TRUE	1	0.441683451002783	2		398	482	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84390203	84390203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138594808	NA	P-0015727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	108	378	0	ENST00000321945.7:c.578G>A	p.Arg193Gln	p.R193Q	ENST00000321945	NM_139076.2	193	cGa/cAa	6/9	1	2	FACETS	0.88	0.792	0.972	0.88	0.792	0.972	CLONAL	1	TRUE	1	0.441683451002783	2		378	556	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704647	117704647	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	86	224	0	ENST00000368508.3:c.2329G>T	p.Gly777Ter	p.G777*	ENST00000368508	NM_002944.2	777	Gga/Tga	16/43	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.441683451002783	2		224	349	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230428	46230428	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	82	379	0	ENST00000334344.6:c.762C>G	p.Asn254Lys	p.N254K	ENST00000334344	NM_152641.2	254	aaC/aaG	7/21	0.536509211927761	3	FACETS	0.734	0.649	0.825	0.367	0.324	0.413	SUBCLONAL	1	TRUE	1	0.536509211927761	3		379	528	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945302	54945302	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	39	268	0	ENST00000312783.6:c.1124G>A	p.Arg375Lys	p.R375K	ENST00000312783	NM_198436.1	375	aGa/aAa	10/10	NA	2	FACETS	0.643	0.538	0.759			1	INDETERMINATE	1	TRUE	NA	0.536509211927761	2		268	226	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439889	52439889	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0015728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	113	500	0	ENST00000460680.1:c.823A>T	p.Lys275Ter	p.K275*	ENST00000460680	NM_004656.3	275	Aag/Tag	10/17	0.509661661522594	1	FACETS	0.734	0.665	0.805	0.734	0.665	0.805	SUBCLONAL	1	TRUE	0	0.536509211927761	1		500	420	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	64	507	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.251599982274002	1	FACETS	0.74	0.641	0.848	0.74	0.641	0.848	SUBCLONAL	1	TRUE	0	0.256746240419831	1		507	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0015729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	162	467	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.251599982274002	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.256746240419831	1		468	1043	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891277	101891277	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	82	569	1	ENST00000374994.4:c.238C>T	p.Arg80Ter	p.R80*	ENST00000374994	NM_004612.2	80	Cga/Tga	2/9	0.256746240419831	1	FACETS	0.756	0.667	0.853	0.756	0.667	0.853	SUBCLONAL	1	TRUE	0	0.256746240419831	1		570	736	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456737	32456737	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	160	486	1	ENST00000332351.3:c.155G>A	p.Arg52His	p.R52H	ENST00000332351	NM_024426.4	52	cGt/cAt	1/10	0.256746240419831	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.256746240419831	1		487	1030	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257412	19257412	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1528	230	1024	2	ENST00000162023.5:c.721C>A	p.Pro241Thr	p.P241T	ENST00000162023		241	Ccc/Acc	11/13	0.251599982274002	1	FACETS	0.888	0.825	0.954	0.888	0.825	0.954	CLONAL	1	TRUE	0	0.256746240419831	1		1026	1758	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248729	212248729	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	64	301	0	ENST00000342788.4:c.3538C>T	p.Leu1180Phe	p.L1180F	ENST00000342788	NM_005235.2	1180	Ctt/Ttt	28/28	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.256746240419831	2		301	496	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0015730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	124	754	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.358259661356139	2		755	670	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0015730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	172	630	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.358259661356139	2		631	717	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0015730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	120	398	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.358259661356139	2		398	589	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0015730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	110	496	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	NA	2	FACETS	1	0.946	1			1	INDETERMINATE	1	TRUE	NA	0.358259661356139	2		496	571	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450648	70450648	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	152	514	0	ENST00000373644.4:c.5488A>T	p.Thr1830Ser	p.T1830S	ENST00000373644	NM_030625.2	1830	Act/Tct	12/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.358259661356139	2		514	699	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549162	21549162	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs45510199	NA	P-0015730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	169	787	0	ENST00000382592.4:c.3114C>A	p.Tyr1038Ter	p.Y1038*	ENST00000382592	NM_014572.2	1038	taC/taA	8/8	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.358259661356139	2		787	848	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003149	42003149	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1225212904	NA	P-0015730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	300	702	0	ENST00000219905.7:c.2686C>T	p.Arg896Ter	p.R896*	ENST00000219905	NM_001164273.1	896	Cga/Tga	8/24	0.358259661356139	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.358259661356139	2		702	826	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229083	36229083	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	139	676	0	ENST00000222270.7:c.7863C>A	p.Tyr2621Ter	p.Y2621*	ENST00000222270	NM_014727.1	2621	taC/taA	36/37	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.358259661356139	2		676	769	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62316879	62316879	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	106	606	0	ENST00000360203.5:c.1195G>T	p.Val399Leu	p.V399L	ENST00000360203	NM_001283009.1	399	Gtg/Ttg	15/35	1	2	FACETS	0.926	0.832	1	0.926	0.832	1	CLONAL	1	TRUE	1	0.358259661356139	2		606	639	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177984	56177986	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs754402779	NA	P-0015730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	102	493	1	ENST00000399503.3:c.2965_2967del	p.Ser989del	p.S989del	ENST00000399503	NM_005921.1	986	cCTTct/cct	14/20	1	2	FACETS	0.957	0.858	1	0.957	0.858	1	CLONAL	1	TRUE	1	0.358259661356139	2		494	595	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258744	115258744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434596	NA	P-0015731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	161	500	0	ENST00000369535.4:c.38G>A	p.Gly13Asp	p.G13D	ENST00000369535	NM_002524.4	13	gGt/gAt	2/7	1	2	FACETS	0.577	0.53	0.626	0.577	0.53	0.626	SUBCLONAL	1	TRUE	1	0.745182626569146	2		500	749	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0015731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	14	319	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	1	2	FACETS	0.075	0.053	0.101	0.075	0.053	0.101	SUBCLONAL	1	TRUE	1	0.745182626569146	2		319	504	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0015731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	81	508	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	0.29	0.255	0.328	0.29	0.255	0.328	SUBCLONAL	1	TRUE	1	0.745182626569146	2		508	749	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400023	139400023	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	272	773	1	ENST00000277541.6:c.4325del	p.Pro1442ArgfsTer3	p.P1442Rfs*3	ENST00000277541	NM_017617.3	1442	cCg/cg	25/34	1	2	FACETS	0.573	0.537	0.611	0.573	0.537	0.611	SUBCLONAL	1	TRUE	1	0.745182626569146	2		774	1273	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167772	56167772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	76	461	0	ENST00000399503.3:c.1337G>A	p.Cys446Tyr	p.C446Y	ENST00000399503	NM_005921.1	446	tGc/tAc	7/20	1	2	FACETS	0.344	0.302	0.389	0.344	0.302	0.389	SUBCLONAL	1	TRUE	1	0.745182626569146	2		461	593	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0015732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	201	467	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.356954790821755	2	FACETS	0.983	0.917	1	0.983	0.917	1	CLONAL	2	TRUE	0	0.356954790821755	2		468	573	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920422	114920422	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	65	408	0	ENST00000543371.1:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000543371	NM_001198531.1	455	Cga/Tga	13/14	0.246938938353913	3	FACETS	0.631	0.547	0.723	0.316	0.273	0.362	SUBCLONAL	1	TRUE	1	0.356954790821755	3		408	680	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94200981	94200981	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs372411821	NA	P-0015732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	82	233	0	ENST00000323929.3:c.1096C>T	p.Arg366Ter	p.R366*	ENST00000323929	NM_005591.3	366	Cga/Tga	10/20	0.356954790821755	3	FACETS	0.927	0.827	1	0.927	0.827	1	CLONAL	2	TRUE	1	0.356954790821755	3		233	292	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383860	15383867	+	frameshift_variant	Frame_Shift_Del	DEL	CATTACTG	CATTACTG	-	novel	NA	P-0015732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	115	534	0	ENST00000263377.2:c.44_51del	p.Pro15ArgfsTer37	p.P15Rfs*37	ENST00000263377	NM_058243.2	15	cCAGTAATG/c	2/20	0.356954790821755	3	FACETS	1	0.944	1	0.534	0.481	0.59	CLONAL	1	TRUE	1	0.356954790821755	3		534	711	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321450	62321450	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs372284625	NA	P-0015732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	69	534	0	ENST00000360203.5:c.2152G>C	p.Ala718Pro	p.A718P	ENST00000360203	NM_001283009.1	718	Gcc/Ccc	25/35	0.356954790821755	5	FACETS	0.554	0.481	0.634	0.139	0.12	0.159	SUBCLONAL	1	TRUE	1	0.356954790821755	5		534	1071	SUCCESS
APC	324	MSKCC	GRCh37	5	112157629	112157653	+	frameshift_variant	Frame_Shift_Del	DEL	TGTGTGTTCTAATGAAACTTTCATT	TGTGTGTTCTAATGAAACTTTCATT	-	novel	NA	P-0015732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	34	326	0	ENST00000257430.4:c.1351_1375del	p.Cys451MetfsTer8	p.C451Mfs*8	ENST00000257430	NM_000038.5	450	gTGTGTGTTCTAATGAAACTTTCATTt/gt	11/16	1	2	FACETS	0.593	0.486	0.714	0.593	0.486	0.714	SUBCLONAL	1	TRUE	1	0.356954790821755	2		326	321	SUCCESS
APC	324	MSKCC	GRCh37	5	112174851	112174854	+	frameshift_variant	Frame_Shift_Del	DEL	TTCC	TTCC	-	novel	NA	P-0015732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	30	197	0	ENST00000257430.4:c.3563_3566del	p.Pro1188HisfsTer76	p.P1188Hfs*76	ENST00000257430	NM_000038.5	1187	aTTCCt/at	16/16	1	2	FACETS	0.721	0.584	0.875	0.721	0.584	0.875	SUBCLONAL	1	TRUE	1	0.356954790821755	2		197	233	SUCCESS
APC	324	MSKCC	GRCh37	5	112175312	112175312	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	38	203	0	ENST00000257430.4:c.4021A>G	p.Ser1341Gly	p.S1341G	ENST00000257430	NM_000038.5	1341	Agt/Ggt	16/16	1	2	FACETS	0.873	0.726	1	0.873	0.726	1	CLONAL	1	TRUE	1	0.356954790821755	2		203	244	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0015734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	675	860	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.542954309401624	4	FACETS	0.994	0.969	1			1	CLONAL	4	TRUE	NA	0.539867257831597	4		861	968	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374166	118374182	+	frameshift_variant	Frame_Shift_Del	DEL	AACGCACAGTCAAAGTG	AACGCACAGTCAAAGTG	-	novel	NA	P-0015734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	275	441	0	ENST00000534358.1:c.7560_7576del	p.Lys2520AsnfsTer10	p.K2520Nfs*10	ENST00000534358	NM_005933.3	2520	aAACGCACAGTCAAAGTG/a	27/36	0.542954309401624	4	FACETS	1	0.99	1	0.858	0.819	0.897	CLONAL	3	TRUE	0	0.539867257831597	4		441	457	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912363	32912374	+	inframe_deletion	In_Frame_Del	DEL	CAACTGATATTA	CAACTGATATTA	-	novel	NA	P-0015734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	50	315	0	ENST00000380152.3:c.3874_3885del	p.Leu1292_Gln1295del	p.L1292_Q1295del	ENST00000380152		1291	CAACTGATATTA/-	11/27	0.542954309401624	4	FACETS	0.739	0.629	0.859	0.369	0.314	0.43	SUBCLONAL	1	TRUE	2	0.539867257831597	4		315	386	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271562	15271562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751851528	NA	P-0015734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	550	984	1	ENST00000263388.2:c.6877C>T	p.Pro2293Ser	p.P2293S	ENST00000263388	NM_000435.2	2293	Ccc/Tcc	33/33	0.542954309401624	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	2	0.539867257831597	4		985	1398	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0015735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	170	475	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.607756892553737	2		475	539	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	162	414	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	0.607756892553737	2		414	527	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0015735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	137	441	1	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	0.843	0.771	0.918	0.843	0.771	0.918	CLONAL	1	TRUE	1	0.607756892553737	2		442	535	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0015735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	324	824	1	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	0.607756892553737	1	FACETS	0.965	0.917	1	0.965	0.917	1	CLONAL	1	TRUE	0	0.607756892553737	1		825	769	SUCCESS
APC	324	MSKCC	GRCh37	5	112174571	112174571	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	107	448	0	ENST00000257430.4:c.3281del	p.Gly1094AspfsTer32	p.G1094Dfs*32	ENST00000257430	NM_000038.5	1094	Gga/ga	16/16	1	2	FACETS	0.859	0.776	0.945	0.859	0.776	0.945	CLONAL	1	TRUE	1	0.607756892553737	2		448	410	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504308	8504308	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1563902484	NA	P-0015735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	215	531	0	ENST00000356435.5:c.1775G>T	p.Gly592Val	p.G592V	ENST00000356435		592	gGc/gTc	12/35	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.607756892553737	2		531	699	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934345	39934345	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121434618	NA	P-0015735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	256	678	1	ENST00000378444.4:c.254C>T	p.Pro85Leu	p.P85L	ENST00000378444	NM_001123385.1	85	cCg/cTg	4/15	1	2	FACETS	0.996	0.935	1	0.996	0.935	1	CLONAL	1	TRUE	1	0.607756892553737	2		679	846	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	553	580	0	ENST00000263967.3:c.278G>T	p.Arg93Leu	p.R93L	ENST00000263967	NM_006218.2	93	cGg/cTg	2/21	0.271474745624927	8	FACETS	1	0.976	1			1	CLONAL	7	TRUE	NA	0.271474745624927	8		580	1042	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578438	7578467	+	inframe_deletion	In_Frame_Del	DEL	CTTGTAGATGGCCATGGCGCGGACGCGGGT	CTTGTAGATGGCCATGGCGCGGACGCGGGT	-	novel	NA	P-0015737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	189	603	0	ENST00000269305.4:c.463_492del	p.Thr155_Lys164del	p.T155_K164del	ENST00000269305	NM_001126112.2	155	ACCCGCGTCCGCGCCATGGCCATCTACAAG/-	5/11	0.187322312548061	2	FACETS	1	0.99	1	0.731	0.676	0.789	CLONAL	1	TRUE	0	0.271474745624927	2		603	952	SUCCESS
AXL	558	MSKCC	GRCh37	19	41749549	41749549	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs780942273	NA	P-0015737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	91	656	0	ENST00000301178.4:c.1474G>C	p.Gly492Arg	p.G492R	ENST00000301178	NM_021913.4	492	Ggt/Cgt	12/20	0.246738071580929	3	FACETS	0.619	0.548	0.696	0.31	0.274	0.348	SUBCLONAL	1	TRUE	1	0.271474745624927	3		656	1230	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591204	67591257	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCAGGATGAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGGTTGACT	TTCAGGATGAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGGTTGACT	-	novel	NA	P-0015737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	49	281	0	ENST00000274335.5:c.1746-44_1755del		p.X582_splice	ENST00000274335		582		13/15	0.187322312548061	2	FACETS	1	0.955	1	0.669	0.57	0.775	CLONAL	1	TRUE	0	0.271474745624927	2		281	270	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056263	26056263	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	33	325	0	ENST00000343677.2:c.394G>T	p.Val132Phe	p.V132F	ENST00000343677	NM_005319.3	132	Gtt/Ttt	1/1	1	2	FACETS	0.44	0.357	0.533	0.44	0.357	0.533	SUBCLONAL	1	TRUE	1	0.271474745624927	2		325	553	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752957	128752957	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	215	386	1	ENST00000377970.2:c.1118C>G	p.Thr373Arg	p.T373R	ENST00000377970	NM_002467.4	373	aCa/aGa	3/3	0.271474745624927	4	FACETS	1	0.985	1	0.804	0.749	0.861	CLONAL	2	TRUE	1	0.271474745624927	4		387	835	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951994	178951994	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	52	537	0	ENST00000263967.3:c.3049G>C	p.Asp1017His	p.D1017H	ENST00000263967	NM_006218.2	1017	Gat/Cat	21/21	1	2	FACETS	0.815	0.694	0.946	0.815	0.694	0.946	CLONAL	1	TRUE	1	0.273399723714243	2		537	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578549	+	inframe_deletion	In_Frame_Del	DEL	GGG	GGG	-	novel	NA	P-0015739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1361	449	1307	1	ENST00000269305.4:c.381_383del	p.Pro128del	p.P128del	ENST00000269305	NM_001126112.2	127	tcCCCt/tct	5/11	0.27303725572599	2	FACETS	0.907	0.864	0.952	0.907	0.864	0.952	CLONAL	2	TRUE	0	0.273399723714243	2		1308	1810	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0015740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	91	278	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.92	0.82	1	0.92	0.82	1	CLONAL	1	TRUE	1	0.389265361470766	2		278	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0015741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	663	662	3	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	0.858654134435827	2	FACETS	0.956	0.937	0.973	0.956	0.937	0.973	CLONAL	2	TRUE	0	0.87499363050913	2		665	793	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478851	56478851	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	494	632	5	ENST00000267101.3:c.307C>G	p.Arg103Gly	p.R103G	ENST00000267101	NM_001982.3	103	Cgc/Ggc	3/28	0.865290292036899	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.87499363050913	1		637	612	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696179	52696179	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	423	596	6	ENST00000394830.3:c.498del	p.Gln167LysfsTer7	p.Q167Kfs*7	ENST00000394830	NM_018313.4	166	ggG/gg	5/30	0.87499363050913	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.87499363050913	1		602	535	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855029	76855029	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1557085898	NA	P-0015741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	10	201	0	ENST00000373344.5:c.5807A>G	p.Lys1936Arg	p.K1936R	ENST00000373344	NM_000489.3	1936	aAg/aGg	25/35	1	1	FACETS	0.036	0.024	0.051	0.036	0.024	0.051	SUBCLONAL	1	TRUE	0	0.87499363050913	1		201	360	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288924	11288924	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	114	392	0	ENST00000361445.4:c.2831A>C	p.Asp944Ala	p.D944A	ENST00000361445	NM_004958.3	944	gAt/gCt	19/58	0.368098988485439	3	FACETS	0.457	0.411	0.505	0.152	0.137	0.169	INDETERMINATE	1	TRUE	0	0.87499363050913	3		392	820	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862111	68862112	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	221	647	0	ENST00000261769.5:c.2200dup	p.Arg734LysfsTer14	p.R734Kfs*14	ENST00000261769	NM_004360.3	733	-/A	14/16	0.881340563048743	1	FACETS	0.998	0.96	1	0.998	0.96	1	CLONAL	1	TRUE	0	0.881340563048743	1		647	281	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101063	26101063	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	188	644	0	ENST00000435504.4:c.29del	p.Gly10AlafsTer12	p.G10Afs*12	ENST00000435504		10	gGc/gc	1/13	1	2	FACETS	0.857	0.799	0.916	0.857	0.799	0.916	CLONAL	1	TRUE	1	0.881340563048743	2		644	498	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0015743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	254	541	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.168017247778124	4	FACETS	0.831	0.779	0.883	0.831	0.779	0.883	INDETERMINATE	2	TRUE	2	0.581252295439493	4		541	832	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844220	68844220	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	216	523	0	ENST00000261769.5:c.808del	p.Ser270LeufsTer12	p.S270Lfs*12	ENST00000261769	NM_004360.3	270	Tct/ct	6/16	0.592780999411955	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.581252295439493	1		523	404	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87322758	87322758	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	64	535	0	ENST00000277120.3:c.360-1G>A		p.X120_splice	ENST00000277120		120			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		535	205	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87322758	87322758	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015744-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	179	535	0	ENST00000277120.3:c.360-1G>A		p.X120_splice	ENST00000277120		120			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		535	998	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0015745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2360	1076	541	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.833919982444274	7	FACETS	1	0.996	1	0.386	0.374	0.398	CLONAL	2	TRUE	1	0.833919982444274	7		541	3436	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0015745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	904	684	0	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	1	2	FACETS	1	0.996	1	1	0.999	1	CLONAL	2	TRUE	1	0.833919982444274	2		684	1045	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968673	55968673	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs755067067	NA	P-0015745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	311	517	3	ENST00000263923.4:c.1990C>T	p.Arg664Cys	p.R664C	ENST00000263923	NM_002253.2	664	Cgt/Tgt	14/30	1	2	FACETS	0.927	0.878	0.976	0.927	0.878	0.976	CLONAL	1	TRUE	1	0.833919982444274	2		520	805	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65304180	65304180	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1320196357	NA	P-0015745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	190	520	0	ENST00000342505.4:c.2935C>T	p.Gln979Ter	p.Q979*	ENST00000342505	NM_002227.2	979	Cag/Tag	21/25	0.833919982444274	1	FACETS	0.552	0.515	0.59	0.552	0.515	0.59	SUBCLONAL	1	TRUE	0	0.833919982444274	1		520	481	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257565	19257565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	533	764	0	ENST00000162023.5:c.661G>A	p.Gly221Arg	p.G221R	ENST00000162023		221	Gga/Aga	10/13	1	2	FACETS	0.983	0.944	1	0.983	0.944	1	CLONAL	1	TRUE	1	0.833919982444274	2		764	1300	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568501	41568501	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0015745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	277	356	0	ENST00000263253.7:c.4453-2A>G		p.X1485_splice	ENST00000263253	NM_001429.3	1485			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.833919982444274	2		356	655	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970971	21970971	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	85	915	0	ENST00000304494.5:c.387C>A	p.Tyr129Ter	p.Y129*	ENST00000304494	NM_000077.4	129	taC/taA	2/3	0.291650023191531	3	FACETS	0.903	0.818	0.988	1	0.972	1	CLONAL	4	FALSE	0	0.291650023191531	3		915	185	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412252	139412252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057523819	NA	P-0015747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	80	917	1	ENST00000277541.6:c.1393G>A	p.Ala465Thr	p.A465T	ENST00000277541	NM_017617.3	465	Gcc/Acc	8/34	0.291650023191531	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	3	FALSE	0	0.291650023191531	3		918	183	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577102	7577102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793881	NA	P-0015747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	80	800	1	ENST00000269305.4:c.836G>A	p.Gly279Glu	p.G279E	ENST00000269305	NM_001126112.2	279	gGg/gAg	8/11	0.291650023191531	3	FACETS	1	0.95	1	1	0.983	1	CLONAL	3	FALSE	1	0.291650023191531	3		801	192	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954642	17954643	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	27	1076	0	ENST00000458235.1:c.251dup	p.Ser85GlufsTer46	p.S85Efs*46	ENST00000458235	NM_000215.3	84	ccg/ccCg	3/24	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	FALSE	1	0.291650023191531	2		1076	157	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605835	46605835	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765477973	NA	P-0015747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	19	765	1	ENST00000263734.3:c.1483G>A	p.Asp495Asn	p.D495N	ENST00000263734	NM_001430.4	495	Gac/Aac	11/16	0.100294654510903	0	FACETS	0.855	0.658	1			1	INDETERMINATE	1	FALSE	0	0.291650023191531	0		766	108	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628525	187628528	+	frameshift_variant	Frame_Shift_Del	DEL	TGGA	TGGA	-	novel	NA	P-0015747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	49	804	0	ENST00000441802.2:c.2454_2457del	p.Pro820SerfsTer11	p.P820Sfs*11	ENST00000441802	NM_005245.3	818	aaTCCA/aa	2/27	0.126016840614461	0	FACETS	1	0.9	1			1	INDETERMINATE	2	FALSE	0	0.291650023191531	0		804	115	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992720	68992720	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs182978151	NA	P-0015747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	16	734	3	ENST00000288368.4:c.1685G>A	p.Arg562His	p.R562H	ENST00000288368	NM_024870.2	562	cGt/cAt	16/40	0.126016840614461	0	FACETS	0.688	0.514	0.89			1	INDETERMINATE	1	FALSE	0	0.291650023191531	0		737	113	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0015749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	233	549	0	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	0.306320271959592	2	FACETS	0.901	0.842	0.961	0.901	0.842	0.961	CLONAL	2	TRUE	0	0.31740611977846	2		549	815	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100713	8100713	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	295	679	0	ENST00000346208.3:c.687C>A	p.Tyr229Ter	p.Y229*	ENST00000346208		229	taC/taA	3/6	0.249248219529063	3	FACETS	0.977	0.92	1	0.977	0.92	1	CLONAL	2	TRUE	1	0.31740611977846	3		679	1102	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332268	70332268	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	97	349	0	ENST00000373644.4:c.174del	p.Lys59ArgfsTer16	p.K59Rfs*16	ENST00000373644	NM_030625.2	58	gTt/gt	2/12	0.249248219529063	3	FACETS	0.964	0.859	1	0.482	0.429	0.538	CLONAL	1	TRUE	1	0.31740611977846	3		349	735	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702232	47702232	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	88	468	0	ENST00000233146.2:c.1828C>G	p.His610Asp	p.H610D	ENST00000233146	NM_000251.2	610	Cac/Gac	12/16	0.31740611977846	4	FACETS	0.653	0.577	0.735	0.326	0.288	0.368	SUBCLONAL	1	TRUE	2	0.31740611977846	4		468	1119	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702337	47702337	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs267607982	NA	P-0015749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	96	339	0	ENST00000233146.2:c.1933C>G	p.Gln645Glu	p.Q645E	ENST00000233146	NM_000251.2	645	Caa/Gaa	12/16	0.31740611977846	4	FACETS	0.824	0.733	0.922	0.412	0.366	0.461	CLONAL	1	TRUE	2	0.31740611977846	4		339	967	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703705	47703705	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	72	339	0	ENST00000233146.2:c.2205C>G	p.Ile735Met	p.I735M	ENST00000233146	NM_000251.2	735	atC/atG	13/16	0.31740611977846	4	FACETS	0.802	0.7	0.913	0.401	0.35	0.457	CLONAL	1	TRUE	2	0.31740611977846	4		339	745	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150040	202150040	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs746401108	NA	P-0015749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	128	471	2	ENST00000358485.4:c.1481G>A	p.Arg494Gln	p.R494Q	ENST00000358485	NM_001080125.1	494	cGa/cAa	8/9	0.31740611977846	4	FACETS	0.979	0.886	1	0.49	0.443	0.539	CLONAL	1	TRUE	2	0.31740611977846	4		473	1085	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495267	212495267	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	141	587	1	ENST00000342788.4:c.1999G>T	p.Val667Leu	p.V667L	ENST00000342788	NM_005235.2	667	Gtg/Ttg	17/28	0.242223325452936	4	FACETS	0.988	0.898	1			1	CLONAL	1	TRUE	NA	0.31740611977846	4		588	1185	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864464	151864464	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0015749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	52	207	0	ENST00000262189.6:c.9518-1G>C		p.X3173_splice	ENST00000262189	NM_170606.2	3173			1	2	FACETS	0.958	0.82	1	0.958	0.82	1	CLONAL	1	TRUE	1	0.31740611977846	2		207	342	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426735	47426735	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	126	246	0	ENST00000377045.4:c.980G>T	p.Gly327Val	p.G327V	ENST00000377045	NM_001654.4	327	gGg/gTg	10/16	1	1	FACETS	0.801	0.731	0.873	1	0.988	1	CLONAL	2	TRUE	0	0.31740611977846	1		246	417	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	471	414	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.89903948481993	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.905257176037516	3		414	753	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0015750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	175	279	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.409542883332194	4	FACETS	1	0.97	1	1	0.97	1	INDETERMINATE	2	TRUE	2	0.905257176037516	4		279	348	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088787	27088788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	269	493	1	ENST00000324856.7:c.2402dup	p.Gln802SerfsTer15	p.Q802Sfs*15	ENST00000324856	NM_006015.4	799	cag/caGg	7/20	0.905257176037516	1	FACETS	0.946	0.913	0.977	0.946	0.913	0.977	CLONAL	1	TRUE	0	0.905257176037516	1		494	344	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726236	46726236	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	233	339	1	ENST00000371975.4:c.430G>T	p.Val144Phe	p.V144F	ENST00000371975	NM_003579.3	144	Gtt/Ttt	6/18	0.448432070536523	3	FACETS	1	0.962	1	0.519	0.486	0.552	INDETERMINATE	1	TRUE	1	0.905257176037516	3		340	721	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828461	72828461	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139821312	NA	P-0015750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	129	414	0	ENST00000268489.5:c.8120C>T	p.Ala2707Val	p.A2707V	ENST00000268489	NM_006885.3	2707	gCg/gTg	9/10	1	2	FACETS	0.448	0.407	0.491	0.448	0.407	0.491	SUBCLONAL	1	TRUE	1	0.905257176037516	2		414	636	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223390	53223390	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	365	627	0	ENST00000375401.3:c.3969G>T	p.Glu1323Asp	p.E1323D	ENST00000375401	NM_004187.3	1323	gaG/gaT	23/26	1	2	FACETS	0.891	0.848	0.934	0.891	0.848	0.934	CLONAL	1	TRUE	1	0.905257176037516	2		627	905	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220555	123220555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	148	475	1	ENST00000218089.9:c.3212G>A	p.Arg1071Gln	p.R1071Q	ENST00000218089	NM_001042749.1	1071	cGg/cAg	30/35	1	2	FACETS	0.452	0.413	0.492	0.452	0.413	0.492	SUBCLONAL	1	TRUE	1	0.905257176037516	2		476	724	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0015751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	669	704	1	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.071297540610936	4	FACETS	0.948	0.925	0.97			1	INDETERMINATE	4	TRUE	NA	0.634471512864735	4		705	909	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0015757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	197	704	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.898	0.831	0.968	0.898	0.831	0.968	CLONAL	1	TRUE	1	0.41007587588855	2		705	1070	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577501	7577501	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	rs1427471466	NA	P-0015757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	197	546	0	ENST00000269305.4:c.780del	p.Ser261ValfsTer84	p.S261Vfs*84	ENST00000269305	NM_001126112.2	260	tcC/tc	7/11	0.41007587588855	1	FACETS	0.906	0.84	0.974	0.906	0.84	0.974	CLONAL	1	TRUE	0	0.41007587588855	1		546	843	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615539	43615539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1451004715	NA	P-0015757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	180	526	0	ENST00000355710.3:c.2618G>A	p.Arg873Gln	p.R873Q	ENST00000355710	NM_020975.4	873	cGg/cAg	15/20	0.305635028243669	3	FACETS	0.956	0.88	1	0.478	0.44	0.518	CLONAL	1	TRUE	1	0.41007587588855	3		526	1107	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206606	108206606	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555128350	NA	P-0015757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	185	510	0	ENST00000278616.4:c.8186A>C	p.Gln2729Pro	p.Q2729P	ENST00000278616	NM_000051.3	2729	cAa/cCa	56/63	1	2	FACETS	0.99	0.915	1	0.99	0.915	1	CLONAL	1	TRUE	1	0.41007587588855	2		510	911	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0015758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	278	605	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.89	0.837	0.945	1	0.996	1	CLONAL	4	TRUE	1	0.15	2		606	1041	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1567548223	NA	P-0015758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	74	626	1	ENST00000269305.4:c.797del	p.Gly266AspfsTer79	p.G266Dfs*79	ENST00000269305	NM_001126112.2	266	gGa/ga	8/11	1	2	FACETS	0.864	0.754	0.984	0.864	0.754	0.984	CLONAL	1	TRUE	1	0.15	2		627	1142	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253775	30253775	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	69	490	0	ENST00000307677.4:c.679G>T	p.Gly227Cys	p.G227C	ENST00000307677	NM_138578.1	227	Ggc/Tgc	3/3	1	2	FACETS	0.857	0.744	0.98	0.857	0.744	0.98	CLONAL	1	TRUE	1	0.15	2		490	1074	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521723	89521723	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	40	394	0	ENST00000336596.2:c.2800G>T	p.Gly934Cys	p.G934C	ENST00000336596	NM_005233.5	934	Ggt/Tgt	16/17	1	2	FACETS	0.685	0.567	0.816	0.685	0.567	0.816	SUBCLONAL	1	TRUE	1	0.15	2		394	779	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527814	157527814	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	65	452	0	ENST00000346085.5:c.5539C>T	p.Pro1847Ser	p.P1847S	ENST00000346085	NM_020732.3	1847	Cct/Tct	20/20	1	2	FACETS	0.917	0.793	1	0.917	0.793	1	CLONAL	1	TRUE	1	0.15	2		452	945	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040974	47040974	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	87	618	0	ENST00000377604.3:c.1505del	p.Gly502ValfsTer202	p.G502Vfs*202	ENST00000377604	NM_001204468.1	502	Ggt/gt	14/24	1	2	FACETS	0.927	0.818	1	0.927	0.818	1	CLONAL	1	TRUE	1	0.15	2		618	1251	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0015759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	314	458	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	0.427231579455367	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.439065608988298	2		458	625	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0015759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	344	620	1	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.374397704735736	2	FACETS	0.989	0.942	1	0.989	0.942	1	CLONAL	2	TRUE	0	0.439065608988298	2		621	792	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610265	10610265	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	391	827	3	ENST00000171111.5:c.445G>A	p.Glu149Lys	p.E149K	ENST00000171111	NM_203500.1	149	Gag/Aag	2/6	0.439065608988298	2	FACETS	0.933	0.89	0.977	0.933	0.89	0.977	CLONAL	2	TRUE	0	0.439065608988298	2		830	954	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023420	27023420	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	318	560	1	ENST00000324856.7:c.526C>T	p.Gln176Ter	p.Q176*	ENST00000324856	NM_006015.4	176	Caa/Taa	1/20	0.391863679043689	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.439065608988298	3		561	849	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112745438	112745438	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	141	726	0	ENST00000369452.4:c.756C>A	p.His252Gln	p.H252Q	ENST00000369452	NM_007373.3	252	caC/caA	3/9	0.391863679043689	3	FACETS	0.988	0.901	1	0.494	0.45	0.54	CLONAL	1	TRUE	1	0.439065608988298	3		726	793	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435723	49435723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	365	643	2	ENST00000301067.7:c.6160G>A	p.Ala2054Thr	p.A2054T	ENST00000301067	NM_003482.3	2054	Gca/Aca	29/54	0.289733565401943	4	FACETS	0.994	0.943	1	0.994	0.943	1	CLONAL	2	TRUE	2	0.439065608988298	4		645	1204	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548264	41548264	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	248	554	1	ENST00000263253.7:c.3052G>C	p.Glu1018Gln	p.E1018Q	ENST00000263253	NM_001429.3	1018	Gag/Cag	16/31	0.334432528383746	5	FACETS	0.869	0.812	0.927	0.579	0.541	0.618	CLONAL	2	TRUE	2	0.439065608988298	5		555	1078	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156609	55156609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1376909345	NA	P-0015759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	366	639	0	ENST00000257290.5:c.3010G>A	p.Glu1004Lys	p.E1004K	ENST00000257290	NM_006206.4	1004	Gag/Aag	22/23	0.439173204981023	3	FACETS	0.913	0.867	0.96			1	CLONAL	2	TRUE	NA	0.439065608988298	3		639	1113	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164830	106164830	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	271	544	3	ENST00000380013.4:c.3698G>T	p.Trp1233Leu	p.W1233L	ENST00000380013	NM_001127208.2	1233	tGg/tTg	6/11	0.289733565401943	4	FACETS	0.98	0.922	1	0.98	0.922	1	CLONAL	2	TRUE	2	0.439065608988298	4		547	906	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190854	106190854	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	245	509	0	ENST00000380013.4:c.4132T>C	p.Cys1378Arg	p.C1378R	ENST00000380013	NM_001127208.2	1378	Tgt/Cgt	9/11	0.289733565401943	4	FACETS	0.926	0.867	0.986	0.926	0.867	0.986	CLONAL	2	TRUE	2	0.439065608988298	4		509	867	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050825	5050825	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	111	603	0	ENST00000381652.3:c.608C>G	p.Ser203Cys	p.S203C	ENST00000381652	NM_004972.3	203	tCt/tGt	6/25	0.427231579455367	2	FACETS	0.853	0.768	0.941	0.426	0.384	0.471	CLONAL	1	TRUE	0	0.439065608988298	2		603	593	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938516	44938516	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	36	305	0	ENST00000377967.4:c.3064C>A	p.His1022Asn	p.H1022N	ENST00000377967	NM_021140.2	1022	Cat/Aat	20/29	1	1	FACETS	0.323	0.265	0.388	0.323	0.265	0.388	SUBCLONAL	1	TRUE	0	0.37000280313751	1		305	491	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226351	2226351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1331463984	NA	P-0015762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	27	469	0	ENST00000326181.6:c.1964G>A	p.Arg655Gln	p.R655Q	ENST00000326181	NM_032271.2	655	cGa/cAa	20/21	0.3	1	FACETS	0.157	0.125	0.194	0.157	0.125	0.194	INDETERMINATE	1	TRUE	0	0.75	1		469	286	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118835	115118835	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772182165	NA	P-0015763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	363	657	2	ENST00000257566.3:c.506G>A	p.Arg169Gln	p.R169Q	ENST00000257566	NM_016569.3	169	cGg/cAg	2/8	1	2	FACETS	0.988	0.941	1	0.988	0.941	1	CLONAL	1	TRUE	1	0.836608891730937	2		659	878	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40682085	40682085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761530012	NA	P-0015763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	246	767	0	ENST00000249776.8:c.640C>T	p.Arg214Trp	p.R214W	ENST00000249776	NM_033286.3	214	Cgg/Tgg	6/9	0.395131086929217	1	FACETS	0.394	0.368	0.419	0.394	0.368	0.419	INDETERMINATE	1	TRUE	0	0.836608891730937	1		767	869	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89809237	89809237	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	116	816	0	ENST00000389301.3:c.3736C>G	p.Leu1246Val	p.L1246V	ENST00000389301	NM_000135.2	1246	Cta/Gta	37/43	1	2	FACETS	0.229	0.206	0.254	0.229	0.206	0.254	SUBCLONAL	1	TRUE	1	0.836608891730937	2		816	1210	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299899	15299899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	474	970	1	ENST00000263388.2:c.1279C>T	p.Arg427Cys	p.R427C	ENST00000263388	NM_000435.2	427	Cgc/Tgc	8/33	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.836608891730937	2		971	1120	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051608	30051608	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1362524399	NA	P-0015763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	306	539	0	ENST00000338641.4:c.542C>T	p.Pro181Leu	p.P181L	ENST00000338641	NM_000268.3	181	cCg/cTg	6/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.836608891730937	2		539	692	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274888	142274889	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0015763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1520	768	864	0	ENST00000350721.4:c.2171_2172del	p.Leu724HisfsTer10	p.L724Hfs*10	ENST00000350721	NM_001184.3	724	cTG/c	10/47	0.836608891730937	4	FACETS	1	0.997	1	0.368	0.355	0.382	CLONAL	1	TRUE	0	0.836608891730937	4		864	2288	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154241	2154242	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755455183	NA	P-0015764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	85	548	3	ENST00000434045.2:c.686dup	p.Glu230ArgfsTer50	p.E230Rfs*50	ENST00000434045	NM_001127598.1	229	cca/ccCa	5/5	NA	2	FACETS	0.8	0.707	0.899			1	INDETERMINATE	1	TRUE	NA	0.311222888993935	2		551	683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0015764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	240	641	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.311222888993935	3	FACETS	0.866	0.809	0.925	0.866	0.809	0.925	CLONAL	2	TRUE	1	0.311222888993935	3		641	1029	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0015764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1188	288	801	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.311222888993935	6	FACETS	1	0.952	1			1	CLONAL	2	TRUE	NA	0.311222888993935	6		801	1476	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40462652	40462652	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139614126	NA	P-0015764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	123	464	0	ENST00000345506.4:c.2350G>A	p.Gly784Ser	p.G784S	ENST00000345506	NM_003152.3	784	Ggt/Agt	20/20	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.311222888993935	2		464	784	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855610	45855610	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs41556519	NA	P-0015764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	77	446	2	ENST00000391945.4:c.2047C>T	p.Arg683Trp	p.R683W	ENST00000391945	NM_000400.3	683	Cgg/Tgg	22/23	1	2	FACETS	0.839	0.737	0.948	0.839	0.737	0.948	CLONAL	1	TRUE	1	0.311222888993935	2		448	590	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	70	435	2	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	0.689	0.6	0.785	0.689	0.6	0.785	SUBCLONAL	1	TRUE	1	0.311222888993935	2		437	653	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0015764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	122	552	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.28260482303321	3	FACETS	1	0.982	1	0.682	0.618	0.75	CLONAL	1	TRUE	1	0.311222888993935	3		552	664	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517833	187517833	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	39	282	0	ENST00000441802.2:c.12861del	p.Phe4287LeufsTer62	p.F4287Lfs*62	ENST00000441802	NM_005245.3	4287	ttT/tt	25/27	1	2	FACETS	0.568	0.471	0.677	0.568	0.471	0.677	SUBCLONAL	1	TRUE	1	0.311222888993935	2		282	441	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	214	248	0				ENST00000310581	NM_198253.2	-/1132			0.337384708498507	4	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.729890264977722	4		248	761	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024003	27024003	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	104	163	0	ENST00000324856.7:c.1109G>T	p.Gly370Val	p.G370V	ENST00000324856	NM_006015.4	370	gGg/gTg	1/20	0.653220718372485	4	FACETS	0.913	0.831	0.997	0.913	0.831	0.997	CLONAL	2	TRUE	2	0.729890264977722	4		163	270	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206941996	206941996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	202	447	0	ENST00000423557.1:c.522G>A	p.Met174Ile	p.M174I	ENST00000423557	NM_000572.2	174	atG/atA	5/5	0.653220718372485	4	FACETS	0.814	0.76	0.87	0.814	0.76	0.87	CLONAL	2	TRUE	2	0.729890264977722	4		447	588	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719980	18719980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs889775181	NA	P-0015766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	258	543	1	ENST00000266497.5:c.3877G>A	p.Glu1293Lys	p.E1293K	ENST00000266497		1293	Gaa/Aaa	27/31	0.712802155325734	4	FACETS	0.922	0.869	0.976	0.922	0.869	0.976	CLONAL	2	TRUE	2	0.729890264977722	4		544	663	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287416	46287416	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	195	442	1	ENST00000334344.6:c.5275G>T	p.Glu1759Ter	p.E1759*	ENST00000334344	NM_152641.2	1759	Gaa/Taa	20/21	0.712802155325734	4	FACETS	0.851	0.794	0.91	0.851	0.794	0.91	CLONAL	2	TRUE	2	0.729890264977722	4		443	543	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041237	29041237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	333	607	0	ENST00000282397.4:c.191C>T	p.Pro64Leu	p.P64L	ENST00000282397	NM_002019.4	64	cCt/cTt	3/30	0.712802155325734	4	FACETS	0.881	0.836	0.927	0.881	0.836	0.927	CLONAL	2	TRUE	2	0.729890264977722	4		607	896	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	279	511	1	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	0.729890264977722	4	FACETS	0.927	0.876	0.979			1	CLONAL	2	TRUE	NA	0.729890264977722	4		512	713	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89833590	89833590	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	415	655	0	ENST00000389301.3:c.2560G>C	p.Asp854His	p.D854H	ENST00000389301	NM_000135.2	854	Gat/Cat	27/43	0.653220718372485	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.729890264977722	4		655	980	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29105996	29105996	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	132	400	0	ENST00000328354.6:c.844C>G	p.His282Asp	p.H282D	ENST00000328354	NM_007194.3	282	Cat/Gat	7/15	0.653220718372485	4	FACETS	1	0.983	1	0.659	0.602	0.717	CLONAL	1	TRUE	2	0.729890264977722	4		400	475	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29106038	29106038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766462610	NA	P-0015766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	179	413	0	ENST00000328354.6:c.802C>T	p.Leu268Phe	p.L268F	ENST00000328354	NM_007194.3	268	Ctc/Ttc	7/15	0.653220718372485	4	FACETS	0.769	0.713	0.825	0.769	0.713	0.825	SUBCLONAL	2	TRUE	2	0.729890264977722	4		413	552	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021828	71021828	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0015766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	204	265	0	ENST00000318789.4:c.1531-1G>C		p.X511_splice	ENST00000318789	NM_032682.5	511			0.713879382822375	4	FACETS	0.962	0.912	1	0.962	0.912	1	CLONAL	3	TRUE	1	0.729890264977722	4		265	335	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0015766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	785	874	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	0.670578842835422	4	FACETS	0.991	0.965	1	0.991	0.965	1	CLONAL	3	TRUE	1	0.729890264977722	4		874	1251	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176619016	176619016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1309337861	NA	P-0015766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	147	587	0	ENST00000439151.2:c.1059G>A	p.Met353Ile	p.M353I	ENST00000439151	NM_022455.4	353	atG/atA	3/23	0.70414335352566	3	FACETS	1	0.933	1	0.509	0.467	0.552	CLONAL	1	TRUE	1	0.729890264977722	3		587	540	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171599	32171602	+	missense_variant	Missense_Mutation	ONP	GTCC	GTCC	CTCT	novel	NA	P-0015766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	830	804	0	ENST00000375023.3:c.3176_3179delinsAGAG	p.Gly1059_Thr1060delinsGluSer	p.G1059_T1060delinsES	ENST00000375023	NM_004557.3	1059	gGGACc/gAGAGc	20/30	0.714505645456951	5	FACETS	0.953	0.93	0.976	0.953	0.93	0.976	CLONAL	4	TRUE	1	0.729890264977722	5		804	1250	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878464	151878464	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	436	875	0	ENST00000262189.6:c.6481C>T	p.Gln2161Ter	p.Q2161*	ENST00000262189	NM_170606.2	2161	Caa/Taa	36/59	0.712802155325734	4	FACETS	0.915	0.875	0.956	0.915	0.875	0.956	CLONAL	2	TRUE	2	0.729890264977722	4		875	1129	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922817	44922826	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGCCTGCC	CCTGCCTGCC	-	novel	NA	P-0015766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	277	245	0	ENST00000377967.4:c.1679_1688del	p.Pro560LeufsTer30	p.P560Lfs*30	ENST00000377967	NM_021140.2	560	CCTGCCTGCCct/ct	16/29	0.650705295062512	2	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.729890264977722	2		245	341	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039408	47039408	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	414	381	0	ENST00000377604.3:c.1031G>C	p.Gly344Ala	p.G344A	ENST00000377604	NM_001204468.1	344	gGc/gCc	10/24	0.650705295062512	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.729890264977722	2		381	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0015767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	22	467	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.155	0.119	0.196	0.155	0.119	0.196	SUBCLONAL	1	FALSE	1	0.378125897890254	2		468	753	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111958699	111958699	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0015767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	74	693	0	ENST00000375549.3:c.169+2T>C		p.X57_splice	ENST00000375549	NM_003002.3	57			1	2	FACETS	0.347	0.303	0.396	0.347	0.303	0.396	SUBCLONAL	1	FALSE	1	0.378125897890254	2		693	1127	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366456	118366456	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	52	492	0	ENST00000534358.1:c.5405A>G	p.Asp1802Gly	p.D1802G	ENST00000534358	NM_005933.3	1802	gAc/gGc	19/36	1	2	FACETS	0.354	0.3	0.413	0.354	0.3	0.413	SUBCLONAL	1	FALSE	1	0.378125897890254	2		492	778	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9928076	9928076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	45	475	0	ENST00000330684.3:c.1663G>A	p.Ala555Thr	p.A555T	ENST00000330684	NM_001134407.1	555	Gcc/Acc	8/13	1	2	FACETS	0.289	0.242	0.342	0.289	0.242	0.342	SUBCLONAL	1	FALSE	1	0.378125897890254	2		475	823	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74858992	74858992	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	65	301	0	ENST00000284811.8:c.212C>A	p.Ser71Ter	p.S71*	ENST00000284811		71	tCg/tAg	4/4	0.378125897890254	3	FACETS	0.676	0.586	0.773	0.338	0.293	0.387	SUBCLONAL	1	FALSE	1	0.378125897890254	3		301	605	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058687	47058687	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	90	623	0	ENST00000409792.3:c.7591G>T	p.Glu2531Ter	p.E2531*	ENST00000409792	NM_014159.6	2531	Gag/Tag	21/21	0.3	1	FACETS	0.944	0.839	1	0.944	0.839	1	CLONAL	1	TRUE	0	0.27	1		623	611	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939033	48939033	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	75	303	0	ENST00000267163.4:c.865A>C	p.Lys289Gln	p.K289Q	ENST00000267163	NM_000321.2	289	Aaa/Caa	9/27	0.118186703609964	3	FACETS	1	0.921	1	0.533	0.468	0.604	INDETERMINATE	1	TRUE	1	0.27	3		303	591	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651336	52651336	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	118	529	0	ENST00000394830.3:c.1760T>C	p.Ile587Thr	p.I587T	ENST00000394830	NM_018313.4	587	aTa/aCa	15/30	0.3	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.27	1		529	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578541	7578541	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1131691013	NA	P-0015769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	300	891	0	ENST00000269305.4:c.389T>C	p.Leu130Pro	p.L130P	ENST00000269305	NM_001126112.2	130	cTc/cCc	5/11	0.417649771442295	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.417649771442295	1		891	1112	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0015769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	387	568	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.10364003165945	5	FACETS	1	0.989	1			1	INDETERMINATE	3	TRUE	NA	0.417649771442295	5		568	906	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243776993	243776993	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	54	706	1	ENST00000263826.5:c.676G>T	p.Glu226Ter	p.E226*	ENST00000263826	NM_005465.4	226	Gaa/Taa	7/13	0.14301366682259	5	FACETS	0.483	0.412	0.563			1	INDETERMINATE	1	TRUE	NA	0.417649771442295	5		707	870	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243777014	243777014	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	43	599	0	ENST00000263826.5:c.655G>A	p.Asp219Asn	p.D219N	ENST00000263826	NM_005465.4	219	Gac/Aac	7/13	0.14301366682259	5	FACETS	0.458	0.382	0.543			1	INDETERMINATE	1	TRUE	NA	0.417649771442295	5		599	731	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23640590	23640590	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs180177116	NA	P-0015769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	173	609	1	ENST00000261584.4:c.2521del	p.Thr841GlnfsTer10	p.T841Qfs*10	ENST00000261584	NM_024675.3	841	Aca/ca	6/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.417649771442295	2		610	672	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	27	507	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.787	0.63	0.963	0.787	0.63	0.963	CLONAL	1	TRUE	1	0.33	2		507	208	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578399	+	frameshift_variant	Frame_Shift_Del	DEL	GGTGG	GGTGG	-	novel	NA	P-0015771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	26	612	0	ENST00000269305.4:c.531_535del	p.His178Ter	p.H178*	ENST00000269305	NM_001126112.2	177	ccCCACCat/ccat	5/11	1	2	FACETS	0.651	0.518	0.803	0.651	0.518	0.803	SUBCLONAL	1	TRUE	1	0.33	2		612	242	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880997	37880998	+	protein_altering_variant	In_Frame_Ins	INS	-	-	TGT	rs397516979	NA	P-0015774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	178	874	0	ENST00000269571.5:c.2326_2327insTGT	p.Gly776delinsValCys	p.G776delinsVC	ENST00000269571		776	ggt/gTGTgt	20/27	0.196190618268452	3	FACETS	0.759	0.699	0.822	0.759	0.699	0.822	SUBCLONAL	2	TRUE	1	0.261492612075281	3		874	1014	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857812	57857812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	137	955	2	ENST00000228682.2:c.131C>T	p.Ala44Val	p.A44V	ENST00000228682	NM_005269.2	44	gCt/gTt	3/12	0.196190618268452	3	FACETS	1	0.941	1	0.524	0.476	0.576	CLONAL	1	TRUE	1	0.261492612075281	3		957	1130	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66679698	66679698	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0015774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	104	762	0	ENST00000307102.5:c.13A>T	p.Lys5Ter	p.K5*	ENST00000307102	NM_002755.3	5	Aag/Tag	1/11	1	2	FACETS	0.917	0.821	1	0.917	0.821	1	CLONAL	1	TRUE	1	0.261492612075281	2		762	867	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0015775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	318	612	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.5884114621547	1	FACETS	0.994	0.945	1	0.994	0.945	1	CLONAL	1	TRUE	0	0.624975544811256	1		612	704	SUCCESS
APC	324	MSKCC	GRCh37	5	112116517	112116517	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs869312753	NA	P-0015775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	159	354	0	ENST00000257430.4:c.562C>T	p.Gln188Ter	p.Q188*	ENST00000257430	NM_000038.5	188	Caa/Taa	6/16	0.5884114621547	1	FACETS	0.817	0.757	0.879	0.817	0.757	0.879	CLONAL	1	TRUE	0	0.624975544811256	1		354	428	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0015777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	373	574	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.533099693810809	4	FACETS	0.885	0.84	0.931			1	CLONAL	2	TRUE	NA	0.533099693810809	4		574	1212	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0015777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	1115	641	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.426176789488649	4	FACETS	1	0.998	1			1	CLONAL	4	TRUE	NA	0.533099693810809	4		641	1452	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435150	18435150	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	88	488	0	ENST00000266497.5:c.135T>A	p.Asp45Glu	p.D45E	ENST00000266497		45	gaT/gaA	1/31	0.458678335062716	4	FACETS	1	0.923	1	0.349	0.31	0.391	CLONAL	1	TRUE	1	0.533099693810809	4		488	483	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480395	56480395	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	802	654	2	ENST00000267101.3:c.502A>G	p.Arg168Gly	p.R168G	ENST00000267101	NM_001982.3	168	Agg/Ggg	4/28	0.533099693810809	5	FACETS	0.995	0.968	1	0.995	0.968	1	CLONAL	4	TRUE	1	0.533099693810809	5		656	1360	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39721145	39721145	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	86	679	2	ENST00000361337.2:c.648G>T	p.Lys216Asn	p.K216N	ENST00000361337	NM_003286.2	216	aaG/aaT	9/21	0.533099693810809	6	FACETS	0.613	0.54	0.691	0.153	0.135	0.173	SUBCLONAL	1	TRUE	2	0.533099693810809	6		681	1088	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	398	507	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.387446660598834	3	FACETS	0.99	0.942	1	0.99	0.942	1	CLONAL	2	TRUE	1	0.387876660842688	3		507	1237	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207021	1207021	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913324	NA	P-0015780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	414	594	2	ENST00000326873.7:c.109C>T	p.Gln37Ter	p.Q37*	ENST00000326873	NM_000455.4	37	Cag/Tag	1/10	0.387876660842688	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.387876660842688	2		596	1038	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609742	28609742	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	443	742	0	ENST00000241453.7:c.1487T>G	p.Val496Gly	p.V496G	ENST00000241453	NM_004119.2	496	gTg/gGg	12/24	0.387876660842688	2	FACETS	0.971	0.928	1	0.971	0.928	1	CLONAL	2	TRUE	0	0.387876660842688	2		742	1176	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095840	178095898	+	frameshift_variant	Frame_Shift_Del	DEL	TAATGCAAGTTGAGCTTCATTGAACTGCTCTTTGGACATCATTTCGTTGAAGTCAACAA	TAATGCAAGTTGAGCTTCATTGAACTGCTCTTTGGACATCATTTCGTTGAAGTCAACAA	-	novel	NA	P-0015780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	72	495	0	ENST00000397062.3:c.1433_1491del	p.Val478AspfsTer6	p.V478Dfs*6	ENST00000397062	NM_006164.4	478	gTTGTTGACTTCAACGAAATGATGTCCAAAGAGCAGTTCAATGAAGCTCAACTTGCATTA/g	5/5	0.387446660598834	3	FACETS	0.423	0.368	0.482	0.211	0.184	0.241	SUBCLONAL	1	TRUE	1	0.387876660842688	3		495	1049	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508847	31508847	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1214	100	596	0	ENST00000344624.3:c.1468G>T	p.Asp490Tyr	p.D490Y	ENST00000344624		490	Gac/Tac	7/33	0.291968146574466	4	FACETS	0.545	0.485	0.609	0.136	0.121	0.153	SUBCLONAL	1	TRUE	0	0.387876660842688	4		596	1314	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339299	116339299	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	174	523	0	ENST00000397752.3:c.161A>T	p.Asn54Ile	p.N54I	ENST00000397752	NM_000245.2	54	aAt/aTt	2/21	0.370899370199755	4	FACETS	1	0.976	1	0.578	0.531	0.627	CLONAL	1	TRUE	2	0.387876660842688	4		523	1077	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5078309	5078309	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	115	403	0	ENST00000381652.3:c.1996G>T	p.Glu666Ter	p.E666*	ENST00000381652	NM_004972.3	666	Gaa/Taa	16/25	1	2	FACETS	0.854	0.771	0.943	0.854	0.771	0.943	CLONAL	1	TRUE	1	0.387876660842688	2		403	694	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	188	507	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.457051878861857	3	FACETS	1	0.99	1	0.734	0.68	0.789	CLONAL	1	TRUE	1	0.456074453837467	3		507	690	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0015781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	427	790	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.448685971103327	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.456074453837467	2		792	925	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633395	3633395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771200478	NA	P-0015781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	413	909	1	ENST00000294008.3:c.4856C>T	p.Pro1619Leu	p.P1619L	ENST00000294008	NM_032444.2	1619	cCg/cTg	14/15	0.161750820625797	6	FACETS	0.841	0.801	0.883	0.841	0.801	0.883	INDETERMINATE	3	TRUE	3	0.456074453837467	6		910	1372	SUCCESS
APC	324	MSKCC	GRCh37	5	112175761	112175762	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0015781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	122	361	0	ENST00000257430.4:c.4472_4473del	p.Phe1491CysfsTer22	p.F1491Cfs*22	ENST00000257430	NM_000038.5	1490	caTTtt/catt	16/16	NA	2	FACETS	0.794	0.727	0.863			1	INDETERMINATE	2	TRUE	NA	0.456074453837467	2		361	337	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0015782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	142	475	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.48097066966094	5	FACETS	0.793	0.725	0.864	0.529	0.483	0.576	SUBCLONAL	2	TRUE	2	0.48097066966094	5		475	641	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0015782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	256	860	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.48097066966094	3	FACETS	1	0.985	1	0.58	0.543	0.619	CLONAL	1	TRUE	1	0.48097066966094	3		861	1138	SUCCESS
APC	324	MSKCC	GRCh37	5	112175600	112175600	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	405	635	0	ENST00000257430.4:c.4312del	p.Thr1438HisfsTer35	p.T1438Hfs*35	ENST00000257430	NM_000038.5	1437	Aaa/aa	16/16	0.460911056878875	3	FACETS	0.933	0.896	0.971	0.933	0.896	0.971	CLONAL	3	TRUE	0	0.48097066966094	3		635	746	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330537	65330537	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	329	663	0	ENST00000342505.4:c.1109del	p.Pro370LeufsTer7	p.P370Lfs*7	ENST00000342505	NM_002227.2	370	cCt/ct	8/25	0.48097066966094	3	FACETS	0.937	0.888	0.986	0.624	0.592	0.657	CLONAL	2	TRUE	0	0.48097066966094	3		663	906	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108091	30108091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80271647	NA	P-0015782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	352	718	0	ENST00000331968.5:c.716C>T	p.Ser239Leu	p.S239L	ENST00000331968	NM_002742.2	239	tCg/tTg	5/18	0.480533074970305	4	FACETS	1	0.986	1	0.734	0.696	0.771	CLONAL	2	TRUE	1	0.48097066966094	4		718	985	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991866	72991866	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201721439	NA	P-0015782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	736	904	2	ENST00000268489.5:c.2179C>T	p.Arg727Cys	p.R727C	ENST00000268489	NM_006885.3	727	Cgc/Tgc	2/10	0.48097066966094	5	FACETS	0.98	0.951	1	0.98	0.951	1	CLONAL	4	TRUE	1	0.48097066966094	5		906	1344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	DEL	C	C	-	rs1567550969	NA	P-0015782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	409	868	0	ENST00000269305.4:c.672+1del		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.48097066966094	3	FACETS	0.916	0.873	0.959	0.916	0.873	0.959	CLONAL	2	TRUE	1	0.48097066966094	3		868	1152	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39690102	39690102	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1687	149	673	0	ENST00000361337.2:c.127G>C	p.Asp43His	p.D43H	ENST00000361337	NM_003286.2	43	Gac/Cac	3/21	0.48097066966094	8	FACETS	0.824	0.75	0.903	0.118	0.107	0.129	CLONAL	1	TRUE	1	0.48097066966094	8		673	1836	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729658	41729658	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	129	571	1	ENST00000242208.4:c.871C>A	p.Pro291Thr	p.P291T	ENST00000242208	NM_002192.2	291	Cct/Act	3/3	0.438812551851198	5	FACETS	1	0.958	1	0.275	0.249	0.302	CLONAL	1	TRUE	1	0.48097066966094	5		572	840	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245325	53245325	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	444	785	0	ENST00000375401.3:c.712A>G	p.Ile238Val	p.I238V	ENST00000375401	NM_004187.3	238	Atc/Gtc	6/26	0.48097066966094	5	FACETS	1	0.993	1	0.815	0.778	0.853	CLONAL	2	TRUE	2	0.48097066966094	5		785	1300	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555687605	NA	P-0015783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	80	538	0	ENST00000342988.3:c.1610A>G	p.Asp537Gly	p.D537G	ENST00000342988	NM_005359.5	537	gAc/gGc	12/12	0.564207382031603	1	FACETS	0.271	0.238	0.307	0.271	0.238	0.307	SUBCLONAL	1	TRUE	0	0.564207382031603	1		538	751	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0015783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	292	720	1	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.564207382031603	1	FACETS	0.891	0.841	0.941	0.891	0.841	0.941	CLONAL	1	TRUE	0	0.564207382031603	1		721	834	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867533	78867533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs185118480	NA	P-0015783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	263	616	0	ENST00000306801.3:c.2269G>A	p.Gly757Arg	p.G757R	ENST00000306801	NM_020761.2	757	Gga/Aga	20/34	1	2	FACETS	0.957	0.898	1	0.957	0.898	1	CLONAL	1	TRUE	1	0.564207382031603	2		616	974	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266010	41266578	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTG	TTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTG	-	novel	NA	P-0015783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	112	255	0	ENST00000349496.5:c.14-7_375del		p.X5_splice	ENST00000349496	NM_001904.3	5		3-4/15	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.564207382031603	2		255	372	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277264	41277264	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	222	504	0	ENST00000349496.5:c.1733A>G	p.His578Arg	p.H578R	ENST00000349496	NM_001904.3	578	cAc/cGc	11/15	1	2	FACETS	0.986	0.92	1	0.986	0.92	1	CLONAL	1	TRUE	1	0.564207382031603	2		504	798	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0015784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	15	541	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.275172689064336	14	FACETS	0.853	0.63	1	0.32	0.236	0.418	CLONAL	3	FALSE	6	0.275172689064336	14		541	113	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577296	64577296	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	68	887	0	ENST00000312049.6:c.286C>T	p.Gln96Ter	p.Q96*	ENST00000312049	NM_130799.2	96	Cag/Tag	2/10	0.275172689064336	4	FACETS	1	0.912	1	1	0.975	1	CLONAL	4	FALSE	1	0.275172689064336	4		887	154	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818783	170818783	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	10	369	0	ENST00000296930.5:c.332T>A	p.Ile111Asn	p.I111N	ENST00000296930	NM_002520.6	111	aTt/aAt	4/11	0.275172689064336	8	FACETS	1	0.763	1	0.231	0.157	0.322	CLONAL	1	FALSE	3	0.275172689064336	8		369	115	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	490	414	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.26310028031635	3	FACETS	0.806	0.771	0.841	0.806	0.771	0.841	INDETERMINATE	2	TRUE	1	0.559117795022604	3		414	1392	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17355201	17355201	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs934514080	NA	P-0015785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	168	704	0	ENST00000375499.3:c.317A>G	p.Asn106Ser	p.N106S	ENST00000375499	NM_003000.2	106	aAt/aGt	4/8	0.498028742990154	2	FACETS	0.541	0.496	0.588	0.27	0.248	0.294	SUBCLONAL	1	TRUE	0	0.559117795022604	2		704	1111	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514038	69514038	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	361	582	0	ENST00000294312.3:c.643G>A	p.Glu215Lys	p.E215K	ENST00000294312	NM_005117.2	215	Gag/Aag	3/3	1	2	FACETS	0.952	0.902	1	0.952	0.902	1	CLONAL	1	TRUE	1	0.559117795022604	2		582	1356	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716386	18716386	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1179	346	638	0	ENST00000266497.5:c.3733C>A	p.Leu1245Ile	p.L1245I	ENST00000266497		1245	Ctt/Att	26/31	0.26310028031635	3	FACETS	1	0.969	1	0.519	0.49	0.549	INDETERMINATE	1	TRUE	1	0.559117795022604	3		638	1525	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437296	121437296	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1445	319	904	1	ENST00000257555.6:c.1634C>T	p.Ser545Leu	p.S545L	ENST00000257555		545	tCa/tTa	9/10	0.498028742990154	2	FACETS	0.647	0.608	0.687	0.323	0.304	0.344	SUBCLONAL	1	TRUE	0	0.559117795022604	2		905	1764	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336073	73336073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	141	275	0	ENST00000377767.4:c.2330C>T	p.Ser777Leu	p.S777L	ENST00000377767	NM_014953.3	777	tCa/tTa	17/21	1	2	FACETS	0.959	0.879	1	0.959	0.879	1	CLONAL	1	TRUE	1	0.559117795022604	2		275	526	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882998	89882998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752776388	NA	P-0015785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	95	393	0	ENST00000389301.3:c.26C>T	p.Ser9Phe	p.S9F	ENST00000389301	NM_000135.2	9	tCc/tTc	1/43	1	2	FACETS	0.404	0.359	0.452	0.404	0.359	0.452	SUBCLONAL	1	TRUE	1	0.559117795022604	2		393	841	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572962	7572974	+	frameshift_variant	Frame_Shift_Del	DEL	GTTTTTTATGGCG	GTTTTTTATGGCG	-	novel	NA	P-0015785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	296	574	0	ENST00000269305.4:c.1135_1147del	p.Arg379SerfsTer39	p.R379Sfs*39	ENST00000269305	NM_001126112.2	379	CGCCATAAAAAACtc/tc	11/11	0.559117795022604	1	FACETS	0.819	0.773	0.867	0.819	0.773	0.867	CLONAL	1	TRUE	0	0.559117795022604	1		574	931	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556877	29556877	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	72	396	0	ENST00000356175.3:c.2875C>T	p.Gln959Ter	p.Q959*	ENST00000356175	NM_000267.3	959	Caa/Taa	22/57	1	2	FACETS	0.365	0.319	0.416	0.365	0.319	0.416	SUBCLONAL	1	TRUE	1	0.559117795022604	2		396	705	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604673	48604673	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060500738	NA	P-0015785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	316	460	0	ENST00000342988.3:c.1495T>C	p.Cys499Arg	p.C499R	ENST00000342988	NM_005359.5	499	Tgc/Cgc	12/12	0.559117795022604	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.559117795022604	1		460	743	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718761	190718761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	90	464	0	ENST00000441310.2:c.919G>A	p.Asp307Asn	p.D307N	ENST00000441310	NM_000534.4	307	Gat/Aat	8/13	1	2	FACETS	0.385	0.341	0.432	0.385	0.341	0.432	SUBCLONAL	1	TRUE	1	0.559117795022604	2		464	836	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0015785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	187	329	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.559117795022604	2		329	667	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735464	40735464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	503	741	0	ENST00000373198.4:c.3409G>A	p.Glu1137Lys	p.E1137K	ENST00000373198	NM_133170.3	1137	Gag/Aag	25/32	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.559117795022604	2		741	1748	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42842606	42842606	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778628616	NA	P-0015785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	173	734	0	ENST00000398585.3:c.1251G>A	p.Trp417Ter	p.W417*	ENST00000398585	NM_001135099.1	417	tgG/tgA	11/14	0.338993481418766	1	FACETS	0.35	0.321	0.38	0.35	0.321	0.38	SUBCLONAL	1	TRUE	0	0.559117795022604	1		734	1274	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129600	47129600	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0015785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	79	589	0	ENST00000409792.3:c.5277+3G>A		p.X1759_splice	ENST00000409792	NM_014159.6	1759			0.559117795022604	1	FACETS	0.253	0.222	0.286	0.253	0.222	0.286	SUBCLONAL	1	TRUE	0	0.559117795022604	1		589	805	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598142	52598142	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	394	718	0	ENST00000394830.3:c.3724C>T	p.Gln1242Ter	p.Q1242*	ENST00000394830	NM_018313.4	1242	Cag/Tag	24/30	0.559117795022604	1	FACETS	0.968	0.922	1	0.968	0.922	1	CLONAL	1	TRUE	0	0.559117795022604	1		718	1049	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226925	142226925	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	126	662	0	ENST00000350721.4:c.4879C>T	p.Gln1627Ter	p.Q1627*	ENST00000350721	NM_001184.3	1627	Cag/Tag	28/47	0.498028742990154	2	FACETS	0.453	0.409	0.499	0.226	0.204	0.25	SUBCLONAL	1	TRUE	0	0.559117795022604	2		662	995	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751931	57751931	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55768901	NA	P-0015785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	304	618	0	ENST00000274289.3:c.1306G>A	p.Glu436Lys	p.E436K	ENST00000274289	NM_006622.3	436	Gaa/Aaa	10/14	1	2	FACETS	0.933	0.879	0.989	0.933	0.879	0.989	CLONAL	1	TRUE	1	0.559117795022604	2		618	1165	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681829	30681829	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs774216207	NA	P-0015785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	412	707	1	ENST00000376406.3:c.268C>T	p.Arg90Ter	p.R90*	ENST00000376406	NM_014641.2	90	Cga/Tga	3/15	1	2	FACETS	0.927	0.881	0.974	0.927	0.881	0.974	CLONAL	1	TRUE	1	0.559117795022604	2		708	1590	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339898	116339898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	132	589	0	ENST00000397752.3:c.760G>A	p.Glu254Lys	p.E254K	ENST00000397752	NM_000245.2	254	Gaa/Aaa	2/21	1	2	FACETS	0.406	0.367	0.446	0.406	0.367	0.446	SUBCLONAL	1	TRUE	1	0.559117795022604	2		589	1164	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896396	151896396	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1390364171	NA	P-0015785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	135	662	0	ENST00000262189.6:c.4241C>T	p.Ser1414Leu	p.S1414L	ENST00000262189	NM_170606.2	1414	tCa/tTa	27/59	1	2	FACETS	0.399	0.362	0.439	0.399	0.362	0.439	SUBCLONAL	1	TRUE	1	0.559117795022604	2		662	1210	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942825	68942825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753863699	NA	P-0015785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1601	196	807	1	ENST00000288368.4:c.637G>A	p.Glu213Lys	p.E213K	ENST00000288368	NM_024870.2	213	Gag/Aag	6/40	0.26310028031635	3	FACETS	0.499	0.46	0.54	0.25	0.23	0.27	INDETERMINATE	1	TRUE	1	0.559117795022604	3		808	1797	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465542	8465542	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	413	775	0	ENST00000356435.5:c.3638G>A	p.Gly1213Glu	p.G1213E	ENST00000356435		1213	gGa/gAa	21/35	0.559117795022604	1	FACETS	0.961	0.916	1	0.961	0.916	1	CLONAL	1	TRUE	0	0.559117795022604	1		775	1108	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342695	87342695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	377	711	0	ENST00000277120.3:c.980C>T	p.Ser327Phe	p.S327F	ENST00000277120		327	tCc/tTc	9/19	0.559117795022604	1	FACETS	0.965	0.918	1	0.965	0.918	1	CLONAL	1	TRUE	0	0.559117795022604	1		711	1007	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915922	127915922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	163	706	1	ENST00000373547.4:c.559C>T	p.His187Tyr	p.H187Y	ENST00000373547	NM_002721.4	187	Cat/Tat	6/7	0.559117795022604	1	FACETS	0.382	0.35	0.416	0.382	0.35	0.416	SUBCLONAL	1	TRUE	0	0.559117795022604	1		707	1100	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341625	70341625	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	494	816	0	ENST00000374080.3:c.1060C>G	p.Gln354Glu	p.Q354E	ENST00000374080		354	Cag/Gag	7/45	0.559117795022604	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.559117795022604	1		816	1212	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443695	29443695	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs863225281	NA	P-0121592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	386	613	0	ENST00000389048.3:c.3522C>A	p.Phe1174Leu	p.F1174L	ENST00000389048	NM_004304.4	1174	ttC/ttA	23/29	0.654269326686533	3	FACETS	0.996	0.953	1	0.996	0.953	1	CLONAL	2	NA	1	0.654269326686533	3		613	786	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38960546	38960546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1230911017	NA	P-0121592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	36	376	2	ENST00000357387.3:c.1805C>T	p.Thr602Met	p.T602M	ENST00000357387	NM_152756.3	602	aCg/aTg	20/38	0.654269326686533	4	FACETS	0.271	0.222	0.326	0.135	0.111	0.163	SUBCLONAL	1	NA	2	0.654269326686533	4		378	672	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809531	36809531	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0121592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	294	752	0	ENST00000373129.3:c.934G>C	p.Val312Leu	p.V312L	ENST00000373129	NM_032017.1	312	Gtc/Ctc	10/12	0.654269326686533	3	FACETS	1	0.989	1	0.593	0.558	0.628	CLONAL	1	NA	1	0.654269326686533	3		752	1006	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46736441	46736441	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0121592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	166	561	1	ENST00000371975.4:c.1153A>T	p.Thr385Ser	p.T385S	ENST00000371975	NM_003579.3	385	Acc/Tcc	10/18	0.654269326686533	3	FACETS	0.899	0.828	0.973	0.45	0.414	0.487	CLONAL	1	NA	1	0.654269326686533	3		562	749	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303999	91303999	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	42	737	1	ENST00000355112.3:c.1396G>T	p.Gly466Trp	p.G466W	ENST00000355112	NM_000057.2	466	Ggg/Tgg	7/22	0.654269326686533	2	FACETS	0.227	0.189	0.27	0.114	0.094	0.135	SUBCLONAL	1	NA	0	0.654269326686533	2		738	565	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273236	18273236	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0121592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	96	719	0	ENST00000222254.8:c.1029A>C	p.Lys343Asn	p.K343N	ENST00000222254	NM_005027.3	343	aaA/aaC	9/16	0.654269326686533	3	FACETS	0.463	0.411	0.517	0.231	0.205	0.259	SUBCLONAL	1	NA	1	0.654269326686533	3		719	842	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47710031	47710031	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0121592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	89	447	0	ENST00000233146.2:c.2748A>G	p.Ile916Met	p.I916M	ENST00000233146	NM_000251.2	916	atA/atG	16/16	0.654269326686533	3	FACETS	0.593	0.526	0.664	0.296	0.263	0.332	SUBCLONAL	1	NA	1	0.654269326686533	3		447	609	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660501	227660501	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0121592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	171	397	0	ENST00000305123.5:c.2954G>C	p.Ser985Thr	p.S985T	ENST00000305123	NM_005544.2	985	aGc/aCc	1/2	0.654269326686533	3	FACETS	1	0.974	1	0.56	0.518	0.604	CLONAL	1	NA	1	0.654269326686533	3		397	619	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631182	176631182	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0121592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	59	593	0	ENST00000439151.2:c.1125A>C	p.Arg375Ser	p.R375S	ENST00000439151	NM_022455.4	375	agA/agC	4/23	0.654269326686533	3	FACETS	0.278	0.239	0.322	0.139	0.119	0.161	SUBCLONAL	1	NA	1	0.654269326686533	3		593	860	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923802	39923802	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	346	867	0	ENST00000378444.4:c.3289G>T	p.Asp1097Tyr	p.D1097Y	ENST00000378444	NM_001123385.1	1097	Gac/Tac	7/15	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	NA	NA	0.654269326686533	2		867	919	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354984	70354984	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0121592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	211	651	0	ENST00000374080.3:c.4906C>G	p.Arg1636Gly	p.R1636G	ENST00000374080		1636	Cgc/Ggc	36/45	1	2	FACETS	0.949	0.885	1	0.949	0.885	1	CLONAL	1	NA	1	0.654269326686533	2		651	680	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829793	76829793	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0121592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	202	678	0	ENST00000373344.5:c.6248A>G	p.Tyr2083Cys	p.Y2083C	ENST00000373344	NM_000489.3	2083	tAt/tGt	28/35	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	NA	1	0.654269326686533	2		678	614	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577075	7577075	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	82	746	0	ENST00000269305.4:c.863del	p.Asn288IlefsTer57	p.N288Ifs*57	ENST00000269305	NM_001126112.2	288	aAt/at	8/11	0.442183999021477	2	FACETS	0.933	0.83	1	0.467	0.415	0.522	CLONAL	1	TRUE	0	0.500569487409122	2		746	351	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088723	27088723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs990194975	NA	P-0015787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	97	672	0	ENST00000324856.7:c.2332G>A	p.Gly778Arg	p.G778R	ENST00000324856	NM_006015.4	778	Gga/Aga	7/20	0.410074903501614	1	FACETS	0.862	0.777	0.951	0.862	0.777	0.951	CLONAL	1	TRUE	0	0.500569487409122	1		672	337	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	202	414	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.3	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.27	3		414	749	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433388	49433388	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555191598	NA	P-0015789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	119	798	0	ENST00000301067.7:c.8059C>T	p.Arg2687Ter	p.R2687*	ENST00000301067	NM_003482.3	2687	Cga/Tga	32/54	1	2	FACETS	0.999	0.901	1	0.999	0.901	1	CLONAL	1	TRUE	1	0.27	2		798	882	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412958	49412958	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	130	723	0	ENST00000418115.1:c.65T>C	p.Leu22Pro	p.L22P	ENST00000418115	NM_001664.2	22	cTc/cCc	2/5	1	2	FACETS	0.998	0.904	1	0.998	0.904	1	CLONAL	1	TRUE	1	0.27	2		723	965	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545804	41545804	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs201054979	NA	P-0015789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	141	773	0	ENST00000263253.7:c.2419A>G	p.Ile807Val	p.I807V	ENST00000263253	NM_001429.3	807	Ata/Gta	14/31	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.27	2		773	915	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894800	101894800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370568025	NA	P-0015789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	54	286	0	ENST00000374994.4:c.353C>T	p.Ser118Leu	p.S118L	ENST00000374994	NM_004612.2	118	tCa/tTa	3/9	0.265449874157265	1	FACETS	0.856	0.734	0.99	0.856	0.734	0.99	CLONAL	1	TRUE	0	0.27	1		286	404	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894910	101894910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751679796	NA	P-0015789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	69	353	0	ENST00000374994.4:c.463C>T	p.His155Tyr	p.H155Y	ENST00000374994	NM_004612.2	155	Cac/Tac	3/9	0.265449874157265	1	FACETS	0.957	0.836	1	0.957	0.836	1	CLONAL	1	TRUE	0	0.27	1		353	462	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894962	101894962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	54	349	0	ENST00000374994.4:c.515C>T	p.Ser172Leu	p.S172L	ENST00000374994	NM_004612.2	172	tCa/tTa	3/9	0.265449874157265	1	FACETS	0.81	0.694	0.937	0.81	0.694	0.937	CLONAL	1	TRUE	0	0.27	1		349	427	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894864	101894866	+	missense_variant	Missense_Mutation	TNP	CTC	CTC	TTT	novel	NA	P-0015789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	62	309	0	ENST00000374994.4:c.417_419delinsTTT	p.Ser140Leu	p.S140L	ENST00000374994	NM_004612.2	139	atCTCa/atTTTa	3/9	0.265449874157265	1	FACETS	0.967	0.838	1	0.967	0.838	1	CLONAL	1	TRUE	0	0.27	1		309	411	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	63	414	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	0.15	2		414	772	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0015790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	54	568	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.150279964895795	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.15	1		568	588	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0015790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	50	480	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.936	0.793	1	0.936	0.793	1	CLONAL	1	TRUE	1	0.15	2		481	712	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0015790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	25	424	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	0.601	0.472	0.749	0.601	0.472	0.749	SUBCLONAL	1	TRUE	1	0.15	2		424	555	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030486	49030486	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	63	344	2	ENST00000267163.4:c.1960+1G>A		p.X654_splice	ENST00000267163	NM_000321.2	654			0.150279964895795	3	FACETS	0.818	0.708	0.937	0.818	0.708	0.937	CLONAL	2	TRUE	1	0.15	3		346	552	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0015790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	45	422	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	1	0.844	1	1	0.844	1	CLONAL	1	TRUE	1	0.15	2		422	597	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	24	247	0	ENST00000257430.4:c.3919dup	p.Ile1307AsnfsTer8	p.I1307Nfs*8	ENST00000257430	NM_000038.5	1306	gaa/gAaa	16/16	1	2	FACETS	0.746	0.584	0.933	0.746	0.584	0.933	CLONAL	1	TRUE	1	0.15	2		247	429	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0015791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	118	704	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.540704291543754	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	4	TRUE	0	0.540704291543754	4		705	156	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0015791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	57	604	1				ENST00000310581	NM_198253.2	-/1132			0.432927637712625	4	FACETS	1	0.919	1	1	0.919	1	CLONAL	2	TRUE	2	0.540704291543754	4		605	153	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804304	43804304	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763568293	NA	P-0015791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	30	644	1	ENST00000372470.3:c.304C>T	p.Arg102Cys	p.R102C	ENST00000372470	NM_005373.2	102	Cgt/Tgt	3/12	1	2	FACETS	0.965	0.794	1	0.965	0.794	1	CLONAL	1	TRUE	1	0.540704291543754	2		645	115	SUCCESS
RET	5979	MSKCC	GRCh37	10	43613889	43613889	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	17	815	0	ENST00000355710.3:c.2353C>A	p.Pro785Thr	p.P785T	ENST00000355710	NM_020975.4	785	Cca/Aca	13/20	0.433489323547868	3	FACETS	0.563	0.423	0.725	0.281	0.211	0.363	SUBCLONAL	1	TRUE	1	0.540704291543754	3		815	142	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243946	46243947	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0015791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	32	590	0	ENST00000334344.6:c.2041_2042del	p.Val681PhefsTer25	p.V681Ffs*25	ENST00000334344	NM_152641.2	680	acTGtt/actt	15/21	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.540704291543754	2		590	101	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562956	95562956	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	33	441	0	ENST00000393063.1:c.4301A>G	p.Glu1434Gly	p.E1434G	ENST00000393063	NM_030621.3	1434	gAa/gGa	24/28	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.540704291543754	2		441	87	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979022	7979022	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	35	602	0	ENST00000319144.4:c.1545G>C	p.Glu515Asp	p.E515D	ENST00000319144	NM_001139.2	515	gaG/gaC	12/15	0.353951734957338	4	FACETS	1	0.846	1	0.341	0.282	0.406	CLONAL	1	TRUE	1	0.540704291543754	4		602	195	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16055258	16055258	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0015791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	41	529	0	ENST00000268712.3:c.842+2T>C		p.X281_splice	ENST00000268712	NM_006311.3	281			0.353951734957338	4	FACETS	0.99	0.846	1	0.66	0.564	0.761	CLONAL	2	TRUE	1	0.540704291543754	4		529	118	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441093	149441093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	75	831	1	ENST00000286301.3:c.1819G>A	p.Glu607Lys	p.E607K	ENST00000286301	NM_005211.3	607	Gag/Aag	13/22	0.432927637712625	4	FACETS	1	0.91	1	1	0.91	1	CLONAL	2	TRUE	2	0.540704291543754	4		832	209	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111502	8111503	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	61	673	0	ENST00000346208.3:c.990dup	p.Asn331GlufsTer21	p.N331Efs*21	ENST00000346208		330	agg/aGgg	5/6	0.229979421529015	3	FACETS	0.604	0.52	0.698	0.302	0.26	0.349	SUBCLONAL	1	TRUE	1	0.21	3		673	1062	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239419	105239419	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	117	605	0	ENST00000349310.3:c.968A>G	p.Asp323Gly	p.D323G	ENST00000349310	NM_001014432.1	323	gAc/gGc	12/15	0.229979421529015	3	FACETS	1	0.979	1	0.671	0.605	0.742	CLONAL	1	TRUE	1	0.21	3		605	917	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743611	46743757	+	splice_acceptor_variant,splice_donor_variant,frameshift_variant,stop_lost,intron_variant	Splice_Site	DEL	GTTTATCCTGGATGAAGCTAGCCTCAGTGACACACATGACAGGTGGGGAAGTGCCCTAACCATTATCTCTAAGCTACCCACACAGTAGGGAGATGGGATCTGTAGTGACTTCAGCTGTGCCTTCTGTCCCTAGGTTGCACTGCCGAC	GTTTATCCTGGATGAAGCTAGCCTCAGTGACACACATGACAGGTGGGGAAGTGCCCTAACCATTATCTCTAAGCTACCCACACAGTAGGGAGATGGGATCTGTAGTGACTTCAGCTGTGCCTTCTGTCCCTAGGTTGCACTGCCGAC	-	novel	NA	P-0015794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	59	629	1	ENST00000371975.4:c.1995_2050del		p.X665_splice	ENST00000371975	NM_003579.3	665	ctGTTTATCCTGGATGAAGCTAGCCTCAGTGACACACATGACAGGTGGGGAAGTGCCCTAACCATTATCTCTAAGCTACCCACACAGTAGGGAGATGGGATCTGTAGTGACTTCAGCTGTGCCTTCTGTCCCTAGGTTGCACTGCCGACgt/ctgt	17-18/18	1	2	FACETS	0.541	0.464	0.626	0.541	0.464	0.626	SUBCLONAL	1	TRUE	1	0.21	2		630	1038	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250347	39250347	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	44	732	0	ENST00000402219.2:c.1222T>C	p.Tyr408His	p.Y408H	ENST00000402219	NM_005633.3	408	Tat/Cat	10/23	1	2	FACETS	0.55	0.46	0.65	0.55	0.46	0.65	SUBCLONAL	1	TRUE	1	0.21	2		732	762	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982134	93982134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773950345	NA	P-0015794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	39	377	1	ENST00000369303.4:c.1331C>T	p.Ser444Leu	p.S444L	ENST00000369303	NM_004440.3	444	tCg/tTg	6/17	0.138261985476045	0	FACETS	0.56	0.464	0.668			1	SUBCLONAL	1	TRUE	0	0.21	0		378	524	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	686	414	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.463939182340163	9	FACETS	1	0.979	1	0.883	0.858	0.908	CLONAL	7	TRUE	1	0.463939182340163	9		414	1098	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0015795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	352	597	0	ENST00000269305.4:c.994-1G>T		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.463939182340163	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.463939182340163	2		597	694	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39567844	39567844	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	35	416	0	ENST00000262039.4:c.600A>C	p.Glu200Asp	p.E200D	ENST00000262039	NM_002647.2	200	gaA/gaC	5/25	0.463939182340163	1	FACETS	0.574	0.474	0.683	0.574	0.474	0.683	SUBCLONAL	1	TRUE	0	0.463939182340163	1		416	202	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095913	178095914	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1323566743	NA	P-0015795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	69	500	0	ENST00000397062.3:c.1417dup	p.Ile473AsnfsTer3	p.I473Nfs*3	ENST00000397062	NM_006164.4	473	atc/aAtc	5/5	0.461258536487154	5	FACETS	0.765	0.666	0.873	0.255	0.222	0.291	SUBCLONAL	1	TRUE	2	0.463939182340163	5		500	659	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422405	225422405	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	68	644	0	ENST00000264414.4:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000264414	NM_003590.4	79	Gaa/Caa	2/16	0.461258536487154	5	FACETS	0.666	0.579	0.761	0.222	0.193	0.254	SUBCLONAL	1	TRUE	2	0.463939182340163	5		644	746	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0015810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	395	624	1	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.597499784365652	2	FACETS	0.919	0.885	0.953	0.919	0.885	0.953	CLONAL	2	FALSE	0	0.683125991941519	2		625	629	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15365053	15365053	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	176	672	0	ENST00000263377.2:c.2068G>T	p.Ala690Ser	p.A690S	ENST00000263377	NM_058243.2	690	Gcc/Tcc	11/20	0.611344960513269	4	FACETS	0.839	0.772	0.909	0.419	0.386	0.455	CLONAL	1	FALSE	2	0.683125991941519	4		672	1034	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942060	71942113	+	inframe_deletion	In_Frame_Del	DEL	GTGACATCCTGGTTCACATCGAAGGGTCTGGGGAAGACCCTGGACGAGGTCACA	GTGACATCCTGGTTCACATCGAAGGGTCTGGGGAAGACCCTGGACGAGGTCACA	-	novel	NA	P-0015810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	172	840	1	ENST00000298229.2:c.1329_1382del	p.Ser444_Thr461del	p.S444_T461del	ENST00000298229	NM_001567.3	442	GTGACATCCTGGTTCACATCGAAGGGTCTGGGGAAGACCCTGGACGAGGTCACA/-	12/28	0.665341090827319	4	FACETS	0.723	0.664	0.784	0.181	0.166	0.196	SUBCLONAL	1	FALSE	0	0.683125991941519	4		841	1173	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204782	94204782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	74	477	0	ENST00000323929.3:c.803G>A	p.Ser268Asn	p.S268N	ENST00000323929	NM_005591.3	268	aGc/aAc	8/20	0.683125991941519	3	FACETS	0.792	0.698	0.892			1	SUBCLONAL	1	FALSE	NA	0.683125991941519	3		477	367	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885481	111885481	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	162	585	0	ENST00000341259.2:c.1258G>C	p.Glu420Gln	p.E420Q	ENST00000341259	NM_005475.2	420	Gag/Cag	7/8	0.260228222847326	6	FACETS	1	0.978	1			1	INDETERMINATE	1	FALSE	NA	0.683125991941519	6		585	945	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28903784	28903784	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	186	672	0	ENST00000282397.4:c.2675T>C	p.Val892Ala	p.V892A	ENST00000282397	NM_002019.4	892	gTt/gCt	19/30	0.611344960513269	4	FACETS	0.93	0.858	1	0.465	0.429	0.502	CLONAL	1	FALSE	2	0.683125991941519	4		672	986	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40864505	40864505	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0015810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	168	562	0	ENST00000428826.2:c.1205-2A>G		p.X402_splice	ENST00000428826		402			0.620711315641901	2	FACETS	0.901	0.833	0.97	0.45	0.416	0.485	CLONAL	1	FALSE	0	0.683125991941519	2		562	546	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243037	41243037	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	187	563	0	ENST00000357654.3:c.4109C>G	p.Ser1370Cys	p.S1370C	ENST00000357654	NM_007294.3	1370	tCt/tGt	11/23	0.620711315641901	2	FACETS	0.952	0.885	1	0.476	0.442	0.511	CLONAL	1	FALSE	0	0.683125991941519	2		563	575	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143226671	143226671	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs865964158	NA	P-0015810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	108	417	1	ENST00000262992.4:c.443C>T	p.Ala148Val	p.A148V	ENST00000262992	NM_001101669.1	148	gCc/gTc	7/24	NA	2	FACETS	0.755	0.682	0.83			1	INDETERMINATE	1	FALSE	NA	0.683125991941519	2		418	419	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109321749	109321750	+	missense_variant	Missense_Mutation	DNP	TC	TC	GG	novel	NA	P-0015810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	171	829	1	ENST00000436639.2:c.673_674delinsCC	p.Glu225Pro	p.E225P	ENST00000436639	NM_014454.2	225	GAa/CCa	4/10	0.683125991941519	4	FACETS	0.693	0.636	0.753	0.231	0.212	0.251	SUBCLONAL	1	FALSE	1	0.683125991941519	4		830	1216	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	250	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.976	0.92	1	1	0.995	1	CLONAL	2	TRUE	1	0.426122351765816	2		248	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0015811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	49	467	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.206	0.174	0.243	0.206	0.174	0.243	SUBCLONAL	1	TRUE	1	0.426122351765816	2		468	1114	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453136	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	rs397516897	NA	P-0015811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	224	594	0	ENST00000288602.6:c.1799_1801del	p.Val600_Lys601delinsGlu	p.V600_K601delinsE	ENST00000288602	NM_004333.4	600	gTGAaa/gaa	15/18	1	2	FACETS	0.852	0.798	0.906	1	0.994	1	CLONAL	2	TRUE	1	0.426122351765816	2		594	617	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427345	427345	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs775852708	NA	P-0015811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	427	541	0	ENST00000399788.2:c.2824A>G	p.Met942Val	p.M942V	ENST00000399788	NM_001042603.1	942	Atg/Gtg	19/28	1	2	FACETS	1	0.987	1	1	0.997	1	CLONAL	2	TRUE	1	0.426122351765816	2		541	935	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796882	42796883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761345552	NA	P-0015812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1671	307	863	0	ENST00000575354.2:c.3347dup	p.Ser1117LysfsTer34	p.S1117Kfs*34	ENST00000575354	NM_015125.3	1114	gcc/gCcc	14/20	0.766145073861968	4	FACETS	0.702	0.659	0.747	0.234	0.219	0.249	SUBCLONAL	1	TRUE	1	0.79173022553784	4		863	1978	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0015812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	311	581	1	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	0.79173022553784	2		582	732	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0015812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	272	596	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	1	2	FACETS	0.899	0.848	0.952	0.899	0.848	0.952	CLONAL	1	TRUE	1	0.79173022553784	2		596	764	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436227	110436227	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1394911868	NA	P-0015812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	61	445	0	ENST00000375856.3:c.2174del	p.Gly725AlafsTer102	p.G725Afs*102	ENST00000375856	NM_003749.2	725	gGc/gc	1/2	0.362995906035303	3	FACETS	0.423	0.365	0.485	0.211	0.182	0.243	INDETERMINATE	1	TRUE	1	0.79173022553784	3		445	509	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255141	16255142	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0015812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	61	497	1	ENST00000375759.3:c.2417_2418dup	p.Arg807AspfsTer3	p.R807Dfs*3	ENST00000375759	NM_015001.2	802	-/GA	11/15	NA	2	FACETS	0.188	0.161	0.217			1	INDETERMINATE	1	TRUE	NA	0.79173022553784	2		498	821	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980314	201980314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326760178	NA	P-0015812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1617	164	783	2	ENST00000359651.3:c.50C>T	p.Ala17Val	p.A17V	ENST00000359651		17	gCg/gTg	1/8	0.328093601073983	6	FACETS	0.601	0.549	0.655	0.2	0.183	0.219	INDETERMINATE	1	TRUE	3	0.79173022553784	6		785	1781	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8284909	8284909	+	start_lost	Translation_Start_Site	SNP	T	T	A	novel	NA	P-0015812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	73	492	2	ENST00000335790.3:c.1A>T	p.Met1?	p.M1?	ENST00000335790	NM_002315.2	1	Atg/Ttg	1/4	0.79173022553784	3	FACETS	0.278	0.242	0.316	0.139	0.121	0.158	SUBCLONAL	1	TRUE	1	0.79173022553784	3		494	927	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028815	42028815	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	54	584	1	ENST00000219905.7:c.4357del	p.Tyr1453MetfsTer27	p.Y1453Mfs*27	ENST00000219905	NM_001164273.1	1451	ccT/cc	13/24	0.79173022553784	2	FACETS	0.162	0.137	0.188	0.081	0.068	0.094	SUBCLONAL	1	TRUE	0	0.79173022553784	2		585	844	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38504646	38504646	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	297	637	0	ENST00000254066.5:c.257A>C	p.Lys86Thr	p.K86T	ENST00000254066	NM_000964.3	86	aAg/aCg	3/9	0.79173022553784	3	FACETS	0.827	0.778	0.878	0.414	0.389	0.439	CLONAL	1	TRUE	1	0.79173022553784	3		637	1266	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207151	1207151	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	33	928	0	ENST00000326873.7:c.239T>G	p.Leu80Arg	p.L80R	ENST00000326873	NM_000455.4	80	cTc/cGc	1/10	0.79173022553784	1	FACETS	0.076	0.062	0.093	0.076	0.062	0.093	SUBCLONAL	1	TRUE	0	0.79173022553784	1		928	660	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141549439	141549439	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1330	75	269	0	ENST00000220592.5:c.2149T>C	p.Cys717Arg	p.C717R	ENST00000220592	NM_012154.3	717	Tgc/Cgc	16/19	0.79173022553784	8	FACETS	0.455	0.397	0.518	0.065	0.056	0.074	SUBCLONAL	1	TRUE	1	0.79173022553784	8		269	1405	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81904434	81904507	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTCACTTTTTTCATATTTACAGGAAATAGGAGCACACAAAGATGAGCTCAGCTTTGAACAGTTCCATCTCTTC	GGTCACTTTTTTCATATTTACAGGAAATAGGAGCACACAAAGATGAGCTCAGCTTTGAACAGTTCCATCTCTTC	TTATGATTTTCATGT	novel	NA	P-0015812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	44	388	0	ENST00000359376.3:c.565-23_615delinsTTATGATTTTCATGT		p.X189_splice	ENST00000359376	NM_002661.3	189		7/33	0.79173022553784	2	FACETS	0.344	0.29	0.404	0.172	0.145	0.202	SUBCLONAL	1	TRUE	0	0.79173022553784	2		388	323	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0015813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	13	636	1	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.363	0.257	0.492	0.363	0.257	0.492	SUBCLONAL	1	TRUE	1	0.15	2		637	478	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266611	198266611	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs755415626	NA	P-0015813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	30	467	0	ENST00000335508.6:c.2225G>A	p.Gly742Asp	p.G742D	ENST00000335508	NM_012433.2	742	gGt/gAt	16/25	1	2	FACETS	1	0.84	1	1	0.84	1	CLONAL	1	TRUE	1	0.15	2		467	382	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572186	64572186	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1254459338	NA	P-0015813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	29	328	2	ENST00000312049.6:c.1453C>T	p.Arg485Trp	p.R485W	ENST00000312049	NM_130799.2	485	Cgg/Tgg	10/10	1	2	FACETS	0.732	0.586	0.899	0.732	0.586	0.899	SUBCLONAL	1	TRUE	1	0.15	2		330	528	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775597	9775597	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0015813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	37	456	0	ENST00000377346.4:c.142-2A>G		p.X48_splice	ENST00000377346	NM_005026.3	48			1	2	FACETS	0.678	0.557	0.814	0.678	0.557	0.814	SUBCLONAL	1	TRUE	1	0.15	2		456	728	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943789	71943789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773085707	NA	P-0015813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	76	773	3	ENST00000298229.2:c.1832G>A	p.Arg611His	p.R611H	ENST00000298229	NM_001567.3	611	cGc/cAc	15/28	1	2	FACETS	0.918	0.803	1	0.918	0.803	1	CLONAL	1	TRUE	1	0.15	2		776	1104	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335546	73335546	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs35653839	NA	P-0015813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	29	474	0	ENST00000377767.4:c.2625del	p.Phe875LeufsTer22	p.F875Lfs*22	ENST00000377767	NM_014953.3	875	ttT/tt	19/21	1	2	FACETS	0.897	0.72	1	0.897	0.72	1	CLONAL	1	TRUE	1	0.15	2		474	431	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813674	50813674	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	103	955	2	ENST00000398568.2:c.1228G>A	p.Glu410Lys	p.E410K	ENST00000398568	NM_001042412.1	410	Gag/Aag	8/18	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.15	2		957	1179	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0015815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	259	605	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.307839783074826	1	FACETS	0.869	0.818	0.921	0.869	0.818	0.921	INDETERMINATE	1	TRUE	0	0.56876065757646	1		606	750	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610247	10610247	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	441	761	0	ENST00000171111.5:c.463G>T	p.Val155Phe	p.V155F	ENST00000171111	NM_203500.1	155	Gtc/Ttc	2/6	0.56876065757646	1	FACETS	0.948	0.905	0.99	0.948	0.905	0.99	CLONAL	1	TRUE	0	0.56876065757646	1		761	1171	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410650	32410650	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	291	503	0	ENST00000332351.3:c.1508A>T	p.His503Leu	p.H503L	ENST00000332351	NM_024426.4	503	cAc/cTc	10/10	1	2	FACETS	0.914	0.86	0.969	0.914	0.86	0.969	CLONAL	1	TRUE	1	0.56876065757646	2		503	1120	SUCCESS
EED	8726	MSKCC	GRCh37	11	85956294	85956294	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372992816	NA	P-0015815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	122	213	0	ENST00000263360.6:c.23C>T	p.Thr8Ile	p.T8I	ENST00000263360	NM_003797.3	8	aCt/aTt	1/12	1	2	FACETS	0.894	0.813	0.978	0.894	0.813	0.978	CLONAL	1	TRUE	1	0.56876065757646	2		213	480	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221975	1221975	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	380	660	0	ENST00000326873.7:c.890G>C	p.Arg297Thr	p.R297T	ENST00000326873	NM_000455.4	297	aGg/aCg	7/10	0.56876065757646	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.56876065757646	1		660	945	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25498374	25498374	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	260	377	0	ENST00000264709.3:c.487A>T	p.Met163Leu	p.M163L	ENST00000264709	NM_175629.2	163	Atg/Ttg	5/23	1	2	FACETS	0.995	0.934	1	0.995	0.934	1	CLONAL	1	TRUE	1	0.56876065757646	2		377	919	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981671	70981671	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1585	165	781	0	ENST00000276594.2:c.425del	p.Pro142ArgfsTer8	p.P142Rfs*8	ENST00000276594	NM_024504.3	142	cCg/cg	2/8	1	2	FACETS	0.332	0.303	0.362	0.332	0.303	0.362	SUBCLONAL	1	TRUE	1	0.56876065757646	2		781	1750	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0015816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	48	339	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.158437596180501	4	FACETS	1	0.951	1	1	0.951	1	INDETERMINATE	2	TRUE	2	0.49	4		339	120	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0015816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	291	641	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.311754356278821	16	FACETS	1	0.991	1			1	CLONAL	17	TRUE	NA	0.49	16		641	305	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425787	49425788	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0015816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	13	660	0	ENST00000301067.7:c.12700_12701del	p.Gln4235GlyfsTer98	p.Q4235Gfs*98	ENST00000301067	NM_003482.3	4234	AGt/t	39/54	0.311754356278821	11	FACETS	1	0.804	1			1	CLONAL	1	TRUE	NA	0.49	11		660	146	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938408	76938414	+	frameshift_variant	Frame_Shift_Del	DEL	TTTCCTT	TTTCCTT	-	novel	NA	P-0015816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	45	369	0	ENST00000373344.5:c.2334_2340del	p.Lys778AsnfsTer23	p.K778Nfs*23	ENST00000373344	NM_000489.3	778	aaAAGGAAA/aa	9/35	0.311754356278821	2	FACETS	1	0.964	1	1	0.98	1	CLONAL	3	TRUE	0	0.49	2		369	55	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0015817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	42	626	1	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	0.159076333517007	5	FACETS	0.923	0.78	1	0.923	0.78	1	CLONAL	3	FALSE	2	0.194958381244829	5		627	201	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0015818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1215	283	670	1	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.933	0.874	0.993	0.933	0.874	0.993	CLONAL	1	TRUE	1	0.405052172429612	2		671	1498	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	383	414	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.215235477954309	3	FACETS	0.823	0.781	0.866	0.823	0.781	0.866	INDETERMINATE	2	TRUE	1	0.405052172429612	3		414	1381	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107135	27107136	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	499	593	0	ENST00000324856.7:c.6747dup	p.Glu2250ArgfsTer28	p.E2250Rfs*28	ENST00000324856	NM_006015.4	2249	tca/tcAa	20/20	1	2	FACETS	0.993	0.952	1	1	0.997	1	CLONAL	2	TRUE	1	0.405052172429612	2		593	1241	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1962801	1962801	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772470710	NA	P-0015818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	226	516	2	ENST00000382891.5:c.3295G>A	p.Glu1099Lys	p.E1099K	ENST00000382891	NM_133335.3	1099	Gag/Aag	18/22	1	2	FACETS	0.952	0.886	1	0.952	0.886	1	CLONAL	1	TRUE	1	0.405052172429612	2		518	1172	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578530	7578539	+	protein_altering_variant	In_Frame_Del	DEL	ACATCTTGTT	ACATCTTGTT	G	novel	NA	P-0015818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1205	359	1101	0	ENST00000269305.4:c.391_400delinsC	p.Asn131_Phe134delinsLeu	p.N131_F134delinsL	ENST00000269305	NM_001126112.2	131	AACAAGATGTtt/Ctt	5/11	0.405052172429612	1	FACETS	0.904	0.855	0.954	0.904	0.855	0.954	CLONAL	1	TRUE	0	0.405052172429612	1		1101	1564	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481806	56481806	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	160	614	0	ENST00000267101.3:c.734C>T	p.Ala245Val	p.A245V	ENST00000267101	NM_001982.3	245	gCc/gTc	7/28	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.326949326347169	2		614	963	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	158	507	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.754	0.691	0.82	1	0.988	1	SUBCLONAL	2	TRUE	1	0.25	2		507	838	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0015820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	164	785	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.20035986953455	2	FACETS	0.819	0.753	0.888	0.819	0.753	0.888	CLONAL	2	TRUE	0	0.25	2		785	801	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	311	541	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.350774078024297	3	FACETS	0.986	0.931	1	0.986	0.931	1	CLONAL	2	TRUE	1	0.350774078024297	3		541	1057	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	499	583	0				ENST00000310581	NM_198253.2	-/1132			0.350774078024297	7	FACETS	1	0.989	1	1	0.989	1	CLONAL	5	TRUE	2	0.350774078024297	7		583	1000	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578530	7578530	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs267605077	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1588	276	972	0	ENST00000269305.4:c.400T>A	p.Phe134Ile	p.F134I	ENST00000269305	NM_001126112.2	134	Ttt/Att	5/11	0.350774078024297	3	FACETS	0.992	0.928	1	0.496	0.464	0.53	CLONAL	1	TRUE	1	0.350774078024297	3		972	1864	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	109	431	0	ENST00000304494.5:c.143C>T	p.Pro48Leu	p.P48L	ENST00000304494	NM_000077.4	48	cCg/cTg	1/3	0.335811024602497	3	FACETS	0.899	0.807	0.996			1	CLONAL	1	TRUE	NA	0.350774078024297	3		431	813	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412488	63412488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	187	817	0	ENST00000330258.3:c.679G>A	p.Glu227Lys	p.E227K	ENST00000330258	NM_152424.3	227	Gaa/Aaa	2/2	0.192364366685928	3	FACETS	0.997	0.919	1			1	INDETERMINATE	1	TRUE	NA	0.350774078024297	3		817	1257	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630695	187630695	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	360	587	0	ENST00000441802.2:c.287T>C	p.Leu96Pro	p.L96P	ENST00000441802	NM_005245.3	96	cTa/cCa	2/27	0.350075264996632	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.350774078024297	2		587	1007	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113155	209113155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371567806	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	120	401	0	ENST00000345146.2:c.352C>T	p.Pro118Ser	p.P118S	ENST00000345146	NM_005896.2	118	Ccc/Tcc	4/10	NA	2	FACETS	0.957	0.865	1			1	INDETERMINATE	1	TRUE	NA	0.350774078024297	2		401	715	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066550	94066550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	249	496	0	ENST00000369303.4:c.1209G>A	p.Met403Ile	p.M403I	ENST00000369303	NM_004440.3	403	atG/atA	5/17	0.350774078024297	2	FACETS	0.955	0.897	1	0.955	0.897	1	CLONAL	2	TRUE	0	0.350774078024297	2		496	743	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259165	16259165	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	332	624	0	ENST00000375759.3:c.6430C>T	p.Pro2144Ser	p.P2144S	ENST00000375759	NM_015001.2	2144	Cca/Tca	11/15	0.214338406140166	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.350774078024297	2		624	930	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363517	40363517	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	135	600	0	ENST00000397332.2:c.712C>T	p.His238Tyr	p.H238Y	ENST00000397332	NM_001033082.2	238	Cat/Tat	3/3	0.350774078024297	3	FACETS	0.872	0.792	0.958	0.436	0.396	0.479	CLONAL	1	TRUE	1	0.350774078024297	3		600	1037	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465361	120465361	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	178	556	0	ENST00000256646.2:c.4900C>T	p.Gln1634Ter	p.Q1634*	ENST00000256646	NM_024408.3	1634	Caa/Taa	27/34	0.350774078024297	3	FACETS	1	0.976	1	0.575	0.529	0.623	CLONAL	1	TRUE	1	0.350774078024297	3		556	1037	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510721	120510721	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	393	689	0	ENST00000256646.2:c.1243G>A	p.Asp415Asn	p.D415N	ENST00000256646	NM_024408.3	415	Gat/Aat	7/34	0.350774078024297	3	FACETS	0.976	0.927	1	0.976	0.927	1	CLONAL	2	TRUE	1	0.350774078024297	3		689	1349	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731157	162731157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1274236205	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	345	453	0	ENST00000367921.3:c.1012C>T	p.Leu338Phe	p.L338F	ENST00000367921	NM_006182.2	338	Ctc/Ttc	9/18	0.350774078024297	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.350774078024297	3		453	930	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248570	8248589	+	frameshift_variant	Frame_Shift_Del	DEL	TCCCGGGCCCGCATCACCAT	TCCCGGGCCCGCATCACCAT	-	novel	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1169	149	734	0	ENST00000335790.3:c.298_317del	p.Met100GlnfsTer37	p.M100Qfs*37	ENST00000335790	NM_002315.2	100	ATGGTGATGCGGGCCCGGGAc/c	3/4	0.350774078024297	3	FACETS	0.758	0.69	0.829	0.379	0.345	0.415	SUBCLONAL	1	TRUE	1	0.350774078024297	3		734	1318	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870930	12870930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	98	347	0	ENST00000228872.4:c.157G>A	p.Glu53Lys	p.E53K	ENST00000228872	NM_004064.3	53	Gaa/Aaa	1/3	1	2	FACETS	0.916	0.819	1	0.916	0.819	1	CLONAL	1	TRUE	1	0.350774078024297	2		347	610	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856527	111856527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1235385153	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	180	365	0	ENST00000341259.2:c.578C>T	p.Pro193Leu	p.P193L	ENST00000341259	NM_005475.2	193	cCc/cTc	2/8	0.350774078024297	3	FACETS	0.919	0.851	0.99	0.919	0.851	0.99	CLONAL	2	TRUE	1	0.350774078024297	3		365	656	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435375	121435376	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	349	769	0	ENST00000257555.6:c.1408_1409insG	p.Pro470ArgfsTer79	p.P470Rfs*79	ENST00000257555		470	ccc/cGcc	7/10	0.350774078024297	3	FACETS	0.953	0.902	1	0.953	0.902	1	CLONAL	2	TRUE	1	0.350774078024297	3		769	1227	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578371	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TA	novel	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	207	454	0	ENST00000269305.4:c.559_559+1delinsTA		p.X187_splice	ENST00000269305	NM_001126112.2	187		5/11	0.350774078024297	3	FACETS	0.915	0.852	0.98	0.915	0.852	0.98	CLONAL	2	TRUE	1	0.350774078024297	3		454	758	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122401	17122401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	290	621	0	ENST00000285071.4:c.994C>T	p.Leu332Phe	p.L332F	ENST00000285071	NM_144997.5	332	Ctc/Ttc	9/14	0.350774078024297	3	FACETS	0.904	0.851	0.959	0.904	0.851	0.959	CLONAL	2	TRUE	1	0.350774078024297	3		621	1075	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684020	29684020	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774781617	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	395	737	1	ENST00000356175.3:c.7718G>A	p.Arg2573His	p.R2573H	ENST00000356175	NM_000267.3	2573	cGt/cAt	52/57	0.350774078024297	3	FACETS	0.919	0.873	0.967	0.919	0.873	0.967	CLONAL	2	TRUE	1	0.350774078024297	3		738	1440	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40461481	40461481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	403	944	1	ENST00000345506.4:c.2201C>T	p.Pro734Leu	p.P734L	ENST00000345506	NM_003152.3	734	cCc/cTc	19/20	0.350774078024297	3	FACETS	0.848	0.805	0.892	0.848	0.805	0.892	CLONAL	2	TRUE	1	0.350774078024297	3		945	1592	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208058	5208058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139519201	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	223	400	0	ENST00000357368.4:c.5653G>A	p.Gly1885Ser	p.G1885S	ENST00000357368	NM_002850.3	1885	Ggc/Agc	37/38	0.350075264996632	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.350774078024297	2		400	627	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243965	5243965	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	167	589	0	ENST00000357368.4:c.1517C>T	p.Ser506Phe	p.S506F	ENST00000357368	NM_002850.3	506	tCc/tTc	11/38	0.350075264996632	2	FACETS	1	0.979	1	0.591	0.543	0.64	CLONAL	1	TRUE	0	0.350774078024297	2		589	806	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210696	36210697	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	160	707	4	ENST00000222270.7:c.447_448delinsTT	p.Arg150Ter	p.R150*	ENST00000222270	NM_014727.1	149	ccCCga/ccTTga	3/37	NA	2	FACETS	0.881	0.807	0.959			1	INDETERMINATE	1	TRUE	NA	0.350774078024297	2		711	1035	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443669	29443669	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	377	654	0	ENST00000389048.3:c.3548T>A	p.Ile1183Asn	p.I1183N	ENST00000389048	NM_004304.4	1183	aTt/aAt	23/29	0.350774078024297	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.350774078024297	3		654	1235	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022435	31022437	+	frameshift_variant	Frame_Shift_Del	DEL	CAT	CAT	TA	novel	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	125	197	0	ENST00000375687.4:c.1920_1922delinsTA	p.Ile641ThrfsTer62	p.I641Tfs*62	ENST00000375687	NM_015338.5	640	gcCATc/gcTAc	13/13	0.273594920324598	5	FACETS	0.923	0.843	1	0.923	0.843	1	CLONAL	3	TRUE	2	0.350774078024297	5		197	393	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156729	106156729	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	297	473	0	ENST00000380013.4:c.1630C>G	p.Arg544Gly	p.R544G	ENST00000380013	NM_001127208.2	544	Cga/Gga	3/11	0.350774078024297	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.350774078024297	3		473	914	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927054	131927071	+	inframe_deletion	In_Frame_Del	DEL	CATACAACAACACGTACC	CATACAACAACACGTACC	-	novel	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	205	535	0	ENST00000265335.6:c.1593_1610del	p.His531_Thr536del	p.H531_T536del	ENST00000265335		531	CATACAACAACACGTACC/-	10/25	0.350774078024297	3	FACETS	0.792	0.736	0.851	0.792	0.736	0.851	SUBCLONAL	2	TRUE	1	0.350774078024297	3		535	867	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554398	141554398	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368519674	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1393	209	766	0	ENST00000220592.5:c.1753C>T	p.Pro585Ser	p.P585S	ENST00000220592	NM_012154.3	585	Ccg/Tcg	14/19	0.320528731954101	4	FACETS	1	0.929	1	0.335	0.31	0.361	CLONAL	1	TRUE	1	0.350774078024297	4		766	1602	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974675	21974675	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	287	455	0	ENST00000304494.5:c.150+2T>A		p.X50_splice	ENST00000304494	NM_000077.4	50			0.335811024602497				0.984	1				CLONAL	2	TRUE	NA	0.350774078024297	3		455	863	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27173259	27173259	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1460	163	698	0	ENST00000380036.4:c.800G>C	p.Arg267Thr	p.R267T	ENST00000380036	NM_000459.3	267	aGg/aCg	6/23	0.301732260736345	4	FACETS	0.773	0.707	0.843			1	SUBCLONAL	1	TRUE	NA	0.350774078024297	4		698	1623	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396263	139396263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	255	811	1	ENST00000277541.6:c.5575G>A	p.Ala1859Thr	p.A1859T	ENST00000277541	NM_017617.3	1859	Gcc/Acc	30/34	0.350774078024297	3	FACETS	1	0.987	1	0.608	0.567	0.649	CLONAL	1	TRUE	1	0.350774078024297	3		812	1406	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139411723	139411723	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	351	751	0	ENST00000277541.6:c.1555+1G>A		p.X519_splice	ENST00000277541	NM_017617.3	519			0.350774078024297	3	FACETS	0.995	0.943	1	0.995	0.943	1	CLONAL	2	TRUE	1	0.350774078024297	3		751	1182	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413085	139413086	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	177	628	3	ENST00000277541.6:c.1056_1057delinsTT	p.Arg353Cys	p.R353C	ENST00000277541	NM_017617.3	352	gaCCgt/gaTTgt	6/34	0.350774078024297	3	FACETS	1	0.941	1	0.514	0.472	0.557	CLONAL	1	TRUE	1	0.350774078024297	3		631	1155	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413103	139413103	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs746187371	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	223	694	1	ENST00000277541.6:c.1039G>T	p.Gly347Cys	p.G347C	ENST00000277541	NM_017617.3	347	Ggc/Tgc	6/34	0.350774078024297	3	FACETS	1	0.978	1	0.564	0.523	0.605	CLONAL	1	TRUE	1	0.350774078024297	3		695	1326	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683677	162683678	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	T	novel	NA	P-0015821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	279	520	0	ENST00000366898.1:c.291_292delinsA	p.Glu98SerfsTer5	p.E98Sfs*5	ENST00000366898	NM_004562.2	97	cgGGag/cgAag	3/12	0.350774078024297	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.350774078024297	2		520	781	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923699	39923699	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs758883383	NA	P-0015822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	92	692	1	ENST00000378444.4:c.3392G>T	p.Arg1131Leu	p.R1131L	ENST00000378444	NM_001123385.1	1131	cGg/cTg	7/15	0.338693160574028	1	FACETS	0.936	0.838	1	0.936	0.838	1	CLONAL	1	TRUE	0	0.422629626753851	1		693	367	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	442	507	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.557162924284732	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.603317667066307	3		507	824	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	19	321	0	ENST00000288602.6:c.1742A>T	p.Asn581Ile	p.N581I	ENST00000288602	NM_004333.4	581	aAt/aTt	15/18	1	2	FACETS	0.209	0.158	0.269	0.209	0.158	0.269	SUBCLONAL	1	TRUE	1	0.603317667066307	2		321	301	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37092133	37092133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs864622445	NA	P-0015823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	42	371	1	ENST00000231790.2:c.2260G>A	p.Glu754Lys	p.E754K	ENST00000231790	NM_000249.3	754	Gag/Aag	19/19	1	2	FACETS	0.27	0.225	0.32	0.27	0.225	0.32	SUBCLONAL	1	TRUE	1	0.603317667066307	2		372	515	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521902	157521902	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	185	443	0	ENST00000346085.5:c.4174T>G	p.Tyr1392Asp	p.Y1392D	ENST00000346085	NM_020732.3	1392	Tac/Gac	18/20	1	2	FACETS	0.781	0.723	0.842	0.781	0.723	0.842	SUBCLONAL	1	TRUE	1	0.603317667066307	2		443	785	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987353	2987353	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	296	588	0	ENST00000396946.4:c.76G>T	p.Val26Leu	p.V26L	ENST00000396946	NM_032415.4	26	Gtg/Ttg	3/25	1	2	FACETS	0.93	0.878	0.984	0.93	0.878	0.984	CLONAL	1	TRUE	1	0.689429251270943	2		588	923	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32931931	32931934	+	frameshift_variant	Frame_Shift_Ins	INS	CAGA	CAGA	TCTGCATTTTTAACAGCAAAAAT	novel	NA	P-0015828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	90	380	0	ENST00000380152.3:c.7670_7673delinsTCTGCATTTTTAACAGCAAAAAT	p.Ala2557ValfsTer15	p.A2557Vfs*15	ENST00000380152		2557	gCAGAg/gTCTGCATTTTTAACAGCAAAAATg	16/27	0.687871093652044	1	FACETS	0.567	0.508	0.627	0.567	0.508	0.627	SUBCLONAL	1	TRUE	0	0.689429251270943	1		380	302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0015829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	210	812	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.283018573541018	2	FACETS	0.881	0.823	0.94	0.881	0.823	0.94	CLONAL	2	TRUE	0	0.384595737929159	2		812	620	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	176	507	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.268026645517362	4	FACETS	0.841	0.777	0.908	0.841	0.777	0.908	CLONAL	2	TRUE	2	0.384595737929159	4		507	753	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205102	123205102	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	102	725	0	ENST00000218089.9:c.2462T>G	p.Leu821Trp	p.L821W	ENST00000218089	NM_001042749.1	821	tTg/tGg	25/35	0.384595737929159	3	FACETS	0.913	0.817	1	0.456	0.408	0.507	CLONAL	1	TRUE	1	0.384595737929159	3		725	693	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119784	17119784	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	572	870	0	ENST00000285071.4:c.1210C>G	p.Pro404Ala	p.P404A	ENST00000285071	NM_144997.5	404	Cca/Gca	11/14	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	2	FALSE	NA	0.478105317326547	2		870	1168	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953050	2953050	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1170949848	NA	P-0015831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	242	973	1	ENST00000396946.4:c.2890A>G	p.Ser964Gly	p.S964G	ENST00000396946	NM_032415.4	964	Agc/Ggc	22/25	NA	2	FACETS	0.97	0.906	1			1	INDETERMINATE	1	FALSE	NA	0.478105317326547	2		974	1044	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509237	106509237	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1224	188	773	0	ENST00000359195.3:c.1231A>C	p.Asn411His	p.N411H	ENST00000359195	NM_002649.2	411	Aat/Cat	2/11	0.291053154743483	5	FACETS	0.956	0.881	1			1	CLONAL	1	FALSE	NA	0.478105317326547	5		773	1412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0015833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	784	531	1	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.770743878697931	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.770743878697931	3		532	903	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242685	16242685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2037	300	717	0	ENST00000375759.3:c.1306G>A	p.Ala436Thr	p.A436T	ENST00000375759	NM_015001.2	436	Gca/Aca	6/15	0.770743878697931	9	FACETS	1	0.989	1			1	CLONAL	1	TRUE	NA	0.770743878697931	9		717	2337	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660192	12660192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144637992	NA	P-0015833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	248	604	0	ENST00000251849.4:c.29C>T	p.Thr10Met	p.T10M	ENST00000251849	NM_002880.3	10	aCg/aTg	2/17	0.770743878697931	3	FACETS	1	0.968	1	0.525	0.492	0.559	CLONAL	1	TRUE	1	0.770743878697931	3		604	849	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0015835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	41	868	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.473	0.393	0.563	0.473	0.393	0.563	SUBCLONAL	1	TRUE	1	0.22	2		868	788	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0015835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	41	337	0	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.22	2		337	350	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41222997	41222997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	55	986	0	ENST00000357654.3:c.4934G>A	p.Arg1645Lys	p.R1645K	ENST00000357654	NM_007294.3	1645	aGg/aAg	15/23	1	2	FACETS	0.486	0.414	0.566	0.486	0.414	0.566	SUBCLONAL	1	TRUE	1	0.22	2		986	1028	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554545	63554545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	31	609	0	ENST00000307078.5:c.194C>T	p.Pro65Leu	p.P65L	ENST00000307078	NM_004655.3	65	cCg/cTg	2/11	1	2	FACETS	0.456	0.368	0.557	0.456	0.368	0.557	SUBCLONAL	1	TRUE	1	0.22	2		609	618	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848013	151848013	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	29	425	0	ENST00000262189.6:c.12746C>A	p.Thr4249Asn	p.T4249N	ENST00000262189	NM_170606.2	4249	aCt/aAt	51/59	1	2	FACETS	0.506	0.405	0.621	0.506	0.405	0.621	SUBCLONAL	1	TRUE	1	0.22	2		425	521	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692820	89692820	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587782641	NA	P-0015836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4	17	253	0	ENST00000371953.3:c.306del	p.Lys102AsnfsTer11	p.K102Nfs*11	ENST00000371953	NM_000314.4	102	Aaa/aa	5/9	1	2	FACETS	0.984	0.846	1	1	0.956	1	CLONAL	3	TRUE	1	0.548258452190534	2		253	21	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038878	12038878	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	34	590	0	ENST00000396373.4:c.1171T>G	p.Tyr391Asp	p.Y391D	ENST00000396373	NM_001987.4	391	Tat/Gat	7/8	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.548258452190534	2		590	101	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054498	42054498	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	13	656	1	ENST00000219905.7:c.7682T>A	p.Met2561Lys	p.M2561K	ENST00000219905	NM_001164273.1	2561	aTg/aAg	22/24	1	2	FACETS	0.539	0.39	0.715	0.539	0.39	0.715	SUBCLONAL	1	TRUE	1	0.548258452190534	2		657	88	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0015837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	320	668	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.955	1	1	0.996	1	CLONAL	2	TRUE	1	0.407245476155544	2		671	781	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0015837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	224	892	7	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	0.407245476155544	2		899	1020	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0015837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	32	552	0	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	0.273	0.221	0.332	0.273	0.221	0.332	SUBCLONAL	1	TRUE	1	0.407245476155544	2		552	576	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118713	115118713	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	46	669	0	ENST00000257566.3:c.628A>G	p.Thr210Ala	p.T210A	ENST00000257566	NM_016569.3	210	Acc/Gcc	2/8	1	2	FACETS	0.283	0.238	0.334	0.283	0.238	0.334	SUBCLONAL	1	TRUE	1	0.407245476155544	2		669	797	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913920	32913920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358766	NA	P-0015837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	133	738	1	ENST00000380152.3:c.5428G>A	p.Val1810Ile	p.V1810I	ENST00000380152		1810	Gtt/Att	11/27	1	2	FACETS	0.912	0.83	0.999	0.912	0.83	0.999	CLONAL	1	TRUE	1	0.407245476155544	2		739	716	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060989	38060990	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTGGGGG	novel	NA	P-0015837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	67	371	1	ENST00000250448.2:c.993_999dup	p.Thr334ProfsTer83	p.T334Pfs*83	ENST00000250448	NM_004496.3	333	-/CCCCCAG	2/2	1	2	FACETS	0.769	0.67	0.874	0.769	0.67	0.874	SUBCLONAL	1	TRUE	1	0.407245476155544	2		372	428	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829314	72829314	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	47	755	0	ENST00000268489.5:c.7267del	p.Thr2423GlnfsTer105	p.T2423Qfs*105	ENST00000268489	NM_006885.3	2423	Aca/ca	9/10	1	2	FACETS	0.277	0.232	0.326	0.277	0.232	0.326	SUBCLONAL	1	TRUE	1	0.407245476155544	2		755	834	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11032336	11032336	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	155	851	0	ENST00000327064.4:c.1730A>C	p.His577Pro	p.H577P	ENST00000327064	NM_199141.1	577	cAc/cCc	16/16	1	2	FACETS	0.925	0.847	1	0.925	0.847	1	CLONAL	1	TRUE	1	0.407245476155544	2		851	823	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273869	18273869	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	225	1014	0	ENST00000222254.8:c.1202T>G	p.Leu401Arg	p.L401R	ENST00000222254	NM_005027.3	401	cTc/cGc	10/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.407245476155544	2		1014	988	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37038181	37038181	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1064795693	NA	P-0015837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	84	467	0	ENST00000231790.2:c.188A>G	p.Asp63Gly	p.D63G	ENST00000231790	NM_000249.3	63	gAc/gGc	2/19	0.294918923621911	1	FACETS	0.853	0.759	0.953	0.853	0.759	0.953	CLONAL	1	TRUE	0	0.407245476155544	1		467	385	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356477	70356477	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	40	573	1	ENST00000374080.3:c.5372A>G	p.Lys1791Arg	p.K1791R	ENST00000374080		1791	aAa/aGa	37/45	1	1	FACETS	0.273	0.226	0.325	0.273	0.226	0.325	SUBCLONAL	1	TRUE	0	0.407245476155544	1		574	573	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692775	89692775	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554898053	NA	P-0015839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	114	440	0	ENST00000371953.3:c.259C>T	p.Gln87Ter	p.Q87*	ENST00000371953	NM_000314.4	87	Caa/Taa	5/9	0.37492576884575	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.37492576884575	1		440	488	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662481	227662481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	76	537	0	ENST00000305123.5:c.974G>A	p.Arg325His	p.R325H	ENST00000305123	NM_005544.2	325	cGt/cAt	1/2	1	2	FACETS	0.937	0.822	1	0.937	0.822	1	CLONAL	1	TRUE	1	0.283246613746336	2		537	573	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584583	52584583	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	128	842	2	ENST00000394830.3:c.4430del	p.Pro1477LeufsTer12	p.P1477Lfs*12	ENST00000394830	NM_018313.4	1477	cCt/ct	29/30	0.283246613746336	1	FACETS	0.886	0.802	0.974	0.886	0.802	0.974	CLONAL	1	TRUE	0	0.283246613746336	1		844	876	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998824	100998824	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	89	971	0	ENST00000325455.5:c.978C>G	p.Asp326Glu	p.D326E	ENST00000325455	NM_001202474.3	326	gaC/gaG	1/8	1	2	FACETS	0.627	0.555	0.705	0.627	0.555	0.705	SUBCLONAL	1	TRUE	1	0.283246613746336	2		971	1002	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110015	115110015	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	111	1172	1	ENST00000257566.3:c.1863C>A	p.Ser621Arg	p.S621R	ENST00000257566	NM_016569.3	621	agC/agA	8/8	1	2	FACETS	0.666	0.597	0.739	0.666	0.597	0.739	SUBCLONAL	1	TRUE	1	0.283246613746336	2		1173	1177	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556119	29556119	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	46	177	0	ENST00000356175.3:c.2486C>G	p.Ser829Cys	p.S829C	ENST00000356175	NM_000267.3	829	tCt/tGt	21/57	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.283246613746336	2		177	224	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376685	31376685	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	60	557	0	ENST00000328111.2:c.680A>G	p.Asp227Gly	p.D227G	ENST00000328111	NM_006892.3	227	gAc/gGc	7/23	1	2	FACETS	0.728	0.627	0.838	0.728	0.627	0.838	SUBCLONAL	1	TRUE	1	0.283246613746336	2		557	582	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99823067	99823067	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	83	530	0	ENST00000280892.6:c.145G>C	p.Ala49Pro	p.A49P	ENST00000280892	NM_001130678.1	49	Gct/Cct	2/7	1	2	FACETS	0.838	0.74	0.944	0.838	0.74	0.944	CLONAL	1	TRUE	1	0.283246613746336	2		530	699	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738750	145738750	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1343306408	NA	P-0015840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	162	1193	1	ENST00000428558.2:c.2314G>A	p.Val772Met	p.V772M	ENST00000428558	NM_004260.3	772	Gtg/Atg	15/22	1	2	FACETS	0.983	0.9	1	0.983	0.9	1	CLONAL	1	TRUE	1	0.283246613746336	2		1194	1164	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519966	NA	P-0015842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	241	866	0	ENST00000347630.2:c.397T>A	p.Phe133Ile	p.F133I	ENST00000347630	NM_001007230.1	133	Ttc/Atc	6/11	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	FALSE	1	0.515707723986886	2		866	933	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117799	108117799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202160435	NA	P-0015843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	79	533	2	ENST00000278616.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000278616	NM_000051.3	337	cGt/cAt	8/63	0.212158971164005	2	FACETS	0.948	0.834	1	0.474	0.417	0.535	CLONAL	1	TRUE	0	0.260540930770744	2		535	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0015843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	346	1081	1	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.212158971164005	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.260540930770744	2		1082	1208	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691039	NA	P-0015845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	271	554	0	ENST00000269305.4:c.919+1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.100761671405265	3	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.270605309660138	3		554	918	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761170	59761170	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587781666	NA	P-0015845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	60	622	0	ENST00000259008.2:c.3237T>G	p.Ile1079Met	p.I1079M	ENST00000259008	NM_032043.2	1079	atT/atG	20/20	0.270605309660138	6	FACETS	0.8	0.688	0.923	0.267	0.229	0.308	CLONAL	1	TRUE	3	0.270605309660138	6		622	854	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279450	1279450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs973201915	NA	P-0015845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	150	852	1	ENST00000310581.5:c.2086C>T	p.Arg696Cys	p.R696C	ENST00000310581	NM_198253.2	696	Cgt/Tgt	5/16	0.257911703110934	3	FACETS	0.988	0.901	1	0.494	0.45	0.54	CLONAL	1	TRUE	1	0.270605309660138	3		853	1274	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872193	76872200	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	TTTCCTCT	TTTCCTCT	-	novel	NA	P-0015845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	63	230	0	ENST00000373344.5:c.5449-2_5454del		p.X1817_splice	ENST00000373344	NM_000489.3	1817		22/35	0.260098135643596	2	FACETS	1	0.959	1			1	CLONAL	2	TRUE	NA	0.270605309660138	2		230	191	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99180083	99180083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777486763	NA	P-0015847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	105	428	2	ENST00000074304.5:c.2026G>A	p.Val676Met	p.V676M	ENST00000074304	NM_001134224.1	676	Gtg/Atg	19/26	0.311265396969631	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.311265396969631	1		430	542	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31466323	31466323	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	145	679	0	ENST00000344624.3:c.2432A>G	p.Lys811Arg	p.K811R	ENST00000344624		811	aAa/aGa	16/33	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.311265396969631	2		679	905	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0015848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	18	414	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.49	0.367	0.635	0.49	0.367	0.635	SUBCLONAL	1	TRUE	1	0.15	2		414	490	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950588	38950588	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0015848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	30	569	0	ENST00000357387.3:c.3362C>G	p.Ser1121Ter	p.S1121*	ENST00000357387	NM_152756.3	1121	tCa/tGa	31/38	1	2	FACETS	0.709	0.57	0.868	0.709	0.57	0.868	SUBCLONAL	1	TRUE	1	0.15	2		569	564	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170926	56170926	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	26	334	0	ENST00000399503.3:c.1755del	p.Arg585SerfsTer71	p.R585Sfs*71	ENST00000399503	NM_005921.1	585	aGg/ag	10/20	1	2	FACETS	0.7	0.553	0.869	0.7	0.553	0.869	SUBCLONAL	1	TRUE	1	0.15	2		334	495	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020240	123020240	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	65	654	0	ENST00000355640.3:c.728C>G	p.Ala243Gly	p.A243G	ENST00000355640		243	gCt/gGt	2/7	0.3	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.15	1		654	618	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0015850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	23	552	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	1	2	FACETS	0.115	0.089	0.146	0.115	0.089	0.146	SUBCLONAL	1	TRUE	1	0.595768116841446	2		552	670	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0015851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	170	704	1	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	0.45	2		705	755	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0015851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	192	399	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.45	2		399	837	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0015851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	42	549	0	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	1	2	FACETS	0.181	0.15	0.215	0.181	0.15	0.215	SUBCLONAL	1	TRUE	1	0.45	2		549	1033	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0015851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	151	398	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.9	0.824	0.979	0.9	0.824	0.979	CLONAL	1	TRUE	1	0.45	2		398	746	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0015851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	144	356	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.893	0.816	0.973	0.893	0.816	0.973	CLONAL	1	TRUE	1	0.45	2		356	717	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0015851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	135	496	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.995	0.908	1	0.995	0.908	1	CLONAL	1	TRUE	1	0.45	2		496	603	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0015851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	126	391	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.951	0.864	1	0.951	0.864	1	CLONAL	1	TRUE	1	0.45	2		391	589	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0015851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	98	285	0	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	1	2	FACETS	0.953	0.855	1	0.953	0.855	1	CLONAL	1	TRUE	1	0.45	2		285	457	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851104	63851104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148232588	NA	P-0015851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	217	498	0	ENST00000279873.7:c.1882G>A	p.Val628Met	p.V628M	ENST00000279873	NM_032199.2	628	Gtg/Atg	10/10	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.45	2		498	964	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	243	777	0	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.897	0.837	0.959	0.897	0.837	0.959	CLONAL	1	TRUE	1	0.45	2		777	1204	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226573330	226573330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781235145	NA	P-0015851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	176	474	1	ENST00000366794.5:c.886G>A	p.Glu296Lys	p.E296K	ENST00000366794	NM_001618.3	296	Gag/Aag	7/23	1	2	FACETS	0.915	0.843	0.989	0.915	0.843	0.989	CLONAL	1	TRUE	1	0.45	2		475	855	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563021	21563021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	252	696	2	ENST00000382592.4:c.898G>A	p.Ala300Thr	p.A300T	ENST00000382592	NM_014572.2	300	Gcc/Acc	4/8	1	2	FACETS	0.974	0.911	1	0.974	0.911	1	CLONAL	1	TRUE	1	0.45	2		698	1150	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119050	70119050	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	203	496	0	ENST00000245479.2:c.622C>T	p.Gln208Ter	p.Q208*	ENST00000245479	NM_000346.3	208	Cag/Tag	2/3	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.45	2		496	760	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11210203	11210203	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	438	492	0	ENST00000361445.4:c.4550C>T	p.Ala1517Val	p.A1517V	ENST00000361445	NM_004958.3	1517	gCt/gTt	31/58	0.3	2	FACETS	0.999	0.957	1			1	CLONAL	2	TRUE	NA	0.45	2		492	974	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139625	202139626	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	140	322	0	ENST00000358485.4:c.790dup	p.Val264GlyfsTer13	p.V264Gfs*13	ENST00000358485	NM_001080125.1	262	-/G	6/9	1	2	FACETS	0.949	0.866	1	0.949	0.866	1	CLONAL	1	TRUE	1	0.45	2		322	656	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063359	67063359	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	194	457	1	ENST00000412916.2:c.54del	p.Phe18LeufsTer4	p.F18Lfs*4	ENST00000412916		17	Ttt/tt	1/6	1	2	FACETS	0.997	0.923	1	0.997	0.923	1	CLONAL	1	TRUE	1	0.45	2		458	865	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654856	29654856	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1049849034	NA	P-0015851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	75	206	0	ENST00000356175.3:c.5545C>T	p.Arg1849Trp	p.R1849W	ENST00000356175	NM_000267.3	1849	Cgg/Tgg	37/57	1	2	FACETS	0.868	0.765	0.978	0.868	0.765	0.978	CLONAL	1	TRUE	1	0.45	2		206	384	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052633	42052633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	221	466	1	ENST00000219905.7:c.7304G>A	p.Arg2435Gln	p.R2435Q	ENST00000219905	NM_001164273.1	2435	cGg/cAg	20/24	1	2	FACETS	0.999	0.93	1	0.999	0.93	1	CLONAL	1	TRUE	1	0.45	2		467	983	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925318	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0015851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	76	402	0	ENST00000543371.1:c.1402_1403del	p.Lys468ValfsTer8	p.K468Vfs*8	ENST00000543371	NM_001198531.1	465	agAAaa/agaa	14/14	1	2	FACETS	0.485	0.425	0.549	0.485	0.425	0.549	SUBCLONAL	1	TRUE	1	0.45	2		402	697	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0015851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	294	739	1	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	0.45	2		740	1299	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843515	156843515	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368769883	NA	P-0015851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	232	549	0	ENST00000524377.1:c.941G>A	p.Arg314His	p.R314H	ENST00000524377	NM_002529.3	314	cGc/cAc	8/17	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.45	2		549	950	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100762	8100762	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766641914	NA	P-0015851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	174	656	2	ENST00000346208.3:c.736G>A	p.Gly246Ser	p.G246S	ENST00000346208		246	Ggc/Agc	3/6	1	2	FACETS	0.885	0.815	0.957	0.885	0.815	0.957	CLONAL	1	TRUE	1	0.45	2		658	874	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371775	118371775	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782301554	NA	P-0015851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	152	380	0	ENST00000534358.1:c.6232C>T	p.Arg2078Cys	p.R2078C	ENST00000534358	NM_005933.3	2078	Cgt/Tgt	25/36	1	2	FACETS	0.894	0.818	0.972	0.894	0.818	0.972	CLONAL	1	TRUE	1	0.45	2		380	756	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2224304	2224304	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	288	692	0	ENST00000326181.6:c.1316A>G	p.Asp439Gly	p.D439G	ENST00000326181	NM_032271.2	439	gAt/gGt	14/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.45	2		692	1205	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214675	5214675	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1274728310	NA	P-0015851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	293	684	0	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	0.45	2		684	1191	SUCCESS
AXL	558	MSKCC	GRCh37	19	41737096	41737096	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1327166268	NA	P-0015851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	64	688	1	ENST00000301178.4:c.676C>A	p.Gln226Lys	p.Q226K	ENST00000301178	NM_021913.4	226	Cag/Aag	6/20	1	2	FACETS	0.234	0.202	0.27	0.234	0.202	0.27	SUBCLONAL	1	TRUE	1	0.45	2		689	1214	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690273	47690273	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	140	448	0	ENST00000233146.2:c.1490T>C	p.Ile497Thr	p.I497T	ENST00000233146	NM_000251.2	497	aTa/aCa	9/16	1	2	FACETS	0.766	0.698	0.838	0.766	0.698	0.838	SUBCLONAL	1	TRUE	1	0.45	2		448	812	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62320897	62320897	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	271	794	0	ENST00000360203.5:c.1921G>A	p.Val641Met	p.V641M	ENST00000360203	NM_001283009.1	641	Gtg/Atg	23/35	1	2	FACETS	0.92	0.862	0.98	0.92	0.862	0.98	CLONAL	1	TRUE	1	0.45	2		794	1309	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090393	37090393	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs267607883	NA	P-0015851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	158	377	0	ENST00000231790.2:c.1990-2A>G		p.X664_splice	ENST00000231790	NM_000249.3	664			1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.45	2		377	679	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607255	189607255	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	70	660	0	ENST00000264731.3:c.1634C>T	p.Thr545Ile	p.T545I	ENST00000264731	NM_003722.4	545	aCa/aTa	12/14	1	2	FACETS	0.304	0.264	0.348	0.304	0.264	0.348	SUBCLONAL	1	TRUE	1	0.45	2		660	1023	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519339	137519340	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	66	242	0	ENST00000367739.4:c.1298dup	p.Asn433LysfsTer2	p.N433Kfs*2	ENST00000367739	NM_000416.2	433	aat/aaAt	7/7	1	2	FACETS	0.889	0.777	1	0.889	0.777	1	CLONAL	1	TRUE	1	0.45	2		242	330	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240767	55240767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770193776	NA	P-0015851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	247	701	0	ENST00000275493.2:c.2011C>T	p.Arg671Cys	p.R671C	ENST00000275493	NM_005228.3	671	Cgc/Tgc	17/28	1	2	FACETS	0.986	0.922	1	0.986	0.922	1	CLONAL	1	TRUE	1	0.45	2		701	1113	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058536	69058536	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61753703	NA	P-0015851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	183	604	0	ENST00000288368.4:c.4180C>T	p.Arg1394Trp	p.R1394W	ENST00000288368	NM_024870.2	1394	Cgg/Tgg	34/40	1	2	FACETS	0.96	0.887	1	0.96	0.887	1	CLONAL	1	TRUE	1	0.45	2		604	847	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400044	139400044	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	269	714	0	ENST00000277541.6:c.4304G>T	p.Gly1435Val	p.G1435V	ENST00000277541	NM_017617.3	1435	gGg/gTg	25/34	1	2	FACETS	0.969	0.908	1	0.969	0.908	1	CLONAL	1	TRUE	1	0.45	2		714	1234	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652397	48652397	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	239	392	1	ENST00000376670.3:c.1073del	p.Pro358GlnfsTer74	p.P358Qfs*74	ENST00000376670	NM_002049.3	356	ggC/gg	6/6	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.45	1		393	567	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934603	9934603	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747838255	NA	P-0015852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	50	474	2	ENST00000330684.3:c.1552C>T	p.Arg518Cys	p.R518C	ENST00000330684	NM_001134407.1	518	Cgt/Tgt	7/13	1	2	FACETS	0.18	0.152	0.211	0.18	0.152	0.211	SUBCLONAL	1	TRUE	1	0.687665396132125	2		476	809	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175413	108175413	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	160	723	0	ENST00000278616.4:c.5508del	p.Cys1838ValfsTer8	p.C1838Vfs*8	ENST00000278616	NM_000051.3	1836	gaC/ga	37/63	0.687665396132125	1	FACETS	0.951	0.888	1	0.951	0.888	1	CLONAL	1	TRUE	0	0.687665396132125	1		723	321	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175413	108175413	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015852-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	131	723	0	ENST00000278616.4:c.5508del	p.Cys1838ValfsTer8	p.C1838Vfs*8	ENST00000278616	NM_000051.3	1836	gaC/ga	37/63	0.369545246463271	1	FACETS	0.9	0.819	0.985	0.9	0.819	0.985	CLONAL	1	TRUE	0	0.369545246463271	1		723	642	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	150	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.938	0.865	1	0.938	0.865	1	CLONAL	1	TRUE	1	0.709096372402643	2		248	451	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913403	NA	P-0015853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	203	251	0	ENST00000349496.5:c.110C>A	p.Ser37Tyr	p.S37Y	ENST00000349496	NM_001904.3	37	tCt/tAt	3/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.709096372402643	2		251	551	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439874	52439874	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	245	935	0	ENST00000460680.1:c.838C>T	p.Gln280Ter	p.Q280*	ENST00000460680	NM_004656.3	280	Cag/Tag	10/17	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.709096372402643	2		935	690	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023253	27023268	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCCGGCGGCGGCGG	CGCCCGGCGGCGGCGG	-	novel	NA	P-0015853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	308	406	0	ENST00000324856.7:c.359_374del	p.Pro120LeufsTer107	p.P120Lfs*107	ENST00000324856	NM_006015.4	120	cCGCCCGGCGGCGGCGGt/ct	1/20	0.679211819443557	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.709096372402643	2		406	407	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165632	118165632	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	170	621	0	ENST00000369448.3:c.142C>A	p.Leu48Met	p.L48M	ENST00000369448	NM_017709.3	48	Ctg/Atg	2/2	0.607743525987246	3	FACETS	0.924	0.852	0.998	0.462	0.426	0.499	CLONAL	1	TRUE	1	0.709096372402643	3		621	703	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651118	206651118	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	561	1171	1	ENST00000367120.3:c.728C>A	p.Ala243Asp	p.A243D	ENST00000367120	NM_014002.3	243	gCt/gAt	8/22	0.607743525987246	3	FACETS	0.959	0.924	0.993	0.959	0.924	0.993	CLONAL	2	TRUE	1	0.709096372402643	3		1172	1118	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914689	32914689	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	208	845	0	ENST00000380152.3:c.6197T>G	p.Val2066Gly	p.V2066G	ENST00000380152		2066	gTt/gGt	11/27	1	2	FACETS	0.921	0.86	0.984	0.921	0.86	0.984	CLONAL	1	TRUE	1	0.709096372402643	2		845	637	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412218	139412218	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	279	1077	1	ENST00000277541.6:c.1427G>T	p.Cys476Phe	p.C476F	ENST00000277541	NM_017617.3	476	tGc/tTc	8/34	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.709096372402643	2		1078	775	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0015855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	280	583	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.802113591273894	2		583	640	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0015855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	959	657	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.802113591273894	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.802113591273894	2		657	1186	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39074439	39074439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1298143494	NA	P-0015855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	369	414	0	ENST00000357387.3:c.41G>A	p.Arg14Gln	p.R14Q	ENST00000357387	NM_152756.3	14	cGa/cAa	1/38	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.802113591273894	2		414	858	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227888	55227888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1226827460	NA	P-0015855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	309	344	1	ENST00000275493.2:c.1355C>T	p.Ser452Phe	p.S452F	ENST00000275493	NM_005228.3	452	tCc/tTc	12/28	1	2	FACETS	0.989	0.937	1	0.989	0.937	1	CLONAL	1	TRUE	1	0.802113591273894	2		345	779	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692914	89692915	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AATG	novel	NA	P-0015855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	299	458	0	ENST00000371953.3:c.400_403dup	p.Ile135AsnfsTer46	p.I135Nfs*46	ENST00000371953	NM_000314.4	133	gta/gtAATGa	5/9	0.802113591273894	1	FACETS	0.849	0.81	0.887	0.849	0.81	0.887	CLONAL	1	TRUE	0	0.802113591273894	1		458	526	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218970	133218970	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	533	695	0	ENST00000320574.5:c.4966C>T	p.Pro1656Ser	p.P1656S	ENST00000320574	NM_006231.2	1656	Ccc/Tcc	38/49	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.802113591273894	2		695	1284	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273289	18273289	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	326	416	0	ENST00000222254.8:c.1082T>A	p.Ile361Asn	p.I361N	ENST00000222254	NM_005027.3	361	aTc/aAc	9/16	1	2	FACETS	0.991	0.941	1	0.991	0.941	1	CLONAL	1	TRUE	1	0.802113591273894	2		416	820	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274712	198274712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	298	304	0	ENST00000335508.6:c.686C>T	p.Ser229Phe	p.S229F	ENST00000335508	NM_012433.2	229	tCc/tTc	7/25	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.802113591273894	2		304	739	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652797	212652798	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	301	489	0	ENST00000342788.4:c.508_509delinsTT	p.Pro170Leu	p.P170L	ENST00000342788	NM_005235.2	170	CCa/TTa	4/28	1	2	FACETS	0.737	0.695	0.78	0.737	0.695	0.78	SUBCLONAL	1	TRUE	1	0.802113591273894	2		489	1018	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543904	41543905	+	missense_variant	Missense_Mutation	DNP	CT	CT	TA	novel	NA	P-0015855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1157	437	551	0	ENST00000263253.7:c.2195_2196delinsTA	p.Pro732Leu	p.P732L	ENST00000263253	NM_001429.3	732	cCT/cTA	12/31	0.739114236202638	3	FACETS	0.958	0.912	1			1	CLONAL	1	TRUE	NA	0.802113591273894	3		551	1594	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39002707	39002707	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	358	445	0	ENST00000357387.3:c.322C>T	p.Arg108Ter	p.R108*	ENST00000357387	NM_152756.3	108	Cga/Tga	5/38	1	2	FACETS	0.927	0.881	0.973	0.927	0.881	0.973	CLONAL	1	TRUE	1	0.802113591273894	2		445	963	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528050	157528051	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	305	425	3	ENST00000346085.5:c.5775_5776delinsTT	p.Arg1926Ter	p.R1926*	ENST00000346085	NM_020732.3	1925	agCCga/agTTga	20/20	1	2	FACETS	0.91	0.861	0.959	0.91	0.861	0.959	CLONAL	1	TRUE	1	0.802113591273894	2		428	836	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534542	140534542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	378	404	0	ENST00000288602.6:c.371C>T	p.Ser124Phe	p.S124F	ENST00000288602	NM_004333.4	124	tCc/tTc	3/18	1	2	FACETS	0.971	0.924	1	0.971	0.924	1	CLONAL	1	TRUE	1	0.802113591273894	2		404	971	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	36	414	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.622	0.51	0.748	0.622	0.51	0.748	SUBCLONAL	1	TRUE	1	0.18	2		414	643	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974734	21974753	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCGCCCGCACCTCCTCTA	CAGCGCCCGCACCTCCTCTA	-	novel	NA	P-0015857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	31	320	0	ENST00000304494.5:c.74_93del	p.Val25AlafsTer12	p.V25Afs*12	ENST00000304494	NM_000077.4	25	gTAGAGGAGGTGCGGGCGCTG/g	1/3	1	2	FACETS	0.706	0.57	0.86	0.706	0.57	0.86	SUBCLONAL	1	TRUE	1	0.18	2		320	488	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916644	178916665	+	protein_altering_variant	In_Frame_Del	DEL	TGGGGCATCCACTTGATGCCCC	TGGGGCATCCACTTGATGCCCC	GGGG	novel	NA	P-0015861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	58	346	2	ENST00000263967.3:c.31_52delinsGGGG	p.Trp11_Pro18delinsGlyAla	p.W11_P18delinsGA	ENST00000263967	NM_006218.2	11	TGGGGCATCCACTTGATGCCCCca/GGGGca	2/21	1	2	FACETS	0.952	0.824	1	0.952	0.824	1	CLONAL	1	TRUE	1	0.420192290680769	2		348	290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0015862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	341	513	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.390754829721192	3	FACETS	0.927	0.883	0.972	0.927	0.883	0.972	CLONAL	3	TRUE	0	0.390754829721192	3		513	750	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220679	1220679	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	288	729	0	ENST00000326873.7:c.698del	p.Gly233AlafsTer54	p.G233Afs*54	ENST00000326873	NM_000455.4	233	Ggc/gc	5/10	0.390754829721192	2	FACETS	0.991	0.937	1	0.991	0.937	1	CLONAL	2	TRUE	0	0.390754829721192	2		729	744	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602292	10602292	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	317	642	0	ENST00000171111.5:c.1286G>T	p.Gly429Val	p.G429V	ENST00000171111	NM_203500.1	429	gGc/gTc	3/6	0.390754829721192	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.390754829721192	2		642	717	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17949085	17949085	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	248	661	0	ENST00000458235.1:c.1556A>G	p.Asp519Gly	p.D519G	ENST00000458235	NM_000215.3	519	gAc/gGc	11/24	0.390754829721192	2	FACETS	0.925	0.87	0.981	0.925	0.87	0.981	CLONAL	2	TRUE	0	0.390754829721192	2		661	686	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138589	55138589	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	136	563	0	ENST00000257290.5:c.1266T>A	p.Asp422Glu	p.D422E	ENST00000257290	NM_006206.4	422	gaT/gaA	9/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.390754829721192	2		563	596	SUCCESS
APC	324	MSKCC	GRCh37	5	112174736	112174736	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	119	325	0	ENST00000257430.4:c.3445G>T	p.Glu1149Ter	p.E1149*	ENST00000257430	NM_000038.5	1149	Gaa/Taa	16/16	0.390754829721192	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.390754829721192	2		325	277	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864478	162864478	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	127	467	0	ENST00000366898.1:c.35G>C	p.Gly12Ala	p.G12A	ENST00000366898	NM_004562.2	12	gGt/gCt	2/12	0.182370923183439	3	FACETS	1	0.981	1	0.657	0.597	0.72	INDETERMINATE	1	TRUE	1	0.390754829721192	3		467	591	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808594	1808594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	564	741	0	ENST00000260795.2:c.2207C>T	p.Ser736Phe	p.S736F	ENST00000260795		736	tCc/tTc	16/17	0.530266781900322	6	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.698887585555795	6		741	1595	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35857082	35857082	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs868017120	NA	P-0015863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	151	219	0	ENST00000303115.3:c.3G>A	p.Met1?	p.M1?	ENST00000303115	NM_002185.3	1	atG/atA	1/8	0.561754234235883	5	FACETS	0.95	0.875	1	0.633	0.583	0.684	CLONAL	2	TRUE	2	0.698887585555795	5		219	466	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35857138	35857138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	116	212	0	ENST00000303115.3:c.59G>A	p.Gly20Glu	p.G20E	ENST00000303115	NM_002185.3	20	gGa/gAa	1/8	0.561754234235883	5	FACETS	0.821	0.746	0.899	0.547	0.497	0.6	CLONAL	2	TRUE	2	0.698887585555795	5		212	414	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652063	36652064	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0015863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	1055	658	0	ENST00000244741.5:c.186dup	p.Phe63LeufsTer26	p.F63Lfs*26	ENST00000244741	NM_000389.4	62	gac/gaCc	2/3	0.698887585555795	4	FACETS	0.983	0.966	0.998	0.983	0.966	0.998	CLONAL	4	TRUE	0	0.698887585555795	4		658	1305	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0015864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	220	655	2	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.414126404049247	2		657	1028	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061208	38061208	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	117	469	1	ENST00000250448.2:c.781C>A	p.Arg261Ser	p.R261S	ENST00000250448	NM_004496.3	261	Cgc/Agc	2/2	1	2	FACETS	0.937	0.847	1	0.937	0.847	1	CLONAL	1	TRUE	1	0.414126404049247	2		470	603	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849604	68849604	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	199	675	0	ENST00000261769.5:c.1507C>T	p.Gln503Ter	p.Q503*	ENST00000261769	NM_004360.3	503	Cag/Tag	10/16	0.414126404049247	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.414126404049247	1		675	746	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181878	56181878	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	51	353	0	ENST00000399503.3:c.4102A>G	p.Arg1368Gly	p.R1368G	ENST00000399503	NM_005921.1	1368	Aga/Gga	17/20	0.373889778287895	1	FACETS	0.371	0.315	0.432	0.371	0.315	0.432	SUBCLONAL	1	TRUE	0	0.414126404049247	1		353	527	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049691	16049691	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	169	605	0	ENST00000268712.3:c.1081C>T	p.Arg361Ter	p.R361*	ENST00000268712	NM_006311.3	361	Cga/Tga	10/46	0.341177765418203	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.341177765418203	1		605	670	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049691	16049691	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015865-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	56	605	0	ENST00000268712.3:c.1081C>T	p.Arg361Ter	p.R361*	ENST00000268712	NM_006311.3	361	Cga/Tga	10/46	0.220421569309173	1	FACETS	0.543	0.464	0.63	0.543	0.464	0.63	SUBCLONAL	1	FALSE	0	0.220421569309173	1		605	833	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933342	39933342	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015865-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	69	865	0	ENST00000378444.4:c.1257A>T	p.Lys419Asn	p.K419N	ENST00000378444	NM_001123385.1	419	aaA/aaT	4/15	0.220421569309173	1	FACETS	0.597	0.519	0.682	0.597	0.519	0.682	SUBCLONAL	1	FALSE	0	0.220421569309173	1		865	933	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0015867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	193	835	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.18536000227682	3	FACETS	1	0.989	1	0.683	0.634	0.733	INDETERMINATE	1	TRUE	1	0.51332722528123	3		836	692	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	385	507	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.36135646574021	5	FACETS	0.977	0.932	1			1	CLONAL	3	TRUE	NA	0.51332722528123	5		507	906	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0015867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	209	574	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.51332722528123	3	FACETS	0.832	0.777	0.888	0.832	0.777	0.888	CLONAL	2	TRUE	1	0.51332722528123	3		574	615	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577586	7577586	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587781589	NA	P-0015867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	172	603	0	ENST00000269305.4:c.695T>G	p.Ile232Ser	p.I232S	ENST00000269305	NM_001126112.2	232	aTc/aGc	7/11	0.18536000227682	3	FACETS	1	0.983	1	0.616	0.569	0.666	INDETERMINATE	1	TRUE	1	0.51332722528123	3		603	683	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873401	151873401	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1003155450	NA	P-0015867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	179	307	0	ENST00000262189.6:c.9137T>G	p.Leu3046Arg	p.L3046R	ENST00000262189	NM_170606.2	3046	cTt/cGt	38/59	0.51332722528123	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.51332722528123	2		307	343	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	23	860	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.268	0.207	0.339	0.268	0.207	0.339	SUBCLONAL	1	TRUE	1	0.17	2		861	1010	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716212	52716212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555791268	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	42	385	0	ENST00000322088.6:c.656C>T	p.Ser219Leu	p.S219L	ENST00000322088	NM_014225.5	219	tCg/tTg	6/15	1	2	FACETS	0.892	0.744	1	0.892	0.744	1	CLONAL	1	TRUE	1	0.17	2		385	554	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922301	178922301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	35	420	0	ENST00000263967.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000263967	NM_006218.2	357	cGa/cAa	6/21	1	2	FACETS	0.82	0.672	0.988	0.82	0.672	0.988	CLONAL	1	TRUE	1	0.17	2		420	502	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	38	394	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.17	2		394	420	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	31	373	0	ENST00000263967.3:c.333G>T	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaT	2/21	1	2	FACETS	0.862	0.697	1	0.862	0.697	1	CLONAL	1	TRUE	1	0.17	2		373	423	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589168	67589168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	16	283	0	ENST00000274335.5:c.1156C>T	p.Arg386Ter	p.R386*	ENST00000274335		386	Cga/Tga	9/15	1	2	FACETS	0.738	0.546	0.968	0.738	0.546	0.968	CLONAL	1	TRUE	1	0.17	2		283	255	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259477	89259477	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200567888	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	33	392	0	ENST00000336596.2:c.621G>T	p.Lys207Asn	p.K207N	ENST00000336596	NM_005233.5	207	aaG/aaT	3/17	1	2	FACETS	0.805	0.655	0.975	0.805	0.655	0.975	CLONAL	1	TRUE	1	0.17	2		392	482	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126730	5126730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1437629509	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	62	405	0	ENST00000381652.3:c.3338G>A	p.Arg1113His	p.R1113H	ENST00000381652	NM_004972.3	1113	cGc/cAc	25/25	1	2	FACETS	0.844	0.731	0.966	1	0.975	1	CLONAL	2	TRUE	1	0.17	2		405	432	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891035	112891035	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs755619262	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	21	322	0	ENST00000351677.2:c.369G>T	p.Glu123Asp	p.E123D	ENST00000351677	NM_002834.3	123	gaG/gaT	4/16	1	2	FACETS	0.677	0.521	0.859	0.677	0.521	0.859	SUBCLONAL	1	TRUE	1	0.17	2		322	365	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089730	27089730	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	42	587	0	ENST00000324856.7:c.2686G>T	p.Glu896Ter	p.E896*	ENST00000324856	NM_006015.4	896	Gaa/Taa	8/20	1	2	FACETS	0.629	0.524	0.747	0.629	0.524	0.747	SUBCLONAL	1	TRUE	1	0.17	2		587	785	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413662	138413662	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1331108652	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	53	474	0	ENST00000289153.2:c.1858C>T	p.Arg620Ter	p.R620*	ENST00000289153	NM_006219.2	620	Cga/Tga	12/22	1	2	FACETS	0.97	0.826	1	0.97	0.826	1	CLONAL	1	TRUE	1	0.17	2		474	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578528	7578528	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1249	67	860	0	ENST00000269305.4:c.402T>G	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	ttT/ttG	5/11	1	2	FACETS	0.599	0.518	0.687	0.599	0.518	0.687	SUBCLONAL	1	TRUE	1	0.17	2		860	1316	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577073	7577073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	55	630	0	ENST00000269305.4:c.865C>T	p.Leu289Phe	p.L289F	ENST00000269305	NM_001126112.2	289	Ctc/Ttc	8/11	1	2	FACETS	0.679	0.579	0.789	0.679	0.579	0.789	SUBCLONAL	1	TRUE	1	0.17	2		630	953	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	20	290	0	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	1	2	FACETS	0.674	0.515	0.861	0.674	0.515	0.861	SUBCLONAL	1	TRUE	1	0.17	2		290	349	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332628	65332628	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748142963	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	27	332	1	ENST00000342505.4:c.911C>T	p.Ser304Leu	p.S304L	ENST00000342505	NM_002227.2	304	tCg/tTg	7/25	1	2	FACETS	0.756	0.601	0.934	0.756	0.601	0.934	CLONAL	1	TRUE	1	0.17	2		333	420	SUCCESS
AR	367	MSKCC	GRCh37	X	66937442	66937442	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555996863	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	49	549	2	ENST00000374690.3:c.2296G>A	p.Ala766Thr	p.A766T	ENST00000374690	NM_000044.3	766	Gcc/Acc	5/8	1	2	FACETS	0.886	0.749	1	0.886	0.749	1	CLONAL	1	TRUE	1	0.17	2		551	651	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913023	32913023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376338226	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	39	590	0	ENST00000380152.3:c.4531G>A	p.Glu1511Lys	p.E1511K	ENST00000380152		1511	Gaa/Aaa	11/27	1	2	FACETS	0.787	0.651	0.939	0.787	0.651	0.939	CLONAL	1	TRUE	1	0.17	2		590	583	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645665	215645665	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1060501297	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	35	368	0	ENST00000260947.4:c.933G>T	p.Lys311Asn	p.K311N	ENST00000260947	NM_000465.2	311	aaG/aaT	4/11	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.17	2		368	391	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584500	189584500	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	21	378	1	ENST00000264731.3:c.796C>T	p.Arg266Ter	p.R266*	ENST00000264731	NM_003722.4	266	Cga/Tga	6/14	1	2	FACETS	0.673	0.518	0.855	0.673	0.518	0.855	SUBCLONAL	1	TRUE	1	0.17	2		379	367	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629147	86629147	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	26	324	0	ENST00000274376.6:c.892G>T	p.Glu298Ter	p.E298*	ENST00000274376	NM_002890.2	298	Gaa/Taa	4/25	1	2	FACETS	0.792	0.627	0.982	0.792	0.627	0.982	CLONAL	1	TRUE	1	0.17	2		324	386	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216568	108216568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs767845728	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	24	319	1	ENST00000278616.4:c.8517C>A	p.Phe2839Leu	p.F2839L	ENST00000278616	NM_000051.3	2839	ttC/ttA	58/63	1	2	FACETS	0.743	0.582	0.929	0.743	0.582	0.929	CLONAL	1	TRUE	1	0.17	2		320	380	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29090089	29090089	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764396738	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	23	157	0	ENST00000328354.6:c.1392G>T	p.Lys464Asn	p.K464N	ENST00000328354	NM_007194.3	464	aaG/aaT	13/15	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.17	2		157	231	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	35	382	0	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	1	2	FACETS	0.712	0.583	0.859	0.712	0.583	0.859	SUBCLONAL	1	TRUE	1	0.17	2		382	578	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198263220	198263220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	36	440	0	ENST00000335508.6:c.3099G>T	p.Glu1033Asp	p.E1033D	ENST00000335508	NM_012433.2	1033	gaG/gaT	21/25	1	2	FACETS	0.789	0.647	0.947	0.789	0.647	0.947	CLONAL	1	TRUE	1	0.17	2		440	537	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201816	66201816	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556854839	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	31	388	0	ENST00000273854.3:c.2686C>T	p.Arg896Cys	p.R896C	ENST00000273854	NM_004439.5	896	Cgt/Tgt	16/18	1	2	FACETS	0.743	0.6	0.905	0.743	0.6	0.905	CLONAL	1	TRUE	1	0.17	2		388	491	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098800	178098800	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	47	554	0	ENST00000397062.3:c.245A>G	p.Glu82Gly	p.E82G	ENST00000397062	NM_006164.4	82	gAa/gGa	2/5	1	2	FACETS	0.791	0.666	0.93	0.791	0.666	0.93	CLONAL	1	TRUE	1	0.17	2		554	699	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934887	9934887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	42	558	1	ENST00000330684.3:c.1403C>T	p.Ser468Phe	p.S468F	ENST00000330684	NM_001134407.1	468	tCc/tTc	6/13	1	2	FACETS	0.845	0.704	1	0.845	0.704	1	CLONAL	1	TRUE	1	0.17	2		559	585	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542861	187542861	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1340793072	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	19	366	0	ENST00000441802.2:c.4879C>T	p.Arg1627Ter	p.R1627*	ENST00000441802	NM_005245.3	1627	Cga/Tga	10/27	1	2	FACETS	0.642	0.487	0.826	0.642	0.487	0.826	SUBCLONAL	1	TRUE	1	0.17	2		366	348	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942686	48942686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767011440	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	23	292	0	ENST00000267163.4:c.1073G>A	p.Arg358Gln	p.R358Q	ENST00000267163	NM_000321.2	358	cGa/cAa	11/27	1	2	FACETS	0.663	0.516	0.834	0.663	0.516	0.834	SUBCLONAL	1	TRUE	1	0.17	2		292	408	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37056036	37056036	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs267607789	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	33	386	1	ENST00000231790.2:c.790+1G>A		p.X264_splice	ENST00000231790	NM_000249.3	264			1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.17	2		387	336	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851574	134851574	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747682274	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	31	457	0	ENST00000398015.3:c.980G>A	p.Arg327His	p.R327H	ENST00000398015	NM_004441.4	327	cGc/cAc	5/16	1	2	FACETS	0.62	0.5	0.757	0.62	0.5	0.757	SUBCLONAL	1	TRUE	1	0.17	2		457	588	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649005	86649005	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	34	404	0	ENST00000274376.6:c.1285G>T	p.Glu429Ter	p.E429*	ENST00000274376	NM_002890.2	429	Gaa/Taa	9/25	1	2	FACETS	0.897	0.733	1	0.897	0.733	1	CLONAL	1	TRUE	1	0.17	2		404	446	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137487	202137487	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	41	548	1	ENST00000358485.4:c.715G>T	p.Glu239Ter	p.E239*	ENST00000358485	NM_001080125.1	239	Gaa/Taa	4/9	1	2	FACETS	0.804	0.669	0.955	0.804	0.669	0.955	CLONAL	1	TRUE	1	0.17	2		549	600	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027661	48027661	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	21	271	0	ENST00000234420.5:c.2539G>T	p.Glu847Ter	p.E847*	ENST00000234420	NM_000179.2	847	Gaa/Taa	4/10	1	2	FACETS	0.8	0.616	1	0.8	0.616	1	CLONAL	1	TRUE	1	0.17	2		271	309	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249857	133249857	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1565972665	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	29	348	0	ENST00000320574.5:c.1366G>C	p.Ala456Pro	p.A456P	ENST00000320574	NM_006231.2	456	Gcc/Ccc	14/49	1	2	FACETS	0.666	0.534	0.818	0.666	0.534	0.818	SUBCLONAL	1	TRUE	1	0.17	2		348	512	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584747	187584747	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1358297166	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	27	393	0	ENST00000441802.2:c.3286C>T	p.Arg1096Ter	p.R1096*	ENST00000441802	NM_005245.3	1096	Cga/Tga	3/27	1	2	FACETS	0.784	0.624	0.968	0.784	0.624	0.968	CLONAL	1	TRUE	1	0.17	2		393	405	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463578	25463578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770938712	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	49	463	1	ENST00000264709.3:c.2104G>A	p.Asp702Asn	p.D702N	ENST00000264709	NM_175629.2	702	Gat/Aat	18/23	1	2	FACETS	0.89	0.752	1	0.89	0.752	1	CLONAL	1	TRUE	1	0.17	2		464	648	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281660	49281660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61735175	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	58	667	2	ENST00000282018.3:c.707C>T	p.Ser236Leu	p.S236L	ENST00000282018	NM_020377.2	236	tCg/tTg	1/1	1	2	FACETS	0.867	0.743	1	0.867	0.743	1	CLONAL	1	TRUE	1	0.17	2		669	787	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748117	72748117	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	34	455	0	ENST00000357731.5:c.61C>T	p.Leu21Phe	p.L21F	ENST00000357731	NM_173808.2	21	Ctc/Ttc	1/7	1	2	FACETS	0.673	0.549	0.814	0.673	0.549	0.814	SUBCLONAL	1	TRUE	1	0.17	2		455	594	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429846	78429846	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	17	254	0	ENST00000370768.2:c.942T>G	p.Asp314Glu	p.D314E	ENST00000370768	NM_003902.3	314	gaT/gaG	12/20	1	2	FACETS	0.664	0.495	0.865	0.664	0.495	0.865	SUBCLONAL	1	TRUE	1	0.17	2		254	301	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120502047	120502047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs189684879	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	33	419	1	ENST00000256646.2:c.1994G>A	p.Arg665His	p.R665H	ENST00000256646	NM_024408.3	665	cGc/cAc	12/34	1	2	FACETS	0.828	0.674	1	0.828	0.674	1	CLONAL	1	TRUE	1	0.17	2		420	469	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724565	162724565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397514747	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	63	527	0	ENST00000367921.3:c.337G>A	p.Glu113Lys	p.E113K	ENST00000367921	NM_006182.2	113	Gag/Aag	5/18	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.17	2		527	572	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518514	204518514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	26	304	0	ENST00000367182.3:c.1177G>A	p.Glu393Lys	p.E393K	ENST00000367182	NM_001278516.1	393	Gaa/Aaa	11/11	1	2	FACETS	0.894	0.709	1	0.894	0.709	1	CLONAL	1	TRUE	1	0.17	2		304	342	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759904	63759904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	35	297	0	ENST00000279873.7:c.557G>A	p.Arg186Gln	p.R186Q	ENST00000279873	NM_032199.2	186	cGg/cAg	4/10	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.17	2		297	374	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717774	89717774	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	A	A	T	rs1554825261	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	22	345	0	ENST00000371953.3:c.799A>T	p.Lys267Ter	p.K267*	ENST00000371953	NM_000314.4	267	Aag/Tag	7/9	1	2	FACETS	0.789	0.612	0.995	0.789	0.612	0.995	CLONAL	1	TRUE	1	0.17	2		345	328	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720871	89720871	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	22	348	0	ENST00000371953.3:c.1022T>G	p.Phe341Cys	p.F341C	ENST00000371953	NM_000314.4	341	tTt/tGt	8/9	1	2	FACETS	0.601	0.464	0.759	0.601	0.464	0.759	SUBCLONAL	1	TRUE	1	0.17	2		348	431	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128989	64128989	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	59	590	2	ENST00000334205.4:c.619G>A	p.Glu207Lys	p.E207K	ENST00000334205	NM_003942.2	207	Gaa/Aaa	6/17	1	2	FACETS	0.818	0.702	0.944	0.818	0.702	0.944	CLONAL	1	TRUE	1	0.17	2		592	849	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172502	108172502	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	26	333	0	ENST00000278616.4:c.5305A>T	p.Thr1769Ser	p.T1769S	ENST00000278616	NM_000051.3	1769	Aca/Tca	35/63	1	2	FACETS	1	0.84	1	1	0.84	1	CLONAL	1	TRUE	1	0.17	2		333	286	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103196	119103196	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	41	525	0	ENST00000264033.4:c.234G>T	p.Lys78Asn	p.K78N	ENST00000264033	NM_005188.3	78	aaG/aaT	2/16	1	2	FACETS	0.809	0.673	0.961	0.809	0.673	0.961	CLONAL	1	TRUE	1	0.17	2		525	596	SUCCESS
CBL	867	MSKCC	GRCh37	11	119158563	119158563	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	34	499	0	ENST00000264033.4:c.1943G>T	p.Ser648Ile	p.S648I	ENST00000264033	NM_005188.3	648	aGt/aTt	12/16	1	2	FACETS	0.723	0.59	0.874	0.723	0.59	0.874	SUBCLONAL	1	TRUE	1	0.17	2		499	553	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435052	18435052	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	27	325	2	ENST00000266497.5:c.37G>T	p.Glu13Ter	p.E13*	ENST00000266497		13	Gaa/Taa	1/31	1	2	FACETS	0.775	0.616	0.956	0.775	0.616	0.956	CLONAL	1	TRUE	1	0.17	2		327	410	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231418	46231418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	36	409	0	ENST00000334344.6:c.1258G>A	p.Glu420Lys	p.E420K	ENST00000334344	NM_152641.2	420	Gag/Aag	10/21	1	2	FACETS	0.971	0.799	1	0.971	0.799	1	CLONAL	1	TRUE	1	0.17	2		409	436	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861224	57861224	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	49	514	1	ENST00000228682.2:c.1021G>A	p.Ala341Thr	p.A341T	ENST00000228682	NM_005269.2	341	Gcc/Acc	9/12	1	2	FACETS	0.839	0.709	0.982	0.839	0.709	0.982	CLONAL	1	TRUE	1	0.17	2		515	687	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864550	57864550	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs200775132	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	74	705	0	ENST00000228682.2:c.2027T>G	p.Phe676Cys	p.F676C	ENST00000228682	NM_005269.2	676	tTt/tGt	12/12	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.17	2		705	823	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120554412	120554412	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	22	201	0	ENST00000229340.5:c.43G>A	p.Gly15Ser	p.G15S	ENST00000229340	NM_006861.6	15	Ggc/Agc	1/6	1	2	FACETS	1	0.794	1	1	0.794	1	CLONAL	1	TRUE	1	0.17	2		201	253	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28886159	28886159	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	33	443	1	ENST00000282397.4:c.3463G>T	p.Gly1155Cys	p.G1155C	ENST00000282397	NM_002019.4	1155	Ggt/Tgt	26/30	1	2	FACETS	0.791	0.643	0.957	0.791	0.643	0.957	CLONAL	1	TRUE	1	0.17	2		444	491	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972663	32972663	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	40	433	0	ENST00000380152.3:c.10013C>A	p.Ser3338Ter	p.S3338*	ENST00000380152		3338	tCa/tAa	27/27	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.17	2		433	455	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027158	49027158	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	37	421	0	ENST00000267163.4:c.1725A>C	p.Gln575His	p.Q575H	ENST00000267163	NM_000321.2	575	caA/caC	18/27	1	2	FACETS	0.946	0.78	1	0.946	0.78	1	CLONAL	1	TRUE	1	0.17	2		421	460	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528224	103528224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768302699	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	45	402	0	ENST00000355739.4:c.3532C>T	p.Arg1178Cys	p.R1178C	ENST00000355739	NM_000123.3	1178	Cgt/Tgt	15/15	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.17	2		402	517	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100175	30100175	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	50	513	0	ENST00000331968.5:c.1445T>C	p.Leu482Ser	p.L482S	ENST00000331968	NM_002742.2	482	tTa/tCa	10/18	1	2	FACETS	0.926	0.785	1	0.926	0.785	1	CLONAL	1	TRUE	1	0.17	2		513	635	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100208	30100208	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	34	363	0	ENST00000331968.5:c.1412T>G	p.Ile471Ser	p.I471S	ENST00000331968	NM_002742.2	471	aTt/aGt	10/18	1	2	FACETS	0.844	0.689	1	0.844	0.689	1	CLONAL	1	TRUE	1	0.17	2		363	474	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68290283	68290283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867530891	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	25	380	1	ENST00000487270.1:c.23G>A	p.Arg8Gln	p.R8Q	ENST00000487270	NM_133509.3	8	cGa/cAa	2/11	1	2	FACETS	0.598	0.47	0.745	0.598	0.47	0.745	SUBCLONAL	1	TRUE	1	0.17	2		381	492	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40678613	40678613	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	51	586	1	ENST00000249776.8:c.355G>T	p.Glu119Ter	p.E119*	ENST00000249776	NM_033286.3	119	Gaa/Taa	3/9	1	2	FACETS	0.77	0.653	0.9	0.77	0.653	0.9	SUBCLONAL	1	TRUE	1	0.17	2		587	779	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817835	3817835	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	44	559	0	ENST00000262367.5:c.3136A>C	p.Met1046Leu	p.M1046L	ENST00000262367	NM_004380.2	1046	Atg/Ctg	16/31	1	2	FACETS	0.731	0.612	0.864	0.731	0.612	0.864	SUBCLONAL	1	TRUE	1	0.17	2		559	708	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857172	9857172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555481986	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	25	384	1	ENST00000330684.3:c.4229C>T	p.Ser1410Leu	p.S1410L	ENST00000330684	NM_001134407.1	1410	tCg/tTg	13/13	1	2	FACETS	0.617	0.485	0.769	0.617	0.485	0.769	SUBCLONAL	1	TRUE	1	0.17	2		385	477	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357164	89357164	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	47	600	0	ENST00000301030.4:c.470C>A	p.Thr157Asn	p.T157N	ENST00000301030	NM_001256183.1	157	aCc/aAc	6/13	1	2	FACETS	0.698	0.587	0.821	0.698	0.587	0.821	SUBCLONAL	1	TRUE	1	0.17	2		600	792	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983797	15983797	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	44	477	0	ENST00000268712.3:c.3325G>T	p.Glu1109Ter	p.E1109*	ENST00000268712	NM_006311.3	1109	Gaa/Taa	25/46	1	2	FACETS	0.924	0.775	1	0.924	0.775	1	CLONAL	1	TRUE	1	0.17	2		477	560	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627509	37627509	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs371684674	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	54	543	0	ENST00000447079.4:c.1424C>A	p.Ser475Tyr	p.S475Y	ENST00000447079	NM_015083.1	475	tCt/tAt	2/14	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.17	2		543	606	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40857132	40857132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316478374	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	47	502	0	ENST00000428826.2:c.1909G>A	p.Glu637Lys	p.E637K	ENST00000428826		637	Gaa/Aaa	17/21	1	2	FACETS	0.792	0.667	0.931	0.792	0.667	0.931	CLONAL	1	TRUE	1	0.17	2		502	698	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40865353	40865353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1454055017	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	40	573	0	ENST00000428826.2:c.1078C>T	p.Arg360Cys	p.R360C	ENST00000428826		360	Cgt/Tgt	11/21	1	2	FACETS	0.644	0.533	0.767	0.644	0.533	0.767	SUBCLONAL	1	TRUE	1	0.17	2		573	731	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210688	36210688	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	48	539	2	ENST00000222270.7:c.439C>T	p.Arg147Ter	p.R147*	ENST00000222270	NM_014727.1	147	Cga/Tga	3/37	1	2	FACETS	0.823	0.695	0.965	0.823	0.695	0.965	CLONAL	1	TRUE	1	0.17	2		541	686	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912052	50912052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773180520	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	66	722	0	ENST00000440232.2:c.1786G>A	p.Val596Ile	p.V596I	ENST00000440232	NM_002691.3	596	Gtc/Atc	15/27	1	2	FACETS	0.843	0.73	0.966	0.843	0.73	0.966	CLONAL	1	TRUE	1	0.17	2		722	921	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966716	25966716	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	40	449	1	ENST00000435504.4:c.2490G>T	p.Glu830Asp	p.E830D	ENST00000435504		830	gaG/gaT	13/13	1	2	FACETS	0.8	0.664	0.953	0.8	0.664	0.953	CLONAL	1	TRUE	1	0.17	2		450	588	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543705	29543705	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	65	629	1	ENST00000389048.3:c.1458C>A	p.Phe486Leu	p.F486L	ENST00000389048	NM_004304.4	486	ttC/ttA	7/29	1	2	FACETS	0.979	0.848	1	0.979	0.848	1	CLONAL	1	TRUE	1	0.17	2		630	781	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198262755	198262755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	40	477	1	ENST00000335508.6:c.3220C>T	p.Arg1074Cys	p.R1074C	ENST00000335508	NM_012433.2	1074	Cgt/Tgt	22/25	1	2	FACETS	0.82	0.68	0.976	0.82	0.68	0.976	CLONAL	1	TRUE	1	0.17	2		478	574	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735645	204735645	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	27	314	1	ENST00000302823.3:c.446T>A	p.Ile149Asn	p.I149N	ENST00000302823	NM_005214.4	149	aTt/aAt	2/4	1	2	FACETS	0.854	0.679	1	0.854	0.679	1	CLONAL	1	TRUE	1	0.17	2		315	372	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076885	41076885	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	40	434	0	ENST00000373198.4:c.1535C>T	p.Thr512Ile	p.T512I	ENST00000373198	NM_133170.3	512	aCc/aTc	9/32	1	2	FACETS	0.919	0.763	1	0.919	0.763	1	CLONAL	1	TRUE	1	0.17	2		434	512	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531817	41531817	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	37	425	0	ENST00000263253.7:c.1529G>A	p.Ser510Asn	p.S510N	ENST00000263253	NM_001429.3	510	aGt/aAt	7/31	1	2	FACETS	0.994	0.82	1	0.994	0.82	1	CLONAL	1	TRUE	1	0.17	2		425	438	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637690	52637690	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	39	426	0	ENST00000394830.3:c.2626C>A	p.Arg876Ser	p.R876S	ENST00000394830	NM_018313.4	876	Cgt/Agt	18/30	1	2	FACETS	0.839	0.694	1	0.839	0.694	1	CLONAL	1	TRUE	1	0.17	2		426	547	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457232	89457232	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	23	358	0	ENST00000336596.2:c.1713G>T	p.Lys571Asn	p.K571N	ENST00000336596	NM_005233.5	571	aaG/aaT	9/17	1	2	FACETS	0.703	0.547	0.883	0.703	0.547	0.883	SUBCLONAL	1	TRUE	1	0.17	2		358	385	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947212	178947212	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	20	210	0	ENST00000263967.3:c.2648A>G	p.Asp883Gly	p.D883G	ENST00000263967	NM_006218.2	883	gAc/gGc	18/21	1	2	FACETS	0.875	0.67	1	0.875	0.67	1	CLONAL	1	TRUE	1	0.17	2		210	269	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502483	186502483	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	15	198	0	ENST00000323963.5:c.206A>G	p.Lys69Arg	p.K69R	ENST00000323963		69	aAa/aGa	3/11	1	2	FACETS	0.878	0.644	1	0.878	0.644	1	CLONAL	1	TRUE	1	0.17	2		198	201	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502876	186502876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	27	452	1	ENST00000323963.5:c.334G>A	p.Glu112Lys	p.E112K	ENST00000323963		112	Gaa/Aaa	4/11	1	2	FACETS	0.667	0.53	0.825	0.667	0.53	0.825	SUBCLONAL	1	TRUE	1	0.17	2		453	476	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565843	55565843	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	44	525	0	ENST00000288135.5:c.667C>A	p.Leu223Ile	p.L223I	ENST00000288135	NM_000222.2	223	Ctt/Att	4/21	1	2	FACETS	0.83	0.695	0.98	0.83	0.695	0.98	CLONAL	1	TRUE	1	0.17	2		525	624	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524555	187524555	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	34	579	0	ENST00000441802.2:c.11125A>T	p.Lys3709Ter	p.K3709*	ENST00000441802	NM_005245.3	3709	Aaa/Taa	19/27	1	2	FACETS	0.614	0.501	0.743	0.614	0.501	0.743	SUBCLONAL	1	TRUE	1	0.17	2		579	651	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410883	31410883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	54	540	1	ENST00000344624.3:c.3637C>T	p.Arg1213Cys	p.R1213C	ENST00000344624		1213	Cgc/Tgc	28/33	1	2	FACETS	0.772	0.658	0.898	0.772	0.658	0.898	SUBCLONAL	1	TRUE	1	0.17	2		541	823	SUCCESS
APC	324	MSKCC	GRCh37	5	112155038	112155038	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	50	418	0	ENST00000257430.4:c.1309C>T	p.Pro437Ser	p.P437S	ENST00000257430	NM_000038.5	437	Cca/Tca	10/16	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.17	2		418	502	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818393	170818393	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	11	166	0	ENST00000296930.5:c.223A>G	p.Thr75Ala	p.T75A	ENST00000296930	NM_002520.6	75	Aca/Gca	3/11	1	2	FACETS	0.892	0.619	1	0.892	0.619	1	CLONAL	1	TRUE	1	0.17	2		166	145	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637786	176637786	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	34	597	2	ENST00000439151.2:c.2386G>T	p.Glu796Ter	p.E796*	ENST00000439151	NM_022455.4	796	Gaa/Taa	5/23	1	2	FACETS	0.596	0.486	0.721	0.596	0.486	0.721	SUBCLONAL	1	TRUE	1	0.17	2		599	671	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721741	176721741	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	31	362	0	ENST00000439151.2:c.7372C>T	p.Leu2458Phe	p.L2458F	ENST00000439151	NM_022455.4	2458	Ctc/Ttc	23/23	1	2	FACETS	0.844	0.682	1	0.844	0.682	1	CLONAL	1	TRUE	1	0.17	2		362	432	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31946708	31946708	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	47	497	0	ENST00000375333.2:c.596G>T	p.Arg199Ile	p.R199I	ENST00000375333	NM_032454.1	199	aGa/aTa	4/8	1	2	FACETS	0.753	0.634	0.885	0.753	0.634	0.885	SUBCLONAL	1	TRUE	1	0.17	2		497	734	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798417	32798417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770778501	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	49	546	0	ENST00000374899.4:c.1439G>A	p.Arg480His	p.R480H	ENST00000374899	NM_018833.2	480	cGc/cAc	8/12	1	2	FACETS	0.818	0.691	0.958	0.818	0.691	0.958	CLONAL	1	TRUE	1	0.17	2		546	705	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805714	32805714	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	34	543	0	ENST00000374899.4:c.297G>A	p.Trp99Ter	p.W99*	ENST00000374899	NM_018833.2	99	tgG/tgA	2/12	1	2	FACETS	0.601	0.489	0.727	0.601	0.489	0.727	SUBCLONAL	1	TRUE	1	0.17	2		543	666	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106543547	106543547	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	24	325	0	ENST00000369096.4:c.349A>C	p.Ile117Leu	p.I117L	ENST00000369096	NM_001198.3	117	Ata/Cta	3/7	1	2	FACETS	0.646	0.506	0.809	0.646	0.506	0.809	SUBCLONAL	1	TRUE	1	0.17	2		325	437	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109415106	109415106	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	89	766	0	ENST00000436639.2:c.171G>T	p.Glu57Asp	p.E57D	ENST00000436639	NM_014454.2	57	gaG/gaT	1/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.17	2		766	845	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715823	117715823	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	37	399	0	ENST00000368508.3:c.935A>G	p.Glu312Gly	p.E312G	ENST00000368508	NM_002944.2	312	gAa/gGa	9/43	1	2	FACETS	0.987	0.814	1	0.987	0.814	1	CLONAL	1	TRUE	1	0.17	2		399	441	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985520	2985520	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	48	550	0	ENST00000396946.4:c.291T>G	p.Phe97Leu	p.F97L	ENST00000396946	NM_032415.4	97	ttT/ttG	4/25	1	2	FACETS	0.796	0.672	0.934	0.796	0.672	0.934	CLONAL	1	TRUE	1	0.17	2		550	709	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92247397	92247397	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	17	220	0	ENST00000265734.4:c.823G>T	p.Asp275Tyr	p.D275Y	ENST00000265734	NM_001259.6	275	Gac/Tac	7/8	1	2	FACETS	0.631	0.47	0.822	0.631	0.47	0.822	SUBCLONAL	1	TRUE	1	0.17	2		220	317	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92404095	92404095	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	40	394	1	ENST00000265734.4:c.284C>A	p.Thr95Asn	p.T95N	ENST00000265734	NM_001259.6	95	aCt/aAt	3/8	1	2	FACETS	0.943	0.783	1	0.943	0.783	1	CLONAL	1	TRUE	1	0.17	2		395	499	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395492	116395492	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	24	398	0	ENST00000397752.3:c.1785A>C	p.Lys595Asn	p.K595N	ENST00000397752	NM_000245.2	595	aaA/aaC	6/21	1	2	FACETS	0.679	0.531	0.849	0.679	0.531	0.849	SUBCLONAL	1	TRUE	1	0.17	2		398	416	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412036	116412036	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	55	627	1	ENST00000397752.3:c.3021T>A	p.Phe1007Leu	p.F1007L	ENST00000397752	NM_000245.2	1007	ttT/ttA	14/21	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.17	2		628	618	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981315	68981315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866864487	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	20	349	0	ENST00000288368.4:c.1387C>T	p.Arg463Cys	p.R463C	ENST00000288368	NM_024870.2	463	Cgc/Tgc	12/40	1	2	FACETS	0.731	0.559	0.932	0.731	0.559	0.932	CLONAL	1	TRUE	1	0.17	2		349	322	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965728	90965728	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs920311188	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	17	235	1	ENST00000265433.3:c.1589C>A	p.Ser530Tyr	p.S530Y	ENST00000265433	NM_002485.4	530	tCt/tAt	11/16	1	2	FACETS	0.746	0.557	0.971	0.746	0.557	0.971	CLONAL	1	TRUE	1	0.17	2		236	268	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126334	5126334	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	29	213	0	ENST00000381652.3:c.3179A>G	p.Glu1060Gly	p.E1060G	ENST00000381652	NM_004972.3	1060	gAa/gGa	24/25	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.17	2		213	270	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484298	8484298	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs7869444	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	47	446	0	ENST00000356435.5:c.3234G>T	p.Glu1078Asp	p.E1078D	ENST00000356435		1078	gaG/gaT	19/35	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.17	2		446	537	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27183575	27183575	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	28	399	0	ENST00000380036.4:c.1149G>T	p.Met383Ile	p.M383I	ENST00000380036	NM_000459.3	383	atG/atT	8/23	1	2	FACETS	0.656	0.523	0.808	0.656	0.523	0.808	SUBCLONAL	1	TRUE	1	0.17	2		399	502	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133729585	133729585	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	50	569	0	ENST00000318560.5:c.214T>G	p.Phe72Val	p.F72V	ENST00000318560	NM_005157.4	72	Ttt/Gtt	2/11	1	2	FACETS	0.8	0.678	0.936	0.8	0.678	0.936	CLONAL	1	TRUE	1	0.17	2		569	735	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913224	39913224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769982436	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	50	556	0	ENST00000378444.4:c.4891G>A	p.Asp1631Asn	p.D1631N	ENST00000378444	NM_001123385.1	1631	Gat/Aat	14/15	1	2	FACETS	0.874	0.74	1	0.874	0.74	1	CLONAL	1	TRUE	1	0.17	2		556	673	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347888	70347888	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	45	560	0	ENST00000374080.3:c.3127C>A	p.Leu1043Ile	p.L1043I	ENST00000374080		1043	Ctt/Att	22/45	1	2	FACETS	0.673	0.564	0.794	0.673	0.564	0.794	SUBCLONAL	1	TRUE	1	0.17	2		560	787	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937913	76937914	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	30	422	0	ENST00000373344.5:c.2834dup	p.Ser946GlufsTer10	p.S946Efs*10	ENST00000373344	NM_000489.3	945	aag/aaAg	9/35	1	2	FACETS	0.618	0.497	0.757	0.618	0.497	0.757	SUBCLONAL	1	TRUE	1	0.17	2		422	571	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944361	76944361	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	32	576	1	ENST00000373344.5:c.544C>A	p.Gln182Lys	p.Q182K	ENST00000373344	NM_000489.3	182	Caa/Aaa	7/35	1	2	FACETS	0.708	0.573	0.86	0.708	0.573	0.86	SUBCLONAL	1	TRUE	1	0.17	2		577	532	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504048	123504048	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	19	287	0	ENST00000371139.4:c.224G>T	p.Arg75Ile	p.R75I	ENST00000371139	NM_001114937.2	75	aGa/aTa	3/4	1	2	FACETS	0.626	0.475	0.805	0.626	0.475	0.805	SUBCLONAL	1	TRUE	1	0.17	2		287	357	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	473	707	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	NA	2	FACETS	0.884	0.846	0.922			1	INDETERMINATE	3	TRUE	NA	0.291159289879829	2		707	1225	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683747	162683747	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	144	513	1	ENST00000366898.1:c.222G>T	p.Trp74Cys	p.W74C	ENST00000366898	NM_004562.2	74	tgG/tgT	3/12	0.247569460515108	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.291159289879829	1		514	827	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106662	27106662	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	169	573	0	ENST00000324856.7:c.6273G>A	p.Trp2091Ter	p.W2091*	ENST00000324856	NM_006015.4	2091	tgG/tgA	20/20	0.291159289879829	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.291159289879829	1		573	712	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	430249	430249	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1242334605	NA	P-0015870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	107	375	0	ENST00000399788.2:c.2453G>A	p.Arg818Gln	p.R818Q	ENST00000399788	NM_001042603.1	818	cGg/cAg	18/28	0.123854810457853	3	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.291159289879829	3		375	624	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675245	40675245	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	34	497	0	ENST00000249776.8:c.209G>T	p.Gly70Val	p.G70V	ENST00000249776	NM_033286.3	70	gGg/gTg	1/9	0.291159289879829	1	FACETS	0.321	0.262	0.389	0.321	0.262	0.389	SUBCLONAL	1	TRUE	0	0.291159289879829	1		497	621	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119808	70119808	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	234	704	2	ENST00000245479.2:c.811del	p.Arg271AlafsTer8	p.R271Afs*8	ENST00000245479	NM_000346.3	270	ttC/tt	3/3	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.291159289879829	2		706	1090	SUCCESS
APC	324	MSKCC	GRCh37	5	112174475	112174475	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	71	264	0	ENST00000257430.4:c.3184del	p.Gln1062LysfsTer64	p.Q1062Kfs*64	ENST00000257430	NM_000038.5	1062	Caa/aa	16/16	0.273342100131228	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.291159289879829	1		264	365	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397163	397163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	135	464	1	ENST00000380956.4:c.548C>T	p.Pro183Leu	p.P183L	ENST00000380956	NM_001195286.1	183	cCg/cTg	5/9	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.291159289879829	2		465	727	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0015871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	104	670	1	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.972	0.869	1	0.972	0.869	1	CLONAL	1	TRUE	1	0.24	2		671	892	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0015871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	147	414	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.249283045979148	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.24	3		414	587	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795743	42795743	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs535815082	NA	P-0015871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	107	842	0	ENST00000575354.2:c.2732C>T	p.Pro911Leu	p.P911L	ENST00000575354	NM_015125.3	911	cCg/cTg	11/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.24	2		842	779	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259192	36259192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	87	704	0	ENST00000300305.3:c.299C>T	p.Ser100Phe	p.S100F	ENST00000300305		100	tCc/tTc	3/8	1	2	FACETS	0.972	0.86	1	0.972	0.86	1	CLONAL	1	TRUE	1	0.24	2		704	746	SUCCESS
BLM	641	MSKCC	GRCh37	15	91295082	91295082	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	29	404	0	ENST00000355112.3:c.865A>T	p.Ile289Phe	p.I289F	ENST00000355112	NM_000057.2	289	Att/Ttt	4/22	1	2	FACETS	0.931	0.746	1	0.931	0.746	1	CLONAL	1	TRUE	1	0.14	2		404	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578480	7578480	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	72	728	0	ENST00000269305.4:c.450del	p.Pro152ArgfsTer18	p.P152Rfs*18	ENST00000269305	NM_001126112.2	150	acA/ac	5/11	1	2	FACETS	0.878	0.765	1	0.878	0.765	1	CLONAL	1	TRUE	1	0.14	2		728	1171	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792895	33792896	+	missense_variant	Missense_Mutation	DNP	CC	CC	GA	novel	NA	P-0015872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	19	167	0	ENST00000498907.2:c.425_426delinsTC	p.Arg142Ile	p.R142I	ENST00000498907	NM_004364.3	142	aGG/aTC	1/1	1	2	FACETS	1	0.775	1	1	0.775	1	CLONAL	1	TRUE	1	0.14	2		167	266	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001525	150001534	+	frameshift_variant	Frame_Shift_Del	DEL	GATGTAATTA	GATGTAATTA	-	novel	NA	P-0015872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	38	419	0	ENST00000253339.5:c.2070_2079del	p.Asn691ValfsTer13	p.N691Vfs*13	ENST00000253339		690	tcTAATTACATC/tc	4/7	1	2	FACETS	0.949	0.783	1	0.949	0.783	1	CLONAL	1	TRUE	1	0.14	2		419	572	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398284	+	missense_variant	Missense_Mutation	TNP	CAC	CAC	AAG	novel	NA	P-0015872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	25	472	0	ENST00000311936.3:c.35_37delinsCTT	p.Gly12_Gly13delinsAlaCys	p.G12_G13delinsAC	ENST00000311936	NM_004985.3	12	gGTGgc/gCTTgc	2/5	1	2	FACETS	0.647	0.508	0.807	0.647	0.508	0.807	SUBCLONAL	1	TRUE	1	0.14	2		472	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577123	7577123	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876660333	NA	P-0015874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	589	714	0	ENST00000269305.4:c.815T>G	p.Val272Gly	p.V272G	ENST00000269305	NM_001126112.2	272	gTg/gGg	8/11	0.450461488104414	3	FACETS	0.97	0.937	1	0.97	0.937	1	CLONAL	3	TRUE	0	0.450461488104414	3		714	1101	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804352	43804352	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	253	537	2	ENST00000372470.3:c.352C>A	p.Gln118Lys	p.Q118K	ENST00000372470	NM_005373.2	118	Cag/Aag	3/12	0.417444832126121	3	FACETS	0.939	0.883	0.996	0.939	0.883	0.996	CLONAL	2	TRUE	1	0.450461488104414	3		539	733	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724304	112724304	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	309	571	1	ENST00000369452.4:c.188G>T	p.Gly63Val	p.G63V	ENST00000369452	NM_007373.3	63	gGg/gTg	2/9	0.306359029624423	3	FACETS	0.917	0.867	0.967	0.917	0.867	0.967	CLONAL	2	TRUE	1	0.450461488104414	3		572	917	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81968132	81968132	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	210	509	0	ENST00000359376.3:c.2838C>A	p.Asn946Lys	p.N946K	ENST00000359376	NM_002661.3	946	aaC/aaA	26/33	0.450461488104414	2	FACETS	0.827	0.773	0.881	0.827	0.773	0.881	CLONAL	2	TRUE	0	0.450461488104414	2		509	564	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182608	99182608	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs757400396	NA	P-0015874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	103	269	0	ENST00000074304.5:c.2411A>G	p.Asn804Ser	p.N804S	ENST00000074304	NM_001134224.1	804	aAt/aGt	22/26	0.401144586614423	5	FACETS	1	0.956	1	0.375	0.336	0.417	CLONAL	1	TRUE	2	0.450461488104414	5		269	681	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165272	47165272	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	134	300	0	ENST00000409792.3:c.854A>G	p.His285Arg	p.H285R	ENST00000409792	NM_014159.6	285	cAt/cGt	3/21	0.444421874282619	2	FACETS	0.896	0.826	0.967	0.896	0.826	0.967	CLONAL	2	TRUE	0	0.450461488104414	2		300	332	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213797	66213797	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	149	461	1	ENST00000273854.3:c.2633C>A	p.Pro878His	p.P878H	ENST00000273854	NM_004439.5	878	cCc/cAc	15/18	0.450461488104414	2	FACETS	0.833	0.77	0.898	0.833	0.77	0.898	CLONAL	2	TRUE	0	0.450461488104414	2		462	397	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286552	33286552	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	149	502	0	ENST00000374542.5:c.2191G>C	p.Glu731Gln	p.E731Q	ENST00000374542	NM_001141970.1	731	Gaa/Caa	8/8	0.450461488104414	2	FACETS	0.993	0.91	1	0.497	0.455	0.54	CLONAL	1	TRUE	0	0.450461488104414	2		502	666	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781449	135781450	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0015874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	193	405	0	ENST00000298552.3:c.1515_1516del	p.Pro506LeufsTer28	p.P506Lfs*28	ENST00000298552	NM_001162426.1	505	tcTCcc/tccc	15/23	0.450461488104414	2	FACETS	0.813	0.758	0.869	0.813	0.758	0.869	CLONAL	2	TRUE	0	0.450461488104414	2		405	527	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	228	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.992	0.93	1	0.992	0.93	1	CLONAL	1	TRUE	1	0.700481332196909	2		248	656	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164805	47164805	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	249	312	0	ENST00000409792.3:c.1321C>T	p.Arg441Ter	p.R441*	ENST00000409792	NM_014159.6	441	Cga/Tga	3/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.700481332196909	2		312	683	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134688	41134688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1034299550	NA	P-0015882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	225	399	0	ENST00000379561.5:c.940C>T	p.Arg314Cys	p.R314C	ENST00000379561	NM_002015.3	314	Cgc/Tgc	2/3	1	2	FACETS	0.973	0.911	1	0.973	0.911	1	CLONAL	1	TRUE	1	0.700481332196909	2		399	660	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938406	76938406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	281	614	0	ENST00000373344.5:c.2342G>A	p.Arg781Gln	p.R781Q	ENST00000373344	NM_000489.3	781	cGa/cAa	9/35	1	2	FACETS	0.907	0.854	0.96	0.907	0.854	0.96	CLONAL	1	TRUE	1	0.700481332196909	2		614	885	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410556	63410556	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	377	674	2	ENST00000330258.3:c.2611C>T	p.Arg871Ter	p.R871*	ENST00000330258	NM_152424.3	871	Cga/Tga	2/2	1	2	FACETS	0.988	0.939	1	0.988	0.939	1	CLONAL	1	TRUE	1	0.700481332196909	2		676	1090	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781326	3781326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1445723787	NA	P-0015882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	493	891	1	ENST00000262367.5:c.5039C>T	p.Ser1680Phe	p.S1680F	ENST00000262367	NM_004380.2	1680	tCc/tTc	30/31	0.700481332196909	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.700481332196909	1		892	885	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248234	59248234	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	31	79	0	ENST00000371222.2:c.509A>T	p.Tyr170Phe	p.Y170F	ENST00000371222	NM_002228.3	170	tAc/tTc	1/1	0.700481332196909	1	FACETS	0.747	0.627	0.871	0.747	0.627	0.871	SUBCLONAL	1	TRUE	0	0.700481332196909	1		79	77	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204506575	204506575	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1487408075	NA	P-0015882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	346	587	2	ENST00000367182.3:c.361G>A	p.Ala121Thr	p.A121T	ENST00000367182	NM_001278516.1	121	Gct/Act	6/11	1	2	FACETS	0.969	0.92	1	0.969	0.92	1	CLONAL	1	TRUE	1	0.700481332196909	2		589	1019	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023104	33023105	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	223	462	1	ENST00000300177.4:c.213_214delinsAA	p.Glu72Lys	p.E72K	ENST00000300177	NM_001191322.1	71	gaGGag/gaAAag	2/2	1	2	FACETS	0.924	0.864	0.985	0.924	0.864	0.985	CLONAL	1	TRUE	1	0.700481332196909	2		463	689	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857061	9857061	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	164	284	0	ENST00000330684.3:c.4340C>T	p.Ser1447Phe	p.S1447F	ENST00000330684	NM_001134407.1	1447	tCc/tTc	13/13	0.700481332196909	1	FACETS	0.985	0.922	1	0.985	0.922	1	CLONAL	1	TRUE	0	0.700481332196909	1		284	309	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830414	72830414	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	160	246	0	ENST00000268489.5:c.6167C>T	p.Pro2056Leu	p.P2056L	ENST00000268489	NM_006885.3	2056	cCt/cTt	9/10	0.700481332196909	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.700481332196909	1		246	271	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550536	29550536	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1131691130	NA	P-0015882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	241	465	1	ENST00000356175.3:c.1796G>A	p.Trp599Ter	p.W599*	ENST00000356175	NM_000267.3	599	tGg/tAg	16/57	1	2	FACETS	0.941	0.883	1	0.941	0.883	1	CLONAL	1	TRUE	1	0.700481332196909	2		466	731	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676137	29676137	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	139	355	0	ENST00000356175.3:c.7127-1G>A		p.X2376_splice	ENST00000356175	NM_000267.3	2376			1	2	FACETS	0.876	0.804	0.951	0.876	0.804	0.951	CLONAL	1	TRUE	1	0.700481332196909	2		355	453	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40468827	40468827	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	416	749	0	ENST00000264657.5:c.2237C>T	p.Pro746Leu	p.P746L	ENST00000264657	NM_139276.2	746	cCc/cTc	23/24	1	2	FACETS	0.964	0.919	1	0.964	0.919	1	CLONAL	1	TRUE	1	0.700481332196909	2		749	1232	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303058	15303059	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	409	908	4	ENST00000263388.2:c.391_392delinsAA	p.Gly131Asn	p.G131N	ENST00000263388	NM_000435.2	131	GGt/AAt	4/33	1	2	FACETS	0.92	0.875	0.964	0.92	0.875	0.964	CLONAL	1	TRUE	1	0.700481332196909	2		912	1270	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222997	36222997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	449	847	1	ENST00000222270.7:c.5626C>T	p.Pro1876Ser	p.P1876S	ENST00000222270	NM_014727.1	1876	Ccc/Tcc	27/37	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.700481332196909	2		848	1276	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212484001	212484001	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0015882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	139	356	0	ENST00000342788.4:c.2203-1G>A		p.X735_splice	ENST00000342788	NM_005235.2	735			1	2	FACETS	0.925	0.85	1	0.925	0.85	1	CLONAL	1	TRUE	1	0.700481332196909	2		356	429	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439997	220439998	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	495	1034	2	ENST00000243786.2:c.850_851delinsTT	p.Pro284Phe	p.P284F	ENST00000243786	NM_002191.3	284	CCc/TTc	2/2	1	2	FACETS	0.935	0.895	0.977	0.935	0.895	0.977	CLONAL	1	TRUE	1	0.700481332196909	2		1036	1511	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730868	40730868	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	345	720	1	ENST00000373198.4:c.3667G>A	p.Asp1223Asn	p.D1223N	ENST00000373198	NM_133170.3	1223	Gat/Aat	27/32	1	2	FACETS	0.98	0.93	1	0.98	0.93	1	CLONAL	1	TRUE	1	0.700481332196909	2		721	1005	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533725	41533725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	375	671	0	ENST00000263253.7:c.1691C>T	p.Thr564Ile	p.T564I	ENST00000263253	NM_001429.3	564	aCt/aTt	8/31	1	2	FACETS	0.982	0.934	1	0.982	0.934	1	CLONAL	1	TRUE	1	0.700481332196909	2		671	1090	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573516	41573516	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	429	754	1	ENST00000263253.7:c.5801G>A	p.Arg1934Lys	p.R1934K	ENST00000263253	NM_001429.3	1934	aGa/aAa	31/31	1	2	FACETS	0.997	0.952	1	0.997	0.952	1	CLONAL	1	TRUE	1	0.700481332196909	2		755	1228	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162459	47162459	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	213	440	0	ENST00000409792.3:c.3667C>T	p.Gln1223Ter	p.Q1223*	ENST00000409792	NM_014159.6	1223	Caa/Taa	3/21	1	2	FACETS	0.968	0.905	1	0.968	0.905	1	CLONAL	1	TRUE	1	0.700481332196909	2		440	628	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161402	185161402	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	326	537	0	ENST00000265026.3:c.829C>T	p.His277Tyr	p.H277Y	ENST00000265026	NM_004721.4	277	Cat/Tat	4/14	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.700481332196909	2		537	857	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604223	189604224	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	353	678	2	ENST00000264731.3:c.1390_1391delinsTT	p.Pro464Leu	p.P464L	ENST00000264731	NM_003722.4	464	CCa/TTa	11/14	1	2	FACETS	0.904	0.857	0.952	0.904	0.857	0.952	CLONAL	1	TRUE	1	0.700481332196909	2		680	1115	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254487	1254488	+	missense_variant	Missense_Mutation	DNP	CC	CC	TG	novel	NA	P-0015882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	315	662	1	ENST00000310581.5:c.3290_3291delinsCA	p.Arg1097Thr	p.R1097T	ENST00000310581	NM_198253.2	1097	aGG/aCA	15/16	1	2	FACETS	0.857	0.81	0.906	0.857	0.81	0.906	CLONAL	1	TRUE	1	0.700481332196909	2		663	1049	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509774	106509774	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	343	640	0	ENST00000359195.3:c.1768C>T	p.Pro590Ser	p.P590S	ENST00000359195	NM_002649.2	590	Cct/Tct	2/11	1	2	FACETS	0.99	0.939	1	0.99	0.939	1	CLONAL	1	TRUE	1	0.700481332196909	2		640	989	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68993059	68993059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	350	396	1	ENST00000288368.4:c.1864G>A	p.Gly622Arg	p.G622R	ENST00000288368	NM_024870.2	622	Gga/Aga	17/40	0.673674037338206	2	FACETS	0.965	0.929	0.999	0.965	0.929	0.999	CLONAL	2	TRUE	0	0.700481332196909	2		397	518	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933265	39933265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	449	795	1	ENST00000378444.4:c.1334C>T	p.Ser445Phe	p.S445F	ENST00000378444	NM_001123385.1	445	tCt/tTt	4/15	1	2	FACETS	0.969	0.925	1	0.969	0.925	1	CLONAL	1	TRUE	1	0.700481332196909	2		796	1323	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650623	48650623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	359	717	0	ENST00000376670.3:c.593C>T	p.Pro198Leu	p.P198L	ENST00000376670	NM_002049.3	198	cCc/cTc	3/6	1	2	FACETS	0.971	0.922	1	0.971	0.922	1	CLONAL	1	TRUE	1	0.700481332196909	2		717	1056	SUCCESS
AR	367	MSKCC	GRCh37	X	66765277	66765277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329298379	NA	P-0015882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	344	631	0	ENST00000374690.3:c.289C>T	p.Pro97Ser	p.P97S	ENST00000374690	NM_000044.3	97	Ccc/Tcc	1/8	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.700481332196909	2		631	976	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	26	507	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.837	1	1	0.837	1	CLONAL	1	TRUE	1	0.228353690295135	2		507	215	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	rs886039483	NA	P-0015883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	21	913	0	ENST00000269305.4:c.376T>G	p.Tyr126Asp	p.Y126D	ENST00000269305	NM_001126112.2	126	Tac/Gac	5/11	1	2	FACETS	0.684	0.527	0.866	0.684	0.527	0.866	SUBCLONAL	1	TRUE	1	0.228353690295135	2		913	269	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951118	48951130	+	frameshift_variant	Frame_Shift_Del	DEL	AAGAGAAATTTGC	AAGAGAAATTTGC	-	novel	NA	P-0015883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	40	473	0	ENST00000267163.4:c.1280_1292del	p.Lys427IlefsTer26	p.K427Ifs*26	ENST00000267163	NM_000321.2	427	aAAGAGAAATTTGCt/at	13/27	0.17318604406952	3	FACETS	0.961	0.807	1	0.641	0.538	0.753	CLONAL	2	TRUE	0	0.228353690295135	3		473	203	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828125	72828125	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	47	761	1	ENST00000268489.5:c.8456C>T	p.Ser2819Phe	p.S2819F	ENST00000268489	NM_006885.3	2819	tCc/tTc	9/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.228353690295135	2		762	304	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573586	48573587	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0015883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	14	370	1	ENST00000342988.3:c.170_171del	p.Leu57TyrfsTer12	p.L57Yfs*12	ENST00000342988	NM_005359.5	57	tTA/t	2/12	1	2	FACETS	0.619	0.448	0.825	0.619	0.448	0.825	SUBCLONAL	1	TRUE	1	0.228353690295135	2		371	198	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0015884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	453	796	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.498429125192642	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.498429125192642	2		796	907	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020768	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs926053251	NA	P-0015884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	200	602	2	ENST00000358127.4:c.77T>G	p.Val26Gly	p.V26G	ENST00000358127	NM_001280556.1	26	gTt/gGt	2/10	0.211453139374483	5	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.498429125192642	5		604	944	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0015884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	108	355	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	1	2	FACETS	0.957	0.864	1	0.957	0.864	1	CLONAL	1	TRUE	1	0.498429125192642	2		355	453	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469503	25469503	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	154	514	0	ENST00000264709.3:c.1265T>C	p.Leu422Pro	p.L422P	ENST00000264709	NM_175629.2	422	cTg/cCg	10/23	0.498429125192642	3	FACETS	0.918	0.84	0.999	0.459	0.42	0.5	CLONAL	1	TRUE	1	0.498429125192642	3		514	841	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426808	121426808	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371759652	NA	P-0015884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	180	509	0	ENST00000257555.6:c.499G>A	p.Val167Ile	p.V167I	ENST00000257555		167	Gtc/Atc	2/10	0.498429125192642	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.498429125192642	1		509	523	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005327	29005327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759189221	NA	P-0015884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	95	491	1	ENST00000282397.4:c.934C>T	p.Arg312Cys	p.R312C	ENST00000282397	NM_002019.4	312	Cgt/Tgt	7/30	NA	2	FACETS	0.557	0.496	0.622			1	INDETERMINATE	1	TRUE	NA	0.498429125192642	2		492	684	SUCCESS
APC	324	MSKCC	GRCh37	5	112174916	112174916	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	100	260	0	ENST00000257430.4:c.3625G>T	p.Glu1209Ter	p.E1209*	ENST00000257430	NM_000038.5	1209	Gaa/Taa	16/16	1	2	FACETS	0.991	0.891	1	0.991	0.891	1	CLONAL	1	TRUE	1	0.498429125192642	2		260	405	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221957	98221957	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	92	433	2	ENST00000331920.6:c.2812C>T	p.Gln938Ter	p.Q938*	ENST00000331920	NM_000264.3	938	Cag/Tag	17/24	0.435327211256713	3	FACETS	0.653	0.58	0.731	0.327	0.29	0.366	SUBCLONAL	1	TRUE	1	0.498429125192642	3		435	706	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391547	139391547	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1401419952	NA	P-0015884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	362	754	1	ENST00000277541.6:c.6644C>T	p.Ser2215Leu	p.S2215L	ENST00000277541	NM_017617.3	2215	tCg/tTg	34/34	0.421730110549135	4	FACETS	0.843	0.799	0.888	0.562	0.532	0.592	CLONAL	2	TRUE	1	0.498429125192642	4		755	1291	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0015888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	127	339	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.846	0.775	0.918	0.846	0.775	0.918	CLONAL	1	TRUE	1	0.838754739331982	2		339	358	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0015888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	245	583	0				ENST00000310581	NM_198253.2	-/1132			0.298519718691507	1	FACETS	0.726	0.688	0.764	0.726	0.688	0.764	INDETERMINATE	1	TRUE	0	0.838754739331982	1		583	467	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794460	42794460	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	318	765	2	ENST00000575354.2:c.1544del	p.Pro515GlnfsTer8	p.P515Qfs*8	ENST00000575354	NM_015125.3	514	Ccc/cc	10/20	0.838754739331982	1	FACETS	0.811	0.776	0.846	0.811	0.776	0.846	CLONAL	1	TRUE	0	0.838754739331982	1		767	543	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952372	38952372	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	60	349	0	ENST00000357387.3:c.3053T>C	p.Ile1018Thr	p.I1018T	ENST00000357387	NM_152756.3	1018	aTc/aCc	30/38	0.298519718691507	1	FACETS	0.205	0.177	0.235	0.205	0.177	0.235	INDETERMINATE	1	TRUE	0	0.838754739331982	1		349	406	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338702	70338702	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	205	520	0	ENST00000374080.3:c.98A>G	p.Glu33Gly	p.E33G	ENST00000374080		33	gAg/gGg	1/45	1	2	FACETS	0.703	0.655	0.753	0.703	0.655	0.753	SUBCLONAL	1	TRUE	1	0.838754739331982	2		520	695	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0015889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	339	486	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	1	2	FACETS	0.983	0.932	1	0.983	0.932	1	CLONAL	1	TRUE	1	0.708113016496607	2		486	974	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494006	56494006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	348	608	2	ENST00000267101.3:c.3178G>A	p.Gly1060Ser	p.G1060S	ENST00000267101	NM_001982.3	1060	Ggt/Agt	26/28	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.708113016496607	2		610	974	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73333955	73333955	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1371184216	NA	P-0015889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	305	411	0	ENST00000377767.4:c.2855A>C	p.Lys952Thr	p.K952T	ENST00000377767	NM_014953.3	952	aAg/aCg	21/21	0.708113016496607	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.708113016496607	1		411	554	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630681	187630681	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1422225593	NA	P-0015889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	340	533	0	ENST00000441802.2:c.301A>G	p.Lys101Glu	p.K101E	ENST00000441802	NM_005245.3	101	Aaa/Gaa	2/27	1	2	FACETS	0.928	0.879	0.977	0.928	0.879	0.977	CLONAL	1	TRUE	1	0.708113016496607	2		533	1035	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106497	27106498	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0015890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	120	764	0	ENST00000324856.7:c.6109dup	p.Gln2037ProfsTer62	p.Q2037Pfs*62	ENST00000324856	NM_006015.4	2036	-/C	20/20	1	2	FACETS	0.79	0.713	0.872	0.79	0.713	0.872	SUBCLONAL	1	TRUE	1	0.334547590159104	2		764	908	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	401951	401952	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0015890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	70	357	1	ENST00000399788.2:c.4839_4840del	p.Asn1614LeufsTer15	p.N1614Lfs*15	ENST00000399788	NM_001042603.1	1613	caGAac/caac	27/28	0.334547590159104	3	FACETS	0.842	0.735	0.958	0.421	0.367	0.479	CLONAL	1	TRUE	1	0.334547590159104	3		358	580	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159749	20159749	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	121	516	0	ENST00000379607.5:c.10A>C	p.Asn4His	p.N4H	ENST00000379607	NM_001412.3	4	Aat/Cat	1/7	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.334547590159104	2		516	591	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0015891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	165	279	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.848004844872973	1	FACETS	0.893	0.844	0.941	0.893	0.844	0.941	CLONAL	1	TRUE	0	0.848004844872973	1		279	251	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0015893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	146	475	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	TRUE	1	0.544415012939813	2		475	431	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711874	89711874	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs786204862	NA	P-0015893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	114	334	1	ENST00000371953.3:c.493-1G>A		p.X165_splice	ENST00000371953	NM_000314.4	165			1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.544415012939813	2		335	397	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs770248150	NA	P-0015893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	243	430	0	ENST00000311936.3:c.351A>T	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaT	4/5	0.544415012939813	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.544415012939813	3		430	545	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720853	89720854	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATACT	novel	NA	P-0015893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	119	296	0	ENST00000371953.3:c.1005_1009dup	p.Phe337TyrfsTer9	p.F337Yfs*9	ENST00000371953	NM_000314.4	335	cga/cgATACTa	8/9	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.544415012939813	2		296	386	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604652	48604652	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	106	262	0	ENST00000342988.3:c.1474G>T	p.Val492Phe	p.V492F	ENST00000342988	NM_005359.5	492	Gtt/Ttt	12/12	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.544415012939813	2		262	357	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274899	41274899	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	124	456	0	ENST00000349496.5:c.1149G>T	p.Trp383Cys	p.W383C	ENST00000349496	NM_001904.3	383	tgG/tgT	8/15	1	2	FACETS	0.885	0.804	0.968	0.885	0.804	0.968	CLONAL	1	TRUE	1	0.544415012939813	2		456	515	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453132	140453132	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913365	NA	P-0015893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	450	469	0	ENST00000288602.6:c.1803A>C	p.Lys601Asn	p.K601N	ENST00000288602	NM_004333.4	601	aaA/aaC	15/18	0.544415012939813	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	1	0.544415012939813	4		469	812	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133392	38133392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	94	252	0	ENST00000317025.8:c.4081G>A	p.Glu1361Lys	p.E1361K	ENST00000317025	NM_023034.1	1361	Gag/Aag	24/24	0.544415012939813	3	FACETS	0.974	0.871	1	0.487	0.435	0.542	CLONAL	1	TRUE	1	0.544415012939813	3		252	451	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325683	87325683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	155	380	0	ENST00000277120.3:c.560C>T	p.Ala187Val	p.A187V	ENST00000277120		187	gCa/gTa	6/19	0.544415012939813	3	FACETS	1	0.943	1	0.517	0.475	0.562	CLONAL	1	TRUE	1	0.544415012939813	3		380	700	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	123	248	0				ENST00000310581	NM_198253.2	-/1132			0.249187726402702	3	FACETS	0.955	0.867	1	0.955	0.867	1	CLONAL	2	TRUE	1	0.249187726402702	3		248	581	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0015895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	96	704	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.233216949752056	3	FACETS	0.982	0.88	1	0.655	0.587	0.727	CLONAL	2	TRUE	0	0.249187726402702	3		705	441	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0015895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	141	519	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.249187726402702	6	FACETS	0.88	0.804	0.96	0.88	0.804	0.96	CLONAL	3	TRUE	3	0.249187726402702	6		519	642	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0015895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	217	844	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	0.249187726402702	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.249187726402702	3		844	931	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0015895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	383	805	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.248612849745841	2	FACETS	0.975	0.928	1	1	0.995	1	CLONAL	3	TRUE	0	0.249187726402702	2		807	1051	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945647	206945647	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550164520	NA	P-0015895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	147	518	0	ENST00000423557.1:c.134G>A	p.Arg45Gln	p.R45Q	ENST00000423557	NM_000572.2	45	cGa/cAa	1/5	0.249187726402702	3	FACETS	0.999	0.915	1	0.999	0.915	1	CLONAL	2	TRUE	1	0.249187726402702	3		518	664	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446309	70446309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	114	734	1	ENST00000373644.4:c.5249C>T	p.Pro1750Leu	p.P1750L	ENST00000373644	NM_030625.2	1750	cCt/cTt	11/12	0.249187726402702	3	FACETS	1	0.942	1	0.534	0.48	0.592	CLONAL	1	TRUE	1	0.249187726402702	3		735	963	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572104	64572104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141679530	NA	P-0015895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	383	619	0	ENST00000312049.6:c.1535C>T	p.Ser512Leu	p.S512L	ENST00000312049	NM_130799.2	512	tCa/tTa	10/10	0.249187726402702	5	FACETS	0.883	0.84	0.928	1	0.991	1	CLONAL	4	TRUE	2	0.249187726402702	5		619	1195	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930723	32930723	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507388	NA	P-0015895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	139	510	0	ENST00000380152.3:c.7594C>T	p.Pro2532Ser	p.P2532S	ENST00000380152		2532	Ccc/Tcc	15/27	0.249187726402702	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	1	0.249187726402702	3		510	595	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281001	49281001	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	92	676	0	ENST00000282018.3:c.48A>C	p.Glu16Asp	p.E16D	ENST00000282018	NM_020377.2	16	gaA/gaC	1/1	0.249187726402702	3	FACETS	1	0.979	1	0.726	0.646	0.81	CLONAL	1	TRUE	1	0.249187726402702	3		676	572	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828836	72828836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1317112594	NA	P-0015895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	179	500	0	ENST00000268489.5:c.7745C>T	p.Pro2582Leu	p.P2582L	ENST00000268489	NM_006885.3	2582	cCa/cTa	9/10	0.249187726402702	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.249187726402702	3		500	739	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117173	7117173	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764041031	NA	P-0015895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	224	630	0	ENST00000302850.5:c.4043C>T	p.Ser1348Leu	p.S1348L	ENST00000302850	NM_000208.2	1348	tCg/tTg	22/22	0.249187726402702	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.249187726402702	3		630	860	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872492	136872492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	33	283	0	ENST00000241393.3:c.1006G>A	p.Gly336Arg	p.G336R	ENST00000241393	NM_003467.2	336	Gga/Aga	2/2	1	2	FACETS	0.742	0.605	0.896	0.742	0.605	0.896	SUBCLONAL	1	TRUE	1	0.249187726402702	2		283	357	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164865	36164865	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	192	680	5	ENST00000300305.3:c.1010C>T	p.Pro337Leu	p.P337L	ENST00000300305		337	cCc/cTc	8/8	0.249187726402702	3	FACETS	1	0.985	1	0.636	0.587	0.688	CLONAL	1	TRUE	1	0.249187726402702	3		685	1362	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199940	138199940	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	156	408	0	ENST00000237289.4:c.1358C>T	p.Ser453Phe	p.S453F	ENST00000237289	NM_001270507.1	453	tCc/tTc	7/9	0.249187726402702	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.249187726402702	3		408	610	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161990433	161990433	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1257682809	NA	P-0015895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	92	633	0	ENST00000366898.1:c.887C>A	p.Ser296Tyr	p.S296Y	ENST00000366898	NM_004562.2	296	tCc/tAc	8/12	0.249187726402702	3	FACETS	1	0.977	1	0.705	0.627	0.787	CLONAL	1	TRUE	1	0.249187726402702	3		633	589	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90976659	90976659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	72	553	0	ENST00000265433.3:c.973C>T	p.Pro325Ser	p.P325S	ENST00000265433	NM_002485.4	325	Cct/Tct	8/16	0.249187726402702	3	FACETS	1	0.97	1	0.694	0.608	0.786	CLONAL	1	TRUE	1	0.249187726402702	3		553	468	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	169	248	0				ENST00000310581	NM_198253.2	-/1132			0.231319391700356	2	FACETS	1	0.99	1	0.742	0.687	0.798	INDETERMINATE	1	TRUE	0	0.451065346292335	2		248	505	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0015895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	314	704	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.236069953797559	3	FACETS	0.962	0.91	1	0.641	0.607	0.676	INDETERMINATE	2	TRUE	0	0.451065346292335	3		705	887	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0015895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	647	519	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.451065346292335	5	FACETS	0.926	0.895	0.957	1	0.996	1	CLONAL	4	TRUE	2	0.451065346292335	5		519	1299	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0015895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	297	844	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	1	2	FACETS	0.974	0.916	1	0.974	0.916	1	CLONAL	1	TRUE	1	0.451065346292335	2		844	1352	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0015895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	638	805	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.451065346292335	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.451065346292335	2		807	1326	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945647	206945647	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550164520	NA	P-0015895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	177	518	0	ENST00000423557.1:c.134G>A	p.Arg45Gln	p.R45Q	ENST00000423557	NM_000572.2	45	cGa/cAa	1/5	1	2	FACETS	0.912	0.841	0.985	0.912	0.841	0.985	CLONAL	1	TRUE	1	0.451065346292335	2		518	861	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446309	70446309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	264	734	1	ENST00000373644.4:c.5249C>T	p.Pro1750Leu	p.P1750L	ENST00000373644	NM_030625.2	1750	cCt/cTt	11/12	0.27587619722153	3	FACETS	1	0.953	1	0.512	0.478	0.546	CLONAL	1	TRUE	1	0.451065346292335	3		735	1402	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572104	64572104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141679530	NA	P-0015895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	307	619	0	ENST00000312049.6:c.1535C>T	p.Ser512Leu	p.S512L	ENST00000312049	NM_130799.2	512	tCa/tTa	10/10	0.210075086249897	4	FACETS	0.857	0.808	0.908	0.857	0.808	0.908	INDETERMINATE	2	TRUE	2	0.451065346292335	4		619	1152	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828836	72828836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1317112594	NA	P-0015895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	182	500	0	ENST00000268489.5:c.7745C>T	p.Pro2582Leu	p.P2582L	ENST00000268489	NM_006885.3	2582	cCa/cTa	9/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.451065346292335	2		500	741	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117173	7117173	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764041031	NA	P-0015895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	246	630	0	ENST00000302850.5:c.4043C>T	p.Ser1348Leu	p.S1348L	ENST00000302850	NM_000208.2	1348	tCg/tTg	22/22	0.190151356168677	3	FACETS	1	0.986	1	0.594	0.555	0.635	INDETERMINATE	1	TRUE	1	0.451065346292335	3		630	1125	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872492	136872492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	184	283	0	ENST00000241393.3:c.1006G>A	p.Gly336Arg	p.G336R	ENST00000241393	NM_003467.2	336	Gga/Aga	2/2	0.341588349302494	2	FACETS	0.791	0.736	0.847	0.791	0.736	0.847	SUBCLONAL	2	TRUE	0	0.451065346292335	2		283	516	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164865	36164865	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	134	680	5	ENST00000300305.3:c.1010C>T	p.Pro337Leu	p.P337L	ENST00000300305		337	cCc/cTc	8/8	0.312905491620594	1	FACETS	0.469	0.425	0.515	0.469	0.425	0.515	SUBCLONAL	1	TRUE	0	0.451065346292335	1		685	981	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199940	138199940	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	140	408	0	ENST00000237289.4:c.1358C>T	p.Ser453Phe	p.S453F	ENST00000237289	NM_001270507.1	453	tCc/tTc	7/9	0.283140683268901	1	FACETS	0.917	0.84	0.997	0.917	0.84	0.997	CLONAL	1	TRUE	0	0.451065346292335	1		408	524	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161990433	161990433	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1257682809	NA	P-0015895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	169	633	0	ENST00000366898.1:c.887C>A	p.Ser296Tyr	p.S296Y	ENST00000366898	NM_004562.2	296	tCc/tAc	8/12	0.283140683268901	1	FACETS	0.742	0.683	0.803	0.742	0.683	0.803	SUBCLONAL	1	TRUE	0	0.451065346292335	1		633	782	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90976659	90976659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	124	553	0	ENST00000265433.3:c.973C>T	p.Pro325Ser	p.P325S	ENST00000265433	NM_002485.4	325	Cct/Tct	8/16	1	2	FACETS	0.867	0.786	0.952	0.867	0.786	0.952	CLONAL	1	TRUE	1	0.451065346292335	2		553	634	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151174470	151174470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	60	521	0	ENST00000262187.5:c.224C>T	p.Ser75Phe	p.S75F	ENST00000262187	NM_005614.3	75	tCc/tTc	4/8	0.236069953797559	3	FACETS	0.487	0.419	0.562	0.162	0.139	0.188	INDETERMINATE	1	TRUE	0	0.451065346292335	3		521	669	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0015896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	182	790	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.244891800561092	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.244891800561092	1		792	942	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948136	178948136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	51	229	0	ENST00000263967.3:c.2908G>A	p.Glu970Lys	p.E970K	ENST00000263967	NM_006218.2	970	Gaa/Aaa	20/21	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.244891800561092	2		229	358	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727430	66727430	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910099707	NA	P-0015896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	61	319	0	ENST00000307102.5:c.146G>A	p.Arg49His	p.R49H	ENST00000307102	NM_002755.3	49	cGc/cAc	2/11	1	2	FACETS	0.825	0.711	0.948	0.825	0.711	0.948	CLONAL	1	TRUE	1	0.244891800561092	2		319	604	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745474	162745474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	49	402	0	ENST00000367921.3:c.1889C>T	p.Ser630Phe	p.S630F	ENST00000367921	NM_006182.2	630	tCt/tTt	15/18	0.553166194570338	6	FACETS	0.382	0.322	0.448	0.076	0.064	0.09	SUBCLONAL	1	TRUE	1	0.553166194570338	6		402	977	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778728	76778728	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0015903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	278	493	0	ENST00000373344.5:c.6849+2T>C		p.X2283_splice	ENST00000373344	NM_000489.3	2283			0.553168652016087	4	FACETS	1	0.977	1			1	CLONAL	2	TRUE	NA	0.553166194570338	4		493	733	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0015904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	363	467	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.331766985018126	3	FACETS	0.983	0.939	1	0.983	0.939	1	CLONAL	3	TRUE	0	0.378097096060878	3		468	774	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0015904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	109	279	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.378097096060878	6	FACETS	0.952	0.858	1			1	CLONAL	2	TRUE	NA	0.378097096060878	6		279	532	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265427	152265427	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	96	535	0	ENST00000206249.3:c.880A>C	p.Ser294Arg	p.S294R	ENST00000206249	NM_000125.3	294	Agc/Cgc	4/8	0.372111785042842	3	FACETS	0.852	0.759	0.95	0.426	0.379	0.475	CLONAL	1	TRUE	1	0.378097096060878	3		535	709	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877391	40877391	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372713520	NA	P-0015904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	140	664	0	ENST00000373198.4:c.2305G>A	p.Val769Met	p.V769M	ENST00000373198	NM_133170.3	769	Gtg/Atg	15/32	NA	2	FACETS	0.983	0.897	1			1	INDETERMINATE	1	TRUE	NA	0.378097096060878	2		664	753	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604624	43604624	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	143	685	2	ENST00000355710.3:c.1209C>A	p.His403Gln	p.H403Q	ENST00000355710	NM_020975.4	403	caC/caA	6/20	1	2	FACETS	0.955	0.871	1	0.955	0.871	1	CLONAL	1	TRUE	1	0.378097096060878	2		687	792	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135307	2135307	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	138	708	0	ENST00000219476.3:c.4646A>T	p.Tyr1549Phe	p.Y1549F	ENST00000219476	NM_000548.3	1549	tAt/tTt	36/42	0.303066827264569	4	FACETS	1	0.933	1	0.344	0.312	0.377	CLONAL	1	TRUE	1	0.378097096060878	4		708	975	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844140	68844140	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	124	645	0	ENST00000261769.5:c.728A>G	p.Glu243Gly	p.E243G	ENST00000261769	NM_004360.3	243	gAg/gGg	6/16	1	2	FACETS	0.869	0.786	0.955	0.869	0.786	0.955	CLONAL	1	TRUE	1	0.378097096060878	2		645	755	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229356	5229356	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	novel	NA	P-0015904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	145	825	0	ENST00000357368.4:c.2350-3C>T		p.X784_splice	ENST00000357368	NM_002850.3	784			1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.378097096060878	2		825	766	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314611	30314613	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0015904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	133	687	0	ENST00000262643.3:c.1163_1165del	p.Pro388del	p.P388del	ENST00000262643	NM_001238.2	387	tCTCct/tct	12/12	1	2	FACETS	0.858	0.779	0.941	0.858	0.779	0.941	CLONAL	1	TRUE	1	0.378097096060878	2		687	820	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098765	47098765	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs754096506	NA	P-0015904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	150	740	0	ENST00000409792.3:c.6509G>T	p.Gly2170Val	p.G2170V	ENST00000409792	NM_014159.6	2170	gGt/gTt	15/21	0.364435550488554	2	FACETS	1	0.952	1	0.529	0.484	0.576	CLONAL	1	TRUE	0	0.378097096060878	2		740	750	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673798	176673798	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0015904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	87	545	2	ENST00000439151.2:c.4497+1G>T		p.X1499_splice	ENST00000439151	NM_022455.4	1499			0.372111785042842	3	FACETS	0.804	0.711	0.902	0.402	0.355	0.451	CLONAL	1	TRUE	1	0.378097096060878	3		547	681	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790884	89790884	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747140961	NA	P-0015904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	224	614	0	ENST00000336032.3:c.271C>T	p.Arg91Trp	p.R91W	ENST00000336032	NM_006813.2	91	Cgg/Tgg	1/2	0.378097096060878	2	FACETS	0.85	0.795	0.906	0.85	0.795	0.906	CLONAL	2	TRUE	0	0.378097096060878	2		614	697	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760789	133760789	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	224	644	0	ENST00000318560.5:c.3112G>T	p.Ala1038Ser	p.A1038S	ENST00000318560	NM_005157.4	1038	Gcg/Tcg	11/11	0.25892341678014	4	FACETS	0.965	0.9	1	0.965	0.9	1	CLONAL	2	TRUE	2	0.378097096060878	4		644	846	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0015905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	116	644	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	0.498472033537759	3	FACETS	0.956	0.864	1	0.478	0.432	0.527	CLONAL	1	TRUE	1	0.498472033537759	3		644	608	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0015905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	262	467	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.478594854282894	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.498472033537759	2		468	503	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758774	41758774	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs758985963	NA	P-0015905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	46	625	3	ENST00000301178.4:c.1828C>T	p.Arg610Ter	p.R610*	ENST00000301178	NM_021913.4	610	Cga/Tga	16/20	NA	2	FACETS	0.287	0.241	0.339			1	INDETERMINATE	1	TRUE	NA	0.498472033537759	2		628	642	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211778	36211778	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1206043749	NA	P-0015905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	72	669	0	ENST00000222270.7:c.1529G>C	p.Ser510Thr	p.S510T	ENST00000222270	NM_014727.1	510	aGt/aCt	3/37	NA	2	FACETS	0.474	0.414	0.539			1	INDETERMINATE	1	TRUE	NA	0.498472033537759	2		669	609	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267008	41267008	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	158	350	0	ENST00000349496.5:c.679G>T	p.Gly227Cys	p.G227C	ENST00000349496	NM_001904.3	227	Ggc/Tgc	5/15	0.498472033537759	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.498472033537759	1		350	475	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0015907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	77	414	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	0.235460151853211	2		414	586	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458572	12458572	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	100	618	0	ENST00000287820.6:c.1189G>C	p.Glu397Gln	p.E397Q	ENST00000287820	NM_015869.4	397	Gag/Cag	6/7	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.235460151853211	2		618	839	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894228	NA	P-0015910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	59	462	0	ENST00000451590.1:c.37G>C	p.Gly13Arg	p.G13R	ENST00000451590	NM_001130442.1	13	Ggt/Cgt	2/5	0.193183589289468	0	FACETS	0.297	0.255	0.342			1	INDETERMINATE	1	TRUE	0	0.41	0		462	572	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842076	68842596	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTGGACACTAAGAAGGATAAAAAGAGAATGCAGTCTTTACGATATAGCAAAGGGTCTCATTGGTTTTTGTTTTGATTGGTCATTTTGGTGGATATATATAATTTGTCATTGATAAGAGAATGTGTCATTAAATTCAAACTGTACACTGCCCACAGAAGGCTGGGGACGCTGTCTGGCTAGGTTGGACTGTTAGACCTGAAGTATCCGTCTTGAATTGTCTTATCTTGTTCCTCATCTTCTTTCCTTTTAGGCCTCCGTTTCTGGAATCCAAGCAGAATTGCTCACATTTCCCAACTCCTCTCCTGGCCTCAGAAGACAGAAGAGAGACTGGGTTATTCCTCCCATCAGCTGCCCAGAAAATGAAAAAGGCCCATTTCCTAAAAACCTGGTTCAGGTAGAGAAAGAAGTTCTCTGTTTCTCTGGGAGGGATTTGGCAGAGAAGTACCAAGGAGAGAAAGGGAAAAGACCCAGTGTTGGGATCCTTCTTTACTAATTCTTTTTCTTTCATTTTGTCTTCAGA	TCTGGACACTAAGAAGGATAAAAAGAGAATGCAGTCTTTACGATATAGCAAAGGGTCTCATTGGTTTTTGTTTTGATTGGTCATTTTGGTGGATATATATAATTTGTCATTGATAAGAGAATGTGTCATTAAATTCAAACTGTACACTGCCCACAGAAGGCTGGGGACGCTGTCTGGCTAGGTTGGACTGTTAGACCTGAAGTATCCGTCTTGAATTGTCTTATCTTGTTCCTCATCTTCTTTCCTTTTAGGCCTCCGTTTCTGGAATCCAAGCAGAATTGCTCACATTTCCCAACTCCTCTCCTGGCCTCAGAAGACAGAAGAGAGACTGGGTTATTCCTCCCATCAGCTGCCCAGAAAATGAAAAAGGCCCATTTCCTAAAAACCTGGTTCAGGTAGAGAAAGAAGTTCTCTGTTTCTCTGGGAGGGATTTGGCAGAGAAGTACCAAGGAGAGAAAGGGAAAAGACCCAGTGTTGGGATCCTTCTTTACTAATTCTTTTTCTTTCATTTTGTCTTCAGA	-	novel	NA	P-0015910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1	57	5	0	ENST00000261769.5:c.388-249_534del		p.X130_splice	ENST00000261769	NM_004360.3	130		4-5/16	1	2	FACETS		NA	1	1	0.987	1	NA	5	TRUE	1	0.41	2		5	58	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521633	89521633	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	20	157	2	ENST00000336596.2:c.2710G>T	p.Asp904Tyr	p.D904Y	ENST00000336596	NM_005233.5	904	Gac/Tac	16/17	0.181395801691762	2	FACETS	0.407	0.311	0.519	0.204	0.155	0.26	INDETERMINATE	1	TRUE	0	0.34	2		159	289	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513012	106513012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758968659	NA	P-0015911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	66	67	0	ENST00000359195.3:c.2026G>A	p.Ala676Thr	p.A676T	ENST00000359195	NM_002649.2	676	Gcc/Acc	3/11	1	2	FACETS	0.783	0.688	0.883	1	0.976	1	SUBCLONAL	2	TRUE	1	0.34	2		67	248	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889128	76889128	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	17	119	0	ENST00000373344.5:c.4882C>G	p.Leu1628Val	p.L1628V	ENST00000373344	NM_000489.3	1628	Ctt/Gtt	18/35	0.190224008297367	2	FACETS	0.472	0.353	0.612	0.236	0.176	0.306	INDETERMINATE	1	TRUE	0	0.34	2		119	212	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11270884	11270884	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	23	59	0	ENST00000361445.4:c.3641G>T	p.Cys1214Phe	p.C1214F	ENST00000361445	NM_004958.3	1214	tGc/tTc	24/58	0.290976635466527	3	FACETS	0.638	0.499	0.798			1	SUBCLONAL	1	TRUE	NA	0.34	3		59	248	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741517	17741517	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs147517396	NA	P-0015911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	42	56	0	ENST00000250003.3:c.188C>A	p.Ser63Ter	p.S63*	ENST00000250003	NM_002478.4	63	tCg/tAg	1/3	1	2	FACETS	0.642	0.537	0.758	0.642	0.537	0.758	SUBCLONAL	1	TRUE	1	0.34	2		56	385	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77051795	77051830	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCCCACGAGGTAACTGCAGGAATACAGATAAAGGG	CTCCCACGAGGTAACTGCAGGAATACAGATAAAGGG	-	novel	NA	P-0015911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	44	142	0	ENST00000356341.3:c.999-22_1012del		p.X333_splice	ENST00000356341	NM_002576.4	333		11/15	1	2	FACETS	0.735	0.619	0.864	0.735	0.619	0.864	SUBCLONAL	1	TRUE	1	0.34	2		142	352	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446793	49446793	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	27	73	0	ENST00000301067.7:c.1017G>A	p.Trp339Ter	p.W339*	ENST00000301067	NM_003482.3	339	tgG/tgA	8/54	0.3	1	FACETS	0.342	0.272	0.423	0.342	0.272	0.423	SUBCLONAL	1	TRUE	0	0.34	1		73	385	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869578	102869578	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0015911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	33	141	0	ENST00000307046.8:c.64-1G>A		p.X22_splice	ENST00000307046	NM_001111285.1	22			NA	2	FACETS	0.484	0.394	0.585			1	INDETERMINATE	1	TRUE	NA	0.34	2		141	401	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878166	48878166	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	31	50	0	ENST00000267163.4:c.118G>T	p.Glu40Ter	p.E40*	ENST00000267163	NM_000321.2	40	Gag/Tag	1/27	0.3	1	FACETS	0.823	0.672	0.99	0.823	0.672	0.99	CLONAL	1	TRUE	0	0.34	1		50	184	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897394	78897394	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	74	75	0	ENST00000306801.3:c.2729G>T	p.Gly910Val	p.G910V	ENST00000306801	NM_020761.2	910	gGc/gTc	23/34	1	2	FACETS	0.978	0.86	1	0.978	0.86	1	CLONAL	1	TRUE	1	0.34	2		75	445	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220476	1220477	+	missense_variant	Missense_Mutation	DNP	TC	TC	CT	novel	NA	P-0015911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	85	98	0	ENST00000326873.7:c.569_570delinsCT	p.Leu190Pro	p.L190P	ENST00000326873	NM_000455.4	190	cTC/cCT	4/10	0.290976635466527	3	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.34	3		98	399	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299979	15299979	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	85	45	0	ENST00000263388.2:c.1199A>T	p.Asn400Ile	p.N400I	ENST00000263388	NM_000435.2	400	aAc/aTc	8/33	0.247307785672659	4	FACETS	0.891	0.793	0.994			1	CLONAL	2	TRUE	NA	0.34	4		45	376	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877463	40877463	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0015911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	23	63	0	ENST00000373198.4:c.2234-1G>C		p.X745_splice	ENST00000373198	NM_133170.3	745			1	2	FACETS	0.541	0.423	0.677	0.541	0.423	0.677	SUBCLONAL	1	TRUE	1	0.34	2		63	250	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542249	187542249	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	29	48	0	ENST00000441802.2:c.5491A>G	p.Thr1831Ala	p.T1831A	ENST00000441802	NM_005245.3	1831	Aca/Gca	10/27	NA	2	FACETS	0.669	0.539	0.815			1	INDETERMINATE	1	TRUE	NA	0.34	2		48	255	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739669	41739669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	72	116	0	ENST00000242208.4:c.304G>A	p.Glu102Lys	p.E102K	ENST00000242208	NM_002192.2	102	Gag/Aag	2/3	1	2	FACETS	0.952	0.835	1	0.952	0.835	1	CLONAL	1	TRUE	1	0.34	2		116	445	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339536	81339536	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	37	174	0	ENST00000222390.5:c.1468del	p.Thr490ArgfsTer7	p.T490Rfs*7	ENST00000222390	NM_000601.4	490	Acg/cg	13/18	1	2	FACETS	0.6	0.495	0.716	0.6	0.495	0.716	SUBCLONAL	1	TRUE	1	0.34	2		174	363	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157988	27157988	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	56	143	0	ENST00000380036.4:c.212C>G	p.Pro71Arg	p.P71R	ENST00000380036	NM_000459.3	71	cCg/cGg	2/23	1	2	FACETS	0.898	0.772	1	0.898	0.772	1	CLONAL	1	TRUE	1	0.34	2		143	367	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341485	70341485	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	31	90	0	ENST00000374080.3:c.920T>A	p.Leu307Gln	p.L307Q	ENST00000374080		307	cTg/cAg	7/45	0.190224008297367	2	FACETS	0.413	0.333	0.502	0.206	0.166	0.251	INDETERMINATE	1	TRUE	0	0.34	2		90	442	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813107	76813107	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	28	117	0	ENST00000373344.5:c.6514del	p.Glu2172LysfsTer9	p.E2172Kfs*9	ENST00000373344	NM_000489.3	2172	Gaa/aa	30/35	0.190224008297367	2	FACETS	0.92	0.742	1	0.46	0.371	0.56	INDETERMINATE	1	TRUE	0	0.34	2		117	179	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152857997	152857997	+	synonymous_variant	Silent	SNP	G	G	T	novel	NA	P-0015911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	49	29	0	ENST00000406277.2:c.618C>A	p.Pro206=	p.P206=	ENST00000406277	NM_152274.4	206	ccC/ccA	6/7	0.190224008297367	2	FACETS	1	0.962	1	0.71	0.609	0.818	INDETERMINATE	1	TRUE	0	0.34	2		29	203	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0015911-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	494	563	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	NA	2	FACETS	1	0.968	1			1	INDETERMINATE	2	TRUE	NA	0.548663461346184	2		564	896	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0015911-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	76	668	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.44680318044894	3	FACETS	0.63	0.554	0.713	0.21	0.184	0.238	SUBCLONAL	1	TRUE	0	0.548663461346184	3		671	560	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282214	38282214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121909645	NA	P-0015911-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	120	57	0	ENST00000425967.3:c.842G>A	p.Arg281Gln	p.R281Q	ENST00000425967	NM_001174067.1	281	cGg/cAg	8/19	0.21475145076089	3	FACETS	1	0.961	1	0.554	0.503	0.608	INDETERMINATE	1	TRUE	1	0.548663461346184	3		57	503	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035935	47035935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015911-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	67	78	0	ENST00000377604.3:c.613C>T	p.His205Tyr	p.H205Y	ENST00000377604	NM_001204468.1	205	Cac/Tac	7/24	0.548663461346184	4	FACETS	0.421	0.365	0.482	0.14	0.121	0.161	SUBCLONAL	1	TRUE	1	0.548663461346184	4		78	898	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0015912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	72	339	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	0.985	1	CLONAL	2	TRUE	1	0.316870584824213	2		339	204	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0015912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	760	796	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.316870584824213	2	FACETS	1	0.997	1	1	0.999	1	CLONAL	5	TRUE	0	0.316870584824213	2		796	886	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76919020	76919020	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0015912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	76	106	0	ENST00000373344.5:c.3971C>G	p.Ser1324Ter	p.S1324*	ENST00000373344	NM_000489.3	1324	tCa/tGa	12/35	1	1	FACETS	1	0.976	1	1	0.99	1	CLONAL	4	TRUE	0	0.316870584824213	1		106	92	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76919036	76919036	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	56	85	0	ENST00000373344.5:c.3955C>G	p.Gln1319Glu	p.Q1319E	ENST00000373344	NM_000489.3	1319	Caa/Gaa	12/35	1	1	FACETS	1	0.964	1	1	0.987	1	CLONAL	4	TRUE	0	0.316870584824213	1		85	69	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593580	55593606	+	splice_acceptor_variant,coding_sequence_variant	In_Frame_Del	DEL	AGAAACCCATGTATGAAGTACAGTGGA	AGAAACCCATGTATGAAGTACAGTGGA	-	rs121913234	NA	P-0015913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	201	393	0	ENST00000288135.5:c.1648_1674del		p.K550_K558del	ENST00000288135	NM_000222.2	550		11/21	0.750824235999253	4	FACETS	1	0.944	1			1	CLONAL	2	TRUE	NA	0.750824235999253	4		393	465	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249029	55249029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs483352806	NA	P-0015913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	8	530	1	ENST00000275493.2:c.2327G>A	p.Arg776His	p.R776H	ENST00000275493	NM_005228.3	776	cGc/cAc	20/28	0.259058805554283	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.750824235999253	0		531	287	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038879	47038879	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	71	715	0	ENST00000377604.3:c.886G>T	p.Glu296Ter	p.E296*	ENST00000377604	NM_001204468.1	296	Gag/Tag	9/24	0.559898309865885	1	FACETS	0.325	0.285	0.367	0.325	0.285	0.367	SUBCLONAL	1	TRUE	0	0.750824235999253	1		715	364	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861518	152861533	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCAAGTAAATTGAA	GGCCAAGTAAATTGAA	-	novel	NA	P-0015913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	79	520	0	ENST00000406277.2:c.219_234del	p.Ser74AlafsTer49	p.S74Afs*49	ENST00000406277	NM_152274.4	73	tcTTCAATTTACTTGGCC/tc	4/7	0.559898309865885		FACETS		0.416	0.522				SUBCLONAL	1	TRUE	0	0.750824235999253	1		520	281	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0015915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	352	480	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.99	0.944	1	0.99	0.944	1	CLONAL	1	TRUE	1	0.928780808265351	2		481	766	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475063	40475063	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	445	535	0	ENST00000264657.5:c.1847A>G	p.Glu616Gly	p.E616G	ENST00000264657	NM_139276.2	616	gAa/gGa	20/24	1	2	FACETS	0.99	0.949	1	0.99	0.949	1	CLONAL	1	TRUE	1	0.928780808265351	2		535	968	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415656	49415656	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1057520667	NA	P-0015915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	213	265	0	ENST00000301067.7:c.16522-1G>A		p.X5508_splice	ENST00000301067	NM_003482.3	5508			1	2	FACETS	0.877	0.822	0.932	0.877	0.822	0.932	CLONAL	1	TRUE	1	0.928780808265351	2		265	523	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832607	72832607	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	190	219	2	ENST00000268489.5:c.3974C>T	p.Ser1325Leu	p.S1325L	ENST00000268489	NM_006885.3	1325	tCa/tTa	9/10	0.928780808265351	3	FACETS	1	0.966	1	0.531	0.494	0.569	CLONAL	1	TRUE	1	0.928780808265351	3		221	564	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591111	67591137	+	inframe_deletion	In_Frame_Del	DEL	AGACCTTATCCAGCTGAGAAAGACGAG	AGACCTTATCCAGCTGAGAAAGACGAG	-	novel	NA	P-0015915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	145	347	0	ENST00000274335.5:c.1709_1735del	p.Leu570_Asp578del	p.L570_D578del	ENST00000274335		568	ccAGACCTTATCCAGCTGAGAAAGACGAGa/cca	12/15	1	2	FACETS	0.648	0.595	0.702	0.648	0.595	0.702	SUBCLONAL	1	TRUE	1	0.928780808265351	2		347	482	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	226	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.791012306686262	2		248	560	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589149	67589151	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	novel	NA	P-0015919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	52	252	0	ENST00000274335.5:c.1138_1140del	p.Leu380del	p.L380del	ENST00000274335		379	aaATTa/aaa	9/15	1	2	FACETS	0.932	0.813	1	0.932	0.813	1	CLONAL	1	TRUE	1	0.791012306686262	2		252	141	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937094	48937094	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	68	190	0	ENST00000267163.4:c.861+1G>A		p.X287_splice	ENST00000267163	NM_000321.2	287			0.791012306686262	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.791012306686262	1		190	99	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857399	9857399	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	68	400	0	ENST00000330684.3:c.4002C>G	p.Ser1334Arg	p.S1334R	ENST00000330684	NM_001134407.1	1334	agC/agG	13/13	1	2	FACETS	0.292	0.254	0.334	0.292	0.254	0.334	SUBCLONAL	1	TRUE	1	0.791012306686262	2		400	588	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0015921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	135	697	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.244786309581245	4	FACETS	1	0.981	1	0.443	0.401	0.486	CLONAL	1	TRUE	1	0.244786309581245	4		698	1034	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0015921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	249	787	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.244786309581245	4	FACETS	1	0.979	1	0.742	0.693	0.792	CLONAL	2	TRUE	1	0.244786309581245	4		787	1138	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353790	68353790	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	185	294	0	ENST00000487270.1:c.625C>G	p.Leu209Val	p.L209V	ENST00000487270	NM_133509.3	209	Ctt/Gtt	7/11	0.244786309581245	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.244786309581245	3		294	734	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874470	151874470	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	63	267	0	ENST00000262189.6:c.8068G>A	p.Asp2690Asn	p.D2690N	ENST00000262189	NM_170606.2	2690	Gat/Aat	38/59	1	2	FACETS	0.872	0.755	1	0.872	0.755	1	CLONAL	1	TRUE	1	0.244786309581245	2		267	590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0015921-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	44	948	0	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.253535281784885	1	FACETS	0.496	0.415	0.585	0.496	0.415	0.585	SUBCLONAL	1	TRUE	0	0.256672900222472	1		948	603	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0015921-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	264	787	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.235343408901233	5	FACETS	1	0.973	1	0.797	0.748	0.846	CLONAL	3	TRUE	1	0.256672900222472	5		787	894	SUCCESS
ATR	545	MSKCC	GRCh37	3	142183989	142183989	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015921-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	58	916	0	ENST00000350721.4:c.6991G>T	p.Asp2331Tyr	p.D2331Y	ENST00000350721	NM_001184.3	2331	Gac/Tac	41/47	1	2	FACETS	0.552	0.473	0.638	0.552	0.473	0.638	SUBCLONAL	1	TRUE	1	0.256672900222472	2		916	819	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0015924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	136	414	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.314628574402595	4	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	FALSE	2	0.372272857810014	4		414	489	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0015924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	190	617	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.337001311740628	2	FACETS	0.902	0.839	0.966	0.902	0.839	0.966	CLONAL	2	FALSE	0	0.372272857810014	2		617	566	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795066	42795066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537583557	NA	P-0015924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	152	728	2	ENST00000575354.2:c.2146C>T	p.Arg716Trp	p.R716W	ENST00000575354	NM_015125.3	716	Cgg/Tgg	10/20	0.349592895309318	3	FACETS	0.828	0.761	0.898	0.828	0.761	0.898	CLONAL	2	FALSE	1	0.372272857810014	3		730	585	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884550	151884550	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0015924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	134	316	0	ENST00000262189.6:c.4805C>G	p.Ser1602Ter	p.S1602*	ENST00000262189	NM_170606.2	1602	tCa/tGa	33/59	0.372272857810014	3	FACETS	0.85	0.783	0.918	1	0.984	1	CLONAL	3	FALSE	1	0.372272857810014	3		316	335	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940490	31940490	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	73	846	0	ENST00000375333.2:c.523G>C	p.Val175Leu	p.V175L	ENST00000375333	NM_032454.1	175	Gtg/Ctg	3/8	0.185657662312595	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		846	821	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603023	48603023	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555687378	NA	P-0015926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	33	256	0	ENST00000342988.3:c.1324C>T	p.Gln442Ter	p.Q442*	ENST00000342988	NM_005359.5	442	Cag/Tag	11/12	1	2	FACETS	0.724	0.59	0.874	0.724	0.59	0.874	SUBCLONAL	1	TRUE	1	0.248394613350249	2		256	367	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412045	116412045	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0015926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	244	725	0	ENST00000397752.3:c.3028+2T>C		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.248394613350249	4	FACETS	0.905	0.844	0.968	0.905	0.844	0.968	CLONAL	2	TRUE	2	0.248394613350249	4		725	1355	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250250	133250250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs483352909	NA	P-0015926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	98	643	0	ENST00000320574.5:c.1270C>T	p.Leu424Phe	p.L424F	ENST00000320574	NM_006231.2	424	Ctc/Ttc	13/49	0.248394613350249	2	FACETS	0.966	0.861	1	0.483	0.43	0.539	CLONAL	1	TRUE	0	0.248394613350249	2		643	817	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99192893	99192893	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	50	389	0	ENST00000268035.6:c.83C>A	p.Thr28Lys	p.T28K	ENST00000268035	NM_000875.3	28	aCg/aAg	1/21	1	2	FACETS	0.818	0.695	0.954	0.818	0.695	0.954	CLONAL	1	TRUE	1	0.248394613350249	2		389	492	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259470	89259470	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	84	543	0	ENST00000336596.2:c.614C>A	p.Thr205Lys	p.T205K	ENST00000336596	NM_005233.5	205	aCa/aAa	3/17	0.248394613350249	3	FACETS	0.938	0.827	1	0.469	0.413	0.528	CLONAL	1	TRUE	1	0.248394613350249	3		543	811	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499126	149499126	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	70	509	0	ENST00000261799.4:c.2702G>T	p.Gly901Val	p.G901V	ENST00000261799	NM_002609.3	901	gGc/gTc	20/23	0.248394613350249	3	FACETS	0.999	0.871	1	0.5	0.435	0.569	CLONAL	1	TRUE	1	0.248394613350249	3		509	634	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411566	116411567	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	108	315	0	ENST00000397752.3:c.2745_2746insG	p.Ser916ValfsTer47	p.S916Vfs*47	ENST00000397752	NM_000245.2	915	-/G	13/21	0.248394613350249	4	FACETS	1	0.9	1	1	0.9	1	CLONAL	2	TRUE	2	0.248394613350249	4		315	543	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0015927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	220	541	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.395105067375261	4	FACETS	0.949	0.885	1	0.949	0.885	1	CLONAL	2	TRUE	2	0.400111777857113	4		541	811	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0015927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	162	315	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.395105067375261	4	FACETS	0.926	0.854	1	0.926	0.854	1	CLONAL	2	TRUE	2	0.400111777857113	4		315	612	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717714	89717718	+	frameshift_variant	Frame_Shift_Del	DEL	TTACC	TTACC	-	novel	NA	P-0015927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	255	391	0	ENST00000371953.3:c.740_744del	p.Leu247CysfsTer4	p.L247Cfs*4	ENST00000371953	NM_000314.4	247	TTACCt/t	7/9	0.400111777857113	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.400111777857113	2		391	598	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939032	48939033	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	158	237	0	ENST00000267163.4:c.869dup	p.Asn290LysfsTer20	p.N290Kfs*20	ENST00000267163	NM_000321.2	288	-/A	9/27	0.400111777857113	3	FACETS	0.87	0.809	0.932	0.87	0.809	0.932	CLONAL	3	TRUE	0	0.400111777857113	3		237	363	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322943	31322943	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	147	729	0	ENST00000412585.2:c.953T>G	p.Leu318Arg	p.L318R	ENST00000412585	NM_005514.6	318	cTa/cGa	5/8	0.400111777857113	4	FACETS	0.827	0.753	0.905	0.276	0.251	0.302	CLONAL	1	TRUE	1	0.400111777857113	4		729	1244	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs483352695	NA	P-0015928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	154	538	0	ENST00000269305.4:c.736A>T	p.Met246Leu	p.M246L	ENST00000269305	NM_001126112.2	246	Atg/Ttg	7/11	0.288859194471814	1	FACETS	0.947	0.868	1	0.947	0.868	1	CLONAL	1	TRUE	0	0.34398548354173	1		538	783	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122662	108122662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	40	428	0	ENST00000278616.4:c.1706G>T	p.Ser569Ile	p.S569I	ENST00000278616	NM_000051.3	569	aGc/aTc	11/63	0.194582431606062	1	FACETS	0.275	0.227	0.328	0.275	0.227	0.328	INDETERMINATE	1	TRUE	0	0.34398548354173	1		428	701	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237686	133237686	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	146	588	0	ENST00000320574.5:c.2929G>T	p.Gly977Trp	p.G977W	ENST00000320574	NM_006231.2	977	Ggg/Tgg	25/49	0.194582431606062	1	FACETS	0.671	0.611	0.733	0.671	0.611	0.733	INDETERMINATE	1	TRUE	0	0.34398548354173	1		588	1048	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313232	30313232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	207	466	0	ENST00000262643.3:c.926C>T	p.Ser309Leu	p.S309L	ENST00000262643	NM_001238.2	309	tCa/tTa	10/12	0.178689626972483	3	FACETS	1	0.99	1	0.71	0.659	0.763	INDETERMINATE	1	TRUE	1	0.34398548354173	3		466	993	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313431	30313431	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0015928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	226	504	0	ENST00000262643.3:c.1031C>G	p.Ser344Ter	p.S344*	ENST00000262643	NM_001238.2	344	tCa/tGa	11/12	0.178689626972483	3	FACETS	1	0.99	1	0.688	0.64	0.738	INDETERMINATE	1	TRUE	1	0.34398548354173	3		504	1119	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004879	150004879	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs769204431	NA	P-0015928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	148	356	0	ENST00000253339.5:c.1346A>G	p.His449Arg	p.H449R	ENST00000253339		449	cAt/cGt	3/7	0.252825239178064	2	FACETS	1	0.987	1	0.708	0.649	0.769	CLONAL	1	TRUE	0	0.34398548354173	2		356	608	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508251	106508251	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	100	236	0	ENST00000359195.3:c.245G>A	p.Ser82Asn	p.S82N	ENST00000359195	NM_002649.2	82	aGc/aAc	2/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.34398548354173	2		236	489	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787846	135787846	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	rs118203440	NA	P-0015928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	88	294	0	ENST00000298552.3:c.738-2A>T		p.X246_splice	ENST00000298552	NM_001162426.1	246			0.34398548354173	1	FACETS	0.969	0.863	1	0.969	0.863	1	CLONAL	1	TRUE	0	0.34398548354173	1		294	437	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0015929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	302	605	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.239509600479078	4	FACETS	1	0.95	1	1	0.95	1	CLONAL	3	TRUE	1	0.248105033531409	4		606	1005	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0015929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	76	425	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.248105033531409	5	FACETS	0.956	0.837	1			1	CLONAL	1	TRUE	NA	0.248105033531409	5		425	879	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0015929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	105	684	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	0.242560369093856	3	FACETS	0.95	0.85	1	0.475	0.425	0.529	CLONAL	1	TRUE	1	0.248105033531409	3		684	1001	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256568	16256568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	112	664	0	ENST00000375759.3:c.3833C>T	p.Ser1278Phe	p.S1278F	ENST00000375759	NM_015001.2	1278	tCc/tTc	11/15	1	2	FACETS	0.943	0.847	1	0.943	0.847	1	CLONAL	1	TRUE	1	0.248105033531409	2		664	957	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957441	175957441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	333	577	0	ENST00000367669.3:c.1955G>A	p.Gly652Glu	p.G652E	ENST00000367669	NM_022457.5	652	gGa/gAa	17/20	0.248105033531409	6	FACETS	0.962	0.911	1	0.962	0.911	1	CLONAL	4	TRUE	2	0.248105033531409	6		577	1044	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094797	2094797	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1324289477	NA	P-0015929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	120	565	1	ENST00000219066.1:c.383G>T	p.Arg128Leu	p.R128L	ENST00000219066	NM_002528.5	128	cGc/cTc	3/6	0.241126142257982	4	FACETS	1	0.975	1	0.624	0.563	0.689	CLONAL	1	TRUE	2	0.248105033531409	4		566	967	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312692	30312692	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	99	662	1	ENST00000262643.3:c.673G>A	p.Glu225Lys	p.E225K	ENST00000262643	NM_001238.2	225	Gaa/Aaa	8/12	0.242560369093856	3	FACETS	0.823	0.733	0.919	0.411	0.366	0.46	CLONAL	1	TRUE	1	0.248105033531409	3		663	1090	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172088	99172088	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	323	488	0	ENST00000074304.5:c.1654G>T	p.Glu552Ter	p.E552*	ENST00000074304	NM_001134224.1	552	Gag/Tag	17/26	0.248105033531409	5	FACETS	0.971	0.92	1	0.971	0.92	1	CLONAL	4	TRUE	1	0.248105033531409	5		488	920	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548306	41548306	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	184	536	1	ENST00000263253.7:c.3094A>T	p.Thr1032Ser	p.T1032S	ENST00000263253	NM_001429.3	1032	Act/Tct	16/31	0.242560369093856	3	FACETS	0.927	0.856	1	0.927	0.856	1	CLONAL	2	TRUE	1	0.248105033531409	3		537	899	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984897	55984897	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	164	571	0	ENST00000263923.4:c.232G>T	p.Glu78Ter	p.E78*	ENST00000263923	NM_002253.2	78	Gag/Tag	3/30	0.241126142257982	4	FACETS	0.904	0.83	0.981	0.904	0.83	0.981	CLONAL	2	TRUE	2	0.248105033531409	4		571	913	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067044	143067044	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	77	515	0	ENST00000262992.4:c.1669G>C	p.Asp557His	p.D557H	ENST00000262992	NM_001101669.1	557	Gat/Cat	16/24	0.241126142257982	4	FACETS	0.829	0.726	0.94	0.414	0.363	0.47	CLONAL	1	TRUE	2	0.248105033531409	4		515	935	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861077	35861077	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	79	434	0	ENST00000303115.3:c.206T>C	p.Leu69Pro	p.L69P	ENST00000303115	NM_002185.3	69	cTg/cCg	2/8	0.239509600479078	4	FACETS	1	0.891	1	0.338	0.297	0.383	CLONAL	1	TRUE	1	0.248105033531409	4		434	783	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120283	94120283	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	50	337	0	ENST00000369303.4:c.768G>T	p.Trp256Cys	p.W256C	ENST00000369303	NM_004440.3	256	tgG/tgT	3/17	1	2	FACETS	0.894	0.759	1	0.894	0.759	1	CLONAL	1	TRUE	1	0.248105033531409	2		337	451	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983095	149983095	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	98	582	0	ENST00000253339.5:c.3163G>C	p.Glu1055Gln	p.E1055Q	ENST00000253339		1055	Gaa/Caa	7/7	1	2	FACETS	0.94	0.838	1	0.94	0.838	1	CLONAL	1	TRUE	1	0.248105033531409	2		582	840	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845126	151845126	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	68	499	0	ENST00000262189.6:c.13886C>A	p.Ser4629Ter	p.S4629*	ENST00000262189	NM_170606.2	4629	tCa/tAa	52/59	0.248105033531409	5	FACETS	0.814	0.706	0.931	0.271	0.235	0.311	CLONAL	1	TRUE	2	0.248105033531409	5		499	924	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371984	55371984	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	137	655	2	ENST00000297316.4:c.674C>A	p.Ser225Tyr	p.S225Y	ENST00000297316	NM_022454.3	225	tCc/tAc	2/2	0.248105033531409	5	FACETS	1	0.972	1	0.296	0.268	0.325	CLONAL	1	TRUE	1	0.248105033531409	5		657	1282	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028091	69028091	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776025075	NA	P-0015929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1250	286	906	3	ENST00000288368.4:c.3250C>T	p.Arg1084Trp	p.R1084W	ENST00000288368	NM_024870.2	1084	Cgg/Tgg	26/40	0.248105033531409	5	FACETS	1	0.959	1	0.515	0.483	0.548	CLONAL	2	TRUE	1	0.248105033531409	5		909	1536	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006014	22006014	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	417	714	2	ENST00000276925.6:c.389G>T	p.Gly130Val	p.G130V	ENST00000276925	NM_004936.3	130	gGg/gTg	2/2	0.248105033531409	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	3	TRUE	0	0.248105033531409	3		716	1241	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	186	792	1	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	1	2	FACETS	0.881	0.812	0.954	0.881	0.812	0.954	CLONAL	1	TRUE	1	0.322889339792227	2		793	1307	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115755	8115879	+	frameshift_variant	Frame_Shift_Del	DEL	AATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAGAACAGCTCGTTTAACCCGGCCGCCCTCTCCAGACACATGTCCTCCCTGAGCCACATCTCGCCCT	AATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAGAACAGCTCGTTTAACCCGGCCGCCCTCTCCAGACACATGTCCTCCCTGAGCCACATCTCGCCCT	-	novel	NA	P-0015930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	104	670	0	ENST00000346208.3:c.1101_1225del	p.Lys367AsnfsTer98	p.K367Nfs*98	ENST00000346208		367	aaAATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAGAACAGCTCGTTTAACCCGGCCGCCCTCTCCAGACACATGTCCTCCCTGAGCCACATCTCGCCCTtc/aatc	6/6	1	2	FACETS	0.585	0.522	0.651	0.585	0.522	0.651	SUBCLONAL	1	TRUE	1	0.322889339792227	2		670	1102	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278093	41278093	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	111	373	0	ENST00000349496.5:c.1969G>A	p.Ala657Thr	p.A657T	ENST00000349496	NM_001904.3	657	Gct/Act	13/15	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.322889339792227	2		373	676	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056999	180056999	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1237	191	878	0	ENST00000261937.6:c.620A>T	p.Glu207Val	p.E207V	ENST00000261937	NM_182925.4	207	gAg/gTg	5/30	1	2	FACETS	0.828	0.764	0.896	0.828	0.764	0.896	CLONAL	1	TRUE	1	0.322889339792227	2		878	1428	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248151	110248151	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	152	455	0	ENST00000374672.4:c.1321G>T	p.Asp441Tyr	p.D441Y	ENST00000374672	NM_004235.4	441	Gat/Tat	5/5	1	2	FACETS	0.982	0.897	1	0.982	0.897	1	CLONAL	1	TRUE	1	0.322889339792227	2		455	959	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0015931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	319	641	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.534026898748218	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	0	0.534026898748218	1		641	872	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	240	776	1	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.534026898748218	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	0	0.534026898748218	1		777	648	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259141	36259141	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	222	599	0	ENST00000300305.3:c.350del	p.Lys117ArgfsTer5	p.K117Rfs*5	ENST00000300305		117	aAg/ag	3/8	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.534026898748218	2		599	794	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44910951	44910951	+	splice_region_variant,intron_variant	Splice_Region	SNP	T	T	C	rs1024351607	NA	P-0015931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	157	445	2	ENST00000377967.4:c.655-3T>C		p.X219_splice	ENST00000377967	NM_021140.2	219			1	2	FACETS	0.92	0.846	0.997	0.92	0.846	0.997	CLONAL	1	FALSE	1	0.534026898748218	2		447	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0015932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	433	719	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.457616549291864	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.454660205120406	2		720	812	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023918	27023918	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	55	136	0	ENST00000324856.7:c.1024G>C	p.Ala342Pro	p.A342P	ENST00000324856	NM_006015.4	342	Gcg/Ccg	1/20	0.290409650170065	2	FACETS	1	0.962	1	0.657	0.572	0.747	CLONAL	1	TRUE	0	0.454660205120406	2		136	184	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746141	162746141	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	108	350	0	ENST00000367921.3:c.2264C>G	p.Ser755Cys	p.S755C	ENST00000367921	NM_006182.2	755	tCt/tGt	16/18	0.454660205120406	6	FACETS	1	0.96	1	0.228	0.205	0.254	CLONAL	1	TRUE	1	0.454660205120406	6		350	794	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333688	70333694	+	protein_altering_variant	In_Frame_Del	DEL	CCAACTC	CCAACTC	AAAT	novel	NA	P-0015932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	199	585	3	ENST00000373644.4:c.1593_1599delinsAAAT	p.Gln532_Leu533delinsAsn	p.Q532_L533delinsN	ENST00000373644	NM_030625.2	531	gcCCAACTC/gcAAAT	2/12	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.454660205120406	2		588	643	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857787	57857799	+	frameshift_variant	Frame_Shift_Del	DEL	TCTGGCCCGCCCT	TCTGGCCCGCCCT	-	novel	NA	P-0015932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	158	732	0	ENST00000228682.2:c.110_122del	p.Gly37AlafsTer37	p.G37Afs*37	ENST00000228682	NM_005269.2	36	TCTGGCCCGCCCTtc/tc	3/12	NA	2	FACETS	0.741	0.679	0.806			1	INDETERMINATE	1	TRUE	NA	0.454660205120406	2		732	938	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18956781	18956802	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGCTGCAGGTTGGGCCCGAAGG	TGCTGCAGGTTGGGCCCGAAGG	-	novel	NA	P-0015932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	285	424	0	ENST00000262803.5:c.232-8_245del		p.X78_splice	ENST00000262803	NM_002911.3	78		2/24	0.457616549291864	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.454660205120406	3		424	619	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554880	187554911	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGTTGTAGTTTGACTTCTGTTCTGCATCAA	GAGGTTGTAGTTTGACTTCTGTTCTGCATCAA	-	novel	NA	P-0015932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	102	612	0	ENST00000441802.2:c.4250_4281del	p.Leu1417HisfsTer24	p.L1417Hfs*24	ENST00000441802	NM_005245.3	1417	cTTGATGCAGAACAGAAGTCAAACTACAACCTC/c	7/27	0.457616549291864	1	FACETS	0.818	0.736	0.903	0.818	0.736	0.903	CLONAL	1	TRUE	0	0.454660205120406	1		612	424	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793221	139793221	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	119	790	1	ENST00000247668.2:c.29G>T	p.Gly10Val	p.G10V	ENST00000247668	NM_021138.3	10	gGc/gTc	2/11	0.457616549291864	2	FACETS	0.541	0.487	0.598	0.27	0.243	0.299	SUBCLONAL	1	TRUE	0	0.454660205120406	2		791	968	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0015933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	239	541	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.426361417123503	2	FACETS	0.833	0.783	0.884	0.833	0.783	0.884	CLONAL	2	TRUE	0	0.461851123931238	2		541	621	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259161	36259161	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	228	660	0	ENST00000300305.3:c.330G>T	p.Lys110Asn	p.K110N	ENST00000300305		110	aaG/aaT	3/8	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.461851123931238	2		660	931	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965567	15965567	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs747836235	NA	P-0015933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	75	185	1	ENST00000268712.3:c.5239C>T	p.Arg1747Ter	p.R1747*	ENST00000268712	NM_006311.3	1747	Cga/Tga	36/46	0.422997945478525	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.461851123931238	1		186	230	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691039	NA	P-0015934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	116	554	0	ENST00000269305.4:c.919+1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.213088688287308	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.213088688287308	1		554	938	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682398	52682398	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	78	489	0	ENST00000394830.3:c.775G>T	p.Ala259Ser	p.A259S	ENST00000394830	NM_018313.4	259	Gcc/Tcc	8/30	0.213088688287308	1	FACETS	0.77	0.676	0.873	0.77	0.676	0.873	SUBCLONAL	1	TRUE	0	0.213088688287308	1		489	849	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829740	76829740	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	87	626	1	ENST00000373344.5:c.6301G>T	p.Glu2101Ter	p.E2101*	ENST00000373344	NM_000489.3	2101	Gaa/Taa	28/35	1	2	FACETS	0.799	0.706	0.899	0.799	0.706	0.899	SUBCLONAL	1	TRUE	1	0.213088688287308	2		627	1022	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523498	106523498	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	65	354	0	ENST00000359195.3:c.2650G>C	p.Asp884His	p.D884H	ENST00000359195	NM_002649.2	884	Gac/Cac	8/11	1	2	FACETS	0.844	0.731	0.967	0.844	0.731	0.967	CLONAL	1	TRUE	1	0.213088688287308	2		354	723	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695853	117695853	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	133	722	1	ENST00000369458.3:c.584C>A	p.Ser195Tyr	p.S195Y	ENST00000369458	NM_024626.3	195	tCc/tAc	4/6	0.213088688287308	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.213088688287308	1		723	1046	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333986	70333987	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0015934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	56	428	2	ENST00000373644.4:c.1891_1892delinsAA	p.Pro631Lys	p.P631K	ENST00000373644	NM_030625.2	631	CCa/AAa	2/12	1	2	FACETS	0.68	0.581	0.788	0.68	0.581	0.788	SUBCLONAL	1	TRUE	1	0.213088688287308	2		430	773	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123353319	123353319	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1346210003	NA	P-0015934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	118	699	1	ENST00000358487.5:c.13G>T	p.Gly5Cys	p.G5C	ENST00000358487	NM_000141.4	5	Ggt/Tgt	2/18	1	2	FACETS	0.987	0.888	1	0.987	0.888	1	CLONAL	1	TRUE	1	0.213088688287308	2		700	1122	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518038	69518038	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1248010792	NA	P-0015934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	83	599	0	ENST00000294312.3:c.327G>T	p.Met109Ile	p.M109I	ENST00000294312	NM_005117.2	109	atG/atT	2/3	1	2	FACETS	0.947	0.834	1	0.947	0.834	1	CLONAL	1	TRUE	1	0.213088688287308	2		599	823	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244161	133244162	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0015934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	96	569	3	ENST00000320574.5:c.2246_2247delinsTT	p.Arg749Leu	p.R749L	ENST00000320574	NM_006231.2	749	cGG/cTT	20/49	1	2	FACETS	0.924	0.822	1	0.924	0.822	1	CLONAL	1	TRUE	1	0.213088688287308	2		572	975	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253182	133253182	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	133	604	0	ENST00000320574.5:c.859G>T	p.Asp287Tyr	p.D287Y	ENST00000320574	NM_006231.2	287	Gat/Tat	9/49	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.213088688287308	2		604	1016	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41011048	41011048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	222	672	1	ENST00000267868.3:c.481G>A	p.Asp161Asn	p.D161N	ENST00000267868	NM_002875.4	161	Gac/Aac	6/10	0.192470550150239	2	FACETS	0.88	0.818	0.944	0.88	0.818	0.944	CLONAL	2	TRUE	0	0.213088688287308	2		673	1184	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476311	88476311	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	320	733	0	ENST00000360948.2:c.1821C>A	p.Cys607Ter	p.C607*	ENST00000360948	NM_001012338.2	607	tgC/tgA	15/19	0.192470550150239	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.213088688287308	2		733	1241	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678454	88678454	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	375	675	0	ENST00000360948.2:c.1082G>T	p.Gly361Val	p.G361V	ENST00000360948	NM_001012338.2	361	gGc/gTc	9/19	0.213088688287308	3	FACETS	1	0.978	1			1	CLONAL	3	TRUE	NA	0.213088688287308	3		675	1234	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550464	29550464	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	G	rs915463951	NA	P-0015934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	33	212	0	ENST00000356175.3:c.1724C>G	p.Ser575Ter	p.S575*	ENST00000356175	NM_000267.3	575	tCa/tGa	16/57	0.213088688287308	1	FACETS	0.767	0.625	0.926	0.767	0.625	0.926	CLONAL	1	TRUE	0	0.213088688287308	1		212	361	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39570486	39570486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	27	287	0	ENST00000262039.4:c.682G>A	p.Asp228Asn	p.D228N	ENST00000262039	NM_002647.2	228	Gat/Aat	6/25	1	2	FACETS	0.517	0.411	0.64	0.517	0.411	0.64	SUBCLONAL	1	TRUE	1	0.213088688287308	2		287	490	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600362	10600362	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	139	726	0	ENST00000171111.5:c.1493G>C	p.Arg498Pro	p.R498P	ENST00000171111	NM_203500.1	498	cGa/cCa	4/6	0.213088688287308	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.213088688287308	1		726	1144	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143981	11143981	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	82	487	0	ENST00000358026.2:c.3562G>T	p.Asp1188Tyr	p.D1188Y	ENST00000358026	NM_001128849.1	1188	Gac/Tac	26/36	0.213088688287308	1	FACETS	0.902	0.795	1	0.902	0.795	1	CLONAL	1	TRUE	0	0.213088688287308	1		487	762	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27016124	27016124	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	86	444	1	ENST00000335756.4:c.400G>T	p.Gly134Cys	p.G134C	ENST00000335756	NM_001809.3	134	Ggc/Tgc	4/5	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.213088688287308	2		445	737	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561051	9561051	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	44	334	0	ENST00000353224.5:c.731G>A	p.Gly244Glu	p.G244E	ENST00000353224	NM_177990.2	244	gGg/gAg	4/10	1	2	FACETS	0.802	0.672	0.945	0.802	0.672	0.945	CLONAL	1	TRUE	1	0.213088688287308	2		334	515	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739097	40739097	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	76	573	0	ENST00000373198.4:c.3187del	p.Leu1063SerfsTer37	p.L1063Sfs*37	ENST00000373198	NM_133170.3	1063	Ctc/tc	24/32	0.213088688287308	1	FACETS	0.728	0.637	0.826	0.728	0.637	0.826	SUBCLONAL	1	TRUE	0	0.213088688287308	1		573	876	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182253	38182253	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	53	407	0	ENST00000396334.3:c.689G>T	p.Arg230Leu	p.R230L	ENST00000396334	NM_002468.4	230	cGc/cTc	4/5	0.213088688287308	1	FACETS	0.641	0.546	0.746	0.641	0.546	0.746	SUBCLONAL	1	TRUE	0	0.213088688287308	1		407	693	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242743	66242743	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	84	499	0	ENST00000273854.3:c.1829G>T	p.Cys610Phe	p.C610F	ENST00000273854	NM_004439.5	610	tGc/tTc	9/18	1	2	FACETS	0.844	0.744	0.952	0.844	0.744	0.952	CLONAL	1	TRUE	1	0.213088688287308	2		499	934	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519147	187519147	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	77	580	0	ENST00000441802.2:c.12236G>T	p.Arg4079Ile	p.R4079I	ENST00000441802	NM_005245.3	4079	aGa/aTa	23/27	0.213088688287308	1	FACETS	0.712	0.624	0.807	0.712	0.624	0.807	SUBCLONAL	1	TRUE	0	0.213088688287308	1		580	907	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874575	35874575	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	80	543	0	ENST00000303115.3:c.731C>A	p.Thr244Asn	p.T244N	ENST00000303115	NM_002185.3	244	aCc/aAc	6/8	0.213088688287308	1	FACETS	0.772	0.678	0.873	0.772	0.678	0.873	SUBCLONAL	1	TRUE	0	0.213088688287308	1		543	869	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523073	176523073	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	95	620	0	ENST00000292408.4:c.1837C>A	p.Leu613Met	p.L613M	ENST00000292408	NM_213647.1	613	Ctg/Atg	14/18	1	2	FACETS	0.9	0.799	1	0.9	0.799	1	CLONAL	1	TRUE	1	0.213088688287308	2		620	991	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453115	140453115	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	93	577	0	ENST00000288602.6:c.1820C>T	p.Ser607Phe	p.S607F	ENST00000288602	NM_004333.4	607	tCc/tTc	15/18	1	2	FACETS	0.876	0.778	0.982	0.876	0.778	0.982	CLONAL	1	TRUE	1	0.213088688287308	2		577	996	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058572	69058572	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	111	719	0	ENST00000288368.4:c.4216G>T	p.Val1406Phe	p.V1406F	ENST00000288368	NM_024870.2	1406	Gtt/Ttt	34/40	1	2	FACETS	0.833	0.746	0.925	0.833	0.746	0.925	CLONAL	1	TRUE	1	0.213088688287308	2		719	1251	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570209	87570209	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	44	263	0	ENST00000277120.3:c.1949C>A	p.Pro650His	p.P650H	ENST00000277120		650	cCt/cAt	17/19	0.213088688287308	1	FACETS	0.941	0.791	1	0.941	0.791	1	CLONAL	1	TRUE	0	0.213088688287308	1		263	392	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123025090	123025090	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	50	547	0	ENST00000355640.3:c.980G>T	p.Cys327Phe	p.C327F	ENST00000355640		327	tGc/tTc	4/7	NA	2	FACETS	0.512	0.433	0.599			1	INDETERMINATE	1	TRUE	NA	0.213088688287308	2		547	917	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0015935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	272	590	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.793756713555739	1	FACETS	0.97	0.928	1	0.97	0.928	1	CLONAL	1	TRUE	0	0.793756713555739	1		590	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659675	NA	P-0015935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	299	600	1	ENST00000269305.4:c.764T>C	p.Ile255Thr	p.I255T	ENST00000269305	NM_001126112.2	255	aTc/aCc	7/11	0.793756713555739	1	FACETS	0.986	0.945	1	0.986	0.945	1	CLONAL	1	TRUE	0	0.793756713555739	1		601	461	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65349082	65349082	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	265	532	0	ENST00000342505.4:c.83A>G	p.Asn28Ser	p.N28S	ENST00000342505	NM_002227.2	28	aAc/aGc	3/25	0.793756713555739	3	FACETS	0.899	0.844	0.957	0.45	0.422	0.479	CLONAL	1	TRUE	1	0.793756713555739	3		532	1037	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119831	108119831	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0015935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	123	303	0	ENST00000278616.4:c.1235+2T>C		p.X412_splice	ENST00000278616	NM_000051.3	412			0.793756713555739	3	FACETS	0.851	0.773	0.931	0.425	0.386	0.466	CLONAL	1	TRUE	1	0.793756713555739	3		303	509	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108064	30108064	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	360	707	1	ENST00000331968.5:c.743A>T	p.Asn248Ile	p.N248I	ENST00000331968	NM_002742.2	248	aAt/aTt	5/18	0.737469405029574	4	FACETS	1	0.979	1	0.534	0.505	0.564	CLONAL	1	TRUE	2	0.793756713555739	4		708	1523	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029140	14029140	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	160	347	0	ENST00000311895.7:c.1351A>G	p.Met451Val	p.M451V	ENST00000311895	NM_005236.2	451	Atg/Gtg	8/11	0.772448706129271	3	FACETS	0.88	0.81	0.953	0.44	0.405	0.477	CLONAL	1	TRUE	1	0.793756713555739	3		347	640	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853188	68853188	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	255	515	1	ENST00000261769.5:c.1571G>T	p.Arg524Leu	p.R524L	ENST00000261769	NM_004360.3	524	cGg/cTg	11/16	0.772448706129271	3	FACETS	0.983	0.922	1	0.492	0.461	0.523	CLONAL	1	TRUE	1	0.793756713555739	3		516	913	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696721	47696721	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	212	502	0	ENST00000347630.2:c.227T>C	p.Leu76Ser	p.L76S	ENST00000347630	NM_001007230.1	76	tTa/tCa	5/11	0.793756713555739	3	FACETS	0.881	0.82	0.944	0.44	0.41	0.472	CLONAL	1	TRUE	1	0.793756713555739	3		502	847	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295745	212295745	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	292	583	1	ENST00000342788.4:c.2568T>A	p.His856Gln	p.H856Q	ENST00000342788	NM_005235.2	856	caT/caA	21/28	1	2	FACETS	0.986	0.933	1	0.986	0.933	1	CLONAL	1	TRUE	1	0.793756713555739	2		584	746	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164569	36164569	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	248	528	0	ENST00000300305.3:c.1306T>C	p.Ser436Pro	p.S436P	ENST00000300305		436	Tcc/Ccc	8/8	1	2	FACETS	0.969	0.912	1	0.969	0.912	1	CLONAL	1	TRUE	1	0.793756713555739	2		528	645	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449829	149449829	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	342	907	1	ENST00000286301.3:c.1235A>G	p.Asn412Ser	p.N412S	ENST00000286301	NM_005211.3	412	aAc/aGc	9/22	0.793756713555739	3	FACETS	0.913	0.863	0.964	0.457	0.431	0.482	CLONAL	1	TRUE	1	0.793756713555739	3		908	1318	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221313	1221314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs121913321	NA	P-0015936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	184	665	0	ENST00000326873.7:c.842dup	p.Leu282AlafsTer3	p.L282Afs*3	ENST00000326873	NM_000455.4	279	ggc/ggCc	6/10	0.453251871169922	1	FACETS	0.832	0.769	0.896	0.832	0.769	0.896	CLONAL	1	TRUE	0	0.453251871169922	1		665	755	SUCCESS
APC	324	MSKCC	GRCh37	5	112174502	112174502	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876659539	NA	P-0015936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	103	392	0	ENST00000257430.4:c.3211C>T	p.Gln1071Ter	p.Q1071*	ENST00000257430	NM_000038.5	1071	Caa/Taa	16/16	0.395817754000151	1	FACETS	0.778	0.7	0.859	0.778	0.7	0.859	SUBCLONAL	1	TRUE	0	0.453251871169922	1		392	452	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346880	89346880	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1272359896	NA	P-0015936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	14	214	0	ENST00000301030.4:c.6070C>T	p.Pro2024Ser	p.P2024S	ENST00000301030	NM_001256183.1	2024	Ccg/Tcg	9/13	1	2	FACETS	0.262	0.189	0.35	0.262	0.189	0.35	SUBCLONAL	1	TRUE	1	0.453251871169922	2		214	236	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600005	10600005	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	259	712	0	ENST00000171111.5:c.1571del	p.Gly524AlafsTer8	p.G524Afs*8	ENST00000171111	NM_203500.1	524	gGc/gc	5/6	0.453251871169922	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.453251871169922	1		712	876	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219958	36219958	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1311032384	NA	P-0015936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	182	519	0	ENST00000222270.7:c.4760A>T	p.Tyr1587Phe	p.Y1587F	ENST00000222270	NM_014727.1	1587	tAc/tTc	21/37	1	2	FACETS	0.979	0.905	1	0.979	0.905	1	CLONAL	1	TRUE	1	0.453251871169922	2		519	820	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902742	50902742	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	221	758	1	ENST00000440232.2:c.316+1G>A		p.X106_splice	ENST00000440232	NM_002691.3	106			NA	2	FACETS	0.955	0.889	1			1	INDETERMINATE	1	TRUE	NA	0.453251871169922	2		759	1021	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0015937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	1669	618	2	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.477478210508269	25	FACETS	1	0.992	1			1	CLONAL	24	TRUE	NA	0.477478210508269	25		620	1885	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0015937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	122	558	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.477478210508269	2	FACETS	0.913	0.839	0.986	0.913	0.839	0.986	CLONAL	2	TRUE	0	0.477478210508269	2		558	280	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858738	9858738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149698593	NA	P-0015937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	24	209	0	ENST00000330684.3:c.2663C>T	p.Thr888Met	p.T888M	ENST00000330684	NM_001134407.1	888	aCg/aTg	13/13	0.154309352306928	3	FACETS	0.769	0.608	0.95	0.256	0.202	0.317	INDETERMINATE	1	TRUE	0	0.477478210508269	3		209	162	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606826	43606826	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	30	854	0	ENST00000355710.3:c.1435G>C	p.Ala479Pro	p.A479P	ENST00000355710	NM_020975.4	479	Gcc/Ccc	7/20	0.306425444239085	3	FACETS	0.417	0.336	0.509			1	SUBCLONAL	1	TRUE	NA	0.477478210508269	3		854	373	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120787	115120787	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	34	617	0	ENST00000257566.3:c.219G>C	p.Glu73Asp	p.E73D	ENST00000257566	NM_016569.3	73	gaG/gaC	1/8	0.327031219857276	3	FACETS	0.479	0.392	0.577	0.24	0.196	0.289	SUBCLONAL	1	TRUE	1	0.477478210508269	3		617	368	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911939	32911939	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660471	NA	P-0015937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	26	565	3	ENST00000380152.3:c.3447G>A	p.Met1149Ile	p.M1149I	ENST00000380152		1149	atG/atA	11/27	0.477478210508269	2	FACETS	0.539	0.43	0.663	0.27	0.215	0.332	SUBCLONAL	1	TRUE	0	0.477478210508269	2		568	202	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426001	138426003	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0015937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	16	444	0	ENST00000289153.2:c.1528_1530del	p.Lys510del	p.K510del	ENST00000289153	NM_006219.2	510	AAG/-	9/22	0.421083573664054	4	FACETS	0.436	0.323	0.571	0.145	0.107	0.191	SUBCLONAL	1	TRUE	1	0.477478210508269	4		444	227	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540391	187540391	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0015937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	26	480	0	ENST00000441802.2:c.7349C>G	p.Ser2450Ter	p.S2450*	ENST00000441802	NM_005245.3	2450	tCa/tGa	10/27	0.395485881281199	5	FACETS	0.551	0.437	0.682	0.184	0.145	0.228	SUBCLONAL	1	TRUE	2	0.477478210508269	5		480	339	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821517	32821517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767728168	NA	P-0015937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	27	857	1	ENST00000354258.4:c.77C>T	p.Pro26Leu	p.P26L	ENST00000354258	NM_000593.5	26	cCa/cTa	1/11	0.477478210508269	2	FACETS	0.287	0.228	0.355	0.144	0.114	0.178	SUBCLONAL	1	TRUE	0	0.477478210508269	2		858	394	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511219	157511219	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs772973856	NA	P-0015937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	29	631	1	ENST00000346085.5:c.3737C>A	p.Ser1246Ter	p.S1246*	ENST00000346085	NM_020732.3	1246	tCa/tAa	15/20	0.477478210508269	2	FACETS	0.492	0.396	0.599	0.246	0.198	0.3	SUBCLONAL	1	TRUE	0	0.477478210508269	2		632	247	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500790	8500790	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	52	341	0	ENST00000356435.5:c.2092G>C	p.Glu698Gln	p.E698Q	ENST00000356435		698	Gag/Cag	13/35	0.477478210508269	3	FACETS	0.782	0.669	0.905	0.391	0.334	0.453	CLONAL	1	TRUE	1	0.477478210508269	3		341	345	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923169	39923169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772367454	NA	P-0015937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	18	573	1	ENST00000378444.4:c.3539C>T	p.Ser1180Phe	p.S1180F	ENST00000378444	NM_001123385.1	1180	tCt/tTt	8/15	0.438126154013737	1	FACETS	0.29	0.219	0.373	0.29	0.219	0.373	SUBCLONAL	1	TRUE	0	0.477478210508269	1		574	198	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0015937-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	6204	618	2	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.645597050655922	10	FACETS	1	0.999	1			1	CLONAL	10	TRUE	NA	0.645597050655922	10		620	6811	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0015937-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	405	558	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.645597050655922	1	FACETS	0.979	0.937	1	0.979	0.937	1	CLONAL	1	TRUE	0	0.645597050655922	1		558	868	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858738	9858738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149698593	NA	P-0015937-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	74	209	0	ENST00000330684.3:c.2663C>T	p.Thr888Met	p.T888M	ENST00000330684	NM_001134407.1	888	aCg/aTg	13/13	1	2	FACETS	0.529	0.465	0.598	0.529	0.465	0.598	SUBCLONAL	1	TRUE	1	0.645597050655922	2		209	433	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911939	32911939	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660471	NA	P-0015937-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	84	565	3	ENST00000380152.3:c.3447G>A	p.Met1149Ile	p.M1149I	ENST00000380152		1149	atG/atA	11/27	0.645597050655922	1	FACETS	0.229	0.202	0.258	0.229	0.202	0.258	SUBCLONAL	1	TRUE	0	0.645597050655922	1		568	770	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511219	157511219	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs772973856	NA	P-0015937-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	351	631	1	ENST00000346085.5:c.3737C>A	p.Ser1246Ter	p.S1246*	ENST00000346085	NM_020732.3	1246	tCa/tAa	15/20	0.645597050655922	1	FACETS	0.615	0.582	0.648	0.615	0.582	0.648	SUBCLONAL	1	TRUE	0	0.645597050655922	1		632	1198	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500790	8500790	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015937-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	94	341	0	ENST00000356435.5:c.2092G>C	p.Glu698Gln	p.E698Q	ENST00000356435		698	Gag/Cag	13/35	0.62206337765795	1	FACETS	0.264	0.234	0.295	0.264	0.234	0.295	SUBCLONAL	1	TRUE	0	0.645597050655922	1		341	747	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923169	39923169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772367454	NA	P-0015937-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	77	573	1	ENST00000378444.4:c.3539C>T	p.Ser1180Phe	p.S1180F	ENST00000378444	NM_001123385.1	1180	tCt/tTt	8/15	0.536785660853992	0	FACETS	0.138	0.121	0.156			1	SUBCLONAL	1	TRUE	0	0.645597050655922	0		574	614	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976739	2977584	+	splice_donor_variant,splice_acceptor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	CCCGCCGCACCATCTCGATCCTCATCTCGTCGTTCTTCTCCTCCAGCTCGCGGATCTGCTTCCTGTACTTGTCCTTTTCGATTAAGCACTGCGAGTACTGTGTCTGAGCTTCATCTCGGGAGTGGAAGGCCTGCCAGGGAGAAGCGGGACGAAGGCTGCTTTGGGGGTTGCACCCCAGCCAAATCCAGCTGGGCCCAGGGACAGGCATCATCCCAACCCAGGGGCCAGCCACATCGTCTGTGGCTCTCGTCTGCAGTCTGACCCCTGGGCGTGTCAGTCACTACCTTCTTCATTAACGCGATCACAGAGCCGATGGTCCGACCCTTGCTAGTGGCAGGCTCTGTGTTGAGAGCTTTGATGCAGTGTCCCTGGAAGGCCACAGCCTGTCCCTATGAGGCGGTGCTACCGTAATTATCCCCATTTTACAGATGAGGGCACTGAGGTCAGGGGTGGCAGCTTGCCTATGGGCATACACCTTATGAATGACAGGGCTGGATCTGAACCCATCCTCTCACCCGAGAGAACACACAACATTTAAGAACCATGCTTGGTCGTGGGAGCTGCTGGAGCCCAGCTCGGATCCCCCTGCTACCCAAACGCCTGTGACTTCCAAAAAAGCCTTTTGGAATTCATCTTTTAGAATTCATCTTTGGAACAGAAATGGGAAAGATGGATTCAGGAGTGATCCCTGCATTGTCAGTGATGTTGCACTGGACAAAACACTCTGAAGGAGCCGGTGGTCTGGGGTGCGGGCCCCGCTGTGCAGCCTCGCCGCCCTGCACGCTGCAGGTGGTGCCTGTACCTGGTCCCGCTCCCGCTCCACCTCCTCCAGCTGCAGCATGACCG	CCCGCCGCACCATCTCGATCCTCATCTCGTCGTTCTTCTCCTCCAGCTCGCGGATCTGCTTCCTGTACTTGTCCTTTTCGATTAAGCACTGCGAGTACTGTGTCTGAGCTTCATCTCGGGAGTGGAAGGCCTGCCAGGGAGAAGCGGGACGAAGGCTGCTTTGGGGGTTGCACCCCAGCCAAATCCAGCTGGGCCCAGGGACAGGCATCATCCCAACCCAGGGGCCAGCCACATCGTCTGTGGCTCTCGTCTGCAGTCTGACCCCTGGGCGTGTCAGTCACTACCTTCTTCATTAACGCGATCACAGAGCCGATGGTCCGACCCTTGCTAGTGGCAGGCTCTGTGTTGAGAGCTTTGATGCAGTGTCCCTGGAAGGCCACAGCCTGTCCCTATGAGGCGGTGCTACCGTAATTATCCCCATTTTACAGATGAGGGCACTGAGGTCAGGGGTGGCAGCTTGCCTATGGGCATACACCTTATGAATGACAGGGCTGGATCTGAACCCATCCTCTCACCCGAGAGAACACACAACATTTAAGAACCATGCTTGGTCGTGGGAGCTGCTGGAGCCCAGCTCGGATCCCCCTGCTACCCAAACGCCTGTGACTTCCAAAAAAGCCTTTTGGAATTCATCTTTTAGAATTCATCTTTGGAACAGAAATGGGAAAGATGGATTCAGGAGTGATCCCTGCATTGTCAGTGATGTTGCACTGGACAAAACACTCTGAAGGAGCCGGTGGTCTGGGGTGCGGGCCCCGCTGTGCAGCCTCGCCGCCCTGCACGCTGCAGGTGGTGCCTGTACCTGGTCCCGCTCCCGCTCCACCTCCTCCAGCTGCAGCATGACCG	-	novel	NA	P-0015937-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1254	167	616	0	ENST00000396946.4:c.1100_1273del		p.X367_splice	ENST00000396946	NM_032415.4	367	aCGGTCATGCTGCAGCTGGAGGAGGTGGAGCGGGAGCGGGACCAGGTACAGGCACCACCTGCAGCGTGCAGGGCGGCGAGGCTGCACAGCGGGGCCCGCACCCCAGACCACCGGCTCCTTCAGAGTGTTTTGTCCAGTGCAACATCACTGACAATGCAGGGATCACTCCTGAATCCATCTTTCCCATTTCTGTTCCAAAGATGAATTCTAAAAGATGAATTCCAAAAGGCTTTTTTGGAAGTCACAGGCGTTTGGGTAGCAGGGGGATCCGAGCTGGGCTCCAGCAGCTCCCACGACCAAGCATGGTTCTTAAATGTTGTGTGTTCTCTCGGGTGAGAGGATGGGTTCAGATCCAGCCCTGTCATTCATAAGGTGTATGCCCATAGGCAAGCTGCCACCCCTGACCTCAGTGCCCTCATCTGTAAAATGGGGATAATTACGGTAGCACCGCCTCATAGGGACAGGCTGTGGCCTTCCAGGGACACTGCATCAAAGCTCTCAACACAGAGCCTGCCACTAGCAAGGGTCGGACCATCGGCTCTGTGATCGCGTTAATGAAGAAGGTAGTGACTGACACGCCCAGGGGTCAGACTGCAGACGAGAGCCACAGACGATGTGGCTGGCCCCTGGGTTGGGATGATGCCTGTCCCTGGGCCCAGCTGGATTTGGCTGGGGTGCAACCCCCAAAGCAGCCTTCGTCCCGCTTCTCCCTGGCAGGCCTTCCACTCCCGAGATGAAGCTCAGACACAGTACTCGCAGTGCTTAATCGAAAAGGACAAGTACAGGAAGCAGATCCGCGAGCTGGAGGAGAAGAACGACGAGATGAGGATCGAGATGGTGCGGCGGGag/aag	8-9/25	0.355127438992528	2	FACETS	0.364	0.333	0.397	0.182	0.166	0.199	INDETERMINATE	1	TRUE	0	0.645597050655922	2		616	1421	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428615	78428615	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015937-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	68	283	0	ENST00000370768.2:c.1184G>C	p.Gly395Ala	p.G395A	ENST00000370768	NM_003902.3	395	gGa/gCa	14/20	0.586483159014556	1	FACETS	0.325	0.283	0.37	0.325	0.283	0.37	SUBCLONAL	1	TRUE	0	0.645597050655922	1		283	439	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490896	56490896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015937-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	123	521	0	ENST00000267101.3:c.2342C>T	p.Ser781Leu	p.S781L	ENST00000267101	NM_001982.3	781	tCa/tTa	20/28	0.177800344123793	2	FACETS	0.293	0.264	0.324	0.147	0.132	0.162	INDETERMINATE	1	TRUE	0	0.645597050655922	2		521	1299	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105240314	105240314	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015937-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1265	90	564	0	ENST00000349310.3:c.637C>G	p.Leu213Val	p.L213V	ENST00000349310	NM_001014432.1	213	Ctg/Gtg	9/15	0.378164632473913	3	FACETS	0.272	0.24	0.307	0.091	0.08	0.103	INDETERMINATE	1	TRUE	0	0.645597050655922	3		564	1355	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027818	48027818	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015937-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	131	334	0	ENST00000234420.5:c.2696A>T	p.Glu899Val	p.E899V	ENST00000234420	NM_000179.2	899	gAa/gTa	4/10	0.445346554263255	1	FACETS	0.436	0.396	0.477	0.436	0.396	0.477	SUBCLONAL	1	TRUE	0	0.645597050655922	1		334	631	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62297356	62297356	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0015937-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	72	423	0	ENST00000360203.5:c.539-1G>C		p.X180_splice	ENST00000360203	NM_001283009.1	180			0.18508118050077	2	FACETS	0.22	0.191	0.251	0.11	0.095	0.126	INDETERMINATE	1	TRUE	0	0.645597050655922	2		423	1016	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584702	52584792	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTTCTGAGAAGGATAACTCGAATTCTGTCAAGTCCTAGAAAATCAAACTGGGAGGCTCACCTGTTGTCCATATGGACTTCCACCTGGTGC	TGTTCTGAGAAGGATAACTCGAATTCTGTCAAGTCCTAGAAAATCAAACTGGGAGGCTCACCTGTTGTCCATATGGACTTCCACCTGGTGC	-	novel	NA	P-0015937-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	39	415	0	ENST00000394830.3:c.4330_4360-49del		p.X1444_splice	ENST00000394830	NM_018313.4	1444		28/30	0.586483159014556	1	FACETS	0.134	0.11	0.16	0.134	0.11	0.16	SUBCLONAL	1	TRUE	0	0.645597050655922	1		415	612	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31424571	31424571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1186040397	NA	P-0015937-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1254	70	634	0	ENST00000344624.3:c.3224G>A	p.Arg1075His	p.R1075H	ENST00000344624		1075	cGc/cAc	25/33	0.182794076585806	5	FACETS	0.322	0.28	0.369	0.107	0.093	0.123	INDETERMINATE	1	TRUE	2	0.645597050655922	5		634	1324	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889086	76889086	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015937-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	98	592	1	ENST00000373344.5:c.4924C>A	p.Gln1642Lys	p.Q1642K	ENST00000373344	NM_000489.3	1642	Caa/Aaa	18/35	0.391396509850212	0	FACETS	0.158	0.141	0.177			1	SUBCLONAL	1	TRUE	0	0.645597050655922	0		593	680	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0015938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	82	414	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.229848345347855	2		414	685	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263935	104263935	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1332258864	NA	P-0015938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	10	193	2	ENST00000369902.3:c.30del	p.Gly11AlafsTer85	p.G11Afs*85	ENST00000369902	NM_016169.3	9	gCc/gc	1/12	1	2	FACETS	0.458	0.31	0.644	0.458	0.31	0.644	SUBCLONAL	1	TRUE	1	0.229848345347855	2		195	190	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864757	57864757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138157845	NA	P-0015938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	83	683	2	ENST00000228682.2:c.2234C>T	p.Ala745Val	p.A745V	ENST00000228682	NM_005269.2	745	gCg/gTg	12/12	1	2	FACETS	0.936	0.825	1	0.936	0.825	1	CLONAL	1	TRUE	1	0.229848345347855	2		685	772	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	66	507	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.243764188647038	3	FACETS	1	0.943	1	0.579	0.504	0.661	CLONAL	1	TRUE	1	0.26	3		507	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0015939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1278	228	563	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.26	2		564	1506	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998774	100998774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769453610	NA	P-0015939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1227	87	612	0	ENST00000325455.5:c.1028G>A	p.Arg343Gln	p.R343Q	ENST00000325455	NM_001202474.3	343	cGg/cAg	1/8	1	2	FACETS	0.509	0.449	0.574	0.509	0.449	0.574	SUBCLONAL	1	TRUE	1	0.26	2		612	1314	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197253	26197253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238004407	NA	P-0015939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	52	325	0	ENST00000356476.2:c.226G>A	p.Ala76Thr	p.A76T	ENST00000356476		76	Gcg/Acg	1/1	0.131956778267959	3	FACETS	0.597	0.507	0.696	0.299	0.253	0.348	INDETERMINATE	1	TRUE	1	0.26	3		325	757	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971118	21971118	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	180	466	0	ENST00000304494.5:c.240del	p.Val82CysfsTer64	p.V82Cfs*64	ENST00000304494	NM_000077.4	80	cgA/cg	2/3	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.26	2		466	1169	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0015940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	104	444	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.975	0.871	1	0.975	0.871	1	CLONAL	1	TRUE	1	0.21	2		444	1016	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	90	414	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.929	0.823	1	0.929	0.823	1	CLONAL	1	TRUE	1	0.21	2		414	923	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0015940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	74	364	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.28591921549363	1	FACETS	0.957	0.838	1	0.957	0.838	1	CLONAL	1	TRUE	0	0.21	1		364	659	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39537654	39537654	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	54	285	0	ENST00000262039.4:c.188T>C	p.Val63Ala	p.V63A	ENST00000262039	NM_002647.2	63	gTt/gCt	2/25	1	2	FACETS	0.927	0.791	1	0.927	0.791	1	CLONAL	1	TRUE	1	0.21	2		285	555	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459759	149459759	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374166176	NA	P-0015940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	89	501	2	ENST00000286301.3:c.448C>T	p.Arg150Cys	p.R150C	ENST00000286301	NM_005211.3	150	Cgc/Tgc	4/22	1	2	FACETS	0.676	0.598	0.761	0.676	0.598	0.761	SUBCLONAL	1	TRUE	1	0.21	2		503	1253	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876658468	NA	P-0015942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	264	583	1	ENST00000269305.4:c.577C>A	p.His193Asn	p.H193N	ENST00000269305	NM_001126112.2	193	Cat/Aat	6/11	0.49079919007474	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.49079919007474	1		584	721	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876117	35876117	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	48	331	0	ENST00000303115.3:c.909C>A	p.Phe303Leu	p.F303L	ENST00000303115	NM_002185.3	303	ttC/ttA	8/8	1	2	FACETS	0.34	0.287	0.398	0.34	0.287	0.398	SUBCLONAL	1	TRUE	1	0.49079919007474	2		331	576	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0015944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	152	279	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.367561241304221	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.385121239491033	3		279	442	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0015944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	86	552	1	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	0.367561241304221	3	FACETS	0.55	0.485	0.62	0.275	0.242	0.31	SUBCLONAL	1	TRUE	1	0.385121239491033	3		553	968	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835562	68835599	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGCCCTGCAGTGAATTTTGAAGATTGCACCGGTCGAC	CTGCCCTGCAGTGAATTTTGAAGATTGCACCGGTCGAC	-	novel	NA	P-0015944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	161	301	1	ENST00000261769.5:c.164-11_190del		p.X55_splice	ENST00000261769	NM_004360.3	55		3/16	0.385121239491033	2	FACETS	0.925	0.856	0.995	0.925	0.856	0.995	CLONAL	2	TRUE	0	0.385121239491033	2		302	452	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0015944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	275	479	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.367561241304221	3	FACETS	0.947	0.891	1	0.947	0.891	1	CLONAL	2	TRUE	1	0.385121239491033	3		479	899	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524678	187524678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769237577	NA	P-0015944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	173	744	1	ENST00000441802.2:c.11002C>T	p.Arg3668Trp	p.R3668W	ENST00000441802	NM_005245.3	3668	Cgg/Tgg	19/27	0.367561241304221	3	FACETS	0.829	0.761	0.9	0.415	0.38	0.45	CLONAL	1	TRUE	1	0.385121239491033	3		745	1292	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884453	151884453	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	72	289	0	ENST00000262189.6:c.4902A>T	p.Arg1634Ser	p.R1634S	ENST00000262189	NM_170606.2	1634	agA/agT	33/59	0.367561241304221	3	FACETS	0.743	0.65	0.844	0.372	0.325	0.422	SUBCLONAL	1	TRUE	1	0.385121239491033	3		289	600	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0015945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	397	482	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.639973648859605	2		482	1222	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440395	52440409	+	splice_region_variant,intron_variant	Splice_Region	DEL	GCAGTCACAGCCGCA	GCAGTCACAGCCGCA	-	novel	NA	P-0015945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	181	317	0	ENST00000460680.1:c.660-17_660-3del		p.X220_splice	ENST00000460680	NM_004656.3	220			0.639973648859605	1	FACETS	0.769	0.716	0.824	0.769	0.716	0.824	SUBCLONAL	1	TRUE	0	0.639973648859605	1		317	500	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	183	414	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.294280650082248	3	FACETS	0.823	0.762	0.887	0.549	0.508	0.591	CLONAL	2	TRUE	0	0.366803433012925	3		414	717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0015946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	131	641	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.284254229971252	1	FACETS	0.778	0.706	0.853	0.778	0.706	0.853	SUBCLONAL	1	TRUE	0	0.366803433012925	1		641	750	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591888	48591888	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	49	296	0	ENST00000342988.3:c.1051G>T	p.Asp351Tyr	p.D351Y	ENST00000342988	NM_005359.5	351	Gat/Tat	9/12	1	2	FACETS	0.738	0.627	0.859	0.738	0.627	0.859	SUBCLONAL	1	TRUE	1	0.366803433012925	2		296	362	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480466	89480466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446890859	NA	P-0015946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	66	244	1	ENST00000336596.2:c.2303C>T	p.Ser768Leu	p.S768L	ENST00000336596	NM_005233.5	768	tCg/tTg	13/17	1	2	FACETS	0.811	0.706	0.923	0.811	0.706	0.923	CLONAL	1	TRUE	1	0.366803433012925	2		245	444	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281157	142281157	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	41	369	0	ENST00000350721.4:c.1087T>C	p.Ser363Pro	p.S363P	ENST00000350721	NM_001184.3	363	Tct/Cct	4/47	1	2	FACETS	0.423	0.352	0.503	0.423	0.352	0.503	SUBCLONAL	1	TRUE	1	0.366803433012925	2		369	528	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092710	27092710	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0015947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	51	349	0	ENST00000324856.7:c.2733-2A>T		p.X911_splice	ENST00000324856	NM_006015.4	911			1	2	FACETS	0.72	0.611	0.839	0.72	0.611	0.839	SUBCLONAL	1	TRUE	1	0.250886442838324	2		349	565	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712011	89712012	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	35	228	0	ENST00000371953.3:c.631dup	p.Cys211LeufsTer32	p.C211Lfs*32	ENST00000371953	NM_000314.4	210	act/acTt	6/9	1	2	FACETS	0.779	0.64	0.935	0.779	0.64	0.935	CLONAL	1	TRUE	1	0.250886442838324	2		228	358	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346351	89346351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764833948	NA	P-0015947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	40	434	0	ENST00000301030.4:c.6599C>T	p.Pro2200Leu	p.P2200L	ENST00000301030	NM_001256183.1	2200	cCt/cTt	9/13	0.250886442838324	1	FACETS	0.595	0.494	0.707	0.595	0.494	0.707	SUBCLONAL	1	TRUE	0	0.250886442838324	1		434	469	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259334	36259334	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	36	502	0	ENST00000300305.3:c.157A>G	p.Ser53Gly	p.S53G	ENST00000300305		53	Agc/Ggc	3/8	1	2	FACETS	0.417	0.341	0.501	0.417	0.341	0.501	SUBCLONAL	1	TRUE	1	0.250886442838324	2		502	689	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483931	88483931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	245	565	0	ENST00000360948.2:c.1639G>A	p.Gly547Arg	p.G547R	ENST00000360948	NM_001012338.2	547	Gga/Aga	14/19	1	2	FACETS	0.864	0.81	0.92	0.864	0.81	0.92	CLONAL	1	TRUE	1	0.668621881593785	2		565	848	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189361	56189361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	214	349	0	ENST00000399503.3:c.4393G>A	p.Ala1465Thr	p.A1465T	ENST00000399503	NM_005921.1	1465	Gct/Act	20/20	0.668621881593785	3	FACETS	1	0.955	1	0.516	0.481	0.553	CLONAL	1	TRUE	1	0.668621881593785	3		349	827	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205043	123205043	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	224	338	0	ENST00000218089.9:c.2403G>C	p.Gln801His	p.Q801H	ENST00000218089	NM_001042749.1	801	caG/caC	25/35	0.556086382326156	3	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.668621881593785	3		338	774	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226574099	226574115	+	frameshift_variant	Frame_Shift_Del	DEL	TTTCTTTAGCTCGTCCT	TTTCTTTAGCTCGTCCT	G	novel	NA	P-0015948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	173	394	0	ENST00000366794.5:c.746_762delinsC	p.Lys249ThrfsTer8	p.K249Tfs*8	ENST00000366794	NM_001618.3	249	aAGGACGAGCTAAAGAAA/aC	6/23	0.668621881593785	3	FACETS	0.816	0.752	0.883	0.408	0.376	0.442	CLONAL	1	TRUE	1	0.668621881593785	3		394	846	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847277	68847277	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	301	514	0	ENST00000261769.5:c.1199A>T	p.Asp400Val	p.D400V	ENST00000261769	NM_004360.3	400	gAt/gTt	9/16	0.649535397360804	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.649535397360804	1		514	558	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100213	157100253	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCGGGGCCGCGAGCCTCAGCAAGGCGGCCGCCGGCTC	GGCGGCGGGGCCGCGAGCCTCAGCAAGGCGGCCGCCGGCTC	-	novel	NA	P-0015950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	82	53	0	ENST00000346085.5:c.1160_1200del	p.Ala387GlyfsTer134	p.A387Gfs*134	ENST00000346085	NM_020732.3	384	GGCGGCGGGGCCGCGAGCCTCAGCAAGGCGGCCGCCGGCTCg/g	1/20	0.292669545616319	1	FACETS	1	0.981	1	1	0.981	1	INDETERMINATE	1	TRUE	0	0.594034824313415	1		53	144	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881001	37881002	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGCTCCCC	rs397516981	NA	P-0015950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	462	553	0	ENST00000269571.5:c.2331_2339dup	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	gtg/gtGGGCTCCCCg	20/27	0.331827093357287	3	FACETS	0.754	0.72	0.788	0.754	0.72	0.788	INDETERMINATE	2	TRUE	1	0.594034824313415	3		553	1338	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953730	48953730	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs3092891	NA	P-0015950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	131	179	2	ENST00000267163.4:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000267163	NM_000321.2	445	Cga/Tga	14/27	0.594034824313415	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.594034824313415	1		181	309	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0015950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	277	498	1	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	0.594034824313415	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.594034824313415	1		499	630	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394101	31394101	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	106	418	0	ENST00000328111.2:c.2388A>T	p.Lys796Asn	p.K796N	ENST00000328111	NM_006892.3	796	aaA/aaT	22/23	0.285377292977899	3	FACETS	0.46	0.411	0.511	0.153	0.137	0.171	INDETERMINATE	1	TRUE	0	0.594034824313415	3		418	1007	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0015951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	141	475	1	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.302508514636899	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.302508514636899	1		476	758	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0015952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	481	588	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.791536820383482	2	FACETS	1	0.996	1	0.642	0.617	0.666	CLONAL	1	TRUE	0	0.791536820383482	2		588	947	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445680	49445680	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2320	171	1121	1	ENST00000301067.7:c.1786G>T	p.Ala596Ser	p.A596S	ENST00000301067	NM_003482.3	596	Gca/Tca	10/54	1	2	FACETS	0.173	0.158	0.189	0.173	0.158	0.189	SUBCLONAL	1	TRUE	1	0.791536820383482	2		1122	2491	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979279	93979279	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	32	402	0	ENST00000369303.4:c.1549G>T	p.Ala517Ser	p.A517S	ENST00000369303	NM_004440.3	517	Gct/Tct	7/17	0.411204380429035	1	FACETS	0.103	0.083	0.126	0.103	0.083	0.126	INDETERMINATE	1	TRUE	0	0.791536820383482	1		402	474	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997443	149997443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747123108	NA	P-0015952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	76	616	0	ENST00000253339.5:c.2836G>A	p.Gly946Arg	p.G946R	ENST00000253339		946	Gga/Aga	6/7	0.411204380429035	1	FACETS	0.095	0.083	0.109	0.095	0.083	0.109	INDETERMINATE	1	TRUE	0	0.791536820383482	1		616	1216	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0015953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	1033	796	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.894023319401341	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.894023319401341	1		796	1181	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0015953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	654	441	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.894023319401341	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.894023319401341	1		441	734	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131402	17131402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398124537	NA	P-0015953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	75	483	0	ENST00000285071.4:c.50G>A	p.Arg17His	p.R17H	ENST00000285071	NM_144997.5	17	cGc/cAc	4/14	0.894023319401341	1	FACETS	0.11	0.095	0.125	0.11	0.095	0.125	SUBCLONAL	1	TRUE	0	0.894023319401341	1		483	846	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913407	NA	P-0015953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	405	475	0	ENST00000349496.5:c.133T>G	p.Ser45Ala	p.S45A	ENST00000349496	NM_001904.3	45	Tct/Gct	3/15	0.894023319401341	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.894023319401341	1		475	458	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920173	76920173	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	301	486	0	ENST00000373344.5:c.3904del	p.Arg1302GlufsTer44	p.R1302Efs*44	ENST00000373344	NM_000489.3	1302	Aga/ga	11/35	0.894023319401341	1	FACETS	0.856	0.823	0.888	0.856	0.823	0.888	CLONAL	1	TRUE	0	0.894023319401341	1		486	435	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101063	27101063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	67	629	0	ENST00000324856.7:c.4345G>A	p.Gly1449Ser	p.G1449S	ENST00000324856	NM_006015.4	1449	Ggc/Agc	18/20	0.894023319401341	1	FACETS	0.073	0.063	0.084	0.073	0.063	0.084	SUBCLONAL	1	TRUE	0	0.894023319401341	1		629	1132	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307348	118307348	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	35	33	0	ENST00000534358.1:c.126del	p.Pro45ArgfsTer105	p.P45Rfs*105	ENST00000534358	NM_005933.3	41	Ccc/cc	1/36	0.894023319401341	1	FACETS	0.984	0.888	1	0.984	0.888	1	CLONAL	1	TRUE	0	0.894023319401341	1		33	44	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431760	49431760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748336297	NA	P-0015953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	279	554	2	ENST00000301067.7:c.9379C>T	p.Arg3127Cys	p.R3127C	ENST00000301067	NM_003482.3	3127	Cgc/Tgc	34/54	0.273942604611815	2	FACETS	0.611	0.575	0.649	0.306	0.287	0.325	INDETERMINATE	1	TRUE	0	0.894023319401341	2		556	1021	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445500	49445500	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs886042284	NA	P-0015953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1483	196	747	2	ENST00000301067.7:c.1966del	p.Leu656CysfsTer274	p.L656Cfs*274	ENST00000301067	NM_003482.3	656	Ctg/tg	10/54	0.273942604611815	2	FACETS	0.261	0.24	0.283	0.131	0.12	0.142	INDETERMINATE	1	TRUE	0	0.894023319401341	2		749	1679	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859426	57859426	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756656703	NA	P-0015953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	341	391	0	ENST00000228682.2:c.571C>T	p.Arg191Trp	p.R191W	ENST00000228682	NM_005269.2	191	Cgg/Tgg	6/12	0.273942604611815	2	FACETS	0.722	0.684	0.76	0.361	0.342	0.38	INDETERMINATE	1	TRUE	0	0.894023319401341	2		391	1057	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2089939	2089939	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1337853224	NA	P-0015953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	62	501	0	ENST00000219066.1:c.925G>A	p.Ala309Thr	p.A309T	ENST00000219066	NM_002528.5	309	Gcc/Acc	6/6	0.556578795952341	1	FACETS	0.103	0.088	0.119	0.103	0.088	0.119	SUBCLONAL	1	TRUE	0	0.894023319401341	1		501	746	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777990	3777990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1423752547	NA	P-0015953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1315	375	912	4	ENST00000262367.5:c.7058G>A	p.Arg2353Gln	p.R2353Q	ENST00000262367	NM_004380.2	2353	cGg/cAg	31/31	0.556578795952341	1	FACETS	0.274	0.259	0.29	0.274	0.259	0.29	SUBCLONAL	1	TRUE	0	0.894023319401341	1		916	1690	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831418	89831418	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	553	519	0	ENST00000389301.3:c.2658G>T	p.Glu886Asp	p.E886D	ENST00000389301	NM_000135.2	886	gaG/gaT	28/43	0.403273081240336	1	FACETS	0.669	0.645	0.692	0.669	0.645	0.692	INDETERMINATE	1	TRUE	0	0.894023319401341	1		519	1023	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29662025	29662025	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	415	351	0	ENST00000356175.3:c.5923del	p.Ile1975TyrfsTer16	p.I1975Yfs*16	ENST00000356175	NM_000267.3	1973	gcA/gc	39/57	0.894023319401341	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.894023319401341	1		351	497	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880264	37880264	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1375812476	NA	P-0015953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	44	519	1	ENST00000269571.5:c.2307+1G>A		p.X769_splice	ENST00000269571		769			0.894023319401341	1	FACETS	0.065	0.054	0.077	0.065	0.054	0.077	SUBCLONAL	1	TRUE	0	0.894023319401341	1		520	837	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78866606	78866606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	1581	482	4	ENST00000306801.3:c.2179C>T	p.Arg727Cys	p.R727C	ENST00000306801	NM_020761.2	727	Cgt/Tgt	19/34	0.894023319401341	3	FACETS	0.998	0.989	1	0.998	0.989	1	CLONAL	3	TRUE	0	0.894023319401341	3		486	1710	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942533	17942533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	811	562	1	ENST00000458235.1:c.2755G>A	p.Ala919Thr	p.A919T	ENST00000458235	NM_000215.3	919	Gcg/Acg	20/24	0.209828733976072	4	FACETS	0.999	0.968	1	0.999	0.968	1	INDETERMINATE	2	TRUE	2	0.894023319401341	4		563	1720	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965985	18965985	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	811	542	0	ENST00000262803.5:c.1478C>T	p.Pro493Leu	p.P493L	ENST00000262803	NM_002911.3	493	cCg/cTg	11/24	0.209828733976072	4	FACETS	0.976	0.946	1	0.976	0.946	1	INDETERMINATE	2	TRUE	2	0.894023319401341	4		542	1760	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656943	47656943	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0015953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	462	315	0	ENST00000233146.2:c.1139T>A	p.Leu380Ter	p.L380*	ENST00000233146	NM_000251.2	380	tTa/tAa	7/16	0.894023319401341	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.894023319401341	1		315	519	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630600	158630600	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	312	244	1	ENST00000263640.3:c.643G>A	p.Gly215Arg	p.G215R	ENST00000263640	NM_001105.4	215	Ggg/Agg	6/11	0.894023319401341	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.894023319401341	1		245	354	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735465	204735465	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1559591751	NA	P-0015953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	75	350	0	ENST00000302823.3:c.266A>G	p.Tyr89Cys	p.Y89C	ENST00000302823	NM_005214.4	89	tAc/tGc	2/4	0.894023319401341	1	FACETS	0.166	0.145	0.188	0.166	0.145	0.188	SUBCLONAL	1	TRUE	0	0.894023319401341	1		350	559	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515324	31515324	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs187981384	NA	P-0015953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	451	432	1	ENST00000344624.3:c.1061G>A	p.Arg354His	p.R354H	ENST00000344624		354	cGc/cAc	5/33	0.312676784590934	2	FACETS	1	0.995	1	0.602	0.579	0.625	INDETERMINATE	1	TRUE	0	0.894023319401341	2		433	838	SUCCESS
APC	324	MSKCC	GRCh37	5	112176153	112176154	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0015953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	312	419	0	ENST00000257430.4:c.4864_4865del	p.Asn1622GlnfsTer9	p.N1622Qfs*9	ENST00000257430	NM_000038.5	1621	cAA/c	16/16	0.312676784590934	2	FACETS	0.723	0.684	0.764	0.362	0.342	0.382	INDETERMINATE	1	TRUE	0	0.894023319401341	2		419	965	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946226	13946230	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TAAAT	TAAAT	-	novel	NA	P-0015953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	386	320	0	ENST00000405192.2:c.872-6_872-2del		p.X291_splice	ENST00000405192	NM_001163147.1	291			0.312676784590934	2	FACETS	1	0.994	1	0.612	0.586	0.637	INDETERMINATE	1	TRUE	0	0.894023319401341	2		320	706	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93626940	93626940	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199886319	NA	P-0015953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	471	399	0	ENST00000375746.1:c.787G>A	p.Gly263Ser	p.G263S	ENST00000375746	NM_001174167.1	263	Ggc/Agc	5/14	0.209828733976072	4	FACETS	0.837	0.801	0.873	0.837	0.801	0.873	INDETERMINATE	2	TRUE	2	0.894023319401341	4		399	1192	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231199	98231199	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	607	452	0	ENST00000331920.6:c.2084A>G	p.Asp695Gly	p.D695G	ENST00000331920	NM_000264.3	695	gAc/gGc	14/24	0.336909253178177	4	FACETS	0.916	0.883	0.949	0.916	0.883	0.949	INDETERMINATE	2	TRUE	2	0.894023319401341	4		452	1404	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0015954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	308	356	0	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	TRUE	1	NA	2		356	751	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022253	31022253	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0015954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	200	282	0	ENST00000375687.4:c.1738A>T	p.Lys580Ter	p.K580*	ENST00000375687	NM_015338.5	580	Aaa/Taa	13/13	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		282	491	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0015955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	61	605	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.979	0.846	1	0.979	0.846	1	CLONAL	1	TRUE	1	0.24	2		606	519	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0015955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	68	707	3	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	1	2	FACETS	0.827	0.719	0.944	0.827	0.719	0.944	CLONAL	1	TRUE	1	0.24	2		710	685	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243560	46243560	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs779708870	NA	P-0015955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	34	237	0	ENST00000334344.6:c.1912+1G>A		p.X638_splice	ENST00000334344	NM_152641.2	638			1	2	FACETS	0.974	0.799	1	0.974	0.799	1	CLONAL	1	TRUE	1	0.24	2		237	291	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865223	57865223	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	60	717	0	ENST00000228682.2:c.2700T>G	p.Asn900Lys	p.N900K	ENST00000228682	NM_005269.2	900	aaT/aaG	12/12	1	2	FACETS	0.773	0.665	0.89	0.773	0.665	0.89	SUBCLONAL	1	TRUE	1	0.24	2		717	647	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041755	29041755	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0015955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	21	259	0	ENST00000282397.4:c.65-1G>T		p.X22_splice	ENST00000282397	NM_002019.4	22			1	2	FACETS	0.57	0.439	0.723	0.57	0.439	0.723	SUBCLONAL	1	TRUE	1	0.24	2		259	307	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274099	10274099	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	28	608	0	ENST00000330684.3:c.170C>G	p.Pro57Arg	p.P57R	ENST00000330684	NM_001134407.1	57	cCc/cGc	2/13	1	2	FACETS	0.417	0.333	0.515	0.417	0.333	0.515	SUBCLONAL	1	TRUE	1	0.24	2		608	559	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602785	10602785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	43	867	0	ENST00000171111.5:c.793C>T	p.Gln265Ter	p.Q265*	ENST00000171111	NM_203500.1	265	Cag/Tag	3/6	1	2	FACETS	0.525	0.438	0.621	0.525	0.438	0.621	SUBCLONAL	1	TRUE	1	0.24	2		867	683	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197795	123197795	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	36	552	0	ENST00000218089.9:c.1919G>T	p.Cys640Phe	p.C640F	ENST00000218089	NM_001042749.1	640	tGt/tTt	20/35	NA	2	FACETS	0.645	0.53	0.774			1	INDETERMINATE	1	TRUE	NA	0.24	2		552	465	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152093	55152093	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121908585	NA	P-0015956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	364	402	0	ENST00000257290.5:c.2525A>T	p.Asp842Val	p.D842V	ENST00000257290	NM_006206.4	842	gAc/gTc	18/23	0.829002775542699	1	FACETS	0.977	0.943	1	0.977	0.943	1	CLONAL	1	TRUE	0	0.829002775542699	1		402	526	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	61	503	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.15	0.129	0.174	0.15	0.129	0.174	SUBCLONAL	1	TRUE	1	0.784421352705488	2		503	1035	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024001	27024002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	12	118	1	ENST00000324856.7:c.1113dup	p.Gln372AlafsTer28	p.Q372Afs*28	ENST00000324856	NM_006015.4	369	-/G	1/20	1	2	FACETS	0.127	0.089	0.175	0.127	0.089	0.175	SUBCLONAL	1	TRUE	1	0.784421352705488	2		119	240	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716352	52716352	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	389	482	0	ENST00000322088.6:c.796A>C	p.Lys266Gln	p.K266Q	ENST00000322088	NM_014225.5	266	Aag/Cag	6/15	1	2	FACETS	0.973	0.927	1	0.973	0.927	1	CLONAL	1	TRUE	1	0.784421352705488	2		482	1019	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250242	110250242	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1222896190	NA	P-0015957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	439	600	1	ENST00000374672.4:c.433C>T	p.Pro145Ser	p.P145S	ENST00000374672	NM_004235.4	145	Ccc/Tcc	3/5	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.784421352705488	2		601	1061	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844193	68844193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121964873	NA	P-0015958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	159	709	2	ENST00000261769.5:c.781G>A	p.Glu261Lys	p.E261K	ENST00000261769	NM_004360.3	261	Gaa/Aaa	6/16	0.165462741335042	0	FACETS	0.419	0.385	0.455			1	INDETERMINATE	1	TRUE	0	0.510099767106865	0		711	729	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652147	3652147	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775151113	NA	P-0015958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	130	881	3	ENST00000294008.3:c.922G>A	p.Val308Met	p.V308M	ENST00000294008	NM_032444.2	308	Gtg/Atg	4/15	0.154749173749772	2	FACETS	0.501	0.453	0.551	0.25	0.226	0.276	INDETERMINATE	1	TRUE	0	0.510099767106865	2		884	1018	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876520	59876520	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	151	576	0	ENST00000259008.2:c.1281C>A	p.Asn427Lys	p.N427K	ENST00000259008	NM_032043.2	427	aaC/aaA	9/20	0.199242867493412	2	FACETS	0.61	0.557	0.665	0.305	0.278	0.333	INDETERMINATE	1	TRUE	0	0.510099767106865	2		576	971	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535378	66535378	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	163	869	0	ENST00000273854.3:c.83T>A	p.Leu28Gln	p.L28Q	ENST00000273854	NM_004439.5	28	cTg/cAg	1/18	0.435636044987792	2	FACETS	0.731	0.671	0.794	0.366	0.335	0.397	SUBCLONAL	1	TRUE	0	0.510099767106865	2		869	874	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	482	248	0				ENST00000310581	NM_198253.2	-/1132			0.798954723198721	3	FACETS	0.931	0.896	0.965	0.931	0.896	0.965	CLONAL	2	TRUE	1	0.798954723198721	3		248	907	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0015959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	297	235	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.798954723198721	3	FACETS	0.967	0.922	1	0.645	0.615	0.675	CLONAL	2	TRUE	0	0.798954723198721	3		235	538	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0015959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	1002	588	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.798954723198721	3	FACETS	0.997	0.982	1	0.997	0.982	1	CLONAL	3	TRUE	0	0.798954723198721	3		588	1174	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714396	117714396	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	183	350	0	ENST00000368508.3:c.1253C>T	p.Ser418Leu	p.S418L	ENST00000368508	NM_002944.2	418	tCa/tTa	11/43	1	2	FACETS	0.981	0.914	1	0.981	0.914	1	CLONAL	1	TRUE	1	0.798954723198721	2		350	467	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312683	91312683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759330541	NA	P-0015959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	143	264	0	ENST00000355112.3:c.2422C>T	p.Arg808Cys	p.R808C	ENST00000355112	NM_000057.2	808	Cgt/Tgt	12/22	0.791602148522773	4	FACETS	0.899	0.821	0.981	0.3	0.273	0.327	CLONAL	1	TRUE	1	0.798954723198721	4		264	716	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325023	123325023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	267	528	1	ENST00000358487.5:c.305C>T	p.Ser102Phe	p.S102F	ENST00000358487	NM_000141.4	102	tCc/tTc	3/18	1	2	FACETS	0.85	0.801	0.901	0.85	0.801	0.901	CLONAL	1	TRUE	1	0.798954723198721	2		529	786	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100062	30100062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1182	275	584	0	ENST00000331968.5:c.1558C>T	p.Leu520Phe	p.L520F	ENST00000331968	NM_002742.2	520	Ctc/Ttc	10/18	0.744852971870842	4	FACETS	0.85	0.796	0.906	0.425	0.398	0.453	CLONAL	1	TRUE	2	0.798954723198721	4		584	1457	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50830259	50830259	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	425	410	0	ENST00000398568.2:c.2702C>T	p.Pro901Leu	p.P901L	ENST00000398568	NM_001042412.1	901	cCt/cTt	18/18	0.798954723198721	3	FACETS	0.945	0.908	0.982	0.945	0.908	0.982	CLONAL	2	TRUE	1	0.798954723198721	3		410	788	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366369	15366369	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	336	304	0	ENST00000263377.2:c.1786C>T	p.Pro596Ser	p.P596S	ENST00000263377	NM_058243.2	596	Cct/Tct	10/20	0.670793748278412	4	FACETS	0.913	0.867	0.959	0.913	0.867	0.959	CLONAL	2	TRUE	2	0.798954723198721	4		304	829	SUCCESS
AXL	558	MSKCC	GRCh37	19	41759558	41759558	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	625	709	0	ENST00000301178.4:c.1981G>A	p.Glu661Lys	p.E661K	ENST00000301178	NM_021913.4	661	Gag/Aag	17/20	0.523110214427183	4	FACETS	0.892	0.859	0.925	0.892	0.859	0.925	CLONAL	2	TRUE	2	0.798954723198721	4		709	1578	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190742017	190742017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	190	408	0	ENST00000441310.2:c.2654C>T	p.Ser885Phe	p.S885F	ENST00000441310	NM_000534.4	885	tCc/tTc	13/13	0.798954723198721	3	FACETS	0.828	0.767	0.891	0.414	0.383	0.446	CLONAL	1	TRUE	1	0.798954723198721	3		408	804	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251637	212251637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	441	350	0	ENST00000342788.4:c.3422C>T	p.Pro1141Leu	p.P1141L	ENST00000342788	NM_005235.2	1141	cCa/cTa	27/28	0.798954723198721	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.798954723198721	3		350	742	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980769	40980769	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	283	458	1	ENST00000373198.4:c.1717G>A	p.Gly573Ser	p.G573S	ENST00000373198	NM_133170.3	573	Ggc/Agc	10/32	0.744852971870842	4	FACETS	1	0.952	1	0.508	0.476	0.54	CLONAL	1	TRUE	2	0.798954723198721	4		459	1255	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164735	36164735	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	713	680	1	ENST00000300305.3:c.1140C>A	p.Tyr380Ter	p.Y380*	ENST00000300305		380	taC/taA	8/8	0.798954723198721	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.798954723198721	3		681	1215	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795337	39795337	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	232	431	0	ENST00000288319.7:c.383C>T	p.Pro128Leu	p.P128L	ENST00000288319	NM_182918.3	128	cCa/cTa	3/10	0.798954723198721	3	FACETS	0.984	0.92	1	0.492	0.46	0.525	CLONAL	1	TRUE	1	0.798954723198721	3		431	826	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747924	41747924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	609	606	1	ENST00000226382.2:c.845C>T	p.Ser282Phe	p.S282F	ENST00000226382	NM_003924.3	282	tCc/tTc	3/3	0.798954723198721	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.798954723198721	2		607	756	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971152	55971152	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0015959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	536	439	0	ENST00000263923.4:c.1646-1G>A		p.X549_splice	ENST00000263923	NM_002253.2	549			0.798954723198721	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.798954723198721	2		439	658	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164055	106164055	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	285	296	0	ENST00000380013.4:c.3565A>C	p.Ser1189Arg	p.S1189R	ENST00000380013	NM_001127208.2	1189	Agt/Cgt	5/11	0.798954723198721	2	FACETS	0.98	0.947	1	0.98	0.947	1	CLONAL	2	TRUE	0	0.798954723198721	2		296	364	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159060	143159060	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	289	328	0	ENST00000262992.4:c.793C>T	p.Pro265Ser	p.P265S	ENST00000262992	NM_001101669.1	265	Cct/Tct	10/24	0.798954723198721	2	FACETS	0.994	0.961	1	0.994	0.961	1	CLONAL	2	TRUE	0	0.798954723198721	2		328	364	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499586	149499586	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	434	499	1	ENST00000261799.4:c.2687T>G	p.Ile896Ser	p.I896S	ENST00000261799	NM_002609.3	896	aTc/aGc	19/23	0.798954723198721	3	FACETS	0.904	0.868	0.94	0.904	0.868	0.94	CLONAL	2	TRUE	1	0.798954723198721	3		500	841	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178633	32178633	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	1040	656	1	ENST00000375023.3:c.2761G>A	p.Gly921Arg	p.G921R	ENST00000375023	NM_004557.3	921	Gga/Aga	18/30	0.798954723198721	4	FACETS	0.987	0.965	1	0.987	0.965	1	CLONAL	3	TRUE	1	0.798954723198721	4		657	1582	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956573	93956573	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	172	317	0	ENST00000369303.4:c.2663G>A	p.Gly888Glu	p.G888E	ENST00000369303	NM_004440.3	888	gGa/gAa	15/17	0.798954723198721	4	FACETS	0.949	0.875	1	0.316	0.291	0.343	CLONAL	1	TRUE	1	0.798954723198721	4		317	816	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979485	2979485	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	321	555	2	ENST00000396946.4:c.762G>T	p.Lys254Asn	p.K254N	ENST00000396946	NM_032415.4	254	aaG/aaT	6/25	0.798954723198721	4	FACETS	0.95	0.895	1	0.475	0.447	0.504	CLONAL	1	TRUE	2	0.798954723198721	4		557	1521	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950455	68950455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	265	406	0	ENST00000288368.4:c.767C>T	p.Ser256Phe	p.S256F	ENST00000288368	NM_024870.2	256	tCt/tTt	7/40	0.798954723198721	3	FACETS	0.961	0.902	1	0.481	0.451	0.511	CLONAL	1	TRUE	1	0.798954723198721	3		406	966	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633401	8633401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	434	422	0	ENST00000356435.5:c.268C>T	p.Pro90Ser	p.P90S	ENST00000356435		90	Ccg/Tcg	3/35	0.670793748278412	4	FACETS	0.927	0.887	0.968	0.927	0.887	0.968	CLONAL	2	TRUE	2	0.798954723198721	4		422	1054	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44970634	44970634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	514	210	0	ENST00000377967.4:c.4184C>T	p.Pro1395Leu	p.P1395L	ENST00000377967	NM_021140.2	1395	cCa/cTa	29/29	0.682898911079643	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.798954723198721	2		210	558	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061313	38061313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1204900727	NA	P-0015960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1214	547	781	0	ENST00000250448.2:c.676G>A	p.Asp226Asn	p.D226N	ENST00000250448	NM_004496.3	226	Gac/Aac	2/2	0.158342098660852	5	FACETS	1	0.974	1	0.681	0.653	0.711	INDETERMINATE	2	TRUE	2	0.558496202514816	5		781	1761	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99460053	99460053	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	68	454	0	ENST00000268035.6:c.2149G>C	p.Glu717Gln	p.E717Q	ENST00000268035	NM_000875.3	717	Gaa/Caa	10/21	0.169438459887238	2	FACETS	0.282	0.244	0.322	0.141	0.122	0.161	INDETERMINATE	1	TRUE	0	0.558496202514816	2		454	865	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589606	67589611	+	inframe_deletion	In_Frame_Del	DEL	CAAGAA	CAAGAA	-	novel	NA	P-0015960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	113	286	0	ENST00000274335.5:c.1369_1374del	p.Gln457_Glu458del	p.Q457_E458del	ENST00000274335		457	CAAGAA/-	10/15	0.316265948965533	1	FACETS	0.746	0.677	0.817	0.746	0.677	0.817	INDETERMINATE	1	TRUE	0	0.558496202514816	1		286	391	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202925	27202925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749958421	NA	P-0015960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1390	155	466	0	ENST00000380036.4:c.2017C>T	p.Arg673Cys	p.R673C	ENST00000380036	NM_000459.3	673	Cgt/Tgt	13/23	0.558496202514816	4	FACETS	0.56	0.511	0.612	0.187	0.17	0.204	SUBCLONAL	1	TRUE	1	0.558496202514816	4		466	1545	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775719	9775719	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	88	613	0	ENST00000377346.4:c.262C>A	p.Arg88Ser	p.R88S	ENST00000377346	NM_005026.3	88	Cgt/Agt	4/24	0.148710920050336	3	FACETS	0.726	0.641	0.817	0.363	0.32	0.409	SUBCLONAL	1	TRUE	1	0.216190834523511	3		613	1243	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988452	41988455	+	frameshift_variant	Frame_Shift_Del	DEL	CAAA	CAAA	-	novel	NA	P-0015962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	467	448	0	ENST00000219905.7:c.1246_1249del	p.Asn416ValfsTer7	p.N416Vfs*7	ENST00000219905	NM_001164273.1	415	tCAAAc/tc	3/24	0.452917491531226	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.524316281909272	3		448	979	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105512	30105512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768104173	NA	P-0015962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	82	361	0	ENST00000331968.5:c.1174G>A	p.Ala392Thr	p.A392T	ENST00000331968	NM_002742.2	392	Gcc/Acc	7/18	0.362455236462339	4	FACETS	0.433	0.38	0.49			1	SUBCLONAL	1	TRUE	NA	0.524316281909272	4		361	1101	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687288	37687288	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	266	363	0	ENST00000447079.4:c.4192C>A	p.Pro1398Thr	p.P1398T	ENST00000447079	NM_015083.1	1398	Cca/Aca	14/14	0.257830043238916	4	FACETS	0.829	0.778	0.881	0.829	0.778	0.881	INDETERMINATE	2	TRUE	2	0.524316281909272	4		363	933	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091809	29091809	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202089930	NA	P-0015962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	506	496	0	ENST00000328354.6:c.1148C>T	p.Thr383Ile	p.T383I	ENST00000328354	NM_007194.3	383	aCc/aTc	11/15	0.524316281909272	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.524316281909272	3		496	1100	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729382	41729382	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	190	433	0	ENST00000242208.4:c.1147C>G	p.Pro383Ala	p.P383A	ENST00000242208	NM_002192.2	383	Ccc/Gcc	3/3	0.15405693281148	3	FACETS	1	0.987	1	0.646	0.6	0.693	INDETERMINATE	1	TRUE	1	0.616278044499889	3		433	624	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352367	70352367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	103	482	0	ENST00000374080.3:c.4394G>A	p.Arg1465His	p.R1465H	ENST00000374080		1465	cGt/cAt	31/45	0.616278044499889	1	FACETS	0.577	0.52	0.636	0.577	0.52	0.636	SUBCLONAL	1	TRUE	0	0.616278044499889	1		482	401	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0015964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	251	541	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.541638059046432	6	FACETS	1	0.978	1	0.277	0.258	0.296	INDETERMINATE	1	TRUE	2	0.921513617448758	6		541	1399	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0015964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	207	467	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.839028384415964	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.921513617448758	1		468	235	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	334	354	1	ENST00000263967.3:c.3012G>A	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atA	21/21	0.541638059046432	6	FACETS	1	0.967	1	0.514	0.486	0.541	INDETERMINATE	2	TRUE	2	0.921513617448758	6		355	1003	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770065	56770065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752608224	NA	P-0015964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	116	463	0	ENST00000337432.4:c.61C>T	p.Pro21Ser	p.P21S	ENST00000337432	NM_058216.2	21	Cca/Tca	1/9	0.839028384415964	1	FACETS	0.552	0.508	0.596	0.552	0.508	0.596	SUBCLONAL	1	TRUE	0	0.921513617448758	1		463	246	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175891	176175891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1227884588	NA	P-0015964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	31	145	0	ENST00000367669.3:c.224C>T	p.Ser75Leu	p.S75L	ENST00000367669	NM_022457.5	75	tCg/tTg	1/20	NA	2	FACETS	0.53	0.436	0.631			1	INDETERMINATE	1	TRUE	NA	0.921513617448758	2		145	127	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114901023	114901023	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs979684293	NA	P-0015964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	239	584	0	ENST00000543371.1:c.633C>A	p.Phe211Leu	p.F211L	ENST00000543371	NM_001198531.1	211	ttC/ttA	6/14	0.432195969265131	1	FACETS	0.639	0.605	0.672	0.639	0.605	0.672	INDETERMINATE	1	TRUE	0	0.921513617448758	1		584	438	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494962	56494962	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	204	441	0	ENST00000267101.3:c.3319G>C	p.Glu1107Gln	p.E1107Q	ENST00000267101	NM_001982.3	1107	Gag/Cag	27/28	0.8030905329315	3	FACETS	1	0.982	1	0.571	0.534	0.61	CLONAL	1	TRUE	1	0.921513617448758	3		441	566	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987165	36987165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	145	756	0	ENST00000354822.5:c.524C>T	p.Ser175Leu	p.S175L	ENST00000354822	NM_001079668.2	175	tCg/tTg	3/3	0.425616178143163	1	FACETS	0.392	0.361	0.424	0.392	0.361	0.424	INDETERMINATE	1	TRUE	0	0.921513617448758	1		756	433	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39595513	39595513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746929631	NA	P-0015964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	152	327	1	ENST00000262039.4:c.1399G>A	p.Asp467Asn	p.D467N	ENST00000262039	NM_002647.2	467	Gat/Aat	12/25	0.921513617448758	1	FACETS	0.589	0.549	0.629	0.589	0.549	0.629	SUBCLONAL	1	TRUE	0	0.921513617448758	1		328	302	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3094724	3094724	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	173	527	0	ENST00000078429.4:c.75C>G	p.Ile25Met	p.I25M	ENST00000078429	NM_002067.2	25	atC/atG	1/7	0.921513617448758	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.921513617448758	1		527	197	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660992	227660992	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	291	410	1	ENST00000305123.5:c.2463C>A	p.Cys821Ter	p.C821*	ENST00000305123	NM_005544.2	821	tgC/tgA	1/2	0.921513617448758	5	FACETS	0.964	0.912	1			1	CLONAL	2	TRUE	NA	0.921513617448758	5		411	780	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662172	227662172	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	390	586	2	ENST00000305123.5:c.1283C>A	p.Ser428Ter	p.S428*	ENST00000305123	NM_005544.2	428	tCg/tAg	1/2	0.921513617448758	5	FACETS	0.928	0.883	0.973			1	CLONAL	2	TRUE	NA	0.921513617448758	5		588	1087	SUCCESS
ATR	545	MSKCC	GRCh37	3	142218544	142218544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	215	349	0	ENST00000350721.4:c.5305G>A	p.Glu1769Lys	p.E1769K	ENST00000350721	NM_001184.3	1769	Gaa/Aaa	31/47	0.541638059046432	6	FACETS	1	0.991	1	0.368	0.342	0.394	INDETERMINATE	1	TRUE	2	0.921513617448758	6		349	902	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952478	38952478	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	122	276	0	ENST00000357387.3:c.2947G>C	p.Asp983His	p.D983H	ENST00000357387	NM_152756.3	983	Gat/Cat	30/38	0.304222324490184	4	FACETS	0.96	0.872	1	0.48	0.436	0.526	INDETERMINATE	1	TRUE	2	0.921513617448758	4		276	530	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176561	56176561	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1561198459	NA	P-0015964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	301	355	0	ENST00000399503.3:c.2111C>G	p.Ser704Ter	p.S704*	ENST00000399503	NM_005921.1	704	tCa/tGa	12/20	0.574997652170001	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.921513617448758	1		355	337	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031939	26031939	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	169	291	0	ENST00000244661.2:c.350G>A	p.Arg117Gln	p.R117Q	ENST00000244661	NM_003537.3	117	cGa/cAa	1/1	0.8030905329315	3	FACETS	1	0.988	1	0.661	0.616	0.708	CLONAL	1	TRUE	1	0.921513617448758	3		291	405	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679733	30679733	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	240	484	1	ENST00000376406.3:c.1986G>T	p.Gln662His	p.Q662H	ENST00000376406	NM_014641.2	662	caG/caT	5/15	0.202112462575005	4	FACETS	0.941	0.887	0.994	0.941	0.887	0.994	INDETERMINATE	2	TRUE	2	0.921513617448758	4		485	532	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965690	93965690	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	336	430	2	ENST00000369303.4:c.2238G>C	p.Met746Ile	p.M746I	ENST00000369303	NM_004440.3	746	atG/atC	13/17	0.304222324490184	4	FACETS	0.973	0.927	1	0.973	0.927	1	INDETERMINATE	2	TRUE	2	0.921513617448758	4		432	720	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976761	2976761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	78	739	1	ENST00000396946.4:c.1251G>A	p.Met417Ile	p.M417I	ENST00000396946	NM_032415.4	417	atG/atA	9/25	0.921513617448758	1	FACETS	0.348	0.31	0.389	0.348	0.31	0.389	SUBCLONAL	1	TRUE	0	0.921513617448758	1		740	262	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975403	13975403	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	176	405	1	ENST00000405192.2:c.484G>T	p.Asp162Tyr	p.D162Y	ENST00000405192	NM_001163147.1	162	Gac/Tac	7/12	0.69049606246223	1	FACETS	0.601	0.563	0.638	0.601	0.563	0.638	SUBCLONAL	1	TRUE	0	0.921513617448758	1		406	343	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862873	117862875	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0015964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1253	246	381	0	ENST00000297338.2:c.1602_1604del	p.Glu534del	p.E534del	ENST00000297338	NM_006265.2	534	gaAGAt/gat	12/14	0.541638059046432	6	FACETS	1	0.943	1	0.253	0.236	0.271	INDETERMINATE	1	TRUE	2	0.921513617448758	6		381	1499	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	66	248	0				ENST00000310581	NM_198253.2	-/1132			0.164922427094393	2	FACETS	1	0.938	1	0.563	0.492	0.64	INDETERMINATE	1	TRUE	0	0.333826822402793	2		248	351	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030364	49030364	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	55	216	0	ENST00000267163.4:c.1841del	p.Lys614ArgfsTer9	p.K614Rfs*9	ENST00000267163	NM_000321.2	613	ccA/cc	19/27	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.333826822402793	2		216	298	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803172	1803172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775241791	NA	P-0015965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	119	560	2	ENST00000260795.2:c.524G>A	p.Arg175His	p.R175H	ENST00000260795		175	cGc/cAc	4/17	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.333826822402793	2		562	657	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30668406	30668406	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	107	281	0	ENST00000376406.3:c.6106C>T	p.Gln2036Ter	p.Q2036*	ENST00000376406	NM_014641.2	2036	Cag/Tag	15/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.333826822402793	2		281	521	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	1911	507	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.32777492854134	6	FACETS	1	0.997	1	1	0.999	1	CLONAL	7	TRUE	1	0.32777492854134	6		507	2652	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602340	10602340	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	265	956	0	ENST00000171111.5:c.1238G>T	p.Arg413Leu	p.R413L	ENST00000171111	NM_203500.1	413	cGt/cTt	3/6	0.32777492854134	1	FACETS	0.872	0.821	0.924	1	0.995	1	CLONAL	2	TRUE	0	0.32777492854134	1		956	775	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220792	1221631	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGTGGGCGCAGGGCGTGGCCACCGGCCCAGACCCTCTCTGGCCACAGCCGCTAGGGGGTGCTTACTTTATGGAAATGTAACTCATACGGCAGATGGTGGTTCACCCGTGTGAAGTGCAGCCTGGCCCGTCAGGGATCTTCACAGAGTGGCACGGCCGACCCTCCTCCCAGAGCCCCACAGGGAAGCTGGGCGGGTGACAGCAGCTCCAGGCCCCTTCCCCGGGTGGGTCCAGAGGACACTCCCCTCCTACCCCGTAGCCTCCACTAGTGGAAGGTGGTGAAGACAGAGGTGTCCTTGAGTCCACAGGGCCTCTGGTCCAGCAGCCACGGGACGCCTCTGTCCCTGGGGTAGAGCTGGGGCTCCTAGGGCGTCAACCACCTTGACTGACCACGCCTTTCTTCCCTCCCCTCGAAATGAAGCTACAACATCACCACGGGTCTGTACCCCTTCGAAGGGGACAACATCTACAAGTTGTTTGAGAACATCGGGAAGGGGAGCTACGCCATCCCGGGCGACTGTGGCCCCCCGCTCTCTGACCTGCTGAAAGGTGGGAGCCTCATCCCTCTGCCCGCAGCCCCAGGGAGGCGGGGCTTTTGTGCAGAAATGTAGGGTTGGGGGTGTCAGGTGGGGGGCTATTGGCCCCGAGACCCCAGCAGGCATTGAGAGGACTGAGTGGAGAGGCCGACCTCCCCGCAGGGCCTGGTTTGCCAGGTCCCTCAGCTCCACCCTGCTTCTGGGCCCTGTTCACCCTCCGAACTCCCACCCCAGAGGGCAGTGCTGCCCTGCGCCTCCCCCAGCCCCACCCTCGGGGGCTCCCTGGCTTGCAGGGTCTGTCAGGG	CTGTGGGCGCAGGGCGTGGCCACCGGCCCAGACCCTCTCTGGCCACAGCCGCTAGGGGGTGCTTACTTTATGGAAATGTAACTCATACGGCAGATGGTGGTTCACCCGTGTGAAGTGCAGCCTGGCCCGTCAGGGATCTTCACAGAGTGGCACGGCCGACCCTCCTCCCAGAGCCCCACAGGGAAGCTGGGCGGGTGACAGCAGCTCCAGGCCCCTTCCCCGGGTGGGTCCAGAGGACACTCCCCTCCTACCCCGTAGCCTCCACTAGTGGAAGGTGGTGAAGACAGAGGTGTCCTTGAGTCCACAGGGCCTCTGGTCCAGCAGCCACGGGACGCCTCTGTCCCTGGGGTAGAGCTGGGGCTCCTAGGGCGTCAACCACCTTGACTGACCACGCCTTTCTTCCCTCCCCTCGAAATGAAGCTACAACATCACCACGGGTCTGTACCCCTTCGAAGGGGACAACATCTACAAGTTGTTTGAGAACATCGGGAAGGGGAGCTACGCCATCCCGGGCGACTGTGGCCCCCCGCTCTCTGACCTGCTGAAAGGTGGGAGCCTCATCCCTCTGCCCGCAGCCCCAGGGAGGCGGGGCTTTTGTGCAGAAATGTAGGGTTGGGGGTGTCAGGTGGGGGGCTATTGGCCCCGAGACCCCAGCAGGCATTGAGAGGACTGAGTGGAGAGGCCGACCTCCCCGCAGGGCCTGGTTTGCCAGGTCCCTCAGCTCCACCCTGCTTCTGGGCCCTGTTCACCCTCCGAACTCCCACCCCAGAGGGCAGTGCTGCCCTGCGCCTCCCCCAGCCCCACCCTCGGGGGCTCCCTGGCTTGCAGGGTCTGTCAGGG	-	novel	NA	P-0015967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	51	195	0	ENST00000326873.7:c.734+76_862+292del		p.X245_splice	ENST00000326873	NM_000455.4	245		6/10	0.32777492854134	1	FACETS	1	0.893	1	1	0.979	1	CLONAL	2	TRUE	0	0.32777492854134	1		195	127	SUCCESS
ATR	545	MSKCC	GRCh37	3	142224024	142224025	+	missense_variant	Missense_Mutation	DNP	GC	GC	AT	novel	NA	P-0015967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	151	798	1	ENST00000350721.4:c.5152_5153delinsAT	p.Ala1718Ile	p.A1718I	ENST00000350721	NM_001184.3	1718	GCc/ATc	29/47	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.32777492854134	2		799	864	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	186	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.981	0.913	1	0.981	0.913	1	CLONAL	1	TRUE	1	0.7019717737741	2		248	540	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0015968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	295	704	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	0.7019717737741	2		705	823	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612028	189612028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs900140738	NA	P-0015968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	212	465	0	ENST00000264731.3:c.1780C>T	p.Arg594Ter	p.R594*	ENST00000264731	NM_003722.4	594	Cga/Tga	14/14	1	2	FACETS	0.941	0.879	1	0.941	0.879	1	CLONAL	1	TRUE	1	0.7019717737741	2		465	642	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707876	43707876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	367	573	0	ENST00000382044.4:c.5005C>T	p.Leu1669Phe	p.L1669F	ENST00000382044	NM_001141980.1	1669	Ctc/Ttc	23/28	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.7019717737741	2		573	994	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680635	88680635	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	165	262	0	ENST00000360948.2:c.622G>A	p.Asp208Asn	p.D208N	ENST00000360948	NM_001012338.2	208	Gac/Aac	6/19	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.7019717737741	2		262	436	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463583	25463583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772368909	NA	P-0015968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	198	367	0	ENST00000264709.3:c.2099C>T	p.Pro700Leu	p.P700L	ENST00000264709	NM_175629.2	700	cCa/cTa	18/23	1	2	FACETS	0.861	0.801	0.923	0.861	0.801	0.923	CLONAL	1	TRUE	1	0.7019717737741	2		367	655	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197369	26197369	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	238	227	0	ENST00000356476.2:c.110A>T	p.Lys37Met	p.K37M	ENST00000356476		37	aAg/aTg	1/1	0.689347213760441	3	FACETS	0.931	0.88	0.983	0.931	0.88	0.983	CLONAL	2	TRUE	1	0.7019717737741	3		227	492	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841231	15841242	+	inframe_deletion	In_Frame_Del	DEL	AGCCGGAGCCGG	AGCCGGAGCCGG	-	rs752736259	NA	P-0015968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	129	154	0	ENST00000307771.7:c.1332_1343del	p.Ser445_Arg448del	p.S445_R448del	ENST00000307771	NM_005089.3	439	AGCCGGAGCCGG/-	11/11	1	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.7019717737741	1		154	235	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144148	55144148	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519700	NA	P-0015969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	189	533	0	ENST00000257290.5:c.1977C>A	p.Asn659Lys	p.N659K	ENST00000257290	NM_006206.4	659	aaC/aaA	14/23	1	2	FACETS	0.943	0.873	1	0.943	0.873	1	CLONAL	1	TRUE	1	0.493013004728173	2		533	813	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0015970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	438	605	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.420799158036927	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	1	0.44254755749162	3		606	1003	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220644	1220644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1167609100	NA	P-0015970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	671	814	0	ENST00000326873.7:c.662C>T	p.Pro221Leu	p.P221L	ENST00000326873	NM_000455.4	221	cCg/cTg	5/10	0.44254755749162	3	FACETS	0.877	0.847	0.906			1	CLONAL	3	TRUE	NA	0.44254755749162	3		814	1408	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296182	15296182	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519101	NA	P-0015970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	205	709	0	ENST00000263388.2:c.2182C>T	p.Arg728Cys	p.R728C	ENST00000263388	NM_000435.2	728	Cgc/Tgc	14/33	0.421556800332816	3	FACETS	0.903	0.836	0.973	0.301	0.278	0.325	CLONAL	1	TRUE	0	0.44254755749162	3		709	1253	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141777	108141843	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCTACCATCTTAGTATCTAATGCTTTTAAAGGAGCTTCCTGGAGAAGAGTACCCCTTGCCAATGGA	TCCTACCATCTTAGTATCTAATGCTTTTAAAGGAGCTTCCTGGAGAAGAGTACCCCTTGCCAATGGA	-	novel	NA	P-0015970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	67	411	0	ENST00000278616.4:c.2839-14_2891del		p.X947_splice	ENST00000278616	NM_000051.3	947		19/63	0.44254755749162	3	FACETS	1	0.96	1	0.414	0.362	0.468	CLONAL	1	TRUE	0	0.44254755749162	3		411	298	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748601	40748601	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	98	412	0	ENST00000373198.4:c.2915G>T	p.Arg972Leu	p.R972L	ENST00000373198	NM_133170.3	972	cGa/cTa	21/32	0.207831809668026	5	FACETS	0.963	0.859	1	0.321	0.286	0.358	INDETERMINATE	1	TRUE	2	0.44254755749162	5		412	765	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439247	52439247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772070350	NA	P-0015970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	135	638	0	ENST00000460680.1:c.995C>T	p.Pro332Leu	p.P332L	ENST00000460680	NM_004656.3	332	cCc/cTc	11/17	1	2	FACETS	0.65	0.59	0.713	0.65	0.59	0.713	SUBCLONAL	1	TRUE	1	0.44254755749162	2		638	939	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361106	66361106	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs757242674	NA	P-0015970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	139	329	0	ENST00000273854.3:c.1066A>G	p.Arg356Gly	p.R356G	ENST00000273854	NM_004439.5	356	Aga/Gga	4/18	0.269256795735404	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.44254755749162	1		329	374	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964382	93964382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	104	482	0	ENST00000369303.4:c.2515G>A	p.Asp839Asn	p.D839N	ENST00000369303	NM_004440.3	839	Gac/Aac	14/17	0.44254755749162	2	FACETS	0.933	0.839	1	0.466	0.419	0.516	CLONAL	1	TRUE	0	0.44254755749162	2		482	504	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	140	414	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.951	0.868	1	0.951	0.868	1	CLONAL	1	TRUE	1	0.420454234066916	2		414	700	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0015971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	151	467	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.404817819556993	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.420454234066916	1		468	555	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430818	78430818	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	170	679	0	ENST00000370768.2:c.571A>C	p.Met191Leu	p.M191L	ENST00000370768	NM_003902.3	191	Atg/Ctg	8/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.420454234066916	2		679	760	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581195	48581195	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	112	520	1	ENST00000342988.3:c.499G>T	p.Glu167Ter	p.E167*	ENST00000342988	NM_005359.5	167	Gag/Tag	5/12	0.404817819556993	1	FACETS	0.842	0.761	0.926	0.842	0.761	0.926	CLONAL	1	TRUE	0	0.420454234066916	1		521	500	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0015972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	206	512	1	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	0.311929431416601	5	FACETS	1	0.962	1	0.704	0.654	0.756	CLONAL	2	TRUE	2	0.311929431416601	5		513	918	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407561	139407563	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	rs587778561	NA	P-0015972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	153	829	0	ENST00000277541.6:c.2377_2379del	p.Asn793del	p.N793del	ENST00000277541	NM_017617.3	793	AAC/-	15/34	0.311929431416601	3	FACETS	0.943	0.86	1	0.471	0.43	0.515	CLONAL	1	TRUE	1	0.311929431416601	3		829	1203	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579415	7579415	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	238	648	0	ENST00000269305.4:c.272G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tGg/tAg	4/11	0.367203815494931	3	FACETS	0.896	0.844	0.949	1	0.992	1	CLONAL	3	TRUE	1	0.367054774084562	3		648	571	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136019	64136019	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199674030	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	94	665	1	ENST00000334205.4:c.1280G>A	p.Arg427His	p.R427H	ENST00000334205	NM_003942.2	427	cGc/cAc	11/17	0.367203815494931	3	FACETS	1	0.936	1	0.535	0.477	0.597	CLONAL	1	TRUE	1	0.367054774084562	3		666	566	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900171	101900171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564161322	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	48	274	0	ENST00000374994.4:c.605C>T	p.Ala202Val	p.A202V	ENST00000374994	NM_004612.2	202	gCg/gTg	4/9	0.324520166312061	3	FACETS	0.776	0.657	0.906	0.388	0.328	0.453	CLONAL	1	TRUE	1	0.367054774084562	3		274	399	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402517	139402517	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	79	695	1	ENST00000277541.6:c.3400C>T	p.Gln1134Ter	p.Q1134*	ENST00000277541	NM_017617.3	1134	Cag/Tag	21/34	1	2	FACETS	0.774	0.682	0.873	0.774	0.682	0.873	SUBCLONAL	1	TRUE	1	0.367054774084562	2		696	556	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664814	138664814	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	61	267	1	ENST00000330315.3:c.751C>A	p.Pro251Thr	p.P251T	ENST00000330315	NM_023067.3	251	Ccg/Acg	1/1	0.298296084934478	5	FACETS	0.924	0.804	1	0.616	0.536	0.701	CLONAL	2	TRUE	2	0.367054774084562	5		268	279	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797769	32797769	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs78328107	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	186	617	1	ENST00000374899.4:c.1733C>T	p.Ala578Val	p.A578V	ENST00000374899	NM_018833.2	578	gCg/gTg	10/12	0.199878798377921	5	FACETS	0.948	0.877	1	0.632	0.584	0.681	INDETERMINATE	2	TRUE	2	0.367054774084562	5		618	829	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783310	9783310	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	46	747	0	ENST00000377346.4:c.2554A>C	p.Lys852Gln	p.K852Q	ENST00000377346	NM_005026.3	852	Aag/Cag	20/24	0.255690529621347	4	FACETS	0.51	0.428	0.6	0.255	0.214	0.3	SUBCLONAL	1	TRUE	2	0.367054774084562	4		747	672	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497745	120497745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	87	544	1	ENST00000256646.2:c.2137C>T	p.His713Tyr	p.H713Y	ENST00000256646	NM_024408.3	713	Cat/Tat	13/34	0.199878798377921	5	FACETS	1	0.928	1	0.355	0.314	0.399	INDETERMINATE	1	TRUE	2	0.367054774084562	5		545	690	SUCCESS
FH	2271	MSKCC	GRCh37	1	241665839	241665839	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	79	513	2	ENST00000366560.3:c.1140G>T	p.Met380Ile	p.M380I	ENST00000366560	NM_000143.3	380	atG/atT	8/10	0.226218601010955	3	FACETS	0.83	0.73	0.936	0.277	0.243	0.312	CLONAL	1	TRUE	0	0.367054774084562	3		515	614	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385387	4385387	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	76	251	0	ENST00000261254.3:c.411+1G>A		p.X137_splice	ENST00000261254	NM_001759.3	137			0.279540541483509	3	FACETS	1	0.921	1	0.695	0.619	0.774	CLONAL	2	TRUE	0	0.367054774084562	3		251	235	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865680	57865680	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	159	876	0	ENST00000228682.2:c.3157C>A	p.Leu1053Met	p.L1053M	ENST00000228682	NM_005269.2	1053	Ctg/Atg	12/12	0.199878798377921	5	FACETS	0.894	0.821	0.97	0.596	0.547	0.647	INDETERMINATE	2	TRUE	2	0.367054774084562	5		876	751	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813309	102813309	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	63	394	0	ENST00000307046.8:c.380C>A	p.Thr127Asn	p.T127N	ENST00000307046	NM_001111285.1	127	aCc/aAc	3/4	0.199878798377921	5	FACETS	1	0.934	1	0.376	0.326	0.43	INDETERMINATE	1	TRUE	2	0.367054774084562	5		394	472	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110017	115110017	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	126	944	0	ENST00000257566.3:c.1861A>T	p.Ser621Cys	p.S621C	ENST00000257566	NM_016569.3	621	Agc/Tgc	8/8	0.199878798377921	5	FACETS	1	0.982	1	0.461	0.417	0.507	INDETERMINATE	1	TRUE	2	0.367054774084562	5		944	770	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26911778	26911778	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	64	523	2	ENST00000381527.3:c.203C>A	p.Ala68Glu	p.A68E	ENST00000381527	NM_001260.1	68	gCa/gAa	2/13	0.324520166312061	3	FACETS	0.634	0.549	0.727	0.317	0.274	0.364	SUBCLONAL	1	TRUE	1	0.367054774084562	3		525	651	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046560	30046560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs541601115	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	92	587	0	ENST00000331968.5:c.2623G>A	p.Glu875Lys	p.E875K	ENST00000331968	NM_002742.2	875	Gag/Aag	18/18	0.367203815494931	3	FACETS	0.878	0.78	0.981	0.439	0.39	0.491	CLONAL	1	TRUE	1	0.367054774084562	3		587	676	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544628	65544628	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	49	446	0	ENST00000358664.4:c.295+3G>A		p.X99_splice	ENST00000358664	NM_002382.4	99			0.367203815494931	3	FACETS	0.671	0.569	0.783	0.335	0.284	0.392	SUBCLONAL	1	TRUE	1	0.367054774084562	3		446	471	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786051	3786051	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	212	839	0	ENST00000262367.5:c.4714A>T	p.Ser1572Cys	p.S1572C	ENST00000262367	NM_004380.2	1572	Agt/Tgt	28/31	0.321494900665325	2	FACETS	0.923	0.862	0.984	0.923	0.862	0.984	CLONAL	2	TRUE	0	0.367054774084562	2		839	626	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864531	56864531	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	166	546	0	ENST00000308159.5:c.1019G>C	p.Arg340Pro	p.R340P	ENST00000308159	NM_014669.4	340	cGa/cCa	10/22	0.306922457337402	3	FACETS	0.85	0.784	0.918			1	CLONAL	2	TRUE	NA	0.367054774084562	3		546	630	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223042	41223042	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	99	710	0	ENST00000357654.3:c.4889A>G	p.Glu1630Gly	p.E1630G	ENST00000357654	NM_007294.3	1630	gAa/gGa	15/23	1	2	FACETS	0.821	0.734	0.914	0.821	0.734	0.914	CLONAL	1	TRUE	1	0.367054774084562	2		710	657	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438224	56438225	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	193	624	2	ENST00000407977.2:c.768_769delinsTT	p.Gly257Cys	p.G257C	ENST00000407977		256	cgGGgt/cgTTgt	7/10	0.348515412614565	4	FACETS	0.892	0.832	0.954	0.892	0.832	0.954	CLONAL	3	TRUE	1	0.367054774084562	4		626	537	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211673	5211673	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	141	622	0	ENST00000357368.4:c.5162G>T	p.Arg1721Leu	p.R1721L	ENST00000357368	NM_002850.3	1721	cGg/cTg	33/38	0.340734104947295	2	FACETS	0.948	0.873	1	0.948	0.873	1	CLONAL	2	TRUE	0	0.367054774084562	2		622	405	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906783	50906783	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555790565	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	148	998	1	ENST00000440232.2:c.1171G>A	p.Asp391Asn	p.D391N	ENST00000440232	NM_002691.3	391	Gac/Aac	10/27	0.158393282710634	4	FACETS	0.763	0.698	0.831	0.763	0.698	0.831	INDETERMINATE	2	TRUE	2	0.367054774084562	4		999	722	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25468911	25468911	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	306	817	0	ENST00000264709.3:c.1452del	p.Gln485ArgfsTer166	p.Q485Rfs*166	ENST00000264709	NM_175629.2	484	cgG/cg	12/23	0.367054774084562	3	FACETS	0.902	0.856	0.949	0.902	0.856	0.949	CLONAL	3	TRUE	0	0.367054774084562	3		817	729	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128028923	128028923	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	90	641	0	ENST00000285398.2:c.1934G>C	p.Arg645Pro	p.R645P	ENST00000285398	NM_000122.1	645	cGa/cCa	12/15	0.306922457337402	3	FACETS	0.859	0.762	0.961			1	CLONAL	1	TRUE	NA	0.367054774084562	3		641	676	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660271	227660271	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	87	470	1	ENST00000305123.5:c.3184G>T	p.Gly1062Cys	p.G1062C	ENST00000305123	NM_005544.2	1062	Ggc/Tgc	1/2	0.359780653438942	4	FACETS	1	0.974	1	0.676	0.601	0.756	CLONAL	1	TRUE	2	0.367054774084562	4		471	479	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661380	227661380	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	118	438	0	ENST00000305123.5:c.2075G>T	p.Gly692Val	p.G692V	ENST00000305123	NM_005544.2	692	gGg/gTg	1/2	0.359780653438942	4	FACETS	0.964	0.875	1	0.964	0.875	1	CLONAL	2	TRUE	2	0.367054774084562	4		438	456	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713377	40713377	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	193	637	0	ENST00000373198.4:c.4138G>C	p.Glu1380Gln	p.E1380Q	ENST00000373198	NM_133170.3	1380	Gag/Cag	30/32	0.298296084934478	5	FACETS	0.901	0.834	0.97	0.601	0.556	0.647	CLONAL	2	TRUE	2	0.367054774084562	5		637	905	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730901	40730901	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	158	577	0	ENST00000373198.4:c.3634G>T	p.Asp1212Tyr	p.D1212Y	ENST00000373198	NM_133170.3	1212	Gac/Tac	27/32	0.298296084934478	5	FACETS	0.993	0.913	1	0.662	0.608	0.718	CLONAL	2	TRUE	2	0.367054774084562	5		577	672	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262936	46262936	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	196	537	0	ENST00000371998.3:c.1109A>T	p.Gln370Leu	p.Q370L	ENST00000371998		370	cAg/cTg	10/23	0.298296084934478	5	FACETS	0.97	0.899	1	0.646	0.599	0.695	CLONAL	2	TRUE	2	0.367054774084562	5		537	854	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292814	62292814	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	61	304	0	ENST00000360203.5:c.266G>T	p.Trp89Leu	p.W89L	ENST00000360203	NM_001283009.1	89	tGg/tTg	3/35	0.298296084934478	5	FACETS	0.81	0.704	0.924	0.54	0.469	0.616	CLONAL	2	TRUE	2	0.367054774084562	5		304	318	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259509	89259509	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	62	384	0	ENST00000336596.2:c.653T>A	p.Met218Lys	p.M218K	ENST00000336596	NM_005233.5	218	aTg/aAg	3/17	0.194028643395153	3	FACETS	0.921	0.798	1			1	INDETERMINATE	1	TRUE	NA	0.367054774084562	3		384	434	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119666128	119666128	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	43	537	0	ENST00000316626.5:c.353C>A	p.Ser118Tyr	p.S118Y	ENST00000316626		118	tCc/tAc	3/12	0.298296084934478	5	FACETS	0.428	0.357	0.508	0.143	0.119	0.17	SUBCLONAL	1	TRUE	2	0.367054774084562	5		537	848	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199939	128199939	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	61	391	0	ENST00000341105.2:c.1366C>A	p.Pro456Thr	p.P456T	ENST00000341105	NM_032638.4	456	Ccg/Acg	6/6	0.298296084934478	5	FACETS	0.753	0.654	0.861	0.502	0.436	0.574	SUBCLONAL	2	TRUE	2	0.367054774084562	5		391	342	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430645	181430645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	136	527	0	ENST00000325404.1:c.497G>T	p.Trp166Leu	p.W166L	ENST00000325404	NM_003106.3	166	tGg/tTg	1/1	0.298296084934478	5	FACETS	1	0.919	1	0.671	0.612	0.732	CLONAL	2	TRUE	2	0.367054774084562	5		527	571	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456518	189456518	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	153	540	2	ENST00000264731.3:c.279G>T	p.Met93Ile	p.M93I	ENST00000264731	NM_003722.4	93	atG/atT	3/14	0.298296084934478	5	FACETS	0.812	0.744	0.883	0.541	0.496	0.589	CLONAL	2	TRUE	2	0.367054774084562	5		542	796	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231729	66231729	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	45	533	1	ENST00000273854.3:c.1971G>T	p.Glu657Asp	p.E657D	ENST00000273854	NM_004439.5	657	gaG/gaT	11/18	0.266067487703458	3	FACETS	0.527	0.442	0.62	0.176	0.147	0.207	SUBCLONAL	1	TRUE	0	0.367054774084562	3		534	551	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143043316	143043316	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	103	570	0	ENST00000262992.4:c.2100A>T	p.Lys700Asn	p.K700N	ENST00000262992	NM_001101669.1	700	aaA/aaT	19/24	0.266067487703458	3	FACETS	1	0.899	1	0.334	0.299	0.372	CLONAL	1	TRUE	0	0.367054774084562	3		570	662	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094911	143094911	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	166	524	1	ENST00000262992.4:c.1233G>T	p.Lys411Asn	p.K411N	ENST00000262992	NM_001101669.1	411	aaG/aaT	14/24	0.266067487703458	3	FACETS	0.9	0.83	0.971	0.6	0.553	0.647	CLONAL	2	TRUE	0	0.367054774084562	3		525	595	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525133	187525133	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	120	374	0	ENST00000441802.2:c.10549-2A>T		p.X3517_splice	ENST00000441802	NM_005245.3	3517			0.293793495085755	2	FACETS	0.879	0.802	0.958	0.879	0.802	0.958	CLONAL	2	TRUE	0	0.367054774084562	2		374	372	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876268	35876268	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	181	533	0	ENST00000303115.3:c.1060G>T	p.Val354Leu	p.V354L	ENST00000303115	NM_002185.3	354	Gta/Tta	8/8	0.359780653438942	4	FACETS	0.939	0.869	1	0.939	0.869	1	CLONAL	2	TRUE	2	0.367054774084562	4		533	718	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527580	157527580	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	260	635	0	ENST00000346085.5:c.5305G>T	p.Asp1769Tyr	p.D1769Y	ENST00000346085	NM_020732.3	1769	Gac/Tac	20/20	0.367203815494931	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.367054774084562	3		635	775	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971315	13971315	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	158	438	0	ENST00000405192.2:c.614G>T	p.Arg205Met	p.R205M	ENST00000405192	NM_001163147.1	205	aGg/aTg	8/12	0.367203815494931	3	FACETS	0.921	0.849	0.996	0.921	0.849	0.996	CLONAL	2	TRUE	1	0.367054774084562	3		438	553	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729460	41729460	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	81	516	1	ENST00000242208.4:c.1069C>A	p.His357Asn	p.H357N	ENST00000242208	NM_002192.2	357	Cat/Aat	3/3	0.367203815494931	3	FACETS	0.912	0.804	1	0.456	0.402	0.513	CLONAL	1	TRUE	1	0.367054774084562	3		517	573	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729999	41729999	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	220	585	0	ENST00000242208.4:c.530A>T	p.Gln177Leu	p.Q177L	ENST00000242208	NM_002192.2	177	cAg/cTg	3/3	0.367203815494931	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.367054774084562	3		585	679	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151893043	151893043	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1406863036	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	93	514	1	ENST00000262189.6:c.4327G>A	p.Asp1443Asn	p.D1443N	ENST00000262189	NM_170606.2	1443	Gac/Aac	28/59	0.359780653438942	4	FACETS	0.794	0.705	0.889	0.397	0.352	0.445	SUBCLONAL	1	TRUE	2	0.367054774084562	4		515	873	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742147	145742147	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs997621519	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	50	397	0	ENST00000428558.2:c.356C>T	p.Ala119Val	p.A119V	ENST00000428558	NM_004260.3	119	gCc/gTc	5/22	0.277946692195981	3	FACETS	1	0.885	1			1	CLONAL	1	TRUE	NA	0.367054774084562	3		397	309	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319966	8319966	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs748716978	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	54	289	0	ENST00000356435.5:c.5535C>G	p.Ser1845Arg	p.S1845R	ENST00000356435		1845	agC/agG	34/35	0.293793495085755	2	FACETS	0.911	0.783	1	0.455	0.391	0.525	CLONAL	1	TRUE	0	0.367054774084562	2		289	323	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633452	8633452	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	96	441	2	ENST00000356435.5:c.217G>T	p.Glu73Ter	p.E73*	ENST00000356435		73	Gag/Tag	3/35	0.293793495085755	2	FACETS	1	0.974	1	0.641	0.575	0.71	CLONAL	1	TRUE	0	0.367054774084562	2		443	408	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342662	87342662	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	210	795	0	ENST00000277120.3:c.947A>G	p.Gln316Arg	p.Q316R	ENST00000277120		316	cAg/cGg	9/19	0.324520166312061	3	FACETS	0.783	0.728	0.84	0.783	0.728	0.84	SUBCLONAL	2	TRUE	1	0.367054774084562	3		795	865	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019521	123019521	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	72	491	0	ENST00000355640.3:c.9T>A	p.Phe3Leu	p.F3L	ENST00000355640		3	ttT/ttA	2/7	0.324520166312061	3	FACETS	0.745	0.651	0.847	0.373	0.325	0.424	SUBCLONAL	1	TRUE	1	0.367054774084562	3		491	623	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696435	47696435	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	482	639	0	ENST00000347630.2:c.388G>C	p.Asp130His	p.D130H	ENST00000347630	NM_001007230.1	130	Gac/Cac	6/11	0.605248889365547	2	FACETS	0.924	0.891	0.957	0.924	0.891	0.957	CLONAL	2	TRUE	0	0.617383864620105	2		639	845	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836263	89836263	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1320172669	NA	P-0015974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	249	725	0	ENST00000389301.3:c.2486C>T	p.Ser829Phe	p.S829F	ENST00000389301	NM_000135.2	829	tCc/tTc	26/43	1	2	FACETS	0.838	0.785	0.894	0.838	0.785	0.894	CLONAL	1	TRUE	1	0.617383864620105	2		725	962	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325693	30325693	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	165	303	0	ENST00000322652.5:c.1891C>T	p.Gln631Ter	p.Q631*	ENST00000322652	NM_015355.2	631	Caa/Taa	16/16	0.605248889365547	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.617383864620105	2		303	246	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0015974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	419	540	0	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			NA	2	FACETS	0.932	0.897	0.968			1	INDETERMINATE	2	TRUE	NA	0.617383864620105	2		540	728	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851560	63851560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	275	763	1	ENST00000279873.7:c.2338C>T	p.Arg780Ter	p.R780*	ENST00000279873	NM_032199.2	780	Cga/Tga	10/10	0.47577089160448	1	FACETS	0.899	0.849	0.949	0.899	0.849	0.949	CLONAL	1	TRUE	0	0.617383864620105	1		764	685	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88635782	88635782	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	85	287	0	ENST00000372037.3:c.7C>G	p.Gln3Glu	p.Q3E	ENST00000372037	NM_004329.2	3	Cag/Gag	3/13	0.617383864620105	3	FACETS	1	0.975	1	0.66	0.591	0.732	CLONAL	1	TRUE	1	0.617383864620105	3		287	273	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037905	49037917	+	frameshift_variant	Frame_Shift_Del	DEL	GAATATAGACCTT	GAATATAGACCTT	-	novel	NA	P-0015974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	174	562	0	ENST00000267163.4:c.2145_2157del	p.Ile717SerfsTer5	p.I717Sfs*5	ENST00000267163	NM_000321.2	715	aaGAATATAGACCTT/aa	21/27	0.617383864620105	2	FACETS	0.883	0.83	0.937	0.883	0.83	0.937	CLONAL	2	TRUE	0	0.617383864620105	2		562	319	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99491909	99491909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1432	243	627	0	ENST00000268035.6:c.3694G>A	p.Asp1232Asn	p.D1232N	ENST00000268035	NM_000875.3	1232	Gac/Aac	20/21	0.617383864620105	5	FACETS	0.905	0.843	0.97	0.226	0.21	0.243	CLONAL	1	TRUE	1	0.617383864620105	5		627	1675	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104355	2104355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	316	721	0	ENST00000219476.3:c.395C>T	p.Ser132Phe	p.S132F	ENST00000219476	NM_000548.3	132	tCc/tTc	5/42	1	2	FACETS	0.937	0.885	0.991	0.937	0.885	0.991	CLONAL	1	TRUE	1	0.617383864620105	2		721	1092	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191111	2191111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	278	751	1	ENST00000398665.3:c.365C>T	p.Pro122Leu	p.P122L	ENST00000398665	NM_032482.2	122	cCc/cTc	5/28	0.617383864620105	3	FACETS	0.905	0.849	0.963	0.453	0.424	0.482	CLONAL	1	TRUE	1	0.617383864620105	3		752	1302	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2202721	2202721	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	202	635	0	ENST00000398665.3:c.730G>C	p.Ala244Pro	p.A244P	ENST00000398665	NM_032482.2	244	Gcc/Ccc	9/28	0.617383864620105	3	FACETS	0.8	0.741	0.861	0.4	0.37	0.431	SUBCLONAL	1	TRUE	1	0.617383864620105	3		635	1071	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521052	187521052	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	225	325	0	ENST00000441802.2:c.12103G>A	p.Gly4035Ser	p.G4035S	ENST00000441802	NM_005245.3	4035	Ggt/Agt	22/27	0.617383864620105	2	FACETS	0.939	0.891	0.987	0.939	0.891	0.987	CLONAL	2	TRUE	0	0.617383864620105	2		325	388	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673239	30673239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	255	503	0	ENST00000376406.3:c.3721G>A	p.Glu1241Lys	p.E1241K	ENST00000376406	NM_014641.2	1241	Gaa/Aaa	10/15	0.617383864620105	3	FACETS	1	0.984	1	0.57	0.534	0.607	CLONAL	1	TRUE	1	0.617383864620105	3		503	948	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513314	106513314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559655430	NA	P-0015974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	351	480	0	ENST00000359195.3:c.2218G>A	p.Glu740Lys	p.E740K	ENST00000359195	NM_002649.2	740	Gag/Aag	4/11	0.605248889365547	2	FACETS	0.894	0.856	0.932	0.894	0.856	0.932	CLONAL	2	TRUE	0	0.617383864620105	2		480	636	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860046	151860046	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1369146356	NA	P-0015974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	282	346	0	ENST00000262189.6:c.10616T>G	p.Leu3539Arg	p.L3539R	ENST00000262189	NM_170606.2	3539	cTt/cGt	43/59	0.605248889365547	2	FACETS	0.928	0.885	0.971	0.928	0.885	0.971	CLONAL	2	TRUE	0	0.617383864620105	2		346	492	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194616	29194616	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	301	855	2	ENST00000240100.2:c.1112C>T	p.Ser371Phe	p.S371F	ENST00000240100	NM_001394.6	371	tCc/tTc	4/4	0.617383864620105	3	FACETS	1	0.943	1	0.501	0.471	0.532	CLONAL	1	TRUE	1	0.617383864620105	3		857	1273	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613678	100613678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	461	286	0	ENST00000308731.7:c.901G>A	p.Glu301Lys	p.E301K	ENST00000308731	NM_000061.2	301	Gaa/Aaa	11/19	0.500673368299205	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.617383864620105	2		286	650	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480588	123480589	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	258	210	0	ENST00000371139.4:c.96_97delinsAA	p.Asp33Asn	p.D33N	ENST00000371139	NM_001114937.2	32	agGGac/agAAac	1/4	0.500673368299205	2	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.617383864620105	2		210	384	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0015977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	265	424	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	0.771541697226461	2		424	683	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594221	55594221	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913512	NA	P-0015977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	2209	437	0	ENST00000288135.5:c.1924A>G	p.Lys642Glu	p.K642E	ENST00000288135	NM_000222.2	642	Aaa/Gaa	13/21	0.771541697226461	10	FACETS	1	0.998	1			1	CLONAL	9	TRUE	NA	0.771541697226461	10		437	2481	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066765	30066765	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	95	482	0	ENST00000331968.5:c.2366T>G	p.Ile789Arg	p.I789R	ENST00000331968	NM_002742.2	789	aTa/aGa	16/18	1	2	FACETS	0.277	0.246	0.311	0.277	0.246	0.311	SUBCLONAL	1	TRUE	1	0.771541697226461	2		482	888	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	339	414	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.35900227821587	3	FACETS	0.842	0.797	0.888	0.842	0.797	0.888	CLONAL	2	TRUE	1	0.420806531473084	3		414	1158	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0015980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	251	790	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.420806531473084	1	FACETS	0.994	0.931	1	0.994	0.931	1	CLONAL	1	TRUE	0	0.420806531473084	1		792	948	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7168069	7168069	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	407	657	1	ENST00000302850.5:c.1520C>A	p.Thr507Lys	p.T507K	ENST00000302850	NM_000208.2	507	aCa/aAa	7/22	0.35900227821587	3	FACETS	0.892	0.849	0.936	0.892	0.849	0.936	CLONAL	2	TRUE	1	0.420806531473084	3		658	1312	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403116	116403116	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45440991	NA	P-0015980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	98	387	1	ENST00000397752.3:c.2377C>T	p.Arg793Cys	p.R793C	ENST00000397752	NM_000245.2	793	Cgc/Tgc	11/21	1	2	FACETS	0.561	0.5	0.626	0.561	0.5	0.626	SUBCLONAL	1	TRUE	1	0.420806531473084	2		388	830	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0015981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	30	425	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.353	0.283	0.433	0.353	0.283	0.433	SUBCLONAL	1	TRUE	1	0.21763439660589	2		425	781	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106138	27106138	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	73	464	0	ENST00000324856.7:c.5749A>G	p.Thr1917Ala	p.T1917A	ENST00000324856	NM_006015.4	1917	Act/Gct	20/20	1	2	FACETS	0.856	0.747	0.973	0.856	0.747	0.973	CLONAL	1	TRUE	1	0.21763439660589	2		464	784	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692780	89692780	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1554898056	NA	P-0015981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	87	505	0	ENST00000371953.3:c.264T>A	p.Tyr88Ter	p.Y88*	ENST00000371953	NM_000314.4	88	taT/taA	5/9	0.179299096527314	0	FACETS	0.877	0.777	0.985			1	CLONAL	1	TRUE	0	0.21763439660589	0		505	713	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835622	68835622	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	75	564	0	ENST00000261769.5:c.213del	p.Asp72ThrfsTer11	p.D72Tfs*11	ENST00000261769	NM_004360.3	71	ctC/ct	3/16	0.21763439660589	1	FACETS	0.744	0.65	0.844	0.744	0.65	0.844	SUBCLONAL	1	TRUE	0	0.21763439660589	1		564	826	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332914	152332914	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	58	294	0	ENST00000206249.3:c.1220A>T	p.Asn407Ile	p.N407I	ENST00000206249	NM_000125.3	407	aAc/aTc	5/8	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.21763439660589	2		294	480	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298141	123298141	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	78	673	0	ENST00000358487.5:c.713G>A	p.Gly238Glu	p.G238E	ENST00000358487	NM_000141.4	238	gGg/gAg	6/18	1	2	FACETS	0.798	0.703	0.899	0.798	0.703	0.899	SUBCLONAL	1	TRUE	1	0.402983941418049	2		673	485	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183750	10183750	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	172	704	0	ENST00000256474.2:c.220del	p.Val74SerfsTer85	p.V74Sfs*85	ENST00000256474	NM_000551.3	73	caG/ca	1/3	0.402983941418049	1	FACETS	0.943	0.87	1	0.943	0.87	1	CLONAL	1	TRUE	0	0.402983941418049	1		704	723	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47088106	47088107	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0015983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	50	418	0	ENST00000409792.3:c.6968_6969del	p.Tyr2323CysfsTer45	p.Y2323Cfs*45	ENST00000409792	NM_014159.6	2323	tAT/t	16/21	0.402983941418049	1	FACETS	0.812	0.696	0.937	0.812	0.696	0.937	CLONAL	1	TRUE	0	0.402983941418049	1		418	244	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441261	52441261	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	116	525	0	ENST00000460680.1:c.509T>C	p.Phe170Ser	p.F170S	ENST00000460680	NM_004656.3	170	tTt/tCt	7/17	0.402983941418049	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.402983941418049	1		525	419	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595828	52595828	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	108	567	0	ENST00000394830.3:c.4087del	p.Thr1363GlnfsTer17	p.T1363Qfs*17	ENST00000394830	NM_018313.4	1363	Aca/ca	26/30	0.402983941418049	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.402983941418049	1		567	409	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271218	26271218	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	29	427	0	ENST00000305910.3:c.395G>A	p.Arg132His	p.R132H	ENST00000305910	NM_003534.2	132	cGt/cAt	1/1	0.402983941418049	6	FACETS	0.515	0.412	0.632	0.172	0.137	0.211	SUBCLONAL	1	TRUE	3	0.402983941418049	6		427	505	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	260	507	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.423547902196001	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.42203349941735	3		507	642	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0015986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	47	251	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.423547902196001	3	FACETS	1	0.873	1	0.515	0.437	0.599	CLONAL	1	TRUE	1	0.42203349941735	3		251	262	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0015986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	254	485	2	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	0.423547902196001	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.42203349941735	3		487	610	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952088	178952088	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553826184	NA	P-0015986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	83	478	0	ENST00000263967.3:c.3143A>G	p.His1048Arg	p.H1048R	ENST00000263967	NM_006218.2	1048	cAt/cGt	21/21	0.423547902196001	3	FACETS	1	0.916	1	0.52	0.461	0.583	CLONAL	1	TRUE	1	0.42203349941735	3		478	458	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057784	27057784	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	291	1140	0	ENST00000324856.7:c.1493del	p.Pro498LeufsTer121	p.P498Lfs*121	ENST00000324856	NM_006015.4	498	Cct/ct	3/20	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.42203349941735	2		1140	1092	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158171	47158172	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0015986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	147	623	0	ENST00000409792.3:c.4527_4528del	p.Arg1509SerfsTer4	p.R1509Sfs*4	ENST00000409792	NM_014159.6	1509	agAGct/agct	4/21	0.423547902196001	3	FACETS	1	0.973	1	0.575	0.526	0.627	CLONAL	1	TRUE	1	0.42203349941735	3		623	733	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	1350	507	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.700868547392676	7	FACETS	0.925	0.908	0.942	1	0.998	1	CLONAL	6	TRUE	2	0.700868547392676	7		507	1910	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220395	1220395	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	886	674	2	ENST00000326873.7:c.488G>T	p.Gly163Val	p.G163V	ENST00000326873	NM_000455.4	163	gGc/gTc	4/10	0.700868547392676	3	FACETS	1	0.996	1			1	CLONAL	3	TRUE	NA	0.700868547392676	3		676	1079	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158325	108158325	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs587782276	NA	P-0015987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	241	392	0	ENST00000278616.4:c.3994-2A>G		p.X1332_splice	ENST00000278616	NM_000051.3	1332			0.700868547392676	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.700868547392676	2		392	335	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390971	89390971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	333	614	0	ENST00000336596.2:c.1037G>A	p.Ser346Asn	p.S346N	ENST00000336596	NM_005233.5	346	aGt/aAt	5/17	0.689006388200616	4	FACETS	0.867	0.822	0.913	0.867	0.822	0.913	CLONAL	2	TRUE	2	0.700868547392676	4		614	932	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513470	149513470	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	393	686	0	ENST00000261799.4:c.733T>A	p.Phe245Ile	p.F245I	ENST00000261799	NM_002609.3	245	Ttc/Atc	5/23	0.355713254033014	5	FACETS	1	0.987	1	0.733	0.698	0.768	INDETERMINATE	2	TRUE	2	0.700868547392676	5		686	1046	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039638	47039638	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1556778349	NA	P-0015987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	525	825	0	ENST00000377604.3:c.1090C>T	p.Gln364Ter	p.Q364*	ENST00000377604	NM_001204468.1	364	Cag/Tag	11/24	0.355713254033014	5	FACETS	1	0.995	1	0.814	0.781	0.846	INDETERMINATE	2	TRUE	2	0.700868547392676	5		825	1259	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344860	70344860	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	405	712	1	ENST00000374080.3:c.2090G>A	p.Gly697Asp	p.G697D	ENST00000374080		697	gGc/gAc	15/45	0.355713254033014	5	FACETS	1	0.98	1	0.701	0.668	0.735	INDETERMINATE	2	TRUE	2	0.700868547392676	5		713	1127	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630303	100630303	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0015987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	155	243	0	ENST00000308731.7:c.-30-1G>T		p.X10_splice	ENST00000308731	NM_000061.2	10			0.6239128931731	4	FACETS	0.962	0.892	1	0.962	0.892	1	CLONAL	2	TRUE	2	0.700868547392676	4		243	391	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179126	123179126	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	337	668	0	ENST00000218089.9:c.575A>T	p.Tyr192Phe	p.Y192F	ENST00000218089	NM_001042749.1	192	tAt/tTt	8/35	0.6239128931731	4	FACETS	0.855	0.811	0.9	0.855	0.811	0.9	CLONAL	2	TRUE	2	0.700868547392676	4		668	956	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0015989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	1819	605	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.734701304293258	6	FACETS	0.999	0.984	1	0.999	0.984	1	CLONAL	5	FALSE	1	0.734701304293258	6		606	2449	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859397	57859397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	294	390	0	ENST00000228682.2:c.542C>T	p.Ser181Phe	p.S181F	ENST00000228682	NM_005269.2	181	tCt/tTt	6/12	0.658743356004416	6	FACETS	1	0.992	1			1	CLONAL	1	FALSE	NA	0.734701304293258	6		390	1423	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859638	57859638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777659251	NA	P-0015989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1181	464	448	0	ENST00000228682.2:c.692C>T	p.Ser231Phe	p.S231F	ENST00000228682	NM_005269.2	231	tCt/tTt	7/12	0.658743356004416	6	FACETS	0.948	0.904	0.993			1	CLONAL	2	FALSE	NA	0.734701304293258	6		448	1645	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285041	15285041	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	1229	479	0	ENST00000263388.2:c.4574T>C	p.Leu1525Pro	p.L1525P	ENST00000263388	NM_000435.2	1525	cTg/cCg	25/33	0.569072942956345	10	FACETS	0.974	0.964	0.983	1	0.998	1	CLONAL	11	TRUE	0	0.569072942956345	10		479	1321	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959247	2959247	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0015990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	81	364	0	ENST00000396946.4:c.2270-1G>T		p.X757_splice	ENST00000396946	NM_032415.4	757			NA	2	FACETS	0.699	0.62	0.784			1	INDETERMINATE	1	TRUE	NA	0.569072942956345	2		364	407	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769886672	NA	P-0015991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	86	243	1	ENST00000405192.2:c.414dup	p.Thr139HisfsTer24	p.T139Hfs*24	ENST00000405192	NM_001163147.1	138	-/C	7/12	1	2	FACETS	0.653	0.58	0.731	0.653	0.58	0.731	SUBCLONAL	1	TRUE	1	0.556530552717775	2		244	473	SUCCESS
AR	367	MSKCC	GRCh37	X	66943552	66943552	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137852578	NA	P-0015991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2503	913	235	1	ENST00000374690.3:c.2632A>G	p.Thr878Ala	p.T878A	ENST00000374690	NM_000044.3	878	Act/Gct	8/8	0.556530552717775	12	FACETS	0.908	0.878	0.939			1	CLONAL	4	TRUE	NA	0.556530552717775	12		236	3416	SUCCESS
APC	324	MSKCC	GRCh37	5	112175651	112175651	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	200	488	0	ENST00000257430.4:c.4364del	p.Asn1455IlefsTer18	p.N1455Ifs*18	ENST00000257430	NM_000038.5	1454	Aaa/aa	16/16	0.556530552717775	1	FACETS	0.928	0.866	0.991	0.928	0.866	0.991	CLONAL	1	TRUE	0	0.556530552717775	1		488	559	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306928	65306928	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	178	366	0	ENST00000342505.4:c.2649G>C	p.Glu883Asp	p.E883D	ENST00000342505	NM_002227.2	883	gaG/gaC	19/25	1	2	FACETS	0.968	0.895	1	0.968	0.895	1	CLONAL	1	TRUE	1	0.556530552717775	2		366	661	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99460038	99460038	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	213	431	2	ENST00000268035.6:c.2134G>A	p.Glu712Lys	p.E712K	ENST00000268035	NM_000875.3	712	Gag/Aag	10/21	1	2	FACETS	0.985	0.918	1	0.985	0.918	1	CLONAL	1	TRUE	1	0.556530552717775	2		433	777	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222383	2222383	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777184095	NA	P-0015993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	72	539	3	ENST00000398665.3:c.3215G>A	p.Arg1072His	p.R1072H	ENST00000398665	NM_032482.2	1072	cGt/cAt	24/28	0.273686210015955	2	FACETS	0.828	0.731	0.93	0.414	0.365	0.465	INDETERMINATE	1	TRUE	0	0.619219471742092	2		542	281	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29099492	29099492	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs587781699	NA	P-0015993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	204	580	1	ENST00000328354.6:c.908+1G>A		p.X303_splice	ENST00000328354	NM_007194.3	303			0.617616603418944	2	FACETS	0.874	0.824	0.923	0.874	0.824	0.923	CLONAL	2	TRUE	0	0.619219471742092	2		581	377	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509592	106509592	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	135	572	0	ENST00000359195.3:c.1586T>A	p.Leu529Gln	p.L529Q	ENST00000359195	NM_002649.2	529	cTg/cAg	2/11	0.619219471742092	4	FACETS	1	0.952	1	0.356	0.324	0.389	CLONAL	1	TRUE	1	0.619219471742092	4		572	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0016000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	277	525	1	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.748709731171776	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.748709731171776	1		526	462	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106817	27106817	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	498	448	0	ENST00000324856.7:c.6428G>T	p.Arg2143Leu	p.R2143L	ENST00000324856	NM_006015.4	2143	cGc/cTc	20/20	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	2	TRUE	NA	0.748709731171776	2		448	656	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001293	29001293	+	splice_region_variant,intron_variant	Splice_Region	SNP	T	T	C	novel	NA	P-0016000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	147	275	0	ENST00000282397.4:c.1436+3A>G		p.X479_splice	ENST00000282397	NM_002019.4	479			1	2	FACETS	0.946	0.873	1	0.946	0.873	1	CLONAL	1	TRUE	1	0.748709731171776	2		275	415	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951172	48951172	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0016000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	204	381	0	ENST00000267163.4:c.1332+2T>C		p.X444_splice	ENST00000267163	NM_000321.2	444			0.703826935256665	1	FACETS	0.926	0.875	0.978	0.926	0.875	0.978	CLONAL	1	TRUE	0	0.748709731171776	1		381	368	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469137	25469137	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	331	631	1	ENST00000264709.3:c.1321G>T	p.Val441Leu	p.V441L	ENST00000264709	NM_175629.2	441	Gtg/Ttg	11/23	1	2	FACETS	0.931	0.882	0.98	0.931	0.882	0.98	CLONAL	1	TRUE	1	0.748709731171776	2		632	950	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805516	1805516	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	305	658	0	ENST00000260795.2:c.1028A>G	p.Asn343Ser	p.N343S	ENST00000260795		343	aAt/aGt	7/17	0.748709731171776	1	FACETS	0.977	0.933	1	0.977	0.933	1	CLONAL	1	TRUE	0	0.748709731171776	1		658	522	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151882680	151882680	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	326	452	0	ENST00000262189.6:c.5045G>A	p.Trp1682Ter	p.W1682*	ENST00000262189	NM_170606.2	1682	tGg/tAg	34/59	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.748709731171776	2		452	793	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993110	90993110	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876659320	NA	P-0016000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	228	392	0	ENST00000265433.3:c.332A>G	p.Glu111Gly	p.E111G	ENST00000265433	NM_002485.4	111	gAg/gGg	4/16	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.748709731171776	2		392	608	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050743	5050743	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	274	467	0	ENST00000381652.3:c.526G>A	p.Glu176Lys	p.E176K	ENST00000381652	NM_004972.3	176	Gaa/Aaa	6/25	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.748709731171776	2		467	714	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0016002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	420	745	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.494738115515942	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.494738115515942	1		745	959	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	136	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.494738115515942	2		248	480	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0016002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	172	657	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.917	0.846	0.992	0.917	0.846	0.992	CLONAL	1	TRUE	1	0.494738115515942	2		657	758	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156732	20156732	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	153	397	0	ENST00000379607.5:c.25G>C	p.Gly9Arg	p.G9R	ENST00000379607	NM_001412.3	9	Ggt/Cgt	2/7	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.494738115515942	2		397	556	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	80	414	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.131020032021602	3	FACETS	0.815	0.719	0.916	0.815	0.719	0.916	INDETERMINATE	2	FALSE	1	0.22686762690385	3		414	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0016003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	16	796	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.22686762690385	1	FACETS	0.229	0.169	0.303	0.229	0.169	0.303	SUBCLONAL	1	FALSE	0	0.22686762690385	1		796	545	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49413010	49413010	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519952	NA	P-0016003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	136	681	1	ENST00000418115.1:c.13C>T	p.Arg5Trp	p.R5W	ENST00000418115	NM_001664.2	5	Cgg/Tgg	2/5	0.131020032021602	3	FACETS	1	0.954	1	1	0.954	1	INDETERMINATE	2	FALSE	1	0.22686762690385	3		682	623	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469672	NA	P-0016003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	39	677	1	ENST00000374080.3:c.131G>A	p.Gly44Asp	p.G44D	ENST00000374080		44	gGt/gAt	2/45	0.22686762690385	0	FACETS	0.504	0.417	0.601			1	SUBCLONAL	1	FALSE	0	0.22686762690385	0		678	527	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075122	16075122	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0016003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	122	240	0	ENST00000268712.3:c.430A>T	p.Lys144Ter	p.K144*	ENST00000268712	NM_006311.3	144	Aag/Tag	4/46	0.22686762690385	7	FACETS	1	0.956	1			1	CLONAL	4	FALSE	NA	0.22686762690385	7		240	391	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842656	68842657	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0016003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	135	683	0	ENST00000261769.5:c.597_598dup	p.Pro200HisfsTer16	p.P200Hfs*16	ENST00000261769	NM_004360.3	198	gac/gACac	5/16	0.22686762690385	1	FACETS	1	0.97	1	1	0.992	1	CLONAL	2	FALSE	0	0.22686762690385	1		683	468	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115710	8115711	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0016003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	66	556	0	ENST00000346208.3:c.1059_1060dup	p.Leu354ProfsTer2	p.L354Pfs*2	ENST00000346208		352	-/CC	6/6	0.22686762690385	1	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	FALSE	0	0.22686762690385	1		556	512	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115416	115115416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	181	647	1	ENST00000257566.3:c.910C>T	p.Arg304Trp	p.R304W	ENST00000257566	NM_016569.3	304	Cgg/Tgg	5/8	0.143151479312544	0	FACETS	0.66	0.609	0.714			1	SUBCLONAL	2	FALSE	0	0.22686762690385	0		648	934	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0016004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	26	320	3	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.519	0.412	0.641	0.519	0.412	0.641	SUBCLONAL	1	TRUE	1	0.345583287252559	2		323	290	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753008	128753008	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1460956206	NA	P-0016004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	145	446	0	ENST00000377970.2:c.1169T>G	p.Phe390Cys	p.F390C	ENST00000377970	NM_002467.4	390	tTt/tGt	3/3	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.345583287252559	2		446	765	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555526268	NA	P-0016005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	431	688	0	ENST00000269305.4:c.406C>G	p.Gln136Glu	p.Q136E	ENST00000269305	NM_001126112.2	136	Caa/Gaa	5/11	0.776177853846397	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.776177853846397	1		688	641	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482425	56482425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	629	387	0	ENST00000267101.3:c.973G>A	p.Gly325Arg	p.G325R	ENST00000267101	NM_001982.3	325	Gga/Aga	8/28	0.776177853846397	4	FACETS	0.954	0.926	0.982			1	CLONAL	3	TRUE	NA	0.776177853846397	4		387	1006	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913274	NA	P-0016005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	41	443	0	ENST00000263967.3:c.1634A>C	p.Glu545Ala	p.E545A	ENST00000263967	NM_006218.2	545	gAg/gCg	10/21	0.370235847825479	3	FACETS	0.362	0.302	0.429	0.121	0.1	0.143	INDETERMINATE	1	TRUE	0	0.776177853846397	3		443	405	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076785	72076785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576347795	NA	P-0016005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	116	419	0	ENST00000357731.5:c.712G>A	p.Gly238Arg	p.G238R	ENST00000357731	NM_173808.2	238	Gga/Aga	5/7	0.230759779429431	2	FACETS	0.497	0.449	0.548	0.249	0.224	0.274	INDETERMINATE	1	TRUE	0	0.776177853846397	2		419	601	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115251272	115251272	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	45	329	0	ENST00000369535.4:c.454G>A	p.Val152Ile	p.V152I	ENST00000369535	NM_002524.4	152	Gtt/Att	5/7	0.230759779429431	2	FACETS	0.246	0.207	0.29	0.123	0.103	0.145	INDETERMINATE	1	TRUE	0	0.776177853846397	2		329	471	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0016007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	330	605	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.501441063099477	3	FACETS	0.925	0.885	0.966	0.925	0.885	0.966	CLONAL	3	TRUE	0	0.501441063099477	3		606	593	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148936	119148936	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	344	533	0	ENST00000264033.4:c.1156G>T	p.Glu386Ter	p.E386*	ENST00000264033	NM_005188.3	386	Gaa/Taa	8/16	0.4863805526268	4	FACETS	0.918	0.881	0.954	0.918	0.881	0.954	CLONAL	4	TRUE	0	0.501441063099477	4		533	561	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579515	7579524	+	frameshift_variant	Frame_Shift_Del	DEL	GGTCTTCAGT	GGTCTTCAGT	-	novel	NA	P-0016007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	195	695	0	ENST00000269305.4:c.163_172del	p.Thr55GlnfsTer65	p.T55Qfs*65	ENST00000269305	NM_001126112.2	55	ACTGAAGACCca/ca	4/11	0.441591225165899	2	FACETS	1	0.99	1	0.682	0.636	0.73	CLONAL	1	TRUE	0	0.501441063099477	2		695	570	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339953	70339962	+	frameshift_variant	Frame_Shift_Del	DEL	GACCTGTGCC	GACCTGTGCC	-	novel	NA	P-0016007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	38	440	0	ENST00000374080.3:c.486_495del	p.Met162IlefsTer55	p.M162Ifs*55	ENST00000374080		162	atGACCTGTGCC/at	4/45	0.454765131021639	1	FACETS	0.297	0.246	0.355	0.297	0.246	0.355	SUBCLONAL	1	TRUE	0	0.501441063099477	1		440	382	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330628	65330628	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0016008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	288	351	0	ENST00000342505.4:c.1018A>T	p.Lys340Ter	p.K340*	ENST00000342505	NM_002227.2	340	Aaa/Taa	8/25	0.79066342070012	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.79066342070012	1		351	433	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29120968	29120968	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	224	419	0	ENST00000328354.6:c.589A>G	p.Lys197Glu	p.K197E	ENST00000328354	NM_007194.3	197	Aaa/Gaa	4/15	0.79066342070012	1	FACETS	0.976	0.929	1	0.976	0.929	1	CLONAL	1	TRUE	0	0.79066342070012	1		419	351	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940079	49940079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778931500	NA	P-0016008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	249	538	6	ENST00000296474.3:c.964C>T	p.Arg322Trp	p.R322W	ENST00000296474	NM_002447.2	322	Cgg/Tgg	1/20	0.79066342070012	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.79066342070012	1		544	339	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295382	1295382	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0016008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	100	241	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.988	0.898	1	0.988	0.898	1	CLONAL	1	TRUE	1	0.79066342070012	2		241	256	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662622	117662622	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1456345928	NA	P-0016008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	262	424	0	ENST00000368508.3:c.4843A>G	p.Asn1615Asp	p.N1615D	ENST00000368508	NM_002944.2	1615	Aat/Gat	29/43	1	2	FACETS	0.931	0.877	0.986	0.931	0.877	0.986	CLONAL	1	TRUE	1	0.79066342070012	2		424	712	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	75	414	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.3	3	FACETS	0.893	0.782	1	0.446	0.391	0.506	CLONAL	1	FALSE	1	0.3	3		414	644	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0016009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	119	790	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.256747406621852	3	FACETS	0.864	0.778	0.955			1	CLONAL	1	FALSE	NA	0.3	3		792	1056	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881001	37881002	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGCTCCCC	rs397516981	NA	P-0016009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	88	553	0	ENST00000269571.5:c.2331_2339dup	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	gtg/gtGGGCTCCCCg	20/27	0.197055462215677	4	FACETS	0.757	0.669	0.852	0.252	0.223	0.284	SUBCLONAL	1	FALSE	1	0.3	4		553	1007	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346641	225346641	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	38	363	0	ENST00000264414.4:c.1997C>T	p.Thr666Ile	p.T666I	ENST00000264414	NM_003590.4	666	aCa/aTa	14/16	0.189374399306995	3	FACETS	0.487	0.402	0.583	0.244	0.201	0.292	SUBCLONAL	1	FALSE	1	0.3	3		363	598	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0016012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	392	485	1	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.658989999914577	2	FACETS	0.986	0.951	1	0.986	0.951	1	CLONAL	2	TRUE	0	0.658989999914577	2		486	603	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630303	187630303	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774143174	NA	P-0016012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	255	537	1	ENST00000441802.2:c.679C>T	p.Arg227Cys	p.R227C	ENST00000441802	NM_005245.3	227	Cgt/Tgt	2/27	0.154278323833345	3	FACETS	1	0.993	1	0.722	0.679	0.765	INDETERMINATE	1	TRUE	1	0.658989999914577	3		538	713	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118353158	118353158	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	131	543	0	ENST00000534358.1:c.4034A>G	p.Lys1345Arg	p.K1345R	ENST00000534358	NM_005933.3	1345	aAa/aGa	8/36	0.658989999914577	4	FACETS	0.546	0.494	0.601	0.182	0.164	0.201	SUBCLONAL	1	TRUE	1	0.658989999914577	4		543	1209	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163928	47163928	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	115	348	0	ENST00000409792.3:c.2198A>G	p.Asp733Gly	p.D733G	ENST00000409792	NM_014159.6	733	gAt/gGt	3/21	0.658989999914577	4	FACETS	0.926	0.836	1	0.309	0.278	0.341	CLONAL	1	TRUE	1	0.658989999914577	4		348	625	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0016013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	263	605	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.381658206957717	2	FACETS	0.944	0.889	1	0.944	0.889	1	CLONAL	2	TRUE	0	0.38275738630204	2		606	728	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0016013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	222	467	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.379052114302094	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.38275738630204	2		468	527	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0016013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	137	496	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.175966803699168	3	FACETS	1	0.984	1	0.681	0.621	0.744	INDETERMINATE	1	TRUE	1	0.38275738630204	3		496	626	SUCCESS
APC	324	MSKCC	GRCh37	5	112175525	112175525	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	82	346	1	ENST00000257430.4:c.4234G>T	p.Gly1412Ter	p.G1412*	ENST00000257430	NM_000038.5	1412	Gga/Tga	16/16	0.175966803699168	3	FACETS	1	0.9	1	0.509	0.45	0.572	INDETERMINATE	1	TRUE	1	0.38275738630204	3		347	501	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961059	55961059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530419081	NA	P-0016013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	237	744	1	ENST00000263923.4:c.2881C>T	p.Arg961Trp	p.R961W	ENST00000263923	NM_002253.2	961	Cgg/Tgg	21/30	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.38275738630204	2		745	916	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376680	118376680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	49	594	0	ENST00000534358.1:c.10073G>A	p.Ser3358Asn	p.S3358N	ENST00000534358	NM_005933.3	3358	aGt/aAt	27/36	0.20010043167607	5	FACETS	0.491	0.414	0.576	0.098	0.082	0.116	INDETERMINATE	1	TRUE	0	0.38275738630204	5		594	821	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66525055	66525055	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	48	246	0	ENST00000358598.2:c.814G>A	p.Glu272Lys	p.E272K	ENST00000358598	NM_212471.2	272	Gaa/Aaa	9/11	1	2	FACETS	0.74	0.628	0.862	0.74	0.628	0.862	SUBCLONAL	1	TRUE	1	0.38275738630204	2		246	339	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226826	2226826	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1259363492	NA	P-0016013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	246	465	2	ENST00000398665.3:c.4306G>A	p.Gly1436Arg	p.G1436R	ENST00000398665	NM_032482.2	1436	Gga/Aga	27/28	0.365627257647803	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.38275738630204	3		467	723	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0016014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	16	541	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.069	0.05	0.091	0.069	0.05	0.091	SUBCLONAL	1	TRUE	1	0.613364048196099	2		541	760	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207162	1207162	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs137853076	NA	P-0016014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	164	765	0	ENST00000326873.7:c.250A>T	p.Lys84Ter	p.K84*	ENST00000326873	NM_000455.4	84	Aag/Tag	1/10	0.613364048196099	1	FACETS	0.531	0.489	0.575	0.531	0.489	0.575	SUBCLONAL	1	TRUE	0	0.613364048196099	1		765	698	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720339	43720339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	175	588	1	ENST00000382044.4:c.3703C>T	p.Pro1235Ser	p.P1235S	ENST00000382044	NM_001141980.1	1235	Cct/Tct	18/28	1	2	FACETS	0.7	0.646	0.757	0.7	0.646	0.757	SUBCLONAL	1	TRUE	1	0.613364048196099	2		589	815	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117509	4117509	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	13	261	0	ENST00000262948.5:c.211G>A	p.Asp71Asn	p.D71N	ENST00000262948	NM_030662.3	71	Gac/Aac	2/11	0.613364048196099	1	FACETS	0.153	0.109	0.207	0.153	0.109	0.207	SUBCLONAL	1	TRUE	0	0.613364048196099	1		261	192	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0016015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	308	606	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.793984441753254	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.793984441753254	1		606	400	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797744	42797744	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	208	566	0	ENST00000575354.2:c.3796G>T	p.Ala1266Ser	p.A1266S	ENST00000575354	NM_015125.3	1266	Gcc/Tcc	16/20	1	2	FACETS	0.819	0.764	0.875	0.819	0.764	0.875	CLONAL	1	TRUE	1	0.793984441753254	2		566	640	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0016016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	117	605	1	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	0.99	1	CLONAL	2	TRUE	1	0.217206323236044	2		606	470	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207021	1207021	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913324	NA	P-0016016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	383	594	2	ENST00000326873.7:c.109C>T	p.Gln37Ter	p.Q37*	ENST00000326873	NM_000455.4	37	Cag/Tag	1/10	0.067442857139659	3	FACETS	1	0.984	1			1	INDETERMINATE	3	TRUE	NA	0.217206323236044	3		596	1203	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420561	49420561	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	107	433	0	ENST00000301067.7:c.15188C>G	p.Ala5063Gly	p.A5063G	ENST00000301067	NM_003482.3	5063	gCc/gGc	48/54	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.217206323236044	2		433	869	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524749	103524749	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0016016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	22	190	0	ENST00000355739.4:c.2879+1A>T		p.X960_splice	ENST00000355739	NM_000123.3	960			1	2	FACETS	0.631	0.489	0.796	0.631	0.489	0.796	SUBCLONAL	1	TRUE	1	0.217206323236044	2		190	321	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500562	99500562	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	71	437	0	ENST00000268035.6:c.3995G>T	p.Gly1332Val	p.G1332V	ENST00000268035	NM_000875.3	1332	gGg/gTg	21/21	0.067442857139659	3	FACETS	0.777	0.676	0.886			1	INDETERMINATE	1	TRUE	NA	0.217206323236044	3		437	933	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068349	26068349	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0016016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	42	248	0	ENST00000435504.4:c.140+1G>T		p.X47_splice	ENST00000435504		47			0.150163321370402	3	FACETS	1	0.938	1	0.634	0.531	0.748	CLONAL	1	TRUE	1	0.217206323236044	3		248	338	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526261	189526261	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	130	438	0	ENST00000264731.3:c.525C>A	p.His175Gln	p.H175Q	ENST00000264731	NM_003722.4	175	caC/caA	4/14	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.217206323236044	2		438	1091	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510327	187510327	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	58	246	0	ENST00000441802.2:c.13186G>T	p.Asp4396Tyr	p.D4396Y	ENST00000441802	NM_005245.3	4396	Gac/Tac	27/27	0.198541833226558	3	FACETS	1	0.942	1	0.594	0.511	0.685	CLONAL	1	TRUE	1	0.217206323236044	3		246	498	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793535	89793535	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	42	312	0	ENST00000336032.3:c.604G>A	p.Gly202Ser	p.G202S	ENST00000336032	NM_006813.2	202	Ggt/Agt	2/2	0.217206323236044	1	FACETS	0.868	0.726	1	0.868	0.726	1	CLONAL	1	TRUE	0	0.217206323236044	1		312	397	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016236	150016236	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	45	255	0	ENST00000253339.5:c.470G>T	p.Arg157Ile	p.R157I	ENST00000253339		157	aGa/aTa	2/7	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.217206323236044	2		255	391	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851547	128851547	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	160	512	1	ENST00000249373.3:c.1872G>T	p.Lys624Asn	p.K624N	ENST00000249373	NM_005631.4	624	aaG/aaT	11/12	0.149092364916664	4	FACETS	1	0.988	1	0.742	0.678	0.808	CLONAL	1	TRUE	2	0.217206323236044	4		513	1209	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993624	90993625	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0016016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	69	290	0	ENST00000265433.3:c.298_299delinsTT	p.Gly100Leu	p.G100L	ENST00000265433	NM_002485.4	100	GGa/TTa	3/16	0.16905631967707	5	FACETS	0.885	0.773	1	0.59	0.515	0.67	CLONAL	2	TRUE	2	0.217206323236044	5		290	476	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195088	123195103	+	frameshift_variant	Frame_Shift_Del	DEL	AGCATACCTTGTGGAT	AGCATACCTTGTGGAT	-	novel	NA	P-0016016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	32	297	0	ENST00000218089.9:c.1436_1451del	p.Tyr479CysfsTer9	p.Y479Cfs*9	ENST00000218089	NM_001042749.1	477	gcAGCATACCTTGTGGAT/gc	16/35	1	2	FACETS	0.726	0.589	0.88	0.726	0.589	0.88	SUBCLONAL	1	TRUE	1	0.217206323236044	2		297	406	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0016017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	1866	618	2	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.569161621671595	11	FACETS	1	0.986	1			1	CLONAL	9	TRUE	NA	0.569161621671595	11		620	2592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691039	NA	P-0016017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	378	491	0	ENST00000269305.4:c.919+1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.569161621671595	2	FACETS	0.981	0.941	1	0.981	0.941	1	CLONAL	2	TRUE	0	0.569161621671595	2		491	677	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602872	10602872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	296	752	1	ENST00000171111.5:c.706G>A	p.Asp236Asn	p.D236N	ENST00000171111	NM_203500.1	236	Gac/Aac	3/6	0.569161621671595	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.569161621671595	1		753	709	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134251	11134251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1218643327	NA	P-0016017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	238	524	0	ENST00000358026.2:c.2917C>T	p.Arg973Trp	p.R973W	ENST00000358026	NM_001128849.1	973	Cgg/Tgg	20/36	0.569161621671595	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.569161621671595	1		524	596	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092983	27092983	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	150	303	0	ENST00000324856.7:c.2914G>T	p.Asp972Tyr	p.D972Y	ENST00000324856	NM_006015.4	972	Gat/Tat	10/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.569161621671595	2		303	501	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962553	100962553	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778032418	NA	P-0016017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	552	454	2	ENST00000325455.5:c.1844G>A	p.Arg615His	p.R615H	ENST00000325455	NM_001202474.3	615	cGc/cAc	3/8	0.513558735419468	4	FACETS	0.959	0.925	0.993			1	CLONAL	3	TRUE	NA	0.569161621671595	4		456	1058	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479774	67479774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906856	NA	P-0016017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	199	465	1	ENST00000327367.4:c.1081G>A	p.Glu361Lys	p.E361K	ENST00000327367	NM_005902.3	361	Gag/Aag	8/9	0.261345008685326	4	FACETS	0.974	0.901	1	0.243	0.225	0.263	INDETERMINATE	1	TRUE	0	0.569161621671595	4		466	1127	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747086	40747087	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0016017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	160	415	0	ENST00000373198.4:c.2995_2996delinsAA	p.Ser999Asn	p.S999N	ENST00000373198	NM_133170.3	999	TCc/AAc	22/32	0.569161621671595	3	FACETS	0.901	0.827	0.978	0.45	0.413	0.489	CLONAL	1	TRUE	1	0.569161621671595	3		415	802	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217261	66217261	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	117	296	2	ENST00000273854.3:c.2354C>G	p.Ser785Cys	p.S785C	ENST00000273854	NM_004439.5	785	tCt/tGt	14/18	0.569161621671595	1	FACETS	0.952	0.871	1	0.952	0.871	1	CLONAL	1	TRUE	0	0.569161621671595	1		298	309	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0016018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	120	583	0				ENST00000310581	NM_198253.2	-/1132			0.42651487616401	4	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	2	0.42651487616401	4		583	381	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913403	NA	P-0016018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	96	251	0	ENST00000349496.5:c.110C>A	p.Ser37Tyr	p.S37Y	ENST00000349496	NM_001904.3	37	tCt/tAt	3/15	0.42651487616401	5	FACETS	1	0.904	1	0.67	0.602	0.742	CLONAL	2	TRUE	2	0.42651487616401	5		251	367	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198389	138198389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751123351	NA	P-0016018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	30	393	0	ENST00000237289.4:c.982G>A	p.Ala328Thr	p.A328T	ENST00000237289	NM_001270507.1	328	Gca/Aca	6/9	0.332454477566132	3	FACETS	0.579	0.467	0.704	0.289	0.233	0.352	SUBCLONAL	1	TRUE	1	0.42651487616401	3		393	295	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449546	149449546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376388107	NA	P-0016018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	123	597	0	ENST00000286301.3:c.1400C>T	p.Thr467Met	p.T467M	ENST00000286301	NM_005211.3	467	aCg/aTg	10/22	0.382740928671258	4	FACETS	0.76	0.691	0.833	0.76	0.691	0.833	SUBCLONAL	2	TRUE	2	0.42651487616401	4		597	541	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933461	49933461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201953002	NA	P-0016018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	139	578	1	ENST00000296474.3:c.2729G>A	p.Arg910Gln	p.R910Q	ENST00000296474	NM_002447.2	910	cGg/cAg	11/20	0.42651487616401	5	FACETS	0.838	0.765	0.914	0.558	0.51	0.609	CLONAL	2	TRUE	2	0.42651487616401	5		579	638	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111517	8111517	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	75	549	1	ENST00000346208.3:c.1003G>A	p.Asp335Asn	p.D335N	ENST00000346208		335	Gac/Aac	5/6	NA	2	FACETS	1	0.907	1			1	INDETERMINATE	1	TRUE	NA	0.42651487616401	2		550	341	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552660	18552660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758604951	NA	P-0016018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	115	472	0	ENST00000266497.5:c.2071C>T	p.Leu691Phe	p.L691F	ENST00000266497		691	Ctt/Ttt	14/31	0.135646651319572	5	FACETS	1	0.949	1			1	INDETERMINATE	2	TRUE	NA	0.42651487616401	5		472	414	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967593	26967593	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	106	505	0	ENST00000381527.3:c.736C>T	p.Pro246Ser	p.P246S	ENST00000381527	NM_001260.1	246	Cct/Tct	7/13	0.42651487616401	4	FACETS	0.846	0.764	0.932	0.846	0.764	0.932	CLONAL	2	TRUE	2	0.42651487616401	4		505	419	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331790	68331791	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0016018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	110	461	0	ENST00000487270.1:c.386_387delinsTT	p.Thr129Ile	p.T129I	ENST00000487270	NM_133509.3	129	aCC/aTT	5/11	0.42651487616401	4	FACETS	0.809	0.731	0.89	0.809	0.731	0.89	CLONAL	2	TRUE	2	0.42651487616401	4		461	455	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858040	9858040	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs757427207	NA	P-0016018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	62	397	0	ENST00000330684.3:c.3361G>T	p.Asp1121Tyr	p.D1121Y	ENST00000330684	NM_001134407.1	1121	Gat/Tat	13/13	0.382740928671258	4	FACETS	1	0.89	1	0.515	0.446	0.588	CLONAL	1	TRUE	2	0.42651487616401	4		397	403	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627404	37627404	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	202	563	0	ENST00000447079.4:c.1319C>T	p.Ser440Leu	p.S440L	ENST00000447079	NM_015083.1	440	tCa/tTa	2/14	0.390875880317226	5	FACETS	0.885	0.826	0.945			1	CLONAL	3	TRUE	NA	0.42651487616401	5		563	585	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097604	11097604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	118	615	1	ENST00000358026.2:c.784C>T	p.Pro262Ser	p.P262S	ENST00000358026	NM_001128849.1	262	Ccc/Tcc	5/36	0.306550800159154	4	FACETS	0.782	0.709	0.858	0.782	0.709	0.858	SUBCLONAL	2	TRUE	2	0.42651487616401	4		616	505	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455535	189455536	+	missense_variant	Missense_Mutation	DNP	AG	AG	TA	novel	NA	P-0016018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	47	366	2	ENST00000264731.3:c.69_70delinsTA	p.Glu24Lys	p.E24K	ENST00000264731	NM_003722.4	23	gtAGaa/gtTAaa	2/14	0.42651487616401	3	FACETS	0.922	0.783	1	0.461	0.391	0.537	CLONAL	1	TRUE	1	0.42651487616401	3		368	290	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397158	397158	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0016018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	61	435	0	ENST00000380956.4:c.543C>G	p.Tyr181Ter	p.Y181*	ENST00000380956	NM_001195286.1	181	taC/taG	5/9	0.42651487616401	4	FACETS	0.974	0.843	1	0.487	0.421	0.558	CLONAL	1	TRUE	2	0.42651487616401	4		435	419	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331648	8331648	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	61	402	0	ENST00000356435.5:c.5468T>G	p.Phe1823Cys	p.F1823C	ENST00000356435		1823	tTc/tGc	33/35	NA	2	FACETS	0.883	0.767	1			1	INDETERMINATE	1	TRUE	NA	0.42651487616401	2		402	324	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797328	135797328	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057524690	NA	P-0016018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	43	287	0	ENST00000298552.3:c.541C>T	p.His181Tyr	p.H181Y	ENST00000298552	NM_001162426.1	181	Cat/Tat	7/23	1	2	FACETS	0.854	0.721	0.999	0.854	0.721	0.999	CLONAL	1	TRUE	1	0.42651487616401	2		287	236	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220578	1220578	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0016020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	78	493	1	ENST00000326873.7:c.598-2A>T		p.X200_splice	ENST00000326873	NM_000455.4	200			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.189374583286164	2		494	596	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579592	7579592	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs879254212	NA	P-0016020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	77	440	0	ENST00000269305.4:c.97-2A>G		p.X33_splice	ENST00000269305	NM_001126112.2	33			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.189374583286164	2		440	610	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78921151	78921151	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	122	308	0	ENST00000306801.3:c.3265G>A	p.Asp1089Asn	p.D1089N	ENST00000306801	NM_020761.2	1089	Gac/Aac	27/34	0.189374583286164	3	FACETS	0.899	0.816	0.985	0.899	0.816	0.985	CLONAL	3	TRUE	0	0.189374583286164	3		308	523	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0016021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	171	464	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.285436580507407	4	FACETS	0.894	0.823	0.967	0.894	0.823	0.967	CLONAL	2	TRUE	2	0.315356827718183	4		464	798	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	357	713	0	ENST00000269305.4:c.383del	p.Pro128LeufsTer42	p.P128Lfs*42	ENST00000269305	NM_001126112.2	128	cCt/ct	5/11	0.288611486807605	3	FACETS	0.854	0.811	0.898	0.854	0.811	0.898	CLONAL	3	TRUE	0	0.315356827718183	3		713	1023	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427279	49427279	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	122	293	1	ENST00000301067.7:c.11209C>T	p.Gln3737Ter	p.Q3737*	ENST00000301067	NM_003482.3	3737	Cag/Tag	39/54	0.315356827718183	6	FACETS	1	0.974	1			1	CLONAL	2	TRUE	NA	0.315356827718183	6		294	527	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003399	42003399	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	76	357	0	ENST00000219905.7:c.2936A>T	p.Gln979Leu	p.Q979L	ENST00000219905	NM_001164273.1	979	cAg/cTg	8/24	1	2	FACETS	0.938	0.824	1	0.938	0.824	1	CLONAL	1	TRUE	1	0.315356827718183	2		357	514	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892235	9892235	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	144	488	1	ENST00000330684.3:c.2255G>A	p.Ser752Asn	p.S752N	ENST00000330684	NM_001134407.1	752	aGt/aAt	11/13	0.315356827718183	6	FACETS	0.825	0.752	0.901	0.412	0.376	0.451	CLONAL	2	TRUE	2	0.315356827718183	6		489	903	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39573243	39573243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	65	243	0	ENST00000262039.4:c.724G>A	p.Glu242Lys	p.E242K	ENST00000262039	NM_002647.2	242	Gaa/Aaa	7/25	0.315356827718183	3	FACETS	1	0.88	1	0.507	0.44	0.578	CLONAL	1	TRUE	1	0.315356827718183	3		243	471	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56409138	56409138	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	84	302	1	ENST00000348428.3:c.1645G>T	p.Glu549Ter	p.E549*	ENST00000348428	NM_006785.3	549	Gag/Tag	14/17	0.315356827718183	3	FACETS	1	0.975	1	0.693	0.615	0.776	CLONAL	1	TRUE	1	0.315356827718183	3		303	445	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919004	50919004	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	100	548	0	ENST00000440232.2:c.2741G>A	p.Ser914Asn	p.S914N	ENST00000440232	NM_002691.3	914	aGt/aAt	22/27	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.315356827718183	2		548	602	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754905	29754905	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1286011012	NA	P-0016021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	80	365	1	ENST00000389048.3:c.1030C>A	p.His344Asn	p.H344N	ENST00000389048	NM_004304.4	344	Cac/Aac	4/29	0.315356827718183	3	FACETS	1	0.938	1	0.55	0.485	0.619	CLONAL	1	TRUE	1	0.315356827718183	3		366	534	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356240	66356240	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs753971619	NA	P-0016021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	192	472	1	ENST00000273854.3:c.1257C>A	p.Ser419Arg	p.S419R	ENST00000273854	NM_004439.5	419	agC/agA	5/18	0.285436580507407	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	2	0.315356827718183	4		473	769	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467410	66467410	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761454685	NA	P-0016021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	27	162	0	ENST00000273854.3:c.859G>A	p.Gly287Arg	p.G287R	ENST00000273854	NM_004439.5	287	Ggg/Agg	3/18	0.285436580507407	4	FACETS	0.825	0.658	1	0.413	0.329	0.507	CLONAL	1	TRUE	2	0.315356827718183	4		162	273	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971239	13971239	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	140	358	0	ENST00000405192.2:c.690G>T	p.Glu230Asp	p.E230D	ENST00000405192	NM_001163147.1	230	gaG/gaT	8/12	0.285436580507407	4	FACETS	0.856	0.781	0.934	0.856	0.781	0.934	CLONAL	2	TRUE	2	0.315356827718183	4		358	682	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0016022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	441	657	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.956	0.914	0.999	0.956	0.914	0.999	CLONAL	1	TRUE	1	0.784263728562575	2		657	1176	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504939	186504939	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	238	250	0	ENST00000323963.5:c.795T>G	p.Cys265Trp	p.C265W	ENST00000323963		265	tgT/tgG	8/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.784263728562575	2		250	585	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	137	605	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.826	0.755	0.9	0.826	0.755	0.9	CLONAL	1	TRUE	1	0.62	2		606	535	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	121	414	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.845	0.768	0.925	0.845	0.768	0.925	CLONAL	1	TRUE	1	0.62	2		414	462	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	166	355	0	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.62	2		355	513	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	183	509	0	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.62	2		509	500	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692820	89692820	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587782641	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	85	253	0	ENST00000371953.3:c.306del	p.Lys102AsnfsTer11	p.K102Nfs*11	ENST00000371953	NM_000314.4	102	Aaa/aa	5/9	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.62	2		253	267	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	244	590	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.62	2		590	754	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103510737	103510737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146833751	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	192	583	1	ENST00000355739.4:c.641G>A	p.Arg214His	p.R214H	ENST00000355739	NM_000123.3	214	cGc/cAc	6/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.62	2		584	596	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696691	176696691	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	142	372	0	ENST00000439151.2:c.5397del	p.Phe1799LeufsTer22	p.F1799Lfs*22	ENST00000439151	NM_022455.4	1798	Ttt/tt	16/23	1	2	FACETS	0.912	0.837	0.991	0.912	0.837	0.991	CLONAL	1	TRUE	1	0.62	2		372	502	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396889	139396889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777962754	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	47	612	2	ENST00000277541.6:c.5219C>T	p.Ala1740Val	p.A1740V	ENST00000277541	NM_017617.3	1740	gCg/gTg	28/34	1	2	FACETS	0.201	0.169	0.237	0.201	0.169	0.237	SUBCLONAL	1	TRUE	1	0.62	2		614	754	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	65	544	1	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	1	2	FACETS	0.327	0.283	0.374	0.327	0.283	0.374	SUBCLONAL	1	TRUE	1	0.62	2		545	642	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	287	843	1	ENST00000227507.2:c.859C>T	p.Pro287Ser	p.P287S	ENST00000227507	NM_053056.2	287	Ccc/Tcc	5/5	1	2	FACETS	0.96	0.905	1	0.96	0.905	1	CLONAL	1	TRUE	1	0.62	2		844	964	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	129	401	3	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.867	0.791	0.946	0.867	0.791	0.946	CLONAL	1	TRUE	1	0.62	2		404	480	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	167	547	2	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.919	0.849	0.992	0.919	0.849	0.992	CLONAL	1	TRUE	1	0.62	2		549	586	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562285	21562285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749940600	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	282	781	0	ENST00000382592.4:c.1634G>A	p.Arg545His	p.R545H	ENST00000382592	NM_014572.2	545	cGt/cAt	4/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.62	2		781	878	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391799	139391799	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1455334351	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	79	632	1	ENST00000277541.6:c.6392del	p.Gly2131AlafsTer117	p.G2131Afs*117	ENST00000277541	NM_017617.3	2131	gGc/gc	34/34	1	2	FACETS	0.42	0.369	0.474	0.42	0.369	0.474	SUBCLONAL	1	TRUE	1	0.62	2		633	607	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467697	66467697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779449792	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	119	455	0	ENST00000273854.3:c.572G>A	p.Arg191His	p.R191H	ENST00000273854	NM_004439.5	191	cGt/cAt	3/18	1	2	FACETS	0.914	0.832	0.999	0.914	0.832	0.999	CLONAL	1	TRUE	1	0.62	2		455	420	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258889	16258889	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	325	871	4	ENST00000375759.3:c.6158del	p.Asn2053ThrfsTer11	p.N2053Tfs*11	ENST00000375759	NM_015001.2	2052	Aaa/aa	11/15	1	2	FACETS	0.934	0.883	0.987	0.934	0.883	0.987	CLONAL	1	TRUE	1	0.62	2		875	1122	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105892	27105892	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	201	587	0	ENST00000324856.7:c.5503C>T	p.Gln1835Ter	p.Q1835*	ENST00000324856	NM_006015.4	1835	Cag/Tag	20/20	1	2	FACETS	0.942	0.877	1	0.942	0.877	1	CLONAL	1	TRUE	1	0.62	2		587	688	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352238	70352238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1255849432	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	216	612	1	ENST00000374080.3:c.4265G>A	p.Arg1422His	p.R1422H	ENST00000374080		1422	cGc/cAc	31/45	1	2	FACETS	0.94	0.877	1	0.94	0.877	1	CLONAL	1	TRUE	1	0.62	2		613	741	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213961	2213961	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs753146456	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	52	814	1	ENST00000326181.6:c.45del	p.Ser17AlafsTer111	p.S17Afs*111	ENST00000326181	NM_032271.2	14	Ggg/gg	2/21	1	2	FACETS	0.176	0.149	0.205	0.176	0.149	0.205	SUBCLONAL	1	TRUE	1	0.62	2		815	955	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349640	89349641	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs772267579	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	205	604	12	ENST00000301030.4:c.3309dup	p.Asp1104ArgfsTer2	p.D1104Rfs*2	ENST00000301030	NM_001256183.1	1103	-/A	9/13	1	2	FACETS	0.803	0.746	0.861	0.803	0.746	0.861	CLONAL	1	TRUE	1	0.62	2		616	824	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089648	27089648	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	215	651	0	ENST00000324856.7:c.2604T>G	p.Tyr868Ter	p.Y868*	ENST00000324856	NM_006015.4	868	taT/taG	8/20	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.62	2		651	690	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65312326	65312329	+	splice_region_variant,intron_variant	Splice_Region	DEL	ACTT	ACTT	-	novel	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	234	546	0	ENST00000342505.4:c.1987+3_1987+6del		p.X663_splice	ENST00000342505	NM_002227.2	663			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.62	2		546	696	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65312374	65312375	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	252	611	0	ENST00000342505.4:c.1944dup	p.His649ThrfsTer60	p.H649Tfs*60	ENST00000342505	NM_002227.2	648	-/A	14/25	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.62	2		611	806	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720727	89720727	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	21	124	0	ENST00000371953.3:c.878G>T	p.Gly293Val	p.G293V	ENST00000371953	NM_000314.4	293	gGa/gTa	8/9	1	2	FACETS	0.434	0.337	0.545	0.434	0.337	0.545	SUBCLONAL	1	TRUE	1	0.62	2		124	156	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571855	64571855	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	407	1019	4	ENST00000312049.6:c.1784C>A	p.Pro595His	p.P595H	ENST00000312049	NM_130799.2	595	cCt/cAt	10/10	1	2	FACETS	0.96	0.913	1	0.96	0.913	1	CLONAL	1	TRUE	1	0.62	2		1023	1367	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436662	110436662	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1172028943	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	80	995	1	ENST00000375856.3:c.1739C>T	p.Thr580Met	p.T580M	ENST00000375856	NM_003749.2	580	aCg/aTg	1/2	1	2	FACETS	0.247	0.216	0.28	0.247	0.216	0.28	SUBCLONAL	1	TRUE	1	0.62	2		996	1045	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828210	72828210	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	214	668	0	ENST00000268489.5:c.8371A>C	p.Thr2791Pro	p.T2791P	ENST00000268489	NM_006885.3	2791	Acc/Ccc	9/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.62	2		668	638	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028051	48028051	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	122	364	0	ENST00000234420.5:c.2929T>C	p.Tyr977His	p.Y977H	ENST00000234420	NM_000179.2	977	Tac/Cac	4/10	1	2	FACETS	0.974	0.888	1	0.974	0.888	1	CLONAL	1	TRUE	1	0.62	2		364	404	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548348	41548348	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	169	520	0	ENST00000263253.7:c.3140del	p.Lys1047ArgfsTer12	p.K1047Rfs*12	ENST00000263253	NM_001429.3	1046	Aaa/aa	16/31	1	2	FACETS	0.84	0.775	0.907	0.84	0.775	0.907	CLONAL	1	TRUE	1	0.62	2		520	649	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440881	52440881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867416499	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	226	659	0	ENST00000460680.1:c.623G>A	p.Arg208Gln	p.R208Q	ENST00000460680	NM_004656.3	208	cGg/cAg	8/17	1	2	FACETS	0.971	0.907	1	0.971	0.907	1	CLONAL	1	TRUE	1	0.62	2		659	751	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468398	89468398	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1467832547	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	39	310	0	ENST00000336596.2:c.1938del	p.Glu647ArgfsTer9	p.E647Rfs*9	ENST00000336596	NM_005233.5	644	tcA/tc	11/17	1	2	FACETS	0.336	0.279	0.4	0.336	0.279	0.4	SUBCLONAL	1	TRUE	1	0.62	2		310	374	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413638	138413638	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs375492591	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	148	537	0	ENST00000289153.2:c.1882C>T	p.Arg628Ter	p.R628*	ENST00000289153	NM_006219.2	628	Cga/Tga	12/22	1	2	FACETS	0.787	0.721	0.854	0.787	0.721	0.854	SUBCLONAL	1	TRUE	1	0.62	2		537	607	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215273	142215273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	205	633	0	ENST00000350721.4:c.5828C>T	p.Ala1943Val	p.A1943V	ENST00000350721	NM_001184.3	1943	gCt/gTt	34/47	1	2	FACETS	0.915	0.851	0.98	0.915	0.851	0.98	CLONAL	1	TRUE	1	0.62	2		633	723	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561914	55561914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769632130	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	120	364	1	ENST00000288135.5:c.304G>A	p.Gly102Ser	p.G102S	ENST00000288135	NM_000222.2	102	Ggc/Agc	2/21	1	2	FACETS	0.933	0.849	1	0.933	0.849	1	CLONAL	1	TRUE	1	0.62	2		365	415	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584761	187584761	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	131	306	0	ENST00000441802.2:c.3272T>G	p.Ile1091Arg	p.I1091R	ENST00000441802	NM_005245.3	1091	aTa/aGa	3/27	1	2	FACETS	0.98	0.897	1	0.98	0.897	1	CLONAL	1	TRUE	1	0.62	2		306	431	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79968644	79968644	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	197	531	0	ENST00000265081.6:c.994G>A	p.Ala332Thr	p.A332T	ENST00000265081	NM_002439.4	332	Gcc/Acc	6/24	1	2	FACETS	0.958	0.892	1	0.958	0.892	1	CLONAL	1	TRUE	1	0.62	2		531	663	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739789	41739789	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	41	600	0	ENST00000242208.4:c.184A>G	p.Ile62Val	p.I62V	ENST00000242208	NM_002192.2	62	Att/Gtt	2/3	1	2	FACETS	0.183	0.152	0.218	0.183	0.152	0.218	SUBCLONAL	1	TRUE	1	0.62	2		600	722	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741676	145741676	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	242	657	0	ENST00000428558.2:c.827A>G	p.Gln276Arg	p.Q276R	ENST00000428558	NM_004260.3	276	cAg/cGg	5/22	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.62	2		657	711	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87356813	87356813	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	26	404	0	ENST00000277120.3:c.1166A>C	p.Asn389Thr	p.N389T	ENST00000277120		389	aAc/aCc	10/19	1	2	FACETS	0.19	0.15	0.236	0.19	0.15	0.236	SUBCLONAL	1	TRUE	1	0.62	2		404	442	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399315	139399315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369467132	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	338	963	4	ENST00000277541.6:c.4828G>A	p.Ala1610Thr	p.A1610T	ENST00000277541	NM_017617.3	1610	Gca/Aca	26/34	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.62	2		967	1089	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922074	39922074	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	257	812	0	ENST00000378444.4:c.4098del	p.Lys1366AsnfsTer3	p.K1366Nfs*3	ENST00000378444	NM_001123385.1	1366	aaA/aa	9/15	1	2	FACETS	0.858	0.804	0.913	0.858	0.804	0.913	CLONAL	1	TRUE	1	0.62	2		812	966	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214696	5214697	+	missense_variant	Missense_Mutation	DNP	CA	CA	TG	novel	NA	P-0016023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	247	756	0	ENST00000357368.4:c.4369_4370inv	p.Cys1457His	p.C1457H	ENST00000357368	NM_002850.3	1457	TGt/CAt	29/38	1	2	FACETS	0.961	0.901	1	0.961	0.901	1	CLONAL	1	TRUE	1	0.62	2		756	829	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0016026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	166	442	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.35680688457567	2		442	788	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849051	156849051	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	196	587	0	ENST00000524377.1:c.1943A>C	p.His648Pro	p.H648P	ENST00000524377	NM_002529.3	648	cAc/cCc	15/17	0.265204154359515	4	FACETS	1	0.99	1	0.726	0.672	0.783	CLONAL	1	TRUE	2	0.35680688457567	4		587	1026	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914218	32914218	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	69	397	0	ENST00000380152.3:c.5726A>T	p.Asp1909Val	p.D1909V	ENST00000380152		1909	gAt/gTt	11/27	0.181860127765205	1	FACETS	0.634	0.553	0.721	0.634	0.553	0.721	INDETERMINATE	1	TRUE	0	0.35680688457567	1		397	501	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543370	65543370	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	33	456	0	ENST00000358664.4:c.307G>T	p.Glu103Ter	p.E103*	ENST00000358664	NM_002382.4	103	Gag/Tag	5/5	0.35680688457567	1	FACETS	0.315	0.256	0.381	0.315	0.256	0.381	SUBCLONAL	1	TRUE	0	0.35680688457567	1		456	483	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41228556	41228556	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	120	535	0	ENST00000357654.3:c.4433A>G	p.Glu1478Gly	p.E1478G	ENST00000357654	NM_007294.3	1478	gAg/gGg	13/23	0.27044319234529	3	FACETS	0.788	0.71	0.87	0.394	0.355	0.435	SUBCLONAL	1	TRUE	1	0.35680688457567	3		535	1006	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268739	41268739	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	77	341	0	ENST00000349496.5:c.977A>C	p.Asn326Thr	p.N326T	ENST00000349496	NM_001904.3	326	aAt/aCt	7/15	0.270054515130377	2	FACETS	0.712	0.626	0.805	0.356	0.313	0.403	SUBCLONAL	1	TRUE	0	0.35680688457567	2		341	606	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045814	26045814	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	97	292	0	ENST00000540144.1:c.176C>G	p.Thr59Ser	p.T59S	ENST00000540144	NM_003531.2	59	aCc/aGc	1/1	0.310190759270837	3	FACETS	1	0.969	1	0.615	0.55	0.684	CLONAL	1	TRUE	1	0.35680688457567	3		292	521	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	159	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.901	0.831	0.975	0.901	0.831	0.975	CLONAL	1	TRUE	1	0.612423053613013	2		248	576	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254663	16254663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	146	523	0	ENST00000375759.3:c.1928C>T	p.Pro643Leu	p.P643L	ENST00000375759	NM_015001.2	643	cCt/cTt	11/15	0.404407245988726	1	FACETS	0.364	0.332	0.398	0.364	0.332	0.398	SUBCLONAL	1	TRUE	0	0.612423053613013	1		523	909	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100409	8100409	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1268951338	NA	P-0016027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	361	642	1	ENST00000346208.3:c.383G>A	p.Gly128Glu	p.G128E	ENST00000346208		128	gGg/gAg	3/6	0.612423053613013	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.612423053613013	1		643	770	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425728	49425728	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	534	518	0	ENST00000301067.7:c.12760C>T	p.Gln4254Ter	p.Q4254*	ENST00000301067	NM_003482.3	4254	Cag/Tag	39/54	0.592987027042872	2	FACETS	0.981	0.949	1	0.981	0.949	1	CLONAL	2	TRUE	0	0.612423053613013	2		518	889	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858621	57858621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772683970	NA	P-0016027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	590	434	1	ENST00000228682.2:c.359C>T	p.Ser120Phe	p.S120F	ENST00000228682	NM_005269.2	120	tCc/tTc	4/12	0.592987027042872	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.612423053613013	2		435	941	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915797	112915797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	447	357	0	ENST00000351677.2:c.1070C>T	p.Thr357Met	p.T357M	ENST00000351677	NM_002834.3	357	aCg/aTg	9/16	0.592987027042872	2	FACETS	0.992	0.956	1	0.992	0.956	1	CLONAL	2	TRUE	0	0.612423053613013	2		357	736	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43738686	43738686	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	297	474	0	ENST00000382044.4:c.2939C>T	p.Ser980Phe	p.S980F	ENST00000382044	NM_001141980.1	980	tCt/tTt	14/28	1	2	FACETS	0.9	0.848	0.953	0.9	0.848	0.953	CLONAL	1	TRUE	1	0.612423053613013	2		474	1078	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559090	29559090	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1223905930	NA	P-0016027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	46	31	0	ENST00000356175.3:c.3198-1G>A		p.X1066_splice	ENST00000356175	NM_000267.3	1066			1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.612423053613013	2		31	143	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560043	29560043	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs868450405	NA	P-0016027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	130	232	0	ENST00000356175.3:c.3520C>T	p.Gln1174Ter	p.Q1174*	ENST00000356175	NM_000267.3	1174	Cag/Tag	27/57	1	2	FACETS	0.917	0.838	0.999	0.917	0.838	0.999	CLONAL	1	TRUE	1	0.612423053613013	2		232	463	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2220180	2220180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	342	607	0	ENST00000398665.3:c.2765C>T	p.Ala922Val	p.A922V	ENST00000398665	NM_032482.2	922	gCc/gTc	23/28	1	2	FACETS	0.949	0.898	1	0.949	0.898	1	CLONAL	1	TRUE	1	0.612423053613013	2		607	1177	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143072	30143072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	378	680	1	ENST00000389048.3:c.454G>A	p.Glu152Lys	p.E152K	ENST00000389048	NM_004304.4	152	Gag/Aag	1/29	0.352061223029958	1	FACETS	0.787	0.748	0.826	0.787	0.748	0.826	INDETERMINATE	1	TRUE	0	0.612423053613013	1		681	1088	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158215	106158215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111678678	NA	P-0016027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	198	326	0	ENST00000380013.4:c.3116C>T	p.Ser1039Leu	p.S1039L	ENST00000380013	NM_001127208.2	1039	tCg/tTg	3/11	0.352061223029958	1	FACETS	0.76	0.709	0.813	0.76	0.709	0.813	INDETERMINATE	1	TRUE	0	0.612423053613013	1		326	590	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1253870	1253871	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0016027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	208	510	2	ENST00000310581.5:c.3371_3372delinsTT	p.Pro1124Leu	p.P1124L	ENST00000310581	NM_198253.2	1124	cCC/cTT	16/16	1	2	FACETS	0.808	0.751	0.866	0.808	0.751	0.866	CLONAL	1	TRUE	1	0.612423053613013	2		512	841	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515291	149515291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1244128395	NA	P-0016027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	241	474	0	ENST00000261799.4:c.191G>A	p.Arg64Gln	p.R64Q	ENST00000261799	NM_002609.3	64	cGg/cAg	3/23	1	2	FACETS	0.992	0.93	1	0.992	0.93	1	CLONAL	1	TRUE	1	0.612423053613013	2		474	793	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522605	176522605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	320	593	0	ENST00000292408.4:c.1702C>T	p.Pro568Ser	p.P568S	ENST00000292408	NM_213647.1	568	Cca/Tca	13/18	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.612423053613013	2		593	995	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672626	30672626	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	217	406	0	ENST00000376406.3:c.4334C>T	p.Pro1445Leu	p.P1445L	ENST00000376406	NM_014641.2	1445	cCt/cTt	10/15	0.187562464941983	6	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.612423053613013	6		406	1106	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170061	32170061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	365	682	0	ENST00000375023.3:c.3547G>A	p.Gly1183Arg	p.G1183R	ENST00000375023	NM_004557.3	1183	Gga/Aga	21/30	1	2	FACETS	0.971	0.921	1	0.971	0.921	1	CLONAL	1	TRUE	1	0.612423053613013	2		682	1227	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157192782	157192783	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0016027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	192	372	1	ENST00000346085.5:c.1772_1773delinsAA	p.Trp591Ter	p.W591*	ENST00000346085	NM_020732.3	591	tGG/tAA	3/20	1	2	FACETS	0.715	0.662	0.77	0.715	0.662	0.77	SUBCLONAL	1	TRUE	1	0.612423053613013	2		373	877	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220269	55220269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	191	595	0	ENST00000275493.2:c.659C>T	p.Ser220Phe	p.S220F	ENST00000275493	NM_005228.3	220	tCc/tTc	6/28	0.344918233657079	0	FACETS	0.269	0.248	0.29			1	INDETERMINATE	1	TRUE	0	0.612423053613013	0		595	900	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526580	106526580	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	74	296	0	ENST00000359195.3:c.2873G>A	p.Gly958Glu	p.G958E	ENST00000359195	NM_002649.2	958	gGa/gAa	10/11	0.352061223029958	1	FACETS	0.395	0.347	0.447	0.395	0.347	0.447	INDETERMINATE	1	TRUE	0	0.612423053613013	1		296	424	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878301	151878301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	316	445	0	ENST00000262189.6:c.6644C>T	p.Ser2215Phe	p.S2215F	ENST00000262189	NM_170606.2	2215	tCt/tTt	36/59	0.352061223029958	1	FACETS	0.905	0.858	0.952	0.905	0.858	0.952	INDETERMINATE	1	TRUE	0	0.612423053613013	1		445	791	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485897	8485897	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765439647	NA	P-0016027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	142	313	0	ENST00000356435.5:c.2920C>T	p.Pro974Ser	p.P974S	ENST00000356435		974	Cca/Tca	17/35	0.404407245988726	1	FACETS	0.676	0.62	0.733	0.676	0.62	0.733	SUBCLONAL	1	TRUE	0	0.612423053613013	1		313	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578189	7578189	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1567551150	NA	P-0016028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	1194	604	0	ENST00000269305.4:c.660T>A	p.Tyr220Ter	p.Y220*	ENST00000269305	NM_001126112.2	220	taT/taA	6/11	0.64131891306992	5	FACETS	1	0.997	1	0.852	0.84	0.864	CLONAL	4	FALSE	0	0.942771732002115	5		604	1435	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100549	102100549	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	422	484	0	ENST00000282441.5:c.1393A>C	p.Ile465Leu	p.I465L	ENST00000282441	NM_001130145.2	465	Ata/Cta	9/9	0.942771732002115	4	FACETS	0.818	0.781	0.855	0.818	0.781	0.855	CLONAL	2	FALSE	2	0.942771732002115	4		484	1063	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223086	5223086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1251374260	NA	P-0016028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	452	615	1	ENST00000357368.4:c.2717C>T	p.Ala906Val	p.A906V	ENST00000357368	NM_002850.3	906	gCg/gTg	18/38	0.538900175293059	5	FACETS	0.904	0.864	0.945	0.603	0.576	0.63	INDETERMINATE	2	FALSE	2	0.942771732002115	5		616	1280	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0016029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	403	536	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.211954439465921	6	FACETS	0.994	0.945	1			1	CLONAL	4	TRUE	NA	0.211954439465921	6		536	1362	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221228	1221228	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	240	589	1	ENST00000326873.7:c.751G>T	p.Gly251Cys	p.G251C	ENST00000326873	NM_000455.4	251	Ggt/Tgt	6/10	0.211954439465921	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.211954439465921	2		590	1036	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577102	7577102	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	126	632	0	ENST00000269305.4:c.836G>T	p.Gly279Val	p.G279V	ENST00000269305	NM_001126112.2	279	gGg/gTg	8/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.211954439465921	2		632	1105	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600428	10600428	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	274	745	0	ENST00000171111.5:c.1427G>T	p.Gly476Val	p.G476V	ENST00000171111	NM_203500.1	476	gGg/gTg	4/6	0.211954439465921	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.211954439465921	2		745	1248	SUCCESS
ATR	545	MSKCC	GRCh37	3	142286917	142286917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	52	317	0	ENST00000350721.4:c.139G>A	p.Asp47Asn	p.D47N	ENST00000350721	NM_001184.3	47	Gat/Aat	2/47	0.209942921998131	4	FACETS	0.678	0.575	0.791	0.339	0.287	0.396	SUBCLONAL	1	TRUE	2	0.211954439465921	4		317	877	SUCCESS
ATR	545	MSKCC	GRCh37	3	142286925	142286925	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	58	359	0	ENST00000350721.4:c.131T>A	p.Ile44Lys	p.I44K	ENST00000350721	NM_001184.3	44	aTa/aAa	2/47	0.209942921998131	4	FACETS	0.692	0.593	0.801	0.346	0.296	0.401	SUBCLONAL	1	TRUE	2	0.211954439465921	4		359	958	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1940072	1940210	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTCCTTTCTTTTCCTTTTGTTGTTCTTTTTCTTTTTTTTTCCTTTTTTTCTTTTCTTTTTTTTTTCTTTCTTTTTTTTTTTTTTTTTTTTTTTTTAAATAATAGAGAGACACAATCACTGACAAAACGGCCAGAACA	TTTTCCTTTCTTTTCCTTTTGTTGTTCTTTTTCTTTTTTTTTCCTTTTTTTCTTTTCTTTTTTTTTTCTTTCTTTTTTTTTTTTTTTTTTTTTTTTTAAATAATAGAGAGACACAATCACTGACAAAACGGCCAGAACA	-	novel	NA	P-0016029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	38	14	0	ENST00000382891.5:c.1675-106_1707del		p.X559_splice	ENST00000382891	NM_133335.3	559		8/22	NA	2	FACETS	0.934	0.818	1			1	INDETERMINATE	6	TRUE	NA	0.211954439465921	2		14	64	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395252	139395253	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0016029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	205	549	2	ENST00000277541.6:c.5685_5686delinsTT	p.Glu1896Ter	p.E1896*	ENST00000277541	NM_017617.3	1895	ctGGag/ctTTag	31/34	0.209942921998131	4	FACETS	1	0.933	1	1	0.933	1	CLONAL	2	TRUE	2	0.211954439465921	4		551	1163	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0016030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	82	475	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.914	0.814	1	0.914	0.814	1	CLONAL	1	TRUE	1	0.600385226018216	2		475	299	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	255	414	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	0.815	0.772	0.859			1	INDETERMINATE	2	TRUE	NA	0.600385226018216	2		414	521	SUCCESS
APC	324	MSKCC	GRCh37	5	112116517	112116517	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs869312753	NA	P-0016030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	62	354	0	ENST00000257430.4:c.562C>T	p.Gln188Ter	p.Q188*	ENST00000257430	NM_000038.5	188	Caa/Taa	6/16	0.600385226018216	3	FACETS	0.898	0.782	1	0.449	0.391	0.511	CLONAL	1	TRUE	1	0.600385226018216	3		354	299	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0016030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	258	480	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.600385226018216	2		481	791	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	107	309	0	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.600385226018216	2		309	336	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370933	55370933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	336	700	0	ENST00000297316.4:c.235G>A	p.Ala79Thr	p.A79T	ENST00000297316	NM_022454.3	79	Gct/Act	1/2	0.600385226018216	3	FACETS	1	0.955	1	0.506	0.478	0.536	CLONAL	1	TRUE	1	0.600385226018216	3		700	1437	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591902	48591902	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519740	NA	P-0016030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	137	379	0	ENST00000342988.3:c.1065C>A	p.Asp355Glu	p.D355E	ENST00000342988	NM_005359.5	355	gaC/gaA	9/12	1	2	FACETS	0.941	0.862	1	0.941	0.862	1	CLONAL	1	TRUE	1	0.600385226018216	2		379	485	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587133	189587133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	143	418	0	ENST00000264731.3:c.1150G>A	p.Gly384Ser	p.G384S	ENST00000264731	NM_003722.4	384	Ggt/Agt	9/14	1	2	FACETS	0.97	0.891	1	0.97	0.891	1	CLONAL	1	TRUE	1	0.600385226018216	2		418	491	SUCCESS
APC	324	MSKCC	GRCh37	5	112175771	112175772	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	253	277	0	ENST00000257430.4:c.4483dup	p.Ser1495LysfsTer19	p.S1495Kfs*19	ENST00000257430	NM_000038.5	1494	gaa/gAaa	16/16	0.600385226018216	3	FACETS	0.95	0.897	1	0.95	0.897	1	CLONAL	2	TRUE	1	0.600385226018216	3		277	577	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356454	70356454	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	321	358	1	ENST00000374080.3:c.5349G>T	p.Lys1783Asn	p.K1783N	ENST00000374080		1783	aaG/aaT	37/45	0.531017750978608	2	FACETS	1	0.99	1			1	CLONAL	1	TRUE	NA	0.600385226018216	2		359	910	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945965	17945965	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	62	642	0	ENST00000458235.1:c.1974G>T	p.Glu658Asp	p.E658D	ENST00000458235	NM_000215.3	658	gaG/gaT	15/24	0.153192212717317	3	FACETS	0.28	0.241	0.323			1	INDETERMINATE	1	TRUE	NA	0.686113065256311	3		642	866	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937331	76937357	+	frameshift_variant	Frame_Shift_Del	DEL	ATTTCTTCTTTCCCTCAATTCTATTCT	ATTTCTTCTTTCCCTCAATTCTATTCT	G	novel	NA	P-0016032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	190	311	0	ENST00000373344.5:c.3391_3417delinsC	p.Arg1131LeufsTer8	p.R1131Lfs*8	ENST00000373344	NM_000489.3	1131	AGAATAGAATTGAGGGAAAGAAGAAAT/C	9/35	0.408167924893136	6	FACETS	1	0.978	1			1	INDETERMINATE	2	TRUE	NA	0.686113065256311	6		311	584	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0016033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	161	605	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.322430602728502	3	FACETS	0.761	0.699	0.825	0.761	0.699	0.825	SUBCLONAL	2	TRUE	1	0.322430602728502	3		606	762	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579463	7579463	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	285	643	0	ENST00000269305.4:c.224del	p.Pro75LeufsTer48	p.P75Lfs*48	ENST00000269305	NM_001126112.2	75	cCt/ct	4/11	0.227045685449891	2	FACETS	0.95	0.895	1	0.95	0.895	1	CLONAL	2	TRUE	0	0.322430602728502	2		643	930	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197402	94197402	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	80	450	1	ENST00000323929.3:c.1102G>T	p.Asp368Tyr	p.D368Y	ENST00000323929	NM_005591.3	368	Gac/Tac	11/20	0.25887221790648	3	FACETS	0.861	0.758	0.972	0.431	0.379	0.486	CLONAL	1	TRUE	1	0.322430602728502	3		451	669	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592115	67592115	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	68	293	0	ENST00000274335.5:c.1931G>A	p.Gly644Asp	p.G644D	ENST00000274335		644	gGc/gAc	14/15	0.25887221790648	3	FACETS	0.879	0.766	1	0.44	0.383	0.501	CLONAL	1	TRUE	1	0.322430602728502	3		293	557	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045006	47045006	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	286	391	1	ENST00000377604.3:c.2332C>T	p.Gln778Ter	p.Q778*	ENST00000377604	NM_001204468.1	778	Cag/Tag	20/24	0.322430602728502	2	FACETS	0.917	0.869	0.965			1	CLONAL	3	TRUE	NA	0.322430602728502	2		392	645	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319330	11319330	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	165	481	0	ENST00000361445.4:c.137A>T	p.His46Leu	p.H46L	ENST00000361445	NM_004958.3	46	cAc/cTc	2/58	0.259141321460078	3	FACETS	0.798	0.734	0.864	0.798	0.734	0.864	SUBCLONAL	2	TRUE	1	0.322430602728502	3		481	745	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849848	156849848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374918502	NA	P-0016033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	158	458	3	ENST00000524377.1:c.2104C>T	p.Arg702Cys	p.R702C	ENST00000524377	NM_002529.3	702	Cgt/Tgt	16/17	0.322430602728502	3	FACETS	1	0.984	1	0.655	0.6	0.712	CLONAL	1	TRUE	1	0.322430602728502	3		461	869	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306558	163306558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	80	447	3	ENST00000271452.3:c.355C>T	p.Arg119Trp	p.R119W	ENST00000271452	NM_145697.2	119	Cgg/Tgg	6/14	0.322430602728502	3	FACETS	0.898	0.79	1	0.449	0.395	0.506	CLONAL	1	TRUE	1	0.322430602728502	3		450	642	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342446	118342446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	44	309	0	ENST00000534358.1:c.572C>T	p.Ser191Leu	p.S191L	ENST00000534358	NM_005933.3	191	tCa/tTa	3/36	NA	2	FACETS	0.632	0.53	0.744			1	INDETERMINATE	1	TRUE	NA	0.322430602728502	2		309	432	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398085	4398085	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	91	511	0	ENST00000261254.3:c.649G>A	p.Asp217Asn	p.D217N	ENST00000261254	NM_001759.3	217	Gat/Aat	4/5	0.322430602728502	3	FACETS	0.684	0.606	0.768	0.342	0.303	0.384	SUBCLONAL	1	TRUE	1	0.322430602728502	3		511	958	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244780	46244780	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	118	558	2	ENST00000334344.6:c.2874G>T	p.Gln958His	p.Q958H	ENST00000334344	NM_152641.2	958	caG/caT	15/21	0.322430602728502	3	FACETS	0.8	0.72	0.884	0.4	0.36	0.442	SUBCLONAL	1	TRUE	1	0.322430602728502	3		560	1063	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225983	133225983	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs761617609	NA	P-0016033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	330	629	0	ENST00000320574.5:c.3914G>T	p.Gly1305Val	p.G1305V	ENST00000320574	NM_006231.2	1305	gGg/gTg	31/49	0.322430602728502	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	1	0.322430602728502	3		629	1178	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435916	110435916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762957829	NA	P-0016033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	87	654	0	ENST00000375856.3:c.2485C>T	p.Pro829Ser	p.P829S	ENST00000375856	NM_003749.2	829	Ccc/Tcc	1/2	1	2	FACETS	0.611	0.54	0.688	0.611	0.54	0.688	SUBCLONAL	1	TRUE	1	0.322430602728502	2		654	883	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420266	88420266	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	79	554	1	ENST00000360948.2:c.2420G>T	p.Trp807Leu	p.W807L	ENST00000360948	NM_001012338.2	807	tGg/tTg	19/19	0.200124374253619	4	FACETS	0.787	0.691	0.891	0.394	0.345	0.446	SUBCLONAL	1	TRUE	2	0.322430602728502	4		555	823	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679144	88679144	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1187821886	NA	P-0016033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	138	361	0	ENST00000360948.2:c.893C>A	p.Ala298Asp	p.A298D	ENST00000360948	NM_001012338.2	298	gCc/gAc	8/19	0.200124374253619	4	FACETS	0.834	0.76	0.91	0.834	0.76	0.91	CLONAL	2	TRUE	2	0.322430602728502	4		361	679	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007210	62007210	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	304	598	0	ENST00000392795.3:c.472C>A	p.Leu158Met	p.L158M	ENST00000392795	NM_001039933.1	158	Ctg/Atg	4/6	0.233246937973765	5	FACETS	1	0.975	1	0.71	0.668	0.753	CLONAL	2	TRUE	2	0.322430602728502	5		598	1314	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533123	63533123	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs754833574	NA	P-0016033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	231	528	0	ENST00000307078.5:c.1771G>T	p.Ala591Ser	p.A591S	ENST00000307078	NM_004655.3	591	Gcc/Tcc	7/11	0.233246937973765	5	FACETS	1	0.98	1	0.751	0.7	0.802	CLONAL	2	TRUE	2	0.322430602728502	5		528	944	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119075	70119075	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	229	418	1	ENST00000245479.2:c.647C>A	p.Ser216Tyr	p.S216Y	ENST00000245479	NM_000346.3	216	tCc/tAc	2/3	0.233246937973765	5	FACETS	0.888	0.83	0.948	0.888	0.83	0.948	CLONAL	3	TRUE	2	0.322430602728502	5		419	791	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593479	48593479	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	72	325	0	ENST00000342988.3:c.1230G>T	p.Gln410His	p.Q410H	ENST00000342988	NM_005359.5	410	caG/caT	10/12	1	2	FACETS	0.859	0.752	0.974	0.859	0.752	0.974	CLONAL	1	TRUE	1	0.322430602728502	2		325	520	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867806	45867806	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0016033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	93	611	0	ENST00000391945.4:c.595-1G>T		p.X199_splice	ENST00000391945	NM_000400.3	199			0.25887221790648	3	FACETS	0.661	0.586	0.741	0.33	0.293	0.371	SUBCLONAL	1	TRUE	1	0.322430602728502	3		611	1014	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030583	48030583	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs372103816	NA	P-0016033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	58	308	0	ENST00000234420.5:c.3197A>G	p.Tyr1066Cys	p.Y1066C	ENST00000234420	NM_000179.2	1066	tAt/tGt	5/10	0.322430602728502	4	FACETS	0.622	0.533	0.719	0.207	0.177	0.24	SUBCLONAL	1	TRUE	1	0.322430602728502	4		308	765	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935072	49935072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	203	669	0	ENST00000296474.3:c.1927G>A	p.Glu643Lys	p.E643K	ENST00000296474	NM_002447.2	643	Gag/Aag	6/20	0.247832759478222	4	FACETS	0.777	0.72	0.837	0.777	0.72	0.837	SUBCLONAL	2	TRUE	2	0.322430602728502	4		669	1071	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595914	52595914	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	251	608	0	ENST00000394830.3:c.4001A>C	p.Tyr1334Ser	p.Y1334S	ENST00000394830	NM_018313.4	1334	tAc/tCc	26/30	0.247832759478222	4	FACETS	0.888	0.83	0.948	0.888	0.83	0.948	CLONAL	2	TRUE	2	0.322430602728502	4		608	1159	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898707	134898707	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	122	269	0	ENST00000398015.3:c.1765C>A	p.Pro589Thr	p.P589T	ENST00000398015	NM_004441.4	589	Cca/Aca	10/16	0.247832759478222	4	FACETS	0.889	0.806	0.975	0.889	0.806	0.975	CLONAL	2	TRUE	2	0.322430602728502	4		269	563	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159041	143159041	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	78	306	0	ENST00000262992.4:c.812T>A	p.Leu271His	p.L271H	ENST00000262992	NM_001101669.1	271	cTt/cAt	10/24	0.247832759478222	4	FACETS	1	0.975	1	0.719	0.634	0.809	CLONAL	1	TRUE	2	0.322430602728502	4		306	445	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295441	1295441	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0016033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	28	37	0				ENST00000310581	NM_198253.2	-/1132			0.25887221790648	3	FACETS	1	0.836	1	1	0.95	1	CLONAL	3	TRUE	1	0.322430602728502	3		37	67	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39021187	39021187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	80	395	0	ENST00000357387.3:c.149G>A	p.Gly50Glu	p.G50E	ENST00000357387	NM_152756.3	50	gGa/gAa	3/38	0.25887221790648	3	FACETS	0.852	0.75	0.962	0.426	0.375	0.481	CLONAL	1	TRUE	1	0.322430602728502	3		395	676	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522554	176522554	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1471204215	NA	P-0016033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	218	627	0	ENST00000292408.4:c.1651G>T	p.Glu551Ter	p.E551*	ENST00000292408	NM_213647.1	551	Gag/Tag	13/18	0.25887221790648	3	FACETS	0.806	0.75	0.864	0.806	0.75	0.864	CLONAL	2	TRUE	1	0.322430602728502	3		627	974	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386559	81386559	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	186	493	0	ENST00000222390.5:c.428C>A	p.Thr143Asn	p.T143N	ENST00000222390	NM_000601.4	143	aCt/aAt	4/18	0.233246937973765	5	FACETS	0.987	0.913	1	0.658	0.608	0.71	CLONAL	2	TRUE	2	0.322430602728502	5		493	867	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046489	69046489	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	253	509	0	ENST00000288368.4:c.3962A>C	p.Gln1321Pro	p.Q1321P	ENST00000288368	NM_024870.2	1321	cAg/cCg	32/40	0.322430602728502	5	FACETS	1	0.965	1	0.697	0.652	0.744	CLONAL	2	TRUE	2	0.322430602728502	5		509	1113	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430635	80430635	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	80	292	0	ENST00000286548.4:c.373G>T	p.Glu125Ter	p.E125*	ENST00000286548	NM_002072.3	125	Gag/Tag	3/7	0.233246937973765	5	FACETS	0.835	0.738	0.938	0.556	0.492	0.625	CLONAL	2	TRUE	2	0.322430602728502	5		292	441	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133729492	133729492	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	128	504	0	ENST00000318560.5:c.121G>T	p.Gly41Cys	p.G41C	ENST00000318560	NM_005157.4	41	Ggt/Tgt	2/11	0.322430602728502	3	FACETS	1	0.965	1	0.567	0.514	0.623	CLONAL	1	TRUE	1	0.322430602728502	3		504	813	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390923	139390923	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	134	725	0	ENST00000277541.6:c.7268C>T	p.Ser2423Leu	p.S2423L	ENST00000277541	NM_017617.3	2423	tCa/tTa	34/34	0.322430602728502	3	FACETS	0.841	0.763	0.925	0.421	0.381	0.463	CLONAL	1	TRUE	1	0.322430602728502	3		725	1147	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247581	53247581	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0016033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	162	182	0	ENST00000375401.3:c.229-1G>T		p.X77_splice	ENST00000375401	NM_004187.3	77			0.322430602728502	2	FACETS	0.886	0.824	0.949			1	CLONAL	3	TRUE	NA	0.322430602728502	2		182	378	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0016034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	47	754	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.982	0.831	1	0.982	0.831	1	CLONAL	1	TRUE	1	0.258079598836256	2		755	371	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220371	1220371	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0016034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	77	425	0	ENST00000326873.7:c.465-1G>T		p.X155_splice	ENST00000326873	NM_000455.4	155			0.258079598836256	1	FACETS	0.945	0.831	1	0.945	0.831	1	CLONAL	1	TRUE	0	0.258079598836256	1		425	550	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861822	57861822	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	80	591	1	ENST00000228682.2:c.1123G>T	p.Asp375Tyr	p.D375Y	ENST00000228682	NM_005269.2	375	Gat/Tat	10/12	1	2	FACETS	0.751	0.66	0.849	0.751	0.66	0.849	SUBCLONAL	1	TRUE	1	0.258079598836256	2		592	825	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243776996	243776996	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	45	534	0	ENST00000263826.5:c.673A>C	p.Met225Leu	p.M225L	ENST00000263826	NM_005465.4	225	Atg/Ctg	7/13	1	2	FACETS	0.836	0.704	0.982	0.836	0.704	0.982	CLONAL	1	TRUE	1	0.258079598836256	2		534	417	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482347	56482347	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	54	449	0	ENST00000267101.3:c.895A>G	p.Thr299Ala	p.T299A	ENST00000267101	NM_001982.3	299	Aca/Gca	8/28	1	2	FACETS	0.727	0.62	0.843	0.727	0.62	0.843	SUBCLONAL	1	TRUE	1	0.258079598836256	2		449	576	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779743	3779743	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	52	511	0	ENST00000262367.5:c.5305C>T	p.Arg1769Trp	p.R1769W	ENST00000262367	NM_004380.2	1769	Cgg/Tgg	31/31	1	2	FACETS	0.746	0.635	0.868	0.746	0.635	0.868	SUBCLONAL	1	TRUE	1	0.258079598836256	2		511	540	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602688	10602688	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	103	633	0	ENST00000171111.5:c.890G>T	p.Cys297Phe	p.C297F	ENST00000171111	NM_203500.1	297	tGc/tTc	3/6	0.258079598836256	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.258079598836256	1		633	661	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138486	11138486	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	64	480	0	ENST00000358026.2:c.3242A>C	p.Lys1081Thr	p.K1081T	ENST00000358026	NM_001128849.1	1081	aAa/aCa	24/36	0.258079598836256	1	FACETS	0.8	0.693	0.915	0.8	0.693	0.915	CLONAL	1	TRUE	0	0.258079598836256	1		480	540	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965693	18965693	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	85	655	0	ENST00000262803.5:c.1271A>T	p.Gln424Leu	p.Q424L	ENST00000262803	NM_002911.3	424	cAg/cTg	10/24	0.258079598836256	1	FACETS	0.933	0.825	1	0.933	0.825	1	CLONAL	1	TRUE	0	0.258079598836256	1		655	615	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931799	39931799	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	98	585	0	ENST00000378444.4:c.2800G>C	p.Asp934His	p.D934H	ENST00000378444	NM_001123385.1	934	Gat/Cat	4/15	0.204044210566913	1	FACETS	0.899	0.802	1	0.899	0.802	1	CLONAL	1	TRUE	0	0.258079598836256	1		585	736	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345997	70345997	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750730080	NA	P-0016034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	71	519	0	ENST00000374080.3:c.2534C>T	p.Thr845Met	p.T845M	ENST00000374080		845	aCg/aTg	18/45	0.204044210566913	1	FACETS	0.708	0.617	0.806	0.708	0.617	0.806	SUBCLONAL	1	TRUE	0	0.258079598836256	1		519	677	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0016036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	102	536	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.907	0.81	1	0.907	0.81	1	CLONAL	1	TRUE	1	0.243177785714878	2		536	925	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0016036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	37	790	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.261	0.214	0.315	0.261	0.214	0.315	SUBCLONAL	1	TRUE	1	0.243177785714878	2		792	1165	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0016036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	46	364	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.619	0.521	0.728	0.619	0.521	0.728	SUBCLONAL	1	TRUE	1	0.243177785714878	2		364	611	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762215	43762215	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	80	624	0	ENST00000382044.4:c.1230del	p.Gln411ArgfsTer12	p.Q411Rfs*12	ENST00000382044	NM_001141980.1	410	ttT/tt	11/28	1	2	FACETS	0.59	0.518	0.668	0.59	0.518	0.668	SUBCLONAL	1	TRUE	1	0.243177785714878	2		624	1115	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619374	1619374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753007864	NA	P-0016036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	64	654	0	ENST00000344749.5:c.1267G>A	p.Gly423Arg	p.G423R	ENST00000344749	NM_001136139.2	423	Ggg/Agg	15/19	1	2	FACETS	0.58	0.501	0.667	0.58	0.501	0.667	SUBCLONAL	1	TRUE	1	0.243177785714878	2		654	907	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143204	30143204	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1268240399	NA	P-0016036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	42	485	0	ENST00000389048.3:c.322del	p.Val108SerfsTer20	p.V108Sfs*20	ENST00000389048	NM_004304.4	108	Gtc/tc	1/29	1	2	FACETS	0.552	0.46	0.654	0.552	0.46	0.654	SUBCLONAL	1	TRUE	1	0.243177785714878	2		485	626	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180273	38180273	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs779805093	NA	P-0016036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	183	578	0	ENST00000396334.3:c.121C>T	p.Arg41Ter	p.R41*	ENST00000396334	NM_002468.4	41	Cga/Tga	1/5	0.190884417456483	2	FACETS	0.969	0.896	1	0.969	0.896	1	CLONAL	2	TRUE	0	0.243177785714878	2		578	777	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630007	187630007	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	126	587	0	ENST00000441802.2:c.975G>C	p.Trp325Cys	p.W325C	ENST00000441802	NM_005245.3	325	tgG/tgC	2/27	0.243177785714878	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.243177785714878	1		587	787	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228384	228384	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774160524	NA	P-0016036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	51	394	0	ENST00000264932.6:c.706G>A	p.Ala236Thr	p.A236T	ENST00000264932	NM_004168.2	236	Gca/Aca	6/15	0.243177785714878	5	FACETS	0.589	0.499	0.689	0.147	0.124	0.173	SUBCLONAL	1	TRUE	1	0.243177785714878	5		394	972	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225474	26225474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	24	180	0	ENST00000360408.1:c.92C>T	p.Pro31Leu	p.P31L	ENST00000360408	NM_003532.2	31	cCg/cTg	1/1	1	2	FACETS	0.572	0.448	0.715	0.572	0.448	0.715	SUBCLONAL	1	TRUE	1	0.243177785714878	2		180	345	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170136	32170136	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771019003	NA	P-0016036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	69	673	1	ENST00000375023.3:c.3472C>T	p.Arg1158Ter	p.R1158*	ENST00000375023	NM_004557.3	1158	Cga/Tga	21/30	1	2	FACETS	0.591	0.513	0.676	0.591	0.513	0.676	SUBCLONAL	1	TRUE	1	0.243177785714878	2		674	960	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372714	81372714	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	82	396	0	ENST00000222390.5:c.820C>A	p.Leu274Ile	p.L274I	ENST00000222390	NM_000601.4	274	Ctt/Att	7/18	1	2	FACETS	0.968	0.853	1	0.968	0.853	1	CLONAL	1	TRUE	1	0.243177785714878	2		396	697	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737702	145737702	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137853232	NA	P-0016036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	120	543	3	ENST00000428558.2:c.3061C>T	p.Arg1021Trp	p.R1021W	ENST00000428558	NM_004260.3	1021	Cgg/Tgg	19/22	0.243177785714878	4	FACETS	1	0.978	1	0.435	0.392	0.48	CLONAL	1	TRUE	1	0.243177785714878	4		546	940	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1962801	1962801	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772470710	NA	P-0016037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	78	516	2	ENST00000382891.5:c.3295G>A	p.Glu1099Lys	p.E1099K	ENST00000382891	NM_133335.3	1099	Gag/Aag	18/22	0.201993173440702	3	FACETS	0.976	0.856	1	0.488	0.428	0.553	CLONAL	1	TRUE	1	0.201993173440702	3		518	871	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0016037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	196	325	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	0.201993173440702	5	FACETS	0.924	0.859	0.991	0.924	0.859	0.991	CLONAL	4	TRUE	1	0.201993173440702	5		325	684	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712019	89712019	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	C	novel	NA	P-0016037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	90	191	0	ENST00000371953.3:c.634+3A>C		p.X212_splice	ENST00000371953	NM_000314.4	212			0.191102804972685	3	FACETS	1	0.896	1	1	0.896	1	CLONAL	3	TRUE	0	0.201993173440702	3		191	327	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934152	48934152	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0016037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	74	219	0	ENST00000267163.4:c.608-1G>T		p.X203_splice	ENST00000267163	NM_000321.2	203			0.201993173440702	2	FACETS	0.969	0.853	1	0.969	0.853	1	CLONAL	2	TRUE	0	0.201993173440702	2		219	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577596	7577597	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	GTCAGAG	novel	NA	P-0016037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	128	498	0	ENST00000269305.4:c.678_684dup	p.Cys229LeufsTer2	p.C229Lfs*2	ENST00000269305	NM_001126112.2	228	-/CTCTGAC	7/11	0.201993173440702	3	FACETS	0.945	0.858	1	0.945	0.858	1	CLONAL	2	TRUE	1	0.201993173440702	3		498	738	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188817	32188817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	127	643	0	ENST00000375023.3:c.737G>A	p.Gly246Glu	p.G246E	ENST00000375023	NM_004557.3	246	gGg/gAg	4/30	0.182071348473635	4	FACETS	0.863	0.781	0.949	0.863	0.781	0.949	CLONAL	2	TRUE	2	0.201993173440702	4		643	876	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0016039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	63	371	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	1	2	FACETS	0.321	0.277	0.369	0.321	0.277	0.369	SUBCLONAL	1	TRUE	1	0.578339372818499	2		371	679	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131930617	131930617	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	64	377	1	ENST00000265335.6:c.1850G>T	p.Arg617Ile	p.R617I	ENST00000265335		617	aGa/aTa	12/25	1	2	FACETS	0.317	0.274	0.363	0.317	0.274	0.363	SUBCLONAL	1	TRUE	1	0.578339372818499	2		378	699	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0016040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	154	489	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.565764245471483	2	FACETS	0.808	0.752	0.865	0.808	0.752	0.865	CLONAL	2	TRUE	0	0.568816199137304	2		489	335	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119234	3119234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775040372	NA	P-0016040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	11	649	1	ENST00000078429.4:c.766C>T	p.Arg256Trp	p.R256W	ENST00000078429	NM_002067.2	256	Cgg/Tgg	6/7	0.121416962812931	3	FACETS	0.131	0.09	0.182	0.065	0.045	0.091	INDETERMINATE	1	TRUE	1	0.568816199137304	3		650	380	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	176	437	0	ENST00000256196.4:c.68G>A	p.Gly23Asp	p.G23D	ENST00000256196		23	gGc/gAc	1/6	0.565764245471483	2	FACETS	0.979	0.921	1	0.979	0.921	1	CLONAL	2	TRUE	0	0.568816199137304	2		437	316	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0016041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	179	801	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	0.853	0.786	0.923	0.853	0.786	0.923	CLONAL	1	TRUE	1	0.428754767601896	2		801	979	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252994	36252995	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0016041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	118	594	0	ENST00000300305.3:c.366_367dup	p.Asp123GlyfsTer11	p.D123Gfs*11	ENST00000300305		123	gat/gGGat	4/8	1	2	FACETS	0.744	0.671	0.82	0.744	0.671	0.82	SUBCLONAL	1	TRUE	1	0.428754767601896	2		594	740	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842594	68842594	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0016041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	135	553	0	ENST00000261769.5:c.532-2A>G		p.X178_splice	ENST00000261769	NM_004360.3	178			0.428754767601896	1	FACETS	0.923	0.843	1	0.923	0.843	1	CLONAL	1	TRUE	0	0.428754767601896	1		553	536	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180579	56180579	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	35	447	0	ENST00000399503.3:c.3908A>T	p.His1303Leu	p.H1303L	ENST00000399503	NM_005921.1	1303	cAt/cTt	16/20	1	2	FACETS	0.257	0.21	0.31	0.257	0.21	0.31	SUBCLONAL	1	TRUE	1	0.428754767601896	2		447	635	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0016042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	423	657	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	0.824285507651241	2		657	920	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041630	14041630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368096448	NA	P-0016042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	102	429	1	ENST00000311895.7:c.2177G>A	p.Arg726His	p.R726H	ENST00000311895	NM_005236.2	726	cGc/cAc	11/11	0.824285507651241	3	FACETS	0.403	0.36	0.449	0.202	0.18	0.225	SUBCLONAL	1	TRUE	1	0.824285507651241	3		430	867	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0016043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	327	605	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.313447004294126	5	FACETS	0.926	0.879	0.974			1	CLONAL	4	TRUE	NA	0.313447004294126	5		606	828	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204641	108204653	+	frameshift_variant	Frame_Shift_Del	DEL	AATTACTAAACTT	AATTACTAAACTT	-	novel	NA	P-0016043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	51	250	0	ENST00000278616.4:c.7958_7970del	p.Ile2653ArgfsTer3	p.I2653Rfs*3	ENST00000278616	NM_000051.3	2652	ccAATTACTAAACTT/cc	54/63	1	2	FACETS	0.919	0.785	1	0.919	0.785	1	CLONAL	1	TRUE	1	0.313447004294126	2		250	354	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220131	133220131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764904030	NA	P-0016043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	71	701	1	ENST00000320574.5:c.4306C>T	p.Arg1436Trp	p.R1436W	ENST00000320574	NM_006231.2	1436	Cgg/Tgg	34/49	0.261107915920644	1	FACETS	0.658	0.574	0.747	0.658	0.574	0.747	SUBCLONAL	1	TRUE	0	0.313447004294126	1		702	581	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000300	42000300	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0016043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	39	445	2	ENST00000219905.7:c.2321-2A>T		p.X774_splice	ENST00000219905	NM_001164273.1	774			0.313447004294126	1	FACETS	0.755	0.629	0.894	0.755	0.629	0.894	SUBCLONAL	1	TRUE	0	0.313447004294126	1		447	278	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40747919	40747919	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	96	667	1	ENST00000392038.2:c.499A>T	p.Ile167Phe	p.I167F	ENST00000392038	NM_001626.4	167	Atc/Ttc	6/14	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.313447004294126	2		668	600	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877398	40877398	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	69	586	0	ENST00000373198.4:c.2298G>T	p.Met766Ile	p.M766I	ENST00000373198	NM_133170.3	766	atG/atT	15/32	1	2	FACETS	0.755	0.658	0.86	0.755	0.658	0.86	SUBCLONAL	1	TRUE	1	0.313447004294126	2		586	583	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074272	30074272	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	40	581	0	ENST00000338641.4:c.1534A>G	p.Thr512Ala	p.T512A	ENST00000338641	NM_000268.3	512	Act/Gct	14/16	0.313447004294126	1	FACETS	0.434	0.36	0.516	0.434	0.36	0.516	SUBCLONAL	1	TRUE	0	0.313447004294126	1		581	496	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539594	187539594	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs377032665	NA	P-0016043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	61	421	0	ENST00000441802.2:c.8146G>T	p.Val2716Leu	p.V2716L	ENST00000441802	NM_005245.3	2716	Gtg/Ttg	10/27	0.154092622088736	0	FACETS	0.87	0.757	0.992			1	INDETERMINATE	1	TRUE	0	0.313447004294126	0		421	307	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968242	2968242	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	71	725	1	ENST00000396946.4:c.1744C>A	p.Pro582Thr	p.P582T	ENST00000396946	NM_032415.4	582	Ccc/Acc	13/25	1	2	FACETS	0.803	0.702	0.913	0.803	0.702	0.913	CLONAL	1	TRUE	1	0.313447004294126	2		726	564	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335662	81335663	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0016043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	128	571	0	ENST00000222390.5:c.1697dup	p.Asn566LysfsTer10	p.N566Kfs*10	ENST00000222390	NM_000601.4	566	aat/aaAt	15/18	0.112797403173739	4	FACETS	1	0.984	1	0.713	0.647	0.783	INDETERMINATE	1	TRUE	2	0.313447004294126	4		571	752	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350062	81350062	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	66	386	1	ENST00000222390.5:c.1270C>A	p.Arg424Ser	p.R424S	ENST00000222390	NM_000601.4	424	Cgt/Agt	10/18	0.112797403173739	4	FACETS	0.802	0.7	0.91	0.802	0.7	0.91	INDETERMINATE	2	TRUE	2	0.313447004294126	4		387	345	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0016043-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	271	605	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.3	4	FACETS	0.996	0.934	1			1	CLONAL	3	TRUE	NA	0.19	4		606	1136	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220131	133220131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764904030	NA	P-0016043-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	70	701	1	ENST00000320574.5:c.4306C>T	p.Arg1436Trp	p.R1436W	ENST00000320574	NM_006231.2	1436	Cgg/Tgg	34/49	1	2	FACETS	0.905	0.788	1	0.905	0.788	1	CLONAL	1	TRUE	1	0.19	2		702	814	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000300	42000300	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0016043-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	58	445	2	ENST00000219905.7:c.2321-2A>T		p.X774_splice	ENST00000219905	NM_001164273.1	774			1	2	FACETS	0.902	0.774	1	0.902	0.774	1	CLONAL	1	TRUE	1	0.19	2		447	677	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40747919	40747919	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016043-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	61	667	1	ENST00000392038.2:c.499A>T	p.Ile167Phe	p.I167F	ENST00000392038	NM_001626.4	167	Atc/Ttc	6/14	1	2	FACETS	0.773	0.665	0.89	0.773	0.665	0.89	SUBCLONAL	1	TRUE	1	0.19	2		668	831	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877398	40877398	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016043-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	54	586	0	ENST00000373198.4:c.2298G>T	p.Met766Ile	p.M766I	ENST00000373198	NM_133170.3	766	atG/atT	15/32	1	2	FACETS	0.745	0.635	0.866	0.745	0.635	0.866	SUBCLONAL	1	TRUE	1	0.19	2		586	763	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074272	30074272	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016043-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	57	581	0	ENST00000338641.4:c.1534A>G	p.Thr512Ala	p.T512A	ENST00000338641	NM_000268.3	512	Act/Gct	14/16	1	2	FACETS	0.779	0.667	0.902	0.779	0.667	0.902	CLONAL	1	TRUE	1	0.19	2		581	770	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539594	187539594	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs377032665	NA	P-0016043-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	50	421	0	ENST00000441802.2:c.8146G>T	p.Val2716Leu	p.V2716L	ENST00000441802	NM_005245.3	2716	Gtg/Ttg	10/27	1	2	FACETS	0.808	0.685	0.945	0.808	0.685	0.945	CLONAL	1	TRUE	1	0.19	2		421	651	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968242	2968242	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016043-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	66	725	1	ENST00000396946.4:c.1744C>A	p.Pro582Thr	p.P582T	ENST00000396946	NM_032415.4	582	Ccc/Acc	13/25	1	2	FACETS	0.761	0.659	0.872	0.761	0.659	0.872	SUBCLONAL	1	TRUE	1	0.19	2		726	913	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335662	81335663	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0016043-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	77	571	0	ENST00000222390.5:c.1697dup	p.Asn566LysfsTer10	p.N566Kfs*10	ENST00000222390	NM_000601.4	566	aat/aaAt	15/18	1	2	FACETS	0.866	0.758	0.982	0.866	0.758	0.982	CLONAL	1	TRUE	1	0.19	2		571	936	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350062	81350062	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016043-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	40	386	1	ENST00000222390.5:c.1270C>A	p.Arg424Ser	p.R424S	ENST00000222390	NM_000601.4	424	Cgt/Agt	10/18	1	2	FACETS	0.6	0.497	0.715	0.6	0.497	0.715	SUBCLONAL	1	TRUE	1	0.19	2		387	702	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5246048	5246048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781664688	NA	P-0016044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	130	282	0	ENST00000357368.4:c.727G>A	p.Val243Met	p.V243M	ENST00000357368	NM_002850.3	243	Gtg/Atg	10/38	1	2	FACETS	0.941	0.864	1	1	0.99	1	CLONAL	2	TRUE	1	0.376344045047763	2		282	367	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579870	7579870	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	475	631	1	ENST00000269305.4:c.43del	p.Ser15ValfsTer29	p.S15Vfs*29	ENST00000269305	NM_001126112.2	15	Agt/gt	2/11	0.346357662933394	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	0	0.376344045047763	3		632	984	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016618	12016618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	177	338	0	ENST00000353533.5:c.754G>A	p.Gly252Arg	p.G252R	ENST00000353533	NM_003010.3	252	Gga/Aga	7/11	0.346357662933394	3	FACETS	1	0.977	1	0.75	0.696	0.804	CLONAL	2	TRUE	0	0.376344045047763	3		338	497	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971291	13971291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748182764	NA	P-0016044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	135	391	0	ENST00000405192.2:c.638G>A	p.Arg213His	p.R213H	ENST00000405192	NM_001163147.1	213	cGc/cAc	8/12	0.374238856215768	3	FACETS	1	0.962	1	0.553	0.503	0.605	CLONAL	1	TRUE	1	0.376344045047763	3		391	771	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002915	69002915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1393555535	NA	P-0016044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	66	321	2	ENST00000288368.4:c.2215G>A	p.Val739Ile	p.V739I	ENST00000288368	NM_024870.2	739	Gtt/Att	20/40	0.289949254293789	4	FACETS	0.754	0.654	0.862	0.251	0.218	0.288	SUBCLONAL	1	TRUE	1	0.376344045047763	4		323	640	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0016045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	306	541	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.33175054050599	3	FACETS	0.942	0.889	0.996	0.942	0.889	0.996	CLONAL	2	TRUE	1	0.368109037906317	3		541	1045	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675071	40675071	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	49	600	0	ENST00000249776.8:c.35T>G	p.Val12Gly	p.V12G	ENST00000249776	NM_033286.3	12	gTt/gGt	1/9	0.368109037906317	1	FACETS	0.227	0.191	0.267	0.227	0.191	0.267	SUBCLONAL	1	TRUE	0	0.368109037906317	1		600	957	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936051	49936051	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	70	609	1	ENST00000296474.3:c.1619G>A	p.Trp540Ter	p.W540*	ENST00000296474	NM_002447.2	540	tGg/tAg	4/20	1	2	FACETS	0.364	0.316	0.416	0.364	0.316	0.416	SUBCLONAL	1	TRUE	1	0.368109037906317	2		610	1044	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956179	55956180	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CA	CA	-	novel	NA	P-0016045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	85	407	0	ENST00000263923.4:c.3135_3136del	p.Cys1045Ter	p.C1045*	ENST00000263923	NM_002253.2	1045	tgTGac/tgac	23/30	1	2	FACETS	0.574	0.507	0.647	0.574	0.507	0.647	SUBCLONAL	1	TRUE	1	0.368109037906317	2		407	804	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0016046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	130	474	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.929	0.845	1	1	0.989	1	CLONAL	2	TRUE	1	0.214225102768283	2		474	653	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821594	72821596	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	rs374416547	NA	P-0016046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	10	109	1	ENST00000268489.5:c.10579_10581del	p.Gly3527del	p.G3527del	ENST00000268489	NM_006885.3	3527	GGC/-	10/10	1	2	FACETS	0.491	0.333	0.69	0.491	0.333	0.69	SUBCLONAL	1	TRUE	1	0.214225102768283	2		110	190	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923397	9923397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	281	603	0	ENST00000330684.3:c.1890G>A	p.Met630Ile	p.M630I	ENST00000330684	NM_001134407.1	630	atG/atA	9/13	0.203420803902455	3	FACETS	0.887	0.834	0.942	1	0.992	1	CLONAL	3	TRUE	1	0.214225102768283	3		603	1091	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101474	27101568	+	frameshift_variant	Frame_Shift_Del	DEL	TCCAGCCCTGCTCCCCTGCCCCGGCCAATGGAGAACCGCACCTCTCCTAGCAAGTCTCCATTCCTGCACTCTGGGATGAAAATGCAGAAGGCAGG	TCCAGCCCTGCTCCCCTGCCCCGGCCAATGGAGAACCGCACCTCTCCTAGCAAGTCTCCATTCCTGCACTCTGGGATGAAAATGCAGAAGGCAGG	-	novel	NA	P-0016046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	78	740	0	ENST00000324856.7:c.4759_4853del	p.Ser1587ProfsTer29	p.S1587Pfs*29	ENST00000324856	NM_006015.4	1586	TCCAGCCCTGCTCCCCTGCCCCGGCCAATGGAGAACCGCACCTCTCCTAGCAAGTCTCCATTCCTGCACTCTGGGATGAAAATGCAGAAGGCAGGt/t	18/20	0.214225102768283	1	FACETS	0.526	0.46	0.597	0.526	0.46	0.597	SUBCLONAL	1	TRUE	0	0.214225102768283	1		740	1236	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991097	41991097	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	220	482	0	ENST00000219905.7:c.2050G>A	p.Glu684Lys	p.E684K	ENST00000219905	NM_001164273.1	684	Gaa/Aaa	4/24	0.214225102768283	1	FACETS	0.943	0.878	1	1	0.994	1	CLONAL	2	TRUE	0	0.214225102768283	1		482	972	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592204	55592204	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	53	374	0	ENST00000288135.5:c.1528G>T	p.Gly510Cys	p.G510C	ENST00000288135	NM_000222.2	510	Ggt/Tgt	9/21	0.214225102768283	1	FACETS	0.641	0.546	0.746	0.641	0.546	0.746	SUBCLONAL	1	TRUE	0	0.214225102768283	1		374	689	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0016047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	235	618	2	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.241052786404004	4	FACETS	0.995	0.927	1	0.995	0.927	1	CLONAL	2	TRUE	2	0.248540901381551	4		620	1187	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026859	48026859	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	145	317	0	ENST00000234420.5:c.1737T>G	p.Cys579Trp	p.C579W	ENST00000234420	NM_000179.2	579	tgT/tgG	4/10	0.241052786404004	4	FACETS	0.897	0.819	0.979	0.897	0.819	0.979	CLONAL	2	TRUE	2	0.248540901381551	4		317	812	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0016048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	244	598	0	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	1	2	FACETS	0.977	0.921	1	0.977	0.921	1	CLONAL	1	TRUE	1	0.874586460104313	2		598	571	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574002	7574002	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs375338359	NA	P-0016048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	688	826	0	ENST00000269305.4:c.1025G>C	p.Arg342Pro	p.R342P	ENST00000269305	NM_001126112.2	342	cGa/cCa	10/11	0.874586460104313	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.874586460104313	2		826	776	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0016048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	30	71	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	0.425559872655232	1	FACETS	0.576	0.485	0.669	0.576	0.485	0.669	INDETERMINATE	1	TRUE	0	0.874586460104313	1		71	67	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29662044	29662044	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199474751	NA	P-0016048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	359	400	0	ENST00000356175.3:c.5938G>A	p.Gly1980Arg	p.G1980R	ENST00000356175	NM_000267.3	1980	Ggg/Agg	39/57	NA	2	FACETS	0.966	0.941	0.989			1	INDETERMINATE	2	TRUE	NA	0.874586460104313	2		400	425	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939680	76939681	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0016048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	320	729	0	ENST00000373344.5:c.1067dup	p.Leu359ThrfsTer3	p.L359Tfs*3	ENST00000373344	NM_000489.3	356	gca/gcCa	9/35	0.821102008498516	1	FACETS	0.783	0.75	0.815	0.783	0.75	0.815	SUBCLONAL	1	TRUE	0	0.874586460104313	1		729	526	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	112	507	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.333024773095416	1	FACETS	0.957	0.863	1	0.957	0.863	1	CLONAL	1	TRUE	0	0.333024773095416	1		507	586	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923503	9923503	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs551688681	NA	P-0016050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	47	375	0	ENST00000330684.3:c.1784A>G	p.His595Arg	p.H595R	ENST00000330684	NM_001134407.1	595	cAt/cGt	9/13	1	2	FACETS	0.706	0.597	0.825	0.706	0.597	0.825	SUBCLONAL	1	TRUE	1	0.333024773095416	2		375	400	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458054	120458054	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759285634	NA	P-0016050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	56	493	0	ENST00000256646.2:c.7291C>T	p.His2431Tyr	p.H2431Y	ENST00000256646	NM_024408.3	2431	Cac/Tac	34/34	1	2	FACETS	0.642	0.55	0.742	0.642	0.55	0.742	SUBCLONAL	1	TRUE	1	0.333024773095416	2		493	524	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206616	108206616	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	171	444	0	ENST00000278616.4:c.8196C>A	p.Phe2732Leu	p.F2732L	ENST00000278616	NM_000051.3	2732	ttC/ttA	56/63	0.321232758044055	2	FACETS	0.859	0.794	0.925	0.859	0.794	0.925	CLONAL	2	TRUE	0	0.333024773095416	2		444	598	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78704451	78704451	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	82	448	1	ENST00000306801.3:c.599G>T	p.Gly200Val	p.G200V	ENST00000306801	NM_020761.2	200	gGc/gTc	5/34	1	2	FACETS	0.845	0.746	0.95	0.845	0.746	0.95	CLONAL	1	TRUE	1	0.333024773095416	2		449	583	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56367808	56367808	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	82	369	0	ENST00000348428.3:c.634C>T	p.Pro212Ser	p.P212S	ENST00000348428	NM_006785.3	212	Cca/Tca	4/17	1	2	FACETS	0.92	0.813	1	0.92	0.813	1	CLONAL	1	TRUE	1	0.333024773095416	2		369	535	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942535	17942535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753577833	NA	P-0016050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	43	655	3	ENST00000458235.1:c.2753G>A	p.Arg918His	p.R918H	ENST00000458235	NM_000215.3	918	cGc/cAc	20/24	1	2	FACETS	0.365	0.305	0.433	0.365	0.305	0.433	SUBCLONAL	1	TRUE	1	0.333024773095416	2		658	707	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190708715	190708715	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	87	501	0	ENST00000441310.2:c.608T>A	p.Val203Glu	p.V203E	ENST00000441310	NM_000534.4	203	gTa/gAa	6/13	1	2	FACETS	0.907	0.804	1	0.907	0.804	1	CLONAL	1	TRUE	1	0.333024773095416	2		501	576	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495203	212495203	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	97	572	0	ENST00000342788.4:c.2063G>T	p.Arg688Ile	p.R688I	ENST00000342788	NM_005235.2	688	aGa/aTa	17/28	1	2	FACETS	0.827	0.738	0.923	0.827	0.738	0.923	CLONAL	1	TRUE	1	0.333024773095416	2		572	704	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517444	176517444	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs987602724	NA	P-0016050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	117	606	2	ENST00000292408.4:c.145C>A	p.Leu49Ile	p.L49I	ENST00000292408	NM_213647.1	49	Ctt/Att	3/18	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.333024773095416	2		608	544	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163264	32163264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1441887869	NA	P-0016050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	198	1032	2	ENST00000375023.3:c.5962C>T	p.Pro1988Ser	p.P1988S	ENST00000375023	NM_004557.3	1988	Cca/Tca	30/30	0.333024773095416	3	FACETS	1	0.973	1	0.554	0.512	0.598	CLONAL	1	TRUE	1	0.333024773095416	3		1034	1251	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502149	157502149	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	42	548	0	ENST00000346085.5:c.3182A>T	p.Tyr1061Phe	p.Y1061F	ENST00000346085	NM_020732.3	1061	tAc/tTc	12/20	0.333024773095416	1	FACETS	0.371	0.309	0.44	0.371	0.309	0.44	SUBCLONAL	1	TRUE	0	0.333024773095416	1		548	566	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	195	507	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.93	0.867	0.996	0.93	0.867	0.996	CLONAL	1	TRUE	1	0.717733030065107	2		507	584	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0016051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	151	421	1	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.852	0.784	0.921	0.852	0.784	0.921	CLONAL	1	TRUE	1	0.717733030065107	2		422	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0016051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	557	875	3	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.717733030065107	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.717733030065107	1		878	929	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602952	55602952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1237984655	NA	P-0016051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	218	436	0	ENST00000288135.5:c.2662C>T	p.Arg888Trp	p.R888W	ENST00000288135	NM_000222.2	888	Cgg/Tgg	19/21	1	2	FACETS	0.949	0.888	1	0.949	0.888	1	CLONAL	1	TRUE	1	0.717733030065107	2		436	640	SUCCESS
APC	324	MSKCC	GRCh37	5	112175562	112175563	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGAT	novel	NA	P-0016051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	191	508	0	ENST00000257430.4:c.4274_4277dup	p.Ser1426ArgfsTer2	p.S1426Rfs*2	ENST00000257430	NM_000038.5	1424	cca/ccAGATa	16/16	1	2	FACETS	0.945	0.88	1	0.945	0.88	1	CLONAL	1	TRUE	1	0.717733030065107	2		508	563	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273049	55273049	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	426	664	2	ENST00000275493.2:c.3372C>A	p.His1124Gln	p.H1124Q	ENST00000275493	NM_005228.3	1124	caC/caA	28/28	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.717733030065107	2		666	1054	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0016052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	389	467	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.739867117756747	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.739867117756747	2		468	490	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591126	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAGAAAGAC	GAGAAAGAC	-	novel	NA	P-0016052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	158	343	0	ENST00000274335.5:c.1723_1731del	p.Lys575_Arg577del	p.K575_R577del	ENST00000274335		573	ctGAGAAAGACg/ctg	12/15	0.739867117756747	2	FACETS	0.803	0.754	0.851	0.803	0.754	0.851	CLONAL	2	TRUE	0	0.739867117756747	2		343	266	SUCCESS
FH	2271	MSKCC	GRCh37	1	241683004	241683004	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	147	563	0	ENST00000366560.3:c.19C>T	p.Leu7Phe	p.L7F	ENST00000366560	NM_000143.3	7	Ctc/Ttc	1/10	0.625200054425395	4	FACETS	0.861	0.787	0.939			1	CLONAL	1	TRUE	NA	0.739867117756747	4		563	803	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736275	243736275	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	164	563	0	ENST00000263826.5:c.772G>T	p.Ala258Ser	p.A258S	ENST00000263826	NM_005465.4	258	Gcc/Tcc	8/13	0.625200054425395	4	FACETS	0.878	0.806	0.952			1	CLONAL	1	TRUE	NA	0.739867117756747	4		563	879	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302932	15302932	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	152	775	0	ENST00000263388.2:c.518C>A	p.Thr173Asn	p.T173N	ENST00000263388	NM_000435.2	173	aCc/aAc	4/33	0.276781616387693	5	FACETS	0.895	0.818	0.975	0.298	0.272	0.325	INDETERMINATE	1	TRUE	2	0.739867117756747	5		775	969	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984812	55984812	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	114	551	0	ENST00000263923.4:c.317G>T	p.Arg106Leu	p.R106L	ENST00000263923	NM_002253.2	106	cGg/cTg	3/30	0.184489539536443	4	FACETS	0.821	0.741	0.906	0.274	0.247	0.302	INDETERMINATE	1	TRUE	1	0.739867117756747	4		551	653	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752864	57752864	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	36	386	0	ENST00000274289.3:c.1064A>G	p.His355Arg	p.H355R	ENST00000274289	NM_006622.3	355	cAc/cGc	8/14	0.569303869590497	4	FACETS	0.275	0.225	0.331	0.137	0.112	0.166	SUBCLONAL	1	TRUE	2	0.739867117756747	4		386	616	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069935	5069935	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	36	292	0	ENST00000381652.3:c.1524C>A	p.Asn508Lys	p.N508K	ENST00000381652	NM_004972.3	508	aaC/aaA	12/25	0.181045991239098	4	FACETS	0.47	0.387	0.563	0.235	0.193	0.282	INDETERMINATE	1	TRUE	2	0.739867117756747	4		292	360	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247099	53247099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	71	612	1	ENST00000375401.3:c.401G>A	p.Trp134Ter	p.W134*	ENST00000375401	NM_004187.3	134	tGg/tAg	4/26	0.576856070760307	1	FACETS	0.23	0.201	0.262	0.23	0.201	0.262	SUBCLONAL	1	TRUE	0	0.739867117756747	1		613	525	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271875	18271883	+	protein_altering_variant	In_Frame_Ins	INS	AGCGACGTG	AGCGACGTG	CACCCGCAGACT	novel	NA	P-0016052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	162	744	0	ENST00000222254.8:c.478_486delinsCACCCGCAGACT	p.Ser160_Val162delinsHisProGlnThr	p.S160_V162delinsHPQT	ENST00000222254	NM_005027.3	160	AGCGACGTG/CACCCGCAGACT	5/16	0.276781616387693	5	FACETS	0.809	0.741	0.881	0.27	0.247	0.294	INDETERMINATE	1	TRUE	2	0.739867117756747	5		744	1142	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	791	515	3	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.875611005615162	3	FACETS	1	0.987	1	1	0.998	1	CLONAL	3	TRUE	1	0.875611005615162	3		518	866	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	278	355	0	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.875611005615162	2		355	619	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	63	485	2	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.175	0.151	0.202	0.175	0.151	0.202	SUBCLONAL	1	TRUE	1	0.875611005615162	2		487	822	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	264	487	1	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	0.875611005615162	3	FACETS	0.795	0.745	0.847	0.398	0.372	0.424	SUBCLONAL	1	TRUE	1	0.875611005615162	3		488	1090	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092740	27092740	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1557611083	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	317	455	0	ENST00000324856.7:c.2765del	p.Gly922AlafsTer2	p.G922Afs*2	ENST00000324856	NM_006015.4	921	Ggg/gg	9/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.875611005615162	2		455	692	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749415085	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	28	399	0	ENST00000263967.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000263967	NM_006218.2	38	Cgt/Tgt	2/21	1	2	FACETS	0.129	0.103	0.16	0.129	0.103	0.16	SUBCLONAL	1	TRUE	1	0.875611005615162	2		399	495	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007332	143007332	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	209	304	3	ENST00000262992.4:c.2452del	p.Arg818GlufsTer4	p.R818Efs*4	ENST00000262992	NM_001101669.1	818	Aga/ga	22/24	1	2	FACETS	0.978	0.918	1	0.978	0.918	1	CLONAL	1	TRUE	1	0.875611005615162	2		307	488	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931452	131931452	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507178	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	297	390	3	ENST00000265335.6:c.2165del	p.Lys722ArgfsTer14	p.K722Rfs*14	ENST00000265335		719	ctA/ct	13/25	1	2	FACETS	0.962	0.912	1	0.962	0.912	1	CLONAL	1	TRUE	1	0.875611005615162	2		393	705	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	405	594	2	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.875611005615162	2		596	882	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444659	78444659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs908264837	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	88	432	0	ENST00000370768.2:c.30del	p.Ser11LeufsTer43	p.S11Lfs*43	ENST00000370768	NM_003902.3	10	ccC/cc	1/20	1	2	FACETS	0.297	0.263	0.334	0.297	0.263	0.334	SUBCLONAL	1	TRUE	1	0.875611005615162	2		432	676	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732910	44732910	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	248	529	0	ENST00000377967.4:c.117del	p.Ser40AlafsTer2	p.S40Afs*2	ENST00000377967	NM_021140.2	38	tCc/tc	1/29	1	2	FACETS	0.889	0.837	0.942	0.889	0.837	0.942	CLONAL	1	TRUE	1	0.875611005615162	2		529	637	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691872	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs79375991	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	375	395	22	ENST00000295754.5:c.383del	p.Lys128SerfsTer35	p.K128Sfs*35	ENST00000295754	NM_003242.5	125	gAa/ga	3/7	1	2	FACETS	0.843	0.816	0.869	1	0.997	1	CLONAL	2	TRUE	1	0.875611005615162	2		417	508	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67646013	67646014	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs1470210640	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	302	516	4	ENST00000264010.4:c.950_951del	p.Thr317ArgfsTer91	p.T317Rfs*91	ENST00000264010	NM_006565.3	314	aAC/a	4/12	1	2	FACETS	0.817	0.773	0.863	0.817	0.773	0.863	CLONAL	1	TRUE	1	0.875611005615162	2		520	844	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913396	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	191	346	0	ENST00000349496.5:c.95A>C	p.Asp32Ala	p.D32A	ENST00000349496	NM_001904.3	32	gAc/gCc	3/15	1	2	FACETS	0.9	0.84	0.96	0.9	0.84	0.96	CLONAL	1	TRUE	1	0.875611005615162	2		346	485	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105648	27105648	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	300	421	0	ENST00000324856.7:c.5259del	p.Ser1754LeufsTer16	p.S1754Lfs*16	ENST00000324856	NM_006015.4	1753	gtG/gt	20/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.875611005615162	2		421	630	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100648	8100648	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1304	116	807	1	ENST00000346208.3:c.622C>A	p.Leu208Met	p.L208M	ENST00000346208		208	Ctg/Atg	3/6	0.875611005615162	3	FACETS	0.268	0.241	0.298	0.134	0.12	0.149	SUBCLONAL	1	TRUE	1	0.875611005615162	3		808	1420	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949205	71949205	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	442	780	0	ENST00000298229.2:c.3672C>A	p.Asp1224Glu	p.D1224E	ENST00000298229	NM_001567.3	1224	gaC/gaA	27/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.875611005615162	2		780	966	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142060	108142060	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	221	553	0	ENST00000278616.4:c.3004G>T	p.Gly1002Cys	p.G1002C	ENST00000278616	NM_000051.3	1002	Ggt/Tgt	20/63	1	2	FACETS	0.742	0.694	0.792	0.742	0.694	0.792	SUBCLONAL	1	TRUE	1	0.875611005615162	2		553	680	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930609	32930609	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs80358972	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	293	454	1	ENST00000380152.3:c.7480C>T	p.Arg2494Ter	p.R2494*	ENST00000380152		2494	Cga/Tga	15/27	1	2	FACETS	0.884	0.836	0.932	0.884	0.836	0.932	CLONAL	1	TRUE	1	0.875611005615162	2		455	757	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103513896	103513896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	239	418	0	ENST00000355739.4:c.712C>T	p.Leu238Phe	p.L238F	ENST00000355739	NM_000123.3	238	Ctt/Ttt	7/15	1	2	FACETS	0.922	0.868	0.977	0.922	0.868	0.977	CLONAL	1	TRUE	1	0.875611005615162	2		418	592	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354350	354350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764120241	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	338	705	0	ENST00000262320.3:c.1208G>A	p.Arg403Gln	p.R403Q	ENST00000262320	NM_003502.3	403	cGg/cAg	5/11	1	2	FACETS	0.75	0.711	0.79	0.75	0.711	0.79	SUBCLONAL	1	TRUE	1	0.875611005615162	2		705	1029	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842456	68842456	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	348	526	0	ENST00000261769.5:c.521del	p.Asn174ThrfsTer41	p.N174Tfs*41	ENST00000261769	NM_004360.3	173	Aaa/aa	4/16	1	2	FACETS	0.902	0.858	0.947	0.902	0.858	0.947	CLONAL	1	TRUE	1	0.875611005615162	2		526	881	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155990	99155990	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	294	473	0	ENST00000074304.5:c.671-1G>A		p.X224_splice	ENST00000074304	NM_001134224.1	224			1	2	FACETS	0.942	0.892	0.992	0.942	0.892	0.992	CLONAL	1	TRUE	1	0.875611005615162	2		473	713	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99181137	99181137	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	395	585	0	ENST00000074304.5:c.2078T>C	p.Leu693Pro	p.L693P	ENST00000074304	NM_001134224.1	693	cTg/cCg	20/26	1	2	FACETS	0.972	0.928	1	0.972	0.928	1	CLONAL	1	TRUE	1	0.875611005615162	2		585	928	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098012	178098012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	283	398	0	ENST00000397062.3:c.368del	p.Leu123TrpfsTer8	p.L123Wfs*8	ENST00000397062	NM_006164.4	123	tTg/tg	3/5	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.875611005615162	2		398	646	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817382	39817382	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	241	423	1	ENST00000288319.7:c.181C>A	p.Pro61Thr	p.P61T	ENST00000288319	NM_182918.3	61	Cca/Aca	2/10	1	2	FACETS	0.928	0.874	0.983	0.928	0.874	0.983	CLONAL	1	TRUE	1	0.875611005615162	2		424	593	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73108255	73108255	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	34	96	0	ENST00000356692.5:c.355G>T	p.Asp119Tyr	p.D119Y	ENST00000356692		119	Gac/Tac	4/9	1	2	FACETS	0.602	0.501	0.71	0.602	0.501	0.71	SUBCLONAL	1	TRUE	1	0.875611005615162	2		96	129	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55143590	55143590	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138740193	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	47	371	0	ENST00000257290.5:c.1822G>A	p.Val608Ile	p.V608I	ENST00000257290	NM_006206.4	608	Gtt/Att	13/23	1	2	FACETS	0.17	0.143	0.2	0.17	0.143	0.2	SUBCLONAL	1	TRUE	1	0.875611005615162	2		371	631	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007309	143007309	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	178	311	0	ENST00000262992.4:c.2475G>A	p.Trp825Ter	p.W825*	ENST00000262992	NM_001101669.1	825	tgG/tgA	22/24	1	2	FACETS	0.892	0.83	0.954	0.892	0.83	0.954	CLONAL	1	TRUE	1	0.875611005615162	2		311	456	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950782	79950782	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	77	205	0	ENST00000265081.6:c.236T>C	p.Ile79Thr	p.I79T	ENST00000265081	NM_002439.4	79	aTa/aCa	1/24	1	2	FACETS	0.884	0.792	0.978	0.884	0.792	0.978	CLONAL	1	TRUE	1	0.875611005615162	2		205	199	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527727	157527727	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	112	515	1	ENST00000346085.5:c.5452C>T	p.His1818Tyr	p.H1818Y	ENST00000346085	NM_020732.3	1818	Cac/Tac	20/20	1	2	FACETS	0.317	0.284	0.351	0.317	0.284	0.351	SUBCLONAL	1	TRUE	1	0.875611005615162	2		516	808	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412563	116412563	+	intron_variant	Intron	DEL	A	A	-	novel	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1566	545	912	0	ENST00000397752.3:c.3028+526del		p.*1010*	ENST00000397752	NM_000245.2	-/1390			0.875611005615162	3	FACETS	0.848	0.811	0.886	0.424	0.405	0.443	CLONAL	1	TRUE	1	0.875611005615162	3		912	2111	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995527	68995527	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	363	673	0	ENST00000288368.4:c.1935del	p.Phe645LeufsTer2	p.F645Lfs*2	ENST00000288368	NM_024870.2	644	gTt/gt	18/40	1	2	FACETS	0.947	0.901	0.992	0.947	0.901	0.992	CLONAL	1	TRUE	1	0.875611005615162	2		673	876	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982638	90982638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	192	340	0	ENST00000265433.3:c.850G>A	p.Asp284Asn	p.D284N	ENST00000265433	NM_002485.4	284	Gac/Aac	7/16	1	2	FACETS	0.941	0.88	1	0.941	0.88	1	CLONAL	1	TRUE	1	0.875611005615162	2		340	466	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750678	128750678	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	204	460	0	ENST00000377970.2:c.215C>A	p.Pro72His	p.P72H	ENST00000377970	NM_002467.4	72	cCc/cAc	2/3	1	2	FACETS	0.676	0.63	0.724	0.676	0.63	0.724	SUBCLONAL	1	TRUE	1	0.875611005615162	2		460	689	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778026	135778026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1336228562	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	287	444	0	ENST00000298552.3:c.2357G>A	p.Arg786Gln	p.R786Q	ENST00000298552	NM_001162426.1	786	cGa/cAa	18/23	1	2	FACETS	0.914	0.865	0.964	0.914	0.865	0.964	CLONAL	1	TRUE	1	0.875611005615162	2		444	717	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47004885	47004885	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0016053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	364	638	0	ENST00000377604.3:c.-126+1G>A		p.X42_splice	ENST00000377604	NM_001204468.1	42			1	2	FACETS	0.958	0.913	1	0.958	0.913	1	CLONAL	1	TRUE	1	0.875611005615162	2		638	868	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0016054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	131	697	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.314310290945712	5	FACETS	1	0.965	1	0.379	0.343	0.417	CLONAL	1	TRUE	2	0.314310290945712	5		698	1080	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0016054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	182	474	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.314310290945712	5	FACETS	0.924	0.853	0.998	0.616	0.568	0.666	CLONAL	2	TRUE	2	0.314310290945712	5		474	922	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45422926	45422926	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	133	372	0	ENST00000262160.6:c.202C>T	p.Gln68Ter	p.Q68*	ENST00000262160	NM_005901.5	68	Caa/Taa	2/11	0.314310290945712	2	FACETS	0.874	0.799	0.952	0.874	0.799	0.952	CLONAL	2	TRUE	0	0.314310290945712	2		372	484	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392173	81392173	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	53	211	0	ENST00000222390.5:c.104G>C	p.Arg35Thr	p.R35T	ENST00000222390	NM_000601.4	35	aGa/aCa	2/18	0.314310290945712	5	FACETS	1	0.962	1	0.469	0.401	0.542	CLONAL	1	TRUE	2	0.314310290945712	5		211	353	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226125	53226125	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	190	589	0	ENST00000375401.3:c.2724del	p.Arg909GlyfsTer26	p.R909Gfs*26	ENST00000375401	NM_004187.3	908	ggG/gg	19/26	0.314310290945712	2	FACETS	0.836	0.775	0.899	0.836	0.775	0.899	CLONAL	2	TRUE	0	0.314310290945712	2		589	723	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653236	29653236	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	62	395	0	ENST00000356175.3:c.5171A>G	p.Lys1724Arg	p.K1724R	ENST00000356175	NM_000267.3	1724	aAg/aGg	36/57	1	2	FACETS	0.967	0.837	1	0.967	0.837	1	CLONAL	1	TRUE	1	0.259115037153838	2		395	495	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200720	128200720	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	8	817	3	ENST00000341105.2:c.1085G>T	p.Arg362Leu	p.R362L	ENST00000341105	NM_032638.4	362	cGa/cTa	5/6	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		820	383	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960099	151960099	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0016059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	23	567	0	ENST00000262189.6:c.1299+2T>C		p.X433_splice	ENST00000262189	NM_170606.2	433			1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		567	247	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0016060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	499	886	0	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	0.859569085738964	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.859569085738964	1		886	641	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0016062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	202	541	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.463705790277525	4	FACETS	1	0.945	1	0.513	0.474	0.553	CLONAL	1	FALSE	2	0.461965428279565	4		541	1246	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0016062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	16	835	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.463705790277525	1	FACETS	0.156	0.115	0.205	0.156	0.115	0.205	SUBCLONAL	1	FALSE	0	0.461965428279565	1		836	342	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275191	41275191	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770598744	NA	P-0016062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	89	515	0	ENST00000349496.5:c.1357C>T	p.Arg453Trp	p.R453W	ENST00000349496	NM_001904.3	453	Cgg/Tgg	9/15	0.197672032796212	1	FACETS	0.687	0.613	0.766	0.687	0.613	0.766	INDETERMINATE	1	FALSE	0	0.461965428279565	1		515	431	SUCCESS
EED	8726	MSKCC	GRCh37	11	85977189	85977189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775716311	NA	P-0016062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	119	674	0	ENST00000263360.6:c.791G>A	p.Arg264Lys	p.R264K	ENST00000263360	NM_003797.3	264	aGg/aAg	8/12	1	2	FACETS	0.769	0.695	0.847	0.769	0.695	0.847	SUBCLONAL	1	FALSE	1	0.461965428279565	2		674	670	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431850	49431850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	105	756	2	ENST00000301067.7:c.9289G>A	p.Glu3097Lys	p.E3097K	ENST00000301067	NM_003482.3	3097	Gag/Aag	34/54	NA	2	FACETS	1	0.967	1			1	INDETERMINATE	1	FALSE	NA	0.461965428279565	2		758	391	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490299	56490299	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	65	473	0	ENST00000267101.3:c.2068C>G	p.Leu690Val	p.L690V	ENST00000267101	NM_001982.3	690	Ctg/Gtg	18/28	1	2	FACETS	0.741	0.645	0.843	0.741	0.645	0.843	SUBCLONAL	1	FALSE	1	0.461965428279565	2		473	380	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	30	902	0	ENST00000269305.4:c.475del	p.Ala159ProfsTer11	p.A159Pfs*11	ENST00000269305	NM_001126112.2	159	Gcc/cc	5/11	0.463705790277525	1	FACETS	0.25	0.201	0.305	0.25	0.201	0.305	SUBCLONAL	1	FALSE	0	0.461965428279565	1		902	400	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4097296	4097298	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0016062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	119	951	0	ENST00000262948.5:c.963_965del	p.Leu322del	p.L322del	ENST00000262948	NM_030662.3	321	ctCCTg/ctg	8/11	0.253374216368053	0	FACETS	0.569	0.516	0.624			1	INDETERMINATE	1	FALSE	0	0.461965428279565	0		951	487	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281943	39281943	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	86	432	0	ENST00000402219.2:c.532C>G	p.Gln178Glu	p.Q178E	ENST00000402219	NM_005633.3	178	Caa/Gaa	5/23	1	2	FACETS	0.967	0.861	1	0.967	0.861	1	CLONAL	1	FALSE	1	0.461965428279565	2		432	385	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099206	157099206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1015004964	NA	P-0016062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	107	696	1	ENST00000346085.5:c.143C>T	p.Ser48Phe	p.S48F	ENST00000346085	NM_020732.3	48	tCc/tTc	1/20	0.10595117970935	4	FACETS	1	0.968	1	0.593	0.533	0.656	INDETERMINATE	1	FALSE	2	0.461965428279565	4		697	571	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140449195	140449195	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	96	520	0	ENST00000288602.6:c.1884A>T	p.Gln628His	p.Q628H	ENST00000288602	NM_004333.4	628	caA/caT	16/18	1	2	FACETS	0.83	0.742	0.922	0.83	0.742	0.922	CLONAL	1	FALSE	1	0.461965428279565	2		520	501	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965695	90965695	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876658501	NA	P-0016062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	105	512	0	ENST00000265433.3:c.1622C>G	p.Ala541Gly	p.A541G	ENST00000265433	NM_002485.4	541	gCt/gGt	11/16	1	2	FACETS	0.947	0.853	1	0.947	0.853	1	CLONAL	1	FALSE	1	0.461965428279565	2		512	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0016063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	491	720	1	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.636071478360624	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.636071478360624	2		721	748	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015094	37015094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	261	773	0	ENST00000358127.4:c.310C>T	p.Arg104Cys	p.R104C	ENST00000358127	NM_001280556.1	104	Cgc/Tgc	3/10	0.636071478360624	3	FACETS	0.904	0.847	0.964	0.452	0.423	0.482	CLONAL	1	TRUE	1	0.636071478360624	3		773	1196	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037891	49037891	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	163	600	0	ENST00000267163.4:c.2131del	p.Ile711TyrfsTer4	p.I711Yfs*4	ENST00000267163	NM_000321.2	711	Ata/ta	21/27	0.636071478360624	1	FACETS	0.979	0.912	1	0.979	0.912	1	CLONAL	1	TRUE	0	0.636071478360624	1		600	357	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30730003	30730003	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	186	494	0	ENST00000295754.5:c.1524G>C	p.Gln508His	p.Q508H	ENST00000295754	NM_003242.5	508	caG/caC	6/7	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.636071478360624	2		494	562	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696689	47696689	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519972	NA	P-0016064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	44	621	0	ENST00000347630.2:c.259T>A	p.Tyr87Asn	p.Y87N	ENST00000347630	NM_001007230.1	87	Tac/Aac	5/11	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	FALSE	1	0.22490877503369	2		621	336	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601920	43601920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500755	NA	P-0016064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	113	734	0	ENST00000355710.3:c.964G>A	p.Asp322Asn	p.D322N	ENST00000355710	NM_020975.4	322	Gac/Aac	5/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.22490877503369	2		734	756	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	392	414	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.205160561231929	5	FACETS	0.913	0.867	0.96	0.913	0.867	0.96	CLONAL	4	TRUE	1	0.205160561231929	5		414	1368	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94963946	94963946	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0016065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	99	622	0	ENST00000536441.1:c.78+1G>T		p.X26_splice	ENST00000536441	NM_144665.3	26			0.205160561231929	4	FACETS	0.88	0.786	0.979	0.587	0.524	0.653	CLONAL	2	TRUE	1	0.205160561231929	4		622	661	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409039	4409039	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	53	481	0	ENST00000261254.3:c.734C>T	p.Ala245Val	p.A245V	ENST00000261254	NM_001759.3	245	gCt/gTt	5/5	0.205160561231929	5	FACETS	1	0.927	1			1	CLONAL	1	TRUE	NA	0.205160561231929	5		481	588	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212522512	212522512	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	55	616	0	ENST00000342788.4:c.1913G>C	p.Trp638Ser	p.W638S	ENST00000342788	NM_005235.2	638	tGg/tCg	16/28	0.113255769622989	5	FACETS	0.888	0.758	1	0.222	0.189	0.258	INDETERMINATE	1	TRUE	1	0.205160561231929	5		616	790	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133538	55133538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770343276	NA	P-0016065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	48	805	2	ENST00000257290.5:c.842C>T	p.Thr281Met	p.T281M	ENST00000257290	NM_006206.4	281	aCg/aTg	6/23	0.205160561231929	1	FACETS	0.547	0.461	0.642	0.547	0.461	0.642	SUBCLONAL	1	TRUE	0	0.205160561231929	1		807	768	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680299	30680299	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	67	848	0	ENST00000376406.3:c.1420C>T	p.His474Tyr	p.H474Y	ENST00000376406	NM_014641.2	474	Cac/Tac	5/15	0.205160561231929	3	FACETS	0.756	0.656	0.866	0.378	0.328	0.433	SUBCLONAL	1	TRUE	1	0.205160561231929	3		848	952	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	205	414	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.52243898682879	2	FACETS	0.958	0.904	1	0.958	0.904	1	CLONAL	2	TRUE	0	0.572427654575306	2		414	374	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0016066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	168	754	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.20604610492458	3	FACETS	1	0.99	1	0.737	0.683	0.793	INDETERMINATE	1	TRUE	1	0.572427654575306	3		755	512	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0016066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	20	644	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	0.52243898682879	2	FACETS	0.174	0.132	0.223	0.087	0.066	0.112	SUBCLONAL	1	TRUE	0	0.572427654575306	2		644	402	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0016066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	57	410	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.539171532367624	3	FACETS	0.698	0.601	0.802	0.349	0.3	0.401	SUBCLONAL	1	TRUE	1	0.572427654575306	3		410	367	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732969	30732969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893810	NA	P-0016066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	288	455	0	ENST00000295754.5:c.1582C>T	p.Arg528Cys	p.R528C	ENST00000295754	NM_003242.5	528	Cgt/Tgt	7/7	0.52243898682879	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.572427654575306	2		455	480	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411246	63411246	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	348	458	0	ENST00000330258.3:c.1921C>T	p.Arg641Ter	p.R641*	ENST00000330258	NM_152424.3	641	Cga/Tga	2/2	0.437885829940104	2	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.572427654575306	2		458	514	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984229	7984229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	180	842	0	ENST00000319144.4:c.500G>A	p.Arg167Gln	p.R167Q	ENST00000319144	NM_001139.2	167	cGg/cAg	4/15	1	2	FACETS	0.966	0.895	1	0.966	0.895	1	CLONAL	1	TRUE	1	0.572427654575306	2		842	651	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275653	41275653	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	117	594	0	ENST00000349496.5:c.1548T>G	p.Asn516Lys	p.N516K	ENST00000349496	NM_001904.3	516	aaT/aaG	10/15	0.52243898682879	2	FACETS	0.797	0.722	0.875	0.398	0.361	0.438	SUBCLONAL	1	TRUE	0	0.572427654575306	2		594	513	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271273	153271273	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0016066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	69	400	0	ENST00000281708.4:c.505A>T	p.Lys169Ter	p.K169*	ENST00000281708	NM_033632.3	169	Aaa/Taa	3/12	1	2	FACETS	0.861	0.758	0.97	0.861	0.758	0.97	CLONAL	1	TRUE	1	0.572427654575306	2		400	280	SUCCESS
APC	324	MSKCC	GRCh37	5	112174010	112174010	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	185	548	0	ENST00000257430.4:c.2721del	p.Ser908LeufsTer8	p.S908Lfs*8	ENST00000257430	NM_000038.5	907	Ggg/gg	16/16	0.539171532367624	3	FACETS	0.852	0.794	0.911	0.852	0.794	0.911	CLONAL	2	TRUE	1	0.572427654575306	3		548	488	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0016068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	63	697	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.23289841717548	5	FACETS	0.977	0.845	1	0.326	0.281	0.374	CLONAL	1	FALSE	2	0.281800705871185	5		698	651	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0016068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	146	787	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.23289841717548	5	FACETS	0.882	0.809	0.958	0.882	0.809	0.958	CLONAL	3	FALSE	2	0.281800705871185	5		787	557	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0016068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	33	474	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.81	0.662	0.976	0.81	0.662	0.976	CLONAL	1	FALSE	1	0.281800705871185	2		474	289	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222831	5222831	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs2230610	NA	P-0016068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	26	636	2	ENST00000357368.4:c.2972C>T	p.Ala991Val	p.A991V	ENST00000357368	NM_002850.3	991	gCg/gTg	18/38	0.185199438835272	2	FACETS	0.497	0.394	0.616	0.249	0.197	0.308	SUBCLONAL	1	FALSE	0	0.281800705871185	2		638	371	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955090	55955090	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	43	716	0	ENST00000263923.4:c.3455C>G	p.Thr1152Arg	p.T1152R	ENST00000263923	NM_002253.2	1152	aCg/aGg	26/30	1	2	FACETS	0.812	0.681	0.956	0.812	0.681	0.956	CLONAL	1	FALSE	1	0.281800705871185	2		716	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0016069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	233	860	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.394340938593633	2	FACETS	0.99	0.93	1	0.99	0.93	1	CLONAL	2	TRUE	0	0.396375296428049	2		861	594	SUCCESS
YES1	7525	MSKCC	GRCh37	18	746003	746003	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	79	604	0	ENST00000314574.4:c.519G>T	p.Leu173Phe	p.L173F	ENST00000314574	NM_005433.3	173	ttG/ttT	5/12	NA	2	FACETS	0.767	0.676	0.864			1	INDETERMINATE	1	TRUE	NA	0.396375296428049	2		604	520	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593397	48593397	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs377767355	NA	P-0016069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	57	402	0	ENST00000342988.3:c.1148T>A	p.Ile383Lys	p.I383K	ENST00000342988	NM_005359.5	383	aTa/aAa	10/12	0.396375296428049	1	FACETS	0.877	0.759	1	0.877	0.759	1	CLONAL	1	TRUE	0	0.396375296428049	1		402	263	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650553	18650553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	45	457	0	ENST00000266497.5:c.2764G>T	p.Ala922Ser	p.A922S	ENST00000266497		922	Gct/Tct	20/31	0.158407473465188	2	FACETS	0.59	0.497	0.692	0.295	0.248	0.346	INDETERMINATE	1	TRUE	0	0.396375296428049	2		457	385	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867203	68867203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782024	NA	P-0016069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	101	614	0	ENST00000261769.5:c.2450C>T	p.Ala817Val	p.A817V	ENST00000261769	NM_004360.3	817	gCg/gTg	16/16	0.17745256920033	3	FACETS	1	0.967	1			1	INDETERMINATE	1	TRUE	NA	0.396375296428049	3		614	513	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	159	248	0				ENST00000310581	NM_198253.2	-/1132			0.360006755624355	3	FACETS	1	0.967	1	0.696	0.654	0.738	INDETERMINATE	2	TRUE	0	0.793339796765653	3		248	268	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913407	NA	P-0016070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	99	475	0	ENST00000349496.5:c.133T>G	p.Ser45Ala	p.S45A	ENST00000349496	NM_001904.3	45	Tct/Gct	3/15	1	2	FACETS	0.928	0.841	1	0.928	0.841	1	CLONAL	1	TRUE	1	0.793339796765653	2		475	269	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074070	8074100	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGAACATCATATTTGAAATCAGAAAGTGT	CAGGAACATCATATTTGAAATCAGAAAGTGT	-	novel	NA	P-0016070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	154	416	0	ENST00000377482.5:c.559_589del	p.Thr187AlafsTer50	p.T187Afs*50	ENST00000377482	NM_018948.3	187	ACACTTTCTGATTTCAAATATGATGTTCCTGgc/gc	4/4	0.766885212849745	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.793339796765653	1		416	218	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94170345	94170345	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	178	411	1	ENST00000323929.3:c.1924G>A	p.Glu642Lys	p.E642K	ENST00000323929	NM_005591.3	642	Gag/Aag	17/20	0.778106571106916	3	FACETS	0.927	0.87	0.984	0.927	0.87	0.984	CLONAL	2	TRUE	1	0.793339796765653	3		412	338	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991820	72991820	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	199	762	0	ENST00000268489.5:c.2225G>A	p.Ser742Asn	p.S742N	ENST00000268489	NM_006885.3	742	aGt/aAt	2/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.793339796765653	2		762	462	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864703	68864703	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	99	564	0	ENST00000288368.4:c.74T>A	p.Val25Glu	p.V25E	ENST00000288368	NM_024870.2	25	gTg/gAg	1/40	0.324992249626088	1	FACETS	0.568	0.515	0.623	0.568	0.515	0.623	INDETERMINATE	1	TRUE	0	0.793339796765653	1		564	265	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5466803	5466804	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGATACAAACTCAAAG	novel	NA	P-0016070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	66	296	0	ENST00000381577.3:c.826_841dup	p.Lys281ArgfsTer9	p.K281Rfs*9	ENST00000381577	NM_014143.3	275	caa/caAGATACAAACTCAAAGa	6/7	0.183370405315395	1	FACETS	0.456	0.402	0.513	0.456	0.402	0.513	INDETERMINATE	1	TRUE	0	0.793339796765653	1		296	220	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613405	100613405	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	136	741	0	ENST00000308731.7:c.995G>T	p.Arg332Leu	p.R332L	ENST00000308731	NM_000061.2	332	cGt/cTt	12/19	0.183370405315395	1	FACETS	0.567	0.521	0.613	0.567	0.521	0.613	INDETERMINATE	1	TRUE	0	0.793339796765653	1		741	365	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613426	100613426	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0016070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	106	648	0	ENST00000308731.7:c.975-1G>T		p.X325_splice	ENST00000308731	NM_000061.2	325			0.183370405315395	1	FACETS	0.57	0.518	0.622	0.57	0.518	0.622	INDETERMINATE	1	TRUE	0	0.793339796765653	1		648	283	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129731	47129731	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	16	409	1	ENST00000409792.3:c.5149G>T	p.Gly1717Ter	p.G1717*	ENST00000409792	NM_014159.6	1717	Gga/Tga	10/21	1	2	FACETS	0.265	0.195	0.348	0.265	0.195	0.348	SUBCLONAL	1	FALSE	1	0.40789398588455	2		410	296	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400279	139400295	+	frameshift_variant	Frame_Shift_Del	DEL	AGCGCAGGCTGCCGCAG	AGCGCAGGCTGCCGCAG	-	novel	NA	P-0016087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	52	784	0	ENST00000277541.6:c.4053_4069del	p.Cys1352ProfsTer47	p.C1352Pfs*47	ENST00000277541	NM_017617.3	1351	acCTGCGGCAGCCTGCGCTgc/acgc	25/34	1	2	FACETS	0.483	0.411	0.562	0.483	0.411	0.562	SUBCLONAL	1	FALSE	1	0.40789398588455	2		784	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0016088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	31	467	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.859	0.698	1	0.859	0.698	1	CLONAL	1	TRUE	1	0.275453060559555	2		468	262	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244957	41244957	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357003	NA	P-0016088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	18	620	1	ENST00000357654.3:c.2591C>T	p.Ser864Leu	p.S864L	ENST00000357654	NM_007294.3	864	tCa/tTa	10/23	1	2	FACETS	0.871	0.661	1	0.871	0.661	1	CLONAL	1	TRUE	1	0.275453060559555	2		621	150	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578421	7578421	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	8	735	0	ENST00000269305.4:c.509C>A	p.Thr170Lys	p.T170K	ENST00000269305	NM_001126112.2	170	aCg/aAg	5/11	1	2	FACETS	0.2	0.128	0.293	0.2	0.128	0.293	SUBCLONAL	1	TRUE	1	0.275453060559555	2		735	291	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0016089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	1212	618	2	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.683869069496862	6	FACETS	0.979	0.961	0.998			1	CLONAL	5	TRUE	NA	0.683869069496862	6		620	1714	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619172	37619172	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	146	578	0	ENST00000447079.4:c.848C>A	p.Ser283Ter	p.S283*	ENST00000447079	NM_015083.1	283	tCg/tAg	1/14	0.683869069496862	3	FACETS	0.661	0.603	0.721	0.33	0.301	0.361	SUBCLONAL	1	TRUE	1	0.683869069496862	3		578	867	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66523994	66523994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	43	260	0	ENST00000358598.2:c.722G>A	p.Arg241Lys	p.R241K	ENST00000358598	NM_212471.2	241	aGa/aAa	8/11	0.683869069496862	3	FACETS	0.38	0.318	0.449	0.19	0.159	0.225	SUBCLONAL	1	TRUE	1	0.683869069496862	3		260	444	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884031	37884031	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	370	719	1	ENST00000269571.5:c.3502G>T	p.Glu1168Ter	p.E1168*	ENST00000269571		1168	Gaa/Taa	27/27	0.683869069496862	3	FACETS	1	0.993	1	0.644	0.612	0.677	CLONAL	1	TRUE	1	0.683869069496862	3		720	1127	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0016089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	416	990	0	ENST00000269305.4:c.394A>T	p.Lys132Ter	p.K132*	ENST00000269305	NM_001126112.2	132	Aag/Tag	5/11	0.683869069496862	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.683869069496862	1		990	714	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458549	120458549	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	124	581	0	ENST00000256646.2:c.6796G>C	p.Glu2266Gln	p.E2266Q	ENST00000256646	NM_024408.3	2266	Gag/Cag	34/34	0.286761855529028	1	FACETS	0.34	0.308	0.374	0.34	0.308	0.374	INDETERMINATE	1	TRUE	0	0.683869069496862	1		581	701	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922156	100922156	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	239	387	0	ENST00000325455.5:c.2356G>T	p.Glu786Ter	p.E786*	ENST00000325455	NM_001202474.3	786	Gaa/Taa	5/8	0.334594858280235	2	FACETS	1	0.993	1	0.703	0.664	0.742	INDETERMINATE	1	TRUE	0	0.683869069496862	2		387	497	SUCCESS
ATM	472	MSKCC	GRCh37	11	108137924	108137925	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0016089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	33	415	2	ENST00000278616.4:c.2493_2494delinsAT	p.Asp831_Arg832delinsGluCys	p.D831_R832delinsEC	ENST00000278616	NM_000051.3	831	gaCCgt/gaATgt	17/63	0.334594858280235	2	FACETS	0.182	0.148	0.221	0.091	0.074	0.111	INDETERMINATE	1	TRUE	0	0.683869069496862	2		417	529	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240613	133240613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201115064	NA	P-0016089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	87	482	0	ENST00000320574.5:c.2683G>A	p.Ala895Thr	p.A895T	ENST00000320574	NM_006231.2	895	Gcc/Acc	23/49	1	2	FACETS	0.461	0.409	0.516	0.461	0.409	0.516	SUBCLONAL	1	TRUE	1	0.683869069496862	2		482	552	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039201	49039201	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	280	579	0	ENST00000267163.4:c.2279T>C	p.Phe760Ser	p.F760S	ENST00000267163	NM_000321.2	760	tTc/tCc	22/27	0.683869069496862	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.683869069496862	1		579	529	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194859	30194859	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	150	589	0	ENST00000331968.5:c.286G>T	p.Gly96Ter	p.G96*	ENST00000331968	NM_002742.2	96	Gga/Tga	2/18	0.460340405062207	3	FACETS	0.661	0.604	0.721	0.331	0.302	0.361	SUBCLONAL	1	TRUE	1	0.683869069496862	3		589	890	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646990	23646990	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	132	617	0	ENST00000261584.4:c.877G>C	p.Gly293Arg	p.G293R	ENST00000261584	NM_024675.3	293	Ggc/Cgc	4/13	0.253380076303394	3	FACETS	0.587	0.533	0.645	0.196	0.177	0.215	INDETERMINATE	1	TRUE	0	0.683869069496862	3		617	882	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619037	37619037	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	167	694	0	ENST00000447079.4:c.713C>G	p.Ser238Trp	p.S238W	ENST00000447079	NM_015083.1	238	tCg/tGg	1/14	0.683869069496862	3	FACETS	0.631	0.579	0.686	0.316	0.289	0.343	SUBCLONAL	1	TRUE	1	0.683869069496862	3		694	1038	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982118	10982511	+	coding_sequence_variant,5_prime_UTR_variant	Frame_Shift_Del	DEL	GCCCAGGACGGCCGGCAGAGGGCGCTGCGCCACGGGGCCGGGCCGCGGCGACGGTGGCGGCGGCGGCGGCGAGGCGGCGCGTGGCCGGCAGGCGGCGCTGCCCGGCTCGGCCTCGGCCTGCACGGCGGCTGCGGCGGCGGTAGCGGCAGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCAGCGGCGGCGGCCTGGGCCCGGGCGCAGCGGCGGCGGCGGCGGGGCCTGGAGCCGGATCTAAGATGGCAGCGGCGGCGGCGGCGGTGGGGCCGGGCGCGGGCGGCGCGGGGTCGGCGGTCCCGGGCGGCGCGGGGCCCTGCGCTACCGTGTCGGTGTTCCCCGGCGCCCGCCTCCTCACCATCGGCGACGCGAACG	GCCCAGGACGGCCGGCAGAGGGCGCTGCGCCACGGGGCCGGGCCGCGGCGACGGTGGCGGCGGCGGCGGCGAGGCGGCGCGTGGCCGGCAGGCGGCGCTGCCCGGCTCGGCCTCGGCCTGCACGGCGGCTGCGGCGGCGGTAGCGGCAGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCAGCGGCGGCGGCCTGGGCCCGGGCGCAGCGGCGGCGGCGGCGGGGCCTGGAGCCGGATCTAAGATGGCAGCGGCGGCGGCGGCGGTGGGGCCGGGCGCGGGCGGCGCGGGGTCGGCGGTCCCGGGCGGCGCGGGGCCCTGCGCTACCGTGTCGGTGTTCCCCGGCGCCCGCCTCCTCACCATCGGCGACGCGAACG	-	novel	NA	P-0016089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	2	33	0				ENST00000327064	NM_199141.1	?-45/608		1/16	0.665666270862264	2	FACETS	0.031	0.012	0.065	0.016	0.006	0.033	SUBCLONAL	1	TRUE	0	0.683869069496862	2		33	186	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797942	42797942	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	218	817	0	ENST00000575354.2:c.3994A>G	p.Lys1332Glu	p.K1332E	ENST00000575354	NM_015125.3	1332	Aag/Gag	16/20	0.683869069496862	2	FACETS	0.57	0.53	0.612	0.285	0.265	0.306	SUBCLONAL	1	TRUE	0	0.683869069496862	2		817	1118	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660831	227660831	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	25	421	0	ENST00000305123.5:c.2624G>C	p.Arg875Pro	p.R875P	ENST00000305123	NM_005544.2	875	cGa/cCa	1/2	1	2	FACETS	0.164	0.128	0.204	0.164	0.128	0.204	SUBCLONAL	1	TRUE	1	0.683869069496862	2		421	447	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682459	52682459	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0016089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	72	330	0	ENST00000394830.3:c.715-1G>A		p.X239_splice	ENST00000394830	NM_018313.4	239			0.631133976009184	1	FACETS	0.412	0.363	0.465	0.412	0.363	0.465	SUBCLONAL	1	TRUE	0	0.683869069496862	1		330	336	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186823	142186823	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	223	410	0	ENST00000350721.4:c.6640G>C	p.Asp2214His	p.D2214H	ENST00000350721	NM_001184.3	2214	Gat/Cat	39/47	0.383508934482351	3	FACETS	1	0.993	1	0.747	0.7	0.794	INDETERMINATE	1	TRUE	1	0.683869069496862	3		410	586	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31468146	31468146	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	89	594	0	ENST00000344624.3:c.2266C>T	p.Gln756Ter	p.Q756*	ENST00000344624		756	Caa/Taa	15/33	0.353007187725008	5	FACETS	0.489	0.432	0.55	0.163	0.144	0.184	INDETERMINATE	1	TRUE	2	0.683869069496862	5		594	1078	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0016091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	337	790	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.61615808722189	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.61615808722189	1		792	717	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0016091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	89	259	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.61615808722189	1	FACETS	0.947	0.858	1	0.947	0.858	1	CLONAL	1	TRUE	0	0.61615808722189	1		259	211	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0016091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	77	456	1	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.947	0.842	1	0.947	0.842	1	CLONAL	1	TRUE	1	0.61615808722189	2		457	264	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913237	NA	P-0016091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	126	541	0	ENST00000369535.4:c.35G>C	p.Gly12Ala	p.G12A	ENST00000369535	NM_002524.4	12	gGt/gCt	2/7	0.61615808722189	1	FACETS	0.724	0.662	0.788	0.724	0.662	0.788	SUBCLONAL	1	TRUE	0	0.61615808722189	1		541	391	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43806160	43806160	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	205	511	0	ENST00000372470.3:c.956G>T	p.Arg319Met	p.R319M	ENST00000372470	NM_005373.2	319	aGg/aTg	6/12	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.61615808722189	2		511	573	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911579	114911579	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	38	749	0	ENST00000543371.1:c.1097C>G	p.Ala366Gly	p.A366G	ENST00000543371	NM_001198531.1	366	gCa/gGa	10/14	0.61615808722189	1	FACETS	0.126	0.103	0.151	0.126	0.103	0.151	SUBCLONAL	1	TRUE	0	0.61615808722189	1		749	680	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647918	3647918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1273526453	NA	P-0016091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	201	903	1	ENST00000294008.3:c.1246G>A	p.Ala416Thr	p.A416T	ENST00000294008	NM_032444.2	416	Gca/Aca	6/15	1	2	FACETS	0.642	0.594	0.691	0.642	0.594	0.691	SUBCLONAL	1	TRUE	1	0.61615808722189	2		904	1017	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051642	30051642	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0016091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	30	374	0	ENST00000338641.4:c.576C>G	p.Tyr192Ter	p.Y192*	ENST00000338641	NM_000268.3	192	taC/taG	6/16	0.61615808722189	1	FACETS	0.196	0.158	0.24	0.196	0.158	0.24	SUBCLONAL	1	TRUE	0	0.61615808722189	1		374	343	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324112	31324125	+	frameshift_variant	Frame_Shift_Del	DEL	TCAGGGCGATGTAA	TCAGGGCGATGTAA	-	novel	NA	P-0016091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	38	134	0	ENST00000412585.2:c.438_451del	p.Asp146GlufsTer26	p.D146Efs*26	ENST00000412585	NM_005514.6	146	gaTTACATCGCCCTGAac/gaac	3/8	0.61615808722189	1	FACETS	0.589	0.495	0.689	0.589	0.495	0.689	SUBCLONAL	1	TRUE	0	0.61615808722189	1		134	145	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512047	148512047	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	170	471	0	ENST00000320356.2:c.1631C>T	p.Ala544Val	p.A544V	ENST00000320356	NM_004456.4	544	gCa/gTa	14/20	1	2	FACETS	0.97	0.897	1	0.97	0.897	1	CLONAL	1	TRUE	1	0.61615808722189	2		471	569	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	146	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.82	2		248	355	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692897	89692912	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGGGACGAACTGGT	AAAGGGACGAACTGGT	-	novel	NA	P-0016092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	97	518	0	ENST00000371953.3:c.381_396del	p.Lys128Ter	p.K128*	ENST00000371953	NM_000314.4	127	ggAAAGGGACGAACTGGT/gg	5/9	0.3	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.82	0		518	132	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100362	8100362	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	108	913	1	ENST00000346208.3:c.336G>A	p.Trp112Ter	p.W112*	ENST00000346208		112	tgG/tgA	3/6	1	2	FACETS	0.957	0.858	1	0.957	0.858	1	CLONAL	1	TRUE	1	0.265175038946895	2		914	851	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115843	8115844	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0016093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	99	763	0	ENST00000346208.3:c.1191dup	p.Arg398GlnfsTer109	p.R398Qfs*109	ENST00000346208		397	tcc/tCcc	6/6	1	2	FACETS	0.957	0.854	1	0.957	0.854	1	CLONAL	1	TRUE	1	0.265175038946895	2		763	780	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41276073	41276073	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	117	677	0	ENST00000357654.3:c.41T>A	p.Val14Asp	p.V14D	ENST00000357654	NM_007294.3	14	gTc/gAc	2/23	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.265175038946895	2		677	810	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020902	26020902	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	48	291	0	ENST00000357647.3:c.186del	p.Ile63PhefsTer28	p.I63Ffs*28	ENST00000357647	NM_003529.2	62	cTt/ct	1/1	1	2	FACETS	0.973	0.825	1	0.973	0.825	1	CLONAL	1	TRUE	1	0.265175038946895	2		291	372	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371783	55371783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	54	298	0	ENST00000297316.4:c.473G>A	p.Gly158Asp	p.G158D	ENST00000297316	NM_022454.3	158	gGc/gAc	2/2	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.265175038946895	2		298	313	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314993	1314993	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375729637	NA	P-0016093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	54	723	0	ENST00000400841.2:c.668C>T	p.Thr223Met	p.T223M	ENST00000400841		223	aCg/aTg	6/6	1	2	FACETS	0.516	0.44	0.6	0.516	0.44	0.6	SUBCLONAL	1	TRUE	1	0.265175038946895	2		723	789	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786474	135786496	+	frameshift_variant	Frame_Shift_Del	DEL	AACCATAGATGGGCTCCAAAGAG	AACCATAGATGGGCTCCAAAGAG	T	novel	NA	P-0016093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	66	684	0	ENST00000298552.3:c.1034_1056delinsA	p.Thr345AsnfsTer4	p.T345Nfs*4	ENST00000298552	NM_001162426.1	345	aCTCTTTGGAGCCCATCTATGGTT/aA	11/23	0.265175038946895	1	FACETS	0.708	0.614	0.809	0.708	0.614	0.809	SUBCLONAL	1	TRUE	0	0.265175038946895	1		684	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0016093-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	128	465	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.171806905874099	2	FACETS	0.962	0.87	1	0.481	0.435	0.53	CLONAL	1	TRUE	0	0.244071377224242	2		465	1090	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611793	100611793	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs782133950	NA	P-0016093-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	54	392	0	ENST00000308731.7:c.1328T>C	p.Ile443Thr	p.I443T	ENST00000308731	NM_000061.2	443	aTt/aCt	14/19	0.242361569892972	0	FACETS	0.49	0.417	0.569			1	SUBCLONAL	1	TRUE	0	0.244071377224242	0		392	683	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61711225	61711225	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016093-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	78	437	0	ENST00000401558.2:c.2524C>G	p.Pro842Ala	p.P842A	ENST00000401558	NM_003400.3	842	Cct/Gct	21/25	1	2	FACETS	0.845	0.742	0.957	0.845	0.742	0.957	CLONAL	1	TRUE	1	0.244071377224242	2		437	756	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0016094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	66	279	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.633866577319553	3	FACETS	0.854	0.747	0.969	0.427	0.373	0.485	CLONAL	1	TRUE	1	0.633866577319553	3		279	321	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930282	39930282	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	114	404	0	ENST00000378444.4:c.3182del	p.Lys1061SerfsTer52	p.K1061Sfs*52	ENST00000378444	NM_001123385.1	1061	aAg/ag	6/15	1	1	FACETS	0.541	0.49	0.594	0.541	0.49	0.594	SUBCLONAL	1	TRUE	0	0.633866577319553	1		404	454	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102198796	102198797	+	inframe_insertion	In_Frame_Ins	INS	-	-	TAAGAATTAAAGGACAGGAGT	novel	NA	P-0016094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	81	440	0	ENST00000263464.3:c.969_989dup	p.Glu329_Phe330insLeuArgIleLysGlyGlnGlu	p.E329_F330insLRIKGQE	ENST00000263464	NM_001165.4	323	ata/aTAAGAATTAAAGGACAGGAGTta	4/9	1	2	FACETS	0.623	0.552	0.699	0.623	0.552	0.699	SUBCLONAL	1	TRUE	1	0.633866577319553	2		440	410	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0016097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	47	279	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.535	0.455	0.622	0.535	0.455	0.622	SUBCLONAL	1	TRUE	1	0.7	2		279	251	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857867	89857867	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148473140	NA	P-0016097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	40	684	1	ENST00000389301.3:c.1303C>T	p.Arg435Cys	p.R435C	ENST00000389301	NM_000135.2	435	Cgc/Tgc	14/43	1	2	FACETS	0.236	0.195	0.28	0.236	0.195	0.28	SUBCLONAL	1	TRUE	1	0.7	2		685	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0016098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	82	947	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.3	2		949	544	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0016098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	104	541	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	0.3	2		541	637	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0016098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	91	552	1	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.3	2		553	561	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720809	89720809	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	48	322	0	ENST00000371953.3:c.961del	p.Thr321GlnfsTer23	p.T321Qfs*23	ENST00000371953	NM_000314.4	320	ttA/tt	8/9	1	2	FACETS	0.653	0.552	0.764	0.653	0.552	0.764	SUBCLONAL	1	TRUE	1	0.3	2		322	490	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729775	41729775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	36	316	0	ENST00000242208.4:c.754G>A	p.Ala252Thr	p.A252T	ENST00000242208	NM_002192.2	252	Gcc/Acc	3/3	1	2	FACETS	0.992	0.821	1	0.992	0.821	1	CLONAL	1	TRUE	1	0.3	2		316	242	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375108	31375108	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375097618	NA	P-0016098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	81	821	0	ENST00000328111.2:c.505G>A	p.Asp169Asn	p.D169N	ENST00000328111	NM_006892.3	169	Gac/Aac	6/23	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.3	2		821	517	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023208	27023229	+	frameshift_variant	Frame_Shift_Del	DEL	GGAACGCGGGCCCTAGGCCCGC	GGAACGCGGGCCCTAGGCCCGC	-	novel	NA	P-0016098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	30	306	0	ENST00000324856.7:c.314_335del	p.Gly105AlafsTer2	p.G105Afs*2	ENST00000324856	NM_006015.4	105	gGGAACGCGGGCCCTAGGCCCGCc/gc	1/20	1	2	FACETS	0.787	0.637	0.956	0.787	0.637	0.956	CLONAL	1	TRUE	1	0.3	2		306	254	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466019	69466019	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	76	732	0	ENST00000227507.2:c.857C>A	p.Thr286Lys	p.T286K	ENST00000227507	NM_053056.2	286	aCa/aAa	5/5	1	2	FACETS	0.906	0.796	1	0.906	0.796	1	CLONAL	1	TRUE	1	0.3	2		732	559	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660475	67660475	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	54	401	1	ENST00000264010.4:c.1375C>T	p.Gln459Ter	p.Q459*	ENST00000264010	NM_006565.3	459	Cag/Tag	8/12	1	2	FACETS	0.809	0.692	0.936	0.809	0.692	0.936	CLONAL	1	TRUE	1	0.3	2		402	445	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0016108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	39	470	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.19	2		470	370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0016108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	45	707	3	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	1	2	FACETS	0.652	0.546	0.769	0.652	0.546	0.769	SUBCLONAL	1	TRUE	1	0.19	2		710	727	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17116977	17116977	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	23	454	0	ENST00000285071.4:c.1732C>G	p.Arg578Gly	p.R578G	ENST00000285071	NM_144997.5	578	Cgg/Ggg	14/14	1	2	FACETS	0.537	0.418	0.675	0.537	0.418	0.675	SUBCLONAL	1	TRUE	1	0.19	2		454	451	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120214	70120214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	51	656	0	ENST00000245479.2:c.1216C>T	p.His406Tyr	p.H406Y	ENST00000245479	NM_000346.3	406	Cac/Tac	3/3	1	2	FACETS	0.718	0.609	0.838	0.718	0.609	0.838	SUBCLONAL	1	TRUE	1	0.19	2		656	748	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424220	47424220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	36	584	0	ENST00000377045.4:c.225C>A	p.Asp75Glu	p.D75E	ENST00000377045	NM_001654.4	75	gaC/gaA	4/16	1	2	FACETS	0.651	0.534	0.783	0.651	0.534	0.783	SUBCLONAL	1	TRUE	1	0.19	2		584	582	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781504	NA	P-0016111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	534	765	1	ENST00000269305.4:c.314G>T	p.Gly105Val	p.G105V	ENST00000269305	NM_001126112.2	105	gGc/gTc	4/11	0.891022386536005	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.897728928625858	1		766	628	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473779	67473779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906850	NA	P-0016111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	566	600	1	ENST00000327367.4:c.859C>T	p.Arg287Trp	p.R287W	ENST00000327367	NM_005902.3	287	Cgg/Tgg	6/9	0.897728928625858	2	FACETS	0.982	0.964	0.999	0.982	0.964	0.999	CLONAL	2	TRUE	0	0.897728928625858	2		601	642	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793382	18793382	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs77070108	NA	P-0016111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	261	549	1	ENST00000266497.5:c.4079C>T	p.Ala1360Val	p.A1360V	ENST00000266497		1360	gCg/gTg	30/31	1	2	FACETS	0.922	0.87	0.974	0.922	0.87	0.974	CLONAL	1	TRUE	1	0.897728928625858	2		550	631	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917794	29917794	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201750304	NA	P-0016111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	443	705	1	ENST00000389048.3:c.874C>T	p.Arg292Cys	p.R292C	ENST00000389048	NM_004304.4	292	Cgc/Tgc	3/29	1	2	FACETS	0.962	0.921	1	0.962	0.921	1	CLONAL	1	TRUE	1	0.897728928625858	2		706	1026	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22008871	22008871	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	447	724	0	ENST00000276925.6:c.82G>T	p.Glu28Ter	p.E28*	ENST00000276925	NM_004936.3	28	Gag/Tag	1/2	0.897728928625858	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.897728928625858	1		724	527	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	66	583	0				ENST00000310581	NM_198253.2	-/1132			0.616559664955003	3	FACETS	0.653	0.569	0.744	0.327	0.284	0.372	SUBCLONAL	1	FALSE	1	0.637695475654005	3		583	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	432	796	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.637695475654005	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	FALSE	0	0.637695475654005	1		796	784	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781201	161781201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55830907	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	232	575	1	ENST00000366898.1:c.1204C>T	p.Arg402Cys	p.R402C	ENST00000366898	NM_004562.2	402	Cgt/Tgt	11/12	1	2	FACETS	0.95	0.889	1	0.95	0.889	1	CLONAL	1	FALSE	1	0.637695475654005	2		576	766	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087515	27087516	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	335	718	2	ENST00000324856.7:c.2089_2090delinsTT	p.Pro697Leu	p.P697L	ENST00000324856	NM_006015.4	697	CCg/TTg	5/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.637695475654005	2		720	953	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089703	27089703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	261	722	1	ENST00000324856.7:c.2659C>T	p.Pro887Ser	p.P887S	ENST00000324856	NM_006015.4	887	Cca/Tca	8/20	1	2	FACETS	0.977	0.918	1	0.977	0.918	1	CLONAL	1	FALSE	1	0.637695475654005	2		723	838	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731176	162731176	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775649903	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	187	470	0	ENST00000367921.3:c.1031G>A	p.Ser344Asn	p.S344N	ENST00000367921	NM_006182.2	344	aGt/aAt	9/18	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.637695475654005	2		470	558	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306595	163306595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	246	638	1	ENST00000271452.3:c.392G>A	p.Arg131Lys	p.R131K	ENST00000271452	NM_145697.2	131	aGa/aAa	6/14	1	2	FACETS	0.943	0.884	1	0.943	0.884	1	CLONAL	1	FALSE	1	0.637695475654005	2		639	818	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193121552	193121552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	161	423	0	ENST00000367435.3:c.950G>A	p.Gly317Asp	p.G317D	ENST00000367435	NM_024529.4	317	gGt/gAt	10/17	1	2	FACETS	0.935	0.863	1	0.935	0.863	1	CLONAL	1	FALSE	1	0.637695475654005	2		423	540	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980428	201980428	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1202654721	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	244	557	0	ENST00000359651.3:c.163+1G>A		p.X55_splice	ENST00000359651		55			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.637695475654005	2		557	678	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200508	67200508	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	333	615	0	ENST00000312629.5:c.702G>T	p.Glu234Asp	p.E234D	ENST00000312629	NM_003952.2	234	gaG/gaT	8/15	0.637695475654005	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	0	0.637695475654005	1		615	655	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170524	108170524	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	271	644	0	ENST00000278616.4:c.5089A>T	p.Thr1697Ser	p.T1697S	ENST00000278616	NM_000051.3	1697	Acc/Tcc	34/63	0.637695475654005	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	0	0.637695475654005	1		644	560	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205299	46205299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	164	638	0	ENST00000334344.6:c.383C>T	p.Pro128Leu	p.P128L	ENST00000334344	NM_152641.2	128	cCa/cTa	4/21	0.355364445834951	1	FACETS	0.552	0.508	0.597	0.552	0.508	0.597	INDETERMINATE	1	FALSE	0	0.637695475654005	1		638	635	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420853	49420854	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	141	503	0	ENST00000301067.7:c.14895_14896delinsTT	p.Arg4966Trp	p.R4966W	ENST00000301067	NM_003482.3	4965	gcCCgg/gcTTgg	48/54	1	2	FACETS	0.79	0.723	0.859	0.79	0.723	0.859	SUBCLONAL	1	FALSE	1	0.637695475654005	2		503	560	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114247	115114247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	265	704	1	ENST00000257566.3:c.970G>A	p.Val324Met	p.V324M	ENST00000257566	NM_016569.3	324	Gtg/Atg	6/8	0.355364445834951	1	FACETS	0.743	0.699	0.787	0.743	0.699	0.787	INDETERMINATE	1	FALSE	0	0.637695475654005	1		705	762	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916851	48916851	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1131690902	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	190	385	0	ENST00000267163.4:c.380+1G>A		p.X127_splice	ENST00000267163	NM_000321.2	127			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.637695475654005	2		385	552	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942662	48942662	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	179	433	0	ENST00000267163.4:c.1050-1G>A		p.X350_splice	ENST00000267163	NM_000321.2	350			1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	FALSE	1	0.637695475654005	2		433	557	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95573993	95573993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	130	464	0	ENST00000393063.1:c.2756C>T	p.Pro919Leu	p.P919L	ENST00000393063	NM_030621.3	919	cCc/cTc	18/28	0.355364445834951	1	FACETS	0.564	0.515	0.616	0.564	0.515	0.616	INDETERMINATE	1	FALSE	0	0.637695475654005	1		464	492	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007621	45007621	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	110	292	0	ENST00000558401.1:c.68G>A	p.Arg23His	p.R23H	ENST00000558401	NM_004048.2	23	cGt/cAt	2/4	0.273978157078151	1	FACETS	0.628	0.57	0.689	0.628	0.57	0.689	INDETERMINATE	1	FALSE	0	0.637695475654005	1		292	374	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129190	2129190	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	384	754	1	ENST00000219476.3:c.3124C>A	p.Pro1042Thr	p.P1042T	ENST00000219476	NM_000548.3	1042	Ccg/Acg	27/42	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	1	FALSE	NA	0.637695475654005	2		755	830	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860603	3860603	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	251	582	1	ENST00000262367.5:c.975+1G>A		p.X325_splice	ENST00000262367	NM_004380.2	325			0.636045892294037	1	FACETS	0.903	0.852	0.954	0.903	0.852	0.954	CLONAL	1	FALSE	0	0.637695475654005	1		583	594	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597434	10597434	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	300	852	0	ENST00000171111.5:c.1769C>T	p.Thr590Ile	p.T590I	ENST00000171111	NM_203500.1	590	aCc/aTc	6/6	0.355364445834951	1	FACETS	0.71	0.67	0.75	0.71	0.67	0.75	INDETERMINATE	1	FALSE	0	0.637695475654005	1		852	903	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271588	15271588	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	194	974	0	ENST00000263388.2:c.6851C>T	p.Thr2284Ile	p.T2284I	ENST00000263388	NM_000435.2	2284	aCt/aTt	33/33	0.355364445834951	1	FACETS	0.546	0.506	0.587	0.546	0.506	0.587	INDETERMINATE	1	FALSE	0	0.637695475654005	1		974	759	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032088	48032088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376799914	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	101	402	1	ENST00000234420.5:c.3478G>A	p.Val1160Ile	p.V1160I	ENST00000234420	NM_000179.2	1160	Gtc/Atc	6/10	0.355364445834951	1	FACETS	0.46	0.413	0.509	0.46	0.413	0.509	INDETERMINATE	1	FALSE	0	0.637695475654005	1		403	469	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659859	227659859	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372040825	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	133	579	0	ENST00000305123.5:c.3596C>T	p.Pro1199Leu	p.P1199L	ENST00000305123	NM_005544.2	1199	cCg/cTg	1/2	0.273978157078151	1	FACETS	0.555	0.507	0.605	0.555	0.507	0.605	INDETERMINATE	1	FALSE	0	0.637695475654005	1		579	512	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021191	31021191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757102293	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	167	631	1	ENST00000375687.4:c.1190G>A	p.Arg397His	p.R397H	ENST00000375687	NM_015338.5	397	cGt/cAt	12/13	0.420286366119472	1	FACETS	0.584	0.539	0.63	0.584	0.539	0.63	SUBCLONAL	1	FALSE	0	0.637695475654005	1		632	611	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31369183	31369183	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764811687	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	295	647	0	ENST00000328111.2:c.167C>T	p.Ser56Phe	p.S56F	ENST00000328111	NM_006892.3	56	tCc/tTc	3/23	0.420286366119472	1	FACETS	0.898	0.851	0.945	0.898	0.851	0.945	CLONAL	1	FALSE	0	0.637695475654005	1		647	702	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262885	46262885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761607812	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	156	671	2	ENST00000371998.3:c.1058G>A	p.Arg353Gln	p.R353Q	ENST00000371998		353	cGa/cAa	10/23	0.420286366119472	1	FACETS	0.433	0.397	0.47	0.433	0.397	0.47	SUBCLONAL	1	FALSE	0	0.637695475654005	1		673	770	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54956583	54956583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	272	644	1	ENST00000312783.6:c.611C>T	p.Thr204Ile	p.T204I	ENST00000312783	NM_198436.1	204	aCc/aTc	7/10	0.207195608990661	2	FACETS	1	0.992	1	0.642	0.607	0.678	INDETERMINATE	1	FALSE	0	0.637695475654005	2		645	664	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057259	30057259	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	273	624	0	ENST00000338641.4:c.741G>C	p.Glu247Asp	p.E247D	ENST00000338641	NM_000268.3	247	gaG/gaC	8/16	1	2	FACETS	0.981	0.923	1	0.981	0.923	1	CLONAL	1	FALSE	1	0.637695475654005	2		624	873	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713438	30713438	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	256	574	1	ENST00000295754.5:c.763T>A	p.Phe255Ile	p.F255I	ENST00000295754	NM_003242.5	255	Ttt/Att	4/7	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.637695475654005	2		575	741	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934976	49934976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1277564624	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	252	601	2	ENST00000296474.3:c.2023G>A	p.Val675Met	p.V675M	ENST00000296474	NM_002447.2	675	Gtg/Atg	6/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.637695475654005	2		603	717	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026871	71026871	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	185	376	0	ENST00000318789.4:c.1351G>A	p.Asp451Asn	p.D451N	ENST00000318789	NM_032682.5	451	Gat/Aat	16/21	1	2	FACETS	0.99	0.92	1	0.99	0.92	1	CLONAL	1	FALSE	1	0.637695475654005	2		376	586	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185200237	185200237	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	200	546	0	ENST00000265026.3:c.2894C>T	p.Thr965Ile	p.T965I	ENST00000265026	NM_004721.4	965	aCc/aTc	14/14	1	2	FACETS	0.935	0.87	1	0.935	0.87	1	CLONAL	1	FALSE	1	0.637695475654005	2		546	671	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127323	55127324	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	197	611	2	ENST00000257290.5:c.111_112delinsAA	p.Val38Ile	p.V38I	ENST00000257290	NM_006206.4	37	aaGGtt/aaAAtt	3/23	1	2	FACETS	0.821	0.762	0.881	0.821	0.762	0.881	CLONAL	1	FALSE	1	0.637695475654005	2		613	753	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155268	55155268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752010861	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	175	514	2	ENST00000257290.5:c.2867G>A	p.Gly956Glu	p.G956E	ENST00000257290	NM_006206.4	956	gGa/gAa	21/23	1	2	FACETS	0.851	0.787	0.917	0.851	0.787	0.917	CLONAL	1	FALSE	1	0.637695475654005	2		516	645	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067143	143067143	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs992654738	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	238	581	0	ENST00000262992.4:c.1570G>T	p.Val524Leu	p.V524L	ENST00000262992	NM_001101669.1	524	Gtg/Ttg	16/24	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	1	0.637695475654005	2		581	732	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542633	187542633	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	208	564	0	ENST00000441802.2:c.5107G>A	p.Asp1703Asn	p.D1703N	ENST00000441802	NM_005245.3	1703	Gat/Aat	10/27	1	2	FACETS	0.94	0.876	1	0.94	0.876	1	CLONAL	1	FALSE	1	0.637695475654005	2		564	694	SUCCESS
APC	324	MSKCC	GRCh37	5	112178255	112178255	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	226	607	1	ENST00000257430.4:c.6964C>T	p.Gln2322Ter	p.Q2322*	ENST00000257430	NM_000038.5	2322	Cag/Tag	16/16	0.62980228641989	1	FACETS	0.998	0.94	1	0.998	0.94	1	CLONAL	1	FALSE	0	0.637695475654005	1		608	484	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053117	180053117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1268798979	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	143	608	0	ENST00000261937.6:c.1252G>A	p.Val418Met	p.V418M	ENST00000261937	NM_182925.4	418	Gtg/Atg	9/30	0.637695475654005	1	FACETS	0.952	0.882	1	0.952	0.882	1	CLONAL	1	FALSE	0	0.637695475654005	1		608	321	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965590	93965590	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1408104586	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	216	679	0	ENST00000369303.4:c.2338T>C	p.Ser780Pro	p.S780P	ENST00000369303	NM_004440.3	780	Tcc/Ccc	13/17	1	2	FACETS	0.928	0.866	0.992	0.928	0.866	0.992	CLONAL	1	FALSE	1	0.637695475654005	2		679	730	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6048626	6048626	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	178	644	0	ENST00000265849.7:c.23+2T>A		p.X8_splice	ENST00000265849	NM_000535.5	8			1	2	FACETS	0.855	0.791	0.921	0.855	0.791	0.921	CLONAL	1	FALSE	1	0.637695475654005	2		644	653	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439661	140439661	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs766692331	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	111	461	0	ENST00000288602.6:c.2078T>C	p.Met693Thr	p.M693T	ENST00000288602	NM_004333.4	693	aTg/aCg	17/18	1	2	FACETS	0.897	0.814	0.984	0.897	0.814	0.984	CLONAL	1	FALSE	1	0.637695475654005	2		461	388	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372490	55372490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758620469	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1413	291	955	1	ENST00000297316.4:c.1180G>A	p.Ala394Thr	p.A394T	ENST00000297316	NM_022454.3	394	Gcc/Acc	2/2	0.637695475654005	4	FACETS	0.877	0.822	0.934	0.219	0.205	0.234	CLONAL	1	FALSE	0	0.637695475654005	4		956	1704	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992729	68992729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779079528	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1277	258	795	0	ENST00000288368.4:c.1694C>T	p.Ser565Leu	p.S565L	ENST00000288368	NM_024870.2	565	tCg/tTg	16/40	0.637695475654005	4	FACETS	0.863	0.806	0.923	0.216	0.201	0.231	CLONAL	1	FALSE	0	0.637695475654005	4		795	1535	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046338	69046338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	239	483	0	ENST00000288368.4:c.3811C>T	p.Leu1271Phe	p.L1271F	ENST00000288368	NM_024870.2	1271	Ctt/Ttt	32/40	0.637695475654005	4	FACETS	1	0.979	1	0.28	0.261	0.299	CLONAL	1	FALSE	0	0.637695475654005	4		483	1097	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741941	145741941	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769976284	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	988	608	1	ENST00000428558.2:c.562C>T	p.Pro188Ser	p.P188S	ENST00000428558	NM_004260.3	188	Cct/Tct	5/22	0.637695475654005	5	FACETS	0.994	0.977	1			1	CLONAL	5	FALSE	NA	0.637695475654005	5		609	1220	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97873861	97873861	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	254	815	0	ENST00000289081.3:c.1213G>A	p.Glu405Lys	p.E405K	ENST00000289081	NM_000136.2	405	Gag/Aag	13/15	0.355364445834951	1	FACETS	0.647	0.607	0.688	0.647	0.607	0.688	INDETERMINATE	1	FALSE	0	0.637695475654005	1		815	839	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209378	98209378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs552921967	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	91	482	0	ENST00000331920.6:c.4160C>T	p.Pro1387Leu	p.P1387L	ENST00000331920	NM_000264.3	1387	cCt/cTt	23/24	0.355364445834951	1	FACETS	0.591	0.53	0.655	0.591	0.53	0.655	INDETERMINATE	1	FALSE	0	0.637695475654005	1		482	329	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412660	139412661	+	missense_variant	Missense_Mutation	DNP	TT	TT	AG	novel	NA	P-0016112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	199	729	1	ENST00000277541.6:c.1183_1184delinsCT	p.Lys395Leu	p.K395L	ENST00000277541	NM_017617.3	395	AAg/CTg	7/34	0.355364445834951	1	FACETS	0.64	0.596	0.686	0.64	0.596	0.686	INDETERMINATE	1	FALSE	0	0.637695475654005	1		730	664	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274794	123274794	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913478	NA	P-0016114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	691	655	0	ENST00000358487.5:c.1124A>G	p.Tyr375Cys	p.Y375C	ENST00000358487	NM_000141.4	375	tAc/tGc	9/18	0.649612072516738	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.649612072516738	2		655	1034	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057657	180057657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775457696	NA	P-0016114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	309	778	0	ENST00000261937.6:c.298G>A	p.Glu100Lys	p.E100K	ENST00000261937	NM_182925.4	100	Gag/Aag	3/30	0.194418410237349	0	FACETS	0.301	0.283	0.318			1	INDETERMINATE	1	TRUE	0	0.649612072516738	0		778	1109	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	229	704	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.998	0.933	1	0.998	0.933	1	CLONAL	1	TRUE	1	0.574451490050545	2		705	799	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	340	668	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.973	0.932	1	1	0.997	1	CLONAL	2	TRUE	1	0.574451490050545	2		671	608	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272336	15272337	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs771517374	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	225	1127	5	ENST00000263388.2:c.6102dup	p.Gly2035ArgfsTer60	p.G2035Rfs*60	ENST00000263388	NM_000435.2	2034	-/C	33/33	1	2	FACETS	0.937	0.875	1	0.937	0.875	1	CLONAL	1	TRUE	1	0.574451490050545	2		1132	836	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	182	609	2	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.978	0.906	1	0.978	0.906	1	CLONAL	1	TRUE	1	0.574451490050545	2		611	648	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100175	27100176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	111	666	0	ENST00000324856.7:c.3977dup	p.Gln1327AlafsTer11	p.Q1327Afs*11	ENST00000324856	NM_006015.4	1324	tac/taCc	16/20	1	2	FACETS	0.677	0.61	0.747	0.677	0.61	0.747	SUBCLONAL	1	TRUE	1	0.574451490050545	2		666	571	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405953	49405953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	64	1142	0	ENST00000418115.1:c.185G>A	p.Gly62Glu	p.G62E	ENST00000418115	NM_001664.2	62	gGg/gAg	3/5	1	2	FACETS	0.208	0.18	0.24	0.208	0.18	0.24	SUBCLONAL	1	TRUE	1	0.574451490050545	2		1142	1069	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	183	798	1	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	0.91	0.843	0.98	0.91	0.843	0.98	CLONAL	1	TRUE	1	0.574451490050545	2		799	700	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521543	8521543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868728165	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	40	677	0	ENST00000356435.5:c.695G>A	p.Arg232His	p.R232H	ENST00000356435		232	cGc/cAc	9/35	1	2	FACETS	0.213	0.176	0.254	0.213	0.176	0.254	SUBCLONAL	1	TRUE	1	0.574451490050545	2		677	653	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	106	457	3	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	1	2	FACETS	0.868	0.784	0.957	0.868	0.784	0.957	CLONAL	1	TRUE	1	0.574451490050545	2		460	425	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070577	67070578	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	80	493	0	ENST00000412916.2:c.207dup	p.Pro70SerfsTer13	p.P70Sfs*13	ENST00000412916		67	-/T	3/6	1	2	FACETS	0.527	0.464	0.593	0.527	0.464	0.593	SUBCLONAL	1	TRUE	1	0.574451490050545	2		493	529	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032560	47032560	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	273	820	0	ENST00000377604.3:c.466G>A	p.Ala156Thr	p.A156T	ENST00000377604	NM_001204468.1	156	Gca/Aca	5/24	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.574451490050545	2		820	874	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209298	133209298	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060500809	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	126	910	1	ENST00000320574.5:c.6088del	p.Ala2030ProfsTer18	p.A2030Pfs*18	ENST00000320574	NM_006231.2	2030	Gcc/cc	44/49	1	2	FACETS	0.608	0.551	0.667	0.608	0.551	0.667	SUBCLONAL	1	TRUE	1	0.574451490050545	2		911	722	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857932	89857932	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201385829	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	134	900	0	ENST00000389301.3:c.1238G>A	p.Arg413His	p.R413H	ENST00000389301	NM_000135.2	413	cGt/cAt	14/43	1	2	FACETS	0.634	0.576	0.694	0.634	0.576	0.694	SUBCLONAL	1	TRUE	1	0.574451490050545	2		900	736	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519505	137519506	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs780346130	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	174	573	6	ENST00000367739.4:c.1132_1133del	p.Ser378PhefsTer6	p.S378Ffs*6	ENST00000367739	NM_000416.2	378	AGt/t	7/7	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.574451490050545	2		579	605	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784962	9784962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	43	736	0	ENST00000377346.4:c.2965C>T	p.Leu989Phe	p.L989F	ENST00000377346	NM_005026.3	989	Ctc/Ttc	23/24	1	2	FACETS	0.225	0.188	0.267	0.225	0.188	0.267	SUBCLONAL	1	TRUE	1	0.574451490050545	2		736	664	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242743	16242743	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756096700	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	278	1032	3	ENST00000375759.3:c.1364G>A	p.Arg455His	p.R455H	ENST00000375759	NM_015001.2	455	cGc/cAc	6/15	1	2	FACETS	0.819	0.769	0.871	0.819	0.769	0.871	CLONAL	1	TRUE	1	0.574451490050545	2		1035	1182	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259612	16259612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	147	934	0	ENST00000375759.3:c.6877G>A	p.Ala2293Thr	p.A2293T	ENST00000375759	NM_015001.2	2293	Gcc/Acc	11/15	1	2	FACETS	0.63	0.576	0.687	0.63	0.576	0.687	SUBCLONAL	1	TRUE	1	0.574451490050545	2		934	812	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46733255	46733255	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs746152916	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	152	852	0	ENST00000371975.4:c.1016T>C	p.Val339Ala	p.V339A	ENST00000371975	NM_003579.3	339	gTa/gCa	9/18	1	2	FACETS	0.588	0.538	0.641	0.588	0.538	0.641	SUBCLONAL	1	TRUE	1	0.574451490050545	2		852	900	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841430	156841430	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	143	665	0	ENST00000524377.1:c.733C>T	p.Pro245Ser	p.P245S	ENST00000524377	NM_002529.3	245	Cca/Tca	7/17	1	2	FACETS	0.886	0.812	0.963	0.886	0.812	0.963	CLONAL	1	TRUE	1	0.574451490050545	2		665	562	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446226	70446226	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	207	808	2	ENST00000373644.4:c.5166G>T	p.Lys1722Asn	p.K1722N	ENST00000373644	NM_030625.2	1722	aaG/aaT	11/12	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.574451490050545	2		810	696	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911519	114911519	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	103	572	0	ENST00000543371.1:c.1037A>G	p.Lys346Arg	p.K346R	ENST00000543371	NM_001198531.1	346	aAg/aGg	10/14	1	2	FACETS	0.601	0.539	0.666	0.601	0.539	0.666	SUBCLONAL	1	TRUE	1	0.574451490050545	2		572	597	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589762	69589762	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779951764	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	11	156	1	ENST00000168712.1:c.91G>A	p.Ala31Thr	p.A31T	ENST00000168712	NM_002007.2	31	Gca/Aca	1/3	1	2	FACETS	0.221	0.153	0.306	0.221	0.153	0.306	SUBCLONAL	1	TRUE	1	0.574451490050545	2		157	173	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435192	49435193	+	missense_variant	Missense_Mutation	DNP	CA	CA	GG	novel	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	51	477	5	ENST00000301067.7:c.6360_6361delinsCC	p.Ala2121Pro	p.A2121P	ENST00000301067	NM_003482.3	2120	gcTGcc/gcCCcc	31/54	1	2	FACETS	0.48	0.409	0.557	0.48	0.409	0.557	SUBCLONAL	1	TRUE	1	0.574451490050545	2		482	370	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219301	133219301	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	41	777	0	ENST00000320574.5:c.4743del	p.Thr1583HisfsTer11	p.T1583Hfs*11	ENST00000320574	NM_006231.2	1581	ggG/gg	37/49	1	2	FACETS	0.21	0.174	0.25	0.21	0.174	0.25	SUBCLONAL	1	TRUE	1	0.574451490050545	2		777	679	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514607	103514607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372636507	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	140	538	0	ENST00000355739.4:c.1108C>T	p.Arg370Cys	p.R370C	ENST00000355739	NM_000123.3	370	Cgt/Tgt	8/15	1	2	FACETS	0.954	0.874	1	0.954	0.874	1	CLONAL	1	TRUE	1	0.574451490050545	2		538	511	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527843	103527843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	107	801	1	ENST00000355739.4:c.3151G>A	p.Ala1051Thr	p.A1051T	ENST00000355739	NM_000123.3	1051	Gca/Aca	15/15	1	2	FACETS	0.519	0.465	0.575	0.519	0.465	0.575	SUBCLONAL	1	TRUE	1	0.574451490050545	2		802	718	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782948	66782948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200442489	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	209	577	3	ENST00000307102.5:c.1177G>A	p.Val393Ile	p.V393I	ENST00000307102	NM_002755.3	393	Gtc/Atc	11/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.574451490050545	2		580	623	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646467	23646467	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881906	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	241	924	0	ENST00000261584.4:c.1400G>A	p.Gly467Asp	p.G467D	ENST00000261584	NM_024675.3	467	gGc/gAc	4/13	1	2	FACETS	0.926	0.866	0.988	0.926	0.866	0.988	CLONAL	1	TRUE	1	0.574451490050545	2		924	906	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647133	23647133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571063157	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	56	1053	3	ENST00000261584.4:c.734C>T	p.Ala245Val	p.A245V	ENST00000261584	NM_024675.3	245	gCg/gTg	4/13	1	2	FACETS	0.184	0.157	0.214	0.184	0.157	0.214	SUBCLONAL	1	TRUE	1	0.574451490050545	2		1056	1058	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826530	50826530	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	212	628	0	ENST00000398568.2:c.2255A>C	p.Gln752Pro	p.Q752P	ENST00000398568	NM_001042412.1	752	cAg/cCg	15/18	1	2	FACETS	0.856	0.797	0.918	0.856	0.797	0.918	CLONAL	1	TRUE	1	0.574451490050545	2		628	862	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829644	72829644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769074546	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	239	980	0	ENST00000268489.5:c.6937C>T	p.Arg2313Cys	p.R2313C	ENST00000268489	NM_006885.3	2313	Cgt/Tgt	9/10	1	2	FACETS	0.891	0.833	0.951	0.891	0.833	0.951	CLONAL	1	TRUE	1	0.574451490050545	2		980	934	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989642	15989642	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	41	442	0	ENST00000268712.3:c.3131T>C	p.Val1044Ala	p.V1044A	ENST00000268712	NM_006311.3	1044	gTg/gCg	23/46	1	2	FACETS	0.279	0.232	0.332	0.279	0.232	0.332	SUBCLONAL	1	TRUE	1	0.574451490050545	2		442	511	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354379	40354379	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	287	1333	2	ENST00000293328.3:c.2216A>G	p.His739Arg	p.H739R	ENST00000293328	NM_012448.3	739	cAc/cGc	18/19	1	2	FACETS	0.9	0.847	0.955	0.9	0.847	0.955	CLONAL	1	TRUE	1	0.574451490050545	2		1335	1110	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191128	2191128	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	271	1103	0	ENST00000398665.3:c.382T>C	p.Tyr128His	p.Y128H	ENST00000398665	NM_032482.2	128	Tac/Cac	5/28	1	2	FACETS	0.966	0.907	1	0.966	0.907	1	CLONAL	1	TRUE	1	0.574451490050545	2		1103	977	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961494	18961494	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	114	407	0	ENST00000262803.5:c.630-3C>T		p.X210_splice	ENST00000262803	NM_002911.3	210			1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.574451490050545	2		407	376	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223601	36223601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773621382	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	161	1043	3	ENST00000222270.7:c.6151G>A	p.Ala2051Thr	p.A2051T	ENST00000222270	NM_014727.1	2051	Gct/Act	28/37	1	2	FACETS	0.645	0.592	0.701	0.645	0.592	0.701	SUBCLONAL	1	TRUE	1	0.574451490050545	2		1046	869	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514781	44514781	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	42	641	0	ENST00000291552.4:c.466C>T	p.Arg156Cys	p.R156C	ENST00000291552	NM_006758.2	156	Cgt/Tgt	6/8	1	2	FACETS	0.226	0.188	0.268	0.226	0.188	0.268	SUBCLONAL	1	TRUE	1	0.574451490050545	2		641	648	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655163	45655163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	138	501	0	ENST00000407780.3:c.689G>A	p.Ser230Asn	p.S230N	ENST00000407780	NM_001283052.1	230	aGc/aAc	4/7	1	2	FACETS	0.987	0.904	1	0.987	0.904	1	CLONAL	1	TRUE	1	0.574451490050545	2		501	487	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458270	12458270	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	244	924	2	ENST00000287820.6:c.892del	p.Leu298CysfsTer38	p.L298Cfs*38	ENST00000287820	NM_015869.4	296	aCc/ac	6/7	1	2	FACETS	0.965	0.904	1	0.965	0.904	1	CLONAL	1	TRUE	1	0.574451490050545	2		926	880	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935635	49935635	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	213	807	0	ENST00000296474.3:c.1729del	p.His577ThrfsTer5	p.H577Tfs*5	ENST00000296474	NM_002447.2	577	Cac/ac	5/20	1	2	FACETS	0.967	0.901	1	0.967	0.901	1	CLONAL	1	TRUE	1	0.574451490050545	2		807	767	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940877	49940877	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	52	929	0	ENST00000296474.3:c.166C>T	p.Gln56Ter	p.Q56*	ENST00000296474	NM_002447.2	56	Cag/Tag	1/20	1	2	FACETS	0.2	0.169	0.234	0.2	0.169	0.234	SUBCLONAL	1	TRUE	1	0.574451490050545	2		929	905	SUCCESS
ATR	545	MSKCC	GRCh37	3	142212111	142212111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	279	857	0	ENST00000350721.4:c.5941G>A	p.Glu1981Lys	p.E1981K	ENST00000350721	NM_001184.3	1981	Gaa/Aaa	35/47	1	2	FACETS	0.967	0.91	1	0.967	0.91	1	CLONAL	1	TRUE	1	0.574451490050545	2		857	1004	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	202	855	4	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	1	2	FACETS	0.925	0.86	0.993	0.925	0.86	0.993	CLONAL	1	TRUE	1	0.574451490050545	2		859	760	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245393	153245393	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	457	967	0	ENST00000281708.4:c.1798G>T	p.Asp600Tyr	p.D600Y	ENST00000281708	NM_033632.3	600	Gat/Tat	11/12	0.573734204055306	2	FACETS	0.911	0.876	0.946	0.911	0.876	0.946	CLONAL	2	TRUE	0	0.574451490050545	2		967	873	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519189	187519189	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	263	926	1	ENST00000441802.2:c.12194del	p.Gly4065AlafsTer141	p.G4065Afs*141	ENST00000441802	NM_005245.3	4065	gGc/gc	23/27	0.573734204055306	2	FACETS	1	0.959	1	0.513	0.482	0.545	CLONAL	1	TRUE	0	0.574451490050545	2		927	892	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31431755	31431755	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	239	914	0	ENST00000344624.3:c.3073G>A	p.Ala1025Thr	p.A1025T	ENST00000344624		1025	Gct/Act	23/33	1	2	FACETS	0.885	0.827	0.945	0.885	0.827	0.945	CLONAL	1	TRUE	1	0.574451490050545	2		914	940	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500450	149500450	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs112566969	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	44	629	0	ENST00000261799.4:c.2586+1G>A		p.X862_splice	ENST00000261799	NM_002609.3	862			1	2	FACETS	0.259	0.216	0.306	0.259	0.216	0.306	SUBCLONAL	1	TRUE	1	0.574451490050545	2		629	592	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517791	176517791	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	75	1016	2	ENST00000292408.4:c.401G>T	p.Arg134Met	p.R134M	ENST00000292408	NM_213647.1	134	aGg/aTg	4/18	1	2	FACETS	0.285	0.249	0.324	0.285	0.249	0.324	SUBCLONAL	1	TRUE	1	0.574451490050545	2		1018	916	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945695	151945695	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	238	879	1	ENST00000262189.6:c.1824A>T	p.Gln608His	p.Q608H	ENST00000262189	NM_170606.2	608	caA/caT	14/59	1	2	FACETS	0.866	0.809	0.924	0.866	0.809	0.924	CLONAL	1	TRUE	1	0.574451490050545	2		880	957	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538979	23538979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771028824	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	174	789	0	ENST00000380871.4:c.460C>T	p.Arg154Trp	p.R154W	ENST00000380871	NM_006167.3	154	Cgg/Tgg	2/2	1	2	FACETS	0.851	0.786	0.918	0.851	0.786	0.918	CLONAL	1	TRUE	1	0.574451490050545	2		789	712	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005894	69005894	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	118	891	3	ENST00000288368.4:c.2305C>T	p.Gln769Ter	p.Q769*	ENST00000288368	NM_024870.2	769	Caa/Taa	21/40	1	2	FACETS	0.508	0.458	0.561	0.508	0.458	0.561	SUBCLONAL	1	TRUE	1	0.574451490050545	2		894	808	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319854	8319854	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	173	705	0	ENST00000356435.5:c.5647C>T	p.Arg1883Ter	p.R1883*	ENST00000356435		1883	Cga/Tga	34/35	1	2	FACETS	0.842	0.777	0.91	0.842	0.777	0.91	CLONAL	1	TRUE	1	0.574451490050545	2		705	715	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486067	8486067	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	167	845	0	ENST00000356435.5:c.2750T>C	p.Val917Ala	p.V917A	ENST00000356435		917	gTa/gCa	17/35	1	2	FACETS	0.894	0.825	0.966	0.894	0.825	0.966	CLONAL	1	TRUE	1	0.574451490050545	2		845	650	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36846912	36846912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139738432	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	129	601	0	ENST00000358127.4:c.1027G>A	p.Gly343Arg	p.G343R	ENST00000358127	NM_001280556.1	343	Ggg/Agg	9/10	1	2	FACETS	0.818	0.745	0.894	0.818	0.745	0.894	CLONAL	1	TRUE	1	0.574451490050545	2		601	549	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781060	135781061	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs118203597	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	209	874	2	ENST00000298552.3:c.1904_1905del	p.Thr635ArgfsTer52	p.T635Rfs*52	ENST00000298552	NM_001162426.1	635	aCA/a	15/23	1	2	FACETS	0.823	0.765	0.883	0.823	0.765	0.883	CLONAL	1	TRUE	1	0.574451490050545	2		876	884	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426094	47426094	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	58	1204	0	ENST00000377045.4:c.619del	p.Leu207TyrfsTer85	p.L207Yfs*85	ENST00000377045	NM_001654.4	205	gCc/gc	7/16	1	2	FACETS	0.189	0.162	0.22	0.189	0.162	0.22	SUBCLONAL	1	TRUE	1	0.574451490050545	2		1204	1066	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	73	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.269531019522648	2		248	530	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271991	15271991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777802431	NA	P-0016116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	82	684	0	ENST00000263388.2:c.6448C>T	p.Arg2150Cys	p.R2150C	ENST00000263388	NM_000435.2	2150	Cgc/Tgc	33/33	0.241835659044417	3	FACETS	0.815	0.718	0.92	0.408	0.359	0.46	CLONAL	1	TRUE	1	0.269531019522648	3		684	847	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690302	117690302	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	88	428	0	ENST00000369458.3:c.827G>A	p.Ser276Asn	p.S276N	ENST00000369458	NM_024626.3	276	aGc/aAc	5/6	1	2	FACETS	0.992	0.88	1	0.992	0.88	1	CLONAL	1	TRUE	1	0.269531019522648	2		428	658	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199979	138199979	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	65	404	1	ENST00000237289.4:c.1397G>A	p.Ser466Asn	p.S466N	ENST00000237289	NM_001270507.1	466	aGc/aAc	7/9	1	2	FACETS	0.75	0.65	0.859	0.75	0.65	0.859	SUBCLONAL	1	TRUE	1	0.269531019522648	2		405	643	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137524714	137524716	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs587776858	NA	P-0016117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	192	641	0	ENST00000367739.4:c.653_655del	p.Glu218del	p.E218del	ENST00000367739	NM_000416.2	218	gAAGga/gga	5/7	0.621666084717734	4	FACETS	0.947	0.875	1			1	CLONAL	1	TRUE	NA	0.708897124726327	4		641	978	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061152	38061185	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCG	CCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCG	-	novel	NA	P-0016117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	256	212	0	ENST00000250448.2:c.804_837del	p.Cys268Ter	p.C268*	ENST00000250448	NM_004496.3	268	tgCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGG/tg	2/2	1	2	FACETS	0.896	0.855	0.936	1	0.996	1	CLONAL	2	TRUE	1	0.708897124726327	2		212	403	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618817	37618817	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	191	616	1	ENST00000447079.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000447079	NM_015083.1	165	Cag/Tag	1/14	0.635704849920747	3	FACETS	0.926	0.858	0.997			1	CLONAL	1	TRUE	NA	0.708897124726327	3		617	788	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627854	37627854	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0016117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	517	591	0	ENST00000447079.4:c.1769C>G	p.Ser590Ter	p.S590*	ENST00000447079	NM_015083.1	590	tCa/tGa	2/14	0.635704849920747	3	FACETS	0.985	0.949	1			1	CLONAL	2	TRUE	NA	0.708897124726327	3		591	1003	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38960562	38960562	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	120	402	0	ENST00000357387.3:c.1789A>G	p.Lys597Glu	p.K597E	ENST00000357387	NM_152756.3	597	Aag/Gag	20/38	0.504404067922457	3	FACETS	0.969	0.881	1			1	CLONAL	1	TRUE	NA	0.708897124726327	3		402	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0016119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	363	558	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.335753881741311	3	FACETS	0.835	0.794	0.877	0.835	0.794	0.877	CLONAL	3	TRUE	0	0.335753881741311	3		558	1008	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456842	32456842	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	163	529	0	ENST00000332351.3:c.50C>A	p.Thr17Lys	p.T17K	ENST00000332351	NM_024426.4	17	aCg/aAg	1/10	0.229381020610161	2	FACETS	1	0.987	1	0.692	0.636	0.749	CLONAL	1	TRUE	0	0.335753881741311	2		529	702	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243439	46243439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	80	461	0	ENST00000334344.6:c.1792G>A	p.Gly598Arg	p.G598R	ENST00000334344	NM_152641.2	598	Gga/Aga	14/21	0.335753881741311	3	FACETS	0.647	0.569	0.732	0.324	0.284	0.366	SUBCLONAL	1	TRUE	1	0.335753881741311	3		461	860	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487254	56487254	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	91	694	0	ENST00000267101.3:c.1400C>G	p.Ser467Cys	p.S467C	ENST00000267101	NM_001982.3	467	tCt/tGt	12/28	0.335753881741311	3	FACETS	0.519	0.459	0.584	0.26	0.229	0.292	SUBCLONAL	1	TRUE	1	0.335753881741311	3		694	1219	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041164	29041164	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	201	690	0	ENST00000282397.4:c.264C>A	p.Phe88Leu	p.F88L	ENST00000282397	NM_002019.4	88	ttC/ttA	3/30	0.251735647198058	3	FACETS	1	0.989	1	0.682	0.632	0.734	CLONAL	1	TRUE	1	0.335753881741311	3		690	1025	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657075	47657075	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs200429136	NA	P-0016119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	155	354	0	ENST00000233146.2:c.1271A>G	p.His424Arg	p.H424R	ENST00000233146	NM_000251.2	424	cAt/cGt	7/16	0.335753881741311	3	FACETS	0.845	0.776	0.916	0.845	0.776	0.916	CLONAL	2	TRUE	1	0.335753881741311	3		354	638	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152643	99152643	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	80	591	0	ENST00000074304.5:c.439A>G	p.Arg147Gly	p.R147G	ENST00000074304	NM_001134224.1	147	Agg/Ggg	7/26	1	2	FACETS	0.585	0.514	0.661	0.585	0.514	0.661	SUBCLONAL	1	TRUE	1	0.335753881741311	2		591	815	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634703	158634703	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs766295467	NA	P-0016119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	65	368	0	ENST00000263640.3:c.483C>A	p.Asp161Glu	p.D161E	ENST00000263640	NM_001105.4	161	gaC/gaA	5/11	1	2	FACETS	0.707	0.613	0.808	0.707	0.613	0.808	SUBCLONAL	1	TRUE	1	0.335753881741311	2		368	548	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39706246	39706246	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	91	283	0	ENST00000361337.2:c.304A>G	p.Ile102Val	p.I102V	ENST00000361337	NM_003286.2	102	Ata/Gta	5/21	0.254017073360799	3	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.335753881741311	3		283	437	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280432	1280432	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	86	480	0	ENST00000310581.5:c.1791G>C	p.Gln597His	p.Q597H	ENST00000310581	NM_198253.2	597	caG/caC	4/16	0.335753881741311	4	FACETS	0.705	0.623	0.795	0.353	0.311	0.398	SUBCLONAL	1	TRUE	2	0.335753881741311	4		480	970	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372744	81372744	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	142	509	0	ENST00000222390.5:c.790G>T	p.Asp264Tyr	p.D264Y	ENST00000222390	NM_000601.4	264	Gat/Tat	7/18	0.335753881741311	3	FACETS	1	0.973	1	0.583	0.531	0.637	CLONAL	1	TRUE	1	0.335753881741311	3		509	847	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624460	140624460	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	99	219	0	ENST00000288602.6:c.44del	p.Gly15AlafsTer39	p.G15Afs*39	ENST00000288602	NM_004333.4	15	gGc/gc	1/18	0.335753881741311	5	FACETS	1	0.969	1	0.797	0.717	0.88	CLONAL	2	TRUE	2	0.335753881741311	5		219	371	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989650	68989650	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	235	528	0	ENST00000288368.4:c.1588G>T	p.Glu530Ter	p.E530*	ENST00000288368	NM_024870.2	530	Gaa/Taa	15/40	0.335753881741311	3	FACETS	0.947	0.885	1	0.947	0.885	1	CLONAL	2	TRUE	1	0.335753881741311	3		528	863	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966713	36966713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	142	269	0	ENST00000358127.4:c.613G>A	p.Glu205Lys	p.E205K	ENST00000358127	NM_001280556.1	205	Gag/Aag	6/10	0.335753881741311	3	FACETS	0.867	0.793	0.943			1	CLONAL	2	TRUE	NA	0.335753881741311	3		269	570	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40457652	40457652	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	353	617	0	ENST00000345506.4:c.1405A>G	p.Ile469Val	p.I469V	ENST00000345506	NM_003152.3	469	Atc/Gtc	13/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.861400705593341	2		617	792	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	251	507	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.847	0.791	0.904	1	0.994	1	CLONAL	2	TRUE	1	0.247574420929823	2		507	1197	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934578	NA	P-0016127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	96	554	0	ENST00000269305.4:c.524G>T	p.Arg175Leu	p.R175L	ENST00000269305	NM_001126112.2	175	cGc/cTc	5/11	1	2	FACETS	0.842	0.749	0.942	0.842	0.749	0.942	CLONAL	1	TRUE	1	0.247574420929823	2		554	921	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944853	131944853	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	68	438	0	ENST00000265335.6:c.2874G>T	p.Met958Ile	p.M958I	ENST00000265335		958	atG/atT	18/25	1	2	FACETS	0.775	0.673	0.885	0.775	0.673	0.885	SUBCLONAL	1	TRUE	1	0.247574420929823	2		438	709	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098975	178098975	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	76	382	0	ENST00000397062.3:c.70T>A	p.Trp24Arg	p.W24R	ENST00000397062	NM_006164.4	24	Tgg/Agg	2/5	1	2	FACETS	0.952	0.835	1	0.952	0.835	1	CLONAL	1	TRUE	1	0.247574420929823	2		382	645	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207011	1207026	+	frameshift_variant	Frame_Shift_Del	DEL	GGTCATCTACCAGCCG	GGTCATCTACCAGCCG	-	novel	NA	P-0016127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	106	565	0	ENST00000326873.7:c.99_114del	p.Glu33AspfsTer13	p.E33Dfs*13	ENST00000326873	NM_000455.4	33	gaGGTCATCTACCAGCCG/ga	1/10	0.247574420929823	1	FACETS	0.851	0.762	0.945	0.851	0.762	0.945	CLONAL	1	TRUE	0	0.247574420929823	1		565	882	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615709	100615709	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	130	648	0	ENST00000308731.7:c.623C>A	p.Ala208Glu	p.A208E	ENST00000308731	NM_000061.2	208	gCa/gAa	8/19	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.247574420929823	2		648	1049	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806119	1806119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931614	NA	P-0016128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	12	722	0	ENST00000260795.2:c.1138G>A	p.Gly380Arg	p.G380R	ENST00000260795		380	Ggg/Agg	8/17	1	2	FACETS	0.128	0.089	0.176	0.128	0.089	0.176	SUBCLONAL	1	TRUE	1	0.361783909373004	2		722	519	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115928	8115929	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	364	445	0	ENST00000346208.3:c.1275dup	p.Ser426IlefsTer81	p.S426Ifs*81	ENST00000346208		425	cca/ccAa	6/6	1	2	FACETS	1	0.968	1	1	0.996	1	CLONAL	2	TRUE	1	0.361783909373004	2		445	983	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101445	27101446	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	279	549	0	ENST00000324856.7:c.4729dup	p.Ser1577LysfsTer26	p.S1577Kfs*26	ENST00000324856	NM_006015.4	1576	cca/ccAa	18/20	0.314887145911184	4	FACETS	1	0.945	1	1	0.994	1	CLONAL	3	TRUE	2	0.361783909373004	4		549	700	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274172	10274172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567354612	NA	P-0016128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	51	420	0	ENST00000330684.3:c.97G>A	p.Ala33Thr	p.A33T	ENST00000330684	NM_001134407.1	33	Gcg/Acg	2/13	1	2	FACETS	0.993	0.864	1	1	0.978	1	CLONAL	2	TRUE	1	0.361783909373004	2		420	142	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69998263	69998263	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	86	671	0	ENST00000394351.3:c.503T>C	p.Leu168Pro	p.L168P	ENST00000394351	NM_000248.3	168	cTc/cCc	5/9	0.265618114642716	4	FACETS	0.955	0.845	1	0.477	0.422	0.536	CLONAL	1	TRUE	2	0.361783909373004	4		671	678	SUCCESS
MET	4233	MSKCC	GRCh37	7	116399465	116399465	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	129	557	0	ENST00000397752.3:c.2285G>A	p.Gly762Asp	p.G762D	ENST00000397752	NM_000245.2	762	gGt/gAt	10/21	0.361783909373004	6	FACETS	1	0.977	1			1	CLONAL	2	TRUE	NA	0.361783909373004	6		557	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0016129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	136	947	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.329272680357025	1	FACETS	0.857	0.78	0.939	0.857	0.78	0.939	CLONAL	1	TRUE	0	0.329272680357025	1		949	805	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222369	2222382	+	frameshift_variant	Frame_Shift_Del	DEL	GACCGCCAGCGCCC	GACCGCCAGCGCCC	-	novel	NA	P-0016129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	129	647	0	ENST00000398665.3:c.3202_3215del	p.Thr1068TrpfsTer61	p.T1068Wfs*61	ENST00000398665	NM_032482.2	1067	ctGACCGCCAGCGCCCgt/ctgt	24/28	0.329272680357025	1	FACETS	0.921	0.836	1	0.921	0.836	1	CLONAL	1	TRUE	0	0.329272680357025	1		647	711	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035184	6035184	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs369763423	NA	P-0016129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	146	630	0	ENST00000265849.7:c.884G>T	p.Arg295Leu	p.R295L	ENST00000265849	NM_000535.5	295	cGg/cTg	8/15	0.329272680357025	1	FACETS	0.924	0.844	1	0.924	0.844	1	CLONAL	1	TRUE	0	0.329272680357025	1		630	802	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874177	151874183	+	frameshift_variant	Frame_Shift_Del	DEL	ATTATCT	ATTATCT	TTG	novel	NA	P-0016129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	84	682	2	ENST00000262189.6:c.8355_8361delinsCAA	p.Leu2785PhefsTer37	p.L2785Ffs*37	ENST00000262189	NM_170606.2	2785	ttAGATAAT/ttCAA	38/59	1	2	FACETS	0.555	0.489	0.626	0.555	0.489	0.626	SUBCLONAL	1	TRUE	1	0.329272680357025	2		684	919	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939132	76939132	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	177	773	1	ENST00000373344.5:c.1616A>T	p.Gln539Leu	p.Q539L	ENST00000373344	NM_000489.3	539	cAg/cTg	9/35	0.329272680357025	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.329272680357025	1		774	895	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559817	29559818	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	C	novel	NA	P-0016129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	93	452	0	ENST00000356175.3:c.3414_3415delinsC	p.Ala1139HisfsTer3	p.A1139Hfs*3	ENST00000356175	NM_000267.3	1138	ctGGca/ctCca	26/57	0.329272680357025	1	FACETS	0.798	0.711	0.891	0.798	0.711	0.891	SUBCLONAL	1	TRUE	0	0.329272680357025	1		452	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0016130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1330	443	889	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	1	2	FACETS	0.833	0.792	0.874	0.833	0.792	0.874	CLONAL	1	TRUE	1	0.6	2		889	1773	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936552	49936552	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	462	734	0	ENST00000296474.3:c.1375G>C	p.Val459Leu	p.V459L	ENST00000296474	NM_002447.2	459	Gtc/Ctc	2/20	0.487939083034039	3	FACETS	0.998	0.955	1	0.998	0.955	1	CLONAL	2	TRUE	1	0.487939083034039	3		734	1180	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874869	151874869	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	147	377	0	ENST00000262189.6:c.7669G>T	p.Ala2557Ser	p.A2557S	ENST00000262189	NM_170606.2	2557	Gca/Tca	38/59	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.487939083034039	2		377	531	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	97	414	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.836	0.745	0.933	0.836	0.745	0.933	CLONAL	1	TRUE	1	0.291243873328802	2		414	797	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578493	7578493	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1206165503	NA	P-0016134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	288	923	0	ENST00000269305.4:c.437G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tGg/tAg	5/11	1	2	FACETS	0.863	0.817	0.908	1	0.995	1	CLONAL	2	TRUE	1	0.505070347322557	2		923	661	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495732	72495732	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	190	609	0	ENST00000477973.2:c.338del	p.Trp114GlyfsTer22	p.W114Gfs*22	ENST00000477973	NM_012234.5	114	Tgg/gg	1/4	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.505070347322557	2		609	694	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0016135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	188	399	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.369838198047314	3	FACETS	0.877	0.814	0.943	0.877	0.814	0.943	CLONAL	2	TRUE	1	0.373529088017531	3		399	681	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458435	120458436	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs771237928	NA	P-0016135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	36	454	0	ENST00000256646.2:c.6909dup	p.Ile2304HisfsTer9	p.I2304Hfs*9	ENST00000256646	NM_024408.3	2303	-/C	34/34	0.236185468265435	1	FACETS	0.321	0.263	0.385	0.321	0.263	0.385	SUBCLONAL	1	TRUE	0	0.373529088017531	1		454	489	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842686	68842686	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	187	652	0	ENST00000261769.5:c.622G>T	p.Glu208Ter	p.E208*	ENST00000261769	NM_004360.3	208	Gaa/Taa	5/16	0.373529088017531	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.373529088017531	1		652	770	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0016136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	330	475	1	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	NA	2	FACETS	0.969	0.935	1			1	INDETERMINATE	2	TRUE	NA	0.755168186825497	2		476	451	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266845	18266845	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	227	654	0	ENST00000222254.8:c.156G>C	p.Gln52His	p.Q52H	ENST00000222254	NM_005027.3	52	caG/caC	2/16	0.655762324881399	4	FACETS	1	0.942	1	0.506	0.471	0.542	CLONAL	1	TRUE	2	0.755168186825497	4		654	1042	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015133	37015133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223489007	NA	P-0016136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	609	734	0	ENST00000358127.4:c.271G>A	p.Ala91Thr	p.A91T	ENST00000358127	NM_001280556.1	91	Gcc/Acc	3/10	0.655762324881399	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	2	0.755168186825497	4		734	1403	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380722	118380722	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	235	733	1	ENST00000534358.1:c.10960C>A	p.Gln3654Lys	p.Q3654K	ENST00000534358	NM_005933.3	3654	Cag/Aag	30/36	0.750223946925068	3	FACETS	0.882	0.823	0.942	0.441	0.411	0.471	CLONAL	1	TRUE	1	0.755168186825497	3		734	972	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843446	3843446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200933101	NA	P-0016136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	244	576	0	ENST00000262367.5:c.1157G>A	p.Arg386Gln	p.R386Q	ENST00000262367	NM_004380.2	386	cGa/cAa	4/31	0.678505219030328	4	FACETS	1	0.962	1			1	CLONAL	1	TRUE	NA	0.755168186825497	4		576	1089	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612398	1612398	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	621	757	0	ENST00000344749.5:c.1621G>T	p.Asp541Tyr	p.D541Y	ENST00000344749	NM_001136139.2	541	Gac/Tac	18/19	0.655762324881399	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.755168186825497	4		757	1391	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158228	47158228	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	189	467	0	ENST00000409792.3:c.4471C>G	p.His1491Asp	p.H1491D	ENST00000409792	NM_014159.6	1491	Cat/Gat	4/21	0.755168186825497	2	FACETS	0.948	0.883	1	0.474	0.441	0.507	CLONAL	1	TRUE	0	0.755168186825497	2		467	528	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628314	187628314	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	537	646	0	ENST00000441802.2:c.2668G>C	p.Glu890Gln	p.E890Q	ENST00000441802	NM_005245.3	890	Gag/Cag	2/27	0.748787770612888	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.755168186825497	3		646	958	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393181	393181	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	162	385	0	ENST00000380956.4:c.29G>C	p.Gly10Ala	p.G10A	ENST00000380956	NM_001195286.1	10	gGa/gCa	2/9	0.746827501241983	4	FACETS	0.95	0.872	1	0.317	0.29	0.344	CLONAL	1	TRUE	1	0.755168186825497	4		385	793	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117874123	117874123	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	235	608	0	ENST00000297338.2:c.331C>G	p.Pro111Ala	p.P111A	ENST00000297338	NM_006265.2	111	Cct/Gct	4/14	0.746827501241983	4	FACETS	1	0.971	1	0.357	0.333	0.382	CLONAL	1	TRUE	1	0.755168186825497	4		608	1020	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	62	414	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.347173588754381	5	FACETS	1	0.966	1	0.458	0.398	0.522	CLONAL	1	FALSE	2	0.463935203816339	5		414	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0016137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	61	467	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.2015097170562	3	FACETS	0.942	0.83	1	0.628	0.553	0.706	INDETERMINATE	2	FALSE	0	0.463935203816339	3		468	172	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974732	21974732	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	29	248	0	ENST00000304494.5:c.95T>A	p.Leu32Gln	p.L32Q	ENST00000304494	NM_000077.4	32	cTg/cAg	1/3	0.463935203816339	1	FACETS	0.99	0.815	1	0.99	0.815	1	CLONAL	1	FALSE	0	0.463935203816339	1		248	97	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851601	134851601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs961044599	NA	P-0016137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	35	382	0	ENST00000398015.3:c.1007C>T	p.Thr336Met	p.T336M	ENST00000398015	NM_004441.4	336	aCg/aTg	5/16	0.364040688675772	0	FACETS	0.647	0.541	0.76			1	SUBCLONAL	1	FALSE	0	0.463935203816339	0		382	125	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0016139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	1241	531	1	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.764737312924813	3	FACETS	1	0.991	1			1	CLONAL	3	TRUE	NA	0.764737312924813	3		532	1484	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249011	55249012	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAACCCCCACGG	novel	NA	P-0016139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	780	497	0	ENST00000275493.2:c.2320_2321insGCAACCCCCACG	p.His773_Val774insGlyAsnProHis	p.H773_V774insGNPH	ENST00000275493	NM_005228.3	770	gac/gaCAACCCCCACGGc	20/28	0.764737312924813	5	FACETS	1	0.996	1	0.805	0.779	0.831	CLONAL	2	TRUE	2	0.764737312924813	5		497	1814	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0016141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	61	485	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.18910090741885	3	FACETS	0.815	0.703	0.938	0.408	0.351	0.469	CLONAL	1	TRUE	1	0.257136463879014	3		485	657	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057835	27057835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	103	686	0	ENST00000324856.7:c.1543C>T	p.Gln515Ter	p.Q515*	ENST00000324856	NM_006015.4	515	Cag/Tag	3/20	0.18910090741885	3	FACETS	0.99	0.885	1	0.495	0.442	0.551	CLONAL	1	TRUE	1	0.257136463879014	3		686	913	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847363	68847368	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGTG	CCAGTG	AA	novel	NA	P-0016141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	44	461	2	ENST00000261769.5:c.1285_1290delinsAA	p.Pro429LysfsTer7	p.P429Kfs*7	ENST00000261769	NM_004360.3	429	CCAGTG/AA	9/16	0.257136591442272	1	FACETS	0.981	0.827	1	0.981	0.827	1	CLONAL	1	TRUE	0	0.257136463879014	1		463	304	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880188	37880188	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	77	459	0	ENST00000269571.5:c.2232G>T	p.Glu744Asp	p.E744D	ENST00000269571		744	gaG/gaT	19/27	0.18910090741885	3	FACETS	1	0.975	1	0.73	0.643	0.823	CLONAL	1	TRUE	1	0.257136463879014	3		459	463	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	320	414	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.430175910333137	3	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.660453817836107	3		414	532	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197399	26197399	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	61	163	0	ENST00000356476.2:c.80G>T	p.Arg27Leu	p.R27L	ENST00000356476		27	cGa/cTa	1/1	0.379501379262128	5	FACETS	1	0.951	1	0.402	0.349	0.458	INDETERMINATE	1	TRUE	2	0.660453817836107	5		163	305	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715883	117715883	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	117	436	1	ENST00000368508.3:c.875G>T	p.Trp292Leu	p.W292L	ENST00000368508	NM_002944.2	292	tGg/tTg	9/43	0.659424340944367	4	FACETS	0.89	0.804	0.981	0.297	0.268	0.327	CLONAL	1	TRUE	1	0.660453817836107	4		437	661	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016146-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	142	507	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.461093317110264	3	FACETS	0.858	0.789	0.928	0.858	0.789	0.928	CLONAL	2	TRUE	1	0.476918291700458	3		507	430	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663346	227663346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024227751	NA	P-0016146-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	34	422	0	ENST00000305123.5:c.109G>A	p.Glu37Lys	p.E37K	ENST00000305123	NM_005544.2	37	Gag/Aag	1/2	1	2	FACETS	0.487	0.399	0.585	0.487	0.399	0.585	SUBCLONAL	1	TRUE	1	0.476918291700458	2		422	293	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165634	118165648	+	inframe_deletion	In_Frame_Del	DEL	GAAGGACATCGTCCA	GAAGGACATCGTCCA	-	novel	NA	P-0016146-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	47	346	0	ENST00000369448.3:c.146_160del	p.Lys49_Gln53del	p.K49_Q53del	ENST00000369448	NM_017709.3	48	ctGAAGGACATCGTCCAg/ctg	2/2	0.350796430102579	3	FACETS	0.495	0.418	0.58	0.248	0.209	0.29	SUBCLONAL	1	TRUE	1	0.476918291700458	3		346	493	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154873	2154873	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016146-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	152	848	0	ENST00000434045.2:c.348C>G	p.Ser116Arg	p.S116R	ENST00000434045	NM_001127598.1	116	agC/agG	4/5	1	2	FACETS	0.996	0.914	1	0.996	0.914	1	CLONAL	1	TRUE	1	0.476918291700458	2		848	640	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724875	43724875	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016146-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	63	372	0	ENST00000382044.4:c.3192G>C	p.Arg1064Ser	p.R1064S	ENST00000382044	NM_001141980.1	1064	agG/agC	17/28	0.25248908773504	1	FACETS	0.915	0.802	1	0.915	0.802	1	INDETERMINATE	1	TRUE	0	0.476918291700458	1		372	220	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114679	73114679	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016146-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	50	650	0	ENST00000356692.5:c.1060G>A	p.Ala354Thr	p.A354T	ENST00000356692		354	Gct/Act	9/9	0.25248908773504	1	FACETS	0.365	0.31	0.425	0.365	0.31	0.425	INDETERMINATE	1	TRUE	0	0.476918291700458	1		650	438	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	129	248	0				ENST00000310581	NM_198253.2	-/1132			0.202252426581039	5	FACETS	1	0.98	1	0.429	0.389	0.471	INDETERMINATE	1	TRUE	2	0.5007850282409	5		248	701	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0016149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	593	563	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.282047834468907	3	FACETS	1	0.996	1	0.832	0.803	0.861	INDETERMINATE	2	TRUE	0	0.5007850282409	3		564	1187	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480341	56480341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	290	377	0	ENST00000267101.3:c.448G>A	p.Glu150Lys	p.E150K	ENST00000267101	NM_001982.3	150	Gag/Aag	4/28	0.419428851608507	2	FACETS	0.803	0.76	0.847	0.803	0.76	0.847	CLONAL	2	TRUE	0	0.5007850282409	2		377	721	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651893	36651894	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0016149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	182	363	0	ENST00000244741.5:c.19dup	p.Asp7GlyfsTer29	p.D7Gfs*29	ENST00000244741	NM_000389.4	5	-/G	2/3	0.27086611357313	3	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.5007850282409	3		363	794	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495016	56495016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776728303	NA	P-0016149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	341	368	0	ENST00000267101.3:c.3373C>T	p.Arg1125Trp	p.R1125W	ENST00000267101	NM_001982.3	1125	Cgg/Tgg	27/28	0.419428851608507	2	FACETS	0.832	0.792	0.874	0.832	0.792	0.874	CLONAL	2	TRUE	0	0.5007850282409	2		368	818	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276950	123276950	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	56	408	0	ENST00000358487.5:c.967G>C	p.Glu323Gln	p.E323Q	ENST00000358487	NM_000141.4	323	Gag/Cag	8/18	NA	2	FACETS	0.292	0.249	0.338			1	INDETERMINATE	1	TRUE	NA	0.5007850282409	2		408	767	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416799	416799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	181	262	0	ENST00000399788.2:c.3751G>A	p.Glu1251Lys	p.E1251K	ENST00000399788	NM_001042603.1	1251	Gaa/Aaa	23/28	0.23188164374848	5	FACETS	0.814	0.752	0.877	0.542	0.501	0.585	INDETERMINATE	2	TRUE	2	0.5007850282409	5		262	778	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481830	56481830	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	454	471	0	ENST00000267101.3:c.758G>T	p.Gly253Val	p.G253V	ENST00000267101	NM_001982.3	253	gGa/gTa	7/28	0.419428851608507	2	FACETS	0.879	0.843	0.916	0.879	0.843	0.916	CLONAL	2	TRUE	0	0.5007850282409	2		471	1031	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941727	48941728	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0016149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	193	258	0	ENST00000267163.4:c.1039dup	p.Ser347PhefsTer6	p.S347Ffs*6	ENST00000267163	NM_000321.2	346	gat/gaTt	10/27	0.5007850282409	2	FACETS	0.818	0.765	0.872	0.818	0.765	0.872	CLONAL	2	TRUE	0	0.5007850282409	2		258	471	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807863	3807863	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	368	437	0	ENST00000262367.5:c.3556G>C	p.Glu1186Gln	p.E1186Q	ENST00000262367	NM_004380.2	1186	Gag/Cag	18/31	0.419428851608507	2	FACETS	0.792	0.754	0.83	0.792	0.754	0.83	SUBCLONAL	2	TRUE	0	0.5007850282409	2		437	928	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817853	3817853	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	377	506	0	ENST00000262367.5:c.3118G>C	p.Glu1040Gln	p.E1040Q	ENST00000262367	NM_004380.2	1040	Gag/Cag	16/31	0.419428851608507	2	FACETS	1	0.995	1	0.72	0.685	0.756	CLONAL	1	TRUE	0	0.5007850282409	2		506	1045	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820785	3820785	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0016149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	435	570	0	ENST00000262367.5:c.2666C>G	p.Ser889Ter	p.S889*	ENST00000262367	NM_004380.2	889	tCa/tGa	14/31	0.419428851608507	2	FACETS	0.759	0.725	0.793	0.759	0.725	0.793	SUBCLONAL	2	TRUE	0	0.5007850282409	2		570	1145	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049694	16049694	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	365	405	0	ENST00000268712.3:c.1078C>T	p.Gln360Ter	p.Q360*	ENST00000268712	NM_006311.3	360	Cag/Tag	10/46	0.282047834468907	3	FACETS	1	0.982	1	0.707	0.674	0.741	INDETERMINATE	2	TRUE	0	0.5007850282409	3		405	859	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663734	29663734	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	377	470	0	ENST00000356175.3:c.6166G>A	p.Asp2056Asn	p.D2056N	ENST00000356175	NM_000267.3	2056	Gat/Aat	41/57	0.365546160282227	4	FACETS	0.897	0.851	0.943			1	CLONAL	2	TRUE	NA	0.5007850282409	4		470	1260	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78933914	78933914	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	293	443	0	ENST00000306801.3:c.3514C>A	p.Leu1172Met	p.L1172M	ENST00000306801	NM_020761.2	1172	Ctg/Atg	30/34	0.23188164374848	5	FACETS	0.776	0.729	0.824	0.517	0.486	0.549	INDETERMINATE	2	TRUE	2	0.5007850282409	5		443	1321	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250949	10250949	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	284	405	0	ENST00000340748.4:c.3531C>G	p.Phe1177Leu	p.F1177L	ENST00000340748		1177	ttC/ttG	32/40	0.202252426581039	5	FACETS	0.896	0.843	0.952	0.598	0.562	0.635	INDETERMINATE	2	TRUE	2	0.5007850282409	5		405	1108	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439764	220439764	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1373497202	NA	P-0016149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	49	391	1	ENST00000243786.2:c.617C>T	p.Ser206Leu	p.S206L	ENST00000243786	NM_002191.3	206	tCa/tTa	2/2	1	2	FACETS	0.225	0.189	0.264	0.225	0.189	0.264	SUBCLONAL	1	TRUE	1	0.5007850282409	2		392	871	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266985	41266985	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	112	316	0	ENST00000349496.5:c.656A>G	p.His219Arg	p.H219R	ENST00000349496	NM_001904.3	219	cAt/cGt	5/15	0.331635766507674	6	FACETS	0.796	0.714	0.883	0.199	0.178	0.221	SUBCLONAL	1	TRUE	2	0.5007850282409	6		316	1125	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515070	148515070	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0016149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	260	312	0	ENST00000320356.2:c.1139C>G	p.Ser380Ter	p.S380*	ENST00000320356	NM_004456.4	380	tCa/tGa	10/20	0.463187118195039	4	FACETS	1	0.992	1	0.705	0.66	0.751	CLONAL	1	TRUE	2	0.5007850282409	4		312	1105	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798280	45798280	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	182	379	0	ENST00000450313.1:c.656C>T	p.Thr219Ile	p.T219I	ENST00000450313	NM_012222.2	219	aCa/aTa	8/16	1	2	FACETS	0.836	0.774	0.9	0.836	0.774	0.9	CLONAL	1	TRUE	1	0.650773410968042	2		379	669	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348715	118348715	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	173	337	0	ENST00000534358.1:c.3368A>G	p.Glu1123Gly	p.E1123G	ENST00000534358	NM_005933.3	1123	gAa/gGa	5/36	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.650773410968042	2		337	523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574035	7574035	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs867389695	NA	P-0016150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	361	427	0	ENST00000269305.4:c.994-2A>G		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.650773410968042	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.650773410968042	1		427	707	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441262	52441262	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	245	330	0	ENST00000460680.1:c.508T>G	p.Phe170Val	p.F170V	ENST00000460680	NM_004656.3	170	Ttt/Gtt	7/17	0.650773410968042	1	FACETS	0.994	0.94	1	0.994	0.94	1	CLONAL	1	TRUE	0	0.650773410968042	1		330	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0016151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	482	947	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.296771805602965	3	FACETS	0.987	0.947	1			1	CLONAL	3	TRUE	NA	0.328358889167521	3		949	1154	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348795	11348795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1355566958	NA	P-0016151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	79	396	1	ENST00000332029.2:c.541C>T	p.Arg181Cys	p.R181C	ENST00000332029	NM_003745.1	181	Cgc/Tgc	2/2	0.328358889167521	2	FACETS	1	0.955	1	0.583	0.515	0.655	CLONAL	1	TRUE	0	0.328358889167521	2		397	413	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255617	16255617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	129	654	0	ENST00000375759.3:c.2883del	p.Lys962SerfsTer12	p.K962Sfs*12	ENST00000375759	NM_015001.2	961	aGg/ag	11/15	0.328358889167521	3	FACETS	0.992	0.899	1	0.496	0.449	0.546	CLONAL	1	TRUE	1	0.328358889167521	3		654	922	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692932	89692932	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	78	865	0	ENST00000371953.3:c.416T>C	p.Leu139Ser	p.L139S	ENST00000371953	NM_000314.4	139	tTa/tCa	5/9	0.31285003291428	1	FACETS	0.437	0.383	0.495	0.437	0.383	0.495	SUBCLONAL	1	TRUE	0	0.328358889167521	1		865	909	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778095	27778099	+	frameshift_variant	Frame_Shift_Del	DEL	GACTT	GACTT	C	novel	NA	P-0016151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	80	249	0	ENST00000369163.2:c.244_248delinsC	p.Asp82ArgfsTer8	p.D82Rfs*8	ENST00000369163	NM_003536.2	82	GACTTg/Cg	1/1	0.328358889167521	3	FACETS	0.798	0.702	0.901	0.399	0.351	0.451	CLONAL	1	TRUE	1	0.328358889167521	3		249	711	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0016151-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	311	947	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.260079141582621	3	FACETS	1	0.988	1	0.77	0.728	0.812	CLONAL	2	TRUE	0	0.338271572816045	3		949	931	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348795	11348795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1355566958	NA	P-0016151-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	61	396	1	ENST00000332029.2:c.541C>T	p.Arg181Cys	p.R181C	ENST00000332029	NM_003745.1	181	Cgc/Tgc	2/2	0.280360221706114	2	FACETS	1	0.929	1	0.555	0.482	0.633	CLONAL	1	TRUE	0	0.338271572816045	2		397	325	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255617	16255617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016151-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	91	654	0	ENST00000375759.3:c.2883del	p.Lys962SerfsTer12	p.K962Sfs*12	ENST00000375759	NM_015001.2	961	aGg/ag	11/15	0.280263227877843	3	FACETS	0.912	0.81	1	0.456	0.405	0.51	CLONAL	1	TRUE	1	0.338271572816045	3		654	690	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692932	89692932	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016151-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	107	865	0	ENST00000371953.3:c.416T>C	p.Leu139Ser	p.L139S	ENST00000371953	NM_000314.4	139	tTa/tCa	5/9	1	2	FACETS	0.922	0.828	1	0.922	0.828	1	CLONAL	1	TRUE	1	0.338271572816045	2		865	686	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778099	27778099	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016151-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	97	856	2	ENST00000369163.2:c.248T>C	p.Leu83Ser	p.L83S	ENST00000369163	NM_003536.2	83	tTg/tCg	1/1	0.338271572816045	7	FACETS	1	0.967	1	0.306	0.272	0.342	CLONAL	1	TRUE	3	0.338271572816045	7		858	865	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778095	27778098	+	frameshift_variant	Frame_Shift_Del	DEL	GACT	GACT	-	novel	NA	P-0016151-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	97	850	0	ENST00000369163.2:c.244_247del	p.Asp82CysfsTer8	p.D82Cfs*8	ENST00000369163	NM_003536.2	82	GACTtg/tg	1/1	0.338271572816045	7	FACETS	1	0.967	1	0.306	0.272	0.342	CLONAL	1	TRUE	3	0.338271572816045	7		850	865	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575157	48575157	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0016151-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	65	671	0	ENST00000342988.3:c.351T>G	p.Tyr117Ter	p.Y117*	ENST00000342988	NM_005359.5	117	taT/taG	3/12	0.260308194744037	2	FACETS	0.555	0.48	0.635	0.277	0.24	0.318	SUBCLONAL	1	TRUE	0	0.338271572816045	2		671	693	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0016159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	237	467	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.410468575778016	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.410468575778016	1		468	761	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954187	48954187	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1555286568	NA	P-0016159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	112	286	0	ENST00000267163.4:c.1390-2A>G		p.X464_splice	ENST00000267163	NM_000321.2	464			0.410468575778016	1	FACETS	0.988	0.895	1	0.988	0.895	1	CLONAL	1	TRUE	0	0.410468575778016	1		286	439	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	1071	653	1	ENST00000269571.5:c.829G>T	p.Asp277Tyr	p.D277Y	ENST00000269571		277	Gac/Tac	7/27	0.270805369127436	6	FACETS	0.939	0.918	0.96			1	CLONAL	6	TRUE	NA	0.410468575778016	6		654	1686	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30099946	30099946	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs758403249	NA	P-0121470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	76	332	0	ENST00000331968.5:c.1672+2T>C		p.X558_splice	ENST00000331968	NM_002742.2	558			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		332	489	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	153	507	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.936	0.858	1	0.936	0.858	1	CLONAL	1	TRUE	1	0.41	2		507	797	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986670	36986674	+	frameshift_variant	Frame_Shift_Del	DEL	CCACC	CCACC	-	novel	NA	P-0016161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	18	34	0	ENST00000354822.5:c.1015_1019del	p.Gly339ArgfsTer98	p.G339Rfs*98	ENST00000354822	NM_001079668.2	339	GGTGGc/c	3/3	0.410174650816824	1	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	0	0.41	1		34	51	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964501	93964501	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	57	380	0	ENST00000369303.4:c.2396del	p.Pro799GlnfsTer2	p.P799Qfs*2	ENST00000369303	NM_004440.3	799	cCa/ca	14/17	1	2	FACETS	0.573	0.492	0.661	0.573	0.492	0.661	SUBCLONAL	1	TRUE	1	0.41	2		380	485	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645919	67645919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	77	626	1	ENST00000264010.4:c.847C>T	p.Arg283Cys	p.R283C	ENST00000264010	NM_006565.3	283	Cgt/Tgt	4/12	0.263993388794212	1	FACETS	0.374	0.328	0.424	0.374	0.328	0.424	SUBCLONAL	1	TRUE	0	0.413692823501011	1		627	789	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160648	56160663	+	frameshift_variant	Frame_Shift_Del	DEL	GTTAACAAAGTGATGC	GTTAACAAAGTGATGC	-	novel	NA	P-0016162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	47	488	0	ENST00000399503.3:c.923_938del	p.Val308GlyfsTer10	p.V308Gfs*10	ENST00000399503	NM_005921.1	308	GTTAACAAAGTGATGCgg/gg	4/20	1	2	FACETS	0.364	0.306	0.427	0.364	0.306	0.427	SUBCLONAL	1	TRUE	1	0.413692823501011	2		488	625	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178643	56178643	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	36	296	0	ENST00000399503.3:c.3617del	p.Pro1206LeufsTer39	p.P1206Lfs*39	ENST00000399503	NM_005921.1	1206	Cct/ct	14/20	1	2	FACETS	0.416	0.342	0.499	0.416	0.342	0.499	SUBCLONAL	1	TRUE	1	0.413692823501011	2		296	418	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0016165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	188	669	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.295831286622213	3	FACETS	1	0.989	1	0.719	0.665	0.776	CLONAL	1	TRUE	1	0.327492740622586	3		669	929	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677814	47677814	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	93	699	0	ENST00000347630.2:c.1051G>C	p.Glu351Gln	p.E351Q	ENST00000347630	NM_001007230.1	351	Gag/Cag	11/11	0.295831286622213	3	FACETS	0.661	0.586	0.741	0.33	0.293	0.371	SUBCLONAL	1	TRUE	1	0.327492740622586	3		699	1000	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109322692	109322692	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0016165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	77	583	0	ENST00000436639.2:c.346-1G>A		p.X116_splice	ENST00000436639	NM_014454.2	116			1	2	FACETS	0.624	0.548	0.707	0.624	0.548	0.707	SUBCLONAL	1	TRUE	1	0.327492740622586	2		583	753	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554344	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	137	822	1	ENST00000220592.5:c.1807G>T	p.Ala603Ser	p.A603S	ENST00000220592	NM_012154.3	603	Gcc/Tcc	14/19	1	2	FACETS	0.767	0.696	0.841	0.767	0.696	0.841	SUBCLONAL	1	TRUE	1	0.327492740622586	2		823	1091	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0016166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	91	339	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.244109540736621	4	FACETS	0.964	0.863	1	0.964	0.863	1	CLONAL	2	TRUE	2	0.331489449235641	4		339	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1131691023	NA	P-0016166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	500	718	0	ENST00000269305.4:c.470T>A	p.Val157Asp	p.V157D	ENST00000269305	NM_001126112.2	157	gTc/gAc	5/11	0.280693594256196	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	4	TRUE	0	0.331489449235641	4		718	922	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719638	190719638	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	37	327	0	ENST00000441310.2:c.1640A>C	p.Asn547Thr	p.N547T	ENST00000441310	NM_000534.4	547	aAc/aCc	9/13	0.244109540736621	4	FACETS	0.754	0.623	0.902	0.377	0.311	0.451	CLONAL	1	TRUE	2	0.331489449235641	4		327	394	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719698	190719698	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	80	377	0	ENST00000441310.2:c.1700G>C	p.Ser567Thr	p.S567T	ENST00000441310	NM_000534.4	567	aGc/aCc	9/13	0.244109540736621	4	FACETS	1	0.957	1	0.592	0.522	0.667	CLONAL	1	TRUE	2	0.331489449235641	4		377	543	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0016167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	59	704	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.813	0.702	0.934	0.813	0.702	0.934	CLONAL	1	TRUE	1	0.33353138173032	2		705	435	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412032	116412032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	80	858	1	ENST00000397752.3:c.3017C>T	p.Thr1006Ile	p.T1006I	ENST00000397752	NM_000245.2	1006	aCt/aTt	14/21	1	2	FACETS	0.903	0.797	1	0.903	0.797	1	CLONAL	1	TRUE	1	0.33353138173032	2		859	531	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058009	27058010	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0016167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	101	548	0	ENST00000324856.7:c.1720_1721del	p.Ser574ProfsTer48	p.S574Pfs*48	ENST00000324856	NM_006015.4	573	CTc/c	3/20	1	2	FACETS	0.932	0.834	1	0.932	0.834	1	CLONAL	1	TRUE	1	0.33353138173032	2		548	650	SUCCESS
APC	324	MSKCC	GRCh37	5	112175307	112175307	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	8	354	0	ENST00000257430.4:c.4016G>T	p.Gly1339Val	p.G1339V	ENST00000257430	NM_000038.5	1339	gGt/gTt	16/16	1	2	FACETS	0.145	0.093	0.213	0.145	0.093	0.213	SUBCLONAL	1	TRUE	1	0.33353138173032	2		354	331	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101909953	101909954	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	27	288	0	ENST00000374994.4:c.1275dup	p.Leu426ThrfsTer5	p.L426Tfs*5	ENST00000374994	NM_004612.2	425	caa/cAaa	8/9	0.33353138173032	1	FACETS	0.605	0.484	0.742	0.605	0.484	0.742	SUBCLONAL	1	TRUE	0	0.33353138173032	1		288	223	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0016168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	166	339	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.912	0.846	0.98	0.912	0.846	0.98	CLONAL	1	TRUE	1	0.792722502046409	2		339	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0016168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	468	790	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.792722502046409	2		792	1157	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939812	76939813	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0016168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	282	354	0	ENST00000373344.5:c.935dup	p.Ser313IlefsTer9	p.S313Ifs*9	ENST00000373344	NM_000489.3	312	aca/acCa	9/35	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.792722502046409	1		354	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0016169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	295	546	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.568587785967619	1	FACETS	0.998	0.945	1	0.998	0.945	1	CLONAL	1	FALSE	0	0.568587785967619	1		546	744	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	256	726	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	FALSE	1	0.568587785967619	2		726	888	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675248	176675248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201483724	NA	P-0016169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	139	311	1	ENST00000439151.2:c.4564G>A	p.Asp1522Asn	p.D1522N	ENST00000439151	NM_022455.4	1522	Gat/Aat	11/23	1	2	FACETS	0.873	0.798	0.951	0.873	0.798	0.951	CLONAL	1	FALSE	1	0.568587785967619	2		312	560	SUCCESS
APC	324	MSKCC	GRCh37	5	112173669	112173670	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0016169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	197	436	0	ENST00000257430.4:c.2379_2380del	p.Tyr796TrpfsTer2	p.Y796Wfs*2	ENST00000257430	NM_000038.5	793	cAA/c	16/16	1	2	FACETS	0.983	0.913	1	0.983	0.913	1	CLONAL	1	FALSE	1	0.568587785967619	2		436	705	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653829	89653829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554893808	NA	P-0016169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	151	530	0	ENST00000371953.3:c.127G>A	p.Glu43Lys	p.E43K	ENST00000371953	NM_000314.4	43	Gaa/Aaa	2/9	0.568587785967619	1	FACETS	0.953	0.881	1	0.953	0.881	1	CLONAL	1	FALSE	0	0.568587785967619	1		530	399	SUCCESS
APC	324	MSKCC	GRCh37	5	112175747	112175748	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0016169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	134	340	0	ENST00000257430.4:c.4456_4457del	p.Asp1486TyrfsTer27	p.D1486Yfs*27	ENST00000257430	NM_000038.5	1486	GAt/t	16/16	1	2	FACETS	0.843	0.769	0.92	0.843	0.769	0.92	CLONAL	1	FALSE	1	0.568587785967619	2		340	559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	329	936	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.178491155907054	6	FACETS	0.862	0.815	0.91			1	INDETERMINATE	3	TRUE	NA	0.394437861398106	6		938	1154	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	220	599	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	0.178491155907054	6	FACETS	0.848	0.792	0.907			1	INDETERMINATE	3	TRUE	NA	0.394437861398106	6		599	784	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913351	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	76	595	0	ENST00000288602.6:c.1397G>C	p.Gly466Ala	p.G466A	ENST00000288602	NM_004333.4	466	gGa/gCa	11/18	0.381155057489845	3	FACETS	0.741	0.65	0.838	0.37	0.325	0.419	SUBCLONAL	1	TRUE	1	0.394437861398106	3		595	623	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220578	1220578	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	197	580	0	ENST00000326873.7:c.598-2A>T		p.X200_splice	ENST00000326873	NM_000455.4	200			0.278450032201408	3	FACETS	1	0.985	1			1	CLONAL	2	TRUE	NA	0.394437861398106	3		580	505	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936802	32936802	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	67	539	0	ENST00000380152.3:c.7948G>C	p.Glu2650Gln	p.E2650Q	ENST00000380152		2650	Gaa/Caa	17/27	1	2	FACETS	0.673	0.586	0.767	0.673	0.586	0.767	SUBCLONAL	1	TRUE	1	0.394437861398106	2		539	505	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098975	178098975	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1328994103	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	174	411	0	ENST00000397062.3:c.70T>C	p.Trp24Arg	p.W24R	ENST00000397062	NM_006164.4	24	Tgg/Cgg	2/5	0.389270431137832	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.394437861398106	2		411	426	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027676	48027678	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs587782858	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	68	390	0	ENST00000234420.5:c.2561_2563del	p.Lys854del	p.K854del	ENST00000234420	NM_000179.2	852	AAG/-	4/10	0.394437861398106	5	FACETS	0.802	0.697	0.916	0.201	0.174	0.229	CLONAL	1	TRUE	1	0.394437861398106	5		390	684	SUCCESS
APC	324	MSKCC	GRCh37	5	112164664	112164664	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1060503259	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	28	351	1	ENST00000257430.4:c.1742del	p.Lys581ArgfsTer9	p.K581Rfs*9	ENST00000257430	NM_000038.5	580	Aaa/aa	14/16	0.389270431137832	2	FACETS	0.32	0.255	0.394	0.16	0.127	0.197	SUBCLONAL	1	TRUE	0	0.394437861398106	2		352	444	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295247	1295247	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	47	319	2				ENST00000310581	NM_198253.2	-/1132			0.394437861398106	5	FACETS	0.692	0.584	0.812	0.173	0.146	0.203	SUBCLONAL	1	TRUE	1	0.394437861398106	5		321	548	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489905	2489905	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	195	497	0	ENST00000355716.4:c.302C>T	p.Pro101Leu	p.P101L	ENST00000355716	NM_003820.2	101	cCa/cTa	3/8	0.133738424938904	4	FACETS	1	0.982	1			1	INDETERMINATE	2	TRUE	NA	0.394437861398106	4		497	597	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058650	72058650	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	178	388	0	ENST00000357731.5:c.790C>T	p.Leu264Phe	p.L264F	ENST00000357731	NM_173808.2	264	Ctc/Ttc	6/7	0.394437861398106	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.394437861398106	2		388	432	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551592	150551592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	222	543	0	ENST00000369026.2:c.415G>T	p.Ala139Ser	p.A139S	ENST00000369026	NM_021960.4	139	Gct/Tct	1/3	0.394437861398106	6	FACETS	0.987	0.919	1	0.329	0.306	0.353	CLONAL	2	TRUE	0	0.394437861398106	6		543	1020	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845885	156845885	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	440	740	0	ENST00000524377.1:c.1515C>G	p.Ile505Met	p.I505M	ENST00000524377	NM_002529.3	505	atC/atG	13/17	0.394437861398106	6	FACETS	0.999	0.953	1	0.499	0.476	0.523	CLONAL	3	TRUE	0	0.394437861398106	6		740	1332	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851265	156851265	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	363	512	0	ENST00000524377.1:c.2222C>A	p.Thr741Lys	p.T741K	ENST00000524377	NM_002529.3	741	aCg/aAg	17/17	0.394437861398106	6	FACETS	1	0.988	1	0.557	0.529	0.585	CLONAL	3	TRUE	0	0.394437861398106	6		512	986	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596156	43596156	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	86	506	0	ENST00000355710.3:c.323A>G	p.Lys108Arg	p.K108R	ENST00000355710	NM_020975.4	108	aAg/aGg	2/20	0.381155057489845	3	FACETS	0.854	0.757	0.959	0.427	0.378	0.48	CLONAL	1	TRUE	1	0.394437861398106	3		506	611	SUCCESS
EED	8726	MSKCC	GRCh37	11	85963238	85963238	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	103	566	1	ENST00000263360.6:c.316A>G	p.Lys106Glu	p.K106E	ENST00000263360	NM_003797.3	106	Aaa/Gaa	3/12	0.381155057489845	3	FACETS	0.911	0.816	1	0.456	0.408	0.506	CLONAL	1	TRUE	1	0.394437861398106	3		567	686	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94211990	94211990	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	125	693	2	ENST00000323929.3:c.455A>T	p.His152Leu	p.H152L	ENST00000323929	NM_005591.3	152	cAc/cTc	6/20	0.381155057489845	3	FACETS	0.849	0.768	0.934	0.424	0.384	0.467	CLONAL	1	TRUE	1	0.394437861398106	3		695	894	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	163	752	2	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	0.381155057489845	3	FACETS	0.87	0.797	0.946	0.435	0.398	0.473	CLONAL	1	TRUE	1	0.394437861398106	3		754	1138	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347560	118347560	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	130	514	0	ENST00000534358.1:c.3197C>A	p.Pro1066His	p.P1066H	ENST00000534358	NM_005933.3	1066	cCc/cAc	4/36	0.381155057489845	3	FACETS	1	0.969	1	0.574	0.522	0.63	CLONAL	1	TRUE	1	0.394437861398106	3		514	687	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287411	46287411	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	108	505	0	ENST00000334344.6:c.5272-2A>T		p.X1758_splice	ENST00000334344	NM_152641.2	1758			0.394437861398106	3	FACETS	1	0.906	1	0.504	0.453	0.558	CLONAL	1	TRUE	1	0.394437861398106	3		505	650	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120663	115120663	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	139	770	0	ENST00000257566.3:c.343C>A	p.Gln115Lys	p.Q115K	ENST00000257566	NM_016569.3	115	Cag/Aag	1/8	0.37480022895488	3	FACETS	0.865	0.787	0.948	0.433	0.393	0.474	CLONAL	1	TRUE	1	0.394437861398106	3		770	975	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245293	133245293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	296	656	0	ENST00000320574.5:c.1954G>A	p.Ala652Thr	p.A652T	ENST00000320574	NM_006231.2	652	Gct/Act	18/49	0.37480022895488	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.394437861398106	3		656	820	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562265	21562265	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	159	731	0	ENST00000382592.4:c.1654G>T	p.Glu552Ter	p.E552*	ENST00000382592	NM_014572.2	552	Gag/Tag	4/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.394437861398106	2		731	724	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563212	21563212	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	137	734	0	ENST00000382592.4:c.707G>T	p.Gly236Val	p.G236V	ENST00000382592	NM_014572.2	236	gGt/gTt	4/8	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.394437861398106	2		734	614	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240127	41240127	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	22	92	0	ENST00000379561.5:c.223A>T	p.Ser75Cys	p.S75C	ENST00000379561	NM_002015.3	75	Agc/Tgc	1/3	1	2	FACETS	0.764	0.598	0.952	0.764	0.598	0.952	CLONAL	1	TRUE	1	0.394437861398106	2		92	146	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515352	103515352	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	29	447	0	ENST00000355739.4:c.1853T>C	p.Ile618Thr	p.I618T	ENST00000355739	NM_000123.3	618	aTc/aCc	8/15	1	2	FACETS	0.286	0.229	0.351	0.286	0.229	0.351	SUBCLONAL	1	TRUE	1	0.394437861398106	2		447	514	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515442	103515442	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	75	341	0	ENST00000355739.4:c.1943G>C	p.Ser648Thr	p.S648T	ENST00000355739	NM_000123.3	648	aGt/aCt	8/15	1	2	FACETS	0.946	0.833	1	0.946	0.833	1	CLONAL	1	TRUE	1	0.394437861398106	2		341	402	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610405	81610405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	117	575	1	ENST00000298171.2:c.2003C>T	p.Pro668Leu	p.P668L	ENST00000298171	NM_000369.2	668	cCa/cTa	10/10	0.37480022895488	3	FACETS	1	0.926	1	0.515	0.465	0.568	CLONAL	1	TRUE	1	0.394437861398106	3		576	689	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122253	2122253	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs45462192	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	216	582	0	ENST00000219476.3:c.2109G>A	p.Trp703Ter	p.W703*	ENST00000219476	NM_000548.3	703	tgG/tgA	20/42	0.348742108585221	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.394437861398106	3		582	619	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654705	67654705	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	108	647	0	ENST00000264010.4:c.1192A>G	p.Met398Val	p.M398V	ENST00000264010	NM_006565.3	398	Atg/Gtg	6/12	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.394437861398106	2		647	535	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992672	72992672	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1474036205	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	66	598	0	ENST00000268489.5:c.1373C>T	p.Pro458Leu	p.P458L	ENST00000268489	NM_006885.3	458	cCa/cTa	2/10	1	2	FACETS	0.7	0.609	0.798	0.7	0.609	0.798	SUBCLONAL	1	TRUE	1	0.394437861398106	2		598	478	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29662047	29662047	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1567615941	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	91	502	0	ENST00000356175.3:c.5941C>T	p.Gln1981Ter	p.Q1981*	ENST00000356175	NM_000267.3	1981	Cag/Tag	39/57	0.344310552678133	3	FACETS	0.983	0.875	1			1	CLONAL	1	TRUE	NA	0.394437861398106	3		502	562	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683983	29683983	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	232	754	0	ENST00000356175.3:c.7681C>T	p.Gln2561Ter	p.Q2561*	ENST00000356175	NM_000267.3	2561	Cag/Tag	52/57	0.344310552678133	3	FACETS	0.902	0.843	0.961			1	CLONAL	2	TRUE	NA	0.394437861398106	3		754	781	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858120	40858120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	159	715	1	ENST00000428826.2:c.1744G>A	p.Asp582Asn	p.D582N	ENST00000428826		582	Gac/Aac	16/21	1	2	FACETS	0.859	0.787	0.934	0.859	0.787	0.934	CLONAL	1	TRUE	1	0.394437861398106	2		716	939	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226398	41226398	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs41293457	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	161	783	0	ENST00000357654.3:c.4625C>G	p.Ser1542Cys	p.S1542C	ENST00000357654	NM_007294.3	1542	tCt/tGt	14/23	1	2	FACETS	0.938	0.861	1	0.938	0.861	1	CLONAL	1	TRUE	1	0.394437861398106	2		783	870	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376212	15376212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	58	341	0	ENST00000263377.2:c.802del	p.Val268TyrfsTer15	p.V268Yfs*15	ENST00000263377	NM_058243.2	268	Gta/ta	5/20	0.389270431137832	2	FACETS	0.828	0.715	0.95	0.414	0.357	0.475	CLONAL	1	TRUE	0	0.394437861398106	2		341	355	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723068	52723068	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1486388431	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	57	404	0	ENST00000322088.6:c.1253G>A	p.Arg418Gln	p.R418Q	ENST00000322088	NM_014225.5	418	cGg/cAg	10/15	0.37480022895488	3	FACETS	0.688	0.591	0.794	0.344	0.295	0.397	SUBCLONAL	1	TRUE	1	0.394437861398106	3		404	503	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455173	29455173	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746442213	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	97	446	0	ENST00000389048.3:c.2629G>A	p.Ala877Thr	p.A877T	ENST00000389048	NM_004304.4	877	Gca/Aca	15/29	0.37480022895488	3	FACETS	1	0.945	1	0.544	0.486	0.605	CLONAL	1	TRUE	1	0.394437861398106	3		446	541	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574119	46574119	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	75	664	0	ENST00000263734.3:c.134A>G	p.His45Arg	p.H45R	ENST00000263734	NM_001430.4	45	cAc/cGc	2/16	0.394437861398106	5	FACETS	0.664	0.58	0.754	0.166	0.145	0.189	SUBCLONAL	1	TRUE	1	0.394437861398106	5		664	912	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46603815	46603815	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	117	650	1	ENST00000263734.3:c.1172C>A	p.Thr391Asn	p.T391N	ENST00000263734	NM_001430.4	391	aCc/aAc	9/16	0.394437861398106	5	FACETS	0.904	0.813	1	0.226	0.203	0.25	CLONAL	1	TRUE	1	0.394437861398106	5		651	1045	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593669	215593669	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	161	438	0	ENST00000260947.4:c.2065G>C	p.Asp689His	p.D689H	ENST00000260947	NM_000465.2	689	Gac/Cac	11/11	0.389270431137832	2	FACETS	0.907	0.84	0.976	0.907	0.84	0.976	CLONAL	2	TRUE	0	0.394437861398106	2		438	450	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054189	30054189	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	77	431	0	ENST00000338641.4:c.611A>G	p.Glu204Gly	p.E204G	ENST00000338641	NM_000268.3	204	gAa/gGa	7/16	0.394437861398106	3	FACETS	0.966	0.85	1	0.322	0.283	0.363	CLONAL	1	TRUE	0	0.394437861398106	3		431	484	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880886	134880886	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	196	532	0	ENST00000398015.3:c.1449G>T	p.Met483Ile	p.M483I	ENST00000398015	NM_004441.4	483	atG/atT	7/16	0.389270431137832	2	FACETS	0.924	0.862	0.987	0.924	0.862	0.987	CLONAL	2	TRUE	0	0.394437861398106	2		532	538	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665061	182665061	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	133	724	0	ENST00000292782.4:c.665T>C	p.Met222Thr	p.M222T	ENST00000292782	NM_020640.2	222	aTg/aCg	6/7	0.389270431137832	2	FACETS	0.903	0.821	0.989	0.451	0.41	0.495	CLONAL	1	TRUE	0	0.394437861398106	2		724	747	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167696	185167696	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	241	569	0	ENST00000265026.3:c.1019G>T	p.Gly340Val	p.G340V	ENST00000265026	NM_004721.4	340	gGa/gTa	6/14	0.389270431137832	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.394437861398106	2		569	601	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542342	187542342	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	55	387	0	ENST00000441802.2:c.5398G>T	p.Asp1800Tyr	p.D1800Y	ENST00000441802	NM_005245.3	1800	Gat/Tat	10/27	0.37480022895488	3	FACETS	0.795	0.682	0.918	0.397	0.341	0.459	CLONAL	1	TRUE	1	0.394437861398106	3		387	420	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557177	187557177	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	82	465	0	ENST00000441802.2:c.4183+2T>C		p.X1395_splice	ENST00000441802	NM_005245.3	1395			0.37480022895488	3	FACETS	0.929	0.821	1	0.464	0.41	0.522	CLONAL	1	TRUE	1	0.394437861398106	3		465	536	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959914	38959914	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	74	463	0	ENST00000357387.3:c.2018T>C	p.Val673Ala	p.V673A	ENST00000357387	NM_152756.3	673	gTt/gCt	21/38	0.394437861398106	5	FACETS	0.941	0.824	1	0.235	0.206	0.267	CLONAL	1	TRUE	1	0.394437861398106	5		463	635	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39002649	39002649	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	226	562	0	ENST00000357387.3:c.380A>G	p.Tyr127Cys	p.Y127C	ENST00000357387	NM_152756.3	127	tAt/tGt	5/38	0.389270431137832	2	FACETS	1	0.989	1	0.644	0.6	0.688	CLONAL	1	TRUE	0	0.394437861398106	2		562	890	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562742	176562742	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	504	789	0	ENST00000439151.2:c.638G>T	p.Ser213Ile	p.S213I	ENST00000439151	NM_022455.4	213	aGc/aTc	2/23	0.344310552678133	3	FACETS	0.973	0.936	1			1	CLONAL	3	TRUE	NA	0.394437861398106	3		789	1048	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964470	93964470	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	107	616	0	ENST00000369303.4:c.2427G>C	p.Gln809His	p.Q809H	ENST00000369303	NM_004440.3	809	caG/caC	14/17	0.381155057489845	3	FACETS	0.948	0.851	1	0.474	0.425	0.526	CLONAL	1	TRUE	1	0.394437861398106	3		616	685	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642549	117642549	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867259158	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	120	738	0	ENST00000368508.3:c.5650A>G	p.Arg1884Gly	p.R1884G	ENST00000368508	NM_002944.2	1884	Aga/Gga	35/43	0.381155057489845	3	FACETS	0.742	0.669	0.819	0.371	0.334	0.41	SUBCLONAL	1	TRUE	1	0.394437861398106	3		738	982	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962396	2962396	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	62	493	0	ENST00000396946.4:c.2143-2A>C		p.X715_splice	ENST00000396946	NM_032415.4	715			0.394437861398106	1	FACETS	0.636	0.551	0.727	0.636	0.551	0.727	SUBCLONAL	1	TRUE	0	0.394437861398106	1		493	397	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508158	106508158	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs144650421	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	37	235	0	ENST00000359195.3:c.152G>T	p.Cys51Phe	p.C51F	ENST00000359195	NM_002649.2	51	tGc/tTc	2/11	0.381155057489845	3	FACETS	1	0.884	1	0.54	0.449	0.639	CLONAL	1	TRUE	1	0.394437861398106	3		235	208	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570329	87570329	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	94	672	0	ENST00000277120.3:c.2069A>G	p.His690Arg	p.H690R	ENST00000277120		690	cAc/cGc	17/19	0.394437861398106	2	FACETS	0.813	0.725	0.907	0.407	0.362	0.454	CLONAL	1	TRUE	0	0.394437861398106	2		672	586	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782740	135782742	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	366	527	0	ENST00000298552.3:c.1279_1281del	p.Ser427del	p.S427del	ENST00000298552	NM_001162426.1	427	TCT/-	13/23	0.394437861398106	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	TRUE	0	0.394437861398106	3		527	725	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321322	1321322	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	251	576	0	ENST00000400841.2:c.433G>T	p.Asp145Tyr	p.D145Y	ENST00000400841		145	Gat/Tat	4/6	0.178491155907054	3	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.394437861398106	3		576	620	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345936	70345936	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	269	310	0	ENST00000374080.3:c.2473A>T	p.Thr825Ser	p.T825S	ENST00000374080		825	Act/Tct	18/45	0.178491155907054	3	FACETS	0.889	0.848	0.931			1	INDETERMINATE	4	TRUE	NA	0.394437861398106	3		310	459	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592724	28592725	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AC	AC	T	novel	NA	P-0016171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	111	533	0	ENST00000241453.7:c.2420_2421delinsA	p.Cys807Ter	p.C807*	ENST00000241453	NM_004119.2	807	tGT/tA	20/24	1	2	FACETS	0.912	0.822	1	0.912	0.822	1	CLONAL	1	TRUE	1	0.394437861398106	2		533	617	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40367491	40367491	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	10	30	0	ENST00000397332.2:c.70G>T	p.Gly24Cys	p.G24C	ENST00000397332	NM_001033082.2	24	Ggc/Tgc	1/3	1	2	FACETS	0.968	0.672	1	0.968	0.672	1	CLONAL	1	TRUE	1	0.39	2		30	53	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318761	163318761	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	136	723	0	ENST00000271452.3:c.1151G>T	p.Arg384Ile	p.R384I	ENST00000271452	NM_145697.2	384	aGa/aTa	13/14	0.30206164945731	6	FACETS	1	0.971	1	0.233	0.211	0.256	CLONAL	1	TRUE	1	0.39	6		723	1064	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106098	8106098	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	79	438	0	ENST00000346208.3:c.918G>T	p.Arg306Ser	p.R306S	ENST00000346208		306	agG/agT	4/6	0.206553378698032	4	FACETS	0.838	0.737	0.946	0.419	0.368	0.473	INDETERMINATE	1	TRUE	2	0.39	4		438	672	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852781	63852781	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1255716370	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	50	436	0	ENST00000279873.7:c.3559A>G	p.Lys1187Glu	p.K1187E	ENST00000279873	NM_032199.2	1187	Aaa/Gaa	10/10	0.208621485666639	2	FACETS	0.485	0.411	0.566	0.242	0.205	0.283	INDETERMINATE	1	TRUE	0	0.39	2		436	529	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310883	123310883	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	142	456	0	ENST00000358487.5:c.545G>T	p.Gly182Val	p.G182V	ENST00000358487	NM_000141.4	182	gGg/gTg	5/18	0.208621485666639	2	FACETS	1	0.986	1	0.695	0.637	0.755	INDETERMINATE	1	TRUE	0	0.39	2		456	524	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589655	69589655	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	26	119	0	ENST00000168712.1:c.198G>T	p.Glu66Asp	p.E66D	ENST00000168712	NM_002007.2	66	gaG/gaT	1/3	0.206553378698032	4	FACETS	1	0.836	1	0.527	0.42	0.646	INDETERMINATE	1	TRUE	2	0.39	4		119	176	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148933	119148933	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	179	611	0	ENST00000264033.4:c.1153G>T	p.Ala385Ser	p.A385S	ENST00000264033	NM_005188.3	385	Gct/Tct	8/16	0.206553378698032	4	FACETS	0.926	0.857	0.998	0.926	0.857	0.998	INDETERMINATE	2	TRUE	2	0.39	4		611	689	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	256	791	1	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.244090126631814	3	FACETS	0.834	0.782	0.888	0.834	0.782	0.888	CLONAL	2	TRUE	1	0.39	3		792	940	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134018	41134018	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	64	344	0	ENST00000379561.5:c.1610G>T	p.Arg537Leu	p.R537L	ENST00000379561	NM_002015.3	537	cGt/cTt	2/3	0.167353714494552	4	FACETS	0.945	0.82	1	0.472	0.41	0.54	INDETERMINATE	1	TRUE	2	0.39	4		344	483	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437878	110437878	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1213249755	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	19	84	2	ENST00000375856.3:c.523G>T	p.Ala175Ser	p.A175S	ENST00000375856	NM_003749.2	175	Gcc/Tcc	1/2	0.167353714494552	4	FACETS	0.928	0.71	1	0.464	0.355	0.589	INDETERMINATE	1	TRUE	2	0.39	4		86	146	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726646	88726646	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	A	novel	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	79	468	0	ENST00000360948.2:c.395+3G>T		p.X132_splice	ENST00000360948	NM_001012338.2	132			0.30206164945731	2	FACETS	0.904	0.799	1	0.452	0.399	0.509	CLONAL	1	TRUE	0	0.39	2		468	448	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81971386	81971386	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs774452862	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	51	535	0	ENST00000359376.3:c.3076G>T	p.Ala1026Ser	p.A1026S	ENST00000359376	NM_002661.3	1026	Gca/Tca	28/33	0.167353714494552	4	FACETS	0.552	0.469	0.645	0.276	0.234	0.323	INDETERMINATE	1	TRUE	2	0.39	4		535	658	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057520005	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	361	765	0	ENST00000269305.4:c.820G>T	p.Val274Phe	p.V274F	ENST00000269305	NM_001126112.2	274	Gtt/Ttt	8/11	0.18649262225826	3	FACETS	1	0.992	1	0.809	0.769	0.848	INDETERMINATE	2	TRUE	0	0.39	3		765	912	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559143	29559151	+	inframe_deletion	In_Frame_Del	DEL	CCTCTGCAG	CCTCTGCAG	-	novel	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	85	358	0	ENST00000356175.3:c.3253_3261del	p.Leu1085_Pro1087del	p.L1085_P1087del	ENST00000356175	NM_000267.3	1084	CCTCTGCAG/-	25/57	0.18649262225826	3	FACETS	1	0.948	1	0.373	0.331	0.418	INDETERMINATE	1	TRUE	0	0.39	3		358	465	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58711260	58711260	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	263	651	1	ENST00000305921.3:c.748C>T	p.Arg250Ter	p.R250*	ENST00000305921	NM_003620.3	250	Cga/Tga	3/6	0.18649262225826	3	FACETS	0.927	0.871	0.985	0.618	0.581	0.657	INDETERMINATE	2	TRUE	0	0.39	3		652	869	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942170	17942170	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	75	485	0	ENST00000458235.1:c.2845G>T	p.Asp949Tyr	p.D949Y	ENST00000458235	NM_000215.3	949	Gac/Tac	21/24	0.11856218125961	3	FACETS	0.74	0.649	0.838	0.247	0.216	0.28	INDETERMINATE	1	TRUE	0	0.39	3		485	621	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463268	25463268	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs749282210	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	46	526	0	ENST00000264709.3:c.2225G>C	p.Arg742Pro	p.R742P	ENST00000264709	NM_175629.2	742	cGg/cCg	19/23	1	2	FACETS	0.353	0.296	0.415	0.353	0.296	0.415	SUBCLONAL	1	TRUE	1	0.39	2		526	669	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652843	212652843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	38	551	0	ENST00000342788.4:c.463C>T	p.Leu155Phe	p.L155F	ENST00000342788	NM_005235.2	155	Ctt/Ttt	4/28	0.30206164945731	4	FACETS	0.369	0.303	0.442	0.123	0.101	0.148	SUBCLONAL	1	TRUE	1	0.39	4		551	735	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458235	12458235	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	263	496	0	ENST00000287820.6:c.852G>A	p.Met284Ile	p.M284I	ENST00000287820	NM_015869.4	284	atG/atA	6/7	0.279125111682043	3	FACETS	1	0.989	1	0.797	0.752	0.843	CLONAL	2	TRUE	0	0.39	3		496	674	SUCCESS
ATR	545	MSKCC	GRCh37	3	142286997	142286997	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	159	441	0	ENST00000350721.4:c.60-1G>C		p.X20_splice	ENST00000350721	NM_001184.3	20			0.11856218125961	3	FACETS	0.809	0.745	0.876	0.54	0.497	0.584	INDETERMINATE	2	TRUE	0	0.39	3		441	602	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956195	55956195	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	112	597	0	ENST00000263923.4:c.3120C>A	p.Asn1040Lys	p.N1040K	ENST00000263923	NM_002253.2	1040	aaC/aaA	23/30	0.160881758597329	2	FACETS	0.66	0.593	0.731	0.33	0.296	0.366	INDETERMINATE	1	TRUE	0	0.39	2		597	870	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157911	106157911	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	74	418	0	ENST00000380013.4:c.2812A>T	p.Thr938Ser	p.T938S	ENST00000380013	NM_001127208.2	938	Act/Tct	3/11	0.160881758597329	2	FACETS	0.639	0.56	0.724	0.319	0.28	0.362	INDETERMINATE	1	TRUE	0	0.39	2		418	594	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094924	143094924	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	46	493	0	ENST00000262992.4:c.1220C>G	p.Thr407Arg	p.T407R	ENST00000262992	NM_001101669.1	407	aCa/aGa	14/24	0.160881758597329	2	FACETS	0.401	0.337	0.472	0.201	0.168	0.236	INDETERMINATE	1	TRUE	0	0.39	2		493	588	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1255515	1255515	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	99	470	0	ENST00000310581.5:c.3044G>T	p.Cys1015Phe	p.C1015F	ENST00000310581	NM_198253.2	1015	tGt/tTt	14/16	0.30206164945731	9	FACETS	1	0.951	1			1	CLONAL	1	TRUE	NA	0.39	9		470	1070	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526384	31526384	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	509	929	0	ENST00000344624.3:c.656G>T	p.Arg219Ile	p.R219I	ENST00000344624		219	aGa/aTa	2/33	0.30206164945731	5	FACETS	0.981	0.94	1	0.981	0.94	1	CLONAL	3	TRUE	2	0.39	5		929	1406	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876172	35876172	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	331	491	0	ENST00000303115.3:c.964G>C	p.Gly322Arg	p.G322R	ENST00000303115	NM_002185.3	322	Ggt/Cgt	8/8	0.30206164945731	5	FACETS	0.982	0.931	1	0.982	0.931	1	CLONAL	3	TRUE	2	0.39	5		491	913	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	72	305	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.18649262225826	3	FACETS	0.663	0.579	0.753	0.221	0.193	0.251	INDETERMINATE	1	TRUE	0	0.39	3		305	666	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673436	30673436	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	79	442	0	ENST00000376406.3:c.3524A>T	p.Asp1175Val	p.D1175V	ENST00000376406	NM_014641.2	1175	gAc/gTc	10/15	0.167353714494552	4	FACETS	0.887	0.78	1	0.443	0.39	0.501	INDETERMINATE	1	TRUE	2	0.39	4		442	635	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967900	93967900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373761211	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	94	691	1	ENST00000369303.4:c.2027G>A	p.Arg676Lys	p.R676K	ENST00000369303	NM_004440.3	676	aGg/aAg	11/17	0.160881758597329	2	FACETS	0.636	0.566	0.711	0.318	0.283	0.356	INDETERMINATE	1	TRUE	0	0.39	2		692	758	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739753	41739753	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	63	614	0	ENST00000242208.4:c.220G>T	p.Val74Phe	p.V74F	ENST00000242208	NM_002192.2	74	Gtc/Ttc	2/3	0.167353714494552	4	FACETS	0.544	0.47	0.626	0.272	0.235	0.313	INDETERMINATE	1	TRUE	2	0.39	4		614	825	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389359	8389359	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	88	596	1	ENST00000356435.5:c.4259G>T	p.Arg1420Met	p.R1420M	ENST00000356435		1420	aGg/aTg	26/35	0.167353714494552	4	FACETS	0.82	0.726	0.921	0.41	0.363	0.461	INDETERMINATE	1	TRUE	2	0.39	4		597	765	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485815	8485815	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	94	297	0	ENST00000356435.5:c.3002G>T	p.Gly1001Val	p.G1001V	ENST00000356435		1001	gGg/gTg	17/35	0.167353714494552	4	FACETS	0.765	0.684	0.85	0.765	0.684	0.85	INDETERMINATE	2	TRUE	2	0.39	4		297	438	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528612	8528612	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	84	452	2	ENST00000356435.5:c.520C>A	p.Arg174Ser	p.R174S	ENST00000356435		174	Cgt/Agt	4/35	0.167353714494552	4	FACETS	0.936	0.827	1	0.468	0.413	0.526	INDETERMINATE	1	TRUE	2	0.39	4		454	640	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528672	8528672	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	72	363	1	ENST00000356435.5:c.460G>T	p.Asp154Tyr	p.D154Y	ENST00000356435		154	Gat/Tat	4/35	0.167353714494552	4	FACETS	0.888	0.776	1	0.444	0.388	0.504	INDETERMINATE	1	TRUE	2	0.39	4		364	578	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750337	133750337	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	88	532	0	ENST00000318560.5:c.1168G>A	p.Gly390Arg	p.G390R	ENST00000318560	NM_005157.4	390	Ggg/Agg	7/11	0.11856218125961	3	FACETS	0.828	0.734	0.929	0.276	0.244	0.31	INDETERMINATE	1	TRUE	0	0.39	3		532	651	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038822	47038822	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	104	678	0	ENST00000377604.3:c.829C>T	p.Gln277Ter	p.Q277*	ENST00000377604	NM_001204468.1	277	Cag/Tag	9/24	0.131466905184634	0	FACETS	0.639	0.575	0.707			1	INDETERMINATE	1	TRUE	0	0.39	0		678	509	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223539	53223539	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	55	386	0	ENST00000375401.3:c.3820G>C	p.Glu1274Gln	p.E1274Q	ENST00000375401	NM_004187.3	1274	Gag/Cag	23/26	0.131466905184634	0	FACETS	0.482	0.414	0.556			1	INDETERMINATE	1	TRUE	0	0.39	0		386	357	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763931	76763931	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	82	524	0	ENST00000373344.5:c.7377G>T	p.Met2459Ile	p.M2459I	ENST00000373344	NM_000489.3	2459	atG/atT	35/35	0.131466905184634	0	FACETS	0.472	0.417	0.531			1	INDETERMINATE	1	TRUE	0	0.39	0		524	543	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0016173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	364	509	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.325124417377469	3	FACETS	0.963	0.917	1	0.963	0.917	1	CLONAL	3	TRUE	0	0.342557086929005	3		509	862	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923160	48923160	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587776789	NA	P-0016173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	92	425	0	ENST00000267163.4:c.607+1G>T		p.X203_splice	ENST00000267163	NM_000321.2	203			0.181363820751392	3	FACETS	0.837	0.749	0.928	0.837	0.749	0.928	INDETERMINATE	2	TRUE	1	0.342557086929005	3		425	376	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335667	81335667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	85	643	0	ENST00000222390.5:c.1693C>T	p.Leu565Phe	p.L565F	ENST00000222390	NM_000601.4	565	Ctc/Ttc	15/18	0.193075006549694	5	FACETS	1	0.906	1	0.343	0.303	0.386	INDETERMINATE	1	TRUE	2	0.342557086929005	5		643	730	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505595	186505595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	62	402	1	ENST00000323963.5:c.1003C>T	p.Arg335Cys	p.R335C	ENST00000323963		335	Cgc/Tgc	10/11	0.342557086929005	3	FACETS	0.784	0.677	0.899	0.392	0.338	0.45	SUBCLONAL	1	TRUE	1	0.342557086929005	3		403	541	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925711	114925711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752060378	NA	P-0016173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	33	490	0	ENST00000543371.1:c.1789G>A	p.Val597Ile	p.V597I	ENST00000543371	NM_001198531.1	597	Gtc/Atc	14/14	NA	2	FACETS	0.315	0.256	0.383			1	INDETERMINATE	1	TRUE	NA	0.342557086929005	2		490	611	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267359	198267359	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs377023736	NA	P-0016173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	186	908	0	ENST00000335508.6:c.1998G>T	p.Lys666Asn	p.K666N	ENST00000335508	NM_012433.2	666	aaG/aaT	14/25	0.181363820751392	3	FACETS	0.809	0.749	0.872	0.809	0.749	0.872	INDETERMINATE	2	TRUE	1	0.342557086929005	3		908	786	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291782	15291782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs940948912	NA	P-0016173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	62	619	0	ENST00000263388.2:c.2984C>T	p.Pro995Leu	p.P995L	ENST00000263388	NM_000435.2	995	cCg/cTg	18/33	0.324289265942085	2	FACETS	0.852	0.738	0.974	0.426	0.369	0.487	CLONAL	1	TRUE	0	0.342557086929005	2		619	425	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317040	11317040	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763938203	NA	P-0016173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	232	432	3	ENST00000361445.4:c.454G>A	p.Ala152Thr	p.A152T	ENST00000361445	NM_004958.3	152	Gcc/Acc	4/58	0.271966121682012	3	FACETS	0.849	0.797	0.902	0.849	0.797	0.902	CLONAL	3	TRUE	0	0.342557086929005	3		435	623	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803598	43803598	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	22	517	2	ENST00000372470.3:c.79G>A	p.Asp27Asn	p.D27N	ENST00000372470	NM_005373.2	27	Gat/Aat	1/12	0.271966121682012	3	FACETS	0.347	0.268	0.439	0.116	0.089	0.147	SUBCLONAL	1	TRUE	0	0.342557086929005	3		519	434	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741616	17741616	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	60	241	0	ENST00000250003.3:c.287G>T	p.Trp96Leu	p.W96L	ENST00000250003	NM_002478.4	96	tGg/tTg	1/3	0.266364698170207	3	FACETS	1	0.966	1	0.693	0.602	0.791	CLONAL	1	TRUE	1	0.342557086929005	3		241	296	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242706	46242706	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	231	511	0	ENST00000334344.6:c.1668A>T	p.Leu556Phe	p.L556F	ENST00000334344	NM_152641.2	556	ttA/ttT	13/21	0.325124417377469	3	FACETS	0.908	0.853	0.963	0.908	0.853	0.963	CLONAL	3	TRUE	0	0.342557086929005	3		511	580	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914267	32914267	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	109	525	0	ENST00000380152.3:c.5775G>T	p.Gln1925His	p.Q1925H	ENST00000380152		1925	caG/caT	11/27	0.181363820751392	3	FACETS	1	0.978	1	0.664	0.598	0.734	INDETERMINATE	1	TRUE	1	0.342557086929005	3		525	561	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944663	32944663	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1555287655	NA	P-0016173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	138	554	0	ENST00000380152.3:c.8456A>T	p.Asp2819Val	p.D2819V	ENST00000380152		2819	gAt/gTt	19/27	0.181363820751392	3	FACETS	1	0.986	1	0.735	0.671	0.802	INDETERMINATE	1	TRUE	1	0.342557086929005	3		554	642	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724576	43724576	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	89	786	1	ENST00000382044.4:c.3491G>T	p.Cys1164Phe	p.C1164F	ENST00000382044	NM_001141980.1	1164	tGt/tTt	17/28	1	2	FACETS	0.711	0.63	0.797	0.711	0.63	0.797	SUBCLONAL	1	TRUE	1	0.342557086929005	2		787	731	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678508	88678508	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs183806623	NA	P-0016173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	63	439	3	ENST00000360948.2:c.1028G>T	p.Arg343Leu	p.R343L	ENST00000360948	NM_001012338.2	343	cGg/cTg	9/19	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.342557086929005	2		442	349	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226265	2226265	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0016173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	104	526	0	ENST00000326181.6:c.1879-1G>T		p.X627_splice	ENST00000326181	NM_032271.2	627			0.181363820751392	3	FACETS	1	0.975	1	0.643	0.577	0.712	INDETERMINATE	1	TRUE	1	0.342557086929005	3		526	553	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972403	81972403	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	G	novel	NA	P-0016173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	75	357	0	ENST00000359376.3:c.3199-3C>G		p.X1067_splice	ENST00000359376	NM_002661.3	1067			0.181363820751392	3	FACETS	1	0.886	1	0.505	0.443	0.571	INDETERMINATE	1	TRUE	1	0.342557086929005	3		357	508	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046263	128046263	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1308398082	NA	P-0016173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	108	509	2	ENST00000285398.2:c.1000C>T	p.Arg334Cys	p.R334C	ENST00000285398	NM_000122.1	334	Cgt/Tgt	7/15	0.181363820751392	3	FACETS	0.965	0.867	1	0.483	0.433	0.535	INDETERMINATE	1	TRUE	1	0.342557086929005	3		511	765	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743901	40743901	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	122	590	0	ENST00000373198.4:c.3094G>T	p.Val1032Phe	p.V1032F	ENST00000373198	NM_133170.3	1032	Gtc/Ttc	23/32	0.342557086929005	3	FACETS	1	0.968	1	0.579	0.524	0.638	CLONAL	1	TRUE	1	0.342557086929005	3		590	720	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72873629	72873629	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1197235374	NA	P-0016173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	76	567	0	ENST00000325599.8:c.673A>G	p.Lys225Glu	p.K225E	ENST00000325599	NM_018130.2	225	Aaa/Gaa	6/11	0.185368990056274	3	FACETS	0.719	0.63	0.815	0.24	0.21	0.272	INDETERMINATE	1	TRUE	0	0.342557086929005	3		567	723	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391007	89391007	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	67	596	0	ENST00000336596.2:c.1073C>A	p.Thr358Asn	p.T358N	ENST00000336596	NM_005233.5	358	aCc/aAc	5/17	0.185368990056274	3	FACETS	0.685	0.595	0.783	0.228	0.198	0.261	INDETERMINATE	1	TRUE	0	0.342557086929005	3		596	669	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84406209	84406209	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	86	379	0	ENST00000321945.7:c.17C>A	p.Thr6Lys	p.T6K	ENST00000321945	NM_139076.2	6	aCg/aAg	1/9	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.342557086929005	2		379	418	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526324	31526324	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	147	731	0	ENST00000344624.3:c.716G>T	p.Gly239Val	p.G239V	ENST00000344624		239	gGg/gTg	2/33	0.342557086929005	3	FACETS	1	0.921	1	0.505	0.46	0.552	CLONAL	1	TRUE	1	0.342557086929005	3		731	995	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514333	149514333	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	66	402	1	ENST00000261799.4:c.611A>T	p.Tyr204Phe	p.Y204F	ENST00000261799	NM_002609.3	204	tAc/tTc	4/23	0.104204861916331	0	FACETS	0.572	0.498	0.652			1	INDETERMINATE	1	TRUE	0	0.342557086929005	0		403	443	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707798	176707798	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	121	500	0	ENST00000439151.2:c.5855G>T	p.Arg1952Leu	p.R1952L	ENST00000439151	NM_022455.4	1952	cGg/cTg	18/23	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.342557086929005	2		500	642	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168950	32168950	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	336	686	0	ENST00000375023.3:c.4083G>C	p.Glu1361Asp	p.E1361D	ENST00000375023	NM_004557.3	1361	gaG/gaC	22/30	0.342557086929005	4	FACETS	0.95	0.901	1	1	0.994	1	CLONAL	3	TRUE	2	0.342557086929005	4		686	924	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117730786	117730786	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	212	569	0	ENST00000368508.3:c.248G>T	p.Gly83Val	p.G83V	ENST00000368508	NM_002944.2	83	gGc/gTc	4/43	0.223624892661137	2	FACETS	0.921	0.86	0.984	0.921	0.86	0.984	CLONAL	2	TRUE	0	0.342557086929005	2		569	672	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367257	50367257	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1245618829	NA	P-0016173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	73	376	0	ENST00000331340.3:c.64G>C	p.Asp22His	p.D22H	ENST00000331340	NM_006060.4	22	Gat/Cat	3/8	0.193075006549694	5	FACETS	1	0.954	1	0.398	0.348	0.451	INDETERMINATE	1	TRUE	2	0.342557086929005	5		376	541	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945044	151945044	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764420905	NA	P-0016173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	26	458	0	ENST00000262189.6:c.2475G>T	p.Met825Ile	p.M825I	ENST00000262189	NM_170606.2	825	atG/atT	14/59	0.193075006549694	5	FACETS	0.487	0.385	0.604	0.162	0.128	0.202	INDETERMINATE	1	TRUE	2	0.342557086929005	5		458	472	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741634	145741634	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	182	624	0	ENST00000428558.2:c.869G>T	p.Gly290Val	p.G290V	ENST00000428558	NM_004260.3	290	gGg/gTg	5/22	0.342557086929005	7	FACETS	0.974	0.898	1	0.389	0.359	0.421	CLONAL	2	TRUE	2	0.342557086929005	7		624	1013	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518262	8518262	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	173	294	0	ENST00000356435.5:c.1129C>A	p.Arg377Ser	p.R377S	ENST00000356435		377	Cgc/Agc	10/35	0.30037447849602	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	3	TRUE	0	0.342557086929005	3		294	378	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403335	139403335	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	156	421	0	ENST00000277541.6:c.3158G>T	p.Gly1053Val	p.G1053V	ENST00000277541	NM_017617.3	1053	gGc/gTc	19/34	0.30037447849602	3	FACETS	0.914	0.848	0.982	0.914	0.848	0.982	CLONAL	3	TRUE	0	0.342557086929005	3		421	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579376	+	missense_variant	Missense_Mutation	TNP	CCT	CCT	ACA	novel	NA	P-0016173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	607	226	0	ENST00000269305.4:c.311_313delinsTGT	p.Gln104_Gly105delinsLeuCys	p.Q104_G105delinsLC	ENST00000269305	NM_001126112.2	104	cAGGgc/cTGTgc	4/11	0.330819854951728	2	FACETS	0.876	0.849	0.903	1	0.998	1	CLONAL	4	TRUE	0	0.342557086929005	2		226	1011	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0016175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	557	2255	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.375368857031826	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	TRUE	1	0.379968616372753	4		2255	1331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0016175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	362	710	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.304993331495482	2	FACETS	0.951	0.904	0.999	0.951	0.904	0.999	CLONAL	2	TRUE	0	0.379968616372753	2		710	1002	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576120	88576120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147160868	NA	P-0016175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	114	706	0	ENST00000360948.2:c.1553G>A	p.Arg518His	p.R518H	ENST00000360948	NM_001012338.2	518	cGt/cAt	13/19	1	2	FACETS	0.71	0.639	0.786	0.71	0.639	0.786	SUBCLONAL	1	TRUE	1	0.379968616372753	2		706	845	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221228	1221228	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	155	700	0	ENST00000326873.7:c.751G>T	p.Gly251Cys	p.G251C	ENST00000326873	NM_000455.4	251	Ggt/Tgt	6/10	0.35584455341205	1	FACETS	0.729	0.668	0.794	0.729	0.668	0.794	SUBCLONAL	1	TRUE	0	0.379968616372753	1		700	906	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615044	43615044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	109	629	0	ENST00000355710.3:c.2458C>T	p.Arg820Cys	p.R820C	ENST00000355710	NM_020975.4	820	Cgc/Tgc	14/20	1	2	FACETS	0.821	0.738	0.909	0.821	0.738	0.909	CLONAL	1	TRUE	1	0.379968616372753	2		629	699	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998264	100998264	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	47	195	0	ENST00000325455.5:c.1538C>A	p.Pro513His	p.P513H	ENST00000325455	NM_001202474.3	513	cCt/cAt	1/8	1	2	FACETS	0.896	0.762	1	0.896	0.762	1	CLONAL	1	TRUE	1	0.379968616372753	2		195	276	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702643	52702643	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0016175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	164	495	0	ENST00000394830.3:c.255T>A	p.Tyr85Ter	p.Y85*	ENST00000394830	NM_018313.4	85	taT/taA	4/30	0.35584455341205	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.379968616372753	1		495	638	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515154	31515154	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	299	798	0	ENST00000344624.3:c.1231G>T	p.Val411Leu	p.V411L	ENST00000344624		411	Gtg/Ttg	5/33	0.164669987627367	3	FACETS	0.778	0.733	0.825	0.778	0.733	0.825	INDETERMINATE	2	TRUE	1	0.379968616372753	3		798	1203	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69000039	69000039	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	465	481	0	ENST00000288368.4:c.2108G>T	p.Gly703Val	p.G703V	ENST00000288368	NM_024870.2	703	gGa/gTa	19/40	0.379968616372753	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	1	0.379968616372753	4		481	1058	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636316	21636316	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0016175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	118	591	0	ENST00000421138.2:c.694A>T	p.Arg232Ter	p.R232*	ENST00000421138		232	Aga/Tga	7/16	0.375368857031826	4	FACETS	0.797	0.717	0.881	0.266	0.239	0.294	SUBCLONAL	1	TRUE	1	0.379968616372753	4		591	1076	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247478	71247478	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	171	623	0	ENST00000318789.4:c.55G>T	p.Gly19Trp	p.G19W	ENST00000318789	NM_032682.5	19	Ggg/Tgg	6/21	0.35584455341205	1	FACETS	0.935	0.861	1	0.935	0.861	1	CLONAL	1	TRUE	0	0.379968616372753	1		623	780	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141089	55141089	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	109	450	0	ENST00000257290.5:c.1735C>A	p.Gln579Lys	p.Q579K	ENST00000257290	NM_006206.4	579	Cag/Aag	12/23	1	2	FACETS	0.911	0.819	1	0.911	0.819	1	CLONAL	1	TRUE	1	0.379968616372753	2		450	630	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955945	55955945	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	137	579	0	ENST00000263923.4:c.3217del	p.Ala1073ProfsTer29	p.A1073Pfs*29	ENST00000263923	NM_002253.2	1073	Gcc/cc	24/30	1	2	FACETS	0.925	0.842	1	0.925	0.842	1	CLONAL	1	TRUE	1	0.379968616372753	2		579	780	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467794	66467794	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	94	410	0	ENST00000273854.3:c.475G>T	p.Asp159Tyr	p.D159Y	ENST00000273854	NM_004439.5	159	Gat/Tat	3/18	1	2	FACETS	0.815	0.726	0.909	0.815	0.726	0.909	CLONAL	1	TRUE	1	0.379968616372753	2		410	607	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525001	187525001	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	125	612	2	ENST00000441802.2:c.10679C>A	p.Ser3560Ter	p.S3560*	ENST00000441802	NM_005245.3	3560	tCa/tAa	19/27	1	2	FACETS	0.845	0.765	0.929	0.845	0.765	0.929	CLONAL	1	TRUE	1	0.379968616372753	2		614	779	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499121	149499121	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	111	487	1	ENST00000261799.4:c.2707C>A	p.Pro903Thr	p.P903T	ENST00000261799	NM_002609.3	903	Cct/Act	20/23	1	2	FACETS	0.903	0.813	0.998	0.903	0.813	0.998	CLONAL	1	TRUE	1	0.379968616372753	2		488	647	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874746	151874746	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	176	334	0	ENST00000262189.6:c.7792G>T	p.Asp2598Tyr	p.D2598Y	ENST00000262189	NM_170606.2	2598	Gac/Tac	38/59	0.326931222388813	3	FACETS	0.851	0.787	0.917	0.851	0.787	0.917	CLONAL	2	TRUE	1	0.379968616372753	3		334	648	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0016177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	251	599	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.254981642790358	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.254981642790358	3		599	975	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0016177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	80	683	0				ENST00000310581	NM_198253.2	-/1132			0.254981642790358	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.254981642790358	1		683	479	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637579	52637579	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	76	541	0	ENST00000394830.3:c.2737G>T	p.Glu913Ter	p.E913*	ENST00000394830	NM_018313.4	913	Gaa/Taa	18/30	0.254981642790358	1	FACETS	0.599	0.524	0.679	0.599	0.524	0.679	SUBCLONAL	1	TRUE	0	0.254981642790358	1		541	869	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711903	89711903	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs864622341	NA	P-0016177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	118	497	0	ENST00000371953.3:c.521A>G	p.Tyr174Cys	p.Y174C	ENST00000371953	NM_000314.4	174	tAt/tGt	6/9	0.254981642790358	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.254981642790358	1		497	753	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47604194	47604194	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	58	475	2	ENST00000263735.4:c.533C>A	p.Pro178Gln	p.P178Q	ENST00000263735	NM_002354.2	178	cCa/cAa	5/9	0.254981642790358	1	FACETS	0.508	0.436	0.588	0.508	0.436	0.588	SUBCLONAL	1	TRUE	0	0.254981642790358	1		477	781	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582406	119582406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs72548709	NA	P-0016177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	45	257	0	ENST00000316626.5:c.995G>A	p.Arg332His	p.R332H	ENST00000316626		332	cGt/cAt	10/12	1	2	FACETS	0.767	0.645	0.902	0.767	0.645	0.902	CLONAL	1	TRUE	1	0.254981642790358	2		257	460	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781419	135781419	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	188	363	1	ENST00000298552.3:c.1546C>T	p.Gln516Ter	p.Q516*	ENST00000298552	NM_001162426.1	516	Cag/Tag	15/23	0.541342567634041	2	FACETS	0.941	0.884	0.998	0.941	0.884	0.998	CLONAL	2	TRUE	0	0.541342567634041	2		364	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0016178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	392	590	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.541342567634041	2	FACETS	0.992	0.951	1	0.992	0.951	1	CLONAL	2	TRUE	0	0.541342567634041	2		590	730	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353757	68353757	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	170	286	0	ENST00000487270.1:c.592G>A	p.Glu198Lys	p.E198K	ENST00000487270	NM_133509.3	198	Gaa/Aaa	7/11	0.541342567634041	3	FACETS	0.969	0.902	1	0.969	0.902	1	CLONAL	2	TRUE	1	0.541342567634041	3		286	412	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438066	49438066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024285765	NA	P-0016178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	381	504	1	ENST00000301067.7:c.5105G>A	p.Arg1702Gln	p.R1702Q	ENST00000301067	NM_003482.3	1702	cGa/cAa	21/54	0.430307984121841	5	FACETS	0.923	0.88	0.966			1	CLONAL	3	TRUE	NA	0.541342567634041	5		505	921	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90645579	90645579	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	62	112	0	ENST00000330062.3:c.44C>T	p.Ser15Leu	p.S15L	ENST00000330062	NM_002168.2	15	tCa/tTa	1/11	0.541342567634041	3	FACETS	0.851	0.751	0.955	0.851	0.751	0.955	CLONAL	2	TRUE	1	0.541342567634041	3		112	171	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303823	91303823	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0016178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	124	252	0	ENST00000355112.3:c.1221-1G>C		p.X407_splice	ENST00000355112	NM_000057.2	407			0.541342567634041	3	FACETS	0.841	0.77	0.914	0.841	0.77	0.914	CLONAL	2	TRUE	1	0.541342567634041	3		252	346	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	364577	364577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754764999	NA	P-0016178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	51	585	0	ENST00000262320.3:c.985G>A	p.Asp329Asn	p.D329N	ENST00000262320	NM_003502.3	329	Gat/Aat	3/11	0.541342567634041	2	FACETS	0.319	0.27	0.372	0.159	0.135	0.186	SUBCLONAL	1	TRUE	0	0.541342567634041	2		585	591	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347759	89347759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1334528543	NA	P-0016178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	352	344	0	ENST00000301030.4:c.5191G>A	p.Asp1731Asn	p.D1731N	ENST00000301030	NM_001256183.1	1731	Gac/Aac	9/13	0.541342567634041	6	FACETS	0.999	0.955	1	0.999	0.955	1	CLONAL	4	TRUE	2	0.541342567634041	6		344	678	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347895	89347895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	444	368	0	ENST00000301030.4:c.5055G>A	p.Met1685Ile	p.M1685I	ENST00000301030	NM_001256183.1	1685	atG/atA	9/13	0.541342567634041	6	FACETS	1	0.983	1	1	0.983	1	CLONAL	4	TRUE	2	0.541342567634041	6		368	821	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348047	89348047	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	885	747	0	ENST00000301030.4:c.4903C>G	p.Leu1635Val	p.L1635V	ENST00000301030	NM_001256183.1	1635	Ctg/Gtg	9/13	0.541342567634041	6	FACETS	1	0.985	1	1	0.985	1	CLONAL	4	TRUE	2	0.541342567634041	6		747	1670	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348656	89348656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	879	754	0	ENST00000301030.4:c.4294G>A	p.Asp1432Asn	p.D1432N	ENST00000301030	NM_001256183.1	1432	Gat/Aat	9/13	0.541342567634041	6	FACETS	0.972	0.944	0.999	0.972	0.944	0.999	CLONAL	4	TRUE	2	0.541342567634041	6		754	1740	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352030	89352030	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	656	582	0	ENST00000301030.4:c.920C>G	p.Ser307Cys	p.S307C	ENST00000301030	NM_001256183.1	307	tCc/tGc	9/13	0.541342567634041	6	FACETS	0.945	0.913	0.976			1	CLONAL	4	TRUE	NA	0.541342567634041	6		582	1336	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89825085	89825085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	252	417	1	ENST00000389301.3:c.2881G>A	p.Glu961Lys	p.E961K	ENST00000389301	NM_000135.2	961	Gag/Aag	30/43	0.541342567634041	6	FACETS	0.982	0.92	1			1	CLONAL	2	TRUE	NA	0.541342567634041	6		418	987	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556281	29556281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	124	439	0	ENST00000356175.3:c.2648C>T	p.Ser883Leu	p.S883L	ENST00000356175	NM_000267.3	883	tCa/tTa	21/57	0.541342567634041	3	FACETS	0.86	0.779	0.945	0.43	0.389	0.473	CLONAL	1	TRUE	1	0.541342567634041	3		439	677	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761160	59761160	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1567728614	NA	P-0016178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	487	505	0	ENST00000259008.2:c.3247C>G	p.Leu1083Val	p.L1083V	ENST00000259008	NM_032043.2	1083	Ctt/Gtt	20/20	0.518232280104813	5	FACETS	1	0.966	1			1	CLONAL	3	TRUE	NA	0.541342567634041	5		505	1080	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372127	45372127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	333	627	0	ENST00000262160.6:c.1042G>A	p.Glu348Lys	p.E348K	ENST00000262160	NM_005901.5	348	Gag/Aag	9/11	NA	2	FACETS	0.933	0.891	0.976			1	INDETERMINATE	2	TRUE	NA	0.541342567634041	2		627	659	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198260853	198260853	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	166	594	0	ENST00000335508.6:c.3466G>C	p.Glu1156Gln	p.E1156Q	ENST00000335508	NM_012433.2	1156	Gaa/Caa	23/25	0.541342567634041	3	FACETS	0.901	0.828	0.977	0.45	0.414	0.489	CLONAL	1	TRUE	1	0.541342567634041	3		594	865	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39704812	39704812	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	92	388	0	ENST00000361337.2:c.157G>C	p.Glu53Gln	p.E53Q	ENST00000361337	NM_003286.2	53	Gaa/Caa	4/21	0.46468517063738	4	FACETS	0.805	0.716	0.9			1	CLONAL	1	TRUE	NA	0.541342567634041	4		388	651	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171597	36171598	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	TTGA	novel	NA	P-0016178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	107	149	0	ENST00000300305.3:c.964_967dup	p.Thr323IlefsTer278	p.T323Ifs*278	ENST00000300305		323	acg/aTCAAcg		0.541342567634041	3	FACETS	1	0.918	1	1	0.918	1	CLONAL	2	TRUE	1	0.541342567634041	3		149	250	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259355	89259355	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	264	385	0	ENST00000336596.2:c.499G>A	p.Glu167Lys	p.E167K	ENST00000336596	NM_005233.5	167	Gag/Aag	3/17	0.464485364667082	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.541342567634041	4		385	696	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500880	149500880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	164	415	0	ENST00000261799.4:c.2350G>A	p.Glu784Lys	p.E784K	ENST00000261799	NM_002609.3	784	Gag/Aag	17/23	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.541342567634041	2		415	540	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721223	176721223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	85	432	0	ENST00000439151.2:c.6854G>A	p.Arg2285Lys	p.R2285K	ENST00000439151	NM_022455.4	2285	aGa/aAa	23/23	1	2	FACETS	0.885	0.788	0.986	0.885	0.788	0.986	CLONAL	1	TRUE	1	0.541342567634041	2		432	355	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956586	93956586	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	105	396	0	ENST00000369303.4:c.2650G>A	p.Glu884Lys	p.E884K	ENST00000369303	NM_004440.3	884	Gaa/Aaa	15/17	1	2	FACETS	0.827	0.745	0.913	0.827	0.745	0.913	CLONAL	1	TRUE	1	0.541342567634041	2		396	469	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624403	140624404	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGGCGC	rs397507458	NA	P-0016178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	10	84	2	ENST00000288602.6:c.95_100dup	p.Gly32_Ala33dup	p.G32_A33dup	ENST00000288602	NM_004333.4	32	gcg/gGCGCCGcg	1/18	0.541342567634041	2	FACETS	0.528	0.363	0.727	0.264	0.181	0.364	SUBCLONAL	1	TRUE	0	0.541342567634041	2		86	70	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412544	80412544	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	91	301	0	ENST00000286548.4:c.497G>T	p.Arg166Leu	p.R166L	ENST00000286548	NM_002072.3	166	cGc/cTc	4/7	0.541342567634041	2	FACETS	0.963	0.863	1	0.482	0.431	0.534	CLONAL	1	TRUE	0	0.541342567634041	2		301	349	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339268	87339268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759501723	NA	P-0016178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	282	420	0	ENST00000277120.3:c.850C>T	p.His284Tyr	p.H284Y	ENST00000277120		284	Cat/Tat	8/19	0.541342567634041	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.541342567634041	2		420	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574024	7574025	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0016179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	112	616	0	ENST00000269305.4:c.1002dup	p.Arg335AlafsTer2	p.R335Afs*2	ENST00000269305	NM_001126112.2	334	-/G	10/11	0.29638909432432	1	FACETS	0.89	0.802	0.983	1	0.987	1	CLONAL	2	TRUE	0	0.18	1		616	636	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202123028	202123028	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs34210251	NA	P-0016179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	31	534	0	ENST00000358485.4:c.74C>T	p.Pro25Leu	p.P25L	ENST00000358485	NM_001080125.1	25	cCc/cTc	1/9	1	2	FACETS	0.621	0.501	0.757	0.621	0.501	0.757	SUBCLONAL	1	TRUE	1	0.18	2		534	555	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540841	187540841	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761083769	NA	P-0016179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	63	414	0	ENST00000441802.2:c.6899C>T	p.Thr2300Met	p.T2300M	ENST00000441802	NM_005245.3	2300	aCg/aTg	10/27	0.0609133834285602	3	FACETS	1	0.967	1	0.706	0.611	0.809	INDETERMINATE	1	TRUE	1	0.18	3		414	540	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541084	187541084	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	36	367	0	ENST00000441802.2:c.6656C>A	p.Thr2219Lys	p.T2219K	ENST00000441802	NM_005245.3	2219	aCa/aAa	10/27	0.0609133834285602	3	FACETS	0.956	0.786	1	0.478	0.393	0.574	INDETERMINATE	1	TRUE	1	0.18	3		367	456	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541660	187541660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745765579	NA	P-0016179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	32	366	0	ENST00000441802.2:c.6080G>A	p.Arg2027His	p.R2027H	ENST00000441802	NM_005245.3	2027	cGc/cAc	10/27	0.0609133834285602	3	FACETS	0.859	0.697	1	0.43	0.348	0.522	INDETERMINATE	1	TRUE	1	0.18	3		366	451	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	259	486	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.336183663972172	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.336183663972172	2		486	708	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0016180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	250	896	1	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.26366794904448	2	FACETS	0.916	0.859	0.974	0.916	0.859	0.974	CLONAL	2	TRUE	0	0.336183663972172	2		897	812	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468490	89468490	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	127	389	0	ENST00000336596.2:c.2024G>T	p.Gly675Val	p.G675V	ENST00000336596	NM_005233.5	675	gGa/gTa	11/17	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.336183663972172	2		389	724	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262360	115262360	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	82	414	0	ENST00000438362.2:c.2194G>C	p.Gly732Arg	p.G732R	ENST00000438362	NM_001242891.1	732	Ggc/Cgc	18/20	1	2	FACETS	0.782	0.69	0.88	0.782	0.69	0.88	SUBCLONAL	1	TRUE	1	0.336183663972172	2		414	624	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176145047	176145047	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	110	489	0	ENST00000367669.3:c.564G>T	p.Leu188Phe	p.L188F	ENST00000367669	NM_022457.5	188	ttG/ttT	3/20	0.336183663972172	3	FACETS	0.749	0.671	0.831	0.374	0.335	0.416	SUBCLONAL	1	TRUE	1	0.336183663972172	3		489	1021	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245192	46245192	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	122	395	1	ENST00000334344.6:c.3286C>T	p.Gln1096Ter	p.Q1096*	ENST00000334344	NM_152641.2	1096	Cag/Tag	15/21	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.336183663972172	2		396	714	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246344	46246344	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	111	396	0	ENST00000334344.6:c.4438G>T	p.Gly1480Ter	p.G1480*	ENST00000334344	NM_152641.2	1480	Gga/Tga	15/21	1	2	FACETS	0.945	0.85	1	0.945	0.85	1	CLONAL	1	TRUE	1	0.336183663972172	2		396	699	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494854	56494854	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	97	325	0	ENST00000267101.3:c.3211G>C	p.Val1071Leu	p.V1071L	ENST00000267101	NM_001982.3	1071	Gtt/Ctt	27/28	1	2	FACETS	0.988	0.883	1	0.988	0.883	1	CLONAL	1	TRUE	1	0.336183663972172	2		325	584	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112032	115112032	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	118	617	3	ENST00000257566.3:c.1708C>A	p.Leu570Met	p.L570M	ENST00000257566	NM_016569.3	570	Ctg/Atg	7/8	1	2	FACETS	0.885	0.799	0.977	0.885	0.799	0.977	CLONAL	1	TRUE	1	0.336183663972172	2		620	793	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941675	48941675	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	33	328	0	ENST00000267163.4:c.985A>G	p.Lys329Glu	p.K329E	ENST00000267163	NM_000321.2	329	Aaa/Gaa	10/27	0.298005741300459	3	FACETS	0.356	0.289	0.432	0.119	0.096	0.144	SUBCLONAL	1	TRUE	0	0.336183663972172	3		328	644	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961400	41961400	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	192	319	3	ENST00000219905.7:c.308G>T	p.Arg103Leu	p.R103L	ENST00000219905	NM_001164273.1	103	cGc/cTc	2/24	0.336183663972172	2	FACETS	0.924	0.859	0.991	0.924	0.859	0.991	CLONAL	2	TRUE	0	0.336183663972172	2		322	618	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220715	2220715	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	73	317	0	ENST00000326181.6:c.332A>G	p.Glu111Gly	p.E111G	ENST00000326181	NM_032271.2	111	gAg/gGg	5/21	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.336183663972172	2		317	434	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858649	9858649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778940856	NA	P-0016180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	78	349	0	ENST00000330684.3:c.2752C>T	p.Pro918Ser	p.P918S	ENST00000330684	NM_001134407.1	918	Ccc/Tcc	13/13	1	2	FACETS	0.851	0.749	0.961	0.851	0.749	0.961	CLONAL	1	TRUE	1	0.336183663972172	2		349	545	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676230	29676230	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0016180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	210	526	0	ENST00000356175.3:c.7219A>T	p.Lys2407Ter	p.K2407*	ENST00000356175	NM_000267.3	2407	Aaa/Taa	48/57	0.281940773028099	4	FACETS	0.772	0.716	0.83	0.772	0.716	0.83	SUBCLONAL	2	TRUE	2	0.336183663972172	4		526	1081	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683558	29683558	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060500295	NA	P-0016180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	272	563	0	ENST00000356175.3:c.7638del	p.Met2548Ter	p.M2548*	ENST00000356175	NM_000267.3	2545	Ccc/cc	51/57	0.281940773028099	4	FACETS	0.95	0.891	1	0.95	0.891	1	CLONAL	2	TRUE	2	0.336183663972172	4		563	1138	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395769	45395769	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	79	501	0	ENST00000262160.6:c.365G>A	p.Gly122Glu	p.G122E	ENST00000262160	NM_005901.5	122	gGa/gAa	4/11	0.179262721224219	2	FACETS	0.697	0.613	0.788	0.349	0.306	0.394	INDETERMINATE	1	TRUE	0	0.336183663972172	2		501	674	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244098	5244098	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	217	495	0	ENST00000357368.4:c.1384G>T	p.Val462Phe	p.V462F	ENST00000357368	NM_002850.3	462	Gtc/Ttc	11/38	0.336183663972172	2	FACETS	0.935	0.874	0.999	0.935	0.874	0.999	CLONAL	2	TRUE	0	0.336183663972172	2		495	690	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918147	50918147	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	437	684	1	ENST00000440232.2:c.2464G>T	p.Asp822Tyr	p.D822Y	ENST00000440232	NM_002691.3	822	Gac/Tac	20/27	0.310477204649013	3	FACETS	1	0.971	1			1	CLONAL	3	TRUE	NA	0.336183663972172	3		685	994	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47607083	47607083	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778825812	NA	P-0016180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	89	499	0	ENST00000263735.4:c.833C>T	p.Ala278Val	p.A278V	ENST00000263735	NM_002354.2	278	gCa/gTa	7/9	0.336183663972172	5	FACETS	0.729	0.644	0.82	0.243	0.214	0.274	SUBCLONAL	1	TRUE	2	0.336183663972172	5		499	1093	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47613751	47613751	+	stop_lost	Nonstop_Mutation	SNP	A	A	T	novel	NA	P-0016180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	172	332	0	ENST00000263735.4:c.944A>T	p.Ter315LeuextTer12	p.*315Lext*12	ENST00000263735	NM_002354.2	315	tAa/tTa	9/9	0.336183663972172	5	FACETS	0.859	0.791	0.93	0.573	0.527	0.62	CLONAL	2	TRUE	2	0.336183663972172	5		332	896	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72891517	72891517	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1173444435	NA	P-0016180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	124	509	0	ENST00000325599.8:c.245G>C	p.Gly82Ala	p.G82A	ENST00000325599	NM_018130.2	82	gGc/gCc	3/11	1	2	FACETS	0.989	0.895	1	0.989	0.895	1	CLONAL	1	TRUE	1	0.336183663972172	2		509	746	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670469	134670469	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	241	434	1	ENST00000398015.3:c.380C>A	p.Ala127Asp	p.A127D	ENST00000398015	NM_004441.4	127	gCc/gAc	3/16	0.336183663972172	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.336183663972172	2		435	707	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1977109	1977124	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCGGGGATAGACCA	CCTCGGGGATAGACCA	-	novel	NA	P-0016180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	277	769	0	ENST00000382891.5:c.3603_3618del	p.Phe1201LeufsTer123	p.F1201Lfs*123	ENST00000382891	NM_133335.3	1201	ttCCTCGGGGATAGACCA/tt	20/22	0.310477204649013	3	FACETS	0.911	0.855	0.967			1	CLONAL	2	TRUE	NA	0.336183663972172	3		769	1057	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003199	143003199	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	193	489	0	ENST00000262992.4:c.2627T>A	p.Leu876Gln	p.L876Q	ENST00000262992	NM_001101669.1	876	cTg/cAg	23/24	0.23642656186735	3	FACETS	0.958	0.889	1	0.958	0.889	1	CLONAL	2	TRUE	1	0.336183663972172	3		489	700	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007369	143007369	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	87	338	0	ENST00000262992.4:c.2415G>T	p.Leu805Phe	p.L805F	ENST00000262992	NM_001101669.1	805	ttG/ttT	22/24	0.23642656186735	3	FACETS	1	0.906	1	0.512	0.454	0.574	CLONAL	1	TRUE	1	0.336183663972172	3		338	590	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149452879	149452879	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	193	402	0	ENST00000286301.3:c.1067C>A	p.Thr356Asn	p.T356N	ENST00000286301	NM_005211.3	356	aCc/aAc	7/22	0.336183663972172	3	FACETS	0.966	0.897	1	0.966	0.897	1	CLONAL	2	TRUE	1	0.336183663972172	3		402	694	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149498414	149498414	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	222	386	0	ENST00000261799.4:c.2800T>A	p.Tyr934Asn	p.Y934N	ENST00000261799	NM_002609.3	934	Tat/Aat	21/23	0.336183663972172	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.336183663972172	3		386	741	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517390	157517390	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	131	437	0	ENST00000346085.5:c.3954G>C	p.Met1318Ile	p.M1318I	ENST00000346085	NM_020732.3	1318	atG/atC	16/20	0.332485237175222	4	FACETS	1	0.971	1	0.391	0.354	0.429	CLONAL	1	TRUE	1	0.336183663972172	4		437	888	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879363	151879363	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	159	328	0	ENST00000262189.6:c.5582G>C	p.Arg1861Pro	p.R1861P	ENST00000262189	NM_170606.2	1861	cGg/cCg	36/59	0.336183663972172	3	FACETS	0.891	0.82	0.965	0.891	0.82	0.965	CLONAL	2	TRUE	1	0.336183663972172	3		328	620	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317294	87317294	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	273	508	0	ENST00000277120.3:c.319G>T	p.Ala107Ser	p.A107S	ENST00000277120		107	Gct/Tct	4/19	0.336183663972172	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.336183663972172	2		508	796	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039610	47039610	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0016180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	185	221	0	ENST00000377604.3:c.1063-1G>T		p.X355_splice	ENST00000377604	NM_001204468.1	355			0.282487943794137	2	FACETS	0.895	0.837	0.953			1	CLONAL	3	TRUE	NA	0.336183663972172	2		221	410	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	308	486	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.485080516807161	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.490744614633324	2		486	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0016180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	308	896	1	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.399349089891165	2	FACETS	0.924	0.878	0.971	0.924	0.878	0.971	CLONAL	2	TRUE	0	0.490744614633324	2		897	679	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468490	89468490	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	156	389	0	ENST00000336596.2:c.2024G>T	p.Gly675Val	p.G675V	ENST00000336596	NM_005233.5	675	gGa/gTa	11/17	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.490744614633324	2		389	633	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262360	115262360	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	142	414	0	ENST00000438362.2:c.2194G>C	p.Gly732Arg	p.G732R	ENST00000438362	NM_001242891.1	732	Ggc/Cgc	18/20	1	2	FACETS	0.935	0.855	1	0.935	0.855	1	CLONAL	1	TRUE	1	0.490744614633324	2		414	619	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176145047	176145047	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	161	489	0	ENST00000367669.3:c.564G>T	p.Leu188Phe	p.L188F	ENST00000367669	NM_022457.5	188	ttG/ttT	3/20	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.490744614633324	NA		489	1017	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245192	46245192	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	128	395	1	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	0.490744614633324	2		396	501	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246344	46246344	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	124	396	0	ENST00000334344.6:c.4438G>T	p.Gly1480Ter	p.G1480*	ENST00000334344	NM_152641.2	1480	Gga/Tga	15/21	1	2	FACETS	0.893	0.811	0.979	0.893	0.811	0.979	CLONAL	1	TRUE	1	0.490744614633324	2		396	566	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494854	56494854	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	118	325	0	ENST00000267101.3:c.3211G>C	p.Val1071Leu	p.V1071L	ENST00000267101	NM_001982.3	1071	Gtt/Ctt	27/28	1	2	FACETS	0.907	0.822	0.996	0.907	0.822	0.996	CLONAL	1	TRUE	1	0.490744614633324	2		325	530	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112032	115112032	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	149	617	3	ENST00000257566.3:c.1708C>A	p.Leu570Met	p.L570M	ENST00000257566	NM_016569.3	570	Ctg/Atg	7/8	1	2	FACETS	0.854	0.782	0.929	0.854	0.782	0.929	CLONAL	1	TRUE	1	0.490744614633324	2		620	711	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941675	48941675	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	39	328	0	ENST00000267163.4:c.985A>G	p.Lys329Glu	p.K329E	ENST00000267163	NM_000321.2	329	Aaa/Gaa	10/27	0.341025068197342	3	FACETS	0.314	0.259	0.375	0.105	0.086	0.125	SUBCLONAL	1	TRUE	0	0.490744614633324	3		328	631	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961400	41961400	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	249	319	3	ENST00000219905.7:c.308G>T	p.Arg103Leu	p.R103L	ENST00000219905	NM_001164273.1	103	cGc/cTc	2/24	0.485080516807161	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.490744614633324	2		322	505	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220715	2220715	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	96	317	0	ENST00000326181.6:c.332A>G	p.Glu111Gly	p.E111G	ENST00000326181	NM_032271.2	111	gAg/gGg	5/21	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.490744614633324	2		317	389	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858649	9858649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778940856	NA	P-0016180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	123	349	0	ENST00000330684.3:c.2752C>T	p.Pro918Ser	p.P918S	ENST00000330684	NM_001134407.1	918	Ccc/Tcc	13/13	1	2	FACETS	0.991	0.901	1	0.991	0.901	1	CLONAL	1	TRUE	1	0.490744614633324	2		349	506	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676230	29676230	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0016180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	329	526	0	ENST00000356175.3:c.7219A>T	p.Lys2407Ter	p.K2407*	ENST00000356175	NM_000267.3	2407	Aaa/Taa	48/57	0.300339022775462	5	FACETS	1	0.971	1	0.693	0.655	0.731	CLONAL	2	TRUE	2	0.490744614633324	5		526	1120	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683558	29683558	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060500295	NA	P-0016180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	374	563	0	ENST00000356175.3:c.7638del	p.Met2548Ter	p.M2548*	ENST00000356175	NM_000267.3	2545	Ccc/cc	51/57	0.300339022775462	5	FACETS	1	0.987	1	0.741	0.704	0.779	CLONAL	2	TRUE	2	0.490744614633324	5		563	1190	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244098	5244098	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	298	495	0	ENST00000357368.4:c.1384G>T	p.Val462Phe	p.V462F	ENST00000357368	NM_002850.3	462	Gtc/Ttc	11/38	0.485080516807161	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.490744614633324	2		495	596	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918147	50918147	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	531	684	1	ENST00000440232.2:c.2464G>T	p.Asp822Tyr	p.D822Y	ENST00000440232	NM_002691.3	822	Gac/Tac	20/27	0.488220522684637	3	FACETS	0.98	0.947	1			1	CLONAL	3	TRUE	NA	0.490744614633324	3		685	917	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47607083	47607083	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778825812	NA	P-0016180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	122	499	0	ENST00000263735.4:c.833C>T	p.Ala278Val	p.A278V	ENST00000263735	NM_002354.2	278	gCa/gTa	7/9	0.351655979789079	6	FACETS	0.82	0.739	0.905	0.205	0.184	0.227	CLONAL	1	TRUE	2	0.490744614633324	6		499	1202	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47613751	47613751	+	stop_lost	Nonstop_Mutation	SNP	A	A	T	novel	NA	P-0016180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	247	332	0	ENST00000263735.4:c.944A>T	p.Ter315LeuextTer12	p.*315Lext*12	ENST00000263735	NM_002354.2	315	tAa/tTa	9/9	0.351655979789079	6	FACETS	1	0.96	1	0.518	0.484	0.552	CLONAL	2	TRUE	2	0.490744614633324	6		332	963	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72891517	72891517	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1173444435	NA	P-0016180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	185	509	0	ENST00000325599.8:c.245G>C	p.Gly82Ala	p.G82A	ENST00000325599	NM_018130.2	82	gGc/gCc	3/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.490744614633324	2		509	727	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670469	134670469	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	272	434	1	ENST00000398015.3:c.380C>A	p.Ala127Asp	p.A127D	ENST00000398015	NM_004441.4	127	gCc/gAc	3/16	0.485080516807161	2	FACETS	0.91	0.861	0.959	0.91	0.861	0.959	CLONAL	2	TRUE	0	0.490744614633324	2		435	609	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1977109	1977124	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCGGGGATAGACCA	CCTCGGGGATAGACCA	-	novel	NA	P-0016180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	358	769	0	ENST00000382891.5:c.3603_3618del	p.Phe1201LeufsTer123	p.F1201Lfs*123	ENST00000382891	NM_133335.3	1201	ttCCTCGGGGATAGACCA/tt	20/22	0.458186952548272	3	FACETS	0.873	0.829	0.918			1	CLONAL	2	TRUE	NA	0.490744614633324	3		769	1041	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003199	143003199	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	230	489	0	ENST00000262992.4:c.2627T>A	p.Leu876Gln	p.L876Q	ENST00000262992	NM_001101669.1	876	cTg/cAg	23/24	0.490744614633324	3	FACETS	0.994	0.934	1	0.994	0.934	1	CLONAL	2	TRUE	1	0.490744614633324	3		489	587	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007369	143007369	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	128	338	0	ENST00000262992.4:c.2415G>T	p.Leu805Phe	p.L805F	ENST00000262992	NM_001101669.1	805	ttG/ttT	22/24	0.490744614633324	3	FACETS	0.973	0.883	1	0.486	0.441	0.533	CLONAL	1	TRUE	1	0.490744614633324	3		338	668	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149452879	149452879	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	282	402	0	ENST00000286301.3:c.1067C>A	p.Thr356Asn	p.T356N	ENST00000286301	NM_005211.3	356	aCc/aAc	7/22	0.490744614633324	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.490744614633324	3		402	691	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149498414	149498414	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	216	386	0	ENST00000261799.4:c.2800T>A	p.Tyr934Asn	p.Y934N	ENST00000261799	NM_002609.3	934	Tat/Aat	21/23	0.490744614633324	3	FACETS	0.887	0.83	0.945	0.887	0.83	0.945	CLONAL	2	TRUE	1	0.490744614633324	3		386	618	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517390	157517390	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	157	437	0	ENST00000346085.5:c.3954G>C	p.Met1318Ile	p.M1318I	ENST00000346085	NM_020732.3	1318	atG/atC	16/20	0.490744614633324	4	FACETS	0.969	0.887	1	0.323	0.295	0.352	CLONAL	1	TRUE	1	0.490744614633324	4		437	984	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879363	151879363	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	201	328	0	ENST00000262189.6:c.5582G>C	p.Arg1861Pro	p.R1861P	ENST00000262189	NM_170606.2	1861	cGg/cCg	36/59	0.490744614633324	3	FACETS	0.977	0.914	1	0.977	0.914	1	CLONAL	2	TRUE	1	0.490744614633324	3		328	522	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317294	87317294	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	333	508	0	ENST00000277120.3:c.319G>T	p.Ala107Ser	p.A107S	ENST00000277120		107	Gct/Tct	4/19	0.485080516807161	2	FACETS	0.933	0.889	0.978	0.933	0.889	0.978	CLONAL	2	TRUE	0	0.490744614633324	2		508	727	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039610	47039610	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0016180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	276	221	0	ENST00000377604.3:c.1063-1G>T		p.X355_splice	ENST00000377604	NM_001204468.1	355			0.339805114367621	2	FACETS	0.886	0.848	0.923			1	CLONAL	3	TRUE	NA	0.490744614633324	2		221	423	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358417	91358417	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	64	710	0	ENST00000355112.3:c.4162G>A	p.Ala1388Thr	p.A1388T	ENST00000355112	NM_000057.2	1388	Gcg/Acg	22/22	0.485080516807161	2	FACETS	0.29	0.25	0.333	0.145	0.125	0.167	SUBCLONAL	1	TRUE	0	0.490744614633324	2		710	900	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139264	37139264	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	24	242	0	ENST00000373509.5:c.604G>C	p.Asp202His	p.D202H	ENST00000373509	NM_002648.3	202	Gat/Cat	4/6	0.351655979789079	6	FACETS	0.407	0.318	0.51	0.102	0.079	0.128	SUBCLONAL	1	TRUE	2	0.490744614633324	6		242	476	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	133	599	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.79	0.717	0.866	0.79	0.717	0.866	SUBCLONAL	1	TRUE	1	0.389946198930997	2		599	864	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391024	89391024	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	145	636	0	ENST00000336596.2:c.1095del	p.Lys365AsnfsTer6	p.K365Nfs*6	ENST00000336596	NM_005233.5	364	Aaa/aa	5/17	1	2	FACETS	0.842	0.768	0.92	0.842	0.768	0.92	CLONAL	1	TRUE	1	0.389946198930997	2		636	883	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	138	547	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	0.389946198930997	2		547	697	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736166	204736166	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	110	374	2	ENST00000302823.3:c.529del	p.Tyr177IlefsTer10	p.Y177Ifs*10	ENST00000302823	NM_005214.4	175	Ttt/tt	3/4	1	2	FACETS	0.907	0.817	1	0.907	0.817	1	CLONAL	1	TRUE	1	0.389946198930997	2		376	622	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979987	7979987	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746723399	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	148	561	0	ENST00000319144.4:c.1350del	p.Leu451SerfsTer16	p.L451Sfs*16	ENST00000319144	NM_001139.2	450	ggG/gg	10/15	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.389946198930997	2		561	717	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	250	314	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.958	1	1	0.995	1	CLONAL	2	TRUE	1	0.389946198930997	2		318	628	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101268	27101268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	128	622	0	ENST00000324856.7:c.4555del	p.Gln1519ArgfsTer8	p.Q1519Rfs*8	ENST00000324856	NM_006015.4	1517	gCc/gc	18/20	1	2	FACETS	0.87	0.789	0.955	0.87	0.789	0.955	CLONAL	1	TRUE	1	0.389946198930997	2		622	755	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141426	11141426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	75	430	0	ENST00000358026.2:c.3403C>T	p.Arg1135Trp	p.R1135W	ENST00000358026	NM_001128849.1	1135	Cgg/Tgg	25/36	1	2	FACETS	0.479	0.419	0.544	0.479	0.419	0.544	SUBCLONAL	1	TRUE	1	0.389946198930997	2		430	803	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	31	137	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	0.691	0.562	0.835	0.691	0.562	0.835	SUBCLONAL	1	TRUE	1	0.389946198930997	2		137	230	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553591	106553591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376600972	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	82	338	0	ENST00000369096.4:c.1556C>T	p.Ala519Val	p.A519V	ENST00000369096	NM_001198.3	519	gCg/gTg	5/7	1	2	FACETS	0.908	0.804	1	0.908	0.804	1	CLONAL	1	TRUE	1	0.389946198930997	2		338	463	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215787	98215787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376844749	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	151	575	1	ENST00000331920.6:c.3422C>T	p.Ala1141Val	p.A1141V	ENST00000331920	NM_000264.3	1141	gCg/gTg	20/24	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.389946198930997	2		576	720	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217234	11217234	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1031980569	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	134	557	0	ENST00000361445.4:c.4444C>T	p.Arg1482Cys	p.R1482C	ENST00000361445	NM_004958.3	1482	Cgc/Tgc	30/58	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.389946198930997	2		557	661	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852118	63852118	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	122	608	0	ENST00000279873.7:c.2901del	p.Lys967AsnfsTer15	p.K967Nfs*15	ENST00000279873	NM_032199.2	966	Aaa/aa	10/10	1	2	FACETS	0.725	0.655	0.799	0.725	0.655	0.799	SUBCLONAL	1	TRUE	1	0.389946198930997	2		608	863	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097624	11097625	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1165714406	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	79	681	1	ENST00000358026.2:c.810dup	p.Gly271ArgfsTer16	p.G271Rfs*16	ENST00000358026	NM_001128849.1	268	-/C	5/36	1	2	FACETS	0.494	0.433	0.559	0.494	0.433	0.559	SUBCLONAL	1	TRUE	1	0.389946198930997	2		682	821	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375459	40375459	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	157	662	2	ENST00000293328.3:c.491del	p.Lys164SerfsTer17	p.K164Sfs*17	ENST00000293328	NM_012448.3	164	aAg/ag	5/19	1	2	FACETS	0.915	0.838	0.995	0.915	0.838	0.995	CLONAL	1	TRUE	1	0.389946198930997	2		664	880	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435128	110435129	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs772322568	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	104	595	1	ENST00000375856.3:c.3272dup	p.Lys1092GlufsTer233	p.K1092Efs*233	ENST00000375856	NM_003749.2	1091	ccg/ccCg	1/2	1	2	FACETS	0.698	0.625	0.776	0.698	0.625	0.776	SUBCLONAL	1	TRUE	1	0.389946198930997	2		596	764	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129130	152129130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	164	687	2	ENST00000206249.3:c.83G>A	p.Arg28His	p.R28H	ENST00000206249	NM_000125.3	28	cGt/cAt	1/8	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.389946198930997	2		689	788	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265353	152265353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188957694	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	75	390	0	ENST00000206249.3:c.806G>A	p.Arg269His	p.R269H	ENST00000206249	NM_000125.3	269	cGc/cAc	4/8	1	2	FACETS	0.757	0.665	0.856	0.757	0.665	0.856	SUBCLONAL	1	TRUE	1	0.389946198930997	2		390	508	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	105	556	3	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	1	2	FACETS	0.874	0.785	0.969	0.874	0.785	0.969	CLONAL	1	TRUE	1	0.389946198930997	2		559	616	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943776	9943776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1277595711	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	112	448	0	ENST00000330684.3:c.1165G>A	p.Val389Met	p.V389M	ENST00000330684	NM_001134407.1	389	Gtg/Atg	5/13	1	2	FACETS	0.936	0.843	1	0.936	0.843	1	CLONAL	1	TRUE	1	0.389946198930997	2		448	614	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	147	673	0	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	0.765	0.697	0.835	0.765	0.697	0.835	SUBCLONAL	1	TRUE	1	0.389946198930997	2		673	986	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912346	32912346	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359406	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	115	283	0	ENST00000380152.3:c.3860del	p.Asn1287IlefsTer6	p.N1287Ifs*6	ENST00000380152		1285	gAa/ga	11/27	1	2	FACETS	0.815	0.734	0.899	0.815	0.734	0.899	CLONAL	1	TRUE	1	0.389946198930997	2		283	724	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478130	138478130	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148660928	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	49	510	1	ENST00000289153.2:c.56C>T	p.Ala19Val	p.A19V	ENST00000289153	NM_006219.2	19	gCg/gTg	1/22	1	2	FACETS	0.343	0.29	0.402	0.343	0.29	0.402	SUBCLONAL	1	TRUE	1	0.389946198930997	2		511	732	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784944	9784944	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	137	540	0	ENST00000377346.4:c.2947G>A	p.Ala983Thr	p.A983T	ENST00000377346	NM_005026.3	983	Gcg/Acg	23/24	1	2	FACETS	0.971	0.884	1	0.971	0.884	1	CLONAL	1	TRUE	1	0.389946198930997	2		540	724	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303205	11303205	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	147	584	1	ENST00000361445.4:c.1378C>T	p.Arg460Ter	p.R460*	ENST00000361445	NM_004958.3	460	Cga/Tga	9/58	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.389946198930997	2		585	744	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406444	70406444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149434944	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	176	584	2	ENST00000373644.4:c.3958C>T	p.Arg1320Trp	p.R1320W	ENST00000373644	NM_030625.2	1320	Cgg/Tgg	4/12	1	2	FACETS	0.96	0.885	1	0.96	0.885	1	CLONAL	1	TRUE	1	0.389946198930997	2		586	940	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406445	70406445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781773145	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	189	585	0	ENST00000373644.4:c.3959G>A	p.Arg1320Gln	p.R1320Q	ENST00000373644	NM_030625.2	1320	cGg/cAg	4/12	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.389946198930997	2		585	945	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88676898	88676898	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747371306	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	191	513	0	ENST00000372037.3:c.683G>A	p.Arg228Gln	p.R228Q	ENST00000372037	NM_004329.2	228	cGa/cAa	9/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.389946198930997	2		513	839	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903697	114903697	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	64	690	0	ENST00000543371.1:c.701C>A	p.Pro234Gln	p.P234Q	ENST00000543371	NM_001198531.1	234	cCg/cAg	7/14	1	2	FACETS	0.354	0.306	0.408	0.354	0.306	0.408	SUBCLONAL	1	TRUE	1	0.389946198930997	2		690	926	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941004	71941004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	144	675	0	ENST00000298229.2:c.884del	p.Pro295GlnfsTer20	p.P295Qfs*20	ENST00000298229	NM_001567.3	294	Ccc/cc	8/28	1	2	FACETS	0.825	0.752	0.902	0.825	0.752	0.902	CLONAL	1	TRUE	1	0.389946198930997	2		675	895	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998981	100998981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1321866717	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	75	472	2	ENST00000325455.5:c.821G>A	p.Arg274His	p.R274H	ENST00000325455	NM_001202474.3	274	cGc/cAc	1/8	1	2	FACETS	0.857	0.753	0.967	0.857	0.753	0.967	CLONAL	1	TRUE	1	0.389946198930997	2		474	449	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111959695	111959695	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	55	327	0	ENST00000375549.3:c.274G>A	p.Asp92Asn	p.D92N	ENST00000375549	NM_003002.3	92	Gac/Aac	3/4	1	2	FACETS	0.463	0.396	0.537	0.463	0.396	0.537	SUBCLONAL	1	TRUE	1	0.389946198930997	2		327	609	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415917	49415917	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	61	395	1	ENST00000301067.7:c.16430del	p.Cys5477LeufsTer10	p.C5477Lfs*10	ENST00000301067	NM_003482.3	5477	tGt/tt	53/54	1	2	FACETS	0.558	0.481	0.641	0.558	0.481	0.641	SUBCLONAL	1	TRUE	1	0.389946198930997	2		396	561	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445287	49445287	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	158	769	0	ENST00000301067.7:c.2179C>T	p.Pro727Ser	p.P727S	ENST00000301067	NM_003482.3	727	Cca/Tca	10/54	1	2	FACETS	0.875	0.802	0.952	0.875	0.802	0.952	CLONAL	1	TRUE	1	0.389946198930997	2		769	926	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235899	133235899	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	68	379	0	ENST00000320574.5:c.3257G>T	p.Gly1086Val	p.G1086V	ENST00000320574	NM_006231.2	1086	gGc/gTc	26/49	1	2	FACETS	0.789	0.689	0.897	0.789	0.689	0.897	SUBCLONAL	1	TRUE	1	0.389946198930997	2		379	442	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108083	30108084	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	169	589	0	ENST00000331968.5:c.723dup	p.Gly242TrpfsTer19	p.G242Wfs*19	ENST00000331968	NM_002742.2	241	-/T	5/18	1	2	FACETS	0.976	0.898	1	0.976	0.898	1	CLONAL	1	TRUE	1	0.389946198930997	2		589	888	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396475	30396475	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1474657301	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	32	419	0	ENST00000331968.5:c.244T>C	p.Cys82Arg	p.C82R	ENST00000331968	NM_002742.2	82	Tgc/Cgc	1/18	1	2	FACETS	0.282	0.228	0.343	0.282	0.228	0.343	SUBCLONAL	1	TRUE	1	0.389946198930997	2		419	583	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986679	36986679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	11	17	0	ENST00000354822.5:c.1010G>A	p.Gly337Asp	p.G337D	ENST00000354822	NM_001079668.2	337	gGc/gAc	3/3	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.389946198930997	2		17	38	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007726	45007729	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	109	408	0	ENST00000558401.1:c.176_179del	p.Leu59Ter	p.L59*	ENST00000558401	NM_004048.2	58	gACTTa/ga	2/4	0.389946198930997	1	FACETS	0.862	0.777	0.951	0.862	0.777	0.951	CLONAL	1	TRUE	0	0.389946198930997	1		408	522	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66777482	66777482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144080051	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	128	461	2	ENST00000307102.5:c.848C>T	p.Ala283Val	p.A283V	ENST00000307102	NM_002755.3	283	gCg/gTg	7/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.389946198930997	2		463	625	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121819	2121819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137854168	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	125	599	1	ENST00000219476.3:c.1981G>A	p.Gly661Ser	p.G661S	ENST00000219476	NM_000548.3	661	Ggc/Agc	19/42	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.389946198930997	2		600	603	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777892	3777892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1171889477	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	178	794	1	ENST00000262367.5:c.7156G>A	p.Gly2386Arg	p.G2386R	ENST00000262367	NM_004380.2	2386	Gga/Aga	31/31	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.389946198930997	2		795	885	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128558	30128558	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	138	503	0	ENST00000263025.4:c.824T>C	p.Met275Thr	p.M275T	ENST00000263025	NM_002746.2	275	aTg/aCg	6/9	1	2	FACETS	0.948	0.863	1	0.948	0.863	1	CLONAL	1	TRUE	1	0.389946198930997	2		503	747	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991703	72991703	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201821212	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	26	263	0	ENST00000268489.5:c.2342C>T	p.Ala781Val	p.A781V	ENST00000268489	NM_006885.3	781	gCg/gTg	2/10	1	2	FACETS	0.593	0.472	0.73	0.593	0.472	0.73	SUBCLONAL	1	TRUE	1	0.389946198930997	2		263	225	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993536	72993536	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	93	452	0	ENST00000268489.5:c.509T>C	p.Phe170Ser	p.F170S	ENST00000268489	NM_006885.3	170	tTc/tCc	2/10	1	2	FACETS	0.824	0.734	0.919	0.824	0.734	0.919	CLONAL	1	TRUE	1	0.389946198930997	2		452	579	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351923	89351923	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147744268	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	174	839	3	ENST00000301030.4:c.1027G>A	p.Val343Ile	p.V343I	ENST00000301030	NM_001256183.1	343	Gtc/Atc	9/13	1	2	FACETS	0.871	0.801	0.943	0.871	0.801	0.943	CLONAL	1	TRUE	1	0.389946198930997	2		842	1025	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805768	46805768	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199813155	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	100	524	0	ENST00000290295.7:c.188G>A	p.Cys63Tyr	p.C63Y	ENST00000290295	NM_006361.5	63	tGc/tAc	1/2	1	2	FACETS	0.9	0.806	0.999	0.9	0.806	0.999	CLONAL	1	TRUE	1	0.389946198930997	2		524	570	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733223	74733223	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	107	479	0	ENST00000359995.5:c.20del	p.Pro7LeufsTer7	p.P7Lfs*7	ENST00000359995	NM_001195427.1	7	cCt/ct	1/3	1	2	FACETS	0.919	0.827	1	0.919	0.827	1	CLONAL	1	TRUE	1	0.389946198930997	2		479	597	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121052	3121052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777133920	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	178	719	1	ENST00000078429.4:c.955G>A	p.Asp319Asn	p.D319N	ENST00000078429	NM_002067.2	319	Gac/Aac	7/7	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.389946198930997	2		720	842	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248625	10248625	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	62	472	0	ENST00000340748.4:c.4128G>T	p.Glu1376Asp	p.E1376D	ENST00000340748		1376	gaG/gaT	35/40	1	2	FACETS	0.558	0.482	0.64	0.558	0.482	0.64	SUBCLONAL	1	TRUE	1	0.389946198930997	2		472	570	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095950	11095950	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	119	548	0	ENST00000358026.2:c.224C>A	p.Pro75His	p.P75H	ENST00000358026	NM_001128849.1	75	cCc/cAc	3/36	1	2	FACETS	0.952	0.861	1	0.952	0.861	1	CLONAL	1	TRUE	1	0.389946198930997	2		548	641	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272170	15272170	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	102	433	0	ENST00000263388.2:c.6269G>C	p.Gly2090Ala	p.G2090A	ENST00000263388	NM_000435.2	2090	gGc/gCc	33/33	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.389946198930997	2		433	459	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216712	36216712	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780411851	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	36	391	2	ENST00000222270.7:c.3878G>A	p.Arg1293His	p.R1293H	ENST00000222270	NM_014727.1	1293	cGc/cAc	13/37	1	2	FACETS	0.369	0.303	0.444	0.369	0.303	0.444	SUBCLONAL	1	TRUE	1	0.389946198930997	2		393	500	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227874	36227875	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	81	734	0	ENST00000222270.7:c.7363_7364del	p.Ser2455LeufsTer2	p.S2455Lfs*2	ENST00000222270	NM_014727.1	2453	caTCtc/catc	32/37	1	2	FACETS	0.51	0.448	0.576	0.51	0.448	0.576	SUBCLONAL	1	TRUE	1	0.389946198930997	2		734	815	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085755	16085755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	112	552	3	ENST00000281043.3:c.931G>A	p.Gly311Arg	p.G311R	ENST00000281043	NM_005378.4	311	Ggg/Agg	3/3	1	2	FACETS	0.895	0.806	0.988	0.895	0.806	0.988	CLONAL	1	TRUE	1	0.389946198930997	2		555	642	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39294788	39294788	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	125	522	0	ENST00000402219.2:c.194G>A	p.Arg65Gln	p.R65Q	ENST00000402219	NM_005633.3	65	cGa/cAa	2/23	1	2	FACETS	0.817	0.739	0.898	0.817	0.739	0.898	CLONAL	1	TRUE	1	0.389946198930997	2		522	785	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574053	46574053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1320324950	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	141	509	1	ENST00000263734.3:c.68C>T	p.Ala23Val	p.A23V	ENST00000263734	NM_001430.4	23	gCg/gTg	2/16	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.389946198930997	2		510	716	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99154342	99154342	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774761280	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	96	404	0	ENST00000074304.5:c.484C>T	p.Arg162Cys	p.R162C	ENST00000074304	NM_001134224.1	162	Cgt/Tgt	8/26	1	2	FACETS	0.917	0.819	1	0.917	0.819	1	CLONAL	1	TRUE	1	0.389946198930997	2		404	537	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273135	198273135	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	66	490	0	ENST00000335508.6:c.1075C>G	p.Pro359Ala	p.P359A	ENST00000335508	NM_012433.2	359	Cca/Gca	8/25	1	2	FACETS	0.424	0.367	0.485	0.424	0.367	0.485	SUBCLONAL	1	TRUE	1	0.389946198930997	2		490	799	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434237	12434237	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	128	512	0	ENST00000287820.6:c.605G>T	p.Gly202Val	p.G202V	ENST00000287820	NM_015869.4	202	gGg/gTg	4/7	1	2	FACETS	0.794	0.719	0.872	0.794	0.719	0.872	SUBCLONAL	1	TRUE	1	0.389946198930997	2		512	827	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161871	47161871	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	59	509	1	ENST00000409792.3:c.4255G>T	p.Gly1419Cys	p.G1419C	ENST00000409792	NM_014159.6	1419	Ggt/Tgt	3/21	1	2	FACETS	0.337	0.289	0.39	0.337	0.289	0.39	SUBCLONAL	1	TRUE	1	0.389946198930997	2		510	898	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205850	128205850	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	58	253	0	ENST00000341105.2:c.25C>T	p.Arg9Cys	p.R9C	ENST00000341105	NM_032638.4	9	Cgc/Tgc	2/6	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.389946198930997	2		253	285	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953109	38953109	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	35	335	0	ENST00000357387.3:c.2875T>G	p.Cys959Gly	p.C959G	ENST00000357387	NM_152756.3	959	Tgt/Ggt	29/38	1	2	FACETS	0.341	0.279	0.411	0.341	0.279	0.411	SUBCLONAL	1	TRUE	1	0.389946198930997	2		335	527	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500798	149500798	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	143	531	1	ENST00000261799.4:c.2432C>T	p.Ala811Val	p.A811V	ENST00000261799	NM_002609.3	811	gCc/gTc	17/23	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.389946198930997	2		532	659	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043956	180043956	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	77	626	0	ENST00000261937.6:c.3040C>G	p.Leu1014Val	p.L1014V	ENST00000261937	NM_182925.4	1014	Ctt/Gtt	22/30	NA	2	FACETS	0.539	0.472	0.61			1	INDETERMINATE	1	TRUE	NA	0.389946198930997	2		626	733	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170042	32170042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	189	683	0	ENST00000375023.3:c.3566C>T	p.Ala1189Val	p.A1189V	ENST00000375023	NM_004557.3	1189	gCt/gTt	21/30	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.389946198930997	2		683	922	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700222	117700222	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs979014772	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	116	507	0	ENST00000368508.3:c.2597G>A	p.Ser866Asn	p.S866N	ENST00000368508	NM_002944.2	866	aGc/aAc	17/43	1	2	FACETS	0.866	0.782	0.955	0.866	0.782	0.955	CLONAL	1	TRUE	1	0.389946198930997	2		507	687	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543608	148543608	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	76	580	0	ENST00000320356.2:c.200C>A	p.Pro67His	p.P67H	ENST00000320356	NM_004456.4	67	cCt/cAt	3/20	1	2	FACETS	0.43	0.376	0.489	0.43	0.376	0.489	SUBCLONAL	1	TRUE	1	0.389946198930997	2		580	906	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151882716	151882716	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	22	239	0	ENST00000262189.6:c.5009A>T	p.Asp1670Val	p.D1670V	ENST00000262189	NM_170606.2	1670	gAt/gTt	34/59	1	2	FACETS	0.289	0.223	0.365	0.289	0.223	0.365	SUBCLONAL	1	TRUE	1	0.389946198930997	2		239	391	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300040	137300040	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	148	968	4	ENST00000481739.1:c.331del	p.Leu111TrpfsTer57	p.L111Wfs*57	ENST00000481739	NM_002957.4	109	Ccc/cc	3/10	1	2	FACETS	0.896	0.819	0.977	0.896	0.819	0.977	CLONAL	1	TRUE	1	0.389946198930997	2		972	847	SUCCESS
AR	367	MSKCC	GRCh37	X	66765317	66765317	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	67	672	0	ENST00000374690.3:c.329T>A	p.Leu110Gln	p.L110Q	ENST00000374690	NM_000044.3	110	cTg/cAg	1/8	1	2	FACETS	0.502	0.435	0.573	0.502	0.435	0.573	SUBCLONAL	1	TRUE	1	0.389946198930997	2		672	685	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70350027	70350027	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	79	513	0	ENST00000374080.3:c.4013del	p.Asn1338ThrfsTer7	p.N1338Tfs*7	ENST00000374080		1337	gAa/ga	28/45	1	2	FACETS	0.641	0.564	0.724	0.641	0.564	0.724	SUBCLONAL	1	TRUE	1	0.389946198930997	2		513	632	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360589	70360597	+	inframe_deletion	In_Frame_Del	DEL	AGCAGCAGC	AGCAGCAGC	-	rs769857818	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	83	511	0	ENST00000374080.3:c.6159_6167del	p.Gln2074_Gln2076del	p.Q2074_Q2076del	ENST00000374080		2050	gAGCAGCAGCag/gag	42/45	1	2	FACETS	0.605	0.533	0.681	0.605	0.533	0.681	SUBCLONAL	1	TRUE	1	0.389946198930997	2		511	704	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939674	76939674	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	117	741	0	ENST00000373344.5:c.1074del	p.Lys358AsnfsTer2	p.K358Nfs*2	ENST00000373344	NM_000489.3	358	aaA/aa	9/35	1	2	FACETS	0.658	0.593	0.727	0.658	0.593	0.727	SUBCLONAL	1	TRUE	1	0.389946198930997	2		741	912	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152864462	152864462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	15	127	0	ENST00000406277.2:c.64G>A	p.Ala22Thr	p.A22T	ENST00000406277	NM_152274.4	22	Gcc/Acc	3/7	1		FACETS		0.405	0.721				SUBCLONAL	1	TRUE	1	0.389946198930997	2		127	140	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993832	72993832	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	77	305	2	ENST00000268489.5:c.213del	p.Ser72ProfsTer37	p.S72Pfs*37	ENST00000268489	NM_006885.3	71	ccC/cc	2/10	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.389946198930997	2		307	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0016181-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	231	869	3	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.312549684439952	2	FACETS	0.651	0.607	0.697	0.325	0.303	0.349	INDETERMINATE	1	TRUE	0	0.654085527991889	2		872	1085	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156068	99156068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016181-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	113	652	0	ENST00000074304.5:c.748G>A	p.Ala250Thr	p.A250T	ENST00000074304	NM_001134224.1	250	Gca/Aca	10/26	1	2	FACETS	0.521	0.469	0.576	0.521	0.469	0.576	SUBCLONAL	1	TRUE	1	0.654085527991889	2		652	663	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955966	55955966	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757722266	NA	P-0016181-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	105	670	0	ENST00000263923.4:c.3196C>T	p.Arg1066Cys	p.R1066C	ENST00000263923	NM_002253.2	1066	Cgc/Tgc	24/30	0.102505770181378	5	FACETS	0.7	0.626	0.778			1	INDETERMINATE	1	TRUE	NA	0.654085527991889	5		670	909	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240171	41240171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1291996842	NA	P-0016181-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	18	64	0	ENST00000379561.5:c.179C>T	p.Ser60Leu	p.S60L	ENST00000379561	NM_002015.3	60	tCg/tTg	1/3	0.654085527991889	1	FACETS	0.529	0.409	0.662	0.529	0.409	0.662	SUBCLONAL	1	TRUE	0	0.654085527991889	1		64	70	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574035	7574035	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0016181-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	384	720	1	ENST00000269305.4:c.994-2A>T		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.312549684439952	2	FACETS	1	0.996	1	0.727	0.695	0.76	INDETERMINATE	1	TRUE	0	0.654085527991889	2		721	807	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456582	32456582	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016181-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	21	40	0	ENST00000332351.3:c.310C>T	p.Pro104Ser	p.P104S	ENST00000332351	NM_024426.4	104	Ccg/Tcg	1/10	0.518759668738229	1	FACETS	0.675	0.538	0.822	0.675	0.538	0.822	SUBCLONAL	1	TRUE	0	0.654085527991889	1		40	64	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610447	81610447	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016181-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	97	562	0	ENST00000298171.2:c.2045C>A	p.Thr682Asn	p.T682N	ENST00000298171	NM_000369.2	682	aCc/aAc	10/10	0.619878119953875	3	FACETS	0.455	0.405	0.508	0.228	0.202	0.254	SUBCLONAL	1	TRUE	1	0.654085527991889	3		562	865	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028481	42028481	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0016181-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	459	643	1	ENST00000219905.7:c.4019C>G	p.Ser1340Ter	p.S1340*	ENST00000219905	NM_001164273.1	1340	tCa/tGa	13/24	0.654085527991889	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.654085527991889	1		644	760	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813818	50813818	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016181-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	324	921	1	ENST00000398568.2:c.1372G>T	p.Ala458Ser	p.A458S	ENST00000398568	NM_001042412.1	458	Gcc/Tcc	8/18	0.642756803483618	2	FACETS	0.987	0.934	1	0.493	0.467	0.521	CLONAL	1	TRUE	0	0.654085527991889	2		922	1004	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796914	78796914	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016181-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	370	705	4	ENST00000306801.3:c.1027G>T	p.Val343Leu	p.V343L	ENST00000306801	NM_020761.2	343	Gtg/Ttg	9/34	0.312549684439952	2	FACETS	1	0.996	1	0.74	0.707	0.773	INDETERMINATE	1	TRUE	0	0.654085527991889	2		709	764	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589827	55589827	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016181-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	96	542	0	ENST00000288135.5:c.1309A>G	p.Thr437Ala	p.T437A	ENST00000288135	NM_000222.2	437	Aca/Gca	8/21	0.102505770181378	5	FACETS	0.655	0.583	0.732			1	INDETERMINATE	1	TRUE	NA	0.654085527991889	5		542	888	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722098	176722098	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016181-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	535	553	2	ENST00000439151.2:c.7729G>T	p.Val2577Leu	p.V2577L	ENST00000439151	NM_022455.4	2577	Gtg/Ttg	23/23	0.602096462740795	4	FACETS	1	0.972	1	0.754	0.729	0.779	CLONAL	3	TRUE	0	0.654085527991889	4		555	897	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679762	30679762	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016181-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	90	650	0	ENST00000376406.3:c.1957G>C	p.Asp653His	p.D653H	ENST00000376406	NM_014641.2	653	Gac/Cac	5/15	0.367064455407699	3	FACETS	0.443	0.393	0.497	0.222	0.196	0.249	INDETERMINATE	1	TRUE	1	0.654085527991889	3		650	824	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346637	81346637	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016181-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	285	430	0	ENST00000222390.5:c.1316A>C	p.Tyr439Ser	p.Y439S	ENST00000222390	NM_000601.4	439	tAc/tCc	11/18	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.654085527991889	2		430	678	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140500172	140500172	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016181-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1230	218	1029	0	ENST00000288602.6:c.970G>C	p.Asp324His	p.D324H	ENST00000288602	NM_004333.4	324	Gac/Cac	7/18	0.102505770181378	5	FACETS	0.912	0.846	0.981			1	INDETERMINATE	1	TRUE	NA	0.654085527991889	5		1029	1448	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146952	38146952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016181-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1417	197	1022	2	ENST00000317025.8:c.3190G>A	p.Glu1064Lys	p.E1064K	ENST00000317025	NM_023034.1	1064	Gaa/Aaa	18/24	0.619878119953875	3	FACETS	0.495	0.457	0.536	0.248	0.228	0.268	SUBCLONAL	1	TRUE	1	0.654085527991889	3		1024	1614	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939463	68939463	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016181-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	476	622	0	ENST00000288368.4:c.448A>G	p.Met150Val	p.M150V	ENST00000288368	NM_024870.2	150	Atg/Gtg	5/40	0.619878119953875	3	FACETS	0.861	0.825	0.897	0.861	0.825	0.897	CLONAL	2	TRUE	1	0.654085527991889	3		622	1122	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0016182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	130	580	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	1	2	FACETS	0.831	0.753	0.912	0.831	0.753	0.912	CLONAL	1	TRUE	1	0.369996872674599	2		580	846	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0016182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	140	714	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	0.78	0.71	0.854	0.78	0.71	0.854	SUBCLONAL	1	TRUE	1	0.369996872674599	2		714	970	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0016182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	101	257	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.883	0.791	0.981	0.883	0.791	0.981	CLONAL	1	TRUE	1	0.369996872674599	2		257	618	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604758	48604759	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCACTTACACCGGGCCC	novel	NA	P-0016182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	85	478	0	ENST00000342988.3:c.1583_1599dup	p.Gln534ThrfsTer9	p.Q534Tfs*9	ENST00000342988	NM_005359.5	527	att/atTCACTTACACCGGGCCCt	12/12	0.315806704455712	1	FACETS	0.563	0.498	0.633	0.563	0.498	0.633	SUBCLONAL	1	TRUE	0	0.369996872674599	1		478	665	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0016183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	433	796	1	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.808575212377713	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.808575212377713	1		797	555	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0016184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	62	731	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.617	0.531	0.71	0.617	0.531	0.71	SUBCLONAL	1	TRUE	1	0.220938435159013	2		731	910	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380331	14380338	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGACTT	GCCGACTT	-	novel	NA	P-0016184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	56	276	0	ENST00000256196.4:c.79_86del	p.Lys27AlafsTer15	p.K27Afs*15	ENST00000256196		27	AAGTCGGCg/g	1/6	1	2	FACETS	0.883	0.757	1	0.883	0.757	1	CLONAL	1	TRUE	1	0.220938435159013	2		276	574	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266500	55266500	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	148	592	0	ENST00000275493.2:c.2792A>G	p.Glu931Gly	p.E931G	ENST00000275493	NM_005228.3	931	gAa/gGa	23/28	1	2	FACETS	0.78	0.712	0.851	1	0.988	1	SUBCLONAL	2	TRUE	1	0.220938435159013	2		592	859	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1287	83	641	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	0.11	2		641	1370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs786201057	NA	P-0016184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	52	457	0	ENST00000269305.4:c.374C>G	p.Thr125Arg	p.T125R	ENST00000269305	NM_001126112.2	125	aCg/aGg	4/11	1	2	FACETS	0.957	0.812	1	0.957	0.812	1	CLONAL	1	TRUE	1	0.11	2		457	988	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633363	3633363	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776578234	NA	P-0016184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1321	73	586	2	ENST00000294008.3:c.4888G>A	p.Ala1630Thr	p.A1630T	ENST00000294008	NM_032444.2	1630	Gcc/Acc	14/15	1	2	FACETS	0.952	0.829	1	0.952	0.829	1	CLONAL	1	TRUE	1	0.11	2		588	1394	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610208	10610208	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	164	657	0	ENST00000171111.5:c.502G>T	p.Val168Phe	p.V168F	ENST00000171111	NM_203500.1	168	Gtc/Ttc	2/6	0.417023111741977	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.417023111741977	1		657	421	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428629	49428629	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	210	723	3	ENST00000301067.7:c.10321C>T	p.Gln3441Ter	p.Q3441*	ENST00000301067	NM_003482.3	3441	Cag/Tag	35/54	0.283377277339928	4	FACETS	0.909	0.846	0.974	0.909	0.846	0.974	CLONAL	2	TRUE	2	0.417023111741977	4		726	785	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805885	46805885	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	105	382	0	ENST00000290295.7:c.71G>T	p.Gly24Val	p.G24V	ENST00000290295	NM_006361.5	24	gGg/gTg	1/2	1	2	FACETS	0.782	0.709	0.857	1	0.985	1	SUBCLONAL	2	TRUE	1	0.417023111741977	2		382	322	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207078	1207083	+	inframe_deletion	In_Frame_Del	DEL	GGGGAA	GGGGAA	-	novel	NA	P-0016185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	149	673	0	ENST00000326873.7:c.168_173del	p.Glu57_Gly58del	p.E57_G58del	ENST00000326873	NM_000455.4	56	GGGGAA/-	1/10	0.417023111741977	1	FACETS	0.756	0.7	0.814	1	0.99	1	SUBCLONAL	2	TRUE	0	0.417023111741977	1		673	374	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141395	11141452	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTGCCCGTCAGGAACCACGAAGGCGGAGGACCGGGGCATGCTGCTGAAAACCTTCAAC	GTGCCCGTCAGGAACCACGAAGGCGGAGGACCGGGGCATGCTGCTGAAAACCTTCAAC	-	novel	NA	P-0016185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	60	454	1	ENST00000358026.2:c.3383-10_3430del		p.X1128_splice	ENST00000358026	NM_001128849.1	1128		25/36	0.409980262142643	2	FACETS	1	0.952	1	0.602	0.525	0.684	CLONAL	1	TRUE	0	0.417023111741977	2		455	239	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223212	36223212	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	138	873	1	ENST00000222270.7:c.5762C>T	p.Pro1921Leu	p.P1921L	ENST00000222270	NM_014727.1	1921	cCc/cTc	28/37	0.417023111741977	7	FACETS	1	0.948	1			1	CLONAL	1	TRUE	NA	0.417023111741977	7		874	1268	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528635	89528635	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	79	355	0	ENST00000336596.2:c.2935G>T	p.Gly979Cys	p.G979C	ENST00000336596	NM_005233.5	979	Ggc/Tgc	17/17	0.417023111741977	3	FACETS	0.758	0.667	0.855	0.379	0.333	0.428	SUBCLONAL	1	TRUE	1	0.417023111741977	3		355	604	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984923	101984923	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	29	336	0	ENST00000282441.5:c.370C>G	p.Arg124Gly	p.R124G	ENST00000282441	NM_001130145.2	124	Cga/Gga	2/9	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		336	373	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1231	172	726	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.433560947569443	3	FACETS	0.568	0.521	0.617	0.284	0.26	0.309	SUBCLONAL	1	TRUE	1	0.550466731647877	3		726	1403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0016187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	540	800	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.497600496011718	2	FACETS	0.939	0.905	0.972	0.939	0.905	0.972	CLONAL	2	TRUE	0	0.550466731647877	2		801	1045	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0016187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	151	619	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	NA	2	FACETS	0.502	0.458	0.549			1	INDETERMINATE	1	TRUE	NA	0.550466731647877	2		619	1092	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971116	21971116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552823	NA	P-0016187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	270	529	0	ENST00000304494.5:c.242C>T	p.Pro81Leu	p.P81L	ENST00000304494	NM_000077.4	81	cCc/cTc	2/3	0.550466731647877	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.550466731647877	1		529	511	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916922	178916927	+	inframe_deletion	In_Frame_Del	DEL	ACCAGT	ACCAGT	-	novel	NA	P-0016187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	156	662	0	ENST00000263967.3:c.310_315del	p.Pro104_Val105del	p.P104_V105del	ENST00000263967	NM_006218.2	103	gaACCAGTa/gaa	2/21	0.129251497207569	5	FACETS	1	0.974	1	0.385	0.352	0.419	INDETERMINATE	1	TRUE	2	0.550466731647877	5		662	896	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099071	27099071	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	331	652	0	ENST00000324856.7:c.3488del	p.Pro1163GlnfsTer17	p.P1163Qfs*17	ENST00000324856	NM_006015.4	1163	Cca/ca	13/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.550466731647877	2		652	1039	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982299	201982364	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGTCCCCACAGATGGTTTTCGTGACTGCAAGAAGGGGGATCCCAAGCACGGGAAGCGGAAACGAGG	CGTCCCCACAGATGGTTTTCGTGACTGCAAGAAGGGGGATCCCAAGCACGGGAAGCGGAAACGAGG	-	novel	NA	P-0016187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	146	573	0	ENST00000359651.3:c.689-10_744del		p.X230_splice	ENST00000359651		230		6/8	0.354522454154142	3	FACETS	0.629	0.573	0.688	0.315	0.286	0.344	SUBCLONAL	1	TRUE	1	0.550466731647877	3		573	1075	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481649	56481649	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	246	592	3	ENST00000267101.3:c.684T>A	p.His228Gln	p.H228Q	ENST00000267101	NM_001982.3	228	caT/caA	6/28	0.433560947569443	3	FACETS	1	0.96	1	0.519	0.484	0.554	CLONAL	1	TRUE	1	0.550466731647877	3		595	1099	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286225	66286225	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	130	470	0	ENST00000273854.3:c.1461G>C	p.Leu487Phe	p.L487F	ENST00000273854	NM_004439.5	487	ttG/ttC	6/18	0.254623193838344	3	FACETS	1	0.911	1	0.5	0.455	0.548	INDETERMINATE	1	TRUE	1	0.550466731647877	3		470	602	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619391	1619391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779358744	NA	P-0016189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	48	605	1	ENST00000344749.5:c.1250C>T	p.Thr417Met	p.T417M	ENST00000344749	NM_001136139.2	417	aCg/aTg	15/19	1	2	FACETS	0.902	0.761	1	0.902	0.761	1	CLONAL	1	TRUE	1	0.154644932401951	2		606	688	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579427	7579427	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	58	593	0	ENST00000269305.4:c.260del	p.Pro87GlnfsTer36	p.P87Qfs*36	ENST00000269305	NM_001126112.2	87	cCa/ca	4/11	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.154644932401951	2		593	693	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971116	21971116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552823	NA	P-0016190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	314	529	0	ENST00000304494.5:c.242C>T	p.Pro81Leu	p.P81L	ENST00000304494	NM_000077.4	81	cCc/cTc	2/3	0.558973420365417	2	FACETS	0.964	0.919	1	0.964	0.919	1	CLONAL	2	TRUE	0	0.558973420365417	2		529	583	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0016190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	503	765	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.52748209223514	2	FACETS	0.966	0.931	1	0.966	0.931	1	CLONAL	2	TRUE	0	0.558973420365417	2		765	932	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396516	30396516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs537554301	NA	P-0016190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	336	621	1	ENST00000331968.5:c.203C>T	p.Ser68Leu	p.S68L	ENST00000331968	NM_002742.2	68	tCg/tTg	1/18	0.214027318999447	4	FACETS	0.888	0.841	0.936	0.888	0.841	0.936	INDETERMINATE	2	TRUE	2	0.558973420365417	4		622	1055	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949099	151949100	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0016190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	379	654	0	ENST00000262189.6:c.1545_1546del	p.Met515IlefsTer3	p.M515Ifs*3	ENST00000262189	NM_170606.2	515	atGTat/atat	11/59	NA	2	FACETS	0.955	0.915	0.995			1	INDETERMINATE	2	TRUE	NA	0.558973420365417	2		654	710	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0016191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	114	547	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	0.216262878125954	2		547	704	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	59	423	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.978	0.849	1	1	0.978	1	CLONAL	2	TRUE	1	0.216262878125954	2		423	279	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581229	48581229	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs377767331	NA	P-0016191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	128	761	0	ENST00000342988.3:c.533C>G	p.Ser178Ter	p.S178*	ENST00000342988	NM_005359.5	178	tCa/tGa	5/12	0.216262878125954	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.216262878125954	1		761	817	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441974	6441974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	173	772	0	ENST00000356142.4:c.533C>T	p.Ala178Val	p.A178V	ENST00000356142	NM_018890.3	178	gCg/gTg	7/7	1	2	FACETS	0.847	0.779	0.917	1	0.991	1	CLONAL	2	TRUE	1	0.216262878125954	2		772	945	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0016191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	181	520	1	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.216262878125954	2	FACETS	0.975	0.905	1	1	0.99	1	CLONAL	3	TRUE	0	0.216262878125954	2		521	572	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468036	120468036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs919872084	NA	P-0016191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	78	661	0	ENST00000256646.2:c.4403C>T	p.Ser1468Phe	p.S1468F	ENST00000256646	NM_024408.3	1468	tCc/tTc	25/34	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.216262878125954	2		661	676	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201675	67201675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	93	540	1	ENST00000312629.5:c.976C>T	p.Pro326Ser	p.P326S	ENST00000312629	NM_003952.2	326	Ccc/Tcc	12/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.216262878125954	2		541	647	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431604	6431604	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	40	218	0	ENST00000356142.4:c.157C>A	p.Leu53Met	p.L53M	ENST00000356142	NM_018890.3	53	Ctg/Atg	3/7	1	2	FACETS	0.841	0.705	0.989	1	0.963	1	CLONAL	2	TRUE	1	0.216262878125954	2		218	220	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139414006	139414006	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	199	609	0	ENST00000277541.6:c.754C>T	p.Gln252Ter	p.Q252*	ENST00000277541	NM_017617.3	252	Cag/Tag	5/34	0.216262878125954	2	FACETS	1	0.945	1	1	0.992	1	CLONAL	3	TRUE	0	0.216262878125954	2		609	604	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356252	70356252	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1215330787	NA	P-0016191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	99	350	1	ENST00000374080.3:c.5147G>A	p.Arg1716Gln	p.R1716Q	ENST00000374080		1716	cGa/cAa	37/45	1	1	FACETS	1	0.951	1	1	0.988	1	CLONAL	2	TRUE	0	0.216262878125954	1		351	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0016192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	385	485	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.454075905129099	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.460410991969072	2		486	814	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012383	176012386	+	frameshift_variant	Frame_Shift_Del	DEL	CCAA	CCAA	-	novel	NA	P-0016192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	312	684	2	ENST00000367669.3:c.1548_1551del	p.Cys516Ter	p.C516*	ENST00000367669	NM_022457.5	516	tgTTGG/tg	14/20	0.453433922149217	4	FACETS	0.816	0.769	0.864	0.816	0.769	0.864	CLONAL	2	TRUE	2	0.460410991969072	4		686	1213	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970971	21970971	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	229	786	1	ENST00000304494.5:c.387C>A	p.Tyr129Ter	p.Y129*	ENST00000304494	NM_000077.4	129	taC/taA	2/3	0.478051931658952	1	FACETS	0.748	0.7	0.798	0.748	0.7	0.798	SUBCLONAL	1	TRUE	0	0.58128884725951	1		787	747	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596072	43596072	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	174	739	0	ENST00000355710.3:c.239T>G	p.Leu80Arg	p.L80R	ENST00000355710	NM_020975.4	80	cTg/cGg	2/20	1	2	FACETS	0.659	0.607	0.714	0.659	0.607	0.714	SUBCLONAL	1	TRUE	1	0.58128884725951	2		739	908	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793064	33793064	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016193-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	31	292	0	ENST00000498907.2:c.257G>C	p.Arg86Pro	p.R86P	ENST00000498907	NM_004364.3	86	cGg/cCg	1/1	1	2	FACETS	0.233	0.188	0.284	0.233	0.188	0.284	SUBCLONAL	1	TRUE	1	0.590869815311227	2		292	450	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862767	9862767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1285952756	NA	P-0016195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	146	674	0	ENST00000330684.3:c.2536C>T	p.Arg846Cys	p.R846C	ENST00000330684	NM_001134407.1	846	Cgc/Tgc	12/13	0.514062987454079	1	FACETS	0.921	0.848	0.997	0.921	0.848	0.997	CLONAL	1	TRUE	0	0.514062987454079	1		674	458	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437286	52437286	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	161	847	0	ENST00000460680.1:c.1758del	p.Arg587AspfsTer30	p.R587Dfs*30	ENST00000460680	NM_004656.3	586	atC/at	14/17	0.514062987454079	1	FACETS	0.974	0.9	1	0.974	0.9	1	CLONAL	1	TRUE	0	0.514062987454079	1		847	478	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	174	486	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.32463206301339	3	FACETS	0.912	0.844	0.982	0.912	0.844	0.982	CLONAL	2	TRUE	1	0.385769539972332	3		486	590	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	119	540	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	1	2	FACETS	0.841	0.759	0.926	0.841	0.759	0.926	CLONAL	1	TRUE	1	0.385769539972332	2		540	734	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528335	157528335	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	159	731	0	ENST00000346085.5:c.6060G>C	p.Leu2020Phe	p.L2020F	ENST00000346085	NM_020732.3	2020	ttG/ttC	20/20	1	2	FACETS	0.761	0.697	0.829	0.761	0.697	0.829	SUBCLONAL	1	TRUE	1	0.385769539972332	2		731	1083	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209357	98209357	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748812637	NA	P-0016196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	65	449	0	ENST00000331920.6:c.4181G>A	p.Arg1394Gln	p.R1394Q	ENST00000331920	NM_000264.3	1394	cGa/cAa	23/24	0.385769539972332	1	FACETS	0.548	0.476	0.626	0.548	0.476	0.626	SUBCLONAL	1	TRUE	0	0.385769539972332	1		449	496	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162323	47162323	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs773098323	NA	P-0016196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	89	404	0	ENST00000409792.3:c.3803C>G	p.Ser1268Cys	p.S1268C	ENST00000409792	NM_014159.6	1268	tCt/tGt	3/21	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.385769539972332	2		404	385	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717609	89717609	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs876661024	NA	P-0016196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	97	425	0	ENST00000371953.3:c.635-1G>C		p.X212_splice	ENST00000371953	NM_000314.4	212			NA	2	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.385769539972332	2		425	416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0016196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	185	470	0	ENST00000269305.4:c.673-2A>C		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.385769539972332	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.385769539972332	1		470	563	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552763	18552763	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	28	532	0	ENST00000266497.5:c.2174T>G	p.Leu725Arg	p.L725R	ENST00000266497		725	cTt/cGt	14/31	1	2	FACETS	0.301	0.24	0.371	0.301	0.24	0.371	SUBCLONAL	1	TRUE	1	0.385769539972332	2		532	482	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	121	423	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.91	0.83	0.992	0.91	0.83	0.992	CLONAL	1	TRUE	1	0.707451450613471	2		423	376	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310572	65310572	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	160	491	0	ENST00000342505.4:c.2116G>A	p.Glu706Lys	p.E706K	ENST00000342505	NM_002227.2	706	Gag/Aag	16/25	1	2	FACETS	0.896	0.827	0.966	0.896	0.827	0.966	CLONAL	1	TRUE	1	0.707451450613471	2		491	505	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0016197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	539	1585	1	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.370356111133848	4	FACETS	1	0.995	1			1	INDETERMINATE	2	TRUE	NA	0.707451450613471	4		1586	1060	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247617	123247617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	321	630	0	ENST00000358487.5:c.1874G>A	p.Arg625Gln	p.R625Q	ENST00000358487	NM_000141.4	625	cGa/cAa	14/18	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.707451450613471	2		630	819	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421568	32421568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267602851	NA	P-0016197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	176	519	0	ENST00000332351.3:c.1024G>A	p.Asp342Asn	p.D342N	ENST00000332351	NM_024426.4	342	Gat/Aat	6/10	0.701653638323662	3	FACETS	0.832	0.767	0.899	0.416	0.383	0.45	CLONAL	1	TRUE	1	0.707451450613471	3		519	810	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200951	108200951	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1565529306	NA	P-0016197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	151	378	0	ENST00000278616.4:c.7318A>G	p.Lys2440Glu	p.K2440E	ENST00000278616	NM_000051.3	2440	Aag/Gag	50/63	0.707451450613471	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.707451450613471	1		378	274	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515210	103515210	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141763734	NA	P-0016197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	199	537	0	ENST00000355739.4:c.1711C>T	p.Pro571Ser	p.P571S	ENST00000355739	NM_000123.3	571	Ccg/Tcg	8/15	1	2	FACETS	0.904	0.843	0.968	0.904	0.843	0.968	CLONAL	1	TRUE	1	0.707451450613471	2		537	622	SUCCESS
BLM	641	MSKCC	GRCh37	15	91333991	91333991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs944867688	NA	P-0016197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	515	704	2	ENST00000355112.3:c.2936G>A	p.Arg979Lys	p.R979K	ENST00000355112	NM_000057.2	979	aGa/aAa	15/22	0.707451450613471	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.707451450613471	3		706	976	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9928072	9928072	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780349	NA	P-0016197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	197	531	0	ENST00000330684.3:c.1667C>T	p.Ser556Phe	p.S556F	ENST00000330684	NM_001134407.1	556	tCt/tTt	8/13	1	2	FACETS	0.975	0.909	1	0.975	0.909	1	CLONAL	1	TRUE	1	0.707451450613471	2		531	571	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274231	10274231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367543131	NA	P-0016197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	136	361	1	ENST00000330684.3:c.38C>T	p.Pro13Leu	p.P13L	ENST00000330684	NM_001134407.1	13	cCg/cTg	2/13	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.707451450613471	2		362	380	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829181	72829181	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	208	566	0	ENST00000268489.5:c.7400C>T	p.Pro2467Leu	p.P2467L	ENST00000268489	NM_006885.3	2467	cCc/cTc	9/10	1	2	FACETS	0.974	0.909	1	0.974	0.909	1	CLONAL	1	TRUE	1	0.707451450613471	2		566	604	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984478	72984478	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	217	662	0	ENST00000268489.5:c.3106A>G	p.Asn1036Asp	p.N1036D	ENST00000268489	NM_006885.3	1036	Aac/Gac	3/10	1	2	FACETS	0.88	0.822	0.94	0.88	0.822	0.94	CLONAL	1	TRUE	1	0.707451450613471	2		662	697	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570066	212570066	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	268	599	2	ENST00000342788.4:c.1175T>A	p.Phe392Tyr	p.F392Y	ENST00000342788	NM_005235.2	392	tTt/tAt	10/28	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.707451450613471	2		601	730	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439983	220439983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	314	919	0	ENST00000243786.2:c.836G>A	p.Trp279Ter	p.W279*	ENST00000243786	NM_002191.3	279	tGg/tAg	2/2	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.707451450613471	2		919	832	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713365	40713365	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	318	691	0	ENST00000373198.4:c.4150G>A	p.Glu1384Lys	p.E1384K	ENST00000373198	NM_133170.3	1384	Gag/Aag	30/32	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.707451450613471	2		691	777	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475603	12475603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	272	556	0	ENST00000287820.6:c.1477C>T	p.Leu493Phe	p.L493F	ENST00000287820	NM_015869.4	493	Ctt/Ttt	7/7	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.707451450613471	2		556	740	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266444	41266444	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0016197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	151	406	0	ENST00000349496.5:c.242-1G>A		p.X81_splice	ENST00000349496	NM_001904.3	81			1	2	FACETS	0.91	0.839	0.983	0.91	0.839	0.983	CLONAL	1	TRUE	1	0.707451450613471	2		406	469	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713720	52713720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	183	418	0	ENST00000394830.3:c.8C>T	p.Ser3Phe	p.S3F	ENST00000394830	NM_018313.4	3	tCc/tTc	2/30	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.707451450613471	2		418	461	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873103	134873104	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0016197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	191	676	2	ENST00000398015.3:c.1407_1408delinsTT	p.Arg470Trp	p.R470W	ENST00000398015	NM_004441.4	469	atCCgg/atTTgg	6/16	1	2	FACETS	0.879	0.818	0.943	0.879	0.818	0.943	CLONAL	1	TRUE	1	0.707451450613471	2		678	614	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149245705	149245705	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs747447921	NA	P-0016197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	272	639	0	ENST00000360632.3:c.823G>C	p.Val275Leu	p.V275L	ENST00000360632	NM_015472.4	275	Gtt/Ctt	5/7	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.707451450613471	2		639	707	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455608	189455608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	342	747	0	ENST00000264731.3:c.142G>A	p.Glu48Lys	p.E48K	ENST00000264731	NM_003722.4	48	Gaa/Aaa	2/14	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.707451450613471	2		747	858	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189585631	189585631	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	198	545	0	ENST00000264731.3:c.892G>A	p.Glu298Lys	p.E298K	ENST00000264731	NM_003722.4	298	Gaa/Aaa	7/14	1	2	FACETS	0.901	0.839	0.965	0.901	0.839	0.965	CLONAL	1	TRUE	1	0.707451450613471	2		545	621	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976866	55976866	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1824302	NA	P-0016197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	316	768	0	ENST00000263923.4:c.1046G>A	p.Arg349Lys	p.R349K	ENST00000263923	NM_002253.2	349	aGa/aAa	8/30	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.707451450613471	2		768	874	SUCCESS
APC	324	MSKCC	GRCh37	5	112175322	112175322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	131	357	0	ENST00000257430.4:c.4031C>T	p.Ser1344Leu	p.S1344L	ENST00000257430	NM_000038.5	1344	tCa/tTa	16/16	1	2	FACETS	0.834	0.763	0.908	0.834	0.763	0.908	CLONAL	1	TRUE	1	0.707451450613471	2		357	444	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524328	176524328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	238	722	0	ENST00000292408.4:c.2189C>T	p.Pro730Leu	p.P730L	ENST00000292408	NM_213647.1	730	cCc/cTc	17/18	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.707451450613471	2		722	642	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673415	30673415	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	419	489	0	ENST00000376406.3:c.3545C>T	p.Pro1182Leu	p.P1182L	ENST00000376406	NM_014641.2	1182	cCc/cTc	10/15	0.707451450613471	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.707451450613471	3		489	790	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622236	117622236	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866580908	NA	P-0016197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	222	654	0	ENST00000368508.3:c.6634C>T	p.Gln2212Ter	p.Q2212*	ENST00000368508	NM_002944.2	2212	Cag/Tag	42/43	0.707451450613471	1	FACETS	0.954	0.902	1	0.954	0.902	1	CLONAL	1	TRUE	0	0.707451450613471	1		654	425	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997822	149997822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	289	750	2	ENST00000253339.5:c.2645C>T	p.Pro882Leu	p.P882L	ENST00000253339		882	cCc/cTc	5/7	0.707451450613471	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.707451450613471	1		752	505	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435945	116435945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1395763398	NA	P-0016197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	223	644	0	ENST00000397752.3:c.3940G>A	p.Glu1314Lys	p.E1314K	ENST00000397752	NM_000245.2	1314	Gaa/Aaa	21/21	0.316374956670938	3	FACETS	1	0.982	1	0.57	0.532	0.608	INDETERMINATE	1	TRUE	1	0.707451450613471	3		644	749	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465534	8465534	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	270	773	1	ENST00000356435.5:c.3646A>T	p.Asn1216Tyr	p.N1216Y	ENST00000356435		1216	Aac/Tac	21/35	0.707451450613471	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.707451450613471	1		774	488	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500753	8500753	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0016197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	174	441	0	ENST00000356435.5:c.2128+1G>A		p.X710_splice	ENST00000356435		710			0.707451450613471	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.707451450613471	1		441	317	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958423	90958423	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs6413508	NA	P-0016197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	195	604	1	ENST00000265433.3:c.2015C>T	p.Pro672Leu	p.P672L	ENST00000265433	NM_002485.4	672	cCa/cTa	13/16	0.701653638323662	3	FACETS	0.868	0.804	0.934	0.434	0.402	0.467	CLONAL	1	TRUE	1	0.707451450613471	3		605	860	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	119	486	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.994	0.902	1	0.994	0.902	1	CLONAL	1	TRUE	1	0.458530243475035	2		486	522	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870920	12870965	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAGACATGGAAGAGGCGAGCCAGCGCAAGTGGAATTTCGATTTT	CAGAGACATGGAAGAGGCGAGCCAGCGCAAGTGGAATTTCGATTTT	-	novel	NA	P-0016198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	30	319	0	ENST00000228872.4:c.151_196del	p.Asp51IlefsTer5	p.D51Ifs*5	ENST00000228872	NM_004064.3	49	tgCAGAGACATGGAAGAGGCGAGCCAGCGCAAGTGGAATTTCGATTTT/tg	1/3	1	2	FACETS	0.27	0.217	0.331	0.27	0.217	0.331	SUBCLONAL	1	TRUE	1	0.458530243475035	2		319	484	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183308	56183308	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	181	462	0	ENST00000399503.3:c.4220del	p.Gly1407AspfsTer15	p.G1407Dfs*15	ENST00000399503	NM_005921.1	1406	caG/ca	18/20	0.45409726237526	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.458530243475035	1		462	526	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896545	151896545	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0016198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	95	345	0	ENST00000262189.6:c.4093-1G>T		p.X1365_splice	ENST00000262189	NM_170606.2	1365			1	2	FACETS	0.94	0.841	1	0.94	0.841	1	CLONAL	1	TRUE	1	0.458530243475035	2		345	441	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0016199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1616	172	580	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.378440493022948	3	FACETS	0.331	0.303	0.36	0.165	0.151	0.18	INDETERMINATE	1	TRUE	1	0.820186093636622	3		580	1788	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0016199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1242	788	978	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	0.378440493022948	3	FACETS	1	0.997	1	0.667	0.645	0.69	INDETERMINATE	1	TRUE	1	0.820186093636622	3		978	2030	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122706	108122706	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	1044	682	1	ENST00000278616.4:c.1750C>T	p.Gln584Ter	p.Q584*	ENST00000278616	NM_000051.3	584	Cag/Tag	11/63	NA	2	FACETS	0.978	0.962	0.994			1	INDETERMINATE	2	TRUE	NA	0.820186093636622	2		683	1301	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041888	42041888	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	401	591	1	ENST00000219905.7:c.6086del	p.Gly2029ValfsTer73	p.G2029Vfs*73	ENST00000219905	NM_001164273.1	2028	aGg/ag	17/24	0.589338573703681	0	FACETS		NA	1			1	NA	1	TRUE	0	0.820186093636622	0		592	686	SUCCESS
APC	324	MSKCC	GRCh37	5	112174029	112174029	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs762572576	NA	P-0016199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	147	482	0	ENST00000257430.4:c.2738A>G	p.His913Arg	p.H913R	ENST00000257430	NM_000038.5	913	cAt/cGt	16/16	0.820186093636622	1	FACETS	0.267	0.243	0.291	0.267	0.243	0.291	SUBCLONAL	1	TRUE	0	0.820186093636622	1		482	793	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946352	2946353	+	missense_variant	Missense_Mutation	DNP	CT	CT	TA	novel	NA	P-0016199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1675	200	764	0	ENST00000396946.4:c.3384_3385delinsTA	p.Glu1129Lys	p.E1129K	ENST00000396946	NM_032415.4	1128	gtAGag/gtTAag	25/25	1	2	FACETS	0.26	0.24	0.282	0.26	0.24	0.282	SUBCLONAL	1	TRUE	1	0.820186093636622	2		764	1875	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277253	38277253	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	146	571	2	ENST00000425967.3:c.1175C>T	p.Ala392Val	p.A392V	ENST00000425967	NM_001174067.1	392	gCc/gTc	10/19	0.820186093636622	1	FACETS	0.394	0.361	0.428	0.394	0.361	0.428	SUBCLONAL	1	TRUE	0	0.820186093636622	1		573	533	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0016202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	75	192	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.339899867151581	2		192	425	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913471	NA	P-0016202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	169	616	0	ENST00000269571.5:c.2329G>C	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ctg	20/27	1	2	FACETS	0.968	0.889	1	0.968	0.889	1	CLONAL	1	TRUE	1	0.339899867151581	2		616	1027	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958501	175958501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	53	501	0	ENST00000367669.3:c.1844C>T	p.Ser615Phe	p.S615F	ENST00000367669	NM_022457.5	615	tCt/tTt	16/20	0.339899867151581	3	FACETS	0.365	0.31	0.426	0.183	0.155	0.213	SUBCLONAL	1	TRUE	1	0.339899867151581	3		501	999	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871757	12871757	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0016202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	144	261	0	ENST00000228872.4:c.476-2A>G		p.X159_splice	ENST00000228872	NM_004064.3	159			0.338579476122697	2	FACETS	0.981	0.903	1	0.981	0.903	1	CLONAL	2	TRUE	0	0.339899867151581	2		261	432	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117458	115117458	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0016202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	148	297	0	ENST00000257566.3:c.718-2A>G		p.X240_splice	ENST00000257566	NM_016569.3	240			0.338579476122697	2	FACETS	0.862	0.793	0.934	0.862	0.793	0.934	CLONAL	2	TRUE	0	0.339899867151581	2		297	505	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844102	68844122	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CTTCTCTCACGCTGTGTCATC	CTTCTCTCACGCTGTGTCATC	-	novel	NA	P-0016202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	110	399	1	ENST00000261769.5:c.691_711del	p.Phe231_Ser237del	p.F231_S237del	ENST00000261769	NM_004360.3	230	ctCTTCTCTCACGCTGTGTCATCc/ctc	6/16	0.339899867151581	1	FACETS	0.977	0.881	1	0.977	0.881	1	CLONAL	1	TRUE	0	0.339899867151581	1		400	550	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0016203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	49	523	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.883	0.746	1	0.883	0.746	1	CLONAL	1	TRUE	1	0.14	2		523	793	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0016203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	39	470	0	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS	0.777	0.642	0.928	0.777	0.642	0.928	CLONAL	1	TRUE	1	0.14	2		470	717	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151289	202151290	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	54	591	0	ENST00000358485.4:c.1596dup	p.Leu533ThrfsTer6	p.L533Tfs*6	ENST00000358485	NM_001080125.1	530	aga/agAa	9/9	1	2	FACETS	0.837	0.712	0.974	0.837	0.712	0.974	CLONAL	1	TRUE	1	0.14	2		591	922	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0016203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1264	37	552	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.406	0.333	0.489	0.406	0.333	0.489	SUBCLONAL	1	TRUE	1	0.14	2		552	1301	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624296	89624296	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs786201995	NA	P-0016203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	56	609	0	ENST00000371953.3:c.70G>C	p.Asp24His	p.D24H	ENST00000371953	NM_000314.4	24	Gac/Cac	1/9	1	2	FACETS	0.787	0.672	0.913	0.787	0.672	0.913	CLONAL	1	TRUE	1	0.14	2		609	1017	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225530	26225530	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	30	272	0	ENST00000360408.1:c.148C>T	p.Arg50Cys	p.R50C	ENST00000360408	NM_003532.2	50	Cgc/Tgc	1/1	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.14	2		272	352	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466026	69466028	+	inframe_deletion	In_Frame_Del	DEL	CGA	CGA	-	novel	NA	P-0016203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	49	502	0	ENST00000227507.2:c.866_868del	p.Asp289del	p.D289del	ENST00000227507	NM_053056.2	288	acCGAc/acc	5/5	1	2	FACETS	0.931	0.787	1	0.931	0.787	1	CLONAL	1	TRUE	1	0.14	2		502	752	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850704	63850705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	64	502	0	ENST00000279873.7:c.1489dup	p.Ile497AsnfsTer31	p.I497Nfs*31	ENST00000279873	NM_032199.2	494	-/A	10/10	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.14	2		502	755	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0016203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	97	443	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.859	0.765	0.958	1	0.984	1	CLONAL	2	TRUE	1	0.14	2		444	807	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099075	27099081	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCAGC	CTCCAGC	-	novel	NA	P-0016203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	53	651	0	ENST00000324856.7:c.3491_3497del	p.Thr1164AsnfsTer14	p.T1164Nfs*14	ENST00000324856	NM_006015.4	1164	aCTCCAGCa/aa	13/20	1	2	FACETS	0.847	0.72	0.987	0.847	0.72	0.987	CLONAL	1	TRUE	1	0.14	2		651	894	SUCCESS
ATM	472	MSKCC	GRCh37	11	108128247	108128247	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	66	464	1	ENST00000278616.4:c.2294del	p.Asn765IlefsTer12	p.N765Ifs*12	ENST00000278616	NM_000051.3	764	Aaa/aa	15/63	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.14	2		465	942	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	461379	461379	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	74	498	2	ENST00000399788.2:c.1141C>T	p.Pro381Ser	p.P381S	ENST00000399788	NM_001042603.1	381	Cca/Tca	9/28	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.14	2		500	880	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424478	49424478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	53	560	0	ENST00000301067.7:c.13745G>A	p.Gly4582Asp	p.G4582D	ENST00000301067	NM_003482.3	4582	gGc/gAc	41/54	1	2	FACETS	0.999	0.85	1	0.999	0.85	1	CLONAL	1	TRUE	1	0.14	2		560	758	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281963	49281963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749053455	NA	P-0016203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	72	655	1	ENST00000282018.3:c.1010G>A	p.Ser337Asn	p.S337N	ENST00000282018	NM_020377.2	337	aGt/aAt	1/1	1	2	FACETS	0.956	0.833	1	0.956	0.833	1	CLONAL	1	TRUE	1	0.14	2		656	1076	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16062165	16062165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	59	567	0	ENST00000268712.3:c.641C>T	p.Ala214Val	p.A214V	ENST00000268712	NM_006311.3	214	gCt/gTt	6/46	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.14	2		567	821	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	66	1083	2	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.836	0.723	0.959	0.836	0.723	0.959	CLONAL	1	TRUE	1	0.14	2		1085	1128	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731487	47731487	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs982080768	NA	P-0016203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	10	46	0	ENST00000449228.1:c.305G>A	p.Arg102His	p.R102H	ENST00000449228	NM_001127240.2	102	cGt/cAt	2/4	1	2	FACETS	1	0.8	1	1	0.9	1	CLONAL	2	TRUE	1	0.14	2		46	58	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264868	46264868	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	49	512	1	ENST00000371998.3:c.1738G>C	p.Val580Leu	p.V580L	ENST00000371998		580	Gtg/Ctg	12/23	1	2	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	TRUE	1	0.14	2		513	691	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089141	37089141	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	33	347	0	ENST00000231790.2:c.1863G>A	p.Met621Ile	p.M621I	ENST00000231790	NM_000249.3	621	atG/atA	16/19	1	2	FACETS	0.829	0.673	1	0.829	0.673	1	CLONAL	1	TRUE	1	0.14	2		347	569	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405821	157405822	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0016203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	28	373	0	ENST00000346085.5:c.2067dup	p.Thr690HisfsTer73	p.T690Hfs*73	ENST00000346085	NM_020732.3	688	ctc/ctCc	6/20	1	2	FACETS	0.729	0.581	0.898	0.729	0.581	0.898	SUBCLONAL	1	TRUE	1	0.14	2		373	549	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958182	2958182	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	60	612	0	ENST00000396946.4:c.2550G>A	p.Met850Ile	p.M850I	ENST00000396946	NM_032415.4	850	atG/atA	19/25	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.14	2		612	740	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444372	50444372	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	32	318	0	ENST00000331340.3:c.302G>T	p.Ser101Ile	p.S101I	ENST00000331340	NM_006060.4	101	aGc/aTc	4/8	1	2	FACETS	0.977	0.792	1	0.977	0.792	1	CLONAL	1	TRUE	1	0.14	2		318	468	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760879	133760879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749413196	NA	P-0016203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	75	821	1	ENST00000318560.5:c.3202G>A	p.Val1068Met	p.V1068M	ENST00000318560	NM_005157.4	1068	Gtg/Atg	11/11	1	2	FACETS	0.92	0.804	1	0.92	0.804	1	CLONAL	1	TRUE	1	0.14	2		822	1164	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933419	39933419	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	38	511	0	ENST00000378444.4:c.1180C>T	p.Pro394Ser	p.P394S	ENST00000378444	NM_001123385.1	394	Ccc/Tcc	4/15	1	2	FACETS	0.859	0.709	1	0.859	0.709	1	CLONAL	1	TRUE	1	0.14	2		511	632	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0016204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	105	731	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.999	0.895	1	0.999	0.895	1	CLONAL	1	TRUE	1	0.266167237765068	2		731	790	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165730	108165730	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs765759912	NA	P-0016204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	98	448	1	ENST00000278616.4:c.4853G>T	p.Arg1618Leu	p.R1618L	ENST00000278616	NM_000051.3	1618	cGa/cTa	32/63	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.266167237765068	2		449	678	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68878207	68878207	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	138	353	2	ENST00000487270.1:c.920G>T	p.Arg307Leu	p.R307L	ENST00000487270	NM_133509.3	307	cGg/cTg	9/11	0.153803045296766	3	FACETS	1	0.97	1	0.756	0.692	0.823	INDETERMINATE	2	TRUE	0	0.266167237765068	3		355	518	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030041	36030041	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1289307625	NA	P-0016204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	32	630	1	ENST00000358208.4:c.1076A>G	p.Lys359Arg	p.K359R	ENST00000358208		359	aAg/aGg	9/12	1	2	FACETS	0.408	0.33	0.497	0.408	0.33	0.497	SUBCLONAL	1	TRUE	1	0.266167237765068	2		631	589	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035952	47035953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0016204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	133	828	0	ENST00000377604.3:c.633dup	p.Lys212GlnfsTer4	p.K212Qfs*4	ENST00000377604	NM_001204468.1	210	-/C	7/24	1	2	FACETS	0.965	0.875	1	0.965	0.875	1	CLONAL	1	TRUE	1	0.266167237765068	2		828	1036	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0016205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	165	591	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.397875706479988	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.397875706479988	1		592	649	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115928	8115929	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	120	385	0	ENST00000346208.3:c.1275dup	p.Ser426IlefsTer81	p.S426Ifs*81	ENST00000346208		425	cca/ccAa	6/6	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.397875706479988	2		385	601	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847399	68847399	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs886039685	NA	P-0016205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	35	439	0	ENST00000261769.5:c.1320+1G>C		p.X440_splice	ENST00000261769	NM_004360.3	440			0.397875706479988	1	FACETS	0.262	0.214	0.316	0.262	0.214	0.316	SUBCLONAL	1	TRUE	0	0.397875706479988	1		439	538	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	172	641	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.989	0.909	1	0.989	0.909	1	CLONAL	1	TRUE	1	0.313015618168835	2		641	1111	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578476	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTGCCGGGCGG	GGGTGCCGGGCGG	-	rs876659215	NA	P-0016206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	205	678	3	ENST00000269305.4:c.454_466del	p.Pro152AlafsTer14	p.P152Afs*14	ENST00000269305	NM_001126112.2	152	CCGCCCGGCACCCgc/gc	5/11	0.313015618168835	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.313015618168835	1		681	978	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021809	71021809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	74	272	0	ENST00000318789.4:c.1549C>T	p.Leu517Phe	p.L517F	ENST00000318789	NM_032682.5	517	Ctt/Ttt	18/21	1	2	FACETS	0.987	0.867	1	0.987	0.867	1	CLONAL	1	TRUE	1	0.313015618168835	2		272	479	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442488	52442488	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0016207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	346	529	0	ENST00000460680.1:c.255+2T>G		p.X85_splice	ENST00000460680	NM_004656.3	85			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		529	625	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0016209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	300	683	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	1	0.912081655316715	2		683	561	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0016209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2486	177	637	1	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.912081655316715	7	FACETS	0.478	0.438	0.521			1	SUBCLONAL	1	FALSE	NA	0.912081655316715	7		638	2663	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281176	49281176	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758137158	NA	P-0016209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	333	744	3	ENST00000282018.3:c.223G>A	p.Val75Ile	p.V75I	ENST00000282018	NM_020377.2	75	Gtt/Att	1/1	0.293614663131262	1	FACETS	0.502	0.477	0.527	0.502	0.477	0.527	INDETERMINATE	1	FALSE	0	0.912081655316715	1		747	791	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763455	41763455	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	338	512	0	ENST00000301178.4:c.2254G>A	p.Gly752Ser	p.G752S	ENST00000301178	NM_021913.4	752	Ggc/Agc	19/20	1	2	FACETS	0.907	0.862	0.952	0.907	0.862	0.952	CLONAL	1	FALSE	1	0.912081655316715	2		512	817	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0016210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	95	605	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.475548167108245	2		605	334	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098495	47098495	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759979231	NA	P-0016210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	108	332	1	ENST00000409792.3:c.6779C>T	p.Pro2260Leu	p.P2260L	ENST00000409792	NM_014159.6	2260	cCg/cTg	15/21	0.475548167108245	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.475548167108245	1		333	242	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788657	3788657	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	137	559	0	ENST00000262367.5:c.4297T>A	p.Tyr1433Asn	p.Y1433N	ENST00000262367	NM_004380.2	1433	Tat/Aat	26/31	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.475548167108245	2		559	490	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911600	114911600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750718467	NA	P-0016210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	59	564	2	ENST00000543371.1:c.1118C>T	p.Thr373Met	p.T373M	ENST00000543371	NM_001198531.1	373	aCg/aTg	10/14	1	2	FACETS	0.816	0.707	0.933	0.816	0.707	0.933	CLONAL	1	TRUE	1	0.475548167108245	2		566	304	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023248	33023248	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	94	695	0	ENST00000300177.4:c.357C>A	p.Tyr119Ter	p.Y119*	ENST00000300177	NM_001191322.1	119	taC/taA	2/2	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.475548167108245	2		695	355	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578264	7578304	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GATAAGATGCTGAGGAGGGGCCAGACCTAAGAGCAATCAGT	GATAAGATGCTGAGGAGGGGCCAGACCTAAGAGCAATCAGT	-	novel	NA	P-0016211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	376	623	2	ENST00000269305.4:c.560-15_585del		p.X187_splice	ENST00000269305	NM_001126112.2	187		6/11	0.566877797315179	2	FACETS	0.892	0.853	0.93	0.892	0.853	0.93	CLONAL	2	TRUE	0	0.566877797315179	2		625	744	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145561	24145561	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	58	518	0	ENST00000263121.7:c.580G>C	p.Glu194Gln	p.E194Q	ENST00000263121	NM_003073.3	194	Gag/Cag	5/9	0.369558867469442	3	FACETS	0.267	0.229	0.31	0.134	0.114	0.155	SUBCLONAL	1	TRUE	1	0.566877797315179	3		518	982	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523501	106523501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373006568	NA	P-0016211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	125	305	0	ENST00000359195.3:c.2653G>A	p.Ala885Thr	p.A885T	ENST00000359195	NM_002649.2	885	Gcc/Acc	8/11	0.30504213503371	1	FACETS	0.554	0.503	0.608	0.554	0.503	0.608	INDETERMINATE	1	TRUE	0	0.566877797315179	1		305	570	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932659	39932659	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	136	711	0	ENST00000378444.4:c.1940G>T	p.Arg647Met	p.R647M	ENST00000378444	NM_001123385.1	647	aGg/aTg	4/15	1	2	FACETS	0.478	0.434	0.525	0.478	0.434	0.525	SUBCLONAL	1	TRUE	1	0.566877797315179	2		711	1003	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	162	405	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.94	0.866	1	0.94	0.866	1	CLONAL	1	TRUE	1	0.572748739039713	2		405	602	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573826	64573826	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	111	324	0	ENST00000312049.6:c.927del	p.Lys310ArgfsTer58	p.K310Rfs*58	ENST00000312049	NM_130799.2	309	gcC/gc	7/10	0.54906859342348	1	FACETS	0.775	0.704	0.848	0.775	0.704	0.848	SUBCLONAL	1	TRUE	0	0.572748739039713	1		324	357	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151174424	151174431	+	frameshift_variant	Frame_Shift_Del	DEL	GATTGATG	GATTGATG	-	novel	NA	P-0016212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	153	475	0	ENST00000262187.5:c.263_270del	p.Thr88LysfsTer4	p.T88Kfs*4	ENST00000262187	NM_005614.3	88	aCATCAATC/a	4/8	1	2	FACETS	0.755	0.692	0.82	0.755	0.692	0.82	SUBCLONAL	1	TRUE	1	0.572748739039713	2		475	708	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108044	30108044	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs765821685	NA	P-0016213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	147	616	1	ENST00000331968.5:c.763C>T	p.Arg255Ter	p.R255*	ENST00000331968	NM_002742.2	255	Cga/Tga	5/18	1	2	FACETS	0.828	0.755	0.905	0.828	0.755	0.905	CLONAL	1	TRUE	1	0.349374249704164	2		617	1016	SUCCESS
FH	2271	MSKCC	GRCh37	1	241676905	241676905	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	201	412	1	ENST00000366560.3:c.376G>A	p.Glu126Lys	p.E126K	ENST00000366560	NM_000143.3	126	Gag/Aag	3/10	1	2	FACETS	0.84	0.783	0.899	0.84	0.783	0.899	CLONAL	1	TRUE	1	0.766634808351955	2		413	624	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720732	89720732	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	21	163	0	ENST00000371953.3:c.883del	p.Leu295TyrfsTer12	p.L295Yfs*12	ENST00000371953	NM_000314.4	295	Cta/ta	8/9	0.766634808351955	1	FACETS	0.356	0.279	0.441	0.356	0.279	0.441	SUBCLONAL	1	TRUE	0	0.766634808351955	1		163	95	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442977	49442977	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	258	473	0	ENST00000301067.7:c.3931del	p.Arg1311AspfsTer19	p.R1311Dfs*19	ENST00000301067	NM_003482.3	1311	Aga/ga	12/54	1	2	FACETS	0.846	0.795	0.898	0.846	0.795	0.898	CLONAL	1	TRUE	1	0.766634808351955	2		473	796	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194859	30194859	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1186546402	NA	P-0016214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	372	523	0	ENST00000331968.5:c.286G>A	p.Gly96Arg	p.G96R	ENST00000331968	NM_002742.2	96	Gga/Aga	2/18	NA	2	FACETS	0.972	0.925	1			1	INDETERMINATE	1	TRUE	NA	0.766634808351955	2		523	998	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33446588	33446588	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	204	530	1	ENST00000345365.6:c.45G>T	p.Glu15Asp	p.E15D	ENST00000345365	NM_002878.3	15	gaG/gaT	1/10	1	2	FACETS	0.64	0.594	0.687	0.64	0.594	0.687	SUBCLONAL	1	TRUE	1	0.766634808351955	2		531	832	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657062	45657062	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368372298	NA	P-0016214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	260	325	0	ENST00000407780.3:c.94G>A	p.Asp32Asn	p.D32N	ENST00000407780	NM_001283052.1	32	Gac/Aac	3/7	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.766634808351955	2		325	628	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873549	151873549	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	260	436	0	ENST00000262189.6:c.8989C>G	p.Gln2997Glu	p.Q2997E	ENST00000262189	NM_170606.2	2997	Caa/Gaa	38/59	1	2	FACETS	0.965	0.909	1	0.965	0.909	1	CLONAL	1	TRUE	1	0.766634808351955	2		436	703	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873797	151873797	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0016214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	154	286	0	ENST00000262189.6:c.8741C>G	p.Ser2914Ter	p.S2914*	ENST00000262189	NM_170606.2	2914	tCa/tGa	38/59	1	2	FACETS	0.774	0.713	0.837	0.774	0.713	0.837	SUBCLONAL	1	TRUE	1	0.766634808351955	2		286	519	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577049	7577049	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	528	600	0	ENST00000269305.4:c.889del	p.His297ThrfsTer48	p.H297Tfs*48	ENST00000269305	NM_001126112.2	297	Cac/ac	8/11	0.554960442164939	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.548786304446276	2		600	872	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577049	7577049	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016215-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	286	600	0	ENST00000269305.4:c.889del	p.His297ThrfsTer48	p.H297Tfs*48	ENST00000269305	NM_001126112.2	297	Cac/ac	8/11	0.294941180432963	2	FACETS	0.972	0.915	1	0.972	0.915	1	CLONAL	2	TRUE	0	0.294941180432963	2		600	998	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776783	NA	P-0016217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	54	363	1	ENST00000267163.4:c.1215+1G>A		p.X405_splice	ENST00000267163	NM_000321.2	405			0.146302720773202	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.740786149755027	0		364	170	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997499	149997499	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	14	396	0	ENST00000253339.5:c.2780A>G	p.Tyr927Cys	p.Y927C	ENST00000253339		927	tAc/tGc	6/7	0.412769854362911	1	FACETS	0.107	0.077	0.143	0.107	0.077	0.143	INDETERMINATE	1	FALSE	0	0.740786149755027	1		396	222	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016273	150016273	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	14	377	0	ENST00000253339.5:c.433G>T	p.Asp145Tyr	p.D145Y	ENST00000253339		145	Gat/Tat	2/7	0.412769854362911	1	FACETS	0.113	0.081	0.151	0.113	0.081	0.151	INDETERMINATE	1	FALSE	0	0.740786149755027	1		377	211	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0016219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	194	669	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	0.895	0.829	0.963	0.895	0.829	0.963	CLONAL	1	TRUE	1	0.516111511081391	2		669	840	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044978	47044978	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	226	700	0	ENST00000377604.3:c.2307del	p.Ser770AlafsTer32	p.S770Afs*32	ENST00000377604	NM_001204468.1	768	ttC/tt	20/24	1	2	FACETS	0.999	0.932	1	0.999	0.932	1	CLONAL	1	TRUE	1	0.516111511081391	2		700	877	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138389	37138389	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	52	442	0	ENST00000373509.5:c.38G>C	p.Arg13Pro	p.R13P	ENST00000373509	NM_002648.3	13	cGc/cCc	1/6	0.15830403369994	3	FACETS	0.375	0.319	0.438	0.188	0.159	0.219	INDETERMINATE	1	TRUE	1	0.52034000125129	3		442	671	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024546	31024546	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	242	465	0	ENST00000375687.4:c.4031C>T	p.Ser1344Phe	p.S1344F	ENST00000375687	NM_015338.5	1344	tCc/tTc	13/13	0.168386580842993	3	FACETS	0.997	0.939	1	0.664	0.626	0.704	INDETERMINATE	2	TRUE	0	0.52034000125129	3		465	588	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159048	143159048	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	127	348	0	ENST00000262992.4:c.805A>T	p.Ile269Phe	p.I269F	ENST00000262992	NM_001101669.1	269	Att/Ttt	10/24	0.506915706333819	3	FACETS	0.816	0.74	0.896	0.408	0.37	0.448	CLONAL	1	TRUE	1	0.52034000125129	3		348	754	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115952	8115953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0016222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	131	389	0	ENST00000346208.3:c.1300dup	p.His434ProfsTer73	p.H434Pfs*73	ENST00000346208		433	cac/caCc	6/6	0.558324620599599	1	FACETS	0.649	0.597	0.702	0.649	0.597	0.702	SUBCLONAL	1	TRUE	0	0.754711989878836	1		389	333	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73047225	73047225	+	splice_region_variant,intron_variant	Splice_Region	SNP	T	T	C	rs754339156	NA	P-0016222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	74	455	0	ENST00000356692.5:c.35-3T>C		p.X12_splice	ENST00000356692		12			0.160073999781746	1	FACETS	0.236	0.206	0.267	0.236	0.206	0.267	INDETERMINATE	1	TRUE	0	0.754711989878836	1		455	518	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553043	106553043	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	157	857	0	ENST00000369096.4:c.1011del	p.Ser338LeufsTer40	p.S338Lfs*40	ENST00000369096	NM_001198.3	336	agC/ag	5/7	NA	2	FACETS	0.8	0.738	0.864			1	INDETERMINATE	1	TRUE	NA	0.754711989878836	2		857	520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	463	496	2	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	NA	2	FACETS	0.978	0.936	1			1	INDETERMINATE	1	TRUE	NA	0.792172375432855	2		498	1195	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023909	27023923	+	inframe_deletion	In_Frame_Del	DEL	GCTGCGGCGGCGGCA	GCTGCGGCGGCGGCA	-	rs751352361	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	13	36	0	ENST00000324856.7:c.1029_1043del	p.Ala345_Ala349del	p.A345_A349del	ENST00000324856	NM_006015.4	339	GCTGCGGCGGCGGCA/-	1/20	NA	2	FACETS	0.49	0.357	0.644			1	INDETERMINATE	1	TRUE	NA	0.792172375432855	2		36	67	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654737	29654737	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs771529172	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	262	319	0	ENST00000356175.3:c.5426G>T	p.Arg1809Leu	p.R1809L	ENST00000356175	NM_000267.3	1809	cGc/cTc	37/57	0.404168945118371	3	FACETS	1	0.985	1	0.57	0.536	0.605	INDETERMINATE	1	TRUE	1	0.792172375432855	3		319	810	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521481	8521481	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760428875	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	154	530	1	ENST00000356435.5:c.757G>A	p.Val253Ile	p.V253I	ENST00000356435		253	Gtt/Att	9/35	0.425419939735371	1	FACETS	0.336	0.308	0.366	0.336	0.308	0.366	INDETERMINATE	1	TRUE	0	0.792172375432855	1		531	698	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100408	8100408	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	437	708	3	ENST00000346208.3:c.382G>T	p.Gly128Trp	p.G128W	ENST00000346208		128	Ggg/Tgg	3/6	NA	2	FACETS	0.84	0.801	0.879			1	INDETERMINATE	1	TRUE	NA	0.792172375432855	2		711	1314	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259745	16259745	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	395	591	1	ENST00000375759.3:c.7010G>T	p.Arg2337Leu	p.R2337L	ENST00000375759	NM_015001.2	2337	cGa/cTa	11/15	0.252733833476463	3	FACETS	1	0.985	1	0.543	0.516	0.57	INDETERMINATE	1	TRUE	1	0.792172375432855	3		592	1283	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439770	51439772	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	185	201	0	ENST00000262662.1:c.338_340del	p.Glu113del	p.E113del	ENST00000262662		112	aAAGaa/aaa	4/4	0.349715775329338	2	FACETS	1	0.969	1	0.532	0.497	0.568	INDETERMINATE	1	TRUE	0	0.792172375432855	2		201	439	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248628	59248628	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	725	667	0	ENST00000371222.2:c.115A>C	p.Thr39Pro	p.T39P	ENST00000371222	NM_002228.3	39	Acc/Ccc	1/1	0.349715775329338	2	FACETS	1	0.998	1	0.73	0.709	0.751	INDETERMINATE	1	TRUE	0	0.792172375432855	2		667	1254	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65311249	65311249	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1312736393	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	138	449	0	ENST00000342505.4:c.2062A>G	p.Thr688Ala	p.T688A	ENST00000342505	NM_002227.2	688	Aca/Gca	15/25	0.349715775329338	2	FACETS	0.457	0.416	0.5	0.229	0.208	0.25	INDETERMINATE	1	TRUE	0	0.792172375432855	2		449	762	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243675649	243675650	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	77	322	0	ENST00000263826.5:c.1330_1331del	p.Ile444TyrfsTer6	p.I444Yfs*6	ENST00000263826	NM_005465.4	444	ATt/t	12/13	0.422599920546824	3	FACETS	0.528	0.464	0.596			1	INDETERMINATE	1	TRUE	NA	0.792172375432855	3		322	514	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741885	17741885	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	20	47	0	ENST00000250003.3:c.556C>A	p.Pro186Thr	p.P186T	ENST00000250003	NM_002478.4	186	Ccg/Acg	1/3	NA	2	FACETS	0.505	0.393	0.631			1	INDETERMINATE	1	TRUE	NA	0.792172375432855	2		47	100	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245280	46245280	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	262	363	2	ENST00000334344.6:c.3374A>T	p.Gln1125Leu	p.Q1125L	ENST00000334344	NM_152641.2	1125	cAa/cTa	15/21	0.224366146864929	3	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.792172375432855	3		365	692	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246477	46246477	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	266	306	1	ENST00000334344.6:c.4571G>T	p.Arg1524Met	p.R1524M	ENST00000334344	NM_152641.2	1524	aGg/aTg	15/21	0.224366146864929	3	FACETS	0.854	0.809	0.899			1	INDETERMINATE	2	TRUE	NA	0.792172375432855	3		307	549	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601364	28601364	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	164	435	0	ENST00000241453.7:c.2068A>G	p.Ile690Val	p.I690V	ENST00000241453	NM_004119.2	690	Att/Gtt	17/24	0.788968954142305	2	FACETS	0.681	0.628	0.736	0.341	0.314	0.368	SUBCLONAL	1	TRUE	0	0.792172375432855	2		435	608	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914376	32914376	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs747406932	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	126	416	0	ENST00000380152.3:c.5884A>G	p.Ile1962Val	p.I1962V	ENST00000380152		1962	Ata/Gta	11/27	NA	2	FACETS	0.499	0.452	0.547			1	INDETERMINATE	1	TRUE	NA	0.792172375432855	2		416	638	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947540	48947540	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	528	530	0	ENST00000267163.4:c.1128-1G>T		p.X376_splice	ENST00000267163	NM_000321.2	376			NA	2	FACETS	0.98	0.955	1			1	INDETERMINATE	2	TRUE	NA	0.792172375432855	2		530	680	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81528510	81528510	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	421	443	0	ENST00000298171.2:c.189C>A	p.His63Gln	p.H63Q	ENST00000298171	NM_000369.2	63	caC/caA	2/10	0.792172375432855	2	FACETS	0.973	0.946	1	0.973	0.946	1	CLONAL	2	TRUE	0	0.792172375432855	2		443	546	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42053954	42053954	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	108	364	0	ENST00000219905.7:c.7418del	p.Gly2473AspfsTer2	p.G2473Dfs*2	ENST00000219905	NM_001164273.1	2472	caG/ca	21/24	0.425419939735371	1	FACETS	0.348	0.314	0.384	0.348	0.314	0.384	INDETERMINATE	1	TRUE	0	0.792172375432855	1		364	473	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678358	88678358	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	369	475	0	ENST00000360948.2:c.1178del	p.Gly393AlafsTer21	p.G393Afs*21	ENST00000360948	NM_001012338.2	393	gGc/gc	9/19	1	2	FACETS	0.967	0.921	1	0.967	0.921	1	CLONAL	1	TRUE	1	0.792172375432855	2		475	963	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690618	88690618	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	243	393	0	ENST00000360948.2:c.412C>G	p.Arg138Gly	p.R138G	ENST00000360948	NM_001012338.2	138	Cgg/Ggg	5/19	1	2	FACETS	0.857	0.804	0.91	0.857	0.804	0.91	CLONAL	1	TRUE	1	0.792172375432855	2		393	716	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478243	99478243	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	86	238	0	ENST00000268035.6:c.3147C>G	p.Asn1049Lys	p.N1049K	ENST00000268035	NM_000875.3	1049	aaC/aaG	16/21	1	2	FACETS	0.543	0.483	0.606	0.543	0.483	0.606	SUBCLONAL	1	TRUE	1	0.792172375432855	2		238	400	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835791	68835791	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376152506	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	319	443	0	ENST00000261769.5:c.382C>T	p.His128Tyr	p.H128Y	ENST00000261769	NM_004360.3	128	Cat/Tat	3/16	1	2	FACETS	0.904	0.856	0.953	0.904	0.856	0.953	CLONAL	1	TRUE	1	0.792172375432855	2		443	891	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829422	72829422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	302	314	0	ENST00000268489.5:c.7159C>T	p.Pro2387Ser	p.P2387S	ENST00000268489	NM_006885.3	2387	Ccc/Tcc	9/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.792172375432855	2		314	709	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81891922	81891922	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	417	511	0	ENST00000359376.3:c.392A>T	p.Gln131Leu	p.Q131L	ENST00000359376	NM_002661.3	131	cAg/cTg	4/33	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.792172375432855	2		511	1052	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81891959	81891959	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	334	353	2	ENST00000359376.3:c.429G>T	p.Glu143Asp	p.E143D	ENST00000359376	NM_002661.3	143	gaG/gaT	4/33	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.792172375432855	2		355	791	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836401	89836401	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	458	353	0	ENST00000389301.3:c.2348G>C	p.Gly783Ala	p.G783A	ENST00000389301	NM_000135.2	783	gGg/gCg	26/43	NA	2	FACETS	0.942	0.915	0.968			1	INDETERMINATE	2	TRUE	NA	0.792172375432855	2		353	614	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983735	15983735	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	251	359	0	ENST00000268712.3:c.3387A>T	p.Glu1129Asp	p.E1129D	ENST00000268712	NM_006311.3	1129	gaA/gaT	25/46	NA	2	FACETS	0.926	0.872	0.982			1	INDETERMINATE	1	TRUE	NA	0.792172375432855	2		359	684	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245620	41245620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	356	514	0	ENST00000357654.3:c.1928G>A	p.Ser643Asn	p.S643N	ENST00000357654	NM_007294.3	643	aGt/aAt	10/23	0.404168945118371	3	FACETS	1	0.992	1	0.614	0.583	0.646	INDETERMINATE	1	TRUE	1	0.792172375432855	3		514	1022	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437549	56437549	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	198	551	2	ENST00000407977.2:c.913C>T	p.Gln305Ter	p.Q305*	ENST00000407977		305	Cag/Tag	8/10	0.404168945118371	3	FACETS	0.536	0.495	0.579	0.268	0.247	0.29	INDETERMINATE	1	TRUE	1	0.792172375432855	3		553	1302	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009138	27009138	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	128	139	1	ENST00000335756.4:c.74G>T	p.Gly25Val	p.G25V	ENST00000335756	NM_001809.3	25	gGc/gTc	1/5	0.436203744620184	1	FACETS	0.849	0.789	0.907	0.849	0.789	0.907	INDETERMINATE	1	TRUE	0	0.792172375432855	1		140	230	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416141	29416141	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs753750497	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	234	391	0	ENST00000389048.3:c.4812C>A	p.Tyr1604Ter	p.Y1604*	ENST00000389048	NM_004304.4	1604	taC/taA	29/29	0.436203744620184	1	FACETS	0.751	0.709	0.793	0.751	0.709	0.793	INDETERMINATE	1	TRUE	0	0.792172375432855	1		391	475	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39708734	39708734	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	483	540	0	ENST00000361337.2:c.345A>T	p.Gln115His	p.Q115H	ENST00000361337	NM_003286.2	115	caA/caT	6/21	0.257046180717819	4	FACETS	1	0.985	1	1	0.985	1	INDETERMINATE	2	TRUE	2	0.792172375432855	4		540	1042	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264184	46264184	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	249	185	0	ENST00000371998.3:c.1231A>T	p.Met411Leu	p.M411L	ENST00000371998		411	Atg/Ttg	11/23	0.257046180717819	4	FACETS	1	0.982	1	1	0.982	1	INDETERMINATE	2	TRUE	2	0.792172375432855	4		185	517	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129661	47129661	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	376	561	0	ENST00000409792.3:c.5219G>T	p.Arg1740Leu	p.R1740L	ENST00000409792	NM_014159.6	1740	cGg/cTg	10/21	0.77593553352108	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.792172375432855	1		561	545	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970819	55970819	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	140	385	0	ENST00000263923.4:c.1978A>T	p.Thr660Ser	p.T660S	ENST00000263923	NM_002253.2	660	Aca/Tca	13/30	NA	2	FACETS	0.451	0.411	0.493			1	INDETERMINATE	1	TRUE	NA	0.792172375432855	2		385	784	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35857105	35857105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs776642878	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	144	268	0	ENST00000303115.3:c.26G>C	p.Gly9Ala	p.G9A	ENST00000303115	NM_002185.3	9	gGc/gCc	1/8	0.377007080977625	6	FACETS	1	0.984	1	0.337	0.308	0.368	INDETERMINATE	1	TRUE	2	0.792172375432855	6		268	697	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569844	67569844	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	T	novel	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	220	204	0	ENST00000274335.5:c.502+3G>T		p.X168_splice	ENST00000274335		168			0.766190807866447	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.792172375432855	2		204	277	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819945	170819947	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	rs764976369	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	80	263	0	ENST00000296930.5:c.492_494del	p.Asp168del	p.D168del	ENST00000296930	NM_002520.6	163	GAT/-	6/11	0.766190807866447	2	FACETS	0.549	0.486	0.615	0.274	0.243	0.308	SUBCLONAL	1	TRUE	0	0.792172375432855	2		263	368	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117707014	117707014	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	633	506	0	ENST00000368508.3:c.2136G>A	p.Trp712Ter	p.W712*	ENST00000368508	NM_002944.2	712	tgG/tgA	15/43	0.792172375432855	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.792172375432855	3		506	1090	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415529	152415529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	216	470	1	ENST00000206249.3:c.1379C>T	p.Thr460Ile	p.T460I	ENST00000206249	NM_000125.3	460	aCa/aTa	7/8	0.792172375432855	3	FACETS	0.581	0.539	0.625	0.29	0.269	0.313	SUBCLONAL	1	TRUE	1	0.792172375432855	3		471	1311	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467654	50467654	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	381	476	0	ENST00000331340.3:c.889G>T	p.Ala297Ser	p.A297S	ENST00000331340	NM_006060.4	297	Gcc/Tcc	8/8	0.422599920546824	3	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.792172375432855	3		476	1104	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336665	81336665	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1258858592	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	186	388	2	ENST00000222390.5:c.1557C>A	p.Cys519Ter	p.C519*	ENST00000222390	NM_000601.4	519	tgC/tgA	14/18	1	2	FACETS	0.997	0.93	1	0.997	0.93	1	CLONAL	1	TRUE	1	0.792172375432855	2		390	471	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554317	141554317	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	252	745	0	ENST00000220592.5:c.1834G>C	p.Ala612Pro	p.A612P	ENST00000220592	NM_012154.3	612	Gcc/Ccc	14/19	1	2	FACETS	0.459	0.429	0.491	0.459	0.429	0.491	SUBCLONAL	1	TRUE	1	0.792172375432855	2		745	1385	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485243	8485243	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	276	472	1	ENST00000356435.5:c.3137C>A	p.Ser1046Tyr	p.S1046Y	ENST00000356435		1046	tCc/tAc	18/35	0.425419939735371	1	FACETS	0.705	0.668	0.742	0.705	0.668	0.742	INDETERMINATE	1	TRUE	0	0.792172375432855	1		473	597	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8501029	8501029	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs757562644	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	68	310	0	ENST00000356435.5:c.1853G>T	p.Cys618Phe	p.C618F	ENST00000356435		618	tGc/tTc	13/35	0.425419939735371	1	FACETS	0.327	0.286	0.37	0.327	0.286	0.37	INDETERMINATE	1	TRUE	0	0.792172375432855	1		310	317	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410720	63410720	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	593	249	0	ENST00000330258.3:c.2447G>T	p.Arg816Leu	p.R816L	ENST00000330258	NM_152424.3	816	cGg/cTg	2/2	0.641257674076843	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.792172375432855	2		249	678	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504132	123504134	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs748078276	NA	P-0016223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	124	254	0	ENST00000371139.4:c.313_315del	p.Lys105del	p.K105del	ENST00000371139	NM_001114937.2	103	gAGAag/gag	3/4	0.744817189055116	2	FACETS	0.494	0.448	0.542			1	SUBCLONAL	1	TRUE	NA	0.792172375432855	2		254	634	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0016224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	242	516	1	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	0.841	0.789	0.895	1	0.994	1	CLONAL	2	TRUE	1	0.383082799914656	2		517	751	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247351	153247351	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	144	447	0	ENST00000281708.4:c.1451G>T	p.Arg484Met	p.R484M	ENST00000281708	NM_033632.3	484	aGg/aTg	10/12	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.383082799914656	2		447	741	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206590	108206590	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	283	321	0	ENST00000278616.4:c.8170C>A	p.Gln2724Lys	p.Q2724K	ENST00000278616	NM_000051.3	2724	Caa/Aaa	56/63	0.344267340411858	5	FACETS	1	0.986	1			1	CLONAL	3	TRUE	NA	0.383082799914656	5		321	694	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280661	115280661	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	162	548	0	ENST00000438362.2:c.370C>G	p.Arg124Gly	p.R124G	ENST00000438362	NM_001242891.1	124	Cgg/Ggg	4/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.383082799914656	2		548	791	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163307884	163307884	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0016224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	73	326	0	ENST00000271452.3:c.509+1G>T		p.X170_splice	ENST00000271452	NM_145697.2	170			0.247791134499899	3	FACETS	0.987	0.866	1	0.494	0.433	0.559	CLONAL	1	TRUE	1	0.383082799914656	3		326	460	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14300905	14300905	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	30	138	1	ENST00000256196.4:c.593G>T	p.Gly198Val	p.G198V	ENST00000256196		198	gGc/gTc	6/6	1	2	FACETS	0.949	0.774	1	0.949	0.774	1	CLONAL	1	TRUE	1	0.383082799914656	2		139	165	SUCCESS
ATM	472	MSKCC	GRCh37	11	108138048	108138048	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	98	353	0	ENST00000278616.4:c.2617G>T	p.Gly873Ter	p.G873*	ENST00000278616	NM_000051.3	873	Gga/Tga	17/63	0.344267340411858	5	FACETS	1	0.914	1			1	CLONAL	1	TRUE	NA	0.383082799914656	5		353	783	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213964	2213964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1455	169	681	0	ENST00000326181.6:c.43G>A	p.Gly15Arg	p.G15R	ENST00000326181	NM_032271.2	15	Ggg/Agg	2/21	0.246736785856969	3	FACETS	0.647	0.593	0.705			1	SUBCLONAL	1	TRUE	NA	0.383082799914656	3		681	1624	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533281	29533281	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	41	231	0	ENST00000356175.3:c.1284G>C	p.Lys428Asn	p.K428N	ENST00000356175	NM_000267.3	428	aaG/aaC	12/57	1	2	FACETS	0.575	0.48	0.681	0.575	0.48	0.681	SUBCLONAL	1	TRUE	1	0.383082799914656	2		231	372	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812308	212812308	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs201678258	NA	P-0016224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	40	340	0	ENST00000342788.4:c.268G>T	p.Ala90Ser	p.A90S	ENST00000342788	NM_005235.2	90	Gct/Tct	3/28	1	2	FACETS	0.419	0.347	0.498	0.419	0.347	0.498	SUBCLONAL	1	TRUE	1	0.383082799914656	2		340	499	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543672	9543672	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0016224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	103	343	0	ENST00000353224.5:c.1483-1G>T		p.X495_splice	ENST00000353224	NM_177990.2	495			0.383082799914656	3	FACETS	0.974	0.873	1	0.487	0.436	0.541	CLONAL	1	TRUE	1	0.383082799914656	3		343	658	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739091	40739092	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0016224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	294	419	1	ENST00000373198.4:c.3192_3193delinsAA	p.Phe1064_His1065delinsLeuAsn	p.F1064_H1065delinsLN	ENST00000373198	NM_133170.3	1064	ttCCac/ttAAac	24/32	0.383082799914656	3	FACETS	0.886	0.835	0.939	0.886	0.835	0.939	CLONAL	2	TRUE	1	0.383082799914656	3		420	1032	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133718	55133718	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0016224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	117	406	0	ENST00000257290.5:c.932-1G>T		p.X311_splice	ENST00000257290	NM_006206.4	311			1	2	FACETS	0.979	0.885	1	0.979	0.885	1	CLONAL	1	TRUE	1	0.383082799914656	2		406	624	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149436894	149436894	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	173	484	0	ENST00000286301.3:c.2275T>A	p.Ser759Thr	p.S759T	ENST00000286301	NM_005211.3	759	Tcc/Acc	17/22	1	2	FACETS	0.931	0.857	1	0.931	0.857	1	CLONAL	1	TRUE	1	0.383082799914656	2		484	970	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439423	149439423	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	159	426	0	ENST00000286301.3:c.1972C>A	p.Pro658Thr	p.P658T	ENST00000286301	NM_005211.3	658	Cct/Act	15/22	1	2	FACETS	0.949	0.87	1	0.949	0.87	1	CLONAL	1	TRUE	1	0.383082799914656	2		426	875	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199821	138199821	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	169	460	1	ENST00000237289.4:c.1239G>T	p.Lys413Asn	p.K413N	ENST00000237289	NM_001270507.1	413	aaG/aaT	7/9	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.383082799914656	2		461	842	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68984770	68984770	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	138	509	0	ENST00000288368.4:c.1534A>G	p.Met512Val	p.M512V	ENST00000288368	NM_024870.2	512	Atg/Gtg	14/40	0.203889762531629	3	FACETS	0.752	0.687	0.819	0.752	0.687	0.819	INDETERMINATE	2	TRUE	1	0.383082799914656	3		509	571	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500937	8500937	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs932334009	NA	P-0016224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	52	336	0	ENST00000356435.5:c.1945T>A	p.Tyr649Asn	p.Y649N	ENST00000356435		649	Tac/Aac	13/35	1	2	FACETS	0.433	0.368	0.504	0.433	0.368	0.504	SUBCLONAL	1	TRUE	1	0.383082799914656	2		336	627	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911460	101911460	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0016224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	30	188	0	ENST00000374994.4:c.1387-2A>T		p.X463_splice	ENST00000374994	NM_004612.2	463			1	2	FACETS	0.614	0.497	0.746	0.614	0.497	0.746	SUBCLONAL	1	TRUE	1	0.383082799914656	2		188	255	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039709	47039709	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0016224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	218	731	1	ENST00000377604.3:c.1160+1G>A		p.X387_splice	ENST00000377604	NM_001204468.1	387			0.383082799914656	1	FACETS	0.934	0.869	1	0.934	0.869	1	CLONAL	1	TRUE	0	0.383082799914656	1		732	985	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412928	63412928	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	210	757	0	ENST00000330258.3:c.239G>T	p.Gly80Val	p.G80V	ENST00000330258	NM_152424.3	80	gGt/gTt	2/2	1	2	FACETS	0.908	0.841	0.976	0.908	0.841	0.976	CLONAL	1	TRUE	1	0.383082799914656	2		757	1208	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	517	405	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.719861664374718	3	FACETS	0.977	0.941	1	0.977	0.941	1	CLONAL	2	TRUE	1	0.719861664374718	3		405	1000	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619792	1619792	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	365	625	0	ENST00000344749.5:c.1154del	p.Gly385ValfsTer9	p.G385Vfs*9	ENST00000344749	NM_001136139.2	385	gGt/gt	14/19	1	2	FACETS	0.949	0.901	0.997	0.949	0.901	0.997	CLONAL	1	TRUE	1	0.719861664374718	2		625	1069	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026871	71026871	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	147	343	1	ENST00000318789.4:c.1351G>T	p.Asp451Tyr	p.D451Y	ENST00000318789	NM_032682.5	451	Gat/Tat	16/21	0.719861664374718	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.719861664374718	1		344	257	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187393	38187393	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	236	390	1	ENST00000317025.8:c.1084C>T	p.Gln362Ter	p.Q362*	ENST00000317025	NM_023034.1	362	Cag/Tag	6/24	1	2	FACETS	0.938	0.88	0.998	0.938	0.88	0.998	CLONAL	1	TRUE	1	0.719861664374718	2		391	699	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0016227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	36	591	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.816	0.669	0.982	0.816	0.669	0.982	CLONAL	1	TRUE	1	0.14	2		592	630	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793340	242793340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201540918	NA	P-0016227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	66	794	0	ENST00000334409.5:c.737C>T	p.Thr246Met	p.T246M	ENST00000334409	NM_005018.2	246	aCg/aTg	5/5	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.14	2		794	888	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467988	50467988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	30	436	3	ENST00000331340.3:c.1223G>A	p.Arg408His	p.R408H	ENST00000331340	NM_006060.4	408	cGc/cAc	8/8	1	2	FACETS	0.862	0.694	1	0.862	0.694	1	CLONAL	1	TRUE	1	0.14	2		439	497	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0016228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	42	683	0				ENST00000310581	NM_198253.2	-/1132			0.193619680149723	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.841013385555079	0		683	76	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0016228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	6863	415	0	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.841013385555079	82	FACETS	1	0.997	1			1	CLONAL	71	FALSE	NA	0.841013385555079	82		415	7928	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589583	67589585	+	inframe_deletion	In_Frame_Del	DEL	TAC	TAC	-	novel	NA	P-0016228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	71	354	2	ENST00000274335.5:c.1346_1348del	p.Leu449_His450delinsTyr	p.L449_H450delinsY	ENST00000274335		449	tTACat/tat	10/15	0.727483982894777	3	FACETS	1	0.962	1			1	CLONAL	1	FALSE	NA	0.841013385555079	3		356	200	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023559	27023560	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0016229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	79	347	0	ENST00000324856.7:c.671dup	p.Pro225AlafsTer175	p.P225Afs*175	ENST00000324856	NM_006015.4	222	tac/taCc	1/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.18	2		347	788	SUCCESS
AR	367	MSKCC	GRCh37	X	66766208	66766208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	27	252	1	ENST00000374690.3:c.1220G>A	p.Arg407His	p.R407H	ENST00000374690	NM_000044.3	407	cGc/cAc	1/8	1	2	FACETS	0.571	0.454	0.707	0.571	0.454	0.707	SUBCLONAL	1	TRUE	1	0.18	2		253	525	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119024	70119024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	60	410	2	ENST00000245479.2:c.600del	p.Asn201ThrfsTer18	p.N201Tfs*18	ENST00000245479	NM_000346.3	199	tCc/tc	2/3	1	2	FACETS	0.831	0.715	0.959	0.831	0.715	0.959	CLONAL	1	TRUE	1	0.18	2		412	802	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390153	89390153	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	38	269	0	ENST00000336596.2:c.902C>A	p.Ser301Ter	p.S301*	ENST00000336596	NM_005233.5	301	tCa/tAa	4/17	1	2	FACETS	0.639	0.527	0.765	0.639	0.527	0.765	SUBCLONAL	1	TRUE	1	0.18	2		269	661	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0016230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	24	552	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.32	0.249	0.402	0.32	0.249	0.402	SUBCLONAL	1	TRUE	1	0.16	2		552	938	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253151	133253151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	72	458	0	ENST00000320574.5:c.890C>T	p.Ser297Phe	p.S297F	ENST00000320574	NM_006231.2	297	tCc/tTc	9/49	1	2	FACETS	0.849	0.74	0.968	0.849	0.74	0.968	CLONAL	1	TRUE	1	0.16	2		458	1060	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562746	29562746	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs199474742	NA	P-0016231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	152	478	1	ENST00000356175.3:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000356175	NM_000267.3	1276	Cga/Tga	28/57	0.731008275362646	1	FACETS	0.923	0.862	0.983	0.923	0.862	0.983	CLONAL	1	TRUE	0	0.731008275362646	1		479	286	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246021910	246021910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759589293	NA	P-0016231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	222	543	1	ENST00000388985.4:c.964G>A	p.Asp322Asn	p.D322N	ENST00000388985		322	Gat/Aat	10/12	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.731008275362646	2		544	575	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922008	39922008	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	AAGAGGTACCTT	novel	NA	P-0016231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	108	245	0	ENST00000378444.4:c.4164delinsAAGGTACCTCTT	p.Asp1389ArgfsTer8	p.D1389Rfs*8	ENST00000378444	NM_001123385.1	1388	gcC/gcAAGGTACCTCTT	9/15	1	1	FACETS	0.971	0.898	1	0.971	0.898	1	CLONAL	1	TRUE	0	0.731008275362646	1		245	193	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0016232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	544	936	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.674614366577496	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.698225418400686	1		938	1001	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0016233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	154	591	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.511668998264683	1	FACETS	0.877	0.808	0.948	0.877	0.808	0.948	CLONAL	1	TRUE	0	0.511668998264683	1		592	511	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911069	94911069	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	106	505	0	ENST00000536441.1:c.1061A>G	p.Tyr354Cys	p.Y354C	ENST00000536441	NM_144665.3	354	tAt/tGt	8/10	0.511668998264683	3	FACETS	0.859	0.78	0.939	0.859	0.78	0.939	CLONAL	2	TRUE	1	0.511668998264683	3		505	303	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945120	32945120	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs758884639	NA	P-0016233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	59	405	0	ENST00000380152.3:c.8515T>C	p.Tyr2839His	p.Y2839H	ENST00000380152		2839	Tac/Cac	20/27	0.231439020028121	5	FACETS	1	0.873	1	0.337	0.291	0.387	INDETERMINATE	1	TRUE	2	0.511668998264683	5		405	403	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465417	99465417	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs147969557	NA	P-0016233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	183	423	0	ENST00000268035.6:c.2242A>G	p.Thr748Ala	p.T748A	ENST00000268035	NM_000875.3	748	Acc/Gcc	11/21	0.511668998264683	3	FACETS	0.99	0.914	1	0.495	0.457	0.535	CLONAL	1	TRUE	1	0.511668998264683	3		423	907	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020438	69020438	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	109	595	0	ENST00000288368.4:c.2810A>T	p.Asn937Ile	p.N937I	ENST00000288368	NM_024870.2	937	aAc/aTc	24/40	0.511668998264683	3	FACETS	0.939	0.845	1	0.469	0.422	0.519	CLONAL	1	TRUE	1	0.511668998264683	3		595	570	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0016234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	175	2255	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.194953111257979	2	FACETS	0.956	0.881	1	0.956	0.881	1	CLONAL	2	TRUE	0	0.204811207927019	2		2255	894	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0016234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	74	397	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	1	2	FACETS	0.778	0.679	0.885	0.778	0.679	0.885	SUBCLONAL	1	TRUE	1	0.204811207927019	2		397	929	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107180	27107180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1308037041	NA	P-0016234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	76	380	0	ENST00000324856.7:c.6791C>T	p.Ser2264Leu	p.S2264L	ENST00000324856	NM_006015.4	2264	tCa/tTa	20/20	1	2	FACETS	0.83	0.727	0.942	0.83	0.727	0.942	CLONAL	1	TRUE	1	0.204811207927019	2		380	894	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916734	48916734	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0016234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	62	272	0	ENST00000267163.4:c.265-1G>T		p.X89_splice	ENST00000267163	NM_000321.2	89			1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.204811207927019	2		272	534	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106024	27106024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369894428	NA	P-0016234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	58	320	2	ENST00000324856.7:c.5635C>T	p.Arg1879Trp	p.R1879W	ENST00000324856	NM_006015.4	1879	Cgg/Tgg	20/20	1	2	FACETS	0.787	0.675	0.909	0.787	0.675	0.909	CLONAL	1	TRUE	1	0.204811207927019	2		322	720	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561045	9561045	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	26	229	0	ENST00000353224.5:c.737C>T	p.Ser246Phe	p.S246F	ENST00000353224	NM_177990.2	246	tCc/tTc	4/10	0.16785907637143	2	FACETS	0.527	0.416	0.654	0.263	0.208	0.327	SUBCLONAL	1	TRUE	0	0.204811207927019	2		229	482	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099864	27099864	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	65	355	0	ENST00000324856.7:c.3743C>A	p.Ser1248Ter	p.S1248*	ENST00000324856	NM_006015.4	1248	tCa/tAa	15/20	1	2	FACETS	0.904	0.783	1	0.904	0.783	1	CLONAL	1	TRUE	1	0.204811207927019	2		355	702	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106676	27106676	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0016234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	80	421	0	ENST00000324856.7:c.6287C>G	p.Ser2096Ter	p.S2096*	ENST00000324856	NM_006015.4	2096	tCa/tGa	20/20	1	2	FACETS	0.948	0.833	1	0.948	0.833	1	CLONAL	1	TRUE	1	0.204811207927019	2		421	824	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288518	21288518	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	113	348	0	ENST00000354336.3:c.763G>T	p.Ala255Ser	p.A255S	ENST00000354336	NM_005207.3	255	Gcc/Tcc	2/3	0.16785907637143	2	FACETS	1	0.977	1	0.654	0.588	0.724	CLONAL	1	TRUE	0	0.204811207927019	2		348	843	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035138	37035138	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	38	227	0	ENST00000231790.2:c.100G>C	p.Glu34Gln	p.E34Q	ENST00000231790	NM_000249.3	34	Gag/Cag	1/19	0.16785907637143	2	FACETS	0.628	0.518	0.751	0.314	0.259	0.376	SUBCLONAL	1	TRUE	0	0.204811207927019	2		227	591	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521726	89521726	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	100	359	0	ENST00000336596.2:c.2803G>T	p.Val935Leu	p.V935L	ENST00000336596	NM_005233.5	935	Gtg/Ttg	16/17	0.16785907637143	2	FACETS	1	0.955	1	0.566	0.505	0.632	CLONAL	1	TRUE	0	0.204811207927019	2		359	862	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056756	180056756	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	209	497	3	ENST00000261937.6:c.756C>A	p.Cys252Ter	p.C252*	ENST00000261937	NM_182925.4	252	tgC/tgA	6/30	0.16785907637143	2	FACETS	0.829	0.768	0.892	0.829	0.768	0.892	CLONAL	2	TRUE	0	0.204811207927019	2		500	1231	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559297	141559297	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	97	394	0	ENST00000220592.5:c.1504G>C	p.Glu502Gln	p.E502Q	ENST00000220592	NM_012154.3	502	Gag/Cag	12/19	0.204811207927019	3	FACETS	1	0.959	1	0.387	0.344	0.433	CLONAL	1	TRUE	0	0.204811207927019	3		394	899	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0016235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	137	936	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.9	0.818	0.986	0.9	0.818	0.986	CLONAL	1	TRUE	1	0.340903592481256	2		938	893	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0016235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	211	1585	1	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.340903592481256	2		1586	931	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678568	88678568	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	36	260	0	ENST00000360948.2:c.968T>C	p.Phe323Ser	p.F323S	ENST00000360948	NM_001012338.2	323	tTt/tCt	9/19	0.171713022172074	0	FACETS	0.392	0.323	0.47			1	INDETERMINATE	1	TRUE	0	0.340903592481256	0		260	355	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81922878	81922878	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	46	322	0	ENST00000359376.3:c.867+1del		p.E289fs	ENST00000359376	NM_002661.3	289	gaG/ga	10/33	0.247522864125393	3	FACETS	0.529	0.445	0.622	0.265	0.222	0.311	SUBCLONAL	1	TRUE	1	0.340903592481256	3		322	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0016235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	151	521	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.340903592481256	2		523	664	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752826	42752826	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	347	683	0	ENST00000222329.4:c.1438C>T	p.Leu480Phe	p.L480F	ENST00000222329	NM_006494.2	480	Ctc/Ttc	4/4	0.234771863246742	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.340903592481256	2		683	975	SUCCESS
APC	324	MSKCC	GRCh37	5	112154869	112154870	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCA	novel	NA	P-0016235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	41	470	0	ENST00000257430.4:c.1142_1145dup	p.Arg382SerfsTer16	p.R382Sfs*16	ENST00000257430	NM_000038.5	380	-/GCCA	10/16	0.221495309342073	2	FACETS	0.336	0.279	0.4	0.168	0.139	0.2	SUBCLONAL	1	TRUE	0	0.340903592481256	2		470	715	SUCCESS
APC	324	MSKCC	GRCh37	5	112174268	112174277	+	frameshift_variant	Frame_Shift_Del	DEL	AAGTTTTGCA	AAGTTTTGCA	-	novel	NA	P-0016235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	170	369	0	ENST00000257430.4:c.2977_2986del	p.Lys993ValfsTer9	p.K993Vfs*9	ENST00000257430	NM_000038.5	993	AAGTTTTGCAgt/gt	16/16	0.221495309342073	2	FACETS	0.777	0.717	0.838	0.777	0.717	0.838	SUBCLONAL	2	TRUE	0	0.340903592481256	2		369	642	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0016235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	44	277	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.221495309342073	2	FACETS	0.463	0.388	0.547	0.232	0.194	0.274	SUBCLONAL	1	TRUE	0	0.340903592481256	2		277	557	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202230	138202230	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	69	418	0	ENST00000237289.4:c.2147G>C	p.Cys716Ser	p.C716S	ENST00000237289	NM_001270507.1	716	tGc/tCc	9/9	1	2	FACETS	0.534	0.464	0.61	0.534	0.464	0.61	SUBCLONAL	1	TRUE	1	0.340903592481256	2		418	758	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942756	44942757	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0016235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	178	299	0	ENST00000377967.4:c.3336_3337insAA	p.Val1113LysfsTer8	p.V1113Kfs*8	ENST00000377967	NM_021140.2	1112	-/AA	23/29	1	1	FACETS	0.984	0.917	1	1	0.993	1	CLONAL	2	TRUE	0	0.340903592481256	1		299	440	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579433	7579433	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1064793279	NA	P-0016236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	94	465	1	ENST00000269305.4:c.254del	p.Pro85LeufsTer38	p.P85Lfs*38	ENST00000269305	NM_001126112.2	85	cCt/ct	4/11	0.237845871110956	1	FACETS	0.73	0.649	0.816	0.73	0.649	0.816	SUBCLONAL	1	FALSE	0	0.3	1		466	730	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354806	40354806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567653213	NA	P-0016236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	125	539	0	ENST00000293328.3:c.2098G>A	p.Val700Met	p.V700M	ENST00000293328	NM_012448.3	700	Gtg/Atg	17/19	1	2	FACETS	0.874	0.79	0.962	0.874	0.79	0.962	CLONAL	1	FALSE	1	0.3	2		539	954	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105870	27105870	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	154	388	0	ENST00000324856.7:c.5481C>A	p.Cys1827Ter	p.C1827*	ENST00000324856	NM_006015.4	1827	tgC/tgA	20/20	1	2	FACETS	0.65	0.596	0.707	0.65	0.596	0.707	SUBCLONAL	1	TRUE	1	0.619809672537561	2		388	764	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549724	187549724	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs570583897	NA	P-0016237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	201	377	0	ENST00000441802.2:c.4517G>A	p.Arg1506His	p.R1506H	ENST00000441802	NM_005245.3	1506	cGt/cAt	8/27	0.619809672537561	3	FACETS	0.917	0.851	0.987	0.459	0.425	0.494	CLONAL	1	TRUE	1	0.619809672537561	3		377	926	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	160	423	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.753	0.693	0.814	0.753	0.693	0.814	SUBCLONAL	1	TRUE	1	0.701408956774538	2		423	606	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653800	89653802	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	novel	NA	P-0016238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	150	308	0	ENST00000371953.3:c.98_100del	p.Ile33_Ala34delinsThr	p.I33_A34delinsT	ENST00000371953	NM_000314.4	33	aTTGct/act	2/9	0.701408956774538	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.701408956774538	1		308	272	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197757	66197757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770802873	NA	P-0016238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	305	452	1	ENST00000273854.3:c.2942G>A	p.Arg981Gln	p.R981Q	ENST00000273854	NM_004439.5	981	cGg/cAg	17/18	1	2	FACETS	0.962	0.909	1	0.962	0.909	1	CLONAL	1	TRUE	1	0.701408956774538	2		453	904	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0016239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	192	414	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	0.946	0.876	1	0.946	0.876	1	CLONAL	1	TRUE	1	0.440089398914825	2		414	922	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097836	8097836	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	158	457	0	ENST00000346208.3:c.218A>T	p.Gln73Leu	p.Q73L	ENST00000346208		73	cAg/cTg	2/6	1	2	FACETS	0.794	0.728	0.864	0.794	0.728	0.864	SUBCLONAL	1	TRUE	1	0.440089398914825	2		457	904	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0016240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	170	546	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.415117702837802	3	FACETS	1	0.988	1	0.693	0.639	0.749	CLONAL	1	TRUE	1	0.415117702837802	3		546	714	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	77	423	0				ENST00000310581	NM_198253.2	-/1132			0.415117702837802	3	FACETS	1	0.97	1	0.659	0.583	0.739	CLONAL	1	TRUE	1	0.415117702837802	3		423	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0016240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	275	521	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.415117702837802	3	FACETS	0.836	0.791	0.881	1	0.991	1	CLONAL	3	TRUE	1	0.415117702837802	3		523	638	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805789	46805789	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	92	311	0	ENST00000290295.7:c.167C>T	p.Ser56Leu	p.S56L	ENST00000290295	NM_006361.5	56	tCg/tTg	1/2	0.18377129958726	5	FACETS	0.831	0.742	0.924			1	INDETERMINATE	2	TRUE	NA	0.415117702837802	5		311	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0016241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	227	610	2	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.62163168270309	2	FACETS	0.978	0.931	1	0.978	0.931	1	CLONAL	2	TRUE	0	0.646275593862958	2		612	359	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937905	36937905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201890478	NA	P-0016241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	234	445	0	ENST00000361632.4:c.931C>T	p.Arg311Cys	p.R311C	ENST00000361632		311	Cgc/Tgc	7/16	0.646275593862958	11	FACETS	0.99	0.921	1			1	CLONAL	2	TRUE	NA	0.646275593862958	11		445	1430	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21643196	21643196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	570	516	1	ENST00000421138.2:c.331C>T	p.Leu111Phe	p.L111F	ENST00000421138		111	Ctt/Ttt	5/16	0.646275593862958	12	FACETS	0.982	0.957	1			1	CLONAL	10	TRUE	NA	0.646275593862958	12		517	760	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105238710	105238710	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	178	365	0	ENST00000349310.3:c.1252G>T	p.Glu418Ter	p.E418*	ENST00000349310	NM_001014432.1	418	Gag/Tag	13/15	0.646275593862958	4	FACETS	0.877	0.815	0.941			1	CLONAL	2	TRUE	NA	0.646275593862958	4		365	517	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705457	43705457	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	183	410	0	ENST00000382044.4:c.5165A>G	p.Glu1722Gly	p.E1722G	ENST00000382044	NM_001141980.1	1722	gAg/gGg	24/28	0.646275593862958	4	FACETS	0.854	0.793	0.916	0.854	0.793	0.916	CLONAL	2	TRUE	2	0.646275593862958	4		410	546	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647490	3647490	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs143831403	NA	P-0016241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	194	455	0	ENST00000294008.3:c.1573C>A	p.Arg525Ser	p.R525S	ENST00000294008	NM_032444.2	525	Cgc/Agc	7/15	0.607101993365373	4	FACETS	0.864	0.805	0.924	0.864	0.805	0.924	CLONAL	2	TRUE	2	0.646275593862958	4		455	572	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439559	220439559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	167	303	0	ENST00000243786.2:c.412G>A	p.Asp138Asn	p.D138N	ENST00000243786	NM_002191.3	138	Gac/Aac	2/2	0.607101993365373	4	FACETS	0.915	0.848	0.983	0.915	0.848	0.983	CLONAL	2	TRUE	2	0.646275593862958	4		303	465	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163524	47163524	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	108	254	0	ENST00000409792.3:c.2602G>A	p.Asp868Asn	p.D868N	ENST00000409792	NM_014159.6	868	Gat/Aat	3/21	0.550295786611398	3	FACETS	1	0.982	1	0.814	0.755	0.873	CLONAL	2	TRUE	0	0.646275593862958	3		254	181	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026656	6026656	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	117	593	0	ENST00000265849.7:c.1740A>C	p.Lys580Asn	p.K580N	ENST00000265849	NM_000535.5	580	aaA/aaC	11/15	0.646275593862958	3	FACETS	0.949	0.86	1	0.474	0.43	0.521	CLONAL	1	TRUE	1	0.646275593862958	3		593	505	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197884	123197885	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	98	282	0	ENST00000218089.9:c.2010dup	p.Asp671ArgfsTer7	p.D671Rfs*7	ENST00000218089	NM_001042749.1	670	gaa/gAaa	20/35	0.545204437039611	4	FACETS	0.995	0.903	1			1	CLONAL	2	TRUE	NA	0.646275593862958	4		282	251	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	711	641	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.411645039121031	4	FACETS	0.881	0.854	0.909	1	0.996	1	CLONAL	4	TRUE	1	0.411645039121031	4		641	1383	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371734	55371734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	139	456	1	ENST00000297316.4:c.424C>T	p.Arg142Cys	p.R142C	ENST00000297316	NM_022454.3	142	Cgc/Tgc	2/2	0.411645039121031	4	FACETS	0.889	0.808	0.975	0.296	0.269	0.325	CLONAL	1	TRUE	1	0.411645039121031	4		457	1072	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579344	7579345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0016242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	423	637	0	ENST00000269305.4:c.342dup	p.His115AlafsTer34	p.H115Afs*34	ENST00000269305	NM_001126112.2	114	-/G	4/11	0.411645039121031	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.411645039121031	2		637	1003	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437556	56437556	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	398	628	0	ENST00000407977.2:c.906G>A	p.Trp302Ter	p.W302*	ENST00000407977		302	tgG/tgA	8/10	0.411645039121031	2	FACETS	0.998	0.952	1	0.998	0.952	1	CLONAL	2	TRUE	0	0.411645039121031	2		628	969	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268418	142268418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771309709	NA	P-0016242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	318	520	0	ENST00000350721.4:c.3074G>A	p.Arg1025His	p.R1025H	ENST00000350721	NM_001184.3	1025	cGt/cAt	15/47	0.397616995500152	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.411645039121031	3		520	889	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971077	21971077	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	250	365	0	ENST00000304494.5:c.281T>A	p.Leu94Gln	p.L94Q	ENST00000304494	NM_000077.4	94	cTg/cAg	2/3	0.411645039121031	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.411645039121031	2		365	586	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0016244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	118	547	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.801838470333217	2	FACETS	0.59	0.535	0.648	0.295	0.267	0.324	SUBCLONAL	1	TRUE	0	0.807755066046273	2		547	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0016244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	409	505	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.807755066046273	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.807755066046273	1		505	585	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306653	41306653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	166	430	0	ENST00000373198.4:c.1006G>A	p.Glu336Lys	p.E336K	ENST00000373198	NM_133170.3	336	Gag/Aag	7/32	1	2	FACETS	0.502	0.461	0.544	0.502	0.461	0.544	SUBCLONAL	1	TRUE	1	0.807755066046273	2		430	819	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131787	2131787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1020561347	NA	P-0016244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	336	361	0	ENST00000219476.3:c.3802C>T	p.Arg1268Cys	p.R1268C	ENST00000219476	NM_000548.3	1268	Cgc/Tgc	31/42	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.807755066046273	2		361	803	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256832	16256832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs887977680	NA	P-0016244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	381	497	2	ENST00000375759.3:c.4097G>A	p.Arg1366Gln	p.R1366Q	ENST00000375759	NM_015001.2	1366	cGa/cAa	11/15	0.768267153743174	1	FACETS	0.992	0.957	1	0.992	0.957	1	CLONAL	1	TRUE	0	0.807755066046273	1		499	567	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132948	30132948	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	64	400	2	ENST00000331968.5:c.653C>A	p.Ser218Ter	p.S218*	ENST00000331968	NM_002742.2	218	tCa/tAa	4/18	0.330473346488335	1	FACETS	0.123	0.106	0.142	0.123	0.106	0.142	INDETERMINATE	1	TRUE	0	0.807755066046273	1		402	765	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827727	72827727	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	34	364	0	ENST00000268489.5:c.8854C>G	p.Gln2952Glu	p.Q2952E	ENST00000268489	NM_006885.3	2952	Caa/Gaa	9/10	0.807755066046273	1	FACETS	0.082	0.066	0.099	0.082	0.066	0.099	SUBCLONAL	1	TRUE	0	0.807755066046273	1		364	613	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619264	37619264	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2975	228	325	0	ENST00000447079.4:c.940G>A	p.Glu314Lys	p.E314K	ENST00000447079	NM_015083.1	314	Gaa/Aaa	1/14	0.807755066046273	12	FACETS	0.888	0.822	0.957			1	CLONAL	1	TRUE	NA	0.807755066046273	12		325	3203	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1650196	1650196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199639167	NA	P-0016244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	484	481	0	ENST00000344749.5:c.52G>A	p.Asp18Asn	p.D18N	ENST00000344749	NM_001136139.2	18	Gac/Aac	2/19	0.807755066046273	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.807755066046273	1		481	663	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271782	18271782	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	T	novel	NA	P-0016244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	501	489	0	ENST00000222254.8:c.466+3G>T		p.X156_splice	ENST00000222254	NM_005027.3	156			0.807755066046273	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.807755066046273	1		489	654	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193530	99193530	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	195	387	0	ENST00000074304.5:c.2725G>C	p.Glu909Gln	p.E909Q	ENST00000074304	NM_001134224.1	909	Gag/Cag	25/26	0.418962561889458	1	FACETS	0.418	0.388	0.448	0.418	0.388	0.448	INDETERMINATE	1	TRUE	0	0.807755066046273	1		387	689	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165621	47165621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	19	284	0	ENST00000409792.3:c.505C>T	p.His169Tyr	p.H169Y	ENST00000409792	NM_014159.6	169	Cat/Tat	3/21	0.807755066046273	1	FACETS	0.075	0.056	0.096	0.075	0.056	0.096	SUBCLONAL	1	TRUE	0	0.807755066046273	1		284	376	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294132	1294132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147056740	NA	P-0016244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	541	606	0	ENST00000310581.5:c.869C>T	p.Ser290Phe	p.S290F	ENST00000310581	NM_198253.2	290	tCt/tTt	2/16	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.807755066046273	2		606	1268	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509249	106509249	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	365	455	0	ENST00000359195.3:c.1243G>C	p.Glu415Gln	p.E415Q	ENST00000359195	NM_002649.2	415	Gag/Cag	2/11	0.807755066046273	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.807755066046273	1		455	513	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992734	68992734	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	230	508	0	ENST00000288368.4:c.1699G>A	p.Glu567Lys	p.E567K	ENST00000288368	NM_024870.2	567	Gag/Aag	16/40	0.627349460037023	3	FACETS	0.788	0.734	0.843	0.394	0.367	0.422	SUBCLONAL	1	TRUE	1	0.807755066046273	3		508	1015	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424202	47424202	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	47	340	0	ENST00000377045.4:c.207G>C	p.Lys69Asn	p.K69N	ENST00000377045	NM_001654.4	69	aaG/aaC	4/16	0.51896141755112	1	FACETS	0.125	0.105	0.147	0.125	0.105	0.147	SUBCLONAL	1	TRUE	0	0.807755066046273	1		340	557	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0016245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	143	244	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.262589474134138	3	FACETS	0.828	0.763	0.893	0.828	0.763	0.893	INDETERMINATE	2	TRUE	1	0.57296443416996	3		244	388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574006	7574013	+	frameshift_variant	Frame_Shift_Del	DEL	ACATCTCG	ACATCTCG	-	novel	NA	P-0016246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	474	481	0	ENST00000269305.4:c.1014_1021del	p.Glu339ProfsTer5	p.E339Pfs*5	ENST00000269305	NM_001126112.2	338	ttCGAGATGTtc/tttc	10/11	0.819289071268393	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.819289071268393	1		481	666	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033252	69033252	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	405	387	1	ENST00000288368.4:c.3692C>A	p.Thr1231Asn	p.T1231N	ENST00000288368	NM_024870.2	1231	aCt/aAt	30/40	1	2	FACETS	0.971	0.927	1	0.971	0.927	1	CLONAL	1	TRUE	1	0.819289071268393	2		388	1018	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	207	486	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.845	0.788	0.905	0.845	0.788	0.905	CLONAL	1	TRUE	1	0.70564223761798	2		486	694	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	60	318	5	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.245	0.211	0.283	0.245	0.211	0.283	SUBCLONAL	1	TRUE	1	0.70564223761798	2		323	694	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	75	402	0	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	2	FACETS	0.21	0.184	0.24	0.21	0.184	0.24	SUBCLONAL	1	TRUE	1	0.70564223761798	2		402	1010	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913403	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	57	249	0	ENST00000349496.5:c.110C>A	p.Ser37Tyr	p.S37Y	ENST00000349496	NM_001904.3	37	tCt/tAt	3/15	1	2	FACETS	0.256	0.219	0.296	0.256	0.219	0.296	SUBCLONAL	1	TRUE	1	0.70564223761798	2		249	631	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	276	376	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	0.70564223761798	2		376	749	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	490	1492	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	0.956	0.914	0.998	0.956	0.914	0.998	CLONAL	1	TRUE	1	0.70564223761798	2		1492	1453	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	298	320	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.921	0.869	0.974	0.921	0.869	0.974	CLONAL	1	TRUE	1	0.70564223761798	2		321	917	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	274	396	2	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.70564223761798	2		398	774	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	276	394	9	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.757	0.711	0.804	0.757	0.711	0.804	SUBCLONAL	1	TRUE	1	0.70564223761798	2		403	1033	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	104	329	1	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	1	2	FACETS	0.356	0.319	0.397	0.356	0.319	0.397	SUBCLONAL	1	TRUE	1	0.70564223761798	2		330	827	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	127	443	0	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	1	2	FACETS	0.32	0.289	0.353	0.32	0.289	0.353	SUBCLONAL	1	TRUE	1	0.70564223761798	2		443	1125	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121909229	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	489	361	0	ENST00000371953.3:c.389G>C	p.Arg130Pro	p.R130P	ENST00000371953	NM_000314.4	130	cGa/cCa	5/9	0.70564223761798	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.70564223761798	2		361	647	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921551	178921551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	191	350	0	ENST00000263967.3:c.1033A>G	p.Asn345Asp	p.N345D	ENST00000263967	NM_006218.2	345	Aat/Gat	5/21	1	2	FACETS	0.932	0.867	0.998	0.932	0.867	0.998	CLONAL	1	TRUE	1	0.70564223761798	2		350	581	SUCCESS
APC	324	MSKCC	GRCh37	5	112111408	112111411	+	frameshift_variant	Frame_Shift_Del	DEL	ATAG	ATAG	-	rs387906231	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	148	399	0	ENST00000257430.4:c.509_512del	p.Asp170ValfsTer4	p.D170Vfs*4	ENST00000257430	NM_000038.5	169	ATAGat/at	5/16	1	2	FACETS	0.633	0.579	0.688	0.633	0.579	0.688	SUBCLONAL	1	TRUE	1	0.70564223761798	2		399	663	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	249	278	2	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.98	0.921	1	0.98	0.921	1	CLONAL	1	TRUE	1	0.70564223761798	2		280	720	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	253	672	0	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	1	2	FACETS	0.702	0.657	0.749	0.702	0.657	0.749	SUBCLONAL	1	TRUE	1	0.70564223761798	2		672	1021	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831357	72831358	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTG	rs34918837	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	66	173	1	ENST00000268489.5:c.5221_5223dup	p.Gln1741dup	p.Q1741dup	ENST00000268489	NM_006885.3	1741	-/CAA	9/10	1	2	FACETS	0.457	0.398	0.521	0.457	0.398	0.521	SUBCLONAL	1	TRUE	1	0.70564223761798	2		174	409	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796882	42796883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761345552	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	423	560	6	ENST00000575354.2:c.3347dup	p.Ser1117LysfsTer34	p.S1117Kfs*34	ENST00000575354	NM_015125.3	1114	gcc/gCcc	14/20	1	2	FACETS	0.902	0.859	0.946	0.902	0.859	0.946	CLONAL	1	TRUE	1	0.70564223761798	2		566	1329	SUCCESS
APC	324	MSKCC	GRCh37	5	112151245	112151246	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs1114167567	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	126	324	0	ENST00000257430.4:c.893_894del	p.His298LeufsTer28	p.H298Lfs*28	ENST00000257430	NM_000038.5	296	agCAca/agca	9/16	1	2	FACETS	0.39	0.353	0.43	0.39	0.353	0.43	SUBCLONAL	1	TRUE	1	0.70564223761798	2		324	915	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829404	72829404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200268844	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	357	339	0	ENST00000268489.5:c.7177G>A	p.Ala2393Thr	p.A2393T	ENST00000268489	NM_006885.3	2393	Gcc/Acc	9/10	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.70564223761798	2		339	856	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510166	149510166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747109578	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	105	367	1	ENST00000261799.4:c.1303C>T	p.Arg435Cys	p.R435C	ENST00000261799	NM_002609.3	435	Cgc/Tgc	9/23	1	2	FACETS	0.287	0.256	0.32	0.287	0.256	0.32	SUBCLONAL	1	TRUE	1	0.70564223761798	2		368	1036	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298068	11298068	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	410	408	0	ENST00000361445.4:c.2040C>G	p.Asp680Glu	p.D680E	ENST00000361445	NM_004958.3	680	gaC/gaG	13/58	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.70564223761798	2		408	1108	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262156	16262156	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	91	134	0	ENST00000375759.3:c.9421C>T	p.Gln3141Ter	p.Q3141*	ENST00000375759	NM_015001.2	3141	Cag/Tag	11/15	1	2	FACETS	0.874	0.786	0.966	0.874	0.786	0.966	CLONAL	1	TRUE	1	0.70564223761798	2		134	295	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057968	27057969	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	368	434	0	ENST00000324856.7:c.1676_1677del	p.Pro559LeufsTer63	p.P559Lfs*63	ENST00000324856	NM_006015.4	559	cCT/c	3/20	1	2	FACETS	0.98	0.932	1	0.98	0.932	1	CLONAL	1	TRUE	1	0.70564223761798	2		434	1064	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366987	40366987	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	307	411	4	ENST00000397332.2:c.210del	p.Thr71ArgfsTer69	p.T71Rfs*69	ENST00000397332	NM_001033082.2	70	ccC/cc	2/3	1	2	FACETS	0.842	0.794	0.89	0.842	0.794	0.89	CLONAL	1	TRUE	1	0.70564223761798	2		415	1034	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115279477	115279477	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs112486926	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	81	383	2	ENST00000438362.2:c.541-1G>A		p.X181_splice	ENST00000438362	NM_001242891.1	181			1	2	FACETS	0.275	0.241	0.311	0.275	0.241	0.311	SUBCLONAL	1	TRUE	1	0.70564223761798	2		385	836	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456461	32456461	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	307	299	1	ENST00000332351.3:c.431C>T	p.Pro144Leu	p.P144L	ENST00000332351	NM_024426.4	144	cCg/cTg	1/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.70564223761798	2		300	755	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427959	49427959	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	300	417	1	ENST00000301067.7:c.10631C>T	p.Ala3544Val	p.A3544V	ENST00000301067	NM_003482.3	3544	gCc/gTc	38/54	1	2	FACETS	0.775	0.73	0.821	0.775	0.73	0.821	SUBCLONAL	1	TRUE	1	0.70564223761798	2		418	1097	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487954	56487954	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	213	385	1	ENST00000267101.3:c.1685C>T	p.Thr562Ile	p.T562I	ENST00000267101	NM_001982.3	562	aCt/aTt	14/28	1	2	FACETS	0.646	0.6	0.693	0.646	0.6	0.693	SUBCLONAL	1	TRUE	1	0.70564223761798	2		386	935	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74000797	74000797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	44	235	0	ENST00000318443.5:c.1487G>A	p.Cys496Tyr	p.C496Y	ENST00000318443	NM_001024736.1	496	tGt/tAt	7/10	1	2	FACETS	0.205	0.172	0.243	0.205	0.172	0.243	SUBCLONAL	1	TRUE	1	0.70564223761798	2		235	607	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353968	15353968	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	21	90	0	ENST00000263377.2:c.2912A>T	p.Gln971Leu	p.Q971L	ENST00000263377	NM_058243.2	971	cAg/cTg	14/20	1	2	FACETS	0.235	0.181	0.298	0.235	0.181	0.298	SUBCLONAL	1	TRUE	1	0.70564223761798	2		90	253	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210440	36210440	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	353	472	0	ENST00000222270.7:c.433C>T	p.Arg145Ter	p.R145*	ENST00000222270	NM_014727.1	145	Cga/Tga	2/37	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.70564223761798	2		472	992	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797834	42797834	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	94	394	1	ENST00000575354.2:c.3886G>A	p.Ala1296Thr	p.A1296T	ENST00000575354	NM_015125.3	1296	Gcc/Acc	16/20	1	2	FACETS	0.302	0.268	0.338	0.302	0.268	0.338	SUBCLONAL	1	TRUE	1	0.70564223761798	2		395	883	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635555	47635556	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs63749848	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	55	289	0	ENST00000233146.2:c.229_230del	p.Ser77CysfsTer4	p.S77Cfs*4	ENST00000233146	NM_000251.2	76	cAG/c	2/16	1	2	FACETS	0.195	0.166	0.227	0.195	0.166	0.227	SUBCLONAL	1	TRUE	1	0.70564223761798	2		289	799	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29115393	29115393	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1342011335	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	53	445	0	ENST00000328354.6:c.673del	p.Thr225LeufsTer10	p.T225Lfs*10	ENST00000328354	NM_007194.3	225	Act/ct	5/15	1	2	FACETS	0.155	0.131	0.181	0.155	0.131	0.181	SUBCLONAL	1	TRUE	1	0.70564223761798	2		445	968	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70005612	70005614	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs1553704814	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	59	421	0	ENST00000394351.3:c.649_651del	p.Arg217del	p.R217del	ENST00000394351	NM_000248.3	214	cGAAga/cga	7/9	1	2	FACETS	0.254	0.218	0.293	0.254	0.218	0.293	SUBCLONAL	1	TRUE	1	0.70564223761798	2		421	659	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449680	187449680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	101	400	2	ENST00000232014.4:c.200G>A	p.Cys67Tyr	p.C67Y	ENST00000232014	NM_001130845.1	67	tGc/tAc	4/10	1	2	FACETS	0.29	0.259	0.324	0.29	0.259	0.324	SUBCLONAL	1	TRUE	1	0.70564223761798	2		402	986	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449788	149449788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	380	448	0	ENST00000286301.3:c.1276del	p.Gln426SerfsTer4	p.Q426Sfs*4	ENST00000286301	NM_005211.3	426	Cag/ag	9/22	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.70564223761798	2		448	1022	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679819	30679819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316478659	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	85	307	0	ENST00000376406.3:c.1900G>A	p.Val634Met	p.V634M	ENST00000376406	NM_014641.2	634	Gtg/Atg	5/15	1	2	FACETS	0.323	0.285	0.363	0.323	0.285	0.363	SUBCLONAL	1	TRUE	1	0.70564223761798	2		307	747	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117739645	117739645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	270	367	0	ENST00000368508.3:c.148C>T	p.Pro50Ser	p.P50S	ENST00000368508	NM_002944.2	50	Cca/Tca	2/43	1	2	FACETS	0.938	0.883	0.994	0.938	0.883	0.994	CLONAL	1	TRUE	1	0.70564223761798	2		367	816	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220494	98220494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	95	383	0	ENST00000331920.6:c.2969C>T	p.Ala990Val	p.A990V	ENST00000331920	NM_000264.3	990	gCa/gTa	18/24	1	2	FACETS	0.248	0.22	0.278	0.248	0.22	0.278	SUBCLONAL	1	TRUE	1	0.70564223761798	2		383	1086	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300837	137300837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	74	471	0	ENST00000481739.1:c.482G>A	p.Arg161Gln	p.R161Q	ENST00000481739	NM_002957.4	161	cGg/cAg	4/10	1	2	FACETS	0.179	0.155	0.204	0.179	0.155	0.204	SUBCLONAL	1	TRUE	1	0.70564223761798	2		471	1175	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044750	47044750	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868946632	NA	P-0016247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	279	495	0	ENST00000377604.3:c.2150C>T	p.Ala717Val	p.A717V	ENST00000377604	NM_001204468.1	717	gCc/gTc	19/24	1	2	FACETS	0.688	0.646	0.731	0.688	0.646	0.731	SUBCLONAL	1	TRUE	1	0.70564223761798	2		495	1150	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911482	131911482	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	45	361	0	ENST00000265335.6:c.227C>G	p.Thr76Arg	p.T76R	ENST00000265335		76	aCa/aGa	3/25	0.925399541815854	1	FACETS	0.133	0.111	0.156	0.133	0.111	0.156	SUBCLONAL	1	TRUE	0	0.925399541815854	1		361	394	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966622	36966622	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	598	362	0	ENST00000358127.4:c.704A>G	p.Glu235Gly	p.E235G	ENST00000358127	NM_001280556.1	235	gAg/gGg	6/10	1	2	FACETS	1	0.988	1	1	0.998	1	CLONAL	2	TRUE	1	0.925399541815854	2		362	645	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0016250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	70	279	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.847	0.738	0.964	0.847	0.738	0.964	CLONAL	1	TRUE	1	0.26	2		279	636	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0016250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	81	534	0	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	1	2	FACETS	0.89	0.784	1	0.89	0.784	1	CLONAL	1	TRUE	1	0.26	2		534	700	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0016250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	79	526	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	1	2	FACETS	0.95	0.835	1	0.95	0.835	1	CLONAL	1	TRUE	1	0.26	2		526	640	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743501	46743503	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs746553748	NA	P-0016250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	28	310	0	ENST00000371975.4:c.1885_1887del	p.Glu629del	p.E629del	ENST00000371975	NM_003579.3	628	GAG/-	17/18	1	2	FACETS	0.538	0.43	0.662	0.538	0.43	0.662	SUBCLONAL	1	TRUE	1	0.26	2		310	400	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518305	204518305	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	48	445	0	ENST00000367182.3:c.968G>T	p.Cys323Phe	p.C323F	ENST00000367182	NM_001278516.1	323	tGt/tTt	11/11	1	2	FACETS	0.571	0.482	0.669	0.571	0.482	0.669	SUBCLONAL	1	TRUE	1	0.26	2		445	647	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594086	55594086	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	52	315	0	ENST00000288135.5:c.1872G>T	p.Met624Ile	p.M624I	ENST00000288135	NM_000222.2	624	atG/atT	12/21	1	2	FACETS	0.729	0.62	0.848	0.729	0.62	0.848	SUBCLONAL	1	TRUE	1	0.26	2		315	549	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356130	66356130	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	91	390	0	ENST00000273854.3:c.1367A>T	p.Gln456Leu	p.Q456L	ENST00000273854	NM_004439.5	456	cAg/cTg	5/18	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.26	2		390	689	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356445	70356446	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0016250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	80	654	1	ENST00000374080.3:c.5340_5341delinsTT	p.Glu1780_Glu1781delinsAspTer	p.E1780_E1781delinsD*	ENST00000374080		1780	gaGGaa/gaTTaa	37/45	0.141016632677261	0	FACETS	0.669	0.588	0.755			1	INDETERMINATE	1	TRUE	0	0.26	0		655	681	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	424	423	0				ENST00000310581	NM_198253.2	-/1132			0.300570229479486	7	FACETS	0.968	0.93	1	0.968	0.93	1	CLONAL	6	TRUE	1	0.37	7		423	760	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0016251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	378	997	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.300570229479486	3	FACETS	0.882	0.841	0.924	0.882	0.841	0.924	CLONAL	3	TRUE	0	0.37	3		997	915	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022913	27022938	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGCCGCCGCCAGCAGCCTGGGCAA	CCCGCCGCCGCCAGCAGCCTGGGCAA	-	rs797045262	NA	P-0016251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	19	32	0	ENST00000324856.7:c.31_56del	p.Ser11AlafsTer91	p.S11Afs*91	ENST00000324856	NM_006015.4	7	CCCGCCGCCGCCAGCAGCCTGGGCAAc/c	1/20	0.300570229479486	3	FACETS	0.79	0.615	0.985	0.79	0.615	0.985	CLONAL	2	TRUE	1	0.37	3		32	77	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267597	7267597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	101	425	0	ENST00000302850.5:c.411G>A	p.Met137Ile	p.M137I	ENST00000302850	NM_000208.2	137	atG/atA	2/22	1	2	FACETS	0.714	0.638	0.794	0.714	0.638	0.794	SUBCLONAL	1	TRUE	1	0.37	2		425	765	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651994	36651995	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0016251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	145	343	0	ENST00000244741.5:c.119dup	p.Cys41LeufsTer7	p.C41Lfs*7	ENST00000244741	NM_000389.4	39	gcg/gcGg	2/3	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.37	2		343	759	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435950	49435950	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	328	446	0	ENST00000301067.7:c.6031G>T	p.Glu2011Ter	p.E2011*	ENST00000301067	NM_003482.3	2011	Gag/Tag	28/54	0.300570229479486	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.37	2		446	797	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951053	48951053	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0016251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	92	171	0	ENST00000267163.4:c.1216-1G>C		p.X406_splice	ENST00000267163	NM_000321.2	406			0.271289642010485	2	FACETS	0.869	0.783	0.959	0.869	0.783	0.959	CLONAL	2	TRUE	0	0.37	2		171	286	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061525	38061528	+	frameshift_variant	Frame_Shift_Del	DEL	CCGC	CCGC	-	novel	NA	P-0016251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	57	156	0	ENST00000250448.2:c.461_464del	p.Gly154AlafsTer39	p.G154Afs*39	ENST00000250448	NM_004496.3	154	gGCGGc/gc	2/2	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.37	2		156	307	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061829	38061855	+	inframe_deletion	In_Frame_Del	DEL	TCATGGTGTTCATGGTCATGTAGGTGT	TCATGGTGTTCATGGTCATGTAGGTGT	-	novel	NA	P-0016251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	99	481	0	ENST00000250448.2:c.134_160del	p.Asn45_Met53del	p.N45_M53del	ENST00000250448	NM_004496.3	45	aACACCTACATGACCATGAACACCATGAct/act	2/2	1	2	FACETS	0.613	0.546	0.684	0.613	0.546	0.684	SUBCLONAL	1	TRUE	1	0.37	2		481	873	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89846317	89846317	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	103	417	0	ENST00000389301.3:c.1675G>C	p.Glu559Gln	p.E559Q	ENST00000389301	NM_000135.2	559	Gag/Cag	18/43	0.300570229479486	3	FACETS	0.757	0.676	0.842	0.378	0.338	0.421	SUBCLONAL	1	TRUE	1	0.37	3		417	872	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578555	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	AC	AC	TT	novel	NA	P-0016251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	64	481	2	ENST00000269305.4:c.376-1_376delinsAA		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	0.300570229479486	3	FACETS	0.469	0.405	0.539	0.156	0.135	0.18	SUBCLONAL	1	TRUE	0	0.37	3		483	874	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123040842	123040842	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	342	244	0	ENST00000355640.3:c.1305T>G	p.Ile435Met	p.I435M	ENST00000355640		435	atT/atG	7/7	0.300570229479486	3	FACETS	0.922	0.883	0.961			1	CLONAL	4	TRUE	NA	0.37	3		244	594	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0016252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	201	683	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.473082714232102	2		683	574	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259154	36259154	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	214	455	0	ENST00000300305.3:c.337C>G	p.Pro113Ala	p.P113A	ENST00000300305		113	Ccc/Gcc	3/8	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.473082714232102	2		455	726	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	13	726	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.215	0.152	0.292	0.215	0.152	0.292	SUBCLONAL	1	TRUE	1	0.27	2		726	448	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444766	49444767	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	29	1304	1	ENST00000301067.7:c.2699dup	p.Ser901ValfsTer2	p.S901Vfs*2	ENST00000301067	NM_003482.3	900	ctg/ctTg	10/54	1	2	FACETS	0.403	0.323	0.495	0.403	0.323	0.495	SUBCLONAL	1	TRUE	1	0.27	2		1305	533	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	280	423	0				ENST00000310581	NM_198253.2	-/1132			0.799351648449545	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	TRUE	1	0.799351648449545	4		423	410	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0016254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	143	660	2	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	0.972	0.898	1	0.972	0.898	1	CLONAL	1	TRUE	1	0.799351648449545	2		662	368	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100312	27100312	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	323	1143	2	ENST00000324856.7:c.4024C>T	p.Gln1342Ter	p.Q1342*	ENST00000324856	NM_006015.4	1342	Cag/Tag	17/20	1	2	FACETS	0.999	0.948	1	0.999	0.948	1	CLONAL	1	TRUE	1	0.799351648449545	2		1145	809	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0016254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	289	976	2	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.799351648449545	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.799351648449545	1		978	430	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981539	201981540	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0016254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	870	1186	2	ENST00000359651.3:c.453_454delinsTT	p.Gln151_Glu152delinsHisTer	p.Q151_E152delinsH*	ENST00000359651		151	caGGag/caTTag	3/8	0.788009155096111	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.799351648449545	3		1188	999	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445917	49445917	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	652	1308	1	ENST00000301067.7:c.1549G>T	p.Glu517Ter	p.E517*	ENST00000301067	NM_003482.3	517	Gag/Tag	10/54	0.725610090334461	3	FACETS	0.916	0.887	0.946	0.916	0.887	0.946	CLONAL	2	TRUE	1	0.799351648449545	3		1309	1246	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68290282	68290282	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs138727212	NA	P-0016254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	178	785	5	ENST00000487270.1:c.22C>T	p.Arg8Ter	p.R8*	ENST00000487270	NM_133509.3	8	Cga/Tga	2/11	1	2	FACETS	0.966	0.899	1	0.966	0.899	1	CLONAL	1	TRUE	1	0.799351648449545	2		790	461	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729884	30729884	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1407331537	NA	P-0016254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	98	447	0	ENST00000295754.5:c.1405G>C	p.Asp469His	p.D469H	ENST00000295754	NM_003242.5	469	Gat/Cat	6/7	1	2	FACETS	0.892	0.807	0.978	0.892	0.807	0.978	CLONAL	1	TRUE	1	0.799351648449545	2		447	275	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851507	128851507	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0016254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	212	836	0	ENST00000249373.3:c.1832C>G	p.Ser611Ter	p.S611*	ENST00000249373	NM_005631.4	611	tCa/tGa	11/12	0.799351648449545	1	FACETS	0.945	0.897	0.991	0.945	0.897	0.991	CLONAL	1	TRUE	0	0.799351648449545	1		836	337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0016255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	761	1003	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.822173532350867	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.837870669317732	2		1003	887	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144469	58144469	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1228840061	NA	P-0016255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	387	477	0	ENST00000257904.6:c.602G>A	p.Gly201Asp	p.G201D	ENST00000257904	NM_000075.3	201	gGc/gAc	5/8	0.818799711387411	3	FACETS	0.972	0.934	1	0.972	0.934	1	CLONAL	2	TRUE	1	0.837870669317732	3		477	674	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115251200	115251200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	557	926	1	ENST00000369535.4:c.526G>T	p.Asp176Tyr	p.D176Y	ENST00000369535	NM_002524.4	176	Gat/Tat	5/7	0.818799711387411	3	FACETS	0.976	0.944	1	0.976	0.944	1	CLONAL	2	TRUE	1	0.837870669317732	3		927	966	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658579	206658579	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	312	490	0	ENST00000367120.3:c.1552G>A	p.Glu518Lys	p.E518K	ENST00000367120	NM_014002.3	518	Gag/Aag	15/22	0.6004365521225	4	FACETS	0.931	0.884	0.979	0.931	0.884	0.979	CLONAL	2	TRUE	2	0.837870669317732	4		490	735	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434497	110434497	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	287	769	0	ENST00000375856.3:c.3904A>G	p.Thr1302Ala	p.T1302A	ENST00000375856	NM_003749.2	1302	Acc/Gcc	1/2	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.837870669317732	2		769	641	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218415	1218415	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs112675807	NA	P-0016255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	570	916	0	ENST00000326873.7:c.291-1G>A		p.X97_splice	ENST00000326873	NM_000455.4	97			0.837870669317732	2	FACETS	0.982	0.96	1	0.982	0.96	1	CLONAL	2	TRUE	0	0.837870669317732	2		916	693	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101913	11101913	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	665	904	0	ENST00000358026.2:c.1333C>T	p.Gln445Ter	p.Q445*	ENST00000358026	NM_001128849.1	445	Cag/Tag	8/36	0.837870669317732	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.837870669317732	2		904	765	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39240642	39240642	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	256	851	0	ENST00000402219.2:c.2126A>T	p.Tyr709Phe	p.Y709F	ENST00000402219	NM_005633.3	709	tAt/tTt	13/23	0.818799711387411	3	FACETS	0.963	0.904	1	0.482	0.452	0.513	CLONAL	1	TRUE	1	0.837870669317732	3		851	900	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097188	178097188	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	247	705	0	ENST00000397062.3:c.526G>C	p.Asp176His	p.D176H	ENST00000397062	NM_006164.4	176	Gat/Cat	4/5	0.818799711387411	3	FACETS	1	0.947	1	0.506	0.474	0.538	CLONAL	1	TRUE	1	0.837870669317732	3		705	827	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403173	213403173	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	359	485	0	ENST00000342788.4:c.82G>T	p.Val28Leu	p.V28L	ENST00000342788	NM_005235.2	28	Gtg/Ttg	1/28	0.818799711387411	3	FACETS	0.923	0.883	0.962	0.923	0.883	0.962	CLONAL	2	TRUE	1	0.837870669317732	3		485	659	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561060	9561060	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	139	367	1	ENST00000353224.5:c.722G>T	p.Gly241Val	p.G241V	ENST00000353224	NM_177990.2	241	gGg/gTg	4/10	0.119756380773092	5	FACETS	1	0.974	1	0.564	0.521	0.608	INDETERMINATE	2	TRUE	1	0.837870669317732	5		368	332	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964319	55964319	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	182	539	0	ENST00000263923.4:c.2494G>T	p.Asp832Tyr	p.D832Y	ENST00000263923	NM_002253.2	832	Gac/Tac	17/30	0.787619180867502	3	FACETS	0.944	0.875	1	0.472	0.437	0.508	CLONAL	1	TRUE	1	0.837870669317732	3		539	653	SUCCESS
APC	324	MSKCC	GRCh37	5	112103007	112103010	+	frameshift_variant	Frame_Shift_Del	DEL	TATG	TATG	AAT	novel	NA	P-0016255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	468	584	2	ENST00000257430.4:c.342_345delinsAAT	p.Gly116ValfsTer9	p.G116Vfs*9	ENST00000257430	NM_000038.5	114	ccTATG/ccAAT	4/16	0.827665902646181	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.837870669317732	2		586	554	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222612	157222612	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	271	678	0	ENST00000346085.5:c.1879G>T	p.Ala627Ser	p.A627S	ENST00000346085	NM_020732.3	627	Gcg/Tcg	4/20	0.836913162468443	4	FACETS	0.979	0.917	1	0.326	0.305	0.348	CLONAL	1	TRUE	1	0.837870669317732	4		678	1215	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0016256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	77	683	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.775	0.682	0.874	0.775	0.682	0.874	SUBCLONAL	1	TRUE	1	0.396619696745827	2		683	501	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0016256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15993	1819	446	1	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.396619696745827	48	FACETS	1	0.992	1			1	CLONAL	5	TRUE	NA	0.396619696745827	48		447	17812	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692802	89692802	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123320	NA	P-0016256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	111	596	0	ENST00000371953.3:c.286C>T	p.Pro96Ser	p.P96S	ENST00000371953	NM_000314.4	96	Cca/Tca	5/9	0.396619696745827	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.396619696745827	1		596	437	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114799872	114799872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753187602	NA	P-0016256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	60	959	1	ENST00000543371.1:c.539C>T	p.Pro180Leu	p.P180L	ENST00000543371	NM_001198531.1	180	cCg/cTg	5/14	0.396619696745827	1	FACETS	0.349	0.3	0.402	0.349	0.3	0.402	SUBCLONAL	1	TRUE	0	0.396619696745827	1		960	695	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340047	116340047	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1200423161	NA	P-0016256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	81	480	0	ENST00000397752.3:c.909G>C	p.Lys303Asn	p.K303N	ENST00000397752	NM_000245.2	303	aaG/aaC	2/21	0.383595269078709	3	FACETS	0.831	0.733	0.936	0.415	0.366	0.468	CLONAL	1	TRUE	1	0.396619696745827	3		480	589	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0016257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	342	819	2	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.673988199039914	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.673988199039914	2		821	500	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0016257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	119	318	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.934	0.852	1	0.934	0.852	1	CLONAL	1	TRUE	1	0.673988199039914	2		318	378	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952145	76952146	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0016257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	200	478	0	ENST00000373344.5:c.289_290del	p.Pro97PhefsTer3	p.P97Ffs*3	ENST00000373344	NM_000489.3	97	CCt/t	5/35	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.673988199039914	1		478	319	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0016258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	762	2255	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.434858272598347	5	FACETS	0.993	0.968	1	0.993	0.968	1	CLONAL	5	TRUE	0	0.434858272598347	5		2255	1166	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220698	1220698	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	320	1112	1	ENST00000326873.7:c.716G>T	p.Trp239Leu	p.W239L	ENST00000326873	NM_000455.4	239	tGg/tTg	5/10	0.434858272598347	2	FACETS	0.896	0.85	0.943	0.896	0.85	0.943	CLONAL	2	TRUE	0	0.434858272598347	2		1113	821	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11318653	11318653	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	T	novel	NA	P-0016258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	241	875	0	ENST00000361445.4:c.163-3C>A		p.X55_splice	ENST00000361445	NM_004958.3	55			0.434858272598347	3	FACETS	0.877	0.822	0.934	0.877	0.822	0.934	CLONAL	2	TRUE	1	0.434858272598347	3		875	769	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107140	27107140	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	259	815	0	ENST00000324856.7:c.6753del	p.Phe2251LeufsTer16	p.F2251Lfs*16	ENST00000324856	NM_006015.4	2251	Ttt/tt	20/20	0.434858272598347	2	FACETS	0.973	0.919	1	0.973	0.919	1	CLONAL	2	TRUE	0	0.434858272598347	2		815	612	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224583	108224583	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730881329	NA	P-0016258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	158	538	0	ENST00000278616.4:c.8762C>A	p.Thr2921Lys	p.T2921K	ENST00000278616	NM_000051.3	2921	aCg/aAg	60/63	0.434858272598347	2	FACETS	0.956	0.888	1	0.956	0.888	1	CLONAL	2	TRUE	0	0.434858272598347	2		538	380	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415640	49415641	+	missense_variant	Missense_Mutation	DNP	GA	GA	TG	novel	NA	P-0016258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	95	654	2	ENST00000301067.7:c.16536_16537delinsCA	p.Gln5513Lys	p.Q5513K	ENST00000301067	NM_003482.3	5512	taTCag/taCAag	54/54	0.431783752721123	3	FACETS	0.925	0.826	1	0.463	0.413	0.516	CLONAL	1	TRUE	1	0.434858272598347	3		656	575	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813339	102813339	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	121	685	0	ENST00000307046.8:c.350C>A	p.Ser117Ter	p.S117*	ENST00000307046	NM_001111285.1	117	tCa/tAa	3/4	0.431783752721123	3	FACETS	1	0.962	1	0.559	0.506	0.614	CLONAL	1	TRUE	1	0.434858272598347	3		685	606	SUCCESS
ALK	238	MSKCC	GRCh37	2	29450455	29450455	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	645	1402	1	ENST00000389048.3:c.2899A>T	p.Thr967Ser	p.T967S	ENST00000389048	NM_004304.4	967	Acc/Tcc	17/29	0.393595766972454	4	FACETS	0.912	0.879	0.945	0.912	0.879	0.945	CLONAL	3	TRUE	1	0.434858272598347	4		1403	1556	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058698	180058698	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	363	1257	0	ENST00000261937.6:c.139C>A	p.Leu47Met	p.L47M	ENST00000261937	NM_182925.4	47	Ctg/Atg	2/30	0.366540247931555	4	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	2	0.434858272598347	4		1257	1192	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367248	50367248	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs931548912	NA	P-0016258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	110	604	0	ENST00000331340.3:c.55C>A	p.Pro19Thr	p.P19T	ENST00000331340	NM_006060.4	19	Cct/Act	3/8	0.218756443160612	4	FACETS	1	0.983	1	0.739	0.667	0.814	INDETERMINATE	1	TRUE	2	0.434858272598347	4		604	491	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341973	8341973	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	200	653	2	ENST00000356435.5:c.4667G>T	p.Gly1556Val	p.G1556V	ENST00000356435		1556	gGa/gTa	29/35	0.434858272598347	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	0	0.434858272598347	2		655	457	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937220	76937220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	79	1008	1	ENST00000373344.5:c.3528G>T	p.Lys1176Asn	p.K1176N	ENST00000373344	NM_000489.3	1176	aaG/aaT	9/35	0.248569403053399	3	FACETS	0.713	0.628	0.805	0.238	0.209	0.269	INDETERMINATE	1	TRUE	0	0.434858272598347	3		1009	620	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241679	55241681	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	rs397517086	NA	P-0016259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	182	681	0	ENST00000275493.2:c.2127_2129del	p.Glu709_Thr710delinsAsp	p.E709_T710delinsD	ENST00000275493	NM_005228.3	709	gaAACt/gat	18/28	0.241632524132747	6	FACETS	0.9	0.828	0.974			1	CLONAL	2	TRUE	NA	0.241632524132747	6		681	1242	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7119529	7119529	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	107	703	0	ENST00000302850.5:c.3725A>C	p.Asn1242Thr	p.N1242T	ENST00000302850	NM_000208.2	1242	aAt/aCt	21/22	0.190931478047602	3	FACETS	0.962	0.861	1	0.481	0.43	0.535	CLONAL	1	TRUE	1	0.241632524132747	3		703	1032	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144092	11144092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	108	808	0	ENST00000358026.2:c.3673G>A	p.Asp1225Asn	p.D1225N	ENST00000358026	NM_001128849.1	1225	Gac/Aac	26/36	0.190931478047602	3	FACETS	0.869	0.778	0.966	0.434	0.389	0.483	CLONAL	1	TRUE	1	0.241632524132747	3		808	1153	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0016260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	185	731	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.272912857764704	3	FACETS	0.944	0.873	1	0.944	0.873	1	CLONAL	2	TRUE	1	0.272912857764704	3		731	816	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0016261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	93	2255	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.507	0.45	0.568	0.507	0.45	0.568	SUBCLONAL	1	TRUE	1	0.440195082661662	2		2255	833	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220443	1220443	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	76	967	0	ENST00000326873.7:c.536C>G	p.Pro179Arg	p.P179R	ENST00000326873	NM_000455.4	179	cCg/cGg	4/10	1	2	FACETS	0.476	0.417	0.539	0.476	0.417	0.539	SUBCLONAL	1	TRUE	1	0.440195082661662	2		967	726	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679765	88679765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	34	784	1	ENST00000360948.2:c.698G>A	p.Gly233Asp	p.G233D	ENST00000360948	NM_001012338.2	233	gGc/gAc	7/19	1	2	FACETS	0.285	0.232	0.345	0.285	0.232	0.345	SUBCLONAL	1	TRUE	1	0.440195082661662	2		785	542	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443829	18443829	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	49	632	0	ENST00000266497.5:c.802T>A	p.Ser268Thr	p.S268T	ENST00000266497		268	Tct/Act	3/31	1	2	FACETS	0.403	0.341	0.471	0.403	0.341	0.471	SUBCLONAL	1	TRUE	1	0.440195082661662	2		632	553	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356278	66356278	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	35	773	0	ENST00000273854.3:c.1219G>C	p.Glu407Gln	p.E407Q	ENST00000273854	NM_004439.5	407	Gag/Cag	5/18	1	2	FACETS	0.275	0.224	0.331	0.275	0.224	0.331	SUBCLONAL	1	TRUE	1	0.440195082661662	2		773	579	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889081	76889081	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	74	887	0	ENST00000373344.5:c.4929G>T	p.Glu1643Asp	p.E1643D	ENST00000373344	NM_000489.3	1643	gaG/gaT	18/35	1	2	FACETS	0.375	0.327	0.426	0.375	0.327	0.426	SUBCLONAL	1	TRUE	1	0.440195082661662	2		887	897	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0016262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	8	488	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.588439056742462	1	FACETS	0.048	0.03	0.071	0.048	0.03	0.071	SUBCLONAL	1	TRUE	0	0.588439056742462	1		490	400	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115970	8116001	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	TCACCGCCATGGGTTAGAGCCCTGCTCGATGC	TCACCGCCATGGGTTAGAGCCCTGCTCGATGC	-	novel	NA	P-0016262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	32	548	0	ENST00000346208.3:c.1320_*19del		p.*440*	ENST00000346208		439		6/6	1	2	FACETS	0.235	0.19	0.286	0.235	0.19	0.286	SUBCLONAL	1	TRUE	1	0.588439056742462	2		548	463	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259394	11259394	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	151	935	2	ENST00000361445.4:c.4174G>A	p.Ala1392Thr	p.A1392T	ENST00000361445	NM_004958.3	1392	Gca/Aca	28/58	1	2	FACETS	0.936	0.859	1	0.936	0.859	1	CLONAL	1	TRUE	1	0.518910851483251	2		937	622	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0016263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	158	963	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	0.507608430521458	1	FACETS	0.845	0.779	0.912	0.845	0.779	0.912	CLONAL	1	TRUE	0	0.518910851483251	1		963	534	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs121913468	NA	P-0016263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	231	1271	0	ENST00000269571.5:c.2305G>C	p.Asp769His	p.D769H	ENST00000269571		769	Gac/Cac	19/27	0.518910851483251	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.518910851483251	1		1271	651	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519895	NA	P-0016263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	190	1065	1	ENST00000281708.4:c.1394G>T	p.Arg465Leu	p.R465L	ENST00000281708	NM_033632.3	465	cGt/cTt	9/12	0.338923075743795	1	FACETS	0.774	0.718	0.831	0.774	0.718	0.831	SUBCLONAL	1	TRUE	0	0.518910851483251	1		1066	701	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227869	123227869	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	32	389	1	ENST00000218089.9:c.3580C>T	p.Arg1194Trp	p.R1194W	ENST00000218089	NM_001042749.1	1194	Cgg/Tgg	33/35	1	2	FACETS	0.478	0.39	0.577	0.478	0.39	0.577	SUBCLONAL	1	TRUE	1	0.518910851483251	2		390	258	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117308	115117309	+	splice_donor_variant	Splice_Site	INS	-	-	C	novel	NA	P-0016264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	37	537	0	ENST00000257566.3:c.864+1dup		p.X288_splice	ENST00000257566	NM_016569.3	288			0.142934587305191	3	FACETS	0.517	0.426	0.62	0.172	0.142	0.207	INDETERMINATE	1	TRUE	0	0.325388774718401	3		537	511	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849464	68849483	+	frameshift_variant	Frame_Shift_Del	DEL	TGACGAATGTGGTACCTTTT	TGACGAATGTGGTACCTTTT	-	novel	NA	P-0016264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	94	894	0	ENST00000261769.5:c.1367_1386del	p.Val456GlyfsTer20	p.V456Gfs*20	ENST00000261769	NM_004360.3	456	gTGACGAATGTGGTACCTTTT/g	10/16	0.325388774718401	1	FACETS	0.82	0.731	0.914	0.82	0.731	0.914	CLONAL	1	TRUE	0	0.325388774718401	1		894	590	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177812	56177813	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0016264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	123	559	1	ENST00000399503.3:c.2789_2790del	p.Arg930ThrfsTer10	p.R930Tfs*10	ENST00000399503	NM_005921.1	929	GAg/g	14/20	0.142934587305191	3	FACETS	0.921	0.838	1	0.614	0.559	0.672	INDETERMINATE	2	TRUE	0	0.325388774718401	3		560	477	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913517	NA	P-0016265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	370	823	0	ENST00000288135.5:c.1676T>C	p.Val559Ala	p.V559A	ENST00000288135	NM_000222.2	559	gTt/gCt	11/21	0.681464192439786	2	FACETS	0.987	0.952	1	0.987	0.952	1	CLONAL	2	TRUE	0	0.681464192439786	2		823	550	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10305575	10305575	+	start_lost	Translation_Start_Site	SNP	T	T	C	rs753525461	NA	P-0016265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	92	724	1	ENST00000340748.4:c.1A>G	p.Met1?	p.M1?	ENST00000340748		1	Atg/Gtg	1/40	1	2	FACETS	0.813	0.73	0.9	0.813	0.73	0.9	CLONAL	1	TRUE	1	0.681464192439786	2		725	332	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	323	641	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.507158847311505	2	FACETS	0.963	0.919	1	0.963	0.919	1	CLONAL	2	FALSE	0	0.545133901226251	2		641	615	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0016266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	124	467	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	0.144542820203047	0	FACETS	0.432	0.393	0.473			1	INDETERMINATE	1	FALSE	0	0.545133901226251	0		467	479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0016266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	468	607	1	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.545133901226251	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	0	0.545133901226251	1		608	1139	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518424	204518424	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	401	756	1	ENST00000367182.3:c.1087C>T	p.Arg363Ter	p.R363*	ENST00000367182	NM_001278516.1	363	Cga/Tga	11/11	0.248447788201002	4	FACETS	0.913	0.874	0.952			1	INDETERMINATE	3	FALSE	NA	0.545133901226251	4		757	830	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849819	156849819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765477124	NA	P-0016266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	173	721	0	ENST00000524377.1:c.2075G>A	p.Arg692His	p.R692H	ENST00000524377	NM_002529.3	692	cGc/cAc	16/17	1	2	FACETS	0.834	0.769	0.901	0.834	0.769	0.901	CLONAL	1	FALSE	1	0.545133901226251	2		721	761	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390695	118390695	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	156	612	0	ENST00000534358.1:c.11345A>G	p.Asn3782Ser	p.N3782S	ENST00000534358	NM_005933.3	3782	aAc/aGc	33/36	1	2	FACETS	0.911	0.838	0.988	0.911	0.838	0.988	CLONAL	1	FALSE	1	0.545133901226251	2		612	628	SUCCESS
APC	324	MSKCC	GRCh37	5	112175346	112175351	+	frameshift_variant	Frame_Shift_Del	DEL	TTGAAT	TTGAAT	A	novel	NA	P-0016266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	94	480	0	ENST00000257430.4:c.4055_4060delinsA	p.Val1352AspfsTer21	p.V1352Dfs*21	ENST00000257430	NM_000038.5	1352	gTTGAATtt/gAtt	16/16	0.144542820203047	0	FACETS	0.353	0.316	0.393			1	INDETERMINATE	1	FALSE	0	0.545133901226251	0		480	444	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	137	726	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.985	0.895	1	0.985	0.895	1	CLONAL	1	TRUE	1	0.270105841048224	2		726	1030	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0016267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	89	675	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.868	0.769	0.974	0.868	0.769	0.974	CLONAL	1	TRUE	1	0.270105841048224	2		675	759	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0016267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	104	346	1	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	0.270105841048224	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.270105841048224	1		347	558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579462	7579463	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1567556454	NA	P-0016267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	100	852	0	ENST00000269305.4:c.224dup	p.Ala76CysfsTer73	p.A76Cfs*73	ENST00000269305	NM_001126112.2	75	cct/ccCt	4/11	0.270105841048224	1	FACETS	0.92	0.822	1	0.92	0.822	1	CLONAL	1	TRUE	0	0.270105841048224	1		852	696	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87338487	87338487	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0016267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	63	519	0	ENST00000277120.3:c.584-1G>A		p.X195_splice	ENST00000277120		195			1	2	FACETS	0.916	0.794	1	0.916	0.794	1	CLONAL	1	TRUE	1	0.270105841048224	2		519	509	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0016268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	87	807	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.156133152240315	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		807	1090	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0016268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	84	644	0	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.156133152240315	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		644	1024	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691929	30691929	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	31	345	0	ENST00000295754.5:c.431A>G	p.Asn144Ser	p.N144S	ENST00000295754	NM_003242.5	144	aAt/aGt	3/7	0.156133152240315	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		345	600	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300900	137300900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148741267	NA	P-0016268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	89	616	0	ENST00000481739.1:c.545G>A	p.Arg182Gln	p.R182Q	ENST00000481739	NM_002957.4	182	cGg/cAg	4/10	0.156133152240315	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		616	888	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218912	133218912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1011938171	NA	P-0016269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	23	662	4	ENST00000320574.5:c.5024G>A	p.Arg1675His	p.R1675H	ENST00000320574	NM_006231.2	1675	cGc/cAc	38/49	1	2	FACETS	0.137	0.106	0.173	0.137	0.106	0.173	SUBCLONAL	1	TRUE	1	0.818505308393435	2		666	410	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420011	152420011	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	13	484	1	ENST00000206249.3:c.1698C>A	p.Ser566Arg	p.S566R	ENST00000206249	NM_000125.3	566	agC/agA	8/8	1	2	FACETS	0.291	0.21	0.389	0.291	0.21	0.389	SUBCLONAL	1	TRUE	1	0.818505308393435	2		485	109	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132464	11132468	+	stop_gained	Nonsense_Mutation	ONP	ACGCA	ACGCA	TAGCT	novel	NA	P-0016269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	27	576	0	ENST00000358026.2:c.2680_2684delinsTAGCT	p.Thr894_Gln895delinsTer	p.T894_Q895delins*	ENST00000358026	NM_001128849.1	894	ACGCAg/TAGCTg	19/36	0.189597235737714	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.818505308393435	0		576	338	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948719	71948719	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs778488376	NA	P-0016269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	119	504	1	ENST00000298229.2:c.3431C>A	p.Ala1144Glu	p.A1144E	ENST00000298229	NM_001567.3	1144	gCg/gAg	26/28	0.818505308393435	3	FACETS	0.909	0.826	0.995	0.454	0.413	0.498	CLONAL	1	TRUE	1	0.818505308393435	3		505	451	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805055	89805055	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	10	552	0	ENST00000389301.3:c.4322A>G	p.Gln1441Arg	p.Q1441R	ENST00000389301	NM_000135.2	1441	cAg/cGg	43/43	0.818505308393435	3	FACETS	0.177	0.12	0.25	0.089	0.06	0.125	SUBCLONAL	1	TRUE	1	0.818505308393435	3		552	194	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805065	89805065	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	12	519	1	ENST00000389301.3:c.4312A>T	p.Ser1438Cys	p.S1438C	ENST00000389301	NM_000135.2	1438	Agc/Tgc	43/43	0.818505308393435	3	FACETS	0.211	0.148	0.288	0.105	0.074	0.144	SUBCLONAL	1	TRUE	1	0.818505308393435	3		520	196	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866648	37866648	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	16	596	0	ENST00000269571.5:c.815T>G	p.Val272Gly	p.V272G	ENST00000269571		272	gTc/gGc	7/27	1	2	FACETS	0.261	0.194	0.34	0.261	0.194	0.34	SUBCLONAL	1	TRUE	1	0.818505308393435	2		596	150	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302813	15302814	+	missense_variant	Missense_Mutation	DNP	TG	TG	CA	novel	NA	P-0016269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	19	596	0	ENST00000263388.2:c.636_637inv	p.Arg213Gly	p.R213G	ENST00000263388	NM_000435.2	212	tgCAgg/tgTGgg	4/33	1	2	FACETS	0.128	0.097	0.165	0.128	0.097	0.165	SUBCLONAL	1	TRUE	1	0.818505308393435	2		596	363	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730828	40730828	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	15	658	0	ENST00000373198.4:c.3707G>C	p.Cys1236Ser	p.C1236S	ENST00000373198	NM_133170.3	1236	tGc/tCc	27/32	0.176683152373717	1	FACETS	0.118	0.086	0.155	0.118	0.086	0.155	INDETERMINATE	1	TRUE	0	0.818505308393435	1		658	184	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515621	31515621	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	11	581	0	ENST00000344624.3:c.998T>C	p.Leu333Ser	p.L333S	ENST00000344624		333	tTa/tCa	4/33	0.818505308393435	3	FACETS	0.357	0.249	0.49	0.179	0.124	0.245	SUBCLONAL	1	TRUE	1	0.818505308393435	3		581	106	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741761	145741761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540719285	NA	P-0016269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	89	519	0	ENST00000428558.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000428558	NM_004260.3	248	Cgt/Tgt	5/22	1	2	FACETS	0.95	0.858	1	0.95	0.858	1	CLONAL	1	TRUE	1	0.818505308393435	2		519	229	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287313	38287313	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs760780809	NA	P-0016269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	13	620	0	ENST00000425967.3:c.344C>G	p.Thr115Arg	p.T115R	ENST00000425967	NM_001174067.1	115	aCa/aGa	4/19	1	2	FACETS	0.194	0.138	0.261	0.194	0.138	0.261	SUBCLONAL	1	TRUE	1	0.818505308393435	2		620	164	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876522	35876523	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0016269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	10	568	0	ENST00000303115.3:c.1315_1316dup	p.Ser440LeufsTer24	p.S440Lfs*24	ENST00000303115	NM_002185.3	438	-/AC	8/8	0.818505308393435	3	FACETS	0.196	0.132	0.275	0.098	0.066	0.138	SUBCLONAL	1	TRUE	1	0.818505308393435	3		568	176	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0016270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	172	547	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.948	0.875	1	0.948	0.875	1	CLONAL	1	TRUE	1	0.491593411049621	2		547	738	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151181846	151181846	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	128	417	0	ENST00000262187.5:c.169C>T	p.Gln57Ter	p.Q57*	ENST00000262187	NM_005614.3	57	Caa/Taa	3/8	1	2	FACETS	0.895	0.814	0.979	0.895	0.814	0.979	CLONAL	1	TRUE	1	0.491593411049621	2		417	582	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117387	115117388	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0016270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	134	413	0	ENST00000257566.3:c.785_786dup	p.Leu263AsnfsTer20	p.L263Nfs*20	ENST00000257566	NM_016569.3	262	-/AA	4/8	1	2	FACETS	0.988	0.902	1	0.988	0.902	1	CLONAL	1	TRUE	1	0.491593411049621	2		413	552	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647589	23647589	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761863504	NA	P-0016270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	165	523	0	ENST00000261584.4:c.278G>A	p.Gly93Glu	p.G93E	ENST00000261584	NM_024675.3	93	gGa/gAa	4/13	0.457094861690806	3	FACETS	1	0.924	1	0.503	0.462	0.545	CLONAL	1	TRUE	1	0.491593411049621	3		523	832	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772259	68772260	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0016270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	202	730	0	ENST00000261769.5:c.109dup	p.Tyr37LeufsTer22	p.Y37Lfs*22	ENST00000261769	NM_004360.3	36	-/T	2/16	0.491593411049621	1	FACETS	0.985	0.918	1	0.985	0.918	1	CLONAL	1	TRUE	0	0.491593411049621	1		730	629	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096309	178096309	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	31	386	0	ENST00000397062.3:c.1022del	p.Asp341ValfsTer8	p.D341Vfs*8	ENST00000397062	NM_006164.4	341	gAt/gt	5/5	1	2	FACETS	0.242	0.195	0.295	0.242	0.195	0.295	SUBCLONAL	1	TRUE	1	0.491593411049621	2		386	522	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0016271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	300	754	0	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	0.234153751885233	2	FACETS	0.9	0.847	0.955	0.9	0.847	0.955	CLONAL	2	TRUE	0	0.264689169286155	2		754	1259	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398286	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0016271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	282	579	0	ENST00000311936.3:c.33_34delinsCT	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	11	gcTGgt/gcCTgt	2/5	0.264689169286155	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	2	0.264689169286155	4		579	1308	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782387	9782387	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370932461	NA	P-0016271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	111	674	2	ENST00000377346.4:c.2320G>A	p.Val774Met	p.V774M	ENST00000377346	NM_005026.3	774	Gtg/Atg	18/24	0.234153751885233	2	FACETS	0.69	0.619	0.767	0.345	0.309	0.384	SUBCLONAL	1	TRUE	0	0.264689169286155	2		676	1215	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961050	15961050	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	80	238	0	ENST00000268712.3:c.6170A>G	p.Gln2057Arg	p.Q2057R	ENST00000268712	NM_006311.3	2057	cAa/cGa	40/46	0.234153751885233	2	FACETS	0.844	0.749	0.945	0.844	0.749	0.945	CLONAL	2	TRUE	0	0.264689169286155	2		238	358	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207054	1207054	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0016271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	266	618	1	ENST00000326873.7:c.142A>T	p.Lys48Ter	p.K48*	ENST00000326873	NM_000455.4	48	Aag/Tag	1/10	0.233463664693734	2	FACETS	0.937	0.879	0.997	0.937	0.879	0.997	CLONAL	2	TRUE	0	0.264689169286155	2		619	1072	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602253	10602254	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0016271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	171	451	0	ENST00000171111.5:c.1324_1325del	p.Arg442ValfsTer2	p.R442Vfs*2	ENST00000171111	NM_203500.1	442	AGg/g	3/6	0.233463664693734	2	FACETS	0.847	0.78	0.916	0.847	0.78	0.916	CLONAL	2	TRUE	0	0.264689169286155	2		451	763	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739078	40739078	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	87	472	0	ENST00000373198.4:c.3206G>A	p.Trp1069Ter	p.W1069*	ENST00000373198	NM_133170.3	1069	tGg/tAg	24/32	0.21134535734334	4	FACETS	0.918	0.811	1	0.459	0.405	0.516	CLONAL	1	TRUE	2	0.264689169286155	4		472	906	SUCCESS
APC	324	MSKCC	GRCh37	5	112178245	112178250	+	inframe_deletion	In_Frame_Del	DEL	TAGACC	TAGACC	-	novel	NA	P-0016271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	79	437	0	ENST00000257430.4:c.6956_6961del	p.Arg2319_Pro2320del	p.R2319_P2320del	ENST00000257430	NM_000038.5	2318	agTAGACCt/agt	16/16	1	2	FACETS	0.646	0.567	0.731	0.646	0.567	0.731	SUBCLONAL	1	TRUE	1	0.264689169286155	2		437	924	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	82	486	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.876	0.774	0.985	0.876	0.774	0.985	CLONAL	1	TRUE	1	0.34722893506083	2		486	539	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	20	284	0	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	0.34722893506083	1	FACETS	0.272	0.207	0.348	0.272	0.207	0.348	SUBCLONAL	1	TRUE	0	0.34722893506083	1		284	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578528	7578528	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	193	872	2	ENST00000269305.4:c.402T>A	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	ttT/ttA	5/11	0.34722893506083	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.34722893506083	1		874	919	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0016275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	121	257	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	0.334146580297193	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	2	0.45	4		257	325	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441952	52441982	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGATGAAGGCACTGCAGCCTACCTCAGGGCT	GGATGAAGGCACTGCAGCCTACCTCAGGGCT	-	novel	NA	P-0016276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	81	257	0	ENST00000460680.1:c.367_375+22del		p.X123_splice	ENST00000460680	NM_004656.3	123		5/17	0.184277751511907	2	FACETS	0.87	0.777	0.967	1	0.973	1	CLONAL	3	TRUE	0	0.236965378123918	2		257	262	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950676	38950676	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	78	344	0	ENST00000357387.3:c.3274A>G	p.Lys1092Glu	p.K1092E	ENST00000357387	NM_152756.3	1092	Aaa/Gaa	31/38	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.236965378123918	2		344	507	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045764	26045764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	31	265	0	ENST00000540144.1:c.127del	p.Arg43AlafsTer20	p.R43Afs*20	ENST00000540144	NM_003531.2	42	taC/ta	1/1	0.236965378123918	5	FACETS	1	0.921	1	0.427	0.346	0.517	CLONAL	1	TRUE	2	0.236965378123918	5		265	277	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662589	117662589	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	50	409	0	ENST00000368508.3:c.4876T>G	p.Ser1626Ala	p.S1626A	ENST00000368508	NM_002944.2	1626	Tct/Gct	29/43	0.236965378123918	3	FACETS	0.75	0.636	0.877	0.375	0.318	0.439	SUBCLONAL	1	TRUE	1	0.236965378123918	3		409	629	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663674	117663674	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	64	349	0	ENST00000368508.3:c.4558T>G	p.Leu1520Val	p.L1520V	ENST00000368508	NM_002944.2	1520	Tta/Gta	28/43	0.236965378123918	3	FACETS	0.843	0.729	0.966	0.421	0.364	0.483	CLONAL	1	TRUE	1	0.236965378123918	3		349	717	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005852	69005852	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	64	445	0	ENST00000288368.4:c.2263C>A	p.Gln755Lys	p.Q755K	ENST00000288368	NM_024870.2	755	Caa/Aaa	21/40	0.236965378123918	7	FACETS	0.955	0.825	1	0.159	0.137	0.183	CLONAL	1	TRUE	1	0.236965378123918	7		445	901	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971137	21971137	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs200429615	NA	P-0016276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	39	262	0	ENST00000304494.5:c.221A>C	p.Asp74Ala	p.D74A	ENST00000304494	NM_000077.4	74	gAc/gCc	2/3	0.19156051858359	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.236965378123918	1		262	224	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172272	99172272	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs374507988	NA	P-0016277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	39	374	1	ENST00000074304.5:c.1837+1G>A		p.X613_splice	ENST00000074304	NM_001134224.1	613			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		375	305	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0016278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	164	277	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.911	0.843	0.982	0.911	0.843	0.982	CLONAL	1	TRUE	1	0.714091567750242	2		277	504	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0016278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	367	554	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.972	0.924	1	0.972	0.924	1	CLONAL	1	TRUE	1	0.714091567750242	2		554	1057	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0016278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	204	373	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.714091567750242	2		373	549	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411276	63411276	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	350	234	0	ENST00000330258.3:c.1891C>T	p.Arg631Ter	p.R631*	ENST00000330258	NM_152424.3	631	Cga/Tga	2/2	NA	2	FACETS	0.967	0.917	1			1	INDETERMINATE	1	TRUE	NA	0.714091567750242	2		234	1014	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591894	48591894	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	221	455	0	ENST00000342988.3:c.1057T>C	p.Tyr353His	p.Y353H	ENST00000342988	NM_005359.5	353	Tac/Cac	9/12	0.714091567750242	1	FACETS	0.98	0.927	1	0.98	0.927	1	CLONAL	1	TRUE	0	0.714091567750242	1		455	406	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812115	43812115	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0016278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	229	486	0	ENST00000372470.3:c.981-1G>T		p.X327_splice	ENST00000372470	NM_005373.2	327			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.714091567750242	2		486	609	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457325	67457326	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCACGAGCTGCGGGCCATGGAGCTGTGTGAGTTCG	novel	NA	P-0016278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	28	643	0	ENST00000327367.4:c.308_309insGCGGGCCATGGAGCTGTGTGAGTTCGCCACGAGCT	p.Phe113ThrfsTer15	p.F113Tfs*15	ENST00000327367	NM_005902.3	100	cac/caCCACGAGCTGCGGGCCATGGAGCTGTGTGAGTTCGc	2/9	0.714091567750242	1	FACETS	0.091	0.072	0.113	0.091	0.072	0.113	SUBCLONAL	1	TRUE	0	0.714091567750242	1		643	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577115	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	AAACACGCACCTCAAAGCTGTTCCGTCCCAGTAGATTACCACTACTCAGGAT	novel	NA	P-0016278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	222	1019	0	ENST00000269305.4:c.783-11_823dup	p.Cys275TyrfsTer4	p.C275Yfs*4	ENST00000269305	NM_001126112.2	275	tgt/tATCCTGAGTAGTGGTAATCTACTGGGACGGAACAGCTTTGAGGTGCGTGTTTgt	8/11	0.714091567750242	1	FACETS	0.327	0.303	0.351	0.327	0.303	0.351	SUBCLONAL	1	TRUE	0	0.714091567750242	1		1019	1223	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497895	25497895	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	69	571	0	ENST00000264709.3:c.554T>G	p.Met185Arg	p.M185R	ENST00000264709	NM_175629.2	185	aTg/aGg	6/23	1	2	FACETS	0.274	0.238	0.313	0.274	0.238	0.313	SUBCLONAL	1	TRUE	1	0.714091567750242	2		571	705	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977626	2977626	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1880	358	1089	0	ENST00000396946.4:c.1058C>T	p.Thr353Ile	p.T353I	ENST00000396946	NM_032415.4	353	aCc/aTc	8/25	0.639227154938486	4	FACETS	0.768	0.724	0.813	0.256	0.241	0.271	SUBCLONAL	1	TRUE	1	0.714091567750242	4		1089	2238	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035190	6035190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1274671450	NA	P-0016280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	209	486	0	ENST00000265849.7:c.878A>G	p.Asn293Ser	p.N293S	ENST00000265849	NM_000535.5	293	aAc/aGc	8/15	0.3	5	FACETS	0.924	0.857	0.994	0.616	0.571	0.663	CLONAL	2	FALSE	2	0.3	5		486	1093	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0016281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	47	547	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.473	0.398	0.555	0.473	0.398	0.555	SUBCLONAL	1	FALSE	1	0.35327936914596	2		547	563	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0016281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	62	596	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.438	0.377	0.504	0.438	0.377	0.504	SUBCLONAL	1	FALSE	1	0.35327936914596	2		596	802	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760298	133760298	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	37	424	0	ENST00000318560.5:c.2621G>A	p.Arg874Lys	p.R874K	ENST00000318560	NM_005157.4	874	aGa/aAa	11/11	1	2	FACETS	0.335	0.275	0.402	0.335	0.275	0.402	SUBCLONAL	1	FALSE	1	0.35327936914596	2		424	625	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	140	486	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.346379057255825	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	0	0.455500504310577	1		486	432	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	208	530	1	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.283010703531788	0	FACETS	0.834	0.779	0.89			1	CLONAL	1	FALSE	0	0.455500504310577	0		531	596	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101198	27101198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1553153231	NA	P-0016283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	74	240	0	ENST00000324856.7:c.4480C>T	p.Gln1494Ter	p.Q1494*	ENST00000324856	NM_006015.4	1494	Caa/Taa	18/20	0.346379057255825	1	FACETS	0.481	0.421	0.544	0.481	0.421	0.544	SUBCLONAL	1	FALSE	0	0.455500504310577	1		240	522	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745093	41745094	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0016283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	127	237	0	ENST00000301178.4:c.1159_1160del	p.Gln387ArgfsTer99	p.Q387Rfs*99	ENST00000301178	NM_021913.4	387	CAa/a	9/20	0.243965179210641	1	FACETS	0.744	0.676	0.814	0.744	0.676	0.814	INDETERMINATE	1	FALSE	0	0.455500504310577	1		237	579	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994336	25994336	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	108	188	0	ENST00000435504.4:c.477G>T	p.Gln159His	p.Q159H	ENST00000435504		159	caG/caT	6/13	1	2	FACETS	0.958	0.864	1	0.958	0.864	1	CLONAL	1	FALSE	1	0.455500504310577	2		188	495	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285888	39285888	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	74	65	0	ENST00000402219.2:c.271C>G	p.Gln91Glu	p.Q91E	ENST00000402219	NM_005633.3	91	Caa/Gaa	3/23	1	2	FACETS	0.591	0.518	0.669	0.591	0.518	0.669	SUBCLONAL	1	FALSE	1	0.455500504310577	2		65	550	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397139	397139	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	39	193	0	ENST00000380956.4:c.524A>G	p.Asp175Gly	p.D175G	ENST00000380956	NM_001195286.1	175	gAc/gGc	5/9	0.244617559472207	1	FACETS	0.284	0.235	0.339	0.284	0.235	0.339	INDETERMINATE	1	FALSE	0	0.455500504310577	1		193	465	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247516	53247516	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	97	202	0	ENST00000375401.3:c.293C>G	p.Ser98Cys	p.S98C	ENST00000375401	NM_004187.3	98	tCc/tGc	3/26	0.346379057255825	1	FACETS	0.43	0.383	0.48	0.43	0.383	0.48	SUBCLONAL	1	FALSE	0	0.455500504310577	1		202	765	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267359	198267359	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs377023736	NA	P-0016284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	20	908	0	ENST00000335508.6:c.1998G>T	p.Lys666Asn	p.K666N	ENST00000335508	NM_012433.2	666	aaG/aaT	14/25	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		908	822	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	31	837	1	ENST00000269305.4:c.859G>T	p.Glu287Ter	p.E287*	ENST00000269305	NM_001126112.2	287	Gag/Tag	8/11	0.685109054242998	1	FACETS	0.085	0.068	0.104	0.085	0.068	0.104	SUBCLONAL	1	TRUE	0	0.704335966825282	1		838	671	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111523	8111524	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0016285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	296	759	0	ENST00000346208.3:c.1010dup	p.Cys338LeufsTer14	p.C338Lfs*14	ENST00000346208		337	gtc/gTtc	5/6	1	2	FACETS	0.968	0.915	1	0.968	0.915	1	CLONAL	1	TRUE	1	0.704335966825282	2		759	868	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032549	12032568	+	frameshift_variant	Frame_Shift_Del	DEL	AGTAATTCTGAGGAAAGGGA	AGTAATTCTGAGGAAAGGGA	-	novel	NA	P-0016285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	119	463	0	ENST00000353533.5:c.986_1005del	p.Ser329IlefsTer17	p.S329Ifs*17	ENST00000353533	NM_003010.3	329	AGTAATTCTGAGGAAAGGGAa/a	9/11	0.685109054242998	1	FACETS	0.782	0.718	0.847	0.782	0.718	0.847	SUBCLONAL	1	TRUE	0	0.704335966825282	1		463	280	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251737	212251737	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	174	331	1	ENST00000342788.4:c.3322A>T	p.Asn1108Tyr	p.N1108Y	ENST00000342788	NM_005235.2	1108	Aat/Tat	27/28	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.704335966825282	2		332	469	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0016287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	282	998	2	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.62421759379979	2		1000	872	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	228	807	0	ENST00000335508.6:c.1874G>T	p.Arg625Leu	p.R625L	ENST00000335508	NM_012433.2	625	cGt/cTt	14/25	1	2	FACETS	0.987	0.923	1	0.987	0.923	1	CLONAL	1	TRUE	1	0.62421759379979	2		807	740	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0016287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	70	271	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	0.62421759379979	1	FACETS	0.941	0.841	1	0.941	0.841	1	CLONAL	1	TRUE	0	0.62421759379979	1		271	164	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974782	21974782	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs138677674	NA	P-0016287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	10	261	0	ENST00000304494.5:c.45G>A	p.Trp15Ter	p.W15*	ENST00000304494	NM_000077.4	15	tgG/tgA	1/3	0.62421759379979				0.095	0.197				SUBCLONAL	1	TRUE	0	0.62421759379979	1		261	157	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690799	89690810	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTAGTTGTGCTG	TTAGTTGTGCTG	-	novel	NA	P-0016287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	132	629	1	ENST00000371953.3:c.210-4_217del		p.X70_splice	ENST00000371953	NM_000314.4	70		4/9	0.62421759379979	1	FACETS	0.824	0.758	0.892	0.824	0.758	0.892	CLONAL	1	TRUE	0	0.62421759379979	1		630	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555526097	NA	P-0016288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	542	446	0	ENST00000269305.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000269305	NM_001126112.2	167	Cag/Tag	5/11	0.365538262682243	4	FACETS	1	0.994	1			1	CLONAL	3	TRUE	NA	0.376310006755645	4		446	1137	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998886	100998886	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1380505844	NA	P-0016288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	325	966	0	ENST00000325455.5:c.916G>C	p.Val306Leu	p.V306L	ENST00000325455	NM_001202474.3	306	Gtg/Ctg	1/8	0.363227635941297	4	FACETS	0.924	0.872	0.977	0.924	0.872	0.977	CLONAL	2	TRUE	2	0.376310006755645	4		966	1287	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21629878	21629878	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	122	1049	0	ENST00000421138.2:c.916A>C	p.Lys306Gln	p.K306Q	ENST00000421138		306	Aag/Cag	9/16	0.210636389048404	5	FACETS	0.895	0.807	0.989			1	INDETERMINATE	1	TRUE	NA	0.376310006755645	5		1049	1133	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829989	72829990	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0016288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	301	869	0	ENST00000268489.5:c.6591_6592del	p.Phe2198GlnfsTer6	p.F2198Qfs*6	ENST00000268489	NM_006885.3	2197	ctCTtc/cttc	9/10	0.376310006755645	2	FACETS	0.979	0.926	1	0.979	0.926	1	CLONAL	2	TRUE	0	0.376310006755645	2		869	817	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993196	72993196	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	416	1330	2	ENST00000268489.5:c.849G>T	p.Met283Ile	p.M283I	ENST00000268489	NM_006885.3	283	atG/atT	2/10	0.376310006755645	2	FACETS	0.947	0.903	0.992	0.947	0.903	0.992	CLONAL	2	TRUE	0	0.376310006755645	2		1332	1167	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993399	72993399	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1243611387	NA	P-0016288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	339	1401	0	ENST00000268489.5:c.646C>T	p.Pro216Ser	p.P216S	ENST00000268489	NM_006885.3	216	Ccg/Tcg	2/10	0.376310006755645	2	FACETS	0.971	0.921	1	0.971	0.921	1	CLONAL	2	TRUE	0	0.376310006755645	2		1401	928	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045687	26045687	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	87	277	0	ENST00000540144.1:c.49C>A	p.Pro17Thr	p.P17T	ENST00000540144	NM_003531.2	17	Ccg/Acg	1/1	0.376310006755645	4	FACETS	0.829	0.739	0.923	0.829	0.739	0.923	CLONAL	2	TRUE	2	0.376310006755645	4		277	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0016289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	500	730	1	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.463010488956937	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.463010488956937	2		731	1019	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220295	55220295	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	546	933	0	ENST00000275493.2:c.685A>T	p.Ser229Cys	p.S229C	ENST00000275493	NM_005228.3	229	Agt/Tgt	6/28	0.329890314488599	4	FACETS	0.94	0.904	0.975	0.94	0.904	0.975	CLONAL	3	TRUE	1	0.463010488956937	4		933	1224	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485708	40485708	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs869312887	NA	P-0016289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	334	724	0	ENST00000264657.5:c.1032G>C	p.Gln344His	p.Q344H	ENST00000264657	NM_139276.2	344	caG/caC	10/24	0.463010488956937	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.463010488956937	2		724	712	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715601	30715601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	42	305	0	ENST00000295754.5:c.1259G>A	p.Gly420Glu	p.G420E	ENST00000295754	NM_003242.5	420	gGa/gAa	5/7	0.463010488956937	1	FACETS	0.797	0.675	0.928	0.797	0.675	0.928	CLONAL	1	TRUE	0	0.463010488956937	1		305	175	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0016290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	466	480	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.430535983537037	4	FACETS	0.89	0.857	0.922	0.89	0.857	0.922	CLONAL	4	TRUE	0	0.466847356701137	4		480	823	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0016290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	1348	1232	1	ENST00000311936.3:c.34_35delinsAT	p.Gly12Ile	p.G12I	ENST00000311936	NM_004985.3	12	GGt/ATt	2/5	0.466847356701137	7	FACETS	1	0.997	1			1	CLONAL	7	TRUE	NA	0.466847356701137	7		1233	1714	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602583	10602584	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0016290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	255	1027	1	ENST00000171111.5:c.994_995delinsAT	p.Gly332Ile	p.G332I	ENST00000171111	NM_203500.1	332	GGc/ATc	3/6	0.466847356701137	2	FACETS	0.975	0.922	1	0.975	0.922	1	CLONAL	2	TRUE	0	0.466847356701137	2		1028	560	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293132	212293132	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0016290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	132	830	1	ENST00000342788.4:c.2719+1G>T		p.X907_splice	ENST00000342788	NM_005235.2	907			0.466847356701137	3	FACETS	1	0.929	1	0.512	0.466	0.561	CLONAL	1	TRUE	1	0.466847356701137	3		831	681	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662985	227662985	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	361	1015	0	ENST00000305123.5:c.470G>T	p.Gly157Val	p.G157V	ENST00000305123	NM_005544.2	157	gGa/gTa	1/2	0.466847356701137	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.466847356701137	3		1015	912	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187560926	187560926	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs374385969	NA	P-0016290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	110	872	0	ENST00000441802.2:c.3592A>G	p.Thr1198Ala	p.T1198A	ENST00000441802	NM_005245.3	1198	Act/Gct	4/27	0.466847356701137	3	FACETS	0.804	0.723	0.89	0.402	0.361	0.445	CLONAL	1	TRUE	1	0.466847356701137	3		872	723	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638003	176638003	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	203	1410	0	ENST00000439151.2:c.2603C>G	p.Ser868Cys	p.S868C	ENST00000439151	NM_022455.4	868	tCt/tGt	5/23	1	2	FACETS	0.993	0.922	1	0.993	0.922	1	CLONAL	1	TRUE	1	0.466847356701137	2		1410	876	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974669	21974669	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	G	novel	NA	P-0016290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	152	974	0	ENST00000304494.5:c.150+8G>C		p.X50_splice	ENST00000304494	NM_000077.4	50			0.466847356701137	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.466847356701137	1		974	484	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045431	47045474	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCCAACATTCACATACACATACAAACTTTCAGCAAATGAAGTA	CCCCAACATTCACATACACATACAAACTTTCAGCAAATGAAGTA	-	novel	NA	P-0016290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	104	732	0	ENST00000377604.3:c.2431-31_2443del		p.X811_splice	ENST00000377604	NM_001204468.1	811		22/24	0.466847356701137	1	FACETS	0.938	0.848	1	0.938	0.848	1	CLONAL	1	TRUE	0	0.466847356701137	1		732	364	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0016293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	373	488	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.627636020945771	2	FACETS	0.977	0.941	1	0.977	0.941	1	CLONAL	2	TRUE	0	0.66737224740738	2		490	572	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0016293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	254	362	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.66737224740738	3	FACETS	0.945	0.906	0.983	0.945	0.906	0.983	CLONAL	3	TRUE	0	0.66737224740738	3		362	358	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	136	472	1	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	0.66737224740738	3	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	1	0.66737224740738	3		473	267	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022592	31022592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs373221034	NA	P-0016293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1597	395	674	0	ENST00000375687.4:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000375687	NM_015338.5	693	Cga/Tga	13/13	0.66737224740738	8	FACETS	0.892	0.845	0.94	0.297	0.281	0.314	CLONAL	2	TRUE	2	0.66737224740738	8		674	1992	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100980	41100980	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868706902	NA	P-0016293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	218	602	0	ENST00000373198.4:c.1376G>A	p.Arg459Gln	p.R459Q	ENST00000373198	NM_133170.3	459	cGg/cAg	8/32	0.66737224740738	6	FACETS	1	0.989	1			1	CLONAL	1	TRUE	NA	0.66737224740738	6		602	1140	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	167	384	0	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	0.66737224740738	3	FACETS	0.913	0.841	0.988	0.457	0.42	0.494	CLONAL	1	TRUE	1	0.66737224740738	3		384	731	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244020	5244020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752283871	NA	P-0016293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	532	625	2	ENST00000357368.4:c.1462G>A	p.Val488Met	p.V488M	ENST00000357368	NM_002850.3	488	Gtg/Atg	11/38	0.605334463740764	4	FACETS	0.925	0.893	0.957	0.925	0.893	0.957	CLONAL	3	TRUE	1	0.66737224740738	4		627	958	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092759	27092759	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	214	745	0	ENST00000324856.7:c.2780G>A	p.Gly927Glu	p.G927E	ENST00000324856	NM_006015.4	927	gGa/gAa	9/20	1	2	FACETS	0.987	0.922	1	0.987	0.922	1	CLONAL	1	TRUE	1	0.66737224740738	2		745	650	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604646	43604646	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	175	740	0	ENST00000355710.3:c.1231T>C	p.Ser411Pro	p.S411P	ENST00000355710	NM_020975.4	411	Tcc/Ccc	6/20	0.66737224740738	3	FACETS	0.9	0.83	0.972	0.45	0.415	0.486	CLONAL	1	TRUE	1	0.66737224740738	3		740	777	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609029	43609029	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1204846773	NA	P-0016293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	256	681	1	ENST00000355710.3:c.1785G>T	p.Glu595Asp	p.E595D	ENST00000355710	NM_020975.4	595	gaG/gaT	10/20	0.66737224740738	3	FACETS	0.904	0.854	0.954	0.904	0.854	0.954	CLONAL	2	TRUE	1	0.66737224740738	3		682	566	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779359	3779359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	291	434	1	ENST00000262367.5:c.5689C>T	p.Pro1897Ser	p.P1897S	ENST00000262367	NM_004380.2	1897	Ccc/Tcc	31/31	0.66737224740738	3	FACETS	0.964	0.916	1	0.964	0.916	1	CLONAL	2	TRUE	1	0.66737224740738	3		435	603	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866732	37866732	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs1191408638	NA	P-0016293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	241	780	0	ENST00000269571.5:c.899C>G	p.Pro300Arg	p.P300R	ENST00000269571		300	cCc/cGc	7/27	0.659739463378931	4	FACETS	1	0.945	1	0.507	0.473	0.543	CLONAL	1	TRUE	2	0.66737224740738	4		780	1187	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0016293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	43	488	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.863	0.72	1	0.863	0.72	1	CLONAL	1	TRUE	1	0.14	2		490	712	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022592	31022592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs373221034	NA	P-0016293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	53	674	0	ENST00000375687.4:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000375687	NM_015338.5	693	Cga/Tga	13/13	1	2	FACETS	0.779	0.662	0.908	0.779	0.662	0.908	CLONAL	1	TRUE	1	0.14	2		674	972	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	26	384	0	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	1	2	FACETS	0.372	0.293	0.464	0.372	0.293	0.464	SUBCLONAL	1	TRUE	1	0.14	2		384	998	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244020	5244020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752283871	NA	P-0016293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	61	625	2	ENST00000357368.4:c.1462G>A	p.Val488Met	p.V488M	ENST00000357368	NM_002850.3	488	Gtg/Atg	11/38	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.14	2		627	811	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779359	3779359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	30	434	1	ENST00000262367.5:c.5689C>T	p.Pro1897Ser	p.P1897S	ENST00000262367	NM_004380.2	1897	Ccc/Tcc	31/31	1	2	FACETS	0.778	0.625	0.952	0.778	0.625	0.952	CLONAL	1	TRUE	1	0.14	2		435	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0016296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	187	612	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.274389789731943	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.274389789731943	2		612	590	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945141	32945141	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs886040781	NA	P-0016296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	97	708	2	ENST00000380152.3:c.8536G>T	p.Glu2846Ter	p.E2846*	ENST00000380152		2846	Gag/Tag	20/27	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.274389789731943	2		710	655	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281602	198281602	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	90	535	0	ENST00000335508.6:c.529A>G	p.Lys177Glu	p.K177E	ENST00000335508	NM_012433.2	177	Aaa/Gaa	6/25	0.231597945056646	4	FACETS	1	0.95	1	0.377	0.334	0.422	CLONAL	1	TRUE	1	0.274389789731943	4		535	740	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978790	13978790	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	119	688	0	ENST00000405192.2:c.317A>C	p.Glu106Ala	p.E106A	ENST00000405192	NM_001163147.1	106	gAa/gCa	6/12	0.274389789731943	3	FACETS	1	0.961	1	0.564	0.508	0.622	CLONAL	1	TRUE	1	0.274389789731943	3		688	875	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696431	47696431	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519969	NA	P-0016305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	168	720	0	ENST00000347630.2:c.392G>C	p.Trp131Ser	p.W131S	ENST00000347630	NM_001007230.1	131	tGg/tCg	6/11	0.292944369488903	1	FACETS	0.867	0.796	0.942	0.867	0.796	0.942	CLONAL	1	TRUE	0	0.292944369488903	1		720	1129	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254714	46254714	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	119	488	0	ENST00000334344.6:c.4904T>C	p.Leu1635Pro	p.L1635P	ENST00000334344	NM_152641.2	1635	cTg/cCg	16/21	0.34356881378712	4	FACETS	0.97	0.874	1	0.485	0.437	0.536	CLONAL	1	TRUE	2	0.349798866723205	4		488	947	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577107	7577108	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0016307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	214	874	0	ENST00000269305.4:c.830_831del	p.Cys277SerfsTer28	p.C277Sfs*28	ENST00000269305	NM_001126112.2	277	tGT/t	8/11	0.349798866723205	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.349798866723205	1		874	738	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420101	41420101	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	79	316	0	ENST00000373198.4:c.220T>G	p.Phe74Val	p.F74V	ENST00000373198	NM_133170.3	74	Ttc/Gtc	3/32	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.349798866723205	2		316	364	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1391	1216	641	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.109936243419933	5	FACETS	1	0.994	1	1	0.999	1	CLONAL	7	TRUE	1	0.154944723615448	5		641	2607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0016308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	176	397	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	NA	2	FACETS	0.881	0.81	0.956			1	INDETERMINATE	2	TRUE	NA	0.154944723615448	2		397	1289	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743924	40743924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199514226	NA	P-0016308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	141	602	1	ENST00000373198.4:c.3071C>T	p.Thr1024Met	p.T1024M	ENST00000373198	NM_133170.3	1024	aCg/aTg	23/32	1	2	FACETS	0.798	0.726	0.875	1	0.988	1	SUBCLONAL	2	TRUE	1	0.154944723615448	2		603	1140	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0016308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	112	672	1	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	0.154944723615448	3	FACETS	1	0.982	1	0.73	0.655	0.81	CLONAL	1	TRUE	1	0.154944723615448	3		673	1067	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843736	156843736	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1008878777	NA	P-0016308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1669	132	955	2	ENST00000524377.1:c.1162G>A	p.Glu388Lys	p.E388K	ENST00000524377	NM_002529.3	388	Gag/Aag	8/17	0.154944723615448	5	FACETS	1	0.968	1			1	CLONAL	1	TRUE	NA	0.154944723615448	5		957	1801	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546044	29546044	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778548	NA	P-0016308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1490	198	734	0	ENST00000356175.3:c.1549G>A	p.Glu517Lys	p.E517K	ENST00000356175	NM_000267.3	517	Gaa/Aaa	14/57	0.154944723615448	3	FACETS	0.816	0.753	0.882	0.816	0.753	0.882	CLONAL	2	TRUE	1	0.154944723615448	3		734	1688	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332894	65332894	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	G	novel	NA	P-0016308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	28	238	0	ENST00000342505.4:c.648-3T>C		p.X216_splice	ENST00000342505	NM_002227.2	216			1	2	FACETS	0.767	0.612	0.945	0.767	0.612	0.945	CLONAL	1	TRUE	1	0.154944723615448	2		238	471	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475152	475152	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1421	364	1010	0	ENST00000399788.2:c.485A>G	p.Tyr162Cys	p.Y162C	ENST00000399788	NM_001042603.1	162	tAt/tGt	4/28	0.0197363355366997	3	FACETS	0.945	0.894	0.999			1	INDETERMINATE	3	TRUE	NA	0.154944723615448	3		1010	1785	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285231	212285231	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	141	615	0	ENST00000342788.4:c.3070del	p.Val1024SerfsTer128	p.V1024Sfs*128	ENST00000342788	NM_005235.2	1024	Gtc/tc	25/28	0.154944723615448	3	FACETS	1	0.986	1	0.741	0.673	0.812	CLONAL	1	TRUE	1	0.154944723615448	3		615	1324	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739099	40739099	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	71	524	0	ENST00000373198.4:c.3185G>C	p.Arg1062Pro	p.R1062P	ENST00000373198	NM_133170.3	1062	cGc/cCc	24/32	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.154944723615448	2		524	889	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35857082	35857082	+	start_lost	Translation_Start_Site	SNP	G	G	T	novel	NA	P-0016308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	98	339	0	ENST00000303115.3:c.3G>T	p.Met1?	p.M1?	ENST00000303115	NM_002185.3	1	atG/atT	1/8	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.154944723615448	2		339	909	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672330	86672330	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1256	188	578	1	ENST00000274376.6:c.2132G>T	p.Arg711Leu	p.R711L	ENST00000274376	NM_002890.2	711	cGa/cTa	16/25	1	2	FACETS	0.84	0.774	0.91	1	0.991	1	CLONAL	2	TRUE	1	0.154944723615448	2		579	1444	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201826	152201826	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	166	589	0	ENST00000206249.3:c.680G>A	p.Cys227Tyr	p.C227Y	ENST00000206249	NM_000125.3	227	tGc/tAc	3/8	1	2	FACETS	0.924	0.848	1	1	0.991	1	CLONAL	2	TRUE	1	0.154944723615448	2		589	1159	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501252	140501252	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1392	221	697	0	ENST00000288602.6:c.820A>G	p.Thr274Ala	p.T274A	ENST00000288602	NM_004333.4	274	Aca/Gca	6/18	0.154944723615448	5	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	3	0.154944723615448	5		697	1613	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891537	151891537	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	207	455	0	ENST00000262189.6:c.4495A>G	p.Met1499Val	p.M1499V	ENST00000262189	NM_170606.2	1499	Atg/Gtg	29/59	0.154944723615448	5	FACETS	0.897	0.831	0.965	1	0.988	1	CLONAL	3	TRUE	3	0.154944723615448	5		455	1224	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039695	47039695	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0016308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1268	223	907	0	ENST00000377604.3:c.1147A>T	p.Lys383Ter	p.K383*	ENST00000377604	NM_001204468.1	383	Aag/Tag	11/24	1	2	FACETS	0.965	0.896	1	1	0.994	1	CLONAL	2	TRUE	1	0.154944723615448	2		907	1491	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410964	63410964	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1222	151	742	1	ENST00000330258.3:c.2203G>T	p.Ala735Ser	p.A735S	ENST00000330258	NM_152424.3	735	Gca/Tca	2/2	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.154944723615448	2		743	1373	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972626	76972626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1507	86	698	0	ENST00000373344.5:c.115G>A	p.Ala39Thr	p.A39T	ENST00000373344	NM_000489.3	39	Gca/Aca	2/35	1	2	FACETS	0.697	0.614	0.787	0.697	0.614	0.787	SUBCLONAL	1	TRUE	1	0.154944723615448	2		698	1593	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0016309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	190	714	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.218864795435287	3	FACETS	0.89	0.822	0.961	0.89	0.822	0.961	CLONAL	2	TRUE	1	0.218864795435287	3		714	1082	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591895	48591895	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs377767346	NA	P-0016309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	28	510	0	ENST00000342988.3:c.1058A>G	p.Tyr353Cys	p.Y353C	ENST00000342988	NM_005359.5	353	tAc/tGc	9/12	0.175268795761348	1	FACETS	0.416	0.331	0.513	0.416	0.331	0.513	SUBCLONAL	1	TRUE	0	0.218864795435287	1		510	548	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11301665	11301665	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	55	622	0	ENST00000361445.4:c.1486G>C	p.Gly496Arg	p.G496R	ENST00000361445	NM_004958.3	496	Ggc/Cgc	10/58	0.218864795435287	3	FACETS	0.709	0.605	0.823	0.354	0.302	0.412	SUBCLONAL	1	TRUE	1	0.218864795435287	3		622	787	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884632	111884632	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	63	563	0	ENST00000341259.2:c.808G>C	p.Asp270His	p.D270H	ENST00000341259	NM_005475.2	270	Gac/Cac	3/8	1	2	FACETS	0.924	0.799	1	0.924	0.799	1	CLONAL	1	TRUE	1	0.218864795435287	2		563	623	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144110	11144110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	58	788	2	ENST00000358026.2:c.3691G>A	p.Ala1231Thr	p.A1231T	ENST00000358026	NM_001128849.1	1231	Gcc/Acc	26/36	0.218864795435287	2	FACETS	0.64	0.549	0.74	0.32	0.274	0.37	SUBCLONAL	1	TRUE	0	0.218864795435287	2		790	828	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0016311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	201	372	0	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	0.19082593806631	3	FACETS	1	0.99	1	0.733	0.679	0.79	CLONAL	1	TRUE	1	0.31	3		372	1021	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518602	69518602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	107	477	0	ENST00000294312.3:c.43G>A	p.Gly15Ser	p.G15S	ENST00000294312	NM_005117.2	15	Ggc/Agc	1/3	0.19082593806631	3	FACETS	0.683	0.61	0.76	0.341	0.305	0.38	SUBCLONAL	1	TRUE	1	0.31	3		477	1168	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911551	32911551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1440156136	NA	P-0016311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	25	306	0	ENST00000380152.3:c.3059C>T	p.Ser1020Phe	p.S1020F	ENST00000380152		1020	tCt/tTt	11/27	1	2	FACETS	0.501	0.395	0.623	0.501	0.395	0.623	SUBCLONAL	1	TRUE	1	0.31	2		306	322	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131951721	131951721	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	51	339	0	ENST00000265335.6:c.3063C>A	p.Asn1021Lys	p.N1021K	ENST00000265335		1021	aaC/aaA	20/25	1	2	FACETS	0.648	0.551	0.754	0.648	0.551	0.754	SUBCLONAL	1	TRUE	1	0.31	2		339	508	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061317	38061317	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	360	662	0	ENST00000250448.2:c.672C>A	p.Phe224Leu	p.F224L	ENST00000250448	NM_004496.3	224	ttC/ttA	2/2	0.355549941584038	3	FACETS	1	0.99	1	0.59	0.559	0.622	INDETERMINATE	1	TRUE	1	0.59359331394706	3		662	1333	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0016315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	332	561	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.392869784056418	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.392869784056418	2		561	736	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578415	7578415	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	170	548	0	ENST00000269305.4:c.515T>A	p.Val172Asp	p.V172D	ENST00000269305	NM_001126112.2	172	gTt/gAt	5/11	0.392869784056418	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.392869784056418	1		548	658	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906453	50906453	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs960226186	NA	P-0016315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	206	655	1	ENST00000440232.2:c.1114G>A	p.Glu372Lys	p.E372K	ENST00000440232	NM_002691.3	372	Gag/Aag	9/27	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.392869784056418	2		656	854	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908795	101908795	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	47	421	0	ENST00000374994.4:c.1159T>G	p.Ser387Ala	p.S387A	ENST00000374994	NM_004612.2	387	Tcc/Gcc	7/9	1	2	FACETS	0.688	0.582	0.803	0.688	0.582	0.803	SUBCLONAL	1	TRUE	1	0.392869784056418	2		421	348	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0016316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	87	491	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.3	3	FACETS	0.793	0.703	0.89			1	SUBCLONAL	2	TRUE	NA	0.18	3		492	664	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0016316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	104	687	1	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	0.221554107543413	4	FACETS	0.794	0.71	0.883	0.794	0.71	0.883	SUBCLONAL	2	TRUE	2	0.18	4		688	859	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520183	9520183	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781425219	NA	P-0016316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	47	536	2	ENST00000353224.5:c.2086G>A	p.Gly696Arg	p.G696R	ENST00000353224	NM_177990.2	696	Gga/Aga	10/10	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.18	2		538	439	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468309	50468309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1159541845	NA	P-0016316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	36	598	1	ENST00000331340.3:c.1544G>A	p.Arg515His	p.R515H	ENST00000331340	NM_006060.4	515	cGc/cAc	8/8	0.3	1	FACETS	0.774	0.636	0.929	0.774	0.636	0.929	CLONAL	1	TRUE	0	0.18	1		599	470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0016318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	240	936	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.399952490858411	1	FACETS	0.853	0.796	0.912	0.853	0.796	0.912	CLONAL	1	TRUE	0	0.410237929629287	1		938	1090	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776783	NA	P-0016318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	174	363	1	ENST00000267163.4:c.1215+1G>A		p.X405_splice	ENST00000267163	NM_000321.2	405			0.340038252688897	1	FACETS	0.963	0.89	1	0.963	0.89	1	CLONAL	1	TRUE	0	0.410237929629287	1		364	700	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0016318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	271	670	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.410237929629287	2		670	1269	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0016318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	186	643	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.410237929629287	2		643	787	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	140	306	0	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	1	2	FACETS	0.985	0.899	1	0.985	0.899	1	CLONAL	1	TRUE	1	0.410237929629287	2		306	693	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910752	114910753	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	CTAGGTTCCCTCCCCATATGGTCCCACTC	novel	NA	P-0016318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	148	468	0	ENST00000543371.1:c.898_899insTCCTAGGTTCCCTCCCCATATGGTCCCAC		p.X300_splice	ENST00000543371	NM_001198531.1	300			1	2	FACETS	0.659	0.601	0.72	0.659	0.601	0.72	SUBCLONAL	1	TRUE	1	0.410237929629287	2		468	1095	SUCCESS
APC	324	MSKCC	GRCh37	5	112174344	112174345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGGAGAACTAGATACACCAATAAATTATAGTCTTAAATATTCAGATGAGCAG	novel	NA	P-0016318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	57	366	0	ENST00000257430.4:c.3055_3106dup	p.Leu1036TrpfsTer10	p.L1036Wfs*10	ENST00000257430	NM_000038.5	1018	gat/gaTGGAGAACTAGATACACCAATAAATTATAGTCTTAAATATTCAGATGAGCAGt	16/16	1	2	FACETS	0.322	0.276	0.374	0.322	0.276	0.374	SUBCLONAL	1	TRUE	1	0.410237929629287	2		366	862	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964333	70964333	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	99	249	1	ENST00000276594.2:c.1695G>A	p.Met565Ile	p.M565I	ENST00000276594	NM_024504.3	565	atG/atA	8/8	1	2	FACETS	0.946	0.848	1	0.946	0.848	1	CLONAL	1	TRUE	1	0.410237929629287	2		250	510	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94906474	94906474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1173588660	NA	P-0016320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	46	457	0	ENST00000536441.1:c.1424G>A	p.Arg475Gln	p.R475Q	ENST00000536441	NM_144665.3	475	cGa/cAa	10/10	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		457	645	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420670	49420670	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs797045659	NA	P-0016320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	31	351	0	ENST00000301067.7:c.15079C>T	p.Arg5027Ter	p.R5027*	ENST00000301067	NM_003482.3	5027	Cga/Tga	48/54	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		351	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0016321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	935	485	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.813311190508999	4	FACETS	1	0.995	1			1	CLONAL	4	TRUE	NA	0.847600246357517	4		486	1008	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193219820	193219820	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	108	346	0	ENST00000367435.3:c.1574A>T	p.His525Leu	p.H525L	ENST00000367435	NM_024529.4	525	cAt/cTt	17/17	0.431438822226622	4	FACETS	0.59	0.529	0.655			1	INDETERMINATE	1	TRUE	NA	0.847600246357517	4		346	798	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100768	8100768	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	119	445	0	ENST00000346208.3:c.742G>C	p.Gly248Arg	p.G248R	ENST00000346208		248	Gga/Cga	3/6	0.25257182138002	3	FACETS	0.781	0.708	0.857	0.26	0.236	0.286	INDETERMINATE	1	TRUE	0	0.847600246357517	3		445	512	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858048	152858048	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	126	263	0	ENST00000406277.2:c.567del	p.Ile189MetfsTer155	p.I189Mfs*155	ENST00000406277	NM_152274.4	189	atC/at	6/7	0.847600246357517	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.847600246357517	1		263	165	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0016322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	726	1050	1	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	NA	2	FACETS	0.992	0.973	1			1	INDETERMINATE	2	TRUE	NA	0.837245955577797	2		1051	874	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619849	1619849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758087547	NA	P-0016322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	434	527	0	ENST00000344749.5:c.1097C>T	p.Thr366Met	p.T366M	ENST00000344749	NM_001136139.2	366	aCg/aTg	14/19	0.821210657509797	2	FACETS	0.955	0.929	0.979	0.955	0.929	0.979	CLONAL	2	TRUE	0	0.837245955577797	2		527	543	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528324	157528324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180102689	NA	P-0016322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	554	557	1	ENST00000346085.5:c.6049C>T	p.Leu2017Phe	p.L2017F	ENST00000346085	NM_020732.3	2017	Ctc/Ttc	20/20	0.833376051565043	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.837245955577797	2		558	650	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	213	423	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.975	0.914	1	0.975	0.914	1	CLONAL	1	TRUE	1	0.82	2		423	533	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0016324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	258	318	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.82	2		318	612	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0016324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	272	352	1	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	0.839234058442003	1	FACETS	0.976	0.936	1	0.976	0.936	1	CLONAL	1	TRUE	0	0.82	1		353	401	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117028	193117028	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	411	376	0	ENST00000367435.3:c.762del	p.Gln254HisfsTer3	p.Q254Hfs*3	ENST00000367435	NM_024529.4	254	cAa/ca	8/17	1	2	FACETS	0.756	0.719	0.793	0.756	0.719	0.793	SUBCLONAL	1	TRUE	1	0.82	2		376	1326	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791005	42791005	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	295	368	0	ENST00000575354.2:c.153del	p.Ser52ProfsTer153	p.S52Pfs*153	ENST00000575354	NM_015125.3	50	gaC/ga	2/20	0.839234058442003	1	FACETS	0.945	0.907	0.983	0.945	0.907	0.983	CLONAL	1	TRUE	0	0.82	1		368	449	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663388	67663388	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	267	370	0	ENST00000264010.4:c.1789G>T	p.Gly597Ter	p.G597*	ENST00000264010	NM_006565.3	597	Gga/Tga	10/12	1	2	FACETS	0.852	0.8	0.904	0.852	0.8	0.904	CLONAL	1	FALSE	1	0.690488876157044	2		370	908	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665562	138665562	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0016325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	175	280	0	ENST00000330315.3:c.3G>A	p.Met1?	p.M1?	ENST00000330315	NM_023067.3	1	atG/atA	1/1	1	2	FACETS	0.862	0.798	0.928	0.862	0.798	0.928	CLONAL	1	FALSE	1	0.690488876157044	2		280	588	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564534	86564534	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	37	256	0	ENST00000274376.6:c.266G>C	p.Gly89Ala	p.G89A	ENST00000274376	NM_002890.2	89	gGa/gCa	1/25	1	2	FACETS	0.193	0.158	0.231	0.193	0.158	0.231	SUBCLONAL	1	FALSE	1	0.690488876157044	2		256	556	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750975	128750975	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs990645227	NA	P-0016325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	40	230	2	ENST00000377970.2:c.512G>T	p.Arg171Leu	p.R171L	ENST00000377970	NM_002467.4	171	cGc/cTc	2/3	1	2	FACETS	0.205	0.169	0.244	0.205	0.169	0.244	SUBCLONAL	1	FALSE	1	0.690488876157044	2		232	566	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244368	5244368	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	286	475	1	ENST00000357368.4:c.1114C>T	p.Gln372Ter	p.Q372*	ENST00000357368	NM_002850.3	372	Caa/Taa	11/38	0.143140481836182	0	FACETS	0.367	0.346	0.39			1	INDETERMINATE	1	TRUE	0	0.614949805743383	0		476	975	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442623	52442623	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs1060503732	NA	P-0016326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	123	216	0	ENST00000460680.1:c.123-1G>C		p.X41_splice	ENST00000460680	NM_004656.3	41			0.614949805743383	1	FACETS	0.879	0.807	0.954	0.879	0.807	0.954	CLONAL	1	TRUE	0	0.614949805743383	1		216	315	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750257	133750257	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	185	303	0	ENST00000318560.5:c.1088A>G	p.Asp363Gly	p.D363G	ENST00000318560	NM_005157.4	363	gAt/gGt	7/11	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.614949805743383	2		303	598	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0016327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	253	683	0				ENST00000310581	NM_198253.2	-/1132			0.688760569559071	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.688760569559071	1		683	466	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0016327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	759	619	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.683466465646449	2	FACETS	0.954	0.93	0.978	0.954	0.93	0.978	CLONAL	2	TRUE	0	0.688760569559071	2		619	1155	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984848	9984848	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	264	482	0	ENST00000330684.3:c.1117G>A	p.Glu373Lys	p.E373K	ENST00000330684	NM_001134407.1	373	Gaa/Aaa	4/13	NA	2	FACETS	0.913	0.858	0.968			1	INDETERMINATE	1	TRUE	NA	0.688760569559071	2		482	840	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612073	189612073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142762485	NA	P-0016327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	308	487	3	ENST00000264731.3:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000264731	NM_003722.4	609	Gaa/Aaa	14/14	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.688760569559071	2		490	854	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0016327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	485	470	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.587438032412185	3	FACETS	0.848	0.814	0.883	0.848	0.814	0.883	CLONAL	2	TRUE	1	0.688760569559071	3		470	1116	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047693	180047693	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	324	534	0	ENST00000261937.6:c.2322G>A	p.Met774Ile	p.M774I	ENST00000261937	NM_182925.4	774	atG/atA	16/30	0.688760569559071	1	FACETS	0.952	0.907	0.996	0.952	0.907	0.996	CLONAL	1	TRUE	0	0.688760569559071	1		534	648	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801065	135801065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs118203361	NA	P-0016327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	544	483	0	ENST00000298552.3:c.272C>T	p.Ser91Leu	p.S91L	ENST00000298552	NM_001162426.1	91	tCg/tTg	5/23	0.587438032412185	3	FACETS	0.822	0.79	0.854	0.822	0.79	0.854	CLONAL	2	TRUE	1	0.688760569559071	3		483	1292	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222978	5222978	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293966082	NA	P-0016327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	351	521	0	ENST00000357368.4:c.2825C>T	p.Ser942Leu	p.S942L	ENST00000357368	NM_002850.3	942	tCg/tTg	18/38	1	2	FACETS	0.986	0.935	1	0.986	0.935	1	CLONAL	1	TRUE	1	0.688760569559071	2		521	1034	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367239	50367239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1045233686	NA	P-0016327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	222	282	0	ENST00000331340.3:c.46G>A	p.Glu16Lys	p.E16K	ENST00000331340	NM_006060.4	16	Gaa/Aaa	3/8	0.135673332543897	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.688760569559071	0		282	627	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615574	43615574	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201487882	NA	P-0016327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	324	504	0	ENST00000355710.3:c.2653G>A	p.Gly885Arg	p.G885R	ENST00000355710	NM_020975.4	885	Ggg/Agg	15/20	0.688760569559071	1	FACETS	0.97	0.925	1	0.97	0.925	1	CLONAL	1	TRUE	0	0.688760569559071	1		504	636	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251941	8251941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	344	482	2	ENST00000335790.3:c.136G>A	p.Glu46Lys	p.E46K	ENST00000335790	NM_002315.2	46	Gaa/Aaa	2/4	0.135673332543897	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.688760569559071	0		484	881	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21553849	21553849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868208801	NA	P-0016327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	346	516	0	ENST00000382592.4:c.2753C>T	p.Pro918Leu	p.P918L	ENST00000382592	NM_014572.2	918	cCc/cTc	7/8	0.592120848690617	3	FACETS	1	0.966	1	0.514	0.486	0.543	CLONAL	1	TRUE	1	0.688760569559071	3		516	1313	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877393	28877393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs991429591	NA	P-0016327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	434	376	0	ENST00000282397.4:c.3928G>A	p.Asp1310Asn	p.D1310N	ENST00000282397	NM_002019.4	1310	Gac/Aac	30/30	0.592120848690617	3	FACETS	0.898	0.861	0.936	0.898	0.861	0.936	CLONAL	2	TRUE	1	0.688760569559071	3		376	943	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519887	29519887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1486865549	NA	P-0016327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	304	487	1	ENST00000389048.3:c.1684G>A	p.Gly562Arg	p.G562R	ENST00000389048	NM_004304.4	562	Gga/Aga	9/29	1	2	FACETS	0.909	0.858	0.961	0.909	0.858	0.961	CLONAL	1	TRUE	1	0.688760569559071	2		488	971	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606709	29606709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	337	434	0	ENST00000389048.3:c.1171G>A	p.Gly391Arg	p.G391R	ENST00000389048	NM_004304.4	391	Gga/Aga	5/29	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.688760569559071	2		434	940	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458579	12458579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	374	538	0	ENST00000287820.6:c.1196C>T	p.Ala399Val	p.A399V	ENST00000287820	NM_015869.4	399	gCt/gTt	6/7	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.688760569559071	2		538	1042	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706940	117706940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	440	530	1	ENST00000368508.3:c.2210C>T	p.Ser737Leu	p.S737L	ENST00000368508	NM_002944.2	737	tCa/tTa	15/43	0.688760569559071	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.688760569559071	1		531	795	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946462	2946462	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758055212	NA	P-0016327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	269	408	0	ENST00000396946.4:c.3275G>A	p.Arg1092Gln	p.R1092Q	ENST00000396946	NM_032415.4	1092	cGa/cAa	25/25	1	2	FACETS	0.962	0.906	1	0.962	0.906	1	CLONAL	1	TRUE	1	0.688760569559071	2		408	812	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50358661	50358661	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	163	278	1	ENST00000331340.3:c.4G>A	p.Asp2Asn	p.D2N	ENST00000331340	NM_006060.4	2	Gat/Aat	2/8	0.135673332543897	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.688760569559071	0		279	540	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465627	8465627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	315	523	1	ENST00000356435.5:c.3553G>A	p.Glu1185Lys	p.E1185K	ENST00000356435		1185	Gaa/Aaa	21/35	0.688760569559071	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.688760569559071	1		524	591	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486035	8486035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	294	383	0	ENST00000356435.5:c.2782G>A	p.Glu928Lys	p.E928K	ENST00000356435		928	Gaa/Aaa	17/35	0.688760569559071	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.688760569559071	1		383	538	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390915	89390917	+	stop_gained	Nonsense_Mutation	TNP	TTC	TTC	CTA	novel	NA	P-0016327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	239	420	0	ENST00000336596.2:c.981_983delinsCTA	p.Ser328Ter	p.S328*	ENST00000336596	NM_005233.5	327	tcTTCa/tcCTAa	5/17	0.206499719221697	1	FACETS	0.683	0.641	0.726	0.683	0.641	0.726	INDETERMINATE	1	TRUE	0	0.688760569559071	1		420	666	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0016328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	825	683	0				ENST00000310581	NM_198253.2	-/1132			0.58001752042442	7	FACETS	1	0.995	1	1	0.995	1	CLONAL	6	TRUE	1	0.58001752042442	7		683	1102	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0016328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	527	1585	1	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.58001752042442	2	FACETS	0.981	0.948	1	0.981	0.948	1	CLONAL	2	TRUE	0	0.58001752042442	2		1586	926	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993645	90993645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs12721593	NA	P-0016328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	332	551	1	ENST00000265433.3:c.278C>T	p.Ser93Leu	p.S93L	ENST00000265433	NM_002485.4	93	tCg/tTg	3/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.58001752042442	2		552	1090	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244913	123244913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1224606327	NA	P-0016328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	243	614	2	ENST00000358487.5:c.2191G>A	p.Glu731Lys	p.E731K	ENST00000358487	NM_000141.4	731	Gaa/Aaa	16/18	1	2	FACETS	0.916	0.857	0.976	0.916	0.857	0.976	CLONAL	1	TRUE	1	0.58001752042442	2		616	915	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135659	64135659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779393153	NA	P-0016328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	263	500	1	ENST00000334205.4:c.1127C>T	p.Thr376Ile	p.T376I	ENST00000334205	NM_003942.2	376	aCc/aTc	10/17	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.58001752042442	2		501	830	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047298	77047298	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	187	425	1	ENST00000356341.3:c.1246C>T	p.Pro416Ser	p.P416S	ENST00000356341	NM_002576.4	416	Cca/Tca	13/15	1	2	FACETS	0.867	0.803	0.933	0.867	0.803	0.933	CLONAL	1	TRUE	1	0.58001752042442	2		426	744	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375890	118375890	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	238	516	0	ENST00000534358.1:c.9283C>T	p.Gln3095Ter	p.Q3095*	ENST00000534358	NM_005933.3	3095	Caa/Taa	27/36	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.58001752042442	2		516	812	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699372	47699372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	287	557	2	ENST00000347630.2:c.136G>A	p.Glu46Lys	p.E46K	ENST00000347630	NM_001007230.1	46	Gag/Aag	4/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.58001752042442	2		559	940	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219978	36219978	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0016328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	153	444	1	ENST00000222270.7:c.4779+1G>T		p.X1593_splice	ENST00000222270	NM_014727.1	1593			1	2	FACETS	0.986	0.908	1	0.986	0.908	1	CLONAL	1	TRUE	1	0.58001752042442	2		445	535	SUCCESS
REL	5966	MSKCC	GRCh37	2	61121601	61121601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	274	667	1	ENST00000295025.8:c.223C>T	p.His75Tyr	p.H75Y	ENST00000295025	NM_002908.2	75	Cat/Tat	3/11	1	2	FACETS	0.97	0.912	1	0.97	0.912	1	CLONAL	1	TRUE	1	0.58001752042442	2		668	974	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575439	67575439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	138	295	0	ENST00000274335.5:c.512C>T	p.Ser171Phe	p.S171F	ENST00000274335		171	tCc/tTc	4/15	1	2	FACETS	0.919	0.841	0.999	0.919	0.841	0.999	CLONAL	1	TRUE	1	0.58001752042442	2		295	518	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671296	30671296	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1562080084	NA	P-0016328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	142	338	0	ENST00000376406.3:c.5581C>T	p.Pro1861Ser	p.P1861S	ENST00000376406	NM_014641.2	1861	Cca/Tca	11/15	0.149656536545334	3	FACETS	1	0.98	1	0.616	0.564	0.669	INDETERMINATE	1	TRUE	1	0.58001752042442	3		338	513	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350157	81350157	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	346	389	0	ENST00000222390.5:c.1175A>T	p.Tyr392Phe	p.Y392F	ENST00000222390	NM_000601.4	392	tAt/tTt	10/18	0.58001752042442	3	FACETS	0.894	0.85	0.938	0.894	0.85	0.938	CLONAL	2	TRUE	1	0.58001752042442	3		389	861	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950461	68950461	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	260	503	0	ENST00000288368.4:c.773G>A	p.Gly258Glu	p.G258E	ENST00000288368	NM_024870.2	258	gGa/gAa	7/40	1	2	FACETS	0.984	0.924	1	0.984	0.924	1	CLONAL	1	TRUE	1	0.58001752042442	2		503	911	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492925	8492925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	204	492	0	ENST00000356435.5:c.2404G>A	p.Ala802Thr	p.A802T	ENST00000356435		802	Gcc/Acc	16/35	0.223888337597435	3	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.58001752042442	3		492	851	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0016329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	245	599	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.719169093808001	2		599	661	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	107	423	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.804	0.728	0.883	0.804	0.728	0.883	CLONAL	1	TRUE	1	0.719169093808001	2		423	370	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110689	2110689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs911600402	NA	P-0016329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	328	446	1	ENST00000219476.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000219476	NM_000548.3	332	Gag/Aag	11/42	0.719169093808001	3	FACETS	0.907	0.856	0.96	0.454	0.428	0.48	CLONAL	1	TRUE	1	0.719169093808001	3		447	1367	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0016335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	133	519	1	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.792	0.719	0.868	0.792	0.719	0.868	SUBCLONAL	1	TRUE	1	0.403737766418248	2		520	832	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771319	68771319	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1555509622	NA	P-0016335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	49	107	0	ENST00000261769.5:c.1A>G	p.Met1?	p.M1?	ENST00000261769	NM_004360.3	1	Atg/Gtg	1/16	0.403737766418248	1	FACETS	0.91	0.78	1	0.91	0.78	1	CLONAL	1	TRUE	0	0.403737766418248	1		107	213	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16021255	16021259	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	TAAAA	TAAAA	-	novel	NA	P-0016335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	98	262	0	ENST00000268712.3:c.1998_2002del	p.Tyr666Ter	p.Y666*	ENST00000268712	NM_006311.3	666	taTTTTAac/taac	18/46	0.379545970745433	1	FACETS	0.656	0.586	0.729	0.656	0.586	0.729	SUBCLONAL	1	TRUE	0	0.403737766418248	1		262	591	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0016335-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	154	519	1	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.933	0.854	1	0.933	0.854	1	CLONAL	1	TRUE	1	0.358320091242107	2		520	921	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771319	68771319	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1555509622	NA	P-0016335-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	23	107	0	ENST00000261769.5:c.1A>G	p.Met1?	p.M1?	ENST00000261769	NM_004360.3	1	Atg/Gtg	1/16	0.358320091242107	1	FACETS	0.579	0.454	0.721	0.579	0.454	0.721	SUBCLONAL	1	TRUE	0	0.358320091242107	1		107	182	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0016337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	135	616	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.833	0.756	0.915	0.833	0.756	0.915	CLONAL	1	TRUE	1	0.285291170276965	2		616	1136	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720828	89720828	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0016337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	96	298	0	ENST00000371953.3:c.979A>T	p.Lys327Ter	p.K327*	ENST00000371953	NM_000314.4	327	Aaa/Taa	8/9	0.285291170276965	1	FACETS	0.899	0.802	1	0.899	0.802	1	CLONAL	1	TRUE	0	0.285291170276965	1		298	642	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589656	67589670	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATCCCAGGTGAGTTT	ATCCCAGGTGAGTTT	-	novel	NA	P-0016337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	89	412	0	ENST00000274335.5:c.1419_1425+8del		p.X473_splice	ENST00000274335		473		10/15	1	2	FACETS	0.666	0.589	0.748	0.666	0.589	0.748	SUBCLONAL	1	TRUE	1	0.285291170276965	2		412	937	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151882717	151882717	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0016337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	25	247	0	ENST00000262189.6:c.5009-1G>A		p.X1670_splice	ENST00000262189	NM_170606.2	1670			1	2	FACETS	0.367	0.289	0.458	0.367	0.289	0.458	SUBCLONAL	1	TRUE	1	0.285291170276965	2		247	477	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0016338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	229	450	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.907	0.848	0.968	0.907	0.848	0.968	CLONAL	1	TRUE	1	0.649707559441221	2		450	777	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519985	NA	P-0016338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	451	658	0	ENST00000269305.4:c.857A>T	p.Glu286Val	p.E286V	ENST00000269305	NM_001126112.2	286	gAa/gTa	8/11	0.649707559441221	1	FACETS	0.992	0.952	1	0.992	0.952	1	CLONAL	1	TRUE	0	0.649707559441221	1		658	945	SUCCESS
APC	324	MSKCC	GRCh37	5	112175273	112175273	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123121	NA	P-0016338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	229	340	0	ENST00000257430.4:c.3982C>T	p.Gln1328Ter	p.Q1328*	ENST00000257430	NM_000038.5	1328	Cag/Tag	16/16	1	2	FACETS	0.947	0.886	1	0.947	0.886	1	CLONAL	1	TRUE	1	0.649707559441221	2		340	744	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727429	66727429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	283	399	1	ENST00000307102.5:c.145C>T	p.Arg49Cys	p.R49C	ENST00000307102	NM_002755.3	49	Cgc/Tgc	2/11	0.368638548207234	1	FACETS	0.811	0.767	0.856	0.811	0.767	0.856	INDETERMINATE	1	TRUE	0	0.649707559441221	1		400	725	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006090	22006090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753878524	NA	P-0016338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	272	417	1	ENST00000276925.6:c.313C>T	p.Arg105Trp	p.R105W	ENST00000276925	NM_004936.3	105	Cgg/Tgg	2/2	0.649707559441221	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.649707559441221	1		418	508	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047957	180047957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1460398148	NA	P-0016339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	97	459	1	ENST00000261937.6:c.2218G>A	p.Glu740Lys	p.E740K	ENST00000261937	NM_182925.4	740	Gag/Aag	15/30	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	FALSE	1	0.673430158167489	2		460	284	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0016340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	346	488	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.397332788462723	2	FACETS	0.781	0.743	0.82	0.781	0.743	0.82	SUBCLONAL	2	TRUE	0	0.540669466349053	2		490	819	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285894	39285894	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	146	489	2	ENST00000402219.2:c.265G>T	p.Asp89Tyr	p.D89Y	ENST00000402219	NM_005633.3	89	Gat/Tat	3/23	0.430100525377911	3	FACETS	0.758	0.692	0.828	0.379	0.346	0.414	SUBCLONAL	1	TRUE	1	0.540669466349053	3		491	905	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736166	204736166	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	210	374	2	ENST00000302823.3:c.529del	p.Tyr177IlefsTer10	p.Y177Ifs*10	ENST00000302823	NM_005214.4	175	Ttt/tt	3/4	1	2	FACETS	0.573	0.533	0.613	0.573	0.533	0.613	SUBCLONAL	1	TRUE	1	0.96140817457462	2		376	763	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	126	376	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.371	0.336	0.407	0.371	0.336	0.407	SUBCLONAL	1	TRUE	1	0.96140817457462	2		376	707	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0016341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	75	324	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.307	0.269	0.347	0.307	0.269	0.347	SUBCLONAL	1	TRUE	1	0.96140817457462	2		325	509	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106078	27106078	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	175	467	0	ENST00000324856.7:c.5693del	p.Pro1898HisfsTer25	p.P1898Hfs*25	ENST00000324856	NM_006015.4	1897	Ccc/cc	20/20	1	2	FACETS	0.469	0.432	0.506	0.469	0.432	0.506	SUBCLONAL	1	TRUE	1	0.96140817457462	2		467	777	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0016341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	50	424	0	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	1	2	FACETS	0.117	0.099	0.138	0.117	0.099	0.138	SUBCLONAL	1	TRUE	1	0.96140817457462	2		424	888	SUCCESS
AR	367	MSKCC	GRCh37	X	66766105	66766105	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	114	524	1	ENST00000374690.3:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000374690	NM_000044.3	373	Gga/Aga	1/8	1	2	FACETS	0.261	0.234	0.289	0.261	0.234	0.289	SUBCLONAL	1	TRUE	1	0.96140817457462	2		525	909	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482927	140482927	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	180	599	3	ENST00000288602.6:c.1208del	p.Pro403LeufsTer8	p.P403Lfs*8	ENST00000288602	NM_004333.4	403	cCt/ct	10/18	1	2	FACETS	0.409	0.377	0.442	0.409	0.377	0.442	SUBCLONAL	1	TRUE	1	0.96140817457462	2		602	916	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0016341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	84	176	0	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.489	0.435	0.546	0.489	0.435	0.546	SUBCLONAL	1	TRUE	1	0.96140817457462	2		176	357	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617589	158617589	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121912679	NA	P-0016341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	42	326	0	ENST00000263640.3:c.1067G>A	p.Gly356Asp	p.G356D	ENST00000263640	NM_001105.4	356	gGc/gAc	9/11	1	2	FACETS	0.144	0.119	0.171	0.144	0.119	0.171	SUBCLONAL	1	TRUE	1	0.96140817457462	2		326	608	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696688	47696688	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519971	NA	P-0016341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	61	537	0	ENST00000347630.2:c.260A>G	p.Tyr87Cys	p.Y87C	ENST00000347630	NM_001007230.1	87	tAc/tGc	5/11	1	2	FACETS	0.139	0.119	0.16	0.139	0.119	0.16	SUBCLONAL	1	TRUE	1	0.96140817457462	2		537	916	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777676	9777676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	209	428	0	ENST00000377346.4:c.1012C>T	p.Arg338Trp	p.R338W	ENST00000377346	NM_005026.3	338	Cgg/Tgg	8/24	1	2	FACETS	0.526	0.489	0.564	0.526	0.489	0.564	SUBCLONAL	1	TRUE	1	0.96140817457462	2		428	826	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630626	158630626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912678	NA	P-0016341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	68	428	3	ENST00000263640.3:c.617G>A	p.Arg206His	p.R206H	ENST00000263640	NM_001105.4	206	cGc/cAc	6/11	1	2	FACETS	0.182	0.157	0.208	0.182	0.157	0.208	SUBCLONAL	1	TRUE	1	0.96140817457462	2		431	779	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186804	11186804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755115241	NA	P-0016341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	59	428	0	ENST00000361445.4:c.6401G>A	p.Arg2134Gln	p.R2134Q	ENST00000361445	NM_004958.3	2134	cGg/cAg	46/58	1	2	FACETS	0.163	0.139	0.188	0.163	0.139	0.188	SUBCLONAL	1	TRUE	1	0.96140817457462	2		428	754	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797114	45797114	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587780084	NA	P-0016341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	81	539	0	ENST00000450313.1:c.1301C>A	p.Thr434Lys	p.T434K	ENST00000450313	NM_012222.2	434	aCg/aAg	13/16	1	2	FACETS	0.164	0.144	0.186	0.164	0.144	0.186	SUBCLONAL	1	TRUE	1	0.96140817457462	2		539	1028	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982311	201982311	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1343	249	596	0	ENST00000359651.3:c.690T>A	p.Asp230Glu	p.D230E	ENST00000359651		230	gaT/gaA	6/8	0.96140817457462	3	FACETS	0.482	0.449	0.516	0.241	0.224	0.258	SUBCLONAL	1	TRUE	1	0.96140817457462	3		596	1592	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692769	89692769	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0016341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	160	479	0	ENST00000371953.3:c.254-1G>T		p.X85_splice	ENST00000371953	NM_000314.4	85			1	2	FACETS	0.46	0.423	0.499	0.46	0.423	0.499	SUBCLONAL	1	TRUE	1	0.96140817457462	2		479	723	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692983	89692983	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	54	441	0	ENST00000371953.3:c.467G>T	p.Gly156Val	p.G156V	ENST00000371953	NM_000314.4	156	gGg/gTg	5/9	1	2	FACETS	0.163	0.138	0.189	0.163	0.138	0.189	SUBCLONAL	1	TRUE	1	0.96140817457462	2		441	691	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717712	89717712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782350	NA	P-0016341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	24	501	1	ENST00000371953.3:c.737C>T	p.Pro246Leu	p.P246L	ENST00000371953	NM_000314.4	246	cCg/cTg	7/9	1	2	FACETS	0.067	0.052	0.085	0.067	0.052	0.085	SUBCLONAL	1	TRUE	1	0.96140817457462	2		502	740	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118353205	118353205	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	156	313	0	ENST00000534358.1:c.4081G>T	p.Glu1361Ter	p.E1361*	ENST00000534358	NM_005933.3	1361	Gaa/Taa	8/36	1	2	FACETS	0.545	0.501	0.59	0.545	0.501	0.59	SUBCLONAL	1	TRUE	1	0.96140817457462	2		313	596	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426022	49426022	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	48	473	3	ENST00000301067.7:c.12466del	p.Gln4156AsnfsTer5	p.Q4156Nfs*5	ENST00000301067	NM_003482.3	4156	Caa/aa	39/54	1	2	FACETS	0.128	0.107	0.15	0.128	0.107	0.15	SUBCLONAL	1	TRUE	1	0.96140817457462	2		476	782	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432244	49432245	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0016341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	79	644	0	ENST00000301067.7:c.8894dup	p.Asn2965LysfsTer8	p.N2965Kfs*8	ENST00000301067	NM_003482.3	2965	aac/aaAc	34/54	1	2	FACETS	0.136	0.119	0.155	0.136	0.119	0.155	SUBCLONAL	1	TRUE	1	0.96140817457462	2		644	1206	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347553	89347553	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	201	434	0	ENST00000301030.4:c.5397del	p.Glu1800ArgfsTer163	p.E1800Rfs*163	ENST00000301030	NM_001256183.1	1799	ccC/cc	9/13	1	2	FACETS	0.491	0.456	0.528	0.491	0.456	0.528	SUBCLONAL	1	TRUE	1	0.96140817457462	2		434	851	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976593	7976593	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1333287390	NA	P-0016341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	200	474	1	ENST00000319144.4:c.1799G>A	p.Arg600Gln	p.R600Q	ENST00000319144	NM_001139.2	600	cGg/cAg	14/15	1	2	FACETS	0.507	0.471	0.545	0.507	0.471	0.545	SUBCLONAL	1	TRUE	1	0.96140817457462	2		475	820	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29686022	29686022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	40	340	0	ENST00000356175.3:c.8086C>T	p.Pro2696Ser	p.P2696S	ENST00000356175	NM_000267.3	2696	Ccg/Tcg	55/57	1	2	FACETS	0.163	0.135	0.194	0.163	0.135	0.194	SUBCLONAL	1	TRUE	1	0.96140817457462	2		340	512	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792837	33792848	+	inframe_deletion	In_Frame_Del	DEL	GCTTGATCACCA	GCTTGATCACCA	-	novel	NA	P-0016341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	66	222	1	ENST00000498907.2:c.473_484del	p.Leu158_Lys161del	p.L158_K161del	ENST00000498907	NM_004364.3	158	cTGGTGATCAAGCag/cag	1/1	1	2	FACETS	0.312	0.271	0.356	0.312	0.271	0.356	SUBCLONAL	1	TRUE	1	0.96140817457462	2		223	440	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99175934	99175934	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	212	479	0	ENST00000074304.5:c.1850del	p.Pro617LeufsTer18	p.P617Lfs*18	ENST00000074304	NM_001134224.1	616	Ccc/cc	18/26	1	2	FACETS	0.488	0.453	0.523	0.488	0.453	0.523	SUBCLONAL	1	TRUE	1	0.96140817457462	2		479	904	SUCCESS
ATR	545	MSKCC	GRCh37	3	142238625	142238625	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	92	306	0	ENST00000350721.4:c.4268A>G	p.Glu1423Gly	p.E1423G	ENST00000350721	NM_001184.3	1423	gAg/gGg	24/47	1	2	FACETS	0.448	0.4	0.499	0.448	0.4	0.499	SUBCLONAL	1	TRUE	1	0.96140817457462	2		306	427	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509927	187509927	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555931755	NA	P-0016341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	44	266	1	ENST00000441802.2:c.13586C>T	p.Ala4529Val	p.A4529V	ENST00000441802	NM_005245.3	4529	gCg/gTg	27/27	1	2	FACETS	0.179	0.15	0.212	0.179	0.15	0.212	SUBCLONAL	1	TRUE	1	0.96140817457462	2		267	511	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534385	187534385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778337700	NA	P-0016341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	66	405	1	ENST00000441802.2:c.9341C>T	p.Thr3114Met	p.T3114M	ENST00000441802	NM_005245.3	3114	aCg/aTg	13/27	1	2	FACETS	0.154	0.133	0.177	0.154	0.133	0.177	SUBCLONAL	1	TRUE	1	0.96140817457462	2		406	890	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183343	56183343	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	33	340	0	ENST00000399503.3:c.4253C>A	p.Pro1418His	p.P1418H	ENST00000399503	NM_005921.1	1418	cCt/cAt	18/20	1	2	FACETS	0.131	0.106	0.159	0.131	0.106	0.159	SUBCLONAL	1	TRUE	1	0.96140817457462	2		340	523	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522664	67522664	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	142	319	0	ENST00000274335.5:c.161G>T	p.Gly54Val	p.G54V	ENST00000274335		54	gGc/gTc	1/15	1	2	FACETS	0.558	0.512	0.607	0.558	0.512	0.607	SUBCLONAL	1	TRUE	1	0.96140817457462	2		319	529	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589155	67589156	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAAATA	novel	NA	P-0016341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	81	340	0	ENST00000274335.5:c.1144_1149dup	p.Lys382_Ile383dup	p.K382_I383dup	ENST00000274335		382	-/AAAATA	9/15	1	2	FACETS	0.357	0.315	0.401	0.357	0.315	0.401	SUBCLONAL	1	TRUE	1	0.96140817457462	2		340	472	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469956	157469956	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	172	403	1	ENST00000346085.5:c.2754del	p.Ser919ValfsTer20	p.S919Vfs*20	ENST00000346085	NM_020732.3	917	aCc/ac	9/20	1	2	FACETS	0.516	0.476	0.558	0.516	0.476	0.558	SUBCLONAL	1	TRUE	1	0.96140817457462	2		404	693	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517346	157517346	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	65	490	0	ENST00000346085.5:c.3910A>C	p.Ser1304Arg	p.S1304R	ENST00000346085	NM_020732.3	1304	Agc/Cgc	16/20	1	2	FACETS	0.141	0.122	0.163	0.141	0.122	0.163	SUBCLONAL	1	TRUE	1	0.96140817457462	2		490	957	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938677	76938678	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0016341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	94	542	0	ENST00000373344.5:c.2070dup	p.Leu691ThrfsTer10	p.L691Tfs*10	ENST00000373344	NM_000489.3	690	-/A	9/35	1	2	FACETS	0.199	0.176	0.223	0.199	0.176	0.223	SUBCLONAL	1	TRUE	1	0.96140817457462	2		542	984	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061223	38061228	+	inframe_deletion	In_Frame_Del	DEL	TCTCGA	TCTCGA	-	novel	NA	P-0016342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	174	402	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	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.59158471861044	2		402	517	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50483668	50483668	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	94	201	0	ENST00000394963.4:c.774del	p.Trp258CysfsTer15	p.W258Cfs*15	ENST00000394963	NM_003076.4	258	tGg/tg	7/13	1	2	FACETS	0.709	0.634	0.788	0.709	0.634	0.788	SUBCLONAL	1	TRUE	1	0.59158471861044	2		201	448	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694649	176694657	+	frameshift_variant	Frame_Shift_Del	DEL	TGCAATGAC	TGCAATGAC	GCAATGA	novel	NA	P-0016342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	174	479	2	ENST00000439151.2:c.5233_5241delinsGCAATGA	p.Cys1745AlafsTer4	p.C1745Afs*4	ENST00000439151	NM_022455.4	1745	TGCAATGAC/GCAATGA	15/23	1	2	FACETS	0.82	0.757	0.886	0.82	0.757	0.886	CLONAL	1	TRUE	1	0.59158471861044	2		481	717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28934577	NA	P-0016345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	453	401	0	ENST00000269305.4:c.770T>C	p.Leu257Pro	p.L257P	ENST00000269305	NM_001126112.2	257	cTg/cCg	7/11	0.627478752585064	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.627478752585064	2		401	618	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274018	10274018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1354238435	NA	P-0016345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	193	588	0	ENST00000330684.3:c.251C>T	p.Thr84Met	p.T84M	ENST00000330684	NM_001134407.1	84	aCg/aTg	2/13	0.53332280661719	3	FACETS	0.901	0.834	0.97			1	CLONAL	1	TRUE	NA	0.627478752585064	3		588	897	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22413312	22413312	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	89	162	0	ENST00000344548.3:c.439C>T	p.Arg147Cys	p.R147C	ENST00000344548	NM_001039802.1	147	Cgt/Tgt	6/7	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.627478752585064	2		162	262	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456341	32456341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	212	586	0	ENST00000332351.3:c.551C>T	p.Pro184Leu	p.P184L	ENST00000332351	NM_024426.4	184	cCg/cTg	1/10	0.627036740103969	2	FACETS	0.957	0.893	1	0.479	0.446	0.512	CLONAL	1	TRUE	0	0.627478752585064	2		586	706	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033834	49033934	+	frameshift_variant	Frame_Shift_Del	DEL	AGCCTATCTCCGGCTAAATACACTTTGTGAACGCCTTCTGTCTGAGCACCCAGAATTAGAACATATCATCTGGACCCTTTTCCAGCACACCCTGCAGAATG	AGCCTATCTCCGGCTAAATACACTTTGTGAACGCCTTCTGTCTGAGCACCCAGAATTAGAACATATCATCTGGACCCTTTTCCAGCACACCCTGCAGAATG	-	novel	NA	P-0016345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	261	359	0	ENST00000267163.4:c.1973_2073del	p.Ala658ValfsTer2	p.A658Vfs*2	ENST00000267163	NM_000321.2	657	ctAGCCTATCTCCGGCTAAATACACTTTGTGAACGCCTTCTGTCTGAGCACCCAGAATTAGAACATATCATCTGGACCCTTTTCCAGCACACCCTGCAGAATGag/ctag	20/27	0.576234550761997	3	FACETS	0.837	0.798	0.876	0.837	0.798	0.876	CLONAL	3	TRUE	0	0.627478752585064	3		359	435	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469088	25469093	+	inframe_deletion	In_Frame_Del	DEL	GGCTTT	GGCTTT	-	novel	NA	P-0016345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	252	513	0	ENST00000264709.3:c.1365_1370del	p.Lys455_Pro457delinsAsn	p.K455_P457delinsN	ENST00000264709	NM_175629.2	455	aaAAAGCCc/aac	11/23	0.627478752585064	3	FACETS	0.946	0.884	1			1	CLONAL	1	TRUE	NA	0.627478752585064	3		513	1116	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251578	212251578	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	324	318	0	ENST00000342788.4:c.3481G>A	p.Glu1161Lys	p.E1161K	ENST00000342788	NM_005235.2	1161	Gaa/Aaa	27/28	0.514964905853712	3	FACETS	1	0.993	1	0.816	0.781	0.851	CLONAL	2	TRUE	0	0.627478752585064	3		318	554	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467559	66467559	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	196	389	0	ENST00000273854.3:c.710T>C	p.Val237Ala	p.V237A	ENST00000273854	NM_004439.5	237	gTa/gCa	3/18	0.576234550761997	3	FACETS	1	0.988	1	0.432	0.402	0.463	CLONAL	1	TRUE	0	0.627478752585064	3		389	633	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328347	137328347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	279	571	0	ENST00000481739.1:c.1276C>T	p.Arg426Cys	p.R426C	ENST00000481739	NM_002957.4	426	Cgc/Tgc	10/10	0.627478752585064	2	FACETS	1	0.979	1	0.54	0.509	0.572	CLONAL	1	TRUE	0	0.627478752585064	2		571	823	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	102	641	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.3	2		641	656	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0016348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	72	523	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.996	0.872	1	0.996	0.872	1	CLONAL	1	TRUE	1	0.3	2		523	482	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0016348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	117	332	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.3	2		332	581	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692887	89692887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660535	NA	P-0016348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	53	491	0	ENST00000371953.3:c.371G>A	p.Cys124Tyr	p.C124Y	ENST00000371953	NM_000314.4	124	tGt/tAt	5/9	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.3	2		491	340	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716212	52716212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555791268	NA	P-0016348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	78	513	0	ENST00000322088.6:c.656C>T	p.Ser219Leu	p.S219L	ENST00000322088	NM_014225.5	219	tCg/tTg	6/15	1	2	FACETS	0.868	0.764	0.98	0.868	0.764	0.98	CLONAL	1	TRUE	1	0.3	2		513	599	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159746	20159746	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	58	602	0	ENST00000379607.5:c.13A>G	p.Lys5Glu	p.K5E	ENST00000379607	NM_001412.3	5	Aaa/Gaa	1/7	1	2	FACETS	0.684	0.588	0.789	0.684	0.588	0.789	SUBCLONAL	1	TRUE	1	0.3	2		602	565	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150330	108150330	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	67	446	1	ENST00000278616.4:c.3397G>T	p.Glu1133Ter	p.E1133*	ENST00000278616	NM_000051.3	1133	Gaa/Taa	23/63	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.3	2		447	412	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563080	21563080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1466832911	NA	P-0016348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	94	878	0	ENST00000382592.4:c.839C>T	p.Pro280Leu	p.P280L	ENST00000382592	NM_014572.2	280	cCg/cTg	4/8	1	2	FACETS	0.711	0.631	0.795	0.711	0.631	0.795	SUBCLONAL	1	TRUE	1	0.3	2		878	882	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589147	67589147	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	128	465	0	ENST00000274335.5:c.1135A>G	p.Lys379Glu	p.K379E	ENST00000274335		379	Aaa/Gaa	9/15	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.535479333186307	2		465	474	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097266	178097266	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	280	714	1	ENST00000397062.3:c.448C>T	p.His150Tyr	p.H150Y	ENST00000397062	NM_006164.4	150	Cac/Tac	4/5	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.535479333186307	2		715	1010	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720803	89720804	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs786204892	NA	P-0016349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	51	328	0	ENST00000371953.3:c.955dup	p.Thr319AsnfsTer6	p.T319Nfs*6	ENST00000371953	NM_000314.4	318	-/A	8/9	0.535479333186307	1	FACETS	0.674	0.58	0.774	0.674	0.58	0.774	SUBCLONAL	1	TRUE	0	0.535479333186307	1		328	207	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141569588	141569588	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	260	757	1	ENST00000220592.5:c.696G>T	p.Glu232Asp	p.E232D	ENST00000220592	NM_012154.3	232	gaG/gaT	6/19	1	2	FACETS	0.894	0.838	0.952	0.894	0.838	0.952	CLONAL	1	TRUE	1	0.535479333186307	2		758	1086	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0016350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	104	731	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.174974517742643	5	FACETS	1	0.969	1	0.41	0.366	0.457	CLONAL	1	TRUE	2	0.208379649877773	5		731	1064	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578528	7578528	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	181	872	2	ENST00000269305.4:c.402T>A	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	ttT/ttA	5/11	NA	2	FACETS	0.751	0.692	0.814			1	INDETERMINATE	2	TRUE	NA	0.208379649877773	2		874	1156	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215252	142215252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	77	549	0	ENST00000350721.4:c.5849C>T	p.Ser1950Leu	p.S1950L	ENST00000350721	NM_001184.3	1950	tCa/tTa	34/47	1	2	FACETS	0.935	0.82	1	0.935	0.82	1	CLONAL	1	TRUE	1	0.208379649877773	2		549	790	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382150	152382150	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	74	382	0	ENST00000206249.3:c.1260del	p.Met421TrpfsTer17	p.M421Wfs*17	ENST00000206249	NM_000125.3	420	ggC/gg	6/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.208379649877773	2		382	496	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	217	423	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.674962878924878	2		423	630	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592303	29592303	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1060500303	NA	P-0016352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	185	555	0	ENST00000356175.3:c.4718A>G	p.Tyr1573Cys	p.Y1573C	ENST00000356175	NM_000267.3	1573	tAc/tGc	35/57	0.652786442249372	1	FACETS	0.995	0.934	1	0.995	0.934	1	CLONAL	1	TRUE	0	0.674962878924878	1		555	365	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115397	115115397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866796237	NA	P-0016352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	364	893	1	ENST00000257566.3:c.929G>A	p.Arg310Gln	p.R310Q	ENST00000257566	NM_016569.3	310	cGa/cAa	5/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.674962878924878	2		894	1048	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685583	29685583	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	250	854	3	ENST00000356175.3:c.7993C>T	p.Gln2665Ter	p.Q2665*	ENST00000356175	NM_000267.3	2665	Cag/Tag	54/57	1	2	FACETS	0.83	0.778	0.884	0.83	0.778	0.884	CLONAL	1	TRUE	1	0.674962878924878	2		857	892	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954248	17954248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776850935	NA	P-0016352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	386	990	0	ENST00000458235.1:c.361C>T	p.Arg121Cys	p.R121C	ENST00000458235	NM_000215.3	121	Cgc/Tgc	4/24	1	2	FACETS	0.944	0.898	0.992	0.944	0.898	0.992	CLONAL	1	TRUE	1	0.674962878924878	2		990	1211	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540332	187540332	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	335	715	0	ENST00000441802.2:c.7408G>T	p.Gly2470Ter	p.G2470*	ENST00000441802	NM_005245.3	2470	Gga/Tga	10/27	1	2	FACETS	0.993	0.941	1	0.993	0.941	1	CLONAL	1	TRUE	1	0.674962878924878	2		715	1000	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	40	726	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.837	0.696	0.992	0.837	0.696	0.992	CLONAL	1	TRUE	1	0.245189326601746	2		726	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0016353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	53	488	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.159390009236447	1	FACETS	0.776	0.662	0.9	0.776	0.662	0.9	SUBCLONAL	1	TRUE	0	0.245189326601746	1		490	489	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840006	27840006	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	48	356	0	ENST00000328488.2:c.88G>A	p.Ala30Thr	p.A30T	ENST00000328488	NM_003533.2	30	Gct/Act	1/1	0.189422237034881	5	FACETS	1	0.958	1	0.474	0.401	0.553	CLONAL	1	TRUE	2	0.245189326601746	5		356	377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0016355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	416	800	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.315494347029295	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.334896176772002	2		801	1223	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0016355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	51	514	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.453	0.384	0.528	0.453	0.384	0.528	SUBCLONAL	1	TRUE	1	0.334896176772002	2		514	673	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911541	134911541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	68	531	0	ENST00000398015.3:c.2006C>T	p.Ala669Val	p.A669V	ENST00000398015	NM_004441.4	669	gCg/gTg	11/16	1	2	FACETS	0.408	0.354	0.467	0.408	0.354	0.467	SUBCLONAL	1	TRUE	1	0.334896176772002	2		531	995	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622131	43622131	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	163	662	2	ENST00000355710.3:c.3148C>T	p.Arg1050Ter	p.R1050*	ENST00000355710	NM_020975.4	1050	Cga/Tga	19/20	1	2	FACETS	0.931	0.853	1	0.931	0.853	1	CLONAL	1	TRUE	1	0.334896176772002	2		664	1046	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794062	42794062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	167	582	2	ENST00000575354.2:c.1423G>A	p.Glu475Lys	p.E475K	ENST00000575354	NM_015125.3	475	Gag/Aag	9/20	0.11574103740543	3	FACETS	1	0.985	1	0.651	0.598	0.706	INDETERMINATE	1	TRUE	1	0.334896176772002	3		584	894	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070282	37070283	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	37	423	0	ENST00000231790.2:c.1418dup	p.His473GlnfsTer6	p.H473Qfs*6	ENST00000231790	NM_000249.3	473	cat/cAat	13/19	1	2	FACETS	0.525	0.433	0.628	0.525	0.433	0.628	SUBCLONAL	1	TRUE	1	0.334896176772002	2		423	421	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856016	151856016	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	160	798	0	ENST00000262189.6:c.11602del	p.Arg3868GlyfsTer21	p.R3868Gfs*21	ENST00000262189	NM_170606.2	3868	Agg/gg	44/59	1	2	FACETS	0.51	0.467	0.555	0.51	0.467	0.555	SUBCLONAL	1	TRUE	1	0.637541939126708	2		798	984	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	48	486	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.7	0.59	0.822	0.7	0.59	0.822	SUBCLONAL	1	TRUE	1	0.17	2		486	807	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155700	56155701	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1338345984	NA	P-0016358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	73	603	0	ENST00000399503.3:c.793_794del	p.Glu265IlefsTer35	p.E265Ifs*35	ENST00000399503	NM_005921.1	264	tcAGaa/tcaa	3/20	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.17	2		603	806	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160538	56160577	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAATAAAAAAAAATGTTGTGAAGTTTCAGAGTGGCAGAAT	TAATAAAAAAAAATGTTGTGAAGTTTCAGAGTGGCAGAAT	-	novel	NA	P-0016358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	27	314	0	ENST00000399503.3:c.835-23_851del		p.X279_splice	ENST00000399503	NM_005921.1	279		4/20	1	2	FACETS	0.689	0.547	0.851	0.689	0.547	0.851	SUBCLONAL	1	TRUE	1	0.17	2		314	461	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836323	151836323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	62	613	0	ENST00000262189.6:c.14482del	p.Arg4828AlafsTer7	p.R4828Afs*7	ENST00000262189	NM_170606.2	4828	Cgc/gc	57/59	1	2	FACETS	0.814	0.701	0.937	0.814	0.701	0.937	CLONAL	1	TRUE	1	0.17	2		613	896	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0016361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	883	936	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	2	TRUE	NA	0.598690601216092	2		938	1344	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0016361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	231	547	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.598690601216092	3	FACETS	1	0.975	1	0.545	0.508	0.583	CLONAL	1	TRUE	1	0.598690601216092	3		547	920	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0016361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	211	393	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.598690601216092	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.598690601216092	1		393	456	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	234	256	0	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.598690601216092	2		256	763	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610306	10610306	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	493	654	0	ENST00000171111.5:c.404G>T	p.Arg135Leu	p.R135L	ENST00000171111	NM_203500.1	135	cGc/cTc	2/6	0.598690601216092	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.598690601216092	1		654	1026	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019807	123019807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1174668840	NA	P-0016361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	269	555	0	ENST00000355640.3:c.295G>A	p.Glu99Lys	p.E99K	ENST00000355640		99	Gaa/Aaa	2/7	1	2	FACETS	0.884	0.83	0.94	0.884	0.83	0.94	CLONAL	1	TRUE	1	0.598690601216092	2		555	1016	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1042200	1042200	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	983	675	0	ENST00000358495.3:c.25C>G	p.Leu9Val	p.L9V	ENST00000358495	NM_134424.2	9	Ctt/Gtt	2/12	0.488248606078186	4	FACETS	0.953	0.928	0.977	0.953	0.928	0.977	CLONAL	3	TRUE	1	0.598690601216092	4		675	1837	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843390	3843390	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	214	311	0	ENST00000262367.5:c.1213C>T	p.Gln405Ter	p.Q405*	ENST00000262367	NM_004380.2	405	Caa/Taa	4/31	1	2	FACETS	0.987	0.921	1	0.987	0.921	1	CLONAL	1	TRUE	1	0.598690601216092	2		311	724	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785816	50785816	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	150	364	0	ENST00000398568.2:c.806T>C	p.Met269Thr	p.M269T	ENST00000398568	NM_001042412.1	269	aTg/aCg	4/18	1	2	FACETS	0.949	0.873	1	0.949	0.873	1	CLONAL	1	TRUE	1	0.598690601216092	2		364	528	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782190	56782190	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	211	327	0	ENST00000308159.5:c.31C>T	p.Gln11Ter	p.Q11*	ENST00000308159	NM_014669.4	11	Cag/Tag	2/22	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.598690601216092	2		327	686	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78519576	78519576	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	297	410	0	ENST00000306801.3:c.147G>C	p.Trp49Cys	p.W49C	ENST00000306801	NM_020761.2	49	tgG/tgC	1/34	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.598690601216092	2		410	907	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290010	15290010	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2096	393	643	0	ENST00000263388.2:c.3544T>C	p.Cys1182Arg	p.C1182R	ENST00000263388	NM_000435.2	1182	Tgc/Cgc	22/33	0.598690601216092	5	FACETS	1	0.947	1			1	CLONAL	1	TRUE	NA	0.598690601216092	5		643	2489	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257764	198257764	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	303	595	1	ENST00000335508.6:c.3688G>T	p.Val1230Phe	p.V1230F	ENST00000335508	NM_012433.2	1230	Gtt/Ttt	24/25	1	2	FACETS	0.949	0.894	1	0.949	0.894	1	CLONAL	1	TRUE	1	0.598690601216092	2		596	1067	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30954244	30954244	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	247	523	0	ENST00000375687.4:c.115G>C	p.Glu39Gln	p.E39Q	ENST00000375687	NM_015338.5	39	Gag/Cag	2/13	1	2	FACETS	0.869	0.814	0.927	0.869	0.814	0.927	CLONAL	1	TRUE	1	0.598690601216092	2		523	949	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171749	36171749	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	171	304	0	ENST00000300305.3:c.816G>T	p.Gln272His	p.Q272H	ENST00000300305		272	caG/caT	7/8	1	2	FACETS	0.905	0.836	0.976	0.905	0.836	0.976	CLONAL	1	TRUE	1	0.598690601216092	2		304	631	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86681123	86681123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs925782039	NA	P-0016361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	149	323	0	ENST00000274376.6:c.2764C>T	p.Pro922Ser	p.P922S	ENST00000274376	NM_002890.2	922	Cca/Tca	22/25	0.30182680254179	1	FACETS	0.794	0.732	0.858	0.794	0.732	0.858	INDETERMINATE	1	TRUE	0	0.598690601216092	1		323	439	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932369	39932369	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	519	682	0	ENST00000378444.4:c.2230G>C	p.Glu744Gln	p.E744Q	ENST00000378444	NM_001123385.1	744	Gag/Cag	4/15	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.598690601216092	2		682	1496	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888737	76888737	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	285	670	0	ENST00000373344.5:c.5092C>G	p.Arg1698Gly	p.R1698G	ENST00000373344	NM_000489.3	1698	Cgg/Ggg	19/35	1	2	FACETS	0.895	0.842	0.949	0.895	0.842	0.949	CLONAL	1	TRUE	1	0.598690601216092	2		670	1064	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039504	49039506	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	GGT	GGT	C	novel	NA	P-0016361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	587	530	0	ENST00000267163.4:c.2489_2489+2delinsC		p.X830_splice	ENST00000267163	NM_000321.2	830		23/27	0.542619704607789	3	FACETS	0.904	0.876	0.931	0.904	0.876	0.931	CLONAL	3	TRUE	0	0.598690601216092	3		530	940	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	56	423	0				ENST00000310581	NM_198253.2	-/1132			0.160256533476917	0	FACETS	0.681	0.603	0.76			1	INDETERMINATE	1	FALSE	0	0.5780564839083	0		423	120	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339624	70339624	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	12	355	0	ENST00000374080.3:c.293A>G	p.Gln98Arg	p.Q98R	ENST00000374080		98	cAg/cGg	3/45	1	1	FACETS	0.138	0.097	0.189	0.138	0.097	0.189	SUBCLONAL	1	FALSE	0	0.5780564839083	1		355	214	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	455	726	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.297852079801186	5	FACETS	1	0.991	1	1	0.996	1	CLONAL	5	FALSE	1	0.329216821848129	5		726	764	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577569	7577569	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519981	NA	P-0016364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	335	501	1	ENST00000269305.4:c.712T>C	p.Cys238Arg	p.C238R	ENST00000269305	NM_001126112.2	238	Tgt/Cgt	7/11	0.515173613845993	2	FACETS	0.977	0.932	1	0.977	0.932	1	CLONAL	2	TRUE	0	0.517430690891974	2		502	663	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589580	67589606	+	inframe_deletion	In_Frame_Del	DEL	AATTACATGAATATAACACTCAGTTTC	AATTACATGAATATAACACTCAGTTTC	-	novel	NA	P-0016364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	324	434	0	ENST00000274335.5:c.1345_1371del	p.Leu449_Gln457del	p.L449_Q457del	ENST00000274335		448	aAATTACATGAATATAACACTCAGTTTCaa/aaa	10/15	0.517430690891974	3	FACETS	0.905	0.858	0.953			1	CLONAL	2	TRUE	NA	0.517430690891974	3		434	871	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003199	143003199	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	372	489	0	ENST00000262992.4:c.2627T>A	p.Leu876Gln	p.L876Q	ENST00000262992	NM_001101669.1	876	cTg/cAg	23/24	0.778426816218946	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.778426816218946	3		489	616	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	764	496	2	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.778426816218946	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.778426816218946	3		498	883	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	143	393	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.778426816218946	3	FACETS	1	0.931	1	0.508	0.466	0.552	CLONAL	1	TRUE	1	0.778426816218946	3		393	502	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	366	483	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.757505490643701	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	2	0.778426816218946	4		483	820	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740623	58740624	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs763475304	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	711	739	2	ENST00000305921.3:c.1535dup	p.Asn512LysfsTer16	p.N512Kfs*16	ENST00000305921	NM_003620.3	510	caa/cAaa	6/6	0.778426816218946	5	FACETS	0.882	0.853	0.91	0.882	0.853	0.91	CLONAL	3	TRUE	2	0.778426816218946	5		741	1497	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068427	16068427	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	11	107	0	ENST00000268712.3:c.484G>T	p.Gly162Trp	p.G162W	ENST00000268712	NM_006311.3	162	Ggg/Tgg	5/46	0.778426816218946	3	FACETS	0.312	0.216	0.429	0.104	0.072	0.143	SUBCLONAL	1	TRUE	0	0.778426816218946	3		107	126	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87338624	87338624	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	157	446	1	ENST00000277120.3:c.720G>T	p.Met240Ile	p.M240I	ENST00000277120		240	atG/atT	7/19	0.778426816218946	3	FACETS	1	0.922	1	0.5	0.461	0.541	CLONAL	1	TRUE	1	0.778426816218946	3		447	560	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221340	1221340	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	441	488	1	ENST00000326873.7:c.862+1G>C		p.X288_splice	ENST00000326873	NM_000455.4	288			0.356873945387356	4	FACETS	0.98	0.958	1			1	INDETERMINATE	4	TRUE	NA	0.778426816218946	4		489	514	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096864	11096864	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	578	789	0	ENST00000358026.2:c.356-1G>T		p.X119_splice	ENST00000358026	NM_001128849.1	119			0.778426816218946	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.778426816218946	2		789	681	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189795	11189795	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	143	337	0	ENST00000361445.4:c.5714G>A	p.Arg1905Lys	p.R1905K	ENST00000361445	NM_004958.3	1905	aGa/aAa	40/58	0.778426816218946	3	FACETS	1	0.952	1	0.526	0.483	0.571	CLONAL	1	TRUE	1	0.778426816218946	3		337	485	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245421	16245421	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	115	346	0	ENST00000375759.3:c.1396G>T	p.Asp466Tyr	p.D466Y	ENST00000375759	NM_015001.2	466	Gat/Tat	7/15	0.778426816218946	3	FACETS	0.786	0.711	0.865	0.393	0.355	0.433	SUBCLONAL	1	TRUE	1	0.778426816218946	3		346	522	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933472	36933472	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	436	571	0	ENST00000361632.4:c.1815G>T	p.Gln605His	p.Q605H	ENST00000361632		605	caG/caT	13/16	0.778426816218946	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.778426816218946	3		571	725	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652423	206652424	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	198	581	0	ENST00000367120.3:c.1135dup	p.Leu379ProfsTer10	p.L379Pfs*10	ENST00000367120	NM_014002.3	377	agc/agCc	10/22	0.757505490643701	4	FACETS	0.855	0.791	0.921	0.428	0.395	0.461	CLONAL	1	TRUE	2	0.778426816218946	4		581	1058	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226551695	226551695	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	557	596	0	ENST00000366794.5:c.2735A>C	p.Gln912Pro	p.Q912P	ENST00000366794	NM_001618.3	912	cAg/cCg	20/23	0.757505490643701	4	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	2	0.778426816218946	4		596	1092	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552753	226552753	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	460	451	0	ENST00000366794.5:c.2608G>C	p.Ala870Pro	p.A870P	ENST00000366794	NM_001618.3	870	Gct/Cct	19/23	0.757505490643701	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	2	0.778426816218946	4		451	947	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332609	70332609	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	280	638	1	ENST00000373644.4:c.514C>A	p.Leu172Ile	p.L172I	ENST00000373644	NM_030625.2	172	Cta/Ata	2/12	0.778426816218946	3	FACETS	1	0.99	1	0.607	0.572	0.643	CLONAL	1	TRUE	1	0.778426816218946	3		639	823	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405200	70405200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	442	684	0	ENST00000373644.4:c.2714C>T	p.Ser905Leu	p.S905L	ENST00000373644	NM_030625.2	905	tCa/tTa	4/12	0.778426816218946	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.778426816218946	3		684	711	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450967	70450967	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	239	622	0	ENST00000373644.4:c.5807C>G	p.Pro1936Arg	p.P1936R	ENST00000373644	NM_030625.2	1936	cCt/cGt	12/12	0.778426816218946	3	FACETS	1	0.984	1	0.573	0.537	0.61	CLONAL	1	TRUE	1	0.778426816218946	3		622	744	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633552	69633552	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs281860301	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	323	291	1	ENST00000334134.2:c.150C>A	p.Cys50Ter	p.C50*	ENST00000334134	NM_005247.2	50	tgC/tgA	1/3	0.775365381110069	4	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.778426816218946	4		292	664	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948306	71948306	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1199544899	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	610	794	0	ENST00000298229.2:c.3018G>T	p.Arg1006Ser	p.R1006S	ENST00000298229	NM_001567.3	1006	agG/agT	26/28	0.775365381110069	4	FACETS	1	0.987	1			1	CLONAL	2	TRUE	NA	0.778426816218946	4		794	1328	SUCCESS
EED	8726	MSKCC	GRCh37	11	85956305	85956305	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	109	251	0	ENST00000263360.6:c.34G>T	p.Gly12Ter	p.G12*	ENST00000263360	NM_003797.3	12	Gga/Tga	1/12	0.778426816218946	5	FACETS	0.823	0.739	0.911	0.165	0.147	0.183	CLONAL	1	TRUE	0	0.778426816218946	5		251	738	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998256	100998256	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1344139364	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	413	219	0	ENST00000325455.5:c.1546G>T	p.Gly516Cys	p.G516C	ENST00000325455	NM_001202474.3	516	Ggc/Tgc	1/8	0.778426816218946	5	FACETS	1	0.991	1	0.657	0.632	0.682	CLONAL	3	TRUE	0	0.778426816218946	5		219	700	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106396	108106396	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	300	237	0	ENST00000278616.4:c.332-1G>T		p.X111_splice	ENST00000278616	NM_000051.3	111			0.778426816218946	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	4	TRUE	0	0.778426816218946	4		237	341	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190784	108190784	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	151	387	0	ENST00000278616.4:c.6451A>T	p.Arg2151Ter	p.R2151*	ENST00000278616	NM_000051.3	2151	Aga/Tga	44/63	0.778426816218946	4	FACETS	1	0.959	1	0.268	0.246	0.292	CLONAL	1	TRUE	0	0.778426816218946	4		387	643	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435986	49435986	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	380	544	0	ENST00000301067.7:c.5995A>G	p.Asn1999Asp	p.N1999D	ENST00000301067	NM_003482.3	1999	Aac/Gac	28/54	0.750927588653558	5	FACETS	1	0.957	1			1	CLONAL	2	TRUE	NA	0.778426816218946	5		544	1052	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112197	115112197	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	313	437	0	ENST00000257566.3:c.1543G>T	p.Gly515Trp	p.G515W	ENST00000257566	NM_016569.3	515	Ggg/Tgg	7/8	0.681188545091166	4	FACETS	0.964	0.915	1	0.964	0.915	1	CLONAL	2	TRUE	2	0.778426816218946	4		437	742	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215877	133215877	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	200	262	0	ENST00000320574.5:c.5386A>G	p.Lys1796Glu	p.K1796E	ENST00000320574	NM_006231.2	1796	Aag/Gag	40/49	0.681188545091166	4	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	2	0.778426816218946	4		262	456	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592634	28592634	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	219	656	0	ENST00000241453.7:c.2511G>T	p.Met837Ile	p.M837I	ENST00000241453	NM_004119.2	837	atG/atT	20/24	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.778426816218946	2		656	552	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515036	103515036	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	131	309	0	ENST00000355739.4:c.1537G>C	p.Ala513Pro	p.A513P	ENST00000355739	NM_000123.3	513	Gca/Cca	8/15	0.737632353731962	3	FACETS	1	0.94	1	0.517	0.473	0.563	CLONAL	1	TRUE	1	0.778426816218946	3		309	452	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435972	110435972	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1171816938	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	553	692	0	ENST00000375856.3:c.2429A>G	p.Tyr810Cys	p.Y810C	ENST00000375856	NM_003749.2	810	tAc/tGc	1/2	0.737632353731962	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.778426816218946	3		692	939	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437019	110437019	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	40	75	0	ENST00000375856.3:c.1382C>G	p.Pro461Arg	p.P461R	ENST00000375856	NM_003749.2	461	cCg/cGg	1/2	0.737632353731962	3	FACETS	1	0.852	1	0.503	0.426	0.585	CLONAL	1	TRUE	1	0.778426816218946	3		75	142	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557641	95557641	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	521	735	2	ENST00000393063.1:c.5426G>T	p.Gly1809Val	p.G1809V	ENST00000393063	NM_030621.3	1809	gGg/gTg	26/28	0.778426816218946	3	FACETS	0.974	0.939	1	0.974	0.939	1	CLONAL	2	TRUE	1	0.778426816218946	3		737	955	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643430	38643434	+	frameshift_variant	Frame_Shift_Del	DEL	TAAGT	TAAGT	-	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	252	655	0	ENST00000299084.4:c.906_910del	p.Leu302PhefsTer9	p.L302Ffs*9	ENST00000299084	NM_152594.2	300	acTAAGTta/acta	7/7	0.773435791498424	3	FACETS	1	0.955	1	0.511	0.479	0.544	CLONAL	1	TRUE	1	0.778426816218946	3		655	880	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632578	3632578	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	210	720	0	ENST00000294008.3:c.5270G>A	p.Arg1757Lys	p.R1757K	ENST00000294008	NM_032444.2	1757	aGg/aAg	15/15	0.226558946634246	4	FACETS	1	0.973	1	0.273	0.253	0.293	INDETERMINATE	1	TRUE	0	0.778426816218946	4		720	880	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857424	9857424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1036750557	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	171	450	0	ENST00000330684.3:c.3977G>A	p.Gly1326Asp	p.G1326D	ENST00000330684	NM_001134407.1	1326	gGc/gAc	13/13	0.226558946634246	4	FACETS	1	0.985	1	0.315	0.291	0.34	INDETERMINATE	1	TRUE	0	0.778426816218946	4		450	620	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349055	11349055	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	158	366	0	ENST00000332029.2:c.281G>C	p.Arg94Pro	p.R94P	ENST00000332029	NM_003745.1	94	cGc/cCc	2/2	0.226558946634246	4	FACETS	1	0.987	1	0.346	0.319	0.374	INDETERMINATE	1	TRUE	0	0.778426816218946	4		366	521	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134479	30134479	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	214	435	2	ENST00000263025.4:c.52G>T	p.Glu18Ter	p.E18*	ENST00000263025	NM_002746.2	18	Gag/Tag	1/9	0.226558946634246	4	FACETS	0.78	0.729	0.832	0.39	0.364	0.416	INDETERMINATE	2	TRUE	0	0.778426816218946	4		437	627	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50810107	50810107	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	145	558	0	ENST00000398568.2:c.931A>T	p.Arg311Trp	p.R311W	ENST00000398568	NM_001042412.1	311	Agg/Tgg	6/18	0.226558946634246	4	FACETS	1	0.943	1	0.26	0.237	0.283	INDETERMINATE	1	TRUE	0	0.778426816218946	4		558	638	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50810140	50810140	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1261828777	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	444	667	0	ENST00000398568.2:c.964G>T	p.Gly322Cys	p.G322C	ENST00000398568	NM_001042412.1	322	Ggt/Tgt	6/18	0.226558946634246	4	FACETS	0.967	0.934	1	0.726	0.7	0.75	INDETERMINATE	3	TRUE	0	0.778426816218946	4		667	699	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984642	72984642	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	233	660	0	ENST00000268489.5:c.2942G>T	p.Gly981Val	p.G981V	ENST00000268489	NM_006885.3	981	gGg/gTg	3/10	0.226558946634246	4	FACETS	1	0.989	1	0.318	0.297	0.34	INDETERMINATE	1	TRUE	0	0.778426816218946	4		660	837	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667841	37667841	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	448	573	2	ENST00000447079.4:c.2726G>T	p.Gly909Val	p.G909V	ENST00000447079	NM_015083.1	909	gGa/gTa	8/14	0.778426816218946	5	FACETS	1	0.963	1	0.672	0.642	0.703	CLONAL	2	TRUE	2	0.778426816218946	5		575	1237	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868590	37868590	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	181	434	1	ENST00000269571.5:c.1037G>T	p.Gly346Val	p.G346V	ENST00000269571		346	gGc/gTc	9/27	0.778426816218946	5	FACETS	1	0.969	1	0.366	0.337	0.395	CLONAL	1	TRUE	2	0.778426816218946	5		435	919	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226531	41226531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	322	486	0	ENST00000357654.3:c.4492C>T	p.Pro1498Ser	p.P1498S	ENST00000357654	NM_007294.3	1498	Cct/Tct	14/23	0.778426816218946	5	FACETS	0.922	0.873	0.973	0.615	0.582	0.649	CLONAL	2	TRUE	2	0.778426816218946	5		486	972	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110161	3110161	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	354	438	1	ENST00000078429.4:c.151G>T	p.Gly51Trp	p.G51W	ENST00000078429	NM_002067.2	51	Ggg/Tgg	2/7	0.778426816218946	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.778426816218946	2		439	423	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11172484	11172484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	553	556	0	ENST00000358026.2:c.5032G>A	p.Glu1678Lys	p.E1678K	ENST00000358026	NM_001128849.1	1678	Gaa/Aaa	36/36	0.778426816218946	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.778426816218946	2		556	683	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281190	15281190	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	566	719	0	ENST00000263388.2:c.5066G>T	p.Gly1689Val	p.G1689V	ENST00000263388	NM_000435.2	1689	gGt/gTt	27/33	0.778426816218946	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.778426816218946	2		719	642	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349664	15349664	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	179	526	0	ENST00000263377.2:c.3910G>T	p.Val1304Leu	p.V1304L	ENST00000263377	NM_058243.2	1304	Gtg/Ttg	19/20	0.778426816218946	2	FACETS	1	0.968	1	0.532	0.496	0.569	CLONAL	1	TRUE	0	0.778426816218946	2		526	432	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902217	50902217	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	539	658	0	ENST00000440232.2:c.109G>T	p.Asp37Tyr	p.D37Y	ENST00000440232	NM_002691.3	37	Gac/Tac	2/27	0.737632353731962	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.778426816218946	3		658	881	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716208	52716208	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	163	442	0	ENST00000322088.6:c.652G>T	p.Asp218Tyr	p.D218Y	ENST00000322088	NM_014225.5	218	Gac/Tac	6/15	0.737632353731962	3	FACETS	1	0.964	1	0.537	0.495	0.579	CLONAL	1	TRUE	1	0.778426816218946	3		442	542	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467169	25467169	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	207	510	0	ENST00000264709.3:c.1706C>G	p.Pro569Arg	p.P569R	ENST00000264709	NM_175629.2	569	cCg/cGg	15/23	0.737632353731962	3	FACETS	1	0.96	1	0.521	0.485	0.558	CLONAL	1	TRUE	1	0.778426816218946	3		510	709	SUCCESS
ALK	238	MSKCC	GRCh37	2	29430103	29430103	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	425	562	0	ENST00000389048.3:c.3872T>A	p.Leu1291Gln	p.L1291Q	ENST00000389048	NM_004304.4	1291	cTg/cAg	26/29	0.737632353731962	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.778426816218946	3		562	740	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010438	48010438	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	252	532	0	ENST00000234420.5:c.66G>T	p.Lys22Asn	p.K22N	ENST00000234420	NM_000179.2	22	aaG/aaT	1/10	0.737632353731962	3	FACETS	1	0.982	1	0.557	0.522	0.592	CLONAL	1	TRUE	1	0.778426816218946	3		532	808	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248497	212248497	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	485	379	0	ENST00000342788.4:c.3770A>T	p.Asp1257Val	p.D1257V	ENST00000342788	NM_005235.2	1257	gAc/gTc	28/28	0.778426816218946	5	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	2	0.778426816218946	5		379	842	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514462	41514462	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	546	528	0	ENST00000373198.4:c.199C>G	p.Gln67Glu	p.Q67E	ENST00000373198	NM_133170.3	67	Cag/Gag	2/32	0.778426816218946	5	FACETS	0.975	0.94	1	0.975	0.94	1	CLONAL	3	TRUE	2	0.778426816218946	5		528	1040	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458266	12458266	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	507	615	2	ENST00000287820.6:c.883A>T	p.Ile295Phe	p.I295F	ENST00000287820	NM_015869.4	295	Atc/Ttc	6/7	0.778426816218946	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.778426816218946	2		617	627	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72881562	72881562	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	409	421	0	ENST00000325599.8:c.557G>C	p.Arg186Pro	p.R186P	ENST00000325599	NM_018130.2	186	cGc/cCc	5/11	0.778426816218946	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.778426816218946	3		421	713	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259500	89259500	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	182	458	0	ENST00000336596.2:c.644C>A	p.Thr215Lys	p.T215K	ENST00000336596	NM_005233.5	215	aCg/aAg	3/17	0.778426816218946	3	FACETS	1	0.98	1	0.578	0.537	0.62	CLONAL	1	TRUE	1	0.778426816218946	3		458	562	SUCCESS
ATR	545	MSKCC	GRCh37	3	142218552	142218552	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	196	525	0	ENST00000350721.4:c.5297G>A	p.Trp1766Ter	p.W1766*	ENST00000350721	NM_001184.3	1766	tGg/tAg	31/47	0.778426816218946	3	FACETS	0.925	0.859	0.994	0.463	0.429	0.497	CLONAL	1	TRUE	1	0.778426816218946	3		525	756	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961433	1961433	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	245	575	1	ENST00000382891.5:c.3221G>T	p.Gly1074Val	p.G1074V	ENST00000382891	NM_133335.3	1074	gGg/gTg	17/22	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.778426816218946	2		576	564	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129934	55129934	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	257	625	0	ENST00000257290.5:c.468G>T	p.Glu156Asp	p.E156D	ENST00000257290	NM_006206.4	156	gaG/gaT	4/23	0.778426816218946	3	FACETS	1	0.956	1	0.512	0.48	0.545	CLONAL	1	TRUE	1	0.778426816218946	3		625	896	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143129682	143129682	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	322	436	0	ENST00000262992.4:c.968G>A	p.Gly323Glu	p.G323E	ENST00000262992	NM_001101669.1	323	gGg/gAg	12/24	0.778426816218946	3	FACETS	0.994	0.95	1	0.994	0.95	1	CLONAL	2	TRUE	1	0.778426816218946	3		436	578	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541321	187541321	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	311	425	0	ENST00000441802.2:c.6419A>C	p.Gln2140Pro	p.Q2140P	ENST00000441802	NM_005245.3	2140	cAa/cCa	10/27	0.778426816218946	3	FACETS	0.97	0.926	1	0.97	0.926	1	CLONAL	2	TRUE	1	0.778426816218946	3		425	572	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659229	86659229	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	341	436	0	ENST00000274376.6:c.1518T>G	p.Tyr506Ter	p.Y506*	ENST00000274376	NM_002890.2	506	taT/taG	11/25	0.778426816218946	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.778426816218946	2		436	406	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031947	26031947	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	139	342	0	ENST00000244661.2:c.342T>A	p.His114Gln	p.H114Q	ENST00000244661	NM_003537.3	114	caT/caA	1/1	0.778426816218946	3	FACETS	1	0.978	1	0.591	0.543	0.64	CLONAL	1	TRUE	1	0.778426816218946	3		342	420	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032071	26032071	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	133	325	0	ENST00000244661.2:c.218G>C	p.Arg73Pro	p.R73P	ENST00000244661	NM_003537.3	73	cGa/cCa	1/1	0.778426816218946	3	FACETS	0.963	0.88	1	0.481	0.44	0.525	CLONAL	1	TRUE	1	0.778426816218946	3		325	493	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679762	30679762	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	183	510	0	ENST00000376406.3:c.1957G>T	p.Asp653Tyr	p.D653Y	ENST00000376406	NM_014641.2	653	Gac/Tac	5/15	0.778426816218946	3	FACETS	1	0.955	1	0.52	0.482	0.559	CLONAL	1	TRUE	1	0.778426816218946	3		510	628	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120786	94120786	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	481	560	0	ENST00000369303.4:c.265T>A	p.Trp89Arg	p.W89R	ENST00000369303	NM_004440.3	89	Tgg/Agg	3/17	0.681188545091166	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.778426816218946	4		560	1045	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015880	112015880	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	504	625	0	ENST00000368678.4:c.1061G>T	p.Gly354Val	p.G354V	ENST00000368678		354	gGa/gTa	10/13	0.681188545091166	4	FACETS	0.991	0.951	1	0.991	0.951	1	CLONAL	2	TRUE	2	0.778426816218946	4		625	1162	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117650564	117650564	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	519	736	0	ENST00000368508.3:c.5294G>T	p.Ser1765Ile	p.S1765I	ENST00000368508	NM_002944.2	1765	aGt/aTt	32/43	0.681188545091166	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	2	0.778426816218946	4		736	1186	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522167	157522167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	462	487	0	ENST00000346085.5:c.4439G>A	p.Gly1480Asp	p.G1480D	ENST00000346085	NM_020732.3	1480	gGc/gAc	18/20	0.778426816218946	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.778426816218946	2		487	521	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346550	81346550	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	252	365	0	ENST00000222390.5:c.1403G>T	p.Arg468Leu	p.R468L	ENST00000222390	NM_000601.4	468	cGt/cTt	11/18	0.681188545091166	4	FACETS	0.915	0.863	0.969	0.915	0.863	0.969	CLONAL	2	TRUE	2	0.778426816218946	4		365	629	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942860	68942860	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	241	656	0	ENST00000288368.4:c.672A>T	p.Leu224Phe	p.L224F	ENST00000288368	NM_024870.2	224	ttA/ttT	6/40	0.778426816218946	3	FACETS	0.981	0.918	1	0.49	0.459	0.523	CLONAL	1	TRUE	1	0.778426816218946	3		656	877	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956825	68956825	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs184081186	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	363	483	0	ENST00000288368.4:c.943G>A	p.Ala315Thr	p.A315T	ENST00000288368	NM_024870.2	315	Gct/Act	8/40	0.778426816218946	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.778426816218946	3		483	625	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68999994	68999994	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	445	649	0	ENST00000288368.4:c.2063G>T	p.Gly688Val	p.G688V	ENST00000288368	NM_024870.2	688	gGc/gTc	19/40	0.778426816218946	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.778426816218946	3		649	794	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375935	8375935	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	155	322	0	ENST00000356435.5:c.4661+1G>T		p.X1554_splice	ENST00000356435		1554			0.778426816218946	3	FACETS	1	0.926	1	0.335	0.308	0.363	CLONAL	1	TRUE	0	0.778426816218946	3		322	550	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389306	8389306	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	776	675	0	ENST00000356435.5:c.4312G>T	p.Asp1438Tyr	p.D1438Y	ENST00000356435		1438	Gac/Tac	26/35	0.778426816218946	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.778426816218946	3		675	903	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974739	21974739	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	235	289	0	ENST00000304494.5:c.88G>T	p.Ala30Ser	p.A30S	ENST00000304494	NM_000077.4	30	Gcg/Tcg	1/3	0.778426816218946	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.778426816218946	1		289	283	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158131	27158131	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	161	495	0	ENST00000380036.4:c.355C>G	p.Arg119Gly	p.R119G	ENST00000380036	NM_000459.3	119	Cgt/Ggt	2/23	0.778426816218946	1	FACETS	0.679	0.632	0.727	0.679	0.632	0.727	SUBCLONAL	1	TRUE	0	0.778426816218946	1		495	372	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285691	87285691	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	305	411	0	ENST00000277120.3:c.28C>A	p.Pro10Thr	p.P10T	ENST00000277120		10	Ccc/Acc	2/19	0.778426816218946	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.778426816218946	3		411	503	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342754	87342754	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	472	629	0	ENST00000277120.3:c.1039C>A	p.Gln347Lys	p.Q347K	ENST00000277120		347	Cag/Aag	9/19	0.778426816218946	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.778426816218946	3		629	768	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211371	98211371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs970679518	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	358	530	0	ENST00000331920.6:c.3784C>T	p.Pro1262Ser	p.P1262S	ENST00000331920	NM_000264.3	1262	Ccc/Tcc	22/24	0.778426816218946	3	FACETS	0.955	0.914	0.996	0.955	0.914	0.996	CLONAL	2	TRUE	1	0.778426816218946	3		530	669	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904874	101904874	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	183	415	0	ENST00000374994.4:c.862C>G	p.Leu288Val	p.L288V	ENST00000374994	NM_004612.2	288	Ctt/Gtt	5/9	0.778426816218946	3	FACETS	1	0.962	1	0.528	0.49	0.568	CLONAL	1	TRUE	1	0.778426816218946	3		415	618	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759791	133759791	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	324	406	1	ENST00000318560.5:c.2114G>T	p.Gly705Val	p.G705V	ENST00000318560	NM_005157.4	705	gGc/gTc	11/11	0.778426816218946	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.778426816218946	3		407	516	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391520	139391520	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	508	696	0	ENST00000277541.6:c.6671A>T	p.Gln2224Leu	p.Q2224L	ENST00000277541	NM_017617.3	2224	cAg/cTg	34/34	0.778426816218946	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.778426816218946	3		696	834	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814841	139814841	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	261	668	0	ENST00000247668.2:c.834G>T	p.Lys278Asn	p.K278N	ENST00000247668	NM_021138.3	278	aaG/aaT	8/11	0.778426816218946	3	FACETS	0.997	0.936	1	0.499	0.468	0.53	CLONAL	1	TRUE	1	0.778426816218946	3		668	934	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932609	39932609	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	506	738	0	ENST00000378444.4:c.1990G>C	p.Glu664Gln	p.E664Q	ENST00000378444	NM_001123385.1	664	Gag/Cag	4/15	0.622415002107372	4	FACETS	0.963	0.924	1	0.963	0.924	1	CLONAL	2	TRUE	2	0.778426816218946	4		738	1201	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39935723	39935723	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	369	502	0	ENST00000378444.4:c.149C>T	p.Pro50Leu	p.P50L	ENST00000378444	NM_001123385.1	50	cCc/cTc	3/15	0.622415002107372	4	FACETS	0.996	0.95	1	0.996	0.95	1	CLONAL	2	TRUE	2	0.778426816218946	4		502	846	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410407	63410407	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	381	649	1	ENST00000330258.3:c.2760G>T	p.Glu920Asp	p.E920D	ENST00000330258	NM_152424.3	920	gaG/gaT	2/2	0.622415002107372	4	FACETS	0.925	0.882	0.969	0.925	0.882	0.969	CLONAL	2	TRUE	2	0.778426816218946	4		650	941	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411375	63411375	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	311	539	0	ENST00000330258.3:c.1792G>C	p.Ala598Pro	p.A598P	ENST00000330258	NM_152424.3	598	Gcc/Ccc	2/2	0.622415002107372	4	FACETS	0.939	0.89	0.987	0.939	0.89	0.987	CLONAL	2	TRUE	2	0.778426816218946	4		539	757	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412083	63412083	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	556	755	0	ENST00000330258.3:c.1084C>G	p.Leu362Val	p.L362V	ENST00000330258	NM_152424.3	362	Ctg/Gtg	2/2	0.622415002107372	4	FACETS	0.97	0.933	1	0.97	0.933	1	CLONAL	2	TRUE	2	0.778426816218946	4		755	1310	SUCCESS
AR	367	MSKCC	GRCh37	X	66766279	66766279	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	354	465	0	ENST00000374690.3:c.1291G>C	p.Ala431Pro	p.A431P	ENST00000374690	NM_000044.3	431	Gct/Cct	1/8	0.622415002107372	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.778426816218946	4		465	791	SUCCESS
AR	367	MSKCC	GRCh37	X	66937446	66937446	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	387	536	1	ENST00000374690.3:c.2300C>A	p.Pro767His	p.P767H	ENST00000374690	NM_000044.3	767	cCt/cAt	5/8	0.622415002107372	4	FACETS	0.951	0.907	0.995	0.951	0.907	0.995	CLONAL	2	TRUE	2	0.778426816218946	4		537	930	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541316	187541316	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	AA	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	289	424	0	ENST00000441802.2:c.6424delinsTT	p.Glu2142LeufsTer3	p.E2142Lfs*3	ENST00000441802	NM_005245.3	2142	Gag/TTag	10/27	0.778426816218946	3	FACETS	0.916	0.871	0.961	0.916	0.871	0.961	CLONAL	2	TRUE	1	0.778426816218946	3		424	563	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044977	47044977	+	frameshift_variant	Frame_Shift_Ins	INS	T	T	AC	novel	NA	P-0016365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	516	642	0	ENST00000377604.3:c.2303delinsAC	p.Phe768TyrfsTer22	p.F768Yfs*22	ENST00000377604	NM_001204468.1	768	tTc/tACc	20/24	0.622415002107372	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.778426816218946	4		642	1144	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0016366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	487	714	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.789181344093325	4	FACETS	1	0.996	1	0.714	0.682	0.746	CLONAL	1	TRUE	2	0.789181344093325	4		714	1546	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0016366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	177	384	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.789181344093325	2		384	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0016367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	216	488	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.737642147776051	1	FACETS	0.913	0.862	0.963	0.913	0.862	0.963	CLONAL	1	TRUE	0	0.737642147776051	1		490	405	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218538	5218538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767763908	NA	P-0016367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	330	605	0	ENST00000357368.4:c.3941G>A	p.Arg1314His	p.R1314H	ENST00000357368	NM_002850.3	1314	cGc/cAc	25/38	1	2	FACETS	0.978	0.927	1	0.978	0.927	1	CLONAL	1	TRUE	1	0.737642147776051	2		605	915	SUCCESS
APC	324	MSKCC	GRCh37	5	112175351	112175352	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0016367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	142	348	0	ENST00000257430.4:c.4062_4063del	p.Ser1355PhefsTer19	p.S1355Ffs*19	ENST00000257430	NM_000038.5	1354	TTt/t	16/16	0.737642147776051	1	FACETS	0.853	0.793	0.913	0.853	0.793	0.913	CLONAL	1	TRUE	0	0.737642147776051	1		348	285	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118944	70118944	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0016367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	321	664	0	ENST00000245479.2:c.516C>G	p.Tyr172Ter	p.Y172*	ENST00000245479	NM_000346.3	172	taC/taG	2/3	1	2	FACETS	0.936	0.886	0.987	0.936	0.886	0.987	CLONAL	1	TRUE	1	0.737642147776051	2		664	930	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710553	40710553	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778726076	NA	P-0016367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	606	578	1	ENST00000373198.4:c.4298G>A	p.Arg1433His	p.R1433H	ENST00000373198	NM_133170.3	1433	cGt/cAt	31/32	0.737642147776051	4	FACETS	0.991	0.954	1	0.495	0.477	0.514	CLONAL	2	TRUE	0	0.737642147776051	4		579	1441	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937569	76937569	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	rs375733148	NA	P-0016367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	174	537	0	ENST00000373344.5:c.3179T>G	p.Leu1060Ter	p.L1060*	ENST00000373344	NM_000489.3	1060	tTa/tGa	9/35	0.343867553801479	1	FACETS	0.516	0.478	0.556	0.516	0.478	0.556	INDETERMINATE	1	TRUE	0	0.737642147776051	1		537	577	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0016369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	278	383	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	0.764644020665096	1	FACETS	0.962	0.918	1	0.962	0.918	1	CLONAL	1	TRUE	0	0.764644020665096	1		383	467	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175212	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	227	265	0	ENST00000257430.4:c.3924del	p.Glu1309LysfsTer12	p.E1309Kfs*12	ENST00000257430	NM_000038.5	1307	atA/at	16/16	0.764644020665096	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.764644020665096	1		265	352	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781005	135781016	+	frameshift_variant	Frame_Shift_Del	DEL	GTATCAGTCTGT	GTATCAGTCTGT	A	novel	NA	P-0016369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	273	435	0	ENST00000298552.3:c.1949_1960delinsT	p.Asp650ValfsTer34	p.D650Vfs*34	ENST00000298552	NM_001162426.1	650	gACAGACTGATACag/gTag	15/23	0.764644020665096	1	FACETS	0.991	0.946	1	0.991	0.946	1	CLONAL	1	TRUE	0	0.764644020665096	1		435	445	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0016370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	82	772	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.671	0.592	0.756	0.671	0.592	0.756	SUBCLONAL	1	TRUE	1	0.372151838762103	2		772	657	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8497259	8497259	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	92	565	0	ENST00000356435.5:c.2332G>T	p.Asp778Tyr	p.D778Y	ENST00000356435		778	Gat/Tat	15/35	1	2	FACETS	0.763	0.679	0.853	0.763	0.679	0.853	SUBCLONAL	1	TRUE	1	0.372151838762103	2		565	648	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251851	8251851	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	31	376	0	ENST00000335790.3:c.226C>A	p.Arg76Ser	p.R76S	ENST00000335790	NM_002315.2	76	Cgc/Agc	2/4	1	2	FACETS	0.409	0.331	0.498	0.409	0.331	0.498	SUBCLONAL	1	TRUE	1	0.372151838762103	2		376	407	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56857734	56857734	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	44	351	0	ENST00000308159.5:c.770A>T	p.Gln257Leu	p.Q257L	ENST00000308159	NM_014669.4	257	cAg/cTg	8/22	1	2	FACETS	0.534	0.448	0.629	0.534	0.448	0.629	SUBCLONAL	1	TRUE	1	0.372151838762103	2		351	443	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267496	198267496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764445898	NA	P-0016370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	56	455	1	ENST00000335508.6:c.1861G>A	p.Asp621Asn	p.D621N	ENST00000335508	NM_012433.2	621	Gat/Aat	14/25	1	2	FACETS	0.534	0.457	0.617	0.534	0.457	0.617	SUBCLONAL	1	TRUE	1	0.372151838762103	2		456	564	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041247	47041247	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	67	766	0	ENST00000377604.3:c.1675G>T	p.Glu559Ter	p.E559*	ENST00000377604	NM_001204468.1	559	Gaa/Taa	15/24	1	2	FACETS	0.515	0.447	0.589	0.515	0.447	0.589	SUBCLONAL	1	TRUE	1	0.372151838762103	2		766	699	SUCCESS
AR	367	MSKCC	GRCh37	X	66765851	66765851	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	52	767	0	ENST00000374690.3:c.863C>A	p.Ala288Asp	p.A288D	ENST00000374690	NM_000044.3	288	gCc/gAc	1/8	1	2	FACETS	0.41	0.348	0.478	0.41	0.348	0.478	SUBCLONAL	1	TRUE	1	0.372151838762103	2		767	682	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115871	8115872	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0016371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	110	614	0	ENST00000346208.3:c.1219_1220del	p.Ser407AlafsTer99	p.S407Afs*99	ENST00000346208		406	aTC/a	6/6	1	2	FACETS	0.705	0.633	0.781	0.705	0.633	0.781	SUBCLONAL	1	TRUE	1	0.410190329028083	2		614	761	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575049	64575049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs386134259	NA	P-0016371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	100	464	0	ENST00000312049.6:c.758C>T	p.Ser253Leu	p.S253L	ENST00000312049	NM_130799.2	253	tCg/tTg	4/10	0.410190329028083	1	FACETS	0.777	0.697	0.861	0.777	0.697	0.861	SUBCLONAL	1	TRUE	0	0.410190329028083	1		464	499	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318779	163318779	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs116669228	NA	P-0016371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	195	764	2	ENST00000271452.3:c.1169G>A	p.Arg390Gln	p.R390Q	ENST00000271452	NM_145697.2	390	cGa/cAa	13/14	0.339758172292526	3	FACETS	1	0.957	1	0.525	0.485	0.566	CLONAL	1	TRUE	1	0.410190329028083	3		766	1092	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	94	726	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.208444977011161	1	FACETS	0.804	0.714	0.901	0.804	0.714	0.901	CLONAL	1	TRUE	0	0.208444977011161	1		726	1005	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578523	7578523	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1567554216	NA	P-0016372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	114	741	0	ENST00000269305.4:c.407A>C	p.Gln136Pro	p.Q136P	ENST00000269305	NM_001126112.2	136	cAa/cCa	5/11	0.208444977011161	1	FACETS	0.821	0.737	0.911	0.821	0.737	0.911	CLONAL	1	TRUE	0	0.208444977011161	1		741	1193	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032329	42032331	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	rs781754335	NA	P-0016372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	98	587	0	ENST00000219905.7:c.4518_4520del	p.Ser1507del	p.S1507del	ENST00000219905	NM_001164273.1	1505	TCC/-	14/24	0.208444977011161	1	FACETS	0.835	0.743	0.933	0.835	0.743	0.933	CLONAL	1	TRUE	0	0.208444977011161	1		587	1009	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6037000	6037000	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1181	134	691	0	ENST00000265849.7:c.760G>C	p.Glu254Gln	p.E254Q	ENST00000265849	NM_000535.5	254	Gag/Cag	7/15	1	2	FACETS	0.978	0.886	1	0.978	0.886	1	CLONAL	1	TRUE	1	0.208444977011161	2		691	1315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577515	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016374-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	418	617	0	ENST00000269305.4:c.766del	p.Thr256HisfsTer89	p.T256Hfs*89	ENST00000269305	NM_001126112.2	256	Aca/ca	7/11	0.824265365577088	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	FALSE	0	0.824265365577088	2		617	476	SUCCESS
AXL	558	MSKCC	GRCh37	19	41759540	41759540	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016374-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	296	664	0	ENST00000301178.4:c.1963G>C	p.Asp655His	p.D655H	ENST00000301178	NM_021913.4	655	Gac/Cac	17/20	0.256550000849435	3	FACETS	0.887	0.844	0.929	0.887	0.844	0.929	INDETERMINATE	2	FALSE	1	0.824265365577088	3		664	572	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0016375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	368	731	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.220193527804089	3	FACETS	0.795	0.756	0.835	0.795	0.756	0.835	INDETERMINATE	2	TRUE	1	0.561232578202235	3		731	1056	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039658	47039659	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	348	623	0	ENST00000377604.3:c.1111dup	p.Thr371AsnfsTer10	p.T371Nfs*10	ENST00000377604	NM_001204468.1	370	-/A	11/24	1	2	FACETS	0.941	0.89	0.993	0.941	0.89	0.993	CLONAL	1	TRUE	1	0.561232578202235	2		623	1318	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246021826	246021826	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	71	498	0	ENST00000388985.4:c.1048T>C	p.Tyr350His	p.Y350H	ENST00000388985		350	Tat/Cat	10/12	0.220193527804089	3	FACETS	0.321	0.279	0.366	0.16	0.139	0.183	INDETERMINATE	1	TRUE	1	0.561232578202235	3		498	1010	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376469	118376469	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	265	514	0	ENST00000534358.1:c.9862A>G	p.Ile3288Val	p.I3288V	ENST00000534358	NM_005933.3	3288	Atc/Gtc	27/36	NA	2	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.561232578202235	2		514	901	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197399	26197399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	20	200	0	ENST00000356476.2:c.80G>A	p.Arg27Gln	p.R27Q	ENST00000356476		27	cGa/cAa	1/1	0.302465331489713	5	FACETS	0.349	0.266	0.446	0.116	0.088	0.149	INDETERMINATE	1	TRUE	2	0.561232578202235	5		200	376	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0016376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1274	152	2255	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	0.19	2		2255	1426	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	57	486	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.524	0.448	0.609	0.524	0.448	0.609	SUBCLONAL	1	TRUE	1	0.19	2		486	1144	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0016376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1265	90	896	1	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	1	2	FACETS	0.699	0.618	0.787	0.699	0.618	0.787	SUBCLONAL	1	TRUE	1	0.19	2		897	1355	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0016377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	51	807	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.763	0.645	0.892	0.763	0.645	0.892	SUBCLONAL	1	TRUE	1	0.11	2		807	1216	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782082	NA	P-0016377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	32	660	0	ENST00000269305.4:c.745A>T	p.Arg249Trp	p.R249W	ENST00000269305	NM_001126112.2	249	Agg/Tgg	7/11	1	2	FACETS	0.697	0.563	0.849	0.697	0.563	0.849	SUBCLONAL	1	TRUE	1	0.11	2		660	835	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910621	50910621	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	76	891	3	ENST00000440232.2:c.1724C>T	p.Ser575Leu	p.S575L	ENST00000440232	NM_002691.3	575	tCa/tTa	14/27	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.11	2		894	1094	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0016378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	102	978	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.13	2		978	1133	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480595	50480595	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	55	906	0	ENST00000394963.4:c.465G>C	p.Arg155Ser	p.R155S	ENST00000394963	NM_003076.4	155	agG/agC	4/13	1	2	FACETS	0.863	0.735	1	0.863	0.735	1	CLONAL	1	TRUE	1	0.13	2		906	981	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109315722	109315722	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1688	94	1202	0	ENST00000436639.2:c.1063G>T	p.Glu355Ter	p.E355*	ENST00000436639	NM_014454.2	355	Gag/Tag	6/10	1	2	FACETS	0.812	0.719	0.912	0.812	0.719	0.912	CLONAL	1	TRUE	1	0.13	2		1202	1782	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0016379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	63	643	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.784	0.676	0.901	0.784	0.676	0.901	CLONAL	1	TRUE	1	0.2	2		643	804	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492623	56492623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	104	657	0	ENST00000267101.3:c.2773G>A	p.Glu925Lys	p.E925K	ENST00000267101	NM_001982.3	925	Gag/Aag	23/28	1	2	FACETS	0.952	0.851	1	0.952	0.851	1	CLONAL	1	TRUE	1	0.2	2		657	1092	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226101	133226101	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs984562653	NA	P-0016379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	63	724	0	ENST00000320574.5:c.3796G>A	p.Glu1266Lys	p.E1266K	ENST00000320574	NM_006231.2	1266	Gag/Aag	31/49	1	2	FACETS	0.738	0.636	0.848	0.738	0.636	0.848	SUBCLONAL	1	TRUE	1	0.2	2		724	854	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719923	18719923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1540	108	944	1	ENST00000266497.5:c.3820C>T	p.His1274Tyr	p.H1274Y	ENST00000266497		1274	Cac/Tac	27/31	1	2	FACETS	0.655	0.585	0.73	0.655	0.585	0.73	SUBCLONAL	1	TRUE	1	0.2	2		945	1648	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138498	2138498	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777006583	NA	P-0016379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1258	96	885	0	ENST00000219476.3:c.5311C>T	p.Pro1771Ser	p.P1771S	ENST00000219476	NM_000548.3	1771	Ccg/Tcg	42/42	1	2	FACETS	0.709	0.629	0.795	0.709	0.629	0.795	SUBCLONAL	1	TRUE	1	0.2	2		885	1354	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	112	515	0	ENST00000308159.5:c.43C>G	p.Gln15Glu	p.Q15E	ENST00000308159	NM_014669.4	15	Cag/Gag	2/22	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.2	2		515	897	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000081	30000081	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373337083	NA	P-0016379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	96	875	1	ENST00000338641.4:c.94G>A	p.Glu32Lys	p.E32K	ENST00000338641	NM_000268.3	32	Gag/Aag	1/16	1	2	FACETS	0.841	0.747	0.942	0.841	0.747	0.942	CLONAL	1	TRUE	1	0.2	2		876	1141	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221930	98221930	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	53	622	1	ENST00000331920.6:c.2839G>T	p.Glu947Ter	p.E947*	ENST00000331920	NM_000264.3	947	Gaa/Taa	17/24	1	2	FACETS	0.651	0.554	0.758	0.651	0.554	0.758	SUBCLONAL	1	TRUE	1	0.2	2		623	814	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928273	178928273	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	149	591	0	ENST00000263967.3:c.1459C>T	p.Pro487Ser	p.P487S	ENST00000263967	NM_006218.2	487	Cca/Tca	9/21	1	2	FACETS	0.825	0.759	0.892	0.825	0.759	0.892	CLONAL	1	TRUE	1	0.752814321065121	2		591	480	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	158	423	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.67371684162652	2		423	459	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0016383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	110	318	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.949	0.862	1	0.949	0.862	1	CLONAL	1	TRUE	1	0.67371684162652	2		318	344	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591085	67591085	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519839	NA	P-0016383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	133	537	0	ENST00000274335.5:c.1678G>T	p.Asp560Tyr	p.D560Y	ENST00000274335		560	Gac/Tac	12/15	1	2	FACETS	0.975	0.894	1	0.975	0.894	1	CLONAL	1	TRUE	1	0.67371684162652	2		537	405	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0016383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	10	542	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	0.072	0.048	0.103	0.072	0.048	0.103	SUBCLONAL	1	TRUE	1	0.67371684162652	2		542	410	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413070	139413072	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0016383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	55	609	0	ENST00000277541.6:c.1070_1072del	p.Phe357del	p.F357del	ENST00000277541	NM_017617.3	357	tTCTac/tac	6/34	1	2	FACETS	0.265	0.226	0.307	0.265	0.226	0.307	SUBCLONAL	1	TRUE	1	0.67371684162652	2		609	617	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544748	65544748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	12	543	1	ENST00000358664.4:c.178C>T	p.Arg60Trp	p.R60W	ENST00000358664	NM_002382.4	60	Cgg/Tgg	4/5	1	2	FACETS	0.059	0.041	0.082	0.059	0.041	0.082	SUBCLONAL	1	TRUE	1	0.67371684162652	2		544	599	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132532	11132532	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	238	755	0	ENST00000358026.2:c.2748C>G	p.Asn916Lys	p.N916K	ENST00000358026	NM_001128849.1	916	aaC/aaG	19/36	1	2	FACETS	0.805	0.752	0.858	0.805	0.752	0.858	CLONAL	1	TRUE	1	0.67371684162652	2		755	878	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523054	25523054	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199643287	NA	P-0016383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	278	687	1	ENST00000264709.3:c.131C>T	p.Thr44Met	p.T44M	ENST00000264709	NM_175629.2	44	aCg/aTg	3/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.67371684162652	2		688	765	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0016384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	351	547	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.740299192894631	5	FACETS	1	0.979	1	0.703	0.668	0.739	CLONAL	2	TRUE	2	0.740299192894631	5		547	949	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46276097	46276097	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	526	454	0	ENST00000371998.3:c.3533T>C	p.Leu1178Pro	p.L1178P	ENST00000371998		1178	cTg/cCg	18/23	0.740299192894631	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	2	0.740299192894631	4		454	1224	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0016385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	36	279	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	NA	2	FACETS	0.304	0.249	0.366			1	INDETERMINATE	1	TRUE	NA	0.326755694878153	2		279	725	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0016385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	81	570	1	ENST00000311936.3:c.34_35delinsTT	p.Gly12Phe	p.G12F	ENST00000311936	NM_004985.3	12	GGt/TTt	2/5	1	2	FACETS	0.628	0.552	0.709	0.628	0.552	0.709	SUBCLONAL	1	TRUE	1	0.326755694878153	2		571	790	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964087	28964087	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	58	462	0	ENST00000282397.4:c.1815C>A	p.Ser605Arg	p.S605R	ENST00000282397	NM_002019.4	605	agC/agA	13/30	1	2	FACETS	0.534	0.458	0.617	0.534	0.458	0.617	SUBCLONAL	1	TRUE	1	0.326755694878153	2		462	665	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336222	73336222	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	29	341	0	ENST00000377767.4:c.2181G>T	p.Gln727His	p.Q727H	ENST00000377767	NM_014953.3	727	caG/caT	17/21	1	2	FACETS	0.351	0.281	0.432	0.351	0.281	0.432	SUBCLONAL	1	TRUE	1	0.326755694878153	2		341	505	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905143	50905143	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	126	706	0	ENST00000440232.2:c.425A>T	p.His142Leu	p.H142L	ENST00000440232	NM_002691.3	142	cAc/cTc	4/27	1	2	FACETS	0.725	0.655	0.799	0.725	0.655	0.799	SUBCLONAL	1	TRUE	1	0.326755694878153	2		706	1064	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041263	47041273	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACCGTGAGTAG	ACCGTGAGTAG	-	novel	NA	P-0016385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	39	332	0	ENST00000377604.3:c.1691_1693+8del		p.X564_splice	ENST00000377604	NM_001204468.1	564		15/24	0.208790854820572	0	FACETS	0.331	0.274	0.395			1	SUBCLONAL	1	TRUE	NA	0.326755694878153	0		332	485	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	394	641	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.231619144338885	4	FACETS	0.895	0.851	0.939	0.895	0.851	0.939	CLONAL	4	TRUE	0	0.231619144338885	4		641	1171	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0016390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	190	342	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	0.198114369484324	2	FACETS	0.829	0.767	0.895	0.829	0.767	0.895	CLONAL	2	TRUE	0	0.231619144338885	2		342	989	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577129	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519986	NA	P-0016390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1173	302	568	0	ENST00000269305.4:c.809T>G	p.Phe270Cys	p.F270C	ENST00000269305	NM_001126112.2	270	tTt/tGt	8/11	0.213224763584055	3	FACETS	0.986	0.927	1	0.658	0.618	0.698	CLONAL	2	TRUE	0	0.231619144338885	3		568	1475	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573573	48573573	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	70	337	1	ENST00000342988.3:c.157G>T	p.Glu53Ter	p.E53*	ENST00000342988	NM_005359.5	53	Gaa/Taa	2/12	1	2	FACETS	0.97	0.846	1	0.97	0.846	1	CLONAL	1	TRUE	1	0.231619144338885	2		338	623	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934574	NA	P-0016391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	403	536	0	ENST00000269305.4:c.844C>G	p.Arg282Gly	p.R282G	ENST00000269305	NM_001126112.2	282	Cgg/Ggg	8/11	0.633520929688769	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.633520929688769	1		536	862	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332633	153332634	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0016391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	214	323	0	ENST00000281708.4:c.322dup	p.Gln108ProfsTer3	p.Q108Pfs*3	ENST00000281708	NM_033632.3	108	caa/cCaa	2/12	0.633520929688769	1	FACETS	0.91	0.855	0.967	0.91	0.855	0.967	CLONAL	1	TRUE	0	0.633520929688769	1		323	507	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137524708	137524708	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	48	523	0	ENST00000367739.4:c.661T>G	p.Leu221Val	p.L221V	ENST00000367739	NM_000416.2	221	Tta/Gta	5/7	0.633520929688769	1	FACETS	0.108	0.09	0.127	0.108	0.09	0.127	SUBCLONAL	1	TRUE	0	0.633520929688769	1		523	960	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534423	140534423	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	127	323	0	ENST00000288602.6:c.490A>G	p.Lys164Glu	p.K164E	ENST00000288602	NM_004333.4	164	Aaa/Gaa	3/18	0.578365457128981	3	FACETS	0.548	0.495	0.603	0.274	0.247	0.302	SUBCLONAL	1	TRUE	1	0.633520929688769	3		323	964	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372230	55372230	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	133	345	0	ENST00000297316.4:c.920G>C	p.Gly307Ala	p.G307A	ENST00000297316	NM_022454.3	307	gGc/gCc	2/2	1	2	FACETS	0.729	0.665	0.796	0.729	0.665	0.796	SUBCLONAL	1	TRUE	1	0.633520929688769	2		345	576	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0016392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	113	332	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.214252657832431	5	FACETS	1	0.965	1	0.745	0.679	0.812	INDETERMINATE	2	TRUE	2	0.608169187307411	5		332	318	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220275	55220275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751295137	NA	P-0016392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	11	610	3	ENST00000275493.2:c.665G>A	p.Arg222His	p.R222H	ENST00000275493	NM_005228.3	222	cGc/cAc	6/28	NA	2	FACETS	0.113	0.078	0.158			1	INDETERMINATE	1	TRUE	NA	0.608169187307411	2		613	319	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117311	115117311	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	137	368	0	ENST00000257566.3:c.863A>G	p.Lys288Arg	p.K288R	ENST00000257566	NM_016569.3	288	aAg/aGg	4/8	0.224975535578543	4	FACETS	0.846	0.777	0.918	0.846	0.777	0.918	INDETERMINATE	2	TRUE	2	0.608169187307411	4		368	428	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696688	47696688	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519971	NA	P-0016393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	173	456	0	ENST00000347630.2:c.260A>C	p.Tyr87Ser	p.Y87S	ENST00000347630	NM_001007230.1	87	tAc/tCc	5/11	1	2	FACETS	0.99	0.911	1	0.99	0.911	1	CLONAL	1	TRUE	1	0.377986337158696	2		456	925	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380285	25380285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104894364	NA	P-0016394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	364	500	1	ENST00000311936.3:c.173C>T	p.Thr58Ile	p.T58I	ENST00000311936	NM_004985.3	58	aCa/aTa	3/5	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.61208504511455	2		501	1128	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274645	123274645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	197	277	0	ENST00000358487.5:c.1273C>T	p.Arg425Trp	p.R425W	ENST00000358487	NM_000141.4	425	Cgg/Tgg	9/18	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.61208504511455	2		277	632	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725192	49725192	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs766477367	NA	P-0016394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	74	165	0	ENST00000449682.2:c.233T>C	p.Met78Thr	p.M78T	ENST00000449682	NM_020998.3	78	aTg/aCg	2/18	1	2	FACETS	0.715	0.631	0.805	0.715	0.631	0.805	SUBCLONAL	1	TRUE	1	0.61208504511455	2		165	338	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964925	55964925	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	636	440	0	ENST00000263923.4:c.2312C>A	p.Thr771Lys	p.T771K	ENST00000263923	NM_002253.2	771	aCg/aAg	16/30	0.61208504511455	3	FACETS	0.978	0.944	1	0.978	0.944	1	CLONAL	2	TRUE	1	0.61208504511455	3		440	1387	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	46	423	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.751	0.631	0.884	0.751	0.631	0.884	SUBCLONAL	1	TRUE	1	0.17	2		423	721	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951964	178951964	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	22	475	0	ENST00000263967.3:c.3019G>C	p.Gly1007Arg	p.G1007R	ENST00000263967	NM_006218.2	1007	Ggc/Cgc	21/21	1	2	FACETS	0.305	0.235	0.387	0.305	0.235	0.387	SUBCLONAL	1	TRUE	1	0.17	2		475	848	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682991	241682991	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1226883651	NA	P-0016395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	86	266	0	ENST00000366560.3:c.32C>G	p.Ser11Trp	p.S11W	ENST00000366560	NM_000143.3	11	tCg/tGg	1/10	1	2	FACETS	0.921	0.812	1	0.921	0.812	1	CLONAL	1	TRUE	1	0.17	2		266	1099	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412245	63412245	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1421	110	618	1	ENST00000330258.3:c.922C>A	p.Pro308Thr	p.P308T	ENST00000330258	NM_152424.3	308	Cca/Aca	2/2	1	2	FACETS	0.845	0.756	0.94	0.845	0.756	0.94	CLONAL	1	TRUE	1	0.17	2		619	1531	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412332	63412332	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	110	494	1	ENST00000330258.3:c.835A>T	p.Ser279Cys	p.S279C	ENST00000330258	NM_152424.3	279	Agt/Tgt	2/2	1	2	FACETS	0.998	0.894	1	0.998	0.894	1	CLONAL	1	TRUE	1	0.17	2		495	1297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0016396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	637	449	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.863806470184226	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.863806470184226	1		449	789	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217609	7217609	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0016396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	242	622	0	ENST00000380728.2:c.317+1G>T		p.X106_splice	ENST00000380728		106			0.863806470184226	1	FACETS	0.968	0.929	1	0.968	0.929	1	CLONAL	1	TRUE	0	0.863806470184226	1		622	329	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0016397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	181	931	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.200659295790675	6	FACETS	0.857	0.79	0.927	0.857	0.79	0.927	CLONAL	3	FALSE	3	0.200659295790675	6		931	983	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579399	7579400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAAGATGACAG	novel	NA	P-0016397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	60	944	0	ENST00000269305.4:c.277_287dup	p.Val97CysfsTer30	p.V97Cfs*30	ENST00000269305	NM_001126112.2	96	tct/tcCTGTCATCTTCt	4/11	0.200659295790675	1	FACETS	0.777	0.669	0.896	0.777	0.669	0.896	SUBCLONAL	1	FALSE	0	0.200659295790675	1		944	692	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206728	36206729	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGGGTTAT	novel	NA	P-0016397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	37	687	0	ENST00000300305.3:c.783_784insATAACCCT	p.Gln262IlefsTer52	p.Q262Ifs*52	ENST00000300305		261	-/ATAACCCT	6/8	1	2	FACETS	0.592	0.487	0.71	0.592	0.487	0.71	SUBCLONAL	1	FALSE	1	0.200659295790675	2		687	623	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340844	70340844	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	91	804	0	ENST00000374080.3:c.577T>C	p.Tyr193His	p.Y193H	ENST00000374080		193	Tac/Cac	5/45	0.200659295790675	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	0	0.200659295790675	1		804	701	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0016398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	59	332	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.566	0.487	0.653	0.566	0.487	0.653	SUBCLONAL	1	TRUE	1	0.327594804293738	2		332	636	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556447	29556447	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	86	731	0	ENST00000356175.3:c.2814G>C	p.Lys938Asn	p.K938N	ENST00000356175	NM_000267.3	938	aaG/aaC	21/57	1	2	FACETS	0.673	0.595	0.757	0.673	0.595	0.757	SUBCLONAL	1	TRUE	1	0.327594804293738	2		731	780	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880449	155880449	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs869025189	NA	P-0016400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	220	676	0	ENST00000368323.3:c.104G>C	p.Ser35Thr	p.S35T	ENST00000368323	NM_006912.5	35	aGt/aCt	2/6	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.526036894754752	2		676	688	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902873	1902873	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	237	1055	0	ENST00000382891.5:c.492G>T	p.Lys164Asn	p.K164N	ENST00000382891	NM_133335.3	164	aaG/aaT	2/22	1	2	FACETS	0.943	0.88	1	0.943	0.88	1	CLONAL	1	TRUE	1	0.526036894754752	2		1055	956	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932278	39932278	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	336	716	0	ENST00000378444.4:c.2321A>T	p.Lys774Met	p.K774M	ENST00000378444	NM_001123385.1	774	aAg/aTg	4/15	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.526036894754752	1		716	670	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	42	423	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.384907846384748	NA		423	96	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0016401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	103	1585	1	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.22001534238057	4	FACETS	1	0.924	1	1	0.924	1	INDETERMINATE	2	TRUE	2	0.384907846384748	4		1586	361	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0016402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	12	643	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		643	577	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894230	NA	P-0016402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	13	902	0	ENST00000451590.1:c.35G>A	p.Gly12Asp	p.G12D	ENST00000451590	NM_001130442.1	12	gGc/gAc	2/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		902	435	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0016403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	55	561	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.2	2		561	376	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148991	119148991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs192712314	NA	P-0016403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	15	868	1	ENST00000264033.4:c.1211G>A	p.Cys404Tyr	p.C404Y	ENST00000264033	NM_005188.3	404	tGt/tAt	8/16	1	2	FACETS	0.394	0.287	0.523	0.394	0.287	0.523	SUBCLONAL	1	TRUE	1	0.2	2		869	381	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599928	10599928	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	39	1109	0	ENST00000171111.5:c.1648A>T	p.Met550Leu	p.M550L	ENST00000171111	NM_203500.1	550	Atg/Ttg	5/6	1	2	FACETS	0.501	0.413	0.599	0.501	0.413	0.599	SUBCLONAL	1	TRUE	1	0.2	2		1109	779	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0016404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	435	997	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.3	2	FACETS	1	0.988	1			1	CLONAL	3	TRUE	NA	0.26	2		997	1025	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0016404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	53	318	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	0.26	2		318	304	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938029	76938029	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	56	846	2	ENST00000373344.5:c.2719C>T	p.Arg907Ter	p.R907*	ENST00000373344	NM_000489.3	907	Cga/Tga	9/35	1	2	FACETS	0.97	0.833	1	0.97	0.833	1	CLONAL	1	TRUE	1	0.26	2		848	444	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939927	76939927	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0016404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	40	1044	2	ENST00000373344.5:c.821T>A	p.Leu274Ter	p.L274*	ENST00000373344	NM_000489.3	274	tTg/tAg	9/35	1	2	FACETS	0.603	0.501	0.718	0.603	0.501	0.718	SUBCLONAL	1	TRUE	1	0.26	2		1046	510	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591135	67591149	+	inframe_deletion	In_Frame_Del	DEL	GAGAGACCAATACTT	GAGAGACCAATACTT	-	novel	NA	P-0016405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	79	467	0	ENST00000274335.5:c.1730_1744del	p.Arg577_Leu581del	p.R577_L581del	ENST00000274335		576	acGAGAGACCAATACTTg/acg	12/15	1	2	FACETS	0.504	0.445	0.567	0.504	0.445	0.567	SUBCLONAL	1	TRUE	1	0.698607699293748	2		467	449	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226124	53226124	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs951268570	NA	P-0016406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	195	836	1	ENST00000375401.3:c.2725C>T	p.Arg909Trp	p.R909W	ENST00000375401	NM_004187.3	909	Cgg/Tgg	19/26	0.350131702539424	4	FACETS	1	0.952	1	1	0.952	1	INDETERMINATE	2	TRUE	2	0.759841088842865	4		837	443	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733414	85733414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1755	215	666	0	ENST00000370580.1:c.598G>A	p.Ala200Thr	p.A200T	ENST00000370580	NM_003921.4	200	Gct/Act	3/3	0.759841088842865	6	FACETS	0.724	0.67	0.78			1	SUBCLONAL	1	TRUE	NA	0.759841088842865	6		666	1970	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103798	47103798	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	247	702	0	ENST00000409792.3:c.6148C>T	p.Gln2050Ter	p.Q2050*	ENST00000409792	NM_014159.6	2050	Caa/Taa	14/21	0.759841088842865	2	FACETS	0.997	0.959	1	0.997	0.959	1	CLONAL	2	TRUE	0	0.759841088842865	2		702	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0016412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	74	488	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.486956550342447	1	FACETS	0.756	0.668	0.849	0.756	0.668	0.849	SUBCLONAL	1	TRUE	0	0.486956550342447	1		490	304	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407575	407575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748516736	NA	P-0016412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	152	549	0	ENST00000380956.4:c.1333C>T	p.Arg445Cys	p.R445C	ENST00000380956	NM_001195286.1	445	Cgc/Tgc	9/9	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.486956550342447	2		549	445	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49054148	49054148	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	57	411	0	ENST00000267163.4:c.2728C>T	p.Arg910Ter	p.R910*	ENST00000267163	NM_000321.2	910	Cga/Tga	27/27	1	2	FACETS	0.689	0.594	0.791	0.689	0.594	0.791	SUBCLONAL	1	TRUE	1	0.486956550342447	2		411	340	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778906	3778906	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771638045	NA	P-0016412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	53	321	0	ENST00000262367.5:c.6142G>A	p.Val2048Met	p.V2048M	ENST00000262367	NM_004380.2	2048	Gtg/Atg	31/31	0.324668748503299	1	FACETS	0.773	0.668	0.885	0.773	0.668	0.885	SUBCLONAL	1	TRUE	0	0.486956550342447	1		321	213	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063663	67063663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	93	498	2	ENST00000412916.2:c.112G>A	p.Glu38Lys	p.E38K	ENST00000412916		38	Gag/Aag	2/6	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.486956550342447	2		500	359	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223385	36223385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	95	961	0	ENST00000222270.7:c.5935G>A	p.Asp1979Asn	p.D1979N	ENST00000222270	NM_014727.1	1979	Gac/Aac	28/37	0.147428308468834	2	FACETS	0.724	0.646	0.806	0.362	0.323	0.403	INDETERMINATE	1	TRUE	0	0.486956550342447	2		961	539	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058449	69058449	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	77	443	1	ENST00000288368.4:c.4093C>T	p.Pro1365Ser	p.P1365S	ENST00000288368	NM_024870.2	1365	Cct/Tct	34/40	1	2	FACETS	0.953	0.843	1	0.953	0.843	1	CLONAL	1	TRUE	1	0.486956550342447	2		444	332	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599320	55599320	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913506	NA	P-0016415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	262	609	0	ENST00000288135.5:c.2446G>T	p.Asp816Tyr	p.D816Y	ENST00000288135	NM_000222.2	816	Gac/Tac	17/21	0.418014326753766	3	FACETS	0.779	0.731	0.828	0.519	0.487	0.552	SUBCLONAL	2	TRUE	0	0.439616873723319	3		609	933	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681478	30681478	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	193	507	0	ENST00000376406.3:c.534G>C	p.Arg178Ser	p.R178S	ENST00000376406	NM_014641.2	178	agG/agC	4/15	0.415735254313664	4	FACETS	0.934	0.861	1	0.467	0.43	0.505	CLONAL	1	TRUE	2	0.439616873723319	4		507	1354	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0016416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	85	683	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.506683393846765	2		683	322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs863224683	NA	P-0016416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	229	905	0	ENST00000269305.4:c.388C>G	p.Leu130Val	p.L130V	ENST00000269305	NM_001126112.2	130	Ctc/Gtc	5/11	1	2	FACETS	0.999	0.932	1	0.999	0.932	1	CLONAL	1	TRUE	1	0.506683393846765	2		905	905	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916728	178916728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	123	524	0	ENST00000263967.3:c.115G>A	p.Glu39Lys	p.E39K	ENST00000263967	NM_006218.2	39	Gag/Aag	2/21	0.506683393846765	3	FACETS	0.975	0.884	1	0.488	0.442	0.536	CLONAL	1	TRUE	1	0.506683393846765	3		524	624	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015461	176015461	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0016416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	105	408	2	ENST00000367669.3:c.1278-1G>A		p.X426_splice	ENST00000367669	NM_022457.5	426			1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.506683393846765	2		410	401	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690821	89690821	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs1554897866	NA	P-0016416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	133	334	0	ENST00000371953.3:c.228T>G	p.Tyr76Ter	p.Y76*	ENST00000371953	NM_000314.4	76	taT/taG	4/9	0.506683393846765	1	FACETS	0.978	0.897	1	0.978	0.897	1	CLONAL	1	TRUE	0	0.506683393846765	1		334	401	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244974	46244974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs577713771	NA	P-0016416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	194	647	1	ENST00000334344.6:c.3068C>T	p.Pro1023Leu	p.P1023L	ENST00000334344	NM_152641.2	1023	cCa/cTa	15/21	1	2	FACETS	0.984	0.913	1	0.984	0.913	1	CLONAL	1	TRUE	1	0.506683393846765	2		648	778	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646163	215646163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	151	899	0	ENST00000260947.4:c.435G>A	p.Met145Ile	p.M145I	ENST00000260947	NM_000465.2	145	atG/atA	4/11	1	2	FACETS	0.528	0.481	0.576	0.528	0.481	0.576	SUBCLONAL	1	TRUE	1	0.51	2		899	1122	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	1623	726	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.667142766209438	5	FACETS	0.979	0.962	0.995			1	CLONAL	4	TRUE	NA	0.738665240065702	5		726	2366	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0016420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	159	683	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.638757575626658	2		683	389	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112479	115112479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs912240752	NA	P-0016420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	308	609	2	ENST00000257566.3:c.1261C>T	p.Arg421Trp	p.R421W	ENST00000257566	NM_016569.3	421	Cgg/Tgg	7/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.638757575626658	2		611	896	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591246	67591246	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0016420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	218	357	1	ENST00000274335.5:c.1746-2A>T		p.X582_splice	ENST00000274335		582			1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.638757575626658	2		358	680	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339469	81339469	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	52	420	0	ENST00000222390.5:c.1535G>T	p.Arg512Ile	p.R512I	ENST00000222390	NM_000601.4	512	aGa/aTa	13/18	0.638757575626658	3	FACETS	0.211	0.178	0.246	0.105	0.089	0.123	SUBCLONAL	1	TRUE	1	0.638757575626658	3		420	1020	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308300	15308317	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGGCACTCACAGGCAGG	CAGGCACTCACAGGCAGG	-	novel	NA	P-0016421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	64	567	0	ENST00000263388.2:c.191_197+11del		p.X64_splice	ENST00000263388	NM_000435.2	64		2/33	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		567	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0016423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	187	556	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.255047139339622	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.255047139339622	1		556	1182	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206667324	206667324	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	152	529	0	ENST00000367120.3:c.2117G>T	p.Arg706Leu	p.R706L	ENST00000367120	NM_014002.3	706	cGg/cTg	21/22	1	2	FACETS	0.933	0.851	1	0.933	0.851	1	CLONAL	1	TRUE	1	0.255047139339622	2		529	1277	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546575	9546575	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777430875	NA	P-0016423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	118	477	0	ENST00000353224.5:c.1447C>T	p.Arg483Trp	p.R483W	ENST00000353224	NM_177990.2	483	Cgg/Tgg	5/10	1	2	FACETS	0.972	0.876	1	0.972	0.876	1	CLONAL	1	TRUE	1	0.255047139339622	2		477	952	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141105	55141105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	88	395	0	ENST00000257290.5:c.1751C>T	p.Ser584Leu	p.S584L	ENST00000257290	NM_006206.4	584	tCa/tTa	12/23	1	2	FACETS	0.893	0.79	1	0.893	0.79	1	CLONAL	1	TRUE	1	0.255047139339622	2		395	773	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681424	88681424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	140	530	0	ENST00000372037.3:c.1314G>T	p.Trp438Cys	p.W438C	ENST00000372037	NM_004329.2	438	tgG/tgT	11/13	0.219558846508358	1	FACETS	0.921	0.837	1	0.921	0.837	1	CLONAL	1	TRUE	0	0.255047139339622	1		530	1040	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933379	100933379	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	114	512	1	ENST00000325455.5:c.2011C>A	p.Gln671Lys	p.Q671K	ENST00000325455	NM_001202474.3	671	Cag/Aag	4/8	1	2	FACETS	0.891	0.801	0.987	0.891	0.801	0.987	CLONAL	1	TRUE	1	0.255047139339622	2		513	1003	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404794	404794	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	106	518	0	ENST00000399788.2:c.4400G>T	p.Arg1467Leu	p.R1467L	ENST00000399788	NM_001042603.1	1467	cGg/cTg	26/28	1	2	FACETS	0.798	0.714	0.887	0.798	0.714	0.887	SUBCLONAL	1	TRUE	1	0.255047139339622	2		518	1042	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864465	57864465	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	126	547	0	ENST00000228682.2:c.1942C>A	p.Arg648Ser	p.R648S	ENST00000228682	NM_005269.2	648	Cgt/Agt	12/12	1	2	FACETS	0.988	0.893	1	0.988	0.893	1	CLONAL	1	TRUE	1	0.255047139339622	2		547	1000	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112386	115112386	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	68	290	0	ENST00000257566.3:c.1354G>C	p.Glu452Gln	p.E452Q	ENST00000257566	NM_016569.3	452	Gag/Cag	7/8	1	2	FACETS	0.831	0.722	0.948	0.831	0.722	0.948	CLONAL	1	TRUE	1	0.255047139339622	2		290	642	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219531	133219531	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	84	455	0	ENST00000320574.5:c.4603G>C	p.Gly1535Arg	p.G1535R	ENST00000320574	NM_006231.2	1535	Ggc/Cgc	36/49	1	2	FACETS	0.831	0.733	0.936	0.831	0.733	0.936	CLONAL	1	TRUE	1	0.255047139339622	2		455	793	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560401	95560401	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	124	413	0	ENST00000393063.1:c.5188G>T	p.Gly1730Trp	p.G1730W	ENST00000393063	NM_030621.3	1730	Ggg/Tgg	25/28	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.255047139339622	2		413	957	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456348	99456348	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	95	438	0	ENST00000268035.6:c.1665C>A	p.Asp555Glu	p.D555E	ENST00000268035	NM_000875.3	555	gaC/gaA	8/21	1	2	FACETS	0.868	0.772	0.971	0.868	0.772	0.971	CLONAL	1	TRUE	1	0.255047139339622	2		438	858	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533364	29533364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	73	281	0	ENST00000356175.3:c.1367C>T	p.Ala456Val	p.A456V	ENST00000356175	NM_000267.3	456	gCa/gTa	12/57	1	2	FACETS	0.901	0.789	1	0.901	0.789	1	CLONAL	1	TRUE	1	0.255047139339622	2		281	635	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098409	11098409	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	131	536	0	ENST00000358026.2:c.928del	p.Arg310AlafsTer16	p.R310Afs*16	ENST00000358026	NM_001128849.1	309	ggC/gg	6/36	0.255047139339622	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.255047139339622	1		536	824	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965881	25965881	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	158	542	0	ENST00000435504.4:c.3325G>T	p.Gly1109Cys	p.G1109C	ENST00000435504		1109	Ggt/Tgt	13/13	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.255047139339622	2		542	1194	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519873	29519873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	194	639	0	ENST00000389048.3:c.1698G>T	p.Leu566Phe	p.L566F	ENST00000389048	NM_004304.4	566	ttG/ttT	9/29	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.255047139339622	2		639	1217	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021091	31021091	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	117	391	0	ENST00000375687.4:c.1090G>T	p.Gly364Cys	p.G364C	ENST00000375687	NM_015338.5	364	Ggt/Tgt	12/13	1	2	FACETS	0.972	0.875	1	0.972	0.875	1	CLONAL	1	TRUE	1	0.255047139339622	2		391	944	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286231	66286231	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	80	419	0	ENST00000273854.3:c.1455C>G	p.Ile485Met	p.I485M	ENST00000273854	NM_004439.5	485	atC/atG	6/18	1	2	FACETS	0.83	0.73	0.937	0.83	0.73	0.937	CLONAL	1	TRUE	1	0.255047139339622	2		419	756	SUCCESS
APC	324	MSKCC	GRCh37	5	112177053	112177053	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786204093	NA	P-0016423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1460	182	726	0	ENST00000257430.4:c.5762G>T	p.Gly1921Val	p.G1921V	ENST00000257430	NM_000038.5	1921	gGt/gTt	16/16	1	2	FACETS	0.869	0.799	0.943	0.869	0.799	0.943	CLONAL	1	TRUE	1	0.255047139339622	2		726	1642	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274823	38274823	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0016423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	87	301	0	ENST00000425967.3:c.1756+1G>T		p.X586_splice	ENST00000425967	NM_001174067.1	586			1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.255047139339622	2		301	681	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500810	8500810	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	90	397	0	ENST00000356435.5:c.2072C>G	p.Thr691Arg	p.T691R	ENST00000356435		691	aCa/aGa	13/35	1	2	FACETS	0.764	0.676	0.858	0.764	0.676	0.858	SUBCLONAL	1	TRUE	1	0.255047139339622	2		397	924	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940056	76940056	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	178	387	0	ENST00000373344.5:c.692G>T	p.Cys231Phe	p.C231F	ENST00000373344	NM_000489.3	231	tGt/tTt	9/35	1	1	FACETS	0.817	0.755	0.882	1	0.991	1	CLONAL	2	TRUE	0	0.255047139339622	1		387	745	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243908	46243908	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	95	459	0	ENST00000334344.6:c.2002T>G	p.Ser668Ala	p.S668A	ENST00000334344	NM_152641.2	668	Tct/Gct	15/21	0.729017505907329	3	FACETS	0.957	0.859	1			1	CLONAL	1	FALSE	NA	0.717551867052951	3		459	376	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167753	185167753	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774495315	NA	P-0016430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	55	491	0	ENST00000265026.3:c.1076C>T	p.Ser359Leu	p.S359L	ENST00000265026	NM_004721.4	359	tCa/tTa	6/14	0.444847840282535	4	FACETS	0.468	0.4	0.542			1	SUBCLONAL	1	FALSE	NA	0.717551867052951	4		491	563	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0016431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	31	2255	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.843	0.684	1	0.843	0.684	1	CLONAL	1	FALSE	1	0.267557596046326	2		2255	275	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207118	1207118	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	53	704	0	ENST00000326873.7:c.206C>A	p.Ser69Ter	p.S69*	ENST00000326873	NM_000455.4	69	tCg/tAg	1/10	0.267557596046326	1	FACETS	0.945	0.809	1	0.945	0.809	1	CLONAL	1	FALSE	0	0.267557596046326	1		704	363	SUCCESS
AR	367	MSKCC	GRCh37	X	66766357	66766386	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	-	rs746853821	NA	P-0016431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	12	99	1	ENST00000374690.3:c.1391_1420del	p.Gly464_Gly473del	p.G464_G473del	ENST00000374690	NM_000044.3	457	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGC/-	1/8	0.267557596046326	1	FACETS	0.863	0.614	1	0.863	0.614	1	CLONAL	1	FALSE	0	0.267557596046326	1		100	90	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304375	91304375	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	22	551	1	ENST00000355112.3:c.1772G>T	p.Arg591Leu	p.R591L	ENST00000355112	NM_000057.2	591	cGg/cTg	7/22	0.181181257998937	0	FACETS	0.533	0.414	0.67			1	SUBCLONAL	1	FALSE	0	0.267557596046326	0		552	226	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577572	7577572	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882004	NA	P-0016431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	47	441	0	ENST00000269305.4:c.709A>G	p.Met237Val	p.M237V	ENST00000269305	NM_001126112.2	237	Atg/Gtg	7/11	0.267557596046326	1	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	FALSE	0	0.267557596046326	1		441	292	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294268	11294268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879251235	NA	P-0016431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	27	462	3	ENST00000361445.4:c.2263C>T	p.Arg755Cys	p.R755C	ENST00000361445	NM_004958.3	755	Cgc/Tgc	14/58	1	2	FACETS	0.57	0.454	0.703	0.57	0.454	0.703	SUBCLONAL	1	FALSE	1	0.267557596046326	2		465	354	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73352342	73352342	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	61	387	1	ENST00000377767.4:c.563G>T	p.Gly188Val	p.G188V	ENST00000377767	NM_014953.3	188	gGa/gTa	3/21	0.267557596046326	4	FACETS	0.954	0.836	1	0.954	0.836	1	CLONAL	3	FALSE	1	0.267557596046326	4		388	202	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135397	30135397	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	42	353	0	ENST00000331968.5:c.421G>C	p.Asp141His	p.D141H	ENST00000331968	NM_002742.2	141	Gac/Cac	3/18	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	1	0.267557596046326	2		353	247	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984874	9984874	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	46	566	2	ENST00000330684.3:c.1091T>C	p.Ile364Thr	p.I364T	ENST00000330684	NM_001134407.1	364	aTt/aCt	4/13	0.267557596046326	1	FACETS	0.768	0.648	0.899	0.768	0.648	0.899	SUBCLONAL	1	FALSE	0	0.267557596046326	1		568	388	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448544	89448544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	40	460	0	ENST00000336596.2:c.1508C>T	p.Thr503Ile	p.T503I	ENST00000336596	NM_005233.5	503	aCt/aTt	7/17	0.267557596046326	1	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	FALSE	0	0.267557596046326	1		460	241	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696757	176696757	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs752685166	NA	P-0016431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	33	305	0	ENST00000439151.2:c.5458G>T	p.Val1820Leu	p.V1820L	ENST00000439151	NM_022455.4	1820	Gtg/Ttg	16/23	0.267557596046326	1	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	FALSE	0	0.267557596046326	1		305	184	SUCCESS
AR	367	MSKCC	GRCh37	X	66766226	66766226	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	31	302	0	ENST00000374690.3:c.1238G>T	p.Ser413Ile	p.S413I	ENST00000374690	NM_000044.3	413	aGc/aTc	1/8	0.267557596046326	1	FACETS	0.974	0.794	1	0.974	0.794	1	CLONAL	1	FALSE	0	0.267557596046326	1		302	206	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0016432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	910	607	1	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.39052865703472	3	FACETS	1	0.986	1			1	CLONAL	3	TRUE	NA	0.626490084623192	3		608	1259	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	608	387	0	ENST00000256196.4:c.68G>A	p.Gly23Asp	p.G23D	ENST00000256196		23	gGc/gAc	1/6	0.626490084623192	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	0	0.626490084623192	3		387	839	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578369	7578369	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0016433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	191	388	0	ENST00000269305.4:c.559+2T>G		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.321756387334941	2	FACETS	0.888	0.826	0.951	0.888	0.826	0.951	CLONAL	2	TRUE	0	0.368380584325521	2		388	584	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6027103	6027103	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	89	67	0	ENST00000265849.7:c.1293G>C	p.Glu431Asp	p.E431D	ENST00000265849	NM_000535.5	431	gaG/gaC	11/15	0.368380584325521	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	3	TRUE	1	0.368380584325521	4		67	192	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	193	726	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.295323494380795	2		726	957	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48586250	48586250	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	89	583	0	ENST00000342988.3:c.919G>T	p.Glu307Ter	p.E307*	ENST00000342988	NM_005359.5	307	Gag/Tag	8/12	0.261254930066151	1	FACETS	0.803	0.712	0.899	0.803	0.712	0.899	CLONAL	1	TRUE	0	0.295323494380795	1		583	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0016434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	134	653	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.295323494380795	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.295323494380795	1		653	659	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	119	641	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	0.161687631851542	2		641	1278	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105757	27105757	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	52	254	0	ENST00000324856.7:c.5371del	p.Ser1791GlnfsTer15	p.S1791Qfs*15	ENST00000324856	NM_006015.4	1790	Ttt/tt	20/20	0.161687631851542	1	FACETS	0.994	0.845	1	0.994	0.845	1	CLONAL	1	TRUE	0	0.161687631851542	1		254	595	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620644	52620645	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	TGATTCACAGACAAAAACATCCTCA	novel	NA	P-0016436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	49	443	1	ENST00000394830.3:c.3084_3108dup	p.Arg1037Ter	p.R1037*	ENST00000394830	NM_018313.4	1036	-/TGAGGATGTTTTTGTCTGTGAATCA	21/30	0.161687631851542	1	FACETS	0.629	0.531	0.738	0.629	0.531	0.738	SUBCLONAL	1	TRUE	0	0.161687631851542	1		444	885	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0016437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	103	591	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.375011111357412	1	FACETS	0.873	0.785	0.967	0.873	0.785	0.967	CLONAL	1	TRUE	0	0.375011111357412	1		592	511	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713390	30713390	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	65	413	0	ENST00000295754.5:c.715A>G	p.Thr239Ala	p.T239A	ENST00000295754	NM_003242.5	239	Aca/Gca	4/7	1	2	FACETS	0.462	0.399	0.529	0.462	0.399	0.529	SUBCLONAL	1	TRUE	1	0.375011111357412	2		413	751	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0016440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	88	346	1	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	1	2	FACETS	0.758	0.672	0.85	1	0.979	1	SUBCLONAL	2	TRUE	1	0.17772936724056	2		347	653	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0016440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	174	643	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.17772936724056	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.17772936724056	3		643	860	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0016440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	129	438	1	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	1	2	FACETS	0.807	0.731	0.887	1	0.987	1	CLONAL	2	TRUE	1	0.17772936724056	2		439	899	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057835	27057835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1434	109	836	0	ENST00000324856.7:c.1543C>T	p.Gln515Ter	p.Q515*	ENST00000324856	NM_006015.4	515	Cag/Tag	3/20	1	2	FACETS	0.795	0.711	0.885	0.795	0.711	0.885	SUBCLONAL	1	TRUE	1	0.17772936724056	2		836	1543	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426909	49426909	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	26	326	0	ENST00000301067.7:c.11579A>G	p.Gln3860Arg	p.Q3860R	ENST00000301067	NM_003482.3	3860	cAg/cGg	39/54	1	2	FACETS	0.341	0.269	0.423	0.341	0.269	0.423	SUBCLONAL	1	TRUE	1	0.372363541439121	2		326	410	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92252389	92252389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369229292	NA	P-0016442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	43	472	0	ENST00000265734.4:c.659G>A	p.Arg220His	p.R220H	ENST00000265734	NM_001259.6	220	cGt/cAt	6/8	1	2	FACETS	0.272	0.227	0.323	0.272	0.227	0.323	SUBCLONAL	1	TRUE	1	0.372363541439121	2		472	849	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	83	641	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.2	2		641	810	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0016443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	94	449	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.862	0.765	0.966	0.862	0.765	0.966	CLONAL	1	TRUE	1	0.2	2		449	1091	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016443-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	58	641	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.653	0.562	0.752	0.653	0.562	0.752	SUBCLONAL	1	TRUE	1	0.37	2		641	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0016443-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	88	449	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.574	0.508	0.646	0.574	0.508	0.646	SUBCLONAL	1	TRUE	1	0.37	2		449	828	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0016444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	396	523	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.731114906303113	2	FACETS	0.997	0.967	1	0.997	0.967	1	CLONAL	2	TRUE	0	0.759321677432671	2		523	523	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0016444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	555	643	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.624256577397443	5	FACETS	0.984	0.95	1			1	CLONAL	3	TRUE	NA	0.759321677432671	5		643	1059	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0016444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	203	457	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.576656564186826	3	FACETS	0.934	0.868	1	0.467	0.434	0.501	CLONAL	1	TRUE	1	0.759321677432671	3		457	790	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0016444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	449	472	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.702551325697975	2	FACETS	0.979	0.95	1	0.979	0.95	1	CLONAL	2	TRUE	0	0.759321677432671	2		472	604	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524486	44524486	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	79	377	0	ENST00000291552.4:c.71T>C	p.Ile24Thr	p.I24T	ENST00000291552	NM_006758.2	24	aTt/aCt	2/8	0.329341827219879	1	FACETS	0.355	0.314	0.398	0.355	0.314	0.398	INDETERMINATE	1	TRUE	0	0.759321677432671	1		377	364	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36819977	36819977	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	256	595	0	ENST00000373129.3:c.611T>C	p.Val204Ala	p.V204A	ENST00000373129	NM_032017.1	204	gTg/gCg	7/12	0.575758374846977	3	FACETS	0.95	0.89	1	0.475	0.445	0.506	CLONAL	1	TRUE	1	0.759321677432671	3		595	979	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197289	94197289	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	28	540	0	ENST00000323929.3:c.1215G>T	p.Lys405Asn	p.K405N	ENST00000323929	NM_005591.3	405	aaG/aaT	11/20	0.711367828609242	1	FACETS	0.122	0.097	0.151	0.122	0.097	0.151	SUBCLONAL	1	TRUE	0	0.759321677432671	1		540	374	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732421	74732421	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	113	227	0	ENST00000359995.5:c.488C>G	p.Ser163Cys	p.S163C	ENST00000359995	NM_001195427.1	163	tCc/tGc	2/3	0.576656564186826	3	FACETS	1	0.949	1	0.533	0.484	0.584	CLONAL	1	TRUE	1	0.759321677432671	3		227	385	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250272	39250272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397517147	NA	P-0016444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	663	996	1	ENST00000402219.2:c.1297G>A	p.Glu433Lys	p.E433K	ENST00000402219	NM_005633.3	433	Gag/Aag	10/23	0.597223386605148	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	2	0.759321677432671	4		997	1534	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84406180	84406180	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	167	472	0	ENST00000321945.7:c.46G>C	p.Gly16Arg	p.G16R	ENST00000321945	NM_139076.2	16	Ggc/Cgc	1/9	0.702551325697975	2	FACETS	0.806	0.745	0.868	0.403	0.372	0.434	CLONAL	1	TRUE	0	0.759321677432671	2		472	546	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259439	55259439	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs397517126	NA	P-0016445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	519	401	0	ENST00000275493.2:c.2497T>G	p.Leu833Val	p.L833V	ENST00000275493	NM_005228.3	833	Ttg/Gtg	21/28	0.721976835650034	5	FACETS	1	0.995	1	0.855	0.828	0.881	CLONAL	3	TRUE	1	0.887835491742676	5		401	797	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0016445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	544	577	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.729621559285599	3	FACETS	0.873	0.852	0.892	0.873	0.852	0.892	CLONAL	3	TRUE	0	0.887835491742676	3		577	676	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249022	55249022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567477136	NA	P-0016445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	613	489	0	ENST00000275493.2:c.2320G>A	p.Val774Met	p.V774M	ENST00000275493	NM_005228.3	774	Gtg/Atg	20/28	0.721976835650034	5	FACETS	1	0.996	1	0.866	0.842	0.891	CLONAL	3	TRUE	1	0.887835491742676	5		489	929	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106031	8106031	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	149	486	0	ENST00000346208.3:c.851G>A	p.Cys284Tyr	p.C284Y	ENST00000346208		284	tGc/tAc	4/6	0.765464633168243	3	FACETS	0.925	0.85	1	0.462	0.425	0.501	CLONAL	1	TRUE	1	0.887835491742676	3		486	524	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417954	32417954	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0016445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	148	397	0	ENST00000332351.3:c.1099-1G>T		p.X367_splice	ENST00000332351	NM_024426.4	367			0.738000050671969	2	FACETS	0.807	0.745	0.871	0.404	0.372	0.436	CLONAL	1	TRUE	0	0.887835491742676	2		397	413	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791854	42791854	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	379	607	0	ENST00000575354.2:c.740A>G	p.Gln247Arg	p.Q247R	ENST00000575354	NM_015125.3	247	cAg/cGg	5/20	NA	2	FACETS	0.818	0.791	0.844			1	INDETERMINATE	2	TRUE	NA	0.887835491742676	2		607	522	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455105	50455105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756772861	NA	P-0016445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	131	387	0	ENST00000331340.3:c.652G>A	p.Glu218Lys	p.E218K	ENST00000331340	NM_006060.4	218	Gaa/Aaa	6/8	0.721976835650034	5	FACETS	0.868	0.788	0.952	0.217	0.197	0.238	CLONAL	1	TRUE	1	0.887835491742676	5		387	793	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0016446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	24	138	1	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.856471806942276	2		139	54	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0016446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	154	475	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	0.374801144362549	3	FACETS	0.793	0.738	0.848	0.793	0.738	0.848	INDETERMINATE	2	TRUE	1	0.856471806942276	3		475	324	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0016446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	184	608	9	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	0.374801144362549	3	FACETS	1	0.981	1	0.579	0.538	0.62	INDETERMINATE	1	TRUE	1	0.856471806942276	3		617	530	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176338	24176338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	9	636	1	ENST00000263121.7:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000263121	NM_003073.3	377	Cgt/Tgt	9/9	0.224141530697653	1	FACETS	0.027	0.018	0.04	0.027	0.018	0.04	INDETERMINATE	1	TRUE	0	0.856471806942276	1		637	440	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432543	49432543	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	168	471	0	ENST00000301067.7:c.8596G>T	p.Glu2866Ter	p.E2866*	ENST00000301067	NM_003482.3	2866	Gag/Tag	34/54	0.37938927922533	4	FACETS	0.958	0.893	1	0.958	0.893	1	INDETERMINATE	2	TRUE	2	0.856471806942276	4		471	380	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	83	423	0				ENST00000310581	NM_198253.2	-/1132			0.230730177612944	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.73	0		423	177	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0016449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	209	1585	1	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.73	2		1586	543	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987061	69987068	+	frameshift_variant	Frame_Shift_Del	DEL	CAAATAAA	CAAATAAA	-	novel	NA	P-0016449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	207	559	0	ENST00000394351.3:c.124_131del	p.Asn42CysfsTer37	p.N42Cfs*37	ENST00000394351	NM_000248.3	41	gCAAATAAA/g	2/9	1	2	FACETS	0.998	0.933	1	0.998	0.933	1	CLONAL	1	TRUE	1	0.73	2		559	568	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034458	47034459	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0016449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	363	325	0	ENST00000377604.3:c.543_544del	p.Gln182GlyfsTer26	p.Q182Gfs*26	ENST00000377604	NM_001204468.1	181	ttGCag/ttag	6/24	1	1	FACETS		NA	1	1	0.997	1	NA	2	TRUE	0	0.73	1		325	411	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0016450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	311	570	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	0.927	0.877	0.977	0.927	0.877	0.977	CLONAL	1	TRUE	1	0.769829113951053	2		570	872	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432096	49432096	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	128	685	0	ENST00000301067.7:c.9043G>A	p.Gly3015Ser	p.G3015S	ENST00000301067	NM_003482.3	3015	Ggt/Agt	34/54	0.225708436567286	3	FACETS	1	0.972	1			1	CLONAL	1	TRUE	NA	0.225708436567286	3		685	1058	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0016452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	143	496	2	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	1	2	FACETS	0.808	0.736	0.884	1	0.988	1	CLONAL	2	TRUE	1	0.183634367656004	2		498	964	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998537	100998537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1005434284	NA	P-0016452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	82	409	0	ENST00000325455.5:c.1265C>T	p.Pro422Leu	p.P422L	ENST00000325455	NM_001202474.3	422	cCg/cTg	1/8	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.183634367656004	2		409	730	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521558	46521558	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	68	646	0	ENST00000262741.5:c.850C>A	p.Gln284Lys	p.Q284K	ENST00000262741	NM_003629.3	284	Caa/Aaa	7/10	0.183634367656004	2	FACETS	0.733	0.635	0.838	0.366	0.317	0.419	SUBCLONAL	1	TRUE	0	0.183634367656004	2		646	1011	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572932	7572932	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1192921623	NA	P-0016452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	70	342	0	ENST00000269305.4:c.1177G>A	p.Asp393Asn	p.D393N	ENST00000269305	NM_001126112.2	393	Gac/Aac	11/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.183634367656004	2		342	626	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780563	56780563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782332	NA	P-0016452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	68	420	0	ENST00000337432.4:c.578G>A	p.Arg193Gln	p.R193Q	ENST00000337432	NM_058216.2	193	cGa/cAa	4/9	0.183634367656004	1	FACETS	0.733	0.636	0.838	0.733	0.636	0.838	SUBCLONAL	1	TRUE	0	0.183634367656004	1		420	918	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610589	10610589	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	125	495	1	ENST00000171111.5:c.121G>T	p.Glu41Ter	p.E41*	ENST00000171111	NM_203500.1	41	Gag/Tag	2/6	0.183634367656004	2	FACETS	0.834	0.755	0.918	0.834	0.755	0.918	CLONAL	2	TRUE	0	0.183634367656004	2		496	816	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795012	42795012	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	76	631	0	ENST00000575354.2:c.2092G>A	p.Glu698Lys	p.E698K	ENST00000575354	NM_015125.3	698	Gag/Aag	10/20	1	2	FACETS	0.77	0.673	0.875	0.77	0.673	0.875	SUBCLONAL	1	TRUE	1	0.183634367656004	2		631	1075	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714712	52714712	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs111525410	NA	P-0016452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	48	470	1	ENST00000322088.6:c.470G>A	p.Arg157Gln	p.R157Q	ENST00000322088	NM_014225.5	157	cGa/cAa	4/15	NA	2	FACETS	0.64	0.539	0.751			1	INDETERMINATE	1	TRUE	NA	0.183634367656004	2		471	817	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570070	212570070	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs745408040	NA	P-0016452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	89	457	0	ENST00000342788.4:c.1171G>T	p.Val391Phe	p.V391F	ENST00000342788	NM_005235.2	391	Gtc/Ttc	10/28	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.183634367656004	2		457	835	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702662	52702662	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0016452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	76	227	0	ENST00000394830.3:c.237-1G>T		p.X79_splice	ENST00000394830	NM_018313.4	79			0.183634367656004	2	FACETS	0.904	0.795	1	0.904	0.795	1	CLONAL	2	TRUE	0	0.183634367656004	2		227	458	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498460	89498460	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	47	257	0	ENST00000336596.2:c.2432G>T	p.Gly811Val	p.G811V	ENST00000336596	NM_005233.5	811	gGg/gTg	14/17	0.183634367656004	3	FACETS	1	0.929	1	0.591	0.499	0.692	CLONAL	1	TRUE	1	0.183634367656004	3		257	473	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199908	128199908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	56	261	0	ENST00000341105.2:c.1397C>T	p.Ser466Phe	p.S466F	ENST00000341105	NM_032638.4	466	tCc/tTc	6/6	0.183634367656004	3	FACETS	1	0.966	1	0.742	0.637	0.856	CLONAL	1	TRUE	1	0.183634367656004	3		261	449	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279118	142279118	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	129	411	0	ENST00000350721.4:c.1528C>G	p.Gln510Glu	p.Q510E	ENST00000350721	NM_001184.3	510	Caa/Gaa	6/47	0.183634367656004	3	FACETS	0.968	0.878	1	0.968	0.878	1	CLONAL	2	TRUE	1	0.183634367656004	3		411	792	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356239	66356239	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	123	477	0	ENST00000273854.3:c.1258G>T	p.Gly420Cys	p.G420C	ENST00000273854	NM_004439.5	420	Ggc/Tgc	5/18	0.183634367656004	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.183634367656004	1		477	867	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137325971	137325971	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs755663805	NA	P-0016452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	142	520	0	ENST00000481739.1:c.1159G>T	p.Ala387Ser	p.A387S	ENST00000481739	NM_002957.4	387	Gcc/Tcc	9/10	0.183634367656004	1	FACETS	0.75	0.683	0.821	1	0.987	1	SUBCLONAL	2	TRUE	0	0.183634367656004	1		520	936	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0016454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	635	563	2	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.452432327249273	2	FACETS	0.891	0.86	0.922	0.891	0.86	0.922	CLONAL	2	TRUE	0	0.506905530416226	2		565	1406	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	223	440	1	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	1	2	FACETS	0.999	0.931	1	0.999	0.931	1	CLONAL	1	TRUE	1	0.506905530416226	2		441	881	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855957	68855957	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	326	1030	0	ENST00000261769.5:c.1766del	p.Asn589MetfsTer24	p.N589Mfs*24	ENST00000261769	NM_004360.3	589	Aat/at	12/16	0.506905530416226	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.506905530416226	1		1030	937	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871298	35871298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375672744	NA	P-0016454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	208	721	2	ENST00000303115.3:c.520G>A	p.Asp174Asn	p.D174N	ENST00000303115	NM_002185.3	174	Gat/Aat	4/8	0.253448726089335	1	FACETS	0.819	0.763	0.877	0.819	0.763	0.877	INDETERMINATE	1	TRUE	0	0.506905530416226	1		723	748	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0016454-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	142	563	2	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.16389646834625	2	FACETS	1	0.986	1	0.714	0.651	0.78	CLONAL	1	TRUE	0	0.25	2		565	795	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855957	68855957	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016454-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	104	1030	0	ENST00000261769.5:c.1766del	p.Asn589MetfsTer24	p.N589Mfs*24	ENST00000261769	NM_004360.3	589	Aat/at	12/16	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.25	2		1030	809	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871298	35871298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375672744	NA	P-0016454-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	81	721	2	ENST00000303115.3:c.520G>A	p.Asp174Asn	p.D174N	ENST00000303115	NM_002185.3	174	Gat/Aat	4/8	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.25	2		723	641	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	144	423	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.921	0.848	0.997	0.921	0.848	0.997	CLONAL	1	TRUE	1	0.710344762388076	2		423	440	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0016455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	424	411	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.25738802309489	4	FACETS	1	0.987	1			1	INDETERMINATE	3	TRUE	NA	0.710344762388076	4		411	651	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774771	73774771	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	125	575	1	ENST00000254810.4:c.316G>A	p.Glu106Lys	p.E106K	ENST00000254810	NM_005324.3	106	Gaa/Aaa	4/4	0.447194458357334	3	FACETS	0.43	0.388	0.474	0.215	0.194	0.237	SUBCLONAL	1	TRUE	1	0.710344762388076	3		576	1110	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252166	226252167	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	novel	NA	P-0016455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	58	155	0	ENST00000366813.1:c.114_115delinsTT	p.Lys38_Pro39delinsAsnSer	p.K38_P39delinsNS	ENST00000366813		38	aaACct/aaTTct	1/3	1	2	FACETS	0.923	0.808	1	0.923	0.808	1	CLONAL	1	TRUE	1	0.710344762388076	2		155	177	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203498	108203498	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	30	310	0	ENST00000278616.4:c.7798G>C	p.Glu2600Gln	p.E2600Q	ENST00000278616	NM_000051.3	2600	Gag/Cag	53/63	1	2	FACETS	0.191	0.153	0.233	0.191	0.153	0.233	SUBCLONAL	1	TRUE	1	0.710344762388076	2		310	443	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203511	108203511	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	35	340	0	ENST00000278616.4:c.7811G>C	p.Arg2604Thr	p.R2604T	ENST00000278616	NM_000051.3	2604	aGa/aCa	53/63	1	2	FACETS	0.197	0.161	0.237	0.197	0.161	0.237	SUBCLONAL	1	TRUE	1	0.710344762388076	2		340	501	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443530	49443530	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	80	443	0	ENST00000301067.7:c.3841G>T	p.Gly1281Ter	p.G1281*	ENST00000301067	NM_003482.3	1281	Gga/Tga	11/54	1	2	FACETS	0.329	0.289	0.371	0.329	0.289	0.371	SUBCLONAL	1	TRUE	1	0.710344762388076	2		443	685	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008982	152008982	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	291	501	0	ENST00000262189.6:c.640C>T	p.Gln214Ter	p.Q214*	ENST00000262189	NM_170606.2	214	Cag/Tag	5/59	1	2	FACETS	0.925	0.872	0.978	0.925	0.872	0.978	CLONAL	1	TRUE	1	0.710344762388076	2		501	886	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782740	135782740	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	155	473	0	ENST00000298552.3:c.1281del	p.Ala428GlnfsTer12	p.A428Qfs*12	ENST00000298552	NM_001162426.1	427	tcT/tc	13/23	0.710344762388076	1	FACETS	0.592	0.547	0.64	0.592	0.547	0.64	SUBCLONAL	1	TRUE	0	0.710344762388076	1		473	475	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0016456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	210	332	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.954	0.89	1	0.954	0.89	1	CLONAL	1	TRUE	1	0.659887284584985	2		332	667	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100685	67100685	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	225	519	0	ENST00000412916.2:c.383A>G	p.Asp128Gly	p.D128G	ENST00000412916		128	gAt/gGt	4/6	0.659887284584985	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.659887284584985	1		519	451	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249102	55249103	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TATGTCCGGGAACACAAAGACAATATTGGCTCCCAGTACCTGCTCAA	novel	NA	P-0016456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	18	680	0	ENST00000275493.2:c.2401_2447dup	p.Trp817MetfsTer25	p.W817Mfs*25	ENST00000275493	NM_005228.3	800	-/TATGTCCGGGAACACAAAGACAATATTGGCTCCCAGTACCTGCTCAA	20/28	1	2	FACETS	0.062	0.046	0.081	0.062	0.046	0.081	SUBCLONAL	1	TRUE	1	0.659887284584985	2		680	879	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949643	151949643	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	223	510	0	ENST00000262189.6:c.1457del	p.Asn486IlefsTer9	p.N486Ifs*9	ENST00000262189	NM_170606.2	486	aAt/at	10/59	1	2	FACETS	0.97	0.907	1	0.97	0.907	1	CLONAL	1	TRUE	1	0.659887284584985	2		510	697	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855029	76855029	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1557085898	NA	P-0016457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	12	428	0	ENST00000373344.5:c.5807A>G	p.Lys1936Arg	p.K1936R	ENST00000373344	NM_000489.3	1936	aAg/aGg	25/35	0.153272840989242	0	FACETS	0.055	0.038	0.076			1	INDETERMINATE	1	TRUE	0	0.455601359323317	0		428	525	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159041	24159042	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0016457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	205	514	0	ENST00000263121.7:c.716_717dup	p.Ala240LeufsTer28	p.A240Lfs*28	ENST00000263121	NM_003073.3	238	gcc/gcCTc	6/9	0.455601359323317	1	FACETS	0.972	0.905	1	0.972	0.905	1	CLONAL	1	TRUE	0	0.455601359323317	1		514	715	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0016458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	28	547	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.187	0.148	0.232	0.187	0.148	0.232	SUBCLONAL	1	TRUE	1	0.310135679334204	2		547	965	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849449	68849449	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	187	449	0	ENST00000261769.5:c.1353del	p.Leu452TyrfsTer3	p.L452Yfs*3	ENST00000261769	NM_004360.3	451	aTt/at	10/16	0.310135679334204	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.310135679334204	1		449	704	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859623	151859623	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0016458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	85	252	0	ENST00000262189.6:c.11039T>G	p.Leu3680Ter	p.L3680*	ENST00000262189	NM_170606.2	3680	tTa/tGa	43/59	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.310135679334204	2		252	441	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	244	423	0				ENST00000310581	NM_198253.2	-/1132			0.183188331096031	4	FACETS	1	0.988	1	1	0.988	1	INDETERMINATE	2	TRUE	2	0.922074410937958	4		423	445	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0016462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	399	381	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	0.183188331096031	4	FACETS	0.99	0.947	1	0.99	0.947	1	INDETERMINATE	2	TRUE	2	0.922074410937958	4		381	840	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413049	139413049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064795070	NA	P-0016462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	23	357	0	ENST00000277541.6:c.1093C>T	p.Arg365Cys	p.R365C	ENST00000277541	NM_017617.3	365	Cgc/Tgc	6/34	0.919440194930523	1	FACETS	0.069	0.053	0.087	0.069	0.053	0.087	SUBCLONAL	1	TRUE	0	0.922074410937958	1		357	390	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650810	48650810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	730	703	3	ENST00000376670.3:c.679G>A	p.Ala227Thr	p.A227T	ENST00000376670	NM_002049.3	227	Gcc/Acc	4/6	0.183188331096031	4	FACETS	0.982	0.95	1	0.982	0.95	1	INDETERMINATE	2	TRUE	2	0.922074410937958	4		706	1550	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430916	78430916	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0016462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	338	389	0	ENST00000370768.2:c.474-1G>A		p.X158_splice	ENST00000370768	NM_003902.3	158			0.922074410937958	1	FACETS	0.971	0.944	0.996	0.971	0.944	0.996	CLONAL	1	TRUE	0	0.922074410937958	1		389	407	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42790971	42790972	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTTAGTCCCCTTCCTGGCACCCAGCCAGCCTGACCCCT	novel	NA	P-0016462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	353	520	0	ENST00000575354.2:c.118_155dup	p.Val53Ter	p.V53*	ENST00000575354	NM_015125.3	39	tcc/tcCTTAGTCCCCTTCCTGGCACCCAGCCAGCCTGACCCCTc	2/20	0.922074410937958	1	FACETS	0.459	0.436	0.482	0.459	0.436	0.482	SUBCLONAL	1	TRUE	0	0.922074410937958	1		520	900	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121805	2121807	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs137854104	NA	P-0016463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1360	163	523	0	ENST00000219476.3:c.1973_1975del	p.Lys658del	p.K658del	ENST00000219476	NM_000548.3	656	gAGAag/gag	19/42	0.498099869559233	5	FACETS	0.751	0.687	0.818	0.25	0.229	0.273	SUBCLONAL	1	TRUE	2	0.498099869559233	5		523	1523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578496	7578496	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	689	758	0	ENST00000269305.4:c.434T>G	p.Leu145Arg	p.L145R	ENST00000269305	NM_001126112.2	145	cTg/cGg	5/11	0.437881969165932	1	FACETS	0.751	0.726	0.775	1	0.997	1	SUBCLONAL	2	TRUE	0	0.498099869559233	1		758	1384	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0016463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	151	276	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	0.498099869559233	3	FACETS	0.904	0.827	0.984	0.452	0.413	0.492	CLONAL	1	TRUE	1	0.498099869559233	3		276	838	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16203058	16203058	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	252	410	0	ENST00000375759.3:c.766C>G	p.Gln256Glu	p.Q256E	ENST00000375759	NM_015001.2	256	Cag/Gag	3/15	0.498099869559233	4	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.498099869559233	4		410	1305	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652976	29652979	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	rs1085307459	NA	P-0016463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	614	404	1	ENST00000356175.3:c.4914_4917del	p.Lys1640GlyfsTer36	p.K1640Gfs*36	ENST00000356175	NM_000267.3	1637	ttTCTC/tt	36/57	0.441522435859916	4	FACETS	0.981	0.947	1	0.736	0.71	0.761	CLONAL	3	TRUE	0	0.498099869559233	4		405	1255	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589610	67589611	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAAAAGTCGAGAATATGATAGATT	novel	NA	P-0016463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	268	318	0	ENST00000274335.5:c.1375_1398dup	p.Lys459_Leu466dup	p.K459_L466dup	ENST00000274335		459	gaa/gaAAAAAGTCGAGAATATGATAGATTa	10/15	0.43819429448926	3	FACETS	1	0.991	1	0.438	0.41	0.465	CLONAL	1	TRUE	0	0.498099869559233	3		318	1024	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148669	20148669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	256	544	0	ENST00000379607.5:c.394G>A	p.Asp132Asn	p.D132N	ENST00000379607	NM_001412.3	132	Gat/Aat	6/7	0.149267579021506	3	FACETS	1	0.979	1	0.369	0.345	0.394	INDETERMINATE	1	TRUE	0	0.498099869559233	3		544	1160	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028886	47028886	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	89	198	0	ENST00000377604.3:c.190C>T	p.Gln64Ter	p.Q64*	ENST00000377604	NM_001204468.1	64	Cag/Tag	3/24	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.551793115531479	1		198	166	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117799	108117799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202160435	NA	P-0016464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	144	367	0	ENST00000278616.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000278616	NM_000051.3	337	cGt/cAt	8/63	0.534508259222836	1	FACETS	0.724	0.664	0.786	0.724	0.664	0.786	SUBCLONAL	1	TRUE	0	0.551793115531479	1		367	522	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604787	48604787	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519741	NA	P-0016464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	28	383	0	ENST00000342988.3:c.1609G>T	p.Asp537Tyr	p.D537Y	ENST00000342988	NM_005359.5	537	Gac/Tac	12/12	0.232980351845373	5	FACETS	0.257	0.204	0.317			1	INDETERMINATE	1	TRUE	NA	0.551793115531479	5		383	722	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110032	115110032	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	147	641	0	ENST00000257566.3:c.1846T>A	p.Ser616Thr	p.S616T	ENST00000257566	NM_016569.3	616	Tct/Act	8/8	0.547120793804053	3	FACETS	1	0.946	1	0.522	0.478	0.568	CLONAL	1	TRUE	1	0.551793115531479	3		641	651	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435004	110435004	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	200	543	1	ENST00000375856.3:c.3397G>T	p.Ala1133Ser	p.A1133S	ENST00000375856	NM_003749.2	1133	Gcc/Tcc	1/2	1	2	FACETS	0.896	0.832	0.962	0.896	0.832	0.962	CLONAL	1	TRUE	1	0.551793115531479	2		544	809	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554234	29554234	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0016464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	130	354	1	ENST00000356175.3:c.2252-2A>T		p.X751_splice	ENST00000356175	NM_000267.3	751			0.378271134076005	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.551793115531479	1		355	292	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113778	11113778	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	164	554	0	ENST00000358026.2:c.1886C>G	p.Thr629Arg	p.T629R	ENST00000358026	NM_001128849.1	629	aCa/aGa	12/36	1	2	FACETS	0.819	0.753	0.887	0.819	0.753	0.887	CLONAL	1	TRUE	1	0.551793115531479	2		554	726	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180651	56180651	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	74	319	0	ENST00000399503.3:c.3980C>T	p.Ala1327Val	p.A1327V	ENST00000399503	NM_005921.1	1327	gCa/gTa	16/20	0.276966227603095	2	FACETS	0.593	0.521	0.671	0.297	0.26	0.336	INDETERMINATE	1	TRUE	0	0.551793115531479	2		319	452	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562798	176562798	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	133	607	0	ENST00000439151.2:c.694C>G	p.Gln232Glu	p.Q232E	ENST00000439151	NM_022455.4	232	Cag/Gag	2/23	1	2	FACETS	0.449	0.407	0.494	0.449	0.407	0.494	SUBCLONAL	1	TRUE	1	0.551793115531479	2		607	1073	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030369	180030369	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	206	547	0	ENST00000261937.6:c.3915T>G	p.Asn1305Lys	p.N1305K	ENST00000261937	NM_182925.4	1305	aaT/aaG	30/30	1	2	FACETS	0.861	0.8	0.924	0.861	0.8	0.924	CLONAL	1	TRUE	1	0.551793115531479	2		547	867	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969150	93969150	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	56	359	1	ENST00000369303.4:c.1846G>T	p.Asp616Tyr	p.D616Y	ENST00000369303	NM_004440.3	616	Gac/Tac	10/17	1	2	FACETS	0.49	0.421	0.565	0.49	0.421	0.565	SUBCLONAL	1	TRUE	1	0.551793115531479	2		360	414	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969156	93969156	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	31	349	0	ENST00000369303.4:c.1840T>C	p.Tyr614His	p.Y614H	ENST00000369303	NM_004440.3	614	Tat/Cat	10/17	1	2	FACETS	0.264	0.213	0.322	0.264	0.213	0.322	SUBCLONAL	1	TRUE	1	0.551793115531479	2		349	425	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8339020	8339020	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	75	436	0	ENST00000356435.5:c.5281G>A	p.Glu1761Lys	p.E1761K	ENST00000356435		1761	Gaa/Aaa	32/35	0.303841038336306	0	FACETS	0.225	0.197	0.255			1	INDETERMINATE	1	TRUE	0	0.551793115531479	0		436	542	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608342	100608342	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	G	novel	NA	P-0016464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	168	264	0	ENST00000308731.7:c.1751-3T>C		p.X584_splice	ENST00000308731	NM_000061.2	584			1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.551793115531479	1		264	342	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0016464-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	103	486	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	1	2	FACETS	0.808	0.723	0.898	0.808	0.723	0.898	CLONAL	1	FALSE	1	0.333856693961508	2		486	764	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0016464-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	136	413	1	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	FALSE	1	0.333856693961508	2		414	800	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604701	48604701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555687572	NA	P-0016464-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	99	305	0	ENST00000342988.3:c.1523G>A	p.Gly508Asp	p.G508D	ENST00000342988	NM_005359.5	508	gGc/gAc	12/12	0.333856693961508	1	FACETS	0.922	0.826	1	0.922	0.826	1	CLONAL	1	FALSE	0	0.333856693961508	1		305	536	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245481	46245481	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1443868779	NA	P-0016464-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	31	248	0	ENST00000334344.6:c.3575C>G	p.Ala1192Gly	p.A1192G	ENST00000334344	NM_152641.2	1192	gCa/gGa	15/21	1	2	FACETS	0.439	0.355	0.534	0.439	0.355	0.534	SUBCLONAL	1	FALSE	1	0.333856693961508	2		248	423	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661847	227661847	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016464-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	65	701	0	ENST00000305123.5:c.1608C>G	p.His536Gln	p.H536Q	ENST00000305123	NM_005544.2	536	caC/caG	1/2	1	2	FACETS	0.357	0.308	0.411	0.357	0.308	0.411	SUBCLONAL	1	FALSE	1	0.333856693961508	2		701	1090	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057520005	NA	P-0016465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	848	765	0	ENST00000269305.4:c.820G>T	p.Val274Phe	p.V274F	ENST00000269305	NM_001126112.2	274	Gtt/Ttt	8/11	0.697340831558926	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.697340831558926	1		765	1404	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199946	108199947	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	412	335	0	ENST00000278616.4:c.7289dup	p.His2430GlnfsTer2	p.H2430Qfs*2	ENST00000278616	NM_000051.3	2430	cat/cAat	49/63	0.697340831558926	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.697340831558926	1		335	716	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954379	48954379	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0016465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	414	292	0	ENST00000267163.4:c.1498+2T>G		p.X500_splice	ENST00000267163	NM_000321.2	500			0.697340831558926	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.697340831558926	1		292	674	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745103	41745103	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs751098286	NA	P-0016465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	283	645	0	ENST00000301178.4:c.1169C>A	p.Thr390Asn	p.T390N	ENST00000301178	NM_021913.4	390	aCc/aAc	9/20	0.697340831558926	1	FACETS	0.712	0.672	0.751	0.712	0.672	0.751	SUBCLONAL	1	TRUE	0	0.697340831558926	1		645	743	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630140	100630140	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	46	434	0	ENST00000308731.7:c.133G>C	p.Glu45Gln	p.E45Q	ENST00000308731	NM_000061.2	45	Gaa/Caa	2/19	0.501803055418953	1	FACETS	0.098	0.082	0.116	0.098	0.082	0.116	SUBCLONAL	1	TRUE	0	0.697340831558926	1		434	875	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0016466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	72	547	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	0.86	0.754	0.657	0.86	SUBCLONAL	1	FALSE	1	0.186456709521763	2		547	1024	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829039	128829040	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs570242755	NA	P-0016466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	11	20	0	ENST00000249373.3:c.67_69dup	p.Leu23dup	p.L23dup	ENST00000249373	NM_005631.4	23	ggg/ggGCTg	1/12	1	2	FACETS	0.936	0.671	1	1	0.916	1	CLONAL	3	FALSE	1	0.186456709521763	2		20	42	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115971	8115972	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	157	266	0	ENST00000346208.3:c.1318dup	p.Thr440AsnfsTer67	p.T440Nfs*67	ENST00000346208		439	-/A	6/6	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.520114509997689	2		266	527	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78704367	78704367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780768526	NA	P-0016468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	180	345	0	ENST00000306801.3:c.515C>T	p.Thr172Met	p.T172M	ENST00000306801	NM_020761.2	172	aCg/aTg	5/34	0.430199763611763	5	FACETS	1	0.984	1	0.312	0.287	0.338	CLONAL	1	TRUE	1	0.520114509997689	5		345	988	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063718	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0016469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	59	188	0	ENST00000412916.2:c.165+2dup		p.X55_splice	ENST00000412916		55			0.449528366180557	1	FACETS	0.913	0.796	1	0.913	0.796	1	CLONAL	1	TRUE	0	0.449528366180557	1		188	223	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115750	8115750	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs104894164	NA	P-0016469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	198	564	0	ENST00000346208.3:c.1096C>T	p.Arg366Ter	p.R366*	ENST00000346208		366	Cga/Tga	6/6	1	2	FACETS	0.923	0.855	0.994	0.923	0.855	0.994	CLONAL	1	TRUE	1	0.449528366180557	2		564	954	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562547	21562547	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	20	30	0	ENST00000382592.4:c.1372G>A	p.Val458Met	p.V458M	ENST00000382592	NM_014572.2	458	Gtg/Atg	4/8	1	2	FACETS	0.767	0.61	0.936	1	0.929	1	CLONAL	2	TRUE	1	0.449528366180557	2		30	58	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590713	95590713	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	93	305	1	ENST00000393063.1:c.1196A>T	p.Glu399Val	p.E399V	ENST00000393063	NM_030621.3	399	gAg/gTg	9/28	0.217204045257759	2	FACETS	0.838	0.748	0.933	0.419	0.374	0.467	INDETERMINATE	1	TRUE	0	0.449528366180557	2		306	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0016470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	20	435	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	1	2	FACETS	0.298	0.227	0.382	0.298	0.227	0.382	SUBCLONAL	1	TRUE	1	0.2	2		435	671	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913499	NA	P-0016470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	48	219	0	ENST00000345146.2:c.394C>A	p.Arg132Ser	p.R132S	ENST00000345146	NM_005896.2	132	Cgt/Agt	4/10	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.2	2		219	395	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917805	29917805	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	107	697	2	ENST00000389048.3:c.863G>A	p.Trp288Ter	p.W288*	ENST00000389048	NM_004304.4	288	tGg/tAg	3/29	1	2	FACETS	0.843	0.758	0.934	0.843	0.758	0.934	CLONAL	1	TRUE	1	0.38917877113819	2		699	652	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0016473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	643	547	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	0.985	1	CLONAL	1	TRUE	1	0.850003873755049	2		547	1460	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919231	178919231	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	391	363	0	ENST00000263967.3:c.716T>G	p.Leu239Arg	p.L239R	ENST00000263967	NM_006218.2	239	cTa/cGa	4/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.850003873755049	2		363	888	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061461	38061461	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	336	283	0	ENST00000250448.2:c.528C>G	p.Ile176Met	p.I176M	ENST00000250448	NM_004496.3	176	atC/atG	2/2	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.850003873755049	2		283	783	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804317	43804317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750046020	NA	P-0016473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	546	526	1	ENST00000372470.3:c.317C>T	p.Pro106Leu	p.P106L	ENST00000372470	NM_005373.2	106	cCg/cTg	3/12	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.850003873755049	2		527	1219	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031871	10031871	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567186996	NA	P-0016473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	510	524	0	ENST00000330684.3:c.952G>A	p.Ala318Thr	p.A318T	ENST00000330684	NM_001134407.1	318	Gcc/Acc	3/13	0.480978540996161	4	FACETS	1	0.995	1			1	INDETERMINATE	1	TRUE	NA	0.850003873755049	4		524	1717	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367267	50367267	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs919149752	NA	P-0016473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	362	363	0	ENST00000331340.3:c.74A>T	p.Asp25Val	p.D25V	ENST00000331340	NM_006060.4	25	gAt/gTt	3/8	0.850003873755049	3	FACETS	0.957	0.907	1	0.479	0.453	0.504	CLONAL	1	TRUE	1	0.850003873755049	3		363	1268	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874644	151874645	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0016473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	324	316	0	ENST00000262189.6:c.7893_7894del	p.Gln2632ThrfsTer24	p.Q2632Tfs*24	ENST00000262189	NM_170606.2	2631	tcTCaa/tcaa	38/59	0.850003873755049	3	FACETS	0.975	0.922	1	0.488	0.461	0.515	CLONAL	1	TRUE	1	0.850003873755049	3		316	1114	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258907	16258907	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200349060	NA	P-0016474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	180	738	2	ENST00000375759.3:c.6172G>A	p.Ala2058Thr	p.A2058T	ENST00000375759	NM_015001.2	2058	Gcc/Acc	11/15	0.437373834147513	1	FACETS	0.43	0.398	0.463	0.43	0.398	0.463	INDETERMINATE	1	FALSE	0	0.811487295484887	1		740	613	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285570	46285570	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs78222561	NA	P-0016474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	59	212	0	ENST00000334344.6:c.4930C>T	p.Gln1644Ter	p.Q1644*	ENST00000334344	NM_152641.2	1644	Cag/Tag	17/21	1	2	FACETS	0.586	0.51	0.668	0.586	0.51	0.668	SUBCLONAL	1	FALSE	1	0.811487295484887	2		212	248	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012485	29012485	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	novel	NA	P-0016474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	39	327	0	ENST00000282397.4:c.389-3C>T		p.X130_splice	ENST00000282397	NM_002019.4	130			1	2	FACETS	0.275	0.229	0.327	0.275	0.229	0.327	SUBCLONAL	1	FALSE	1	0.811487295484887	2		327	349	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56832399	56832399	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	72	342	0	ENST00000308159.5:c.309G>C	p.Lys103Asn	p.K103N	ENST00000308159	NM_014669.4	103	aaG/aaC	4/22	0.811487295484887	1	FACETS	0.401	0.354	0.45	0.401	0.354	0.45	SUBCLONAL	1	FALSE	0	0.811487295484887	1		342	263	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063640	67063640	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	171	383	0	ENST00000412916.2:c.89C>G	p.Thr30Arg	p.T30R	ENST00000412916		30	aCg/aGg	2/6	0.811487295484887	1	FACETS	0.998	0.946	1	0.998	0.946	1	CLONAL	1	FALSE	0	0.811487295484887	1		383	251	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856002	68856002	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	327	546	3	ENST00000261769.5:c.1810G>T	p.Glu604Ter	p.E604*	ENST00000261769	NM_004360.3	604	Gag/Tag	12/16	0.811487295484887	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	0	0.811487295484887	1		549	456	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762475	41762475	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	115	426	0	ENST00000301178.4:c.2155G>A	p.Glu719Lys	p.E719K	ENST00000301178	NM_021913.4	719	Gag/Aag	18/20	1	2	FACETS	0.456	0.411	0.502	0.456	0.411	0.502	SUBCLONAL	1	FALSE	1	0.811487295484887	2		426	622	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271393	26271393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	96	314	0	ENST00000305910.3:c.220G>A	p.Glu74Lys	p.E74K	ENST00000305910	NM_003534.2	74	Gaa/Aaa	1/1	0.269225890081756	2	FACETS	0.708	0.638	0.782	0.354	0.319	0.391	INDETERMINATE	1	FALSE	0	0.811487295484887	2		314	334	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851412	151851412	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	149	568	0	ENST00000262189.6:c.12079G>T	p.Glu4027Ter	p.E4027*	ENST00000262189	NM_170606.2	4027	Gag/Tag	47/59	NA	2	FACETS	0.658	0.604	0.714			1	INDETERMINATE	1	FALSE	NA	0.811487295484887	2		568	558	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753130	128753130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	125	428	0	ENST00000377970.2:c.1291G>A	p.Glu431Lys	p.E431K	ENST00000377970	NM_002467.4	431	Gaa/Aaa	3/3	NA	2	FACETS	0.664	0.605	0.725			1	INDETERMINATE	1	FALSE	NA	0.811487295484887	2		428	464	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022096	5022096	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	93	471	0	ENST00000381652.3:c.109C>T	p.Pro37Ser	p.P37S	ENST00000381652	NM_004972.3	37	Cca/Tca	3/25	1	2	FACETS	0.516	0.461	0.574	0.516	0.461	0.574	SUBCLONAL	1	FALSE	1	0.811487295484887	2		471	444	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939175	76939175	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	94	552	1	ENST00000373344.5:c.1573C>A	p.Pro525Thr	p.P525T	ENST00000373344	NM_000489.3	525	Cca/Aca	9/35	0.113585162423053	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.811487295484887	0		553	440	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	171	349	0	ENST00000206249.3:c.1607T>A	p.Leu536His	p.L536H	ENST00000206249	NM_000125.3	536	cTc/cAc	8/8	0.44349678275745	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.44349678275745	1		349	589	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844109	68844110	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	164	429	0	ENST00000261769.5:c.698dup	p.His233GlnfsTer11	p.H233Qfs*11	ENST00000261769	NM_004360.3	233	cac/cAac	6/16	0.44349678275745	1	FACETS	0.937	0.864	1	0.937	0.864	1	CLONAL	1	TRUE	0	0.44349678275745	1		429	614	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240271	5240271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145504993	NA	P-0016475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	239	611	0	ENST00000357368.4:c.1643C>T	p.Pro548Leu	p.P548L	ENST00000357368	NM_002850.3	548	cCg/cTg	12/38	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.44349678275745	2		611	996	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520017	NA	P-0016478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	337	699	1	ENST00000326873.7:c.647C>T	p.Ser216Phe	p.S216F	ENST00000326873	NM_000455.4	216	tCc/tTc	5/10	0.621940438123563	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.735022262363566	1		700	578	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259089	153259089	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0016478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	40	207	0	ENST00000281708.4:c.727-1G>C		p.X243_splice	ENST00000281708	NM_033632.3	243			0.674281766696904	2	FACETS	1	0.931	1	0.573	0.493	0.655	CLONAL	1	TRUE	0	0.735022262363566	2		207	95	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798075	45798075	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553127975	NA	P-0016478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	174	544	0	ENST00000450313.1:c.776C>T	p.Ser259Phe	p.S259F	ENST00000450313	NM_012222.2	259	tCc/tTc	9/16	0.53255397391336	4	FACETS	1	0.988	1	0.457	0.423	0.492	CLONAL	1	TRUE	1	0.735022262363566	4		544	599	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32899272	32899272	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555280859	NA	P-0016478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	77	437	1	ENST00000380152.3:c.376C>T	p.Gln126Ter	p.Q126*	ENST00000380152		126	Caa/Taa	4/27	0.628369981672431	3	FACETS	1	0.954	1	0.381	0.338	0.424	CLONAL	1	TRUE	0	0.735022262363566	3		438	251	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981195	55981195	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	53	471	0	ENST00000263923.4:c.504G>C	p.Lys168Asn	p.K168N	ENST00000263923	NM_002253.2	168	aaG/aaC	5/30	0.674281766696904	2	FACETS	1	0.892	1	0.511	0.447	0.578	CLONAL	1	TRUE	0	0.735022262363566	2		471	141	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753175	57753175	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	49	274	0	ENST00000274289.3:c.841G>A	p.Glu281Lys	p.E281K	ENST00000274289	NM_006622.3	281	Gaa/Aaa	7/14	0.670344656748934	4	FACETS	1	0.881	1	0.516	0.442	0.596	CLONAL	1	TRUE	2	0.735022262363566	4		274	224	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002653	37002653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	66	304	0	ENST00000358127.4:c.596G>A	p.Arg199Lys	p.R199K	ENST00000358127	NM_001280556.1	199	aGa/aAa	5/10	0.632894476178428	4	FACETS	0.809	0.706	0.92	0.405	0.353	0.46	CLONAL	1	TRUE	2	0.735022262363566	4		304	385	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0016479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	172	561	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.967	0.892	1	0.967	0.892	1	CLONAL	1	TRUE	1	0.492266014177944	2		561	723	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103410	2103410	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1478204355	NA	P-0016479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	89	601	1	ENST00000219476.3:c.293G>A	p.Arg98Gln	p.R98Q	ENST00000219476	NM_000548.3	98	cGg/cAg	4/42	1	2	FACETS	0.371	0.328	0.417	0.371	0.328	0.417	SUBCLONAL	1	TRUE	1	0.492266014177944	2		602	974	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223853	53223853	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1157	138	965	0	ENST00000375401.3:c.3506C>T	p.Ser1169Leu	p.S1169L	ENST00000375401	NM_004187.3	1169	tCg/tTg	23/26	NA	2	FACETS	0.433	0.393	0.476			1	INDETERMINATE	1	TRUE	NA	0.492266014177944	2		965	1295	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016479-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	215	423	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.819065102452235	2		423	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0016479-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	378	505	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.819065102452235	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.819065102452235	1		505	511	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692851	89692851	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016479-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	203	267	0	ENST00000371953.3:c.335T>A	p.Leu112Gln	p.L112Q	ENST00000371953	NM_000314.4	112	cTa/cAa	5/9	0.819065102452235	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.819065102452235	2		267	240	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670897	30670897	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016479-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	340	791	0	ENST00000376406.3:c.5849del	p.Leu1950ArgfsTer21	p.L1950Rfs*21	ENST00000376406	NM_014641.2	1950	cTg/cg	12/15	0.49403769561438	4	FACETS	1	0.992	1	0.414	0.391	0.437	CLONAL	1	TRUE	1	0.819065102452235	4		791	1217	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0016481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	81	806	3	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.352037936843783	1	FACETS	0.76	0.671	0.854	0.76	0.671	0.854	SUBCLONAL	1	TRUE	0	0.352037936843783	1		809	499	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941654	48941654	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs776534331	NA	P-0016481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	37	334	0	ENST00000267163.4:c.964G>T	p.Glu322Ter	p.E322*	ENST00000267163	NM_000321.2	322	Gaa/Taa	10/27	0.352037936843783	1	FACETS	0.946	0.79	1	0.946	0.79	1	CLONAL	1	TRUE	0	0.352037936843783	1		334	183	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	8	495	0	ENST00000269305.4:c.528C>A	p.Cys176Ter	p.C176*	ENST00000269305	NM_001126112.2	176	tgC/tgA	5/11	0.352037936843783	1	FACETS	0.117	0.075	0.173	0.117	0.075	0.173	SUBCLONAL	1	TRUE	0	0.352037936843783	1		495	319	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841345	15841345	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	34	358	0	ENST00000307771.7:c.1429C>T	p.Gln477Ter	p.Q477*	ENST00000307771	NM_005089.3	477	Cag/Tag	11/11	1	1	FACETS	0.776	0.64	0.927	0.776	0.64	0.927	CLONAL	1	TRUE	0	0.352037936843783	1		358	205	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097742	27097742	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	65	719	0	ENST00000324856.7:c.3331G>T	p.Glu1111Ter	p.E1111*	ENST00000324856	NM_006015.4	1111	Gaa/Taa	12/20	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.352037936843783	2		719	368	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120508112	120508112	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	19	525	1	ENST00000256646.2:c.1645G>T	p.Asp549Tyr	p.D549Y	ENST00000256646	NM_024408.3	549	Gat/Tat	10/34	1	2	FACETS	0.371	0.281	0.476	0.371	0.281	0.476	SUBCLONAL	1	TRUE	1	0.352037936843783	2		526	291	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851298	156851298	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	116	714	1	ENST00000524377.1:c.2255G>T	p.Cys752Phe	p.C752F	ENST00000524377	NM_002529.3	752	tGc/tTc	17/17	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.352037936843783	2		715	456	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737021	162737021	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	35	408	0	ENST00000367921.3:c.1165C>G	p.Pro389Ala	p.P389A	ENST00000367921	NM_006182.2	389	Cca/Gca	11/18	1	2	FACETS	0.808	0.667	0.965	0.808	0.667	0.965	CLONAL	1	TRUE	1	0.352037936843783	2		408	246	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333034	70333034	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	66	905	0	ENST00000373644.4:c.939C>A	p.Asn313Lys	p.N313K	ENST00000373644	NM_030625.2	313	aaC/aaA	2/12	0.320280330635262	1	FACETS	0.975	0.853	1	0.975	0.853	1	CLONAL	1	TRUE	0	0.352037936843783	1		905	317	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444313	49444313	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	81	741	0	ENST00000301067.7:c.3058C>T	p.Leu1020Phe	p.L1020F	ENST00000301067	NM_003482.3	1020	Ctt/Ttt	11/54	1	2	FACETS	0.971	0.858	1	0.971	0.858	1	CLONAL	1	TRUE	1	0.352037936843783	2		741	474	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245312	133245312	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	80	716	0	ENST00000320574.5:c.1935G>C	p.Met645Ile	p.M645I	ENST00000320574	NM_006231.2	645	atG/atC	18/49	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.352037936843783	2		716	398	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335944	73335944	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	32	434	0	ENST00000377767.4:c.2351A>T	p.Asp784Val	p.D784V	ENST00000377767	NM_014953.3	784	gAt/gTt	18/21	0.352037936843783	1	FACETS	0.925	0.76	1	0.925	0.76	1	CLONAL	1	TRUE	0	0.352037936843783	1		434	162	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220687	1220687	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	107	798	0	ENST00000326873.7:c.706del	p.Val236TrpfsTer51	p.V236Wfs*51	ENST00000326873	NM_000455.4	235	aaG/aa	5/10	0.352037936843783	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.352037936843783	1		798	403	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212692	36212692	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	66	684	0	ENST00000222270.7:c.2443G>T	p.Ala815Ser	p.A815S	ENST00000222270	NM_014727.1	815	Gca/Tca	3/37	1	2	FACETS	0.826	0.719	0.941	0.826	0.719	0.941	CLONAL	1	TRUE	1	0.352037936843783	2		684	454	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474059	29474059	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	39	674	0	ENST00000389048.3:c.2116C>A	p.Gln706Lys	p.Q706K	ENST00000389048	NM_004304.4	706	Cag/Aag	12/29	1	2	FACETS	0.57	0.473	0.677	0.57	0.473	0.677	SUBCLONAL	1	TRUE	1	0.352037936843783	2		674	389	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546622	9546622	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	19	471	0	ENST00000353224.5:c.1400C>A	p.Thr467Asn	p.T467N	ENST00000353224	NM_177990.2	467	aCc/aAc	5/10	1	2	FACETS	0.398	0.302	0.511	0.398	0.302	0.511	SUBCLONAL	1	TRUE	1	0.352037936843783	2		471	271	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801174	1801174	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	57	766	0	ENST00000260795.2:c.303C>G	p.His101Gln	p.H101Q	ENST00000260795		101	caC/caG	2/17	0.333742630123718	1	FACETS	0.691	0.595	0.795	0.691	0.595	0.795	SUBCLONAL	1	TRUE	0	0.352037936843783	1		766	386	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152569	56152569	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	104	270	0	ENST00000399503.3:c.625G>T	p.Gly209Trp	p.G209W	ENST00000399503	NM_005921.1	209	Ggg/Tgg	2/20	0.179338939382285	3	FACETS	0.881	0.802	0.961			1	INDETERMINATE	3	TRUE	NA	0.352037936843783	3		270	263	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045838	26045838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755131918	NA	P-0016481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	60	338	0	ENST00000540144.1:c.200C>T	p.Pro67Leu	p.P67L	ENST00000540144	NM_003531.2	67	cCg/cTg	1/1	0.16957260261757	3	FACETS	1	0.925	1	0.552	0.478	0.632	INDETERMINATE	1	TRUE	1	0.352037936843783	3		338	363	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200086	138200086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765245305	NA	P-0016481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	52	372	0	ENST00000237289.4:c.1504C>T	p.Arg502Trp	p.R502W	ENST00000237289	NM_001270507.1	502	Cgg/Tgg	7/9	0.16957260261757	3	FACETS	1	0.861	1	0.504	0.43	0.583	INDETERMINATE	1	TRUE	1	0.352037936843783	3		372	345	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992764	68992764	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs769067107	NA	P-0016481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	27	763	0	ENST00000288368.4:c.1729C>T	p.Arg577Ter	p.R577*	ENST00000288368	NM_024870.2	577	Cga/Tga	16/40	0.352037936843783	1	FACETS	0.43	0.343	0.529	0.43	0.343	0.529	SUBCLONAL	1	TRUE	0	0.352037936843783	1		763	294	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436594	8436594	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	25	559	0	ENST00000356435.5:c.4084G>T	p.Glu1362Ter	p.E1362*	ENST00000356435		1362	Gag/Tag	24/35	0.352037936843783	1	FACETS	0.61	0.484	0.752	0.61	0.484	0.752	SUBCLONAL	1	TRUE	0	0.352037936843783	1		559	192	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486032	8486032	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	15	500	0	ENST00000356435.5:c.2785G>T	p.Gly929Cys	p.G929C	ENST00000356435		929	Ggc/Tgc	17/35	0.352037936843783	1	FACETS	0.355	0.26	0.468	0.355	0.26	0.468	SUBCLONAL	1	TRUE	0	0.352037936843783	1		500	198	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398262	25398262	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913538	NA	P-0016482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	19	680	0	ENST00000311936.3:c.57G>T	p.Leu19Phe	p.L19F	ENST00000311936	NM_004985.3	19	ttG/ttT	2/5	0.251866237106563	4	FACETS	0.662	0.501	0.852	0.331	0.25	0.426	SUBCLONAL	1	TRUE	2	0.15	4		680	440	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994365	25994365	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	16	345	0	ENST00000435504.4:c.448C>G	p.Pro150Ala	p.P150A	ENST00000435504		150	Cca/Gca	6/13	0.3	3	FACETS	0.757	0.559	0.994			1	CLONAL	1	TRUE	NA	0.15	3		345	303	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437439	49437439	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	188	600	0	ENST00000301067.7:c.5446G>T	p.Glu1816Ter	p.E1816*	ENST00000301067	NM_003482.3	1816	Gaa/Taa	23/54	0.195066956717727	4	FACETS	0.818	0.76	0.877	0.818	0.76	0.877	INDETERMINATE	2	TRUE	2	0.61304042065201	4		600	605	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992619	72992619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	154	431	0	ENST00000268489.5:c.1426G>A	p.Glu476Lys	p.E476K	ENST00000268489	NM_006885.3	476	Gag/Aag	2/10	0.310551051293013	4	FACETS	0.917	0.847	0.988			1	INDETERMINATE	2	TRUE	NA	0.61304042065201	4		431	442	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965707	93965707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752253692	NA	P-0016483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	104	538	0	ENST00000369303.4:c.2221G>A	p.Gly741Arg	p.G741R	ENST00000369303	NM_004440.3	741	Gga/Aga	13/17	0.281689456813826	4	FACETS	0.56	0.501	0.624	0.28	0.25	0.312	INDETERMINATE	1	TRUE	2	0.61304042065201	4		538	977	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs786203436	NA	P-0016484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	60	602	0	ENST00000269305.4:c.487T>G	p.Tyr163Asp	p.Y163D	ENST00000269305	NM_001126112.2	163	Tac/Gac	5/11	1	2	FACETS	0.893	0.767	1	0.893	0.767	1	CLONAL	1	TRUE	1	0.16	2		602	840	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202843	133202843	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369748519	NA	P-0016484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	33	648	0	ENST00000320574.5:c.6391C>T	p.Arg2131Cys	p.R2131C	ENST00000320574	NM_006231.2	2131	Cgc/Tgc	46/49	0.170853801717663	1	FACETS	0.601	0.488	0.73	0.601	0.488	0.73	SUBCLONAL	1	TRUE	0	0.16	1		648	631	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348948	11348948	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	47	529	0	ENST00000332029.2:c.388T>C	p.Phe130Leu	p.F130L	ENST00000332029	NM_003745.1	130	Ttt/Ctt	2/2	1	2	FACETS	0.705	0.593	0.83	0.705	0.593	0.83	SUBCLONAL	1	TRUE	1	0.16	2		529	833	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290223	15290223	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	143	653	0	ENST00000263388.2:c.3412A>C	p.Ile1138Leu	p.I1138L	ENST00000263388	NM_000435.2	1138	Att/Ctt	21/33	1	2	FACETS	0.819	0.745	0.897	1	0.988	1	CLONAL	2	TRUE	1	0.16	2		653	1091	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495481	149495481	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	70	817	1	ENST00000261799.4:c.3166T>A	p.Ser1056Thr	p.S1056T	ENST00000261799	NM_002609.3	1056	Tca/Aca	23/23	1	2	FACETS	0.78	0.678	0.891	0.78	0.678	0.891	SUBCLONAL	1	TRUE	1	0.16	2		818	1122	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70967599	70967599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	59	625	0	ENST00000276594.2:c.1424G>A	p.Ser475Asn	p.S475N	ENST00000276594	NM_024504.3	475	aGc/aAc	7/8	1	2	FACETS	0.838	0.719	0.968	0.838	0.719	0.968	CLONAL	1	TRUE	1	0.16	2		625	880	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs786203436	NA	P-0016484-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	419	602	0	ENST00000269305.4:c.487T>G	p.Tyr163Asp	p.Y163D	ENST00000269305	NM_001126112.2	163	Tac/Gac	5/11	0.39101361597398	2	FACETS	0.975	0.931	1	0.975	0.931	1	CLONAL	2	TRUE	0	0.393543559515276	2		602	1092	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348948	11348948	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016484-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	218	529	0	ENST00000332029.2:c.388T>C	p.Phe130Leu	p.F130L	ENST00000332029	NM_003745.1	130	Ttt/Ctt	2/2	0.393543559515276	4	FACETS	1	0.961	1			1	CLONAL	1	TRUE	NA	0.393543559515276	4		529	1463	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290223	15290223	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016484-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	736	653	0	ENST00000263388.2:c.3412A>C	p.Ile1138Leu	p.I1138L	ENST00000263388	NM_000435.2	1138	Att/Ctt	21/33	0.393543559515276	5	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	2	0.393543559515276	5		653	1925	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495481	149495481	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016484-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	293	817	1	ENST00000261799.4:c.3166T>A	p.Ser1056Thr	p.S1056T	ENST00000261799	NM_002609.3	1056	Tca/Aca	23/23	0.39101361597398	2	FACETS	1	0.976	1	0.537	0.504	0.571	CLONAL	1	TRUE	0	0.393543559515276	2		818	1386	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70967599	70967599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016484-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	400	625	0	ENST00000276594.2:c.1424G>A	p.Ser475Asn	p.S475N	ENST00000276594	NM_024504.3	475	aGc/aAc	7/8	0.275137144784664	4	FACETS	0.94	0.892	0.988			1	CLONAL	2	TRUE	NA	0.393543559515276	4		625	1507	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114901042	114901042	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016484-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	192	597	0	ENST00000543371.1:c.652C>G	p.Pro218Ala	p.P218A	ENST00000543371	NM_001198531.1	218	Cca/Gca	6/14	0.393543559515276	3	FACETS	0.914	0.843	0.987	0.457	0.421	0.494	CLONAL	1	TRUE	1	0.393543559515276	3		597	1278	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633698	69633698	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016484-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	16	37	0	ENST00000334134.2:c.4G>C	p.Gly2Arg	p.G2R	ENST00000334134	NM_005247.2	2	Ggc/Cgc	1/3	0.393543559515276	3	FACETS	1	0.827	1	0.566	0.426	0.726	CLONAL	1	TRUE	1	0.393543559515276	3		37	86	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817409	39817435	+	protein_altering_variant	In_Frame_Del	DEL	GGACGCGTGGGCTCATCTTGGAAGTCT	GGACGCGTGGGCTCATCTTGGAAGTCT	AGATTACAGCAG	novel	NA	P-0016484-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	125	461	2	ENST00000288319.7:c.128_154delinsCTGCTGTAATCT	p.Gln43_Pro52delinsProAlaValIleSer	p.Q43_P52delinsPAVIS	ENST00000288319	NM_182918.3	43	cAGACTTCCAAGATGAGCCCACGCGTCCct/cCTGCTGTAATCTct	2/10	0.393543559515276	3	FACETS	0.799	0.722	0.88	0.399	0.361	0.44	SUBCLONAL	1	TRUE	1	0.393543559515276	3		463	952	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143352321	143352321	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0016484-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1206	122	459	0	ENST00000262992.4:c.91+1G>T		p.X31_splice	ENST00000262992	NM_001101669.1	31			0.393543559515276	6	FACETS	0.834	0.752	0.922	0.139	0.125	0.154	CLONAL	1	TRUE	0	0.393543559515276	6		459	1328	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652109	36652109	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016484-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	178	521	0	ENST00000244741.5:c.231C>A	p.Tyr77Ter	p.Y77*	ENST00000244741	NM_000389.4	77	taC/taA	2/3	0.393543559515276	4	FACETS	1	0.926	1	0.252	0.231	0.273	CLONAL	1	TRUE	0	0.393543559515276	4		521	1251	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982735	90982735	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016484-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1470	187	584	1	ENST00000265433.3:c.753G>T	p.Leu251Phe	p.L251F	ENST00000265433	NM_002485.4	251	ttG/ttT	7/16	0.393543559515276	5	FACETS	0.912	0.839	0.988	0.228	0.209	0.247	CLONAL	1	TRUE	1	0.393543559515276	5		585	1657	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752879	128752879	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016484-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	151	393	0	ENST00000377970.2:c.1040T>A	p.Val347Asp	p.V347D	ENST00000377970	NM_002467.4	347	gTc/gAc	3/3	0.393543559515276	5	FACETS	0.993	0.906	1	0.248	0.226	0.272	CLONAL	1	TRUE	1	0.393543559515276	5		393	1229	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519988	NA	P-0016485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	384	711	1	ENST00000269305.4:c.808T>C	p.Phe270Leu	p.F270L	ENST00000269305	NM_001126112.2	270	Ttt/Ctt	8/11	0.609554007204135	1	FACETS	0.936	0.894	0.98	0.936	0.894	0.98	CLONAL	1	TRUE	0	0.630356114546624	1		712	891	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277065	38277065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369096310	NA	P-0016485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	136	390	0	ENST00000425967.3:c.1363C>T	p.Arg455Cys	p.R455C	ENST00000425967	NM_001174067.1	455	Cgc/Tgc	10/19	0.630356114546624	1	FACETS	0.498	0.455	0.544	0.498	0.455	0.544	SUBCLONAL	1	TRUE	0	0.630356114546624	1		390	593	SUCCESS
APC	324	MSKCC	GRCh37	5	112175213	112175213	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0016485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	74	223	0	ENST00000257430.4:c.3922A>T	p.Lys1308Ter	p.K1308*	ENST00000257430	NM_000038.5	1308	Aaa/Taa	16/16	0.326699530008084	1	FACETS	0.396	0.348	0.447	0.396	0.348	0.447	INDETERMINATE	1	TRUE	0	0.630356114546624	1		223	406	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418624	49418624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1459471282	NA	P-0016485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	89	519	2	ENST00000301067.7:c.15890C>T	p.Thr5297Met	p.T5297M	ENST00000301067	NM_003482.3	5297	aCg/aTg	49/54	0.285237232739608	1	FACETS	0.219	0.194	0.247	0.219	0.194	0.247	INDETERMINATE	1	TRUE	0	0.630356114546624	1		521	882	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876603	59876603	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764711572	NA	P-0016485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	273	414	0	ENST00000259008.2:c.1198G>T	p.Asp400Tyr	p.D400Y	ENST00000259008	NM_032043.2	400	Gac/Tac	9/20	1	2	FACETS	0.893	0.839	0.948	0.893	0.839	0.948	CLONAL	1	TRUE	1	0.630356114546624	2		414	970	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675186	30675186	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	141	540	0	ENST00000376406.3:c.3059T>C	p.Ile1020Thr	p.I1020T	ENST00000376406	NM_014641.2	1020	aTc/aCc	9/15	0.624825332411146	2	FACETS	0.416	0.378	0.456	0.208	0.189	0.228	SUBCLONAL	1	TRUE	0	0.630356114546624	2		540	1075	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	36	641	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.433	0.354	0.523	0.433	0.354	0.523	SUBCLONAL	1	TRUE	1	0.15	2		641	1108	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0016486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	41	279	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.7	0.581	0.833	0.7	0.581	0.833	SUBCLONAL	1	TRUE	1	0.15	2		279	781	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0016486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	37	491	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.609	0.5	0.732	0.609	0.5	0.732	SUBCLONAL	1	TRUE	1	0.15	2		492	810	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0016487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	157	277	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.506113459063735	2		277	598	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0016487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	472	514	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.777	0.743	0.81	1	0.996	1	SUBCLONAL	2	TRUE	1	0.506113459063735	2		514	1201	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0016487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	338	806	3	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.506113459063735	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.506113459063735	1		809	942	SUCCESS
APC	324	MSKCC	GRCh37	5	112173656	112173656	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123117	NA	P-0016487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	120	374	0	ENST00000257430.4:c.2365C>T	p.Gln789Ter	p.Q789*	ENST00000257430	NM_000038.5	789	Cag/Tag	16/16	1	2	FACETS	0.754	0.682	0.829	0.754	0.682	0.829	SUBCLONAL	1	TRUE	1	0.506113459063735	2		374	629	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110030	115110031	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0016487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	252	678	0	ENST00000257566.3:c.1847_1848del	p.Ser616CysfsTer75	p.S616Cfs*75	ENST00000257566	NM_016569.3	616	tCT/t	8/8	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.506113459063735	2		678	957	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707791	43707791	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs778285528	NA	P-0016487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	225	513	0	ENST00000382044.4:c.5089+1G>T		p.X1697_splice	ENST00000382044	NM_001141980.1	1697			1	2	FACETS	0.911	0.849	0.975	0.911	0.849	0.975	CLONAL	1	TRUE	1	0.506113459063735	2		513	976	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538873	23538873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	123	321	0	ENST00000380871.4:c.566G>A	p.Gly189Glu	p.G189E	ENST00000380871	NM_006167.3	189	gGa/gAa	2/2	0.506113459063735	1	FACETS	0.96	0.878	1	0.96	0.878	1	CLONAL	1	TRUE	0	0.506113459063735	1		321	378	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412438	63412438	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	260	819	0	ENST00000330258.3:c.729del	p.Glu244AsnfsTer38	p.E244Nfs*38	ENST00000330258	NM_152424.3	243	ccA/cc	2/2	1	2	FACETS	0.946	0.886	1	0.946	0.886	1	CLONAL	1	TRUE	1	0.506113459063735	2		819	1086	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0016488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	630	904	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.26466699533888	1	FACETS	1	0.997	1	1	0.997	1	INDETERMINATE	1	TRUE	0	0.771768910348609	1		905	859	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856604	111856604	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	90	166	0	ENST00000341259.2:c.655C>G	p.Arg219Gly	p.R219G	ENST00000341259	NM_005475.2	219	Cgc/Ggc	2/8	1	2	FACETS	0.801	0.72	0.886	0.801	0.72	0.886	CLONAL	1	TRUE	1	0.771768910348609	2		166	291	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657651	37657652	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0016488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	458	570	2	ENST00000447079.4:c.2568_2569delinsTT	p.His857Tyr	p.H857Y	ENST00000447079	NM_015083.1	856	ctGCat/ctTTat	6/14	0.747524340181032	2	FACETS	0.914	0.886	0.942	0.914	0.886	0.942	CLONAL	2	TRUE	0	0.771768910348609	2		572	649	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0016491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	260	2255	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	2	TRUE	NA	0.733279493619859	2		2255	333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0016491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	134	610	2	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.413651543182769	3	FACETS	1	0.984	1	0.662	0.609	0.718	INDETERMINATE	1	TRUE	1	0.733279493619859	3		612	377	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165782	118165782	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1293686110	NA	P-0016491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	64	354	0	ENST00000369448.3:c.292G>C	p.Ala98Pro	p.A98P	ENST00000369448	NM_017709.3	98	Gct/Cct	2/2	1	2	FACETS	0.737	0.646	0.832	0.737	0.646	0.832	SUBCLONAL	1	TRUE	1	0.733279493619859	2		354	237	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742459	17742459	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	44	528	0	ENST00000250003.3:c.641G>T	p.Ser214Ile	p.S214I	ENST00000250003	NM_002478.4	214	aGc/aTc	2/3	0.733279493619859	1	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	0	0.733279493619859	1		528	75	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198475	108198475	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	115	432	0	ENST00000278616.4:c.7079A>C	p.Tyr2360Ser	p.Y2360S	ENST00000278616	NM_000051.3	2360	tAt/tCt	48/63	0.733279493619859	3	FACETS	1	0.974	1			1	CLONAL	1	TRUE	NA	0.733279493619859	3		432	360	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109809	115109809	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	61	717	0	ENST00000257566.3:c.2069C>G	p.Ser690Cys	p.S690C	ENST00000257566	NM_016569.3	690	tCt/tGt	8/8	NA	2	FACETS	0.973	0.857	1			1	INDETERMINATE	1	TRUE	NA	0.733279493619859	2		717	171	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214645	133214645	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	85	422	1	ENST00000320574.5:c.5633G>T	p.Arg1878Leu	p.R1878L	ENST00000320574	NM_006231.2	1878	cGc/cTc	41/49	NA	2	FACETS	0.987	0.887	1			1	INDETERMINATE	1	TRUE	NA	0.733279493619859	2		423	235	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678476	88678476	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	61	559	0	ENST00000360948.2:c.1060C>A	p.Gln354Lys	p.Q354K	ENST00000360948	NM_001012338.2	354	Caa/Aaa	9/19	0.733279493619859	1	FACETS	0.68	0.601	0.761	0.68	0.601	0.761	SUBCLONAL	1	TRUE	0	0.733279493619859	1		559	155	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576923	7576928	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGTGCT	AGTGCT	-	novel	NA	P-0016491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	99	537	0	ENST00000269305.4:c.920-2_923del		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	0.413651543182769	3	FACETS	1	0.98	1	0.671	0.608	0.736	INDETERMINATE	1	TRUE	1	0.733279493619859	3		537	275	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40859988	40859988	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	108	469	0	ENST00000428826.2:c.1648T>C	p.Cys550Arg	p.C550R	ENST00000428826		550	Tgc/Cgc	15/21	0.413651543182769	3	FACETS	1	0.982	1	0.68	0.619	0.743	INDETERMINATE	1	TRUE	1	0.733279493619859	3		469	296	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602797	10602797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	139	763	0	ENST00000171111.5:c.781C>T	p.Arg261Trp	p.R261W	ENST00000171111	NM_203500.1	261	Cgg/Tgg	3/6	0.733279493619859	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.733279493619859	1		763	224	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171732	36171732	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759227406	NA	P-0016491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	122	319	1	ENST00000300305.3:c.833C>T	p.Pro278Leu	p.P278L	ENST00000300305		278	cCg/cTg	7/8	0.733279493619859	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.733279493619859	1		320	182	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133824	55133825	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0016491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	83	529	1	ENST00000257290.5:c.1037_1038delinsTT	p.Arg346Ile	p.R346I	ENST00000257290	NM_006206.4	346	aGG/aTT	7/23	1	2	FACETS	0.963	0.864	1	0.963	0.864	1	CLONAL	1	TRUE	1	0.733279493619859	2		530	235	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231751	66231751	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	53	441	1	ENST00000273854.3:c.1949A>T	p.Tyr650Phe	p.Y650F	ENST00000273854	NM_004439.5	650	tAc/tTc	11/18	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.733279493619859	2		442	144	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900170	101900170	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	71	234	0	ENST00000374994.4:c.604G>A	p.Ala202Thr	p.A202T	ENST00000374994	NM_004612.2	202	Gcg/Acg	4/9	0.733279493619859	1	FACETS	0.909	0.821	0.996	0.909	0.821	0.996	CLONAL	1	TRUE	0	0.733279493619859	1		234	135	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	97	423	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.761	0.679	0.848	0.761	0.679	0.848	SUBCLONAL	1	TRUE	1	0.392110660773374	2		423	650	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0016496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	177	521	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.353452214388	1	FACETS	0.751	0.691	0.812	0.751	0.691	0.812	SUBCLONAL	1	TRUE	0	0.392110660773374	1		523	967	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0016496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1453	211	541	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	0.392110660773374	5	FACETS	1	0.946	1			1	CLONAL	1	TRUE	NA	0.392110660773374	5		541	1664	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533548	533548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	781	497	0	ENST00000451590.1:c.355G>A	p.Asp119Asn	p.D119N	ENST00000451590	NM_001130442.1	119	Gac/Aac	4/5	0.392110660773374	5	FACETS	1	0.995	1			1	CLONAL	3	TRUE	NA	0.392110660773374	5		497	1849	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420067	152420067	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141662120	NA	P-0016496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	139	274	0	ENST00000206249.3:c.1754C>T	p.Thr585Met	p.T585M	ENST00000206249	NM_000125.3	585	aCg/aTg	8/8	1	2	FACETS	0.871	0.793	0.953	0.871	0.793	0.953	CLONAL	1	TRUE	1	0.392110660773374	2		274	814	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845354	156845354	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	178	438	1	ENST00000524377.1:c.1397T>C	p.Leu466Pro	p.L466P	ENST00000524377	NM_002529.3	466	cTg/cCg	12/17	1	2	FACETS	0.872	0.803	0.944	0.872	0.803	0.944	CLONAL	1	TRUE	1	0.392110660773374	2		439	1041	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447080	49447080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	163	383	0	ENST00000301067.7:c.864G>A	p.Met288Ile	p.M288I	ENST00000301067	NM_003482.3	288	atG/atA	7/54	1	2	FACETS	0.868	0.796	0.943	0.868	0.796	0.943	CLONAL	1	TRUE	1	0.392110660773374	2		383	958	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244224	133244224	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	113	292	0	ENST00000320574.5:c.2184del	p.Ala730ProfsTer62	p.A730Pfs*62	ENST00000320574	NM_006231.2	728	cgG/cg	20/49	NA	2	FACETS	0.793	0.714	0.876			1	INDETERMINATE	1	TRUE	NA	0.392110660773374	2		292	727	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	47	726	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.745	0.627	0.877	0.745	0.627	0.877	SUBCLONAL	1	TRUE	1	0.15	2		726	841	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433507	138433507	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759331142	NA	P-0016497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	43	367	1	ENST00000289153.2:c.1105G>A	p.Val369Ile	p.V369I	ENST00000289153	NM_006219.2	369	Gta/Ata	7/22	1	2	FACETS	0.883	0.738	1	0.883	0.738	1	CLONAL	1	TRUE	1	0.15	2		368	649	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145645	11145645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	323	384	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	0.98	1	CLONAL	1	TRUE	1	0.842339288137184	2		384	725	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836798	151836798	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	692	675	2	ENST00000262189.6:c.14422G>T	p.Glu4808Ter	p.E4808*	ENST00000262189	NM_170606.2	4808	Gaa/Taa	56/59	0.839306990994873	3	FACETS	0.988	0.959	1	0.988	0.959	1	CLONAL	2	TRUE	1	0.842339288137184	3		677	1182	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836798	151836798	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016498-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	428	675	2	ENST00000262189.6:c.14422G>T	p.Glu4808Ter	p.E4808*	ENST00000262189	NM_170606.2	4808	Gaa/Taa	56/59	0.671801419138239	3	FACETS	0.987	0.947	1	0.987	0.947	1	CLONAL	2	TRUE	1	0.671801419138239	3		677	862	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989630	212989630	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0016498-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	40	347	0	ENST00000342788.4:c.83-2A>C		p.X28_splice	ENST00000342788	NM_005235.2	28			1	2	FACETS	0.341	0.284	0.404	0.341	0.284	0.404	SUBCLONAL	1	TRUE	1	0.671801419138239	2		347	349	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151932966	151932966	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016498-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	26	34	0	ENST00000262189.6:c.2705C>A	p.Ser902Ter	p.S902*	ENST00000262189	NM_170606.2	902	tCg/tAg	16/59	0.671801419138239	3	FACETS	0.976	0.816	1	0.976	0.816	1	CLONAL	2	TRUE	1	0.671801419138239	3		34	53	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692780	89692780	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1554898056	NA	P-0016499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	322	469	0	ENST00000371953.3:c.264T>A	p.Tyr88Ter	p.Y88*	ENST00000371953	NM_000314.4	88	taT/taA	5/9	0.514843446218252	2	FACETS	0.963	0.919	1	0.963	0.919	1	CLONAL	2	TRUE	0	0.534065525451017	2		469	626	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098493	47098493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	114	351	0	ENST00000409792.3:c.6781G>A	p.Ala2261Thr	p.A2261T	ENST00000409792	NM_014159.6	2261	Gcc/Acc	15/21	0.248688931226708	5	FACETS	1	0.958	1	0.371	0.335	0.41	INDETERMINATE	1	TRUE	2	0.534065525451017	5		351	690	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200428	138200428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	163	421	0	ENST00000237289.4:c.1846G>A	p.Gly616Arg	p.G616R	ENST00000237289	NM_001270507.1	616	Ggg/Agg	7/9	0.534195718572631	3	FACETS	0.977	0.897	1	0.488	0.448	0.53	CLONAL	1	TRUE	1	0.534065525451017	3		421	792	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380276	+	missense_variant	Missense_Mutation	DNP	TT	TT	CA	novel	NA	P-0016500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	169	567	0	ENST00000311936.3:c.182_183delinsTG	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAA/cTG	3/5	0.43208708498677	2	FACETS	0.818	0.759	0.879	0.818	0.759	0.879	CLONAL	2	TRUE	0	0.43208708498677	2		567	478	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110712	2110712	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	246	642	0	ENST00000219476.3:c.1018del	p.Leu340CysfsTer23	p.L340Cfs*23	ENST00000219476	NM_000548.3	339	gtC/gt	11/42	0.43208708498677	3	FACETS	1	0.974	1	0.542	0.505	0.579	CLONAL	1	TRUE	1	0.43208708498677	3		642	1278	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126167	2126183	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTAAGGTGGGCTCAGGG	CTAAGGTGGGCTCAGGG	-	novel	NA	P-0016500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	247	422	0	ENST00000219476.3:c.2739_2742+13del		p.X913_splice	ENST00000219476	NM_000548.3	913		24/42	0.43208708498677	3	FACETS	0.841	0.788	0.894	0.841	0.788	0.894	CLONAL	2	TRUE	1	0.43208708498677	3		422	827	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439721	51439722	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0016502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	185	248	0	ENST00000262662.1:c.287_288dup	p.Asn97LeufsTer28	p.N97Lfs*28	ENST00000262662		96	gtt/gTTtt	4/4	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.331039443487075	2		248	768	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578371	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	GT	novel	NA	P-0016502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	199	289	1	ENST00000269305.4:c.559_559+1delinsAC		p.X187_splice	ENST00000269305	NM_001126112.2	187		5/11	0.331039495904227	1	FACETS	0.81	0.755	0.867	1	0.992	1	CLONAL	2	TRUE	0	0.331039443487075	1		290	619	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572510	41572510	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748485911	NA	P-0016502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	127	306	1	ENST00000263253.7:c.5039G>A	p.Arg1680His	p.R1680H	ENST00000263253	NM_001429.3	1680	cGc/cAc	30/31	1	2	FACETS	0.834	0.755	0.918	0.834	0.755	0.918	CLONAL	1	TRUE	1	0.331039443487075	2		307	920	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0016503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	720	731	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.556312055033725	5	FACETS	0.959	0.927	0.991	0.959	0.927	0.991	CLONAL	3	TRUE	2	0.556312055033725	5		731	1650	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420670	49420670	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs797045659	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	79	351	0	ENST00000301067.7:c.15079C>T	p.Arg5027Ter	p.R5027*	ENST00000301067	NM_003482.3	5027	Cga/Tga	48/54	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.17	2		351	854	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720870	89720870	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1554825652	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	72	304	0	ENST00000371953.3:c.1021T>G	p.Phe341Val	p.F341V	ENST00000371953	NM_000314.4	341	Ttt/Gtt	8/9	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.17	2		304	628	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	82	502	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	0.911	0.801	1	0.911	0.801	1	CLONAL	1	TRUE	1	0.17	2		502	1059	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210733	5210733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779302415	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	60	472	0	ENST00000357368.4:c.5318C>T	p.Ser1773Leu	p.S1773L	ENST00000357368	NM_002850.3	1773	tCg/tTg	34/38	1	2	FACETS	0.744	0.639	0.859	0.744	0.639	0.859	SUBCLONAL	1	TRUE	1	0.17	2		472	949	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480483	57480483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	50	318	0	ENST00000371085.3:c.478C>T	p.Arg160Cys	p.R160C	ENST00000371085	NM_000516.4	160	Cgt/Tgt	6/13	1	2	FACETS	0.848	0.718	0.991	0.848	0.718	0.991	CLONAL	1	TRUE	1	0.17	2		318	694	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556696	41556696	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	52	410	0	ENST00000263253.7:c.3641C>A	p.Ser1214Tyr	p.S1214Y	ENST00000263253	NM_001429.3	1214	tCt/tAt	20/31	1	2	FACETS	0.723	0.614	0.844	0.723	0.614	0.844	SUBCLONAL	1	TRUE	1	0.17	2		410	846	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	67	404	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	0.885	0.767	1	0.885	0.767	1	CLONAL	1	TRUE	1	0.17	2		404	891	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539951	187539951	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs777631605	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	67	300	0	ENST00000441802.2:c.7789C>T	p.Arg2597Ter	p.R2597*	ENST00000441802	NM_005245.3	2597	Cga/Tga	10/27	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.17	2		300	623	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	33	271	1	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	1	2	FACETS	0.706	0.574	0.855	0.706	0.574	0.855	SUBCLONAL	1	TRUE	1	0.17	2		272	550	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428511	78428511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408536007	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	59	430	1	ENST00000370768.2:c.1288C>T	p.Arg430Cys	p.R430C	ENST00000370768	NM_003902.3	430	Cgt/Tgt	14/20	1	2	FACETS	0.698	0.599	0.807	0.698	0.599	0.807	SUBCLONAL	1	TRUE	1	0.17	2		431	994	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267600319	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	35	264	0	ENST00000257430.4:c.4199C>T	p.Ser1400Leu	p.S1400L	ENST00000257430	NM_000038.5	1400	tCg/tTg	16/16	1	2	FACETS	0.682	0.557	0.822	0.682	0.557	0.822	SUBCLONAL	1	TRUE	1	0.17	2		264	604	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	56	442	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.838	0.717	0.972	0.838	0.717	0.972	CLONAL	1	TRUE	1	0.17	2		442	786	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941654	48941654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776534331	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	36	309	0	ENST00000267163.4:c.964G>A	p.Glu322Lys	p.E322K	ENST00000267163	NM_000321.2	322	Gaa/Aaa	10/27	1	2	FACETS	0.756	0.621	0.909	0.756	0.621	0.909	CLONAL	1	TRUE	1	0.17	2		309	560	SUCCESS
APC	324	MSKCC	GRCh37	5	112177368	112177368	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	46	343	0	ENST00000257430.4:c.6077C>A	p.Ser2026Tyr	p.S2026Y	ENST00000257430	NM_000038.5	2026	tCt/tAt	16/16	1	2	FACETS	0.822	0.691	0.968	0.822	0.691	0.968	CLONAL	1	TRUE	1	0.17	2		343	658	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950304	15950304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763924640	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	105	586	1	ENST00000268712.3:c.6640C>T	p.Arg2214Cys	p.R2214C	ENST00000268712	NM_006311.3	2214	Cgt/Tgt	42/46	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.17	2		587	1133	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281778	39281778	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519963	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	54	390	0	ENST00000402219.2:c.697A>T	p.Asn233Tyr	p.N233Y	ENST00000402219	NM_005633.3	233	Aat/Tat	5/23	1	2	FACETS	0.821	0.699	0.954	0.821	0.699	0.954	CLONAL	1	TRUE	1	0.17	2		390	774	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528078	103528078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368829739	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	61	326	0	ENST00000355739.4:c.3386C>T	p.Ser1129Leu	p.S1129L	ENST00000355739	NM_000123.3	1129	tCg/tTg	15/15	1	2	FACETS	0.991	0.854	1	0.991	0.854	1	CLONAL	1	TRUE	1	0.17	2		326	724	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724542	162724542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1041487062	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	47	323	2	ENST00000367921.3:c.314G>A	p.Arg105His	p.R105H	ENST00000367921	NM_006182.2	105	cGc/cAc	5/18	1	2	FACETS	0.811	0.683	0.953	0.811	0.683	0.953	CLONAL	1	TRUE	1	0.17	2		325	682	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101309	27101309	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	58	533	0	ENST00000324856.7:c.4591G>T	p.Glu1531Ter	p.E1531*	ENST00000324856	NM_006015.4	1531	Gaa/Taa	18/20	1	2	FACETS	0.705	0.604	0.816	0.705	0.604	0.816	SUBCLONAL	1	TRUE	1	0.17	2		533	968	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65349125	65349125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	44	434	0	ENST00000342505.4:c.40G>A	p.Ala14Thr	p.A14T	ENST00000342505	NM_002227.2	14	Gct/Act	3/25	1	2	FACETS	0.61	0.51	0.721	0.61	0.51	0.721	SUBCLONAL	1	TRUE	1	0.17	2		434	849	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115251236	115251236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	59	416	0	ENST00000369535.4:c.490C>T	p.Arg164Cys	p.R164C	ENST00000369535	NM_002524.4	164	Cgc/Tgc	5/7	1	2	FACETS	0.713	0.612	0.825	0.713	0.612	0.825	SUBCLONAL	1	TRUE	1	0.17	2		416	973	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870376	155870376	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	82	439	0	ENST00000368323.3:c.463G>T	p.Glu155Ter	p.E155*	ENST00000368323	NM_006912.5	155	Gaa/Taa	6/6	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.17	2		439	962	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720822	89720822	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	48	270	0	ENST00000371953.3:c.973C>T	p.Leu325Phe	p.L325F	ENST00000371953	NM_000314.4	325	Ctt/Ttt	8/9	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.17	2		270	546	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909867	100909867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	34	266	0	ENST00000325455.5:c.2782C>T	p.Leu928Phe	p.L928F	ENST00000325455	NM_001202474.3	928	Ctt/Ttt	8/8	1	2	FACETS	0.851	0.695	1	0.851	0.695	1	CLONAL	1	TRUE	1	0.17	2		266	470	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907120	32907120	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	74	474	0	ENST00000380152.3:c.1505A>C	p.Lys502Thr	p.K502T	ENST00000380152		502	aAa/aCa	10/27	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.17	2		474	788	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56873505	56873505	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	58	384	0	ENST00000308159.5:c.2209T>G	p.Phe737Val	p.F737V	ENST00000308159	NM_014669.4	737	Ttc/Gtc	20/22	1	2	FACETS	0.928	0.796	1	0.928	0.796	1	CLONAL	1	TRUE	1	0.17	2		384	735	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993339	72993339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368995910	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	84	512	1	ENST00000268489.5:c.706G>A	p.Val236Met	p.V236M	ENST00000268489	NM_006885.3	236	Gtg/Atg	2/10	1	2	FACETS	0.899	0.792	1	0.899	0.792	1	CLONAL	1	TRUE	1	0.17	2		513	1099	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322591	30322591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	57	368	0	ENST00000322652.5:c.1604G>A	p.Arg535Gln	p.R535Q	ENST00000322652	NM_015355.2	535	cGa/cAa	14/16	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.17	2		368	663	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59878807	59878807	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	34	283	0	ENST00000259008.2:c.947T>G	p.Val316Gly	p.V316G	ENST00000259008	NM_032043.2	316	gTt/gGt	8/20	1	2	FACETS	0.722	0.589	0.872	0.722	0.589	0.872	SUBCLONAL	1	TRUE	1	0.17	2		283	554	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021790	71021790	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	62	294	0	ENST00000318789.4:c.1568T>A	p.Phe523Tyr	p.F523Y	ENST00000318789	NM_032682.5	523	tTt/tAt	18/21	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.17	2		294	712	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72866487	72866487	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	60	391	0	ENST00000325599.8:c.776A>C	p.Lys259Thr	p.K259T	ENST00000325599	NM_018130.2	259	aAa/aCa	7/11	1	2	FACETS	0.792	0.681	0.914	0.792	0.681	0.914	CLONAL	1	TRUE	1	0.17	2		391	891	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916948	178916950	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	48	560	0	ENST00000263967.3:c.337_339del	p.Leu113del	p.L113del	ENST00000263967	NM_006218.2	112	aTCCtc/atc	2/21	1	2	FACETS	0.682	0.575	0.801	0.682	0.575	0.801	SUBCLONAL	1	TRUE	1	0.17	2		560	828	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467954	66467954	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs907974082	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	50	347	0	ENST00000273854.3:c.315G>T	p.Met105Ile	p.M105I	ENST00000273854	NM_004439.5	105	atG/atT	3/18	1	2	FACETS	0.95	0.805	1	0.95	0.805	1	CLONAL	1	TRUE	1	0.17	2		347	619	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539242	187539242	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749995439	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	47	286	0	ENST00000441802.2:c.8498C>T	p.Ala2833Val	p.A2833V	ENST00000441802	NM_005245.3	2833	gCa/gTa	10/27	1	2	FACETS	0.973	0.821	1	0.973	0.821	1	CLONAL	1	TRUE	1	0.17	2		286	568	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117639384	117639384	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	63	527	0	ENST00000368508.3:c.5972A>C	p.Lys1991Thr	p.K1991T	ENST00000368508	NM_002944.2	1991	aAg/aCg	37/43	1	2	FACETS	0.772	0.666	0.888	0.772	0.666	0.888	SUBCLONAL	1	TRUE	1	0.17	2		527	960	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001146	150001146	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	49	464	0	ENST00000253339.5:c.2458C>A	p.His820Asn	p.H820N	ENST00000253339		820	Cat/Aat	4/7	1	2	FACETS	0.589	0.497	0.692	0.589	0.497	0.692	SUBCLONAL	1	TRUE	1	0.17	2		464	978	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001305	150001305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568586257	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	70	496	1	ENST00000253339.5:c.2299C>T	p.Arg767Cys	p.R767C	ENST00000253339		767	Cgt/Tgt	4/7	1	2	FACETS	0.841	0.731	0.961	0.841	0.731	0.961	CLONAL	1	TRUE	1	0.17	2		497	979	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730455	133730455	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	38	302	0	ENST00000318560.5:c.521A>G	p.Tyr174Cys	p.Y174C	ENST00000318560	NM_005157.4	174	tAc/tGc	3/11	1	2	FACETS	0.87	0.718	1	0.87	0.718	1	CLONAL	1	TRUE	1	0.17	2		302	514	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197860	123197860	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	82	423	0	ENST00000218089.9:c.1984G>A	p.Ala662Thr	p.A662T	ENST00000218089	NM_001042749.1	662	Gca/Aca	20/35	1	2	FACETS	0.966	0.849	1	0.966	0.849	1	CLONAL	1	TRUE	1	0.17	2		423	999	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0016506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	77	1585	1	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.13	2		1586	1178	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0016506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	30	378	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	1	2	FACETS	0.491	0.394	0.603	0.491	0.394	0.603	SUBCLONAL	1	TRUE	1	0.13	2		378	940	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243999	53243999	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	53	513	3	ENST00000375401.3:c.994C>T	p.Arg332Ter	p.R332*	ENST00000375401	NM_004187.3	332	Cga/Tga	8/26	1	2	FACETS	0.86	0.731	1	0.86	0.731	1	CLONAL	1	TRUE	1	0.13	2		516	948	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164800	32164800	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	52	422	0	ENST00000375023.3:c.5102G>A	p.Gly1701Glu	p.G1701E	ENST00000375023	NM_004557.3	1701	gGg/gAg	28/30	1	2	FACETS	0.971	0.824	1	0.971	0.824	1	CLONAL	1	TRUE	1	0.13	2		422	824	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476264	88476264	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	259	433	1	ENST00000360948.2:c.1868G>A	p.Gly623Glu	p.G623E	ENST00000360948	NM_001012338.2	623	gGa/gAa	15/19	0.592829696173322	3	FACETS	0.917	0.858	0.978	0.459	0.429	0.489	CLONAL	1	TRUE	1	0.592829696173322	3		434	1235	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751095	57751141	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAAGCCACAGTACTTACATCCATGAGGTTCTCCTCCATGTAATGAGA	AAAGCCACAGTACTTACATCCATGAGGTTCTCCTCCATGTAATGAGA	-	novel	NA	P-0016507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	64	187	0	ENST00000274289.3:c.1726_1755+17del		p.X576_splice	ENST00000274289	NM_006622.3	576		12/14	1	2	FACETS	0.529	0.46	0.604	0.529	0.46	0.604	SUBCLONAL	1	TRUE	1	0.592829696173322	2		187	408	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971155	21971164	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCCGTGGA	GCGCCGTGGA	-	novel	NA	P-0016507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	337	233	0	ENST00000304494.5:c.194_203del	p.Leu65ArgfsTer78	p.L65Rfs*78	ENST00000304494	NM_000077.4	65	cTCCACGGCGCg/cg	2/3	0.592829696173322	2	FACETS	0.997	0.956	1	0.997	0.956	1	CLONAL	2	TRUE	0	0.592829696173322	2		233	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0016508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	368	546	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.723223743354157	1	FACETS	0.995	0.955	1	0.995	0.955	1	CLONAL	1	TRUE	0	0.749658907076521	1		546	617	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0016508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	792	554	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.749658907076521	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.749658907076521	2		554	1011	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350155	81350155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758567520	NA	P-0016508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	388	324	0	ENST00000222390.5:c.1177C>T	p.Arg393Cys	p.R393C	ENST00000222390	NM_000601.4	393	Cgt/Tgt	10/18	0.729103231746269	4	FACETS	0.921	0.878	0.965	0.921	0.878	0.965	CLONAL	2	TRUE	2	0.749658907076521	4		324	983	SUCCESS
APC	324	MSKCC	GRCh37	5	112175240	112175256	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGATCCTGTGAGCGA	GAAGATCCTGTGAGCGA	-	novel	NA	P-0016508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	311	250	0	ENST00000257430.4:c.3949_3965del	p.Glu1317SerfsTer9	p.E1317Sfs*9	ENST00000257430	NM_000038.5	1317	GAAGATCCTGTGAGCGAa/a	16/16	0.717815224108292	3	FACETS	0.897	0.865	0.928	0.897	0.865	0.928	CLONAL	3	TRUE	0	0.749658907076521	3		250	424	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354159	15354159	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016515-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	150	434	1	ENST00000263377.2:c.2721A>T	p.Gln907His	p.Q907H	ENST00000263377	NM_058243.2	907	caA/caT	14/20	1	2	FACETS	0.96	0.889	1	0.96	0.889	1	CLONAL	1	TRUE	1	0.863234290349359	2		435	362	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778081	27778081	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016515-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	177	402	0	ENST00000369163.2:c.230A>T	p.Gln77Leu	p.Q77L	ENST00000369163	NM_003536.2	77	cAg/cTg	1/1	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.863234290349359	2		402	409	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0016521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	8	2255	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.168037647342647	0	FACETS	0.226	0.144	0.332			1	SUBCLONAL	1	FALSE	0	0.168037647342647	0		2255	351	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	307	1083	2	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.852	0.804	0.902	0.852	0.804	0.902	CLONAL	1	TRUE	1	0.668230642152285	2		1085	1078	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	317	672	0	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	0.668230642152285	3	FACETS	1	0.952	1	0.505	0.476	0.535	CLONAL	1	TRUE	1	0.668230642152285	3		672	1253	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	308	514	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.668230642152285	2		514	818	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478082	99478082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1416018269	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	186	349	1	ENST00000268035.6:c.2986C>T	p.Arg996Trp	p.R996W	ENST00000268035	NM_000875.3	996	Cgg/Tgg	16/21	1	2	FACETS	0.939	0.872	1	0.939	0.872	1	CLONAL	1	TRUE	1	0.668230642152285	2		350	593	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	96	229	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	0.871	0.784	0.961	0.871	0.784	0.961	CLONAL	1	TRUE	1	0.668230642152285	2		229	330	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	198	496	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.668230642152285	2		496	592	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741707	145741707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543009701	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	142	502	3	ENST00000428558.2:c.796G>A	p.Glu266Lys	p.E266K	ENST00000428558	NM_004260.3	266	Gag/Aag	5/22	1	2	FACETS	0.491	0.447	0.537	0.491	0.447	0.537	SUBCLONAL	1	TRUE	1	0.668230642152285	2		505	866	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460401	149460401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	239	421	0	ENST00000286301.3:c.236C>T	p.Thr79Met	p.T79M	ENST00000286301	NM_005211.3	79	aCg/aTg	3/22	1	2	FACETS	0.919	0.861	0.979	0.919	0.861	0.979	CLONAL	1	TRUE	1	0.668230642152285	2		421	778	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591132	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	rs1057519842	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	179	410	0	ENST00000274335.5:c.1727_1729del	p.Thr576del	p.T576del	ENST00000274335		575	aaGACg/aag	12/15	1	2	FACETS	0.875	0.811	0.942	0.875	0.811	0.942	CLONAL	1	TRUE	1	0.668230642152285	2		410	612	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	289	699	1	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.908	0.855	0.961	0.908	0.855	0.961	CLONAL	1	TRUE	1	0.668230642152285	2		700	953	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440912	52440912	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1205668341	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	51	488	0	ENST00000460680.1:c.592del	p.Glu198ArgfsTer33	p.E198Rfs*33	ENST00000460680	NM_004656.3	198	Gag/ag	8/17	1	2	FACETS	0.17	0.143	0.199	0.17	0.143	0.199	SUBCLONAL	1	TRUE	1	0.668230642152285	2		488	899	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779084	135779084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769566267	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	81	390	3	ENST00000298552.3:c.2162G>A	p.Arg721His	p.R721H	ENST00000298552	NM_001162426.1	721	cGc/cAc	17/23	1	2	FACETS	0.355	0.312	0.401	0.355	0.312	0.401	SUBCLONAL	1	TRUE	1	0.668230642152285	2		393	683	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	302	536	0	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	0.964	0.91	1	0.964	0.91	1	CLONAL	1	TRUE	1	0.668230642152285	2		536	938	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268793	98268793	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1554708751	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	92	516	1	ENST00000331920.6:c.290del	p.Asn97ThrfsTer20	p.N97Tfs*20	ENST00000331920	NM_000264.3	97	aAc/ac	2/24	1	2	FACETS	0.264	0.234	0.297	0.264	0.234	0.297	SUBCLONAL	1	TRUE	1	0.668230642152285	2		517	1042	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910346	29910346	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	93	410	0	ENST00000376809.5:c.19del	p.Arg7GlufsTer13	p.R7Efs*13	ENST00000376809	NM_002116.7	6	Ccc/cc	1/8	1	2	FACETS	0.364	0.323	0.407	0.364	0.323	0.407	SUBCLONAL	1	TRUE	1	0.668230642152285	2		410	765	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	86	461	0	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.283	0.25	0.319	0.283	0.25	0.319	SUBCLONAL	1	TRUE	1	0.668230642152285	2		461	909	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56872937	56872937	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	73	355	2	ENST00000308159.5:c.2097del	p.Phe699LeufsTer19	p.F699Lfs*19	ENST00000308159	NM_014669.4	698	Ttt/tt	19/22	1	2	FACETS	0.318	0.278	0.362	0.318	0.278	0.362	SUBCLONAL	1	TRUE	1	0.668230642152285	2		357	687	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052632	42052632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779811318	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	327	436	1	ENST00000219905.7:c.7303C>T	p.Arg2435Trp	p.R2435W	ENST00000219905	NM_001164273.1	2435	Cgg/Tgg	20/24	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.668230642152285	2		437	942	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722906	49722906	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	rs747477010	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	53	126	0	ENST00000449682.2:c.1421del	p.Pro474GlnfsTer52	p.P474Qfs*52	ENST00000449682	NM_020998.3	474	cCa/ca	12/18	1	2	FACETS	0.77	0.666	0.881	0.77	0.666	0.881	SUBCLONAL	1	TRUE	1	0.668230642152285	2		126	206	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110155	3110155	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	194	381	0	ENST00000078429.4:c.145G>A	p.Glu49Lys	p.E49K	ENST00000078429	NM_002067.2	49	Gag/Aag	2/7	1	2	FACETS	0.989	0.921	1	0.989	0.921	1	CLONAL	1	TRUE	1	0.668230642152285	2		381	587	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526499	66526499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	64	387	1	ENST00000358598.2:c.1055G>A	p.Arg352Gln	p.R352Q	ENST00000358598	NM_212471.2	352	cGa/cAa	11/11	1	2	FACETS	0.237	0.205	0.272	0.237	0.205	0.272	SUBCLONAL	1	TRUE	1	0.668230642152285	2		388	808	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138137	64138137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	282	554	0	ENST00000334205.4:c.2060C>T	p.Thr687Met	p.T687M	ENST00000334205	NM_003942.2	687	aCg/aTg	16/17	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.668230642152285	2		554	828	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682810	190682810	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	135	569	2	ENST00000441310.2:c.492del	p.Lys164AsnfsTer6	p.K164Nfs*6	ENST00000441310	NM_000534.4	162	gcA/gc	5/13	1	2	FACETS	0.483	0.439	0.53	0.483	0.439	0.53	SUBCLONAL	1	TRUE	1	0.668230642152285	2		571	836	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468269	50468269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	48	544	0	ENST00000331340.3:c.1504C>T	p.Arg502Trp	p.R502W	ENST00000331340	NM_006060.4	502	Cgg/Tgg	8/8	1	2	FACETS	0.153	0.129	0.181	0.153	0.129	0.181	SUBCLONAL	1	TRUE	1	0.668230642152285	2		544	937	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085996	16085996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	102	500	0	ENST00000281043.3:c.1172G>A	p.Arg391His	p.R391H	ENST00000281043	NM_005378.4	391	cGc/cAc	3/3	1	2	FACETS	0.335	0.299	0.373	0.335	0.299	0.373	SUBCLONAL	1	TRUE	1	0.668230642152285	2		500	912	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279831	46279836	+	inframe_deletion	In_Frame_Del	DEL	CAGCAA	CAGCAA	-	rs764026511	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	29	364	0	ENST00000371998.3:c.3762_3767del	p.Gln1275_Gln1276del	p.Q1275_Q1276del	ENST00000371998		1253	CAGCAA/-	20/23	1	2	FACETS	0.157	0.125	0.193	0.157	0.125	0.193	SUBCLONAL	1	TRUE	1	0.668230642152285	2		364	552	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32814943	32814943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs760014590	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	300	473	0	ENST00000354258.4:c.2122C>T	p.Arg708Ter	p.R708*	ENST00000354258	NM_000593.5	708	Cga/Tga	10/11	1	2	FACETS	0.933	0.881	0.987	0.933	0.881	0.987	CLONAL	1	TRUE	1	0.668230642152285	2		473	962	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	391	756	2	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.983	0.935	1	0.983	0.935	1	CLONAL	1	TRUE	1	0.668230642152285	2		758	1191	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023909	27023909	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	134	140	0	ENST00000324856.7:c.1015G>T	p.Ala339Ser	p.A339S	ENST00000324856	NM_006015.4	339	Gct/Tct	1/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.668230642152285	2		140	324	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099017	27099017	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	347	556	1	ENST00000324856.7:c.3433C>T	p.Gln1145Ter	p.Q1145*	ENST00000324856	NM_006015.4	1145	Cag/Tag	13/20	1	2	FACETS	0.917	0.869	0.967	0.917	0.869	0.967	CLONAL	1	TRUE	1	0.668230642152285	2		557	1132	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115975	8115975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	136	271	0	ENST00000346208.3:c.1321G>A	p.Ala441Thr	p.A441T	ENST00000346208		441	Gcc/Acc	6/6	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.668230642152285	2		271	406	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219171	94219171	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	337	639	0	ENST00000323929.3:c.233T>C	p.Leu78Ser	p.L78S	ENST00000323929	NM_005591.3	78	tTa/tCa	4/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.668230642152285	2		639	994	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375464	118375464	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	76	312	0	ENST00000534358.1:c.8857G>T	p.Ala2953Ser	p.A2953S	ENST00000534358	NM_005933.3	2953	Gct/Tct	27/36	1	2	FACETS	0.386	0.339	0.437	0.386	0.339	0.437	SUBCLONAL	1	TRUE	1	0.668230642152285	2		312	589	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28980033	28980033	+	splice_acceptor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	96	336	0	ENST00000282397.4:c.1437-2del		p.X479_splice	ENST00000282397	NM_002019.4	479			0.668230642152285	3	FACETS	0.607	0.542	0.677	0.304	0.271	0.339	SUBCLONAL	1	TRUE	1	0.668230642152285	3		336	631	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304351	91304351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	325	593	0	ENST00000355112.3:c.1748C>T	p.Ala583Val	p.A583V	ENST00000355112	NM_000057.2	583	gCc/gTc	7/22	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.668230642152285	2		593	960	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40879742	40879742	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	109	545	0	ENST00000428826.2:c.157A>G	p.Thr53Ala	p.T53A	ENST00000428826		53	Acc/Gcc	4/21	1	2	FACETS	0.293	0.262	0.326	0.293	0.262	0.326	SUBCLONAL	1	TRUE	1	0.668230642152285	2		545	1113	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438238	56438238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	267	399	1	ENST00000407977.2:c.755G>A	p.Cys252Tyr	p.C252Y	ENST00000407977		252	tGc/tAc	7/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.668230642152285	2		400	737	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007739	62007739	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	102	210	0	ENST00000392795.3:c.128C>A	p.Ala43Asp	p.A43D	ENST00000392795	NM_001039933.1	43	gCt/gAt	3/6	1	2	FACETS	0.763	0.688	0.842	0.763	0.688	0.842	SUBCLONAL	1	TRUE	1	0.668230642152285	2		210	400	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906370	50906370	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs749601227	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	45	529	1	ENST00000440232.2:c.1036del	p.Glu346SerfsTer47	p.E346Sfs*47	ENST00000440232	NM_002691.3	344	tGg/tg	9/27	1	2	FACETS	0.153	0.128	0.181	0.153	0.128	0.181	SUBCLONAL	1	TRUE	1	0.668230642152285	2		530	881	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25536832	25536832	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781229619	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	198	421	0	ENST00000264709.3:c.22G>A	p.Gly8Ser	p.G8S	ENST00000264709	NM_175629.2	8	Ggc/Agc	2/23	1	2	FACETS	0.878	0.817	0.941	0.878	0.817	0.941	CLONAL	1	TRUE	1	0.668230642152285	2		421	675	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266155	198266155	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	38	463	0	ENST00000335508.6:c.2465G>T	p.Arg822Met	p.R822M	ENST00000335508	NM_012433.2	822	aGg/aTg	17/25	1	2	FACETS	0.179	0.147	0.214	0.179	0.147	0.214	SUBCLONAL	1	TRUE	1	0.668230642152285	2		463	637	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437353	220437353	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1389002726	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	150	542	0	ENST00000243786.2:c.257T>C	p.Phe86Ser	p.F86S	ENST00000243786	NM_002191.3	86	tTc/tCc	1/2	1	2	FACETS	0.474	0.432	0.517	0.474	0.432	0.517	SUBCLONAL	1	TRUE	1	0.668230642152285	2		542	948	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662184	227662184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	291	638	2	ENST00000305123.5:c.1271G>A	p.Gly424Asp	p.G424D	ENST00000305123	NM_005544.2	424	gGt/gAt	1/2	1	2	FACETS	0.863	0.813	0.915	0.863	0.813	0.915	CLONAL	1	TRUE	1	0.668230642152285	2		640	1009	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795061	242795061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1203794937	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	296	649	4	ENST00000334409.5:c.148G>A	p.Ala50Thr	p.A50T	ENST00000334409	NM_005018.2	50	Gcc/Acc	2/5	1	2	FACETS	0.911	0.859	0.965	0.911	0.859	0.965	CLONAL	1	TRUE	1	0.668230642152285	2		653	972	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485766	57485766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	167	381	0	ENST00000371085.3:c.1067G>A	p.Arg356His	p.R356H	ENST00000371085	NM_000516.4	356	cGt/cAt	13/13	1	2	FACETS	0.807	0.745	0.872	0.807	0.745	0.872	CLONAL	1	TRUE	1	0.668230642152285	2		381	619	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159112	24159112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1341827515	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	238	360	0	ENST00000263121.7:c.784G>A	p.Val262Ile	p.V262I	ENST00000263121	NM_003073.3	262	Gtc/Atc	6/9	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.668230642152285	2		360	702	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948079	178948079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	188	377	0	ENST00000263967.3:c.2851C>T	p.Arg951Cys	p.R951C	ENST00000263967	NM_006218.2	951	Cgt/Tgt	20/21	1	2	FACETS	0.883	0.82	0.948	0.883	0.82	0.948	CLONAL	1	TRUE	1	0.668230642152285	2		377	637	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806690	1806690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1388464798	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	94	471	0	ENST00000260795.2:c.1406G>A	p.Arg469Gln	p.R469Q	ENST00000260795		469	cGg/cAg	9/17	NA	2	FACETS	0.31	0.275	0.347			1	INDETERMINATE	1	TRUE	NA	0.668230642152285	2		471	909	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539653	187539653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201751862	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	211	411	0	ENST00000441802.2:c.8087C>T	p.Pro2696Leu	p.P2696L	ENST00000441802	NM_005245.3	2696	cCg/cTg	10/27	1	2	FACETS	0.938	0.876	1	0.938	0.876	1	CLONAL	1	TRUE	1	0.668230642152285	2		411	673	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32790089	32790089	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	173	320	0	ENST00000374899.4:c.1939C>A	p.Leu647Ile	p.L647I	ENST00000374899	NM_018833.2	647	Ctt/Att	12/12	1	2	FACETS	0.921	0.853	0.991	0.921	0.853	0.991	CLONAL	1	TRUE	1	0.668230642152285	2		320	562	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793332	139793332	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376801177	NA	P-0016522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	61	467	0	ENST00000247668.2:c.140C>T	p.Ala47Val	p.A47V	ENST00000247668	NM_021138.3	47	gCg/gTg	2/11	1	2	FACETS	0.2	0.172	0.231	0.2	0.172	0.231	SUBCLONAL	1	TRUE	1	0.668230642152285	2		467	913	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8501029	8501029	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs757562644	NA	P-0016524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	77	310	0	ENST00000356435.5:c.1853G>T	p.Cys618Phe	p.C618F	ENST00000356435		618	tGc/tTc	13/35	0.22594088540687	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	FALSE	0	0.22594088540687	1		310	548	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471762	120471762	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	64	541	1	ENST00000256646.2:c.3729T>A	p.Asp1243Glu	p.D1243E	ENST00000256646	NM_024408.3	1243	gaT/gaA	23/34	1	2	FACETS	0.651	0.562	0.748	0.651	0.562	0.748	SUBCLONAL	1	FALSE	1	0.22594088540687	2		542	870	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514107	69514107	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	143	554	0	ENST00000294312.3:c.574C>A	p.Leu192Met	p.L192M	ENST00000294312	NM_005117.2	192	Ctg/Atg	3/3	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.22594088540687	2		554	962	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207745	102207745	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	38	472	0	ENST00000263464.3:c.1727T>C	p.Val576Ala	p.V576A	ENST00000263464	NM_001165.4	576	gTa/gCa	9/9	1	2	FACETS	0.46	0.379	0.551	0.46	0.379	0.551	SUBCLONAL	1	FALSE	1	0.22594088540687	2		472	731	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40678575	40678575	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	121	560	1	ENST00000249776.8:c.317G>T	p.Arg106Leu	p.R106L	ENST00000249776	NM_033286.3	106	cGg/cTg	3/9	0.122903463814231	0	FACETS	0.806	0.727	0.89			1	INDETERMINATE	1	FALSE	0	0.22594088540687	0		561	1028	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs985033810	NA	P-0016524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	101	502	0	ENST00000269305.4:c.731G>T	p.Gly244Val	p.G244V	ENST00000269305	NM_001126112.2	244	gGc/gTc	7/11	0.22594088540687	1	FACETS	0.984	0.879	1	0.984	0.879	1	CLONAL	1	FALSE	0	0.22594088540687	1		502	806	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220599	1220617	+	frameshift_variant	Frame_Shift_Del	DEL	CGGACGACACCTGCCGGAC	CGGACGACACCTGCCGGAC	TGT	novel	NA	P-0016524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	177	599	3	ENST00000326873.7:c.617_635delinsTGT	p.Ala206ValfsTer76	p.A206Vfs*76	ENST00000326873	NM_000455.4	206	gCGGACGACACCTGCCGGACc/gTGTc	5/10	0.184164255270286	2	FACETS	0.802	0.738	0.868	0.802	0.738	0.868	CLONAL	2	FALSE	0	0.22594088540687	2		602	977	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171681	36171681	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	63	308	0	ENST00000300305.3:c.884C>A	p.Ser295Tyr	p.S295Y	ENST00000300305		295	tCt/tAt	7/8	0.184164255270286	2	FACETS	0.931	0.805	1	0.465	0.402	0.534	CLONAL	1	FALSE	0	0.22594088540687	2		308	599	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455552	189455552	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	155	555	0	ENST00000264731.3:c.86T>C	p.Phe29Ser	p.F29S	ENST00000264731	NM_003722.4	29	tTc/tCc	2/14	0.184164255270286	2	FACETS	1	0.986	1	0.7	0.64	0.763	CLONAL	1	FALSE	0	0.22594088540687	2		555	980	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671636	30671636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	51	438	0	ENST00000376406.3:c.5324C>T	p.Ser1775Phe	p.S1775F	ENST00000376406	NM_014641.2	1775	tCt/tTt	10/15	0.186503265523659	1	FACETS	0.529	0.448	0.618	0.529	0.448	0.618	SUBCLONAL	1	FALSE	0	0.22594088540687	1		438	757	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346634	81346634	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	84	334	0	ENST00000222390.5:c.1319G>T	p.Cys440Phe	p.C440F	ENST00000222390	NM_000601.4	440	tGc/tTc	11/18	0.0904337471368031	3	FACETS	1	0.967	1			1	INDETERMINATE	1	FALSE	NA	0.22594088540687	3		334	654	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453145	140453145	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913366	NA	P-0016524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	395	489	0	ENST00000288602.6:c.1790T>A	p.Leu597Gln	p.L597Q	ENST00000288602	NM_004333.4	597	cTa/cAa	15/18	0.22594088540687	5	FACETS	0.987	0.939	1			1	CLONAL	4	FALSE	NA	0.22594088540687	5		489	1186	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87475992	87475992	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1223	133	868	0	ENST00000277120.3:c.1434A>T	p.Arg478Ser	p.R478S	ENST00000277120		478	agA/agT	13/19	0.22594088540687	1	FACETS	0.77	0.697	0.847	0.77	0.697	0.847	SUBCLONAL	1	FALSE	0	0.22594088540687	1		868	1356	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044557	47044557	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	81	330	1	ENST00000377604.3:c.2054G>T	p.Arg685Leu	p.R685L	ENST00000377604	NM_001204468.1	685	cGg/cTg	18/24	0.22594088540687	0	FACETS	1	0.892	1			1	CLONAL	1	FALSE	NA	0.22594088540687	0		331	549	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0016526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	344	936	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.59762019481499	1	FACETS	0.969	0.922	1	0.969	0.922	1	CLONAL	1	TRUE	0	0.59762019481499	1		938	833	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451131	70451131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769757590	NA	P-0016526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	305	463	1	ENST00000373644.4:c.5971G>A	p.Asp1991Asn	p.D1991N	ENST00000373644	NM_030625.2	1991	Gat/Aat	12/12	1	2	FACETS	0.93	0.876	0.984	0.93	0.876	0.984	CLONAL	1	TRUE	1	0.59762019481499	2		464	1098	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914298	32914298	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1566233265	NA	P-0016526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	336	454	0	ENST00000380152.3:c.5806A>G	p.Met1936Val	p.M1936V	ENST00000380152		1936	Atg/Gtg	11/27	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.59762019481499	2		454	1034	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867029	45867029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367741538	NA	P-0016526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	229	373	0	ENST00000391945.4:c.1090C>T	p.Arg364Cys	p.R364C	ENST00000391945	NM_000400.3	364	Cgc/Tgc	11/23	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.59762019481499	2		373	766	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665402	138665402	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	344	572	0	ENST00000330315.3:c.163C>G	p.Pro55Ala	p.P55A	ENST00000330315	NM_023067.3	55	Ccc/Gcc	1/1	1	2	FACETS	0.987	0.935	1	0.987	0.935	1	CLONAL	1	TRUE	1	0.59762019481499	2		572	1166	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0016527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	129	570	1	ENST00000311936.3:c.34_35delinsTT	p.Gly12Phe	p.G12F	ENST00000311936	NM_004985.3	12	GGt/TTt	2/5	1	2	FACETS	0.787	0.712	0.867	0.787	0.712	0.867	SUBCLONAL	1	TRUE	1	0.30538955199717	2		571	1073	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0016527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	105	365	2	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.30538955199717	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.30538955199717	1		367	511	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219381	1219381	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	126	464	0	ENST00000326873.7:c.433G>T	p.Glu145Ter	p.E145*	ENST00000326873	NM_000455.4	145	Gag/Tag	3/10	0.30538955199717	1	FACETS	0.971	0.88	1	0.971	0.88	1	CLONAL	1	TRUE	0	0.30538955199717	1		464	720	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599969	10599969	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	176	631	0	ENST00000171111.5:c.1607G>C	p.Arg536Pro	p.R536P	ENST00000171111	NM_203500.1	536	cGc/cCc	5/6	0.30538955199717	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.30538955199717	1		631	949	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11151992	11151992	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	103	387	2	ENST00000358026.2:c.4276G>T	p.Glu1426Ter	p.E1426*	ENST00000358026	NM_001128849.1	1426	Gag/Tag	31/36	0.30538955199717	1	FACETS	0.953	0.854	1	0.953	0.854	1	CLONAL	1	TRUE	0	0.30538955199717	1		389	600	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538329	187538329	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	124	416	0	ENST00000441802.2:c.8905G>T	p.Val2969Phe	p.V2969F	ENST00000441802	NM_005245.3	2969	Gtt/Ttt	11/27	1	2	FACETS	0.895	0.809	0.986	0.895	0.809	0.986	CLONAL	1	TRUE	1	0.30538955199717	2		416	907	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877899	151877899	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	82	318	0	ENST00000262189.6:c.7046T>A	p.Phe2349Tyr	p.F2349Y	ENST00000262189	NM_170606.2	2349	tTc/tAc	36/59	1	2	FACETS	0.947	0.837	1	0.947	0.837	1	CLONAL	1	TRUE	1	0.30538955199717	2		318	567	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177635	56177635	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs755905626	NA	P-0016529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	244	355	0	ENST00000399503.3:c.2608C>T	p.Gln870Ter	p.Q870*	ENST00000399503	NM_005921.1	870	Cag/Tag	14/20	1	2	FACETS	0.98	0.923	1	0.98	0.923	1	CLONAL	1	TRUE	1	0.791338883381201	2		355	629	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520006	NA	P-0016531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	467	603	0	ENST00000269305.4:c.821T>G	p.Val274Gly	p.V274G	ENST00000269305	NM_001126112.2	274	gTt/gGt	8/11	NA	2	FACETS	0.971	0.928	1			1	INDETERMINATE	1	TRUE	NA	0.683374217243977	2		603	1407	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855019	76855019	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	304	271	1	ENST00000373344.5:c.5817del	p.Asp1940IlefsTer15	p.D1940Ifs*15	ENST00000373344	NM_000489.3	1939	aaA/aa	25/35	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.683374217243977	1		272	537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	463	574	0	ENST00000269305.4:c.814del	p.Val272CysfsTer73	p.V272Cfs*73	ENST00000269305	NM_001126112.2	272	Gtg/tg	8/11	NA	2	FACETS	0.99	0.946	1			1	INDETERMINATE	1	TRUE	NA	0.683374217243977	2		574	1369	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220507	1220507	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	T	novel	NA	P-0016531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	250	497	0	ENST00000326873.7:c.597+3A>T		p.X199_splice	ENST00000326873	NM_000455.4	199			0.683374217243977	1	FACETS	0.907	0.858	0.957	0.907	0.858	0.957	CLONAL	1	TRUE	0	0.683374217243977	1		497	531	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593602	55593613	+	inframe_deletion	In_Frame_Del	DEL	GTGGAAGGTTGT	GTGGAAGGTTGT	-	novel	NA	P-0016532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	228	503	0	ENST00000288135.5:c.1668_1679del	p.Gln556_Val560delinsHis	p.Q556_V560delinsH	ENST00000288135	NM_000222.2	556	caGTGGAAGGTTGTt/cat	11/21	1	2	FACETS	0.712	0.664	0.761	0.712	0.664	0.761	SUBCLONAL	1	TRUE	1	0.717162635333535	2		503	893	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22412959	22412959	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	135	197	0	ENST00000344548.3:c.206C>G	p.Pro69Arg	p.P69R	ENST00000344548	NM_001039802.1	69	cCg/cGg	5/7	1	2	FACETS	0.939	0.862	1	0.939	0.862	1	CLONAL	1	TRUE	1	0.717162635333535	2		197	401	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115753	108115753	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	54	341	0	ENST00000278616.4:c.901G>T	p.Gly301Cys	p.G301C	ENST00000278616	NM_000051.3	301	Ggt/Tgt	7/63	1	2	FACETS	0.79	0.676	0.914	0.79	0.676	0.914	CLONAL	1	TRUE	1	0.309885646342905	2		341	441	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675403	241675405	+	inframe_deletion	In_Frame_Del	DEL	ACC	ACC	-	novel	NA	P-0016535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	25	403	0	ENST00000366560.3:c.417_419del	p.Val140del	p.V140del	ENST00000366560	NM_000143.3	139	gtGGTa/gta	4/10	0.186489327045522	1	FACETS	0.849	0.688	1	0.849	0.688	1	INDETERMINATE	1	TRUE	0	0.51	1		403	86	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554324	81554324	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	19	577	0	ENST00000298171.2:c.344C>A	p.Thr115Asn	p.T115N	ENST00000298171	NM_000369.2	115	aCt/aAt	4/10	1	2	FACETS	0.92	0.715	1	0.92	0.715	1	CLONAL	1	TRUE	1	0.51	2		577	81	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584772	52584772	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0016535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	18	490	0	ENST00000394830.3:c.4350T>A	p.Tyr1450Ter	p.Y1450*	ENST00000394830	NM_018313.4	1450	taT/taA	28/30	0.3	1	FACETS	0.835	0.649	1	0.835	0.649	1	INDETERMINATE	1	TRUE	0	0.51	1		490	63	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948523	31948523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756991872	NA	P-0016535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	10	175	0	ENST00000375333.2:c.1006C>T	p.Arg336Trp	p.R336W	ENST00000375333	NM_032454.1	336	Cgg/Tgg	7/8	1	2	FACETS	0.53	0.364	0.731	0.53	0.364	0.731	SUBCLONAL	1	TRUE	1	0.51	2		175	74	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983483	90983483	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587780099	NA	P-0016535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	26	511	0	ENST00000265433.3:c.620G>T	p.Ser207Ile	p.S207I	ENST00000265433	NM_002485.4	207	aGt/aTt	6/16	1	2	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	TRUE	1	0.51	2		511	96	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874321	76874321	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0016535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	25	314	0	ENST00000373344.5:c.5401A>T	p.Lys1801Ter	p.K1801*	ENST00000373344	NM_000489.3	1801	Aaa/Taa	21/35	0.236744330919882	2	FACETS	1	0.906	1			1	INDETERMINATE	2	TRUE	NA	0.51	2		314	44	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0016536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	180	309	1	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	0.995	1	CLONAL	4	FALSE	1	0.201869937256314	2		310	433	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123022468	123022468	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0016536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	38	640	0	ENST00000355640.3:c.878-1G>A		p.X293_splice	ENST00000355640		293			0.175404494417407	0	FACETS	0.871	0.722	1			1	CLONAL	1	FALSE	0	0.201869937256314	0		640	345	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0016537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	28	547	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.113790840425179	3	FACETS	0.987	0.788	1	0.494	0.394	0.608	CLONAL	1	TRUE	1	0.12	3		547	501	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0016537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	61	332	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.113790840425179	3	FACETS	0.855	0.74	0.98	1	0.958	1	CLONAL	3	TRUE	1	0.12	3		332	420	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913396	NA	P-0016537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	48	284	0	ENST00000349496.5:c.95A>T	p.Asp32Val	p.D32V	ENST00000349496	NM_001904.3	32	gAc/gTc	3/15	0.113790840425179	3	FACETS	0.961	0.818	1	1	0.96	1	CLONAL	3	TRUE	1	0.12	3		284	294	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412493	80412493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514698	NA	P-0016537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	11	350	0	ENST00000286548.4:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000286548	NM_002072.3	183	cGa/cAa	4/7	0.113790840425179	3	FACETS	0.364	0.25	0.507	0.182	0.125	0.254	SUBCLONAL	1	TRUE	1	0.12	3		350	534	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338671	70338671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	103	495	0	ENST00000374080.3:c.67G>T	p.Asp23Tyr	p.D23Y	ENST00000374080		23	Gat/Tat	1/45	1	2	FACETS	1	0.96	1	1	0.988	1	CLONAL	2	TRUE	1	0.12	2		495	748	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617533	158617533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751000395	NA	P-0016537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	32	366	1	ENST00000263640.3:c.1123C>T	p.Arg375Cys	p.R375C	ENST00000263640	NM_001105.4	375	Cgt/Tgt	9/11	0.113790840425179	3	FACETS	1	0.819	1	0.506	0.409	0.615	CLONAL	1	TRUE	1	0.12	3		367	559	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617539	158617539	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	44	356	0	ENST00000263640.3:c.1117A>T	p.Asn373Tyr	p.N373Y	ENST00000263640	NM_001105.4	373	Aat/Tat	9/11	0.113790840425179	3	FACETS	0.767	0.643	0.904	0.767	0.643	0.904	CLONAL	2	TRUE	1	0.12	3		356	507	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991703	72991703	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201821212	NA	P-0016538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	146	263	0	ENST00000268489.5:c.2342C>T	p.Ala781Val	p.A781V	ENST00000268489	NM_006885.3	781	gCg/gTg	2/10	0.213861544768676	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	0	0.278764770124879	2		263	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	155	471	0	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.278764770124879	2		471	869	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820582	3820582	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1429	232	387	0	ENST00000262367.5:c.2869C>G	p.Pro957Ala	p.P957A	ENST00000262367	NM_004380.2	957	Cct/Gct	14/31	0.278764770124879	9	FACETS	0.99	0.92	1			1	CLONAL	2	TRUE	NA	0.278764770124879	9		387	1661	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711875	89711875	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587782603	NA	P-0016538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	114	388	0	ENST00000371953.3:c.493G>A	p.Gly165Arg	p.G165R	ENST00000371953	NM_000314.4	165	Gga/Aga	6/9	0.213861544768676	2	FACETS	1	0.965	1	0.577	0.52	0.637	CLONAL	1	TRUE	0	0.278764770124879	2		388	709	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820660	3820660	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1835	308	483	0	ENST00000262367.5:c.2791C>G	p.Gln931Glu	p.Q931E	ENST00000262367	NM_004380.2	931	Caa/Gaa	14/31	0.278764770124879	9	FACETS	1	0.953	1			1	CLONAL	2	TRUE	NA	0.278764770124879	9		483	2143	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56787292	56787292	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374196453	NA	P-0016538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1256	352	573	1	ENST00000337432.4:c.778C>T	p.Arg260Trp	p.R260W	ENST00000337432	NM_058216.2	260	Cgg/Tgg	5/9	0.27876477012488	4	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	2	0.278764770124879	4		574	1608	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980814	40980814	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	127	532	0	ENST00000373198.4:c.1672C>A	p.Pro558Thr	p.P558T	ENST00000373198	NM_133170.3	558	Cca/Aca	10/32	0.27876477012488	4	FACETS	0.898	0.811	0.991	0.449	0.405	0.496	CLONAL	1	TRUE	2	0.278764770124879	4		532	1297	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	275	641	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.336903635968948	2		641	1344	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552774	226552774	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	331	447	0	ENST00000366794.5:c.2587G>T	p.Gly863Trp	p.G863W	ENST00000366794	NM_001618.3	863	Ggg/Tgg	19/23	0.336903635968948	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.336903635968948	3		447	1075	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861856	57861856	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	154	450	0	ENST00000228682.2:c.1157T>A	p.Val386Glu	p.V386E	ENST00000228682	NM_005269.2	386	gTg/gAg	10/12	1	2	FACETS	0.983	0.899	1	0.983	0.899	1	CLONAL	1	TRUE	1	0.336903635968948	2		450	930	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152082	11152082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866735560	NA	P-0016539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	164	413	0	ENST00000358026.2:c.4366C>T	p.Pro1456Ser	p.P1456S	ENST00000358026	NM_001128849.1	1456	Ccg/Tcg	31/36	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.336903635968948	2		413	887	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044839	47044839	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0016539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	158	457	0	ENST00000377604.3:c.2167-2A>G		p.X723_splice	ENST00000377604	NM_001204468.1	723			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.336903635968948	2		457	839	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0016541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	642	1585	1	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.986	0.95	1	0.986	0.95	1	CLONAL	1	TRUE	1	0.82	2		1586	1588	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047173	77047173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	489	437	0	ENST00000356341.3:c.1371G>A	p.Met457Ile	p.M457I	ENST00000356341	NM_002576.4	457	atG/atA	13/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.82	2		437	1182	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061169	38061169	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	162	204	0	ENST00000250448.2:c.820G>A	p.Ala274Thr	p.A274T	ENST00000250448	NM_004496.3	274	Gcc/Acc	2/2	1	2	FACETS	0.906	0.84	0.974	0.906	0.84	0.974	CLONAL	1	TRUE	1	0.82	2		204	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0016542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	581	496	2	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.51152914399961	2	FACETS	0.967	0.934	1	0.967	0.934	1	CLONAL	2	TRUE	0	0.547246704287353	2		498	1098	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0016542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	290	462	5	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	1	2	FACETS	0.972	0.915	1	0.972	0.915	1	CLONAL	1	TRUE	1	0.547246704287353	2		467	1090	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710649	40710649	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	270	404	1	ENST00000373198.4:c.4202G>T	p.Gly1401Val	p.G1401V	ENST00000373198	NM_133170.3	1401	gGa/gTa	31/32	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.547246704287353	2		405	920	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056425	26056427	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	rs774779034	NA	P-0016542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	80	212	0	ENST00000343677.2:c.230_232del	p.Asn77del	p.N77del	ENST00000343677	NM_005319.3	77	aACAgc/agc	1/1	0.236875879955271	1	FACETS	0.385	0.34	0.434	0.385	0.34	0.434	INDETERMINATE	1	TRUE	0	0.547246704287353	1		212	551	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729974	30729974	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs397516840	NA	P-0016542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	263	378	0	ENST00000295754.5:c.1495G>T	p.Glu499Ter	p.E499*	ENST00000295754	NM_003242.5	499	Gaa/Taa	6/7	0.547246704287353	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.547246704287353	1		378	671	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435612	110435612	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1240327417	NA	P-0016542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	189	385	0	ENST00000375856.3:c.2789G>A	p.Arg930His	p.R930H	ENST00000375856	NM_003749.2	930	cGc/cAc	1/2	0.541698862669162	2	FACETS	0.668	0.617	0.721	0.334	0.308	0.361	SUBCLONAL	1	TRUE	0	0.547246704287353	2		385	1034	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575551	64575551	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1085307471	NA	P-0016542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	300	399	0	ENST00000312049.6:c.466G>C	p.Gly156Arg	p.G156R	ENST00000312049	NM_130799.2	156	Ggt/Cgt	3/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.547246704287353	2		399	1046	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156266	119156266	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	246	341	0	ENST00000264033.4:c.1931A>G	p.Asp644Gly	p.D644G	ENST00000264033	NM_005188.3	644	gAt/gGt	11/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.547246704287353	2		341	838	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859410	57859410	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	232	325	0	ENST00000228682.2:c.555G>T	p.Met185Ile	p.M185I	ENST00000228682	NM_005269.2	185	atG/atT	6/12	1	2	FACETS	0.971	0.907	1	0.971	0.907	1	CLONAL	1	TRUE	1	0.547246704287353	2		325	873	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26927976	26927976	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	181	422	0	ENST00000381527.3:c.415A>T	p.Ile139Phe	p.I139F	ENST00000381527	NM_001260.1	139	Att/Ttt	4/13	0.547246704287353	1	FACETS	0.823	0.763	0.884	0.823	0.763	0.884	CLONAL	1	TRUE	0	0.547246704287353	1		422	584	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560341	95560341	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	250	356	0	ENST00000393063.1:c.5248G>C	p.Val1750Leu	p.V1750L	ENST00000393063	NM_030621.3	1750	Gta/Cta	25/28	1	2	FACETS	0.992	0.929	1	0.992	0.929	1	CLONAL	1	TRUE	1	0.547246704287353	2		356	921	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857977	9857977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1163517430	NA	P-0016542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	128	417	0	ENST00000330684.3:c.3424C>T	p.Pro1142Ser	p.P1142S	ENST00000330684	NM_001134407.1	1142	Ccc/Tcc	13/13	0.290268136351068	1	FACETS	0.388	0.351	0.427	0.388	0.351	0.427	INDETERMINATE	1	TRUE	0	0.547246704287353	1		417	875	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119918	70119918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202028563	NA	P-0016542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	163	394	0	ENST00000245479.2:c.920C>T	p.Pro307Leu	p.P307L	ENST00000245479	NM_000346.3	307	cCg/cTg	3/3	0.51152914399961	2	FACETS	0.69	0.634	0.749	0.345	0.317	0.375	SUBCLONAL	1	TRUE	0	0.547246704287353	2		394	863	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872759	136872759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	75	257	1	ENST00000241393.3:c.739G>A	p.Ala247Thr	p.A247T	ENST00000241393	NM_003467.2	247	Gct/Act	2/2	0.312477759649257	1	FACETS	0.329	0.288	0.373	0.329	0.288	0.373	INDETERMINATE	1	TRUE	0	0.547246704287353	1		258	605	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620643	52620643	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	267	430	0	ENST00000394830.3:c.3110G>C	p.Arg1037Pro	p.R1037P	ENST00000394830	NM_018313.4	1037	cGg/cCg	21/30	0.547246704287353	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.547246704287353	1		430	685	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672730	86672730	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0016542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	158	315	0	ENST00000274376.6:c.2217T>A	p.Tyr739Ter	p.Y739*	ENST00000274376	NM_002890.2	739	taT/taA	17/25	0.547246704287353	1	FACETS	0.887	0.819	0.956	0.887	0.819	0.956	CLONAL	1	TRUE	0	0.547246704287353	1		315	473	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043391	180043391	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	134	518	0	ENST00000261937.6:c.3195C>A	p.Asp1065Glu	p.D1065E	ENST00000261937	NM_182925.4	1065	gaC/gaA	23/30	0.547246704287353	1	FACETS	0.446	0.405	0.489	0.446	0.405	0.489	SUBCLONAL	1	TRUE	0	0.547246704287353	1		518	798	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965698	93965698	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	204	401	0	ENST00000369303.4:c.2230G>T	p.Ala744Ser	p.A744S	ENST00000369303	NM_004440.3	744	Gct/Tct	13/17	0.290268136351068	1	FACETS	0.707	0.657	0.758	0.707	0.657	0.758	INDETERMINATE	1	TRUE	0	0.547246704287353	1		401	766	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041061	112041061	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	228	335	0	ENST00000368678.4:c.194G>T	p.Gly65Val	p.G65V	ENST00000368678		65	gGa/gTa	3/13	0.290268136351068	1	FACETS	0.872	0.817	0.929	0.872	0.817	0.929	INDETERMINATE	1	TRUE	0	0.547246704287353	1		335	694	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981936	70981937	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0016542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	303	508	2	ENST00000276594.2:c.159_160delinsAA	p.Phe53Leu	p.F53L	ENST00000276594	NM_024504.3	53	ttCCgg/ttAAgg	2/8	0.236875879955271	1	FACETS	0.885	0.836	0.935	0.885	0.836	0.935	INDETERMINATE	1	TRUE	0	0.547246704287353	1		510	909	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750831	128750831	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	628	469	0	ENST00000377970.2:c.368G>T	p.Gly123Val	p.G123V	ENST00000377970	NM_002467.4	123	gGa/gTa	2/3	0.547246704287353	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	1	0.547246704287353	3		469	1228	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738762	145738762	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	861	585	0	ENST00000428558.2:c.2302G>T	p.Val768Leu	p.V768L	ENST00000428558	NM_004260.3	768	Gtg/Ttg	15/22	0.547246704287353	3	FACETS	0.85	0.826	0.873	1	0.997	1	CLONAL	3	TRUE	1	0.547246704287353	3		585	1572	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	428	530	1	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.660027789595083	1	FACETS	0.99	0.949	1	0.99	0.949	1	CLONAL	1	TRUE	0	0.660027789595083	1		531	878	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0016543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	366	480	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.645689858643786	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.660027789595083	1		480	719	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0016543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	963	563	2	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.604901755331269	3	FACETS	0.986	0.959	1			1	CLONAL	2	TRUE	NA	0.660027789595083	3		565	1968	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105630	30105631	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0016543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	454	657	1	ENST00000331968.5:c.1055_1056delinsAA	p.Arg352Lys	p.R352K	ENST00000331968	NM_002742.2	352	aGG/aAA	7/18	1	2	FACETS	0.885	0.844	0.927	0.885	0.844	0.927	CLONAL	1	TRUE	1	0.660027789595083	2		658	1554	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061191	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	280	476	0	ENST00000250448.2:c.798C>G	p.Phe266Leu	p.F266L	ENST00000250448	NM_004496.3	266	ttC/ttG	2/2	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.660027789595083	2		476	777	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618629	37618629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1279	433	533	0	ENST00000447079.4:c.305C>T	p.Ser102Leu	p.S102L	ENST00000447079	NM_015083.1	102	tCa/tTa	1/14	0.604901755331269	3	FACETS	1	0.966	1			1	CLONAL	1	TRUE	NA	0.660027789595083	3		533	1712	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618658	37618658	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1430	445	579	1	ENST00000447079.4:c.334C>T	p.Arg112Cys	p.R112C	ENST00000447079	NM_015083.1	112	Cgt/Tgt	1/14	0.604901755331269	3	FACETS	0.956	0.91	1			1	CLONAL	1	TRUE	NA	0.660027789595083	3		580	1875	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619145	37619145	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1197	397	461	0	ENST00000447079.4:c.821C>G	p.Ser274Trp	p.S274W	ENST00000447079	NM_015083.1	274	tCg/tGg	1/14	0.604901755331269	3	FACETS	1	0.952	1			1	CLONAL	1	TRUE	NA	0.660027789595083	3		461	1594	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40379633	40379633	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	375	515	0	ENST00000293328.3:c.199G>C	p.Glu67Gln	p.E67Q	ENST00000293328	NM_012448.3	67	Gag/Cag	3/19	NA	2	FACETS	0.918	0.871	0.965			1	INDETERMINATE	1	TRUE	NA	0.660027789595083	2		515	1238	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10264986	10264986	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	241	300	0	ENST00000340748.4:c.1954C>T	p.Arg652Ter	p.R652*	ENST00000340748		652	Cga/Tga	21/40	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.660027789595083	2		300	726	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748577	40748577	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1321	88	430	0	ENST00000392038.2:c.305C>A	p.Ala102Asp	p.A102D	ENST00000392038	NM_001626.4	102	gCc/gAc	5/14	0.604901755331269	3	FACETS	0.252	0.222	0.284			1	SUBCLONAL	1	TRUE	NA	0.660027789595083	3		430	1409	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37081709	37081709	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764663152	NA	P-0016543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	403	546	0	ENST00000231790.2:c.1591G>A	p.Val531Met	p.V531M	ENST00000231790	NM_000249.3	531	Gtg/Atg	14/19	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.660027789595083	2		546	1205	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538311	187538311	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	380	550	0	ENST00000441802.2:c.8923G>A	p.Glu2975Lys	p.E2975K	ENST00000441802	NM_005245.3	2975	Gaa/Aaa	11/27	1	2	FACETS	0.892	0.847	0.938	0.892	0.847	0.938	CLONAL	1	TRUE	1	0.660027789595083	2		550	1291	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410981	31410981	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	434	528	0	ENST00000344624.3:c.3539C>G	p.Ser1180Cys	p.S1180C	ENST00000344624		1180	tCt/tGt	28/33	1	2	FACETS	0.988	0.942	1	0.988	0.942	1	CLONAL	1	TRUE	1	0.660027789595083	2		528	1331	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803122	32803122	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745356167	NA	P-0016543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	371	380	3	ENST00000374899.4:c.754C>T	p.Arg252Trp	p.R252W	ENST00000374899	NM_018833.2	252	Cgg/Tgg	5/12	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.660027789595083	2		383	1081	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522604	106522604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	274	390	0	ENST00000359195.3:c.2581G>A	p.Asp861Asn	p.D861N	ENST00000359195	NM_002649.2	861	Gat/Aat	7/11	1	2	FACETS	0.832	0.782	0.883	0.832	0.782	0.883	CLONAL	1	TRUE	1	0.660027789595083	2		390	998	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0016544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1389	188	772	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	0.209146464928008	2		772	1577	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971177	21971177	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913382	NA	P-0016544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	89	277	0	ENST00000304494.5:c.181G>T	p.Glu61Ter	p.E61*	ENST00000304494	NM_000077.4	61	Gag/Tag	2/3	0.209146464928008	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.209146464928008	1		277	615	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235837	108235837	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	203	312	0	ENST00000278616.4:c.8879G>T	p.Trp2960Leu	p.W2960L	ENST00000278616	NM_000051.3	2960	tGg/tTg	62/63	0.202060533911447	2	FACETS	0.808	0.748	0.871	0.808	0.748	0.871	CLONAL	2	TRUE	0	0.209146464928008	2		312	1201	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112769514	112769514	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1404	80	565	0	ENST00000369452.4:c.1466G>T	p.Gly489Val	p.G489V	ENST00000369452	NM_007373.3	489	gGc/gTc	8/9	1	2	FACETS	0.516	0.452	0.585	0.516	0.452	0.585	SUBCLONAL	1	TRUE	1	0.209146464928008	2		565	1484	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466960	18466960	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1179	146	439	0	ENST00000266497.5:c.1099C>T	p.Gln367Ter	p.Q367*	ENST00000266497		367	Cag/Tag	5/31	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.209146464928008	2		439	1325	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093386	30093386	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1329	80	483	0	ENST00000331968.5:c.1877A>T	p.Gln626Leu	p.Q626L	ENST00000331968	NM_002742.2	626	cAg/cTg	13/18	1	2	FACETS	0.543	0.476	0.616	0.543	0.476	0.616	SUBCLONAL	1	TRUE	1	0.209146464928008	2		483	1409	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584366	39584366	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	78	268	0	ENST00000262039.4:c.1031A>T	p.Glu344Val	p.E344V	ENST00000262039	NM_002647.2	344	gAg/gTg	10/25	1	2	FACETS	0.985	0.865	1	0.985	0.865	1	CLONAL	1	TRUE	1	0.209146464928008	2		268	757	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945794	17945794	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	86	408	0	ENST00000458235.1:c.2066C>A	p.Pro689His	p.P689H	ENST00000458235	NM_000215.3	689	cCc/cAc	16/24	1	2	FACETS	0.775	0.684	0.873	0.775	0.684	0.873	SUBCLONAL	1	TRUE	1	0.209146464928008	2		408	1061	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955857	55955857	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0016544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	125	402	0	ENST00000263923.4:c.3304+1G>T		p.X1102_splice	ENST00000263923	NM_002253.2	1102			1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.209146464928008	2		402	1181	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508754	148508754	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	100	353	0	ENST00000320356.2:c.1910T>G	p.Val637Gly	p.V637G	ENST00000320356	NM_004456.4	637	gTg/gGg	16/20	1	2	FACETS	0.757	0.674	0.846	0.757	0.674	0.846	SUBCLONAL	1	TRUE	1	0.209146464928008	2		353	1263	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44920609	44920609	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1348	181	425	0	ENST00000377967.4:c.1370A>T	p.His457Leu	p.H457L	ENST00000377967	NM_021140.2	457	cAt/cTt	14/29	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.209146464928008	2		425	1529	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039817	47039817	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0016544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	170	575	0	ENST00000377604.3:c.1161-1G>T		p.X387_splice	ENST00000377604	NM_001204468.1	387			NA	2	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.209146464928008	2		575	1366	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89791110	89791111	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	T	novel	NA	P-0016544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	45	112	0	ENST00000336032.3:c.497_498delinsT	p.Pro166LeufsTer17	p.P166Lfs*17	ENST00000336032	NM_006813.2	166	cCG/cT	1/2	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.209146464928008	2		112	290	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	338	530	1	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.635195581411673	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.635195581411673	1		531	705	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214891	36214891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201094135	NA	P-0016545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	395	574	1	ENST00000222270.7:c.3317G>A	p.Arg1106Gln	p.R1106Q	ENST00000222270	NM_014727.1	1106	cGg/cAg	8/37	1	2	FACETS	0.963	0.916	1	0.963	0.916	1	CLONAL	1	TRUE	1	0.635195581411673	2		575	1291	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880219	37880220	+	missense_variant	Missense_Mutation	DNP	TT	TT	CC	rs121913469	NA	P-0016547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	71	671	0	ENST00000269571.5:c.2263_2264delinsCC	p.Leu755Pro	p.L755P	ENST00000269571		755	TTg/CCg	19/27	0.4043037179615	4	FACETS	1	0.936	1			1	CLONAL	2	TRUE	NA	0.403295120775307	4		671	228	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174838	56174848	+	frameshift_variant	Frame_Shift_Del	DEL	CTTGCCACAGT	CTTGCCACAGT	-	novel	NA	P-0016547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	52	401	0	ENST00000399503.3:c.1997_2007del	p.Pro666LeufsTer27	p.P666Lfs*27	ENST00000399503	NM_005921.1	666	cCTTGCCACAGT/c	11/20	0.4043037179615	4	FACETS	1	0.932	1			1	CLONAL	1	TRUE	NA	0.403295120775307	4		401	313	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183324	56183340	+	frameshift_variant	Frame_Shift_Del	DEL	ACAATTGCATTTATGGC	ACAATTGCATTTATGGC	-	novel	NA	P-0016547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	50	398	0	ENST00000399503.3:c.4236_4252del	p.Ile1413Ter	p.I1413*	ENST00000399503	NM_005921.1	1412	ACAATTGCATTTATGGCa/a	18/20	0.4043037179615	4	FACETS	1	0.947	1			1	CLONAL	1	TRUE	NA	0.403295120775307	4		398	279	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920167	76920167	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	29	569	0	ENST00000373344.5:c.3910G>T	p.Gly1304Ter	p.G1304*	ENST00000373344	NM_000489.3	1304	Gga/Tga	11/35	1	2	FACETS	0.639	0.516	0.778	0.639	0.516	0.778	SUBCLONAL	1	TRUE	1	0.403295120775307	2		569	225	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0016548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	162	277	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.441766596178008	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.441766596178008	1		277	523	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591285	67591285	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	151	346	0	ENST00000274335.5:c.1784del	p.Asn595ThrfsTer67	p.N595Tfs*67	ENST00000274335		595	Aac/ac	13/15	0.441766596178008	1	FACETS	0.934	0.859	1	0.934	0.859	1	CLONAL	1	TRUE	0	0.441766596178008	1		346	570	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0016549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	613	731	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.609233118530865	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.609233118530865	3		731	1254	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40498589	40498589	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	175	311	0	ENST00000264657.5:c.271C>T	p.Gln91Ter	p.Q91*	ENST00000264657	NM_139276.2	91	Cag/Tag	3/24	0.609233118530865	3	FACETS	1	0.986	1	0.644	0.596	0.693	CLONAL	1	TRUE	1	0.609233118530865	3		311	582	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088759	27088759	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	481	574	1	ENST00000324856.7:c.2368C>T	p.Gln790Ter	p.Q790*	ENST00000324856	NM_006015.4	790	Cag/Tag	7/20	0.609233118530865	2	FACETS	0.987	0.953	1	0.987	0.953	1	CLONAL	2	TRUE	0	0.609233118530865	2		575	800	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305323	65305323	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	326	606	0	ENST00000342505.4:c.2805G>C	p.Glu935Asp	p.E935D	ENST00000342505	NM_002227.2	935	gaG/gaC	20/25	0.609233118530865	2	FACETS	0.947	0.895	1	0.474	0.447	0.5	CLONAL	1	TRUE	0	0.609233118530865	2		606	1130	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614833	23614833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200283306	NA	P-0016549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	301	630	0	ENST00000261584.4:c.3508C>T	p.His1170Tyr	p.H1170Y	ENST00000261584	NM_024675.3	1170	Cat/Tat	13/13	1	2	FACETS	0.889	0.838	0.942	0.889	0.838	0.942	CLONAL	1	TRUE	1	0.609233118530865	2		630	1111	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141479	11141479	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	237	512	1	ENST00000358026.2:c.3456C>A	p.Phe1152Leu	p.F1152L	ENST00000358026	NM_001128849.1	1152	ttC/ttA	25/36	1	2	FACETS	0.912	0.853	0.973	0.912	0.853	0.973	CLONAL	1	TRUE	1	0.609233118530865	2		513	853	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0016550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	439	936	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.370838669495773	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.370838669495773	2		938	1076	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0016550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	285	599	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.370838669495773	3	FACETS	0.911	0.857	0.966	0.911	0.857	0.966	CLONAL	2	TRUE	1	0.370838669495773	3		599	1000	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	109	486	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.146947172554042	3	FACETS	1	0.949	1	0.544	0.489	0.601	INDETERMINATE	1	TRUE	1	0.370838669495773	3		486	641	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562729	21562729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1474280181	NA	P-0016550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	792	465	0	ENST00000382592.4:c.1190G>A	p.Arg397Gln	p.R397Q	ENST00000382592	NM_014572.2	397	cGg/cAg	4/8	0.370838669495773	6	FACETS	1	0.994	1	1	0.994	1	CLONAL	5	TRUE	1	0.370838669495773	6		465	1378	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17117112	17117112	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398124532	NA	P-0016550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	179	557	0	ENST00000285071.4:c.1597C>T	p.Gln533Ter	p.Q533*	ENST00000285071	NM_144997.5	533	Cag/Tag	14/14	0.370838669495773	2	FACETS	0.977	0.9	1	0.489	0.45	0.529	CLONAL	1	TRUE	0	0.370838669495773	2		557	988	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043992	180043992	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	147	443	0	ENST00000261937.6:c.3004G>T	p.Glu1002Ter	p.E1002*	ENST00000261937	NM_182925.4	1002	Gag/Tag	22/30	0.370838669495773	2	FACETS	1	0.945	1	0.522	0.477	0.569	CLONAL	1	TRUE	0	0.370838669495773	2		443	759	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184140	123184140	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	103	363	0	ENST00000218089.9:c.998G>C	p.Gly333Ala	p.G333A	ENST00000218089	NM_001042749.1	333	gGt/gCt	11/35	0.212504473784961	5	FACETS	1	0.981	1	0.485	0.435	0.538	INDETERMINATE	1	TRUE	2	0.370838669495773	5		363	594	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	191	405	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.762199105406914	2	FACETS	0.887	0.826	0.95	0.444	0.413	0.475	CLONAL	1	TRUE	0	0.762199105406914	2		405	565	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0016551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	30	643	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.762199105406914	3	FACETS	0.182	0.145	0.223	0.091	0.072	0.112	SUBCLONAL	1	TRUE	1	0.762199105406914	3		643	599	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937623	32937623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1302254513	NA	P-0016551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	235	401	0	ENST00000380152.3:c.8284C>T	p.Pro2762Ser	p.P2762S	ENST00000380152		2762	Cct/Tct	18/27	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.762199105406914	2		401	615	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463245	25463245	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	228	401	0	ENST00000264709.3:c.2248C>T	p.Pro750Ser	p.P750S	ENST00000264709	NM_175629.2	750	Ccc/Tcc	19/23	0.762199105406914	3	FACETS	0.996	0.93	1	0.498	0.465	0.532	CLONAL	1	TRUE	1	0.762199105406914	3		401	830	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934239	39934240	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0016551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	481	477	0	ENST00000378444.4:c.359_360del	p.Pro120ArgfsTer65	p.P120Rfs*65	ENST00000378444	NM_001123385.1	120	cCA/c	4/15	0.743841596491912	3	FACETS	0.94	0.905	0.976			1	CLONAL	2	TRUE	NA	0.762199105406914	3		477	927	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0016552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	203	591	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.313332750425107	2	FACETS	0.853	0.794	0.914	0.853	0.794	0.914	CLONAL	2	TRUE	0	0.336710161547147	2		592	707	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0016552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	70	277	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.336710161547147	1	FACETS	0.753	0.659	0.855	0.753	0.659	0.855	SUBCLONAL	1	TRUE	0	0.336710161547147	1		277	459	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39567846	39567846	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs747761836	NA	P-0016552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	66	289	1	ENST00000262039.4:c.602T>A	p.Ile201Lys	p.I201K	ENST00000262039	NM_002647.2	201	aTa/aAa	5/25	0.291828660846756	3	FACETS	0.859	0.747	0.981	0.43	0.373	0.491	CLONAL	1	TRUE	1	0.336710161547147	3		290	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0016553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	704	488	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.76140149004218	3	FACETS	0.91	0.892	0.927	0.91	0.892	0.927	CLONAL	3	TRUE	0	0.852367331886808	3		490	863	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81563032	81563032	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	40	383	0	ENST00000298171.2:c.595G>C	p.Gly199Arg	p.G199R	ENST00000298171	NM_000369.2	199	Ggg/Cgg	7/10	1	2	FACETS	0.145	0.12	0.173	0.145	0.12	0.173	SUBCLONAL	1	TRUE	1	0.852367331886808	2		383	647	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726544	41726544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs891614619	NA	P-0016554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	154	494	1	ENST00000301178.4:c.89C>T	p.Thr30Met	p.T30M	ENST00000301178	NM_021913.4	30	aCg/aTg	2/20	1	2	FACETS	0.95	0.868	1	0.95	0.868	1	CLONAL	1	TRUE	1	0.28	2		495	1158	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs587781702	NA	P-0016554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	136	529	1	ENST00000269305.4:c.920-1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.28	2		530	953	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41525969	41525970	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0016554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1195	76	635	0	ENST00000263253.7:c.1249dup	p.Leu417ProfsTer6	p.L417Pfs*6	ENST00000263253	NM_001429.3	415	ctc/ctCc	5/31	1	2	FACETS	0.427	0.373	0.486	0.427	0.373	0.486	SUBCLONAL	1	TRUE	1	0.28	2		635	1271	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349882	70349882	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0016554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	190	307	1	ENST00000374080.3:c.3868-3C>T		p.X1290_splice	ENST00000374080		1290			0.232336127350391	2	FACETS	0.991	0.919	1			1	CLONAL	2	TRUE	NA	0.28	2		308	685	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0016556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	40	552	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.682	0.564	0.814	0.682	0.564	0.814	SUBCLONAL	1	TRUE	1	0.11	2		552	1067	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947827	178947827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	23	256	0	ENST00000263967.3:c.2702G>T	p.Cys901Phe	p.C901F	ENST00000263967	NM_006218.2	901	tGt/tTt	19/21	1	2	FACETS	0.977	0.761	1	0.977	0.761	1	CLONAL	1	TRUE	1	0.11	2		256	428	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0016556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	39	341	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.825	0.681	0.986	0.825	0.681	0.986	CLONAL	1	TRUE	1	0.11	2		341	860	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443345	187443345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	24	304	0	ENST00000232014.4:c.1781G>A	p.Arg594Gln	p.R594Q	ENST00000232014	NM_001130845.1	594	cGa/cAa	8/10	1	2	FACETS	0.57	0.445	0.716	0.57	0.445	0.716	SUBCLONAL	1	TRUE	1	0.11	2		304	765	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672842	86672842	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	22	232	0	ENST00000274376.6:c.2329G>T	p.Glu777Ter	p.E777*	ENST00000274376	NM_002890.2	777	Gaa/Taa	17/25	1	2	FACETS	0.976	0.755	1	0.976	0.755	1	CLONAL	1	TRUE	1	0.11	2		232	410	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542357	187542357	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs769432838	NA	P-0016556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	31	243	0	ENST00000441802.2:c.5383C>T	p.Arg1795Ter	p.R1795*	ENST00000441802	NM_005245.3	1795	Cga/Tga	10/27	1	2	FACETS	1	0.827	1	1	0.827	1	CLONAL	1	TRUE	1	0.11	2		243	549	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14303198	14303198	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	76	487	1	ENST00000256196.4:c.477G>T	p.Lys159Asn	p.K159N	ENST00000256196		159	aaG/aaT	5/6	1	2	FACETS	0.824	0.722	0.935	1	0.978	1	CLONAL	2	TRUE	1	0.11	2		488	838	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398665	116398665	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1351264833	NA	P-0016556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	30	403	0	ENST00000397752.3:c.2255C>A	p.Ser752Tyr	p.S752Y	ENST00000397752	NM_000245.2	752	tCt/tAt	9/21	1	2	FACETS	0.986	0.793	1	0.986	0.793	1	CLONAL	1	TRUE	1	0.11	2		403	553	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41489061	41489062	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0016557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	41	400	0	ENST00000263253.7:c.54dup	p.Ser19LeufsTer20	p.S19Lfs*20	ENST00000263253	NM_001429.3	18	ctc/ctCc	1/31	0.123688823675331	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		400	677	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096183	71096183	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	260	275	0	ENST00000318789.4:c.574del	p.Gln192SerfsTer14	p.Q192Sfs*14	ENST00000318789	NM_032682.5	192	Cag/ag	10/21	0.551124617418617	2	FACETS	0.938	0.892	0.985	0.938	0.892	0.985	CLONAL	2	TRUE	0	0.584523016654006	2		275	474	SUCCESS
APC	324	MSKCC	GRCh37	5	112163676	112163677	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0016558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	311	408	0	ENST00000257430.4:c.1601_1602del	p.Lys534IlefsTer2	p.K534Ifs*2	ENST00000257430	NM_000038.5	533	ctAAaa/ctaa	13/16	0.551124617418617	2	FACETS	0.842	0.801	0.882	0.842	0.801	0.882	CLONAL	2	TRUE	0	0.584523016654006	2		408	632	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	208	486	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	0.373059561201441	2		486	1014	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0016560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	228	591	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.373059561201441	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.373059561201441	1		592	964	SUCCESS
APC	324	MSKCC	GRCh37	5	112173730	112173730	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	138	338	0	ENST00000257430.4:c.2442del	p.Phe814LeufsTer6	p.F814Lfs*6	ENST00000257430	NM_000038.5	813	aaT/aa	16/16	0.329033308879787	1	FACETS	0.805	0.733	0.88	0.805	0.733	0.88	CLONAL	1	TRUE	0	0.373059561201441	1		338	748	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435316	49435316	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	113	381	0	ENST00000301067.7:c.6237G>T	p.Gln2079His	p.Q2079H	ENST00000301067	NM_003482.3	2079	caG/caT	31/54	1	2	FACETS	0.644	0.579	0.714	0.644	0.579	0.714	SUBCLONAL	1	TRUE	1	0.373059561201441	2		381	940	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003805	45003805	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	140	261	0	ENST00000558401.1:c.61A>G	p.Ile21Val	p.I21V	ENST00000558401	NM_004048.2	21	Atc/Gtc	1/4	1	2	FACETS	0.811	0.738	0.887	0.811	0.738	0.887	CLONAL	1	TRUE	1	0.373059561201441	2		261	926	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0016562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	653	2255	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	0.865941353587242	2		2255	1443	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs104886003	NA	P-0016562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	474	503	0	ENST00000263967.3:c.1633G>C	p.Glu545Gln	p.E545Q	ENST00000263967	NM_006218.2	545	Gag/Cag	10/21	0.865941353587242	3	FACETS	1	0.958	1	0.502	0.479	0.525	CLONAL	1	TRUE	1	0.865941353587242	3		503	1564	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127164	22127164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057519911	NA	P-0016562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	311	378	0	ENST00000215832.6:c.964G>A	p.Glu322Lys	p.E322K	ENST00000215832	NM_002745.4	322	Gag/Aag	7/9	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.865941353587242	2		378	702	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294454	1294454	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	327	470	0	ENST00000310581.5:c.547C>G	p.Gln183Glu	p.Q183E	ENST00000310581	NM_198253.2	183	Cag/Gag	2/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.865941353587242	2		470	702	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745588	162745588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754868982	NA	P-0016562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	479	515	1	ENST00000367921.3:c.2003G>A	p.Arg668His	p.R668H	ENST00000367921	NM_006182.2	668	cGc/cAc	15/18	1	2	FACETS	0.983	0.942	1	0.983	0.942	1	CLONAL	1	TRUE	1	0.865941353587242	2		516	1126	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106549	27106549	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	568	777	0	ENST00000324856.7:c.6160G>T	p.Glu2054Ter	p.E2054*	ENST00000324856	NM_006015.4	2054	Gag/Tag	20/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.865941353587242	2		777	1253	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660675	190660675	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	275	266	0	ENST00000441310.2:c.313G>A	p.Glu105Lys	p.E105K	ENST00000441310	NM_000534.4	105	Gag/Aag	3/13	1	2	FACETS	0.945	0.893	0.998	0.945	0.893	0.998	CLONAL	1	TRUE	1	0.865941353587242	2		266	672	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274890	142274890	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1328	528	556	0	ENST00000350721.4:c.2170C>G	p.Leu724Val	p.L724V	ENST00000350721	NM_001184.3	724	Ctg/Gtg	10/47	0.865941353587242	3	FACETS	0.942	0.901	0.983	0.471	0.45	0.492	CLONAL	1	TRUE	1	0.865941353587242	3		556	1856	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26021044	26021045	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0016562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	173	299	0	ENST00000357647.3:c.327_328del	p.Leu110ValfsTer?	p.L110Vfs*?	ENST00000357647	NM_003529.2	109	aaCCtg/aatg	1/1	1	2	FACETS	0.81	0.752	0.87	0.81	0.752	0.87	CLONAL	1	TRUE	1	0.865941353587242	2		299	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578192	7578192	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	184	562	0	ENST00000269305.4:c.657del	p.Tyr220MetfsTer27	p.Y220Mfs*27	ENST00000269305	NM_001126112.2	219	ccC/cc	6/11	0.454523514108239	2	FACETS	0.892	0.833	0.951	0.892	0.833	0.951	CLONAL	2	TRUE	0	0.485630416044402	2		562	425	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602767	10602767	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	166	510	1	ENST00000171111.5:c.811G>T	p.Val271Leu	p.V271L	ENST00000171111	NM_203500.1	271	Gtg/Ttg	3/6	0.44093045834077	2	FACETS	0.944	0.881	1	0.944	0.881	1	CLONAL	2	TRUE	0	0.485630416044402	2		511	362	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462122	120462122	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	72	419	0	ENST00000256646.2:c.5594A>G	p.Gln1865Arg	p.Q1865R	ENST00000256646	NM_024408.3	1865	cAg/cGg	31/34	0.485630416044402	3	FACETS	0.853	0.748	0.965			1	CLONAL	1	TRUE	NA	0.485630416044402	3		419	432	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188115	108188115	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	58	315	0	ENST00000278616.4:c.6214G>C	p.Gly2072Arg	p.G2072R	ENST00000278616	NM_000051.3	2072	Gga/Cga	43/63	0.485630416044402	5	FACETS	0.871	0.75	1	0.29	0.25	0.335	CLONAL	1	TRUE	2	0.485630416044402	5		315	474	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022522	12022522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762232508	NA	P-0016563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	73	447	1	ENST00000396373.4:c.628C>T	p.Arg210Cys	p.R210C	ENST00000396373	NM_001987.4	210	Cgc/Tgc	5/8	1	2	FACETS	0.884	0.779	0.996	0.884	0.779	0.996	CLONAL	1	TRUE	1	0.485630416044402	2		448	340	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120791116	120791116	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	171	441	0	ENST00000257552.2:c.719C>A	p.Thr240Asn	p.T240N	ENST00000257552	NM_002442.3	240	aCc/aAc	10/15	0.485630416044402	3	FACETS	0.943	0.876	1	0.943	0.876	1	CLONAL	2	TRUE	1	0.485630416044402	3		441	464	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127409	17127409	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	148	456	0	ENST00000285071.4:c.445G>T	p.Gly149Cys	p.G149C	ENST00000285071	NM_144997.5	149	Ggc/Tgc	6/14	0.454523514108239	2	FACETS	0.926	0.86	0.994	0.926	0.86	0.994	CLONAL	2	TRUE	0	0.485630416044402	2		456	329	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131364	17131364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	139	401	0	ENST00000285071.4:c.88C>T	p.Pro30Ser	p.P30S	ENST00000285071	NM_144997.5	30	Cct/Tct	4/14	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.485630416044402	NA		401	344	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221457	36221457	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	198	503	0	ENST00000222270.7:c.5216C>G	p.Ser1739Cys	p.S1739C	ENST00000222270	NM_014727.1	1739	tCc/tGc	25/37	0.331185018371876	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.485630416044402	4		503	496	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1955149	1955149	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	63	545	0	ENST00000382891.5:c.2236A>C	p.Lys746Gln	p.K746Q	ENST00000382891	NM_133335.3	746	Aaa/Caa	12/22	0.204208857258141	1	FACETS	0.532	0.463	0.607	0.532	0.463	0.607	INDETERMINATE	1	TRUE	0	0.485630416044402	1		545	369	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1955215	1955215	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	55	397	0	ENST00000382891.5:c.2302C>T	p.His768Tyr	p.H768Y	ENST00000382891	NM_133335.3	768	Cat/Tat	12/22	0.204208857258141	1	FACETS	0.533	0.458	0.613	0.533	0.458	0.613	INDETERMINATE	1	TRUE	0	0.485630416044402	1		397	322	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294553	1294553	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	127	427	0	ENST00000310581.5:c.448G>T	p.Val150Phe	p.V150F	ENST00000310581	NM_198253.2	150	Gtt/Ttt	2/16	0.409296326819139	4	FACETS	1	0.916	1	1	0.916	1	CLONAL	2	TRUE	2	0.485630416044402	4		427	388	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940502	31940502	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	151	415	1	ENST00000375333.2:c.535G>T	p.Val179Leu	p.V179L	ENST00000375333	NM_032454.1	179	Gtg/Ttg	3/8	0.432898959462115	2	FACETS	0.937	0.87	1	0.937	0.87	1	CLONAL	2	TRUE	0	0.485630416044402	2		416	332	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92354974	92354974	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	111	219	0	ENST00000265734.4:c.503G>T	p.Arg168Leu	p.R168L	ENST00000265734	NM_001259.6	168	cGc/cTc	4/8	0.485630416044402	4	FACETS	0.935	0.849	1	0.935	0.849	1	CLONAL	2	TRUE	2	0.485630416044402	4		219	363	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0016565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	179	305	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.507627270364274	2		305	701	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0016565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	315	509	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.421012410742289	3	FACETS	0.914	0.866	0.963	0.914	0.866	0.963	CLONAL	2	TRUE	1	0.507627270364274	3		509	851	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412095	63412095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852217	NA	P-0016565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	317	332	0	ENST00000330258.3:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000330258	NM_152424.3	358	Cga/Tga	2/2	0.302186163138384	2	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.507627270364274	2		332	515	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052636	42052636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1054243525	NA	P-0016565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	211	411	0	ENST00000219905.7:c.7307G>A	p.Arg2436His	p.R2436H	ENST00000219905	NM_001164273.1	2436	cGt/cAt	20/24	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.507627270364274	2		411	742	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258311	16258311	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	199	476	0	ENST00000375759.3:c.5576G>T	p.Arg1859Leu	p.R1859L	ENST00000375759	NM_015001.2	1859	cGg/cTg	11/15	0.491906425359727	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.507627270364274	1		476	568	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041728	29041728	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	122	369	0	ENST00000282397.4:c.91G>C	p.Asp31His	p.D31H	ENST00000282397	NM_002019.4	31	Gat/Cat	2/30	0.507627270364274	3	FACETS	0.76	0.687	0.837	0.38	0.343	0.419	SUBCLONAL	1	TRUE	1	0.507627270364274	3		369	793	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30293216	30293216	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0016565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	111	353	0	ENST00000322652.5:c.505+1G>T		p.X169_splice	ENST00000322652	NM_015355.2	169			1	2	FACETS	0.703	0.633	0.777	0.703	0.633	0.777	SUBCLONAL	1	TRUE	1	0.507627270364274	2		353	622	SUCCESS
APC	324	MSKCC	GRCh37	5	112173260	112173261	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs863225322	NA	P-0016565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	98	238	0	ENST00000257430.4:c.1974_1975del	p.Asn659GlnfsTer14	p.N659Qfs*14	ENST00000257430	NM_000038.5	657	AGa/a	16/16	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.507627270364274	2		238	357	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	160	423	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.953	1			1	INDETERMINATE	1	TRUE	NA	0.604055971476564	2		423	508	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0016566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	1204	446	1	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.604055971476564	6	FACETS	0.976	0.953	0.999			1	CLONAL	4	TRUE	NA	0.604055971476564	6		447	2255	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0016566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	65	161	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.604055971476564	1	FACETS	0.546	0.478	0.618	0.546	0.478	0.618	SUBCLONAL	1	TRUE	0	0.604055971476564	1		161	275	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226561945	226561957	+	frameshift_variant	Frame_Shift_Del	DEL	TTTCTTCATACTT	TTTCTTCATACTT	-	novel	NA	P-0016566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	133	448	0	ENST00000366794.5:c.2040_2052del	p.Ser681ProfsTer17	p.S681Pfs*17	ENST00000366794	NM_001618.3	680	gaAAGTATGAAGAAA/ga	14/23	1	2	FACETS	0.608	0.553	0.666	0.608	0.553	0.666	SUBCLONAL	1	TRUE	1	0.604055971476564	2		448	724	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210026	55210026	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	1058	389	0	ENST00000275493.2:c.136G>T	p.Asp46Tyr	p.D46Y	ENST00000275493	NM_005228.3	46	Gat/Tat	2/28	0.604055971476564	6	FACETS	1	0.994	1			1	CLONAL	4	TRUE	NA	0.604055971476564	6		389	1834	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0016567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	809	1585	1	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.84586552758675	2	FACETS	0.995	0.978	1	0.995	0.978	1	CLONAL	2	TRUE	0	0.84586552758675	2		1586	961	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145436	58145436	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	289	314	0	ENST00000257904.6:c.65A>G	p.Lys22Arg	p.K22R	ENST00000257904	NM_000075.3	22	aAg/aGg	2/8	1	2	FACETS	0.958	0.907	1	0.958	0.907	1	CLONAL	1	TRUE	1	0.84586552758675	2		314	713	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69032453	69032453	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1210	446	524	0	ENST00000288368.4:c.3527T>A	p.Leu1176Gln	p.L1176Q	ENST00000288368	NM_024870.2	1176	cTa/cAa	29/40	0.825093264919531	3	FACETS	0.906	0.863	0.95	0.453	0.431	0.475	CLONAL	1	TRUE	1	0.84586552758675	3		524	1656	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0016568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	70	279	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.667	0.58	0.762	0.667	0.58	0.762	SUBCLONAL	1	TRUE	1	0.21	2		279	999	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918596	44918597	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0016568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	49	234	0	ENST00000377967.4:c.1083_1084del	p.Tyr362Ter	p.Y362*	ENST00000377967	NM_021140.2	360	aCT/a	12/29	1	1	FACETS	0.735	0.622	0.86	0.735	0.622	0.86	SUBCLONAL	1	TRUE	0	0.21	1		234	568	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190670480	190670480	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	72	329	0	ENST00000441310.2:c.418G>T	p.Gly140Cys	p.G140C	ENST00000441310	NM_000534.4	140	Ggt/Tgt	4/13	1	2	FACETS	0.77	0.671	0.877	0.77	0.671	0.877	SUBCLONAL	1	TRUE	1	0.21	2		329	891	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178152	56178152	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	234	392	0	ENST00000399503.3:c.3127del	p.Ser1043ProfsTer39	p.S1043Pfs*39	ENST00000399503	NM_005921.1	1042	cTt/ct	14/20	0.215845225895409	4	FACETS	0.836	0.78	0.894	0.836	0.78	0.894	CLONAL	3	TRUE	1	0.215845225895409	4		392	1051	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612866	228612866	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138699472	NA	P-0016570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	109	275	0	ENST00000366696.1:c.161G>A	p.Arg54His	p.R54H	ENST00000366696	NM_003493.2	54	cGc/cAc	1/1	0.374686008574652	3	FACETS	0.862	0.776	0.953	0.431	0.388	0.477	CLONAL	1	TRUE	1	0.527339877045727	3		275	606	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399783	139399783	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	150	388	0	ENST00000277541.6:c.4565A>C	p.Gln1522Pro	p.Q1522P	ENST00000277541	NM_017617.3	1522	cAg/cCg	25/34	0.527339877045727	3	FACETS	0.771	0.704	0.84	0.385	0.352	0.42	SUBCLONAL	1	TRUE	1	0.527339877045727	3		388	933	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0016571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	223	561	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.405723409576932	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.412699764508481	2		561	527	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106182989	106182989	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	240	365	0	ENST00000380013.4:c.4028A>G	p.Asp1343Gly	p.D1343G	ENST00000380013	NM_001127208.2	1343	gAt/gGt	8/11	0.405723409576932	2	FACETS	0.862	0.809	0.915	0.862	0.809	0.915	CLONAL	2	TRUE	0	0.412699764508481	2		365	675	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447803	49447804	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	AA	novel	NA	P-0016571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	118	406	1	ENST00000301067.7:c.630_631delinsTT	p.Gln211Ter	p.Q211*	ENST00000301067	NM_003482.3	210	ctGCag/ctTTag	5/54	0.412699764508481	3	FACETS	0.842	0.76	0.93	0.421	0.38	0.465	CLONAL	1	TRUE	1	0.412699764508481	3		407	819	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070564	67070564	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs771119364	NA	P-0016571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	258	258	0	ENST00000412916.2:c.188A>G	p.Asn63Ser	p.N63S	ENST00000412916		63	aAt/aGt	3/6	0.410885042353703	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.412699764508481	2		258	570	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36253009	36253013	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACCTA	ACCTA	-	novel	NA	P-0016571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	317	432	0	ENST00000300305.3:c.352-3_353del		p.X118_splice	ENST00000300305		118		4/8	0.280575309408506	2	FACETS	0.974	0.924	1	0.974	0.924	1	CLONAL	2	TRUE	0	0.412699764508481	2		432	789	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859638	151859638	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	131	247	0	ENST00000262189.6:c.11024del	p.Gln3675ArgfsTer6	p.Q3675Rfs*6	ENST00000262189	NM_170606.2	3675	cAg/cg	43/59	0.405298541099822	4	FACETS	1	0.986	1	0.734	0.668	0.803	CLONAL	1	TRUE	2	0.412699764508481	4		247	611	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877860	151877878	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGTTGGCACAGGTCCAG	GAAGTTGGCACAGGTCCAG	-	novel	NA	P-0016571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	197	255	0	ENST00000262189.6:c.7067_7085del	p.Pro2356GlnfsTer3	p.P2356Qfs*3	ENST00000262189	NM_170606.2	2356	cCTGGACCTGTGCCAACTTCa/ca	36/59	0.405298541099822	4	FACETS	0.891	0.827	0.957	0.891	0.827	0.957	CLONAL	2	TRUE	2	0.412699764508481	4		255	757	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	111	423	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.912	1			1	INDETERMINATE	1	TRUE	NA	0.660589817109514	2		423	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0016572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	467	476	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	NA	2	FACETS	0.997	0.965	1			1	INDETERMINATE	2	TRUE	NA	0.660589817109514	2		476	709	SUCCESS
AR	367	MSKCC	GRCh37	X	66937337	66937337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137852571	NA	P-0016572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	47	320	0	ENST00000374690.3:c.2191G>A	p.Val731Met	p.V731M	ENST00000374690	NM_000044.3	731	Gtg/Atg	5/8	0.455330391528102	3	FACETS	0.238	0.199	0.28			1	SUBCLONAL	1	TRUE	NA	0.660589817109514	3		320	797	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685315	89685315	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0016572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	230	355	0	ENST00000371953.3:c.209+1G>C		p.X70_splice	ENST00000371953	NM_000314.4	70			0.660589817109514	1	FACETS	0.935	0.881	0.988	0.935	0.881	0.988	CLONAL	1	TRUE	0	0.660589817109514	1		355	499	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192671	94192671	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1805367	NA	P-0016572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	286	419	0	ENST00000323929.3:c.1403A>G	p.Asp468Gly	p.D468G	ENST00000323929	NM_005591.3	468	gAt/gGt	13/20	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.660589817109514	2		419	856	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259574	89259574	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	150	251	0	ENST00000336596.2:c.718C>T	p.Pro240Ser	p.P240S	ENST00000336596	NM_005233.5	240	Cca/Tca	3/17	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.660589817109514	2		251	446	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981893	70981893	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1440556377	NA	P-0016572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	182	424	2	ENST00000276594.2:c.203C>A	p.Pro68His	p.P68H	ENST00000276594	NM_024504.3	68	cCc/cAc	2/8	1	2	FACETS	0.822	0.762	0.885	0.822	0.762	0.885	CLONAL	1	TRUE	1	0.660589817109514	2		426	670	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	480	641	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.327010411558273	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.327010411558273	3		641	1053	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	215	384	0	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.327010411558273	2		384	985	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163500	108163500	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	224	249	0	ENST00000278616.4:c.4591C>T	p.Gln1531Ter	p.Q1531*	ENST00000278616	NM_000051.3	1531	Cag/Tag	30/63	0.216037849275701	2	FACETS	0.938	0.877	1	0.938	0.877	1	CLONAL	2	TRUE	0	0.327010411558273	2		249	730	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16021243	16021243	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	100	167	0	ENST00000268712.3:c.2014C>T	p.Arg672Ter	p.R672*	ENST00000268712	NM_006311.3	672	Cga/Tga	18/46	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.327010411558273	2		167	607	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120124	70120124	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	75	72	0	ENST00000245479.2:c.1126C>T	p.Gln376Ter	p.Q376*	ENST00000245479	NM_000346.3	376	Cag/Tag	3/3	1	2	FACETS	0.796	0.705	0.892	1	0.979	1	SUBCLONAL	2	TRUE	1	0.327010411558273	2		72	288	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253844	153253844	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	158	230	0	ENST00000281708.4:c.889G>T	p.Glu297Ter	p.E297*	ENST00000281708	NM_033632.3	297	Gaa/Taa	6/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.327010411558273	2		230	783	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485285	8485285	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	95	383	0	ENST00000356435.5:c.3095C>T	p.Thr1032Ile	p.T1032I	ENST00000356435		1032	aCt/aTt	18/35	1	2	FACETS	0.531	0.471	0.595	0.531	0.471	0.595	SUBCLONAL	1	TRUE	1	0.327010411558273	2		383	1094	SUCCESS
APC	324	MSKCC	GRCh37	5	112175556	112175575	+	frameshift_variant	Frame_Shift_Del	DEL	ATCTTCCAGATAGCCCTGGA	ATCTTCCAGATAGCCCTGGA	G	novel	NA	P-0016573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	78	229	0	ENST00000257430.4:c.4265_4284delinsG	p.Asp1422GlyfsTer45	p.D1422Gfs*45	ENST00000257430	NM_000038.5	1422	gATCTTCCAGATAGCCCTGGA/gG	16/16	0.215946487767255	1	FACETS	0.59	0.518	0.668	0.59	0.518	0.668	SUBCLONAL	1	TRUE	0	0.327010411558273	1		229	676	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0016574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	135	683	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.41981740964582	2		683	605	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690819	89690820	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0016574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	114	420	0	ENST00000371953.3:c.227_228del	p.Tyr76Ter	p.Y76*	ENST00000371953	NM_000314.4	76	TAt/t	4/9	0.41981740964582	1	FACETS	0.911	0.825	1	0.911	0.825	1	CLONAL	1	TRUE	0	0.41981740964582	1		420	471	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911782	32911782	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	229	587	0	ENST00000380152.3:c.3290T>G	p.Phe1097Cys	p.F1097C	ENST00000380152		1097	tTt/tGt	11/27	1	2	FACETS	0.994	0.925	1	0.994	0.925	1	CLONAL	1	TRUE	1	0.41981740964582	2		587	1098	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128033	30128036	+	frameshift_variant	Frame_Shift_Del	DEL	GGAA	GGAA	-	novel	NA	P-0016574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	174	469	0	ENST00000263025.4:c.1093_1096del	p.Phe365ArgfsTer138	p.F365Rfs*138	ENST00000263025	NM_002746.2	365	TTCCag/ag	8/9	1	2	FACETS	0.912	0.84	0.987	0.912	0.84	0.987	CLONAL	1	TRUE	1	0.41981740964582	2		469	909	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0016575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	158	2255	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.829	0.758	0.903	0.829	0.758	0.903	CLONAL	1	TRUE	1	0.348107734032725	2		2255	1095	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604787	48604787	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	149	313	0	ENST00000342988.3:c.1609G>C	p.Asp537His	p.D537H	ENST00000342988	NM_005359.5	537	Gac/Cac	12/12	0.348107734032725	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.348107734032725	1		313	683	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246498718	246498718	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	152	343	0	ENST00000388985.4:c.287G>T	p.Arg96Ile	p.R96I	ENST00000388985		96	aGa/aTa	3/12	0.348107734032725	3	FACETS	0.918	0.838	1	0.459	0.419	0.501	CLONAL	1	TRUE	1	0.348107734032725	3		343	1117	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670685	67670685	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	138	430	0	ENST00000264010.4:c.1930del	p.Ala644ProfsTer42	p.A644Pfs*42	ENST00000264010	NM_006565.3	644	Gcc/cc	11/12	1	2	FACETS	0.846	0.769	0.927	0.846	0.769	0.927	CLONAL	1	TRUE	1	0.348107734032725	2		430	937	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218419	1218439	+	inframe_deletion	In_Frame_Del	DEL	AATTCAACTACTGAGGAGGTT	AATTCAACTACTGAGGAGGTT	-	novel	NA	P-0016575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	216	406	0	ENST00000326873.7:c.295_315del	p.Ile99_Leu105del	p.I99_L105del	ENST00000326873	NM_000455.4	98	gaAATTCAACTACTGAGGAGGTTa/gaa	2/10	0.348107734032725	2	FACETS	1	0.988	1	0.64	0.595	0.687	CLONAL	1	TRUE	0	0.348107734032725	2		406	969	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210770	36210770	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	161	465	0	ENST00000222270.7:c.521C>G	p.Pro174Arg	p.P174R	ENST00000222270	NM_014727.1	174	cCa/cGa	3/37	1	2	FACETS	0.734	0.671	0.799	0.734	0.671	0.799	SUBCLONAL	1	TRUE	1	0.348107734032725	2		465	1261	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247453	71247453	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	133	308	0	ENST00000318789.4:c.80T>A	p.Leu27Gln	p.L27Q	ENST00000318789	NM_032682.5	27	cTa/cAa	6/21	1	2	FACETS	0.983	0.894	1	0.983	0.894	1	CLONAL	1	TRUE	1	0.348107734032725	2		308	777	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162189	38162191	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0016575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	153	392	0	ENST00000317025.8:c.2525_2527del	p.Ser842del	p.S842del	ENST00000317025	NM_023034.1	842	tCCTac/tac	14/24	1	2	FACETS	0.878	0.803	0.957	0.878	0.803	0.957	CLONAL	1	TRUE	1	0.348107734032725	2		392	1001	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370926	55370926	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	165	358	0	ENST00000297316.4:c.228G>C	p.Met76Ile	p.M76I	ENST00000297316	NM_022454.3	76	atG/atC	1/2	1	2	FACETS	0.934	0.857	1	0.934	0.857	1	CLONAL	1	TRUE	1	0.348107734032725	2		358	1015	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141426	11141426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	62	430	0	ENST00000358026.2:c.3403C>T	p.Arg1135Trp	p.R1135W	ENST00000358026	NM_001128849.1	1135	Cgg/Tgg	25/36	1	2	FACETS	0.209	0.18	0.241	0.209	0.18	0.241	SUBCLONAL	1	TRUE	1	0.59	2		430	1005	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0016576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	215	318	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.59	2		318	558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0016576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	890	449	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.81388359308587	2	FACETS	0.936	0.92	0.952	1	0.998	1	CLONAL	3	TRUE	0	0.59	2		449	1074	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332751	65332751	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375997338	NA	P-0016576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	61	291	0	ENST00000342505.4:c.788C>T	p.Thr263Met	p.T263M	ENST00000342505	NM_002227.2	263	aCg/aTg	7/25	1	2	FACETS	0.243	0.209	0.281	0.243	0.209	0.281	SUBCLONAL	1	TRUE	1	0.59	2		291	850	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159088	143159088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	143	370	0	ENST00000262992.4:c.765G>A	p.Met255Ile	p.M255I	ENST00000262992	NM_001101669.1	255	atG/atA	10/24	1	2	FACETS	0.566	0.516	0.618	0.566	0.516	0.618	SUBCLONAL	1	TRUE	1	0.59	2		370	857	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141565	11141565	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	52	340	0	ENST00000358026.2:c.3542A>C	p.His1181Pro	p.H1181P	ENST00000358026	NM_001128849.1	1181	cAc/cCc	25/36	1	2	FACETS	0.205	0.174	0.24	0.205	0.174	0.24	SUBCLONAL	1	TRUE	1	0.59	2		340	860	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61712928	61712928	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	131	301	0	ENST00000401558.2:c.2483A>C	p.Glu828Ala	p.E828A	ENST00000401558	NM_003400.3	828	gAa/gCa	20/25	1	2	FACETS	0.492	0.446	0.541	0.492	0.446	0.541	SUBCLONAL	1	TRUE	1	0.59	2		301	902	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459498	50459498	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777862077	NA	P-0016576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	171	257	2	ENST00000331340.3:c.787G>A	p.Val263Met	p.V263M	ENST00000331340	NM_006060.4	263	Gtg/Atg	7/8	1	2	FACETS	0.706	0.65	0.764	0.706	0.65	0.764	SUBCLONAL	1	TRUE	1	0.59	2		259	821	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937600	76937603	+	frameshift_variant	Frame_Shift_Del	DEL	TTAT	TTAT	-	novel	NA	P-0016576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	340	126	0	ENST00000373344.5:c.3145_3148del	p.Ile1049GlufsTer68	p.I1049Efs*68	ENST00000373344	NM_000489.3	1049	ATAAga/ga	9/35	1	1	FACETS	0.889	0.859	0.918	1	0.997	1	CLONAL	2	TRUE	0	0.59	1		126	457	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61712945	61712948	+	missense_variant	Missense_Mutation	ONP	TATT	TATT	CATG	novel	NA	P-0016576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	143	338	0	ENST00000401558.2:c.2463_2466delinsCATG	p.Gln821_Ile822delinsHisMet	p.Q821_I822delinsHM	ENST00000401558	NM_003400.3	821	caAATA/caCATG	20/25	1	2	FACETS	0.471	0.428	0.515	0.471	0.428	0.515	SUBCLONAL	1	TRUE	1	0.59	2		338	1030	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	366	726	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.215644698940325	3	FACETS	0.821	0.778	0.865	0.821	0.778	0.865	INDETERMINATE	2	TRUE	1	0.39149896660656	3		726	1362	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0016577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	352	405	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.39149896660656	2	FACETS	0.945	0.898	0.993	0.945	0.898	0.993	CLONAL	2	TRUE	0	0.39149896660656	2		405	951	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723453	52723453	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	52	336	0	ENST00000322088.6:c.1314C>A	p.Phe438Leu	p.F438L	ENST00000322088	NM_014225.5	438	ttC/ttA	11/15	0.215644698940325	3	FACETS	0.325	0.275	0.379	0.162	0.137	0.19	INDETERMINATE	1	TRUE	1	0.39149896660656	3		336	978	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717777	89717777	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0016578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	331	319	0	ENST00000371953.3:c.801+1G>T		p.X267_splice	ENST00000371953	NM_000314.4	267			0.36857181712001	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	0	0.373345021860611	3		319	681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0016578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	38	386	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	1	2	FACETS	0.269	0.221	0.322	0.269	0.221	0.322	SUBCLONAL	1	TRUE	1	0.373345021860611	2		386	758	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106497	27106498	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0016578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	132	591	0	ENST00000324856.7:c.6109dup	p.Gln2037ProfsTer62	p.Q2037Pfs*62	ENST00000324856	NM_006015.4	2036	-/C	20/20	1	2	FACETS	0.544	0.492	0.599	0.544	0.492	0.599	SUBCLONAL	1	TRUE	1	0.373345021860611	2		591	1300	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058081	27058082	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0016578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	109	353	0	ENST00000324856.7:c.1789_1790del	p.Phe597ProfsTer25	p.F597Pfs*25	ENST00000324856	NM_006015.4	597	TTc/c	3/20	1	2	FACETS	0.891	0.802	0.986	0.891	0.802	0.986	CLONAL	1	TRUE	1	0.373345021860611	2		353	655	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466022	69466022	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	80	514	0	ENST00000227507.2:c.860C>G	p.Pro287Arg	p.P287R	ENST00000227507	NM_053056.2	287	cCc/cGc	5/5	1	2	FACETS	0.5	0.439	0.566	0.5	0.439	0.566	SUBCLONAL	1	TRUE	1	0.373345021860611	2		514	857	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591107	67591108	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACC	novel	NA	P-0016578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	127	339	0	ENST00000274335.5:c.1702_1704dup	p.Pro568dup	p.P568dup	ENST00000274335		568	aaa/aaACCa	12/15	1	2	FACETS	0.908	0.824	0.997	0.908	0.824	0.997	CLONAL	1	TRUE	1	0.373345021860611	2		339	749	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964467	70964467	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	120	399	0	ENST00000276594.2:c.1561T>C	p.Tyr521His	p.Y521H	ENST00000276594	NM_024504.3	521	Tac/Cac	8/8	0.309479533374294	3	FACETS	0.816	0.737	0.899	0.408	0.368	0.45	CLONAL	1	TRUE	1	0.484877517598928	3		399	754	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685307	89685307	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123317	NA	P-0016581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	162	396	0	ENST00000371953.3:c.202T>C	p.Tyr68His	p.Y68H	ENST00000371953	NM_000314.4	68	Tac/Cac	3/9	0.477359272595445	1	FACETS	0.982	0.907	1	0.982	0.907	1	CLONAL	1	TRUE	0	0.477359272595445	1		396	526	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0016581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	261	500	1	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	0.477359272595445	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.477359272595445	1		501	825	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820744	3820744	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	310	516	0	ENST00000262367.5:c.2707C>T	p.Pro903Ser	p.P903S	ENST00000262367	NM_004380.2	903	Cct/Tct	14/31	0.477359272595445	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.477359272595445	1		516	931	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576851	7576851	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0016581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	397	384	0	ENST00000269305.4:c.993+2T>G		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.466731940241809	2	FACETS	0.95	0.909	0.993	0.95	0.909	0.993	CLONAL	2	TRUE	0	0.477359272595445	2		384	875	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588972	67588985	+	frameshift_variant	Frame_Shift_Del	DEL	TTTTTGGTACGAGA	TTTTTGGTACGAGA	AAAAAGC	novel	NA	P-0016581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	79	233	1	ENST00000274335.5:c.1063_1076delinsAAAAAGC	p.Phe355LysfsTer16	p.F355Kfs*16	ENST00000274335		355	TTTTTGGTACGAGAt/AAAAAGCt	8/15	0.477359272595445	1	FACETS	0.759	0.673	0.85	0.759	0.673	0.85	SUBCLONAL	1	TRUE	0	0.477359272595445	1		234	332	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415703	152415703	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	176	316	0	ENST00000206249.3:c.1553G>C	p.Ser518Thr	p.S518T	ENST00000206249	NM_000125.3	518	aGt/aCt	7/8	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.477359272595445	2		316	737	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0016582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	482	1492	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.427110194136406	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.469763085543253	3		1492	1147	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793663	NA	P-0016582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	493	541	2	ENST00000263967.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000263967	NM_006218.2	93	cGg/cAg	2/21	0.439906808596912	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.469763085543253	4		543	1509	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046290	128046290	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs368191279	NA	P-0016582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	307	442	1	ENST00000285398.2:c.973C>T	p.Arg325Ter	p.R325*	ENST00000285398	NM_000122.1	325	Cga/Tga	7/15	0.439906808596912	4	FACETS	0.902	0.851	0.954	0.902	0.851	0.954	CLONAL	2	TRUE	2	0.469763085543253	4		443	1065	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245241	46245241	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	34	302	0	ENST00000334344.6:c.3335A>G	p.Gln1112Arg	p.Q1112R	ENST00000334344	NM_152641.2	1112	cAg/cGg	15/21	0.469763085543253	3	FACETS	0.281	0.228	0.34	0.14	0.114	0.17	SUBCLONAL	1	TRUE	1	0.469763085543253	3		302	637	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577567	7577568	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs1555525539	NA	P-0016582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	154	365	0	ENST00000269305.4:c.713_714del	p.Cys238Ter	p.C238*	ENST00000269305	NM_001126112.2	238	tGT/t	7/11	0.427110194136406	3	FACETS	0.986	0.903	1	0.493	0.451	0.537	CLONAL	1	TRUE	1	0.469763085543253	3		365	821	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37882072	37882072	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1259746959	NA	P-0016582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	212	353	0	ENST00000269571.5:c.2838C>G	p.Ile946Met	p.I946M	ENST00000269571		946	atC/atG	23/27	0.469763085543253	4	FACETS	0.776	0.722	0.832			1	SUBCLONAL	2	TRUE	NA	0.469763085543253	4		353	855	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0016583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	183	546	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.223018089332884	2		546	1156	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	194	726	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.203323106432106	4	FACETS	0.783	0.722	0.846	0.783	0.722	0.846	SUBCLONAL	2	TRUE	2	0.223018089332884	4		726	1359	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405948	49405948	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	217	681	0	ENST00000418115.1:c.190G>A	p.Glu64Lys	p.E64K	ENST00000418115	NM_001664.2	64	Gaa/Aaa	3/5	0.223018089332884	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.223018089332884	1		681	1246	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105646	27105647	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTC	novel	NA	P-0016583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	93	327	0	ENST00000324856.7:c.5259_5262dup	p.Ser1755ValfsTer2	p.S1755Vfs*2	ENST00000324856	NM_006015.4	1753	gtg/gTGTCtg	20/20	0.223018089332884	1	FACETS	0.967	0.86	1	0.967	0.86	1	CLONAL	1	TRUE	0	0.223018089332884	1		327	766	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999574	100999574	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1192	213	667	1	ENST00000325455.5:c.228C>A	p.Asp76Glu	p.D76E	ENST00000325455	NM_001202474.3	76	gaC/gaA	1/8	0.155540123662659	3	FACETS	0.756	0.7	0.813	0.756	0.7	0.813	SUBCLONAL	2	TRUE	1	0.223018089332884	3		668	1405	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131343	17131343	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1179	193	525	0	ENST00000285071.4:c.109G>A	p.Asp37Asn	p.D37N	ENST00000285071	NM_144997.5	37	Gac/Aac	4/14	0.223018089332884	4	FACETS	0.771	0.712	0.834			1	SUBCLONAL	2	TRUE	NA	0.223018089332884	4		525	1372	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469546	25469546	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	91	582	1	ENST00000264709.3:c.1222G>T	p.Glu408Ter	p.E408*	ENST00000264709	NM_175629.2	408	Gaa/Taa	10/23	1	2	FACETS	0.699	0.619	0.786	0.699	0.619	0.786	SUBCLONAL	1	TRUE	1	0.223018089332884	2		583	1167	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131350	17131358	+	missense_variant	Missense_Mutation	ONP	CCCATCCCC	CCCATCCCC	TCCATTCCT	novel	NA	P-0016583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	154	496	0	ENST00000285071.4:c.94_102delinsAGGAATGGA	p.Gly32_Asp33delinsArgAsn	p.G32_D33delinsRN	ENST00000285071	NM_144997.5	32	GGGGATGGG/AGGAATGGA	4/14	0.223018089332884	4	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.223018089332884	4		496	1245	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0016584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	63	730	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.233719397518657	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.233719397518657	1		730	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0016584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	215	429	1	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.203187456901344	2	FACETS	0.849	0.793	0.908	1	0.988	1	CLONAL	3	TRUE	0	0.233719397518657	2		430	722	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0016584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	539	455	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	0.233719397518657	5	FACETS	1	0.989	1	1	0.989	1	CLONAL	4	TRUE	1	0.233719397518657	5		455	1445	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577492	64577493	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0016585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	353	473	0	ENST00000312049.6:c.89_90insC	p.Glu30AspfsTer87	p.E30Dfs*87	ENST00000312049	NM_130799.2	30	gag/gaCg	2/10	0.945143058292875	1	FACETS	0.959	0.935	0.981	0.959	0.935	0.981	CLONAL	1	TRUE	0	0.945143058292875	1		473	411	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218351	133218351	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1402161985	NA	P-0016585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	463	513	0	ENST00000320574.5:c.5260A>G	p.Met1754Val	p.M1754V	ENST00000320574	NM_006231.2	1754	Atg/Gtg	39/49	1	2	FACETS	0.971	0.932	1	0.971	0.932	1	CLONAL	1	TRUE	1	0.945143058292875	2		513	1009	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104350	2104350	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	562	634	0	ENST00000219476.3:c.390C>A	p.Tyr130Ter	p.Y130*	ENST00000219476	NM_000548.3	130	taC/taA	5/42	0.945143058292875	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.945143058292875	1		634	612	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287946	33287949	+	frameshift_variant	Frame_Shift_Del	DEL	TCTG	TCTG	-	novel	NA	P-0016585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	409	397	0	ENST00000374542.5:c.1304_1307del	p.Thr435MetfsTer92	p.T435Mfs*92	ENST00000374542	NM_001141970.1	435	aCAGAt/at	5/8	0.945143058292875	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.945143058292875	1		397	445	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015038	27015038	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016589-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	224	340	0	ENST00000335756.4:c.140G>A	p.Trp47Ter	p.W47*	ENST00000335756	NM_001809.3	47	tGg/tAg	2/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		340	637	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911588	39911588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372913827	NA	P-0016589-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	295	455	1	ENST00000378444.4:c.5042G>A	p.Arg1681His	p.R1681H	ENST00000378444	NM_001123385.1	1681	cGc/cAc	15/15	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		456	873	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0016593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	210	730	1	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.269130077893764	1	FACETS	0.974	0.903	1	0.974	0.903	1	CLONAL	1	TRUE	0	0.269130077893764	1		731	1386	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922292	178922293	+	inframe_insertion,splice_region_variant	In_Frame_Ins	INS	-	-	CTATGTTCGAACAGGTATCTACCATGG	novel	NA	P-0016593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	70	366	0	ENST00000263967.3:c.1062_1088dup	p.Tyr355_Gly363dup	p.Y355_G363dup	ENST00000263967	NM_006218.2	355	atc/atCTATGTTCGAACAGGTATCTACCATGGc	6/21	0.156884363854994	3	FACETS	0.565	0.491	0.646	0.283	0.245	0.323	INDETERMINATE	1	TRUE	1	0.269130077893764	3		366	1044	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196544	106196544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1322028048	NA	P-0016593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	83	310	0	ENST00000380013.4:c.4877C>T	p.Thr1626Ile	p.T1626I	ENST00000380013	NM_001127208.2	1626	aCc/aTc	11/11	1	2	FACETS	0.765	0.674	0.863	0.765	0.674	0.863	SUBCLONAL	1	TRUE	1	0.269130077893764	2		310	806	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267369	198267369	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239341681	NA	P-0016594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	43	476	1	ENST00000335508.6:c.1988C>T	p.Thr663Ile	p.T663I	ENST00000335508	NM_012433.2	663	aCt/aTt	14/25	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.203420626390607	2		477	318	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120672	115120672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	84	678	1	ENST00000257566.3:c.334C>T	p.Leu112Phe	p.L112F	ENST00000257566	NM_016569.3	112	Ctt/Ttt	1/8	0.203420626390607	19	FACETS	0.908	0.801	1			1	CLONAL	3	TRUE	NA	0.203420626390607	19		679	827	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851591	134851591	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748976557	NA	P-0016594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	38	422	0	ENST00000398015.3:c.997G>A	p.Val333Ile	p.V333I	ENST00000398015	NM_004441.4	333	Gtc/Atc	5/16	1	2	FACETS	1	0.869	1	1	0.969	1	CLONAL	2	TRUE	1	0.203420626390607	2		422	179	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254165	133254165	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	11	350	0	ENST00000320574.5:c.719T>G	p.Val240Gly	p.V240G	ENST00000320574	NM_006231.2	240	gTg/gGg	7/49	0.192132037720266	3	FACETS	0.319	0.22	0.442	0.16	0.11	0.221	INDETERMINATE	1	TRUE	1	0.421143284422875	3		350	198	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0016596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	175	683	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.982	0.909	1	0.982	0.909	1	CLONAL	1	TRUE	1	0.607460696513746	2		683	587	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0016596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	295	1585	1	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.977	0.921	1	0.977	0.921	1	CLONAL	1	TRUE	1	0.607460696513746	2		1586	994	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673806	37673806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201661022	NA	P-0016596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	309	416	0	ENST00000447079.4:c.2960C>T	p.Ser987Phe	p.S987F	ENST00000447079	NM_015083.1	987	tCt/tTt	10/14	1	2	FACETS	0.974	0.92	1	0.974	0.92	1	CLONAL	1	TRUE	1	0.607460696513746	2		416	1044	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230691	46230691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424958105	NA	P-0016596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	157	369	0	ENST00000334344.6:c.940C>T	p.Arg314Cys	p.R314C	ENST00000334344	NM_152641.2	314	Cgt/Tgt	8/21	1	2	FACETS	0.804	0.739	0.871	0.804	0.739	0.871	CLONAL	1	TRUE	1	0.607460696513746	2		369	643	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435061	18435061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267603400	NA	P-0016596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	245	464	0	ENST00000266497.5:c.46G>A	p.Glu16Lys	p.E16K	ENST00000266497		16	Gaa/Aaa	1/31	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.607460696513746	2		464	776	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449788	8449788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1267613597	NA	P-0016596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	233	456	0	ENST00000356435.5:c.3925G>A	p.Glu1309Lys	p.E1309K	ENST00000356435		1309	Gag/Aag	23/35	0.607460696513746	1	FACETS	0.86	0.808	0.913	0.86	0.808	0.913	CLONAL	1	TRUE	0	0.607460696513746	1		456	621	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18762514	18762514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	188	423	0	ENST00000266497.5:c.4010C>T	p.Ser1337Phe	p.S1337F	ENST00000266497		1337	tCc/tTc	29/31	1	2	FACETS	0.821	0.76	0.883	0.821	0.76	0.883	CLONAL	1	TRUE	1	0.607460696513746	2		423	754	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261697	16261697	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	301	458	0	ENST00000375759.3:c.8962C>A	p.Pro2988Thr	p.P2988T	ENST00000375759	NM_015001.2	2988	Cct/Act	11/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.607460696513746	2		458	927	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724702	112724702	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1367984118	NA	P-0016596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	270	532	0	ENST00000369452.4:c.586A>G	p.Thr196Ala	p.T196A	ENST00000369452	NM_007373.3	196	Act/Gct	2/9	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.607460696513746	2		532	851	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573794	64573794	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1114167469	NA	P-0016596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	250	342	0	ENST00000312049.6:c.959C>T	p.Pro320Leu	p.P320L	ENST00000312049	NM_130799.2	320	cCc/cTc	7/10	0.607460696513746	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.607460696513746	1		342	515	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231108	46231108	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0016596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	174	360	0	ENST00000334344.6:c.1028T>G	p.Leu343Ter	p.L343*	ENST00000334344	NM_152641.2	343	tTa/tGa	9/21	1	2	FACETS	0.839	0.775	0.905	0.839	0.775	0.905	CLONAL	1	TRUE	1	0.607460696513746	2		360	683	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245366	46245366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746181283	NA	P-0016596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	241	411	2	ENST00000334344.6:c.3460C>T	p.Pro1154Ser	p.P1154S	ENST00000334344	NM_152641.2	1154	Cca/Tca	15/21	1	2	FACETS	0.949	0.889	1	0.949	0.889	1	CLONAL	1	TRUE	1	0.607460696513746	2		413	836	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281939	49281940	+	missense_variant	Missense_Mutation	DNP	AG	AG	CA	novel	NA	P-0016596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	302	537	1	ENST00000282018.3:c.986_987delinsCA	p.Lys329Thr	p.K329T	ENST00000282018	NM_020377.2	329	aAG/aCA	1/1	1	2	FACETS	0.944	0.89	0.999	0.944	0.89	0.999	CLONAL	1	TRUE	1	0.607460696513746	2		538	1053	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81528494	81528494	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	183	404	0	ENST00000298171.2:c.173A>C	p.Lys58Thr	p.K58T	ENST00000298171	NM_000369.2	58	aAg/aCg	2/10	1	2	FACETS	0.872	0.807	0.939	0.872	0.807	0.939	CLONAL	1	TRUE	1	0.607460696513746	2		404	691	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098633	2098633	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758239066	NA	P-0016596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	256	378	0	ENST00000219476.3:c.17G>A	p.Ser6Asn	p.S6N	ENST00000219476	NM_000548.3	6	aGc/aAc	2/42	1	2	FACETS	0.978	0.918	1	0.978	0.918	1	CLONAL	1	TRUE	1	0.607460696513746	2		378	862	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640980	3640980	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	417	661	0	ENST00000294008.3:c.2659T>C	p.Ser887Pro	p.S887P	ENST00000294008	NM_032444.2	887	Tct/Cct	12/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.607460696513746	2		661	1255	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953189	81953189	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	139	273	0	ENST00000359376.3:c.2155T>G	p.Tyr719Asp	p.Y719D	ENST00000359376	NM_002661.3	719	Tac/Gac	20/33	0.358279356878226	1	FACETS	0.669	0.614	0.727	0.669	0.614	0.727	INDETERMINATE	1	TRUE	0	0.607460696513746	1		273	476	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357484	89357484	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	198	497	0	ENST00000301030.4:c.334T>G	p.Ser112Ala	p.S112A	ENST00000301030	NM_001256183.1	112	Tcc/Gcc	5/13	0.358279356878226	1	FACETS	0.636	0.591	0.682	0.636	0.591	0.682	INDETERMINATE	1	TRUE	0	0.607460696513746	1		497	714	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40500436	40500436	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	216	377	0	ENST00000264657.5:c.99T>A	p.Phe33Leu	p.F33L	ENST00000264657	NM_139276.2	33	ttT/ttA	2/24	1	2	FACETS	0.854	0.795	0.914	0.854	0.795	0.914	CLONAL	1	TRUE	1	0.607460696513746	2		377	833	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198262742	198262742	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	221	398	0	ENST00000335508.6:c.3233T>C	p.Val1078Ala	p.V1078A	ENST00000335508	NM_012433.2	1078	gTc/gCc	22/25	1	2	FACETS	0.898	0.838	0.96	0.898	0.838	0.96	CLONAL	1	TRUE	1	0.607460696513746	2		398	810	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101029	41101029	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	176	337	0	ENST00000373198.4:c.1327A>G	p.Thr443Ala	p.T443A	ENST00000373198	NM_133170.3	443	Acc/Gcc	8/32	1	2	FACETS	0.932	0.862	1	0.932	0.862	1	CLONAL	1	TRUE	1	0.607460696513746	2		337	622	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47205375	47205375	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	271	417	0	ENST00000409792.3:c.40G>A	p.Asp14Asn	p.D14N	ENST00000409792	NM_014159.6	14	Gat/Aat	1/21	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.607460696513746	2		417	807	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976826	55976826	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	267	438	0	ENST00000263923.4:c.1086A>G	p.Ile362Met	p.I362M	ENST00000263923	NM_002253.2	362	atA/atG	8/30	1	2	FACETS	0.961	0.903	1	0.961	0.903	1	CLONAL	1	TRUE	1	0.607460696513746	2		438	915	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106162526	106162526	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	226	335	0	ENST00000380013.4:c.3440T>A	p.Phe1147Tyr	p.F1147Y	ENST00000380013	NM_001127208.2	1147	tTt/tAt	4/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.607460696513746	2		335	679	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540919	187540919	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	151	261	0	ENST00000441802.2:c.6821A>G	p.Asp2274Gly	p.D2274G	ENST00000441802	NM_005245.3	2274	gAc/gGc	10/27	1	2	FACETS	0.928	0.853	1	0.928	0.853	1	CLONAL	1	TRUE	1	0.607460696513746	2		261	536	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541237	187541237	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	196	303	0	ENST00000441802.2:c.6503T>C	p.Val2168Ala	p.V2168A	ENST00000441802	NM_005245.3	2168	gTt/gCt	10/27	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.607460696513746	2		303	628	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294202	1294202	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	189	684	0	ENST00000310581.5:c.799G>C	p.Asp267His	p.D267H	ENST00000310581	NM_198253.2	267	Gac/Cac	2/16	1	2	FACETS	0.5	0.461	0.541	0.5	0.461	0.541	SUBCLONAL	1	TRUE	1	0.607460696513746	2		684	1245	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80074585	80074585	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	259	492	0	ENST00000265081.6:c.2365T>G	p.Tyr789Asp	p.Y789D	ENST00000265081	NM_002439.4	789	Tac/Gac	17/24	1	2	FACETS	0.917	0.86	0.975	0.917	0.86	0.975	CLONAL	1	TRUE	1	0.607460696513746	2		492	930	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157454245	157454245	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	265	400	0	ENST00000346085.5:c.2455T>G	p.Ser819Ala	p.S819A	ENST00000346085	NM_020732.3	819	Tct/Gct	8/20	1	2	FACETS	0.983	0.923	1	0.983	0.923	1	CLONAL	1	TRUE	1	0.607460696513746	2		400	888	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846133	151846134	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0016596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	150	318	1	ENST00000262189.6:c.12878_12879delinsTT	p.Pro4293Leu	p.P4293L	ENST00000262189	NM_170606.2	4293	cCC/cTT	52/59	1	2	FACETS	0.901	0.828	0.977	0.901	0.828	0.977	CLONAL	1	TRUE	1	0.607460696513746	2		319	548	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965427	68965427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	290	667	1	ENST00000288368.4:c.1039G>A	p.Glu347Lys	p.E347K	ENST00000288368	NM_024870.2	347	Gaa/Aaa	9/40	1	2	FACETS	0.915	0.861	0.969	0.915	0.861	0.969	CLONAL	1	TRUE	1	0.607460696513746	2		668	1044	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518360	8518360	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	108	179	0	ENST00000356435.5:c.1031A>T	p.Asp344Val	p.D344V	ENST00000356435		344	gAc/gTc	10/35	0.607460696513746	1	FACETS	0.952	0.87	1	0.952	0.87	1	CLONAL	1	TRUE	0	0.607460696513746	1		179	260	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157973	27157973	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs770461384	NA	P-0016596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	302	489	0	ENST00000380036.4:c.197A>G	p.Asn66Ser	p.N66S	ENST00000380036	NM_000459.3	66	aAc/aGc	2/23	0.607460696513746	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.607460696513746	1		489	682	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	595	726	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.354905344399502	4	FACETS	1	0.973	1			1	CLONAL	3	TRUE	NA	0.354905344399502	4		726	1494	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0016597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	139	486	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.354905344399502	2		486	722	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437594	56437595	+	missense_variant	Missense_Mutation	DNP	AG	AG	TA	novel	NA	P-0016597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	269	404	2	ENST00000407977.2:c.867_868delinsTA	p.Cys290Ser	p.C290S	ENST00000407977		289	tcCTgc/tcTAgc	8/10	0.354905344399502	2	FACETS	0.989	0.932	1	0.989	0.932	1	CLONAL	2	TRUE	0	0.354905344399502	2		406	766	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591926	48591926	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0016597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	121	290	1	ENST00000342988.3:c.1089T>A	p.Cys363Ter	p.C363*	ENST00000342988	NM_005359.5	363	tgT/tgA	9/12	0.297596919782516	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.354905344399502	1		291	523	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971154	21971155	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0016597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	196	393	0	ENST00000304494.5:c.203_204del	p.Ala68GlyfsTer51	p.A68Gfs*51	ENST00000304494	NM_000077.4	68	gCG/g	2/3	0.354905344399502	2	FACETS	0.908	0.846	0.972	0.908	0.846	0.972	CLONAL	2	TRUE	0	0.354905344399502	2		393	608	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034426	47034427	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0016597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	155	256	0	ENST00000377604.3:c.514_515dup	p.Phe173AlafsTer94	p.F173Afs*94	ENST00000377604	NM_001204468.1	171	cgg/cGGgg	6/24	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.354905344399502	1		256	483	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0016598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	176	269	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.89392096579565	1	FACETS	0.767	0.724	0.809	0.767	0.724	0.809	SUBCLONAL	1	TRUE	0	0.89392096579565	1		269	284	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577115	7577115	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519983	NA	P-0016599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	87	518	0	ENST00000269305.4:c.823T>C	p.Cys275Arg	p.C275R	ENST00000269305	NM_001126112.2	275	Tgt/Cgt	8/11	1	2	FACETS	0.846	0.747	0.953	0.846	0.747	0.953	CLONAL	1	TRUE	1	0.203587923105263	2		518	1010	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	174	423	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.697702556659542	2		423	498	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588943	67588943	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	182	205	0	ENST00000274335.5:c.1034A>G	p.Glu345Gly	p.E345G	ENST00000274335		345	gAa/gGa	8/15	1	2	FACETS	0.954	0.886	1	0.954	0.886	1	CLONAL	1	TRUE	1	0.697702556659542	2		205	547	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0016603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	106	547	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.814	0.729	0.905	0.814	0.729	0.905	CLONAL	1	TRUE	1	0.294197135311636	2		547	885	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0016603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	74	373	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.687	0.601	0.78	0.687	0.601	0.78	SUBCLONAL	1	TRUE	1	0.294197135311636	2		373	732	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0016603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	33	352	1	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	1	2	FACETS	0.348	0.282	0.422	0.348	0.282	0.422	SUBCLONAL	1	TRUE	1	0.294197135311636	2		353	645	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0016603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	209	514	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.192367649090033	3	FACETS	1	0.99	1	0.706	0.655	0.76	CLONAL	1	TRUE	1	0.294197135311636	3		514	1154	SUCCESS
APC	324	MSKCC	GRCh37	5	112175651	112175651	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	71	418	0	ENST00000257430.4:c.4364del	p.Asn1455IlefsTer18	p.N1455Ifs*18	ENST00000257430	NM_000038.5	1454	Aaa/aa	16/16	1	2	FACETS	0.66	0.576	0.752	0.66	0.576	0.752	SUBCLONAL	1	TRUE	1	0.294197135311636	2		418	731	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781321	3781321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200112956	NA	P-0016603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	166	684	1	ENST00000262367.5:c.5044C>T	p.Arg1682Cys	p.R1682C	ENST00000262367	NM_004380.2	1682	Cgc/Tgc	30/31	0.192367649090033	3	FACETS	1	0.959	1	0.538	0.493	0.585	CLONAL	1	TRUE	1	0.294197135311636	3		685	1204	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871800	12871800	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	43	346	1	ENST00000228872.4:c.517A>G	p.Asn173Asp	p.N173D	ENST00000228872	NM_004064.3	173	Aat/Gat	2/3	0.192367649090033	3	FACETS	0.392	0.326	0.465	0.196	0.163	0.233	SUBCLONAL	1	TRUE	1	0.294197135311636	3		347	856	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713750	30713750	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	36	388	0	ENST00000295754.5:c.1075G>C	p.Ala359Pro	p.A359P	ENST00000295754	NM_003242.5	359	Gct/Cct	4/7	1	2	FACETS	0.417	0.342	0.501	0.417	0.342	0.501	SUBCLONAL	1	TRUE	1	0.294197135311636	2		388	587	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836855	151836855	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	117	568	1	ENST00000262189.6:c.14365C>T	p.Arg4789Ter	p.R4789*	ENST00000262189	NM_170606.2	4789	Cga/Tga	56/59	NA	2	FACETS	0.753	0.678	0.833			1	INDETERMINATE	1	TRUE	NA	0.294197135311636	2		569	1056	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061240	38061240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	65	498	0	ENST00000250448.2:c.749C>T	p.Ser250Phe	p.S250F	ENST00000250448	NM_004496.3	250	tCc/tTc	2/2	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.12	2		498	957	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913273	NA	P-0016604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	16	469	0	ENST00000263967.3:c.1624G>C	p.Glu542Gln	p.E542Q	ENST00000263967	NM_006218.2	542	Gaa/Caa	10/21	1	2	FACETS	0.444	0.326	0.585	0.444	0.326	0.585	SUBCLONAL	1	TRUE	1	0.12	2		469	601	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563266	21563266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1320375890	NA	P-0016604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	86	629	2	ENST00000382592.4:c.653G>A	p.Gly218Glu	p.G218E	ENST00000382592	NM_014572.2	218	gGa/gAa	4/8	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.12	2		631	1198	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31939941	31939941	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	86	408	1	ENST00000375333.2:c.168G>T	p.Trp56Cys	p.W56C	ENST00000375333	NM_032454.1	56	tgG/tgT	1/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.12	2		409	999	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563501	87563501	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	58	460	0	ENST00000277120.3:c.1889T>C	p.Ile630Thr	p.I630T	ENST00000277120		630	aTc/aCc	16/19	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.12	2		460	947	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555526097	NA	P-0016605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	236	446	0	ENST00000269305.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000269305	NM_001126112.2	167	Cag/Tag	5/11	0.425381330664974	1	FACETS	0.962	0.899	1	0.962	0.899	1	CLONAL	1	TRUE	0	0.430410355423103	1		446	895	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0016605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	398	670	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.151476570679703	4	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.430410355423103	4		670	1195	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603007	48603008	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	GTCTT	novel	NA	P-0016605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	90	196	0	ENST00000342988.3:c.1309_1313dup	p.Phe438LeufsTer40	p.F438Lfs*40	ENST00000342988	NM_005359.5	436	-/GTCTT		0.430410355423103	1	FACETS	0.878	0.785	0.975	0.878	0.785	0.975	CLONAL	1	TRUE	0	0.430410355423103	1		196	374	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759968	133759968	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs575721187	NA	P-0016605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	287	599	0	ENST00000318560.5:c.2291G>A	p.Arg764Gln	p.R764Q	ENST00000318560	NM_005157.4	764	cGg/cAg	11/11	1	2	FACETS	0.955	0.896	1	0.955	0.896	1	CLONAL	1	TRUE	1	0.430410355423103	2		599	1397	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0016606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	387	505	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.590471775928556	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.590471775928556	1		505	778	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730916	40730916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765075213	NA	P-0016606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1300	254	336	0	ENST00000373198.4:c.3619C>T	p.Arg1207Cys	p.R1207C	ENST00000373198	NM_133170.3	1207	Cgt/Tgt	27/32	0.393049852693107	6	FACETS	1	0.986	1	0.302	0.281	0.323	CLONAL	1	TRUE	2	0.590471775928556	6		336	1554	SUCCESS
APC	324	MSKCC	GRCh37	5	112174096	112174096	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs137854575	NA	P-0016606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	58	294	0	ENST00000257430.4:c.2805C>G	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	taC/taG	16/16	0.353571897505392	1	FACETS	0.337	0.29	0.388	0.337	0.29	0.388	INDETERMINATE	1	TRUE	0	0.590471775928556	1		294	411	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778896	9778896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1454291091	NA	P-0016606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	207	376	1	ENST00000377346.4:c.1165C>T	p.Arg389Cys	p.R389C	ENST00000377346	NM_005026.3	389	Cgt/Tgt	9/24	0.327136099511239	1	FACETS	0.441	0.408	0.474	0.441	0.408	0.474	INDETERMINATE	1	TRUE	0	0.590471775928556	1		377	1121	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431915	49431915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	208	556	0	ENST00000301067.7:c.9224C>T	p.Ser3075Leu	p.S3075L	ENST00000301067	NM_003482.3	3075	tCg/tTg	34/54	0.353571897505392	1	FACETS	0.414	0.383	0.446	0.414	0.383	0.446	INDETERMINATE	1	TRUE	0	0.590471775928556	1		556	1199	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058858	42058858	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1012955328	NA	P-0016606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	83	233	0	ENST00000219905.7:c.8578C>T	p.Arg2860Trp	p.R2860W	ENST00000219905	NM_001164273.1	2860	Cgg/Tgg	24/24	0.590471775928556	1	FACETS	0.368	0.325	0.413	0.368	0.325	0.413	SUBCLONAL	1	TRUE	0	0.590471775928556	1		233	539	SUCCESS
APC	324	MSKCC	GRCh37	5	112103015	112103015	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1064793535	NA	P-0016606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	156	340	0	ENST00000257430.4:c.350C>A	p.Ser117Ter	p.S117*	ENST00000257430	NM_000038.5	117	tCa/tAa	4/16	0.353571897505392	1	FACETS	0.675	0.621	0.73	0.675	0.621	0.73	INDETERMINATE	1	TRUE	0	0.590471775928556	1		340	552	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	37	641	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.45	0.369	0.541	0.45	0.369	0.541	SUBCLONAL	1	TRUE	1	0.15	2		641	1097	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0016607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1260	72	622	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			1	2	FACETS	0.721	0.627	0.823	0.721	0.627	0.823	SUBCLONAL	1	TRUE	1	0.15	2		622	1332	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713694	30713695	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0016607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	42	276	0	ENST00000295754.5:c.1019_1020del	p.His340ArgfsTer24	p.H340Rfs*24	ENST00000295754	NM_003242.5	340	cAT/c	4/7	1	2	FACETS	0.77	0.641	0.914	0.77	0.641	0.914	CLONAL	1	TRUE	1	0.15	2		276	727	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0016608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	252	616	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.297333554646251	3	FACETS	0.868	0.811	0.926			1	CLONAL	2	TRUE	NA	0.297333554646251	3		616	1122	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624264	89624267	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	novel	NA	P-0016608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	192	277	0	ENST00000371953.3:c.38_41del	p.Lys13ArgfsTer10	p.K13Rfs*10	ENST00000371953	NM_000314.4	13	aAAAGg/ag	1/9	0.297333554646251	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.297333554646251	2		277	536	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412046	116412046	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	T	novel	NA	P-0016611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	316	603	0	ENST00000397752.3:c.3028+3A>T		p.X1010_splice	ENST00000397752	NM_000245.2	1010			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		603	1406	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0016612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	679	754	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.436751024347016	2	FACETS	0.89	0.859	0.921	0.89	0.859	0.921	CLONAL	2	TRUE	0	0.468838988299588	2		754	1627	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434074	49434074	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	203	446	1	ENST00000301067.7:c.7479del	p.Phe2494SerfsTer49	p.F2494Sfs*49	ENST00000301067	NM_003482.3	2493	ggG/gg	31/54	0.43709808555446	3	FACETS	0.92	0.852	0.991	0.46	0.426	0.496	CLONAL	1	TRUE	1	0.468838988299588	3		447	1162	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610144	10610144	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	572	550	0	ENST00000171111.5:c.566A>T	p.Asn189Ile	p.N189I	ENST00000171111	NM_203500.1	189	aAc/aTc	2/6	0.461057408437586	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.468838988299588	2		550	1212	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141453	11141453	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	560	575	0	ENST00000358026.2:c.3430G>T	p.Glu1144Ter	p.E1144*	ENST00000358026	NM_001128849.1	1144	Gag/Tag	25/36	0.461057408437586	2	FACETS	0.947	0.912	0.983	0.947	0.912	0.983	CLONAL	2	TRUE	0	0.468838988299588	2		575	1261	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299859	15299859	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	584	638	0	ENST00000263388.2:c.1319G>T	p.Cys440Phe	p.C440F	ENST00000263388	NM_000435.2	440	tGc/tTc	8/33	0.461057408437586	2	FACETS	0.939	0.905	0.974	0.939	0.905	0.974	CLONAL	2	TRUE	0	0.468838988299588	2		638	1326	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463172	25463172	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	352	485	0	ENST00000264709.3:c.2321A>T	p.Glu774Val	p.E774V	ENST00000264709	NM_175629.2	774	gAg/gTg	19/23	0.267882264461242	3	FACETS	0.793	0.751	0.835	0.793	0.751	0.835	INDETERMINATE	2	TRUE	1	0.468838988299588	3		485	1169	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225449673	225449682	+	frameshift_variant	Frame_Shift_Del	DEL	GATCCGCATC	GATCCGCATC	-	novel	NA	P-0016612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	221	353	0	ENST00000264414.4:c.45_54del	p.Lys15AsnfsTer6	p.K15Nfs*6	ENST00000264414	NM_003590.4	15	aaGATGCGGATC/aa	1/16	0.469073327785998	3	FACETS	1	0.992	1	0.734	0.685	0.784	CLONAL	1	TRUE	1	0.468838988299588	3		353	793	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249463	153249463	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	533	545	0	ENST00000281708.4:c.1315A>G	p.Thr439Ala	p.T439A	ENST00000281708	NM_033632.3	439	Aca/Gca	9/12	0.436751024347016	2	FACETS	0.971	0.934	1	0.971	0.934	1	CLONAL	2	TRUE	0	0.468838988299588	2		545	1171	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340250	116340250	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	199	371	0	ENST00000397752.3:c.1112A>C	p.Asn371Thr	p.N371T	ENST00000397752	NM_000245.2	371	aAc/aCc	2/21	0.43709808555446	3	FACETS	0.995	0.921	1	0.498	0.46	0.536	CLONAL	1	TRUE	1	0.468838988299588	3		371	1053	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340288	116340288	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0016612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	375	365	0	ENST00000397752.3:c.1150A>T	p.Arg384Ter	p.R384*	ENST00000397752	NM_000245.2	384	Aga/Tga	2/21	0.43709808555446	3	FACETS	0.942	0.896	0.989	0.942	0.896	0.989	CLONAL	2	TRUE	1	0.468838988299588	3		365	1048	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412655	139412655	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	227	583	0	ENST00000277541.6:c.1189A>G	p.Ile397Val	p.I397V	ENST00000277541	NM_017617.3	397	Atc/Gtc	7/34	1	2	FACETS	0.914	0.851	0.978	0.914	0.851	0.978	CLONAL	1	TRUE	1	0.468838988299588	2		583	1060	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853332	151853332	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	GCA	novel	NA	P-0016612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	367	428	0	ENST00000262189.6:c.11770delinsTGC	p.Glu3924CysfsTer11	p.E3924Cfs*11	ENST00000262189	NM_170606.2	3924	Gaa/TGCaa	45/59	0.43709808555446	3	FACETS	0.912	0.866	0.958	0.912	0.866	0.958	CLONAL	2	TRUE	1	0.468838988299588	3		428	1060	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0016613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	739	731	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.292818302196614	7	FACETS	1	0.986	1			1	CLONAL	6	TRUE	NA	0.292818302196614	7		731	1418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0016613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	168	610	2	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.292818302196614	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.292818302196614	1		612	906	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030325	180030325	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115824945	NA	P-0016613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	140	522	0	ENST00000261937.6:c.3959G>A	p.Arg1320Gln	p.R1320Q	ENST00000261937	NM_182925.4	1320	cGg/cAg	30/30	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.292818302196614	2		522	807	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838410	156838410	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	105	482	0	ENST00000524377.1:c.688A>T	p.Thr230Ser	p.T230S	ENST00000524377	NM_002529.3	230	Aca/Tca	6/17	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.292818302196614	2		482	684	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741541	17741541	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs773231763	NA	P-0016613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	134	391	0	ENST00000250003.3:c.212C>A	p.Pro71Gln	p.P71Q	ENST00000250003	NM_002478.4	71	cCg/cAg	1/3	0.217301677672746	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.292818302196614	1		391	559	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222294	39222294	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	121	452	0	ENST00000402219.2:c.3316G>C	p.Asp1106His	p.D1106H	ENST00000402219	NM_005633.3	1106	Gat/Cat	20/23	1	2	FACETS	0.904	0.816	0.997	0.904	0.816	0.997	CLONAL	1	TRUE	1	0.292818302196614	2		452	914	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710652	40710652	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	98	418	0	ENST00000373198.4:c.4199G>T	p.Gly1400Val	p.G1400V	ENST00000373198	NM_133170.3	1400	gGg/gTg	31/32	1	2	FACETS	0.94	0.839	1	0.94	0.839	1	CLONAL	1	TRUE	1	0.292818302196614	2		418	712	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932677	49932677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754028685	NA	P-0016613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	98	621	0	ENST00000296474.3:c.3194C>T	p.Ala1065Val	p.A1065V	ENST00000296474	NM_002447.2	1065	gCg/gTg	14/20	1	2	FACETS	0.749	0.667	0.836	0.749	0.667	0.836	SUBCLONAL	1	TRUE	1	0.292818302196614	2		621	894	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873119	134873119	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0016613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	48	427	0	ENST00000398015.3:c.1422+1G>T		p.X474_splice	ENST00000398015	NM_004441.4	474			1	2	FACETS	0.529	0.446	0.62	0.529	0.446	0.62	SUBCLONAL	1	TRUE	1	0.292818302196614	2		427	620	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449459	149449459	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	75	357	0	ENST00000286301.3:c.1487G>T	p.Trp496Leu	p.W496L	ENST00000286301	NM_005211.3	496	tGg/tTg	10/22	0.217301677672746	1	FACETS	0.799	0.702	0.904	0.799	0.702	0.904	CLONAL	1	TRUE	0	0.292818302196614	1		357	547	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55260504	55260504	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	849	454	0	ENST00000275493.2:c.2671T>G	p.Tyr891Asp	p.Y891D	ENST00000275493	NM_005228.3	891	Tat/Gat	22/28	0.292818302196614	7	FACETS	1	0.982	1			1	CLONAL	6	TRUE	NA	0.292818302196614	7		454	1651	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92355007	92355007	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	74	230	0	ENST00000265734.4:c.470G>T	p.Gly157Val	p.G157V	ENST00000265734	NM_001259.6	157	gGa/gTa	4/8	1	2	FACETS	0.948	0.832	1	0.948	0.832	1	CLONAL	1	TRUE	1	0.292818302196614	2		230	533	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933860	39933860	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	32	470	0	ENST00000378444.4:c.739del	p.Leu247CysfsTer19	p.L247Cfs*19	ENST00000378444	NM_001123385.1	247	Ctg/tg	4/15	0.217301677672746	1	FACETS	0.292	0.236	0.356	0.292	0.236	0.356	SUBCLONAL	1	TRUE	0	0.292818302196614	1		470	638	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044472	47044472	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	145	643	1	ENST00000377604.3:c.1969C>A	p.Arg657Ser	p.R657S	ENST00000377604	NM_001204468.1	657	Cgc/Agc	18/24	0.217301677672746	1	FACETS	0.838	0.763	0.916	0.838	0.763	0.916	CLONAL	1	TRUE	0	0.292818302196614	1		644	1009	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76764003	76764003	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	111	546	2	ENST00000373344.5:c.7305C>A	p.His2435Gln	p.H2435Q	ENST00000373344	NM_000489.3	2435	caC/caA	35/35	1	2	FACETS	0.887	0.797	0.982	0.887	0.797	0.982	CLONAL	1	TRUE	1	0.292818302196614	2		548	855	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	150	2255	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.287820694879808	1	FACETS	0.946	0.864	1	0.946	0.864	1	CLONAL	1	TRUE	0	0.287820694879808	1		2255	943	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912660	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	149	621	0	ENST00000269305.4:c.839G>T	p.Arg280Ile	p.R280I	ENST00000269305	NM_001126112.2	280	aGa/aTa	8/11	0.287820694879808	1	FACETS	0.951	0.868	1	0.951	0.868	1	CLONAL	1	TRUE	0	0.287820694879808	1		621	932	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040650	47040650	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	96	536	2	ENST00000377604.3:c.1285G>T	p.Glu429Ter	p.E429*	ENST00000377604	NM_001204468.1	429	Gag/Tag	13/24	1	2	FACETS	0.871	0.776	0.972	0.871	0.776	0.972	CLONAL	1	TRUE	1	0.287820694879808	2		538	766	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076719	72076719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	103	505	0	ENST00000357731.5:c.778G>A	p.Gly260Arg	p.G260R	ENST00000357731	NM_173808.2	260	Gga/Aga	5/7	1	2	FACETS	0.784	0.7	0.873	0.784	0.7	0.873	SUBCLONAL	1	TRUE	1	0.287820694879808	2		505	913	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101278	27101278	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	92	458	0	ENST00000324856.7:c.4563del	p.Ala1522ProfsTer5	p.A1522Pfs*5	ENST00000324856	NM_006015.4	1520	ggC/gg	18/20	1	2	FACETS	0.881	0.782	0.985	0.881	0.782	0.985	CLONAL	1	TRUE	1	0.287820694879808	2		458	726	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80160631	80160631	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	110	538	1	ENST00000265081.6:c.3001-1G>T		p.X1001_splice	ENST00000265081	NM_002439.4	1001			1	2	FACETS	0.698	0.626	0.775	0.698	0.626	0.775	SUBCLONAL	1	TRUE	1	0.287820694879808	2		539	1095	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405025	70405025	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	153	605	3	ENST00000373644.4:c.2539G>T	p.Ala847Ser	p.A847S	ENST00000373644	NM_030625.2	847	Gct/Tct	4/12	1	2	FACETS	0.983	0.898	1	0.983	0.898	1	CLONAL	1	TRUE	1	0.287820694879808	2		608	1082	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450972	70450972	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	94	453	0	ENST00000373644.4:c.5812C>T	p.Gln1938Ter	p.Q1938*	ENST00000373644	NM_030625.2	1938	Cag/Tag	12/12	1	2	FACETS	0.812	0.722	0.909	0.812	0.722	0.909	CLONAL	1	TRUE	1	0.287820694879808	2		453	804	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692877	89692877	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	68	237	0	ENST00000371953.3:c.361G>T	p.Ala121Ser	p.A121S	ENST00000371953	NM_000314.4	121	Gca/Tca	5/9	1	2	FACETS	0.955	0.832	1	0.955	0.832	1	CLONAL	1	TRUE	1	0.287820694879808	2		237	495	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742871	17742871	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	109	540	1	ENST00000250003.3:c.779C>A	p.Ser260Tyr	p.S260Y	ENST00000250003	NM_002478.4	260	tCc/tAc	3/3	0.287820694879808	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.287820694879808	1		541	606	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625219	69625219	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	115	524	0	ENST00000334134.2:c.574del	p.Arg192GlyfsTer?	p.R192Gfs*?	ENST00000334134	NM_005247.2	192	Cgg/gg	3/3	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.287820694879808	2		524	703	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233753	133233753	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	115	316	0	ENST00000320574.5:c.3551G>T	p.Ser1184Ile	p.S1184I	ENST00000320574	NM_006231.2	1184	aGt/aTt	29/49	0.287820694879808	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.287820694879808	1		316	587	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054513	42054513	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	72	513	1	ENST00000219905.7:c.7697G>T	p.Arg2566Met	p.R2566M	ENST00000219905	NM_001164273.1	2566	aGg/aTg	22/24	1	2	FACETS	0.584	0.509	0.666	0.584	0.509	0.666	SUBCLONAL	1	TRUE	1	0.287820694879808	2		514	856	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29701161	29701161	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	95	260	0	ENST00000356175.3:c.8445G>T	p.Lys2815Asn	p.K2815N	ENST00000356175	NM_000267.3	2815	aaG/aaT	57/57	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.287820694879808	2		260	582	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354386	40354386	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	150	819	0	ENST00000293328.3:c.2209C>T	p.Gln737Ter	p.Q737*	ENST00000293328	NM_012448.3	737	Cag/Tag	18/19	1	2	FACETS	0.828	0.755	0.905	0.828	0.755	0.905	CLONAL	1	TRUE	1	0.287820694879808	2		819	1259	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58701104	58701104	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	78	424	1	ENST00000305921.3:c.695G>T	p.Gly232Val	p.G232V	ENST00000305921	NM_003620.3	232	gGt/gTt	2/6	1	2	FACETS	0.683	0.599	0.773	0.683	0.599	0.773	SUBCLONAL	1	TRUE	1	0.287820694879808	2		425	794	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732966	74732966	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	59	223	0	ENST00000359995.5:c.277G>T	p.Gly93Cys	p.G93C	ENST00000359995	NM_001195427.1	93	Ggc/Tgc	1/3	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.287820694879808	2		223	368	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210450	2210450	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	107	545	0	ENST00000398665.3:c.1057G>C	p.Ala353Pro	p.A353P	ENST00000398665	NM_032482.2	353	Gcg/Ccg	13/28	0.287820694879808	1	FACETS	0.999	0.898	1	0.999	0.898	1	CLONAL	1	TRUE	0	0.287820694879808	1		545	637	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7163179	7163180	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	118	500	0	ENST00000302850.5:c.1892dup	p.Ser632ValfsTer2	p.S632Vfs*2	ENST00000302850	NM_000208.2	631	gtg/gtTg	9/22	0.287820694879808	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.287820694879808	1		500	694	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602398	10602398	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	155	652	0	ENST00000171111.5:c.1180G>T	p.Asp394Tyr	p.D394Y	ENST00000171111	NM_203500.1	394	Gac/Tac	3/6	0.287820694879808	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.287820694879808	1		652	786	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637233	47637234	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GC	GC	AT	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	84	283	0	ENST00000233146.2:c.367_368delinsAT	p.Ala123Ile	p.A123I	ENST00000233146	NM_000251.2	123	GCt/ATt	3/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.287820694879808	2		283	517	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024759	31024759	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	171	446	0	ENST00000375687.4:c.4244G>T	p.Arg1415Leu	p.R1415L	ENST00000375687	NM_015338.5	1415	cGa/cTa	13/13	0.22090526683762	3	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	1	0.287820694879808	3		446	670	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655244	45655244	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	64	484	0	ENST00000407780.3:c.608T>A	p.Leu203Gln	p.L203Q	ENST00000407780	NM_001283052.1	203	cTg/cAg	4/7	1	2	FACETS	0.598	0.517	0.686	0.598	0.517	0.686	SUBCLONAL	1	TRUE	1	0.287820694879808	2		484	744	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475436	12475436	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	141	555	1	ENST00000287820.6:c.1310T>A	p.Ile437Asn	p.I437N	ENST00000287820	NM_015869.4	437	aTt/aAt	7/7	0.238490883083732	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.287820694879808	1		556	808	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259244	89259244	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	71	282	0	ENST00000336596.2:c.388G>T	p.Asp130Tyr	p.D130Y	ENST00000336596	NM_005233.5	130	Gat/Tat	3/17	0.238490883083732	1	FACETS	0.902	0.79	1	0.902	0.79	1	CLONAL	1	TRUE	0	0.287820694879808	1		282	468	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259670	89259670	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs374955351	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	37	128	0	ENST00000336596.2:c.814G>T	p.Ala272Ser	p.A272S	ENST00000336596	NM_005233.5	272	Gct/Tct	3/17	0.238490883083732	1	FACETS	0.957	0.795	1	0.957	0.795	1	CLONAL	1	TRUE	0	0.287820694879808	1		128	230	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971034	55971034	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	123	430	0	ENST00000263923.4:c.1763C>A	p.Pro588Gln	p.P588Q	ENST00000263923	NM_002253.2	588	cCa/cAa	13/30	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.287820694879808	2		430	679	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467520	66467520	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	65	285	1	ENST00000273854.3:c.749C>A	p.Ala250Asp	p.A250D	ENST00000273854	NM_004439.5	250	gCt/gAt	3/18	1	2	FACETS	0.914	0.794	1	0.914	0.794	1	CLONAL	1	TRUE	1	0.287820694879808	2		286	494	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247157	153247157	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	61	224	0	ENST00000281708.4:c.1644+1G>T		p.X548_splice	ENST00000281708	NM_033632.3	548			1	2	FACETS	0.997	0.863	1	0.997	0.863	1	CLONAL	1	TRUE	1	0.287820694879808	2		224	425	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268177	153268177	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	85	223	0	ENST00000281708.4:c.631G>T	p.Asp211Tyr	p.D211Y	ENST00000281708	NM_033632.3	211	Gac/Tac	4/12	1	2	FACETS	0.991	0.877	1	0.991	0.877	1	CLONAL	1	TRUE	1	0.287820694879808	2		223	596	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518278	187518278	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	38	184	1	ENST00000441802.2:c.12416G>T	p.Gly4139Val	p.G4139V	ENST00000441802	NM_005245.3	4139	gGg/gTg	25/27	1	2	FACETS	0.877	0.728	1	0.877	0.728	1	CLONAL	1	TRUE	1	0.287820694879808	2		185	301	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876319	35876319	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	83	348	0	ENST00000303115.3:c.1111G>C	p.Ala371Pro	p.A371P	ENST00000303115	NM_002185.3	371	Gct/Cct	8/8	1	2	FACETS	0.901	0.796	1	0.901	0.796	1	CLONAL	1	TRUE	1	0.287820694879808	2		348	640	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524568	176524568	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	87	776	1	ENST00000292408.4:c.2300C>A	p.Ser767Tyr	p.S767Y	ENST00000292408	NM_213647.1	767	tCt/tAt	18/18	1	2	FACETS	0.611	0.539	0.687	0.611	0.539	0.687	SUBCLONAL	1	TRUE	1	0.287820694879808	2		777	990	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137528153	137528153	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	41	349	0	ENST00000367739.4:c.147G>T	p.Glu49Asp	p.E49D	ENST00000367739	NM_000416.2	49	gaG/gaT	2/7	0.120445156203179	0	FACETS	0.301	0.25	0.359			1	INDETERMINATE	1	TRUE	0	0.287820694879808	0		349	673	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969931	161969931	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	41	426	0	ENST00000366898.1:c.1038C>A	p.Asp346Glu	p.D346E	ENST00000366898	NM_004562.2	346	gaC/gaA	9/12	0.120445156203179	0	FACETS	0.351	0.292	0.417			1	INDETERMINATE	1	TRUE	0	0.287820694879808	0		426	578	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50358697	50358697	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	53	234	0	ENST00000331340.3:c.40G>C	p.Gly14Arg	p.G14R	ENST00000331340	NM_006060.4	14	Ggg/Cgg	2/8	1	2	FACETS	0.89	0.761	1	0.89	0.761	1	CLONAL	1	TRUE	1	0.287820694879808	2		234	414	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526582	106526582	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	98	341	0	ENST00000359195.3:c.2875A>C	p.Asn959His	p.N959H	ENST00000359195	NM_002649.2	959	Aac/Cac	10/11	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.287820694879808	2		341	631	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398635	116398635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	108	489	2	ENST00000397752.3:c.2225C>T	p.Pro742Leu	p.P742L	ENST00000397752	NM_000245.2	742	cCc/cTc	9/21	1	2	FACETS	0.864	0.774	0.958	0.864	0.774	0.958	CLONAL	1	TRUE	1	0.287820694879808	2		491	869	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956772	68956772	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	81	494	0	ENST00000288368.4:c.890G>C	p.Arg297Pro	p.R297P	ENST00000288368	NM_024870.2	297	cGt/cCt	8/40	1	2	FACETS	0.574	0.504	0.649	0.574	0.504	0.649	SUBCLONAL	1	TRUE	1	0.287820694879808	2		494	981	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894966	101894966	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	99	350	0	ENST00000374994.4:c.519G>T	p.Glu173Asp	p.E173D	ENST00000374994	NM_004612.2	173	gaG/gaT	3/9	0.287820694879808	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.287820694879808	1		350	557	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39935742	39935742	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	142	532	0	ENST00000378444.4:c.130G>C	p.Glu44Gln	p.E44Q	ENST00000378444	NM_001123385.1	44	Gaa/Caa	3/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.287820694879808	2		532	885	SUCCESS
AR	367	MSKCC	GRCh37	X	66765448	66765448	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	92	538	0	ENST00000374690.3:c.460G>T	p.Asp154Tyr	p.D154Y	ENST00000374690	NM_000044.3	154	Gac/Tac	1/8	1	2	FACETS	0.912	0.811	1	0.912	0.811	1	CLONAL	1	TRUE	1	0.287820694879808	2		538	701	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339664	70339664	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	172	610	0	ENST00000374080.3:c.333T>A	p.Ser111Arg	p.S111R	ENST00000374080		111	agT/agA	3/45	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.287820694879808	2		610	1017	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361778	70361778	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	207	707	1	ENST00000374080.3:c.6454G>T	p.Ala2152Ser	p.A2152S	ENST00000374080		2152	Gca/Tca	44/45	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.287820694879808	2		708	1215	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217359	123217359	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	133	592	0	ENST00000218089.9:c.3013G>T	p.Glu1005Ter	p.E1005*	ENST00000218089	NM_001042749.1	1005	Gaa/Taa	29/35	1	2	FACETS	0.828	0.75	0.91	0.828	0.75	0.91	CLONAL	1	TRUE	1	0.287820694879808	2		592	1116	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858045	152858045	+	synonymous_variant	Silent	SNP	G	G	T	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	62	306	0	ENST00000406277.2:c.570C>A	p.Ala190=	p.A190=	ENST00000406277	NM_152274.4	190	gcC/gcA	6/7	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.287820694879808	2		306	421	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860077	152860077	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	130	615	0	ENST00000406277.2:c.351C>G	p.Asp117Glu	p.D117E	ENST00000406277	NM_152274.4	117	gaC/gaG	5/7	1		FACETS		0.863	1				CLONAL	1	TRUE	1	0.287820694879808	2		615	949	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016613-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	696	641	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.337467624576364	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	0	0.337467624576364	3		641	1566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0016613-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	332	652	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.337467624576364	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.337467624576364	1		652	1470	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780896	9780896	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016613-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	84	552	1	ENST00000377346.4:c.1618G>T	p.Glu540Ter	p.E540*	ENST00000377346	NM_005026.3	540	Gag/Tag	13/24	0.337467624576364	1	FACETS	0.351	0.308	0.396	0.351	0.308	0.396	SUBCLONAL	1	TRUE	0	0.337467624576364	1		553	1180	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885903	23885903	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016613-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	55	233	0	ENST00000374561.5:c.15C>G	p.Ser5Arg	p.S5R	ENST00000374561	NM_002167.4	5	agC/agG	1/3	0.337467624576364	1	FACETS	0.528	0.452	0.611	0.528	0.452	0.611	SUBCLONAL	1	TRUE	0	0.337467624576364	1		233	513	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606751	43606751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016613-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1299	82	615	0	ENST00000355710.3:c.1360G>A	p.Val454Met	p.V454M	ENST00000355710	NM_020975.4	454	Gtg/Atg	7/20	0.337467624576364	1	FACETS	0.293	0.257	0.331	0.293	0.257	0.331	SUBCLONAL	1	TRUE	0	0.337467624576364	1		615	1381	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118353173	118353173	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016613-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1248	247	522	0	ENST00000534358.1:c.4049G>T	p.Arg1350Leu	p.R1350L	ENST00000534358	NM_005933.3	1350	cGc/cTc	8/36	1	2	FACETS	0.979	0.913	1	0.979	0.913	1	CLONAL	1	TRUE	1	0.337467624576364	2		522	1495	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865695	57865695	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016613-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	346	660	0	ENST00000228682.2:c.3172G>T	p.Gly1058Trp	p.G1058W	ENST00000228682	NM_005269.2	1058	Ggg/Tgg	12/12	0.320850438037612	2	FACETS	1	0.994	1	0.737	0.697	0.779	CLONAL	1	TRUE	0	0.337467624576364	2		660	1391	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860728	3860728	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016613-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	120	442	1	ENST00000262367.5:c.851G>T	p.Gly284Val	p.G284V	ENST00000262367	NM_004380.2	284	gGa/gTa	3/31	0.280187478644668	1	FACETS	0.6	0.541	0.663	0.6	0.541	0.663	SUBCLONAL	1	TRUE	0	0.337467624576364	1		443	985	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992294	72992294	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016613-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1409	195	692	0	ENST00000268489.5:c.1751del	p.Gly584AlafsTer76	p.G584Afs*76	ENST00000268489	NM_006885.3	584	gGc/gc	2/10	0.280187478644668	1	FACETS	0.599	0.552	0.648	0.599	0.552	0.648	SUBCLONAL	1	TRUE	0	0.337467624576364	1		692	1604	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627748	37627748	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016613-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1591	160	689	1	ENST00000447079.4:c.1663C>T	p.Pro555Ser	p.P555S	ENST00000447079	NM_015083.1	555	Cct/Tct	2/14	1	2	FACETS	0.542	0.494	0.591	0.542	0.494	0.591	SUBCLONAL	1	TRUE	1	0.337467624576364	2		690	1751	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223182	41223182	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016613-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	201	432	0	ENST00000357654.3:c.4749A>T	p.Arg1583Ser	p.R1583S	ENST00000357654	NM_007294.3	1583	agA/agT	15/23	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.337467624576364	2		432	953	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213884	2213884	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016613-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	139	643	0	ENST00000398665.3:c.1696C>T	p.Gln566Ter	p.Q566*	ENST00000398665	NM_032482.2	566	Caa/Taa	18/28	0.337467624576364	1	FACETS	0.536	0.487	0.589	0.536	0.487	0.589	SUBCLONAL	1	TRUE	0	0.337467624576364	1		643	1277	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982532	10982532	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016613-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	31	165	0	ENST00000327064.4:c.154G>T	p.Glu52Ter	p.E52*	ENST00000327064	NM_199141.1	52	Gag/Tag	1/16	0.337467624576364	1	FACETS	0.457	0.37	0.555	0.457	0.37	0.555	SUBCLONAL	1	TRUE	0	0.337467624576364	1		165	334	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724361	52724361	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016613-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	118	453	0	ENST00000322088.6:c.1493G>T	p.Arg498Leu	p.R498L	ENST00000322088	NM_014225.5	498	cGc/cTc	12/15	0.280187478644668	1	FACETS	0.556	0.501	0.615	0.556	0.501	0.615	SUBCLONAL	1	TRUE	0	0.337467624576364	1		453	1045	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576776	212576776	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016613-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	100	491	0	ENST00000342788.4:c.1123G>T	p.Gly375Trp	p.G375W	ENST00000342788	NM_005235.2	375	Ggg/Tgg	9/28	0.280187478644668	1	FACETS	0.474	0.422	0.529	0.474	0.422	0.529	SUBCLONAL	1	TRUE	0	0.337467624576364	1		491	1040	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794377	242794377	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016613-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	144	664	1	ENST00000334409.5:c.565G>T	p.Ala189Ser	p.A189S	ENST00000334409	NM_005018.2	189	Gcc/Tcc	3/5	0.280187478644668	1	FACETS	0.586	0.533	0.642	0.586	0.533	0.642	SUBCLONAL	1	TRUE	0	0.337467624576364	1		665	1210	SUCCESS
ATR	545	MSKCC	GRCh37	3	142185265	142185265	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016613-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	239	546	1	ENST00000350721.4:c.6798G>T	p.Met2266Ile	p.M2266I	ENST00000350721	NM_001184.3	2266	atG/atT	40/47	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.337467624576364	2		547	1018	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003205	143003205	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016613-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	128	426	0	ENST00000262992.4:c.2621G>T	p.Arg874Leu	p.R874L	ENST00000262992	NM_001101669.1	874	cGa/cTa	23/24	1	2	FACETS	0.769	0.696	0.847	0.769	0.696	0.847	SUBCLONAL	1	TRUE	1	0.337467624576364	2		426	986	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539978	187539978	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016613-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	170	389	0	ENST00000441802.2:c.7762G>T	p.Asp2588Tyr	p.D2588Y	ENST00000441802	NM_005245.3	2588	Gat/Tat	10/27	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.337467624576364	2		389	965	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630979	187630979	+	start_lost	Translation_Start_Site	SNP	C	C	A	novel	NA	P-0016613-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	146	491	0	ENST00000441802.2:c.3G>T	p.Met1?	p.M1?	ENST00000441802	NM_005245.3	1	atG/atT	2/27	1	2	FACETS	0.736	0.67	0.805	0.736	0.67	0.805	SUBCLONAL	1	TRUE	1	0.337467624576364	2		491	1176	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94067982	94067982	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016613-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	105	369	0	ENST00000369303.4:c.980C>G	p.Ala327Gly	p.A327G	ENST00000369303	NM_004440.3	327	gCg/gGg	4/17	0.280187478644668	1	FACETS	0.682	0.611	0.758	0.682	0.611	0.758	SUBCLONAL	1	TRUE	0	0.337467624576364	1		369	758	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508266	106508266	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016613-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	126	251	1	ENST00000359195.3:c.260T>A	p.Phe87Tyr	p.F87Y	ENST00000359195	NM_002649.2	87	tTc/tAc	2/11	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.337467624576364	2		252	739	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508708	106508708	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016613-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1446	157	549	0	ENST00000359195.3:c.702G>T	p.Lys234Asn	p.K234N	ENST00000359195	NM_002649.2	234	aaG/aaT	2/11	1	2	FACETS	0.58	0.53	0.634	0.58	0.53	0.634	SUBCLONAL	1	TRUE	1	0.337467624576364	2		549	1603	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341805	8341805	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016613-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	150	635	0	ENST00000356435.5:c.4835C>A	p.Ala1612Glu	p.A1612E	ENST00000356435		1612	gCa/gAa	29/35	0.337467624576364	1	FACETS	0.706	0.644	0.771	0.706	0.644	0.771	SUBCLONAL	1	TRUE	0	0.337467624576364	1		635	1047	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639851	93639851	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0016613-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	122	232	0	ENST00000375746.1:c.1182-2A>T		p.X394_splice	ENST00000375746	NM_001174167.1	394			0.337467624576364	1	FACETS	0.985	0.893	1	0.985	0.893	1	CLONAL	1	TRUE	0	0.337467624576364	1		232	610	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	96	641	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.965	0.86	1	0.965	0.86	1	CLONAL	1	TRUE	1	0.308117223113814	2		641	646	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220414	1220414	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	151	518	0	ENST00000326873.7:c.508del	p.Gln170ArgfsTer117	p.Q170Rfs*117	ENST00000326873	NM_000455.4	169	agC/ag	4/10	0.308117223113814	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.308117223113814	1		518	825	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610511	10610511	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1454940381	NA	P-0016614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	115	371	0	ENST00000171111.5:c.199A>G	p.Met67Val	p.M67V	ENST00000171111	NM_203500.1	67	Atg/Gtg	2/6	0.308117223113814	1	FACETS	0.911	0.822	1	0.911	0.822	1	CLONAL	1	TRUE	0	0.308117223113814	1		371	693	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132527	11132527	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	146	475	3	ENST00000358026.2:c.2743C>T	p.Gln915Ter	p.Q915*	ENST00000358026	NM_001128849.1	915	Cag/Tag	19/36	0.308117223113814	1	FACETS	0.921	0.841	1	0.921	0.841	1	CLONAL	1	TRUE	0	0.308117223113814	1		478	870	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141514	11141514	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	111	494	0	ENST00000358026.2:c.3491A>G	p.Asn1164Ser	p.N1164S	ENST00000358026	NM_001128849.1	1164	aAc/aGc	25/36	0.308117223113814	1	FACETS	0.786	0.707	0.871	0.786	0.707	0.871	SUBCLONAL	1	TRUE	0	0.308117223113814	1		494	775	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911534	101911534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111426349	NA	P-0016614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	108	411	1	ENST00000374994.4:c.1459C>T	p.Arg487Trp	p.R487W	ENST00000374994	NM_004612.2	487	Cgg/Tgg	9/9	0.308117223113814	1	FACETS	0.845	0.759	0.936	0.845	0.759	0.936	CLONAL	1	TRUE	0	0.308117223113814	1		412	702	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028895	47028895	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	80	287	0	ENST00000377604.3:c.199G>T	p.Glu67Ter	p.E67*	ENST00000377604	NM_001204468.1	67	Gag/Tag	3/24	1	2	FACETS	0.864	0.761	0.974	0.864	0.761	0.974	CLONAL	1	TRUE	1	0.308117223113814	2		287	601	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030516	47030517	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CG	novel	NA	P-0016614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	142	525	0	ENST00000377604.3:c.292_293dup	p.Asp99GlufsTer36	p.D99Efs*36	ENST00000377604	NM_001204468.1	97	-/CG	4/24	1	2	FACETS	0.843	0.767	0.924	0.843	0.767	0.924	CLONAL	1	TRUE	1	0.308117223113814	2		525	1093	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651652	48651652	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	195	604	0	ENST00000376670.3:c.818C>A	p.Ala273Asp	p.A273D	ENST00000376670	NM_002049.3	273	gCc/gAc	5/6	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.308117223113814	2		604	1152	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860891	151860894	+	frameshift_variant	Frame_Shift_Del	DEL	TTCT	TTCT	-	novel	NA	P-0016617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	151	279	0	ENST00000262189.6:c.9768_9771del	p.Lys3256AsnfsTer5	p.K3256Nfs*5	ENST00000262189	NM_170606.2	3256	aaAGAA/aa	43/59	1	2	FACETS	0.843	0.776	0.911	0.843	0.776	0.911	CLONAL	1	TRUE	1	0.75145875500609	2		279	477	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0016618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1340	50	1033	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	1	2	FACETS	0.36	0.303	0.422	0.36	0.303	0.422	SUBCLONAL	1	TRUE	1	0.2	2		1033	1390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0016619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	696	869	3	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA	2	FACETS	0.971	0.936	1			1	INDETERMINATE	2	TRUE	NA	0.392908131975658	2		872	1825	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0016619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1292	380	723	0	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	0.392908131975658	1	FACETS	0.93	0.88	0.98	0.93	0.88	0.98	CLONAL	1	TRUE	0	0.392908131975658	1		723	1672	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938230	76938230	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	221	456	2	ENST00000373344.5:c.2518del	p.Arg840GlufsTer29	p.R840Efs*29	ENST00000373344	NM_000489.3	840	Aga/ga	9/35	0.392908131975658	1	FACETS	0.814	0.756	0.873	0.814	0.756	0.873	CLONAL	1	TRUE	0	0.392908131975658	1		458	1111	SUCCESS
APC	324	MSKCC	GRCh37	5	112176863	112176863	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1270783041	NA	P-0016619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	193	321	0	ENST00000257430.4:c.5572C>T	p.Arg1858Ter	p.R1858*	ENST00000257430	NM_000038.5	1858	Cga/Tga	16/16	1	2	FACETS	0.947	0.876	1	0.947	0.876	1	CLONAL	1	TRUE	1	0.392908131975658	2		321	1037	SUCCESS
APC	324	MSKCC	GRCh37	5	112178936	112178936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199539353	NA	P-0016619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	197	319	0	ENST00000257430.4:c.7645C>T	p.Arg2549Cys	p.R2549C	ENST00000257430	NM_000038.5	2549	Cgt/Tgt	16/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.392908131975658	2		319	928	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101750	71101751	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0016619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	85	136	0	ENST00000318789.4:c.447dup	p.Gln150ThrfsTer20	p.Q150Tfs*20	ENST00000318789	NM_032682.5	149	-/A	9/21	1	2	FACETS	0.818	0.725	0.917	0.818	0.725	0.917	CLONAL	1	TRUE	1	0.392908131975658	2		136	529	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136804	55136804	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	138	277	1	ENST00000257290.5:c.1126C>T	p.Arg376Ter	p.R376*	ENST00000257290	NM_006206.4	376	Cga/Tga	8/23	1	2	FACETS	0.863	0.786	0.944	0.863	0.786	0.944	CLONAL	1	TRUE	1	0.392908131975658	2		278	814	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518737	176518737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753812223	NA	P-0016619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1579	282	534	0	ENST00000292408.4:c.655C>T	p.Arg219Cys	p.R219C	ENST00000292408	NM_213647.1	219	Cgc/Tgc	6/18	0.392908131975658	3	FACETS	0.923	0.864	0.984	0.461	0.432	0.492	CLONAL	1	TRUE	1	0.392908131975658	3		534	1861	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629420	187629420	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376472322	NA	P-0016619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	310	571	2	ENST00000441802.2:c.1562C>T	p.Thr521Met	p.T521M	ENST00000441802	NM_005245.3	521	aCg/aTg	2/27	0.384106300758873	1	FACETS	0.967	0.911	1	0.967	0.911	1	CLONAL	1	TRUE	0	0.392908131975658	1		573	1311	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2492097	2492097	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs772088410	NA	P-0016619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1764	390	701	0	ENST00000355716.4:c.500del	p.Pro167ArgfsTer23	p.P167Rfs*23	ENST00000355716	NM_003820.2	165	tgC/tg	5/8	0.354725415027019	2	FACETS	0.922	0.872	0.973	0.461	0.436	0.487	CLONAL	1	TRUE	0	0.392908131975658	2		701	2154	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726496	46726496	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs766404630	NA	P-0016619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	141	261	0	ENST00000371975.4:c.575A>G	p.Gln192Arg	p.Q192R	ENST00000371975	NM_003579.3	192	cAg/cGg	7/18	0.392908131975658	1	FACETS	0.949	0.867	1	0.949	0.867	1	CLONAL	1	TRUE	0	0.392908131975658	1		261	608	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841421	156841421	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1558102649	NA	P-0016619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	173	337	1	ENST00000524377.1:c.728del	p.Gly243ValfsTer7	p.G243Vfs*7	ENST00000524377	NM_002529.3	242	Ggg/gg	7/17	0.373091948912588	3	FACETS	1	0.922	1	0.334	0.307	0.363	CLONAL	1	TRUE	0	0.392908131975658	3		338	1051	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828153	243828153	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771617244	NA	P-0016619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	189	316	0	ENST00000263826.5:c.205C>T	p.Pro69Ser	p.P69S	ENST00000263826	NM_005465.4	69	Cca/Tca	3/13	0.392908131975658	1	FACETS	0.805	0.744	0.869	0.805	0.744	0.869	CLONAL	1	TRUE	0	0.392908131975658	1		316	960	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205535	61205535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs535627239	NA	P-0016619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	410	446	0	ENST00000301761.2:c.320G>A	p.Arg107His	p.R107H	ENST00000301761	NM_017841.2	107	cGc/cAc	3/4	0.354725415027019	2	FACETS	0.82	0.781	0.86	0.82	0.781	0.86	CLONAL	2	TRUE	0	0.392908131975658	2		446	1272	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924638	94924638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754657751	NA	P-0016619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	315	545	1	ENST00000536441.1:c.272G>A	p.Arg91Gln	p.R91Q	ENST00000536441	NM_144665.3	91	cGg/cAg	3/10	0.392908131975658	1	FACETS	0.99	0.933	1	0.99	0.933	1	CLONAL	1	TRUE	0	0.392908131975658	1		546	1301	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027153	49027156	+	frameshift_variant	Frame_Shift_Del	DEL	AAAC	AAAC	-	novel	NA	P-0016619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	225	419	0	ENST00000267163.4:c.1722_1725del	p.Lys574AsnfsTer36	p.K574Nfs*36	ENST00000267163	NM_000321.2	574	AAACaa/aa	18/27	0.376302746463506	1	FACETS	0.875	0.814	0.937	0.875	0.814	0.937	CLONAL	1	TRUE	0	0.392908131975658	1		419	1052	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093455	30093455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776034417	NA	P-0016619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	145	325	0	ENST00000331968.5:c.1808G>A	p.Arg603His	p.R603H	ENST00000331968	NM_002742.2	603	cGt/cAt	13/18	1	2	FACETS	0.876	0.799	0.956	0.876	0.799	0.956	CLONAL	1	TRUE	1	0.392908131975658	2		325	843	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500315	99500315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	197	417	1	ENST00000268035.6:c.3748C>T	p.Gln1250Ter	p.Q1250*	ENST00000268035	NM_000875.3	1250	Cag/Tag	21/21	1	2	FACETS	0.876	0.81	0.944	0.876	0.81	0.944	CLONAL	1	TRUE	1	0.392908131975658	2		418	1145	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343696	343696	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1454	126	740	2	ENST00000262320.3:c.1978C>T	p.Gln660Ter	p.Q660*	ENST00000262320	NM_003502.3	660	Cag/Tag	8/11	0.392908131975658	1	FACETS	0.326	0.294	0.361	0.326	0.294	0.361	SUBCLONAL	1	TRUE	0	0.392908131975658	1		742	1580	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347912	347912	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1445	389	868	0	ENST00000262320.3:c.1594C>T	p.His532Tyr	p.H532Y	ENST00000262320	NM_003502.3	532	Cac/Tac	6/11	0.392908131975658	1	FACETS	0.868	0.822	0.915	0.868	0.822	0.915	CLONAL	1	TRUE	0	0.392908131975658	1		868	1834	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830750	72830750	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs983793348	NA	P-0016619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	94	446	0	ENST00000268489.5:c.5831C>T	p.Ala1944Val	p.A1944V	ENST00000268489	NM_006885.3	1944	gCc/gTc	9/10	1	2	FACETS	0.389	0.345	0.437	0.389	0.345	0.437	SUBCLONAL	1	TRUE	1	0.392908131975658	2		446	1230	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349578	89349578	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1386	260	595	0	ENST00000301030.4:c.3372G>T	p.Glu1124Asp	p.E1124D	ENST00000301030	NM_001256183.1	1124	gaG/gaT	9/13	1	2	FACETS	0.804	0.751	0.859	0.804	0.751	0.859	CLONAL	1	TRUE	1	0.392908131975658	2		595	1646	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40874872	40874874	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0016619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1266	377	688	0	ENST00000428826.2:c.426_428del	p.Glu142del	p.E142del	ENST00000428826		142	gaAGAt/gat	6/21	0.392908131975658	1	FACETS	0.939	0.889	0.99	0.939	0.889	0.99	CLONAL	1	TRUE	0	0.392908131975658	1		688	1643	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7132235	7132235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs911929963	NA	P-0016619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1449	268	518	1	ENST00000302850.5:c.2776C>T	p.Arg926Trp	p.R926W	ENST00000302850	NM_000208.2	926	Cgg/Tgg	14/22	0.392908131975658	3	FACETS	0.951	0.888	1	0.475	0.444	0.508	CLONAL	1	TRUE	1	0.392908131975658	3		519	1717	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285902	39285902	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	193	415	0	ENST00000402219.2:c.257C>T	p.Ala86Val	p.A86V	ENST00000402219	NM_005633.3	86	gCa/gTa	3/23	0.392908131975658	1	FACETS	0.876	0.811	0.944	0.876	0.811	0.944	CLONAL	1	TRUE	0	0.392908131975658	1		415	901	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657041	47657041	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs863225387	NA	P-0016619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	204	382	2	ENST00000233146.2:c.1237C>T	p.Gln413Ter	p.Q413*	ENST00000233146	NM_000251.2	413	Caa/Taa	7/16	0.392908131975658	1	FACETS	0.976	0.906	1	0.976	0.906	1	CLONAL	1	TRUE	0	0.392908131975658	1		384	855	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264659	46264659	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	122	202	0	ENST00000371998.3:c.1529C>G	p.Ser510Cys	p.S510C	ENST00000371998		510	tCt/tGt	12/23	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.392908131975658	2		202	614	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626462	12626462	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs532786413	NA	P-0016619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	215	350	3	ENST00000251849.4:c.1687C>T	p.Arg563Ter	p.R563*	ENST00000251849	NM_002880.3	563	Cga/Tga	16/17	1	2	FACETS	0.991	0.921	1	0.991	0.921	1	CLONAL	1	TRUE	1	0.392908131975658	2		353	1104	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49724707	49724708	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0016619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1334	203	579	0	ENST00000449682.2:c.481_482del	p.Thr161SerfsTer12	p.T161Sfs*12	ENST00000449682	NM_020998.3	161	ACt/t	5/18	1	2	FACETS	0.672	0.621	0.726	0.672	0.621	0.726	SUBCLONAL	1	TRUE	1	0.392908131975658	2		579	1537	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508746	31508746	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1388	303	534	0	ENST00000344624.3:c.1569G>T	p.Trp523Cys	p.W523C	ENST00000344624		523	tgG/tgT	7/33	1	2	FACETS	0.912	0.857	0.969	0.912	0.857	0.969	CLONAL	1	TRUE	1	0.392908131975658	2		534	1691	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944636	38944636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746712836	NA	P-0016619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	198	324	0	ENST00000357387.3:c.4825C>T	p.Arg1609Cys	p.R1609C	ENST00000357387	NM_152756.3	1609	Cgt/Tgt	36/38	1	2	FACETS	0.953	0.882	1	0.953	0.882	1	CLONAL	1	TRUE	1	0.392908131975658	2		324	1058	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0016620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	79	332	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.21	2		332	751	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0016622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	243	683	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.430755749943204	2		683	1023	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0016622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	480	554	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.430755749943204	2	FACETS	0.941	0.902	0.981	0.941	0.902	0.981	CLONAL	2	TRUE	0	0.430755749943204	2		554	1184	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482927	140482927	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	184	599	3	ENST00000288602.6:c.1208del	p.Pro403LeufsTer8	p.P403Lfs*8	ENST00000288602	NM_004333.4	403	cCt/ct	10/18	1	2	FACETS	0.716	0.66	0.775	0.716	0.66	0.775	SUBCLONAL	1	TRUE	1	0.430755749943204	2		602	1193	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916948	178916950	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0016622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	311	560	0	ENST00000263967.3:c.337_339del	p.Leu113del	p.L113del	ENST00000263967	NM_006218.2	112	aTCCtc/atc	2/21	0.307769789702992	2	FACETS	0.766	0.724	0.808	0.766	0.724	0.808	SUBCLONAL	2	TRUE	0	0.430755749943204	2		560	943	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0016622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	192	288	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.430755749943204	2		288	842	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101099	27101099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	668	921	1	ENST00000324856.7:c.4381C>T	p.Arg1461Ter	p.R1461*	ENST00000324856	NM_006015.4	1461	Cga/Tga	18/20	0.430755749943204	2	FACETS	0.969	0.935	1	0.969	0.935	1	CLONAL	2	TRUE	0	0.430755749943204	2		922	1601	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653809	89653809	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	286	421	0	ENST00000371953.3:c.107G>T	p.Gly36Val	p.G36V	ENST00000371953	NM_000314.4	36	gGa/gTa	2/9	0.430755749943204	2	FACETS	0.987	0.934	1	0.987	0.934	1	CLONAL	2	TRUE	0	0.430755749943204	2		421	673	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864432	57864432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200606293	NA	P-0016622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	208	604	1	ENST00000228682.2:c.1909C>T	p.Arg637Trp	p.R637W	ENST00000228682	NM_005269.2	637	Cgg/Tgg	12/12	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.430755749943204	2		605	946	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799116	42799116	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760743180	NA	P-0016622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1563	439	1188	0	ENST00000575354.2:c.4600C>T	p.Pro1534Ser	p.P1534S	ENST00000575354	NM_015125.3	1534	Cct/Tct	20/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.430755749943204	2		1188	2002	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131976370	131976370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501944	NA	P-0016622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	146	482	0	ENST00000265335.6:c.3625G>A	p.Ala1209Thr	p.A1209T	ENST00000265335		1209	Gcc/Acc	24/25	1	2	FACETS	0.657	0.599	0.718	0.657	0.599	0.718	SUBCLONAL	1	TRUE	1	0.430755749943204	2		482	1032	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	79	137	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	0.85	0.751	0.957	1	0.981	1	CLONAL	2	TRUE	1	0.201956397448659	2		137	460	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	345	556	3	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	0.201956397448659	1	FACETS	1	0.985	1	1	0.996	1	CLONAL	2	TRUE	0	0.201956397448659	1		559	1383	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912346	32912346	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359406	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	114	283	0	ENST00000380152.3:c.3860del	p.Asn1287IlefsTer6	p.N1287Ifs*6	ENST00000380152		1285	gAa/ga	11/27	1	2	FACETS	0.946	0.854	1	1	0.988	1	CLONAL	2	TRUE	1	0.201956397448659	2		283	597	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300040	137300040	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2193	500	968	4	ENST00000481739.1:c.331del	p.Leu111TrpfsTer57	p.L111Wfs*57	ENST00000481739	NM_002957.4	109	Ccc/cc	3/10	0.201956397448659	1	FACETS	0.827	0.787	0.867	1	0.996	1	CLONAL	2	TRUE	0	0.201956397448659	1		972	2693	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	68	192	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.196713026478105	3	FACETS	0.766	0.668	0.872	0.766	0.668	0.872	SUBCLONAL	2	TRUE	1	0.201956397448659	3		192	484	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2125	736	1083	2	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.849	0.817	0.882	1	0.998	1	CLONAL	3	TRUE	1	0.201956397448659	2		1085	2861	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	161	324	1	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	0.992	1	CLONAL	2	TRUE	1	0.201956397448659	2		325	786	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	139	176	0	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	0.201956397448659	1	FACETS	1	0.981	1	1	0.992	1	CLONAL	2	TRUE	0	0.201956397448659	1		176	496	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	207	361	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.949	1	1	0.994	1	CLONAL	2	TRUE	1	0.201956397448659	2		362	997	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486262	8486262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	141	236	0	ENST00000356435.5:c.2555C>T	p.Pro852Leu	p.P852L	ENST00000356435		852	cCt/cTt	17/35	0.201956397448659	1	FACETS	0.887	0.809	0.967	1	0.99	1	CLONAL	2	TRUE	0	0.201956397448659	1		236	708	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097751	27097751	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1317	325	543	0	ENST00000324856.7:c.3344del	p.Pro1115GlnfsTer46	p.P1115Qfs*46	ENST00000324856	NM_006015.4	1114	Ccc/cc	12/20	1	2	FACETS	0.98	0.923	1	1	0.996	1	CLONAL	2	TRUE	1	0.201956397448659	2		543	1642	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141498	11141498	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1375	391	671	2	ENST00000358026.2:c.3480del	p.Leu1161SerfsTer3	p.L1161Sfs*3	ENST00000358026	NM_001128849.1	1159	Ggg/gg	25/36	1	2	FACETS	1	0.985	1	1	0.997	1	CLONAL	2	TRUE	1	0.201956397448659	2		673	1766	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509085	66509085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	167	381	0	ENST00000273854.3:c.242del	p.Asn81MetfsTer24	p.N81Mfs*24	ENST00000273854	NM_004439.5	81	aAt/at	2/18	0.201956397448659	1	FACETS	0.943	0.868	1	1	0.992	1	CLONAL	2	TRUE	0	0.201956397448659	1		381	788	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524993	187524993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371987657	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	127	471	0	ENST00000441802.2:c.10687G>A	p.Val3563Ile	p.V3563I	ENST00000441802	NM_005245.3	3563	Gtc/Atc	19/27	0.201956397448659	1	FACETS	0.931	0.841	1	0.931	0.841	1	CLONAL	1	TRUE	0	0.201956397448659	1		471	1214	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	344	400	2	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	0.196713026478105	3	FACETS	0.853	0.806	0.901	1	0.992	1	CLONAL	3	TRUE	1	0.201956397448659	3		402	1466	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630303	187630303	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774143174	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	161	496	1	ENST00000441802.2:c.679C>T	p.Arg227Cys	p.R227C	ENST00000441802	NM_005245.3	227	Cgt/Tgt	2/27	0.201956397448659	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.201956397448659	1		497	1223	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562345	21562345	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1204055851	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1389	408	759	0	ENST00000382592.4:c.1574G>A	p.Arg525His	p.R525H	ENST00000382592	NM_014572.2	525	cGc/cAc	4/8	1	2	FACETS	1	0.988	1	1	0.997	1	CLONAL	2	TRUE	1	0.201956397448659	2		759	1797	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776099	9776099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748146002	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1442	303	662	2	ENST00000377346.4:c.563G>A	p.Arg188Gln	p.R188Q	ENST00000377346	NM_005026.3	188	cGg/cAg	5/24	1	2	FACETS	0.86	0.807	0.914	1	0.995	1	CLONAL	2	TRUE	1	0.201956397448659	2		664	1745	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793010	33793010	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs974386262	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	120	148	1	ENST00000498907.2:c.311G>A	p.Gly104Asp	p.G104D	ENST00000498907	NM_004364.3	104	gGc/gAc	1/1	1	2	FACETS	0.894	0.813	0.978	1	0.991	1	CLONAL	3	TRUE	1	0.201956397448659	2		149	443	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186895	142186895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866304619	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	140	270	0	ENST00000350721.4:c.6568C>T	p.Arg2190Cys	p.R2190C	ENST00000350721	NM_001184.3	2190	Cgt/Tgt	39/47	0.196713026478105	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	1	0.201956397448659	3		270	717	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692847	89692847	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123321	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	99	189	0	ENST00000371953.3:c.331T>C	p.Trp111Arg	p.W111R	ENST00000371953	NM_000314.4	111	Tgg/Cgg	5/9	1	2	FACETS	1	0.952	1	1	0.988	1	CLONAL	2	TRUE	1	0.201956397448659	2		189	444	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696461	47696461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	251	617	0	ENST00000347630.2:c.362G>A	p.Arg121Gln	p.R121Q	ENST00000347630	NM_001007230.1	121	cGg/cAg	6/11	1	2	FACETS	1	0.966	1	1	0.995	1	CLONAL	2	TRUE	1	0.201956397448659	2		617	1183	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060912	38060912	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	189	373	1	ENST00000250448.2:c.1077del	p.Ile360Ter	p.I360*	ENST00000250448	NM_004496.3	359	ccC/cc	2/2	1	2	FACETS	1	0.981	1	1	0.994	1	CLONAL	2	TRUE	1	0.201956397448659	2		374	795	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355256	81355256	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1258267427	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	142	261	0	ENST00000222390.5:c.1118G>A	p.Arg373Gln	p.R373Q	ENST00000222390	NM_000601.4	373	cGa/cAa	9/18	1	2	FACETS	0.928	0.846	1	1	0.99	1	CLONAL	2	TRUE	1	0.201956397448659	2		261	758	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291921	15291921	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2058	635	1020	0	ENST00000263388.2:c.2845C>A	p.Leu949Met	p.L949M	ENST00000263388	NM_000435.2	949	Ctg/Atg	18/33	1	2	FACETS	1	0.994	1	1	0.998	1	CLONAL	2	TRUE	1	0.201956397448659	2		1020	2693	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142910	30142910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141093002	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2187	297	983	1	ENST00000389048.3:c.616G>A	p.Ala206Thr	p.A206T	ENST00000389048	NM_004304.4	206	Gcg/Acg	1/29	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.201956397448659	2		984	2484	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380346	14380346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	289	558	0	ENST00000256196.4:c.71G>A	p.Gly24Asp	p.G24D	ENST00000256196		24	gGc/gAc	1/6	0.201956397448659	1	FACETS	0.925	0.868	0.983	1	0.995	1	CLONAL	2	TRUE	0	0.201956397448659	1		558	1391	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599234	28599234	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1834	582	877	2	ENST00000253063.3:c.685del	p.Gln229ArgfsTer18	p.Q229Rfs*18	ENST00000253063	NM_031459.4	227	gCc/gc	5/10	1	2	FACETS	1	0.994	1	1	0.998	1	CLONAL	2	TRUE	1	0.201956397448659	2		879	2416	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779743	3779743	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	134	414	0	ENST00000262367.5:c.5305C>T	p.Arg1769Trp	p.R1769W	ENST00000262367	NM_004380.2	1769	Cgg/Tgg	31/31	0.201956397448659	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.201956397448659	1		414	1080	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28595728	28595728	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769967309	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	338	579	1	ENST00000253063.3:c.125G>A	p.Arg42Gln	p.R42Q	ENST00000253063	NM_031459.4	42	cGa/cAa	2/10	1	2	FACETS	1	0.981	1	1	0.996	1	CLONAL	2	TRUE	1	0.201956397448659	2		580	1537	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43806113	43806113	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	327	530	0	ENST00000372470.3:c.909G>A	p.Trp303Ter	p.W303*	ENST00000372470	NM_005373.2	303	tgG/tgA	6/12	1	2	FACETS	1	0.986	1	1	0.996	1	CLONAL	2	TRUE	1	0.201956397448659	2		530	1428	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192108	108192108	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	247	401	0	ENST00000278616.4:c.6533C>T	p.Ala2178Val	p.A2178V	ENST00000278616	NM_000051.3	2178	gCc/gTc	45/63	0.201956397448659	1	FACETS	0.99	0.925	1	1	0.994	1	CLONAL	2	TRUE	0	0.201956397448659	1		401	1111	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416416	49416416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123734	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	311	424	0	ENST00000301067.7:c.16295G>A	p.Arg5432Gln	p.R5432Q	ENST00000301067	NM_003482.3	5432	cGg/cAg	51/54	1	2	FACETS	1	0.985	1	1	0.996	1	CLONAL	2	TRUE	1	0.201956397448659	2		424	1355	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420144	49420144	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	310	474	0	ENST00000301067.7:c.15605C>T	p.Ala5202Val	p.A5202V	ENST00000301067	NM_003482.3	5202	gCc/gTc	48/54	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.201956397448659	2		474	1245	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447923	49447923	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs770105193	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	182	272	1	ENST00000301067.7:c.511C>T	p.Arg171Cys	p.R171C	ENST00000301067	NM_003482.3	171	Cgc/Tgc	5/54	1	2	FACETS	1	0.97	1	1	0.993	1	CLONAL	2	TRUE	1	0.201956397448659	2		273	820	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001982	29001982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369255421	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	200	411	0	ENST00000282397.4:c.1183G>A	p.Val395Ile	p.V395I	ENST00000282397	NM_002019.4	395	Gta/Ata	9/30	1	2	FACETS	0.9	0.833	0.97	1	0.993	1	CLONAL	2	TRUE	1	0.201956397448659	2		411	1100	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046723	42046723	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1561	454	655	0	ENST00000219905.7:c.7097A>G	p.His2366Arg	p.H2366R	ENST00000219905	NM_001164273.1	2366	cAc/cGc	18/24	1	2	FACETS	1	0.988	1	1	0.997	1	CLONAL	2	TRUE	1	0.201956397448659	2		655	2015	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129044	2129044	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137854410	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	130	399	0	ENST00000219476.3:c.2978C>T	p.Thr993Met	p.T993M	ENST00000219476	NM_000548.3	993	aCg/aTg	27/42	0.201956397448659	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.201956397448659	1		399	1126	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946261	81946261	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	163	547	0	ENST00000359376.3:c.1994G>A	p.Arg665Gln	p.R665Q	ENST00000359376	NM_002661.3	665	cGg/cAg	19/33	0.201956397448659	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.201956397448659	1		547	1374	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434867	56434867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1157	268	487	0	ENST00000407977.2:c.2270G>A	p.Cys757Tyr	p.C757Y	ENST00000407977		757	tGc/tAc	9/10	1	2	FACETS	0.931	0.871	0.993	1	0.995	1	CLONAL	2	TRUE	1	0.201956397448659	2		487	1425	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554542	63554542	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	262	343	0	ENST00000307078.5:c.197A>G	p.Glu66Gly	p.E66G	ENST00000307078	NM_004655.3	66	gAg/gGg	2/11	1	2	FACETS	1	0.981	1	1	0.995	1	CLONAL	2	TRUE	1	0.201956397448659	2		343	1164	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215538	5215538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267605547	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	359	485	0	ENST00000357368.4:c.4165G>A	p.Asp1389Asn	p.D1389N	ENST00000357368	NM_002850.3	1389	Gac/Aac	27/38	1	2	FACETS	1	0.99	1	1	0.997	1	CLONAL	2	TRUE	1	0.201956397448659	2		485	1482	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11018783	11018783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2040	606	876	0	ENST00000327064.4:c.415G>A	p.Glu139Lys	p.E139K	ENST00000327064	NM_199141.1	139	Gag/Aag	3/16	1	2	FACETS	1	0.992	1	1	0.998	1	CLONAL	2	TRUE	1	0.201956397448659	2		876	2646	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031171	11031171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568357607	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1620	430	720	0	ENST00000327064.4:c.1256G>A	p.Arg419Gln	p.R419Q	ENST00000327064	NM_199141.1	419	cGg/cAg	11/16	1	2	FACETS	1	0.974	1	1	0.997	1	CLONAL	2	TRUE	1	0.201956397448659	2		720	2050	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211504	36211504	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1830	514	839	0	ENST00000222270.7:c.1259del	p.Pro420LeufsTer55	p.P420Lfs*55	ENST00000222270	NM_014727.1	419	Ccc/cc	3/37	1	2	FACETS	1	0.987	1	1	0.997	1	CLONAL	2	TRUE	1	0.201956397448659	2		839	2344	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656906	47656906	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	179	280	0	ENST00000233146.2:c.1102G>T	p.Glu368Ter	p.E368*	ENST00000233146	NM_000251.2	368	Gaa/Taa	7/16	1	2	FACETS	1	0.97	1	1	0.993	1	CLONAL	2	TRUE	1	0.201956397448659	2		280	808	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703591	47703591	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs63750872	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	256	441	0	ENST00000233146.2:c.2091T>A	p.Cys697Ter	p.C697*	ENST00000233146	NM_000251.2	697	tgT/tgA	13/16	1	2	FACETS	1	0.974	1	1	0.995	1	CLONAL	2	TRUE	1	0.201956397448659	2		441	1177	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101048	41101048	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	195	416	0	ENST00000373198.4:c.1308G>T	p.Glu436Asp	p.E436D	ENST00000373198	NM_133170.3	436	gaG/gaT	8/32	1	2	FACETS	0.975	0.903	1	1	0.993	1	CLONAL	2	TRUE	1	0.201956397448659	2		416	990	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264098	46264098	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	196	254	0	ENST00000371998.3:c.1145C>A	p.Pro382His	p.P382H	ENST00000371998		382	cCt/cAt	11/23	1	2	FACETS	1	0.984	1	1	0.994	1	CLONAL	2	TRUE	1	0.201956397448659	2		254	805	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523588	41523588	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1204	309	484	1	ENST00000263253.7:c.1004G>A	p.Arg335His	p.R335H	ENST00000263253	NM_001429.3	335	cGc/cAc	4/31	1	2	FACETS	1	0.95	1	1	0.996	1	CLONAL	2	TRUE	1	0.201956397448659	2		485	1513	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125832	47125832	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	109	208	0	ENST00000409792.3:c.5438del	p.Asn1813IlefsTer25	p.N1813Ifs*25	ENST00000409792	NM_014159.6	1813	aAt/at	12/21	0.196713026478105	3	FACETS	0.92	0.827	1	0.92	0.827	1	CLONAL	2	TRUE	1	0.201956397448659	3		208	646	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277508	142277508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759350161	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	316	463	0	ENST00000350721.4:c.1843G>A	p.Ala615Thr	p.A615T	ENST00000350721	NM_001184.3	615	Gct/Act	8/47	0.196713026478105	3	FACETS	0.945	0.892	1	1	0.993	1	CLONAL	3	TRUE	1	0.201956397448659	3		463	1215	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013719	170013719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388201066	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	305	417	1	ENST00000295797.4:c.1438C>T	p.Arg480Cys	p.R480C	ENST00000295797	NM_002740.5	480	Cgc/Tgc	15/18	0.196713026478105	3	FACETS	0.895	0.843	0.949	1	0.992	1	CLONAL	3	TRUE	1	0.201956397448659	3		418	1238	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803630	1803630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780147591	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1407	471	843	0	ENST00000260795.2:c.808G>A	p.Asp270Asn	p.D270N	ENST00000260795		270	Gac/Aac	6/17	0.201956397448659	1	FACETS	1	0.989	1	1	0.997	1	CLONAL	2	TRUE	0	0.201956397448659	1		843	1878	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920288	1920288	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1393	184	543	0	ENST00000382891.5:c.1348C>T	p.Arg450Ter	p.R450*	ENST00000382891	NM_133335.3	450	Cga/Tga	5/22	0.201956397448659	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.201956397448659	1		543	1577	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55143552	55143552	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	125	183	1	ENST00000257290.5:c.1787-3C>T		p.X596_splice	ENST00000257290	NM_006206.4	596			0.201956397448659	1	FACETS	1	0.937	1	1	0.99	1	CLONAL	2	TRUE	0	0.201956397448659	1		184	536	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750406	57750421	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	TCTTTCAGTTACATCT	TCTTTCAGTTACATCT	-	novel	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	134	304	0	ENST00000274289.3:c.2047_*4del		p.*683*	ENST00000274289	NM_006622.3	683		14/14	1	2	FACETS	0.881	0.801	0.965	1	0.989	1	CLONAL	2	TRUE	1	0.201956397448659	2		304	753	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26046035	26046035	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767901516	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	143	227	0	ENST00000540144.1:c.400del	p.Glu134LysfsTer?	p.E134Kfs*?	ENST00000540144	NM_003531.2	133	Ggg/gg	1/1	1	2	FACETS	0.971	0.887	1	1	0.991	1	CLONAL	2	TRUE	1	0.201956397448659	2		227	729	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553519	106553519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1203176627	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	93	257	0	ENST00000369096.4:c.1484C>T	p.Ala495Val	p.A495V	ENST00000369096	NM_001198.3	495	gCc/gTc	5/7	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.201956397448659	2		257	722	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129421	152129421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	222	375	0	ENST00000206249.3:c.374G>A	p.Gly125Asp	p.G125D	ENST00000206249	NM_000125.3	125	gGc/gAc	1/8	1	2	FACETS	1	0.979	1	1	0.994	1	CLONAL	2	TRUE	1	0.201956397448659	2		375	975	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946463	2946463	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs777458922	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1320	317	573	2	ENST00000396946.4:c.3274C>T	p.Arg1092Ter	p.R1092*	ENST00000396946	NM_032415.4	1092	Cga/Tga	25/25	1	2	FACETS	0.959	0.902	1	1	0.995	1	CLONAL	2	TRUE	1	0.201956397448659	2		575	1637	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268927	55268927	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1289194907	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1555	458	778	0	ENST00000275493.2:c.2993A>G	p.Tyr998Cys	p.Y998C	ENST00000275493	NM_005228.3	998	tAc/tGc	25/28	1	2	FACETS	1	0.989	1	1	0.997	1	CLONAL	2	TRUE	1	0.201956397448659	2		778	2013	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878320	151878320	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	185	356	0	ENST00000262189.6:c.6625del	p.Thr2209HisfsTer30	p.T2209Hfs*30	ENST00000262189	NM_170606.2	2209	Aca/ca	36/59	1	2	FACETS	0.933	0.861	1	1	0.992	1	CLONAL	2	TRUE	1	0.201956397448659	2		356	982	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739394	145739394	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1336325647	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1326	830	655	1	ENST00000428558.2:c.1976C>T	p.Ala659Val	p.A659V	ENST00000428558	NM_004260.3	659	gCt/gTt	12/22	0.201956397448659	4	FACETS	0.916	0.887	0.946	1	0.998	1	CLONAL	5	TRUE	1	0.201956397448659	4		656	2156	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209397	98209397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs187104739	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	164	348	0	ENST00000331920.6:c.4141G>A	p.Val1381Met	p.V1381M	ENST00000331920	NM_000264.3	1381	Gtg/Atg	23/24	0.201956397448659	1	FACETS	0.871	0.8	0.945	1	0.991	1	CLONAL	2	TRUE	0	0.201956397448659	1		348	838	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796805	135796805	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203427	NA	P-0016626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	146	337	0	ENST00000298552.3:c.682C>T	p.Arg228Ter	p.R228*	ENST00000298552	NM_001162426.1	228	Cga/Tga	8/23	0.201956397448659	1	FACETS	0.796	0.727	0.869	1	0.988	1	SUBCLONAL	2	TRUE	0	0.201956397448659	1		337	816	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115955	8115956	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0016627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	112	376	0	ENST00000346208.3:c.1305dup	p.Ser436LeufsTer71	p.S436Lfs*71	ENST00000346208		434	cac/caCc	6/6	0.357830679944723	5	FACETS	0.853	0.767	0.943	0.171	0.153	0.189	INDETERMINATE	1	FALSE	0	0.733994195279176	5		376	752	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530077	63530077	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7960	1643	656	0	ENST00000307078.5:c.2358G>C	p.Leu786Phe	p.L786F	ENST00000307078	NM_004655.3	786	ttG/ttC	10/11	0.733994195279176	23	FACETS	1	0.984	1			1	CLONAL	4	FALSE	NA	0.733994195279176	23		656	9603	SUCCESS
BTK	695	MSKCC	GRCh37	X	100612524	100612524	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	157	403	0	ENST00000308731.7:c.1150G>A	p.Ala384Thr	p.A384T	ENST00000308731	NM_000061.2	384	Gca/Aca	13/19	NA	2	FACETS	0.782	0.721	0.846			1	INDETERMINATE	1	FALSE	NA	0.733994195279176	2		403	547	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	4203	726	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.579511013103565	1	FACETS	1	0.997	1			1	CLONAL	2	TRUE	0	0.579511013103565	1		726	5102	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0016628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	563	869	3	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.576981928560671	1	FACETS	0.963	0.925	1	0.963	0.925	1	CLONAL	1	TRUE	0	0.579511013103565	1		872	1433	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423601	88423601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	309	527	0	ENST00000360948.2:c.2234G>A	p.Arg745Gln	p.R745Q	ENST00000360948	NM_001012338.2	745	cGg/cAg	18/19	1	2	FACETS	0.908	0.856	0.962	0.908	0.856	0.962	CLONAL	1	TRUE	1	0.579511013103565	2		527	1174	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492700	56492700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	698	575	0	ENST00000407977.2:c.239G>A	p.Gly80Glu	p.G80E	ENST00000407977		80	gGa/gAa	2/10	0.579511013103565	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.579511013103565	2		575	1171	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579439	7579439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201717599	NA	P-0016628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	440	644	0	ENST00000269305.4:c.248C>T	p.Ala83Val	p.A83V	ENST00000269305	NM_001126112.2	83	gCg/gTg	4/11	0.576981928560671	1	FACETS	0.955	0.913	0.998	0.955	0.913	0.998	CLONAL	1	TRUE	0	0.579511013103565	1		644	1129	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230399	46230399	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	218	321	0	ENST00000334344.6:c.733G>T	p.Glu245Ter	p.E245*	ENST00000334344	NM_152641.2	245	Gaa/Taa	7/21	1	2	FACETS	0.881	0.821	0.943	0.881	0.821	0.943	CLONAL	1	TRUE	1	0.579511013103565	2		321	854	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246078935	246078935	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	319	444	0	ENST00000388985.4:c.710T>C	p.Ile237Thr	p.I237T	ENST00000388985		237	aTc/aCc	8/12	1	2	FACETS	0.981	0.927	1	0.981	0.927	1	CLONAL	1	TRUE	1	0.579511013103565	2		444	1122	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683228	88683228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876658515	NA	P-0016628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	283	458	0	ENST00000372037.3:c.1438C>T	p.Arg480Trp	p.R480W	ENST00000372037	NM_004329.2	480	Cgg/Tgg	12/13	1	2	FACETS	0.984	0.926	1	0.984	0.926	1	CLONAL	1	TRUE	1	0.579511013103565	2		458	993	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522565	106522565	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	234	312	0	ENST00000359195.3:c.2542C>G	p.Leu848Val	p.L848V	ENST00000359195	NM_002649.2	848	Cta/Gta	7/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.579511013103565	2		312	718	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593613	55593613	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913521	NA	P-0016629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	334	472	0	ENST00000288135.5:c.1679T>A	p.Val560Asp	p.V560D	ENST00000288135	NM_000222.2	560	gTt/gAt	11/21	0.80771530234478	1	FACETS	0.982	0.945	1	0.982	0.945	1	CLONAL	1	TRUE	0	0.80771530234478	1		472	502	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641753	12641753	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	300	495	0	ENST00000251849.4:c.888C>G	p.Ser296Arg	p.S296R	ENST00000251849	NM_002880.3	296	agC/agG	9/17	1	2	FACETS	0.818	0.773	0.865	0.818	0.773	0.865	CLONAL	1	TRUE	1	0.80771530234478	2		495	908	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271263	153271263	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0016629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	16	356	0	ENST00000281708.4:c.515T>A	p.Leu172Ter	p.L172*	ENST00000281708	NM_033632.3	172	tTg/tAg	3/12	0.80771530234478	1	FACETS	0.077	0.056	0.101	0.077	0.056	0.101	SUBCLONAL	1	TRUE	0	0.80771530234478	1		356	307	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332538	153332539	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0016629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	54	367	0	ENST00000281708.4:c.417_418insTA	p.Thr140Ter	p.T140*	ENST00000281708	NM_033632.3	139	-/TA	2/12	0.80771530234478	1	FACETS	0.186	0.159	0.215	0.186	0.159	0.215	SUBCLONAL	1	TRUE	0	0.80771530234478	1		367	429	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977949	134977949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56186270	NA	P-0016630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	78	564	1	ENST00000398015.3:c.2942C>T	p.Thr981Met	p.T981M	ENST00000398015	NM_004441.4	981	aCg/aTg	16/16	1	2	FACETS	0.893	0.789	1	1	0.982	1	CLONAL	2	TRUE	1	0.22	2		565	397	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0016632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	232	480	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.214292782254292	2	FACETS	0.979	0.914	1	0.979	0.914	1	CLONAL	2	TRUE	0	0.26727213111667	2		480	887	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321690	62321690	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	118	479	1	ENST00000360203.5:c.2309G>T	p.Gly770Val	p.G770V	ENST00000360203	NM_001283009.1	770	gGa/gTa	26/35	NA	2	FACETS	0.787	0.708	0.871			1	INDETERMINATE	1	TRUE	NA	0.26727213111667	2		480	1122	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449764	8449764	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	258	420	0	ENST00000356435.5:c.3949G>T	p.Asp1317Tyr	p.D1317Y	ENST00000356435		1317	Gac/Tac	23/35	0.26727213111667	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.26727213111667	3		420	1054	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0016634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	336	399	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.557261313194646	3	FACETS	0.944	0.905	0.981	0.944	0.905	0.981	CLONAL	3	TRUE	0	0.554310275516965	3		399	547	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074019	8074019	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	151	282	1	ENST00000377482.5:c.640del	p.Thr214ProfsTer33	p.T214Pfs*33	ENST00000377482	NM_018948.3	214	Acc/cc	4/4	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.554310275516965	2		283	509	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105679	11105785	+	splice_donor_variant,intron_variant	Splice_Site	DEL	TATGGTCCTGCCTTCTTGACGTGCGCTCTTCTACATGTGTAGCTGGTACTGCGGGCTCCAGGGGTCACTCCCCAGGGTTACGCCAAGGCATTTCACAGCTCGGAGTT	TATGGTCCTGCCTTCTTGACGTGCGCTCTTCTACATGTGTAGCTGGTACTGCGGGCTCCAGGGGTCACTCCCCAGGGTTACGCCAAGGCATTTCACAGCTCGGAGTT	-	novel	NA	P-0016634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	168	301	0	ENST00000358026.2:c.1593+2_1593+108del		p.X531_splice	ENST00000358026	NM_001128849.1	531			0.557261313194646	3	FACETS	1	0.99	1	0.498	0.461	0.536	CLONAL	1	TRUE	0	0.554310275516965	3		301	518	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142864	30142864	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	80	539	0	ENST00000389048.3:c.662G>T	p.Gly221Val	p.G221V	ENST00000389048	NM_004304.4	221	gGg/gTg	1/29	0.409993619159686	0	FACETS	0.445	0.396	0.497			1	SUBCLONAL	1	TRUE	0	0.554310275516965	0		539	289	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99162516	99162516	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	119	363	0	ENST00000074304.5:c.1034T>A	p.Val345Asp	p.V345D	ENST00000074304	NM_001134224.1	345	gTt/gAt	12/26	0.557261313194646	4	FACETS	1	0.954	1			1	CLONAL	1	TRUE	NA	0.554310275516965	4		363	612	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017766	31017766	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	158	418	0	ENST00000375687.4:c.628C>A	p.Leu210Met	p.L210M	ENST00000375687	NM_015338.5	210	Ctg/Atg	8/13	0.557261313194646	3	FACETS	1	0.945	1	0.519	0.476	0.563	CLONAL	1	TRUE	1	0.554310275516965	3		418	702	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164547	47164588	+	inframe_deletion	In_Frame_Del	DEL	TTGCTTCATTTTCTGAAGTCCTTTTAGATTCTCTTTCTAGTT	TTGCTTCATTTTCTGAAGTCCTTTTAGATTCTCTTTCTAGTT	-	novel	NA	P-0016634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	126	267	0	ENST00000409792.3:c.1538_1579del	p.Lys513_Ala526del	p.K513_A526del	ENST00000409792	NM_014159.6	513	aAACTAGAAAGAGAATCTAAAAGGACTTCAGAAAATGAAGCAAtt/att	3/21	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.554310275516965	2		267	348	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403386	138403590	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGGCCCTACTACTCCCATAAGGCAGTGACTTTCTGCTTGCTATTCATAGGAGATTCACTGCGCAAAGCACAGTCACTTACTAGAGTTCTGAGAGGATAACACATGGGTTCAGGGGTGACTGCAGGTCAGAGAGGGCTTCCCGGTAAGCACTCTGTTTTAAACAGGTATGCATGGCCTCCTTCCCTTTGGCTCTGTTTAACTTCA	CTGGCCCTACTACTCCCATAAGGCAGTGACTTTCTGCTTGCTATTCATAGGAGATTCACTGCGCAAAGCACAGTCACTTACTAGAGTTCTGAGAGGATAACACATGGGTTCAGGGGTGACTGCAGGTCAGAGAGGGCTTCCCGGTAAGCACTCTGTTTTAAACAGGTATGCATGGCCTCCTTCCCTTTGGCTCTGTTTAACTTCA	-	novel	NA	P-0016634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	88	51	0	ENST00000289153.2:c.2192_2315+81del		p.X731_splice	ENST00000289153	NM_006219.2	731		15/22	0.557261313194646	4	FACETS	0.991	0.905	1	0.991	0.905	1	CLONAL	3	TRUE	1	0.554310275516965	4		51	166	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244278	153244278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	109	234	0	ENST00000281708.4:c.1879G>A	p.Val627Met	p.V627M	ENST00000281708	NM_033632.3	627	Gtg/Atg	12/12	0.557261313194646	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.554310275516965	1		234	209	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525936	148525946	+	frameshift_variant	Frame_Shift_Del	DEL	AACTCCACAAA	AACTCCACAAA	-	novel	NA	P-0016634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1228	195	708	0	ENST00000320356.2:c.511_521del	p.Phe171GlyfsTer8	p.F171Gfs*8	ENST00000320356	NM_004456.4	171	TTTGTGGAGTTg/g	6/20	0.554310275516965	5	FACETS	0.906	0.836	0.979	0.302	0.278	0.327	CLONAL	1	TRUE	2	0.554310275516965	5		708	1423	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	183	486	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.951	0.878	1	0.951	0.878	1	CLONAL	1	TRUE	1	0.419260767443717	2		486	918	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198888	67198888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751194292	NA	P-0016636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	181	442	0	ENST00000312629.5:c.359G>A	p.Arg120Gln	p.R120Q	ENST00000312629	NM_003952.2	120	cGg/cAg	5/15	1	2	FACETS	0.934	0.862	1	0.934	0.862	1	CLONAL	1	TRUE	1	0.419260767443717	2		442	924	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12043203	12043203	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0016636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	140	290	0	ENST00000353533.5:c.1086+2T>C		p.X362_splice	ENST00000353533	NM_003010.3	362			0.372745177433133	1	FACETS	0.951	0.87	1	0.951	0.87	1	CLONAL	1	TRUE	0	0.419260767443717	1		290	555	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16046917	16046917	+	splice_region_variant,intron_variant	Splice_Region	SNP	T	T	A	novel	NA	P-0016636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	160	345	0	ENST00000268712.3:c.1173+3A>T		p.X391_splice	ENST00000268712	NM_006311.3	391			0.372745177433133	1	FACETS	0.997	0.918	1	0.997	0.918	1	CLONAL	1	TRUE	0	0.419260767443717	1		345	605	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498333	29498333	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	104	528	0	ENST00000389048.3:c.1847G>T	p.Gly616Val	p.G616V	ENST00000389048	NM_004304.4	616	gGa/gTa	10/29	0.248087038784948	0	FACETS	0.307	0.274	0.342			1	INDETERMINATE	1	TRUE	0	0.419260767443717	0		528	939	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579437	7579437	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	126	684	0	ENST00000269305.4:c.250del	p.Ala84ProfsTer39	p.A84Pfs*39	ENST00000269305	NM_001126112.2	84	Gcc/cc	4/11	1	2	FACETS	0.991	0.898	1	0.991	0.898	1	CLONAL	1	TRUE	1	0.342257436531878	2		684	743	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0016637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	210	930	2	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.342257436531878	2		932	1211	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207064	1207065	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1131690917	NA	P-0016637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	202	810	0	ENST00000326873.7:c.157dup	p.Asp53GlyfsTer110	p.D53Gfs*110	ENST00000326873	NM_000455.4	51	atg/atGg	1/10	0.342257436531878	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.342257436531878	1		810	731	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691093	18691093	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	138	440	0	ENST00000266497.5:c.3204C>A	p.Asp1068Glu	p.D1068E	ENST00000266497		1068	gaC/gaA	23/31	1	2	FACETS	0.97	0.883	1	0.97	0.883	1	CLONAL	1	TRUE	1	0.342257436531878	2		440	831	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420273	49420273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1205083140	NA	P-0016637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	85	794	0	ENST00000301067.7:c.15476G>A	p.Arg5159Gln	p.R5159Q	ENST00000301067	NM_003482.3	5159	cGg/cAg	48/54	1	2	FACETS	0.489	0.431	0.552	0.489	0.431	0.552	SUBCLONAL	1	TRUE	1	0.342257436531878	2		794	1015	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320958	30320958	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1247	296	808	0	ENST00000322652.5:c.1368C>A	p.Asn456Lys	p.N456K	ENST00000322652	NM_015355.2	456	aaC/aaA	12/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.342257436531878	2		808	1543	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687049	37687049	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs151051059	NA	P-0016637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	64	582	0	ENST00000447079.4:c.3953A>G	p.His1318Arg	p.H1318R	ENST00000447079	NM_015083.1	1318	cAt/cGt	14/14	1	2	FACETS	0.439	0.379	0.504	0.439	0.379	0.504	SUBCLONAL	1	TRUE	1	0.342257436531878	2		582	852	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120373	70120373	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1648	259	1717	0	ENST00000245479.2:c.1375G>T	p.Gly459Cys	p.G459C	ENST00000245479	NM_000346.3	459	Ggc/Tgc	3/3	1	2	FACETS	0.794	0.74	0.849	0.794	0.74	0.849	SUBCLONAL	1	TRUE	1	0.342257436531878	2		1717	1907	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599929	10599931	+	inframe_deletion	In_Frame_Del	DEL	GGG	GGG	-	novel	NA	P-0016637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	277	935	0	ENST00000171111.5:c.1645_1647del	p.Pro549del	p.P549del	ENST00000171111	NM_203500.1	549	CCC/-	5/6	0.342257436531878	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.342257436531878	1		935	1054	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509361	106509361	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	228	592	0	ENST00000359195.3:c.1355C>A	p.Ser452Tyr	p.S452Y	ENST00000359195	NM_002649.2	452	tCt/tAt	2/11	0.284453174675882	2	FACETS	1	0.992	1	0.74	0.691	0.791	CLONAL	1	TRUE	0	0.342257436531878	2		592	900	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411325	63411325	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1295086973	NA	P-0016637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	183	788	0	ENST00000330258.3:c.1842C>A	p.His614Gln	p.H614Q	ENST00000330258	NM_152424.3	614	caC/caA	2/2	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.342257436531878	2		788	981	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937930	76937930	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	215	692	0	ENST00000373344.5:c.2818G>T	p.Ala940Ser	p.A940S	ENST00000373344	NM_000489.3	940	Gct/Tct	9/35	1	2	FACETS	0.992	0.921	1	0.992	0.921	1	CLONAL	1	TRUE	1	0.342257436531878	2		692	1266	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0016638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	364	561	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.761893238685047	2		561	937	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100585	67100585	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	289	200	0	ENST00000412916.2:c.283G>T	p.Val95Leu	p.V95L	ENST00000412916		95	Gta/Tta	4/6	0.761893238685047	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.761893238685047	1		200	440	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980034	7980034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369807670	NA	P-0016638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	440	412	0	ENST00000319144.4:c.1303G>A	p.Val435Ile	p.V435I	ENST00000319144	NM_001139.2	435	Gtc/Atc	10/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.761893238685047	2		412	1131	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0016638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	394	501	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.995	0.949	1	0.995	0.949	1	CLONAL	1	TRUE	1	0.761893238685047	2		501	1039	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256412	16256416	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	novel	NA	P-0016638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	517	482	0	ENST00000375759.3:c.3682_3686del	p.Lys1228AspfsTer7	p.K1228Dfs*7	ENST00000375759	NM_015001.2	1226	aAAAAG/a	11/15	1	2	FACETS	0.987	0.946	1	0.987	0.946	1	CLONAL	1	TRUE	1	0.761893238685047	2		482	1375	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261081	16261082	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	381	352	0	ENST00000375759.3:c.8347dup	p.Ser2783LysfsTer30	p.S2783Kfs*30	ENST00000375759	NM_015001.2	2782	-/A	11/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.761893238685047	2		352	970	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804287	43804287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	431	377	0	ENST00000372470.3:c.287C>T	p.Pro96Leu	p.P96L	ENST00000372470	NM_005373.2	96	cCa/cTa	3/12	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.761893238685047	2		377	1130	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959446	26959448	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0016638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	339	361	0	ENST00000381527.3:c.616_618del	p.Leu206del	p.L206del	ENST00000381527	NM_001260.1	205	CTT/-	6/13	1	2	FACETS	0.876	0.83	0.922	0.876	0.83	0.922	CLONAL	1	TRUE	1	0.761893238685047	2		361	1016	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0016639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	276	547	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.332710951777852	3	FACETS	1	0.992	1	0.681	0.639	0.725	CLONAL	1	TRUE	1	0.372935717308975	3		547	1289	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131505	202131505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	123	351	0	ENST00000358485.4:c.473C>T	p.Ser158Phe	p.S158F	ENST00000358485	NM_001080125.1	158	tCt/tTt	2/9	0.332710951777852	3	FACETS	1	0.963	1	0.562	0.509	0.618	CLONAL	1	TRUE	1	0.372935717308975	3		351	696	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127676	2127676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	227	602	1	ENST00000219476.3:c.2915C>T	p.Ala972Val	p.A972V	ENST00000219476	NM_000548.3	972	gCc/gTc	26/42	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.372935717308975	2		603	1030	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820749	3820749	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	271	742	0	ENST00000262367.5:c.2702del	p.Pro901ArgfsTer26	p.P901Rfs*26	ENST00000262367	NM_004380.2	901	cCg/cg	14/31	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.372935717308975	2		742	1364	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533950	63533950	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	58	183	0	ENST00000307078.5:c.1204G>A	p.Glu402Lys	p.E402K	ENST00000307078	NM_004655.3	402	Gaa/Aaa	6/11	0.372935717308975	2	FACETS	0.871	0.752	1	0.436	0.376	0.5	CLONAL	1	TRUE	0	0.372935717308975	2		183	357	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680215	30680215	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	245	563	0	ENST00000376406.3:c.1504G>C	p.Asp502His	p.D502H	ENST00000376406	NM_014641.2	502	Gat/Cat	5/15	0.157850133740406	4	FACETS	1	0.992	1	0.747	0.697	0.798	INDETERMINATE	1	TRUE	2	0.372935717308975	4		563	1208	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894866	101894866	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0016639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	83	257	0	ENST00000374994.4:c.419C>G	p.Ser140Ter	p.S140*	ENST00000374994	NM_004612.2	140	tCa/tGa	3/9	0.372935717308975	2	FACETS	0.991	0.879	1	0.496	0.439	0.556	CLONAL	1	TRUE	0	0.372935717308975	2		257	449	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0016641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	301	599	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.323123374649257	4	FACETS	1	0.993	1	0.718	0.675	0.761	CLONAL	1	TRUE	2	0.497173757221284	4		599	1263	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631839	90631839	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519906	NA	P-0016641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	171	446	0	ENST00000330062.3:c.514A>T	p.Arg172Trp	p.R172W	ENST00000330062	NM_002168.2	172	Agg/Tgg	4/11	1	2	FACETS	0.923	0.851	0.998	0.923	0.851	0.998	CLONAL	1	TRUE	1	0.497173757221284	2		446	745	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246170	46246170	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	156	351	0	ENST00000334344.6:c.4264A>C	p.Thr1422Pro	p.T1422P	ENST00000334344	NM_152641.2	1422	Act/Cct	15/21	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.497173757221284	2		351	611	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210659	2210659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200547302	NA	P-0016641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	308	746	0	ENST00000398665.3:c.1156G>A	p.Val386Met	p.V386M	ENST00000398665	NM_032482.2	386	Gtg/Atg	14/28	1	2	FACETS	0.995	0.938	1	0.995	0.938	1	CLONAL	1	TRUE	1	0.497173757221284	2		746	1245	SUCCESS
APC	324	MSKCC	GRCh37	5	112175842	112175842	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	98	259	0	ENST00000257430.4:c.4551del	p.Asp1519MetfsTer4	p.D1519Mfs*4	ENST00000257430	NM_000038.5	1517	caG/ca	16/16	1	2	FACETS	0.878	0.788	0.973	0.878	0.788	0.973	CLONAL	1	TRUE	1	0.497173757221284	2		259	449	SUCCESS
APC	324	MSKCC	GRCh37	5	112175865	112175896	+	frameshift_variant	Frame_Shift_Del	DEL	TGCCTCCAGTTCAGGAAAATGACAATGGGAAT	TGCCTCCAGTTCAGGAAAATGACAATGGGAAT	-	novel	NA	P-0016641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	84	284	0	ENST00000257430.4:c.4574_4605del	p.Met1525ArgfsTer8	p.M1525Rfs*8	ENST00000257430	NM_000038.5	1525	aTGCCTCCAGTTCAGGAAAATGACAATGGGAAT/a	16/16	1	2	FACETS	0.701	0.621	0.786	0.701	0.621	0.786	SUBCLONAL	1	TRUE	1	0.497173757221284	2		284	482	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55209982	55209982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	141	320	0	ENST00000275493.2:c.92G>A	p.Cys31Tyr	p.C31Y	ENST00000275493	NM_005228.3	31	tGc/tAc	2/28	0.323123374649257	4	FACETS	1	0.921	1	0.505	0.46	0.553	CLONAL	1	TRUE	2	0.497173757221284	4		320	840	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0016642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1417	426	2255	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.648077496422779	4	FACETS	1	0.991	1	0.392	0.372	0.412	CLONAL	1	TRUE	1	0.648077496422779	4		2255	1843	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722761	49722761	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs62262682	NA	P-0016642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	16	22	0	ENST00000449682.2:c.1478G>T	p.Arg493Leu	p.R493L	ENST00000449682	NM_020998.3	493	cGt/cTt	13/18	1	2	FACETS	0.695	0.526	0.886	0.695	0.526	0.886	SUBCLONAL	1	TRUE	1	0.648077496422779	2		22	71	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471614	120471614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1399178397	NA	P-0016642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	145	260	0	ENST00000256646.2:c.3877C>T	p.Arg1293Cys	p.R1293C	ENST00000256646	NM_024408.3	1293	Cgt/Tgt	23/34	1	2	FACETS	0.732	0.671	0.797	0.732	0.671	0.797	SUBCLONAL	1	TRUE	1	0.648077496422779	2		260	611	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124621	108124621	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1298234172	NA	P-0016642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	278	422	0	ENST00000278616.4:c.1979T>C	p.Met660Thr	p.M660T	ENST00000278616	NM_000051.3	660	aTg/aCg	13/63	0.648077496422779	1	FACETS	0.789	0.745	0.834	0.789	0.745	0.834	SUBCLONAL	1	TRUE	0	0.648077496422779	1		422	735	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190718	108190718	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	283	532	0	ENST00000278616.4:c.6385T>A	p.Tyr2129Asn	p.Y2129N	ENST00000278616	NM_000051.3	2129	Tac/Aac	44/63	0.648077496422779	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.648077496422779	1		532	583	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554270	63554270	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs951973598	NA	P-0016642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	541	437	0	ENST00000307078.5:c.469A>G	p.Ile157Val	p.I157V	ENST00000307078	NM_004655.3	157	Ata/Gta	2/11	0.316093320385092	3	FACETS	1	0.988	1	0.703	0.678	0.728	INDETERMINATE	2	TRUE	0	0.648077496422779	3		437	1048	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221309	1221310	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs587776659	NA	P-0016642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	629	524	0	ENST00000326873.7:c.834_835del	p.Cys278TrpfsTer6	p.C278Wfs*6	ENST00000326873	NM_000455.4	278	TGt/t	6/10	0.629505155856635	2	FACETS	0.897	0.869	0.925	0.897	0.869	0.925	CLONAL	2	TRUE	0	0.648077496422779	2		524	1082	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521667	89521667	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	268	416	0	ENST00000336596.2:c.2744C>A	p.Thr915Lys	p.T915K	ENST00000336596	NM_005233.5	915	aCa/aAa	16/17	1	2	FACETS	0.896	0.842	0.951	0.896	0.842	0.951	CLONAL	1	TRUE	1	0.648077496422779	2		416	923	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409851	63409851	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	136	240	0	ENST00000330258.3:c.3316A>G	p.Ser1106Gly	p.S1106G	ENST00000330258	NM_152424.3	1106	Agc/Ggc	2/2	0.336374761069919	1	FACETS	0.628	0.575	0.682	0.628	0.575	0.682	INDETERMINATE	1	TRUE	0	0.648077496422779	1		240	452	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546988	9546988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	187	169	0	ENST00000353224.5:c.1034C>T	p.Ser345Leu	p.S345L	ENST00000353224	NM_177990.2	345	tCa/tTa	5/10	NA	2	FACETS	0.949	0.888	1			1	INDETERMINATE	2	TRUE	NA	0.483056008290938	2		169	408	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097608	27097608	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0016643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	634	526	0	ENST00000324856.7:c.3199-2A>T		p.X1067_splice	ENST00000324856	NM_006015.4	1067			0.483056008290938	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.483056008290938	2		526	1285	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736274	243736274	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	567	487	0	ENST00000263826.5:c.773C>A	p.Ala258Asp	p.A258D	ENST00000263826	NM_005465.4	258	gCc/gAc	8/13	0.483056008290938	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.483056008290938	3		487	1390	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104268976	104268976	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	657	515	0	ENST00000369902.3:c.233G>T	p.Gly78Val	p.G78V	ENST00000369902	NM_016169.3	78	gGg/gTg	2/12	0.483056008290938	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.483056008290938	3		515	1681	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041308	42041308	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0016643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	425	385	0	ENST00000219905.7:c.5504-1G>T		p.X1835_splice	ENST00000219905	NM_001164273.1	1835			0.483056008290938	2	FACETS	0.982	0.941	1	0.982	0.941	1	CLONAL	2	TRUE	0	0.483056008290938	2		385	896	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778017	3778017	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1407	871	926	0	ENST00000262367.5:c.7031G>T	p.Arg2344Leu	p.R2344L	ENST00000262367	NM_004380.2	2344	cGg/cTg	31/31	0.427211707278434	3	FACETS	0.983	0.952	1	0.983	0.952	1	CLONAL	2	TRUE	1	0.483056008290938	3		926	2278	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50810138	50810138	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	551	526	0	ENST00000398568.2:c.962G>T	p.Arg321Ile	p.R321I	ENST00000398568	NM_001042412.1	321	aGa/aTa	6/18	0.483056008290938	3	FACETS	0.975	0.936	1	0.975	0.936	1	CLONAL	2	TRUE	1	0.483056008290938	3		526	1452	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528145	29528146	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0016643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	710	640	0	ENST00000356175.3:c.1153_1154insT	p.Arg385LeufsTer11	p.R385Lfs*11	ENST00000356175	NM_000267.3	385	cgt/cTgt	10/57	0.483056008290938	2	FACETS	0.946	0.915	0.977	0.946	0.915	0.977	CLONAL	2	TRUE	0	0.483056008290938	2		640	1554	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311601	15311601	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	259	67	0	ENST00000263388.2:c.116C>T	p.Ala39Val	p.A39V	ENST00000263388	NM_000435.2	39	gCa/gTa	1/33	0.483056008290938	5	FACETS	1	0.98	1			1	CLONAL	4	TRUE	NA	0.483056008290938	5		67	439	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199900	128199900	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	270	180	0	ENST00000341105.2:c.1405C>A	p.His469Asn	p.H469N	ENST00000341105	NM_032638.4	469	Cac/Aac	6/6	0.483056008290938	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.483056008290938	3		180	641	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356195	66356195	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	507	386	0	ENST00000273854.3:c.1302C>A	p.His434Gln	p.H434Q	ENST00000273854	NM_004439.5	434	caC/caA	5/18	0.425984916779861	4	FACETS	0.988	0.946	1			1	CLONAL	2	TRUE	NA	0.483056008290938	4		386	1575	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564739	86564739	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	331	548	0	ENST00000274376.6:c.471C>G	p.Asp157Glu	p.D157E	ENST00000274376	NM_002890.2	157	gaC/gaG	1/25	0.483056008290938	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.483056008290938	1		548	957	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86676400	86676400	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	137	204	0	ENST00000274376.6:c.2678del	p.Thr893LysfsTer18	p.T893Kfs*18	ENST00000274376	NM_002890.2	893	aCa/aa	20/25	0.483056008290938	1	FACETS	0.973	0.893	1	0.973	0.893	1	CLONAL	1	TRUE	0	0.483056008290938	1		204	442	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671684	30671684	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	476	361	1	ENST00000376406.3:c.5276G>A	p.Gly1759Glu	p.G1759E	ENST00000376406	NM_014641.2	1759	gGa/gAa	10/15	0.483056008290938	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.483056008290938	3		362	1166	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967854	93967854	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1169	302	550	0	ENST00000369303.4:c.2073C>A	p.His691Gln	p.H691Q	ENST00000369303	NM_004440.3	691	caC/caA	11/17	1	2	FACETS	0.85	0.799	0.903	0.85	0.799	0.903	CLONAL	1	TRUE	1	0.483056008290938	2		550	1471	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224349	55224349	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	595	348	0	ENST00000275493.2:c.1130G>T	p.Arg377Met	p.R377M	ENST00000275493	NM_005228.3	377	aGg/aTg	9/28	0.483056008290938	5	FACETS	0.954	0.918	0.991	0.954	0.918	0.991	CLONAL	3	TRUE	2	0.483056008290938	5		348	1484	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372332	55372332	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2654	446	802	0	ENST00000297316.4:c.1022C>A	p.Pro341His	p.P341H	ENST00000297316	NM_022454.3	341	cCc/cAc	2/2	0.483056008290938	6	FACETS	1	0.99	1	0.234	0.222	0.247	CLONAL	1	TRUE	1	0.483056008290938	6		802	3100	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90970980	90970980	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	651	231	0	ENST00000265433.3:c.1097A>G	p.Asp366Gly	p.D366G	ENST00000265433	NM_002485.4	366	gAc/gGc	9/16	0.483056008290938	6	FACETS	0.94	0.912	0.969	0.94	0.912	0.969	CLONAL	5	TRUE	1	0.483056008290938	6		231	1127	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635173	87635173	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	199	338	0	ENST00000277120.3:c.2225T>A	p.Met742Lys	p.M742K	ENST00000277120		742	aTg/aAg	18/19	0.483056008290938	2	FACETS	0.934	0.866	1	0.467	0.433	0.502	CLONAL	1	TRUE	0	0.483056008290938	2		338	882	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250422	110250422	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	603	560	0	ENST00000374672.4:c.253G>T	p.Gly85Cys	p.G85C	ENST00000374672	NM_004235.4	85	Ggt/Tgt	3/5	0.483056008290938	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.483056008290938	2		560	1130	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938566	76938566	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	206	420	0	ENST00000373344.5:c.2182A>T	p.Asn728Tyr	p.N728Y	ENST00000373344	NM_000489.3	728	Aat/Tat	9/35	0.483056008290938	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.483056008290938	1		420	634	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009101	27009102	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	T	novel	NA	P-0016643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	286	258	0	ENST00000335756.4:c.37_38delinsT	p.Pro13Ter	p.P13*	ENST00000335756	NM_001809.3	13	CCg/Tg	1/5	0.483056008290938	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.483056008290938	3		258	706	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	244	423	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.826	0.777	0.876	1	0.994	1	CLONAL	2	TRUE	1	0.455122366203426	2		423	649	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0016645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	692	649	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.455122366203426	1	FACETS	0.949	0.921	0.978	1	0.998	1	CLONAL	2	TRUE	0	0.455122366203426	1		649	1237	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166347	7166347	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	473	740	1	ENST00000302850.5:c.1679A>T	p.Asp560Val	p.D560V	ENST00000302850	NM_000208.2	560	gAc/gTc	8/22	1	2	FACETS	0.781	0.747	0.815	1	0.996	1	SUBCLONAL	2	TRUE	1	0.455122366203426	2		741	1331	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202184	138202184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772293188	NA	P-0016645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	254	374	0	ENST00000237289.4:c.2101C>T	p.Arg701Cys	p.R701C	ENST00000237289	NM_001270507.1	701	Cgc/Tgc	9/9	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.455122366203426	2		374	794	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0016646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	25	476	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	1	2	FACETS	0.093	0.073	0.117	0.093	0.073	0.117	SUBCLONAL	1	TRUE	1	0.461558756276323	2		476	1162	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602757	10602757	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	352	795	0	ENST00000171111.5:c.821A>G	p.His274Arg	p.H274R	ENST00000171111	NM_203500.1	274	cAc/cGc	3/6	0.453848006403909	1	FACETS	0.877	0.83	0.925	0.877	0.83	0.925	CLONAL	1	TRUE	0	0.461558756276323	1		795	1338	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937145	36937145	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	92	604	0	ENST00000361632.4:c.1174G>C	p.Glu392Gln	p.E392Q	ENST00000361632		392	Gag/Cag	9/16	1	2	FACETS	0.32	0.283	0.359	0.32	0.283	0.359	SUBCLONAL	1	TRUE	1	0.461558756276323	2		604	1247	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938243	36938243	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	111	615	2	ENST00000361632.4:c.718G>A	p.Glu240Lys	p.E240K	ENST00000361632		240	Gaa/Aaa	6/16	1	2	FACETS	0.373	0.334	0.415	0.373	0.334	0.415	SUBCLONAL	1	TRUE	1	0.461558756276323	2		617	1289	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999787	100999787	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	231	603	0	ENST00000325455.5:c.15G>T	p.Lys5Asn	p.K5N	ENST00000325455	NM_001202474.3	5	aaG/aaT	1/8	0.453848006403909	1	FACETS	0.982	0.919	1	0.982	0.919	1	CLONAL	1	TRUE	0	0.461558756276323	1		603	784	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989162	41989162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	133	605	0	ENST00000219905.7:c.1954G>A	p.Asp652Asn	p.D652N	ENST00000219905	NM_001164273.1	652	Gat/Aat	3/24	1	2	FACETS	0.456	0.413	0.502	0.456	0.413	0.502	SUBCLONAL	1	TRUE	1	0.461558756276323	2		605	1264	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223403	2223403	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	C	novel	NA	P-0016646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	60	543	0	ENST00000326181.6:c.1012+3G>C		p.X338_splice	ENST00000326181	NM_032271.2	338			1	2	FACETS	0.257	0.22	0.297	0.257	0.22	0.297	SUBCLONAL	1	TRUE	1	0.461558756276323	2		543	1012	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586096	29586096	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	76	509	0	ENST00000356175.3:c.4316A>C	p.His1439Pro	p.H1439P	ENST00000356175	NM_000267.3	1439	cAt/cCt	32/57	1	2	FACETS	0.312	0.272	0.354	0.312	0.272	0.354	SUBCLONAL	1	TRUE	1	0.461558756276323	2		509	1057	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219349	1219349	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	262	668	1	ENST00000326873.7:c.401del	p.Cys134LeufsTer27	p.C134Lfs*27	ENST00000326873	NM_000455.4	134	tGt/tt	3/10	0.453848006403909	1	FACETS	0.832	0.78	0.886	0.832	0.78	0.886	CLONAL	1	TRUE	0	0.461558756276323	1		669	1049	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52676029	52676029	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0016646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1527	94	728	0	ENST00000394830.3:c.1028C>G	p.Ser343Ter	p.S343*	ENST00000394830	NM_018313.4	343	tCa/tGa	11/30	1	2	FACETS	0.251	0.222	0.282	0.251	0.222	0.282	SUBCLONAL	1	TRUE	1	0.461558756276323	2		728	1621	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293946	1293946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2054	593	1382	2	ENST00000310581.5:c.1055C>A	p.Pro352His	p.P352H	ENST00000310581	NM_198253.2	352	cCc/cAc	2/16	1	2	FACETS	0.971	0.929	1	0.971	0.929	1	CLONAL	1	TRUE	1	0.461558756276323	2		1384	2647	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394708	45394709	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0016647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	29	375	0	ENST00000262160.6:c.640_641del	p.Ser214Ter	p.S214*	ENST00000262160	NM_005901.5	214	AGt/t	5/11	0.477588566681081	2	FACETS	0.317	0.254	0.389	0.159	0.127	0.195	SUBCLONAL	1	TRUE	0	0.477588566681081	2		375	383	SUCCESS
APC	324	MSKCC	GRCh37	5	112177478	112177478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	92	621	0	ENST00000257430.4:c.6187C>T	p.His2063Tyr	p.H2063Y	ENST00000257430	NM_000038.5	2063	Cat/Tat	16/16	0.40135832790982	5	FACETS	1	0.947	1	0.542	0.487	0.599	CLONAL	2	TRUE	1	0.477588566681081	5		621	305	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250704	26250704	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	225	626	1	ENST00000446824.2:c.130C>T	p.Pro44Ser	p.P44S	ENST00000446824	NM_021018.2	44	Cct/Tct	1/1	0.477588566681081	18	FACETS	0.951	0.888	1			1	CLONAL	6	TRUE	NA	0.477588566681081	18		627	796	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016647-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	179	423	0				ENST00000310581	NM_198253.2	-/1132			0.228620352570455	5	FACETS	1	0.98	1			1	INDETERMINATE	1	FALSE	NA	0.633117133903258	5		423	930	SUCCESS
APC	324	MSKCC	GRCh37	5	112177478	112177478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016647-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	116	621	0	ENST00000257430.4:c.6187C>T	p.His2063Tyr	p.H2063Y	ENST00000257430	NM_000038.5	2063	Cat/Tat	16/16	0.633117133903258	3	FACETS	0.697	0.629	0.769	0.349	0.314	0.385	SUBCLONAL	1	FALSE	1	0.633117133903258	3		621	692	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250704	26250704	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016647-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	147	626	1	ENST00000446824.2:c.130C>T	p.Pro44Ser	p.P44S	ENST00000446824	NM_021018.2	44	Cct/Tct	1/1	0.633117133903258	3	FACETS	0.794	0.726	0.865	0.397	0.363	0.433	SUBCLONAL	1	FALSE	1	0.633117133903258	3		627	770	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741885	17741885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016647-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	26	281	1	ENST00000250003.3:c.556C>T	p.Pro186Ser	p.P186S	ENST00000250003	NM_002478.4	186	Ccg/Tcg	1/3	0.468443854608702	5	FACETS	0.536	0.425	0.662	0.179	0.141	0.221	SUBCLONAL	1	FALSE	2	0.633117133903258	5		282	299	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664717	138664717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1045933002	NA	P-0016647-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	133	370	0	ENST00000330315.3:c.848C>T	p.Ala283Val	p.A283V	ENST00000330315	NM_023067.3	283	gCa/gTa	1/1	0.633117133903258	3	FACETS	1	0.933	1	0.513	0.468	0.56	CLONAL	1	FALSE	1	0.633117133903258	3		370	539	SUCCESS
APC	324	MSKCC	GRCh37	5	112176395	112176395	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016647-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	56	468	0	ENST00000257430.4:c.5104G>T	p.Gly1702Ter	p.G1702*	ENST00000257430	NM_000038.5	1702	Gga/Tga	16/16	0.633117133903258	3	FACETS	0.431	0.369	0.499	0.216	0.184	0.25	SUBCLONAL	1	FALSE	1	0.633117133903258	3		468	540	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117737429	117737429	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016647-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	47	711	1	ENST00000368508.3:c.220T>A	p.Leu74Ile	p.L74I	ENST00000368508	NM_002944.2	74	Tta/Ata	3/43	0.468836409171366	3	FACETS	0.244	0.205	0.287	0.122	0.102	0.144	SUBCLONAL	1	FALSE	1	0.633117133903258	3		712	801	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835946	151835946	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016647-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	197	771	0	ENST00000262189.6:c.14578G>T	p.Val4860Leu	p.V4860L	ENST00000262189	NM_170606.2	4860	Gtg/Ttg	58/59	0.28057206374027	5	FACETS	1	0.98	1	0.389	0.36	0.42	INDETERMINATE	1	FALSE	2	0.633117133903258	5		771	1039	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772007	135772007	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016647-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	35	432	0	ENST00000298552.3:c.3110G>T	p.Gly1037Val	p.G1037V	ENST00000298552	NM_001162426.1	1037	gGc/gTc	23/23	0.633117133903258	3	FACETS	0.294	0.24	0.354	0.147	0.12	0.177	SUBCLONAL	1	FALSE	1	0.633117133903258	3		432	495	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041236	47041236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016647-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1312	71	1285	0	ENST00000377604.3:c.1664C>T	p.Pro555Leu	p.P555L	ENST00000377604	NM_001204468.1	555	cCc/cTc	15/24	0.633117133903258	3	FACETS	0.214	0.185	0.244	0.107	0.092	0.122	SUBCLONAL	1	FALSE	1	0.633117133903258	3		1285	1383	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533857	533858	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCGCTGTACTCCTCCTGGCC	novel	NA	P-0016648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	416	698	0	ENST00000451590.1:c.178_198dup	p.Gly60_Ala66dup	p.G60_A66dup	ENST00000451590	NM_001130442.1	60	-/GGCCAGGAGGAGTACAGCGCC	3/5	0.732900011044716	2	FACETS	1	0.992	1	0.584	0.558	0.61	CLONAL	1	TRUE	0	0.73785853488307	2		698	966	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533146	63533146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777186938	NA	P-0016648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1564	295	760	2	ENST00000307078.5:c.1748G>A	p.Gly583Glu	p.G583E	ENST00000307078	NM_004655.3	583	gGg/gAg	7/11	0.3168846701814	6	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.73785853488307	6		762	1859	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0016651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	120	636	1	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	NA	2	FACETS	1	0.95	1			1	INDETERMINATE	1	FALSE	NA	0.21063300055187	2		637	1048	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372238	55372238	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	91	612	1	ENST00000297316.4:c.928G>A	p.Gly310Ser	p.G310S	ENST00000297316	NM_022454.3	310	Ggc/Agc	2/2	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	FALSE	1	0.21063300055187	2		613	864	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563093	21563093	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	131	856	1	ENST00000382592.4:c.826C>T	p.Gln276Ter	p.Q276*	ENST00000382592	NM_014572.2	276	Cag/Tag	4/8	0.447385999774857	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.447385999774857	1		857	307	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0016653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	266	599	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.873	0.819	0.928	1	0.994	1	CLONAL	2	TRUE	1	0.291692013873344	2		599	1045	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	139	423	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.81	0.741	0.883	1	0.989	1	CLONAL	2	TRUE	1	0.291692013873344	2		423	588	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115952	8115953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0016655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	104	287	0	ENST00000346208.3:c.1299_1300dup	p.His434ProfsTer42	p.H434Pfs*42	ENST00000346208		433	cac/caCCc	6/6	1	2	FACETS	0.843	0.756	0.934	0.843	0.756	0.934	CLONAL	1	TRUE	1	0.39	2		287	633	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0016656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	68	519	1	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.961	0.838	1	0.961	0.838	1	CLONAL	1	TRUE	1	0.27	2		520	524	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772210	68772210	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121964875	NA	P-0016656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	170	687	0	ENST00000261769.5:c.59G>A	p.Trp20Ter	p.W20*	ENST00000261769	NM_004360.3	20	tGg/tAg	2/16	0.288909031805933	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.27	1		687	1052	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023008	27023010	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs587779737	NA	P-0016656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	10	57	0	ENST00000324856.7:c.126_128del	p.Ala45del	p.A45del	ENST00000324856	NM_006015.4	38	gaGGCg/gag	1/20	1	2	FACETS	0.565	0.385	0.79	0.565	0.385	0.79	SUBCLONAL	1	TRUE	1	0.27	2		57	131	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118815	115118816	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	126	346	1	ENST00000257566.3:c.525_526insT	p.Ala176CysfsTer51	p.A176Cfs*51	ENST00000257566	NM_016569.3	175	-/T	2/8	0.3	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.27	1		347	722	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	101	329	1	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	1	2	FACETS	0.966	0.865	1	1	0.987	1	CLONAL	2	TRUE	1	0.17	2		330	615	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210440	36210440	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	134	472	0	ENST00000222270.7:c.433C>T	p.Arg145Ter	p.R145*	ENST00000222270	NM_014727.1	145	Cga/Tga	2/37	1	2	FACETS	0.851	0.773	0.934	1	0.988	1	CLONAL	2	TRUE	1	0.17	2		472	926	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	27	514	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.274	0.217	0.341	0.274	0.217	0.341	SUBCLONAL	1	TRUE	1	0.17	2		514	1158	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	40	411	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.48	0.397	0.573	0.48	0.397	0.573	SUBCLONAL	1	TRUE	1	0.17	2		411	981	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760967	59760967	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	115	286	0	ENST00000259008.2:c.3440del	p.Asn1147MetfsTer3	p.N1147Mfs*3	ENST00000259008	NM_032043.2	1147	aAt/at	20/20	1	2	FACETS	0.856	0.771	0.946	1	0.986	1	CLONAL	2	TRUE	1	0.17	2		286	790	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553478	29553478	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781807	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1455	87	722	2	ENST00000356175.3:c.2033del	p.Pro678ArgfsTer10	p.P678Rfs*10	ENST00000356175	NM_000267.3	676	aCc/ac	18/57	1	2	FACETS	0.664	0.585	0.749	0.664	0.585	0.749	SUBCLONAL	1	TRUE	1	0.17	2		724	1542	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78923339	78923339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1441841406	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	53	318	0	ENST00000306801.3:c.3362C>T	p.Thr1121Met	p.T1121M	ENST00000306801	NM_020761.2	1121	aCg/aTg	28/34	1	2	FACETS	0.958	0.816	1	0.958	0.816	1	CLONAL	1	TRUE	1	0.17	2		318	651	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	61	325	0	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	0.736	0.633	0.849	0.736	0.633	0.849	SUBCLONAL	1	TRUE	1	0.17	2		325	975	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372193	55372193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753081636	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	117	585	0	ENST00000297316.4:c.883G>A	p.Val295Met	p.V295M	ENST00000297316	NM_022454.3	295	Gtg/Atg	2/2	0.157025491277062	3	FACETS	1	0.981	1	0.699	0.628	0.773	CLONAL	1	TRUE	1	0.17	3		585	1069	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952435	38952435	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138880117	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	58	190	0	ENST00000357387.3:c.2990G>A	p.Arg997His	p.R997H	ENST00000357387	NM_152756.3	997	cGc/cAc	30/38	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.17	2		190	549	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246532	41246532	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357569	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	76	417	2	ENST00000357654.3:c.1016del	p.Lys339ArgfsTer2	p.K339Rfs*2	ENST00000357654	NM_007294.3	339	aAg/ag	10/23	1	2	FACETS	0.835	0.73	0.948	0.835	0.73	0.948	CLONAL	1	TRUE	1	0.17	2		419	1071	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633406	8633406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	123	350	0	ENST00000356435.5:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000356435		88	cGg/cAg	3/35	1	2	FACETS	0.892	0.807	0.982	1	0.988	1	CLONAL	2	TRUE	1	0.17	2		350	811	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125634	47125634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1357325164	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	30	171	1	ENST00000409792.3:c.5636G>A	p.Arg1879His	p.R1879H	ENST00000409792	NM_014159.6	1879	cGc/cAc	12/21	1	2	FACETS	0.846	0.682	1	0.846	0.682	1	CLONAL	1	TRUE	1	0.17	2		172	417	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443655	29443655	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	149	526	0	ENST00000389048.3:c.3562C>T	p.Gln1188Ter	p.Q1188*	ENST00000389048	NM_004304.4	1188	Caa/Taa	23/29	1	2	FACETS	0.862	0.786	0.941	1	0.989	1	CLONAL	2	TRUE	1	0.17	2		526	1017	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131422	202131422	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	41	291	0	ENST00000358485.4:c.390A>T	p.Arg130Ser	p.R130S	ENST00000358485	NM_001080125.1	130	agA/agT	2/9	1	2	FACETS	0.636	0.528	0.757	0.636	0.528	0.757	SUBCLONAL	1	TRUE	1	0.17	2		291	758	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606334	93606334	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs796052158	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	61	533	1	ENST00000375746.1:c.154G>A	p.Ala52Thr	p.A52T	ENST00000375746	NM_001174167.1	52	Gcc/Acc	2/14	1	2	FACETS	0.817	0.703	0.942	0.817	0.703	0.942	CLONAL	1	TRUE	1	0.17	2		534	878	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656840	45656840	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	52	457	1	ENST00000407780.3:c.316del	p.Gln106ArgfsTer11	p.Q106Rfs*11	ENST00000407780	NM_001283052.1	106	Cag/ag	3/7	1	2	FACETS	0.664	0.564	0.775	0.664	0.564	0.775	SUBCLONAL	1	TRUE	1	0.17	2		458	921	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1570	124	814	5	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	0.399845622044195	3	FACETS	0.934	0.842	1	0.467	0.421	0.517	CLONAL	1	TRUE	1	0.17	3		819	1694	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259730	16259730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764509266	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	124	490	0	ENST00000375759.3:c.6995G>A	p.Arg2332His	p.R2332H	ENST00000375759	NM_015001.2	2332	cGc/cAc	11/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.17	2		490	1225	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32449539	32449539	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1271732325	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	83	644	1	ENST00000332351.3:c.835G>A	p.Gly279Ser	p.G279S	ENST00000332351	NM_024426.4	279	Ggc/Agc	3/10	0.291309445961608	2	FACETS	0.81	0.713	0.916	0.405	0.356	0.458	CLONAL	1	TRUE	0	0.17	2		645	1205	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	472178	472178	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372866054	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	150	376	0	ENST00000399788.2:c.623G>A	p.Gly208Asp	p.G208D	ENST00000399788	NM_001042603.1	208	gGc/gAc	5/28	1	2	FACETS	0.9	0.822	0.982	1	0.99	1	CLONAL	2	TRUE	1	0.17	2		376	980	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354604	91354604	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	61	352	0	ENST00000355112.3:c.4048del	p.Thr1350LeufsTer56	p.T1350Lfs*56	ENST00000355112	NM_000057.2	1348	agA/ag	21/22	1	2	FACETS	0.775	0.667	0.894	0.775	0.667	0.894	SUBCLONAL	1	TRUE	1	0.17	2		352	926	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121855	2121855	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	103	421	0	ENST00000219476.3:c.2017G>A	p.Ala673Thr	p.A673T	ENST00000219476	NM_000548.3	673	Gcg/Acg	19/42	1	2	FACETS	0.811	0.726	0.902	1	0.984	1	CLONAL	2	TRUE	1	0.17	2		421	747	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640750	3640750	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	42	373	0	ENST00000294008.3:c.2889G>T	p.Arg963Ser	p.R963S	ENST00000294008	NM_032444.2	963	agG/agT	12/15	1	2	FACETS	0.749	0.624	0.888	0.749	0.624	0.888	SUBCLONAL	1	TRUE	1	0.17	2		373	660	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830791	3830791	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	124	325	0	ENST00000262367.5:c.1765A>G	p.Arg589Gly	p.R589G	ENST00000262367	NM_004380.2	589	Agg/Ggg	8/31	1	2	FACETS	0.938	0.849	1	1	0.989	1	CLONAL	2	TRUE	1	0.17	2		325	778	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826564	50826565	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	88	169	0	ENST00000398568.2:c.2296dup	p.Ile766AsnfsTer14	p.I766Nfs*14	ENST00000398568	NM_001042412.1	763	-/A	15/18	1	2	FACETS	0.941	0.836	1	1	0.984	1	CLONAL	2	TRUE	1	0.17	2		169	550	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559108	29559108	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	23	121	0	ENST00000356175.3:c.3215G>C	p.Ser1072Thr	p.S1072T	ENST00000356175	NM_000267.3	1072	aGc/aCc	25/57	1	2	FACETS	0.798	0.622	1	0.798	0.622	1	CLONAL	1	TRUE	1	0.17	2		121	339	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677765	47677765	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	103	320	1	ENST00000347630.2:c.1100del	p.Pro367HisfsTer5	p.P367Hfs*5	ENST00000347630	NM_001007230.1	367	cCa/ca	11/11	1	2	FACETS	0.787	0.704	0.875	1	0.983	1	SUBCLONAL	2	TRUE	1	0.17	2		321	770	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435833	56435834	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	75	222	0	ENST00000407977.2:c.1303_1304insA	p.Leu435HisfsTer8	p.L435Hfs*8	ENST00000407977		435	cta/cAta	9/10	1	2	FACETS	0.925	0.813	1	1	0.981	1	CLONAL	2	TRUE	1	0.17	2		222	477	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63531786	63531786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373911689	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	155	451	1	ENST00000307078.5:c.2195C>T	p.Thr732Met	p.T732M	ENST00000307078	NM_004655.3	732	aCg/aTg	9/11	1	2	FACETS	0.842	0.769	0.918	1	0.99	1	CLONAL	2	TRUE	1	0.17	2		452	1083	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303293	15303293	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	244	786	0	ENST00000263388.2:c.235del	p.Glu79ArgfsTer157	p.E79Rfs*157	ENST00000263388	NM_000435.2	79	Gag/ag	3/33	1	2	FACETS	1	0.97	1	1	0.995	1	CLONAL	2	TRUE	1	0.17	2		786	1343	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906781	50906781	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1440	107	898	0	ENST00000440232.2:c.1169C>A	p.Pro390His	p.P390H	ENST00000440232	NM_002691.3	390	cCc/cAc	10/27	1	2	FACETS	0.814	0.727	0.907	0.814	0.727	0.907	CLONAL	1	TRUE	1	0.17	2		898	1547	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939998	49939998	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1230	104	711	0	ENST00000296474.3:c.1045del	p.Val349SerfsTer3	p.V349Sfs*3	ENST00000296474	NM_002447.2	349	Gtc/tc	1/20	1	2	FACETS	0.917	0.818	1	0.917	0.818	1	CLONAL	1	TRUE	1	0.17	2		711	1334	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518298	187518299	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	32	139	0	ENST00000441802.2:c.12395_12396del	p.Ser4132TrpfsTer11	p.S4132Wfs*11	ENST00000441802	NM_005245.3	4132	tCT/t	25/27	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.17	2		139	313	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520527	176520527	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	204	680	0	ENST00000292408.4:c.1372C>T	p.Pro458Ser	p.P458S	ENST00000292408	NM_213647.1	458	Cca/Tca	10/18	1	2	FACETS	0.952	0.881	1	1	0.993	1	CLONAL	2	TRUE	1	0.17	2		680	1261	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20483144	20483144	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	80	293	0	ENST00000346618.3:c.877A>G	p.Asn293Asp	p.N293D	ENST00000346618	NM_001949.4	293	Aat/Gat	4/7	0.157025491277062	3	FACETS	1	0.972	1	0.697	0.613	0.787	CLONAL	1	TRUE	1	0.17	3		293	733	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911111	29911119	+	inframe_deletion	In_Frame_Del	DEL	ACCGGCAGG	ACCGGCAGG	-	rs1554316318	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	94	459	0	ENST00000376809.5:c.412_420del	p.Arg138_Asp140del	p.R138_D140del	ENST00000376809	NM_002116.7	137	tACCGGCAGGac/tac	3/8	0.157025491277062	3	FACETS	1	0.977	1	0.701	0.623	0.784	CLONAL	1	TRUE	1	0.17	3		459	856	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522526	157522526	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1448	212	901	0	ENST00000346085.5:c.4802del	p.Pro1601GlnfsTer13	p.P1601Qfs*13	ENST00000346085	NM_020732.3	1600	Ccc/cc	18/20	1	2	FACETS	0.751	0.695	0.81	1	0.991	1	SUBCLONAL	2	TRUE	1	0.17	2		901	1660	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729771	41729771	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	67	241	0	ENST00000242208.4:c.758G>T	p.Ser253Ile	p.S253I	ENST00000242208	NM_002192.2	253	aGc/aTc	3/3	1	2	FACETS	0.759	0.661	0.866	1	0.973	1	SUBCLONAL	2	TRUE	1	0.17	2		241	519	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859766	151859767	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	25	151	0	ENST00000262189.6:c.10895dup	p.Pro3633ThrfsTer19	p.P3633Tfs*19	ENST00000262189	NM_170606.2	3632	cca/ccCa	43/59	1	2	FACETS	0.786	0.62	0.978	0.786	0.62	0.978	CLONAL	1	TRUE	1	0.17	2		151	374	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880171	151880171	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	50	323	0	ENST00000262189.6:c.5153G>T	p.Arg1718Met	p.R1718M	ENST00000262189	NM_170606.2	1718	aGg/aTg	35/59	1	2	FACETS	0.723	0.611	0.846	0.723	0.611	0.846	SUBCLONAL	1	TRUE	1	0.17	2		323	814	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117875468	117875468	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	104	359	1	ENST00000297338.2:c.175C>T	p.Leu59Phe	p.L59F	ENST00000297338	NM_006265.2	59	Ctc/Ttc	3/14	0.399845622044195	3	FACETS	1	0.97	1	0.621	0.555	0.692	CLONAL	1	TRUE	1	0.17	3		360	1069	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929412	44929415	+	frameshift_variant	Frame_Shift_Del	DEL	ACAA	ACAA	-	rs786205676	NA	P-0016657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	214	390	0	ENST00000377967.4:c.2515_2518del	p.Asn839ValfsTer27	p.N839Vfs*27	ENST00000377967	NM_021140.2	838	ACAAac/ac	17/29	1	1	FACETS	0.92	0.856	0.985	1	0.995	1	CLONAL	3	TRUE	0	0.17	1		390	835	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0016659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	84	683	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		683	1069	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	273	641	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.9	0.844	0.958	1	0.995	1	CLONAL	2	TRUE	1	0.253213912723667	2		641	1198	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0016660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	125	379	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.253213912723667	2		380	735	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577595	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0016660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	152	413	0	ENST00000269305.4:c.686dup	p.Cys229TrpfsTer11	p.C229Wfs*11	ENST00000269305	NM_001126112.2	229	tgt/tgGt	7/11	0.203447051939746	2	FACETS	1	0.986	1	0.703	0.643	0.766	CLONAL	1	TRUE	0	0.253213912723667	2		413	854	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974758	21974771	+	frameshift_variant	Frame_Shift_Del	DEL	ACCCCGGGCCGCGG	ACCCCGGGCCGCGG	C	novel	NA	P-0016660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	66	247	0	ENST00000304494.5:c.56_69delinsG	p.Ala19GlyfsTer3	p.A19Gfs*3	ENST00000304494	NM_000077.4	19	gCCGCGGCCCGGGGT/gG	1/3	0.253213912723667	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.253213912723667	1		247	420	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0016661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	43	730	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	1	2	FACETS	0.977	0.817	1	0.977	0.817	1	CLONAL	1	TRUE	1	0.17	2		730	518	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36824360	36824360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755810424	NA	P-0016661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	77	465	2	ENST00000373129.3:c.176C>T	p.Thr59Met	p.T59M	ENST00000373129	NM_032017.1	59	aCg/aTg	4/12	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.17	2		467	668	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202276	138202276	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	39	503	0	ENST00000237289.4:c.2193G>T	p.Glu731Asp	p.E731D	ENST00000237289	NM_001270507.1	731	gaG/gaT	9/9	0.245972218971842	5	FACETS	0.862	0.713	1			1	CLONAL	1	TRUE	NA	0.17	5		503	668	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0016663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	245	591	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.605301073474707	1	FACETS	0.938	0.883	0.993	0.938	0.883	0.993	CLONAL	1	TRUE	0	0.605301073474707	1		592	602	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0016663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	207	514	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.794	0.738	0.852	0.794	0.738	0.852	SUBCLONAL	1	TRUE	1	0.605301073474707	2		514	861	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028790	47028790	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	433	390	1	ENST00000377604.3:c.94C>T	p.Arg32Ter	p.R32*	ENST00000377604	NM_001204468.1	32	Cga/Tga	3/24	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.605301073474707	1		391	759	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670492	246670492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	289	578	1	ENST00000388985.4:c.28G>A	p.Ala10Thr	p.A10T	ENST00000388985		10	Gca/Aca	1/12	1	2	FACETS	0.922	0.868	0.977	0.922	0.868	0.977	CLONAL	1	TRUE	1	0.605301073474707	2		579	1036	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265684	41266624	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACCTTTTGCTCCATTTTCTGCTCACTCCTCCTAATGGCTTGGTGAAATAGCAAACAAGCCACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTA	ACCTTTTGCTCCATTTTCTGCTCACTCCTCCTAATGGCTTGGTGAAATAGCAAACAAGCCACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTA	-	novel	NA	P-0016663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	179	56	0	ENST00000349496.5:c.13+114_423del		p.X5_splice	ENST00000349496	NM_001904.3	5		3-4/15	1	2	FACETS	1	0.972	1	1	0.994	1	CLONAL	2	TRUE	1	0.605301073474707	2		56	283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0016665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	143	904	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.210763383886328	1	FACETS	0.875	0.795	0.959	0.875	0.795	0.959	CLONAL	1	TRUE	0	0.210763383886328	1		905	1388	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0016667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	272	547	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.410759549659342	3	FACETS	0.918	0.864	0.974	0.918	0.864	0.974	CLONAL	2	TRUE	1	0.410333752781056	3		547	870	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561492	141561492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1620	141	443	0	ENST00000220592.5:c.1313G>A	p.Arg438Gln	p.R438Q	ENST00000220592	NM_012154.3	438	cGg/cAg	11/19	0.410333752781056	8	FACETS	0.871	0.79	0.956	0.145	0.131	0.16	CLONAL	1	TRUE	2	0.410333752781056	8		443	1761	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	157	423	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.620274143973203	2		423	458	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888189	112888189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507511	NA	P-0016684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	150	1103	0	ENST00000351677.2:c.205G>A	p.Glu69Lys	p.E69K	ENST00000351677	NM_002834.3	69	Gag/Aag	3/16	1	2	FACETS	0.904	0.831	0.979	0.904	0.831	0.979	CLONAL	1	TRUE	1	0.620274143973203	2		1103	535	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679366	29679366	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs866445127	NA	P-0016684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	147	677	0	ENST00000356175.3:c.7486C>T	p.Arg2496Ter	p.R2496*	ENST00000356175	NM_000267.3	2496	Cga/Tga	50/57	1	2	FACETS	0.924	0.849	1	0.924	0.849	1	CLONAL	1	TRUE	1	0.620274143973203	2		677	513	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667616	29667616	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1060500359	NA	P-0016684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	220	1133	1	ENST00000356175.3:c.6952G>T	p.Glu2318Ter	p.E2318*	ENST00000356175	NM_000267.3	2318	Gaa/Taa	46/57	1	2	FACETS	0.938	0.876	1	0.938	0.876	1	CLONAL	1	TRUE	1	0.620274143973203	2		1134	756	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	177	486	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.183404681665865	2	FACETS	0.874	0.807	0.943	1	0.986	1	CLONAL	3	TRUE	0	0.183404681665865	2		486	736	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0016686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	167	1033	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.183404681665865	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.183404681665865	1		1033	1187	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0016686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	258	853	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	0.183404681665865	2	FACETS	0.859	0.804	0.915	1	0.99	1	CLONAL	3	TRUE	0	0.183404681665865	2		853	1092	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458085	120458086	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0016686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	50	422	0	ENST00000256646.2:c.7259_7260del	p.Glu2420ValfsTer3	p.E2420Vfs*3	ENST00000256646	NM_024408.3	2420	gAG/g	34/34	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.183404681665865	2		422	507	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060782	38060784	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0016686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	84	1188	1	ENST00000250448.2:c.1205_1207del	p.Ile402del	p.I402del	ENST00000250448	NM_004496.3	402	aTCAac/aac	2/2	1	2	FACETS	0.897	0.79	1	0.897	0.79	1	CLONAL	1	TRUE	1	0.183404681665865	2		1189	1021	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354375	354375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910854855	NA	P-0016686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	104	728	1	ENST00000262320.3:c.1183C>T	p.Arg395Cys	p.R395C	ENST00000262320	NM_003502.3	395	Cgc/Tgc	5/11	0.183404681665865	3	FACETS	1	0.965	1	0.595	0.532	0.663	CLONAL	1	TRUE	1	0.183404681665865	3		729	1040	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779598	3779598	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	148	934	0	ENST00000262367.5:c.5450C>T	p.Pro1817Leu	p.P1817L	ENST00000262367	NM_004380.2	1817	cCg/cTg	31/31	0.183404681665865	3	FACETS	1	0.984	1	0.689	0.627	0.754	CLONAL	1	TRUE	1	0.183404681665865	3		934	1279	SUCCESS
ATR	545	MSKCC	GRCh37	3	142285047	142285047	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	46	650	0	ENST00000350721.4:c.208G>C	p.Asp70His	p.D70H	ENST00000350721	NM_001184.3	70	Gat/Cat	3/47	0.183404681665865	2	FACETS	0.68	0.571	0.8	0.34	0.285	0.4	SUBCLONAL	1	TRUE	0	0.183404681665865	2		650	738	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751896	57751896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	54	611	0	ENST00000274289.3:c.1341G>A	p.Met447Ile	p.M447I	ENST00000274289	NM_006622.3	447	atG/atA	10/14	0.183404681665865	1	FACETS	0.773	0.659	0.898	0.773	0.659	0.898	SUBCLONAL	1	TRUE	0	0.183404681665865	1		611	692	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540162	23540162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	23	490	0	ENST00000380871.4:c.241C>T	p.Arg81Cys	p.R81C	ENST00000380871	NM_006167.3	81	Cgc/Tgc	1/2	0.183404681665865	1	FACETS	0.699	0.545	0.877	0.699	0.545	0.877	SUBCLONAL	1	TRUE	0	0.183404681665865	1		490	326	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043465	180043465	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1451816005	NA	P-0016687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	117	690	3	ENST00000261937.6:c.3121C>T	p.Arg1041Trp	p.R1041W	ENST00000261937	NM_182925.4	1041	Cgg/Tgg	23/30	0.581744780612619	2	FACETS	0.956	0.869	1	0.478	0.434	0.524	CLONAL	1	TRUE	0	0.580030540028044	2		693	422	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778359	3778359	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	21	486	0	ENST00000262367.5:c.6689A>C	p.Gln2230Pro	p.Q2230P	ENST00000262367	NM_004380.2	2230	cAg/cCg	31/31	0.581744780612619	4	FACETS	0.311	0.239	0.395	0.104	0.079	0.132	SUBCLONAL	1	TRUE	1	0.580030540028044	4		486	368	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825543	50825543	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	253	612	0	ENST00000398568.2:c.2174C>G	p.Pro725Arg	p.P725R	ENST00000398568	NM_001042412.1	725	cCc/cGc	14/18	0.581744780612619	4	FACETS	0.992	0.933	1			1	CLONAL	2	TRUE	NA	0.580030540028044	4		612	695	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574005	7574008	+	frameshift_variant	Frame_Shift_Del	DEL	AACA	AACA	-	novel	NA	P-0016687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	850	955	0	ENST00000269305.4:c.1019_1022del	p.Met340ThrfsTer4	p.M340Tfs*4	ENST00000269305	NM_001126112.2	340	aTGTTc/ac	10/11	0.580030540028044	7	FACETS	0.977	0.959	0.994			1	CLONAL	7	TRUE	NA	0.580030540028044	7		955	1050	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17940883	17940914	+	splice_region_variant,intron_variant	Splice_Region	DEL	ACTGGGAAACTGAGGCTAGCCCTGCGGCGCTC	ACTGGGAAACTGAGGCTAGCCCTGCGGCGCTC	-	novel	NA	P-0016687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	97	947	0	ENST00000458235.1:c.3207+3_3207+34del		p.X1069_splice	ENST00000458235	NM_000215.3	1069			0.581744780612619	3	FACETS	0.612	0.546	0.683	0.306	0.273	0.342	SUBCLONAL	1	TRUE	1	0.580030540028044	3		947	705	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799267	42799267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1228159994	NA	P-0016687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	73	585	0	ENST00000575354.2:c.4751G>A	p.Gly1584Glu	p.G1584E	ENST00000575354	NM_015125.3	1584	gGa/gAa	20/20	0.581744780612619	2	FACETS	0.809	0.714	0.91	0.405	0.357	0.455	CLONAL	1	TRUE	0	0.580030540028044	2		585	311	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470570	25470583	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGCAGTTTCCCC	CCCGCAGTTTCCCC	TCCA	novel	NA	P-0016687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	142	1155	5	ENST00000264709.3:c.891_904delinsTGGA	p.Trp297CysfsTer16	p.W297Cfs*16	ENST00000264709	NM_175629.2	297	tgGGGGAAACTGCGGGgc/tgTGGAgc	8/23	0.581744780612619	3	FACETS	0.779	0.71	0.851	0.389	0.355	0.426	SUBCLONAL	1	TRUE	1	0.580030540028044	3		1160	811	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023753	27023753	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1383675220	NA	P-0016689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	102	865	1	ENST00000324856.7:c.862del	p.Gln288SerfsTer75	p.Q288Sfs*75	ENST00000324856	NM_006015.4	287	Ccc/cc	1/20	1	2	FACETS	0.62	0.556	0.688	0.62	0.556	0.688	SUBCLONAL	1	TRUE	1	0.565308258852311	2		866	582	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692816	89692817	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554898084	NA	P-0016689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	269	509	0	ENST00000371953.3:c.301dup	p.Ile101AsnfsTer6	p.I101Nfs*6	ENST00000371953	NM_000314.4	100	-/A	5/9	0.524605869696449	2	FACETS	0.983	0.935	1	0.983	0.935	1	CLONAL	2	TRUE	0	0.565308258852311	2		509	484	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871244	35871244	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	176	703	0	ENST00000216797.5:c.929T>G	p.Phe310Cys	p.F310C	ENST00000216797	NM_020529.2	310	tTt/tGt	6/6	1	2	FACETS	0.875	0.808	0.944	0.875	0.808	0.944	CLONAL	1	TRUE	1	0.565308258852311	2		703	712	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844099	68844099	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0016689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	132	618	0	ENST00000261769.5:c.688-1G>A		p.X230_splice	ENST00000261769	NM_004360.3	230			0.559877963396331	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.565308258852311	1		618	326	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402786	139402786	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	184	1061	1	ENST00000277541.6:c.3223T>A	p.Trp1075Arg	p.W1075R	ENST00000277541	NM_017617.3	1075	Tgg/Agg	20/34	1	2	FACETS	0.875	0.81	0.942	0.875	0.81	0.942	CLONAL	1	TRUE	1	0.565308258852311	2		1062	744	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061191	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016689-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	18	476	0	ENST00000250448.2:c.798C>G	p.Phe266Leu	p.F266L	ENST00000250448	NM_004496.3	266	ttC/ttG	2/2	1	2	FACETS	0.209	0.157	0.269	0.209	0.157	0.269	SUBCLONAL	1	TRUE	1	0.685008131302537	2		476	252	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692816	89692817	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554898084	NA	P-0016689-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	377	509	0	ENST00000371953.3:c.301dup	p.Ile101AsnfsTer6	p.I101Nfs*6	ENST00000371953	NM_000314.4	100	-/A	5/9	0.685008131302537	2	FACETS	0.966	0.931	1	0.966	0.931	1	CLONAL	2	TRUE	0	0.685008131302537	2		509	570	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871244	35871244	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016689-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	246	703	0	ENST00000216797.5:c.929T>G	p.Phe310Cys	p.F310C	ENST00000216797	NM_020529.2	310	tTt/tGt	6/6	1	2	FACETS	0.981	0.921	1	0.981	0.921	1	CLONAL	1	TRUE	1	0.685008131302537	2		703	732	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844099	68844099	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0016689-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	172	618	0	ENST00000261769.5:c.688-1G>A		p.X230_splice	ENST00000261769	NM_004360.3	230			0.685008131302537	1	FACETS	0.907	0.848	0.967	0.907	0.848	0.967	CLONAL	1	TRUE	0	0.685008131302537	1		618	364	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402786	139402786	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016689-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	334	1061	1	ENST00000277541.6:c.3223T>A	p.Trp1075Arg	p.W1075R	ENST00000277541	NM_017617.3	1075	Tgg/Agg	20/34	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.685008131302537	2		1062	934	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0016690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	216	791	1	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.210164130499961	4	FACETS	0.991	0.92	1	0.991	0.92	1	CLONAL	2	TRUE	2	0.233610948526979	4		792	1151	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209090	133209090	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	98	341	0	ENST00000320574.5:c.6141G>C	p.Met2047Ile	p.M2047I	ENST00000320574	NM_006231.2	2047	atG/atC	45/49	0.220927126007692	2	FACETS	0.976	0.876	1	0.976	0.876	1	CLONAL	2	TRUE	0	0.233610948526979	2		341	430	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845547	128845547	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	165	700	0	ENST00000249373.3:c.844C>A	p.Leu282Met	p.L282M	ENST00000249373	NM_005631.4	282	Ctg/Atg	4/12	0.210164130499961	4	FACETS	0.892	0.818	0.968	0.892	0.818	0.968	CLONAL	2	TRUE	2	0.233610948526979	4		700	977	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032374	42032374	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	63	597	0	ENST00000219905.7:c.4558G>C	p.Ala1520Pro	p.A1520P	ENST00000219905	NM_001164273.1	1520	Gcg/Ccg	14/24	0.220535048358655	1	FACETS	0.742	0.641	0.851	0.742	0.641	0.851	SUBCLONAL	1	TRUE	0	0.233610948526979	1		597	642	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88671966	88671966	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0016690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	96	804	0	ENST00000360948.2:c.1205-1G>A		p.X402_splice	ENST00000360948	NM_001012338.2	402			1	2	FACETS	0.821	0.73	0.919	0.821	0.73	0.919	CLONAL	1	TRUE	1	0.233610948526979	2		804	1001	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577148	7577163	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GATTACCACTACTCAG	GATTACCACTACTCAG	-	novel	NA	P-0016690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	273	868	0	ENST00000269305.4:c.783-8_790del		p.X261_splice	ENST00000269305	NM_001126112.2	261		8/11	0.233610948526979	3	FACETS	1	0.987	1			1	CLONAL	2	TRUE	NA	0.233610948526979	3		868	1104	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541477	29541478	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0016690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	103	363	0	ENST00000356175.3:c.1401_1402del	p.Phe468Ter	p.F468*	ENST00000356175	NM_000267.3	467	acATtt/actt	13/57	NA	2	FACETS	0.87	0.781	0.962			1	INDETERMINATE	2	TRUE	NA	0.233610948526979	2		363	507	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660678	227660678	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	271	743	0	ENST00000305123.5:c.2777A>G	p.Gln926Arg	p.Q926R	ENST00000305123	NM_005544.2	926	cAg/cGg	1/2	0.166003360838332	3	FACETS	0.896	0.842	0.951	0.896	0.842	0.951	CLONAL	3	TRUE	0	0.233610948526979	3		743	964	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610644	52610647	+	frameshift_variant	Frame_Shift_Del	DEL	TTTC	TTTC	-	novel	NA	P-0016690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	178	685	0	ENST00000394830.3:c.3526_3529del	p.Glu1176GlnfsTer16	p.E1176Qfs*16	ENST00000394830	NM_018313.4	1176	GAAAca/ca	23/30	0.220927126007692	2	FACETS	0.881	0.812	0.952	0.881	0.812	0.952	CLONAL	2	TRUE	0	0.233610948526979	2		685	865	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335615	81335615	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	168	641	1	ENST00000222390.5:c.1745T>A	p.Met582Lys	p.M582K	ENST00000222390	NM_000601.4	582	aTg/aAg	15/18	0.210164130499961	4	FACETS	0.955	0.878	1	0.955	0.878	1	CLONAL	2	TRUE	2	0.233610948526979	4		642	929	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038858	47038894	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CAGGGCTCGGAGCCAAGCTCAGAGAACGCCAATGACA	CAGGGCTCGGAGCCAAGCTCAGAGAACGCCAATGACA	ATGATG	novel	NA	P-0016690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	56	495	0	ENST00000377604.3:c.865_901delinsATGATG	p.Gln289MetfsTer9	p.Q289Mfs*9	ENST00000377604	NM_001204468.1	289	CAGGGCTCGGAGCCAAGCTCAGAGAACGCCAATGACAcc/ATGATGcc	9/24	1	1	FACETS	0.873	0.749	1	0.873	0.749	1	CLONAL	1	TRUE	0	0.233610948526979	1		495	485	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	213	423	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.690346114254804	2		423	535	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711992	89711992	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	90	436	0	ENST00000371953.3:c.611del	p.Pro204GlnfsTer17	p.P204Qfs*17	ENST00000371953	NM_000314.4	204	Cca/ca	6/9	0.690346114254804	1	FACETS	0.981	0.896	1	0.981	0.896	1	CLONAL	1	TRUE	0	0.690346114254804	1		436	174	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026871	71026871	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	138	343	1	ENST00000318789.4:c.1351G>T	p.Asp451Tyr	p.D451Y	ENST00000318789	NM_032682.5	451	Gat/Tat	16/21	0.756787457182376	2	FACETS	0.97	0.918	1	0.97	0.918	1	CLONAL	2	TRUE	0	0.756787457182376	2		344	188	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258696	115258696	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	314	405	0	ENST00000369535.4:c.86T>C	p.Val29Ala	p.V29A	ENST00000369535	NM_002524.4	29	gTa/gCa	2/7	0.338714965629858	4	FACETS	1	0.991	1	1	0.991	1	INDETERMINATE	2	TRUE	2	0.756787457182376	4		405	628	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850850	63850850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	464	615	1	ENST00000279873.7:c.1628C>T	p.Pro543Leu	p.P543L	ENST00000279873	NM_032199.2	543	cCa/cTa	10/10	0.756787457182376	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.756787457182376	2		616	613	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998537	100998538	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0016692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	479	625	1	ENST00000325455.5:c.1264_1265delinsAA	p.Pro422Lys	p.P422K	ENST00000325455	NM_001202474.3	422	CCg/AAg	1/8	0.580302685315491	4	FACETS	0.842	0.806	0.879	0.842	0.806	0.879	CLONAL	2	TRUE	2	0.756787457182376	4		626	1320	SUCCESS
CBL	867	MSKCC	GRCh37	11	119158586	119158586	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	479	999	0	ENST00000264033.4:c.1967del	p.Gly656ValfsTer46	p.G656Vfs*46	ENST00000264033	NM_005188.3	656	Ggt/gt	12/16	NA	2	FACETS	0.965	0.937	0.992			1	INDETERMINATE	2	TRUE	NA	0.756787457182376	2		999	656	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112127	115112127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	1257	1053	0	ENST00000257566.3:c.1613G>C	p.Gly538Ala	p.G538A	ENST00000257566	NM_016569.3	538	gGc/gCc	7/8	0.756787457182376	5	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	2	0.756787457182376	5		1053	2232	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027168	49027168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913305	NA	P-0016692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	177	797	1	ENST00000267163.4:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	579	Cga/Tga	18/27	0.756787457182376	2	FACETS	0.995	0.95	1	0.995	0.95	1	CLONAL	2	TRUE	0	0.756787457182376	2		798	235	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031814	10031814	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0016692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	561	589	0	ENST00000330684.3:c.1007+2T>A		p.X336_splice	ENST00000330684	NM_001134407.1	336			0.756787457182376	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.756787457182376	2		589	690	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782177	NA	P-0016692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	1031	795	1	ENST00000269305.4:c.644G>T	p.Ser215Ile	p.S215I	ENST00000269305	NM_001126112.2	215	aGt/aTt	6/11	0.756787457182376	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.756787457182376	2		796	1319	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600470	10600470	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	1434	992	0	ENST00000171111.5:c.1385G>T	p.Gly462Val	p.G462V	ENST00000171111	NM_203500.1	462	gGg/gTg	4/6	0.756787457182376	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.756787457182376	3		992	1693	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383074	42383074	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	183	438	2	ENST00000221972.3:c.94G>T	p.Ala32Ser	p.A32S	ENST00000221972	NM_021601.3	32	Gcc/Tcc	2/5	0.5278353191143	3	FACETS	1	0.951	1			1	CLONAL	1	TRUE	NA	0.756787457182376	3		440	645	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549409	187549409	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	559	721	2	ENST00000441802.2:c.4709G>T	p.Arg1570Leu	p.R1570L	ENST00000441802	NM_005245.3	1570	cGg/cTg	9/27	0.706367110101209	3	FACETS	0.951	0.917	0.984	0.951	0.917	0.984	CLONAL	2	TRUE	1	0.756787457182376	3		723	1071	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117746757	117746757	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	228	747	1	ENST00000368508.3:c.63G>C	p.Trp21Cys	p.W21C	ENST00000368508	NM_002944.2	21	tgG/tgC	1/43	0.756787457182376	6	FACETS	0.838	0.782	0.896			1	CLONAL	2	TRUE	NA	0.756787457182376	6		748	904	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945004	151945004	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0016692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	11	81	0	ENST00000262189.6:c.2515A>T	p.Arg839Ter	p.R839*	ENST00000262189	NM_170606.2	839	Aga/Tga	14/59	0.755424343666864	3	FACETS	0.89	0.636	1	0.297	0.212	0.395	CLONAL	1	TRUE	0	0.756787457182376	3		81	45	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	605	641	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.388325773574172	8	FACETS	1	0.989	1			1	CLONAL	7	TRUE	NA	0.388325773574172	8		641	931	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0016693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	70	486	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.388325773574172	12	FACETS	0.86	0.747	0.983			1	CLONAL	1	TRUE	NA	0.388325773574172	12		486	1233	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942685	48942685	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913301	NA	P-0016693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	141	569	1	ENST00000267163.4:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000267163	NM_000321.2	358	Cga/Tga	11/27	NA	2	FACETS	1	0.939	1			1	INDETERMINATE	2	TRUE	NA	0.388325773574172	2		570	356	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123353315	123353315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3750819	NA	P-0016693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	300	944	0	ENST00000358487.5:c.17G>A	p.Arg6His	p.R6H	ENST00000358487	NM_000141.4	6	cGt/cAt	2/18	0.388325773574172	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.388325773574172	3		944	868	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578530	7578530	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs267605077	NA	P-0016693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	565	1372	0	ENST00000269305.4:c.400T>A	p.Phe134Ile	p.F134I	ENST00000269305	NM_001126112.2	134	Ttt/Att	5/11	0.388325773574172	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.388325773574172	3		1372	1093	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152567	56152581	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGGGCCTGTGGTAA	GAGGGCCTGTGGTAA	-	novel	NA	P-0016693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	63	327	0	ENST00000399503.3:c.624_633+5del		p.X208_splice	ENST00000399503	NM_005921.1	208		2/20	0.388325773574172	4	FACETS	1	0.972	1	0.743	0.648	0.845	CLONAL	1	TRUE	2	0.388325773574172	4		327	303	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394867	394867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202124383	NA	P-0016693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	228	462	1	ENST00000380956.4:c.263C>T	p.Pro88Leu	p.P88L	ENST00000380956	NM_001195286.1	88	cCg/cTg	3/9	0.388325773574172	5	FACETS	0.988	0.927	1	0.988	0.927	1	CLONAL	3	TRUE	2	0.388325773574172	5		463	627	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220281	55220281	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759106015	NA	P-0016693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	261	862	8	ENST00000275493.2:c.671G>A	p.Arg224His	p.R224H	ENST00000275493	NM_005228.3	224	cGt/cAt	6/28	0.388325773574172	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	1	0.388325773574172	3		870	795	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	43	641	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.719	0.6	0.853	0.719	0.6	0.853	SUBCLONAL	1	FALSE	1	0.13983928181816	2		641	855	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0016694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	27	480	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.688	0.546	0.852	0.688	0.546	0.852	SUBCLONAL	1	FALSE	1	0.13983928181816	2		480	561	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879549	151879549	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	25	367	0	ENST00000262189.6:c.5396C>A	p.Ser1799Ter	p.S1799*	ENST00000262189	NM_170606.2	1799	tCa/tAa	36/59	1	2	FACETS	0.924	0.728	1	0.924	0.728	1	CLONAL	1	FALSE	1	0.13983928181816	2		367	387	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015010	37015010	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	23	462	0	ENST00000358127.4:c.394G>T	p.Val132Phe	p.V132F	ENST00000358127	NM_001280556.1	132	Gtc/Ttc	3/10	0.13983928181816	1	FACETS	0.737	0.574	0.927	0.737	0.574	0.927	CLONAL	1	FALSE	0	0.13983928181816	1		462	415	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0016695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	96	731	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.163066483578018	4	FACETS	1	0.957	1	0.572	0.51	0.639	INDETERMINATE	1	TRUE	2	0.327404203431391	4		731	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577505	7577505	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs745425759	NA	P-0016695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	54	526	0	ENST00000269305.4:c.776A>T	p.Asp259Val	p.D259V	ENST00000269305	NM_001126112.2	259	gAc/gTc	7/11	1	2	FACETS	0.773	0.661	0.894	0.773	0.661	0.894	SUBCLONAL	1	TRUE	1	0.327404203431391	2		526	427	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074288	8074288	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	55	572	0	ENST00000377482.5:c.371G>T	p.Cys124Phe	p.C124F	ENST00000377482	NM_018948.3	124	tGt/tTt	4/4	1	2	FACETS	0.61	0.522	0.706	0.61	0.522	0.706	SUBCLONAL	1	TRUE	1	0.327404203431391	2		572	551	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118911	115118911	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	62	441	0	ENST00000257566.3:c.430G>T	p.Asp144Tyr	p.D144Y	ENST00000257566	NM_016569.3	144	Gat/Tat	2/8	0.240056935871658	2	FACETS	0.997	0.865	1	0.498	0.432	0.569	CLONAL	1	TRUE	0	0.327404203431391	2		441	380	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805571	46805571	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	57	994	0	ENST00000290295.7:c.385T>C	p.Phe129Leu	p.F129L	ENST00000290295	NM_006361.5	129	Ttc/Ctc	1/2	0.327404203431391	3	FACETS	0.466	0.398	0.54			1	SUBCLONAL	1	TRUE	NA	0.327404203431391	3		994	870	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58700884	58700884	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	22	420	0	ENST00000305921.3:c.475G>A	p.Glu159Lys	p.E159K	ENST00000305921	NM_003620.3	159	Gaa/Aaa	2/6	1	2	FACETS	0.325	0.251	0.412	0.325	0.251	0.412	SUBCLONAL	1	TRUE	1	0.327404203431391	2		420	413	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985887	60985887	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	39	583	0	ENST00000333681.4:c.13G>C	p.Gly5Arg	p.G5R	ENST00000333681		5	Ggg/Cgg	2/3	1	2	FACETS	0.472	0.391	0.562	0.472	0.391	0.562	SUBCLONAL	1	TRUE	1	0.327404203431391	2		583	505	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247373	153247373	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	53	486	1	ENST00000281708.4:c.1429G>T	p.Gly477Cys	p.G477C	ENST00000281708	NM_033632.3	477	Ggt/Tgt	10/12	0.163066483578018	4	FACETS	0.73	0.622	0.848	0.365	0.311	0.424	INDETERMINATE	1	TRUE	2	0.327404203431391	4		487	589	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0016696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	928	488	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.5563559153042	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.5563559153042	3		490	1272	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518340	204518340	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	109	378	0	ENST00000367182.3:c.1003T>A	p.Ser335Thr	p.S335T	ENST00000367182	NM_001278516.1	335	Tca/Aca	11/11	0.5563559153042	3	FACETS	0.513	0.46	0.57	0.171	0.153	0.19	SUBCLONAL	1	TRUE	0	0.5563559153042	3		378	976	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784020	120784020	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1509	430	804	0	ENST00000257552.2:c.965C>A	p.Ala322Glu	p.A322E	ENST00000257552	NM_002442.3	322	gCg/gAg	13/15	0.5563559153042	3	FACETS	1	0.965	1	0.509	0.484	0.536	CLONAL	1	TRUE	1	0.5563559153042	3		804	1939	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175391	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0016696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	233	229	0	ENST00000257430.4:c.4101_4102dup	p.Thr1368ArgfsTer48	p.T1368Rfs*48	ENST00000257430	NM_000038.5	1367	cag/cAGag	16/16	0.5563559153042	3	FACETS	0.88	0.827	0.935	0.88	0.827	0.935	CLONAL	2	TRUE	1	0.5563559153042	3		229	608	SUCCESS
APC	324	MSKCC	GRCh37	5	112175476	112175477	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0016696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	161	273	0	ENST00000257430.4:c.4187_4188del	p.Phe1396Ter	p.F1396*	ENST00000257430	NM_000038.5	1395	agTTtt/agtt	16/16	0.5563559153042	3	FACETS	1	0.975	1	0.573	0.527	0.62	CLONAL	1	TRUE	1	0.5563559153042	3		273	646	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56339083	56339084	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	AG	AG	CC	novel	NA	P-0016698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	24	62	0	ENST00000348428.3:c.208_209delinsCC	p.Ser70Pro	p.S70P	ENST00000348428	NM_006785.3	70	AGt/CCt	1/17	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.37	2		62	110	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538940	23538940	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	59	327	0	ENST00000380871.4:c.499C>G	p.Gln167Glu	p.Q167E	ENST00000380871	NM_006167.3	167	Caa/Gaa	2/2	1	2	FACETS	0.824	0.712	0.945	0.824	0.712	0.945	CLONAL	1	TRUE	1	0.37	2		327	387	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	186	349	0	ENST00000206249.3:c.1607T>A	p.Leu536His	p.L536H	ENST00000206249	NM_000125.3	536	cTc/cAc	8/8	0.22909977898721	1	FACETS	0.753	0.695	0.813	0.753	0.695	0.813	INDETERMINATE	1	TRUE	0	0.412498294273769	1		349	951	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104264077	104264077	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	321	644	0	ENST00000369902.3:c.168del	p.Ile57SerfsTer39	p.I57Sfs*39	ENST00000369902	NM_016169.3	56	gcT/gc	1/12	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.412498294273769	2		644	1508	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	199	726	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.5	0.462	0.54	0.5	0.462	0.54	SUBCLONAL	1	TRUE	1	0.572835384472555	2		726	1389	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0016701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	99	288	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.439	0.391	0.489	0.439	0.391	0.489	SUBCLONAL	1	TRUE	1	0.572835384472555	2		288	788	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864909	57864909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1281	143	520	0	ENST00000228682.2:c.2386C>A	p.Leu796Ile	p.L796I	ENST00000228682	NM_005269.2	796	Cta/Ata	12/12	1	2	FACETS	0.351	0.318	0.385	0.351	0.318	0.385	SUBCLONAL	1	TRUE	1	0.572835384472555	2		520	1424	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28886222	28886222	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	99	380	0	ENST00000282397.4:c.3400C>G	p.Leu1134Val	p.L1134V	ENST00000282397	NM_002019.4	1134	Ctg/Gtg	26/30	1	2	FACETS	0.345	0.307	0.385	0.345	0.307	0.385	SUBCLONAL	1	TRUE	1	0.572835384472555	2		380	1003	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633270	3633270	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1459274777	NA	P-0016701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1740	184	822	0	ENST00000294008.3:c.4981A>G	p.Lys1661Glu	p.K1661E	ENST00000294008	NM_032444.2	1661	Aag/Gag	14/15	1	2	FACETS	0.334	0.307	0.363	0.334	0.307	0.363	SUBCLONAL	1	TRUE	1	0.572835384472555	2		822	1924	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143198	24143198	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1387	191	620	1	ENST00000263121.7:c.430G>T	p.Ala144Ser	p.A144S	ENST00000263121	NM_003073.3	144	Gcc/Tcc	4/9	1	2	FACETS	0.423	0.389	0.458	0.423	0.389	0.458	SUBCLONAL	1	TRUE	1	0.572835384472555	2		621	1578	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660111	12660111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	94	323	0	ENST00000251849.4:c.110G>A	p.Gly37Asp	p.G37D	ENST00000251849	NM_002880.3	37	gGc/gAc	2/17	1	2	FACETS	0.344	0.305	0.385	0.344	0.305	0.385	SUBCLONAL	1	TRUE	1	0.572835384472555	2		323	955	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332823	152332823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	94	335	0	ENST00000206249.3:c.1129C>T	p.His377Tyr	p.H377Y	ENST00000206249	NM_000125.3	377	Cac/Tac	5/8	1	2	FACETS	0.347	0.307	0.388	0.347	0.307	0.388	SUBCLONAL	1	TRUE	1	0.572835384472555	2		335	947	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021700	69021700	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	166	373	0	ENST00000288368.4:c.2989del	p.Ala997ProfsTer19	p.A997Pfs*19	ENST00000288368	NM_024870.2	996	gcG/gc	25/40	0.206915971430313	3	FACETS	0.646	0.592	0.702	0.323	0.296	0.351	INDETERMINATE	1	TRUE	1	0.572835384472555	3		373	1154	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391403	139391403	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	147	488	1	ENST00000277541.6:c.6788G>T	p.Arg2263Leu	p.R2263L	ENST00000277541	NM_017617.3	2263	cGg/cTg	34/34	1	2	FACETS	0.47	0.429	0.514	0.47	0.429	0.514	SUBCLONAL	1	TRUE	1	0.572835384472555	2		489	1091	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0016702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	35	757	1	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	1	2	FACETS	0.137	0.112	0.167	0.137	0.112	0.167	SUBCLONAL	1	TRUE	1	0.516424438436411	2		758	986	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506444	148506444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	11	481	1	ENST00000320356.2:c.2068C>T	p.Arg690Cys	p.R690C	ENST00000320356	NM_004456.4	690	Cgt/Tgt	18/20	0.516424438436411	3	FACETS	0.1	0.068	0.139	0.05	0.034	0.07	SUBCLONAL	1	TRUE	1	0.516424438436411	3		482	537	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945761	206945763	+	inframe_deletion	In_Frame_Del	DEL	AGC	AGC	-	novel	NA	P-0016702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	103	318	0	ENST00000423557.1:c.18_20del	p.Leu7del	p.L7del	ENST00000423557	NM_000572.2	6	ctGCTc/ctc	1/5	1	2	FACETS	0.915	0.824	1	0.915	0.824	1	CLONAL	1	TRUE	1	0.516424438436411	2		318	436	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033376	48033376	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	100	591	0	ENST00000234420.5:c.3680T>C	p.Ile1227Thr	p.I1227T	ENST00000234420	NM_000179.2	1227	aTa/aCa	8/10	1	2	FACETS	0.903	0.811	0.998	0.903	0.811	0.998	CLONAL	1	TRUE	1	0.516424438436411	2		591	429	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183692	10183693	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	132	777	0	ENST00000256474.2:c.161_162insA	p.Met54IlefsTer78	p.M54Ifs*78	ENST00000256474	NM_000551.3	54	atg/atAg	1/3	0.516424438436411	1	FACETS	0.899	0.823	0.977	0.899	0.823	0.977	CLONAL	1	TRUE	0	0.516424438436411	1		777	422	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542485	187542485	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	103	532	0	ENST00000441802.2:c.5255T>C	p.Leu1752Pro	p.L1752P	ENST00000441802	NM_005245.3	1752	cTa/cCa	10/27	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.516424438436411	2		532	370	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891199	101891199	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	22	392	0	ENST00000374994.4:c.160T>C	p.Cys54Arg	p.C54R	ENST00000374994	NM_004612.2	54	Tgc/Cgc	2/9	0.461840976980926	1	FACETS	0.257	0.199	0.323	0.257	0.199	0.323	SUBCLONAL	1	TRUE	0	0.516424438436411	1		392	246	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0016703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	419	2255	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.285562063582053	4	FACETS	0.958	0.915	1	0.719	0.686	0.752	CLONAL	3	TRUE	0	0.379294514272918	4		2255	1060	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0016703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	203	279	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.227785069402117	5	FACETS	1	0.983	1	0.784	0.73	0.84	CLONAL	2	TRUE	2	0.379294514272918	5		279	714	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976745	2976745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748839211	NA	P-0016703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	129	462	2	ENST00000396946.4:c.1267C>T	p.Arg423Trp	p.R423W	ENST00000396946	NM_032415.4	423	Cgg/Tgg	9/25	0.379294514272918	6	FACETS	0.922	0.834	1	0.231	0.208	0.254	CLONAL	1	TRUE	2	0.379294514272918	6		464	1297	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212457	5212457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	100	425	2	ENST00000357368.4:c.4660G>A	p.Ala1554Thr	p.A1554T	ENST00000357368	NM_002850.3	1554	Gcg/Acg	31/38	0.281015065766802	4	FACETS	0.822	0.733	0.916	0.411	0.366	0.458	CLONAL	1	TRUE	2	0.379294514272918	4		427	885	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106862	27106862	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142069738	NA	P-0016703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	91	255	0	ENST00000324856.7:c.6473G>A	p.Arg2158Gln	p.R2158Q	ENST00000324856	NM_006015.4	2158	cGa/cAa	20/20	0.379294514272918	3	FACETS	1	0.941	1	0.544	0.484	0.607	CLONAL	1	TRUE	1	0.379294514272918	3		255	525	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729744	162729744	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	88	349	1	ENST00000367921.3:c.830G>T	p.Arg277Leu	p.R277L	ENST00000367921	NM_006182.2	277	cGc/cTc	8/18	0.379294514272918	8	FACETS	0.818	0.723	0.922	0.136	0.12	0.154	CLONAL	1	TRUE	2	0.379294514272918	8		350	1212	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497807	120497807	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782026650	NA	P-0016703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	152	422	1	ENST00000256646.2:c.2075G>A	p.Arg692His	p.R692H	ENST00000256646	NM_024408.3	692	cGc/cAc	13/34	0.379294514272918	3	FACETS	1	0.963	1	0.547	0.5	0.596	CLONAL	1	TRUE	1	0.379294514272918	3		423	872	SUCCESS
FH	2271	MSKCC	GRCh37	1	241665814	241665814	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1365	120	333	0	ENST00000366560.3:c.1165G>T	p.Gly389Trp	p.G389W	ENST00000366560	NM_000143.3	389	Ggg/Tgg	8/10	0.379294514272918	8	FACETS	0.911	0.82	1	0.152	0.136	0.168	CLONAL	1	TRUE	2	0.379294514272918	8		333	1485	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597802	43597802	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763295929	NA	P-0016703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	132	453	0	ENST00000355710.3:c.350C>A	p.Pro117His	p.P117H	ENST00000355710	NM_020975.4	117	cCc/cAc	3/20	0.355047831892844	4	FACETS	0.891	0.808	0.98	0.297	0.269	0.327	CLONAL	1	TRUE	1	0.379294514272918	4		453	1077	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851413	63851413	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	251	375	0	ENST00000279873.7:c.2191A>T	p.Ser731Cys	p.S731C	ENST00000279873	NM_032199.2	731	Agt/Tgt	10/10	0.355047831892844	4	FACETS	1	0.942	1	0.67	0.628	0.714	CLONAL	2	TRUE	1	0.379294514272918	4		375	908	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121672	108121672	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	124	383	2	ENST00000278616.4:c.1480G>T	p.Gly494Cys	p.G494C	ENST00000278616	NM_000051.3	494	Ggt/Tgt	10/63	0.379294514272918	3	FACETS	0.896	0.81	0.987	0.299	0.27	0.329	CLONAL	1	TRUE	0	0.379294514272918	3		385	868	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281957	49281957	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	146	508	0	ENST00000282018.3:c.1004C>A	p.Pro335His	p.P335H	ENST00000282018	NM_020377.2	335	cCt/cAt	1/1	0.379294514272918	3	FACETS	0.885	0.806	0.967	0.442	0.403	0.484	CLONAL	1	TRUE	1	0.379294514272918	3		508	1035	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858014	9858014	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	122	356	0	ENST00000330684.3:c.3387C>A	p.His1129Gln	p.H1129Q	ENST00000330684	NM_001134407.1	1129	caC/caA	13/13	0.227785069402117	5	FACETS	1	0.957	1	0.369	0.333	0.407	CLONAL	1	TRUE	2	0.379294514272918	5		356	911	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89806405	89806405	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	256	387	0	ENST00000389301.3:c.3931A>T	p.Ser1311Cys	p.S1311C	ENST00000389301	NM_000135.2	1311	Agt/Tgt	39/43	0.379294514272918	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.379294514272918	3		387	788	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618820	37618820	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	276	415	0	ENST00000447079.4:c.496G>C	p.Val166Leu	p.V166L	ENST00000447079	NM_015083.1	166	Gta/Cta	1/14	0.355047831892844	4	FACETS	1	0.964	1	0.689	0.648	0.731	CLONAL	2	TRUE	1	0.379294514272918	4		415	971	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353863	40353863	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	156	274	0	ENST00000293328.3:c.2257A>T	p.Thr753Ser	p.T753S	ENST00000293328	NM_012448.3	753	Acc/Tcc	19/19	0.355047831892844	4	FACETS	0.861	0.791	0.934	0.574	0.527	0.623	CLONAL	2	TRUE	1	0.379294514272918	4		274	659	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78599550	78599552	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0016703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	105	248	0	ENST00000306801.3:c.222_224del	p.Asp74_Val75delinsGlu	p.D74_V75delinsE	ENST00000306801	NM_020761.2	74	gaTGTg/gag	2/34	0.379294514272918	6	FACETS	1	0.965	1	0.236	0.211	0.263	CLONAL	1	TRUE	1	0.379294514272918	6		248	824	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211650	5211650	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	96	318	1	ENST00000357368.4:c.5185G>T	p.Gly1729Cys	p.G1729C	ENST00000357368	NM_002850.3	1729	Ggt/Tgt	33/38	0.281015065766802	4	FACETS	0.902	0.803	1	0.451	0.401	0.504	CLONAL	1	TRUE	2	0.379294514272918	4		319	774	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919755	50919755	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	122	478	0	ENST00000440232.2:c.2923G>C	p.Gly975Arg	p.G975R	ENST00000440232	NM_002691.3	975	Ggc/Cgc	23/27	0.281015065766802	4	FACETS	0.966	0.872	1	0.483	0.436	0.533	CLONAL	1	TRUE	2	0.379294514272918	4		478	919	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426627	212426627	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0016703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	355	370	2	ENST00000342788.4:c.2487+1G>T		p.X829_splice	ENST00000342788	NM_005235.2	829			0.379294514272918	5	FACETS	0.924	0.876	0.972	0.924	0.876	0.972	CLONAL	3	TRUE	2	0.379294514272918	5		372	1060	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374344	31374344	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	105	381	1	ENST00000328111.2:c.343G>T	p.Glu115Ter	p.E115*	ENST00000328111	NM_006892.3	115	Gag/Tag	5/23	0.227785069402117	5	FACETS	1	0.925	1	0.347	0.311	0.386	CLONAL	1	TRUE	2	0.379294514272918	5		382	834	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40828012	40828012	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	76	226	0	ENST00000373198.4:c.2416C>G	p.Gln806Glu	p.Q806E	ENST00000373198	NM_133170.3	806	Cag/Gag	17/32	NA	2	FACETS	1	0.883	1			1	INDETERMINATE	1	TRUE	NA	0.379294514272918	2		226	400	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958197	54958197	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1621	175	546	0	ENST00000312783.6:c.410G>T	p.Arg137Leu	p.R137L	ENST00000312783	NM_198436.1	137	cGc/cTc	6/10	0.379294514272918	7	FACETS	1	0.918	1	0.2	0.183	0.218	CLONAL	1	TRUE	2	0.379294514272918	7		546	1796	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035138	30035138	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	282	449	0	ENST00000338641.4:c.300T>G	p.Phe100Leu	p.F100L	ENST00000338641	NM_000268.3	100	ttT/ttG	3/16	0.281015065766802	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.379294514272918	4		449	949	SUCCESS
ATR	545	MSKCC	GRCh37	3	142218475	142218475	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	144	363	0	ENST00000350721.4:c.5374G>T	p.Ala1792Ser	p.A1792S	ENST00000350721	NM_001184.3	1792	Gca/Tca	31/47	0.379294514272918	3	FACETS	1	0.961	1	0.546	0.498	0.596	CLONAL	1	TRUE	1	0.379294514272918	3		363	827	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430866	181430866	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	404	748	0	ENST00000325404.1:c.718A>T	p.Met240Leu	p.M240L	ENST00000325404	NM_003106.3	240	Atg/Ttg	1/1	0.379294514272918	4	FACETS	0.936	0.889	0.985	0.624	0.593	0.657	CLONAL	2	TRUE	1	0.379294514272918	4		748	1569	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152116	55152116	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	158	449	0	ENST00000257290.5:c.2548G>T	p.Val850Leu	p.V850L	ENST00000257290	NM_006206.4	850	Gtg/Ttg	18/23	0.379294514272918	3	FACETS	1	0.918	1	0.501	0.459	0.546	CLONAL	1	TRUE	1	0.379294514272918	3		449	989	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161671	56161671	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	109	375	0	ENST00000399503.3:c.1168C>T	p.Gln390Ter	p.Q390*	ENST00000399503	NM_005921.1	390	Cag/Tag	6/20	0.379294514272918	3	FACETS	0.836	0.75	0.927	0.418	0.375	0.464	CLONAL	1	TRUE	1	0.379294514272918	3		375	818	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631153	176631153	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	107	305	0	ENST00000439151.2:c.1096G>T	p.Val366Leu	p.V366L	ENST00000439151	NM_022455.4	366	Gtg/Ttg	4/23	0.379294514272918	3	FACETS	1	0.898	1	0.5	0.449	0.554	CLONAL	1	TRUE	1	0.379294514272918	3		305	671	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835952	151835952	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1188	149	338	0	ENST00000262189.6:c.14572G>T	p.Glu4858Ter	p.E4858*	ENST00000262189	NM_170606.2	4858	Gaa/Taa	58/59	0.379294514272918	6	FACETS	1	0.936	1	0.258	0.235	0.283	CLONAL	1	TRUE	2	0.379294514272918	6		338	1337	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8525030	8525030	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	77	188	0	ENST00000356435.5:c.574C>A	p.Leu192Ile	p.L192I	ENST00000356435		192	Ctt/Att	7/35	0.227785069402117	5	FACETS	1	0.956	1	0.396	0.348	0.448	CLONAL	1	TRUE	2	0.379294514272918	5		188	536	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636759	8636759	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1318804406	NA	P-0016703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	94	270	0	ENST00000356435.5:c.150C>A	p.Asp50Glu	p.D50E	ENST00000356435		50	gaC/gaA	2/35	0.227785069402117	5	FACETS	0.975	0.867	1	0.325	0.289	0.364	CLONAL	1	TRUE	2	0.379294514272918	5		270	798	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972661	76972661	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	152	380	0	ENST00000373344.5:c.80A>T	p.Glu27Val	p.E27V	ENST00000373344	NM_000489.3	27	gAa/gTa	2/35	0.379294514272918	2	FACETS	1	0.947	1	0.522	0.478	0.569	CLONAL	1	TRUE	0	0.379294514272918	2		380	767	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846052	128846053	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	A	novel	NA	P-0016703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1194	252	492	0	ENST00000249373.3:c.982_983delinsA	p.Gly328MetfsTer59	p.G328Mfs*59	ENST00000249373	NM_005631.4	328	GGt/At	5/12	0.379294514272918	6	FACETS	0.808	0.754	0.864	0.404	0.377	0.432	CLONAL	2	TRUE	2	0.379294514272918	6		492	1446	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0016704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	42	305	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.397025315684475	2	FACETS	0.22	0.183	0.262	0.11	0.091	0.131	SUBCLONAL	1	TRUE	0	0.487562870380317	2		305	782	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	363	641	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.232702605760343	2	FACETS	1	0.995	1	0.731	0.694	0.768	INDETERMINATE	1	TRUE	0	0.487562870380317	2		641	1019	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411276	63411276	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	343	234	0	ENST00000330258.3:c.1891C>T	p.Arg631Ter	p.R631*	ENST00000330258	NM_152424.3	631	Cga/Tga	2/2	0.37318392759371	2	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.487562870380317	2		234	578	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	121	384	0	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	0.26521144998174	1	FACETS	0.45	0.406	0.496	0.45	0.406	0.496	INDETERMINATE	1	TRUE	0	0.487562870380317	1		384	835	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0016704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	186	341	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.26521144998174	1	FACETS	0.913	0.847	0.981	0.913	0.847	0.981	INDETERMINATE	1	TRUE	0	0.487562870380317	1		341	632	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455075	50455075	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	162	237	0	ENST00000331340.3:c.622C>T	p.Arg208Ter	p.R208*	ENST00000331340	NM_006060.4	208	Cga/Tga	6/8	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.487562870380317	2		237	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	653	735	1	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.463068661642675	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.487562870380317	1		736	1510	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620541	52620541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141958485	NA	P-0016704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	291	384	0	ENST00000394830.3:c.3212G>A	p.Arg1071His	p.R1071H	ENST00000394830	NM_018313.4	1071	cGc/cAc	21/30	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.487562870380317	2		384	939	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741513	17741513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1178137322	NA	P-0016704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	149	541	1	ENST00000250003.3:c.184C>T	p.His62Tyr	p.H62Y	ENST00000250003	NM_002478.4	62	Cac/Tac	1/3	1	2	FACETS	0.625	0.57	0.682	0.625	0.57	0.682	SUBCLONAL	1	TRUE	1	0.487562870380317	2		542	978	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436431	110436431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1532	133	657	0	ENST00000375856.3:c.1970C>T	p.Thr657Met	p.T657M	ENST00000375856	NM_003749.2	657	aCg/aTg	1/2	0.210424778777391	4	FACETS	0.487	0.441	0.537	0.244	0.22	0.269	INDETERMINATE	1	TRUE	2	0.487562870380317	4		657	1665	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821732	72821732	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	31	249	0	ENST00000268489.5:c.10443G>C	p.Arg3481Ser	p.R3481S	ENST00000268489	NM_006885.3	3481	agG/agC	10/10	0.487562870380317	1	FACETS	0.212	0.171	0.259	0.212	0.171	0.259	SUBCLONAL	1	TRUE	0	0.487562870380317	1		249	453	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368253	45368253	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	259	328	0	ENST00000262160.6:c.1349A>G	p.Asp450Gly	p.D450G	ENST00000262160	NM_005901.5	450	gAc/gGc	11/11	0.487562870380317	2	FACETS	0.942	0.891	0.993	0.942	0.891	0.993	CLONAL	2	TRUE	0	0.487562870380317	2		328	564	SUCCESS
APC	324	MSKCC	GRCh37	5	112175351	112175351	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	170	171	0	ENST00000257430.4:c.4063del	p.Ser1355LeufsTer60	p.S1355Lfs*60	ENST00000257430	NM_000038.5	1354	Ttt/tt	16/16	0.397025315684475	2	FACETS	0.896	0.835	0.958	0.896	0.835	0.958	CLONAL	2	TRUE	0	0.487562870380317	2		171	389	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020378	69020379	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	A	novel	NA	P-0016704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	54	443	0	ENST00000288368.4:c.2750_2751delinsA	p.Thr917AsnfsTer26	p.T917Nfs*26	ENST00000288368	NM_024870.2	917	aCT/aA	24/40	0.155930503798712	2	FACETS	0.244	0.207	0.284	0.122	0.103	0.142	INDETERMINATE	1	TRUE	0	0.487562870380317	2		443	909	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577520	7577520	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	557	359	1	ENST00000269305.4:c.761T>A	p.Ile254Asn	p.I254N	ENST00000269305	NM_001126112.2	254	aTc/aAc	7/11	0.435196021846264	3	FACETS	0.948	0.914	0.982	0.948	0.914	0.982	CLONAL	3	TRUE	0	0.435196021846264	3		360	1096	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400125	41400125	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1462	175	463	0	ENST00000373198.4:c.634C>G	p.Gln212Glu	p.Q212E	ENST00000373198	NM_133170.3	212	Cag/Gag	5/32	0.419233227977979	5	FACETS	0.812	0.745	0.882	0.203	0.186	0.221	CLONAL	1	TRUE	1	0.435196021846264	5		463	1637	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099788	157099804	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGCCCCGGCGGCCGC	GCGGCCCCGGCGGCCGC	-	novel	NA	P-0016705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	523	496	0	ENST00000346085.5:c.727_743del	p.Gly243TrpfsTer5	p.G243Wfs*5	ENST00000346085	NM_020732.3	242	gGCGGCCCCGGCGGCCGC/g	1/20	0.435196021846264	4	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	2	0.435196021846264	4		496	1406	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0016706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	75	512	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	1	2	FACETS	0.897	0.786	1	0.897	0.786	1	CLONAL	1	TRUE	1	0.261795700294973	2		512	639	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	260	423	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.962	0.912	1	1	0.997	1	CLONAL	6	TRUE	1	0.172208671559674	2		423	523	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0016707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	222	554	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.120921487702952	3	FACETS	0.943	0.887	0.999	1	0.995	1	CLONAL	6	TRUE	1	0.172208671559674	3		554	495	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0016708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	187	2255	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.341622313953635	4	FACETS	0.881	0.82	0.942	0.881	0.82	0.942	CLONAL	3	TRUE	1	0.374988091150291	4		2255	519	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138480	11138480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	140	999	1	ENST00000358026.2:c.3236C>T	p.Ser1079Leu	p.S1079L	ENST00000358026	NM_001128849.1	1079	tCg/tTg	24/36	0.326000454656298	2	FACETS	0.847	0.778	0.918	0.847	0.778	0.918	CLONAL	2	TRUE	0	0.374988091150291	2		1000	441	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190670442	190670442	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	73	747	0	ENST00000441310.2:c.380G>T	p.Gly127Val	p.G127V	ENST00000441310	NM_000534.4	127	gGc/gTc	4/13	0.307074505559561	5	FACETS	1	0.975	1	0.492	0.432	0.556	CLONAL	1	TRUE	2	0.374988091150291	5		747	412	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793287	242793287	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	205	1387	1	ENST00000334409.5:c.790C>A	p.Arg264Ser	p.R264S	ENST00000334409	NM_005018.2	264	Cgc/Agc	5/5	0.307074505559561	5	FACETS	1	0.987	1	0.831	0.774	0.89	CLONAL	2	TRUE	2	0.374988091150291	5		1388	685	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024578	31024578	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	48	795	0	ENST00000375687.4:c.4063G>A	p.Asp1355Asn	p.D1355N	ENST00000375687	NM_015338.5	1355	Gac/Aac	13/13	0.374988091150291	3	FACETS	0.756	0.641	0.883	0.378	0.32	0.442	SUBCLONAL	1	TRUE	1	0.374988091150291	3		795	402	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739119	40739119	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	42	635	0	ENST00000373198.4:c.3165C>A	p.Tyr1055Ter	p.Y1055*	ENST00000373198	NM_133170.3	1055	taC/taA	24/32	0.374988091150291	3	FACETS	0.66	0.552	0.78	0.33	0.276	0.39	SUBCLONAL	1	TRUE	1	0.374988091150291	3		635	403	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1953902	1953902	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	148	1315	1	ENST00000382891.5:c.2081G>T	p.Cys694Phe	p.C694F	ENST00000382891	NM_133335.3	694	tGc/tTc	11/22	0.317611665852889	3	FACETS	0.792	0.726	0.86	0.792	0.726	0.86	SUBCLONAL	2	TRUE	1	0.374988091150291	3		1316	592	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64290041	64290041	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	78	1027	0	ENST00000370651.3:c.484G>A	p.Asp162Asn	p.D162N	ENST00000370651	NM_003463.4	162	Gat/Aat	6/6	1	2	FACETS	0.835	0.736	0.941	0.835	0.736	0.941	CLONAL	1	TRUE	1	0.374988091150291	2		1027	498	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021735	69021735	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	72	936	3	ENST00000288368.4:c.3023G>A	p.Gly1008Asp	p.G1008D	ENST00000288368	NM_024870.2	1008	gGc/gAc	25/40	0.374988091150291	3	FACETS	0.844	0.739	0.958	0.422	0.369	0.479	CLONAL	1	TRUE	1	0.374988091150291	3		939	540	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970900	21970900	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0016708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	88	1420	2	ENST00000304494.5:c.457+1G>A		p.X153_splice	ENST00000304494	NM_000077.4	153			0.326000454656298	2	FACETS	0.958	0.852	1	0.479	0.426	0.535	CLONAL	1	TRUE	0	0.374988091150291	2		1422	490	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034417	47034418	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	TT	novel	NA	P-0016708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	108	904	3	ENST00000377604.3:c.503-1_503delinsTT		p.X168_splice	ENST00000377604	NM_001204468.1	168		6/24	0.201876071278921	4	FACETS	0.75	0.676	0.828	0.75	0.676	0.828	INDETERMINATE	2	TRUE	2	0.374988091150291	4		907	528	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412830	63412831	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	A	novel	NA	P-0016708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	120	1069	0	ENST00000330258.3:c.336_337delinsT	p.Glu112AspfsTer58	p.E112Dfs*58	ENST00000330258	NM_152424.3	112	gaAGga/gaTga	2/2	0.201876071278921	4	FACETS	0.764	0.692	0.839	0.764	0.692	0.839	INDETERMINATE	2	TRUE	2	0.374988091150291	4		1069	576	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219351	1219352	+	frameshift_variant	Frame_Shift_Ins	INS	GG	GG	TTT	novel	NA	P-0016708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	112	1042	0	ENST00000326873.7:c.403_404delinsTTT	p.Gly135PhefsTer28	p.G135Ffs*28	ENST00000326873	NM_000455.4	135	GGc/TTTc	3/10	0.326000454656298	2	FACETS	1	0.982	1	0.698	0.632	0.766	CLONAL	1	TRUE	0	0.374988091150291	2		1042	428	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211602	46211602	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	89	600	0	ENST00000334344.6:c.568G>T	p.Val190Phe	p.V190F	ENST00000334344	NM_152641.2	190	Gtc/Ttc	5/21	1	2	FACETS	0.988	0.891	1	0.988	0.891	1	CLONAL	1	TRUE	1	0.732063197696512	2		600	246	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	143	726	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.260410816204795	2	FACETS	1	0.987	1	0.738	0.675	0.803	CLONAL	1	TRUE	0	0.321899591818487	2		726	602	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0016710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	142	869	3	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.321899591818487	1	FACETS	0.909	0.829	0.993	0.909	0.829	0.993	CLONAL	1	TRUE	0	0.321899591818487	1		872	814	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934174	49934174	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs149428633	NA	P-0016710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	70	1116	0	ENST00000296474.3:c.2333A>G	p.Asn778Ser	p.N778S	ENST00000296474	NM_002447.2	778	aAc/aGc	8/20	1	2	FACETS	0.54	0.469	0.616	0.54	0.469	0.616	SUBCLONAL	1	TRUE	1	0.321899591818487	2		1116	806	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151167659	151167659	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	120	853	0	ENST00000262187.5:c.460C>T	p.Gln154Ter	p.Q154*	ENST00000262187	NM_005614.3	154	Cag/Tag	7/8	0.227859801316533	3	FACETS	1	0.978	1	0.641	0.58	0.706	CLONAL	1	TRUE	1	0.321899591818487	3		853	675	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	120	423	0				ENST00000310581	NM_198253.2	-/1132			0.19655245689727	3	FACETS	0.996	0.901	1	0.996	0.901	1	CLONAL	2	TRUE	1	0.19655245689727	3		423	673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578551	7578551	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	304	1394	0	ENST00000269305.4:c.379T>A	p.Ser127Thr	p.S127T	ENST00000269305	NM_001126112.2	127	Tcc/Acc	5/11	0.19655245689727	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.19655245689727	2		1394	1333	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0016713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	154	519	1	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.705300864997965	3	FACETS	0.99	0.925	1	0.99	0.925	1	CLONAL	2	TRUE	1	0.732700803811637	3		520	290	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0016713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	114	519	1	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.694749013340242	3	FACETS	0.89	0.819	0.961	0.89	0.819	0.961	CLONAL	2	TRUE	1	0.740833097990459	3		520	237	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0016714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	545	1492	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.333373325496995	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.392070870302244	2		1492	1356	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0016714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	173	730	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.392070870302244	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.392070870302244	1		730	650	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941658	48941658	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs765678030	NA	P-0016714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	67	465	0	ENST00000267163.4:c.968A>G	p.Glu323Gly	p.E323G	ENST00000267163	NM_000321.2	323	gAa/gGa	10/27	0.392070870302244	1	FACETS	0.968	0.849	1	0.968	0.849	1	CLONAL	1	TRUE	0	0.392070870302244	1		465	284	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650569	18650569	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750864969	NA	P-0016714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	121	662	1	ENST00000266497.5:c.2780G>A	p.Arg927His	p.R927H	ENST00000266497		927	cGt/cAt	20/31	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.392070870302244	2		663	587	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432024	121432024	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	333	1358	0	ENST00000257555.6:c.771C>A	p.Asn257Lys	p.N257K	ENST00000257555		257	aaC/aaA	4/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.392070870302244	2		1358	1516	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2114373	2114373	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	361	1213	0	ENST00000219476.3:c.1544del	p.Leu515ArgfsTer20	p.L515Rfs*20	ENST00000219476	NM_000548.3	515	cTg/cg	15/42	0.392070870302244	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.392070870302244	1		1213	1020	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943729	9943729	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	286	840	1	ENST00000330684.3:c.1212C>A	p.Asn404Lys	p.N404K	ENST00000330684	NM_001134407.1	404	aaC/aaA	5/13	0.333373325496995	2	FACETS	0.883	0.833	0.934	0.883	0.833	0.934	CLONAL	2	TRUE	0	0.392070870302244	2		841	826	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976400	18976400	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1297	293	1518	0	ENST00000262803.5:c.3050G>C	p.Arg1017Pro	p.R1017P	ENST00000262803	NM_002911.3	1017	cGt/cCt	22/24	0.228097935657695	1	FACETS	0.756	0.709	0.804	0.756	0.709	0.804	INDETERMINATE	1	TRUE	0	0.392070870302244	1		1518	1590	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661612	227661612	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	121	622	0	ENST00000305123.5:c.1843A>T	p.Met615Leu	p.M615L	ENST00000305123	NM_005544.2	615	Atg/Ttg	1/2	0.249539945141097	1	FACETS	0.758	0.686	0.833	0.758	0.686	0.833	SUBCLONAL	1	TRUE	0	0.392070870302244	1		622	655	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158242	47158242	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	95	519	0	ENST00000409792.3:c.4457A>T	p.Lys1486Met	p.K1486M	ENST00000409792	NM_014159.6	1486	aAg/aTg	4/21	0.392070870302244	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.392070870302244	1		519	371	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542429	187542429	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs755310203	NA	P-0016714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	178	570	0	ENST00000441802.2:c.5311A>G	p.Thr1771Ala	p.T1771A	ENST00000441802	NM_005245.3	1771	Aca/Gca	10/27	0.163084481736975	3	FACETS	0.813	0.752	0.876			1	INDETERMINATE	2	TRUE	NA	0.392070870302244	3		570	668	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068039	94068039	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	164	623	0	ENST00000369303.4:c.923C>G	p.Ser308Cys	p.S308C	ENST00000369303	NM_004440.3	308	tCc/tGc	4/17	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.392070870302244	2		623	680	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374390	81374390	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	109	697	0	ENST00000222390.5:c.672T>A	p.Asp224Glu	p.D224E	ENST00000222390	NM_000601.4	224	gaT/gaA	6/18	0.246151502007723	1	FACETS	0.611	0.548	0.677	0.611	0.548	0.677	SUBCLONAL	1	TRUE	0	0.392070870302244	1		697	732	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	196	641	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	0.485181319242433	2		641	794	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0016715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	10	393	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.133	0.09	0.189	0.133	0.09	0.189	SUBCLONAL	1	TRUE	1	0.485181319242433	2		393	309	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0016715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	8	415	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.103	0.066	0.152	0.103	0.066	0.152	SUBCLONAL	1	TRUE	1	0.485181319242433	2		415	320	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0016715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	17	775	2	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	0.278766558875848	1	FACETS	0.12	0.089	0.157	0.12	0.089	0.157	INDETERMINATE	1	TRUE	0	0.485181319242433	1		777	443	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451921	29451921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	143	1140	1	ENST00000389048.3:c.2644G>A	p.Gly882Ser	p.G882S	ENST00000389048	NM_004304.4	882	Ggc/Agc	16/29	1	2	FACETS	0.867	0.792	0.945	0.867	0.792	0.945	CLONAL	1	TRUE	1	0.485181319242433	2		1141	680	SUCCESS
APC	324	MSKCC	GRCh37	5	112111332	112111332	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	75	490	0	ENST00000257430.4:c.429G>T	p.Leu143Phe	p.L143F	ENST00000257430	NM_000038.5	143	ttG/ttT	5/16	1	2	FACETS	0.852	0.751	0.958	0.852	0.751	0.958	CLONAL	1	TRUE	1	0.485181319242433	2		490	363	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374316	81374316	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	96	374	0	ENST00000222390.5:c.746G>T	p.Arg249Ile	p.R249I	ENST00000222390	NM_000601.4	249	aGa/aTa	6/18	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.485181319242433	2		374	361	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914672	39914672	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0016715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	175	968	0	ENST00000378444.4:c.4690A>T	p.Arg1564Ter	p.R1564*	ENST00000378444	NM_001123385.1	1564	Aga/Tga	12/15	1	2	FACETS	0.972	0.897	1	0.972	0.897	1	CLONAL	1	TRUE	1	0.485181319242433	2		968	742	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574544	64574544	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1565645563	NA	P-0016716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	481	825	0	ENST00000312049.6:c.851C>A	p.Ala284Glu	p.A284E	ENST00000312049	NM_130799.2	284	gCa/gAa	6/10	0.820815100416313	1	FACETS	0.973	0.943	1	0.973	0.943	1	CLONAL	1	TRUE	0	0.820815100416313	1		825	710	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631341	117631341	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	60	685	0	ENST00000368508.3:c.6337G>T	p.Asp2113Tyr	p.D2113Y	ENST00000368508	NM_002944.2	2113	Gat/Tat	40/43	0.390523031330261	1	FACETS	0.1	0.086	0.116	0.1	0.086	0.116	INDETERMINATE	1	TRUE	0	0.820815100416313	1		685	858	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	75	726	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	0.13	2		726	990	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0016717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1548	80	800	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.756	0.662	0.857	0.756	0.662	0.857	SUBCLONAL	1	TRUE	1	0.13	2		801	1628	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100324	27100324	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1612	95	1488	1	ENST00000324856.7:c.4036C>T	p.Gln1346Ter	p.Q1346*	ENST00000324856	NM_006015.4	1346	Caa/Taa	17/20	1	2	FACETS	0.856	0.759	0.961	0.856	0.759	0.961	CLONAL	1	TRUE	1	0.13	2		1489	1707	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974787	21974799	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCCGAAGGCTC	CAGCCGAAGGCTC	-	novel	NA	P-0016717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	15	309	0	ENST00000304494.5:c.28_40del	p.Glu10ThrfsTer12	p.E10Tfs*12	ENST00000304494	NM_000077.4	10	GAGCCTTCGGCTGac/ac	1/3	1	2	FACETS	1	0.735	1	1	0.735	1	CLONAL	1	TRUE	1	0.13	2		309	230	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0016718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	402	998	2	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	0.506618374602037	4	FACETS	0.963	0.917	1	0.963	0.917	1	CLONAL	2	TRUE	2	0.571720786619294	4		1000	1148	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084108	47084108	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	377	912	3	ENST00000409792.3:c.7181A>G	p.Asn2394Ser	p.N2394S	ENST00000409792	NM_014159.6	2394	aAc/aGc	17/21	0.571720786619294	2	FACETS	0.927	0.888	0.966	0.927	0.888	0.966	CLONAL	2	TRUE	0	0.571720786619294	2		915	711	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162687	47162687	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	269	667	3	ENST00000409792.3:c.3439C>T	p.Gln1147Ter	p.Q1147*	ENST00000409792	NM_014159.6	1147	Cag/Tag	3/21	0.571720786619294	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.571720786619294	2		670	467	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436652	52436654	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0016718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	322	854	0	ENST00000460680.1:c.2020_2022del	p.Phe674del	p.F674del	ENST00000460680	NM_004656.3	674	TTC/-	16/17	0.571720786619294	2	FACETS	0.959	0.917	1	0.959	0.917	1	CLONAL	2	TRUE	0	0.571720786619294	2		854	587	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112356	115112357	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0016719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	104	536	0	ENST00000257566.3:c.1382_1383dup	p.Thr462AlafsTer171	p.T462Afs*171	ENST00000257566	NM_016569.3	461	-/GC	7/8	1	2	FACETS	0.883	0.795	0.977	0.883	0.795	0.977	CLONAL	1	TRUE	1	0.478513537317619	2		536	492	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118894	115118894	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	152	621	0	ENST00000257566.3:c.447del	p.Tyr149Ter	p.Y149*	ENST00000257566	NM_016569.3	149	taC/ta	2/8	1	2	FACETS	0.862	0.79	0.937	0.862	0.79	0.937	CLONAL	1	TRUE	1	0.478513537317619	2		621	737	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772295	68772298	+	frameshift_variant	Frame_Shift_Del	DEL	AGGC	AGGC	-	novel	NA	P-0016719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	223	1042	0	ENST00000261769.5:c.144_147del	p.Arg48SerfsTer7	p.R48Sfs*7	ENST00000261769	NM_004360.3	48	agAGGC/ag	2/16	0.478513537317619	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.478513537317619	1		1042	669	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470480	25470480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760854242	NA	P-0016720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	142	661	2	ENST00000264709.3:c.994G>A	p.Gly332Arg	p.G332R	ENST00000264709	NM_175629.2	332	Gga/Aga	8/23	0.152981204182963	2	FACETS	0.535	0.486	0.586	0.267	0.243	0.293	INDETERMINATE	1	TRUE	0	0.509759478209968	2		663	1042	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614977	23614977	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540276838	NA	P-0016720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	36	316	0	ENST00000261584.4:c.3364G>A	p.Asp1122Asn	p.D1122N	ENST00000261584	NM_024675.3	1122	Gac/Aac	13/13	0.509759478209968	1	FACETS	0.21	0.172	0.253	0.21	0.172	0.253	SUBCLONAL	1	TRUE	0	0.509759478209968	1		316	500	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614979	23614979	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	37	302	0	ENST00000261584.4:c.3362G>T	p.Gly1121Val	p.G1121V	ENST00000261584	NM_024675.3	1121	gGt/gTt	13/13	0.509759478209968	1	FACETS	0.22	0.181	0.264	0.22	0.181	0.264	SUBCLONAL	1	TRUE	0	0.509759478209968	1		302	491	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251477	10251477	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	119	629	0	ENST00000340748.4:c.3455C>T	p.Ser1152Leu	p.S1152L	ENST00000340748		1152	tCg/tTg	31/40	0.375997399040682	3	FACETS	0.61	0.549	0.674	0.305	0.274	0.337	SUBCLONAL	1	TRUE	1	0.509759478209968	3		629	961	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873344	151873344	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	60	201	0	ENST00000262189.6:c.9194A>G	p.Glu3065Gly	p.E3065G	ENST00000262189	NM_170606.2	3065	gAa/gGa	38/59	0.379704481770751	1	FACETS	0.5	0.433	0.572	0.5	0.433	0.572	SUBCLONAL	1	TRUE	0	0.509759478209968	1		201	351	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56879387	56879387	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	57	556	1	ENST00000519728.1:c.904C>T	p.Leu302Phe	p.L302F	ENST00000519728	NM_002350.3	302	Ctc/Ttc	9/13	1	2	FACETS	0.254	0.217	0.294	0.254	0.217	0.294	SUBCLONAL	1	TRUE	1	0.509759478209968	2		557	881	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692911	89692911	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121909241	NA	P-0016721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	69	615	2	ENST00000371953.3:c.395G>T	p.Gly132Val	p.G132V	ENST00000371953	NM_000314.4	132	gGt/gTt	5/9	1	2	FACETS	0.515	0.447	0.587	0.515	0.447	0.587	SUBCLONAL	1	TRUE	1	0.369914116310493	2		617	725	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382214	152382214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	105	399	0	ENST00000206249.3:c.1324G>A	p.Gly442Arg	p.G442R	ENST00000206249	NM_000125.3	442	Gga/Aga	6/8	0.30111627143558	2	FACETS	0.617	0.552	0.686	0.309	0.276	0.343	SUBCLONAL	1	TRUE	0	0.369914116310493	2		399	920	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303175	11303175	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	128	397	0	ENST00000361445.4:c.1408C>T	p.His470Tyr	p.H470Y	ENST00000361445	NM_004958.3	470	Cat/Tat	9/58	1	2	FACETS	0.912	0.827	1	0.912	0.827	1	CLONAL	1	TRUE	1	0.369914116310493	2		397	759	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579407	7579414	+	frameshift_variant	Frame_Shift_Del	DEL	ACAGGGGC	ACAGGGGC	CCGGGGG	novel	NA	P-0016721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	137	642	1	ENST00000269305.4:c.273_280delinsCCCCCGG	p.Trp91CysfsTer32	p.W91Cfs*32	ENST00000269305	NM_001126112.2	91	tgGCCCCTGTca/tgCCCCCGGca	4/11	0.369914116310493	1	FACETS	0.612	0.556	0.671	0.612	0.556	0.671	SUBCLONAL	1	TRUE	0	0.369914116310493	1		643	987	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236714	236714	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	rs759041443	NA	P-0016721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	47	203	0	ENST00000264932.6:c.1432G>T	p.Gly478Ter	p.G478*	ENST00000264932	NM_004168.2	478	Gga/Tga	10/15	0.139455144066019	4	FACETS	0.784	0.662	0.918			1	INDETERMINATE	1	TRUE	NA	0.369914116310493	4		203	444	SUCCESS
APC	324	MSKCC	GRCh37	5	112175030	112175030	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	23	220	0	ENST00000257430.4:c.3739G>T	p.Ala1247Ser	p.A1247S	ENST00000257430	NM_000038.5	1247	Gcc/Tcc	16/16	0.323268916397938	3	FACETS	0.465	0.362	0.583			1	SUBCLONAL	1	TRUE	NA	0.369914116310493	3		220	317	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106543490	106543490	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1487656517	NA	P-0016721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	66	302	0	ENST00000369096.4:c.292G>T	p.Val98Phe	p.V98F	ENST00000369096	NM_001198.3	98	Gtt/Ttt	3/7	1	2	FACETS	0.762	0.663	0.869	0.762	0.663	0.869	SUBCLONAL	1	TRUE	1	0.369914116310493	2		302	468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0016722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1597	146	869	3	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.618	0.561	0.677	0.618	0.561	0.677	SUBCLONAL	1	TRUE	1	0.271237535137702	2		872	1743	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974765	21974765	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1329324238	NA	P-0016722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	87	184	0	ENST00000304494.5:c.62C>A	p.Ala21Asp	p.A21D	ENST00000304494	NM_000077.4	21	gCc/gAc	1/3	0.271237535137702	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.271237535137702	1		184	455	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247442	71247442	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs750746668	NA	P-0016722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	203	390	0	ENST00000318789.4:c.91G>T	p.Gly31Cys	p.G31C	ENST00000318789	NM_032682.5	31	Ggt/Tgt	6/21	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.271237535137702	2		390	1171	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577088	7577088	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1204379654	NA	P-0016722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1413	300	600	0	ENST00000269305.4:c.850A>C	p.Thr284Pro	p.T284P	ENST00000269305	NM_001126112.2	284	Aca/Cca	8/11	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.271237535137702	2		600	1713	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803598	43803598	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	99	353	0	ENST00000372470.3:c.79G>T	p.Asp27Tyr	p.D27Y	ENST00000372470	NM_005373.2	27	Gat/Tat	1/12	1	2	FACETS	0.633	0.563	0.707	0.633	0.563	0.707	SUBCLONAL	1	TRUE	1	0.271237535137702	2		353	1154	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956229	175956229	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	150	323	0	ENST00000367669.3:c.1983T>A	p.Asn661Lys	p.N661K	ENST00000367669	NM_022457.5	661	aaT/aaA	18/20	1	2	FACETS	0.969	0.883	1	0.969	0.883	1	CLONAL	1	TRUE	1	0.271237535137702	2		323	1142	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457796	69457796	+	splice_region_variant,intron_variant	Splice_Region	SNP	T	T	C	novel	NA	P-0016722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	41	244	0	ENST00000227507.2:c.199-3T>C		p.X67_splice	ENST00000227507	NM_053056.2	67			1	2	FACETS	0.394	0.327	0.469	0.394	0.327	0.469	SUBCLONAL	1	TRUE	1	0.271237535137702	2		244	768	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844107	68844107	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	96	340	0	ENST00000261769.5:c.695C>T	p.Ser232Phe	p.S232F	ENST00000261769	NM_004360.3	232	tCt/tTt	6/16	0.271237535137702	1	FACETS	0.587	0.522	0.657	0.587	0.522	0.657	SUBCLONAL	1	TRUE	0	0.271237535137702	1		340	1042	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41249267	41249267	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1706	155	604	0	ENST00000357654.3:c.587A>C	p.Tyr196Ser	p.Y196S	ENST00000357654	NM_007294.3	196	tAt/tCt	8/23	1	2	FACETS	0.614	0.56	0.672	0.614	0.56	0.672	SUBCLONAL	1	TRUE	1	0.271237535137702	2		604	1861	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610225	10610225	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1206	242	508	0	ENST00000171111.5:c.485A>G	p.Tyr162Cys	p.Y162C	ENST00000171111	NM_203500.1	162	tAc/tGc	2/6	0.271237535137702	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.271237535137702	1		508	1448	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626736	12626736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149580968	NA	P-0016722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	72	314	0	ENST00000251849.4:c.1553G>A	p.Arg518Gln	p.R518Q	ENST00000251849	NM_002880.3	518	cGa/cAa	15/17	0.271237535137702	1	FACETS	0.466	0.406	0.531	0.466	0.406	0.531	SUBCLONAL	1	TRUE	0	0.271237535137702	1		314	985	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948503	31948503	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	162	415	0	ENST00000375333.2:c.986G>T	p.Arg329Leu	p.R329L	ENST00000375333	NM_032454.1	329	cGg/cTg	7/8	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.271237535137702	2		415	1159	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679105	117679105	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs56192249	NA	P-0016722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	258	393	0	ENST00000368508.3:c.3716A>T	p.Tyr1239Phe	p.Y1239F	ENST00000368508	NM_002944.2	1239	tAc/tTc	24/43	0.216019571031961	2	FACETS	0.839	0.785	0.894	0.839	0.785	0.894	CLONAL	2	TRUE	0	0.271237535137702	2		393	1134	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372684	81372684	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	45	202	0	ENST00000222390.5:c.850G>C	p.Ala284Pro	p.A284P	ENST00000222390	NM_000601.4	284	Gca/Cca	7/18	1	2	FACETS	0.538	0.451	0.634	0.538	0.451	0.634	SUBCLONAL	1	TRUE	1	0.271237535137702	2		202	617	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633229	12633229	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs368807126	NA	P-0016724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1169	140	442	0	ENST00000251849.4:c.1171A>T	p.Arg391Trp	p.R391W	ENST00000251849	NM_002880.3	391	Agg/Tgg	11/17	1	2	FACETS	0.894	0.812	0.981	0.894	0.812	0.981	CLONAL	1	TRUE	1	0.239147029805199	2		442	1309	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101300	27101300	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1423	203	609	1	ENST00000324856.7:c.4582C>T	p.Arg1528Ter	p.R1528*	ENST00000324856	NM_006015.4	1528	Cga/Tga	18/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.239147029805199	2		610	1626	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24134006	24134006	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	164	496	2	ENST00000263121.7:c.157C>T	p.Arg53Ter	p.R53*	ENST00000263121	NM_003073.3	53	Cga/Tga	2/9	0.239147029805199	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.239147029805199	1		498	1186	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0016727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1285	361	800	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	NA	2	FACETS	0.968	0.915	1			1	INDETERMINATE	2	TRUE	NA	0.226649466907671	2		801	1646	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0016727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	395	643	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.226649466907671	4	FACETS	0.968	0.919	1	1	0.995	1	CLONAL	3	TRUE	2	0.226649466907671	4		643	1472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0016729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	191	397	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.242900391217585	2	FACETS	0.842	0.779	0.906	0.842	0.779	0.906	CLONAL	2	TRUE	0	0.269140722305198	2		397	843	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0016729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	124	458	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	0.269140722305198	6	FACETS	1	0.967	1			1	CLONAL	1	TRUE	NA	0.269140722305198	6		458	1217	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591269	67591345	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCGGCAAAAGAAGTTGAACGAGTGGTTGGGCAATGAAAACACTGAAGAGTAAGTAGTTACTAAAGATGGTGATAGCA	TCGGCAAAAGAAGTTGAACGAGTGGTTGGGCAATGAAAACACTGAAGAGTAAGTAGTTACTAAAGATGGTGATAGCA	-	novel	NA	P-0016729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	60	289	0	ENST00000274335.5:c.1767_1814+29del		p.X589_splice	ENST00000274335		589		13/15	0.25585735410307	4	FACETS	0.8	0.689	0.922	0.4	0.344	0.461	CLONAL	1	TRUE	2	0.269140722305198	4		289	707	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877813	151877814	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0016729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	162	181	0	ENST00000262189.6:c.7131_7132del	p.Thr2378ArgfsTer11	p.T2378Rfs*11	ENST00000262189	NM_170606.2	2377	gaTAca/gaca	36/59	0.260381379972275	3	FACETS	0.998	0.925	1	0.998	0.925	1	CLONAL	3	TRUE	0	0.269140722305198	3		181	456	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835780	68835781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0016730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	43	1178	2	ENST00000261769.5:c.377dup	p.Pro127AlafsTer41	p.P127Afs*41	ENST00000261769	NM_004360.3	124	cgc/cgCc	3/16	1	2	FACETS	0.348	0.29	0.413	0.348	0.29	0.413	SUBCLONAL	1	TRUE	1	0.33272989421254	2		1180	742	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929262	32929262	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	75	1590	1	ENST00000380152.3:c.7272G>T	p.Arg2424Ser	p.R2424S	ENST00000380152		2424	agG/agT	14/27	1	2	FACETS	0.359	0.313	0.409	0.359	0.313	0.409	SUBCLONAL	1	TRUE	1	0.33272989421254	2		1591	1255	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	620	486	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.460168473921622	5	FACETS	1	0.992	1	1	0.992	1	CLONAL	4	TRUE	1	0.460168473921622	5		486	1062	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0016732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	117	501	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			0.253995952096967	1	FACETS	0.702	0.635	0.772	0.702	0.635	0.772	INDETERMINATE	1	TRUE	0	0.460168473921622	1		501	558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577518	7577518	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519995	NA	P-0016732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	364	629	0	ENST00000269305.4:c.763A>T	p.Ile255Phe	p.I255F	ENST00000269305	NM_001126112.2	255	Atc/Ttc	7/11	0.393495890209089	3	FACETS	0.874	0.835	0.913	0.874	0.835	0.913	CLONAL	3	TRUE	0	0.460168473921622	3		629	742	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56811497	56811497	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1567818564	NA	P-0016732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	252	663	0	ENST00000337432.4:c.1045A>G	p.Thr349Ala	p.T349A	ENST00000337432	NM_058216.2	349	Act/Gct	9/9	0.460168473921622	4	FACETS	1	0.989	1	0.638	0.596	0.681	CLONAL	1	TRUE	2	0.460168473921622	4		663	1254	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78921143	78921143	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	121	473	1	ENST00000306801.3:c.3257C>T	p.Thr1086Met	p.T1086M	ENST00000306801	NM_020761.2	1086	aCg/aTg	27/34	0.2035284850958	5	FACETS	1	0.98	1	0.44	0.398	0.484	INDETERMINATE	1	TRUE	2	0.460168473921622	5		474	674	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259167	36259167	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	445	680	1	ENST00000300305.3:c.324C>A	p.Cys108Ter	p.C108*	ENST00000300305		108	tgC/tgA	3/8	0.460168473921622	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.460168473921622	3		681	1159	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813370	32813370	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1510	257	828	1	ENST00000354258.4:c.2413G>T	p.Asp805Tyr	p.D805Y	ENST00000354258	NM_000593.5	805	Gat/Tat	11/11	0.406683327798132	4	FACETS	0.923	0.861	0.987	0.462	0.43	0.494	CLONAL	1	TRUE	2	0.460168473921622	4		829	1767	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016732-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	644	486	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.692330602979429	5	FACETS	1	0.989	1	1	0.989	1	CLONAL	4	TRUE	1	0.692330602979429	5		486	922	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0016732-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	142	501	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			NA	2	FACETS	0.941	0.865	1			1	INDETERMINATE	1	TRUE	NA	0.692330602979429	2		501	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577518	7577518	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519995	NA	P-0016732-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	402	629	0	ENST00000269305.4:c.763A>T	p.Ile255Phe	p.I255F	ENST00000269305	NM_001126112.2	255	Atc/Ttc	7/11	0.60131299285057	3	FACETS	0.889	0.859	0.919	0.889	0.859	0.919	CLONAL	3	TRUE	0	0.692330602979429	3		629	586	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56811497	56811497	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1567818564	NA	P-0016732-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	294	663	0	ENST00000337432.4:c.1045A>G	p.Thr349Ala	p.T349A	ENST00000337432	NM_058216.2	349	Act/Gct	9/9	0.691433086107189	5	FACETS	0.908	0.857	0.961	0.606	0.571	0.641	CLONAL	2	TRUE	2	0.692330602979429	5		663	953	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78921143	78921143	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016732-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	121	473	1	ENST00000306801.3:c.3257C>T	p.Thr1086Met	p.T1086M	ENST00000306801	NM_020761.2	1086	aCg/aTg	27/34	0.692330602979429	4	FACETS	0.951	0.861	1	0.317	0.287	0.349	CLONAL	1	TRUE	1	0.692330602979429	4		474	622	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259167	36259167	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016732-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	329	680	1	ENST00000300305.3:c.324C>A	p.Cys108Ter	p.C108*	ENST00000300305		108	tgC/tgA	3/8	0.692330602979429	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.692330602979429	3		681	632	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813370	32813370	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016732-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	167	828	1	ENST00000354258.4:c.2413G>T	p.Asp805Tyr	p.D805Y	ENST00000354258	NM_000593.5	805	Gat/Tat	11/11	0.535814671488314	4	FACETS	0.785	0.72	0.853	0.393	0.36	0.427	SUBCLONAL	1	TRUE	2	0.692330602979429	4		829	1040	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993399	72993399	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1243611387	NA	P-0016733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	57	1401	0	ENST00000268489.5:c.646C>T	p.Pro216Ser	p.P216S	ENST00000268489	NM_006885.3	216	Ccg/Tcg	2/10	0.3	0	FACETS	0.404	0.346	0.467			1	SUBCLONAL	1	TRUE	0	0.32	0		1401	600	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63810652	63810652	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs753041204	NA	P-0016733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	260	675	0	ENST00000279873.7:c.739A>G	p.Asn247Asp	p.N247D	ENST00000279873	NM_032199.2	247	Aat/Gat	5/10	NA	2	FACETS	1	0.954	1			1	INDETERMINATE	2	TRUE	NA	0.32	2		675	799	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220012	133220012	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	85	1035	0	ENST00000320574.5:c.4425G>C	p.Gln1475His	p.Q1475H	ENST00000320574	NM_006231.2	1475	caG/caC	34/49	0.210570637584447	0	FACETS	0.667	0.59	0.748			1	SUBCLONAL	1	TRUE	0	0.32	0		1035	542	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609721	28609721	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	83	1471	1	ENST00000241453.7:c.1508T>A	p.Met503Lys	p.M503K	ENST00000241453	NM_004119.2	503	aTg/aAg	12/24	0.3	1	FACETS	0.473	0.416	0.534	0.473	0.416	0.534	SUBCLONAL	1	TRUE	0	0.32	1		1472	921	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56339014	56339014	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	23	158	1	ENST00000348428.3:c.139C>T	p.Gln47Ter	p.Q47*	ENST00000348428	NM_006785.3	47	Cag/Tag	1/17	0.3	1	FACETS	0.745	0.586	0.926	0.745	0.586	0.926	CLONAL	1	TRUE	0	0.32	1		159	162	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29099511	29099535	+	frameshift_variant	Frame_Shift_Del	DEL	TAATCTTCTGCATCAAAAAAGTTTT	TAATCTTCTGCATCAAAAAAGTTTT	-	novel	NA	P-0016733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	93	1415	0	ENST00000328354.6:c.866_890del	p.Lys289IlefsTer7	p.K289Ifs*7	ENST00000328354	NM_007194.3	289	aAAAACTTTTTTGATGCAGAAGATTAt/at	8/15	1	2	FACETS	0.587	0.52	0.658	0.587	0.52	0.658	SUBCLONAL	1	TRUE	1	0.32	2		1415	991	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427700	72427700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	156	586	1	ENST00000477973.2:c.790G>A	p.Glu264Lys	p.E264K	ENST00000477973	NM_012234.5	264	Gaa/Aaa	4/4	1	2	FACETS	0.916	0.844	0.991	1	0.991	1	CLONAL	2	TRUE	1	0.32	2		587	532	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84406180	84406180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	208	1129	1	ENST00000321945.7:c.46G>A	p.Gly16Ser	p.G16S	ENST00000321945	NM_139076.2	16	Ggc/Agc	1/9	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.32	2		1130	892	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960216	151960216	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0016733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	78	503	0	ENST00000262189.6:c.1185-1G>C		p.X395_splice	ENST00000262189	NM_170606.2	395			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.32	2		503	348	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206665080	206665080	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	160	736	1	ENST00000367120.3:c.1833G>A	p.Met611Ile	p.M611I	ENST00000367120	NM_014002.3	611	atG/atA	18/22	NA	2	FACETS	0.333	0.304	0.363			1	INDETERMINATE	1	TRUE	NA	0.777208225145814	2		737	1236	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115861	8115886	+	frameshift_variant	Frame_Shift_Del	DEL	CTGAGCCACATCTCGCCCTTCAGCCA	CTGAGCCACATCTCGCCCTTCAGCCA	-	novel	NA	P-0016734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1647	254	1451	0	ENST00000346208.3:c.1209_1234del	p.Ser404GlnfsTer94	p.S404Qfs*94	ENST00000346208		403	CTGAGCCACATCTCGCCCTTCAGCCAc/c	6/6	0.461625789459884	3	FACETS	0.477	0.445	0.511	0.239	0.222	0.256	INDETERMINATE	1	TRUE	1	0.777208225145814	3		1451	1901	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47684718	47684718	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs369378549	NA	P-0016734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	998	1342	2	ENST00000347630.2:c.731A>G	p.Asn244Ser	p.N244S	ENST00000347630	NM_001007230.1	244	aAt/aGt	9/11	0.40299495727754	2	FACETS	0.751	0.733	0.77	0.751	0.733	0.77	INDETERMINATE	2	TRUE	0	0.777208225145814	2		1344	1709	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973231	25973231	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	171	665	0	ENST00000435504.4:c.1194T>A	p.Asp398Glu	p.D398E	ENST00000435504		398	gaT/gaA	12/13	0.388233995083946	1	FACETS	0.365	0.336	0.394	0.365	0.336	0.394	INDETERMINATE	1	TRUE	0	0.777208225145814	1		665	738	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401430	401430	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199834880	NA	P-0016734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	74	324	1	ENST00000380956.4:c.752G>A	p.Arg251Gln	p.R251Q	ENST00000380956	NM_001195286.1	251	cGg/cAg	7/9	NA	2	FACETS	0.643	0.569	0.722			1	INDETERMINATE	1	TRUE	NA	0.777208225145814	2		325	296	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	144	423	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.951	0.875	1	0.951	0.875	1	CLONAL	1	TRUE	1	0.701349469003854	2		423	432	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692908	89692908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514560	NA	P-0016735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	431	1317	0	ENST00000371953.3:c.392C>T	p.Thr131Ile	p.T131I	ENST00000371953	NM_000314.4	131	aCt/aTt	5/9	0.701349469003854	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.701349469003854	1		1317	777	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6045561	6045561	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	323	1348	0	ENST00000265849.7:c.125T>C	p.Leu42Ser	p.L42S	ENST00000265849	NM_000535.5	42	tTa/tCa	2/15	0.701349469003854	3	FACETS	0.912	0.86	0.965	0.456	0.43	0.483	CLONAL	1	TRUE	1	0.701349469003854	3		1348	1364	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339387	116339387	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs751158831	NA	P-0016736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	115	660	0	ENST00000397752.3:c.249G>C	p.Glu83Asp	p.E83D	ENST00000397752	NM_000245.2	83	gaG/gaC	2/21	0.170938853456876	2	FACETS	0.973	0.878	1	0.973	0.878	1	CLONAL	2	TRUE	0	0.17	2		660	695	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411877	116411888	+	intron_variant	Intron	DEL	AGCTCTTTCTTT	AGCTCTTTCTTT	-	novel	NA	P-0016736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1668	314	2083	0	ENST00000397752.3:c.2888-26_2888-15del		p.*963*	ENST00000397752	NM_000245.2	-/1390			0.170938853456876	2	FACETS	0.932	0.876	0.99	0.932	0.876	0.99	CLONAL	2	TRUE	0	0.17	2		2083	1982	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0016736-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	246	731	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	0.357772036273422	2		731	1017	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0016736-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	24	623	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.357772036273422	1	FACETS	0.176	0.137	0.221	0.176	0.137	0.221	SUBCLONAL	1	TRUE	0	0.357772036273422	1		623	626	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039684	47039684	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016736-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	181	478	0	ENST00000377604.3:c.1136T>A	p.Val379Asp	p.V379D	ENST00000377604	NM_001204468.1	379	gTt/gAt	11/24	1	1	FACETS	0.754	0.7	0.809	1	0.991	1	SUBCLONAL	2	TRUE	0	0.357772036273422	1		478	551	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0016737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	14	585	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	0.194743103121585	3	FACETS	1	0.731	1	0.5	0.365	0.659	CLONAL	1	TRUE	1	0.311077776363144	3		585	104	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023903	27023910	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGGGGC	TGGGGGGC	-	novel	NA	P-0016737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	13	365	0	ENST00000324856.7:c.1011_1018del	p.Trp337CysfsTer60	p.W337Cfs*60	ENST00000324856	NM_006015.4	337	TGGGGGGCt/t	1/20	1	2	FACETS	1	0.824	1	1	0.824	1	CLONAL	1	TRUE	1	0.311077776363144	2		365	70	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0016737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	27	1620	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.311077776363144	2		1620	123	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713589	52713610	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CAGGATCTACAGTTGGAAGATT	CAGGATCTACAGTTGGAAGATT	-	novel	NA	P-0016737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	23	905	0	ENST00000394830.3:c.118_138+1del		p.X40_splice	ENST00000394830	NM_018313.4	40		2/30	0.311077776363144	1	FACETS	0.873	0.689	1	0.873	0.689	1	CLONAL	1	TRUE	0	0.311077776363144	1		905	143	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249399	153249399	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	32	1203	1	ENST00000281708.4:c.1379A>G	p.His460Arg	p.H460R	ENST00000281708	NM_033632.3	460	cAt/cGt	9/12	0.194743103121585	3	FACETS	0.868	0.716	1	0.868	0.716	1	CLONAL	2	TRUE	1	0.311077776363144	3		1204	137	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346903	89346903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1190073937	NA	P-0016738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	42	121	0	ENST00000301030.4:c.6047C>T	p.Pro2016Leu	p.P2016L	ENST00000301030	NM_001256183.1	2016	cCc/cTc	9/13	0.238489530278087	3	FACETS	0.939	0.792	1	0.626	0.528	0.732	CLONAL	2	FALSE	0	0.238489530278087	3		121	210	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170701	7170701	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1344	180	674	0	ENST00000302850.5:c.1330C>G	p.His444Asp	p.H444D	ENST00000302850	NM_000208.2	444	Cac/Gac	6/22	0.238489530278087	5	FACETS	1	0.986	1	0.672	0.618	0.73	CLONAL	1	FALSE	3	0.238489530278087	5		674	1524	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960134	134960134	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	154	427	0	ENST00000398015.3:c.2491C>A	p.Gln831Lys	p.Q831K	ENST00000398015	NM_004441.4	831	Caa/Aaa	13/16	0.238489530278087	3	FACETS	0.754	0.69	0.822	0.754	0.69	0.822	SUBCLONAL	2	FALSE	1	0.238489530278087	3		427	958	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	428	486	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.358195094269369	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.358195094269369	3		486	858	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023307	27023307	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0016739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	83	278	0	ENST00000324856.7:c.413C>G	p.Ser138Ter	p.S138*	ENST00000324856	NM_006015.4	138	tCa/tGa	1/20	1	2	FACETS	0.784	0.693	0.882	0.784	0.693	0.882	SUBCLONAL	1	TRUE	1	0.358195094269369	2		278	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578518	7578518	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934875	NA	P-0016739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	534	969	0	ENST00000269305.4:c.412G>C	p.Ala138Pro	p.A138P	ENST00000269305	NM_001126112.2	138	Gcc/Ccc	5/11	0.358195094269369	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.358195094269369	1		969	1661	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518911	187518911	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	435	481	0	ENST00000441802.2:c.12293G>T	p.Cys4098Phe	p.C4098F	ENST00000441802	NM_005245.3	4098	tGt/tTt	24/27	1	2	FACETS	0.935	0.896	0.975	0.935	0.896	0.975	CLONAL	1	TRUE	1	0.961745947416433	2		481	967	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244700	46244700	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	988	559	0	ENST00000334344.6:c.2795del	p.Pro932GlnfsTer31	p.P932Qfs*31	ENST00000334344	NM_152641.2	932	Cca/ca	15/21	0.875132091540941	4	FACETS	0.935	0.909	0.961	0.935	0.909	0.961	CLONAL	2	TRUE	2	0.961745947416433	4		559	2156	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427507	49427507	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	864	386	0	ENST00000301067.7:c.10981G>C	p.Gly3661Arg	p.G3661R	ENST00000301067	NM_003482.3	3661	Ggt/Cgt	39/54	0.875132091540941	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.961745947416433	4		386	1733	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934162	48934162	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0016740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	456	287	0	ENST00000267163.4:c.617T>G	p.Leu206Ter	p.L206*	ENST00000267163	NM_000321.2	206	tTa/tGa	7/27	NA	2	FACETS	1	0.997	1			1	INDETERMINATE	2	TRUE	NA	0.961745947416433	2		287	461	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042217	42042217	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	895	473	0	ENST00000219905.7:c.6412A>T	p.Ser2138Cys	p.S2138C	ENST00000219905	NM_001164273.1	2138	Agt/Tgt	17/24	0.961745947416433	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.961745947416433	2		473	918	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136847	2136847	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	494	511	0	ENST00000219476.3:c.4964A>T	p.Glu1655Val	p.E1655V	ENST00000219476	NM_000548.3	1655	gAg/gTg	38/42	1	2	FACETS	0.955	0.917	0.992	0.955	0.917	0.992	CLONAL	1	TRUE	1	0.961745947416433	2		511	1076	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578480	+	inframe_deletion	In_Frame_Del	DEL	GGGGGT	GGGGGT	-	novel	NA	P-0016740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	2317	744	0	ENST00000269305.4:c.450_455del	p.Pro152_Pro153del	p.P152_P153del	ENST00000269305	NM_001126112.2	150	acACCCCCg/acg	5/11	0.958375248396255	3	FACETS	0.996	0.991	1	0.996	0.991	1	CLONAL	3	TRUE	0	0.961745947416433	3		744	2388	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41276049	41276049	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs80357438	NA	P-0016740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1308	403	475	1	ENST00000357654.3:c.65T>A	p.Leu22Ter	p.L22*	ENST00000357654	NM_007294.3	22	tTa/tAa	2/23	0.961745947416433	4	FACETS	0.961	0.912	1	0.32	0.304	0.337	CLONAL	1	TRUE	1	0.961745947416433	4		476	1711	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659968	227659968	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	484	597	0	ENST00000305123.5:c.3487C>A	p.Pro1163Thr	p.P1163T	ENST00000305123	NM_005544.2	1163	Cca/Aca	1/2	1	2	FACETS	0.983	0.944	1	0.983	0.944	1	CLONAL	1	TRUE	1	0.961745947416433	2		597	1024	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143352342	143352342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	371	408	0	ENST00000262992.4:c.71C>T	p.Pro24Leu	p.P24L	ENST00000262992	NM_001101669.1	24	cCc/cTc	2/24	1	2	FACETS	0.99	0.946	1	0.99	0.946	1	CLONAL	1	TRUE	1	0.961745947416433	2		408	779	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053029	180053029	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs776682740	NA	P-0016740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	1383	611	0	ENST00000261937.6:c.1261C>T	p.Pro421Ser	p.P421S	ENST00000261937	NM_182925.4	421	Ccc/Tcc	10/30	0.961745947416433	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.961745947416433	2		611	1431	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863280	56863280	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	318	516	0	ENST00000519728.1:c.424C>T	p.Gln142Ter	p.Q142*	ENST00000519728	NM_002350.3	142	Cag/Tag	6/13	0.948619055509415	3	FACETS	0.845	0.797	0.894	0.422	0.398	0.447	CLONAL	1	TRUE	1	0.961745947416433	3		516	1159	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	200	423	0				ENST00000310581	NM_198253.2	-/1132			0.193910968105205	3	FACETS	0.953	0.887	1	0.953	0.887	1	INDETERMINATE	2	TRUE	1	0.381609884365323	3		423	655	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894228	NA	P-0016742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	245	663	0	ENST00000451590.1:c.37G>C	p.Gly13Arg	p.G13R	ENST00000451590	NM_001130442.1	13	Ggt/Cgt	2/5	0.193910968105205	3	FACETS	0.835	0.781	0.89	0.835	0.781	0.89	INDETERMINATE	2	TRUE	1	0.381609884365323	3		663	916	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0016742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	305	545	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.381609884365323	3	FACETS	0.976	0.922	1	0.976	0.922	1	CLONAL	2	TRUE	1	0.381609884365323	3		545	975	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092809	27092809	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	91	563	1	ENST00000324856.7:c.2830C>T	p.Gln944Ter	p.Q944*	ENST00000324856	NM_006015.4	944	Cag/Tag	9/20	1	2	FACETS	0.538	0.477	0.604	0.538	0.477	0.604	SUBCLONAL	1	TRUE	1	0.381609884365323	2		564	886	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905397	11905397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	54	306	0	ENST00000396373.4:c.47C>T	p.Ser16Leu	p.S16L	ENST00000396373	NM_001987.4	16	tCa/tTa	2/8	0.193910968105205	3	FACETS	0.552	0.471	0.64	0.276	0.235	0.32	INDETERMINATE	1	TRUE	1	0.381609884365323	3		306	611	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs863224683	NA	P-0016743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1380	64	905	0	ENST00000269305.4:c.388C>G	p.Leu130Val	p.L130V	ENST00000269305	NM_001126112.2	130	Ctc/Gtc	5/11	1	2	FACETS	0.739	0.637	0.85	0.739	0.637	0.85	SUBCLONAL	1	TRUE	1	0.12	2		905	1444	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913274	NA	P-0016743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	28	597	0	ENST00000263967.3:c.1634A>C	p.Glu545Ala	p.E545A	ENST00000263967	NM_006218.2	545	gAg/gCg	10/21	0.3	9	FACETS	1	0.831	1			1	CLONAL	1	TRUE	NA	0.12	9		597	632	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	95	423	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.998	0.889	1	0.998	0.889	1	CLONAL	1	TRUE	1	0.26	2		423	732	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0016744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	284	568	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.27914217246569	3	FACETS	0.837	0.785	0.891	0.837	0.785	0.891	CLONAL	2	TRUE	1	0.26	3		568	1474	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251839	212251839	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	32	239	0	ENST00000342788.4:c.3220G>A	p.Glu1074Lys	p.E1074K	ENST00000342788	NM_005235.2	1074	Gaa/Aaa	27/28	1	2	FACETS	0.457	0.37	0.555	0.457	0.37	0.555	SUBCLONAL	1	TRUE	1	0.26	2		239	539	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186757	108186757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs864622251	NA	P-0016744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	201	534	0	ENST00000278616.4:c.6115G>A	p.Glu2039Lys	p.E2039K	ENST00000278616	NM_000051.3	2039	Gaa/Aaa	42/63	0.29913387465684	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.26	1		534	1196	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156680	2156680	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1236	91	591	1	ENST00000434045.2:c.242C>A	p.Ala81Asp	p.A81D	ENST00000434045	NM_001127598.1	81	gCt/gAt	3/5	1	2	FACETS	0.528	0.466	0.593	0.528	0.466	0.593	SUBCLONAL	1	TRUE	1	0.26	2		592	1327	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953214	81953214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369516453	NA	P-0016744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	67	217	0	ENST00000359376.3:c.2180G>A	p.Arg727Gln	p.R727Q	ENST00000359376	NM_002661.3	727	cGa/cAa	20/33	0.29913387465684	1	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	0	0.26	1		217	441	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618499	37618499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	70	418	1	ENST00000447079.4:c.175G>A	p.Glu59Lys	p.E59K	ENST00000447079	NM_015083.1	59	Gaa/Aaa	1/14	0.27914217246569	3	FACETS	0.531	0.462	0.607	0.266	0.231	0.304	SUBCLONAL	1	TRUE	1	0.26	3		419	1145	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17124884	17124890	+	stop_gained	Nonsense_Mutation	DEL	CGGTCGG	CGGTCGG	A	novel	NA	P-0016744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	163	535	1	ENST00000285071.4:c.832_838delinsT	p.Pro278_Glu280delinsTer	p.P278_E280delins*	ENST00000285071	NM_144997.5	278	CCGACCGag/Tag	8/14	0.29913387465684	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.26	1		536	935	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0016746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	42	2255	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.641	0.534	0.761	0.641	0.534	0.761	SUBCLONAL	1	TRUE	1	0.18	2		2255	728	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0016747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	3804	547	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.401343560091282	15	FACETS	0.988	0.978	0.997			1	CLONAL	14	TRUE	NA	0.401343560091282	15		547	4947	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578292	7578292	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	C	rs763746485	NA	P-0016747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	190	437	0	ENST00000269305.4:c.560-3T>G		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.401343560091282	1	FACETS	0.916	0.848	0.987	0.916	0.848	0.987	CLONAL	1	TRUE	0	0.401343560091282	1		437	826	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434494	140434494	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1436193121	NA	P-0016747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	155	341	0	ENST00000288602.6:c.2204G>A	p.Arg735Gln	p.R735Q	ENST00000288602	NM_004333.4	735	cGg/cAg	18/18	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.401343560091282	2		341	734	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0016749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	948	533	2	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	0.567975623175795	5	FACETS	0.951	0.938	0.962			1	CLONAL	5	TRUE	NA	0.881053638274034	5		535	1051	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242436	55242436	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	282	431	0	ENST00000275493.2:c.2206G>A	p.Glu736Lys	p.E736K	ENST00000275493	NM_005228.3	736	Gag/Aag	19/28	0.881053638274034	5	FACETS	0.998	0.936	1	0.333	0.312	0.355	CLONAL	1	TRUE	2	0.881053638274034	5		431	1489	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670356	246670356	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	116	325	1	ENST00000388985.4:c.164G>A	p.Gly55Glu	p.G55E	ENST00000388985		55	gGg/gAg	1/12	0.462447345149302	6	FACETS	1	0.979	1	0.438	0.396	0.482	INDETERMINATE	1	TRUE	3	0.881053638274034	6		326	554	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59924535	59924535	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	767	291	0	ENST00000259008.2:c.554C>A	p.Ala185Glu	p.A185E	ENST00000259008	NM_032043.2	185	gCa/gAa	6/20	0.881053638274034	5	FACETS	1	0.998	1	1	0.998	1	CLONAL	5	TRUE	0	0.881053638274034	5		291	789	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	148	423	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.66	2		423	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0016751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	25	521	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.08	0.062	0.1	0.08	0.062	0.1	SUBCLONAL	1	TRUE	1	0.66	2		523	950	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	77	423	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.412765934823035	2		423	289	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0016761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	127	480	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.412765934823035	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.412765934823035	1		480	471	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534285	534285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894226	NA	P-0016761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	320	622	0	ENST00000451590.1:c.38G>T	p.Gly13Val	p.G13V	ENST00000451590	NM_001130442.1	13	gGt/gTt	2/5	0.0797273904591747	4	FACETS	0.952	0.904	1	1	0.994	1	INDETERMINATE	3	TRUE	2	0.412765934823035	4		622	767	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098801	178098801	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	231	716	0	ENST00000397062.3:c.244G>C	p.Glu82Gln	p.E82Q	ENST00000397062	NM_006164.4	82	Gaa/Caa	2/5	1	2	FACETS	0.874	0.813	0.937	0.874	0.813	0.937	CLONAL	1	TRUE	1	0.412765934823035	2		716	1281	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569964	95569964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	195	513	0	ENST00000393063.1:c.3769G>A	p.Val1257Met	p.V1257M	ENST00000393063	NM_030621.3	1257	Gtg/Atg	22/28	0.412765934823035	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.412765934823035	2		513	457	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858758	9858760	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs766019656	NA	P-0016761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	28	265	0	ENST00000330684.3:c.2641_2643del	p.Lys881del	p.K881del	ENST00000330684	NM_001134407.1	881	AAG/-	13/13	1	2	FACETS	0.678	0.546	0.827	0.678	0.546	0.827	SUBCLONAL	1	TRUE	1	0.412765934823035	2		265	200	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541414	187541415	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0016761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	133	420	0	ENST00000441802.2:c.6325_6326del	p.Asp2109GlnfsTer16	p.D2109Qfs*16	ENST00000441802	NM_005245.3	2109	GAc/c	10/27	0.0797273904591747	4	FACETS	0.834	0.761	0.91	0.834	0.761	0.91	INDETERMINATE	2	TRUE	2	0.412765934823035	4		420	546	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0016763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	727	643	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.849300663663543	3	FACETS	0.999	0.971	1	0.999	0.971	1	CLONAL	2	TRUE	1	0.88238606354674	3		643	1189	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087551	27087566	+	frameshift_variant	Frame_Shift_Del	DEL	TCTCGCTCAGGACCAC	TCTCGCTCAGGACCAC	-	novel	NA	P-0016763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	271	672	0	ENST00000324856.7:c.2131_2146del	p.Ser711LeufsTer26	p.S711Lfs*26	ENST00000324856	NM_006015.4	709	TCTCGCTCAGGACCACtc/tc	5/20	NA	2	FACETS	0.775	0.73	0.82			1	INDETERMINATE	1	TRUE	NA	0.88238606354674	2		672	793	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134561	41134561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780271950	NA	P-0016763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	651	498	0	ENST00000379561.5:c.1067C>T	p.Ala356Val	p.A356V	ENST00000379561	NM_002015.3	356	gCc/gTc	2/3	0.88238606354674	2	FACETS	0.986	0.969	1	0.986	0.969	1	CLONAL	2	TRUE	0	0.88238606354674	2		498	748	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919223	48919244	+	frameshift_variant	Frame_Shift_Del	DEL	AAATTCTTTAACTTACTAAAAG	AAATTCTTTAACTTACTAAAAG	-	novel	NA	P-0016763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	261	256	1	ENST00000267163.4:c.393_414del	p.Phe131LeufsTer15	p.F131Lfs*15	ENST00000267163	NM_000321.2	130	AAATTCTTTAACTTACTAAAAGaa/aa	4/27	0.88238606354674	2	FACETS	0.967	0.938	0.993	0.967	0.938	0.993	CLONAL	2	TRUE	0	0.88238606354674	2		257	306	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71161707	71161707	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	257	469	0	ENST00000318789.4:c.262G>T	p.Asp88Tyr	p.D88Y	ENST00000318789	NM_032682.5	88	Gac/Tac	7/21	0.88238606354674	1	FACETS	0.917	0.88	0.952	0.917	0.88	0.952	CLONAL	1	TRUE	0	0.88238606354674	1		469	355	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008947	152008947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	403	712	0	ENST00000262189.6:c.675G>A	p.Trp225Ter	p.W225*	ENST00000262189	NM_170606.2	225	tgG/tgA	5/59	0.88238606354674	1	FACETS	0.995	0.967	1	0.995	0.967	1	CLONAL	1	TRUE	0	0.88238606354674	1		712	513	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0016764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	124	1585	1	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.270584570563913	2		1586	831	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519988	NA	P-0016764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	72	711	1	ENST00000269305.4:c.808T>C	p.Phe270Leu	p.F270L	ENST00000269305	NM_001126112.2	270	Ttt/Ctt	8/11	1	2	FACETS	0.629	0.548	0.716	0.629	0.548	0.716	SUBCLONAL	1	TRUE	1	0.270584570563913	2		712	846	SUCCESS
APC	324	MSKCC	GRCh37	5	112157682	112157682	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1060503340	NA	P-0016764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	75	308	0	ENST00000257430.4:c.1402G>T	p.Glu468Ter	p.E468*	ENST00000257430	NM_000038.5	468	Gaa/Taa	11/16	0.260467408757907	2	FACETS	1	0.976	1	0.737	0.65	0.83	CLONAL	1	TRUE	0	0.270584570563913	2		308	376	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411777	63411777	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	97	814	0	ENST00000330258.3:c.1390del	p.Ala464ProfsTer77	p.A464Pfs*77	ENST00000330258	NM_152424.3	464	Gcc/cc	2/2	0.270584570563913	1	FACETS	0.973	0.869	1	0.973	0.869	1	CLONAL	1	TRUE	0	0.270584570563913	1		814	637	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0016765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	383	309	1	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		310	1028	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0016766-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	47	2255	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.241285252495275	3	FACETS	0.981	0.864	1	1	0.964	1	CLONAL	4	TRUE	0	0.311167627622882	3		2255	89	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132464	11132468	+	stop_gained	Nonsense_Mutation	ONP	ACGCA	ACGCA	TAGCT	novel	NA	P-0016766-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	14	576	0	ENST00000358026.2:c.2680_2684delinsTAGCT	p.Thr894_Gln895delinsTer	p.T894_Q895delins*	ENST00000358026	NM_001128849.1	894	ACGCAg/TAGCTg	19/36	0.311167627622882	3	FACETS	0.867	0.632	1	0.433	0.316	0.573	CLONAL	1	TRUE	1	0.311167627622882	3		576	120	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0016766-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	15	553	2	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	1	2	FACETS	0.765	0.575	0.98	1	0.901	1	CLONAL	2	TRUE	1	0.311167627622882	2		555	63	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619172	43619172	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016766-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	35	473	0	ENST00000355710.3:c.2855A>G	p.Tyr952Cys	p.Y952C	ENST00000355710	NM_020975.4	952	tAt/tGt	17/20	0.311167627622882	4	FACETS	1	0.921	1	1	0.921	1	CLONAL	2	TRUE	2	0.311167627622882	4		473	125	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43769885	43769885	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016766-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	14	496	1	ENST00000382044.4:c.861A>T	p.Gln287His	p.Q287H	ENST00000382044	NM_001141980.1	287	caA/caT	8/28	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.311167627622882	2		497	67	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630660	158630660	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016766-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	18	430	0	ENST00000263640.3:c.583G>T	p.Gly195Cys	p.G195C	ENST00000263640	NM_001105.4	195	Ggt/Tgt	6/11	0.311167627622882	3	FACETS	1	0.861	1	1	0.861	1	CLONAL	2	TRUE	1	0.311167627622882	3		430	58	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326191	62326191	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016766-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	20	495	2	ENST00000360203.5:c.3207G>T	p.Arg1069Ser	p.R1069S	ENST00000360203	NM_001283009.1	1069	agG/agT	32/35	0.311167627622882	8	FACETS	0.963	0.753	1			1	CLONAL	3	TRUE	NA	0.311167627622882	8		497	86	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143006	47143006	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016766-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	42	621	0	ENST00000409792.3:c.4957A>C	p.Thr1653Pro	p.T1653P	ENST00000409792	NM_014159.6	1653	Acc/Ccc	8/21	0.223312202097385	3	FACETS	1	0.892	1	1	0.892	1	CLONAL	2	TRUE	1	0.311167627622882	3		621	147	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890135	76890135	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016766-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	38	615	0	ENST00000373344.5:c.4759G>T	p.Gly1587Cys	p.G1587C	ENST00000373344	NM_000489.3	1587	Ggt/Tgt	17/35	0.235805746538414	2	FACETS	1	0.876	1	1	0.965	1	CLONAL	3	TRUE	0	0.311167627622882	2		615	80	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0016767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	443	936	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.534173792534538	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.534173792534538	2		938	778	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	271	641	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.534173792534538	3	FACETS	0.978	0.925	1	0.978	0.925	1	CLONAL	2	TRUE	1	0.534173792534538	3		641	657	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052636	42052636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1054243525	NA	P-0016767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	201	411	0	ENST00000219905.7:c.7307G>A	p.Arg2436His	p.R2436H	ENST00000219905	NM_001164273.1	2436	cGt/cAt	20/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.534173792534538	2		411	634	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0016767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	80	338	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.534173792534538	2		338	250	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245447	153245447	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	286	507	0	ENST00000281708.4:c.1744T>C	p.Ser582Pro	p.S582P	ENST00000281708	NM_033632.3	582	Tcg/Ccg	11/12	0.534173792534538	3	FACETS	0.92	0.87	0.971	0.92	0.87	0.971	CLONAL	2	TRUE	1	0.534173792534538	3		507	737	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099089	27099089	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	182	529	2	ENST00000324856.7:c.3505C>A	p.Pro1169Thr	p.P1169T	ENST00000324856	NM_006015.4	1169	Cca/Aca	13/20	0.534173792534538	3	FACETS	1	0.968	1	0.544	0.502	0.587	CLONAL	1	TRUE	1	0.534173792534538	3		531	794	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176176017	176176017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1165280945	NA	P-0016767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	145	457	0	ENST00000367669.3:c.98C>T	p.Ser33Phe	p.S33F	ENST00000367669	NM_022457.5	33	tCt/tTt	1/20	0.534173792534538	3	FACETS	1	0.971	1	0.567	0.519	0.616	CLONAL	1	TRUE	1	0.534173792534538	3		457	607	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88672029	88672029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749780872	NA	P-0016767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	109	447	0	ENST00000372037.3:c.563G>A	p.Arg188His	p.R188H	ENST00000372037	NM_004329.2	188	cGt/cAt	8/13	0.534173792534538	3	FACETS	0.993	0.895	1	0.496	0.447	0.548	CLONAL	1	TRUE	1	0.534173792534538	3		447	521	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182001	38182001	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853064	NA	P-0016767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	156	367	0	ENST00000396334.3:c.625C>T	p.Arg209Cys	p.R209C	ENST00000396334	NM_002468.4	209	Cgc/Tgc	3/5	0.534173792534538	3	FACETS	1	0.966	1	0.365	0.335	0.397	CLONAL	1	TRUE	0	0.534173792534538	3		367	675	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721518	49721519	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0016767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	179	481	0	ENST00000449682.2:c.2119_2120dup	p.Phe708SerfsTer16	p.F708Sfs*16	ENST00000449682	NM_020998.3	707	gtc/gtGTc	18/18	0.534173792534538	3	FACETS	0.969	0.894	1	0.485	0.447	0.524	CLONAL	1	TRUE	1	0.534173792534538	3		481	876	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143043279	143043279	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0016767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	38	384	0	ENST00000262992.4:c.2135+2T>A		p.X712_splice	ENST00000262992	NM_001101669.1	712			0.534173792534538	3	FACETS	0.366	0.302	0.437	0.183	0.151	0.219	SUBCLONAL	1	TRUE	1	0.534173792534538	3		384	493	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245380	153245380	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	160	493	0	ENST00000281708.4:c.1811A>C	p.Lys604Thr	p.K604T	ENST00000281708	NM_033632.3	604	aAa/aCa	11/12	0.534173792534538	3	FACETS	0.969	0.89	1	0.485	0.445	0.526	CLONAL	1	TRUE	1	0.534173792534538	3		493	783	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875096	151875097	+	splice_acceptor_variant	Splice_Site	INS	-	-	TT	rs753425356	NA	P-0016767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	13	51	1	ENST00000262189.6:c.7443-3_7443-2dup		p.X2481_splice	ENST00000262189	NM_170606.2	2481			0.534173792534538	4	FACETS	0.754	0.544	1	0.377	0.272	0.502	CLONAL	1	TRUE	2	0.534173792534538	4		52	99	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27203118	27203118	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0016767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	168	468	2	ENST00000380036.4:c.2209+1G>T		p.X737_splice	ENST00000380036	NM_000459.3	737			0.534173792534538	3	FACETS	1	0.965	1	0.542	0.499	0.587	CLONAL	1	TRUE	1	0.534173792534538	3		470	735	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611203	100611203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555977836	NA	P-0016767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	353	410	1	ENST00000308731.7:c.1403G>A	p.Arg468His	p.R468H	ENST00000308731	NM_000061.2	468	cGc/cAc	15/19	0.534173792534538	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	1	0.534173792534538	4		411	630	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106058	8106058	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	222	366	0	ENST00000346208.3:c.878T>A	p.Met293Lys	p.M293K	ENST00000346208		293	aTg/aAg	4/6	0.28022104339405	4	FACETS	0.968	0.904	1	0.968	0.904	1	CLONAL	2	TRUE	2	0.420197423622077	4		366	775	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0016770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	341	547	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.285638503794389	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	3	TRUE	0	0.307275230215406	3		547	849	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0016770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	146	651	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.187949799399825	2	FACETS	1	0.981	1	0.627	0.573	0.683	CLONAL	1	TRUE	0	0.307275230215406	2		651	758	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444680	78444680	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	28	491	0	ENST00000370768.2:c.9C>G	p.Asp3Glu	p.D3E	ENST00000370768	NM_003902.3	3	gaC/gaG	1/20	0.253070670753213	1	FACETS	0.298	0.238	0.368	0.298	0.238	0.368	SUBCLONAL	1	TRUE	0	0.307275230215406	1		491	517	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411983	63411983	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	37	755	1	ENST00000330258.3:c.1184A>T	p.Glu395Val	p.E395V	ENST00000330258	NM_152424.3	395	gAg/gTg	2/2	0.307275230215406	1	FACETS	0.301	0.247	0.362	0.301	0.247	0.362	SUBCLONAL	1	TRUE	0	0.307275230215406	1		756	677	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	678	726	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.611291252870598	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.611291252870598	3		726	1401	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0016775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	756	1227	2	ENST00000269305.4:c.394A>T	p.Lys132Ter	p.K132*	ENST00000269305	NM_001126112.2	132	Aag/Tag	5/11	0.710838034324018	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.710838034324018	1		1229	1300	SUCCESS
APC	324	MSKCC	GRCh37	5	112116462	112116492	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTTTTTTATTATTTGTGGTTTTAGTTTTCC	ACTTTTTTATTATTTGTGGTTTTAGTTTTCC	-	novel	NA	P-0016775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	141	278	0	ENST00000257430.4:c.532-25_537del		p.X178_splice	ENST00000257430	NM_000038.5	178		6/16	0.710838034324018	1	FACETS	0.951	0.885	1	0.951	0.885	1	CLONAL	1	TRUE	0	0.710838034324018	1		278	269	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0016776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	188	419	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	0.760491010959929	3	FACETS	0.973	0.903	1	0.487	0.451	0.524	CLONAL	1	TRUE	1	0.760491010959929	3		419	701	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22405041	22405041	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	168	265	0	ENST00000344548.3:c.70A>G	p.Thr24Ala	p.T24A	ENST00000344548	NM_001039802.1	24	Aca/Gca	3/7	1	2	FACETS	0.687	0.634	0.742	0.687	0.634	0.742	SUBCLONAL	1	TRUE	1	0.760491010959929	2		265	643	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027162	49027171	+	frameshift_variant	Frame_Shift_Del	DEL	AAGGACCGAG	AAGGACCGAG	-	novel	NA	P-0016777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	227	720	0	ENST00000267163.4:c.1736_1745del	p.Arg579GlnfsTer29	p.R579Qfs*29	ENST00000267163	NM_000321.2	577	AAGGACCGAGaa/aa	18/27	0.538797162231121	1	FACETS	0.842	0.788	0.898	0.842	0.788	0.898	CLONAL	1	TRUE	0	0.538797162231121	1		720	731	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149290705	149290705	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	355	625	0	ENST00000360632.3:c.514G>C	p.Val172Leu	p.V172L	ENST00000360632	NM_015472.4	172	Gtc/Ctc	3/7	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.538797162231121	2		625	1203	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659257	86659257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	201	477	0	ENST00000274376.6:c.1546C>G	p.Pro516Ala	p.P516A	ENST00000274376	NM_002890.2	516	Cca/Gca	11/25	1	2	FACETS	0.955	0.888	1	0.955	0.888	1	CLONAL	1	TRUE	1	0.538797162231121	2		477	781	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341273	70341273	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	218	443	0	ENST00000374080.3:c.833del	p.Pro278LeufsTer35	p.P278Lfs*35	ENST00000374080		278	Cct/ct	6/45	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.538797162231121	2		443	754	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0016779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	272	499	1	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.572179942525918	2		500	820	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578188	7578188	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201592	NA	P-0016779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	347	746	1	ENST00000269305.4:c.661G>T	p.Glu221Ter	p.E221*	ENST00000269305	NM_001126112.2	221	Gag/Tag	6/11	1	2	FACETS	0.813	0.769	0.86	0.813	0.769	0.86	CLONAL	1	TRUE	1	0.572179942525918	2		747	1491	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546985	9546985	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	108	236	0	ENST00000353224.5:c.1037G>T	p.Gly346Val	p.G346V	ENST00000353224	NM_177990.2	346	gGg/gTg	5/10	0.120897497057963	3	FACETS	1	0.981	1	0.68	0.616	0.746	INDETERMINATE	1	TRUE	1	0.572179942525918	3		236	357	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027248	49027248	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0016779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	275	498	0	ENST00000267163.4:c.1814+1G>A		p.X605_splice	ENST00000267163	NM_000321.2	605			0.572179942525918	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.572179942525918	1		498	674	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138172	64138172	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	150	686	1	ENST00000334205.4:c.2095C>T	p.Arg699Cys	p.R699C	ENST00000334205	NM_003942.2	699	Cgc/Tgc	16/17	1	2	FACETS	0.492	0.449	0.538	0.492	0.449	0.538	SUBCLONAL	1	TRUE	1	0.572179942525918	2		687	1065	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163700	72163700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	316	581	0	ENST00000357731.5:c.658G>A	p.Val220Ile	p.V220I	ENST00000357731	NM_173808.2	220	Gtt/Att	4/7	0.111156687238231	4	FACETS	0.818	0.772	0.864	0.818	0.772	0.864	INDETERMINATE	2	TRUE	2	0.572179942525918	4		581	1062	SUCCESS
FH	2271	MSKCC	GRCh37	1	241665808	241665808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	387	550	0	ENST00000366560.3:c.1171C>T	p.His391Tyr	p.H391Y	ENST00000366560	NM_000143.3	391	Cat/Tat	8/10	0.28321865359414	4	FACETS	0.815	0.774	0.857	0.815	0.774	0.857	INDETERMINATE	2	TRUE	2	0.572179942525918	4		550	1304	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563057	21563057	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	347	761	0	ENST00000382592.4:c.862A>C	p.Ser288Arg	p.S288R	ENST00000382592	NM_014572.2	288	Agc/Cgc	4/8	NA	2	FACETS	1	0.957	1			1	INDETERMINATE	1	TRUE	NA	0.572179942525918	2		761	1199	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100041	30100041	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	291	558	0	ENST00000331968.5:c.1579G>T	p.Asp527Tyr	p.D527Y	ENST00000331968	NM_002742.2	527	Gat/Tat	10/18	0.111156687238231	4	FACETS	0.776	0.731	0.823	0.776	0.731	0.823	INDETERMINATE	2	TRUE	2	0.572179942525918	4		558	1030	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220370	1220371	+	splice_acceptor_variant	Splice_Site	DNP	AG	AG	TC	novel	NA	P-0016779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	249	477	2	ENST00000326873.7:c.465-2_465-1delinsTC		p.X155_splice	ENST00000326873	NM_000455.4	155			0.572179942525918	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.572179942525918	1		479	531	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602581	10602581	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	291	524	0	ENST00000171111.5:c.997G>C	p.Gly333Arg	p.G333R	ENST00000171111	NM_203500.1	333	Ggc/Cgc	3/6	0.572179942525918	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.572179942525918	1		524	631	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213313	36213313	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	245	736	0	ENST00000222270.7:c.2510C>G	p.Ser837Cys	p.S837C	ENST00000222270	NM_014727.1	837	tCc/tGc	4/37	0.572179942525918	1	FACETS	0.612	0.572	0.653	0.612	0.572	0.653	SUBCLONAL	1	TRUE	0	0.572179942525918	1		736	999	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793440	242793440	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	320	621	2	ENST00000334409.5:c.637C>A	p.Pro213Thr	p.P213T	ENST00000334409	NM_005018.2	213	Ccc/Acc	5/5	0.186576482391241	2	FACETS	1	0.992	1	0.619	0.586	0.653	INDETERMINATE	1	TRUE	0	0.572179942525918	2		623	903	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199890	128199890	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779338723	NA	P-0016779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	87	236	0	ENST00000341105.2:c.1415C>A	p.Pro472Gln	p.P472Q	ENST00000341105	NM_032638.4	472	cCg/cAg	6/6	0.186576482391241	2	FACETS	0.842	0.752	0.938	0.421	0.376	0.469	INDETERMINATE	1	TRUE	0	0.572179942525918	2		236	361	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447318	187447318	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	40	445	0	ENST00000232014.4:c.875C>G	p.Pro292Arg	p.P292R	ENST00000232014	NM_001130845.1	292	cCc/cGc	5/10	0.540192752363766	1	FACETS	0.172	0.142	0.205	0.172	0.142	0.205	SUBCLONAL	1	TRUE	0	0.572179942525918	1		445	582	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542261	187542261	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	130	357	0	ENST00000441802.2:c.5479G>T	p.Gly1827Cys	p.G1827C	ENST00000441802	NM_005245.3	1827	Ggt/Tgt	10/27	0.186576482391241	2	FACETS	0.794	0.723	0.869	0.397	0.361	0.435	INDETERMINATE	1	TRUE	0	0.572179942525918	2		357	572	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528630	157528630	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	369	675	0	ENST00000346085.5:c.6355G>T	p.Val2119Phe	p.V2119F	ENST00000346085	NM_020732.3	2119	Gtt/Ttt	20/20	0.111156687238231	4	FACETS	0.755	0.715	0.795	0.755	0.715	0.795	INDETERMINATE	2	TRUE	2	0.572179942525918	4		675	1343	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729425	41729425	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	99	425	0	ENST00000242208.4:c.1104C>A	p.Phe368Leu	p.F368L	ENST00000242208	NM_002192.2	368	ttC/ttA	3/3	0.182491264833092	2	FACETS	0.589	0.526	0.654	0.294	0.263	0.327	INDETERMINATE	1	TRUE	0	0.572179942525918	2		425	588	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380109	116380109	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	375	653	0	ENST00000397752.3:c.1498G>T	p.Gly500Cys	p.G500C	ENST00000397752	NM_000245.2	500	Ggc/Tgc	4/21	0.182491264833092	2	FACETS	1	0.994	1	0.677	0.645	0.71	INDETERMINATE	1	TRUE	0	0.572179942525918	2		653	968	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285821	87285821	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	285	561	0	ENST00000277120.3:c.158T>A	p.Val53Glu	p.V53E	ENST00000277120		53	gTg/gAg	2/19	0.182491264833092	2	FACETS	1	0.99	1	0.602	0.568	0.637	INDETERMINATE	1	TRUE	0	0.572179942525918	2		561	827	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937815	76937815	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	197	311	2	ENST00000373344.5:c.2933C>A	p.Ser978Tyr	p.S978Y	ENST00000373344	NM_000489.3	978	tCt/tAt	9/35	0.418374158406351	0	FACETS	0.659	0.617	0.701			1	SUBCLONAL	1	TRUE	NA	0.572179942525918	0		313	447	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0016780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	110	772	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.311935993488441	2		772	492	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs112445441	NA	P-0016780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	49	777	0	ENST00000311936.3:c.38G>T	p.Gly13Val	p.G13V	ENST00000311936	NM_004985.3	13	gGc/gTc	2/5	1	2	FACETS	0.642	0.544	0.75	0.642	0.544	0.75	SUBCLONAL	1	TRUE	1	0.311935993488441	2		777	489	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544682	65544682	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	74	679	0	ENST00000358664.4:c.244C>T	p.Gln82Ter	p.Q82*	ENST00000358664	NM_002382.4	82	Cag/Tag	4/5	1	2	FACETS	0.949	0.833	1	0.949	0.833	1	CLONAL	1	TRUE	1	0.311935993488441	2		679	500	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430851	78430851	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778377	NA	P-0016780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	76	689	0	ENST00000370768.2:c.538G>T	p.Gly180Cys	p.G180C	ENST00000370768	NM_003902.3	180	Ggc/Tgc	8/20	1	2	FACETS	0.839	0.736	0.949	0.839	0.736	0.949	CLONAL	1	TRUE	1	0.311935993488441	2		689	581	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574023	7574043	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGCCCACGGATCTGCAGCAAC	CGCCCACGGATCTGCAGCAAC	-	novel	NA	P-0016780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	91	820	2	ENST00000269305.4:c.994-10_1004del		p.X332_splice	ENST00000269305	NM_001126112.2	332		10/11	0.311935993488441	1	FACETS	0.943	0.84	1	0.943	0.84	1	CLONAL	1	TRUE	0	0.311935993488441	1		822	522	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054391	13054391	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	106	699	0	ENST00000316448.5:c.1001A>G	p.Asn334Ser	p.N334S	ENST00000316448	NM_004343.3	334	aAc/aGc	8/9	1	2	FACETS	0.991	0.889	1	0.991	0.889	1	CLONAL	1	TRUE	1	0.311935993488441	2		699	686	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866394	42866394	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	75	738	0	ENST00000398585.3:c.238C>T	p.Gln80Ter	p.Q80*	ENST00000398585	NM_001135099.1	80	Cag/Tag	3/14	1	2	FACETS	0.851	0.747	0.963	0.851	0.747	0.963	CLONAL	1	TRUE	1	0.311935993488441	2		738	565	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435894	149435894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs690016548	NA	P-0016780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	74	673	0	ENST00000286301.3:c.2330G>A	p.Arg777Gln	p.R777Q	ENST00000286301	NM_005211.3	777	cGg/cAg	18/22	1	2	FACETS	0.756	0.662	0.857	0.756	0.662	0.857	SUBCLONAL	1	TRUE	1	0.311935993488441	2		673	628	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395132	139395132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs997320046	NA	P-0016780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	134	577	2	ENST00000277541.6:c.5806G>A	p.Ala1936Thr	p.A1936T	ENST00000277541	NM_017617.3	1936	Gcc/Acc	31/34	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.311935993488441	2		579	609	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038816	47038864	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTACCAGGCCCAGGGAGTCCTGGCCTCCCAAGCCCTGTCACAGGGCT	CCCTACCAGGCCCAGGGAGTCCTGGCCTCCCAAGCCCTGTCACAGGGCT	-	novel	NA	P-0016780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	122	779	0	ENST00000377604.3:c.824_872del	p.Pro275ArgfsTer17	p.P275Rfs*17	ENST00000377604	NM_001204468.1	275	CCCTACCAGGCCCAGGGAGTCCTGGCCTCCCAAGCCCTGTCACAGGGCTcg/cg	9/24	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.311935993488441	2		779	670	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555525857	NA	P-0016781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	122	716	0	ENST00000269305.4:c.596G>A	p.Gly199Glu	p.G199E	ENST00000269305	NM_001126112.2	199	gGa/gAa	6/11	1	2	FACETS	0.932	0.843	1	0.932	0.843	1	CLONAL	1	TRUE	1	0.326361406347001	2		716	802	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989562	85989562	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs767548896	NA	P-0016781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	64	329	0	ENST00000263360.6:c.1321C>T	p.Arg441Ter	p.R441*	ENST00000263360	NM_003797.3	441	Cga/Tga	12/12	1	2	FACETS	0.78	0.676	0.892	0.78	0.676	0.892	SUBCLONAL	1	TRUE	1	0.326361406347001	2		329	503	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220707	1220707	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	129	626	0	ENST00000326873.7:c.725G>T	p.Gly242Val	p.G242V	ENST00000326873	NM_000455.4	242	gGg/gTg	5/10	0.326361406347001	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.326361406347001	1		626	547	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498424	89498424	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1176464192	NA	P-0016781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	41	273	2	ENST00000336596.2:c.2396G>A	p.Arg799His	p.R799H	ENST00000336596	NM_005233.5	799	cGc/cAc	14/17	0.326361406347001	1	FACETS	0.655	0.548	0.773	0.655	0.548	0.773	SUBCLONAL	1	TRUE	0	0.326361406347001	1		275	321	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610454	10610454	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	94	534	0	ENST00000171111.5:c.256C>T	p.Gln86Ter	p.Q86*	ENST00000171111	NM_203500.1	86	Cag/Tag	2/6	0.326361406347001	1	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	0	0.326361406347001	1		534	478	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724696	112724696	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	99	547	0	ENST00000369452.4:c.580C>G	p.Leu194Val	p.L194V	ENST00000369452	NM_007373.3	194	Ctc/Gtc	2/9	1	2	FACETS	0.832	0.743	0.927	0.832	0.743	0.927	CLONAL	1	TRUE	1	0.326361406347001	2		547	729	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590578	95590578	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	89	459	0	ENST00000393063.1:c.1331G>A	p.Gly444Glu	p.G444E	ENST00000393063	NM_030621.3	444	gGa/gAa	9/28	1	2	FACETS	0.742	0.658	0.832	0.742	0.658	0.832	SUBCLONAL	1	TRUE	1	0.326361406347001	2		459	735	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007806	45007807	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0016781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	73	419	0	ENST00000558401.1:c.253_254del	p.Leu85ValfsTer4	p.L85Vfs*4	ENST00000558401	NM_004048.2	85	TTg/g	2/4	0.326361406347001	1	FACETS	0.791	0.694	0.896	0.791	0.694	0.896	SUBCLONAL	1	TRUE	0	0.326361406347001	1		419	473	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476325	88476325	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs763974843	NA	P-0016781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	33	652	0	ENST00000360948.2:c.1807T>A	p.Phe603Ile	p.F603I	ENST00000360948	NM_001012338.2	603	Ttc/Atc	15/19	0.323461512548074	2	FACETS	0.317	0.258	0.385	0.159	0.129	0.193	SUBCLONAL	1	TRUE	0	0.326361406347001	2		652	637	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038621	14038621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	117	507	0	ENST00000311895.7:c.1946G>A	p.Arg649Lys	p.R649K	ENST00000311895	NM_005236.2	649	aGa/aAa	10/11	1	2	FACETS	0.926	0.836	1	0.926	0.836	1	CLONAL	1	TRUE	1	0.326361406347001	2		507	774	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584709	48584709	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0016781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	94	501	0	ENST00000342988.3:c.788-1G>C		p.X263_splice	ENST00000342988	NM_005359.5	263			0.326361406347001	1	FACETS	0.976	0.872	1	0.976	0.872	1	CLONAL	1	TRUE	0	0.326361406347001	1		501	494	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662167	227662167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	98	619	0	ENST00000305123.5:c.1288G>A	p.Glu430Lys	p.E430K	ENST00000305123	NM_005544.2	430	Gag/Aag	1/2	1	2	FACETS	0.983	0.878	1	0.983	0.878	1	CLONAL	1	TRUE	1	0.326361406347001	2		619	611	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662909	52662909	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0016781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	91	420	0	ENST00000394830.3:c.1443+1G>C		p.X481_splice	ENST00000394830	NM_018313.4	481			0.326361406347001	1	FACETS	0.841	0.748	0.939	0.841	0.748	0.939	CLONAL	1	TRUE	0	0.326361406347001	1		420	555	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498472	89498472	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	32	281	0	ENST00000336596.2:c.2446del	p.Glu816ArgfsTer2	p.E816Rfs*2	ENST00000336596	NM_005233.5	815	tGg/tg	14/17	0.326361406347001	1	FACETS	0.57	0.464	0.688	0.57	0.464	0.688	SUBCLONAL	1	TRUE	0	0.326361406347001	1		281	288	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505342	186505342	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0016781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	70	320	0	ENST00000323963.5:c.968C>G	p.Ser323Ter	p.S323*	ENST00000323963		323	tCa/tGa	9/11	1	2	FACETS	0.884	0.773	1	0.884	0.773	1	CLONAL	1	TRUE	1	0.326361406347001	2		320	485	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032210	26032210	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	32	167	0	ENST00000244661.2:c.79C>A	p.Arg27Ser	p.R27S	ENST00000244661	NM_003537.3	27	Cgc/Agc	1/1	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.326361406347001	2		167	154	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120582	94120582	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	73	445	0	ENST00000369303.4:c.469C>A	p.Gln157Lys	p.Q157K	ENST00000369303	NM_004440.3	157	Caa/Aaa	3/17	0.326361406347001	1	FACETS	0.777	0.681	0.879	0.777	0.681	0.879	SUBCLONAL	1	TRUE	0	0.326361406347001	1		445	482	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372142	55372142	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	173	665	0	ENST00000297316.4:c.832C>A	p.Pro278Thr	p.P278T	ENST00000297316	NM_022454.3	278	Ccc/Acc	2/2	0.204252919663719	3	FACETS	0.901	0.832	0.973	0.901	0.832	0.973	CLONAL	2	TRUE	1	0.326361406347001	3		665	684	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88677042	88677054	+	frameshift_variant	Frame_Shift_Del	DEL	AAATCTACCAAAC	AAATCTACCAAAC	-	novel	NA	P-0016781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	449	81	0	ENST00000372037.3:c.827_839del	p.Glu276ValfsTer3	p.E276Vfs*3	ENST00000372037	NM_004329.2	276	gAAATCTACCAAACt/gt	9/13	1	2	FACETS	1	0.977	1	1	0.998	1	CLONAL	3	TRUE	1	0.326361406347001	2		81	896	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	125	726	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.813	0.736	0.895	1	0.987	1	CLONAL	2	TRUE	1	0.183202415545868	2		726	839	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	106	441	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	0.162858239950305	2	FACETS	0.843	0.757	0.935	0.843	0.757	0.935	CLONAL	2	TRUE	0	0.183202415545868	2		441	686	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247207	153247207	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1179476070	NA	P-0016782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	65	599	0	ENST00000281708.4:c.1595C>T	p.Thr532Ile	p.T532I	ENST00000281708	NM_033632.3	532	aCc/aTc	10/12	1	2	FACETS	0.897	0.776	1	0.897	0.776	1	CLONAL	1	TRUE	1	0.183202415545868	2		599	791	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0016782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	88	723	2	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	1	2	FACETS	0.848	0.749	0.954	0.848	0.749	0.954	CLONAL	1	TRUE	1	0.183202415545868	2		725	1133	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523321	9523321	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	58	541	1	ENST00000353224.5:c.1916G>T	p.Gly639Val	p.G639V	ENST00000353224	NM_177990.2	639	gGc/gTc	9/10	1	2	FACETS	0.621	0.531	0.719	0.621	0.531	0.719	SUBCLONAL	1	TRUE	1	0.183202415545868	2		542	1020	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291496	15291496	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs774701967	NA	P-0016782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	68	465	0	ENST00000263388.2:c.3138G>C	p.Gln1046His	p.Q1046H	ENST00000263388	NM_000435.2	1046	caG/caC	19/33	0.162858239950305	2	FACETS	0.785	0.681	0.898	0.392	0.34	0.449	SUBCLONAL	1	TRUE	0	0.183202415545868	2		465	946	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602921	10602923	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0016782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1351	223	902	0	ENST00000171111.5:c.655_657del	p.Glu219del	p.E219del	ENST00000171111	NM_203500.1	219	GAG/-	3/6	0.162858239950305	2	FACETS	0.773	0.718	0.831	0.773	0.718	0.831	SUBCLONAL	2	TRUE	0	0.183202415545868	2		902	1574	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225637	133225637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs556821288	NA	P-0016782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	74	550	2	ENST00000320574.5:c.4027G>A	p.Gly1343Ser	p.G1343S	ENST00000320574	NM_006231.2	1343	Ggc/Agc	32/49	1	2	FACETS	0.675	0.589	0.769	0.675	0.589	0.769	SUBCLONAL	1	TRUE	1	0.183202415545868	2		552	1196	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436717	110436717	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1744	154	923	1	ENST00000375856.3:c.1684del	p.Asp562ThrfsTer17	p.D562Tfs*17	ENST00000375856	NM_003749.2	562	Gac/ac	1/2	1	2	FACETS	0.886	0.807	0.969	0.886	0.807	0.969	CLONAL	1	TRUE	1	0.183202415545868	2		924	1898	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779419	3779419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370389591	NA	P-0016782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	91	533	0	ENST00000262367.5:c.5629G>A	p.Val1877Met	p.V1877M	ENST00000262367	NM_004380.2	1877	Gtg/Atg	31/31	1	2	FACETS	0.991	0.878	1	0.991	0.878	1	CLONAL	1	TRUE	1	0.183202415545868	2		533	1002	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827310	72827310	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	103	674	1	ENST00000268489.5:c.9271C>A	p.Leu3091Ile	p.L3091I	ENST00000268489	NM_006885.3	3091	Ctt/Att	9/10	1	2	FACETS	0.913	0.815	1	0.913	0.815	1	CLONAL	1	TRUE	1	0.183202415545868	2		675	1231	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007704	62007704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	36	324	0	ENST00000392795.3:c.163G>A	p.Ala55Thr	p.A55T	ENST00000392795	NM_001039933.1	55	Gcc/Acc	3/6	0.15071187743227	3	FACETS	0.601	0.492	0.723	0.3	0.246	0.362	SUBCLONAL	1	TRUE	1	0.183202415545868	3		324	714	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533802	63533802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	53	422	0	ENST00000307078.5:c.1352G>A	p.Gly451Asp	p.G451D	ENST00000307078	NM_004655.3	451	gGc/gAc	6/11	0.15071187743227	3	FACETS	0.809	0.688	0.942	0.404	0.344	0.471	CLONAL	1	TRUE	1	0.183202415545868	3		422	781	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727933	78727933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	86	498	0	ENST00000306801.3:c.778G>A	p.Ala260Thr	p.A260T	ENST00000306801	NM_020761.2	260	Gct/Act	6/34	0.15071187743227	3	FACETS	0.891	0.786	1	0.446	0.393	0.503	CLONAL	1	TRUE	1	0.183202415545868	3		498	1150	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57567428	57567428	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1322	142	557	0	ENST00000316660.6:c.19C>G	p.Arg7Gly	p.R7G	ENST00000316660	NM_021127.2	7	Cgc/Ggc	1/2	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.183202415545868	2		557	1464	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138600	11138600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370466670	NA	P-0016782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	96	557	1	ENST00000358026.2:c.3356G>A	p.Arg1119His	p.R1119H	ENST00000358026	NM_001128849.1	1119	cGc/cAc	24/36	0.162858239950305	2	FACETS	0.904	0.803	1	0.452	0.401	0.506	CLONAL	1	TRUE	0	0.183202415545868	2		558	1159	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209197	36209202	+	inframe_deletion	In_Frame_Del	DEL	CGGGGA	CGGGGA	-	novel	NA	P-0016782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	32	138	0	ENST00000222270.7:c.282_287del	p.Arg99_Gly100del	p.R99_G100del	ENST00000222270	NM_014727.1	93	CGGGGA/-	1/37	0.183202415545868	3	FACETS	0.978	0.794	1	0.489	0.397	0.593	CLONAL	1	TRUE	1	0.183202415545868	3		138	390	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214738	36214738	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	143	467	0	ENST00000222270.7:c.3164G>T	p.Arg1055Leu	p.R1055L	ENST00000222270	NM_014727.1	1055	cGg/cTg	8/37	0.183202415545868	3	FACETS	0.861	0.784	0.942	0.861	0.784	0.942	CLONAL	2	TRUE	1	0.183202415545868	3		467	990	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705652	47705652	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0016782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	107	375	0	ENST00000233146.2:c.2452A>T	p.Lys818Ter	p.K818*	ENST00000233146	NM_000251.2	818	Aag/Tag	14/16	0.183202415545868	2	FACETS	0.927	0.833	1	0.927	0.833	1	CLONAL	2	TRUE	0	0.183202415545868	2		375	630	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38946591	38946591	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	40	438	0	ENST00000357387.3:c.4378G>A	p.Ala1460Thr	p.A1460T	ENST00000357387	NM_152756.3	1460	Gca/Aca	33/38	0.183202415545868	3	FACETS	0.71	0.589	0.846	0.355	0.294	0.423	SUBCLONAL	1	TRUE	1	0.183202415545868	3		438	671	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86648978	86648978	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	35	399	0	ENST00000274376.6:c.1261del	p.Asp421ThrfsTer3	p.D421Tfs*3	ENST00000274376	NM_002890.2	420	Ggg/gg	9/25	1	2	FACETS	0.738	0.604	0.888	0.738	0.604	0.888	SUBCLONAL	1	TRUE	1	0.183202415545868	2		399	518	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225488	26225488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	44	192	1	ENST00000360408.1:c.106G>A	p.Val36Met	p.V36M	ENST00000360408	NM_003532.2	36	Gtg/Atg	1/1	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.183202415545868	2		193	445	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140886	37140886	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	63	442	0	ENST00000373509.5:c.722C>A	p.Pro241His	p.P241H	ENST00000373509	NM_002648.3	241	cCt/cAt	5/6	1	2	FACETS	0.725	0.626	0.835	0.725	0.626	0.835	SUBCLONAL	1	TRUE	1	0.183202415545868	2		442	948	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900060	151900060	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	64	620	1	ENST00000262189.6:c.4051del	p.Arg1351GlyfsTer23	p.R1351Gfs*23	ENST00000262189	NM_170606.2	1351	Agg/gg	26/59	0.15071187743227	3	FACETS	1	0.912	1	0.536	0.464	0.615	CLONAL	1	TRUE	1	0.183202415545868	3		621	711	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128206856	128206856	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757660392	NA	P-0016782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	57	332	0	ENST00000265960.3:c.1367C>T	p.Thr456Met	p.T456M	ENST00000265960	NM_001006617.1	456	aCg/aTg	11/12	0.183202415545868	3	FACETS	0.904	0.775	1	0.452	0.387	0.524	CLONAL	1	TRUE	1	0.183202415545868	3		332	751	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741694	17741694	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	865	718	0	ENST00000250003.3:c.365T>G	p.Leu122Arg	p.L122R	ENST00000250003	NM_002478.4	122	cTg/cGg	1/3	0.925871547992889	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.942715096936988	2		718	914	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	56	423	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		423	556	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653867	89653867	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1554893835	NA	P-0016784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	34	475	0	ENST00000371953.3:c.164+1G>T		p.X55_splice	ENST00000371953	NM_000314.4	55			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		475	368	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161731	56161756	+	frameshift_variant	Frame_Shift_Del	DEL	AAGTTTGTTTCACGCATGTCAAATTC	AAGTTTGTTTCACGCATGTCAAATTC	-	novel	NA	P-0016785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	161	696	0	ENST00000399503.3:c.1228_1253del	p.Lys410SerfsTer7	p.K410Sfs*7	ENST00000399503	NM_005921.1	410	AAGTTTGTTTCACGCATGTCAAATTCt/t	6/20	0.398947180285339	4	FACETS	1	0.947	1			1	CLONAL	1	TRUE	NA	0.398947180285339	4		696	1079	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184142	56184142	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	225	407	0	ENST00000399503.3:c.4347G>A	p.Trp1449Ter	p.W1449*	ENST00000399503	NM_005921.1	1449	tgG/tgA	19/20	0.398947180285339	4	FACETS	1	0.976	1			1	CLONAL	2	TRUE	NA	0.398947180285339	4		407	725	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0016786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	314	547	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.544764022466566	2		547	988	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913283	NA	P-0016786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	188	435	1	ENST00000263967.3:c.3129G>T	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atT	21/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.544764022466566	2		436	643	SUCCESS
AR	367	MSKCC	GRCh37	X	66943543	66943543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852581	NA	P-0016786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	185	410	1	ENST00000374690.3:c.2623C>T	p.His875Tyr	p.H875Y	ENST00000374690	NM_000044.3	875	Cat/Tat	8/8	1	2	FACETS	0.996	0.923	1	0.996	0.923	1	CLONAL	1	TRUE	1	0.544764022466566	2		411	682	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431460	121431460	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	218	456	0	ENST00000257555.6:c.664A>C	p.Lys222Gln	p.K222Q	ENST00000257555		222	Aag/Cag	3/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.544764022466566	2		456	752	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842405	68842409	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGT	TGGGT	-	novel	NA	P-0016786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	224	654	1	ENST00000261769.5:c.467_471del	p.Trp156TyrfsTer10	p.W156Yfs*10	ENST00000261769	NM_004360.3	156	TGGGTt/t	4/16	0.508943273419072	1	FACETS	0.778	0.727	0.831	0.778	0.727	0.831	SUBCLONAL	1	TRUE	0	0.544764022466566	1		655	769	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	719	726	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.348737901472559	2	FACETS	0.9	0.868	0.931	0.9	0.868	0.931	CLONAL	2	TRUE	0	0.420249030875742	2		726	1902	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237704	16237704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1263387333	NA	P-0016791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1965	315	657	0	ENST00000375759.3:c.1151G>A	p.Arg384Gln	p.R384Q	ENST00000375759	NM_015001.2	384	cGg/cAg	5/15	0.28750090980423	3	FACETS	0.796	0.747	0.846	0.398	0.373	0.423	SUBCLONAL	1	TRUE	1	0.420249030875742	3		657	2280	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649421	23649421	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	419	354	0	ENST00000261584.4:c.78G>T	p.Arg26Ser	p.R26S	ENST00000261584	NM_024675.3	26	agG/agT	2/13	0.28750090980423	3	FACETS	0.842	0.801	0.884	0.842	0.801	0.884	CLONAL	2	TRUE	1	0.420249030875742	3		354	1433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0016791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1537	737	802	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.309761439264582	2	FACETS	0.771	0.743	0.799	0.771	0.743	0.799	SUBCLONAL	2	TRUE	0	0.420249030875742	2		802	2274	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376106	225376106	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1519	267	698	0	ENST00000264414.4:c.848G>T	p.Gly283Val	p.G283V	ENST00000264414	NM_003590.4	283	gGg/gTg	6/16	NA	2	FACETS	0.711	0.665	0.76			1	INDETERMINATE	1	TRUE	NA	0.420249030875742	2		698	1786	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146836	185146836	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	210	381	0	ENST00000265026.3:c.467A>C	p.Gln156Pro	p.Q156P	ENST00000265026	NM_004721.4	156	cAg/cCg	2/14	0.309761439264582	2	FACETS	0.892	0.827	0.959	0.446	0.413	0.48	CLONAL	1	TRUE	0	0.420249030875742	2		381	1121	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143029344	143029344	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0016791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	192	290	0	ENST00000262992.4:c.2277-1G>T		p.X759_splice	ENST00000262992	NM_001101669.1	759			0.348737901472559	2	FACETS	0.844	0.78	0.911	0.422	0.39	0.456	CLONAL	1	TRUE	0	0.420249030875742	2		290	1082	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501506	149501506	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1222	535	700	0	ENST00000261799.4:c.2281G>T	p.Val761Phe	p.V761F	ENST00000261799	NM_002609.3	761	Gtc/Ttc	16/23	0.314919930547406	2	FACETS	1	0.996	1	0.725	0.694	0.756	CLONAL	1	TRUE	0	0.420249030875742	2		700	1757	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517847	8517847	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0016791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	211	247	0	ENST00000356435.5:c.1543+1G>T		p.X515_splice	ENST00000356435		515			1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.420249030875742	2		247	855	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0016792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	195	591	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.288214288193758	2	FACETS	0.956	0.888	1	0.956	0.888	1	CLONAL	2	TRUE	0	0.289823088480619	2		592	704	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0016792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	154	561	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.289823088480619	3	FACETS	0.887	0.814	0.963	0.887	0.814	0.963	CLONAL	2	TRUE	1	0.289823088480619	3		561	686	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902838	1902838	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	293	575	0	ENST00000382891.5:c.457C>G	p.Gln153Glu	p.Q153E	ENST00000382891	NM_133335.3	153	Cag/Gag	2/22	0.288214288193758	2	FACETS	0.997	0.939	1	0.997	0.939	1	CLONAL	2	TRUE	0	0.289823088480619	2		575	1014	SUCCESS
APC	324	MSKCC	GRCh37	5	112178655	112178655	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	75	388	0	ENST00000257430.4:c.7364A>C	p.Lys2455Thr	p.K2455T	ENST00000257430	NM_000038.5	2455	aAa/aCa	16/16	0.289823088480619	3	FACETS	0.779	0.682	0.884	0.389	0.341	0.442	SUBCLONAL	1	TRUE	1	0.289823088480619	3		388	761	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	338	486	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.754298867121261	4	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.754298867121261	4		486	1404	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	185	423	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.96	0.894	1	0.96	0.894	1	CLONAL	1	TRUE	1	0.754298867121261	2		423	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0016793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	478	649	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.754298867121261	2		649	1193	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0016793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	379	553	2	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	1	2	FACETS	0.956	0.91	1	0.956	0.91	1	CLONAL	1	TRUE	1	0.754298867121261	2		555	1051	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753136	57753136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	192	297	2	ENST00000274289.3:c.880G>A	p.Glu294Lys	p.E294K	ENST00000274289	NM_006622.3	294	Gaa/Aaa	7/14	1	2	FACETS	0.911	0.848	0.975	0.911	0.848	0.975	CLONAL	1	TRUE	1	0.754298867121261	2		299	559	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572413	41572413	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1410	185	494	0	ENST00000263253.7:c.4942C>T	p.Gln1648Ter	p.Q1648*	ENST00000263253	NM_001429.3	1648	Cag/Tag	30/31	0.576011311070048	7	FACETS	0.983	0.904	1			1	CLONAL	1	TRUE	NA	0.576011311070048	7		494	1595	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577595	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0016795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	288	433	0	ENST00000269305.4:c.686_687del	p.Cys229TyrfsTer10	p.C229Yfs*10	ENST00000269305	NM_001126112.2	229	tGT/t	7/11	NA	2	FACETS	0.928	0.883	0.972			1	INDETERMINATE	2	TRUE	NA	0.576011311070048	2		433	539	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271744	18271744	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1310	441	633	0	ENST00000222254.8:c.431C>G	p.Ser144Cys	p.S144C	ENST00000222254	NM_005027.3	144	tCt/tGt	4/16	0.576011311070048	6	FACETS	0.941	0.895	0.988			1	CLONAL	2	TRUE	NA	0.576011311070048	6		633	1751	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633583	69633583	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	168	194	0	ENST00000334134.2:c.119G>T	p.Gly40Val	p.G40V	ENST00000334134	NM_005247.2	40	gGc/gTc	1/3	0.575657609925933	4	FACETS	1	0.977	1			1	CLONAL	2	TRUE	NA	0.576011311070048	4		194	410	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253493	226253493	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	164	400	0	ENST00000366813.1:c.265G>A	p.Ala89Thr	p.A89T	ENST00000366813		89	Gct/Act	2/3	NA	2	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.576011311070048	2		400	539	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925481	114925481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	192	537	0	ENST00000543371.1:c.1559C>T	p.Ser520Phe	p.S520F	ENST00000543371	NM_001198531.1	520	tCc/tTc	14/14	0.564757306171522	2	FACETS	0.867	0.804	0.932	0.433	0.402	0.466	CLONAL	1	TRUE	0	0.576011311070048	2		537	769	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112910815	112910817	+	frameshift_variant	Frame_Shift_Del	DEL	ACA	ACA	CC	novel	NA	P-0016795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	262	609	1	ENST00000351677.2:c.824_826delinsCC	p.Asn275ThrfsTer64	p.N275Tfs*64	ENST00000351677	NM_002834.3	275	aACAaa/aCCaa	7/16	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.576011311070048	2		610	864	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281879	49281879	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	135	504	0	ENST00000282018.3:c.926G>C	p.Gly309Ala	p.G309A	ENST00000282018	NM_020377.2	309	gGg/gCg	1/1	NA	2	FACETS	0.704	0.641	0.769			1	INDETERMINATE	1	TRUE	NA	0.576011311070048	2		504	666	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256279	41256279	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs80358116	NA	P-0016795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	303	213	0	ENST00000357654.3:c.302-1G>A		p.X101_splice	ENST00000357654	NM_007294.3	101			0.576011311070048	6	FACETS	0.956	0.91	1	0.956	0.91	1	CLONAL	4	TRUE	2	0.576011311070048	6		213	592	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31381390	31381390	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	119	372	0	ENST00000328111.2:c.1115C>T	p.Ser372Leu	p.S372L	ENST00000328111	NM_006892.3	372	tCa/tTa	10/23	0.575657609925933	3	FACETS	0.799	0.722	0.88	0.4	0.361	0.44	SUBCLONAL	1	TRUE	1	0.576011311070048	3		372	666	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751386	57751386	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	170	228	0	ENST00000274289.3:c.1605G>C	p.Met535Ile	p.M535I	ENST00000274289	NM_006622.3	535	atG/atC	11/14	0.575657609925933	3	FACETS	0.89	0.828	0.954	0.89	0.828	0.954	CLONAL	2	TRUE	1	0.576011311070048	3		228	427	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751101	128751101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1221801220	NA	P-0016795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1340	172	480	0	ENST00000377970.2:c.638C>G	p.Pro213Arg	p.P213R	ENST00000377970	NM_002467.4	213	cCt/cGt	2/3	0.576011311070048	7	FACETS	0.964	0.884	1			1	CLONAL	1	TRUE	NA	0.576011311070048	7		480	1512	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108787	2108788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs137854024	NA	P-0016796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	246	455	0	ENST00000219476.3:c.894dup	p.Val299CysfsTer39	p.V299Cfs*39	ENST00000219476	NM_000548.3	296	-/T	10/42	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		455	733	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579584	7579585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0016798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	302	407	0	ENST00000269305.4:c.102dup	p.Pro36AlafsTer7	p.P36Afs*7	ENST00000269305	NM_001126112.2	34	-/C	4/11	0.510013001396232	3	FACETS	0.843	0.804	0.882	0.843	0.804	0.882	CLONAL	3	TRUE	0	0.550596646222854	3		407	553	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371683	55371683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753693798	NA	P-0016798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	131	463	4	ENST00000297316.4:c.373C>T	p.Arg125Cys	p.R125C	ENST00000297316	NM_022454.3	125	Cgc/Tgc	2/2	0.550596646222854	6	FACETS	1	0.942	1	0.351	0.318	0.386	CLONAL	1	TRUE	3	0.550596646222854	6		467	950	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610581	81610581	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764711377	NA	P-0016798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	165	350	0	ENST00000298171.2:c.2179G>A	p.Glu727Lys	p.E727K	ENST00000298171	NM_000369.2	727	Gag/Aag	10/10	0.522867247096305	2	FACETS	0.903	0.844	0.962	0.903	0.844	0.962	CLONAL	2	TRUE	0	0.550596646222854	2		350	332	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247761	59247761	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	122	408	0	ENST00000371222.2:c.982T>A	p.Leu328Met	p.L328M	ENST00000371222	NM_002228.3	328	Ttg/Atg	1/1	1	2	FACETS	0.987	0.898	1	0.987	0.898	1	CLONAL	1	TRUE	1	0.550596646222854	2		408	449	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366966	15366966	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0016798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	139	477	0	ENST00000263377.2:c.1660A>T	p.Lys554Ter	p.K554*	ENST00000263377	NM_058243.2	554	Aaa/Taa	9/20	0.527987461118042	2	FACETS	0.962	0.88	1	0.481	0.44	0.523	CLONAL	1	TRUE	0	0.550596646222854	2		477	525	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259284	36259298	+	inframe_deletion	In_Frame_Del	DEL	GCCGGCCAGGGCAGC	GCCGGCCAGGGCAGC	-	novel	NA	P-0016798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	83	317	1	ENST00000300305.3:c.193_207del	p.Ala65_Gly69del	p.A65_G69del	ENST00000300305		65	GCTGCCCTGGCCGGC/-	3/8	0.348283451649744	4	FACETS	1	0.942	1	0.367	0.325	0.411	CLONAL	1	TRUE	1	0.550596646222854	4		318	425	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37622771	37622771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542730360	NA	P-0016798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	182	456	1	ENST00000249071.6:c.521G>A	p.Arg174Gln	p.R174Q	ENST00000249071	NM_002872.4	174	cGg/cAg	6/7	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.550596646222854	2		457	553	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430258	181430258	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	81	271	0	ENST00000325404.1:c.110G>T	p.Ser37Ile	p.S37I	ENST00000325404	NM_003106.3	37	aGc/aTc	1/1	0.550596646222854	3	FACETS	0.809	0.715	0.908	0.404	0.357	0.454	CLONAL	1	TRUE	1	0.550596646222854	3		271	464	SUCCESS
APC	324	MSKCC	GRCh37	5	112176902	112176902	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	52	357	0	ENST00000257430.4:c.5611G>A	p.Asp1871Asn	p.D1871N	ENST00000257430	NM_000038.5	1871	Gat/Aat	16/16	0.550596646222854	1	FACETS	0.405	0.346	0.469	0.405	0.346	0.469	SUBCLONAL	1	TRUE	0	0.550596646222854	1		357	338	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	62	423	0				ENST00000310581	NM_198253.2	-/1132			0.441739422229708	1	FACETS	0.676	0.594	0.763	0.676	0.594	0.763	SUBCLONAL	1	TRUE	0	0.626363088822966	1		423	201	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0016800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	296	1585	1	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	0.626363088822966	2		1586	835	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979350	40979350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747923769	NA	P-0016800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	71	729	1	ENST00000373198.4:c.1783G>A	p.Asp595Asn	p.D595N	ENST00000373198	NM_133170.3	595	Gac/Aac	11/32	0.561934507342087	0	FACETS	0.307	0.27	0.345			1	SUBCLONAL	1	TRUE	0	0.626363088822966	0		730	276	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28979972	28979972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	157	1486	0	ENST00000282397.4:c.1496G>A	p.Gly499Glu	p.G499E	ENST00000282397	NM_002019.4	499	gGa/gAa	11/30	NA	2	FACETS	0.716	0.658	0.777			1	INDETERMINATE	1	TRUE	NA	0.626363088822966	2		1486	700	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39214610	39214614	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTACC	TTACC	-	novel	NA	P-0016800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	141	1038	0	ENST00000402219.2:c.3510_3510+4del		p.X1170_splice	ENST00000402219	NM_005633.3	1170		22/23	1	2	FACETS	0.688	0.629	0.751	0.688	0.629	0.751	SUBCLONAL	1	TRUE	1	0.626363088822966	2		1038	654	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127916000	127916000	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	138	1099	0	ENST00000373547.4:c.481del	p.Cys161ValfsTer70	p.C161Vfs*70	ENST00000373547	NM_002721.4	161	Tgt/gt	6/7	0.626363088822966	1	FACETS	0.782	0.719	0.846	0.782	0.719	0.846	SUBCLONAL	1	TRUE	0	0.626363088822966	1		1099	387	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20153932	20153932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	235	555	0	ENST00000379607.5:c.128G>A	p.Gly43Glu	p.G43E	ENST00000379607	NM_001412.3	43	gGa/gAa	3/7	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.626363088822966	1		555	392	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	142	726	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.3	2		726	908	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	68	314	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.958	0.836	1	0.958	0.836	1	CLONAL	1	TRUE	1	0.3	2		318	473	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466026	69466028	+	inframe_deletion	In_Frame_Del	DEL	CGA	CGA	-	novel	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	144	502	0	ENST00000227507.2:c.866_868del	p.Asp289del	p.D289del	ENST00000227507	NM_053056.2	288	acCGAc/acc	5/5	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.3	2		502	790	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	93	443	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.972	0.865	1	0.972	0.865	1	CLONAL	1	TRUE	1	0.3	2		444	638	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328347	137328347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	133	571	0	ENST00000481739.1:c.1276C>T	p.Arg426Cys	p.R426C	ENST00000481739	NM_002957.4	426	Cgc/Tgc	10/10	1	2	FACETS	0.91	0.826	0.999	0.91	0.826	0.999	CLONAL	1	TRUE	1	0.3	2		571	974	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338671	70338671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	121	495	0	ENST00000374080.3:c.67G>T	p.Asp23Tyr	p.D23Y	ENST00000374080		23	Gat/Tat	1/45	1	2	FACETS	0.97	0.876	1	0.97	0.876	1	CLONAL	1	TRUE	1	0.3	2		495	832	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	207	330	0	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	1	0.972	1	1	0.994	1	CLONAL	2	TRUE	1	0.3	2		330	641	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	128	497	1	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	0.846	0.765	0.931	0.846	0.765	0.931	CLONAL	1	TRUE	1	0.3	2		498	1009	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692893	89692893	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	76	302	0	ENST00000371953.3:c.377C>A	p.Ala126Asp	p.A126D	ENST00000371953	NM_000314.4	126	gCt/gAt	5/9	1	2	FACETS	0.839	0.736	0.949	0.839	0.736	0.949	CLONAL	1	TRUE	1	0.3	2		302	604	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427754	72427754	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	59	178	0	ENST00000477973.2:c.736C>T	p.Gln246Ter	p.Q246*	ENST00000477973	NM_012234.5	246	Cag/Tag	4/4	1	2	FACETS	0.974	0.841	1	0.974	0.841	1	CLONAL	1	TRUE	1	0.3	2		178	404	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874637	35874637	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	61	297	2	ENST00000303115.3:c.799del	p.Arg267GlyfsTer28	p.R267Gfs*28	ENST00000303115	NM_002185.3	265	Aaa/aa	6/8	1	2	FACETS	0.788	0.681	0.905	0.788	0.681	0.905	CLONAL	1	TRUE	1	0.3	2		299	516	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750639	128750639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775522201	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	79	318	1	ENST00000377970.2:c.176C>T	p.Ala59Val	p.A59V	ENST00000377970	NM_002467.4	59	gCg/gTg	2/3	1	2	FACETS	0.972	0.856	1	0.972	0.856	1	CLONAL	1	TRUE	1	0.3	2		319	542	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794441	42794441	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	152	701	1	ENST00000575354.2:c.1526del	p.Pro509HisfsTer14	p.P509Hfs*14	ENST00000575354	NM_015125.3	507	cgC/cg	10/20	1	2	FACETS	0.85	0.776	0.928	0.85	0.776	0.928	CLONAL	1	TRUE	1	0.3	2		702	1192	SUCCESS
BLM	641	MSKCC	GRCh37	15	91295028	91295030	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs587779895	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	73	277	0	ENST00000355112.3:c.819_821del	p.Lys273del	p.K273del	ENST00000355112	NM_000057.2	271	AAG/-	4/22	1	2	FACETS	0.857	0.75	0.972	0.857	0.75	0.972	CLONAL	1	TRUE	1	0.3	2		277	568	SUCCESS
ATM	472	MSKCC	GRCh37	11	108213967	108213967	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876659872	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	84	234	3	ENST00000278616.4:c.8287C>T	p.Arg2763Ter	p.R2763*	ENST00000278616	NM_000051.3	2763	Cga/Tga	57/63	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.3	2		237	482	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793677	89793677	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	105	405	2	ENST00000336032.3:c.752del	p.Lys251SerfsTer14	p.K251Sfs*14	ENST00000336032	NM_006813.2	249	gAa/ga	2/2	1	2	FACETS	0.857	0.767	0.952	0.857	0.767	0.952	CLONAL	1	TRUE	1	0.3	2		407	817	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543606	148543606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	81	463	0	ENST00000320356.2:c.202G>A	p.Val68Met	p.V68M	ENST00000320356	NM_004456.4	68	Gtg/Atg	3/20	1	2	FACETS	0.556	0.488	0.628	0.556	0.488	0.628	SUBCLONAL	1	TRUE	1	0.3	2		463	972	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822586	72822586	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	65	226	0	ENST00000268489.5:c.9589del	p.Gln3197SerfsTer44	p.Q3197Sfs*44	ENST00000268489	NM_006885.3	3197	Cag/ag	10/10	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.3	2		226	417	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	174	550	8	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.903	0.829	0.98	0.903	0.829	0.98	CLONAL	1	TRUE	1	0.3	2		558	1285	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16247392	16247392	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	67	199	0	ENST00000375759.3:c.1663G>A	p.Ala555Thr	p.A555T	ENST00000375759	NM_015001.2	555	Gcc/Acc	9/15	1	2	FACETS	0.923	0.804	1	0.923	0.804	1	CLONAL	1	TRUE	1	0.3	2		199	484	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36814324	36814324	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	55	339	0	ENST00000373129.3:c.716A>G	p.Tyr239Cys	p.Y239C	ENST00000373129	NM_032017.1	239	tAc/tGc	8/12	1	2	FACETS	0.616	0.527	0.714	0.616	0.527	0.714	SUBCLONAL	1	TRUE	1	0.3	2		339	595	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115272881	115272882	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	95	386	0	ENST00000438362.2:c.1491_1492del	p.Lys498GlyfsTer3	p.K498Gfs*3	ENST00000438362	NM_001242891.1	497	gaGAag/gaag	12/20	1	2	FACETS	0.817	0.727	0.913	0.817	0.727	0.913	CLONAL	1	TRUE	1	0.3	2		386	775	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720672	89720677	+	inframe_deletion	In_Frame_Del	DEL	GTAAAT	GTAAAT	-	novel	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	59	177	0	ENST00000371953.3:c.823_828del	p.Val275_Asn276del	p.V275_N276del	ENST00000371953	NM_000314.4	275	GTAAAT/-	8/9	1	2	FACETS	0.848	0.731	0.975	0.848	0.731	0.975	CLONAL	1	TRUE	1	0.3	2		177	464	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936153	71936153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	24	248	0	ENST00000298229.2:c.125G>A	p.Gly42Asp	p.G42D	ENST00000298229	NM_001567.3	42	gGc/gAc	1/28	1	2	FACETS	0.488	0.382	0.609	0.488	0.382	0.609	SUBCLONAL	1	TRUE	1	0.3	2		248	328	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	493318	493318	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	118	345	0	ENST00000399788.2:c.245C>T	p.Ala82Val	p.A82V	ENST00000399788	NM_001042603.1	82	gCa/gTa	3/28	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.3	2		345	762	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424178	49424178	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs886040960	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	66	257	0	ENST00000301067.7:c.13884del	p.Thr4629ProfsTer11	p.T4629Pfs*11	ENST00000301067	NM_003482.3	4628	ccC/cc	42/54	1	2	FACETS	0.833	0.724	0.951	0.833	0.724	0.951	CLONAL	1	TRUE	1	0.3	2		257	528	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435009	110435009	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	150	618	0	ENST00000375856.3:c.3392G>A	p.Arg1131His	p.R1131H	ENST00000375856	NM_003749.2	1131	cGc/cAc	1/2	1	2	FACETS	0.903	0.824	0.987	0.903	0.824	0.987	CLONAL	1	TRUE	1	0.3	2		618	1107	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435727	110435727	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776486519	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	84	372	1	ENST00000375856.3:c.2674C>T	p.Arg892Cys	p.R892C	ENST00000375856	NM_003749.2	892	Cgc/Tgc	1/2	1	2	FACETS	0.995	0.88	1	0.995	0.88	1	CLONAL	1	TRUE	1	0.3	2		373	563	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031919	10031919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs901717931	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	98	379	1	ENST00000330684.3:c.904G>A	p.Ala302Thr	p.A302T	ENST00000330684	NM_001134407.1	302	Gct/Act	3/13	1	2	FACETS	0.996	0.89	1	0.996	0.89	1	CLONAL	1	TRUE	1	0.3	2		380	656	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351057	89351057	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	136	537	0	ENST00000301030.4:c.1893del	p.Lys631AsnfsTer22	p.K631Nfs*22	ENST00000301030	NM_001256183.1	631	aaA/aa	9/13	1	2	FACETS	0.836	0.758	0.917	0.836	0.758	0.917	CLONAL	1	TRUE	1	0.3	2		537	1085	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40376852	40376852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs892570954	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	114	464	0	ENST00000293328.3:c.320G>A	p.Arg107His	p.R107H	ENST00000293328	NM_012448.3	107	cGc/cAc	4/19	1	2	FACETS	0.875	0.787	0.968	0.875	0.787	0.968	CLONAL	1	TRUE	1	0.3	2		464	869	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436049	56436049	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376002987	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	43	204	0	ENST00000407977.2:c.1088G>A	p.Arg363Gln	p.R363Q	ENST00000407977		363	cGg/cAg	9/10	1	2	FACETS	0.856	0.719	1	0.856	0.719	1	CLONAL	1	TRUE	1	0.3	2		204	335	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211880	36211880	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759918812	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1221	186	726	0	ENST00000222270.7:c.1631G>A	p.Arg544Gln	p.R544Q	ENST00000222270	NM_014727.1	544	cGg/cAg	3/37	1	2	FACETS	0.881	0.812	0.954	0.881	0.812	0.954	CLONAL	1	TRUE	1	0.3	2		726	1407	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222842	36222842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	147	640	1	ENST00000222270.7:c.5471C>T	p.Thr1824Ile	p.T1824I	ENST00000222270	NM_014727.1	1824	aCa/aTa	27/37	1	2	FACETS	0.866	0.79	0.947	0.866	0.79	0.947	CLONAL	1	TRUE	1	0.3	2		641	1131	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223274	36223274	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	234	794	0	ENST00000222270.7:c.5828del	p.Pro1943LeufsTer44	p.P1943Lfs*44	ENST00000222270	NM_014727.1	1942	Ccc/cc	28/37	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.3	2		794	1454	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027175	48027175	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	113	404	0	ENST00000234420.5:c.2053G>A	p.Gly685Ser	p.G685S	ENST00000234420	NM_000179.2	685	Ggt/Agt	4/10	1	2	FACETS	0.971	0.874	1	0.971	0.874	1	CLONAL	1	TRUE	1	0.3	2		404	776	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587240	212587240	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	89	329	0	ENST00000342788.4:c.761A>G	p.Asp254Gly	p.D254G	ENST00000342788	NM_005235.2	254	gAc/gGc	7/28	1	2	FACETS	0.93	0.825	1	0.93	0.825	1	CLONAL	1	TRUE	1	0.3	2		329	638	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158134	47158134	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	111	556	0	ENST00000409792.3:c.4565A>G	p.Asn1522Ser	p.N1522S	ENST00000409792	NM_014159.6	1522	aAt/aGt	4/21	1	2	FACETS	0.658	0.59	0.73	0.658	0.59	0.73	SUBCLONAL	1	TRUE	1	0.3	2		556	1125	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134514526	134514526	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1428579099	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	107	375	0	ENST00000398015.3:c.53T>C	p.Met18Thr	p.M18T	ENST00000398015	NM_004441.4	18	aTg/aCg	1/16	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.3	2		375	657	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80088602	80088602	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	147	530	0	ENST00000265081.6:c.2594C>A	p.Pro865His	p.P865H	ENST00000265081	NM_002439.4	865	cCt/cAt	19/24	1	2	FACETS	0.95	0.866	1	0.95	0.866	1	CLONAL	1	TRUE	1	0.3	2		530	1032	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056328	180056328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	80	522	0	ENST00000261937.6:c.916G>A	p.Gly306Ser	p.G306S	ENST00000261937	NM_182925.4	306	Ggc/Agc	7/30	1	2	FACETS	0.598	0.525	0.676	0.598	0.525	0.676	SUBCLONAL	1	TRUE	1	0.3	2		522	892	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553156	106553156	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	69	317	0	ENST00000369096.4:c.1121A>G	p.Tyr374Cys	p.Y374C	ENST00000369096	NM_001198.3	374	tAc/tGc	5/7	1	2	FACETS	0.741	0.645	0.844	0.741	0.645	0.844	SUBCLONAL	1	TRUE	1	0.3	2		317	621	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133258	38133258	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	76	409	0	ENST00000317025.8:c.4215C>G	p.Cys1405Trp	p.C1405W	ENST00000317025	NM_023034.1	1405	tgC/tgG	24/24	1	2	FACETS	0.637	0.557	0.722	0.637	0.557	0.722	SUBCLONAL	1	TRUE	1	0.3	2		409	796	SUCCESS
AR	367	MSKCC	GRCh37	X	66765719	66765719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1319	185	743	0	ENST00000374690.3:c.731C>T	p.Ser244Leu	p.S244L	ENST00000374690	NM_000044.3	244	tCg/tTg	1/8	1	2	FACETS	0.82	0.755	0.889	0.82	0.755	0.889	CLONAL	1	TRUE	1	0.3	2		743	1504	SUCCESS
AR	367	MSKCC	GRCh37	X	66766594	66766594	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	136	596	0	ENST00000374690.3:c.1609del	p.Asp537ThrfsTer25	p.D537Tfs*25	ENST00000374690	NM_000044.3	536	Ggg/gg	1/8	1	2	FACETS	0.841	0.763	0.923	0.841	0.763	0.923	CLONAL	1	TRUE	1	0.3	2		596	1078	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591242	67591246	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TTTCA	TTTCA	G	novel	NA	P-0016801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	80	269	0	ENST00000274335.5:c.1746-6_1746-2delinsG		p.X582_splice	ENST00000274335		582			1	2	FACETS	0.798	0.703	0.901	0.798	0.703	0.901	CLONAL	1	TRUE	1	0.3	2		269	668	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	34	486	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.586	0.477	0.708	0.586	0.477	0.708	SUBCLONAL	1	TRUE	1	0.21	2		486	553	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0016802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	17	192	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.514	0.383	0.67	0.514	0.383	0.67	SUBCLONAL	1	TRUE	1	0.21	2		192	315	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206842	36206846	+	frameshift_variant	Frame_Shift_Del	DEL	GCTCG	GCTCG	-	novel	NA	P-0016802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	30	200	0	ENST00000300305.3:c.666_670del	p.Glu223AlafsTer3	p.E223Afs*3	ENST00000300305		222	tcCGAGCgg/tcgg	6/8	1	2	FACETS	0.794	0.64	0.968	0.794	0.64	0.968	CLONAL	1	TRUE	1	0.21	2		200	360	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	550	486	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.356292309050987	6	FACETS	0.95	0.916	0.985	0.95	0.916	0.985	CLONAL	5	TRUE	1	0.356292309050987	6		486	1113	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106058	8106058	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	94	366	0	ENST00000346208.3:c.878T>A	p.Met293Lys	p.M293K	ENST00000346208		293	aTg/aAg	4/6	1	2	FACETS	0.884	0.788	0.986	0.884	0.788	0.986	CLONAL	1	TRUE	1	0.356292309050987	2		366	597	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	166	423	0				ENST00000310581	NM_198253.2	-/1132			0.424553358791152	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	FALSE	0	0.424553358791152	2		423	389	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100507	8100507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1158297550	NA	P-0016806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	417	883	2	ENST00000346208.3:c.481G>A	p.Val161Ile	p.V161I	ENST00000346208		161	Gtc/Atc	3/6	0.424553358791152	3	FACETS	0.998	0.952	1	0.998	0.952	1	CLONAL	2	FALSE	1	0.424553358791152	3		885	1193	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717678	89717679	+	stop_gained,inframe_insertion	Nonsense_Mutation	INS	-	-	AAGACAAGTTCATGT	novel	NA	P-0016806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	256	697	0	ENST00000371953.3:c.705_719dup	p.Met239_Tyr240insTer	p.M239_Y240ins*	ENST00000371953	NM_000314.4	235	gaa/gAAGACAAGTTCATGTaa	7/9	0.424553358791152	2	FACETS	1	0.993	1	0.72	0.675	0.765	CLONAL	1	FALSE	0	0.424553358791152	2		697	838	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095925	178095925	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	137	395	0	ENST00000397062.3:c.1406C>A	p.Pro469His	p.P469H	ENST00000397062	NM_006164.4	469	cCt/cAt	5/5	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.424553358791152	2		395	567	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38942967	38942967	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	116	561	0	ENST00000357387.3:c.5020C>A	p.Gln1674Lys	p.Q1674K	ENST00000357387	NM_152756.3	1674	Caa/Aaa	37/38	0.424553358791152	2	FACETS	0.688	0.62	0.76	0.344	0.31	0.38	SUBCLONAL	1	FALSE	0	0.424553358791152	2		561	794	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505039	149505059	+	inframe_deletion	In_Frame_Del	DEL	CGTGGAGTCATAGGGCAGCTG	CGTGGAGTCATAGGGCAGCTG	-	novel	NA	P-0016806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	306	542	0	ENST00000261799.4:c.1756_1776del	p.Gln586_Thr592del	p.Q586_T592del	ENST00000261799	NM_002609.3	586	CAGCTGCCCTATGACTCCACG/-	12/23	0.424553358791152	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	FALSE	0	0.424553358791152	2		542	681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0016807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	103	514	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.336954439706105	0	FACETS	0.414	0.371	0.459			1	SUBCLONAL	1	TRUE	0	0.461153067692854	0		514	582	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332909	70332909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	132	713	0	ENST00000373644.4:c.814G>A	p.Glu272Lys	p.E272K	ENST00000373644	NM_030625.2	272	Gag/Aag	2/12	1	2	FACETS	0.631	0.572	0.693	0.631	0.572	0.693	SUBCLONAL	1	TRUE	1	0.461153067692854	2		713	907	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038857	12038857	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	G	rs750329786	NA	P-0016807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	250	415	0	ENST00000396373.4:c.1153-3C>G		p.X385_splice	ENST00000396373	NM_001987.4	385			0.43113724615776	2	FACETS	0.856	0.807	0.907	0.856	0.807	0.907	CLONAL	2	TRUE	0	0.461153067692854	2		415	633	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69214123	69214123	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	62	434	0	ENST00000462284.1:c.327C>G	p.Ile109Met	p.I109M	ENST00000462284	NM_002392.5	109	atC/atG	5/11	0.260177942055468	2	FACETS	0.577	0.499	0.661	0.289	0.249	0.331	INDETERMINATE	1	TRUE	0	0.461153067692854	2		434	466	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966313	25966313	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	223	496	0	ENST00000435504.4:c.2893G>C	p.Glu965Gln	p.E965Q	ENST00000435504		965	Gag/Cag	13/13	0.160625656043743	3	FACETS	0.784	0.732	0.837	0.784	0.732	0.837	INDETERMINATE	2	TRUE	1	0.461153067692854	3		496	759	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579408	7579460	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTG	CAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTG	-	rs1555526610	NA	P-0016808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	775	501	0	ENST00000269305.4:c.227_279del	p.Ala76ValfsTer55	p.A76Vfs*55	ENST00000269305	NM_001126112.2	76	gCACCAGCAGCTCCTACACCGGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTG/g	4/11	0.594637985013342	3	FACETS	0.943	0.922	0.963			1	CLONAL	3	TRUE	NA	0.72284212943494	3		501	1032	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17359608	17359612	+	frameshift_variant	Frame_Shift_Del	DEL	TTGAT	TTGAT	-	novel	NA	P-0016808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	145	512	0	ENST00000375499.3:c.229_233del	p.Ile77AspfsTer2	p.I77Dfs*2	ENST00000375499	NM_003000.2	77	ATCAAg/g	3/8	0.721839996843647	2	FACETS	0.451	0.411	0.493	0.226	0.205	0.247	SUBCLONAL	1	TRUE	0	0.72284212943494	2		512	889	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426811	121426811	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764434453	NA	P-0016808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	402	446	0	ENST00000257555.6:c.502C>T	p.Arg168Cys	p.R168C	ENST00000257555		168	Cgc/Tgc	2/10	0.72284212943494	3	FACETS	0.939	0.9	0.979	0.939	0.9	0.979	CLONAL	2	TRUE	1	0.72284212943494	3		446	806	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432028	121432028	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	149	683	0	ENST00000257555.6:c.775G>T	p.Val259Phe	p.V259F	ENST00000257555		259	Gtc/Ttc	4/10	0.72284212943494	3	FACETS	0.468	0.426	0.512	0.234	0.213	0.256	SUBCLONAL	1	TRUE	1	0.72284212943494	3		683	1199	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437266	52437266	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	365	424	0	ENST00000460680.1:c.1778del	p.Gln593ArgfsTer24	p.Q593Rfs*24	ENST00000460680	NM_004656.3	593	cAg/cg	14/17	0.708939194802168	2	FACETS	0.923	0.889	0.956	0.923	0.889	0.956	CLONAL	2	TRUE	0	0.72284212943494	2		424	547	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950487	68950487	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	99	318	0	ENST00000288368.4:c.799C>A	p.Leu267Ile	p.L267I	ENST00000288368	NM_024870.2	267	Ctt/Att	7/40	0.72284212943494	3	FACETS	0.479	0.428	0.534	0.24	0.214	0.267	SUBCLONAL	1	TRUE	1	0.72284212943494	3		318	778	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0016809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	98	936	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.156379267070175	3	FACETS	0.838	0.746	0.936	0.419	0.373	0.468	CLONAL	1	TRUE	1	0.256286539838668	3		938	1030	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249810	39249810	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1458063607	NA	P-0016809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	59	592	0	ENST00000402219.2:c.1759A>G	p.Ile587Val	p.I587V	ENST00000402219	NM_005633.3	587	Ata/Gta	10/23	NA	2	FACETS	0.646	0.555	0.745			1	INDETERMINATE	1	TRUE	NA	0.256286539838668	2		592	713	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945675	54945675	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	22	487	0	ENST00000312783.6:c.895G>C	p.Glu299Gln	p.E299Q	ENST00000312783	NM_198436.1	299	Gaa/Caa	9/10	1	2	FACETS	0.422	0.326	0.533	0.422	0.326	0.533	SUBCLONAL	1	TRUE	1	0.256286539838668	2		487	407	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888844	76888844	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	43	667	0	ENST00000373344.5:c.4985C>A	p.Pro1662His	p.P1662H	ENST00000373344	NM_000489.3	1662	cCt/cAt	19/35	1	2	FACETS	0.415	0.346	0.492	0.415	0.346	0.492	SUBCLONAL	1	TRUE	1	0.256286539838668	2		667	809	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0016810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	275	561	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.631543244404907	3	FACETS	0.901	0.863	0.937	1	0.995	1	CLONAL	3	FALSE	1	0.658407197977731	3		561	411	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188317	32188317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144492578	NA	P-0016810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	126	842	2	ENST00000375023.3:c.1024G>A	p.Val342Met	p.V342M	ENST00000375023	NM_004557.3	342	Gtg/Atg	6/30	0.147903303191571	4	FACETS	0.789	0.721	0.86	0.789	0.721	0.86	INDETERMINATE	2	FALSE	2	0.658407197977731	4		844	402	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600446	10600446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	14	958	2	ENST00000171111.5:c.1409G>A	p.Arg470His	p.R470H	ENST00000171111	NM_203500.1	470	cGt/cAt	4/6	1	2	FACETS	0.061	0.043	0.083	0.061	0.043	0.083	SUBCLONAL	1	FALSE	1	0.658407197977731	2		960	696	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412958	49412958	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	136	1081	0	ENST00000418115.1:c.65T>G	p.Leu22Arg	p.L22R	ENST00000418115	NM_001664.2	22	cTc/cGc	2/5	1	2	FACETS	0.93	0.853	1	0.93	0.853	1	CLONAL	1	FALSE	1	0.658407197977731	2		1081	444	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117410	115117411	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0016810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	92	453	1	ENST00000257566.3:c.763_764del	p.Val255LysfsTer4	p.V255Kfs*4	ENST00000257566	NM_016569.3	255	GTa/a	4/8	1	2	FACETS	0.967	0.87	1	0.967	0.87	1	CLONAL	1	FALSE	1	0.658407197977731	2		454	289	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061096	38061096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	10	158	0	ENST00000250448.2:c.893C>T	p.Ser298Phe	p.S298F	ENST00000250448	NM_004496.3	298	tCt/tTt	2/2	0.631543244404907	3	FACETS	0.313	0.213	0.438	0.156	0.106	0.219	SUBCLONAL	1	FALSE	1	0.658407197977731	3		158	129	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846148	68846185	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GATCTTCAATCCCACCACGGTAATTCTATAACTCCTTA	GATCTTCAATCCCACCACGGTAATTCTATAACTCCTTA	-	novel	NA	P-0016810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	149	961	0	ENST00000261769.5:c.1121_1137+21del		p.X374_splice	ENST00000261769	NM_004360.3	374		8/16	0.617051392838327	2	FACETS	1	0.986	1	0.652	0.604	0.7	CLONAL	1	FALSE	0	0.658407197977731	2		961	347	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664450	138664450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	130	495	0	ENST00000330315.3:c.1115C>T	p.Ser372Leu	p.S372L	ENST00000330315	NM_023067.3	372	tCg/tTg	1/1	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	FALSE	1	0.658407197977731	2		495	382	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241737	55241737	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0016810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	145	542	0	ENST00000275493.2:c.2184+1G>T		p.X728_splice	ENST00000275493	NM_005228.3	728			0.383036870897591	4	FACETS	0.812	0.747	0.878	0.812	0.747	0.878	INDETERMINATE	2	FALSE	2	0.658407197977731	4		542	450	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44919298	44919298	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	20	384	0	ENST00000377967.4:c.1226T>C	p.Leu409Pro	p.L409P	ENST00000377967	NM_021140.2	409	cTa/cCa	13/29	0.697338617708051	1	FACETS	0.126	0.096	0.161	0.126	0.096	0.161	SUBCLONAL	1	TRUE	0	0.708943359504247	1		384	289	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444737	49444737	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	540	791	0	ENST00000301067.7:c.2729C>G	p.Pro910Arg	p.P910R	ENST00000301067	NM_003482.3	910	cCt/cGt	10/54	0.637147920884693	2	FACETS	0.879	0.851	0.906	0.879	0.851	0.906	CLONAL	2	TRUE	0	0.708943359504247	2		791	867	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954343	48954344	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCGCTCT	novel	NA	P-0016811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	327	378	0	ENST00000267163.4:c.1467_1474dup	p.Glu492AlafsTer6	p.E492Afs*6	ENST00000267163	NM_000321.2	488	-/TGCGCTCT	16/27	0.708943359504247	4	FACETS	1	0.976	1	0.521	0.495	0.547	CLONAL	2	TRUE	0	0.708943359504247	4		378	756	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823802	3823802	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	298	381	0	ENST00000262367.5:c.2413del	p.Ala805ArgfsTer2	p.A805Rfs*2	ENST00000262367	NM_004380.2	805	Gcg/cg	13/31	0.498189659426136	3	FACETS	1	0.988	1	0.733	0.7	0.766	CLONAL	2	TRUE	0	0.708943359504247	3		381	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576858	7576858	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	483	447	0	ENST00000269305.4:c.988del	p.Leu330PhefsTer15	p.L330Ffs*15	ENST00000269305	NM_001126112.2	330	Ctt/tt	9/11	0.617351212538637	3	FACETS	0.89	0.863	0.917	0.89	0.863	0.917	CLONAL	3	TRUE	0	0.708943359504247	3		447	691	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383230	42383230	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	120	460	0	ENST00000221972.3:c.250G>A	p.Gly84Ser	p.G84S	ENST00000221972	NM_021601.3	84	Ggc/Agc	2/5	0.242825759725574	4	FACETS	0.741	0.669	0.816	0.185	0.167	0.204	INDETERMINATE	1	TRUE	0	0.708943359504247	4		460	781	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42384967	42384967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	123	497	0	ENST00000221972.3:c.601G>A	p.Asp201Asn	p.D201N	ENST00000221972	NM_021601.3	201	Gac/Aac	5/5	0.242825759725574	4	FACETS	0.809	0.732	0.89	0.202	0.183	0.223	INDETERMINATE	1	TRUE	0	0.708943359504247	4		497	733	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375163	31375163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774622592	NA	P-0016811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	123	599	1	ENST00000328111.2:c.560C>T	p.Pro187Leu	p.P187L	ENST00000328111	NM_006892.3	187	cCc/cTc	6/23	0.274575859011173	5	FACETS	0.693	0.626	0.765	0.231	0.208	0.255	INDETERMINATE	1	TRUE	2	0.708943359504247	5		600	1033	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114546	73114547	+	splice_acceptor_variant	Splice_Site	DEL	AG	AG	-	novel	NA	P-0016811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	197	193	0	ENST00000356692.5:c.929_930del		p.X310_splice	ENST00000356692		310			0.61658011996201	2	FACETS	0.948	0.902	0.994	0.948	0.902	0.994	CLONAL	2	TRUE	0	0.708943359504247	2		193	293	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574026	7574026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	25	678	0	ENST00000269305.4:c.1001G>T	p.Gly334Val	p.G334V	ENST00000269305	NM_001126112.2	334	gGg/gTg	10/11	1	2	FACETS	0.064	0.05	0.08	0.064	0.05	0.08	SUBCLONAL	1	TRUE	1	0.683457958983051	2		678	1147	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856313	111856313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747913408	NA	P-0016813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	30	65	0	ENST00000341259.2:c.364G>A	p.Glu122Lys	p.E122K	ENST00000341259	NM_005475.2	122	Gag/Aag	2/8	0.196622185994622	3	FACETS	1	0.925	1	0.62	0.513	0.734	INDETERMINATE	1	TRUE	1	0.683457958983051	3		65	95	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754323	57754501	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CACCTTTCTTGCTTTCAAAATATGAGCCATTGACTAAGAAGAGGAGAAGGAAAAAAGAGAATCTGTCAAAACAGTTATCAAAATCACTGGTTTCCCTTTGCAGGATGAGCAATGAAAGTTAACTTTGCAGTGTAAGTGCTGCCACAGCTAAAATCCCAGATAAAATACTCTTTGAATAC	CACCTTTCTTGCTTTCAAAATATGAGCCATTGACTAAGAAGAGGAGAAGGAAAAAAGAGAATCTGTCAAAACAGTTATCAAAATCACTGGTTTCCCTTTGCAGGATGAGCAATGAAAGTTAACTTTGCAGTGTAAGTGCTGCCACAGCTAAAATCCCAGATAAAATACTCTTTGAATAC	-	novel	NA	P-0016813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	13	406	0	ENST00000274289.3:c.495+51_528del		p.X165_splice	ENST00000274289	NM_006622.3	165		4/14	0.669760379374171	0	FACETS		NA	1			1	NA	1	TRUE	0	0.683457958983051	0		406	260	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821125	32821125	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0016813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	370	882	0	ENST00000354258.4:c.469A>T	p.Lys157Ter	p.K157*	ENST00000354258	NM_000593.5	157	Aag/Tag	1/11	1	2	FACETS	0.915	0.869	0.963	0.915	0.869	0.963	CLONAL	1	TRUE	1	0.683457958983051	2		882	1183	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	92	423	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.55	2		423	292	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0016814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	84	318	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.185442635805332	4	FACETS	1	0.969	1	0.63	0.56	0.703	INDETERMINATE	1	TRUE	2	0.55	4		318	376	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430767	78430768	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0016814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	75	665	0	ENST00000370768.2:c.621_622insTT	p.Ile208LeufsTer15	p.I208Lfs*15	ENST00000370768	NM_003902.3	207	-/TT	8/20	0.55075181948921	1	FACETS	0.286	0.25	0.324	0.286	0.25	0.324	SUBCLONAL	1	TRUE	0	0.55	1		665	692	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104658	209104658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	57	403	1	ENST00000345146.2:c.920C>T	p.Ala307Val	p.A307V	ENST00000345146	NM_005896.2	307	gCt/gTt	8/10	0.185442635805332	4	FACETS	0.513	0.44	0.593	0.257	0.22	0.297	INDETERMINATE	1	TRUE	2	0.55	4		404	626	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	245	486	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.361935598886106	3	FACETS	0.918	0.861	0.977	0.918	0.861	0.977	CLONAL	2	TRUE	1	0.392696112945842	3		486	813	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0016815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	278	1050	1	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.392696112945842	1	FACETS	0.813	0.762	0.866	0.813	0.762	0.866	CLONAL	1	TRUE	0	0.392696112945842	1		1051	1399	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061222	38061222	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	183	583	0	ENST00000250448.2:c.767A>T	p.Asn256Ile	p.N256I	ENST00000250448	NM_004496.3	256	aAc/aTc	2/2	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.392696112945842	2		583	882	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858935	45858935	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	115	824	0	ENST00000391945.4:c.1531C>T	p.Arg511Trp	p.R511W	ENST00000391945	NM_000400.3	511	Cgg/Tgg	16/23	0.352830726285247	1	FACETS	0.408	0.367	0.453	0.408	0.367	0.453	SUBCLONAL	1	TRUE	0	0.392696112945842	1		824	1153	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526682	106526682	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	69	518	0	ENST00000359195.3:c.2975T>A	p.Leu992His	p.L992H	ENST00000359195	NM_002649.2	992	cTc/cAc	10/11	1	2	FACETS	0.444	0.386	0.507	0.444	0.386	0.507	SUBCLONAL	1	TRUE	1	0.392696112945842	2		518	791	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0016816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	162	461	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.397618219149352	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.397618219149352	1		461	602	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126757	5126757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775495966	NA	P-0016816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	106	443	2	ENST00000381652.3:c.3365G>A	p.Arg1122Gln	p.R1122Q	ENST00000381652	NM_004972.3	1122	cGa/cAa	25/25	1	2	FACETS	0.657	0.588	0.729	0.657	0.588	0.729	SUBCLONAL	1	TRUE	1	0.397618219149352	2		445	812	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954019	32954019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80359162	NA	P-0016816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	220	553	2	ENST00000380152.3:c.9086C>T	p.Ala3029Val	p.A3029V	ENST00000380152		3029	gCg/gTg	23/27	0.397618219149352	1	FACETS	0.873	0.813	0.936	0.873	0.813	0.936	CLONAL	1	TRUE	0	0.397618219149352	1		555	1015	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528231	103528231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	79	386	1	ENST00000355739.4:c.3539G>A	p.Arg1180Lys	p.R1180K	ENST00000355739	NM_000123.3	1180	aGg/aAg	15/15	0.368843503157351	3	FACETS	0.671	0.59	0.758	0.224	0.196	0.253	SUBCLONAL	1	TRUE	0	0.397618219149352	3		387	710	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993108	72993108	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	230	662	1	ENST00000268489.5:c.937G>A	p.Glu313Lys	p.E313K	ENST00000268489	NM_006885.3	313	Gag/Aag	2/10	0.397618219149352	1	FACETS	0.909	0.847	0.972	0.909	0.847	0.972	CLONAL	1	TRUE	0	0.397618219149352	1		663	1020	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224170	39224170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1558460622	NA	P-0016816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	114	385	0	ENST00000402219.2:c.2974G>A	p.Glu992Lys	p.E992K	ENST00000402219	NM_005633.3	992	Gaa/Aaa	19/23	1	2	FACETS	0.84	0.757	0.927	0.84	0.757	0.927	CLONAL	1	TRUE	1	0.397618219149352	2		385	683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0016816-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	243	461	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.493739045933881	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.493739045933881	1		461	724	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126757	5126757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775495966	NA	P-0016816-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	114	443	2	ENST00000381652.3:c.3365G>A	p.Arg1122Gln	p.R1122Q	ENST00000381652	NM_004972.3	1122	cGa/cAa	25/25	0.151741605966211	3	FACETS	1	0.969	1	0.586	0.53	0.645	INDETERMINATE	1	TRUE	1	0.493739045933881	3		445	491	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954019	32954019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80359162	NA	P-0016816-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	223	553	2	ENST00000380152.3:c.9086C>T	p.Ala3029Val	p.A3029V	ENST00000380152		3029	gCg/gTg	23/27	0.493739045933881	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.493739045933881	1		555	621	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993108	72993108	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016816-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	284	662	1	ENST00000268489.5:c.937G>A	p.Glu313Lys	p.E313K	ENST00000268489	NM_006885.3	313	Gag/Aag	2/10	0.424814282544898	1	FACETS	0.977	0.921	1	0.977	0.921	1	CLONAL	1	TRUE	0	0.493739045933881	1		663	887	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224170	39224170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1558460622	NA	P-0016816-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	129	385	0	ENST00000402219.2:c.2974G>A	p.Glu992Lys	p.E992K	ENST00000402219	NM_005633.3	992	Gaa/Aaa	19/23	0.171615240723757	1	FACETS	0.839	0.766	0.915	0.839	0.766	0.915	INDETERMINATE	1	TRUE	0	0.493739045933881	1		385	469	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	80	641	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.237791152320081	4	FACETS	1	0.974	1	0.726	0.637	0.821	CLONAL	1	TRUE	2	0.13	4		641	958	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031171	11031171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568357607	NA	P-0016817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	42	720	0	ENST00000327064.4:c.1256G>A	p.Arg419Gln	p.R419Q	ENST00000327064	NM_199141.1	419	cGg/cAg	11/16	0.313966094099681	4	FACETS	1	0.849	1	0.511	0.425	0.606	CLONAL	1	TRUE	2	0.13	4		720	715	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457239	67457246	+	frameshift_variant	Frame_Shift_Del	DEL	GGATGGCC	GGATGGCC	-	novel	NA	P-0016817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	24	404	0	ENST00000327367.4:c.215_222del	p.Asp72ValfsTer36	p.D72Vfs*36	ENST00000327367	NM_005902.3	71	ctGGATGGCCgg/ctgg	2/9	0.403897178452013	3	FACETS	0.821	0.642	1	0.41	0.321	0.514	CLONAL	1	TRUE	1	0.13	3		404	479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578523	7578542	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCAAAACATCTTGTTGAG	TGGCAAAACATCTTGTTGAG	-	novel	NA	P-0016817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	54	955	0	ENST00000269305.4:c.388_407del	p.Leu130ThrfsTer12	p.L130Tfs*12	ENST00000269305	NM_001126112.2	130	CTCAACAAGATGTTTTGCCAa/a	5/11	0.403897178452013	3	FACETS	0.839	0.714	0.977	0.42	0.357	0.489	CLONAL	1	TRUE	1	0.13	3		955	1054	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229433	98229433	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	22	259	0	ENST00000331920.6:c.2525A>T	p.Lys842Ile	p.K842I	ENST00000331920	NM_000264.3	842	aAa/aTa	15/24	0.403897178452013	3	FACETS	0.999	0.773	1	0.499	0.386	0.63	CLONAL	1	TRUE	1	0.13	3		259	361	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0016818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	152	497	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	1	2	FACETS	0.965	0.883	1	0.965	0.883	1	CLONAL	1	TRUE	1	0.410379965487891	2		497	768	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177011	56177014	+	frameshift_variant	Frame_Shift_Del	DEL	ATAG	ATAG	-	novel	NA	P-0016818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	116	305	0	ENST00000399503.3:c.2286_2289del	p.Arg763CysfsTer35	p.R763Cfs*35	ENST00000399503	NM_005921.1	761	ATAGat/at	13/20	1	2	FACETS	0.887	0.802	0.978	0.887	0.802	0.978	CLONAL	1	TRUE	1	0.410379965487891	2		305	637	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161175	56161176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0016818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	107	321	0	ENST00000399503.3:c.1047_1048dup	p.Ala350ValfsTer13	p.A350Vfs*13	ENST00000399503	NM_005921.1	348	-/TG	5/20	1	2	FACETS	0.801	0.72	0.887	0.801	0.72	0.887	CLONAL	1	TRUE	1	0.410379965487891	2		321	651	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545763	106545763	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	185	453	0	ENST00000359195.3:c.3240G>T	p.Trp1080Cys	p.W1080C	ENST00000359195	NM_002649.2	1080	tgG/tgT	11/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.410379965487891	2		453	864	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856020	68856020	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	130	573	0	ENST00000261769.5:c.1828C>T	p.Gln610Ter	p.Q610*	ENST00000261769	NM_004360.3	610	Cag/Tag	12/16	0.376577466865501	1	FACETS	0.961	0.875	1	0.961	0.875	1	CLONAL	1	TRUE	0	0.376577466865501	1		573	583	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248848	133248876	+	frameshift_variant	Frame_Shift_Del	DEL	CAAGGGCGTGGCGCAAGGTCTTCTCAACC	CAAGGGCGTGGCGCAAGGTCTTCTCAACC	-	novel	NA	P-0016819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	46	500	0	ENST00000320574.5:c.1719_1747del	p.Val574GlyfsTer14	p.V574Gfs*14	ENST00000320574	NM_006231.2	573	cgGGTTGAGAAGACCTTGCGCCACGCCCTTGag/cgag	16/49	1	2	FACETS	0.378	0.317	0.445	0.378	0.317	0.445	SUBCLONAL	1	TRUE	1	0.376577466865501	2		500	647	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518615	103518615	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	28	254	0	ENST00000355739.4:c.2203G>C	p.Glu735Gln	p.E735Q	ENST00000355739	NM_000123.3	735	Gag/Cag	10/15	1	2	FACETS	0.425	0.34	0.522	0.425	0.34	0.522	SUBCLONAL	1	TRUE	1	0.376577466865501	2		254	350	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22153354	22153354	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	71	427	0	ENST00000215832.6:c.556G>C	p.Glu186Gln	p.E186Q	ENST00000215832	NM_002745.4	186	Gaa/Caa	4/9	1	2	FACETS	0.513	0.447	0.584	0.513	0.447	0.584	SUBCLONAL	1	TRUE	1	0.376577466865501	2		427	735	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825328	134825328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	70	225	0	ENST00000398015.3:c.844G>A	p.Glu282Lys	p.E282K	ENST00000398015	NM_004441.4	282	Gaa/Aaa	4/16	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.376577466865501	2		225	333	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184158	56184158	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	83	294	0	ENST00000399503.3:c.4363T>C	p.Ser1455Pro	p.S1455P	ENST00000399503	NM_005921.1	1455	Tcc/Ccc	19/20	0.376577466865501	3	FACETS	0.885	0.782	0.995	0.442	0.391	0.498	CLONAL	1	TRUE	1	0.376577466865501	3		294	592	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589631	67589632	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATTATATGAAGA	novel	NA	P-0016819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	165	326	0	ENST00000274335.5:c.1397_1408dup	p.Leu466_Glu469dup	p.L466_E469dup	ENST00000274335		466	aga/agATTATATGAAGAa	10/15	0.376577466865501	3	FACETS	1	0.989	1	0.737	0.679	0.798	CLONAL	1	TRUE	1	0.376577466865501	3		326	706	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426051	47426051	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372462744	NA	P-0016819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	124	619	0	ENST00000377045.4:c.571C>T	p.His191Tyr	p.H191Y	ENST00000377045	NM_001654.4	191	Cac/Tac	7/16	1	2	FACETS	0.934	0.846	1	0.934	0.846	1	CLONAL	1	TRUE	1	0.376577466865501	2		619	705	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191766	123191766	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	90	381	0	ENST00000218089.9:c.1355G>T	p.Gly452Val	p.G452V	ENST00000218089	NM_001042749.1	452	gGa/gTa	15/35	NA	2	FACETS	0.77	0.684	0.861			1	INDETERMINATE	1	TRUE	NA	0.376577466865501	2		381	621	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0016820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	25	670	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.359369354080125	3	FACETS	0.222	0.174	0.278	0.111	0.087	0.139	SUBCLONAL	1	TRUE	1	0.359369354080125	3		670	740	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782177	NA	P-0016820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	191	795	1	ENST00000269305.4:c.644G>T	p.Ser215Ile	p.S215I	ENST00000269305	NM_001126112.2	215	aGt/aTt	6/11	0.305001407399261	1	FACETS	0.773	0.714	0.835	0.773	0.714	0.835	SUBCLONAL	1	TRUE	0	0.359369354080125	1		796	1128	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0016821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	262	599	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		599	926	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	92	423	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		423	386	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0016822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	180	509	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.206489414359022	3	FACETS	0.76	0.701	0.821	0.76	0.701	0.821	SUBCLONAL	2	FALSE	1	0.291236832994495	3		509	932	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	195	486	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.944	0.877	1	1	0.993	1	CLONAL	2	FALSE	1	0.291236832994495	2		486	709	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0016822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	20	480	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.188	0.143	0.242	0.188	0.143	0.242	SUBCLONAL	1	FALSE	1	0.291236832994495	2		480	729	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306996	65306997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0016822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	93	259	3	ENST00000342505.4:c.2580dup	p.Pro861ThrfsTer4	p.P861Tfs*4	ENST00000342505	NM_002227.2	860	-/A	19/25	0.177884824949484	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	0	0.291236832994495	1		262	497	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562734	29562734	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	336	383	0	ENST00000356175.3:c.3814C>T	p.Gln1272Ter	p.Q1272*	ENST00000356175	NM_000267.3	1272	Cag/Tag	28/57	0.294581634967876	3	FACETS	0.905	0.862	0.949	1	0.992	1	CLONAL	4	FALSE	0	0.291236832994495	3		383	730	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	266	486	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.482095646688031	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.482095646688031	3		486	623	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	112	423	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.482095646688031	2		423	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0016823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	167	591	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.482095646688031	2		592	635	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961833	55961833	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0016823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	99	424	0	ENST00000263923.4:c.2729-1G>C		p.X910_splice	ENST00000263923	NM_002253.2	910			1	2	FACETS	0.909	0.816	1	0.909	0.816	1	CLONAL	1	TRUE	1	0.482095646688031	2		424	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577019	7577043	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CTCGCTTAGTGCTCCCTGGGGGCAG	CTCGCTTAGTGCTCCCTGGGGGCAG	-	novel	NA	P-0016824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	37	448	0	ENST00000269305.4:c.895_919del	p.Leu299HisfsTer38	p.L299Hfs*38	ENST00000269305	NM_001126112.2	299	CTGCCCCCAGGGAGCACTAAGCGAGca/ca	8/11	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.12	2		448	573	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143044	47143044	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	42	431	0	ENST00000409792.3:c.4919G>A	p.Trp1640Ter	p.W1640*	ENST00000409792	NM_014159.6	1640	tGg/tAg	8/21	1	2	FACETS	0.958	0.797	1	0.958	0.797	1	CLONAL	1	TRUE	1	0.12	2		431	731	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	211	605	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	1	2	FACETS	0.921	0.857	0.987	0.921	0.857	0.987	CLONAL	1	TRUE	1	0.55	2		605	833	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696461	47696461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	194	617	0	ENST00000347630.2:c.362G>A	p.Arg121Gln	p.R121Q	ENST00000347630	NM_001007230.1	121	cGg/cAg	6/11	1	2	FACETS	0.88	0.815	0.946	0.88	0.815	0.946	CLONAL	1	TRUE	1	0.55	2		617	802	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255096	16255096	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	209	728	1	ENST00000375759.3:c.2361A>T	p.Lys787Asn	p.K787N	ENST00000375759	NM_015001.2	787	aaA/aaT	11/15	1	2	FACETS	0.866	0.805	0.929	0.866	0.805	0.929	CLONAL	1	TRUE	1	0.55	2		729	878	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851361	156851361	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	174	780	0	ENST00000524377.1:c.2318G>T	p.Ser773Ile	p.S773I	ENST00000524377	NM_002529.3	773	aGc/aTc	17/17	1	2	FACETS	0.817	0.754	0.883	0.817	0.754	0.883	CLONAL	1	TRUE	1	0.55	2		780	774	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850948	63850948	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	229	756	0	ENST00000279873.7:c.1726G>T	p.Glu576Ter	p.E576*	ENST00000279873	NM_032199.2	576	Gaa/Taa	10/10	1	2	FACETS	0.812	0.757	0.87	0.812	0.757	0.87	CLONAL	1	TRUE	1	0.55	2		756	1025	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685281	89685281	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	177	520	0	ENST00000371953.3:c.176C>A	p.Ser59Ter	p.S59*	ENST00000371953	NM_000314.4	59	tCa/tAa	3/9	1	2	FACETS	0.99	0.916	1	0.99	0.916	1	CLONAL	1	TRUE	1	0.55	2		520	650	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	213	737	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.983	0.916	1	0.983	0.916	1	CLONAL	1	TRUE	1	0.55	2		737	788	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239530	123239530	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	393	1143	0	ENST00000358487.5:c.2307C>A	p.Tyr769Ter	p.Y769*	ENST00000358487	NM_000141.4	769	taC/taA	18/18	1	2	FACETS	0.962	0.913	1	0.962	0.913	1	CLONAL	1	TRUE	1	0.55	2		1143	1485	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941264	71941264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772985547	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	229	828	1	ENST00000298229.2:c.1039C>T	p.Arg347Trp	p.R347W	ENST00000298229	NM_001567.3	347	Cgg/Tgg	9/28	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.55	2		829	824	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942155	71942155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	572	1044	3	ENST00000298229.2:c.1419G>T	p.Glu473Asp	p.E473D	ENST00000298229	NM_001567.3	473	gaG/gaT	12/28	1	2	FACETS	0.924	0.891	0.956	1	0.998	1	CLONAL	2	TRUE	1	0.55	2		1047	1126	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195394	102195394	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	141	432	0	ENST00000263464.3:c.154C>T	p.Arg52Cys	p.R52C	ENST00000263464	NM_001165.4	52	Cgt/Tgt	2/9	1	2	FACETS	0.922	0.844	1	0.922	0.844	1	CLONAL	1	TRUE	1	0.55	2		432	556	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160347	108160347	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	45	415	0	ENST00000278616.4:c.4255C>A	p.Leu1419Ile	p.L1419I	ENST00000278616	NM_000051.3	1419	Ctt/Att	29/63	1	2	FACETS	0.3	0.251	0.353	0.3	0.251	0.353	SUBCLONAL	1	TRUE	1	0.55	2		415	546	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50488306	50488306	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	72	785	0	ENST00000394963.4:c.1220T>G	p.Phe407Cys	p.F407C	ENST00000394963	NM_003076.4	407	tTt/tGt	10/13	1	2	FACETS	0.262	0.228	0.299	0.262	0.228	0.299	SUBCLONAL	1	TRUE	1	0.55	2		785	1000	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249857	133249857	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1565972665	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	146	477	0	ENST00000320574.5:c.1366G>C	p.Ala456Pro	p.A456P	ENST00000320574	NM_006231.2	456	Gcc/Ccc	14/49	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.55	2		477	525	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28611324	28611324	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	53	698	0	ENST00000241453.7:c.1307G>T	p.Arg436Ile	p.R436I	ENST00000241453	NM_004119.2	436	aGa/aTa	10/24	1	2	FACETS	0.205	0.174	0.239	0.205	0.174	0.239	SUBCLONAL	1	TRUE	1	0.55	2		698	942	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626787	28626787	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	203	583	0	ENST00000241453.7:c.509G>T	p.Arg170Ile	p.R170I	ENST00000241453	NM_004119.2	170	aGa/aTa	5/24	1	2	FACETS	0.94	0.874	1	0.94	0.874	1	CLONAL	1	TRUE	1	0.55	2		583	785	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914745	32914745	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs761996223	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	106	863	0	ENST00000380152.3:c.6253T>G	p.Leu2085Val	p.L2085V	ENST00000380152		2085	Tta/Gta	11/27	1	2	FACETS	0.424	0.379	0.471	0.424	0.379	0.471	SUBCLONAL	1	TRUE	1	0.55	2		863	910	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726669	88726669	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	81	621	0	ENST00000360948.2:c.375G>T	p.Lys125Asn	p.K125N	ENST00000360948	NM_001012338.2	125	aaG/aaT	4/19	1	2	FACETS	0.403	0.355	0.456	0.403	0.355	0.456	SUBCLONAL	1	TRUE	1	0.55	2		621	730	SUCCESS
BLM	641	MSKCC	GRCh37	15	91337480	91337480	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	206	652	0	ENST00000355112.3:c.3103G>A	p.Glu1035Lys	p.E1035K	ENST00000355112	NM_000057.2	1035	Gaa/Aaa	16/22	1	2	FACETS	0.901	0.838	0.967	0.901	0.838	0.967	CLONAL	1	TRUE	1	0.55	2		652	831	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781331	3781331	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs752125051	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	310	968	0	ENST00000262367.5:c.5034C>A	p.Phe1678Leu	p.F1678L	ENST00000262367	NM_004380.2	1678	ttC/ttA	30/31	1	2	FACETS	0.96	0.905	1	0.96	0.905	1	CLONAL	1	TRUE	1	0.55	2		968	1174	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832852	3832852	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	51	563	0	ENST00000262367.5:c.1406C>A	p.Ser469Tyr	p.S469Y	ENST00000262367	NM_004380.2	469	tCt/tAt	6/31	1	2	FACETS	0.262	0.222	0.306	0.262	0.222	0.306	SUBCLONAL	1	TRUE	1	0.55	2		563	709	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923366	9923366	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	91	694	0	ENST00000330684.3:c.1921T>G	p.Phe641Val	p.F641V	ENST00000330684	NM_001134407.1	641	Ttc/Gtc	9/13	1	2	FACETS	0.422	0.374	0.473	0.422	0.374	0.473	SUBCLONAL	1	TRUE	1	0.55	2		694	785	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032064	10032064	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	59	665	3	ENST00000330684.3:c.759C>A	p.Phe253Leu	p.F253L	ENST00000330684	NM_001134407.1	253	ttC/ttA	3/13	1	2	FACETS	0.282	0.242	0.326	0.282	0.242	0.326	SUBCLONAL	1	TRUE	1	0.55	2		668	760	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646762	23646762	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	314	931	1	ENST00000261584.4:c.1105C>A	p.Leu369Ile	p.L369I	ENST00000261584	NM_024675.3	369	Ctt/Att	4/13	1	2	FACETS	0.994	0.938	1	0.994	0.938	1	CLONAL	1	TRUE	1	0.55	2		932	1149	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819546	81819546	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	77	202	0	ENST00000359376.3:c.-47-2A>C		p.X16_splice	ENST00000359376	NM_002661.3	16			1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.55	2		202	247	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348354	89348354	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1191	99	1013	0	ENST00000301030.4:c.4596G>T	p.Glu1532Asp	p.E1532D	ENST00000301030	NM_001256183.1	1532	gaG/gaT	9/13	1	2	FACETS	0.279	0.248	0.312	0.279	0.248	0.312	SUBCLONAL	1	TRUE	1	0.55	2		1013	1290	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979656	7979656	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	30	495	0	ENST00000319144.4:c.1369T>C	p.Ser457Pro	p.S457P	ENST00000319144	NM_001139.2	457	Tcc/Ccc	11/15	1	2	FACETS	0.211	0.169	0.258	0.211	0.169	0.258	SUBCLONAL	1	TRUE	1	0.55	2		495	518	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325762	30325762	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs771704089	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	203	610	1	ENST00000322652.5:c.1960C>T	p.Arg654Ter	p.R654*	ENST00000322652	NM_015355.2	654	Cga/Tga	16/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.55	2		611	671	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696462	47696462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	205	610	1	ENST00000347630.2:c.361C>T	p.Arg121Trp	p.R121W	ENST00000347630	NM_001007230.1	121	Cgg/Tgg	6/11	1	2	FACETS	0.948	0.882	1	0.948	0.882	1	CLONAL	1	TRUE	1	0.55	2		611	786	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212215	36212215	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1010777622	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	245	875	0	ENST00000222270.7:c.1966G>A	p.Glu656Lys	p.E656K	ENST00000222270	NM_014727.1	656	Gaa/Aaa	3/37	1	2	FACETS	0.932	0.872	0.994	0.932	0.872	0.994	CLONAL	1	TRUE	1	0.55	2		875	956	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027541	48027541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587779923	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	132	459	1	ENST00000234420.5:c.2419G>A	p.Glu807Lys	p.E807K	ENST00000234420	NM_000179.2	807	Gaa/Aaa	4/10	1	2	FACETS	0.996	0.91	1	0.996	0.91	1	CLONAL	1	TRUE	1	0.55	2		460	482	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137487	202137487	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1218	125	1025	0	ENST00000358485.4:c.715G>T	p.Glu239Ter	p.E239*	ENST00000358485	NM_001080125.1	239	Gaa/Taa	4/9	1	2	FACETS	0.338	0.305	0.374	0.338	0.305	0.374	SUBCLONAL	1	TRUE	1	0.55	2		1025	1343	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39762950	39762950	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	198	735	2	ENST00000288319.7:c.886C>A	p.Leu296Ile	p.L296I	ENST00000288319	NM_182918.3	296	Ctt/Att	9/10	1	2	FACETS	0.768	0.712	0.827	0.768	0.712	0.827	SUBCLONAL	1	TRUE	1	0.55	2		737	937	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092909	29092909	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	74	882	0	ENST00000328354.6:c.1075G>T	p.Glu359Ter	p.E359*	ENST00000328354	NM_007194.3	359	Gaa/Taa	10/15	1	2	FACETS	0.242	0.211	0.276	0.242	0.211	0.276	SUBCLONAL	1	TRUE	1	0.55	2		882	1112	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713129	30713129	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	52	419	0	ENST00000295754.5:c.455-1G>T		p.X152_splice	ENST00000295754	NM_003242.5	152			1	2	FACETS	0.38	0.324	0.442	0.38	0.324	0.442	SUBCLONAL	1	TRUE	1	0.55	2		419	497	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931589	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	122	410	0	ENST00000349496.5:c.101G>A	p.Gly34Glu	p.G34E	ENST00000349496	NM_001904.3	34	gGa/gAa	3/15	1	2	FACETS	0.875	0.795	0.958	0.875	0.795	0.958	CLONAL	1	TRUE	1	0.55	2		410	507	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163797	47163797	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	189	592	0	ENST00000409792.3:c.2329G>T	p.Glu777Ter	p.E777*	ENST00000409792	NM_014159.6	777	Gaa/Taa	3/21	1	2	FACETS	0.907	0.84	0.976	0.907	0.84	0.976	CLONAL	1	TRUE	1	0.55	2		592	758	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259477	89259477	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200567888	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	192	561	0	ENST00000336596.2:c.621G>T	p.Lys207Asn	p.K207N	ENST00000336596	NM_005233.5	207	aaG/aaT	3/17	1	2	FACETS	0.938	0.87	1	0.938	0.87	1	CLONAL	1	TRUE	1	0.55	2		561	744	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526268	189526268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	79	744	4	ENST00000264731.3:c.532G>A	p.Asp178Asn	p.D178N	ENST00000264731	NM_003722.4	178	Gac/Aac	4/14	1	2	FACETS	0.312	0.273	0.353	0.312	0.273	0.353	SUBCLONAL	1	TRUE	1	0.55	2		748	921	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573317	55573317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752061752	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	286	809	1	ENST00000288135.5:c.979G>A	p.Asp327Asn	p.D327N	ENST00000288135	NM_000222.2	327	Gat/Aat	6/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.55	2		810	992	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958799	55958799	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	301	926	0	ENST00000263923.4:c.3054C>A	p.Phe1018Leu	p.F1018L	ENST00000263923	NM_002253.2	1018	ttC/ttA	22/30	1	2	FACETS	0.978	0.922	1	0.978	0.922	1	CLONAL	1	TRUE	1	0.55	2		926	1119	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189873	66189873	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1032457637	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	76	650	0	ENST00000273854.3:c.3073G>T	p.Glu1025Ter	p.E1025*	ENST00000273854	NM_004439.5	1025	Gaa/Taa	18/18	1	2	FACETS	0.327	0.286	0.371	0.327	0.286	0.371	SUBCLONAL	1	TRUE	1	0.55	2		650	846	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538912	187538912	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201085583	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	148	495	0	ENST00000441802.2:c.8828C>T	p.Thr2943Met	p.T2943M	ENST00000441802	NM_005245.3	2943	aCg/aTg	10/27	1	2	FACETS	0.858	0.787	0.933	0.858	0.787	0.933	CLONAL	1	TRUE	1	0.55	2		495	627	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672800	86672800	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764802465	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	154	416	0	ENST00000274376.6:c.2287G>A	p.Glu763Lys	p.E763K	ENST00000274376	NM_002890.2	763	Gaa/Aaa	17/25	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.55	2		416	547	SUCCESS
APC	324	MSKCC	GRCh37	5	112154933	112154933	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660612	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	116	786	1	ENST00000257430.4:c.1204C>T	p.Arg402Cys	p.R402C	ENST00000257430	NM_000038.5	402	Cgt/Tgt	10/16	1	2	FACETS	0.419	0.377	0.464	0.419	0.377	0.464	SUBCLONAL	1	TRUE	1	0.55	2		787	1007	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722165	176722165	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	162	585	0	ENST00000439151.2:c.7796C>A	p.Ser2599Tyr	p.S2599Y	ENST00000439151	NM_022455.4	2599	tCt/tAt	23/23	1	2	FACETS	0.898	0.827	0.972	0.898	0.827	0.972	CLONAL	1	TRUE	1	0.55	2		585	656	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64286880	64286880	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1029378671	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	249	751	0	ENST00000370651.3:c.95A>C	p.Lys32Thr	p.K32T	ENST00000370651	NM_003463.4	32	aAa/aCa	2/6	1	2	FACETS	0.996	0.933	1	0.996	0.933	1	CLONAL	1	TRUE	1	0.55	2		751	909	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001395	150001395	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	254	845	0	ENST00000253339.5:c.2209C>T	p.Arg737Ter	p.R737*	ENST00000253339		737	Cga/Tga	4/7	1	2	FACETS	0.962	0.902	1	0.962	0.902	1	CLONAL	1	TRUE	1	0.55	2		845	960	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522565	106522565	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	153	432	0	ENST00000359195.3:c.2542C>A	p.Leu848Ile	p.L848I	ENST00000359195	NM_002649.2	848	Cta/Ata	7/11	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.55	2		432	541	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187329	38187329	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2234552	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	240	723	2	ENST00000317025.8:c.1148G>A	p.Arg383Gln	p.R383Q	ENST00000317025	NM_023034.1	383	cGa/cAa	6/24	1	2	FACETS	0.965	0.903	1	0.965	0.903	1	CLONAL	1	TRUE	1	0.55	2		725	904	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87322770	87322770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781137734	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	204	562	1	ENST00000277120.3:c.371G>A	p.Arg124Gln	p.R124Q	ENST00000277120		124	cGa/cAa	5/19	1	2	FACETS	0.847	0.786	0.909	0.847	0.786	0.909	CLONAL	1	TRUE	1	0.55	2		563	876	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771828	135771828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779599439	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	287	918	1	ENST00000298552.3:c.3289C>T	p.Arg1097Cys	p.R1097C	ENST00000298552	NM_001162426.1	1097	Cgt/Tgt	23/23	1	2	FACETS	0.9	0.846	0.956	0.9	0.846	0.956	CLONAL	1	TRUE	1	0.55	2		919	1159	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15827432	15827432	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	239	777	0	ENST00000307771.7:c.548T>C	p.Phe183Ser	p.F183S	ENST00000307771	NM_005089.3	183	tTt/tCt	7/11	1	2	FACETS	0.973	0.91	1	0.973	0.91	1	CLONAL	1	TRUE	1	0.55	2		777	893	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70355017	70355017	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	86	884	1	ENST00000374080.3:c.4939G>T	p.Asp1647Tyr	p.D1647Y	ENST00000374080		1647	Gat/Tat	36/45	1	2	FACETS	0.269	0.237	0.303	0.269	0.237	0.303	SUBCLONAL	1	TRUE	1	0.55	2		885	1164	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937401	76937401	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	219	785	0	ENST00000373344.5:c.3347C>A	p.Ser1116Tyr	p.S1116Y	ENST00000373344	NM_000489.3	1116	tCc/tAc	9/35	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.55	2		785	773	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938229	76938229	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs191682105	NA	P-0016825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	295	872	2	ENST00000373344.5:c.2519G>T	p.Arg840Ile	p.R840I	ENST00000373344	NM_000489.3	840	aGa/aTa	9/35	1	2	FACETS	0.977	0.92	1	0.977	0.92	1	CLONAL	1	TRUE	1	0.55	2		874	1098	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	102	423	0				ENST00000310581	NM_198253.2	-/1132			0.786662311485682	2	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.86	2		423	190	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0016826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	2357	411	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.786662311485682	27	FACETS	1	0.997	1			1	CLONAL	24	TRUE	NA	0.86	27		411	2648	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779172	135779172	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203631	NA	P-0016826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	270	354	0	ENST00000298552.3:c.2074C>T	p.Arg692Ter	p.R692*	ENST00000298552	NM_001162426.1	692	Cga/Tga	17/23	0.87880923370786	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.86	2		354	313	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930727	32930727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80358987	NA	P-0016826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	359	371	0	ENST00000380152.3:c.7598C>T	p.Ser2533Phe	p.S2533F	ENST00000380152		2533	tCt/tTt	15/27	0.442532471652412	7	FACETS	1	0.99	1	0.854	0.815	0.893	INDETERMINATE	3	TRUE	3	0.86	7		371	770	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937643	44937643	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0016826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	573	248	0	ENST00000377967.4:c.2833-2A>G		p.X945_splice	ENST00000377967	NM_021140.2	945			0.786662311485682	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.86	2		248	620	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578393	7578393	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876660821	NA	P-0016827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	315	501	0	ENST00000269305.4:c.537T>A	p.His179Gln	p.H179Q	ENST00000269305	NM_001126112.2	179	caT/caA	5/11	0.453643335504232	2	FACETS	0.991	0.95	1	0.991	0.95	1	CLONAL	2	TRUE	0	0.639662337284685	2		501	497	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286205	66286205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777851171	NA	P-0016827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	197	324	0	ENST00000273854.3:c.1481G>A	p.Arg494His	p.R494H	ENST00000273854	NM_004439.5	494	cGt/cAt	6/18	0.626284528261211	2	FACETS	0.846	0.797	0.894	0.846	0.797	0.894	CLONAL	2	TRUE	0	0.639662337284685	2		324	364	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107909	30107909	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	29	429	0	ENST00000331968.5:c.898C>T	p.Gln300Ter	p.Q300*	ENST00000331968	NM_002742.2	300	Cag/Tag	5/18	0.639662337284685	2	FACETS	0.162	0.129	0.2	0.081	0.064	0.1	SUBCLONAL	1	TRUE	0	0.639662337284685	2		429	559	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091740	29091740	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	277	265	0	ENST00000328354.6:c.1217G>T	p.Arg406Leu	p.R406L	ENST00000328354	NM_007194.3	406	cGt/cTt	11/15	0.639662337284685	4	FACETS	1	0.977	1			1	CLONAL	2	TRUE	NA	0.639662337284685	4		265	669	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612039	189612039	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2660	904	447	0	ENST00000264731.3:c.1791C>G	p.Ile597Met	p.I597M	ENST00000264731	NM_003722.4	597	atC/atG	14/14	0.639662337284685	11	FACETS	1	0.982	1			1	CLONAL	3	TRUE	NA	0.639662337284685	11		447	3564	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612080	189612080	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2855	1002	493	0	ENST00000264731.3:c.1832C>G	p.Ser611Cys	p.S611C	ENST00000264731	NM_003722.4	611	tCc/tGc	14/14	0.639662337284685	11	FACETS	1	0.99	1			1	CLONAL	3	TRUE	NA	0.639662337284685	11		493	3857	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057553	180057553	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0016827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	81	399	0	ENST00000261937.6:c.400+2T>C		p.X134_splice	ENST00000261937	NM_182925.4	134			0.639662337284685	2	FACETS	0.546	0.482	0.613	0.273	0.241	0.307	SUBCLONAL	1	TRUE	0	0.639662337284685	2		399	464	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856050	68856050	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	590	590	0	ENST00000261769.5:c.1859del	p.Pro620LeufsTer11	p.P620Lfs*11	ENST00000261769	NM_004360.3	620	Cct/ct	12/16	0.580743263065405	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.580743263065405	2		590	1016	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176970	56176973	+	frameshift_variant	Frame_Shift_Del	DEL	AATC	AATC	-	novel	NA	P-0016828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	288	265	0	ENST00000399503.3:c.2242_2245del	p.Ser748ThrfsTer13	p.S748Tfs*13	ENST00000399503	NM_005921.1	747	gAATCa/ga	13/20	0.580743263065405	3	FACETS	0.878	0.83	0.926	0.878	0.83	0.926	CLONAL	2	TRUE	1	0.580743263065405	3		265	729	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0016829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	198	683	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.509781731563978	2		683	746	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518725	176518725	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	301	730	0	ENST00000292408.4:c.643G>A	p.Val215Met	p.V215M	ENST00000292408	NM_213647.1	215	Gtg/Atg	6/18	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.509781731563978	2		730	996	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287432	46287435	+	frameshift_variant	Frame_Shift_Del	DEL	TAAC	TAAC	-	novel	NA	P-0016829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	96	591	0	ENST00000334344.6:c.5294_5297del	p.Thr1765AsnfsTer5	p.T1765Nfs*5	ENST00000334344	NM_152641.2	1764	aTAACt/at	20/21	1	2	FACETS	0.778	0.696	0.865	0.778	0.696	0.865	SUBCLONAL	1	TRUE	1	0.509781731563978	2		591	484	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202462	123202462	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs762388218	NA	P-0016829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	83	842	0	ENST00000218089.9:c.2314T>C	p.Cys772Arg	p.C772R	ENST00000218089	NM_001042749.1	772	Tgt/Cgt	24/35	1	2	FACETS	0.844	0.749	0.943	0.844	0.749	0.943	CLONAL	1	TRUE	1	0.509781731563978	2		842	386	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	540	726	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.219027739301828	1	FACETS	0.893	0.859	0.928	0.893	0.859	0.928	INDETERMINATE	1	TRUE	0	0.644958493728218	1		726	1270	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0016830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	438	869	3	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.617208176066491	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.644958493728218	1		872	860	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0016830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	309	696	2	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	0.617208176066491	1	FACETS	0.99	0.941	1	0.99	0.941	1	CLONAL	1	TRUE	0	0.644958493728218	1		698	656	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339175	65339175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180823763	NA	P-0016830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	212	420	0	ENST00000342505.4:c.361G>A	p.Asp121Asn	p.D121N	ENST00000342505	NM_002227.2	121	Gac/Aac	5/25	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.644958493728218	2		420	594	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221084	5221084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371881792	NA	P-0016830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	148	520	0	ENST00000357368.4:c.3382G>A	p.Val1128Ile	p.V1128I	ENST00000357368	NM_002850.3	1128	Gtc/Atc	20/38	0.32823093073642	1	FACETS	0.749	0.691	0.809	0.749	0.691	0.809	INDETERMINATE	1	TRUE	0	0.644958493728218	1		520	415	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435658	18435658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143896492	NA	P-0016830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	110	354	0	ENST00000266497.5:c.643G>A	p.Gly215Arg	p.G215R	ENST00000266497		215	Gga/Aga	1/31	0.219027739301828	1	FACETS	0.39	0.351	0.431	0.39	0.351	0.431	INDETERMINATE	1	TRUE	0	0.644958493728218	1		354	592	SUCCESS
APC	324	MSKCC	GRCh37	5	112174736	112174736	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	201	394	0	ENST00000257430.4:c.3445G>T	p.Glu1149Ter	p.E1149*	ENST00000257430	NM_000038.5	1149	Gaa/Taa	16/16	1	2	FACETS	0.919	0.856	0.985	0.919	0.856	0.985	CLONAL	1	TRUE	1	0.644958493728218	2		394	678	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444231	49444231	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	171	892	0	ENST00000301067.7:c.3140T>C	p.Leu1047Pro	p.L1047P	ENST00000301067	NM_003482.3	1047	cTa/cCa	11/54	0.198013753596726	3	FACETS	0.619	0.569	0.673	0.206	0.189	0.225	INDETERMINATE	1	TRUE	0	0.644958493728218	3		892	1132	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965326	25965326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs984403631	NA	P-0016830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	57	531	0	ENST00000435504.4:c.3880C>T	p.Leu1294Phe	p.L1294F	ENST00000435504		1294	Ctt/Ttt	13/13	0.259949496151106	2	FACETS	0.26	0.222	0.301	0.13	0.111	0.151	INDETERMINATE	1	TRUE	0	0.644958493728218	2		531	681	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096526	178096526	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	36	292	1	ENST00000397062.3:c.805A>T	p.Asn269Tyr	p.N269Y	ENST00000397062	NM_006164.4	269	Aac/Tac	5/5	1	2	FACETS	0.231	0.189	0.277	0.231	0.189	0.277	SUBCLONAL	1	TRUE	1	0.644958493728218	2		293	484	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69998247	69998247	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	269	741	0	ENST00000394351.3:c.487C>G	p.Leu163Val	p.L163V	ENST00000394351	NM_000248.3	163	Ctg/Gtg	5/9	1	2	FACETS	0.752	0.705	0.8	0.752	0.705	0.8	SUBCLONAL	1	TRUE	1	0.644958493728218	2		741	1109	SUCCESS
APC	324	MSKCC	GRCh37	5	112175575	112175575	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	152	528	0	ENST00000257430.4:c.4284del	p.Gln1429LysfsTer44	p.Q1429Kfs*44	ENST00000257430	NM_000038.5	1428	ggA/gg	16/16	1	2	FACETS	0.736	0.676	0.8	0.736	0.676	0.8	SUBCLONAL	1	TRUE	1	0.644958493728218	2		528	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0016831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	285	480	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.0800276666100947	4	FACETS	1	0.987	1			1	INDETERMINATE	3	TRUE	NA	0.39306131162047	4		480	602	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0016831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	172	560	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	0.159838260684206	5	FACETS	0.812	0.747	0.879	0.541	0.498	0.586	INDETERMINATE	2	TRUE	2	0.39306131162047	5		560	857	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805287	89805287	+	splice_region_variant,intron_variant	Splice_Region	SNP	T	T	G	novel	NA	P-0016831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	81	374	0	ENST00000389301.3:c.4260+3A>C		p.X1420_splice	ENST00000389301	NM_000135.2	1420			0.39306131162047	2	FACETS	0.888	0.786	0.998	0.444	0.393	0.499	CLONAL	1	TRUE	0	0.39306131162047	2		374	464	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845721	151845721	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	219	494	0	ENST00000262189.6:c.13291A>G	p.Asn4431Asp	p.N4431D	ENST00000262189	NM_170606.2	4431	Aac/Gac	52/59	0.302018783132764	4	FACETS	0.965	0.9	1	0.965	0.9	1	CLONAL	2	TRUE	2	0.39306131162047	4		494	804	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574027	7574027	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882028	NA	P-0016832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	203	479	1	ENST00000269305.4:c.1000G>T	p.Gly334Trp	p.G334W	ENST00000269305	NM_001126112.2	334	Ggg/Tgg	10/11	0.22589875829907	2	FACETS	0.93	0.863	0.999	0.93	0.863	0.999	CLONAL	2	TRUE	0	0.254753385498936	2		480	857	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712017	89712017	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs1114167622	NA	P-0016832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	57	191	0	ENST00000371953.3:c.634+1G>C		p.X212_splice	ENST00000371953	NM_000314.4	212			0.22589875829907	2	FACETS	0.78	0.674	0.893	0.78	0.674	0.893	SUBCLONAL	2	TRUE	0	0.254753385498936	2		191	287	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240308	41240308	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	110	408	0	ENST00000379561.5:c.42C>G	p.Phe14Leu	p.F14L	ENST00000379561	NM_002015.3	14	ttC/ttG	1/3	0.195650453344298	2	FACETS	0.878	0.792	0.967	0.878	0.792	0.967	CLONAL	2	TRUE	0	0.254753385498936	2		408	492	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0016833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	301	616	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.94	0.89	0.991	0.94	0.89	0.991	CLONAL	1	TRUE	1	0.82	2		616	781	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602749	10602749	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	61	592	0	ENST00000171111.5:c.829A>C	p.Thr277Pro	p.T277P	ENST00000171111	NM_203500.1	277	Acg/Ccg	3/6	1	2	FACETS	0.224	0.193	0.258	0.224	0.193	0.258	SUBCLONAL	1	TRUE	1	0.82	2		592	664	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	198	256	0	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.927011100654463	2		256	418	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0016835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	1552	398	1	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	0.927011100654463	6	FACETS	0.991	0.973	1	0.991	0.973	1	CLONAL	4	TRUE	2	0.927011100654463	6		399	2410	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729968	30729968	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs863223852	NA	P-0016835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	281	268	0	ENST00000295754.5:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000295754	NM_003242.5	497	Cga/Tga	6/7	0.927011100654463	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.927011100654463	1		268	325	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481581	40481581	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	306	310	0	ENST00000264657.5:c.1224C>G	p.Phe408Leu	p.F408L	ENST00000264657	NM_139276.2	408	ttC/ttG	13/24	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.927011100654463	2		310	660	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058536	69058536	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61753703	NA	P-0016835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	505	494	2	ENST00000288368.4:c.4180C>T	p.Arg1394Trp	p.R1394W	ENST00000288368	NM_024870.2	1394	Cgg/Tgg	34/40	1	2	FACETS	0.938	0.9	0.975	0.938	0.9	0.975	CLONAL	1	TRUE	1	0.927011100654463	2		496	1162	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46527686	46527686	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	402	380	1	ENST00000262741.5:c.679G>T	p.Glu227Ter	p.E227*	ENST00000262741	NM_003629.3	227	Gaa/Taa	6/10	1	2	FACETS	0.977	0.934	1	0.977	0.934	1	CLONAL	1	TRUE	1	0.927011100654463	2		381	888	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224507	53224507	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	388	484	0	ENST00000375401.3:c.3206G>C	p.Arg1069Thr	p.R1069T	ENST00000375401	NM_004187.3	1069	aGa/aCa	21/26	NA	2	FACETS	0.933	0.891	0.976			1	INDETERMINATE	1	TRUE	NA	0.927011100654463	2		484	897	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0016836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	283	547	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.350487579204318	3	FACETS	0.924	0.87	0.979	0.924	0.87	0.979	CLONAL	2	TRUE	1	0.382983037788105	3		547	953	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55963925	55963925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	112	333	0	ENST00000263923.4:c.2518C>T	p.Leu840Phe	p.L840F	ENST00000263923	NM_002253.2	840	Ctt/Ttt	18/30	1	2	FACETS	0.973	0.878	1	0.973	0.878	1	CLONAL	1	TRUE	1	0.382983037788105	2		333	601	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0016838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	126	2255	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	0.207914730917294	2		2255	993	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1064795203	NA	P-0016838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	122	1730	0	ENST00000269305.4:c.532C>G	p.His178Asp	p.H178D	ENST00000269305	NM_001126112.2	178	Cac/Gac	5/11	0.158882626085928	2	FACETS	1	0.981	1	0.685	0.619	0.755	CLONAL	1	TRUE	0	0.207914730917294	2		1730	856	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423511	88423511	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0016838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	91	2056	0	ENST00000360948.2:c.2324C>G	p.Ser775Ter	p.S775*	ENST00000360948	NM_001012338.2	775	tCa/tGa	18/19	0.158882626085928	2	FACETS	0.831	0.736	0.932	0.415	0.368	0.466	CLONAL	1	TRUE	0	0.207914730917294	2		2056	1054	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220382	1220382	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	145	1735	1	ENST00000326873.7:c.475C>T	p.Gln159Ter	p.Q159*	ENST00000326873	NM_000455.4	159	Cag/Tag	4/10	NA	2	FACETS	0.846	0.773	0.924			1	INDETERMINATE	2	TRUE	NA	0.207914730917294	2		1736	824	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035169	30035169	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	116	2149	3	ENST00000338641.4:c.331C>T	p.Gln111Ter	p.Q111*	ENST00000338641	NM_000268.3	111	Cag/Tag	3/16	0.207914730917294	1	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	0	0.207914730917294	1		2152	988	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845528	63845528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs993996582	NA	P-0016838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	92	2351	3	ENST00000279873.7:c.1267C>T	p.Arg423Trp	p.R423W	ENST00000279873	NM_032199.2	423	Cgg/Tgg	9/10	1	2	FACETS	0.755	0.669	0.848	0.755	0.669	0.848	SUBCLONAL	1	TRUE	1	0.207914730917294	2		2354	1172	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962543	100962543	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	137	1935	3	ENST00000325455.5:c.1854C>A	p.Asn618Lys	p.N618K	ENST00000325455	NM_001202474.3	618	aaC/aaA	3/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.207914730917294	2		1938	977	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111965530	111965530	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	44	893	0	ENST00000375549.3:c.316G>T	p.Gly106Cys	p.G106C	ENST00000375549	NM_003002.3	106	Ggc/Tgc	4/4	1	2	FACETS	0.977	0.821	1	0.977	0.821	1	CLONAL	1	TRUE	1	0.207914730917294	2		893	433	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112884083	112884083	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs79203122	NA	P-0016838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	101	1596	0	ENST00000351677.2:c.18G>T	p.Trp6Cys	p.W6C	ENST00000351677	NM_002834.3	6	tgG/tgT	2/16	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.207914730917294	2		1596	929	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233726	133233726	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	66	1171	0	ENST00000320574.5:c.3578G>C	p.Arg1193Thr	p.R1193T	ENST00000320574	NM_006231.2	1193	aGa/aCa	29/49	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.207914730917294	2		1171	635	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248909	133248909	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs11833773	NA	P-0016838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	90	1823	0	ENST00000320574.5:c.1687-1G>A		p.X563_splice	ENST00000320574	NM_006231.2	563			1	2	FACETS	0.886	0.785	0.995	0.886	0.785	0.995	CLONAL	1	TRUE	1	0.207914730917294	2		1823	977	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293133	91293133	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	90	1890	3	ENST00000355112.3:c.635C>A	p.Ser212Tyr	p.S212Y	ENST00000355112	NM_000057.2	212	tCc/tAc	3/22	0.158882626085928	2	FACETS	0.893	0.79	1	0.446	0.395	0.501	CLONAL	1	TRUE	0	0.207914730917294	2		1893	970	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341262	341262	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	151	2233	0	ENST00000262320.3:c.2222G>T	p.Cys741Phe	p.C741F	ENST00000262320	NM_003502.3	741	tGc/tTc	9/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.207914730917294	2		2233	1137	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640400	3640400	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0016838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1325	114	2460	0	ENST00000294008.3:c.3239C>G	p.Ser1080Ter	p.S1080*	ENST00000294008	NM_032444.2	1080	tCa/tGa	12/15	1	2	FACETS	0.762	0.684	0.846	0.762	0.684	0.846	SUBCLONAL	1	TRUE	1	0.207914730917294	2		2460	1439	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777756	3777756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772690401	NA	P-0016838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1420	176	2885	7	ENST00000262367.5:c.7292C>T	p.Thr2431Met	p.T2431M	ENST00000262367	NM_004380.2	2431	aCg/aTg	31/31	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.207914730917294	2		2892	1596	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40500455	40500455	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	116	1724	2	ENST00000264657.5:c.80C>T	p.Pro27Leu	p.P27L	ENST00000264657	NM_139276.2	27	cCa/cTa	2/24	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.207914730917294	2		1726	956	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58700911	58700911	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	61	1648	0	ENST00000305921.3:c.502C>G	p.Pro168Ala	p.P168A	ENST00000305921	NM_003620.3	168	Cct/Gct	2/6	1	2	FACETS	0.657	0.565	0.758	0.657	0.565	0.758	SUBCLONAL	1	TRUE	1	0.207914730917294	2		1648	893	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744512	41744512	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	140	2008	1	ENST00000301178.4:c.1132G>A	p.Glu378Lys	p.E378K	ENST00000301178	NM_021913.4	378	Gag/Aag	8/20	0.158882626085928	2	FACETS	1	0.983	1	0.684	0.622	0.749	CLONAL	1	TRUE	0	0.207914730917294	2		2009	985	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128016882	128016882	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587778276	NA	P-0016838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	95	1997	0	ENST00000285398.2:c.2207G>C	p.Arg736Thr	p.R736T	ENST00000285398	NM_000122.1	736	aGa/aCa	14/15	1	2	FACETS	0.972	0.864	1	0.972	0.864	1	CLONAL	1	TRUE	1	0.207914730917294	2		1997	940	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561734	55561734	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	65	1147	3	ENST00000288135.5:c.124G>T	p.Gly42Ter	p.G42*	ENST00000288135	NM_000222.2	42	Gga/Tga	2/21	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.207914730917294	2		1150	588	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196972	138196972	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	64	901	0	ENST00000237289.4:c.634G>T	p.Asp212Tyr	p.D212Y	ENST00000237289	NM_001270507.1	212	Gac/Tac	4/9	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.207914730917294	2		901	520	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128206833	128206833	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	96	1504	0	ENST00000265960.3:c.1390A>G	p.Lys464Glu	p.K464E	ENST00000265960	NM_001006617.1	464	Aaa/Gaa	11/12	0.207914730917294	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.207914730917294	1		1504	684	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444890	49444893	+	missense_variant	Missense_Mutation	ONP	GGTG	GGTG	TGTC	novel	NA	P-0016838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	112	2113	2	ENST00000301067.7:c.2573_2576delinsGACA	p.Pro858_Pro859delinsArgHis	p.P858_P859delinsRH	ENST00000301067	NM_003482.3	858	cCACCc/cGACAc	10/54	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.207914730917294	2		2115	1007	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0016839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	322	599	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	FALSE	1	0.876200432885576	2		599	713	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	74	423	0				ENST00000310581	NM_198253.2	-/1132			0.273588025600267	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.876200432885576	0		423	149	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122754	108122754	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	186	405	1	ENST00000278616.4:c.1798del	p.His600ThrfsTer14	p.H600Tfs*14	ENST00000278616	NM_000051.3	600	Cac/ac	11/63	0.87494237734604	1	FACETS	0.947	0.903	0.988	0.947	0.903	0.988	CLONAL	1	FALSE	0	0.876200432885576	1		406	252	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	137	290	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.759	0.692	0.828	0.759	0.692	0.828	SUBCLONAL	1	TRUE	1	0.58162653361232	2		290	621	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0016840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	56	433	2	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS	0.299	0.256	0.347	0.299	0.256	0.347	SUBCLONAL	1	TRUE	1	0.58162653361232	2		435	643	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041165	29041165	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	77	542	0	ENST00000282397.4:c.263del	p.Phe88SerfsTer5	p.F88Sfs*5	ENST00000282397	NM_002019.4	88	tTc/tc	3/30	1	2	FACETS	0.313	0.274	0.355	0.313	0.274	0.355	SUBCLONAL	1	TRUE	1	0.58162653361232	2		542	846	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070573	67070573	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	96	284	0	ENST00000412916.2:c.197del	p.Leu66ProfsTer23	p.L66Pfs*23	ENST00000412916		66	cTc/cc	3/6	0.58162653361232	1	FACETS	0.624	0.561	0.691	0.624	0.561	0.691	SUBCLONAL	1	TRUE	0	0.58162653361232	1		284	375	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729858	41729858	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	85	485	1	ENST00000242208.4:c.671C>A	p.Ser224Tyr	p.S224Y	ENST00000242208	NM_002192.2	224	tCc/tAc	3/3	1	2	FACETS	0.814	0.725	0.908	0.814	0.725	0.908	CLONAL	1	TRUE	1	0.58162653361232	2		486	359	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878375	151878375	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	100	437	0	ENST00000262189.6:c.6570del	p.Phe2190LeufsTer5	p.F2190Lfs*5	ENST00000262189	NM_170606.2	2190	ttT/tt	36/59	1	2	FACETS	0.643	0.576	0.713	0.643	0.576	0.713	SUBCLONAL	1	TRUE	1	0.58162653361232	2		437	535	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016840-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	93	290	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.804	0.717	0.896	0.804	0.717	0.896	CLONAL	1	TRUE	1	0.42535575309369	2		290	544	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729858	41729858	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016840-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	53	485	1	ENST00000242208.4:c.671C>A	p.Ser224Tyr	p.S224Y	ENST00000242208	NM_002192.2	224	tCc/tAc	3/3	1	2	FACETS	0.781	0.67	0.902	0.781	0.67	0.902	CLONAL	1	TRUE	1	0.42535575309369	2		486	319	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0016841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	74	500	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	0.138655777893074	3	FACETS	1	0.969	1	0.677	0.593	0.767	CLONAL	1	FALSE	1	0.20572249421238	3		500	586	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842603	68842603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	99	496	0	ENST00000261769.5:c.539C>T	p.Ser180Phe	p.S180F	ENST00000261769	NM_004360.3	180	tCc/tTc	5/16	0.133314921170129	0	FACETS	0.757	0.678	0.84			1	SUBCLONAL	2	FALSE	0	0.20572249421238	0		496	505	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627742	37627742	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	47	740	0	ENST00000447079.4:c.1657C>T	p.Pro553Ser	p.P553S	ENST00000447079	NM_015083.1	553	Cct/Tct	2/14	1	2	FACETS	0.587	0.494	0.691	0.587	0.494	0.691	SUBCLONAL	1	FALSE	1	0.20572249421238	2		740	778	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212134	5212134	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	60	534	4	ENST00000357368.4:c.4897C>T	p.Gln1633Ter	p.Q1633*	ENST00000357368	NM_002850.3	1633	Cag/Tag	32/38	0.133314921170129	0	FACETS	0.994	0.858	1			1	CLONAL	1	FALSE	0	0.20572249421238	0		538	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0016842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	274	410	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.491307733034441	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.514428576139952	2		410	467	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857895	9857895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761399460	NA	P-0016842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	118	334	1	ENST00000330684.3:c.3506G>A	p.Arg1169Gln	p.R1169Q	ENST00000330684	NM_001134407.1	1169	cGg/cAg	13/13	0.479354967349625	3	FACETS	1	0.95	1	0.538	0.487	0.591	CLONAL	1	TRUE	1	0.514428576139952	3		335	536	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164085	106164086	+	splice_donor_variant	Splice_Site	INS	-	-	T	rs1396345080	NA	P-0016842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	50	212	0	ENST00000380013.4:c.3594+2dup		p.X1198_splice	ENST00000380013	NM_001127208.2	1198			0.514428576139952	3	FACETS	0.73	0.622	0.847	0.365	0.311	0.424	SUBCLONAL	1	TRUE	1	0.514428576139952	3		212	335	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075367	8075367	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0016842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	38	158	0	ENST00000377482.5:c.202+1G>T		p.X68_splice	ENST00000377482	NM_018948.3	68			0.514428576139952	2	FACETS	0.455	0.377	0.541	0.227	0.188	0.271	SUBCLONAL	1	TRUE	0	0.514428576139952	2		158	325	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943361	71943361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	75	350	0	ENST00000298229.2:c.1693G>A	p.Gly565Arg	p.G565R	ENST00000298229	NM_001567.3	565	Gga/Aga	14/28	NA	2	FACETS	0.546	0.479	0.618			1	INDETERMINATE	1	TRUE	NA	0.514428576139952	2		350	534	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779323	3779323	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	97	275	0	ENST00000262367.5:c.5725C>T	p.Pro1909Ser	p.P1909S	ENST00000262367	NM_004380.2	1909	Ccc/Tcc	31/31	0.479354967349625	3	FACETS	1	0.97	1	0.606	0.544	0.671	CLONAL	1	TRUE	1	0.514428576139952	3		275	391	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40469210	40469210	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	84	235	0	ENST00000264657.5:c.2134T>G	p.Cys712Gly	p.C712G	ENST00000264657	NM_139276.2	712	Tgt/Ggt	22/24	0.514428576139952	2	FACETS	0.8	0.711	0.895	0.4	0.355	0.448	SUBCLONAL	1	TRUE	0	0.514428576139952	2		235	408	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349687	89349687	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1335	205	672	0	ENST00000301030.4:c.3263A>C	p.Glu1088Ala	p.E1088A	ENST00000301030	NM_001256183.1	1088	gAg/gCg	9/13	0.881291728575943	3	FACETS	0.435	0.402	0.47	0.218	0.201	0.235	SUBCLONAL	1	TRUE	1	0.881291728575943	3		672	1540	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0016845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	48	390	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.24	2		392	386	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0016845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	524	879	1	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.3	5	FACETS	1	0.965	1	1	0.995	1	CLONAL	5	TRUE	1	0.24	5		880	1183	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589597	67589597	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	52	435	0	ENST00000274335.5:c.1360A>C	p.Thr454Pro	p.T454P	ENST00000274335		454	Act/Cct	10/15	1	2	FACETS	0.954	0.814	1	0.954	0.814	1	CLONAL	1	TRUE	1	0.24	2		435	454	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268978	55268978	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1365	140	526	0	ENST00000275493.2:c.3044A>G	p.Glu1015Gly	p.E1015G	ENST00000275493	NM_005228.3	1015	gAg/gGg	25/28	0.3	5	FACETS	1	0.943	1	0.264	0.239	0.29	CLONAL	1	TRUE	1	0.24	5		526	1505	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	93	408	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.212397782982444	3	FACETS	0.914	0.816	1	0.914	0.816	1	CLONAL	2	TRUE	1	0.246971225593049	3		408	463	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943641	9943641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	95	738	2	ENST00000330684.3:c.1300G>A	p.Val434Met	p.V434M	ENST00000330684	NM_001134407.1	434	Gtg/Atg	5/13	0.247000733826439	3	FACETS	0.738	0.655	0.827	0.369	0.327	0.414	SUBCLONAL	1	TRUE	1	0.246971225593049	3		740	1171	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577137	7577137	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	280	797	0	ENST00000269305.4:c.801del	p.Asn268ThrfsTer77	p.N268Tfs*77	ENST00000269305	NM_001126112.2	267	cgG/cg	8/11	0.239023422962554	2	FACETS	0.961	0.902	1	0.961	0.902	1	CLONAL	2	TRUE	0	0.246971225593049	2		797	1180	SUCCESS
APC	324	MSKCC	GRCh37	5	112137081	112137081	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0016847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	25	432	0	ENST00000257430.4:c.834+1G>C		p.X278_splice	ENST00000257430	NM_000038.5	278			1	2	FACETS	0.552	0.434	0.686	0.552	0.434	0.686	SUBCLONAL	1	TRUE	1	0.246971225593049	2		432	367	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873032	136873032	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1442655114	NA	P-0016847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	40	400	0	ENST00000241393.3:c.466G>T	p.Val156Phe	p.V156F	ENST00000241393	NM_003467.2	156	Gtc/Ttc	2/2	1	2	FACETS	0.438	0.363	0.523	0.438	0.363	0.523	SUBCLONAL	1	TRUE	1	0.246971225593049	2		400	739	SUCCESS
APC	324	MSKCC	GRCh37	5	112174759	112174762	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs786203020	NA	P-0016847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	30	470	0	ENST00000257430.4:c.3471_3474del	p.Glu1157AspfsTer7	p.E1157Dfs*7	ENST00000257430	NM_000038.5	1156	gaAGAG/ga	16/16	1	2	FACETS	0.92	0.745	1	0.92	0.745	1	CLONAL	1	TRUE	1	0.246971225593049	2		470	264	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912013	127912013	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	39	506	0	ENST00000373547.4:c.857G>T	p.Arg286Leu	p.R286L	ENST00000373547	NM_002721.4	286	cGg/cTg	7/7	0.204601871089965	3	FACETS	0.592	0.49	0.707	0.296	0.245	0.354	SUBCLONAL	1	TRUE	1	0.246971225593049	3		506	599	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0016849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	599	459	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.86113519952926	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.86113519952926	2		459	670	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124258	2124258	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768683470	NA	P-0016849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	164	612	0	ENST00000219476.3:c.2413G>A	p.Val805Ile	p.V805I	ENST00000219476	NM_000548.3	805	Gtc/Atc	22/42	0.409190563116723	3	FACETS	0.491	0.45	0.535	0.246	0.225	0.268	INDETERMINATE	1	TRUE	1	0.86113519952926	3		612	1109	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518587	69518587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs114327249	NA	P-0016849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	163	446	1	ENST00000294312.3:c.58G>A	p.Val20Met	p.V20M	ENST00000294312	NM_005117.2	20	Gtg/Atg	1/3	0.86113519952926	3	FACETS	0.561	0.514	0.609	0.28	0.257	0.305	SUBCLONAL	1	TRUE	1	0.86113519952926	3		447	966	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650419	12650419	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	167	353	0	ENST00000251849.4:c.427C>G	p.Arg143Gly	p.R143G	ENST00000251849	NM_002880.3	143	Cgg/Ggg	5/17	0.444486501396205	3	FACETS	0.669	0.615	0.725	0.335	0.307	0.363	INDETERMINATE	1	TRUE	1	0.86113519952926	3		353	829	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27209227	27209227	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	150	569	0	ENST00000380036.4:c.2684G>C	p.Arg895Pro	p.R895P	ENST00000380036	NM_000459.3	895	cGa/cCa	16/23	0.635932955966206	3	FACETS	0.452	0.412	0.494	0.151	0.137	0.165	SUBCLONAL	1	TRUE	0	0.86113519952926	3		569	1102	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0016850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	103	401	3	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.688	0.613	0.767	0.688	0.613	0.767	SUBCLONAL	1	TRUE	1	0.259397225477447	2		404	1155	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0016850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	75	421	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.74	0.648	0.84	0.74	0.648	0.84	SUBCLONAL	1	TRUE	1	0.259397225477447	2		421	781	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	111	634	1	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	1	2	FACETS	0.804	0.721	0.892	0.804	0.721	0.892	CLONAL	1	TRUE	1	0.259397225477447	2		635	1065	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0016850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	64	568	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.259397225477447	1	FACETS	0.66	0.571	0.756	0.66	0.571	0.756	SUBCLONAL	1	TRUE	0	0.259397225477447	1		568	651	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	119	752	0	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	1	2	FACETS	0.853	0.768	0.943	0.853	0.768	0.943	CLONAL	1	TRUE	1	0.259397225477447	2		752	1076	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45805907	45805907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	96	547	3	ENST00000450313.1:c.20G>A	p.Arg7His	p.R7H	ENST00000450313	NM_012222.2	7	cGc/cAc	1/16	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.259397225477447	2		550	725	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243984	5243984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173811578	NA	P-0016850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	46	534	2	ENST00000357368.4:c.1498C>T	p.Arg500Trp	p.R500W	ENST00000357368	NM_002850.3	500	Cgg/Tgg	11/38	1	2	FACETS	0.602	0.506	0.708	0.602	0.506	0.708	SUBCLONAL	1	TRUE	1	0.259397225477447	2		536	589	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928292	69928292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752026814	NA	P-0016850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	107	473	0	ENST00000352241.4:c.112G>A	p.Ala38Thr	p.A38T	ENST00000352241	NM_198159.2	38	Gcc/Acc	2/10	0.182895464601605	2	FACETS	1	0.974	1	0.635	0.57	0.703	CLONAL	1	TRUE	0	0.259397225477447	2		473	650	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358979	81358979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754502188	NA	P-0016850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	92	726	3	ENST00000222390.5:c.982C>T	p.Arg328Cys	p.R328C	ENST00000222390	NM_000601.4	328	Cgt/Tgt	8/18	1	2	FACETS	0.757	0.671	0.849	0.757	0.671	0.849	SUBCLONAL	1	TRUE	1	0.259397225477447	2		729	937	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0016852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	107	638	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	1	2	FACETS	0.822	0.736	0.913	0.822	0.736	0.913	CLONAL	1	TRUE	1	0.288712551688387	2		638	902	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249037	55249038	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0016852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	328	526	2	ENST00000275493.2:c.2335_2336delinsTT	p.Gly779Phe	p.G779F	ENST00000275493	NM_005228.3	779	GGc/TTc	20/28	0.288712551688387	5	FACETS	1	0.985	1	0.829	0.785	0.874	CLONAL	3	TRUE	1	0.288712551688387	5		528	982	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189379	56189379	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	110	581	0	ENST00000399503.3:c.4411C>A	p.Pro1471Thr	p.P1471T	ENST00000399503	NM_005921.1	1471	Cca/Aca	20/20	1	2	FACETS	0.823	0.738	0.913	0.823	0.738	0.913	CLONAL	1	TRUE	1	0.288712551688387	2		581	926	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733341	85733341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	170	631	1	ENST00000370580.1:c.671C>T	p.Pro224Leu	p.P224L	ENST00000370580	NM_003921.4	224	cCc/cTc	3/3	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.288712551688387	2		632	1116	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892140	9892140	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	97	582	0	ENST00000330684.3:c.2350G>T	p.Gly784Cys	p.G784C	ENST00000330684	NM_001134407.1	784	Ggt/Tgt	11/13	1	2	FACETS	0.73	0.649	0.815	0.73	0.649	0.815	SUBCLONAL	1	TRUE	1	0.288712551688387	2		582	921	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754901	29754901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1558370551	NA	P-0016852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	33	347	0	ENST00000389048.3:c.1034G>A	p.Cys345Tyr	p.C345Y	ENST00000389048	NM_004304.4	345	tGc/tAc	4/29	1	2	FACETS	0.558	0.454	0.674	0.558	0.454	0.674	SUBCLONAL	1	TRUE	1	0.288712551688387	2		347	410	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917835	29917835	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	124	717	1	ENST00000389048.3:c.833del	p.Pro278LeufsTer57	p.P278Lfs*57	ENST00000389048	NM_004304.4	278	cCt/ct	3/29	1	2	FACETS	0.811	0.732	0.895	0.811	0.732	0.895	CLONAL	1	TRUE	1	0.288712551688387	2		718	1059	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161387	185161387	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	96	577	1	ENST00000265026.3:c.814C>T	p.Leu272Phe	p.L272F	ENST00000265026	NM_004721.4	272	Ctc/Ttc	4/14	1	2	FACETS	0.687	0.611	0.769	0.687	0.611	0.769	SUBCLONAL	1	TRUE	1	0.288712551688387	2		578	968	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358956	81358956	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs757186641	NA	P-0016852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	126	555	0	ENST00000222390.5:c.1005C>A	p.His335Gln	p.H335Q	ENST00000222390	NM_000601.4	335	caC/caA	8/18	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.288712551688387	2		555	842	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020347	69020347	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	170	465	0	ENST00000288368.4:c.2719T>A	p.Ser907Thr	p.S907T	ENST00000288368	NM_024870.2	907	Tct/Act	24/40	0.108296037124812	3	FACETS	0.858	0.791	0.929	0.858	0.791	0.929	INDETERMINATE	2	TRUE	1	0.288712551688387	3		465	785	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033823	49033823	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0016854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	78	372	2	ENST00000267163.4:c.1961-1G>T		p.X654_splice	ENST00000267163	NM_000321.2	654			0.441133091817628	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.727718142089646	4		374	150	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1555525585	NA	P-0016854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	67	518	0	ENST00000269305.4:c.673-2A>G		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.705706614581168	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.727718142089646	2		518	81	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163309249	163309250	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0016854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	41	516	0	ENST00000271452.3:c.588_589delinsCT	p.Gln196_Asp197delinsHisTyr	p.Q196_D197delinsHY	ENST00000271452	NM_145697.2	196	caGGat/caCTat	8/14	0.595643144133048	4	FACETS	0.869	0.744	0.999	0.869	0.744	0.999	CLONAL	2	TRUE	2	0.727718142089646	4		516	112	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425365	49425365	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	78	626	0	ENST00000301067.7:c.13123G>T	p.Gly4375Ter	p.G4375*	ENST00000301067	NM_003482.3	4375	Gga/Tga	39/54	0.595643144133048	4	FACETS	0.945	0.848	1	0.945	0.848	1	CLONAL	2	TRUE	2	0.727718142089646	4		626	196	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916758	48916759	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAAC	novel	NA	P-0016854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	44	543	0	ENST00000267163.4:c.289_292dup	p.Leu98ArgfsTer13	p.L98Rfs*13	ENST00000267163	NM_000321.2	96	-/GAAC	3/27	0.441133091817628	4	FACETS	0.941	0.813	1	0.941	0.813	1	CLONAL	2	TRUE	2	0.727718142089646	4		543	111	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438208	110438208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	26	150	0	ENST00000375856.3:c.193G>A	p.Gly65Arg	p.G65R	ENST00000375856	NM_003749.2	65	Ggg/Agg	1/2	0.297879793478081	6	FACETS	1	0.838	1			1	INDETERMINATE	3	TRUE	NA	0.727718142089646	6		150	58	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3795343	3795343	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	101	561	0	ENST00000262367.5:c.3849C>G	p.Cys1283Trp	p.C1283W	ENST00000262367	NM_004380.2	1283	tgC/tgG	22/31	0.594919358633853	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.727718142089646	3		561	167	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845391	89845391	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	50	702	0	ENST00000389301.3:c.1736A>C	p.Tyr579Ser	p.Y579S	ENST00000389301	NM_000135.2	579	tAc/tCc	19/43	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.727718142089646	2		702	111	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221122	5221122	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	63	520	0	ENST00000357368.4:c.3344C>T	p.Ala1115Val	p.A1115V	ENST00000357368	NM_002850.3	1115	gCc/gTc	20/38	0.282404065134958	5	FACETS	1	0.945	1	0.745	0.66	0.833	INDETERMINATE	2	TRUE	2	0.727718142089646	5		520	162	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935998	49935998	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	95	749	0	ENST00000296474.3:c.1672T>A	p.Cys558Ser	p.C558S	ENST00000296474	NM_002447.2	558	Tgt/Agt	4/20	0.705706614581168	2	FACETS	0.997	0.931	1	0.997	0.931	1	CLONAL	2	TRUE	0	0.727718142089646	2		749	131	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331646	8331646	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1177261686	NA	P-0016854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	72	526	0	ENST00000356435.5:c.5470A>G	p.Ile1824Val	p.I1824V	ENST00000356435		1824	Atc/Gtc	33/35	0.441133091817628	4	FACETS	0.846	0.753	0.942	0.846	0.753	0.942	CLONAL	2	TRUE	2	0.727718142089646	4		526	202	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019658	123019658	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	67	579	0	ENST00000355640.3:c.146G>C	p.Arg49Pro	p.R49P	ENST00000355640		49	cGa/cCa	2/7	0.282404065134958	5	FACETS	1	0.926	1	0.705	0.626	0.788	INDETERMINATE	2	TRUE	2	0.727718142089646	5		579	182	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	53	301	4				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.756	0.646	0.876	0.756	0.646	0.876	SUBCLONAL	1	TRUE	1	0.329840148634042	2		305	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0016855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	153	495	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.329840148634042	1	FACETS	0.986	0.903	1	0.986	0.903	1	CLONAL	1	TRUE	0	0.329840148634042	1		495	786	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426688	49426689	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	AG	novel	NA	P-0016855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	67	162	0	ENST00000301067.7:c.11799_11800delinsCT	p.Gln3933_Gln3934delinsHisTer	p.Q3933_Q3934delinsH*	ENST00000301067	NM_003482.3	3933	caGCag/caCTag	39/54	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.329840148634042	2		162	337	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447802	49447802	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	176	482	0	ENST00000301067.7:c.632del	p.Gln211ArgfsTer50	p.Q211Rfs*50	ENST00000301067	NM_003482.3	211	cAg/cg	5/54	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.329840148634042	2		482	1029	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66679731	66679731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	85	532	0	ENST00000307102.5:c.46G>A	p.Asp16Asn	p.D16N	ENST00000307102	NM_002755.3	16	Gac/Aac	1/11	1	2	FACETS	0.555	0.49	0.626	0.555	0.49	0.626	SUBCLONAL	1	TRUE	1	0.329840148634042	2		532	928	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50818298	50818298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1467188617	NA	P-0016855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1221	124	590	0	ENST00000398568.2:c.1876G>A	p.Asp626Asn	p.D626N	ENST00000398568	NM_001042412.1	626	Gat/Aat	11/18	1	2	FACETS	0.559	0.504	0.618	0.559	0.504	0.618	SUBCLONAL	1	TRUE	1	0.329840148634042	2		590	1345	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026284	48026284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	80	296	0	ENST00000234420.5:c.1162C>T	p.His388Tyr	p.H388Y	ENST00000234420	NM_000179.2	388	Cac/Tac	4/10	0.329840148634042	3	FACETS	0.795	0.699	0.897	0.397	0.349	0.449	SUBCLONAL	1	TRUE	1	0.329840148634042	3		296	711	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820724	3820725	+	frameshift_variant	Frame_Shift_Ins	INS	AG	AG	GCT	novel	NA	P-0016855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1284	238	760	0	ENST00000262367.5:c.2726_2727delinsAGC	p.Ala909GlufsTer61	p.A909Efs*61	ENST00000262367	NM_004380.2	909	gCT/gAGC	14/31	1	2	FACETS	0.948	0.882	1	0.948	0.882	1	CLONAL	1	TRUE	1	0.329840148634042	2		760	1522	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114238	115114241	+	missense_variant	Missense_Mutation	ONP	CATC	CATC	TATT	novel	NA	P-0016855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	188	638	0	ENST00000257566.3:c.976_979delinsAATA	p.Asp326_Glu327delinsAsnLys	p.D326_E327delinsNK	ENST00000257566	NM_016569.3	326	GATGaa/AATAaa	6/8	1	2	FACETS	0.872	0.804	0.944	0.872	0.804	0.944	CLONAL	1	TRUE	1	0.329840148634042	2		638	1307	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	69	290	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		290	698	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862174	68862174	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	50	702	0	ENST00000261769.5:c.2262del	p.Tyr755MetfsTer15	p.Y755Mfs*15	ENST00000261769	NM_004360.3	754	taC/ta	14/16	0.124818580562307	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		702	677	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	436	525	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	0.283081158997815	NA		525	802	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343903	118343903	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	146	364	0	ENST00000534358.1:c.2029C>T	p.Arg677Ter	p.R677*	ENST00000534358	NM_005933.3	677	Cga/Tga	3/36	0.367366131383738	3	FACETS	1	0.958	1	0.36	0.329	0.394	CLONAL	1	TRUE	0	0.367366131383738	3		364	870	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925143	81925143	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	84	461	1	ENST00000359376.3:c.934C>A	p.Gln312Lys	p.Q312K	ENST00000359376	NM_002661.3	312	Cag/Aag	11/33	1	2	FACETS	0.47	0.414	0.53	0.47	0.414	0.53	SUBCLONAL	1	TRUE	1	0.367366131383738	2		462	973	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0016866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	276	520	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.367366131383738	2		520	1002	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007713	62007713	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	116	251	0	ENST00000392795.3:c.154C>G	p.Arg52Gly	p.R52G	ENST00000392795	NM_001039933.1	52	Cgt/Ggt	3/6	0.367366131383738	3	FACETS	1	0.964	1	0.382	0.344	0.421	CLONAL	1	TRUE	0	0.367366131383738	3		251	653	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222767	5222851	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTCGCACTTGGAGGTCATAGGCCGTGTCGGGCTTCAGGCCCTGCAGCGTGAGCGCGTTCTCCGCGCCCGGCTCAGCCGCTGCC	GGCTCGCACTTGGAGGTCATAGGCCGTGTCGGGCTTCAGGCCCTGCAGCGTGAGCGCGTTCTCCGCGCCCGGCTCAGCCGCTGCC	-	novel	NA	P-0016866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	61	522	1	ENST00000357368.4:c.2952_3036del	p.Ala985ThrfsTer30	p.A985Tfs*30	ENST00000357368	NM_002850.3	984	ccGGCAGCGGCTGAGCCGGGCGCGGAGAACGCGCTCACGCTGCAGGGCCTGAAGCCCGACACGGCCTATGACCTCCAAGTGCGAGCC/cc	18/38	0.348012365972625	2	FACETS	0.444	0.382	0.511	0.222	0.191	0.256	SUBCLONAL	1	TRUE	0	0.367366131383738	2		523	748	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566556	41566556	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756061989	NA	P-0016866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	64	319	2	ENST00000263253.7:c.4433G>A	p.Arg1478His	p.R1478H	ENST00000263253	NM_001429.3	1478	cGt/cAt	27/31	0.311939302584123	5	FACETS	0.482	0.416	0.555			1	SUBCLONAL	1	TRUE	NA	0.367366131383738	5		321	1121	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056638	26056638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775071187	NA	P-0016866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	26	152	0	ENST00000343677.2:c.19G>A	p.Ala7Thr	p.A7T	ENST00000343677	NM_005319.3	7	Gcc/Acc	1/1	0.367366131383738	4	FACETS	0.465	0.368	0.577	0.155	0.122	0.193	SUBCLONAL	1	TRUE	1	0.367366131383738	4		152	416	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359060	81359060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	95	419	0	ENST00000222390.5:c.901G>A	p.Glu301Lys	p.E301K	ENST00000222390	NM_000601.4	301	Gaa/Aaa	8/18	0.367366131383738	3	FACETS	0.481	0.427	0.539	0.16	0.142	0.18	SUBCLONAL	1	TRUE	0	0.367366131383738	3		419	1273	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508083	106508083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339698935	NA	P-0016866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	29	141	0	ENST00000359195.3:c.77G>A	p.Arg26His	p.R26H	ENST00000359195	NM_002649.2	26	cGc/cAc	2/11	0.367366131383738	3	FACETS	0.556	0.447	0.68	0.185	0.149	0.227	SUBCLONAL	1	TRUE	0	0.367366131383738	3		141	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0016867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	170	822	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.812	0.745	0.882	1	0.99	1	CLONAL	2	TRUE	1	0.18	2		822	1163	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0016867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	57	517	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.743	0.636	0.861	0.743	0.636	0.861	SUBCLONAL	1	TRUE	1	0.18	2		517	852	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991910	72991910	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	41	391	2	ENST00000268489.5:c.2135G>T	p.Arg712Leu	p.R712L	ENST00000268489	NM_006885.3	712	cGg/cTg	2/10	1	2	FACETS	0.712	0.592	0.846	0.712	0.592	0.846	SUBCLONAL	1	TRUE	1	0.18	2		393	640	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100073	27100074	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CG	CG	TT	novel	NA	P-0016867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	44	492	1	ENST00000324856.7:c.3869_3870delinsTT	p.Thr1290Ile	p.T1290I	ENST00000324856	NM_006015.4	1290	aCG/aTT	16/20	1	2	FACETS	0.632	0.528	0.747	0.632	0.528	0.747	SUBCLONAL	1	TRUE	1	0.18	2		493	774	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106724	27106724	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	52	490	0	ENST00000324856.7:c.6337del	p.Ser2113ProfsTer22	p.S2113Pfs*22	ENST00000324856	NM_006015.4	2112	cTt/ct	20/20	1	2	FACETS	0.78	0.662	0.909	0.78	0.662	0.909	CLONAL	1	TRUE	1	0.18	2		490	741	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805047	43805047	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	51	536	1	ENST00000372470.3:c.497G>A	p.Arg166Lys	p.R166K	ENST00000372470	NM_005373.2	166	aGg/aAg	4/12	1	2	FACETS	0.716	0.607	0.837	0.716	0.607	0.837	SUBCLONAL	1	TRUE	1	0.18	2		537	791	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999596	100999597	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0016867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	93	640	1	ENST00000325455.5:c.205_206delinsAA	p.Pro69Asn	p.P69N	ENST00000325455	NM_001202474.3	69	CCc/AAc	1/8	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.18	2		641	961	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641541	18641541	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	53	409	0	ENST00000266497.5:c.2540C>A	p.Ser847Tyr	p.S847Y	ENST00000266497		847	tCt/tAt	17/31	1	2	FACETS	0.809	0.688	0.941	0.809	0.688	0.941	CLONAL	1	TRUE	1	0.18	2		409	728	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230371	46230371	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0016867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	65	262	0	ENST00000334344.6:c.706-1G>A		p.X236_splice	ENST00000334344	NM_152641.2	236			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.18	2		262	553	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396242	396242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	70	470	4	ENST00000262320.3:c.784G>A	p.Ala262Thr	p.A262T	ENST00000262320	NM_003502.3	262	Gct/Act	2/11	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.18	2		474	770	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81954848	81954848	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	65	548	0	ENST00000359376.3:c.2281G>C	p.Asp761His	p.D761H	ENST00000359376	NM_002661.3	761	Gat/Cat	21/33	1	2	FACETS	0.771	0.666	0.885	0.771	0.666	0.885	SUBCLONAL	1	TRUE	1	0.18	2		548	937	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281148	46281148	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0016867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	35	365	1	ENST00000371998.3:c.3947-2A>T		p.X1316_splice	ENST00000371998		1316			1	2	FACETS	0.599	0.49	0.723	0.599	0.49	0.723	SUBCLONAL	1	TRUE	1	0.18	2		366	649	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670687	134670687	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	56	448	2	ENST00000398015.3:c.598G>T	p.Val200Leu	p.V200L	ENST00000398015	NM_004441.4	200	Gtg/Ttg	3/16	1	2	FACETS	0.73	0.624	0.847	0.73	0.624	0.847	SUBCLONAL	1	TRUE	1	0.18	2		450	852	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196606	106196606	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1402182437	NA	P-0016867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	59	410	0	ENST00000380013.4:c.4939G>T	p.Gly1647Cys	p.G1647C	ENST00000380013	NM_001127208.2	1647	Ggt/Tgt	11/11	1	2	FACETS	0.98	0.842	1	0.98	0.842	1	CLONAL	1	TRUE	1	0.18	2		410	669	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639144	176639144	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	106	495	0	ENST00000439151.2:c.3744A>T	p.Glu1248Asp	p.E1248D	ENST00000439151	NM_022455.4	1248	gaA/gaT	5/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.18	2		495	819	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665752	29665755	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1555535032	NA	P-0016868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	354	413	0	ENST00000356175.3:c.6789_6792del	p.Tyr2264ThrfsTer5	p.Y2264Tfs*5	ENST00000356175	NM_000267.3	2263	ACTTac/ac	45/57	0.33119348377738	2	FACETS	0.943	0.894	0.993	0.943	0.894	0.993	CLONAL	2	TRUE	0	0.33119348377738	2		413	1133	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0016869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	196	401	3	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.3782891576343	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	1	0.3782891576343	3		404	598	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259353	11259353	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	67	437	0	ENST00000361445.4:c.4215G>C	p.Gln1405His	p.Q1405H	ENST00000361445	NM_004958.3	1405	caG/caC	28/58	1	2	FACETS	0.78	0.68	0.888	0.78	0.68	0.888	SUBCLONAL	1	TRUE	1	0.3782891576343	2		437	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577138	7577138	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587780075	NA	P-0016869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	162	577	0	ENST00000269305.4:c.800G>C	p.Arg267Pro	p.R267P	ENST00000269305	NM_001126112.2	267	cGg/cCg	8/11	NA	2	FACETS	0.848	0.784	0.914			1	INDETERMINATE	2	TRUE	NA	0.3782891576343	2		577	505	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468258	120468258	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	78	391	0	ENST00000256646.2:c.4181A>T	p.Gln1394Leu	p.Q1394L	ENST00000256646	NM_024408.3	1394	cAg/cTg	25/34	0.3782891576343	4	FACETS	1	0.92	1			1	CLONAL	1	TRUE	NA	0.3782891576343	4		391	537	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94906474	94906474	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	67	442	0	ENST00000536441.1:c.1424G>C	p.Arg475Pro	p.R475P	ENST00000536441	NM_144665.3	475	cGa/cCa	10/10	0.3782891576343	3	FACETS	0.829	0.722	0.945	0.415	0.361	0.473	CLONAL	1	TRUE	1	0.3782891576343	3		442	508	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483937	88483937	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	60	466	0	ENST00000360948.2:c.1633G>A	p.Gly545Ser	p.G545S	ENST00000360948	NM_001012338.2	545	Ggt/Agt	14/19	0.360658542519188	2	FACETS	0.702	0.606	0.806	0.351	0.303	0.403	SUBCLONAL	1	TRUE	0	0.3782891576343	2		466	452	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99451967	99451967	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	97	407	0	ENST00000268035.6:c.1301G>T	p.Trp434Leu	p.W434L	ENST00000268035	NM_000875.3	434	tGg/tTg	6/21	0.360658542519188	2	FACETS	1	0.938	1	0.533	0.477	0.592	CLONAL	1	TRUE	0	0.3782891576343	2		407	481	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7978963	7978963	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	75	502	0	ENST00000319144.4:c.1604C>G	p.Ser535Cys	p.S535C	ENST00000319144	NM_001139.2	535	tCt/tGt	12/15	NA	2	FACETS	0.897	0.789	1			1	INDETERMINATE	1	TRUE	NA	0.3782891576343	2		502	442	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243027	41243027	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	91	537	0	ENST00000357654.3:c.4119G>C	p.Glu1373Asp	p.E1373D	ENST00000357654	NM_007294.3	1373	gaG/gaC	11/23	0.3782891576343	3	FACETS	0.877	0.78	0.982	0.439	0.39	0.491	CLONAL	1	TRUE	1	0.3782891576343	3		537	652	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120284	70120284	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	107	751	1	ENST00000245479.2:c.1286G>T	p.Ser429Ile	p.S429I	ENST00000245479	NM_000346.3	429	aGc/aTc	3/3	0.3782891576343	3	FACETS	1	0.921	1	0.515	0.462	0.571	CLONAL	1	TRUE	1	0.3782891576343	3		752	653	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602698	10602698	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	162	612	3	ENST00000171111.5:c.880G>T	p.Asp294Tyr	p.D294Y	ENST00000171111	NM_203500.1	294	Gac/Tac	3/6	0.357330638621871	2	FACETS	0.987	0.915	1	0.987	0.915	1	CLONAL	2	TRUE	0	0.3782891576343	2		615	434	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521695	89521695	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	86	450	0	ENST00000336596.2:c.2772G>T	p.Trp924Cys	p.W924C	ENST00000336596	NM_005233.5	924	tgG/tgT	16/17	0.3782891576343	4	FACETS	0.948	0.839	1	0.474	0.419	0.533	CLONAL	1	TRUE	2	0.3782891576343	4		450	661	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946160	55946160	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	47	292	0	ENST00000263923.4:c.4019C>A	p.Ala1340Asp	p.A1340D	ENST00000263923	NM_002253.2	1340	gCc/gAc	30/30	0.3782891576343	3	FACETS	0.805	0.681	0.941	0.403	0.34	0.471	CLONAL	1	TRUE	1	0.3782891576343	3		292	367	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217211	66217211	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	66	445	0	ENST00000273854.3:c.2404G>T	p.Ala802Ser	p.A802S	ENST00000273854	NM_004439.5	802	Gct/Tct	14/18	0.3782891576343	3	FACETS	0.74	0.642	0.845	0.37	0.321	0.423	SUBCLONAL	1	TRUE	1	0.3782891576343	3		445	561	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280292	1280292	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	194	638	0	ENST00000310581.5:c.1931C>A	p.Thr644Lys	p.T644K	ENST00000310581	NM_198253.2	644	aCg/aAg	4/16	0.332391030340908	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.3782891576343	4		638	638	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959941	38959941	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	51	314	0	ENST00000357387.3:c.1991G>T	p.Gly664Val	p.G664V	ENST00000357387	NM_152756.3	664	gGa/gTa	21/38	0.332391030340908	4	FACETS	0.909	0.774	1	0.454	0.387	0.528	CLONAL	1	TRUE	2	0.3782891576343	4		314	409	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490443	20490443	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs115470365	NA	P-0016869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	239	446	0	ENST00000346618.3:c.1180A>G	p.Met394Val	p.M394V	ENST00000346618	NM_001949.4	394	Atg/Gtg	7/7	0.3782891576343	4	FACETS	0.938	0.882	0.995			1	CLONAL	3	TRUE	NA	0.3782891576343	4		446	619	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846097	128846097	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	196	623	0	ENST00000249373.3:c.1027T>G	p.Phe343Val	p.F343V	ENST00000249373	NM_005631.4	343	Ttc/Gtc	5/12	0.3782891576343	4	FACETS	1	0.93	1			1	CLONAL	2	TRUE	NA	0.3782891576343	4		623	713	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501356	140501356	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	44	352	0	ENST00000288602.6:c.716G>T	p.Arg239Leu	p.R239L	ENST00000288602	NM_004333.4	239	cGa/cTa	6/18	0.292899881253963	3	FACETS	0.668	0.561	0.786			1	SUBCLONAL	1	TRUE	NA	0.3782891576343	3		352	414	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937961	76937961	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs782283059	NA	P-0016869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	140	237	0	ENST00000373344.5:c.2787G>C	p.Gln929His	p.Q929H	ENST00000373344	NM_000489.3	929	caG/caC	9/35	0.3782891576343	2	FACETS	0.937	0.862	1			1	CLONAL	2	TRUE	NA	0.3782891576343	2		237	395	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938232	76938232	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	133	273	0	ENST00000373344.5:c.2516A>C	p.Lys839Thr	p.K839T	ENST00000373344	NM_000489.3	839	aAa/aCa	9/35	0.3782891576343	2	FACETS	0.966	0.888	1			1	CLONAL	2	TRUE	NA	0.3782891576343	2		273	364	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0016870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	64	401	3	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	0.14	2		404	772	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0016870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	62	304	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.14	2		304	754	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235838	108235838	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	38	360	0	ENST00000278616.4:c.8880G>T	p.Trp2960Cys	p.W2960C	ENST00000278616	NM_000051.3	2960	tgG/tgT	62/63	1	2	FACETS	0.982	0.81	1	0.982	0.81	1	CLONAL	1	TRUE	1	0.14	2		360	553	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870853	12870853	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	31	111	0	ENST00000228872.4:c.80C>A	p.Ser27Ter	p.S27*	ENST00000228872	NM_004064.3	27	tCg/tAg	1/3	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.14	2		111	328	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019443	42019443	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	38	451	1	ENST00000219905.7:c.3496G>T	p.Glu1166Ter	p.E1166*	ENST00000219905	NM_001164273.1	1166	Gaa/Taa	10/24	1	2	FACETS	0.742	0.611	0.888	0.742	0.611	0.888	SUBCLONAL	1	TRUE	1	0.14	2		452	732	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670886	134670886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1432628958	NA	P-0016870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	16	158	0	ENST00000398015.3:c.797C>T	p.Ala266Val	p.A266V	ENST00000398015	NM_004441.4	266	gCa/gTa	3/16	1	2	FACETS	0.85	0.628	1	0.85	0.628	1	CLONAL	1	TRUE	1	0.14	2		158	269	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0016872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	180	469	1	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.426789065566856	1	FACETS	0.912	0.844	0.981	0.912	0.844	0.981	CLONAL	1	TRUE	0	0.467636134075535	1		470	647	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0016872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	528	634	2	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.312426513582417	5	FACETS	1	0.989	1			1	CLONAL	3	TRUE	NA	0.467636134075535	5		636	1192	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652129	36652129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34916193	NA	P-0016872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	171	304	1	ENST00000244741.5:c.251G>A	p.Arg84Gln	p.R84Q	ENST00000244741	NM_000389.4	84	cGa/cAa	2/3	0.426789065566856	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.467636134075535	1		305	556	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045006	47045006	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	190	261	0	ENST00000377604.3:c.2332C>T	p.Gln778Ter	p.Q778*	ENST00000377604	NM_001204468.1	778	Cag/Tag	20/24	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.467636134075535	1		261	456	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851501	151851502	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0016872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	132	319	0	ENST00000262189.6:c.11989dup	p.Thr3997AsnfsTer3	p.T3997Nfs*3	ENST00000262189	NM_170606.2	3997	act/aAct	47/59	1	2	FACETS	0.866	0.788	0.947	0.866	0.788	0.947	CLONAL	1	TRUE	1	0.467636134075535	2		319	652	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486271	8486271	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	109	288	0	ENST00000356435.5:c.2546C>A	p.Thr849Lys	p.T849K	ENST00000356435		849	aCa/aAa	17/35	0.467636134075535	1	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	0	0.467636134075535	1		288	356	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	29	408	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.972	0.78	1	0.972	0.78	1	CLONAL	1	TRUE	1	0.154137518816088	2		408	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0016873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	29	418	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.121933045235495	1	FACETS	1	0.806	1	1	0.806	1	CLONAL	1	TRUE	0	0.154137518816088	1		420	346	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414297	32414297	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	29	353	0	ENST00000332351.3:c.1254G>C	p.Glu418Asp	p.E418D	ENST00000332351	NM_024426.4	418	gaG/gaC	8/10	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.154137518816088	2		353	329	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907119	32907120	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs886038066	NA	P-0016873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	37	521	1	ENST00000380152.3:c.1507_1508del	p.Lys503ValfsTer10	p.K503Vfs*10	ENST00000380152		502	AAa/a	10/27	0.154137518816088	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.154137518816088	1		522	322	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46603751	46603751	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1233737038	NA	P-0016873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	39	752	1	ENST00000263734.3:c.1108A>G	p.Met370Val	p.M370V	ENST00000263734	NM_001430.4	370	Atg/Gtg	9/16	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.154137518816088	2		753	427	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0016875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	50	308	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.11	2		308	637	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577115	7577115	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519983	NA	P-0016875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	73	529	0	ENST00000269305.4:c.823T>C	p.Cys275Arg	p.C275R	ENST00000269305	NM_001126112.2	275	Tgt/Cgt	8/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.11	2		529	1183	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799156	42799156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778746549	NA	P-0016875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	62	502	0	ENST00000575354.2:c.4640C>T	p.Pro1547Leu	p.P1547L	ENST00000575354	NM_015125.3	1547	cCt/cTt	20/20	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.11	2		502	1118	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261381	16261382	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0016875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	62	435	0	ENST00000375759.3:c.8647_8648dup	p.Ser2884IlefsTer6	p.S2884Ifs*6	ENST00000375759	NM_015001.2	2882	-/CA	11/15	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.11	2		435	914	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11032332	11032332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	62	441	0	ENST00000327064.4:c.1726G>A	p.Ala576Thr	p.A576T	ENST00000327064	NM_199141.1	576	Gcc/Acc	16/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.11	2		441	923	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93973618	93973618	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	39	415	0	ENST00000369303.4:c.1758C>A	p.Ser586Arg	p.S586R	ENST00000369303	NM_004440.3	586	agC/agA	9/17	0.242839343937733	1	FACETS	0.819	0.68	0.974	1	0.959	1	CLONAL	2	TRUE	0	0.11	1		415	409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0016876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	114	410	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.44	2		410	511	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061185	38061202	+	inframe_deletion	In_Frame_Del	DEL	GCACTTGAAGCGCTTCTG	GCACTTGAAGCGCTTCTG	-	novel	NA	P-0016876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	93	252	0	ENST00000250448.2:c.787_804del	p.Gln263_Cys268del	p.Q263_C268del	ENST00000250448	NM_004496.3	263	CAGAAGCGCTTCAAGTGC/-	2/2	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.44	2		252	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577567	7577567	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920789	NA	P-0016877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	320	379	0	ENST00000269305.4:c.714T>G	p.Cys238Trp	p.C238W	ENST00000269305	NM_001126112.2	238	tgT/tgG	7/11	0.280546405867626	0	FACETS	1	0.953	1			1	CLONAL	2	FALSE	0	0.323743939063917	0		379	668	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868157	56868157	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs770464790	NA	P-0016877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	81	366	0	ENST00000308159.5:c.1655A>G	p.Tyr552Cys	p.Y552C	ENST00000308159	NM_014669.4	552	tAt/tGt	14/22	1	2	FACETS	0.564	0.495	0.637	0.564	0.495	0.637	SUBCLONAL	1	FALSE	1	0.323743939063917	2		366	888	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	132	290	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.28359082413602	3	FACETS	1	0.982	1	0.674	0.612	0.739	CLONAL	1	TRUE	1	0.28359082413602	3		290	789	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453145	140453145	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913366	NA	P-0016878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	25	539	0	ENST00000288602.6:c.1790T>G	p.Leu597Arg	p.L597R	ENST00000288602	NM_004333.4	597	cTa/cGa	15/18	1	2	FACETS	0.181	0.141	0.227	0.181	0.141	0.227	SUBCLONAL	1	TRUE	1	0.28359082413602	2		539	975	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900715	32900715	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	164	415	0	ENST00000380152.3:c.596C>G	p.Ala199Gly	p.A199G	ENST00000380152		199	gCt/gGt	7/27	0.190437614131108	2	FACETS	1	0.982	1	0.622	0.571	0.675	CLONAL	1	TRUE	0	0.28359082413602	2		415	930	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340426	8340426	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	299	406	0	ENST00000356435.5:c.5170A>T	p.Thr1724Ser	p.T1724S	ENST00000356435		1724	Acc/Tcc	31/35	0.850106182819974	3	FACETS	1	0.955	1	0.507	0.478	0.536	CLONAL	1	TRUE	1	0.850106182819974	3		406	989	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969494	44969497	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTA	AGTA	-	novel	NA	P-0016883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	576	291	0	ENST00000377967.4:c.4176+3_4176+6del		p.X1392_splice	ENST00000377967	NM_021140.2	1392		28/29	0.830717838453861	2	FACETS	1	0.981	1			1	CLONAL	2	TRUE	NA	0.850106182819974	2		291	677	SUCCESS
AR	367	MSKCC	GRCh37	X	66943553	66943553	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs137852580	NA	P-0016883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	358	265	0	ENST00000374690.3:c.2633C>G	p.Thr878Ser	p.T878S	ENST00000374690	NM_000044.3	878	aCt/aGt	8/8	0.830717838453861	2	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.850106182819974	2		265	787	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	340	290	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.295633110896053	3	FACETS	0.834	0.791	0.877	0.834	0.791	0.877	CLONAL	3	TRUE	0	0.348106433995467	3		290	917	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267481	198267481	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs769888451	NA	P-0016884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	102	503	0	ENST00000335508.6:c.1876A>G	p.Asn626Asp	p.N626D	ENST00000335508	NM_012433.2	626	Aac/Gac	14/25	1	2	FACETS	0.877	0.785	0.975	0.877	0.785	0.975	CLONAL	1	TRUE	1	0.348106433995467	2		503	668	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41542778	41542778	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	284	608	0	ENST00000263253.7:c.2089A>T	p.Ser697Cys	p.S697C	ENST00000263253	NM_001429.3	697	Agt/Tgt	11/31	1	2	FACETS	0.887	0.836	0.939	0.887	0.836	0.939	CLONAL	1	TRUE	1	0.730379381626324	2		608	877	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170834741	170834741	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs754700741	NA	P-0016885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	143	403	0	ENST00000296930.5:c.809A>G	p.Asn270Ser	p.N270S	ENST00000296930	NM_002520.6	270	aAt/aGt	10/11	1	2	FACETS	0.849	0.781	0.92	0.849	0.781	0.92	CLONAL	1	TRUE	1	0.730379381626324	2		403	461	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818803	32818803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	305	557	0	ENST00000354258.4:c.1148G>A	p.Gly383Glu	p.G383E	ENST00000354258	NM_000593.5	383	gGa/gAa	4/11	1	2	FACETS	0.928	0.877	0.98	0.928	0.877	0.98	CLONAL	1	TRUE	1	0.730379381626324	2		557	900	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577274	64577275	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGTCGGC	novel	NA	P-0016888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	157	560	0	ENST00000312049.6:c.307_308insGCCGACC	p.Leu103ArgfsTer16	p.L103Rfs*16	ENST00000312049	NM_130799.2	103	ctg/cGCCGACCtg	2/10	0.540400724482475	1	FACETS	0.76	0.7	0.822	0.76	0.7	0.822	SUBCLONAL	1	TRUE	0	0.540400724482475	1		560	558	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274164	18274164	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	258	715	0	ENST00000222254.8:c.1382A>T	p.Asp461Val	p.D461V	ENST00000222254	NM_005027.3	461	gAc/gTc	11/16	1	2	FACETS	0.952	0.892	1	0.952	0.892	1	CLONAL	1	TRUE	1	0.540400724482475	2		715	1003	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271226	38271226	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2203	154	540	0	ENST00000425967.3:c.2482T>G	p.Ser828Ala	p.S828A	ENST00000425967	NM_001174067.1	828	Tct/Gct	19/19	0.540400724482475	11	FACETS	0.83	0.755	0.909			1	CLONAL	1	TRUE	NA	0.540400724482475	11		540	2357	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0016889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	88	330	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.749745776412064	3	FACETS	0.358	0.316	0.402	0.179	0.158	0.201	SUBCLONAL	1	TRUE	1	0.759522345123596	3		330	894	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829039	128829040	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs570242755	NA	P-0016889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	13	24	0	ENST00000249373.3:c.67_69dup	p.Leu23dup	p.L23dup	ENST00000249373	NM_005631.4	23	ggg/ggGCTg	1/12	1	2	FACETS	0.713	0.527	0.923	0.713	0.527	0.923	CLONAL	1	TRUE	1	0.759522345123596	2		24	48	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107227	27107227	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	207	261	0	ENST00000324856.7:c.6842del	p.Leu2281Ter	p.L2281*	ENST00000324856	NM_006015.4	2280	Ttt/tt	20/20	0.29451804918194	1	FACETS	0.733	0.689	0.779	0.733	0.689	0.779	INDETERMINATE	1	TRUE	0	0.759522345123596	1		261	461	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37863335	37863335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	231	615	0	ENST00000269571.5:c.166G>A	p.Val56Met	p.V56M	ENST00000269571		56	Gtg/Atg	2/27	0.395728512829794	3	FACETS	0.616	0.573	0.661	0.308	0.286	0.331	INDETERMINATE	1	TRUE	1	0.759522345123596	3		615	1362	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	293	525	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.429700754179629	3	FACETS	0.917	0.865	0.97	0.917	0.865	0.97	CLONAL	2	TRUE	1	0.424618726325987	3		525	912	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727077	40727077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	11	384	0	ENST00000373198.4:c.3887A>T	p.Glu1296Val	p.E1296V	ENST00000373198	NM_133170.3	1296	gAg/gTg	28/32	0.429700754179629	0	FACETS	0.266	0.185	0.365			1	SUBCLONAL	1	TRUE	0	0.424618726325987	0		384	112	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098600	108098600	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	104	242	2	ENST00000278616.4:c.170G>T	p.Trp57Leu	p.W57L	ENST00000278616	NM_000051.3	57	tGg/tTg	3/63	0.429700754179629	3	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.424618726325987	3		244	476	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257336	16257336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557759530	NA	P-0016891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	65	589	1	ENST00000375759.3:c.4601C>T	p.Ser1534Leu	p.S1534L	ENST00000375759	NM_015001.2	1534	tCa/tTa	11/15	0.429700754179629	4	FACETS	0.892	0.775	1			1	CLONAL	1	TRUE	NA	0.424618726325987	4		590	489	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115980	8115980	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	41	208	0	ENST00000346208.3:c.1326G>C	p.Met442Ile	p.M442I	ENST00000346208		442	atG/atC	6/6	0.165706880501757	0	FACETS	0.556	0.468	0.651			1	INDETERMINATE	1	TRUE	0	0.424618726325987	0		208	200	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426895	49426895	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	31	262	0	ENST00000301067.7:c.11593C>T	p.Gln3865Ter	p.Q3865*	ENST00000301067	NM_003482.3	3865	Caa/Taa	39/54	0.424618726325987	5	FACETS	0.902	0.733	1	0.301	0.244	0.364	CLONAL	1	TRUE	2	0.424618726325987	5		262	265	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961579	41961579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	42	414	0	ENST00000219905.7:c.487C>T	p.Pro163Ser	p.P163S	ENST00000219905	NM_001164273.1	163	Cct/Tct	2/24	0.142514450968262	5	FACETS	0.641	0.535	0.759			1	INDETERMINATE	1	TRUE	NA	0.424618726325987	5		414	505	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669511	88669511	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	21	551	0	ENST00000360948.2:c.1387G>T	p.Gly463Ter	p.G463*	ENST00000360948	NM_001012338.2	463	Gga/Tga	12/19	0.303300435305635	0	FACETS	0.243	0.187	0.308			1	SUBCLONAL	1	TRUE	0	0.424618726325987	0		551	234	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019171	31019171	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	101	616	0	ENST00000375687.4:c.766G>T	p.Gly256Trp	p.G256W	ENST00000375687	NM_015338.5	256	Ggg/Tgg	9/13	NA	2	FACETS	1	0.932	1			1	INDETERMINATE	1	TRUE	NA	0.424618726325987	2		616	454	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264746	46264746	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	33	432	1	ENST00000371998.3:c.1616C>G	p.Ser539Cys	p.S539C	ENST00000371998		539	tCt/tGt	12/23	0.307033313844038	4	FACETS	0.462	0.376	0.56	0.231	0.188	0.28	SUBCLONAL	1	TRUE	2	0.424618726325987	4		433	479	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098781	47098782	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	98	558	0	ENST00000409792.3:c.6492dup	p.Ala2165CysfsTer19	p.A2165Cfs*19	ENST00000409792	NM_014159.6	2164	-/T	15/21	0.289613321610288	5	FACETS	0.792	0.71	0.879	0.528	0.473	0.586	SUBCLONAL	2	TRUE	2	0.424618726325987	5		558	477	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748320	41748320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	25	628	0	ENST00000226382.2:c.449G>A	p.Arg150His	p.R150H	ENST00000226382	NM_003924.3	150	cGc/cAc	3/3	NA	2	FACETS	0.493	0.39	0.61			1	INDETERMINATE	1	TRUE	NA	0.424618726325987	2		628	239	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007374	143007374	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	21	258	0	ENST00000262992.4:c.2410G>C	p.Ala804Pro	p.A804P	ENST00000262992	NM_001101669.1	804	Gca/Cca	22/24	NA	2	FACETS	0.307	0.236	0.39			1	INDETERMINATE	1	TRUE	NA	0.424618726325987	2		258	322	SUCCESS
APC	324	MSKCC	GRCh37	5	112176806	112176806	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	39	385	0	ENST00000257430.4:c.5515G>C	p.Ala1839Pro	p.A1839P	ENST00000257430	NM_000038.5	1839	Gct/Cct	16/16	0.381839954983036	3	FACETS	0.577	0.479	0.686	0.288	0.239	0.343	SUBCLONAL	1	TRUE	1	0.424618726325987	3		385	386	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247141	53247167	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACCACAATCTGAAAAAACAAGTAGGAA	ACCACAATCTGAAAAAACAAGTAGGAA	-	novel	NA	P-0016891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	36	413	0	ENST00000375401.3:c.352-19_359del		p.X118_splice	ENST00000375401	NM_004187.3	118		4/26	0.429700754179629	0	FACETS	0.577	0.481	0.682			1	SUBCLONAL	1	TRUE	0	0.424618726325987	0		413	169	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057937	27057937	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	166	567	0	ENST00000324856.7:c.1650del	p.Tyr551ThrfsTer68	p.Y551Tfs*68	ENST00000324856	NM_006015.4	549	Ccc/cc	3/20	0.445941388284203	3	FACETS	1	0.975	1	0.574	0.528	0.623	CLONAL	1	TRUE	1	0.448323828283922	3		567	789	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088681	27088682	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	370	688	0	ENST00000324856.7:c.2296dup	p.Gln766ProfsTer51	p.Q766Pfs*51	ENST00000324856	NM_006015.4	764	tcc/tCcc	7/20	0.445941388284203	3	FACETS	0.965	0.917	1	0.965	0.917	1	CLONAL	2	TRUE	1	0.448323828283922	3		688	1047	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429978	78429978	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	272	460	1	ENST00000370768.2:c.901del	p.Ile301TyrfsTer22	p.I301Yfs*22	ENST00000370768	NM_003902.3	301	Ata/ta	11/20	0.445941388284203	3	FACETS	0.873	0.821	0.925	0.873	0.821	0.925	CLONAL	2	TRUE	1	0.448323828283922	3		461	851	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100630	8100630	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761929509	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	332	616	1	ENST00000346208.3:c.604C>T	p.Arg202Cys	p.R202C	ENST00000346208		202	Cgt/Tgt	3/6	0.431108321208767	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.448323828283922	4		617	969	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653867	89653867	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	184	347	0	ENST00000371953.3:c.164+1G>A		p.X55_splice	ENST00000371953	NM_000314.4	55			0.431108321208767	4	FACETS	0.922	0.854	0.991	0.922	0.854	0.991	CLONAL	2	TRUE	2	0.448323828283922	4		347	645	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	178	453	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	0.431108321208767	4	FACETS	0.935	0.866	1	0.935	0.866	1	CLONAL	2	TRUE	2	0.448323828283922	4		454	615	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	128	508	0	ENST00000227507.2:c.859C>G	p.Pro287Ala	p.P287A	ENST00000227507	NM_053056.2	287	Ccc/Gcc	5/5	0.445941388284203	3	FACETS	1	0.914	1	0.504	0.457	0.553	CLONAL	1	TRUE	1	0.448323828283922	3		508	694	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216590	108216590	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	98	328	0	ENST00000278616.4:c.8539G>C	p.Glu2847Gln	p.E2847Q	ENST00000278616	NM_000051.3	2847	Gag/Cag	58/63	0.445941388284203	3	FACETS	0.947	0.847	1	0.474	0.423	0.527	CLONAL	1	TRUE	1	0.448323828283922	3		328	565	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342601	118342601	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	142	409	2	ENST00000534358.1:c.727G>T	p.Glu243Ter	p.E243*	ENST00000534358	NM_005933.3	243	Gag/Tag	3/36	0.445941388284203	3	FACETS	1	0.959	1	0.542	0.495	0.592	CLONAL	1	TRUE	1	0.448323828283922	3		411	715	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427562	427563	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	172	460	0	ENST00000399788.2:c.2606dup	p.Asp870ArgfsTer14	p.D870Rfs*14	ENST00000399788	NM_001042603.1	869	cca/ccCa	19/28	0.382186635020837	3	FACETS	1	0.976	1			1	CLONAL	1	TRUE	NA	0.448323828283922	3		460	820	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246555	46246555	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	61	205	0	ENST00000334344.6:c.4649G>T	p.Ser1550Ile	p.S1550I	ENST00000334344	NM_152641.2	1550	aGc/aTc	15/21	0.445941388284203	3	FACETS	0.931	0.807	1	0.465	0.403	0.532	CLONAL	1	TRUE	1	0.448323828283922	3		205	358	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424210	49424210	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	93	115	0	ENST00000301067.7:c.13852A>C	p.Asn4618His	p.N4618H	ENST00000301067	NM_003482.3	4618	Aac/Cac	42/54	0.445941388284203	3	FACETS	0.873	0.796	0.95	1	0.98	1	CLONAL	3	TRUE	1	0.448323828283922	3		115	194	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443578	49443578	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	280	501	1	ENST00000301067.7:c.3793C>A	p.Pro1265Thr	p.P1265T	ENST00000301067	NM_003482.3	1265	Cca/Aca	11/54	0.445941388284203	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.448323828283922	3		502	682	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444932	49444933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs767415197	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	40	264	0	ENST00000301067.7:c.2533dup	p.Arg845ProfsTer3	p.R845Pfs*3	ENST00000301067	NM_003482.3	845	cgg/cCgg	10/54	0.445941388284203	3	FACETS	0.57	0.475	0.677	0.285	0.237	0.339	SUBCLONAL	1	TRUE	1	0.448323828283922	3		264	383	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243045	105243045	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	324	569	0	ENST00000349310.3:c.238T>C	p.Trp80Arg	p.W80R	ENST00000349310	NM_001014432.1	80	Tgg/Cgg	5/15	0.445941388284203	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.448323828283922	3		569	836	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973749	15973749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148246943	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	233	324	0	ENST00000268712.3:c.4243C>T	p.Arg1415Cys	p.R1415C	ENST00000268712	NM_006311.3	1415	Cgt/Tgt	31/46	0.431108321208767	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.448323828283922	4		324	701	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	171	459	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.431108321208767	4	FACETS	0.962	0.89	1	0.962	0.89	1	CLONAL	2	TRUE	2	0.448323828283922	4		460	574	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223300	5223300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141070507	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	137	468	0	ENST00000357368.4:c.2503C>T	p.Arg835Cys	p.R835C	ENST00000357368	NM_002850.3	835	Cgc/Tgc	18/38	0.445941388284203	3	FACETS	1	0.985	1	0.688	0.629	0.749	CLONAL	1	TRUE	1	0.448323828283922	3		468	544	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280066	18280072	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGCCC	CGCGCCC	-	novel	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	60	105	0	ENST00000222254.8:c.2151_2157del	p.Gly720AlafsTer152	p.G720Afs*152	ENST00000222254	NM_005027.3	717	CGCGCCCcg/cg	16/16	0.445941388284203	3	FACETS	0.791	0.692	0.896	0.791	0.692	0.896	SUBCLONAL	2	TRUE	1	0.448323828283922	3		105	207	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416532	29416532	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	213	436	0	ENST00000389048.3:c.4421del	p.Gly1474AspfsTer3	p.G1474Dfs*3	ENST00000389048	NM_004304.4	1474	gGa/ga	29/29	0.431108321208767	4	FACETS	0.886	0.825	0.948	0.886	0.825	0.948	CLONAL	2	TRUE	2	0.448323828283922	4		436	777	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46611663	46611663	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	156	615	0	ENST00000263734.3:c.2477T>C	p.Leu826Pro	p.L826P	ENST00000263734	NM_001430.4	826	cTg/cCg	16/16	0.431108321208767	4	FACETS	0.863	0.789	0.941	0.431	0.394	0.471	CLONAL	1	TRUE	2	0.448323828283922	4		615	1168	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193540	99193540	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	113	486	0	ENST00000074304.5:c.2735T>C	p.Leu912Pro	p.L912P	ENST00000074304	NM_001134224.1	912	cTg/cCg	25/26	0.431108321208767	4	FACETS	0.931	0.838	1	0.466	0.419	0.515	CLONAL	1	TRUE	2	0.448323828283922	4		486	784	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264985	46264985	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	118	471	0	ENST00000371998.3:c.1860del	p.Lys620AsnfsTer18	p.K620Nfs*18	ENST00000371998		619	Aaa/aa	12/23	0.367261821288993	4	FACETS	0.89	0.802	0.982	0.445	0.401	0.491	CLONAL	1	TRUE	2	0.448323828283922	4		471	857	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165548	47165548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs77310684	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	167	548	1	ENST00000409792.3:c.578C>T	p.Pro193Leu	p.P193L	ENST00000409792	NM_014159.6	193	cCg/cTg	3/21	0.445941388284203	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.448323828283922	3		549	433	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	312	180	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.445941388284203	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.448323828283922	3		180	821	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806153	1806153	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28931615	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	67	662	2	ENST00000260795.2:c.1172C>T	p.Ala391Val	p.A391V	ENST00000260795		391	gCg/gTg	8/17	0.445941388284203	3	FACETS	0.407	0.353	0.466	0.203	0.176	0.233	SUBCLONAL	1	TRUE	1	0.448323828283922	3		664	899	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250879	153250879	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	138	500	0	ENST00000281708.4:c.1181T>C	p.Ile394Thr	p.I394T	ENST00000281708	NM_033632.3	394	aTa/aCa	8/12	0.445941388284203	3	FACETS	0.825	0.751	0.904	0.413	0.375	0.452	CLONAL	1	TRUE	1	0.448323828283922	3		500	913	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627818	187627818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149283579	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	140	606	0	ENST00000441802.2:c.3164C>T	p.Thr1055Met	p.T1055M	ENST00000441802	NM_005245.3	1055	aCg/aTg	2/27	0.445941388284203	3	FACETS	0.812	0.739	0.889	0.406	0.369	0.445	CLONAL	1	TRUE	1	0.448323828283922	3		606	941	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589541	67589579	+	inframe_deletion	In_Frame_Del	DEL	AAGTTGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAA	AAGTTGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAA	-	novel	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	135	266	0	ENST00000274335.5:c.1306_1344del	p.Val436_Lys448del	p.V436_K448del	ENST00000274335		435	cAAGTTGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAAaa/caa	10/15	0.431108321208767	4	FACETS	0.869	0.794	0.946	0.869	0.794	0.946	CLONAL	2	TRUE	2	0.448323828283922	4		266	502	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591076	67591076	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	179	305	0	ENST00000274335.5:c.1669C>T	p.Arg557Ter	p.R557*	ENST00000274335		557	Cga/Tga	12/15	0.431108321208767	4	FACETS	0.853	0.789	0.919	0.853	0.789	0.919	CLONAL	2	TRUE	2	0.448323828283922	4		305	678	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	91	316	1	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	0.431108321208767	4	FACETS	1	0.967	1	0.614	0.547	0.684	CLONAL	1	TRUE	2	0.448323828283922	4		317	479	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045997	26045997	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	70	261	0	ENST00000540144.1:c.359T>G	p.Ile120Ser	p.I120S	ENST00000540144	NM_003531.2	120	aTc/aGc	1/1	0.445941388284203	3	FACETS	0.775	0.678	0.881	0.388	0.339	0.441	SUBCLONAL	1	TRUE	1	0.448323828283922	3		261	493	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120680	94120680	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	38	351	0	ENST00000369303.4:c.371A>T	p.Asn124Ile	p.N124I	ENST00000369303	NM_004440.3	124	aAt/aTt	3/17	0.445941388284203	3	FACETS	0.366	0.302	0.438	0.183	0.151	0.219	SUBCLONAL	1	TRUE	1	0.448323828283922	3		351	567	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993697	90993697	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	279	435	0	ENST00000265433.3:c.226A>G	p.Thr76Ala	p.T76A	ENST00000265433	NM_002485.4	76	Acc/Gcc	3/16	0.445941388284203	3	FACETS	0.935	0.881	0.989	0.935	0.881	0.989	CLONAL	2	TRUE	1	0.448323828283922	3		435	815	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90995027	90995028	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs864622253	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	126	510	0	ENST00000265433.3:c.93_94del	p.Ala32HisfsTer4	p.A32Hfs*4	ENST00000265433	NM_002485.4	31	tgTGcc/tgcc	2/16	0.445941388284203	3	FACETS	0.754	0.683	0.83	0.377	0.341	0.415	SUBCLONAL	1	TRUE	1	0.448323828283922	3		510	912	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	233	446	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.431108321208767	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.448323828283922	4		446	696	SUCCESS
AR	367	MSKCC	GRCh37	X	66863208	66863208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	106	454	0	ENST00000374690.3:c.1727C>T	p.Thr576Ile	p.T576I	ENST00000374690	NM_000044.3	576	aCa/aTa	2/8	0.431108321208767	4	FACETS	0.825	0.739	0.916	0.413	0.369	0.458	CLONAL	1	TRUE	2	0.448323828283922	4		454	830	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692991	89692993	+	missense_variant	Missense_Mutation	TNP	AGG	AGG	TGC	novel	NA	P-0016893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	184	390	0	ENST00000371953.3:c.475_477delinsTGC	p.Arg159Cys	p.R159C	ENST00000371953	NM_000314.4	159	AGG/TGC	5/9	0.407601818398365	2	FACETS	0.835	0.777	0.894	0.835	0.777	0.894	CLONAL	2	TRUE	0	0.430580120282912	2		390	512	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599320	55599320	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913506	NA	P-0016894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	387	709	0	ENST00000288135.5:c.2446G>C	p.Asp816His	p.D816H	ENST00000288135	NM_000222.2	816	Gac/Cac	17/21	1	2	FACETS	0.931	0.887	0.975	0.931	0.887	0.975	CLONAL	1	TRUE	1	0.857297931191084	2		709	970	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913517	NA	P-0016894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	312	550	0	ENST00000288135.5:c.1676T>A	p.Val559Asp	p.V559D	ENST00000288135	NM_000222.2	559	gTt/gAt	11/21	1	2	FACETS	0.906	0.859	0.954	0.906	0.859	0.954	CLONAL	1	TRUE	1	0.857297931191084	2		550	803	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0016894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	240	526	0	ENST00000269305.4:c.559+1G>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.650423726697228	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.857297931191084	1		526	314	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916829	48916829	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs983885759	NA	P-0016894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	391	618	1	ENST00000267163.4:c.359T>A	p.Leu120Gln	p.L120Q	ENST00000267163	NM_000321.2	120	cTa/cAa	3/27	0.848141330162985	1	FACETS	0.911	0.88	0.942	0.911	0.88	0.942	CLONAL	1	TRUE	0	0.857297931191084	1		619	572	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544649	65544649	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555340540	NA	P-0016894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	331	615	0	ENST00000358664.4:c.277G>C	p.Ala93Pro	p.A93P	ENST00000358664	NM_002382.4	93	Gct/Cct	4/5	0.857297931191084	1	FACETS	0.919	0.885	0.952	0.919	0.885	0.952	CLONAL	1	TRUE	0	0.857297931191084	1		615	480	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019537	42019537	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	501	844	0	ENST00000219905.7:c.3590del	p.Thr1197MetfsTer2	p.T1197Mfs*2	ENST00000219905	NM_001164273.1	1197	aCt/at	10/24	0.848141330162985	1	FACETS	0.965	0.937	0.992	0.965	0.937	0.992	CLONAL	1	TRUE	0	0.857297931191084	1		844	692	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330467	65330468	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	A	novel	NA	P-0016895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	38	388	0	ENST00000342505.4:c.1176+2dup		p.X392_splice	ENST00000342505	NM_002227.2	392			0.252120701174563	1	FACETS	0.416	0.343	0.498	0.416	0.343	0.498	SUBCLONAL	1	TRUE	0	0.25507302675629	1		388	625	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717715	89717716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0016895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	104	490	1	ENST00000371953.3:c.741_742insAA	p.Pro248AsnfsTer9	p.P248Nfs*9	ENST00000371953	NM_000314.4	247	tta/ttAAa	7/9	0.25507302675629	1	FACETS	0.83	0.743	0.923	0.83	0.743	0.923	CLONAL	1	TRUE	0	0.25507302675629	1		491	857	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70971044	70971044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1458	88	834	0	ENST00000276594.2:c.1217G>A	p.Gly406Glu	p.G406E	ENST00000276594	NM_024504.3	406	gGg/gAg	6/8	1	2	FACETS	0.446	0.393	0.503	0.446	0.393	0.503	SUBCLONAL	1	TRUE	1	0.25507302675629	2		834	1546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0016896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	813	708	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.859515156226969	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.859515156226969	2		708	937	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0016896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	98	195	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.919	0.835	1	0.919	0.835	1	CLONAL	1	TRUE	1	0.859515156226969	2		195	248	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814303	76814306	+	frameshift_variant	Frame_Shift_Del	DEL	ATAA	ATAA	-	novel	NA	P-0016896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	104	242	0	ENST00000373344.5:c.6338_6341del	p.Phe2113SerfsTer9	p.F2113Sfs*9	ENST00000373344	NM_000489.3	2113	tTTATc/tc	29/35	1	1	FACETS	0.92	0.859	0.978	0.92	0.859	0.978	CLONAL	1	TRUE	0	0.859515156226969	1		242	150	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120496232	120496232	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	572	594	1	ENST00000256646.2:c.2299C>T	p.Gln767Ter	p.Q767*	ENST00000256646	NM_024408.3	767	Cag/Tag	14/34	1	2	FACETS	0.992	0.954	1	0.992	0.954	1	CLONAL	1	TRUE	1	0.839513343902475	2		595	1374	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720699	89720699	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs786202840	NA	P-0016898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	84	134	0	ENST00000371953.3:c.850G>T	p.Glu284Ter	p.E284*	ENST00000371953	NM_000314.4	284	Gag/Tag	8/9	0.839513343902475	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.839513343902475	1		134	115	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247204	153247204	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	467	478	1	ENST00000281708.4:c.1598G>T	p.Cys533Phe	p.C533F	ENST00000281708	NM_033632.3	533	tGt/tTt	10/12	0.393532785461185	1	FACETS	0.68	0.653	0.707	0.68	0.653	0.707	INDETERMINATE	1	TRUE	0	0.839513343902475	1		479	949	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319430	11319430	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	432	418	3	ENST00000361445.4:c.37G>T	p.Ala13Ser	p.A13S	ENST00000361445	NM_004958.3	13	Gcc/Tcc	2/58	1	2	FACETS	0.933	0.892	0.975	0.933	0.892	0.975	CLONAL	1	TRUE	1	0.839513343902475	2		421	1103	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099303	193099303	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0016898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	235	271	0	ENST00000367435.3:c.238-1G>C		p.X80_splice	ENST00000367435	NM_024529.4	80			NA	2	FACETS	0.994	0.936	1			1	INDETERMINATE	1	TRUE	NA	0.839513343902475	2		271	563	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254726	46254726	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs77129625	NA	P-0016898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	247	317	0	ENST00000334344.6:c.4916G>T	p.Cys1639Phe	p.C1639F	ENST00000334344	NM_152641.2	1639	tGt/tTt	16/21	1	2	FACETS	0.884	0.831	0.937	0.884	0.831	0.937	CLONAL	1	TRUE	1	0.839513343902475	2		317	666	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878148	48878148	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	172	138	1	ENST00000267163.4:c.100G>T	p.Glu34Ter	p.E34*	ENST00000267163	NM_000321.2	34	Gag/Tag	1/27	0.839513343902475	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.839513343902475	1		139	230	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014128	14014128	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	505	416	0	ENST00000311895.7:c.106G>T	p.Ala36Ser	p.A36S	ENST00000311895	NM_005236.2	36	Gcc/Tcc	1/11	NA	2	FACETS	1	0.961	1			1	INDETERMINATE	1	TRUE	NA	0.839513343902475	2		416	1201	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627783	187627783	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	314	583	0	ENST00000441802.2:c.3199G>T	p.Gly1067Trp	p.G1067W	ENST00000441802	NM_005245.3	1067	Ggg/Tgg	2/27	0.393532785461185	1	FACETS	0.403	0.38	0.426	0.403	0.38	0.426	INDETERMINATE	1	TRUE	0	0.839513343902475	1		583	1078	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866496	56866496	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	592	523	0	ENST00000519728.1:c.743A>G	p.Lys248Arg	p.K248R	ENST00000519728	NM_002350.3	248	aAg/aGg	8/13	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.839513343902475	2		523	1386	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129873	69129873	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	37	245	0	ENST00000288368.4:c.4627G>T	p.Glu1543Ter	p.E1543*	ENST00000288368	NM_024870.2	1543	Gag/Tag	38/40	1	2	FACETS	0.144	0.118	0.173	0.144	0.118	0.173	SUBCLONAL	1	TRUE	1	0.839513343902475	2		245	611	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352784	70352784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1369442321	NA	P-0016898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	644	320	0	ENST00000374080.3:c.4505C>T	p.Ser1502Phe	p.S1502F	ENST00000374080		1502	tCc/tTc	32/45	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.839513343902475	1		320	764	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1269	460	408	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.243573675225535	5	FACETS	1	0.986	1	0.722	0.688	0.757	CLONAL	2	TRUE	2	0.388894575199665	5		408	1729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579584	7579585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0016899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	251	501	0	ENST00000269305.4:c.102dup	p.Pro36AlafsTer7	p.P36Afs*7	ENST00000269305	NM_001126112.2	34	-/C	4/11	0.322443147492444	2	FACETS	0.803	0.753	0.853	0.803	0.753	0.853	CLONAL	2	TRUE	0	0.388894575199665	2		501	804	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11552822	NA	P-0016899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	272	237	0	ENST00000304494.5:c.250G>T	p.Asp84Tyr	p.D84Y	ENST00000304494	NM_000077.4	84	Gac/Tac	2/3	0.336741615528781	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.388894575199665	2		237	633	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138596	2138596	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	420	455	0	ENST00000219476.3:c.5409del	p.Phe1803LeufsTer23	p.F1803Lfs*23	ENST00000219476	NM_000548.3	1803	ttC/tt	42/42	0.768043381596488	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.768043381596488	1		455	642	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288789	33288789	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	281	346	0	ENST00000374542.5:c.763C>T	p.Gln255Ter	p.Q255*	ENST00000374542	NM_001141970.1	255	Cag/Tag	3/8	0.768043381596488	1	FACETS	0.914	0.871	0.957	0.914	0.871	0.957	CLONAL	1	TRUE	0	0.768043381596488	1		346	493	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945532	151945532	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	23	452	1	ENST00000262189.6:c.1987C>T	p.Gln663Ter	p.Q663*	ENST00000262189	NM_170606.2	663	Cag/Tag	14/59	1	2	FACETS	0.148	0.114	0.186	0.148	0.114	0.186	SUBCLONAL	1	TRUE	1	0.768043381596488	2		453	406	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485287	8485287	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	151	613	0	ENST00000356435.5:c.3093G>C	p.Lys1031Asn	p.K1031N	ENST00000356435		1031	aaG/aaC	18/35	0.758522265612712	1	FACETS	0.816	0.76	0.871	0.816	0.76	0.871	CLONAL	1	TRUE	0	0.768043381596488	1		613	297	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0016903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	74	268	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.823	0.721	0.933	0.823	0.721	0.933	CLONAL	1	TRUE	1	0.317081511336739	2		268	567	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118930	115118930	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	95	317	0	ENST00000257566.3:c.411A>T	p.Lys137Asn	p.K137N	ENST00000257566	NM_016569.3	137	aaA/aaT	2/8	0.180998122172332	3	FACETS	1	0.912	1	0.342	0.305	0.382	INDETERMINATE	1	TRUE	0	0.317081511336739	3		317	676	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	85	330	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.435	0.385	0.49	0.435	0.385	0.49	SUBCLONAL	1	TRUE	1	0.575051293677467	2		330	679	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	199	446	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.997	0.928	1	0.997	0.928	1	CLONAL	1	TRUE	1	0.575051293677467	2		446	694	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	53	439	1	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.388	0.331	0.45	0.388	0.331	0.45	SUBCLONAL	1	TRUE	1	0.575051293677467	2		440	475	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	347	590	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.575051293677467	2		590	1194	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789591	3789591	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	49	394	0	ENST00000262367.5:c.4268del	p.Pro1423LeufsTer36	p.P1423Lfs*36	ENST00000262367	NM_004380.2	1423	cCt/ct	25/31	1	2	FACETS	0.183	0.154	0.215	0.183	0.154	0.215	SUBCLONAL	1	TRUE	1	0.575051293677467	2		394	931	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	218	417	1	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.776	0.722	0.832	0.776	0.722	0.832	SUBCLONAL	1	TRUE	1	0.575051293677467	2		418	977	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	261	606	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.743	0.695	0.792	0.743	0.695	0.792	SUBCLONAL	1	TRUE	1	0.575051293677467	2		606	1222	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845583	72845583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769603301	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	102	407	1	ENST00000268489.5:c.3757C>T	p.Arg1253Cys	p.R1253C	ENST00000268489	NM_006885.3	1253	Cgc/Tgc	7/10	0.575051293677467	1	FACETS	0.453	0.406	0.502	0.453	0.406	0.502	SUBCLONAL	1	TRUE	0	0.575051293677467	1		408	558	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165602	118165602	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs921184290	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	36	306	0	ENST00000369448.3:c.112C>T	p.Arg38Ter	p.R38*	ENST00000369448	NM_017709.3	38	Cga/Tga	2/2	1	2	FACETS	0.191	0.156	0.23	0.191	0.156	0.23	SUBCLONAL	1	TRUE	1	0.575051293677467	2		306	655	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785964	135785964	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs118203506	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	54	342	1	ENST00000298552.3:c.1257del	p.Arg420GlyfsTer20	p.R420Gfs*20	ENST00000298552	NM_001162426.1	419	ccC/cc	12/23	1	2	FACETS	0.27	0.23	0.314	0.27	0.23	0.314	SUBCLONAL	1	TRUE	1	0.575051293677467	2		343	695	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346158	89346158	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs878855327	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	46	99	1	ENST00000301030.4:c.6792del	p.Ala2265ProfsTer72	p.A2265Pfs*72	ENST00000301030	NM_001256183.1	2264	ccC/cc	9/13	0.575051293677467	1	FACETS	0.974	0.844	1	0.974	0.844	1	CLONAL	1	TRUE	0	0.575051293677467	1		100	117	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	43	387	0	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	0.306	0.256	0.361	0.306	0.256	0.361	SUBCLONAL	1	TRUE	1	0.575051293677467	2		387	489	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076870	41076870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751972373	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	55	368	0	ENST00000373198.4:c.1550C>T	p.Thr517Met	p.T517M	ENST00000373198	NM_133170.3	517	aCg/aTg	9/32	1	2	FACETS	0.249	0.212	0.289	0.249	0.212	0.289	SUBCLONAL	1	TRUE	1	0.575051293677467	2		368	768	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245024	133245024	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs752846614	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	108	456	2	ENST00000320574.5:c.2091del	p.Leu698CysfsTer94	p.L698Cfs*94	ENST00000320574	NM_006231.2	697	ccC/cc	19/49	1	2	FACETS	0.388	0.347	0.431	0.388	0.347	0.431	SUBCLONAL	1	TRUE	1	0.575051293677467	2		458	969	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850704	63850705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	75	390	0	ENST00000279873.7:c.1489dup	p.Ile497AsnfsTer31	p.I497Nfs*31	ENST00000279873	NM_032199.2	494	-/A	10/10	1	2	FACETS	0.258	0.225	0.293	0.258	0.225	0.293	SUBCLONAL	1	TRUE	1	0.575051293677467	2		390	1012	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851685	134851685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377348490	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	54	324	0	ENST00000398015.3:c.1091G>A	p.Arg364Gln	p.R364Q	ENST00000398015	NM_004441.4	364	cGg/cAg	5/16	1	2	FACETS	0.3	0.256	0.349	0.3	0.256	0.349	SUBCLONAL	1	TRUE	1	0.575051293677467	2		324	625	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021422	42021422	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	159	414	0	ENST00000219905.7:c.3718C>T	p.Arg1240Ter	p.R1240*	ENST00000219905	NM_001164273.1	1240	Cga/Tga	11/24	1	2	FACETS	0.591	0.542	0.643	0.591	0.542	0.643	SUBCLONAL	1	TRUE	1	0.575051293677467	2		414	935	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574679	41574679	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	365	575	2	ENST00000263253.7:c.6970del	p.His2324ThrfsTer29	p.H2324Tfs*29	ENST00000263253	NM_001429.3	2322	Ccc/cc	31/31	1	2	FACETS	0.99	0.939	1	0.99	0.939	1	CLONAL	1	TRUE	1	0.575051293677467	2		577	1282	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435777	56435777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1055597951	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	52	308	0	ENST00000407977.2:c.1360C>T	p.Arg454Cys	p.R454C	ENST00000407977		454	Cgc/Tgc	9/10	1	2	FACETS	0.335	0.285	0.39	0.335	0.285	0.39	SUBCLONAL	1	TRUE	1	0.575051293677467	2		308	540	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	126	570	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.51	0.462	0.561	0.51	0.462	0.561	SUBCLONAL	1	TRUE	1	0.575051293677467	2		571	859	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	269	533	0	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	1	2	FACETS	0.912	0.856	0.969	0.912	0.856	0.969	CLONAL	1	TRUE	1	0.575051293677467	2		533	1026	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023070	27023088	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGCCCCGCCGTGGGGCC	AGGGCCCCGCCGTGGGGCC	-	novel	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	30	68	0	ENST00000324856.7:c.176_194del	p.Glu59GlyfsTer36	p.E59Gfs*36	ENST00000324856	NM_006015.4	59	gAGGGCCCCGCCGTGGGGCCg/gg	1/20	1	2	FACETS	0.705	0.576	0.847	0.705	0.576	0.847	SUBCLONAL	1	TRUE	1	0.575051293677467	2		68	148	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243859002	243859003	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	49	320	0	ENST00000263826.5:c.62dup	p.Asn21LysfsTer19	p.N21Kfs*19	ENST00000263826	NM_005465.4	21	aac/aaAc	2/13	0.497785167141827	3	FACETS	0.332	0.28	0.389	0.166	0.14	0.195	SUBCLONAL	1	TRUE	1	0.575051293677467	3		320	661	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653769	89653785	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTAAAGTACTCAGATAT	CTAAAGTACTCAGATAT	-	novel	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	96	314	0	ENST00000371953.3:c.80-13_83del		p.X27_splice	ENST00000371953	NM_000314.4	27		2/9	1	2	FACETS	0.776	0.696	0.861	0.776	0.696	0.861	SUBCLONAL	1	TRUE	1	0.575051293677467	2		314	430	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144613	119144613	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	61	377	0	ENST00000264033.4:c.626T>C	p.Leu209Pro	p.L209P	ENST00000264033	NM_005188.3	209	cTa/cCa	4/16	1	2	FACETS	0.308	0.265	0.355	0.308	0.265	0.355	SUBCLONAL	1	TRUE	1	0.575051293677467	2		377	689	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434940	49434940	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	32	290	0	ENST00000301067.7:c.6613del	p.Ala2205ProfsTer59	p.A2205Pfs*59	ENST00000301067	NM_003482.3	2205	Gcc/cc	31/54	1	2	FACETS	0.228	0.184	0.277	0.228	0.184	0.277	SUBCLONAL	1	TRUE	1	0.575051293677467	2		290	489	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218429	133218430	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	141	468	0	ENST00000320574.5:c.5180_5181dup	p.Glu1728TrpfsTer34	p.E1728Wfs*34	ENST00000320574	NM_006231.2	1727	-/TG	39/49	1	2	FACETS	0.523	0.476	0.573	0.523	0.476	0.573	SUBCLONAL	1	TRUE	1	0.575051293677467	2		468	937	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570104	95570104	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	49	296	0	ENST00000393063.1:c.3629C>A	p.Pro1210His	p.P1210H	ENST00000393063	NM_030621.3	1210	cCc/cAc	22/28	1	2	FACETS	0.254	0.215	0.298	0.254	0.215	0.298	SUBCLONAL	1	TRUE	1	0.575051293677467	2		296	670	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614463	38614463	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	59	456	0	ENST00000299084.4:c.234del	p.Asp79ThrfsTer42	p.D79Tfs*42	ENST00000299084	NM_152594.2	77	Aaa/aa	3/7	1	2	FACETS	0.254	0.218	0.294	0.254	0.218	0.294	SUBCLONAL	1	TRUE	1	0.575051293677467	2		456	807	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779317	3779317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1417577046	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	125	263	0	ENST00000262367.5:c.5731C>T	p.Pro1911Ser	p.P1911S	ENST00000262367	NM_004380.2	1911	Ccc/Tcc	31/31	1	2	FACETS	0.764	0.694	0.837	0.764	0.694	0.837	SUBCLONAL	1	TRUE	1	0.575051293677467	2		263	569	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982767	7982767	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	82	482	0	ENST00000319144.4:c.1018del	p.Leu340SerfsTer12	p.L340Sfs*12	ENST00000319144	NM_001139.2	340	Ctc/tc	8/15	1	2	FACETS	0.334	0.294	0.377	0.334	0.294	0.377	SUBCLONAL	1	TRUE	1	0.575051293677467	2		482	854	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110889	8110889	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs146036524	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	101	515	2	ENST00000585124.1:c.206C>T	p.Thr69Met	p.T69M	ENST00000585124	NM_004217.3	69	aCg/aTg	4/9	1	2	FACETS	0.352	0.313	0.392	0.352	0.313	0.392	SUBCLONAL	1	TRUE	1	0.575051293677467	2		517	999	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39542545	39542545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750067845	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	43	426	0	ENST00000262039.4:c.349G>A	p.Gly117Arg	p.G117R	ENST00000262039	NM_002647.2	117	Gga/Aga	3/25	1	2	FACETS	0.186	0.155	0.221	0.186	0.155	0.221	SUBCLONAL	1	TRUE	1	0.575051293677467	2		426	803	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219356	1219356	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786202544	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	229	538	0	ENST00000326873.7:c.408G>A	p.Met136Ile	p.M136I	ENST00000326873	NM_000455.4	136	atG/atA	3/10	1	2	FACETS	0.789	0.736	0.845	0.789	0.736	0.845	SUBCLONAL	1	TRUE	1	0.575051293677467	2		538	1009	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184411	7184411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375845481	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	175	460	0	ENST00000302850.5:c.890G>A	p.Arg297Gln	p.R297Q	ENST00000302850	NM_000208.2	297	cGg/cAg	3/22	1	2	FACETS	0.578	0.532	0.626	0.578	0.532	0.626	SUBCLONAL	1	TRUE	1	0.575051293677467	2		460	1053	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602334	10602334	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1379198956	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	103	585	1	ENST00000171111.5:c.1244G>A	p.Arg415His	p.R415H	ENST00000171111	NM_203500.1	415	cGc/cAc	3/6	1	2	FACETS	0.328	0.292	0.366	0.328	0.292	0.366	SUBCLONAL	1	TRUE	1	0.575051293677467	2		586	1093	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218125	36218125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1345863391	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	51	308	0	ENST00000222270.7:c.4072G>A	p.Ala1358Thr	p.A1358T	ENST00000222270	NM_014727.1	1358	Gca/Aca	15/37	1	2	FACETS	0.29	0.246	0.338	0.29	0.246	0.338	SUBCLONAL	1	TRUE	1	0.575051293677467	2		308	612	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753752	42753757	+	inframe_deletion	In_Frame_Del	DEL	GAAGAT	GAAGAT	-	rs749503353	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	211	521	0	ENST00000222329.4:c.507_512del	p.Ser170_Ser171del	p.S170_S171del	ENST00000222329	NM_006494.2	169	tcATCTTCc/tcc	4/4	1	2	FACETS	0.71	0.659	0.762	0.71	0.659	0.762	SUBCLONAL	1	TRUE	1	0.575051293677467	2		521	1034	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437223	220437223	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	322	709	2	ENST00000243786.2:c.132del	p.Ala45ArgfsTer2	p.A45Rfs*2	ENST00000243786	NM_002191.3	43	Ccc/cc	1/2	1	2	FACETS	0.969	0.915	1	0.969	0.915	1	CLONAL	1	TRUE	1	0.575051293677467	2		711	1156	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149238728	149238728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1389152577	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1181	101	636	3	ENST00000360632.3:c.1067G>A	p.Arg356His	p.R356H	ENST00000360632	NM_015472.4	356	cGt/cAt	7/7	1	2	FACETS	0.274	0.244	0.306	0.274	0.244	0.306	SUBCLONAL	1	TRUE	1	0.575051293677467	2		639	1282	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155475	106155475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768227565	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	47	363	0	ENST00000380013.4:c.376G>A	p.Gly126Arg	p.G126R	ENST00000380013	NM_001127208.2	126	Ggg/Agg	3/11	1	2	FACETS	0.176	0.148	0.208	0.176	0.148	0.208	SUBCLONAL	1	TRUE	1	0.575051293677467	2		363	927	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160585	56160585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	72	317	0	ENST00000399503.3:c.862del	p.Arg288GlufsTer24	p.R288Efs*24	ENST00000399503	NM_005921.1	287	Ccc/cc	4/20	1	2	FACETS	0.298	0.26	0.34	0.298	0.26	0.34	SUBCLONAL	1	TRUE	1	0.575051293677467	2		317	840	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137524702	137524702	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	62	579	1	ENST00000367739.4:c.667G>A	p.Val223Met	p.V223M	ENST00000367739	NM_000416.2	223	Gtg/Atg	5/7	1	2	FACETS	0.199	0.171	0.229	0.199	0.171	0.229	SUBCLONAL	1	TRUE	1	0.575051293677467	2		580	1086	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776158	135776158	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	53	500	0	ENST00000298552.3:c.2569G>C	p.Glu857Gln	p.E857Q	ENST00000298552	NM_001162426.1	857	Gag/Cag	20/23	1	2	FACETS	0.176	0.149	0.206	0.176	0.149	0.206	SUBCLONAL	1	TRUE	1	0.575051293677467	2		500	1047	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786024	135786025	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	68	443	0	ENST00000298552.3:c.1196dup	p.Leu400ThrfsTer6	p.L400Tfs*6	ENST00000298552	NM_001162426.1	399	cca/ccCa	12/23	1	2	FACETS	0.268	0.232	0.307	0.268	0.232	0.307	SUBCLONAL	1	TRUE	1	0.575051293677467	2		443	882	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620085	21620086	+	missense_variant	Missense_Mutation	DNP	TT	TT	CC	novel	NA	P-0016904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	143	452	0	ENST00000382592.4:c.80_81delinsGG	p.Lys27Arg	p.K27R	ENST00000382592	NM_014572.2	27	aAA/aGG	2/8	1	2	FACETS	0.481	0.438	0.527	0.481	0.438	0.527	SUBCLONAL	1	TRUE	1	0.575051293677467	2		452	1034	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578400	7578400	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs751477326	NA	P-0016905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	118	342	0	ENST00000269305.4:c.530C>G	p.Pro177Arg	p.P177R	ENST00000269305	NM_001126112.2	177	cCc/cGc	5/11	0.161628489924505	2	FACETS	0.995	0.897	1	0.498	0.448	0.549	INDETERMINATE	1	TRUE	0	0.283033564376835	2		342	838	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884145	37884145	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	80	542	0	ENST00000269571.5:c.3616C>G	p.Gln1206Glu	p.Q1206E	ENST00000269571		1206	Cag/Gag	27/27	0.161628489924505	2	FACETS	0.5	0.439	0.567	0.25	0.219	0.284	INDETERMINATE	1	TRUE	0	0.283033564376835	2		542	1130	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	96	290	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.814	0.723	0.911	0.814	0.723	0.911	CLONAL	1	TRUE	1	0.22	2		290	1072	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953529	32953529	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs4987047	NA	P-0016906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	103	523	0	ENST00000380152.3:c.8830A>T	p.Ile2944Phe	p.I2944F	ENST00000380152		2944	Atc/Ttc	22/27	1	2	FACETS	0.75	0.669	0.837	0.75	0.669	0.837	SUBCLONAL	1	TRUE	1	0.22	2		523	1248	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110073	115110073	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	165	651	0	ENST00000257566.3:c.1805del	p.Pro602LeufsTer30	p.P602Lfs*30	ENST00000257566	NM_016569.3	602	cCt/ct	8/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.22	2		651	1314	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857396	68857397	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0016906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	178	565	0	ENST00000261769.5:c.2033_2034dup	p.Thr679Ter	p.T679*	ENST00000261769	NM_004360.3	677	-/GT	13/16	0.3	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.22	1		565	1202	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231824	36231830	+	frameshift_variant	Frame_Shift_Del	DEL	GCGACTT	GCGACTT	-	novel	NA	P-0016906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1276	119	555	0	ENST00000300305.3:c.554_560del	p.Gln185ProfsTer24	p.Q185Pfs*24	ENST00000300305		185	cAAGTCGCc/cc	5/8	1	2	FACETS	0.775	0.697	0.859	0.775	0.697	0.859	SUBCLONAL	1	TRUE	1	0.22	2		555	1395	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180512	56180512	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	101	314	0	ENST00000399503.3:c.3841del	p.Ser1281LeufsTer7	p.S1281Lfs*7	ENST00000399503	NM_005921.1	1281	Tct/ct	16/20	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.22	2		314	904	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0016907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	33	390	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.843	0.685	1	0.843	0.685	1	CLONAL	1	FALSE	1	0.124720300768108	2		392	628	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0016907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	72	307	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	1	2	FACETS	0.943	0.824	1	1	0.981	1	CLONAL	2	FALSE	1	0.124720300768108	2		307	612	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099023	27099023	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	91	436	0	ENST00000324856.7:c.3442del	p.Gln1148SerfsTer13	p.Q1148Sfs*13	ENST00000324856	NM_006015.4	1147	Ccc/cc	13/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.124720300768108	2		436	1060	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920785	100920785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371165895	NA	P-0016907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	68	290	0	ENST00000325455.5:c.2363G>A	p.Arg788Gln	p.R788Q	ENST00000325455	NM_001202474.3	788	cGg/cAg	6/8	1	2	FACETS	1	0.876	1	1	0.981	1	CLONAL	2	FALSE	1	0.124720300768108	2		290	542	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	133	253	0	ENST00000256196.4:c.68G>A	p.Gly23Asp	p.G23D	ENST00000256196		23	gGc/gAc	1/6	1	2	FACETS	1	0.941	1	1	0.992	1	CLONAL	3	FALSE	1	0.124720300768108	2		253	681	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685310	89685310	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	176	281	0	ENST00000371953.3:c.206del	p.Asn69IlefsTer30	p.N69Ifs*30	ENST00000371953	NM_000314.4	69	Aat/at	3/9	0.124720300768108	3	FACETS	0.963	0.891	1	1	0.991	1	CLONAL	5	FALSE	0	0.124720300768108	3		281	623	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922328	178922328	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	68	425	0	ENST00000263967.3:c.1097C>G	p.Pro366Arg	p.P366R	ENST00000263967	NM_006218.2	366	cCc/cGc	6/21	1	2	FACETS	0.767	0.666	0.876	1	0.973	1	SUBCLONAL	2	FALSE	1	0.124720300768108	2		425	711	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426121	47426121	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519786	NA	P-0016907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1154	150	531	0	ENST00000377045.4:c.641C>G	p.Ser214Cys	p.S214C	ENST00000377045	NM_001654.4	214	tCc/tGc	7/16	0.124720300768108	1	FACETS	0.865	0.788	0.946	1	0.989	1	CLONAL	2	FALSE	0	0.124720300768108	1		531	1304	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200039	123200040	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	65	277	0	ENST00000218089.9:c.2114dup	p.Trp706ValfsTer7	p.W706Vfs*7	ENST00000218089	NM_001042749.1	704	tca/tcAa	22/35	0.124720300768108	1	FACETS	1	0.906	1	1	0.981	1	CLONAL	2	FALSE	0	0.124720300768108	1		277	464	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	782	629	1	ENST00000397752.3:c.3028G>T	p.Asp1010Tyr	p.D1010Y	ENST00000397752	NM_000245.2	1010	Gat/Tat	14/21	0.39342742424572	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	0	0.39342742424572	3		630	1561	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575694	55575694	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	213	381	0	ENST00000288135.5:c.1220T>C	p.Val407Ala	p.V407A	ENST00000288135	NM_000222.2	407	gTt/gCt	7/21	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.39342742424572	2		381	918	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357757	70357757	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1185	444	666	0	ENST00000374080.3:c.6012del	p.Thr2005ProfsTer6	p.T2005Pfs*6	ENST00000374080		2003	gCc/gc	41/45	0.334807259389942	3	FACETS	0.829	0.789	0.869	0.829	0.789	0.869	CLONAL	2	TRUE	1	0.39342742424572	3		666	1629	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0016911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	378	487	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	0.919	0.873	0.965	0.919	0.873	0.965	CLONAL	1	TRUE	1	0.74	2		487	1112	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578393	7578393	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876660821	NA	P-0016912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	53	353	0	ENST00000269305.4:c.537T>A	p.His179Gln	p.H179Q	ENST00000269305	NM_001126112.2	179	caT/caA	5/11	0.241183991397449	1	FACETS	0.865	0.739	1	0.865	0.739	1	CLONAL	1	TRUE	0	0.241183991397449	1		353	447	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110251257	110251257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	48	378	0	ENST00000374672.4:c.80C>T	p.Pro27Leu	p.P27L	ENST00000374672	NM_004235.4	27	cCg/cTg	2/5	0.241183991397449	1	FACETS	0.695	0.587	0.813	0.695	0.587	0.813	SUBCLONAL	1	TRUE	0	0.241183991397449	1		378	504	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0016913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	226	638	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.785718508549043	2		638	473	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267359	198267359	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs377023736	NA	P-0016913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	210	653	0	ENST00000335508.6:c.1998G>T	p.Lys666Asn	p.K666N	ENST00000335508	NM_012433.2	666	aaG/aaT	14/25	1	2	FACETS	0.994	0.931	1	0.994	0.931	1	CLONAL	1	TRUE	1	0.785718508549043	2		653	538	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825569	50825569	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	42	438	0	ENST00000398568.2:c.2200T>C	p.Ser734Pro	p.S734P	ENST00000398568	NM_001042412.1	734	Tct/Cct	14/18	0.785718508549043	1	FACETS	0.269	0.226	0.316	0.269	0.226	0.316	SUBCLONAL	1	TRUE	0	0.785718508549043	1		438	241	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165667	47165667	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	105	416	0	ENST00000409792.3:c.459del	p.Arg154GlyfsTer10	p.R154Gfs*10	ENST00000409792	NM_014159.6	153	tcC/tc	3/21	0.785718508549043	1	FACETS	0.927	0.859	0.994	0.927	0.859	0.994	CLONAL	1	TRUE	0	0.785718508549043	1		416	175	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157656	106157657	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1560546209	NA	P-0016913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	47	395	0	ENST00000380013.4:c.2562dup	p.Ala855CysfsTer17	p.A855Cfs*17	ENST00000380013	NM_001127208.2	853	ctt/cTtt	3/11	1	2	FACETS	0.322	0.273	0.377	0.322	0.273	0.377	SUBCLONAL	1	TRUE	1	0.785718508549043	2		395	371	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180793	106180793	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	88	298	0	ENST00000380013.4:c.3821A>C	p.Gln1274Pro	p.Q1274P	ENST00000380013	NM_001127208.2	1274	cAg/cCg	7/11	1	2	FACETS	0.907	0.817	1	0.907	0.817	1	CLONAL	1	TRUE	1	0.785718508549043	2		298	247	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717695	89717695	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs190070312	NA	P-0016914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	140	420	1	ENST00000371953.3:c.720C>G	p.Tyr240Ter	p.Y240*	ENST00000371953	NM_000314.4	240	taC/taG	7/9	0.381760397804723	1	FACETS	0.758	0.691	0.828	0.758	0.691	0.828	SUBCLONAL	1	TRUE	0	0.381760397804723	1		421	783	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129189	64129189	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	147	443	0	ENST00000334205.4:c.727G>T	p.Glu243Ter	p.E243*	ENST00000334205	NM_003942.2	243	Gag/Tag	7/17	0.279206734308862	3	FACETS	1	0.915	1			1	CLONAL	1	TRUE	NA	0.381760397804723	3		443	915	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060711	38060711	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0016914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1343	80	629	0	ENST00000250448.2:c.1278C>G	p.Tyr426Ter	p.Y426*	ENST00000250448	NM_004496.3	426	taC/taG	2/2	1	2	FACETS	0.295	0.258	0.334	0.295	0.258	0.334	SUBCLONAL	1	TRUE	1	0.381760397804723	2		629	1423	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612164	43612164	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	10	174	1	ENST00000355710.3:c.2269G>A	p.Val757Met	p.V757M	ENST00000355710	NM_020975.4	757	Gtg/Atg	12/20	1	2	FACETS	0.149	0.1	0.209	0.149	0.1	0.209	SUBCLONAL	1	TRUE	1	0.715040109788505	2		175	188	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117849	70117849	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	129	308	0	ENST00000245479.2:c.317A>G	p.Lys106Arg	p.K106R	ENST00000245479	NM_000346.3	106	aAg/aGg	1/3	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.715040109788505	2		308	324	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0016918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	731	178	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.311630881374883	8	FACETS	0.995	0.966	1			1	CLONAL	7	TRUE	NA	0.311630881374883	8		178	1303	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379426	225379426	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	216	829	0	ENST00000264414.4:c.442C>T	p.Arg148Ter	p.R148*	ENST00000264414	NM_003590.4	148	Cga/Tga	4/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.311630881374883	2		829	1251	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432120	49432120	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	189	690	1	ENST00000301067.7:c.9019G>T	p.Glu3007Ter	p.E3007*	ENST00000301067	NM_003482.3	3007	Gaa/Taa	34/54	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.311630881374883	2		691	1088	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100684	67100684	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	71	478	0	ENST00000412916.2:c.382G>C	p.Asp128His	p.D128H	ENST00000412916		128	Gat/Cat	4/6	1	2	FACETS	0.527	0.459	0.601	0.527	0.459	0.601	SUBCLONAL	1	TRUE	1	0.311630881374883	2		478	864	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676293	37676293	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	124	630	0	ENST00000447079.4:c.3048G>C	p.Gln1016His	p.Q1016H	ENST00000447079	NM_015083.1	1016	caG/caC	11/14	1	2	FACETS	0.673	0.607	0.743	0.673	0.607	0.743	SUBCLONAL	1	TRUE	1	0.311630881374883	2		630	1182	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217023	2217023	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	150	607	0	ENST00000398665.3:c.2478C>G	p.Ser826Arg	p.S826R	ENST00000398665	NM_032482.2	826	agC/agG	21/28	1	2	FACETS	0.912	0.832	0.995	0.912	0.832	0.995	CLONAL	1	TRUE	1	0.311630881374883	2		607	1056	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212309	36212309	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576228442	NA	P-0016918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	153	591	0	ENST00000222270.7:c.2060C>T	p.Ser687Phe	p.S687F	ENST00000222270	NM_014727.1	687	tCt/tTt	3/37	NA	2	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.311630881374883	2		591	928	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714517	52714517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs950558629	NA	P-0016918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	118	376	0	ENST00000322088.6:c.275C>T	p.Pro92Leu	p.P92L	ENST00000322088	NM_014225.5	92	cCg/cTg	4/15	0.311630881374883	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.311630881374883	1		376	579	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29115468	29115468	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	203	405	0	ENST00000328354.6:c.598G>T	p.Val200Phe	p.V200F	ENST00000328354	NM_007194.3	200	Gtc/Ttc	5/15	NA	2	FACETS	0.968	0.901	1			1	INDETERMINATE	2	TRUE	NA	0.311630881374883	2		405	673	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683381	182683381	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1677	116	564	0	ENST00000292782.4:c.164G>T	p.Ser55Ile	p.S55I	ENST00000292782	NM_020640.2	55	aGt/aTt	2/7	0.311630881374883	8	FACETS	0.803	0.721	0.892			1	CLONAL	1	TRUE	NA	0.311630881374883	8		564	1793	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557352	187557352	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0016918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	85	513	0	ENST00000441802.2:c.4010C>G	p.Ser1337Ter	p.S1337*	ENST00000441802	NM_005245.3	1337	tCa/tGa	6/27	0.311630881374883	1	FACETS	0.6	0.529	0.675	0.6	0.529	0.675	SUBCLONAL	1	TRUE	0	0.311630881374883	1		513	768	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294706	1294706	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	34	418	0	ENST00000310581.5:c.295T>C	p.Phe99Leu	p.F99L	ENST00000310581	NM_198253.2	99	Ttc/Ctc	2/16	1	2	FACETS	0.322	0.262	0.39	0.322	0.262	0.39	SUBCLONAL	1	TRUE	1	0.311630881374883	2		418	677	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526211	31526211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs553006501	NA	P-0016918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	220	681	0	ENST00000344624.3:c.829C>T	p.Arg277Cys	p.R277C	ENST00000344624		277	Cgc/Tgc	2/33	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.311630881374883	2		681	1312	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048176	180048176	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	88	646	0	ENST00000261937.6:c.2097C>G	p.Cys699Trp	p.C699W	ENST00000261937	NM_182925.4	699	tgC/tgG	14/30	0.311630881374883	1	FACETS	0.564	0.499	0.634	0.564	0.499	0.634	SUBCLONAL	1	TRUE	0	0.311630881374883	1		646	845	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576851	7576851	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0016919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	121	357	1	ENST00000269305.4:c.993+2T>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.44078447031086	1	FACETS	0.853	0.774	0.934	0.853	0.774	0.934	CLONAL	1	TRUE	0	0.44078447031086	1		358	502	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143090	30143090	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	173	536	0	ENST00000389048.3:c.436G>A	p.Gly146Ser	p.G146S	ENST00000389048	NM_004304.4	146	Ggc/Agc	1/29	1	2	FACETS	0.945	0.87	1	0.945	0.87	1	CLONAL	1	TRUE	1	0.44078447031086	2		536	831	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480492	89480492	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	61	204	2	ENST00000336596.2:c.2329G>T	p.Ala777Ser	p.A777S	ENST00000336596	NM_005233.5	777	Gct/Tct	13/17	1	2	FACETS	0.713	0.618	0.816	0.713	0.618	0.816	SUBCLONAL	1	TRUE	1	0.44078447031086	2		206	388	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032794	30032794	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121434259	NA	P-0016920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	349	388	0	ENST00000338641.4:c.169C>T	p.Arg57Ter	p.R57*	ENST00000338641	NM_000268.3	57	Cga/Tga	2/16	0.552189963378429	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.561220336498304	2		388	618	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149655	61149655	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs767945446	NA	P-0016920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	66	168	0	ENST00000295025.8:c.1845A>T	p.Glu615Asp	p.E615D	ENST00000295025	NM_002908.2	615	gaA/gaT	11/11	0.56201105666741	4	FACETS	0.748	0.65	0.853	0.374	0.325	0.427	SUBCLONAL	1	TRUE	2	0.561220336498304	4		168	491	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199837	108199837	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057520430	NA	P-0016921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	239	382	0	ENST00000278616.4:c.7179T>G	p.Phe2393Leu	p.F2393L	ENST00000278616	NM_000051.3	2393	ttT/ttG	49/63	0.458088952776541	1	FACETS	0.358	0.335	0.382	0.358	0.335	0.382	INDETERMINATE	1	TRUE	0	0.90764265313639	1		382	803	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200960	108200960	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121434220	NA	P-0016921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	409	287	0	ENST00000278616.4:c.7327C>T	p.Arg2443Ter	p.R2443*	ENST00000278616	NM_000051.3	2443	Cga/Tga	50/63	0.458088952776541	1	FACETS	0.712	0.685	0.739	0.712	0.685	0.739	INDETERMINATE	1	TRUE	0	0.90764265313639	1		287	691	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716407	18716407	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	294	424	0	ENST00000266497.5:c.3754C>G	p.Gln1252Glu	p.Q1252E	ENST00000266497		1252	Cag/Gag	26/31	NA	2	FACETS	0.668	0.63	0.707			1	INDETERMINATE	1	TRUE	NA	0.90764265313639	2		424	970	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539021	23539021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	264	387	0	ENST00000380871.4:c.418G>A	p.Glu140Lys	p.E140K	ENST00000380871	NM_006167.3	140	Gag/Aag	2/2	0.662777544596821	0	FACETS		NA	1			1	NA	1	TRUE	0	0.90764265313639	0		387	374	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483291	120483291	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	24	385	0	ENST00000256646.2:c.3070C>A	p.His1024Asn	p.H1024N	ENST00000256646	NM_024408.3	1024	Cat/Aat	19/34	1	2	FACETS	0.869	0.683	1	0.869	0.683	1	CLONAL	1	FALSE	1	0.2054497213527	2		385	269	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206843	162206843	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	26	472	0	ENST00000366898.1:c.832G>T	p.Val278Phe	p.V278F	ENST00000366898	NM_004562.2	278	Gtt/Ttt	7/12	1	2	FACETS	0.781	0.619	0.966	0.781	0.619	0.966	CLONAL	1	FALSE	1	0.2054497213527	2		472	324	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	177	290	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.653	0.603	0.706	0.653	0.603	0.706	SUBCLONAL	1	TRUE	1	0.67799356668822	2		290	799	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0016924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	165	609	2	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	1	2	FACETS	0.526	0.483	0.571	0.526	0.483	0.571	SUBCLONAL	1	TRUE	1	0.67799356668822	2		611	925	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243777011	243777011	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	16	738	0	ENST00000263826.5:c.658C>G	p.Arg220Gly	p.R220G	ENST00000263826	NM_005465.4	220	Cgt/Ggt	7/13	0.0978281673391481	3	FACETS	0.756	0.568	0.97			1	INDETERMINATE	2	TRUE	NA	0.277139543209685	3		738	87	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0016930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	21	487	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.336324140645529	1	FACETS	0.154	0.118	0.197	0.154	0.118	0.197	SUBCLONAL	1	TRUE	0	0.336324140645529	1		489	673	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224273	98224273	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	30	182	0	ENST00000331920.6:c.2568G>T	p.Gln856His	p.Q856H	ENST00000331920	NM_000264.3	856	caG/caT	16/24	1	2	FACETS	0.646	0.523	0.786	0.646	0.523	0.786	SUBCLONAL	1	TRUE	1	0.336324140645529	2		182	276	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11552822	NA	P-0016931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	209	237	0	ENST00000304494.5:c.250G>T	p.Asp84Tyr	p.D84Y	ENST00000304494	NM_000077.4	84	Gac/Tac	2/3	0.868201950453533	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.868201950453533	1		237	238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0016931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	524	415	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			NA	2	FACETS	0.937	0.915	0.958			1	INDETERMINATE	2	TRUE	NA	0.868201950453533	2		415	644	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805172	43805172	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	343	527	1	ENST00000372470.3:c.622C>T	p.Gln208Ter	p.Q208*	ENST00000372470	NM_005373.2	208	Cag/Tag	4/12	1	2	FACETS	0.986	0.939	1	0.986	0.939	1	CLONAL	1	TRUE	1	0.868201950453533	2		528	801	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390185	89390185	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746351940	NA	P-0016931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	163	325	0	ENST00000336596.2:c.934C>T	p.Arg312Trp	p.R312W	ENST00000336596	NM_005233.5	312	Cgg/Tgg	4/17	0.342184570984132	1	FACETS	0.513	0.476	0.551	0.513	0.476	0.551	INDETERMINATE	1	TRUE	0	0.868201950453533	1		325	414	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221761	55221761	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	316	480	0	ENST00000275493.2:c.805C>G	p.Leu269Val	p.L269V	ENST00000275493	NM_005228.3	269	Ctc/Gtc	7/28	0.182389548095018	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.868201950453533	0		480	802	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	257	408	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.363142273226207	2	FACETS	1	0.992	1	0.648	0.613	0.683	INDETERMINATE	1	TRUE	0	0.72556409444679	2		408	547	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578410	7578410	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	646	481	0	ENST00000269305.4:c.520A>T	p.Arg174Trp	p.R174W	ENST00000269305	NM_001126112.2	174	Agg/Tgg	5/11	0.72556409444679	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.72556409444679	1		481	965	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435984	116435984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	309	650	2	ENST00000397752.3:c.3979C>T	p.Arg1327Cys	p.R1327C	ENST00000397752	NM_000245.2	1327	Cgc/Tgc	21/21	0.430184549258778	3	FACETS	0.995	0.939	1	0.498	0.469	0.527	INDETERMINATE	1	TRUE	1	0.72556409444679	3		652	1166	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660469	67660469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	100	308	1	ENST00000264010.4:c.1369C>T	p.Arg457Ter	p.R457*	ENST00000264010	NM_006565.3	457	Cga/Tga	8/12	0.382834117102134	1	FACETS	0.337	0.302	0.374	0.337	0.302	0.374	INDETERMINATE	1	TRUE	0	0.72556409444679	1		309	521	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175857	24175859	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs875989800	NA	P-0016932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	440	559	0	ENST00000263121.7:c.1091_1093del	p.Lys364del	p.K364del	ENST00000263121	NM_003073.3	362	gAGAag/gag	8/9	0.425628919819776	1	FACETS	0.771	0.738	0.804	0.771	0.738	0.804	INDETERMINATE	1	TRUE	0	0.72556409444679	1		559	1003	SUCCESS
APC	324	MSKCC	GRCh37	5	112175198	112175198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	213	309	0	ENST00000257430.4:c.3907C>T	p.Gln1303Ter	p.Q1303*	ENST00000257430	NM_000038.5	1303	Caa/Taa	16/16	0.659730092352059	2	FACETS	0.92	0.876	0.963	0.92	0.876	0.963	CLONAL	2	TRUE	0	0.72556409444679	2		309	319	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812292	212812292	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778048381	NA	P-0016932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	133	472	0	ENST00000342788.4:c.284G>A	p.Arg95His	p.R95H	ENST00000342788	NM_005235.2	95	cGt/cAt	3/28	0.382834117102134	1	FACETS	0.577	0.529	0.626	0.577	0.529	0.626	INDETERMINATE	1	TRUE	0	0.72556409444679	1		472	405	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0016932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	348	421	1	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	0.72556409444679	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.72556409444679	1		422	528	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174418	11174418	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	625	650	0	ENST00000361445.4:c.7257A>T	p.Glu2419Asp	p.E2419D	ENST00000361445	NM_004958.3	2419	gaA/gaT	53/58	0.72556409444679	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.72556409444679	1		650	903	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514526	103514526	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0016932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	91	273	0	ENST00000355739.4:c.1027A>T	p.Arg343Ter	p.R343*	ENST00000355739	NM_000123.3	343	Aga/Tga	8/15	0.382834117102134	1	FACETS	0.352	0.314	0.392	0.352	0.314	0.392	INDETERMINATE	1	TRUE	0	0.72556409444679	1		273	454	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267614	7267614	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886037750	NA	P-0016932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	311	577	3	ENST00000302850.5:c.394G>A	p.Gly132Ser	p.G132S	ENST00000302850	NM_000208.2	132	Ggc/Agc	2/22	0.382834117102134	1	FACETS	0.39	0.367	0.413	0.39	0.367	0.413	INDETERMINATE	1	TRUE	0	0.72556409444679	1		580	1402	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50138876	50138876	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	916	741	4	ENST00000246792.3:c.614C>A	p.Ala205Asp	p.A205D	ENST00000246792	NM_006270.3	205	gCc/gAc	6/6	0.382834117102134	1	FACETS	0.794	0.77	0.817	0.794	0.77	0.817	INDETERMINATE	1	TRUE	0	0.72556409444679	1		745	2027	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	84	408	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	0.208212829296226	2		408	713	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578410	7578410	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	102	481	0	ENST00000269305.4:c.520A>T	p.Arg174Trp	p.R174W	ENST00000269305	NM_001126112.2	174	Agg/Tgg	5/11	0.208212829296226	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.208212829296226	1		481	595	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435984	116435984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	100	650	2	ENST00000397752.3:c.3979C>T	p.Arg1327Cys	p.R1327C	ENST00000397752	NM_000245.2	1327	Cgc/Tgc	21/21	0.200425871359606	3	FACETS	0.924	0.823	1	0.462	0.411	0.516	CLONAL	1	TRUE	1	0.208212829296226	3		652	1148	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660469	67660469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	69	308	1	ENST00000264010.4:c.1369C>T	p.Arg457Ter	p.R457*	ENST00000264010	NM_006565.3	457	Cga/Tga	8/12	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.208212829296226	2		309	541	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175857	24175859	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs875989800	NA	P-0016932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	93	559	0	ENST00000263121.7:c.1091_1093del	p.Lys364del	p.K364del	ENST00000263121	NM_003073.3	362	gAGAag/gag	8/9	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.208212829296226	2		559	746	SUCCESS
APC	324	MSKCC	GRCh37	5	112175198	112175198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	59	309	0	ENST00000257430.4:c.3907C>T	p.Gln1303Ter	p.Q1303*	ENST00000257430	NM_000038.5	1303	Caa/Taa	16/16	0.208212829296226	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.208212829296226	1		309	412	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812292	212812292	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778048381	NA	P-0016932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	56	472	0	ENST00000342788.4:c.284G>A	p.Arg95His	p.R95H	ENST00000342788	NM_005235.2	95	cGt/cAt	3/28	1	2	FACETS	0.819	0.701	0.948	0.819	0.701	0.948	CLONAL	1	TRUE	1	0.208212829296226	2		472	657	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0016932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	105	421	1	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	0.174392968189034	0	FACETS	1	0.975	1			1	CLONAL	1	TRUE	0	0.208212829296226	0		422	619	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174418	11174418	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	170	650	0	ENST00000361445.4:c.7257A>T	p.Glu2419Asp	p.E2419D	ENST00000361445	NM_004958.3	2419	gaA/gaT	53/58	0.174392968189034	0	FACETS	0.77	0.708	0.833			1	SUBCLONAL	2	TRUE	0	0.208212829296226	0		650	840	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267614	7267614	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886037750	NA	P-0016932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	123	577	3	ENST00000302850.5:c.394G>A	p.Gly132Ser	p.G132S	ENST00000302850	NM_000208.2	132	Ggc/Agc	2/22	0.208212829296226	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.208212829296226	1		580	913	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50138876	50138876	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	84	741	4	ENST00000246792.3:c.614C>A	p.Ala205Asp	p.A205D	ENST00000246792	NM_006270.3	205	gCc/gAc	6/6	0.208212829296226	1	FACETS	0.738	0.651	0.833	0.738	0.651	0.833	SUBCLONAL	1	TRUE	0	0.208212829296226	1		745	979	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266611	198266611	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs755415626	NA	P-0016933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	109	443	0	ENST00000335508.6:c.2225G>A	p.Gly742Asp	p.G742D	ENST00000335508	NM_012433.2	742	gGt/gAt	16/25	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.34	2		443	565	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2199938	2199938	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	98	543	0	ENST00000398665.3:c.707G>C	p.Ser236Thr	p.S236T	ENST00000398665	NM_032482.2	236	aGt/aCt	8/28	1	2	FACETS	0.934	0.835	1	0.934	0.835	1	CLONAL	1	TRUE	1	0.34	2		543	617	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	307	290	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.699284484400004	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.699284484400004	3		290	555	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0016934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	454	583	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.699284484400004	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.699284484400004	2		583	617	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107234	27107234	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	240	357	0	ENST00000324856.7:c.6845T>C	p.Ile2282Thr	p.I2282T	ENST00000324856	NM_006015.4	2282	aTt/aCt	20/20	0.699284484400004	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.699284484400004	3		357	439	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374909	149374909	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	280	552	0	ENST00000360632.3:c.185C>G	p.Ser62Trp	p.S62W	ENST00000360632	NM_015472.4	62	tCg/tGg	2/7	0.68848592549721	4	FACETS	0.871	0.822	0.921	0.871	0.822	0.921	CLONAL	2	TRUE	2	0.699284484400004	4		552	781	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559090	29559090	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0016934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	35	65	0	ENST00000356175.3:c.3198-1G>C		p.X1066_splice	ENST00000356175	NM_000267.3	1066			0.699284484400004	2	FACETS	0.944	0.831	1	0.944	0.831	1	CLONAL	2	TRUE	0	0.699284484400004	2		65	53	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976761	2976761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	786	685	0	ENST00000396946.4:c.1251G>A	p.Met417Ile	p.M417I	ENST00000396946	NM_032415.4	417	atG/atA	9/25	0.699284484400004	6	FACETS	0.97	0.943	0.998	0.97	0.943	0.998	CLONAL	4	TRUE	2	0.699284484400004	6		685	1389	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287202	46287202	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0016934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	235	301	0	ENST00000334344.6:c.5148-1G>T		p.X1716_splice	ENST00000334344	NM_152641.2	1716			0.68848592549721	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.699284484400004	4		301	555	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675231	40675231	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	165	519	0	ENST00000249776.8:c.195C>G	p.Asp65Glu	p.D65E	ENST00000249776	NM_033286.3	65	gaC/gaG	1/9	0.699284484400004	5	FACETS	1	0.985	1	0.325	0.299	0.352	CLONAL	1	TRUE	1	0.699284484400004	5		519	744	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819632	81819632	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1261993965	NA	P-0016934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	118	477	0	ENST00000359376.3:c.38A>C	p.Tyr13Ser	p.Y13S	ENST00000359376	NM_002661.3	13	tAt/tCt	2/33	0.699284484400004	2	FACETS	0.951	0.867	1	0.475	0.433	0.519	CLONAL	1	TRUE	0	0.699284484400004	2		477	355	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728565	190728565	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs764521118	NA	P-0016934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	182	756	0	ENST00000441310.2:c.1958del	p.Lys653ArgfsTer2	p.K653Rfs*2	ENST00000441310	NM_000534.4	651	agA/ag	10/13	0.699284484400004	3	FACETS	0.769	0.709	0.83	0.384	0.354	0.415	SUBCLONAL	1	TRUE	1	0.699284484400004	3		756	914	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36022629	36022629	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	248	732	0	ENST00000358208.4:c.502G>A	p.Ala168Thr	p.A168T	ENST00000358208		168	Gca/Aca	5/12	0.699284484400004	3	FACETS	1	0.963	1	0.52	0.487	0.554	CLONAL	1	TRUE	1	0.699284484400004	3		732	920	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190798	106190798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775677220	NA	P-0016934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	133	441	3	ENST00000380013.4:c.4076G>A	p.Arg1359His	p.R1359H	ENST00000380013	NM_001127208.2	1359	cGt/cAt	9/11	0.699284484400004	3	FACETS	0.836	0.762	0.914	0.418	0.381	0.457	CLONAL	1	TRUE	1	0.699284484400004	3		444	614	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609960	117609998	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTCACCTGTGAAAAAAATATGAATGTTATTCTAGCATG	CTTCACCTGTGAAAAAAATATGAATGTTATTCTAGCATG	TTATTTATTATT	novel	NA	P-0016934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	108	417	4	ENST00000368508.3:c.6734-33_6739delinsAATAATAAATAA		p.X2245_splice	ENST00000368508	NM_002944.2	2245		43/43	0.675698161445739	4	FACETS	0.852	0.766	0.943	0.213	0.191	0.236	CLONAL	1	TRUE	0	0.699284484400004	4		421	616	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0016937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	157	395	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.238007600941163	2	FACETS	0.948	0.872	1	0.948	0.872	1	CLONAL	2	TRUE	0	0.26124007763273	2		397	634	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0016937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	55	356	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	0.26124007763273	1	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	0	0.26124007763273	1		356	336	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38968098	38968098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777143677	NA	P-0016937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	54	848	1	ENST00000357387.3:c.1007G>A	p.Arg336His	p.R336H	ENST00000357387	NM_152756.3	336	cGt/cAt	12/38	0.26124007763273	3	FACETS	0.806	0.688	0.935	0.403	0.344	0.468	CLONAL	1	TRUE	1	0.26124007763273	3		849	580	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553492	29553492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768638173	NA	P-0016937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	162	866	0	ENST00000356175.3:c.2041C>T	p.Arg681Ter	p.R681*	ENST00000356175	NM_000267.3	681	Cga/Tga	18/57	0.238007600941163	2	FACETS	0.812	0.746	0.88	0.812	0.746	0.88	CLONAL	2	TRUE	0	0.26124007763273	2		866	764	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688746	47688746	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200866660	NA	P-0016937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	172	590	0	ENST00000347630.2:c.554G>A	p.Arg185Gln	p.R185Q	ENST00000347630	NM_001007230.1	185	cGg/cAg	7/11	0.238007600941163	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.26124007763273	2		590	632	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696656	47696656	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	69	695	0	ENST00000347630.2:c.292G>C	p.Val98Leu	p.V98L	ENST00000347630	NM_001007230.1	98	Gtt/Ctt	5/11	0.238007600941163	2	FACETS	0.886	0.772	1	0.443	0.386	0.505	CLONAL	1	TRUE	0	0.26124007763273	2		695	596	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11027109	11027109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173812039	NA	P-0016937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	221	983	0	ENST00000327064.4:c.874G>A	p.Val292Ile	p.V292I	ENST00000327064	NM_199141.1	292	Gtc/Atc	7/16	0.238007600941163	2	FACETS	0.958	0.893	1	0.958	0.893	1	CLONAL	2	TRUE	0	0.26124007763273	2		983	883	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	76	453	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.869	0.764	0.981	0.869	0.764	0.981	CLONAL	1	TRUE	1	0.359878580832621	2		454	486	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	63	439	1	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.359878580832621	2		440	348	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912168	114912168	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	86	615	0	ENST00000543371.1:c.1238T>C	p.Leu413Pro	p.L413P	ENST00000543371	NM_001198531.1	413	cTg/cCg	11/14	1	2	FACETS	0.739	0.654	0.829	0.739	0.654	0.829	SUBCLONAL	1	TRUE	1	0.359878580832621	2		615	647	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32449577	32449577	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1060501253	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	297	829	2	ENST00000332351.3:c.797del	p.Pro266ArgfsTer20	p.P266Rfs*20	ENST00000332351	NM_024426.4	266	cCg/cg	3/10	0.359878580832621	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.359878580832621	2		831	772	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942053	71942053	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	74	1041	1	ENST00000298229.2:c.1322del	p.Asn441ThrfsTer2	p.N441Tfs*2	ENST00000298229	NM_001567.3	439	ccA/cc	12/28	1	2	FACETS	0.372	0.324	0.424	0.372	0.324	0.424	SUBCLONAL	1	TRUE	1	0.359878580832621	2		1042	1106	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420745	49420745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768594066	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	81	584	1	ENST00000301067.7:c.15004C>T	p.Arg5002Trp	p.R5002W	ENST00000301067	NM_003482.3	5002	Cgg/Tgg	48/54	1	2	FACETS	0.731	0.644	0.823	0.731	0.644	0.823	SUBCLONAL	1	TRUE	1	0.359878580832621	2		585	616	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438067	49438067	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886043414	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	128	683	2	ENST00000301067.7:c.5104C>T	p.Arg1702Ter	p.R1702*	ENST00000301067	NM_003482.3	1702	Cga/Tga	21/54	1	2	FACETS	0.963	0.873	1	0.963	0.873	1	CLONAL	1	TRUE	1	0.359878580832621	2		685	739	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117358	115117359	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	92	565	0	ENST00000257566.3:c.815dup	p.Leu272PhefsTer6	p.L272Ffs*6	ENST00000257566	NM_016569.3	272	ttg/ttTg	4/8	1	2	FACETS	0.902	0.803	1	0.902	0.803	1	CLONAL	1	TRUE	1	0.359878580832621	2		565	567	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237591	133237591	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	74	682	0	ENST00000320574.5:c.3024G>T	p.Lys1008Asn	p.K1008N	ENST00000320574	NM_006231.2	1008	aaG/aaT	25/49	1	2	FACETS	0.583	0.509	0.661	0.583	0.509	0.661	SUBCLONAL	1	TRUE	1	0.359878580832621	2		682	706	SUCCESS
BLM	641	MSKCC	GRCh37	15	91290624	91290624	+	start_lost	Translation_Start_Site	SNP	T	T	C	rs1057516593	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	111	686	0	ENST00000355112.3:c.2T>C	p.Met1?	p.M1?	ENST00000355112	NM_000057.2	1	aTg/aCg	2/22	1	2	FACETS	0.94	0.847	1	0.94	0.847	1	CLONAL	1	TRUE	1	0.359878580832621	2		686	656	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823846	3823846	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	129	593	0	ENST00000262367.5:c.2369A>G	p.Gln790Arg	p.Q790R	ENST00000262367	NM_004380.2	790	cAg/cGg	13/31	0.359627464838758	2	FACETS	1	0.962	1	0.555	0.504	0.608	CLONAL	1	TRUE	0	0.359878580832621	2		593	646	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577111	7577111	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs786202082	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	50	851	0	ENST00000269305.4:c.827C>G	p.Ala276Gly	p.A276G	ENST00000269305	NM_001126112.2	276	gCc/gGc	8/11	1	2	FACETS	0.265	0.224	0.311	0.265	0.224	0.311	SUBCLONAL	1	TRUE	1	0.359878580832621	2		851	1048	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	111	549	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	1	2	FACETS	0.842	0.757	0.931	0.842	0.757	0.931	CLONAL	1	TRUE	1	0.359878580832621	2		549	733	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	73	593	0	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	1	2	FACETS	0.636	0.556	0.722	0.636	0.556	0.722	SUBCLONAL	1	TRUE	1	0.359878580832621	2		593	638	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8111101	8111101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1362101464	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	100	628	1	ENST00000585124.1:c.106C>T	p.Pro36Ser	p.P36S	ENST00000585124	NM_004217.3	36	Cca/Tca	3/9	1	2	FACETS	0.786	0.702	0.875	0.786	0.702	0.875	SUBCLONAL	1	TRUE	1	0.359878580832621	2		629	707	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374887	45374887	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	198	883	0	ENST00000262160.6:c.956T>C	p.Val319Ala	p.V319A	ENST00000262160	NM_005901.5	319	gTt/gCt	8/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.359878580832621	2		883	924	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119208	3119208	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1208115313	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	187	805	0	ENST00000078429.4:c.740G>A	p.Arg247Gln	p.R247Q	ENST00000078429	NM_002067.2	247	cGg/cAg	6/7	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.359878580832621	2		805	822	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	112	667	3	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	0.91	0.819	1	0.91	0.819	1	CLONAL	1	TRUE	1	0.359878580832621	2		670	684	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222762	5222762	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1391073074	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	39	743	1	ENST00000357368.4:c.3041C>T	p.Thr1014Met	p.T1014M	ENST00000357368	NM_002850.3	1014	aCg/aTg	18/38	1	2	FACETS	0.289	0.238	0.346	0.289	0.238	0.346	SUBCLONAL	1	TRUE	1	0.359878580832621	2		744	750	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231528	5231528	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	36	682	0	ENST00000357368.4:c.1948del	p.Ala650ProfsTer22	p.A650Pfs*22	ENST00000357368	NM_002850.3	650	Gcc/cc	14/38	1	2	FACETS	0.31	0.254	0.373	0.31	0.254	0.373	SUBCLONAL	1	TRUE	1	0.359878580832621	2		682	645	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7128965	7128965	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	123	625	0	ENST00000302850.5:c.2843T>C	p.Leu948Ser	p.L948S	ENST00000302850	NM_000208.2	948	tTa/tCa	15/22	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.359878580832621	2		625	604	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629033	14629035	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs764800868	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	144	641	0	ENST00000254322.2:c.127_129del	p.Glu43del	p.E43del	ENST00000254322	NM_006145.1	43	GAG/-	1/3	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.359878580832621	2		641	713	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17941318	17941318	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	84	563	0	ENST00000458235.1:c.3090del	p.Ser1031ArgfsTer7	p.S1031Rfs*7	ENST00000458235	NM_000215.3	1030	ccC/cc	22/24	1	2	FACETS	0.828	0.732	0.929	0.828	0.732	0.929	CLONAL	1	TRUE	1	0.359878580832621	2		563	564	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224124	36224124	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	176	909	1	ENST00000222270.7:c.6678del	p.Thr2227ArgfsTer34	p.T2227Rfs*34	ENST00000222270	NM_014727.1	2225	tCc/tc	28/37	1	2	FACETS	0.999	0.92	1	0.999	0.92	1	CLONAL	1	TRUE	1	0.359878580832621	2		910	979	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	187	1018	1	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.359878580832621	2		1019	1006	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	195	837	4	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.359878580832621	2		841	948	SUCCESS
ALK	238	MSKCC	GRCh37	2	29473977	29473977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1241282087	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	135	679	0	ENST00000389048.3:c.2198C>T	p.Thr733Ile	p.T733I	ENST00000389048	NM_004304.4	733	aCc/aTc	12/29	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.359878580832621	2		679	660	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368388	225368388	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1366667901	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	119	604	0	ENST00000264414.4:c.1358del	p.Asn453ThrfsTer2	p.N453Tfs*2	ENST00000264414	NM_003590.4	453	aAc/ac	9/16	1	2	FACETS	0.999	0.903	1	0.999	0.903	1	CLONAL	1	TRUE	1	0.359878580832621	2		604	662	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050315	37050315	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs63751101	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	136	710	2	ENST00000231790.2:c.469del	p.Tyr157ThrfsTer3	p.Y157Tfs*3	ENST00000231790	NM_000249.3	155	cTt/ct	6/19	0.359627464838758	2	FACETS	0.967	0.879	1	0.483	0.439	0.529	CLONAL	1	TRUE	0	0.359878580832621	2		712	782	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181908	38181908	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	23	371	0	ENST00000396334.3:c.532A>G	p.Ile178Val	p.I178V	ENST00000396334	NM_002468.4	178	Atc/Gtc	3/5	0.359627464838758	2	FACETS	0.315	0.245	0.396	0.157	0.122	0.198	SUBCLONAL	1	TRUE	0	0.359878580832621	2		371	406	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	126	306	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.359627464838758	2	FACETS	0.919	0.841	0.999	0.919	0.841	0.999	CLONAL	2	TRUE	0	0.359878580832621	2		306	381	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205003	128205004	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	72	481	0	ENST00000341105.2:c.437dup	p.Gly147TrpfsTer38	p.G147Wfs*38	ENST00000341105	NM_032638.4	146	ggt/ggGt	3/6	1	2	FACETS	0.928	0.814	1	0.928	0.814	1	CLONAL	1	TRUE	1	0.359878580832621	2		481	431	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215906	142215906	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	53	507	3	ENST00000350721.4:c.5687C>A	p.Ala1896Asp	p.A1896D	ENST00000350721	NM_001184.3	1896	gCc/gAc	33/47	1	2	FACETS	0.586	0.5	0.68	0.586	0.5	0.68	SUBCLONAL	1	TRUE	1	0.359878580832621	2		510	503	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158231	106158231	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	27	492	0	ENST00000380013.4:c.3132G>T	p.Lys1044Asn	p.K1044N	ENST00000380013	NM_001127208.2	1044	aaG/aaT	3/11	1	2	FACETS	0.293	0.232	0.363	0.293	0.232	0.363	SUBCLONAL	1	TRUE	1	0.359878580832621	2		492	512	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	116	612	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.961	0.867	1	0.961	0.867	1	CLONAL	1	TRUE	1	0.359878580832621	2		612	671	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591149	67591151	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	76	462	0	ENST00000274335.5:c.1744_1745+1del		p.LMdel	ENST00000274335		581	tTGAtg/ttg	12/15	1	2	FACETS	0.967	0.851	1	0.967	0.851	1	CLONAL	1	TRUE	1	0.359878580832621	2		462	437	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495402	149495402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765611204	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	41	806	0	ENST00000261799.4:c.3245C>T	p.Pro1082Leu	p.P1082L	ENST00000261799	NM_002609.3	1082	cCg/cTg	23/23	1	2	FACETS	0.285	0.236	0.34	0.285	0.236	0.34	SUBCLONAL	1	TRUE	1	0.359878580832621	2		806	799	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523098	176523098	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	149	840	0	ENST00000292408.4:c.1862C>G	p.Thr621Ser	p.T621S	ENST00000292408	NM_213647.1	621	aCt/aGt	14/18	1	2	FACETS	0.952	0.87	1	0.952	0.87	1	CLONAL	1	TRUE	1	0.359878580832621	2		840	870	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523142	176523143	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	133	827	1	ENST00000292408.4:c.1906_1907delinsTT	p.Gly636Phe	p.G636F	ENST00000292408	NM_213647.1	636	GGc/TTc	14/18	1	2	FACETS	0.863	0.784	0.947	0.863	0.784	0.947	CLONAL	1	TRUE	1	0.359878580832621	2		828	856	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	168	498	3	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.359878580832621	2		501	820	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32814948	32814948	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	137	677	0	ENST00000354258.4:c.2117del	p.Gly706ValfsTer12	p.G706Vfs*12	ENST00000354258	NM_000593.5	706	gGt/gt	10/11	1	2	FACETS	0.94	0.855	1	0.94	0.855	1	CLONAL	1	TRUE	1	0.359878580832621	2		677	810	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821200	32821200	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	147	790	0	ENST00000354258.4:c.394del	p.Ala132ProfsTer25	p.A132Pfs*25	ENST00000354258	NM_000593.5	132	Gcc/cc	1/11	1	2	FACETS	0.881	0.804	0.962	0.881	0.804	0.962	CLONAL	1	TRUE	1	0.359878580832621	2		790	927	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956568	93956568	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	81	537	0	ENST00000369303.4:c.2668C>A	p.Leu890Ile	p.L890I	ENST00000369303	NM_004440.3	890	Cta/Ata	15/17	1	2	FACETS	0.838	0.74	0.943	0.838	0.74	0.943	CLONAL	1	TRUE	1	0.359878580832621	2		537	537	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	132	547	3	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.359878580832621	2		550	691	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606581	93606581	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	125	605	0	ENST00000375746.1:c.401A>G	p.Gln134Arg	p.Q134R	ENST00000375746	NM_001174167.1	134	cAg/cGg	2/14	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.359878580832621	2		605	624	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224161	98224161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56173896	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	50	269	1	ENST00000331920.6:c.2680G>A	p.Asp894Asn	p.D894N	ENST00000331920	NM_000264.3	894	Gat/Aat	16/24	1	2	FACETS	0.92	0.785	1	0.92	0.785	1	CLONAL	1	TRUE	1	0.359878580832621	2		270	302	SUCCESS
AR	367	MSKCC	GRCh37	X	66766087	66766087	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	159	403	0	ENST00000374690.3:c.1099T>C	p.Phe367Leu	p.F367L	ENST00000374690	NM_000044.3	367	Ttt/Ctt	1/8	1	1	FACETS	0.798	0.738	0.859	1	0.99	1	SUBCLONAL	2	TRUE	0	0.359878580832621	1		403	454	SUCCESS
AR	367	MSKCC	GRCh37	X	66766187	66766187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	75	191	0	ENST00000374690.3:c.1199C>T	p.Ala400Val	p.A400V	ENST00000374690	NM_000044.3	400	gCg/gTg	1/8	1	1	FACETS	0.876	0.784	0.971	1	0.983	1	CLONAL	2	TRUE	0	0.359878580832621	1		191	195	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016938-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	99	301	4				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.308287819238757	2		305	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0016938-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	185	1546	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.308287819238757	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.308287819238757	1		1546	993	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591281	67591282	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0016938-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	161	404	0	ENST00000274335.5:c.1781dup	p.Leu594PhefsTer8	p.L594Ffs*8	ENST00000274335		593	-/T	13/15	0.308287819238757	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.308287819238757	1		404	756	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	144	408	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	0.428547629190968	2		408	658	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0016939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	76	481	2	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.428547629190968	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	0	0.428547629190968	1		483	272	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280031	66280031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867811974	NA	P-0016939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	71	362	1	ENST00000273854.3:c.1658G>A	p.Arg553Gln	p.R553Q	ENST00000273854	NM_004439.5	553	cGa/cAa	7/18	0.182364389425206	3	FACETS	1	0.961	1	0.617	0.543	0.696	INDETERMINATE	1	TRUE	1	0.428547629190968	3		363	326	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057789	27057795	+	frameshift_variant	Frame_Shift_Del	DEL	GTATCAG	GTATCAG	-	novel	NA	P-0016939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	157	1088	1	ENST00000324856.7:c.1497_1503del	p.Tyr500SerfsTer117	p.Y500Sfs*117	ENST00000324856	NM_006015.4	499	tcGTATCAG/tc	3/20	0.428547629190968	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.428547629190968	1		1089	465	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518187	103518187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769956023	NA	P-0016939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	66	327	0	ENST00000355739.4:c.2125G>A	p.Asp709Asn	p.D709N	ENST00000355739	NM_000123.3	709	Gac/Aac	9/15	0.182364389425206	3	FACETS	1	0.966	1	0.656	0.575	0.742	INDETERMINATE	1	TRUE	1	0.428547629190968	3		327	285	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177792	56177792	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	107	447	0	ENST00000399503.3:c.2765C>G	p.Ala922Gly	p.A922G	ENST00000399503	NM_005921.1	922	gCc/gGc	14/20	0.214074606381499	4	FACETS	0.924	0.836	1			1	INDETERMINATE	2	TRUE	NA	0.428547629190968	4		447	386	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178445	56178445	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs373890078	NA	P-0016939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	85	370	0	ENST00000399503.3:c.3418A>G	p.Met1140Val	p.M1140V	ENST00000399503	NM_005921.1	1140	Atg/Gtg	14/20	0.214074606381499	4	FACETS	0.754	0.671	0.841			1	INDETERMINATE	2	TRUE	NA	0.428547629190968	4		370	376	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931991	39931991	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747289594	NA	P-0016939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	117	845	0	ENST00000378444.4:c.2608A>G	p.Thr870Ala	p.T870A	ENST00000378444	NM_001123385.1	870	Act/Gct	4/15	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.428547629190968	2		845	411	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	112	594	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.346960948609308	1	FACETS	0.885	0.798	0.977	0.885	0.798	0.977	CLONAL	1	TRUE	0	0.346960948609308	1		594	603	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55143617	55143617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878854825	NA	P-0016941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	37	358	1	ENST00000257290.5:c.1849C>T	p.Arg617Trp	p.R617W	ENST00000257290	NM_006206.4	617	Cgg/Tgg	13/23	1	2	FACETS	0.263	0.216	0.316	0.263	0.216	0.316	SUBCLONAL	1	TRUE	1	0.417959848097427	2		359	673	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42848519	42848519	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	50	819	0	ENST00000398585.3:c.823del	p.Ser275LeufsTer5	p.S275Lfs*5	ENST00000398585	NM_001135099.1	275	Tct/ct	8/14	0.308481127929701	0	FACETS	0.153	0.129	0.179			1	SUBCLONAL	1	TRUE	0	0.417959848097427	0		819	911	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406492	70406492	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1231	76	825	1	ENST00000373644.4:c.4006A>T	p.Thr1336Ser	p.T1336S	ENST00000373644	NM_030625.2	1336	Aca/Tca	4/12	1	2	FACETS	0.278	0.243	0.317	0.278	0.243	0.317	SUBCLONAL	1	TRUE	1	0.417959848097427	2		826	1307	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0016942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	690	632	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.780262412014459	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.780262412014459	2		634	863	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0016942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	446	489	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.780262412014459	3	FACETS	0.99	0.966	1	0.99	0.966	1	CLONAL	3	TRUE	0	0.780262412014459	3		489	535	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	364	500	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.471650745458266	5	FACETS	0.944	0.903	0.985	0.944	0.903	0.985	CLONAL	3	TRUE	2	0.780262412014459	5		500	715	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379375	225379375	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	147	937	0	ENST00000264414.4:c.493C>G	p.Leu165Val	p.L165V	ENST00000264414	NM_003590.4	165	Cta/Gta	4/16	0.385522410809476	5	FACETS	0.698	0.636	0.764	0.233	0.212	0.255	INDETERMINATE	1	TRUE	2	0.780262412014459	5		937	1171	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0016943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	129	492	1	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.342798573652097	2		493	727	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952100	178952100	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	111	630	0	ENST00000263967.3:c.3155C>A	p.Thr1052Lys	p.T1052K	ENST00000263967	NM_006218.2	1052	aCa/aAa	21/21	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.342798573652097	2		630	571	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842366	68842366	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	153	860	0	ENST00000261769.5:c.429del	p.Asn144ThrfsTer71	p.N144Tfs*71	ENST00000261769	NM_004360.3	143	Ccc/cc	4/16	0.342798573652097	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.342798573652097	1		860	640	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410710	63410710	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	142	369	0	ENST00000330258.3:c.2457A>T	p.Glu819Asp	p.E819D	ENST00000330258	NM_152424.3	819	gaA/gaT	2/2	0.394647357729298	2	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.394647357729298	2		369	604	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937499	76937499	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	214	296	0	ENST00000373344.5:c.3249del	p.Asn1084MetfsTer34	p.N1084Mfs*34	ENST00000373344	NM_000489.3	1083	aaG/aa	9/35	0.394647357729298	2	FACETS	1	0.974	1			1	CLONAL	2	TRUE	NA	0.394647357729298	2		296	508	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273414	38273414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	73	751	1	ENST00000425967.3:c.1921G>A	p.Gly641Ser	p.G641S	ENST00000425967	NM_001174067.1	641	Ggc/Agc	14/19	0.296601381234362	2	FACETS	0.349	0.304	0.398	0.175	0.152	0.199	SUBCLONAL	1	TRUE	0	0.394647357729298	2		752	1059	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0016945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	90	390	2				ENST00000310581	NM_198253.2	-/1132			0.298615900405858	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.807704107546279	0		392	158	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0016945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	239	879	1	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.807704107546279	8	FACETS	1	0.967	1			1	CLONAL	2	FALSE	NA	0.807704107546279	8		880	960	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249022	55249022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567477136	NA	P-0016945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	248	655	1	ENST00000275493.2:c.2320G>A	p.Val774Met	p.V774M	ENST00000275493	NM_005228.3	774	Gtg/Atg	20/28	0.807704107546279	8	FACETS	1	0.957	1			1	CLONAL	2	FALSE	NA	0.807704107546279	8		656	1021	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613206	52613206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	113	738	1	ENST00000394830.3:c.3322G>A	p.Asp1108Asn	p.D1108N	ENST00000394830	NM_018313.4	1108	Gat/Aat	22/30	0.332411638321781	4	FACETS	0.808	0.737	0.881	0.808	0.737	0.881	INDETERMINATE	2	FALSE	2	0.807704107546279	4		739	313	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046327	69046327	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	50	506	0	ENST00000288368.4:c.3800T>G	p.Phe1267Cys	p.F1267C	ENST00000288368	NM_024870.2	1267	tTc/tGc	32/40	1	2	FACETS	0.904	0.786	1	0.904	0.786	1	CLONAL	1	FALSE	1	0.807704107546279	2		506	137	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574030	7574030	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	165	679	2	ENST00000269305.4:c.997del	p.Arg333ValfsTer12	p.R333Vfs*12	ENST00000269305	NM_001126112.2	333	Cgt/gt	10/11	0.635156847327531	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.635156847327531	2		681	258	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406167	70406167	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	86	911	1	ENST00000373644.4:c.3681G>T	p.Arg1227Ser	p.R1227S	ENST00000373644	NM_030625.2	1227	agG/agT	4/12	0.256934308719732	2	FACETS	1	0.948	1	0.544	0.488	0.601	INDETERMINATE	1	TRUE	0	0.635156847327531	2		912	249	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874057	123874057	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1013699873	NA	P-0016946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	17	29	0	ENST00000330479.4:c.88G>C	p.Glu30Gln	p.E30Q	ENST00000330479	NM_020382.3	30	Gag/Cag	2/9	0.635156847327531	2	FACETS	1	0.91	1	0.686	0.542	0.835	CLONAL	1	TRUE	0	0.635156847327531	2		29	39	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058618	42058618	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	35	366	0	ENST00000219905.7:c.8338del	p.Met2780Ter	p.M2780*	ENST00000219905	NM_001164273.1	2780	Atg/tg	24/24	0.184756722866569	2	FACETS	0.896	0.75	1	0.448	0.375	0.526	INDETERMINATE	1	TRUE	0	0.635156847327531	2		366	123	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646818	23646819	+	missense_variant	Missense_Mutation	DNP	TG	TG	AA	novel	NA	P-0016946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	65	754	1	ENST00000261584.4:c.1048_1049delinsTT	p.Gln350Leu	p.Q350L	ENST00000261584	NM_024675.3	350	CAa/TTa	4/13	0.111972230080218	3	FACETS	1	0.93	1	0.362	0.318	0.41	INDETERMINATE	1	TRUE	0	0.635156847327531	3		755	248	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164807	32164807	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	85	492	0	ENST00000375023.3:c.5095G>C	p.Glu1699Gln	p.E1699Q	ENST00000375023	NM_004557.3	1699	Gag/Cag	28/30	0.635156847327531	3	FACETS	0.985	0.878	1	0.493	0.439	0.549	CLONAL	1	TRUE	1	0.635156847327531	3		492	358	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005333	150005333	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	68	459	0	ENST00000253339.5:c.892G>C	p.Glu298Gln	p.E298Q	ENST00000253339		298	Gag/Cag	3/7	0.578519063417634	4	FACETS	1	0.95	1	0.388	0.34	0.438	CLONAL	1	TRUE	1	0.635156847327531	4		459	301	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	83	301	4				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.752953085987998	2		305	196	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807889	1807889	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs78311289	NA	P-0016948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	415	895	0	ENST00000260795.2:c.1948A>G	p.Lys650Glu	p.K650E	ENST00000260795		650	Aag/Gag	13/17	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	1	TRUE	NA	0.752953085987998	2		895	750	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176481	123176481	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	201	348	0	ENST00000218089.9:c.448del	p.Glu150LysfsTer33	p.E150Kfs*33	ENST00000218089	NM_001042749.1	150	Gaa/aa	7/35	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.752953085987998	1		348	278	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692948	89692949	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0016948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	267	890	0	ENST00000371953.3:c.437dup	p.Leu146PhefsTer34	p.L146Ffs*34	ENST00000371953	NM_000314.4	144	-/T	5/9	0.752953085987998	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.752953085987998	1		890	414	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0016949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	101	489	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.973	0.871	1	0.973	0.871	1	CLONAL	1	TRUE	1	0.341595119669277	2		489	608	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063684	67063684	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	116	212	1	ENST00000412916.2:c.133C>T	p.Gln45Ter	p.Q45*	ENST00000412916		45	Cag/Tag	2/6	0.341595119669277	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.341595119669277	1		213	516	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111487	8111487	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	185	221	0	ENST00000346208.3:c.973A>G	p.Thr325Ala	p.T325A	ENST00000346208		325	Acc/Gcc	5/6	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.341595119669277	2		221	1007	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118769	115118771	+	missense_variant	Missense_Mutation	TNP	GGG	GGG	CCC	novel	NA	P-0016949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	115	199	1	ENST00000257566.3:c.570_572inv	p.Ser190_Pro191delinsArgGly	p.S190_P191delinsRG	ENST00000257566	NM_016569.3	190	agCCCc/agGGGc	2/8	1	2	FACETS	0.85	0.766	0.939	0.85	0.766	0.939	CLONAL	1	TRUE	1	0.341595119669277	2		200	792	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817873	3817873	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	125	200	0	ENST00000262367.5:c.3098A>G	p.Lys1033Arg	p.K1033R	ENST00000262367	NM_004380.2	1033	aAa/aGa	16/31	0.341595119669277	3	FACETS	0.818	0.739	0.901	0.409	0.369	0.451	CLONAL	1	TRUE	1	0.341595119669277	3		200	1048	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842691	68842691	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	139	235	0	ENST00000261769.5:c.627del	p.Glu210LysfsTer5	p.E210Kfs*5	ENST00000261769	NM_004360.3	209	agA/ag	5/16	0.341595119669277	1	FACETS	0.838	0.763	0.917	0.838	0.763	0.917	CLONAL	1	TRUE	0	0.341595119669277	1		235	805	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1173	41	525	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.563	0.466	0.671	0.563	0.466	0.671	SUBCLONAL	1	TRUE	1	0.12	2		525	1214	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0016950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	65	487	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.989	0.855	1	0.989	0.855	1	CLONAL	1	TRUE	1	0.12	2		489	1095	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998890	11998890	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0016950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	29	302	0	ENST00000353533.5:c.394-2A>G		p.X132_splice	ENST00000353533	NM_003010.3	132			1	2	FACETS	0.849	0.68	1	0.849	0.68	1	CLONAL	1	TRUE	1	0.12	2		302	569	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0016951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	96	180	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	0.49467961593665	2		180	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577595	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0016951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	89	664	0	ENST00000269305.4:c.686_687del	p.Cys229TyrfsTer10	p.C229Yfs*10	ENST00000269305	NM_001126112.2	229	tGT/t	7/11	0.49467961593665	1	FACETS	0.978	0.879	1	0.978	0.879	1	CLONAL	1	TRUE	0	0.49467961593665	1		664	277	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665110	29665110	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658541	NA	P-0016951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	61	875	2	ENST00000356175.3:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000356175	NM_000267.3	2237	Cga/Tga	44/57	1	2	FACETS	0.859	0.748	0.978	0.859	0.748	0.978	CLONAL	1	TRUE	1	0.49467961593665	2		877	287	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082341	16082341	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	87	1133	0	ENST00000281043.3:c.155A>C	p.Lys52Thr	p.K52T	ENST00000281043	NM_005378.4	52	aAg/aCg	2/3	1	2	FACETS	0.812	0.723	0.907	0.812	0.723	0.907	CLONAL	1	TRUE	1	0.49467961593665	2		1133	433	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252963	36252964	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	ATCACAGT	novel	NA	P-0016951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	107	678	0	ENST00000300305.3:c.391_398dup	p.Met133IlefsTer3	p.M133Ifs*3	ENST00000300305		133	atg/atACTGTGATg	4/8	1	2	FACETS	0.917	0.827	1	0.917	0.827	1	CLONAL	1	TRUE	1	0.49467961593665	2		678	472	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115905	8115906	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	35	510	0	ENST00000346208.3:c.1252dup	p.Thr418AsnfsTer89	p.T418Nfs*89	ENST00000346208		417	-/A	6/6	1	2	FACETS	0.324	0.264	0.391	0.324	0.264	0.391	SUBCLONAL	1	TRUE	1	0.326607141495411	2		510	662	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115905	8115906	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016952-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	288	510	0	ENST00000346208.3:c.1252dup	p.Thr418AsnfsTer89	p.T418Nfs*89	ENST00000346208		417	-/A	6/6	0.201880449406006	5	FACETS	0.908	0.855	0.962	0.605	0.57	0.641	INDETERMINATE	2	TRUE	2	0.634337805227346	5		510	976	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016952-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	330	335	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.233817740184621	4	FACETS	0.927	0.879	0.976	0.927	0.879	0.976	INDETERMINATE	2	TRUE	2	0.634337805227346	4		335	917	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106122	27106147	+	frameshift_variant	Frame_Shift_Del	DEL	GGATGACATGTTGTCTACTCGGTCTA	GGATGACATGTTGTCTACTCGGTCTA	-	novel	NA	P-0016952-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	128	404	0	ENST00000324856.7:c.5734_5759del	p.Asp1912HisfsTer8	p.D1912Hfs*8	ENST00000324856	NM_006015.4	1911	atGGATGACATGTTGTCTACTCGGTCTAgc/atgc	20/20	0.634337805227346	1	FACETS	0.504	0.458	0.551	0.504	0.458	0.551	SUBCLONAL	1	TRUE	0	0.634337805227346	1		404	547	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028614	12028614	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	31	559	2	ENST00000353533.5:c.817G>T	p.Glu273Ter	p.E273*	ENST00000353533	NM_003010.3	273	Gaa/Taa	8/11	0.574423237393378	1	FACETS	0.193	0.156	0.235	0.193	0.156	0.235	SUBCLONAL	1	TRUE	0	0.574423237393378	1		561	399	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170722	7170722	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	92	1085	1	ENST00000302850.5:c.1309C>A	p.Gln437Lys	p.Q437K	ENST00000302850	NM_000208.2	437	Cag/Aag	6/22	1	2	FACETS	0.26	0.23	0.293	0.26	0.23	0.293	SUBCLONAL	1	TRUE	1	0.574423237393378	2		1086	1231	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0016957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	190	195	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.118164537429446	4	FACETS	0.867	0.808	0.927	0.867	0.808	0.927	INDETERMINATE	2	TRUE	2	0.751002498472345	4		195	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519989	NA	P-0016957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	522	654	0	ENST00000269305.4:c.730G>C	p.Gly244Arg	p.G244R	ENST00000269305	NM_001126112.2	244	Ggc/Cgc	7/11	0.700660985466286	2	FACETS	0.963	0.936	0.989	0.963	0.936	0.989	CLONAL	2	TRUE	0	0.751002498472345	2		654	722	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888722	76888725	+	frameshift_variant	Frame_Shift_Del	DEL	TTTC	TTTC	-	novel	NA	P-0016957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	411	808	0	ENST00000373344.5:c.5104_5107del	p.Glu1702TyrfsTer22	p.E1702Yfs*22	ENST00000373344	NM_000489.3	1702	GAAAta/ta	19/35	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.751002498472345	2		808	1023	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0016958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	224	463	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.591516927899009	2		463	729	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247168	153247168	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1560758208	NA	P-0016958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	28	465	0	ENST00000281708.4:c.1634A>G	p.Tyr545Cys	p.Y545C	ENST00000281708	NM_033632.3	545	tAt/tGt	10/12	0.591516927899009	1	FACETS	0.155	0.124	0.192	0.155	0.124	0.192	SUBCLONAL	1	TRUE	0	0.591516927899009	1		465	429	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332882	153332882	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0016958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	70	521	0	ENST00000281708.4:c.74C>G	p.Ser25Ter	p.S25*	ENST00000281708	NM_033632.3	25	tCa/tGa	2/12	0.591516927899009	1	FACETS	0.246	0.214	0.28	0.246	0.214	0.28	SUBCLONAL	1	TRUE	0	0.591516927899009	1		521	678	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733393	85733393	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	62	684	0	ENST00000370580.1:c.619C>G	p.Leu207Val	p.L207V	ENST00000370580	NM_003921.4	207	Cta/Gta	3/3	0.591516927899009	3	FACETS	0.244	0.21	0.282	0.122	0.105	0.141	SUBCLONAL	1	TRUE	1	0.591516927899009	3		684	1111	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355925	73355925	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	433	852	0	ENST00000377767.4:c.46G>T	p.Val16Leu	p.V16L	ENST00000377767	NM_014953.3	16	Gtg/Ttg	1/21	1	2	FACETS	0.981	0.934	1	0.981	0.934	1	CLONAL	1	TRUE	1	0.591516927899009	2		852	1492	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565580	41565580	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	50	651	0	ENST00000263253.7:c.4246G>T	p.Glu1416Ter	p.E1416*	ENST00000263253	NM_001429.3	1416	Gaa/Taa	26/31	1	2	FACETS	0.198	0.167	0.232	0.198	0.167	0.232	SUBCLONAL	1	TRUE	1	0.591516927899009	2		651	854	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729410	41729410	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	48	589	0	ENST00000242208.4:c.1119C>G	p.Ile373Met	p.I373M	ENST00000242208	NM_002192.2	373	atC/atG	3/3	1	2	FACETS	0.2	0.169	0.236	0.2	0.169	0.236	SUBCLONAL	1	TRUE	1	0.591516927899009	2		589	810	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258970	153258970	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0016958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	20	403	0	ENST00000281708.4:c.845C>G	p.Ser282Ter	p.S282*	ENST00000281708	NM_033632.3	282	tCa/tGa	5/12	0.591516927899009	1	FACETS	0.181	0.138	0.231	0.181	0.138	0.231	SUBCLONAL	1	TRUE	0	0.591516927899009	1		403	263	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110815	2110815	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0016959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	117	616	0	ENST00000219476.3:c.1119+1G>T		p.X373_splice	ENST00000219476	NM_000548.3	373			0.0821789893035545	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		616	515	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2114357	2114360	+	frameshift_variant	Frame_Shift_Del	DEL	CAGT	CAGT	AG	novel	NA	P-0016959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	165	936	1	ENST00000219476.3:c.1528_1531delinsAG	p.Gln510SerfsTer78	p.Q510Sfs*78	ENST00000219476	NM_000548.3	510	CAGTtg/AGtg	15/42	0.0821789893035545	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		937	731	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849317	89849317	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1274321707	NA	P-0016960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	253	867	0	ENST00000389301.3:c.1576G>C	p.Glu526Gln	p.E526Q	ENST00000389301	NM_000135.2	526	Gaa/Caa	17/43	0.539542784928486	3	FACETS	0.949	0.887	1	0.316	0.295	0.338	CLONAL	1	TRUE	0	0.539542784928486	3		867	1255	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572924	7572934	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	ATGTCAGTCTG	ATGTCAGTCTG	-	novel	NA	P-0016960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	303	574	0	ENST00000269305.4:c.1175_*3del		p.*392*	ENST00000269305	NM_001126112.2	392		11/11	0.539542784928486	2	FACETS	0.909	0.864	0.953	0.909	0.864	0.953	CLONAL	2	TRUE	0	0.539542784928486	2		574	618	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028636	12028636	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0016960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	379	541	0	ENST00000353533.5:c.839C>G	p.Ser280Ter	p.S280*	ENST00000353533	NM_003010.3	280	tCa/tGa	8/11	0.539542784928486	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.539542784928486	2		541	688	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40476813	40476813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	128	819	3	ENST00000264657.5:c.1516G>A	p.Glu506Lys	p.E506K	ENST00000264657	NM_139276.2	506	Gag/Aag	17/24	0.539542784928486	3	FACETS	0.497	0.449	0.548	0.249	0.224	0.274	SUBCLONAL	1	TRUE	1	0.539542784928486	3		822	1212	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207633	2207633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752264656	NA	P-0016960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	271	928	1	ENST00000398665.3:c.917C>T	p.Thr306Met	p.T306M	ENST00000398665	NM_032482.2	306	aCg/aTg	11/28	1	2	FACETS	0.987	0.927	1	0.987	0.927	1	CLONAL	1	TRUE	1	0.539542784928486	2		929	1018	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753109	128753109	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	420	710	0	ENST00000377970.2:c.1270G>A	p.Glu424Lys	p.E424K	ENST00000377970	NM_002467.4	424	Gag/Aag	3/3	0.536838132628875	4	FACETS	0.944	0.899	0.989	0.944	0.899	0.989	CLONAL	2	TRUE	2	0.539542784928486	4		710	1270	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974779	21974780	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	70	218	0	ENST00000304494.5:c.47dup	p.Ala17GlyfsTer27	p.A17Gfs*27	ENST00000304494	NM_000077.4	16	ctg/ctTg	1/3	0.539542784928486	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.539542784928486	1		218	181	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027060	71027084	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAGGGGCCTTGGGTGACGGGAGT	CAGAGGGGCCTTGGGTGACGGGAGT	-	novel	NA	P-0016961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	106	570	0	ENST00000318789.4:c.1243_1267del	p.Thr415SerfsTer51	p.T415Sfs*51	ENST00000318789	NM_032682.5	415	ACTCCCGTCACCCAAGGCCCCTCTGtc/tc	15/21	1	2	FACETS	0.864	0.78	0.952	0.864	0.78	0.952	CLONAL	1	TRUE	1	0.580037661598232	2		570	423	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0016962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	103	554	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.883	0.788	0.984	0.883	0.788	0.984	CLONAL	1	TRUE	1	0.225678270725913	2		554	1034	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573996	7573996	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121912662	NA	P-0016962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	105	807	0	ENST00000269305.4:c.1031T>C	p.Leu344Pro	p.L344P	ENST00000269305	NM_001126112.2	344	cTg/cCg	10/11	1	2	FACETS	0.77	0.687	0.857	0.77	0.687	0.857	SUBCLONAL	1	TRUE	1	0.225678270725913	2		807	1209	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591889	48591889	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	57	499	0	ENST00000342988.3:c.1052A>G	p.Asp351Gly	p.D351G	ENST00000342988	NM_005359.5	351	gAt/gGt	9/12	1	2	FACETS	0.817	0.701	0.945	0.817	0.701	0.945	CLONAL	1	TRUE	1	0.225678270725913	2		499	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577128	7577128	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	118	763	0	ENST00000269305.4:c.810T>A	p.Phe270Leu	p.F270L	ENST00000269305	NM_001126112.2	270	ttT/ttA	8/11	1	2	FACETS	0.858	0.772	0.949	0.858	0.772	0.949	CLONAL	1	TRUE	1	0.225678270725913	2		763	1219	SUCCESS
APC	324	MSKCC	GRCh37	5	112174262	112174262	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs786202995	NA	P-0016962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	58	422	0	ENST00000257430.4:c.2971G>T	p.Glu991Ter	p.E991*	ENST00000257430	NM_000038.5	991	Gaa/Taa	16/16	1	2	FACETS	0.75	0.644	0.867	0.75	0.644	0.867	SUBCLONAL	1	TRUE	1	0.225678270725913	2		422	685	SUCCESS
APC	324	MSKCC	GRCh37	5	112175350	112175351	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0016962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	45	316	0	ENST00000257430.4:c.4063dup	p.Ser1355PhefsTer20	p.S1355Ffs*20	ENST00000257430	NM_000038.5	1353	-/T	16/16	1	2	FACETS	0.77	0.647	0.906	0.77	0.647	0.906	CLONAL	1	TRUE	1	0.225678270725913	2		316	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0016963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	195	708	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.8	0.741	0.863	1	0.991	1	SUBCLONAL	2	TRUE	1	0.244104534199547	2		708	998	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0016963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	179	525	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.244104534199547	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.244104534199547	2		526	651	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0016963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	184	563	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	0.244104534199547	2		563	1026	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248427	212248427	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	42	298	0	ENST00000342788.4:c.3840G>T	p.Glu1280Asp	p.E1280D	ENST00000342788	NM_005235.2	1280	gaG/gaT	28/28	1	2	FACETS	0.943	0.789	1	0.943	0.789	1	CLONAL	1	TRUE	1	0.244104534199547	2		298	365	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119777	70119778	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0016963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	209	841	2	ENST00000245479.2:c.782_783dup	p.Gly262ArgfsTer18	p.G262Rfs*18	ENST00000245479	NM_000346.3	260	cca/ccAGa	3/3	1	2	FACETS	0.812	0.753	0.872	1	0.992	1	CLONAL	2	TRUE	1	0.244104534199547	2		843	1055	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223649	36223649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs533229757	NA	P-0016963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	168	821	2	ENST00000222270.7:c.6199G>A	p.Gly2067Ser	p.G2067S	ENST00000222270	NM_014727.1	2067	Ggc/Agc	28/37	0.0997911441861441	3	FACETS	1	0.987	1	0.712	0.654	0.774	INDETERMINATE	1	TRUE	1	0.244104534199547	3		823	1084	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779135	135779135	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs752054698	NA	P-0016963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	47	471	0	ENST00000298552.3:c.2111A>G	p.Tyr704Cys	p.Y704C	ENST00000298552	NM_001162426.1	704	tAt/tGt	17/23	1	2	FACETS	0.63	0.531	0.74	0.63	0.531	0.74	SUBCLONAL	1	TRUE	1	0.244104534199547	2		471	611	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	79	301	4				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.974	0.868	1	0.974	0.868	1	CLONAL	1	TRUE	1	0.607289653252935	2		305	267	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACAACCCCC	rs397517115	NA	P-0016964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	103	593	0	ENST00000275493.2:c.2311_2319dup	p.Asn771_His773dup	p.N771_H773dup	ENST00000275493	NM_005228.3	771	gac/gACAACCCCCac	20/28	0.607289653252935	4	FACETS	0.809	0.725	0.898	0.27	0.241	0.3	CLONAL	1	TRUE	1	0.607289653252935	4		593	674	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690817	89690819	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs1554897864	NA	P-0016964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	116	490	0	ENST00000371953.3:c.226_228del	p.Tyr76del	p.Y76del	ENST00000371953	NM_000314.4	75	cATTat/cat	4/9	0.607289653252935	1	FACETS	0.95	0.871	1	0.95	0.871	1	CLONAL	1	TRUE	0	0.607289653252935	1		490	280	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579349	7579349	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	97	752	0	ENST00000269305.4:c.338T>C	p.Phe113Ser	p.F113S	ENST00000269305	NM_001126112.2	113	tTc/tCc	4/11	0.178952575809994	1	FACETS	0.747	0.665	0.835	0.747	0.665	0.835	SUBCLONAL	1	FALSE	0	0.238672738668603	1		752	958	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520017	NA	P-0016965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	95	818	0	ENST00000326873.7:c.647C>T	p.Ser216Phe	p.S216F	ENST00000326873	NM_000455.4	216	tCc/tTc	5/10	0.238672738668603	1	FACETS	0.705	0.626	0.789	0.705	0.626	0.789	SUBCLONAL	1	FALSE	0	0.238672738668603	1		818	995	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0016966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	294	395	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	NA	2	FACETS	0.983	0.946	1			1	INDETERMINATE	2	TRUE	NA	0.726049298561341	2		397	412	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473780	67473780	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730880214	NA	P-0016966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	132	505	0	ENST00000327367.4:c.860G>A	p.Arg287Gln	p.R287Q	ENST00000327367	NM_005902.3	287	cGg/cAg	6/9	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.726049298561341	2		505	352	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	266	490	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	0.726049298561341	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.726049298561341	2		490	357	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385357	4385357	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	62	348	1	ENST00000261254.3:c.382G>A	p.Asp128Asn	p.D128N	ENST00000261254	NM_001759.3	128	Gac/Aac	2/5	0.547491192169189	4	FACETS	0.812	0.705	0.927			1	CLONAL	1	TRUE	NA	0.726049298561341	4		349	363	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266948	18266948	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	98	389	0	ENST00000222254.8:c.259G>T	p.Gly87Cys	p.G87C	ENST00000222254	NM_005027.3	87	Ggc/Tgc	2/16	NA	2	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.726049298561341	2		389	226	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247294	153247294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	344	659	1	ENST00000281708.4:c.1508C>T	p.Ala503Val	p.A503V	ENST00000281708	NM_033632.3	503	gCa/gTa	10/12	0.697718437750278	3	FACETS	0.973	0.929	1	0.973	0.929	1	CLONAL	2	TRUE	1	0.726049298561341	3		660	664	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0016967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	184	418	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.523759603396096	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	0	0.523759603396096	1		420	484	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0016967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	95	525	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.858	0.768	0.952	0.858	0.768	0.952	CLONAL	1	FALSE	1	0.523759603396096	2		526	423	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0016967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	190	563	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.225257268668512	0	FACETS	0.471	0.436	0.506			1	INDETERMINATE	1	FALSE	0	0.523759603396096	0		563	734	SUCCESS
APC	324	MSKCC	GRCh37	5	112175761	112175761	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	67	435	0	ENST00000257430.4:c.4473del	p.Phe1491LeufsTer16	p.F1491Lfs*16	ENST00000257430	NM_000038.5	1490	caT/ca	16/16	1	2	FACETS	0.797	0.698	0.903	0.797	0.698	0.903	CLONAL	1	FALSE	1	0.523759603396096	2		435	321	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243936	46243936	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	159	747	0	ENST00000334344.6:c.2030del	p.Val677GlyfsTer24	p.V677Gfs*24	ENST00000334344	NM_152641.2	677	gTg/gg	15/21	0.186590455970372	3	FACETS	1	0.955	1	0.529	0.486	0.574	INDETERMINATE	1	FALSE	1	0.523759603396096	3		747	724	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118931	70118932	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0016967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	152	950	1	ENST00000245479.2:c.505dup	p.His169ProfsTer83	p.H169Pfs*83	ENST00000245479	NM_000346.3	168	gac/gaCc	2/3	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.523759603396096	2		951	549	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155535	106155535	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	64	486	0	ENST00000380013.4:c.436G>A	p.Asp146Asn	p.D146N	ENST00000380013	NM_001127208.2	146	Gat/Aat	3/11	0.225257268668512	0	FACETS	0.266	0.23	0.304			1	INDETERMINATE	1	FALSE	0	0.523759603396096	0		486	438	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945396	151945396	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	43	748	0	ENST00000262189.6:c.2123C>T	p.Ser708Leu	p.S708L	ENST00000262189	NM_170606.2	708	tCa/tTa	14/59	0.148986324760109	3	FACETS	0.299	0.249	0.354	0.149	0.124	0.177	INDETERMINATE	1	FALSE	1	0.523759603396096	3		748	693	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920685	100920685	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	181	751	2	ENST00000325455.5:c.2463G>T	p.Met821Ile	p.M821I	ENST00000325455	NM_001202474.3	821	atG/atT	6/8	0.553750129537366	3	FACETS	1	0.98	1	0.586	0.542	0.632	CLONAL	1	TRUE	1	0.553750129537366	3		753	712	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948044	178948044	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	165	402	0	ENST00000263967.3:c.2816A>G	p.Asp939Gly	p.D939G	ENST00000263967	NM_006218.2	939	gAt/gGt	20/21	0.537766323215461	4	FACETS	0.996	0.923	1	0.996	0.923	1	CLONAL	2	TRUE	2	0.553750129537366	4		402	465	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309016	137309016	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	309	739	0	ENST00000481739.1:c.623del	p.Glu208GlyfsTer49	p.E208Gfs*49	ENST00000481739	NM_002957.4	208	gAg/gg	5/10	0.553750129537366	2	FACETS	0.988	0.942	1	0.988	0.942	1	CLONAL	2	TRUE	0	0.553750129537366	2		739	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578503	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	430	1072	0	ENST00000269305.4:c.427del	p.Val143CysfsTer27	p.V143Cfs*27	ENST00000269305	NM_001126112.2	143	Gtg/tg	5/11	0.553750129537366	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.553750129537366	2		1072	753	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0016969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	319	689	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.102116085285953	4	FACETS	0.911	0.866	0.956			1	INDETERMINATE	3	TRUE	NA	0.491880349061788	4		690	708	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661621	227661621	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	55	535	0	ENST00000305123.5:c.1834T>C	p.Tyr612His	p.Y612H	ENST00000305123	NM_005544.2	612	Tac/Cac	1/2	0.428019283802956	3	FACETS	0.78	0.671	0.899	0.39	0.335	0.45	SUBCLONAL	1	TRUE	1	0.491880349061788	3		535	357	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928071	178928098	+	protein_altering_variant	In_Frame_Del	DEL	ATGGATTAGAAGATTTGCTGAACCCTAT	ATGGATTAGAAGATTTGCTGAACCCTAT	G	novel	NA	P-0016969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	121	730	0	ENST00000263967.3:c.1349_1376delinsG	p.His450_Ile459delinsArg	p.H450_I459delinsR	ENST00000263967	NM_006218.2	450	cATGGATTAGAAGATTTGCTGAACCCTATt/cGt	8/21	0.491880349061788	3	FACETS	0.854	0.78	0.93	0.569	0.52	0.62	CLONAL	2	TRUE	0	0.491880349061788	3		730	359	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	179	290	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.685814943014974	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.685814943014974	1		290	314	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594258	55594258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913523	NA	P-0016970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	192	552	1	ENST00000288135.5:c.1961T>C	p.Val654Ala	p.V654A	ENST00000288135	NM_000222.2	654	gTg/gCg	13/21	0.685814943014974	2	FACETS	0.955	0.889	1	0.478	0.444	0.512	CLONAL	1	TRUE	0	0.685814943014974	2		553	586	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361126	66361126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303114412	NA	P-0016970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	269	499	0	ENST00000273854.3:c.1046C>T	p.Pro349Leu	p.P349L	ENST00000273854	NM_004439.5	349	cCa/cTa	4/18	0.685814943014974	2	FACETS	0.919	0.878	0.959	0.919	0.878	0.959	CLONAL	2	TRUE	0	0.685814943014974	2		499	427	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593604	55593607	+	protein_altering_variant	In_Frame_Del	DEL	GGAA	GGAA	T	novel	NA	P-0016970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	236	547	0	ENST00000288135.5:c.1670_1673delinsT	p.Trp557_Lys558delinsLeu	p.W557_K558delinsL	ENST00000288135	NM_000222.2	557	tGGAAg/tTg	11/21	0.685814943014974	2	FACETS	0.894	0.85	0.936	0.894	0.85	0.936	CLONAL	2	TRUE	0	0.685814943014974	2		547	385	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510783	120510783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	193	517	1	ENST00000256646.2:c.1181C>T	p.Pro394Leu	p.P394L	ENST00000256646	NM_024408.3	394	cCc/cTc	7/34	1	2	FACETS	0.976	0.909	1	0.976	0.909	1	CLONAL	1	TRUE	1	0.67	2		518	590	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510816	120510817	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0016972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	116	380	0	ENST00000256646.2:c.1147_1148delinsTT	p.Pro383Phe	p.P383F	ENST00000256646	NM_024408.3	383	CCt/TTt	7/34	1	2	FACETS	0.828	0.752	0.907	0.828	0.752	0.907	CLONAL	1	TRUE	1	0.67	2		380	418	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606796	43606796	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772489699	NA	P-0016972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	225	812	1	ENST00000355710.3:c.1405G>A	p.Asp469Asn	p.D469N	ENST00000355710	NM_020975.4	469	Gac/Aac	7/20	1	2	FACETS	0.821	0.766	0.877	0.821	0.766	0.877	CLONAL	1	TRUE	1	0.67	2		813	818	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344207	118344207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	272	739	0	ENST00000534358.1:c.2333C>T	p.Ser778Phe	p.S778F	ENST00000534358	NM_005933.3	778	tCc/tTc	3/36	1	2	FACETS	0.951	0.895	1	0.951	0.895	1	CLONAL	1	TRUE	1	0.67	2		739	854	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420214	49420214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs794727688	NA	P-0016972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	209	704	0	ENST00000301067.7:c.15535C>T	p.Arg5179Cys	p.R5179C	ENST00000301067	NM_003482.3	5179	Cgt/Tgt	48/54	1	2	FACETS	0.894	0.833	0.956	0.894	0.833	0.956	CLONAL	1	TRUE	1	0.67	2		704	698	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588626	28588626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs548609046	NA	P-0016972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	155	637	0	ENST00000241453.7:c.2822C>T	p.Ser941Leu	p.S941L	ENST00000241453	NM_004119.2	941	tCg/tTg	23/24	1	2	FACETS	0.736	0.676	0.798	0.736	0.676	0.798	SUBCLONAL	1	TRUE	1	0.67	2		637	629	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913920	32913920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358766	NA	P-0016972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	126	786	1	ENST00000380152.3:c.5428G>A	p.Val1810Ile	p.V1810I	ENST00000380152		1810	Gtt/Att	11/27	1	2	FACETS	0.825	0.752	0.9	0.825	0.752	0.9	CLONAL	1	TRUE	1	0.67	2		787	456	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436194	110436194	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs918898281	NA	P-0016972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	241	703	0	ENST00000375856.3:c.2207C>T	p.Ser736Phe	p.S736F	ENST00000375856	NM_003749.2	736	tCc/tTc	1/2	1	2	FACETS	0.991	0.93	1	0.991	0.93	1	CLONAL	1	TRUE	1	0.67	2		703	726	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035365	42035365	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780475295	NA	P-0016972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	84	383	0	ENST00000219905.7:c.5207G>A	p.Arg1736Lys	p.R1736K	ENST00000219905	NM_001164273.1	1736	aGa/aAa	15/24	1	2	FACETS	0.764	0.681	0.852	0.764	0.681	0.852	SUBCLONAL	1	TRUE	1	0.67	2		383	328	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112547	2112547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs796053485	NA	P-0016972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	329	865	1	ENST00000219476.3:c.1307C>T	p.Pro436Leu	p.P436L	ENST00000219476	NM_000548.3	436	cCg/cTg	13/42	1	2	FACETS	0.974	0.922	1	0.974	0.922	1	CLONAL	1	TRUE	1	0.67	2		866	1008	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656678	3656678	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	294	875	0	ENST00000294008.3:c.557C>T	p.Ser186Phe	p.S186F	ENST00000294008	NM_032444.2	186	tCc/tTc	3/15	1	2	FACETS	0.906	0.854	0.959	0.906	0.854	0.959	CLONAL	1	TRUE	1	0.67	2		875	969	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032311	10032311	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	157	511	1	ENST00000330684.3:c.512C>T	p.Ser171Phe	p.S171F	ENST00000330684	NM_001134407.1	171	tCc/tTc	3/13	1	2	FACETS	0.888	0.818	0.959	0.888	0.818	0.959	CLONAL	1	TRUE	1	0.67	2		512	528	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351866	89351867	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0016972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	274	1050	2	ENST00000301030.4:c.1083_1084delinsAA	p.Asp362Asn	p.D362N	ENST00000301030	NM_001256183.1	361	gtGGac/gtAAac	9/13	1	2	FACETS	0.762	0.716	0.81	0.762	0.716	0.81	SUBCLONAL	1	TRUE	1	0.67	2		1052	1073	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0016972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	298	924	2	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	1	2	FACETS	0.865	0.816	0.916	0.865	0.816	0.916	CLONAL	1	TRUE	1	0.67	2		926	1028	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276855	15276855	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	236	780	0	ENST00000263388.2:c.5410G>A	p.Glu1804Lys	p.E1804K	ENST00000263388	NM_000435.2	1804	Gag/Aag	30/33	1	2	FACETS	0.905	0.848	0.965	0.905	0.848	0.965	CLONAL	1	TRUE	1	0.67	2		780	778	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223281	36223281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1339231950	NA	P-0016972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	413	1314	0	ENST00000222270.7:c.5831C>T	p.Pro1944Leu	p.P1944L	ENST00000222270	NM_014727.1	1944	cCt/cTt	28/37	1	2	FACETS	0.989	0.942	1	0.989	0.942	1	CLONAL	1	TRUE	1	0.67	2		1314	1247	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45864781	45864781	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0016972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	243	735	1	ENST00000391945.4:c.1237+1G>A		p.X413_splice	ENST00000391945	NM_000400.3	413			1	2	FACETS	0.908	0.851	0.966	0.908	0.851	0.966	CLONAL	1	TRUE	1	0.67	2		736	799	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61760972	61760973	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCTGAAATCAAGCA	novel	NA	P-0016972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	109	588	0	ENST00000401558.2:c.47_60dup	p.Gln21CysfsTer13	p.Q21Cfs*13	ENST00000401558	NM_003400.3	20	-/TGCTTGATTTCAGC	2/25	1	2	FACETS	0.712	0.643	0.784	0.712	0.643	0.784	SUBCLONAL	1	TRUE	1	0.67	2		588	457	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274712	198274712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	117	366	1	ENST00000335508.6:c.686C>T	p.Ser229Phe	p.S229F	ENST00000335508	NM_012433.2	229	tCc/tTc	7/25	1	2	FACETS	0.773	0.701	0.847	0.773	0.701	0.847	SUBCLONAL	1	TRUE	1	0.67	2		367	452	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543858	212543858	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	180	614	0	ENST00000342788.4:c.1541G>A	p.Gly514Glu	p.G514E	ENST00000342788	NM_005235.2	514	gGa/gAa	13/28	1	2	FACETS	0.84	0.778	0.903	0.84	0.778	0.903	CLONAL	1	TRUE	1	0.67	2		614	640	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267784	46267784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753240956	NA	P-0016972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	218	705	4	ENST00000371998.3:c.2545C>T	p.Arg849Cys	p.R849C	ENST00000371998		849	Cgt/Tgt	14/23	1	2	FACETS	0.895	0.836	0.956	0.895	0.836	0.956	CLONAL	1	TRUE	1	0.67	2		709	727	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164159	47164159	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	109	480	1	ENST00000409792.3:c.1967C>T	p.Ser656Phe	p.S656F	ENST00000409792	NM_014159.6	656	tCt/tTt	3/21	1	2	FACETS	0.859	0.778	0.942	0.859	0.778	0.942	CLONAL	1	TRUE	1	0.67	2		481	379	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935589	49935589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	103	840	0	ENST00000296474.3:c.1775C>T	p.Ser592Phe	p.S592F	ENST00000296474	NM_002447.2	592	tCc/tTc	5/20	1	2	FACETS	0.383	0.342	0.426	0.383	0.342	0.426	SUBCLONAL	1	TRUE	1	0.67	2		840	803	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143181675	143181675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377427325	NA	P-0016972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	203	794	2	ENST00000262992.4:c.658G>A	p.Gly220Arg	p.G220R	ENST00000262992	NM_001101669.1	220	Gga/Aga	9/24	1	2	FACETS	0.836	0.778	0.896	0.836	0.778	0.896	CLONAL	1	TRUE	1	0.67	2		796	725	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295253	+	upstream_gene_variant	5'Flank	ONP	GAGG	GAGG	AAGA	novel	NA	P-0016972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	150	571	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.888	0.817	0.962	0.888	0.817	0.962	CLONAL	1	TRUE	1	0.67	2		571	504	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983352	149983352	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	174	584	0	ENST00000253339.5:c.2906T>C	p.Leu969Pro	p.L969P	ENST00000253339		969	cTt/cCt	7/7	1	2	FACETS	0.85	0.786	0.916	0.85	0.786	0.916	CLONAL	1	TRUE	1	0.67	2		584	611	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879009	151879009	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1300239688	NA	P-0016972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	172	513	0	ENST00000262189.6:c.5936C>T	p.Pro1979Leu	p.P1979L	ENST00000262189	NM_170606.2	1979	cCc/cTc	36/59	1	2	FACETS	0.96	0.889	1	0.96	0.889	1	CLONAL	1	TRUE	1	0.67	2		513	535	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317926	8317926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	179	462	0	ENST00000356435.5:c.5687C>T	p.Ser1896Phe	p.S1896F	ENST00000356435		1896	tCc/tTc	35/35	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.67	2		462	463	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242871	98242871	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0016972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	152	418	0	ENST00000331920.6:c.747-1G>A		p.X249_splice	ENST00000331920	NM_000264.3	249			1	2	FACETS	0.961	0.886	1	0.961	0.886	1	CLONAL	1	TRUE	1	0.67	2		418	472	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393653	139393653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	274	708	1	ENST00000277541.6:c.5993C>T	p.Pro1998Leu	p.P1998L	ENST00000277541	NM_017617.3	1998	cCa/cTa	32/34	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.67	2		709	736	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417386	139417393	+	frameshift_variant	Frame_Shift_Del	DEL	CGTAGGGC	CGTAGGGC	-	novel	NA	P-0016972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	53	868	0	ENST00000277541.6:c.651_658del	p.Pro218AlafsTer35	p.P218Afs*35	ENST00000277541	NM_017617.3	217	cgGCCCTACGtg/cgtg	4/34	1	2	FACETS	0.185	0.157	0.216	0.185	0.157	0.216	SUBCLONAL	1	TRUE	1	0.67	2		868	854	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921567	39921568	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0016972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	198	657	2	ENST00000378444.4:c.4252_4253delinsTT	p.Pro1418Phe	p.P1418F	ENST00000378444	NM_001123385.1	1418	CCc/TTc	10/15	1	2	FACETS	0.959	0.894	1	0.959	0.894	1	CLONAL	1	TRUE	1	0.67	2		659	616	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932479	39932479	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	249	853	1	ENST00000378444.4:c.2120C>T	p.Pro707Leu	p.P707L	ENST00000378444	NM_001123385.1	707	cCc/cTc	4/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.67	2		854	723	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347963	70347963	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777724452	NA	P-0016972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	163	629	0	ENST00000374080.3:c.3202C>T	p.Pro1068Ser	p.P1068S	ENST00000374080		1068	Ccc/Tcc	22/45	1	2	FACETS	0.943	0.872	1	0.943	0.872	1	CLONAL	1	TRUE	1	0.67	2		629	516	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	389	525	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.249974139013786	3	FACETS	0.879	0.84	0.919	1	0.995	1	CLONAL	3	TRUE	1	0.412654990003848	3		525	862	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0016973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	117	463	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.412654990003848	2		463	458	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096252	178096252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	106	469	1	ENST00000397062.3:c.1079C>T	p.Ser360Leu	p.S360L	ENST00000397062	NM_006164.4	360	tCa/tTa	5/5	0.412654990003848	3	FACETS	1	0.959	1	0.564	0.507	0.624	CLONAL	1	TRUE	1	0.412654990003848	3		470	549	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713589	30713589	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1553630174	NA	P-0016973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	197	419	13	ENST00000295754.5:c.914T>G	p.Leu305Arg	p.L305R	ENST00000295754	NM_003242.5	305	cTc/cGc	4/7	0.412654990003848	2	FACETS	0.856	0.806	0.905	1	0.99	1	CLONAL	3	TRUE	0	0.412654990003848	2		432	372	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579353	7579356	+	protein_altering_variant	In_Frame_Del	DEL	CCAG	CCAG	T	novel	NA	P-0016973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	228	854	5	ENST00000269305.4:c.331_334delinsA	p.Leu111_Gly112delinsSer	p.L111_G112delinsS	ENST00000269305	NM_001126112.2	111	CTGGgc/Agc	4/11	0.412654990003848	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.412654990003848	2		859	492	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335568	73335571	+	missense_variant	Missense_Mutation	ONP	CCAT	CCAT	ACAA	novel	NA	P-0016973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	244	692	6	ENST00000377767.4:c.2600_2603delinsTTGT	p.Tyr867_Gly868delinsPheVal	p.Y867_G868delinsFV	ENST00000377767	NM_014953.3	867	tATGGt/tTTGTt	19/21	0.365972407061036	4	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	2	0.412654990003848	4		698	822	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0016974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	420	489	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.39544469992405	5	FACETS	1	0.985	1			1	CLONAL	4	TRUE	NA	0.39544469992405	5		489	803	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578502	7578502	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555526241	NA	P-0016974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	165	848	0	ENST00000269305.4:c.428T>G	p.Val143Gly	p.V143G	ENST00000269305	NM_001126112.2	143	gTg/gGg	5/11	0.39544469992405	1	FACETS	0.809	0.743	0.877	0.809	0.743	0.877	CLONAL	1	TRUE	0	0.39544469992405	1		848	828	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845378	89845378	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	114	642	0	ENST00000389301.3:c.1749C>G	p.Phe583Leu	p.F583L	ENST00000389301	NM_000135.2	583	ttC/ttG	19/43	0.39544469992405	1	FACETS	0.695	0.626	0.767	0.695	0.626	0.767	SUBCLONAL	1	TRUE	0	0.39544469992405	1		642	666	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576134	29576134	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0016974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	104	514	0	ENST00000356175.3:c.4107C>G	p.Tyr1369Ter	p.Y1369*	ENST00000356175	NM_000267.3	1369	taC/taG	30/57	0.39544469992405	1	FACETS	0.829	0.745	0.917	0.829	0.745	0.917	CLONAL	1	TRUE	0	0.39544469992405	1		514	509	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7120763	7120763	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	novel	NA	P-0016974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	127	665	0	ENST00000302850.5:c.3530-3C>T		p.X1177_splice	ENST00000302850	NM_000208.2	1177			0.39544469992405	1	FACETS	0.866	0.787	0.949	0.866	0.787	0.949	CLONAL	1	TRUE	0	0.39544469992405	1		665	595	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0016975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	102	180	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.896	0.801	0.996	0.896	0.801	0.996	CLONAL	1	TRUE	1	0.295392105182552	2		180	771	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	342	408	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.267438965758147	7	FACETS	1	0.974	1			1	CLONAL	4	TRUE	NA	0.267438965758147	7		408	1024	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0016976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	198	795	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.267438965758147	2	FACETS	0.943	0.876	1	0.943	0.876	1	CLONAL	2	TRUE	0	0.267438965758147	2		796	785	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085656	16085656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201115523	NA	P-0016976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	64	669	0	ENST00000281043.3:c.832G>A	p.Asp278Asn	p.D278N	ENST00000281043	NM_005378.4	278	Gac/Aac	3/3	0.247427814587341	4	FACETS	0.751	0.649	0.862	0.375	0.324	0.431	SUBCLONAL	1	TRUE	2	0.267438965758147	4		669	808	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679717	88679717	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	29	472	0	ENST00000360948.2:c.746A>C	p.Gln249Pro	p.Q249P	ENST00000360948	NM_001012338.2	249	cAg/cCg	7/19	0.267438965758147	2	FACETS	0.426	0.341	0.523	0.213	0.17	0.262	SUBCLONAL	1	TRUE	0	0.267438965758147	2		472	509	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637994	39637994	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756468687	NA	P-0016976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	59	666	1	ENST00000262039.4:c.2411C>T	p.Thr804Met	p.T804M	ENST00000262039	NM_002647.2	804	aCg/aTg	22/25	1	2	FACETS	0.719	0.618	0.828	0.719	0.618	0.828	SUBCLONAL	1	TRUE	1	0.267438965758147	2		667	614	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430368	181430368	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	35	516	0	ENST00000325404.1:c.220C>T	p.Arg74Cys	p.R74C	ENST00000325404	NM_003106.3	74	Cgc/Tgc	1/1	0.226368141529921	4	FACETS	0.596	0.487	0.718			1	SUBCLONAL	1	TRUE	NA	0.267438965758147	4		516	557	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514402	149514402	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	58	573	1	ENST00000261799.4:c.542G>T	p.Gly181Val	p.G181V	ENST00000261799	NM_002609.3	181	gGt/gTt	4/23	0.235642758142043	4	FACETS	0.851	0.731	0.983	0.425	0.365	0.492	CLONAL	1	TRUE	2	0.267438965758147	4		574	646	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1272353	1272353	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554040129	NA	P-0016977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	127	850	0	ENST00000310581.5:c.2329G>A	p.Val777Met	p.V777M	ENST00000310581	NM_198253.2	777	Gtg/Atg	7/16	0.373976983226787	4	FACETS	0.9	0.815	0.99	0.45	0.407	0.495	CLONAL	1	TRUE	2	0.461016719764073	4		850	894	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0016981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	139	376	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.358151077962244	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.358151077962244	1		376	571	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332591	70332591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115711488	NA	P-0016981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	232	577	1	ENST00000373644.4:c.496C>T	p.Leu166Phe	p.L166F	ENST00000373644	NM_030625.2	166	Ctt/Ttt	2/12	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.358151077962244	2		578	1032	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476376	88476376	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	100	462	2	ENST00000360948.2:c.1756C>A	p.Gln586Lys	p.Q586K	ENST00000360948	NM_001012338.2	586	Cag/Aag	15/19	0.163811428969322	3	FACETS	0.77	0.687	0.859	0.257	0.229	0.287	INDETERMINATE	1	TRUE	0	0.358151077962244	3		464	855	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670492	134670492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	384	531	0	ENST00000398015.3:c.403C>T	p.Leu135Phe	p.L135F	ENST00000398015	NM_004441.4	135	Ctc/Ttc	3/16	0.352661522785116	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.358151077962244	3		531	1079	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0016981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	189	401	0	ENST00000269305.4:c.673-2A>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.358151077962244	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.358151077962244	1		401	643	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609011	43609011	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	172	415	0	ENST00000355710.3:c.1767C>A	p.Ser589Arg	p.S589R	ENST00000355710	NM_020975.4	589	agC/agA	10/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.358151077962244	2		415	693	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456555	32456555	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1253163678	NA	P-0016981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	16	58	0	ENST00000332351.3:c.337G>C	p.Ala113Pro	p.A113P	ENST00000332351	NM_024426.4	113	Gct/Cct	1/10	0.195195932791536	2	FACETS	0.638	0.475	0.83	0.319	0.237	0.415	INDETERMINATE	1	TRUE	0	0.358151077962244	2		58	140	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090428	77090428	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	69	254	0	ENST00000356341.3:c.297G>A	p.Met99Ile	p.M99I	ENST00000356341	NM_002576.4	99	atG/atA	4/15	0.195195932791536	2	FACETS	0.605	0.527	0.69	0.302	0.263	0.345	INDETERMINATE	1	TRUE	0	0.358151077962244	2		254	637	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435953	49435953	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	366	585	0	ENST00000301067.7:c.6028G>T	p.Glu2010Ter	p.E2010*	ENST00000301067	NM_003482.3	2010	Gag/Tag	28/54	0.263322015365956	3	FACETS	0.96	0.91	1	0.96	0.91	1	CLONAL	2	TRUE	1	0.358151077962244	3		585	1255	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244949	133244949	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	282	640	1	ENST00000320574.5:c.2166G>T	p.Arg722Ser	p.R722S	ENST00000320574	NM_006231.2	722	agG/agT	19/49	0.337768692634823	3	FACETS	1	0.993	1			1	CLONAL	1	TRUE	NA	0.358151077962244	3		641	1303	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912919	32912919	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	236	522	1	ENST00000380152.3:c.4427A>T	p.Asp1476Val	p.D1476V	ENST00000380152		1476	gAc/gTc	11/27	0.345932317013981	2	FACETS	0.925	0.868	0.985	0.925	0.868	0.985	CLONAL	2	TRUE	0	0.358151077962244	2		523	712	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609511	81609511	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	97	405	1	ENST00000298171.2:c.1109T>A	p.Leu370His	p.L370H	ENST00000298171	NM_000369.2	370	cTc/cAc	10/10	0.263322015365956	3	FACETS	0.832	0.741	0.928	0.416	0.37	0.464	CLONAL	1	TRUE	1	0.358151077962244	3		406	768	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18943071	18943071	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1252980053	NA	P-0016981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	354	486	0	ENST00000262803.5:c.53C>G	p.Thr18Arg	p.T18R	ENST00000262803	NM_002911.3	18	aCg/aGg	1/24	0.195195932791536	2	FACETS	0.96	0.911	1	0.96	0.911	1	INDETERMINATE	2	TRUE	0	0.358151077962244	2		486	1030	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99169286	99169286	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	335	575	1	ENST00000074304.5:c.1216C>T	p.Gln406Ter	p.Q406*	ENST00000074304	NM_001134224.1	406	Cag/Tag	15/26	0.352661522785116	3	FACETS	0.904	0.855	0.955	0.904	0.855	0.955	CLONAL	2	TRUE	1	0.358151077962244	3		576	1220	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026207	36026207	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	459	663	0	ENST00000358208.4:c.809T>A	p.Leu270Gln	p.L270Q	ENST00000358208		270	cTg/cAg	7/12	0.238212711583831	5	FACETS	0.837	0.798	0.876	0.837	0.798	0.876	CLONAL	3	TRUE	2	0.358151077962244	5		663	1570	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188233	10188233	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs104893831	NA	P-0016981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	375	638	0	ENST00000256474.2:c.376G>C	p.Asp126His	p.D126H	ENST00000256474	NM_000551.3	126	Gat/Cat	2/3	0.358151077962244	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.358151077962244	2		638	939	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136913	55136913	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	118	417	0	ENST00000257290.5:c.1235A>C	p.Gln412Pro	p.Q412P	ENST00000257290	NM_006206.4	412	cAa/cCa	8/23	0.163811428969322	3	FACETS	0.901	0.813	0.995	0.3	0.271	0.332	INDETERMINATE	1	TRUE	0	0.358151077962244	3		417	862	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55963922	55963922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	240	400	0	ENST00000263923.4:c.2521G>A	p.Gly841Ser	p.G841S	ENST00000263923	NM_002253.2	841	Ggc/Agc	18/30	0.163811428969322	3	FACETS	0.974	0.912	1	0.649	0.608	0.692	INDETERMINATE	2	TRUE	0	0.358151077962244	3		400	811	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176684042	176684042	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	398	678	2	ENST00000439151.2:c.4856G>T	p.Cys1619Phe	p.C1619F	ENST00000439151	NM_022455.4	1619	tGt/tTt	13/23	0.345932317013981	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.358151077962244	2		680	1024	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407593	407594	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0016981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	105	428	2	ENST00000380956.4:c.1351_1352delinsAT	p.Glu451Ile	p.E451I	ENST00000380956	NM_001195286.1	451	GAa/ATa	9/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.358151077962244	NA		430	807	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158636	26158636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	89	139	1	ENST00000289316.2:c.239G>A	p.Arg80His	p.R80H	ENST00000289316	NM_138720.2	80	cGc/cAc	1/2	0.238212711583831	5	FACETS	1	0.947	1	0.73	0.653	0.811	CLONAL	2	TRUE	2	0.358151077962244	5		140	349	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286863	33286863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	96	397	1	ENST00000374542.5:c.2074G>A	p.Gly692Ser	p.G692S	ENST00000374542	NM_001141970.1	692	Ggc/Agc	7/8	0.238212711583831	5	FACETS	0.822	0.73	0.919	0.274	0.243	0.307	CLONAL	1	TRUE	2	0.358151077962244	5		398	1003	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521853	157521853	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	259	344	0	ENST00000346085.5:c.4125T>A	p.His1375Gln	p.H1375Q	ENST00000346085	NM_020732.3	1375	caT/caA	18/20	0.315842353157646	2	FACETS	0.98	0.922	1	0.98	0.922	1	CLONAL	2	TRUE	0	0.358151077962244	2		344	738	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5070049	5070049	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	69	340	0	ENST00000381652.3:c.1638A>G	p.Ile546Met	p.I546M	ENST00000381652	NM_004972.3	546	atA/atG	12/25	0.358151077962244	1	FACETS	0.819	0.717	0.929	0.819	0.717	0.929	CLONAL	1	TRUE	0	0.358151077962244	1		340	386	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613672	100613672	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	305	248	0	ENST00000308731.7:c.907G>T	p.Gly303Cys	p.G303C	ENST00000308731	NM_000061.2	303	Ggt/Tgt	11/19	0.358151077962244	2	FACETS	0.998	0.951	1			1	CLONAL	3	TRUE	NA	0.358151077962244	2		248	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578281	7578281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	13	693	2	ENST00000269305.4:c.568C>T	p.Pro190Ser	p.P190S	ENST00000269305	NM_001126112.2	190	Cct/Tct	6/11	0.614728298729761	1	FACETS	0.047	0.033	0.064	0.047	0.033	0.064	SUBCLONAL	1	TRUE	0	0.631302987986966	1		695	601	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674348	86674348	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	33	325	1	ENST00000274376.6:c.2480C>T	p.Ser827Phe	p.S827F	ENST00000274376	NM_002890.2	827	tCt/tTt	18/25	0.211144274641429	3	FACETS	0.228	0.185	0.277	0.076	0.061	0.093	INDETERMINATE	1	TRUE	0	0.631302987986966	3		326	602	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0016982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	327	325	0	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	2	TRUE	NA	0.631302987986966	2		325	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057520005	NA	P-0016983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1300	65	749	0	ENST00000269305.4:c.820G>T	p.Val274Phe	p.V274F	ENST00000269305	NM_001126112.2	274	Gtt/Ttt	8/11	1	2	FACETS	0.595	0.514	0.684	0.595	0.514	0.684	SUBCLONAL	1	TRUE	1	0.16	2		749	1365	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	285	525	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	0.51599437293857	2		525	1034	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0016984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	255	178	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.51599437293857	2		178	820	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0016984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	129	356	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	1	2	FACETS	0.928	0.845	1	0.928	0.845	1	CLONAL	1	TRUE	1	0.51599437293857	2		356	539	SUCCESS
APC	324	MSKCC	GRCh37	5	112175328	112175328	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	110	323	0	ENST00000257430.4:c.4037C>A	p.Ser1346Ter	p.S1346*	ENST00000257430	NM_000038.5	1346	tCa/tAa	16/16	1	2	FACETS	0.923	0.834	1	0.923	0.834	1	CLONAL	1	TRUE	1	0.51599437293857	2		323	462	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186757	108186757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs864622251	NA	P-0016984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	271	678	1	ENST00000278616.4:c.6115G>A	p.Glu2039Lys	p.E2039K	ENST00000278616	NM_000051.3	2039	Gaa/Aaa	42/63	0.51599437293857	1	FACETS	0.975	0.919	1	0.975	0.919	1	CLONAL	1	TRUE	0	0.51599437293857	1		679	799	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799143	45799143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755653922	NA	P-0016984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	269	641	1	ENST00000450313.1:c.290G>A	p.Arg97Gln	p.R97Q	ENST00000450313	NM_012222.2	97	cGa/cAa	3/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.51599437293857	2		642	1012	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372224	55372224	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	40	544	1	ENST00000297316.4:c.914C>T	p.Ala305Val	p.A305V	ENST00000297316	NM_022454.3	305	gCg/gTg	2/2	1	2	FACETS	0.264	0.219	0.315	0.264	0.219	0.315	SUBCLONAL	1	TRUE	1	0.51599437293857	2		545	587	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759665	133759665	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	56	617	0	ENST00000318560.5:c.1988G>T	p.Ser663Ile	p.S663I	ENST00000318560	NM_005157.4	663	aGc/aTc	11/11	1	2	FACETS	0.247	0.211	0.287	0.247	0.211	0.287	SUBCLONAL	1	TRUE	1	0.51599437293857	2		617	879	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0016985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	228	295	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.579270663056633	4	FACETS	0.957	0.899	1	0.957	0.899	1	CLONAL	2	TRUE	2	0.713232626265512	4		295	572	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	230	485	3	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	0.95	0.89	1	0.95	0.89	1	CLONAL	1	TRUE	1	0.713232626265512	2		488	679	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874263	155874263	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1557960039	NA	P-0016985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	1106	527	0	ENST00000368323.3:c.268A>G	p.Met90Val	p.M90V	ENST00000368323	NM_006912.5	90	Atg/Gtg	5/6	0.713232626265512	7	FACETS	0.941	0.92	0.963	0.941	0.92	0.963	CLONAL	5	TRUE	2	0.713232626265512	7		527	1834	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0016987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	115	178	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.417150785871691	4	FACETS	0.529	0.475	0.586	0.265	0.237	0.293	SUBCLONAL	1	TRUE	2	0.663245279277972	4		178	1090	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725021	49725021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs114429531	NA	P-0016987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	165	514	0	ENST00000449682.2:c.323G>A	p.Arg108His	p.R108H	ENST00000449682	NM_020998.3	108	cGt/cAt	3/18	0.417150785871691	4	FACETS	1	0.967	1	0.547	0.503	0.593	CLONAL	1	TRUE	2	0.663245279277972	4		514	756	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577572	7577572	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882004	NA	P-0016987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	429	539	0	ENST00000269305.4:c.709A>G	p.Met237Val	p.M237V	ENST00000269305	NM_001126112.2	237	Atg/Gtg	7/11	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	2	TRUE	NA	0.663245279277972	2		539	644	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640152	3640152	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	477	892	1	ENST00000294008.3:c.3487C>A	p.Leu1163Ile	p.L1163I	ENST00000294008	NM_032444.2	1163	Cta/Ata	12/15	0.325257553431341	3	FACETS	1	0.995	1	0.66	0.631	0.69	INDETERMINATE	1	TRUE	1	0.663245279277972	3		893	1450	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0016988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	65	348	1	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.747	0.648	0.854	0.747	0.648	0.854	SUBCLONAL	1	TRUE	1	0.32	2		349	544	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023830	27023831	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0016988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	57	499	0	ENST00000324856.7:c.941dup	p.Asp315ArgfsTer85	p.D315Rfs*85	ENST00000324856	NM_006015.4	312	-/G	1/20	0.3	1	FACETS	0.568	0.487	0.656	0.568	0.487	0.656	SUBCLONAL	1	TRUE	0	0.32	1		499	527	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099097	27099097	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	43	644	0	ENST00000324856.7:c.3513del	p.Gln1172ArgfsTer8	p.Q1172Rfs*8	ENST00000324856	NM_006015.4	1171	agT/ag	13/20	0.3	1	FACETS	0.311	0.26	0.369	0.311	0.26	0.369	SUBCLONAL	1	TRUE	0	0.32	1		644	725	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652225	36652226	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0016989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	58	503	0	ENST00000244741.5:c.349dup	p.Cys117LeufsTer12	p.C117Lfs*12	ENST00000244741	NM_000389.4	116	tct/tcTt	2/3	1	2	FACETS	0.49	0.419	0.567	0.49	0.419	0.567	SUBCLONAL	1	TRUE	1	0.264770229593152	2		503	895	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7152788	7152788	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1540	108	805	0	ENST00000302850.5:c.2180C>T	p.Ser727Leu	p.S727L	ENST00000302850	NM_000208.2	727	tCg/tTg	10/22	1	2	FACETS	0.495	0.442	0.552	0.495	0.442	0.552	SUBCLONAL	1	TRUE	1	0.264770229593152	2		805	1648	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790828	89790829	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0016989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	439	772	0	ENST00000336032.3:c.216_217del	p.Ala74SerfsTer133	p.A74Sfs*133	ENST00000336032	NM_006813.2	72	cCT/c	1/2	1	2	FACETS	0.97	0.927	1	1	0.997	1	CLONAL	3	TRUE	1	0.264770229593152	2		772	1139	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28607300	28607300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs527560658	NA	P-0016990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	222	430	1	ENST00000253063.3:c.1430G>A	p.Arg477His	p.R477H	ENST00000253063	NM_031459.4	477	cGc/cAc	10/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.611712191776963	2		431	693	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896984	28896984	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	247	568	0	ENST00000282397.4:c.2896T>A	p.Phe966Ile	p.F966I	ENST00000282397	NM_002019.4	966	Ttt/Att	21/30	1	2	FACETS	0.997	0.935	1	0.997	0.935	1	CLONAL	1	TRUE	1	0.611712191776963	2		568	810	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577144	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs879253942	NA	P-0016991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1324	121	690	0	ENST00000269305.4:c.794T>C	p.Leu265Pro	p.L265P	ENST00000269305	NM_001126112.2	265	cTg/cCg	8/11	1	2	FACETS	0.523	0.471	0.579	0.523	0.471	0.579	SUBCLONAL	1	TRUE	1	0.32	2		690	1445	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934154	48934164	+	stop_gained,protein_altering_variant	Nonsense_Mutation	DEL	GGAAGTATTAC	GGAAGTATTAC	AAGATGAA	novel	NA	P-0016991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	147	475	3	ENST00000267163.4:c.609_619delinsAAGATGAA	p.Glu204_Gln207delinsArgTer	p.E204_Q207delinsR*	ENST00000267163	NM_000321.2	203	ggGGAAGTATTACaa/ggAAGATGAAaa	7/27	0.3	3	FACETS	0.96	0.875	1	0.48	0.437	0.525	CLONAL	1	TRUE	1	0.32	3		478	1110	SUCCESS
BLM	641	MSKCC	GRCh37	15	91308599	91308599	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1282	103	647	0	ENST00000355112.3:c.2148G>C	p.Leu716Phe	p.L716F	ENST00000355112	NM_000057.2	716	ttG/ttC	9/22	0.255125419346696	3	FACETS	0.539	0.481	0.602	0.27	0.24	0.301	SUBCLONAL	1	TRUE	1	0.32	3		647	1385	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857818	9857818	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	45	541	0	ENST00000330684.3:c.3583G>C	p.Asp1195His	p.D1195H	ENST00000330684	NM_001134407.1	1195	Gac/Cac	13/13	1	2	FACETS	0.334	0.279	0.394	0.334	0.279	0.394	SUBCLONAL	1	TRUE	1	0.32	2		541	843	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577144	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs879253942	NA	P-0016991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	161	690	0	ENST00000269305.4:c.794T>C	p.Leu265Pro	p.L265P	ENST00000269305	NM_001126112.2	265	cTg/cCg	8/11	0.568315361236733	2	FACETS	0.95	0.892	1	0.95	0.892	1	CLONAL	2	TRUE	0	0.603041390212984	2		690	281	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934154	48934164	+	stop_gained,protein_altering_variant	Nonsense_Mutation	DEL	GGAAGTATTAC	GGAAGTATTAC	AAGATGAA	novel	NA	P-0016991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	388	475	3	ENST00000267163.4:c.609_619delinsAAGATGAA	p.Glu204_Gln207delinsArgTer	p.E204_Q207delinsR*	ENST00000267163	NM_000321.2	203	ggGGAAGTATTACaa/ggAAGATGAAaa	7/27	0.613115124845914	4	FACETS	1	0.991	1	0.825	0.794	0.856	CLONAL	3	TRUE	0	0.603041390212984	4		478	625	SUCCESS
BLM	641	MSKCC	GRCh37	15	91308599	91308599	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	219	647	0	ENST00000355112.3:c.2148G>C	p.Leu716Phe	p.L716F	ENST00000355112	NM_000057.2	716	ttG/ttC	9/22	0.603041390212984	5	FACETS	0.866	0.807	0.926	0.577	0.538	0.617	CLONAL	2	TRUE	2	0.603041390212984	5		647	799	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857818	9857818	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	48	541	0	ENST00000330684.3:c.3583G>C	p.Asp1195His	p.D1195H	ENST00000330684	NM_001134407.1	1195	Gac/Cac	13/13	0.613115124845914	2	FACETS	1	0.873	1	0.507	0.437	0.581	CLONAL	1	TRUE	0	0.603041390212984	2		541	157	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188296	32188296	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561687277	NA	P-0016991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	48	878	2	ENST00000375023.3:c.1045G>A	p.Gly349Ser	p.G349S	ENST00000375023	NM_004557.3	349	Ggc/Agc	6/30	0.613115124845914	4	FACETS	0.713	0.605	0.831	0.238	0.201	0.277	SUBCLONAL	1	TRUE	1	0.603041390212984	4		880	358	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719924	18719924	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1403036730	NA	P-0016991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	71	712	0	ENST00000266497.5:c.3821A>G	p.His1274Arg	p.H1274R	ENST00000266497		1274	cAc/cGc	27/31	0.613115124845914	4	FACETS	0.51	0.445	0.581			1	SUBCLONAL	1	TRUE	NA	0.603041390212984	4		712	740	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120903	115120903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	41	478	0	ENST00000257566.3:c.103G>A	p.Gly35Ser	p.G35S	ENST00000257566	NM_016569.3	35	Ggt/Agt	1/8	0.219774371815776	0	FACETS	0.355	0.301	0.413			1	INDETERMINATE	1	TRUE	0	0.603041390212984	0		478	152	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285164	198285164	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	81	553	0	ENST00000335508.6:c.403C>G	p.Pro135Ala	p.P135A	ENST00000335508	NM_012433.2	135	Cct/Gct	4/25	0.613115124845914	3	FACETS	0.557	0.491	0.628			1	SUBCLONAL	1	TRUE	NA	0.603041390212984	3		553	628	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129456	152129456	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs185717042	NA	P-0016991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	45	435	0	ENST00000206249.3:c.409A>C	p.Ser137Arg	p.S137R	ENST00000206249	NM_000125.3	137	Agc/Cgc	1/8	0.603041390212984	7	FACETS	0.922	0.776	1	0.154	0.129	0.181	CLONAL	1	TRUE	1	0.603041390212984	7		435	406	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	136	408	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.961	0.874	1	0.961	0.874	1	CLONAL	1	TRUE	1	0.351597770176561	2		408	805	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0016992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	181	593	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.351597770176561	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.351597770176561	1		593	817	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988801	41988801	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	165	809	0	ENST00000219905.7:c.1596del	p.Lys532AsnfsTer15	p.K532Nfs*15	ENST00000219905	NM_001164273.1	531	agA/ag	3/24	1	2	FACETS	0.95	0.872	1	0.95	0.872	1	CLONAL	1	TRUE	1	0.351597770176561	2		809	988	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604664	48604664	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	114	422	0	ENST00000342988.3:c.1486del	p.Arg496ValfsTer8	p.R496Vfs*8	ENST00000342988	NM_005359.5	496	Cgt/gt	12/12	0.351597770176561	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.351597770176561	1		422	494	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251330	99251330	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	244	597	0	ENST00000268035.6:c.634C>T	p.Gln212Ter	p.Q212*	ENST00000268035	NM_000875.3	212	Cag/Tag	2/21	NA	2	FACETS	0.891	0.838	0.945			1	INDETERMINATE	1	FALSE	NA	0.85022417974769	2		597	644	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204864	NA	P-0016994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	288	560	3	ENST00000371953.3:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000371953	NM_000314.4	171	Cag/Tag	6/9	0.706968229038631	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.706968229038631	1		563	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	269	761	0	ENST00000269305.4:c.166G>T	p.Glu56Ter	p.E56*	ENST00000269305	NM_001126112.2	56	Gaa/Taa	4/11	0.706968229038631	1	FACETS	0.988	0.939	1	0.988	0.939	1	CLONAL	1	TRUE	0	0.706968229038631	1		761	498	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0016994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	182	422	1	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.706968229038631	2		423	470	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540380	187540380	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202097333	NA	P-0016994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	29	449	1	ENST00000441802.2:c.7360C>T	p.Arg2454Trp	p.R2454W	ENST00000441802	NM_005245.3	2454	Cgg/Tgg	10/27	NA	2	FACETS	0.151	0.12	0.185			1	INDETERMINATE	1	TRUE	NA	0.706968229038631	2		450	545	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120469178	120469178	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	331	1052	0	ENST00000256646.2:c.3949G>A	p.Gly1317Arg	p.G1317R	ENST00000256646	NM_024408.3	1317	Ggg/Agg	24/34	1	2	FACETS	0.687	0.648	0.727	0.687	0.648	0.727	SUBCLONAL	1	TRUE	1	0.706968229038631	2		1052	1363	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195752	102195752	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	470	413	0	ENST00000263464.3:c.512C>G	p.Ala171Gly	p.A171G	ENST00000263464	NM_001165.4	171	gCc/gGc	2/9	0.706968229038631	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.706968229038631	3		413	870	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947599	48947599	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	299	687	0	ENST00000267163.4:c.1187del	p.Pro396LeufsTer5	p.P396Lfs*5	ENST00000267163	NM_000321.2	396	Cct/ct	12/27	0.513998628112363	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.706968229038631	1		687	536	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533093	63533093	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs750354919	NA	P-0016994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	174	488	0	ENST00000307078.5:c.1801G>T	p.Gly601Cys	p.G601C	ENST00000307078	NM_004655.3	601	Ggc/Tgc	7/11	NA	2	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.706968229038631	2		488	437	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400628	56400628	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0016994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	135	240	2	ENST00000348428.3:c.1223-1G>T		p.X408_splice	ENST00000348428	NM_006785.3	408			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.706968229038631	2		242	363	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266990	18266990	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	112	267	0	ENST00000222254.8:c.301C>A	p.Arg101Ser	p.R101S	ENST00000222254	NM_005027.3	101	Cgt/Agt	2/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.706968229038631	2		267	280	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198264842	198264842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	62	831	0	ENST00000335508.6:c.2950G>A	p.Glu984Lys	p.E984K	ENST00000335508	NM_012433.2	984	Gaa/Aaa	20/25	NA	2	FACETS	0.193	0.166	0.223			1	INDETERMINATE	1	TRUE	NA	0.706968229038631	2		831	909	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460450	149460450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	116	574	1	ENST00000286301.3:c.187G>A	p.Asp63Asn	p.D63N	ENST00000286301	NM_005211.3	63	Gat/Aat	3/22	1	2	FACETS	0.533	0.481	0.587	0.533	0.481	0.587	SUBCLONAL	1	TRUE	1	0.706968229038631	2		575	616	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481617	20481617	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	165	439	0	ENST00000346618.3:c.686A>T	p.His229Leu	p.H229L	ENST00000346618	NM_001949.4	229	cAc/cTc	3/7	0.706968229038631	3	FACETS	0.847	0.779	0.917			1	CLONAL	1	TRUE	NA	0.706968229038631	3		439	746	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	448	500	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.519438947369443	2	FACETS	0.874	0.842	0.907	0.874	0.842	0.907	CLONAL	2	TRUE	0	0.637180733516295	2		500	804	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0017000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	335	436	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.637180733516295	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.637180733516295	1		436	658	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936083	178936083	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519927	NA	P-0017000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	505	640	0	ENST00000263967.3:c.1625A>C	p.Glu542Ala	p.E542A	ENST00000263967	NM_006218.2	542	gAa/gCa	10/21	0.266588054737971	3	FACETS	1	0.992	1	0.73	0.703	0.756	INDETERMINATE	2	TRUE	0	0.637180733516295	3		640	955	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112767310	112767310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	62	655	0	ENST00000369452.4:c.1183C>T	p.Pro395Ser	p.P395S	ENST00000369452	NM_007373.3	395	Ccc/Tcc	6/9	1	2	FACETS	0.222	0.191	0.256	0.222	0.191	0.256	SUBCLONAL	1	TRUE	1	0.637180733516295	2		655	878	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185050	123185050	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	217	759	0	ENST00000218089.9:c.1101del	p.Phe367LeufsTer12	p.F367Lfs*12	ENST00000218089	NM_001042749.1	366	cTt/ct	12/35	0.178502317914582	0	FACETS	0.268	0.249	0.288			1	INDETERMINATE	1	TRUE	0	0.637180733516295	0		759	921	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0017001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	257	470	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.281090494563518	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.25	3		470	1009	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276653	15276653	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0017001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	51	662	0	ENST00000263388.2:c.5612C>G	p.Ser1871Ter	p.S1871*	ENST00000263388	NM_000435.2	1871	tCa/tGa	30/33	0.168896827448009	3	FACETS	0.452	0.382	0.529	0.226	0.191	0.265	SUBCLONAL	1	TRUE	1	0.25	3		662	1016	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032566	47032566	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	210	559	0	ENST00000377604.3:c.472G>T	p.Glu158Ter	p.E158*	ENST00000377604	NM_001204468.1	158	Gag/Tag	5/24	0.168896827448009	3	FACETS	0.956	0.888	1	0.956	0.888	1	CLONAL	2	TRUE	1	0.25	3		559	988	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911787	32911787	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	212	759	2	ENST00000380152.3:c.3295T>A	p.Ser1099Thr	p.S1099T	ENST00000380152		1099	Tca/Aca	11/27	1	2	FACETS	0.798	0.741	0.857	1	0.992	1	SUBCLONAL	2	TRUE	1	0.25	2		761	1063	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495704	72495705	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTC	novel	NA	P-0017001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	53	481	0	ENST00000477973.2:c.363_365dup	p.Arg122dup	p.R122dup	ENST00000477973	NM_012234.5	122	aac/aGAAac	1/4	1	2	FACETS	0.596	0.507	0.693	0.596	0.507	0.693	SUBCLONAL	1	TRUE	1	0.25	2		481	712	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434558	140434558	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs555976452	NA	P-0017001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	38	254	0	ENST00000288602.6:c.2140A>G	p.Ile714Val	p.I714V	ENST00000288602	NM_004333.4	714	Att/Gtt	18/18	NA	2	FACETS	1	0.856	1			1	INDETERMINATE	1	TRUE	NA	0.25	2		254	294	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	121	301	4				ENST00000310581	NM_198253.2	-/1132			0.346996762458631	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.346996762458631	1		305	456	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0017003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	289	308	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.346996762458631	3	FACETS	0.976	0.92	1	0.976	0.92	1	CLONAL	2	TRUE	1	0.346996762458631	3		308	1001	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709162	117709162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867987684	NA	P-0017003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	146	442	0	ENST00000368508.3:c.1795G>A	p.Glu599Lys	p.E599K	ENST00000368508	NM_002944.2	599	Gaa/Aaa	13/43	0.312337882998201	2	FACETS	1	0.983	1	0.65	0.595	0.708	CLONAL	1	TRUE	0	0.346996762458631	2		442	647	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561151	9561151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	135	331	0	ENST00000353224.5:c.631G>A	p.Glu211Lys	p.E211K	ENST00000353224	NM_177990.2	211	Gaa/Aaa	4/10	0.342558122483887	3	FACETS	0.82	0.748	0.894	0.82	0.748	0.894	CLONAL	2	TRUE	1	0.346996762458631	3		331	557	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306677	41306677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs724159835	NA	P-0017003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	229	554	3	ENST00000373198.4:c.982C>T	p.Arg328Cys	p.R328C	ENST00000373198	NM_133170.3	328	Cgc/Tgc	7/32	0.342558122483887	3	FACETS	0.819	0.764	0.875	0.819	0.764	0.875	CLONAL	2	TRUE	1	0.346996762458631	3		557	946	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0017003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	77	230	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.346996762458631	1	FACETS	0.845	0.745	0.952	0.845	0.745	0.952	CLONAL	1	TRUE	0	0.346996762458631	1		230	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578196	7578196	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555525743	NA	P-0017003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	415	837	0	ENST00000269305.4:c.653T>G	p.Val218Gly	p.V218G	ENST00000269305	NM_001126112.2	218	gTg/gGg	6/11	0.346996762458631	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.346996762458631	2		837	1196	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729713	41729713	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	94	496	0	ENST00000242208.4:c.816G>T	p.Lys272Asn	p.K272N	ENST00000242208	NM_002192.2	272	aaG/aaT	3/3	0.346996762458631	3	FACETS	0.706	0.628	0.791	0.353	0.314	0.396	SUBCLONAL	1	TRUE	1	0.346996762458631	3		496	900	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11181418	11181418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761004954	NA	P-0017003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	270	662	0	ENST00000361445.4:c.6818C>T	p.Pro2273Leu	p.P2273L	ENST00000361445	NM_004958.3	2273	cCg/cTg	49/58	NA	2	FACETS	0.801	0.752	0.85			1	INDETERMINATE	2	TRUE	NA	0.346996762458631	2		662	972	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439869	51439869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	105	248	0	ENST00000262662.1:c.434G>A	p.Arg145Lys	p.R145K	ENST00000262662		145	aGg/aAg	4/4	0.159400920329939	2	FACETS	0.831	0.752	0.914	0.831	0.752	0.914	INDETERMINATE	2	TRUE	0	0.346996762458631	2		248	364	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414302	32414302	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0017003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	197	368	0	ENST00000332351.3:c.1250-1G>A		p.X417_splice	ENST00000332351	NM_024426.4	417			0.346996762458631	2	FACETS	0.917	0.854	0.982	0.917	0.854	0.982	CLONAL	2	TRUE	0	0.346996762458631	2		368	619	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945648	71945648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	273	509	0	ENST00000298229.2:c.2404C>T	p.Gln802Ter	p.Q802*	ENST00000298229	NM_001567.3	802	Cag/Tag	21/28	0.346996762458631	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.346996762458631	2		509	750	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629065	14629066	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0017003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	96	416	0	ENST00000254322.2:c.96_97delinsAT	p.His32_Pro33delinsGlnSer	p.H32_P33delinsQS	ENST00000254322	NM_006145.1	32	caCCcg/caATcg	1/3	1	2	FACETS	0.857	0.764	0.955	0.857	0.764	0.955	CLONAL	1	TRUE	1	0.346996762458631	2		416	646	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950309	17950309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	177	627	0	ENST00000458235.1:c.1418C>T	p.Ser473Phe	p.S473F	ENST00000458235	NM_000215.3	473	tCc/tTc	10/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.346996762458631	2		627	917	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157053	106157053	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778729965	NA	P-0017003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	83	666	0	ENST00000380013.4:c.1954C>T	p.Gln652Ter	p.Q652*	ENST00000380013	NM_001127208.2	652	Cag/Tag	3/11	0.202698652484258	1	FACETS	0.459	0.404	0.518	0.459	0.404	0.518	INDETERMINATE	1	TRUE	0	0.346996762458631	1		666	861	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860493	151860493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1380777672	NA	P-0017003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	311	482	1	ENST00000262189.6:c.10169C>T	p.Pro3390Leu	p.P3390L	ENST00000262189	NM_170606.2	3390	cCc/cTc	43/59	0.346996762458631	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.346996762458631	3		483	980	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	174	301	4				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.460426670828423	2		305	696	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0017004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	297	591	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.433973940028188	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.460426670828423	1		591	945	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259400	16259400	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	247	425	0	ENST00000375759.3:c.6665T>G	p.Ile2222Ser	p.I2222S	ENST00000375759	NM_015001.2	2222	aTc/aGc	11/15	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.460426670828423	2		425	778	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317619	163317619	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	102	728	0	ENST00000271452.3:c.1015A>C	p.Asn339His	p.N339H	ENST00000271452	NM_145697.2	339	Aat/Cat	12/14	0.229588487554485	2	FACETS	0.462	0.412	0.515	0.231	0.206	0.258	INDETERMINATE	1	TRUE	0	0.460426670828423	2		728	959	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662496	227662496	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	123	347	0	ENST00000305123.5:c.959A>C	p.Lys320Thr	p.K320T	ENST00000305123	NM_005544.2	320	aAg/aCg	1/2	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.460426670828423	2		347	485	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181349	185181351	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0017004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	217	499	0	ENST00000265026.3:c.1295_1297del	p.Glu432del	p.E432del	ENST00000265026	NM_004721.4	430	agAGAa/aga	8/14	0.244279591918215	1	FACETS	0.815	0.759	0.873	0.815	0.759	0.873	INDETERMINATE	1	TRUE	0	0.460426670828423	1		499	890	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965586	93965586	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs372024057	NA	P-0017004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	311	679	1	ENST00000369303.4:c.2342G>T	p.Arg781Leu	p.R781L	ENST00000369303	NM_004440.3	781	cGa/cTa	13/17	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.460426670828423	2		680	1227	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0017007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1258	180	290	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.990440383786403	3	FACETS	0.378	0.347	0.41	0.189	0.173	0.205	SUBCLONAL	1	TRUE	1	0.990440383786403	3		290	1438	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105907	27105907	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	423	457	0	ENST00000324856.7:c.5518G>A	p.Gly1840Ser	p.G1840S	ENST00000324856	NM_006015.4	1840	Ggc/Agc	20/20	1	2	FACETS	0.964	0.924	1	0.964	0.924	1	CLONAL	1	TRUE	1	0.990440383786403	2		457	886	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104264079	104264081	+	inframe_deletion	In_Frame_Del	DEL	TCG	TCG	-	novel	NA	P-0017007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	687	826	0	ENST00000369902.3:c.172_174del	p.Val58del	p.V58del	ENST00000369902	NM_016169.3	57	aTCGtc/atc	1/12	1	2	FACETS	0.957	0.926	0.989	0.957	0.926	0.989	CLONAL	1	TRUE	1	0.990440383786403	2		826	1449	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421528	32421528	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	456	478	0	ENST00000332351.3:c.1064G>T	p.Arg355Ile	p.R355I	ENST00000332351	NM_024426.4	355	aGa/aTa	6/10	1	2	FACETS	0.957	0.918	0.996	0.957	0.918	0.996	CLONAL	1	TRUE	1	0.990440383786403	2		478	962	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425668	49425668	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	403	526	0	ENST00000301067.7:c.12820C>G	p.Leu4274Val	p.L4274V	ENST00000301067	NM_003482.3	4274	Ctc/Gtc	39/54	1	2	FACETS	0.884	0.844	0.923	0.884	0.844	0.923	CLONAL	1	TRUE	1	0.990440383786403	2		526	921	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112581	115112581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	671	929	2	ENST00000257566.3:c.1159C>T	p.Pro387Ser	p.P387S	ENST00000257566	NM_016569.3	387	Ccc/Tcc	7/8	1	2	FACETS	0.889	0.858	0.92	0.889	0.858	0.92	CLONAL	1	TRUE	1	0.990440383786403	2		931	1524	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626689	28626689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	413	439	0	ENST00000241453.7:c.607G>A	p.Gly203Arg	p.G203R	ENST00000241453	NM_004119.2	203	Ggg/Agg	5/24	0.977184506693653	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.990440383786403	1		439	420	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947536	48947537	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	CTAGGACTGTTATGAACACTATCCAA	novel	NA	P-0017007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	408	754	0	ENST00000267163.4:c.1128-3_1150dup		p.X376_splice	ENST00000267163	NM_000321.2	376			0.963311235666837	1	FACETS	0.604	0.581	0.626	0.604	0.581	0.626	SUBCLONAL	1	TRUE	0	0.990440383786403	1		754	689	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781408	3781408	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	447	566	0	ENST00000262367.5:c.4957G>T	p.Asp1653Tyr	p.D1653Y	ENST00000262367	NM_004380.2	1653	Gac/Tac	30/31	1	2	FACETS	0.923	0.885	0.961	0.923	0.885	0.961	CLONAL	1	TRUE	1	0.990440383786403	2		566	978	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782144	NA	P-0017007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	689	739	0	ENST00000269305.4:c.473G>C	p.Arg158Pro	p.R158P	ENST00000269305	NM_001126112.2	158	cGc/cCc	5/11	0.977184506693653	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.990440383786403	1		739	700	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617530	158617530	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	463	517	1	ENST00000263640.3:c.1126G>T	p.Val376Leu	p.V376L	ENST00000263640	NM_001105.4	376	Gtg/Ttg	9/11	1	2	FACETS	0.93	0.892	0.968	0.93	0.892	0.968	CLONAL	1	TRUE	1	0.990440383786403	2		518	1005	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133521	55133521	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	600	761	0	ENST00000257290.5:c.825G>T	p.Leu275Phe	p.L275F	ENST00000257290	NM_006206.4	275	ttG/ttT	6/23	1	2	FACETS	0.94	0.906	0.974	0.94	0.906	0.974	CLONAL	1	TRUE	1	0.990440383786403	2		761	1289	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35860980	35860980	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	386	379	0	ENST00000303115.3:c.109G>C	p.Asp37His	p.D37H	ENST00000303115	NM_002185.3	37	Gac/Cac	2/8	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.990440383786403	2		379	739	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43749815	43749815	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	359	468	0	ENST00000523873.1:c.668G>T	p.Arg223Leu	p.R223L	ENST00000523873		223	cGt/cTt	7/8	0.990440383786403	3	FACETS	0.891	0.845	0.939	0.446	0.422	0.47	CLONAL	1	TRUE	1	0.990440383786403	3		468	1216	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876985	151876985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	388	471	0	ENST00000262189.6:c.7376C>T	p.Pro2459Leu	p.P2459L	ENST00000262189	NM_170606.2	2459	cCa/cTa	37/59	1	2	FACETS	0.926	0.885	0.967	0.926	0.885	0.967	CLONAL	1	TRUE	1	0.990440383786403	2		471	846	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033191	69033191	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	619	764	0	ENST00000288368.4:c.3631C>A	p.Pro1211Thr	p.P1211T	ENST00000288368	NM_024870.2	1211	Cca/Aca	30/40	0.977184506693653	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.990440383786403	1		764	624	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986497	36986498	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	845	890	0	ENST00000354822.5:c.1191_1192insA	p.Gly398ArgfsTer41	p.G398Rfs*41	ENST00000354822	NM_001079668.2	397	-/A	3/3	1	2	FACETS	0.965	0.936	0.993	0.965	0.936	0.993	CLONAL	1	TRUE	1	0.990440383786403	2		890	1769	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0017008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	16	525	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.562	0.413	0.74	0.562	0.413	0.74	SUBCLONAL	1	TRUE	1	0.11	2		525	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0017008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	27	632	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.652	0.517	0.808	0.652	0.517	0.808	SUBCLONAL	1	TRUE	1	0.11	2		634	753	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0017008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	18	411	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.96	0.722	1	0.96	0.722	1	CLONAL	1	TRUE	1	0.11	2		411	341	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302604	15302604	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115836330	NA	P-0017008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	33	883	7	ENST00000263388.2:c.754G>A	p.Val252Met	p.V252M	ENST00000263388	NM_000435.2	252	Gtg/Atg	5/33	1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	1	0.11	2		890	591	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0017010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	153	290	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.208431498392596	4	FACETS	1	0.985	1	0.447	0.41	0.487	INDETERMINATE	1	TRUE	1	0.441871794238342	4		290	744	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256235	16256236	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0017010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	337	647	0	ENST00000375759.3:c.3502_3503del	p.Ser1168LeufsTer10	p.S1168Lfs*10	ENST00000375759	NM_015001.2	1167	cAG/c	11/15	0.439771465711546	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.441871794238342	2		647	733	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117731	108117732	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTATATGATCTGCTAGTGAATGAGATAAGTCATATAGGAAGTAGAGGAAAGTA	novel	NA	P-0017010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	29	373	0	ENST00000278616.4:c.945_997dup	p.Ser333TyrfsTer5	p.S333Yfs*5	ENST00000278616	NM_000051.3	314	-/TTATATGATCTGCTAGTGAATGAGATAAGTCATATAGGAAGTAGAGGAAAGTA	8/63	0.441871794238342	1	FACETS	0.256	0.205	0.314	0.256	0.205	0.314	SUBCLONAL	1	TRUE	0	0.441871794238342	1		373	399	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445485	49445485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371225040	NA	P-0017010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	146	704	2	ENST00000301067.7:c.1981C>T	p.Arg661Cys	p.R661C	ENST00000301067	NM_003482.3	661	Cgc/Tgc	10/54	0.441871794238342	4	FACETS	1	0.916	1	0.335	0.305	0.366	CLONAL	1	TRUE	1	0.441871794238342	4		706	949	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559155	29559155	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	36	444	0	ENST00000356175.3:c.3262G>A	p.Glu1088Lys	p.E1088K	ENST00000356175	NM_000267.3	1088	Gaa/Aaa	25/57	0.441871794238342	2	FACETS	0.286	0.235	0.344	0.143	0.117	0.172	SUBCLONAL	1	TRUE	0	0.441871794238342	2		444	569	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021835	69021835	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	364	498	0	ENST00000288368.4:c.3123G>T	p.Glu1041Asp	p.E1041D	ENST00000288368	NM_024870.2	1041	gaG/gaT	25/40	0.275571939451237	5	FACETS	0.87	0.826	0.914	0.87	0.826	0.914	CLONAL	3	TRUE	2	0.441871794238342	5		498	1050	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607402	46607402	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	294	583	0	ENST00000263734.3:c.1591C>T	p.Pro531Ser	p.P531S	ENST00000263734	NM_001430.4	531	Ccc/Tcc	12/16	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		583	1117	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881002	37881003	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCTCCCCA	rs397516982	NA	P-0017013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	287	732	0	ENST00000269571.5:c.2332_2340dup	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	-/GGCTCCCCA	20/27	0.134013913102623	9	FACETS	0.918	0.863	0.975	0.918	0.863	0.975	CLONAL	6	FALSE	3	0.134013913102623	9		732	1142	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120794	94120794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs570778929	NA	P-0017013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	54	543	0	ENST00000369303.4:c.257G>A	p.Arg86Gln	p.R86Q	ENST00000369303	NM_004440.3	86	cGg/cAg	3/17	0.134013913102623	5	FACETS	1	0.957	1	0.454	0.387	0.528	CLONAL	1	FALSE	2	0.134013913102623	5		543	710	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912291	32912291	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1191600785	NA	P-0017013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	36	556	0	ENST00000380152.3:c.3799G>A	p.Asp1267Asn	p.D1267N	ENST00000380152		1267	Gat/Aat	11/27	0.134013913102623	5	FACETS	1	0.929	1	0.428	0.352	0.515	CLONAL	1	FALSE	2	0.134013913102623	5		556	502	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562606	95562606	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	40	376	0	ENST00000393063.1:c.4651G>C	p.Glu1551Gln	p.E1551Q	ENST00000393063	NM_030621.3	1551	Gag/Cag	24/28	0.134013913102623	6	FACETS	1	0.946	1	0.461	0.383	0.549	CLONAL	1	FALSE	3	0.134013913102623	6		376	547	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448352	56448352	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	57	748	0	ENST00000407977.2:c.295C>G	p.Leu99Val	p.L99V	ENST00000407977		99	Ctg/Gtg	3/10	0.134013913102623	9	FACETS	1	0.93	1	0.192	0.164	0.223	CLONAL	1	FALSE	3	0.134013913102623	9		748	1085	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559255	141559255	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	71	649	1	ENST00000220592.5:c.1546C>T	p.Gln516Ter	p.Q516*	ENST00000220592	NM_012154.3	516	Cag/Tag	12/19	0.0821320426349332	3	FACETS	0.786	0.686	0.895	0.786	0.686	0.895	SUBCLONAL	2	FALSE	1	0.134013913102623	3		650	719	SUCCESS
AR	367	MSKCC	GRCh37	X	66766208	66766208	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	65	380	0	ENST00000374690.3:c.1220G>C	p.Arg407Pro	p.R407P	ENST00000374690	NM_000044.3	407	cGc/cCc	1/8	0.126260517879483	4	FACETS	0.924	0.804	1	0.924	0.804	1	CLONAL	3	FALSE	1	0.134013913102623	4		380	397	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0017015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	201	330	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.480521037605115	2		330	777	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0017015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	108	695	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.194535106986771	1	FACETS	0.338	0.302	0.376	0.338	0.302	0.376	INDETERMINATE	1	TRUE	0	0.480521037605115	1		695	1011	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0017015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	77	533	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.431	0.378	0.489	0.431	0.378	0.489	SUBCLONAL	1	TRUE	1	0.480521037605115	2		533	743	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163720	32163720	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253487294	NA	P-0017015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	31	420	1	ENST00000375023.3:c.5506G>A	p.Glu1836Lys	p.E1836K	ENST00000375023	NM_004557.3	1836	Gag/Aag	30/30	1	2	FACETS	0.21	0.169	0.257	0.21	0.169	0.257	SUBCLONAL	1	TRUE	1	0.480521037605115	2		421	613	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394052	31394052	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	61	599	0	ENST00000328111.2:c.2339C>T	p.Ser780Leu	p.S780L	ENST00000328111	NM_006892.3	780	tCg/tTg	22/23	0.480521037605115	3	FACETS	0.263	0.226	0.304	0.131	0.113	0.152	SUBCLONAL	1	TRUE	1	0.480521037605115	3		599	1198	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466580	120466580	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	148	444	0	ENST00000256646.2:c.4539C>G	p.Phe1513Leu	p.F1513L	ENST00000256646	NM_024408.3	1513	ttC/ttG	26/34	0.22844303544601	3	FACETS	0.908	0.83	0.991	0.454	0.415	0.496	INDETERMINATE	1	TRUE	1	0.480521037605115	3		444	841	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624275	89624275	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786204910	NA	P-0017015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	64	523	0	ENST00000371953.3:c.49C>G	p.Gln17Glu	p.Q17E	ENST00000371953	NM_000314.4	17	Caa/Gaa	1/9	1	2	FACETS	0.336	0.29	0.386	0.336	0.29	0.386	SUBCLONAL	1	TRUE	1	0.480521037605115	2		523	792	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440534	49440534	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1503	134	915	0	ENST00000301067.7:c.4276G>C	p.Glu1426Gln	p.E1426Q	ENST00000301067	NM_003482.3	1426	Gag/Cag	15/54	0.150636757731122	6	FACETS	0.668	0.604	0.736			1	INDETERMINATE	1	TRUE	NA	0.480521037605115	6		915	1637	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028438	42028438	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	52	421	1	ENST00000219905.7:c.3976C>T	p.Gln1326Ter	p.Q1326*	ENST00000219905	NM_001164273.1	1326	Cag/Tag	13/24	0.194535106986771	1	FACETS	0.242	0.205	0.282	0.242	0.205	0.282	INDETERMINATE	1	TRUE	0	0.480521037605115	1		422	680	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472473	88472473	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	122	660	0	ENST00000360948.2:c.2082G>C	p.Lys694Asn	p.K694N	ENST00000360948	NM_001012338.2	694	aaG/aaC	16/19	0.194535106986771	1	FACETS	0.485	0.438	0.534	0.485	0.438	0.534	INDETERMINATE	1	TRUE	0	0.480521037605115	1		660	796	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119881	70119881	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	134	748	0	ENST00000245479.2:c.883G>C	p.Asp295His	p.D295H	ENST00000245479	NM_000346.3	295	Gac/Cac	3/3	0.194535106986771	1	FACETS	0.511	0.464	0.56	0.511	0.464	0.56	INDETERMINATE	1	TRUE	0	0.480521037605115	1		748	830	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207631	2207631	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	105	748	0	ENST00000398665.3:c.915G>C	p.Trp305Cys	p.W305C	ENST00000398665	NM_032482.2	305	tgG/tgC	11/28	1	2	FACETS	0.419	0.374	0.466	0.419	0.374	0.466	SUBCLONAL	1	TRUE	1	0.480521037605115	2		748	1044	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030557	11030557	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	186	639	0	ENST00000327064.4:c.1111G>C	p.Glu371Gln	p.E371Q	ENST00000327064	NM_199141.1	371	Gaa/Caa	10/16	1	2	FACETS	0.857	0.792	0.925	0.857	0.792	0.925	CLONAL	1	TRUE	1	0.480521037605115	2		639	903	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051192	13051192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	100	514	0	ENST00000316448.5:c.628G>A	p.Asp210Asn	p.D210N	ENST00000316448	NM_004343.3	210	Gat/Aat	5/9	1	2	FACETS	0.453	0.404	0.505	0.453	0.404	0.505	SUBCLONAL	1	TRUE	1	0.480521037605115	2		514	919	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378291	225378291	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	103	631	0	ENST00000264414.4:c.604G>T	p.Glu202Ter	p.E202*	ENST00000264414	NM_003590.4	202	Gaa/Taa	5/16	1	2	FACETS	0.389	0.347	0.434	0.389	0.347	0.434	SUBCLONAL	1	TRUE	1	0.480521037605115	2		631	1103	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981164	55981164	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1256	113	608	1	ENST00000263923.4:c.535T>C	p.Trp179Arg	p.W179R	ENST00000263923	NM_002253.2	179	Tgg/Cgg	5/30	0.480521037605115	3	FACETS	0.426	0.382	0.473			1	SUBCLONAL	1	TRUE	NA	0.480521037605115	3		609	1369	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79968660	79968660	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	91	597	0	ENST00000265081.6:c.1010C>G	p.Ser337Cys	p.S337C	ENST00000265081	NM_002439.4	337	tCt/tGt	6/24	1	2	FACETS	0.439	0.389	0.493	0.439	0.389	0.493	SUBCLONAL	1	TRUE	1	0.480521037605115	2		597	862	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131893068	131893068	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	101	400	0	ENST00000265335.6:c.52G>C	p.Glu18Gln	p.E18Q	ENST00000265335		18	Gag/Cag	1/25	0.22844303544601	3	FACETS	0.627	0.56	0.699	0.314	0.28	0.35	INDETERMINATE	1	TRUE	1	0.480521037605115	3		400	831	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020742	26020742	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	26	191	0	ENST00000357647.3:c.25C>T	p.Arg9Trp	p.R9W	ENST00000357647	NM_003529.2	9	Cgg/Tgg	1/1	1	2	FACETS	0.323	0.256	0.4	0.323	0.256	0.4	SUBCLONAL	1	TRUE	1	0.480521037605115	2		191	335	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709172	117709174	+	inframe_deletion	In_Frame_Del	DEL	AAT	AAT	-	novel	NA	P-0017015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	167	442	0	ENST00000368508.3:c.1783_1785del	p.Ile595del	p.I595del	ENST00000368508	NM_002944.2	595	ATT/-	13/43	1	2	FACETS	0.892	0.821	0.966	0.892	0.821	0.966	CLONAL	1	TRUE	1	0.480521037605115	2		442	779	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650575	48650575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	275	866	0	ENST00000376670.3:c.545C>T	p.Ser182Leu	p.S182L	ENST00000376670	NM_002049.3	182	tCa/tTa	3/6	1	2	FACETS	0.899	0.843	0.957	0.899	0.843	0.957	CLONAL	1	TRUE	1	0.480521037605115	2		866	1273	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360490	70360490	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	146	913	1	ENST00000374080.3:c.6050C>T	p.Ser2017Leu	p.S2017L	ENST00000374080		2017	tCa/tTa	42/45	1	2	FACETS	0.451	0.411	0.495	0.451	0.411	0.495	SUBCLONAL	1	TRUE	1	0.480521037605115	2		914	1346	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182858	123182858	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	54	453	0	ENST00000218089.9:c.823C>G	p.Gln275Glu	p.Q275E	ENST00000218089	NM_001042749.1	275	Cag/Gag	10/35	1	2	FACETS	0.285	0.242	0.331	0.285	0.242	0.331	SUBCLONAL	1	TRUE	1	0.480521037605115	2		453	790	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0017017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	448	708	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.283319977297754	2	FACETS	0.795	0.758	0.832	0.795	0.758	0.832	SUBCLONAL	2	TRUE	0	0.405152454890095	2		708	1391	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0017017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	148	195	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.297828742915476	4	FACETS	0.983	0.911	1	1	0.989	1	CLONAL	3	TRUE	2	0.405152454890095	4		195	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0017017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	473	443	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.283319977297754	2	FACETS	1	0.967	1	1	0.997	1	CLONAL	3	TRUE	0	0.405152454890095	2		443	777	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872135	76872135	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	240	303	0	ENST00000373344.5:c.5512del	p.Arg1838GlufsTer2	p.R1838Efs*2	ENST00000373344	NM_000489.3	1838	Aga/ga	22/35	1	1	FACETS		NA	1	1	0.997	1	NA	4	TRUE	0	0.405152454890095	1		303	253	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633424	8633424	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	45	523	0	ENST00000356435.5:c.245T>C	p.Leu82Pro	p.L82P	ENST00000356435		82	cTc/cCc	3/35	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		523	788	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0017020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	80	500	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.2	2		500	783	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913381	NA	P-0017020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	61	505	1	ENST00000304494.5:c.322G>A	p.Asp108Asn	p.D108N	ENST00000304494	NM_000077.4	108	Gat/Aat	2/3	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.2	2		506	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577560	7577560	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520002	NA	P-0017020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	56	513	0	ENST00000269305.4:c.721T>C	p.Ser241Pro	p.S241P	ENST00000269305	NM_001126112.2	241	Tcc/Ccc	7/11	1	2	FACETS	0.93	0.797	1	0.93	0.797	1	CLONAL	1	TRUE	1	0.2	2		513	602	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236213	108236213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778267979	NA	P-0017020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	82	647	1	ENST00000278616.4:c.9149C>T	p.Pro3050Leu	p.P3050L	ENST00000278616	NM_000051.3	3050	cCa/cTa	63/63	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.2	2		648	790	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436375	52436375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1294983956	NA	P-0017020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	41	475	1	ENST00000460680.1:c.2119G>A	p.Gly707Ser	p.G707S	ENST00000460680	NM_004656.3	707	Ggc/Agc	17/17	1	2	FACETS	0.93	0.775	1	0.93	0.775	1	CLONAL	1	TRUE	1	0.2	2		476	441	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0017021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	205	696	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.598387775391373	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.598387775391373	1		696	413	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200946	108200946	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs147604227	NA	P-0017021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	104	271	0	ENST00000278616.4:c.7313C>G	p.Thr2438Arg	p.T2438R	ENST00000278616	NM_000051.3	2438	aCa/aGa	50/63	0.598387775391373	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.598387775391373	1		271	174	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308353	30308353	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	40	669	0	ENST00000262643.3:c.367A>C	p.Lys123Gln	p.K123Q	ENST00000262643	NM_001238.2	123	Aag/Cag	6/12	0.230371545577781	2	FACETS	0.192	0.158	0.229	0.096	0.079	0.115	INDETERMINATE	1	TRUE	0	0.598387775391373	2		669	698	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793186	42793186	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	420	753	1	ENST00000575354.2:c.1078G>A	p.Val360Ile	p.V360I	ENST00000575354	NM_015125.3	360	Gta/Ata	7/20	0.230371545577781	2	FACETS	1	0.996	1	0.737	0.705	0.77	INDETERMINATE	1	TRUE	0	0.598387775391373	2		754	952	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206909	162206909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150562946	NA	P-0017021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	35	381	0	ENST00000366898.1:c.766C>T	p.Arg256Cys	p.R256C	ENST00000366898	NM_004562.2	256	Cgc/Tgc	7/12	0.166342595995332	5	FACETS	0.376	0.307	0.453	0.125	0.102	0.151	INDETERMINATE	1	TRUE	2	0.598387775391373	5		381	591	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123026603	123026603	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	144	719	0	ENST00000355640.3:c.1079C>A	p.Pro360Gln	p.P360Q	ENST00000355640		360	cCa/cAa	5/7	0.356887407558581	1	FACETS	0.469	0.428	0.512	0.469	0.428	0.512	INDETERMINATE	1	TRUE	0	0.598387775391373	1		719	719	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0017022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	437	708	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.598201252454698	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.598201252454698	1		708	864	SUCCESS
APC	324	MSKCC	GRCh37	5	112174096	112174096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs137854575	NA	P-0017022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	197	543	0	ENST00000257430.4:c.2805C>A	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	taC/taA	16/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.598201252454698	2		543	644	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0017022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	192	539	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.884	0.82	0.95	0.884	0.82	0.95	CLONAL	1	TRUE	1	0.598201252454698	2		539	726	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210075	55210075	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	321	686	0	ENST00000275493.2:c.185T>G	p.Leu62Arg	p.L62R	ENST00000275493	NM_005228.3	62	cTt/cGt	2/28	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.598201252454698	2		686	972	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048788	180048788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375315719	NA	P-0017022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	296	864	0	ENST00000261937.6:c.1774C>T	p.Arg592Cys	p.R592C	ENST00000261937	NM_182925.4	592	Cgc/Tgc	13/30	1	2	FACETS	0.918	0.865	0.973	0.918	0.865	0.973	CLONAL	1	TRUE	1	0.598201252454698	2		864	1078	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044541	47044541	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	501	439	1	ENST00000377604.3:c.2038C>T	p.Arg680Ter	p.R680*	ENST00000377604	NM_001204468.1	680	Cga/Tga	18/24	0.466487758137098	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.598201252454698	2		440	704	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105733	27105827	+	frameshift_variant	Frame_Shift_Del	DEL	GTTGAAAATGATGAGGAGATAGCCTTTTCAGGCAAGGACAAGCCAGCTTCAGAGAATAGTGAGGAGAAGCTGATCAGTAAGTTTGACAAGCTTCC	GTTGAAAATGATGAGGAGATAGCCTTTTCAGGCAAGGACAAGCCAGCTTCAGAGAATAGTGAGGAGAAGCTGATCAGTAAGTTTGACAAGCTTCC	-	novel	NA	P-0017022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	135	335	0	ENST00000324856.7:c.5344_5438del	p.Val1782SerfsTer8	p.V1782Sfs*8	ENST00000324856	NM_006015.4	1782	GTTGAAAATGATGAGGAGATAGCCTTTTCAGGCAAGGACAAGCCAGCTTCAGAGAATAGTGAGGAGAAGCTGATCAGTAAGTTTGACAAGCTTCCa/a	20/20	1	2	FACETS	0.95	0.87	1	0.95	0.87	1	CLONAL	1	TRUE	1	0.598201252454698	2		335	475	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115763	8115763	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	158	890	0	ENST00000346208.3:c.1109G>C	p.Ser370Thr	p.S370T	ENST00000346208		370	aGc/aCc	6/6	1	2	FACETS	0.412	0.376	0.45	0.412	0.376	0.45	SUBCLONAL	1	TRUE	1	0.598201252454698	2		890	1282	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710682	114710683	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0017022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	246	610	1	ENST00000543371.1:c.169_170del	p.Asn57GlnfsTer39	p.N57Qfs*39	ENST00000543371	NM_001198531.1	56	cAA/c	1/14	1	2	FACETS	0.989	0.927	1	0.989	0.927	1	CLONAL	1	TRUE	1	0.598201252454698	2		611	832	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541588	29541588	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1555612289	NA	P-0017022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	118	561	0	ENST00000356175.3:c.1514del	p.Lys505SerfsTer21	p.K505Sfs*21	ENST00000356175	NM_000267.3	504	ccA/cc	13/57	0.598201252454698	1	FACETS	0.56	0.507	0.614	0.56	0.507	0.614	SUBCLONAL	1	TRUE	0	0.598201252454698	1		561	494	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281892	39281892	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	277	809	0	ENST00000402219.2:c.583A>G	p.Thr195Ala	p.T195A	ENST00000402219	NM_005633.3	195	Acc/Gcc	5/23	1	2	FACETS	0.875	0.822	0.93	0.875	0.822	0.93	CLONAL	1	TRUE	1	0.598201252454698	2		809	1058	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161949	47161949	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1469670151	NA	P-0017022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	69	420	0	ENST00000409792.3:c.4177T>G	p.Leu1393Val	p.L1393V	ENST00000409792	NM_014159.6	1393	Tta/Gta	3/21	1	2	FACETS	0.361	0.314	0.412	0.361	0.314	0.412	SUBCLONAL	1	TRUE	1	0.598201252454698	2		420	639	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624558	93624558	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867241355	NA	P-0017022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	339	712	1	ENST00000375746.1:c.649C>T	p.Arg217Cys	p.R217C	ENST00000375746	NM_001174167.1	217	Cgc/Tgc	4/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.598201252454698	2		713	1059	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760979	133760979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	237	856	0	ENST00000318560.5:c.3302C>T	p.Pro1101Leu	p.P1101L	ENST00000318560	NM_005157.4	1101	cCg/cTg	11/11	1	2	FACETS	0.622	0.579	0.666	0.622	0.579	0.666	SUBCLONAL	1	TRUE	1	0.598201252454698	2		856	1274	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520006	NA	P-0017023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	261	804	0	ENST00000269305.4:c.821T>G	p.Val274Gly	p.V274G	ENST00000269305	NM_001126112.2	274	gTt/gGt	8/11	NA	2	FACETS	0.953	0.893	1			1	INDETERMINATE	2	TRUE	NA	0.234977357570797	2		804	1165	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	332	357	2	ENST00000322088.6:c.767C>A	p.Ser256Tyr	p.S256Y	ENST00000322088	NM_014225.5	256	tCc/tAc	6/15	0.234977357570797	6	FACETS	0.982	0.93	1	0.982	0.93	1	CLONAL	4	TRUE	2	0.234977357570797	6		359	1057	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605868	46605868	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745977062	NA	P-0017023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	120	677	1	ENST00000263734.3:c.1516G>A	p.Ala506Thr	p.A506T	ENST00000263734	NM_001430.4	506	Gcc/Acc	11/16	0.185048102037608	4	FACETS	1	0.951	1	0.545	0.49	0.602	CLONAL	1	TRUE	2	0.234977357570797	4		678	1158	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0017024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	145	195	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.186242929981122	1	FACETS	1	0.97	1	1	0.97	1	INDETERMINATE	1	TRUE	0	0.544897681921324	1		195	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0017024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	729	487	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	NA	2	FACETS	0.947	0.926	0.967			1	INDETERMINATE	3	TRUE	NA	0.544897681921324	2		489	942	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371740	116371748	+	inframe_deletion	In_Frame_Del	DEL	TCAGGCTGT	TCAGGCTGT	-	novel	NA	P-0017024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	156	303	0	ENST00000397752.3:c.1219_1227del	p.Ser407_Cys409del	p.S407_C409del	ENST00000397752	NM_000245.2	407	TCAGGCTGT/-	3/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.544897681921324	2		303	527	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913508	39913508	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0017024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	275	369	2	ENST00000378444.4:c.4819+1G>A		p.X1607_splice	ENST00000378444	NM_001123385.1	1607			1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.544897681921324	1		371	507	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955550	48955550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913304	NA	P-0017025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	113	448	2	ENST00000267163.4:c.1666C>T	p.Arg556Ter	p.R556*	ENST00000267163	NM_000321.2	556	Cga/Tga	17/27	0.00363923986621106	3	FACETS	0.982	0.887	1			1	INDETERMINATE	2	FALSE	NA	0.216021676786502	3		450	590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0017025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	72	440	0	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	NA	2	FACETS	0.947	0.833	1			1	INDETERMINATE	2	FALSE	NA	0.216021676786502	2		440	352	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741220	40741220	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	103	651	0	ENST00000392038.2:c.1213G>C	p.Glu405Gln	p.E405Q	ENST00000392038	NM_001626.4	405	Gag/Cag	12/14	0.216021676786502	1	FACETS	0.975	0.878	1	1	0.988	1	CLONAL	2	FALSE	0	0.216021676786502	1		651	436	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060922	38060922	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	25	306	0	ENST00000250448.2:c.1067del	p.Thr356MetfsTer5	p.T356Mfs*5	ENST00000250448	NM_004496.3	356	aCt/at	2/2	0.216021676786502	1	FACETS	1	0.834	1	1	0.834	1	CLONAL	1	FALSE	0	0.216021676786502	1		306	195	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42843834	42843834	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	29	605	0	ENST00000398585.3:c.1085G>C	p.Gly362Ala	p.G362A	ENST00000398585	NM_001135099.1	362	gGa/gCa	10/14	0.216021676786502	0	FACETS	0.39	0.312	0.479			1	SUBCLONAL	1	FALSE	0	0.216021676786502	0		605	540	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725537	117725537	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	63	539	1	ENST00000368508.3:c.344T>A	p.Met115Lys	p.M115K	ENST00000368508	NM_002944.2	115	aTg/aAg	5/43	0.216021676786502	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	FALSE	0	0.216021676786502	1		540	439	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912135	76912135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	106	481	0	ENST00000373344.5:c.4129G>A	p.Glu1377Lys	p.E1377K	ENST00000373344	NM_000489.3	1377	Gaa/Aaa	13/35	0.216021676786502	0	FACETS	0.805	0.725	0.888			1	CLONAL	2	FALSE	0	0.216021676786502	0		481	478	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	104	479	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.234804734748106	2	FACETS	1	0.965	1	0.591	0.529	0.656	CLONAL	1	TRUE	0	0.234804734748106	2		479	750	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057835	27057835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1295	214	657	0	ENST00000324856.7:c.1543C>T	p.Gln515Ter	p.Q515*	ENST00000324856	NM_006015.4	515	Cag/Tag	3/20	0.184402055968473	4	FACETS	1	0.991	1	0.746	0.691	0.803	CLONAL	1	TRUE	2	0.234804734748106	4		657	1509	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99192881	99192881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1013771934	NA	P-0017026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	57	409	0	ENST00000268035.6:c.71C>T	p.Ser24Leu	p.S24L	ENST00000268035	NM_000875.3	24	tCg/tTg	1/21	0.234804734748106	3	FACETS	0.84	0.72	0.971	0.42	0.36	0.486	CLONAL	1	TRUE	1	0.234804734748106	3		409	646	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65304149	65304149	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	88	493	0	ENST00000342505.4:c.2966A>C	p.Lys989Thr	p.K989T	ENST00000342505	NM_002227.2	989	aAg/aCg	21/25	0.234804734748106	2	FACETS	1	0.964	1	0.61	0.541	0.684	CLONAL	1	TRUE	0	0.234804734748106	2		493	614	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510124	120510124	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0017026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	201	531	0	ENST00000256646.2:c.1385C>G	p.Ser462Ter	p.S462*	ENST00000256646	NM_024408.3	462	tCa/tGa	8/34	0.234804734748106	9	FACETS	1	0.977	1			1	CLONAL	2	TRUE	NA	0.234804734748106	9		531	1365	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111495	8111496	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGGA	novel	NA	P-0017026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	242	623	0	ENST00000346208.3:c.982_985dup	p.Arg329MetfsTer24	p.R329Mfs*24	ENST00000346208		327	-/TGGA	5/6	0.234804734748106	3	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	1	0.234804734748106	3		623	1138	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622120	43622120	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	103	566	2	ENST00000355710.3:c.3142del	p.Leu1048SerfsTer61	p.L1048Sfs*61	ENST00000355710	NM_020975.4	1046	gCc/gc	19/20	0.234804734748106	3	FACETS	1	0.93	1	0.526	0.47	0.586	CLONAL	1	TRUE	1	0.234804734748106	3		568	931	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434271	49434271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1474738542	NA	P-0017026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1298	305	917	2	ENST00000301067.7:c.7282C>T	p.Arg2428Trp	p.R2428W	ENST00000301067	NM_003482.3	2428	Cgg/Tgg	31/54	0.225108330520157	4	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	2	0.234804734748106	4		919	1603	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945815	17945815	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	rs779747536	NA	P-0017026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	178	551	0	ENST00000458235.1:c.2048-3C>T		p.X683_splice	ENST00000458235	NM_000215.3	683			0.184402055968473	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	2	0.234804734748106	4		551	886	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965430	68965430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	77	719	0	ENST00000288368.4:c.1042G>A	p.Glu348Lys	p.E348K	ENST00000288368	NM_024870.2	348	Gag/Aag	9/40	0.221374609848499	3	FACETS	0.88	0.771	0.997	0.293	0.257	0.333	CLONAL	1	TRUE	0	0.234804734748106	3		719	833	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141557591	141557591	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1598	240	709	0	ENST00000220592.5:c.1724A>T	p.Asn575Ile	p.N575I	ENST00000220592	NM_012154.3	575	aAc/aTc	13/19	0.234804734748106	9	FACETS	1	0.941	1	0.338	0.314	0.363	CLONAL	2	TRUE	3	0.234804734748106	9		709	1838	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0017028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	31	180	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.406940078103331	9	FACETS	0.32	0.257	0.392			1	SUBCLONAL	1	TRUE	NA	0.406940078103331	9		180	1155	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0017028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	169	513	1	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.406940078103331	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.406940078103331	1		514	501	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs730881677	NA	P-0017028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	143	332	0	ENST00000304494.5:c.151-1G>T		p.X51_splice	ENST00000304494	NM_000077.4	51			0.406940078103331	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.406940078103331	1		332	382	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098954	178098954	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	31	325	0	ENST00000397062.3:c.91G>C	p.Gly31Arg	p.G31R	ENST00000397062	NM_006164.4	31	Gga/Cga	2/5	1	2	FACETS	0.364	0.294	0.443	0.364	0.294	0.443	SUBCLONAL	1	TRUE	1	0.406940078103331	2		325	419	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253974	133253974	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	133	493	0	ENST00000320574.5:c.776G>T	p.Arg259Leu	p.R259L	ENST00000320574	NM_006231.2	259	cGc/cTc	8/49	1	2	FACETS	0.984	0.896	1	0.984	0.896	1	CLONAL	1	TRUE	1	0.406940078103331	2		493	664	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4094498	4094498	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0017028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	172	735	0	ENST00000262948.5:c.1047-2A>C		p.X349_splice	ENST00000262948	NM_030662.3	349			1	2	FACETS	0.891	0.819	0.965	0.891	0.819	0.965	CLONAL	1	TRUE	1	0.406940078103331	2		735	949	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954651	17954651	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	254	749	0	ENST00000458235.1:c.243G>C	p.Trp81Cys	p.W81C	ENST00000458235	NM_000215.3	81	tgG/tgC	3/24	0.135531379701099	4	FACETS	0.882	0.826	0.939	0.882	0.826	0.939	INDETERMINATE	2	TRUE	2	0.406940078103331	4		749	996	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170009641	170009641	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0017028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1338	194	456	2	ENST00000295797.4:c.1204-1G>T		p.X402_splice	ENST00000295797	NM_002740.5	402			0.406940078103331	15	FACETS	1	0.975	1			1	CLONAL	2	TRUE	NA	0.406940078103331	15		458	1532	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97876938	97876938	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	181	453	0	ENST00000289081.3:c.1127G>C	p.Arg376Thr	p.R376T	ENST00000289081	NM_000136.2	376	aGa/aCa	12/15	0.406940078103331	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.406940078103331	1		453	504	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265456	198265456	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017029-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	438	580	0	ENST00000335508.6:c.2701C>T	p.Gln901Ter	p.Q901*	ENST00000335508	NM_012433.2	901	Caa/Taa	18/25	0.464217259073424	2	FACETS	0.966	0.925	1	0.483	0.462	0.504	INDETERMINATE	1	TRUE	0	0.91357167931101	2		580	993	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042806	42042806	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	48	256	0	ENST00000219905.7:c.7001T>G	p.Val2334Gly	p.V2334G	ENST00000219905	NM_001164273.1	2334	gTa/gGa	17/24	0.131806183072051	0	FACETS	0.593	0.501	0.695			1	INDETERMINATE	1	TRUE	0	0.223240574763216	0		256	563	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591146	67591156	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTTGATGTAA	ACTTGATGTAA	G	novel	NA	P-0017031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	87	362	0	ENST00000274335.5:c.1739_1745+4delinsG		p.X580_splice	ENST00000274335		580		12/15	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.223240574763216	2		362	771	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0017032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	247	290	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.966	0.906	1	0.966	0.906	1	CLONAL	1	TRUE	1	0.639890909729583	2		290	799	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0017033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	227	195	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.996	0.938	1	0.996	0.938	1	CLONAL	1	TRUE	1	0.905905716072543	2		195	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0017033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	623	632	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.975	0.941	1	0.975	0.941	1	CLONAL	1	TRUE	1	0.905905716072543	2		634	1410	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955572	48955572	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587778863	NA	P-0017033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	405	436	1	ENST00000267163.4:c.1688G>A	p.Trp563Ter	p.W563*	ENST00000267163	NM_000321.2	563	tGg/tAg	17/27	0.905905716072543	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.905905716072543	1		437	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578273	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0017033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	428	600	1	ENST00000269305.4:c.576_577delinsAA	p.His193Asn	p.H193N	ENST00000269305	NM_001126112.2	192	caGCat/caAAat	6/11	1	2	FACETS	0.869	0.83	0.908	0.869	0.83	0.908	CLONAL	1	TRUE	1	0.905905716072543	2		601	1087	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888793	76888794	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	501	792	0	ENST00000373344.5:c.5035dup	p.Met1679AsnfsTer6	p.M1679Nfs*6	ENST00000373344	NM_000489.3	1679	atg/aAtg	19/35	0.443297942243916	1	FACETS	0.658	0.634	0.682	0.658	0.634	0.682	INDETERMINATE	1	TRUE	0	0.905905716072543	1		792	919	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115873	8115874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0017034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	349	621	0	ENST00000346208.3:c.1220dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tCcg	6/6	1	2	FACETS	0.949	0.898	1	0.949	0.898	1	CLONAL	1	TRUE	1	0.587294134594352	2		621	1253	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763254	59763254	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6777	6102	686	1	ENST00000259008.2:c.2848A>G	p.Lys950Glu	p.K950E	ENST00000259008	NM_032043.2	950	Aaa/Gaa	19/20	0.587294134594352	16	FACETS	1	0.998	1			1	CLONAL	8	TRUE	NA	0.587294134594352	16		687	12879	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59924539	59924539	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201047375	NA	P-0017034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1452	5450	455	0	ENST00000259008.2:c.550G>A	p.Asp184Asn	p.D184N	ENST00000259008	NM_032043.2	184	Gat/Aat	6/20	0.587294134594352	16	FACETS	0.982	0.974	0.989			1	CLONAL	14	TRUE	NA	0.587294134594352	16		455	6902	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59934430	59934430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	2789	311	0	ENST00000259008.2:c.368C>T	p.Ser123Leu	p.S123L	ENST00000259008	NM_032043.2	123	tCa/tTa	4/20	0.587294134594352	16	FACETS	0.976	0.964	0.988			1	CLONAL	13	TRUE	NA	0.587294134594352	16		311	3825	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952152	178952162	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	AAAAGATAACT	AAAAGATAACT	-	novel	NA	P-0017034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	205	355	0	ENST00000263967.3:c.3207_*10del		p.*1069*	ENST00000263967	NM_006218.2	1069		21/21	1	2	FACETS	0.962	0.895	1	0.962	0.895	1	CLONAL	1	TRUE	1	0.587294134594352	2		355	726	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675576	86675576	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	240	429	0	ENST00000274376.6:c.2512A>C	p.Asn838His	p.N838H	ENST00000274376	NM_002890.2	838	Aat/Cat	19/25	1	2	FACETS	0.926	0.866	0.987	0.926	0.866	0.987	CLONAL	1	TRUE	1	0.587294134594352	2		429	883	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0017036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	240	290	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.943	0.881	1	0.943	0.881	1	CLONAL	1	TRUE	1	0.506980670738062	2		290	1004	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856113	68856113	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782750	NA	P-0017036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	266	580	0	ENST00000261769.5:c.1921C>T	p.Gln641Ter	p.Q641*	ENST00000261769	NM_004360.3	641	Cag/Tag	12/16	0.506980670738062	1	FACETS	0.928	0.873	0.985	0.928	0.873	0.985	CLONAL	1	TRUE	0	0.506980670738062	1		580	844	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480082	50480082	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	101	495	0	ENST00000394963.4:c.316C>T	p.Gln106Ter	p.Q106*	ENST00000394963	NM_003076.4	106	Cag/Tag	2/13	1	2	FACETS	0.432	0.385	0.481	0.432	0.385	0.481	SUBCLONAL	1	TRUE	1	0.506980670738062	2		495	923	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880169	151880169	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	273	498	1	ENST00000262189.6:c.5155C>T	p.Gln1719Ter	p.Q1719*	ENST00000262189	NM_170606.2	1719	Cag/Tag	35/59	1	2	FACETS	0.913	0.857	0.972	0.913	0.857	0.972	CLONAL	1	TRUE	1	0.506980670738062	2		499	1179	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879852	44879852	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0017036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	168	320	0	ENST00000377967.4:c.444-3C>T		p.X148_splice	ENST00000377967	NM_021140.2	148			1	2	FACETS	0.939	0.865	1	0.939	0.865	1	CLONAL	1	TRUE	1	0.506980670738062	2		320	706	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0017038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	269	470	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.285622798212146	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.285622798212146	4		470	1169	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056132	26056132	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	68	419	0	ENST00000343677.2:c.525G>C	p.Lys175Asn	p.K175N	ENST00000343677	NM_005319.3	175	aaG/aaC	1/1	0.246917752398972	4	FACETS	0.646	0.56	0.739	0.323	0.28	0.37	SUBCLONAL	1	TRUE	2	0.285622798212146	4		419	948	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857881	89857881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772567344	NA	P-0017038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	101	632	3	ENST00000389301.3:c.1289C>T	p.Ala430Val	p.A430V	ENST00000389301	NM_000135.2	430	gCg/gTg	14/43	0.173669236272404	3	FACETS	0.808	0.721	0.901	0.404	0.36	0.451	CLONAL	1	TRUE	1	0.285622798212146	3		635	1000	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858192	9858192	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	67	498	0	ENST00000330684.3:c.3209G>A	p.Cys1070Tyr	p.C1070Y	ENST00000330684	NM_001134407.1	1070	tGc/tAc	13/13	0.285622798212146	4	FACETS	0.685	0.593	0.784			1	SUBCLONAL	1	TRUE	NA	0.285622798212146	4		498	881	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487520	38487520	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs368040095	NA	P-0017038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	65	491	1	ENST00000254066.5:c.50A>G	p.Asn17Ser	p.N17S	ENST00000254066	NM_000964.3	17	aAt/aGt	2/9	0.246917752398972	4	FACETS	0.606	0.524	0.696	0.303	0.262	0.348	SUBCLONAL	1	TRUE	2	0.285622798212146	4		492	965	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119710	70119710	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1341	97	782	1	ENST00000245479.2:c.712C>A	p.Pro238Thr	p.P238T	ENST00000245479	NM_000346.3	238	Ccc/Acc	3/3	0.285622798212146	5	FACETS	0.675	0.599	0.756	0.225	0.199	0.252	SUBCLONAL	1	TRUE	2	0.285622798212146	5		783	1438	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041007	47041008	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	289	316	0	ENST00000377604.3:c.1538dup	p.Ala514GlyfsTer4	p.A514Gfs*4	ENST00000377604	NM_001204468.1	513	gag/gAag	14/24	0.254593944931358	2	FACETS	0.928	0.878	0.979			1	CLONAL	3	TRUE	NA	0.285622798212146	2		316	727	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428127	47428127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	104	311	0	ENST00000377045.4:c.1087C>G	p.His363Asp	p.H363D	ENST00000377045	NM_001654.4	363	Cat/Gat	11/16	0.254593944931358	2	FACETS	1	0.959	1			1	CLONAL	1	TRUE	NA	0.285622798212146	2		311	640	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	332	408	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.125443681604963	3	FACETS	0.86	0.813	0.907	0.573	0.542	0.605	INDETERMINATE	2	TRUE	0	0.427822419187068	3		408	1096	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0017039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	408	395	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.427822419187068	2	FACETS	0.975	0.931	1	0.975	0.931	1	CLONAL	2	TRUE	0	0.427822419187068	2		397	978	SUCCESS
APC	324	MSKCC	GRCh37	5	112175060	112175060	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	93	193	0	ENST00000257430.4:c.3769G>T	p.Glu1257Ter	p.E1257*	ENST00000257430	NM_000038.5	1257	Gaa/Taa	16/16	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.427822419187068	2		193	431	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344383	118344383	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	112	259	0	ENST00000534358.1:c.2509C>T	p.Pro837Ser	p.P837S	ENST00000534358	NM_005933.3	837	Cct/Tct	3/36	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.427822419187068	2		259	499	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343627	343627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1178966552	NA	P-0017039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	262	586	0	ENST00000262320.3:c.2047G>A	p.Val683Met	p.V683M	ENST00000262320	NM_003502.3	683	Gtg/Atg	8/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.427822419187068	2		586	1101	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0017040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	353	410	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.635872993732148	1	FACETS	0.753	0.726	0.779	1	0.996	1	SUBCLONAL	2	TRUE	0	0.635872993732148	1		410	503	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0017040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	440	525	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	0.635872993732148	2		525	1094	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347864	347864	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	271	749	0	ENST00000262320.3:c.1642G>T	p.Glu548Ter	p.E548*	ENST00000262320	NM_003502.3	548	Gag/Tag	6/11	0.635872993732148	1	FACETS	0.799	0.753	0.845	0.799	0.753	0.845	SUBCLONAL	1	TRUE	0	0.635872993732148	1		749	728	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1039241	1039241	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	461	588	0	ENST00000358495.3:c.256C>A	p.His86Asn	p.H86N	ENST00000358495	NM_134424.2	86	Cac/Aac	4/12	0.175523349622536	4	FACETS	1	0.99	1	1	0.99	1	INDETERMINATE	2	TRUE	2	0.635872993732148	4		588	1078	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300845	137300845	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	164	679	0	ENST00000481739.1:c.490C>A	p.Arg164Ser	p.R164S	ENST00000481739	NM_002957.4	164	Cgc/Agc	4/10	1	2	FACETS	0.55	0.505	0.597	0.55	0.505	0.597	SUBCLONAL	1	TRUE	1	0.635872993732148	2		679	938	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0017041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	567	410	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.641368633500491	3	FACETS	0.904	0.881	0.927	0.904	0.881	0.927	CLONAL	3	TRUE	0	0.75160168418502	3		410	765	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93627351	93627351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139520862	NA	P-0017041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	188	446	0	ENST00000375746.1:c.818G>A	p.Arg273His	p.R273H	ENST00000375746	NM_001174167.1	273	cGt/cAt	6/14	0.75160168418502	4	FACETS	0.768	0.708	0.83	0.256	0.236	0.277	SUBCLONAL	1	TRUE	1	0.75160168418502	4		446	1141	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577379	64577379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1319371332	NA	P-0017041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	97	464	0	ENST00000312049.6:c.203C>T	p.Ala68Val	p.A68V	ENST00000312049	NM_130799.2	68	gCc/gTc	2/10	0.404107960696399	6	FACETS	0.602	0.535	0.674			1	INDETERMINATE	1	TRUE	NA	0.75160168418502	6		464	1073	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426879	49426879	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	319	271	0	ENST00000301067.7:c.11609del	p.Met3870ArgfsTer11	p.M3870Rfs*11	ENST00000301067	NM_003482.3	3870	aTg/ag	39/54	0.683380308089019	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	2	0.75160168418502	4		271	644	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602792	10602792	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	272	597	0	ENST00000171111.5:c.786C>G	p.Phe262Leu	p.F262L	ENST00000171111	NM_203500.1	262	ttC/ttG	3/6	1	2	FACETS	0.633	0.593	0.673	0.633	0.593	0.673	SUBCLONAL	1	TRUE	1	0.75160168418502	2		597	1144	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670377	134670377	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	75	387	1	ENST00000398015.3:c.288C>A	p.Cys96Ter	p.C96*	ENST00000398015	NM_004441.4	96	tgC/tgA	3/16	0.253498796143346	5	FACETS	0.556	0.487	0.632			1	INDETERMINATE	1	TRUE	NA	0.75160168418502	5		388	763	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873700	35873700	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	250	434	0	ENST00000303115.3:c.656A>T	p.Glu219Val	p.E219V	ENST00000303115	NM_002185.3	219	gAa/gTa	5/8	0.743654825635619	3	FACETS	1	0.952	1	0.509	0.477	0.542	CLONAL	1	TRUE	1	0.75160168418502	3		434	899	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463307	25463307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757211277	NA	P-0017043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	186	421	1	ENST00000264709.3:c.2186G>A	p.Arg729Gln	p.R729Q	ENST00000264709	NM_175629.2	729	cGg/cAg	19/23	0.351982817309424	1	FACETS	0.397	0.368	0.427	0.397	0.368	0.427	INDETERMINATE	1	TRUE	0	0.835302701277162	1		422	653	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs878854073	NA	P-0017043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	376	482	0	ENST00000269305.4:c.673-1G>A		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.835302701277162	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.835302701277162	1		482	510	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74859029	74859029	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	141	391	0	ENST00000284811.8:c.175G>C	p.Glu59Gln	p.E59Q	ENST00000284811		59	Gag/Cag	4/4	1	2	FACETS	0.496	0.452	0.541	0.496	0.452	0.541	SUBCLONAL	1	TRUE	1	0.835302701277162	2		391	681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0017044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	549	822	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.982	0.944	1	0.982	0.944	1	CLONAL	1	TRUE	1	0.811865086114068	2		822	1377	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748487	40748487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143335817	NA	P-0017044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2521	188	674	2	ENST00000392038.2:c.395C>T	p.Thr132Met	p.T132M	ENST00000392038	NM_001626.4	132	aCg/aTg	5/14	0.601041634208564	6	FACETS	0.449	0.412	0.487			1	SUBCLONAL	1	TRUE	NA	0.811865086114068	6		676	2709	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111855996	111855996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779622961	NA	P-0017044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	156	378	0	ENST00000341259.2:c.47C>T	p.Ser16Leu	p.S16L	ENST00000341259	NM_005475.2	16	tCa/tTa	2/8	1	2	FACETS	0.452	0.413	0.491	0.452	0.413	0.491	SUBCLONAL	1	TRUE	1	0.811865086114068	2		378	851	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257141	198257141	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	99	541	0	ENST00000335508.6:c.3801A>C	p.Lys1267Asn	p.K1267N	ENST00000335508	NM_012433.2	1267	aaA/aaC	25/25	1	2	FACETS	0.465	0.416	0.516	0.465	0.416	0.516	SUBCLONAL	1	TRUE	1	0.811865086114068	2		541	525	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31401565	31401565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1394	660	594	0	ENST00000344624.3:c.4099G>A	p.Asp1367Asn	p.D1367N	ENST00000344624		1367	Gat/Aat	33/33	0.811865086114068	5	FACETS	0.878	0.844	0.912	0.439	0.422	0.456	CLONAL	2	TRUE	1	0.811865086114068	5		594	2054	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843801	151843802	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	437	529	0	ENST00000262189.6:c.13913dup	p.Leu4638PhefsTer12	p.L4638Ffs*12	ENST00000262189	NM_170606.2	4638	ttg/ttTg	53/59	0.782416921970945	2	FACETS	0.899	0.871	0.925	0.899	0.871	0.925	CLONAL	2	TRUE	0	0.811865086114068	2		529	599	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	281	390	2				ENST00000310581	NM_198253.2	-/1132			0.806150546201402	3	FACETS	1	0.991	1	0.629	0.594	0.664	CLONAL	1	TRUE	1	0.9018052441386	3		392	719	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911514	131911514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143802516	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	234	370	0	ENST00000265335.6:c.259C>T	p.Arg87Cys	p.R87C	ENST00000265335		87	Cgt/Tgt	3/25	0.9018052441386	2	FACETS	0.836	0.785	0.887	0.418	0.392	0.444	CLONAL	1	TRUE	0	0.9018052441386	2		370	621	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367321	50367321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1259	198	319	1	ENST00000331340.3:c.128G>A	p.Gly43Glu	p.G43E	ENST00000331340	NM_006060.4	43	gGa/gAa	3/8	0.9018052441386	6	FACETS	0.845	0.78	0.913	0.211	0.195	0.229	CLONAL	1	TRUE	2	0.9018052441386	6		320	1457	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467675	50467675	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759124417	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1406	663	625	0	ENST00000331340.3:c.910G>A	p.Glu304Lys	p.E304K	ENST00000331340	NM_006060.4	304	Gaa/Aaa	8/8	0.9018052441386	6	FACETS	0.996	0.958	1	0.498	0.479	0.518	CLONAL	2	TRUE	2	0.9018052441386	6		625	2069	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	1545	511	2	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.9018052441386	7	FACETS	0.995	0.978	1	0.995	0.978	1	CLONAL	5	TRUE	2	0.9018052441386	7		513	2241	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416876	121416876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	435	720	3	ENST00000257555.6:c.305C>T	p.Ala102Val	p.A102V	ENST00000257555		102	gCc/gTc	1/10	0.9018052441386	3	FACETS	1	0.953	1	0.5	0.476	0.524	CLONAL	1	TRUE	1	0.9018052441386	3		723	1400	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218804	5218804	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773998457	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1154	127	478	0	ENST00000357368.4:c.3929C>T	p.Pro1310Leu	p.P1310L	ENST00000357368	NM_002850.3	1310	cCc/cTc	24/38	0.9018052441386	5	FACETS	0.517	0.467	0.571	0.172	0.155	0.191	SUBCLONAL	1	TRUE	2	0.9018052441386	5		478	1281	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097629	11097629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1212	443	664	0	ENST00000358026.2:c.809C>T	p.Pro270Leu	p.P270L	ENST00000358026	NM_001128849.1	270	cCc/cTc	5/36	0.9018052441386	5	FACETS	1	0.995	1	0.466	0.443	0.489	CLONAL	1	TRUE	2	0.9018052441386	5		664	1655	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631271	117631271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	263	407	0	ENST00000368508.3:c.6407G>A	p.Gly2136Glu	p.G2136E	ENST00000368508	NM_002944.2	2136	gGa/gAa	40/43	0.900529455487027	2	FACETS	0.941	0.889	0.993	0.47	0.444	0.497	CLONAL	1	TRUE	0	0.9018052441386	2		407	620	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560824	9560824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376118527	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	209	316	0	ENST00000353224.5:c.958C>T	p.Arg320Cys	p.R320C	ENST00000353224	NM_177990.2	320	Cgc/Tgc	4/10	0.814170158522168	3	FACETS	1	0.938	1	0.503	0.469	0.537	CLONAL	1	TRUE	1	0.9018052441386	3		316	669	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143093	7143093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1460294044	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	104	428	0	ENST00000302850.5:c.2276G>A	p.Arg759Gln	p.R759Q	ENST00000302850	NM_000208.2	759	cGg/cAg	12/22	0.9018052441386	5	FACETS	0.561	0.501	0.624	0.187	0.167	0.208	SUBCLONAL	1	TRUE	2	0.9018052441386	5		428	968	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	365	696	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	0.237647481156769	4	FACETS	1	0.986	1	0.279	0.264	0.295	INDETERMINATE	1	TRUE	0	0.9018052441386	4		696	1378	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106020	27106021	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	208	402	0	ENST00000324856.7:c.5631_5632delinsTT	p.Pro1878Ser	p.P1878S	ENST00000324856	NM_006015.4	1877	gcCCct/gcTTct	20/20	NA	2	FACETS	0.795	0.743	0.848			1	INDETERMINATE	1	TRUE	NA	0.9018052441386	2		402	580	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248043	59248043	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	146	285	0	ENST00000371222.2:c.700G>C	p.Glu234Gln	p.E234Q	ENST00000371222	NM_002228.3	234	Gag/Cag	1/1	0.730033208834703	3	FACETS	0.834	0.765	0.906			1	CLONAL	1	TRUE	NA	0.9018052441386	3		285	563	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604514	43604514	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	286	550	0	ENST00000355710.3:c.1099A>C	p.Asn367His	p.N367H	ENST00000355710	NM_020975.4	367	Aac/Cac	6/20	1	2	FACETS	0.868	0.82	0.916	0.868	0.82	0.916	CLONAL	1	TRUE	1	0.9018052441386	2		550	731	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310950	123310950	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	351	264	0	ENST00000358487.5:c.478G>A	p.Glu160Lys	p.E160K	ENST00000358487	NM_000141.4	160	Gaa/Aaa	5/18	0.9018052441386	3	FACETS	0.987	0.948	1	0.987	0.948	1	CLONAL	2	TRUE	1	0.9018052441386	3		264	572	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633564	69633685	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGCGCCGGGGCGCCCCGCCAAGGTGCTCGTAGACGCCGCCACGGCCGCCCGCATCGCGCCGCAACCGCGCCCCAGGGCCCGCTGCGGGCCAGCCGGGCTCCAGCAGGCTGAGCAGTAGCA	GCGGCGCCGGGGCGCCCCGCCAAGGTGCTCGTAGACGCCGCCACGGCCGCCCGCATCGCGCCGCAACCGCGCCCCAGGGCCCGCTGCGGGCCAGCCGGGCTCCAGCAGGCTGAGCAGTAGCA	-	novel	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	22	216	0	ENST00000334134.2:c.17_138del	p.Leu6GlnfsTer81	p.L6Qfs*81	ENST00000334134	NM_005247.2	6	cTGCTACTGCTCAGCCTGCTGGAGCCCGGCTGGCCCGCAGCGGGCCCTGGGGCGCGGTTGCGGCGCGATGCGGGCGGCCGTGGCGGCGTCTACGAGCACCTTGGCGGGGCGCCCCGGCGCCGC/c	1/3	0.9018052441386	2	FACETS	0.136	0.105	0.172	0.068	0.052	0.086	SUBCLONAL	1	TRUE	0	0.9018052441386	2		216	359	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133208960	133208961	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	248	442	1	ENST00000320574.5:c.6270_6271delinsTT	p.Pro2091Ser	p.P2091S	ENST00000320574	NM_006231.2	2090	ctCCcc/ctTTcc	45/49	0.9018052441386	3	FACETS	0.816	0.764	0.87	0.408	0.382	0.435	CLONAL	1	TRUE	1	0.9018052441386	3		443	978	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622451	28622451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	255	472	1	ENST00000241453.7:c.1166C>T	p.Ser389Leu	p.S389L	ENST00000241453	NM_004119.2	389	tCa/tTa	9/24	0.5997063475154	4	FACETS	0.913	0.854	0.974			1	CLONAL	1	TRUE	NA	0.9018052441386	4		473	1178	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054037	42054037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1246555872	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	188	385	0	ENST00000219905.7:c.7499C>T	p.Ser2500Leu	p.S2500L	ENST00000219905	NM_001164273.1	2500	tCg/tTg	21/24	0.237647481156769	4	FACETS	1	0.975	1	0.278	0.258	0.3	INDETERMINATE	1	TRUE	0	0.9018052441386	4		385	712	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347750	89347750	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	429	327	0	ENST00000301030.4:c.5200G>A	p.Asp1734Asn	p.D1734N	ENST00000301030	NM_001256183.1	1734	Gac/Aac	9/13	0.724717866798472	3	FACETS	0.978	0.942	1	0.978	0.942	1	CLONAL	2	TRUE	1	0.9018052441386	3		327	706	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554565	29554565	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199474730	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	475	347	0	ENST00000356175.3:c.2350T>C	p.Trp784Arg	p.W784R	ENST00000356175	NM_000267.3	784	Tgg/Cgg	20/57	0.897388428644031	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.9018052441386	2		347	518	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56801451	56801451	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781287	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	654	468	0	ENST00000337432.4:c.955C>T	p.Arg319Ter	p.R319*	ENST00000337432	NM_058216.2	319	Cga/Tga	7/9	0.9018052441386	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.9018052441386	2		468	702	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296322	15296322	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772994625	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	311	440	1	ENST00000263388.2:c.2120G>A	p.Gly707Asp	p.G707D	ENST00000263388	NM_000435.2	707	gGc/gAc	13/33	0.9018052441386	5	FACETS	1	0.994	1	0.483	0.456	0.512	CLONAL	1	TRUE	2	0.9018052441386	5		441	1119	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223545	36223545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs527676065	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	441	691	0	ENST00000222270.7:c.6095C>T	p.Ser2032Phe	p.S2032F	ENST00000222270	NM_014727.1	2032	tCc/tTc	28/37	0.814170158522168	3	FACETS	0.944	0.9	0.99	0.472	0.45	0.495	CLONAL	1	TRUE	1	0.9018052441386	3		691	1503	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973238	25973238	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	165	240	0	ENST00000435504.4:c.1187C>T	p.Pro396Leu	p.P396L	ENST00000435504		396	cCc/cTc	12/13	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.9018052441386	2		240	360	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39729993	39729993	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	246	470	0	ENST00000361337.2:c.1308G>C	p.Lys436Asn	p.K436N	ENST00000361337	NM_003286.2	436	aaG/aaC	13/21	0.814170158522168	3	FACETS	0.898	0.841	0.957	0.449	0.42	0.479	CLONAL	1	TRUE	1	0.9018052441386	3		470	881	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944387	40944387	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	197	337	1	ENST00000373198.4:c.2115C>A	p.Phe705Leu	p.F705L	ENST00000373198	NM_133170.3	705	ttC/ttA	12/32	0.814170158522168	3	FACETS	0.919	0.854	0.985	0.459	0.427	0.493	CLONAL	1	TRUE	1	0.9018052441386	3		338	690	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438560	52438560	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	327	402	0	ENST00000460680.1:c.1159C>T	p.Pro387Ser	p.P387S	ENST00000460680	NM_004656.3	387	Cca/Tca	12/17	0.814170158522168	3	FACETS	0.99	0.936	1	0.495	0.468	0.523	CLONAL	1	TRUE	1	0.9018052441386	3		402	1063	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898764	134898764	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	156	312	0	ENST00000398015.3:c.1822C>G	p.Arg608Gly	p.R608G	ENST00000398015	NM_004441.4	608	Cgg/Ggg	10/16	1	2	FACETS	0.832	0.77	0.895	0.832	0.77	0.895	CLONAL	1	TRUE	1	0.9018052441386	2		312	416	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141066	55141066	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	202	320	0	ENST00000257290.5:c.1712A>G	p.Glu571Gly	p.E571G	ENST00000257290	NM_006206.4	571	gAa/gGa	12/23	0.846918005085279	4	FACETS	0.988	0.917	1	0.329	0.305	0.354	CLONAL	1	TRUE	1	0.9018052441386	4		320	862	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270125	66270125	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	785	493	0	ENST00000273854.3:c.1757T>C	p.Leu586Ser	p.L586S	ENST00000273854	NM_004439.5	586	tTg/tCg	8/18	0.846918005085279	4	FACETS	0.963	0.94	0.986	0.963	0.94	0.986	CLONAL	3	TRUE	1	0.9018052441386	4		493	1146	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875634	35875634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	206	443	2	ENST00000303115.3:c.821C>T	p.Pro274Leu	p.P274L	ENST00000303115	NM_002185.3	274	cCc/cTc	7/8	0.806150546201402	3	FACETS	0.861	0.801	0.923	0.43	0.4	0.462	CLONAL	1	TRUE	1	0.9018052441386	3		445	770	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178364	56178364	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	148	266	0	ENST00000399503.3:c.3337T>C	p.Phe1113Leu	p.F1113L	ENST00000399503	NM_005921.1	1113	Ttc/Ctc	14/20	0.806150546201402	3	FACETS	0.895	0.822	0.97	0.448	0.411	0.485	CLONAL	1	TRUE	1	0.9018052441386	3		266	532	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176715863	176715863	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	368	507	0	ENST00000439151.2:c.6195T>G	p.Asn2065Lys	p.N2065K	ENST00000439151	NM_022455.4	2065	aaT/aaG	21/23	0.9018052441386	2	FACETS	1	0.972	1	0.513	0.489	0.536	CLONAL	1	TRUE	0	0.9018052441386	2		507	796	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680869	30680869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1659	424	625	1	ENST00000376406.3:c.850C>T	p.Pro284Ser	p.P284S	ENST00000376406	NM_014641.2	284	Cca/Tca	5/15	0.522180227259427	6	FACETS	1	0.993	1	0.422	0.4	0.444	INDETERMINATE	1	TRUE	3	0.9018052441386	6		626	2083	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554828	106554828	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758646294	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	75	364	1	ENST00000369096.4:c.1945C>T	p.His649Tyr	p.H649Y	ENST00000369096	NM_001198.3	649	Cac/Tac	7/7	0.264042346332277	5	FACETS	0.44	0.385	0.5			1	INDETERMINATE	1	TRUE	NA	0.9018052441386	5		365	889	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677936	117677936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	255	433	0	ENST00000368508.3:c.3997G>A	p.Glu1333Lys	p.E1333K	ENST00000368508	NM_002944.2	1333	Gaa/Aaa	25/43	0.900529455487027	2	FACETS	0.99	0.936	1	0.495	0.468	0.523	CLONAL	1	TRUE	0	0.9018052441386	2		433	571	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099889	157099889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767529376	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	353	560	3	ENST00000346085.5:c.826G>A	p.Ala276Thr	p.A276T	ENST00000346085	NM_020732.3	276	Gcc/Acc	1/20	0.900529455487027	2	FACETS	0.932	0.887	0.977	0.466	0.443	0.489	CLONAL	1	TRUE	0	0.9018052441386	2		563	840	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099895	157099895	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	375	561	0	ENST00000346085.5:c.832G>T	p.Gly278Cys	p.G278C	ENST00000346085	NM_020732.3	278	Ggc/Tgc	1/20	0.900529455487027	2	FACETS	0.968	0.924	1	0.484	0.462	0.507	CLONAL	1	TRUE	0	0.9018052441386	2		561	859	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392143	81392143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	217	237	0	ENST00000222390.5:c.134C>T	p.Ser45Leu	p.S45L	ENST00000222390	NM_000601.4	45	tCa/tTa	2/18	0.9018052441386	6	FACETS	1	0.991	1	0.373	0.347	0.4	CLONAL	1	TRUE	2	0.9018052441386	6		237	905	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884505	151884505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1403	166	322	0	ENST00000262189.6:c.4850C>T	p.Ser1617Leu	p.S1617L	ENST00000262189	NM_170606.2	1617	tCa/tTa	33/59	0.9018052441386	7	FACETS	0.764	0.699	0.832	0.153	0.139	0.167	SUBCLONAL	1	TRUE	2	0.9018052441386	7		322	1569	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151947944	151947944	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1216156088	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1824	212	454	0	ENST00000262189.6:c.1729C>T	p.Pro577Ser	p.P577S	ENST00000262189	NM_170606.2	577	Cca/Tca	12/59	0.9018052441386	7	FACETS	0.752	0.695	0.811	0.15	0.139	0.163	SUBCLONAL	1	TRUE	2	0.9018052441386	7		454	2036	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922532	56922532	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	232	452	0	ENST00000519728.1:c.1402T>C	p.Cys468Arg	p.C468R	ENST00000519728	NM_002350.3	468	Tgc/Cgc	13/13	0.448341351249565	4	FACETS	1	0.934	1	0.5	0.467	0.535	INDETERMINATE	1	TRUE	2	0.9018052441386	4		452	978	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864769	68864769	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	187	324	0	ENST00000288368.4:c.140C>T	p.Ser47Leu	p.S47L	ENST00000288368	NM_024870.2	47	tCg/tTg	1/40	0.448341351249565	4	FACETS	0.933	0.863	1	0.467	0.431	0.503	INDETERMINATE	1	TRUE	2	0.9018052441386	4		324	845	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104642	69104642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	293	490	3	ENST00000288368.4:c.4486G>A	p.Ala1496Thr	p.A1496T	ENST00000288368	NM_024870.2	1496	Gct/Act	37/40	0.448341351249565	4	FACETS	1	0.982	1	0.552	0.519	0.585	INDETERMINATE	1	TRUE	2	0.9018052441386	4		493	1120	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436684	8436684	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	190	319	2	ENST00000356435.5:c.3994G>A	p.Ala1332Thr	p.A1332T	ENST00000356435		1332	Gct/Act	24/35	0.9018052441386	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.9018052441386	1		321	230	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98222022	98222022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	226	352	0	ENST00000331920.6:c.2747C>T	p.Pro916Leu	p.P916L	ENST00000331920	NM_000264.3	916	cCc/cTc	17/24	0.730033208834703	3	FACETS	0.9	0.841	0.961			1	CLONAL	1	TRUE	NA	0.9018052441386	3		352	808	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760022	133760022	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754674216	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	517	718	1	ENST00000318560.5:c.2345C>T	p.Pro782Leu	p.P782L	ENST00000318560	NM_005157.4	782	cCt/cTt	11/11	0.9018052441386	2	FACETS	1	0.984	1	0.521	0.501	0.541	CLONAL	1	TRUE	0	0.9018052441386	2		719	1101	SUCCESS
AR	367	MSKCC	GRCh37	X	66766497	66766497	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	315	350	0	ENST00000374690.3:c.1509G>A	p.Trp503Ter	p.W503*	ENST00000374690	NM_000044.3	503	tgG/tgA	1/8	0.845598702371128	2	FACETS	0.652	0.616	0.69			1	SUBCLONAL	1	TRUE	NA	0.9018052441386	2		350	1071	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357157	70357157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	273	268	0	ENST00000374080.3:c.5672C>T	p.Ser1891Phe	p.S1891F	ENST00000374080		1891	tCc/tTc	39/45	0.845598702371128	2	FACETS	0.561	0.527	0.597			1	SUBCLONAL	1	TRUE	NA	0.9018052441386	2		268	1079	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480509	123480509	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	136	190	2	ENST00000371139.4:c.17T>C	p.Val6Ala	p.V6A	ENST00000371139	NM_001114937.2	6	gTg/gCg	1/4	0.845598702371128	2	FACETS	0.516	0.471	0.564			1	SUBCLONAL	1	TRUE	NA	0.9018052441386	2		192	584	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	98	301	4				ENST00000310581	NM_198253.2	-/1132			0.23935503295846	3	FACETS	0.89	0.797	0.988			1	CLONAL	2	TRUE	NA	0.23935503295846	3		305	515	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881001	37881002	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGCTCCCC	rs397516981	NA	P-0017048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2062	5778	689	0	ENST00000269571.5:c.2331_2339dup	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	gtg/gtGGGCTCCCCg	20/27	0.23935503295846	52	FACETS	1	0.992	1			1	CLONAL	43	TRUE	NA	0.23935503295846	52		689	7840	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0017048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	109	672	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.227885848425296	1	FACETS	0.929	0.834	1	0.929	0.834	1	CLONAL	1	TRUE	0	0.23935503295846	1		672	863	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512450	38512450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	126	755	1	ENST00000254066.5:c.1361G>A	p.Arg454Lys	p.R454K	ENST00000254066	NM_000964.3	454	aGa/aAa	9/9	0.23935503295846	3	FACETS	1	0.922	1	0.512	0.462	0.564	CLONAL	1	TRUE	1	0.23935503295846	3		756	1152	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186754	108186754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	89	607	0	ENST00000278616.4:c.6112C>T	p.His2038Tyr	p.H2038Y	ENST00000278616	NM_000051.3	2038	Cac/Tac	42/63	0.23935503295846	4	FACETS	0.864	0.764	0.971	0.432	0.382	0.486	CLONAL	1	TRUE	2	0.23935503295846	4		607	1067	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730828	40730828	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	105	700	0	ENST00000373198.4:c.3707G>A	p.Cys1236Tyr	p.C1236Y	ENST00000373198	NM_133170.3	1236	tGc/tAc	27/32	0.23935503295846	3	FACETS	1	0.917	1	0.515	0.46	0.573	CLONAL	1	TRUE	1	0.23935503295846	3		700	954	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041190	47041190	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	217	874	1	ENST00000377604.3:c.1618C>T	p.Gln540Ter	p.Q540*	ENST00000377604	NM_001204468.1	540	Cag/Tag	15/24	0.219308264704003	4	FACETS	0.967	0.898	1	0.967	0.898	1	CLONAL	2	TRUE	2	0.23935503295846	4		875	1162	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0017049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	112	401	3	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.753	0.677	0.833	1	0.983	1	SUBCLONAL	2	TRUE	1	0.184420227885221	2		404	807	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933819	36933819	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	57	446	0	ENST00000361632.4:c.1580C>A	p.Pro527His	p.P527H	ENST00000361632		527	cCc/cAc	12/16	1	2	FACETS	0.865	0.741	1	0.865	0.741	1	CLONAL	1	TRUE	1	0.184420227885221	2		446	715	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380661	118380661	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0017049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	35	379	0	ENST00000534358.1:c.10901-2A>G		p.X3634_splice	ENST00000534358	NM_005933.3	3634			1	2	FACETS	0.573	0.469	0.692	0.573	0.469	0.692	SUBCLONAL	1	TRUE	1	0.184420227885221	2		379	662	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	430221	430221	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	82	445	0	ENST00000399788.2:c.2481G>T	p.Lys827Asn	p.K827N	ENST00000399788	NM_001042603.1	827	aaG/aaT	18/28	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.184420227885221	2		445	679	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032044	10032044	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	61	509	0	ENST00000330684.3:c.779T>C	p.Leu260Ser	p.L260S	ENST00000330684	NM_001134407.1	260	tTg/tCg	3/13	1	2	FACETS	0.78	0.671	0.899	0.78	0.671	0.899	SUBCLONAL	1	TRUE	1	0.184420227885221	2		509	848	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0017049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	79	530	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.184420227885221	2		530	826	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55478800	55478800	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	53	507	0	ENST00000284073.2:c.373G>T	p.Asp125Tyr	p.D125Y	ENST00000284073	NM_138962.2	125	Gat/Tat	6/14	1	2	FACETS	0.694	0.59	0.809	0.694	0.59	0.809	SUBCLONAL	1	TRUE	1	0.184420227885221	2		507	828	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602581	10602581	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	58	503	0	ENST00000171111.5:c.997G>T	p.Gly333Cys	p.G333C	ENST00000171111	NM_203500.1	333	Ggc/Tgc	3/6	1	2	FACETS	0.659	0.564	0.762	0.659	0.564	0.762	SUBCLONAL	1	TRUE	1	0.184420227885221	2		503	955	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645711	12645711	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	22	225	0	ENST00000251849.4:c.758A>G	p.Gln253Arg	p.Q253R	ENST00000251849	NM_002880.3	253	cAg/cGg	7/17	1	2	FACETS	0.71	0.55	0.896	0.71	0.55	0.896	SUBCLONAL	1	TRUE	1	0.184420227885221	2		225	336	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390931	89390931	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	38	446	0	ENST00000336596.2:c.997A>G	p.Ile333Val	p.I333V	ENST00000336596	NM_005233.5	333	Atc/Gtc	5/17	1	2	FACETS	0.617	0.509	0.739	0.617	0.509	0.739	SUBCLONAL	1	TRUE	1	0.184420227885221	2		446	668	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38194902	38194902	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	94	816	0	ENST00000317025.8:c.831G>T	p.Lys277Asn	p.K277N	ENST00000317025	NM_023034.1	277	aaG/aaT	4/24	1	2	FACETS	0.776	0.688	0.87	0.776	0.688	0.87	SUBCLONAL	1	TRUE	1	0.184420227885221	2		816	1314	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	292	500	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.514909827982021	2		500	994	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0017050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	138	192	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	0.514909827982021	2		192	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577095	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519984	NA	P-0017050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	394	741	0	ENST00000269305.4:c.843C>A	p.Asp281Glu	p.D281E	ENST00000269305	NM_001126112.2	281	gaC/gaA	8/11	0.514909827982021	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.514909827982021	1		741	1126	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752411	57752412	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0017050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	95	205	0	ENST00000274289.3:c.1161_1162del	p.Arg387SerfsTer3	p.R387Sfs*3	ENST00000274289	NM_006622.3	387	agAGtg/agtg	9/14	0.509148993832532	1	FACETS	0.774	0.695	0.856	0.774	0.695	0.856	SUBCLONAL	1	TRUE	0	0.514909827982021	1		205	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0017051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	191	523	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.206963713172582	2	FACETS	0.775	0.717	0.836	0.775	0.717	0.836	SUBCLONAL	2	TRUE	0	0.250089790230193	2		523	985	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418670	49418670	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783698	NA	P-0017051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	330	558	1	ENST00000301067.7:c.15844C>T	p.Arg5282Ter	p.R5282*	ENST00000301067	NM_003482.3	5282	Cga/Tga	49/54	0.208020181750941	3	FACETS	0.883	0.835	0.932	0.883	0.835	0.932	CLONAL	3	TRUE	0	0.250089790230193	3		559	1121	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655173	45655173	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	48	360	0	ENST00000407780.3:c.679A>G	p.Thr227Ala	p.T227A	ENST00000407780	NM_001283052.1	227	Act/Gct	4/7	1	2	FACETS	0.499	0.421	0.586	0.499	0.421	0.586	SUBCLONAL	1	TRUE	1	0.250089790230193	2		360	769	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959317	38959317	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1221	150	443	1	ENST00000357387.3:c.2158A>C	p.Ile720Leu	p.I720L	ENST00000357387	NM_152756.3	720	Att/Ctt	22/38	0.250089790230193	5	FACETS	1	0.976	1	0.401	0.365	0.439	CLONAL	1	TRUE	2	0.250089790230193	5		444	1371	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131926965	131926965	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	178	394	1	ENST00000265335.6:c.1502A>C	p.Lys501Thr	p.K501T	ENST00000265335		501	aAa/aCa	10/25	0.214706307985579	2	FACETS	0.922	0.851	0.995	0.922	0.851	0.995	CLONAL	2	TRUE	0	0.250089790230193	2		395	772	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562912	176562912	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	120	753	2	ENST00000439151.2:c.808C>T	p.Gln270Ter	p.Q270*	ENST00000439151	NM_022455.4	270	Caa/Taa	2/23	0.214706307985579	2	FACETS	0.743	0.669	0.822	0.371	0.334	0.411	SUBCLONAL	1	TRUE	0	0.250089790230193	2		755	1292	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0017056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	380	390	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.782964992680287	2		392	908	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591076	67591076	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	185	305	0	ENST00000274335.5:c.1669C>T	p.Arg557Ter	p.R557*	ENST00000274335		557	Cga/Tga	12/15	1	2	FACETS	0.943	0.879	1	0.943	0.879	1	CLONAL	1	TRUE	1	0.782964992680287	2		305	501	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577586	7577586	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	274	467	0	ENST00000269305.4:c.695T>A	p.Ile232Asn	p.I232N	ENST00000269305	NM_001126112.2	232	aTc/aAc	7/11	1	2	FACETS	0.969	0.91	1	0.969	0.91	1	CLONAL	1	TRUE	1	0.556067038220685	2		467	1017	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559305	141559307	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0017057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	249	490	0	ENST00000220592.5:c.1494_1496del	p.Asp499del	p.D499del	ENST00000220592	NM_012154.3	498	gcGGAc/gcc	12/19	0.556067038220685	3	FACETS	0.876	0.817	0.936	0.438	0.408	0.468	CLONAL	1	TRUE	1	0.556067038220685	3		490	1307	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577593	7577603	+	frameshift_variant	Frame_Shift_Del	DEL	TACAGTCAGAG	TACAGTCAGAG	A	novel	NA	P-0017057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	220	438	0	ENST00000269305.4:c.678_688delinsT	p.Ser227ProfsTer17	p.S227Pfs*17	ENST00000269305	NM_001126112.2	226	ggCTCTGACTGTAcc/ggTcc	7/11	1	2	FACETS	0.822	0.765	0.88	0.822	0.765	0.88	CLONAL	1	TRUE	1	0.556067038220685	2		438	963	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0017060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	101	352	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.847	0.757	0.943	0.847	0.757	0.943	CLONAL	1	TRUE	1	0.310555817386561	2		352	768	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0017060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	258	410	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	0.310555817386561	3	FACETS	0.907	0.85	0.966	0.907	0.85	0.966	CLONAL	2	TRUE	1	0.310555817386561	3		410	1058	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0017060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	219	349	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	0.308689905579781	4	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	2	0.310555817386561	4		349	908	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0017060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	204	618	1	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.310555817386561	2		619	1201	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577586	7577587	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0017060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	117	400	0	ENST00000269305.4:c.694_695del	p.Ile232ProfsTer7	p.I232Pfs*7	ENST00000269305	NM_001126112.2	232	ATc/c	7/11	0.310555817386561	3	FACETS	0.881	0.793	0.974	0.441	0.396	0.487	CLONAL	1	TRUE	1	0.310555817386561	3		400	988	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151871214	151871214	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0017065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	129	505	0	ENST00000262189.6:c.9374+2T>G		p.X3125_splice	ENST00000262189	NM_170606.2	3125			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		505	756	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	275	301	4				ENST00000310581	NM_198253.2	-/1132			0.847054791921296	5	FACETS	0.983	0.935	1	0.983	0.935	1	CLONAL	3	TRUE	2	0.847054791921296	5		305	500	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29107910	29107910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	271	479	0	ENST00000328354.6:c.779C>T	p.Ser260Leu	p.S260L	ENST00000328354	NM_007194.3	260	tCa/tTa	6/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.847054791921296	2		479	611	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952498	38952498	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	106	274	0	ENST00000357387.3:c.2927C>G	p.Ala976Gly	p.A976G	ENST00000357387	NM_152756.3	976	gCt/gGt	30/38	0.847054791921296	5	FACETS	0.722	0.647	0.802	0.241	0.215	0.268	SUBCLONAL	1	TRUE	2	0.847054791921296	5		274	787	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857558	9857558	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	155	286	0	ENST00000330684.3:c.3843G>C	p.Lys1281Asn	p.K1281N	ENST00000330684	NM_001134407.1	1281	aaG/aaC	13/13	0.847054791921296	2	FACETS	0.986	0.915	1	0.493	0.457	0.53	CLONAL	1	TRUE	0	0.847054791921296	2		286	371	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248409	59248409	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1184098204	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	119	222	0	ENST00000371222.2:c.334G>C	p.Glu112Gln	p.E112Q	ENST00000371222	NM_002228.3	112	Gag/Cag	1/1	0.847054791921296	4	FACETS	0.919	0.832	1	0.306	0.277	0.337	CLONAL	1	TRUE	1	0.847054791921296	4		222	565	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022853	31022853	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs751021760	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	764	386	0	ENST00000375687.4:c.2338C>T	p.Gln780Ter	p.Q780*	ENST00000375687	NM_015338.5	780	Cag/Tag	13/13	0.847054791921296	6	FACETS	1	0.994	1			1	CLONAL	3	TRUE	NA	0.847054791921296	6		386	1493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578209	7578209	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	698	588	0	ENST00000269305.4:c.640del	p.His214IlefsTer33	p.H214Ifs*33	ENST00000269305	NM_001126112.2	214	Cat/at	6/11	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	2	TRUE	NA	0.847054791921296	2		588	823	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518731	204518731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	182	304	0	ENST00000367182.3:c.1394G>A	p.Arg465Lys	p.R465K	ENST00000367182	NM_001278516.1	465	aGa/aAa	11/11	0.847054791921296	4	FACETS	0.962	0.889	1	0.321	0.296	0.346	CLONAL	1	TRUE	1	0.847054791921296	4		304	825	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259196	16259196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750396773	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	258	372	0	ENST00000375759.3:c.6461C>T	p.Ser2154Phe	p.S2154F	ENST00000375759	NM_015001.2	2154	tCt/tTt	11/15	0.847054791921296	4	FACETS	1	0.979	1	0.367	0.343	0.391	CLONAL	1	TRUE	1	0.847054791921296	4		372	1023	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261140	16261140	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1275384688	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	203	292	0	ENST00000375759.3:c.8405C>T	p.Ser2802Leu	p.S2802L	ENST00000375759	NM_015001.2	2802	tCa/tTa	11/15	0.847054791921296	4	FACETS	1	0.934	1	0.335	0.311	0.361	CLONAL	1	TRUE	1	0.847054791921296	4		292	880	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262414	16262414	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	125	213	0	ENST00000375759.3:c.9679C>G	p.Gln3227Glu	p.Q3227E	ENST00000375759	NM_015001.2	3227	Cag/Gag	11/15	0.847054791921296	4	FACETS	1	0.956	1	0.361	0.328	0.395	CLONAL	1	TRUE	1	0.847054791921296	4		213	504	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263658	16263658	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	145	312	0	ENST00000375759.3:c.10027G>C	p.Gly3343Arg	p.G3343R	ENST00000375759	NM_015001.2	3343	Ggc/Cgc	12/15	0.847054791921296	4	FACETS	0.875	0.799	0.953	0.292	0.266	0.318	CLONAL	1	TRUE	1	0.847054791921296	4		312	723	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023808	27023808	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747283284	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	219	283	0	ENST00000324856.7:c.914C>T	p.Ala305Val	p.A305V	ENST00000324856	NM_006015.4	305	gCc/gTc	1/20	0.723641954248252	4	FACETS	1	0.968	1			1	CLONAL	1	TRUE	NA	0.847054791921296	4		283	896	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305269	39305269	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1604	276	499	0	ENST00000373001.3:c.1156C>G	p.Leu386Val	p.L386V	ENST00000373001	NM_022157.3	386	Ctg/Gtg	7/7	0.847054791921296	6	FACETS	0.934	0.873	0.997			1	CLONAL	1	TRUE	NA	0.847054791921296	6		499	1880	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532729	46532729	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756800675	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	209	378	0	ENST00000262741.5:c.349C>T	p.His117Tyr	p.H117Y	ENST00000262741	NM_003629.3	117	Cac/Tac	4/10	0.847054791921296	4	FACETS	0.866	0.803	0.93	0.289	0.267	0.31	CLONAL	1	TRUE	1	0.847054791921296	4		378	1053	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332884	65332884	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	83	197	1	ENST00000342505.4:c.655C>T	p.Arg219Ter	p.R219*	ENST00000342505	NM_002227.2	219	Cga/Tga	7/25	0.847054791921296	4	FACETS	0.783	0.694	0.878	0.261	0.231	0.293	SUBCLONAL	1	TRUE	1	0.847054791921296	4		198	462	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414974	78414974	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	210	331	0	ENST00000370768.2:c.1792C>T	p.Pro598Ser	p.P598S	ENST00000370768	NM_003902.3	598	Cct/Tct	19/20	0.847054791921296	4	FACETS	0.956	0.888	1	0.319	0.296	0.342	CLONAL	1	TRUE	1	0.847054791921296	4		331	958	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263273	115263273	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	393	614	0	ENST00000438362.2:c.2077C>T	p.Gln693Ter	p.Q693*	ENST00000438362	NM_001242891.1	693	Cag/Tag	17/20	0.847054791921296	4	FACETS	1	0.985	1	0.364	0.345	0.383	CLONAL	1	TRUE	1	0.847054791921296	4		614	1571	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518658	204518658	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	212	330	0	ENST00000367182.3:c.1321G>T	p.Glu441Ter	p.E441*	ENST00000367182	NM_001278516.1	441	Gag/Tag	11/11	0.847054791921296	4	FACETS	0.916	0.851	0.984	0.305	0.283	0.328	CLONAL	1	TRUE	1	0.847054791921296	4		330	1009	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649908	88649908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554888119	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	214	349	0	ENST00000372037.3:c.157G>A	p.Glu53Lys	p.E53K	ENST00000372037	NM_004329.2	53	Gag/Aag	4/13	0.847054791921296	2	FACETS	1	0.945	1	0.503	0.472	0.535	CLONAL	1	TRUE	0	0.847054791921296	2		349	502	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136921	64136921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	146	226	1	ENST00000334205.4:c.1432C>T	p.His478Tyr	p.H478Y	ENST00000334205	NM_003942.2	478	Cac/Tac	13/17	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.847054791921296	2		227	314	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115654	108115654	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs557012154	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	192	418	0	ENST00000278616.4:c.802C>T	p.Gln268Ter	p.Q268*	ENST00000278616	NM_000051.3	268	Caa/Taa	7/63	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.847054791921296	2		418	415	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342434	118342434	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	173	334	0	ENST00000534358.1:c.560C>G	p.Ser187Ter	p.S187*	ENST00000534358	NM_005933.3	187	tCa/tGa	3/36	1	2	FACETS	0.937	0.872	1	0.937	0.872	1	CLONAL	1	TRUE	1	0.847054791921296	2		334	436	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342455	118342455	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	182	322	0	ENST00000534358.1:c.581C>G	p.Ser194Cys	p.S194C	ENST00000534358	NM_005933.3	194	tCt/tGt	3/36	1	2	FACETS	0.99	0.924	1	0.99	0.924	1	CLONAL	1	TRUE	1	0.847054791921296	2		322	434	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342793	118342793	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	245	357	0	ENST00000534358.1:c.919C>G	p.Pro307Ala	p.P307A	ENST00000534358	NM_005933.3	307	Cca/Gca	3/36	1	2	FACETS	0.972	0.916	1	0.972	0.916	1	CLONAL	1	TRUE	1	0.847054791921296	2		357	595	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343343	118343343	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	171	281	0	ENST00000534358.1:c.1469C>G	p.Ser490Cys	p.S490C	ENST00000534358	NM_005933.3	490	tCt/tGt	3/36	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.847054791921296	2		281	389	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344054	118344054	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	193	323	0	ENST00000534358.1:c.2180C>G	p.Ser727Cys	p.S727C	ENST00000534358	NM_005933.3	727	tCt/tGt	3/36	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.847054791921296	2		323	410	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444789	49444789	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	405	622	0	ENST00000301067.7:c.2677C>T	p.Pro893Ser	p.P893S	ENST00000301067	NM_003482.3	893	Ccc/Tcc	10/54	0.847054791921296	3	FACETS	1	0.981	1	0.529	0.503	0.555	CLONAL	1	TRUE	1	0.847054791921296	3		622	1287	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445073	49445073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	202	390	0	ENST00000301067.7:c.2393C>T	p.Ser798Phe	p.S798F	ENST00000301067	NM_003482.3	798	tCc/tTc	10/54	0.847054791921296	3	FACETS	0.841	0.781	0.903	0.421	0.39	0.452	CLONAL	1	TRUE	1	0.847054791921296	3		390	807	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445077	49445077	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	205	408	0	ENST00000301067.7:c.2389C>A	p.Leu797Met	p.L797M	ENST00000301067	NM_003482.3	797	Ctg/Atg	10/54	0.847054791921296	3	FACETS	0.832	0.773	0.893	0.416	0.386	0.447	CLONAL	1	TRUE	1	0.847054791921296	3		408	828	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134211	41134211	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	343	242	0	ENST00000379561.5:c.1417del	p.His473IlefsTer5	p.H473Ifs*5	ENST00000379561	NM_002015.3	473	Cat/at	2/3	NA	2	FACETS	0.971	0.944	0.997			1	INDETERMINATE	2	TRUE	NA	0.847054791921296	2		242	417	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355914	73355914	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	263	434	0	ENST00000377767.4:c.57C>G	p.Ile19Met	p.I19M	ENST00000377767	NM_014953.3	19	atC/atG	1/21	0.796806513413726	4	FACETS	0.932	0.872	0.993	0.466	0.436	0.497	CLONAL	1	TRUE	2	0.847054791921296	4		434	1231	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435067	110435067	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	234	400	0	ENST00000375856.3:c.3334G>C	p.Glu1112Gln	p.E1112Q	ENST00000375856	NM_003749.2	1112	Gag/Cag	1/2	0.796806513413726	4	FACETS	0.877	0.817	0.939	0.438	0.408	0.47	CLONAL	1	TRUE	2	0.847054791921296	4		400	1164	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107922	30107922	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	179	388	0	ENST00000331968.5:c.885C>G	p.Phe295Leu	p.F295L	ENST00000331968	NM_002742.2	295	ttC/ttG	5/18	0.847054791921296	3	FACETS	0.806	0.745	0.87	0.403	0.372	0.435	CLONAL	1	TRUE	1	0.847054791921296	3		388	746	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43738605	43738605	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1364340339	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	44	517	0	ENST00000382044.4:c.3020C>G	p.Ser1007Cys	p.S1007C	ENST00000382044	NM_001141980.1	1007	tCt/tGt	14/28	1	2	FACETS	0.127	0.106	0.15	0.127	0.106	0.15	SUBCLONAL	1	TRUE	1	0.847054791921296	2		517	819	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118631	17118631	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	212	312	0	ENST00000285071.4:c.1301-1G>A		p.X434_splice	ENST00000285071	NM_144997.5	434			0.847054791921296	3	FACETS	0.934	0.87	0.999	0.467	0.435	0.5	CLONAL	1	TRUE	1	0.847054791921296	3		312	763	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40460342	40460342	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	199	289	0	ENST00000345506.4:c.2053C>G	p.Pro685Ala	p.P685A	ENST00000345506	NM_003152.3	685	Cct/Gct	17/20	0.847054791921296	3	FACETS	0.987	0.918	1	0.493	0.459	0.529	CLONAL	1	TRUE	1	0.847054791921296	3		289	678	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56432344	56432344	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	236	354	0	ENST00000407977.2:c.2312C>A	p.Ser771Ter	p.S771*	ENST00000407977		771	tCa/tAa	10/10	0.847054791921296	3	FACETS	1	0.953	1	0.51	0.478	0.544	CLONAL	1	TRUE	1	0.847054791921296	3		354	777	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733044	74733044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	167	353	0	ENST00000359995.5:c.199G>A	p.Asp67Asn	p.D67N	ENST00000359995	NM_001195427.1	67	Gac/Aac	1/3	0.847054791921296	3	FACETS	0.829	0.764	0.896	0.415	0.382	0.448	CLONAL	1	TRUE	1	0.847054791921296	3		353	677	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024711	11024711	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	338	210	0	ENST00000327064.4:c.828G>C	p.Lys276Asn	p.K276N	ENST00000327064	NM_199141.1	276	aaG/aaC	6/16	0.847054791921296	4	FACETS	1	0.971	1	0.683	0.651	0.716	CLONAL	2	TRUE	1	0.847054791921296	4		210	719	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17940961	17940961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1456924832	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	518	497	0	ENST00000458235.1:c.3163G>A	p.Glu1055Lys	p.E1055K	ENST00000458235	NM_000215.3	1055	Gag/Aag	23/24	0.847054791921296	4	FACETS	1	0.962	1	0.667	0.641	0.693	CLONAL	2	TRUE	1	0.847054791921296	4		497	1129	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727866	41727866	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	308	573	0	ENST00000301178.4:c.491G>T	p.Gly164Val	p.G164V	ENST00000301178	NM_021913.4	164	gGa/gTa	4/20	0.847054791921296	4	FACETS	0.967	0.91	1	0.322	0.303	0.342	CLONAL	1	TRUE	1	0.847054791921296	4		573	1389	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856054	45856054	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs922327414	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	799	431	0	ENST00000391945.4:c.1852G>A	p.Val618Ile	p.V618I	ENST00000391945	NM_000400.3	618	Gtc/Atc	20/23	0.847054791921296	4	FACETS	0.966	0.942	0.99	0.966	0.942	0.99	CLONAL	3	TRUE	1	0.847054791921296	4		431	1202	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907693	111907693	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	168	276	0	ENST00000393256.3:c.467G>T	p.Gly156Val	p.G156V	ENST00000393256	NM_006538.4	156	gGa/gTa	3/4	0.847054791921296	3	FACETS	0.932	0.861	1	0.311	0.287	0.335	CLONAL	1	TRUE	0	0.847054791921296	3		276	606	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285240	212285240	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	298	487	0	ENST00000342788.4:c.3061G>C	p.Glu1021Gln	p.E1021Q	ENST00000342788	NM_005235.2	1021	Gag/Cag	25/28	0.847054791921296	3	FACETS	1	0.979	1	0.359	0.339	0.38	CLONAL	1	TRUE	0	0.847054791921296	3		487	930	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281697	142281697	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	271	536	0	ENST00000350721.4:c.547G>C	p.Asp183His	p.D183H	ENST00000350721	NM_001184.3	183	Gat/Cat	4/47	0.847054791921296	4	FACETS	0.894	0.837	0.952	0.447	0.418	0.476	CLONAL	1	TRUE	2	0.847054791921296	4		536	1322	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182679131	182679131	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	206	478	0	ENST00000292782.4:c.403G>A	p.Glu135Lys	p.E135K	ENST00000292782	NM_020640.2	135	Gaa/Aaa	4/7	0.847054791921296	4	FACETS	0.977	0.907	1	0.488	0.453	0.525	CLONAL	1	TRUE	2	0.847054791921296	4		478	920	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940665	131940665	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	211	352	0	ENST00000265335.6:c.2692G>C	p.Val898Leu	p.V898L	ENST00000265335		898	Gtt/Ctt	16/25	0.847054791921296	3	FACETS	0.857	0.797	0.918	0.428	0.398	0.459	CLONAL	1	TRUE	1	0.847054791921296	3		352	828	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032254	26032254	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	86	195	0	ENST00000244661.2:c.35C>A	p.Thr12Asn	p.T12N	ENST00000244661	NM_003537.3	12	aCc/aAc	1/1	0.847054791921296	3	FACETS	0.794	0.708	0.885	0.397	0.354	0.443	SUBCLONAL	1	TRUE	1	0.847054791921296	3		195	364	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271257	26271257	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	351	330	0	ENST00000305910.3:c.356C>A	p.Thr119Asn	p.T119N	ENST00000305910	NM_003534.2	119	aCt/aAt	1/1	0.847054791921296	3	FACETS	0.91	0.871	0.949	0.91	0.871	0.949	CLONAL	2	TRUE	1	0.847054791921296	3		330	648	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839921	27839921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	186	365	1	ENST00000328488.2:c.173C>T	p.Ser58Leu	p.S58L	ENST00000328488	NM_003533.2	58	tCg/tTg	1/1	0.847054791921296	3	FACETS	0.91	0.843	0.979	0.455	0.421	0.49	CLONAL	1	TRUE	1	0.847054791921296	3		366	687	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099616	157099616	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1448942636	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	14	26	0	ENST00000346085.5:c.553G>C	p.Glu185Gln	p.E185Q	ENST00000346085	NM_020732.3	185	Gag/Cag	1/20	0.847054791921296	3	FACETS	0.663	0.489	0.863	0.331	0.244	0.432	SUBCLONAL	1	TRUE	1	0.847054791921296	3		26	71	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405817	157405817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	148	289	0	ENST00000346085.5:c.2059G>A	p.Asp687Asn	p.D687N	ENST00000346085	NM_020732.3	687	Gac/Aac	6/20	0.847054791921296	3	FACETS	0.884	0.811	0.959	0.442	0.405	0.48	CLONAL	1	TRUE	1	0.847054791921296	3		289	563	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836778	151836778	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	249	418	0	ENST00000262189.6:c.14442G>C	p.Glu4814Asp	p.E4814D	ENST00000262189	NM_170606.2	4814	gaG/gaC	56/59	0.847054791921296	3	FACETS	0.932	0.873	0.992	0.466	0.436	0.496	CLONAL	1	TRUE	1	0.847054791921296	3		418	898	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152373128	152373128	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	340	475	0	ENST00000359321.1:c.37G>C	p.Glu13Gln	p.E13Q	ENST00000359321	NM_005431.1	13	Gag/Cag	1/3	0.847054791921296	3	FACETS	1	0.98	1	0.533	0.505	0.562	CLONAL	1	TRUE	1	0.847054791921296	3		475	1072	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341121	8341121	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	287	458	0	ENST00000356435.5:c.5095T>C	p.Tyr1699His	p.Y1699H	ENST00000356435		1699	Tac/Cac	30/35	0.847054791921296	2	FACETS	0.982	0.93	1	0.491	0.465	0.518	CLONAL	1	TRUE	0	0.847054791921296	2		458	690	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650070	93650070	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	251	436	0	ENST00000375746.1:c.1621C>G	p.Pro541Ala	p.P541A	ENST00000375746	NM_001174167.1	541	Ccg/Gcg	12/14	1	2	FACETS	0.983	0.927	1	0.983	0.927	1	CLONAL	1	TRUE	1	0.847054791921296	2		436	603	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041624	47041624	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	831	308	0	ENST00000377604.3:c.1851del	p.Ala618ProfsTer86	p.A618Pfs*86	ENST00000377604	NM_001204468.1	617	Ccc/cc	17/24	0.847054791921296	3	FACETS	0.982	0.967	0.996			1	CLONAL	3	TRUE	NA	0.847054791921296	3		308	948	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020196	123020196	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	643	229	0	ENST00000355640.3:c.684C>G	p.Phe228Leu	p.F228L	ENST00000355640		228	ttC/ttG	2/7	0.779187492014306	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.847054791921296	2		229	711	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	174	301	4				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.486824830876622	2		305	551	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057835	27057835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1858	271	657	0	ENST00000324856.7:c.1543C>T	p.Gln515Ter	p.Q515*	ENST00000324856	NM_006015.4	515	Cag/Tag	3/20	1	2	FACETS	0.523	0.488	0.559	0.523	0.488	0.559	SUBCLONAL	1	TRUE	1	0.486824830876622	2		657	2129	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1339	515	585	0	ENST00000267101.3:c.310G>C	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ctg	3/28	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.486824830876622	2		585	1854	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8733795	8733795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138127948	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	297	382	1	ENST00000356435.5:c.49C>T	p.Arg17Cys	p.R17C	ENST00000356435		17	Cgc/Tgc	1/35	0.486824830876622	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.486824830876622	1		383	893	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006075	22006075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762253433	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	286	257	0	ENST00000276925.6:c.328G>A	p.Asp110Asn	p.D110N	ENST00000276925	NM_004936.3	110	Gat/Aat	2/2	0.486824830876622	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.486824830876622	1		257	647	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257569	16257569	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	391	559	0	ENST00000375759.3:c.4834G>C	p.Asp1612His	p.D1612H	ENST00000375759	NM_015001.2	1612	Gat/Cat	11/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.486824830876622	2		559	1574	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809217	243809217	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1217463895	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	252	427	0	ENST00000263826.5:c.407C>T	p.Ser136Phe	p.S136F	ENST00000263826	NM_005465.4	136	tCt/tTt	4/13	1	2	FACETS	0.899	0.841	0.96	0.899	0.841	0.96	CLONAL	1	TRUE	1	0.486824830876622	2		427	1151	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	432	502	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.486824830876622	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.486824830876622	1		502	1220	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074183	8074183	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	264	339	0	ENST00000377482.5:c.476C>T	p.Ser159Phe	p.S159F	ENST00000377482	NM_018948.3	159	tCt/tTt	4/4	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.486824830876622	2		339	1023	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256888	16256888	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1191	420	485	0	ENST00000375759.3:c.4153G>C	p.Asp1385His	p.D1385H	ENST00000375759	NM_015001.2	1385	Gat/Cat	11/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.486824830876622	2		485	1611	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257995	16257995	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1176124993	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	321	355	0	ENST00000375759.3:c.5260G>A	p.Asp1754Asn	p.D1754N	ENST00000375759	NM_015001.2	1754	Gac/Aac	11/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.486824830876622	2		355	1151	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258394	16258394	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1286	436	528	1	ENST00000375759.3:c.5659C>T	p.Leu1887Phe	p.L1887F	ENST00000375759	NM_015001.2	1887	Ctt/Ttt	11/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.486824830876622	2		529	1722	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435093	49435093	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	278	275	0	ENST00000301067.7:c.6460G>C	p.Asp2154His	p.D2154H	ENST00000301067	NM_003482.3	2154	Gac/Cac	31/54	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.486824830876622	2		275	1077	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434113	121434113	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	409	480	0	ENST00000257555.6:c.1004C>G	p.Ser335Ter	p.S335*	ENST00000257555		335	tCa/tGa	5/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.486824830876622	2		480	1609	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914056	32914056	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	273	502	0	ENST00000380152.3:c.5564C>G	p.Ser1855Ter	p.S1855*	ENST00000380152		1855	tCa/tGa	11/27	0.326619017681428	1	FACETS	0.902	0.848	0.957	0.902	0.848	0.957	CLONAL	1	TRUE	0	0.486824830876622	1		502	941	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878148	48878148	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	37	60	0	ENST00000267163.4:c.100G>C	p.Glu34Gln	p.E34Q	ENST00000267163	NM_000321.2	34	Gag/Cag	1/27	0.326619017681428	1	FACETS	0.431	0.357	0.512	0.431	0.357	0.512	SUBCLONAL	1	TRUE	0	0.486824830876622	1		60	267	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748891	43748891	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1298603817	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1291	510	700	0	ENST00000382044.4:c.1915C>T	p.Arg639Ter	p.R639*	ENST00000382044	NM_001141980.1	639	Cga/Tga	12/28	0.251775102694028	1	FACETS	0.88	0.841	0.92	0.88	0.841	0.92	INDETERMINATE	1	TRUE	0	0.486824830876622	1		700	1801	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727386	66727386	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	110	235	0	ENST00000307102.5:c.102G>C	p.Gln34His	p.Q34H	ENST00000307102	NM_002755.3	34	caG/caC	2/11	0.251775102694028	1	FACETS	0.475	0.427	0.526	0.475	0.427	0.526	INDETERMINATE	1	TRUE	0	0.486824830876622	1		235	720	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100616	67100616	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	464	329	0	ENST00000412916.2:c.314G>A	p.Gly105Glu	p.G105E	ENST00000412916		105	gGa/gAa	4/6	0.430977919382739	2	FACETS	0.909	0.871	0.946	0.909	0.871	0.946	CLONAL	2	TRUE	0	0.486824830876622	2		329	1049	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81941350	81941350	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1154	81	473	0	ENST00000359376.3:c.1528G>C	p.Glu510Gln	p.E510Q	ENST00000359376	NM_002661.3	510	Gaa/Caa	16/33	0.486824830876622	1	FACETS	0.204	0.179	0.231	0.204	0.179	0.231	SUBCLONAL	1	TRUE	0	0.486824830876622	1		473	1235	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587782272	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	332	642	0	ENST00000269305.4:c.994-1G>C		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.486824830876622	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.486824830876622	1		642	1016	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244785	41244785	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1439	459	551	0	ENST00000357654.3:c.2763G>C	p.Gln921His	p.Q921H	ENST00000357654	NM_007294.3	921	caG/caC	10/23	1	2	FACETS	0.994	0.946	1	0.994	0.946	1	CLONAL	1	TRUE	1	0.486824830876622	2		551	1898	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597486	10597486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1188	168	464	0	ENST00000171111.5:c.1717G>A	p.Asp573Asn	p.D573N	ENST00000171111	NM_203500.1	573	Gat/Aat	6/6	0.326619017681428	1	FACETS	0.385	0.353	0.419	0.385	0.353	0.419	SUBCLONAL	1	TRUE	0	0.486824830876622	1		464	1356	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945774	17945774	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1298	374	472	0	ENST00000458235.1:c.2086C>T	p.Leu696Phe	p.L696F	ENST00000458235	NM_000215.3	696	Ctc/Ttc	16/24	0.26965314179184	3	FACETS	1	0.988	1	0.571	0.541	0.603	INDETERMINATE	1	TRUE	1	0.486824830876622	3		472	1672	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765672	41765672	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1589	102	513	0	ENST00000301178.4:c.2548G>C	p.Asp850His	p.D850H	ENST00000301178	NM_021913.4	850	Gat/Cat	20/20	0.26965314179184	3	FACETS	0.308	0.274	0.345	0.154	0.137	0.173	INDETERMINATE	1	TRUE	1	0.486824830876622	3		513	1691	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791509	42791509	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1425	366	475	0	ENST00000575354.2:c.490C>G	p.Leu164Val	p.L164V	ENST00000575354	NM_015125.3	164	Cta/Gta	4/20	0.26965314179184	3	FACETS	1	0.972	1	0.522	0.493	0.551	INDETERMINATE	1	TRUE	1	0.486824830876622	3		475	1791	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605127	46605127	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs760600266	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	122	404	0	ENST00000263734.3:c.1344G>C	p.Gln448His	p.Q448H	ENST00000263734	NM_001430.4	448	caG/caC	10/16	1	2	FACETS	0.397	0.357	0.438	0.397	0.357	0.438	SUBCLONAL	1	TRUE	1	0.486824830876622	2		404	1264	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225367728	225367728	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	158	399	0	ENST00000264414.4:c.1439C>G	p.Ser480Ter	p.S480*	ENST00000264414	NM_003590.4	480	tCa/tGa	10/16	0.326619017681428	1	FACETS	0.442	0.404	0.482	0.442	0.404	0.482	SUBCLONAL	1	TRUE	0	0.486824830876622	1		399	1110	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743936	40743936	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	265	366	0	ENST00000373198.4:c.3059G>C	p.Trp1020Ser	p.W1020S	ENST00000373198	NM_133170.3	1020	tGg/tCg	23/32	1	2	FACETS	0.819	0.767	0.874	0.819	0.767	0.874	CLONAL	1	TRUE	1	0.486824830876622	2		366	1329	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553304	41553304	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	398	483	0	ENST00000263253.7:c.3393T>A	p.Tyr1131Ter	p.Y1131*	ENST00000263253	NM_001429.3	1131	taT/taA	18/31	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.486824830876622	2		483	1618	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539513	187539513	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	222	290	0	ENST00000441802.2:c.8227C>G	p.Pro2743Ala	p.P2743A	ENST00000441802	NM_005245.3	2743	Cca/Gca	10/27	0.486824830876622	1	FACETS	0.941	0.88	1	0.941	0.88	1	CLONAL	1	TRUE	0	0.486824830876622	1		290	733	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540944	187540944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	241	246	0	ENST00000441802.2:c.6796G>A	p.Glu2266Lys	p.E2266K	ENST00000441802	NM_005245.3	2266	Gaa/Aaa	10/27	0.486824830876622	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.486824830876622	1		246	674	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973824	131973824	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	289	354	0	ENST00000265335.6:c.3527C>G	p.Ser1176Cys	p.S1176C	ENST00000265335		1176	tCt/tGt	23/25	0.486824830876622	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.486824830876622	1		354	869	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873299	151873299	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	98	195	0	ENST00000262189.6:c.9239C>T	p.Ser3080Leu	p.S3080L	ENST00000262189	NM_170606.2	3080	tCa/tTa	38/59	0.251775102694028	1	FACETS	0.463	0.413	0.516	0.463	0.413	0.516	INDETERMINATE	1	TRUE	0	0.486824830876622	1		195	658	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737793	145737793	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1266261662	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	151	414	0	ENST00000428558.2:c.3037G>A	p.Asp1013Asn	p.D1013N	ENST00000428558	NM_004260.3	1013	Gac/Aac	18/22	NA	2	FACETS	0.466	0.425	0.51			1	INDETERMINATE	1	TRUE	NA	0.486824830876622	2		414	1331	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738344	145738344	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1418	208	530	0	ENST00000428558.2:c.2641G>C	p.Glu881Gln	p.E881Q	ENST00000428558	NM_004260.3	881	Gag/Cag	16/22	NA	2	FACETS	0.526	0.486	0.567			1	INDETERMINATE	1	TRUE	NA	0.486824830876622	2		530	1626	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949128	44949128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	355	192	0	ENST00000377967.4:c.3689C>T	p.Ala1230Val	p.A1230V	ENST00000377967	NM_021140.2	1230	gCt/gTt	25/29	1	1	FACETS	0.798	0.763	0.834	1	0.996	1	SUBCLONAL	2	TRUE	0	0.486824830876622	1		192	691	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22008907	22008910	+	missense_variant	Missense_Mutation	ONP	CATC	CATC	TATT	novel	NA	P-0017068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	257	393	0	ENST00000276925.6:c.43_46delinsAATA	p.Asp15_Glu16delinsAsnLys	p.D15_E16delinsNK	ENST00000276925	NM_004936.3	15	GATGag/AATAag	1/2	0.486824830876622	1	FACETS	0.814	0.763	0.867	0.814	0.763	0.867	CLONAL	1	TRUE	0	0.486824830876622	1		393	981	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183772	10183772	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	220	473	0	ENST00000256474.2:c.242del	p.Pro81ArgfsTer78	p.P81Rfs*78	ENST00000256474	NM_000551.3	81	Ccg/cg	1/3	0.511670990880484	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.511670990880484	1		473	606	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595952	52595953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	183	438	0	ENST00000394830.3:c.3962dup	p.Lys1322GlufsTer19	p.K1322Efs*19	ENST00000394830	NM_018313.4	1321	aag/aaAg	26/30	0.511670990880484	1	FACETS	0.929	0.863	0.997	0.929	0.863	0.997	CLONAL	1	TRUE	0	0.511670990880484	1		438	573	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402755	20402755	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	130	247	0	ENST00000346618.3:c.292C>A	p.Leu98Ile	p.L98I	ENST00000346618	NM_001949.4	98	Ctc/Atc	1/7	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.511670990880484	2		247	459	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0017071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	111	290	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	0.218489873904713	2		290	750	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0017071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	53	390	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.758	0.646	0.881	0.758	0.646	0.881	SUBCLONAL	1	TRUE	1	0.218489873904713	2		392	640	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0017071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	114	513	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.218489873904713	2		513	814	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122614	108122614	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	51	381	0	ENST00000278616.4:c.1658G>T	p.Gly553Val	p.G553V	ENST00000278616	NM_000051.3	553	gGa/gTa	11/63	0.218489873904713	1	FACETS	0.602	0.51	0.702	0.602	0.51	0.702	SUBCLONAL	1	TRUE	0	0.218489873904713	1		381	691	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122637	108122637	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	65	385	0	ENST00000278616.4:c.1681C>T	p.Gln561Ter	p.Q561*	ENST00000278616	NM_000051.3	561	Caa/Taa	11/63	0.218489873904713	1	FACETS	0.758	0.657	0.869	0.758	0.657	0.869	SUBCLONAL	1	TRUE	0	0.218489873904713	1		385	699	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647519	3647519	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1397	139	511	2	ENST00000294008.3:c.1544G>C	p.Arg515Thr	p.R515T	ENST00000294008	NM_032444.2	515	aGa/aCa	7/15	1	2	FACETS	0.828	0.751	0.91	0.828	0.751	0.91	CLONAL	1	TRUE	1	0.218489873904713	2		513	1536	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705622	47705622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	62	300	1	ENST00000233146.2:c.2422G>A	p.Glu808Lys	p.E808K	ENST00000233146	NM_000251.2	808	Gaa/Aaa	14/16	1	2	FACETS	0.887	0.766	1	0.887	0.766	1	CLONAL	1	TRUE	1	0.218489873904713	2		301	640	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778810	76778810	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	87	515	0	ENST00000373344.5:c.6769C>G	p.Leu2257Val	p.L2257V	ENST00000373344	NM_000489.3	2257	Ctt/Gtt	31/35	0.218489873904713	1	FACETS	0.966	0.855	1	0.966	0.855	1	CLONAL	1	TRUE	0	0.218489873904713	1		515	734	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0017095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	161	308	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.98	0.901	1	0.98	0.901	1	CLONAL	1	TRUE	1	0.495044340782031	2		308	664	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0017096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	190	178	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.45392386411732	2		178	811	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231783	36231783	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	249	602	0	ENST00000300305.3:c.601del	p.Arg201GlufsTer10	p.R201Efs*10	ENST00000300305		201	Cga/ga	5/8	1	2	FACETS	0.946	0.884	1	0.946	0.884	1	CLONAL	1	TRUE	1	0.45392386411732	2		602	1160	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161782	56161783	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTACATCTAGTTCAGA	novel	NA	P-0017096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	144	440	0	ENST00000399503.3:c.1283_1284insATCTAGTTCAGACTAC	p.Glu432AspfsTer4	p.E432Dfs*4	ENST00000399503	NM_005921.1	427	tct/tCTACATCTAGTTCAGAct	6/20	1	2	FACETS	0.697	0.635	0.762	0.697	0.635	0.762	SUBCLONAL	1	TRUE	1	0.45392386411732	2		440	910	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178382	56178382	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0017096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	128	272	1	ENST00000399503.3:c.3355A>T	p.Lys1119Ter	p.K1119*	ENST00000399503	NM_005921.1	1119	Aaa/Taa	14/20	1	2	FACETS	0.938	0.853	1	0.938	0.853	1	CLONAL	1	TRUE	1	0.45392386411732	2		273	601	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0017097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2752	485	415	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.786973713844128	12	FACETS	0.94	0.893	0.987			1	CLONAL	2	TRUE	NA	0.786973713844128	12		415	3237	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100117	157100119	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs797045268	NA	P-0017097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	10	23	0	ENST00000346085.5:c.1069_1071del	p.Gly357del	p.G357del	ENST00000346085	NM_020732.3	352	GGC/-	1/20	0.786973713844128	4	FACETS	0.441	0.301	0.614	0.22	0.15	0.307	SUBCLONAL	1	TRUE	2	0.786973713844128	4		23	103	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578213	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs864309495	NA	P-0017097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	736	642	0	ENST00000269305.4:c.636del	p.Arg213AspfsTer34	p.R213Dfs*34	ENST00000269305	NM_001126112.2	212	ttT/tt	6/11	0.786973713844128	2	FACETS	0.966	0.945	0.987	0.966	0.945	0.987	CLONAL	2	TRUE	0	0.786973713844128	2		642	968	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453138	140453139	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTA	rs727502902	NA	P-0017097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	521	452	0	ENST00000288602.6:c.1794_1796dup	p.Thr599dup	p.T599dup	ENST00000288602	NM_004333.4	599	aca/acTACa	15/18	0.786973713844128	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.786973713844128	4		452	1166	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692889	89692889	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	1846	334	0	ENST00000371953.3:c.375del	p.Ala126LeufsTer8	p.A126Lfs*8	ENST00000371953	NM_000314.4	125	Aaa/aa	5/9	0.786973713844128	12	FACETS	0.996	0.983	1			1	CLONAL	10	TRUE	NA	0.786973713844128	12		334	2325	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479763	67479763	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs140880290	NA	P-0017097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	230	420	0	ENST00000327367.4:c.1070A>G	p.Asn357Ser	p.N357S	ENST00000327367	NM_005902.3	357	aAc/aGc	8/9	1	2	FACETS	0.979	0.919	1	0.979	0.919	1	CLONAL	1	TRUE	1	0.786973713844128	2		420	597	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246929	10246929	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	247	427	2	ENST00000340748.4:c.4476C>G	p.Phe1492Leu	p.F1492L	ENST00000340748		1492	ttC/ttG	37/40	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.786973713844128	2		429	590	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	141	594	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.3	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.26	1		594	822	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0017098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	26	395	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	1	2	FACETS	0.239	0.188	0.297	0.239	0.188	0.297	SUBCLONAL	1	TRUE	1	0.26	2		395	838	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0017098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	108	497	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	1	2	FACETS	0.901	0.808	1	0.901	0.808	1	CLONAL	1	TRUE	1	0.26	2		497	922	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005582	42005587	+	inframe_deletion	In_Frame_Del	DEL	AGATCC	AGATCC	-	novel	NA	P-0017098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	121	397	0	ENST00000219905.7:c.3320_3325del	p.Asp1107_Pro1108del	p.D1107_P1108del	ENST00000219905	NM_001164273.1	1106	cgAGATCCa/cga	9/24	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.26	2		397	923	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0017099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	145	290	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.258597803477843	2		290	871	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842326	68842326	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0017099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	133	487	1	ENST00000261769.5:c.388-1G>A		p.X130_splice	ENST00000261769	NM_004360.3	130			0.258597803477843	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.258597803477843	1		488	829	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942871	15942890	+	frameshift_variant	Frame_Shift_Del	DEL	GTCATCAAAGCTTCCCATGA	GTCATCAAAGCTTCCCATGA	-	novel	NA	P-0017099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	68	575	2	ENST00000268712.3:c.6812_6831del	p.Leu2271GlnfsTer3	p.L2271Qfs*3	ENST00000268712	NM_006311.3	2271	cTCATGGGAAGCTTTGATGAC/c	44/46	1	2	FACETS	0.515	0.447	0.59	0.515	0.447	0.59	SUBCLONAL	1	TRUE	1	0.258597803477843	2		577	1021	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055670	152055670	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0017099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	166	608	0	ENST00000262189.6:c.250+2T>C		p.X84_splice	ENST00000262189	NM_170606.2	84			0.160791371024987	3	FACETS	1	0.977	1	0.589	0.54	0.641	CLONAL	1	TRUE	1	0.258597803477843	3		608	1230	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089805	5089805	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	257	339	0	ENST00000381652.3:c.2703C>G	p.Ile901Met	p.I901M	ENST00000381652	NM_004972.3	901	atC/atG	20/25	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.751630043584631	2		339	684	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867546	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGC	GGCGGCGGC	-	rs11466445	NA	P-0017102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	12	31	0	ENST00000374994.4:c.70_78del	p.Ala24_Ala26del	p.A24_A26del	ENST00000374994	NM_004612.2	17	ctGGCGGCGGCg/ctg	1/9	1	2	FACETS	0.516	0.37	0.685	0.516	0.37	0.685	SUBCLONAL	1	TRUE	1	0.738770082970755	2		31	63	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100445	8100445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1157299467	NA	P-0017102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	374	684	0	ENST00000346208.3:c.419C>T	p.Ser140Phe	p.S140F	ENST00000346208		140	tCc/tTc	3/6	1	2	FACETS	0.925	0.88	0.972	0.925	0.88	0.972	CLONAL	1	TRUE	1	0.738770082970755	2		684	1094	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968592	55968593	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCGTGCATGAGACTTCGATGCTTTCCCC	novel	NA	P-0017102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1376	541	615	0	ENST00000263923.4:c.2041_2070dup	p.Gly681_Ala690dup	p.G681_A690dup	ENST00000263923	NM_002253.2	681	-/GGGGAAAGCATCGAAGTCTCATGCACGGCA	14/30	0.738770082970755	3	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.738770082970755	3		615	1917	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0017103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	108	390	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.404912262761285	2		392	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912655	NA	P-0017103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	204	486	0	ENST00000269305.4:c.725G>C	p.Cys242Ser	p.C242S	ENST00000269305	NM_001126112.2	242	tGc/tCc	7/11	1	2	FACETS	0.981	0.91	1	0.981	0.91	1	CLONAL	1	TRUE	1	0.404912262761285	2		486	1027	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942685	48942685	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913301	NA	P-0017103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	203	378	1	ENST00000267163.4:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000267163	NM_000321.2	358	Cga/Tga	11/27	0.404912262761285	1	FACETS	0.926	0.859	0.994	0.926	0.859	0.994	CLONAL	1	TRUE	0	0.404912262761285	1		379	864	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782620	NA	P-0017103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	242	756	1	ENST00000269305.4:c.427G>A	p.Val143Met	p.V143M	ENST00000269305	NM_001126112.2	143	Gtg/Atg	5/11	1	2	FACETS	0.869	0.81	0.931	0.869	0.81	0.931	CLONAL	1	TRUE	1	0.404912262761285	2		757	1375	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720680	89720681	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	69	222	0	ENST00000371953.3:c.833dup	p.Phe279LeufsTer19	p.F279Lfs*19	ENST00000371953	NM_000314.4	277	-/T	8/9	0.404912262761285	1	FACETS	0.581	0.507	0.66	0.581	0.507	0.66	SUBCLONAL	1	TRUE	0	0.404912262761285	1		222	468	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823886	3823886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	162	473	1	ENST00000262367.5:c.2329G>A	p.Gly777Ser	p.G777S	ENST00000262367	NM_004380.2	777	Ggt/Agt	13/31	1	2	FACETS	0.842	0.772	0.915	0.842	0.772	0.915	CLONAL	1	TRUE	1	0.404912262761285	2		474	950	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0017104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1184	69	516	1	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.11	2		517	1253	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0017104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	57	549	1	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	1	2	FACETS	0.904	0.773	1	0.904	0.773	1	CLONAL	1	TRUE	1	0.11	2		550	1146	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0017106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	577	525	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.328966514330387	6	FACETS	0.974	0.938	1	0.974	0.938	1	CLONAL	4	TRUE	2	0.443962224415464	6		525	1260	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0017106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	149	463	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.443962224415464	3	FACETS	1	0.973	1	0.577	0.528	0.628	CLONAL	1	TRUE	1	0.443962224415464	3		463	711	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602413	10602413	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	470	685	0	ENST00000171111.5:c.1165G>T	p.Asp389Tyr	p.D389Y	ENST00000171111	NM_203500.1	389	Gac/Tac	3/6	0.443962224415464	2	FACETS	0.988	0.947	1	0.988	0.947	1	CLONAL	2	TRUE	0	0.443962224415464	2		685	1072	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63662105	63662105	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	204	414	0	ENST00000279873.7:c.209T>C	p.Leu70Ser	p.L70S	ENST00000279873	NM_032199.2	70	tTa/tCa	2/10	0.326314518984014	3	FACETS	1	0.982	1	0.586	0.543	0.63	CLONAL	1	TRUE	1	0.443962224415464	3		414	959	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912153	114912153	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	615	547	0	ENST00000543371.1:c.1223A>G	p.Gln408Arg	p.Q408R	ENST00000543371	NM_001198531.1	408	cAg/cGg	11/14	0.443962224415464	4	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.443962224415464	4		547	1606	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216611	108216612	+	missense_variant	Missense_Mutation	DNP	CG	CG	TT	novel	NA	P-0017106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	149	286	1	ENST00000278616.4:c.8560_8561delinsTT	p.Arg2854Phe	p.R2854F	ENST00000278616	NM_000051.3	2854	CGc/TTc	58/63	0.443962224415464	2	FACETS	0.907	0.84	0.976	0.907	0.84	0.976	CLONAL	2	TRUE	0	0.443962224415464	2		287	370	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858938	57858939	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0017106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	522	642	1	ENST00000228682.2:c.434_435delinsAG	p.Pro145Gln	p.P145Q	ENST00000228682	NM_005269.2	145	cCC/cAG	5/12	0.332986146018367	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.443962224415464	4		643	1582	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033466	48033466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	119	512	0	ENST00000234420.5:c.3770C>T	p.Ser1257Phe	p.S1257F	ENST00000234420	NM_000179.2	1257	tCt/tTt	8/10	0.424995258984272	4	FACETS	0.874	0.788	0.964	0.291	0.262	0.322	CLONAL	1	TRUE	1	0.443962224415464	4		512	886	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971127	13971127	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	111	154	0	ENST00000405192.2:c.802G>T	p.Gly268Cys	p.G268C	ENST00000405192	NM_001163147.1	268	Ggc/Tgc	8/12	0.332986146018367	4	FACETS	0.984	0.893	1	0.984	0.893	1	CLONAL	2	TRUE	2	0.443962224415464	4		154	367	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513225	106513225	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	128	302	0	ENST00000359195.3:c.2129A>C	p.Gln710Pro	p.Q710P	ENST00000359195	NM_002649.2	710	cAg/cCg	4/11	0.443962224415464	3	FACETS	1	0.943	1	0.527	0.478	0.578	CLONAL	1	TRUE	1	0.443962224415464	3		302	669	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	131	301	4				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.975	0.887	1	0.975	0.887	1	CLONAL	1	TRUE	1	0.417451054969655	2		305	644	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	80	180	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.186489661301981	3	FACETS	0.566	0.498	0.64	0.283	0.249	0.32	INDETERMINATE	1	TRUE	1	0.417451054969655	3		180	818	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040629	47040629	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	72	494	1	ENST00000377604.3:c.1264G>A	p.Glu422Lys	p.E422K	ENST00000377604	NM_001204468.1	422	Gag/Aag	13/24	0.320348229976925	1	FACETS	0.316	0.275	0.36	0.316	0.275	0.36	SUBCLONAL	1	TRUE	0	0.417451054969655	1		495	865	SUCCESS
APC	324	MSKCC	GRCh37	5	112174086	112174086	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs878853432	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	64	389	0	ENST00000257430.4:c.2795C>G	p.Ser932Ter	p.S932*	ENST00000257430	NM_000038.5	932	tCa/tGa	16/16	1	2	FACETS	0.344	0.297	0.395	0.344	0.297	0.395	SUBCLONAL	1	TRUE	1	0.417451054969655	2		389	892	SUCCESS
APC	324	MSKCC	GRCh37	5	112174764	112174764	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	63	331	0	ENST00000257430.4:c.3473G>C	p.Arg1158Thr	p.R1158T	ENST00000257430	NM_000038.5	1158	aGa/aCa	16/16	1	2	FACETS	0.391	0.337	0.449	0.391	0.337	0.449	SUBCLONAL	1	TRUE	1	0.417451054969655	2		331	772	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890267	72890267	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1174	111	604	0	ENST00000325599.8:c.415G>C	p.Glu139Gln	p.E139Q	ENST00000325599	NM_018130.2	139	Gaa/Caa	4/11	1	2	FACETS	0.414	0.371	0.46	0.414	0.371	0.46	SUBCLONAL	1	TRUE	1	0.417451054969655	2		604	1285	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164462	36164463	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	135	232	0	ENST00000300305.3:c.1412_1413del	p.Arg471ProfsTer128	p.R471Pfs*128	ENST00000300305		471	cGC/c	8/8	0.417451054969655	3	FACETS	1	0.979	1	0.625	0.57	0.683	CLONAL	1	TRUE	1	0.417451054969655	3		232	625	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045756	26045756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	35	167	0	ENST00000540144.1:c.118C>T	p.His40Tyr	p.H40Y	ENST00000540144	NM_003531.2	40	Cat/Tat	1/1	1	2	FACETS	0.395	0.324	0.476	0.395	0.324	0.476	SUBCLONAL	1	TRUE	1	0.417451054969655	2		167	424	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717609	89717609	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs876661024	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	70	390	0	ENST00000371953.3:c.635-1G>C		p.X212_splice	ENST00000371953	NM_000314.4	212			1	2	FACETS	0.463	0.403	0.527	0.463	0.403	0.527	SUBCLONAL	1	TRUE	1	0.417451054969655	2		390	725	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058045	27058045	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	86	457	1	ENST00000324856.7:c.1753C>T	p.Gln585Ter	p.Q585*	ENST00000324856	NM_006015.4	585	Cag/Tag	3/20	1	2	FACETS	0.429	0.378	0.483	0.429	0.378	0.483	SUBCLONAL	1	TRUE	1	0.417451054969655	2		458	961	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838389	156838389	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1292	123	541	0	ENST00000524377.1:c.667G>C	p.Glu223Gln	p.E223Q	ENST00000524377	NM_002529.3	223	Gag/Cag	6/17	0.28894898243382	3	FACETS	0.503	0.453	0.557	0.252	0.226	0.279	SUBCLONAL	1	TRUE	1	0.417451054969655	3		541	1415	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015393	176015393	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	54	571	0	ENST00000367669.3:c.1345G>C	p.Glu449Gln	p.E449Q	ENST00000367669	NM_022457.5	449	Gaa/Caa	12/20	0.28894898243382	3	FACETS	0.38	0.324	0.443	0.19	0.162	0.222	SUBCLONAL	1	TRUE	1	0.417451054969655	3		571	822	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666440	206666440	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	154	407	0	ENST00000367120.3:c.1920G>C	p.Glu640Asp	p.E640D	ENST00000367120	NM_014002.3	640	gaG/gaC	19/22	1	2	FACETS	0.742	0.679	0.809	0.742	0.679	0.809	SUBCLONAL	1	TRUE	1	0.417451054969655	2		407	994	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809292	243809292	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	53	510	0	ENST00000263826.5:c.332G>A	p.Arg111Lys	p.R111K	ENST00000263826	NM_005465.4	111	aGg/aAg	4/13	1	2	FACETS	0.257	0.218	0.3	0.257	0.218	0.3	SUBCLONAL	1	TRUE	1	0.417451054969655	2		510	988	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717681	89717681	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	85	580	0	ENST00000371953.3:c.706G>C	p.Asp236His	p.D236H	ENST00000371953	NM_000314.4	236	Gac/Cac	7/9	1	2	FACETS	0.399	0.352	0.45	0.399	0.352	0.45	SUBCLONAL	1	TRUE	1	0.417451054969655	2		580	1020	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121729	108121729	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs865985297	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	100	551	0	ENST00000278616.4:c.1537C>T	p.Gln513Ter	p.Q513*	ENST00000278616	NM_000051.3	513	Cag/Tag	10/63	1	2	FACETS	0.429	0.382	0.48	0.429	0.382	0.48	SUBCLONAL	1	TRUE	1	0.417451054969655	2		551	1116	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484278	50484278	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs1313708909	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	121	602	0	ENST00000394963.4:c.1038C>G	p.Ile346Met	p.I346M	ENST00000394963	NM_003076.4	346	atC/atG	9/13	1	2	FACETS	0.46	0.414	0.509	0.46	0.414	0.509	SUBCLONAL	1	TRUE	1	0.417451054969655	2		602	1260	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896960	28896960	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	300	515	0	ENST00000282397.4:c.2920G>C	p.Asp974His	p.D974H	ENST00000282397	NM_002019.4	974	Gat/Cat	21/30	0.28894898243382	3	FACETS	1	0.991	1	0.633	0.595	0.672	CLONAL	1	TRUE	1	0.417451054969655	3		515	1373	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99192836	99192836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	92	398	0	ENST00000268035.6:c.26C>T	p.Ser9Phe	p.S9F	ENST00000268035	NM_000875.3	9	tCc/tTc	1/21	1	2	FACETS	0.485	0.43	0.544	0.485	0.43	0.544	SUBCLONAL	1	TRUE	1	0.417451054969655	2		398	908	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640901	3640901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1394	128	711	0	ENST00000294008.3:c.2738G>A	p.Arg913Lys	p.R913K	ENST00000294008	NM_032444.2	913	aGa/aAa	12/15	1	2	FACETS	0.403	0.364	0.445	0.403	0.364	0.445	SUBCLONAL	1	TRUE	1	0.417451054969655	2		711	1522	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553503	29553503	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	238	502	0	ENST00000356175.3:c.2052G>C	p.Gln684His	p.Q684H	ENST00000356175	NM_000267.3	684	caG/caC	18/57	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.417451054969655	2		502	1084	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649026	37649026	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	146	394	0	ENST00000447079.4:c.2131G>A	p.Glu711Lys	p.E711K	ENST00000447079	NM_015083.1	711	Gaa/Aaa	4/14	1	2	FACETS	0.851	0.777	0.928	0.851	0.777	0.928	CLONAL	1	TRUE	1	0.417451054969655	2		394	822	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649096	37649096	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	212	547	0	ENST00000447079.4:c.2201G>C	p.Gly734Ala	p.G734A	ENST00000447079	NM_015083.1	734	gGa/gCa	4/14	1	2	FACETS	0.965	0.896	1	0.965	0.896	1	CLONAL	1	TRUE	1	0.417451054969655	2		547	1053	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743014	743014	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	90	535	2	ENST00000314574.4:c.964C>T	p.Gln322Ter	p.Q322*	ENST00000314574	NM_005433.3	322	Cag/Tag	8/12	0.234984147621456	2	FACETS	0.416	0.368	0.468	0.208	0.184	0.234	INDETERMINATE	1	TRUE	0	0.417451054969655	2		537	1036	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56415066	56415066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	75	333	0	ENST00000348428.3:c.2467G>A	p.Glu823Lys	p.E823K	ENST00000348428	NM_006785.3	823	Gaa/Aaa	17/17	0.234984147621456	2	FACETS	0.538	0.471	0.61	0.269	0.235	0.305	INDETERMINATE	1	TRUE	0	0.417451054969655	2		333	668	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953247	17953247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767248290	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1223	310	758	0	ENST00000458235.1:c.739C>T	p.Pro247Ser	p.P247S	ENST00000458235	NM_000215.3	247	Cca/Tca	6/24	1	2	FACETS	0.969	0.911	1	0.969	0.911	1	CLONAL	1	TRUE	1	0.417451054969655	2		758	1533	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794581	42794581	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1703	121	641	1	ENST00000575354.2:c.1661C>G	p.Ser554Ter	p.S554*	ENST00000575354	NM_015125.3	554	tCa/tGa	10/20	0.417451054969655	3	FACETS	0.384	0.345	0.426	0.192	0.172	0.213	SUBCLONAL	1	TRUE	1	0.417451054969655	3		642	1824	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116242	209116242	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1248893111	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	73	488	0	ENST00000345146.2:c.34G>C	p.Glu12Gln	p.E12Q	ENST00000345146	NM_005896.2	12	Gag/Cag	3/10	0.41148013899783	2	FACETS	0.35	0.305	0.399	0.175	0.152	0.2	SUBCLONAL	1	TRUE	0	0.417451054969655	2		488	999	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612290	189612290	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	58	303	0	ENST00000264731.3:c.2042G>C	p.Ter681SerextTer12	p.*681Sext*12	ENST00000264731	NM_003722.4	681	tGa/tCa	14/14	0.186489661301981	3	FACETS	0.507	0.435	0.585	0.253	0.217	0.293	INDETERMINATE	1	TRUE	1	0.417451054969655	3		303	663	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751541	57751541	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	80	325	0	ENST00000274289.3:c.1450G>T	p.Glu484Ter	p.E484*	ENST00000274289	NM_006622.3	484	Gaa/Taa	11/14	1	2	FACETS	0.513	0.451	0.58	0.513	0.451	0.58	SUBCLONAL	1	TRUE	1	0.417451054969655	2		325	747	SUCCESS
APC	324	MSKCC	GRCh37	5	112175283	112175283	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	57	288	0	ENST00000257430.4:c.3992G>C	p.Arg1331Thr	p.R1331T	ENST00000257430	NM_000038.5	1331	aGa/aCa	16/16	1	2	FACETS	0.368	0.315	0.426	0.368	0.315	0.426	SUBCLONAL	1	TRUE	1	0.417451054969655	2		288	742	SUCCESS
APC	324	MSKCC	GRCh37	5	112175471	112175471	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	56	277	0	ENST00000257430.4:c.4180G>C	p.Asp1394His	p.D1394H	ENST00000257430	NM_000038.5	1394	Gat/Cat	16/16	1	2	FACETS	0.406	0.347	0.47	0.406	0.347	0.47	SUBCLONAL	1	TRUE	1	0.417451054969655	2		277	661	SUCCESS
APC	324	MSKCC	GRCh37	5	112176351	112176351	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	55	368	0	ENST00000257430.4:c.5060G>T	p.Arg1687Leu	p.R1687L	ENST00000257430	NM_000038.5	1687	cGa/cTa	16/16	1	2	FACETS	0.346	0.295	0.402	0.346	0.295	0.402	SUBCLONAL	1	TRUE	1	0.417451054969655	2		368	761	SUCCESS
APC	324	MSKCC	GRCh37	5	112177589	112177589	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	61	392	0	ENST00000257430.4:c.6298G>C	p.Asp2100His	p.D2100H	ENST00000257430	NM_000038.5	2100	Gat/Cat	16/16	1	2	FACETS	0.38	0.327	0.438	0.38	0.327	0.438	SUBCLONAL	1	TRUE	1	0.417451054969655	2		392	769	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394992	394992	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	86	434	0	ENST00000380956.4:c.388G>T	p.Glu130Ter	p.E130*	ENST00000380956	NM_001195286.1	130	Gag/Tag	3/9	1	2	FACETS	0.438	0.386	0.493	0.438	0.386	0.493	SUBCLONAL	1	TRUE	1	0.417451054969655	2		434	941	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671882	30671882	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	269	600	0	ENST00000376406.3:c.5078C>A	p.Pro1693Gln	p.P1693Q	ENST00000376406	NM_014641.2	1693	cCg/cAg	10/15	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.417451054969655	2		600	1258	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903739	41903739	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	72	412	1	ENST00000372991.4:c.818C>T	p.Ser273Phe	p.S273F	ENST00000372991	NM_001760.3	273	tCc/tTc	5/5	1	2	FACETS	0.362	0.315	0.413	0.362	0.315	0.413	SUBCLONAL	1	TRUE	1	0.417451054969655	2		413	953	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553452	106553452	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	55	232	0	ENST00000369096.4:c.1417G>C	p.Asp473His	p.D473H	ENST00000369096	NM_001198.3	473	Gat/Cat	5/7	1	2	FACETS	0.414	0.354	0.481	0.414	0.354	0.481	SUBCLONAL	1	TRUE	1	0.417451054969655	2		232	636	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152357809	152357809	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	81	479	0	ENST00000359321.1:c.98C>A	p.Ala33Asp	p.A33D	ENST00000359321	NM_005431.1	33	gCt/gAt	2/3	0.417451054969655	1	FACETS	0.341	0.299	0.385	0.341	0.299	0.385	SUBCLONAL	1	TRUE	0	0.417451054969655	1		479	901	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833924	44833924	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0017107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	146	414	0	ENST00000377967.4:c.348C>G	p.Tyr116Ter	p.Y116*	ENST00000377967	NM_021140.2	116	taC/taG	4/29	0.320348229976925	1	FACETS	0.839	0.768	0.913	0.839	0.768	0.913	CLONAL	1	TRUE	0	0.417451054969655	1		414	660	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0017108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	173	418	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	1	2	FACETS	0.449	0.413	0.486	0.449	0.413	0.486	SUBCLONAL	1	TRUE	1	0.81	2		418	952	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560464	95560464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	377	469	0	ENST00000393063.1:c.5125G>A	p.Asp1709Asn	p.D1709N	ENST00000393063	NM_030621.3	1709	Gat/Aat	25/28	1	2	FACETS	0.971	0.925	1	0.971	0.925	1	CLONAL	1	TRUE	1	0.81	2		469	959	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95579503	95579503	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs754081635	NA	P-0017108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	207	421	1	ENST00000393063.1:c.1966C>T	p.Arg656Ter	p.R656*	ENST00000393063	NM_030621.3	656	Cga/Tga	13/28	1	2	FACETS	0.923	0.863	0.983	0.923	0.863	0.983	CLONAL	1	TRUE	1	0.81	2		422	554	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0017112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	737	822	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.831727791174109	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.831727791174109	2		822	869	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0017112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	515	180	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.825985661787184	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.831727791174109	3		180	851	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541542	29541542	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137854557	NA	P-0017112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	25	695	0	ENST00000356175.3:c.1466A>G	p.Tyr489Cys	p.Y489C	ENST00000356175	NM_000267.3	489	tAt/tGt	13/57	0.831727791174109	2	FACETS	0.417	0.333	0.512	0.209	0.166	0.256	SUBCLONAL	1	TRUE	0	0.831727791174109	2		695	144	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63817051	63817051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	257	339	0	ENST00000279873.7:c.1022G>A	p.Arg341Gln	p.R341Q	ENST00000279873	NM_032199.2	341	cGa/cAa	6/10	0.831727791174109	8	FACETS	0.813	0.76	0.868	0.407	0.38	0.434	CLONAL	2	TRUE	4	0.831727791174109	8		339	1328	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164182	108164182	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	119	355	0	ENST00000278616.4:c.4754G>C	p.Arg1585Thr	p.R1585T	ENST00000278616	NM_000051.3	1585	aGa/aCa	31/63	0.825985661787184	3	FACETS	0.927	0.843	1	0.464	0.421	0.508	CLONAL	1	TRUE	1	0.831727791174109	3		355	437	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112126	115112135	+	frameshift_variant	Frame_Shift_Del	DEL	GCCAGCGGCC	GCCAGCGGCC	-	novel	NA	P-0017112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	519	775	0	ENST00000257566.3:c.1605_1614del	p.Ala536TrpfsTer93	p.A536Wfs*93	ENST00000257566	NM_016569.3	535	gcGGCCGCTGGC/gc	7/8	0.674754182516458	3	FACETS	0.902	0.87	0.935	0.902	0.87	0.935	CLONAL	2	TRUE	1	0.831727791174109	3		775	979	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112142	115112142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs566842835	NA	P-0017112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	548	713	2	ENST00000257566.3:c.1598G>A	p.Ser533Asn	p.S533N	ENST00000257566	NM_016569.3	533	aGc/aAc	7/8	0.674754182516458	3	FACETS	0.987	0.954	1	0.987	0.954	1	CLONAL	2	TRUE	1	0.831727791174109	3		715	945	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160744	56160745	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	161	402	0	ENST00000399503.3:c.1019dup	p.Phe341ValfsTer44	p.F341Vfs*44	ENST00000399503	NM_005921.1	340	gtg/gTtg	4/20	0.623533911295786	3	FACETS	1	0.968	1	0.544	0.502	0.586	CLONAL	1	TRUE	1	0.831727791174109	3		402	504	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178091	56178091	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	292	400	0	ENST00000399503.3:c.3064C>T	p.Gln1022Ter	p.Q1022*	ENST00000399503	NM_005921.1	1022	Cag/Tag	14/20	0.623533911295786	3	FACETS	0.945	0.901	0.989	0.945	0.901	0.989	CLONAL	2	TRUE	1	0.831727791174109	3		400	526	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862867	117862867	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	474	604	0	ENST00000297338.2:c.1610A>C	p.Glu537Ala	p.E537A	ENST00000297338	NM_006265.2	537	gAa/gCa	12/14	0.831727791174109	4	FACETS	0.989	0.948	1	0.494	0.474	0.515	CLONAL	2	TRUE	0	0.831727791174109	4		604	1056	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	85	605	1	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	1	2	FACETS	0.67	0.593	0.752	0.67	0.593	0.752	SUBCLONAL	1	TRUE	1	0.44	2		606	577	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884011	37884011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150680317	NA	P-0017113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	78	913	1	ENST00000269571.5:c.3482G>A	p.Arg1161Gln	p.R1161Q	ENST00000269571		1161	cGa/cAa	27/27	0.3	7	FACETS	0.588	0.514	0.667			1	SUBCLONAL	1	TRUE	NA	0.44	7		914	1267	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110082	115110083	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	126	1258	0	ENST00000257566.3:c.1795dup	p.Ser599LysfsTer93	p.S599Kfs*93	ENST00000257566	NM_016569.3	599	agc/aAgc	8/8	1	2	FACETS	0.569	0.515	0.627	0.569	0.515	0.627	SUBCLONAL	1	TRUE	1	0.44	2		1258	1006	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	136	408	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.334690449522387	1	FACETS	0.912	0.83	0.998	0.912	0.83	0.998	CLONAL	1	TRUE	0	0.334690449522387	1		408	742	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0017117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	76	180	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.5	0.437	0.567	0.5	0.437	0.567	SUBCLONAL	1	TRUE	1	0.334690449522387	2		180	909	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578528	7578528	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	268	1142	1	ENST00000269305.4:c.402T>A	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	ttT/ttA	5/11	0.334690449522387	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.334690449522387	1		1143	1148	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682991	241682991	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1226883651	NA	P-0017117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	121	483	0	ENST00000366560.3:c.32C>G	p.Ser11Trp	p.S11W	ENST00000366560	NM_000143.3	11	tCg/tGg	1/10	0.322992684931956	3	FACETS	0.779	0.706	0.854			1	SUBCLONAL	2	TRUE	NA	0.334690449522387	3		483	542	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319899	8319899	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	117	570	1	ENST00000356435.5:c.5602G>T	p.Gly1868Ter	p.G1868*	ENST00000356435		1868	Gga/Tga	34/35	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.334690449522387	2		571	645	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163889	152163889	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	98	577	0	ENST00000206249.3:c.610G>T	p.Gly204Cys	p.G204C	ENST00000206249	NM_000125.3	204	Ggc/Tgc	2/8	0.310160120607255	3	FACETS	0.986	0.881	1	0.493	0.44	0.55	CLONAL	1	TRUE	1	0.334690449522387	3		577	693	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246021942	246021942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1320812485	NA	P-0017117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	142	678	0	ENST00000388985.4:c.932C>T	p.Ala311Val	p.A311V	ENST00000388985		311	gCa/gTa	10/12	0.322992684931956	3	FACETS	0.969	0.882	1			1	CLONAL	1	TRUE	NA	0.334690449522387	3		678	1022	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812574	43812574	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200454070	NA	P-0017117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	74	768	0	ENST00000372470.3:c.1277G>A	p.Arg426Gln	p.R426Q	ENST00000372470	NM_005373.2	426	cGa/cAa	8/12	1	2	FACETS	0.53	0.463	0.603	0.53	0.463	0.603	SUBCLONAL	1	TRUE	1	0.334690449522387	2		768	834	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400977	72400977	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	104	683	0	ENST00000357731.5:c.194G>A	p.Gly65Glu	p.G65E	ENST00000357731	NM_173808.2	65	gGa/gAa	2/7	1	2	FACETS	0.879	0.788	0.976	0.879	0.788	0.976	CLONAL	1	TRUE	1	0.334690449522387	2		683	707	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567311	226567312	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	59	609	0	ENST00000366794.5:c.1574dup	p.Leu525PhefsTer4	p.L525Ffs*4	ENST00000366794	NM_001618.3	525	tta/ttTa	11/23	0.262468691972497	4	FACETS	0.476	0.408	0.551	0.119	0.102	0.138	SUBCLONAL	1	TRUE	0	0.334690449522387	4		609	988	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609108	43609108	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	128	893	0	ENST00000355710.3:c.1864C>A	p.Pro622Thr	p.P622T	ENST00000355710	NM_020975.4	622	Ccc/Acc	10/20	0.291046199687968	1	FACETS	0.71	0.643	0.781	0.71	0.643	0.781	SUBCLONAL	1	TRUE	0	0.334690449522387	1		893	897	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945135	32945135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755783122	NA	P-0017117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	168	669	1	ENST00000380152.3:c.8530G>A	p.Glu2844Lys	p.E2844K	ENST00000380152		2844	Gaa/Aaa	20/27	0.334690449522387	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.334690449522387	1		670	692	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037949	49037950	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0017117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	118	621	0	ENST00000267163.4:c.2191_2192dup	p.Pro732PhefsTer13	p.P732Ffs*13	ENST00000267163	NM_000321.2	730	gat/gaTCt	21/27	0.334690449522387	1	FACETS	0.832	0.751	0.917	0.832	0.751	0.917	CLONAL	1	TRUE	0	0.334690449522387	1		621	706	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117540	4117540	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	41	335	0	ENST00000262948.5:c.180G>C	p.Gln60His	p.Q60H	ENST00000262948	NM_030662.3	60	caG/caC	2/11	1	2	FACETS	0.623	0.52	0.738	0.623	0.52	0.738	SUBCLONAL	1	TRUE	1	0.334690449522387	2		335	393	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265318	10265318	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	53	625	0	ENST00000340748.4:c.1728C>A	p.Phe576Leu	p.F576L	ENST00000340748		576	ttC/ttA	20/40	1	2	FACETS	0.499	0.425	0.58	0.499	0.425	0.58	SUBCLONAL	1	TRUE	1	0.334690449522387	2		625	635	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276782	15276783	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0017117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	60	771	1	ENST00000263388.2:c.5482_5483delinsTT	p.Gly1828Leu	p.G1828L	ENST00000263388	NM_000435.2	1828	GGg/TTg	30/33	1	2	FACETS	0.492	0.423	0.567	0.492	0.423	0.567	SUBCLONAL	1	TRUE	1	0.334690449522387	2		772	729	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955114	17955114	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	181	857	0	ENST00000458235.1:c.113C>T	p.Pro38Leu	p.P38L	ENST00000458235	NM_000215.3	38	cCc/cTc	2/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.334690449522387	2		857	852	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797304	42797304	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	181	945	1	ENST00000575354.2:c.3666G>T	p.Glu1222Asp	p.E1222D	ENST00000575354	NM_015125.3	1222	gaG/gaT	15/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.334690449522387	2		946	865	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47710004	47710004	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	68	687	2	ENST00000233146.2:c.2721G>T	p.Lys907Asn	p.K907N	ENST00000233146	NM_000251.2	907	aaG/aaT	16/16	1	2	FACETS	0.485	0.421	0.555	0.485	0.421	0.555	SUBCLONAL	1	TRUE	1	0.334690449522387	2		689	837	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84390263	84390263	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	67	728	1	ENST00000321945.7:c.518T>A	p.Met173Lys	p.M173K	ENST00000321945	NM_139076.2	173	aTg/aAg	6/9	1	2	FACETS	0.423	0.367	0.485	0.423	0.367	0.485	SUBCLONAL	1	TRUE	1	0.334690449522387	2		729	946	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0017118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	115	290	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	FALSE	1	0.3	2		290	730	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267359	198267359	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs377023736	NA	P-0017120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	82	869	0	ENST00000335508.6:c.1998G>C	p.Lys666Asn	p.K666N	ENST00000335508	NM_012433.2	666	aaG/aaC	14/25	1	2	FACETS	0.705	0.62	0.796	0.705	0.62	0.796	SUBCLONAL	1	TRUE	1	0.259795531763596	2		869	896	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100469	8100469	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451961949	NA	P-0017120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	73	1032	2	ENST00000346208.3:c.443C>T	p.Pro148Leu	p.P148L	ENST00000346208		148	cCg/cTg	3/6	1	2	FACETS	0.531	0.463	0.605	0.531	0.463	0.605	SUBCLONAL	1	TRUE	1	0.259795531763596	2		1034	1058	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023632	27023633	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCA	novel	NA	P-0017120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	37	594	1	ENST00000324856.7:c.741_742insAGCC	p.Gly248SerfsTer153	p.G248Sfs*153	ENST00000324856	NM_006015.4	246	-/GCCA	1/20	1	2	FACETS	0.506	0.416	0.607	0.506	0.416	0.607	SUBCLONAL	1	TRUE	1	0.259795531763596	2		595	563	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446999	49446999	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1565822457	NA	P-0017120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	48	531	0	ENST00000301067.7:c.945del	p.Trp315Ter	p.W315*	ENST00000301067	NM_003482.3	315	tgG/tg	7/54	0.107235128823692	3	FACETS	0.652	0.551	0.765	0.326	0.275	0.383	INDETERMINATE	1	TRUE	1	0.259795531763596	3		531	640	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951089	17951089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750687910	NA	P-0017120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	69	891	1	ENST00000458235.1:c.1204C>T	p.Arg402Cys	p.R402C	ENST00000458235	NM_000215.3	402	Cgc/Tgc	9/24	1	2	FACETS	0.618	0.537	0.706	0.618	0.537	0.706	SUBCLONAL	1	TRUE	1	0.259795531763596	2		892	860	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86686618	86686618	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	35	606	0	ENST00000274376.6:c.3062A>C	p.His1021Pro	p.H1021P	ENST00000274376	NM_002890.2	1021	cAc/cCc	25/25	1	2	FACETS	0.457	0.373	0.551	0.457	0.373	0.551	SUBCLONAL	1	TRUE	1	0.259795531763596	2		606	590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0017121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	61	418	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.2	2		420	606	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0017121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	56	547	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.905	0.775	1	0.905	0.775	1	CLONAL	1	TRUE	1	0.2	2		547	619	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584560	48584560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	50	697	1	ENST00000342988.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000342988	NM_005359.5	245	Cag/Tag	6/12	1	2	FACETS	0.876	0.743	1	0.876	0.743	1	CLONAL	1	TRUE	1	0.2	2		698	571	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971088	21971088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746459174	NA	P-0017121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	32	547	0	ENST00000579755.1:c.313C>T	p.Pro105Ser	p.P105S	ENST00000579755		105	Cct/Tct	2/3	0.202991021976083	1	FACETS	0.742	0.603	0.9	0.742	0.603	0.9	SUBCLONAL	1	TRUE	0	0.2	1		547	388	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971095	21971099	+	frameshift_variant	Frame_Shift_Del	DEL	TCCCG	TCCCG	-	novel	NA	P-0017121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	24	532	0	ENST00000304494.5:c.259_263del	p.Arg87GlyfsTer31	p.R87Gfs*31	ENST00000304494	NM_000077.4	87	CGGGAg/g	2/3	0.202991021976083				0.452	0.722				SUBCLONAL	1	TRUE	0	0.2	1		532	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0017121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	26	418	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.4	0.317	0.495	0.4	0.317	0.495	SUBCLONAL	1	TRUE	1	0.383736767238947	2		420	339	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0017121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	24	547	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.53	0.417	0.659	0.53	0.417	0.659	SUBCLONAL	1	TRUE	1	0.383736767238947	2		547	236	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584560	48584560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	26	697	1	ENST00000342988.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000342988	NM_005359.5	245	Cag/Tag	6/12	1	2	FACETS	0.467	0.371	0.578	0.467	0.371	0.578	SUBCLONAL	1	TRUE	1	0.383736767238947	2		698	290	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971088	21971088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746459174	NA	P-0017121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	16	547	0	ENST00000579755.1:c.313C>T	p.Pro105Ser	p.P105S	ENST00000579755		105	Cct/Tct	2/3	1	2	FACETS	0.376	0.278	0.492	0.376	0.278	0.492	SUBCLONAL	1	TRUE	1	0.383736767238947	2		547	222	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971095	21971099	+	frameshift_variant	Frame_Shift_Del	DEL	TCCCG	TCCCG	-	novel	NA	P-0017121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	13	532	0	ENST00000304494.5:c.259_263del	p.Arg87GlyfsTer31	p.R87Gfs*31	ENST00000304494	NM_000077.4	87	CGGGAg/g	2/3	1				0.224	0.423				SUBCLONAL	1	TRUE	1	0.383736767238947	2		532	216	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860693	3860693	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	25	763	1	ENST00000262367.5:c.886C>T	p.Gln296Ter	p.Q296*	ENST00000262367	NM_004380.2	296	Cag/Tag	3/31	1	2	FACETS	0.449	0.355	0.558	0.449	0.355	0.558	SUBCLONAL	1	TRUE	1	0.383736767238947	2		764	290	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0017122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	37	306	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	0.588	0.484	0.703	0.588	0.484	0.703	SUBCLONAL	1	TRUE	1	0.290828942162475	2		306	433	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0017122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	113	568	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.290828942162475	3	FACETS	1	0.965	1	0.581	0.523	0.643	CLONAL	1	TRUE	1	0.290828942162475	3		569	766	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692910	89692910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	227	637	0	ENST00000371953.3:c.394G>A	p.Gly132Ser	p.G132S	ENST00000371953	NM_000314.4	132	Ggt/Agt	5/9	0.290828942162475	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.290828942162475	3		637	850	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589623	67589634	+	inframe_deletion	In_Frame_Del	DEL	ATATGATAGATT	ATATGATAGATT	-	novel	NA	P-0017122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	64	503	0	ENST00000274335.5:c.1392_1403del	p.Asp464_Tyr467del	p.D464_Y467del	ENST00000274335		462	gaATATGATAGATTa/gaa	10/15	1	2	FACETS	0.669	0.579	0.767	0.669	0.579	0.767	SUBCLONAL	1	TRUE	1	0.290828942162475	2		503	658	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180627	56180661	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACAATCTCTTCATTGAATGGATGGCAGGTATGTTA	ACAATCTCTTCATTGAATGGATGGCAGGTATGTTA	TAAAACATTAACAT	novel	NA	P-0017122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	36	492	3	ENST00000399503.3:c.3956_3982+8delinsTAAAACATTAACAT		p.X1319_splice	ENST00000399503	NM_005921.1	1319		16/20	1	2	FACETS	0.434	0.356	0.521	0.434	0.356	0.521	SUBCLONAL	1	TRUE	1	0.290828942162475	2		495	571	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885616	111885616	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374482426	NA	P-0017123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	648	1035	0	ENST00000341259.2:c.1393G>A	p.Val465Ile	p.V465I	ENST00000341259	NM_005475.2	465	Gtc/Atc	7/8	1	2	FACETS	0.973	0.946	0.999	1	0.998	1	CLONAL	2	TRUE	1	0.682599877264146	2		1035	976	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331973	81331973	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	185	743	0	ENST00000222390.5:c.2111G>T	p.Gly704Val	p.G704V	ENST00000222390	NM_000601.4	704	gGt/gTt	18/18	1	2	FACETS	0.933	0.867	1	0.933	0.867	1	CLONAL	1	TRUE	1	0.682599877264146	2		743	581	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829116	128829116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	66	41	0	ENST00000249373.3:c.124C>T	p.Arg42Trp	p.R42W	ENST00000249373	NM_005631.4	42	Cgg/Tgg	1/12	0.65443716675002	4	FACETS	0.935	0.845	1			1	CLONAL	3	TRUE	NA	0.682599877264146	4		41	116	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859384	151859397	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGACTCTGTGCT	GAGGACTCTGTGCT	-	novel	NA	P-0017123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	184	650	0	ENST00000262189.6:c.11265_11278del	p.Ala3756ProfsTer15	p.A3756Pfs*15	ENST00000262189	NM_170606.2	3755	tcAGCACAGAGTCCTCcc/tccc	43/59	0.674755404009358	3	FACETS	0.838	0.774	0.904	0.279	0.258	0.302	CLONAL	1	TRUE	0	0.682599877264146	3		650	863	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0017124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	62	439	1	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	0.159605711365677	3	FACETS	1	0.879	1	0.508	0.439	0.581	INDETERMINATE	1	TRUE	1	0.321563592307373	3		440	441	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0017124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	31	252	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.159605711365677	3	FACETS	0.638	0.516	0.775	0.319	0.258	0.388	INDETERMINATE	1	TRUE	1	0.321563592307373	3		252	351	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444505	49444505	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	64	730	1	ENST00000301067.7:c.2866G>T	p.Glu956Ter	p.E956*	ENST00000301067	NM_003482.3	956	Gag/Tag	11/54	1	2	FACETS	0.595	0.515	0.682	0.595	0.515	0.682	SUBCLONAL	1	TRUE	1	0.321563592307373	2		731	669	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916920	178916925	+	inframe_deletion	In_Frame_Del	DEL	GAACCA	GAACCA	-	novel	NA	P-0017124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	44	874	0	ENST00000263967.3:c.308_313del	p.Glu103_Pro104del	p.E103_P104del	ENST00000263967	NM_006218.2	103	GAACCA/-	2/21	1	2	FACETS	0.39	0.326	0.462	0.39	0.326	0.462	SUBCLONAL	1	TRUE	1	0.321563592307373	2		874	701	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372526	55372527	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	93	1214	0	ENST00000297316.4:c.1217dup	p.Tyr407IlefsTer7	p.Y407Ifs*7	ENST00000297316	NM_022454.3	406	gta/gTta	2/2	1	2	FACETS	0.479	0.424	0.538	0.479	0.424	0.538	SUBCLONAL	1	TRUE	1	0.321563592307373	2		1214	1208	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	25	301	4				ENST00000310581	NM_198253.2	-/1132			0.3	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		305	98	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0017152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	130	308	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		308	715	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950066	44950066	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs863224886	NA	P-0017154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	120	478	1	ENST00000377967.4:c.3835C>T	p.Arg1279Ter	p.R1279*	ENST00000377967	NM_021140.2	1279	Cga/Tga	26/29	0.228931078390934	1	FACETS	0.913	0.824	1	0.913	0.824	1	CLONAL	1	TRUE	0	0.241006426391855	1		479	959	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577152	7577154	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	ACC	ACC	-	rs1567548347	NA	P-0017154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	100	441	0	ENST00000269305.4:c.784_786del	p.Gly262del	p.G262del	ENST00000269305	NM_001126112.2	262	GGT/-	8/11	0.228931078390934	1	FACETS	0.746	0.665	0.832	0.746	0.665	0.832	SUBCLONAL	1	TRUE	0	0.241006426391855	1		441	979	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416459	49416459	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	61	398	0	ENST00000301067.7:c.16252G>C	p.Glu5418Gln	p.E5418Q	ENST00000301067	NM_003482.3	5418	Gaa/Caa	51/54	0.228931078390934	1	FACETS	0.534	0.459	0.615	0.534	0.459	0.615	SUBCLONAL	1	TRUE	0	0.241006426391855	1		398	834	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246018	41246018	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357735	NA	P-0017154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	143	513	0	ENST00000357654.3:c.1530del	p.Gly511AlafsTer21	p.G511Afs*21	ENST00000357654	NM_007294.3	510	tcA/tc	10/23	0.228931078390934	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.241006426391855	1		513	1009	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612002	189612002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	89	363	0	ENST00000264731.3:c.1754C>T	p.Ala585Val	p.A585V	ENST00000264731	NM_003722.4	585	gCa/gTa	14/14	0.241006426391855	3	FACETS	1	0.917	1	0.522	0.462	0.586	CLONAL	1	TRUE	1	0.241006426391855	3		363	793	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908296	41908296	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	62	629	0	ENST00000372991.4:c.226G>C	p.Glu76Gln	p.E76Q	ENST00000372991	NM_001760.3	76	Gaa/Caa	2/5	1	2	FACETS	0.478	0.411	0.551	0.478	0.411	0.551	SUBCLONAL	1	TRUE	1	0.241006426391855	2		629	1076	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950066	44950066	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs863224886	NA	P-0017154-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	313	478	1	ENST00000377967.4:c.3835C>T	p.Arg1279Ter	p.R1279*	ENST00000377967	NM_021140.2	1279	Cga/Tga	26/29	0.59820301277463	1	FACETS	0.985	0.934	1	0.985	0.934	1	CLONAL	1	TRUE	0	0.59820301277463	1		479	745	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577152	7577154	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	ACC	ACC	-	rs1567548347	NA	P-0017154-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	520	441	0	ENST00000269305.4:c.784_786del	p.Gly262del	p.G262del	ENST00000269305	NM_001126112.2	262	GGT/-	8/11	0.550234666722439	2	FACETS	0.896	0.864	0.928	0.896	0.864	0.928	CLONAL	2	TRUE	0	0.59820301277463	2		441	970	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416459	49416459	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017154-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	46	398	0	ENST00000301067.7:c.16252G>C	p.Glu5418Gln	p.E5418Q	ENST00000301067	NM_003482.3	5418	Gaa/Caa	51/54	0.574493010337996	1	FACETS	0.151	0.126	0.178	0.151	0.126	0.178	SUBCLONAL	1	TRUE	0	0.59820301277463	1		398	716	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246018	41246018	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357735	NA	P-0017154-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	440	513	0	ENST00000357654.3:c.1530del	p.Gly511AlafsTer21	p.G511Afs*21	ENST00000357654	NM_007294.3	510	tcA/tc	10/23	0.59820301277463	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.59820301277463	1		513	912	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612002	189612002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017154-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	288	363	0	ENST00000264731.3:c.1754C>T	p.Ala585Val	p.A585V	ENST00000264731	NM_003722.4	585	gCa/gTa	14/14	0.59820301277463	3	FACETS	1	0.986	1	0.575	0.541	0.611	CLONAL	1	TRUE	1	0.59820301277463	3		363	1087	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	83	408	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.584	0.514	0.659	0.584	0.514	0.659	SUBCLONAL	1	TRUE	1	0.29	2		408	981	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560494	65560494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	62	441	0	ENST00000358664.4:c.103C>T	p.Arg35Cys	p.R35C	ENST00000358664	NM_002382.4	35	Cgt/Tgt	3/5	0.138603032768147	1	FACETS	0.508	0.438	0.584	0.508	0.438	0.584	INDETERMINATE	1	TRUE	0	0.29	1		441	720	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462923	120462923	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	31	361	0	ENST00000256646.2:c.5408C>T	p.Pro1803Leu	p.P1803L	ENST00000256646	NM_024408.3	1803	cCa/cTa	30/34	1	2	FACETS	0.419	0.338	0.511	0.419	0.338	0.511	SUBCLONAL	1	TRUE	1	0.29	2		361	510	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646588	23646588	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	69	442	0	ENST00000261584.4:c.1279del	p.Ala427LeufsTer25	p.A427Lfs*25	ENST00000261584	NM_024675.3	427	Gct/ct	4/13	1	2	FACETS	0.602	0.524	0.688	0.602	0.524	0.688	SUBCLONAL	1	TRUE	1	0.29	2		442	790	SUCCESS
APC	324	MSKCC	GRCh37	5	112179128	112179128	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	48	404	0	ENST00000257430.4:c.7837A>G	p.Arg2613Gly	p.R2613G	ENST00000257430	NM_000038.5	2613	Aga/Gga	16/16	1	2	FACETS	0.476	0.402	0.559	0.476	0.402	0.559	SUBCLONAL	1	TRUE	1	0.29	2		404	695	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0017155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	15	308	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		308	660	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0017156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	83	180	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.805	0.709	0.907	0.805	0.709	0.907	CLONAL	1	TRUE	1	0.248254602037101	2		180	831	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881440	37881440	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	88	550	0	ENST00000269571.5:c.2632C>T	p.His878Tyr	p.H878Y	ENST00000269571		878	Cat/Tat	21/27	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.248254602037101	2		550	683	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171607	36171607	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1569008655	NA	P-0017156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	82	217	0	ENST00000300305.3:c.958C>T	p.Arg320Ter	p.R320*	ENST00000300305		320	Cga/Tga	7/8	0.20689540569019	3	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	1	0.248254602037101	3		217	351	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857530	68857531	+	splice_donor_variant	Splice_Site	DEL	GT	GT	-	novel	NA	P-0017156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	69	377	0	ENST00000261769.5:c.2164+1_2164+2del		p.X722_splice	ENST00000261769	NM_004360.3	722			0.248254602037101	1	FACETS	0.958	0.836	1	0.958	0.836	1	CLONAL	1	TRUE	0	0.248254602037101	1		377	508	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475137	40475137	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	90	492	0	ENST00000264657.5:c.1773G>C	p.Lys591Asn	p.K591N	ENST00000264657	NM_139276.2	591	aaG/aaC	20/24	1	2	FACETS	0.965	0.856	1	0.965	0.856	1	CLONAL	1	TRUE	1	0.248254602037101	2		492	751	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0017157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	108	525	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	0.16	2		525	1140	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728701	190728701	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	53	554	0	ENST00000441310.2:c.2089G>T	p.Val697Leu	p.V697L	ENST00000441310	NM_000534.4	697	Gta/Tta	10/13	1	2	FACETS	0.843	0.717	0.981	0.843	0.717	0.981	CLONAL	1	TRUE	1	0.16	2		554	786	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436662	52436662	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	61	688	0	ENST00000460680.1:c.2012A>G	p.Tyr671Cys	p.Y671C	ENST00000460680	NM_004656.3	671	tAc/tGc	16/17	1	2	FACETS	0.813	0.699	0.937	0.813	0.699	0.937	CLONAL	1	TRUE	1	0.16	2		688	938	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941820	44941820	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0017157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	58	240	2	ENST00000377967.4:c.3145-1G>T		p.X1049_splice	ENST00000377967	NM_021140.2	1049			1	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.16	1		242	475	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84393376	84393377	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	TTAA	novel	NA	P-0017158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	14	396	0	ENST00000321945.7:c.280_281insTTAA	p.Lys94IlefsTer21	p.K94Ifs*21	ENST00000321945	NM_139076.2	94	aag/aTTAAag	4/9	1	2	FACETS	0.659	0.476	0.88	0.659	0.476	0.88	SUBCLONAL	1	TRUE	1	0.18	2		396	236	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	88	301	4				ENST00000310581	NM_198253.2	-/1132			0.332763274932102	2	FACETS	0.856	0.77	0.945	0.856	0.77	0.945	CLONAL	2	TRUE	0	0.401358050141721	2		305	256	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	147	387	0	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	0.15148462897189	3	FACETS	0.75	0.688	0.815	0.75	0.688	0.815	INDETERMINATE	2	TRUE	1	0.401358050141721	3		387	586	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	378	632	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.289262221140899	2	FACETS	0.836	0.795	0.879	0.836	0.795	0.879	CLONAL	2	TRUE	0	0.401358050141721	2		634	1126	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	36	252	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.332763274932102	2	FACETS	0.846	0.702	1	0.423	0.351	0.503	CLONAL	1	TRUE	0	0.401358050141721	2		252	212	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799108	45799108	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765123255	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	129	723	2	ENST00000450313.1:c.325C>T	p.Arg109Trp	p.R109W	ENST00000450313	NM_012222.2	109	Cgg/Tgg	3/16	0.302601838626706	3	FACETS	0.647	0.585	0.713	0.216	0.195	0.238	SUBCLONAL	1	TRUE	0	0.401358050141721	3		725	1192	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	309	432	1	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	0.302601838626706	3	FACETS	1	0.983	1	0.725	0.686	0.765	CLONAL	2	TRUE	0	0.401358050141721	3		433	850	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468307	120468307	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	97	473	0	ENST00000256646.2:c.4132T>C	p.Cys1378Arg	p.C1378R	ENST00000256646	NM_024408.3	1378	Tgt/Cgt	25/34	0.302601838626706	3	FACETS	0.76	0.677	0.848	0.253	0.225	0.283	SUBCLONAL	1	TRUE	0	0.401358050141721	3		473	764	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609948	43609948	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs75076352	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	193	733	0	ENST00000355710.3:c.1900T>C	p.Cys634Arg	p.C634R	ENST00000355710	NM_020975.4	634	Tgc/Cgc	11/20	0.332763274932102	2	FACETS	0.795	0.734	0.858	0.397	0.367	0.429	SUBCLONAL	1	TRUE	0	0.401358050141721	2		733	1210	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871053	12871053	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	80	283	0	ENST00000228872.4:c.285del	p.Gly97ValfsTer22	p.G97Vfs*22	ENST00000228872	NM_004064.3	94	Ccc/cc	1/3	0.332763274932102	2	FACETS	0.925	0.818	1	0.462	0.409	0.52	CLONAL	1	TRUE	0	0.401358050141721	2		283	431	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245040	46245040	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776897929	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	141	574	1	ENST00000334344.6:c.3134C>T	p.Ser1045Leu	p.S1045L	ENST00000334344	NM_152641.2	1045	tCg/tTg	15/21	0.332763274932102	2	FACETS	0.784	0.714	0.858	0.392	0.357	0.429	SUBCLONAL	1	TRUE	0	0.401358050141721	2		575	896	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811605	102811605	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1565968684	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	149	620	1	ENST00000307046.8:c.579del	p.Gly194GlufsTer8	p.G194Efs*8	ENST00000307046	NM_001111285.1	193	aaA/aa	4/4	0.332763274932102	2	FACETS	0.954	0.873	1	0.477	0.436	0.52	CLONAL	1	TRUE	0	0.401358050141721	2		621	778	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263841	133263841	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	24	115	0	ENST00000320574.5:c.61A>G	p.Arg21Gly	p.R21G	ENST00000320574	NM_006231.2	21	Agg/Ggg	1/49	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.401358050141721	NA		115	206	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563176	21563176	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	123	499	0	ENST00000382592.4:c.743T>C	p.Leu248Pro	p.L248P	ENST00000382592	NM_014572.2	248	cTg/cCg	4/8	0.332763274932102	2	FACETS	0.781	0.706	0.859	0.39	0.353	0.43	SUBCLONAL	1	TRUE	0	0.401358050141721	2		499	785	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041350	42041350	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	322	648	0	ENST00000219905.7:c.5545T>C	p.Ser1849Pro	p.S1849P	ENST00000219905	NM_001164273.1	1849	Tct/Cct	17/24	0.332763274932102	2	FACETS	0.845	0.8	0.891	0.845	0.8	0.891	CLONAL	2	TRUE	0	0.401358050141721	2		648	949	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43700278	43700278	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1353202985	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	137	574	1	ENST00000382044.4:c.5609G>A	p.Arg1870His	p.R1870H	ENST00000382044	NM_001141980.1	1870	cGt/cAt	27/28	0.332763274932102	2	FACETS	0.863	0.786	0.944	0.432	0.393	0.472	CLONAL	1	TRUE	0	0.401358050141721	2		575	791	SUCCESS
BLM	641	MSKCC	GRCh37	15	91328244	91328244	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	135	491	0	ENST00000355112.3:c.2756A>G	p.His919Arg	p.H919R	ENST00000355112	NM_000057.2	919	cAt/cGt	14/22	0.332763274932102	2	FACETS	0.902	0.821	0.987	0.451	0.41	0.494	CLONAL	1	TRUE	0	0.401358050141721	2		491	746	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3651034	3651034	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	119	509	0	ENST00000294008.3:c.1109C>A	p.Ala370Asp	p.A370D	ENST00000294008	NM_032444.2	370	gCt/gAt	5/15	1	2	FACETS	0.755	0.682	0.833	0.755	0.682	0.833	SUBCLONAL	1	TRUE	1	0.401358050141721	2		509	785	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778993	3778993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372852842	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	70	282	0	ENST00000262367.5:c.6055G>A	p.Gly2019Arg	p.G2019R	ENST00000262367	NM_004380.2	2019	Ggg/Agg	31/31	1	2	FACETS	0.906	0.794	1	0.906	0.794	1	CLONAL	1	TRUE	1	0.401358050141721	2		282	385	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661945	29661945	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854552	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	254	611	1	ENST00000356175.3:c.5839C>T	p.Arg1947Ter	p.R1947*	ENST00000356175	NM_000267.3	1947	Cga/Tga	39/57	0.289262221140899	2	FACETS	0.858	0.806	0.91	0.858	0.806	0.91	CLONAL	2	TRUE	0	0.401358050141721	2		612	738	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30311757	30311757	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	54	333	0	ENST00000262643.3:c.609+2T>C		p.X203_splice	ENST00000262643	NM_001238.2	203			0.15148462897189	3	FACETS	0.572	0.488	0.663	0.286	0.244	0.332	INDETERMINATE	1	TRUE	1	0.401358050141721	3		333	565	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221328	36221328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1308156549	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	337	702	2	ENST00000222270.7:c.5162C>T	p.Thr1721Met	p.T1721M	ENST00000222270	NM_014727.1	1721	aCg/aTg	24/37	0.15148462897189	3	FACETS	1	0.994	1	0.736	0.695	0.778	INDETERMINATE	1	TRUE	1	0.401358050141721	3		704	1370	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50916770	50916770	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	168	495	1	ENST00000440232.2:c.2242A>G	p.Ser748Gly	p.S748G	ENST00000440232	NM_002691.3	748	Agt/Ggt	18/27	0.15148462897189	3	FACETS	1	0.966	1	0.546	0.502	0.593	INDETERMINATE	1	TRUE	1	0.401358050141721	3		496	920	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918992	50918992	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568638496	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	180	565	0	ENST00000440232.2:c.2729G>A	p.Arg910Gln	p.R910Q	ENST00000440232	NM_002691.3	910	cGg/cAg	22/27	0.15148462897189	3	FACETS	1	0.98	1	0.59	0.544	0.638	INDETERMINATE	1	TRUE	1	0.401358050141721	3		565	913	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657047	47657047	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	187	466	0	ENST00000233146.2:c.1244del	p.Pro415LeufsTer23	p.P415Lfs*23	ENST00000233146	NM_000251.2	415	Cct/ct	7/16	0.332763274932102	2	FACETS	0.856	0.797	0.917	0.856	0.797	0.917	CLONAL	2	TRUE	0	0.401358050141721	2		466	544	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546847	9546847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	154	279	0	ENST00000353224.5:c.1175C>T	p.Ser392Leu	p.S392L	ENST00000353224	NM_177990.2	392	tCg/tTg	5/10	0.15148462897189	3	FACETS	0.852	0.784	0.921	0.852	0.784	0.921	INDETERMINATE	2	TRUE	1	0.401358050141721	3		279	541	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852431	42852431	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757262240	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	109	521	2	ENST00000398585.3:c.655C>T	p.Arg219Trp	p.R219W	ENST00000398585	NM_001135099.1	219	Cgg/Tgg	6/14	0.337555204710996	2	FACETS	0.711	0.638	0.788	0.355	0.319	0.394	SUBCLONAL	1	TRUE	0	0.401358050141721	2		523	764	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24134036	24134036	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	173	624	0	ENST00000263121.7:c.187A>G	p.Ile63Val	p.I63V	ENST00000263121	NM_003073.3	63	Ata/Gta	2/9	0.289262221140899	2	FACETS	0.966	0.89	1	0.483	0.445	0.523	CLONAL	1	TRUE	0	0.401358050141721	2		624	892	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191054	185191054	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	141	705	0	ENST00000265026.3:c.1935del	p.Pro646LeufsTer18	p.P646Lfs*18	ENST00000265026	NM_004721.4	645	ccT/cc	11/14	0.332763274932102	2	FACETS	0.7	0.637	0.766	0.35	0.318	0.383	SUBCLONAL	1	TRUE	0	0.401358050141721	2		705	1004	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007332	143007332	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	148	436	0	ENST00000262992.4:c.2452del	p.Arg818GlufsTer4	p.R818Efs*4	ENST00000262992	NM_001101669.1	818	Aga/ga	22/24	0.260310355624725	3	FACETS	1	0.987	1	0.71	0.65	0.771	CLONAL	1	TRUE	1	0.401358050141721	3		436	624	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521299	187521299	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1166479124	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	141	651	0	ENST00000441802.2:c.11856del	p.Phe3952LeufsTer31	p.F3952Lfs*31	ENST00000441802	NM_005245.3	3952	ttT/tt	22/27	0.260310355624725	3	FACETS	0.812	0.739	0.889	0.406	0.369	0.445	CLONAL	1	TRUE	1	0.401358050141721	3		651	1039	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163761	32163761	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	93	380	0	ENST00000375023.3:c.5465C>G	p.Ala1822Gly	p.A1822G	ENST00000375023	NM_004557.3	1822	gCt/gGt	30/30	0.332763274932102	2	FACETS	0.852	0.76	0.95	0.426	0.38	0.475	CLONAL	1	TRUE	0	0.401358050141721	2		380	544	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004496	150004496	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs768555460	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	122	550	0	ENST00000253339.5:c.1729A>G	p.Ser577Gly	p.S577G	ENST00000253339		577	Agt/Ggt	3/7	0.332763274932102	2	FACETS	0.801	0.724	0.882	0.4	0.362	0.441	CLONAL	1	TRUE	0	0.401358050141721	2		550	759	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879672	151879672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	29	171	0	ENST00000262189.6:c.5273G>A	p.Arg1758His	p.R1758H	ENST00000262189	NM_170606.2	1758	cGt/cAt	36/59	0.272712638742364	4	FACETS	0.779	0.628	0.949	0.389	0.314	0.475	CLONAL	1	TRUE	2	0.401358050141721	4		171	260	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974678	21974678	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs587778189	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	199	409	0	ENST00000304494.5:c.149A>G	p.Gln50Arg	p.Q50R	ENST00000304494	NM_000077.4	50	cAg/cGg	1/3	0.332763274932102	2	FACETS	0.792	0.738	0.848	0.792	0.738	0.848	SUBCLONAL	2	TRUE	0	0.401358050141721	2		409	626	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27192562	27192562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138894008	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	233	501	2	ENST00000380036.4:c.1565G>A	p.Arg522His	p.R522H	ENST00000380036	NM_000459.3	522	cGt/cAt	11/23	0.332763274932102	2	FACETS	1	0.992	1	0.717	0.67	0.764	CLONAL	1	TRUE	0	0.401358050141721	2		503	810	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	96	414	1	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	0.332763274932102	2	FACETS	0.68	0.606	0.758	0.34	0.303	0.379	SUBCLONAL	1	TRUE	0	0.401358050141721	2		415	704	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412607	139412607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373770404	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	105	435	1	ENST00000277541.6:c.1237G>A	p.Val413Met	p.V413M	ENST00000277541	NM_017617.3	413	Gtg/Atg	7/34	0.332763274932102	2	FACETS	0.719	0.644	0.798	0.359	0.322	0.399	SUBCLONAL	1	TRUE	0	0.401358050141721	2		436	728	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039314	47039314	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1251	161	799	0	ENST00000377604.3:c.937A>G	p.Met313Val	p.M313V	ENST00000377604	NM_001204468.1	313	Atg/Gtg	10/24	0.0534450582817683	3	FACETS	0.682	0.624	0.744			1	INDETERMINATE	1	TRUE	NA	0.401358050141721	3		799	1412	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938173	76938174	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	108	697	0	ENST00000373344.5:c.2574dup	p.Gly859ArgfsTer4	p.G859Rfs*4	ENST00000373344	NM_000489.3	858	-/A	9/35	0.113141673071369	6	FACETS	0.948	0.849	1	0.316	0.283	0.352	INDETERMINATE	1	TRUE	3	0.401358050141721	6		697	1023	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	50	301	4				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.27748491302705	2		305	264	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0017163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	200	388	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.27748491302705	2		388	1092	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0017163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	281	628	1	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.27748491302705	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.27748491302705	1		629	1212	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156720	20156720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	91	220	2	ENST00000379607.5:c.37C>T	p.Arg13Cys	p.R13C	ENST00000379607	NM_001412.3	13	Cgc/Tgc	2/7	0.24598991334109	0	FACETS	1	0.949	1			1	CLONAL	1	TRUE	NA	0.27748491302705	0		222	428	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123836	46123836	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	86	272	0	ENST00000334344.6:c.102T>A	p.Phe34Leu	p.F34L	ENST00000334344	NM_152641.2	34	ttT/ttA	2/21	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.27748491302705	2		272	523	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051011	180051011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146167161	NA	P-0017163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	220	526	2	ENST00000261937.6:c.1472C>T	p.Ala491Val	p.A491V	ENST00000261937	NM_182925.4	491	gCg/gTg	11/30	0.27748491302705	1	FACETS	0.755	0.704	0.809	1	0.992	1	SUBCLONAL	2	TRUE	0	0.27748491302705	1		528	904	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305412	65305412	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	126	498	1	ENST00000342505.4:c.2716G>T	p.Ala906Ser	p.A906S	ENST00000342505	NM_002227.2	906	Gct/Tct	20/25	NA	2	FACETS	1	0.943	1			1	INDETERMINATE	1	TRUE	NA	0.27748491302705	2		499	858	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410667	32410667	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	136	423	1	ENST00000332351.3:c.1491T>A	p.Asp497Glu	p.D497E	ENST00000332351	NM_024426.4	497	gaT/gaA	10/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.27748491302705	2		424	874	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480477	89480477	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1411035734	NA	P-0017163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	86	264	0	ENST00000336596.2:c.2314G>C	p.Glu772Gln	p.E772Q	ENST00000336596	NM_005233.5	772	Gag/Cag	13/17	0.27748491302705	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.27748491302705	1		264	497	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937125	39937125	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	106	301	0	ENST00000378444.4:c.58G>T	p.Val20Phe	p.V20F	ENST00000378444	NM_001123385.1	20	Gtc/Ttc	2/15	0.24598991334109	0	FACETS	1	0.901	1			1	CLONAL	1	TRUE	NA	0.27748491302705	0		301	551	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0017164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	171	489	1	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.812	0.75	0.876	0.812	0.75	0.876	CLONAL	1	TRUE	1	0.648844118543745	2		490	649	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094308	27094308	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	182	412	0	ENST00000324856.7:c.3016G>A	p.Glu1006Lys	p.E1006K	ENST00000324856	NM_006015.4	1006	Gag/Aag	11/20	1	2	FACETS	0.912	0.846	0.98	0.912	0.846	0.98	CLONAL	1	TRUE	1	0.648844118543745	2		412	615	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094386	27094386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	228	479	1	ENST00000324856.7:c.3094G>A	p.Glu1032Lys	p.E1032K	ENST00000324856	NM_006015.4	1032	Gag/Aag	11/20	1	2	FACETS	0.987	0.924	1	0.987	0.924	1	CLONAL	1	TRUE	1	0.648844118543745	2		480	712	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39537555	39537555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	114	372	0	ENST00000262039.4:c.89G>A	p.Arg30Lys	p.R30K	ENST00000262039	NM_002647.2	30	aGa/aAa	2/25	1	2	FACETS	0.843	0.765	0.924	0.843	0.765	0.924	CLONAL	1	TRUE	1	0.648844118543745	2		372	417	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317207	11317207	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	237	438	0	ENST00000361445.4:c.287T>C	p.Val96Ala	p.V96A	ENST00000361445	NM_004958.3	96	gTg/gCg	4/58	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.648844118543745	2		438	625	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100147	27100147	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	243	484	0	ENST00000324856.7:c.3943G>C	p.Asp1315His	p.D1315H	ENST00000324856	NM_006015.4	1315	Gac/Cac	16/20	1	2	FACETS	0.951	0.891	1	0.951	0.891	1	CLONAL	1	TRUE	1	0.648844118543745	2		484	788	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151744	108151758	+	frameshift_variant	Frame_Shift_Del	DEL	AAACTTTGGATGAAA	AAACTTTGGATGAAA	TAAC	novel	NA	P-0017164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	88	347	2	ENST00000278616.4:c.3425_3439delinsTAAC	p.Glu1142ValfsTer4	p.E1142Vfs*4	ENST00000278616	NM_000051.3	1142	gAAACTTTGGATGAAAtt/gTAACtt	24/63	1	2	FACETS	0.678	0.605	0.756	0.678	0.605	0.756	SUBCLONAL	1	TRUE	1	0.648844118543745	2		349	400	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479178	50479178	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	150	201	0	ENST00000394963.4:c.26C>T	p.Ser9Phe	p.S9F	ENST00000394963	NM_003076.4	9	tCt/tTt	1/13	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.648844118543745	2		201	432	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855951	68855951	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	247	666	0	ENST00000261769.5:c.1759G>A	p.Asp587Asn	p.D587N	ENST00000261769	NM_004360.3	587	Gat/Aat	12/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.648844118543745	2		666	753	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866096	37866096	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	316	497	0	ENST00000269571.5:c.605C>A	p.Ser202Tyr	p.S202Y	ENST00000269571		202	tCc/tAc	5/27	0.465736685898676	3	FACETS	1	0.946	1			1	CLONAL	1	TRUE	NA	0.648844118543745	3		497	1286	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56415027	56415027	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	165	479	1	ENST00000348428.3:c.2428G>T	p.Glu810Ter	p.E810*	ENST00000348428	NM_006785.3	810	Gaa/Taa	17/17	1	2	FACETS	0.869	0.802	0.938	0.869	0.802	0.938	CLONAL	1	TRUE	1	0.648844118543745	2		480	585	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355551	15355551	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	330	627	0	ENST00000263377.2:c.2181G>C	p.Lys727Asn	p.K727N	ENST00000263377	NM_058243.2	727	aaG/aaC	12/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.648844118543745	2		627	999	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15365071	15365071	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	62	591	0	ENST00000263377.2:c.2050G>A	p.Glu684Lys	p.E684K	ENST00000263377	NM_058243.2	684	Gag/Aag	11/20	1	2	FACETS	0.221	0.19	0.255	0.221	0.19	0.255	SUBCLONAL	1	TRUE	1	0.648844118543745	2		591	865	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18956931	18956931	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	novel	NA	P-0017164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	157	304	0	ENST00000262803.5:c.371+3G>A		p.X124_splice	ENST00000262803	NM_002911.3	124			1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.648844118543745	2		304	468	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212422	36212422	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	686	623	0	ENST00000222270.7:c.2173C>A	p.Pro725Thr	p.P725T	ENST00000222270	NM_014727.1	725	Cca/Aca	3/37	0.603164466453154	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.648844118543745	3		623	1345	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723470	52723470	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	243	468	0	ENST00000322088.6:c.1331A>G	p.Asn444Ser	p.N444S	ENST00000322088	NM_014225.5	444	aAc/aGc	11/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.648844118543745	2		468	713	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145513	24145513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	260	491	0	ENST00000263121.7:c.532G>A	p.Glu178Lys	p.E178K	ENST00000263121	NM_003073.3	178	Gag/Aag	5/9	1	2	FACETS	0.999	0.939	1	0.999	0.939	1	CLONAL	1	TRUE	1	0.648844118543745	2		491	802	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176683982	176683982	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	194	534	0	ENST00000439151.2:c.4796G>T	p.Ser1599Ile	p.S1599I	ENST00000439151	NM_022455.4	1599	aGt/aTt	13/23	1	2	FACETS	0.868	0.806	0.931	0.868	0.806	0.931	CLONAL	1	TRUE	1	0.648844118543745	2		534	689	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777935	27777935	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	82	189	0	ENST00000369163.2:c.84G>C	p.Lys28Asn	p.K28N	ENST00000369163	NM_003536.2	28	aaG/aaC	1/1	0.648844118543745	2	FACETS	0.976	0.873	1	0.488	0.436	0.542	CLONAL	1	TRUE	0	0.648844118543745	2		189	259	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0017166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	163	410	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	0.916	0.844	0.99			1	INDETERMINATE	2	TRUE	NA	0.293251405910944	2		410	607	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0017166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	416	470	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.233425449436628	4	FACETS	0.999	0.952	1	0.999	0.952	1	CLONAL	3	TRUE	1	0.293251405910944	4		470	1224	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0017166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	132	374	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.233425449436628	4	FACETS	1	0.968	1	0.384	0.348	0.422	CLONAL	1	TRUE	1	0.293251405910944	4		375	1010	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602255	10602255	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	33	546	1	ENST00000171111.5:c.1323G>T	p.Glu441Asp	p.E441D	ENST00000171111	NM_203500.1	441	gaG/gaT	3/6	1	2	FACETS	0.354	0.287	0.429	0.354	0.287	0.429	SUBCLONAL	1	TRUE	1	0.293251405910944	2		547	636	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468065	50468065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749084924	NA	P-0017166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	140	378	0	ENST00000331340.3:c.1300G>A	p.Ala434Thr	p.A434T	ENST00000331340	NM_006060.4	434	Gcc/Acc	8/8	0.233425449436628	4	FACETS	0.975	0.897	1	0.975	0.897	1	CLONAL	3	TRUE	1	0.293251405910944	4		378	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0017167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	364	822	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.328631623981035	2	FACETS	0.976	0.927	1	0.976	0.927	1	CLONAL	2	TRUE	0	0.337510567179106	2		822	1105	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101273	27101273	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	302	926	0	ENST00000324856.7:c.4555C>T	p.Gln1519Ter	p.Q1519*	ENST00000324856	NM_006015.4	1519	Cag/Tag	18/20	0.328631623981035	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.337510567179106	2		926	848	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986899	36986899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	188	626	1	ENST00000354822.5:c.790G>A	p.Gly264Ser	p.G264S	ENST00000354822	NM_001079668.2	264	Ggc/Agc	3/3	0.334095389862371	3	FACETS	0.948	0.879	1	0.632	0.586	0.679	CLONAL	2	TRUE	0	0.337510567179106	3		627	687	SUCCESS
AXL	558	MSKCC	GRCh37	19	41736908	41736908	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs370473880	NA	P-0017167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	211	1232	0	ENST00000301178.4:c.623A>G	p.His208Arg	p.H208R	ENST00000301178	NM_021913.4	208	cAt/cGt	5/20	0.328631623981035	2	FACETS	1	0.966	1	0.534	0.495	0.574	CLONAL	1	TRUE	0	0.337510567179106	2		1232	1171	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515615	31515615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	168	1006	0	ENST00000344624.3:c.1004G>A	p.Gly335Glu	p.G335E	ENST00000344624		335	gGg/gAg	4/33	0.328631623981035	2	FACETS	1	0.929	1	0.506	0.464	0.549	CLONAL	1	TRUE	0	0.337510567179106	2		1006	984	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956691	93956691	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	75	616	0	ENST00000369303.4:c.2545A>T	p.Ile849Leu	p.I849L	ENST00000369303	NM_004440.3	849	Ata/Tta	15/17	0.300374014919876	3	FACETS	0.748	0.655	0.849	0.374	0.327	0.425	SUBCLONAL	1	TRUE	1	0.337510567179106	3		616	694	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120240	94120240	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	72	453	0	ENST00000369303.4:c.811C>G	p.Gln271Glu	p.Q271E	ENST00000369303	NM_004440.3	271	Caa/Gaa	3/17	0.300374014919876	3	FACETS	1	0.898	1	0.514	0.45	0.583	CLONAL	1	TRUE	1	0.337510567179106	3		453	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780071	NA	P-0017170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	416	989	2	ENST00000269305.4:c.580C>T	p.Leu194Phe	p.L194F	ENST00000269305	NM_001126112.2	194	Ctt/Ttt	6/11	0.514102965245735	2	FACETS	0.815	0.781	0.849	0.815	0.781	0.849	CLONAL	2	TRUE	0	0.603078957083261	2		991	846	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974800	15974800	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	255	665	0	ENST00000268712.3:c.4075A>C	p.Ile1359Leu	p.I1359L	ENST00000268712	NM_006311.3	1359	Att/Ctt	30/46	0.514102965245735	2	FACETS	0.849	0.805	0.893	0.849	0.805	0.893	CLONAL	2	TRUE	0	0.603078957083261	2		665	498	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212264	36212264	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	101	892	0	ENST00000222270.7:c.2015G>A	p.Gly672Glu	p.G672E	ENST00000222270	NM_014727.1	672	gGg/gAg	3/37	0.539699839852392	3	FACETS	0.458	0.409	0.511	0.229	0.204	0.256	SUBCLONAL	1	TRUE	1	0.603078957083261	3		892	951	SUCCESS
APC	324	MSKCC	GRCh37	5	112175158	112175159	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	145	367	0	ENST00000257430.4:c.3869dup	p.Asn1290LysfsTer11	p.N1290Kfs*11	ENST00000257430	NM_000038.5	1289	-/A	16/16	0.514102965245735	2	FACETS	1	0.989	1	0.742	0.688	0.797	CLONAL	1	TRUE	0	0.603078957083261	2		367	324	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061178	38061195	+	inframe_deletion	In_Frame_Del	DEL	GCTTCTCGCACTTGAAGC	GCTTCTCGCACTTGAAGC	-	novel	NA	P-0017172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	44	343	1	ENST00000250448.2:c.794_811del	p.Arg265_Lys270del	p.R265_K270del	ENST00000250448	NM_004496.3	265	cGCTTCAAGTGCGAGAAGCag/cag	2/2	1	2	FACETS	0.549	0.463	0.642	0.549	0.463	0.642	SUBCLONAL	1	TRUE	1	0.594151427164345	2		344	270	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835758	68835794	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AATACAGTGGGGCACCACCACCGCCCCCCGCCCCATC	AATACAGTGGGGCACCACCACCGCCCCCCGCCCCATC	-	novel	NA	P-0017172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	102	820	0	ENST00000261769.5:c.350_386del	p.Asn117ArgfsTer86	p.N117Rfs*86	ENST00000261769	NM_004360.3	117	AATACAGTGGGGCACCACCACCGCCCCCCGCCCCATCag/ag	3/16	0.518725768246024	1	FACETS	0.421	0.377	0.467	0.421	0.377	0.467	SUBCLONAL	1	TRUE	0	0.594151427164345	1		820	573	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0017174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	2451	1008	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.371647569437478	15	FACETS	1	0.996	1	0.948	0.935	0.96	CLONAL	13	TRUE	1	0.371647569437478	15		1008	3396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0017174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	285	1220	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	0.329765674390734	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.371647569437478	1		1220	1165	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30956886	30956889	+	frameshift_variant	Frame_Shift_Del	DEL	TTTA	TTTA	-	novel	NA	P-0017174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	232	810	0	ENST00000375687.4:c.213_216del	p.Phe71LeufsTer48	p.F71Lfs*48	ENST00000375687	NM_015338.5	71	tTTTAt/tt	4/13	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.371647569437478	2		810	964	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032579	47032579	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	189	419	0	ENST00000377604.3:c.485del	p.Met162SerfsTer104	p.M162Sfs*104	ENST00000377604	NM_001204468.1	162	aTg/ag	5/24	0.181787760444101	2	FACETS	1	0.977	1			1	INDETERMINATE	2	TRUE	NA	0.371647569437478	2		419	462	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0017174-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2555	1319	374	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.3	19	FACETS	0.958	0.933	0.984	0.479	0.466	0.492	CLONAL	9	TRUE	1	0.24	19		375	3874	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0017174-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1191	2842	1008	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.3	19	FACETS	0.992	0.979	1	0.992	0.979	1	CLONAL	18	TRUE	1	0.24	19		1008	4033	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0017174-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1179	227	1220	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	0.294125318856137	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.24	1		1220	1406	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30956886	30956889	+	frameshift_variant	Frame_Shift_Del	DEL	TTTA	TTTA	-	novel	NA	P-0017174-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	153	810	0	ENST00000375687.4:c.213_216del	p.Phe71LeufsTer48	p.F71Lfs*48	ENST00000375687	NM_015338.5	71	tTTTAt/tt	4/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.24	2		810	1089	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032579	47032579	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017174-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	603	419	0	ENST00000377604.3:c.485del	p.Met162SerfsTer104	p.M162Sfs*104	ENST00000377604	NM_001204468.1	162	aTg/ag	5/24	0.3	4	FACETS	0.99	0.958	1			1	CLONAL	6	TRUE	NA	0.24	4		419	1049	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918659	94918659	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	novel	NA	P-0017174-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	43	526	0	ENST00000536441.1:c.526-3C>T		p.X176_splice	ENST00000536441	NM_144665.3	176			0.136854408569369	3	FACETS	0.59	0.493	0.699	0.295	0.246	0.35	INDETERMINATE	1	TRUE	1	0.24	3		526	680	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355087	73355087	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017174-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	87	717	0	ENST00000377767.4:c.283C>G	p.Leu95Val	p.L95V	ENST00000377767	NM_014953.3	95	Ctt/Gtt	2/21	0.294125318856137	1	FACETS	0.723	0.639	0.813	0.723	0.639	0.813	SUBCLONAL	1	TRUE	0	0.24	1		717	883	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873297	151873297	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017174-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	36	412	0	ENST00000262189.6:c.9241G>C	p.Glu3081Gln	p.E3081Q	ENST00000262189	NM_170606.2	3081	Gaa/Caa	38/59	0.136854408569369	3	FACETS	0.581	0.477	0.699	0.291	0.238	0.35	INDETERMINATE	1	TRUE	1	0.24	3		412	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0017175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	500	487	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.16369169527962	3	FACETS	0.94	0.903	0.977			1	INDETERMINATE	3	TRUE	NA	0.384024163428012	3		489	1101	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944946	31944946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	81	538	2	ENST00000340398.3:c.155G>A	p.Arg52His	p.R52H	ENST00000340398	NM_001013699.2	52	cGt/cAt	1/1	0.384024163428012	4	FACETS	0.647	0.568	0.731	0.216	0.189	0.244	SUBCLONAL	1	TRUE	1	0.384024163428012	4		540	903	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344471	118344471	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	136	389	0	ENST00000534358.1:c.2597A>G	p.Lys866Arg	p.K866R	ENST00000534358	NM_005933.3	866	aAg/aGg	3/36	0.318542118009369	3	FACETS	1	0.959	1	0.712	0.655	0.772	CLONAL	2	TRUE	0	0.384024163428012	3		389	395	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028674	42028674	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	68	733	0	ENST00000219905.7:c.4212C>A	p.Asp1404Glu	p.D1404E	ENST00000219905	NM_001164273.1	1404	gaC/gaA	13/24	0.384024163428012	2	FACETS	0.631	0.55	0.719	0.316	0.275	0.36	SUBCLONAL	1	TRUE	0	0.384024163428012	2		733	561	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41228554	41228554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	151	1080	1	ENST00000357654.3:c.4435G>A	p.Val1479Met	p.V1479M	ENST00000357654	NM_007294.3	1479	Gtg/Atg	13/23	0.384024163428012	2	FACETS	1	0.943	1	0.519	0.475	0.565	CLONAL	1	TRUE	0	0.384024163428012	2		1081	758	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0017176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	340	1134	0	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.391193481046846	2		1134	1299	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0017176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	135	476	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.391193481046846	2		477	544	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453145	140453145	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913366	NA	P-0017176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	526	803	0	ENST00000288602.6:c.1790T>A	p.Leu597Gln	p.L597Q	ENST00000288602	NM_004333.4	597	cTa/cAa	15/18	0.391193481046846	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.391193481046846	3		803	1010	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522449	187522449	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1342860045	NA	P-0017176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	170	660	0	ENST00000441802.2:c.11614C>T	p.Arg3872Ter	p.R3872*	ENST00000441802	NM_005245.3	3872	Cga/Tga	21/27	1	2	FACETS	0.966	0.888	1	0.966	0.888	1	CLONAL	1	TRUE	1	0.391193481046846	2		660	900	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874197	155874197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375724784	NA	P-0017176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	257	845	0	ENST00000368323.3:c.334C>T	p.Arg112Cys	p.R112C	ENST00000368323	NM_006912.5	112	Cgt/Tgt	5/6	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.391193481046846	2		845	1067	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273267	198273267	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	221	630	1	ENST00000335508.6:c.943C>T	p.Arg315Ter	p.R315*	ENST00000335508	NM_012433.2	315	Cga/Tga	8/25	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.391193481046846	2		631	997	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740225	162740225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	182	692	0	ENST00000367921.3:c.1427C>T	p.Pro476Leu	p.P476L	ENST00000367921	NM_006182.2	476	cCc/cTc	12/18	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.391193481046846	2		692	854	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376107	118376107	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	193	603	1	ENST00000534358.1:c.9500C>T	p.Ser3167Phe	p.S3167F	ENST00000534358	NM_005933.3	3167	tCc/tTc	27/36	0.391193481046846	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.391193481046846	1		604	681	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432248	432248	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	182	683	0	ENST00000399788.2:c.2275G>A	p.Asp759Asn	p.D759N	ENST00000399788	NM_001042603.1	759	Gat/Aat	16/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.391193481046846	2		683	823	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864099	57864099	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs752987640	NA	P-0017176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	893	464	0	ENST00000228682.2:c.1577-1G>A		p.X526_splice	ENST00000228682	NM_005269.2	526			0.391193481046846	9	FACETS	1	0.986	1			1	CLONAL	8	TRUE	NA	0.391193481046846	9		464	1335	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727805	41727805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	212	933	0	ENST00000301178.4:c.430G>A	p.Glu144Lys	p.E144K	ENST00000301178	NM_021913.4	144	Gag/Aag	4/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.391193481046846	2		933	1075	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190368	32190368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	197	781	0	ENST00000375023.3:c.371C>T	p.Pro124Leu	p.P124L	ENST00000375023	NM_004557.3	124	cCc/cTc	3/30	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.391193481046846	2		781	915	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505402	157505402	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1408001716	NA	P-0017176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	174	662	0	ENST00000346085.5:c.3383A>G	p.Asn1128Ser	p.N1128S	ENST00000346085	NM_020732.3	1128	aAc/aGc	13/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.391193481046846	2		662	767	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524631	106524631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	283	360	1	ENST00000359195.3:c.2792C>T	p.Ser931Phe	p.S931F	ENST00000359195	NM_002649.2	931	tCc/tTc	9/11	0.391193481046846	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	0	0.391193481046846	3		361	555	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435988	116435988	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755043272	NA	P-0017176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	522	826	1	ENST00000397752.3:c.3983C>T	p.Pro1328Leu	p.P1328L	ENST00000397752	NM_000245.2	1328	cCa/cTa	21/21	0.391193481046846	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	0	0.391193481046846	3		827	1051	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942842	68942842	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	218	813	1	ENST00000288368.4:c.654G>A	p.Met218Ile	p.M218I	ENST00000288368	NM_024870.2	218	atG/atA	6/40	0.391193481046846	3	FACETS	1	0.957	1	0.521	0.484	0.56	CLONAL	1	TRUE	1	0.391193481046846	3		814	1278	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968149	68968149	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1257	250	987	0	ENST00000288368.4:c.1178G>A	p.Gly393Glu	p.G393E	ENST00000288368	NM_024870.2	393	gGa/gAa	10/40	0.391193481046846	3	FACETS	1	0.944	1	0.507	0.473	0.543	CLONAL	1	TRUE	1	0.391193481046846	3		987	1507	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549189	87549189	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	377	446	0	ENST00000277120.3:c.1746G>T	p.Lys582Asn	p.K582N	ENST00000277120		582	aaG/aaT	15/19	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	NA	1	0.869334950902957	2		446	787	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945615	206945615	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0121551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	111	403	0	ENST00000423557.1:c.165+1G>T		p.X55_splice	ENST00000423557	NM_000572.2	55			1	2	FACETS	0.423	0.381	0.467	0.423	0.381	0.467	SUBCLONAL	1	NA	1	0.869334950902957	2		403	604	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805571	46805571	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0121551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1516	156	754	1	ENST00000290295.7:c.385T>A	p.Phe129Ile	p.F129I	ENST00000290295	NM_006361.5	129	Ttc/Atc	1/2	0.847693207677416	4	FACETS	0.401	0.366	0.439	0.134	0.122	0.147	SUBCLONAL	1	NA	1	0.869334950902957	4		755	1672	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278063	15278063	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0121551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	88	494	0	ENST00000263388.2:c.5359C>G	p.Pro1787Ala	p.P1787A	ENST00000263388	NM_000435.2	1787	Cca/Gca	29/33	1	2	FACETS	0.362	0.321	0.405	0.362	0.321	0.405	SUBCLONAL	1	NA	1	0.869334950902957	2		494	560	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636706	176636706	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0121551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	65	493	1	ENST00000439151.2:c.1306G>A	p.Gly436Arg	p.G436R	ENST00000439151	NM_022455.4	436	Ggg/Agg	5/23	1	2	FACETS	0.186	0.161	0.214	0.186	0.161	0.214	SUBCLONAL	1	NA	1	0.869334950902957	2		494	802	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675189	30675189	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0121551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	78	604	0	ENST00000376406.3:c.3056G>A	p.Arg1019Lys	p.R1019K	ENST00000376406	NM_014641.2	1019	aGg/aAg	9/15	1	2	FACETS	0.225	0.197	0.255	0.225	0.197	0.255	SUBCLONAL	1	NA	1	0.869334950902957	2		604	797	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220382	1220382	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	432	595	1	ENST00000326873.7:c.475C>T	p.Gln159Ter	p.Q159*	ENST00000326873	NM_000455.4	159	Cag/Tag	4/10	0.48405562329121	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.495287801116437	2		596	830	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131412	202131412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339962485	NA	P-0017180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	219	658	1	ENST00000358485.4:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000358485	NM_001080125.1	127	cGa/cAa	2/9	1	2	FACETS	0.965	0.899	1	0.965	0.899	1	CLONAL	1	TRUE	1	0.495287801116437	2		659	916	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222339	2222339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771191963	NA	P-0017180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	238	856	0	ENST00000326181.6:c.623G>A	p.Arg208Gln	p.R208Q	ENST00000326181	NM_032271.2	208	cGa/cAa	8/21	1	2	FACETS	0.99	0.925	1	0.99	0.925	1	CLONAL	1	TRUE	1	0.495287801116437	2		856	971	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884543	151884543	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	333	451	0	ENST00000262189.6:c.4812del	p.Phe1604LeufsTer61	p.F1604Lfs*61	ENST00000262189	NM_170606.2	1604	ttT/tt	33/59	0.495287801116437	3	FACETS	0.972	0.923	1	0.972	0.923	1	CLONAL	2	TRUE	1	0.495287801116437	3		451	863	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372195	55372202	+	frameshift_variant	Frame_Shift_Del	DEL	GTACTACG	GTACTACG	-	novel	NA	P-0017180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	31	222	0	ENST00000297316.4:c.886_893del	p.Tyr296ArgfsTer66	p.Y296Rfs*66	ENST00000297316	NM_022454.3	295	gtGTACTACGgc/gtgc	2/2	1	2	FACETS	0.469	0.381	0.568	0.469	0.381	0.568	SUBCLONAL	1	TRUE	1	0.495287801116437	2		222	267	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	193	335	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.687744029222149	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.687744029222149	1		335	350	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0017181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	237	736	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	0.846	0.791	0.901	0.846	0.791	0.901	CLONAL	1	TRUE	1	0.687744029222149	2		736	815	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512330	120512343	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCAGGCATTCAT	CAGCAGGCATTCAT	-	novel	NA	P-0017182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	137	416	0	ENST00000256646.2:c.899_912del	p.Asp300AlafsTer30	p.D300Afs*30	ENST00000256646	NM_024408.3	300	gATGAATGCCTGCTG/g	6/34	0.140442084808662	3	FACETS	0.838	0.763	0.916			1	INDETERMINATE	2	TRUE	NA	0.241889871861971	3		416	758	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025619	1025619	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	179	396	0	ENST00000358495.3:c.756G>C	p.Glu252Asp	p.E252D	ENST00000358495	NM_134424.2	252	gaG/gaC	9/12	0.140442084808662	3	FACETS	1	0.961	1			1	INDETERMINATE	2	TRUE	NA	0.241889871861971	3		396	780	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67132612	67132658	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GGCAAGAAGACAACAAGACCCTAGTCCTGGTTCCAATTTAGGTGGTG	GGCAAGAAGACAACAAGACCCTAGTCCTGGTTCCAATTTAGGTGGTG	-	novel	NA	P-0017182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	31	526	0	ENST00000412916.2:c.496_542del		p.X166_splice	ENST00000412916		166		6/6	0.177538312018581	3	FACETS	0.542	0.437	0.661	0.181	0.145	0.221	SUBCLONAL	1	TRUE	0	0.241889871861971	3		526	530	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37038180	37038180	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	100	296	1	ENST00000231790.2:c.187G>T	p.Asp63Tyr	p.D63Y	ENST00000231790	NM_000249.3	63	Gac/Tac	2/19	0.164488160900319	5	FACETS	0.95	0.851	1	0.633	0.567	0.704	CLONAL	2	TRUE	2	0.241889871861971	5		297	593	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852276	128852276	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1475027326	NA	P-0017182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	182	544	0	ENST00000249373.3:c.2348C>T	p.Ala783Val	p.A783V	ENST00000249373	NM_005631.4	783	gCa/gTa	12/12	0.241889871861971	3	FACETS	1	0.988	1	0.466	0.429	0.505	CLONAL	1	TRUE	0	0.241889871861971	3		544	1206	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	30	301	4				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.355964769776793	2		305	157	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685591	29685603	+	frameshift_variant	Frame_Shift_Del	DEL	GGTGTACCATGAA	GGTGTACCATGAA	-	novel	NA	P-0017183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	114	918	0	ENST00000356175.3:c.8002_8014del	p.Val2668AsnfsTer46	p.V2668Nfs*46	ENST00000356175	NM_000267.3	2667	gtGGTGTACCATGAA/gt	54/57	1	2	FACETS	0.824	0.742	0.911	0.824	0.742	0.911	CLONAL	1	TRUE	1	0.355964769776793	2		918	777	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40477043	40477044	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0017183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	52	515	0	ENST00000264657.5:c.1401_1402del	p.Ile467MetfsTer81	p.I467Mfs*81	ENST00000264657	NM_139276.2	467	atCTgt/atgt	16/24	1	2	FACETS	0.468	0.398	0.545	0.468	0.398	0.545	SUBCLONAL	1	TRUE	1	0.355964769776793	2		515	624	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0017184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	116	589	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.110896229227827	4	FACETS	0.827	0.743	0.916	0.413	0.371	0.458	INDETERMINATE	1	TRUE	2	0.29	4		589	1248	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044719	47044719	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	131	699	0	ENST00000377604.3:c.2119C>T	p.Gln707Ter	p.Q707*	ENST00000377604	NM_001204468.1	707	Cag/Tag	19/24	1	2	FACETS	0.772	0.699	0.85	0.772	0.699	0.85	SUBCLONAL	1	TRUE	1	0.29	2		699	1170	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737780	145737780	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	79	527	0	ENST00000428558.2:c.3050G>C	p.Arg1017Thr	p.R1017T	ENST00000428558	NM_004260.3	1017	aGg/aCg	18/22	NA	2	FACETS	0.561	0.492	0.635			1	INDETERMINATE	1	TRUE	NA	0.29	2		527	972	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0017185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	419	290	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	NA	2	FACETS	0.939	0.905	0.972			1	INDETERMINATE	2	TRUE	NA	0.667132023434553	2		290	669	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0017185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	383	483	0	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.637558755010031	3	FACETS	0.883	0.851	0.914	0.883	0.851	0.914	CLONAL	3	TRUE	0	0.667132023434553	3		483	578	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943329	71943329	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1221876161	NA	P-0017185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	554	754	0	ENST00000298229.2:c.1661C>T	p.Ser554Leu	p.S554L	ENST00000298229	NM_001567.3	554	tCa/tTa	14/28	0.667132023434553	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.667132023434553	3		754	1103	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481842	56481842	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	263	737	0	ENST00000267101.3:c.770C>G	p.Pro257Arg	p.P257R	ENST00000267101	NM_001982.3	257	cCt/cGt	7/28	0.612744178619257	2	FACETS	1	0.983	1	0.556	0.524	0.589	CLONAL	1	TRUE	0	0.667132023434553	2		737	709	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133236077	133236077	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	308	522	0	ENST00000320574.5:c.3079T>G	p.Ser1027Ala	p.S1027A	ENST00000320574	NM_006231.2	1027	Tct/Gct	26/49	0.612744178619257	2	FACETS	0.902	0.863	0.94	0.902	0.863	0.94	CLONAL	2	TRUE	0	0.667132023434553	2		522	512	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872909	136872909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	206	429	0	ENST00000241393.3:c.589G>T	p.Val197Phe	p.V197F	ENST00000241393	NM_003467.2	197	Gtt/Ttt	2/2	0.208744477895376	4	FACETS	0.862	0.805	0.921			1	INDETERMINATE	2	TRUE	NA	0.667132023434553	4		429	597	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191506	10191506	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs5030820	NA	P-0017186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	71	503	0	ENST00000256474.2:c.499C>G	p.Arg167Gly	p.R167G	ENST00000256474	NM_000551.3	167	Cgg/Ggg	3/3	0.390932912531972	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.390932912531972	1		503	267	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0017187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	352	290	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.425643490727537	4	FACETS	1	0.97	1	0.762	0.729	0.795	CLONAL	3	TRUE	0	0.560464128208467	4		290	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	506	518	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.441914341016936	4	FACETS	1	0.992	1	0.816	0.788	0.844	CLONAL	3	TRUE	0	0.560464128208467	4		518	863	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176118142	176118143	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0017187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	134	401	1	ENST00000367669.3:c.830_831del	p.Glu277AlafsTer17	p.E277Afs*17	ENST00000367669	NM_022457.5	277	gAG/g	6/20	0.336715043451092	4	FACETS	1	0.985	1	0.692	0.632	0.755	CLONAL	1	TRUE	2	0.560464128208467	4		402	539	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653785	89653785	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1355570425	NA	P-0017187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	251	416	2	ENST00000371953.3:c.83T>C	p.Ile28Thr	p.I28T	ENST00000371953	NM_000314.4	28	aTt/aCt	2/9	0.459574522932567	3	FACETS	1	0.992	1	0.827	0.785	0.869	CLONAL	2	TRUE	0	0.560464128208467	3		418	462	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676271	29676271	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0017187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	165	541	0	ENST00000356175.3:c.7258+2T>C		p.X2420_splice	ENST00000356175	NM_000267.3	2420			0.468996912959755	2	FACETS	0.767	0.713	0.82	0.767	0.713	0.82	SUBCLONAL	2	TRUE	0	0.560464128208467	2		541	384	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522635	176522636	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0017187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	387	692	0	ENST00000292408.4:c.1734dup	p.Ser579GlufsTer3	p.S579Efs*3	ENST00000292408	NM_213647.1	578	cgg/cGgg	13/18	0.560464128208467	5	FACETS	1	0.983	1	0.537	0.511	0.564	CLONAL	2	TRUE	1	0.560464128208467	5		692	1183	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967893	93967893	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	569	728	1	ENST00000369303.4:c.2034C>A	p.Asp678Glu	p.D678E	ENST00000369303	NM_004440.3	678	gaC/gaA	11/17	0.560464128208467	6	FACETS	0.854	0.819	0.889			1	CLONAL	3	TRUE	NA	0.560464128208467	6		729	1681	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0017189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	122	547	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.956	0.863	1	0.956	0.863	1	CLONAL	1	FALSE	1	0.24441181865879	2		547	1044	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0017189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	131	670	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.177433587822202	2	FACETS	1	0.985	1	0.726	0.66	0.796	CLONAL	1	FALSE	0	0.24441181865879	2		670	738	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906754	32906754	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs780798665	NA	P-0017189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	104	857	0	ENST00000380152.3:c.1139G>C	p.Ser380Thr	p.S380T	ENST00000380152		380	aGt/aCt	10/27	0.127205062208976	3	FACETS	0.962	0.86	1	0.481	0.43	0.536	INDETERMINATE	1	FALSE	1	0.24441181865879	3		857	993	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440614	56440652	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTGGAGGTCTAGTGTGCTTACCCAGGCCGGGGGCTCCT	TCTGGAGGTCTAGTGTGCTTACCCAGGCCGGGGGCTCCT	-	novel	NA	P-0017189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	79	479	0	ENST00000407977.2:c.566_582+22del		p.X189_splice	ENST00000407977		189		5/10	0.177433587822202	2	FACETS	1	0.971	1	0.676	0.597	0.761	CLONAL	1	FALSE	0	0.24441181865879	2		479	478	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533656	63533687	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGGGGGCAGGCGCCCGGCGAGGCGGCCGCG	GGAGGGGGCAGGCGCCCGGCGAGGCGGCCGCG	-	novel	NA	P-0017189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	100	457	0	ENST00000307078.5:c.1467_1498del	p.Ala490ArgfsTer127	p.A490Rfs*127	ENST00000307078	NM_004655.3	489	ccCGCGGCCGCCTCGCCGGGCGCCTGCCCCCTCCtc/cctc	6/11	0.177433587822202	2	FACETS	0.919	0.826	1	0.919	0.826	1	CLONAL	2	FALSE	0	0.24441181865879	2		457	445	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70355033	70355059	+	inframe_deletion	In_Frame_Del	DEL	AGCCACAGGGCTCCCTTATCGATACCA	AGCCACAGGGCTCCCTTATCGATACCA	-	novel	NA	P-0017189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	72	859	0	ENST00000374080.3:c.4957_4983del	p.Pro1653_Lys1661del	p.P1653_K1661del	ENST00000374080		1652	gAGCCACAGGGCTCCCTTATCGATACCAag/gag	36/45	1	2	FACETS	0.718	0.627	0.818	0.718	0.627	0.818	SUBCLONAL	1	FALSE	1	0.24441181865879	2		859	820	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0017190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	100	418	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.269728595971453	2		420	723	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0017190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	46	178	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.0875879659730425	3	FACETS	0.469	0.394	0.553	0.235	0.197	0.277	INDETERMINATE	1	TRUE	1	0.269728595971453	3		178	825	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245391	46245391	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	73	370	0	ENST00000334344.6:c.3485C>A	p.Thr1162Asn	p.T1162N	ENST00000334344	NM_152641.2	1162	aCc/aAc	15/21	0.0875879659730425	3	FACETS	0.732	0.639	0.833	0.366	0.319	0.417	INDETERMINATE	1	TRUE	1	0.269728595971453	3		370	839	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643695	38643695	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	52	433	1	ENST00000299084.4:c.1165G>A	p.Asp389Asn	p.D389N	ENST00000299084	NM_152594.2	389	Gat/Aat	7/7	1	2	FACETS	0.423	0.359	0.494	0.423	0.359	0.494	SUBCLONAL	1	TRUE	1	0.269728595971453	2		434	912	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561868	55561868	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	32	329	0	ENST00000288135.5:c.258G>C	p.Lys86Asn	p.K86N	ENST00000288135	NM_000222.2	86	aaG/aaC	2/21	0.269728595971453	1	FACETS	0.327	0.264	0.398	0.327	0.264	0.398	SUBCLONAL	1	TRUE	0	0.269728595971453	1		329	628	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636924	176636924	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	68	480	2	ENST00000439151.2:c.1524G>T	p.Arg508Ser	p.R508S	ENST00000439151	NM_022455.4	508	agG/agT	5/23	0.269728595971453	1	FACETS	0.446	0.387	0.511	0.446	0.387	0.511	SUBCLONAL	1	TRUE	0	0.269728595971453	1		482	977	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444326	50444326	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	28	241	0	ENST00000331340.3:c.256G>C	p.Asp86His	p.D86H	ENST00000331340	NM_006060.4	86	Gat/Cat	4/8	1	2	FACETS	0.433	0.345	0.533	0.433	0.345	0.533	SUBCLONAL	1	TRUE	1	0.269728595971453	2		241	480	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0017191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	243	525	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.177964440502981	4	FACETS	1	0.971	1			1	CLONAL	2	TRUE	NA	0.289723412690734	4		525	1012	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0017191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	30	201	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	0.199396649753094	2	FACETS	0.797	0.653	0.953	0.797	0.653	0.953	CLONAL	2	TRUE	0	0.289723412690734	2		201	130	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578447	+	frameshift_variant	Frame_Shift_Del	DEL	GCTTGTAGATG	GCTTGTAGATG	-	novel	NA	P-0017191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	134	930	0	ENST00000269305.4:c.483_493del	p.Ile162ValfsTer15	p.I162Vfs*15	ENST00000269305	NM_001126112.2	161	gcCATCTACAAGCag/gcag	5/11	0.207323962994514	2	FACETS	0.793	0.724	0.866	0.793	0.724	0.866	SUBCLONAL	2	TRUE	0	0.289723412690734	2		930	583	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38506095	38506100	+	inframe_deletion	In_Frame_Del	DEL	CTGCAT	CTGCAT	-	novel	NA	P-0017191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	119	940	0	ENST00000254066.5:c.388_393del	p.Cys130_Ile131del	p.C130_I131del	ENST00000254066	NM_000964.3	129	aaCTGCATc/aac	4/9	0.139867555462927	4	FACETS	1	0.982	1	0.696	0.628	0.767	INDETERMINATE	1	TRUE	2	0.289723412690734	4		940	761	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575107	48575107	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	38	682	0	ENST00000342988.3:c.301T>C	p.Trp101Arg	p.W101R	ENST00000342988	NM_005359.5	101	Tgg/Cgg	3/12	0.289723412690734	1	FACETS	0.539	0.446	0.643	0.539	0.446	0.643	SUBCLONAL	1	TRUE	0	0.289723412690734	1		682	416	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306544	41306544	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751487270	NA	P-0017191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	93	733	0	ENST00000373198.4:c.1115C>T	p.Pro372Leu	p.P372L	ENST00000373198	NM_133170.3	372	cCg/cTg	7/32	0.102544398303024	4	FACETS	0.784	0.699	0.874	0.784	0.699	0.874	INDETERMINATE	2	TRUE	2	0.289723412690734	4		733	528	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011138	12011138	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1191386417	NA	P-0017193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	43	499	0	ENST00000353533.5:c.545C>G	p.Ser182Cys	p.S182C	ENST00000353533	NM_003010.3	182	tCt/tGt	5/11	1	2	FACETS	0.53	0.443	0.627	0.53	0.443	0.627	SUBCLONAL	1	TRUE	1	0.282055682572492	2		499	575	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188803	32188803	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	121	651	0	ENST00000375023.3:c.751C>A	p.Leu251Met	p.L251M	ENST00000375023	NM_004557.3	251	Ctg/Atg	4/30	0.282055682572492	3	FACETS	1	0.966	1	0.578	0.522	0.637	CLONAL	1	TRUE	1	0.282055682572492	3		651	847	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0017195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	95	390	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.948	0.85	1	0.948	0.85	1	CLONAL	1	TRUE	1	0.495840590095561	2		392	404	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0017195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	63	195	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.882	0.77	1	0.882	0.77	1	CLONAL	1	TRUE	1	0.495840590095561	2		195	288	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0017196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	216	470	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.34890188048162	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.34890188048162	3		470	673	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045872	47045872	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0017196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	160	388	0	ENST00000377604.3:c.2668-1G>T		p.X890_splice	ENST00000377604	NM_001204468.1	890			0.34890188048162	2	FACETS	1	0.984	1			1	CLONAL	3	TRUE	NA	0.34890188048162	2		388	266	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591892	48591892	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	67	558	0	ENST00000342988.3:c.1055G>T	p.Gly352Val	p.G352V	ENST00000342988	NM_005359.5	352	gGa/gTa	9/12	0.34890188048162	1	FACETS	0.93	0.813	1	0.93	0.813	1	CLONAL	1	TRUE	0	0.34890188048162	1		558	341	SUCCESS
ALK	238	MSKCC	GRCh37	2	29448339	29448339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375889530	NA	P-0017196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	154	1236	2	ENST00000389048.3:c.3160G>A	p.Gly1054Ser	p.G1054S	ENST00000389048	NM_004304.4	1054	Ggc/Agc	19/29	NA	2	FACETS	0.925	0.846	1			1	INDETERMINATE	1	TRUE	NA	0.34890188048162	2		1238	954	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	263	408	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.98	0.919	1	0.98	0.919	1	CLONAL	1	TRUE	1	0.507095287176761	2		408	1058	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0017197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	287	708	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.507095287176761	1	FACETS	0.935	0.881	0.989	0.935	0.881	0.989	CLONAL	1	TRUE	0	0.507095287176761	1		708	904	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058057	27058057	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	72	474	0	ENST00000324856.7:c.1765C>T	p.Gln589Ter	p.Q589*	ENST00000324856	NM_006015.4	589	Caa/Taa	3/20	1	2	FACETS	0.387	0.337	0.44	0.387	0.337	0.44	SUBCLONAL	1	TRUE	1	0.507095287176761	2		474	734	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445499	49445499	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772870804	NA	P-0017197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	260	658	1	ENST00000301067.7:c.1967del	p.Leu656ArgfsTer274	p.L656Rfs*274	ENST00000301067	NM_003482.3	656	cTg/cg	10/54	1	2	FACETS	0.955	0.894	1	0.955	0.894	1	CLONAL	1	TRUE	1	0.507095287176761	2		659	1074	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581273	48581273	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	302	721	0	ENST00000342988.3:c.577G>T	p.Glu193Ter	p.E193*	ENST00000342988	NM_005359.5	193	Gag/Tag	5/12	0.507095287176761	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.507095287176761	1		721	832	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0017198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	818	470	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.325218496913257	10	FACETS	1	0.993	1			1	CLONAL	8	FALSE	NA	0.325218496913257	10		470	1373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577526	7577526	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121912653	NA	P-0017198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	173	746	0	ENST00000269305.4:c.755T>C	p.Leu252Pro	p.L252P	ENST00000269305	NM_001126112.2	252	cTc/cCc	7/11	0.325218496913257	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	FALSE	0	0.325218496913257	2		746	528	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044898	47044898	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	123	1100	2	ENST00000377604.3:c.2224C>T	p.Gln742Ter	p.Q742*	ENST00000377604	NM_001204468.1	742	Cag/Tag	20/24	0.300251897149105	4	FACETS	1	0.912	1	0.337	0.304	0.372	CLONAL	1	FALSE	1	0.325218496913257	4		1102	992	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186697	11186697	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	88	633	0	ENST00000361445.4:c.6508del	p.Arg2170GlyfsTer3	p.R2170Gfs*3	ENST00000361445	NM_004958.3	2170	Cgg/gg	46/58	0.0574036734022632	3	FACETS	1	0.912	1			1	INDETERMINATE	1	FALSE	NA	0.325218496913257	3		633	609	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254582	1254582	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	173	776	4	ENST00000310581.5:c.3196C>T	p.Pro1066Ser	p.P1066S	ENST00000310581	NM_198253.2	1066	Ccc/Tcc	15/16	0.325218496913257	5	FACETS	1	0.945	1	0.687	0.633	0.743	CLONAL	2	FALSE	2	0.325218496913257	5		780	768	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123022474	123022474	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	41	915	0	ENST00000355640.3:c.883G>T	p.Gly295Cys	p.G295C	ENST00000355640		295	Ggt/Tgt	3/7	0.300251897149105	4	FACETS	0.452	0.375	0.538	0.151	0.125	0.18	SUBCLONAL	1	FALSE	1	0.325218496913257	4		915	739	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696713	47696713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	134	686	0	ENST00000347630.2:c.235G>A	p.Glu79Lys	p.E79K	ENST00000347630	NM_001007230.1	79	Gaa/Aaa	5/11	0.231652842883749	3	FACETS	0.92	0.836	1	0.46	0.418	0.505	INDETERMINATE	1	TRUE	1	0.40252166318218	3		686	869	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555685	21555685	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747591469	NA	P-0017199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	43	798	3	ENST00000382592.4:c.2585G>A	p.Arg862Gln	p.R862Q	ENST00000382592	NM_014572.2	862	cGg/cAg	6/8	1	2	FACETS	0.301	0.251	0.357	0.301	0.251	0.357	SUBCLONAL	1	TRUE	1	0.40252166318218	2		801	710	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625189	69625189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782491968	NA	P-0017199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	117	821	0	ENST00000334134.2:c.604C>T	p.Pro202Ser	p.P202S	ENST00000334134	NM_005247.2	202	Cct/Tct	3/3	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.40252166318218	2		821	580	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26911701	26911701	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0017199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	40	504	0	ENST00000381527.3:c.129-3C>T		p.X43_splice	ENST00000381527	NM_001260.1	43			1	2	FACETS	0.406	0.337	0.483	0.406	0.337	0.483	SUBCLONAL	1	TRUE	1	0.40252166318218	2		504	489	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064321	30064322	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GA	GA	TT	novel	NA	P-0017199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	35	386	2	ENST00000338641.4:c.886-1_886delinsTT		p.X296_splice	ENST00000338641	NM_000268.3	296		10/16	1	2	FACETS	0.515	0.422	0.617	0.515	0.422	0.617	SUBCLONAL	1	TRUE	1	0.40252166318218	2		388	338	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0017201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	234	401	3	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.183988044446241	4	FACETS	1	0.95	1	1	0.95	1	CLONAL	4	TRUE	0	0.183988044446241	4		404	741	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986993	36986993	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	102	744	2	ENST00000354822.5:c.696del	p.Thr233ArgfsTer14	p.T233Rfs*14	ENST00000354822	NM_001079668.2	232	ccC/cc	3/3	0.179830098033736	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.183988044446241	2		746	476	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513572	41513572	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	68	756	1	ENST00000263253.7:c.476A>G	p.Asn159Ser	p.N159S	ENST00000263253	NM_001429.3	159	aAt/aGt	2/31	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.183988044446241	2		757	565	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207672	29207672	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	97	654	1	ENST00000240100.2:c.124G>T	p.Gly42Cys	p.G42C	ENST00000240100	NM_001394.6	42	Ggc/Tgc	1/4	0.183988044446241	1	FACETS	0.908	0.813	1	1	0.985	1	CLONAL	2	TRUE	0	0.183988044446241	1		655	527	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0017203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	277	410	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.533192820054217	2	FACETS	0.934	0.887	0.981	0.934	0.887	0.981	CLONAL	2	TRUE	0	0.53808241070878	2		410	551	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226589590	226590017	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCCTGTGTGGTGGGAGGGGGAGGGGGTACTGGAAACTCTTTGTTCTTTGCTTACTTTTGCCATGAACAAAAATAAAGTATATTAAAAACAAAACAACTTTAAAGGCTACATTCCAAGCACCTGGAAAAACAAAATACCAAATATCATGCAACAGATGATGCTGAGTCCAGGAGGTGTTGCTGAAATAACATGGGCACCATACGCTTGATCTGCACATGTGGGAGAGGGCAAGCTGGGGGAGGTTTGCTTTGCTCTCTGAGACGAGGCCCTCCTGGGAGCTTCAGGGTGGGGGCTGAATGCCCATGCTGCCCCAGTATGTACACACCTGTCACTCCTCCAGCTTCCGCTGTCTTCTTGACTTTCTGCTGGTCATCCCACCGAAGCTCAGAGAACCCATCCACCTCAACGTCAGGGTGCCGGATGGAGTG	GCCTGTGTGGTGGGAGGGGGAGGGGGTACTGGAAACTCTTTGTTCTTTGCTTACTTTTGCCATGAACAAAAATAAAGTATATTAAAAACAAAACAACTTTAAAGGCTACATTCCAAGCACCTGGAAAAACAAAATACCAAATATCATGCAACAGATGATGCTGAGTCCAGGAGGTGTTGCTGAAATAACATGGGCACCATACGCTTGATCTGCACATGTGGGAGAGGGCAAGCTGGGGGAGGTTTGCTTTGCTCTCTGAGACGAGGCCCTCCTGGGAGCTTCAGGGTGGGGGCTGAATGCCCATGCTGCCCCAGTATGTACACACCTGTCACTCCTCCAGCTTCCGCTGTCTTCTTGACTTTCTGCTGGTCATCCCACCGAAGCTCAGAGAACCCATCCACCTCAACGTCAGGGTGCCGGATGGAGTG	-	novel	NA	P-0017203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	74	2	0	ENST00000366794.5:c.184_286+325del		p.X62_splice	ENST00000366794	NM_001618.3	62		2/23	0.53808241070878	3	FACETS	0.354	0.309	0.403	0.177	0.154	0.202	SUBCLONAL	1	TRUE	1	0.53808241070878	3		2	985	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206732	102206732	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	158	635	0	ENST00000263464.3:c.1360C>A	p.Leu454Ile	p.L454I	ENST00000263464	NM_001165.4	454	Ctt/Att	7/9	0.226758769513841	3	FACETS	0.863	0.791	0.938	0.288	0.263	0.313	INDETERMINATE	1	TRUE	0	0.53808241070878	3		635	864	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910617	32910617	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs80358489	NA	P-0017203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	174	752	0	ENST00000380152.3:c.2125C>G	p.Leu709Val	p.L709V	ENST00000380152		709	Ctg/Gtg	11/27	0.533192820054217	2	FACETS	1	0.952	1	0.52	0.481	0.56	CLONAL	1	TRUE	0	0.53808241070878	2		752	622	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610393	81610393	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	148	610	0	ENST00000298171.2:c.1991T>C	p.Val664Ala	p.V664A	ENST00000298171	NM_000369.2	664	gTa/gCa	10/10	0.533192820054217	2	FACETS	0.957	0.878	1	0.478	0.439	0.519	CLONAL	1	TRUE	0	0.53808241070878	2		610	575	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610402	81610402	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	146	605	0	ENST00000298171.2:c.2000A>C	p.Tyr667Ser	p.Y667S	ENST00000298171	NM_000369.2	667	tAt/tCt	10/10	0.533192820054217	2	FACETS	0.974	0.894	1	0.487	0.447	0.529	CLONAL	1	TRUE	0	0.53808241070878	2		605	557	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955034	93955034	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	167	361	0	ENST00000369303.4:c.2864T>A	p.Val955Glu	p.V955E	ENST00000369303	NM_004440.3	955	gTa/gAa	16/17	0.53808241070878	5	FACETS	1	0.967	1	0.72	0.667	0.776	CLONAL	2	TRUE	2	0.53808241070878	5		361	519	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911801	32911803	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	novel	NA	P-0017203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	227	864	0	ENST00000380152.3:c.3310_3312del	p.Thr1104del	p.T1104del	ENST00000380152		1103	ttAACa/tta	11/27	0.533192820054217	2	FACETS	0.989	0.923	1	0.495	0.461	0.529	CLONAL	1	TRUE	0	0.53808241070878	2		864	853	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	51	301	4				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.94	0.799	1	0.94	0.799	1	CLONAL	1	TRUE	1	0.23	2		305	472	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780226	9780226	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	109	924	0	ENST00000377346.4:c.1396G>A	p.Asp466Asn	p.D466N	ENST00000377346	NM_005026.3	466	Gat/Aat	11/24	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.23	2		924	852	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936201	71936201	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	50	483	0	ENST00000298229.2:c.173T>C	p.Leu58Pro	p.L58P	ENST00000298229	NM_001567.3	58	cTc/cCc	1/28	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.23	2		483	375	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591621	38591621	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0017204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	65	650	0	ENST00000299084.4:c.80C>G	p.Ser27Ter	p.S27*	ENST00000299084	NM_152594.2	27	tCa/tGa	2/7	1	2	FACETS	0.928	0.805	1	0.928	0.805	1	CLONAL	1	TRUE	1	0.23	2		650	609	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220561	1220582	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGCACGGCACCGCCACAGGCA	CTGCACGGCACCGCCACAGGCA	-	novel	NA	P-0017204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	82	667	0	ENST00000326873.7:c.598-13_606del		p.X200_splice	ENST00000326873	NM_000455.4	200		5/10	0.287492543238028	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.23	1		667	509	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077510	30077510	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	108	874	1	ENST00000338641.4:c.1657G>T	p.Glu553Ter	p.E553*	ENST00000338641	NM_000268.3	553	Gag/Tag	15/16	0.287492543238028	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.23	1		875	747	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114601	73114601	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	50	607	0	ENST00000356692.5:c.982G>C	p.Glu328Gln	p.E328Q	ENST00000356692		328	Gaa/Caa	9/9	1	2	FACETS	0.651	0.551	0.761	0.651	0.551	0.761	SUBCLONAL	1	TRUE	1	0.23	2		607	668	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851696	134851696	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576710309	NA	P-0017204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	43	574	1	ENST00000398015.3:c.1102C>T	p.Arg368Trp	p.R368W	ENST00000398015	NM_004441.4	368	Cgg/Tgg	5/16	1	2	FACETS	0.752	0.629	0.889	0.752	0.629	0.889	SUBCLONAL	1	TRUE	1	0.23	2		575	497	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324148	31324148	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	79	406	0	ENST00000412585.2:c.415C>T	p.Gln139Ter	p.Q139*	ENST00000412585	NM_005514.6	139	Cag/Tag	3/8	1	2	FACETS	1	0.907	1	1	0.985	1	CLONAL	2	TRUE	1	0.23	2		406	335	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0017207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	335	492	1	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.605828232460497	2		493	1045	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168803	56168804	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0017207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	274	519	0	ENST00000399503.3:c.1658dup	p.Tyr553Ter	p.Y553*	ENST00000399503	NM_005921.1	553	tac/tAac	9/20	0.593700145117684	3	FACETS	0.97	0.91	1	0.485	0.455	0.516	CLONAL	1	TRUE	1	0.605828232460497	3		519	1215	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94963996	94963996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	117	169	1	ENST00000536441.1:c.29C>T	p.Ala10Val	p.A10V	ENST00000536441	NM_144665.3	10	gCc/gTc	1/10	0.605828232460497	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.605828232460497	1		170	252	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944983	31944983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1175067252	NA	P-0017207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	535	582	0	ENST00000340398.3:c.118C>T	p.Arg40Cys	p.R40C	ENST00000340398	NM_001013699.2	40	Cgc/Tgc	1/1	0.593700145117684	3	FACETS	0.932	0.896	0.968	0.932	0.896	0.968	CLONAL	2	TRUE	1	0.605828232460497	3		582	1235	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659851	227659851	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	243	389	0	ENST00000305123.5:c.3604C>T	p.Pro1202Ser	p.P1202S	ENST00000305123	NM_005544.2	1202	Ccc/Tcc	1/2	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.605828232460497	2		389	782	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177079	56177080	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0017207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	308	255	0	ENST00000399503.3:c.2350_2351dup	p.Glu785LeufsTer15	p.E785Lfs*15	ENST00000399503	NM_005921.1	783	-/GC	13/20	0.593700145117684	3	FACETS	0.874	0.828	0.92	0.874	0.828	0.92	CLONAL	2	TRUE	1	0.605828232460497	3		255	758	SUCCESS
APC	324	MSKCC	GRCh37	5	112175773	112175773	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	194	339	0	ENST00000257430.4:c.4482A>C	p.Glu1494Asp	p.E1494D	ENST00000257430	NM_000038.5	1494	gaA/gaC	16/16	NA	2	FACETS	1	0.952	1			1	INDETERMINATE	1	TRUE	NA	0.605828232460497	2		339	622	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922097	39922097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1249334408	NA	P-0017209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	131	682	1	ENST00000378444.4:c.4075G>A	p.Gly1359Arg	p.G1359R	ENST00000378444	NM_001123385.1	1359	Ggg/Agg	9/15	0.263870663825611	3	FACETS	0.771	0.699	0.847	0.386	0.349	0.424	INDETERMINATE	1	TRUE	1	0.464676590324972	3		683	901	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030486	49030486	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0017211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	361	461	0	ENST00000267163.4:c.1960+1G>A		p.X654_splice	ENST00000267163	NM_000321.2	654			0.845156870154614	1	FACETS	0.977	0.943	1	0.977	0.943	1	CLONAL	1	TRUE	0	0.845156870154614	1		461	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587780070	NA	P-0017211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	531	499	0	ENST00000269305.4:c.535C>A	p.His179Asn	p.H179N	ENST00000269305	NM_001126112.2	179	Cat/Aat	5/11	0.845156870154614	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.845156870154614	2		499	598	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185169143	185169143	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	511	692	0	ENST00000265026.3:c.1238A>G	p.Asp413Gly	p.D413G	ENST00000265026	NM_004721.4	413	gAt/gGt	7/14	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.845156870154614	2		692	1097	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0017213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	94	410	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.737827428349328	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.775153196394683	1		410	143	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0017213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	79	178	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.775153196394683	4	FACETS	1	0.908	1	0.343	0.303	0.384	CLONAL	1	TRUE	1	0.775153196394683	4		178	352	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371734	55371734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	44	437	0	ENST00000297316.4:c.424C>T	p.Arg142Cys	p.R142C	ENST00000297316	NM_022454.3	142	Cgc/Tgc	2/2	0.15246234181071	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.775153196394683	0		437	109	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480335	56480335	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	151	552	0	ENST00000267101.3:c.442T>C	p.Tyr148His	p.Y148H	ENST00000267101	NM_001982.3	148	Tat/Cat	4/28	0.347610249386535	5	FACETS	1	0.952	1			1	INDETERMINATE	2	TRUE	NA	0.775153196394683	5		552	405	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544145	18544145	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	98	591	0	ENST00000266497.5:c.1962A>G	p.Ile654Met	p.I654M	ENST00000266497		654	atA/atG	13/31	1	2	FACETS	0.919	0.833	1	0.919	0.833	1	CLONAL	1	TRUE	1	0.775153196394683	2		591	275	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39239343	39239343	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	29	729	0	ENST00000402219.2:c.2314G>C	p.Glu772Gln	p.E772Q	ENST00000402219	NM_005633.3	772	Gag/Cag	14/23	1	2	FACETS	0.282	0.227	0.345	0.282	0.227	0.345	SUBCLONAL	1	TRUE	1	0.775153196394683	2		729	265	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458486	12458486	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	90	729	0	ENST00000287820.6:c.1103T>C	p.Leu368Pro	p.L368P	ENST00000287820	NM_015869.4	368	cTc/cCc	6/7	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.775153196394683	2		729	216	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860113	151860113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	77	471	0	ENST00000262189.6:c.10549C>T	p.Pro3517Ser	p.P3517S	ENST00000262189	NM_170606.2	3517	Cct/Tct	43/59	NA	2	FACETS	1	0.942	1			1	INDETERMINATE	1	TRUE	NA	0.775153196394683	2		471	185	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922523	56922550	+	frameshift_variant	Frame_Shift_Del	DEL	GTGGAGAACTGCCCAGATGAGCTCTATG	GTGGAGAACTGCCCAGATGAGCTCTATG	-	novel	NA	P-0017213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	31	543	0	ENST00000519728.1:c.1393_1420del	p.Val465ThrfsTer3	p.V465Tfs*3	ENST00000519728	NM_002350.3	465	GTGGAGAACTGCCCAGATGAGCTCTATGac/ac	13/13	0.15246234181071	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.775153196394683	0		543	233	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0017214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1441	64	632	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.607	0.523	0.7	0.607	0.523	0.7	SUBCLONAL	1	TRUE	1	0.14	2		634	1505	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	138	301	4				ENST00000310581	NM_198253.2	-/1132			0.494389501537164	4	FACETS	1	0.928	1	0.674	0.619	0.73	CLONAL	2	TRUE	1	0.506887924219292	4		305	406	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509639	29509639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	531	433	0	ENST00000356175.3:c.844C>T	p.Gln282Ter	p.Q282*	ENST00000356175	NM_000267.3	282	Cag/Tag	8/57	0.506887924219292	8	FACETS	0.988	0.952	1			1	CLONAL	5	TRUE	NA	0.506887924219292	8		433	1069	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939108	48939108	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0017215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	143	213	0	ENST00000267163.4:c.939+1G>A		p.X313_splice	ENST00000267163	NM_000321.2	313			0.460992556111161	5	FACETS	1	0.94	1	0.514	0.472	0.558	CLONAL	2	TRUE	1	0.506887924219292	5		213	483	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458876	120458876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	396	479	0	ENST00000256646.2:c.6469C>T	p.Pro2157Ser	p.P2157S	ENST00000256646	NM_024408.3	2157	Cct/Tct	34/34	0.506887924219292	8	FACETS	0.891	0.849	0.934	0.713	0.679	0.747	CLONAL	4	TRUE	3	0.506887924219292	8		479	1105	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180961	108180961	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	380	294	0	ENST00000278616.4:c.5837A>C	p.Gln1946Pro	p.Q1946P	ENST00000278616	NM_000051.3	1946	cAg/cCg	39/63	0.505728486408609	2	FACETS		NA	1	1	0.998	1	NA	4	TRUE	0	0.506887924219292	2		294	401	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934512	9934512	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	639	655	0	ENST00000330684.3:c.1643C>T	p.Ala548Val	p.A548V	ENST00000330684	NM_001134407.1	548	gCt/gTt	7/13	0.506887924219292	6	FACETS	0.948	0.916	0.98			1	CLONAL	4	TRUE	NA	0.506887924219292	6		655	1339	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56855458	56855458	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	519	698	0	ENST00000308159.5:c.607C>T	p.Pro203Ser	p.P203S	ENST00000308159	NM_014669.4	203	Cct/Tct	7/22	0.205384868780065	3	FACETS	1	0.968	1			1	INDETERMINATE	3	TRUE	NA	0.506887924219292	3		698	855	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971312	15971312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1441094420	NA	P-0017215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	176	414	0	ENST00000268712.3:c.4637C>T	p.Pro1546Leu	p.P1546L	ENST00000268712	NM_006311.3	1546	cCg/cTg	32/46	0.505728486408609	4	FACETS	1	0.959	1	0.523	0.486	0.561	CLONAL	2	TRUE	0	0.506887924219292	4		414	500	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127294	17127294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	163	432	0	ENST00000285071.4:c.560C>T	p.Pro187Leu	p.P187L	ENST00000285071	NM_144997.5	187	cCc/cTc	6/14	0.505728486408609	4	FACETS	1	0.961	1	0.529	0.49	0.569	CLONAL	2	TRUE	0	0.506887924219292	4		432	458	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585486	29585486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	174	267	0	ENST00000356175.3:c.4235C>T	p.Pro1412Leu	p.P1412L	ENST00000356175	NM_000267.3	1412	cCt/cTt	31/57	0.506887924219292	8	FACETS	0.941	0.871	1			1	CLONAL	3	TRUE	NA	0.506887924219292	8		267	613	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587499	29587499	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1567862991	NA	P-0017215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	414	460	0	ENST00000356175.3:c.4480C>T	p.Gln1494Ter	p.Q1494*	ENST00000356175	NM_000267.3	1494	Cag/Tag	33/57	0.506887924219292	8	FACETS	0.973	0.929	1			1	CLONAL	4	TRUE	NA	0.506887924219292	8		460	1058	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653002	29653002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	589	638	0	ENST00000356175.3:c.4937C>T	p.Pro1646Leu	p.P1646L	ENST00000356175	NM_000267.3	1646	cCt/cTt	36/57	0.506887924219292	8	FACETS	1	0.989	1			1	CLONAL	4	TRUE	NA	0.506887924219292	8		638	1371	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459445	40459445	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	1238	1227	0	ENST00000345506.4:c.1706C>T	p.Thr569Ile	p.T569I	ENST00000345506	NM_003152.3	569	aCc/aTc	15/20	0.506887924219292	6	FACETS	0.97	0.949	0.991			1	CLONAL	5	TRUE	NA	0.506887924219292	6		1227	2028	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918195	50918195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	542	1175	0	ENST00000440232.2:c.2512C>T	p.Pro838Ser	p.P838S	ENST00000440232	NM_002691.3	838	Ccc/Tcc	20/27	0.283690280254644	4	FACETS	0.935	0.9	0.97			1	INDETERMINATE	3	TRUE	NA	0.506887924219292	4		1175	1149	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523232	9523232	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs867668739	NA	P-0017215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	447	561	0	ENST00000353224.5:c.2004+1G>A		p.X668_splice	ENST00000353224	NM_177990.2	668			0.506887924219292	7	FACETS	1	0.99	1	1	0.99	1	CLONAL	4	TRUE	3	0.506887924219292	7		561	916	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191278	185191278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	283	321	0	ENST00000265026.3:c.2159C>T	p.Pro720Leu	p.P720L	ENST00000265026	NM_004721.4	720	cCc/cTc	11/14	0.506887924219292	5	FACETS	1	0.987	1			1	CLONAL	3	TRUE	NA	0.506887924219292	5		321	587	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982109	38982109	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	208	435	0	ENST00000357387.3:c.613C>T	p.Arg205Ter	p.R205*	ENST00000357387	NM_152756.3	205	Cga/Tga	8/38	0.505728486408609	4	FACETS	0.883	0.823	0.945	0.589	0.549	0.63	CLONAL	2	TRUE	1	0.506887924219292	4		435	700	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30668285	30668285	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1295	276	595	0	ENST00000376406.3:c.6227C>T	p.Pro2076Leu	p.P2076L	ENST00000376406	NM_014641.2	2076	cCa/cTa	15/15	0.506887924219292	10	FACETS	1	0.967	1	0.233	0.218	0.249	CLONAL	2	TRUE	1	0.506887924219292	10		595	1571	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166472	32166472	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1455	304	809	0	ENST00000375023.3:c.4571G>A	p.Gly1524Glu	p.G1524E	ENST00000375023	NM_004557.3	1524	gGa/gAa	25/30	0.506887924219292	10	FACETS	1	0.962	1	0.229	0.215	0.244	CLONAL	2	TRUE	1	0.506887924219292	10		809	1759	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787845	135787845	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1564490210	NA	P-0017215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	148	331	0	ENST00000298552.3:c.738-1G>A		p.X246_splice	ENST00000298552	NM_001162426.1	246			0.494389501537164	4	FACETS	0.942	0.867	1	0.628	0.578	0.68	CLONAL	2	TRUE	1	0.506887924219292	4		331	467	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732855	44732855	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1271145433	NA	P-0017215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	389	263	0	ENST00000377967.4:c.58G>A	p.Asp20Asn	p.D20N	ENST00000377967	NM_021140.2	20	Gat/Aat	1/29	0.498541104609685	2	FACETS		NA	1			1	NA	4	TRUE	NA	0.506887924219292	2		263	407	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934654	9934654	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	107	425	0	ENST00000330684.3:c.1501G>A	p.Val501Ile	p.V501I	ENST00000330684	NM_001134407.1	501	Gtc/Atc	7/13	0.506887924219292	6	FACETS	0.999	0.895	1			1	CLONAL	1	TRUE	NA	0.506887924219292	6		425	851	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0017224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	640	401	3	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.568886124299207	3	FACETS	0.953	0.919	0.987	0.953	0.919	0.987	CLONAL	2	TRUE	1	0.568886124299207	3		404	1516	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913315	NA	P-0017224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	426	643	0	ENST00000326873.7:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000326873	NM_000455.4	194	Gac/Tac	4/10	0.568886124299207	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.568886124299207	1		643	1064	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610208	10610208	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	511	734	0	ENST00000171111.5:c.502G>T	p.Val168Phe	p.V168F	ENST00000171111	NM_203500.1	168	Gtc/Ttc	2/6	0.568886124299207	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.568886124299207	1		734	1143	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610123	10610123	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	469	745	0	ENST00000171111.5:c.587G>T	p.Cys196Phe	p.C196F	ENST00000171111	NM_203500.1	196	tGt/tTt	2/6	0.568886124299207	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.568886124299207	1		745	1153	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237617	133237617	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	432	697	2	ENST00000320574.5:c.2998del	p.Glu1000LysfsTer7	p.E1000Kfs*7	ENST00000320574	NM_006231.2	1000	Gaa/aa	25/49	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.568886124299207	2		699	1463	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134859	41134859	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	221	399	0	ENST00000379561.5:c.769A>G	p.Met257Val	p.M257V	ENST00000379561	NM_002015.3	257	Atg/Gtg	2/3	1	2	FACETS	0.99	0.924	1	0.99	0.924	1	CLONAL	1	TRUE	1	0.568886124299207	2		399	785	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061725	38061726	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs766493600	NA	P-0017224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	126	344	0	ENST00000250448.2:c.263dup	p.Ser89LeufsTer138	p.S89Lfs*138	ENST00000250448	NM_004496.3	88	ggc/ggGc	2/2	1	2	FACETS	0.747	0.679	0.819	0.747	0.679	0.819	SUBCLONAL	1	TRUE	1	0.568886124299207	2		344	593	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885992	59885992	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	269	584	0	ENST00000259008.2:c.754A>T	p.Thr252Ser	p.T252S	ENST00000259008	NM_032043.2	252	Aca/Tca	7/20	1	2	FACETS	0.901	0.845	0.958	0.901	0.845	0.958	CLONAL	1	TRUE	1	0.568886124299207	2		584	1050	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022341	31022341	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1292056366	NA	P-0017224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	196	321	0	ENST00000375687.4:c.1826C>T	p.Thr609Ile	p.T609I	ENST00000375687	NM_015338.5	609	aCt/aTt	13/13	1	2	FACETS	0.976	0.907	1	0.976	0.907	1	CLONAL	1	TRUE	1	0.568886124299207	2		321	706	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356362	66356362	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	303	556	1	ENST00000273854.3:c.1135C>A	p.Pro379Thr	p.P379T	ENST00000273854	NM_004439.5	379	Ccg/Acg	5/18	1	2	FACETS	0.943	0.888	0.998	0.943	0.888	0.998	CLONAL	1	TRUE	1	0.568886124299207	2		557	1130	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180952	32180952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	312	452	0	ENST00000375023.3:c.2398C>T	p.Pro800Ser	p.P800S	ENST00000375023	NM_004557.3	800	Ccg/Tcg	15/30	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.568886124299207	2		452	1085	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74858968	74858968	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	59	517	0	ENST00000284811.8:c.236A>G	p.Tyr79Cys	p.Y79C	ENST00000284811		79	tAc/tGc	4/4	0.440800507496021	1	FACETS	0.911	0.794	1	0.911	0.794	1	CLONAL	1	TRUE	0	0.440800507496021	1		517	229	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347625	118347625	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	150	685	0	ENST00000534358.1:c.3262G>T	p.Asp1088Tyr	p.D1088Y	ENST00000534358	NM_005933.3	1088	Gat/Tat	4/36	0.108877069916429	4	FACETS	0.828	0.76	0.899	0.828	0.76	0.899	INDETERMINATE	2	TRUE	2	0.440800507496021	4		685	592	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400866	72400866	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	22	361	0	ENST00000357731.5:c.305G>T	p.Ser102Ile	p.S102I	ENST00000357731	NM_173808.2	102	aGc/aTc	2/7	1	2	FACETS	0.525	0.408	0.66	0.525	0.408	0.66	SUBCLONAL	1	TRUE	1	0.33	2		361	254	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0017228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	363	776	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.391051332335412	3	FACETS	0.925	0.877	0.973	0.925	0.877	0.973	CLONAL	2	TRUE	1	0.391051332335412	3		776	1200	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781440	135781440	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203542	NA	P-0017228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	309	322	1	ENST00000298552.3:c.1525C>T	p.Arg509Ter	p.R509*	ENST00000298552	NM_001162426.1	509	Cga/Tga	15/23	0.391051332335412	5	FACETS	1	0.948	1	1	0.948	1	CLONAL	3	TRUE	2	0.391051332335412	5		323	835	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555273	226555273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781122492	NA	P-0017228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	120	458	0	ENST00000366794.5:c.2314G>A	p.Glu772Lys	p.E772K	ENST00000366794	NM_001618.3	772	Gag/Aag	17/23	0.31192302447989	4	FACETS	0.897	0.809	0.99			1	CLONAL	1	TRUE	NA	0.391051332335412	4		458	952	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115957	8115960	+	frameshift_variant	Frame_Shift_Del	DEL	CCCT	CCCT	-	novel	NA	P-0017228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	160	341	0	ENST00000346208.3:c.1305_1308del	p.Ser436AlafsTer38	p.S436Afs*38	ENST00000346208		435	CCCTcc/cc	6/6	0.245835067533933	4	FACETS	0.769	0.707	0.834	0.769	0.707	0.834	SUBCLONAL	2	TRUE	2	0.391051332335412	4		341	740	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954172	32954172	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs200924727	NA	P-0121531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	302	479	0	ENST00000380152.3:c.9146A>G	p.Tyr3049Cys	p.Y3049C	ENST00000380152		3049	tAc/tGc	24/27	1	2	FACETS	0.929	0.881	0.979	0.929	0.881	0.979	CLONAL	1	NA	1	0.867700870835454	2		479	749	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435187	18435187	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0121531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	44	407	0	ENST00000266497.5:c.172A>G	p.Ile58Val	p.I58V	ENST00000266497		58	Att/Gtt	1/31	1	2	FACETS	0.17	0.142	0.201	0.17	0.142	0.201	SUBCLONAL	1	NA	1	0.867700870835454	2		407	596	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986928	36986928	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1422890661	NA	P-0121531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	420	659	1	ENST00000354822.5:c.761C>A	p.Ala254Glu	p.A254E	ENST00000354822	NM_001079668.2	254	gCg/gAg	3/3	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	NA	1	0.867700870835454	2		660	904	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0017231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	262	470	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.41624164515369	2		470	1096	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259439	55259439	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs397517126	NA	P-0017231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	173	404	0	ENST00000275493.2:c.2497T>G	p.Leu833Val	p.L833V	ENST00000275493	NM_005228.3	833	Ttg/Gtg	21/28	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.41624164515369	2		404	798	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224337	55224337	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	170	539	0	ENST00000275493.2:c.1118C>T	p.Pro373Leu	p.P373L	ENST00000275493	NM_005228.3	373	cCg/cTg	9/28	1	2	FACETS	0.888	0.817	0.962	0.888	0.817	0.962	CLONAL	1	TRUE	1	0.41624164515369	2		539	920	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730876	40730876	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372862828	NA	P-0017231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	200	656	0	ENST00000373198.4:c.3659G>A	p.Arg1220Gln	p.R1220Q	ENST00000373198	NM_133170.3	1220	cGg/cAg	27/32	1	2	FACETS	0.903	0.836	0.973	0.903	0.836	0.973	CLONAL	1	TRUE	1	0.41624164515369	2		656	1064	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0017231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	191	549	0	ENST00000269305.4:c.560-1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.41624164515369	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.41624164515369	1		549	723	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309941	30309941	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	176	473	0	ENST00000307677.4:c.81T>A	p.Phe27Leu	p.F27L	ENST00000307677	NM_138578.1	27	ttT/ttA	2/3	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.41624164515369	2		473	833	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047299	180047299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	158	514	0	ENST00000261937.6:c.2416G>A	p.Ala806Thr	p.A806T	ENST00000261937	NM_182925.4	806	Gca/Aca	17/30	1	2	FACETS	0.999	0.917	1	0.999	0.917	1	CLONAL	1	TRUE	1	0.41624164515369	2		514	760	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397128	397128	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	126	364	1	ENST00000380956.4:c.513G>T	p.Met171Ile	p.M171I	ENST00000380956	NM_001195286.1	171	atG/atT	5/9	1	2	FACETS	0.902	0.819	0.99	0.902	0.819	0.99	CLONAL	1	TRUE	1	0.41624164515369	2		365	671	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650797	93650797	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	33	227	0	ENST00000375746.1:c.1723G>A	p.Gly575Arg	p.G575R	ENST00000375746	NM_001174167.1	575	Ggg/Agg	13/14	0.220994910954326	1	FACETS	0.339	0.276	0.41	0.339	0.276	0.41	INDETERMINATE	1	TRUE	0	0.41624164515369	1		227	370	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218030	108218030	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555139540	NA	P-0017232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	326	380	0	ENST00000278616.4:c.8609A>G	p.Asp2870Gly	p.D2870G	ENST00000278616	NM_000051.3	2870	gAt/gGt	59/63	0.760108144203252	2	FACETS	0.979	0.946	1	0.979	0.946	1	CLONAL	2	TRUE	0	0.760108144203252	2		380	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0017233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	87	591	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	1	2	FACETS	0.689	0.608	0.776	0.689	0.608	0.776	SUBCLONAL	1	FALSE	1	0.226685581673199	2		591	1114	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130576	29130576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs558321010	NA	P-0017233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	34	341	0	ENST00000328354.6:c.134C>T	p.Thr45Met	p.T45M	ENST00000328354	NM_007194.3	45	aCg/aTg	2/15	1	2	FACETS	0.471	0.384	0.57	0.471	0.384	0.57	SUBCLONAL	1	FALSE	1	0.226685581673199	2		341	637	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245912960	245912960	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	37	314	0	ENST00000388985.4:c.1192G>T	p.Asp398Tyr	p.D398Y	ENST00000388985		398	Gat/Tat	12/12	0.214301771430713	3	FACETS	0.582	0.478	0.698	0.291	0.239	0.349	SUBCLONAL	1	FALSE	1	0.226685581673199	3		314	625	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823845	3823845	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	74	516	0	ENST00000262367.5:c.2370G>T	p.Gln790His	p.Q790H	ENST00000262367	NM_004380.2	790	caG/caT	13/31	1	2	FACETS	0.692	0.604	0.787	0.692	0.604	0.787	SUBCLONAL	1	FALSE	1	0.226685581673199	2		516	944	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411880	116411897	+	splice_region_variant,intron_variant	Splice_Region	DEL	TCTTTCTTTCTCTCTGTT	TCTTTCTTTCTCTCTGTT	-	novel	NA	P-0017233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	121	899	0	ENST00000397752.3:c.2888-22_2888-5del		p.X963_splice	ENST00000397752	NM_000245.2	963			0.225461424974531	1	FACETS	0.762	0.686	0.842	0.762	0.686	0.842	SUBCLONAL	1	FALSE	0	0.226685581673199	1		899	1242	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182871	123182871	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	20	277	0	ENST00000218089.9:c.836A>G	p.Asp279Gly	p.D279G	ENST00000218089	NM_001042749.1	279	gAt/gGt	10/35	1	2	FACETS	0.483	0.369	0.618	0.483	0.369	0.618	SUBCLONAL	1	FALSE	1	0.226685581673199	2		277	365	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137085	64137085	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	27	296	0	ENST00000334205.4:c.1596del	p.Lys532AsnfsTer16	p.K532Nfs*16	ENST00000334205	NM_003942.2	532	aaG/aa	13/17	1	2	FACETS	0.777	0.618	0.959	0.777	0.618	0.959	CLONAL	1	TRUE	1	0.18	2		296	386	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279910	46279910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1330	103	952	1	ENST00000371998.3:c.3836C>T	p.Ala1279Val	p.A1279V	ENST00000371998		1279	gCc/gTc	20/23	1	2	FACETS	0.799	0.712	0.891	0.799	0.712	0.891	SUBCLONAL	1	TRUE	1	0.18	2		953	1433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578517	7578517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750600586	NA	P-0017238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	379	823	0	ENST00000269305.4:c.413C>T	p.Ala138Val	p.A138V	ENST00000269305	NM_001126112.2	138	gCc/gTc	5/11	0.260458234190297	3	FACETS	1	0.991	1	0.784	0.745	0.822	CLONAL	2	TRUE	0	0.357129995390134	3		823	1064	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581229	48581229	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs377767331	NA	P-0017238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	205	669	0	ENST00000342988.3:c.533C>G	p.Ser178Ter	p.S178*	ENST00000342988	NM_005359.5	178	tCa/tGa	5/12	0.357129995390134	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.357129995390134	1		669	755	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220691	1220691	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs878853247	NA	P-0017238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	192	636	0	ENST00000326873.7:c.709G>C	p.Asp237His	p.D237H	ENST00000326873	NM_000455.4	237	Gac/Cac	5/10	0.357129995390134	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.357129995390134	1		636	666	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600428	10600428	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	268	852	1	ENST00000171111.5:c.1427G>T	p.Gly476Val	p.G476V	ENST00000171111	NM_203500.1	476	gGg/gTg	4/6	0.357129995390134	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.357129995390134	1		853	1039	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420213	88420213	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	86	504	0	ENST00000360948.2:c.2473C>A	p.His825Asn	p.H825N	ENST00000360948	NM_001012338.2	825	Cat/Aat	19/19	0.357129995390134	0	FACETS	0.815	0.726	0.909			1	CLONAL	1	TRUE	0	0.357129995390134	0		504	380	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33430564	33430564	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0017238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	202	636	0	ENST00000345365.6:c.577-1G>C		p.X193_splice	ENST00000345365	NM_002878.3	193			0.182861378770686	3	FACETS	0.869	0.808	0.932			1	INDETERMINATE	2	TRUE	NA	0.357129995390134	3		636	767	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47710071	47710071	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	116	419	0	ENST00000233146.2:c.2788A>C	p.Ile930Leu	p.I930L	ENST00000233146	NM_000251.2	930	Ata/Cta	16/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.357129995390134	2		419	486	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235454	235454	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	105	789	0	ENST00000264932.6:c.1260G>C	p.Gln420His	p.Q420H	ENST00000264932	NM_004168.2	420	caG/caC	9/15	0.232470969828602	4	FACETS	0.707	0.632	0.787	0.236	0.21	0.263	SUBCLONAL	1	TRUE	1	0.357129995390134	4		789	1129	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868472	117868472	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	280	562	0	ENST00000297338.2:c.870G>T	p.Met290Ile	p.M290I	ENST00000297338	NM_006265.2	290	atG/atT	8/14	0.232470969828602	4	FACETS	1	0.988	1	0.784	0.738	0.831	CLONAL	2	TRUE	1	0.357129995390134	4		562	905	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	71	301	4				ENST00000310581	NM_198253.2	-/1132			0.36167912043736	1	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	0	0.36167912043736	1		305	308	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577129	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519986	NA	P-0017239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	220	716	0	ENST00000269305.4:c.809T>G	p.Phe270Cys	p.F270C	ENST00000269305	NM_001126112.2	270	tTt/tGt	8/11	0.36167912043736	1	FACETS	0.922	0.857	0.989	0.922	0.857	0.989	CLONAL	1	TRUE	0	0.36167912043736	1		716	1081	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99169415	99169415	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	96	342	0	ENST00000074304.5:c.1345G>T	p.Ala449Ser	p.A449S	ENST00000074304	NM_001134224.1	449	Gcc/Tcc	15/26	1	2	FACETS	0.978	0.874	1	0.978	0.874	1	CLONAL	1	TRUE	1	0.36167912043736	2		342	543	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044281	128044281	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	118	415	1	ENST00000285398.2:c.1340C>T	p.Pro447Leu	p.P447L	ENST00000285398	NM_000122.1	447	cCa/cTa	8/15	1	2	FACETS	0.967	0.873	1	0.967	0.873	1	CLONAL	1	TRUE	1	0.36167912043736	2		416	675	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386301	31386301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	156	555	0	ENST00000328111.2:c.1526G>A	p.Gly509Asp	p.G509D	ENST00000328111	NM_006892.3	509	gGc/gAc	15/23	1	2	FACETS	0.952	0.872	1	0.952	0.872	1	CLONAL	1	TRUE	1	0.36167912043736	2		555	906	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	99	301	4				ENST00000310581	NM_198253.2	-/1132			0.308896803480019	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.308896803480019	3		305	298	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0017241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	179	418	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.843	0.78	0.909	1	0.992	1	CLONAL	2	TRUE	1	0.308896803480019	2		420	687	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023952	27023952	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	23	66	0	ENST00000324856.7:c.1060del	p.Gln354AsnfsTer9	p.Q354Nfs*9	ENST00000324856	NM_006015.4	353	gCc/gc	1/20	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.308896803480019	2		66	104	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039501	49039501	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	120	546	0	ENST00000267163.4:c.2486C>A	p.Ser829Ter	p.S829*	ENST00000267163	NM_000321.2	829	tCa/tAa	23/27	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.308896803480019	2		546	749	SUCCESS
ALK	238	MSKCC	GRCh37	2	29448402	29448402	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	172	904	3	ENST00000389048.3:c.3097C>A	p.Leu1033Ile	p.L1033I	ENST00000389048	NM_004304.4	1033	Ctc/Atc	19/29	1	2	FACETS	0.972	0.893	1	0.972	0.893	1	CLONAL	1	TRUE	1	0.308896803480019	2		907	1146	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252853	36252853	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0017241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	128	374	0	ENST00000300305.3:c.508+1del		p.X170_splice	ENST00000300305		170			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.308896803480019	2		374	665	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907621	76907621	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	250	552	0	ENST00000373344.5:c.4540C>T	p.Arg1514Ter	p.R1514*	ENST00000373344	NM_000489.3	1514	Cga/Tga	15/35	1	2	FACETS	0.883	0.827	0.941	0.883	0.827	0.941	CLONAL	1	TRUE	1	0.600465889125604	2		552	943	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503838	149503838	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs864309711	NA	P-0017242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	281	428	0	ENST00000261799.4:c.1998C>G	p.Asn666Lys	p.N666K	ENST00000261799	NM_002609.3	666	aaC/aaG	14/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.600465889125604	2		428	862	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	119	408	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.401770834618277	3	FACETS	0.905	0.824	0.988	0.905	0.824	0.988	CLONAL	2	TRUE	1	0.401770834618277	3		408	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0017243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	367	457	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.349006937502434	3	FACETS	0.844	0.805	0.885	0.844	0.805	0.885	CLONAL	3	TRUE	0	0.401770834618277	3		457	866	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237689	133237689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500820	NA	P-0017243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	348	786	0	ENST00000320574.5:c.2926C>T	p.Arg976Cys	p.R976C	ENST00000320574	NM_006231.2	976	Cgc/Tgc	25/49	0.401770834618277	3	FACETS	0.84	0.795	0.886	0.84	0.795	0.886	CLONAL	2	TRUE	1	0.401770834618277	3		786	1238	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0017243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	61	383	2	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	0.401770834618277	3	FACETS	1	0.969	1	0.709	0.618	0.806	CLONAL	1	TRUE	1	0.401770834618277	3		385	257	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245380	153245380	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	115	695	0	ENST00000281708.4:c.1811A>C	p.Lys604Thr	p.K604T	ENST00000281708	NM_033632.3	604	aAa/aCa	11/12	0.18205207602326	4	FACETS	0.814	0.737	0.894	0.814	0.737	0.894	INDETERMINATE	2	TRUE	2	0.401770834618277	4		695	493	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251918	153251919	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	94	603	0	ENST00000281708.4:c.1087dup	p.Thr363AsnfsTer2	p.T363Nfs*2	ENST00000281708	NM_033632.3	363	act/aAct	7/12	0.18205207602326	4	FACETS	1	0.923	1	1	0.923	1	INDETERMINATE	2	TRUE	2	0.401770834618277	4		603	318	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189458	56189458	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	228	734	0	ENST00000399503.3:c.4490C>A	p.Pro1497His	p.P1497H	ENST00000399503	NM_005921.1	1497	cCt/cAt	20/20	0.401770834618277	3	FACETS	0.968	0.906	1	0.968	0.906	1	CLONAL	2	TRUE	1	0.401770834618277	3		734	704	SUCCESS
APC	324	MSKCC	GRCh37	5	112174369	112174369	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	28	437	0	ENST00000257430.4:c.3079del	p.Tyr1027IlefsTer10	p.Y1027Ifs*10	ENST00000257430	NM_000038.5	1026	aaT/aa	16/16	0.401770834618277	3	FACETS	0.9	0.725	1	0.45	0.362	0.548	CLONAL	1	TRUE	1	0.401770834618277	3		437	186	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44910961	44910963	+	inframe_deletion	In_Frame_Del	DEL	ATC	ATC	-	novel	NA	P-0017243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	41	549	0	ENST00000377967.4:c.664_666del	p.His222del	p.H222del	ENST00000377967	NM_021140.2	221	tATCat/tat	9/29	0.383710489918855	3	FACETS	0.946	0.794	1	0.473	0.397	0.557	CLONAL	1	TRUE	1	0.401770834618277	3		549	259	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0017244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	172	290	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.692274042162513	3	FACETS	1	0.969	1			1	CLONAL	1	TRUE	NA	0.763075063889748	3		290	572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0017244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	44	583	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.713166819210632	1	FACETS	0.15	0.126	0.177	0.15	0.126	0.177	SUBCLONAL	1	TRUE	0	0.763075063889748	1		583	475	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909491	50909491	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139557851	NA	P-0017244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	313	717	0	ENST00000440232.2:c.1295G>A	p.Arg432Gln	p.R432Q	ENST00000440232	NM_002691.3	432	cGg/cAg	11/27	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.763075063889748	2		717	807	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601995	43601995	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1467660660	NA	P-0017244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	268	628	0	ENST00000355710.3:c.1039G>A	p.Val347Met	p.V347M	ENST00000355710	NM_020975.4	347	Gtg/Atg	5/20	1	2	FACETS	0.903	0.85	0.956	0.903	0.85	0.956	CLONAL	1	TRUE	1	0.763075063889748	2		628	778	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910773	114910774	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0017244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	233	470	0	ENST00000543371.1:c.893_894dup	p.Pro299SerfsTer17	p.P299Sfs*17	ENST00000543371	NM_001198531.1	298	gtc/gTCtc	9/14	1	2	FACETS	0.941	0.883	1	0.941	0.883	1	CLONAL	1	TRUE	1	0.763075063889748	2		470	649	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577513	7577514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTGA	novel	NA	P-0017244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	59	406	0	ENST00000269305.4:c.764_767dup	p.Leu257HisfsTer8	p.L257Hfs*8	ENST00000269305	NM_001126112.2	256	aca/acTCACa	7/11	0.713166819210632	1	FACETS	0.225	0.194	0.259	0.225	0.194	0.259	SUBCLONAL	1	TRUE	0	0.763075063889748	1		406	425	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155416	47155417	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	190	485	0	ENST00000409792.3:c.4664dup	p.Leu1556ThrfsTer32	p.L1556Tfs*32	ENST00000409792	NM_014159.6	1555	ata/atTa	5/21	0.763075063889748	2	FACETS	0.975	0.909	1	0.487	0.454	0.521	CLONAL	1	TRUE	0	0.763075063889748	2		485	511	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900372	101900372	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0017244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	105	207	0	ENST00000374994.4:c.805+1G>A		p.X269_splice	ENST00000374994	NM_004612.2	269			1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.763075063889748	2		207	268	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	171	301	4				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.861058728330609	2		305	342	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	278	346	1	ENST00000304494.5:c.143C>T	p.Pro48Leu	p.P48L	ENST00000304494	NM_000077.4	48	cCg/cTg	1/3	1	2	FACETS	0.959	0.907	1	0.959	0.907	1	CLONAL	1	TRUE	1	0.861058728330609	2		347	673	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726656	88726656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1222707412	NA	P-0017246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	294	354	2	ENST00000360948.2:c.388C>T	p.Arg130Cys	p.R130C	ENST00000360948	NM_001012338.2	130	Cgt/Tgt	4/19	1	2	FACETS	0.96	0.91	1	0.96	0.91	1	CLONAL	1	TRUE	1	0.861058728330609	2		356	711	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129353	2129353	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	395	498	0	ENST00000219476.3:c.3208A>C	p.Thr1070Pro	p.T1070P	ENST00000219476	NM_000548.3	1070	Acg/Ccg	28/42	0.861058728330609	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.861058728330609	1		498	495	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436434	52436434	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1559584779	NA	P-0017246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	218	270	0	ENST00000460680.1:c.2060T>C	p.Met687Thr	p.M687T	ENST00000460680	NM_004656.3	687	aTg/aCg	17/17	1	2	FACETS	0.966	0.907	1	0.966	0.907	1	CLONAL	1	TRUE	1	0.861058728330609	2		270	524	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428940	47428940	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1212825155	NA	P-0017246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	366	258	0	ENST00000377045.4:c.1303A>G	p.Ile435Val	p.I435V	ENST00000377045	NM_001654.4	435	Atc/Gtc	13/16	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.861058728330609	1		258	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	281	656	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.503297916333591	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.503297916333591	1		656	733	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804985	43804985	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs757759824	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	251	405	0	ENST00000372470.3:c.435C>A	p.Ser145Arg	p.S145R	ENST00000372470	NM_005373.2	145	agC/agA	4/12	0.146310498973452	4	FACETS	0.919	0.868	0.969	0.689	0.651	0.727	INDETERMINATE	3	TRUE	0	0.503297916333591	4		405	544	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795040	45795040	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs147923905	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	97	562	0	ENST00000450313.1:c.1588G>T	p.Asp530Tyr	p.D530Y	ENST00000450313	NM_012222.2	530	Gat/Tat	16/16	0.146310498973452	4	FACETS	0.731	0.651	0.816	0.183	0.162	0.204	INDETERMINATE	1	TRUE	0	0.503297916333591	4		562	793	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546374	46546374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	228	544	0	ENST00000262741.5:c.155G>T	p.Gly52Val	p.G52V	ENST00000262741	NM_003629.3	52	gGa/gTa	2/10	0.146310498973452	4	FACETS	1	0.984	1	0.568	0.533	0.604	INDETERMINATE	2	TRUE	0	0.503297916333591	4		544	599	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957480	175957480	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	87	554	0	ENST00000367669.3:c.1916A>T	p.His639Leu	p.H639L	ENST00000367669	NM_022457.5	639	cAt/cTt	17/20	0.170788424042274	3	FACETS	0.712	0.631	0.798	0.237	0.21	0.266	INDETERMINATE	1	TRUE	0	0.503297916333591	3		554	608	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555952	226555953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	120	488	0	ENST00000366794.5:c.2223_2224dup	p.His742ProfsTer6	p.H742Pfs*6	ENST00000366794	NM_001618.3	742	cac/cCCac	16/23	0.170788424042274	3	FACETS	0.804	0.727	0.886	0.268	0.242	0.296	INDETERMINATE	1	TRUE	0	0.503297916333591	3		488	742	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115975	8115975	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	86	269	1	ENST00000346208.3:c.1321G>T	p.Ala441Ser	p.A441S	ENST00000346208		441	Gcc/Tcc	6/6	0.170031007048373	3	FACETS	1	0.968	1	0.616	0.55	0.686	INDETERMINATE	1	TRUE	1	0.503297916333591	3		270	347	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32449504	32449504	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	81	483	0	ENST00000332351.3:c.870C>A	p.Ser290Arg	p.S290R	ENST00000332351	NM_024426.4	290	agC/agA	3/10	0.287973215689659	0	FACETS	0.368	0.326	0.414			1	INDETERMINATE	1	TRUE	0	0.503297916333591	0		483	434	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178629	108178629	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	38	235	1	ENST00000278616.4:c.5680G>A	p.Glu1894Lys	p.E1894K	ENST00000278616	NM_000051.3	1894	Gag/Aag	38/63	1	2	FACETS	0.634	0.528	0.751	0.634	0.528	0.751	SUBCLONAL	1	TRUE	1	0.503297916333591	2		236	238	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366540	118366540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	121	659	0	ENST00000534358.1:c.5489C>T	p.Pro1830Leu	p.P1830L	ENST00000534358	NM_005933.3	1830	cCc/cTc	19/36	NA	2	FACETS	0.591	0.533	0.651			1	INDETERMINATE	1	TRUE	NA	0.503297916333591	2		659	814	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524215	18524215	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs769408892	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	155	720	0	ENST00000266497.5:c.1727C>A	p.Ala576Glu	p.A576E	ENST00000266497		576	gCg/gAg	11/31	0.503297916333591	1	FACETS	0.943	0.87	1	0.943	0.87	1	CLONAL	1	TRUE	0	0.503297916333591	1		720	489	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125019	46125019	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	88	229	0	ENST00000334344.6:c.209del	p.Gly70GlufsTer20	p.G70Efs*20	ENST00000334344	NM_152641.2	69	tGg/tg	3/21	0.447480433887664	2	FACETS	1	0.98	1	0.711	0.64	0.784	CLONAL	1	TRUE	0	0.503297916333591	2		229	246	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518688	103518688	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	196	389	0	ENST00000355739.4:c.2276G>C	p.Arg759Pro	p.R759P	ENST00000355739	NM_000123.3	759	cGg/cCg	10/15	0.43117105691588	2	FACETS	0.854	0.8	0.909	0.854	0.8	0.909	CLONAL	2	TRUE	0	0.503297916333591	2		389	456	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569984	95569984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	127	455	0	ENST00000393063.1:c.3749C>T	p.Ser1250Phe	p.S1250F	ENST00000393063	NM_030621.3	1250	tCt/tTt	22/28	0.170031007048373	3	FACETS	1	0.982	1	0.662	0.604	0.723	INDETERMINATE	1	TRUE	1	0.503297916333591	3		455	477	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867235	68867235	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	91	602	0	ENST00000261769.5:c.2482G>A	p.Asp828Asn	p.D828N	ENST00000261769	NM_004360.3	828	Gat/Aat	16/16	0.503297916333591	1	FACETS	0.45	0.4	0.504	0.45	0.4	0.504	SUBCLONAL	1	TRUE	0	0.503297916333591	1		602	601	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81927349	81927350	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	198	633	1	ENST00000359376.3:c.1022_1023delinsAT	p.Ser341Tyr	p.S341Y	ENST00000359376	NM_002661.3	341	tCC/tAT	12/33	0.503297916333591	1	FACETS	0.917	0.854	0.982	0.917	0.854	0.982	CLONAL	1	TRUE	0	0.503297916333591	1		634	642	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969845	81969845	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	216	723	0	ENST00000359376.3:c.2914G>T	p.Val972Phe	p.V972F	ENST00000359376	NM_002661.3	972	Gtc/Ttc	27/33	0.503297916333591	1	FACETS	0.99	0.925	1	0.99	0.925	1	CLONAL	1	TRUE	0	0.503297916333591	1		723	649	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66521929	66521929	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	170	349	0	ENST00000358598.2:c.584G>T	p.Gly195Val	p.G195V	ENST00000358598	NM_212471.2	195	gGg/gTg	7/11	0.170788424042274	3	FACETS	0.894	0.829	0.96	0.596	0.553	0.64	INDETERMINATE	2	TRUE	0	0.503297916333591	3		349	473	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965599	25965599	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	58	567	0	ENST00000435504.4:c.3607C>T	p.Gln1203Ter	p.Q1203*	ENST00000435504		1203	Cag/Tag	13/13	0.10827218350776	5	FACETS	0.506	0.434	0.586			1	INDETERMINATE	1	TRUE	NA	0.503297916333591	5		567	799	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25990587	25990587	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	102	507	0	ENST00000435504.4:c.640del	p.Glu214LysfsTer30	p.E214Kfs*30	ENST00000435504		214	Gaa/aa	8/13	0.10827218350776	5	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.503297916333591	5		507	605	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267451	198267451	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	143	534	0	ENST00000335508.6:c.1906G>T	p.Ala636Ser	p.A636S	ENST00000335508	NM_012433.2	636	Gcc/Tcc	14/25	0.170289944969392	3	FACETS	1	0.982	1	0.636	0.583	0.692	INDETERMINATE	1	TRUE	1	0.503297916333591	3		534	559	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388675	31388675	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	108	549	1	ENST00000328111.2:c.1940G>A	p.Gly647Asp	p.G647D	ENST00000328111	NM_006892.3	647	gGc/gAc	18/23	1	2	FACETS	0.596	0.535	0.661	0.596	0.535	0.661	SUBCLONAL	1	TRUE	1	0.503297916333591	2		550	720	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514510	41514510	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	226	710	3	ENST00000373198.4:c.151G>T	p.Gly51Trp	p.G51W	ENST00000373198	NM_133170.3	51	Ggg/Tgg	2/32	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.503297916333591	2		713	877	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946306	55946306	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	84	216	0	ENST00000263923.4:c.3873G>T	p.Arg1291Ser	p.R1291S	ENST00000263923	NM_002253.2	1291	agG/agT	30/30	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.503297916333591	2		216	270	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197806	66197806	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	53	448	0	ENST00000273854.3:c.2893G>T	p.Gly965Trp	p.G965W	ENST00000273854	NM_004439.5	965	Ggg/Tgg	17/18	1	2	FACETS	0.459	0.392	0.532	0.459	0.392	0.532	SUBCLONAL	1	TRUE	1	0.503297916333591	2		448	459	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143043366	143043366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	163	546	1	ENST00000262992.4:c.2050G>T	p.Val684Phe	p.V684F	ENST00000262992	NM_001101669.1	684	Gtt/Ttt	19/24	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.503297916333591	2		547	573	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527229	187527229	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1024949982	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	93	438	0	ENST00000441802.2:c.10345A>T	p.Ile3449Phe	p.I3449F	ENST00000441802	NM_005245.3	3449	Atc/Ttc	17/27	0.503297916333591	1	FACETS	0.58	0.518	0.646	0.58	0.518	0.646	SUBCLONAL	1	TRUE	0	0.503297916333591	1		438	477	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541661	187541661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199867416	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	45	279	0	ENST00000441802.2:c.6079C>T	p.Arg2027Cys	p.R2027C	ENST00000441802	NM_005245.3	2027	Cgc/Tgc	10/27	0.503297916333591	1	FACETS	0.509	0.431	0.594	0.509	0.431	0.594	SUBCLONAL	1	TRUE	0	0.503297916333591	1		279	263	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542897	187542897	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	43	433	0	ENST00000441802.2:c.4843G>T	p.Val1615Phe	p.V1615F	ENST00000441802	NM_005245.3	1615	Gtc/Ttc	10/27	0.503297916333591	1	FACETS	0.36	0.302	0.424	0.36	0.302	0.424	SUBCLONAL	1	TRUE	0	0.503297916333591	1		433	355	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512322	149512322	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	98	321	0	ENST00000261799.4:c.1118del	p.Ser373TrpfsTer9	p.S373Wfs*9	ENST00000261799	NM_002609.3	373	tCg/tg	7/23	0.503297916333591	1	FACETS	0.978	0.884	1	0.978	0.884	1	CLONAL	1	TRUE	0	0.503297916333591	1		321	298	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514370	149514370	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	121	492	0	ENST00000261799.4:c.574A>T	p.Thr192Ser	p.T192S	ENST00000261799	NM_002609.3	192	Acc/Tcc	4/23	0.503297916333591	1	FACETS	0.814	0.741	0.89	0.814	0.741	0.89	CLONAL	1	TRUE	0	0.503297916333591	1		492	442	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407480	407480	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	206	468	0	ENST00000380956.4:c.1238T>C	p.Leu413Pro	p.L413P	ENST00000380956	NM_001195286.1	413	cTa/cCa	9/9	0.441579712533915	2	FACETS	0.882	0.828	0.937	0.882	0.828	0.937	CLONAL	2	TRUE	0	0.503297916333591	2		468	464	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910647	29910647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	93	865	1	ENST00000376809.5:c.187G>A	p.Asp63Asn	p.D63N	ENST00000376809	NM_002116.7	63	Gac/Aac	2/8	0.441579712533915	2	FACETS	0.49	0.435	0.548	0.245	0.217	0.274	SUBCLONAL	1	TRUE	0	0.503297916333591	2		866	754	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165365	32165365	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	279	665	0	ENST00000375023.3:c.4763T>A	p.Val1588Glu	p.V1588E	ENST00000375023	NM_004557.3	1588	gTg/gAg	27/30	0.441579712533915	2	FACETS	0.798	0.754	0.842	0.798	0.754	0.842	SUBCLONAL	2	TRUE	0	0.503297916333591	2		665	695	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112025292	112025292	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	81	502	0	ENST00000368678.4:c.457A>T	p.Lys153Ter	p.K153*	ENST00000368678		153	Aaa/Taa	6/13	1	2	FACETS	0.602	0.531	0.677	0.602	0.531	0.677	SUBCLONAL	1	TRUE	1	0.503297916333591	2		502	535	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150022977	150022977	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	73	509	0	ENST00000253339.5:c.286C>G	p.Arg96Gly	p.R96G	ENST00000253339		96	Cgg/Ggg	1/7	1	2	FACETS	0.714	0.628	0.807	0.714	0.628	0.807	SUBCLONAL	1	TRUE	1	0.503297916333591	2		509	406	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521881	157521881	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1554235505	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	87	452	0	ENST00000346085.5:c.4153A>T	p.Lys1385Ter	p.K1385*	ENST00000346085	NM_020732.3	1385	Aag/Tag	18/20	1	2	FACETS	0.708	0.629	0.792	0.708	0.629	0.792	SUBCLONAL	1	TRUE	1	0.503297916333591	2		452	488	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161807870	161807870	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1348629802	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	93	573	0	ENST00000366898.1:c.1123G>T	p.Gly375Trp	p.G375W	ENST00000366898	NM_004562.2	375	Ggg/Tgg	10/12	1	2	FACETS	0.748	0.668	0.833	0.748	0.668	0.833	SUBCLONAL	1	TRUE	1	0.503297916333591	2		573	494	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739909	41739909	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	299	479	2	ENST00000242208.4:c.64C>A	p.Pro22Thr	p.P22T	ENST00000242208	NM_002192.2	22	Ccc/Acc	2/3	0.399933587132426	3	FACETS	0.913	0.871	0.955	0.913	0.871	0.955	CLONAL	3	TRUE	0	0.503297916333591	3		481	543	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146933	38146933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	87	921	2	ENST00000317025.8:c.3209C>T	p.Pro1070Leu	p.P1070L	ENST00000317025	NM_023034.1	1070	cCc/cTc	18/24	0.455356344144565	1	FACETS	0.411	0.364	0.462	0.411	0.364	0.462	SUBCLONAL	1	TRUE	0	0.503297916333591	1		923	629	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38314996	38314996	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	311	821	0	ENST00000425967.3:c.68C>A	p.Ala23Asp	p.A23D	ENST00000425967	NM_001174067.1	23	gCc/gAc	3/19	0.455356344144565	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.503297916333591	1		821	781	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449742	8449742	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	148	477	0	ENST00000356435.5:c.3971T>A	p.Leu1324His	p.L1324H	ENST00000356435		1324	cTt/cAt	23/35	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.503297916333591	2		477	585	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180322	27180322	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	75	420	0	ENST00000380036.4:c.986G>A	p.Cys329Tyr	p.C329Y	ENST00000380036	NM_000459.3	329	tGt/tAt	7/23	1	2	FACETS	0.549	0.482	0.621	0.549	0.482	0.621	SUBCLONAL	1	TRUE	1	0.503297916333591	2		420	543	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410361	63410361	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	228	885	0	ENST00000330258.3:c.2806G>C	p.Glu936Gln	p.E936Q	ENST00000330258	NM_152424.3	936	Gaa/Caa	2/2	0.503297916333591	1	FACETS	0.977	0.915	1	0.977	0.915	1	CLONAL	1	TRUE	0	0.503297916333591	1		885	694	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855290	76855290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	124	434	0	ENST00000373344.5:c.5698-1G>A		p.X1900_splice	ENST00000373344	NM_000489.3	1900			0.503297916333591	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.503297916333591	1		434	332	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888751	76888751	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	173	783	0	ENST00000373344.5:c.5078G>A	p.Arg1693Lys	p.R1693K	ENST00000373344	NM_000489.3	1693	aGg/aAg	19/35	0.503297916333591	1	FACETS	0.919	0.851	0.988	0.919	0.851	0.988	CLONAL	1	TRUE	0	0.503297916333591	1		783	560	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613415	100613415	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	120	543	0	ENST00000308731.7:c.985G>T	p.Gly329Trp	p.G329W	ENST00000308731	NM_000061.2	329	Ggg/Tgg	12/19	0.503297916333591	1	FACETS	0.937	0.854	1	0.937	0.854	1	CLONAL	1	TRUE	0	0.503297916333591	1		543	381	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	79	408	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.245	0.215	0.278	0.245	0.215	0.278	SUBCLONAL	1	TRUE	1	0.53014039407037	2		408	1215	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	112	408	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.124024824806332	4	FACETS	0.764	0.689	0.843	0.764	0.689	0.843	INDETERMINATE	2	TRUE	2	0.331998244351486	4		408	588	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0017249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	109	180	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.124024824806332	4	FACETS	0.919	0.829	1	0.919	0.829	1	INDETERMINATE	2	TRUE	2	0.331998244351486	4		180	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0017249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	147	395	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.331998244351486	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.331998244351486	2		397	361	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0017249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	46	312	1	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.19001448431057	3	FACETS	0.976	0.826	1	0.488	0.413	0.571	INDETERMINATE	1	TRUE	1	0.331998244351486	3		313	331	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670327	134670327	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373140258	NA	P-0017249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	26	263	1	ENST00000398015.3:c.238C>T	p.Arg80Trp	p.R80W	ENST00000398015	NM_004441.4	80	Cgg/Tgg	3/16	NA	2	FACETS	0.728	0.58	0.896			1	INDETERMINATE	1	TRUE	NA	0.331998244351486	2		264	215	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259173	89259173	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	47	288	0	ENST00000336596.2:c.317G>T	p.Cys106Phe	p.C106F	ENST00000336596	NM_005233.5	106	tGc/tTc	3/17	0.19001448431057	3	FACETS	1	0.939	1	0.609	0.517	0.709	INDETERMINATE	1	TRUE	1	0.331998244351486	3		288	271	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149238690	149238690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765794546	NA	P-0017249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	73	456	0	ENST00000360632.3:c.1105G>A	p.Val369Ile	p.V369I	ENST00000360632	NM_015472.4	369	Gtt/Att	7/7	0.124024824806332	4	FACETS	1	0.937	1	0.556	0.487	0.63	INDETERMINATE	1	TRUE	2	0.331998244351486	4		456	527	SUCCESS
APC	324	MSKCC	GRCh37	5	112175640	112175640	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	87	298	0	ENST00000257430.4:c.4349del	p.Arg1450GlnfsTer23	p.R1450Qfs*23	ENST00000257430	NM_000038.5	1450	cGa/ca	16/16	0.19001448431057	3	FACETS	0.756	0.674	0.844	0.756	0.674	0.844	INDETERMINATE	2	TRUE	1	0.331998244351486	3		298	404	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30682862	30682862	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	167	411	0	ENST00000376406.3:c.91G>A	p.Val31Ile	p.V31I	ENST00000376406	NM_014641.2	31	Gta/Ata	2/15	0.331998244351486	6	FACETS	1	0.971	1			1	CLONAL	2	TRUE	NA	0.331998244351486	6		411	753	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172054	32172054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	52	390	0	ENST00000375023.3:c.2978C>T	p.Ala993Val	p.A993V	ENST00000375023	NM_004557.3	993	gCc/gTc	19/30	0.177906912540865	4	FACETS	0.846	0.721	0.983	0.423	0.36	0.492	INDETERMINATE	1	TRUE	2	0.331998244351486	4		390	493	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066683	94066683	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	82	363	0	ENST00000369303.4:c.1076del	p.Gly359GlufsTer5	p.G359Efs*5	ENST00000369303	NM_004440.3	359	gGa/ga	5/17	0.331998244351486	4	FACETS	1	0.972	1	0.674	0.596	0.757	CLONAL	1	TRUE	2	0.331998244351486	4		363	488	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937028	48937028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	294	482	0	ENST00000267163.4:c.796C>T	p.Gln266Ter	p.Q266*	ENST00000267163	NM_000321.2	266	Caa/Taa	8/27	0.490284722198054	2	FACETS	0.841	0.796	0.886	0.841	0.796	0.886	CLONAL	2	TRUE	0	0.490565501775252	2		482	713	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274894	41274894	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1275515249	NA	P-0017250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	73	518	0	ENST00000349496.5:c.1144C>G	p.Leu382Val	p.L382V	ENST00000349496	NM_001904.3	382	Ctt/Gtt	8/15	0.490565501775252	3	FACETS	0.427	0.372	0.486	0.213	0.186	0.243	SUBCLONAL	1	TRUE	1	0.490565501775252	3		518	868	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961234	1961234	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	131	560	0	ENST00000382891.5:c.3022G>T	p.Ala1008Ser	p.A1008S	ENST00000382891	NM_133335.3	1008	Gcg/Tcg	17/22	0.490565501775252	3	FACETS	0.924	0.839	1	0.462	0.419	0.506	CLONAL	1	TRUE	1	0.490565501775252	3		560	720	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0121490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	108	485	0	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	0.251953932498167	3	FACETS	1	0.975	1	0.639	0.574	0.709	CLONAL	1	NA	1	0.26	3		485	734	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0017253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	226	401	3	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.201881625216517	4	FACETS	0.856	0.798	0.917	1	0.988	1	CLONAL	3	TRUE	2	0.205540242202798	4		404	1032	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206609	108206609	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	139	444	0	ENST00000278616.4:c.8189A>C	p.Gln2730Pro	p.Q2730P	ENST00000278616	NM_000051.3	2730	cAg/cCg	56/63	0.205540242202798	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.205540242202798	2		444	634	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244155	46244155	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	56	325	0	ENST00000334344.6:c.2249G>A	p.Gly750Glu	p.G750E	ENST00000334344	NM_152641.2	750	gGg/gAg	15/21	0.205540242202798	3	FACETS	1	0.88	1	0.515	0.441	0.596	CLONAL	1	TRUE	1	0.205540242202798	3		325	583	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245035	46245035	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	158	562	0	ENST00000334344.6:c.3129A>T	p.Gln1043His	p.Q1043H	ENST00000334344	NM_152641.2	1043	caA/caT	15/21	0.205540242202798	3	FACETS	1	0.917	1	1	0.917	1	CLONAL	2	TRUE	1	0.205540242202798	3		562	848	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226349	133226349	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	93	748	0	ENST00000320574.5:c.3709G>T	p.Glu1237Ter	p.E1237*	ENST00000320574	NM_006231.2	1237	Gag/Tag	30/49	1	2	FACETS	0.933	0.828	1	0.933	0.828	1	CLONAL	1	TRUE	1	0.205540242202798	2		748	970	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041983	42041983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	173	517	1	ENST00000219905.7:c.6178del	p.Gln2060LysfsTer42	p.Q2060Kfs*42	ENST00000219905	NM_001164273.1	2060	Caa/aa	17/24	0.205540242202798	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.205540242202798	2		518	790	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942532	17942532	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	73	591	0	ENST00000458235.1:c.2756C>A	p.Ala919Glu	p.A919E	ENST00000458235	NM_000215.3	919	gCg/gAg	20/24	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.205540242202798	2		591	691	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951146	17951146	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	101	496	1	ENST00000458235.1:c.1147G>T	p.Asp383Tyr	p.D383Y	ENST00000458235	NM_000215.3	383	Gac/Tac	9/24	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.205540242202798	2		497	712	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215595153	215595154	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0017253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	46	476	1	ENST00000260947.4:c.1982_1983delinsAT	p.Arg661Asn	p.R661N	ENST00000260947	NM_000465.2	661	aGG/aAT	10/11	0.205540242202798	3	FACETS	0.638	0.535	0.751	0.319	0.267	0.376	SUBCLONAL	1	TRUE	1	0.205540242202798	3		477	774	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902560	1902560	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	91	662	5	ENST00000382891.5:c.179G>T	p.Gly60Val	p.G60V	ENST00000382891	NM_133335.3	60	gGg/gTg	2/22	NA	2	FACETS	1	0.942	1			1	INDETERMINATE	1	TRUE	NA	0.205540242202798	2		667	807	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144597	55144597	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	57	442	0	ENST00000257290.5:c.2071G>C	p.Asp691His	p.D691H	ENST00000257290	NM_006206.4	691	Gat/Cat	15/23	0.179124908471465	4	FACETS	0.902	0.773	1			1	CLONAL	1	TRUE	NA	0.205540242202798	4		442	741	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525028	187525028	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	86	494	0	ENST00000441802.2:c.10652T>A	p.Phe3551Tyr	p.F3551Y	ENST00000441802	NM_005245.3	3551	tTc/tAc	19/27	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.205540242202798	2		494	828	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056173	26056173	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	122	344	0	ENST00000343677.2:c.484G>T	p.Ala162Ser	p.A162S	ENST00000343677	NM_005319.3	162	Gcc/Tcc	1/1	0.201881625216517	4	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	2	0.205540242202798	4		344	637	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704560	117704560	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	70	474	0	ENST00000368508.3:c.2416C>T	p.Leu806Phe	p.L806F	ENST00000368508	NM_002944.2	806	Ctc/Ttc	16/43	1	2	FACETS	0.983	0.856	1	0.983	0.856	1	CLONAL	1	TRUE	1	0.205540242202798	2		474	693	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468033	50468033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	52	367	2	ENST00000331340.3:c.1268G>A	p.Arg423His	p.R423H	ENST00000331340	NM_006060.4	423	cGc/cAc	8/8	0.201881625216517	4	FACETS	1	0.93	1	0.581	0.495	0.676	CLONAL	1	TRUE	2	0.205540242202798	4		369	525	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494107	140494107	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1368590056	NA	P-0017253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	57	606	0	ENST00000288602.6:c.1140+1G>A		p.X380_splice	ENST00000288602	NM_004333.4	380			0.201881625216517	4	FACETS	0.619	0.529	0.717	0.309	0.264	0.359	SUBCLONAL	1	TRUE	2	0.205540242202798	4		606	1081	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	97	231	0	ENST00000304494.5:c.247C>A	p.His83Asn	p.H83N	ENST00000304494	NM_000077.4	83	Cac/Aac	2/3	0.329179937981431	2	FACETS	0.875	0.791	0.962	0.875	0.791	0.962	CLONAL	2	TRUE	0	0.390126634261353	2		231	284	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593582	55593598	+	protein_altering_variant,splice_region_variant	In_Frame_Del	DEL	AAACCCATGTATGAAGT	AAACCCATGTATGAAGT	CA	novel	NA	P-0017255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	230	412	2	ENST00000288135.5:c.1648_1664delinsCA	p.Lys550_Val555delinsGln	p.K550_V555delinsQ	ENST00000288135	NM_000222.2	550	AAACCCATGTATGAAGTa/CAa	11/21	0.7018343378659	3	FACETS	0.877	0.826	0.928	0.877	0.826	0.928	CLONAL	2	TRUE	1	0.7018343378659	3		414	505	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	371	479	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.564319194107072	3	FACETS	0.989	0.944	1	0.989	0.944	1	CLONAL	2	TRUE	1	0.564319194107072	3		479	852	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052636	42052636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1054243525	NA	P-0017257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	226	525	1	ENST00000219905.7:c.7307G>A	p.Arg2436His	p.R2436H	ENST00000219905	NM_001164273.1	2436	cGt/cAt	20/24	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.564319194107072	2		526	676	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061163	38061175	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCGGCCCCCGG	CGCCGGCCCCCGG	-	novel	NA	P-0017257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	105	144	0	ENST00000250448.2:c.814_826del	p.Pro272AlafsTer45	p.P272Afs*45	ENST00000250448	NM_004496.3	272	CCGGGGGCCGGCGgc/gc	2/2	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.564319194107072	2		144	251	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778017	3778017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753595183	NA	P-0017257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1393	302	1040	1	ENST00000262367.5:c.7031G>A	p.Arg2344Gln	p.R2344Q	ENST00000262367	NM_004380.2	2344	cGg/cAg	31/31	0.554415955644338	4	FACETS	0.988	0.928	1	0.494	0.464	0.525	CLONAL	1	TRUE	2	0.564319194107072	4		1041	1695	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844172	68844172	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1555515445	NA	P-0017257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	564	847	0	ENST00000261769.5:c.760G>T	p.Asp254Tyr	p.D254Y	ENST00000261769	NM_004360.3	254	Gat/Tat	6/16	0.564319194107072	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.564319194107072	2		847	980	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832529	72832529	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	306	422	0	ENST00000268489.5:c.4052del	p.Pro1351GlnfsTer4	p.P1351Qfs*4	ENST00000268489	NM_006885.3	1351	cCa/ca	9/10	0.564319194107072	2	FACETS	0.997	0.952	1	0.997	0.952	1	CLONAL	2	TRUE	0	0.564319194107072	2		422	544	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020225	123020225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	213	790	0	ENST00000355640.3:c.713G>A	p.Arg238Gln	p.R238Q	ENST00000355640		238	cGa/cAa	2/7	1	2	FACETS	0.999	0.931	1	0.999	0.931	1	CLONAL	1	TRUE	1	0.564319194107072	2		790	756	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0017260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	274	180	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.197502205810332	3	FACETS	0.987	0.93	1	1	0.994	1	CLONAL	3	FALSE	1	0.256041642716596	3		180	815	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111475	8111476	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	135	588	1	ENST00000346208.3:c.962dup	p.Thr322AspfsTer30	p.T322Dfs*30	ENST00000346208		321	cag/cAag	5/6	0.196055520460261	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	0	0.256041642716596	1		589	797	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917611	151917611	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs938655561	NA	P-0017260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	156	682	0	ENST00000262189.6:c.3709C>T	p.Arg1237Ter	p.R1237*	ENST00000262189	NM_170606.2	1237	Cga/Tga	23/59	1	2	FACETS	0.83	0.762	0.901	1	0.99	1	CLONAL	2	FALSE	1	0.256041642716596	2		682	734	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569881	95569881	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	66	315	0	ENST00000393063.1:c.3852del	p.Tyr1285ThrfsTer17	p.Y1285Tfs*17	ENST00000393063	NM_030621.3	1284	ggG/gg	22/28	1	2	FACETS	0.621	0.539	0.709	0.621	0.539	0.709	SUBCLONAL	1	TRUE	1	0.40114744702153	2		315	530	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871182	12871182	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1328655695	NA	P-0017261-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	62	223	0	ENST00000228872.4:c.410del	p.Pro137ArgfsTer8	p.P137Rfs*8	ENST00000228872	NM_004064.3	137	Ccg/cg	1/3	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.29477352117245	2		223	398	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483093	29483093	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017261-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	195	689	0	ENST00000356175.3:c.153T>G	p.Phe51Leu	p.F51L	ENST00000356175	NM_000267.3	51	ttT/ttG	2/57	1	2	FACETS	0.941	0.868	1	0.941	0.868	1	CLONAL	1	TRUE	1	0.29477352117245	2		689	1406	SUCCESS
ATM	472	MSKCC	GRCh37	11	108214042	108214042	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	116	333	0	ENST00000278616.4:c.8362C>T	p.His2788Tyr	p.H2788Y	ENST00000278616	NM_000051.3	2788	Cat/Tat	57/63	1	2	FACETS	0.763	0.691	0.839	0.763	0.691	0.839	SUBCLONAL	1	TRUE	1	0.583279548278639	2		333	521	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212558	36212558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	287	778	0	ENST00000222270.7:c.2309C>T	p.Pro770Leu	p.P770L	ENST00000222270	NM_014727.1	770	cCt/cTt	3/37	1	2	FACETS	0.903	0.849	0.958	0.903	0.849	0.958	CLONAL	1	TRUE	1	0.583279548278639	2		778	1090	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0017263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	171	695	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.279901884708169	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.279901884708169	1		695	810	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154755	2154755	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	106	724	3	ENST00000434045.2:c.466G>A	p.Val156Met	p.V156M	ENST00000434045	NM_001127598.1	156	Gtg/Atg	4/5	1	2	FACETS	0.891	0.798	0.99	0.891	0.798	0.99	CLONAL	1	TRUE	1	0.279901884708169	2		727	850	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10244380	10244380	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	novel	NA	P-0017263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	63	611	1	ENST00000340748.4:c.4817-3C>T		p.X1606_splice	ENST00000340748		1606			1	2	FACETS	0.494	0.426	0.568	0.494	0.426	0.568	SUBCLONAL	1	TRUE	1	0.279901884708169	2		612	912	SUCCESS
APC	324	MSKCC	GRCh37	5	112173841	112173841	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	118	409	0	ENST00000257430.4:c.2551del	p.Ser851ValfsTer10	p.S851Vfs*10	ENST00000257430	NM_000038.5	850	agA/ag	16/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.279901884708169	2		409	649	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0017264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	156	178	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.42	2		178	654	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0017264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	261	415	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.130296946416424	3	FACETS	0.752	0.705	0.8	0.752	0.705	0.8	INDETERMINATE	2	TRUE	1	0.42	3		415	1000	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717615	89717615	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909227	NA	P-0017264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	164	386	0	ENST00000371953.3:c.640C>T	p.Gln214Ter	p.Q214*	ENST00000371953	NM_000314.4	214	Cag/Tag	7/9	0.130296946416424	3	FACETS	1	0.979	1	0.596	0.548	0.646	INDETERMINATE	1	TRUE	1	0.42	3		386	793	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0017264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	139	256	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.923	0.842	1	0.923	0.842	1	CLONAL	1	TRUE	1	0.42	2		256	717	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260317	16260317	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	193	435	0	ENST00000375759.3:c.7582G>A	p.Asp2528Asn	p.D2528N	ENST00000375759	NM_015001.2	2528	Gac/Aac	11/15	1	2	FACETS	0.891	0.824	0.961	0.891	0.824	0.961	CLONAL	1	TRUE	1	0.42	2		435	1031	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518802	204518802	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	93	214	0	ENST00000367182.3:c.1465A>G	p.Ile489Val	p.I489V	ENST00000367182	NM_001278516.1	489	Ata/Gta	11/11	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.42	2		214	433	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219962	5219962	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	210	544	0	ENST00000357368.4:c.3753G>C	p.Gln1251His	p.Q1251H	ENST00000357368	NM_002850.3	1251	caG/caC	22/38	1	2	FACETS	0.82	0.76	0.883	0.82	0.76	0.883	CLONAL	1	TRUE	1	0.42	2		544	1219	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270698	10270698	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	193	454	0	ENST00000340748.4:c.1037C>G	p.Ser346Cys	p.S346C	ENST00000340748		346	tCc/tGc	14/40	1	2	FACETS	0.865	0.799	0.933	0.865	0.799	0.933	CLONAL	1	TRUE	1	0.42	2		454	1063	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430160	181430160	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	55	130	0	ENST00000325404.1:c.12G>T	p.Met4Ile	p.M4I	ENST00000325404	NM_003106.3	4	atG/atT	1/1	1	2	FACETS	0.992	0.856	1	0.992	0.856	1	CLONAL	1	TRUE	1	0.42	2		130	264	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437714	52437714	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	243	360	0	ENST00000460680.1:c.1447C>T	p.Gln483Ter	p.Q483*	ENST00000460680	NM_004656.3	483	Cag/Tag	13/17	0.433673469781416	2	FACETS	0.831	0.783	0.879	0.831	0.783	0.879	CLONAL	2	TRUE	0	0.505201767507018	2		360	579	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037931	49037931	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	259	454	0	ENST00000267163.4:c.2172del	p.Ile724MetfsTer2	p.I724Mfs*2	ENST00000267163	NM_000321.2	724	aTt/at	21/27	0.505201767507018	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.505201767507018	1		454	751	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11032119	11032119	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	114	436	0	ENST00000327064.4:c.1684G>C	p.Gly562Arg	p.G562R	ENST00000327064	NM_199141.1	562	Ggg/Cgg	15/16	1	2	FACETS	0.493	0.443	0.546	0.493	0.443	0.546	SUBCLONAL	1	TRUE	1	0.505201767507018	2		436	915	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0017266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	213	710	1	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.327929340427718	1	FACETS	0.979	0.909	1	0.979	0.909	1	CLONAL	1	TRUE	0	0.327929340427718	1		711	1109	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456429	32456430	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTC	novel	NA	P-0017267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	88	487	0	ENST00000332351.3:c.460_462dup	p.Glu154dup	p.E154dup	ENST00000332351	NM_024426.4	154	-/GAG	1/10	0.331856168476598	2	FACETS	0.526	0.465	0.592	0.263	0.232	0.296	SUBCLONAL	1	TRUE	0	0.359475541940766	2		487	930	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109903	115109903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1182290035	NA	P-0017267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	71	451	1	ENST00000257566.3:c.1975G>A	p.Ala659Thr	p.A659T	ENST00000257566	NM_016569.3	659	Gcc/Acc	8/8	0.169716922950463	4	FACETS	0.563	0.49	0.642	0.281	0.245	0.321	INDETERMINATE	1	TRUE	2	0.359475541940766	4		452	954	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830810	72830810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1522	257	473	2	ENST00000268489.5:c.5771G>A	p.Gly1924Glu	p.G1924E	ENST00000268489	NM_006885.3	1924	gGg/gAg	9/10	0.359475541940766	6	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.359475541940766	6		475	1779	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559851	29559857	+	frameshift_variant	Frame_Shift_Del	DEL	TCAAACT	TCAAACT	-	novel	NA	P-0017267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	176	308	0	ENST00000356175.3:c.3449_3455del	p.Ser1150TyrfsTer6	p.S1150Yfs*6	ENST00000356175	NM_000267.3	1150	TCAAACTta/ta	26/57	0.241605876016092	3	FACETS	0.801	0.74	0.864	0.801	0.74	0.864	CLONAL	2	TRUE	1	0.359475541940766	3		308	721	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128036773	128036773	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	163	509	0	ENST00000285398.2:c.1706A>G	p.Lys569Arg	p.K569R	ENST00000285398	NM_000122.1	569	aAg/aGg	10/15	1	2	FACETS	0.78	0.714	0.849	0.78	0.714	0.849	SUBCLONAL	1	TRUE	1	0.359475541940766	2		509	1163	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138641	55138641	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1038766927	NA	P-0017267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	102	438	0	ENST00000257290.5:c.1318A>T	p.Thr440Ser	p.T440S	ENST00000257290	NM_006206.4	440	Acg/Tcg	9/23	0.359475541940766	3	FACETS	0.614	0.547	0.685	0.307	0.273	0.343	SUBCLONAL	1	TRUE	1	0.359475541940766	3		438	1091	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709133	117709133	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	119	529	1	ENST00000368508.3:c.1824G>A	p.Trp608Ter	p.W608*	ENST00000368508	NM_002944.2	608	tgG/tgA	13/43	0.359475541940766	1	FACETS	0.627	0.566	0.692	0.627	0.566	0.692	SUBCLONAL	1	TRUE	0	0.359475541940766	1		530	866	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517865	8517865	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	39	314	0	ENST00000356435.5:c.1526T>A	p.Val509Asp	p.V509D	ENST00000356435		509	gTc/gAc	10/35	0.335069678111822	3	FACETS	0.363	0.299	0.433	0.121	0.099	0.145	SUBCLONAL	1	TRUE	0	0.359475541940766	3		314	706	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0017271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	378	542	0	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	0.837931161641859	1	FACETS	0.832	0.8	0.864	0.832	0.8	0.864	CLONAL	1	TRUE	0	0.842700063004218	1		542	624	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433374	138433374	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746292811	NA	P-0017271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	484	576	2	ENST00000289153.2:c.1238C>T	p.Thr413Met	p.T413M	ENST00000289153	NM_006219.2	413	aCg/aTg	7/22	0.199975047540332	3	FACETS	0.789	0.757	0.82	0.789	0.757	0.82	INDETERMINATE	2	TRUE	1	0.842700063004218	3		578	1035	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573397	55573397	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	123	513	0	ENST00000288135.5:c.1059A>T	p.Arg353Ser	p.R353S	ENST00000288135	NM_000222.2	353	agA/agT	6/21	1	2	FACETS	0.262	0.236	0.29	0.262	0.236	0.29	SUBCLONAL	1	TRUE	1	0.842700063004218	2		513	1113	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0017273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	44	410	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.14	2		410	575	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0017273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	20	388	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.312	0.237	0.4	0.312	0.237	0.4	SUBCLONAL	1	TRUE	1	0.14	2		388	917	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0017273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	67	501	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.0917067034897192	3	FACETS	0.926	0.802	1	0.463	0.401	0.531	CLONAL	1	TRUE	1	0.14	3		501	1106	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587781525	NA	P-0017275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	492	614	0	ENST00000269305.4:c.842A>G	p.Asp281Gly	p.D281G	ENST00000269305	NM_001126112.2	281	gAc/gGc	8/11	NA	2	FACETS	0.979	0.94	1			1	INDETERMINATE	2	TRUE	NA	0.469891149573562	2		614	1070	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165078	47165078	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	266	270	0	ENST00000409792.3:c.1048G>C	p.Asp350His	p.D350H	ENST00000409792	NM_014159.6	350	Gat/Cat	3/21	0.469233927984909	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.469891149573562	2		270	561	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587780070	NA	P-0017276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	211	361	0	ENST00000269305.4:c.535C>G	p.His179Asp	p.H179D	ENST00000269305	NM_001126112.2	179	Cat/Gat	5/11	0.163795393785701	2	FACETS	1	0.971	1	1	0.992	1	CLONAL	3	FALSE	0	0.163795393785701	2		361	795	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436416	49436416	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0017276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	113	357	0	ENST00000301067.7:c.5795T>A	p.Leu1932Ter	p.L1932*	ENST00000301067	NM_003482.3	1932	tTg/tAg	27/54	0.163795393785701	5	FACETS	0.836	0.754	0.924	0.836	0.754	0.924	CLONAL	3	FALSE	2	0.163795393785701	5		357	685	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836597	89836597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1367874692	NA	P-0017276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	87	435	0	ENST00000389301.3:c.2293C>T	p.Leu765Phe	p.L765F	ENST00000389301	NM_000135.2	765	Ctc/Ttc	25/43	0.163795393785701	6	FACETS	1	0.957	1	0.295	0.26	0.333	CLONAL	1	FALSE	2	0.163795393785701	6		435	1195	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17947999	17947999	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1380	92	455	0	ENST00000458235.1:c.1725G>C	p.Leu575Phe	p.L575F	ENST00000458235	NM_000215.3	575	ttG/ttC	13/24	0.163795393785701	8	FACETS	1	0.951	1	0.228	0.201	0.256	CLONAL	1	FALSE	3	0.163795393785701	8		455	1472	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250676	26250676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	73	306	0	ENST00000446824.2:c.158G>A	p.Arg53His	p.R53H	ENST00000446824	NM_021018.2	53	cGc/cAc	1/1	0.163795393785701	13	FACETS	0.932	0.813	1			1	CLONAL	2	FALSE	NA	0.163795393785701	13		306	909	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223707	53223707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1288544172	NA	P-0017276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	61	268	1	ENST00000375401.3:c.3652C>T	p.Arg1218Cys	p.R1218C	ENST00000375401	NM_004187.3	1218	Cgc/Tgc	23/26	0.163795393785701	3	FACETS	1	0.91	1			1	CLONAL	1	FALSE	NA	0.163795393785701	3		269	749	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0017284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	373	470	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.340491758446124	8	FACETS	1	0.987	1	1	0.987	1	CLONAL	5	TRUE	3	0.340491758446124	8		470	815	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0017284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	483	750	1	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.340491758446124	8	FACETS	1	0.98	1	1	0.98	1	CLONAL	5	TRUE	3	0.340491758446124	8		751	1110	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11210251	11210251	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	91	482	0	ENST00000361445.4:c.4502G>A	p.Trp1501Ter	p.W1501*	ENST00000361445	NM_004958.3	1501	tGg/tAg	31/58	0.340491758446124	3	FACETS	0.759	0.678	0.844			1	SUBCLONAL	2	TRUE	NA	0.340491758446124	3		482	412	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741658	17741658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	60	347	0	ENST00000250003.3:c.329G>A	p.Arg110His	p.R110H	ENST00000250003	NM_002478.4	110	cGc/cAc	1/3	0.274576284047687	3	FACETS	0.806	0.695	0.926	0.403	0.347	0.463	CLONAL	1	TRUE	1	0.340491758446124	3		347	512	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030426	49030426	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	53	310	0	ENST00000267163.4:c.1901C>A	p.Ser634Ter	p.S634*	ENST00000267163	NM_000321.2	634	tCa/tAa	19/27	0.271873572992187	2	FACETS	1	0.932	1	0.572	0.492	0.659	CLONAL	1	TRUE	0	0.340491758446124	2		310	272	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0017284-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	1225	470	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.639842744072248	10	FACETS	1	0.995	1	0.911	0.891	0.932	CLONAL	6	TRUE	3	0.639842744072248	10		470	2137	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0017284-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1605	2176	750	1	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.639842744072248	10	FACETS	1	0.997	1	0.915	0.899	0.93	CLONAL	6	TRUE	3	0.639842744072248	10		751	3781	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11210251	11210251	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017284-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	576	482	0	ENST00000361445.4:c.4502G>A	p.Trp1501Ter	p.W1501*	ENST00000361445	NM_004958.3	1501	tGg/tAg	31/58	0.53930609990659	5	FACETS	0.888	0.855	0.922	0.888	0.855	0.922	CLONAL	3	TRUE	2	0.639842744072248	5		482	1324	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030426	49030426	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017284-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	232	310	0	ENST00000267163.4:c.1901C>A	p.Ser634Ter	p.S634*	ENST00000267163	NM_000321.2	634	tCa/tAa	19/27	0.563101667676142	2	FACETS	0.902	0.856	0.947	0.902	0.856	0.947	CLONAL	2	TRUE	0	0.639842744072248	2		310	402	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843416	3843417	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0017285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	300	471	0	ENST00000262367.5:c.1186_1187del	p.Thr396AlafsTer30	p.T396Afs*30	ENST00000262367	NM_004380.2	396	ACg/g	4/31	0.339322600791141	1	FACETS	0.668	0.631	0.705	0.668	0.631	0.705	INDETERMINATE	1	TRUE	0	0.688682919434439	1		471	855	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0017286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	99	390	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.260049974522284	2		392	716	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374245	138374245	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	60	542	0	ENST00000289153.2:c.3199G>T	p.Asp1067Tyr	p.D1067Y	ENST00000289153	NM_006219.2	1067	Gac/Tac	22/22	1	2	FACETS	0.582	0.5	0.671	0.582	0.5	0.671	SUBCLONAL	1	TRUE	1	0.260049974522284	2		542	793	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907433	32907434	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs879255327	NA	P-0017286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	82	609	0	ENST00000380152.3:c.1821dup	p.Asp608ArgfsTer8	p.D608Rfs*8	ENST00000380152		606	-/A	10/27	1	2	FACETS	0.755	0.665	0.852	0.755	0.665	0.852	SUBCLONAL	1	TRUE	1	0.260049974522284	2		609	835	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560484	95560484	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	107	465	0	ENST00000393063.1:c.5105A>T	p.Gln1702Leu	p.Q1702L	ENST00000393063	NM_030621.3	1702	cAg/cTg	25/28	0.260049974522284	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.260049974522284	1		465	639	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131149	55131149	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2193	1825	630	0	ENST00000257290.5:c.692T>C	p.Ile231Thr	p.I231T	ENST00000257290	NM_006206.4	231	aTt/aCt	5/23	0.260049974522284	26	FACETS	1	0.993	1			1	CLONAL	14	TRUE	NA	0.260049974522284	26		630	4018	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538984	187538984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573293048	NA	P-0017286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	91	534	1	ENST00000441802.2:c.8756C>T	p.Thr2919Met	p.T2919M	ENST00000441802	NM_005245.3	2919	aCg/aTg	10/27	1	2	FACETS	0.827	0.734	0.928	0.827	0.734	0.928	CLONAL	1	TRUE	1	0.260049974522284	2		535	846	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821207	72821227	+	inframe_deletion	In_Frame_Del	DEL	TGGCATCGAGGGCTGAACCCC	TGGCATCGAGGGCTGAACCCC	-	novel	NA	P-0017287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	282	438	1	ENST00000268489.5:c.10948_10968del	p.Gly3650_Pro3656del	p.G3650_P3656del	ENST00000268489	NM_006885.3	3650	GGGGTTCAGCCCTCGATGCCA/-	10/10	0.782805434601962	1	FACETS	0.967	0.926	1	0.967	0.926	1	CLONAL	1	TRUE	0	0.807146637724449	1		439	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572954	7572954	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	280	426	0	ENST00000269305.4:c.1155del	p.Phe385LeufsTer37	p.F385Lfs*37	ENST00000269305	NM_001126112.2	385	ttC/tt	11/11	0.606140539124756	1	FACETS	0.831	0.792	0.87	0.831	0.792	0.87	CLONAL	1	TRUE	0	0.807146637724449	1		426	498	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0017288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	249	546	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.318647561195081	2	FACETS	1	0.99	1	0.651	0.608	0.695	CLONAL	1	TRUE	0	0.344656236471344	2		547	1110	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197564	106197564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754215085	NA	P-0017288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	107	419	1	ENST00000380013.4:c.5897G>A	p.Arg1966His	p.R1966H	ENST00000380013	NM_001127208.2	1966	cGt/cAt	11/11	1	2	FACETS	0.637	0.57	0.708	0.637	0.57	0.708	SUBCLONAL	1	TRUE	1	0.344656236471344	2		420	975	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885695	23885695	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762512538	NA	P-0017288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	283	490	1	ENST00000374561.5:c.223G>A	p.Asp75Asn	p.D75N	ENST00000374561	NM_002167.4	75	Gac/Aac	1/3	0.166103279858779	3	FACETS	0.76	0.714	0.808	0.76	0.714	0.808	INDETERMINATE	2	TRUE	1	0.344656236471344	3		491	1266	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944965	31944965	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	104	460	0	ENST00000340398.3:c.136G>A	p.Val46Met	p.V46M	ENST00000340398	NM_001013699.2	46	Gtg/Atg	1/1	0.184940163360344	4	FACETS	0.737	0.658	0.821	0.369	0.329	0.411	INDETERMINATE	1	TRUE	2	0.344656236471344	4		460	1101	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233726	133233733	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCTGCC	CTCCTGCC	-	novel	NA	P-0017288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	60	339	0	ENST00000320574.5:c.3571_3578del	p.Gly1191ThrfsTer18	p.G1191Tfs*18	ENST00000320574	NM_006231.2	1191	GGCAGGAGa/a	29/49	1	2	FACETS	0.527	0.453	0.607	0.527	0.453	0.607	SUBCLONAL	1	TRUE	1	0.344656236471344	2		339	661	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218417	1218417	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	2932	592	0	ENST00000326873.7:c.292G>A	p.Glu98Lys	p.E98K	ENST00000326873	NM_000455.4	98	Gaa/Aaa	2/10	0.344656236471344	17	FACETS	0.996	0.985	1			1	CLONAL	16	TRUE	NA	0.344656236471344	17		592	3826	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218486	1218486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1316669124	NA	P-0017288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	2085	572	0	ENST00000326873.7:c.361G>A	p.Glu121Lys	p.E121K	ENST00000326873	NM_000455.4	121	Gag/Aag	2/10	0.344656236471344	17	FACETS	0.997	0.983	1			1	CLONAL	15	TRUE	NA	0.344656236471344	17		572	2901	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	58	301	4				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.746	0.649	0.848	0.746	0.649	0.848	SUBCLONAL	1	TRUE	1	0.707124968887777	2		305	220	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223531	55223533	+	inframe_deletion	In_Frame_Del	DEL	GTG	GTG	-	novel	NA	P-0017289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	279	643	0	ENST00000275493.2:c.901_903del	p.Val301del	p.V301del	ENST00000275493	NM_005228.3	300	GTG/-	8/28	0.707124968887777	6	FACETS	1	0.992	1	0.347	0.325	0.37	CLONAL	1	TRUE	2	0.707124968887777	6		643	1373	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589663	67589663	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587777709	NA	P-0017289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	92	418	0	ENST00000274335.5:c.1425+1G>A		p.X475_splice	ENST00000274335		475			1	2	FACETS	0.429	0.382	0.48	0.429	0.382	0.48	SUBCLONAL	1	TRUE	1	0.707124968887777	2		418	606	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	55	335	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.201584810898161	1	FACETS	0.526	0.448	0.611	0.526	0.448	0.611	SUBCLONAL	1	TRUE	0	0.201584810898161	1		335	933	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143044504	143044504	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	64	491	0	ENST00000262992.4:c.1958T>A	p.Leu653Gln	p.L653Q	ENST00000262992	NM_001101669.1	653	cTa/cAa	18/24	1	2	FACETS	0.663	0.572	0.762	0.663	0.572	0.762	SUBCLONAL	1	TRUE	1	0.201584810898161	2		491	958	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106482	27106482	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0017293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	340	614	0	ENST00000324856.7:c.6093T>A	p.Tyr2031Ter	p.Y2031*	ENST00000324856	NM_006015.4	2031	taT/taA	20/20	0.548456563179351	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.548456563179351	1		614	844	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38504591	38504591	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	261	583	0	ENST00000254066.5:c.202T>C	p.Ser68Pro	p.S68P	ENST00000254066	NM_000964.3	68	Tct/Cct	3/9	1	2	FACETS	0.794	0.744	0.847	0.794	0.744	0.847	SUBCLONAL	1	TRUE	1	0.548456563179351	2		583	1198	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270593	98270595	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	rs756897237	NA	P-0017295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	10	79	0	ENST00000331920.6:c.49_51del	p.Gly17del	p.G17del	ENST00000331920	NM_000264.3	17	GGC/-	1/24	1	2	FACETS	0.247	0.167	0.347	0.247	0.167	0.347	SUBCLONAL	1	TRUE	1	0.5	2		79	162	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2105417	2105417	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45517111	NA	P-0017295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	349	524	1	ENST00000219476.3:c.496C>T	p.Gln166Ter	p.Q166*	ENST00000219476	NM_000548.3	166	Cag/Tag	6/42	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.5	2		525	1056	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138540	2138610	+	frameshift_variant,stop_lost	Frame_Shift_Del	DEL	ACACCTGGCTATGAGGTGGGCCAGCGGAAGCGCCTCATCTCCTCGGTGGAGGACTTCACCGAGTTTGTGTG	ACACCTGGCTATGAGGTGGGCCAGCGGAAGCGCCTCATCTCCTCGGTGGAGGACTTCACCGAGTTTGTGTG	-	novel	NA	P-0017295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	276	605	0	ENST00000219476.3:c.5354_5424del	p.Thr1785ArgfsTer?	p.T1785Rfs*?	ENST00000219476	NM_000548.3	1785	ACACCTGGCTATGAGGTGGGCCAGCGGAAGCGCCTCATCTCCTCGGTGGAGGACTTCACCGAGTTTGTGTGa/a	42/42	1	2	FACETS	0.881	0.826	0.938	0.881	0.826	0.938	CLONAL	1	TRUE	1	0.5	2		605	1253	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0017296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	891	180	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.593831232916484	7	FACETS	1	0.991	1	0.877	0.858	0.895	CLONAL	6	TRUE	0	0.593831232916484	7		180	1215	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574002	7574002	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	353	648	0	ENST00000269305.4:c.1025del	p.Arg342GlnfsTer3	p.R342Qfs*3	ENST00000269305	NM_001126112.2	342	cGa/ca	10/11	0.593831232916484	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.593831232916484	1		648	609	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933574	39933574	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	94	410	0	ENST00000378444.4:c.1025G>A	p.Arg342Gln	p.R342Q	ENST00000378444	NM_001123385.1	342	cGa/cAa	4/15	0.255137019074435	5	FACETS	1	0.978	1	0.46	0.411	0.511	INDETERMINATE	1	TRUE	2	0.593831232916484	5		410	434	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268766	41268766	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	419	614	0	ENST00000349496.5:c.1004A>T	p.Lys335Ile	p.K335I	ENST00000349496	NM_001904.3	335	aAa/aTa	7/15	0.419092405215941	3	FACETS	0.994	0.948	1	0.994	0.948	1	CLONAL	2	TRUE	1	0.423591860250399	3		614	1206	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911535	101911535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113605875	NA	P-0017297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	379	564	1	ENST00000374994.4:c.1460G>A	p.Arg487Gln	p.R487Q	ENST00000374994	NM_004612.2	487	cGg/cAg	9/9	0.423591860250399	2	FACETS	0.933	0.889	0.978	0.933	0.889	0.978	CLONAL	2	TRUE	0	0.423591860250399	2		565	959	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220494	1220494	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519858	NA	P-0017297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	370	658	0	ENST00000326873.7:c.587G>T	p.Gly196Val	p.G196V	ENST00000326873	NM_000455.4	196	gGc/gTc	4/10	0.423591860250399	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.423591860250399	2		658	868	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517863	8517863	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs776072591	NA	P-0017297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	183	382	0	ENST00000356435.5:c.1528A>G	p.Ile510Val	p.I510V	ENST00000356435		510	Atc/Gtc	10/35	0.423591860250399	2	FACETS	0.841	0.782	0.9	0.841	0.782	0.9	CLONAL	2	TRUE	0	0.423591860250399	2		382	514	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69202261	69202261	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	245	325	0	ENST00000462284.1:c.4G>C	p.Val2Leu	p.V2L	ENST00000462284	NM_002392.5	2	Gtg/Ctg	1/11	0.419092405215941	3	FACETS	0.978	0.918	1	0.978	0.918	1	CLONAL	2	TRUE	1	0.423591860250399	3		325	717	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2164215	2164215	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	130	475	3	ENST00000398665.3:c.32C>T	p.Ser11Leu	p.S11L	ENST00000398665	NM_032482.2	11	tCg/tTg	1/28	0.423591860250399	2	FACETS	1	0.979	1	0.625	0.57	0.682	CLONAL	1	TRUE	0	0.423591860250399	2		478	491	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247951	10247951	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	268	352	0	ENST00000340748.4:c.4251G>C	p.Met1417Ile	p.M1417I	ENST00000340748		1417	atG/atC	36/40	0.423591860250399	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.423591860250399	2		352	595	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602590	10602590	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	328	551	0	ENST00000171111.5:c.988A>C	p.Thr330Pro	p.T330P	ENST00000171111	NM_203500.1	330	Acc/Ccc	3/6	0.423591860250399	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.423591860250399	2		551	718	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439975	220439975	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	520	836	1	ENST00000243786.2:c.828G>T	p.Trp276Cys	p.W276C	ENST00000243786	NM_002191.3	276	tgG/tgT	2/2	0.293491899357435	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	2	0.423591860250399	4		837	1541	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71019894	71019894	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	90	244	0	ENST00000318789.4:c.1715C>G	p.Ala572Gly	p.A572G	ENST00000318789	NM_032682.5	572	gCt/gGt	19/21	0.419092405215941	3	FACETS	0.992	0.883	1	0.496	0.441	0.554	CLONAL	1	TRUE	1	0.423591860250399	3		244	519	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940419	31940419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	313	599	1	ENST00000375333.2:c.452C>T	p.Ser151Leu	p.S151L	ENST00000375333	NM_032454.1	151	tCa/tTa	3/8	0.423591860250399	2	FACETS	0.997	0.947	1	0.997	0.947	1	CLONAL	2	TRUE	0	0.423591860250399	2		600	741	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0017298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	211	459	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.502778316603456	2	FACETS	0.882	0.833	0.932	0.882	0.833	0.932	CLONAL	2	TRUE	0	0.596356009402505	2		459	401	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005423	29005423	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	105	361	0	ENST00000282397.4:c.838C>T	p.Arg280Ter	p.R280*	ENST00000282397	NM_002019.4	280	Cga/Tga	7/30	0.548060714807178	3	FACETS	1	0.914	1	0.508	0.458	0.561	CLONAL	1	TRUE	1	0.596356009402505	3		361	450	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142950049	142950049	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	114	429	0	ENST00000262992.4:c.2661G>T	p.Glu887Asp	p.E887D	ENST00000262992	NM_001101669.1	887	gaG/gaT	24/24	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.596356009402505	2		429	340	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	283	459	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.584700760235321	2		460	945	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	206	316	1	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.894	0.832	0.959	0.894	0.832	0.959	CLONAL	1	TRUE	1	0.584700760235321	2		317	788	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	288	570	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.963	0.907	1	0.963	0.907	1	CLONAL	1	TRUE	1	0.584700760235321	2		571	1023	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	290	547	3	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.913	0.859	0.968	0.913	0.859	0.968	CLONAL	1	TRUE	1	0.584700760235321	2		550	1087	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11270924	11270924	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	281	655	1	ENST00000361445.4:c.3601C>T	p.Arg1201Ter	p.R1201*	ENST00000361445	NM_004958.3	1201	Cga/Tga	24/58	1	2	FACETS	0.904	0.85	0.96	0.904	0.85	0.96	CLONAL	1	TRUE	1	0.584700760235321	2		656	1063	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255340	16255340	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	382	660	2	ENST00000375759.3:c.2609del	p.Asn870ThrfsTer11	p.N870Tfs*11	ENST00000375759	NM_015001.2	869	Aaa/aa	11/15	1	2	FACETS	0.847	0.803	0.893	0.847	0.803	0.893	CLONAL	1	TRUE	1	0.584700760235321	2		662	1542	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255472	16255472	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	80	622	0	ENST00000375759.3:c.2737C>A	p.Leu913Met	p.L913M	ENST00000375759	NM_015001.2	913	Ctg/Atg	11/15	1	2	FACETS	0.226	0.198	0.256	0.226	0.198	0.256	SUBCLONAL	1	TRUE	1	0.584700760235321	2		622	1212	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258563	16258563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764002157	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	287	476	0	ENST00000375759.3:c.5828C>T	p.Ala1943Val	p.A1943V	ENST00000375759	NM_015001.2	1943	gCg/gTg	11/15	1	2	FACETS	0.972	0.915	1	0.972	0.915	1	CLONAL	1	TRUE	1	0.584700760235321	2		476	1010	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258889	16258889	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1305	481	881	1	ENST00000375759.3:c.6158del	p.Asn2053ThrfsTer11	p.N2053Tfs*11	ENST00000375759	NM_015001.2	2052	Aaa/aa	11/15	1	2	FACETS	0.921	0.879	0.964	0.921	0.879	0.964	CLONAL	1	TRUE	1	0.584700760235321	2		882	1786	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261246	16261246	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1466090335	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	277	468	0	ENST00000375759.3:c.8516del	p.Pro2839ArgfsTer50	p.P2839Rfs*50	ENST00000375759	NM_015001.2	2837	atC/at	11/15	1	2	FACETS	0.995	0.936	1	0.995	0.936	1	CLONAL	1	TRUE	1	0.584700760235321	2		468	952	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	237	409	2	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.938	0.877	1	0.938	0.877	1	CLONAL	1	TRUE	1	0.584700760235321	2		411	864	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937725	36937725	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	285	506	0	ENST00000361632.4:c.1013T>C	p.Leu338Pro	p.L338P	ENST00000361632		338	cTg/cCg	8/16	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.584700760235321	2		506	962	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812466	43812466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1298113648	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	225	401	0	ENST00000372470.3:c.1169G>A	p.Arg390His	p.R390H	ENST00000372470	NM_005373.2	390	cGc/cAc	8/12	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.584700760235321	2		401	758	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798329	45798329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780748	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	84	541	0	ENST00000450313.1:c.607C>T	p.Arg203Cys	p.R203C	ENST00000450313	NM_012222.2	203	Cgt/Tgt	8/16	1	2	FACETS	0.247	0.218	0.28	0.247	0.218	0.28	SUBCLONAL	1	TRUE	1	0.584700760235321	2		541	1161	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606768	43606768	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1564494424	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	372	676	0	ENST00000355710.3:c.1377G>T	p.Glu459Asp	p.E459D	ENST00000355710	NM_020975.4	459	gaG/gaT	7/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.584700760235321	2		676	1251	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851524	63851524	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	310	689	0	ENST00000279873.7:c.2302A>G	p.Thr768Ala	p.T768A	ENST00000279873	NM_032199.2	768	Acc/Gcc	10/10	1	2	FACETS	0.803	0.756	0.851	0.803	0.756	0.851	CLONAL	1	TRUE	1	0.584700760235321	2		689	1321	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692865	89692865	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	105	224	0	ENST00000371953.3:c.349A>G	p.Asn117Asp	p.N117D	ENST00000371953	NM_000314.4	117	Aat/Gat	5/9	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.584700760235321	2		224	355	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244949	123244949	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	377	722	0	ENST00000358487.5:c.2155G>T	p.Gly719Ter	p.G719*	ENST00000358487	NM_000141.4	719	Gga/Tga	16/18	1	2	FACETS	0.96	0.911	1	0.96	0.911	1	CLONAL	1	TRUE	1	0.584700760235321	2		722	1343	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132907	64132907	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	362	655	0	ENST00000334205.4:c.1046del	p.Pro349HisfsTer26	p.P349Hfs*26	ENST00000334205	NM_003942.2	347	agC/ag	9/17	1	2	FACETS	0.968	0.917	1	0.968	0.917	1	CLONAL	1	TRUE	1	0.584700760235321	2		655	1279	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577526	64577526	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	194	357	0	ENST00000312049.6:c.56T>C	p.Val19Ala	p.V19A	ENST00000312049	NM_130799.2	19	gTg/gCg	2/10	1	2	FACETS	0.958	0.889	1	0.958	0.889	1	CLONAL	1	TRUE	1	0.584700760235321	2		357	693	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998862	100998862	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767505462	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	355	670	1	ENST00000325455.5:c.940G>A	p.Ala314Thr	p.A314T	ENST00000325455	NM_001202474.3	314	Gcc/Acc	1/8	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.584700760235321	2		671	1204	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307291	118307291	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	13	71	0	ENST00000534358.1:c.69del	p.Arg24AlafsTer4	p.R24Afs*4	ENST00000534358	NM_005933.3	22	Ggg/gg	1/36	1	2	FACETS	0.523	0.379	0.693	0.523	0.379	0.693	SUBCLONAL	1	TRUE	1	0.584700760235321	2		71	85	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344955	118344955	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	259	367	3	ENST00000534358.1:c.3086del	p.Lys1029ArgfsTer65	p.K1029Rfs*65	ENST00000534358	NM_005933.3	1027	ctA/ct	3/36	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.584700760235321	2		370	825	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466897	18466897	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1324647652	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	241	522	0	ENST00000266497.5:c.1036G>A	p.Asp346Asn	p.D346N	ENST00000266497		346	Gac/Aac	5/31	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.584700760235321	2		522	824	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534783	18534783	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs752024499	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	302	511	0	ENST00000266497.5:c.1841A>G	p.Asp614Gly	p.D614G	ENST00000266497		614	gAt/gGt	12/31	1	2	FACETS	0.95	0.896	1	0.95	0.896	1	CLONAL	1	TRUE	1	0.584700760235321	2		511	1087	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715795	18715795	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769054495	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	172	501	0	ENST00000266497.5:c.3626C>T	p.Thr1209Ile	p.T1209I	ENST00000266497		1209	aCa/aTa	25/31	1	2	FACETS	0.864	0.798	0.933	0.864	0.798	0.933	CLONAL	1	TRUE	1	0.584700760235321	2		501	681	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	287	618	4	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.85	0.799	0.902	0.85	0.799	0.902	CLONAL	1	TRUE	1	0.584700760235321	2		622	1155	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438211	49438211	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	396	627	0	ENST00000301067.7:c.5058del	p.Lys1686AsnfsTer36	p.K1686Nfs*36	ENST00000301067	NM_003482.3	1686	aaA/aa	20/54	1	2	FACETS	0.89	0.845	0.936	0.89	0.845	0.936	CLONAL	1	TRUE	1	0.584700760235321	2		627	1522	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444986	49444987	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	185	426	0	ENST00000301067.7:c.2479dup	p.Gln827ProfsTer3	p.Q827Pfs*3	ENST00000301067	NM_003482.3	827	caa/cCaa	10/54	1	2	FACETS	0.794	0.734	0.856	0.794	0.734	0.856	SUBCLONAL	1	TRUE	1	0.584700760235321	2		426	797	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233240	69233240	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	175	374	2	ENST00000462284.1:c.1111del	p.Thr371LeufsTer2	p.T371Lfs*2	ENST00000462284	NM_002392.5	369	Aaa/aa	11/11	1	2	FACETS	0.882	0.815	0.951	0.882	0.815	0.951	CLONAL	1	TRUE	1	0.584700760235321	2		376	679	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112292	115112292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1282046318	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	92	106	0	ENST00000257566.3:c.1448C>T	p.Thr483Met	p.T483M	ENST00000257566	NM_016569.3	483	aCg/aTg	7/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.584700760235321	2		106	218	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112362	115112362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1440126149	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	206	327	0	ENST00000257566.3:c.1378G>A	p.Glu460Lys	p.E460K	ENST00000257566	NM_016569.3	460	Gag/Aag	7/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.584700760235321	2		327	645	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123892069	123892069	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	194	398	0	ENST00000330479.4:c.878T>C	p.Leu293Pro	p.L293P	ENST00000330479	NM_020382.3	293	cTa/cCa	8/9	1	2	FACETS	0.863	0.8	0.927	0.863	0.8	0.927	CLONAL	1	TRUE	1	0.584700760235321	2		398	769	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237658	133237658	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	443	705	0	ENST00000320574.5:c.2957A>G	p.Gln986Arg	p.Q986R	ENST00000320574	NM_006231.2	986	cAa/cGa	25/49	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.584700760235321	2		705	1451	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562142	21562142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1421513550	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1417	550	1011	1	ENST00000382592.4:c.1777C>T	p.Arg593Cys	p.R593C	ENST00000382592	NM_014572.2	593	Cgc/Tgc	4/8	1	2	FACETS	0.956	0.916	0.998	0.956	0.916	0.998	CLONAL	1	TRUE	1	0.584700760235321	2		1012	1967	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589348	28589348	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	312	630	0	ENST00000241453.7:c.2699A>C	p.Lys900Thr	p.K900T	ENST00000241453	NM_004119.2	900	aAa/aCa	22/24	1	2	FACETS	0.888	0.837	0.94	0.888	0.837	0.94	CLONAL	1	TRUE	1	0.584700760235321	2		630	1202	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592705	28592705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201208287	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	321	533	2	ENST00000241453.7:c.2440G>A	p.Ala814Thr	p.A814T	ENST00000241453	NM_004119.2	814	Gcc/Acc	20/24	1	2	FACETS	0.88	0.83	0.931	0.88	0.83	0.931	CLONAL	1	TRUE	1	0.584700760235321	2		535	1248	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907421	32907421	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359306	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	201	575	4	ENST00000380152.3:c.1813del	p.Ile605TyrfsTer9	p.I605Yfs*9	ENST00000380152		602	ggA/gg	10/27	1	2	FACETS	0.766	0.711	0.824	0.766	0.711	0.824	SUBCLONAL	1	TRUE	1	0.584700760235321	2		579	897	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643372	38643372	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1427402192	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	273	619	2	ENST00000299084.4:c.842A>G	p.Gln281Arg	p.Q281R	ENST00000299084	NM_152594.2	281	cAg/cGg	7/7	1	2	FACETS	0.972	0.913	1	0.972	0.913	1	CLONAL	1	TRUE	1	0.584700760235321	2		621	961	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003510	42003510	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	312	642	0	ENST00000219905.7:c.3047G>A	p.Arg1016Gln	p.R1016Q	ENST00000219905	NM_001164273.1	1016	cGa/cAa	8/24	1	2	FACETS	0.94	0.887	0.995	0.94	0.887	0.995	CLONAL	1	TRUE	1	0.584700760235321	2		642	1135	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	212	377	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.584700760235321	2		377	547	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774126	66774126	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	486	805	1	ENST00000307102.5:c.602G>A	p.Arg201His	p.R201H	ENST00000307102	NM_002755.3	201	cGt/cAt	6/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.584700760235321	2		806	1590	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996278	73996278	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	19	6	0	ENST00000318443.5:c.1012T>C	p.Phe338Leu	p.F338L	ENST00000318443	NM_001024736.1	338	Ttc/Ctc	5/10	1	2	FACETS	0.985	0.809	1	1	0.949	1	CLONAL	2	TRUE	1	0.584700760235321	2		6	33	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90627543	90627545	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	262	462	0	ENST00000330062.3:c.1312_1314del	p.Leu438del	p.L438del	ENST00000330062	NM_002168.2	438	CTC/-	11/11	1	2	FACETS	0.872	0.817	0.928	0.872	0.817	0.928	CLONAL	1	TRUE	1	0.584700760235321	2		462	1028	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304140	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	254	702	0	ENST00000355112.3:c.1543_1544del	p.Asn515Ter	p.N515*	ENST00000355112	NM_000057.2	512	ggAAaa/ggaa	7/22	1	2	FACETS	0.766	0.717	0.817	0.766	0.717	0.817	SUBCLONAL	1	TRUE	1	0.584700760235321	2		702	1134	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779211	3779211	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783507	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	93	248	0	ENST00000262367.5:c.5837del	p.Pro1946HisfsTer30	p.P1946Hfs*30	ENST00000262367	NM_004380.2	1946	cCa/ca	31/31	1	2	FACETS	0.818	0.732	0.907	0.818	0.732	0.907	CLONAL	1	TRUE	1	0.584700760235321	2		248	389	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807837	3807837	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	315	575	0	ENST00000262367.5:c.3582G>T	p.Gln1194His	p.Q1194H	ENST00000262367	NM_004380.2	1194	caG/caT	18/31	1	2	FACETS	0.954	0.9	1	0.954	0.9	1	CLONAL	1	TRUE	1	0.584700760235321	2		575	1130	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	216	415	0	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	0.864	0.805	0.925	0.864	0.805	0.925	CLONAL	1	TRUE	1	0.584700760235321	2		415	855	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825519	50825519	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	178	511	2	ENST00000398568.2:c.2156del	p.Asn719MetfsTer13	p.N719Mfs*13	ENST00000398568	NM_001042412.1	717	gAa/ga	14/18	1	2	FACETS	0.716	0.661	0.774	0.716	0.661	0.774	SUBCLONAL	1	TRUE	1	0.584700760235321	2		513	850	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835781	68835781	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060501215	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	339	510	0	ENST00000261769.5:c.377del	p.Pro126ArgfsTer89	p.P126Rfs*89	ENST00000261769	NM_004360.3	124	cgC/cg	3/16	1	2	FACETS	0.854	0.807	0.902	0.854	0.807	0.902	CLONAL	1	TRUE	1	0.584700760235321	2		510	1358	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	491	763	1	ENST00000269305.4:c.403del	p.Cys135AlafsTer35	p.C135Afs*35	ENST00000269305	NM_001126112.2	135	Tgc/gc	5/11	0.584700760235321	1	FACETS	0.942	0.903	0.982	0.942	0.903	0.982	CLONAL	1	TRUE	0	0.584700760235321	1		764	1261	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17120457	17120457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767714543	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	421	690	1	ENST00000285071.4:c.1102G>A	p.Val368Ile	p.V368I	ENST00000285071	NM_144997.5	368	Gtt/Att	10/14	1	2	FACETS	0.925	0.88	0.971	0.925	0.88	0.971	CLONAL	1	TRUE	1	0.584700760235321	2		691	1557	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509607	29509607	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	287	677	0	ENST00000356175.3:c.812T>C	p.Ile271Thr	p.I271T	ENST00000356175	NM_000267.3	271	aTc/aCc	8/57	1	2	FACETS	0.839	0.789	0.891	0.839	0.789	0.891	CLONAL	1	TRUE	1	0.584700760235321	2		677	1170	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560227	29560227	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	121	220	1	ENST00000356175.3:c.3704A>G	p.Gln1235Arg	p.Q1235R	ENST00000356175	NM_000267.3	1235	cAg/cGg	27/57	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.584700760235321	2		221	381	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879877	37879877	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	303	693	0	ENST00000269571.5:c.2172G>T	p.Lys724Asn	p.K724N	ENST00000269571		724	aaG/aaT	18/27	1	2	FACETS	0.862	0.811	0.913	0.862	0.811	0.913	CLONAL	1	TRUE	1	0.584700760235321	2		693	1203	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533905	63533905	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	536	355	0	ENST00000307078.5:c.1249del	p.Ala417ArgfsTer41	p.A417Rfs*41	ENST00000307078	NM_004655.3	417	Gcg/cg	6/11	0.578493168313553	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.584700760235321	2		355	853	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117951	70117951	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	275	238	0	ENST00000245479.2:c.419G>T	p.Gly140Val	p.G140V	ENST00000245479	NM_000346.3	140	gGc/gTc	1/3	0.578493168313553	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.584700760235321	2		238	452	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	37	160	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	0.584700760235321	3	FACETS	0.389	0.321	0.466	0.195	0.16	0.233	SUBCLONAL	1	TRUE	1	0.584700760235321	3		160	420	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170598	7170598	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750676016	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	341	583	0	ENST00000302850.5:c.1433G>A	p.Arg478His	p.R478H	ENST00000302850	NM_000208.2	478	cGc/cAc	6/22	0.584700760235321	3	FACETS	0.989	0.934	1	0.495	0.467	0.523	CLONAL	1	TRUE	1	0.584700760235321	3		583	1524	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254533	10254533	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	295	497	0	ENST00000340748.4:c.2977A>G	p.Ile993Val	p.I993V	ENST00000340748		993	Att/Gtt	28/40	0.584700760235321	3	FACETS	0.962	0.904	1	0.481	0.452	0.511	CLONAL	1	TRUE	1	0.584700760235321	3		497	1356	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031532	11031532	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1573	385	769	0	ENST00000327064.4:c.1451del	p.Pro484HisfsTer37	p.P484Hfs*37	ENST00000327064	NM_199141.1	483	Ccc/cc	13/16	0.584700760235321	3	FACETS	0.869	0.823	0.917	0.435	0.411	0.459	CLONAL	1	TRUE	1	0.584700760235321	3		769	1958	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098591	11098591	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854197	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	599	556	0	ENST00000358026.2:c.1109G>A	p.Arg370His	p.R370H	ENST00000358026	NM_001128849.1	370	cGc/cAc	6/36	0.584700760235321	3	FACETS	0.944	0.91	0.979	0.944	0.91	0.979	CLONAL	2	TRUE	1	0.584700760235321	3		556	1402	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18960950	18960950	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1635	145	652	0	ENST00000262803.5:c.532del	p.Glu178ArgfsTer55	p.E178Rfs*55	ENST00000262803	NM_002911.3	176	ctG/ct	4/24	0.584700760235321	3	FACETS	0.36	0.327	0.395	0.18	0.163	0.198	SUBCLONAL	1	TRUE	1	0.584700760235321	3		652	1780	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210688	36210688	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	597	577	1	ENST00000222270.7:c.439C>T	p.Arg147Ter	p.R147*	ENST00000222270	NM_014727.1	147	Cga/Tga	3/37	0.584700760235321	3	FACETS	0.953	0.918	0.989	0.953	0.918	0.989	CLONAL	2	TRUE	1	0.584700760235321	3		578	1384	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216652	36216652	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1205441044	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1210	312	608	0	ENST00000222270.7:c.3818A>G	p.His1273Arg	p.H1273R	ENST00000222270	NM_014727.1	1273	cAt/cGt	13/37	0.584700760235321	3	FACETS	0.906	0.853	0.961	0.453	0.426	0.481	CLONAL	1	TRUE	1	0.584700760235321	3		608	1522	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223175	36223175	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1676	464	898	4	ENST00000222270.7:c.5730del	p.Arg1911AspfsTer23	p.R1911Dfs*23	ENST00000222270	NM_014727.1	1909	Ccc/cc	28/37	0.584700760235321	3	FACETS	0.958	0.912	1	0.479	0.456	0.503	CLONAL	1	TRUE	1	0.584700760235321	3		902	2140	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741981	40741981	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	828	714	0	ENST00000392038.2:c.991del	p.Val331TrpfsTer13	p.V331Wfs*13	ENST00000392038	NM_001626.4	331	Gtg/tg	11/14	0.584700760235321	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.584700760235321	3		714	1779	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902297	50902297	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	726	627	0	ENST00000440232.2:c.193del	p.Val65LeufsTer11	p.V65Lfs*11	ENST00000440232	NM_002691.3	63	gaG/ga	2/27	0.584700760235321	3	FACETS	0.974	0.941	1	0.974	0.941	1	CLONAL	2	TRUE	1	0.584700760235321	3		627	1648	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909668	50909668	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1191	327	619	0	ENST00000440232.2:c.1388T>C	p.Leu463Pro	p.L463P	ENST00000440232	NM_002691.3	463	cTg/cCg	12/27	0.584700760235321	3	FACETS	0.952	0.898	1	0.476	0.449	0.504	CLONAL	1	TRUE	1	0.584700760235321	3		619	1518	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724316	52724317	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	308	615	0	ENST00000322088.6:c.1452dup	p.Lys485GlnfsTer26	p.K485Qfs*26	ENST00000322088	NM_014225.5	483	atc/atCc	12/15	0.584700760235321	3	FACETS	0.924	0.869	0.98	0.462	0.434	0.49	CLONAL	1	TRUE	1	0.584700760235321	3		615	1474	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082313	16082314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs780080562	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	341	780	1	ENST00000281043.3:c.134dup	p.Glu47GlyfsTer8	p.E47Gfs*8	ENST00000281043	NM_005378.4	43	acc/aCcc	2/3	1	2	FACETS	0.778	0.735	0.823	0.778	0.735	0.823	SUBCLONAL	1	TRUE	1	0.584700760235321	2		781	1499	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574179	46574179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756121061	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	282	553	0	ENST00000263734.3:c.194G>A	p.Arg65Gln	p.R65Q	ENST00000263734	NM_001430.4	65	cGa/cAa	2/16	1	2	FACETS	0.949	0.893	1	0.949	0.893	1	CLONAL	1	TRUE	1	0.584700760235321	2		553	1016	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661664	227661664	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs761880048	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	200	393	5	ENST00000305123.5:c.1791del	p.His598ThrfsTer38	p.H598Tfs*38	ENST00000305123	NM_005544.2	597	ggG/gg	1/2	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.584700760235321	2		398	666	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395665	31395665	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1182001726	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	330	496	0	ENST00000328111.2:c.2518C>T	p.Arg840Ter	p.R840*	ENST00000328111	NM_006892.3	840	Cga/Tga	23/23	1	2	FACETS	0.976	0.922	1	0.976	0.922	1	CLONAL	1	TRUE	1	0.584700760235321	2		496	1157	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660196	12660196	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	292	629	0	ENST00000251849.4:c.25A>G	p.Lys9Glu	p.K9E	ENST00000251849	NM_002880.3	9	Aag/Gag	2/17	1	2	FACETS	0.894	0.841	0.948	0.894	0.841	0.948	CLONAL	1	TRUE	1	0.584700760235321	2		629	1117	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089123	37089125	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs63751247	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	207	409	0	ENST00000231790.2:c.1852_1854del	p.Lys618del	p.K618del	ENST00000231790	NM_000249.3	615	ctGAAg/ctg	16/19	1	2	FACETS	0.825	0.767	0.885	0.825	0.767	0.885	CLONAL	1	TRUE	1	0.584700760235321	2		409	858	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721499	49721500	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs1429953365	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	317	424	0	ENST00000449682.2:c.2139_2140del	p.Phe714CysfsTer?	p.F714Cfs*?	ENST00000449682	NM_020998.3	713	gtGTtt/gttt	18/18	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.584700760235321	2		424	969	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643687	52643687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	209	538	0	ENST00000394830.3:c.2209A>G	p.Thr737Ala	p.T737A	ENST00000394830	NM_018313.4	737	Aca/Gca	17/30	1	2	FACETS	0.825	0.767	0.884	0.825	0.767	0.884	CLONAL	1	TRUE	1	0.584700760235321	2		538	867	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204992	128204992	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	193	428	0	ENST00000341105.2:c.449del	p.Gly150GlufsTer68	p.G150Efs*68	ENST00000341105	NM_032638.4	150	gGa/ga	3/6	1	2	FACETS	0.898	0.833	0.965	0.898	0.833	0.965	CLONAL	1	TRUE	1	0.584700760235321	2		428	735	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665143	138665143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1266774038	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	338	585	4	ENST00000330315.3:c.422G>A	p.Gly141Asp	p.G141D	ENST00000330315	NM_023067.3	141	gGc/gAc	1/1	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.584700760235321	2		589	1095	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	226	444	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.931	0.87	0.995	0.931	0.87	0.995	CLONAL	1	TRUE	1	0.584700760235321	2		444	830	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143043368	143043368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1290824576	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	285	524	1	ENST00000262992.4:c.2048C>T	p.Ala683Val	p.A683V	ENST00000262992	NM_001101669.1	683	gCc/gTc	19/24	1	2	FACETS	0.965	0.908	1	0.965	0.908	1	CLONAL	1	TRUE	1	0.584700760235321	2		525	1010	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045802	143045802	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766650822	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	298	530	0	ENST00000262992.4:c.1832C>T	p.Ala611Val	p.A611V	ENST00000262992	NM_001101669.1	611	gCg/gTg	17/24	1	2	FACETS	0.825	0.776	0.875	0.825	0.776	0.875	CLONAL	1	TRUE	1	0.584700760235321	2		530	1236	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549364	187549364	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs111886222	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	408	646	1	ENST00000441802.2:c.4754C>T	p.Thr1585Met	p.T1585M	ENST00000441802	NM_005245.3	1585	aCg/aTg	9/27	1	2	FACETS	0.959	0.912	1	0.959	0.912	1	CLONAL	1	TRUE	1	0.584700760235321	2		647	1455	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31401598	31401598	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	298	699	0	ENST00000344624.3:c.4066A>G	p.Arg1356Gly	p.R1356G	ENST00000344624		1356	Agg/Ggg	33/33	1	2	FACETS	0.838	0.788	0.888	0.838	0.788	0.888	CLONAL	1	TRUE	1	0.584700760235321	2		699	1217	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	605	778	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.803	0.775	0.832	1	0.997	1	CLONAL	2	TRUE	1	0.584700760235321	2		782	1288	SUCCESS
APC	324	MSKCC	GRCh37	5	112174437	112174437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs876658667	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	205	491	0	ENST00000257430.4:c.3146G>A	p.Trp1049Ter	p.W1049*	ENST00000257430	NM_000038.5	1049	tGg/tAg	16/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.584700760235321	2		491	687	SUCCESS
APC	324	MSKCC	GRCh37	5	112178033	112178033	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs773874693	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	300	592	5	ENST00000257430.4:c.6747del	p.Gly2250AlafsTer29	p.G2250Afs*29	ENST00000257430	NM_000038.5	2248	Aaa/aa	16/16	1	2	FACETS	0.9	0.848	0.954	0.9	0.848	0.954	CLONAL	1	TRUE	1	0.584700760235321	2		597	1140	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047659	180047659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1006377301	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	603	611	3	ENST00000261937.6:c.2356G>A	p.Ala786Thr	p.A786T	ENST00000261937	NM_182925.4	786	Gct/Act	16/30	0.258285749700238	3	FACETS	0.829	0.798	0.861			1	INDETERMINATE	2	TRUE	NA	0.584700760235321	3		614	1607	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402537	20402537	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	196	416	0	ENST00000346618.3:c.74T>C	p.Val25Ala	p.V25A	ENST00000346618	NM_001949.4	25	gTc/gCc	1/7	1	2	FACETS	0.883	0.82	0.949	0.883	0.82	0.949	CLONAL	1	TRUE	1	0.584700760235321	2		416	759	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402834	20402839	+	inframe_deletion	In_Frame_Del	DEL	GCGGCG	GCGGCG	-	rs746263274	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	23	54	0	ENST00000346618.3:c.382_387del	p.Gly128_Gly129del	p.G128_G129del	ENST00000346618	NM_001949.4	124	aGCGGCGgc/agc	1/7	1	2	FACETS	0.915	0.731	1	0.915	0.731	1	CLONAL	1	TRUE	1	0.584700760235321	2		54	86	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197084	26197084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866960721	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	167	302	0	ENST00000356476.2:c.395G>A	p.Arg132His	p.R132H	ENST00000356476		132	cGt/cAt	1/1	1	2	FACETS	0.877	0.809	0.948	0.877	0.809	0.948	CLONAL	1	TRUE	1	0.584700760235321	2		302	651	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790908	89790910	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs746966684	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	216	438	0	ENST00000336032.3:c.301_303del	p.Lys101del	p.K101del	ENST00000336032	NM_006813.2	99	AAG/-	1/2	1	2	FACETS	0.869	0.81	0.931	0.869	0.81	0.931	CLONAL	1	TRUE	1	0.584700760235321	2		438	850	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708118	117708118	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	178	664	0	ENST00000368508.3:c.2059T>C	p.Trp687Arg	p.W687R	ENST00000368508	NM_002944.2	687	Tgg/Cgg	14/43	1	2	FACETS	0.61	0.562	0.66	0.61	0.562	0.66	SUBCLONAL	1	TRUE	1	0.584700760235321	2		664	998	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714409	117714409	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	273	481	0	ENST00000368508.3:c.1240del	p.Ile414LeufsTer14	p.I414Lfs*14	ENST00000368508	NM_002944.2	414	Att/tt	11/43	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.584700760235321	2		481	820	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004721	150004721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1034620976	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	241	463	1	ENST00000253339.5:c.1504C>T	p.Arg502Cys	p.R502C	ENST00000253339		502	Cgt/Tgt	3/7	1	2	FACETS	0.951	0.89	1	0.951	0.89	1	CLONAL	1	TRUE	1	0.584700760235321	2		464	867	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265525	152265525	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs749411323	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	154	536	0	ENST00000206249.3:c.978A>G	p.Ile326Met	p.I326M	ENST00000206249	NM_000125.3	326	atA/atG	4/8	1	2	FACETS	0.561	0.513	0.611	0.561	0.513	0.611	SUBCLONAL	1	TRUE	1	0.584700760235321	2		536	939	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099424	157099426	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	rs754060642	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	62	272	0	ENST00000346085.5:c.363_365del	p.Gln131del	p.Q131del	ENST00000346085	NM_020732.3	121	CAA/-	1/20	1	2	FACETS	0.37	0.32	0.425	0.37	0.32	0.425	SUBCLONAL	1	TRUE	1	0.584700760235321	2		272	573	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2969661	2969661	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112690795	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	296	508	0	ENST00000396946.4:c.1618G>A	p.Gly540Arg	p.G540R	ENST00000396946	NM_032415.4	540	Gga/Aga	12/25	1	2	FACETS	0.972	0.916	1	0.972	0.916	1	CLONAL	1	TRUE	1	0.584700760235321	2		508	1042	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843242	128843242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs912880810	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	261	529	0	ENST00000249373.3:c.349C>T	p.Arg117Cys	p.R117C	ENST00000249373	NM_005631.4	117	Cgc/Tgc	2/12	1	2	FACETS	0.914	0.857	0.972	0.914	0.857	0.972	CLONAL	1	TRUE	1	0.584700760235321	2		529	977	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878109	151878109	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	213	374	0	ENST00000262189.6:c.6836del	p.Pro2279LeufsTer26	p.P2279Lfs*26	ENST00000262189	NM_170606.2	2279	cCt/ct	36/59	1	2	FACETS	0.94	0.876	1	0.94	0.876	1	CLONAL	1	TRUE	1	0.584700760235321	2		374	775	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020342	69020342	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	378	439	0	ENST00000288368.4:c.2716-2A>C		p.X906_splice	ENST00000288368	NM_024870.2	906			0.584700760235321	3	FACETS	1	0.995	1	0.739	0.703	0.777	CLONAL	1	TRUE	1	0.584700760235321	3		439	1130	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993676	90993676	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1288	257	608	3	ENST00000265433.3:c.247del	p.Met83CysfsTer9	p.M83Cfs*9	ENST00000265433	NM_002485.4	83	Atg/tg	3/16	0.584700760235321	3	FACETS	0.735	0.686	0.786	0.368	0.343	0.393	SUBCLONAL	1	TRUE	1	0.584700760235321	3		611	1545	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882049	36882050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs780753361	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	250	672	2	ENST00000358127.4:c.963dup	p.Ala322ArgfsTer19	p.A322Rfs*19	ENST00000358127	NM_001280556.1	321	-/C	8/10	1	2	FACETS	0.596	0.555	0.637	0.596	0.555	0.637	SUBCLONAL	1	TRUE	1	0.584700760235321	2		674	1436	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250135	110250136	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	263	518	0	ENST00000374672.4:c.539dup	p.Pro181SerfsTer76	p.P181Sfs*76	ENST00000374672	NM_004235.4	180	cct/ccCt	3/5	1	2	FACETS	0.986	0.926	1	0.986	0.926	1	CLONAL	1	TRUE	1	0.584700760235321	2		518	912	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391832	139391832	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766836819	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	565	524	0	ENST00000277541.6:c.6359G>A	p.Arg2120His	p.R2120H	ENST00000277541	NM_017617.3	2120	cGc/cAc	34/34	0.571205848081875	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.584700760235321	3		524	1246	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400029	139400029	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs778742968	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	290	515	0	ENST00000277541.6:c.4319T>C	p.Ile1440Thr	p.I1440T	ENST00000277541	NM_017617.3	1440	aTc/aCc	25/34	0.571205848081875	3	FACETS	0.895	0.84	0.951	0.447	0.42	0.476	CLONAL	1	TRUE	1	0.584700760235321	3		515	1433	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	318	561	2	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	0.571205848081875	3	FACETS	0.987	0.93	1	0.494	0.465	0.523	CLONAL	1	TRUE	1	0.584700760235321	3		563	1424	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	310	259	2	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	0.584700760235321	1		261	587	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0017300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	276	446	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.22127090702924	1	FACETS	0.703	0.662	0.744	0.703	0.662	0.744	INDETERMINATE	1	TRUE	0	0.65899675580978	1		446	799	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913400	NA	P-0017300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	242	319	0	ENST00000349496.5:c.98C>A	p.Ser33Tyr	p.S33Y	ENST00000349496	NM_001904.3	33	tCt/tAt	3/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.65899675580978	2		319	675	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0017300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	301	570	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.878	0.827	0.929	0.878	0.827	0.929	CLONAL	1	TRUE	1	0.65899675580978	2		570	1041	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	312	680	0	ENST00000227507.2:c.859C>T	p.Pro287Ser	p.P287S	ENST00000227507	NM_053056.2	287	Ccc/Tcc	5/5	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.65899675580978	2		680	904	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	197	407	1	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.902	0.839	0.967	0.902	0.839	0.967	CLONAL	1	TRUE	1	0.65899675580978	2		408	663	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0017300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	291	440	7	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	0.991	0.935	1	0.991	0.935	1	CLONAL	1	TRUE	1	0.65899675580978	2		447	891	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831357	72831358	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTG	rs34918837	NA	P-0017300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	86	243	3	ENST00000268489.5:c.5221_5223dup	p.Gln1741dup	p.Q1741dup	ENST00000268489	NM_006885.3	1741	-/CAA	9/10	1	2	FACETS	0.574	0.509	0.642	0.574	0.509	0.642	SUBCLONAL	1	TRUE	1	0.65899675580978	2		246	455	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720803	89720804	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs786204892	NA	P-0017300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	74	256	0	ENST00000371953.3:c.955dup	p.Thr319AsnfsTer6	p.T319Nfs*6	ENST00000371953	NM_000314.4	318	-/A	8/9	1	2	FACETS	0.55	0.484	0.621	0.55	0.484	0.621	SUBCLONAL	1	TRUE	1	0.65899675580978	2		256	408	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774681	73774682	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0017300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	44	99	0	ENST00000254810.4:c.405_406del	p.Arg135SerfsTer12	p.R135Sfs*12	ENST00000254810	NM_005324.3	135	agAGct/agct	4/4	1	2	FACETS	0.568	0.481	0.663	0.568	0.481	0.663	SUBCLONAL	1	TRUE	1	0.65899675580978	2		99	235	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952088	178952088	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553826184	NA	P-0017300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	363	550	0	ENST00000263967.3:c.3143A>G	p.His1048Arg	p.H1048R	ENST00000263967	NM_006218.2	1048	cAt/cGt	21/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.65899675580978	2		550	1063	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088659	27088659	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	488	817	2	ENST00000324856.7:c.2272del	p.Gln758ArgfsTer75	p.Q758Rfs*75	ENST00000324856	NM_006015.4	756	aaC/aa	7/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.65899675580978	2		819	1477	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107008	27107008	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	254	453	0	ENST00000324856.7:c.6619C>T	p.Gln2207Ter	p.Q2207*	ENST00000324856	NM_006015.4	2207	Cag/Tag	20/20	1	2	FACETS	0.965	0.906	1	0.965	0.906	1	CLONAL	1	TRUE	1	0.65899675580978	2		453	799	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822586	72822586	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	208	404	1	ENST00000268489.5:c.9589del	p.Gln3197SerfsTer44	p.Q3197Sfs*44	ENST00000268489	NM_006885.3	3197	Cag/ag	10/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.65899675580978	2		405	577	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402421	139402421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754815022	NA	P-0017300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	404	673	2	ENST00000277541.6:c.3496G>A	p.Gly1166Ser	p.G1166S	ENST00000277541	NM_017617.3	1166	Ggc/Agc	21/34	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.65899675580978	2		675	1012	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213961	2213961	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs753146456	NA	P-0017300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	382	747	2	ENST00000326181.6:c.45del	p.Ser17AlafsTer111	p.S17Afs*111	ENST00000326181	NM_032271.2	14	Ggg/gg	2/21	0.22127090702924	1	FACETS	0.714	0.679	0.749	0.714	0.679	0.749	INDETERMINATE	1	TRUE	0	0.65899675580978	1		749	1089	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798461	45798461	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779997419	NA	P-0017300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	454	705	1	ENST00000450313.1:c.550C>T	p.Arg184Trp	p.R184W	ENST00000450313	NM_012222.2	184	Cgg/Tgg	7/16	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.65899675580978	2		706	1212	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78435627	78435627	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs759271820	NA	P-0017300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	460	748	0	ENST00000370768.2:c.193del	p.Arg65AspfsTer3	p.R65Dfs*3	ENST00000370768	NM_003902.3	65	Aga/ga	2/20	1	2	FACETS	0.938	0.895	0.982	0.938	0.895	0.982	CLONAL	1	TRUE	1	0.65899675580978	2		748	1488	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246518381	246518381	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1202	362	544	0	ENST00000388985.4:c.180G>A	p.Met60Ile	p.M60I	ENST00000388985		60	atG/atA	2/12	0.617388561059212	3	FACETS	0.934	0.883	0.986	0.467	0.441	0.493	CLONAL	1	TRUE	1	0.65899675580978	3		544	1564	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692927	89692953	+	inframe_deletion	In_Frame_Del	DEL	ATATTTATTACATCGGGGCAAATTTTT	ATATTTATTACATCGGGGCAAATTTTT	-	novel	NA	P-0017300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	301	571	0	ENST00000371953.3:c.412_438del	p.Tyr138_Leu146del	p.Y138_L146del	ENST00000371953	NM_000314.4	137	gcATATTTATTACATCGGGGCAAATTTTTa/gca	5/9	1	2	FACETS	0.811	0.764	0.859	0.811	0.764	0.859	CLONAL	1	TRUE	1	0.65899675580978	2		571	1127	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865076	57865076	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462976482	NA	P-0017300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	500	907	3	ENST00000228682.2:c.2557del	p.Gln853SerfsTer93	p.Q853Sfs*93	ENST00000228682	NM_005269.2	851	taC/ta	12/12	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.65899675580978	2		910	1476	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865760	57865761	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1488325542	NA	P-0017300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	367	738	0	ENST00000228682.2:c.3243dup	p.Asn1082GlnfsTer24	p.N1082Qfs*24	ENST00000228682	NM_005269.2	1079	-/C	12/12	1	2	FACETS	0.974	0.925	1	0.974	0.925	1	CLONAL	1	TRUE	1	0.65899675580978	2		738	1143	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976226	7976228	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-	novel	NA	P-0017300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	201	400	0	ENST00000319144.4:c.1967_1969del	p.Glu656del	p.E656del	ENST00000319144	NM_001139.2	656	gAGGcc/gcc	15/15	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.65899675580978	2		400	603	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044498	12044498	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs889363169	NA	P-0017300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	280	496	0	ENST00000353533.5:c.1121C>T	p.Ala374Val	p.A374V	ENST00000353533	NM_003010.3	374	gCc/gTc	11/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.65899675580978	2		496	804	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880240	37880240	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	467	780	0	ENST00000269571.5:c.2284A>C	p.Lys762Gln	p.K762Q	ENST00000269571		762	Aaa/Caa	19/27	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.65899675580978	2		780	1316	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288814	15288814	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	86	111	0	ENST00000263388.2:c.3925del	p.Arg1309AlafsTer111	p.R1309Afs*111	ENST00000263388	NM_000435.2	1309	Cgc/gc	24/33	0.22127090702924	1	FACETS	0.774	0.698	0.853	0.774	0.698	0.853	INDETERMINATE	1	TRUE	0	0.65899675580978	1		111	226	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214398	36214398	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs868041281	NA	P-0017300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	331	768	3	ENST00000222270.7:c.3057del	p.Gly1020AlafsTer4	p.G1020Afs*4	ENST00000222270	NM_014727.1	1018	Aaa/aa	7/37	0.22127090702924	1	FACETS	0.523	0.494	0.553	0.523	0.494	0.553	INDETERMINATE	1	TRUE	0	0.65899675580978	1		771	1287	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40761117	40761117	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	346	630	1	ENST00000392038.2:c.235C>T	p.Gln79Ter	p.Q79*	ENST00000392038	NM_001626.4	79	Cag/Tag	4/14	0.22127090702924	1	FACETS	0.698	0.662	0.735	0.698	0.662	0.735	INDETERMINATE	1	TRUE	0	0.65899675580978	1		631	1008	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526285	31526285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201151813	NA	P-0017300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	454	808	2	ENST00000344624.3:c.755G>A	p.Arg252Gln	p.R252Q	ENST00000344624		252	cGa/cAa	2/33	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.65899675580978	2		810	1299	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591177	67591281	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TACATGAATAATTGGTGATTGCTACAATTCAGGATGAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGGTTGACTCAAAAAGGTGTTCGGCAAAAGAAG	TACATGAATAATTGGTGATTGCTACAATTCAGGATGAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGGTTGACTCAAAAAGGTGTTCGGCAAAAGAAG	-	novel	NA	P-0017300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	210	386	0	ENST00000274335.5:c.1745+26_1780del		p.X582_splice	ENST00000274335		582		13/15	1	2	FACETS	0.878	0.818	0.939	0.878	0.818	0.939	CLONAL	1	TRUE	1	0.65899675580978	2		386	726	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055948	180055948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1309857166	NA	P-0017300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	349	760	0	ENST00000261937.6:c.1037C>T	p.Thr346Met	p.T346M	ENST00000261937	NM_182925.4	346	aCg/aTg	8/30	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.65899675580978	2		760	979	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129501	152129501	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0017300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	33	121	0	ENST00000206249.3:c.452+2T>C		p.X151_splice	ENST00000206249	NM_000125.3	151			1	2	FACETS	0.622	0.513	0.741	0.622	0.513	0.741	SUBCLONAL	1	TRUE	1	0.65899675580978	2		121	161	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100396	157100397	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0017300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	41	111	0	ENST00000346085.5:c.1334dup	p.Pro446AlafsTer89	p.P446Afs*89	ENST00000346085	NM_020732.3	445	gcg/gCcg	1/20	1	2	FACETS	0.604	0.508	0.708	0.604	0.508	0.708	SUBCLONAL	1	TRUE	1	0.65899675580978	2		111	206	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	130	301	4				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.908	0.835	0.983	0.908	0.835	0.983	CLONAL	1	TRUE	1	0.84225448007877	2		305	340	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0017301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	157	195	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.951	0.882	1	0.951	0.882	1	CLONAL	1	TRUE	1	0.84225448007877	2		195	392	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791826	42791826	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	413	500	0	ENST00000575354.2:c.712T>C	p.Trp238Arg	p.W238R	ENST00000575354	NM_015125.3	238	Tgg/Cgg	5/20	0.84225448007877	1	FACETS	0.986	0.954	1	0.986	0.954	1	CLONAL	1	TRUE	0	0.84225448007877	1		500	576	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0017302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	133	230	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	1	2	FACETS	0.812	0.737	0.891	1	0.987	1	CLONAL	2	TRUE	1	0.19	2		230	862	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0017302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	40	192	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.826	0.686	0.982	0.826	0.686	0.982	CLONAL	1	TRUE	1	0.19	2		192	510	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952006	178952006	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	72	467	0	ENST00000263967.3:c.3061T>C	p.Tyr1021His	p.Y1021H	ENST00000263967	NM_006218.2	1021	Tac/Cac	21/21	1	2	FACETS	0.647	0.563	0.738	0.647	0.563	0.738	SUBCLONAL	1	TRUE	1	0.19	2		467	1171	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0017302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1239	121	492	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	0.937	0.843	1	0.937	0.843	1	CLONAL	1	TRUE	1	0.19	2		492	1360	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660553	67660553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1342	126	488	2	ENST00000264010.4:c.1453C>T	p.His485Tyr	p.H485Y	ENST00000264010	NM_006565.3	485	Cat/Tat	8/12	1	2	FACETS	0.903	0.815	0.997	0.903	0.815	0.997	CLONAL	1	TRUE	1	0.19	2		490	1468	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101685	27101686	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0017302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1483	152	531	1	ENST00000324856.7:c.4969_4970dup	p.Arg1658GlyfsTer5	p.R1658Gfs*5	ENST00000324856	NM_006015.4	1656	agg/agGAg	18/20	1	2	FACETS	0.979	0.892	1	0.979	0.892	1	CLONAL	1	TRUE	1	0.19	2		532	1635	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717739	89717740	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	114	379	0	ENST00000371953.3:c.765dup	p.Glu256ArgfsTer42	p.E256Rfs*42	ENST00000371953	NM_000314.4	255	gta/gtAa	7/9	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.19	2		379	1177	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944764	71944775	+	inframe_deletion	In_Frame_Del	DEL	ACCTCCCAGTTC	ACCTCCCAGTTC	-	novel	NA	P-0017302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1476	93	584	0	ENST00000298229.2:c.2189_2200del	p.Thr730_Phe733del	p.T730_F733del	ENST00000298229	NM_001567.3	730	ACCTCCCAGTTC/-	19/28	1	2	FACETS	0.624	0.552	0.701	0.624	0.552	0.701	SUBCLONAL	1	TRUE	1	0.19	2		584	1569	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409060	4409060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781695497	NA	P-0017302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	60	324	2	ENST00000261254.3:c.755C>T	p.Ala252Val	p.A252V	ENST00000261254	NM_001759.3	252	gCg/gTg	5/5	1	2	FACETS	0.757	0.651	0.874	0.757	0.651	0.874	SUBCLONAL	1	TRUE	1	0.19	2		326	834	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207537	29207537	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	69	344	0	ENST00000240100.2:c.259del	p.Leu87CysfsTer140	p.L87Cfs*140	ENST00000240100	NM_001394.6	87	Ctg/tg	1/4	1	2	FACETS	0.867	0.753	0.99	0.867	0.753	0.99	CLONAL	1	TRUE	1	0.19	2		344	838	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0017303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	463	543	2	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.478110588850545	3	FACETS	0.979	0.936	1	0.979	0.936	1	CLONAL	2	TRUE	1	0.478110588850545	3		545	1226	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862850	9862850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751455326	NA	P-0017303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	200	428	0	ENST00000330684.3:c.2453C>T	p.Ala818Val	p.A818V	ENST00000330684	NM_001134407.1	818	gCg/gTg	12/13	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.478110588850545	2		428	726	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0017304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	228	290	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.121764425010199	4	FACETS	0.806	0.749	0.865	0.806	0.749	0.865	INDETERMINATE	2	TRUE	2	0.257487878975401	4		290	1381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1402	262	617	1	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.160416877253426	2	FACETS	1	0.987	1	0.611	0.571	0.654	CLONAL	1	TRUE	0	0.257487878975401	2		618	1664	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604787	48604787	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	58	381	0	ENST00000342988.3:c.1609G>C	p.Asp537His	p.D537H	ENST00000342988	NM_005359.5	537	Gac/Cac	12/12	0.220568844661521	1	FACETS	0.433	0.371	0.501	0.433	0.371	0.501	SUBCLONAL	1	TRUE	0	0.257487878975401	1		381	907	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880255	37880255	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	240	519	0	ENST00000269571.5:c.2299A>T	p.Ile767Phe	p.I767F	ENST00000269571		767	Atc/Ttc	19/27	0.160416877253426	2	FACETS	1	0.988	1	0.633	0.59	0.679	CLONAL	1	TRUE	0	0.257487878975401	2		519	1472	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911550	134911550	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	177	422	1	ENST00000398015.3:c.2015T>A	p.Met672Lys	p.M672K	ENST00000398015	NM_004441.4	672	aTg/aAg	11/16	0.121764425010199	4	FACETS	1	0.984	1	0.645	0.593	0.7	INDETERMINATE	1	TRUE	2	0.257487878975401	4		423	1340	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864336	151864336	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	146	425	0	ENST00000262189.6:c.9645del	p.Lys3215AsnfsTer34	p.K3215Nfs*34	ENST00000262189	NM_170606.2	3215	aaA/aa	42/59	0.257487878975401	1	FACETS	0.893	0.814	0.977	0.893	0.814	0.977	CLONAL	1	TRUE	0	0.257487878975401	1		425	1106	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400040	49400040	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	474	402	2	ENST00000418115.1:c.297G>T	p.Trp99Cys	p.W99C	ENST00000418115	NM_001664.2	99	tgG/tgT	4/5	0.894272965393807	3	FACETS	1	0.996	1	0.464	0.444	0.483	CLONAL	1	FALSE	0	0.894272965393807	3		404	1103	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123156380	123156380	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0017305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	67	100	0	ENST00000218089.9:c.-97-1G>A		p.X33_splice	ENST00000218089	NM_001042749.1	33			0.894272965393807	3	FACETS	1	0.923	1	0.353	0.311	0.395	CLONAL	1	FALSE	0	0.894272965393807	3		100	205	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0017307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	1146	708	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.674643031472268	2	FACETS		NA	1	1	0.999	1	NA	3	TRUE	0	0.674643031472268	2		708	1288	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0017307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	301	195	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.674643031472268	2		195	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0017308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	297	457	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	NA	2	FACETS	0.872	0.824	0.921			1	INDETERMINATE	2	TRUE	NA	0.404314057810417	2		457	842	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450300	50450300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	148	408	0	ENST00000331340.3:c.484C>T	p.Arg162Trp	p.R162W	ENST00000331340	NM_006060.4	162	Cgg/Tgg	5/8	0.404314057810417	3	FACETS	0.851	0.776	0.93	0.426	0.388	0.465	CLONAL	1	TRUE	1	0.404314057810417	3		408	1034	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783245	9783245	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756497515	NA	P-0017308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	261	553	0	ENST00000377346.4:c.2489G>A	p.Arg830His	p.R830H	ENST00000377346	NM_005026.3	830	cGt/cAt	20/24	0.373554055876177	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.404314057810417	1		553	929	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213950	2213950	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	92	528	0	ENST00000326181.6:c.29A>T	p.Asn10Ile	p.N10I	ENST00000326181	NM_032271.2	10	aAc/aTc	2/21	1	2	FACETS	0.418	0.37	0.469	0.418	0.37	0.469	SUBCLONAL	1	TRUE	1	0.404314057810417	2		528	1090	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556250	29556250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199474739	NA	P-0017308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	84	308	1	ENST00000356175.3:c.2617C>T	p.Arg873Cys	p.R873C	ENST00000356175	NM_000267.3	873	Cgt/Tgt	21/57	0.209092566468316	5	FACETS	0.701	0.618	0.791	0.234	0.206	0.264	INDETERMINATE	1	TRUE	2	0.404314057810417	5		309	952	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156541	55156541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368266633	NA	P-0017308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	193	460	1	ENST00000257290.5:c.2942G>A	p.Arg981His	p.R981H	ENST00000257290	NM_006206.4	981	cGt/cAt	22/23	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.404314057810417	2		461	954	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295425	1295425	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0017308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	44	52	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.777	0.666	0.895	1	0.966	1	SUBCLONAL	2	TRUE	1	0.404314057810417	2		53	140	SUCCESS
APC	324	MSKCC	GRCh37	5	112137018	112137018	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	177	488	0	ENST00000257430.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000257430	NM_000038.5	258	Gag/Tag	8/16	1	2	FACETS	0.821	0.756	0.89	0.821	0.756	0.89	CLONAL	1	TRUE	1	0.404314057810417	2		488	1066	SUCCESS
APC	324	MSKCC	GRCh37	5	112175581	112175582	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATGCCACCAAGCAG	novel	NA	P-0017308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	115	469	0	ENST00000257430.4:c.4292_4305dup	p.Ser1436CysfsTer42	p.S1436Cfs*42	ENST00000257430	NM_000038.5	1430	-/ATGCCACCAAGCAG	16/16	1	2	FACETS	0.585	0.526	0.648	0.585	0.526	0.648	SUBCLONAL	1	TRUE	1	0.404314057810417	2		469	972	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640896	3640920	+	frameshift_variant	Frame_Shift_Del	DEL	CATCTCTTCCTGGCTCCAACGGCTC	CATCTCTTCCTGGCTCCAACGGCTC	-	novel	NA	P-0017310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	387	567	0	ENST00000294008.3:c.2719_2743del	p.Glu907ArgfsTer86	p.E907Rfs*86	ENST00000294008	NM_032444.2	907	GAGCCGTTGGAGCCAGGAAGAGATGag/ag	12/15	0.359360133489507	4	FACETS	0.925	0.877	0.974			1	CLONAL	2	TRUE	NA	0.359360133489507	4		567	1583	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217695	7217695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	285	376	0	ENST00000380728.2:c.232G>A	p.Ala78Thr	p.A78T	ENST00000380728		78	Gct/Act	4/11	0.357536156482963	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.359360133489507	2		376	779	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-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	259	581	1	ENST00000269305.4:c.560-22_595del		p.X187_splice	ENST00000269305	NM_001126112.2	187		6/11	0.357536156482963	2	FACETS	0.763	0.716	0.812	0.763	0.716	0.812	SUBCLONAL	2	TRUE	0	0.359360133489507	2		582	944	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856064	68856081	+	frameshift_variant	Frame_Shift_Del	DEL	TCCCTTCACAGCAGAACT	TCCCTTCACAGCAGAACT	CC	novel	NA	P-0017310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	486	559	0	ENST00000261769.5:c.1872_1889delinsCC	p.Pro625GlnfsTer23	p.P625Qfs*23	ENST00000261769	NM_004360.3	624	tcTCCCTTCACAGCAGAACTa/tcCCa	12/16	0.359360133489507	3	FACETS	1	0.994	1	0.811	0.777	0.846	CLONAL	2	TRUE	0	0.359360133489507	3		559	1311	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573998	7573999	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0017311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	322	593	0	ENST00000269305.4:c.1028_1029del	p.Glu343AlafsTer3	p.E343Afs*3	ENST00000269305	NM_001126112.2	343	gAG/g	10/11	0.495875430881564	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.495875430881564	1		593	814	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41201213	41201213	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397509264	NA	P-0017311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	483	541	1	ENST00000357654.3:c.5333-2A>G		p.X1778_splice	ENST00000357654	NM_007294.3	1778			0.495875430881564	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.495875430881564	2		542	919	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462032	120462032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201996575	NA	P-0017312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	143	321	1	ENST00000256646.2:c.5684G>A	p.Arg1895His	p.R1895H	ENST00000256646	NM_024408.3	1895	cGt/cAt	31/34	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.40645019369541	2		322	625	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0017313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	458	644	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.313892139729372	2	FACETS	0.879	0.842	0.916	0.879	0.842	0.916	CLONAL	2	TRUE	0	0.493529486666846	2		644	1056	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655272	45655272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764295138	NA	P-0017313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	111	615	1	ENST00000407780.3:c.580C>T	p.Arg194Trp	p.R194W	ENST00000407780	NM_001283052.1	194	Cgg/Tgg	4/7	NA	2	FACETS	0.357	0.319	0.397			1	INDETERMINATE	1	TRUE	NA	0.493529486666846	2		616	1261	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912478	32912478	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	44	521	0	ENST00000380152.3:c.3986G>C	p.Arg1329Thr	p.R1329T	ENST00000380152		1329	aGa/aCa	11/27	0.286234274364807	4	FACETS	0.538	0.451	0.634	0.269	0.225	0.317	INDETERMINATE	1	TRUE	2	0.493529486666846	4		521	495	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740824	145740824	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	169	541	0	ENST00000428558.2:c.1276G>C	p.Asp426His	p.D426H	ENST00000428558	NM_004260.3	426	Gat/Cat	7/22	1	2	FACETS	0.876	0.806	0.948	0.876	0.806	0.948	CLONAL	1	TRUE	1	0.493529486666846	2		541	782	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0017314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	1265	448	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.561326767067139	8	FACETS	1	0.995	1	1	0.995	1	CLONAL	6	TRUE	2	0.561326767067139	8		448	1926	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0017314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	307	437	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.541737109429658	2	FACETS	0.878	0.835	0.92	0.878	0.835	0.92	CLONAL	2	TRUE	0	0.561326767067139	2		437	623	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6414399	6414399	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	154	219	0	ENST00000356142.4:c.33C>G	p.Asp11Glu	p.D11E	ENST00000356142	NM_018890.3	11	gaC/gaG	1/7	0.561963219408741	3	FACETS	0.874	0.809	0.94	0.874	0.809	0.94	CLONAL	2	TRUE	1	0.561326767067139	3		219	402	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569955	95569955	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763425076	NA	P-0017314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	85	344	0	ENST00000393063.1:c.3778G>A	p.Val1260Ile	p.V1260I	ENST00000393063	NM_030621.3	1260	Gta/Ata	22/28	0.138892790701097	3	FACETS	0.735	0.651	0.824	0.245	0.217	0.275	INDETERMINATE	1	TRUE	0	0.561326767067139	3		344	528	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715657	61715761	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTTAAGGCAGTAGAAGAGAAGTGGTTTGTTTATACTGCATTGTGTAAGAAATCAGAATCACCTACCATTAGCTTGGATAGCTGCAGAAATATTTTCACTGAGGC	ACTTAAGGCAGTAGAAGAGAAGTGGTTTGTTTATACTGCATTGTGTAAGAAATCAGAATCACCTACCATTAGCTTGGATAGCTGCAGAAATATTTTCACTGAGGC	-	novel	NA	P-0017314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	15	98	0	ENST00000401558.2:c.2168_2206+66del		p.X723_splice	ENST00000401558	NM_003400.3	723		18/25	0.305076354171483	5	FACETS	0.467	0.342	0.616	0.156	0.114	0.206	INDETERMINATE	1	TRUE	2	0.561326767067139	5		98	211	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0017315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	119	421	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	NA	2	FACETS	0.69	0.624	0.76			1	INDETERMINATE	1	TRUE	NA	0.514651203769823	2		421	670	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0017315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	182	525	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.931	0.861	1	0.931	0.861	1	CLONAL	1	TRUE	1	0.514651203769823	2		525	760	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0017315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	287	525	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.514651203769823	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.514651203769823	1		525	765	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739911	41739911	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	379	334	0	ENST00000242208.4:c.62C>T	p.Ser21Phe	p.S21F	ENST00000242208	NM_002192.2	21	tCc/tTc	2/3	0.514651203769823	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.514651203769823	3		334	833	SUCCESS
FH	2271	MSKCC	GRCh37	1	241665762	241665762	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	221	409	0	ENST00000366560.3:c.1217A>G	p.Asn406Ser	p.N406S	ENST00000366560	NM_000143.3	406	aAt/aGt	8/10	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.514651203769823	2		409	842	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40468891	40468891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	35	286	1	ENST00000264657.5:c.2173C>A	p.Pro725Thr	p.P725T	ENST00000264657	NM_139276.2	725	Ccg/Acg	23/24	1	2	FACETS	0.209	0.171	0.253	0.209	0.171	0.253	SUBCLONAL	1	TRUE	1	0.514651203769823	2		287	650	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0017316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	220	795	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.264667220395354	2	FACETS	0.935	0.872	1	0.935	0.872	1	CLONAL	2	TRUE	0	0.265460708688694	2		796	886	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750269	133750269	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	34	471	0	ENST00000318560.5:c.1100G>A	p.Arg367Gln	p.R367Q	ENST00000318560	NM_005157.4	367	cGa/cAa	7/11	0.264667220395354	2	FACETS	0.4	0.325	0.484	0.2	0.162	0.242	SUBCLONAL	1	TRUE	0	0.265460708688694	2		471	641	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154243	2154243	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs11545014	NA	P-0017316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	236	457	0	ENST00000434045.2:c.685C>G	p.Pro229Ala	p.P229A	ENST00000434045	NM_001127598.1	229	Cca/Gca	5/5	NA	2	FACETS	0.923	0.867	0.98			1	INDETERMINATE	3	TRUE	NA	0.265460708688694	2		457	642	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527392	41527392	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	186	518	2	ENST00000263253.7:c.1283C>T	p.Pro428Leu	p.P428L	ENST00000263253	NM_001429.3	428	cCa/cTa	6/31	NA	2	FACETS	0.997	0.924	1			1	INDETERMINATE	2	TRUE	NA	0.265460708688694	2		520	703	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681543	117681559	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCCCTTAGATGTAAA	GGCCCCTTAGATGTAAA	-	novel	NA	P-0017316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	135	556	0	ENST00000368508.3:c.3391_3407del	p.Phe1131ArgfsTer5	p.F1131Rfs*5	ENST00000368508	NM_002944.2	1131	TTTACATCTAAGGGGCCa/a	22/43	0.265460708688694	4	FACETS	0.848	0.771	0.928	0.565	0.514	0.619	CLONAL	2	TRUE	1	0.265460708688694	4		556	759	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016264	150016264	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs761339008	NA	P-0017316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	159	505	0	ENST00000253339.5:c.442C>G	p.Arg148Gly	p.R148G	ENST00000253339		148	Cga/Gga	2/7	0.265460708688694	6	FACETS	0.887	0.812	0.965			1	CLONAL	2	TRUE	NA	0.265460708688694	6		505	1034	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134744	41134744	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	278	282	0	ENST00000379561.5:c.884G>A	p.Trp295Ter	p.W295*	ENST00000379561	NM_002015.3	295	tGg/tAg	2/3	0.797679944115527	1	FACETS	0.993	0.951	1	0.993	0.951	1	CLONAL	1	TRUE	0	0.797679944115527	1		282	422	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914168	32914404	+	inframe_deletion	In_Frame_Del	DEL	TTGTTACGAGGCATTGGATGATTCAGAGGATATTCTTCATAACTCTCTAGATAATGATGAATGTAGCACGCATTCACATAAGGTTTTTGCTGACATTCAGAGTGAAGAAATTTTACAACATAACCAAAATATGTCTGGATTGGAGAAAGTTTCTAAAATATCACCTTGTGATGTTAGTTTGGAAACTTCAGATATATGTAAATGTAGTATAGGGAAGCTTCATAAGTCAGTCTCATC	TTGTTACGAGGCATTGGATGATTCAGAGGATATTCTTCATAACTCTCTAGATAATGATGAATGTAGCACGCATTCACATAAGGTTTTTGCTGACATTCAGAGTGAAGAAATTTTACAACATAACCAAAATATGTCTGGATTGGAGAAAGTTTCTAAAATATCACCTTGTGATGTTAGTTTGGAAACTTCAGATATATGTAAATGTAGTATAGGGAAGCTTCATAAGTCAGTCTCATC	-	novel	NA	P-0017317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	449	512	0	ENST00000380152.3:c.5677_5913del	p.Cys1893_Ser1971del	p.C1893_S1971del	ENST00000380152		1892	ggTTGTTACGAGGCATTGGATGATTCAGAGGATATTCTTCATAACTCTCTAGATAATGATGAATGTAGCACGCATTCACATAAGGTTTTTGCTGACATTCAGAGTGAAGAAATTTTACAACATAACCAAAATATGTCTGGATTGGAGAAAGTTTCTAAAATATCACCTTGTGATGTTAGTTTGGAAACTTCAGATATATGTAAATGTAGTATAGGGAAGCTTCATAAGTCAGTCTCATCt/ggt	11/27	0.797679944115527	1	FACETS	0.935	0.902	0.967	0.935	0.902	0.967	CLONAL	1	TRUE	0	0.797679944115527	1		512	724	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849335	68849631	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGCAACAGTTAAGGATTTAATTTTATTTTTACTAACACAAAATGTTTCGTTTTGTTTTTAACTTCATTGTTTCTGCTCTCTAGGGCTTGGATTTTGAGGCCAAGCAGCAGTACATTCTACACGTAGCAGTGACGAATGTGGTACCTTTTGAGGTCTCTCTCACCACCTCCACAGCCACCGTCACCGTGGATGTGCTGGATGTGAATGAAGCCCCCATCTTTGTGCCTCCTGAAAAGAGAGTGGAAGTGTCCGAGGACTTTGGCGTGGGCCAGGAAATCACATCCTACACTGCCCAGG	AGCAACAGTTAAGGATTTAATTTTATTTTTACTAACACAAAATGTTTCGTTTTGTTTTTAACTTCATTGTTTCTGCTCTCTAGGGCTTGGATTTTGAGGCCAAGCAGCAGTACATTCTACACGTAGCAGTGACGAATGTGGTACCTTTTGAGGTCTCTCTCACCACCTCCACAGCCACCGTCACCGTGGATGTGCTGGATGTGAATGAAGCCCCCATCTTTGTGCCTCCTGAAAAGAGAGTGGAAGTGTCCGAGGACTTTGGCGTGGGCCAGGAAATCACATCCTACACTGCCCAGG	-	novel	NA	P-0017317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	67	82	0	ENST00000261769.5:c.1321-80_1537del		p.X441_splice	ENST00000261769	NM_004360.3	441		10/16	0.797679944115527	1	FACETS	0.863	0.781	0.944	0.863	0.781	0.944	CLONAL	1	TRUE	0	0.797679944115527	1		82	117	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38960511	38960511	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	279	261	0	ENST00000357387.3:c.1840G>C	p.Glu614Gln	p.E614Q	ENST00000357387	NM_152756.3	614	Gaa/Caa	20/38	1	2	FACETS	0.989	0.935	1	0.989	0.935	1	CLONAL	1	TRUE	1	0.797679944115527	2		261	707	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523519	106523519	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	369	336	0	ENST00000359195.3:c.2671A>T	p.Ile891Phe	p.I891F	ENST00000359195	NM_002649.2	891	Att/Ttt	8/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.797679944115527	2		336	922	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027794	152027794	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	533	514	0	ENST00000262189.6:c.281C>G	p.Ala94Gly	p.A94G	ENST00000262189	NM_170606.2	94	gCt/gGt	3/59	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.797679944115527	2		514	1287	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0017318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	294	390	2				ENST00000310581	NM_198253.2	-/1132			1				0.981	1				CLONAL	1	TRUE	1	0.784450978099167	2		392	697	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0017318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	140	220	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.784450978099167	2		220	305	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0017318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	11002	382	0	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.784450978099167	20	FACETS	1	0.999	1			1	CLONAL	19	TRUE	NA	0.784450978099167	20		382	11782	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644487	18644487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	244	392	0	ENST00000266497.5:c.2665C>T	p.His889Tyr	p.H889Y	ENST00000266497		889	Cac/Tac	18/31	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.784450978099167	2		392	544	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967494	38967494	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1180880225	NA	P-0017318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	208	335	0	ENST00000357387.3:c.1096G>C	p.Asp366His	p.D366H	ENST00000357387	NM_152756.3	366	Gat/Cat	13/38	1	2	FACETS	0.827	0.772	0.884	0.827	0.772	0.884	CLONAL	1	TRUE	1	0.784450978099167	2		335	641	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0017319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	173	374	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.296321876592628	5	FACETS	0.876	0.806	0.95	0.584	0.537	0.633	CLONAL	2	TRUE	2	0.28	5		375	1001	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28929495	NA	P-0017319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	288	423	1	ENST00000275493.2:c.2155G>T	p.Gly719Cys	p.G719C	ENST00000275493	NM_005228.3	719	Ggc/Tgc	18/28	0.296321876592628	5	FACETS	0.939	0.884	0.995	0.939	0.884	0.995	CLONAL	3	TRUE	2	0.28	5		424	1037	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0017319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	180	291	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.296321876592628	5	FACETS	1	0.981	1	0.793	0.733	0.856	CLONAL	2	TRUE	2	0.28	5		291	767	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577521	7577521	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	229	380	1	ENST00000269305.4:c.760A>T	p.Ile254Phe	p.I254F	ENST00000269305	NM_001126112.2	254	Atc/Ttc	7/11	NA	2	FACETS	1	0.962	1			1	INDETERMINATE	2	TRUE	NA	0.28	2		381	786	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242742	46242742	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0017319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	61	304	0	ENST00000334344.6:c.1704T>A	p.Tyr568Ter	p.Y568*	ENST00000334344	NM_152641.2	568	taT/taA	13/21	0.277924665062274	3	FACETS	0.753	0.649	0.866	0.251	0.216	0.289	SUBCLONAL	1	TRUE	0	0.28	3		304	660	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772349	56772349	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	100	385	0	ENST00000337432.4:c.203G>T	p.Cys68Phe	p.C68F	ENST00000337432	NM_058216.2	68	tGt/tTt	2/9	0.296321876592628	3	FACETS	0.852	0.759	0.95	0.426	0.379	0.475	CLONAL	1	TRUE	1	0.28	3		385	956	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063636	67063641	+	frameshift_variant	Frame_Shift_Del	DEL	TACACG	TACACG	GGACC	novel	NA	P-0017320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	65	383	1	ENST00000412916.2:c.85_90delinsGGACC	p.Tyr29GlyfsTer60	p.Y29Gfs*60	ENST00000412916		29	TACACG/GGACC	2/6	0.22427852603213	1	FACETS	0.73	0.633	0.836	0.73	0.633	0.836	SUBCLONAL	1	TRUE	0	0.24527536640987	1		384	637	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0017321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	101	470	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.844	0.752	0.942	0.844	0.752	0.942	CLONAL	1	TRUE	1	0.205261746109727	2		470	1166	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579368	7579368	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	131	659	0	ENST00000269305.4:c.319T>G	p.Tyr107Asp	p.Y107D	ENST00000269305	NM_001126112.2	107	Tac/Gac	4/11	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.205261746109727	2		659	1271	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0017322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	32	401	3	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.474	0.383	0.579	0.474	0.383	0.579	SUBCLONAL	1	TRUE	1	0.12	2		404	1124	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56879441	56879441	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	72	499	0	ENST00000519728.1:c.958G>T	p.Glu320Ter	p.E320*	ENST00000519728	NM_002350.3	320	Gag/Tag	9/13	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.12	2		499	1051	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0017323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	238	514	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.49	2		514	969	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16235971	16235971	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	78	379	0	ENST00000375759.3:c.1037C>G	p.Ser346Cys	p.S346C	ENST00000375759	NM_015001.2	346	tCt/tGt	4/15	1	2	FACETS	0.346	0.303	0.392	0.346	0.303	0.392	SUBCLONAL	1	TRUE	1	0.49	2		379	921	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180538	94180538	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	185	361	1	ENST00000323929.3:c.1630G>A	p.Asp544Asn	p.D544N	ENST00000323929	NM_005591.3	544	Gac/Aac	15/20	1	2	FACETS	0.994	0.92	1	0.994	0.92	1	CLONAL	1	TRUE	1	0.49	2		362	760	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398286	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0017324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	321	524	1	ENST00000311936.3:c.33_34delinsCT	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	11	gcTGgt/gcCTgt	2/5	0.251911584292759	3	FACETS	0.831	0.786	0.878	0.831	0.786	0.878	INDETERMINATE	2	TRUE	1	0.44736262275304	3		525	1056	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599120	28599120	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	197	634	0	ENST00000253063.3:c.566G>T	p.Trp189Leu	p.W189L	ENST00000253063	NM_031459.4	189	tGg/tTg	5/10	1	2	FACETS	0.985	0.913	1	0.985	0.913	1	CLONAL	1	TRUE	1	0.44736262275304	2		634	894	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869514	102869514	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	133	435	0	ENST00000307046.8:c.127A>T	p.Thr43Ser	p.T43S	ENST00000307046	NM_001111285.1	43	Acc/Tcc	2/4	0.251911584292759	3	FACETS	0.955	0.868	1	0.477	0.434	0.523	INDETERMINATE	1	TRUE	1	0.44736262275304	3		435	762	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144880	47144880	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	378	466	0	ENST00000409792.3:c.4873C>A	p.Arg1625Ser	p.R1625S	ENST00000409792	NM_014159.6	1625	Cgt/Agt	7/21	0.446754249626199	2	FACETS	0.959	0.915	1	0.959	0.915	1	CLONAL	2	TRUE	0	0.44736262275304	2		466	881	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856060	151856060	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	83	475	0	ENST00000262189.6:c.11558G>T	p.Arg3853Leu	p.R3853L	ENST00000262189	NM_170606.2	3853	cGg/cTg	44/59	1	2	FACETS	0.442	0.389	0.499	0.442	0.389	0.499	SUBCLONAL	1	TRUE	1	0.44736262275304	2		475	839	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465657	8465657	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs543399765	NA	P-0017324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	118	385	0	ENST00000356435.5:c.3523A>G	p.Arg1175Gly	p.R1175G	ENST00000356435		1175	Agg/Ggg	21/35	1	2	FACETS	0.888	0.804	0.977	0.888	0.804	0.977	CLONAL	1	TRUE	1	0.44736262275304	2		385	594	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418184	139418184	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	225	524	0	ENST00000277541.6:c.388C>T	p.Pro130Ser	p.P130S	ENST00000277541	NM_017617.3	130	Ccg/Tcg	3/34	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.44736262275304	2		524	925	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348172	70348172	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	193	464	0	ENST00000374080.3:c.3236C>A	p.Ala1079Glu	p.A1079E	ENST00000374080		1079	gCa/gAa	23/45	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.44736262275304	2		464	808	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782329	NA	P-0017325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	613	490	1	ENST00000269305.4:c.746G>A	p.Arg249Lys	p.R249K	ENST00000269305	NM_001126112.2	249	aGg/aAg	7/11	0.628995636562253	2	FACETS	0.993	0.964	1	0.993	0.964	1	CLONAL	2	TRUE	0	0.628995636562253	2		491	981	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495686	56495686	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	416	435	0	ENST00000267101.3:c.3876G>A	p.Met1292Ile	p.M1292I	ENST00000267101	NM_001982.3	1292	atG/atA	28/28	0.628995636562253	5	FACETS	0.907	0.863	0.952	0.605	0.575	0.635	CLONAL	2	TRUE	2	0.628995636562253	5		435	1417	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970831	55970831	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	248	458	0	ENST00000263923.4:c.1966G>T	p.Val656Phe	p.V656F	ENST00000263923	NM_002253.2	656	Gtc/Ttc	13/30	0.565981006823622	4	FACETS	0.968	0.903	1	0.484	0.451	0.518	CLONAL	1	TRUE	2	0.628995636562253	4		458	1327	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0017326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	287	599	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.204246799375457	7	FACETS	0.924	0.871	0.978			1	CLONAL	5	TRUE	NA	0.204246799375457	7		599	919	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032594	47032594	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	35	527	0	ENST00000377604.3:c.500del	p.Ser167Ter	p.S167*	ENST00000377604	NM_001204468.1	167	tCa/ta	5/24	0.204246799375457	1	FACETS	0.656	0.537	0.79	0.656	0.537	0.79	SUBCLONAL	1	TRUE	0	0.204246799375457	1		527	469	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	83	301	4				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.799	0.707	0.898	0.799	0.707	0.898	SUBCLONAL	1	TRUE	1	0.384501581968291	2		305	540	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699369	47699369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	169	522	0	ENST00000347630.2:c.139G>A	p.Glu47Lys	p.E47K	ENST00000347630	NM_001007230.1	47	Gaa/Aaa	4/11	0.384501581968291	3	FACETS	0.878	0.805	0.954	0.439	0.402	0.477	CLONAL	1	TRUE	1	0.384501581968291	3		522	1194	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241679	55241681	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	rs397517086	NA	P-0017328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1184	238	579	0	ENST00000275493.2:c.2127_2129del	p.Glu709_Thr710delinsAsp	p.E709_T710delinsD	ENST00000275493	NM_005228.3	709	gaAACt/gat	18/28	1	2	FACETS	0.697	0.649	0.747	0.697	0.649	0.747	SUBCLONAL	1	TRUE	1	0.480418675194774	2		579	1422	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199963	108199963	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1160508407	NA	P-0017328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	41	353	0	ENST00000278616.4:c.7305C>A	p.Asn2435Lys	p.N2435K	ENST00000278616	NM_000051.3	2435	aaC/aaA	49/63	1	2	FACETS	0.228	0.189	0.272	0.228	0.189	0.272	SUBCLONAL	1	TRUE	1	0.480418675194774	2		353	747	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47685280	47685280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	164	587	0	ENST00000347630.2:c.670G>A	p.Val224Ile	p.V224I	ENST00000347630	NM_001007230.1	224	Gtt/Att	8/11	1	2	FACETS	0.539	0.493	0.587	0.539	0.493	0.587	SUBCLONAL	1	TRUE	1	0.480418675194774	2		587	1267	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971177	21971177	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913382	NA	P-0017329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	156	318	0	ENST00000304494.5:c.181G>T	p.Glu61Ter	p.E61*	ENST00000304494	NM_000077.4	61	Gag/Tag	2/3	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.278067354306238	2		318	1014	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882019	NA	P-0017329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1370	423	636	1	ENST00000269305.4:c.455del	p.Pro152ArgfsTer18	p.P152Rfs*18	ENST00000269305	NM_001126112.2	152	cCg/cg	5/11	0.224431228287495	2	FACETS	0.848	0.806	0.892	0.848	0.806	0.892	CLONAL	2	TRUE	0	0.278067354306238	2		637	1793	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602767	10602767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1389	296	571	1	ENST00000171111.5:c.811G>A	p.Val271Met	p.V271M	ENST00000171111	NM_203500.1	271	Gtg/Atg	3/6	0.278067354306238	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.278067354306238	1		572	1685	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0017329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1340	129	536	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	0.632	0.57	0.697	0.632	0.57	0.697	SUBCLONAL	1	TRUE	1	0.278067354306238	2		536	1469	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233120	46233120	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	92	193	0	ENST00000334344.6:c.1339G>T	p.Val447Leu	p.V447L	ENST00000334344	NM_152641.2	447	Gtg/Ttg	11/21	1	2	FACETS	0.908	0.806	1	0.908	0.806	1	CLONAL	1	TRUE	1	0.278067354306238	2		193	729	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432753	49432753	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	169	388	3	ENST00000301067.7:c.8386C>T	p.Gln2796Ter	p.Q2796*	ENST00000301067	NM_003482.3	2796	Caa/Taa	34/54	1	2	FACETS	0.91	0.834	0.989	0.91	0.834	0.989	CLONAL	1	TRUE	1	0.278067354306238	2		391	1336	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444978	49444978	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	117	256	0	ENST00000301067.7:c.2488G>T	p.Glu830Ter	p.E830*	ENST00000301067	NM_003482.3	830	Gaa/Taa	10/54	1	2	FACETS	0.832	0.748	0.92	0.832	0.748	0.92	CLONAL	1	TRUE	1	0.278067354306238	2		256	1012	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120785281	120785281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	189	408	0	ENST00000257552.2:c.827C>T	p.Ala276Val	p.A276V	ENST00000257552	NM_002442.3	276	gCa/gTa	12/15	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.278067354306238	2		408	1347	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29422373	29422373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520334	NA	P-0017329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1314	400	462	1	ENST00000356175.3:c.46C>T	p.Arg16Cys	p.R16C	ENST00000356175	NM_000267.3	16	Cgc/Tgc	1/57	0.224431228287495	2	FACETS	0.839	0.796	0.884	0.839	0.796	0.884	CLONAL	2	TRUE	0	0.278067354306238	2		463	1714	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288413	15288413	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	195	364	0	ENST00000263388.2:c.4326C>A	p.Cys1442Ter	p.C1442*	ENST00000263388	NM_000435.2	1442	tgC/tgA	24/33	0.278067354306238	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.278067354306238	1		364	1114	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223748	36223748	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1729	246	589	0	ENST00000222270.7:c.6298G>C	p.Gly2100Arg	p.G2100R	ENST00000222270	NM_014727.1	2100	Ggg/Cgg	28/37	1	2	FACETS	0.896	0.834	0.961	0.896	0.834	0.961	CLONAL	1	TRUE	1	0.278067354306238	2		589	1975	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443618	29443618	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1316	236	443	1	ENST00000389048.3:c.3599C>A	p.Ala1200Glu	p.A1200E	ENST00000389048	NM_004304.4	1200	gCg/gAg	23/29	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.278067354306238	2		444	1552	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165861	47165861	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	156	369	0	ENST00000409792.3:c.265C>G	p.Leu89Val	p.L89V	ENST00000409792	NM_014159.6	89	Ctc/Gtc	3/21	0.278067354306238	1	FACETS	0.97	0.887	1	0.97	0.887	1	CLONAL	1	TRUE	0	0.278067354306238	1		369	996	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127387	55127387	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1401	96	530	0	ENST00000257290.5:c.175T>A	p.Tyr59Asn	p.Y59N	ENST00000257290	NM_006206.4	59	Tac/Aac	3/23	1	2	FACETS	0.461	0.409	0.517	0.461	0.409	0.517	SUBCLONAL	1	TRUE	1	0.278067354306238	2		530	1497	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38966750	38966750	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	131	343	0	ENST00000357387.3:c.1292T>C	p.Leu431Ser	p.L431S	ENST00000357387	NM_152756.3	431	tTa/tCa	15/38	0.278067354306238	3	FACETS	0.88	0.796	0.968	0.44	0.398	0.484	CLONAL	1	TRUE	1	0.278067354306238	3		343	1220	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453145	140453145	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913366	NA	P-0121563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	420	539	0	ENST00000288602.6:c.1790T>G	p.Leu597Arg	p.L597R	ENST00000288602	NM_004333.4	597	cTa/cGa	15/18	0.452775763170274	3	FACETS	0.922	0.879	0.966	0.922	0.879	0.966	CLONAL	2	NA	1	0.452775763170274	3		539	1234	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0017331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	332	708	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	NA	2	FACETS	0.773	0.73	0.816			1	INDETERMINATE	2	TRUE	NA	0.340538341499796	2		708	1262	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955145	17955145	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	299	577	0	ENST00000458235.1:c.82G>A	p.Val28Met	p.V28M	ENST00000458235	NM_000215.3	28	Gtg/Atg	2/24	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.340538341499796	2		577	1386	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0017332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	253	290	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.286597933626057	4	FACETS	0.963	0.9	1	0.963	0.9	1	CLONAL	2	TRUE	2	0.286597933626057	4		290	1180	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158225	47158225	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	79	382	0	ENST00000409792.3:c.4474C>T	p.Arg1492Ter	p.R1492*	ENST00000409792	NM_014159.6	1492	Cga/Tga	4/21	1	2	FACETS	0.602	0.528	0.681	0.602	0.528	0.681	SUBCLONAL	1	TRUE	1	0.286597933626057	2		382	916	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28605739	28605739	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150802897	NA	P-0017332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	161	478	4	ENST00000253063.3:c.1343G>A	p.Arg448His	p.R448H	ENST00000253063	NM_031459.4	448	cGc/cAc	9/10	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.286597933626057	2		482	1105	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170220	119170220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	47	236	0	ENST00000264033.4:c.2450C>T	p.Ser817Phe	p.S817F	ENST00000264033	NM_005188.3	817	tCc/tTc	16/16	1	2	FACETS	0.524	0.441	0.615	0.524	0.441	0.615	SUBCLONAL	1	TRUE	1	0.286597933626057	2		236	626	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579340	7579341	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	231	515	0	ENST00000269305.4:c.346dup	p.Ser116PhefsTer33	p.S116Ffs*33	ENST00000269305	NM_001126112.2	116	tct/tTct	4/11	0.191096086040796	2	FACETS	1	0.991	1	0.72	0.671	0.771	CLONAL	1	TRUE	0	0.286597933626057	2		515	1119	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691926	30691926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	90	392	0	ENST00000295754.5:c.428G>A	p.Cys143Tyr	p.C143Y	ENST00000295754	NM_003242.5	143	tGc/tAc	3/7	1	2	FACETS	0.814	0.721	0.912	0.814	0.721	0.912	CLONAL	1	TRUE	1	0.286597933626057	2		392	772	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413147	139413147	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	438	599	2	ENST00000277541.6:c.995G>T	p.Cys332Phe	p.C332F	ENST00000277541	NM_017617.3	332	tGc/tTc	6/34	0.286597933626057	3	FACETS	0.871	0.831	0.912	0.871	0.831	0.912	CLONAL	3	TRUE	0	0.286597933626057	3		601	1337	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933241	39933241	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1394	74	685	1	ENST00000378444.4:c.1358C>T	p.Ser453Phe	p.S453F	ENST00000378444	NM_001123385.1	453	tCc/tTc	4/15	1	2	FACETS	0.352	0.306	0.401	0.352	0.306	0.401	SUBCLONAL	1	TRUE	1	0.286597933626057	2		686	1468	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	276	408	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.985	0.926	1	0.985	0.926	1	CLONAL	1	TRUE	1	0.574436416463359	2		408	976	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121594	108121595	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs587781347	NA	P-0017333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	271	578	0	ENST00000278616.4:c.1402_1403del	p.Lys468GlufsTer18	p.K468Efs*18	ENST00000278616	NM_000051.3	468	AAg/g	10/63	1	2	FACETS	0.975	0.916	1	0.975	0.916	1	CLONAL	1	TRUE	1	0.574436416463359	2		578	968	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125507402	125507403	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	280	631	1	ENST00000428830.2:c.783dup	p.Asp262ArgfsTer2	p.D262Rfs*2	ENST00000428830	NM_001114121.2	259	-/A	8/14	NA	2	FACETS	0.922	0.867	0.979			1	INDETERMINATE	1	TRUE	NA	0.574436416463359	2		632	1057	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578181	7578192	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCTCATAG	GGCGGCTCATAG	-	rs876660749	NA	P-0017333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	188	616	0	ENST00000269305.4:c.657_668del	p.Tyr220_Pro223del	p.Y220_P223del	ENST00000269305	NM_001126112.2	219	ccCTATGAGCCGCCt/cct	6/11	0.574436416463359	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.574436416463359	1		616	463	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974697	21974698	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0017333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	186	368	0	ENST00000304494.5:c.129_130del	p.Ser43ArgfsTer76	p.S43Rfs*76	ENST00000304494	NM_000077.4	43	agTTac/agac	1/3	0.574436416463359	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.574436416463359	1		368	394	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44911048	44911048	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0017333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	240	257	0	ENST00000377967.4:c.748+1G>C		p.X250_splice	ENST00000377967	NM_021140.2	250			1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.574436416463359	1		257	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0017334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	695	627	0	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.874828815319406	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.874828815319406	1		627	886	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786131	3786131	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1696	738	681	0	ENST00000262367.5:c.4634G>T	p.Trp1545Leu	p.W1545L	ENST00000262367	NM_004380.2	1545	tGg/tTg	28/31	0.874828815319406	3	FACETS	0.996	0.96	1	0.498	0.48	0.517	CLONAL	1	TRUE	1	0.874828815319406	3		681	2434	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712001	89712001	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	161	278	0	ENST00000371953.3:c.619A>G	p.Ser207Gly	p.S207G	ENST00000371953	NM_000314.4	207	Agt/Ggt	6/9	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.874828815319406	2		278	343	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601305	28601305	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	476	593	1	ENST00000241453.7:c.2127A>T	p.Lys709Asn	p.K709N	ENST00000241453	NM_004119.2	709	aaA/aaT	17/24	1	2	FACETS	0.969	0.929	1	0.969	0.929	1	CLONAL	1	TRUE	1	0.874828815319406	2		594	1123	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28611427	28611427	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0017334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	304	335	0	ENST00000241453.7:c.1206-2A>T		p.X402_splice	ENST00000241453	NM_004119.2	402			1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.874828815319406	2		335	627	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953729	48953729	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0017334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	295	275	0	ENST00000267163.4:c.1333-1G>A		p.X445_splice	ENST00000267163	NM_000321.2	445			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.874828815319406	2		275	637	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039246	49039246	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	398	559	0	ENST00000267163.4:c.2325+1del		p.R775fs	ENST00000267163	NM_000321.2	775	aGg/ag	22/27	1	2	FACETS	0.93	0.888	0.973	0.93	0.888	0.973	CLONAL	1	TRUE	1	0.874828815319406	2		559	978	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42050027	42050028	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0017334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	191	439	0	ENST00000219905.7:c.7181_7182delinsTT	p.Arg2394Ile	p.R2394I	ENST00000219905	NM_001164273.1	2394	aGG/aTT	19/24	1	2	FACETS	0.835	0.778	0.893	0.835	0.778	0.893	CLONAL	1	TRUE	1	0.874828815319406	2		439	523	SUCCESS
BLM	641	MSKCC	GRCh37	15	91290653	91290653	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	462	615	0	ENST00000355112.3:c.31G>T	p.Glu11Ter	p.E11*	ENST00000355112	NM_000057.2	11	Gag/Tag	2/22	1	2	FACETS	0.976	0.935	1	0.976	0.935	1	CLONAL	1	TRUE	1	0.874828815319406	2		615	1082	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627294	37627294	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	533	575	0	ENST00000447079.4:c.1209G>C	p.Lys403Asn	p.K403N	ENST00000447079	NM_015083.1	403	aaG/aaC	2/14	1	2	FACETS	0.985	0.947	1	0.985	0.947	1	CLONAL	1	TRUE	1	0.874828815319406	2		575	1237	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59861722	59861722	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	474	629	0	ENST00000259008.2:c.1537G>T	p.Ala513Ser	p.A513S	ENST00000259008	NM_032043.2	513	Gca/Tca	11/20	1	2	FACETS	0.982	0.942	1	0.982	0.942	1	CLONAL	1	TRUE	1	0.874828815319406	2		629	1103	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989619	212989619	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	324	330	0	ENST00000342788.4:c.92G>T	p.Gly31Val	p.G31V	ENST00000342788	NM_005235.2	31	gGa/gTa	2/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.874828815319406	2		330	687	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794889	242794889	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	514	482	0	ENST00000334409.5:c.320A>G	p.His107Arg	p.H107R	ENST00000334409	NM_005018.2	107	cAc/cGc	2/5	1	2	FACETS	0.958	0.919	0.996	0.958	0.919	0.996	CLONAL	1	TRUE	1	0.874828815319406	2		482	1227	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866466	42866466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	738	825	0	ENST00000398585.3:c.166G>A	p.Gly56Arg	p.G56R	ENST00000398585	NM_001135099.1	56	Gga/Aga	3/14	1	2	FACETS	0.982	0.95	1	0.982	0.95	1	CLONAL	1	TRUE	1	0.874828815319406	2		825	1718	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691920	30691920	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	374	456	0	ENST00000295754.5:c.422A>T	p.Asp141Val	p.D141V	ENST00000295754	NM_003242.5	141	gAt/gTt	3/7	0.874828815319406	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.874828815319406	1		456	476	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177519	56177519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751612650	NA	P-0017334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	333	428	0	ENST00000399503.3:c.2492C>T	p.Pro831Leu	p.P831L	ENST00000399503	NM_005921.1	831	cCc/cTc	14/20	1	2	FACETS	0.932	0.885	0.979	0.932	0.885	0.979	CLONAL	1	TRUE	1	0.874828815319406	2		428	817	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0017336-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	639	347	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.88242847776265	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.88242847776265	3		347	1029	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176334	24176339	+	inframe_deletion	In_Frame_Del	DEL	GAGGCG	GAGGCG	-	novel	NA	P-0017336-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	385	520	1	ENST00000263121.7:c.1125_1130del	p.Met375_Arg377delinsIle	p.M375_R377delinsI	ENST00000263121	NM_003073.3	375	atGAGGCGt/att	9/9	0.88242847776265	2	FACETS	0.957	0.913	1	0.478	0.456	0.501	CLONAL	1	TRUE	0	0.88242847776265	2		521	912	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587136	189587136	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017336-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	263	358	0	ENST00000264731.3:c.1153A>T	p.Ile385Phe	p.I385F	ENST00000264731	NM_003722.4	385	Atc/Ttc	9/14	0.88242847776265	2	FACETS	0.92	0.868	0.972	0.46	0.434	0.486	CLONAL	1	TRUE	0	0.88242847776265	2		358	648	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195625	123195628	+	frameshift_variant	Frame_Shift_Del	DEL	AACA	AACA	-	novel	NA	P-0017336-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	113	307	0	ENST00000218089.9:c.1539_1542del	p.Thr514IlefsTer7	p.T514Ifs*7	ENST00000218089	NM_001042749.1	513	ctAACA/ct	17/35	0.88242847776265	3	FACETS	0.589	0.531	0.65	0.294	0.265	0.325	SUBCLONAL	1	TRUE	1	0.88242847776265	3		307	627	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572549	64572549	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	429	558	0	ENST00000312049.6:c.1307G>T	p.Trp436Leu	p.W436L	ENST00000312049	NM_130799.2	436	tGg/tTg	9/10	0.570657244545257	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.570657244545257	2		558	733	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2125942	2126472	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCCTTGCGGCAGAAAGCCCCGGCAGCCTTTGTCCCCAAGGCCTGAGCGCCTCGGTTTTTTGCACTTCATGCCCTGGGGATGTTTCCCTGCTGCCAGGATGGAGTGCCAGCCCCCTTCTCATCTCAGGTTTAATCAGTACATCGTGTGTCTGGCCCATCACGTCATAGCCATGTGGTTCATCAGGTGCCGCCTGCCCTTCCGGAAGGATTTTGTCCCTTTCATCACTAAGGTGGGCTCAGGGCCGGTGAAGGCTGTGTCTCTCGGTAGGCCAGGGCTTGCTTTGCCCTTGGCTGTCCATGGTCGGGCAGAGTGACAGGCAGGTGGAGGGCAGTGGGAGGGTGTTTGGGGCTGTGCCTGTGGCGCTGGGGGCTCTGCTGGGCAGCCTGCAGGGCTTTGATGCGCGGCAGGCATTGAGGGGTGGGAGCTGGGTGCCGCCGCCTTGCCCCTAGCCTGCAGCTTGTCCCTGGCCAGGGGGCACCCGGCAGGCCTGGTGAGGGCCTCCAGCCCCCATTGCCACCCCTCACTGTCTG	GGCCTTGCGGCAGAAAGCCCCGGCAGCCTTTGTCCCCAAGGCCTGAGCGCCTCGGTTTTTTGCACTTCATGCCCTGGGGATGTTTCCCTGCTGCCAGGATGGAGTGCCAGCCCCCTTCTCATCTCAGGTTTAATCAGTACATCGTGTGTCTGGCCCATCACGTCATAGCCATGTGGTTCATCAGGTGCCGCCTGCCCTTCCGGAAGGATTTTGTCCCTTTCATCACTAAGGTGGGCTCAGGGCCGGTGAAGGCTGTGTCTCTCGGTAGGCCAGGGCTTGCTTTGCCCTTGGCTGTCCATGGTCGGGCAGAGTGACAGGCAGGTGGAGGGCAGTGGGAGGGTGTTTGGGGCTGTGCCTGTGGCGCTGGGGGCTCTGCTGGGCAGCCTGCAGGGCTTTGATGCGCGGCAGGCATTGAGGGGTGGGAGCTGGGTGCCGCCGCCTTGCCCCTAGCCTGCAGCTTGTCCCTGGCCAGGGGGCACCCGGCAGGCCTGGTGAGGGCCTCCAGCCCCCATTGCCACCCCTCACTGTCTG	-	novel	NA	P-0017348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	543	367	0	ENST00000219476.3:c.2639+51_2743-18del		p.X880_splice	ENST00000219476	NM_000548.3	880		24/42	0.570657244545257	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.570657244545257	2		367	802	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855029	76855029	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	166	526	1	ENST00000373344.5:c.5807del	p.Lys1936ArgfsTer19	p.K1936Rfs*19	ENST00000373344	NM_000489.3	1936	aAg/ag	25/35	0.570657244545257	1	FACETS	0.888	0.823	0.955	0.888	0.823	0.955	CLONAL	1	TRUE	0	0.570657244545257	1		527	468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0017350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	464	385	1	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.810161842269351	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.810161842269351	1		386	640	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439134	52439134	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	192	390	0	ENST00000460680.1:c.1108C>G	p.Pro370Ala	p.P370A	ENST00000460680	NM_004656.3	370	Ccc/Gcc	11/17	1	2	FACETS	0.44	0.406	0.475	0.44	0.406	0.475	SUBCLONAL	1	TRUE	1	0.810161842269351	2		390	1078	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0017352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	19	195	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.099	0.074	0.128	0.099	0.074	0.128	SUBCLONAL	1	TRUE	1	0.741632233836964	2		195	518	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572092	64572093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs767319284	NA	P-0017352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	60	497	1	ENST00000312049.6:c.1546dup	p.Arg516ProfsTer15	p.R516Pfs*15	ENST00000312049	NM_130799.2	516	cgg/cCgg	10/10	0.741632233836964	1	FACETS	0.207	0.179	0.239	0.207	0.179	0.239	SUBCLONAL	1	TRUE	0	0.741632233836964	1		498	491	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115915	8115915	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	290	424	0	ENST00000346208.3:c.1262del	p.Pro421ArgfsTer54	p.P421Rfs*54	ENST00000346208		421	Ccg/cg	6/6	1	2	FACETS	0.979	0.925	1	0.979	0.925	1	CLONAL	1	TRUE	1	0.741632233836964	2		424	799	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608650	189608650	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	68	537	0	ENST00000264731.3:c.1725G>T	p.Gln575His	p.Q575H	ENST00000264731	NM_003722.4	575	caG/caT	13/14	1	2	FACETS	0.191	0.166	0.219	0.191	0.166	0.219	SUBCLONAL	1	TRUE	1	0.741632233836964	2		537	959	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0017354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	542	514	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	0.74799003415812	3	FACETS	0.987	0.952	1	0.987	0.952	1	CLONAL	2	TRUE	1	0.74799003415812	3		514	1009	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0017355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	44	401	3	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.13	2		404	611	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782620	NA	P-0017355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	38	756	1	ENST00000269305.4:c.427G>A	p.Val143Met	p.V143M	ENST00000269305	NM_001126112.2	143	Gtg/Atg	5/11	1	2	FACETS	0.718	0.592	0.861	0.718	0.592	0.861	SUBCLONAL	1	TRUE	1	0.13	2		757	814	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11554273	NA	P-0017355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	16	426	0	ENST00000371085.3:c.601C>A	p.Arg201Ser	p.R201S	ENST00000371085	NM_000516.4	201	Cgt/Agt	8/13	0.3	3	FACETS	0.497	0.366	0.656			1	SUBCLONAL	1	TRUE	NA	0.13	3		426	527	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436621	110436621	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	42	748	0	ENST00000375856.3:c.1780T>G	p.Ser594Ala	p.S594A	ENST00000375856	NM_003749.2	594	Tcg/Gcg	1/2	1	2	FACETS	0.935	0.779	1	0.935	0.779	1	CLONAL	1	TRUE	1	0.13	2		748	691	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426882	49426882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1346721444	NA	P-0017358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	63	253	0	ENST00000301067.7:c.11606C>T	p.Ser3869Phe	p.S3869F	ENST00000301067	NM_003482.3	3869	tCc/tTc	39/54	0.80054394871971	2	FACETS	0.288	0.25	0.33	0.144	0.125	0.165	SUBCLONAL	1	TRUE	0	0.888003738078565	2		253	492	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754050	42754050	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	71	476	0	ENST00000222329.4:c.302G>A	p.Arg101Gln	p.R101Q	ENST00000222329	NM_006494.2	101	cGg/cAg	3/4	0.888003738078565	2	FACETS	0.169	0.147	0.193	0.085	0.073	0.097	SUBCLONAL	1	TRUE	0	0.888003738078565	2		476	945	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0017359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	192	180	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.589111980728827	2		180	643	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0017359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	156	349	1	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.589111980728827	2		350	475	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063656	67063673	+	inframe_deletion	In_Frame_Del	DEL	GCCCCACGAGGAACGCCA	GCCCCACGAGGAACGCCA	-	novel	NA	P-0017359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	169	501	0	ENST00000412916.2:c.106_123del	p.Pro36_Gln41del	p.P36_Q41del	ENST00000412916		35	cgGCCCCACGAGGAACGCCAg/cgg	2/6	0.589111980728827	1	FACETS	0.98	0.912	1	0.98	0.912	1	CLONAL	1	TRUE	0	0.589111980728827	1		501	413	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	293	408	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.952	0.9	1	0.952	0.9	1	CLONAL	1	TRUE	1	0.748463197624644	2		408	822	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0017360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	174	415	2	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.684	0.632	0.738	0.684	0.632	0.738	SUBCLONAL	1	TRUE	1	0.748463197624644	2		417	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs864622237	NA	P-0017360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	70	398	0	ENST00000269305.4:c.700T>C	p.Tyr234His	p.Y234H	ENST00000269305	NM_001126112.2	234	Tac/Cac	7/11	1	2	FACETS	0.286	0.249	0.327	0.286	0.249	0.327	SUBCLONAL	1	TRUE	1	0.748463197624644	2		398	653	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143985	11143985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	195	322	3	ENST00000358026.2:c.3566G>A	p.Arg1189Gln	p.R1189Q	ENST00000358026	NM_001128849.1	1189	cGa/cAa	26/36	1	2	FACETS	0.972	0.907	1	0.972	0.907	1	CLONAL	1	TRUE	1	0.748463197624644	2		325	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576881	7576881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	247	418	0	ENST00000269305.4:c.965C>T	p.Pro322Leu	p.P322L	ENST00000269305	NM_001126112.2	322	cCa/cTa	9/11	1	2	FACETS	0.826	0.775	0.879	0.826	0.775	0.879	CLONAL	1	TRUE	1	0.748463197624644	2		418	799	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653187	29653187	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	65	354	1	ENST00000356175.3:c.5122G>T	p.Ala1708Ser	p.A1708S	ENST00000356175	NM_000267.3	1708	Gcc/Tcc	36/57	1	2	FACETS	0.321	0.278	0.367	0.321	0.278	0.367	SUBCLONAL	1	TRUE	1	0.748463197624644	2		355	541	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210730	5210730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753489907	NA	P-0017360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	162	497	0	ENST00000357368.4:c.5321C>T	p.Thr1774Met	p.T1774M	ENST00000357368	NM_002850.3	1774	aCg/aTg	34/38	1	2	FACETS	0.631	0.58	0.683	0.631	0.58	0.683	SUBCLONAL	1	TRUE	1	0.748463197624644	2		497	686	SUCCESS
APC	324	MSKCC	GRCh37	5	112170691	112170691	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1554083134	NA	P-0017360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	184	355	1	ENST00000257430.4:c.1787C>G	p.Ser596Ter	p.S596*	ENST00000257430	NM_000038.5	596	tCa/tGa	15/16	1	2	FACETS	0.854	0.793	0.916	0.854	0.793	0.916	CLONAL	1	TRUE	1	0.748463197624644	2		356	576	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410100	63410100	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	127	425	0	ENST00000330258.3:c.3067C>G	p.Pro1023Ala	p.P1023A	ENST00000330258	NM_152424.3	1023	Ccc/Gcc	2/2	1	2	FACETS	0.707	0.644	0.772	0.707	0.644	0.772	SUBCLONAL	1	TRUE	1	0.748463197624644	2		425	480	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	31	301	4				ENST00000310581	NM_198253.2	-/1132			0.195039564552899	1	FACETS	0.661	0.534	0.805	0.661	0.534	0.805	SUBCLONAL	1	FALSE	0	0.195039564552899	1		305	434	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0017361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	85	554	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.170896460958577	3	FACETS	0.765	0.677	0.86	0.765	0.677	0.86	SUBCLONAL	2	FALSE	1	0.195039564552899	3		554	625	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93636534	93636534	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	27	495	1	ENST00000375746.1:c.964C>T	p.Pro322Ser	p.P322S	ENST00000375746	NM_001174167.1	322	Ccg/Tcg	8/14	0.195039564552899	0	FACETS	0.415	0.329	0.514			1	SUBCLONAL	1	FALSE	0	0.195039564552899	0		496	537	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670708	134670708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	56	480	0	ENST00000398015.3:c.619C>T	p.Pro207Ser	p.P207S	ENST00000398015	NM_004441.4	207	Cca/Tca	3/16	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	1	0.195039564552899	2		480	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578202	7578202	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520004	NA	P-0017361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	46	673	0	ENST00000269305.4:c.647T>G	p.Val216Gly	p.V216G	ENST00000269305	NM_001126112.2	216	gTg/gGg	6/11	1	2	FACETS	0.532	0.446	0.627	0.532	0.446	0.627	SUBCLONAL	1	FALSE	1	0.195039564552899	2		673	887	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612028	189612028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs900140738	NA	P-0017361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	23	398	0	ENST00000264731.3:c.1780C>T	p.Arg594Ter	p.R594*	ENST00000264731	NM_003722.4	594	Cga/Tga	14/14	1	2	FACETS	0.518	0.403	0.652	0.518	0.403	0.652	SUBCLONAL	1	FALSE	1	0.195039564552899	2		398	455	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486206	8486206	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426671700	NA	P-0017361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	16	352	1	ENST00000356435.5:c.2611C>T	p.Leu871Phe	p.L871F	ENST00000356435		871	Ctt/Ttt	17/35	0.195039564552899	0	FACETS	0.442	0.326	0.58			1	SUBCLONAL	1	FALSE	0	0.195039564552899	0		353	299	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149242	119149242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779039234	NA	P-0017361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	62	460	0	ENST00000264033.4:c.1250C>T	p.Pro417Leu	p.P417L	ENST00000264033	NM_005188.3	417	cCt/cTt	9/16	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.195039564552899	2		460	540	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209253	133209253	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	46	545	0	ENST00000320574.5:c.6133C>T	p.Pro2045Ser	p.P2045S	ENST00000320574	NM_006231.2	2045	Ccc/Tcc	44/49	0.195039564552899	1	FACETS	0.629	0.528	0.74	0.629	0.528	0.74	SUBCLONAL	1	FALSE	0	0.195039564552899	1		545	677	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244226	133244226	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	25	384	0	ENST00000320574.5:c.2182C>G	p.Arg728Gly	p.R728G	ENST00000320574	NM_006231.2	728	Cgg/Ggg	20/49	0.195039564552899	1	FACETS	0.523	0.412	0.652	0.523	0.412	0.652	SUBCLONAL	1	FALSE	0	0.195039564552899	1		384	442	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881544	48881544	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0017361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	73	198	0	ENST00000267163.4:c.264+2T>C		p.X88_splice	ENST00000267163	NM_000321.2	88			0.195039564552899	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	2	FALSE	0	0.195039564552899	2		198	368	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000019	42000019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	40	656	1	ENST00000219905.7:c.2282C>T	p.Pro761Leu	p.P761L	ENST00000219905	NM_001164273.1	761	cCt/cTt	6/24	0.195039564552899	1	FACETS	0.51	0.422	0.608	0.51	0.422	0.608	SUBCLONAL	1	FALSE	0	0.195039564552899	1		657	726	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134569	2134569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759004251	NA	P-0017361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	47	638	0	ENST00000219476.3:c.4346C>T	p.Ser1449Phe	p.S1449F	ENST00000219476	NM_000548.3	1449	tCc/tTc	34/42	1	2	FACETS	0.639	0.538	0.752	0.639	0.538	0.752	SUBCLONAL	1	FALSE	1	0.195039564552899	2		638	754	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271923	15271923	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	82	646	0	ENST00000263388.2:c.6516G>A	p.Trp2172Ter	p.W2172*	ENST00000263388	NM_000435.2	2172	tgG/tgA	33/33	0.170896460958577	3	FACETS	1	0.963	1	0.621	0.547	0.7	CLONAL	1	FALSE	1	0.195039564552899	3		646	743	SUCCESS
ALK	238	MSKCC	GRCh37	2	29420543	29420543	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0017361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	25	327	0	ENST00000389048.3:c.3939-1G>A		p.X1313_splice	ENST00000389048	NM_004304.4	1313			1	2	FACETS	0.633	0.498	0.788	0.633	0.498	0.788	SUBCLONAL	1	FALSE	1	0.195039564552899	2		327	405	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250128	39250128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	31	588	1	ENST00000402219.2:c.1441C>T	p.Pro481Ser	p.P481S	ENST00000402219	NM_005633.3	481	Cct/Tct	10/23	1	2	FACETS	0.527	0.425	0.643	0.527	0.425	0.643	SUBCLONAL	1	FALSE	1	0.195039564552899	2		589	603	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458428	12458428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	33	671	0	ENST00000287820.6:c.1045G>A	p.Gly349Arg	p.G349R	ENST00000287820	NM_015869.4	349	Gga/Aga	6/7	1	2	FACETS	0.542	0.44	0.658	0.542	0.44	0.658	SUBCLONAL	1	FALSE	1	0.195039564552899	2		671	624	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180252	38180252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	37	456	0	ENST00000396334.3:c.100C>T	p.Pro34Ser	p.P34S	ENST00000396334	NM_002468.4	34	Ccc/Tcc	1/5	1	2	FACETS	0.609	0.501	0.731	0.609	0.501	0.731	SUBCLONAL	1	FALSE	1	0.195039564552899	2		456	623	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186901	142186901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	43	389	0	ENST00000350721.4:c.6562C>T	p.Pro2188Ser	p.P2188S	ENST00000350721	NM_001184.3	2188	Ccc/Tcc	39/47	1	2	FACETS	0.976	0.817	1	0.976	0.817	1	CLONAL	1	FALSE	1	0.195039564552899	2		389	452	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041073	180041073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	102	709	0	ENST00000261937.6:c.3326C>T	p.Ser1109Phe	p.S1109F	ENST00000261937	NM_182925.4	1109	tCt/tTt	24/30	0.195039564552899	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	0	0.195039564552899	1		709	867	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839699	27839699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	25	331	2	ENST00000328488.2:c.395G>A	p.Arg132Gln	p.R132Q	ENST00000328488	NM_003533.2	132	cGa/cAa	1/1	1	2	FACETS	0.532	0.418	0.663	0.532	0.418	0.663	SUBCLONAL	1	FALSE	1	0.195039564552899	2		333	482	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866480	56866480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	41	560	2	ENST00000519728.1:c.727C>T	p.Pro243Ser	p.P243S	ENST00000519728	NM_002350.3	243	Ccc/Tcc	8/13	0.195039564552899	1	FACETS	0.519	0.431	0.617	0.519	0.431	0.617	SUBCLONAL	1	FALSE	0	0.195039564552899	1		562	731	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104681	69104681	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	49	406	0	ENST00000288368.4:c.4525G>A	p.Gly1509Arg	p.G1509R	ENST00000288368	NM_024870.2	1509	Gga/Aga	37/40	0.195039564552899	1	FACETS	0.782	0.662	0.914	0.782	0.662	0.914	CLONAL	1	FALSE	0	0.195039564552899	1		406	580	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115919	8115920	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0017362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	114	384	0	ENST00000346208.3:c.1266dup	p.His423AlafsTer84	p.H423Afs*84	ENST00000346208		422	atg/atGg	6/6	0.291334630950793	4	FACETS	1	0.967	1	0.583	0.525	0.643	CLONAL	1	TRUE	2	0.404888143419991	4		384	679	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0017366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	77	308	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.3	2	FACETS	1	0.932	1			1	CLONAL	1	TRUE	NA	0.22	2		308	641	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438203	49438203	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	48	740	3	ENST00000301067.7:c.5066G>A	p.Arg1689His	p.R1689H	ENST00000301067	NM_003482.3	1689	cGt/cAt	20/54	1	2	FACETS	0.531	0.447	0.623	0.531	0.447	0.623	SUBCLONAL	1	TRUE	1	0.22	2		743	822	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397581	116397647	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTCTCCTATGTGGTAAGGAAGATTCTATCCTATCATGTTTGATTTTTACTTAATCTATTTAAATTA	ATTCTCCTATGTGGTAAGGAAGATTCTATCCTATCATGTTTGATTTTTACTTAATCTATTTAAATTA	-	novel	NA	P-0017366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	71	735	0	ENST00000397752.3:c.1953_1966-45del		p.X651_splice	ENST00000397752	NM_000245.2	651		7/21	1	2	FACETS	0.895	0.781	1	0.895	0.781	1	CLONAL	1	TRUE	1	0.22	2		735	721	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578517	7578517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750600586	NA	P-0017368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	904	823	0	ENST00000269305.4:c.413C>T	p.Ala138Val	p.A138V	ENST00000269305	NM_001126112.2	138	gCc/gTc	5/11	NA	2	FACETS	1	0.997	1			1	INDETERMINATE	2	TRUE	NA	0.689611917708264	2		823	1208	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557286	29557286	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753082620	NA	P-0017368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	120	338	0	ENST00000356175.3:c.2999G>A	p.Arg1000His	p.R1000H	ENST00000356175	NM_000267.3	1000	cGt/cAt	23/57	0.689293604285443	4	FACETS	0.879	0.795	0.967			1	CLONAL	1	TRUE	NA	0.689611917708264	4		338	669	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268918	115269150	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTCTTGGAGTTAGAATTACGACCTAAAAGTCGCACACAAGTTGCAACCTGCTGTCCAGGCCTCTGTTTGTCACTAATACTAAATTCAACCTGTGAAAATTAAGGATGCTCATTAACACCATATCACTTCCACACCAATCTCCTTAACTCAGAAAACAAGACCTATAACTCCCCCAGCGCATGCTTTTCATTCCAAATATCCTTTGTTATTACTTCAATGAAATTGATTTTCA	CCTCTTGGAGTTAGAATTACGACCTAAAAGTCGCACACAAGTTGCAACCTGCTGTCCAGGCCTCTGTTTGTCACTAATACTAAATTCAACCTGTGAAAATTAAGGATGCTCATTAACACCATATCACTTCCACACCAATCTCCTTAACTCAGAAAACAAGACCTATAACTCCCCCAGCGCATGCTTTTCATTCCAAATATCCTTTGTTATTACTTCAATGAAATTGATTTTCA	-	novel	NA	P-0017368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	120	611	0	ENST00000438362.2:c.1603-143_1692del		p.X535_splice	ENST00000438362	NM_001242891.1	535		14/20	0.330574945022569	6	FACETS	0.634	0.57	0.701	0.158	0.142	0.176	INDETERMINATE	1	TRUE	2	0.689611917708264	6		611	1307	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124644	108124644	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	292	501	1	ENST00000278616.4:c.2002G>C	p.Glu668Gln	p.E668Q	ENST00000278616	NM_000051.3	668	Gaa/Caa	13/63	0.689293604285443	4	FACETS	0.923	0.873	0.974	0.923	0.873	0.974	CLONAL	2	TRUE	2	0.689611917708264	4		502	775	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030345	49030345	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	321	341	0	ENST00000267163.4:c.1822del	p.Ser608LeufsTer3	p.S608Lfs*3	ENST00000267163	NM_000321.2	607	cTt/ct	19/27	0.689293604285443	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.689611917708264	2		341	455	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965113	81965113	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	203	496	0	ENST00000359376.3:c.2593C>G	p.Gln865Glu	p.Q865E	ENST00000359376	NM_002661.3	865	Cag/Gag	25/33	0.689293604285443	2	FACETS	0.903	0.841	0.966	0.451	0.42	0.483	CLONAL	1	TRUE	0	0.689611917708264	2		496	652	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36253004	36253004	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1286	245	475	1	ENST00000300305.3:c.358G>A	p.Ala120Thr	p.A120T	ENST00000300305		120	Gcc/Acc	4/8	0.689293604285443	5	FACETS	0.944	0.88	1			1	CLONAL	1	TRUE	NA	0.689611917708264	5		476	1531	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440861	52440861	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1407261660	NA	P-0017368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	247	504	0	ENST00000460680.1:c.643G>A	p.Gly215Ser	p.G215S	ENST00000460680	NM_004656.3	215	Ggc/Agc	8/17	0.689293604285443	3	FACETS	0.987	0.924	1			1	CLONAL	1	TRUE	NA	0.689611917708264	3		504	976	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413679	138414013	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAGTTGAAATCCAGAAGCTCTAGGGCCTCCCGGGGGGGCAGTTTAGGCCAAATCTGAAGCAGCGCCTGAAGCTGTTTAAAAAATGAAACTGGTTCAGAAATAATGGGGGACAAAAGTAATCTAATTTTCCTTGACACACAGGAGCACCAAGATAGGTCAAAAGAAGGCAAAGCTCACTTTTAATTATTGATGCCTCAAAAATCCATTCCTGTTAATAGAGACTAATAAAGATTGTCTTTGTTGTTGAAACATTCTATAGATTAAGTCTGAAAAGCTATGAAGTACTTACCCCCAAATAAATTTTATGGGTGAGAGAGAAAAAAATGTTGAATTTG	TAGTTGAAATCCAGAAGCTCTAGGGCCTCCCGGGGGGGCAGTTTAGGCCAAATCTGAAGCAGCGCCTGAAGCTGTTTAAAAAATGAAACTGGTTCAGAAATAATGGGGGACAAAAGTAATCTAATTTTCCTTGACACACAGGAGCACCAAGATAGGTCAAAAGAAGGCAAAGCTCACTTTTAATTATTGATGCCTCAAAAATCCATTCCTGTTAATAGAGACTAATAAAGATTGTCTTTGTTGTTGAAACATTCTATAGATTAAGTCTGAAAAGCTATGAAGTACTTACCCCCAAATAAATTTTATGGGTGAGAGAGAAAAAAATGTTGAATTTG	-	novel	NA	P-0017368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1253	141	436	0	ENST00000289153.2:c.1771-264_1841del		p.X591_splice	ENST00000289153	NM_006219.2	591		12/22	0.689293604285443	5	FACETS	0.597	0.542	0.655	0.199	0.18	0.219	SUBCLONAL	1	TRUE	2	0.689611917708264	5		436	1394	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449570	187449570	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	168	347	0	ENST00000232014.4:c.310G>T	p.Ala104Ser	p.A104S	ENST00000232014	NM_001130845.1	104	Gct/Tct	4/10	0.689293604285443	5	FACETS	0.989	0.909	1	0.33	0.303	0.358	CLONAL	1	TRUE	2	0.689611917708264	5		347	1002	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449495	31449495	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs886369396	NA	P-0017368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	201	335	0	ENST00000344624.3:c.2714A>G	p.Asn905Ser	p.N905S	ENST00000344624		905	aAt/aGt	19/33	0.64719026814802	4	FACETS	1	0.964	1			1	CLONAL	1	TRUE	NA	0.689611917708264	4		335	925	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911410	39911411	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0017368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	252	512	0	ENST00000378444.4:c.5219_5220del	p.Ser1740CysfsTer8	p.S1740Cfs*8	ENST00000378444	NM_001123385.1	1740	tCT/t	15/15	0.689293604285443	2	FACETS	0.965	0.907	1	0.483	0.453	0.513	CLONAL	1	TRUE	0	0.689611917708264	2		512	757	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	30	301	4				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.332	0.266	0.406	0.332	0.266	0.406	SUBCLONAL	1	TRUE	1	0.34	2		305	532	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947852	178947852	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	99	361	0	ENST00000263967.3:c.2727C>G	p.Phe909Leu	p.F909L	ENST00000263967	NM_006218.2	909	ttC/ttG	19/21	0.3	3	FACETS	1	0.981	1	0.739	0.663	0.819	CLONAL	1	TRUE	1	0.34	3		361	461	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242729	46242729	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	42	487	0	ENST00000334344.6:c.1691del	p.Ser564Ter	p.S564*	ENST00000334344	NM_152641.2	564	tCa/ta	13/21	1	2	FACETS	0.572	0.478	0.676	0.572	0.478	0.676	SUBCLONAL	1	TRUE	1	0.34	2		487	432	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404926	70404926	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	63	611	0	ENST00000373644.4:c.2440G>T	p.Asp814Tyr	p.D814Y	ENST00000373644	NM_030625.2	814	Gat/Tat	4/12	1	2	FACETS	0.52	0.449	0.597	0.52	0.449	0.597	SUBCLONAL	1	TRUE	1	0.34	2		611	713	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359363	118359363	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	36	354	1	ENST00000534358.1:c.4367A>T	p.His1456Leu	p.H1456L	ENST00000534358	NM_005933.3	1456	cAc/cTc	11/36	1	2	FACETS	0.496	0.408	0.595	0.496	0.408	0.595	SUBCLONAL	1	TRUE	1	0.34	2		355	427	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127446	55127446	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	79	730	0	ENST00000257290.5:c.234C>A	p.Ser78Arg	p.S78R	ENST00000257290	NM_006206.4	78	agC/agA	3/23	1	2	FACETS	0.522	0.458	0.591	0.522	0.458	0.591	SUBCLONAL	1	TRUE	1	0.34	2		730	891	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675447	30675447	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	58	481	0	ENST00000376406.3:c.2909G>C	p.Gly970Ala	p.G970A	ENST00000376406	NM_014641.2	970	gGg/gCg	8/15	1	2	FACETS	0.563	0.483	0.65	0.563	0.483	0.65	SUBCLONAL	1	TRUE	1	0.34	2		481	606	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	278	634	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	0.412187754240808	2		636	1072	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	198	708	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.73	0.674	0.788	0.73	0.674	0.788	SUBCLONAL	1	TRUE	1	0.412187754240808	2		708	1316	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	93	414	1	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.689	0.613	0.77	0.689	0.613	0.77	SUBCLONAL	1	TRUE	1	0.412187754240808	2		415	655	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1162	227	778	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.793	0.737	0.851	0.793	0.737	0.851	SUBCLONAL	1	TRUE	1	0.412187754240808	2		782	1389	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	53	351	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	0.375	0.319	0.436	0.375	0.319	0.436	SUBCLONAL	1	TRUE	1	0.412187754240808	2		351	686	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696802	176696802	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	73	209	2	ENST00000439151.2:c.5508del	p.Ala1837LeufsTer12	p.A1837Lfs*12	ENST00000439151	NM_022455.4	1835	Aaa/aa	16/23	1	2	FACETS	0.862	0.757	0.973	0.862	0.757	0.973	CLONAL	1	TRUE	1	0.412187754240808	2		211	411	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143984	11143984	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs267607070	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	221	505	1	ENST00000358026.2:c.3565C>T	p.Arg1189Ter	p.R1189*	ENST00000358026	NM_001128849.1	1189	Cga/Tga	26/36	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.412187754240808	2		506	842	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165213	47165213	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	70	335	0	ENST00000409792.3:c.913del	p.Thr305GlnfsTer35	p.T305Qfs*35	ENST00000409792	NM_014159.6	305	Aca/ca	3/21	1	2	FACETS	0.487	0.424	0.555	0.487	0.424	0.555	SUBCLONAL	1	TRUE	1	0.412187754240808	2		335	698	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	201	1074	7	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.781	0.722	0.842	0.781	0.722	0.842	SUBCLONAL	1	TRUE	1	0.412187754240808	2		1081	1249	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646085	215646085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	71	654	0	ENST00000260947.4:c.513del	p.Asp172MetfsTer40	p.D172Mfs*40	ENST00000260947	NM_000465.2	171	aaA/aa	4/11	1	2	FACETS	0.33	0.287	0.377	0.33	0.287	0.377	SUBCLONAL	1	TRUE	1	0.412187754240808	2		654	1044	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676254	29676254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659856	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	55	571	0	ENST00000356175.3:c.7243G>A	p.Val2415Met	p.V2415M	ENST00000356175	NM_000267.3	2415	Gtg/Atg	48/57	1	2	FACETS	0.275	0.234	0.319	0.275	0.234	0.319	SUBCLONAL	1	TRUE	1	0.412187754240808	2		571	972	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675570	86675571	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	121	374	0	ENST00000274376.6:c.2513dup	p.Asn838LysfsTer2	p.N838Kfs*2	ENST00000274376	NM_002890.2	836	gaa/gAaa	19/25	1	2	FACETS	0.883	0.799	0.971	0.883	0.799	0.971	CLONAL	1	TRUE	1	0.412187754240808	2		374	665	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562949	21562949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1461231287	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	55	583	1	ENST00000382592.4:c.970G>A	p.Ala324Thr	p.A324T	ENST00000382592	NM_014572.2	324	Gcg/Acg	4/8	1	2	FACETS	0.301	0.256	0.35	0.301	0.256	0.35	SUBCLONAL	1	TRUE	1	0.412187754240808	2		584	887	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900661	3900661	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	36	389	0	ENST00000262367.5:c.435del	p.Ala146LeufsTer6	p.A146Lfs*6	ENST00000262367	NM_004380.2	145	ccC/cc	2/31	1	2	FACETS	0.263	0.215	0.316	0.263	0.215	0.316	SUBCLONAL	1	TRUE	1	0.412187754240808	2		389	665	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916730	178916730	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	95	488	0	ENST00000263967.3:c.117G>T	p.Glu39Asp	p.E39D	ENST00000263967	NM_006218.2	39	gaG/gaT	2/21	1	2	FACETS	0.51	0.453	0.571	0.51	0.453	0.571	SUBCLONAL	1	TRUE	1	0.412187754240808	2		488	904	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434182	12434182	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776687	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	169	598	1	ENST00000287820.6:c.556del	p.Ser186ValfsTer47	p.S186Vfs*47	ENST00000287820	NM_015869.4	184	Aaa/aa	4/7	1	2	FACETS	0.748	0.687	0.812	0.748	0.687	0.812	SUBCLONAL	1	TRUE	1	0.412187754240808	2		599	1096	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1490	87	924	0	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.268	0.236	0.302	0.268	0.236	0.302	SUBCLONAL	1	TRUE	1	0.412187754240808	2		924	1577	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106916	27106917	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	94	397	0	ENST00000324856.7:c.6532dup	p.Asp2178GlyfsTer47	p.D2178Gfs*47	ENST00000324856	NM_006015.4	2176	cag/caGg	20/20	1	2	FACETS	0.722	0.643	0.806	0.722	0.643	0.806	SUBCLONAL	1	TRUE	1	0.412187754240808	2		397	632	SUCCESS
ATM	472	MSKCC	GRCh37	11	108168077	108168077	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	114	451	0	ENST00000278616.4:c.4973C>T	p.Ala1658Val	p.A1658V	ENST00000278616	NM_000051.3	1658	gCa/gTa	33/63	1	2	FACETS	0.686	0.618	0.759	0.686	0.618	0.759	SUBCLONAL	1	TRUE	1	0.412187754240808	2		451	806	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342775	118342775	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	205	494	2	ENST00000534358.1:c.901C>T	p.Arg301Ter	p.R301*	ENST00000534358	NM_005933.3	301	Cga/Tga	3/36	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.412187754240808	2		496	793	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1042164	1042164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776681920	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1240	87	706	1	ENST00000358495.3:c.61G>A	p.Gly21Ser	p.G21S	ENST00000358495	NM_134424.2	21	Ggc/Agc	2/12	1	2	FACETS	0.318	0.28	0.359	0.318	0.28	0.359	SUBCLONAL	1	TRUE	1	0.412187754240808	2		707	1327	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479220	50479220	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	64	518	0	ENST00000394963.4:c.68G>A	p.Gly23Asp	p.G23D	ENST00000394963	NM_003076.4	23	gGc/gAc	1/13	1	2	FACETS	0.398	0.344	0.457	0.398	0.344	0.457	SUBCLONAL	1	TRUE	1	0.412187754240808	2		518	780	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434477	110434477	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747968639	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	54	564	3	ENST00000375856.3:c.3924del	p.Pro1309ArgfsTer22	p.P1309Rfs*22	ENST00000375856	NM_003749.2	1308	ggG/gg	1/2	1	2	FACETS	0.283	0.241	0.33	0.283	0.241	0.33	SUBCLONAL	1	TRUE	1	0.412187754240808	2		567	925	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094794	2094794	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	141	559	0	ENST00000219066.1:c.386G>T	p.Arg129Met	p.R129M	ENST00000219066	NM_002528.5	129	aGg/aTg	3/6	1	2	FACETS	0.733	0.667	0.802	0.733	0.667	0.802	SUBCLONAL	1	TRUE	1	0.412187754240808	2		559	933	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384726	17384726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368554117	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1214	239	867	0	ENST00000359435.4:c.358G>A	p.Ala120Thr	p.A120T	ENST00000359435	NM_001033549.1	120	Gcc/Acc	4/9	1	2	FACETS	0.798	0.743	0.855	0.798	0.743	0.855	SUBCLONAL	1	TRUE	1	0.412187754240808	2		867	1453	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211525	36211525	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	175	638	0	ENST00000222270.7:c.1280del	p.Pro427HisfsTer48	p.P427Hfs*48	ENST00000222270	NM_014727.1	426	Ccc/cc	3/37	1	2	FACETS	0.749	0.688	0.812	0.749	0.688	0.812	SUBCLONAL	1	TRUE	1	0.412187754240808	2		638	1134	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905312	50905312	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749334182	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1262	77	834	1	ENST00000440232.2:c.520C>T	p.Arg174Trp	p.R174W	ENST00000440232	NM_002691.3	174	Cgg/Tgg	5/27	1	2	FACETS	0.279	0.244	0.317	0.279	0.244	0.317	SUBCLONAL	1	TRUE	1	0.412187754240808	2		835	1339	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660324	227660324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748385460	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	27	244	2	ENST00000305123.5:c.3131C>T	p.Pro1044Leu	p.P1044L	ENST00000305123	NM_005544.2	1044	cCg/cTg	1/2	1	2	FACETS	0.296	0.235	0.366	0.296	0.235	0.366	SUBCLONAL	1	TRUE	1	0.412187754240808	2		246	442	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839705	42839705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1346752687	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1361	163	888	2	ENST00000398585.3:c.1534G>A	p.Gly512Arg	p.G512R	ENST00000398585	NM_001135099.1	512	Ggg/Agg	13/14	1	2	FACETS	0.519	0.474	0.566	0.519	0.474	0.566	SUBCLONAL	1	TRUE	1	0.412187754240808	2		890	1524	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641707	12641707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs555034652	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	132	512	0	ENST00000251849.4:c.934G>A	p.Val312Met	p.V312M	ENST00000251849	NM_002880.3	312	Gtg/Atg	9/17	1	2	FACETS	0.796	0.722	0.873	0.796	0.722	0.873	SUBCLONAL	1	TRUE	1	0.412187754240808	2		512	805	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281480	142281480	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	222	720	0	ENST00000350721.4:c.764T>C	p.Leu255Pro	p.L255P	ENST00000350721	NM_001184.3	255	cTt/cCt	4/47	1	2	FACETS	0.791	0.734	0.85	0.791	0.734	0.85	SUBCLONAL	1	TRUE	1	0.412187754240808	2		720	1362	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177485	56177485	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	111	360	0	ENST00000399503.3:c.2458T>G	p.Tyr820Asp	p.Y820D	ENST00000399503	NM_005921.1	820	Tac/Gac	14/20	1	2	FACETS	0.677	0.608	0.749	0.677	0.608	0.749	SUBCLONAL	1	TRUE	1	0.412187754240808	2		360	796	SUCCESS
APC	324	MSKCC	GRCh37	5	112177150	112177150	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	217	481	0	ENST00000257430.4:c.5862del	p.Phe1954LeufsTer16	p.F1954Lfs*16	ENST00000257430	NM_000038.5	1953	aaT/aa	16/16	0.412187754240808	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.412187754240808	1		481	649	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480181	20480181	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	122	426	0	ENST00000346618.3:c.498T>A	p.Ser166Arg	p.S166R	ENST00000346618	NM_001949.4	166	agT/agA	2/7	1	2	FACETS	0.746	0.674	0.821	0.746	0.674	0.821	SUBCLONAL	1	TRUE	1	0.412187754240808	2		426	794	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777877	27777877	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	34	201	0	ENST00000369163.2:c.26G>T	p.Arg9Leu	p.R9L	ENST00000369163	NM_003536.2	9	cGc/cTc	1/1	1	2	FACETS	0.585	0.48	0.702	0.585	0.48	0.702	SUBCLONAL	1	TRUE	1	0.412187754240808	2		201	282	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066524	94066524	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	97	422	0	ENST00000369303.4:c.1235C>G	p.Thr412Ser	p.T412S	ENST00000369303	NM_004440.3	412	aCt/aGt	5/17	1	2	FACETS	0.645	0.575	0.719	0.645	0.575	0.719	SUBCLONAL	1	TRUE	1	0.412187754240808	2		422	730	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149982903	149982903	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	107	442	0	ENST00000253339.5:c.3355G>T	p.Gly1119Cys	p.G1119C	ENST00000253339		1119	Ggc/Tgc	7/7	1	2	FACETS	0.735	0.66	0.815	0.735	0.66	0.815	SUBCLONAL	1	TRUE	1	0.412187754240808	2		442	706	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023219	150023219	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	154	594	0	ENST00000253339.5:c.44C>A	p.Pro15His	p.P15H	ENST00000253339		15	cCt/cAt	1/7	1	2	FACETS	0.741	0.678	0.808	0.741	0.678	0.808	SUBCLONAL	1	TRUE	1	0.412187754240808	2		594	1008	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341197	8341198	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	56	464	0	ENST00000356435.5:c.5018dup	p.Asn1673LysfsTer5	p.N1673Kfs*5	ENST00000356435		1673	aat/aaAt	30/35	1	2	FACETS	0.331	0.283	0.385	0.331	0.283	0.385	SUBCLONAL	1	TRUE	1	0.412187754240808	2		464	820	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038811	47038811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	41	342	0	ENST00000377604.3:c.818C>T	p.Pro273Leu	p.P273L	ENST00000377604	NM_001204468.1	273	cCg/cTg	9/24	1	1	FACETS	0.299	0.248	0.355	0.299	0.248	0.355	SUBCLONAL	1	TRUE	0	0.412187754240808	1		342	529	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410854	63410854	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	65	343	0	ENST00000330258.3:c.2313G>T	p.Gln771His	p.Q771H	ENST00000330258	NM_152424.3	771	caG/caT	2/2	1	1	FACETS	0.428	0.371	0.49	0.428	0.371	0.49	SUBCLONAL	1	TRUE	0	0.412187754240808	1		343	585	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332670	153332670	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0121439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	323	323	0	ENST00000281708.4:c.286G>T	p.Glu96Ter	p.E96*	ENST00000281708	NM_033632.3	96	Gaa/Taa	2/12	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	NA	1	0.931115080380635	2		323	692	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939091	76939091	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0121439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	181	416	0	ENST00000373344.5:c.1657G>T	p.Glu553Ter	p.E553*	ENST00000373344	NM_000489.3	553	Gaa/Taa	9/35	0.546107920779064	1	FACETS	0.341	0.315	0.366	0.341	0.315	0.366	INDETERMINATE	1	NA	0	0.931115080380635	1		416	610	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	178	408	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.817	0.754	0.882	0.817	0.754	0.882	CLONAL	1	TRUE	1	0.564513043491293	2		408	772	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0017373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	24	501	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	0.199	0.155	0.249	0.199	0.155	0.249	SUBCLONAL	1	TRUE	1	0.564513043491293	2		501	428	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624274	89624274	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs587782187	NA	P-0017373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	382	392	0	ENST00000371953.3:c.48T>A	p.Tyr16Ter	p.Y16*	ENST00000371953	NM_000314.4	16	taT/taA	1/9	0.564513043491293	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.564513043491293	3		392	842	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822585	72822586	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs764626362	NA	P-0017373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	79	292	0	ENST00000268489.5:c.9589dup	p.Gln3197ProfsTer42	p.Q3197Pfs*42	ENST00000268489	NM_006885.3	3197	cag/cCag	10/10	1	2	FACETS	0.63	0.557	0.709	0.63	0.557	0.709	SUBCLONAL	1	TRUE	1	0.564513043491293	2		292	444	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630626	158630626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912678	NA	P-0017373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	137	371	1	ENST00000263640.3:c.617G>A	p.Arg206His	p.R206H	ENST00000263640	NM_001105.4	206	cGc/cAc	6/11	1	2	FACETS	0.802	0.732	0.875	0.802	0.732	0.875	CLONAL	1	TRUE	1	0.564513043491293	2		372	605	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106544	27106550	+	frameshift_variant	Frame_Shift_Del	DEL	GCTTGGA	GCTTGGA	-	novel	NA	P-0017373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	213	776	2	ENST00000324856.7:c.6156_6162del	p.Cys2052Ter	p.C2052*	ENST00000324856	NM_006015.4	2052	tGCTTGGAg/tg	20/20	1	2	FACETS	0.727	0.675	0.781	0.727	0.675	0.781	SUBCLONAL	1	TRUE	1	0.564513043491293	2		778	1038	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	443410	443410	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	143	391	0	ENST00000399788.2:c.1487A>G	p.His496Arg	p.H496R	ENST00000399788	NM_001042603.1	496	cAc/cGc	11/28	NA	2	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.564513043491293	2		391	444	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226032	133226032	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770036124	NA	P-0017373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	116	622	0	ENST00000320574.5:c.3865C>T	p.Arg1289Cys	p.R1289C	ENST00000320574	NM_006231.2	1289	Cgc/Tgc	31/49	1	2	FACETS	0.539	0.486	0.596	0.539	0.486	0.596	SUBCLONAL	1	TRUE	1	0.564513043491293	2		622	762	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637714	23637714	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	175	570	0	ENST00000261584.4:c.2591C>A	p.Pro864His	p.P864H	ENST00000261584	NM_024675.3	864	cCt/cAt	7/13	1	2	FACETS	0.827	0.763	0.893	0.827	0.763	0.893	CLONAL	1	TRUE	1	0.564513043491293	2		570	750	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662740	227662740	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	69	615	0	ENST00000305123.5:c.715C>T	p.Gln239Ter	p.Q239*	ENST00000305123	NM_005544.2	239	Cag/Tag	1/2	1	2	FACETS	0.218	0.189	0.249	0.218	0.189	0.249	SUBCLONAL	1	TRUE	1	0.564513043491293	2		615	1123	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368137	31368138	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGACACC	novel	NA	P-0017373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	128	523	0	ENST00000328111.2:c.11_17dup	p.Leu8GlnfsTer78	p.L8Qfs*78	ENST00000328111	NM_006892.3	3	gga/ggAGACACCa	2/23	1	2	FACETS	0.658	0.597	0.722	0.658	0.597	0.722	SUBCLONAL	1	TRUE	1	0.564513043491293	2		523	689	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326521	62326523	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs777014655	NA	P-0017373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	41	630	1	ENST00000360203.5:c.3451_3453del	p.Glu1151del	p.E1151del	ENST00000360203	NM_001283009.1	1149	cAGGag/cag	33/35	1	2	FACETS	0.179	0.148	0.213	0.179	0.148	0.213	SUBCLONAL	1	TRUE	1	0.564513043491293	2		631	812	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629012	187629012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	193	488	0	ENST00000441802.2:c.1970del	p.Leu657TyrfsTer5	p.L657Yfs*5	ENST00000441802	NM_005245.3	657	tTa/ta	2/27	1	2	FACETS	0.958	0.889	1	0.958	0.889	1	CLONAL	1	TRUE	1	0.564513043491293	2		488	714	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31493382	31493382	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	153	415	0	ENST00000344624.3:c.1774A>C	p.Ile592Leu	p.I592L	ENST00000344624		592	Ata/Cta	10/33	1	2	FACETS	0.916	0.841	0.992	0.916	0.841	0.992	CLONAL	1	TRUE	1	0.564513043491293	2		415	592	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591129	67591130	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0017373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	141	345	0	ENST00000274335.5:c.1723_1724del	p.Lys575AspfsTer26	p.K575Dfs*26	ENST00000274335		574	agAAag/agag	12/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.564513043491293	2		345	460	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591313	67591314	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0017373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	88	318	0	ENST00000274335.5:c.1811_1812del	p.Glu604GlyfsTer9	p.E604Gfs*9	ENST00000274335		604	gAA/g	13/15	1	2	FACETS	0.688	0.612	0.768	0.688	0.612	0.768	SUBCLONAL	1	TRUE	1	0.564513043491293	2		318	453	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752961	128752962	+	inframe_insertion	In_Frame_Ins	INS	-	-	AACGTCTTGGAGCGCCAGAGGAGG	novel	NA	P-0017373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	129	460	0	ENST00000377970.2:c.1127_1150dup	p.Val376_Asn383dup	p.V376_N383dup	ENST00000377970	NM_002467.4	376	-/AACGTCTTGGAGCGCCAGAGGAGG	3/3	1	2	FACETS	0.486	0.44	0.535	0.486	0.44	0.535	SUBCLONAL	1	TRUE	1	0.564513043491293	2		460	940	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712004	89712005	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	A	novel	NA	P-0017373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	87	215	0	ENST00000371953.3:c.622_623delinsA	p.Gly208ThrfsTer13	p.G208Tfs*13	ENST00000371953	NM_000314.4	208	GGc/Ac	6/9	0.564513043491293	3	FACETS	1	0.953	1	0.563	0.502	0.627	CLONAL	1	TRUE	1	0.564513043491293	3		215	351	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99440049	99440049	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0121566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	85	606	0	ENST00000268035.6:c.1017G>C	p.Lys339Asn	p.K339N	ENST00000268035	NM_000875.3	339	aaG/aaC	4/21	1	2	FACETS	0.594	0.524	0.669	0.594	0.524	0.669	SUBCLONAL	1	NA	1	0.32074449441816	2		606	893	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0017375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	654	591	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.657558532905521	2	FACETS	0.949	0.922	0.976	0.949	0.922	0.976	CLONAL	2	TRUE	0	0.675411941449938	2		591	1020	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943632	9943632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	296	482	0	ENST00000330684.3:c.1309C>T	p.Arg437Trp	p.R437W	ENST00000330684	NM_001134407.1	437	Cgg/Tgg	5/13	NA	2	FACETS	0.932	0.88	0.986			1	INDETERMINATE	1	TRUE	NA	0.675411941449938	2		482	940	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677279	29677279	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	505	470	0	ENST00000356175.3:c.7337del	p.Ser2446Ter	p.S2446*	ENST00000356175	NM_000267.3	2446	tCa/ta	49/57	0.657558532905521	2	FACETS	0.887	0.857	0.917	0.887	0.857	0.917	CLONAL	2	TRUE	0	0.675411941449938	2		470	843	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302291	15302291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1381	180	710	0	ENST00000263388.2:c.980C>T	p.Ala327Val	p.A327V	ENST00000263388	NM_000435.2	327	gCc/gTc	6/33	0.186831228930804	4	FACETS	0.572	0.525	0.621	0.286	0.262	0.311	INDETERMINATE	1	TRUE	2	0.675411941449938	4		710	1561	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0017376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	111	489	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.582	0.523	0.645	0.582	0.523	0.645	SUBCLONAL	1	TRUE	1	0.477410534260348	2		489	799	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578491	7578491	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1567553924	NA	P-0017376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	366	875	1	ENST00000269305.4:c.439del	p.Val147LeufsTer23	p.V147Lfs*23	ENST00000269305	NM_001126112.2	147	Gtt/tt	5/11	0.477410534260348	1	FACETS	0.988	0.937	1	0.988	0.937	1	CLONAL	1	TRUE	0	0.477410534260348	1		876	1182	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032526	12032526	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	157	388	0	ENST00000353533.5:c.962T>G	p.Val321Gly	p.V321G	ENST00000353533	NM_003010.3	321	gTg/gGg	9/11	0.477410534260348	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.477410534260348	1		388	491	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78865440	78865547	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGTGACTCAAGTCTCACTGCTGCTCCACAATCATTTTCCAGCCCCAGTGACTGTTATTGTCCCTTCTCCCTCTCGGCAGGAGCTGGTGGTGGCTCTGAGTCATCTTG	TGGTGACTCAAGTCTCACTGCTGCTCCACAATCATTTTCCAGCCCCAGTGACTGTTATTGTCCCTTCTCCCTCTCGGCAGGAGCTGGTGGTGGCTCTGAGTCATCTTG	-	novel	NA	P-0017376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	24	131	0	ENST00000306801.3:c.1984-76_2015del		p.X662_splice	ENST00000306801	NM_020761.2	662		18/34	1	2	FACETS	0.433	0.341	0.539	0.433	0.341	0.539	SUBCLONAL	1	TRUE	1	0.477410534260348	2		131	232	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78865567	78865567	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	215	687	0	ENST00000306801.3:c.2033del	p.Phe678SerfsTer9	p.F678Sfs*9	ENST00000306801	NM_020761.2	677	aaT/aa	18/34	1	2	FACETS	0.848	0.788	0.91	0.848	0.788	0.91	CLONAL	1	TRUE	1	0.477410534260348	2		687	1062	SUCCESS
APC	324	MSKCC	GRCh37	5	112175918	112175918	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	160	378	0	ENST00000257430.4:c.4629del	p.Glu1544AsnfsTer21	p.E1544Nfs*21	ENST00000257430	NM_000038.5	1543	Aaa/aa	16/16	0.477410534260348	1	FACETS	0.976	0.901	1	0.976	0.901	1	CLONAL	1	TRUE	0	0.477410534260348	1		378	523	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0017378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	168	401	3	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.20376963700069	4	FACETS	0.899	0.828	0.973	0.899	0.828	0.973	CLONAL	3	TRUE	1	0.20376963700069	4		404	736	SUCCESS
AR	367	MSKCC	GRCh37	X	66766501	66766501	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	90	674	0	ENST00000374690.3:c.1513C>G	p.Pro505Ala	p.P505A	ENST00000374690	NM_000044.3	505	Cct/Gct	1/8	0.143812441195062	1	FACETS	0.987	0.875	1	0.987	0.875	1	CLONAL	1	TRUE	0	0.20376963700069	1		674	804	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838403	156838403	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	168	568	1	ENST00000524377.1:c.681G>T	p.Trp227Cys	p.W227C	ENST00000524377	NM_002529.3	227	tgG/tgT	6/17	0.17409211449509	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.20376963700069	3		569	830	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999186	100999186	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	57	555	0	ENST00000325455.5:c.616T>A	p.Ser206Thr	p.S206T	ENST00000325455	NM_001202474.3	206	Tcc/Acc	1/8	0.17409211449509	3	FACETS	1	0.895	1	0.526	0.451	0.608	CLONAL	1	TRUE	1	0.20376963700069	3		555	586	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163473	108163473	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	57	534	0	ENST00000278616.4:c.4564G>C	p.Gly1522Arg	p.G1522R	ENST00000278616	NM_000051.3	1522	Ggt/Cgt	30/63	0.17409211449509	3	FACETS	1	0.911	1	0.543	0.465	0.627	CLONAL	1	TRUE	1	0.20376963700069	3		534	568	SUCCESS
ATM	472	MSKCC	GRCh37	11	108181043	108181043	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0017378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	28	232	0	ENST00000278616.4:c.5918+1G>T		p.X1973_splice	ENST00000278616	NM_000051.3	1973			0.17409211449509	3	FACETS	1	0.856	1	0.543	0.435	0.665	CLONAL	1	TRUE	1	0.20376963700069	3		232	279	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435145	18435145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201124495	NA	P-0017378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	151	435	1	ENST00000266497.5:c.130G>A	p.Val44Ile	p.V44I	ENST00000266497		44	Gta/Ata	1/31	0.20376963700069	4	FACETS	0.958	0.879	1	0.958	0.879	1	CLONAL	3	TRUE	1	0.20376963700069	4		436	621	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444936	49444937	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0017378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	82	378	1	ENST00000301067.7:c.2529_2530delinsTT	p.Pro844Ser	p.P844S	ENST00000301067	NM_003482.3	843	tcCCcc/tcTTcc	10/54	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.20376963700069	2		379	620	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467228	99467228	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	35	299	0	ENST00000268035.6:c.2609G>T	p.Gly870Val	p.G870V	ENST00000268035	NM_000875.3	870	gGa/gTa	12/21	0.143812441195062	1	FACETS	0.806	0.661	0.968	0.806	0.661	0.968	CLONAL	1	TRUE	0	0.20376963700069	1		299	383	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641037	3641037	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	56	902	0	ENST00000294008.3:c.2602G>C	p.Glu868Gln	p.E868Q	ENST00000294008	NM_032444.2	868	Gaa/Caa	12/15	1	2	FACETS	0.516	0.44	0.599	0.516	0.44	0.599	SUBCLONAL	1	TRUE	1	0.20376963700069	2		902	1065	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519767	29519767	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	105	514	0	ENST00000389048.3:c.1804G>T	p.Asp602Tyr	p.D602Y	ENST00000389048	NM_004304.4	602	Gat/Tat	9/29	1	2	FACETS	0.776	0.696	0.861	1	0.983	1	SUBCLONAL	2	TRUE	1	0.20376963700069	2		514	664	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573968	41573968	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	38	588	0	ENST00000263253.7:c.6253A>T	p.Ile2085Phe	p.I2085F	ENST00000263253	NM_001429.3	2085	Atc/Ttc	31/31	1	2	FACETS	0.512	0.422	0.613	0.512	0.422	0.613	SUBCLONAL	1	TRUE	1	0.20376963700069	2		588	729	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390171	89390171	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	55	298	1	ENST00000336596.2:c.920A>T	p.Glu307Val	p.E307V	ENST00000336596	NM_005233.5	307	gAg/gTg	4/17	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.20376963700069	2		299	423	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670814	134670814	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	26	310	0	ENST00000398015.3:c.725G>T	p.Gly242Val	p.G242V	ENST00000398015	NM_004441.4	242	gGg/gTg	3/16	0.116093887040325	5	FACETS	0.78	0.617	0.968	0.195	0.154	0.242	INDETERMINATE	1	TRUE	1	0.20376963700069	5		310	427	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984804	55984804	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	79	588	0	ENST00000263923.4:c.325G>T	p.Asp109Tyr	p.D109Y	ENST00000263923	NM_002253.2	109	Gac/Tac	3/30	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.20376963700069	2		588	728	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213923	66213923	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0017378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	56	400	0	ENST00000273854.3:c.2509-2A>T		p.X837_splice	ENST00000273854	NM_004439.5	837			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.20376963700069	2		400	394	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729733	41729733	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	56	457	0	ENST00000242208.4:c.796G>C	p.Glu266Gln	p.E266Q	ENST00000242208	NM_002192.2	266	Gag/Cag	3/3	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.20376963700069	2		457	520	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922045	39922045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	84	680	0	ENST00000378444.4:c.4127G>A	p.Gly1376Glu	p.G1376E	ENST00000378444	NM_001123385.1	1376	gGa/gAa	9/15	0.143812441195062	1	FACETS	0.806	0.71	0.909	0.806	0.71	0.909	CLONAL	1	TRUE	0	0.20376963700069	1		680	919	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933273	39933273	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	80	702	0	ENST00000378444.4:c.1326del	p.Leu443CysfsTer8	p.L443Cfs*8	ENST00000378444	NM_001123385.1	442	gaC/ga	4/15	0.143812441195062	1	FACETS	0.745	0.654	0.843	0.745	0.654	0.843	SUBCLONAL	1	TRUE	0	0.20376963700069	1		702	947	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040946	47040946	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	103	741	0	ENST00000377604.3:c.1476del	p.Met493CysfsTer211	p.M493Cfs*211	ENST00000377604	NM_001204468.1	492	tcG/tc	14/24	0.143812441195062	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.20376963700069	1		741	871	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0017379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	601	410	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.848804595295417	2	FACETS	0.971	0.952	0.988	0.971	0.952	0.988	CLONAL	2	TRUE	0	0.887139866801499	2		410	698	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481857	56481857	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519817	NA	P-0017379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	700	533	0	ENST00000267101.3:c.785C>A	p.Pro262His	p.P262H	ENST00000267101	NM_001982.3	262	cCt/cAt	7/28	0.85892987112645	2	FACETS	0.971	0.953	0.987	0.971	0.953	0.987	CLONAL	2	TRUE	0	0.887139866801499	2		533	813	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983251	7983251	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	94	369	0	ENST00000319144.4:c.763G>C	p.Ala255Pro	p.A255P	ENST00000319144	NM_001139.2	255	Gcc/Ccc	7/15	0.848804595295417	2	FACETS	0.346	0.308	0.387	0.173	0.154	0.194	SUBCLONAL	1	TRUE	0	0.887139866801499	2		369	612	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214806	36214806	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1843	352	579	0	ENST00000222270.7:c.3232C>T	p.Arg1078Cys	p.R1078C	ENST00000222270	NM_014727.1	1078	Cgc/Tgc	8/37	0.887139866801499	6	FACETS	1	0.946	1	0.251	0.236	0.266	CLONAL	1	TRUE	2	0.887139866801499	6		579	2195	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546095	41546095	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	728	600	0	ENST00000263253.7:c.2710G>C	p.Ala904Pro	p.A904P	ENST00000263253	NM_001429.3	904	Gca/Cca	14/31	0.833871695840945	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.887139866801499	4		600	1525	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253974	133253974	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	416	493	0	ENST00000320574.5:c.776G>T	p.Arg259Leu	p.R259L	ENST00000320574	NM_006231.2	259	cGc/cTc	8/49	0.567356569719708	3	FACETS	0.918	0.877	0.959	0.918	0.877	0.959	CLONAL	2	TRUE	1	0.588313153170404	3		493	997	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0017385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	193	451	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.588313153170404	2		451	645	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577499	7577499	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	165	358	0	ENST00000269305.4:c.782G>T	p.Ser261Ile	p.S261I	ENST00000269305	NM_001126112.2	261	aGt/aTt	7/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.588313153170404	2		358	532	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144147	11144147	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	224	496	0	ENST00000358026.2:c.3728G>T	p.Arg1243Leu	p.R1243L	ENST00000358026	NM_001128849.1	1243	cGg/cTg	26/36	0.588313153170404	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.588313153170404	1		496	479	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877349	40877349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747289224	NA	P-0017385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	250	346	1	ENST00000373198.4:c.2347G>A	p.Val783Met	p.V783M	ENST00000373198	NM_133170.3	783	Gtg/Atg	15/32	0.418825692034127	4	FACETS	0.961	0.904	1			1	CLONAL	2	TRUE	NA	0.588313153170404	4		347	702	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792638	33792638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	70	98	0	ENST00000498907.2:c.683C>T	p.Pro228Leu	p.P228L	ENST00000498907	NM_004364.3	228	cCg/cTg	1/1	0.536950999453196	4	FACETS	1	0.894	1			1	CLONAL	2	TRUE	NA	0.588313153170404	4		98	188	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843647	156843647	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1227	517	689	0	ENST00000524377.1:c.1073A>T	p.Asn358Ile	p.N358I	ENST00000524377	NM_002529.3	358	aAc/aTc	8/17	0.588313153170404	5	FACETS	0.949	0.907	0.991	0.632	0.605	0.661	CLONAL	2	TRUE	2	0.588313153170404	5		689	1744	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206942016	206942016	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	253	273	0	ENST00000423557.1:c.502A>T	p.Ile168Leu	p.I168L	ENST00000423557	NM_000572.2	168	Ata/Tta	5/5	0.588313153170404	5	FACETS	0.946	0.887	1	0.63	0.591	0.671	CLONAL	2	TRUE	2	0.588313153170404	5		273	856	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600523	43600523	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	189	542	0	ENST00000355710.3:c.749G>T	p.Arg250Leu	p.R250L	ENST00000355710	NM_020975.4	250	cGc/cTc	4/20	0.581175613428965	3	FACETS	0.893	0.826	0.963	0.447	0.413	0.482	CLONAL	1	TRUE	1	0.588313153170404	3		542	931	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998888	100998888	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	545	608	0	ENST00000325455.5:c.914A>G	p.His305Arg	p.H305R	ENST00000325455	NM_001202474.3	305	cAc/cGc	1/8	0.572300277114437	4	FACETS	0.913	0.881	0.946	0.913	0.881	0.946	CLONAL	3	TRUE	1	0.588313153170404	4		608	1074	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905432	11905432	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs34966596	NA	P-0017385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	282	342	4	ENST00000396373.4:c.82G>T	p.Ala28Ser	p.A28S	ENST00000396373	NM_001987.4	28	Gct/Tct	2/8	0.58615972491477	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.588313153170404	2		346	458	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427986	49427986	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	389	417	0	ENST00000301067.7:c.10604A>C	p.His3535Pro	p.H3535P	ENST00000301067	NM_003482.3	3535	cAc/cCc	38/54	0.57752874936916	4	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	2	0.588313153170404	4		417	1037	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493683	56493683	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	342	397	0	ENST00000267101.3:c.2999T>C	p.Leu1000Pro	p.L1000P	ENST00000267101	NM_001982.3	1000	cTa/cCa	25/28	0.57752874936916	4	FACETS	0.988	0.937	1	0.988	0.937	1	CLONAL	2	TRUE	2	0.588313153170404	4		397	935	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240732	133240732	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	150	398	0	ENST00000320574.5:c.2564G>C	p.Arg855Thr	p.R855T	ENST00000320574	NM_006231.2	855	aGg/aCg	23/49	0.567356569719708	3	FACETS	0.979	0.897	1	0.49	0.448	0.532	CLONAL	1	TRUE	1	0.588313153170404	3		398	674	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679808	88679808	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	153	332	0	ENST00000360948.2:c.655C>A	p.Leu219Met	p.L219M	ENST00000360948	NM_001012338.2	219	Ctg/Atg	7/19	0.581175613428965	3	FACETS	1	0.924	1	0.504	0.462	0.547	CLONAL	1	TRUE	1	0.588313153170404	3		332	668	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339592	339592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	616	510	1	ENST00000262320.3:c.2310G>T	p.Arg770Ser	p.R770S	ENST00000262320	NM_003502.3	770	agG/agT	10/11	0.588313153170404	4	FACETS	0.987	0.955	1	0.987	0.955	1	CLONAL	3	TRUE	1	0.588313153170404	4		511	1123	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40871136	40871136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	169	405	1	ENST00000428826.2:c.754G>A	p.Asp252Asn	p.D252N	ENST00000428826		252	Gac/Aac	8/21	0.588313153170404	4	FACETS	0.989	0.909	1	0.33	0.303	0.358	CLONAL	1	TRUE	1	0.588313153170404	4		406	923	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220394	1220395	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0017385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	193	464	1	ENST00000326873.7:c.487_488delinsTT	p.Gly163Phe	p.G163F	ENST00000326873	NM_000455.4	163	GGc/TTc	4/10	0.588313153170404	1	FACETS	0.898	0.837	0.959	0.898	0.837	0.959	CLONAL	1	TRUE	0	0.588313153170404	1		465	516	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1650234	1650234	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	171	510	0	ENST00000344749.5:c.14A>T	p.Gln5Leu	p.Q5L	ENST00000344749	NM_001136139.2	5	cAg/cTg	2/19	0.588313153170404	1	FACETS	0.906	0.842	0.971	0.906	0.842	0.971	CLONAL	1	TRUE	0	0.588313153170404	1		510	453	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792795	33792795	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	155	156	0	ENST00000498907.2:c.526G>T	p.Ala176Ser	p.A176S	ENST00000498907	NM_004364.3	176	Gcc/Tcc	1/1	0.536950999453196	4	FACETS	1	0.967	1			1	CLONAL	2	TRUE	NA	0.588313153170404	4		156	389	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383227	31383227	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148132847	NA	P-0017385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	354	459	1	ENST00000328111.2:c.1139G>A	p.Arg380Gln	p.R380Q	ENST00000328111	NM_006892.3	380	cGa/cAa	11/23	0.57752874936916	4	FACETS	0.976	0.927	1	0.976	0.927	1	CLONAL	2	TRUE	2	0.588313153170404	4		460	979	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306761	41306761	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	212	267	1	ENST00000373198.4:c.898G>T	p.Val300Leu	p.V300L	ENST00000373198	NM_133170.3	300	Gtg/Ttg	7/32	0.418825692034127	4	FACETS	0.978	0.915	1			1	CLONAL	2	TRUE	NA	0.588313153170404	4		268	585	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069428	30069429	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0017385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	216	321	2	ENST00000338641.4:c.1293_1294delinsTT	p.Glu432Ter	p.E432*	ENST00000338641	NM_000268.3	431	ctGGaa/ctTTaa	12/16	0.588313153170404	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.588313153170404	2		323	364	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266170	41266170	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	108	259	0	ENST00000349496.5:c.167A>T	p.Asp56Val	p.D56V	ENST00000349496	NM_001904.3	56	gAt/gTt	3/15	1	2	FACETS	0.932	0.843	1	0.932	0.843	1	CLONAL	1	TRUE	1	0.588313153170404	2		259	394	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247469	71247469	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	140	519	0	ENST00000318789.4:c.64G>C	p.Gly22Arg	p.G22R	ENST00000318789	NM_032682.5	22	Ggc/Cgc	6/21	1	2	FACETS	0.8	0.731	0.871	0.8	0.731	0.871	SUBCLONAL	1	TRUE	1	0.588313153170404	2		519	595	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430325	181430325	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	211	301	1	ENST00000325404.1:c.177G>T	p.Met59Ile	p.M59I	ENST00000325404	NM_003106.3	59	atG/atT	1/1	0.57752874936916	4	FACETS	0.961	0.898	1	0.961	0.898	1	CLONAL	2	TRUE	2	0.588313153170404	4		302	593	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980326	55980326	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	452	503	0	ENST00000263923.4:c.765del	p.Ile256LeufsTer18	p.I256Lfs*18	ENST00000263923	NM_002253.2	255	ggG/gg	6/30	0.530013862757647	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.588313153170404	4		503	1171	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467839	66467839	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	217	282	0	ENST00000273854.3:c.430C>A	p.Leu144Met	p.L144M	ENST00000273854	NM_004439.5	144	Ctg/Atg	3/18	0.530013862757647	4	FACETS	0.931	0.871	0.993	0.931	0.871	0.993	CLONAL	2	TRUE	2	0.588313153170404	4		282	629	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965545	93965545	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0017385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	369	313	0	ENST00000369303.4:c.2382+1G>T		p.X794_splice	ENST00000369303	NM_004440.3	794			0.569859840879747	3	FACETS	0.935	0.899	0.969	0.935	0.899	0.969	CLONAL	3	TRUE	0	0.588313153170404	3		313	579	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066551	94066551	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	372	349	0	ENST00000369303.4:c.1208T>A	p.Met403Lys	p.M403K	ENST00000369303	NM_004440.3	403	aTg/aAg	5/17	0.569859840879747	3	FACETS	0.931	0.896	0.965	0.931	0.896	0.965	CLONAL	3	TRUE	0	0.588313153170404	3		349	586	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542675	141542675	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	425	410	0	ENST00000220592.5:c.2311G>T	p.Asp771Tyr	p.D771Y	ENST00000220592	NM_012154.3	771	Gac/Tac	18/19	0.588313153170404	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.588313153170404	3		410	879	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465548	8465548	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	212	527	1	ENST00000356435.5:c.3632A>G	p.Tyr1211Cys	p.Y1211C	ENST00000356435		1211	tAt/tGt	21/35	0.588313153170404	1	FACETS	0.897	0.84	0.956	0.897	0.84	0.956	CLONAL	1	TRUE	0	0.588313153170404	1		528	567	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231097	53231097	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	349	227	0	ENST00000375401.3:c.1805A>G	p.His602Arg	p.H602R	ENST00000375401	NM_004187.3	602	cAc/cGc	13/26	0.536950999453196	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.588313153170404	2		227	481	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202483	123202483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	410	171	0	ENST00000218089.9:c.2335G>A	p.Val779Met	p.V779M	ENST00000218089	NM_001042749.1	779	Gtg/Atg	24/35	0.536950999453196	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.588313153170404	2		171	561	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0017386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	1022	367	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.290279017568396	14	FACETS	0.955	0.93	0.98			1	CLONAL	10	TRUE	NA	0.290279017568396	14		367	2022	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577088	7577088	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1204379654	NA	P-0017386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	217	667	0	ENST00000269305.4:c.850A>C	p.Thr284Pro	p.T284P	ENST00000269305	NM_001126112.2	284	Aca/Cca	8/11	1	2	FACETS	0.764	0.711	0.82	1	0.992	1	SUBCLONAL	2	TRUE	1	0.290279017568396	2		667	978	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521327	8521327	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	161	330	0	ENST00000356435.5:c.911C>G	p.Ala304Gly	p.A304G	ENST00000356435		304	gCt/gGt	9/35	0.27996973577755	2	FACETS	0.948	0.874	1	0.948	0.874	1	CLONAL	2	TRUE	0	0.290279017568396	2		330	585	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593615	+	inframe_deletion	In_Frame_Del	DEL	AGTGGAAGGTTGTTG	AGTGGAAGGTTGTTG	-	novel	NA	P-0017387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	311	376	0	ENST00000288135.5:c.1669_1683del	p.Trp557_Glu561del	p.W557_E561del	ENST00000288135	NM_000222.2	556	cAGTGGAAGGTTGTTGag/cag	11/21	0.180967428434786	4	FACETS	0.911	0.866	0.955			1	INDETERMINATE	3	TRUE	NA	0.54697377939236	4		376	644	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0017388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	322	536	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	0.207961205184755	5	FACETS	0.854	0.809	0.9	0.854	0.809	0.9	INDETERMINATE	3	TRUE	2	0.465759582330328	5		536	917	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577555	7577555	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs375874539	NA	P-0017388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	302	480	0	ENST00000269305.4:c.726C>G	p.Cys242Trp	p.C242W	ENST00000269305	NM_001126112.2	242	tgC/tgG	7/11	NA	2	FACETS	0.982	0.933	1			1	INDETERMINATE	2	TRUE	NA	0.465759582330328	2		480	660	SUCCESS
ATM	472	MSKCC	GRCh37	11	108127026	108127026	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	238	427	0	ENST00000278616.4:c.2209G>A	p.Glu737Lys	p.E737K	ENST00000278616	NM_000051.3	737	Gaa/Aaa	14/63	0.407677906488844	4	FACETS	0.828	0.774	0.883			1	CLONAL	2	TRUE	NA	0.465759582330328	4		427	905	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880464	155880464	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	367	481	0	ENST00000368323.3:c.89G>T	p.Gly30Val	p.G30V	ENST00000368323	NM_006912.5	30	gGt/gTt	2/6	0.412177281488604	4	FACETS	0.876	0.835	0.918	0.876	0.835	0.918	CLONAL	3	TRUE	1	0.465759582330328	4		481	879	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28980027	28980027	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	173	361	0	ENST00000282397.4:c.1441G>T	p.Asp481Tyr	p.D481Y	ENST00000282397	NM_002019.4	481	Gac/Tac	11/30	0.421389472724883	4	FACETS	0.893	0.825	0.962	0.893	0.825	0.962	CLONAL	2	TRUE	2	0.465759582330328	4		361	610	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003513	42003513	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	144	494	0	ENST00000219905.7:c.3050C>T	p.Ala1017Val	p.A1017V	ENST00000219905	NM_001164273.1	1017	gCa/gTa	8/24	0.207961205184755	5	FACETS	1	0.984	1	0.454	0.414	0.496	INDETERMINATE	1	TRUE	2	0.465759582330328	5		494	771	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041614	14041614	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	195	365	0	ENST00000311895.7:c.2161G>T	p.Glu721Ter	p.E721*	ENST00000311895	NM_005236.2	721	Gaa/Taa	11/11	0.207961205184755	5	FACETS	1	0.983	1	0.786	0.732	0.842	INDETERMINATE	2	TRUE	2	0.465759582330328	5		365	603	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78882665	78882665	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	177	580	0	ENST00000306801.3:c.2456C>G	p.Ala819Gly	p.A819G	ENST00000306801	NM_020761.2	819	gCt/gGt	21/34	0.338817468648604	3	FACETS	1	0.976	1	0.572	0.528	0.618	CLONAL	1	TRUE	1	0.465759582330328	3		580	819	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610085	10610085	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs756706383	NA	P-0017388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	414	644	0	ENST00000171111.5:c.625A>G	p.Met209Val	p.M209V	ENST00000171111	NM_203500.1	209	Atg/Gtg	2/6	0.465759582330328	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.465759582330328	2		644	851	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098821	178099325	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTAACTGAGCGAAAAAGGCTTTCTCTTGCTCCTTTTGGAGTTGTTCTTGTCTTTCCTTTTCAAGTTTTTTCTGTTTTTCCAGCTCATACTCTTTCCGTCGCTGACTGAAGTCAAATACTTCTCGACTTACTCCAAGATCTATATCTTGCCTCCAAAGTATGTCAATCAAATCCATGTCCTATGTTTAAGACAAAAAAAGGAAGGAGAGAGCTCATGTTTTTTAAATGACAGATACCACATAAATTAATTCACATTATGCCACTGTTGATGGTGGGAAGTGGGGAGATTACAAATACAATCTAAATGAGAACACAGATCCAATGTTCTAGAAGAGCACAGTTAATTCCATTCAATGAATCTATTCATTAAAGACAACAAACAACCTACAAACACATAGCCATCCATTCTAATCACTTGGATCATTAATGATAGGGTGATGGTAGAGGTCACTAAAGGGCAAAGTCACAAATGGTTTGAATGAGAAGAAATCCCACCCTTGTTTAA	TGTAACTGAGCGAAAAAGGCTTTCTCTTGCTCCTTTTGGAGTTGTTCTTGTCTTTCCTTTTCAAGTTTTTTCTGTTTTTCCAGCTCATACTCTTTCCGTCGCTGACTGAAGTCAAATACTTCTCGACTTACTCCAAGATCTATATCTTGCCTCCAAAGTATGTCAATCAAATCCATGTCCTATGTTTAAGACAAAAAAAGGAAGGAGAGAGCTCATGTTTTTTAAATGACAGATACCACATAAATTAATTCACATTATGCCACTGTTGATGGTGGGAAGTGGGGAGATTACAAATACAATCTAAATGAGAACACAGATCCAATGTTCTAGAAGAGCACAGTTAATTCCATTCAATGAATCTATTCATTAAAGACAACAAACAACCTACAAACACATAGCCATCCATTCTAATCACTTGGATCATTAATGATAGGGTGATGGTAGAGGTCACTAAAGGGCAAAGTCACAAATGGTTTGAATGAGAAGAAATCCCACCCTTGTTTAA	-	novel	NA	P-0017388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	118	597	0	ENST00000397062.3:c.46-326_224del		p.X16_splice	ENST00000397062	NM_006164.4	16		2/5	0.444071761551263	3	FACETS	0.765	0.69	0.844	0.382	0.345	0.422	SUBCLONAL	1	TRUE	1	0.465759582330328	3		597	817	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121090	29121090	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1555927004	NA	P-0017388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	328	642	1	ENST00000328354.6:c.467A>T	p.Tyr156Phe	p.Y156F	ENST00000328354	NM_007194.3	156	tAc/tTc	4/15	0.239779787148224	5	FACETS	1	0.978	1	0.711	0.672	0.751	INDETERMINATE	2	TRUE	2	0.465759582330328	5		643	1122	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217116	66217116	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	40	380	3	ENST00000273854.3:c.2499C>A	p.Tyr833Ter	p.Y833*	ENST00000273854	NM_004439.5	833	taC/taA	14/18	0.207961205184755	5	FACETS	0.487	0.404	0.58	0.162	0.134	0.194	INDETERMINATE	1	TRUE	2	0.465759582330328	5		383	599	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081671	143081671	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	28	329	0	ENST00000262992.4:c.1403G>C	p.Ser468Thr	p.S468T	ENST00000262992	NM_001101669.1	468	aGt/aCt	15/24	0.207961205184755	5	FACETS	0.438	0.35	0.54	0.146	0.116	0.18	INDETERMINATE	1	TRUE	2	0.465759582330328	5		329	466	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	45	408	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.785	0.659	0.925	0.785	0.659	0.925	CLONAL	1	TRUE	1	0.18	2		408	637	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987177	36987177	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs886041803	NA	P-0017389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	126	609	3	ENST00000354822.5:c.512del	p.Gly171AlafsTer9	p.G171Afs*9	ENST00000354822	NM_001079668.2	171	gGc/gc	3/3	1	2	FACETS	0.782	0.708	0.861	1	0.986	1	SUBCLONAL	2	TRUE	1	0.18	2		612	895	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578517	7578520	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	novel	NA	P-0017389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1231	114	821	0	ENST00000269305.4:c.410_413del	p.Leu137ProfsTer32	p.L137Pfs*32	ENST00000269305	NM_001126112.2	137	cTGGCc/cc	5/11	1	2	FACETS	0.942	0.845	1	0.942	0.845	1	CLONAL	1	TRUE	1	0.18	2		821	1345	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0017390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	237	367	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.322922635661235	4	FACETS	0.789	0.735	0.844	0.789	0.735	0.844	SUBCLONAL	2	TRUE	2	0.324073201544794	4		367	1228	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624299	89624299	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs398123326	NA	P-0017390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	146	465	0	ENST00000371953.3:c.73T>G	p.Leu25Val	p.L25V	ENST00000371953	NM_000314.4	25	Ttg/Gtg	1/9	1	2	FACETS	0.97	0.885	1	0.97	0.885	1	CLONAL	1	TRUE	1	0.324073201544794	2		465	929	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	73	301	4				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.365873421980999	2		305	301	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971116	21971116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552823	NA	P-0017412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	112	442	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	0.365873421980999	2		442	594	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136107	11136107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749947536	NA	P-0017412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	113	491	0	ENST00000358026.2:c.3091G>A	p.Gly1031Ser	p.G1031S	ENST00000358026	NM_001128849.1	1031	Ggc/Agc	22/36	1	2	FACETS	0.993	0.896	1	0.993	0.896	1	CLONAL	1	TRUE	1	0.365873421980999	2		491	622	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136325	2136325	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	148	436	0	ENST00000219476.3:c.4794del	p.Asp1598GlufsTer27	p.D1598Efs*27	ENST00000219476	NM_000548.3	1598	gaC/ga	37/42	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.365873421980999	2		436	659	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2137938	2137939	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	133	390	0	ENST00000219476.3:c.5067dup	p.Asp1690ArgfsTer16	p.D1690Rfs*16	ENST00000219476	NM_000548.3	1688	-/A	39/42	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.365873421980999	2		390	516	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416431	29416431	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764315254	NA	P-0017412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	89	496	0	ENST00000389048.3:c.4522G>A	p.Gly1508Ser	p.G1508S	ENST00000389048	NM_004304.4	1508	Ggc/Agc	29/29	1	2	FACETS	0.885	0.786	0.989	0.885	0.786	0.989	CLONAL	1	TRUE	1	0.365873421980999	2		496	550	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140449179	140449179	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	52	340	0	ENST00000288602.6:c.1900A>G	p.Ser634Gly	p.S634G	ENST00000288602	NM_004333.4	634	Agc/Ggc	16/18	1	2	FACETS	0.994	0.852	1	0.994	0.852	1	CLONAL	1	TRUE	1	0.365873421980999	2		340	286	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017412-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	95	301	4				ENST00000310581	NM_198253.2	-/1132			0.144901098275011	2	FACETS	0.84	0.751	0.933	1	0.972	1	CLONAL	3	FALSE	0	0.163996939154018	2		305	460	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971116	21971116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552823	NA	P-0017412-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	123	442	0	ENST00000304494.5:c.242C>T	p.Pro81Leu	p.P81L	ENST00000304494	NM_000077.4	81	cCc/cTc	2/3	0.144901098275011	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	FALSE	0	0.163996939154018	2		442	606	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136107	11136107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749947536	NA	P-0017412-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	180	491	0	ENST00000358026.2:c.3091G>A	p.Gly1031Ser	p.G1031S	ENST00000358026	NM_001128849.1	1031	Ggc/Agc	22/36	0.144901098275011	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	FALSE	0	0.163996939154018	2		491	962	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136325	2136325	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017412-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	169	436	0	ENST00000219476.3:c.4794del	p.Asp1598GlufsTer27	p.D1598Efs*27	ENST00000219476	NM_000548.3	1598	gaC/ga	37/42	0.144901098275011	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	FALSE	0	0.163996939154018	2		436	913	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2137938	2137939	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017412-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	164	390	0	ENST00000219476.3:c.5067dup	p.Asp1690ArgfsTer16	p.D1690Rfs*16	ENST00000219476	NM_000548.3	1688	-/A	39/42	0.144901098275011	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	FALSE	0	0.163996939154018	2		390	841	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416431	29416431	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764315254	NA	P-0017412-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	232	496	0	ENST00000389048.3:c.4522G>A	p.Gly1508Ser	p.G1508S	ENST00000389048	NM_004304.4	1508	Ggc/Agc	29/29	0.144901098275011	2	FACETS	0.883	0.823	0.945	1	0.99	1	CLONAL	3	FALSE	0	0.163996939154018	2		496	1068	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140449179	140449179	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017412-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	123	340	0	ENST00000288602.6:c.1900A>G	p.Ser634Gly	p.S634G	ENST00000288602	NM_004333.4	634	Agc/Ggc	16/18	0.144901098275011	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	FALSE	0	0.163996939154018	2		340	609	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166382	118166382	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017412-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	239	326	0	ENST00000369448.3:c.892G>A	p.Glu298Lys	p.E298K	ENST00000369448	NM_017709.3	298	Gaa/Aaa	2/2	1	2	FACETS	1	0.984	1	1	0.996	1	CLONAL	3	FALSE	1	0.163996939154018	2		326	841	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332424	70332424	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017412-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	234	501	0	ENST00000373644.4:c.329C>G	p.Ser110Cys	p.S110C	ENST00000373644	NM_030625.2	110	tCt/tGt	2/12	0.144901098275011	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	FALSE	0	0.163996939154018	2		501	1304	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028390	42028390	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs779824999	NA	P-0017412-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	35	206	0	ENST00000219905.7:c.3928A>C	p.Lys1310Gln	p.K1310Q	ENST00000219905	NM_001164273.1	1310	Aag/Cag	13/24	0.144901098275011	2	FACETS	0.845	0.692	1	0.423	0.346	0.509	CLONAL	1	FALSE	0	0.163996939154018	2		206	505	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420005	41420005	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017412-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	88	319	1	ENST00000373198.4:c.316C>A	p.His106Asn	p.H106N	ENST00000373198	NM_133170.3	106	Cat/Aat	3/32	0.144901098275011	2	FACETS	1	0.976	1	0.707	0.626	0.794	CLONAL	1	FALSE	0	0.163996939154018	2		320	759	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72866432	72866435	+	frameshift_variant	Frame_Shift_Del	DEL	ATCA	ATCA	-	rs571329853	NA	P-0017412-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	83	324	0	ENST00000325599.8:c.828_831del	p.Asp277SerfsTer27	p.D277Sfs*27	ENST00000325599	NM_018130.2	276	atTGAT/at	7/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.163996939154018	2		324	817	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0017413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	110	290	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	0.271311738133582	2		290	656	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0017413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	84	368	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.886	0.782	0.997	0.886	0.782	0.997	CLONAL	1	TRUE	1	0.271311738133582	2		368	699	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258035	123258035	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	141	466	0	ENST00000358487.5:c.1646A>C	p.Asn549Thr	p.N549T	ENST00000358487	NM_000141.4	549	aAt/aCt	12/18	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.271311738133582	2		466	975	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023208	27023227	+	frameshift_variant	Frame_Shift_Del	DEL	GGAACGCGGGCCCTAGGCCC	GGAACGCGGGCCCTAGGCCC	-	novel	NA	P-0017413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	71	203	0	ENST00000324856.7:c.315_334del	p.Asn106ProfsTer4	p.N106Pfs*4	ENST00000324856	NM_006015.4	105	gGGAACGCGGGCCCTAGGCCC/g	1/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.271311738133582	2		203	465	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101650	27101669	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTGTTGAAGCCACACAGC	CTCTGTTGAAGCCACACAGC	-	novel	NA	P-0017413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	152	597	0	ENST00000324856.7:c.4934_4953del	p.Ser1645CysfsTer46	p.S1645Cfs*46	ENST00000324856	NM_006015.4	1644	ggCTCTGTTGAAGCCACACAGCct/ggct	18/20	1	2	FACETS	0.876	0.799	0.957	0.876	0.799	0.957	CLONAL	1	TRUE	1	0.271311738133582	2		597	1279	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100546	157100547	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	68	229	0	ENST00000346085.5:c.1486dup	p.Arg496LysfsTer39	p.R496Kfs*39	ENST00000346085	NM_020732.3	495	caa/cAaa	1/20	1	2	FACETS	0.948	0.826	1	0.948	0.826	1	CLONAL	1	TRUE	1	0.271311738133582	2		229	529	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	51	301	4				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.21	2		305	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519998	NA	P-0017415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	120	467	1	ENST00000269305.4:c.581T>A	p.Leu194His	p.L194H	ENST00000269305	NM_001126112.2	194	cTt/cAt	6/11	0.178550066436158	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.21	1		468	983	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551083	41551083	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	103	429	0	ENST00000263253.7:c.3227G>A	p.Arg1076His	p.R1076H	ENST00000263253	NM_001429.3	1076	cGt/cAt	17/31	1	2	FACETS	0.866	0.773	0.965	0.866	0.773	0.965	CLONAL	1	TRUE	1	0.21	2		429	1133	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251236	99251236	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	88	447	0	ENST00000268035.6:c.540C>A	p.Asp180Glu	p.D180E	ENST00000268035	NM_000875.3	180	gaC/gaA	2/21	1	2	FACETS	0.775	0.685	0.872	0.775	0.685	0.872	SUBCLONAL	1	TRUE	1	0.21	2		447	1081	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993648	72993648	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	67	373	0	ENST00000268489.5:c.397A>G	p.Ile133Val	p.I133V	ENST00000268489	NM_006885.3	133	Atc/Gtc	2/10	1	2	FACETS	0.738	0.64	0.844	0.738	0.64	0.844	SUBCLONAL	1	TRUE	1	0.21	2		373	865	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013711	12013711	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	78	350	0	ENST00000353533.5:c.653A>C	p.His218Pro	p.H218P	ENST00000353533	NM_003010.3	218	cAc/cCc	6/11	0.178550066436158	1	FACETS	0.77	0.675	0.872	0.77	0.675	0.872	SUBCLONAL	1	TRUE	0	0.21	1		350	864	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383813	15383813	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	68	406	0	ENST00000263377.2:c.98C>G	p.Ala33Gly	p.A33G	ENST00000263377	NM_058243.2	33	gCc/gGc	2/20	1	2	FACETS	0.718	0.623	0.821	0.718	0.623	0.821	SUBCLONAL	1	TRUE	1	0.21	2		406	902	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149553	202149553	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	66	372	0	ENST00000358485.4:c.994A>C	p.Thr332Pro	p.T332P	ENST00000358485	NM_001080125.1	332	Acc/Ccc	8/9	0.178550066436158	1	FACETS	0.73	0.632	0.836	0.73	0.632	0.836	SUBCLONAL	1	TRUE	0	0.21	1		372	771	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643374	52643374	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	103	523	0	ENST00000394830.3:c.2522A>G	p.Gln841Arg	p.Q841R	ENST00000394830	NM_018313.4	841	cAa/cGa	17/30	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.21	2		523	931	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434070	121434070	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766770471	NA	P-0017416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	66	332	1	ENST00000257555.6:c.961C>T	p.Arg321Cys	p.R321C	ENST00000257555		321	Cgc/Tgc	5/10	0.722402846108969	2	FACETS	0.257	0.222	0.294	0.128	0.111	0.147	SUBCLONAL	1	TRUE	0	0.722402846108969	2		333	711	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549431	187549431	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	486	390	0	ENST00000441802.2:c.4687A>G	p.Thr1563Ala	p.T1563A	ENST00000441802	NM_005245.3	1563	Acc/Gcc	9/27	0.573859415105518	4	FACETS	0.896	0.858	0.935	0.896	0.858	0.935	CLONAL	2	TRUE	2	0.722402846108969	4		390	1293	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005003	150005003	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	142	249	1	ENST00000253339.5:c.1222T>G	p.Ser408Ala	p.S408A	ENST00000253339		408	Tct/Gct	3/7	0.295919341770146	2	FACETS	0.655	0.599	0.713	0.328	0.299	0.357	INDETERMINATE	1	TRUE	0	0.722402846108969	2		250	600	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937949	76937950	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0017416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	549	448	0	ENST00000373344.5:c.2798_2799del	p.Ser933PhefsTer4	p.S933Ffs*4	ENST00000373344	NM_000489.3	933	tCT/t	9/35	0.247770100212753	3	FACETS	1	0.974	1			1	INDETERMINATE	2	TRUE	NA	0.722402846108969	3		448	1023	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0017417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	124	390	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.716046729336946	2		392	317	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0017417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	157	308	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.884	0.816	0.954	0.884	0.816	0.954	CLONAL	1	TRUE	1	0.716046729336946	2		308	496	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781440	135781440	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203542	NA	P-0017418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	32	322	1	ENST00000298552.3:c.1525C>T	p.Arg509Ter	p.R509*	ENST00000298552	NM_001162426.1	509	Cga/Tga	15/23	0.86821690438664	1	FACETS	0.097	0.078	0.118	0.097	0.078	0.118	SUBCLONAL	1	TRUE	0	0.86821690438664	1		323	430	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922927	39922927	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	450	234	1	ENST00000378444.4:c.3781del	p.Arg1261GlyfsTer33	p.R1261Gfs*33	ENST00000378444	NM_001123385.1	1261	Agg/gg	8/15	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.86821690438664	1		235	543	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164962	123164962	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	209	116	0	ENST00000218089.9:c.275A>G	p.Lys92Arg	p.K92R	ENST00000218089	NM_001042749.1	92	aAg/aGg	5/35	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.86821690438664	1		116	238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	139	518	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.156016097405724	5	FACETS	1	0.942	1	0.524	0.476	0.575	CLONAL	2	TRUE	1	0.156016097405724	5		518	1049	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008017	29008017	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	42	295	0	ENST00000282397.4:c.752A>T	p.Asn251Ile	p.N251I	ENST00000282397	NM_002019.4	251	aAt/aTt	6/30	0.131089395713259	4	FACETS	1	0.943	1	0.662	0.553	0.783	CLONAL	1	TRUE	2	0.156016097405724	4		295	470	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041687	42041706	+	frameshift_variant	Frame_Shift_Del	DEL	AGCATGTTGCTTCCCTTCAG	AGCATGTTGCTTCCCTTCAG	-	novel	NA	P-0017421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	39	428	0	ENST00000219905.7:c.5883_5902del	p.Gln1961HisfsTer13	p.Q1961Hfs*13	ENST00000219905	NM_001164273.1	1961	cAGCATGTTGCTTCCCTTCAG/c	17/24	0.151532956024052	3	FACETS	0.712	0.588	0.851	0.356	0.294	0.426	SUBCLONAL	1	TRUE	1	0.156016097405724	3		428	757	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923386	9923386	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	124	503	0	ENST00000330684.3:c.1901G>T	p.Trp634Leu	p.W634L	ENST00000330684	NM_001134407.1	634	tGg/tTg	9/13	0.156016097405724	3	FACETS	0.994	0.899	1	0.994	0.899	1	CLONAL	2	TRUE	1	0.156016097405724	3		503	862	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063353	67063353	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	142	328	0	ENST00000412916.2:c.43G>C	p.Glu15Gln	p.E15Q	ENST00000412916		15	Gag/Cag	1/6	0.156016097405724	7	FACETS	1	0.978	1			1	CLONAL	2	TRUE	NA	0.156016097405724	7		328	1019	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456514	29456514	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1213	143	571	0	ENST00000389048.3:c.2404G>C	p.Glu802Gln	p.E802Q	ENST00000389048	NM_004304.4	802	Gaa/Caa	14/29	0.156016097405724	8	FACETS	0.992	0.902	1	0.397	0.36	0.435	CLONAL	2	TRUE	3	0.156016097405724	8		571	1356	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391745	139391753	+	inframe_deletion	In_Frame_Del	DEL	AGGCTGCCC	AGGCTGCCC	-	novel	NA	P-0017421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	66	447	0	ENST00000277541.6:c.6438_6446del	p.Gly2147_Leu2149del	p.G2147_L2149del	ENST00000277541	NM_017617.3	2146	ctGGGCAGCCTc/ctc	34/34	0.156016097405724	8	FACETS	1	0.905	1	0.212	0.183	0.243	CLONAL	1	TRUE	3	0.156016097405724	8		447	1174	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0017422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	300	178	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.394078981650083	3	FACETS	0.854	0.808	0.901	0.854	0.808	0.901	CLONAL	2	TRUE	1	0.559248238564734	3		178	804	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952141	178952142	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0017422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	231	415	2	ENST00000263967.3:c.3196_3197delinsTT	p.Ala1066Leu	p.A1066L	ENST00000263967	NM_006218.2	1066	GCa/TTa	21/21	0.394078981650083	3	FACETS	1	0.993	1	0.75	0.702	0.798	CLONAL	1	TRUE	1	0.559248238564734	3		417	705	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874092	151874092	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	161	555	0	ENST00000262189.6:c.8446T>A	p.Ser2816Thr	p.S2816T	ENST00000262189	NM_170606.2	2816	Tcc/Acc	38/59	0.550362556143111	1	FACETS	0.578	0.532	0.627	0.578	0.532	0.627	SUBCLONAL	1	TRUE	0	0.559248238564734	1		555	717	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0017424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	373	180	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.893	0.849	0.937	0.893	0.849	0.937	CLONAL	1	TRUE	1	0.809685282089771	2		180	1032	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0017424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	532	606	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.881	0.845	0.918	0.881	0.845	0.918	CLONAL	1	TRUE	1	0.809685282089771	2		606	1491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0017424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	559	632	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.809884987680157	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.809685282089771	1		634	769	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16021200	16021200	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0017424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	232	248	0	ENST00000268712.3:c.2055+2T>G		p.X685_splice	ENST00000268712	NM_006311.3	685			0.809884987680157	1	FACETS	0.974	0.93	1	0.974	0.93	1	CLONAL	1	TRUE	0	0.809685282089771	1		248	350	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220154	36220154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1460	338	499	1	ENST00000222270.7:c.4874C>T	p.Ser1625Phe	p.S1625F	ENST00000222270	NM_014727.1	1625	tCc/tTc	22/37	0.809884987680157	3	FACETS	0.652	0.615	0.691			1	SUBCLONAL	1	TRUE	NA	0.809685282089771	3		500	1798	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259084	153259084	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	163	201	0	ENST00000281708.4:c.731G>A	p.Trp244Ter	p.W244*	ENST00000281708	NM_033632.3	244	tGg/tAg	5/12	1	2	FACETS	0.939	0.871	1	0.939	0.871	1	CLONAL	1	TRUE	1	0.809685282089771	2		201	429	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0017426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	168	463	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.193585732093353	4	FACETS	0.772	0.709	0.839	0.772	0.709	0.839	SUBCLONAL	2	FALSE	2	0.258771091102076	4		463	1058	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0017426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	337	696	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.258771091102076	2	FACETS	0.944	0.891	0.997	0.944	0.891	0.997	CLONAL	2	FALSE	0	0.258771091102076	2		696	1380	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132833	64132833	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1447050686	NA	P-0017426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1309	130	644	1	ENST00000334205.4:c.967C>T	p.Arg323Cys	p.R323C	ENST00000334205	NM_003942.2	323	Cgc/Tgc	9/17	0.193585732093353	4	FACETS	0.879	0.794	0.969	0.439	0.397	0.485	CLONAL	1	FALSE	2	0.258771091102076	4		645	1439	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	218	601	0	ENST00000269305.4:c.569del	p.Pro190LeufsTer57	p.P190Lfs*57	ENST00000269305	NM_001126112.2	190	cCt/ct	6/11	0.209474279087063	2	FACETS	1	0.991	1	0.736	0.684	0.791	CLONAL	1	FALSE	0	0.258771091102076	2		601	1144	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105635	27105635	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs370901533	NA	P-0017426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	122	377	0	ENST00000324856.7:c.5246G>T	p.Arg1749Met	p.R1749M	ENST00000324856	NM_006015.4	1749	aGg/aTg	20/20	0.258771091102076	3	FACETS	1	0.972	1	0.601	0.543	0.663	CLONAL	1	FALSE	1	0.258771091102076	3		377	886	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217206	66217207	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0017426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	135	526	1	ENST00000273854.3:c.2408_2409delinsAA	p.Ala803Glu	p.A803E	ENST00000273854	NM_004439.5	803	gCC/gAA	14/18	0.214098262960207	3	FACETS	1	0.965	1	0.563	0.511	0.618	CLONAL	1	FALSE	1	0.258771091102076	3		527	1046	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213898	66213898	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	104	522	0	ENST00000273854.3:c.2532G>T	p.Trp844Cys	p.W844C	ENST00000273854	NM_004439.5	844	tgG/tgT	15/18	0.214098262960207	3	FACETS	0.811	0.724	0.904	0.406	0.362	0.452	CLONAL	1	FALSE	1	0.258771091102076	3		522	1119	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843473	156843473	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	123	416	0	ENST00000524377.1:c.899G>T	p.Cys300Phe	p.C300F	ENST00000524377	NM_002529.3	300	tGc/tTc	8/17	0.258771091102076	3	FACETS	1	0.918	1	0.509	0.459	0.562	CLONAL	1	FALSE	1	0.258771091102076	3		416	1054	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163313579	163313579	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	266	550	0	ENST00000271452.3:c.730del	p.Ile244LeufsTer8	p.I244Lfs*8	ENST00000271452	NM_145697.2	242	acA/ac	10/14	0.258771091102076	3	FACETS	0.967	0.906	1	0.967	0.906	1	CLONAL	2	FALSE	1	0.258771091102076	3		550	1200	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	465599	465599	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	109	567	0	ENST00000399788.2:c.777A>T	p.Glu259Asp	p.E259D	ENST00000399788	NM_001042603.1	259	gaA/gaT	6/28	0.258771091102076	2	FACETS	0.684	0.613	0.761	0.342	0.306	0.381	SUBCLONAL	1	FALSE	0	0.258771091102076	2		567	1231	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858597	57858597	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1206	117	635	1	ENST00000228682.2:c.335C>A	p.Ser112Ter	p.S112*	ENST00000228682	NM_005269.2	112	tCg/tAg	4/12	0.202327778785617	3	FACETS	0.772	0.694	0.855	0.257	0.231	0.285	SUBCLONAL	1	FALSE	0	0.258771091102076	3		636	1323	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28882990	28882990	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	109	700	0	ENST00000282397.4:c.3710C>A	p.Ser1237Tyr	p.S1237Y	ENST00000282397	NM_002019.4	1237	tCc/tAc	28/30	1	2	FACETS	0.738	0.661	0.821	0.738	0.661	0.821	SUBCLONAL	1	FALSE	1	0.258771091102076	2		700	1141	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858219	59858219	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	146	493	0	ENST00000259008.2:c.1776G>T	p.Trp592Cys	p.W592C	ENST00000259008	NM_032043.2	592	tgG/tgT	12/20	0.258771091102076	5	FACETS	1	0.981	1	0.432	0.393	0.473	CLONAL	1	FALSE	2	0.258771091102076	5		493	1209	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248538	212248539	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0017426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	151	440	1	ENST00000342788.4:c.3728_3729delinsTT	p.Trp1243Phe	p.W1243F	ENST00000342788	NM_005235.2	1243	tGG/tTT	28/28	0.193585732093353	4	FACETS	0.751	0.686	0.819	0.751	0.686	0.819	SUBCLONAL	2	FALSE	2	0.258771091102076	4		441	978	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462302	89462302	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1463230067	NA	P-0017426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	154	535	0	ENST00000336596.2:c.1774G>T	p.Gly592Cys	p.G592C	ENST00000336596	NM_005233.5	592	Ggt/Tgt	10/17	0.258771091102076	3	FACETS	1	0.984	1	0.663	0.606	0.723	CLONAL	1	FALSE	1	0.258771091102076	3		535	1013	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873092	134873092	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	213	610	0	ENST00000398015.3:c.1396G>T	p.Asp466Tyr	p.D466Y	ENST00000398015	NM_004441.4	466	Gac/Tac	6/16	0.258771091102076	3	FACETS	0.773	0.717	0.832	0.773	0.717	0.832	SUBCLONAL	2	FALSE	1	0.258771091102076	3		610	1202	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55143626	55143626	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	68	391	1	ENST00000257290.5:c.1858C>A	p.Pro620Thr	p.P620T	ENST00000257290	NM_006206.4	620	Cct/Act	13/23	0.214098262960207	3	FACETS	0.764	0.664	0.873	0.382	0.332	0.437	SUBCLONAL	1	FALSE	1	0.258771091102076	3		392	777	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639041	176639139	+	inframe_deletion	In_Frame_Del	DEL	TTGAGGAACCACTGACAGAGCAAAATCATGCTGACTGCTTAGATTCAGCTGGGCCACGGTTAAATGTTTGTGATAAATCCAGTGCCAGCATTGGTGACA	TTGAGGAACCACTGACAGAGCAAAATCATGCTGACTGCTTAGATTCAGCTGGGCCACGGTTAAATGTTTGTGATAAATCCAGTGCCAGCATTGGTGACA	-	novel	NA	P-0017426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	129	566	0	ENST00000439151.2:c.3642_3740del	p.Glu1216_Glu1248del	p.E1216_E1248del	ENST00000439151	NM_022455.4	1214	cTTGAGGAACCACTGACAGAGCAAAATCATGCTGACTGCTTAGATTCAGCTGGGCCACGGTTAAATGTTTGTGATAAATCCAGTGCCAGCATTGGTGACAtg/ctg	5/23	0.203679973619197	3	FACETS	1	0.905	1	0.5	0.452	0.551	CLONAL	1	FALSE	1	0.258771091102076	3		566	1126	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053182	180053182	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	195	690	1	ENST00000261937.6:c.1187C>A	p.Thr396Asn	p.T396N	ENST00000261937	NM_182925.4	396	aCc/aAc	9/30	0.200585298092163	3	FACETS	1	0.988	1			1	CLONAL	1	FALSE	NA	0.258771091102076	3		691	1261	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388038	81388038	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	239	626	0	ENST00000222390.5:c.337G>C	p.Gly113Arg	p.G113R	ENST00000222390	NM_000601.4	113	Ggc/Cgc	3/18	0.193585732093353	4	FACETS	0.866	0.807	0.928	0.866	0.807	0.928	CLONAL	2	FALSE	2	0.258771091102076	4		626	1342	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410394	63410394	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1241	166	657	0	ENST00000330258.3:c.2773C>A	p.Gln925Lys	p.Q925K	ENST00000330258	NM_152424.3	925	Cag/Aag	2/2	0.214098262960207	3	FACETS	1	0.938	1	0.515	0.471	0.561	CLONAL	1	FALSE	1	0.258771091102076	3		657	1407	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042434	16042434	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1568277803	NA	P-0017428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	91	671	1	ENST00000268712.3:c.1240C>T	p.Arg414Ter	p.R414*	ENST00000268712	NM_006311.3	414	Cga/Tga	12/46	1	2	FACETS	0.624	0.553	0.701	0.624	0.553	0.701	SUBCLONAL	1	TRUE	1	0.29	2		672	1005	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687471	37687472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs760014508	NA	P-0017428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	154	247	0	ENST00000447079.4:c.4382dup	p.Thr1463AsnfsTer50	p.T1463Nfs*50	ENST00000447079	NM_015083.1	1459	tgg/tGgg	14/14	0.3	7	FACETS	0.874	0.801	0.949			1	CLONAL	3	TRUE	NA	0.29	7		247	699	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579355	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519997	NA	P-0017428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	123	680	1	ENST00000269305.4:c.332T>A	p.Leu111Gln	p.L111Q	ENST00000269305	NM_001126112.2	111	cTg/cAg	4/11	1	2	FACETS	0.636	0.573	0.703	0.636	0.573	0.703	SUBCLONAL	1	TRUE	1	0.29	2		681	1334	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252988	36252990	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0017428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	82	552	1	ENST00000300305.3:c.372_374del	p.Pro125del	p.P125del	ENST00000300305		124	gtTCCa/gta	4/8	1	2	FACETS	0.476	0.418	0.539	0.476	0.418	0.539	SUBCLONAL	1	TRUE	1	0.29	2		553	1187	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0017429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	84	525	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.955	0.842	1	0.955	0.842	1	CLONAL	1	TRUE	1	0.192741049233583	2		525	913	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0017429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	102	395	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.192741049233583	2		397	1044	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	145	301	4				ENST00000310581	NM_198253.2	-/1132			0.393537709030685	1	FACETS	0.715	0.657	0.775	0.715	0.657	0.775	SUBCLONAL	1	TRUE	0	0.596413635756918	1		305	477	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426908	6426908	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	175	470	0	ENST00000356142.4:c.101C>G	p.Pro34Arg	p.P34R	ENST00000356142	NM_018890.3	34	cCt/cGt	2/7	0.596413635756918	1	FACETS	0.536	0.494	0.579	0.536	0.494	0.579	SUBCLONAL	1	TRUE	0	0.596413635756918	1		470	769	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549277	21549277	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	98	573	0	ENST00000382592.4:c.2999C>A	p.Ser1000Ter	p.S1000*	ENST00000382592	NM_014572.2	1000	tCg/tAg	8/8	0.532957469483629	1	FACETS	0.228	0.203	0.256	0.228	0.203	0.256	SUBCLONAL	1	TRUE	0	0.596413635756918	1		573	1010	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24129429	24129432	+	protein_altering_variant	In_Frame_Del	DEL	TTCT	TTCT	A	novel	NA	P-0017431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	201	370	0	ENST00000263121.7:c.73_76delinsA	p.Phe25_Tyr26delinsAsn	p.F25_Y26delinsN	ENST00000263121	NM_003073.3	25	TTCTac/Aac	1/9	0.596413635756918	1	FACETS	0.855	0.799	0.913	0.855	0.799	0.913	CLONAL	1	TRUE	0	0.596413635756918	1		370	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0017432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	203	410	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.272882812956468	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.272882812956468	1		410	1043	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913315	NA	P-0017432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	209	643	0	ENST00000326873.7:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000326873	NM_000455.4	194	Gac/Tac	4/10	0.272882812956468	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.272882812956468	1		643	1166	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202231	108202231	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	207	599	0	ENST00000278616.4:c.7576A>G	p.Arg2526Gly	p.R2526G	ENST00000278616	NM_000051.3	2526	Aga/Gga	51/63	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.272882812956468	2		599	1326	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0017432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1314	1201	606	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.272882812956468	4	FACETS	1	0.996	1			1	CLONAL	4	TRUE	NA	0.272882812956468	4		606	2515	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743392	743392	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	129	409	0	ENST00000314574.4:c.748A>C	p.Lys250Gln	p.K250Q	ENST00000314574	NM_005433.3	250	Aag/Cag	7/12	0.272882812956468	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.272882812956468	1		409	797	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292385	15292385	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0017432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	116	411	0	ENST00000263388.2:c.2792+2T>G		p.X931_splice	ENST00000263388	NM_000435.2	931			1	2	FACETS	0.929	0.837	1	0.929	0.837	1	CLONAL	1	TRUE	1	0.272882812956468	2		411	915	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81399215	81399215	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866838534	NA	P-0017432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	185	494	1	ENST00000222390.5:c.73G>T	p.Ala25Ser	p.A25S	ENST00000222390	NM_000601.4	25	Gcc/Tcc	1/18	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.272882812956468	2		495	1164	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159743	20159743	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	185	433	0	ENST00000379607.5:c.16G>A	p.Gly6Ser	p.G6S	ENST00000379607	NM_001412.3	6	Ggt/Agt	1/7	0.154706977417531	1	FACETS	1	0.988	1	1	0.988	1	INDETERMINATE	1	TRUE	0	0.272882812956468	1		433	864	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112347	115112347	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1291364957	NA	P-0017436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	67	142	0	ENST00000257566.3:c.1393G>A	p.Ala465Thr	p.A465T	ENST00000257566	NM_016569.3	465	Gcc/Acc	7/8	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.39560605529039	2		142	283	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0017437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	245	497	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.392973053019208	3	FACETS	0.786	0.736	0.838	0.786	0.736	0.838	SUBCLONAL	2	TRUE	1	0.402007554181301	3		497	931	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0017437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	60	301	1	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.38825822958557	1	FACETS	0.545	0.47	0.625	0.545	0.47	0.625	SUBCLONAL	1	TRUE	0	0.402007554181301	1		302	438	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41962039	41962039	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	161	505	0	ENST00000219905.7:c.947C>T	p.Thr316Ile	p.T316I	ENST00000219905	NM_001164273.1	316	aCa/aTa	2/24	0.260141977800161	1	FACETS	0.888	0.816	0.962	0.888	0.816	0.962	CLONAL	1	TRUE	0	0.402007554181301	1		505	721	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665752	29665755	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1555535032	NA	P-0017438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	320	413	0	ENST00000356175.3:c.6789_6792del	p.Tyr2264ThrfsTer5	p.Y2264Tfs*5	ENST00000356175	NM_000267.3	2263	ACTTac/ac	45/57	NA	2	FACETS	0.813	0.771	0.855			1	INDETERMINATE	2	TRUE	NA	0.491619170904717	2		413	801	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0017438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	180	178	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.491619170904717	2		178	726	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577560	7577560	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520002	NA	P-0017438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	292	357	0	ENST00000269305.4:c.721T>G	p.Ser241Ala	p.S241A	ENST00000269305	NM_001126112.2	241	Tcc/Gcc	7/11	0.452450523346498	2	FACETS	0.919	0.872	0.967	0.919	0.872	0.967	CLONAL	2	TRUE	0	0.491619170904717	2		357	646	SUCCESS
FH	2271	MSKCC	GRCh37	1	241676932	241676932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	223	444	0	ENST00000366560.3:c.349G>A	p.Ala117Thr	p.A117T	ENST00000366560	NM_000143.3	117	Gct/Act	3/10	1	2	FACETS	0.856	0.796	0.918	0.856	0.796	0.918	CLONAL	1	TRUE	1	0.441873955331661	2		444	1179	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720728	89720728	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	19	91	0	ENST00000371953.3:c.880del	p.Ser294ValfsTer13	p.S294Vfs*13	ENST00000371953	NM_000314.4	293	ggA/gg	8/9	0.435219774392112	1	FACETS	0.325	0.247	0.416	0.325	0.247	0.416	SUBCLONAL	1	TRUE	0	0.441873955331661	1		91	206	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211653	46211653	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	156	309	0	ENST00000334344.6:c.619G>T	p.Ala207Ser	p.A207S	ENST00000334344	NM_152641.2	207	Gcc/Tcc	5/21	1	2	FACETS	0.842	0.771	0.915	0.842	0.771	0.915	CLONAL	1	TRUE	1	0.441873955331661	2		309	839	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435958	49435958	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	197	524	2	ENST00000301067.7:c.6023A>T	p.Lys2008Met	p.K2008M	ENST00000301067	NM_003482.3	2008	aAg/aTg	28/54	1	2	FACETS	0.915	0.847	0.985	0.915	0.847	0.985	CLONAL	1	TRUE	1	0.441873955331661	2		526	975	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347466	91347466	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	227	466	0	ENST00000355112.3:c.3628C>G	p.Gln1210Glu	p.Q1210E	ENST00000355112	NM_000057.2	1210	Cag/Gag	19/22	1	2	FACETS	0.847	0.788	0.908	0.847	0.788	0.908	CLONAL	1	TRUE	1	0.441873955331661	2		466	1213	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858574	9858574	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	167	386	0	ENST00000330684.3:c.2827T>A	p.Tyr943Asn	p.Y943N	ENST00000330684	NM_001134407.1	943	Tac/Aac	13/13	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.441873955331661	2		386	720	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916122	9916122	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	160	377	0	ENST00000330684.3:c.2167G>T	p.Gly723Trp	p.G723W	ENST00000330684	NM_001134407.1	723	Ggg/Tgg	10/13	1	2	FACETS	0.895	0.822	0.972	0.895	0.822	0.972	CLONAL	1	TRUE	1	0.441873955331661	2		377	809	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578530	7578530	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	271	650	0	ENST00000269305.4:c.400T>G	p.Phe134Val	p.F134V	ENST00000269305	NM_001126112.2	134	Ttt/Gtt	5/11	0.442509835500678	1	FACETS	0.963	0.905	1	0.963	0.905	1	CLONAL	1	TRUE	0	0.441873955331661	1		650	992	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586075	29586075	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	189	334	0	ENST00000356175.3:c.4295T>G	p.Val1432Gly	p.V1432G	ENST00000356175	NM_000267.3	1432	gTt/gGt	32/57	1	2	FACETS	0.94	0.869	1	0.94	0.869	1	CLONAL	1	TRUE	1	0.441873955331661	2		334	910	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315462	30315462	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	297	510	0	ENST00000322652.5:c.1147G>C	p.Glu383Gln	p.E383Q	ENST00000322652	NM_015355.2	383	Gag/Cag	10/16	1	2	FACETS	0.998	0.938	1	0.998	0.938	1	CLONAL	1	TRUE	1	0.441873955331661	2		510	1347	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40458324	40458324	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	69	141	1	ENST00000345506.4:c.1539G>A	p.Met513Ile	p.M513I	ENST00000345506	NM_003152.3	513	atG/atA	14/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.441873955331661	2		142	235	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780607	56780607	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs771078849	NA	P-0017439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	310	526	0	ENST00000337432.4:c.622A>G	p.Ile208Val	p.I208V	ENST00000337432	NM_058216.2	208	Att/Gtt	4/9	1	2	FACETS	0.983	0.925	1	0.983	0.925	1	CLONAL	1	TRUE	1	0.441873955331661	2		526	1428	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581234	48581234	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767332	NA	P-0017439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	221	501	0	ENST00000342988.3:c.538C>T	p.Gln180Ter	p.Q180*	ENST00000342988	NM_005359.5	180	Caa/Taa	5/12	0.435219774392112	1	FACETS	0.872	0.812	0.933	0.872	0.812	0.933	CLONAL	1	TRUE	0	0.441873955331661	1		501	894	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610499	10610499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs541663797	NA	P-0017439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	151	404	1	ENST00000171111.5:c.211C>T	p.Arg71Trp	p.R71W	ENST00000171111	NM_203500.1	71	Cgg/Tgg	2/6	0.442509835500678	1	FACETS	0.893	0.82	0.969	0.893	0.82	0.969	CLONAL	1	TRUE	0	0.441873955331661	1		405	596	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101925	11101925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	236	585	1	ENST00000358026.2:c.1345G>A	p.Glu449Lys	p.E449K	ENST00000358026	NM_001128849.1	449	Gag/Aag	8/36	0.442509835500678	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.441873955331661	1		586	750	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524084	187524084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	243	466	0	ENST00000441802.2:c.11455C>T	p.Pro3819Ser	p.P3819S	ENST00000441802	NM_005245.3	3819	Ccc/Tcc	20/27	0.435219774392112	1	FACETS	0.96	0.898	1	0.96	0.898	1	CLONAL	1	TRUE	0	0.441873955331661	1		466	893	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235365	235365	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs376597185	NA	P-0017439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	156	418	0	ENST00000264932.6:c.1171G>T	p.Ala391Ser	p.A391S	ENST00000264932	NM_004168.2	391	Gct/Tct	9/15	NA	2	FACETS	0.875	0.802	0.951			1	INDETERMINATE	1	TRUE	NA	0.441873955331661	2		418	807	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39002721	39002721	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	229	369	0	ENST00000357387.3:c.308G>A	p.Gly103Glu	p.G103E	ENST00000357387	NM_152756.3	103	gGg/gAg	5/38	0.426489738785819	3	FACETS	0.982	0.913	1	0.491	0.456	0.527	CLONAL	1	TRUE	1	0.441873955331661	3		369	1289	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39074458	39074458	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	166	309	0	ENST00000357387.3:c.22C>A	p.Arg8Ser	p.R8S	ENST00000357387	NM_152756.3	8	Cgc/Agc	1/38	0.426489738785819	3	FACETS	1	0.954	1	0.527	0.484	0.572	CLONAL	1	TRUE	1	0.441873955331661	3		309	870	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109309850	109309850	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	479	503	1	ENST00000436639.2:c.1465G>T	p.Asp489Tyr	p.D489Y	ENST00000436639	NM_014454.2	489	Gat/Tat	9/10	0.383447880240515	2	FACETS	0.86	0.824	0.897	0.86	0.824	0.897	CLONAL	2	TRUE	0	0.441873955331661	2		504	1260	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730075	41730075	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	264	387	0	ENST00000242208.4:c.454C>G	p.Arg152Gly	p.R152G	ENST00000242208	NM_002192.2	152	Cgt/Ggt	3/3	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.441873955331661	2		387	979	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513302	106513302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	71	374	3	ENST00000359195.3:c.2206G>T	p.Val736Phe	p.V736F	ENST00000359195	NM_002649.2	736	Gtc/Ttc	4/11	0.279124536705353	1	FACETS	0.324	0.282	0.37	0.324	0.282	0.37	SUBCLONAL	1	TRUE	0	0.441873955331661	1		377	772	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545788	106545788	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	190	408	0	ENST00000359195.3:c.3265C>T	p.His1089Tyr	p.H1089Y	ENST00000359195	NM_002649.2	1089	Cat/Tat	11/11	0.279124536705353	1	FACETS	0.726	0.671	0.783	0.726	0.671	0.783	SUBCLONAL	1	TRUE	0	0.441873955331661	1		408	923	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955596	90955596	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0017439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	145	279	0	ENST00000265433.3:c.2071-2A>G		p.X691_splice	ENST00000265433	NM_002485.4	691			1	2	FACETS	0.872	0.796	0.95	0.872	0.796	0.95	CLONAL	1	TRUE	1	0.441873955331661	2		279	753	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224522	53224522	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	226	263	0	ENST00000375401.3:c.3191G>C	p.Gly1064Ala	p.G1064A	ENST00000375401	NM_004187.3	1064	gGg/gCg	21/26	1	1	FACETS	0.771	0.725	0.817	1	0.993	1	SUBCLONAL	2	TRUE	0	0.441873955331661	1		263	517	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874340	76874341	+	missense_variant	Missense_Mutation	DNP	CA	CA	AT	novel	NA	P-0017439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	318	251	0	ENST00000373344.5:c.5381_5382delinsAT	p.Met1794Asn	p.M1794N	ENST00000373344	NM_000489.3	1794	aTG/aAT	21/35	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.441873955331661	1		251	759	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509786	187509786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142057401	NA	P-0017441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	27	174	0	ENST00000441802.2:c.13727C>T	p.Thr4576Met	p.T4576M	ENST00000441802	NM_005245.3	4576	aCg/aTg	27/27	0.219170624077527	2	FACETS	0.509	0.405	0.627	0.254	0.202	0.314	SUBCLONAL	1	TRUE	0	0.316964257528124	2		174	335	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587117	212587117	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0017441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	37	225	0	ENST00000342788.4:c.883+1G>A		p.X295_splice	ENST00000342788	NM_005235.2	295			0.208254965079768	3	FACETS	0.626	0.516	0.749	0.313	0.258	0.375	SUBCLONAL	1	TRUE	1	0.316964257528124	3		225	432	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779620	3779620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	262	629	0	ENST00000262367.5:c.5428C>T	p.Arg1810Cys	p.R1810C	ENST00000262367	NM_004380.2	1810	Cgc/Tgc	31/31	0.518279796825431	3	FACETS	0.985	0.921	1	0.492	0.46	0.525	CLONAL	1	TRUE	1	0.518279796825431	3		629	1293	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157975	106157986	+	inframe_deletion	In_Frame_Del	DEL	AGCAAGAACAGC	AGCAAGAACAGC	-	novel	NA	P-0017442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	172	429	0	ENST00000380013.4:c.2881_2892del	p.Glu961_Gln964del	p.E961_Q964del	ENST00000380013	NM_001127208.2	959	aAGCAAGAACAGCag/aag	3/11	0.276552710521883	1	FACETS	0.665	0.613	0.718	0.665	0.613	0.718	INDETERMINATE	1	TRUE	0	0.518279796825431	1		429	740	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690812	89690816	+	frameshift_variant	Frame_Shift_Del	DEL	AAGAC	AAGAC	-	novel	NA	P-0017443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	108	365	0	ENST00000371953.3:c.220_224del	p.Arg74LeufsTer2	p.R74Lfs*2	ENST00000371953	NM_000314.4	73	gaAAGACat/gaat	4/9	1	2	FACETS	0.822	0.74	0.909	0.822	0.74	0.909	CLONAL	1	TRUE	1	0.450555208290195	2		365	583	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411862	116411898	+	splice_region_variant,intron_variant	Splice_Region	DEL	TAGCCGTCTTTAACAAGCTCTTTCTTTCTCTCTGTTT	TAGCCGTCTTTAACAAGCTCTTTCTTTCTCTCTGTTT	-	novel	NA	P-0017443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	388	702	0	ENST00000397752.3:c.2888-39_2888-3del		p.X963_splice	ENST00000397752	NM_000245.2	963			0.210173007832843	3	FACETS	1	0.995	1	0.48	0.455	0.505	INDETERMINATE	1	TRUE	0	0.450555208290195	3		702	1467	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489803	2489803	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	220	501	2	ENST00000355716.4:c.200G>T	p.Cys67Phe	p.C67F	ENST00000355716	NM_003820.2	67	tGc/tTc	3/8	1	2	FACETS	0.813	0.758	0.869	0.813	0.758	0.869	CLONAL	1	TRUE	1	0.662454132112873	2		503	817	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598357	28598357	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	278	593	0	ENST00000253063.3:c.329C>G	p.Ser110Cys	p.S110C	ENST00000253063	NM_031459.4	110	tCc/tGc	3/10	1	2	FACETS	0.985	0.928	1	0.985	0.928	1	CLONAL	1	TRUE	1	0.662454132112873	2		593	852	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588791	69588791	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0017444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	35	543	0	ENST00000168712.1:c.444+1G>A		p.X148_splice	ENST00000168712	NM_002007.2	148			0.523201463497812	1	FACETS	0.112	0.091	0.135	0.112	0.091	0.135	SUBCLONAL	1	TRUE	0	0.662454132112873	1		543	631	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951156	48951156	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	276	434	1	ENST00000267163.4:c.1318G>T	p.Glu440Ter	p.E440*	ENST00000267163	NM_000321.2	440	Gaa/Taa	13/27	0.550747958496934	1	FACETS	0.932	0.883	0.981	0.932	0.883	0.981	CLONAL	1	TRUE	0	0.662454132112873	1		435	598	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428220	33428220	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	137	348	0	ENST00000345365.6:c.903G>T	p.Gln301His	p.Q301H	ENST00000345365	NM_002878.3	301	caG/caT	9/10	1	2	FACETS	0.955	0.877	1	0.955	0.877	1	CLONAL	1	TRUE	1	0.662454132112873	2		348	433	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602840	10602840	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	353	789	0	ENST00000171111.5:c.738C>G	p.Phe246Leu	p.F246L	ENST00000171111	NM_203500.1	246	ttC/ttG	3/6	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.662454132112873	2		789	754	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732851	44732851	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	226	256	0	ENST00000377967.4:c.54C>G	p.Phe18Leu	p.F18L	ENST00000377967	NM_021140.2	18	ttC/ttG	1/29	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.662454132112873	1		256	377	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426058	49426058	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398123712	NA	P-0017444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	278	526	0	ENST00000301067.7:c.12430C>T	p.Gln4144Ter	p.Q4144*	ENST00000301067	NM_003482.3	4144	Cag/Tag	39/54	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.662454132112873	2		526	813	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437604	52437605	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0017445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	50	368	0	ENST00000460680.1:c.1556_1557del	p.Pro519LeufsTer17	p.P519Lfs*17	ENST00000460680	NM_004656.3	519	cCC/c	13/17	1	2	FACETS	0.945	0.799	1	0.945	0.799	1	CLONAL	1	TRUE	1	0.11	2		368	962	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0017446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	209	578	1	ENST00000311936.3:c.180_181delinsAA	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggAAaa	3/5	1	2	FACETS	0.753	0.701	0.807	1	0.991	1	SUBCLONAL	2	TRUE	1	0.352767275015294	2		579	787	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685515	29685516	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1555536882	NA	P-0017446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	217	370	0	ENST00000356175.3:c.7926dup	p.Lys2643Ter	p.K2643*	ENST00000356175	NM_000267.3	2642	tct/tcTt	54/57	0.294038723984013	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.352767275015294	3		370	595	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119840	70119853	+	frameshift_variant	Frame_Shift_Del	DEL	ACGTCATCTCCAAC	ACGTCATCTCCAAC	-	novel	NA	P-0017446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	301	573	0	ENST00000245479.2:c.843_856del	p.Val282ArgfsTer9	p.V282Rfs*9	ENST00000245479	NM_000346.3	281	gACGTCATCTCCAAC/g	3/3	0.294038723984013	3	FACETS	0.823	0.774	0.872	0.823	0.774	0.872	CLONAL	2	TRUE	1	0.352767275015294	3		573	1220	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729908	30729908	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0017446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	33	386	0	ENST00000295754.5:c.1429A>T	p.Lys477Ter	p.K477*	ENST00000295754	NM_003242.5	477	Aag/Tag	6/7	0.352767275015294	1	FACETS	0.268	0.218	0.326	0.268	0.218	0.326	SUBCLONAL	1	TRUE	0	0.352767275015294	1		386	574	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249348	110249348	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	519	577	0	ENST00000374672.4:c.1225A>C	p.Lys409Gln	p.K409Q	ENST00000374672	NM_004235.4	409	Aag/Cag	4/5	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.89	2		577	1095	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225556	2225556	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	289	432	0	ENST00000326181.6:c.1559A>G	p.Asn520Ser	p.N520S	ENST00000326181	NM_032271.2	520	aAc/aGc	17/21	1	2	FACETS	0.908	0.86	0.958	0.908	0.86	0.958	CLONAL	1	TRUE	1	0.89	2		432	715	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0017448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	183	525	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.801	0.739	0.866	1	0.991	1	CLONAL	2	TRUE	1	0.220270968394176	2		525	1037	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112389	115112389	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	66	336	0	ENST00000257566.3:c.1351G>A	p.Ala451Thr	p.A451T	ENST00000257566	NM_016569.3	451	Gcg/Acg	7/8	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.220270968394176	2		336	494	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913495	NA	P-0017448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	1561	423	1	ENST00000371085.3:c.602G>T	p.Arg201Leu	p.R201L	ENST00000371085	NM_000516.4	201	cGt/cTt	8/13	0.220270968394176	11	FACETS	1	0.992	1			1	CLONAL	12	TRUE	NA	0.220270968394176	11		424	2312	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162688924	162688924	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	220	413	0	ENST00000367921.3:c.71A>T	p.Gln24Leu	p.Q24L	ENST00000367921	NM_006182.2	24	cAg/cTg	3/18	0.220270968394176	5	FACETS	1	0.986	1	0.818	0.761	0.877	CLONAL	2	TRUE	2	0.220270968394176	5		413	1083	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23640525	23640525	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	193	474	1	ENST00000261584.4:c.2586G>T	p.Lys862Asn	p.K862N	ENST00000261584	NM_024675.3	862	aaG/aaT	6/13	0.132176379829031	4	FACETS	0.841	0.776	0.909			1	CLONAL	2	TRUE	NA	0.220270968394176	4		475	1271	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353737	15353737	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	197	552	0	ENST00000263377.2:c.3143A>C	p.His1048Pro	p.H1048P	ENST00000263377	NM_058243.2	1048	cAc/cCc	14/20	1	2	FACETS	0.805	0.744	0.868	1	0.991	1	CLONAL	2	TRUE	1	0.220270968394176	2		552	1111	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432674	29432674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770027238	NA	P-0017448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	89	490	0	ENST00000389048.3:c.3814G>A	p.Gly1272Arg	p.G1272R	ENST00000389048	NM_004304.4	1272	Ggg/Agg	25/29	0.220270968394176	1	FACETS	0.871	0.771	0.977	0.871	0.771	0.977	CLONAL	1	TRUE	0	0.220270968394176	1		490	826	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436360	52436360	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	120	392	0	ENST00000460680.1:c.2134C>T	p.Gln712Ter	p.Q712*	ENST00000460680	NM_004656.3	712	Cag/Tag	17/17	1	2	FACETS	0.805	0.728	0.886	1	0.986	1	CLONAL	2	TRUE	1	0.220270968394176	2		392	677	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953788	55953788	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	82	463	0	ENST00000263923.4:c.3648C>A	p.Asn1216Lys	p.N1216K	ENST00000263923	NM_002253.2	1216	aaC/aaA	27/30	0.220270968394176	1	FACETS	0.815	0.718	0.92	0.815	0.718	0.92	CLONAL	1	TRUE	0	0.220270968394176	1		463	813	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945094	151945096	+	inframe_deletion	In_Frame_Del	DEL	CAG	CAG	-	novel	NA	P-0017448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	70	615	0	ENST00000262189.6:c.2423_2425del	p.Ala808del	p.A808del	ENST00000262189	NM_170606.2	808	gCTGga/gga	14/59	1	2	FACETS	0.657	0.571	0.75	0.657	0.571	0.75	SUBCLONAL	1	TRUE	1	0.220270968394176	2		615	968	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480595	123480595	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	166	342	0	ENST00000371139.4:c.103G>T	p.Glu35Ter	p.E35*	ENST00000371139	NM_001114937.2	35	Gag/Tag	1/4	1	2	FACETS	1	0.966	1	1	0.993	1	CLONAL	2	TRUE	1	0.220270968394176	2		342	694	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0017449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	1357	689	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.394106693430461	6	FACETS	0.993	0.979	1	0.993	0.979	1	CLONAL	6	FALSE	0	0.643642898909107	6		690	1619	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913499	NA	P-0017449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	154	285	0	ENST00000345146.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000345146	NM_005896.2	132	Cgt/Ggt	4/10	0.193644457425285	4	FACETS	1	0.942	1	1	0.942	1	INDETERMINATE	2	FALSE	2	0.643642898909107	4		285	386	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101118	41101118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751886972	NA	P-0017449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	52	475	2	ENST00000373198.4:c.1238C>T	p.Ala413Val	p.A413V	ENST00000373198	NM_133170.3	413	gCg/gTg	8/32	0.3203918609596	4	FACETS	0.388	0.329	0.452	0.194	0.164	0.226	INDETERMINATE	1	FALSE	2	0.643642898909107	4		477	685	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7174668	7174668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	57	444	0	ENST00000302850.5:c.1049C>T	p.Ser350Leu	p.S350L	ENST00000302850	NM_000208.2	350	tCg/tTg	4/22	0.343540734121683	5	FACETS	0.362	0.309	0.42	0.121	0.103	0.14	INDETERMINATE	1	FALSE	2	0.643642898909107	5		444	962	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798174	42798175	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGT	novel	NA	P-0017449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	273	552	0	ENST00000575354.2:c.4130_4133dup	p.Leu1379ValfsTer63	p.L1379Vfs*63	ENST00000575354	NM_015125.3	1376	-/CAGT	17/20	0.638889133105294	2	FACETS	0.845	0.804	0.886	0.845	0.804	0.886	CLONAL	2	FALSE	0	0.643642898909107	2		552	502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0017458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	334	418	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	NA	2	FACETS	0.974	0.934	1			1	INDETERMINATE	2	TRUE	NA	0.62097137098924	2		420	552	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	192	357	2	ENST00000322088.6:c.767C>A	p.Ser256Tyr	p.S256Y	ENST00000322088	NM_014225.5	256	tCc/tAc	6/15	NA	2	FACETS	1	0.944	1			1	INDETERMINATE	1	TRUE	NA	0.62097137098924	2		359	608	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40490813	40490813	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	136	415	0	ENST00000264657.5:c.486G>T	p.Met162Ile	p.M162I	ENST00000264657	NM_139276.2	162	atG/atT	6/24	0.0969649270507905	5	FACETS	0.768	0.697	0.844			1	INDETERMINATE	1	TRUE	NA	0.62097137098924	5		415	1101	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741464	39741464	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	701	387	1	ENST00000361337.2:c.1356del	p.Lys452AsnfsTer19	p.K452Nfs*19	ENST00000361337	NM_003286.2	451	Aaa/aa	14/21	0.621933294791111	4	FACETS	0.996	0.966	1			1	CLONAL	3	TRUE	NA	0.62097137098924	4		388	1225	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443345	187443346	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	456	337	0	ENST00000232014.4:c.1780_1781insA	p.Arg594GlnfsTer34	p.R594Qfs*34	ENST00000232014	NM_001130845.1	594	cga/cAga	8/10	0.621933294791111	5	FACETS	1	0.991	1	0.823	0.791	0.854	CLONAL	3	TRUE	1	0.62097137098924	5		337	862	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611843	100611843	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	362	516	0	ENST00000308731.7:c.1278C>G	p.Asp426Glu	p.D426E	ENST00000308731	NM_000061.2	426	gaC/gaG	14/19	0.621933294791111	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.62097137098924	1		516	638	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0017459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	168	308	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.197116795545905	5	FACETS	0.866	0.797	0.936	0.866	0.797	0.936	CLONAL	3	TRUE	2	0.243709228757347	5		308	725	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0017459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	198	441	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	0.243709228757347	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	3	TRUE	0	0.243709228757347	3		441	597	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607568	43607568	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1468917724	NA	P-0017459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	87	466	1	ENST00000355710.3:c.1544G>T	p.Cys515Phe	p.C515F	ENST00000355710	NM_020975.4	515	tGc/tTc	8/20	0.242159396645572	3	FACETS	1	0.965	1	0.618	0.547	0.693	CLONAL	1	TRUE	1	0.243709228757347	3		467	648	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492938	56492938	+	start_lost	Translation_Start_Site	SNP	T	T	A	novel	NA	P-0017459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	72	164	0	ENST00000407977.2:c.1A>T	p.Met1?	p.M1?	ENST00000407977		1	Atg/Ttg	2/10	0.243709228757347	3	FACETS	1	0.93	1	1	0.93	1	CLONAL	3	TRUE	0	0.243709228757347	3		164	208	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	223598	223598	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	35	211	0	ENST00000264932.6:c.65G>A	p.Trp22Ter	p.W22*	ENST00000264932	NM_004168.2	22	tGg/tAg	2/15	0.197116795545905	5	FACETS	1	0.884	1	0.368	0.302	0.442	CLONAL	1	TRUE	2	0.243709228757347	5		211	355	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	223618	223618	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	52	343	0	ENST00000264932.6:c.85G>T	p.Gly29Ter	p.G29*	ENST00000264932	NM_004168.2	29	Gga/Tga	2/15	0.197116795545905	5	FACETS	1	0.869	1	0.341	0.29	0.397	CLONAL	1	TRUE	2	0.243709228757347	5		343	570	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	223645	223645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	69	493	0	ENST00000264932.6:c.112G>A	p.Asp38Asn	p.D38N	ENST00000264932	NM_004168.2	38	Gat/Aat	2/15	0.197116795545905	5	FACETS	0.897	0.78	1	0.299	0.26	0.342	CLONAL	1	TRUE	2	0.243709228757347	5		493	862	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528133	157528133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	71	404	0	ENST00000346085.5:c.5858G>A	p.Arg1953His	p.R1953H	ENST00000346085	NM_020732.3	1953	cGt/cAt	20/20	0.197116795545905	5	FACETS	1	0.96	1	0.418	0.365	0.476	CLONAL	1	TRUE	2	0.243709228757347	5		404	634	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372203	55372203	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	59	283	0	ENST00000297316.4:c.893G>C	p.Gly298Ala	p.G298A	ENST00000297316	NM_022454.3	298	gGc/gCc	2/2	0.197116795545905	5	FACETS	0.767	0.662	0.881	0.511	0.441	0.588	SUBCLONAL	2	TRUE	2	0.243709228757347	5		283	431	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372514	55372514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768972880	NA	P-0017459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	175	684	1	ENST00000297316.4:c.1204G>A	p.Ala402Thr	p.A402T	ENST00000297316	NM_022454.3	402	Gcc/Acc	2/2	0.197116795545905	5	FACETS	1	0.989	1	0.497	0.457	0.54	CLONAL	1	TRUE	2	0.243709228757347	5		685	1314	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	78	301	4				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.27	2		305	570	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588751	29588751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760703505	NA	P-0017460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	96	342	2	ENST00000356175.3:c.4537C>T	p.Arg1513Ter	p.R1513*	ENST00000356175	NM_000267.3	1513	Cga/Tga	34/57	1	2	FACETS	0.973	0.867	1	0.973	0.867	1	CLONAL	1	TRUE	1	0.27	2		344	731	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560139	29560139	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	98	303	0	ENST00000356175.3:c.3616G>T	p.Glu1206Ter	p.E1206*	ENST00000356175	NM_000267.3	1206	Gag/Tag	27/57	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.27	2		303	726	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664448	138664448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	132	348	0	ENST00000330315.3:c.1117C>T	p.Arg373Cys	p.R373C	ENST00000330315	NM_023067.3	373	Cgc/Tgc	1/1	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.27	2		348	883	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053210	180053210	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	161	563	0	ENST00000261937.6:c.1159A>C	p.Lys387Gln	p.K387Q	ENST00000261937	NM_182925.4	387	Aag/Cag	9/30	1	2	FACETS	0.971	0.889	1	0.971	0.889	1	CLONAL	1	TRUE	1	0.27	2		563	1228	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339544	116339544	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199701987	NA	P-0017460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	102	272	0	ENST00000397752.3:c.406G>A	p.Val136Ile	p.V136I	ENST00000397752	NM_000245.2	136	Gtc/Atc	2/21	0.260692324777171	3	FACETS	1	0.963	1	0.584	0.522	0.65	CLONAL	1	TRUE	1	0.27	3		272	734	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0017461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	175	308	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.827	0.762	0.894	1	0.991	1	CLONAL	2	TRUE	1	0.255006330157138	2		308	830	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981253	201981253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1184837452	NA	P-0017461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	122	496	1	ENST00000359651.3:c.332G>A	p.Arg111His	p.R111H	ENST00000359651		111	cGt/cAt	2/8	0.15438867180369	4	FACETS	0.981	0.889	1	0.981	0.889	1	CLONAL	2	TRUE	2	0.255006330157138	4		497	612	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160452	108160452	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0017461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	195	455	0	ENST00000278616.4:c.4360A>T	p.Lys1454Ter	p.K1454*	ENST00000278616	NM_000051.3	1454	Aaa/Taa	29/63	0.255006330157138	4	FACETS	1	0.978	1			1	CLONAL	2	TRUE	NA	0.255006330157138	4		455	841	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366173	15366173	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	94	462	1	ENST00000263377.2:c.1982C>T	p.Pro661Leu	p.P661L	ENST00000263377	NM_058243.2	661	cCg/cTg	10/20	0.255006330157138	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.255006330157138	1		463	480	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421239	12421239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	111	484	1	ENST00000287820.6:c.119C>T	p.Pro40Leu	p.P40L	ENST00000287820	NM_015869.4	40	cCc/cTc	2/7	0.107863331245637	4	FACETS	1	0.982	1	0.735	0.661	0.814	INDETERMINATE	1	TRUE	2	0.255006330157138	4		485	743	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64288876	64288876	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1249	288	421	0	ENST00000370651.3:c.272A>G	p.Lys91Arg	p.K91R	ENST00000370651	NM_003463.4	91	aAg/aGg	4/6	0.255006330157138	8	FACETS	0.865	0.811	0.92	0.519	0.486	0.552	CLONAL	3	TRUE	3	0.255006330157138	8		421	1537	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520111	106520111	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0017461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	86	229	0	ENST00000359195.3:c.2538+1G>A		p.X846_splice	ENST00000359195	NM_002649.2	846			0.255006330157138	5	FACETS	1	0.959	1	0.777	0.692	0.867	CLONAL	2	TRUE	2	0.255006330157138	5		229	400	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528650	8528650	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	81	334	0	ENST00000356435.5:c.482A>T	p.Lys161Ile	p.K161I	ENST00000356435		161	aAa/aTa	4/35	0.255006330157138	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.255006330157138	1		334	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0017462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	772	795	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.493678138797424	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.494038311450576	3		796	1218	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692837	89692837	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	38	161	0	ENST00000371953.3:c.321T>A	p.Asp107Glu	p.D107E	ENST00000371953	NM_000314.4	107	gaT/gaA	5/9	0.493678138797424	1	FACETS	0.666	0.558	0.783	0.666	0.558	0.783	SUBCLONAL	1	TRUE	0	0.494038311450576	1		161	174	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849440	89849440	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	263	486	0	ENST00000389301.3:c.1541C>G	p.Ala514Gly	p.A514G	ENST00000389301	NM_000135.2	514	gCc/gGc	16/43	0.493678138797424	4	FACETS	1	0.991	1	0.456	0.427	0.486	CLONAL	1	TRUE	1	0.494038311450576	4		486	1162	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120846	94120846	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1300929218	NA	P-0017462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	212	508	0	ENST00000369303.4:c.205C>G	p.Arg69Gly	p.R69G	ENST00000369303	NM_004440.3	69	Cga/Gga	3/17	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.494038311450576	2		508	843	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137540458	137540458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1406767058	NA	P-0017462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	153	289	2	ENST00000367739.4:c.7C>T	p.Leu3Phe	p.L3F	ENST00000367739	NM_000416.2	3	Ctc/Ttc	1/7	0.493678138797424	3	FACETS	1	0.955	1	0.531	0.487	0.578	CLONAL	1	TRUE	1	0.494038311450576	3		291	727	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56839415	56839415	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0017462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1252	141	347	0	ENST00000308159.5:c.361-1G>C		p.X121_splice	ENST00000308159	NM_014669.4	121			0.494038311450576	7	FACETS	0.916	0.832	1			1	CLONAL	1	TRUE	NA	0.494038311450576	7		347	1393	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40709552	40709552	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0017462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	201	524	0	ENST00000373198.4:c.4350C>G	p.Tyr1450Ter	p.Y1450*	ENST00000373198	NM_133170.3	1450	taC/taG	32/32	0.493678138797424	3	FACETS	1	0.935	1	0.505	0.468	0.544	CLONAL	1	TRUE	1	0.494038311450576	3		524	1005	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217319	66217319	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	novel	NA	P-0017462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	79	204	2	ENST00000273854.3:c.2299-3C>T		p.X767_splice	ENST00000273854	NM_004439.5	767			0.493678138797424	3	FACETS	1	0.886	1	0.501	0.443	0.563	CLONAL	1	TRUE	1	0.494038311450576	3		206	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0017462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	338	795	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.598709373951242	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.631445810797635	1		796	713	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849440	89849440	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	322	486	0	ENST00000389301.3:c.1541C>G	p.Ala514Gly	p.A514G	ENST00000389301	NM_000135.2	514	gCc/gGc	16/43	0.542933459869092	4	FACETS	0.754	0.712	0.796	0.502	0.474	0.531	SUBCLONAL	2	TRUE	1	0.631445810797635	4		486	1104	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120846	94120846	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1300929218	NA	P-0017462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	71	508	0	ENST00000369303.4:c.205C>G	p.Arg69Gly	p.R69G	ENST00000369303	NM_004440.3	69	Cga/Gga	3/17	0.294494544105227	2	FACETS	0.388	0.339	0.442	0.194	0.169	0.221	INDETERMINATE	1	TRUE	0	0.631445810797635	2		508	579	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137540458	137540458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1406767058	NA	P-0017462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	227	289	2	ENST00000367739.4:c.7C>T	p.Leu3Phe	p.L3F	ENST00000367739	NM_000416.2	3	Ctc/Ttc	1/7	0.440059379537553	3	FACETS	1	0.988	1	0.62	0.579	0.662	CLONAL	1	TRUE	1	0.631445810797635	3		291	763	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691234	18691234	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	49	328	0	ENST00000266497.5:c.3345C>A	p.Asn1115Lys	p.N1115K	ENST00000266497		1115	aaC/aaA	23/31	1	2	FACETS	0.446	0.379	0.519	0.446	0.379	0.519	SUBCLONAL	1	TRUE	1	0.631445810797635	2		328	348	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945055	151945055	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0017462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	26	566	0	ENST00000262189.6:c.2464A>T	p.Lys822Ter	p.K822*	ENST00000262189	NM_170606.2	822	Aaa/Taa	14/59	0.598709373951242	1	FACETS	0.133	0.104	0.165	0.133	0.104	0.165	SUBCLONAL	1	TRUE	0	0.631445810797635	1		566	425	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0017463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	148	195	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	0.568986268210387	2		195	439	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577152	7577154	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	ACC	ACC	-	rs1567548347	NA	P-0017463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	488	441	0	ENST00000269305.4:c.784_786del	p.Gly262del	p.G262del	ENST00000269305	NM_001126112.2	262	GGT/-	8/11	0.568986268210387	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.568986268210387	2		441	855	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940000	76940000	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1311466929	NA	P-0017463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	204	528	0	ENST00000373344.5:c.748C>T	p.Arg250Ter	p.R250*	ENST00000373344	NM_000489.3	250	Cga/Tga	9/35	0.182780870228523	0	FACETS	0.439	0.408	0.47			1	INDETERMINATE	1	TRUE	0	0.568986268210387	0		528	704	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830829	156830829	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1204319733	NA	P-0017464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	181	351	0	ENST00000524377.1:c.103C>T	p.Pro35Ser	p.P35S	ENST00000524377	NM_002529.3	35	Ccc/Tcc	1/17	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.804405961232818	2		351	398	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722210	176722210	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	170	392	0	ENST00000439151.2:c.7844del	p.Lys2615ArgfsTer4	p.K2615Rfs*4	ENST00000439151	NM_022455.4	2614	gAa/ga	23/23	0.333931002622871	6	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.804405961232818	6		392	793	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741958	145741958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs565903685	NA	P-0017464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	171	440	0	ENST00000428558.2:c.545G>A	p.Arg182Gln	p.R182Q	ENST00000428558	NM_004260.3	182	cGg/cAg	5/22	0.794581752925115	3	FACETS	1	0.925	1	0.5	0.462	0.539	CLONAL	1	TRUE	1	0.804405961232818	3		440	596	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0017465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	429	708	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	2	TRUE	NA	0.545343596020775	2		708	772	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	104	305	0	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	1	2	FACETS	0.824	0.742	0.91	0.824	0.742	0.91	CLONAL	1	TRUE	1	0.545343596020775	2		305	463	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0017465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	184	459	1	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	0.85	0.786	0.916	0.85	0.786	0.916	CLONAL	1	TRUE	1	0.545343596020775	2		460	794	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022592	31022592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs373221034	NA	P-0017465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	335	552	2	ENST00000375687.4:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000375687	NM_015338.5	693	Cga/Tga	13/13	0.545343596020775	4	FACETS	1	0.994	1	0.493	0.465	0.521	CLONAL	1	TRUE	1	0.545343596020775	4		554	1284	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498078	29498078	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	43	449	0	ENST00000389048.3:c.1928A>G	p.Lys643Arg	p.K643R	ENST00000389048	NM_004304.4	643	aAg/aGg	11/29	0.545343596020775	3	FACETS	0.24	0.2	0.285	0.12	0.1	0.143	SUBCLONAL	1	TRUE	1	0.545343596020775	3		449	836	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410609	63410609	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	31	283	0	ENST00000330258.3:c.2558A>C	p.Asn853Thr	p.N853T	ENST00000330258	NM_152424.3	853	aAc/aCc	2/2	0.48883217885264	2	FACETS	0.218	0.175	0.266			1	SUBCLONAL	1	TRUE	NA	0.545343596020775	2		283	522	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106034	8106034	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	59	438	0	ENST00000346208.3:c.854A>G	p.Asn285Ser	p.N285S	ENST00000346208		285	aAc/aGc	4/6	0.535327317454881	2	FACETS	0.384	0.33	0.443	0.192	0.165	0.222	SUBCLONAL	1	TRUE	0	0.545343596020775	2		438	563	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762147	43762159	+	frameshift_variant	Frame_Shift_Del	DEL	ACAGTGGACTCAG	ACAGTGGACTCAG	-	novel	NA	P-0017465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	206	609	0	ENST00000382044.4:c.1286_1298del	p.Pro429HisfsTer58	p.P429Hfs*58	ENST00000382044	NM_001141980.1	429	cCTGAGTCCACTGTa/ca	11/28	0.535327317454881	2	FACETS	1	0.932	1	0.501	0.466	0.537	CLONAL	1	TRUE	0	0.545343596020775	2		609	754	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56801442	56801442	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	247	617	0	ENST00000337432.4:c.946C>A	p.His316Asn	p.H316N	ENST00000337432	NM_058216.2	316	Cat/Aat	7/9	0.535327317454881	2	FACETS	0.963	0.901	1	0.481	0.45	0.513	CLONAL	1	TRUE	0	0.545343596020775	2		617	941	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573585	48573585	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	187	469	0	ENST00000342988.3:c.169T>G	p.Leu57Val	p.L57V	ENST00000342988	NM_005359.5	57	Tta/Gta	2/12	0.545343596020775	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.545343596020775	1		469	454	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129102	152129102	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	67	596	0	ENST00000206249.3:c.55C>G	p.Gln19Glu	p.Q19E	ENST00000206249	NM_000125.3	19	Caa/Gaa	1/8	0.531151717087732	3	FACETS	0.399	0.346	0.457	0.2	0.173	0.229	SUBCLONAL	1	TRUE	1	0.545343596020775	3		596	783	SUCCESS
AR	367	MSKCC	GRCh37	X	66766030	66766030	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1399658214	NA	P-0017465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	48	345	0	ENST00000374690.3:c.1042T>C	p.Tyr348His	p.Y348H	ENST00000374690	NM_000044.3	348	Tac/Cac	1/8	0.48883217885264	2	FACETS	0.299	0.253	0.351			1	SUBCLONAL	1	TRUE	NA	0.545343596020775	2		345	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0017466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1335	43	822	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.072	0.06	0.086	0.072	0.06	0.086	SUBCLONAL	1	TRUE	1	0.862686014284984	2		822	1378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs863224683	NA	P-0017466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	310	629	0	ENST00000269305.4:c.388C>G	p.Leu130Val	p.L130V	ENST00000269305	NM_001126112.2	130	Ctc/Gtc	5/11	1	2	FACETS	0.48	0.451	0.51	0.48	0.451	0.51	SUBCLONAL	1	TRUE	1	0.862686014284984	2		629	1497	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94910994	94910994	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	498	560	0	ENST00000536441.1:c.1136T>C	p.Phe379Ser	p.F379S	ENST00000536441	NM_144665.3	379	tTt/tCt	8/10	0.862686014284984	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.862686014284984	1		560	656	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122849	2122849	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs45517218	NA	P-0017466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	28	424	0	ENST00000219476.3:c.2221-1G>A		p.X741_splice	ENST00000219476	NM_000548.3	741			0.862686014284984	1	FACETS	0.068	0.053	0.084	0.068	0.053	0.084	SUBCLONAL	1	TRUE	0	0.862686014284984	1		424	546	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131595	2131595	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs45517302	NA	P-0017466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	48	463	0	ENST00000219476.3:c.3611-1G>A		p.X1204_splice	ENST00000219476	NM_000548.3	1204			0.862686014284984	1	FACETS	0.118	0.099	0.138	0.118	0.099	0.138	SUBCLONAL	1	TRUE	0	0.862686014284984	1		463	537	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581348	48581348	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	372	422	0	ENST00000342988.3:c.653del	p.Pro218LeufsTer23	p.P218Lfs*23	ENST00000342988	NM_005359.5	218	Cct/ct	5/12	0.862686014284984	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.862686014284984	1		422	473	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286552	33286552	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	406	385	0	ENST00000374542.5:c.2191G>T	p.Glu731Ter	p.E731*	ENST00000374542	NM_001141970.1	731	Gaa/Taa	8/8	0.852001476614516	1	FACETS	0.951	0.92	0.98	0.951	0.92	0.98	CLONAL	1	TRUE	0	0.862686014284984	1		385	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0017467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	699	689	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.212085686777034	6	FACETS	1	0.971	1			1	CLONAL	6	TRUE	NA	0.212085686777034	6		690	1556	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156981	106156981	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	237	528	2	ENST00000380013.4:c.1882G>T	p.Glu628Ter	p.E628*	ENST00000380013	NM_001127208.2	628	Gag/Tag	3/11	0.212085686777034	3	FACETS	0.902	0.843	0.963	0.902	0.843	0.963	CLONAL	3	TRUE	0	0.212085686777034	3		530	913	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141497	11141498	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs797045982	NA	P-0017467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	200	629	0	ENST00000358026.2:c.3480dup	p.Leu1161AlafsTer15	p.L1161Afs*15	ENST00000358026	NM_001128849.1	1158	-/G	25/36	0.212085686777034	3	FACETS	1	0.983	1	0.8	0.742	0.86	CLONAL	2	TRUE	0	0.212085686777034	3		629	869	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994138	21994138	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	162	462	0	ENST00000579755.1:c.193G>A	p.Gly65Ser	p.G65S	ENST00000579755		65	Ggt/Agt	1/3	0.167889219787773		FACETS		0.976	1				CLONAL	2	TRUE	0	0.212085686777034	3		462	733	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781816	9781841	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGCTCCGAGATGCACGTGCCGTCGG	CAGCTCCGAGATGCACGTGCCGTCGG	-	novel	NA	P-0017467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	96	514	0	ENST00000377346.4:c.1956-3_1978del		p.X652_splice	ENST00000377346	NM_005026.3	652		16/24	0.212085686777034	3	FACETS	0.756	0.674	0.843	0.504	0.449	0.562	SUBCLONAL	2	TRUE	0	0.212085686777034	3		514	662	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231153	46231153	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	108	377	0	ENST00000334344.6:c.1073C>G	p.Thr358Ser	p.T358S	ENST00000334344	NM_152641.2	358	aCt/aGt	9/21	0.212085686777034	6	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.212085686777034	6		377	1068	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008313	29008313	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	153	331	0	ENST00000282397.4:c.558G>T	p.Trp186Cys	p.W186C	ENST00000282397	NM_002019.4	186	tgG/tgT	5/30	0.212085686777034	3	FACETS	0.945	0.869	1	0.945	0.869	1	CLONAL	3	TRUE	0	0.212085686777034	3		331	563	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32899264	32899264	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	92	428	1	ENST00000380152.3:c.368A>T	p.Lys123Ile	p.K123I	ENST00000380152		123	aAa/aTa	4/27	0.212085686777034	3	FACETS	1	0.945	1	0.369	0.327	0.414	CLONAL	1	TRUE	0	0.212085686777034	3		429	867	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281744	49281744	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs754174807	NA	P-0017467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	251	675	0	ENST00000282018.3:c.791A>G	p.His264Arg	p.H264R	ENST00000282018	NM_020377.2	264	cAc/cGc	1/1	0.212085686777034	3	FACETS	1	0.988	1	0.815	0.762	0.869	CLONAL	2	TRUE	0	0.212085686777034	3		675	1071	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576129	88576129	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	89	536	1	ENST00000360948.2:c.1544A>T	p.Gln515Leu	p.Q515L	ENST00000360948	NM_001012338.2	515	cAg/cTg	13/19	0.212449889646598	4	FACETS	1	0.905	1	0.513	0.453	0.576	CLONAL	1	TRUE	2	0.212085686777034	4		537	992	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673767	37673767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1212731319	NA	P-0017467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1243	79	696	2	ENST00000447079.4:c.2921C>T	p.Pro974Leu	p.P974L	ENST00000447079	NM_015083.1	974	cCg/cTg	10/14	0.212085686777034	5	FACETS	0.743	0.651	0.843	0.371	0.325	0.422	SUBCLONAL	1	TRUE	3	0.212085686777034	5		698	1322	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740509	58740509	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	288	582	0	ENST00000305921.3:c.1414G>T	p.Glu472Ter	p.E472*	ENST00000305921	NM_003620.3	472	Gaa/Taa	6/6	0.212449889646598	4	FACETS	0.979	0.921	1	0.979	0.921	1	CLONAL	3	TRUE	1	0.212085686777034	4		582	1121	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220611	1220611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	243	557	0	ENST00000326873.7:c.629del	p.Cys210SerfsTer77	p.C210Sfs*77	ENST00000326873	NM_000455.4	210	tGc/tc	5/10	0.212085686777034	3	FACETS	0.957	0.896	1	0.957	0.896	1	CLONAL	3	TRUE	0	0.212085686777034	3		557	883	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19261495	19261496	+	missense_variant	Missense_Mutation	DNP	CG	CG	GA	novel	NA	P-0017467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	217	555	1	ENST00000162023.5:c.49_50delinsTC	p.Arg17Ser	p.R17S	ENST00000162023		17	CGg/TCg	6/13	0.212085686777034	3	FACETS	0.878	0.818	0.94	0.878	0.818	0.94	CLONAL	3	TRUE	0	0.212085686777034	3		556	859	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133613	55133613	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	178	472	0	ENST00000257290.5:c.917C>A	p.Thr306Asn	p.T306N	ENST00000257290	NM_006206.4	306	aCt/aAt	6/23	0.212085686777034	5	FACETS	0.841	0.776	0.909	0.841	0.776	0.909	CLONAL	3	TRUE	2	0.212085686777034	5		472	877	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280161	66280162	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0017467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	94	217	1	ENST00000273854.3:c.1528-1_1528delinsTT		p.X510_splice	ENST00000273854	NM_004439.5	510		7/18	0.212085686777034	3	FACETS	1	0.967	1	0.801	0.717	0.889	CLONAL	2	TRUE	0	0.212085686777034	3		218	408	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683691	162683691	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	66	458	0	ENST00000366898.1:c.278del	p.Gly93GlufsTer10	p.G93Efs*10	ENST00000366898	NM_004562.2	93	gGa/ga	3/12	0.150501802180879	4	FACETS	0.976	0.846	1			1	CLONAL	1	TRUE	NA	0.212085686777034	4		458	773	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874263	155874263	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1557960039	NA	P-0017469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	156	527	0	ENST00000368323.3:c.268A>G	p.Met90Val	p.M90V	ENST00000368323	NM_006912.5	90	Atg/Gtg	5/6	0.114637453156228	4	FACETS	0.865	0.79	0.943	0.865	0.79	0.943	CLONAL	2	TRUE	2	0.184964413226713	4		527	1156	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602583	10602583	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	124	422	0	ENST00000171111.5:c.995G>T	p.Gly332Val	p.G332V	ENST00000171111	NM_203500.1	332	gGc/gTc	3/6	0.184964413226713	1	FACETS	0.824	0.746	0.906	1	0.987	1	CLONAL	2	TRUE	0	0.184964413226713	1		422	738	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222987	1222987	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057520042	NA	P-0017469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	107	417	0	ENST00000326873.7:c.924G>C	p.Trp308Cys	p.W308C	ENST00000326873	NM_000455.4	308	tgG/tgC	8/10	0.184964413226713	1	FACETS	0.786	0.706	0.871	1	0.984	1	SUBCLONAL	2	TRUE	0	0.184964413226713	1		417	668	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135023	11135047	+	frameshift_variant	Frame_Shift_Del	DEL	AGTGCGACATGTCTGCGCTGCAGCG	AGTGCGACATGTCTGCGCTGCAGCG	-	novel	NA	P-0017469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	121	468	0	ENST00000358026.2:c.2995_3019del	p.Asp999SerfsTer12	p.D999Sfs*12	ENST00000358026	NM_001128849.1	997	aAGTGCGACATGTCTGCGCTGCAGCGa/aa	21/36	0.184964413226713	1	FACETS	0.767	0.693	0.845	1	0.985	1	SUBCLONAL	2	TRUE	0	0.184964413226713	1		468	774	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494659	2494659	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	105	558	0	ENST00000355716.4:c.799G>T	p.Val267Leu	p.V267L	ENST00000355716	NM_003820.2	267	Gtg/Ttg	8/8	0.184964413226713	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.184964413226713	1		558	901	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0017470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	584	403	1	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.583719416110805	3	FACETS	0.932	0.903	0.959	0.932	0.903	0.959	CLONAL	3	TRUE	0	0.583719416110805	3		404	925	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16062075	16062075	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	393	299	0	ENST00000268712.3:c.731G>C	p.Arg244Pro	p.R244P	ENST00000268712	NM_006311.3	244	cGg/cCg	6/46	0.583719416110805	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	0	0.583719416110805	3		299	567	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736808	736808	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	325	456	0	ENST00000314574.4:c.1291G>T	p.Gly431Cys	p.G431C	ENST00000314574	NM_005433.3	431	Ggt/Tgt	10/12	0.451137632914872	4	FACETS	1	0.956	1			1	CLONAL	2	TRUE	NA	0.583719416110805	4		456	874	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735653	204735653	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	123	249	0	ENST00000302823.3:c.454A>C	p.Ile152Leu	p.I152L	ENST00000302823	NM_005214.4	152	Att/Ctt	2/4	0.583719416110805	3	FACETS	0.99	0.899	1	0.495	0.449	0.543	CLONAL	1	TRUE	1	0.583719416110805	3		249	550	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959143	2959143	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	219	406	1	ENST00000396946.4:c.2373C>A	p.Cys791Ter	p.C791*	ENST00000396946	NM_032415.4	791	tgC/tgA	18/25	0.538434728722137	2	FACETS	0.914	0.852	0.978	0.457	0.426	0.489	CLONAL	1	TRUE	0	0.583719416110805	2		407	821	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0017472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	25	410	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.124	0.097	0.155	0.124	0.097	0.155	SUBCLONAL	1	TRUE	1	0.537012412997478	2		410	753	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	361	301	4				ENST00000310581	NM_198253.2	-/1132			0.537012412997478	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	1	0.537012412997478	4		305	653	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0017472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	197	418	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.929	0.862	0.998	0.929	0.862	0.998	CLONAL	1	TRUE	1	0.537012412997478	2		420	790	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111855996	111855996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779622961	NA	P-0017472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	180	378	0	ENST00000341259.2:c.47C>T	p.Ser16Leu	p.S16L	ENST00000341259	NM_005475.2	16	tCa/tTa	2/8	1	2	FACETS	0.905	0.836	0.975	0.905	0.836	0.975	CLONAL	1	TRUE	1	0.537012412997478	2		378	741	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0017472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	233	342	1	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.537012412997478	2		343	718	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916836	178916836	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	103	596	0	ENST00000263967.3:c.223C>G	p.Gln75Glu	p.Q75E	ENST00000263967	NM_006218.2	75	Caa/Gaa	2/21	0.14542757998405	3	FACETS	0.55	0.491	0.612	0.275	0.245	0.306	INDETERMINATE	1	TRUE	1	0.537012412997478	3		596	885	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434943	56434943	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775335997	NA	P-0017472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	215	448	0	ENST00000407977.2:c.2194C>T	p.Arg732Cys	p.R732C	ENST00000407977		732	Cgc/Tgc	9/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.537012412997478	2		448	772	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952142	178952142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253171657	NA	P-0017472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	153	332	0	ENST00000263967.3:c.3197C>T	p.Ala1066Val	p.A1066V	ENST00000263967	NM_006218.2	1066	gCa/gTa	21/21	0.14542757998405	3	FACETS	1	0.988	1	0.729	0.671	0.788	INDETERMINATE	1	TRUE	1	0.537012412997478	3		332	496	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178002	56178002	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs775205606	NA	P-0017472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	186	437	0	ENST00000399503.3:c.2975C>G	p.Ser992Cys	p.S992C	ENST00000399503	NM_005921.1	992	tCt/tGt	14/20	0.537012412997478	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.537012412997478	1		437	488	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446420	70446420	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0017472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	118	561	0	ENST00000373644.4:c.5360C>G	p.Ser1787Ter	p.S1787*	ENST00000373644	NM_030625.2	1787	tCa/tGa	11/12	1	2	FACETS	0.45	0.405	0.498	0.45	0.405	0.498	SUBCLONAL	1	TRUE	1	0.537012412997478	2		561	976	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625349	69625349	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	249	447	0	ENST00000334134.2:c.444C>A	p.Ser148Arg	p.S148R	ENST00000334134	NM_005247.2	148	agC/agA	3/3	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.537012412997478	2		447	800	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376124	118376124	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	96	482	0	ENST00000534358.1:c.9517C>G	p.Gln3173Glu	p.Q3173E	ENST00000534358	NM_005933.3	3173	Caa/Gaa	27/36	1	2	FACETS	0.455	0.405	0.508	0.455	0.405	0.508	SUBCLONAL	1	TRUE	1	0.537012412997478	2		482	786	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037873	49037874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0017472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	135	376	0	ENST00000267163.4:c.2117_2118dup	p.Ser707ValfsTer9	p.S707Vfs*9	ENST00000267163	NM_000321.2	705	atg/aTGtg	21/27	0.537012412997478	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.537012412997478	1		376	349	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792449	33792449	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	311	546	0	ENST00000498907.2:c.872G>C	p.Arg291Pro	p.R291P	ENST00000498907	NM_004364.3	291	cGc/cCc	1/1	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.537012412997478	2		546	940	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469490	25469490	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	105	444	0	ENST00000264709.3:c.1278A>C	p.Glu426Asp	p.E426D	ENST00000264709	NM_175629.2	426	gaA/gaC	10/23	0.323935739726623	1	FACETS	0.46	0.413	0.51	0.46	0.413	0.51	SUBCLONAL	1	TRUE	0	0.537012412997478	1		444	622	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61720152	61720152	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	81	504	0	ENST00000401558.2:c.1282G>C	p.Glu428Gln	p.E428Q	ENST00000401558	NM_003400.3	428	Gag/Cag	13/25	0.323935739726623	1	FACETS	0.262	0.23	0.297	0.262	0.23	0.297	SUBCLONAL	1	TRUE	0	0.537012412997478	1		504	841	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794506	242794506	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0017472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	118	447	0	ENST00000334409.5:c.437-1G>T		p.X146_splice	ENST00000334409	NM_005018.2	146			0.323935739726623	1	FACETS	0.454	0.41	0.501	0.454	0.41	0.501	SUBCLONAL	1	TRUE	0	0.537012412997478	1		447	708	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41526001	41526001	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	172	434	0	ENST00000263253.7:c.1276C>G	p.Gln426Glu	p.Q426E	ENST00000263253	NM_001429.3	426	Caa/Gaa	5/31	0.437006150065778	0	FACETS	0.713	0.664	0.763			1	SUBCLONAL	1	TRUE	0	0.537012412997478	0		434	416	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531867	41531867	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	209	523	0	ENST00000263253.7:c.1579C>G	p.Leu527Val	p.L527V	ENST00000263253	NM_001429.3	527	Ctt/Gtt	7/31	0.437006150065778	0	FACETS	0.605	0.565	0.645			1	SUBCLONAL	1	TRUE	0	0.537012412997478	0		523	596	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556674	41556674	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	122	441	0	ENST00000263253.7:c.3619G>A	p.Glu1207Lys	p.E1207K	ENST00000263253	NM_001429.3	1207	Gag/Aag	20/31	0.437006150065778	0	FACETS	0.464	0.422	0.508			1	SUBCLONAL	1	TRUE	0	0.537012412997478	0		441	453	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499444	89499444	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	134	429	0	ENST00000336596.2:c.2614G>C	p.Glu872Gln	p.E872Q	ENST00000336596	NM_005233.5	872	Gag/Cag	15/17	0.14542757998405	3	FACETS	0.934	0.85	1	0.467	0.425	0.511	INDETERMINATE	1	TRUE	1	0.537012412997478	3		429	678	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569835	67569835	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772253669	NA	P-0017472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	47	249	0	ENST00000274335.5:c.496G>A	p.Asp166Asn	p.D166N	ENST00000274335		166	Gat/Aat	3/15	0.537012412997478	1	FACETS	0.414	0.351	0.483	0.414	0.351	0.483	SUBCLONAL	1	TRUE	0	0.537012412997478	1		249	309	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490581	20490581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	201	411	1	ENST00000346618.3:c.1318G>A	p.Glu440Lys	p.E440K	ENST00000346618	NM_001949.4	440	Gag/Aag	7/7	1	2	FACETS	0.999	0.929	1	0.999	0.929	1	CLONAL	1	TRUE	1	0.537012412997478	2		412	749	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652324	36652324	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0017472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	156	281	0	ENST00000244741.5:c.445+1G>T		p.X149_splice	ENST00000244741	NM_000389.4	149			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.537012412997478	2		281	512	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135804167	135804167	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	155	356	0	ENST00000298552.3:c.93G>C	p.Glu31Asp	p.E31D	ENST00000298552	NM_001162426.1	31	gaG/gaC	3/23	1	2	FACETS	0.881	0.809	0.956	0.881	0.809	0.956	CLONAL	1	TRUE	1	0.537012412997478	2		356	655	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0017475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	206	195	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.291061497203887	4	FACETS	0.853	0.796	0.91	0.853	0.796	0.91	INDETERMINATE	2	TRUE	2	0.695552161324743	4		195	589	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201059	NA	P-0017475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	1270	401	0	ENST00000269305.4:c.856G>T	p.Glu286Ter	p.E286*	ENST00000269305	NM_001126112.2	286	Gaa/Taa	8/11	0.695552161324743	3	FACETS	1	0.999	1	1	0.999	1	CLONAL	3	TRUE	0	0.695552161324743	3		401	1417	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939681	76939681	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	371	219	0	ENST00000373344.5:c.1067del	p.Ala356GlufsTer4	p.A356Efs*4	ENST00000373344	NM_000489.3	356	gCa/ga	9/35	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.695552161324743	1		219	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0017477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	396	487	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.722471613794992	1	FACETS	0.967	0.928	1	0.967	0.928	1	CLONAL	1	TRUE	0	0.722471613794992	1		489	724	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187718	11187718	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	417	577	0	ENST00000361445.4:c.6179G>T	p.Arg2060Leu	p.R2060L	ENST00000361445	NM_004958.3	2060	cGg/cTg	44/58	0.722471613794992	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.722471613794992	1		577	688	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246093241	246093241	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0017477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	300	419	0	ENST00000388985.4:c.532-2A>T		p.X178_splice	ENST00000388985		178			1	2	FACETS	0.986	0.932	1	0.986	0.932	1	CLONAL	1	TRUE	1	0.722471613794992	2		419	842	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560130	29560130	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	216	276	0	ENST00000356175.3:c.3607G>T	p.Asp1203Tyr	p.D1203Y	ENST00000356175	NM_000267.3	1203	Gat/Tat	27/57	NA	2	FACETS	0.971	0.908	1			1	INDETERMINATE	1	TRUE	NA	0.722471613794992	2		276	616	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663659	29663659	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	280	373	0	ENST00000356175.3:c.6091G>T	p.Gly2031Ter	p.G2031*	ENST00000356175	NM_000267.3	2031	Gga/Tga	41/57	NA	2	FACETS	0.946	0.892	1			1	INDETERMINATE	1	TRUE	NA	0.722471613794992	2		373	819	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649017	37649017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	298	331	1	ENST00000447079.4:c.2122C>T	p.Arg708Cys	p.R708C	ENST00000447079	NM_015083.1	708	Cgt/Tgt	4/14	1	2	FACETS	0.984	0.93	1	0.984	0.93	1	CLONAL	1	TRUE	1	0.722471613794992	2		332	838	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599958	10599958	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	379	612	0	ENST00000171111.5:c.1618del	p.Glu540LysfsTer8	p.E540Kfs*8	ENST00000171111	NM_203500.1	540	Gaa/aa	5/6	0.722471613794992	1	FACETS	0.987	0.947	1	0.987	0.947	1	CLONAL	1	TRUE	0	0.722471613794992	1		612	679	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113836	11113836	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0017477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	227	361	1	ENST00000358026.2:c.1943+1G>A		p.X648_splice	ENST00000358026	NM_001128849.1	648			0.722471613794992	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.722471613794992	1		362	390	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155394	47155394	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	371	489	0	ENST00000409792.3:c.4687G>T	p.Gly1563Cys	p.G1563C	ENST00000409792	NM_014159.6	1563	Ggc/Tgc	5/21	0.722471613794992	1	FACETS	0.988	0.947	1	0.988	0.947	1	CLONAL	1	TRUE	0	0.722471613794992	1		489	664	SUCCESS
APC	324	MSKCC	GRCh37	5	112128170	112128170	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	421	511	0	ENST00000257430.4:c.673G>T	p.Glu225Ter	p.E225*	ENST00000257430	NM_000038.5	225	Gaa/Taa	7/16	0.722471613794992	1	FACETS	0.938	0.9	0.975	0.938	0.9	0.975	CLONAL	1	TRUE	0	0.722471613794992	1		511	794	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782006	NA	P-0017478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	251	554	0	ENST00000269305.4:c.859G>A	p.Glu287Lys	p.E287K	ENST00000269305	NM_001126112.2	287	Gag/Aag	8/11	0.570351525671087	1	FACETS	0.652	0.611	0.693	0.652	0.611	0.693	SUBCLONAL	1	TRUE	0	0.645590475768552	1		554	808	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0017478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	278	417	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.643875946520606	1	FACETS	0.951	0.901	1	0.951	0.901	1	CLONAL	1	TRUE	0	0.645590475768552	1		417	613	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597416	10597416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190115073	NA	P-0017478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	383	518	0	ENST00000171111.5:c.1787G>A	p.Arg596Gln	p.R596Q	ENST00000171111	NM_203500.1	596	cGa/cAa	6/6	1	2	FACETS	0.885	0.84	0.931	0.885	0.84	0.931	CLONAL	1	TRUE	1	0.645590475768552	2		518	1340	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216947	7216947	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	188	383	1	ENST00000380728.2:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000380728		192	Cag/Tag	7/11	0.570351525671087	1	FACETS	0.665	0.618	0.713	0.665	0.618	0.713	SUBCLONAL	1	TRUE	0	0.645590475768552	1		384	593	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092825	27092825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867253777	NA	P-0017478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	55	540	0	ENST00000324856.7:c.2846C>T	p.Ser949Phe	p.S949F	ENST00000324856	NM_006015.4	949	tCc/tTc	9/20	1	2	FACETS	0.156	0.132	0.181	0.156	0.132	0.181	SUBCLONAL	1	TRUE	1	0.645590475768552	2		540	1095	SUCCESS
AR	367	MSKCC	GRCh37	X	66765047	66765047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1297947716	NA	P-0017478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	324	615	1	ENST00000374690.3:c.59G>A	p.Arg20Gln	p.R20Q	ENST00000374690	NM_000044.3	20	cGa/cAa	1/8	NA	2	FACETS	0.815	0.77	0.862			1	INDETERMINATE	1	TRUE	NA	0.645590475768552	2		616	1231	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004625	150004625	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	227	377	0	ENST00000253339.5:c.1600G>C	p.Glu534Gln	p.E534Q	ENST00000253339		534	Gag/Cag	3/7	0.643875946520606	1	FACETS	0.777	0.729	0.826	0.777	0.729	0.826	SUBCLONAL	1	TRUE	0	0.645590475768552	1		377	613	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612071	43612071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	346	542	0	ENST00000355710.3:c.2176C>T	p.Leu726Phe	p.L726F	ENST00000355710	NM_020975.4	726	Ctt/Ttt	12/20	1	2	FACETS	0.989	0.937	1	0.989	0.937	1	CLONAL	1	TRUE	1	0.645590475768552	2		542	1084	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041084	29041084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	257	413	0	ENST00000282397.4:c.344C>T	p.Ser115Leu	p.S115L	ENST00000282397	NM_002019.4	115	tCa/tTa	3/30	0.645590475768552	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.645590475768552	1		413	502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577077	7577079	+	frameshift_variant	Frame_Shift_Del	DEL	CTC	CTC	TT	novel	NA	P-0017478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	251	551	3	ENST00000269305.4:c.859_861delinsAA	p.Glu287LysfsTer58	p.E287Kfs*58	ENST00000269305	NM_001126112.2	287	GAG/AA	8/11	0.570351525671087	1	FACETS	0.648	0.608	0.689	0.648	0.608	0.689	SUBCLONAL	1	TRUE	0	0.645590475768552	1		554	813	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350822	15350822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200902225	NA	P-0017478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	226	416	0	ENST00000263377.2:c.3181G>A	p.Glu1061Lys	p.E1061K	ENST00000263377	NM_058243.2	1061	Gaa/Aaa	15/20	1	2	FACETS	0.801	0.747	0.856	0.801	0.747	0.856	CLONAL	1	TRUE	1	0.645590475768552	2		416	874	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797215	42797215	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	256	478	0	ENST00000575354.2:c.3577G>C	p.Glu1193Gln	p.E1193Q	ENST00000575354	NM_015125.3	1193	Gag/Cag	15/20	1	2	FACETS	0.722	0.676	0.77	0.722	0.676	0.77	SUBCLONAL	1	TRUE	1	0.645590475768552	2		478	1098	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742646	39742646	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	183	255	1	ENST00000361337.2:c.1489G>A	p.Glu497Lys	p.E497K	ENST00000361337	NM_003286.2	497	Gaa/Aaa	15/21	1	2	FACETS	0.942	0.874	1	0.942	0.874	1	CLONAL	1	TRUE	1	0.645590475768552	2		256	602	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445091	89445091	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	159	364	0	ENST00000336596.2:c.1411G>T	p.Glu471Ter	p.E471*	ENST00000336596	NM_005233.5	471	Gag/Tag	6/17	1	2	FACETS	0.72	0.662	0.781	0.72	0.662	0.781	SUBCLONAL	1	TRUE	1	0.645590475768552	2		364	684	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540108	187540108	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	198	387	0	ENST00000441802.2:c.7632G>C	p.Glu2544Asp	p.E2544D	ENST00000441802	NM_005245.3	2544	gaG/gaC	10/27	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.645590475768552	2		387	604	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456971	149456971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	169	347	1	ENST00000286301.3:c.757C>T	p.His253Tyr	p.H253Y	ENST00000286301	NM_005211.3	253	Cat/Tat	6/22	1	2	FACETS	0.798	0.736	0.862	0.798	0.736	0.862	SUBCLONAL	1	TRUE	1	0.645590475768552	2		348	656	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456979	149456979	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	143	304	0	ENST00000286301.3:c.749C>G	p.Ser250Cys	p.S250C	ENST00000286301	NM_005211.3	250	tCt/tGt	6/22	1	2	FACETS	0.738	0.676	0.804	0.738	0.676	0.804	SUBCLONAL	1	TRUE	1	0.645590475768552	2		304	600	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467652	50467652	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	208	414	0	ENST00000331340.3:c.887G>A	p.Ser296Asn	p.S296N	ENST00000331340	NM_006060.4	296	aGc/aAc	8/8	1	2	FACETS	0.823	0.766	0.882	0.823	0.766	0.882	CLONAL	1	TRUE	1	0.645590475768552	2		414	783	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272363	38272363	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	207	415	0	ENST00000425967.3:c.2004G>A	p.Met668Ile	p.M668I	ENST00000425967	NM_001174067.1	668	atG/atA	15/19	1	2	FACETS	0.763	0.71	0.819	0.763	0.71	0.819	SUBCLONAL	1	TRUE	1	0.645590475768552	2		415	840	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576872	7576872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912659	NA	P-0017478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	202	434	0	ENST00000269305.4:c.974G>A	p.Gly325Glu	p.G325E	ENST00000269305	NM_001126112.2	325	gGa/gAa	9/11	0.570351525671087	1	FACETS	0.69	0.643	0.738	0.69	0.643	0.738	SUBCLONAL	1	TRUE	0	0.645590475768552	1		434	614	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692922	89692922	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201044	NA	P-0017481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	36	428	0	ENST00000371953.3:c.406T>C	p.Cys136Arg	p.C136R	ENST00000371953	NM_000314.4	136	Tgt/Cgt	5/9	0.313592945578068	1	FACETS	0.259	0.212	0.312	0.259	0.212	0.312	SUBCLONAL	1	TRUE	0	0.313592945578068	1		428	747	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0017481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	155	438	1	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.313592945578068	2		439	784	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774973	73774973	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	23	190	0	ENST00000254810.4:c.200C>G	p.Pro67Arg	p.P67R	ENST00000254810	NM_005324.3	67	cCc/cGc	3/4	1	2	FACETS	0.332	0.258	0.418	0.332	0.258	0.418	SUBCLONAL	1	TRUE	1	0.313592945578068	2		190	442	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	121	301	4				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.926	0.842	1	0.926	0.842	1	CLONAL	1	TRUE	1	0.559592567936993	2		305	467	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916824	178916824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201269904	NA	P-0017482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	306	500	1	ENST00000263967.3:c.211G>A	p.Val71Ile	p.V71I	ENST00000263967	NM_006218.2	71	Gta/Ata	2/21	1	2	FACETS	0.991	0.934	1	0.991	0.934	1	CLONAL	1	TRUE	1	0.559592567936993	2		501	1104	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644470	18644470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	241	394	0	ENST00000266497.5:c.2648G>A	p.Cys883Tyr	p.C883Y	ENST00000266497		883	tGt/tAt	18/31	1	2	FACETS	0.9	0.841	0.96	0.9	0.841	0.96	CLONAL	1	TRUE	1	0.559592567936993	2		394	957	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928062	178928063	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGT	novel	NA	P-0017482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	266	463	0	ENST00000263967.3:c.1342_1344dup	p.Val448dup	p.V448dup	ENST00000263967	NM_006218.2	448	cca/ccAGTa	8/21	1	2	FACETS	0.873	0.818	0.929	0.873	0.818	0.929	CLONAL	1	TRUE	1	0.559592567936993	2		463	1089	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268722	55269744	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGGAGGCAGCTATAATTTAGAGAACCAAGGGGGATTTCATTATAACAAAATTGGCAAACACACAGGCACCTGCTGGCAATAGACCCCTGCTCCTATAGCCAAGAAGTGGAATAGCATCTCTACGGGCCATTCTAATAGCCTCAAAATCTCTGCACCAGGGGGATGAAAGAATGCATTTGCCAAGTCCTACAGACTCCAACTTCTACCGTGCCCTGATGGATGAAGAAGACATGGACGACGTGGTGGATGCCGACGAGTACCTCATCCCACAGCAGGGCTTCTTCAGCAGCCCCTCCACGTCACGGACTCCCCTCCTGAGCTCTCTGGTATGAAATCTCTGTCTCTCTCTCTCTCTCAAGCTGTGTCTACTCATTTGAACAAATTGAATTTTAGGGAAAATAACCATCTAGTGAAACTCACATGGATATGAAGTCAATTTTAACCAAATGGTAAAATCAAAATCAAAATAAATTAAGTGTATTAATTATTTTGTTGCATTGCAACAACTTGATTGTAAGCCTTTTAGGTCCACTATGGAATGTAATTAAATCAAAACTAAACCTAGTTGCTCTAAAACTAACGATTAAGACAAAAATTAAACACCTTCACAATATACCCTCCATGAGGCACACCACCTGCATTCAGGAAAAGTGGATGAGATGTGGTACAAGCATTCCATGGGCAACTTCTCTGTTTCTTTTTCAGAGTGCAACCAGCAACAATTCCACCGTGGCTTGCATTGATAGAAATGGGGTATGTATGAACACCTTATAAGCCAGAATTTACAGCTCTCCACTATGGCTCTATTTTACATGGAAAATGCCTTAACCTAAATAATTTTAACCCAGATAATCTTGAGTTTTCTTCCTGTGTGGGTTTTTCCCTGCACGGCTGTCACGCCTCACAGTGCCGTTCAAAGCGTGACTCCTGGACCAGTAGTAGCATCGCCTGGCCTTGTTAGAAACGCCATTTTTCAGGCCACTGCCCCAGTTTGACCAAATCAGGACCTCTGGGGGTGGCAC	GGGGAGGCAGCTATAATTTAGAGAACCAAGGGGGATTTCATTATAACAAAATTGGCAAACACACAGGCACCTGCTGGCAATAGACCCCTGCTCCTATAGCCAAGAAGTGGAATAGCATCTCTACGGGCCATTCTAATAGCCTCAAAATCTCTGCACCAGGGGGATGAAAGAATGCATTTGCCAAGTCCTACAGACTCCAACTTCTACCGTGCCCTGATGGATGAAGAAGACATGGACGACGTGGTGGATGCCGACGAGTACCTCATCCCACAGCAGGGCTTCTTCAGCAGCCCCTCCACGTCACGGACTCCCCTCCTGAGCTCTCTGGTATGAAATCTCTGTCTCTCTCTCTCTCTCAAGCTGTGTCTACTCATTTGAACAAATTGAATTTTAGGGAAAATAACCATCTAGTGAAACTCACATGGATATGAAGTCAATTTTAACCAAATGGTAAAATCAAAATCAAAATAAATTAAGTGTATTAATTATTTTGTTGCATTGCAACAACTTGATTGTAAGCCTTTTAGGTCCACTATGGAATGTAATTAAATCAAAACTAAACCTAGTTGCTCTAAAACTAACGATTAAGACAAAAATTAAACACCTTCACAATATACCCTCCATGAGGCACACCACCTGCATTCAGGAAAAGTGGATGAGATGTGGTACAAGCATTCCATGGGCAACTTCTCTGTTTCTTTTTCAGAGTGCAACCAGCAACAATTCCACCGTGGCTTGCATTGATAGAAATGGGGTATGTATGAACACCTTATAAGCCAGAATTTACAGCTCTCCACTATGGCTCTATTTTACATGGAAAATGCCTTAACCTAAATAATTTTAACCCAGATAATCTTGAGTTTTCTTCCTGTGTGGGTTTTTCCCTGCACGGCTGTCACGCCTCACAGTGCCGTTCAAAGCGTGACTCCTGGACCAGTAGTAGCATCGCCTGGCCTTGTTAGAAACGCCATTTTTCAGGCCACTGCCCCAGTTTGACCAAATCAGGACCTCTGGGGGTGGCAC	-	novel	NA	P-0017482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12532	4263	635	3	ENST00000275493.2:c.2947-159_3162+269del		p.X983_splice	ENST00000275493	NM_005228.3	983		25-26/28	0.559592567936993	24	FACETS	1	0.998	1			1	CLONAL	6	TRUE	NA	0.559592567936993	24		638	16795	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0017483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	83	395	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.208056175629385	2		397	682	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	79	357	2	ENST00000322088.6:c.767C>A	p.Ser256Tyr	p.S256Y	ENST00000322088	NM_014225.5	256	tCc/tAc	6/15	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.208056175629385	2		359	689	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936083	178936083	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519927	NA	P-0017483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	214	388	0	ENST00000263967.3:c.1625A>T	p.Glu542Val	p.E542V	ENST00000263967	NM_006218.2	542	gAa/gTa	10/21	0.208056175629385	4	FACETS	0.966	0.903	1			1	CLONAL	4	TRUE	NA	0.208056175629385	4		388	643	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675208	40675208	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	60	420	0	ENST00000249776.8:c.172A>G	p.Ser58Gly	p.S58G	ENST00000249776	NM_033286.3	58	Agc/Ggc	1/9	1	2	FACETS	0.766	0.659	0.883	0.766	0.659	0.883	SUBCLONAL	1	TRUE	1	0.208056175629385	2		420	753	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576871	7576872	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0017483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	55	473	0	ENST00000269305.4:c.974dup	p.Glu326ArgfsTer11	p.E326Rfs*11	ENST00000269305	NM_001126112.2	325	gga/ggGa	9/11	1	2	FACETS	0.704	0.601	0.817	0.704	0.601	0.817	SUBCLONAL	1	TRUE	1	0.208056175629385	2		473	751	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0017484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	243	483	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.330305061281781	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.330305061281781	1		483	1078	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534285	534285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894226	NA	P-0017484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	283	408	0	ENST00000451590.1:c.38G>T	p.Gly13Val	p.G13V	ENST00000451590	NM_001130442.1	13	gGt/gTt	2/5	1	2	FACETS	0.76	0.714	0.807	1	0.994	1	SUBCLONAL	2	TRUE	1	0.330305061281781	2		408	1127	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164505	47164505	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	128	284	2	ENST00000409792.3:c.1621C>T	p.Arg541Ter	p.R541*	ENST00000409792	NM_014159.6	541	Cga/Tga	3/21	0.330305061281781	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.330305061281781	1		286	585	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984519	72984519	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	201	424	0	ENST00000268489.5:c.3065del	p.Gly1022AlafsTer47	p.G1022Afs*47	ENST00000268489	NM_006885.3	1022	gGc/gc	3/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.330305061281781	2		424	975	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560069	29560070	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0017484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	113	256	0	ENST00000356175.3:c.3547_3548del	p.Leu1183AspfsTer11	p.L1183Dfs*11	ENST00000356175	NM_000267.3	1182	gtTCtg/gttg	27/57	0.330305061281781	1	FACETS	0.99	0.894	1	0.99	0.894	1	CLONAL	1	TRUE	0	0.330305061281781	1		256	577	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189926	66189926	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	54	221	0	ENST00000273854.3:c.3020G>T	p.Arg1007Leu	p.R1007L	ENST00000273854	NM_004439.5	1007	cGg/cTg	18/18	1	2	FACETS	0.549	0.468	0.637	0.549	0.468	0.637	SUBCLONAL	1	TRUE	1	0.330305061281781	2		221	596	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549446	187549446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	232	397	0	ENST00000441802.2:c.4672C>T	p.His1558Tyr	p.H1558Y	ENST00000441802	NM_005245.3	1558	Cac/Tac	9/27	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.330305061281781	2		397	945	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750779	57750779	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	162	386	0	ENST00000274289.3:c.1825G>T	p.Asp609Tyr	p.D609Y	ENST00000274289	NM_006622.3	609	Gat/Tat	13/14	1	2	FACETS	0.994	0.911	1	0.994	0.911	1	CLONAL	1	TRUE	1	0.330305061281781	2		386	987	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056181	26056181	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs751702619	NA	P-0017484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	139	288	0	ENST00000343677.2:c.476A>G	p.Lys159Arg	p.K159R	ENST00000343677	NM_005319.3	159	aAg/aGg	1/1	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.330305061281781	2		288	827	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104593	69104593	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	239	458	0	ENST00000288368.4:c.4437G>T	p.Leu1479Phe	p.L1479F	ENST00000288368	NM_024870.2	1479	ttG/ttT	37/40	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.330305061281781	2		458	1252	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521446	8521446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	231	449	0	ENST00000356435.5:c.792G>A	p.Met264Ile	p.M264I	ENST00000356435		264	atG/atA	9/35	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.330305061281781	2		449	1223	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27190538	27190538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753410363	NA	P-0017484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	204	444	1	ENST00000380036.4:c.1339C>T	p.Pro447Ser	p.P447S	ENST00000380036	NM_000459.3	447	Ccc/Tcc	10/23	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.330305061281781	2		445	1140	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778026	135778026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	173	273	2	ENST00000298552.3:c.2357G>T	p.Arg786Leu	p.R786L	ENST00000298552	NM_001162426.1	786	cGa/cTa	18/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.330305061281781	2		275	905	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0017485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	156	290	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	0.343202727426473	2		290	782	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	125	335	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.839	0.759	0.924	0.839	0.759	0.924	CLONAL	1	TRUE	1	0.343202727426473	2		335	868	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099979	27099980	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	188	567	0	ENST00000324856.7:c.3859dup	p.Arg1287LysfsTer11	p.R1287Kfs*11	ENST00000324856	NM_006015.4	1286	-/A	15/20	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.343202727426473	2		567	1087	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2214573	2214573	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	160	497	0	ENST00000398665.3:c.1901A>T	p.Gln634Leu	p.Q634L	ENST00000398665	NM_032482.2	634	cAg/cTg	19/28	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.343202727426473	2		497	902	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0017487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	205	602	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.652762064745604	1	FACETS	0.65	0.606	0.695	0.65	0.606	0.695	SUBCLONAL	1	TRUE	0	0.652762064745604	1		602	651	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	rs886039483	NA	P-0017487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	753	857	0	ENST00000269305.4:c.376T>G	p.Tyr126Asp	p.Y126D	ENST00000269305	NM_001126112.2	126	Tac/Gac	5/11	0.652762064745604	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.652762064745604	1		857	1361	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461979	120461979	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	32	337	0	ENST00000256646.2:c.5737C>A	p.Pro1913Thr	p.P1913T	ENST00000256646	NM_024408.3	1913	Cca/Aca	31/34	0.450080770599772	2	FACETS	0.16	0.129	0.195	0.08	0.064	0.098	SUBCLONAL	1	TRUE	0	0.652762064745604	2		337	612	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0017488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	212	583	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	1	2	FACETS	0.939	0.871	1	0.939	0.871	1	CLONAL	1	TRUE	1	0.374953760932219	2		583	1204	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0017488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	204	551	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	1	2	FACETS	0.921	0.852	0.991	0.921	0.852	0.991	CLONAL	1	TRUE	1	0.374953760932219	2		551	1182	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720900	176720900	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	34	342	1	ENST00000439151.2:c.6531G>A	p.Met2177Ile	p.M2177I	ENST00000439151	NM_022455.4	2177	atG/atA	23/23	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		343	632	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0017492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	369	421	0	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			NA	2	FACETS	0.955	0.93	0.977			1	INDETERMINATE	2	TRUE	NA	0.884633326635452	2		421	437	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849536	68849536	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	89	499	0	ENST00000261769.5:c.1439T>G	p.Val480Gly	p.V480G	ENST00000261769	NM_004360.3	480	gTg/gGg	10/16	0.484045524891286	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.884633326635452	0		499	475	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623103	52623103	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	77	503	0	ENST00000394830.3:c.2948T>G	p.Leu983Arg	p.L983R	ENST00000394830	NM_018313.4	983	cTg/cGg	19/30	0.61894959889099	2	FACETS	0.261	0.229	0.296	0.13	0.114	0.148	SUBCLONAL	1	TRUE	0	0.884633326635452	2		503	667	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225725	26225725	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	304	482	0	ENST00000360408.1:c.343G>T	p.Ala115Ser	p.A115S	ENST00000360408	NM_003532.2	115	Gcc/Tcc	1/1	0.489991355725279	1	FACETS	0.653	0.622	0.684	0.653	0.622	0.684	INDETERMINATE	1	TRUE	0	0.884633326635452	1		482	587	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0017493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	1405	563	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.464428878443803	4	FACETS	0.989	0.974	1			1	CLONAL	4	TRUE	NA	0.626123657099706	4		563	1844	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0017493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	692	436	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.626123657099706	2	FACETS	0.949	0.921	0.976	0.949	0.921	0.976	CLONAL	2	TRUE	0	0.626123657099706	2		436	1165	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207078	1207078	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	837	561	1	ENST00000326873.7:c.166G>T	p.Gly56Trp	p.G56W	ENST00000326873	NM_000455.4	56	Ggg/Tgg	1/10	0.619988346616817	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.626123657099706	2		562	1336	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131457	202131459	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0017493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	297	528	0	ENST00000358485.4:c.430_432del	p.Glu144del	p.E144del	ENST00000358485	NM_001080125.1	142	aAGGag/aag	2/9	0.252527235248561	2	FACETS	0.906	0.854	0.96	0.453	0.427	0.48	INDETERMINATE	1	TRUE	0	0.626123657099706	2		528	1047	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257158	16257158	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	133	557	1	ENST00000375759.3:c.4423C>T	p.Arg1475Ter	p.R1475*	ENST00000375759	NM_015001.2	1475	Cga/Tga	11/15	NA	2	FACETS	0.333	0.302	0.367			1	INDETERMINATE	1	TRUE	NA	0.626123657099706	2		558	1274	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640217	3640217	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1687	205	751	0	ENST00000294008.3:c.3422C>G	p.Ser1141Cys	p.S1141C	ENST00000294008	NM_032444.2	1141	tCt/tGt	12/15	0.416047695135762	2	FACETS	0.346	0.319	0.374	0.173	0.159	0.187	SUBCLONAL	1	TRUE	0	0.626123657099706	2		751	1892	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291061	10291061	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	194	438	0	ENST00000340748.4:c.410C>A	p.Thr137Lys	p.T137K	ENST00000340748		137	aCg/aAg	4/40	0.619988346616817	2	FACETS	0.559	0.516	0.603	0.279	0.258	0.302	SUBCLONAL	1	TRUE	0	0.626123657099706	2		438	1109	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753309	42753309	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1253	532	753	0	ENST00000222329.4:c.955C>G	p.Gln319Glu	p.Q319E	ENST00000222329	NM_006494.2	319	Caa/Gaa	4/4	0.619988346616817	2	FACETS	0.952	0.911	0.994	0.476	0.455	0.497	CLONAL	1	TRUE	0	0.626123657099706	2		753	1785	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99136602	99136602	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	79	365	0	ENST00000074304.5:c.91G>C	p.Gly31Arg	p.G31R	ENST00000074304	NM_001134224.1	31	Ggc/Cgc	3/26	0.252527235248561	2	FACETS	0.303	0.266	0.343	0.152	0.133	0.172	INDETERMINATE	1	TRUE	0	0.626123657099706	2		365	832	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376082	225376082	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	413	478	0	ENST00000264414.4:c.872del	p.Gly291GlufsTer20	p.G291Efs*20	ENST00000264414	NM_003590.4	291	gGa/ga	6/16	0.252527235248561	2	FACETS	1	0.994	1	0.643	0.614	0.672	INDETERMINATE	1	TRUE	0	0.626123657099706	2		478	1026	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40828020	40828020	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	80	262	0	ENST00000373198.4:c.2408C>G	p.Ala803Gly	p.A803G	ENST00000373198	NM_133170.3	803	gCc/gGc	17/32	0.626123657099706	2	FACETS	0.383	0.336	0.432	0.191	0.168	0.216	SUBCLONAL	1	TRUE	0	0.626123657099706	2		262	668	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866466	42866466	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1426	183	736	1	ENST00000398585.3:c.166G>T	p.Gly56Ter	p.G56*	ENST00000398585	NM_001135099.1	56	Gga/Tga	3/14	NA	2	FACETS	0.363	0.334	0.394			1	INDETERMINATE	1	TRUE	NA	0.626123657099706	2		737	1609	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340390	8340391	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0017493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	260	328	0	ENST00000356435.5:c.5205_5206del	p.His1735GlnfsTer13	p.H1735Qfs*13	ENST00000356435		1735	caCAat/caat	31/35	0.626123657099706	1	FACETS	0.956	0.903	1	0.956	0.903	1	CLONAL	1	TRUE	0	0.626123657099706	1		328	597	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696432	47696432	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519968	NA	P-0017494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	71	622	0	ENST00000347630.2:c.391T>G	p.Trp131Gly	p.W131G	ENST00000347630	NM_001007230.1	131	Tgg/Ggg	6/11	1	2	FACETS	0.904	0.788	1	0.904	0.788	1	CLONAL	1	TRUE	1	0.2	2		622	785	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938432	44938442	+	frameshift_variant	Frame_Shift_Del	DEL	AATGAACATAT	AATGAACATAT	-	novel	NA	P-0017494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	48	323	0	ENST00000377967.4:c.2980_2990del	p.Asn994GlyfsTer13	p.N994Gfs*13	ENST00000377967	NM_021140.2	994	AATGAACATATg/g	20/29	1	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.2	1		323	303	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692918	89692918	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	57	671	0	ENST00000371953.3:c.402G>A	p.Met134Ile	p.M134I	ENST00000371953	NM_000314.4	134	atG/atA	5/9	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.2	2		671	471	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813626	50813626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149427272	NA	P-0017495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	83	625	1	ENST00000398568.2:c.1180C>T	p.Arg394Cys	p.R394C	ENST00000398568	NM_001042412.1	394	Cgt/Tgt	8/18	1	2	FACETS	0.566	0.502	0.634	0.566	0.502	0.634	SUBCLONAL	1	TRUE	1	0.693626340089674	2		626	423	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032206	26032206	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	41	148	0	ENST00000244661.2:c.83A>T	p.Lys28Met	p.K28M	ENST00000244661	NM_003537.3	28	aAg/aTg	1/1	0.693626340089674	3	FACETS	1	0.877	1			1	CLONAL	1	TRUE	NA	0.693626340089674	3		148	153	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0017498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	148	525	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.171169536963553	3	FACETS	0.865	0.789	0.945	0.865	0.789	0.945	CLONAL	2	TRUE	1	0.171169536963553	3		525	1085	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0017498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	102	795	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.171169536963553	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.171169536963553	1		796	816	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925111	81925111	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	39	387	0	ENST00000359376.3:c.902T>C	p.Ile301Thr	p.I301T	ENST00000359376	NM_002661.3	301	aTc/aCc	11/33	1	2	FACETS	0.628	0.519	0.75	0.628	0.519	0.75	SUBCLONAL	1	TRUE	1	0.171169536963553	2		387	726	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221050	5221050	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	30	315	0	ENST00000357368.4:c.3416T>A	p.Met1139Lys	p.M1139K	ENST00000357368	NM_002850.3	1139	aTg/aAg	20/38	0.171169536963553	1	FACETS	0.733	0.591	0.896	0.733	0.591	0.896	SUBCLONAL	1	TRUE	0	0.171169536963553	1		315	437	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725049	49725049	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	38	460	0	ENST00000449682.2:c.295C>T	p.Gln99Ter	p.Q99*	ENST00000449682	NM_020998.3	99	Caa/Taa	3/18	1	2	FACETS	0.67	0.552	0.802	0.67	0.552	0.802	SUBCLONAL	1	TRUE	1	0.171169536963553	2		460	663	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0017500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	39	525	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.62	0.512	0.741	0.62	0.512	0.741	SUBCLONAL	1	TRUE	1	0.15	2		525	839	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0017500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	63	536	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	1	2	FACETS	0.96	0.828	1	0.96	0.828	1	CLONAL	1	TRUE	1	0.15	2		536	875	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499449	89499449	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1309775529	NA	P-0017500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	46	397	2	ENST00000336596.2:c.2619G>T	p.Gln873His	p.Q873H	ENST00000336596	NM_005233.5	873	caG/caT	15/17	1	2	FACETS	0.934	0.785	1	0.934	0.785	1	CLONAL	1	TRUE	1	0.15	2		399	657	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037972	49037972	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0017500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	35	262	1	ENST00000267163.4:c.2211+1G>A		p.X737_splice	ENST00000267163	NM_000321.2	737			1	2	FACETS	0.935	0.766	1	0.935	0.766	1	CLONAL	1	TRUE	1	0.15	2		263	499	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32439182	32439182	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	32	463	1	ENST00000332351.3:c.891G>T	p.Met297Ile	p.M297I	ENST00000332351	NM_024426.4	297	atG/atT	4/10	1	2	FACETS	0.672	0.544	0.817	0.672	0.544	0.817	SUBCLONAL	1	TRUE	1	0.15	2		464	635	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119474	193119474	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	55	386	0	ENST00000367435.3:c.869A>G	p.Tyr290Cys	p.Y290C	ENST00000367435	NM_024529.4	290	tAt/tGt	9/17	1	2	FACETS	0.87	0.742	1	0.87	0.742	1	CLONAL	1	TRUE	1	0.15	2		386	843	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604494	43604495	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0017500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	50	520	4	ENST00000355710.3:c.1079_1080delinsTT	p.Arg360Leu	p.R360L	ENST00000355710	NM_020975.4	360	cGG/cTT	6/20	1	2	FACETS	0.992	0.84	1	0.992	0.84	1	CLONAL	1	TRUE	1	0.15	2		524	672	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865260	57865260	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	43	524	0	ENST00000228682.2:c.2741del	p.Gly914AlafsTer32	p.G914Afs*32	ENST00000228682	NM_005269.2	913	Ggg/gg	12/12	1	2	FACETS	0.76	0.635	0.901	0.76	0.635	0.901	CLONAL	1	TRUE	1	0.15	2		524	754	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281716	49281716	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1566110787	NA	P-0017500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	66	639	0	ENST00000282018.3:c.763A>G	p.Ile255Val	p.I255V	ENST00000282018	NM_020377.2	255	Atc/Gtc	1/1	1	2	FACETS	0.854	0.739	0.979	0.854	0.739	0.979	CLONAL	1	TRUE	1	0.15	2		639	1031	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143422	30143422	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	25	346	1	ENST00000389048.3:c.104G>T	p.Gly35Val	p.G35V	ENST00000389048	NM_004304.4	35	gGg/gTg	1/29	1	2	FACETS	0.706	0.555	0.88	0.706	0.555	0.88	SUBCLONAL	1	TRUE	1	0.15	2		347	472	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200700	128200700	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	50	513	0	ENST00000341105.2:c.1105G>T	p.Val369Phe	p.V369F	ENST00000341105	NM_032638.4	369	Gtc/Ttc	5/6	1	2	FACETS	0.869	0.736	1	0.869	0.736	1	CLONAL	1	TRUE	1	0.15	2		513	767	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372220	55372220	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	42	394	0	ENST00000297316.4:c.910G>T	p.Gly304Trp	p.G304W	ENST00000297316	NM_022454.3	304	Ggg/Tgg	2/2	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.15	2		394	511	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69032449	69032449	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1212812244	NA	P-0017500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	40	573	1	ENST00000288368.4:c.3523C>G	p.Leu1175Val	p.L1175V	ENST00000288368	NM_024870.2	1175	Ctc/Gtc	29/40	1	2	FACETS	0.672	0.556	0.801	0.672	0.556	0.801	SUBCLONAL	1	TRUE	1	0.15	2		574	794	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222954	53222954	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0017500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	74	653	0	ENST00000375401.3:c.4117+1G>T		p.X1373_splice	ENST00000375401	NM_004187.3	1373			0.232173817697652	1	FACETS	0.83	0.725	0.945	0.83	0.725	0.945	CLONAL	1	TRUE	0	0.15	1		653	1099	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	160	301	4				ENST00000310581	NM_198253.2	-/1132			0.148176990654296	3	FACETS	0.866	0.799	0.935	0.577	0.532	0.624	INDETERMINATE	2	TRUE	0	0.398547479153228	3		305	556	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032763	30032764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0017502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	124	317	0	ENST00000338641.4:c.140_141dup	p.Asp48LeufsTer76	p.D48Lfs*76	ENST00000338641	NM_000268.3	46	-/TT	2/16	0.365693397503995	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.398547479153228	1		317	439	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0017503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	5759	549	1	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.300056081929091	31	FACETS	1	0.998	1			1	CLONAL	32	TRUE	NA	0.27	31		550	6482	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0017503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	89	320	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.261895888995819	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.27	1		320	495	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610608	52610609	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	200	469	1	ENST00000394830.3:c.3564dup	p.Glu1189ArgfsTer6	p.E1189Rfs*6	ENST00000394830	NM_018313.4	1188	-/A	23/30	0.290699924736365	2	FACETS	0.919	0.853	0.987	0.919	0.853	0.987	CLONAL	2	TRUE	0	0.27	2		470	806	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253911	NA	P-0017503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	103	374	0	ENST00000269305.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000269305	NM_001126112.2	180	Gag/Aag	5/11	0.300056081929091	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.27	1		374	569	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821760	72821760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150891901	NA	P-0017503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	107	384	0	ENST00000268489.5:c.10415C>T	p.Ala3472Val	p.A3472V	ENST00000268489	NM_006885.3	3472	gCg/gTg	10/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.27	2		384	721	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794062	42794062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	62	472	1	ENST00000575354.2:c.1423G>A	p.Glu475Lys	p.E475K	ENST00000575354	NM_015125.3	475	Gag/Aag	9/20	0.261895888995819	1	FACETS	0.52	0.448	0.598	0.52	0.448	0.598	SUBCLONAL	1	TRUE	0	0.27	1		473	764	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435396	56435400	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGC	GAGGC	AAGG	novel	NA	P-0017503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	191	442	1	ENST00000407977.2:c.1737_1741delinsCCTT	p.Arg579SerfsTer121	p.R579Sfs*121	ENST00000407977		579	agGCCTCct/agCCTTct	9/10	0.280479445210682	2	FACETS	0.955	0.885	1	0.955	0.885	1	CLONAL	2	TRUE	0	0.27	2		443	741	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213965	2213965	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	39	395	0	ENST00000398665.3:c.1777C>A	p.Arg593Ser	p.R593S	ENST00000398665	NM_032482.2	593	Cgc/Agc	18/28	0.300056081929091	1	FACETS	0.426	0.353	0.509	0.426	0.353	0.509	SUBCLONAL	1	TRUE	0	0.27	1		395	586	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144185	11144185	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	76	442	1	ENST00000358026.2:c.3766C>T	p.Gln1256Ter	p.Q1256*	ENST00000358026	NM_001128849.1	1256	Cag/Tag	26/36	0.300056081929091	1	FACETS	0.955	0.839	1	0.955	0.839	1	CLONAL	1	TRUE	0	0.27	1		443	510	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183277	56183277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	90	380	0	ENST00000399503.3:c.4187C>T	p.Ala1396Val	p.A1396V	ENST00000399503	NM_005921.1	1396	gCa/gTa	18/20	1	2	FACETS	0.857	0.76	0.961	0.857	0.76	0.961	CLONAL	1	TRUE	1	0.27	2		380	778	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981474	201981475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCTTG	novel	NA	P-0017504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	142	422	0	ENST00000359651.3:c.390_391insTTGCC	p.Ser131LeufsTer26	p.S131Lfs*26	ENST00000359651		130	tcc/tCCTTGcc	3/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.42438604545974	2		422	590	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115650	108115650	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	65	421	0	ENST00000278616.4:c.798G>A	p.Trp266Ter	p.W266*	ENST00000278616	NM_000051.3	266	tgG/tgA	7/63	1	2	FACETS	0.536	0.464	0.613	0.536	0.464	0.613	SUBCLONAL	1	TRUE	1	0.42438604545974	2		421	572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs786201057	NA	P-0017504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	223	395	0	ENST00000269305.4:c.374C>G	p.Thr125Arg	p.T125R	ENST00000269305	NM_001126112.2	125	aCg/aGg	4/11	0.409745449231347	2	FACETS	0.943	0.886	1	0.943	0.886	1	CLONAL	2	TRUE	0	0.42438604545974	2		395	557	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11019849	11019849	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	138	561	0	ENST00000327064.4:c.524C>G	p.Ala175Gly	p.A175G	ENST00000327064	NM_199141.1	175	gCc/gGc	4/16	0.409745449231347	2	FACETS	0.856	0.779	0.936	0.428	0.389	0.468	CLONAL	1	TRUE	0	0.42438604545974	2		561	760	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719838	52719838	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	216	583	1	ENST00000322088.6:c.1050G>T	p.Met350Ile	p.M350I	ENST00000322088	NM_014225.5	350	atG/atT	9/15	NA	2	FACETS	1	0.958	1			1	INDETERMINATE	1	TRUE	NA	0.42438604545974	2		584	977	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131342	202131342	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	184	381	0	ENST00000358485.4:c.310T>C	p.Phe104Leu	p.F104L	ENST00000358485	NM_001080125.1	104	Ttc/Ctc	2/9	0.252543682387701	3	FACETS	0.751	0.695	0.808	0.751	0.695	0.808	INDETERMINATE	2	TRUE	1	0.42438604545974	3		381	700	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564864	41564864	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	241	399	0	ENST00000263253.7:c.4165A>C	p.Asn1389His	p.N1389H	ENST00000263253	NM_001429.3	1389	Aac/Cac	25/31	NA	2	FACETS	0.875	0.822	0.929			1	INDETERMINATE	2	TRUE	NA	0.42438604545974	2		399	649	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539412	187539412	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	42	344	0	ENST00000441802.2:c.8328T>G	p.Phe2776Leu	p.F2776L	ENST00000441802	NM_005245.3	2776	ttT/ttG	10/27	1	2	FACETS	0.369	0.307	0.437	0.369	0.307	0.437	SUBCLONAL	1	TRUE	1	0.42438604545974	2		344	537	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508779	31508779	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	668	585	0	ENST00000344624.3:c.1536G>T	p.Lys512Asn	p.K512N	ENST00000344624		512	aaG/aaT	7/33	0.42438604545974	5	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	2	0.42438604545974	5		585	1565	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946129	13946129	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	197	513	0	ENST00000405192.2:c.967G>T	p.Asp323Tyr	p.D323Y	ENST00000405192	NM_001163147.1	323	Gat/Tat	10/12	0.169119066513477	5	FACETS	0.77	0.713	0.83	0.514	0.475	0.553	INDETERMINATE	2	TRUE	2	0.42438604545974	5		513	986	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	324	301	4				ENST00000310581	NM_198253.2	-/1132			0.365218252455223	4	FACETS	0.89	0.85	0.93	1	0.996	1	CLONAL	4	TRUE	2	0.429179910818282	4		305	606	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971116	21971116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552823	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	305	442	0	ENST00000304494.5:c.242C>T	p.Pro81Leu	p.P81L	ENST00000304494	NM_000077.4	81	cCc/cTc	2/3	0.429179910818282	1	FACETS	0.967	0.935	0.996	1	0.997	1	CLONAL	3	TRUE	0	0.429179910818282	1		442	385	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937067	36937067	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767670169	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	202	409	3	ENST00000361632.4:c.1252C>T	p.Arg418Cys	p.R418C	ENST00000361632		418	Cgt/Tgt	9/16	0.429179910818282	3	FACETS	0.939	0.875	1	0.939	0.875	1	CLONAL	2	TRUE	1	0.429179910818282	3		412	609	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798438	45798445	+	frameshift_variant	Frame_Shift_Del	DEL	CCGAGCTC	CCGAGCTC	-	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	399	624	0	ENST00000450313.1:c.566_573del	p.Gly189GlufsTer61	p.G189Efs*61	ENST00000450313	NM_012222.2	189	gGAGCTCGG/g	7/16	0.429179910818282	3	FACETS	0.883	0.844	0.921	1	0.995	1	CLONAL	3	TRUE	1	0.429179910818282	3		624	853	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263314	115263314	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	267	702	1	ENST00000438362.2:c.2036C>T	p.Pro679Leu	p.P679L	ENST00000438362	NM_001242891.1	679	cCa/cTa	17/20	0.429179910818282	3	FACETS	0.858	0.806	0.91	0.858	0.806	0.91	CLONAL	2	TRUE	1	0.429179910818282	3		703	881	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306558	163306558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	106	560	0	ENST00000271452.3:c.355C>T	p.Arg119Trp	p.R119W	ENST00000271452	NM_145697.2	119	Cgg/Tgg	6/14	0.429179910818282	3	FACETS	0.852	0.772	0.936	0.852	0.772	0.936	CLONAL	2	TRUE	1	0.429179910818282	3		560	352	SUCCESS
RET	5979	MSKCC	GRCh37	10	43595944	43595944	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1564489315	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	519	678	0	ENST00000355710.3:c.111G>A	p.Trp37Ter	p.W37*	ENST00000355710	NM_020975.4	37	tgG/tgA	2/20	0.429179910818282	2	FACETS	1	0.996	1	1	0.998	1	CLONAL	3	TRUE	0	0.429179910818282	2		678	703	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852035	63852035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	198	496	0	ENST00000279873.7:c.2813C>T	p.Ser938Phe	p.S938F	ENST00000279873	NM_032199.2	938	tCc/tTc	10/10	0.429179910818282	3	FACETS	0.844	0.785	0.904	0.563	0.523	0.603	CLONAL	2	TRUE	0	0.429179910818282	3		496	664	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692910	89692910	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	290	563	0	ENST00000371953.3:c.394G>T	p.Gly132Cys	p.G132C	ENST00000371953	NM_000314.4	132	Ggt/Tgt	5/9	0.429179910818282	3	FACETS	0.912	0.883	0.939	1	0.996	1	CLONAL	5	TRUE	0	0.429179910818282	3		563	360	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375513	118375513	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	223	329	0	ENST00000534358.1:c.8906C>T	p.Ser2969Phe	p.S2969F	ENST00000534358	NM_005933.3	2969	tCt/tTt	27/36	0.378534326447417	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	1	0.429179910818282	4		329	432	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375723	118375723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	217	611	1	ENST00000534358.1:c.9116C>T	p.Ser3039Phe	p.S3039F	ENST00000534358	NM_005933.3	3039	tCc/tTc	27/36	0.378534326447417	4	FACETS	0.932	0.87	0.997	0.622	0.58	0.665	CLONAL	2	TRUE	1	0.429179910818282	4		612	775	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148963	119148963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	176	529	0	ENST00000264033.4:c.1183C>T	p.Pro395Ser	p.P395S	ENST00000264033	NM_005188.3	395	Ccc/Tcc	8/16	0.378534326447417	4	FACETS	1	0.945	1	0.682	0.632	0.733	CLONAL	2	TRUE	1	0.429179910818282	4		529	573	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644479	18644479	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	164	508	0	ENST00000266497.5:c.2657G>A	p.Gly886Glu	p.G886E	ENST00000266497		886	gGg/gAg	18/31	NA	2	FACETS	0.844	0.79	0.896			1	INDETERMINATE	3	TRUE	NA	0.429179910818282	2		508	302	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719923	18719923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	156	650	0	ENST00000266497.5:c.3820C>T	p.His1274Tyr	p.H1274Y	ENST00000266497		1274	Cac/Tac	27/31	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.429179910818282	2		650	521	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926257	112926257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	310	409	0	ENST00000351677.2:c.1390G>A	p.Gly464Ser	p.G464S	ENST00000351677	NM_002834.3	464	Ggc/Agc	12/16	0.429179910818282	3	FACETS	1	0.988	1	1	0.996	1	CLONAL	3	TRUE	1	0.429179910818282	3		409	534	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549248	21549248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1407685302	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	471	674	2	ENST00000382592.4:c.3028C>T	p.Pro1010Ser	p.P1010S	ENST00000382592	NM_014572.2	1010	Cct/Tct	8/8	0.365218252455223	4	FACETS	1	0.98	1	1	0.997	1	CLONAL	3	TRUE	2	0.429179910818282	4		676	1013	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557682	21557683	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	376	661	5	ENST00000382592.4:c.2162_2163delinsTT	p.Ala721Val	p.A721V	ENST00000382592	NM_014572.2	721	gCC/gTT	5/8	0.365218252455223	4	FACETS	0.936	0.892	0.98	1	0.995	1	CLONAL	3	TRUE	2	0.429179910818282	4		666	892	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609752	28609752	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	315	648	0	ENST00000241453.7:c.1477G>A	p.Gly493Arg	p.G493R	ENST00000241453	NM_004119.2	493	Gga/Aga	12/24	0.365218252455223	4	FACETS	0.905	0.858	0.952	1	0.994	1	CLONAL	3	TRUE	2	0.429179910818282	4		648	773	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906633	32906633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	227	577	1	ENST00000380152.3:c.1018G>A	p.Glu340Lys	p.E340K	ENST00000380152		340	Gaa/Aaa	10/27	0.365218252455223	4	FACETS	0.988	0.93	1	1	0.993	1	CLONAL	3	TRUE	2	0.429179910818282	4		578	510	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336095	73336095	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780575971	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	68	249	0	ENST00000377767.4:c.2308C>T	p.Pro770Ser	p.P770S	ENST00000377767	NM_014953.3	770	Cca/Tca	17/21	0.429179910818282	4	FACETS	1	0.967	1	0.664	0.581	0.752	CLONAL	1	TRUE	2	0.429179910818282	4		249	341	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40993313	40993313	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	276	487	0	ENST00000267868.3:c.139C>T	p.His47Tyr	p.H47Y	ENST00000267868	NM_002875.4	47	Cat/Tat	3/10	0.429179910818282	4	FACETS	0.891	0.842	0.94	1	0.993	1	CLONAL	3	TRUE	2	0.429179910818282	4		487	688	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000313	42000313	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	259	465	0	ENST00000219905.7:c.2332C>T	p.Pro778Ser	p.P778S	ENST00000219905	NM_001164273.1	778	Ccc/Tcc	7/24	0.429179910818282	4	FACETS	0.93	0.878	0.983	1	0.993	1	CLONAL	3	TRUE	2	0.429179910818282	4		465	618	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019470	42019470	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	303	701	1	ENST00000219905.7:c.3523C>T	p.Pro1175Ser	p.P1175S	ENST00000219905	NM_001164273.1	1175	Ccc/Tcc	10/24	0.429179910818282	4	FACETS	0.916	0.869	0.965	1	0.994	1	CLONAL	3	TRUE	2	0.429179910818282	4		702	734	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3634861	3634861	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs77021998	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	319	535	2	ENST00000294008.3:c.4648C>T	p.Arg1550Trp	p.R1550W	ENST00000294008	NM_032444.2	1550	Cgg/Tgg	13/15	0.330898229478557	4	FACETS	0.859	0.815	0.905			1	CLONAL	3	TRUE	NA	0.429179910818282	4		537	824	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857436	9857436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	230	420	0	ENST00000330684.3:c.3965G>A	p.Gly1322Glu	p.G1322E	ENST00000330684	NM_001134407.1	1322	gGa/gAa	13/13	0.221091558960302	4	FACETS	0.923	0.868	0.979			1	INDETERMINATE	3	TRUE	NA	0.429179910818282	4		420	553	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857529	9857529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1325032512	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	165	316	0	ENST00000330684.3:c.3872C>T	p.Ser1291Phe	p.S1291F	ENST00000330684	NM_001134407.1	1291	tCc/tTc	13/13	0.221091558960302	4	FACETS	0.862	0.8	0.925			1	INDETERMINATE	3	TRUE	NA	0.429179910818282	4		316	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577070	7577070	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	530	725	1	ENST00000269305.4:c.868del	p.Arg290AlafsTer55	p.R290Afs*55	ENST00000269305	NM_001126112.2	290	Cgc/gc	8/11	NA	2	FACETS	0.89	0.867	0.912			1	INDETERMINATE	4	TRUE	NA	0.429179910818282	2		726	694	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528441	29528441	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	193	517	1	ENST00000356175.3:c.1198C>T	p.Gln400Ter	p.Q400*	ENST00000356175	NM_000267.3	400	Cag/Tag	11/57	0.429179910818282	4	FACETS	0.94	0.879	1	1	0.991	1	CLONAL	3	TRUE	2	0.429179910818282	4		518	456	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654653	29654653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	140	376	2	ENST00000356175.3:c.5342C>T	p.Thr1781Ile	p.T1781I	ENST00000356175	NM_000267.3	1781	aCc/aTc	37/57	0.429179910818282	4	FACETS	1	0.982	1	0.657	0.599	0.717	CLONAL	1	TRUE	2	0.429179910818282	4		378	710	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627263	37627263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	198	548	0	ENST00000447079.4:c.1178C>T	p.Ser393Phe	p.S393F	ENST00000447079	NM_015083.1	393	tCc/tTc	2/14	0.429179910818282	4	FACETS	0.778	0.721	0.836	0.778	0.721	0.836	SUBCLONAL	2	TRUE	2	0.429179910818282	4		548	848	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681015	37681015	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	416	586	0	ENST00000447079.4:c.3184C>T	p.Pro1062Ser	p.P1062S	ENST00000447079	NM_015083.1	1062	Cca/Tca	12/14	0.429179910818282	4	FACETS	0.903	0.862	0.944	1	0.995	1	CLONAL	3	TRUE	2	0.429179910818282	4		586	1023	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512438	38512438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs957564687	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	273	856	0	ENST00000254066.5:c.1349C>T	p.Pro450Leu	p.P450L	ENST00000254066	NM_000964.3	450	cCc/cTc	9/9	0.429179910818282	4	FACETS	1	0.992	1	0.703	0.658	0.748	CLONAL	1	TRUE	2	0.429179910818282	4		856	1294	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117524	4117524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371852537	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	208	243	0	ENST00000262948.5:c.196G>A	p.Glu66Lys	p.E66K	ENST00000262948	NM_030662.3	66	Gaa/Aaa	2/11	0.429179910818282	4	FACETS	1	0.953	1	1	0.993	1	CLONAL	3	TRUE	2	0.429179910818282	4		243	454	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243965	5243965	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	314	416	1	ENST00000357368.4:c.1517C>T	p.Ser506Phe	p.S506F	ENST00000357368	NM_002850.3	506	tCc/tTc	11/38	0.429179910818282	4	FACETS	1	0.969	1	1	0.995	1	CLONAL	3	TRUE	2	0.429179910818282	4		417	680	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152077	11152077	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	188	551	0	ENST00000358026.2:c.4361C>T	p.Ser1454Phe	p.S1454F	ENST00000358026	NM_001128849.1	1454	tCc/tTc	31/36	0.429179910818282	4	FACETS	1	0.989	1	0.716	0.662	0.772	CLONAL	1	TRUE	2	0.429179910818282	4		551	874	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291830	15291830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1222604193	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	207	631	0	ENST00000263388.2:c.2936C>T	p.Ala979Val	p.A979V	ENST00000263388	NM_000435.2	979	gCc/gTc	18/33	0.429179910818282	4	FACETS	1	0.99	1	0.711	0.66	0.764	CLONAL	1	TRUE	2	0.429179910818282	4		631	969	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297946	15297947	+	missense_variant	Missense_Mutation	DNP	AC	AC	GT	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	370	689	1	ENST00000263388.2:c.1809_1810inv	p.Tyr604His	p.Y604H	ENST00000263388	NM_000435.2	603	aaGTac/aaACac	11/33	0.429179910818282	4	FACETS	0.846	0.805	0.887	1	0.993	1	CLONAL	3	TRUE	2	0.429179910818282	4		690	971	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223357	36223358	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	463	970	1	ENST00000222270.7:c.5907_5908delinsTT	p.Pro1970Ser	p.P1970S	ENST00000222270	NM_014727.1	1969	ccCCct/ccTTct	28/37	0.429179910818282	4	FACETS	0.836	0.799	0.872	1	0.994	1	CLONAL	3	TRUE	2	0.429179910818282	4		971	1230	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763470	41763470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778081322	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	344	544	2	ENST00000301178.4:c.2269G>A	p.Glu757Lys	p.E757K	ENST00000301178	NM_021913.4	757	Gag/Aag	19/20	0.429179910818282	4	FACETS	0.915	0.87	0.96	1	0.994	1	CLONAL	3	TRUE	2	0.429179910818282	4		546	835	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469167	25469167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	278	522	0	ENST00000264709.3:c.1291C>T	p.Pro431Ser	p.P431S	ENST00000264709	NM_175629.2	431	Ccc/Tcc	11/23	0.146968722867905	4	FACETS	0.905	0.856	0.955	1	0.993	1	INDETERMINATE	3	TRUE	2	0.429179910818282	4		522	682	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743956	40743956	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	239	353	0	ENST00000373198.4:c.3040-1G>A		p.X1014_splice	ENST00000373198	NM_133170.3	1014			0.303895397867963	4	FACETS	1	0.951	1			1	CLONAL	3	TRUE	NA	0.429179910818282	4		353	526	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790093	40790093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1481819261	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	118	453	0	ENST00000373198.4:c.2638C>T	p.Pro880Ser	p.P880S	ENST00000373198	NM_133170.3	880	Ccc/Tcc	18/32	0.303895397867963	4	FACETS	1	0.969	1			1	CLONAL	1	TRUE	NA	0.429179910818282	4		453	667	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306556	41306556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	287	556	1	ENST00000373198.4:c.1103G>A	p.Gly368Glu	p.G368E	ENST00000373198	NM_133170.3	368	gGg/gAg	7/32	0.303895397867963	4	FACETS	0.957	0.906	1			1	CLONAL	3	TRUE	NA	0.429179910818282	4		557	666	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306565	41306565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	310	572	0	ENST00000373198.4:c.1094C>T	p.Pro365Leu	p.P365L	ENST00000373198	NM_133170.3	365	cCa/cTa	7/32	0.303895397867963	4	FACETS	0.975	0.926	1			1	CLONAL	3	TRUE	NA	0.429179910818282	4		572	706	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405884	49405884	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	265	710	1	ENST00000418115.1:c.254C>T	p.Ser85Phe	p.S85F	ENST00000418115	NM_001664.2	85	tCc/tTc	3/5	0.429179910818282	5	FACETS	0.797	0.746	0.85	0.797	0.746	0.85	SUBCLONAL	2	TRUE	3	0.429179910818282	5		711	1273	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89478288	89478288	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	132	327	0	ENST00000336596.2:c.2107G>A	p.Glu703Lys	p.E703K	ENST00000336596	NM_005233.5	703	Gag/Aag	12/17	0.429179910818282	4	FACETS	0.904	0.833	0.977	1	0.986	1	CLONAL	3	TRUE	2	0.429179910818282	4		327	324	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631640	119631640	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	129	386	0	ENST00000316626.5:c.626G>C	p.Arg209Pro	p.R209P	ENST00000316626		209	cGa/cCa	6/12	0.429179910818282	4	FACETS	0.835	0.767	0.904	1	0.982	1	CLONAL	3	TRUE	2	0.429179910818282	4		386	343	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936077	178936077	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	158	481	0	ENST00000263967.3:c.1619T>G	p.Leu540Arg	p.L540R	ENST00000263967	NM_006218.2	540	cTc/cGc	10/21	0.429179910818282	4	FACETS	0.969	0.901	1	1	0.99	1	CLONAL	3	TRUE	2	0.429179910818282	4		481	362	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198153	185198153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	368	589	1	ENST00000265026.3:c.2635G>A	p.Asp879Asn	p.D879N	ENST00000265026	NM_004721.4	879	Gac/Aac	13/14	0.429179910818282	4	FACETS	0.947	0.902	0.991	1	0.995	1	CLONAL	3	TRUE	2	0.429179910818282	4		590	863	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502391	186502391	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	288	405	0	ENST00000323963.5:c.114G>A	p.Met38Ile	p.M38I	ENST00000323963		38	atG/atA	3/11	0.429179910818282	4	FACETS	1	0.969	1	1	0.995	1	CLONAL	3	TRUE	2	0.429179910818282	4		405	621	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612176	189612176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	335	478	0	ENST00000264731.3:c.1928G>A	p.Arg643Gln	p.R643Q	ENST00000264731	NM_003722.4	643	cGa/cAa	14/14	0.429179910818282	4	FACETS	0.989	0.941	1	1	0.995	1	CLONAL	3	TRUE	2	0.429179910818282	4		478	752	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953799	55953799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867819358	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	297	610	0	ENST00000263923.4:c.3637C>T	p.His1213Tyr	p.H1213Y	ENST00000263923	NM_002253.2	1213	Cat/Tat	27/30	0.365218252455223	4	FACETS	0.963	0.913	1	1	0.994	1	CLONAL	3	TRUE	2	0.429179910818282	4		610	685	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156345	106156345	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745997182	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	250	436	0	ENST00000380013.4:c.1246C>T	p.Pro416Ser	p.P416S	ENST00000380013	NM_001127208.2	416	Cct/Tct	3/11	0.365218252455223	4	FACETS	0.881	0.83	0.933	1	0.992	1	CLONAL	3	TRUE	2	0.429179910818282	4		436	630	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628202	187628202	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	657	662	0	ENST00000441802.2:c.2780T>A	p.Phe927Tyr	p.F927Y	ENST00000441802	NM_005245.3	927	tTt/tAt	2/27	0.429179910818282	6	FACETS	0.96	0.93	0.99	1	0.996	1	CLONAL	5	TRUE	2	0.429179910818282	6		662	1185	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260651	1260656	+	frameshift_variant	Frame_Shift_Del	DEL	TGTTCC	TGTTCC	CGACG	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	330	638	2	ENST00000310581.5:c.2903_2908delinsCGTCG	p.Arg968ThrfsTer13	p.R968Tfs*13	ENST00000310581	NM_198253.2	968	aGGAACAtg/aCGTCGtg	12/16	0.365218252455223	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	2	0.429179910818282	4		640	933	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294208	1294208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	251	763	0	ENST00000310581.5:c.793C>T	p.Pro265Ser	p.P265S	ENST00000310581	NM_198253.2	265	Ccg/Tcg	2/16	0.365218252455223	4	FACETS	0.761	0.711	0.811	0.761	0.711	0.811	SUBCLONAL	2	TRUE	2	0.429179910818282	4		763	1099	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80021291	80021291	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs539295465	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	274	504	0	ENST00000265081.6:c.1360C>T	p.Arg454Ter	p.R454*	ENST00000265081	NM_002439.4	454	Cga/Tga	9/24	0.429179910818282	4	FACETS	0.923	0.873	0.974	1	0.993	1	CLONAL	3	TRUE	2	0.429179910818282	4		504	659	SUCCESS
APC	324	MSKCC	GRCh37	5	112173762	112173762	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	118	394	0	ENST00000257430.4:c.2471C>T	p.Pro824Leu	p.P824L	ENST00000257430	NM_000038.5	824	cCa/cTa	16/16	0.429179910818282	4	FACETS	1	0.982	1	0.699	0.633	0.769	CLONAL	1	TRUE	2	0.429179910818282	4		394	562	SUCCESS
APC	324	MSKCC	GRCh37	5	112173824	112173824	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554084249	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	124	385	1	ENST00000257430.4:c.2533C>T	p.Arg845Cys	p.R845C	ENST00000257430	NM_000038.5	845	Cgt/Tgt	16/16	0.429179910818282	4	FACETS	0.756	0.687	0.829	0.756	0.687	0.829	SUBCLONAL	2	TRUE	2	0.429179910818282	4		386	546	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523114	176523114	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	408	732	3	ENST00000292408.4:c.1878G>A	p.Met626Ile	p.M626I	ENST00000292408	NM_213647.1	626	atG/atA	14/18	0.429179910818282	4	FACETS	0.907	0.866	0.948	1	0.995	1	CLONAL	3	TRUE	2	0.429179910818282	4		735	999	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481478	20481478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	320	368	1	ENST00000346618.3:c.547C>T	p.Leu183Phe	p.L183F	ENST00000346618	NM_001949.4	183	Ctt/Ttt	3/7	0.429179910818282	8	FACETS	1	0.981	1	0.649	0.613	0.685	CLONAL	3	TRUE	3	0.429179910818282	8		369	1052	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1828	322	865	1	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	0.429179910818282	7	FACETS	1	0.993	1	0.289	0.272	0.308	CLONAL	1	TRUE	2	0.429179910818282	7		866	2150	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169902	32169902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	991	754	0	ENST00000375023.3:c.3706G>A	p.Glu1236Lys	p.E1236K	ENST00000375023	NM_004557.3	1236	Gaa/Aaa	21/30	0.429179910818282	7	FACETS	0.943	0.92	0.966	1	0.997	1	CLONAL	6	TRUE	2	0.429179910818282	7		754	1692	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803450	32803450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1549	241	758	0	ENST00000374899.4:c.709G>A	p.Asp237Asn	p.D237N	ENST00000374899	NM_018833.2	237	Gac/Aac	4/12	0.429179910818282	7	FACETS	1	0.989	1	0.26	0.242	0.279	CLONAL	1	TRUE	2	0.429179910818282	7		758	1790	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652125	36652125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374965936	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	180	466	1	ENST00000244741.5:c.247C>T	p.Arg83Trp	p.R83W	ENST00000244741	NM_000389.4	83	Cgg/Tgg	2/3	0.429179910818282	8	FACETS	0.878	0.808	0.95			1	CLONAL	2	TRUE	NA	0.429179910818282	8		467	1093	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120336	94120336	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	158	274	0	ENST00000369303.4:c.715G>A	p.Glu239Lys	p.E239K	ENST00000369303	NM_004440.3	239	Gag/Aag	3/17	0.429179910818282	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.429179910818282	4		274	434	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120360	94120360	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs749418654	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	152	302	0	ENST00000369303.4:c.691C>T	p.Arg231Ter	p.R231*	ENST00000369303	NM_004440.3	231	Cga/Tga	3/17	0.429179910818282	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.429179910818282	4		302	424	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683852	117683852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	171	537	0	ENST00000368508.3:c.3295G>A	p.Glu1099Lys	p.E1099K	ENST00000368508	NM_002944.2	1099	Gaa/Aaa	21/43	0.429179910818282	1	FACETS	0.915	0.872	0.955	1	0.995	1	CLONAL	3	TRUE	0	0.429179910818282	1		537	228	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117717390	117717390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370121653	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	290	525	0	ENST00000368508.3:c.817C>T	p.Pro273Ser	p.P273S	ENST00000368508	NM_002944.2	273	Cca/Tca	8/43	0.429179910818282	1	FACETS	0.977	0.946	1	1	0.997	1	CLONAL	3	TRUE	0	0.429179910818282	1		525	362	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55270222	55270222	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755238987	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	379	662	0	ENST00000275493.2:c.3175C>T	p.Pro1059Ser	p.P1059S	ENST00000275493	NM_005228.3	1059	Ccc/Tcc	27/28	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.429179910818282	2		662	822	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392170	81392170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	73	233	0	ENST00000222390.5:c.107G>A	p.Arg36Lys	p.R36K	ENST00000222390	NM_000601.4	36	aGa/aAa	2/18	0.365218252455223	4	FACETS	0.862	0.77	0.956	1	0.972	1	CLONAL	3	TRUE	2	0.429179910818282	4		233	188	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508856	106508856	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376958957	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	134	385	1	ENST00000359195.3:c.850G>A	p.Glu284Lys	p.E284K	ENST00000359195	NM_002649.2	284	Gaa/Aaa	2/11	0.365218252455223	4	FACETS	1	0.986	1	0.727	0.662	0.794	CLONAL	1	TRUE	2	0.429179910818282	4		386	614	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509236	106509236	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	344	636	0	ENST00000359195.3:c.1230G>A	p.Trp410Ter	p.W410*	ENST00000359195	NM_002649.2	410	tgG/tgA	2/11	0.365218252455223	4	FACETS	0.892	0.848	0.937	1	0.994	1	CLONAL	3	TRUE	2	0.429179910818282	4		636	856	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523546	106523546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	257	473	0	ENST00000359195.3:c.2698G>A	p.Gly900Arg	p.G900R	ENST00000359195	NM_002649.2	900	Gga/Aga	8/11	0.365218252455223	4	FACETS	0.938	0.886	0.991	1	0.993	1	CLONAL	3	TRUE	2	0.429179910818282	4		473	608	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545740	106545740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	223	593	1	ENST00000359195.3:c.3217G>A	p.Glu1073Lys	p.E1073K	ENST00000359195	NM_002649.2	1073	Gaa/Aaa	11/11	0.365218252455223	4	FACETS	0.975	0.917	1	1	0.993	1	CLONAL	3	TRUE	2	0.429179910818282	4		594	508	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851484	151851484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	305	532	1	ENST00000262189.6:c.12007C>T	p.Pro4003Ser	p.P4003S	ENST00000262189	NM_170606.2	4003	Ccc/Tcc	47/59	0.365218252455223	4	FACETS	0.876	0.83	0.923	1	0.993	1	CLONAL	3	TRUE	2	0.429179910818282	4		533	773	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980485	70980485	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1285183449	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	214	890	0	ENST00000276594.2:c.892G>A	p.Asp298Asn	p.D298N	ENST00000276594	NM_024504.3	298	Gac/Aac	4/8	0.286435698631612	4	FACETS	1	0.989	1	0.672	0.624	0.721	CLONAL	1	TRUE	2	0.429179910818282	4		890	1061	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566014	141566014	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	291	429	0	ENST00000220592.5:c.1250C>T	p.Ser417Phe	p.S417F	ENST00000220592	NM_012154.3	417	tCc/tTc	10/19	0.429179910818282	4	FACETS	1	0.949	1	1	0.995	1	CLONAL	3	TRUE	2	0.429179910818282	4		429	646	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521431	8521431	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	116	638	0	ENST00000356435.5:c.807G>A	p.Trp269Ter	p.W269*	ENST00000356435		269	tgG/tgA	9/35	0.429179910818282	1	FACETS	0.943	0.856	1	0.943	0.856	1	CLONAL	1	TRUE	0	0.429179910818282	1		638	450	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93636980	93636980	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	160	373	0	ENST00000375746.1:c.1030G>A	p.Asp344Asn	p.D344N	ENST00000375746	NM_001174167.1	344	Gac/Aac	9/14	0.11640075006088	0	FACETS	0.546	0.506	0.585			1	INDETERMINATE	2	TRUE	0	0.429179910818282	0		373	390	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912100	127912100	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	255	374	0	ENST00000373547.4:c.770C>T	p.Ser257Phe	p.S257F	ENST00000373547	NM_002721.4	257	tCt/tTt	7/7	0.429179910818282	4	FACETS	0.913	0.867	0.959	1	0.991	1	CLONAL	4	TRUE	1	0.429179910818282	4		374	465	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417634	139417634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749786734	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	495	781	0	ENST00000277541.6:c.410C>T	p.Ser137Leu	p.S137L	ENST00000277541	NM_017617.3	137	tCg/tTg	4/34	0.429179910818282	4	FACETS	0.905	0.872	0.937	1	0.995	1	CLONAL	4	TRUE	1	0.429179910818282	4		781	911	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932317	39932317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238639795	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	541	408	0	ENST00000378444.4:c.2282G>A	p.Arg761Gln	p.R761Q	ENST00000378444	NM_001123385.1	761	cGg/cAg	4/15	0.429179910818282	2	FACETS	1	0.994	1			1	CLONAL	4	TRUE	NA	0.429179910818282	2		408	612	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933820	39933820	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	191	271	0	ENST00000378444.4:c.779C>T	p.Ser260Phe	p.S260F	ENST00000378444	NM_001123385.1	260	tCc/tTc	4/15	0.429179910818282	2	FACETS	0.978	0.915	1			1	CLONAL	2	TRUE	NA	0.429179910818282	2		271	455	SUCCESS
AR	367	MSKCC	GRCh37	X	66941720	66941720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	398	306	0	ENST00000374690.3:c.2364G>A	p.Met788Ile	p.M788I	ENST00000374690	NM_000044.3	788	atG/atA	6/8	0.221091558960302	2	FACETS	1	0.98	1			1	INDETERMINATE	4	TRUE	NA	0.429179910818282	2		306	462	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0017507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	89	390	2				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.417936231554304	2		392	348	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690805	89690805	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	108	348	0	ENST00000371953.3:c.212G>A	p.Cys71Tyr	p.C71Y	ENST00000371953	NM_000314.4	71	tGt/tAt	4/9	0.417936231554304	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.417936231554304	1		348	388	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439840	51439841	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	104	204	0	ENST00000262662.1:c.407dup	p.Asp138GlyfsTer5	p.D138Gfs*5	ENST00000262662		135	-/A	4/4	0.283143878256219	3	FACETS	0.937	0.849	1	0.937	0.849	1	CLONAL	2	TRUE	1	0.417936231554304	3		204	321	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77034326	77034326	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	101	397	0	ENST00000356341.3:c.1631del	p.Asn544IlefsTer28	p.N544Ifs*28	ENST00000356341	NM_002576.4	544	aAt/at	15/15	1	2	FACETS	0.872	0.782	0.968	0.872	0.782	0.968	CLONAL	1	TRUE	1	0.417936231554304	2		397	554	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293461	1293461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	78	585	0	ENST00000310581.5:c.1540G>A	p.Val514Met	p.V514M	ENST00000310581	NM_198253.2	514	Gtg/Atg	2/16	NA	2	FACETS	0.77	0.678	0.867			1	INDETERMINATE	1	TRUE	NA	0.417936231554304	2		585	485	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	77	301	4				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.849	0.748	0.958	0.849	0.748	0.958	CLONAL	1	TRUE	1	0.362596031659537	2		305	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0017508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	655	551	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.342356940478925	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	TRUE	0	0.362596031659537	3		551	1415	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151246	202151246	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	204	432	0	ENST00000358485.4:c.1550del	p.Asn517ThrfsTer13	p.N517Tfs*13	ENST00000358485	NM_001080125.1	516	Aaa/aa	9/9	0.362596031659537	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.362596031659537	1		432	892	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468073	120468073	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	179	341	0	ENST00000256646.2:c.4366T>C	p.Ser1456Pro	p.S1456P	ENST00000256646	NM_024408.3	1456	Tct/Cct	25/34	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.362596031659537	2		341	803	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584549	187584549	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	137	334	0	ENST00000441802.2:c.3484G>T	p.Glu1162Ter	p.E1162*	ENST00000441802	NM_005245.3	1162	Gag/Tag	3/27	0.362596031659537	1	FACETS	0.953	0.869	1	0.953	0.869	1	CLONAL	1	TRUE	0	0.362596031659537	1		334	649	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584728	187584728	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1161140037	NA	P-0017508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	138	330	0	ENST00000441802.2:c.3305C>A	p.Thr1102Asn	p.T1102N	ENST00000441802	NM_005245.3	1102	aCc/aAc	3/27	0.362596031659537	1	FACETS	0.881	0.804	0.963	0.881	0.804	0.963	CLONAL	1	TRUE	0	0.362596031659537	1		330	707	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	918	676	0	ENST00000397752.3:c.3028G>C	p.Asp1010His	p.D1010H	ENST00000397752	NM_000245.2	1010	Gat/Cat	14/21	0.318133443245232	4	FACETS	0.998	0.969	1	0.998	0.969	1	CLONAL	4	TRUE	0	0.318133443245232	4		676	1906	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599221	28599221	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	119	553	1	ENST00000253063.3:c.667G>T	p.Asp223Tyr	p.D223Y	ENST00000253063	NM_031459.4	223	Gat/Tat	5/10	0.150303369440066	3	FACETS	0.729	0.656	0.806	0.364	0.328	0.403	INDETERMINATE	1	TRUE	1	0.318133443245232	3		554	1190	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932224	36932224	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	133	413	0	ENST00000361632.4:c.2245C>T	p.Gln749Ter	p.Q749*	ENST00000361632		749	Cag/Tag	16/16	0.150303369440066	3	FACETS	1	0.965	1	0.564	0.512	0.619	INDETERMINATE	1	TRUE	1	0.318133443245232	3		413	859	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132933	30132933	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs201537930	NA	P-0017509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	75	426	0	ENST00000331968.5:c.668C>A	p.Ser223Tyr	p.S223Y	ENST00000331968	NM_002742.2	223	tCt/tAt	4/18	0.318133443245232	3	FACETS	0.542	0.473	0.616	0.271	0.236	0.308	SUBCLONAL	1	TRUE	1	0.318133443245232	3		426	1009	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687148	37687172	+	frameshift_variant	Frame_Shift_Del	DEL	TTGACACTGATGAACGAAACTCTGG	TTGACACTGATGAACGAAACTCTGG	-	novel	NA	P-0017509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	63	441	0	ENST00000447079.4:c.4053_4077del	p.Asp1352GlnfsTer3	p.D1352Qfs*3	ENST00000447079	NM_015083.1	1351	aTTGACACTGATGAACGAAACTCTGGt/at	14/14	0.180267700061908	4	FACETS	0.52	0.449	0.599	0.26	0.224	0.3	INDETERMINATE	1	TRUE	2	0.318133443245232	4		441	1003	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226526	41226527	+	stop_gained	Nonsense_Mutation	DNP	AG	AG	TT	novel	NA	P-0017509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	158	405	1	ENST00000357654.3:c.4496_4497delinsAA	p.Ser1499Ter	p.S1499*	ENST00000357654	NM_007294.3	1499	tCT/tAA	14/23	0.180267700061908	4	FACETS	1	0.985	1	0.681	0.623	0.741	INDETERMINATE	1	TRUE	2	0.318133443245232	4		406	962	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257613	19257613	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	99	599	1	ENST00000162023.5:c.613G>T	p.Glu205Ter	p.E205*	ENST00000162023		205	Gaa/Taa	10/13	0.155122831483963	3	FACETS	0.569	0.506	0.637	0.19	0.168	0.213	INDETERMINATE	1	TRUE	0	0.318133443245232	3		600	1267	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478726	57478726	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0017509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	46	256	0	ENST00000371085.3:c.313-1G>C		p.X105_splice	ENST00000371085	NM_000516.4	105			0.167856377874319	3	FACETS	0.62	0.521	0.728			1	INDETERMINATE	1	TRUE	NA	0.318133443245232	3		256	541	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636288	87636288	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	126	515	2	ENST00000277120.3:c.2453G>T	p.Gly818Val	p.G818V	ENST00000277120		818	gGc/gTc	19/19	1	2	FACETS	0.823	0.744	0.906	0.823	0.744	0.906	CLONAL	1	TRUE	1	0.318133443245232	2		517	963	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0017510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	192	178	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.409141276070247	4	FACETS	0.87	0.807	0.935	0.435	0.403	0.468	CLONAL	2	TRUE	0	0.419385155863342	4		178	747	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0017510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	354	342	1	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.288895620891338	3	FACETS	0.915	0.873	0.957	0.915	0.873	0.957	CLONAL	3	TRUE	0	0.419385155863342	3		343	744	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016603	12016603	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	185	255	0	ENST00000353533.5:c.739G>T	p.Asp247Tyr	p.D247Y	ENST00000353533	NM_003010.3	247	Gac/Tac	7/11	0.288895620891338	3	FACETS	1	0.979	1	0.749	0.698	0.8	CLONAL	2	TRUE	0	0.419385155863342	3		255	475	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628326	90628326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147578332	NA	P-0017510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	79	472	0	ENST00000330062.3:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000330062	NM_002168.2	362	cGg/cAg	9/11	0.359917310666416	2	FACETS	0.44	0.386	0.498	0.22	0.193	0.249	SUBCLONAL	1	TRUE	0	0.419385155863342	2		472	856	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398287	25398288	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTC	novel	NA	P-0017510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	279	503	0	ENST00000311936.3:c.29_31dup	p.Gly10dup	p.G10dup	ENST00000311936	NM_004985.3	10	gct/gGAGct	2/5	0.214877392040887	3	FACETS	0.886	0.834	0.939			1	INDETERMINATE	2	TRUE	NA	0.419385155863342	3		503	908	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265911	41266366	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTC	ACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTC	-	novel	NA	P-0017510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	41	31	0	ENST00000349496.5:c.14-101_242-74del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.387964320394858	3	FACETS	0.91	0.805	1	1	0.957	1	CLONAL	4	TRUE	0	0.419385155863342	3		31	65	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0017511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	63	348	1	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.756	0.658	0.861	0.756	0.658	0.861	SUBCLONAL	1	TRUE	1	0.487522171643436	2		349	342	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36217216	36217216	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	227	601	0	ENST00000222270.7:c.3965A>G	p.Tyr1322Cys	p.Y1322C	ENST00000222270	NM_014727.1	1322	tAc/tGc	14/37	1	2	FACETS	0.884	0.823	0.946	0.884	0.823	0.946	CLONAL	1	TRUE	1	0.487522171643436	2		601	1054	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972654	25972654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760621031	NA	P-0017516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	10	245	0	ENST00000435504.4:c.1771C>T	p.Arg591Cys	p.R591C	ENST00000435504		591	Cgc/Tgc	12/13	0.439322832123031	3	FACETS	0.088	0.059	0.124	0.044	0.029	0.062	INDETERMINATE	1	TRUE	1	0.777692632529927	3		245	408	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28624250	28624250	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	68	513	0	ENST00000241453.7:c.724A>C	p.Thr242Pro	p.T242P	ENST00000241453	NM_004119.2	242	Acc/Ccc	6/24	1	2	FACETS	0.428	0.373	0.486	0.428	0.373	0.486	SUBCLONAL	1	TRUE	1	0.777692632529927	2		513	409	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724553	43724553	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	494	805	0	ENST00000382044.4:c.3514G>T	p.Val1172Phe	p.V1172F	ENST00000382044	NM_001141980.1	1172	Gtt/Ttt	17/28	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	1	TRUE	NA	0.777692632529927	2		805	915	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579478	7579478	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	419	525	0	ENST00000269305.4:c.209del	p.Ala70ValfsTer53	p.A70Vfs*53	ENST00000269305	NM_001126112.2	70	gCt/gt	4/11	0.736386206039871	2	FACETS	0.959	0.93	0.986	0.959	0.93	0.986	CLONAL	2	TRUE	0	0.777692632529927	2		525	562	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0017519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	208	448	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	0.885	0.822	0.951	0.885	0.822	0.951	CLONAL	1	TRUE	1	0.505264529691716	2		448	930	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085681	16085681	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762164859	NA	P-0017519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	68	602	0	ENST00000281043.3:c.857G>A	p.Arg286His	p.R286H	ENST00000281043	NM_005378.4	286	cGt/cAt	3/3	1	2	FACETS	0.257	0.222	0.294	0.257	0.222	0.294	SUBCLONAL	1	TRUE	1	0.505264529691716	2		602	1048	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	516	301	4				ENST00000310581	NM_198253.2	-/1132			0.869560427229267	3	FACETS	0.975	0.943	1	0.975	0.943	1	CLONAL	2	TRUE	1	0.878116354744775	3		305	867	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0017520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	234	268	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.878116354744775	2		268	519	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391511	139391511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751456570	NA	P-0017520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	75	531	0	ENST00000277541.6:c.6680C>T	p.Pro2227Leu	p.P2227L	ENST00000277541	NM_017617.3	2227	cCg/cTg	34/34	1	2	FACETS	0.183	0.16	0.209	0.183	0.16	0.209	SUBCLONAL	1	TRUE	1	0.878116354744775	2		531	931	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814258	76814258	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	360	598	0	ENST00000373344.5:c.6386C>A	p.Ala2129Asp	p.A2129D	ENST00000373344	NM_000489.3	2129	gCt/gAt	29/35	0.334812849268207	1	FACETS	0.611	0.583	0.639	0.611	0.583	0.639	INDETERMINATE	1	TRUE	0	0.872764338139417	1		598	761	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584590	52584590	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	485	477	0	ENST00000394830.3:c.4423G>T	p.Gly1475Ter	p.G1475*	ENST00000394830	NM_018313.4	1475	Gga/Tga	29/30	0.872764338139417	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.872764338139417	1		477	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579409	7579409	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1567556114	NA	P-0017521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	527	553	0	ENST00000269305.4:c.278del	p.Leu93ArgfsTer30	p.L93Rfs*30	ENST00000269305	NM_001126112.2	93	cTg/cg	4/11	0.872764338139417	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.872764338139417	1		553	645	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0017522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	50	672	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.381970027390482	5	FACETS	0.765	0.649	0.893			1	SUBCLONAL	1	TRUE	NA	0.38	5		672	540	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63537617	63537617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502160	NA	P-0017522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	80	564	1	ENST00000307078.5:c.1015C>T	p.Arg339Cys	p.R339C	ENST00000307078	NM_004655.3	339	Cgc/Tgc	4/11	0.381970027390482	4	FACETS	1	0.977	1	0.732	0.648	0.821	CLONAL	1	TRUE	2	0.38	4		565	397	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087372	27087421	+	frameshift_variant	Frame_Shift_Del	DEL	TCCCCATGGGGACAGAAGGAGCTCTGAGTCCTGGAGTGAGCACATCAGGG	TCCCCATGGGGACAGAAGGAGCTCTGAGTCCTGGAGTGAGCACATCAGGG	-	novel	NA	P-0017522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	54	494	0	ENST00000324856.7:c.1946_1995del	p.Leu649HisfsTer10	p.L649Hfs*10	ENST00000324856	NM_006015.4	649	cTCCCCATGGGGACAGAAGGAGCTCTGAGTCCTGGAGTGAGCACATCAGGG/c	5/20	0.381970027390482	8	FACETS	1	0.897	1			1	CLONAL	1	TRUE	NA	0.38	8		494	572	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106942	27106943	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	40	287	0	ENST00000324856.7:c.6555dup	p.Ala2186CysfsTer39	p.A2186Cfs*39	ENST00000324856	NM_006015.4	2185	att/aTtt	20/20	0.381970027390482	8	FACETS	1	0.948	1			1	CLONAL	1	TRUE	NA	0.38	8		287	325	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422969	49422969	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	59	711	1	ENST00000301067.7:c.14126C>T	p.Ser4709Leu	p.S4709L	ENST00000301067	NM_003482.3	4709	tCa/tTa	44/54	0.381970027390482	7	FACETS	0.963	0.828	1			1	CLONAL	1	TRUE	NA	0.38	7		712	629	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231782	36231782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs74315450	NA	P-0017523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	14	589	0	ENST00000300305.3:c.602G>A	p.Arg201Gln	p.R201Q	ENST00000300305		201	cGa/cAa	5/8	1	2	FACETS	0.188	0.135	0.254	0.188	0.135	0.254	SUBCLONAL	1	TRUE	1	0.23	2		589	646	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0017523-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	23	549	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	1	2	FACETS	0.461	0.357	0.581	0.461	0.357	0.581	SUBCLONAL	1	TRUE	1	0.13	2		549	768	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515610	31515610	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017523-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	53	459	0	ENST00000344624.3:c.1009A>T	p.Ile337Phe	p.I337F	ENST00000344624		337	Att/Ttt	4/33	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.13	2		459	704	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910455	32910455	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555282375	NA	P-0017524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	252	388	0	ENST00000380152.3:c.1964del	p.Pro655GlnfsTer5	p.P655Qfs*5	ENST00000380152		655	Cca/ca	11/27	0.56524750333197	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.56524750333197	1		388	584	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78426056	78426057	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0017524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	256	448	0	ENST00000370768.2:c.1468_1469del	p.Asn490SerfsTer34	p.N490Sfs*34	ENST00000370768	NM_003902.3	490	AAt/t	15/20	1	2	FACETS	0.979	0.918	1	0.979	0.918	1	CLONAL	1	TRUE	1	0.56524750333197	2		448	925	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375207	118375207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	209	308	0	ENST00000534358.1:c.8600G>A	p.Gly2867Asp	p.G2867D	ENST00000534358	NM_005933.3	2867	gGt/gAt	27/36	0.56524750333197	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.56524750333197	1		308	523	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390346	56390346	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	158	343	0	ENST00000348428.3:c.1085C>G	p.Pro362Arg	p.P362R	ENST00000348428	NM_006785.3	362	cCt/cGt	10/17	0.28629994278475	1	FACETS	0.561	0.515	0.609	0.561	0.515	0.609	INDETERMINATE	1	TRUE	0	0.56524750333197	1		343	715	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091842	29091842	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147877722	NA	P-0017524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	147	236	0	ENST00000328354.6:c.1115C>T	p.Ser372Phe	p.S372F	ENST00000328354	NM_007194.3	372	tCc/tTc	11/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.56524750333197	2		236	470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0017529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	451	474	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.963019268563808	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	FALSE	0	0.963019268563808	1		474	468	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300482	11300482	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	614	614	1	ENST00000361445.4:c.1664del	p.Pro555GlnfsTer45	p.P555Qfs*45	ENST00000361445	NM_004958.3	555	cCa/ca	11/58	0.172527732649904	3	FACETS	0.756	0.73	0.782	0.756	0.73	0.782	INDETERMINATE	2	FALSE	1	0.963019268563808	3		615	1250	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112884155	112884155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	221	391	0	ENST00000351677.2:c.90G>T	p.Leu30Phe	p.L30F	ENST00000351677	NM_002834.3	30	ttG/ttT	2/16	0.168405113157163	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.963019268563808	0		391	557	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955480	48955480	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	267	360	0	ENST00000267163.4:c.1596del	p.Ile532MetfsTer11	p.I532Mfs*11	ENST00000267163	NM_000321.2	532	atC/at	17/27	0.963019268563808	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	FALSE	0	0.963019268563808	1		360	277	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728617	190728617	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	482	637	0	ENST00000441310.2:c.2005A>G	p.Lys669Glu	p.K669E	ENST00000441310	NM_000534.4	669	Aaa/Gaa	10/13	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.963019268563808	2		637	993	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478032	138478032	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	336	490	0	ENST00000289153.2:c.154A>G	p.Ile52Val	p.I52V	ENST00000289153	NM_006219.2	52	Att/Gtt	1/22	1	2	FACETS	0.938	0.893	0.983	0.938	0.893	0.983	CLONAL	1	FALSE	1	0.963019268563808	2		490	744	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191466	185191466	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	365	414	0	ENST00000265026.3:c.2347G>T	p.Gly783Cys	p.G783C	ENST00000265026	NM_004721.4	783	Ggc/Tgc	11/14	0.963019268563808	3	FACETS	0.976	0.926	1	0.325	0.308	0.342	CLONAL	1	FALSE	0	0.963019268563808	3		414	1151	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972035	55972035	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	400	538	0	ENST00000263923.4:c.1609G>C	p.Gly537Arg	p.G537R	ENST00000263923	NM_002253.2	537	Ggg/Cgg	12/30	0.129228514332649	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.963019268563808	0		538	885	SUCCESS
APC	324	MSKCC	GRCh37	5	112176228	112176228	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	41	514	0	ENST00000257430.4:c.4937G>A	p.Gly1646Glu	p.G1646E	ENST00000257430	NM_000038.5	1646	gGg/gAg	16/16	0.963019268563808	1	FACETS	0.089	0.074	0.106	0.089	0.074	0.106	SUBCLONAL	1	FALSE	0	0.963019268563808	1		514	496	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267382	198267382	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017530-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	176	426	0	ENST00000335508.6:c.1975C>G	p.Gln659Glu	p.Q659E	ENST00000335508	NM_012433.2	659	Caa/Gaa	14/25	1	2	FACETS	0.701	0.645	0.76	0.701	0.645	0.76	SUBCLONAL	1	TRUE	1	0.480410378970418	2		426	1045	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593609	55593611	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	rs121913685	NA	P-0017531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	506	408	0	ENST00000288135.5:c.1679_1681del	p.Val560del	p.V560del	ENST00000288135	NM_000222.2	559	GTT/-	11/21	0.914555964145486	2	FACETS	0.929	0.911	0.945	0.929	0.911	0.945	CLONAL	2	TRUE	0	0.954247054009029	2		408	571	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	121	401	3	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.948	0.857	1	0.948	0.857	1	CLONAL	1	TRUE	1	0.341330748837705	2		404	748	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578466	7578466	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786202752	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	179	414	0	ENST00000269305.4:c.464C>A	p.Thr155Asn	p.T155N	ENST00000269305	NM_001126112.2	155	aCc/aAc	5/11	0.341330748837705	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.341330748837705	1		414	715	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911116	29911116	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs199474504	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	104	493	0	ENST00000376809.5:c.415C>T	p.Gln139Ter	p.Q139*	ENST00000376809	NM_002116.7	139	Cag/Tag	3/8	1	2	FACETS	0.85	0.761	0.944	0.85	0.761	0.944	CLONAL	1	TRUE	1	0.341330748837705	2		493	717	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226280	133226280	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	156	503	0	ENST00000320574.5:c.3778G>T	p.Ala1260Ser	p.A1260S	ENST00000320574	NM_006231.2	1260	Gcc/Tcc	30/49	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.341330748837705	2		503	914	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917496	178917496	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	72	231	0	ENST00000263967.3:c.371C>A	p.Pro124Gln	p.P124Q	ENST00000263967	NM_006218.2	124	cCa/cAa	3/21	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.341330748837705	2		231	384	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782629	9782629	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	133	546	0	ENST00000377346.4:c.2391G>T	p.Met797Ile	p.M797I	ENST00000377346	NM_005026.3	797	atG/atT	19/24	1	2	FACETS	0.802	0.727	0.88	0.802	0.727	0.88	CLONAL	1	TRUE	1	0.341330748837705	2		546	972	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101424	27101424	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	210	648	0	ENST00000324856.7:c.4706C>A	p.Pro1569Gln	p.P1569Q	ENST00000324856	NM_006015.4	1569	cCa/cAa	18/20	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.341330748837705	2		648	1207	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933464	36933464	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	277	940	0	ENST00000361632.4:c.1823C>A	p.Ala608Asp	p.A608D	ENST00000361632		608	gCc/gAc	13/16	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.341330748837705	2		940	1497	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937246	36937246	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1248	234	996	0	ENST00000361632.4:c.1073C>A	p.Pro358Gln	p.P358Q	ENST00000361632		358	cCa/cAa	9/16	1	2	FACETS	0.925	0.861	0.992	0.925	0.861	0.992	CLONAL	1	TRUE	1	0.341330748837705	2		996	1482	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466417	120466417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	153	556	1	ENST00000256646.2:c.4702G>A	p.Ala1568Thr	p.A1568T	ENST00000256646	NM_024408.3	1568	Gca/Aca	26/34	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.341330748837705	2		557	813	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512358	120512358	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	84	228	0	ENST00000256646.2:c.884G>T	p.Cys295Phe	p.C295F	ENST00000256646	NM_024408.3	295	tGc/tTc	6/34	0.191606395627881	3	FACETS	1	0.978	1	0.729	0.648	0.815	INDETERMINATE	1	TRUE	1	0.341330748837705	3		228	395	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841431	156841431	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	90	332	0	ENST00000524377.1:c.734C>A	p.Pro245Gln	p.P245Q	ENST00000524377	NM_002529.3	245	cCa/cAa	7/17	0.191606395627881	3	FACETS	0.805	0.714	0.902	0.402	0.357	0.451	INDETERMINATE	1	TRUE	1	0.341330748837705	3		332	767	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226590053	226590053	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	127	496	0	ENST00000366794.5:c.148C>A	p.His50Asn	p.H50N	ENST00000366794	NM_001618.3	50	Cac/Aac	2/23	0.191606395627881	3	FACETS	0.857	0.775	0.943	0.428	0.387	0.472	INDETERMINATE	1	TRUE	1	0.341330748837705	3		496	1017	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404995	70404995	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	126	371	0	ENST00000373644.4:c.2509C>A	p.His837Asn	p.H837N	ENST00000373644	NM_030625.2	837	Cat/Aat	4/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.341330748837705	2		371	641	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201953	67201953	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	120	259	0	ENST00000312629.5:c.1153C>A	p.Leu385Met	p.L385M	ENST00000312629	NM_003952.2	385	Ctg/Atg	13/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.341330748837705	2		259	524	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394800	394800	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	155	477	2	ENST00000399788.2:c.4895G>T	p.Cys1632Phe	p.C1632F	ENST00000399788	NM_001042603.1	1632	tGt/tTt	28/28	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.341330748837705	2		479	801	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416718	416718	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	119	384	0	ENST00000399788.2:c.3832G>T	p.Val1278Leu	p.V1278L	ENST00000399788	NM_001042603.1	1278	Gtg/Ttg	23/28	NA	2	FACETS	0.986	0.891	1			1	INDETERMINATE	1	TRUE	NA	0.341330748837705	2		384	707	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435879	110435879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	36	98	0	ENST00000375856.3:c.2522C>T	p.Pro841Leu	p.P841L	ENST00000375856	NM_003749.2	841	cCt/cTt	1/2	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.341330748837705	2		98	169	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435983	110435983	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	64	217	0	ENST00000375856.3:c.2418G>T	p.Leu806Phe	p.L806F	ENST00000375856	NM_003749.2	806	ttG/ttT	1/2	1	2	FACETS	0.992	0.863	1	0.992	0.863	1	CLONAL	1	TRUE	1	0.341330748837705	2		217	378	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570165	95570165	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	110	379	0	ENST00000393063.1:c.3568G>C	p.Asp1190His	p.D1190H	ENST00000393063	NM_030621.3	1190	Gat/Cat	22/28	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.341330748837705	2		379	622	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779554	3779554	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	149	713	0	ENST00000262367.5:c.5494C>A	p.His1832Asn	p.H1832N	ENST00000262367	NM_004380.2	1832	Cac/Aac	31/31	1	2	FACETS	0.72	0.656	0.788	0.72	0.656	0.788	SUBCLONAL	1	TRUE	1	0.341330748837705	2		713	1212	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829470	72829470	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1235	237	1009	0	ENST00000268489.5:c.7111G>T	p.Ala2371Ser	p.A2371S	ENST00000268489	NM_006885.3	2371	Gcc/Tcc	9/10	1	2	FACETS	0.943	0.878	1	0.943	0.878	1	CLONAL	1	TRUE	1	0.341330748837705	2		1009	1472	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993567	72993567	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	242	899	1	ENST00000268489.5:c.478G>T	p.Gly160Cys	p.G160C	ENST00000268489	NM_006885.3	160	Ggc/Tgc	2/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.341330748837705	2		900	1315	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676174	29676174	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	120	333	0	ENST00000356175.3:c.7163C>G	p.Thr2388Arg	p.T2388R	ENST00000356175	NM_000267.3	2388	aCa/aGa	48/57	0.341330748837705	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.341330748837705	1		333	539	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679295	29679295	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	38	396	0	ENST00000356175.3:c.7415C>A	p.Pro2472Gln	p.P2472Q	ENST00000356175	NM_000267.3	2472	cCa/cAa	50/57	0.341330748837705	1	FACETS	0.299	0.247	0.358	0.299	0.247	0.358	SUBCLONAL	1	TRUE	0	0.341330748837705	1		396	617	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487504	38487504	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	155	422	0	ENST00000254066.5:c.34G>T	p.Gly12Trp	p.G12W	ENST00000254066	NM_000964.3	12	Ggg/Tgg	2/9	0.341330748837705	1	FACETS	0.981	0.899	1	0.981	0.899	1	CLONAL	1	TRUE	0	0.341330748837705	1		422	768	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936852	78936852	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	72	260	1	ENST00000306801.3:c.3934C>A	p.His1312Asn	p.H1312N	ENST00000306801	NM_020761.2	1312	Cac/Aac	33/34	0.340030027162643	2	FACETS	0.726	0.635	0.824	0.363	0.317	0.412	SUBCLONAL	1	TRUE	0	0.341330748837705	2		261	581	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632060	1632060	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1359	353	887	1	ENST00000344749.5:c.275C>A	p.Thr92Lys	p.T92K	ENST00000344749	NM_001136139.2	92	aCa/aAa	5/19	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.341330748837705	2		888	1712	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2206730	2206730	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	195	506	0	ENST00000398665.3:c.790G>T	p.Gly264Cys	p.G264C	ENST00000398665	NM_032482.2	264	Ggc/Tgc	10/28	1	2	FACETS	0.857	0.791	0.925	0.857	0.791	0.925	CLONAL	1	TRUE	1	0.341330748837705	2		506	1334	SUCCESS
CALR	811	MSKCC	GRCh37	19	13049572	13049572	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	267	809	0	ENST00000316448.5:c.79T>A	p.Phe27Ile	p.F27I	ENST00000316448	NM_004343.3	27	Ttt/Att	1/9	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.341330748837705	2		809	1413	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296197	15296197	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	113	428	0	ENST00000263388.2:c.2167G>T	p.Gly723Cys	p.G723C	ENST00000263388	NM_000435.2	723	Ggc/Tgc	14/33	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.341330748837705	2		428	650	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349719	15349719	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	19	157	0	ENST00000263377.2:c.3855G>T	p.Gln1285His	p.Q1285H	ENST00000263377	NM_058243.2	1285	caG/caT	19/20	1	2	FACETS	0.497	0.378	0.636	0.497	0.378	0.636	SUBCLONAL	1	TRUE	1	0.341330748837705	2		157	224	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279310	18279310	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	74	262	0	ENST00000222254.8:c.1762C>A	p.Gln588Lys	p.Q588K	ENST00000222254	NM_005027.3	588	Cag/Aag	14/16	1	2	FACETS	0.796	0.698	0.901	0.796	0.698	0.901	CLONAL	1	TRUE	1	0.341330748837705	2		262	545	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257962	19257962	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	167	500	0	ENST00000162023.5:c.424G>T	p.Val142Leu	p.V142L	ENST00000162023		142	Gtg/Ttg	9/13	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.341330748837705	2		500	864	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792683	33792683	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	88	224	0	ENST00000498907.2:c.638G>T	p.Cys213Phe	p.C213F	ENST00000498907	NM_004364.3	213	tGc/tTc	1/1	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.341330748837705	2		224	503	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469124	25469124	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	155	477	0	ENST00000264709.3:c.1334C>A	p.Ala445Glu	p.A445E	ENST00000264709	NM_175629.2	445	gCa/gAa	11/23	1	2	FACETS	0.985	0.902	1	0.985	0.902	1	CLONAL	1	TRUE	1	0.341330748837705	2		477	922	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309819	30309819	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	123	353	0	ENST00000307677.4:c.203C>A	p.Ala68Asp	p.A68D	ENST00000307677	NM_138578.1	68	gCc/gAc	2/3	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.341330748837705	2		353	657	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024303	31024303	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	120	437	0	ENST00000375687.4:c.3788C>A	p.Pro1263Gln	p.P1263Q	ENST00000375687	NM_015338.5	1263	cCa/cAa	13/13	1	2	FACETS	0.917	0.828	1	0.917	0.828	1	CLONAL	1	TRUE	1	0.341330748837705	2		437	767	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958082	54958082	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	111	337	0	ENST00000312783.6:c.525G>T	p.Glu175Asp	p.E175D	ENST00000312783	NM_198436.1	175	gaG/gaT	6/10	NA	2	FACETS	1	0.933	1			1	INDETERMINATE	1	TRUE	NA	0.341330748837705	2		337	622	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934022	49934022	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	242	763	0	ENST00000296474.3:c.2390G>T	p.Trp797Leu	p.W797L	ENST00000296474	NM_002447.2	797	tGg/tTg	9/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.341330748837705	2		763	1377	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127573	55127573	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	119	173	0	ENST00000257290.5:c.361G>T	p.Val121Leu	p.V121L	ENST00000257290	NM_006206.4	121	Gtg/Ttg	3/23	0.340030027162643	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.341330748837705	2		173	317	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189921	66189921	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	187	320	0	ENST00000273854.3:c.3025G>T	p.Gly1009Ter	p.G1009*	ENST00000273854	NM_004439.5	1009	Gga/Tga	18/18	0.340030027162643	2	FACETS	0.953	0.886	1	0.953	0.886	1	CLONAL	2	TRUE	0	0.341330748837705	2		320	575	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524776	187524776	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	206	399	0	ENST00000441802.2:c.10904C>A	p.Thr3635Lys	p.T3635K	ENST00000441802	NM_005245.3	3635	aCa/aAa	19/27	0.340030027162643	2	FACETS	0.863	0.804	0.924	0.863	0.804	0.924	CLONAL	2	TRUE	0	0.341330748837705	2		399	699	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180645	56180645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	110	277	0	ENST00000399503.3:c.3974G>T	p.Trp1325Leu	p.W1325L	ENST00000399503	NM_005921.1	1325	tGg/tTg	16/20	0.341330748837705	3	FACETS	0.846	0.765	0.931	0.846	0.765	0.931	CLONAL	2	TRUE	1	0.341330748837705	3		277	446	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459660	149459660	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	46	487	0	ENST00000286301.3:c.547G>T	p.Gly183Cys	p.G183C	ENST00000286301	NM_005211.3	183	Ggc/Tgc	4/22	0.330493402434893	2	FACETS	0.311	0.261	0.367	0.156	0.13	0.184	SUBCLONAL	1	TRUE	0	0.341330748837705	2		487	866	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148504755	148504755	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	144	454	1	ENST00000320356.2:c.2239G>T	p.Glu747Ter	p.E747*	ENST00000320356	NM_004456.4	747	Gaa/Taa	20/20	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.341330748837705	2		455	828	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752783	128752783	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1179847000	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	80	324	0	ENST00000377970.2:c.944G>T	p.Cys315Phe	p.C315F	ENST00000377970	NM_002467.4	315	tGc/tTc	3/3	1	2	FACETS	0.803	0.707	0.905	0.803	0.707	0.905	CLONAL	1	TRUE	1	0.341330748837705	2		324	584	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635130	87635130	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	38	314	0	ENST00000277120.3:c.2182C>A	p.His728Asn	p.H728N	ENST00000277120		728	Cac/Aac	18/19	1	2	FACETS	0.41	0.338	0.49	0.41	0.338	0.49	SUBCLONAL	1	TRUE	1	0.341330748837705	2		314	543	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407509	139407509	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	198	428	0	ENST00000277541.6:c.2431G>T	p.Ala811Ser	p.A811S	ENST00000277541	NM_017617.3	811	Gcc/Tcc	15/34	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.341330748837705	2		428	1102	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918616	44918616	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	180	273	0	ENST00000377967.4:c.1099C>A	p.Gln367Lys	p.Q367K	ENST00000377967	NM_021140.2	367	Cag/Aag	12/29	1	1	FACETS	0.81	0.752	0.869	1	0.992	1	CLONAL	2	TRUE	0	0.341330748837705	1		273	540	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426743	47426743	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	48	287	0	ENST00000377045.4:c.988C>A	p.His330Asn	p.H330N	ENST00000377045	NM_001654.4	330	Cat/Aat	10/16	1	1	FACETS	0.354	0.299	0.416	0.354	0.299	0.416	SUBCLONAL	1	TRUE	0	0.341330748837705	1		287	658	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247085	53247085	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	315	392	1	ENST00000375401.3:c.415C>A	p.Gln139Lys	p.Q139K	ENST00000375401	NM_004187.3	139	Cag/Aag	4/26	1	1	FACETS	0.908	0.86	0.956	1	0.996	1	CLONAL	2	TRUE	0	0.341330748837705	1		393	843	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891525	76891525	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	166	328	0	ENST00000373344.5:c.4580C>A	p.Ser1527Ter	p.S1527*	ENST00000373344	NM_000489.3	1527	tCa/tAa	16/35	1	1	FACETS	0.792	0.733	0.853	1	0.991	1	SUBCLONAL	2	TRUE	0	0.341330748837705	1		328	509	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0017533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	171	513	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	NA	2	FACETS	1	0.922	1			1	INDETERMINATE	1	TRUE	NA	0.290240238896295	2		513	1174	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56871637	56871637	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1166462755	NA	P-0017533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1253	112	665	2	ENST00000308159.5:c.2017C>T	p.Arg673Trp	p.R673W	ENST00000308159	NM_014669.4	673	Cgg/Tgg	18/22	0.290240238896295	1	FACETS	0.483	0.433	0.537	0.483	0.433	0.537	SUBCLONAL	1	TRUE	0	0.290240238896295	1		667	1365	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478069	138478125	+	inframe_deletion	In_Frame_Del	DEL	CCCAGTGGGCAAAAGGAAATCCACAGGTATGGAGCCATCAGATGCTATCTGTGAATC	CCCAGTGGGCAAAAGGAAATCCACAGGTATGGAGCCATCAGATGCTATCTGTGAATC	-	novel	NA	P-0017533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	124	584	0	ENST00000289153.2:c.61_117del	p.Asp21_Gly39del	p.D21_G39del	ENST00000289153	NM_006219.2	21	GATTCACAGATAGCATCTGATGGCTCCATACCTGTGGATTTCCTTTTGCCCACTGGG/-	1/22	0.262310465593999	1	FACETS	0.585	0.528	0.646	0.585	0.528	0.646	SUBCLONAL	1	TRUE	0	0.290240238896295	1		584	1248	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239264	105239264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373253729	NA	P-0017533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	86	566	0	ENST00000349310.3:c.1123G>A	p.Glu375Lys	p.E375K	ENST00000349310	NM_001014432.1	375	Gag/Aag	12/15	0.290240238896295	1	FACETS	0.458	0.403	0.516	0.458	0.403	0.516	SUBCLONAL	1	TRUE	0	0.290240238896295	1		566	1107	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573999	7574008	+	frameshift_variant	Frame_Shift_Del	DEL	TCTCGGAACA	TCTCGGAACA	-	novel	NA	P-0017533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1561	240	988	1	ENST00000269305.4:c.1019_1028del	p.Met340SerfsTer2	p.M340Sfs*2	ENST00000269305	NM_001126112.2	340	aTGTTCCGAGAg/ag	10/11	0.290240238896295	1	FACETS	0.785	0.73	0.842	0.785	0.73	0.842	SUBCLONAL	1	TRUE	0	0.290240238896295	1		989	1801	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322647	30322647	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	160	461	0	ENST00000322652.5:c.1660C>T	p.Gln554Ter	p.Q554*	ENST00000322652	NM_015355.2	554	Caa/Taa	14/16	0.290240238896295	1	FACETS	0.984	0.902	1	0.984	0.902	1	CLONAL	1	TRUE	0	0.290240238896295	1		461	958	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260290	10260290	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	92	432	0	ENST00000340748.4:c.2377C>T	p.His793Tyr	p.H793Y	ENST00000340748		793	Cac/Tac	25/40	1	2	FACETS	0.635	0.563	0.713	0.635	0.563	0.713	SUBCLONAL	1	TRUE	1	0.290240238896295	2		432	998	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209108191	209108191	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	77	482	0	ENST00000345146.2:c.658G>A	p.Asp220Asn	p.D220N	ENST00000345146	NM_005896.2	220	Gat/Aat	6/10	0.290240238896295	1	FACETS	0.445	0.389	0.505	0.445	0.389	0.505	SUBCLONAL	1	TRUE	0	0.290240238896295	1		482	1019	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805531	1805531	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1262	324	737	0	ENST00000260795.2:c.1043C>G	p.Ser348Cys	p.S348C	ENST00000260795		348	tCt/tGt	7/17	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.290240238896295	2		737	1586	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127486	55127486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	206	598	3	ENST00000257290.5:c.274G>A	p.Ala92Thr	p.A92T	ENST00000257290	NM_006206.4	92	Gcg/Acg	3/23	0.290240238896295	1	FACETS	0.983	0.911	1	0.983	0.911	1	CLONAL	1	TRUE	0	0.290240238896295	1		601	1234	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868405	117868405	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs778161455	NA	P-0017533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1391	179	698	1	ENST00000297338.2:c.937G>A	p.Val313Ile	p.V313I	ENST00000297338	NM_006265.2	313	Gtt/Att	8/14	1	2	FACETS	0.786	0.722	0.853	0.786	0.722	0.853	SUBCLONAL	1	TRUE	1	0.290240238896295	2		699	1570	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165548	47165548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs77310684	NA	P-0017534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1194	119	548	1	ENST00000409792.3:c.578C>T	p.Pro193Leu	p.P193L	ENST00000409792	NM_014159.6	193	cCg/cTg	3/21	1	2	FACETS	0.406	0.365	0.45	0.406	0.365	0.45	SUBCLONAL	1	TRUE	1	0.446520416708946	2		549	1313	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0017534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	346	470	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.772	0.732	0.812	1	0.995	1	SUBCLONAL	2	TRUE	1	0.446520416708946	2		470	1004	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0017534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	31	357	1	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.261341079402713	1	FACETS	0.216	0.174	0.263	0.216	0.174	0.263	INDETERMINATE	1	TRUE	0	0.446520416708946	1		358	500	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699296	18699296	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	133	341	0	ENST00000266497.5:c.3397G>C	p.Asp1133His	p.D1133H	ENST00000266497		1133	Gac/Cac	24/31	NA	2	FACETS	0.682	0.619	0.748			1	INDETERMINATE	1	TRUE	NA	0.446520416708946	2		341	874	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653826	89653827	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0017534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	150	254	0	ENST00000371953.3:c.125_126dup	p.Glu43LeufsTer12	p.E43Lfs*12	ENST00000371953	NM_000314.4	42	ctt/cTTtt	2/9	0.446520416708946	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.446520416708946	1		254	476	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699259	18699259	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs748575647	NA	P-0017534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	115	279	0	ENST00000266497.5:c.3360G>A	p.Met1120Ile	p.M1120I	ENST00000266497		1120	atG/atA	24/31	NA	2	FACETS	0.742	0.669	0.819			1	INDETERMINATE	1	TRUE	NA	0.446520416708946	2		279	694	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699338	18699338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	115	355	0	ENST00000266497.5:c.3439G>A	p.Asp1147Asn	p.D1147N	ENST00000266497		1147	Gac/Aac	24/31	NA	2	FACETS	0.615	0.553	0.68			1	INDETERMINATE	1	TRUE	NA	0.446520416708946	2		355	838	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217801	2217801	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1265	73	786	2	ENST00000398665.3:c.2578del	p.Glu860SerfsTer208	p.E860Sfs*208	ENST00000398665	NM_032482.2	859	Ggg/gg	22/28	1	2	FACETS	0.244	0.212	0.279	0.244	0.212	0.279	SUBCLONAL	1	TRUE	1	0.446520416708946	2		788	1338	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039369	47039369	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1198	498	868	0	ENST00000377604.3:c.992T>A	p.Val331Glu	p.V331E	ENST00000377604	NM_001204468.1	331	gTg/gAg	10/24	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.446520416708946	2		868	1696	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	230	301	4				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.794628821356838	2		305	543	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725043	89725043	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1057517809	NA	P-0017537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	376	361	0	ENST00000371953.3:c.1027-1G>A		p.X343_splice	ENST00000371953	NM_000314.4	343			0.794628821356838	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.794628821356838	1		361	532	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496924	29496927	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs786201874	NA	P-0017537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	211	177	0	ENST00000356175.3:c.499_502del	p.Cys167GlnfsTer10	p.C167Qfs*10	ENST00000356175	NM_000267.3	165	acTGTT/ac	5/57	1	2	FACETS	0.89	0.832	0.949	0.89	0.832	0.949	CLONAL	1	TRUE	1	0.794628821356838	2		177	597	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888195	112888195	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs397507512	NA	P-0017537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	478	474	0	ENST00000351677.2:c.211T>C	p.Phe71Leu	p.F71L	ENST00000351677	NM_002834.3	71	Ttt/Ctt	3/16	1	2	FACETS	0.898	0.859	0.937	0.898	0.859	0.937	CLONAL	1	TRUE	1	0.794628821356838	2		474	1340	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352510	89352510	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs978728438	NA	P-0017537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1437	968	995	0	ENST00000301030.4:c.829C>T	p.Pro277Ser	p.P277S	ENST00000301030	NM_001256183.1	277	Ccc/Tcc	8/13	0.102128386669722	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.794628821356838	0		995	2405	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657489	29657489	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	187	256	0	ENST00000356175.3:c.5722G>T	p.Glu1908Ter	p.E1908*	ENST00000356175	NM_000267.3	1908	Gag/Tag	38/57	1	2	FACETS	0.898	0.836	0.961	0.898	0.836	0.961	CLONAL	1	TRUE	1	0.794628821356838	2		256	524	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	138	308	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.561	0.513	0.611	0.561	0.513	0.611	SUBCLONAL	1	TRUE	1	0.912057234098622	2		308	539	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	73	178	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.537	0.474	0.604	0.537	0.474	0.604	SUBCLONAL	1	TRUE	1	0.912057234098622	2		178	298	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	221	498	3	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	1	2	FACETS	0.554	0.516	0.593	0.554	0.516	0.593	SUBCLONAL	1	TRUE	1	0.912057234098622	2		501	875	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1332	420	1074	7	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.526	0.499	0.553	0.526	0.499	0.553	SUBCLONAL	1	TRUE	1	0.912057234098622	2		1081	1752	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	229	465	7	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.493	0.46	0.528	0.493	0.46	0.528	SUBCLONAL	1	TRUE	1	0.912057234098622	2		472	1018	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3827631	3827631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141098117	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	218	507	1	ENST00000262367.5:c.2141G>A	p.Arg714His	p.R714H	ENST00000262367	NM_004380.2	714	cGc/cAc	11/31	1	2	FACETS	0.471	0.438	0.506	0.471	0.438	0.506	SUBCLONAL	1	TRUE	1	0.912057234098622	2		508	1014	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39744994	39744994	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	249	570	1	ENST00000361337.2:c.1784C>A	p.Ser595Tyr	p.S595Y	ENST00000361337	NM_003286.2	595	tCc/tAc	17/21	NA	2	FACETS	0.536	0.501	0.572			1	INDETERMINATE	1	TRUE	NA	0.912057234098622	2		571	1019	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456467	99456467	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56248469	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	185	462	0	ENST00000268035.6:c.1784G>A	p.Arg595His	p.R595H	ENST00000268035	NM_000875.3	595	cGt/cAt	8/21	1	2	FACETS	0.532	0.492	0.574	0.532	0.492	0.574	SUBCLONAL	1	TRUE	1	0.912057234098622	2		462	762	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593507	48593507	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1367209662	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	129	245	0	ENST00000342988.3:c.1258C>T	p.Arg420Cys	p.R420C	ENST00000342988	NM_005359.5	420	Cgt/Tgt	10/12	0.638185593165711	3	FACETS	0.531	0.482	0.584	0.266	0.241	0.292	SUBCLONAL	1	TRUE	1	0.912057234098622	3		245	775	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643768	52643768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	150	363	1	ENST00000394830.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000394830	NM_018313.4	710	Cga/Tga	17/30	1	2	FACETS	0.522	0.479	0.567	0.522	0.479	0.567	SUBCLONAL	1	TRUE	1	0.912057234098622	2		364	630	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434361	121434361	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs193922576	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	74	478	0	ENST00000257555.6:c.1129del	p.Leu377SerfsTer7	p.L377Sfs*7	ENST00000257555		375	ggC/gg	6/10	1	2	FACETS	0.228	0.199	0.259	0.228	0.199	0.259	SUBCLONAL	1	TRUE	1	0.912057234098622	2		478	711	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807363	3807364	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	40	281	0	ENST00000262367.5:c.3623dup	p.Gln1209ThrfsTer25	p.Q1209Tfs*25	ENST00000262367	NM_004380.2	1208	cca/ccCa	19/31	1	2	FACETS	0.12	0.099	0.143	0.12	0.099	0.143	SUBCLONAL	1	TRUE	1	0.912057234098622	2		281	731	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276860	15276861	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs753725730	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	157	392	5	ENST00000263388.2:c.5404dup	p.Ala1802GlyfsTer8	p.A1802Gfs*8	ENST00000263388	NM_000435.2	1802	gct/gGct	30/33	1	2	FACETS	0.517	0.475	0.561	0.517	0.475	0.561	SUBCLONAL	1	TRUE	1	0.912057234098622	2		397	666	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355296	15355296	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1282368628	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	44	106	0	ENST00000263377.2:c.2327C>T	p.Pro776Leu	p.P776L	ENST00000263377	NM_058243.2	776	cCg/cTg	13/20	1	2	FACETS	0.592	0.505	0.685	0.592	0.505	0.685	SUBCLONAL	1	TRUE	1	0.912057234098622	2		106	163	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435815	56435815	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755967475	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	84	249	0	ENST00000407977.2:c.1322del	p.Pro441LeufsTer61	p.P441Lfs*61	ENST00000407977		441	cCt/ct	9/10	1	2	FACETS	0.653	0.584	0.725	0.653	0.584	0.725	SUBCLONAL	1	TRUE	1	0.912057234098622	2		249	282	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431395	121431395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs893256143	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	79	508	0	ENST00000257555.6:c.599G>A	p.Arg200Gln	p.R200Q	ENST00000257555		200	cGg/cAg	3/10	1	2	FACETS	0.219	0.192	0.248	0.219	0.192	0.248	SUBCLONAL	1	TRUE	1	0.912057234098622	2		508	792	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180651	56180651	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	24	262	0	ENST00000399503.3:c.3980C>T	p.Ala1327Val	p.A1327V	ENST00000399503	NM_005921.1	1327	gCa/gTa	16/20	1	2	FACETS	0.141	0.11	0.177	0.141	0.11	0.177	SUBCLONAL	1	TRUE	1	0.912057234098622	2		262	373	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199402	11199402	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	195	529	0	ENST00000361445.4:c.5089A>C	p.Thr1697Pro	p.T1697P	ENST00000361445	NM_004958.3	1697	Acc/Ccc	36/58	1	2	FACETS	0.498	0.462	0.536	0.498	0.462	0.536	SUBCLONAL	1	TRUE	1	0.912057234098622	2		529	858	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256448	115256448	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	174	468	0	ENST00000369535.4:c.263A>G	p.Lys88Arg	p.K88R	ENST00000369535	NM_002524.4	88	aAg/aGg	3/7	1	2	FACETS	0.441	0.406	0.477	0.441	0.406	0.477	SUBCLONAL	1	TRUE	1	0.912057234098622	2		468	865	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091437	193091437	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	161	465	0	ENST00000367435.3:c.107T>C	p.Val36Ala	p.V36A	ENST00000367435	NM_024529.4	36	gTg/gCg	1/17	0.889920238553195	3	FACETS	0.431	0.394	0.47	0.216	0.197	0.235	SUBCLONAL	1	TRUE	1	0.912057234098622	3		465	1192	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570740	226570740	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	74	165	0	ENST00000366794.5:c.1156G>T	p.Ala386Ser	p.A386S	ENST00000366794	NM_001618.3	386	Gca/Tca	8/23	0.889920238553195	3	FACETS	0.471	0.413	0.533	0.235	0.206	0.267	SUBCLONAL	1	TRUE	1	0.912057234098622	3		165	502	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226576366	226576366	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1561	147	648	0	ENST00000366794.5:c.708del	p.Ala237ProfsTer2	p.A237Pfs*2	ENST00000366794	NM_001618.3	236	aaA/aa	5/23	0.889920238553195	3	FACETS	0.275	0.249	0.302	0.137	0.124	0.151	SUBCLONAL	1	TRUE	1	0.912057234098622	3		648	1708	SUCCESS
FH	2271	MSKCC	GRCh37	1	241661249	241661249	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	134	311	0	ENST00000366560.3:c.1412T>C	p.Ile471Thr	p.I471T	ENST00000366560	NM_000143.3	471	aTt/aCt	10/10	0.889920238553195	3	FACETS	0.505	0.459	0.554	0.253	0.229	0.277	SUBCLONAL	1	TRUE	1	0.912057234098622	3		311	847	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450676	70450676	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	220	606	0	ENST00000373644.4:c.5516A>G	p.His1839Arg	p.H1839R	ENST00000373644	NM_030625.2	1839	cAc/cGc	12/12	1	2	FACETS	0.46	0.428	0.493	0.46	0.428	0.493	SUBCLONAL	1	TRUE	1	0.912057234098622	2		606	1049	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416961	416961	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	40	422	0	ENST00000399788.2:c.3589del	p.Gln1197LysfsTer12	p.Q1197Kfs*12	ENST00000399788	NM_001042603.1	1197	Caa/aa	23/28	1	2	FACETS	0.11	0.09	0.131	0.11	0.09	0.131	SUBCLONAL	1	TRUE	1	0.912057234098622	2		422	799	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416961	416961	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	148	422	0	ENST00000399788.2:c.3589C>A	p.Gln1197Lys	p.Q1197K	ENST00000399788	NM_001042603.1	1197	Caa/Aaa	23/28	1	2	FACETS	0.406	0.371	0.443	0.406	0.371	0.443	SUBCLONAL	1	TRUE	1	0.912057234098622	2		422	799	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	422302	422302	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	82	516	0	ENST00000399788.2:c.2956G>C	p.Ala986Pro	p.A986P	ENST00000399788	NM_001042603.1	986	Gcc/Ccc	20/28	1	2	FACETS	0.189	0.166	0.214	0.189	0.166	0.214	SUBCLONAL	1	TRUE	1	0.912057234098622	2		516	949	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557483	21557483	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	254	672	0	ENST00000382592.4:c.2362A>G	p.Ile788Val	p.I788V	ENST00000382592	NM_014572.2	788	Atc/Gtc	5/8	1	2	FACETS	0.471	0.44	0.503	0.471	0.44	0.503	SUBCLONAL	1	TRUE	1	0.912057234098622	2		672	1182	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563281	21563281	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	89	582	0	ENST00000382592.4:c.638A>G	p.Asp213Gly	p.D213G	ENST00000382592	NM_014572.2	213	gAc/gGc	4/8	1	2	FACETS	0.242	0.214	0.271	0.242	0.214	0.271	SUBCLONAL	1	TRUE	1	0.912057234098622	2		582	808	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601267	28601267	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	192	489	0	ENST00000241453.7:c.2165A>C	p.Asn722Thr	p.N722T	ENST00000241453	NM_004119.2	722	aAt/aCt	17/24	1	2	FACETS	0.44	0.407	0.475	0.44	0.407	0.475	SUBCLONAL	1	TRUE	1	0.912057234098622	2		489	956	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953761	48953761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769425649	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	103	276	0	ENST00000267163.4:c.1364G>A	p.Arg455Gln	p.R455Q	ENST00000267163	NM_000321.2	455	cGa/cAa	14/27	1	2	FACETS	0.339	0.303	0.376	0.339	0.303	0.376	SUBCLONAL	1	TRUE	1	0.912057234098622	2		276	667	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434454	110434454	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	200	621	0	ENST00000375856.3:c.3947del	p.Pro1316LeufsTer15	p.P1316Lfs*15	ENST00000375856	NM_003749.2	1316	cCt/ct	1/2	1	2	FACETS	0.496	0.459	0.533	0.496	0.459	0.533	SUBCLONAL	1	TRUE	1	0.912057234098622	2		621	885	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574830	95574830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	56	308	0	ENST00000393063.1:c.2267G>A	p.Cys756Tyr	p.C756Y	ENST00000393063	NM_030621.3	756	tGt/tAt	16/28	1	2	FACETS	0.229	0.196	0.265	0.229	0.196	0.265	SUBCLONAL	1	TRUE	1	0.912057234098622	2		308	537	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213960	2213961	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs753146456	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1299	147	798	0	ENST00000326181.6:c.45dup	p.Pro16AlafsTer33	p.P16Afs*33	ENST00000326181	NM_032271.2	13	-/G	2/21	1	2	FACETS	0.223	0.202	0.244	0.223	0.202	0.244	SUBCLONAL	1	TRUE	1	0.912057234098622	2		798	1446	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663407	67663407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763046858	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	195	399	0	ENST00000264010.4:c.1808G>A	p.Arg603His	p.R603H	ENST00000264010	NM_006565.3	603	cGc/cAc	10/12	1	2	FACETS	0.505	0.468	0.544	0.505	0.468	0.544	SUBCLONAL	1	TRUE	1	0.912057234098622	2		399	846	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627658	37627659	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	259	715	0	ENST00000447079.4:c.1577dup	p.Pro527SerfsTer48	p.P527Sfs*48	ENST00000447079	NM_015083.1	525	acc/aCcc	2/14	1	2	FACETS	0.532	0.498	0.567	0.532	0.498	0.567	SUBCLONAL	1	TRUE	1	0.912057234098622	2		715	1067	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508273	38508273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779485530	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	237	570	0	ENST00000254066.5:c.581C>T	p.Ala194Val	p.A194V	ENST00000254066	NM_000964.3	194	gCg/gTg	5/9	1	2	FACETS	0.545	0.509	0.583	0.545	0.509	0.583	SUBCLONAL	1	TRUE	1	0.912057234098622	2		570	953	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459513	40459513	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1268	411	1061	1	ENST00000345506.4:c.1774G>A	p.Gly592Arg	p.G592R	ENST00000345506	NM_003152.3	592	Ggg/Agg	15/20	1	2	FACETS	0.537	0.51	0.565	0.537	0.51	0.565	SUBCLONAL	1	TRUE	1	0.912057234098622	2		1062	1679	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637943	39637944	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1247541427	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	160	410	0	ENST00000262039.4:c.2366dup	p.Thr790HisfsTer4	p.T790Hfs*4	ENST00000262039	NM_002647.2	787	atg/atGg	22/25	0.638185593165711	3	FACETS	0.562	0.515	0.611	0.281	0.257	0.306	SUBCLONAL	1	TRUE	1	0.912057234098622	3		410	909	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143096	7143096	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	120	275	0	ENST00000302850.5:c.2273C>A	p.Ser758Tyr	p.S758Y	ENST00000302850	NM_000208.2	758	tCt/tAt	12/22	1	2	FACETS	0.522	0.474	0.573	0.522	0.474	0.573	SUBCLONAL	1	TRUE	1	0.912057234098622	2		275	504	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610561	10610561	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766652922	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	174	451	0	ENST00000171111.5:c.149G>A	p.Arg50His	p.R50H	ENST00000171111	NM_203500.1	50	cGc/cAc	2/6	1	2	FACETS	0.473	0.436	0.512	0.473	0.436	0.512	SUBCLONAL	1	TRUE	1	0.912057234098622	2		451	806	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290896	15290896	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	315	867	2	ENST00000263388.2:c.3314del	p.Gly1105AlafsTer167	p.G1105Afs*167	ENST00000263388	NM_000435.2	1105	gGc/gc	20/33	1	2	FACETS	0.512	0.482	0.543	0.512	0.482	0.543	SUBCLONAL	1	TRUE	1	0.912057234098622	2		869	1349	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350583	15350583	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1044584643	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	108	380	0	ENST00000263377.2:c.3332A>G	p.Lys1111Arg	p.K1111R	ENST00000263377	NM_058243.2	1111	aAg/aGg	16/20	1	2	FACETS	0.412	0.37	0.456	0.412	0.37	0.456	SUBCLONAL	1	TRUE	1	0.912057234098622	2		380	575	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910429	50910429	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	331	964	0	ENST00000440232.2:c.1684C>T	p.Gln562Ter	p.Q562*	ENST00000440232	NM_002691.3	562	Cag/Tag	13/27	1	2	FACETS	0.494	0.466	0.523	0.494	0.466	0.523	SUBCLONAL	1	TRUE	1	0.912057234098622	2		964	1468	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022346	26022346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	269	624	1	ENST00000435504.4:c.311G>A	p.Gly104Asp	p.G104D	ENST00000435504		104	gGt/gAt	5/13	1	2	FACETS	0.531	0.498	0.566	0.531	0.498	0.566	SUBCLONAL	1	TRUE	1	0.912057234098622	2		625	1110	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641441	47641441	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1338	420	913	0	ENST00000233146.2:c.830del	p.Leu277Ter	p.L277*	ENST00000233146	NM_000251.2	276	Ttt/tt	5/16	1	2	FACETS	0.524	0.497	0.551	0.524	0.497	0.551	SUBCLONAL	1	TRUE	1	0.912057234098622	2		913	1758	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097254	178097254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763327009	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	183	396	0	ENST00000397062.3:c.460C>T	p.Pro154Ser	p.P154S	ENST00000397062	NM_006164.4	154	Cca/Tca	4/5	1	2	FACETS	0.523	0.483	0.563	0.523	0.483	0.563	SUBCLONAL	1	TRUE	1	0.912057234098622	2		396	768	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661891	227661891	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	97	295	0	ENST00000305123.5:c.1564C>T	p.Arg522Ter	p.R522*	ENST00000305123	NM_005544.2	522	Cga/Tga	1/2	1	2	FACETS	0.463	0.415	0.514	0.463	0.415	0.514	SUBCLONAL	1	TRUE	1	0.912057234098622	2		295	459	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394097	31394097	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	122	281	0	ENST00000328111.2:c.2384G>A	p.Gly795Asp	p.G795D	ENST00000328111	NM_006892.3	795	gGc/gAc	22/23	1	2	FACETS	0.475	0.431	0.522	0.475	0.431	0.522	SUBCLONAL	1	TRUE	1	0.912057234098622	2		281	563	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980756	40980756	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	158	361	0	ENST00000373198.4:c.1730del	p.Pro577LeufsTer24	p.P577Lfs*24	ENST00000373198	NM_133170.3	577	cCt/ct	10/32	NA	2	FACETS	0.489	0.449	0.531			1	INDETERMINATE	1	TRUE	NA	0.912057234098622	2		361	708	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485124	57485124	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	55	355	0	ENST00000371085.3:c.958A>G	p.Thr320Ala	p.T320A	ENST00000371085	NM_000516.4	320	Act/Gct	11/13	NA	2	FACETS	0.19	0.162	0.221			1	INDETERMINATE	1	TRUE	NA	0.912057234098622	2		355	635	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259210	36259210	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	219	471	0	ENST00000300305.3:c.281G>A	p.Ser94Asn	p.S94N	ENST00000300305		94	aGc/aAc	3/8	1	2	FACETS	0.617	0.576	0.66	0.617	0.576	0.66	SUBCLONAL	1	TRUE	1	0.912057234098622	2		471	778	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095910	29095910	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	260	603	0	ENST00000328354.6:c.924G>C	p.Glu308Asp	p.E308D	ENST00000328354	NM_007194.3	308	gaG/gaC	9/15	1	2	FACETS	0.486	0.454	0.518	0.486	0.454	0.518	SUBCLONAL	1	TRUE	1	0.912057234098622	2		603	1174	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405933	49405933	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	336	815	0	ENST00000418115.1:c.205C>A	p.Leu69Met	p.L69M	ENST00000418115	NM_001664.2	69	Ctg/Atg	3/5	1	2	FACETS	0.519	0.489	0.548	0.519	0.489	0.548	SUBCLONAL	1	TRUE	1	0.912057234098622	2		815	1421	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499362	89499363	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	47	388	0	ENST00000336596.2:c.2538dup	p.Met847HisfsTer26	p.M847Hfs*26	ENST00000336596	NM_005233.5	844	-/C	15/17	1	2	FACETS	0.143	0.12	0.169	0.143	0.12	0.169	SUBCLONAL	1	TRUE	1	0.912057234098622	2		388	720	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201648	66201648	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	177	557	0	ENST00000273854.3:c.2852+2T>C		p.X951_splice	ENST00000273854	NM_004439.5	951			1	2	FACETS	0.476	0.439	0.515	0.476	0.439	0.515	SUBCLONAL	1	TRUE	1	0.912057234098622	2		557	815	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280092	66280092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	162	455	0	ENST00000273854.3:c.1597G>A	p.Ala533Thr	p.A533T	ENST00000273854	NM_004439.5	533	Gct/Act	7/18	1	2	FACETS	0.457	0.419	0.495	0.457	0.419	0.495	SUBCLONAL	1	TRUE	1	0.912057234098622	2		455	778	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356149	66356149	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	202	408	0	ENST00000273854.3:c.1348T>A	p.Leu450Met	p.L450M	ENST00000273854	NM_004439.5	450	Ttg/Atg	5/18	1	2	FACETS	0.544	0.505	0.584	0.544	0.505	0.584	SUBCLONAL	1	TRUE	1	0.912057234098622	2		408	815	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164880	106164880	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415830017	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	123	296	0	ENST00000380013.4:c.3748G>A	p.Glu1250Lys	p.E1250K	ENST00000380013	NM_001127208.2	1250	Gag/Aag	6/11	1	2	FACETS	0.468	0.425	0.514	0.468	0.425	0.514	SUBCLONAL	1	TRUE	1	0.912057234098622	2		296	576	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629776	187629776	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	195	489	1	ENST00000441802.2:c.1206del	p.Phe402LeufsTer12	p.F402Lfs*12	ENST00000441802	NM_005245.3	402	ttT/tt	2/27	1	2	FACETS	0.427	0.395	0.46	0.427	0.395	0.46	SUBCLONAL	1	TRUE	1	0.912057234098622	2		490	1002	SUCCESS
APC	324	MSKCC	GRCh37	5	112177022	112177022	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	248	653	0	ENST00000257430.4:c.5731C>G	p.Gln1911Glu	p.Q1911E	ENST00000257430	NM_000038.5	1911	Caa/Gaa	16/16	1	2	FACETS	0.522	0.488	0.557	0.522	0.488	0.557	SUBCLONAL	1	TRUE	1	0.912057234098622	2		653	1042	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718186	117718186	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs771923036	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	58	358	0	ENST00000368508.3:c.671C>A	p.Pro224His	p.P224H	ENST00000368508	NM_002944.2	224	cCt/cAt	7/43	1	2	FACETS	0.167	0.143	0.194	0.167	0.143	0.194	SUBCLONAL	1	TRUE	1	0.912057234098622	2		358	760	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202265	138202265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373799889	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	166	430	0	ENST00000237289.4:c.2182C>T	p.Arg728Cys	p.R728C	ENST00000237289	NM_001270507.1	728	Cgc/Tgc	9/9	1	2	FACETS	0.547	0.504	0.591	0.547	0.504	0.591	SUBCLONAL	1	TRUE	1	0.912057234098622	2		430	666	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233127	55233127	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	137	282	1	ENST00000275493.2:c.1877A>G	p.Tyr626Cys	p.Y626C	ENST00000275493	NM_005228.3	626	tAc/tGc	15/28	1	2	FACETS	0.549	0.502	0.598	0.549	0.502	0.598	SUBCLONAL	1	TRUE	1	0.912057234098622	2		283	547	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81399262	81399262	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1049311043	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	64	338	0	ENST00000222390.5:c.26C>T	p.Ala9Val	p.A9V	ENST00000222390	NM_000601.4	9	gCc/gTc	1/18	1	2	FACETS	0.214	0.185	0.246	0.214	0.185	0.246	SUBCLONAL	1	TRUE	1	0.912057234098622	2		338	656	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508650	106508650	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs771142900	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	118	412	0	ENST00000359195.3:c.644T>C	p.Ile215Thr	p.I215T	ENST00000359195	NM_002649.2	215	aTt/aCt	2/11	1	2	FACETS	0.384	0.347	0.423	0.384	0.347	0.423	SUBCLONAL	1	TRUE	1	0.912057234098622	2		412	674	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545779	106545779	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	136	333	0	ENST00000359195.3:c.3256T>C	p.Trp1086Arg	p.W1086R	ENST00000359195	NM_002649.2	1086	Tgg/Cgg	11/11	1	2	FACETS	0.501	0.457	0.547	0.501	0.457	0.547	SUBCLONAL	1	TRUE	1	0.912057234098622	2		333	595	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145736900	145736900	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs765804620	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	92	551	0	ENST00000428558.2:c.3541C>T	p.Arg1181Ter	p.R1181*	ENST00000428558	NM_004260.3	1181	Cga/Tga	22/22	1	2	FACETS	0.216	0.191	0.242	0.216	0.191	0.242	SUBCLONAL	1	TRUE	1	0.912057234098622	2		551	935	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760858	133760858	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs869073622	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	202	618	0	ENST00000318560.5:c.3185del	p.Asn1062ThrfsTer7	p.N1062Tfs*7	ENST00000318560	NM_005157.4	1061	Aaa/aa	11/11	1	2	FACETS	0.469	0.435	0.505	0.469	0.435	0.505	SUBCLONAL	1	TRUE	1	0.912057234098622	2		618	944	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793245	139793245	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1173	442	1024	3	ENST00000247668.2:c.53G>A	p.Gly18Asp	p.G18D	ENST00000247668	NM_021138.3	18	gGc/gAc	2/11	1	2	FACETS	0.6	0.571	0.63	0.6	0.571	0.63	SUBCLONAL	1	TRUE	1	0.912057234098622	2		1027	1615	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15818064	15818064	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	248	276	0	ENST00000307771.7:c.191T>C	p.Leu64Ser	p.L64S	ENST00000307771	NM_005089.3	64	tTg/tCg	3/11	1	1	FACETS	0.542	0.511	0.572	0.542	0.511	0.572	SUBCLONAL	1	TRUE	0	0.912057234098622	1		276	546	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349620	70349620	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1388327076	NA	P-0017538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	342	437	1	ENST00000374080.3:c.3782G>A	p.Arg1261Gln	p.R1261Q	ENST00000374080		1261	cGg/cAg	27/45	1	1	FACETS	0.568	0.542	0.595	0.568	0.542	0.595	SUBCLONAL	1	TRUE	0	0.912057234098622	1		438	718	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0017540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	164	525	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.32459692439448	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.32459692439448	1		525	698	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0017540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	141	348	1	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.32459692439448	2		349	712	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591889	48591889	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1060500741	NA	P-0017540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	204	489	0	ENST00000342988.3:c.1052A>T	p.Asp351Val	p.D351V	ENST00000342988	NM_005359.5	351	gAt/gTt	9/12	0.32459692439448	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.32459692439448	1		489	998	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730915	40730915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753788938	NA	P-0017540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	137	272	0	ENST00000373198.4:c.3620G>A	p.Arg1207His	p.R1207H	ENST00000373198	NM_133170.3	1207	cGt/cAt	27/32	0.32459692439448	3	FACETS	1	0.985	1	0.714	0.651	0.78	CLONAL	1	TRUE	1	0.32459692439448	3		272	687	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101712	27101712	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0017540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	137	361	0	ENST00000324856.7:c.4993+1G>C		p.X1665_splice	ENST00000324856	NM_006015.4	1665			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.32459692439448	2		361	722	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0017542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	265	822	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.321425243208343	2	FACETS	0.903	0.849	0.959	0.903	0.849	0.959	CLONAL	2	TRUE	0	0.337216206291989	2		822	870	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119306	3119306	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	118	758	0	ENST00000078429.4:c.838G>C	p.Glu280Gln	p.E280Q	ENST00000078429	NM_002067.2	280	Gag/Cag	6/7	1	2	FACETS	0.772	0.695	0.852	0.772	0.695	0.852	SUBCLONAL	1	TRUE	1	0.337216206291989	2		758	907	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105237098	105237098	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	84	602	0	ENST00000349310.3:c.1347C>G	p.Ile449Met	p.I449M	ENST00000349310	NM_001014432.1	449	atC/atG	14/15	0.199382673852338	3	FACETS	0.889	0.785	1	0.296	0.261	0.334	INDETERMINATE	1	TRUE	0	0.337216206291989	3		602	655	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256962	41256963	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0017542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	100	364	0	ENST00000357654.3:c.223_224del	p.Glu75LysfsTer5	p.E75Kfs*5	ENST00000357654	NM_007294.3	75	GAa/a	5/23	0.337216206291989	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.337216206291989	1		364	396	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228364	228364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	77	380	0	ENST00000264932.6:c.686G>A	p.Gly229Glu	p.G229E	ENST00000264932	NM_004168.2	229	gGg/gAg	6/15	0.337216206291989	3	FACETS	0.819	0.719	0.926	0.409	0.359	0.463	CLONAL	1	TRUE	1	0.337216206291989	3		380	652	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0017543-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	232	552	0	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	0.448130744070117	2	FACETS	0.953	0.897	1	0.953	0.897	1	CLONAL	2	TRUE	0	0.448130744070117	2		552	543	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061205	38061205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017543-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	128	306	0	ENST00000250448.2:c.784C>T	p.Arg262Cys	p.R262C	ENST00000250448	NM_004496.3	262	Cgc/Tgc	2/2	0.14082412419137	6	FACETS	0.926	0.848	1	0.926	0.848	1	INDETERMINATE	3	TRUE	3	0.448130744070117	6		306	390	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453132	140453132	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913365	NA	P-0017543-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	1095	335	0	ENST00000288602.6:c.1803A>C	p.Lys601Asn	p.K601N	ENST00000288602	NM_004333.4	601	aaA/aaC	15/18	0.448130744070117	14	FACETS	1	0.993	1	1	0.993	1	CLONAL	14	TRUE	0	0.448130744070117	14		335	1272	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226564945	226564945	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017543-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	303	434	0	ENST00000366794.5:c.1805A>T	p.Glu602Val	p.E602V	ENST00000366794	NM_001618.3	602	gAa/gTa	13/23	0.347520586571995	5	FACETS	0.996	0.943	1	0.996	0.943	1	CLONAL	3	TRUE	2	0.448130744070117	5		434	757	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032158	10032158	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017543-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	97	466	0	ENST00000330684.3:c.665T>C	p.Ile222Thr	p.I222T	ENST00000330684	NM_001134407.1	222	aTc/aCc	3/13	0.448130744070117	3	FACETS	1	0.921	1	0.517	0.463	0.575	CLONAL	1	TRUE	1	0.448130744070117	3		466	512	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0017545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	307	367	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.368746838018685	5	FACETS	1	0.991	1	0.832	0.786	0.88	CLONAL	2	TRUE	2	0.392853824674715	5		367	995	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781504	NA	P-0017545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	226	489	0	ENST00000269305.4:c.314G>A	p.Gly105Asp	p.G105D	ENST00000269305	NM_001126112.2	105	gGc/gAc	4/11	0.392853824674715	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.392853824674715	1		489	682	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941669	48941669	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	88	256	0	ENST00000267163.4:c.983del	p.Asn328IlefsTer4	p.N328Ifs*4	ENST00000267163	NM_000321.2	327	Aaa/aa	10/27	0.392853824674715	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.392853824674715	1		256	266	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515025	148515025	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	307	495	1	ENST00000320356.2:c.1184G>A	p.Gly395Glu	p.G395E	ENST00000320356	NM_004456.4	395	gGa/gAa	10/20	0.195194305313206	4	FACETS	0.881	0.83	0.934	0.881	0.83	0.934	INDETERMINATE	2	TRUE	2	0.392853824674715	4		496	1235	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865371	57865371	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2321	235	1214	0	ENST00000228682.2:c.2848C>G	p.Pro950Ala	p.P950A	ENST00000228682	NM_005269.2	950	Cct/Gct	12/12	1	2	FACETS	0.468	0.434	0.504	0.468	0.434	0.504	SUBCLONAL	1	TRUE	1	0.392853824674715	2		1214	2556	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991805	72991805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1668	383	920	0	ENST00000268489.5:c.2240C>T	p.Ser747Phe	p.S747F	ENST00000268489	NM_006885.3	747	tCt/tTt	2/10	0.163504315268482	3	FACETS	1	0.988	1	0.569	0.538	0.6	INDETERMINATE	1	TRUE	1	0.392853824674715	3		920	2051	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498316	29498316	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	203	547	0	ENST00000389048.3:c.1864A>G	p.Ile622Val	p.I622V	ENST00000389048	NM_004304.4	622	Atc/Gtc	10/29	0.226849769281695	1	FACETS	0.763	0.707	0.822	0.763	0.707	0.822	INDETERMINATE	1	TRUE	0	0.392853824674715	1		547	1088	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149498383	149498383	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	217	412	0	ENST00000261799.4:c.2831A>C	p.Lys944Thr	p.K944T	ENST00000261799	NM_002609.3	944	aAg/aCg	21/23	NA	2	FACETS	0.919	0.853	0.987			1	INDETERMINATE	1	TRUE	NA	0.392853824674715	2		412	1202	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0017546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	181	401	3	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.36414767660927	2		404	756	SUCCESS
ATM	472	MSKCC	GRCh37	11	108154953	108154953	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0017546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	63	84	0	ENST00000278616.4:c.3747-1G>T		p.X1249_splice	ENST00000278616	NM_000051.3	1249			0.36414767660927	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.36414767660927	1		84	210	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562744	21562744	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1442338961	NA	P-0017546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	39	137	0	ENST00000382592.4:c.1175C>T	p.Ala392Val	p.A392V	ENST00000382592	NM_014572.2	392	gCg/gTg	4/8	0.305253467768004	1	FACETS	0.664	0.553	0.785	0.664	0.553	0.785	SUBCLONAL	1	TRUE	0	0.36414767660927	1		137	264	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827441	72827441	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1706	113	1064	1	ENST00000268489.5:c.9140A>T	p.Gln3047Leu	p.Q3047L	ENST00000268489	NM_006885.3	3047	cAg/cTg	9/10	NA	2	FACETS	0.341	0.305	0.38			1	INDETERMINATE	1	TRUE	NA	0.36414767660927	2		1065	1819	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654605	29654605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555533569	NA	P-0017546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	73	417	0	ENST00000356175.3:c.5294C>T	p.Ser1765Leu	p.S1765L	ENST00000356175	NM_000267.3	1765	tCg/tTg	37/57	0.190143364843683	3	FACETS	0.449	0.391	0.511	0.224	0.195	0.256	INDETERMINATE	1	TRUE	1	0.36414767660927	3		417	1056	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198228	138198228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	38	177	0	ENST00000237289.4:c.821C>T	p.Pro274Leu	p.P274L	ENST00000237289	NM_001270507.1	274	cCa/cTa	6/9	0.182427784802185	0	FACETS	0.28	0.231	0.335			1	INDETERMINATE	1	TRUE	0	0.36414767660927	0		177	474	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041234	47041234	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1179	391	760	0	ENST00000377604.3:c.1665del	p.Thr556LeufsTer148	p.T556Lfs*148	ENST00000377604	NM_001204468.1	554	agC/ag	15/24	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.36414767660927	2		760	1570	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0017547-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	22	438	1	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	1	0.875	1	1	0.962	1	CLONAL	3	TRUE	1	0.3	2		439	45	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894228	NA	P-0017547-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	15	595	0	ENST00000451590.1:c.37G>C	p.Gly13Arg	p.G13R	ENST00000451590	NM_001130442.1	13	Ggt/Cgt	2/5	1	2	FACETS	1	0.828	1	1	0.932	1	CLONAL	2	TRUE	1	0.3	2		595	45	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	181	438	1	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.918	0.851	0.988	1	0.994	1	CLONAL	3	TRUE	1	0.204975731260445	2		439	641	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894228	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	150	595	0	ENST00000451590.1:c.37G>C	p.Gly13Arg	p.G13R	ENST00000451590	NM_001130442.1	13	Ggt/Cgt	2/5	0.204975731260445	1	FACETS	1	0.967	1	1	0.992	1	CLONAL	2	TRUE	0	0.204975731260445	1		595	595	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056402	180056402	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	98	385	0	ENST00000261937.6:c.842A>G	p.Glu281Gly	p.E281G	ENST00000261937	NM_182925.4	281	gAg/gGg	7/30	1	2	FACETS	0.889	0.795	0.987	1	0.985	1	CLONAL	2	TRUE	1	0.204975731260445	2		385	538	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601963	43601963	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	257	716	0	ENST00000355710.3:c.1007A>C	p.Asn336Thr	p.N336T	ENST00000355710	NM_020975.4	336	aAc/aCc	5/20	1	2	FACETS	0.861	0.807	0.916	1	0.996	1	CLONAL	3	TRUE	1	0.204975731260445	2		716	971	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782319	9782319	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	49	536	0	ENST00000377346.4:c.2252T>A	p.Phe751Tyr	p.F751Y	ENST00000377346	NM_005026.3	751	tTc/tAc	18/24	1	2	FACETS	0.665	0.562	0.779	0.665	0.562	0.779	SUBCLONAL	1	TRUE	1	0.204975731260445	2		536	719	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288816	11288816	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	189	499	0	ENST00000361445.4:c.2939A>G	p.Lys980Arg	p.K980R	ENST00000361445	NM_004958.3	980	aAg/aGg	19/58	1	2	FACETS	1	0.953	1	1	0.995	1	CLONAL	3	TRUE	1	0.204975731260445	2		499	595	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598922	28598922	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	99	614	0	ENST00000253063.3:c.482A>T	p.Glu161Val	p.E161V	ENST00000253063	NM_031459.4	161	gAg/gTg	4/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.204975731260445	2		614	714	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807543	36807543	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	147	569	0	ENST00000373129.3:c.1121A>C	p.Glu374Ala	p.E374A	ENST00000373129	NM_032017.1	374	gAg/gCg	12/12	1	2	FACETS	1	0.957	1	1	0.992	1	CLONAL	2	TRUE	1	0.204975731260445	2		569	669	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736577	85736577	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	58	311	0	ENST00000370580.1:c.70T>G	p.Leu24Val	p.L24V	ENST00000370580	NM_003921.4	24	Tta/Gta	2/3	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.204975731260445	2		311	434	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874212	155874212	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1431	216	672	0	ENST00000368323.3:c.319A>C	p.Ser107Arg	p.S107R	ENST00000368323	NM_006912.5	107	Agt/Cgt	5/6	0.204975731260445	7	FACETS	0.968	0.896	1	0.323	0.298	0.348	CLONAL	2	TRUE	1	0.204975731260445	7		672	1647	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406123	70406123	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	96	804	0	ENST00000373644.4:c.3637A>C	p.Ile1213Leu	p.I1213L	ENST00000373644	NM_030625.2	1213	Att/Ctt	4/12	1	2	FACETS	0.959	0.853	1	0.959	0.853	1	CLONAL	1	TRUE	1	0.204975731260445	2		804	977	SUCCESS
ATM	472	MSKCC	GRCh37	11	108225559	108225559	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	42	492	0	ENST00000278616.4:c.8808A>C	p.Glu2936Asp	p.E2936D	ENST00000278616	NM_000051.3	2936	gaA/gaC	61/63	0.204975731260445	1	FACETS	0.567	0.472	0.672	0.567	0.472	0.672	SUBCLONAL	1	TRUE	0	0.204975731260445	1		492	649	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18576886	18576886	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1338280478	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	214	563	0	ENST00000266497.5:c.2294A>C	p.Lys765Thr	p.K765T	ENST00000266497		765	aAg/aCg	16/31	1	2	FACETS	0.903	0.841	0.966	1	0.995	1	CLONAL	3	TRUE	1	0.204975731260445	2		563	771	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211630	46211630	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	68	455	0	ENST00000334344.6:c.596T>G	p.Ile199Ser	p.I199S	ENST00000334344	NM_152641.2	199	aTc/aGc	5/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.204975731260445	2		455	536	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910749	32910749	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	207	692	0	ENST00000380152.3:c.2257T>G	p.Phe753Val	p.F753V	ENST00000380152		753	Ttt/Gtt	11/27	1	2	FACETS	1	0.984	1	1	0.994	1	CLONAL	2	TRUE	1	0.204975731260445	2		692	843	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911613	32911613	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876658343	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	40	547	0	ENST00000380152.3:c.3121A>G	p.Ser1041Gly	p.S1041G	ENST00000380152		1041	Agt/Ggt	11/27	1	2	FACETS	0.621	0.515	0.74	0.621	0.515	0.74	SUBCLONAL	1	TRUE	1	0.204975731260445	2		547	628	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518642	103518642	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1279680274	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	80	368	0	ENST00000355739.4:c.2230T>G	p.Leu744Val	p.L744V	ENST00000355739	NM_000123.3	744	Tta/Gta	10/15	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.204975731260445	2		368	546	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36989277	36989277	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	75	536	0	ENST00000354822.5:c.58A>G	p.Ser20Gly	p.S20G	ENST00000354822	NM_001079668.2	20	Agc/Ggc	1/3	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.204975731260445	2		536	655	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557441	95557441	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	78	434	0	ENST00000393063.1:c.5533T>G	p.Phe1845Val	p.F1845V	ENST00000393063	NM_030621.3	1845	Ttt/Gtt	27/28	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.204975731260445	2		434	642	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052576	42052576	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	60	466	0	ENST00000219905.7:c.7247A>C	p.Lys2416Thr	p.K2416T	ENST00000219905	NM_001164273.1	2416	aAa/aCa	20/24	1	2	FACETS	0.879	0.757	1	0.879	0.757	1	CLONAL	1	TRUE	1	0.204975731260445	2		466	666	SUCCESS
BLM	641	MSKCC	GRCh37	15	91298126	91298126	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	165	550	0	ENST00000355112.3:c.1045A>G	p.Ser349Gly	p.S349G	ENST00000355112	NM_000057.2	349	Agt/Ggt	5/22	1	2	FACETS	1	0.983	1	1	0.993	1	CLONAL	2	TRUE	1	0.204975731260445	2		550	651	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339526	339526	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	259	788	0	ENST00000262320.3:c.2376A>C	p.Glu792Asp	p.E792D	ENST00000262320	NM_003502.3	792	gaA/gaC	10/11	1	2	FACETS	0.899	0.843	0.956	1	0.996	1	CLONAL	3	TRUE	1	0.204975731260445	2		788	937	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639843	3639843	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	35	568	0	ENST00000294008.3:c.3796A>C	p.Ser1266Arg	p.S1266R	ENST00000294008	NM_032444.2	1266	Agc/Cgc	12/15	1	2	FACETS	0.523	0.427	0.631	0.523	0.427	0.631	SUBCLONAL	1	TRUE	1	0.204975731260445	2		568	653	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670704	67670704	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	159	677	0	ENST00000264010.4:c.1949A>C	p.Lys650Thr	p.K650T	ENST00000264010	NM_006565.3	650	aAg/aCg	11/12	1	2	FACETS	0.898	0.823	0.976	1	0.991	1	CLONAL	2	TRUE	1	0.204975731260445	2		677	864	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81904518	81904518	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	144	386	0	ENST00000359376.3:c.626T>G	p.Leu209Arg	p.L209R	ENST00000359376	NM_002661.3	209	cTt/cGt	7/33	1	2	FACETS	1	0.971	1	1	0.992	1	CLONAL	2	TRUE	1	0.204975731260445	2		386	617	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527466	29527466	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	62	467	0	ENST00000356175.3:c.915A>C	p.Lys305Asn	p.K305N	ENST00000356175	NM_000267.3	305	aaA/aaC	9/57	1	2	FACETS	0.908	0.784	1	0.908	0.784	1	CLONAL	1	TRUE	1	0.204975731260445	2		467	666	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654850	29654850	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	36	260	0	ENST00000356175.3:c.5539A>C	p.Ser1847Arg	p.S1847R	ENST00000356175	NM_000267.3	1847	Agt/Cgt	37/57	1	2	FACETS	0.92	0.757	1	0.92	0.757	1	CLONAL	1	TRUE	1	0.204975731260445	2		260	382	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511533	38511533	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	56	389	0	ENST00000254066.5:c.1031A>T	p.Gln344Leu	p.Q344L	ENST00000254066	NM_000964.3	344	cAg/cTg	8/9	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.204975731260445	2		389	419	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007503	62007503	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	194	490	0	ENST00000392795.3:c.364T>G	p.Phe122Val	p.F122V	ENST00000392795	NM_001039933.1	122	Ttc/Gtc	3/6	1	2	FACETS	0.868	0.806	0.932	1	0.994	1	CLONAL	3	TRUE	1	0.204975731260445	2		490	727	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78765309	78765309	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	79	301	0	ENST00000306801.3:c.890A>C	p.Lys297Thr	p.K297T	ENST00000306801	NM_020761.2	297	aAg/aCg	7/34	1	2	FACETS	0.836	0.738	0.941	1	0.98	1	CLONAL	2	TRUE	1	0.204975731260445	2		301	461	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218422	1218422	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs559620061	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	207	671	0	ENST00000326873.7:c.297T>G	p.Ile99Met	p.I99M	ENST00000326873	NM_000455.4	99	atT/atG	2/10	0.204975731260445	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.204975731260445	2		671	955	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223089	5223089	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	142	704	0	ENST00000357368.4:c.2714T>G	p.Leu905Arg	p.L905R	ENST00000357368	NM_002850.3	905	cTt/cGt	18/38	0.204975731260445	2	FACETS	0.803	0.732	0.877	0.803	0.732	0.877	CLONAL	2	TRUE	0	0.204975731260445	2		704	863	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5225837	5225837	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	146	527	0	ENST00000357368.4:c.2395T>G	p.Leu799Val	p.L799V	ENST00000357368	NM_002850.3	799	Ttg/Gtg	17/38	0.204975731260445	2	FACETS	0.996	0.911	1	0.996	0.911	1	CLONAL	2	TRUE	0	0.204975731260445	2		527	715	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117413	7117413	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	83	372	0	ENST00000302850.5:c.3803T>A	p.Leu1268His	p.L1268H	ENST00000302850	NM_000208.2	1268	cTc/cAc	22/22	0.204975731260445	2	FACETS	0.782	0.692	0.878	0.782	0.692	0.878	SUBCLONAL	2	TRUE	0	0.204975731260445	2		372	518	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248591	10248591	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	39	543	0	ENST00000340748.4:c.4162T>C	p.Tyr1388His	p.Y1388H	ENST00000340748		1388	Tac/Cac	35/40	0.204975731260445	2	FACETS	0.546	0.451	0.652	0.273	0.225	0.326	SUBCLONAL	1	TRUE	0	0.204975731260445	2		543	697	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228539	36228539	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	50	578	0	ENST00000222270.7:c.7553A>C	p.Lys2518Thr	p.K2518T	ENST00000222270	NM_014727.1	2518	aAg/aCg	34/37	0.204975731260445	2	FACETS	0.605	0.511	0.707	0.302	0.255	0.354	SUBCLONAL	1	TRUE	0	0.204975731260445	2		578	807	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867097	45867097	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	153	655	0	ENST00000391945.4:c.1022A>C	p.Lys341Thr	p.K341T	ENST00000391945	NM_000400.3	341	aAg/aCg	11/23	0.204975731260445	2	FACETS	0.947	0.868	1	0.947	0.868	1	CLONAL	2	TRUE	0	0.204975731260445	2		655	788	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965575	25965575	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	254	648	0	ENST00000435504.4:c.3631A>C	p.Ser1211Arg	p.S1211R	ENST00000435504		1211	Agt/Cgt	13/13	1	2	FACETS	0.94	0.882	1	1	0.996	1	CLONAL	3	TRUE	1	0.204975731260445	2		648	879	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965749	25965749	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	110	821	0	ENST00000435504.4:c.3457A>C	p.Ser1153Arg	p.S1153R	ENST00000435504		1153	Agc/Cgc	13/13	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.204975731260445	2		821	1046	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443603	29443603	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	124	657	1	ENST00000389048.3:c.3614A>G	p.Lys1205Arg	p.K1205R	ENST00000389048	NM_004304.4	1205	aAg/aGg	23/29	1	2	FACETS	0.796	0.721	0.875	1	0.986	1	SUBCLONAL	2	TRUE	1	0.204975731260445	2		658	760	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543625	29543625	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	78	470	0	ENST00000389048.3:c.1538A>T	p.Asp513Val	p.D513V	ENST00000389048	NM_004304.4	513	gAc/gTc	7/29	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.204975731260445	2		470	650	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606130	47606130	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	94	525	0	ENST00000263735.4:c.594T>G	p.Asn198Lys	p.N198K	ENST00000263735	NM_002354.2	198	aaT/aaG	6/9	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.204975731260445	2		525	742	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719564	190719564	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	109	389	0	ENST00000441310.2:c.1566A>C	p.Lys522Asn	p.K522N	ENST00000441310	NM_000534.4	522	aaA/aaC	9/13	1	2	FACETS	1	0.974	1	1	0.99	1	CLONAL	2	TRUE	1	0.204975731260445	2		389	435	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738364	190738364	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	73	417	0	ENST00000441310.2:c.2616A>C	p.Lys872Asn	p.K872N	ENST00000441310	NM_000534.4	872	aaA/aaC	12/13	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.204975731260445	2		417	619	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339026	225339026	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	70	668	0	ENST00000264414.4:c.2243T>G	p.Leu748Arg	p.L748R	ENST00000264414	NM_003590.4	748	cTt/cGt	16/16	1	2	FACETS	0.868	0.755	0.99	0.868	0.755	0.99	CLONAL	1	TRUE	1	0.204975731260445	2		668	787	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031215	36031215	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	227	664	0	ENST00000358208.4:c.1334A>C	p.Lys445Thr	p.K445T	ENST00000358208		445	aAg/aCg	11/12	1	2	FACETS	0.923	0.862	0.985	1	0.995	1	CLONAL	3	TRUE	1	0.204975731260445	2		664	800	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256346	46256346	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	91	679	0	ENST00000371998.3:c.574A>C	p.Ser192Arg	p.S192R	ENST00000371998		192	Agc/Cgc	7/23	1	2	FACETS	0.891	0.79	1	0.891	0.79	1	CLONAL	1	TRUE	1	0.204975731260445	2		679	996	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164545	36164545	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	44	393	0	ENST00000300305.3:c.1330C>A	p.Pro444Thr	p.P444T	ENST00000300305		444	Ccc/Acc	8/8	1	2	FACETS	0.91	0.763	1	0.91	0.763	1	CLONAL	1	TRUE	1	0.204975731260445	2		393	472	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513287	41513287	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs761323972	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	229	565	0	ENST00000263253.7:c.191T>G	p.Leu64Arg	p.L64R	ENST00000263253	NM_001429.3	64	cTt/cGt	2/31	1	2	FACETS	0.959	0.896	1	1	0.995	1	CLONAL	3	TRUE	1	0.204975731260445	2		565	777	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259577	89259577	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	72	383	0	ENST00000336596.2:c.721A>G	p.Arg241Gly	p.R241G	ENST00000336596	NM_005233.5	241	Agg/Ggg	3/17	1	2	FACETS	0.806	0.707	0.912	1	0.977	1	CLONAL	2	TRUE	1	0.204975731260445	2		383	436	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447313	187447313	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	80	448	0	ENST00000232014.4:c.880T>G	p.Phe294Val	p.F294V	ENST00000232014	NM_001130845.1	294	Ttc/Gtc	5/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.204975731260445	2		448	599	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55963930	55963930	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	71	420	0	ENST00000263923.4:c.2513A>C	p.Lys838Thr	p.K838T	ENST00000263923	NM_002253.2	838	aAg/aCg	18/30	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.204975731260445	2		420	651	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180868	106180868	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	54	341	0	ENST00000380013.4:c.3896A>G	p.Lys1299Arg	p.K1299R	ENST00000380013	NM_001127208.2	1299	aAg/aGg	7/11	1	2	FACETS	0.992	0.848	1	0.992	0.848	1	CLONAL	1	TRUE	1	0.204975731260445	2		341	531	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094813	143094813	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	22	301	0	ENST00000262992.4:c.1331A>G	p.Lys444Arg	p.K444R	ENST00000262992	NM_001101669.1	444	aAg/aGg	14/24	1	2	FACETS	0.55	0.426	0.695	0.55	0.426	0.695	SUBCLONAL	1	TRUE	1	0.204975731260445	2		301	390	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521382	187521382	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	119	518	0	ENST00000441802.2:c.11773T>G	p.Leu3925Val	p.L3925V	ENST00000441802	NM_005245.3	3925	Ttg/Gtg	22/27	1	2	FACETS	0.859	0.776	0.946	1	0.987	1	CLONAL	2	TRUE	1	0.204975731260445	2		518	676	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950400	38950400	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	137	435	0	ENST00000357387.3:c.3550A>C	p.Lys1184Gln	p.K1184Q	ENST00000357387	NM_152756.3	1184	Aaa/Caa	31/38	0.204975731260445	3	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	1	0.204975731260445	3		435	707	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670712	86670712	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	58	385	0	ENST00000274376.6:c.1990A>G	p.Lys664Glu	p.K664E	ENST00000274376	NM_002890.2	664	Aaa/Gaa	15/25	1	2	FACETS	0.958	0.823	1	0.958	0.823	1	CLONAL	1	TRUE	1	0.204975731260445	2		385	591	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441155	149441155	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	111	610	0	ENST00000286301.3:c.1757A>C	p.Lys586Thr	p.K586T	ENST00000286301	NM_005211.3	586	aAg/aCg	13/22	1	2	FACETS	0.77	0.693	0.852	1	0.984	1	SUBCLONAL	2	TRUE	1	0.204975731260445	2		610	703	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223593	55223593	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	55	459	0	ENST00000275493.2:c.960A>C	p.Glu320Asp	p.E320D	ENST00000275493	NM_005228.3	320	gaA/gaC	8/28	1	2	FACETS	0.94	0.804	1	0.94	0.804	1	CLONAL	1	TRUE	1	0.204975731260445	2		459	571	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55231428	55231428	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	169	509	0	ENST00000275493.2:c.1634A>C	p.Glu545Ala	p.E545A	ENST00000275493	NM_005228.3	545	gAg/gCg	14/28	1	2	FACETS	1	0.98	1	1	0.993	1	CLONAL	2	TRUE	1	0.204975731260445	2		509	698	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371717	55371717	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1194	86	604	0	ENST00000297316.4:c.407A>C	p.Lys136Thr	p.K136T	ENST00000297316	NM_022454.3	136	aAg/aCg	2/2	0.204975731260445	8	FACETS	1	0.921	1	0.151	0.133	0.171	CLONAL	1	TRUE	1	0.204975731260445	8		604	1280	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371747	55371747	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	83	474	0	ENST00000297316.4:c.437A>C	p.Lys146Thr	p.K146T	ENST00000297316	NM_022454.3	146	aAg/aCg	2/2	0.204975731260445	8	FACETS	1	0.972	1	0.195	0.171	0.22	CLONAL	1	TRUE	1	0.204975731260445	8		474	960	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930140	68930140	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	93	565	0	ENST00000288368.4:c.201A>C	p.Glu67Asp	p.E67D	ENST00000288368	NM_024870.2	67	gaA/gaC	2/40	0.204975731260445	8	FACETS	1	0.961	1	0.171	0.151	0.192	CLONAL	1	TRUE	1	0.204975731260445	8		565	1225	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020068	123020068	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017547-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	157	334	2	ENST00000355640.3:c.556A>G	p.Ser186Gly	p.S186G	ENST00000355640		186	Agt/Ggt	2/7	1	1	FACETS	0.909	0.839	0.982	1	0.993	1	CLONAL	3	TRUE	0	0.204975731260445	1		336	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0017548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	121	410	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.343081429071987	2	FACETS	0.973	0.889	1	0.973	0.889	1	CLONAL	2	FALSE	0	0.355305364160824	2		410	350	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550488	29550488	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs199474760	NA	P-0017548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	87	465	0	ENST00000356175.3:c.1748A>G	p.Lys583Arg	p.K583R	ENST00000356175	NM_000267.3	583	aAg/aGg	16/57	0.355305364160824	5	FACETS	1	0.914	1	1	0.914	1	CLONAL	3	FALSE	2	0.355305364160824	5		465	246	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335079	65335079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	78	800	1	ENST00000342505.4:c.562G>A	p.Glu188Lys	p.E188K	ENST00000342505	NM_002227.2	188	Gag/Aag	6/25	0.188742090913635	6	FACETS	1	0.962	1	0.412	0.362	0.466	INDETERMINATE	1	FALSE	3	0.355305364160824	6		801	607	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094832	11094832	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	273	846	0	ENST00000358026.2:c.5C>A	p.Ser2Tyr	p.S2Y	ENST00000358026	NM_001128849.1	2	tCc/tAc	2/36	0.188742090913635	6	FACETS	0.856	0.804	0.909	0.856	0.804	0.909	INDETERMINATE	3	FALSE	3	0.355305364160824	6		846	1024	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411675	116411675	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	14	298	0	ENST00000397752.3:c.2854T>G	p.Phe952Val	p.F952V	ENST00000397752	NM_000245.2	952	Ttc/Gtc	13/21	0.356007855008603	3	FACETS	0.457	0.331	0.61			1	SUBCLONAL	1	FALSE	NA	0.355305364160824	3		298	203	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0017548-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	151	410	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.328304250060732	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.328304250060732	1		410	679	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550488	29550488	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs199474760	NA	P-0017548-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	107	465	0	ENST00000356175.3:c.1748A>G	p.Lys583Arg	p.K583R	ENST00000356175	NM_000267.3	583	aAg/aGg	16/57	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.328304250060732	2		465	487	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335079	65335079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017548-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	76	800	1	ENST00000342505.4:c.562G>A	p.Glu188Lys	p.E188K	ENST00000342505	NM_002227.2	188	Gag/Aag	6/25	1	2	FACETS	0.568	0.497	0.644	0.568	0.497	0.644	SUBCLONAL	1	TRUE	1	0.328304250060732	2		801	815	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094832	11094832	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017548-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	179	846	0	ENST00000358026.2:c.5C>A	p.Ser2Tyr	p.S2Y	ENST00000358026	NM_001128849.1	2	tCc/tAc	2/36	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.328304250060732	2		846	907	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127933444	127933444	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017548-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	84	704	0	ENST00000373547.4:c.91G>C	p.Val31Leu	p.V31L	ENST00000373547	NM_002721.4	31	Gtt/Ctt	2/7	0.299627525438176	3	FACETS	0.605	0.533	0.682	0.302	0.266	0.341	SUBCLONAL	1	TRUE	1	0.328304250060732	3		704	985	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0017549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	1212	357	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	0.70895723139769	9	FACETS	1	0.994	1			1	CLONAL	8	TRUE	NA	0.70895723139769	9		357	1461	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562808	21562808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	36	198	2	ENST00000382592.4:c.1111C>T	p.Pro371Ser	p.P371S	ENST00000382592	NM_014572.2	371	Ccg/Tcg	4/8	1	2	FACETS	0.218	0.179	0.262	0.218	0.179	0.262	SUBCLONAL	1	TRUE	1	0.70895723139769	2		200	465	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559721	29559721	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0017549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	170	305	0	ENST00000356175.3:c.3318C>G	p.Tyr1106Ter	p.Y1106*	ENST00000356175	NM_000267.3	1106	taC/taG	26/57	1	2	FACETS	0.901	0.835	0.97	0.901	0.835	0.97	CLONAL	1	TRUE	1	0.70895723139769	2		305	532	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	131	305	0	ENST00000335508.6:c.1873C>A	p.Arg625Ser	p.R625S	ENST00000335508	NM_012433.2	625	Cgt/Agt	14/25	1	2	FACETS	0.7	0.638	0.764	0.7	0.638	0.764	SUBCLONAL	1	TRUE	1	0.70895723139769	2		305	528	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394978	394978	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	221	270	0	ENST00000380956.4:c.374A>G	p.Tyr125Cys	p.Y125C	ENST00000380956	NM_001195286.1	125	tAc/tGc	3/9	0.70895723139769	3	FACETS	1	0.956	1	0.516	0.481	0.552	CLONAL	1	TRUE	1	0.70895723139769	3		270	818	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223978	2223978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	42	706	2	ENST00000326181.6:c.1192C>T	p.Pro398Ser	p.P398S	ENST00000326181	NM_032271.2	398	Cct/Tct	13/21	0.137159083860571	0	FACETS	0.237	0.197	0.282			1	INDETERMINATE	1	TRUE	0	0.340797989842653	0		708	685	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225938	2225938	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	40	445	0	ENST00000326181.6:c.1730A>G	p.Tyr577Cys	p.Y577C	ENST00000326181	NM_032271.2	577	tAc/tGc	18/21	0.137159083860571	0	FACETS	0.311	0.258	0.37			1	INDETERMINATE	1	TRUE	0	0.340797989842653	0		445	498	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951052	48951052	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0017551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	61	169	0	ENST00000267163.4:c.1216-2A>G		p.X406_splice	ENST00000267163	NM_000321.2	406			1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.253033108939933	2		169	404	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054046	42054046	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	106	393	0	ENST00000219905.7:c.7508C>A	p.Ser2503Ter	p.S2503*	ENST00000219905	NM_001164273.1	2503	tCa/tAa	21/24	0.253033108939933	1	FACETS	0.82	0.735	0.912	0.82	0.735	0.912	CLONAL	1	TRUE	0	0.253033108939933	1		393	892	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836414	89836414	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1196789540	NA	P-0017551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	118	305	0	ENST00000389301.3:c.2335C>G	p.Pro779Ala	p.P779A	ENST00000389301	NM_000135.2	779	Cca/Gca	26/43	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.253033108939933	2		305	669	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782177	NA	P-0017551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1409	335	743	0	ENST00000269305.4:c.644G>A	p.Ser215Asn	p.S215N	ENST00000269305	NM_001126112.2	215	aGt/aAt	6/11	0.20561011955159	2	FACETS	0.759	0.715	0.804	0.759	0.715	0.804	SUBCLONAL	2	TRUE	0	0.253033108939933	2		743	1744	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983127	7983127	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	126	561	0	ENST00000319144.4:c.887C>A	p.Pro296Gln	p.P296Q	ENST00000319144	NM_001139.2	296	cCg/cAg	7/15	0.20561011955159	2	FACETS	0.784	0.707	0.864	0.392	0.353	0.432	SUBCLONAL	1	TRUE	0	0.253033108939933	2		561	1271	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602443	10602443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1321752702	NA	P-0017551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	133	592	0	ENST00000171111.5:c.1135G>A	p.Gly379Ser	p.G379S	ENST00000171111	NM_203500.1	379	Ggc/Agc	3/6	0.253033108939933	1	FACETS	0.858	0.778	0.943	0.858	0.778	0.943	CLONAL	1	TRUE	0	0.253033108939933	1		592	1070	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927998	49927998	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1847	111	895	1	ENST00000296474.3:c.3730C>T	p.His1244Tyr	p.H1244Y	ENST00000296474	NM_002447.2	1244	Cat/Tat	18/20	1	2	FACETS	0.448	0.401	0.499	0.448	0.401	0.499	SUBCLONAL	1	TRUE	1	0.253033108939933	2		896	1958	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920499	134920499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1242	214	535	1	ENST00000398015.3:c.2314G>A	p.Asp772Asn	p.D772N	ENST00000398015	NM_004441.4	772	Gac/Aac	12/16	0.24249268480724	4	FACETS	1	0.99	1	0.728	0.674	0.784	CLONAL	1	TRUE	2	0.253033108939933	4		536	1456	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280067	66280067	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	155	457	0	ENST00000273854.3:c.1622G>T	p.Arg541Leu	p.R541L	ENST00000273854	NM_004439.5	541	cGa/cTa	7/18	0.232644163410259	3	FACETS	1	0.984	1	0.66	0.604	0.72	CLONAL	1	TRUE	1	0.253033108939933	3		457	1045	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44919322	44919322	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	40	302	0	ENST00000377967.4:c.1250C>A	p.Pro417His	p.P417H	ENST00000377967	NM_021140.2	417	cCt/cAt	13/29	1	2	FACETS	0.45	0.373	0.536	0.45	0.373	0.536	SUBCLONAL	1	TRUE	1	0.253033108939933	2		302	703	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0017554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	89	525	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	0.276164217137197	2		525	613	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220494	1220494	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519858	NA	P-0017554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	189	658	0	ENST00000326873.7:c.587G>T	p.Gly196Val	p.G196V	ENST00000326873	NM_000455.4	196	gGc/gTc	4/10	0.276164217137197	2	FACETS	0.84	0.777	0.904	0.84	0.777	0.904	CLONAL	2	TRUE	0	0.276164217137197	2		658	815	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266730	18266730	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	136	366	0	ENST00000222254.8:c.41C>G	p.Pro14Arg	p.P14R	ENST00000222254	NM_005027.3	14	cCg/cGg	2/16	1	2	FACETS	0.942	0.861	1	1	0.99	1	CLONAL	2	TRUE	1	0.276164217137197	2		366	523	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156607	55156607	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	80	533	0	ENST00000257290.5:c.3008G>T	p.Trp1003Leu	p.W1003L	ENST00000257290	NM_006206.4	1003	tGg/tTg	22/23	1	2	FACETS	0.68	0.597	0.769	0.68	0.597	0.769	SUBCLONAL	1	TRUE	1	0.276164217137197	2		533	852	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217283	66217283	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	59	356	0	ENST00000273854.3:c.2332G>T	p.Val778Phe	p.V778F	ENST00000273854	NM_004439.5	778	Gtt/Ttt	14/18	1	2	FACETS	0.958	0.826	1	0.958	0.826	1	CLONAL	1	TRUE	1	0.276164217137197	2		356	446	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467598	66467598	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	105	437	0	ENST00000273854.3:c.671T>A	p.Val224Asp	p.V224D	ENST00000273854	NM_004439.5	224	gTt/gAt	3/18	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.276164217137197	2		437	673	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944829	131944829	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	25	183	0	ENST00000265335.6:c.2850G>T	p.Lys950Asn	p.K950N	ENST00000265335		950	aaG/aaT	18/25	0.259656517997778	1	FACETS	0.729	0.578	0.901	0.729	0.578	0.901	CLONAL	1	TRUE	0	0.276164217137197	1		183	214	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562800	176562800	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	90	521	0	ENST00000439151.2:c.696G>T	p.Gln232His	p.Q232H	ENST00000439151	NM_022455.4	232	caG/caT	2/23	0.276164217137197	4	FACETS	0.865	0.766	0.971	0.288	0.255	0.324	CLONAL	1	TRUE	1	0.276164217137197	4		521	962	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225414	26225414	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1593	242	1325	0	ENST00000360408.1:c.32C>A	p.Ser11Tyr	p.S11Y	ENST00000360408	NM_003532.2	11	tCc/tAc	1/1	1	2	FACETS	0.955	0.889	1	0.955	0.889	1	CLONAL	1	TRUE	1	0.276164217137197	2		1325	1835	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486280	8486280	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	66	315	0	ENST00000356435.5:c.2537C>T	p.Pro846Leu	p.P846L	ENST00000356435		846	cCg/cTg	17/35	1	2	FACETS	0.964	0.838	1	0.964	0.838	1	CLONAL	1	TRUE	1	0.276164217137197	2		315	496	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041022	47041022	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	128	692	1	ENST00000377604.3:c.1552C>T	p.Gln518Ter	p.Q518*	ENST00000377604	NM_001204468.1	518	Cag/Tag	14/24	0.259656517997778	1	FACETS	0.897	0.812	0.986	0.897	0.812	0.986	CLONAL	1	TRUE	0	0.276164217137197	1		693	891	SUCCESS
AR	367	MSKCC	GRCh37	X	66941763	66941763	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	173	977	3	ENST00000374690.3:c.2407C>A	p.Gln803Lys	p.Q803K	ENST00000374690	NM_000044.3	803	Cag/Aag	6/8	0.259656517997778	1	FACETS	0.783	0.718	0.85	0.783	0.718	0.85	SUBCLONAL	1	TRUE	0	0.276164217137197	1		980	1380	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936726	32936728	+	stop_gained	Nonsense_Mutation	TNP	TAG	TAG	AAA	novel	NA	P-0017554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	67	373	1	ENST00000380152.3:c.7872_7874delinsAAA	p.Tyr2624_Arg2625delinsTer	p.Y2624_R2625delins*	ENST00000380152		2624	taTAGa/taAAAa	17/27	1	2	FACETS	0.806	0.701	0.92	0.806	0.701	0.92	CLONAL	1	TRUE	1	0.276164217137197	2		374	602	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023151	27023179	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	-	novel	NA	P-0017555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	123	93	0	ENST00000324856.7:c.267_295del	p.Ser90ProfsTer11	p.S90Pfs*11	ENST00000324856	NM_006015.4	86	gGCGGAGCCGGCAGCGGCGGCGGGCCCGGC/g	1/20	0.251916550996364	1	FACETS	0.963	0.886	1	1	0.992	1	CLONAL	3	TRUE	0	0.263185315676256	1		93	281	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742485	17742485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	139	717	2	ENST00000250003.3:c.667C>T	p.Arg223Trp	p.R223W	ENST00000250003	NM_002478.4	223	Cgg/Tgg	2/3	0.251916550996364	1	FACETS	0.869	0.789	0.952	0.869	0.789	0.952	CLONAL	1	TRUE	0	0.263185315676256	1		719	1056	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797309	135797309	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	71	296	0	ENST00000298552.3:c.560T>C	p.Leu187Pro	p.L187P	ENST00000298552	NM_001162426.1	187	cTc/cCc	7/23	0.263185315676256	1	FACETS	0.837	0.731	0.95	0.837	0.731	0.95	CLONAL	1	TRUE	0	0.263185315676256	1		296	560	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	113	408	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.857	0.772	0.947	0.857	0.772	0.947	CLONAL	1	TRUE	1	0.384830224523235	2		408	685	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0017557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	103	205	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	0.334040286441402	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.384830224523235	1		205	362	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217418	7217421	+	frameshift_variant	Frame_Shift_Del	DEL	AGTT	AGTT	-	novel	NA	P-0017557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	158	593	0	ENST00000380728.2:c.375_378del	p.Thr126IlefsTer218	p.T126Ifs*218	ENST00000380728		125	ggAACT/gg	5/11	0.384830224523235	1	FACETS	0.8	0.733	0.869	0.8	0.733	0.869	SUBCLONAL	1	TRUE	0	0.384830224523235	1		593	829	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578175	7578175	+	splice_donor_variant	Splice_Site	SNP	A	A	T	rs1555525703	NA	P-0017557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	209	635	1	ENST00000269305.4:c.672+2T>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.384830224523235	1	FACETS	0.921	0.856	0.989	0.921	0.856	0.989	CLONAL	1	TRUE	0	0.384830224523235	1		636	952	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813280	89813280	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437529209	NA	P-0017560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	109	396	2	ENST00000389301.3:c.3367G>A	p.Gly1123Arg	p.G1123R	ENST00000389301	NM_000135.2	1123	Gga/Aga	34/43	0.435602719320196	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.435602719320196	1		398	283	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877486	28877486	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	74	227	0	ENST00000282397.4:c.3835A>C	p.Ser1279Arg	p.S1279R	ENST00000282397	NM_002019.4	1279	Agt/Cgt	30/30	0.180301390322211	3	FACETS	0.958	0.853	1	0.639	0.569	0.711	INDETERMINATE	2	TRUE	0	0.435602719320196	3		227	216	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	266	335	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.701872209113222	1	FACETS	0.927	0.879	0.974	0.927	0.879	0.974	CLONAL	1	TRUE	0	0.701872209113222	1		335	531	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727138	40727138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375402843	NA	P-0017562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	357	452	0	ENST00000373198.4:c.3826G>A	p.Val1276Met	p.V1276M	ENST00000373198	NM_133170.3	1276	Gtg/Atg	28/32	1	2	FACETS	0.885	0.84	0.932	0.885	0.84	0.932	CLONAL	1	TRUE	1	0.701872209113222	2		452	1149	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0017564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	495	632	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.627828799605615	2	FACETS	0.839	0.809	0.869	0.839	0.809	0.869	CLONAL	2	TRUE	0	0.653349172454784	2		632	903	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954222	48954237	+	splice_donor_variant,intron_variant	Splice_Site	DEL	TAAATTTTTTACTTTT	TAAATTTTTTACTTTT	AAA	novel	NA	P-0017564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	204	268	1	ENST00000267163.4:c.1421+2_1421+17delinsAAA		p.X474_splice	ENST00000267163	NM_000321.2	474			0.642142789047247	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.653349172454784	1		269	401	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1023835002	NA	P-0017565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	120	383	0	ENST00000558401.1:c.1A>G	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Gtg	1/4	0.594901586190354	1	FACETS	0.363	0.328	0.401	0.363	0.328	0.401	SUBCLONAL	1	TRUE	0	0.594901586190354	1		383	780	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0017565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	189	239	0	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	1	2	FACETS	0.916	0.849	0.984	0.916	0.849	0.984	CLONAL	1	TRUE	1	0.594901586190354	2		239	694	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114817	108114817	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786204543	NA	P-0017565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	195	258	0	ENST00000278616.4:c.640del	p.Ser214ProfsTer16	p.S214Pfs*16	ENST00000278616	NM_000051.3	212	Ttt/tt	6/63	0.582569246254395	1	FACETS	0.956	0.893	1	0.956	0.893	1	CLONAL	1	TRUE	0	0.594901586190354	1		258	482	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007620	45007620	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs111947448	NA	P-0017565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	23	186	0	ENST00000558401.1:c.68-1G>C		p.X23_splice	ENST00000558401	NM_004048.2	23			0.594901586190354	1	FACETS	0.151	0.118	0.19	0.151	0.118	0.19	SUBCLONAL	1	TRUE	0	0.594901586190354	1		186	359	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976198	7976198	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1274525093	NA	P-0017565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	310	334	0	ENST00000319144.4:c.1997G>A	p.Arg666His	p.R666H	ENST00000319144	NM_001139.2	666	cGc/cAc	15/15	0.582569246254395	1	FACETS	0.993	0.943	1	0.993	0.943	1	CLONAL	1	TRUE	0	0.594901586190354	1		334	737	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713463	30713536	+	frameshift_variant	Frame_Shift_Del	DEL	TGAAGCAGAACACTTCAGAGCAGTTTGAGACAGTGGCAGTCAAGATCTTTCCCTATGAGGAGTATGCCTCTTGG	TGAAGCAGAACACTTCAGAGCAGTTTGAGACAGTGGCAGTCAAGATCTTTCCCTATGAGGAGTATGCCTCTTGG	-	novel	NA	P-0017565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	167	277	0	ENST00000295754.5:c.788_861del	p.Leu263GlnfsTer15	p.L263Qfs*15	ENST00000295754	NM_003242.5	263	cTGAAGCAGAACACTTCAGAGCAGTTTGAGACAGTGGCAGTCAAGATCTTTCCCTATGAGGAGTATGCCTCTTGG/c	4/7	0.582569246254395	1	FACETS	0.79	0.732	0.85	0.79	0.732	0.85	SUBCLONAL	1	TRUE	0	0.594901586190354	1		277	499	SUCCESS
APC	324	MSKCC	GRCh37	5	112162945	112162945	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1114167599	NA	P-0017565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	168	270	0	ENST00000257430.4:c.1548+1G>A		p.X516_splice	ENST00000257430	NM_000038.5	516			1	2	FACETS	0.887	0.818	0.957	0.887	0.818	0.957	CLONAL	1	TRUE	1	0.594901586190354	2		270	637	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092809	27092809	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	143	637	0	ENST00000324856.7:c.2830C>T	p.Gln944Ter	p.Q944*	ENST00000324856	NM_006015.4	944	Cag/Tag	9/20	1	2	FACETS	0.794	0.723	0.868	0.794	0.723	0.868	SUBCLONAL	1	TRUE	1	0.38660820367246	2		637	932	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0017581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	98	532	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	1	2	FACETS	0.661	0.589	0.737	0.661	0.589	0.737	SUBCLONAL	1	TRUE	1	0.38660820367246	2		532	767	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0017581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	20	211	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	0.324	0.248	0.414	0.324	0.248	0.414	SUBCLONAL	1	TRUE	1	0.38660820367246	2		211	319	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0017582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	131	401	3	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.912	0.829	0.998	0.912	0.829	0.998	CLONAL	1	TRUE	1	0.436128005348302	2		404	659	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448393	56448393	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	114	389	0	ENST00000407977.2:c.254C>T	p.Ser85Phe	p.S85F	ENST00000407977		85	tCc/tTc	3/10	1	2	FACETS	0.77	0.694	0.85	0.77	0.694	0.85	SUBCLONAL	1	TRUE	1	0.436128005348302	2		389	679	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059450	42059450	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs376097905	NA	P-0017582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1263	315	1081	0	ENST00000219905.7:c.9170G>C	p.Gly3057Ala	p.G3057A	ENST00000219905	NM_001164273.1	3057	gGg/gCg	24/24	0.289893845704476	1	FACETS	0.716	0.673	0.759	0.716	0.673	0.759	SUBCLONAL	1	TRUE	0	0.436128005348302	1		1081	1578	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110608	4110608	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749389113	NA	P-0017582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	148	501	0	ENST00000262948.5:c.349C>T	p.Arg117Cys	p.R117C	ENST00000262948	NM_030662.3	117	Cgc/Tgc	3/11	0.436128005348302	1	FACETS	0.829	0.76	0.901	0.829	0.76	0.901	CLONAL	1	TRUE	0	0.436128005348302	1		501	640	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732958	30732958	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	153	446	0	ENST00000295754.5:c.1571A>G	p.Asp524Gly	p.D524G	ENST00000295754	NM_003242.5	524	gAc/gGc	7/7	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.436128005348302	2		446	650	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250401	110250401	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	166	687	1	ENST00000374672.4:c.274C>A	p.Pro92Thr	p.P92T	ENST00000374672	NM_004235.4	92	Cct/Act	3/5	1	2	FACETS	0.796	0.731	0.864	0.796	0.731	0.864	SUBCLONAL	1	TRUE	1	0.436128005348302	2		688	956	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	306	708	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.155232324538735	0	FACETS	0.81	0.764	0.857			1	CLONAL	4	TRUE	0	0.155232324538735	0		708	1028	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	86	444	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.851	0.757	0.951	1	0.987	1	CLONAL	3	TRUE	1	0.155232324538735	2		444	434	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	359	640	4	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	0.155232324538735	2	FACETS	1	0.987	1	1	0.996	1	CLONAL	3	TRUE	0	0.155232324538735	2		644	1373	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740263	162740263	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs752778008	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	63	507	0	ENST00000367921.3:c.1465C>T	p.Arg489Ter	p.R489*	ENST00000367921	NM_006182.2	489	Cga/Tga	12/18	1	2	FACETS	0.795	0.685	0.915	0.795	0.685	0.915	CLONAL	1	TRUE	1	0.155232324538735	2		507	1021	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	101	255	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.913	0.82	1	1	0.99	1	CLONAL	3	TRUE	1	0.155232324538735	2		255	475	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	30	142	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.155232324538735	0	FACETS	0.989	0.815	1			1	CLONAL	3	TRUE	0	0.155232324538735	0		142	110	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952086	178952086	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	112	390	0	ENST00000263967.3:c.3141T>A	p.His1047Gln	p.H1047Q	ENST00000263967	NM_006218.2	1047	caT/caA	21/21	1	2	FACETS	0.913	0.828	1	1	0.992	1	CLONAL	4	TRUE	1	0.155232324538735	2		390	395	SUCCESS
APC	324	MSKCC	GRCh37	5	112173830	112173831	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	128	382	0	ENST00000257430.4:c.2544dup	p.Asp849ArgfsTer2	p.D849Rfs*2	ENST00000257430	NM_000038.5	847	gaa/gAaa	16/16	1	2	FACETS	0.898	0.817	0.984	1	0.992	1	CLONAL	3	TRUE	1	0.155232324538735	2		382	612	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645694	12645694	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs3730271	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	175	347	0	ENST00000251849.4:c.775T>C	p.Ser259Pro	p.S259P	ENST00000251849	NM_002880.3	259	Tcc/Ccc	7/17	1	2	FACETS	0.997	0.92	1	1	0.994	1	CLONAL	3	TRUE	1	0.155232324538735	2		347	754	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188294	32188295	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs766348245	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	268	731	3	ENST00000375023.3:c.1046dup	p.Thr350HisfsTer4	p.T350Hfs*4	ENST00000375023	NM_004557.3	349	ggc/ggGc	6/30	1	2	FACETS	0.932	0.873	0.993	1	0.996	1	CLONAL	3	TRUE	1	0.155232324538735	2		734	1235	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645974	215645975	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs587780033	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	112	542	0	ENST00000260947.4:c.623dup	p.Lys209GlufsTer5	p.K209Efs*5	ENST00000260947	NM_000465.2	208	aag/aaAg	4/11	1	2	FACETS	0.932	0.842	1	1	0.991	1	CLONAL	3	TRUE	1	0.155232324538735	2		542	516	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384650	31384651	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs756395138	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	205	634	3	ENST00000328111.2:c.1359dup	p.Leu454AlafsTer11	p.L454Afs*11	ENST00000328111	NM_006892.3	451	gag/gaGg	13/23	1	2	FACETS	0.838	0.777	0.901	1	0.994	1	CLONAL	3	TRUE	1	0.155232324538735	2		637	1051	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119780	70119781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	257	575	0	ENST00000245479.2:c.788dup	p.Arg264GlnfsTer32	p.R264Qfs*32	ENST00000245479	NM_000346.3	261	gag/gaGg	3/3	1	2	FACETS	0.97	0.908	1	1	0.996	1	CLONAL	3	TRUE	1	0.155232324538735	2		575	1138	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406237	70406237	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	53	564	1	ENST00000373644.4:c.3751G>T	p.Ala1251Ser	p.A1251S	ENST00000373644	NM_030625.2	1251	Gca/Tca	4/12	1	2	FACETS	0.925	0.787	1	0.925	0.787	1	CLONAL	1	TRUE	1	0.155232324538735	2		565	738	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156696	2156696	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1206	276	863	0	ENST00000434045.2:c.226T>G	p.Ser76Ala	p.S76A	ENST00000434045	NM_001127598.1	76	Tcg/Gcg	3/5	1	2	FACETS	1	0.987	1	1	0.996	1	CLONAL	2	TRUE	1	0.155232324538735	2		863	1482	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137075	64137075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	186	347	1	ENST00000334205.4:c.1586G>A	p.Arg529His	p.R529H	ENST00000334205	NM_003942.2	529	cGc/cAc	13/17	1	2	FACETS	1	0.968	1	1	0.995	1	CLONAL	3	TRUE	1	0.155232324538735	2		348	738	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505377	125505377	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	110	456	0	ENST00000428830.2:c.667G>T	p.Glu223Ter	p.E223*	ENST00000428830	NM_001114121.2	223	Gaa/Taa	7/14	1	2	FACETS	1	0.974	1	1	0.99	1	CLONAL	2	TRUE	1	0.155232324538735	2		456	568	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524621	103524621	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	208	529	0	ENST00000355739.4:c.2752T>A	p.Leu918Ile	p.L918I	ENST00000355739	NM_000123.3	918	Tta/Ata	13/15	1	2	FACETS	0.967	0.898	1	1	0.995	1	CLONAL	3	TRUE	1	0.155232324538735	2		529	924	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007813	45007814	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	43	360	0	ENST00000558401.1:c.262_263del	p.Thr88Ter	p.T88*	ENST00000558401	NM_004048.2	87	tAC/t	2/4	1	2	FACETS	0.949	0.793	1	0.949	0.793	1	CLONAL	1	TRUE	1	0.155232324538735	2		360	584	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134686	2134686	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs999699219	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	138	362	0	ENST00000219476.3:c.4463A>G	p.Asn1488Ser	p.N1488S	ENST00000219476	NM_000548.3	1488	aAt/aGt	34/42	1	2	FACETS	0.883	0.806	0.964	1	0.992	1	CLONAL	3	TRUE	1	0.155232324538735	2		362	671	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831560	72831560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1231624603	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1649	107	1070	2	ENST00000268489.5:c.5021C>T	p.Ala1674Val	p.A1674V	ENST00000268489	NM_006885.3	1674	gCt/gTt	9/10	0.125613150192974	0	FACETS	0.663	0.592	0.739			1	SUBCLONAL	1	TRUE	0	0.155232324538735	0		1072	1756	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350059	89350059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1327	406	1003	3	ENST00000301030.4:c.2891G>A	p.Gly964Asp	p.G964D	ENST00000301030	NM_001256183.1	964	gGc/gAc	9/13	NA	2	FACETS	1	0.954	1			1	INDETERMINATE	3	TRUE	NA	0.155232324538735	2		1006	1733	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924261	11924262	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	11	72	0	ENST00000353533.5:c.63dup	p.Gly22ArgfsTer19	p.G22Rfs*19	ENST00000353533	NM_003010.3	20	acc/aCcc	1/11	0.155232324538735	0	FACETS	0.814	0.565	1			1	CLONAL	1	TRUE	0	0.155232324538735	0		72	147	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032505	12032505	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	39	266	1	ENST00000353533.5:c.941T>C	p.Phe314Ser	p.F314S	ENST00000353533	NM_003010.3	314	tTt/tCt	9/11	0.155232324538735	0	FACETS	0.722	0.601	0.855			1	SUBCLONAL	2	TRUE	0	0.155232324538735	0		267	294	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375458	40375459	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1618	459	1084	0	ENST00000293328.3:c.491dup	p.Leu165AlafsTer54	p.L165Afs*54	ENST00000293328	NM_012448.3	164	aag/aaAg	5/19	1	2	FACETS	0.949	0.903	0.996	1	0.997	1	CLONAL	3	TRUE	1	0.155232324538735	2		1084	2077	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006635	62006635	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1169314441	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	248	617	1	ENST00000392795.3:c.644G>A	p.Arg215Gln	p.R215Q	ENST00000392795	NM_001039933.1	215	cGg/cAg	6/6	1	2	FACETS	0.921	0.86	0.983	1	0.995	1	CLONAL	3	TRUE	1	0.155232324538735	2		618	1157	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532556	63532556	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555577121	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	224	382	0	ENST00000307078.5:c.2023del	p.Arg675ValfsTer14	p.R675Vfs*14	ENST00000307078	NM_004655.3	675	Cgt/gt	8/11	1	2	FACETS	0.917	0.856	0.979	1	0.996	1	CLONAL	4	TRUE	1	0.155232324538735	2		382	787	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615784	1615784	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1771	97	1039	0	ENST00000344749.5:c.1487A>C	p.Glu496Ala	p.E496A	ENST00000344749	NM_001136139.2	496	gAg/gCg	17/19	1	2	FACETS	0.669	0.593	0.75	0.669	0.593	0.75	SUBCLONAL	1	TRUE	1	0.155232324538735	2		1039	1868	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212055	5212055	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749770933	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	197	538	2	ENST00000357368.4:c.4976G>A	p.Arg1659His	p.R1659H	ENST00000357368	NM_002850.3	1659	cGc/cAc	32/38	1	2	FACETS	0.882	0.817	0.95	1	0.994	1	CLONAL	3	TRUE	1	0.155232324538735	2		540	959	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366968	15366968	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	67	645	1	ENST00000263377.2:c.1658G>T	p.Arg553Met	p.R553M	ENST00000263377	NM_058243.2	553	aGg/aTg	9/20	1	2	FACETS	0.685	0.593	0.786	0.685	0.593	0.786	SUBCLONAL	1	TRUE	1	0.155232324538735	2		646	1260	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439836	220439836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1225	394	868	2	ENST00000243786.2:c.689C>T	p.Ala230Val	p.A230V	ENST00000243786	NM_002191.3	230	gCc/gTc	2/2	1	2	FACETS	1	0.975	1	1	0.997	1	CLONAL	3	TRUE	1	0.155232324538735	2		870	1619	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204750	128204750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	335	835	1	ENST00000341105.2:c.691C>T	p.Pro231Ser	p.P231S	ENST00000341105	NM_032638.4	231	Cca/Tca	3/6	1	2	FACETS	0.989	0.934	1	1	0.997	1	CLONAL	3	TRUE	1	0.155232324538735	2		836	1454	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670340	134670340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415689583	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	282	543	1	ENST00000398015.3:c.251G>A	p.Arg84His	p.R84H	ENST00000398015	NM_004441.4	84	cGc/cAc	3/16	1	2	FACETS	1	0.985	1	1	0.996	1	CLONAL	3	TRUE	1	0.155232324538735	2		544	1061	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946218	55946218	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	228	525	0	ENST00000263923.4:c.3961A>G	p.Ser1321Gly	p.S1321G	ENST00000263923	NM_002253.2	1321	Agt/Ggt	30/30	1	2	FACETS	0.984	0.917	1	1	0.995	1	CLONAL	3	TRUE	1	0.155232324538735	2		525	995	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250864	153250864	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	126	475	0	ENST00000281708.4:c.1196A>T	p.Asp399Val	p.D399V	ENST00000281708	NM_033632.3	399	gAt/gTt	8/12	1	2	FACETS	0.892	0.813	0.973	1	0.992	1	CLONAL	4	TRUE	1	0.155232324538735	2		475	455	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541699	187541700	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	235	524	0	ENST00000441802.2:c.6040dup	p.Tyr2014LeufsTer11	p.Y2014Lfs*11	ENST00000441802	NM_005245.3	2014	tat/tTat	10/27	1	2	FACETS	0.987	0.921	1	1	0.995	1	CLONAL	3	TRUE	1	0.155232324538735	2		524	1023	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520249	176520249	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	186	436	0	ENST00000292408.4:c.1168T>C	p.Tyr390His	p.Y390H	ENST00000292408	NM_213647.1	390	Tat/Cat	9/18	1	2	FACETS	0.987	0.913	1	1	0.994	1	CLONAL	3	TRUE	1	0.155232324538735	2		436	809	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176684101	176684101	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs758996271	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	276	592	0	ENST00000439151.2:c.4915A>G	p.Ile1639Val	p.I1639V	ENST00000439151	NM_022455.4	1639	Atc/Gtc	13/23	1	2	FACETS	1	0.983	1	1	0.996	1	CLONAL	3	TRUE	1	0.155232324538735	2		592	1059	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042221	6042221	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs63750871	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	322	671	1	ENST00000265849.7:c.400C>T	p.Arg134Ter	p.R134*	ENST00000265849	NM_000535.5	134	Cga/Tga	5/15	1	2	FACETS	1	0.979	1	1	0.997	1	CLONAL	3	TRUE	1	0.155232324538735	2		672	1283	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476721	140476721	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	135	418	0	ENST00000288602.6:c.1685A>C	p.Gln562Pro	p.Q562P	ENST00000288602	NM_004333.4	562	cAg/cCg	13/18	1	2	FACETS	0.997	0.914	1	1	0.993	1	CLONAL	4	TRUE	1	0.155232324538735	2		418	436	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117874134	117874134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs77749836	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	50	715	0	ENST00000297338.2:c.320C>T	p.Ala107Val	p.A107V	ENST00000297338	NM_006265.2	107	gCc/gTc	4/14	1	2	FACETS	0.957	0.811	1	0.957	0.811	1	CLONAL	1	TRUE	1	0.155232324538735	2		715	673	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397748	139397748	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	197	373	0	ENST00000277541.6:c.5053T>C	p.Cys1685Arg	p.C1685R	ENST00000277541	NM_017617.3	1685	Tgt/Cgt	27/34	1	2	FACETS	1	0.966	1	1	0.995	1	CLONAL	3	TRUE	1	0.155232324538735	2		373	793	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314915	1314917	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs1407876239	NA	P-0017583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	52	578	0	ENST00000400841.2:c.744_746del	p.Leu249del	p.L249del	ENST00000400841		248	ctTCTg/ctg	6/6	1	1	FACETS	0.632	0.536	0.738	0.632	0.536	0.738	SUBCLONAL	1	TRUE	0	0.155232324538735	1		578	978	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0017584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	345	525	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.266791024725169	3	FACETS	0.847	0.802	0.893	1	0.992	1	CLONAL	3	TRUE	1	0.266791024725169	3		525	1154	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587782272	NA	P-0017584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	380	642	0	ENST00000269305.4:c.994-1G>C		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.266791024725169	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.266791024725169	2		642	1410	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828093	243828093	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	285	487	0	ENST00000263826.5:c.265G>C	p.Val89Leu	p.V89L	ENST00000263826	NM_005465.4	89	Gta/Cta	3/13	0.266791024725169	4	FACETS	1	0.988	1	0.789	0.741	0.837	CLONAL	2	TRUE	1	0.266791024725169	4		487	1144	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782323	56782323	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144159027	NA	P-0017584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1598	220	903	2	ENST00000308159.5:c.164C>T	p.Thr55Met	p.T55M	ENST00000308159	NM_014669.4	55	aCg/aTg	2/22	0.217296906611069	1	FACETS	0.786	0.728	0.846	0.786	0.728	0.846	SUBCLONAL	1	TRUE	0	0.266791024725169	1		905	1818	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805690	46805690	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1811	482	1146	0	ENST00000290295.7:c.266C>A	p.Ser89Tyr	p.S89Y	ENST00000290295	NM_006361.5	89	tCc/tAc	1/2	0.266791024725169	3	FACETS	0.893	0.85	0.937	0.893	0.85	0.937	CLONAL	2	TRUE	1	0.266791024725169	3		1146	2293	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220442	1220442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	363	830	0	ENST00000326873.7:c.535C>T	p.Pro179Ser	p.P179S	ENST00000326873	NM_000455.4	179	Ccg/Tcg	4/10	0.266791024725169	2	FACETS	0.913	0.864	0.963	0.913	0.864	0.963	CLONAL	2	TRUE	0	0.266791024725169	2		830	1491	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2199907	2199907	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	374	729	2	ENST00000398665.3:c.676G>T	p.Glu226Ter	p.E226*	ENST00000398665	NM_032482.2	226	Gaa/Taa	8/28	0.266791024725169	2	FACETS	0.936	0.887	0.987	0.936	0.887	0.987	CLONAL	2	TRUE	0	0.266791024725169	2		731	1497	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136182	11136182	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	305	596	0	ENST00000358026.2:c.3166G>T	p.Glu1056Ter	p.E1056*	ENST00000358026	NM_001128849.1	1056	Gag/Tag	22/36	0.266791024725169	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.266791024725169	2		596	1080	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944520	40944520	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	138	600	0	ENST00000373198.4:c.1982T>C	p.Leu661Pro	p.L661P	ENST00000373198	NM_133170.3	661	cTa/cCa	12/32	0.266791024725169	3	FACETS	0.943	0.855	1	0.471	0.427	0.518	CLONAL	1	TRUE	1	0.266791024725169	3		600	1244	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670266	134670266	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	114	569	0	ENST00000398015.3:c.177G>T	p.Gln59His	p.Q59H	ENST00000398015	NM_004441.4	59	caG/caT	3/16	1	2	FACETS	0.827	0.743	0.916	0.827	0.743	0.916	CLONAL	1	TRUE	1	0.266791024725169	2		569	1034	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140449169	140449169	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	36	346	0	ENST00000288602.6:c.1910C>T	p.Ser637Leu	p.S637L	ENST00000288602	NM_004333.4	637	tCa/tTa	16/18	0.266791024725169	4	FACETS	0.56	0.459	0.673	0.187	0.153	0.225	SUBCLONAL	1	TRUE	1	0.266791024725169	4		346	611	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391962	139391962	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1212	402	775	5	ENST00000277541.6:c.6229G>T	p.Ala2077Ser	p.A2077S	ENST00000277541	NM_017617.3	2077	Gcc/Tcc	34/34	0.266791024725169	2	FACETS	0.934	0.886	0.982	0.934	0.886	0.982	CLONAL	2	TRUE	0	0.266791024725169	2		780	1614	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256033	16256033	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	86	489	1	ENST00000375759.3:c.3298del	p.Glu1100LysfsTer20	p.E1100Kfs*20	ENST00000375759	NM_015001.2	1100	Gaa/aa	11/15	0.234054995082446	17	FACETS	1	0.918	1			1	CLONAL	8	FALSE	NA	0.234054995082446	17		490	247	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440843	52440849	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ACCCTGC	ACCCTGC	-	novel	NA	P-0017585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	127	666	0	ENST00000460680.1:c.655_659+2del		p.X219_splice	ENST00000460680	NM_004656.3	219		8/17	0.120767616831162	3	FACETS	0.971	0.925	1			1	INDETERMINATE	8	FALSE	NA	0.234054995082446	3		666	156	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390861	139390861	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	128	492	0	ENST00000277541.6:c.7330C>T	p.Gln2444Ter	p.Q2444*	ENST00000277541	NM_017617.3	2444	Cag/Tag	34/34	0.234054995082446	11	FACETS	1	0.935	1	1	0.986	1	CLONAL	8	FALSE	5	0.234054995082446	11		492	277	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0017586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	276	410	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.498494390557218	2	FACETS	0.985	0.935	1	0.985	0.935	1	CLONAL	2	TRUE	0	0.505610361758342	2		410	554	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106094	8106094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	122	334	0	ENST00000346208.3:c.914G>A	p.Arg305Gln	p.R305Q	ENST00000346208		305	cGa/cAa	4/6	0.15088592207742	3	FACETS	1	0.946	1			1	INDETERMINATE	1	TRUE	NA	0.505610361758342	3		334	570	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380277	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913238	NA	P-0017586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	423	558	1	ENST00000311936.3:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	61	Caa/Aaa	3/5	0.453534389276426	5	FACETS	0.919	0.878	0.961	0.919	0.878	0.961	CLONAL	3	TRUE	2	0.505610361758342	5		559	1067	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440943	56440943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786205215	NA	P-0017586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	435	551	1	ENST00000407977.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000407977		132	Cga/Tga	4/10	0.498494390557218	2	FACETS	0.954	0.915	0.993	0.954	0.915	0.993	CLONAL	2	TRUE	0	0.505610361758342	2		552	902	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223299	5223299	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	58	199	0	ENST00000357368.4:c.2504G>T	p.Arg835Leu	p.R835L	ENST00000357368	NM_002850.3	835	cGc/cTc	18/38	0.505610361758342	4	FACETS	0.954	0.824	1	0.318	0.274	0.365	CLONAL	1	TRUE	1	0.505610361758342	4		199	362	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845319	42845319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778525582	NA	P-0017586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	192	606	0	ENST00000398585.3:c.943G>A	p.Val315Ile	p.V315I	ENST00000398585	NM_001135099.1	315	Gtc/Atc	9/14	1	2	FACETS	0.928	0.86	0.999	0.928	0.86	0.999	CLONAL	1	TRUE	1	0.505610361758342	2		606	818	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	195	301	4				ENST00000310581	NM_198253.2	-/1132			0.242634205900902	3	FACETS	0.849	0.788	0.911	1	0.987	1	CLONAL	3	TRUE	1	0.242634205900902	3		305	708	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786031	135786031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766487204	NA	P-0017587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	47	416	0	ENST00000298552.3:c.1190C>T	p.Pro397Leu	p.P397L	ENST00000298552	NM_001162426.1	397	cCa/cTa	12/23	0.194435973979873	3	FACETS	0.468	0.393	0.551	0.234	0.196	0.276	SUBCLONAL	1	TRUE	1	0.242634205900902	3		416	928	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401225	139401225	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1218	275	555	0	ENST00000277541.6:c.3844C>T	p.Gln1282Ter	p.Q1282*	ENST00000277541	NM_017617.3	1282	Cag/Tag	23/34	0.194435973979873	3	FACETS	0.851	0.797	0.907	0.851	0.797	0.907	CLONAL	2	TRUE	1	0.242634205900902	3		555	1493	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500489	149500491	+	missense_variant	Missense_Mutation	TNP	CTC	CTC	GTT	novel	NA	P-0017587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	246	479	1	ENST00000261799.4:c.2546_2548delinsAAC	p.Arg849_Asp850delinsGlnHis	p.R849_D850delinsQH	ENST00000261799	NM_002609.3	849	cGAGac/cAACac	18/23	0.242634205900902	2	FACETS	0.827	0.772	0.884	0.827	0.772	0.884	CLONAL	2	TRUE	0	0.242634205900902	2		480	1226	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0017588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	38	672	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.320606024218055	1	FACETS	0.664	0.551	0.788	0.664	0.551	0.788	SUBCLONAL	1	TRUE	0	0.320606024218055	1		672	300	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0017588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	14	547	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.97	0.712	1	0.97	0.712	1	CLONAL	1	TRUE	1	0.320606024218055	2		547	90	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578246	28578246	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	26	664	1	ENST00000241453.7:c.2925C>A	p.Phe975Leu	p.F975L	ENST00000241453	NM_004119.2	975	ttC/ttA	24/24	0.320606024218055	1	FACETS	0.757	0.604	0.928	0.757	0.604	0.928	CLONAL	1	TRUE	0	0.320606024218055	1		665	180	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0017590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	154	180	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.288477534513265	3	FACETS	1	0.976	1	1	0.991	1	CLONAL	3	TRUE	1	0.288163836832869	3		180	363	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115737	8115737	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	512	782	0	ENST00000346208.3:c.1083C>G	p.Ile361Met	p.I361M	ENST00000346208		361	atC/atG	6/6	0.288163836832869	4	FACETS	0.959	0.918	1	1	0.996	1	CLONAL	3	TRUE	2	0.288163836832869	4		782	1591	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100631	67100631	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs868631081	NA	P-0017590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	450	501	1	ENST00000412916.2:c.329G>A	p.Trp110Ter	p.W110*	ENST00000412916		110	tGg/tAg	4/6	0.288477534513265	1	FACETS	1	0.993	1	1	0.998	1	CLONAL	3	TRUE	0	0.288163836832869	1		502	790	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840030	27840030	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	645	1038	0	ENST00000328488.2:c.64G>C	p.Ala22Pro	p.A22P	ENST00000328488	NM_003533.2	22	Gcc/Ccc	1/1	0.288477534513265	3	FACETS	1	0.992	1	1	0.997	1	CLONAL	3	TRUE	1	0.288163836832869	3		1038	1558	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090298	77090298	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	294	623	0	ENST00000356341.3:c.427A>C	p.Met143Leu	p.M143L	ENST00000356341	NM_002576.4	143	Atg/Ctg	4/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.61376232936216	2		623	879	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034492	47034492	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0017594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1218	96	771	1	ENST00000377604.3:c.576+1G>A		p.X192_splice	ENST00000377604	NM_001204468.1	192			1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		772	1314	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242483	+	protein_altering_variant	In_Frame_Del	DEL	ATTAAGAGAAGCAACA	ATTAAGAGAAGCAACA	G	novel	NA	P-0017594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	109	445	0	ENST00000275493.2:c.2238_2253delinsG	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACA/gaG	19/28	0.202307626231205	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		445	916	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652129	36652129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34916193	NA	P-0017596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	104	304	1	ENST00000244741.5:c.251G>A	p.Arg84Gln	p.R84Q	ENST00000244741	NM_000389.4	84	cGa/cAa	2/3	0.280493621776871	6	FACETS	1	0.958	1	0.381	0.34	0.424	CLONAL	1	TRUE	3	0.280493621776871	6		305	1013	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584536	189584536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	160	471	0	ENST00000264731.3:c.832G>A	p.Asp278Asn	p.D278N	ENST00000264731	NM_003722.4	278	Gat/Aat	6/14	0.289738071929165	3	FACETS	1	0.979	1	0.605	0.554	0.659	CLONAL	1	TRUE	1	0.280493621776871	3		471	1075	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136978	64136978	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0017596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	226	365	0	ENST00000334205.4:c.1489A>T	p.Lys497Ter	p.K497*	ENST00000334205	NM_003942.2	497	Aag/Tag	13/17	0.284677925050352	4	FACETS	1	0.983	1			1	CLONAL	2	TRUE	NA	0.280493621776871	4		365	891	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608308	28608308	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	101	445	0	ENST00000241453.7:c.1748G>C	p.Gly583Ala	p.G583A	ENST00000241453	NM_004119.2	583	gGc/gCc	14/24	1	2	FACETS	0.753	0.672	0.84	0.753	0.672	0.84	SUBCLONAL	1	TRUE	1	0.280493621776871	2		445	956	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227854	55227854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1166858113	NA	P-0017596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	43	288	0	ENST00000275493.2:c.1321G>A	p.Val441Ile	p.V441I	ENST00000275493	NM_005228.3	441	Gtc/Atc	12/28	0.223394945913156	4	FACETS	0.501	0.418	0.594	0.167	0.139	0.198	SUBCLONAL	1	TRUE	1	0.280493621776871	4		288	783	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501333	140501333	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397516903	NA	P-0017596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	308	210	0	ENST00000288602.6:c.739T>C	p.Phe247Leu	p.F247L	ENST00000288602	NM_004333.4	247	Ttt/Ctt	6/18	0.280493621776871	6	FACETS	0.965	0.92	1			1	CLONAL	6	TRUE	NA	0.280493621776871	6		210	592	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485812	8485812	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	130	382	0	ENST00000356435.5:c.3005C>T	p.Pro1002Leu	p.P1002L	ENST00000356435		1002	cCc/cTc	17/35	NA	2	FACETS	1	0.949	1			1	INDETERMINATE	1	TRUE	NA	0.280493621776871	2		382	866	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044699	47044699	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0017596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	749	284	0	ENST00000377604.3:c.2101-2A>T		p.X701_splice	ENST00000377604	NM_001204468.1	701			0.280493621776871	4	FACETS	0.937	0.912	0.963			1	CLONAL	6	TRUE	NA	0.280493621776871	4		284	1216	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579359	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	A	novel	NA	P-0017596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	252	406	0	ENST00000269305.4:c.328_329delinsT	p.Arg110PhefsTer13	p.R110Ffs*13	ENST00000269305	NM_001126112.2	110	CGt/Tt	4/11	0.280493621776871	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.280493621776871	2		406	873	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158443	108158443	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs879254034	NA	P-0017597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	35	226	1	ENST00000278616.4:c.4109+1G>T		p.X1370_splice	ENST00000278616	NM_000051.3	1370			0.20218079865083	2	FACETS	0.771	0.632	0.928	0.386	0.316	0.464	CLONAL	1	TRUE	0	0.208163922012402	2		227	436	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476272	88476272	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	65	532	2	ENST00000360948.2:c.1860G>A	p.Met620Ile	p.M620I	ENST00000360948	NM_001012338.2	620	atG/atA	15/19	1	2	FACETS	0.615	0.532	0.707	0.615	0.532	0.707	SUBCLONAL	1	TRUE	1	0.208163922012402	2		534	1015	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715595	30715595	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0017597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	43	291	0	ENST00000295754.5:c.1255-2A>C		p.X419_splice	ENST00000295754	NM_003242.5	419			1	2	FACETS	0.696	0.581	0.823	0.696	0.581	0.823	SUBCLONAL	1	TRUE	1	0.208163922012402	2		291	594	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0017598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	33	577	1	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	0.396371365346158	1	FACETS	0.129	0.104	0.157	0.129	0.104	0.157	SUBCLONAL	1	TRUE	0	0.396371365346158	1		578	1035	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577329	64577330	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	rs386134253	NA	P-0017601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	126	493	0	ENST00000312049.6:c.252_253insTT	p.Ile85LeufsTer35	p.I85Lfs*35	ENST00000312049	NM_130799.2	84	-/TT	2/10	0.379820278743465	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.379820278743465	1		493	490	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202741	16202741	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	146	610	0	ENST00000375759.3:c.449G>A	p.Gly150Glu	p.G150E	ENST00000375759	NM_015001.2	150	gGa/gAa	3/15	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.379820278743465	2		610	761	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037972	49037972	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0017602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	142	262	1	ENST00000267163.4:c.2211+1G>A		p.X737_splice	ENST00000267163	NM_000321.2	737			0.942316465410642	3	FACETS	0.713	0.652	0.777	0.357	0.326	0.389	SUBCLONAL	1	TRUE	1	0.946296251429099	3		263	620	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0017602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	452	305	1	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.946296251429099	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.946296251429099	2		306	470	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031955	26031955	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1624	147	771	1	ENST00000244661.2:c.334G>A	p.Ala112Thr	p.A112T	ENST00000244661	NM_003537.3	112	Gcc/Acc	1/1	0.737160940894933	3	FACETS	0.258	0.235	0.284	0.129	0.117	0.142	SUBCLONAL	1	TRUE	1	0.946296251429099	3		772	1771	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115873	8115874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0017603-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	128	621	0	ENST00000346208.3:c.1220dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tCcg	6/6	0.24748810776343	1	FACETS	0.804	0.729	0.883	0.804	0.729	0.883	CLONAL	1	TRUE	0	0.328888038728456	1		621	809	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061636	38061644	+	inframe_deletion	In_Frame_Del	DEL	GCACCCATG	GCACCCATG	-	novel	NA	P-0017603-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	41	179	0	ENST00000250448.2:c.345_353del	p.Met116_Ala118del	p.M116_A118del	ENST00000250448	NM_004496.3	115	gcCATGGGTGCg/gcg	2/2	0.328888038728456	4	FACETS	0.884	0.738	1	0.442	0.369	0.523	CLONAL	1	TRUE	2	0.328888038728456	4		179	375	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0017604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	119	178	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.282264992457273	4	FACETS	0.862	0.784	0.943	0.862	0.784	0.943	CLONAL	3	TRUE	1	0.282264992457273	4		178	418	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088787	27088788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0017604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	115	635	0	ENST00000324856.7:c.2402dup	p.Gln802SerfsTer15	p.Q802Sfs*15	ENST00000324856	NM_006015.4	799	cag/caGg	7/20	1	2	FACETS	0.841	0.756	0.931	0.841	0.756	0.931	CLONAL	1	TRUE	1	0.282264992457273	2		635	969	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105237122	105237124	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0017604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	99	708	0	ENST00000349310.3:c.1321_1323del	p.Glu441del	p.E441del	ENST00000349310	NM_001014432.1	441	GAG/-	14/15	1	2	FACETS	0.627	0.558	0.701	0.627	0.558	0.701	SUBCLONAL	1	TRUE	1	0.282264992457273	2		708	1118	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925546	114925546	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1635	198	1097	0	ENST00000543371.1:c.1624G>T	p.Glu542Ter	p.E542*	ENST00000543371	NM_001198531.1	542	Gag/Tag	14/14	0.279827672370792	3	FACETS	0.873	0.805	0.945	0.437	0.402	0.473	CLONAL	1	TRUE	1	0.282264992457273	3		1097	1833	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32968878	32968878	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	96	405	0	ENST00000380152.3:c.9311del	p.Lys3104SerfsTer4	p.K3104Sfs*4	ENST00000380152		3103	atA/at	25/27	0.279827672370792	3	FACETS	0.918	0.817	1	0.459	0.408	0.513	CLONAL	1	TRUE	1	0.282264992457273	3		405	846	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932666	39932666	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	186	940	1	ENST00000378444.4:c.1933G>C	p.Ala645Pro	p.A645P	ENST00000378444	NM_001123385.1	645	Gca/Cca	4/15	0.282264992457273	1	FACETS	0.868	0.8	0.939	0.868	0.8	0.939	CLONAL	1	TRUE	0	0.282264992457273	1		941	1304	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519975	NA	P-0017605-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	265	430	0	ENST00000269305.4:c.403T>C	p.Cys135Arg	p.C135R	ENST00000269305	NM_001126112.2	135	Tgc/Cgc	5/11	0.466655588447948	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.492609967300729	1		430	660	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911387	32911387	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017605-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	421	920	0	ENST00000380152.3:c.2895G>T	p.Met965Ile	p.M965I	ENST00000380152		965	atG/atT	11/27	0.492609967300729	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.492609967300729	1		920	1203	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	107	408	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.819	0.734	0.911	0.819	0.734	0.911	CLONAL	1	TRUE	1	0.261440914439282	2		408	999	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560477	65560477	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	196	445	0	ENST00000358664.4:c.120del	p.Asp41ThrfsTer24	p.D41Tfs*24	ENST00000358664	NM_002382.4	40	aaA/aa	3/5	0.221693383686046	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.261440914439282	1		445	1064	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726687	88726687	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	75	393	0	ENST00000360948.2:c.357G>T	p.Gln119His	p.Q119H	ENST00000360948	NM_001012338.2	119	caG/caT	4/19	1	2	FACETS	0.574	0.501	0.652	0.574	0.501	0.652	SUBCLONAL	1	TRUE	1	0.261440914439282	2		393	1000	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587781702	NA	P-0017606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	81	270	0	ENST00000269305.4:c.920-1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.261440914439282	1	FACETS	0.905	0.798	1	0.905	0.798	1	CLONAL	1	TRUE	0	0.261440914439282	1		270	595	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111037	193111038	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0017606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	56	263	2	ENST00000367435.3:c.570_571delinsTT	p.Met190_Ala191delinsIleSer	p.M190_A191delinsIS	ENST00000367435	NM_024529.4	190	atGGct/atTTct	7/17	0.163260029984725	3	FACETS	0.691	0.591	0.801	0.346	0.295	0.401	SUBCLONAL	1	TRUE	1	0.261440914439282	3		265	701	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857624	9857624	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	101	359	0	ENST00000330684.3:c.3777C>A	p.Asn1259Lys	p.N1259K	ENST00000330684	NM_001134407.1	1259	aaC/aaA	13/13	1	2	FACETS	0.947	0.846	1	0.947	0.846	1	CLONAL	1	TRUE	1	0.261440914439282	2		359	816	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032027	10032027	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1439	215	653	0	ENST00000330684.3:c.796G>A	p.Glu266Lys	p.E266K	ENST00000330684	NM_001134407.1	266	Gag/Aag	3/13	1	2	FACETS	0.994	0.921	1	0.994	0.921	1	CLONAL	1	TRUE	1	0.261440914439282	2		653	1654	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89806495	89806495	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	112	405	0	ENST00000389301.3:c.3841C>A	p.Leu1281Met	p.L1281M	ENST00000389301	NM_000135.2	1281	Ctg/Atg	39/43	1	2	FACETS	0.919	0.826	1	0.919	0.826	1	CLONAL	1	TRUE	1	0.261440914439282	2		405	932	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652837	29652837	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0017606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	89	255	1	ENST00000356175.3:c.4773-1G>T		p.X1591_splice	ENST00000356175	NM_000267.3	1591			1	2	FACETS	0.844	0.747	0.947	0.844	0.747	0.947	CLONAL	1	TRUE	1	0.261440914439282	2		256	807	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740710	58740710	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1254993767	NA	P-0017606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1852	318	844	2	ENST00000305921.3:c.1615G>T	p.Glu539Ter	p.E539*	ENST00000305921	NM_003620.3	539	Gaa/Taa	6/6	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.261440914439282	2		846	2170	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528641	89528641	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	98	245	0	ENST00000336596.2:c.2941G>T	p.Val981Phe	p.V981F	ENST00000336596	NM_005233.5	981	Gtt/Ttt	17/17	0.163260029984725	3	FACETS	1	0.931	1	0.529	0.472	0.59	CLONAL	1	TRUE	1	0.261440914439282	3		245	801	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196937	106196937	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	143	401	0	ENST00000380013.4:c.5270A>T	p.His1757Leu	p.H1757L	ENST00000380013	NM_001127208.2	1757	cAt/cTt	11/11	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.261440914439282	2		401	1093	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931762	39931762	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1370	221	686	0	ENST00000378444.4:c.2837A>T	p.Glu946Val	p.E946V	ENST00000378444	NM_001123385.1	946	gAg/gTg	4/15	0.226663675828786	1	FACETS	0.924	0.857	0.993	0.924	0.857	0.993	CLONAL	1	TRUE	0	0.261440914439282	1		686	1591	SUCCESS
AR	367	MSKCC	GRCh37	X	66765707	66765707	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1670	113	757	0	ENST00000374690.3:c.719G>C	p.Cys240Ser	p.C240S	ENST00000374690	NM_000044.3	240	tGt/tCt	1/8	0.226663675828786	1	FACETS	0.421	0.377	0.469	0.421	0.377	0.469	SUBCLONAL	1	TRUE	0	0.261440914439282	1		757	1783	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938671	76938671	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	78	494	0	ENST00000373344.5:c.2077G>T	p.Val693Phe	p.V693F	ENST00000373344	NM_000489.3	693	Gtt/Ttt	9/35	0.226663675828786	1	FACETS	0.423	0.37	0.481	0.423	0.37	0.481	SUBCLONAL	1	TRUE	0	0.261440914439282	1		494	1225	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0017607-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	125	469	1	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.285212782538165	1	FACETS	0.935	0.846	1	0.935	0.846	1	CLONAL	1	TRUE	0	0.285212782538165	1		470	804	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0017607-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	86	308	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.954	0.845	1	0.954	0.845	1	CLONAL	1	TRUE	1	0.285212782538165	2		308	632	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059200	47059201	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTCA	novel	NA	P-0017607-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	69	327	0	ENST00000409792.3:c.7457_7460dup	p.Pro2488GlufsTer7	p.P2488Efs*7	ENST00000409792	NM_014159.6	2487	aac/aaTGAAc	20/21	1	2	FACETS	0.692	0.602	0.79	0.692	0.602	0.79	SUBCLONAL	1	TRUE	1	0.285212782538165	2		327	699	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394763	45394779	+	frameshift_variant	Frame_Shift_Del	DEL	AGTCATCCAGAGGCGGA	AGTCATCCAGAGGCGGA	-	novel	NA	P-0017607-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	38	218	0	ENST00000262160.6:c.570_586del	p.Pro191TyrfsTer9	p.P191Yfs*9	ENST00000262160	NM_005901.5	190	ctTCCGCCTCTGGATGACTat/ctat	5/11	1	2	FACETS	0.485	0.4	0.58	0.485	0.4	0.58	SUBCLONAL	1	TRUE	1	0.285212782538165	2		218	549	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127768	47127768	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017607-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	108	306	0	ENST00000409792.3:c.5314G>T	p.Glu1772Ter	p.E1772*	ENST00000409792	NM_014159.6	1772	Gaa/Taa	11/21	1	2	FACETS	0.916	0.821	1	0.916	0.821	1	CLONAL	1	TRUE	1	0.285212782538165	2		306	827	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467706	50467706	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017607-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	158	449	0	ENST00000331340.3:c.941C>G	p.Ala314Gly	p.A314G	ENST00000331340	NM_006060.4	314	gCc/gGc	8/8	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.285212782538165	2		449	1104	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750866	128750866	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1478921898	NA	P-0017607-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	283	591	0	ENST00000377970.2:c.403G>A	p.Asp135Asn	p.D135N	ENST00000377970	NM_002467.4	135	Gac/Aac	2/3	0.272133972758197	3	FACETS	0.944	0.887	1	0.944	0.887	1	CLONAL	2	TRUE	1	0.285212782538165	3		591	1201	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0017608-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	23	290	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.451	0.35	0.569	0.451	0.35	0.569	SUBCLONAL	1	TRUE	1	0.14	2		290	728	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872827	136872827	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017608-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1591	128	980	3	ENST00000241393.3:c.671C>T	p.Ser224Phe	p.S224F	ENST00000241393	NM_003467.2	224	tCc/tTc	2/2	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.14	2		983	1719	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711883	89711884	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0017612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	157	385	0	ENST00000371953.3:c.502_503del	p.Ile168SerfsTer11	p.I168Sfs*11	ENST00000371953	NM_000314.4	167	acTAtt/actt	6/9	0.44144227064641	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.44144227064641	1		385	503	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457283	67457285	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	novel	NA	P-0017612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	182	493	0	ENST00000327367.4:c.259_261del	p.Ile87del	p.I87del	ENST00000327367	NM_005902.3	86	gTCAtc/gtc	2/9	1	2	FACETS	0.979	0.905	1	0.979	0.905	1	CLONAL	1	TRUE	1	0.44144227064641	2		493	842	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270593	98270595	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	rs756897237	NA	P-0017613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	11	79	0	ENST00000331920.6:c.49_51del	p.Gly17del	p.G17del	ENST00000331920	NM_000264.3	17	GGC/-	1/24	1	2	FACETS	0.737	0.509	1	0.737	0.509	1	CLONAL	1	TRUE	1	0.15	2		79	199	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182641	38182641	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs387907272	NA	P-0017613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	93	484	0	ENST00000396334.3:c.794T>C	p.Leu265Pro	p.L265P	ENST00000396334	NM_002468.4	265	cTg/cCg	5/5	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.15	2		484	1023	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0017614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	175	330	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.879	0.814	0.947	0.879	0.814	0.947	CLONAL	1	TRUE	1	0.644105529159274	2		330	618	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892272	9892272	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	316	427	0	ENST00000330684.3:c.2218G>T	p.Gly740Trp	p.G740W	ENST00000330684	NM_001134407.1	740	Ggg/Tgg	11/13	1	2	FACETS	0.925	0.874	0.977	0.925	0.874	0.977	CLONAL	1	TRUE	1	0.644105529159274	2		427	1061	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0017615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	288	344	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.975	0.921	1	0.975	0.921	1	CLONAL	1	TRUE	1	0.772618237943366	2		344	765	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673771	37673772	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAGC	novel	NA	P-0017615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	294	469	0	ENST00000447079.4:c.2928_2931dup	p.Tyr978AlafsTer19	p.Y978Afs*19	ENST00000447079	NM_015083.1	975	-/AAGC	10/14	0.772305820741143	1	FACETS	0.876	0.835	0.917	0.876	0.835	0.917	CLONAL	1	TRUE	0	0.772618237943366	1		469	533	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017616-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	203	454	1	ENST00000206249.3:c.1607T>A	p.Leu536His	p.L536H	ENST00000206249	NM_000125.3	536	cTc/cAc	8/8	0.565745416254082	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.567855292678221	1		455	435	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115956	8115956	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017616-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	127	319	0	ENST00000346208.3:c.1305del	p.Ser436ProfsTer39	p.S436Pfs*39	ENST00000346208		434	caC/ca	6/6	0.182009998758714	4	FACETS	0.762	0.695	0.832	0.762	0.695	0.832	INDETERMINATE	2	TRUE	2	0.567855292678221	4		319	460	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577439	64577440	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0017616-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	212	828	0	ENST00000312049.6:c.142_143del	p.Leu48GlyfsTer68	p.L48Gfs*68	ENST00000312049	NM_130799.2	48	CTg/g	2/10	0.549527374161745	1	FACETS	0.881	0.823	0.939	0.881	0.823	0.939	CLONAL	1	TRUE	0	0.567855292678221	1		828	607	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016562	12016562	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017616-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	114	459	0	ENST00000353533.5:c.698C>T	p.Ser233Phe	p.S233F	ENST00000353533	NM_003010.3	233	tCc/tTc	7/11	0.293379637087356	1	FACETS	0.55	0.497	0.605	0.55	0.497	0.605	INDETERMINATE	1	TRUE	0	0.567855292678221	1		459	523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578191	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs530941076	NA	P-0017617-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	1206	851	2	ENST00000269305.4:c.658T>C	p.Tyr220His	p.Y220H	ENST00000269305	NM_001126112.2	220	Tat/Cat	6/11	0.854821356236767	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.854821356236767	2		853	1318	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335115	65335115	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017617-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	775	655	0	ENST00000342505.4:c.526C>A	p.Pro176Thr	p.P176T	ENST00000342505	NM_002227.2	176	Ccc/Acc	6/25	0.854821356236767	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.854821356236767	4		655	1639	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120548042	120548042	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017617-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	14	73	0	ENST00000256646.2:c.325T>A	p.Cys109Ser	p.C109S	ENST00000256646	NM_024408.3	109	Tgc/Agc	3/34	0.854821356236767	4	FACETS	0.471	0.343	0.623	0.235	0.171	0.312	SUBCLONAL	1	TRUE	2	0.854821356236767	4		73	129	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039400	49039401	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0017617-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	521	803	2	ENST00000267163.4:c.2388dup	p.Arg798ThrfsTer17	p.R798Tfs*17	ENST00000267163	NM_000321.2	795	-/C	23/27	0.854821356236767	2	FACETS	0.986	0.965	1	0.986	0.965	1	CLONAL	2	TRUE	0	0.854821356236767	2		805	618	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296169	15296169	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017617-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	713	611	0	ENST00000263388.2:c.2195G>T	p.Ser732Ile	p.S732I	ENST00000263388	NM_000435.2	732	aGc/aTc	14/33	0.854821356236767	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.854821356236767	2		611	769	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38946575	38946575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017617-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	153	340	0	ENST00000357387.3:c.4394C>T	p.Ala1465Val	p.A1465V	ENST00000357387	NM_152756.3	1465	gCa/gTa	33/38	0.854821356236767	3	FACETS	0.95	0.89	1	0.95	0.89	1	CLONAL	2	TRUE	1	0.854821356236767	3		340	269	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179456	56179456	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017617-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	223	474	0	ENST00000399503.3:c.3769T>C	p.Cys1257Arg	p.C1257R	ENST00000399503	NM_005921.1	1257	Tgt/Cgt	15/20	0.854821356236767	3	FACETS	0.996	0.945	1	0.996	0.945	1	CLONAL	2	TRUE	1	0.854821356236767	3		474	374	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0017619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	138	401	3	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.227117119619071	2	FACETS	0.767	0.699	0.837	0.767	0.699	0.837	SUBCLONAL	2	TRUE	0	0.270255350912174	2		404	666	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0017619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	215	418	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.157259670253058	2	FACETS	0.836	0.777	0.896	0.836	0.777	0.896	INDETERMINATE	2	TRUE	0	0.270255350912174	2		419	952	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408891	41408891	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs547641233	NA	P-0017619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	172	550	0	ENST00000373198.4:c.535G>T	p.Val179Leu	p.V179L	ENST00000373198	NM_133170.3	179	Gtg/Ttg	4/32	0.270255350912174	1	FACETS	0.959	0.881	1	0.959	0.881	1	CLONAL	1	TRUE	0	0.270255350912174	1		550	1148	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198946	67198946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	249	445	0	ENST00000312629.5:c.417G>T	p.Gln139His	p.Q139H	ENST00000312629	NM_003952.2	139	caG/caT	5/15	0.23538097743447	3	FACETS	0.863	0.806	0.922	0.863	0.806	0.922	CLONAL	2	TRUE	1	0.270255350912174	3		445	1212	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480324	56480324	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	128	410	0	ENST00000267101.3:c.431C>A	p.Ser144Ter	p.S144*	ENST00000267101	NM_001982.3	144	tCa/tAa	4/28	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.270255350912174	NA		410	783	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422157	81422157	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	59	425	0	ENST00000298171.2:c.133C>G	p.Gln45Glu	p.Q45E	ENST00000298171	NM_000369.2	45	Caa/Gaa	1/10	1	2	FACETS	0.452	0.387	0.522	0.452	0.387	0.522	SUBCLONAL	1	TRUE	1	0.270255350912174	2		425	967	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610476	81610476	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	180	618	0	ENST00000298171.2:c.2074C>A	p.Leu692Ile	p.L692I	ENST00000298171	NM_000369.2	692	Cta/Ata	10/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.270255350912174	2		618	1179	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239420	105239420	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	146	443	0	ENST00000349310.3:c.967G>C	p.Asp323His	p.D323H	ENST00000349310	NM_001014432.1	323	Gac/Cac	12/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.270255350912174	2		443	834	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156095	106156095	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	214	525	0	ENST00000380013.4:c.998del	p.Pro333HisfsTer14	p.P333Hfs*14	ENST00000380013	NM_001127208.2	332	tgC/tg	3/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.270255350912174	2		525	1238	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675502	30675502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1162	68	653	0	ENST00000376406.3:c.2854G>A	p.Glu952Lys	p.E952K	ENST00000376406	NM_014641.2	952	Gag/Aag	8/15	1	2	FACETS	0.409	0.354	0.469	0.409	0.354	0.469	SUBCLONAL	1	TRUE	1	0.270255350912174	2		653	1230	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675513	30675513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757301316	NA	P-0017619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1267	79	704	1	ENST00000376406.3:c.2843G>A	p.Arg948Lys	p.R948K	ENST00000376406	NM_014641.2	948	aGa/aAa	8/15	1	2	FACETS	0.434	0.38	0.493	0.434	0.38	0.493	SUBCLONAL	1	TRUE	1	0.270255350912174	2		705	1346	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675733	30675733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1550	94	740	1	ENST00000376406.3:c.2623G>A	p.Asp875Asn	p.D875N	ENST00000376406	NM_014641.2	875	Gac/Aac	8/15	1	2	FACETS	0.423	0.375	0.475	0.423	0.375	0.475	SUBCLONAL	1	TRUE	1	0.270255350912174	2		741	1644	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675739	30675739	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1630	99	762	0	ENST00000376406.3:c.2617G>C	p.Glu873Gln	p.E873Q	ENST00000376406	NM_014641.2	873	Gaa/Caa	8/15	1	2	FACETS	0.424	0.376	0.475	0.424	0.376	0.475	SUBCLONAL	1	TRUE	1	0.270255350912174	2		762	1729	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527763	157527764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	79	329	0	ENST00000346085.5:c.5490dup	p.Gln1831SerfsTer5	p.Q1831Sfs*5	ENST00000346085	NM_020732.3	1830	att/aTtt	20/20	0.270255350912174	1	FACETS	0.846	0.744	0.954	0.846	0.744	0.954	CLONAL	1	TRUE	0	0.270255350912174	1		329	598	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372685	81372685	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0017619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	166	503	1	ENST00000222390.5:c.849T>A	p.Cys283Ter	p.C283*	ENST00000222390	NM_000601.4	283	tgT/tgA	7/18	0.151470941852515	3	FACETS	1	0.956	1	0.533	0.488	0.58	INDETERMINATE	1	TRUE	1	0.270255350912174	3		504	1309	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0017620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	293	573	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.690746540006306	2		573	789	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	170	408	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.23133920775991	4	FACETS	0.846	0.78	0.914	0.846	0.78	0.914	CLONAL	3	TRUE	1	0.23133920775991	4		408	713	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0017621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	114	294	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.23133920775991	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.23133920775991	3		294	502	SUCCESS
APC	324	MSKCC	GRCh37	5	112177094	112177095	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0017621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	69	513	0	ENST00000257430.4:c.5803_5804del	p.Gln1935ValfsTer13	p.Q1935Vfs*13	ENST00000257430	NM_000038.5	1935	CAg/g	16/16	0.23133920775991	3	FACETS	0.835	0.726	0.953	0.418	0.363	0.477	CLONAL	1	TRUE	1	0.23133920775991	3		513	797	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0017622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	397	501	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	0.949	0.907	0.99	1	0.997	1	CLONAL	4	TRUE	1	0.247062443182575	2		501	847	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186501402	186501402	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0017622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5895	748	1190	0	ENST00000323963.5:c.3G>A	p.Met1?	p.M1?	ENST00000323963		1	atG/atA	1/11	0.247062443182575	22	FACETS	1	0.985	1			1	CLONAL	3	TRUE	NA	0.247062443182575	22		1190	6643	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056989	180056989	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	120	742	1	ENST00000261937.6:c.630G>A	p.Trp210Ter	p.W210*	ENST00000261937	NM_182925.4	210	tgG/tgA	5/30	0.250843697354705	1	FACETS	0.793	0.714	0.876	0.793	0.714	0.876	SUBCLONAL	1	TRUE	0	0.247062443182575	1		743	1074	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567827	226567827	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	306	438	0	ENST00000366794.5:c.1339A>C	p.Lys447Gln	p.K447Q	ENST00000366794	NM_001618.3	447	Aag/Cag	10/23	1	2	FACETS	0.959	0.911	1	1	0.997	1	CLONAL	4	TRUE	1	0.247062443182575	2		438	646	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781348	3781349	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCT	novel	NA	P-0017622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	406	623	0	ENST00000262367.5:c.5014_5016dup	p.Arg1672dup	p.R1672dup	ENST00000262367	NM_004380.2	1672	-/AGA	30/31	1	2	FACETS	0.899	0.859	0.939	1	0.997	1	CLONAL	4	TRUE	1	0.247062443182575	2		623	914	SUCCESS
APC	324	MSKCC	GRCh37	5	112174187	112174187	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	108	513	0	ENST00000257430.4:c.2896A>C	p.Ser966Arg	p.S966R	ENST00000257430	NM_000038.5	966	Agt/Cgt	16/16	1	2	FACETS	0.947	0.849	1	0.947	0.849	1	CLONAL	1	TRUE	1	0.247062443182575	2		513	923	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0017623-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	78	330	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.45289207158695	4	FACETS	1	0.977	1	0.713	0.634	0.796	CLONAL	1	FALSE	2	0.672445556134064	4		330	272	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0017623-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	417	680	0	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	0.672445556134064	9	FACETS	0.906	0.864	0.948			1	CLONAL	4	FALSE	NA	0.672445556134064	9		680	1148	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117311	115117311	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017623-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	412	550	0	ENST00000257566.3:c.863del	p.Lys288ArgfsTer2	p.K288Rfs*2	ENST00000257566	NM_016569.3	288	aAg/ag	4/8	0.672445556134064	10	FACETS	0.97	0.925	1			1	CLONAL	4	FALSE	NA	0.672445556134064	10		550	1165	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16052795	16052795	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017623-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	40	333	0	ENST00000268712.3:c.879del	p.Phe293LeufsTer33	p.F293Lfs*33	ENST00000268712	NM_006311.3	293	ttT/tt	9/46	0.200440119873049	5	FACETS	0.622	0.518	0.738	0.124	0.103	0.148	INDETERMINATE	1	FALSE	0	0.672445556134064	5		333	384	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100621	8100622	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0017623-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	172	730	0	ENST00000346208.3:c.598dup	p.His200ProfsTer103	p.H200Pfs*103	ENST00000346208		199	tcc/tCcc	3/6	0.400774396487708	4	FACETS	0.789	0.725	0.855	0.394	0.362	0.428	INDETERMINATE	1	FALSE	2	0.672445556134064	4		730	1085	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115111990	115111990	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017623-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	55	307	0	ENST00000257566.3:c.1750C>T	p.Gln584Ter	p.Q584*	ENST00000257566	NM_016569.3	584	Cag/Tag	7/8	0.672445556134064	10	FACETS	0.936	0.8	1			1	CLONAL	1	FALSE	NA	0.672445556134064	10		307	645	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587511	29587511	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017623-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	153	358	0	ENST00000356175.3:c.4494del	p.Gln1499SerfsTer54	p.Q1499Sfs*54	ENST00000356175	NM_000267.3	1498	Ggg/gg	33/57	0.681023854301155	3	FACETS	0.817	0.758	0.878	0.817	0.758	0.878	CLONAL	2	FALSE	1	0.672445556134064	3		358	372	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252972	36252974	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	novel	NA	P-0017623-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	627	361	1	ENST00000300305.3:c.388_390del	p.Val130del	p.V130del	ENST00000300305		130	GTC/-	4/8	0.672445556134064	6	FACETS	0.969	0.933	1	0.726	0.7	0.753	CLONAL	3	FALSE	2	0.672445556134064	6		362	1505	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174833	56174849	+	frameshift_variant	Frame_Shift_Del	DEL	TACTCCTTGCCACAGTT	TACTCCTTGCCACAGTT	-	novel	NA	P-0017623-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	264	543	0	ENST00000399503.3:c.1994_2010del	p.Thr665SerfsTer26	p.T665Sfs*26	ENST00000399503	NM_005921.1	664	taTACTCCTTGCCACAGTTta/tata	11/20	0.672445556134064	9	FACETS	0.95	0.892	1			1	CLONAL	3	FALSE	NA	0.672445556134064	9		543	924	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0017624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	57	180	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.306049834152289	3	FACETS	0.895	0.776	1	0.895	0.776	1	CLONAL	2	TRUE	1	0.306049834152289	3		180	240	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853195	68853195	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886039590	NA	P-0017624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	226	459	0	ENST00000261769.5:c.1578G>A	p.Trp526Ter	p.W526*	ENST00000261769	NM_004360.3	526	tgG/tgA	11/16	NA	2	FACETS	0.964	0.901	1			1	INDETERMINATE	2	TRUE	NA	0.306049834152289	2		459	766	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032846	30032848	+	missense_variant	Missense_Mutation	TNP	GGC	GGC	TGT	novel	NA	P-0017624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	108	433	0	ENST00000338641.4:c.221_223delinsTGT	p.Trp74_Leu75delinsLeuPhe	p.W74_L75delinsLF	ENST00000338641	NM_000268.3	74	tGGCtc/tTGTtc	2/16	1	2	FACETS	0.988	0.888	1	0.988	0.888	1	CLONAL	1	TRUE	1	0.306049834152289	2		433	714	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877429	89877429	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759763556	NA	P-0017625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	586	770	0	ENST00000389301.3:c.334C>T	p.Leu112Phe	p.L112F	ENST00000389301	NM_000135.2	112	Ctc/Ttc	4/43	1	2	FACETS	0.956	0.918	0.994	0.956	0.918	0.994	CLONAL	1	TRUE	1	0.761651117003185	2		770	1610	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051638	30051638	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	81	482	0	ENST00000338641.4:c.572G>A	p.Trp191Ter	p.W191*	ENST00000338641	NM_000268.3	191	tGg/tAg	6/16	0.759532386411271	1	FACETS	0.203	0.179	0.229	0.203	0.179	0.229	SUBCLONAL	1	TRUE	0	0.761651117003185	1		482	648	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440359	52440366	+	protein_altering_variant	In_Frame_Del	DEL	CATCAGGT	CATCAGGT	TA	novel	NA	P-0017625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	378	549	2	ENST00000460680.1:c.686_693delinsTA	p.Asn229_Met231delinsIle	p.N229_M231delinsI	ENST00000460680	NM_004656.3	229	aACCTGATG/aTA	9/17	1	2	FACETS	0.972	0.925	1	0.972	0.925	1	CLONAL	1	TRUE	1	0.761651117003185	2		551	1021	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441465	52441465	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0017625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	430	584	0	ENST00000460680.1:c.387T>A	p.Tyr129Ter	p.Y129*	ENST00000460680	NM_004656.3	129	taT/taA	6/17	1	2	FACETS	0.921	0.879	0.964	0.921	0.879	0.964	CLONAL	1	TRUE	1	0.761651117003185	2		584	1226	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845124	128845124	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs751636409	NA	P-0017625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1233	436	823	2	ENST00000249373.3:c.618G>A	p.Trp206Ter	p.W206*	ENST00000249373	NM_005631.4	206	tgG/tgA	3/12	1	2	FACETS	0.686	0.653	0.72	0.686	0.653	0.72	SUBCLONAL	1	TRUE	1	0.761651117003185	2		825	1669	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0017626-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	134	470	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.193360863918343	5	FACETS	0.85	0.772	0.931	0.566	0.515	0.621	CLONAL	2	TRUE	2	0.287632427669375	5		470	785	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017626-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	145	374	0	ENST00000269305.4:c.475del	p.Ala159ProfsTer11	p.A159Pfs*11	ENST00000269305	NM_001126112.2	159	Gcc/cc	5/11	0.234343837752349	2	FACETS	0.786	0.72	0.856	0.786	0.72	0.856	SUBCLONAL	2	TRUE	0	0.287632427669375	2		374	641	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638185	176638185	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017626-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	51	324	0	ENST00000439151.2:c.2785A>G	p.Thr929Ala	p.T929A	ENST00000439151	NM_022455.4	929	Act/Gct	5/23	0.287632427669375	3	FACETS	0.677	0.575	0.79			1	SUBCLONAL	1	TRUE	NA	0.287632427669375	3		324	599	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206938	162206938	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017626-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	21	203	0	ENST00000366898.1:c.737G>T	p.Ser246Ile	p.S246I	ENST00000366898	NM_004562.2	246	aGc/aTc	7/12	0.230611776877238	2	FACETS	0.467	0.359	0.592	0.233	0.179	0.296	SUBCLONAL	1	TRUE	0	0.287632427669375	2		203	313	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851600	128851600	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017626-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	78	410	0	ENST00000249373.3:c.1925T>G	p.Val642Gly	p.V642G	ENST00000249373	NM_005631.4	642	gTg/gGg	11/12	0.193360863918343	5	FACETS	1	0.887	1	0.337	0.295	0.382	CLONAL	1	TRUE	2	0.287632427669375	5		410	768	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495796	56495796	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	100	296	0	ENST00000267101.3:c.3986G>A	p.Trp1329Ter	p.W1329*	ENST00000267101	NM_001982.3	1329	tGg/tAg	28/28	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.31	NA		296	791	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048253	180048253	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0017627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	90	327	0	ENST00000261937.6:c.2021-1G>T		p.X674_splice	ENST00000261937	NM_182925.4	674			0.295351600004123	6	FACETS	0.882	0.78	0.991	0.176	0.156	0.199	CLONAL	1	TRUE	1	0.31	6		327	1067	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242487	+	protein_altering_variant	In_Frame_Del	DEL	GAATTAAGAGAAGCAACATCTC	GAATTAAGAGAAGCAACATCTC	CTCT	novel	NA	P-0017627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	155	330	1	ENST00000275493.2:c.2236_2257delinsCTCT	p.Glu746_Pro753delinsLeuSer	p.E746_P753delinsLS	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCAACATCTCcg/CTCTcg	19/28	0.295351600004123	5	FACETS	0.835	0.765	0.909	0.557	0.51	0.606	CLONAL	2	TRUE	2	0.31	5		331	877	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740325	145740328	+	frameshift_variant	Frame_Shift_Del	DEL	CATC	CATC	-	novel	NA	P-0017627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	87	352	0	ENST00000428558.2:c.1612_1615del	p.Asp538ThrfsTer19	p.D538Tfs*19	ENST00000428558	NM_004260.3	538	GATGac/ac	9/22	0.295351600004123	6	FACETS	0.84	0.741	0.945			1	CLONAL	1	TRUE	NA	0.31	6		352	1083	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0017628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	405	451	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.666787581851973	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.754312382489214	1		451	648	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0017628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	372	451	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.754312382489214	1	FACETS	0.997	0.958	1	0.997	0.958	1	CLONAL	1	TRUE	0	0.754312382489214	1		451	616	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104298	2104298	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	337	370	0	ENST00000219476.3:c.338G>A	p.Gly113Asp	p.G113D	ENST00000219476	NM_000548.3	113	gGc/gAc	5/42	1	2	FACETS	0.906	0.859	0.954	0.906	0.859	0.954	CLONAL	1	TRUE	1	0.754312382489214	2		370	986	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172166	99172166	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	420	654	0	ENST00000074304.5:c.1732A>G	p.Ser578Gly	p.S578G	ENST00000074304	NM_001134224.1	578	Agc/Ggc	17/26	0.362509657846756	1	FACETS	0.656	0.627	0.686	0.656	0.627	0.686	INDETERMINATE	1	TRUE	0	0.754312382489214	1		654	1057	SUCCESS
ATR	545	MSKCC	GRCh37	3	142180781	142180781	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0017628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	191	353	0	ENST00000350721.4:c.7192+1G>A		p.X2398_splice	ENST00000350721	NM_001184.3	2398			1	2	FACETS	0.514	0.475	0.555	0.514	0.475	0.555	SUBCLONAL	1	TRUE	1	0.754312382489214	2		353	985	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456558	189456558	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs757222487	NA	P-0017628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	311	324	0	ENST00000264731.3:c.319A>G	p.Met107Val	p.M107V	ENST00000264731	NM_003722.4	107	Atg/Gtg	3/14	1	2	FACETS	0.909	0.86	0.959	0.909	0.86	0.959	CLONAL	1	TRUE	1	0.754312382489214	2		324	907	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518254	187518254	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	87	161	0	ENST00000441802.2:c.12440G>T	p.Gly4147Val	p.G4147V	ENST00000441802	NM_005245.3	4147	gGc/gTc	25/27	0.754312382489214	1	FACETS	0.708	0.64	0.776	0.708	0.64	0.776	SUBCLONAL	1	TRUE	0	0.754312382489214	1		161	203	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017630-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	87	301	4				ENST00000310581	NM_198253.2	-/1132			0.294591342951444	3	FACETS	1	0.954	1	0.573	0.508	0.641	CLONAL	1	TRUE	1	0.339056158009556	3		305	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0017630-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	371	795	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.339056158009556	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.339056158009556	1		796	1524	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460359	149460359	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017630-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	236	474	0	ENST00000286301.3:c.278G>T	p.Gly93Val	p.G93V	ENST00000286301	NM_005211.3	93	gGc/gTc	3/22	0.339056158009556	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.339056158009556	1		474	876	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120199	70120199	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017630-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	185	514	0	ENST00000245479.2:c.1201C>A	p.Gln401Lys	p.Q401K	ENST00000245479	NM_000346.3	401	Cag/Aag	3/3	1	2	FACETS	0.935	0.862	1	0.935	0.862	1	CLONAL	1	TRUE	1	0.339056158009556	2		514	1167	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590664	189590664	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017630-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	61	498	0	ENST00000264731.3:c.1229C>A	p.Thr410Asn	p.T410N	ENST00000264731	NM_003722.4	410	aCt/aAt	10/14	1	2	FACETS	0.308	0.265	0.356	0.308	0.265	0.356	SUBCLONAL	1	TRUE	1	0.339056158009556	2		498	1167	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220524	123220524	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017630-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	370	498	0	ENST00000218089.9:c.3181A>C	p.Ser1061Arg	p.S1061R	ENST00000218089	NM_001042749.1	1061	Agt/Cgt	30/35	1	1	FACETS	0.912	0.867	0.957	1	0.996	1	CLONAL	2	TRUE	0	0.339056158009556	1		498	994	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0017632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	124	470	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.273089832390838	4	FACETS	0.913	0.829	1	0.913	0.829	1	CLONAL	2	TRUE	2	0.288100822998836	4		470	607	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153485	108153485	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs587782861	NA	P-0017632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	75	355	0	ENST00000278616.4:c.3627del	p.Phe1209LeufsTer6	p.F1209Lfs*6	ENST00000278616	NM_000051.3	1209	Ttt/tt	25/63	1	2	FACETS	0.74	0.648	0.839	0.74	0.648	0.839	SUBCLONAL	1	TRUE	1	0.288100822998836	2		355	704	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221320	1221320	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587776656	NA	P-0017637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	81	539	0	ENST00000326873.7:c.843del	p.Leu282SerfsTer5	p.L282Sfs*5	ENST00000326873	NM_000455.4	281	ccG/cc	6/10	1	2	FACETS	0.769	0.676	0.868	0.769	0.676	0.868	SUBCLONAL	1	TRUE	1	0.250601804879078	2		539	841	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862837	9862837	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	92	638	1	ENST00000330684.3:c.2466C>A	p.Tyr822Ter	p.Y822*	ENST00000330684	NM_001134407.1	822	taC/taA	12/13	1	2	FACETS	0.689	0.611	0.774	0.689	0.611	0.774	SUBCLONAL	1	TRUE	1	0.250601804879078	2		639	1065	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619360	37619360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	15	190	0	ENST00000447079.4:c.1036C>T	p.Pro346Ser	p.P346S	ENST00000447079	NM_015083.1	346	Cca/Tca	1/14	1	2	FACETS	0.404	0.295	0.536	0.404	0.295	0.536	SUBCLONAL	1	TRUE	1	0.250601804879078	2		190	296	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191141	2191141	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1289	120	863	0	ENST00000398665.3:c.395C>G	p.Ser132Cys	p.S132C	ENST00000398665	NM_032482.2	132	tCc/tGc	5/28	1	2	FACETS	0.68	0.611	0.752	0.68	0.611	0.752	SUBCLONAL	1	TRUE	1	0.250601804879078	2		863	1409	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610288	10610288	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	94	745	1	ENST00000171111.5:c.422A>T	p.Tyr141Phe	p.Y141F	ENST00000171111	NM_203500.1	141	tAc/tTc	2/6	1	2	FACETS	0.718	0.637	0.804	0.718	0.637	0.804	SUBCLONAL	1	TRUE	1	0.250601804879078	2		746	1045	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288486	15288486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	32	395	0	ENST00000263388.2:c.4253C>T	p.Ser1418Leu	p.S1418L	ENST00000263388	NM_000435.2	1418	tCg/tTg	24/33	1	2	FACETS	0.474	0.384	0.576	0.474	0.384	0.576	SUBCLONAL	1	TRUE	1	0.250601804879078	2		395	539	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910756	29910756	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	101	523	0	ENST00000376809.5:c.296G>C	p.Arg99Pro	p.R99P	ENST00000376809	NM_002116.7	99	cGa/cCa	2/8	1	2	FACETS	0.803	0.716	0.895	0.803	0.716	0.895	CLONAL	1	TRUE	1	0.250601804879078	2		523	1004	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44948987	44948987	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0017637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	12	134	0	ENST00000377967.4:c.3549-1G>C		p.X1183_splice	ENST00000377967	NM_021140.2	1183			1	1	FACETS	0.403	0.283	0.55	0.403	0.283	0.55	SUBCLONAL	1	TRUE	0	0.250601804879078	1		134	208	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0017652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	8	667	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.175	0.112	0.257	0.175	0.112	0.257	SUBCLONAL	1	TRUE	1	0.333123981838894	2		668	274	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188200	10188200	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	67	418	0	ENST00000256474.2:c.343C>A	p.His115Asn	p.H115N	ENST00000256474	NM_000551.3	115	Cac/Aac	2/3	0.333123981838894	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.333123981838894	1		418	312	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684347	29684358	+	inframe_deletion	In_Frame_Del	DEL	GCAGAGGCCAGT	GCAGAGGCCAGT	-	novel	NA	P-0017652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	41	521	0	ENST00000356175.3:c.7868_7879del	p.Ala2623_Ser2626del	p.A2623_S2626del	ENST00000356175	NM_000267.3	2623	GCAGAGGCCAGT/-	53/57	1	2	FACETS	0.76	0.635	0.897	0.76	0.635	0.897	SUBCLONAL	1	TRUE	1	0.333123981838894	2		521	324	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7152935	7152935	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	78	298	0	ENST00000302850.5:c.2033T>C	p.Leu678Pro	p.L678P	ENST00000302850	NM_000208.2	678	cTg/cCg	10/22	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.333123981838894	2		298	331	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712525	52712525	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	106	423	0	ENST00000394830.3:c.227del	p.Pro76GlnfsTer19	p.P76Qfs*19	ENST00000394830	NM_018313.4	76	cCa/ca	3/30	0.333123981838894	1	FACETS	0.811	0.736	0.889	1	0.986	1	CLONAL	2	TRUE	0	0.333123981838894	1		423	327	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878961	117878961	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs775766535	NA	P-0017652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	95	526	0	ENST00000297338.2:c.8A>G	p.Tyr3Cys	p.Y3C	ENST00000297338	NM_006265.2	3	tAc/tGc	2/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.333123981838894	2		526	397	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0017653-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	241	941	1	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	0.437422401832249	2		942	964	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017653-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	148	605	1	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.437422401832249	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.437422401832249	1		606	442	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351933	70351933	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017653-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	216	646	1	ENST00000374080.3:c.4130C>T	p.Ser1377Phe	p.S1377F	ENST00000374080		1377	tCc/tTc	30/45	0.404767751348807	0	FACETS	0.929	0.87	0.99			1	CLONAL	1	TRUE	0	0.437422401832249	0		647	598	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0017654-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	711	941	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.194474879858879	8	FACETS	1	0.985	1			1	CLONAL	7	TRUE	NA	0.194474879858879	8		942	1602	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899272	78899272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368064754	NA	P-0017654-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	50	296	0	ENST00000306801.3:c.2911G>A	p.Val971Ile	p.V971I	ENST00000306801	NM_020761.2	971	Gtc/Atc	24/34	1	2	FACETS	0.792	0.671	0.926	0.792	0.671	0.926	CLONAL	1	TRUE	1	0.194474879858879	2		296	649	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118931	70118932	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0017654-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1254	113	659	0	ENST00000245479.2:c.505dup	p.His169ProfsTer83	p.H169Pfs*83	ENST00000245479	NM_000346.3	168	gac/gaCc	2/3	1	2	FACETS	0.85	0.762	0.944	0.85	0.762	0.944	CLONAL	1	TRUE	1	0.194474879858879	2		659	1367	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641197	12641197	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017654-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1253	188	672	0	ENST00000251849.4:c.1101del	p.Lys367AsnfsTer8	p.K367Nfs*8	ENST00000251849	NM_002880.3	367	aaA/aa	10/17	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.194474879858879	2		672	1441	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971116	21971119	+	frameshift_variant	Frame_Shift_Del	DEL	GGTC	GGTC	-	novel	NA	P-0017654-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	83	224	0	ENST00000304494.5:c.239_242del	p.Arg80ProfsTer65	p.R80Pfs*65	ENST00000304494	NM_000077.4	80	cGACCc/cc	2/3	0.194474879858879	2	FACETS	0.785	0.694	0.881	0.785	0.694	0.881	SUBCLONAL	2	TRUE	0	0.194474879858879	2		224	544	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0017654-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	812	941	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.3	6	FACETS	1	0.993	1			1	CLONAL	6	TRUE	NA	0.23	6		942	1606	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899272	78899272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368064754	NA	P-0017654-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	57	296	0	ENST00000306801.3:c.2911G>A	p.Val971Ile	p.V971I	ENST00000306801	NM_020761.2	971	Gtc/Atc	24/34	1	2	FACETS	0.948	0.814	1	0.948	0.814	1	CLONAL	1	TRUE	1	0.23	2		296	523	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118931	70118932	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0017654-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	134	659	0	ENST00000245479.2:c.505dup	p.His169ProfsTer83	p.H169Pfs*83	ENST00000245479	NM_000346.3	168	gac/gaCc	2/3	1	2	FACETS	0.882	0.799	0.97	0.882	0.799	0.97	CLONAL	1	TRUE	1	0.23	2		659	1321	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641197	12641197	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017654-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	143	672	0	ENST00000251849.4:c.1101del	p.Lys367AsnfsTer8	p.K367Nfs*8	ENST00000251849	NM_002880.3	367	aaA/aa	10/17	1	2	FACETS	0.982	0.893	1	0.982	0.893	1	CLONAL	1	TRUE	1	0.23	2		672	1266	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971116	21971119	+	frameshift_variant	Frame_Shift_Del	DEL	GGTC	GGTC	-	novel	NA	P-0017654-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	49	224	0	ENST00000304494.5:c.239_242del	p.Arg80ProfsTer65	p.R80Pfs*65	ENST00000304494	NM_000077.4	80	cGACCc/cc	2/3	0.3	1	FACETS	0.871	0.739	1	0.871	0.739	1	CLONAL	1	TRUE	0	0.23	1		224	433	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0017655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	216	475	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.363271086646668	2	FACETS	0.816	0.763	0.869	0.816	0.763	0.869	CLONAL	2	TRUE	0	0.432571919561373	2		475	612	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0017655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	57	294	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.951	0.823	1	0.951	0.823	1	CLONAL	1	TRUE	1	0.432571919561373	2		294	277	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0017655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	285	642	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.357257622341244	2	FACETS	1	0.993	1	0.724	0.682	0.767	CLONAL	1	TRUE	0	0.432571919561373	2		642	910	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0017655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	80	281	2	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.785	0.694	0.883	0.785	0.694	0.883	SUBCLONAL	1	TRUE	1	0.432571919561373	2		283	471	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923086	39923087	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	249	414	0	ENST00000378444.4:c.3621dup	p.Gln1208ThrfsTer8	p.Q1208Tfs*8	ENST00000378444	NM_001123385.1	1207	-/A	8/15	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.432571919561373	1		414	607	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412095	63412095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852217	NA	P-0017655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	261	351	0	ENST00000330258.3:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000330258	NM_152424.3	358	Cga/Tga	2/2	1	1	FACETS	0.769	0.726	0.812	1	0.994	1	SUBCLONAL	2	TRUE	0	0.432571919561373	1		351	615	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212104	5212104	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751085808	NA	P-0017655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	110	484	0	ENST00000357368.4:c.4927G>A	p.Glu1643Lys	p.E1643K	ENST00000357368	NM_002850.3	1643	Gag/Aag	32/38	0.432571919561373	1	FACETS	0.738	0.666	0.814	0.738	0.666	0.814	SUBCLONAL	1	TRUE	0	0.432571919561373	1		484	540	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93953255	93953255	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	156	654	0	ENST00000369303.4:c.2886T>A	p.Asp962Glu	p.D962E	ENST00000369303	NM_004440.3	962	gaT/gaA	17/17	0.0658143465166974	4	FACETS	1	0.986	1	0.679	0.623	0.738	INDETERMINATE	1	TRUE	2	0.432571919561373	4		654	761	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929077	44929077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2230018	NA	P-0017655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	204	350	1	ENST00000377967.4:c.2177C>T	p.Thr726Met	p.T726M	ENST00000377967	NM_021140.2	726	aCg/aTg	17/29	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.432571919561373	1		351	531	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375050	45375053	+	stop_gained	Nonsense_Mutation	ONP	GCTG	GCTG	ACTA	novel	NA	P-0017655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	57	231	0	ENST00000262160.6:c.790_793delinsTAGT	p.Gln264_Pro265delinsTer	p.Q264_P265delins*	ENST00000262160	NM_005901.5	264	CAGCca/TAGTca	8/11	0.432571919561373	1	FACETS	0.961	0.836	1	0.961	0.836	1	CLONAL	1	TRUE	0	0.432571919561373	1		231	215	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0017656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	118	527	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	0.325534826815189	2		527	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0017656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	25	514	0	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	1	2	FACETS	0.237	0.186	0.296	0.237	0.186	0.296	SUBCLONAL	1	TRUE	1	0.325534826815189	2		514	649	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217917	7217917	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0017656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	58	439	0	ENST00000380728.2:c.95-1G>C		p.X32_splice	ENST00000380728		32			1	2	FACETS	0.456	0.391	0.528	0.456	0.391	0.528	SUBCLONAL	1	TRUE	1	0.325534826815189	2		439	781	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842406	68842409	+	protein_altering_variant	In_Frame_Del	DEL	GGGT	GGGT	A	novel	NA	P-0017656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	120	609	0	ENST00000261769.5:c.467_470delinsA	p.Trp156_Val157delinsTyr	p.W156_V157delinsY	ENST00000261769	NM_004360.3	156	tGGGTt/tAt	4/16	0.301996679781474	1	FACETS	0.697	0.629	0.769	0.697	0.629	0.769	SUBCLONAL	1	TRUE	0	0.325534826815189	1		609	886	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518519	204518519	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	448	310	0	ENST00000367182.3:c.1182C>G	p.Phe394Leu	p.F394L	ENST00000367182	NM_001278516.1	394	ttC/ttG	11/11	0.873280092797603	4	FACETS	0.998	0.957	1	0.998	0.957	1	CLONAL	2	TRUE	2	0.873280092797603	4		310	963	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518706	204518706	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	556	476	0	ENST00000367182.3:c.1369C>G	p.Leu457Val	p.L457V	ENST00000367182	NM_001278516.1	457	Ctt/Gtt	11/11	0.873280092797603	4	FACETS	0.927	0.891	0.962	0.927	0.891	0.962	CLONAL	2	TRUE	2	0.873280092797603	4		476	1287	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912680	100912680	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	378	706	0	ENST00000325455.5:c.2642A>G	p.His881Arg	p.H881R	ENST00000325455	NM_001202474.3	881	cAt/cGt	7/8	0.873280092797603	3	FACETS	0.921	0.874	0.97	0.307	0.291	0.324	CLONAL	1	TRUE	0	0.873280092797603	3		706	1350	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030426	49030426	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0017658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	652	382	0	ENST00000267163.4:c.1901C>G	p.Ser634Ter	p.S634*	ENST00000267163	NM_000321.2	634	tCa/tGa	19/27	0.873280092797603	3	FACETS	0.974	0.958	0.989			1	CLONAL	3	TRUE	NA	0.873280092797603	3		382	734	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0017658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	303	548	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.873280092797603	3	FACETS	0.972	0.917	1			1	CLONAL	1	TRUE	NA	0.873280092797603	3		548	1026	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577543	7577543	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	633	433	0	ENST00000269305.4:c.738G>T	p.Met246Ile	p.M246I	ENST00000269305	NM_001126112.2	246	atG/atT	7/11	0.873280092797603	3	FACETS	1	0.98	1			1	CLONAL	2	TRUE	NA	0.873280092797603	3		433	1028	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880252	37880252	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1691	364	666	0	ENST00000269571.5:c.2296G>C	p.Glu766Gln	p.E766Q	ENST00000269571		766	Gaa/Caa	19/27	0.873280092797603	4	FACETS	0.76	0.718	0.804	0.38	0.359	0.402	SUBCLONAL	1	TRUE	2	0.873280092797603	4		666	2055	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794821	242794821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	21	328	0	ENST00000334409.5:c.388C>T	p.Pro130Ser	p.P130S	ENST00000334409	NM_005018.2	130	Ccc/Tcc	2/5	0.861737820762714	1	FACETS	0.087	0.066	0.11	0.087	0.066	0.11	SUBCLONAL	1	TRUE	0	0.873280092797603	1		328	313	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	525	184	0				ENST00000310581	NM_198253.2	-/1132			0.873280092797603	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	1	0.873280092797603	4		184	717	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056021	26056024	+	frameshift_variant	Frame_Shift_Del	DEL	CTTC	CTTC	TTT	novel	NA	P-0017658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	149	179	1	ENST00000343677.2:c.633_636delinsAAA	p.Lys213AsnfsTer?	p.K213Nfs*?	ENST00000343677	NM_005319.3	211	aaGAAG/aaAAA	1/1	0.218197896166286	1	FACETS	1	0.981	1	1	0.981	1	INDETERMINATE	1	TRUE	0	0.873280092797603	1		180	183	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545734	106545734	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	273	460	1	ENST00000359195.3:c.3211C>T	p.Gln1071Ter	p.Q1071*	ENST00000359195	NM_002649.2	1071	Cag/Tag	11/11	0.873280092797603	4	FACETS	0.928	0.87	0.988	0.464	0.435	0.494	CLONAL	1	TRUE	2	0.873280092797603	4		461	1262	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641271	23641271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199743500	NA	P-0017659-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	138	379	0	ENST00000261584.4:c.2204C>T	p.Pro735Leu	p.P735L	ENST00000261584	NM_024675.3	735	cCa/cTa	5/13	1	2	FACETS	0.805	0.74	0.872	0.805	0.74	0.872	CLONAL	1	TRUE	1	0.859078164651787	2		379	399	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226104	226104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139881415	NA	P-0017659-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	215	248	0	ENST00000264932.6:c.563G>A	p.Arg188Gln	p.R188Q	ENST00000264932	NM_004168.2	188	cGg/cAg	5/15	0.825721031395077	3	FACETS	0.941	0.891	0.992	0.941	0.891	0.992	CLONAL	2	TRUE	1	0.859078164651787	3		248	380	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0017661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	196	478	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.591390963393793	1	FACETS	0.957	0.894	1	0.957	0.894	1	CLONAL	1	TRUE	0	0.591390963393793	1		478	488	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0017661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	188	464	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.579443136283572	2	FACETS	0.978	0.923	1	0.978	0.923	1	CLONAL	2	TRUE	0	0.591390963393793	2		464	325	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0017661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	103	833	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.788	0.709	0.87	0.788	0.709	0.87	SUBCLONAL	1	TRUE	1	0.591390963393793	2		833	442	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710663	114710666	+	frameshift_variant	Frame_Shift_Del	DEL	AATG	AATG	-	novel	NA	P-0017661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	247	785	0	ENST00000543371.1:c.151_154del	p.Glu51GlnfsTer56	p.E51Qfs*56	ENST00000543371	NM_001198531.1	50	AATGaa/aa	1/14	1	2	FACETS	0.84	0.786	0.896	0.84	0.786	0.896	CLONAL	1	TRUE	1	0.591390963393793	2		785	994	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109750	115109750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	223	560	0	ENST00000257566.3:c.2128C>T	p.Leu710Phe	p.L710F	ENST00000257566	NM_016569.3	710	Ctc/Ttc	8/8	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.591390963393793	2		560	738	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604740	48604740	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876659840	NA	P-0017661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	200	416	1	ENST00000342988.3:c.1562C>T	p.Thr521Ile	p.T521I	ENST00000342988	NM_005359.5	521	aCa/aTa	12/12	0.591390963393793	1	FACETS	0.962	0.9	1	0.962	0.9	1	CLONAL	1	TRUE	0	0.591390963393793	1		417	495	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792844	33792844	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	70	275	0	ENST00000498907.2:c.477del	p.Ile160SerfsTer158	p.I160Sfs*158	ENST00000498907	NM_004364.3	159	gtG/gt	1/1	1	2	FACETS	0.536	0.468	0.608	0.536	0.468	0.608	SUBCLONAL	1	TRUE	1	0.591390963393793	2		275	442	SUCCESS
ALK	238	MSKCC	GRCh37	2	29450500	29450500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	239	599	0	ENST00000389048.3:c.2854G>A	p.Gly952Arg	p.G952R	ENST00000389048	NM_004304.4	952	Ggg/Agg	17/29	1	2	FACETS	0.974	0.912	1	0.974	0.912	1	CLONAL	1	TRUE	1	0.591390963393793	2		599	830	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955129	55955129	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	75	403	0	ENST00000263923.4:c.3416T>C	p.Met1139Thr	p.M1139T	ENST00000263923	NM_002253.2	1139	aTg/aCg	26/30	1	2	FACETS	0.402	0.352	0.456	0.402	0.352	0.456	SUBCLONAL	1	TRUE	1	0.591390963393793	2		403	631	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971127	55971127	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	127	305	0	ENST00000263923.4:c.1670C>A	p.Pro557His	p.P557H	ENST00000263923	NM_002253.2	557	cCt/cAt	13/30	1	2	FACETS	0.924	0.842	1	0.924	0.842	1	CLONAL	1	TRUE	1	0.591390963393793	2		305	465	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0017662-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	47	621	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	0.16	2		621	455	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964890	55964890	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017662-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	23	534	0	ENST00000263923.4:c.2347G>T	p.Val783Phe	p.V783F	ENST00000263923	NM_002253.2	783	Gtc/Ttc	16/30	1	2	FACETS	0.861	0.671	1	0.861	0.671	1	CLONAL	1	TRUE	1	0.16	2		534	334	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433943	149433943	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017662-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	44	624	0	ENST00000286301.3:c.2705C>T	p.Thr902Ile	p.T902I	ENST00000286301	NM_005211.3	902	aCc/aTc	21/22	1	2	FACETS	0.866	0.725	1	0.866	0.725	1	CLONAL	1	TRUE	1	0.16	2		624	635	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	128	246	0	ENST00000397752.3:c.3028G>A	p.Asp1010Asn	p.D1010N	ENST00000397752	NM_000245.2	1010	Gat/Aat	14/21	0.288635099507865	4	FACETS	0.99	0.918	1			1	CLONAL	4	TRUE	NA	0.352650998481159	4		246	248	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954270	17954270	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	146	900	0	ENST00000458235.1:c.339G>C	p.Glu113Asp	p.E113D	ENST00000458235	NM_000215.3	113	gaG/gaC	4/24	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.352650998481159	2		900	756	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143029245	143029245	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0017663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	40	277	0	ENST00000262992.4:c.2374+1G>T		p.X792_splice	ENST00000262992	NM_001101669.1	792			1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.352650998481159	2		277	221	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	28	184	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.241353399013429	2		184	158	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0017665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	69	741	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.211003628274512	3	FACETS	0.89	0.78	1	0.89	0.78	1	CLONAL	2	TRUE	1	0.241353399013429	3		741	360	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374293	138374293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	198	667	0	ENST00000289153.2:c.3151G>A	p.Glu1051Lys	p.E1051K	ENST00000289153	NM_006219.2	1051	Gaa/Aaa	22/22	0.108273300536594	5	FACETS	1	0.982	1	0.592	0.548	0.637	INDETERMINATE	2	TRUE	1	0.241353399013429	5		667	944	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0017665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	96	407	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.190350877302713	2	FACETS	1	0.978	1	0.698	0.623	0.777	CLONAL	1	TRUE	0	0.241353399013429	2		407	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0017665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	43	826	1	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.190350877302713	2	FACETS	0.539	0.45	0.638	0.27	0.225	0.319	SUBCLONAL	1	TRUE	0	0.241353399013429	2		827	661	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986867	36986874	+	protein_altering_variant	In_Frame_Del	DEL	GCACCCGG	GCACCCGG	CA	novel	NA	P-0017665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	59	100	1	ENST00000354822.5:c.815_822delinsTG	p.Thr272_Cys274delinsMet	p.T272_C274delinsM	ENST00000354822	NM_001079668.2	272	aCCGGGTGC/aTG	3/3	0.211003628274512	3	FACETS	1	0.927	1	1	0.976	1	CLONAL	3	TRUE	1	0.241353399013429	3		101	169	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374344	138374344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752742313	NA	P-0017665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	140	462	0	ENST00000289153.2:c.3100G>A	p.Glu1034Lys	p.E1034K	ENST00000289153	NM_006219.2	1034	Gaa/Aaa	22/22	0.108273300536594	5	FACETS	1	0.979	1	0.617	0.564	0.673	INDETERMINATE	2	TRUE	1	0.241353399013429	5		462	640	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0017667-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	235	523	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.456388187993899	4	FACETS	0.96	0.913	1	0.96	0.913	1	CLONAL	4	TRUE	0	0.4753707697006	4		523	380	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136227	2136227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017667-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	79	454	0	ENST00000219476.3:c.4696C>T	p.His1566Tyr	p.H1566Y	ENST00000219476	NM_000548.3	1566	Cat/Tat	37/42	0.462048679794044	4	FACETS	0.903	0.796	1	0.452	0.398	0.509	CLONAL	1	TRUE	2	0.4753707697006	4		454	543	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578415	7578427	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTCCGTCATGT	ACCTCCGTCATGT	-	novel	NA	P-0017667-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	135	355	0	ENST00000269305.4:c.503_515del	p.His168LeufsTer2	p.H168Lfs*2	ENST00000269305	NM_001126112.2	168	cACATGACGGAGGTt/ct	5/11	0.4753707697006	2	FACETS	0.986	0.913	1	0.986	0.913	1	CLONAL	2	TRUE	0	0.4753707697006	2		355	288	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169000	32169000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017667-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	348	895	0	ENST00000375023.3:c.4033G>A	p.Ala1345Thr	p.A1345T	ENST00000375023	NM_004557.3	1345	Gcc/Acc	22/30	0.462048679794044	4	FACETS	0.927	0.878	0.977	0.927	0.878	0.977	CLONAL	2	TRUE	2	0.4753707697006	4		895	1165	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0017668-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	66	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.542412026365909	2		306	206	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554283	29554283	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017668-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	137	495	0	ENST00000356175.3:c.2299G>T	p.Glu767Ter	p.E767*	ENST00000356175	NM_000267.3	767	Gag/Tag	19/57	0.504798221500128	1	FACETS	0.956	0.88	1	0.956	0.88	1	CLONAL	1	TRUE	0	0.542412026365909	1		495	385	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590481	67590481	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017668-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	70	245	0	ENST00000274335.5:c.1543G>T	p.Glu515Ter	p.E515*	ENST00000274335		515	Gaa/Taa	11/15	1	2	FACETS	0.884	0.778	0.996	0.884	0.778	0.996	CLONAL	1	TRUE	1	0.542412026365909	2		245	292	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591142	67591143	+	stop_gained,inframe_insertion	Nonsense_Mutation	INS	-	-	AAT	novel	NA	P-0017668-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	14	218	0	ENST00000274335.5:c.1737_1739dup	p.Gln579_Tyr580insTer	p.Q579_Y580ins*	ENST00000274335		579	caa/cAATaa	12/15	1	2	FACETS	0.198	0.142	0.265	0.198	0.142	0.265	SUBCLONAL	1	TRUE	1	0.542412026365909	2		218	261	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0017670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	37	427	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.575	0.474	0.688	0.575	0.474	0.688	SUBCLONAL	1	TRUE	1	0.29	2		427	444	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0017671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	87	427	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	0.423426539885829	2		427	387	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0017671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	35	294	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.423426539885829	1	FACETS	0.938	0.782	1	0.938	0.782	1	CLONAL	1	TRUE	0	0.423426539885829	1		294	139	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042536	37042536	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63751221	NA	P-0017671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	76	430	0	ENST00000231790.2:c.298C>T	p.Arg100Ter	p.R100*	ENST00000231790	NM_000249.3	100	Cga/Tga	3/19	0.423426539885829	1	FACETS	0.913	0.808	1	0.913	0.808	1	CLONAL	1	TRUE	0	0.423426539885829	1		430	310	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220371	1220371	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0017671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	136	563	0	ENST00000326873.7:c.465-1G>T		p.X155_splice	ENST00000326873	NM_000455.4	155			0.423426539885829	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.423426539885829	1		563	428	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602800	10602800	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	89	568	2	ENST00000171111.5:c.778C>T	p.Arg260Ter	p.R260*	ENST00000171111	NM_203500.1	260	Cga/Tga	3/6	0.423426539885829	1	FACETS	0.701	0.624	0.782	0.701	0.624	0.782	SUBCLONAL	1	TRUE	0	0.423426539885829	1		570	473	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161310431	161310431	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	133	602	0	ENST00000367975.2:c.227T>C	p.Ile76Thr	p.I76T	ENST00000367975	NM_003001.3	76	aTt/aCt	4/6	0.423426539885829	3	FACETS	1	0.946	1	0.529	0.481	0.579	CLONAL	1	TRUE	1	0.423426539885829	3		602	720	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333539	70333539	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	100	556	0	ENST00000373644.4:c.1444A>T	p.Asn482Tyr	p.N482Y	ENST00000373644	NM_030625.2	482	Aac/Tac	2/12	1	2	FACETS	0.854	0.765	0.948	0.854	0.765	0.948	CLONAL	1	TRUE	1	0.423426539885829	2		556	553	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557941	21557941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	30	176	0	ENST00000382592.4:c.1904G>A	p.Gly635Glu	p.G635E	ENST00000382592	NM_014572.2	635	gGa/gAa	5/8	1	2	FACETS	0.914	0.746	1	0.914	0.746	1	CLONAL	1	TRUE	1	0.423426539885829	2		176	155	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241312	105241312	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	38	717	1	ENST00000349310.3:c.596A>G	p.Asn199Ser	p.N199S	ENST00000349310	NM_001014432.1	199	aAc/aGc	8/15	1	2	FACETS	0.255	0.21	0.306	0.255	0.21	0.306	SUBCLONAL	1	TRUE	1	0.423426539885829	2		718	703	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152205	11152206	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	89	498	0	ENST00000358026.2:c.4491dup	p.Val1498CysfsTer83	p.V1498Cfs*83	ENST00000358026	NM_001128849.1	1497	att/aTtt	31/36	0.423426539885829	1	FACETS	0.91	0.814	1	0.91	0.814	1	CLONAL	1	TRUE	0	0.423426539885829	1		498	364	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52677299	52677300	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0017671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	140	697	0	ENST00000394830.3:c.958_959dup	p.Gly321LeufsTer42	p.G321Lfs*42	ENST00000394830	NM_018313.4	320	ctt/ctCTt	10/30	0.423426539885829	1	FACETS	0.999	0.915	1	0.999	0.915	1	CLONAL	1	TRUE	0	0.423426539885829	1		697	522	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515406	149515406	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	69	318	0	ENST00000261799.4:c.76G>C	p.Glu26Gln	p.E26Q	ENST00000261799	NM_002609.3	26	Gaa/Caa	3/23	1	2	FACETS	0.947	0.831	1	0.947	0.831	1	CLONAL	1	TRUE	1	0.423426539885829	2		318	344	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169121	32169121	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	109	664	0	ENST00000375023.3:c.3912C>A	p.Ser1304Arg	p.S1304R	ENST00000375023	NM_004557.3	1304	agC/agA	22/30	1	2	FACETS	0.961	0.866	1	0.961	0.866	1	CLONAL	1	TRUE	1	0.423426539885829	2		664	536	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066695	94066695	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	271	1495	2	ENST00000369303.4:c.1064C>T	p.Ala355Val	p.A355V	ENST00000369303	NM_004440.3	355	gCa/gTa	5/17	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.423426539885829	2		1497	1280	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420001	152420001	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763337967	NA	P-0017671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	110	629	1	ENST00000206249.3:c.1688C>T	p.Thr563Met	p.T563M	ENST00000206249	NM_000125.3	563	aCg/aTg	8/8	1	2	FACETS	0.867	0.781	0.958	0.867	0.781	0.958	CLONAL	1	TRUE	1	0.423426539885829	2		630	599	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409805	139409805	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1182867386	NA	P-0017671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	129	547	0	ENST00000277541.6:c.1951G>A	p.Asp651Asn	p.D651N	ENST00000277541	NM_017617.3	651	Gac/Aac	12/34	0.423426539885829	1	FACETS	0.97	0.885	1	0.97	0.885	1	CLONAL	1	TRUE	0	0.423426539885829	1		547	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0017672-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	92	775	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.242956040422788	2	FACETS	0.881	0.789	0.978	0.881	0.789	0.978	CLONAL	2	TRUE	0	0.276266530313794	2		777	378	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0017672-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	33	295	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.252353591553337	4	FACETS	0.824	0.672	0.995	0.275	0.224	0.332	CLONAL	1	TRUE	1	0.276266530313794	4		295	370	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0017672-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	63	380	9	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.252353591553337	4	FACETS	1	0.957	1	0.815	0.714	0.922	CLONAL	2	TRUE	1	0.276266530313794	4		389	238	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391076	89391076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764139832	NA	P-0017672-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	95	575	0	ENST00000336596.2:c.1142G>A	p.Arg381His	p.R381H	ENST00000336596	NM_005233.5	381	cGc/cAc	5/17	0.276266530313794	3	FACETS	1	0.972	1	0.426	0.379	0.475	CLONAL	1	TRUE	0	0.276266530313794	3		575	613	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912188	114912188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017672-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1184	315	1179	1	ENST00000543371.1:c.1258C>T	p.Arg420Trp	p.R420W	ENST00000543371	NM_001198531.1	420	Cgg/Tgg	11/14	0.262581341088996	3	FACETS	0.866	0.815	0.918	0.866	0.815	0.918	CLONAL	2	TRUE	1	0.276266530313794	3		1180	1499	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527977	157527978	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs886041878	NA	P-0017672-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	53	219	0	ENST00000346085.5:c.5703dup	p.Lys1902Ter	p.K1902*	ENST00000346085	NM_020732.3	1901	agt/agTt	20/20	0.276266530313794	3	FACETS	0.86	0.74	0.988	0.86	0.74	0.988	CLONAL	2	TRUE	1	0.276266530313794	3		219	254	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630194	187630194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	103	295	0	ENST00000441802.2:c.788C>T	p.Ser263Leu	p.S263L	ENST00000441802	NM_005245.3	263	tCa/tTa	2/27	1	2	FACETS	1	0.953	1	1	0.991	1	CLONAL	3	TRUE	1	0.27	2		295	238	SUCCESS
ATM	472	MSKCC	GRCh37	11	108214095	108214095	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555135878	NA	P-0017674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	46	213	0	ENST00000278616.4:c.8415G>A	p.Met2805Ile	p.M2805I	ENST00000278616	NM_000051.3	2805	atG/atA	57/63	1	2	FACETS	0.909	0.785	1	1	0.979	1	CLONAL	3	TRUE	1	0.27	2		213	125	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057287	30057287	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777059212	NA	P-0017674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	221	535	0	ENST00000338641.4:c.769C>T	p.Pro257Ser	p.P257S	ENST00000338641	NM_000268.3	257	Ccg/Tcg	8/16	1	2	FACETS	1	0.987	1	1	0.996	1	CLONAL	3	TRUE	1	0.27	2		535	469	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760598	133760598	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	421	1191	0	ENST00000318560.5:c.2925del	p.Ile976SerfsTer93	p.I976Sfs*93	ENST00000318560	NM_005157.4	974	aCc/ac	11/11	1	2	FACETS	1	0.989	1	1	0.997	1	CLONAL	2	TRUE	1	0.27	2		1191	1384	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030465	49030466	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0017676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	39	223	0	ENST00000267163.4:c.1941_1942del	p.Ser648ThrfsTer4	p.S648Tfs*4	ENST00000267163	NM_000321.2	647	cTT/c	19/27	0.605622958827816	3	FACETS	0.888	0.782	0.989	0.888	0.782	0.989	CLONAL	3	TRUE	0	0.605622958827816	3		223	63	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578197	7578197	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	93	1580	1	ENST00000269305.4:c.652del	p.Val218CysfsTer29	p.V218Cfs*29	ENST00000269305	NM_001126112.2	218	Gtg/tg	6/11	0.605622958827816	3	FACETS	0.933	0.864	0.999	0.933	0.864	0.999	CLONAL	3	TRUE	0	0.605622958827816	3		1581	143	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139632	202139632	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	21	520	0	ENST00000358485.4:c.793A>G	p.Met265Val	p.M265V	ENST00000358485	NM_001080125.1	265	Atg/Gtg	6/9	1	2	FACETS	0.889	0.703	1	0.889	0.703	1	CLONAL	1	TRUE	1	0.605622958827816	2		520	78	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627281	86627281	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1554044823	NA	P-0017676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	52	453	0	ENST00000274376.6:c.656C>G	p.Ser219Ter	p.S219*	ENST00000274376	NM_002890.2	219	tCa/tGa	2/25	0.585122283921969	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.605622958827816	2		453	71	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0017678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	348	306	0				ENST00000310581	NM_198253.2	-/1132			0.266531030926632	5	FACETS	1	0.977	1	1	0.994	1	CLONAL	6	TRUE	0	0.266531030926632	5		306	593	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0017678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	116	455	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.15904820256936	3	FACETS	1	0.94	1	0.531	0.478	0.587	INDETERMINATE	1	TRUE	1	0.266531030926632	3		455	929	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0017678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	61	536	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	1	2	FACETS	0.864	0.746	0.992	0.864	0.746	0.992	CLONAL	1	TRUE	1	0.266531030926632	2		536	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579355	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519997	NA	P-0017678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	89	829	0	ENST00000269305.4:c.332T>A	p.Leu111Gln	p.L111Q	ENST00000269305	NM_001126112.2	111	cTg/cAg	4/11	1	2	FACETS	0.815	0.722	0.915	0.815	0.722	0.915	CLONAL	1	TRUE	1	0.266531030926632	2		829	819	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530425	187530425	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0017678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	74	469	0	ENST00000441802.2:c.10118C>G	p.Ser3373Ter	p.S3373*	ENST00000441802	NM_005245.3	3373	tCa/tGa	16/27	0.266531030926632	1	FACETS	0.968	0.85	1	0.968	0.85	1	CLONAL	1	TRUE	0	0.266531030926632	1		469	497	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375704	118375704	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	86	566	0	ENST00000534358.1:c.9097G>C	p.Gly3033Arg	p.G3033R	ENST00000534358	NM_005933.3	3033	Ggc/Cgc	27/36	1	2	FACETS	0.991	0.877	1	0.991	0.877	1	CLONAL	1	TRUE	1	0.266531030926632	2		566	651	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610030	81610030	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	36	334	0	ENST00000298171.2:c.1628T>G	p.Val543Gly	p.V543G	ENST00000298171	NM_000369.2	543	gTt/gGt	10/10	1	2	FACETS	0.736	0.606	0.881	0.736	0.606	0.881	SUBCLONAL	1	TRUE	1	0.266531030926632	2		334	367	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40490827	40490827	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	87	461	0	ENST00000264657.5:c.472C>G	p.Leu158Val	p.L158V	ENST00000264657	NM_139276.2	158	Cta/Gta	6/24	1	2	FACETS	0.889	0.787	0.999	0.889	0.787	0.999	CLONAL	1	TRUE	1	0.266531030926632	2		461	734	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210377	36210377	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	59	685	0	ENST00000222270.7:c.370C>T	p.Gln124Ter	p.Q124*	ENST00000222270	NM_014727.1	124	Cag/Tag	2/37	1	2	FACETS	0.626	0.538	0.723	0.626	0.538	0.723	SUBCLONAL	1	TRUE	1	0.266531030926632	2		685	707	SUCCESS
AXL	558	MSKCC	GRCh37	19	41736888	41736889	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0017678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	101	849	0	ENST00000301178.4:c.605_606del	p.Ser202PhefsTer7	p.S202Ffs*7	ENST00000301178	NM_021913.4	201	tcCTct/tcct	5/20	1	2	FACETS	0.899	0.803	1	0.899	0.803	1	CLONAL	1	TRUE	1	0.266531030926632	2		849	843	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645150	86645150	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	140	394	0	ENST00000274376.6:c.1222C>T	p.Gln408Ter	p.Q408*	ENST00000274376	NM_002890.2	408	Cag/Tag	8/25	0.266531030926632	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.266531030926632	2		394	489	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412683	139412683	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	290	751	0	ENST00000277541.6:c.1161C>G	p.Cys387Trp	p.C387W	ENST00000277541	NM_017617.3	387	tgC/tgG	7/34	0.266531030926632	3	FACETS	0.915	0.863	0.968	0.915	0.863	0.968	CLONAL	3	TRUE	0	0.266531030926632	3		751	898	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0017679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	252	826	1	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.332304460013092	2	FACETS	0.984	0.925	1	0.984	0.925	1	CLONAL	2	TRUE	0	0.337351905822415	2		827	759	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880219	37880220	+	missense_variant	Missense_Mutation	DNP	TT	TT	CC	rs121913469	NA	P-0017679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	371	684	1	ENST00000269571.5:c.2263_2264delinsCC	p.Leu755Pro	p.L755P	ENST00000269571		755	TTg/CCg	19/27	0.337351905822415	6	FACETS	1	0.991	1	0.875	0.831	0.918	CLONAL	3	TRUE	2	0.337351905822415	6		685	1053	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131403	17131403	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs758385503	NA	P-0017679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	153	466	0	ENST00000285071.4:c.49del	p.Arg17AlafsTer38	p.R17Afs*38	ENST00000285071	NM_144997.5	17	Cgc/gc	4/14	0.332304460013092	2	FACETS	0.846	0.779	0.916	0.846	0.779	0.916	CLONAL	2	TRUE	0	0.337351905822415	2		466	536	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793165	42793165	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1135401823	NA	P-0017679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	404	668	1	ENST00000575354.2:c.1057C>T	p.Arg353Ter	p.R353*	ENST00000575354	NM_015125.3	353	Cga/Tga	7/20	0.337351905822415	5	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	2	0.337351905822415	5		669	1152	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027031	48027031	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	129	347	0	ENST00000234420.5:c.1909C>T	p.Leu637Phe	p.L637F	ENST00000234420	NM_000179.2	637	Ctc/Ttc	4/10	0.337351905822415	3	FACETS	0.91	0.83	0.993	0.91	0.83	0.993	CLONAL	2	TRUE	1	0.337351905822415	3		347	491	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624801	9624801	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	293	396	2	ENST00000353224.5:c.176T>A	p.Ile59Asn	p.I59N	ENST00000353224	NM_177990.2	59	aTc/aAc	3/10	0.337351905822415	5	FACETS	1	0.969	1			1	CLONAL	4	TRUE	NA	0.337351905822415	5		398	636	SUCCESS
AR	367	MSKCC	GRCh37	X	66765139	66765139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758522275	NA	P-0017679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	52	340	0	ENST00000374690.3:c.151G>A	p.Gly51Ser	p.G51S	ENST00000374690	NM_000044.3	51	Ggc/Agc	1/8	0.253590649702267	3	FACETS	0.969	0.828	1	0.323	0.276	0.374	CLONAL	1	TRUE	0	0.337351905822415	3		340	372	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0017681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	62	594	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.726	0.627	0.835	0.726	0.627	0.835	SUBCLONAL	1	TRUE	1	0.25	2		594	683	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	55	325	3	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.761	0.651	0.882	0.761	0.651	0.882	SUBCLONAL	1	TRUE	1	0.25	2		328	578	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	65	530	2	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	1	2	FACETS	0.566	0.489	0.649	0.566	0.489	0.649	SUBCLONAL	1	TRUE	1	0.25	2		532	919	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0017681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	66	441	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.641	0.555	0.734	0.641	0.555	0.734	SUBCLONAL	1	TRUE	1	0.25	2		441	824	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	120	528	0	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	0.963	0.868	1	0.963	0.868	1	CLONAL	1	TRUE	1	0.25	2		528	997	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654642	67654642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	39	805	1	ENST00000264010.4:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000264010	NM_006565.3	377	Cgt/Tgt	6/12	1	2	FACETS	0.365	0.301	0.437	0.365	0.301	0.437	SUBCLONAL	1	TRUE	1	0.25	2		806	855	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0017681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	246	1208	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.869	0.812	0.928	1	0.994	1	CLONAL	2	TRUE	1	0.25	2		1208	1132	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0017681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	42	482	3	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	1	2	FACETS	0.463	0.386	0.55	0.463	0.386	0.55	SUBCLONAL	1	TRUE	1	0.25	2		485	725	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020754	37020754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	88	545	1	ENST00000358127.4:c.91C>T	p.Arg31Trp	p.R31W	ENST00000358127	NM_001280556.1	31	Cgg/Tgg	2/10	1	2	FACETS	0.829	0.734	0.932	0.829	0.734	0.932	CLONAL	1	TRUE	1	0.25	2		546	849	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519941	NA	P-0017681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	57	323	0	ENST00000263967.3:c.1031T>C	p.Val344Ala	p.V344A	ENST00000263967	NM_006218.2	344	gTg/gCg	5/21	1	2	FACETS	0.653	0.56	0.756	0.653	0.56	0.756	SUBCLONAL	1	TRUE	1	0.25	2		323	698	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826564	50826565	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	97	346	0	ENST00000398568.2:c.2296dup	p.Ile766AsnfsTer14	p.I766Nfs*14	ENST00000398568	NM_001042412.1	763	-/A	15/18	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.25	2		346	776	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0017681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	123	734	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.25	2		734	941	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319430	11319430	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	79	514	0	ENST00000361445.4:c.37G>A	p.Ala13Thr	p.A13T	ENST00000361445	NM_004958.3	13	Gcc/Acc	2/58	1	2	FACETS	0.821	0.721	0.928	0.821	0.721	0.928	CLONAL	1	TRUE	1	0.25	2		514	770	SUCCESS
RET	5979	MSKCC	GRCh37	10	43595976	43595976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1427186016	NA	P-0017681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	96	672	0	ENST00000355710.3:c.143C>T	p.Thr48Met	p.T48M	ENST00000355710	NM_020975.4	48	aCg/aTg	2/20	1	2	FACETS	0.88	0.783	0.983	0.88	0.783	0.983	CLONAL	1	TRUE	1	0.25	2		672	873	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112397	115112397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1182105031	NA	P-0017681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	78	466	0	ENST00000257566.3:c.1343G>A	p.Gly448Asp	p.G448D	ENST00000257566	NM_016569.3	448	gGc/gAc	7/8	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.25	2		466	595	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034960	42034960	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	100	509	0	ENST00000219905.7:c.4805del	p.Pro1602LeufsTer5	p.P1602Lfs*5	ENST00000219905	NM_001164273.1	1601	aCc/ac	15/24	1	2	FACETS	0.891	0.795	0.993	0.891	0.795	0.993	CLONAL	1	TRUE	1	0.25	2		509	898	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748363	43748363	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs575999589	NA	P-0017681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	119	651	0	ENST00000382044.4:c.2443G>A	p.Val815Ile	p.V815I	ENST00000382044	NM_001141980.1	815	Gta/Ata	12/28	1	2	FACETS	0.927	0.835	1	0.927	0.835	1	CLONAL	1	TRUE	1	0.25	2		651	1027	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435057	56435057	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	125	520	2	ENST00000407977.2:c.2080C>A	p.Pro694Thr	p.P694T	ENST00000407977		694	Cca/Aca	9/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.25	2		522	829	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78820324	78820324	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs758978960	NA	P-0017681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	51	678	0	ENST00000306801.3:c.1264A>G	p.Met422Val	p.M422V	ENST00000306801	NM_020761.2	422	Atg/Gtg	11/34	1	2	FACETS	0.422	0.357	0.494	0.422	0.357	0.494	SUBCLONAL	1	TRUE	1	0.25	2		678	966	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030647	48030649	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs1060502917	NA	P-0017681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	50	474	0	ENST00000234420.5:c.3264_3266del	p.Phe1088del	p.F1088del	ENST00000234420	NM_000179.2	1087	ccCTTc/ccc	5/10	1	2	FACETS	0.491	0.416	0.575	0.491	0.416	0.575	SUBCLONAL	1	TRUE	1	0.25	2		474	814	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442570	52442570	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1404823823	NA	P-0017681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	40	522	1	ENST00000460680.1:c.175C>T	p.Arg59Trp	p.R59W	ENST00000460680	NM_004656.3	59	Cgg/Tgg	4/17	1	2	FACETS	0.417	0.345	0.497	0.417	0.345	0.497	SUBCLONAL	1	TRUE	1	0.25	2		523	768	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026117	71026117	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	90	404	1	ENST00000318789.4:c.1505T>A	p.Phe502Tyr	p.F502Y	ENST00000318789	NM_032682.5	502	tTc/tAc	17/21	1	2	FACETS	0.809	0.717	0.908	0.809	0.717	0.908	CLONAL	1	TRUE	1	0.25	2		405	890	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226913	142226913	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745782942	NA	P-0017681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	134	525	1	ENST00000350721.4:c.4891C>T	p.Arg1631Cys	p.R1631C	ENST00000350721	NM_001184.3	1631	Cgt/Tgt	28/47	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.25	2		526	981	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430906	181430907	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	68	744	0	ENST00000325404.1:c.758_759insA	p.Val254CysfsTer56	p.V254Cfs*56	ENST00000325404	NM_003106.3	253	cct/ccAt	1/1	1	2	FACETS	0.556	0.482	0.636	0.556	0.482	0.636	SUBCLONAL	1	TRUE	1	0.25	2		744	979	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720965	176720965	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs932837462	NA	P-0017681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	53	391	0	ENST00000439151.2:c.6596G>A	p.Arg2199His	p.R2199H	ENST00000439151	NM_022455.4	2199	cGt/cAt	23/23	1	2	FACETS	0.619	0.527	0.72	0.619	0.527	0.72	SUBCLONAL	1	TRUE	1	0.25	2		391	685	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259485	55259485	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148934350	NA	P-0017681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	72	518	0	ENST00000275493.2:c.2543C>T	p.Pro848Leu	p.P848L	ENST00000275493	NM_005228.3	848	cCg/cTg	21/28	1	2	FACETS	0.679	0.592	0.774	0.679	0.592	0.774	SUBCLONAL	1	TRUE	1	0.25	2		518	848	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248085	110248085	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	47	459	0	ENST00000374672.4:c.1387C>T	p.Arg463Ter	p.R463*	ENST00000374672	NM_004235.4	463	Cga/Tga	5/5	1	2	FACETS	0.462	0.389	0.544	0.462	0.389	0.544	SUBCLONAL	1	TRUE	1	0.25	2		459	813	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933584	39933584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	71	471	0	ENST00000378444.4:c.1015C>T	p.Pro339Ser	p.P339S	ENST00000378444	NM_001123385.1	339	Ccg/Tcg	4/15	1	2	FACETS	0.865	0.754	0.984	0.865	0.754	0.984	CLONAL	1	TRUE	1	0.25	2		471	657	SUCCESS
AR	367	MSKCC	GRCh37	X	66766130	66766130	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	74	468	0	ENST00000374690.3:c.1142C>A	p.Pro381His	p.P381H	ENST00000374690	NM_000044.3	381	cCc/cAc	1/8	1	2	FACETS	0.966	0.846	1	0.966	0.846	1	CLONAL	1	TRUE	1	0.25	2		468	613	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0017684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	142	613	1	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.98	0.897	1	0.98	0.897	1	CLONAL	1	TRUE	1	0.525260448235243	2		614	552	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870995	12870995	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0017684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	111	341	0	ENST00000228872.4:c.222C>G	p.Tyr74Ter	p.Y74*	ENST00000228872	NM_004064.3	74	taC/taG	1/3	1	2	FACETS	0.864	0.781	0.952	0.864	0.781	0.952	CLONAL	1	TRUE	1	0.525260448235243	2		341	489	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100702	67100702	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0017684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	164	489	0	ENST00000412916.2:c.399+1G>A		p.X133_splice	ENST00000412916		133			0.525260448235243	1	FACETS	0.869	0.803	0.937	0.869	0.803	0.937	CLONAL	1	TRUE	0	0.525260448235243	1		489	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	360	650	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.360652026712865	2	FACETS	0.836	0.794	0.879	0.836	0.794	0.879	CLONAL	2	TRUE	0	0.426283356989254	2		650	1010	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974696	21974697	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	185	498	0	ENST00000304494.5:c.130dup	p.Tyr44LeufsTer76	p.Y44Lfs*76	ENST00000304494	NM_000077.4	44	tac/tTac	1/3	0.361224845771563	2	FACETS	0.914	0.852	0.976	0.914	0.852	0.976	CLONAL	2	TRUE	0	0.426283356989254	2		498	475	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021721	31021721	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1311986203	NA	P-0017687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	153	484	0	ENST00000375687.4:c.1719+1G>T		p.X573_splice	ENST00000375687	NM_015338.5	573			0.343935418227205	3	FACETS	1	0.917	1	0.501	0.458	0.546	CLONAL	1	TRUE	1	0.426283356989254	3		484	869	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106006	8106006	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs104894162	NA	P-0017687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	141	448	2	ENST00000346208.3:c.826C>T	p.Arg276Ter	p.R276*	ENST00000346208		276	Cga/Tga	4/6	1	2	FACETS	0.964	0.88	1	0.964	0.88	1	CLONAL	1	TRUE	1	0.426283356989254	2		450	686	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396486	30396486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	288	533	0	ENST00000331968.5:c.233G>A	p.Arg78His	p.R78H	ENST00000331968	NM_002742.2	78	cGc/cAc	1/18	0.426283356989254	3	FACETS	0.928	0.875	0.982	0.619	0.583	0.655	CLONAL	2	TRUE	0	0.426283356989254	3		533	883	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584747	187584751	+	frameshift_variant	Frame_Shift_Del	DEL	GATCT	GATCT	-	novel	NA	P-0017687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	100	357	0	ENST00000441802.2:c.3282_3286del	p.Asp1095ThrfsTer4	p.D1095Tfs*4	ENST00000441802	NM_005245.3	1094	tcAGATCga/tcga	3/27	1	2	FACETS	0.769	0.688	0.855	0.769	0.688	0.855	SUBCLONAL	1	TRUE	1	0.426283356989254	2		357	610	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178662	56178662	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1417084083	NA	P-0017687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	59	266	0	ENST00000399503.3:c.3635A>G	p.Asn1212Ser	p.N1212S	ENST00000399503	NM_005921.1	1212	aAt/aGt	14/20	1	2	FACETS	0.771	0.667	0.884	0.771	0.667	0.884	SUBCLONAL	1	TRUE	1	0.426283356989254	2		266	359	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637776	176637776	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	319	755	0	ENST00000439151.2:c.2376C>A	p.Cys792Ter	p.C792*	ENST00000439151	NM_022455.4	792	tgC/tgA	5/23	0.361224845771563	2	FACETS	0.848	0.804	0.894	0.848	0.804	0.894	CLONAL	2	TRUE	0	0.426283356989254	2		755	882	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487556	38487556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	47	488	0	ENST00000254066.5:c.86C>T	p.Pro29Leu	p.P29L	ENST00000254066	NM_000964.3	29	cCc/cTc	2/9	1	2	FACETS	0.881	0.751	1	1	0.978	1	CLONAL	3	TRUE	1	0.15	2		488	237	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847225	68847225	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782798	NA	P-0017694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	63	455	0	ENST00000261769.5:c.1147C>T	p.Gln383Ter	p.Q383*	ENST00000261769	NM_004360.3	383	Cag/Tag	9/16	0.3	1	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	0	0.16	1		455	724	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52621398	52621398	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	77	451	0	ENST00000394830.3:c.3019C>G	p.Leu1007Val	p.L1007V	ENST00000394830	NM_018313.4	1007	Cta/Gta	20/30	1	2	FACETS	0.781	0.683	0.887	0.781	0.683	0.887	SUBCLONAL	1	TRUE	1	0.16	2		451	1233	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0017695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	449	710	5	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.73675160169328	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.746957147137597	1		715	744	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs199469672	NA	P-0017695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	526	674	0	ENST00000374080.3:c.131G>C	p.Gly44Ala	p.G44A	ENST00000374080		44	gGt/gCt	2/45	0.746957147137597	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.746957147137597	1		674	876	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426790	121426790	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201095611	NA	P-0017695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	195	600	5	ENST00000257555.6:c.481G>A	p.Ala161Thr	p.A161T	ENST00000257555		161	Gcc/Acc	2/10	0.20994915618909	1	FACETS	0.311	0.287	0.336	0.311	0.287	0.336	INDETERMINATE	1	TRUE	0	0.746957147137597	1		605	1052	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	100	523	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.9	0.804	1	0.9	0.804	1	CLONAL	1	TRUE	1	0.315627963323972	2		523	704	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101402	27101402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	102	497	2	ENST00000324856.7:c.4689del	p.Met1564Ter	p.M1564*	ENST00000324856	NM_006015.4	1562	Ccc/cc	18/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.315627963323972	2		499	578	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	95	446	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	1	2	FACETS	0.673	0.599	0.753	0.673	0.599	0.753	SUBCLONAL	1	TRUE	1	0.315627963323972	2		446	894	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	131	555	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.315627963323972	2	FACETS	1	0.979	1	0.633	0.575	0.693	CLONAL	1	TRUE	0	0.315627963323972	2		558	656	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	159	914	3	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	0.315627963323972	2		917	830	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325924	65325924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766108549	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	99	520	0	ENST00000342505.4:c.1198G>A	p.Glu400Lys	p.E400K	ENST00000342505	NM_002227.2	400	Gag/Aag	9/25	1	2	FACETS	0.976	0.872	1	0.976	0.872	1	CLONAL	1	TRUE	1	0.315627963323972	2		520	643	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025982	1025982	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	76	446	0	ENST00000358495.3:c.548C>A	p.Pro183His	p.P183H	ENST00000358495	NM_134424.2	183	cCt/cAt	8/12	0.315627963323972	3	FACETS	0.824	0.722	0.933			1	CLONAL	1	TRUE	NA	0.315627963323972	3		446	677	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053022	180053023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750808726	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	86	833	1	ENST00000261937.6:c.1267dup	p.Gln423ProfsTer4	p.Q423Pfs*4	ENST00000261937	NM_182925.4	423	cag/cCag	10/30	0.315627963323972	1	FACETS	0.935	0.83	1	0.935	0.83	1	CLONAL	1	TRUE	0	0.315627963323972	1		834	491	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175857	24175859	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs875989800	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	75	648	0	ENST00000263121.7:c.1091_1093del	p.Lys364del	p.K364del	ENST00000263121	NM_003073.3	362	gAGAag/gag	8/9	1	2	FACETS	0.782	0.685	0.885	0.782	0.685	0.885	SUBCLONAL	1	TRUE	1	0.315627963323972	2		648	608	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475061	40475063	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	124	699	0	ENST00000264657.5:c.1847_1849del	p.Glu616del	p.E616del	ENST00000264657	NM_139276.2	616	gAAGga/gga	20/24	1	2	FACETS	0.813	0.735	0.896	0.813	0.735	0.896	CLONAL	1	TRUE	1	0.315627963323972	2		699	966	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799098	42799098	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	101	842	1	ENST00000575354.2:c.4586del	p.Pro1529LeufsTer91	p.P1529Lfs*91	ENST00000575354	NM_015125.3	1528	Ccc/cc	20/20	1	2	FACETS	0.883	0.789	0.982	0.883	0.789	0.982	CLONAL	1	TRUE	1	0.315627963323972	2		843	725	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260214	16260214	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	61	381	0	ENST00000375759.3:c.7484del	p.Pro2495LeufsTer4	p.P2495Lfs*4	ENST00000375759	NM_015001.2	2493	agC/ag	11/15	1	2	FACETS	0.853	0.738	0.978	0.853	0.738	0.978	CLONAL	1	TRUE	1	0.315627963323972	2		381	453	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	78	503	6	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.315627963323972	2		509	452	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007619	45007619	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs111482205	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	63	221	0	ENST00000558401.1:c.68-2A>G		p.X23_splice	ENST00000558401	NM_004048.2	23			1	2	FACETS	0.955	0.829	1	0.955	0.829	1	CLONAL	1	TRUE	1	0.315627963323972	2		221	418	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141632	202141632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764461240	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	148	664	0	ENST00000358485.4:c.920G>A	p.Arg307Gln	p.R307Q	ENST00000358485	NM_001080125.1	307	cGg/cAg	7/9	0.113706059597023	3	FACETS	1	0.938	1	0.518	0.472	0.566	INDETERMINATE	1	TRUE	1	0.315627963323972	3		664	1048	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257102	19257102	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	71	649	0	ENST00000162023.5:c.861del	p.Ala288ProfsTer?	p.A288Pfs*?	ENST00000162023		287	ccC/cc	12/13	1	2	FACETS	0.891	0.779	1	0.891	0.779	1	CLONAL	1	TRUE	1	0.315627963323972	2		649	505	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239933	41239933	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	13	92	1	ENST00000379561.5:c.417del	p.Ala140ProfsTer193	p.A140Pfs*193	ENST00000379561	NM_002015.3	139	ccC/cc	1/3	1	2	FACETS	0.763	0.549	1	0.763	0.549	1	CLONAL	1	TRUE	1	0.315627963323972	2		93	108	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	89	645	3	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	1	2	FACETS	0.901	0.8	1	0.901	0.8	1	CLONAL	1	TRUE	1	0.315627963323972	2		648	626	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588173	69588173	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	93	682	0	ENST00000168712.1:c.525del	p.Gly176AlafsTer6	p.G176Afs*6	ENST00000168712	NM_002007.2	175	ccC/cc	3/3	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.315627963323972	2		682	554	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954604	17954604	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	108	870	0	ENST00000458235.1:c.290T>C	p.Val97Ala	p.V97A	ENST00000458235	NM_000215.3	97	gTc/gCc	3/24	1	2	FACETS	0.757	0.679	0.84	0.757	0.679	0.84	SUBCLONAL	1	TRUE	1	0.315627963323972	2		870	904	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206575	108206575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138526014	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	88	405	0	ENST00000278616.4:c.8155C>T	p.Arg2719Cys	p.R2719C	ENST00000278616	NM_000051.3	2719	Cgt/Tgt	56/63	1	2	FACETS	0.917	0.814	1	0.917	0.814	1	CLONAL	1	TRUE	1	0.315627963323972	2		405	608	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119910	70119910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1297203260	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	82	658	2	ENST00000245479.2:c.916del	p.Val306CysfsTer77	p.V306Cfs*77	ENST00000245479	NM_000346.3	304	ccG/cc	3/3	0.315627963323972	2	FACETS	1	0.898	1	0.508	0.449	0.571	CLONAL	1	TRUE	0	0.315627963323972	2		660	511	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745962	745963	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	109	627	0	ENST00000314574.4:c.559_560del	p.Ser187Ter	p.S187*	ENST00000314574	NM_005433.3	187	AGt/t	5/12	1	2	FACETS	0.868	0.779	0.962	0.868	0.779	0.962	CLONAL	1	TRUE	1	0.315627963323972	2		627	796	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991709	72991711	+	inframe_deletion	In_Frame_Del	DEL	GCA	GCA	-	rs752963945	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	46	346	1	ENST00000268489.5:c.2334_2336del	p.Ala784del	p.A784del	ENST00000268489	NM_006885.3	778	gcTGCg/gcg	2/10	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.315627963323972	2		347	251	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885550	111885550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775891572	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	87	682	3	ENST00000341259.2:c.1327C>T	p.Arg443Cys	p.R443C	ENST00000341259	NM_005475.2	443	Cgc/Tgc	7/8	0.188672963143204	4	FACETS	0.832	0.735	0.935	0.277	0.245	0.312	INDETERMINATE	1	TRUE	1	0.315627963323972	4		685	872	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741406	17741406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs993043194	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	125	976	2	ENST00000250003.3:c.77C>T	p.Thr26Met	p.T26M	ENST00000250003	NM_002478.4	26	aCg/aTg	1/3	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.315627963323972	2		978	779	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	92	627	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.315627963323972	2		630	533	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939260	71939260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	92	734	1	ENST00000298229.2:c.209G>A	p.Arg70His	p.R70H	ENST00000298229	NM_001567.3	70	cGc/cAc	2/28	1	2	FACETS	0.801	0.711	0.896	0.801	0.711	0.896	CLONAL	1	TRUE	1	0.315627963323972	2		735	728	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825519	50825519	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	107	614	0	ENST00000398568.2:c.2156del	p.Asn719MetfsTer13	p.N719Mfs*13	ENST00000398568	NM_001042412.1	717	gAa/ga	14/18	1	2	FACETS	0.863	0.774	0.957	0.863	0.774	0.957	CLONAL	1	TRUE	1	0.315627963323972	2		614	786	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091782	29091782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373073383	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	113	739	1	ENST00000328354.6:c.1175C>T	p.Ala392Val	p.A392V	ENST00000328354	NM_007194.3	392	gCg/gTg	11/15	1	2	FACETS	0.931	0.838	1	0.931	0.838	1	CLONAL	1	TRUE	1	0.315627963323972	2		740	769	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777990	3777990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1423752547	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	157	1092	0	ENST00000262367.5:c.7058G>A	p.Arg2353Gln	p.R2353Q	ENST00000262367	NM_004380.2	2353	cGg/cAg	31/31	1	2	FACETS	0.968	0.886	1	0.968	0.886	1	CLONAL	1	TRUE	1	0.315627963323972	2		1092	1028	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	126	905	2	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.983	0.89	1	0.983	0.89	1	CLONAL	1	TRUE	1	0.315627963323972	2		907	812	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17349192	17349192	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	78	536	0	ENST00000375499.3:c.676T>G	p.Phe226Val	p.F226V	ENST00000375499	NM_003000.2	226	Ttc/Gtc	7/8	1	2	FACETS	0.858	0.755	0.969	0.858	0.755	0.969	CLONAL	1	TRUE	1	0.315627963323972	2		536	576	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101068	27101068	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	117	807	1	ENST00000324856.7:c.4354del	p.Gln1452ArgfsTer29	p.Q1452Rfs*29	ENST00000324856	NM_006015.4	1450	ggC/gg	18/20	1	2	FACETS	0.856	0.771	0.946	0.856	0.771	0.946	CLONAL	1	TRUE	1	0.315627963323972	2		808	866	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106459	27106459	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	116	636	0	ENST00000324856.7:c.6070C>T	p.Arg2024Trp	p.R2024W	ENST00000324856	NM_006015.4	2024	Cgg/Tgg	20/20	1	2	FACETS	0.824	0.742	0.911	0.824	0.742	0.911	CLONAL	1	TRUE	1	0.315627963323972	2		636	892	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115251276	115251276	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	54	400	0	ENST00000369535.4:c.451-1G>T		p.X151_splice	ENST00000369535	NM_002524.4	151			1	2	FACETS	0.67	0.572	0.776	0.67	0.572	0.776	SUBCLONAL	1	TRUE	1	0.315627963323972	2		400	511	SUCCESS
FH	2271	MSKCC	GRCh37	1	241669439	241669439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	97	426	0	ENST00000366560.3:c.768del	p.Lys256AsnfsTer4	p.K256Nfs*4	ENST00000366560	NM_000143.3	256	aaA/aa	6/10	1	2	FACETS	0.868	0.774	0.968	0.868	0.774	0.968	CLONAL	1	TRUE	1	0.315627963323972	2		426	708	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097650	8097650	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	30	318	0	ENST00000346208.3:c.32T>C	p.Val11Ala	p.V11A	ENST00000346208		11	gTg/gCg	2/6	0.156214706435715	0	FACETS	0.556	0.45	0.674			1	INDETERMINATE	1	TRUE	0	0.315627963323972	0		318	234	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936099	71936099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1001395700	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	41	165	1	ENST00000298229.2:c.71G>A	p.Arg24His	p.R24H	ENST00000298229	NM_001567.3	24	cGc/cAc	1/28	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.315627963323972	2		166	209	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948208	71948209	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs749079348	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	117	1010	3	ENST00000298229.2:c.2927dup	p.Pro977ThrfsTer7	p.P977Tfs*7	ENST00000298229	NM_001567.3	974	gcc/gCcc	26/28	1	2	FACETS	0.829	0.747	0.916	0.829	0.747	0.916	CLONAL	1	TRUE	1	0.315627963323972	2		1013	894	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307537	118307537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	131	798	1	ENST00000534358.1:c.310G>A	p.Ala104Thr	p.A104T	ENST00000534358	NM_005933.3	104	Gcc/Acc	1/36	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.315627963323972	2		799	806	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360525	118360525	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	119	567	0	ENST00000534358.1:c.4498A>G	p.Lys1500Glu	p.K1500E	ENST00000534358	NM_005933.3	1500	Aag/Gag	12/36	1	2	FACETS	0.896	0.808	0.988	0.896	0.808	0.988	CLONAL	1	TRUE	1	0.315627963323972	2		567	842	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421586	49421586	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	99	505	0	ENST00000301067.7:c.14643G>T	p.Gln4881His	p.Q4881H	ENST00000301067	NM_003482.3	4881	caG/caT	47/54	0.188672963143204	4	FACETS	1	0.969	1	0.411	0.367	0.457	INDETERMINATE	1	TRUE	1	0.315627963323972	4		505	670	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422910	49422910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123719	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	224	684	4	ENST00000301067.7:c.14185C>T	p.Arg4729Trp	p.R4729W	ENST00000301067	NM_003482.3	4729	Cgg/Tgg	44/54	0.188672963143204	4	FACETS	1	0.986	1	0.802	0.749	0.857	INDETERMINATE	2	TRUE	1	0.315627963323972	4		688	776	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	137	782	2	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.188672963143204	4	FACETS	1	0.975	1	0.4	0.363	0.439	INDETERMINATE	1	TRUE	1	0.315627963323972	4		784	952	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858943	57858943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	117	720	1	ENST00000228682.2:c.439C>T	p.Pro147Ser	p.P147S	ENST00000228682	NM_005269.2	147	Cct/Tct	5/12	0.188672963143204	4	FACETS	1	0.905	1	0.335	0.301	0.371	INDETERMINATE	1	TRUE	1	0.315627963323972	4		721	970	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21553853	21553853	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs181062581	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	122	707	0	ENST00000382592.4:c.2749A>G	p.Thr917Ala	p.T917A	ENST00000382592	NM_014572.2	917	Act/Gct	7/8	1	2	FACETS	0.964	0.871	1	0.964	0.871	1	CLONAL	1	TRUE	1	0.315627963323972	2		707	802	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959074	28959074	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	113	509	1	ENST00000282397.4:c.2064del	p.Glu689SerfsTer21	p.E689Sfs*21	ENST00000282397	NM_002019.4	688	ccC/cc	14/30	1	2	FACETS	0.977	0.88	1	0.977	0.88	1	CLONAL	1	TRUE	1	0.315627963323972	2		510	733	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95595947	95595947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	116	562	0	ENST00000393063.1:c.596G>A	p.Cys199Tyr	p.C199Y	ENST00000393063	NM_030621.3	199	tGt/tAt	7/28	0.315627963323972	2	FACETS	0.803	0.723	0.888	0.402	0.361	0.444	CLONAL	1	TRUE	0	0.315627963323972	2		562	915	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	359972	359972	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	88	607	2	ENST00000262320.3:c.1116+1G>A		p.X372_splice	ENST00000262320	NM_003502.3	372			1	2	FACETS	0.956	0.849	1	0.956	0.849	1	CLONAL	1	TRUE	1	0.315627963323972	2		609	583	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096132	2096133	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs763525759	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	92	675	2	ENST00000219066.1:c.374dup	p.Val127GlyfsTer43	p.V127Gfs*43	ENST00000219066	NM_002528.5	125	cca/ccCa	2/6	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.315627963323972	2		677	570	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225603	2225603	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	93	680	0	ENST00000326181.6:c.1606G>T	p.Gly536Cys	p.G536C	ENST00000326181	NM_032271.2	536	Ggc/Tgc	17/21	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.315627963323972	2		680	548	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971381	15971381	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	154	663	0	ENST00000268712.3:c.4568del	p.Pro1523LeufsTer20	p.P1523Lfs*20	ENST00000268712	NM_006311.3	1523	cCt/ct	32/46	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.315627963323972	2		663	866	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550566	29550566	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	113	471	0	ENST00000356175.3:c.1826A>T	p.Lys609Ile	p.K609I	ENST00000356175	NM_000267.3	609	aAa/aTa	16/57	1	2	FACETS	0.919	0.827	1	0.919	0.827	1	CLONAL	1	TRUE	1	0.315627963323972	2		471	779	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868595	37868595	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	75	554	0	ENST00000269571.5:c.1042G>C	p.Glu348Gln	p.E348Q	ENST00000269571		348	Gag/Cag	9/27	1	2	FACETS	0.849	0.745	0.96	0.849	0.745	0.96	CLONAL	1	TRUE	1	0.315627963323972	2		554	560	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370173	40370173	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	95	763	0	ENST00000293328.3:c.1165C>T	p.Arg389Cys	p.R389C	ENST00000293328	NM_012448.3	389	Cgc/Tgc	9/19	1	2	FACETS	0.675	0.6	0.755	0.675	0.6	0.755	SUBCLONAL	1	TRUE	1	0.315627963323972	2		763	892	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448271	56448271	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	247	594	0	ENST00000407977.2:c.375+1G>A		p.X125_splice	ENST00000407977		125			0.315627963323972	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.315627963323972	2		594	738	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216482	2216482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372258317	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	104	722	5	ENST00000398665.3:c.2126C>T	p.Pro709Leu	p.P709L	ENST00000398665	NM_032482.2	709	cCg/cTg	20/28	1	2	FACETS	0.978	0.876	1	0.978	0.876	1	CLONAL	1	TRUE	1	0.315627963323972	2		727	674	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212166	5212166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775731386	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	88	777	0	ENST00000357368.4:c.4865C>T	p.Thr1622Met	p.T1622M	ENST00000357368	NM_002850.3	1622	aCg/aTg	32/38	0.315627963323972	0	FACETS	0.735	0.653	0.822			1	SUBCLONAL	1	TRUE	0	0.315627963323972	0		777	519	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223120	5223120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764560600	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	94	889	1	ENST00000357368.4:c.2683G>A	p.Val895Met	p.V895M	ENST00000357368	NM_002850.3	895	Gtg/Atg	18/38	0.315627963323972	0	FACETS	0.778	0.694	0.866			1	SUBCLONAL	1	TRUE	0	0.315627963323972	0		890	524	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5286135	5286135	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	72	687	1	ENST00000357368.4:c.17del	p.Gly6AlafsTer59	p.G6Afs*59	ENST00000357368	NM_002850.3	6	gGc/gc	2/38	0.315627963323972	0	FACETS	0.713	0.625	0.807			1	SUBCLONAL	1	TRUE	0	0.315627963323972	0		688	438	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144491	11144491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	108	746	2	ENST00000358026.2:c.3823G>A	p.Ala1275Thr	p.A1275T	ENST00000358026	NM_001128849.1	1275	Gcc/Acc	27/36	1	2	FACETS	0.949	0.852	1	0.949	0.852	1	CLONAL	1	TRUE	1	0.315627963323972	2		748	721	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350041	15350041	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	123	830	0	ENST00000263377.2:c.3611G>C	p.Ser1204Thr	p.S1204T	ENST00000263377	NM_058243.2	1204	aGc/aCc	18/20	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.315627963323972	2		830	765	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353959	15353959	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1354137520	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	25	222	1	ENST00000263377.2:c.2921C>T	p.Pro974Leu	p.P974L	ENST00000263377	NM_058243.2	974	cCg/cTg	14/20	1	2	FACETS	0.954	0.759	1	0.954	0.759	1	CLONAL	1	TRUE	1	0.315627963323972	2		223	166	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18964138	18964138	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	112	610	0	ENST00000262803.5:c.1135C>A	p.His379Asn	p.H379N	ENST00000262803	NM_002911.3	379	Cac/Aac	8/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.315627963323972	2		610	589	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219934	36219934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	79	633	3	ENST00000222270.7:c.4736G>A	p.Arg1579His	p.R1579H	ENST00000222270	NM_014727.1	1579	cGt/cAt	21/37	1	2	FACETS	0.888	0.782	1	0.888	0.782	1	CLONAL	1	TRUE	1	0.315627963323972	2		636	564	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745213	41745213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1176757863	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	85	554	2	ENST00000301178.4:c.1279C>T	p.Arg427Cys	p.R427C	ENST00000301178	NM_021913.4	427	Cgc/Tgc	9/20	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.315627963323972	2		556	535	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754588	42754589	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	92	749	0	ENST00000222329.4:c.151dup	p.Asp51GlyfsTer11	p.D51Gfs*11	ENST00000222329	NM_006494.2	51	gac/gGac	2/4	1	2	FACETS	0.711	0.631	0.796	0.711	0.631	0.796	SUBCLONAL	1	TRUE	1	0.315627963323972	2		749	820	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731468	47731468	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1284528511	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	29	177	0	ENST00000449228.1:c.324del	p.Phe109SerfsTer120	p.F109Sfs*120	ENST00000449228	NM_001127240.2	108	ggG/gg	2/4	1	2	FACETS	0.888	0.718	1	0.888	0.718	1	CLONAL	1	TRUE	1	0.315627963323972	2		177	207	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967087	25967087	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	80	468	0	ENST00000435504.4:c.2119G>T	p.Gly707Trp	p.G707W	ENST00000435504		707	Ggg/Tgg	13/13	NA	2	FACETS	0.99	0.874	1			1	INDETERMINATE	1	TRUE	NA	0.315627963323972	2		468	512	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702211	47702211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750657	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	115	622	0	ENST00000233146.2:c.1807G>A	p.Asp603Asn	p.D603N	ENST00000233146	NM_000251.2	603	Gat/Aat	12/16	1	2	FACETS	0.883	0.795	0.976	0.883	0.795	0.976	CLONAL	1	TRUE	1	0.315627963323972	2		622	825	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044449	128044449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201840181	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	107	621	1	ENST00000285398.2:c.1172G>A	p.Arg391Gln	p.R391Q	ENST00000285398	NM_000122.1	391	cGg/cAg	8/15	1	2	FACETS	0.897	0.805	0.995	0.897	0.805	0.995	CLONAL	1	TRUE	1	0.315627963323972	2		622	756	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426801	212426801	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	106	527	0	ENST00000342788.4:c.2314A>G	p.Met772Val	p.M772V	ENST00000342788	NM_005235.2	772	Atg/Gtg	20/28	1	2	FACETS	0.888	0.797	0.986	0.888	0.797	0.986	CLONAL	1	TRUE	1	0.315627963323972	2		527	756	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386361	31386361	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767169378	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	79	570	1	ENST00000328111.2:c.1586C>T	p.Pro529Leu	p.P529L	ENST00000328111	NM_006892.3	529	cCg/cTg	15/23	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.315627963323972	2		571	459	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026126	36026126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751268997	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	54	800	1	ENST00000358208.4:c.728G>A	p.Arg243His	p.R243H	ENST00000358208		243	cGc/cAc	7/12	1	2	FACETS	0.542	0.463	0.63	0.542	0.463	0.63	SUBCLONAL	1	TRUE	1	0.315627963323972	2		801	631	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790090	40790090	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	78	593	0	ENST00000373198.4:c.2641del	p.Arg881GlyfsTer20	p.R881Gfs*20	ENST00000373198	NM_133170.3	881	Cgg/gg	18/32	0.315627963323972	0	FACETS	0.709	0.625	0.799			1	SUBCLONAL	1	TRUE	0	0.315627963323972	0		593	477	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817486	39817486	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	108	636	2	ENST00000288319.7:c.77C>A	p.Pro26Gln	p.P26Q	ENST00000288319	NM_182918.3	26	cCa/cAa	2/10	1	2	FACETS	0.98	0.881	1	0.98	0.881	1	CLONAL	1	TRUE	1	0.315627963323972	2		638	698	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37628864	37628864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151307781	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	98	738	0	ENST00000249071.6:c.202C>T	p.Arg68Trp	p.R68W	ENST00000249071	NM_002872.4	68	Cgg/Tgg	3/7	1	2	FACETS	0.793	0.707	0.885	0.793	0.707	0.885	SUBCLONAL	1	TRUE	1	0.315627963323972	2		738	783	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936019	49936019	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	140	782	0	ENST00000296474.3:c.1651A>G	p.Met551Val	p.M551V	ENST00000296474	NM_002447.2	551	Atg/Gtg	4/20	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.315627963323972	2		782	842	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807480	1807480	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	33	664	0	ENST00000260795.2:c.1649C>A	p.Pro550His	p.P550H	ENST00000260795		550	cCc/cAc	12/17	1	2	FACETS	0.412	0.335	0.499	0.412	0.335	0.499	SUBCLONAL	1	TRUE	1	0.315627963323972	2		664	508	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957837	1957837	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	122	691	0	ENST00000382891.5:c.2803C>T	p.Arg935Ter	p.R935*	ENST00000382891	NM_133335.3	935	Cga/Tga	15/22	1	2	FACETS	0.962	0.869	1	0.962	0.869	1	CLONAL	1	TRUE	1	0.315627963323972	2		691	804	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749443	41749443	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	72	491	0	ENST00000226382.2:c.352G>A	p.Ala118Thr	p.A118T	ENST00000226382	NM_003924.3	118	Gcg/Acg	2/3	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.315627963323972	2		491	428	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293440	1293440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1448835821	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	91	572	0	ENST00000310581.5:c.1561C>T	p.Arg521Cys	p.R521C	ENST00000310581	NM_198253.2	521	Cgc/Tgc	2/16	0.156214706435715	0	FACETS	0.824	0.734	0.918			1	INDETERMINATE	1	TRUE	0	0.315627963323972	0		572	479	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31422913	31422913	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	188	822	0	ENST00000344624.3:c.3400G>T	p.Gly1134Ter	p.G1134*	ENST00000344624		1134	Gga/Tga	26/33	0.156214706435715	0	FACETS	0.836	0.772	0.902			1	INDETERMINATE	1	TRUE	0	0.315627963323972	0		822	975	SUCCESS
APC	324	MSKCC	GRCh37	5	112176794	112176794	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs879254181	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	104	465	0	ENST00000257430.4:c.5503A>G	p.Arg1835Gly	p.R1835G	ENST00000257430	NM_000038.5	1835	Aga/Gga	16/16	1	2	FACETS	0.958	0.858	1	0.958	0.858	1	CLONAL	1	TRUE	1	0.315627963323972	2		465	688	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500766	149500766	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs950308789	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	69	465	1	ENST00000261799.4:c.2463+1G>A		p.X821_splice	ENST00000261799	NM_002609.3	821			1	2	FACETS	0.883	0.771	1	0.883	0.771	1	CLONAL	1	TRUE	1	0.315627963323972	2		466	495	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176516607	176516607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs545721160	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	122	674	1	ENST00000292408.4:c.4C>T	p.Arg2Trp	p.R2W	ENST00000292408	NM_213647.1	2	Cgg/Tgg	2/18	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.315627963323972	2		675	723	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017501	112017501	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757587326	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	95	470	0	ENST00000368678.4:c.1012G>A	p.Val338Ile	p.V338I	ENST00000368678		338	Gtc/Atc	9/13	1	2	FACETS	0.859	0.765	0.959	0.859	0.765	0.959	CLONAL	1	TRUE	1	0.315627963323972	2		470	701	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521848	157521848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747088591	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	72	396	0	ENST00000346085.5:c.4120C>T	p.Arg1374Cys	p.R1374C	ENST00000346085	NM_020732.3	1374	Cgc/Tgc	18/20	1	2	FACETS	0.777	0.679	0.882	0.777	0.679	0.882	SUBCLONAL	1	TRUE	1	0.315627963323972	2		396	587	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042213	6042213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064794077	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	151	811	0	ENST00000265849.7:c.408G>A	p.Met136Ile	p.M136I	ENST00000265849	NM_000535.5	136	atG/atA	5/15	1	2	FACETS	0.912	0.833	0.995	0.912	0.833	0.995	CLONAL	1	TRUE	1	0.315627963323972	2		811	1049	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441977	6441977	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	106	668	0	ENST00000356142.4:c.536T>C	p.Leu179Pro	p.L179P	ENST00000356142	NM_018890.3	179	cTc/cCc	7/7	1	2	FACETS	0.693	0.62	0.771	0.693	0.62	0.771	SUBCLONAL	1	TRUE	1	0.315627963323972	2		668	969	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072515	5072515	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	89	465	0	ENST00000381652.3:c.1668del	p.Phe556LeufsTer12	p.F556Lfs*12	ENST00000381652	NM_004972.3	555	acT/ac	13/25	0.315627963323972	3	FACETS	0.77	0.682	0.865	0.385	0.341	0.433	SUBCLONAL	1	TRUE	1	0.315627963323972	3		465	848	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760012	133760012	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	147	933	0	ENST00000318560.5:c.2335A>G	p.Thr779Ala	p.T779A	ENST00000318560	NM_005157.4	779	Aca/Gca	11/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.315627963323972	2		933	753	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401237	139401237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1406056612	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	111	768	3	ENST00000277541.6:c.3832G>A	p.Ala1278Thr	p.A1278T	ENST00000277541	NM_017617.3	1278	Gcc/Acc	23/34	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.315627963323972	2		771	642	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564768	139564768	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	116	748	0	ENST00000308874.7:c.561del	p.Asn188ThrfsTer9	p.N188Tfs*9	ENST00000308874		186	gCc/gc	7/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.315627963323972	2		748	582	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918535	44918535	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	93	525	0	ENST00000377967.4:c.1018G>A	p.Ala340Thr	p.A340T	ENST00000377967	NM_021140.2	340	Gcc/Acc	12/29	0.156214706435715	0	FACETS	0.595	0.529	0.665			1	INDETERMINATE	1	TRUE	0	0.315627963323972	0		525	678	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041603	47041603	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	100	758	0	ENST00000377604.3:c.1831del	p.Glu611ArgfsTer93	p.E611Rfs*93	ENST00000377604	NM_001204468.1	610	Ggg/gg	17/24	0.156214706435715	0	FACETS	0.659	0.589	0.733			1	INDETERMINATE	1	TRUE	0	0.315627963323972	0		758	658	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424712	47424712	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	69	722	1	ENST00000377045.4:c.520C>A	p.Arg174Ser	p.R174S	ENST00000377045	NM_001654.4	174	Cgc/Agc	6/16	0.156214706435715	0	FACETS	0.416	0.361	0.474			1	INDETERMINATE	1	TRUE	0	0.315627963323972	0		723	720	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649712	48649712	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149753411	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	108	779	2	ENST00000376670.3:c.196G>A	p.Ala66Thr	p.A66T	ENST00000376670	NM_002049.3	66	Gct/Act	2/6	0.156214706435715	0	FACETS	0.749	0.674	0.829			1	INDETERMINATE	1	TRUE	0	0.315627963323972	0		781	625	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53241076	53241076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	127	611	0	ENST00000375401.3:c.1135C>T	p.Pro379Ser	p.P379S	ENST00000375401	NM_004187.3	379	Ccc/Tcc	9/26	0.156214706435715	0	FACETS	0.771	0.7	0.847			1	INDETERMINATE	1	TRUE	0	0.315627963323972	0		611	714	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243926	53243926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	100	913	0	ENST00000375401.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000375401	NM_004187.3	356	cCt/cTt	8/26	0.156214706435715	0	FACETS	0.541	0.483	0.603			1	INDETERMINATE	1	TRUE	0	0.315627963323972	0		913	802	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345240	70345240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	111	700	3	ENST00000374080.3:c.2266G>A	p.Val756Ile	p.V756I	ENST00000374080		756	Gta/Ata	16/45	0.156214706435715	0	FACETS	0.771	0.695	0.852			1	INDETERMINATE	1	TRUE	0	0.315627963323972	0		703	624	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81562999	81562999	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	130	509	1	ENST00000298171.2:c.562G>A	p.Gly188Ser	p.G188S	ENST00000298171	NM_000369.2	188	Ggc/Agc	7/10	0.315627963323972	2	FACETS	1	0.986	1	0.741	0.675	0.81	CLONAL	1	TRUE	0	0.315627963323972	2		510	556	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798827	42798836	+	frameshift_variant	Frame_Shift_Ins	INS	CTGGACCAGC	CTGGACCAGC	TGGTCATGCAG	novel	NA	P-0017697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	112	757	0	ENST00000575354.2:c.4399_4408delinsTGGTCATGCAG	p.Leu1467TrpfsTer47	p.L1467Wfs*47	ENST00000575354	NM_015125.3	1467	CTGGACCAGCgc/TGGTCATGCAGgc	19/20	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.315627963323972	2		757	697	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305399	65305399	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	186	499	0	ENST00000342505.4:c.2729T>C	p.Leu910Pro	p.L910P	ENST00000342505	NM_002227.2	910	cTg/cCg	20/25	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.663594706823662	2		499	532	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274911	41274911	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	127	478	0	ENST00000349496.5:c.1161T>G	p.Asn387Lys	p.N387K	ENST00000349496	NM_001904.3	387	aaT/aaG	8/15	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.663594706823662	2		478	367	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106426	27106426	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	173	545	0	ENST00000324856.7:c.6038del	p.Lys2013SerfsTer2	p.K2013Sfs*2	ENST00000324856	NM_006015.4	2013	Aag/ag	20/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.663594706823662	2		545	505	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266107	41266107	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	125	373	0	ENST00000349496.5:c.104T>A	p.Ile35Asn	p.I35N	ENST00000349496	NM_001904.3	35	aTc/aAc	3/15	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.663594706823662	2		373	367	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989651	68989651	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	174	506	0	ENST00000288368.4:c.1589A>G	p.Glu530Gly	p.E530G	ENST00000288368	NM_024870.2	530	gAa/gGa	15/40	0.663594706823662	8	FACETS	1	0.979	1	0.171	0.157	0.187	CLONAL	1	TRUE	1	0.663594706823662	8		506	1307	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0017701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	158	447	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.310377457695734	3	FACETS	1	0.99	1	0.749	0.692	0.806	INDETERMINATE	1	TRUE	1	0.612635464842353	3		447	450	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160837	56161470	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTAAATTTAGATCAATTAATTCCCTATAGTAAACAAAGTTAAACTTAAAATGTATTTTAGGCTAATATTTTTCTTTAATGTATTTATGAGGTTTTACTATCTTAATATACCATAGAATAGAAATTTGATCTATTTAATAAATTCAGTGAAAATGAAAGATTAAATCATGGAAATAGCTGTAGATTTTTCTTATATACAAAGATAATGAAGAATATGAATTAATAGAAACTTTAGTATAAAAAGTTGGAAATATTGTAAAAGTGATAAATTTAGAAGTTCTTGTGAACCACAGATGTATTAACCTATAGGTTTTCTTTTTAACTCTTTAGAACTGCAGCTGTGCACGTGGAACATTCTGTATTCATCTGCTATTTGTGATGCTCCGGGTGTTTCAACTAGAACCTTCAGACCCAATGTTATGGAGAAAAACTTTAAAGAATTTTGAGGTAGTTTTTAATAAATGCTTAGAGTAAAATTGTTAGCATATTCTTAGGATATATTCTTAAAATTTATCCTTCACTAAATTTAGGCAGTGACCATTTTAAAGGTGTGAAGGTATGTAAGAATTAGTTGATGCTTATAAATAGTTCTCATGAGATATTTACTAAACTTTTTCTTCTAGCTTGAAAAAAA	CTTAAATTTAGATCAATTAATTCCCTATAGTAAACAAAGTTAAACTTAAAATGTATTTTAGGCTAATATTTTTCTTTAATGTATTTATGAGGTTTTACTATCTTAATATACCATAGAATAGAAATTTGATCTATTTAATAAATTCAGTGAAAATGAAAGATTAAATCATGGAAATAGCTGTAGATTTTTCTTATATACAAAGATAATGAAGAATATGAATTAATAGAAACTTTAGTATAAAAAGTTGGAAATATTGTAAAAGTGATAAATTTAGAAGTTCTTGTGAACCACAGATGTATTAACCTATAGGTTTTCTTTTTAACTCTTTAGAACTGCAGCTGTGCACGTGGAACATTCTGTATTCATCTGCTATTTGTGATGCTCCGGGTGTTTCAACTAGAACCTTCAGACCCAATGTTATGGAGAAAAACTTTAAAGAATTTTGAGGTAGTTTTTAATAAATGCTTAGAGTAAAATTGTTAGCATATTCTTAGGATATATTCTTAAAATTTATCCTTCACTAAATTTAGGCAGTGACCATTTTAAAGGTGTGAAGGTATGTAAGAATTAGTTGATGCTTATAAATAGTTCTCATGAGATATTTACTAAACTTTTTCTTCTAGCTTGAAAAAAA	-	novel	NA	P-0017701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	43	97	0	ENST00000399503.3:c.1035+77_1153-185del		p.X345_splice	ENST00000399503	NM_005921.1	345		5/20	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.612635464842353	2		97	121	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	157	306	0				ENST00000310581	NM_198253.2	-/1132			0.412902601967374	3	FACETS	1	0.962	1	0.543	0.497	0.59	CLONAL	1	TRUE	1	0.436209612976834	3		306	808	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534285	534286	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	243	599	1	ENST00000451590.1:c.37_38delinsAA	p.Gly13Asn	p.G13N	ENST00000451590	NM_001130442.1	13	GGt/AAt	2/5	0.412902601967374	3	FACETS	0.921	0.864	0.979	0.921	0.864	0.979	CLONAL	2	TRUE	1	0.436209612976834	3		600	737	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351737	89351737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1385566000	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	186	839	0	ENST00000301030.4:c.1213C>T	p.Arg405Cys	p.R405C	ENST00000301030	NM_001256183.1	405	Cgt/Tgt	9/13	1	2	FACETS	0.901	0.832	0.972	0.901	0.832	0.972	CLONAL	1	TRUE	1	0.436209612976834	2		839	947	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400190	41400190	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	134	555	0	ENST00000373198.4:c.569G>A	p.Arg190Lys	p.R190K	ENST00000373198	NM_133170.3	190	aGa/aAa	5/32	0.412902601967374	3	FACETS	0.881	0.801	0.966	0.441	0.4	0.483	CLONAL	1	TRUE	1	0.436209612976834	3		555	849	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20152085	20152085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	169	294	1	ENST00000379607.5:c.245G>A	p.Arg82Gln	p.R82Q	ENST00000379607	NM_001412.3	82	cGa/cAa	4/7	1	1	FACETS	0.755	0.703	0.808	1	0.991	1	SUBCLONAL	2	TRUE	0	0.436209612976834	1		295	401	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561430	9561430	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	150	504	0	ENST00000353224.5:c.352G>A	p.Gly118Ser	p.G118S	ENST00000353224	NM_177990.2	118	Ggc/Agc	4/10	0.412902601967374	3	FACETS	1	0.93	1	0.51	0.466	0.555	CLONAL	1	TRUE	1	0.436209612976834	3		504	822	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560043	29560043	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs868450405	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	101	323	0	ENST00000356175.3:c.3520C>T	p.Gln1174Ter	p.Q1174*	ENST00000356175	NM_000267.3	1174	Cag/Tag	27/57	1	2	FACETS	0.994	0.893	1	0.994	0.893	1	CLONAL	1	TRUE	1	0.436209612976834	2		323	466	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465542	8465542	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	379	654	0	ENST00000356435.5:c.3638G>A	p.Gly1213Glu	p.G1213E	ENST00000356435		1213	gGa/gAa	21/35	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	2	TRUE	NA	0.436209612976834	2		654	812	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776092	9776092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	159	647	1	ENST00000377346.4:c.556C>T	p.Pro186Ser	p.P186S	ENST00000377346	NM_005026.3	186	Ccg/Tcg	5/24	0.405426223322201	1	FACETS	0.961	0.885	1	0.961	0.885	1	CLONAL	1	TRUE	0	0.436209612976834	1		648	593	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257963	16257963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	120	482	0	ENST00000375759.3:c.5228C>T	p.Ser1743Phe	p.S1743F	ENST00000375759	NM_015001.2	1743	tCc/tTc	11/15	0.405426223322201	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.436209612976834	1		482	415	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301823	65301823	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	130	377	0	ENST00000342505.4:c.3216T>A	p.His1072Gln	p.H1072Q	ENST00000342505	NM_002227.2	1072	caT/caA	23/25	0.405426223322201	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.436209612976834	1		377	458	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551799	150551799	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	39	191	0	ENST00000369026.2:c.208A>G	p.Thr70Ala	p.T70A	ENST00000369026	NM_021960.4	70	Acg/Gcg	1/3	1	2	FACETS	0.67	0.558	0.792	0.67	0.558	0.792	SUBCLONAL	1	TRUE	1	0.436209612976834	2		191	267	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849018	156849018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	140	684	1	ENST00000524377.1:c.1910G>A	p.Gly637Glu	p.G637E	ENST00000524377	NM_002529.3	637	gGg/gAg	15/17	1	2	FACETS	0.846	0.771	0.924	0.846	0.771	0.924	CLONAL	1	TRUE	1	0.436209612976834	2		685	759	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258008	123258008	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	125	551	0	ENST00000358487.5:c.1672+1G>A		p.X558_splice	ENST00000358487	NM_000141.4	558			1	2	FACETS	0.792	0.717	0.87	0.792	0.717	0.87	SUBCLONAL	1	TRUE	1	0.436209612976834	2		551	724	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402269	402269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367537993	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	191	661	0	ENST00000399788.2:c.4522C>T	p.Arg1508Trp	p.R1508W	ENST00000399788	NM_001042603.1	1508	Cgg/Tgg	27/28	1	2	FACETS	0.932	0.862	1	0.932	0.862	1	CLONAL	1	TRUE	1	0.436209612976834	2		661	940	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486769	56486769	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	179	591	0	ENST00000267101.3:c.1184-1G>A		p.X395_splice	ENST00000267101	NM_001982.3	395			1	2	FACETS	0.982	0.906	1	0.982	0.906	1	CLONAL	1	TRUE	1	0.436209612976834	2		591	836	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860110	57860110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	176	728	0	ENST00000228682.2:c.850G>A	p.Ala284Thr	p.A284T	ENST00000228682	NM_005269.2	284	Gcc/Acc	8/12	1	2	FACETS	0.978	0.902	1	0.978	0.902	1	CLONAL	1	TRUE	1	0.436209612976834	2		728	825	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218190	69218190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	142	457	0	ENST00000462284.1:c.406G>A	p.Glu136Lys	p.E136K	ENST00000462284	NM_002392.5	136	Gaa/Aaa	6/11	1	2	FACETS	0.934	0.853	1	0.934	0.853	1	CLONAL	1	TRUE	1	0.436209612976834	2		457	697	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109927	115109927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	173	680	1	ENST00000257566.3:c.1951G>A	p.Asp651Asn	p.D651N	ENST00000257566	NM_016569.3	651	Gac/Aac	8/8	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.436209612976834	2		681	751	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120798	115120798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	103	519	0	ENST00000257566.3:c.208G>A	p.Gly70Arg	p.G70R	ENST00000257566	NM_016569.3	70	Ggg/Agg	1/8	1	2	FACETS	0.842	0.755	0.933	0.842	0.755	0.933	CLONAL	1	TRUE	1	0.436209612976834	2		519	561	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914931	32914931	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781476	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	120	449	0	ENST00000380152.3:c.6439C>T	p.His2147Tyr	p.H2147Y	ENST00000380152		2147	Cac/Tac	11/27	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.436209612976834	2		449	519	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923476	9923476	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	149	571	1	ENST00000330684.3:c.1811C>T	p.Ala604Val	p.A604V	ENST00000330684	NM_001134407.1	604	gCt/gTt	9/13	1	2	FACETS	0.994	0.911	1	0.994	0.911	1	CLONAL	1	TRUE	1	0.436209612976834	2		572	687	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992616	72992616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	92	393	0	ENST00000268489.5:c.1429G>A	p.Glu477Lys	p.E477K	ENST00000268489	NM_006885.3	477	Gaa/Aaa	2/10	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.436209612976834	2		393	385	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976222	7976222	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748339571	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	89	489	0	ENST00000319144.4:c.1973C>T	p.Pro658Leu	p.P658L	ENST00000319144	NM_001139.2	658	cCg/cTg	15/15	1	2	FACETS	0.777	0.691	0.869	0.777	0.691	0.869	SUBCLONAL	1	TRUE	1	0.436209612976834	2		489	525	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664492	29664492	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	179	543	1	ENST00000356175.3:c.6472del	p.Arg2158ValfsTer21	p.R2158Vfs*21	ENST00000356175	NM_000267.3	2157	ttC/tt	42/57	1	2	FACETS	0.951	0.877	1	0.951	0.877	1	CLONAL	1	TRUE	1	0.436209612976834	2		544	863	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604625	48604626	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	88	260	1	ENST00000342988.3:c.1448-1_1448delinsAA		p.X483_splice	ENST00000342988	NM_005359.5	483		12/12	0.405426223322201	1	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	0	0.436209612976834	1		261	314	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095607	178095607	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	115	415	0	ENST00000397062.3:c.1724C>T	p.Pro575Leu	p.P575L	ENST00000397062	NM_006164.4	575	cCt/cTt	5/5	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.436209612976834	2		415	521	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215617252	215617252	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	118	415	0	ENST00000260947.4:c.1596T>A	p.Asp532Glu	p.D532E	ENST00000260947	NM_000465.2	532	gaT/gaA	7/11	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.436209612976834	2		415	537	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408926	41408926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	122	482	0	ENST00000373198.4:c.500C>T	p.Ser167Phe	p.S167F	ENST00000373198	NM_133170.3	167	tCc/tTc	4/32	0.412902601967374	3	FACETS	0.883	0.798	0.972	0.441	0.399	0.486	CLONAL	1	TRUE	1	0.436209612976834	3		482	772	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46275890	46275890	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	169	627	0	ENST00000371998.3:c.3326G>A	p.Gly1109Glu	p.G1109E	ENST00000371998		1109	gGa/gAa	18/23	0.412902601967374	3	FACETS	0.885	0.812	0.96	0.442	0.406	0.48	CLONAL	1	TRUE	1	0.436209612976834	3		627	1067	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940541	49940541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs987594044	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	140	717	0	ENST00000296474.3:c.502C>T	p.His168Tyr	p.H168Y	ENST00000296474	NM_002447.2	168	Cat/Tat	1/20	1	2	FACETS	0.788	0.717	0.861	0.788	0.717	0.861	SUBCLONAL	1	TRUE	1	0.436209612976834	2		717	815	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119545690	119545690	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	118	399	0	ENST00000316626.5:c.1247G>C	p.Gly416Ala	p.G416A	ENST00000316626		416	gGa/gCa	12/12	1	2	FACETS	0.873	0.789	0.96	0.873	0.789	0.96	CLONAL	1	TRUE	1	0.436209612976834	2		399	620	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524141	187524141	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	159	510	0	ENST00000441802.2:c.11398C>T	p.Pro3800Ser	p.P3800S	ENST00000441802	NM_005245.3	3800	Cct/Tct	20/27	0.436209612976834	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.436209612976834	1		510	551	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1272338	1272338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	280	754	0	ENST00000310581.5:c.2344G>A	p.Glu782Lys	p.E782K	ENST00000310581	NM_198253.2	782	Gag/Aag	7/16	0.412902601967374	3	FACETS	0.804	0.757	0.853	0.804	0.757	0.853	CLONAL	2	TRUE	1	0.436209612976834	3		754	972	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982036	93982036	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	128	362	0	ENST00000369303.4:c.1429G>T	p.Glu477Ter	p.E477*	ENST00000369303	NM_004440.3	477	Gaa/Taa	6/17	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.436209612976834	2		362	583	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725525	117725525	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	122	579	1	ENST00000368508.3:c.356G>A	p.Trp119Ter	p.W119*	ENST00000368508	NM_002944.2	119	tGg/tAg	5/43	1	2	FACETS	0.798	0.722	0.878	0.798	0.722	0.878	SUBCLONAL	1	TRUE	1	0.436209612976834	2		580	701	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963907	2963907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	161	760	0	ENST00000396946.4:c.1900G>A	p.Glu634Lys	p.E634K	ENST00000396946	NM_032415.4	634	Gag/Aag	15/25	0.412902601967374	3	FACETS	0.9	0.825	0.979	0.45	0.412	0.49	CLONAL	1	TRUE	1	0.436209612976834	3		760	999	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441649	6441649	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	182	876	0	ENST00000356142.4:c.496A>G	p.Lys166Glu	p.K166E	ENST00000356142	NM_018890.3	166	Aag/Gag	6/7	0.412902601967374	3	FACETS	0.844	0.777	0.913	0.422	0.388	0.457	CLONAL	1	TRUE	1	0.436209612976834	3		876	1205	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829887	72829887	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	79	638	0	ENST00000268489.5:c.6694G>T	p.Glu2232Ter	p.E2232*	ENST00000268489	NM_006885.3	2232	Gaa/Taa	9/10	0.257269976788197	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.257269976788197	1		638	500	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618837	37618837	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	197	659	1	ENST00000447079.4:c.513del	p.Ser171ArgfsTer20	p.S171Rfs*20	ENST00000447079	NM_015083.1	171	agC/ag	1/14	1	2	FACETS	1	0.982	1	1	0.994	1	CLONAL	2	TRUE	1	0.257269976788197	2		660	657	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673701	37673701	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	149	539	0	ENST00000447079.4:c.2855G>C	p.Cys952Ser	p.C952S	ENST00000447079	NM_015083.1	952	tGt/tCt	10/14	1	2	FACETS	1	0.952	1	1	0.992	1	CLONAL	2	TRUE	1	0.257269976788197	2		539	551	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0017704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	199	306	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	0.994	1	CLONAL	2	TRUE	1	0.405499235140858	2		307	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577111	7577111	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786202082	NA	P-0017704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	1090	901	3	ENST00000269305.4:c.827C>A	p.Ala276Asp	p.A276D	ENST00000269305	NM_001126112.2	276	gCc/gAc	8/11	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	4	TRUE	NA	0.405499235140858	2		904	1319	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213331	36213331	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765533021	NA	P-0017704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	733	855	3	ENST00000222270.7:c.2528G>A	p.Arg843Gln	p.R843Q	ENST00000222270	NM_014727.1	843	cGg/cAg	4/37	1	2	FACETS	1	0.99	1	1	0.998	1	CLONAL	2	TRUE	1	0.405499235140858	2		858	1708	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536217	106536217	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	283	437	0	ENST00000369096.4:c.184G>T	p.Val62Leu	p.V62L	ENST00000369096	NM_001198.3	62	Gtg/Ttg	2/7	0.180954467821424	1	FACETS	1	0.994	1	1	0.994	1	INDETERMINATE	1	TRUE	0	0.405499235140858	1		437	768	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940500	76940512	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TATTAAAAGAAAA	TATTAAAAGAAAA	-	novel	NA	P-0017704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	285	266	0	ENST00000373344.5:c.595-14_595-2del		p.X199_splice	ENST00000373344	NM_000489.3	199			1	1	FACETS	0.978	0.942	1	1	0.997	1	CLONAL	3	TRUE	0	0.405499235140858	1		266	382	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0017705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	155	427	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.347192913821534	3	FACETS	0.96	0.884	1	0.96	0.884	1	CLONAL	2	TRUE	1	0.347192913821534	3		427	546	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910427	50910427	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750466994	NA	P-0017705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	105	694	0	ENST00000440232.2:c.1682G>A	p.Arg561Gln	p.R561Q	ENST00000440232	NM_002691.3	561	cGg/cAg	13/27	1	2	FACETS	0.865	0.776	0.96	0.865	0.776	0.96	CLONAL	1	TRUE	1	0.347192913821534	2		694	699	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741658	17741658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	140	534	1	ENST00000250003.3:c.329G>A	p.Arg110His	p.R110H	ENST00000250003	NM_002478.4	110	cGc/cAc	1/3	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.347192913821534	2		535	655	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40476776	40476776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765182656	NA	P-0017705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	115	751	2	ENST00000264657.5:c.1553G>A	p.Arg518Gln	p.R518Q	ENST00000264657	NM_139276.2	518	cGa/cAa	17/24	1	2	FACETS	0.768	0.691	0.849	0.768	0.691	0.849	SUBCLONAL	1	TRUE	1	0.347192913821534	2		753	863	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118992	3118992	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	139	683	0	ENST00000078429.4:c.676A>C	p.Ile226Leu	p.I226L	ENST00000078429	NM_002067.2	226	Atc/Ctc	5/7	1	2	FACETS	0.879	0.8	0.962	0.879	0.8	0.962	CLONAL	1	TRUE	1	0.347192913821534	2		683	911	SUCCESS
APC	324	MSKCC	GRCh37	5	112175721	112175723	+	frameshift_variant	Frame_Shift_Del	DEL	AGA	AGA	G	novel	NA	P-0017705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	119	349	0	ENST00000257430.4:c.4430_4432delinsG	p.Gln1477ArgfsTer9	p.Q1477Rfs*9	ENST00000257430	NM_000038.5	1477	cAGAgg/cGgg	16/16	0.347192913821534	2	FACETS	0.907	0.827	0.989	0.907	0.827	0.989	CLONAL	2	TRUE	0	0.347192913821534	2		349	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577086	7577087	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0017706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	513	657	0	ENST00000269305.4:c.851_852del	p.Thr284ArgfsTer21	p.T284Rfs*21	ENST00000269305	NM_001126112.2	284	aCA/a	8/11	0.852940252126806	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.852940252126806	1		657	668	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422716	47422716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1413219188	NA	P-0017706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	321	511	0	ENST00000377045.4:c.188G>A	p.Arg63Gln	p.R63Q	ENST00000377045	NM_001654.4	63	cGa/cAa	3/16	NA	2	FACETS	0.903	0.856	0.95			1	INDETERMINATE	1	TRUE	NA	0.852940252126806	2		511	834	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399516	139399516	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs533102436	NA	P-0017706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	500	650	2	ENST00000277541.6:c.4627G>A	p.Gly1543Arg	p.G1543R	ENST00000277541	NM_017617.3	1543	Ggg/Agg	26/34	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.852940252126806	2		652	1135	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8526626	8526626	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0017706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	34	473	0	ENST00000356435.5:c.568+1G>A		p.X190_splice	ENST00000356435		190			0.82017860939485	1	FACETS	0.077	0.062	0.094	0.077	0.062	0.094	SUBCLONAL	1	TRUE	0	0.852940252126806	1		473	593	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577086	7577087	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0017706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	256	657	0	ENST00000269305.4:c.851_852del	p.Thr284ArgfsTer21	p.T284Rfs*21	ENST00000269305	NM_001126112.2	284	aCA/a	8/11	0.565901720047902	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.565901720047902	1		657	583	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422716	47422716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1413219188	NA	P-0017706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	135	511	0	ENST00000377045.4:c.188G>A	p.Arg63Gln	p.R63Q	ENST00000377045	NM_001654.4	63	cGa/cAa	3/16	1	2	FACETS	0.778	0.71	0.85	0.778	0.71	0.85	SUBCLONAL	1	TRUE	1	0.565901720047902	2		511	613	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399516	139399516	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs533102436	NA	P-0017706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	171	650	2	ENST00000277541.6:c.4627G>A	p.Gly1543Arg	p.G1543R	ENST00000277541	NM_017617.3	1543	Ggg/Agg	26/34	1	2	FACETS	0.894	0.825	0.965	0.894	0.825	0.965	CLONAL	1	TRUE	1	0.565901720047902	2		652	676	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0017708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	210	710	5	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.851	0.801	0.902	1	0.994	1	CLONAL	2	TRUE	1	0.563069175863408	2		715	438	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0017708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	103	339	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	0.96	0.867	1	0.96	0.867	1	CLONAL	1	TRUE	1	0.563069175863408	2		339	381	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432644	49432644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866597679	NA	P-0017708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	245	749	1	ENST00000301067.7:c.8495C>T	p.Ala2832Val	p.A2832V	ENST00000301067	NM_003482.3	2832	gCc/gTc	34/54	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.563069175863408	2		750	779	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039154	49039154	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	28	366	2	ENST00000267163.4:c.2232del	p.Glu746LysfsTer8	p.E746Kfs*8	ENST00000267163	NM_000321.2	744	atC/at	22/27	0.563291837769363	1	FACETS	0.871	0.719	1	0.871	0.719	1	CLONAL	1	TRUE	0	0.563069175863408	1		368	82	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216789	7216790	+	splice_acceptor_variant	Splice_Site	INS	-	-	TGAGAAAGGAAAAGACAGAGCCAT	novel	NA	P-0017708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	77	397	0	ENST00000380728.2:c.635-25_635-2dup		p.X212_splice	ENST00000380728		212			1	2	FACETS	0.553	0.486	0.623	0.553	0.486	0.623	SUBCLONAL	1	TRUE	1	0.563069175863408	2		397	495	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026840	71026909	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCTTATAAAATTCTTGGTTCTGCGCAATATCTGCTGAATAAGAATCATTGTCCTATTAATTATCACTTT	TTCTTATAAAATTCTTGGTTCTGCGCAATATCTGCTGAATAAGAATCATTGTCCTATTAATTATCACTTT	-	novel	NA	P-0017708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	60	378	0	ENST00000318789.4:c.1349-36_1382del		p.X450_splice	ENST00000318789	NM_032682.5	450		16/21	1	2	FACETS	0.923	0.805	1	0.923	0.805	1	CLONAL	1	TRUE	1	0.563069175863408	2		378	231	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937183	36937183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	31	747	0	ENST00000361632.4:c.1136G>A	p.Gly379Asp	p.G379D	ENST00000361632		379	gGc/gAc	9/16	0.363415860553273	3	FACETS	0.364	0.293	0.444	0.182	0.146	0.222	SUBCLONAL	1	FALSE	1	0.366690031366362	3		747	550	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204663	108204663	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	103	336	0	ENST00000278616.4:c.7978G>T	p.Glu2660Ter	p.E2660*	ENST00000278616	NM_000051.3	2660	Gaa/Taa	54/63	0.160459118339754	2	FACETS	1	0.934	1	0.526	0.472	0.583	INDETERMINATE	1	FALSE	0	0.366690031366362	2		336	534	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425553	49425553	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	123	914	0	ENST00000301067.7:c.12935C>G	p.Ser4312Cys	p.S4312C	ENST00000301067	NM_003482.3	4312	tCc/tGc	39/54	0.371632556143503	5	FACETS	1	0.973	1	0.404	0.365	0.445	CLONAL	1	FALSE	2	0.366690031366362	5		914	858	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426384	49426384	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	139	963	0	ENST00000301067.7:c.12104C>T	p.Ser4035Leu	p.S4035L	ENST00000301067	NM_003482.3	4035	tCa/tTa	39/54	0.371632556143503	5	FACETS	1	0.979	1	0.418	0.38	0.459	CLONAL	1	FALSE	2	0.366690031366362	5		963	936	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286216	66286216	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	44	586	0	ENST00000273854.3:c.1470A>T	p.Gln490His	p.Q490H	ENST00000273854	NM_004439.5	490	caA/caT	6/18	0.333069163227373	3	FACETS	0.429	0.359	0.507	0.143	0.119	0.169	SUBCLONAL	1	FALSE	0	0.366690031366362	3		586	662	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31435909	31435909	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	53	540	0	ENST00000344624.3:c.3005C>G	p.Ala1002Gly	p.A1002G	ENST00000344624		1002	gCc/gGc	22/33	0.363415860553273	3	FACETS	0.383	0.325	0.447	0.192	0.162	0.224	SUBCLONAL	1	FALSE	1	0.366690031366362	3		540	893	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741163	145741163	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	47	557	0	ENST00000428558.2:c.1243C>T	p.Gln415Ter	p.Q415*	ENST00000428558	NM_004260.3	415	Cag/Tag	6/22	0.23254189487736	5	FACETS	0.619	0.521	0.727	0.206	0.173	0.243	SUBCLONAL	1	FALSE	2	0.366690031366362	5		557	642	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240351	98240351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	62	416	0	ENST00000331920.6:c.1333G>A	p.Gly445Ser	p.G445S	ENST00000331920	NM_000264.3	445	Ggc/Agc	9/24	0.340186097639359	2	FACETS	1	0.948	1	0.589	0.513	0.67	CLONAL	1	FALSE	0	0.366690031366362	2		416	287	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	67	673	0	ENST00000269305.4:c.880del	p.Glu294SerfsTer51	p.E294Sfs*51	ENST00000269305	NM_001126112.2	294	Gag/ag	8/11	0.159910938049377	3	FACETS	0.896	0.78	1			1	INDETERMINATE	1	FALSE	NA	0.369239523167399	3		673	480	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864183	57864183	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	41	413	0	ENST00000228682.2:c.1660A>C	p.Thr554Pro	p.T554P	ENST00000228682	NM_005269.2	554	Act/Cct	12/12	0.374389840089058	3	FACETS	0.883	0.739	1	0.441	0.369	0.521	CLONAL	1	FALSE	1	0.369239523167399	3		413	298	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403501	138403501	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	98	479	0	ENST00000289153.2:c.2281C>A	p.Pro761Thr	p.P761T	ENST00000289153	NM_006219.2	761	Ccc/Acc	15/22	NA	2	FACETS	0.818	0.73	0.911			1	INDETERMINATE	1	FALSE	NA	0.369239523167399	2		479	649	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0017712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	46	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.745	0.628	0.873	0.745	0.628	0.873	SUBCLONAL	1	TRUE	1	0.275822257001097	2		306	448	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0017712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	215	444	1	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	0.275822257001097	3	FACETS	1	0.985	1			1	CLONAL	2	TRUE	NA	0.275822257001097	3		445	746	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923342	9923342	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397514557	NA	P-0017712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	141	556	0	ENST00000330684.3:c.1945C>G	p.Leu649Val	p.L649V	ENST00000330684	NM_001134407.1	649	Ctg/Gtg	9/13	0.275822257001097	3	FACETS	1	0.984	1	0.693	0.632	0.758	CLONAL	1	TRUE	1	0.275822257001097	3		556	839	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577569	7577569	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519981	NA	P-0017712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	64	528	0	ENST00000269305.4:c.712T>A	p.Cys238Ser	p.C238S	ENST00000269305	NM_001126112.2	238	Tgt/Agt	7/11	1	2	FACETS	0.712	0.616	0.816	0.712	0.616	0.816	SUBCLONAL	1	TRUE	1	0.275822257001097	2		528	652	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982157	201982157	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	69	588	0	ENST00000359651.3:c.684del	p.Ser229AlafsTer25	p.S229Afs*25	ENST00000359651		227	ttC/tt	5/8	1	2	FACETS	0.927	0.808	1	0.927	0.808	1	CLONAL	1	TRUE	1	0.275822257001097	2		588	540	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342460	118342460	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	36	318	0	ENST00000534358.1:c.589del	p.Ser197ProfsTer3	p.S197Pfs*3	ENST00000534358	NM_005933.3	196	Ttt/tt	3/36	1	2	FACETS	0.613	0.504	0.735	0.613	0.504	0.735	SUBCLONAL	1	TRUE	1	0.275822257001097	2		318	426	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352473	118352476	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	novel	NA	P-0017712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	67	560	0	ENST00000534358.1:c.3680_3683del	p.Asp1227AlafsTer7	p.D1227Afs*7	ENST00000534358	NM_005933.3	1226	aaAGAC/aa	7/36	1	2	FACETS	0.545	0.472	0.624	0.545	0.472	0.624	SUBCLONAL	1	TRUE	1	0.275822257001097	2		560	892	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436717	110436717	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	64	811	0	ENST00000375856.3:c.1684G>T	p.Asp562Tyr	p.D562Y	ENST00000375856	NM_003749.2	562	Gac/Tac	1/2	0.184928277293523	2	FACETS	0.558	0.482	0.641	0.279	0.241	0.321	SUBCLONAL	1	TRUE	0	0.275822257001097	2		811	832	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95556982	95556988	+	frameshift_variant	Frame_Shift_Del	DEL	GTAAGTT	GTAAGTT	-	novel	NA	P-0017712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	36	463	0	ENST00000393063.1:c.5616_5622del	p.Tyr1874GlyfsTer9	p.Y1874Gfs*9	ENST00000393063	NM_030621.3	1872	agAACTTAC/ag	28/28	1	2	FACETS	0.391	0.32	0.47	0.391	0.32	0.47	SUBCLONAL	1	TRUE	1	0.275822257001097	2		463	668	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168761	32168761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	80	671	0	ENST00000375023.3:c.4162G>A	p.Asp1388Asn	p.D1388N	ENST00000375023	NM_004557.3	1388	Gat/Aat	23/30	1	2	FACETS	0.953	0.839	1	0.953	0.839	1	CLONAL	1	TRUE	1	0.275822257001097	2		671	609	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	141	833	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.342838061579699	2		833	597	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	121	576	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.342838061579699	2		576	532	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	121	479	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.342838061579699	2		479	706	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	110	689	0	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	1	2	FACETS	0.736	0.66	0.816	0.736	0.66	0.816	SUBCLONAL	1	TRUE	1	0.342838061579699	2		689	872	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	176	508	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.342838061579699	2		509	785	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781324	3781326	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs587783502	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1288	78	843	1	ENST00000262367.5:c.5039_5041del	p.Ser1680del	p.S1680del	ENST00000262367	NM_004380.2	1680	tCCTtg/ttg	30/31	1	2	FACETS	0.333	0.291	0.378	0.333	0.291	0.378	SUBCLONAL	1	TRUE	1	0.342838061579699	2		844	1366	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867541	35867541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	83	515	1	ENST00000303115.3:c.361del	p.Ile121Ter	p.I121*	ENST00000303115	NM_002185.3	119	Aaa/aa	3/8	1	2	FACETS	0.858	0.759	0.965	0.858	0.759	0.965	CLONAL	1	TRUE	1	0.342838061579699	2		516	564	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	85	403	0	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	1	2	FACETS	0.915	0.811	1	0.915	0.811	1	CLONAL	1	TRUE	1	0.342838061579699	2		403	542	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591132	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	rs1057519842	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	101	468	0	ENST00000274335.5:c.1727_1729del	p.Thr576del	p.T576del	ENST00000274335		575	aaGACg/aag	12/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.342838061579699	2		468	469	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	169	716	6	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.883	0.81	0.958	0.883	0.81	0.958	CLONAL	1	TRUE	1	0.342838061579699	2		722	1117	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983994	2983994	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	128	739	0	ENST00000396946.4:c.536G>A	p.Arg179Gln	p.R179Q	ENST00000396946	NM_032415.4	179	cGg/cAg	5/25	1	2	FACETS	0.712	0.644	0.784	0.712	0.644	0.784	SUBCLONAL	1	TRUE	1	0.342838061579699	2		739	1049	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692980	89692980	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1060500126	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	128	569	0	ENST00000371953.3:c.464A>G	p.Tyr155Cys	p.Y155C	ENST00000371953	NM_000314.4	155	tAt/tGt	5/9	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.342838061579699	2		569	539	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750639	128750639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775522201	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	116	485	0	ENST00000377970.2:c.176C>T	p.Ala59Val	p.A59V	ENST00000377970	NM_002467.4	59	gCg/gTg	2/3	1	2	FACETS	0.976	0.881	1	0.976	0.881	1	CLONAL	1	TRUE	1	0.342838061579699	2		485	693	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	64	579	4	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	0.556	0.481	0.637	0.556	0.481	0.637	SUBCLONAL	1	TRUE	1	0.342838061579699	2		583	672	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945033	31945033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	264	709	0	ENST00000340398.3:c.68C>T	p.Thr23Met	p.T23M	ENST00000340398	NM_001013699.2	23	aCg/aTg	1/1	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.342838061579699	2		709	1233	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419897	41419897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs577588058	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	228	597	1	ENST00000373198.4:c.424G>A	p.Val142Ile	p.V142I	ENST00000373198	NM_133170.3	142	Gtc/Atc	3/32	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.342838061579699	2		598	890	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280005	66280005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	51	233	1	ENST00000273854.3:c.1684G>A	p.Val562Met	p.V562M	ENST00000273854	NM_004439.5	562	Gtg/Atg	7/18	1	2	FACETS	0.933	0.797	1	0.933	0.797	1	CLONAL	1	TRUE	1	0.342838061579699	2		234	319	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141487	11141487	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	122	640	0	ENST00000358026.2:c.3464G>T	p.Ser1155Ile	p.S1155I	ENST00000358026	NM_001128849.1	1155	aGc/aTc	25/36	1	2	FACETS	0.655	0.591	0.724	0.655	0.591	0.724	SUBCLONAL	1	TRUE	1	0.342838061579699	2		640	1086	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512402	38512402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	156	688	3	ENST00000254066.5:c.1319del	p.Pro440ArgfsTer203	p.P440Rfs*203	ENST00000254066	NM_000964.3	438	gCc/gc	9/9	1	2	FACETS	0.96	0.879	1	0.96	0.879	1	CLONAL	1	TRUE	1	0.342838061579699	2		691	948	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138431133	138431133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	43	382	0	ENST00000289153.2:c.1316C>T	p.Ala439Val	p.A439V	ENST00000289153	NM_006219.2	439	gCg/gTg	8/22	1	2	FACETS	0.553	0.462	0.652	0.553	0.462	0.652	SUBCLONAL	1	TRUE	1	0.342838061579699	2		382	454	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	167	865	8	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.984	0.904	1	0.984	0.904	1	CLONAL	1	TRUE	1	0.342838061579699	2		873	990	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031969	26031969	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	56	290	0	ENST00000244661.2:c.320A>G	p.Asp107Gly	p.D107G	ENST00000244661	NM_003537.3	107	gAc/gGc	1/1	1	2	FACETS	0.86	0.739	0.99	0.86	0.739	0.99	CLONAL	1	TRUE	1	0.342838061579699	2		290	380	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	88	710	5	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.589	0.521	0.662	0.589	0.521	0.662	SUBCLONAL	1	TRUE	1	0.342838061579699	2		715	871	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073985	8073985	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	82	395	0	ENST00000377482.5:c.674T>C	p.Val225Ala	p.V225A	ENST00000377482	NM_018948.3	225	gTg/gCg	4/4	1	2	FACETS	0.976	0.864	1	0.976	0.864	1	CLONAL	1	TRUE	1	0.342838061579699	2		395	490	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115252251	115252251	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	149	479	1	ENST00000369535.4:c.389C>T	p.Ala130Val	p.A130V	ENST00000369535	NM_002524.4	130	gCc/gTc	4/7	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.342838061579699	2		480	709	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77064630	77064630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	70	597	0	ENST00000356341.3:c.787G>A	p.Val263Met	p.V263M	ENST00000356341	NM_002576.4	263	Gtg/Atg	8/15	1	2	FACETS	0.631	0.55	0.719	0.631	0.55	0.719	SUBCLONAL	1	TRUE	1	0.342838061579699	2		597	647	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203744	94203744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770429536	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	23	381	3	ENST00000323929.3:c.910G>A	p.Val304Met	p.V304M	ENST00000323929	NM_005591.3	304	Gtg/Atg	9/20	1	2	FACETS	0.323	0.251	0.406	0.323	0.251	0.406	SUBCLONAL	1	TRUE	1	0.342838061579699	2		384	416	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022418	12022418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1198	194	893	1	ENST00000396373.4:c.524C>T	p.Thr175Ile	p.T175I	ENST00000396373	NM_001987.4	175	aCc/aTc	5/8	1	2	FACETS	0.813	0.75	0.879	0.813	0.75	0.879	CLONAL	1	TRUE	1	0.342838061579699	2		894	1392	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257270	133257270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	86	499	0	ENST00000320574.5:c.208G>A	p.Glu70Lys	p.E70K	ENST00000320574	NM_006231.2	70	Gag/Aag	3/49	1	2	FACETS	0.686	0.607	0.771	0.686	0.607	0.771	SUBCLONAL	1	TRUE	1	0.342838061579699	2		499	731	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562577	21562577	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1395329857	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	26	91	0	ENST00000382592.4:c.1342C>T	p.Arg448Cys	p.R448C	ENST00000382592	NM_014572.2	448	Cgt/Tgt	4/8	1	2	FACETS	0.45	0.356	0.557	0.45	0.356	0.557	SUBCLONAL	1	TRUE	1	0.342838061579699	2		91	337	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435306	110435306	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	157	370	1	ENST00000375856.3:c.3095C>A	p.Pro1032Gln	p.P1032Q	ENST00000375856	NM_003749.2	1032	cCg/cAg	1/2	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.342838061579699	2		371	681	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040993	42040993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	122	640	3	ENST00000219905.7:c.5371C>T	p.Pro1791Ser	p.P1791S	ENST00000219905	NM_001164273.1	1791	Cct/Tct	16/24	1	2	FACETS	0.761	0.687	0.839	0.761	0.687	0.839	SUBCLONAL	1	TRUE	1	0.342838061579699	2		643	935	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774108	66774108	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	220	724	0	ENST00000307102.5:c.584A>G	p.Asn195Ser	p.N195S	ENST00000307102	NM_002755.3	195	aAc/aGc	6/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.342838061579699	2		724	948	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482864	67482864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555414503	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	95	373	0	ENST00000327367.4:c.1268G>A	p.Ser423Asn	p.S423N	ENST00000327367	NM_005902.3	423	aGt/aAt	9/9	1	2	FACETS	0.832	0.741	0.929	0.832	0.741	0.929	CLONAL	1	TRUE	1	0.342838061579699	2		373	666	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644947	67644978	+	frameshift_variant	Frame_Shift_Del	DEL	TTCAGATGAAGACTGAAGTAATGGAGGGCACA	TTCAGATGAAGACTGAAGTAATGGAGGGCACA	-	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	176	550	0	ENST00000264010.4:c.212_243del	p.Leu71ArgfsTer58	p.L71Rfs*58	ENST00000264010	NM_006565.3	71	cTTCAGATGAAGACTGAAGTAATGGAGGGCACA/c	3/12	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.342838061579699	2		550	723	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654676	67654676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs911815810	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	86	596	0	ENST00000264010.4:c.1163G>A	p.Ser388Asn	p.S388N	ENST00000264010	NM_006565.3	388	aGc/aAc	6/12	1	2	FACETS	0.52	0.459	0.586	0.52	0.459	0.586	SUBCLONAL	1	TRUE	1	0.342838061579699	2		596	964	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351075	89351075	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	88	630	1	ENST00000301030.4:c.1875G>T	p.Glu625Asp	p.E625D	ENST00000301030	NM_001256183.1	625	gaG/gaT	9/13	1	2	FACETS	0.521	0.461	0.586	0.521	0.461	0.586	SUBCLONAL	1	TRUE	1	0.342838061579699	2		631	985	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958212	11958212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760186886	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	55	404	2	ENST00000353533.5:c.122G>A	p.Arg41His	p.R41H	ENST00000353533	NM_003010.3	41	cGc/cAc	2/11	1	2	FACETS	0.627	0.536	0.725	0.627	0.536	0.725	SUBCLONAL	1	TRUE	1	0.342838061579699	2		406	512	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682183	37682183	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	58	614	0	ENST00000447079.4:c.3374G>A	p.Ser1125Asn	p.S1125N	ENST00000447079	NM_015083.1	1125	aGc/aAc	13/14	1	2	FACETS	0.354	0.303	0.41	0.354	0.303	0.41	SUBCLONAL	1	TRUE	1	0.342838061579699	2		614	955	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733237	74733237	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	80	471	0	ENST00000359995.5:c.6C>A	p.Ser2Arg	p.S2R	ENST00000359995	NM_001195427.1	2	agC/agA	1/3	1	2	FACETS	0.752	0.662	0.848	0.752	0.662	0.848	SUBCLONAL	1	TRUE	1	0.342838061579699	2		471	621	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223023	5223023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759129843	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	151	289	0	ENST00000357368.4:c.2780C>T	p.Thr927Met	p.T927M	ENST00000357368	NM_002850.3	927	aCg/aTg	18/38	1	2	FACETS	0.788	0.719	0.86	0.788	0.719	0.86	SUBCLONAL	1	TRUE	1	0.342838061579699	2		289	1118	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098540	11098540	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	127	735	0	ENST00000358026.2:c.1062del	p.Ile355SerfsTer56	p.I355Sfs*56	ENST00000358026	NM_001128849.1	353	aCc/ac	6/36	1	2	FACETS	0.633	0.572	0.697	0.633	0.572	0.697	SUBCLONAL	1	TRUE	1	0.342838061579699	2		735	1171	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141550	11141550	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	73	657	0	ENST00000358026.2:c.3527G>A	p.Ser1176Asn	p.S1176N	ENST00000358026	NM_001128849.1	1176	aGc/aAc	25/36	1	2	FACETS	0.383	0.334	0.437	0.383	0.334	0.437	SUBCLONAL	1	TRUE	1	0.342838061579699	2		657	1112	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273304	18273304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	117	344	1	ENST00000222254.8:c.1097C>T	p.Thr366Met	p.T366M	ENST00000222254	NM_005027.3	366	aCg/aTg	9/16	1	2	FACETS	0.981	0.885	1	0.981	0.885	1	CLONAL	1	TRUE	1	0.342838061579699	2		345	696	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214106	36214107	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	380	953	0	ENST00000222270.7:c.2934_2935del	p.Cys978TrpfsTer16	p.C978Wfs*16	ENST00000222270	NM_014727.1	978	TGt/t	6/37	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.342838061579699	2		953	1483	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61725897	61725897	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	58	583	0	ENST00000401558.2:c.670G>A	p.Ala224Thr	p.A224T	ENST00000401558	NM_003400.3	224	Gca/Aca	9/25	1	2	FACETS	0.495	0.425	0.572	0.495	0.425	0.572	SUBCLONAL	1	TRUE	1	0.342838061579699	2		583	683	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660715	227660715	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	149	723	0	ENST00000305123.5:c.2740G>C	p.Ala914Pro	p.A914P	ENST00000305123	NM_005544.2	914	Gct/Cct	1/2	1	2	FACETS	0.795	0.725	0.868	0.795	0.725	0.868	SUBCLONAL	1	TRUE	1	0.342838061579699	2		723	1094	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624859	9624859	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	83	494	0	ENST00000353224.5:c.118C>T	p.His40Tyr	p.H40Y	ENST00000353224	NM_177990.2	40	Cac/Tac	3/10	1	2	FACETS	0.558	0.492	0.63	0.558	0.492	0.63	SUBCLONAL	1	TRUE	1	0.342838061579699	2		494	867	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012709	36012709	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	73	162	0	ENST00000358208.4:c.153C>A	p.Ser51Arg	p.S51R	ENST00000358208		51	agC/agA	2/12	1	2	FACETS	0.961	0.844	1	0.961	0.844	1	CLONAL	1	TRUE	1	0.342838061579699	2		162	443	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37045933	37045934	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACGAAAACAGCTGATGG	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	91	567	0	ENST00000231790.2:c.350_366dup	p.Lys123ArgfsTer19	p.K123Rfs*19	ENST00000231790	NM_000249.3	116	-/ACGAAAACAGCTGATGG	4/19	1	2	FACETS	0.876	0.779	0.979	0.876	0.779	0.979	CLONAL	1	TRUE	1	0.342838061579699	2		567	606	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182253	38182253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1321587413	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	129	422	0	ENST00000396334.3:c.689G>A	p.Arg230His	p.R230H	ENST00000396334	NM_002468.4	230	cGc/cAc	4/5	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.342838061579699	2		422	636	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125850	47125850	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	29	232	0	ENST00000409792.3:c.5420T>A	p.Leu1807Ter	p.L1807*	ENST00000409792	NM_014159.6	1807	tTg/tAg	12/21	1	2	FACETS	0.505	0.406	0.618	0.505	0.406	0.618	SUBCLONAL	1	TRUE	1	0.342838061579699	2		232	335	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014143	70014143	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	91	634	0	ENST00000394351.3:c.1004T>C	p.Leu335Pro	p.L335P	ENST00000394351	NM_000248.3	335	cTa/cCa	9/9	1	2	FACETS	0.51	0.451	0.573	0.51	0.451	0.573	SUBCLONAL	1	TRUE	1	0.342838061579699	2		634	1041	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431088	181431088	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1197165288	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	188	553	0	ENST00000325404.1:c.940C>T	p.Leu314Phe	p.L314F	ENST00000325404	NM_003106.3	314	Ctc/Ttc	1/1	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.342838061579699	2		553	854	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191178	185191178	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	69	344	2	ENST00000265026.3:c.2059G>A	p.Ala687Thr	p.A687T	ENST00000265026	NM_004721.4	687	Gct/Act	11/14	1	2	FACETS	0.791	0.69	0.899	0.791	0.69	0.899	SUBCLONAL	1	TRUE	1	0.342838061579699	2		346	509	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193845	106193845	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	67	383	0	ENST00000380013.4:c.4307A>G	p.Glu1436Gly	p.E1436G	ENST00000380013	NM_001127208.2	1436	gAg/gGg	10/11	1	2	FACETS	0.7	0.609	0.799	0.7	0.609	0.799	SUBCLONAL	1	TRUE	1	0.342838061579699	2		383	558	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554878	187554878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	80	462	1	ENST00000441802.2:c.4283C>T	p.Thr1428Ile	p.T1428I	ENST00000441802	NM_005245.3	1428	aCa/aTa	7/27	1	2	FACETS	0.729	0.642	0.823	0.729	0.642	0.823	SUBCLONAL	1	TRUE	1	0.342838061579699	2		463	640	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38996949	38996949	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	118	750	0	ENST00000357387.3:c.428G>T	p.Arg143Met	p.R143M	ENST00000357387	NM_152756.3	143	aGg/aTg	6/38	1	2	FACETS	0.838	0.756	0.925	0.838	0.756	0.925	CLONAL	1	TRUE	1	0.342838061579699	2		750	821	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973889	131973889	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs761837416	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	45	381	0	ENST00000265335.6:c.3592C>T	p.Arg1198Ter	p.R1198*	ENST00000265335		1198	Cga/Tga	23/25	1	2	FACETS	0.462	0.388	0.545	0.462	0.388	0.545	SUBCLONAL	1	TRUE	1	0.342838061579699	2		381	568	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457718	149457718	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	153	757	0	ENST00000286301.3:c.686T>C	p.Val229Ala	p.V229A	ENST00000286301	NM_005211.3	229	gTt/gCt	5/22	1	2	FACETS	0.744	0.679	0.813	0.744	0.679	0.813	SUBCLONAL	1	TRUE	1	0.342838061579699	2		757	1199	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912367	29912367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	100	468	1	ENST00000376809.5:c.986C>T	p.Ala329Val	p.A329V	ENST00000376809	NM_002116.7	329	gCc/gTc	5/8	1	2	FACETS	0.744	0.664	0.829	0.744	0.664	0.829	SUBCLONAL	1	TRUE	1	0.342838061579699	2		469	784	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636217	87636217	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	74	372	0	ENST00000277120.3:c.2386del	p.Gln796ArgfsTer6	p.Q796Rfs*6	ENST00000277120		794	tgC/tg	19/19	1	2	FACETS	0.623	0.545	0.707	0.623	0.545	0.707	SUBCLONAL	1	TRUE	1	0.342838061579699	2		372	693	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942794	44942794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	104	754	1	ENST00000377967.4:c.3374C>T	p.Thr1125Ile	p.T1125I	ENST00000377967	NM_021140.2	1125	aCc/aTc	23/29	1	2	FACETS	0.862	0.772	0.957	0.862	0.772	0.957	CLONAL	1	TRUE	1	0.342838061579699	2		755	704	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650793	48650793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	84	767	0	ENST00000376670.3:c.662G>A	p.Gly221Asp	p.G221D	ENST00000376670	NM_002049.3	221	gGc/gAc	4/6	1	2	FACETS	0.38	0.334	0.429	0.38	0.334	0.429	SUBCLONAL	1	TRUE	1	0.342838061579699	2		767	1291	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0017714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	152	684	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.511165567570112	4	FACETS	0.878	0.823	0.931	1	0.985	1	CLONAL	4	TRUE	1	0.511165567570112	4		684	256	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900894	3900894	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0017714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	37	601	0	ENST00000262367.5:c.202A>T	p.Lys68Ter	p.K68*	ENST00000262367	NM_004380.2	68	Aaa/Taa	2/31	0.25292004469861	2	FACETS	0.658	0.547	0.78	0.329	0.273	0.39	INDETERMINATE	1	TRUE	0	0.511165567570112	2		601	220	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682983	241682983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs981562354	NA	P-0017714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	18	479	0	ENST00000366560.3:c.40C>T	p.Leu14Phe	p.L14F	ENST00000366560	NM_000143.3	14	Ctc/Ttc	1/10	0.511165567570112	2	FACETS	0.357	0.27	0.46	0.179	0.135	0.23	SUBCLONAL	1	TRUE	0	0.511165567570112	2		479	197	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472466	88472466	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	27	632	0	ENST00000360948.2:c.2089del	p.Asp697ThrfsTer62	p.D697Tfs*62	ENST00000360948	NM_001012338.2	697	Gac/ac	16/19	0.511165567570112	1	FACETS	0.666	0.54	0.805	0.666	0.54	0.805	SUBCLONAL	1	TRUE	0	0.511165567570112	1		632	118	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578341	212578341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1216559792	NA	P-0017714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	14	388	2	ENST00000342788.4:c.916C>A	p.Arg306Ser	p.R306S	ENST00000342788	NM_005235.2	306	Cgt/Agt	8/28	0.456104918770048	3	FACETS	0.315	0.228	0.421	0.105	0.076	0.141	SUBCLONAL	1	TRUE	0	0.511165567570112	3		390	218	SUCCESS
APC	324	MSKCC	GRCh37	5	112175436	112175484	+	frameshift_variant	Frame_Shift_Del	DEL	TCATGTTTAGCAGATGTACTTCTGTCAGTTCACTTGATAGTTTTGAGAG	TCATGTTTAGCAGATGTACTTCTGTCAGTTCACTTGATAGTTTTGAGAG	-	novel	NA	P-0017714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	28	264	0	ENST00000257430.4:c.4147_4195del	p.Met1383ValfsTer16	p.M1383Vfs*16	ENST00000257430	NM_000038.5	1382	cTCATGTTTAGCAGATGTACTTCTGTCAGTTCACTTGATAGTTTTGAGAGt/ct	16/16	0.493372511755536	3	FACETS	0.969	0.805	1	0.646	0.536	0.76	CLONAL	2	TRUE	0	0.511165567570112	3		264	71	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617671	100617671	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1342391224	NA	P-0017714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	25	302	0	ENST00000308731.7:c.398G>A	p.Arg133Gln	p.R133Q	ENST00000308731	NM_000061.2	133	cGg/cAg	6/19	0.430689909679409	2	FACETS	1	0.879	1			1	CLONAL	1	TRUE	NA	0.511165567570112	2		302	87	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588809	52588809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	202	610	1	ENST00000394830.3:c.4219C>T	p.His1407Tyr	p.H1407Y	ENST00000394830	NM_018313.4	1407	Cac/Tac	27/30	1	2	FACETS	0.675	0.628	0.724	0.675	0.628	0.724	SUBCLONAL	1	TRUE	1	0.793630949374808	2		611	754	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429016	47429016	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	202	285	0	ENST00000377045.4:c.1379C>T	p.Ala460Val	p.A460V	ENST00000377045	NM_001654.4	460	gCc/gTc	13/16	1	1	FACETS	0.721	0.677	0.765	0.721	0.677	0.765	SUBCLONAL	1	TRUE	0	0.793630949374808	1		285	426	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690827	89690828	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0017717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	92	390	0	ENST00000371953.3:c.235dup	p.Ala79GlyfsTer4	p.A79Gfs*4	ENST00000371953	NM_000314.4	78	-/G	4/9	0.584167401030146	1	FACETS	0.57	0.51	0.633	0.57	0.51	0.633	SUBCLONAL	1	TRUE	0	0.599357153849322	1		390	377	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858288	9858288	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	37	284	0	ENST00000330684.3:c.3113C>G	p.Thr1038Arg	p.T1038R	ENST00000330684	NM_001134407.1	1038	aCa/aGa	13/13	1	2	FACETS	0.95	0.799	1	0.95	0.799	1	CLONAL	1	TRUE	1	0.599357153849322	2		284	130	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859555	151859555	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	141	366	0	ENST00000262189.6:c.11107G>T	p.Glu3703Ter	p.E3703*	ENST00000262189	NM_170606.2	3703	Gaa/Taa	43/59	0.599357153849322	2	FACETS	0.964	0.901	1	0.964	0.901	1	CLONAL	2	TRUE	0	0.599357153849322	2		366	244	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244901	41244916	+	protein_altering_variant	In_Frame_Del	DEL	CACATTCCTCTTCTGC	CACATTCCTCTTCTGC	G	novel	NA	P-0017717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	67	577	0	ENST00000357654.3:c.2632_2647delinsC	p.Ala878_Ala883delinsPro	p.A878_A883delinsP	ENST00000357654	NM_007294.3	878	GCAGAAGAGGAATGTGca/Cca	10/23	1	2	FACETS	0.585	0.511	0.665	0.585	0.511	0.665	SUBCLONAL	1	TRUE	1	0.599357153849322	2		577	382	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098955	+	protein_altering_variant	In_Frame_Ins	INS	CCA	CCA	TTGGAGGCAAGATAT	novel	NA	P-0017717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	141	359	0	ENST00000397062.3:c.90_92delinsATATCTTGCCTCCAA	p.Gly31delinsTyrLeuAlaSerLys	p.G31delinsYLASK	ENST00000397062	NM_006164.4	30	ctTGGa/ctATATCTTGCCTCCAAa	2/5	0.599357153849322				0.985	1				CLONAL	1	TRUE	0	0.599357153849322	2		359	361	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858288	9858288	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017717-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	24	284	0	ENST00000330684.3:c.3113C>G	p.Thr1038Arg	p.T1038R	ENST00000330684	NM_001134407.1	1038	aCa/aGa	13/13	1	2	FACETS	0.569	0.448	0.706	0.569	0.448	0.706	SUBCLONAL	1	TRUE	1	0.41998117039316	2		284	201	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859555	151859555	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017717-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	164	366	0	ENST00000262189.6:c.11107G>T	p.Glu3703Ter	p.E3703*	ENST00000262189	NM_170606.2	3703	Gaa/Taa	43/59	0.41998117039316	3	FACETS	0.849	0.791	0.908	0.849	0.791	0.908	CLONAL	3	TRUE	0	0.41998117039316	3		366	371	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098955	+	protein_altering_variant	In_Frame_Ins	INS	CCA	CCA	TTGGAGGCAAGATAT	novel	NA	P-0017717-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	64	352	0	ENST00000397062.3:c.90_92delinsATATCTTGCCTCCAA	p.Gly31delinsTyrLeuAlaSerLys	p.G31delinsYLASK	ENST00000397062	NM_006164.4	30	ctTGGa/ctATATCTTGCCTCCAAa	2/5	0.270426254883263	3	FACETS	1	0.963	1	0.43	0.375	0.488	CLONAL	1	TRUE	0	0.41998117039316	3		352	286	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0017718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	18	294	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.086	0.064	0.112	0.086	0.064	0.112	SUBCLONAL	1	TRUE	1	0.534808212655132	2		294	781	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520087	106520087	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774448553	NA	P-0017718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	90	295	0	ENST00000359195.3:c.2515C>T	p.Arg839Cys	p.R839C	ENST00000359195	NM_002649.2	839	Cgc/Tgc	6/11	1	2	FACETS	0.792	0.707	0.882	0.792	0.707	0.882	SUBCLONAL	1	TRUE	1	0.534808212655132	2		295	425	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0017719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	146	843	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.851	0.78	0.923	0.851	0.78	0.923	CLONAL	1	TRUE	1	0.622971955165934	2		843	551	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021481	31021481	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	172	738	0	ENST00000375687.4:c.1480C>G	p.Pro494Ala	p.P494A	ENST00000375687	NM_015338.5	494	Cca/Gca	12/13	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.622971955165934	2		738	472	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528630	157528630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771871664	NA	P-0017719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	226	1130	2	ENST00000346085.5:c.6355G>A	p.Val2119Ile	p.V2119I	ENST00000346085	NM_020732.3	2119	Gtt/Att	20/20	0.621542517923362	2	FACETS	1	0.98	1	0.556	0.52	0.592	CLONAL	1	TRUE	0	0.622971955165934	2		1132	653	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877455	89877455	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0017720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	74	1021	1	ENST00000389301.3:c.308C>G	p.Ser103Ter	p.S103*	ENST00000389301	NM_000135.2	103	tCa/tGa	4/43	1	2	FACETS	0.299	0.261	0.34	0.299	0.261	0.34	SUBCLONAL	1	TRUE	1	0.589184975848867	2		1022	840	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104353808	104353808	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	49	880	0	ENST00000369902.3:c.742G>C	p.Asp248His	p.D248H	ENST00000369902	NM_016169.3	248	Gat/Cat	6/12	1	2	FACETS	0.264	0.223	0.31	0.264	0.223	0.31	SUBCLONAL	1	TRUE	1	0.589184975848867	2		880	629	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427975	49427975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	206	951	2	ENST00000301067.7:c.10615C>T	p.Arg3539Trp	p.R3539W	ENST00000301067	NM_003482.3	3539	Cgg/Tgg	38/54	1	2	FACETS	0.985	0.917	1	0.985	0.917	1	CLONAL	1	TRUE	1	0.589184975848867	2		953	710	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120842	115120842	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	112	647	0	ENST00000257566.3:c.164C>T	p.Ser55Leu	p.S55L	ENST00000257566	NM_016569.3	55	tCg/tTg	1/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.589184975848867	2		647	316	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727050	41727050	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0017720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	91	895	0	ENST00000301178.4:c.309-1G>A		p.X103_splice	ENST00000301178	NM_021913.4	103			0.589184975848867	1	FACETS	0.413	0.368	0.462	0.413	0.368	0.462	SUBCLONAL	1	TRUE	0	0.589184975848867	1		895	527	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371818	55371818	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	54	237	0	ENST00000297316.4:c.508G>A	p.Glu170Lys	p.E170K	ENST00000297316	NM_022454.3	170	Gag/Aag	2/2	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.589184975848867	2		237	172	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741578	145741578	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554902528	NA	P-0017720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	514	1122	0	ENST00000428558.2:c.925C>T	p.Gln309Ter	p.Q309*	ENST00000428558	NM_004260.3	309	Cag/Tag	5/22	0.529140786219441	5	FACETS	0.898	0.862	0.934	0.898	0.862	0.934	CLONAL	3	TRUE	2	0.589184975848867	5		1122	1220	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44910963	44910963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	93	688	0	ENST00000377967.4:c.664C>T	p.His222Tyr	p.H222Y	ENST00000377967	NM_021140.2	222	Cat/Tat	9/29	NA	2	FACETS	0.655	0.585	0.729			1	INDETERMINATE	1	TRUE	NA	0.589184975848867	2		688	482	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0017722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	14	659	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	0.876	0.632	1	0.876	0.632	1	CLONAL	1	TRUE	1	0.09	2		659	355	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113836	11113836	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0017722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	46	392	1	ENST00000358026.2:c.1943+1G>T		p.X648_splice	ENST00000358026	NM_001128849.1	648			1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.09	2		393	697	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220578	1220578	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0017722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	61	442	1	ENST00000326873.7:c.598-2A>T		p.X200_splice	ENST00000326873	NM_000455.4	200			1	2	FACETS	0.855	0.736	0.984	1	0.974	1	CLONAL	2	TRUE	1	0.09	2		443	793	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602340	10602341	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGG	novel	NA	P-0017722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	61	616	0	ENST00000171111.5:c.1235_1237dup	p.Pro412dup	p.P412dup	ENST00000171111	NM_203500.1	412	cgt/cCCCgt	3/6	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.09	2		616	1109	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032123	48032124	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs63751327	NA	P-0017722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	20	261	0	ENST00000234420.5:c.3514dup	p.Arg1172LysfsTer5	p.R1172Kfs*5	ENST00000234420	NM_000179.2	1171	-/A	6/10	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.09	2		261	379	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259229	36259229	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	65	529	1	ENST00000300305.3:c.262G>T	p.Glu88Ter	p.E88*	ENST00000300305		88	Gag/Tag	3/8	1	2	FACETS	0.902	0.78	1	1	0.977	1	CLONAL	2	TRUE	1	0.09	2		530	801	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0017722-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	222	659	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	0.91	0.851	0.97	0.91	0.851	0.97	CLONAL	1	TRUE	1	0.727130379034737	2		659	671	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113836	11113836	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0017722-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	320	392	1	ENST00000358026.2:c.1943+1G>T		p.X648_splice	ENST00000358026	NM_001128849.1	648			0.692491726662205	1	FACETS	0.858	0.817	0.899	0.858	0.817	0.899	CLONAL	1	TRUE	0	0.727130379034737	1		393	653	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220578	1220578	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0017722-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	416	442	1	ENST00000326873.7:c.598-2A>T		p.X200_splice	ENST00000326873	NM_000455.4	200			0.705361978232449	1	FACETS	0.82	0.785	0.855	0.82	0.785	0.855	CLONAL	1	TRUE	0	0.727130379034737	1		443	888	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602340	10602341	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGG	novel	NA	P-0017722-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	422	616	0	ENST00000171111.5:c.1235_1237dup	p.Pro412dup	p.P412dup	ENST00000171111	NM_203500.1	412	cgt/cCCCgt	3/6	0.692491726662205	1	FACETS	0.726	0.693	0.758	0.726	0.693	0.758	SUBCLONAL	1	TRUE	0	0.727130379034737	1		616	1018	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032123	48032124	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs63751327	NA	P-0017722-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	228	261	0	ENST00000234420.5:c.3514dup	p.Arg1172LysfsTer5	p.R1172Kfs*5	ENST00000234420	NM_000179.2	1171	-/A	6/10	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.727130379034737	2		261	621	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259229	36259229	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017722-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	539	529	1	ENST00000300305.3:c.262G>T	p.Glu88Ter	p.E88*	ENST00000300305		88	Gag/Tag	3/8	0.694239665850261	1	FACETS	0.849	0.818	0.881	0.849	0.818	0.881	CLONAL	1	TRUE	0	0.727130379034737	1		530	1111	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949758	151949758	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017722-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	45	401	0	ENST00000262189.6:c.1342C>T	p.Gln448Ter	p.Q448*	ENST00000262189	NM_170606.2	448	Cag/Tag	10/59	1	2	FACETS	0.19	0.159	0.225	0.19	0.159	0.225	SUBCLONAL	1	TRUE	1	0.727130379034737	2		401	650	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881353	37881353	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017722-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	510	566	0	ENST00000269571.5:c.2545C>G	p.Arg849Gly	p.R849G	ENST00000269571		849	Cgg/Ggg	21/27	1	2	FACETS	0.902	0.863	0.941	0.902	0.863	0.941	CLONAL	1	TRUE	1	0.727130379034737	2		566	1555	SUCCESS
APC	324	MSKCC	GRCh37	5	112173759	112173759	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017722-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	38	301	0	ENST00000257430.4:c.2468C>A	p.Ser823Ter	p.S823*	ENST00000257430	NM_000038.5	823	tCa/tAa	16/16	0.692491726662205	1	FACETS	0.166	0.137	0.198	0.166	0.137	0.198	SUBCLONAL	1	TRUE	0	0.727130379034737	1		301	401	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90976656	90976656	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121908973	NA	P-0017722-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	224	372	1	ENST00000265433.3:c.976C>T	p.Gln326Ter	p.Q326*	ENST00000265433	NM_002485.4	326	Cag/Tag	8/16	0.727130379034737	1	FACETS	0.879	0.83	0.928	0.879	0.83	0.928	CLONAL	1	TRUE	0	0.727130379034737	1		373	446	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578197	7578197	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	603	1580	1	ENST00000269305.4:c.652del	p.Val218CysfsTer29	p.V218Cfs*29	ENST00000269305	NM_001126112.2	218	Gtg/tg	6/11	0.832892631306318	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.832892631306318	1		1581	817	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533552	533552	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	564	1426	0	ENST00000451590.1:c.351G>C	p.Lys117Asn	p.K117N	ENST00000451590	NM_001130442.1	117	aaG/aaC	4/5	0.832892631306318	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.832892631306318	1		1426	750	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998385	100998385	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	108	315	0	ENST00000325455.5:c.1417G>T	p.Gly473Cys	p.G473C	ENST00000325455	NM_001202474.3	473	Ggc/Tgc	1/8	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.832892631306318	2		315	237	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937095	48937095	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0017723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	212	498	1	ENST00000267163.4:c.861+2T>A		p.X287_splice	ENST00000267163	NM_000321.2	287			0.832892631306318	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.832892631306318	1		499	282	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989517	212989517	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	297	927	0	ENST00000342788.4:c.194T>C	p.Ile65Thr	p.I65T	ENST00000342788	NM_005235.2	65	aTa/aCa	2/28	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.832892631306318	2		927	707	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942730	68942730	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0017723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	300	861	0	ENST00000288368.4:c.544-2A>T		p.X182_splice	ENST00000288368	NM_024870.2	182			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.832892631306318	2		861	680	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008291	29008291	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs777429596	NA	P-0017724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	110	490	0	ENST00000282397.4:c.580A>G	p.Ile194Val	p.I194V	ENST00000282397	NM_002019.4	194	Ata/Gta	5/30	NA	2	FACETS	0.655	0.592	0.722			1	INDETERMINATE	1	TRUE	NA	0.729624450401916	2		490	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0017724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	325	492	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.729624450401916	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.729624450401916	1		492	524	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946224	13946224	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	251	458	0	ENST00000405192.2:c.872G>A	p.Gly291Glu	p.G291E	ENST00000405192	NM_001163147.1	291	gGa/gAa	10/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.729624450401916	2		458	659	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0017725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	181	455	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.684021269251715	3	FACETS	0.94	0.897	0.981	0.94	0.897	0.981	CLONAL	3	FALSE	0	0.713713303707031	3		455	244	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0017725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	22	680	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.526443571190984	3	FACETS	0.322	0.25	0.405	0.161	0.125	0.203	SUBCLONAL	1	FALSE	1	0.713713303707031	3		680	260	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032069	26032069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	260	379	0	ENST00000244661.2:c.220G>A	p.Glu74Lys	p.E74K	ENST00000244661	NM_003537.3	74	Gaa/Aaa	1/1	0.713713303707031	27	FACETS	1	0.942	1			1	CLONAL	6	FALSE	NA	0.713713303707031	27		379	1197	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175942	176175942	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	13	104	0	ENST00000367669.3:c.173C>A	p.Ser58Ter	p.S58*	ENST00000367669	NM_022457.5	58	tCg/tAg	1/20	0.403937053460897	4	FACETS	0.299	0.213	0.403	0.149	0.106	0.202	INDETERMINATE	1	FALSE	2	0.713713303707031	4		104	209	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912759	32912759	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs779130725	NA	P-0017725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	36	662	0	ENST00000380152.3:c.4267A>G	p.Thr1423Ala	p.T1423A	ENST00000380152		1423	Act/Gct	11/27	0.713713303707031	5	FACETS	0.701	0.578	0.837	0.234	0.192	0.279	SUBCLONAL	1	FALSE	2	0.713713303707031	5		662	298	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12393128	12393128	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	74	918	1	ENST00000287820.6:c.37G>C	p.Glu13Gln	p.E13Q	ENST00000287820	NM_015869.4	13	Gaa/Caa	1/7	0.652469928019734	4	FACETS	0.438	0.383	0.498	0.11	0.095	0.125	SUBCLONAL	1	FALSE	0	0.713713303707031	4		919	811	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808951	1808951	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	98	774	2	ENST00000260795.2:c.2383C>A	p.Pro795Thr	p.P795T	ENST00000260795		795	Ccc/Acc	17/17	0.526443571190984	3	FACETS	1	0.952	1	0.548	0.494	0.604	CLONAL	1	FALSE	1	0.713713303707031	3		776	340	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714432	117714432	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	44	766	1	ENST00000368508.3:c.1217C>T	p.Pro406Leu	p.P406L	ENST00000368508	NM_002944.2	406	cCc/cTc	11/43	0.304175629428553	1	FACETS	0.944	0.828	1	0.944	0.828	1	INDETERMINATE	1	FALSE	0	0.713713303707031	1		767	84	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949994	44949995	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0017725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	125	381	0	ENST00000377967.4:c.3765dup	p.Tyr1256ValfsTer35	p.Y1256Vfs*35	ENST00000377967	NM_021140.2	1255	cgg/cGgg	26/29	0.580705548783576	3	FACETS	0.949	0.896	0.997			1	CLONAL	3	FALSE	NA	0.713713303707031	3		381	167	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0017726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	224	694	4	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.488919098605901	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.488919098605901	2		698	402	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257884	16257884	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	42	522	0	ENST00000375759.3:c.5149G>A	p.Ala1717Thr	p.A1717T	ENST00000375759	NM_015001.2	1717	Gcg/Acg	11/15	0.179632753973836	2	FACETS	0.513	0.429	0.605	0.256	0.214	0.303	INDETERMINATE	1	TRUE	0	0.488919098605901	2		522	335	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649882	88649882	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0017726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	38	510	0	ENST00000372037.3:c.131C>G	p.Ser44Ter	p.S44*	ENST00000372037	NM_004329.2	44	tCa/tGa	4/13	0.488919098605901	3	FACETS	0.444	0.367	0.53	0.222	0.183	0.265	SUBCLONAL	1	TRUE	1	0.488919098605901	3		510	436	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871149	12871149	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	38	302	1	ENST00000228872.4:c.376G>A	p.Glu126Lys	p.E126K	ENST00000228872	NM_004064.3	126	Gag/Aag	1/3	0.457567226202847	4	FACETS	0.815	0.677	0.967	0.407	0.338	0.484	CLONAL	1	TRUE	2	0.488919098605901	4		303	284	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907133	32907133	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1438502006	NA	P-0017726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	34	601	0	ENST00000380152.3:c.1518C>G	p.Phe506Leu	p.F506L	ENST00000380152		506	ttC/ttG	10/27	0.159127754287196	2	FACETS	0.318	0.26	0.384	0.159	0.13	0.192	INDETERMINATE	1	TRUE	0	0.488919098605901	2		601	437	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634797	158634797	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	133	499	0	ENST00000263640.3:c.389C>G	p.Ser130Cys	p.S130C	ENST00000263640	NM_001105.4	130	tCt/tGt	5/11	0.429107486843565	4	FACETS	1	0.983	1	0.448	0.408	0.49	CLONAL	1	TRUE	1	0.488919098605901	4		499	603	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610520	215610520	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0017726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	156	712	0	ENST00000260947.4:c.1736C>G	p.Ser579Ter	p.S579*	ENST00000260947	NM_000465.2	579	tCa/tGa	8/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.488919098605901	2		712	589	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000020	30000020	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	91	566	0	ENST00000338641.4:c.33C>G	p.Phe11Leu	p.F11L	ENST00000338641	NM_000268.3	11	ttC/ttG	1/16	0.483112371911934	5	FACETS	1	0.974	1	0.441	0.393	0.492	CLONAL	1	TRUE	2	0.488919098605901	5		566	488	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176666781	176666781	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	89	620	0	ENST00000439151.2:c.4217G>C	p.Arg1406Thr	p.R1406T	ENST00000439151	NM_022455.4	1406	aGa/aCa	8/23	1	2	FACETS	0.663	0.589	0.742	0.663	0.589	0.742	SUBCLONAL	1	TRUE	1	0.488919098605901	2		620	549	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335693	81335693	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	84	691	0	ENST00000222390.5:c.1667G>C	p.Arg556Thr	p.R556T	ENST00000222390	NM_000601.4	556	aGa/aCa	15/18	0.488919098605901	3	FACETS	0.715	0.632	0.804	0.358	0.316	0.402	SUBCLONAL	1	TRUE	1	0.488919098605901	3		691	598	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994173	21994173	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	113	776	0	ENST00000579755.1:c.158A>T	p.Gln53Leu	p.Q53L	ENST00000579755		53	cAg/cTg	1/3	0.154932271559452		FACETS		0.789	0.967				INDETERMINATE	1	TRUE	0	0.488919098605901	3		776	657	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128268677	128268677	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	98	780	0	ENST00000265960.3:c.978G>C	p.Glu326Asp	p.E326D	ENST00000265960	NM_001006617.1	326	gaG/gaC	8/12	0.159127754287196	2	FACETS	0.701	0.627	0.779	0.35	0.313	0.39	INDETERMINATE	1	TRUE	0	0.488919098605901	2		780	572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0017727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	279	775	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.446326379922229	2	FACETS	0.846	0.8	0.891	0.846	0.8	0.891	CLONAL	2	TRUE	0	0.503789186996765	2		777	655	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0017727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	436	455	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.226810762855031	4	FACETS	0.866	0.829	0.903	1	0.995	1	INDETERMINATE	3	TRUE	2	0.503789186996765	4		455	1002	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0017727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	852	734	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	0.503789186996765	4	FACETS	1	0.997	1			1	CLONAL	4	TRUE	NA	0.503789186996765	4		734	1145	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0017727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	106	468	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.899	0.81	0.992	0.899	0.81	0.992	CLONAL	1	TRUE	1	0.503789186996765	2		468	468	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0017727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	12	482	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.503789186996765	1	FACETS	0.086	0.06	0.118	0.086	0.06	0.118	SUBCLONAL	1	TRUE	0	0.503789186996765	1		482	415	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201671	66201671	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773217274	NA	P-0017727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	132	690	1	ENST00000273854.3:c.2831C>T	p.Thr944Met	p.T944M	ENST00000273854	NM_004439.5	944	aCg/aTg	16/18	0.503789186996765	1	FACETS	0.825	0.754	0.899	0.825	0.754	0.899	CLONAL	1	TRUE	0	0.503789186996765	1		691	475	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264404	16264404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762946669	NA	P-0017727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	65	874	2	ENST00000375759.3:c.10607G>A	p.Arg3536Gln	p.R3536Q	ENST00000375759	NM_015001.2	3536	cGg/cAg	13/15	0.503789186996765	3	FACETS	0.328	0.283	0.377			1	SUBCLONAL	1	TRUE	NA	0.503789186996765	3		876	985	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107054	27107057	+	frameshift_variant	Frame_Shift_Del	DEL	CCTT	CCTT	-	novel	NA	P-0017727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	100	498	0	ENST00000324856.7:c.6665_6668del	p.Pro2222LeufsTer8	p.P2222Lfs*8	ENST00000324856	NM_006015.4	2222	cCCTTt/ct	20/20	0.307215548945727	1	FACETS	0.741	0.666	0.818	0.741	0.666	0.818	SUBCLONAL	1	TRUE	0	0.503789186996765	1		498	401	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827262	72827262	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	163	742	1	ENST00000268489.5:c.9319C>T	p.Gln3107Ter	p.Q3107*	ENST00000268489	NM_006885.3	3107	Cag/Tag	9/10	0.493176511877873	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.503789186996765	1		743	459	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098922	178098987	+	inframe_deletion	In_Frame_Del	DEL	CTGACTGAAGTCAAATACTTCTCGACTTACTCCAAGATCTATATCTTGCCTCCAAAGTATGTCAAT	CTGACTGAAGTCAAATACTTCTCGACTTACTCCAAGATCTATATCTTGCCTCCAAAGTATGTCAAT	-	novel	NA	P-0017727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	87	509	0	ENST00000397062.3:c.58_123del	p.Ile20_Gln41del	p.I20_Q41del	ENST00000397062	NM_006164.4	20	ATTGACATACTTTGGAGGCAAGATATAGATCTTGGAGTAAGTCGAGAAGTATTTGACTTCAGTCAG/-	2/5	0.23718422435641	3	FACETS	0.597	0.528	0.671			1	INDETERMINATE	1	TRUE	NA	0.503789186996765	3		509	724	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77085379	77085387	+	inframe_deletion	In_Frame_Del	DEL	ATTAGAAGA	ATTAGAAGA	-	novel	NA	P-0121608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	188	745	0	ENST00000356341.3:c.463_471del	p.Ser155_Asn157del	p.S155_N157del	ENST00000356341	NM_002576.4	155	TCTTCTAAT/-	5/15	0.751199964341176	3	FACETS	0.781	0.723	0.842	0.391	0.361	0.421	SUBCLONAL	1	NA	1	0.789773382893294	3		745	850	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487175	56487175	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	181	801	0	ENST00000267101.3:c.1321C>A	p.Leu441Met	p.L441M	ENST00000267101	NM_001982.3	441	Ctg/Atg	12/28	0.751199964341176	3	FACETS	0.826	0.763	0.891	0.413	0.381	0.446	CLONAL	1	NA	1	0.789773382893294	3		801	774	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289678	15289679	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0121608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	301	1099	3	ENST00000263388.2:c.3792_3793delinsAA	p.Ser1264_Pro1265delinsArgThr	p.S1264_P1265delinsRT	ENST00000263388	NM_000435.2	1264	agCCcg/agAAcg	23/33	0.761236460119641	2	FACETS	0.839	0.792	0.886	0.419	0.396	0.443	CLONAL	1	NA	0	0.789773382893294	2		1102	909	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47004910	47004910	+	intron_variant	Intron	SNP	G	G	T	novel	NA	P-0121608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	233	346	0	ENST00000377604.3:c.-126+26G>T		p.*42*	ENST00000377604	NM_001204468.1	-/852			0.749453926541203	2	FACETS	1	0.976	1			1	CLONAL	1	NA	NA	0.789773382893294	2		346	551	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0017729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	169	795	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	NA	2	FACETS	0.941	0.866	1			1	INDETERMINATE	1	TRUE	NA	0.451943629059416	2		795	795	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881617	37881617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777677468	NA	P-0017729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	136	849	3	ENST00000269571.5:c.2687G>A	p.Arg896His	p.R896H	ENST00000269571		896	cGc/cAc	22/27	1	2	FACETS	0.892	0.813	0.974	0.892	0.813	0.974	CLONAL	1	TRUE	1	0.451943629059416	2		852	675	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0017729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	258	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	0.853	0.802	0.904	0.853	0.802	0.904	CLONAL	1	TRUE	1	0.816595226704397	2		795	741	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881617	37881617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777677468	NA	P-0017729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	105	849	3	ENST00000269571.5:c.2687G>A	p.Arg896His	p.R896H	ENST00000269571		896	cGc/cAc	22/27	1	2	FACETS	0.383	0.343	0.425	0.383	0.343	0.425	SUBCLONAL	1	TRUE	1	0.816595226704397	2		852	671	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474404	40474404	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	70	709	0	ENST00000264657.5:c.1997T>G	p.Leu666Arg	p.L666R	ENST00000264657	NM_139276.2	666	cTg/cGg	21/24	0.52322863847759	1	FACETS	0.367	0.32	0.417	0.367	0.32	0.417	SUBCLONAL	1	TRUE	0	0.52322863847759	1		709	539	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434968	49434969	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	C	novel	NA	P-0017730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	40	635	0	ENST00000301067.7:c.6584_6585delinsG	p.Thr2195SerfsTer69	p.T2195Sfs*69	ENST00000301067	NM_003482.3	2195	aCC/aG	31/54	1	2	FACETS	0.297	0.247	0.354	0.297	0.247	0.354	SUBCLONAL	1	TRUE	1	0.52322863847759	2		635	514	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11297903	11297903	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	25	632	1	ENST00000361445.4:c.2205C>G	p.Ile735Met	p.I735M	ENST00000361445	NM_004958.3	735	atC/atG	13/58	0.560788439862203	3	FACETS	0.383	0.302	0.476	0.192	0.151	0.238	SUBCLONAL	1	FALSE	1	0.560788439862203	3		633	298	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0017732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	52	1208	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.919	0.781	1	0.919	0.781	1	CLONAL	1	TRUE	1	0.14	2		1208	808	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653835	89653835	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	43	772	0	ENST00000371953.3:c.133del	p.Val45TyrfsTer9	p.V45Yfs*9	ENST00000371953	NM_000314.4	45	Gta/ta	2/9	0.153182180974849	3	FACETS	1	0.953	1	0.716	0.599	0.845	CLONAL	1	TRUE	1	0.14	3		772	459	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380346	14380346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	30	608	0	ENST00000256196.4:c.71G>A	p.Gly24Asp	p.G24D	ENST00000256196		24	gGc/gAc	1/6	1	2	FACETS	0.786	0.632	0.962	0.786	0.632	0.962	CLONAL	1	TRUE	1	0.14	2		608	545	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830704	72830705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	46	806	0	ENST00000268489.5:c.5876dup	p.Tyr1960ValfsTer2	p.Y1960Vfs*2	ENST00000268489	NM_006885.3	1959	cag/caAg	9/10	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.14	2		806	598	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061240	38061240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	194	830	0	ENST00000250448.2:c.749C>T	p.Ser250Phe	p.S250F	ENST00000250448	NM_004496.3	250	tCc/tTc	2/2	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.559355123706324	2		830	671	SUCCESS
APC	324	MSKCC	GRCh37	5	112175921	112175921	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	176	449	1	ENST00000257430.4:c.4630G>T	p.Glu1544Ter	p.E1544*	ENST00000257430	NM_000038.5	1544	Gaa/Taa	16/16	NA	2	FACETS	0.915	0.857	0.972			1	INDETERMINATE	2	TRUE	NA	0.559355123706324	2		450	344	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696431	47696431	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	163	772	0	ENST00000347630.2:c.392G>T	p.Trp131Leu	p.W131L	ENST00000347630	NM_001007230.1	131	tGg/tTg	6/11	1	2	FACETS	0.973	0.897	1	0.973	0.897	1	CLONAL	1	TRUE	1	0.559355123706324	2		772	599	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748914	41748914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751855310	NA	P-0017734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	50	425	2	ENST00000301178.4:c.1439G>A	p.Arg480His	p.R480H	ENST00000301178	NM_021913.4	480	cGt/cAt	11/20	0.294272568315658	7	FACETS	0.691	0.584	0.808	0.138	0.116	0.162	SUBCLONAL	1	TRUE	2	0.294272568315658	7		427	854	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0017734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	71	444	0	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	0.863	0.754	0.981	0.863	0.754	0.981	CLONAL	1	TRUE	1	0.294272568315658	2		444	559	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715804	117715804	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	100	457	0	ENST00000368508.3:c.954G>T	p.Leu318Phe	p.L318F	ENST00000368508	NM_002944.2	318	ttG/ttT	9/43	0.294272568315658	5	FACETS	0.929	0.828	1	0.232	0.207	0.26	CLONAL	1	TRUE	1	0.294272568315658	5		457	1054	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509420	106509420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs864622026	NA	P-0017734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	109	482	0	ENST00000359195.3:c.1414C>T	p.Arg472Cys	p.R472C	ENST00000359195	NM_002649.2	472	Cgt/Tgt	2/11	0.294272568315658	7	FACETS	1	0.961	1			1	CLONAL	1	TRUE	NA	0.294272568315658	7		482	1115	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0017735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	250	462	0	ENST00000269305.4:c.673-1G>C		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.345102654854289	2	FACETS	0.864	0.812	0.916	0.864	0.812	0.916	CLONAL	2	TRUE	0	0.419454591858908	2		462	690	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416488	49416488	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	231	497	0	ENST00000301067.7:c.16223G>T	p.Gly5408Val	p.G5408V	ENST00000301067	NM_003482.3	5408	gGc/gTc	51/54	0.215414946253867	4	FACETS	0.908	0.848	0.969			1	INDETERMINATE	2	TRUE	NA	0.419454591858908	4		497	861	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288708	15288708	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	18	44	0	ENST00000263388.2:c.4031G>C	p.Cys1344Ser	p.C1344S	ENST00000263388	NM_000435.2	1344	tGt/tCt	24/33	0.357803168653589	3	FACETS	1	0.845	1	0.57	0.437	0.721	CLONAL	1	TRUE	1	0.419454591858908	3		44	91	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735585	204735585	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	210	436	0	ENST00000302823.3:c.386G>A	p.Cys129Tyr	p.C129Y	ENST00000302823	NM_005214.4	129	tGc/tAc	2/4	0.199954631034296	2	FACETS	1	0.991	1	0.713	0.665	0.763	INDETERMINATE	1	TRUE	0	0.419454591858908	2		436	702	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957521	1957521	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	211	690	0	ENST00000382891.5:c.2620G>T	p.Ala874Ser	p.A874S	ENST00000382891	NM_133335.3	874	Gct/Tct	14/22	1	2	FACETS	0.995	0.924	1	0.995	0.924	1	CLONAL	1	TRUE	1	0.419454591858908	2		690	1011	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594233	55594233	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1458	354	429	0	ENST00000288135.5:c.1936T>G	p.Tyr646Asp	p.Y646D	ENST00000288135	NM_000222.2	646	Tac/Gac	13/21	0.419454591858908	9	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.419454591858908	9		429	1812	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598105	55598105	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1647	435	530	0	ENST00000288135.5:c.2302G>C	p.Asp768His	p.D768H	ENST00000288135	NM_000222.2	768	Gac/Cac	16/21	0.419454591858908	9	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.419454591858908	9		530	2082	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599237	55599237	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	286	320	0	ENST00000288135.5:c.2363G>T	p.Cys788Phe	p.C788F	ENST00000288135	NM_000222.2	788	tGt/tTt	17/21	0.419454591858908	9	FACETS	0.905	0.85	0.962			1	CLONAL	3	TRUE	NA	0.419454591858908	9		320	1239	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979549	55979549	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	1172	577	0	ENST00000263923.4:c.898A>G	p.Ser300Gly	p.S300G	ENST00000263923	NM_002253.2	300	Agt/Ggt	7/30	0.419454591858908	9	FACETS	1	0.987	1			1	CLONAL	6	TRUE	NA	0.419454591858908	9		577	2260	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247342	153247343	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0017735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	80	423	0	ENST00000281708.4:c.1459dup	p.Asp487GlyfsTer3	p.D487Gfs*3	ENST00000281708	NM_033632.3	487	gat/gGat	10/12	0.165200688719869	2	FACETS	0.512	0.45	0.579	0.256	0.225	0.29	INDETERMINATE	1	TRUE	0	0.419454591858908	2		423	745	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196926	138196926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	140	328	0	ENST00000237289.4:c.588A>G	p.Ile196Met	p.I196M	ENST00000237289	NM_001270507.1	196	atA/atG	4/9	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.419454591858908	2		328	559	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450363	50450363	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	195	418	0	ENST00000331340.3:c.547C>A	p.Arg183Ser	p.R183S	ENST00000331340	NM_006060.4	183	Cgc/Agc	5/8	0.165200688719869	2	FACETS	1	0.99	1	0.698	0.649	0.749	INDETERMINATE	1	TRUE	0	0.419454591858908	2		418	666	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0017738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	106	427	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	0.223978404556717	2		427	719	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797493	45797493	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	51	613	0	ENST00000450313.1:c.1026C>G	p.Cys342Trp	p.C342W	ENST00000450313	NM_012222.2	342	tgC/tgG	12/16	0.215666094452794	3	FACETS	0.531	0.45	0.621			1	SUBCLONAL	1	TRUE	NA	0.223978404556717	3		613	953	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653386	206653386	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	75	545	0	ENST00000367120.3:c.1270C>T	p.Gln424Ter	p.Q424*	ENST00000367120	NM_014002.3	424	Cag/Tag	12/22	1	2	FACETS	0.668	0.583	0.759	0.668	0.583	0.759	SUBCLONAL	1	TRUE	1	0.223978404556717	2		545	1003	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46240721	46240721	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0017738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	47	301	1	ENST00000334344.6:c.1580+1G>A		p.X527_splice	ENST00000334344	NM_152641.2	527			1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.223978404556717	2		302	330	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589818	28589818	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	46	421	0	ENST00000241453.7:c.2562G>T	p.Trp854Cys	p.W854C	ENST00000241453	NM_004119.2	854	tgG/tgT	21/24	0.223978404556717	1	FACETS	0.565	0.475	0.664	0.565	0.475	0.664	SUBCLONAL	1	TRUE	0	0.223978404556717	1		421	646	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0017738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	105	584	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.223978404556717	2		584	820	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602644	10602644	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0017738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	97	610	0	ENST00000171111.5:c.934A>T	p.Lys312Ter	p.K312*	ENST00000171111	NM_203500.1	312	Aag/Tag	3/6	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.223978404556717	2		610	845	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18975049	18975049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1388907949	NA	P-0017738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	33	282	0	ENST00000262803.5:c.2846G>A	p.Arg949Gln	p.R949Q	ENST00000262803	NM_002911.3	949	cGg/cAg	20/24	1	2	FACETS	0.796	0.649	0.962	0.796	0.649	0.962	CLONAL	1	TRUE	1	0.223978404556717	2		282	370	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463518	25463518	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	38	471	0	ENST00000264709.3:c.2164G>T	p.Gly722Cys	p.G722C	ENST00000264709	NM_175629.2	722	Ggc/Tgc	18/23	1	2	FACETS	0.513	0.423	0.615	0.513	0.423	0.615	SUBCLONAL	1	TRUE	1	0.223978404556717	2		471	661	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753058	57753058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	38	333	0	ENST00000274289.3:c.958G>T	p.Glu320Ter	p.E320*	ENST00000274289	NM_006622.3	320	Gag/Tag	7/14	1	2	FACETS	0.551	0.454	0.659	0.551	0.454	0.659	SUBCLONAL	1	TRUE	1	0.223978404556717	2		333	616	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92355099	92355099	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	52	190	0	ENST00000265734.4:c.378G>C	p.Met126Ile	p.M126I	ENST00000265734	NM_001259.6	126	atG/atC	4/8	0.148591806366976	3	FACETS	1	0.944	1	0.616	0.526	0.715	CLONAL	1	TRUE	1	0.223978404556717	3		190	419	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850272	128850272	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs777204354	NA	P-0017738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	113	588	0	ENST00000249373.3:c.1535G>T	p.Arg512Leu	p.R512L	ENST00000249373	NM_005631.4	512	cGc/cTc	9/12	0.148591806366976	3	FACETS	1	0.936	1	0.529	0.475	0.586	CLONAL	1	TRUE	1	0.223978404556717	3		588	1061	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141549447	141549455	+	inframe_deletion	In_Frame_Del	DEL	CGGGTGTGG	CGGGTGTGG	-	novel	NA	P-0017738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	52	300	0	ENST00000220592.5:c.2133_2141del	p.His711_Arg714delinsGln	p.H711_R714delinsQ	ENST00000220592	NM_012154.3	711	caCCACACCCGg/cag	16/19	1	2	FACETS	0.895	0.762	1	0.895	0.762	1	CLONAL	1	TRUE	1	0.223978404556717	2		300	519	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317545	1317545	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	50	458	0	ENST00000400841.2:c.520G>A	p.Gly174Ser	p.G174S	ENST00000400841		174	Ggc/Agc	5/6	0.223978404556717	1	FACETS	0.525	0.444	0.614	0.525	0.444	0.614	SUBCLONAL	1	TRUE	0	0.223978404556717	1		458	755	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480404	56480404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	232	594	0	ENST00000267101.3:c.511G>A	p.Asp171Asn	p.D171N	ENST00000267101	NM_001982.3	171	Gat/Aat	4/28	1	2	FACETS	0.515	0.479	0.552	0.515	0.479	0.552	SUBCLONAL	1	TRUE	1	0.743647580233096	2		594	1212	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608316	43608317	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTC	novel	NA	P-0017740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	262	719	0	ENST00000355710.3:c.1666_1668dup	p.Ser556dup	p.S556dup	ENST00000355710	NM_020975.4	556	ttc/ttCTCc	9/20	1	2	FACETS	0.724	0.679	0.77	0.724	0.679	0.77	SUBCLONAL	1	TRUE	1	0.743647580233096	2		719	973	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0017742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	329	527	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.39084595372641	3	FACETS	0.857	0.816	0.898	0.571	0.544	0.599	INDETERMINATE	2	TRUE	0	0.766491897392892	3		527	693	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0017742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	80	613	1	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.387	0.341	0.436	0.387	0.341	0.436	SUBCLONAL	1	TRUE	1	0.766491897392892	2		614	539	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	402	184	0				ENST00000310581	NM_198253.2	-/1132			0.727874819574479	2	FACETS	0.988	0.956	1	0.988	0.956	1	CLONAL	2	TRUE	0	0.730739440601882	2		184	557	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0017744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	651	916	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.583019403133757	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	2	0.730739440601882	4		916	1380	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653796	89653798	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs1554893765	NA	P-0017744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	286	362	0	ENST00000371953.3:c.97_99del	p.Ile33del	p.I33del	ENST00000371953	NM_000314.4	32	ATT/-	2/9	0.730739440601882	2	FACETS	0.998	0.961	1	0.998	0.961	1	CLONAL	2	TRUE	0	0.730739440601882	2		362	392	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0017744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	319	357	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.730739440601882	2	FACETS	0.875	0.839	0.91	0.875	0.839	0.91	CLONAL	2	TRUE	0	0.730739440601882	2		357	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0017744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	475	499	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.727874819574479	2	FACETS	0.933	0.903	0.961	0.933	0.903	0.961	CLONAL	2	TRUE	0	0.730739440601882	2		499	697	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858735	9858735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	224	294	0	ENST00000330684.3:c.2666G>A	p.Gly889Glu	p.G889E	ENST00000330684	NM_001134407.1	889	gGa/gAa	13/13	0.300399244976508	5	FACETS	1	0.983	1	0.753	0.707	0.8	INDETERMINATE	2	TRUE	2	0.730739440601882	5		294	569	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340201	116340201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561295443	NA	P-0017744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	324	365	0	ENST00000397752.3:c.1063G>A	p.Glu355Lys	p.E355K	ENST00000397752	NM_000245.2	355	Gaa/Aaa	2/21	0.730739440601882	4	FACETS	0.962	0.913	1	0.962	0.913	1	CLONAL	2	TRUE	2	0.730739440601882	4		365	798	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390905	89390905	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	245	335	0	ENST00000336596.2:c.971G>A	p.Arg324Gln	p.R324Q	ENST00000336596	NM_005233.5	324	cGa/cAa	5/17	0.730739440601882	4	FACETS	0.901	0.848	0.955	0.901	0.848	0.955	CLONAL	2	TRUE	2	0.730739440601882	4		335	644	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468393	89468393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	200	291	0	ENST00000336596.2:c.1927C>T	p.Pro643Ser	p.P643S	ENST00000336596	NM_005233.5	643	Cct/Tct	11/17	0.730739440601882	4	FACETS	0.913	0.853	0.973	0.913	0.853	0.973	CLONAL	2	TRUE	2	0.730739440601882	4		291	519	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851604	134851604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	405	478	0	ENST00000398015.3:c.1010C>T	p.Ser337Phe	p.S337F	ENST00000398015	NM_004441.4	337	tCc/tTc	5/16	0.730739440601882	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.730739440601882	3		478	756	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504949	186504949	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	316	355	0	ENST00000323963.5:c.805G>A	p.Glu269Lys	p.E269K	ENST00000323963		269	Gag/Aag	8/11	0.494769338267637	6	FACETS	1	0.977	1	0.707	0.668	0.746	CLONAL	2	TRUE	3	0.730739440601882	6		355	1004	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510233	187510233	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	447	538	0	ENST00000441802.2:c.13280G>A	p.Gly4427Glu	p.G4427E	ENST00000441802	NM_005245.3	4427	gGa/gAa	27/27	0.730739440601882	2	FACETS	0.944	0.914	0.973	0.944	0.914	0.973	CLONAL	2	TRUE	0	0.730739440601882	2		538	648	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527817	157527817	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs755793592	NA	P-0017744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	393	435	1	ENST00000346085.5:c.5542C>A	p.Pro1848Thr	p.P1848T	ENST00000346085	NM_020732.3	1848	Ccc/Acc	20/20	0.730739440601882	2	FACETS	0.932	0.9	0.963	0.932	0.9	0.963	CLONAL	2	TRUE	0	0.730739440601882	2		436	577	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739726	41739726	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	607	664	0	ENST00000242208.4:c.247C>T	p.Leu83Phe	p.L83F	ENST00000242208	NM_002192.2	83	Ctt/Ttt	2/3	0.686233028461554	4	FACETS	0.985	0.948	1	0.985	0.948	1	CLONAL	2	TRUE	2	0.730739440601882	4		664	1460	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411680	63411680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	610	426	0	ENST00000330258.3:c.1487C>T	p.Pro496Leu	p.P496L	ENST00000330258	NM_152424.3	496	cCc/cTc	2/2	0.520518978520873	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.730739440601882	2		426	738	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182179	11182179	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	427	602	1	ENST00000361445.4:c.6667C>T	p.Gln2223Ter	p.Q2223*	ENST00000361445	NM_004958.3	2223	Cag/Tag	48/58	0.300399244976508	5	FACETS	1	0.954	1	0.667	0.636	0.698	INDETERMINATE	2	TRUE	2	0.730739440601882	5		603	1225	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0017745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	275	306	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		306	567	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0017746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	98	464	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.197570614843379	1	FACETS	0.649	0.581	0.722	0.649	0.581	0.722	INDETERMINATE	1	TRUE	0	0.441943415552725	1		464	532	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955592	55955592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560674167	NA	P-0017746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	143	421	1	ENST00000263923.4:c.3353G>A	p.Arg1118Gln	p.R1118Q	ENST00000263923	NM_002253.2	1118	cGa/cAa	25/30	1	2	FACETS	0.919	0.84	1	0.919	0.84	1	CLONAL	1	TRUE	1	0.441943415552725	2		422	704	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420258	88420258	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	125	386	0	ENST00000360948.2:c.2428G>T	p.Glu810Ter	p.E810*	ENST00000360948	NM_001012338.2	810	Gaa/Taa	19/19	1	2	FACETS	0.817	0.741	0.898	0.817	0.741	0.898	CLONAL	1	TRUE	1	0.441943415552725	2		386	692	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965130	81965130	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	53	453	2	ENST00000359376.3:c.2610G>T	p.Lys870Asn	p.K870N	ENST00000359376	NM_002661.3	870	aaG/aaT	25/33	0.103795677270617	3	FACETS	0.338	0.287	0.394	0.113	0.095	0.132	INDETERMINATE	1	TRUE	0	0.441943415552725	3		455	867	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578456	7578467	+	inframe_deletion	In_Frame_Del	DEL	GCGGACGCGGGT	GCGGACGCGGGT	-	novel	NA	P-0017746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	139	627	0	ENST00000269305.4:c.463_474del	p.Thr155_Arg158del	p.T155_R158del	ENST00000269305	NM_001126112.2	155	ACCCGCGTCCGC/-	5/11	0.426189589990836	1	FACETS	0.576	0.524	0.63	0.576	0.524	0.63	SUBCLONAL	1	TRUE	0	0.441943415552725	1		627	851	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46588157	46588157	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	95	482	0	ENST00000263734.3:c.707A>C	p.Asp236Ala	p.D236A	ENST00000263734	NM_001430.4	236	gAc/gCc	6/16	1	2	FACETS	0.5	0.444	0.559	0.5	0.444	0.559	SUBCLONAL	1	TRUE	1	0.441943415552725	2		482	860	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46255776	46255776	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	124	363	1	ENST00000371998.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371998		130	Cga/Tga	6/23	0.441943415552725	4	FACETS	0.672	0.606	0.742	0.224	0.202	0.248	SUBCLONAL	1	TRUE	1	0.441943415552725	4		364	1204	SUCCESS
APC	324	MSKCC	GRCh37	5	112174916	112174917	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	74	296	0	ENST00000257430.4:c.3627dup	p.His1210ThrfsTer7	p.H1210Tfs*7	ENST00000257430	NM_000038.5	1209	gaa/gAaa	16/16	0.197570614843379	1	FACETS	0.537	0.471	0.607	0.537	0.471	0.607	INDETERMINATE	1	TRUE	0	0.441943415552725	1		296	486	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519704	176519704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143108014	NA	P-0017746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	186	477	0	ENST00000292408.4:c.976G>A	p.Glu326Lys	p.E326K	ENST00000292408	NM_213647.1	326	Gag/Aag	8/18	0.197570614843379	1	FACETS	0.825	0.763	0.889	0.825	0.763	0.889	INDETERMINATE	1	TRUE	0	0.441943415552725	1		477	795	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115928	8115929	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	56	282	0	ENST00000346208.3:c.1275dup	p.Ser426IlefsTer81	p.S426Ifs*81	ENST00000346208		425	cca/ccAa	6/6	1	2	FACETS	0.736	0.631	0.849	0.736	0.631	0.849	SUBCLONAL	1	TRUE	1	0.319904504225786	2		282	476	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112198	115112199	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	187	487	0	ENST00000257566.3:c.1541dup	p.Asn514LysfsTer178	p.N514Kfs*178	ENST00000257566	NM_016569.3	514	aac/aaAc	7/8	0.272192675451408	2	FACETS	0.913	0.848	0.981	0.913	0.848	0.981	CLONAL	2	TRUE	0	0.319904504225786	2		487	640	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068325	30068325	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758594741	NA	P-0017747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	44	258	0	ENST00000331968.5:c.2074G>A	p.Val692Met	p.V692M	ENST00000331968	NM_002742.2	692	Gtg/Atg	15/18	NA	2	FACETS	0.47	0.394	0.555			1	INDETERMINATE	1	TRUE	NA	0.319904504225786	2		258	585	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266611	198266611	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs755415626	NA	P-0017748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	168	336	0	ENST00000335508.6:c.2225G>A	p.Gly742Asp	p.G742D	ENST00000335508	NM_012433.2	742	gGt/gAt	16/25	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.474571198351692	2		336	668	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396284	396284	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0017748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	420	632	0	ENST00000262320.3:c.742A>T	p.Lys248Ter	p.K248*	ENST00000262320	NM_003502.3	248	Aag/Tag	2/11	0.474571198351692	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.474571198351692	2		632	868	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349607	15349607	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	209	698	0	ENST00000263377.2:c.3967C>T	p.Gln1323Ter	p.Q1323*	ENST00000263377	NM_058243.2	1323	Cag/Tag	19/20	1	2	FACETS	0.951	0.884	1	0.951	0.884	1	CLONAL	1	TRUE	1	0.474571198351692	2		698	926	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0017749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	35	518	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.457	0.373	0.552	0.457	0.373	0.552	SUBCLONAL	1	TRUE	1	0.200090696519687	2		518	766	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149511596	149511596	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377445092	NA	P-0017749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	41	504	0	ENST00000261799.4:c.1189C>T	p.Arg397Trp	p.R397W	ENST00000261799	NM_002609.3	397	Cgg/Tgg	8/23	1	2	FACETS	0.67	0.557	0.796	0.67	0.557	0.796	SUBCLONAL	1	TRUE	1	0.200090696519687	2		504	612	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934194	48934194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	56	444	0	ENST00000267163.4:c.649C>T	p.Gln217Ter	p.Q217*	ENST00000267163	NM_000321.2	217	Cag/Tag	7/27	1	2	FACETS	0.74	0.633	0.858	0.74	0.633	0.858	SUBCLONAL	1	TRUE	1	0.200090696519687	2		444	756	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220428	1220428	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	64	663	0	ENST00000326873.7:c.521A>C	p.His174Pro	p.H174P	ENST00000326873	NM_000455.4	174	cAc/cCc	4/10	0.200090696519687	1	FACETS	0.699	0.604	0.802	0.699	0.604	0.802	SUBCLONAL	1	TRUE	0	0.200090696519687	1		663	824	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138461	11138461	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	25	367	0	ENST00000358026.2:c.3217C>G	p.Leu1073Val	p.L1073V	ENST00000358026	NM_001128849.1	1073	Ctg/Gtg	24/36	0.200090696519687	1	FACETS	0.568	0.447	0.707	0.568	0.447	0.707	SUBCLONAL	1	TRUE	0	0.200090696519687	1		367	396	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138564	11138564	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	75	649	1	ENST00000358026.2:c.3320C>T	p.Ser1107Phe	p.S1107F	ENST00000358026	NM_001128849.1	1107	tCc/tTc	24/36	0.200090696519687	1	FACETS	0.792	0.693	0.899	0.792	0.693	0.899	SUBCLONAL	1	TRUE	0	0.200090696519687	1		650	852	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056294	180056294	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	60	598	0	ENST00000261937.6:c.950A>T	p.Gln317Leu	p.Q317L	ENST00000261937	NM_182925.4	317	cAg/cTg	7/30	1	2	FACETS	0.665	0.571	0.767	0.665	0.571	0.767	SUBCLONAL	1	TRUE	1	0.200090696519687	2		598	902	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398904	398904	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	44	340	0	ENST00000380956.4:c.714C>A	p.Ser238Arg	p.S238R	ENST00000380956	NM_001195286.1	238	agC/agA	6/9	1	2	FACETS	0.88	0.738	1	0.88	0.738	1	CLONAL	1	TRUE	1	0.200090696519687	2		340	500	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001502	150001502	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1366946458	NA	P-0017749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	56	462	0	ENST00000253339.5:c.2102A>G	p.Asp701Gly	p.D701G	ENST00000253339		701	gAc/gGc	4/7	1	2	FACETS	0.713	0.609	0.827	0.713	0.609	0.827	SUBCLONAL	1	TRUE	1	0.200090696519687	2		462	785	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0017750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	130	394	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	1	2	FACETS	0.699	0.634	0.767	0.699	0.634	0.767	SUBCLONAL	1	TRUE	1	0.464335572837007	2		394	801	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845821	72845821	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	196	451	0	ENST00000268489.5:c.3646G>A	p.Glu1216Lys	p.E1216K	ENST00000268489	NM_006885.3	1216	Gag/Aag	6/10	0.464335572837007	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.464335572837007	1		451	573	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437155	52437155	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	144	378	0	ENST00000460680.1:c.1889del	p.Lys630ArgfsTer7	p.K630Rfs*7	ENST00000460680	NM_004656.3	630	aAg/ag	14/17	1	2	FACETS	0.936	0.856	1	0.936	0.856	1	CLONAL	1	TRUE	1	0.464335572837007	2		378	663	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0017751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	766	668	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.438991750729424	9	FACETS	0.959	0.932	0.986	0.959	0.932	0.986	CLONAL	7	TRUE	2	0.438991750729424	9		668	1319	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041648	47041648	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	250	289	0	ENST00000377604.3:c.1873G>T	p.Gly625Ter	p.G625*	ENST00000377604	NM_001204468.1	625	Gga/Tga	17/24	0.391419720472049	2	FACETS	0.959	0.914	1			1	CLONAL	3	TRUE	NA	0.438991750729424	2		289	396	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0017752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	177	455	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.997	0.918	1	0.997	0.918	1	CLONAL	1	TRUE	1	0.357333281320857	2		455	994	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727402	66727443	+	inframe_deletion	In_Frame_Del	DEL	CTAGAGCTTGATGAGCAGCAGCGAAAGCGCCTTGAGGCCTTT	CTAGAGCTTGATGAGCAGCAGCGAAAGCGCCTTGAGGCCTTT	-	novel	NA	P-0017752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	108	329	0	ENST00000307102.5:c.120_161del	p.Glu41_Leu54del	p.E41_L54del	ENST00000307102	NM_002755.3	40	CTAGAGCTTGATGAGCAGCAGCGAAAGCGCCTTGAGGCCTTT/-	2/11	1	2	FACETS	0.914	0.822	1	0.914	0.822	1	CLONAL	1	TRUE	1	0.357333281320857	2		329	661	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78831583	78831583	+	splice_region_variant,intron_variant	Splice_Region	DEL	C	C	-	novel	NA	P-0017752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	91	285	0	ENST00000306801.3:c.1399-3del		p.X467_splice	ENST00000306801	NM_020761.2	467			1	2	FACETS	0.807	0.717	0.903	0.807	0.717	0.903	CLONAL	1	TRUE	1	0.357333281320857	2		285	631	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876476	35876476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1242	182	469	0	ENST00000303115.3:c.1268C>T	p.Ser423Phe	p.S423F	ENST00000303115	NM_002185.3	423	tCt/tTt	8/8	0.357333281320857	4	FACETS	0.971	0.893	1	0.485	0.446	0.526	CLONAL	1	TRUE	2	0.357333281320857	4		469	1424	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100523	157100527	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCG	GCCCG	-	novel	NA	P-0017752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	82	285	0	ENST00000346085.5:c.1463_1467del	p.Pro488LeufsTer45	p.P488Lfs*45	ENST00000346085	NM_020732.3	487	aGCCCG/a	1/20	1	2	FACETS	0.918	0.812	1	0.918	0.812	1	CLONAL	1	TRUE	1	0.357333281320857	2		285	500	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-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	113	246	0	ENST00000218089.9:c.377_385+68del		p.X126_splice	ENST00000218089	NM_001042749.1	126		6/35	0.325862027779225	2	FACETS	0.976	0.88	1			1	CLONAL	1	TRUE	NA	0.357333281320857	2		246	648	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593604	55593607	+	protein_altering_variant	In_Frame_Del	DEL	GGAA	GGAA	C	novel	NA	P-0017753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	192	374	0	ENST00000288135.5:c.1670_1673delinsC	p.Trp557_Lys558delinsSer	p.W557_K558delinsS	ENST00000288135	NM_000222.2	557	tGGAAg/tCg	11/21	1	2	FACETS	0.943	0.877	1	0.943	0.877	1	CLONAL	1	TRUE	1	0.7	2		374	582	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201810	66201810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	235	390	1	ENST00000273854.3:c.2692C>T	p.Pro898Ser	p.P898S	ENST00000273854	NM_004439.5	898	Cca/Tca	16/18	0.684059175118567	1	FACETS	0.968	0.915	1	0.968	0.915	1	CLONAL	1	TRUE	0	0.684059175118567	1		391	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579302	7579316	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCAACTGACCGTGC	GGCAACTGACCGTGC	TGA	novel	NA	P-0017755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	260	378	4	ENST00000269305.4:c.371_375+10delinsTCA		p.X124_splice	ENST00000269305	NM_001126112.2	124		4/11	0.684059175118567	1	FACETS	0.955	0.905	1	0.955	0.905	1	CLONAL	1	TRUE	0	0.684059175118567	1		382	524	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058456	69058456	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	156	318	0	ENST00000288368.4:c.4100C>A	p.Thr1367Lys	p.T1367K	ENST00000288368	NM_024870.2	1367	aCa/aAa	34/40	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.684059175118567	2		318	456	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0017756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	785	294	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.31920405415812	6	FACETS	1	0.994	1			1	CLONAL	5	TRUE	NA	0.31920405415812	6		294	1471	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885211	111885211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765614074	NA	P-0017756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	131	436	1	ENST00000341259.2:c.1099G>A	p.Gly367Ser	p.G367S	ENST00000341259	NM_005475.2	367	Ggc/Agc	6/8	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.31920405415812	2		437	787	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	462	184	0				ENST00000310581	NM_198253.2	-/1132			0.818852460974838	3	FACETS	0.977	0.941	1	0.977	0.941	1	CLONAL	2	TRUE	1	0.818852460974838	3		184	814	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0017757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	166	741	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA	2	FACETS	0.833	0.771	0.896			1	INDETERMINATE	1	TRUE	NA	0.818852460974838	2		741	487	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608976	100608976	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	252	423	0	ENST00000308731.7:c.1632G>C	p.Arg544Ser	p.R544S	ENST00000308731	NM_000061.2	544	agG/agC	17/19	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.818852460974838	2		423	605	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0017760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	32	607	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.442352790075132	1	FACETS	0.475	0.388	0.573	0.475	0.388	0.573	SUBCLONAL	1	TRUE	0	0.442352790075132	1		607	237	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907420	32907421	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359306	NA	P-0017760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	52	564	2	ENST00000380152.3:c.1813dup	p.Ile605AsnfsTer11	p.I605Nfs*11	ENST00000380152		602	gga/ggAa	10/27	0.329994631464483	1	FACETS	0.763	0.656	0.877	0.763	0.656	0.877	SUBCLONAL	1	TRUE	0	0.442352790075132	1		566	240	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163315494	163315494	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	38	666	0	ENST00000271452.3:c.834C>G	p.Ile278Met	p.I278M	ENST00000271452	NM_145697.2	278	atC/atG	11/14	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.442352790075132	2		666	153	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998413	100998413	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0017760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	57	311	0	ENST00000325455.5:c.1389C>G	p.Tyr463Ter	p.Y463*	ENST00000325455	NM_001202474.3	463	taC/taG	1/8	1	2	FACETS	0.834	0.72	0.956	0.834	0.72	0.956	CLONAL	1	TRUE	1	0.442352790075132	2		311	309	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482820	67482820	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	260	565	0	ENST00000327367.4:c.1224C>G	p.Asp408Glu	p.D408E	ENST00000327367	NM_005902.3	408	gaC/gaG	9/9	0.308664522285343	2	FACETS	0.995	0.94	1	0.995	0.94	1	CLONAL	2	TRUE	0	0.442352790075132	2		565	591	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55991394	55991394	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	171	784	1	ENST00000263923.4:c.67G>T	p.Gly23Cys	p.G23C	ENST00000263923	NM_002253.2	23	Ggt/Tgt	1/30	0.442352790075132	1	FACETS	0.973	0.899	1	0.973	0.899	1	CLONAL	1	TRUE	0	0.442352790075132	1		785	619	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741257	145741257	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1564804479	NA	P-0017760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	141	687	0	ENST00000428558.2:c.1149G>A	p.Trp383Ter	p.W383*	ENST00000428558	NM_004260.3	383	tgG/tgA	6/22	1	2	FACETS	0.838	0.764	0.915	0.838	0.764	0.915	CLONAL	1	TRUE	1	0.442352790075132	2		687	761	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579361	7579361	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1064796722	NA	P-0017761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	301	1043	0	ENST00000269305.4:c.326T>C	p.Phe109Ser	p.F109S	ENST00000269305	NM_001126112.2	109	tTc/tCc	4/11	0.215331284760764	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	TRUE	0	0.215331284760764	3		1043	976	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0017762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	220	941	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.908	0.855	0.96	1	0.994	1	CLONAL	2	TRUE	1	0.530430085089608	2		942	457	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593477	48593478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0017762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	102	553	1	ENST00000342988.3:c.1229_1230insAA	p.Ser411ArgfsTer5	p.S411Rfs*5	ENST00000342988	NM_005359.5	410	cag/cAAag	10/12	0.530430085089608	1	FACETS	0.924	0.837	1	0.924	0.837	1	CLONAL	1	TRUE	0	0.530430085089608	1		554	306	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551393	141551393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	165	861	1	ENST00000220592.5:c.1904G>A	p.Arg635Gln	p.R635Q	ENST00000220592	NM_012154.3	635	cGg/cAg	15/19	0.475608194594548	3	FACETS	1	0.947	1	0.519	0.477	0.562	CLONAL	1	TRUE	1	0.530430085089608	3		862	759	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971130	21971130	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	164	561	0	ENST00000304494.5:c.228del	p.Thr77LeufsTer69	p.T77Lfs*69	ENST00000304494	NM_000077.4	76	gcC/gc	2/3	0.530430085089608	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.530430085089608	1		561	399	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579343	7579385	+	protein_altering_variant	In_Frame_Del	DEL	TGCAAGAAGCCCAGACGGAAACCGTAGCTGCCCTGGTAGGTTT	TGCAAGAAGCCCAGACGGAAACCGTAGCTGCCCTGGTAGGTTT	A	novel	NA	P-0017762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	90	875	0	ENST00000269305.4:c.302_344delinsT	p.Lys101_His115delinsIle	p.K101_H115delinsI	ENST00000269305	NM_001126112.2	101	aAAACCTACCAGGGCAGCTACGGTTTCCGTCTGGGCTTCTTGCAt/aTt	4/11	0.530430085089608	1	FACETS	0.622	0.555	0.692	0.622	0.555	0.692	SUBCLONAL	1	TRUE	0	0.530430085089608	1		875	401	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0017763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	117	306	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.992	0.907	1	0.992	0.907	1	CLONAL	1	TRUE	1	0.751283814002631	2		307	314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0017763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	313	684	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	0.994	0.942	1	0.994	0.942	1	CLONAL	1	TRUE	1	0.751283814002631	2		684	838	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577578	7577578	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	338	713	1	ENST00000269305.4:c.703A>G	p.Asn235Asp	p.N235D	ENST00000269305	NM_001126112.2	235	Aac/Gac	7/11	1	2	FACETS	0.984	0.934	1	0.984	0.934	1	CLONAL	1	TRUE	1	0.751283814002631	2		714	914	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907621	76907621	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	307	418	1	ENST00000373344.5:c.4540C>T	p.Arg1514Ter	p.R1514*	ENST00000373344	NM_000489.3	1514	Cga/Tga	15/35	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.751283814002631	1		419	410	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143993	11143993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568509370	NA	P-0017763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	44	724	0	ENST00000358026.2:c.3574C>T	p.Arg1192Cys	p.R1192C	ENST00000358026	NM_001128849.1	1192	Cgc/Tgc	26/36	1	2	FACETS	0.139	0.116	0.165	0.139	0.116	0.165	SUBCLONAL	1	TRUE	1	0.751283814002631	2		724	843	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41542772	41542772	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200624197	NA	P-0017763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	53	745	0	ENST00000263253.7:c.2083C>T	p.Arg695Cys	p.R695C	ENST00000263253	NM_001429.3	695	Cgt/Tgt	11/31	1	2	FACETS	0.166	0.141	0.194	0.166	0.141	0.194	SUBCLONAL	1	TRUE	1	0.751283814002631	2		745	848	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375993	8375993	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0017763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	46	522	0	ENST00000356435.5:c.4604T>G	p.Leu1535Ter	p.L1535*	ENST00000356435		1535	tTa/tGa	28/35	1	2	FACETS	0.157	0.131	0.185	0.157	0.131	0.185	SUBCLONAL	1	TRUE	1	0.751283814002631	2		522	782	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0017765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	158	380	9	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.79554207152241	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.79554207152241	1		389	211	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0017765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	427	694	4	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.768954120294077	2	FACETS	0.953	0.926	0.98	0.953	0.926	0.98	CLONAL	2	TRUE	0	0.79554207152241	2		698	563	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394805	45394805	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	113	484	2	ENST00000262160.6:c.544C>T	p.Arg182Ter	p.R182*	ENST00000262160	NM_005901.5	182	Cga/Tga	5/11	0.79554207152241	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.79554207152241	1		486	159	SUCCESS
RET	5979	MSKCC	GRCh37	10	43595979	43595979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	607	883	16	ENST00000355710.3:c.146C>T	p.Pro49Leu	p.P49L	ENST00000355710	NM_020975.4	49	cCc/cTc	2/20	NA	2	FACETS	0.923	0.899	0.946			1	INDETERMINATE	2	TRUE	NA	0.79554207152241	2		899	827	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920430	134920430	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	277	727	3	ENST00000398015.3:c.2245A>C	p.Asn749His	p.N749H	ENST00000398015	NM_004441.4	749	Aac/Cac	12/16	0.487522081902314	1	FACETS	0.808	0.768	0.847	0.808	0.768	0.847	CLONAL	1	TRUE	0	0.79554207152241	1		730	519	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55569990	55569990	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	80	764	5	ENST00000288135.5:c.857G>C	p.Gly286Ala	p.G286A	ENST00000288135	NM_000222.2	286	gGa/gCa	5/21	0.772527668678918	2	FACETS	1	0.923	1	0.516	0.464	0.569	CLONAL	1	TRUE	0	0.79554207152241	2		769	195	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488324	56488324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143726790	NA	P-0017766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	187	803	0	ENST00000267101.3:c.1843G>A	p.Glu615Lys	p.E615K	ENST00000267101	NM_001982.3	615	Gag/Aag	15/28	1	2	FACETS	0.81	0.751	0.872	0.81	0.751	0.872	CLONAL	1	TRUE	1	0.643672860081893	2		803	717	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0017766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	177	805	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	0.98	0.909	1	0.98	0.909	1	CLONAL	1	TRUE	1	0.643672860081893	2		805	561	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916836	178916836	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	155	1034	0	ENST00000263967.3:c.223C>G	p.Gln75Glu	p.Q75E	ENST00000263967	NM_006218.2	75	Caa/Gaa	2/21	1	2	FACETS	0.904	0.832	0.977	0.904	0.832	0.977	CLONAL	1	TRUE	1	0.643672860081893	2		1034	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577505	7577505	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs745425759	NA	P-0017766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	219	800	0	ENST00000269305.4:c.776A>T	p.Asp259Val	p.D259V	ENST00000269305	NM_001126112.2	259	gAc/gTc	7/11	0.643672860081893	1	FACETS	0.886	0.832	0.94	0.886	0.832	0.94	CLONAL	1	TRUE	0	0.643672860081893	1		800	521	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029408	14029408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368830992	NA	P-0017766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	150	572	0	ENST00000311895.7:c.1619C>T	p.Ser540Leu	p.S540L	ENST00000311895	NM_005236.2	540	tCg/tTg	8/11	1	2	FACETS	0.985	0.908	1	0.985	0.908	1	CLONAL	1	TRUE	1	0.643672860081893	2		572	473	SUCCESS
APC	324	MSKCC	GRCh37	5	112175096	112175097	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs786203760	NA	P-0017766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	68	360	0	ENST00000257430.4:c.3807_3808del	p.Ile1269MetfsTer6	p.I1269Mfs*6	ENST00000257430	NM_000038.5	1269	ATa/a	16/16	1	2	FACETS	0.919	0.811	1	0.919	0.811	1	CLONAL	1	TRUE	1	0.643672860081893	2		360	230	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281491	49281491	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	206	764	0	ENST00000282018.3:c.538C>A	p.Gln180Lys	p.Q180K	ENST00000282018	NM_020377.2	180	Cag/Aag	1/1	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.643672860081893	2		764	637	SUCCESS
APC	324	MSKCC	GRCh37	5	112175366	112175367	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0017766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	69	389	0	ENST00000257430.4:c.4076_4077del	p.Lys1359IlefsTer15	p.K1359Ifs*15	ENST00000257430	NM_000038.5	1359	AAa/a	16/16	1	2	FACETS	0.782	0.689	0.881	0.782	0.689	0.881	SUBCLONAL	1	TRUE	1	0.643672860081893	2		389	274	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048635	180048635	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150093355	NA	P-0017766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	301	820	0	ENST00000261937.6:c.1927G>A	p.Val643Ile	p.V643I	ENST00000261937	NM_182925.4	643	Gtc/Atc	13/30	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.643672860081893	2		820	850	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0017767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	83	461	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	0.257531584267125	2		461	521	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842387	68842387	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0017767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	186	656	2	ENST00000261769.5:c.448A>T	p.Arg150Ter	p.R150*	ENST00000261769	NM_004360.3	150	Aga/Tga	4/16	0.257531584267125	1	FACETS	1	0.936	1	1	0.993	1	CLONAL	2	TRUE	0	0.257531584267125	1		658	624	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115439	115115439	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	107	681	1	ENST00000257566.3:c.887A>T	p.Asn296Ile	p.N296I	ENST00000257566	NM_016569.3	296	aAc/aTc	5/8	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.257531584267125	2		682	769	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	99	184	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.795	0.715	0.88	0.795	0.715	0.88	SUBCLONAL	1	TRUE	1	0.608662358546641	2		184	409	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0017768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	141	741	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	0.608662358546641	2		741	442	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40490803	40490803	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	558	579	0	ENST00000264657.5:c.496G>C	p.Glu166Gln	p.E166Q	ENST00000264657	NM_139276.2	166	Gag/Cag	6/24	0.318719889757633	5	FACETS	0.949	0.925	0.973			1	INDETERMINATE	5	TRUE	NA	0.602288888523518	5		579	743	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122912	7122912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316627960	NA	P-0017769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	163	850	1	ENST00000302850.5:c.3347G>A	p.Arg1116His	p.R1116H	ENST00000302850	NM_000208.2	1116	cGt/cAt	18/22	0.602288888523518	3	FACETS	0.917	0.843	0.994	0.459	0.421	0.497	CLONAL	1	TRUE	1	0.602288888523518	3		851	768	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212302	36212302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779172651	NA	P-0017769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	156	705	2	ENST00000222270.7:c.2053G>A	p.Asp685Asn	p.D685N	ENST00000222270	NM_014727.1	685	Gat/Aat	3/37	0.448156987430604	4	FACETS	1	0.934	1			1	CLONAL	1	TRUE	NA	0.602288888523518	4		707	812	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709508	176709508	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	122	606	0	ENST00000439151.2:c.5935G>C	p.Glu1979Gln	p.E1979Q	ENST00000439151	NM_022455.4	1979	Gaa/Caa	19/23	0.602288888523518	3	FACETS	0.893	0.81	0.981	0.298	0.27	0.327	CLONAL	1	TRUE	0	0.602288888523518	3		606	590	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910641	29910641	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs11539959	NA	P-0017769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	66	961	0	ENST00000376809.5:c.181G>T	p.Asp61Tyr	p.D61Y	ENST00000376809	NM_002116.7	61	Gac/Tac	2/8	0.602288888523518	3	FACETS	0.3	0.259	0.344	0.15	0.129	0.172	SUBCLONAL	1	TRUE	1	0.602288888523518	3		961	951	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69011969	69011969	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	170	878	0	ENST00000288368.4:c.2606G>T	p.Ser869Ile	p.S869I	ENST00000288368	NM_024870.2	869	aGc/aTc	23/40	0.553790880906371	4	FACETS	0.866	0.796	0.94	0.433	0.398	0.47	CLONAL	1	TRUE	2	0.602288888523518	4		878	1044	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031672	69031672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	193	558	0	ENST00000288368.4:c.3427G>A	p.Glu1143Lys	p.E1143K	ENST00000288368	NM_024870.2	1143	Gaa/Aaa	28/40	0.553790880906371	4	FACETS	0.802	0.746	0.86	0.802	0.746	0.86	CLONAL	2	TRUE	2	0.602288888523518	4		558	640	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0017770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	124	455	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.548	0.496	0.601	0.548	0.496	0.601	SUBCLONAL	1	TRUE	1	0.713328419589149	2		455	635	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168803	56168804	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0017770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	117	527	0	ENST00000399503.3:c.1658dup	p.Tyr553Ter	p.Y553*	ENST00000399503	NM_005921.1	553	tac/tAac	9/20	1	2	FACETS	0.655	0.593	0.719	0.655	0.593	0.719	SUBCLONAL	1	TRUE	1	0.713328419589149	2		527	501	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174870	56174870	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	134	580	0	ENST00000399503.3:c.2029C>T	p.Gln677Ter	p.Q677*	ENST00000399503	NM_005921.1	677	Cag/Tag	11/20	1	2	FACETS	0.653	0.596	0.713	0.653	0.596	0.713	SUBCLONAL	1	TRUE	1	0.713328419589149	2		580	575	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515002	148515003	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	TTCTTCTTTATCATTG	novel	NA	P-0017770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	92	607	0	ENST00000320356.2:c.1191_1206dup	p.Glu403GlnfsTer2	p.E403Qfs*2	ENST00000320356	NM_004456.4	402	-/CAATGATAAAGAAGAA	10/20	1	2	FACETS	0.479	0.426	0.534	0.479	0.426	0.534	SUBCLONAL	1	TRUE	1	0.713328419589149	2		607	539	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0017771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	97	764	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		764	592	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521514	46521514	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	37	854	0	ENST00000262741.5:c.894C>G	p.Ile298Met	p.I298M	ENST00000262741	NM_003629.3	298	atC/atG	7/10	1	2	FACETS	0.424	0.348	0.509	0.424	0.348	0.509	SUBCLONAL	1	TRUE	1	0.253979051320525	2		854	687	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0017773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	104	471	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.253979051320525	2		471	578	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647224	23647224	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	31	1014	0	ENST00000261584.4:c.643G>C	p.Glu215Gln	p.E215Q	ENST00000261584	NM_024675.3	215	Gaa/Caa	4/13	0.253979051320525	3	FACETS	0.485	0.391	0.592	0.243	0.195	0.296	SUBCLONAL	1	TRUE	1	0.253979051320525	3		1014	567	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246490640	246490640	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0017773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	24	554	0	ENST00000388985.4:c.395-1G>C		p.X132_splice	ENST00000388985		132			0.15224459973969	3	FACETS	0.634	0.497	0.792			1	INDETERMINATE	1	TRUE	NA	0.253979051320525	3		554	336	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418622	49418622	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	92	834	0	ENST00000301067.7:c.15892del	p.Val5298CysfsTer7	p.V5298Cfs*7	ENST00000301067	NM_003482.3	5298	Gtg/tg	49/54	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.253979051320525	2		834	560	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743844	40743844	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	27	645	0	ENST00000373198.4:c.3151C>T	p.Gln1051Ter	p.Q1051*	ENST00000373198	NM_133170.3	1051	Cag/Tag	23/32	1	2	FACETS	0.516	0.41	0.637	0.516	0.41	0.637	SUBCLONAL	1	TRUE	1	0.253979051320525	2		645	412	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38978704	38978704	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	24	762	0	ENST00000357387.3:c.802A>G	p.Thr268Ala	p.T268A	ENST00000357387	NM_152756.3	268	Aca/Gca	9/38	1	2	FACETS	0.407	0.318	0.51	0.407	0.318	0.51	SUBCLONAL	1	TRUE	1	0.253979051320525	2		762	464	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120411	94120411	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs532369845	NA	P-0017773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	42	515	0	ENST00000369303.4:c.640A>G	p.Ile214Val	p.I214V	ENST00000369303	NM_004440.3	214	Atc/Gtc	3/17	1	2	FACETS	0.901	0.754	1	0.901	0.754	1	CLONAL	1	TRUE	1	0.253979051320525	2		515	367	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708970	117708970	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	68	747	1	ENST00000368508.3:c.1987C>T	p.Pro663Ser	p.P663S	ENST00000368508	NM_002944.2	663	Ccc/Tcc	13/43	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.253979051320525	2		748	474	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509249	106509249	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	160	958	0	ENST00000359195.3:c.1243G>T	p.Glu415Ter	p.E415*	ENST00000359195	NM_002649.2	415	Gag/Tag	2/11	0.253979051320525	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.253979051320525	3		958	642	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121086	11121086	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	97	620	0	ENST00000358026.2:c.2153A>G	p.Tyr718Cys	p.Y718C	ENST00000358026	NM_001128849.1	718	tAt/tGt	15/36	1	2	FACETS	0.947	0.846	1	0.947	0.846	1	CLONAL	1	TRUE	1	0.329204555909335	2		620	622	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31939828	31939828	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	82	847	0	ENST00000375333.2:c.55G>C	p.Ala19Pro	p.A19P	ENST00000375333	NM_032454.1	19	Gca/Cca	1/8	1	2	FACETS	0.642	0.565	0.724	0.642	0.565	0.724	SUBCLONAL	1	TRUE	1	0.329204555909335	2		847	776	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257591	19257591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	116	462	0	ENST00000162023.5:c.635C>T	p.Pro212Leu	p.P212L	ENST00000162023		212	cCt/cTt	10/13	0.388726701859364	6	FACETS	0.838	0.758	0.922	0.419	0.379	0.461	CLONAL	2	TRUE	2	0.529788643628963	6		462	538	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0017778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	64	594	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.741	0.646	0.843	0.741	0.646	0.843	SUBCLONAL	1	TRUE	1	0.52	2		594	332	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0017778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	75	844	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.52	2		844	274	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0017778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	55	393	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.52	2		393	196	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101260	27101260	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	87	448	0	ENST00000324856.7:c.4544del	p.Gly1515AlafsTer12	p.G1515Afs*12	ENST00000324856	NM_006015.4	1514	acG/ac	18/20	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.52	2		448	333	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998190	100998193	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	GT	novel	NA	P-0017778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	66	265	0	ENST00000325455.5:c.1609_1612delinsAC	p.Val537ThrfsTer36	p.V537Tfs*36	ENST00000325455	NM_001202474.3	537	GTCTac/ACac	1/8	1	2	FACETS	0.947	0.831	1	0.947	0.831	1	CLONAL	1	TRUE	1	0.52	2		265	268	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117875375	117875375	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	92	443	0	ENST00000297338.2:c.268del	p.Arg90GlyfsTer35	p.R90Gfs*35	ENST00000297338	NM_006265.2	90	Cgg/gg	3/14	1	2	FACETS	0.931	0.834	1	0.931	0.834	1	CLONAL	1	TRUE	1	0.52	2		443	380	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720805	89720805	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	AG	novel	NA	P-0017778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	34	207	0	ENST00000371953.3:c.956delinsAG	p.Thr319LysfsTer6	p.T319Kfs*6	ENST00000371953	NM_000314.4	319	aCt/aAGt	8/9	1	2	FACETS	0.765	0.632	0.909	0.765	0.632	0.909	CLONAL	1	TRUE	1	0.52	2		207	171	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076674	102076674	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	53	347	0	ENST00000282441.5:c.853C>G	p.Leu285Val	p.L285V	ENST00000282441	NM_001130145.2	285	Ctg/Gtg	5/9	0.236077939918819	3	FACETS	1	0.965	1	0.743	0.636	0.858	CLONAL	1	TRUE	1	0.236077939918819	3		347	338	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165327	32165327	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	89	668	0	ENST00000375023.3:c.4801C>A	p.Gln1601Lys	p.Q1601K	ENST00000375023	NM_004557.3	1601	Cag/Aag	27/30	0.103565801367411	4	FACETS	1	0.977	1	0.715	0.634	0.801	INDETERMINATE	1	TRUE	2	0.236077939918819	4		668	652	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242489	+	protein_altering_variant	In_Frame_Del	DEL	TAAGAGAAGCAACATCTCCG	TAAGAGAAGCAACATCTCCG	CT	novel	NA	P-0017780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	81	514	2	ENST00000275493.2:c.2240_2259delinsCT	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCCG/tCT	19/28	0.220621191597864	4	FACETS	1	0.976	1	0.731	0.645	0.823	CLONAL	1	TRUE	2	0.236077939918819	4		516	580	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934574	NA	P-0017781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	694	701	0	ENST00000269305.4:c.844C>G	p.Arg282Gly	p.R282G	ENST00000269305	NM_001126112.2	282	Cgg/Ggg	8/11	0.918547135735268	3	FACETS	0.996	0.984	1	0.996	0.984	1	CLONAL	3	TRUE	0	0.918547135735268	3		701	738	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715777	18715777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1203196085	NA	P-0017781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	70	392	0	ENST00000266497.5:c.3608G>A	p.Arg1203Lys	p.R1203K	ENST00000266497		1203	aGg/aAg	25/31	0.54900411468952	6	FACETS	0.694	0.605	0.79	0.174	0.151	0.198	INDETERMINATE	1	TRUE	2	0.918547135735268	6		392	623	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776783	NA	P-0017781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	236	355	1	ENST00000267163.4:c.1215+1G>A		p.X405_splice	ENST00000267163	NM_000321.2	405			0.897074010537373	2	FACETS	0.952	0.924	0.977	0.952	0.924	0.977	CLONAL	2	TRUE	0	0.918547135735268	2		356	270	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789597	3789597	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	463	513	0	ENST00000262367.5:c.4262G>T	p.Cys1421Phe	p.C1421F	ENST00000262367	NM_004380.2	1421	tGc/tTc	25/31	0.886320484757503	3	FACETS	0.995	0.98	1	0.995	0.98	1	CLONAL	3	TRUE	0	0.918547135735268	3		513	493	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178072	142178072	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1015400677	NA	P-0017781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	259	298	0	ENST00000350721.4:c.7346C>T	p.Ser2449Leu	p.S2449L	ENST00000350721	NM_001184.3	2449	tCa/tTa	43/47	0.721439649001202	4	FACETS	0.897	0.857	0.936	0.897	0.857	0.936	CLONAL	3	TRUE	1	0.918547135735268	4		298	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579355	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519997	NA	P-0017782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	390	658	0	ENST00000269305.4:c.332T>G	p.Leu111Arg	p.L111R	ENST00000269305	NM_001126112.2	111	cTg/cGg	4/11	0.631594477416775	3	FACETS	0.914	0.886	0.941	0.914	0.886	0.941	CLONAL	3	TRUE	0	0.76104983704676	3		658	516	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73108202	73108202	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	31	63	0	ENST00000356692.5:c.302T>C	p.Ile101Thr	p.I101T	ENST00000356692		101	aTt/aCt	4/9	0.638836370572806	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	2	TRUE	0	0.76104983704676	2		63	40	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73108208	73108208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	36	69	0	ENST00000356692.5:c.308G>A	p.Arg103Gln	p.R103Q	ENST00000356692		103	cGa/cAa	4/9	0.638836370572806	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	2	TRUE	0	0.76104983704676	2		69	46	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0017784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	77	514	0	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	0.264003355729141	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.264003355729141	1		514	417	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610498	10610498	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	48	529	0	ENST00000171111.5:c.212G>T	p.Arg71Leu	p.R71L	ENST00000171111	NM_203500.1	71	cGg/cTg	2/6	1	2	FACETS	0.85	0.719	0.992	0.85	0.719	0.992	CLONAL	1	TRUE	1	0.264003355729141	2		529	428	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007774	45007774	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0017784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	29	426	0	ENST00000558401.1:c.221T>A	p.Leu74Ter	p.L74*	ENST00000558401	NM_004048.2	74	tTg/tAg	2/4	0.264003355729141	1	FACETS	0.725	0.584	0.884	0.725	0.584	0.884	SUBCLONAL	1	TRUE	0	0.264003355729141	1		426	263	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136297	2136297	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	77	567	0	ENST00000219476.3:c.4766C>A	p.Pro1589Gln	p.P1589Q	ENST00000219476	NM_000548.3	1589	cCg/cAg	37/42	1	2	FACETS	0.974	0.856	1	0.974	0.856	1	CLONAL	1	TRUE	1	0.264003355729141	2		567	599	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0017785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	112	1080	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.425755328513748	1	FACETS	0.97	0.879	1	0.97	0.879	1	CLONAL	1	TRUE	0	0.425755328513748	1		1080	427	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947596	48947596	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	125	403	0	ENST00000267163.4:c.1183del	p.Gln395AsnfsTer6	p.Q395Nfs*6	ENST00000267163	NM_000321.2	395	Caa/aa	12/27	0.425755328513748	1	FACETS	0.955	0.87	1	0.955	0.87	1	CLONAL	1	TRUE	0	0.425755328513748	1		403	484	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	61	325	3	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.848	0.744	0.957	0.848	0.744	0.957	CLONAL	1	TRUE	1	0.73	2		328	197	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	8	918	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.059	0.037	0.087	0.059	0.037	0.087	SUBCLONAL	1	TRUE	1	0.73	2		918	373	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	145	555	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.856	0.804	0.907	1	0.992	1	CLONAL	2	TRUE	1	0.73	2		558	232	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	127	865	8	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.782	0.714	0.853	0.782	0.714	0.853	SUBCLONAL	1	TRUE	1	0.73	2		873	445	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143994	11143994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	111	466	0	ENST00000358026.2:c.3575G>A	p.Arg1192His	p.R1192H	ENST00000358026	NM_001128849.1	1192	cGc/cAc	26/36	0.0930772978091734	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.73	0		466	295	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573944	7573944	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555524354	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	91	529	0	ENST00000269305.4:c.1083del	p.Ser362AlafsTer8	p.S362Afs*8	ENST00000269305	NM_001126112.2	361	ggG/gg	10/11	1	2	FACETS	0.872	0.784	0.963	0.872	0.784	0.963	CLONAL	1	TRUE	1	0.73	2		529	286	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	162	439	1	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	0.0930772978091734	3	FACETS	1	0.99	1	0.737	0.684	0.791	INDETERMINATE	1	TRUE	1	0.73	3		440	411	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	41	537	2	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.0930772978091734	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.73	0		539	229	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	160	665	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	0.987	0.914	1	0.987	0.914	1	CLONAL	1	TRUE	1	0.73	2		665	444	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	84	255	0	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.967	0.868	1	0.967	0.868	1	CLONAL	1	TRUE	1	0.73	2		255	238	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	137	552	2	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.73	2		554	359	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353819	15353819	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	54	752	2	ENST00000263377.2:c.3061del	p.His1021IlefsTer47	p.H1021Ifs*47	ENST00000263377	NM_058243.2	1021	Cat/at	14/20	0.0930772978091734	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.73	0		754	229	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370236	40370236	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs761761205	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	132	609	7	ENST00000293328.3:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000293328	NM_012448.3	368	Cag/ag	9/19	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.73	2		616	244	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2221594	2221594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766294780	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	147	578	1	ENST00000326181.6:c.463G>A	p.Ala155Thr	p.A155T	ENST00000326181	NM_032271.2	155	Gcc/Acc	7/21	0.0930772978091734	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.73	0		579	339	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905055	50905055	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	71	359	3	ENST00000440232.2:c.342del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	113	Ggg/gg	4/27	0.0930772978091734	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.73	0		362	166	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974770	21974775	+	inframe_deletion	In_Frame_Del	DEL	GGCCGT	GGCCGT	-	novel	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	29	104	0	ENST00000304494.5:c.52_57del	p.Thr18_Ala19del	p.T18_A19del	ENST00000304494	NM_000077.4	18	ACGGCC/-	1/3	1	2	FACETS	0.836	0.689	0.994	0.836	0.689	0.994	CLONAL	1	TRUE	1	0.73	2		104	95	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749491	41749491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	84	363	0	ENST00000226382.2:c.304C>T	p.Arg102Cys	p.R102C	ENST00000226382	NM_003924.3	102	Cgc/Tgc	2/3	0.0930772978091734	3	FACETS	1	0.977	1	0.677	0.608	0.748	INDETERMINATE	1	TRUE	1	0.73	3		363	232	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405953	157405954	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1554294674	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	86	383	2	ENST00000346085.5:c.2201dup	p.Ser736IlefsTer27	p.S736Ifs*27	ENST00000346085	NM_020732.3	732	ccg/ccGg	6/20	0.0930772978091734	3	FACETS	0.911	0.813	1	0.456	0.406	0.508	INDETERMINATE	1	TRUE	1	0.73	3		385	353	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137784	64137784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	131	795	2	ENST00000334205.4:c.1885C>T	p.Arg629Cys	p.R629C	ENST00000334205	NM_003942.2	629	Cgc/Tgc	15/17	1	2	FACETS	0.902	0.826	0.979	0.902	0.826	0.979	CLONAL	1	TRUE	1	0.73	2		797	398	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67646013	67646014	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs1470210640	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	96	468	0	ENST00000264010.4:c.950_951del	p.Thr317ArgfsTer91	p.T317Rfs*91	ENST00000264010	NM_006565.3	314	aAC/a	4/12	1	2	FACETS	0.936	0.846	1	0.936	0.846	1	CLONAL	1	TRUE	1	0.73	2		468	281	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396234	396234	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	110	455	1	ENST00000262320.3:c.792del	p.Gly265GlufsTer149	p.G265Efs*149	ENST00000262320	NM_003502.3	264	ccC/cc	2/11	0.0930772978091734	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.73	0		456	266	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	120	577	1	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	1	2	FACETS	0.886	0.809	0.966	0.886	0.809	0.966	CLONAL	1	TRUE	1	0.73	2		578	371	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	147	859	0	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.97	0.895	1	0.97	0.895	1	CLONAL	1	TRUE	1	0.73	2		859	415	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290896	15290896	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	130	690	3	ENST00000263388.2:c.3314del	p.Gly1105AlafsTer167	p.G1105Afs*167	ENST00000263388	NM_000435.2	1105	gGc/gc	20/33	0.0930772978091734	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.73	0		693	360	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363051	40363051	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	46	270	0	ENST00000397332.2:c.1178G>A	p.Gly393Asp	p.G393D	ENST00000397332	NM_001033082.2	393	gGc/gAc	3/3	1	2	FACETS	0.759	0.65	0.875	0.759	0.65	0.875	SUBCLONAL	1	TRUE	1	0.73	2		270	166	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245912894	245912894	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	93	419	0	ENST00000388985.4:c.1258G>A	p.Glu420Lys	p.E420K	ENST00000388985		420	Gaa/Aaa	12/12	1	2	FACETS	0.947	0.855	1	0.947	0.855	1	CLONAL	1	TRUE	1	0.73	2		419	269	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414212	32414212	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	75	355	2	ENST00000332351.3:c.1339G>A	p.Gly447Ser	p.G447S	ENST00000332351	NM_024426.4	447	Ggt/Agt	8/10	1	2	FACETS	0.886	0.788	0.987	0.886	0.788	0.987	CLONAL	1	TRUE	1	0.73	2		357	232	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869460	102869460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	102	415	0	ENST00000307046.8:c.181G>A	p.Ala61Thr	p.A61T	ENST00000307046	NM_001111285.1	61	Gct/Act	2/4	1	2	FACETS	0.876	0.793	0.962	0.876	0.793	0.962	CLONAL	1	TRUE	1	0.73	2		415	319	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263901	133263901	+	start_lost	Translation_Start_Site	SNP	T	T	C	rs878854847	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	59	209	0	ENST00000320574.5:c.1A>G	p.Met1?	p.M1?	ENST00000320574	NM_006231.2	1	Atg/Gtg	1/49	0.3	1	FACETS	0.646	0.568	0.726	0.646	0.568	0.726	INDETERMINATE	1	TRUE	0	0.73	1		209	159	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986865	36986865	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748087644	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	58	126	0	ENST00000354822.5:c.824C>T	p.Pro275Leu	p.P275L	ENST00000354822	NM_001079668.2	275	cCg/cTg	3/3	0.3	3	FACETS	0.854	0.757	0.952			1	INDETERMINATE	2	TRUE	NA	0.73	3		126	127	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574032	95574032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150510758	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	62	309	0	ENST00000393063.1:c.2717G>A	p.Arg906His	p.R906H	ENST00000393063	NM_030621.3	906	cGc/cAc	18/28	1	2	FACETS	0.813	0.713	0.917	0.813	0.713	0.917	CLONAL	1	TRUE	1	0.73	2		309	209	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347093	347093	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	138	1036	0	ENST00000262320.3:c.1918del	p.Glu640LysfsTer65	p.E640Kfs*65	ENST00000262320	NM_003502.3	640	Gaa/aa	7/11	0.0930772978091734	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.73	0		1036	370	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110677	2110677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	117	509	1	ENST00000219476.3:c.982G>A	p.Ala328Thr	p.A328T	ENST00000219476	NM_000548.3	328	Gca/Aca	11/42	0.0930772978091734	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.73	0		510	322	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658661	3658662	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	150	666	0	ENST00000294008.3:c.304dup	p.Thr102AsnfsTer18	p.T102Nfs*18	ENST00000294008	NM_032444.2	102	acc/aAcc	2/15	0.0930772978091734	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.73	0		666	443	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831608	72831608	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	97	442	0	ENST00000268489.5:c.4973G>C	p.Ser1658Thr	p.S1658T	ENST00000268489	NM_006885.3	1658	aGt/aCt	9/10	1	2	FACETS	0.97	0.878	1	0.97	0.878	1	CLONAL	1	TRUE	1	0.73	2		442	274	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354436	40354436	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	138	596	2	ENST00000293328.3:c.2159del	p.Gly720AlafsTer46	p.G720Afs*46	ENST00000293328	NM_012448.3	720	gGc/gc	18/19	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.73	2		598	375	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760731	59760731	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	19	576	0	ENST00000259008.2:c.3676del	p.Thr1226LeufsTer4	p.T1226Lfs*4	ENST00000259008	NM_032043.2	1226	Act/ct	20/20	1	2	FACETS	0.144	0.109	0.185	0.144	0.109	0.185	SUBCLONAL	1	TRUE	1	0.73	2		576	362	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107195	11107195	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779952581	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	100	447	3	ENST00000358026.2:c.1787C>T	p.Thr596Met	p.T596M	ENST00000358026	NM_001128849.1	596	aCg/aTg	11/36	0.0930772978091734	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.73	0		450	297	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965779	18965779	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1395016855	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	101	683	1	ENST00000262803.5:c.1357G>A	p.Val453Ile	p.V453I	ENST00000262803	NM_002911.3	453	Gta/Ata	10/24	0.0930772978091734	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.73	0		684	329	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967059	18967059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	74	478	0	ENST00000262803.5:c.1774G>A	p.Glu592Lys	p.E592K	ENST00000262803	NM_002911.3	592	Gag/Aag	13/24	0.0930772978091734	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.73	0		478	212	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214728	36214728	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	51	340	2	ENST00000222270.7:c.3159del	p.Arg1055GlyfsTer127	p.R1055Gfs*127	ENST00000222270	NM_014727.1	1052	Ggg/gg	8/37	0.0930772978091734	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.73	0		342	152	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641555	47641555	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	35	117	0	ENST00000233146.2:c.940del	p.Gln314ArgfsTer17	p.Q314Rfs*17	ENST00000233146	NM_000251.2	314	Cag/ag	5/16	1	2	FACETS	0.978	0.826	1	0.978	0.826	1	CLONAL	1	TRUE	1	0.73	2		117	98	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660130	227660130	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	86	367	0	ENST00000305123.5:c.3325A>C	p.Ser1109Arg	p.S1109R	ENST00000305123	NM_005544.2	1109	Agt/Cgt	1/2	0.0930772978091734	3	FACETS	1	0.958	1	0.57	0.511	0.632	INDETERMINATE	1	TRUE	1	0.73	3		367	282	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525016	9525016	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	108	388	0	ENST00000353224.5:c.1869G>T	p.Glu623Asp	p.E623D	ENST00000353224	NM_177990.2	623	gaG/gaT	8/10	0.0930772978091734	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.73	0		388	263	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256371	46256371	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	103	535	0	ENST00000371998.3:c.599T>C	p.Leu200Ser	p.L200S	ENST00000371998		200	tTg/tCg	7/23	0.0930772978091734	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.73	0		535	342	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686293	30686294	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	113	364	0	ENST00000295754.5:c.152_153del	p.Cys51Ter	p.C51*	ENST00000295754	NM_003242.5	50	cTG/c	2/7	1	2	FACETS	0.867	0.789	0.948	0.867	0.789	0.948	CLONAL	1	TRUE	1	0.73	2		364	357	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522693	67522693	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	51	257	0	ENST00000274335.5:c.193del	p.Glu65LysfsTer10	p.E65Kfs*10	ENST00000274335		64	Ggg/gg	1/15	1	2	FACETS	0.682	0.587	0.782	0.682	0.587	0.782	SUBCLONAL	1	TRUE	1	0.73	2		257	205	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395001	395001	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1300046652	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	68	398	2	ENST00000380956.4:c.402del	p.Gly135GlufsTer14	p.G135Efs*14	ENST00000380956	NM_001195286.1	133	Aaa/aa	3/9	0.3	2	FACETS	0.803	0.709	0.902			1	INDETERMINATE	1	TRUE	NA	0.73	2		400	232	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798105	32798105	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1562326716	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	113	530	0	ENST00000374899.4:c.1574del	p.Gly525AspfsTer36	p.G525Dfs*36	ENST00000374899	NM_018833.2	525	gGa/ga	9/12	1	2	FACETS	0.938	0.855	1	0.938	0.855	1	CLONAL	1	TRUE	1	0.73	2		530	330	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020752	112020754	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	146	484	0	ENST00000368678.4:c.817_819del	p.Lys273del	p.K273del	ENST00000368678		273	AAG/-	8/13	0.0930772978091734	3	FACETS	1	0.974	1	0.57	0.524	0.617	INDETERMINATE	1	TRUE	1	0.73	3		484	479	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468098	50468098	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	63	282	1	ENST00000331340.3:c.1333T>C	p.Ser445Pro	p.S445P	ENST00000331340	NM_006060.4	445	Tcg/Ccg	8/8	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.73	2		283	168	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005861	69005861	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	85	444	0	ENST00000288368.4:c.2272T>C	p.Tyr758His	p.Y758H	ENST00000288368	NM_024870.2	758	Tat/Cat	21/40	1	2	FACETS	0.814	0.728	0.904	0.814	0.728	0.904	CLONAL	1	TRUE	1	0.73	2		444	286	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971077	21971077	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	43	199	0	ENST00000304494.5:c.281T>C	p.Leu94Pro	p.L94P	ENST00000304494	NM_000077.4	94	cTg/cCg	2/3	1				0.589	0.805				SUBCLONAL	1	TRUE	1	0.73	2		199	170	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399876	139399876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369915496	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	112	664	2	ENST00000277541.6:c.4472C>T	p.Thr1491Met	p.T1491M	ENST00000277541	NM_017617.3	1491	aCg/aTg	25/34	0.182986178231204	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.73	0		666	312	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15836766	15836766	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	95	394	0	ENST00000307771.7:c.827+1G>A		p.X276_splice	ENST00000307771	NM_005089.3	276			0.0930772978091734	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.73	0		394	283	SUCCESS
AR	367	MSKCC	GRCh37	X	66765743	66765743	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1300639636	NA	P-0017786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	186	820	2	ENST00000374690.3:c.755A>G	p.Glu252Gly	p.E252G	ENST00000374690	NM_000044.3	252	gAg/gGg	1/8	0.0930772978091734	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.73	0		822	544	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164856	47164856	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1278528667	NA	P-0017789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	51	261	0	ENST00000409792.3:c.1270C>T	p.Arg424Ter	p.R424*	ENST00000409792	NM_014159.6	424	Cga/Tga	3/21	1	2	FACETS	0.705	0.604	0.814	0.705	0.604	0.814	SUBCLONAL	1	TRUE	1	0.552109396388751	2		261	262	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562657	29562660	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs1064794276	NA	P-0017789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	128	517	0	ENST00000356175.3:c.3739_3742del	p.Phe1247IlefsTer18	p.F1247Ifs*18	ENST00000356175	NM_000267.3	1246	cTGTTt/ct	28/57	NA	2	FACETS	1	0.916	1			1	INDETERMINATE	1	TRUE	NA	0.552109396388751	2		517	462	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060665	38060665	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	83	733	0	ENST00000250448.2:c.1324G>A	p.Ala442Thr	p.A442T	ENST00000250448	NM_004496.3	442	Gcc/Acc	2/2	1	2	FACETS	0.513	0.453	0.577	0.513	0.453	0.577	SUBCLONAL	1	TRUE	1	0.552109396388751	2		733	586	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259046	89259046	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	34	256	0	ENST00000336596.2:c.190C>A	p.Pro64Thr	p.P64T	ENST00000336596	NM_005233.5	64	Ccc/Acc	3/17	1	2	FACETS	0.513	0.422	0.615	0.513	0.422	0.615	SUBCLONAL	1	TRUE	1	0.552109396388751	2		256	240	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0017796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	46	499	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	0.649	0.545	0.764	0.649	0.545	0.764	SUBCLONAL	1	TRUE	1	0.201453614311194	2		499	704	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325489	1325489	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs752709788	NA	P-0017796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	30	344	0	ENST00000400841.2:c.186C>A	p.Phe62Leu	p.F62L	ENST00000400841		62	ttC/ttA	3/6	1	2	FACETS	0.666	0.536	0.814	0.666	0.536	0.814	SUBCLONAL	1	TRUE	1	0.201453614311194	2		344	447	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	144	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.654507336135668	2		306	419	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400190	41400190	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	193	555	0	ENST00000373198.4:c.569G>A	p.Arg190Lys	p.R190K	ENST00000373198	NM_133170.3	190	aGa/aAa	5/32	1	2	FACETS	0.941	0.875	1	0.941	0.875	1	CLONAL	1	TRUE	1	0.654507336135668	2		555	627	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	263	507	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.654507336135668	2		508	792	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226564885	226564885	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	201	553	2	ENST00000366794.5:c.1865C>T	p.Thr622Ile	p.T622I	ENST00000366794	NM_001618.3	622	aCc/aTc	13/23	1	2	FACETS	0.922	0.859	0.988	0.922	0.859	0.988	CLONAL	1	TRUE	1	0.654507336135668	2		555	666	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942215	71942216	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	164	513	1	ENST00000298229.2:c.1479_1480delinsAT	p.Asp494Tyr	p.D494Y	ENST00000298229	NM_001567.3	493	acGGat/acATat	12/28	0.654507336135668	1	FACETS	0.924	0.86	0.987	0.924	0.86	0.987	CLONAL	1	TRUE	0	0.654507336135668	1		514	365	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699323	18699323	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199904184	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	214	532	0	ENST00000266497.5:c.3424C>T	p.Arg1142Cys	p.R1142C	ENST00000266497		1142	Cgt/Tgt	24/31	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.654507336135668	2		532	550	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944983	31944983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1175067252	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	219	722	0	ENST00000340398.3:c.118C>T	p.Arg40Cys	p.R40C	ENST00000340398	NM_001013699.2	40	Cgc/Tgc	1/1	1	2	FACETS	0.914	0.854	0.976	0.914	0.854	0.976	CLONAL	1	TRUE	1	0.654507336135668	2		722	732	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112028	115112028	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	191	718	0	ENST00000257566.3:c.1712C>T	p.Ser571Phe	p.S571F	ENST00000257566	NM_016569.3	571	tCc/tTc	7/8	1	2	FACETS	0.784	0.727	0.843	0.784	0.727	0.843	SUBCLONAL	1	TRUE	1	0.654507336135668	2		718	744	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112253	115112253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024919027	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	73	152	0	ENST00000257566.3:c.1487G>A	p.Gly496Asp	p.G496D	ENST00000257566	NM_016569.3	496	gGc/gAc	7/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.654507336135668	2		152	174	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636196	28636196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	122	342	0	ENST00000241453.7:c.176C>T	p.Ser59Phe	p.S59F	ENST00000241453	NM_004119.2	59	tCc/tTc	3/24	1	2	FACETS	0.932	0.85	1	0.932	0.85	1	CLONAL	1	TRUE	1	0.654507336135668	2		342	400	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524567	103524567	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	127	367	0	ENST00000355739.4:c.2698C>T	p.Gln900Ter	p.Q900*	ENST00000355739	NM_000123.3	900	Caa/Taa	13/15	1	2	FACETS	0.915	0.836	0.997	0.915	0.836	0.997	CLONAL	1	TRUE	1	0.654507336135668	2		367	424	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923318	9923318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867335598	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	193	573	1	ENST00000330684.3:c.1969G>A	p.Glu657Lys	p.E657K	ENST00000330684	NM_001134407.1	657	Gaa/Aaa	9/13	0.269534142245039	1	FACETS	0.719	0.67	0.769	0.719	0.67	0.769	INDETERMINATE	1	TRUE	0	0.654507336135668	1		574	552	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923328	9923328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	111	572	0	ENST00000330684.3:c.1959G>A	p.Met653Ile	p.M653I	ENST00000330684	NM_001134407.1	653	atG/atA	9/13	0.269534142245039	1	FACETS	0.423	0.382	0.467	0.423	0.382	0.467	INDETERMINATE	1	TRUE	0	0.654507336135668	1		572	539	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031885	10031885	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	175	533	0	ENST00000330684.3:c.938T>A	p.Ile313Asn	p.I313N	ENST00000330684	NM_001134407.1	313	aTc/aAc	3/13	0.269534142245039	1	FACETS	0.701	0.651	0.753	0.701	0.651	0.753	INDETERMINATE	1	TRUE	0	0.654507336135668	1		533	513	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805596	89805596	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184324290	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	215	579	1	ENST00000389301.3:c.4112G>A	p.Gly1371Glu	p.G1371E	ENST00000389301	NM_000135.2	1371	gGg/gAg	41/43	0.654507336135668	1	FACETS	0.957	0.9	1	0.957	0.9	1	CLONAL	1	TRUE	0	0.654507336135668	1		580	462	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734141	58734141	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	285	772	1	ENST00000305921.3:c.1199C>T	p.Ser400Phe	p.S400F	ENST00000305921	NM_003620.3	400	tCc/tTc	5/6	1	2	FACETS	0.874	0.823	0.927	0.874	0.823	0.927	CLONAL	1	TRUE	1	0.654507336135668	2		773	996	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59924491	59924491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	140	421	1	ENST00000259008.2:c.598G>A	p.Glu200Lys	p.E200K	ENST00000259008	NM_032043.2	200	Gaa/Aaa	6/20	1	2	FACETS	0.97	0.891	1	0.97	0.891	1	CLONAL	1	TRUE	1	0.654507336135668	2		422	441	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39600627	39600627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774620242	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	131	417	1	ENST00000262039.4:c.1442C>T	p.Ser481Leu	p.S481L	ENST00000262039	NM_002647.2	481	tCg/tTg	13/25	1	2	FACETS	0.955	0.875	1	0.955	0.875	1	CLONAL	1	TRUE	1	0.654507336135668	2		418	419	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300200	15300200	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1487017745	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	195	615	0	ENST00000263388.2:c.1076C>T	p.Pro359Leu	p.P359L	ENST00000263388	NM_000435.2	359	cCc/cTc	7/33	1	2	FACETS	0.876	0.814	0.94	0.876	0.814	0.94	CLONAL	1	TRUE	1	0.654507336135668	2		615	680	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355186	15355186	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	260	806	0	ENST00000263377.2:c.2437C>T	p.Pro813Ser	p.P813S	ENST00000263377	NM_058243.2	813	Cca/Tca	13/20	1	2	FACETS	0.924	0.868	0.981	0.924	0.868	0.981	CLONAL	1	TRUE	1	0.654507336135668	2		806	860	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228130	36228130	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	192	538	0	ENST00000222270.7:c.7516C>T	p.Pro2506Ser	p.P2506S	ENST00000222270	NM_014727.1	2506	Ccc/Tcc	33/37	1	2	FACETS	0.921	0.856	0.988	0.921	0.856	0.988	CLONAL	1	TRUE	1	0.654507336135668	2		538	637	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765640	41765640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	239	630	0	ENST00000301178.4:c.2516G>A	p.Gly839Glu	p.G839E	ENST00000301178	NM_021913.4	839	gGa/gAa	20/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.654507336135668	2		630	716	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860539	45860539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	175	567	0	ENST00000391945.4:c.1468C>T	p.Leu490Phe	p.L490F	ENST00000391945	NM_000400.3	490	Ctc/Ttc	15/23	1	2	FACETS	0.849	0.785	0.914	0.849	0.785	0.914	CLONAL	1	TRUE	1	0.654507336135668	2		567	630	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551347	29551347	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs372472978	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	164	549	0	ENST00000389048.3:c.1283G>A	p.Gly428Glu	p.G428E	ENST00000389048	NM_004304.4	428	gGa/gAa	6/29	1	2	FACETS	0.973	0.9	1	0.973	0.9	1	CLONAL	1	TRUE	1	0.654507336135668	2		549	515	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158627027	158627027	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	130	390	0	ENST00000263640.3:c.644-1G>A		p.X215_splice	ENST00000263640	NM_001105.4	215			1	2	FACETS	0.858	0.784	0.935	0.858	0.784	0.935	CLONAL	1	TRUE	1	0.654507336135668	2		390	463	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710658	40710658	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	158	454	1	ENST00000373198.4:c.4194-1G>A		p.X1398_splice	ENST00000373198	NM_133170.3	1398			1	2	FACETS	0.973	0.899	1	0.973	0.899	1	CLONAL	1	TRUE	1	0.654507336135668	2		455	496	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945363	54945363	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	237	591	0	ENST00000312783.6:c.1063G>A	p.Gly355Arg	p.G355R	ENST00000312783	NM_198436.1	355	Gga/Aga	10/10	1	2	FACETS	0.983	0.921	1	0.983	0.921	1	CLONAL	1	TRUE	1	0.654507336135668	2		591	737	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645729	12645729	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	105	331	0	ENST00000251849.4:c.740C>T	p.Ser247Phe	p.S247F	ENST00000251849	NM_002880.3	247	tCt/tTt	7/17	1	2	FACETS	0.838	0.757	0.922	0.838	0.757	0.922	CLONAL	1	TRUE	1	0.654507336135668	2		331	383	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931589	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	107	257	0	ENST00000349496.5:c.101G>A	p.Gly34Glu	p.G34E	ENST00000349496	NM_001904.3	34	gGa/gAa	3/15	1	2	FACETS	0.896	0.811	0.984	0.896	0.811	0.984	CLONAL	1	TRUE	1	0.654507336135668	2		257	365	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280793	41280793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	102	329	0	ENST00000349496.5:c.2306G>A	p.Gly769Asp	p.G769D	ENST00000349496	NM_001904.3	769	gGt/gAt	15/15	1	2	FACETS	0.917	0.829	1	0.917	0.829	1	CLONAL	1	TRUE	1	0.654507336135668	2		329	340	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186501428	186501428	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	98	232	0	ENST00000323963.5:c.29G>A	p.Arg10Lys	p.R10K	ENST00000323963		10	aGa/aAa	1/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.654507336135668	2		232	270	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920067	1920067	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1472983214	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	227	690	0	ENST00000382891.5:c.1127C>T	p.Ser376Phe	p.S376F	ENST00000382891	NM_133335.3	376	tCc/tTc	5/22	1	2	FACETS	0.909	0.85	0.97	0.909	0.85	0.97	CLONAL	1	TRUE	1	0.654507336135668	2		690	763	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2952994	2952995	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	168	572	4	ENST00000396946.4:c.2945_2946delinsTT	p.Thr982Ile	p.T982I	ENST00000396946	NM_032415.4	982	aCC/aTT	22/25	1	2	FACETS	0.933	0.863	1	0.933	0.863	1	CLONAL	1	TRUE	1	0.654507336135668	2		576	550	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388032	81388032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	169	595	1	ENST00000222390.5:c.343G>A	p.Glu115Lys	p.E115K	ENST00000222390	NM_000601.4	115	Gaa/Aaa	3/18	1	2	FACETS	0.989	0.916	1	0.989	0.916	1	CLONAL	1	TRUE	1	0.654507336135668	2		596	522	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380023	116380023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373312981	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	183	567	0	ENST00000397752.3:c.1412G>A	p.Gly471Glu	p.G471E	ENST00000397752	NM_000245.2	471	gGa/gAa	4/21	1	2	FACETS	0.911	0.845	0.979	0.911	0.845	0.979	CLONAL	1	TRUE	1	0.654507336135668	2		567	614	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891625	151891626	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	122	420	1	ENST00000262189.6:c.4406_4407delinsTT	p.Ser1469Phe	p.S1469F	ENST00000262189	NM_170606.2	1469	tCC/tTT	29/59	1	2	FACETS	0.946	0.863	1	0.946	0.863	1	CLONAL	1	TRUE	1	0.654507336135668	2		421	394	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285908	38285908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767034103	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	221	479	0	ENST00000425967.3:c.503C>T	p.Ser168Phe	p.S168F	ENST00000425967	NM_001174067.1	168	tCt/tTt	5/19	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.654507336135668	2		479	633	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69011975	69011975	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	279	811	1	ENST00000288368.4:c.2612A>T	p.Asn871Ile	p.N871I	ENST00000288368	NM_024870.2	871	aAt/aTt	23/40	1	2	FACETS	0.924	0.869	0.979	0.924	0.869	0.979	CLONAL	1	TRUE	1	0.654507336135668	2		812	923	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404651	8404651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	99	320	0	ENST00000356435.5:c.4096C>T	p.Pro1366Ser	p.P1366S	ENST00000356435		1366	Cct/Tct	25/35	0.654507336135668	1	FACETS	0.893	0.813	0.973	0.893	0.813	0.973	CLONAL	1	TRUE	0	0.654507336135668	1		320	228	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	163	428	1	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	0.654507336135668	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.654507336135668	1		429	313	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27203102	27203102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	221	597	0	ENST00000380036.4:c.2194C>T	p.Leu732Phe	p.L732F	ENST00000380036	NM_000459.3	732	Ctc/Ttc	13/23	0.654507336135668	1	FACETS	0.909	0.855	0.963	0.909	0.855	0.963	CLONAL	1	TRUE	0	0.654507336135668	1		597	500	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0017802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	57	306	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	0.6331875082938	2		307	135	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0017802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	575	738	1	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	0.6331875082938	4	FACETS	0.957	0.943	0.969	1	0.998	1	CLONAL	5	TRUE	0	0.6331875082938	4		739	620	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928067	178928067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	19	688	0	ENST00000263967.3:c.1345C>T	p.Pro449Ser	p.P449S	ENST00000263967	NM_006218.2	449	Cct/Tct	8/21	0.247747535475137	3	FACETS	0.395	0.301	0.505	0.198	0.15	0.253	INDETERMINATE	1	TRUE	1	0.6331875082938	3		688	200	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456875	149456875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs928018985	NA	P-0017802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	110	630	0	ENST00000286301.3:c.853G>A	p.Gly285Ser	p.G285S	ENST00000286301	NM_005211.3	285	Ggc/Agc	6/22	0.247747535475137	3	FACETS	0.915	0.838	0.993	0.915	0.838	0.993	INDETERMINATE	2	TRUE	1	0.6331875082938	3		630	250	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939688	76939689	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	63	791	0	ENST00000373344.5:c.1059dup	p.Lys354Ter	p.K354*	ENST00000373344	NM_000489.3	353	-/T	9/35	0.6331875082938	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.6331875082938	1		791	114	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	32	455	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.198577280638953	4	FACETS	0.459	0.371	0.559	0.23	0.185	0.28	SUBCLONAL	1	TRUE	2	0.257299520569109	4		455	681	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107125	27107125	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	47	426	0	ENST00000324856.7:c.6736G>T	p.Glu2246Ter	p.E2246*	ENST00000324856	NM_006015.4	2246	Gag/Tag	20/20	1	2	FACETS	0.794	0.671	0.93	0.794	0.671	0.93	CLONAL	1	TRUE	1	0.257299520569109	2		426	460	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602314	10602314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	126	725	1	ENST00000171111.5:c.1264G>A	p.Asp422Asn	p.D422N	ENST00000171111	NM_203500.1	422	Gat/Aat	3/6	0.196852285845735	2	FACETS	0.839	0.762	0.919	0.839	0.762	0.919	CLONAL	2	TRUE	0	0.257299520569109	2		726	584	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816265	89816265	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	37	514	0	ENST00000389301.3:c.3112C>G	p.Leu1038Val	p.L1038V	ENST00000389301	NM_000135.2	1038	Ctc/Gtc	32/43	1	2	FACETS	0.605	0.499	0.725	0.605	0.499	0.725	SUBCLONAL	1	TRUE	1	0.257299520569109	2		514	475	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489247	2489247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	35	583	2	ENST00000355716.4:c.152C>T	p.Ser51Phe	p.S51F	ENST00000355716	NM_003820.2	51	tCc/tTc	2/8	1	2	FACETS	0.504	0.412	0.607	0.504	0.412	0.607	SUBCLONAL	1	TRUE	1	0.257299520569109	2		585	540	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65311270	65311270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	58	503	0	ENST00000342505.4:c.2041C>T	p.Arg681Trp	p.R681W	ENST00000342505	NM_002227.2	681	Cgg/Tgg	15/25	1	2	FACETS	0.867	0.746	0.999	0.867	0.746	0.999	CLONAL	1	TRUE	1	0.257299520569109	2		503	520	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246195	46246195	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	72	491	0	ENST00000334344.6:c.4289G>T	p.Ser1430Ile	p.S1430I	ENST00000334344	NM_152641.2	1430	aGt/aTt	15/21	NA	2	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.257299520569109	2		491	412	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112614	115112614	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1312156913	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	115	895	0	ENST00000257566.3:c.1126G>T	p.Asp376Tyr	p.D376Y	ENST00000257566	NM_016569.3	376	Gac/Tac	7/8	0.18358303085425	2	FACETS	1	0.967	1	0.584	0.526	0.646	CLONAL	1	TRUE	0	0.257299520569109	2		895	765	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226301	133226302	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	80	698	2	ENST00000320574.5:c.3756_3757delinsTT	p.Gln1252_Glu1253delinsHisTer	p.Q1252_E1253delinsH*	ENST00000320574	NM_006231.2	1252	caGGaa/caTTaa	30/49	0.18358303085425	2	FACETS	1	0.881	1	0.5	0.44	0.564	CLONAL	1	TRUE	0	0.257299520569109	2		700	622	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041042	29041042	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	67	391	0	ENST00000282397.4:c.386G>C	p.Ser129Thr	p.S129T	ENST00000282397	NM_002019.4	129	aGt/aCt	3/30	0.202095666916518	2	FACETS	1	0.935	1	0.56	0.488	0.638	CLONAL	1	TRUE	0	0.257299520569109	2		391	465	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988858	41988858	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	72	583	1	ENST00000219905.7:c.1650G>T	p.Gln550His	p.Q550H	ENST00000219905	NM_001164273.1	550	caG/caT	3/24	1	2	FACETS	0.813	0.71	0.925	0.813	0.71	0.925	CLONAL	1	TRUE	1	0.257299520569109	2		584	688	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712503	43712503	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	61	639	0	ENST00000382044.4:c.4681G>T	p.Gly1561Ter	p.G1561*	ENST00000382044	NM_001141980.1	1561	Gga/Tga	21/28	1	2	FACETS	0.725	0.625	0.834	0.725	0.625	0.834	SUBCLONAL	1	TRUE	1	0.257299520569109	2		639	654	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467815	99467815	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	38	464	0	ENST00000268035.6:c.2684G>T	p.Arg895Leu	p.R895L	ENST00000268035	NM_000875.3	895	cGg/cTg	13/21	1	2	FACETS	0.698	0.578	0.833	0.698	0.578	0.833	SUBCLONAL	1	TRUE	1	0.257299520569109	2		464	423	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89851353	89851353	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	41	553	0	ENST00000389301.3:c.1379G>C	p.Arg460Pro	p.R460P	ENST00000389301	NM_000135.2	460	cGa/cCa	15/43	1	2	FACETS	0.653	0.544	0.775	0.653	0.544	0.775	SUBCLONAL	1	TRUE	1	0.257299520569109	2		553	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs878854073	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	113	491	0	ENST00000269305.4:c.673-1G>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.202095666916518	2	FACETS	0.969	0.878	1	0.969	0.878	1	CLONAL	2	TRUE	0	0.257299520569109	2		491	453	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110638	8110638	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	172	706	0	ENST00000585124.1:c.254A>C	p.Lys85Thr	p.K85T	ENST00000585124	NM_004217.3	85	aAa/aCa	5/9	0.202095666916518	2	FACETS	0.931	0.859	1	0.931	0.859	1	CLONAL	2	TRUE	0	0.257299520569109	2		706	718	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428017	33428017	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	133	668	0	ENST00000345365.6:c.942G>T	p.Trp314Cys	p.W314C	ENST00000345365	NM_002878.3	314	tgG/tgT	10/10	0.202095666916518	2	FACETS	0.894	0.815	0.977	0.894	0.815	0.977	CLONAL	2	TRUE	0	0.257299520569109	2		668	578	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619355	37619355	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	17	263	0	ENST00000447079.4:c.1031G>A	p.Arg344Gln	p.R344Q	ENST00000447079	NM_015083.1	344	cGg/cAg	1/14	0.257299520569109	3	FACETS	0.507	0.378	0.661	0.254	0.189	0.331	SUBCLONAL	1	TRUE	1	0.257299520569109	3		263	294	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37876086	37876086	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	54	525	0	ENST00000269571.5:c.1945A>T	p.Ser649Cys	p.S649C	ENST00000269571		649	Agc/Tgc	16/27	0.257299520569109	3	FACETS	0.866	0.74	1	0.433	0.37	0.502	CLONAL	1	TRUE	1	0.257299520569109	3		525	547	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223064	41223064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	65	675	0	ENST00000357654.3:c.4867G>A	p.Ala1623Thr	p.A1623T	ENST00000357654	NM_007294.3	1623	Gct/Act	15/23	0.257299520569109	3	FACETS	0.842	0.73	0.965	0.421	0.365	0.483	CLONAL	1	TRUE	1	0.257299520569109	3		675	677	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119951	70119951	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	40	371	1	ENST00000245479.2:c.953G>A	p.Ser318Asn	p.S318N	ENST00000245479	NM_000346.3	318	aGc/aAc	3/3	0.257299520569109	3	FACETS	1	0.84	1	0.504	0.42	0.597	CLONAL	1	TRUE	1	0.257299520569109	3		372	348	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745968	745968	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	35	635	0	ENST00000314574.4:c.554G>C	p.Arg185Thr	p.R185T	ENST00000314574	NM_005433.3	185	aGa/aCa	5/12	0.196852285845735	2	FACETS	0.409	0.334	0.494	0.205	0.167	0.247	SUBCLONAL	1	TRUE	0	0.257299520569109	2		635	665	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267515	7267515	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	89	613	0	ENST00000302850.5:c.493G>T	p.Asp165Tyr	p.D165Y	ENST00000302850	NM_000208.2	165	Gat/Tat	2/22	0.196852285845735	2	FACETS	1	0.97	1	0.636	0.565	0.711	CLONAL	1	TRUE	0	0.257299520569109	2		613	544	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61709627	61709627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	70	272	1	ENST00000401558.2:c.2860G>A	p.Glu954Lys	p.E954K	ENST00000401558	NM_003400.3	954	Gaa/Aaa	23/25	0.257299520569109	3	FACETS	1	0.971	1	0.711	0.622	0.806	CLONAL	1	TRUE	1	0.257299520569109	3		273	432	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543816	212543816	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	38	593	0	ENST00000342788.4:c.1583G>C	p.Arg528Thr	p.R528T	ENST00000342788	NM_005235.2	528	aGa/aCa	13/28	0.257299520569109	3	FACETS	0.557	0.459	0.666	0.278	0.229	0.333	SUBCLONAL	1	TRUE	1	0.257299520569109	3		593	599	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812225	212812225	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	115	461	0	ENST00000342788.4:c.351G>T	p.Leu117Phe	p.L117F	ENST00000342788	NM_005235.2	117	ttG/ttT	3/28	0.257299520569109	3	FACETS	0.844	0.762	0.929	0.844	0.762	0.929	CLONAL	2	TRUE	1	0.257299520569109	3		461	598	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205808	128205808	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760183425	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	92	422	0	ENST00000341105.2:c.67G>A	p.Asp23Asn	p.D23N	ENST00000341105	NM_032638.4	23	Gac/Aac	2/6	0.24606704994095	3	FACETS	0.893	0.797	0.994			1	CLONAL	2	TRUE	NA	0.257299520569109	3		422	452	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665443	138665443	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	108	588	1	ENST00000330315.3:c.122G>A	p.Gly41Asp	p.G41D	ENST00000330315	NM_023067.3	41	gGc/gAc	1/1	0.257299520569109	5	FACETS	0.871	0.783	0.964	0.581	0.522	0.643	CLONAL	2	TRUE	2	0.257299520569109	5		589	668	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275300	142275300	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	112	718	0	ENST00000350721.4:c.2003G>T	p.Arg668Leu	p.R668L	ENST00000350721	NM_001184.3	668	cGg/cTg	9/47	0.257299520569109	5	FACETS	1	0.973	1	0.418	0.375	0.464	CLONAL	1	TRUE	2	0.257299520569109	5		718	962	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138597	55138597	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs769631321	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	107	538	0	ENST00000257290.5:c.1274A>G	p.His425Arg	p.H425R	ENST00000257290	NM_006206.4	425	cAt/cGt	9/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.257299520569109	2		538	596	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197721	66197721	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	61	582	1	ENST00000273854.3:c.2978C>A	p.Ser993Ter	p.S993*	ENST00000273854	NM_004439.5	993	tCa/tAa	17/18	1	2	FACETS	0.718	0.619	0.827	0.718	0.619	0.827	SUBCLONAL	1	TRUE	1	0.257299520569109	2		583	660	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230786	66230786	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	64	491	0	ENST00000273854.3:c.2185G>T	p.Gly729Ter	p.G729*	ENST00000273854	NM_004439.5	729	Gga/Tga	12/18	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.257299520569109	2		491	457	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629148	187629148	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	66	574	0	ENST00000441802.2:c.1834C>A	p.Leu612Met	p.L612M	ENST00000441802	NM_005245.3	612	Ctg/Atg	2/27	1	2	FACETS	0.919	0.799	1	0.919	0.799	1	CLONAL	1	TRUE	1	0.257299520569109	2		574	558	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293662	1293662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	166	713	0	ENST00000310581.5:c.1339C>A	p.Arg447Ser	p.R447S	ENST00000310581	NM_198253.2	447	Cgc/Agc	2/16	0.257299520569109	5	FACETS	1	0.966	1	0.547	0.503	0.593	CLONAL	2	TRUE	1	0.257299520569109	5		713	817	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294247	1294247	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	75	666	0	ENST00000310581.5:c.754G>T	p.Gly252Trp	p.G252W	ENST00000310581	NM_198253.2	252	Ggg/Tgg	2/16	0.257299520569109	5	FACETS	1	0.918	1	0.266	0.232	0.302	CLONAL	1	TRUE	1	0.257299520569109	5		666	760	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169276	32169276	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	88	455	2	ENST00000375023.3:c.3757C>A	p.Pro1253Thr	p.P1253T	ENST00000375023	NM_004557.3	1253	Cca/Aca	22/30	0.196852285845735	2	FACETS	0.781	0.695	0.871	0.781	0.695	0.871	SUBCLONAL	2	TRUE	0	0.257299520569109	2		457	438	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652073	36652073	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	85	672	0	ENST00000244741.5:c.195G>T	p.Trp65Cys	p.W65C	ENST00000244741	NM_000389.4	65	tgG/tgT	2/3	0.198577280638953	4	FACETS	1	0.963	1	0.611	0.54	0.687	CLONAL	1	TRUE	2	0.257299520569109	4		672	680	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157406022	157406022	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	33	438	0	ENST00000346085.5:c.2264C>G	p.Ser755Cys	p.S755C	ENST00000346085	NM_020732.3	755	tCt/tGt	6/20	0.196852285845735	2	FACETS	0.604	0.491	0.73	0.302	0.245	0.365	SUBCLONAL	1	TRUE	0	0.257299520569109	2		438	425	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978465	2978465	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	88	499	0	ENST00000396946.4:c.865G>T	p.Ala289Ser	p.A289S	ENST00000396946	NM_032415.4	289	Gcc/Tcc	7/25	1	2	FACETS	0.832	0.742	0.928	1	0.983	1	CLONAL	2	TRUE	1	0.257299520569109	2		499	411	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274884	38274884	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	38	753	0	ENST00000425967.3:c.1696A>G	p.Met566Val	p.M566V	ENST00000425967	NM_001174067.1	566	Atg/Gtg	13/19	1	2	FACETS	0.468	0.386	0.56	0.468	0.386	0.56	SUBCLONAL	1	TRUE	1	0.257299520569109	2		753	631	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528774	8528774	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	45	293	1	ENST00000356435.5:c.358C>A	p.Gln120Lys	p.Q120K	ENST00000356435		120	Caa/Aaa	4/35	0.257299520569109	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	0	0.257299520569109	1		294	276	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409494	80409494	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	115	624	0	ENST00000286548.4:c.620G>T	p.Gly207Val	p.G207V	ENST00000286548	NM_002072.3	207	gGg/gTg	5/7	0.196852285845735	2	FACETS	0.765	0.691	0.843	0.765	0.691	0.843	SUBCLONAL	2	TRUE	0	0.257299520569109	2		624	584	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570404	87570404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	110	695	1	ENST00000277120.3:c.2144G>A	p.Arg715Gln	p.R715Q	ENST00000277120		715	cGg/cAg	17/19	0.196852285845735	2	FACETS	1	0.982	1	0.714	0.643	0.788	CLONAL	1	TRUE	0	0.257299520569109	2		696	599	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249348	110249348	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	188	999	0	ENST00000374672.4:c.1225A>G	p.Lys409Glu	p.K409E	ENST00000374672	NM_004235.4	409	Aag/Gag	4/5	0.196852285845735	2	FACETS	0.758	0.7	0.818	0.758	0.7	0.818	SUBCLONAL	2	TRUE	0	0.257299520569109	2		999	964	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399240	139399240	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	97	599	0	ENST00000277541.6:c.4903G>T	p.Ala1635Ser	p.A1635S	ENST00000277541	NM_017617.3	1635	Gcc/Tcc	26/34	0.196852285845735	2	FACETS	0.794	0.711	0.881	0.794	0.711	0.881	SUBCLONAL	2	TRUE	0	0.257299520569109	2		599	475	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314991	1314991	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs764756019	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	63	629	0	ENST00000400841.2:c.670C>G	p.Pro224Ala	p.P224A	ENST00000400841		224	Cct/Gct	6/6	1	1	FACETS	0.692	0.598	0.793	0.692	0.598	0.793	SUBCLONAL	1	TRUE	0	0.257299520569109	1		629	617	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044937	47044937	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	124	437	0	ENST00000377604.3:c.2263G>T	p.Asp755Tyr	p.D755Y	ENST00000377604	NM_001204468.1	755	Gac/Tac	20/24	1	1	FACETS	1	0.963	1	1	0.991	1	CLONAL	2	TRUE	0	0.257299520569109	1		437	382	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611800	100611800	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	66	280	0	ENST00000308731.7:c.1321G>A	p.Glu441Lys	p.E441K	ENST00000308731	NM_000061.2	441	Gaa/Aaa	14/19	1	1	FACETS	0.771	0.675	0.872	1	0.975	1	SUBCLONAL	2	TRUE	0	0.257299520569109	1		280	290	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871724	35871724	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1213	169	512	0	ENST00000216797.5:c.782C>G	p.Pro261Arg	p.P261R	ENST00000216797	NM_020529.2	261	cCa/cGa	5/6	0.277105395817274	17	FACETS	0.906	0.83	0.985			1	CLONAL	3	TRUE	NA	0.277105395817274	17		512	1382	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114674	73114674	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	31	572	0	ENST00000356692.5:c.1055C>G	p.Ser352Cys	p.S352C	ENST00000356692		352	tCt/tGt	9/9	1	2	FACETS	0.448	0.362	0.547	0.448	0.362	0.547	SUBCLONAL	1	TRUE	1	0.277105395817274	2		572	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0017806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	235	710	5	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.584604881144122	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.584604881144122	2		715	385	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0017806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	82	550	1	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.82	0.729	0.916	0.82	0.729	0.916	CLONAL	1	TRUE	1	0.584604881144122	2		551	342	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46725680	46725680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145938974	NA	P-0017806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	127	566	0	ENST00000371975.4:c.316C>T	p.Arg106Cys	p.R106C	ENST00000371975	NM_003579.3	106	Cgc/Tgc	5/18	1	2	FACETS	0.89	0.811	0.972	0.89	0.811	0.972	CLONAL	1	TRUE	1	0.584604881144122	2		566	488	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996856	100996863	+	frameshift_variant	Frame_Shift_Del	DEL	GTATTGTG	GTATTGTG	-	novel	NA	P-0017806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	739	658	0	ENST00000325455.5:c.1664_1671del	p.Pro555GlnfsTer16	p.P555Qfs*16	ENST00000325455	NM_001202474.3	555	cCACAATAC/c	2/8	0.584604881144122	7	FACETS	1	0.989	1			1	CLONAL	6	TRUE	NA	0.584604881144122	7		658	1017	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42384779	42384779	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555844085	NA	P-0017806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	105	522	0	ENST00000221972.3:c.541G>A	p.Glu181Lys	p.E181K	ENST00000221972	NM_021601.3	181	Gaa/Aaa	4/5	1	2	FACETS	0.828	0.746	0.913	0.828	0.746	0.913	CLONAL	1	TRUE	1	0.584604881144122	2		522	434	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262421	39262421	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	123	815	0	ENST00000402219.2:c.1006C>T	p.Gln336Ter	p.Q336*	ENST00000402219	NM_005633.3	336	Caa/Taa	8/23	0.584604881144122	3	FACETS	0.855	0.775	0.939	0.428	0.387	0.47	CLONAL	1	TRUE	1	0.584604881144122	3		815	636	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589585	67589586	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATGAATATAACACTCAGT	novel	NA	P-0017806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	176	449	0	ENST00000274335.5:c.1349_1366dup	p.Gln455_Phe456insTyrGluTyrAsnThrGln	p.Q455_F456insYEYNTQ	ENST00000274335		450	cat/cATGAATATAACACTCAGTat	10/15	0.580916996228783	3	FACETS	0.888	0.827	0.95	0.592	0.551	0.634	CLONAL	2	TRUE	0	0.584604881144122	3		449	438	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845312	76845312	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	82	515	0	ENST00000373344.5:c.6209T>C	p.Ile2070Thr	p.I2070T	ENST00000373344	NM_000489.3	2070	aTt/aCt	27/35	0.584604881144122	1	FACETS	0.534	0.474	0.597	0.534	0.474	0.597	SUBCLONAL	1	TRUE	0	0.584604881144122	1		515	372	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918979	76918979	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	28	485	1	ENST00000373344.5:c.4012C>T	p.His1338Tyr	p.H1338Y	ENST00000373344	NM_000489.3	1338	Cat/Tat	12/35	0.584604881144122	1	FACETS	0.207	0.166	0.255	0.207	0.166	0.255	SUBCLONAL	1	TRUE	0	0.584604881144122	1		486	327	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0017807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	103	833	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.876	0.792	0.964	1	0.987	1	CLONAL	2	FALSE	1	0.327344981407522	2		833	359	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0017807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	105	478	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	0.0593084755630733	3	FACETS	0.838	0.761	0.917	1	0.977	1	INDETERMINATE	3	FALSE	1	0.327344981407522	3		478	297	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0017807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	46	553	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.302820736472587	0	FACETS	0.722	0.623	0.825			1	SUBCLONAL	2	FALSE	0	0.327344981407522	0		553	131	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	53	296	0	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	0.0593084755630733	3	FACETS	1	0.927	1	1	0.982	1	INDETERMINATE	4	FALSE	1	0.327344981407522	3		296	90	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200960	108200960	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121434220	NA	P-0017807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	62	365	1	ENST00000278616.4:c.7327C>T	p.Arg2443Ter	p.R2443*	ENST00000278616	NM_000051.3	2443	Cga/Tga	50/63	0.327344981407522	0	FACETS	0.917	0.815	1			1	CLONAL	2	FALSE	0	0.327344981407522	0		366	139	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248312	59248313	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0017807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	18	73	0	ENST00000371222.2:c.430dup	p.Ala144GlyfsTer166	p.A144Gfs*166	ENST00000371222	NM_002228.3	144	gct/gGct	1/1	0.327344981407522	3	FACETS	1	0.866	1	1	0.866	1	CLONAL	2	FALSE	1	0.327344981407522	3		73	55	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180886	108180886	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0017807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	20	240	0	ENST00000278616.4:c.5763-1G>C		p.X1921_splice	ENST00000278616	NM_000051.3	1921			0.327344981407522	0	FACETS	0.913	0.713	1			1	CLONAL	1	FALSE	0	0.327344981407522	0		240	90	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119786	70119787	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGA	novel	NA	P-0017807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	186	584	0	ENST00000245479.2:c.792_795dup	p.Pro266ThrfsTer31	p.P266Tfs*31	ENST00000245479	NM_000346.3	263	ggc/ggCAGAc	3/3	0.101102796326174	4	FACETS	1	0.937	1	1	0.991	1	INDETERMINATE	3	FALSE	2	0.327344981407522	4		584	500	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660111	12660111	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	31	488	0	ENST00000251849.4:c.110G>C	p.Gly37Ala	p.G37A	ENST00000251849	NM_002880.3	37	gGc/gCc	2/17	0.125057803082663	3	FACETS	0.58	0.469	0.705	0.29	0.234	0.353	INDETERMINATE	1	FALSE	1	0.327344981407522	3		488	380	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016565	12016565	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	78	331	0	ENST00000353533.5:c.701A>T	p.Asn234Ile	p.N234I	ENST00000353533	NM_003010.3	234	aAt/aTt	7/11	0.245562792585049	1	FACETS	0.799	0.702	0.902	0.799	0.702	0.902	CLONAL	1	TRUE	0	0.268438038569771	1		331	630	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696430	47696430	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519970	NA	P-0017810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	116	725	0	ENST00000347630.2:c.393G>T	p.Trp131Cys	p.W131C	ENST00000347630	NM_001007230.1	131	tgG/tgT	6/11	1	2	FACETS	0.99	0.892	1	0.99	0.892	1	CLONAL	1	TRUE	1	0.26	2		725	901	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755554	39755554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs919467999	NA	P-0017810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	140	478	0	ENST00000288319.7:c.1211C>T	p.Pro404Leu	p.P404L	ENST00000288319	NM_182918.3	404	cCg/cTg	10/10	1	2	FACETS	0.811	0.74	0.885	1	0.988	1	CLONAL	2	TRUE	1	0.26	2		478	664	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916929	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519931	NA	P-0017811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	123	482	0	ENST00000263967.3:c.316G>C	p.Gly106Arg	p.G106R	ENST00000263967	NM_006218.2	106	Ggc/Cgc	2/21	1	2	FACETS	0.462	0.419	0.507	0.462	0.419	0.507	SUBCLONAL	1	TRUE	1	0.871282311241017	2		482	611	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0017811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	110	292	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	0.471	0.425	0.52	0.471	0.425	0.52	SUBCLONAL	1	TRUE	1	0.871282311241017	2		292	536	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913517	NA	P-0017811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	435	513	0	ENST00000288135.5:c.1676T>C	p.Val559Ala	p.V559A	ENST00000288135	NM_000222.2	559	gTt/gCt	11/21	0.869859202813906	2	FACETS	0.991	0.969	1	0.991	0.969	1	CLONAL	2	TRUE	0	0.871282311241017	2		513	504	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944387	131944388	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AATACAAGCAACAAAATAGCACAGGATAAAGTAAGATTTCATTTATATATTTACTTATC	novel	NA	P-0017811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	40	558	0	ENST00000265335.6:c.2802_2829+31dup		p.-933fs	ENST00000265335		933	-/AATACAAGCAACAAAATAGCACAGGATAAAGTAAGATTTCATTTATATATTTACTTATC	17/25	1	2	FACETS	0.118	0.097	0.141	0.118	0.097	0.141	SUBCLONAL	1	TRUE	1	0.871282311241017	2		558	781	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851285	156851285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778520978	NA	P-0017813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	210	520	0	ENST00000524377.1:c.2242C>T	p.Arg748Trp	p.R748W	ENST00000524377	NM_002529.3	748	Cgg/Tgg	17/17	0.599099272565585	4	FACETS	1	0.974	1	0.366	0.34	0.394	CLONAL	1	TRUE	1	0.638965504225418	4		520	980	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606304	93606304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	221	603	0	ENST00000375746.1:c.124C>T	p.Arg42Cys	p.R42C	ENST00000375746	NM_001174167.1	42	Cgc/Tgc	2/14	0.638965504225418	3	FACETS	1	0.986	1	0.607	0.567	0.648	CLONAL	1	TRUE	1	0.638965504225418	3		603	752	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862107	68862107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501244	NA	P-0017813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	169	467	0	ENST00000261769.5:c.2195G>A	p.Arg732Gln	p.R732Q	ENST00000261769	NM_004360.3	732	cGg/cAg	14/16	0.638965504225418	1	FACETS	0.945	0.881	1	0.945	0.881	1	CLONAL	1	TRUE	0	0.638965504225418	1		467	381	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061797	38061797	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	328	748	0	ENST00000250448.2:c.192C>G	p.Phe64Leu	p.F64L	ENST00000250448	NM_004496.3	64	ttC/ttG	2/2	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.638965504225418	2		748	904	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0017814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	164	569	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	0.238440345684982	4	FACETS	0.859	0.789	0.931	0.859	0.789	0.931	CLONAL	2	TRUE	2	0.32	4		569	788	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692901	89692901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786204929	NA	P-0017814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	19	433	0	ENST00000371953.3:c.385G>A	p.Gly129Arg	p.G129R	ENST00000371953	NM_000314.4	129	Gga/Aga	5/9	0.271875973116642	3	FACETS	0.208	0.157	0.269	0.104	0.078	0.135	SUBCLONAL	1	TRUE	1	0.32	3		433	661	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203492	108203492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs138941496	NA	P-0017814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	76	226	0	ENST00000278616.4:c.7792C>T	p.Arg2598Ter	p.R2598*	ENST00000278616	NM_000051.3	2598	Cga/Tga	53/63	0.246527527925722	2	FACETS	0.816	0.723	0.914	0.816	0.723	0.914	CLONAL	2	TRUE	0	0.32	2		226	291	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059239	27059239	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	155	445	0	ENST00000324856.7:c.1876G>T	p.Glu626Ter	p.E626*	ENST00000324856	NM_006015.4	626	Gaa/Taa	4/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.32	2		445	724	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120747	115120747	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	93	510	0	ENST00000257566.3:c.259C>G	p.Leu87Val	p.L87V	ENST00000257566	NM_016569.3	87	Ctg/Gtg	1/8	0.291457474995986	3	FACETS	0.667	0.592	0.748	0.333	0.296	0.374	SUBCLONAL	1	TRUE	1	0.32	3		510	1011	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380955	116380955	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	87	489	2	ENST00000397752.3:c.1577G>T	p.Cys526Phe	p.C526F	ENST00000397752	NM_000245.2	526	tGc/tTc	5/21	0.291457474995986	3	FACETS	0.714	0.631	0.803	0.357	0.315	0.402	SUBCLONAL	1	TRUE	1	0.32	3		491	884	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057520007	NA	P-0017815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	669	678	1	ENST00000269305.4:c.614A>C	p.Tyr205Ser	p.Y205S	ENST00000269305	NM_001126112.2	205	tAt/tCt	6/11	0.7380225778935	3	FACETS	0.946	0.925	0.966	0.946	0.925	0.966	CLONAL	3	TRUE	0	0.767385668225245	3		679	850	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148883	119148883	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	193	306	0	ENST00000264033.4:c.1103A>G	p.Tyr368Cys	p.Y368C	ENST00000264033	NM_005188.3	368	tAt/tGt	8/16	0.767385668225245	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.767385668225245	1		306	288	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661986	29661990	+	frameshift_variant	Frame_Shift_Del	DEL	GACCA	GACCA	-	novel	NA	P-0017815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	552	487	1	ENST00000356175.3:c.5880_5884del	p.Met1960IlefsTer3	p.M1960Ifs*3	ENST00000356175	NM_000267.3	1960	atGACCAtc/attc	39/57	0.767385668225245	3	FACETS	0.958	0.935	0.979	1	0.998	1	CLONAL	3	TRUE	1	0.767385668225245	3		488	693	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223633	55223633	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	335	384	3	ENST00000275493.2:c.1000C>T	p.Arg334Cys	p.R334C	ENST00000275493	NM_005228.3	334	Cgc/Tgc	8/28	0.673046518463047	4	FACETS	0.992	0.943	1	0.992	0.943	1	CLONAL	2	TRUE	2	0.767385668225245	4		387	778	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909668	76909668	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	437	407	1	ENST00000373344.5:c.4237G>T	p.Glu1413Ter	p.E1413*	ENST00000373344	NM_000489.3	1413	Gaa/Taa	14/35	0.289530883712197	5	FACETS	0.963	0.932	0.993			1	INDETERMINATE	4	TRUE	NA	0.767385668225245	5		408	636	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0017817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1598	408	668	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.647994652486833	8	FACETS	0.924	0.876	0.973	0.308	0.292	0.325	CLONAL	2	TRUE	2	0.647994652486833	8		668	2006	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190321	32190321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1033015617	NA	P-0017817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	137	455	0	ENST00000375023.3:c.418C>T	p.Arg140Cys	p.R140C	ENST00000375023	NM_004557.3	140	Cgc/Tgc	3/30	0.353685448294778	3	FACETS	0.907	0.828	0.99			1	INDETERMINATE	1	TRUE	NA	0.647994652486833	3		455	617	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798111	45798111	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777335285	NA	P-0017817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	234	605	1	ENST00000450313.1:c.740G>A	p.Arg247Gln	p.R247Q	ENST00000450313	NM_012222.2	247	cGa/cAa	9/16	0.646261709952632	3	FACETS	1	0.938	1	0.502	0.469	0.537	CLONAL	1	TRUE	1	0.647994652486833	3		606	952	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624530	21624530	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	175	922	0	ENST00000421138.2:c.1499T>C	p.Leu500Pro	p.L500P	ENST00000421138		500	cTg/cCg	14/16	0.494241474213057	5	FACETS	1	0.947	1			1	CLONAL	1	TRUE	NA	0.647994652486833	5		922	1027	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110566	4110566	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	359	553	1	ENST00000262948.5:c.391G>T	p.Val131Leu	p.V131L	ENST00000262948	NM_030662.3	131	Gtg/Ttg	3/11	0.595371149395318	3	FACETS	0.809	0.769	0.848	0.809	0.769	0.848	CLONAL	2	TRUE	1	0.647994652486833	3		554	907	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0017818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	71	475	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.205	0.178	0.234	0.205	0.178	0.234	SUBCLONAL	1	TRUE	1	0.726377528199203	2		475	955	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0017818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	184	455	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.571	0.527	0.616	0.571	0.527	0.616	SUBCLONAL	1	TRUE	1	0.726377528199203	2		455	888	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952088	178952088	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553826184	NA	P-0017818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	84	433	0	ENST00000263967.3:c.3143A>G	p.His1048Arg	p.H1048R	ENST00000263967	NM_006218.2	1048	cAt/cGt	21/21	1	2	FACETS	0.283	0.249	0.319	0.283	0.249	0.319	SUBCLONAL	1	TRUE	1	0.726377528199203	2		433	817	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339629	70339629	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	220	640	1	ENST00000374080.3:c.298G>A	p.Asp100Asn	p.D100N	ENST00000374080		100	Gat/Aat	3/45	1	2	FACETS	0.57	0.53	0.612	0.57	0.53	0.612	SUBCLONAL	1	TRUE	1	0.726377528199203	2		641	1062	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593597	55593611	+	inframe_deletion	In_Frame_Del	DEL	GTACAGTGGAAGGTT	GTACAGTGGAAGGTT	-	novel	NA	P-0017819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	227	477	0	ENST00000288135.5:c.1665_1679del	p.Gln556_Val560del	p.Q556_V560del	ENST00000288135	NM_000222.2	555	GTACAGTGGAAGGTT/-	11/21	1	2	FACETS	0.784	0.733	0.837	0.784	0.733	0.837	SUBCLONAL	1	TRUE	1	0.748683449829712	2		477	773	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0017820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	227	523	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.877	0.821	0.933	0.877	0.821	0.933	CLONAL	1	TRUE	1	0.77077343187781	2		523	672	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	288	499	0	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	1	2	FACETS	0.985	0.931	1	0.985	0.931	1	CLONAL	1	TRUE	1	0.77077343187781	2		499	759	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	167	184	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.757	0.7	0.815	0.757	0.7	0.815	SUBCLONAL	1	TRUE	1	0.818801700574541	2		184	539	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807889	1807889	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs78311289	NA	P-0017821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	239	836	0	ENST00000260795.2:c.1948A>G	p.Lys650Glu	p.K650E	ENST00000260795		650	Aag/Gag	13/17	NA	2	FACETS	0.816	0.766	0.868			1	INDETERMINATE	1	TRUE	NA	0.818801700574541	2		836	715	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717624	89717624	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	184	489	0	ENST00000371953.3:c.649G>T	p.Val217Phe	p.V217F	ENST00000371953	NM_000314.4	217	Gtc/Ttc	7/9	0.818801700574541	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.818801700574541	1		489	245	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77085390	77085390	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	266	653	0	ENST00000356341.3:c.460A>G	p.Asn154Asp	p.N154D	ENST00000356341	NM_002576.4	154	Aat/Gat	5/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.818801700574541	2		653	620	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562589	21562589	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	105	323	0	ENST00000382592.4:c.1330G>T	p.Val444Leu	p.V444L	ENST00000382592	NM_014572.2	444	Gtg/Ttg	4/8	1	2	FACETS	0.909	0.827	0.994	0.909	0.827	0.994	CLONAL	1	TRUE	1	0.818801700574541	2		323	282	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480529	123480529	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	16	298	0	ENST00000371139.4:c.37A>T	p.Arg13Trp	p.R13W	ENST00000371139	NM_001114937.2	13	Agg/Tgg	1/4	1	1	FACETS	0.08	0.059	0.106	0.08	0.059	0.106	SUBCLONAL	1	TRUE	0	0.818801700574541	1		298	288	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562657	29562660	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs1064794276	NA	P-0017822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	35	517	0	ENST00000356175.3:c.3739_3742del	p.Phe1247IlefsTer18	p.F1247Ifs*18	ENST00000356175	NM_000267.3	1246	cTGTTt/ct	28/57	0.471320658078399	1	FACETS	0.201	0.164	0.243	0.201	0.164	0.243	SUBCLONAL	1	TRUE	0	0.471320658078399	1		517	564	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376715	31376715	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs964977606	NA	P-0017822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	97	339	0	ENST00000328111.2:c.710C>T	p.Ser237Phe	p.S237F	ENST00000328111	NM_006892.3	237	tCc/tTc	7/23	1	2	FACETS	0.953	0.855	1	0.953	0.855	1	CLONAL	1	TRUE	1	0.471320658078399	2		339	432	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663934	29663934	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0017822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	23	282	0	ENST00000356175.3:c.6364+2T>A		p.X2122_splice	ENST00000356175	NM_000267.3	2122			0.471320658078399	0	FACETS	0.225	0.176	0.282			1	SUBCLONAL	1	TRUE	0	0.471320658078399	0		282	229	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188263	10188263	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs397516442	NA	P-0017823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	213	717	0	ENST00000256474.2:c.408del	p.Phe136LeufsTer23	p.F136Lfs*23	ENST00000256474	NM_000551.3	136	Ttt/tt	2/3	0.3	0	FACETS	0.689	0.644	0.734			1	INDETERMINATE	1	TRUE	0	0.51	0		717	594	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322637	39322637	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	119	720	0	ENST00000373001.3:c.355G>C	p.Gly119Arg	p.G119R	ENST00000373001	NM_022157.3	119	Ggg/Cgg	2/7	0.220139167951382	1	FACETS	0.493	0.445	0.543	0.493	0.445	0.543	INDETERMINATE	1	TRUE	0	0.51	1		720	705	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695815	117695815	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1443124633	NA	P-0017823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	65	487	0	ENST00000369458.3:c.622A>G	p.Met208Val	p.M208V	ENST00000369458	NM_024626.3	208	Atg/Gtg	4/6	1	2	FACETS	0.434	0.376	0.497	0.434	0.376	0.497	SUBCLONAL	1	TRUE	1	0.51	2		487	587	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0017824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	120	523	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.775	0.703	0.851	0.775	0.703	0.851	SUBCLONAL	1	TRUE	1	0.580862576985091	2		523	533	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845764	68845764	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0017824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	96	338	0	ENST00000261769.5:c.1008+2T>G		p.X336_splice	ENST00000261769	NM_004360.3	336			0.508981205455798	1	FACETS	0.702	0.632	0.775	0.702	0.632	0.775	SUBCLONAL	1	TRUE	0	0.580862576985091	1		338	334	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821403	32821403	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	169	681	0	ENST00000354258.4:c.191C>G	p.Ser64Cys	p.S64C	ENST00000354258	NM_000593.5	64	tCt/tGt	1/11	1	2	FACETS	0.786	0.724	0.851	0.786	0.724	0.851	SUBCLONAL	1	TRUE	1	0.580862576985091	2		681	740	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577567	7577568	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs1555525539	NA	P-0017826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	515	549	0	ENST00000269305.4:c.713_714del	p.Cys238Ter	p.C238*	ENST00000269305	NM_001126112.2	238	tGT/t	7/11	NA	2	FACETS	0.949	0.925	0.973			1	INDETERMINATE	2	TRUE	NA	0.809696862192863	2		549	670	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0017827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	267	642	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.581445234820718	3	FACETS	0.882	0.833	0.932	0.882	0.833	0.932	CLONAL	2	FALSE	1	0.581257105129466	3		642	672	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332868	152332868	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745723014	NA	P-0017827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	378	318	0	ENST00000206249.3:c.1174G>A	p.Val392Ile	p.V392I	ENST00000206249	NM_000125.3	392	Gtc/Atc	5/8	0.581445234820718	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	FALSE	1	0.581257105129466	4		318	655	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0017827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	447	958	2	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.581257105129466	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	FALSE	0	0.581257105129466	2		960	746	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0017827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	232	448	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	0.581445234820718	3	FACETS	0.89	0.836	0.944	0.89	0.836	0.944	CLONAL	2	FALSE	1	0.581257105129466	3		448	579	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553470	29553470	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	147	601	2	ENST00000356175.3:c.2019C>A	p.Cys673Ter	p.C673*	ENST00000356175	NM_000267.3	673	tgC/tgA	18/57	0.581445234820718	4	FACETS	0.722	0.658	0.789	0.361	0.329	0.395	SUBCLONAL	1	FALSE	2	0.581257105129466	4		603	1108	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591977	48591977	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0017827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	187	290	0	ENST00000342988.3:c.1139+1G>T		p.X380_splice	ENST00000342988	NM_005359.5	380			0.581257105129466	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	FALSE	0	0.581257105129466	2		290	319	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276650	15276650	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	327	585	0	ENST00000263388.2:c.5615G>C	p.Gly1872Ala	p.G1872A	ENST00000263388	NM_000435.2	1872	gGc/gCc	30/33	0.581445234820718	3	FACETS	0.939	0.893	0.986	0.939	0.893	0.986	CLONAL	2	FALSE	1	0.581257105129466	3		585	773	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15378304	15378305	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	321	558	0	ENST00000263377.2:c.481dup	p.Ile161AsnfsTer3	p.I161Nfs*3	ENST00000263377	NM_058243.2	161	ata/aAta	4/20	0.581445234820718	3	FACETS	0.894	0.849	0.94	0.894	0.849	0.94	CLONAL	2	FALSE	1	0.581257105129466	3		558	797	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61761029	61761029	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	30	292	0	ENST00000401558.2:c.4C>T	p.Pro2Ser	p.P2S	ENST00000401558	NM_003400.3	2	Cca/Tca	2/25	0.581445234820718	4	FACETS	0.283	0.227	0.347	0.142	0.113	0.174	SUBCLONAL	1	FALSE	2	0.581257105129466	4		292	576	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409192	31409192	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	129	609	0	ENST00000344624.3:c.3825A>T	p.Glu1275Asp	p.E1275D	ENST00000344624		1275	gaA/gaT	30/33	0.581445234820718	3	FACETS	0.676	0.613	0.743	0.338	0.306	0.372	SUBCLONAL	1	FALSE	1	0.581257105129466	3		609	847	SUCCESS
APC	324	MSKCC	GRCh37	5	112175455	112175456	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0017827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	87	324	2	ENST00000257430.4:c.4164_4165del	p.Ser1389CysfsTer5	p.S1389Cfs*5	ENST00000257430	NM_000038.5	1388	acTTct/acct	16/16	0.581445234820718	3	FACETS	0.853	0.758	0.953	0.426	0.379	0.477	CLONAL	1	FALSE	1	0.581257105129466	3		326	453	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615635	100615635	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	537	633	2	ENST00000308731.7:c.697C>A	p.Leu233Ile	p.L233I	ENST00000308731	NM_000061.2	233	Cta/Ata	8/19	0.562144115435703	3	FACETS	0.966	0.936	0.995	0.966	0.936	0.995	CLONAL	3	FALSE	0	0.581257105129466	3		635	823	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0017828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	38	518	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.657200845078235	3	FACETS	0.167	0.137	0.2	0.083	0.068	0.1	SUBCLONAL	1	TRUE	1	0.674373199690304	3		518	905	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577035	7577036	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0017828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	591	672	0	ENST00000269305.4:c.902dup	p.Gly302ArgfsTer4	p.G302Rfs*4	ENST00000269305	NM_001126112.2	301	cca/ccCa	8/11	0.674373199690304	2	FACETS	0.994	0.965	1	0.994	0.965	1	CLONAL	2	TRUE	0	0.674373199690304	2		672	882	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0017828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	168	261	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	0.674373199690304	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.674373199690304	2		261	248	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873661	35873661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs193922644	NA	P-0017828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	117	498	1	ENST00000303115.3:c.617G>A	p.Arg206Gln	p.R206Q	ENST00000303115	NM_002185.3	206	cGa/cAa	5/8	0.195530850217395	3	FACETS	0.939	0.851	1	0.313	0.283	0.344	INDETERMINATE	1	TRUE	0	0.674373199690304	3		499	494	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536873	120536873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	324	721	4	ENST00000229340.5:c.313G>A	p.Glu105Lys	p.E105K	ENST00000229340	NM_006861.6	105	Gaa/Aaa	4/6	0.674373199690304	3	FACETS	1	0.983	1	0.55	0.519	0.581	CLONAL	1	TRUE	1	0.674373199690304	3		725	1169	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554161	63554161	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	250	794	1	ENST00000307078.5:c.578C>A	p.Ser193Tyr	p.S193Y	ENST00000307078	NM_004655.3	193	tCt/tAt	2/11	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.674373199690304	2		795	734	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350614	15350614	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201646539	NA	P-0017828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	844	812	0	ENST00000263377.2:c.3301G>A	p.Val1101Met	p.V1101M	ENST00000263377	NM_058243.2	1101	Gtg/Atg	16/20	0.589000811813222	4	FACETS	0.963	0.938	0.989	0.963	0.938	0.989	CLONAL	3	TRUE	1	0.674373199690304	4		812	1450	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917775	29917775	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750435024	NA	P-0017828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	558	650	1	ENST00000389048.3:c.893C>T	p.Ala298Val	p.A298V	ENST00000389048	NM_004304.4	298	gCc/gTc	3/29	0.674373199690304	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.674373199690304	3		651	1105	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420201	420201	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	376	559	0	ENST00000399788.2:c.3066G>C	p.Gln1022His	p.Q1022H	ENST00000399788	NM_001042603.1	1022	caG/caC	21/28	0.533250710205117	6	FACETS	0.86	0.817	0.903	0.645	0.613	0.677	CLONAL	3	TRUE	2	0.533250710205117	6		559	1130	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	85	184	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.419455881986286	2		184	403	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849089	156849089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	199	843	0	ENST00000524377.1:c.1981G>A	p.Gly661Arg	p.G661R	ENST00000524377	NM_002529.3	661	Gga/Aga	15/17	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.419455881986286	2		843	889	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610162	43610162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	133	675	0	ENST00000355710.3:c.2114C>T	p.Ser705Phe	p.S705F	ENST00000355710	NM_020975.4	705	tCc/tTc	11/20	1	2	FACETS	0.926	0.842	1	0.926	0.842	1	CLONAL	1	TRUE	1	0.419455881986286	2		675	685	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588123	69588123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751257747	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	150	579	0	ENST00000168712.1:c.575G>A	p.Arg192Gln	p.R192Q	ENST00000168712	NM_002007.2	192	cGa/cAa	3/3	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.419455881986286	2		579	672	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090994	77090994	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144273203	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	178	650	0	ENST00000356341.3:c.236C>T	p.Ser79Leu	p.S79L	ENST00000356341	NM_002576.4	79	tCa/tTa	3/15	1	2	FACETS	0.982	0.906	1	0.982	0.906	1	CLONAL	1	TRUE	1	0.419455881986286	2		650	864	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204881	94204881	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1226604148	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	143	490	0	ENST00000323929.3:c.704A>G	p.Asp235Gly	p.D235G	ENST00000323929	NM_005591.3	235	gAt/gGt	8/20	1	2	FACETS	0.966	0.882	1	0.966	0.882	1	CLONAL	1	TRUE	1	0.419455881986286	2		490	706	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199914	108199914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	134	457	0	ENST00000278616.4:c.7256G>A	p.Arg2419Lys	p.R2419K	ENST00000278616	NM_000051.3	2419	aGa/aAa	49/63	1	2	FACETS	0.926	0.843	1	0.926	0.843	1	CLONAL	1	TRUE	1	0.419455881986286	2		457	690	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111959680	111959680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1279566824	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	84	330	2	ENST00000375549.3:c.259C>T	p.Pro87Ser	p.P87S	ENST00000375549	NM_003002.3	87	Cct/Tct	3/4	1	2	FACETS	0.942	0.837	1	0.942	0.837	1	CLONAL	1	TRUE	1	0.419455881986286	2		332	425	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409161	4409161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	98	479	0	ENST00000261254.3:c.856G>A	p.Asp286Asn	p.D286N	ENST00000261254	NM_001759.3	286	Gat/Aat	5/5	1	2	FACETS	0.815	0.729	0.907	0.815	0.729	0.907	CLONAL	1	TRUE	1	0.419455881986286	2		479	573	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552600	18552600	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	109	364	0	ENST00000266497.5:c.2011G>A	p.Glu671Lys	p.E671K	ENST00000266497		671	Gaa/Aaa	14/31	1	2	FACETS	0.994	0.896	1	0.994	0.896	1	CLONAL	1	TRUE	1	0.419455881986286	2		364	523	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120795639	120795639	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	144	576	0	ENST00000257552.2:c.514C>T	p.His172Tyr	p.H172Y	ENST00000257552	NM_002442.3	172	Cat/Tat	8/15	1	2	FACETS	0.979	0.895	1	0.979	0.895	1	CLONAL	1	TRUE	1	0.419455881986286	2		576	701	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437154	121437154	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	180	1033	1	ENST00000257555.6:c.1585A>G	p.Asn529Asp	p.N529D	ENST00000257555		529	Aac/Gac	8/10	1	2	FACETS	0.859	0.792	0.929	0.859	0.792	0.929	CLONAL	1	TRUE	1	0.419455881986286	2		1034	999	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30095720	30095720	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	219	800	0	ENST00000331968.5:c.1768G>A	p.Gly590Ser	p.G590S	ENST00000331968	NM_002742.2	590	Ggt/Agt	12/18	1	2	FACETS	0.873	0.811	0.938	0.873	0.811	0.938	CLONAL	1	TRUE	1	0.419455881986286	2		800	1196	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680748	88680748	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	178	670	1	ENST00000360948.2:c.509G>A	p.Trp170Ter	p.W170*	ENST00000360948	NM_001012338.2	170	tGg/tAg	6/19	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.419455881986286	2		671	688	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807367	3807367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	116	456	0	ENST00000262367.5:c.3620C>T	p.Ser1207Phe	p.S1207F	ENST00000262367	NM_004380.2	1207	tCc/tTc	19/31	1	2	FACETS	0.804	0.725	0.887	0.804	0.725	0.887	CLONAL	1	TRUE	1	0.419455881986286	2		456	688	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858202	9858202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	96	450	1	ENST00000330684.3:c.3199C>T	p.Arg1067Trp	p.R1067W	ENST00000330684	NM_001134407.1	1067	Cgg/Tgg	13/13	1	2	FACETS	0.892	0.798	0.992	0.892	0.798	0.992	CLONAL	1	TRUE	1	0.419455881986286	2		451	513	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858660	9858660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	93	408	0	ENST00000330684.3:c.2741G>A	p.Arg914Lys	p.R914K	ENST00000330684	NM_001134407.1	914	aGa/aAa	13/13	1	2	FACETS	0.922	0.823	1	0.922	0.823	1	CLONAL	1	TRUE	1	0.419455881986286	2		408	481	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892188	9892188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	149	698	0	ENST00000330684.3:c.2302G>A	p.Gly768Ser	p.G768S	ENST00000330684	NM_001134407.1	768	Ggc/Agc	11/13	1	2	FACETS	0.897	0.82	0.977	0.897	0.82	0.977	CLONAL	1	TRUE	1	0.419455881986286	2		698	792	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819620	81819620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	81	485	1	ENST00000359376.3:c.26C>T	p.Ser9Phe	p.S9F	ENST00000359376	NM_002661.3	9	tCc/tTc	2/33	1	2	FACETS	0.747	0.66	0.84	0.747	0.66	0.84	SUBCLONAL	1	TRUE	1	0.419455881986286	2		486	517	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346685	89346685	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	57	369	0	ENST00000301030.4:c.6265G>A	p.Val2089Met	p.V2089M	ENST00000301030	NM_001256183.1	2089	Gtg/Atg	9/13	1	2	FACETS	0.912	0.788	1	0.912	0.788	1	CLONAL	1	TRUE	1	0.419455881986286	2		369	298	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557285	29557286	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	109	421	0	ENST00000356175.3:c.2998_2999del	p.Arg1000CysfsTer20	p.R1000Cfs*20	ENST00000356175	NM_000267.3	1000	CGt/t	23/57	1	2	FACETS	0.92	0.829	1	0.92	0.829	1	CLONAL	1	TRUE	1	0.419455881986286	2		421	565	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29662044	29662044	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	123	501	0	ENST00000356175.3:c.5938G>T	p.Gly1980Trp	p.G1980W	ENST00000356175	NM_000267.3	1980	Ggg/Tgg	39/57	1	2	FACETS	0.929	0.843	1	0.929	0.843	1	CLONAL	1	TRUE	1	0.419455881986286	2		501	631	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679366	29679366	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs866445127	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	123	540	0	ENST00000356175.3:c.7486C>T	p.Arg2496Ter	p.R2496*	ENST00000356175	NM_000267.3	2496	Cga/Tga	50/57	1	2	FACETS	0.954	0.865	1	0.954	0.865	1	CLONAL	1	TRUE	1	0.419455881986286	2		540	615	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37882083	37882083	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	108	439	0	ENST00000269571.5:c.2849A>G	p.Asp950Gly	p.D950G	ENST00000269571		950	gAt/gGt	23/27	1	2	FACETS	0.883	0.795	0.976	0.883	0.795	0.976	CLONAL	1	TRUE	1	0.419455881986286	2		439	583	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362470	40362470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1447788988	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	207	802	0	ENST00000293328.3:c.1726G>A	p.Gly576Ser	p.G576S	ENST00000293328	NM_012448.3	576	Ggt/Agt	14/19	1	2	FACETS	0.933	0.865	1	0.933	0.865	1	CLONAL	1	TRUE	1	0.419455881986286	2		802	1058	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41203094	41203094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357428	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	166	757	0	ENST00000357654.3:c.5318C>T	p.Thr1773Ile	p.T1773I	ENST00000357654	NM_007294.3	1773	aCc/aTc	20/23	1	2	FACETS	0.957	0.88	1	0.957	0.88	1	CLONAL	1	TRUE	1	0.419455881986286	2		757	827	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435092	56435092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	139	523	0	ENST00000407977.2:c.2045C>T	p.Pro682Leu	p.P682L	ENST00000407977		682	cCc/cTc	9/10	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.419455881986286	2		523	657	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775165	73775165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	109	525	0	ENST00000254810.4:c.91C>T	p.Pro31Ser	p.P31S	ENST00000254810	NM_005324.3	31	Ccc/Tcc	2/4	1	2	FACETS	0.917	0.826	1	0.917	0.826	1	CLONAL	1	TRUE	1	0.419455881986286	2		525	567	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78882691	78882691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	145	684	0	ENST00000306801.3:c.2482G>A	p.Asp828Asn	p.D828N	ENST00000306801	NM_020761.2	828	Gac/Aac	21/34	1	2	FACETS	0.9	0.822	0.982	0.9	0.822	0.982	CLONAL	1	TRUE	1	0.419455881986286	2		684	768	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227028	2227028	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	146	615	1	ENST00000398665.3:c.4508C>T	p.Ala1503Val	p.A1503V	ENST00000398665	NM_032482.2	1503	gCc/gTc	27/28	1	2	FACETS	0.99	0.906	1	0.99	0.906	1	CLONAL	1	TRUE	1	0.419455881986286	2		616	703	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245945	5245945	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	168	785	0	ENST00000357368.4:c.830A>G	p.Lys277Arg	p.K277R	ENST00000357368	NM_002850.3	277	aAg/aGg	10/38	1	2	FACETS	0.991	0.912	1	0.991	0.912	1	CLONAL	1	TRUE	1	0.419455881986286	2		785	808	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210694	36210694	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	162	689	0	ENST00000222270.7:c.448del	p.Arg150GlufsTer17	p.R150Efs*17	ENST00000222270	NM_014727.1	149	Ccc/cc	3/37	1	2	FACETS	0.944	0.867	1	0.944	0.867	1	CLONAL	1	TRUE	1	0.419455881986286	2		689	818	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211154	36211154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	229	1070	2	ENST00000222270.7:c.905C>T	p.Pro302Leu	p.P302L	ENST00000222270	NM_014727.1	302	cCc/cTc	3/37	1	2	FACETS	0.958	0.892	1	0.958	0.892	1	CLONAL	1	TRUE	1	0.419455881986286	2		1072	1140	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791594	42791594	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754033796	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	130	546	2	ENST00000575354.2:c.575C>T	p.Pro192Leu	p.P192L	ENST00000575354	NM_015125.3	192	cCc/cTc	4/20	1	2	FACETS	0.942	0.856	1	0.942	0.856	1	CLONAL	1	TRUE	1	0.419455881986286	2		548	658	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791782	42791782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	136	598	0	ENST00000575354.2:c.668C>T	p.Pro223Leu	p.P223L	ENST00000575354	NM_015125.3	223	cCc/cTc	5/20	1	2	FACETS	0.874	0.796	0.956	0.874	0.796	0.956	CLONAL	1	TRUE	1	0.419455881986286	2		598	742	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609648	46609648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	209	830	0	ENST00000263734.3:c.2372C>T	p.Pro791Leu	p.P791L	ENST00000263734	NM_001430.4	791	cCc/cTc	15/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.419455881986286	2		830	954	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794364	242794364	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770020786	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	143	843	0	ENST00000334409.5:c.578C>T	p.Ser193Phe	p.S193F	ENST00000334409	NM_005018.2	193	tCc/tTc	3/5	1	2	FACETS	0.875	0.799	0.955	0.875	0.799	0.955	CLONAL	1	TRUE	1	0.419455881986286	2		843	779	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520246	9520246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	155	542	0	ENST00000353224.5:c.2023G>A	p.Gly675Arg	p.G675R	ENST00000353224	NM_177990.2	675	Gga/Aga	10/10	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.419455881986286	2		542	716	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547022	9547022	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs58486349	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	39	165	0	ENST00000353224.5:c.1000G>A	p.Asp334Asn	p.D334N	ENST00000353224	NM_177990.2	334	Gat/Aat	5/10	1	2	FACETS	0.934	0.783	1	0.934	0.783	1	CLONAL	1	TRUE	1	0.419455881986286	2		165	199	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031230	36031230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	157	636	0	ENST00000358208.4:c.1349C>T	p.Ser450Phe	p.S450F	ENST00000358208		450	tCc/tTc	11/12	0.405947198489832	4	FACETS	0.979	0.896	1	0.326	0.298	0.356	CLONAL	1	TRUE	1	0.419455881986286	4		636	1085	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743928	40743928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	252	560	0	ENST00000373198.4:c.3067G>A	p.Asp1023Asn	p.D1023N	ENST00000373198	NM_133170.3	1023	Gac/Aac	23/32	0.405947198489832	4	FACETS	0.885	0.829	0.942	0.59	0.552	0.628	CLONAL	2	TRUE	1	0.419455881986286	4		560	964	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100912	41100912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866253502	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	244	505	0	ENST00000373198.4:c.1444G>A	p.Glu482Lys	p.E482K	ENST00000373198	NM_133170.3	482	Gaa/Aaa	8/32	0.405947198489832	4	FACETS	0.996	0.933	1	0.664	0.622	0.707	CLONAL	2	TRUE	1	0.419455881986286	4		505	829	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420092	41420092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	134	290	0	ENST00000373198.4:c.229G>A	p.Val77Met	p.V77M	ENST00000373198	NM_133170.3	77	Gtg/Atg	3/32	0.405947198489832	4	FACETS	0.939	0.859	1	0.626	0.572	0.681	CLONAL	2	TRUE	1	0.419455881986286	4		290	483	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478737	57478737	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	81	337	0	ENST00000371085.3:c.323C>T	p.Ala108Val	p.A108V	ENST00000371085	NM_000516.4	108	gCc/gTc	5/13	0.405947198489832	4	FACETS	0.896	0.79	1	0.299	0.263	0.337	CLONAL	1	TRUE	1	0.419455881986286	4		337	612	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645683	12645683	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs397516829	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	57	178	0	ENST00000251849.4:c.786T>A	p.Asn262Lys	p.N262K	ENST00000251849	NM_002880.3	262	aaT/aaA	7/17	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.419455881986286	2		178	260	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059133	47059133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	117	553	0	ENST00000409792.3:c.7528C>T	p.Arg2510Cys	p.R2510C	ENST00000409792	NM_014159.6	2510	Cgc/Tgc	20/21	1	2	FACETS	0.853	0.771	0.94	0.853	0.771	0.94	CLONAL	1	TRUE	1	0.419455881986286	2		553	654	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164832	47164832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1017636782	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	82	348	0	ENST00000409792.3:c.1294C>T	p.Arg432Cys	p.R432C	ENST00000409792	NM_014159.6	432	Cgt/Tgt	3/21	1	2	FACETS	0.903	0.8	1	0.903	0.8	1	CLONAL	1	TRUE	1	0.419455881986286	2		348	433	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215915	142215915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746443122	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	110	482	0	ENST00000350721.4:c.5678C>T	p.Ser1893Phe	p.S1893F	ENST00000350721	NM_001184.3	1893	tCc/tTc	33/47	1	2	FACETS	0.889	0.801	0.982	0.889	0.801	0.982	CLONAL	1	TRUE	1	0.419455881986286	2		482	590	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526109	189526109	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	163	682	3	ENST00000264731.3:c.373C>T	p.Gln125Ter	p.Q125*	ENST00000264731	NM_003722.4	125	Cag/Tag	4/14	1	2	FACETS	0.95	0.873	1	0.95	0.873	1	CLONAL	1	TRUE	1	0.419455881986286	2		685	818	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612085	189612085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868285317	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	137	522	0	ENST00000264731.3:c.1837C>T	p.Pro613Ser	p.P613S	ENST00000264731	NM_003722.4	613	Cct/Tct	14/14	1	2	FACETS	0.941	0.858	1	0.941	0.858	1	CLONAL	1	TRUE	1	0.419455881986286	2		522	694	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156730	106156730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1186716961	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	103	438	0	ENST00000380013.4:c.1631G>A	p.Arg544Gln	p.R544Q	ENST00000380013	NM_001127208.2	544	cGa/cAa	3/11	1	2	FACETS	0.901	0.809	0.998	0.901	0.809	0.998	CLONAL	1	TRUE	1	0.419455881986286	2		438	545	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164779	106164779	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs562667223	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	85	364	0	ENST00000380013.4:c.3647G>A	p.Arg1216Gln	p.R1216Q	ENST00000380013	NM_001127208.2	1216	cGa/cAa	6/11	1	2	FACETS	0.947	0.841	1	0.947	0.841	1	CLONAL	1	TRUE	1	0.419455881986286	2		364	428	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538346	187538346	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	143	488	0	ENST00000441802.2:c.8888C>T	p.Pro2963Leu	p.P2963L	ENST00000441802	NM_005245.3	2963	cCt/cTt	11/27	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.419455881986286	2		488	662	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542685	187542685	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs771020867	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	155	522	0	ENST00000441802.2:c.5055C>G	p.Phe1685Leu	p.F1685L	ENST00000441802	NM_005245.3	1685	ttC/ttG	10/27	1	2	FACETS	0.98	0.899	1	0.98	0.899	1	CLONAL	1	TRUE	1	0.419455881986286	2		522	754	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460362	149460362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	98	402	0	ENST00000286301.3:c.275G>A	p.Gly92Glu	p.G92E	ENST00000286301	NM_005211.3	92	gGa/gAa	3/22	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.419455881986286	2		402	441	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520527	176520527	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	152	692	2	ENST00000292408.4:c.1372C>T	p.Pro458Ser	p.P458S	ENST00000292408	NM_213647.1	458	Cca/Tca	10/18	1	2	FACETS	0.934	0.855	1	0.934	0.855	1	CLONAL	1	TRUE	1	0.419455881986286	2		694	776	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185817	32185817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	122	673	0	ENST00000375023.3:c.1579G>A	p.Asp527Asn	p.D527N	ENST00000375023	NM_004557.3	527	Gat/Aat	9/30	0.412296129494522	2	FACETS	0.858	0.777	0.943	0.429	0.388	0.472	CLONAL	1	TRUE	0	0.419455881986286	2		673	678	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286847	33286847	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303730866	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	113	485	0	ENST00000374542.5:c.2090C>T	p.Ser697Phe	p.S697F	ENST00000374542	NM_001141970.1	697	tCc/tTc	7/8	0.412296129494522	2	FACETS	1	0.916	1	0.507	0.458	0.559	CLONAL	1	TRUE	0	0.419455881986286	2		485	531	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015901	112015901	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	128	456	0	ENST00000368678.4:c.1040T>C	p.Leu347Ser	p.L347S	ENST00000368678		347	tTa/tCa	10/13	0.419455881986286	1	FACETS	0.871	0.792	0.952	0.871	0.792	0.952	CLONAL	1	TRUE	0	0.419455881986286	1		456	554	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946289	2946289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1871	299	702	1	ENST00000396946.4:c.3448G>A	p.Asp1150Asn	p.D1150N	ENST00000396946	NM_032415.4	1150	Gac/Aac	25/25	0.419455881986286	11	FACETS	0.949	0.889	1	0.19	0.177	0.202	CLONAL	2	TRUE	1	0.419455881986286	11		703	2170	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963954	2963954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1466	289	560	0	ENST00000396946.4:c.1853C>T	p.Ser618Phe	p.S618F	ENST00000396946	NM_032415.4	618	tCc/tTc	15/25	0.419455881986286	11	FACETS	1	0.983	1	0.227	0.212	0.242	CLONAL	2	TRUE	1	0.419455881986286	11		560	1755	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332070	81332070	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	108	365	0	ENST00000222390.5:c.2014G>A	p.Asp672Asn	p.D672N	ENST00000222390	NM_000601.4	672	Gat/Aat	18/18	0.410289489465022	3	FACETS	1	0.939	1	0.53	0.476	0.586	CLONAL	1	TRUE	1	0.419455881986286	3		365	588	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508561	106508561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	145	266	0	ENST00000359195.3:c.555G>A	p.Met185Ile	p.M185I	ENST00000359195	NM_002649.2	185	atG/atA	2/11	0.410289489465022	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.419455881986286	3		266	372	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371996	55371996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	133	658	0	ENST00000297316.4:c.686G>A	p.Gly229Asp	p.G229D	ENST00000297316	NM_022454.3	229	gGc/gAc	2/2	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.419455881986286	2		658	561	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972918	68972918	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	127	371	0	ENST00000288368.4:c.1243T>C	p.Phe415Leu	p.F415L	ENST00000288368	NM_024870.2	415	Ttt/Ctt	11/40	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.419455881986286	2		371	571	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020539	69020539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	165	594	2	ENST00000288368.4:c.2911G>A	p.Asp971Asn	p.D971N	ENST00000288368	NM_024870.2	971	Gat/Aat	24/40	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.419455881986286	2		596	754	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69050711	69050711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	146	537	0	ENST00000288368.4:c.4046C>T	p.Ser1349Phe	p.S1349F	ENST00000288368	NM_024870.2	1349	tCc/tTc	33/40	1	2	FACETS	0.854	0.78	0.932	0.854	0.78	0.932	CLONAL	1	TRUE	1	0.419455881986286	2		537	815	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964374	70964374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766779014	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	100	381	0	ENST00000276594.2:c.1654G>A	p.Gly552Arg	p.G552R	ENST00000276594	NM_024504.3	552	Ggg/Agg	8/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.419455881986286	2		381	376	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317926	8317926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	96	433	0	ENST00000356435.5:c.5687C>T	p.Ser1896Phe	p.S1896F	ENST00000356435		1896	tCc/tTc	35/35	1	2	FACETS	0.96	0.859	1	0.96	0.859	1	CLONAL	1	TRUE	1	0.419455881986286	2		433	477	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331589	8331589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	123	478	0	ENST00000356435.5:c.5527C>T	p.His1843Tyr	p.H1843Y	ENST00000356435		1843	Cat/Tat	33/35	1	2	FACETS	0.935	0.848	1	0.935	0.848	1	CLONAL	1	TRUE	1	0.419455881986286	2		478	627	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460526	8460526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	165	591	0	ENST00000356435.5:c.3760G>A	p.Asp1254Asn	p.D1254N	ENST00000356435		1254	Gat/Aat	22/35	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.419455881986286	2		591	774	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486082	8486082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	124	576	0	ENST00000356435.5:c.2735C>T	p.Ser912Phe	p.S912F	ENST00000356435		912	tCc/tTc	17/35	1	2	FACETS	0.84	0.761	0.923	0.84	0.761	0.923	CLONAL	1	TRUE	1	0.419455881986286	2		576	704	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521384	8521384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777779009	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	157	694	1	ENST00000356435.5:c.854G>A	p.Gly285Glu	p.G285E	ENST00000356435		285	gGa/gAa	9/35	1	2	FACETS	0.875	0.801	0.951	0.875	0.801	0.951	CLONAL	1	TRUE	1	0.419455881986286	2		695	856	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521502	8521502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	112	563	0	ENST00000356435.5:c.736G>A	p.Glu246Lys	p.E246K	ENST00000356435		246	Gaa/Aaa	9/35	1	2	FACETS	0.805	0.726	0.89	0.805	0.726	0.89	CLONAL	1	TRUE	1	0.419455881986286	2		563	663	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528711	8528711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774617096	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	133	372	1	ENST00000356435.5:c.421C>T	p.Arg141Cys	p.R141C	ENST00000356435		141	Cgc/Tgc	4/35	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.419455881986286	2		373	541	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636812	8636812	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	125	548	0	ENST00000356435.5:c.97C>T	p.Gln33Ter	p.Q33*	ENST00000356435		33	Cag/Tag	2/35	1	2	FACETS	0.937	0.85	1	0.937	0.85	1	CLONAL	1	TRUE	1	0.419455881986286	2		548	636	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970918	21970918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501267	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	195	855	0	ENST00000304494.5:c.440C>T	p.Ala147Val	p.A147V	ENST00000304494	NM_000077.4	147	gCc/gTc	2/3	0.419455881986286	1	FACETS	0.998	0.927	1	0.998	0.927	1	CLONAL	1	TRUE	0	0.419455881986286	1		855	736	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971149	21971149	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786202575	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	74	492	0	ENST00000304494.5:c.209C>T	p.Pro70Leu	p.P70L	ENST00000304494	NM_000077.4	70	cCc/cTc	2/3	0.419455881986286				0.762	0.97				CLONAL	1	TRUE	0	0.419455881986286	1		492	323	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400128	139400128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	198	823	2	ENST00000277541.6:c.4220C>T	p.Ser1407Phe	p.S1407F	ENST00000277541	NM_017617.3	1407	tCc/tTc	25/34	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.419455881986286	2		825	894	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429022	47429022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	114	263	0	ENST00000377045.4:c.1385C>T	p.Pro462Leu	p.P462L	ENST00000377045	NM_001654.4	462	cCc/cTc	13/16	1	1	FACETS	0.814	0.746	0.882	1	0.988	1	CLONAL	2	TRUE	0	0.419455881986286	1		263	264	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0017831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	148	513	1	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.569180135053245	2		514	481	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023151	27023179	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	-	novel	NA	P-0017831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	110	75	1	ENST00000324856.7:c.267_295del	p.Ser90ProfsTer11	p.S90Pfs*11	ENST00000324856	NM_006015.4	86	gGCGGAGCCGGCAGCGGCGGCGGGCCCGGC/g	1/20	0.525576349050867	1	FACETS	0.954	0.898	1	1	0.992	1	CLONAL	2	TRUE	0	0.569180135053245	1		76	145	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579432	7579433	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0017831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	361	584	0	ENST00000269305.4:c.254dup	p.Ala86CysfsTer63	p.A86Cfs*63	ENST00000269305	NM_001126112.2	85	cct/ccCt	4/11	0.569180135053245	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.569180135053245	2		584	625	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631176	69631176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	412	731	1	ENST00000334134.2:c.236C>T	p.Thr79Met	p.T79M	ENST00000334134	NM_005247.2	79	aCg/aTg	2/3	0.484543541801399	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.569180135053245	4		732	1065	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756806	756806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760359350	NA	P-0017831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	145	442	0	ENST00000314574.4:c.22G>A	p.Glu8Lys	p.E8K	ENST00000314574	NM_005433.3	8	Gaa/Aaa	2/12	0.569180135053245	6	FACETS	1	0.919	1	0.252	0.23	0.276	CLONAL	1	TRUE	2	0.569180135053245	6		442	1079	SUCCESS
APC	324	MSKCC	GRCh37	5	112175907	112175907	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0017831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	114	414	0	ENST00000257430.4:c.4616C>G	p.Ser1539Ter	p.S1539*	ENST00000257430	NM_000038.5	1539	tCa/tGa	16/16	0.569180135053245	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.569180135053245	1		414	267	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965643	93965643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762713500	NA	P-0017831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	141	522	1	ENST00000369303.4:c.2285G>A	p.Arg762His	p.R762H	ENST00000369303	NM_004440.3	762	cGc/cAc	13/17	0.440284363112102	4	FACETS	0.968	0.883	1	0.323	0.294	0.353	CLONAL	1	TRUE	1	0.569180135053245	4		523	803	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0017832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	39	427	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.189	0.156	0.227	0.189	0.156	0.227	SUBCLONAL	1	TRUE	1	0.544230418556698	2		427	757	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0017832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1346	37	1080	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	1	2	FACETS	0.098	0.08	0.119	0.098	0.08	0.119	SUBCLONAL	1	TRUE	1	0.544230418556698	2		1080	1383	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0017833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	237	523	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	0.720555415590311	2		523	608	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118892	115118895	+	frameshift_variant	Frame_Shift_Del	DEL	ATGT	ATGT	-	novel	NA	P-0017833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	228	437	0	ENST00000257566.3:c.446_449del	p.Tyr149PhefsTer3	p.Y149Ffs*3	ENST00000257566	NM_016569.3	149	tACATt/tt	2/8	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.720555415590311	2		437	632	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181842	56181842	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	212	535	0	ENST00000399503.3:c.4067del	p.Gly1356AlafsTer21	p.G1356Afs*21	ENST00000399503	NM_005921.1	1356	Ggc/gc	17/20	1	2	FACETS	0.88	0.821	0.94	0.88	0.821	0.94	CLONAL	1	TRUE	1	0.720555415590311	2		535	669	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0017834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	227	741	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.3	3	FACETS	0.849	0.793	0.907	1	0.989	1	CLONAL	3	TRUE	1	0.24	3		741	832	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63829504	63829504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529464997	NA	P-0017837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	50	318	0	ENST00000279873.7:c.1147G>A	p.Gly383Ser	p.G383S	ENST00000279873	NM_032199.2	383	Ggt/Agt	8/10	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		318	519	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0017838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	682	482	0	ENST00000269305.4:c.376-1G>T		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.744497125642143	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.744497125642143	2		482	866	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717644	89717644	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	181	305	0	ENST00000371953.3:c.669G>C	p.Lys223Asn	p.K223N	ENST00000371953	NM_000314.4	223	aaG/aaC	7/9	NA	2	FACETS	0.988	0.92	1			1	INDETERMINATE	1	TRUE	NA	0.744497125642143	2		305	492	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864696	57864696	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	587	457	0	ENST00000228682.2:c.2173C>A	p.Pro725Thr	p.P725T	ENST00000228682	NM_005269.2	725	Cca/Aca	12/12	0.743269374852749	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	2	0.744497125642143	4		457	1298	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29007984	29007984	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	99	178	0	ENST00000282397.4:c.785T>A	p.Val262Asp	p.V262D	ENST00000282397	NM_002019.4	262	gTt/gAt	6/30	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.744497125642143	2		178	251	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008201	29008201	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	98	164	0	ENST00000282397.4:c.670del	p.Arg224AspfsTer7	p.R224Dfs*7	ENST00000282397	NM_002019.4	224	Cga/ga	5/30	1	2	FACETS	0.895	0.81	0.984	0.895	0.81	0.984	CLONAL	1	TRUE	1	0.744497125642143	2		164	294	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135314	30135314	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	55	398	0	ENST00000331968.5:c.504G>T	p.Trp168Cys	p.W168C	ENST00000331968	NM_002742.2	168	tgG/tgT	3/18	0.518631791558358	3	FACETS	0.292	0.249	0.339	0.097	0.083	0.113	SUBCLONAL	1	TRUE	0	0.744497125642143	3		398	695	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476331	88476331	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	212	400	0	ENST00000360948.2:c.1801G>C	p.Val601Leu	p.V601L	ENST00000360948	NM_001012338.2	601	Gtc/Ctc	15/19	0.744497125642143	4	FACETS	0.966	0.897	1	0.322	0.299	0.346	CLONAL	1	TRUE	1	0.744497125642143	4		400	1029	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678534	88678534	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	63	219	0	ENST00000360948.2:c.1002C>A	p.His334Gln	p.H334Q	ENST00000360948	NM_001012338.2	334	caC/caA	9/19	0.744497125642143	4	FACETS	0.604	0.523	0.691	0.201	0.174	0.231	SUBCLONAL	1	TRUE	1	0.744497125642143	4		219	489	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602745	10602745	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	464	386	0	ENST00000171111.5:c.833C>G	p.Pro278Arg	p.P278R	ENST00000171111	NM_203500.1	278	cCg/cGg	3/6	0.744497125642143	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.744497125642143	2		386	619	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42861458	42861458	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	337	251	0	ENST00000398585.3:c.412G>T	p.Ala138Ser	p.A138S	ENST00000398585	NM_001135099.1	138	Gcc/Tcc	4/14	0.744497125642143	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.744497125642143	2		251	443	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32819904	32819904	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	40	398	0	ENST00000354258.4:c.1006T>A	p.Phe336Ile	p.F336I	ENST00000354258	NM_000593.5	336	Ttc/Atc	3/11	1	2	FACETS	0.158	0.13	0.188	0.158	0.13	0.188	SUBCLONAL	1	TRUE	1	0.744497125642143	2		398	682	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874212	151874212	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	176	259	0	ENST00000262189.6:c.8326G>T	p.Glu2776Ter	p.E2776*	ENST00000262189	NM_170606.2	2776	Gaa/Taa	38/59	0.744497125642143	3	FACETS	1	0.964	1	0.534	0.494	0.575	CLONAL	1	TRUE	1	0.744497125642143	3		259	608	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484362	8484362	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	161	282	0	ENST00000356435.5:c.3170G>T	p.Gly1057Val	p.G1057V	ENST00000356435		1057	gGg/gTg	19/35	0.744497125642143	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.744497125642143	1		282	259	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633452	8633452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	94	236	0	ENST00000356435.5:c.217G>A	p.Glu73Lys	p.E73K	ENST00000356435		73	Gag/Aag	3/35	0.744497125642143	1	FACETS	0.686	0.622	0.751	0.686	0.622	0.751	SUBCLONAL	1	TRUE	0	0.744497125642143	1		236	231	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412309	139412309	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	369	394	1	ENST00000277541.6:c.1336G>T	p.Gly446Cys	p.G446C	ENST00000277541	NM_017617.3	446	Ggc/Tgc	8/34	0.690168205620666	4	FACETS	0.966	0.92	1	0.966	0.92	1	CLONAL	2	TRUE	2	0.744497125642143	4		395	895	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	61	642	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.951	0.821	1	0.951	0.821	1	CLONAL	1	TRUE	1	0.23	2		642	558	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	62	455	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.766	0.661	0.88	0.766	0.661	0.88	SUBCLONAL	1	TRUE	1	0.23	2		455	704	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	59	918	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.751	0.645	0.867	0.751	0.645	0.867	SUBCLONAL	1	TRUE	1	0.23	2		918	683	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	66	555	3	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	0.23	2		558	407	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	206	865	8	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.991	0.92	1	1	0.994	1	CLONAL	2	TRUE	1	0.23	2		873	904	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223023	5223023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759129843	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	42	289	0	ENST00000357368.4:c.2780C>T	p.Thr927Met	p.T927M	ENST00000357368	NM_002850.3	927	aCg/aTg	18/38	1	2	FACETS	0.867	0.725	1	0.867	0.725	1	CLONAL	1	TRUE	1	0.23	2		289	421	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	48	255	0	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.23	2		255	375	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106648	27106648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553153748	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	80	786	3	ENST00000324856.7:c.6259G>A	p.Gly2087Arg	p.G2087R	ENST00000324856	NM_006015.4	2087	Gga/Aga	20/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.23	2		789	526	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	50	380	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	0.868	0.737	1	0.868	0.737	1	CLONAL	1	TRUE	1	0.23	2		380	501	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238958	5238958	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	23	222	0	ENST00000357368.4:c.1821del	p.Val608TrpfsTer30	p.V608Wfs*30	ENST00000357368	NM_002850.3	607	ccC/cc	13/38	1	2	FACETS	0.725	0.566	0.908	0.725	0.566	0.908	CLONAL	1	TRUE	1	0.23	2		222	276	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277275	41277275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	49	217	1	ENST00000349496.5:c.1744C>T	p.Arg582Trp	p.R582W	ENST00000349496	NM_001904.3	582	Cgg/Tgg	11/15	1	2	FACETS	0.955	0.81	1	0.955	0.81	1	CLONAL	1	TRUE	1	0.23	2		218	446	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538846	23538846	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746822077	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	27	184	0	ENST00000380871.4:c.593C>T	p.Pro198Leu	p.P198L	ENST00000380871	NM_006167.3	198	cCg/cTg	2/2	1	2	FACETS	0.836	0.667	1	0.836	0.667	1	CLONAL	1	TRUE	1	0.23	2		184	281	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143341	30143341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	53	347	0	ENST00000389048.3:c.185C>T	p.Ser62Leu	p.S62L	ENST00000389048	NM_004304.4	62	tCg/tTg	1/29	1	2	FACETS	0.814	0.694	0.946	0.814	0.694	0.946	CLONAL	1	TRUE	1	0.23	2		347	566	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165282	47165283	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	37	243	0	ENST00000409792.3:c.843dup	p.Glu282ArgfsTer9	p.E282Rfs*9	ENST00000409792	NM_014159.6	281	-/A	3/21	1	2	FACETS	0.663	0.546	0.794	0.663	0.546	0.794	SUBCLONAL	1	TRUE	1	0.23	2		243	485	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050364	13050364	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	55	365	0	ENST00000316448.5:c.320del	p.Gly107AlafsTer4	p.G107Afs*4	ENST00000316448	NM_004343.3	106	Ggg/gg	3/9	1	2	FACETS	0.685	0.585	0.795	0.685	0.585	0.795	SUBCLONAL	1	TRUE	1	0.23	2		365	698	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521525	46521525	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	69	345	1	ENST00000262741.5:c.883del	p.Met295Ter	p.M295*	ENST00000262741	NM_003629.3	295	Atg/tg	7/10	1	2	FACETS	0.929	0.809	1	0.929	0.809	1	CLONAL	1	TRUE	1	0.23	2		346	646	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	33	339	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	0.514	0.418	0.623	0.514	0.418	0.623	SUBCLONAL	1	TRUE	1	0.23	2		339	558	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	56	327	1	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.705	0.603	0.816	0.705	0.603	0.816	SUBCLONAL	1	TRUE	1	0.23	2		328	691	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	54	490	0	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	1	2	FACETS	0.576	0.491	0.67	0.576	0.491	0.67	SUBCLONAL	1	TRUE	1	0.23	2		490	815	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800564	32800564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148663600	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	88	422	0	ENST00000374899.4:c.983C>T	p.Ala328Val	p.A328V	ENST00000374899	NM_018833.2	328	gCg/gTg	6/12	1	2	FACETS	0.984	0.871	1	0.984	0.871	1	CLONAL	1	TRUE	1	0.23	2		422	778	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465973	69465973	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759765773	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	54	315	1	ENST00000227507.2:c.811G>A	p.Ala271Thr	p.A271T	ENST00000227507	NM_053056.2	271	Gcc/Acc	5/5	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.23	2		316	429	SUCCESS
EED	8726	MSKCC	GRCh37	11	85966301	85966301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs183646722	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	48	182	0	ENST00000263360.6:c.398G>A	p.Arg133Gln	p.R133Q	ENST00000263360	NM_003797.3	133	cGg/cAg	4/12	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.23	2		182	335	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118391565	118391565	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	37	242	0	ENST00000534358.1:c.11483del	p.Lys3828ArgfsTer31	p.K3828Rfs*31	ENST00000534358	NM_005933.3	3826	ttA/tt	34/36	1	2	FACETS	0.658	0.542	0.788	0.658	0.542	0.788	SUBCLONAL	1	TRUE	1	0.23	2		242	489	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489540	56489540	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200724560	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	64	279	0	ENST00000267101.3:c.2005C>T	p.Arg669Cys	p.R669C	ENST00000267101	NM_001982.3	669	Cgc/Tgc	17/28	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.23	2		279	530	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133236065	133236065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761261349	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	38	286	4	ENST00000320574.5:c.3091G>A	p.Glu1031Lys	p.E1031K	ENST00000320574	NM_006231.2	1031	Gag/Aag	26/49	1	2	FACETS	0.681	0.563	0.814	0.681	0.563	0.814	SUBCLONAL	1	TRUE	1	0.23	2		290	485	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28624343	28624343	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	67	284	0	ENST00000241453.7:c.631C>T	p.Pro211Ser	p.P211S	ENST00000241453	NM_004119.2	211	Cca/Tca	6/24	1	2	FACETS	0.899	0.781	1	0.899	0.781	1	CLONAL	1	TRUE	1	0.23	2		284	648	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571486	95571486	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	36	230	0	ENST00000393063.1:c.3191T>G	p.Leu1064Arg	p.L1064R	ENST00000393063	NM_030621.3	1064	cTt/cGt	21/28	1	2	FACETS	0.751	0.617	0.9	0.751	0.617	0.9	SUBCLONAL	1	TRUE	1	0.23	2		230	417	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782074	66782075	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	36	252	0	ENST00000307102.5:c.1047_1048del	p.Arg349SerfsTer16	p.R349Sfs*16	ENST00000307102	NM_002755.3	347	gcAGag/gcag	10/11	1	2	FACETS	0.63	0.517	0.756	0.63	0.517	0.756	SUBCLONAL	1	TRUE	1	0.23	2		252	497	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121553	2121553	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45437797	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	67	371	1	ENST00000219476.3:c.1882C>T	p.Arg628Cys	p.R628C	ENST00000219476	NM_000548.3	628	Cgc/Tgc	18/42	1	2	FACETS	0.966	0.84	1	0.966	0.84	1	CLONAL	1	TRUE	1	0.23	2		372	603	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124310	2124310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs936484229	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	76	484	0	ENST00000219476.3:c.2465C>T	p.Ala822Val	p.A822V	ENST00000219476	NM_000548.3	822	gCg/gTg	22/42	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.23	2		484	655	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041768	14041768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1348674133	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	49	299	0	ENST00000311895.7:c.2315G>A	p.Arg772Gln	p.R772Q	ENST00000311895	NM_005236.2	772	cGa/cAa	11/11	1	2	FACETS	0.89	0.754	1	0.89	0.754	1	CLONAL	1	TRUE	1	0.23	2		299	479	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89851308	89851308	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761957732	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	39	383	0	ENST00000389301.3:c.1424C>T	p.Thr475Met	p.T475M	ENST00000389301	NM_000135.2	475	aCg/aTg	15/43	1	2	FACETS	0.562	0.465	0.671	0.562	0.465	0.671	SUBCLONAL	1	TRUE	1	0.23	2		383	603	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108557	8108557	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1466818032	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	66	378	0	ENST00000585124.1:c.838G>A	p.Glu280Lys	p.E280K	ENST00000585124	NM_004217.3	280	Gag/Aag	8/9	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.23	2		378	564	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553610	29553610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1350468182	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	24	153	0	ENST00000356175.3:c.2159G>A	p.Arg720Gln	p.R720Q	ENST00000356175	NM_000267.3	720	cGg/cAg	18/57	1	2	FACETS	0.838	0.659	1	0.838	0.659	1	CLONAL	1	TRUE	1	0.23	2		153	249	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727859	78727859	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778541724	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	52	386	0	ENST00000306801.3:c.704C>T	p.Pro235Leu	p.P235L	ENST00000306801	NM_020761.2	235	cCg/cTg	6/34	1	2	FACETS	0.652	0.554	0.76	0.652	0.554	0.76	SUBCLONAL	1	TRUE	1	0.23	2		386	693	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372130	45372131	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	95	381	1	ENST00000262160.6:c.1038dup	p.Ala347CysfsTer2	p.A347Cfs*2	ENST00000262160	NM_005901.5	346	-/T	9/11	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.23	2		382	781	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745129	41745129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	51	381	0	ENST00000301178.4:c.1195G>A	p.Val399Met	p.V399M	ENST00000301178	NM_021913.4	399	Gtg/Atg	9/20	1	2	FACETS	0.799	0.679	0.931	0.799	0.679	0.931	CLONAL	1	TRUE	1	0.23	2		381	555	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47600710	47600710	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs866758817	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	38	278	1	ENST00000263735.4:c.184+1G>A		p.X62_splice	ENST00000263735	NM_002354.2	62			1	2	FACETS	0.551	0.454	0.659	0.551	0.454	0.659	SUBCLONAL	1	TRUE	1	0.23	2		279	600	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698135	47698135	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63750737	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	82	366	0	ENST00000233146.2:c.1697del	p.Asn566IlefsTer24	p.N566Ifs*24	ENST00000233146	NM_000251.2	565	Aaa/aa	11/16	1	2	FACETS	0.892	0.786	1	0.892	0.786	1	CLONAL	1	TRUE	1	0.23	2		366	799	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025856	48025857	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs267608041	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	21	210	0	ENST00000234420.5:c.741dup	p.Arg248ThrfsTer8	p.R248Tfs*8	ENST00000234420	NM_000179.2	245	ata/atAa	4/10	1	2	FACETS	0.49	0.376	0.622	0.49	0.376	0.622	SUBCLONAL	1	TRUE	1	0.23	2		210	373	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309583	30309583	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	69	399	1	ENST00000307677.4:c.439G>A	p.Gly147Ser	p.G147S	ENST00000307677	NM_138578.1	147	Ggc/Agc	2/3	1	2	FACETS	0.815	0.709	0.93	0.815	0.709	0.93	CLONAL	1	TRUE	1	0.23	2		400	736	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42840391	42840391	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	32	285	0	ENST00000398585.3:c.1357T>C	p.Tyr453His	p.Y453H	ENST00000398585	NM_001135099.1	453	Tat/Cat	12/14	1	2	FACETS	0.566	0.458	0.687	0.566	0.458	0.687	SUBCLONAL	1	TRUE	1	0.23	2		285	492	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266471	41266471	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1369821061	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	32	254	0	ENST00000349496.5:c.268C>T	p.Arg90Ter	p.R90*	ENST00000349496	NM_001904.3	90	Cga/Tga	4/15	1	2	FACETS	0.704	0.572	0.854	0.704	0.572	0.854	SUBCLONAL	1	TRUE	1	0.23	2		254	395	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934764	49934767	+	frameshift_variant	Frame_Shift_Del	DEL	ACAG	ACAG	-	rs1559476985	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	46	426	0	ENST00000296474.3:c.2129_2132del	p.Ser710Ter	p.S710*	ENST00000296474	NM_002447.2	710	tCTGTa/ta	7/20	1	2	FACETS	0.629	0.529	0.74	0.629	0.529	0.74	SUBCLONAL	1	TRUE	1	0.23	2		426	636	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940163	49940163	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747692134	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	53	327	0	ENST00000296474.3:c.880C>T	p.Arg294Trp	p.R294W	ENST00000296474	NM_002447.2	294	Cgg/Tgg	1/20	1	2	FACETS	0.974	0.832	1	0.974	0.832	1	CLONAL	1	TRUE	1	0.23	2		327	473	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1906063	1906063	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	90	508	0	ENST00000382891.5:c.718G>C	p.Val240Leu	p.V240L	ENST00000382891	NM_133335.3	240	Gtt/Ctt	3/22	1	2	FACETS	0.733	0.648	0.823	0.733	0.648	0.823	SUBCLONAL	1	TRUE	1	0.23	2		508	1068	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1941428	1941428	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	111	393	2	ENST00000382891.5:c.1804C>T	p.Arg602Trp	p.R602W	ENST00000382891	NM_133335.3	602	Cgg/Tgg	9/22	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.23	2		395	853	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564482	86564482	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	39	197	0	ENST00000274376.6:c.214C>A	p.Leu72Ile	p.L72I	ENST00000274376	NM_002890.2	72	Cta/Ata	1/25	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.23	2		197	257	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435889	149435889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768825118	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	58	397	0	ENST00000286301.3:c.2335G>A	p.Val779Met	p.V779M	ENST00000286301	NM_005211.3	779	Gtg/Atg	18/22	1	2	FACETS	0.987	0.849	1	0.987	0.849	1	CLONAL	1	TRUE	1	0.23	2		397	511	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225731	26225731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	61	260	0	ENST00000360408.1:c.349C>T	p.Arg117Cys	p.R117C	ENST00000360408	NM_003532.2	117	Cgc/Tgc	1/1	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.23	2		260	482	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346610	81346610	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	29	227	0	ENST00000222390.5:c.1343A>G	p.His448Arg	p.H448R	ENST00000222390	NM_000601.4	448	cAt/cGt	11/18	1	2	FACETS	0.662	0.531	0.81	0.662	0.531	0.81	SUBCLONAL	1	TRUE	1	0.23	2		227	381	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877989	151877989	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1005675691	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	23	127	0	ENST00000262189.6:c.6956C>T	p.Ala2319Val	p.A2319V	ENST00000262189	NM_170606.2	2319	gCc/gTc	36/59	1	2	FACETS	0.797	0.623	0.997	0.797	0.623	0.997	CLONAL	1	TRUE	1	0.23	2		127	251	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738404	145738404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1291628811	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	49	360	0	ENST00000428558.2:c.2581C>T	p.Pro861Ser	p.P861S	ENST00000428558	NM_004260.3	861	Ccc/Tcc	16/22	1	2	FACETS	0.785	0.664	0.917	0.785	0.664	0.917	CLONAL	1	TRUE	1	0.23	2		360	543	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180310	27180310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1286718039	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	53	245	1	ENST00000380036.4:c.974G>A	p.Arg325His	p.R325H	ENST00000380036	NM_000459.3	325	cGc/cAc	7/23	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.23	2		246	454	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781415	135781415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371908551	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	43	228	0	ENST00000298552.3:c.1550G>A	p.Arg517Gln	p.R517Q	ENST00000298552	NM_001162426.1	517	cGg/cAg	15/23	1	2	FACETS	0.932	0.782	1	0.932	0.782	1	CLONAL	1	TRUE	1	0.23	2		228	401	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328439	137328439	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	43	493	0	ENST00000481739.1:c.1368G>T	p.Glu456Asp	p.E456D	ENST00000481739	NM_002957.4	456	gaG/gaT	10/10	1	2	FACETS	0.605	0.505	0.716	0.605	0.505	0.716	SUBCLONAL	1	TRUE	1	0.23	2		493	618	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223371	53223371	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	57	216	0	ENST00000375401.3:c.3988G>A	p.Ala1330Thr	p.A1330T	ENST00000375401	NM_004187.3	1330	Gcc/Acc	23/26	1	1	FACETS	0.764	0.661	0.875	1	0.97	1	SUBCLONAL	2	TRUE	0	0.23	1		216	287	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183797	10183797	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	192	545	0	ENST00000256474.2:c.266T>G	p.Leu89Arg	p.L89R	ENST00000256474	NM_000551.3	89	cTc/cGc	1/3	1	2	FACETS	0.775	0.721	0.831	1	0.992	1	SUBCLONAL	2	TRUE	1	0.417629481178686	2		545	593	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342636	70342636	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	207	232	0	ENST00000374080.3:c.1397A>T	p.His466Leu	p.H466L	ENST00000374080		466	cAt/cTt	10/45	1	1	FACETS	0.902	0.848	0.955	1	0.994	1	CLONAL	2	TRUE	0	0.417629481178686	1		232	435	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0017842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	61	427	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.245501872514976	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	2	TRUE	0	0.310544737162277	2		427	186	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100983	27100983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	136	457	0	ENST00000324856.7:c.4268del	p.Pro1423LeufsTer58	p.P1423Lfs*58	ENST00000324856	NM_006015.4	1422	tCc/tc	18/20	0.175701867546107	4	FACETS	1	0.972	1	1	0.972	1	INDETERMINATE	2	TRUE	2	0.310544737162277	4		457	501	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115415	115115415	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	61	415	1	ENST00000257566.3:c.911G>T	p.Arg304Leu	p.R304L	ENST00000257566	NM_016569.3	304	cGg/cTg	5/8	0.307758820389385	5	FACETS	0.846	0.739	0.958	0.634	0.554	0.719	CLONAL	3	TRUE	1	0.310544737162277	5		416	227	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991495	72991503	+	inframe_deletion	In_Frame_Del	DEL	GAGGCCCAG	GAGGCCCAG	-	novel	NA	P-0017842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	51	415	0	ENST00000268489.5:c.2542_2550del	p.Leu848_Leu850del	p.L848_L850del	ENST00000268489	NM_006885.3	848	CTGGGCCTC/-	2/10	0.310544737162277	5	FACETS	0.951	0.809	1	0.476	0.404	0.554	CLONAL	1	TRUE	3	0.310544737162277	5		415	506	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570097	212570097	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	11	277	0	ENST00000342788.4:c.1144G>T	p.Glu382Ter	p.E382*	ENST00000342788	NM_005235.2	382	Gaa/Taa	10/28	0.242300508150028	5	FACETS	0.818	0.568	1	0.273	0.189	0.375	CLONAL	1	TRUE	2	0.310544737162277	5		277	127	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138419	37138419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs546301253	NA	P-0017842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	96	205	0	ENST00000373509.5:c.68C>T	p.Thr23Ile	p.T23I	ENST00000373509	NM_002648.3	23	aCc/aTc	1/6	0.310544737162277	5	FACETS	1	0.934	1	0.356	0.317	0.398	CLONAL	1	TRUE	2	0.310544737162277	5		205	848	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317219	11317219	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017842-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	100	433	2	ENST00000361445.4:c.275G>T	p.Ser92Ile	p.S92I	ENST00000361445	NM_004958.3	92	aGc/aTc	4/58	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.500220105906796	2		435	400	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206664161	206664161	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017842-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	122	538	0	ENST00000367120.3:c.1703A>G	p.Tyr568Cys	p.Y568C	ENST00000367120	NM_014002.3	568	tAc/tGc	17/22	0.500220105906796	3	FACETS	1	0.954	1	0.543	0.492	0.595	CLONAL	1	TRUE	1	0.500220105906796	3		538	562	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0017842-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	101	662	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	0.841	0.755	0.932	0.841	0.755	0.932	CLONAL	1	TRUE	1	0.500220105906796	2		662	480	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30103727	30103727	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017842-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	93	419	0	ENST00000331968.5:c.1211T>G	p.Ile404Ser	p.I404S	ENST00000331968	NM_002742.2	404	aTc/aGc	8/18	1	2	FACETS	0.997	0.893	1	0.997	0.893	1	CLONAL	1	TRUE	1	0.500220105906796	2		419	373	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245453	41245453	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs876658306	NA	P-0017842-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	141	795	0	ENST00000357654.3:c.2095G>T	p.Glu699Ter	p.E699*	ENST00000357654	NM_007294.3	699	Gag/Tag	10/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.500220105906796	2		795	494	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141502	11141502	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017842-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	254	609	0	ENST00000358026.2:c.3479G>T	p.Gly1160Val	p.G1160V	ENST00000358026	NM_001128849.1	1160	gGg/gTg	25/36	0.500220105906796	2	FACETS	0.973	0.921	1	0.973	0.921	1	CLONAL	2	TRUE	0	0.500220105906796	2		609	522	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111648	56111648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1237362975	NA	P-0017842-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	74	345	0	ENST00000399503.3:c.248C>T	p.Ser83Leu	p.S83L	ENST00000399503	NM_005921.1	83	tCa/tTa	1/20	0.441118752991759	3	FACETS	1	0.91	1	0.519	0.458	0.585	CLONAL	1	TRUE	1	0.500220105906796	3		345	356	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324933	31324933	+	start_lost	Translation_Start_Site	SNP	C	C	G	novel	NA	P-0017842-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	93	427	0	ENST00000412585.2:c.3G>C	p.Met1?	p.M1?	ENST00000412585	NM_005514.6	1	atG/atC	1/8	1	2	FACETS	0.958	0.858	1	0.958	0.858	1	CLONAL	1	TRUE	1	0.500220105906796	2		427	388	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099991	157099991	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017842-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	71	346	0	ENST00000346085.5:c.928G>T	p.Gly310Cys	p.G310C	ENST00000346085	NM_020732.3	310	Ggc/Tgc	1/20	1	2	FACETS	0.94	0.828	1	0.94	0.828	1	CLONAL	1	TRUE	1	0.500220105906796	2		346	302	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946448	2946448	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017842-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	120	610	0	ENST00000396946.4:c.3289G>A	p.Glu1097Lys	p.E1097K	ENST00000396946	NM_032415.4	1097	Gag/Aag	25/25	1	2	FACETS	0.868	0.787	0.952	0.868	0.787	0.952	CLONAL	1	TRUE	1	0.500220105906796	2		610	553	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389266	8389266	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs753837487	NA	P-0017842-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	128	628	0	ENST00000356435.5:c.4352T>C	p.Val1451Ala	p.V1451A	ENST00000356435		1451	gTt/gCt	26/35	0.500220105906796	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.500220105906796	1		628	338	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044710	47044710	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017842-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	129	715	2	ENST00000377604.3:c.2110G>T	p.Ala704Ser	p.A704S	ENST00000377604	NM_001204468.1	704	Gcc/Tcc	19/24	0.185330075694585	1	FACETS	0.669	0.609	0.732	0.669	0.609	0.732	INDETERMINATE	1	TRUE	0	0.500220105906796	1		717	578	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344614	70344614	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017842-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	36	656	2	ENST00000374080.3:c.1975G>T	p.Asp659Tyr	p.D659Y	ENST00000374080		659	Gat/Tat	14/45	0.185330075694585	1	FACETS	0.247	0.203	0.297	0.247	0.203	0.297	INDETERMINATE	1	TRUE	0	0.500220105906796	1		658	437	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182930	123182930	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0017842-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	20	456	0	ENST00000218089.9:c.893+2T>A		p.X298_splice	ENST00000218089	NM_001042749.1	298			0.500220105906796	3	FACETS	0.269	0.205	0.344	0.134	0.102	0.172	SUBCLONAL	1	TRUE	1	0.500220105906796	3		456	372	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106723	27106723	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	34	363	0	ENST00000324856.7:c.6334C>G	p.Leu2112Val	p.L2112V	ENST00000324856	NM_006015.4	2112	Ctt/Gtt	20/20	1	2	FACETS	0.174	0.142	0.211	0.174	0.142	0.211	SUBCLONAL	1	TRUE	1	0.641366048744172	2		363	608	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484206	8484206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768568228	NA	P-0017844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	27	368	0	ENST00000356435.5:c.3326G>A	p.Arg1109His	p.R1109H	ENST00000356435		1109	cGt/cAt	19/35	1	2	FACETS	0.187	0.148	0.232	0.187	0.148	0.232	SUBCLONAL	1	TRUE	1	0.641366048744172	2		368	450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0017847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	317	1081	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.532895831737374	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.587704714830276	2		1082	514	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007747	45007747	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1279144545	NA	P-0017847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	83	188	0	ENST00000558401.1:c.194G>C	p.Arg65Thr	p.R65T	ENST00000558401	NM_004048.2	65	aGa/aCa	2/4	0.587704714830276	2	FACETS	0.745	0.662	0.833	0.373	0.331	0.417	SUBCLONAL	1	TRUE	0	0.587704714830276	2		188	379	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786798	3786798	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	21	238	0	ENST00000262367.5:c.4413C>G	p.Ile1471Met	p.I1471M	ENST00000262367	NM_004380.2	1471	atC/atG	27/31	0.587722596502918	2	FACETS	0.344	0.265	0.434	0.172	0.132	0.217	SUBCLONAL	1	TRUE	0	0.587704714830276	2		238	208	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399344	139399344	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	511	412	2	ENST00000277541.6:c.4799T>A	p.Leu1600Gln	p.L1600Q	ENST00000277541	NM_017617.3	1600	cTg/cAg	26/34	0.587704714830276	8	FACETS	0.995	0.959	1	0.711	0.685	0.736	CLONAL	5	TRUE	1	0.587704714830276	8		414	966	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141036	55141036	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121908586	NA	P-0017851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	126	331	0	ENST00000257290.5:c.1682T>A	p.Val561Asp	p.V561D	ENST00000257290	NM_006206.4	561	gTc/gAc	12/23	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.758939570686477	2		331	320	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136030	64136030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1380280944	NA	P-0017851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	112	542	0	ENST00000334205.4:c.1291C>T	p.Arg431Cys	p.R431C	ENST00000334205	NM_003942.2	431	Cgc/Tgc	11/17	1	2	FACETS	0.607	0.549	0.668	0.607	0.549	0.668	SUBCLONAL	1	TRUE	1	0.758939570686477	2		542	486	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776988	135776988	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	22	380	0	ENST00000298552.3:c.2490G>C	p.Gln830His	p.Q830H	ENST00000298552	NM_001162426.1	830	caG/caC	19/23	1	2	FACETS	0.151	0.117	0.192	0.151	0.117	0.192	SUBCLONAL	1	TRUE	1	0.758939570686477	2		380	383	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0017854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	16	315	0	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	0.252869768699752	4	FACETS	0.263	0.194	0.347	0.132	0.097	0.174	INDETERMINATE	1	TRUE	2	0.468776556386945	4		315	381	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0017854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	102	528	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.381286808217629	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.468776556386945	3		528	233	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220649	1220649	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	383	813	1	ENST00000326873.7:c.667G>T	p.Glu223Ter	p.E223*	ENST00000326873	NM_000455.4	223	Gag/Tag	5/10	0.329328369826166	3	FACETS	0.917	0.879	0.956			1	CLONAL	3	TRUE	NA	0.468776556386945	3		814	733	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068124	94068124	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	122	347	0	ENST00000369303.4:c.838G>T	p.Gly280Cys	p.G280C	ENST00000369303	NM_004440.3	280	Ggc/Tgc	4/17	0.43450376256474	2	FACETS	0.953	0.878	1	0.953	0.878	1	CLONAL	2	TRUE	0	0.468776556386945	2		347	273	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402448	139402448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs549630973	NA	P-0017854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	38	704	2	ENST00000277541.6:c.3469G>A	p.Gly1157Arg	p.G1157R	ENST00000277541	NM_017617.3	1157	Ggg/Agg	21/34	0.43450376256474	2	FACETS	0.27	0.223	0.324	0.135	0.111	0.162	SUBCLONAL	1	TRUE	0	0.468776556386945	2		706	600	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153576	108153601	+	frameshift_variant	Frame_Shift_Del	DEL	TAAACTACACAAATATTGAGGATTTC	TAAACTACACAAATATTGAGGATTTC	-	novel	NA	P-0017854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	79	295	0	ENST00000278616.4:c.3718_3743del	p.Asn1240Ter	p.N1240*	ENST00000278616	NM_000051.3	1239	tTAAACTACACAAATATTGAGGATTTC/t	25/63	0.43450376256474	2	FACETS	0.873	0.785	0.963	0.873	0.785	0.963	CLONAL	2	TRUE	0	0.468776556386945	2		295	193	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42026718	42026718	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0017854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	150	556	0	ENST00000219905.7:c.3844-2A>T		p.X1282_splice	ENST00000219905	NM_001164273.1	1282			NA	2	FACETS	0.925	0.858	0.993			1	INDETERMINATE	2	TRUE	NA	0.468776556386945	2		556	346	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054396	42054396	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	146	480	0	ENST00000219905.7:c.7580A>C	p.Gln2527Pro	p.Q2527P	ENST00000219905	NM_001164273.1	2527	cAa/cCa	22/24	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	2	TRUE	NA	0.468776556386945	2		480	263	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106182995	106182995	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	69	321	0	ENST00000380013.4:c.4034A>G	p.Tyr1345Cys	p.Y1345C	ENST00000380013	NM_001127208.2	1345	tAt/tGt	8/11	0.381286808217629	3	FACETS	1	0.919	1	1	0.919	1	CLONAL	2	TRUE	1	0.468776556386945	3		321	175	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80083461	80083461	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	239	732	0	ENST00000265081.6:c.2513C>G	p.Ala838Gly	p.A838G	ENST00000265081	NM_002439.4	838	gCc/gGc	18/24	0.440808249472995	3	FACETS	0.819	0.768	0.872	0.819	0.768	0.872	CLONAL	2	TRUE	1	0.468776556386945	3		732	768	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517438	176517438	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	120	426	1	ENST00000292408.4:c.139G>T	p.Val47Leu	p.V47L	ENST00000292408	NM_213647.1	47	Gta/Tta	3/18	0.39085890376143	4	FACETS	0.874	0.796	0.956	0.874	0.796	0.956	CLONAL	2	TRUE	2	0.468776556386945	4		427	430	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797268	32797268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770111657	NA	P-0017854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	246	805	1	ENST00000374899.4:c.1841G>A	p.Arg614His	p.R614H	ENST00000374899	NM_018833.2	614	cGt/cAt	11/12	0.351068832894027	5	FACETS	0.88	0.823	0.939	0.586	0.548	0.626	CLONAL	2	TRUE	2	0.468776556386945	5		806	1016	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412259	63412259	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200552684	NA	P-0017854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	191	441	0	ENST00000330258.3:c.908G>A	p.Gly303Asp	p.G303D	ENST00000330258	NM_152424.3	303	gGc/gAc	2/2	0.10892481939313	2	FACETS	1	0.971	1			1	INDETERMINATE	2	TRUE	NA	0.468776556386945	2		441	386	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0017855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	128	941	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.431501638234113	1	FACETS	0.909	0.828	0.993	0.909	0.828	0.993	CLONAL	1	TRUE	0	0.431501638234113	1		942	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0017855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	265	648	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.431501638234113	2	FACETS	0.994	0.939	1	0.994	0.939	1	CLONAL	2	TRUE	0	0.431501638234113	2		648	618	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0017855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	87	609	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.431501638234113	1	FACETS	0.976	0.873	1	0.976	0.873	1	CLONAL	1	TRUE	0	0.431501638234113	1		609	324	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243045	105243045	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	102	638	0	ENST00000349310.3:c.238T>C	p.Trp80Arg	p.W80R	ENST00000349310	NM_001014432.1	80	Tgg/Cgg	5/15	1	2	FACETS	0.825	0.74	0.915	0.825	0.74	0.915	CLONAL	1	TRUE	1	0.431501638234113	2		638	573	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114901001	114901002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0017855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	166	573	2	ENST00000543371.1:c.612dup	p.Thr205HisfsTer5	p.T205Hfs*5	ENST00000543371	NM_001198531.1	204	atc/atCc	6/14	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.431501638234113	2		575	702	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359633	40359633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	264	599	1	ENST00000293328.3:c.2020C>T	p.Pro674Ser	p.P674S	ENST00000293328	NM_012448.3	674	Cca/Tca	16/19	0.431501638234113	2	FACETS	0.954	0.901	1	0.954	0.901	1	CLONAL	2	TRUE	0	0.431501638234113	2		600	641	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509317	149509317	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0017855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	45	222	1	ENST00000261799.4:c.1579+3G>A		p.X527_splice	ENST00000261799	NM_002609.3	527			1	2	FACETS	0.88	0.746	1	0.88	0.746	1	CLONAL	1	TRUE	1	0.431501638234113	2		223	237	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	83	184	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.944	1			1	INDETERMINATE	1	TRUE	NA	0.802279083245789	2		184	194	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700232	117700232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146533107	NA	P-0017856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	223	578	0	ENST00000368508.3:c.2587C>T	p.Arg863Trp	p.R863W	ENST00000368508	NM_002944.2	863	Cgg/Tgg	17/43	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.802279083245789	2		578	504	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0017856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	59	724	2	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.777206970097383	4	FACETS	0.288	0.247	0.333			1	SUBCLONAL	1	TRUE	NA	0.802279083245789	4		726	920	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074064	8074064	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	117	365	0	ENST00000377482.5:c.595C>T	p.Arg199Ter	p.R199*	ENST00000377482	NM_018948.3	199	Cga/Tga	4/4	0.802279083245789	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.802279083245789	1		365	161	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255599	16255599	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs989770862	NA	P-0017856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	138	518	0	ENST00000375759.3:c.2864A>C	p.Glu955Ala	p.E955A	ENST00000375759	NM_015001.2	955	gAa/gCa	11/15	1	2	FACETS	0.994	0.917	1	0.994	0.917	1	CLONAL	1	TRUE	1	0.802279083245789	2		518	346	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307499	118307499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	154	615	1	ENST00000534358.1:c.272C>T	p.Ser91Phe	p.S91F	ENST00000534358	NM_005933.3	91	tCt/tTt	1/36	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.802279083245789	2		616	362	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164218	47164218	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	160	451	1	ENST00000409792.3:c.1908del	p.Phe636LeufsTer6	p.F636Lfs*6	ENST00000409792	NM_014159.6	636	ttT/tt	3/21	1	2	FACETS	0.934	0.866	1	0.934	0.866	1	CLONAL	1	TRUE	1	0.802279083245789	2		452	427	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575506	67575506	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	170	419	0	ENST00000274335.5:c.579del	p.Leu193PhefsTer14	p.L193Ffs*14	ENST00000274335		193	ttA/tt	4/15	1	2	FACETS	0.968	0.899	1	0.968	0.899	1	CLONAL	1	TRUE	1	0.802279083245789	2		419	438	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588143	67588144	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0017856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	240	562	0	ENST00000274335.5:c.973_974del	p.Asn325TyrfsTer7	p.N325Yfs*7	ENST00000274335		325	AAt/t	7/15	1	2	FACETS	0.982	0.924	1	0.982	0.924	1	CLONAL	1	TRUE	1	0.802279083245789	2		562	609	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057021	180057021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752512978	NA	P-0017856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	167	702	1	ENST00000261937.6:c.598G>A	p.Asp200Asn	p.D200N	ENST00000261937	NM_182925.4	200	Gat/Aat	5/30	NA	2	FACETS	0.987	0.917	1			1	INDETERMINATE	1	TRUE	NA	0.802279083245789	2		703	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0017857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	35	775	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.15	2		777	434	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0017857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	16	271	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.824	0.609	1	0.824	0.609	1	CLONAL	1	TRUE	1	0.15	2		271	259	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519896	NA	P-0017857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	21	477	0	ENST00000281708.4:c.1514G>T	p.Arg505Leu	p.R505L	ENST00000281708	NM_033632.3	505	cGc/cTc	10/12	1	2	FACETS	0.523	0.402	0.666	0.523	0.402	0.666	SUBCLONAL	1	TRUE	1	0.15	2		477	535	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0017858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	212	731	1	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.377647521784473	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.377647521784473	3		732	542	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0017858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	2994	578	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.377647521784473	46	FACETS	0.992	0.985	0.999			1	CLONAL	45	TRUE	NA	0.377647521784473	46		578	3307	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272213	15272213	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	46	440	0	ENST00000263388.2:c.6226G>T	p.Gly2076Trp	p.G2076W	ENST00000263388	NM_000435.2	2076	Ggg/Tgg	33/33	0.377647521784473	3	FACETS	0.862	0.729	1	0.431	0.364	0.504	CLONAL	1	TRUE	1	0.377647521784473	3		440	336	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693869	47693869	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs755799226	NA	P-0017858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	108	637	0	ENST00000233146.2:c.1583A>G	p.Lys528Arg	p.K528R	ENST00000233146	NM_000251.2	528	aAg/aGg	10/16	0.377647521784473	6	FACETS	0.806	0.725	0.891	0.403	0.362	0.446	CLONAL	2	TRUE	2	0.377647521784473	6		637	623	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612032	189612032	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	145	510	0	ENST00000264731.3:c.1784A>T	p.His595Leu	p.H595L	ENST00000264731	NM_003722.4	595	cAt/cTt	14/14	0.377647521784473	5	FACETS	1	0.952	1	1	0.952	1	CLONAL	3	TRUE	2	0.377647521784473	5		510	385	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439336	149439336	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	389	573	0	ENST00000286301.3:c.2059C>A	p.Leu687Met	p.L687M	ENST00000286301	NM_005211.3	687	Ctg/Atg	15/22	0.377647521784473	8	FACETS	0.932	0.892	0.972	0.932	0.892	0.972	CLONAL	6	TRUE	2	0.377647521784473	8		573	786	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707624	176707624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1315206249	NA	P-0017858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	55	558	1	ENST00000439151.2:c.5681G>A	p.Arg1894His	p.R1894H	ENST00000439151	NM_022455.4	1894	cGt/cAt	18/23	0.274331626285065	3	FACETS	0.855	0.734	0.987			1	CLONAL	1	TRUE	NA	0.377647521784473	3		559	405	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665365	117665365	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	16	343	0	ENST00000368508.3:c.4382A>G	p.Asn1461Ser	p.N1461S	ENST00000368508	NM_002944.2	1461	aAc/aGc	27/43	0.377647521784473	3	FACETS	0.398	0.294	0.522	0.199	0.147	0.261	SUBCLONAL	1	TRUE	1	0.377647521784473	3		343	253	SUCCESS
BTK	695	MSKCC	GRCh37	X	100629544	100629544	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	177	371	0	ENST00000308731.7:c.220C>A	p.Pro74Thr	p.P74T	ENST00000308731	NM_000061.2	74	Cct/Act	3/19	0.377647521784473	2	FACETS	0.911	0.854	0.967			1	CLONAL	3	TRUE	NA	0.377647521784473	2		371	343	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593607	+	protein_altering_variant	In_Frame_Del	DEL	AGTGGAA	AGTGGAA	G	novel	NA	P-0017859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	228	446	0	ENST00000288135.5:c.1667_1673delinsG	p.Gln556_Lys558delinsArg	p.Q556_K558delinsR	ENST00000288135	NM_000222.2	556	cAGTGGAAg/cGg	11/21	0.703686908599532	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.703686908599532	2		446	313	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631839	90631839	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519906	NA	P-0017860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	29	420	0	ENST00000330062.3:c.514A>T	p.Arg172Trp	p.R172W	ENST00000330062	NM_002168.2	172	Agg/Tgg	4/11	1	2	FACETS	0.591	0.474	0.724	0.591	0.474	0.724	SUBCLONAL	1	TRUE	1	0.235448660512318	2		420	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520008	NA	P-0017860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	93	632	0	ENST00000269305.4:c.613T>G	p.Tyr205Asp	p.Y205D	ENST00000269305	NM_001126112.2	205	Tat/Gat	6/11	0.207800387786236	1	FACETS	0.944	0.84	1	0.944	0.84	1	CLONAL	1	TRUE	0	0.235448660512318	1		632	738	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271257	26271257	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	21	344	0	ENST00000305910.3:c.356C>G	p.Thr119Ser	p.T119S	ENST00000305910	NM_003534.2	119	aCt/aGt	1/1	1	2	FACETS	0.447	0.343	0.568	0.447	0.343	0.568	SUBCLONAL	1	TRUE	1	0.235448660512318	2		344	399	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796781	135796781	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	32	334	0	ENST00000298552.3:c.706G>T	p.Gly236Ter	p.G236*	ENST00000298552	NM_001162426.1	236	Gga/Tga	8/23	0.235448660512318	1	FACETS	0.799	0.651	0.966	0.799	0.651	0.966	CLONAL	1	TRUE	0	0.235448660512318	1		334	300	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	38	918	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.886	0.731	1	0.886	0.731	1	CLONAL	1	TRUE	1	0.14	2		918	613	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375171	31375171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140395707	NA	P-0017861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	63	638	0	ENST00000328111.2:c.568C>T	p.Arg190Cys	p.R190C	ENST00000328111	NM_006892.3	190	Cgc/Tgc	6/23	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.14	2		638	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0017861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	23	404	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			1	2	FACETS	0.792	0.616	0.995	0.792	0.616	0.995	CLONAL	1	TRUE	1	0.14	2		404	415	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132531	11132531	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	31	559	0	ENST00000358026.2:c.2747A>G	p.Asn916Ser	p.N916S	ENST00000358026	NM_001128849.1	916	aAc/aGc	19/36	1	2	FACETS	0.858	0.693	1	0.858	0.693	1	CLONAL	1	TRUE	1	0.14	2		559	516	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548250	41548250	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	32	465	0	ENST00000263253.7:c.3038A>T	p.Glu1013Val	p.E1013V	ENST00000263253	NM_001429.3	1013	gAa/gTa	16/31	1	2	FACETS	0.864	0.7	1	0.864	0.7	1	CLONAL	1	TRUE	1	0.14	2		465	529	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971158	21971161	+	frameshift_variant	Frame_Shift_Del	DEL	CCGT	CCGT	-	novel	NA	P-0017861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	22	281	0	ENST00000304494.5:c.197_200del	p.His66ProfsTer79	p.H66Pfs*79	ENST00000304494	NM_000077.4	66	cACGGc/cc	2/3	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.14	2		281	277	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0017863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	92	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.31639146731886	2		306	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0017863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	179	1001	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.31639146731886	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	0	0.31639146731886	1		1001	846	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224307	55224307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1164954595	NA	P-0017863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	152	605	0	ENST00000275493.2:c.1088C>T	p.Thr363Ile	p.T363I	ENST00000275493	NM_005228.3	363	aCc/aTc	9/28	0.281386514376569	3	FACETS	1	0.985	1	0.677	0.619	0.737	CLONAL	1	FALSE	1	0.31639146731886	3		605	822	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226590076	226590076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	94	454	1	ENST00000366794.5:c.125C>T	p.Pro42Leu	p.P42L	ENST00000366794	NM_001618.3	42	cCc/cTc	2/23	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	FALSE	1	0.31639146731886	2		455	575	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653817	89653817	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	75	459	0	ENST00000371953.3:c.115G>C	p.Ala39Pro	p.A39P	ENST00000371953	NM_000314.4	39	Gca/Cca	2/9	0.31639146731886	1	FACETS	0.924	0.813	1	0.924	0.813	1	CLONAL	1	FALSE	0	0.31639146731886	1		459	432	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934218	48934222	+	frameshift_variant	Frame_Shift_Del	DEL	TATTT	TATTT	-	novel	NA	P-0017863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	101	634	2	ENST00000267163.4:c.677_681del	p.Phe226Ter	p.F226*	ENST00000267163	NM_000321.2	225	TATTTt/t	7/27	0.31639146731886	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	0	0.31639146731886	1		636	491	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	74	184	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.551111838887015	2		184	234	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0017864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6295	2785	557	0	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.551111838887015	43	FACETS	0.978	0.959	0.996	0.318	0.312	0.325	CLONAL	14	TRUE	0	0.551111838887015	43		557	9080	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0017864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7681	208	823	1	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.551111838887015	43	FACETS	1	0.979	1	0.027	0.025	0.03	CLONAL	1	TRUE	0	0.551111838887015	43		824	7889	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169853	32169853	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs751390609	NA	P-0017864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	136	526	0	ENST00000375023.3:c.3755C>T	p.Thr1252Ile	p.T1252I	ENST00000375023	NM_004557.3	1252	aCt/aTt	21/30	1	2	FACETS	0.96	0.878	1	0.96	0.878	1	CLONAL	1	TRUE	1	0.551111838887015	2		526	514	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143246	30143246	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1060500234	NA	P-0017864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	110	474	0	ENST00000389048.3:c.280G>T	p.Asp94Tyr	p.D94Y	ENST00000389048	NM_004304.4	94	Gac/Tac	1/29	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.551111838887015	2		474	358	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952093	178952093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs2108429932	NA	P-0017864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	123	447	3	ENST00000263967.3:c.3148G>A	p.Gly1050Ser	p.G1050S	ENST00000263967	NM_006218.2	1050	Ggc/Agc	21/21	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.551111838887015	2		450	430	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0017865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	155	427	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.246034543247725	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.19	3		427	787	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163456	108163469	+	frameshift_variant	Frame_Shift_Del	DEL	ATCTTCATGTTATT	ATCTTCATGTTATT	-	novel	NA	P-0017865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	48	505	0	ENST00000278616.4:c.4547_4560del	p.His1516ArgfsTer10	p.H1516Rfs*10	ENST00000278616	NM_000051.3	1516	cATCTTCATGTTATT/c	30/63	1	2	FACETS	0.788	0.665	0.924	0.788	0.665	0.924	CLONAL	1	TRUE	1	0.19	2		505	641	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	44	184	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.874	0.735	1	0.874	0.735	1	CLONAL	1	TRUE	1	0.26701681250578	2		184	377	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0017879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	177	916	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.160346032644673	3	FACETS	1	0.982	1	0.62	0.57	0.673	CLONAL	1	TRUE	1	0.26701681250578	3		916	1211	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0017879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	136	958	2	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	1	2	FACETS	0.871	0.79	0.957	0.871	0.79	0.957	CLONAL	1	TRUE	1	0.26701681250578	2		960	1169	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582213	52582213	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	33	366	0	ENST00000394830.3:c.4615A>C	p.Ser1539Arg	p.S1539R	ENST00000394830	NM_018313.4	1539	Agc/Cgc	30/30	1	2	FACETS	0.584	0.476	0.707	0.584	0.476	0.707	SUBCLONAL	1	TRUE	1	0.26701681250578	2		366	423	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148726	20148726	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0017879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	99	741	0	ENST00000379607.5:c.338-1G>T		p.X113_splice	ENST00000379607	NM_001412.3	113			1	2	FACETS	0.878	0.783	0.979	0.878	0.783	0.979	CLONAL	1	TRUE	1	0.26701681250578	2		741	845	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0017882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	421	849	0	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	0.44784246930624	0	FACETS		NA	1			1	NA	3	FALSE	0	0.464493969871875	0		849	522	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341730	8341730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41281783	NA	P-0017882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	144	890	0	ENST00000356435.5:c.4910C>T	p.Thr1637Met	p.T1637M	ENST00000356435		1637	aCg/aTg	29/35	0.464493969871875	2	FACETS	0.598	0.545	0.655	0.299	0.272	0.328	SUBCLONAL	1	FALSE	0	0.464493969871875	2		890	1036	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953041	2953041	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149857605	NA	P-0017882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	171	817	1	ENST00000396946.4:c.2899C>T	p.Arg967Cys	p.R967C	ENST00000396946	NM_032415.4	967	Cgc/Tgc	22/25	0.190955097574913	3	FACETS	0.908	0.835	0.985	0.303	0.278	0.329	INDETERMINATE	1	FALSE	0	0.464493969871875	3		818	999	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	104	579	4	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	0.915	0.824	1	0.915	0.824	1	CLONAL	1	TRUE	1	0.485467413902376	2		583	468	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	163	865	8	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.888	0.817	0.963	0.888	0.817	0.963	CLONAL	1	TRUE	1	0.485467413902376	2		873	756	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	72	477	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.485467413902376	2		477	278	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494690	2494690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770694552	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	174	1110	2	ENST00000355716.4:c.830C>T	p.Thr277Met	p.T277M	ENST00000355716	NM_003820.2	277	aCg/aTg	8/8	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.485467413902376	2		1112	716	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552144	29552144	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	81	376	0	ENST00000356175.3:c.1882del	p.Tyr628ThrfsTer3	p.Y628Tfs*3	ENST00000356175	NM_000267.3	626	cTt/ct	17/57	1	2	FACETS	0.976	0.883	1	1	0.986	1	CLONAL	2	TRUE	1	0.485467413902376	2		376	171	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	24	326	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.51	0.402	0.632	0.51	0.402	0.632	SUBCLONAL	1	TRUE	1	0.485467413902376	2		326	194	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216545	108216545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779872	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	62	602	0	ENST00000278616.4:c.8494C>T	p.Arg2832Cys	p.R2832C	ENST00000278616	NM_000051.3	2832	Cgt/Tgt	58/63	1	2	FACETS	0.837	0.729	0.953	0.837	0.729	0.953	CLONAL	1	TRUE	1	0.485467413902376	2		602	305	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330611	65330611	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	88	680	0	ENST00000342505.4:c.1035del	p.Lys345AsnfsTer32	p.K345Nfs*32	ENST00000342505	NM_002227.2	345	aaA/aa	8/25	1	2	FACETS	0.729	0.648	0.815	0.729	0.648	0.815	SUBCLONAL	1	TRUE	1	0.485467413902376	2		680	497	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796883	42796883	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	192	1267	5	ENST00000575354.2:c.3347del	p.Pro1116GlnfsTer45	p.P1116Qfs*45	ENST00000575354	NM_015125.3	1114	gCc/gc	14/20	1	2	FACETS	0.938	0.869	1	0.938	0.869	1	CLONAL	1	TRUE	1	0.485467413902376	2		1272	843	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	171	689	7	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.485467413902376	2		696	631	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836428	89836428	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759117757	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	79	573	0	ENST00000389301.3:c.2321C>T	p.Pro774Leu	p.P774L	ENST00000389301	NM_000135.2	774	cCg/cTg	26/43	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.485467413902376	2		573	321	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785964	135785964	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs118203506	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	210	646	0	ENST00000298552.3:c.1257del	p.Arg420GlyfsTer20	p.R420Gfs*20	ENST00000298552	NM_001162426.1	419	ccC/cc	12/23	1	2	FACETS	0.949	0.892	1	1	0.994	1	CLONAL	2	TRUE	1	0.485467413902376	2		646	456	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363489	40363489	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749442938	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	119	680	1	ENST00000397332.2:c.740G>A	p.Arg247His	p.R247H	ENST00000397332	NM_001033082.2	247	cGt/cAt	3/3	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.485467413902376	2		681	483	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907421	32907421	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359306	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	97	669	7	ENST00000380152.3:c.1813del	p.Ile605TyrfsTer9	p.I605Yfs*9	ENST00000380152		602	ggA/gg	10/27	1	2	FACETS	0.947	0.85	1	0.947	0.85	1	CLONAL	1	TRUE	1	0.485467413902376	2		676	422	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856305	111856305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777034332	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	10	52	0	ENST00000341259.2:c.356G>A	p.Arg119His	p.R119H	ENST00000341259	NM_005475.2	119	cGc/cAc	2/8	1	2	FACETS	0.777	0.54	1	0.777	0.54	1	CLONAL	1	TRUE	1	0.485467413902376	2		52	53	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061304	38061304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	37	940	0	ENST00000250448.2:c.685G>A	p.Val229Ile	p.V229I	ENST00000250448	NM_004496.3	229	Gtc/Atc	2/2	1	2	FACETS	0.24	0.197	0.288	0.24	0.197	0.288	SUBCLONAL	1	TRUE	1	0.485467413902376	2		940	636	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137325969	137325969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1318249611	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	161	993	3	ENST00000481739.1:c.1157C>T	p.Pro386Leu	p.P386L	ENST00000481739	NM_002957.4	386	cCg/cTg	9/10	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.485467413902376	2		996	640	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37091976	37091976	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	188	530	0	ENST00000231790.2:c.2104-1G>C		p.X702_splice	ENST00000231790	NM_000249.3	702			0.485467413902376	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.485467413902376	2		530	374	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752695	42752695	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1366176199	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	181	890	2	ENST00000222329.4:c.1569del	p.Leu525SerfsTer6	p.L525Sfs*6	ENST00000222329	NM_006494.2	523	ggG/gg	4/4	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.485467413902376	2		892	587	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	160	897	11	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.485467413902376	2		908	553	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430835	78430835	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	155	917	0	ENST00000370768.2:c.554del	p.Asn185MetfsTer7	p.N185Mfs*7	ENST00000370768	NM_003902.3	185	aAt/at	8/20	1	2	FACETS	0.982	0.902	1	0.982	0.902	1	CLONAL	1	TRUE	1	0.485467413902376	2		917	650	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165516	118165516	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	76	275	0	ENST00000369448.3:c.28del	p.Asp10IlefsTer37	p.D10Ifs*37	ENST00000369448	NM_017709.3	9	aGg/ag	2/2	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.485467413902376	2		275	245	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246078896	246078896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs987211168	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	174	846	1	ENST00000388985.4:c.749G>A	p.Arg250Gln	p.R250Q	ENST00000388985		250	cGg/cAg	8/12	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.485467413902376	2		847	715	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608376	43608376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780808	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	263	1288	2	ENST00000355710.3:c.1724C>T	p.Thr575Ile	p.T575I	ENST00000355710	NM_020975.4	575	aCc/aTc	9/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.485467413902376	2		1290	968	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446149	70446149	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1281698688	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	107	660	1	ENST00000373644.4:c.5089G>A	p.Gly1697Ser	p.G1697S	ENST00000373644	NM_030625.2	1697	Ggt/Agt	11/12	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.485467413902376	2		661	441	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17743024	17743024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	155	891	6	ENST00000250003.3:c.932C>T	p.Ala311Val	p.A311V	ENST00000250003	NM_002478.4	311	gCg/gTg	3/3	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.485467413902376	2		897	502	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466022	69466024	+	inframe_deletion	In_Frame_Del	DEL	CCA	CCA	-	novel	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	183	917	0	ENST00000227507.2:c.862_864del	p.Thr288del	p.T288del	ENST00000227507	NM_053056.2	287	cCCAcc/ccc	5/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.485467413902376	2		917	654	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438018	49438018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs111266743	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	206	903	1	ENST00000301067.7:c.5153C>T	p.Ala1718Val	p.A1718V	ENST00000301067	NM_003482.3	1718	gCg/gTg	21/54	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.485467413902376	2		904	747	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992478	72992478	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	268	1093	0	ENST00000268489.5:c.1567C>A	p.Leu523Ile	p.L523I	ENST00000268489	NM_006885.3	523	Ctt/Att	2/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.485467413902376	2		1093	1013	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042481	16042481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	89	788	0	ENST00000268712.3:c.1193G>A	p.Arg398Gln	p.R398Q	ENST00000268712	NM_006311.3	398	cGg/cAg	12/46	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.485467413902376	2		788	355	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428327	33428327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781813	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	161	733	2	ENST00000345365.6:c.796C>T	p.Arg266Cys	p.R266C	ENST00000345365	NM_002878.3	266	Cgc/Tgc	9/10	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.485467413902376	2		735	623	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487540	38487540	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	167	789	2	ENST00000254066.5:c.70T>C	p.Tyr24His	p.Y24H	ENST00000254066	NM_000964.3	24	Tac/Cac	2/9	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.485467413902376	2		791	653	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56809850	56809850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	104	798	1	ENST00000337432.4:c.971C>T	p.Ala324Val	p.A324V	ENST00000337432	NM_058216.2	324	gCa/gTa	8/9	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.485467413902376	2		799	428	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007182	62007182	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147194821	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	160	829	2	ENST00000392795.3:c.500C>T	p.Thr167Met	p.T167M	ENST00000392795	NM_001039933.1	167	aCg/aTg	4/6	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.485467413902376	2		831	574	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727832	78727832	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	225	1122	0	ENST00000306801.3:c.677A>G	p.His226Arg	p.H226R	ENST00000306801	NM_020761.2	226	cAc/cGc	6/34	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.485467413902376	2		1122	923	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985448	60985450	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	200	1154	0	ENST00000333681.4:c.450_452del	p.Phe151del	p.F151del	ENST00000333681		150	ttCTTt/ttt	2/3	1	2	FACETS	0.963	0.893	1	0.963	0.893	1	CLONAL	1	TRUE	1	0.485467413902376	2		1154	856	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600408	10600408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1412883238	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	272	1122	2	ENST00000171111.5:c.1447C>T	p.Arg483Cys	p.R483C	ENST00000171111	NM_203500.1	483	Cgc/Tgc	4/6	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.485467413902376	2		1124	1038	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791008	42791009	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	132	727	0	ENST00000575354.2:c.153_154insA	p.Ser52IlefsTer25	p.S52Ifs*25	ENST00000575354	NM_015125.3	51	-/A	2/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.485467413902376	2		727	422	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471037	25471039	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-	novel	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	211	901	0	ENST00000264709.3:c.722_724del	p.Glu241del	p.E241del	ENST00000264709	NM_175629.2	241	gAGGcc/gcc	7/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.485467413902376	2		901	762	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661186	227661186	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	119	808	0	ENST00000305123.5:c.2269del	p.Gln757SerfsTer186	p.Q757Sfs*186	ENST00000305123	NM_005544.2	757	Cag/ag	1/2	1	2	FACETS	0.761	0.688	0.838	0.761	0.688	0.838	SUBCLONAL	1	TRUE	1	0.485467413902376	2		808	644	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651473	52651474	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	119	922	1	ENST00000394830.3:c.1622_1623del	p.Arg541ThrfsTer3	p.R541Tfs*3	ENST00000394830	NM_018313.4	541	aGA/a	15/30	1	2	FACETS	0.801	0.725	0.881	0.801	0.725	0.881	CLONAL	1	TRUE	1	0.485467413902376	2		923	612	SUCCESS
ATR	545	MSKCC	GRCh37	3	142184046	142184048	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	76	652	0	ENST00000350721.4:c.6932_6934del	p.Lys2311del	p.K2311del	ENST00000350721	NM_001184.3	2311	aAGAtt/att	41/47	1	2	FACETS	0.994	0.88	1	0.994	0.88	1	CLONAL	1	TRUE	1	0.485467413902376	2		652	315	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524581	187524581	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	138	844	0	ENST00000441802.2:c.11099A>G	p.Lys3700Arg	p.K3700R	ENST00000441802	NM_005245.3	3700	aAa/aGa	19/27	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.485467413902376	2		844	511	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557891	187557891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200242253	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	150	494	1	ENST00000441802.2:c.3820G>A	p.Val1274Ile	p.V1274I	ENST00000441802	NM_005245.3	1274	Gtc/Atc	5/27	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.485467413902376	2		495	454	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294255	1294255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1174718400	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	130	709	1	ENST00000310581.5:c.746C>T	p.Thr249Met	p.T249M	ENST00000310581	NM_198253.2	249	aCg/aTg	2/16	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.485467413902376	2		710	449	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591079	67591102	+	inframe_deletion	In_Frame_Del	DEL	GAAATTGACAAACGTATGAACAGC	GAAATTGACAAACGTATGAACAGC	-	novel	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	68	584	0	ENST00000274335.5:c.1672_1695del	p.Glu558_Ser565del	p.E558_S565del	ENST00000274335		558	GAAATTGACAAACGTATGAACAGC/-	12/15	1	2	FACETS	0.862	0.756	0.975	0.862	0.756	0.975	CLONAL	1	TRUE	1	0.485467413902376	2		584	325	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627205	86627205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761101703	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	65	344	1	ENST00000274376.6:c.580C>T	p.Arg194Cys	p.R194C	ENST00000274376	NM_002890.2	194	Cgc/Tgc	2/25	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.485467413902376	2		345	265	SUCCESS
APC	324	MSKCC	GRCh37	5	112178066	112178066	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	147	736	0	ENST00000257430.4:c.6778del	p.Ser2260AlafsTer19	p.S2260Afs*19	ENST00000257430	NM_000038.5	2259	Aaa/aa	16/16	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.485467413902376	2		736	582	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435874	149435874	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs690016564	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	205	859	2	ENST00000286301.3:c.2350G>A	p.Val784Met	p.V784M	ENST00000286301	NM_005211.3	784	Gtg/Atg	18/22	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.485467413902376	2		861	733	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048196	180048196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	235	1090	4	ENST00000261937.6:c.2077G>A	p.Asp693Asn	p.D693N	ENST00000261937	NM_182925.4	693	Gac/Aac	14/30	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.485467413902376	2		1094	833	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056426	180056426	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	65	519	1	ENST00000261937.6:c.818C>T	p.Ala273Val	p.A273V	ENST00000261937	NM_182925.4	273	gCa/gTa	7/30	1	2	FACETS	0.933	0.816	1	0.933	0.816	1	CLONAL	1	TRUE	1	0.485467413902376	2		520	287	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402512	20402512	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	142	840	0	ENST00000346618.3:c.53del	p.Gly18ValfsTer22	p.G18Vfs*22	ENST00000346618	NM_001949.4	17	Ggg/gg	1/7	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.485467413902376	2		840	571	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080657	5080657	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774709145	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	84	707	1	ENST00000381652.3:c.2408G>A	p.Arg803Gln	p.R803Q	ENST00000381652	NM_004972.3	803	cGa/cAa	18/25	1	2	FACETS	0.805	0.714	0.901	0.805	0.714	0.901	CLONAL	1	TRUE	1	0.485467413902376	2		708	430	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238333	98238333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1420410274	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	28	460	0	ENST00000331920.6:c.1711C>T	p.Arg571Trp	p.R571W	ENST00000331920	NM_000264.3	571	Cgg/Tgg	12/24	1	2	FACETS	0.266	0.212	0.327	0.266	0.212	0.327	SUBCLONAL	1	TRUE	1	0.485467413902376	2		460	434	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753870	133753870	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	131	867	1	ENST00000318560.5:c.1339C>T	p.Gln447Ter	p.Q447*	ENST00000318560	NM_005157.4	447	Cag/Tag	8/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.485467413902376	2		868	507	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417373	139417373	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	145	837	1	ENST00000277541.6:c.671C>A	p.Pro224His	p.P224H	ENST00000277541	NM_017617.3	224	cCc/cAc	4/34	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.485467413902376	2		838	499	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793208	139793208	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561210418	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	228	870	2	ENST00000247668.2:c.16G>A	p.Val6Met	p.V6M	ENST00000247668	NM_021138.3	6	Gtg/Atg	2/11	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.485467413902376	2		872	688	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030582	47030582	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs868917893	NA	P-0017883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	180	943	5	ENST00000377604.3:c.357G>T	p.Glu119Asp	p.E119D	ENST00000377604	NM_001204468.1	119	gaG/gaT	4/24	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.485467413902376	2		948	559	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	116	918	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	0.905	0.823	0.99			1	INDETERMINATE	2	TRUE	NA	0.319635084271604	2		918	401	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs730882026	NA	P-0017884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	222	765	0	ENST00000269305.4:c.707A>C	p.Tyr236Ser	p.Y236S	ENST00000269305	NM_001126112.2	236	tAc/tCc	7/11	0.198972086498621	2	FACETS	0.83	0.774	0.887	0.83	0.774	0.887	CLONAL	2	TRUE	0	0.319635084271604	2		765	837	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467748	50467748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	106	718	3	ENST00000331340.3:c.983G>A	p.Arg328His	p.R328H	ENST00000331340	NM_006060.4	328	cGc/cAc	8/8	0.294716821199307	5	FACETS	0.88	0.787	0.979	0.293	0.262	0.327	CLONAL	1	TRUE	2	0.319635084271604	5		721	1115	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0017886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	388	693	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.280423819240548	2	FACETS	0.885	0.843	0.928	1	0.994	1	CLONAL	3	FALSE	0	0.280423819240548	2		693	1042	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223979	36223979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1235	216	1115	0	ENST00000222270.7:c.6529C>T	p.Leu2177Phe	p.L2177F	ENST00000222270	NM_014727.1	2177	Ctt/Ttt	28/37	0.280423819240548	3	FACETS	1	0.984	1	0.605	0.561	0.651	CLONAL	1	FALSE	1	0.280423819240548	3		1115	1451	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028031	48028031	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1054003194	NA	P-0017886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	147	464	0	ENST00000234420.5:c.2913del	p.Ile972LeufsTer25	p.I972Lfs*25	ENST00000234420	NM_000179.2	970	tGg/tg	4/10	0.280423819240548	4	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	FALSE	2	0.280423819240548	4		464	616	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215674235	215674235	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	223	716	0	ENST00000260947.4:c.59C>G	p.Pro20Arg	p.P20R	ENST00000260947	NM_000465.2	20	cCt/cGt	1/11	0.280423819240548	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	FALSE	2	0.280423819240548	4		716	987	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647510	117647510	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	115	834	0	ENST00000368508.3:c.5434A>T	p.Ser1812Cys	p.S1812C	ENST00000368508	NM_002944.2	1812	Agt/Tgt	33/43	0.280423819240548	4	FACETS	1	0.938	1	0.529	0.476	0.586	CLONAL	1	FALSE	2	0.280423819240548	4		834	992	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793310	139793310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1030517939	NA	P-0017886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	254	839	1	ENST00000247668.2:c.118G>A	p.Val40Ile	p.V40I	ENST00000247668	NM_021138.3	40	Gtc/Atc	2/11	0.232636106928514	4	FACETS	0.981	0.917	1	0.981	0.917	1	CLONAL	2	FALSE	2	0.280423819240548	4		840	1182	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	142	918	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.926	0.85	1	0.926	0.85	1	CLONAL	1	TRUE	1	0.635202921734706	2		918	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0017887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	235	1080	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.635202921734706	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.635202921734706	1		1080	491	SUCCESS
ATR	545	MSKCC	GRCh37	3	142284988	142284988	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	54	793	0	ENST00000350721.4:c.267C>A	p.Ser89Arg	p.S89R	ENST00000350721	NM_001184.3	89	agC/agA	3/47	1	2	FACETS	0.371	0.317	0.43	0.371	0.317	0.43	SUBCLONAL	1	TRUE	1	0.635202921734706	2		793	458	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0017889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	69	659	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	0.967	0.859	1	1	0.983	1	CLONAL	2	FALSE	1	0.3715091800266	2		659	192	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398279	25398279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894365	NA	P-0017889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	8	925	1	ENST00000311936.3:c.40G>A	p.Val14Ile	p.V14I	ENST00000311936	NM_004985.3	14	Gta/Ata	2/5	1	2	FACETS	0.144	0.092	0.211	0.144	0.092	0.211	SUBCLONAL	1	FALSE	1	0.3715091800266	2		926	300	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118391545	118391545	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	13	562	0	ENST00000534358.1:c.11458C>T	p.Pro3820Ser	p.P3820S	ENST00000534358	NM_005933.3	3820	Ccc/Tcc	34/36	1	2	FACETS	0.289	0.206	0.391	0.289	0.206	0.391	SUBCLONAL	1	FALSE	1	0.3715091800266	2		562	242	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090671	71090671	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	40	268	0	ENST00000318789.4:c.677del	p.Thr226LysfsTer10	p.T226Kfs*10	ENST00000318789	NM_032682.5	226	aCa/aa	11/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.3715091800266	2		268	148	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519966	NA	P-0017890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	95	669	1	ENST00000347630.2:c.397T>A	p.Phe133Ile	p.F133I	ENST00000347630	NM_001007230.1	133	Ttc/Atc	6/11	0.465024338310245	4	FACETS	1	0.972	1			1	CLONAL	1	TRUE	NA	0.455414274587498	4		670	482	SUCCESS
APC	324	MSKCC	GRCh37	5	112175952	112175952	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587783031	NA	P-0017890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	63	415	0	ENST00000257430.4:c.4666del	p.Thr1556LeufsTer9	p.T1556Lfs*9	ENST00000257430	NM_000038.5	1554	gAa/ga	16/16	0.465024338310245	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.455414274587498	1		415	143	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578278	7578286	+	inframe_deletion	In_Frame_Del	DEL	GAGGGGCCA	GAGGGGCCA	-	novel	NA	P-0017890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	87	737	0	ENST00000269305.4:c.563_571del	p.Leu188_Pro190del	p.L188_P190del	ENST00000269305	NM_001126112.2	188	cTGGCCCCTCct/cct	6/11	0.465024338310245	1	FACETS	0.878	0.801	0.955	1	0.987	1	CLONAL	2	TRUE	0	0.455414274587498	1		737	168	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0017891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	337	507	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.280512911128352	5	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	2	0.280512911128352	5		508	980	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0017892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	116	621	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	0.71	0.641	0.782	0.71	0.641	0.782	SUBCLONAL	1	TRUE	1	0.53921076075935	2		621	606	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0017892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	82	455	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.434	0.382	0.489	0.434	0.382	0.489	SUBCLONAL	1	TRUE	1	0.53921076075935	2		455	701	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0017892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	151	549	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	0.529630935061966	1	FACETS	0.736	0.676	0.797	0.736	0.676	0.797	SUBCLONAL	1	TRUE	0	0.53921076075935	1		549	556	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711887	89711887	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776673	NA	P-0017892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	99	544	2	ENST00000371953.3:c.507del	p.Ser170ValfsTer13	p.S170Vfs*13	ENST00000371953	NM_000314.4	169	Ccc/cc	6/9	0.445519508619946	1	FACETS	0.605	0.543	0.671	0.605	0.543	0.671	SUBCLONAL	1	TRUE	0	0.53921076075935	1		546	443	SUCCESS
ATM	472	MSKCC	GRCh37	11	108159786	108159786	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0017892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	76	408	0	ENST00000278616.4:c.4192A>T	p.Lys1398Ter	p.K1398*	ENST00000278616	NM_000051.3	1398	Aaa/Taa	28/63	1	2	FACETS	0.799	0.705	0.897	0.799	0.705	0.897	SUBCLONAL	1	TRUE	1	0.53921076075935	2		408	353	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555721	21555721	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	169	926	0	ENST00000382592.4:c.2549G>T	p.Cys850Phe	p.C850F	ENST00000382592	NM_014572.2	850	tGt/tTt	6/8	0.529630935061966	1	FACETS	0.822	0.76	0.885	0.822	0.76	0.885	CLONAL	1	TRUE	0	0.53921076075935	1		926	557	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585404	29585404	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	551	825	0	ENST00000356175.3:c.4153G>T	p.Gly1385Ter	p.G1385*	ENST00000356175	NM_000267.3	1385	Gga/Tga	31/57	0.817631987170157	2	FACETS	0.95	0.927	0.973	0.95	0.927	0.973	CLONAL	2	TRUE	0	0.817631987170157	2		825	709	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031919	10031919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs901717931	NA	P-0017895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	255	756	2	ENST00000330684.3:c.904G>A	p.Ala302Thr	p.A302T	ENST00000330684	NM_001134407.1	302	Gct/Act	3/13	1	2	FACETS	0.989	0.932	1	0.989	0.932	1	CLONAL	1	TRUE	1	0.817631987170157	2		758	631	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	162	615	1	ENST00000335508.6:c.1873C>A	p.Arg625Ser	p.R625S	ENST00000335508	NM_012433.2	625	Cgt/Agt	14/25	0.323953159131467	3	FACETS	1	0.966	1	0.54	0.499	0.582	INDETERMINATE	1	TRUE	1	0.817631987170157	3		616	517	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172373	7172373	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	298	755	0	ENST00000302850.5:c.1196G>C	p.Arg399Pro	p.R399P	ENST00000302850	NM_000208.2	399	cGa/cCa	5/22	1	2	FACETS	0.957	0.906	1	0.957	0.906	1	CLONAL	1	TRUE	1	0.817631987170157	2		755	762	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1956924	1956924	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	403	903	0	ENST00000382891.5:c.2375A>G	p.Tyr792Cys	p.Y792C	ENST00000382891	NM_133335.3	792	tAt/tGt	13/22	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.817631987170157	2		903	949	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115718	8115719	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CATA	novel	NA	P-0017898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	157	736	0	ENST00000346208.3:c.1064_1065insCATA	p.Met356IlefsTer16	p.M356Ifs*16	ENST00000346208		355	act/acCATAt	6/6	1	2	FACETS	0.882	0.808	0.958	0.882	0.808	0.958	CLONAL	1	TRUE	1	0.430138357440981	2		736	828	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644856	67644856	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	154	665	0	ENST00000264010.4:c.124del	p.Gln42ArgfsTer20	p.Q42Rfs*20	ENST00000264010	NM_006565.3	41	Ccc/cc	3/12	0.430138357440981	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.430138357440981	1		665	547	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89345543	89345543	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	25	223	0	ENST00000301030.4:c.7407C>A	p.Tyr2469Ter	p.Y2469*	ENST00000301030	NM_001256183.1	2469	taC/taA	9/13	0.430138357440981	1	FACETS	0.604	0.481	0.742	0.604	0.481	0.742	SUBCLONAL	1	TRUE	0	0.430138357440981	1		223	151	SUCCESS
APC	324	MSKCC	GRCh37	5	112175524	112175524	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	26	475	0	ENST00000257430.4:c.4233del	p.Ser1411ArgfsTer4	p.S1411Rfs*4	ENST00000257430	NM_000038.5	1411	agT/ag	16/16	0.259823657946467	1	FACETS	0.4	0.316	0.496	0.4	0.316	0.496	SUBCLONAL	1	TRUE	0	0.26736995813911	1		475	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578493	7578493	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1206165503	NA	P-0017899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	229	972	1	ENST00000269305.4:c.437G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tGg/tAg	5/11	0.26736995813911	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.26736995813911	1		973	1069	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263191	115263191	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1306278892	NA	P-0017899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	48	761	2	ENST00000438362.2:c.2159G>A	p.Arg720His	p.R720H	ENST00000438362	NM_001242891.1	720	cGc/cAc	17/20	1	2	FACETS	0.523	0.441	0.614	0.523	0.441	0.614	SUBCLONAL	1	TRUE	1	0.26736995813911	2		763	686	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477131	67477131	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	158	745	0	ENST00000327367.4:c.938T>A	p.Ile313Asn	p.I313N	ENST00000327367	NM_005902.3	313	aTt/aAt	7/9	0.26736995813911	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.26736995813911	1		745	741	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0017902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	129	722	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.213692934242282	1	FACETS	0.956	0.865	1	0.956	0.865	1	CLONAL	1	FALSE	0	0.213692934242282	1		722	1128	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509630	106509630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	116	859	2	ENST00000359195.3:c.1624C>T	p.Arg542Trp	p.R542W	ENST00000359195	NM_002649.2	542	Cgg/Tgg	2/11	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	1	0.213692934242282	2		861	1042	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937219	36937219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140159756	NA	P-0017902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	97	894	0	ENST00000361632.4:c.1100G>A	p.Arg367Gln	p.R367Q	ENST00000361632		367	cGg/cAg	9/16	1	2	FACETS	0.781	0.694	0.874	0.781	0.694	0.874	SUBCLONAL	1	FALSE	1	0.213692934242282	2		894	1162	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976209	18976209	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	66	1054	1	ENST00000262803.5:c.2969C>A	p.Pro990Gln	p.P990Q	ENST00000262803	NM_002911.3	990	cCa/cAa	21/24	1	2	FACETS	0.476	0.411	0.547	0.476	0.411	0.547	SUBCLONAL	1	FALSE	1	0.213692934242282	2		1055	1298	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129897	69129897	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	37	457	0	ENST00000288368.4:c.4651A>T	p.Ser1551Cys	p.S1551C	ENST00000288368	NM_024870.2	1551	Agc/Tgc	38/40	1	2	FACETS	0.7	0.576	0.838	0.7	0.576	0.838	SUBCLONAL	1	FALSE	1	0.213692934242282	2		457	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781371	NA	P-0017903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	205	982	0	ENST00000269305.4:c.328C>T	p.Arg110Cys	p.R110C	ENST00000269305	NM_001126112.2	110	Cgt/Tgt	4/11	0.575145735174594	1	FACETS	0.814	0.761	0.867	0.814	0.761	0.867	CLONAL	1	TRUE	0	0.646117983192466	1		982	528	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430798	47430798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776912006	NA	P-0017904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	81	1180	1	ENST00000377045.4:c.1763G>A	p.Arg588His	p.R588H	ENST00000377045	NM_001654.4	588	cGc/cAc	16/16	0.122313042318511	3	FACETS	0.489	0.429	0.554	0.245	0.214	0.277	INDETERMINATE	1	TRUE	1	0.318309385747094	3		1181	1206	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242480	55242504	+	protein_altering_variant	In_Frame_Del	DEL	AACATCTCCGAAAGCCAACAAGGAA	AACATCTCCGAAAGCCAACAAGGAA	G	novel	NA	P-0017904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	933	120	0	ENST00000275493.2:c.2250_2274delinsG	p.Thr751_Glu758del	p.T751_E758del	ENST00000275493	NM_005228.3	750	gcAACATCTCCGAAAGCCAACAAGGAA/gcG	19/28	0.318309385747094	3	FACETS	1	0.99	1	1	0.998	1	CLONAL	4	TRUE	1	0.318309385747094	3		120	1650	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967543	26967543	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	49	687	0	ENST00000381527.3:c.686C>G	p.Thr229Arg	p.T229R	ENST00000381527	NM_001260.1	229	aCg/aGg	7/13	0.938535333979951	1	FACETS	0.112	0.094	0.131	0.112	0.094	0.131	SUBCLONAL	1	TRUE	0	0.938535333979951	1		687	497	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	141	184	0				ENST00000310581	NM_198253.2	-/1132			0.311324038914468	4	FACETS	1	0.963	1	1	0.963	1	INDETERMINATE	2	TRUE	2	0.584529014775163	4		184	356	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348252	348252	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1459625721	NA	P-0017908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	340	767	1	ENST00000262320.3:c.1255-1G>A		p.X419_splice	ENST00000262320	NM_003502.3	419			0.572974730906231	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.584529014775163	2		768	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577499	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CC	CC	-	novel	NA	P-0017908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	241	473	0	ENST00000269305.4:c.782_782+1del		p.X261_splice	ENST00000269305	NM_001126112.2	261		7/11	0.570993265925015	2	FACETS	0.941	0.893	0.989	0.941	0.893	0.989	CLONAL	2	TRUE	0	0.584529014775163	2		473	438	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546841	9546841	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	122	259	0	ENST00000353224.5:c.1181A>G	p.Tyr394Cys	p.Y394C	ENST00000353224	NM_177990.2	394	tAc/tGc	5/10	0.584529014775163	4	FACETS	0.837	0.764	0.913	0.837	0.764	0.913	CLONAL	2	TRUE	2	0.584529014775163	4		259	395	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0017909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	21	468	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.197	0.15	0.251	0.197	0.15	0.251	SUBCLONAL	1	TRUE	1	0.29	2		468	737	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782177	NA	P-0017909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	28	790	0	ENST00000269305.4:c.644G>T	p.Ser215Ile	p.S215I	ENST00000269305	NM_001126112.2	215	aGt/aTt	6/11	1	2	FACETS	0.169	0.134	0.21	0.169	0.134	0.21	SUBCLONAL	1	TRUE	1	0.29	2		790	1140	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0017910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	107	941	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.102413969127257	5	FACETS	1	0.974	1	0.427	0.383	0.475	INDETERMINATE	1	TRUE	2	0.28448226673828	5		942	837	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219336	1219336	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	156	685	0	ENST00000326873.7:c.388G>T	p.Glu130Ter	p.E130*	ENST00000326873	NM_000455.4	130	Gag/Tag	3/10	0.28448226673828	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.28448226673828	1		685	657	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578210	226578210	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	36	541	0	ENST00000366794.5:c.518G>T	p.Arg173Leu	p.R173L	ENST00000366794	NM_001618.3	173	cGg/cTg	4/23	0.115770914326477	3	FACETS	0.511	0.419	0.614	0.17	0.139	0.205	INDETERMINATE	1	TRUE	0	0.28448226673828	3		541	566	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332713	70332713	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	58	568	0	ENST00000373644.4:c.618C>A	p.His206Gln	p.H206Q	ENST00000373644	NM_030625.2	206	caC/caA	2/12	0.276684715400946	3	FACETS	0.826	0.71	0.952	0.413	0.355	0.476	CLONAL	1	TRUE	1	0.28448226673828	3		568	564	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741445	17741445	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	59	895	0	ENST00000250003.3:c.116A>T	p.Asp39Val	p.D39V	ENST00000250003	NM_002478.4	39	gAc/gTc	1/3	0.28448226673828	1	FACETS	0.521	0.447	0.601	0.521	0.447	0.601	SUBCLONAL	1	TRUE	0	0.28448226673828	1		895	683	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192148	108192148	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587779856	NA	P-0017910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	111	403	0	ENST00000278616.4:c.6572+1G>A		p.X2191_splice	ENST00000278616	NM_000051.3	2191			0.115770914326477	3	FACETS	0.954	0.863	1	0.636	0.575	0.7	INDETERMINATE	2	TRUE	0	0.28448226673828	3		403	467	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421023	49421023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766131184	NA	P-0017910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	56	339	0	ENST00000301067.7:c.14726C>T	p.Pro4909Leu	p.P4909L	ENST00000301067	NM_003482.3	4909	cCa/cTa	48/54	0.102413969127257	5	FACETS	1	0.961	1	0.457	0.392	0.527	INDETERMINATE	1	TRUE	2	0.28448226673828	5		339	410	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244183	133244183	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	65	547	1	ENST00000320574.5:c.2225G>T	p.Arg742Leu	p.R742L	ENST00000320574	NM_006231.2	742	cGt/cTt	20/49	1	2	FACETS	0.877	0.761	1	0.877	0.761	1	CLONAL	1	TRUE	1	0.28448226673828	2		548	521	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422027	81422027	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs1331241644	NA	P-0017910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	40	272	0	ENST00000298171.2:c.3G>A	p.Met1?	p.M1?	ENST00000298171	NM_000369.2	1	atG/atA	1/10	1	2	FACETS	0.913	0.762	1	0.913	0.762	1	CLONAL	1	TRUE	1	0.28448226673828	2		272	308	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719758	190719758	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	37	389	0	ENST00000441310.2:c.1760C>G	p.Pro587Arg	p.P587R	ENST00000441310	NM_000534.4	587	cCt/cGt	9/13	1	2	FACETS	0.536	0.442	0.642	0.536	0.442	0.642	SUBCLONAL	1	TRUE	1	0.28448226673828	2		389	485	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274548	198274548	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	52	466	0	ENST00000335508.6:c.850G>C	p.Ala284Pro	p.A284P	ENST00000335508	NM_012433.2	284	Gca/Cca	7/25	1	2	FACETS	0.731	0.623	0.85	0.731	0.623	0.85	SUBCLONAL	1	TRUE	1	0.28448226673828	2		466	500	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31504701	31504701	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	102	688	0	ENST00000344624.3:c.1629A>T	p.Arg543Ser	p.R543S	ENST00000344624		543	agA/agT	8/33	0.28448226673828	4	FACETS	1	0.906	1	0.339	0.302	0.377	CLONAL	1	TRUE	1	0.28448226673828	4		688	907	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482254	87482254	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	64	658	0	ENST00000277120.3:c.1541C>A	p.Pro514Gln	p.P514Q	ENST00000277120		514	cCa/cAa	14/19	0.28448226673828	1	FACETS	0.845	0.733	0.965	0.845	0.733	0.965	CLONAL	1	TRUE	0	0.28448226673828	1		658	457	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0017911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	108	627	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	0.937	0.841	1	0.937	0.841	1	CLONAL	1	TRUE	1	0.31	2		627	744	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441231	52441231	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	102	377	0	ENST00000460680.1:c.539T>A	p.Leu180His	p.L180H	ENST00000460680	NM_004656.3	180	cTc/cAc	7/17	0.296995820915698	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.31	1		377	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0017913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1184	480	731	1	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	0.917	0.875	0.959	0.917	0.875	0.959	CLONAL	1	TRUE	1	0.629119288358399	2		732	1664	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0017913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1249	501	834	0	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	1	2	FACETS	0.91	0.87	0.951	0.91	0.87	0.951	CLONAL	1	TRUE	1	0.629119288358399	2		834	1750	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979283	40979283	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	315	452	0	ENST00000373198.4:c.1850G>T	p.Arg617Leu	p.R617L	ENST00000373198	NM_133170.3	617	cGg/cTg	11/32	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.629119288358399	2		452	994	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65349093	65349093	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	383	541	0	ENST00000342505.4:c.72del	p.Thr25LeufsTer3	p.T25Lfs*3	ENST00000342505	NM_002227.2	24	aaG/aa	3/25	0.629119288358399	1	FACETS	0.994	0.949	1	0.994	0.949	1	CLONAL	1	TRUE	0	0.629119288358399	1		541	840	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989443	85989443	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	180	355	0	ENST00000263360.6:c.1202G>A	p.Cys401Tyr	p.C401Y	ENST00000263360	NM_003797.3	401	tGt/tAt	12/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.629119288358399	2		355	491	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913140	32913140	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs80358695	NA	P-0017913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	31	644	0	ENST00000380152.3:c.4648G>C	p.Glu1550Gln	p.E1550Q	ENST00000380152		1550	Gag/Cag	11/27	0.629119288358399	1	FACETS	0.113	0.091	0.138	0.113	0.091	0.138	SUBCLONAL	1	TRUE	0	0.629119288358399	1		644	598	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110515	4110515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	316	456	0	ENST00000262948.5:c.442G>A	p.Glu148Lys	p.E148K	ENST00000262948	NM_030662.3	148	Gaa/Aaa	3/11	1	2	FACETS	0.912	0.861	0.965	0.912	0.861	0.965	CLONAL	1	TRUE	1	0.629119288358399	2		456	1101	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210481	5210481	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	297	453	0	ENST00000357368.4:c.5486G>T	p.Arg1829Leu	p.R1829L	ENST00000357368	NM_002850.3	1829	cGg/cTg	35/38	1	2	FACETS	0.901	0.849	0.954	0.901	0.849	0.954	CLONAL	1	TRUE	1	0.629119288358399	2		453	1048	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523282	9523282	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	383	590	0	ENST00000353224.5:c.1955T>A	p.Met652Lys	p.M652K	ENST00000353224	NM_177990.2	652	aTg/aAg	9/10	1	2	FACETS	0.939	0.891	0.987	0.939	0.891	0.987	CLONAL	1	TRUE	1	0.629119288358399	2		590	1297	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182256	38182256	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	291	456	0	ENST00000396334.3:c.692G>T	p.Arg231Leu	p.R231L	ENST00000396334	NM_002468.4	231	cGg/cTg	4/5	0.629119288358399	1	FACETS	0.84	0.794	0.886	0.84	0.794	0.886	CLONAL	1	TRUE	0	0.629119288358399	1		456	755	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928380	69928380	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	258	354	0	ENST00000352241.4:c.200A>C	p.Gln67Pro	p.Q67P	ENST00000352241	NM_198159.2	67	cAg/cCg	2/10	0.629119288358399	1	FACETS	0.883	0.832	0.933	0.883	0.832	0.933	CLONAL	1	TRUE	0	0.629119288358399	1		354	637	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390206	89390206	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	160	348	0	ENST00000336596.2:c.955T>A	p.Ser319Thr	p.S319T	ENST00000336596	NM_005233.5	319	Tcc/Acc	4/17	0.629119288358399	1	FACETS	0.805	0.746	0.866	0.805	0.746	0.866	CLONAL	1	TRUE	0	0.629119288358399	1		348	433	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952316	38952316	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	119	212	0	ENST00000357387.3:c.3109A>T	p.Ser1037Cys	p.S1037C	ENST00000357387	NM_152756.3	1037	Agt/Tgt	30/38	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.629119288358399	2		212	378	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178535	56178535	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	146	273	0	ENST00000399503.3:c.3508G>C	p.Asp1170His	p.D1170H	ENST00000399503	NM_005921.1	1170	Gat/Cat	14/20	1	2	FACETS	0.85	0.78	0.923	0.85	0.78	0.923	CLONAL	1	TRUE	1	0.629119288358399	2		273	546	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515421	149515421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	331	478	0	ENST00000261799.4:c.61C>T	p.Leu21Phe	p.L21F	ENST00000261799	NM_002609.3	21	Ctc/Ttc	3/23	1	2	FACETS	0.965	0.913	1	0.965	0.913	1	CLONAL	1	TRUE	1	0.629119288358399	2		478	1090	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176678794	176678794	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	570	440	0	ENST00000439151.2:c.4705G>T	p.Glu1569Ter	p.E1569*	ENST00000439151	NM_022455.4	1569	Gag/Tag	12/23	0.626860760796234	2	FACETS	0.992	0.962	1	0.992	0.962	1	CLONAL	2	TRUE	0	0.629119288358399	2		440	913	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271411	26271411	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	303	426	0	ENST00000305910.3:c.202T>C	p.Phe68Leu	p.F68L	ENST00000305910	NM_003534.2	68	Ttc/Ctc	1/1	0.629119288358399	1	FACETS	0.906	0.859	0.953	0.906	0.859	0.953	CLONAL	1	TRUE	0	0.629119288358399	1		426	729	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813545	32813545	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0017913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	227	290	0	ENST00000354258.4:c.2238C>G	p.Tyr746Ter	p.Y746*	ENST00000354258	NM_000593.5	746	taC/taG	11/11	0.629119288358399	1	FACETS	0.854	0.802	0.907	0.854	0.802	0.907	CLONAL	1	TRUE	0	0.629119288358399	1		290	579	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455145	50455145	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	168	328	0	ENST00000331340.3:c.692G>T	p.Gly231Val	p.G231V	ENST00000331340	NM_006060.4	231	gGc/gTc	6/8	0.219096267579895	1	FACETS	0.533	0.491	0.576	0.533	0.491	0.576	INDETERMINATE	1	TRUE	0	0.629119288358399	1		328	687	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402552	139402552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	417	626	0	ENST00000277541.6:c.3365G>A	p.Cys1122Tyr	p.C1122Y	ENST00000277541	NM_017617.3	1122	tGt/tAt	21/34	1	2	FACETS	0.906	0.861	0.951	0.906	0.861	0.951	CLONAL	1	TRUE	1	0.629119288358399	2		626	1464	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53244007	53244007	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	445	322	0	ENST00000375401.3:c.986T>A	p.Met329Lys	p.M329K	ENST00000375401	NM_004187.3	329	aTg/aAg	8/26	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.629119288358399	1		322	740	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	157	184	0				ENST00000310581	NM_198253.2	-/1132			0.354068822667535	4	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.792958984722751	4		184	574	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69202994	69202994	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	126	479	0	ENST00000462284.1:c.21G>C	p.Met7Ile	p.M7I	ENST00000462284	NM_002392.5	7	atG/atC	2/11	1	2	FACETS	0.993	0.912	1	0.993	0.912	1	CLONAL	1	TRUE	1	0.792958984722751	2		479	320	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954339	48954339	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0017914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	125	461	0	ENST00000267163.4:c.1460T>A	p.Leu487Ter	p.L487*	ENST00000267163	NM_000321.2	487	tTg/tAg	16/27	0.792958984722751	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.792958984722751	1		461	190	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423653	88423653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	22	320	0	ENST00000360948.2:c.2182G>A	p.Gly728Arg	p.G728R	ENST00000360948	NM_001012338.2	728	Gga/Aga	18/19	1	2	FACETS	0.188	0.146	0.237	0.188	0.146	0.237	SUBCLONAL	1	TRUE	1	0.792958984722751	2		320	295	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221269	1221330	+	frameshift_variant	Frame_Shift_Del	DEL	TGAGAACATCGGGAAGGGGAGCTACGCCATCCCGGGCGACTGTGGCCCCCCGCTCTCTGACC	TGAGAACATCGGGAAGGGGAGCTACGCCATCCCGGGCGACTGTGGCCCCCCGCTCTCTGACC	-	novel	NA	P-0017914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	27	745	0	ENST00000326873.7:c.794_855del	p.Glu265AlafsTer6	p.E265Afs*6	ENST00000326873	NM_000455.4	264	ttTGAGAACATCGGGAAGGGGAGCTACGCCATCCCGGGCGACTGTGGCCCCCCGCTCTCTGACCtg/tttg	6/10	0.792958984722751	1	FACETS	0.091	0.072	0.113	0.091	0.072	0.113	SUBCLONAL	1	TRUE	0	0.792958984722751	1		745	452	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211336	36211356	+	inframe_deletion	In_Frame_Del	DEL	GACGAGGAAGAAGAGAAGAAA	GACGAGGAAGAAGAGAAGAAA	-	novel	NA	P-0017914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	248	922	0	ENST00000222270.7:c.1089_1109del	p.Asp363_Lys369del	p.D363_K369del	ENST00000222270	NM_014727.1	363	GACGAGGAAGAAGAGAAGAAA/-	3/37	1	2	FACETS	0.98	0.923	1	0.98	0.923	1	CLONAL	1	TRUE	1	0.792958984722751	2		922	638	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	281	623	0	ENST00000391945.4:c.713A>T	p.Asn238Ile	p.N238I	ENST00000391945	NM_000400.3	238	aAc/aTc	8/23	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.792958984722751	2		623	672	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965499	25965499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371883962	NA	P-0017914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	206	718	1	ENST00000435504.4:c.3707C>T	p.Pro1236Leu	p.P1236L	ENST00000435504		1236	cCa/cTa	13/13	0.321927584379616	1	FACETS	0.794	0.748	0.839	0.794	0.748	0.839	INDETERMINATE	1	TRUE	0	0.792958984722751	1		719	395	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342822	225342959	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTGTAAAATTGTTTTTAAAATTAGTTGAATACAATAATTTTGTTAATAATGTTACTGTTTTTTCTATATTAGCCCAGTAGTGAAGAGTCCTCACCTCCGCTACTAGAACATTGTGCTGCATCTTCTTTCTAGATTTC	ATTGTAAAATTGTTTTTAAAATTAGTTGAATACAATAATTTTGTTAATAATGTTACTGTTTTTTCTATATTAGCCCAGTAGTGAAGAGTCCTCACCTCCGCTACTAGAACATTGTGCTGCATCTTCTTTCTAGATTTC	-	novel	NA	P-0017914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	12	76	0	ENST00000264414.4:c.2133_2175+95del		p.X711_splice	ENST00000264414	NM_003590.4	711		15/16	1	2	FACETS	0.841	0.62	1	0.841	0.62	1	CLONAL	1	TRUE	1	0.792958984722751	2		76	36	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371641	225371641	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	148	831	0	ENST00000264414.4:c.963G>C	p.Leu321Phe	p.L321F	ENST00000264414	NM_003590.4	321	ttG/ttC	7/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.792958984722751	2		831	353	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155051	55155051	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	122	448	0	ENST00000257290.5:c.2760C>G	p.His920Gln	p.H920Q	ENST00000257290	NM_006206.4	920	caC/caG	20/23	0.792958984722751	1	FACETS	0.872	0.81	0.933	0.872	0.81	0.933	CLONAL	1	TRUE	0	0.792958984722751	1		448	213	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522602	106522610	+	frameshift_variant	Frame_Shift_Del	DEL	TGGATCTAT	TGGATCTAT	GG	novel	NA	P-0017914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	28	524	1	ENST00000359195.3:c.2579_2587delinsGG	p.Leu860TrpfsTer15	p.L860Wfs*15	ENST00000359195	NM_002649.2	860	tTGGATCTATgc/tGGgc	7/11	0.203868371017887	1	FACETS	0.176	0.141	0.216	0.176	0.141	0.216	INDETERMINATE	1	TRUE	0	0.792958984722751	1		525	242	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	134	918	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.904	0.821	0.991	0.904	0.821	0.991	CLONAL	1	TRUE	1	0.339168958450144	2		918	874	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916614	178916614	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0017915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	57	510	0	ENST00000263967.3:c.1A>G	p.Met1?	p.M1?	ENST00000263967	NM_006218.2	1	Atg/Gtg	2/21	1	2	FACETS	0.641	0.551	0.74	0.641	0.551	0.74	SUBCLONAL	1	TRUE	1	0.339168958450144	2		510	524	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350084	89350084	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	58	694	0	ENST00000301030.4:c.2866G>C	p.Glu956Gln	p.E956Q	ENST00000301030	NM_001256183.1	956	Gag/Cag	9/13	0.339168958450144	1	FACETS	0.444	0.381	0.513	0.444	0.381	0.513	SUBCLONAL	1	TRUE	0	0.339168958450144	1		694	640	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518580	69518580	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	55	653	0	ENST00000294312.3:c.65G>T	p.Gly22Val	p.G22V	ENST00000294312	NM_005117.2	22	gGg/gTg	1/3	0.270714448077296	1	FACETS	0.484	0.413	0.56	0.484	0.413	0.56	SUBCLONAL	1	TRUE	0	0.339168958450144	1		653	557	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349473	73349473	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	153	658	0	ENST00000377767.4:c.863A>C	p.His288Pro	p.H288P	ENST00000377767	NM_014953.3	288	cAc/cCc	6/21	0.253456533953003	2	FACETS	1	0.985	1	0.674	0.619	0.732	CLONAL	1	TRUE	0	0.339168958450144	2		658	669	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348971	89348971	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	67	628	0	ENST00000301030.4:c.3979G>T	p.Glu1327Ter	p.E1327*	ENST00000301030	NM_001256183.1	1327	Gag/Tag	9/13	0.339168958450144	1	FACETS	0.492	0.427	0.562	0.492	0.427	0.562	SUBCLONAL	1	TRUE	0	0.339168958450144	1		628	667	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226598	2226598	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	47	779	0	ENST00000398665.3:c.4078G>A	p.Glu1360Lys	p.E1360K	ENST00000398665	NM_032482.2	1360	Gag/Aag	27/28	1	2	FACETS	0.364	0.306	0.428	0.364	0.306	0.428	SUBCLONAL	1	TRUE	1	0.339168958450144	2		779	762	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794788	242794788	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	47	285	0	ENST00000334409.5:c.421G>T	p.Glu141Ter	p.E141*	ENST00000334409	NM_005018.2	141	Gag/Tag	2/5	1	2	FACETS	0.903	0.766	1	0.903	0.766	1	CLONAL	1	TRUE	1	0.339168958450144	2		285	307	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121067	29121067	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	202	844	0	ENST00000328354.6:c.490A>T	p.Ser164Cys	p.S164C	ENST00000328354	NM_007194.3	164	Agt/Tgt	4/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.339168958450144	2		844	1089	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540896	187540896	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	43	438	0	ENST00000441802.2:c.6844G>T	p.Val2282Leu	p.V2282L	ENST00000441802	NM_005245.3	2282	Gtg/Ttg	10/27	1	2	FACETS	0.563	0.472	0.665	0.563	0.472	0.665	SUBCLONAL	1	TRUE	1	0.339168958450144	2		438	450	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520476	176520476	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	188	827	0	ENST00000292408.4:c.1321A>T	p.Ser441Cys	p.S441C	ENST00000292408	NM_213647.1	441	Agc/Tgc	10/18	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.339168958450144	2		827	984	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157256615	157256615	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	74	549	0	ENST00000346085.5:c.1942G>T	p.Gly648Cys	p.G648C	ENST00000346085	NM_020732.3	648	Ggc/Tgc	5/20	0.133727726174316	0	FACETS	0.423	0.37	0.48			1	INDETERMINATE	1	TRUE	0	0.339168958450144	0		549	682	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128848687	128848687	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	139	537	1	ENST00000249373.3:c.1352G>T	p.Arg451Leu	p.R451L	ENST00000249373	NM_005631.4	451	cGc/cTc	7/12	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.339168958450144	2		538	601	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044905	47044907	+	frameshift_variant	Frame_Shift_Del	DEL	GTG	GTG	TT	novel	NA	P-0017915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	128	841	2	ENST00000377604.3:c.2231_2233delinsTT	p.Arg744LeufsTer58	p.R744Lfs*58	ENST00000377604	NM_001204468.1	744	cGTGgg/cTTgg	20/24	0.339168958450144	1	FACETS	0.785	0.712	0.863	0.785	0.712	0.863	SUBCLONAL	1	TRUE	0	0.339168958450144	1		843	798	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240213	41240213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	10	155	1	ENST00000379561.5:c.137G>A	p.Gly46Asp	p.G46D	ENST00000379561	NM_002015.3	46	gGc/gAc	1/3	NA	3	FACETS	0.67	0.455	0.939	0.335	0.227	0.47	INDETERMINATE	1	TRUE	1	0.21	3		156	157	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251857	212251857	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	114	289	0	ENST00000342788.4:c.3202G>T	p.Asp1068Tyr	p.D1068Y	ENST00000342788	NM_005235.2	1068	Gat/Tat	27/28	1	2	FACETS	0.866	0.786	0.949	1	0.991	1	CLONAL	3	TRUE	1	0.21	2		289	418	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0017918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	176	455	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	0.397183844755562	2		455	762	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049691	16049691	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	152	529	1	ENST00000268712.3:c.1081C>T	p.Arg361Ter	p.R361*	ENST00000268712	NM_006311.3	361	Cga/Tga	10/46	1	2	FACETS	0.852	0.779	0.929	0.852	0.779	0.929	CLONAL	1	TRUE	1	0.397183844755562	2		530	898	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029405	16029406	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0017918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	176	653	1	ENST00000268712.3:c.1624_1625del	p.Glu542ArgfsTer20	p.E542Rfs*20	ENST00000268712	NM_006311.3	542	GAa/a	15/46	1	2	FACETS	0.777	0.714	0.842	0.777	0.714	0.842	SUBCLONAL	1	TRUE	1	0.397183844755562	2		654	1141	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176580	56176581	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	174	452	0	ENST00000399503.3:c.2133dup	p.Gly712ArgfsTer24	p.G712Rfs*24	ENST00000399503	NM_005921.1	710	-/A	12/20	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.397183844755562	2		452	843	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181864	56181875	+	inframe_deletion	In_Frame_Del	DEL	ACCAAATCATTC	ACCAAATCATTC	-	novel	NA	P-0017918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	133	427	0	ENST00000399503.3:c.4090_4101del	p.Gln1364_His1367del	p.Q1364_H1367del	ENST00000399503	NM_005921.1	1363	aACCAAATCATTCac/aac	17/20	1	2	FACETS	0.884	0.803	0.968	0.884	0.803	0.968	CLONAL	1	TRUE	1	0.397183844755562	2		427	758	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0017920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	441	455	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.540858885982837	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.578890315912002	3		455	922	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0017920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	335	630	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.578890315912002	2		630	1154	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070577	67070578	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	165	433	1	ENST00000412916.2:c.207dup	p.Pro70SerfsTer13	p.P70Sfs*13	ENST00000412916		67	-/T	3/6	0.578890315912002	1	FACETS	0.99	0.92	1	0.99	0.92	1	CLONAL	1	TRUE	0	0.578890315912002	1		434	409	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	304	184	0				ENST00000310581	NM_198253.2	-/1132			0.194783354567293	1	FACETS	1	0.988	1	1	0.988	1	INDETERMINATE	1	TRUE	0	0.537354982541507	1		184	731	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0017921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	171	741	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.907	0.836	0.979	0.907	0.836	0.979	CLONAL	1	TRUE	1	0.537354982541507	2		741	702	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577111	7577111	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786202082	NA	P-0017921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	422	901	3	ENST00000269305.4:c.827C>A	p.Ala276Asp	p.A276D	ENST00000269305	NM_001126112.2	276	gCc/gAc	8/11	0.537354982541507	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.537354982541507	1		904	1054	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340456	8340456	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	213	371	0	ENST00000356435.5:c.5140T>G	p.Tyr1714Asp	p.Y1714D	ENST00000356435		1714	Tac/Gac	31/35	0.258773675989107	1	FACETS	1	0.959	1	1	0.959	1	INDETERMINATE	1	TRUE	0	0.537354982541507	1		371	562	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787696	135787711	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTGGTGGTGACATC	GGCTGGTGGTGACATC	-	novel	NA	P-0017921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	139	551	0	ENST00000298552.3:c.871_886del	p.Asp291LeufsTer22	p.D291Lfs*22	ENST00000298552	NM_001162426.1	291	GATGTCACCACCAGCCct/ct	9/23	1	2	FACETS	0.683	0.623	0.747	0.683	0.623	0.747	SUBCLONAL	1	TRUE	1	0.537354982541507	2		551	757	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0017922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	158	306	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.973	0.903	1	0.973	0.903	1	CLONAL	1	TRUE	1	0.854952826891992	2		307	380	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0017922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	916	596	2	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.850168412070365	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.854952826891992	2		598	1035	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912102	76912102	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	189	687	1	ENST00000373344.5:c.4162G>T	p.Gly1388Ter	p.G1388*	ENST00000373344	NM_000489.3	1388	Gga/Tga	13/35	0.481857869212608	1	FACETS	0.652	0.612	0.693	0.652	0.612	0.693	INDETERMINATE	1	TRUE	0	0.854952826891992	1		688	388	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144111	11144111	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	167	873	0	ENST00000358026.2:c.3692C>A	p.Ala1231Asp	p.A1231D	ENST00000358026	NM_001128849.1	1231	gCc/gAc	26/36	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.445293612146113	2		873	735	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	76	555	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.19	2		558	661	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096132	2096133	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs763525759	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	80	675	2	ENST00000219066.1:c.374dup	p.Val127GlyfsTer43	p.V127Gfs*43	ENST00000219066	NM_002528.5	125	cca/ccCa	2/6	1	2	FACETS	0.999	0.878	1	0.999	0.878	1	CLONAL	1	TRUE	1	0.19	2		677	843	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	199	865	8	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.849	0.785	0.916	1	0.992	1	CLONAL	2	TRUE	1	0.19	2		873	1233	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347093	347093	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1260	67	1036	0	ENST00000262320.3:c.1918del	p.Glu640LysfsTer65	p.E640Kfs*65	ENST00000262320	NM_003502.3	640	Gaa/aa	7/11	1	2	FACETS	0.531	0.46	0.61	0.531	0.46	0.61	SUBCLONAL	1	TRUE	1	0.19	2		1036	1327	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	130	535	4	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.933	0.848	1	1	0.989	1	CLONAL	2	TRUE	1	0.19	2		539	733	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	15	155	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	0.596	0.435	0.789	0.596	0.435	0.789	SUBCLONAL	1	TRUE	1	0.19	2		155	265	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945129	32945129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80359104	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	53	537	0	ENST00000380152.3:c.8524C>T	p.Arg2842Cys	p.R2842C	ENST00000380152		2842	Cgc/Tgc	20/27	1	2	FACETS	0.845	0.72	0.983	0.845	0.72	0.983	CLONAL	1	TRUE	1	0.19	2		537	660	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210778	5210778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374377699	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	73	570	2	ENST00000357368.4:c.5273C>T	p.Ala1758Val	p.A1758V	ENST00000357368	NM_002850.3	1758	gCg/gTg	34/38	1	2	FACETS	0.896	0.782	1	0.896	0.782	1	CLONAL	1	TRUE	1	0.19	2		572	858	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172331	7172331	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758151117	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	88	749	0	ENST00000302850.5:c.1238G>A	p.Arg413His	p.R413H	ENST00000302850	NM_000208.2	413	cGt/cAt	5/22	1	2	FACETS	0.813	0.718	0.915	0.813	0.718	0.915	CLONAL	1	TRUE	1	0.19	2		749	1139	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347983	347983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760961378	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	60	878	2	ENST00000262320.3:c.1523del	p.Gly508ValfsTer197	p.G508Vfs*197	ENST00000262320	NM_003502.3	508	gGt/gt	6/11	1	2	FACETS	0.704	0.605	0.813	0.704	0.605	0.813	SUBCLONAL	1	TRUE	1	0.19	2		880	897	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007824	45007825	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	68	508	0	ENST00000558401.1:c.276dup	p.Thr93HisfsTer2	p.T93Hfs*2	ENST00000558401	NM_004048.2	91	acc/aCcc	2/4	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.19	2		508	652	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46715685	46715685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1320236099	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	67	714	0	ENST00000371975.4:c.104G>A	p.Arg35Gln	p.R35Q	ENST00000371975	NM_003579.3	35	cGg/cAg	3/18	1	2	FACETS	0.72	0.624	0.825	0.72	0.624	0.825	SUBCLONAL	1	TRUE	1	0.19	2		714	979	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458467	120458467	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	69	552	1	ENST00000256646.2:c.6878A>G	p.His2293Arg	p.H2293R	ENST00000256646	NM_024408.3	2293	cAc/cGc	34/34	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.19	2		553	670	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658497	117658497	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	56	675	0	ENST00000368508.3:c.5086T>C	p.Tyr1696His	p.Y1696H	ENST00000368508	NM_002944.2	1696	Tac/Cac	31/43	1	2	FACETS	0.842	0.72	0.976	0.842	0.72	0.976	CLONAL	1	TRUE	1	0.19	2		675	700	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467829	50467829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	45	390	0	ENST00000331340.3:c.1064C>T	p.Ala355Val	p.A355V	ENST00000331340	NM_006060.4	355	gCg/gTg	8/8	1	2	FACETS	0.953	0.801	1	0.953	0.801	1	CLONAL	1	TRUE	1	0.19	2		390	497	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499706	8499706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	71	662	1	ENST00000356435.5:c.2263G>A	p.Glu755Lys	p.E755K	ENST00000356435		755	Gaa/Aaa	14/35	1	2	FACETS	0.783	0.681	0.893	0.783	0.681	0.893	SUBCLONAL	1	TRUE	1	0.19	2		663	955	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193850	106193850	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	51	339	0	ENST00000380013.4:c.4317del	p.Lys1439AsnfsTer9	p.K1439Nfs*9	ENST00000380013	NM_001127208.2	1438	Aaa/aa	10/11	1	2	FACETS	0.922	0.784	1	0.922	0.784	1	CLONAL	1	TRUE	1	0.19	2		339	582	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174495	11174495	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	83	689	0	ENST00000361445.4:c.7180G>T	p.Gly2394Cys	p.G2394C	ENST00000361445	NM_004958.3	2394	Ggc/Tgc	53/58	1	2	FACETS	0.959	0.845	1	0.959	0.845	1	CLONAL	1	TRUE	1	0.19	2		689	911	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101168	27101168	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	76	837	0	ENST00000324856.7:c.4450C>T	p.Pro1484Ser	p.P1484S	ENST00000324856	NM_006015.4	1484	Ccc/Tcc	18/20	1	2	FACETS	0.821	0.718	0.932	0.821	0.718	0.932	CLONAL	1	TRUE	1	0.19	2		837	975	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599251	28599251	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1416314446	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	122	886	0	ENST00000253063.3:c.701del	p.Pro234LeufsTer13	p.P234Lfs*13	ENST00000253063	NM_031459.4	233	Ccc/cc	5/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.19	2		886	1206	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263195	115263195	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	72	673	1	ENST00000438362.2:c.2155C>A	p.Leu719Met	p.L719M	ENST00000438362	NM_001242891.1	719	Ctg/Atg	17/20	1	2	FACETS	0.762	0.664	0.869	0.762	0.664	0.869	SUBCLONAL	1	TRUE	1	0.19	2		674	994	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456597	32456597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	22	142	0	ENST00000332351.3:c.295G>A	p.Ala99Thr	p.A99T	ENST00000332351	NM_024426.4	99	Gcg/Acg	1/10	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.19	2		142	198	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212838	94212838	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	58	530	0	ENST00000323929.3:c.402+2T>C		p.X134_splice	ENST00000323929	NM_005591.3	134			1	2	FACETS	0.944	0.81	1	0.944	0.81	1	CLONAL	1	TRUE	1	0.19	2		530	647	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998621	100998621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	82	660	1	ENST00000325455.5:c.1181C>T	p.Ala394Val	p.A394V	ENST00000325455	NM_001202474.3	394	gCg/gTg	1/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.19	2		661	713	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122569	108122569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1565385040	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	48	483	0	ENST00000278616.4:c.1613C>T	p.Ala538Val	p.A538V	ENST00000278616	NM_000051.3	538	gCa/gTa	11/63	1	2	FACETS	0.977	0.826	1	0.977	0.826	1	CLONAL	1	TRUE	1	0.19	2		483	517	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505404	125505404	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	59	614	0	ENST00000428830.2:c.700del	p.Ile234SerfsTer6	p.I234Sfs*6	ENST00000428830	NM_001114121.2	232	Aaa/aa	7/14	1	2	FACETS	0.794	0.682	0.917	0.794	0.682	0.917	CLONAL	1	TRUE	1	0.19	2		614	782	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4387950	4387950	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	58	561	0	ENST00000261254.3:c.436A>G	p.Lys146Glu	p.K146E	ENST00000261254	NM_001759.3	146	Aag/Gag	3/5	1	2	FACETS	0.813	0.697	0.94	0.813	0.697	0.94	CLONAL	1	TRUE	1	0.19	2		561	751	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245519	46245519	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371267186	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	49	429	0	ENST00000334344.6:c.3613G>A	p.Gly1205Arg	p.G1205R	ENST00000334344	NM_152641.2	1205	Gga/Aga	15/21	1	2	FACETS	0.91	0.77	1	0.91	0.77	1	CLONAL	1	TRUE	1	0.19	2		429	567	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426046	49426046	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	84	756	0	ENST00000301067.7:c.12442A>G	p.Met4148Val	p.M4148V	ENST00000301067	NM_003482.3	4148	Atg/Gtg	39/54	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.19	2		756	806	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144530	58144530	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	60	392	0	ENST00000257904.6:c.541C>T	p.Arg181Ter	p.R181*	ENST00000257904	NM_000075.3	181	Cga/Tga	5/8	1	2	FACETS	0.934	0.804	1	0.934	0.804	1	CLONAL	1	TRUE	1	0.19	2		392	676	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245435	133245435	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs754925525	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	84	630	1	ENST00000320574.5:c.1885del	p.Ala629ProfsTer8	p.A629Pfs*8	ENST00000320574	NM_006231.2	629	Gcc/cc	17/49	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.19	2		631	875	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004254	29004254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143093353	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	61	495	0	ENST00000282397.4:c.1039G>A	p.Val347Ile	p.V347I	ENST00000282397	NM_002019.4	347	Gta/Ata	8/30	1	2	FACETS	0.816	0.702	0.94	0.816	0.702	0.94	CLONAL	1	TRUE	1	0.19	2		495	787	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914389	32914389	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs80358823	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	51	631	0	ENST00000380152.3:c.5897A>G	p.His1966Arg	p.H1966R	ENST00000380152		1966	cAt/cGt	11/27	1	2	FACETS	0.748	0.634	0.873	0.748	0.634	0.873	SUBCLONAL	1	TRUE	1	0.19	2		631	718	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38616977	38616977	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	50	644	0	ENST00000299084.4:c.395del	p.Asn132MetfsTer20	p.N132Mfs*20	ENST00000299084	NM_152594.2	130	tcA/tc	4/7	1	2	FACETS	0.775	0.657	0.906	0.775	0.657	0.906	CLONAL	1	TRUE	1	0.19	2		644	679	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423656	88423656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	34	354	0	ENST00000360948.2:c.2179G>A	p.Gly727Arg	p.G727R	ENST00000360948	NM_001012338.2	727	Gga/Aga	18/19	1	2	FACETS	0.797	0.651	0.962	0.797	0.651	0.962	CLONAL	1	TRUE	1	0.19	2		354	449	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631683	90631683	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	71	699	0	ENST00000330062.3:c.586T>G	p.Phe196Val	p.F196V	ENST00000330062	NM_002168.2	196	Ttc/Gtc	5/11	1	2	FACETS	0.725	0.631	0.827	0.725	0.631	0.827	SUBCLONAL	1	TRUE	1	0.19	2		699	1031	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993125	72993125	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1327	106	937	0	ENST00000268489.5:c.920T>C	p.Met307Thr	p.M307T	ENST00000268489	NM_006885.3	307	aTg/aCg	2/10	1	2	FACETS	0.779	0.695	0.868	0.779	0.695	0.868	SUBCLONAL	1	TRUE	1	0.19	2		937	1433	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349556	89349556	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	105	794	0	ENST00000301030.4:c.3394G>T	p.Gly1132Trp	p.G1132W	ENST00000301030	NM_001256183.1	1132	Ggg/Tgg	9/13	1	2	FACETS	0.941	0.84	1	0.941	0.84	1	CLONAL	1	TRUE	1	0.19	2		794	1175	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435079	56435079	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	36	566	0	ENST00000407977.2:c.2058del	p.Ser687ValfsTer13	p.S687Vfs*13	ENST00000407977		686	ccC/cc	9/10	1	2	FACETS	0.527	0.432	0.634	0.527	0.432	0.634	SUBCLONAL	1	TRUE	1	0.19	2		566	719	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899254	78899254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542518961	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	59	518	0	ENST00000306801.3:c.2893C>T	p.Arg965Cys	p.R965C	ENST00000306801	NM_020761.2	965	Cgc/Tgc	24/34	1	2	FACETS	0.861	0.74	0.994	0.861	0.74	0.994	CLONAL	1	TRUE	1	0.19	2		518	721	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302417	15302417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	112	925	1	ENST00000263388.2:c.854G>A	p.Cys285Tyr	p.C285Y	ENST00000263388	NM_000435.2	285	tGc/tAc	6/33	1	2	FACETS	0.982	0.881	1	0.982	0.881	1	CLONAL	1	TRUE	1	0.19	2		926	1200	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355059	15355059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1331196729	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	98	890	4	ENST00000263377.2:c.2564C>T	p.Ala855Val	p.A855V	ENST00000263377	NM_058243.2	855	gCa/gTa	13/20	1	2	FACETS	0.899	0.799	1	0.899	0.799	1	CLONAL	1	TRUE	1	0.19	2		894	1148	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085659	16085659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs794727503	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	110	726	0	ENST00000281043.3:c.835G>A	p.Val279Met	p.V279M	ENST00000281043	NM_005378.4	279	Gtg/Atg	3/3	1	2	FACETS	0.986	0.884	1	0.986	0.884	1	CLONAL	1	TRUE	1	0.19	2		726	1174	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967279	25967279	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	30	392	0	ENST00000435504.4:c.1927C>A	p.Pro643Thr	p.P643T	ENST00000435504		643	Cca/Aca	13/13	1	2	FACETS	0.546	0.439	0.669	0.546	0.439	0.669	SUBCLONAL	1	TRUE	1	0.19	2		392	578	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991697	25991697	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	50	405	0	ENST00000435504.4:c.545G>A	p.Cys182Tyr	p.C182Y	ENST00000435504		182	tGc/tAc	7/13	1	2	FACETS	0.799	0.677	0.933	0.799	0.677	0.933	CLONAL	1	TRUE	1	0.19	2		405	659	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39294894	39294894	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	48	582	0	ENST00000402219.2:c.88G>A	p.Val30Ile	p.V30I	ENST00000402219	NM_005633.3	30	Gtc/Atc	2/23	1	2	FACETS	0.627	0.528	0.736	0.627	0.528	0.736	SUBCLONAL	1	TRUE	1	0.19	2		582	806	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038167	128038167	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	94	610	0	ENST00000285398.2:c.1383C>G	p.His461Gln	p.H461Q	ENST00000285398	NM_000122.1	461	caC/caG	9/15	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.19	2		610	989	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136244	202136244	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1387029323	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	67	518	0	ENST00000358485.4:c.488T>C	p.Met163Thr	p.M163T	ENST00000358485	NM_001080125.1	163	aTg/aCg	3/9	1	2	FACETS	0.914	0.793	1	0.914	0.793	1	CLONAL	1	TRUE	1	0.19	2		518	772	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661614	227661614	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	49	524	0	ENST00000305123.5:c.1841C>T	p.Pro614Leu	p.P614L	ENST00000305123	NM_005544.2	614	cCc/cTc	1/2	1	2	FACETS	0.844	0.714	0.988	0.844	0.714	0.988	CLONAL	1	TRUE	1	0.19	2		524	611	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024202	31024202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	91	742	1	ENST00000375687.4:c.3687G>A	p.Met1229Ile	p.M1229I	ENST00000375687	NM_015338.5	1229	atG/atA	13/13	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.19	2		743	914	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026171	36026171	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	95	834	1	ENST00000358208.4:c.773T>C	p.Leu258Pro	p.L258P	ENST00000358208		258	cTg/cCg	7/12	1	2	FACETS	0.939	0.834	1	0.939	0.834	1	CLONAL	1	TRUE	1	0.19	2		835	1065	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436341	52436341	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1440748203	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	65	489	0	ENST00000460680.1:c.2153G>A	p.Arg718Gln	p.R718Q	ENST00000460680	NM_004656.3	718	cGg/cAg	17/17	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.19	2		489	666	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437157	52437157	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	56	576	0	ENST00000460680.1:c.1887del	p.Lys630ArgfsTer7	p.K630Rfs*7	ENST00000460680	NM_004656.3	629	ccC/cc	14/17	1	2	FACETS	0.772	0.66	0.894	0.772	0.66	0.894	SUBCLONAL	1	TRUE	1	0.19	2		576	764	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665410	138665410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	129	796	1	ENST00000330315.3:c.155C>T	p.Ala52Val	p.A52V	ENST00000330315	NM_023067.3	52	gCg/gTg	1/1	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.19	2		797	1027	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430946	181430946	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1269451539	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	84	759	2	ENST00000325404.1:c.798G>T	p.Gln266His	p.Q266H	ENST00000325404	NM_003106.3	266	caG/caT	1/1	1	2	FACETS	0.936	0.825	1	0.936	0.825	1	CLONAL	1	TRUE	1	0.19	2		761	945	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920189	1920189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745921448	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	144	851	0	ENST00000382891.5:c.1249G>A	p.Asp417Asn	p.D417N	ENST00000382891	NM_133335.3	417	Gac/Aac	5/22	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.19	2		851	1226	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253872	153253872	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	50	423	0	ENST00000281708.4:c.862-1G>A		p.X288_splice	ENST00000281708	NM_033632.3	288			1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.19	2		423	463	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630604	187630605	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	87	761	0	ENST00000441802.2:c.377dup	p.Asn126LysfsTer3	p.N126Kfs*3	ENST00000441802	NM_005245.3	126	aat/aaAt	2/27	1	2	FACETS	0.803	0.708	0.904	0.803	0.708	0.904	CLONAL	1	TRUE	1	0.19	2		761	1141	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80057459	80057459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200337887	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	37	547	0	ENST00000265081.6:c.1858G>A	p.Asp620Asn	p.D620N	ENST00000265081	NM_002439.4	620	Gac/Aac	13/24	1	2	FACETS	0.677	0.557	0.812	0.677	0.557	0.812	SUBCLONAL	1	TRUE	1	0.19	2		547	575	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048698	180048698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771458044	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	49	575	2	ENST00000261937.6:c.1864G>A	p.Ala622Thr	p.A622T	ENST00000261937	NM_182925.4	622	Gcc/Acc	13/30	1	2	FACETS	0.79	0.668	0.924	0.79	0.668	0.924	CLONAL	1	TRUE	1	0.19	2		577	653	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165125	32165125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776703710	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	71	574	1	ENST00000375023.3:c.5003G>A	p.Arg1668His	p.R1668H	ENST00000375023	NM_004557.3	1668	cGc/cAc	27/30	1	2	FACETS	0.982	0.856	1	0.982	0.856	1	CLONAL	1	TRUE	1	0.19	2		575	761	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32819964	32819964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531615408	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1328	115	932	1	ENST00000354258.4:c.946G>A	p.Val316Met	p.V316M	ENST00000354258	NM_000593.5	316	Gtg/Atg	3/11	1	2	FACETS	0.839	0.753	0.931	0.839	0.753	0.931	CLONAL	1	TRUE	1	0.19	2		933	1443	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540353	23540353	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	58	516	0	ENST00000380871.4:c.50C>G	p.Ala17Gly	p.A17G	ENST00000380871	NM_006167.3	17	gCc/gGc	1/2	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.19	2		516	551	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239947	53239947	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	91	788	0	ENST00000375401.3:c.1494G>T	p.Lys498Asn	p.K498N	ENST00000375401	NM_004187.3	498	aaG/aaT	11/26	0.184990931398743	1	FACETS	0.871	0.772	0.978	0.871	0.772	0.978	CLONAL	1	TRUE	0	0.19	1		788	995	SUCCESS
AR	367	MSKCC	GRCh37	X	66766333	66766333	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	28	297	0	ENST00000374690.3:c.1346del	p.Pro449ArgfsTer30	p.P449Rfs*30	ENST00000374690	NM_000044.3	449	Ccg/cg	1/8	0.184990931398743	1	FACETS	0.773	0.618	0.949	0.773	0.618	0.949	CLONAL	1	TRUE	0	0.19	1		297	345	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0017926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	73	294	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		294	786	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	88	184	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.764	0.682	0.851	0.764	0.682	0.851	SUBCLONAL	1	TRUE	1	0.613947065465908	2		184	375	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665752	29665755	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1555535032	NA	P-0017927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	248	553	0	ENST00000356175.3:c.6789_6792del	p.Tyr2264ThrfsTer5	p.Y2264Tfs*5	ENST00000356175	NM_000267.3	2263	ACTTac/ac	45/57	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.613947065465908	2		553	794	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661945	29661945	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854552	NA	P-0017927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	256	611	1	ENST00000356175.3:c.5839C>T	p.Arg1947Ter	p.R1947*	ENST00000356175	NM_000267.3	1947	Cga/Tga	39/57	1	2	FACETS	0.948	0.889	1	0.948	0.889	1	CLONAL	1	TRUE	1	0.613947065465908	2		612	880	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394888	394888	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	195	455	0	ENST00000380956.4:c.284C>G	p.Thr95Arg	p.T95R	ENST00000380956	NM_001195286.1	95	aCg/aGg	3/9	0.613947065465908	1	FACETS	0.998	0.935	1	0.998	0.935	1	CLONAL	1	TRUE	0	0.613947065465908	1		455	441	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0017928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	207	843	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.893	0.829	0.96	0.893	0.829	0.96	CLONAL	1	TRUE	1	0.486749981143414	2		843	952	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0017928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	103	347	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	1	2	FACETS	0.991	0.893	1	0.991	0.893	1	CLONAL	1	TRUE	1	0.486749981143414	2		347	427	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623083	52623084	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	ACCAGCTGAATCCTCCCACAGTCTTTCAATACAGACGATATGTGGTTGTAGG	novel	NA	P-0017928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	97	513	0	ENST00000394830.3:c.2916_2965+2dup		p.X972_splice	ENST00000394830	NM_018313.4	972			0.486749981143414	1	FACETS	0.433	0.386	0.483	0.433	0.386	0.483	SUBCLONAL	1	TRUE	0	0.486749981143414	1		513	697	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0017929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	457	527	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.467577146567757	8	FACETS	0.966	0.924	1			1	CLONAL	4	TRUE	NA	0.467577146567757	8		527	1215	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0017929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	282	710	5	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.441988207488489	2	FACETS	0.926	0.877	0.976	0.926	0.877	0.976	CLONAL	2	TRUE	0	0.467577146567757	2		715	651	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348030	89348030	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1508	251	1002	2	ENST00000301030.4:c.4920G>T	p.Lys1640Asn	p.K1640N	ENST00000301030	NM_001256183.1	1640	aaG/aaT	9/13	0.467577146567757	5	FACETS	1	0.958	1	0.208	0.193	0.223	CLONAL	1	TRUE	0	0.467577146567757	5		1004	1759	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141454	11141454	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1472	192	707	0	ENST00000358026.2:c.3431A>T	p.Glu1144Val	p.E1144V	ENST00000358026	NM_001128849.1	1144	gAg/gTg	25/36	0.467577146567757	6	FACETS	0.955	0.88	1			1	CLONAL	1	TRUE	NA	0.467577146567757	6		707	1664	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607730	46607730	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	234	804	3	ENST00000263734.3:c.1919C>T	p.Pro640Leu	p.P640L	ENST00000263734	NM_001430.4	640	cCc/cTc	12/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.467577146567757	2		807	954	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163555	32163555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779767756	NA	P-0017929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	137	580	0	ENST00000375023.3:c.5671G>A	p.Gly1891Ser	p.G1891S	ENST00000375023	NM_004557.3	1891	Ggc/Agc	30/30	0.432953403286645	4	FACETS	0.868	0.788	0.951	0.434	0.394	0.476	CLONAL	1	TRUE	2	0.467577146567757	4		580	991	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058033	27058033	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	80	467	0	ENST00000324856.7:c.1741C>T	p.Gln581Ter	p.Q581*	ENST00000324856	NM_006015.4	581	Cag/Tag	3/20	1	2	FACETS	0.979	0.863	1	0.979	0.863	1	CLONAL	1	TRUE	1	0.3	2		467	545	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0017930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	121	643	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.3	2		643	765	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584787	48584787	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	143	451	0	ENST00000342988.3:c.865C>T	p.Gln289Ter	p.Q289*	ENST00000342988	NM_005359.5	289	Cag/Tag	7/12	0.295618015621554	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.3	1		451	782	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0017930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	44	587	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	0.359	0.3	0.425	0.359	0.3	0.425	SUBCLONAL	1	TRUE	1	0.3	2		587	817	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49413009	49413009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519953	NA	P-0017930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	151	668	1	ENST00000418115.1:c.14G>A	p.Arg5Gln	p.R5Q	ENST00000418115	NM_001664.2	5	cGg/cAg	2/5	1	2	FACETS	0.93	0.849	1	0.93	0.849	1	CLONAL	1	TRUE	1	0.3	2		669	1082	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720711	89720712	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	26	159	0	ENST00000371953.3:c.867dup	p.Val290SerfsTer8	p.V290Sfs*8	ENST00000371953	NM_000314.4	288	gaa/gAaa	8/9	1	2	FACETS	0.608	0.483	0.751	0.608	0.483	0.751	SUBCLONAL	1	TRUE	1	0.3	2		159	285	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953937	32953937	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80359152	NA	P-0017930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	104	499	0	ENST00000380152.3:c.9004G>A	p.Glu3002Lys	p.E3002K	ENST00000380152		3002	Gaa/Aaa	23/27	1	2	FACETS	0.758	0.677	0.843	0.758	0.677	0.843	SUBCLONAL	1	TRUE	1	0.3	2		499	915	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632519	3632519	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	92	672	0	ENST00000294008.3:c.5329G>C	p.Glu1777Gln	p.E1777Q	ENST00000294008	NM_032444.2	1777	Gag/Cag	15/15	1	2	FACETS	0.765	0.679	0.857	0.765	0.679	0.857	SUBCLONAL	1	TRUE	1	0.3	2		672	802	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857875	9857875	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	60	472	0	ENST00000330684.3:c.3526G>C	p.Glu1176Gln	p.E1176Q	ENST00000330684	NM_001134407.1	1176	Gag/Cag	13/13	1	2	FACETS	0.658	0.567	0.757	0.658	0.567	0.757	SUBCLONAL	1	TRUE	1	0.3	2		472	608	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844175	68844175	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	138	660	0	ENST00000261769.5:c.763C>T	p.Gln255Ter	p.Q255*	ENST00000261769	NM_004360.3	255	Cag/Tag	6/16	0.295618015621554	1	FACETS	0.987	0.899	1	0.987	0.899	1	CLONAL	1	TRUE	0	0.3	1		660	792	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125873	47125873	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0017930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	45	154	0	ENST00000409792.3:c.5398-1G>C		p.X1800_splice	ENST00000409792	NM_014159.6	1800			0.284781896000478	2	FACETS	1	0.876	1	0.521	0.44	0.609	CLONAL	1	TRUE	0	0.3	2		154	288	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451474	187451474	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145456310	NA	P-0017930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	72	345	0	ENST00000232014.4:c.8C>T	p.Ser3Leu	p.S3L	ENST00000232014	NM_001130845.1	3	tCg/tTg	3/10	1	2	FACETS	0.952	0.834	1	0.952	0.834	1	CLONAL	1	TRUE	1	0.3	2		345	504	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468319	50468319	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	80	454	0	ENST00000331340.3:c.1554G>C	p.Met518Ile	p.M518I	ENST00000331340	NM_006060.4	518	atG/atC	8/8	1	2	FACETS	0.915	0.806	1	0.915	0.806	1	CLONAL	1	TRUE	1	0.3	2		454	583	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397678	139397678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778830490	NA	P-0017930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	85	513	0	ENST00000277541.6:c.5123C>T	p.Ser1708Leu	p.S1708L	ENST00000277541	NM_017617.3	1708	tCg/tTg	27/34	1	2	FACETS	0.94	0.832	1	0.94	0.832	1	CLONAL	1	TRUE	1	0.3	2		513	603	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223811	53223811	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	162	838	0	ENST00000375401.3:c.3548C>G	p.Ser1183Cys	p.S1183C	ENST00000375401	NM_004187.3	1183	tCt/tGt	23/26	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.3	2		838	1041	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0017932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	228	621	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	0.896	0.835	0.959	0.896	0.835	0.959	CLONAL	1	TRUE	1	0.504756596530397	2		621	1008	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060711	38060711	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0017932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	181	935	0	ENST00000250448.2:c.1278C>G	p.Tyr426Ter	p.Y426*	ENST00000250448	NM_004496.3	426	taC/taG	2/2	1	2	FACETS	0.575	0.529	0.623	0.575	0.529	0.623	SUBCLONAL	1	TRUE	1	0.504756596530397	2		935	1247	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426268	49426268	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	266	750	0	ENST00000301067.7:c.12220C>A	p.Gln4074Lys	p.Q4074K	ENST00000301067	NM_003482.3	4074	Caa/Aaa	39/54	1	2	FACETS	0.946	0.887	1	0.946	0.887	1	CLONAL	1	TRUE	1	0.504756596530397	2		750	1114	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0017935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	38	549	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	0.176835344124347	1	FACETS	0.886	0.733	1	0.886	0.733	1	CLONAL	1	TRUE	0	0.187750193768563	1		549	414	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711874	89711874	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs786204862	NA	P-0017935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	28	403	0	ENST00000371953.3:c.493-1G>A		p.X165_splice	ENST00000371953	NM_000314.4	165			0.187750193768563	1	FACETS	0.753	0.602	0.925	0.753	0.602	0.925	CLONAL	1	TRUE	0	0.187750193768563	1		403	359	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0017936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	302	447	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.952	0.901	1	0.952	0.901	1	CLONAL	1	TRUE	1	0.794291919320059	2		447	799	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047507	49047507	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0017936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	67	373	0	ENST00000267163.4:c.2501C>G	p.Ser834Ter	p.S834*	ENST00000267163	NM_000321.2	834	tCa/tGa	24/27	0.78442066498735	1	FACETS	0.199	0.173	0.228	0.199	0.173	0.228	SUBCLONAL	1	TRUE	0	0.794291919320059	1		373	510	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0017936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	1030	690	1	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	0.794291919320059	2	FACETS	0.982	0.964	0.999	0.982	0.964	0.999	CLONAL	2	TRUE	0	0.794291919320059	2		691	1321	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0017936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	1042	637	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.794291919320059	2	FACETS	0.988	0.97	1	0.988	0.97	1	CLONAL	2	TRUE	0	0.794291919320059	2		637	1328	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951171	48951171	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587778846	NA	P-0017936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	174	548	0	ENST00000267163.4:c.1332+1G>A		p.X444_splice	ENST00000267163	NM_000321.2	444			0.78442066498735	1	FACETS	0.629	0.586	0.673	0.629	0.586	0.673	SUBCLONAL	1	TRUE	0	0.794291919320059	1		548	420	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097172	11097172	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	428	579	0	ENST00000358026.2:c.663del	p.Pro222HisfsTer81	p.P222Hfs*81	ENST00000358026	NM_001128849.1	221	ccT/cc	4/36	0.794291919320059	1	FACETS	0.99	0.956	1	0.99	0.956	1	CLONAL	1	TRUE	0	0.794291919320059	1		579	656	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729313	41729313	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	578	372	0	ENST00000242208.4:c.1216G>C	p.Asp406His	p.D406H	ENST00000242208	NM_002192.2	406	Gat/Cat	3/3	0.794291919320059	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.794291919320059	3		372	1017	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730069	41730069	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	712	468	0	ENST00000242208.4:c.460G>C	p.Glu154Gln	p.E154Q	ENST00000242208	NM_002192.2	154	Gaa/Caa	3/3	0.794291919320059	3	FACETS	0.971	0.942	1	0.971	0.942	1	CLONAL	2	TRUE	1	0.794291919320059	3		468	1290	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0017940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	159	523	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.191861677829432	4	FACETS	1	0.983	1	0.83	0.764	0.898	CLONAL	2	TRUE	1	0.26	4		523	619	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974747	21974747	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1554656403	NA	P-0017940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	27	209	0	ENST00000304494.5:c.80A>G	p.Glu27Gly	p.E27G	ENST00000304494	NM_000077.4	27	gAg/gGg	1/3	1	2	FACETS	0.999	0.8	1	0.999	0.8	1	CLONAL	1	TRUE	1	0.26	2		209	208	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0017941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	113	455	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.304138363349415	4	FACETS	0.832	0.753	0.915	0.832	0.753	0.915	CLONAL	2	TRUE	2	0.395583492549114	4		455	479	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111526	8111526	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	224	796	0	ENST00000346208.3:c.1012T>C	p.Cys338Arg	p.C338R	ENST00000346208		338	Tgc/Cgc	5/6	0.171580861111706	5	FACETS	0.95	0.885	1	0.633	0.59	0.678	INDETERMINATE	2	TRUE	2	0.395583492549114	5		796	950	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965247	81965247	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	158	484	0	ENST00000359376.3:c.2727G>C	p.Lys909Asn	p.K909N	ENST00000359376	NM_002661.3	909	aaG/aaC	25/33	0.392956137479414	4	FACETS	0.899	0.827	0.973	0.899	0.827	0.973	CLONAL	2	TRUE	2	0.395583492549114	4		484	620	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534432	140534432	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	66	406	0	ENST00000288602.6:c.481C>A	p.Leu161Met	p.L161M	ENST00000288602	NM_004333.4	161	Ctg/Atg	3/18	0.392956137479414	4	FACETS	1	0.971	1	0.721	0.63	0.817	CLONAL	1	TRUE	2	0.395583492549114	4		406	323	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0017943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	26	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.481	0.381	0.596	0.481	0.381	0.596	SUBCLONAL	1	TRUE	1	0.31509162120033	2		306	343	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0017943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	153	507	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.31509162120033	2		508	967	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893589	28893589	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	64	683	0	ENST00000282397.4:c.3257G>A	p.Gly1086Glu	p.G1086E	ENST00000282397	NM_002019.4	1086	gGa/gAa	24/30	0.31509162120033	1	FACETS	0.416	0.359	0.478	0.416	0.359	0.478	SUBCLONAL	1	TRUE	0	0.31509162120033	1		683	823	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259262	89259262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770780950	NA	P-0017943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	67	441	2	ENST00000336596.2:c.406C>T	p.Arg136Ter	p.R136*	ENST00000336596	NM_005233.5	136	Cga/Tga	3/17	1	2	FACETS	0.762	0.663	0.869	0.762	0.663	0.869	SUBCLONAL	1	TRUE	1	0.31509162120033	2		443	558	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16247399	16247399	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	44	425	0	ENST00000375759.3:c.1670T>C	p.Val557Ala	p.V557A	ENST00000375759	NM_015001.2	557	gTt/gCt	9/15	1	2	FACETS	0.431	0.361	0.509	0.431	0.361	0.509	SUBCLONAL	1	TRUE	1	0.31509162120033	2		425	648	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850733	63850733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	159	678	0	ENST00000279873.7:c.1511C>T	p.Ser504Leu	p.S504L	ENST00000279873	NM_032199.2	504	tCa/tTa	10/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.31509162120033	2		678	922	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051199	13051199	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	86	716	0	ENST00000316448.5:c.635A>G	p.Asp212Gly	p.D212G	ENST00000316448	NM_004343.3	212	gAt/gGt	5/9	0.31509162120033	1	FACETS	0.476	0.42	0.536	0.476	0.42	0.536	SUBCLONAL	1	TRUE	0	0.31509162120033	1		716	967	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99162432	99162432	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	92	607	0	ENST00000074304.5:c.950G>A	p.Gly317Glu	p.G317E	ENST00000074304	NM_001134224.1	317	gGg/gAg	12/26	1	2	FACETS	0.673	0.597	0.754	0.673	0.597	0.754	SUBCLONAL	1	TRUE	1	0.31509162120033	2		607	868	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182548	99182548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs942333191	NA	P-0017943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	206	657	1	ENST00000074304.5:c.2351G>A	p.Arg784Gln	p.R784Q	ENST00000074304	NM_001134224.1	784	cGg/cAg	22/26	1	2	FACETS	0.777	0.722	0.834	1	0.992	1	SUBCLONAL	2	TRUE	1	0.31509162120033	2		658	841	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248686	212248686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1380675481	NA	P-0017943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	58	443	0	ENST00000342788.4:c.3581G>A	p.Gly1194Asp	p.G1194D	ENST00000342788	NM_005235.2	1194	gGt/gAt	28/28	1	2	FACETS	0.565	0.485	0.652	0.565	0.485	0.652	SUBCLONAL	1	TRUE	1	0.31509162120033	2		443	652	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128305352	128305352	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	97	878	1	ENST00000265960.3:c.944C>T	p.Ser315Phe	p.S315F	ENST00000265960	NM_001006617.1	315	tCc/tTc	7/12	0.31509162120033	1	FACETS	0.49	0.436	0.549	0.49	0.436	0.549	SUBCLONAL	1	TRUE	0	0.31509162120033	1		879	1058	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0017945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	150	549	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	1	2	FACETS	0.843	0.77	0.92	0.843	0.77	0.92	CLONAL	1	TRUE	1	0.36159286715404	2		549	984	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0017945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	245	1171	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	1	2	FACETS	0.949	0.885	1	0.949	0.885	1	CLONAL	1	TRUE	1	0.36159286715404	2		1171	1428	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495749	72495749	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	127	503	0	ENST00000477973.2:c.323C>T	p.Ala108Val	p.A108V	ENST00000477973	NM_012234.5	108	gCc/gTc	1/4	0.36159286715404	1	FACETS	0.845	0.767	0.927	0.845	0.767	0.927	CLONAL	1	TRUE	0	0.36159286715404	1		503	681	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937094	48937094	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0017945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	86	253	0	ENST00000267163.4:c.861+1G>C		p.X287_splice	ENST00000267163	NM_000321.2	287			0.36159286715404	1	FACETS	0.884	0.785	0.988	0.884	0.785	0.988	CLONAL	1	TRUE	0	0.36159286715404	1		253	441	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732623	190732623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369226504	NA	P-0017945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	160	611	0	ENST00000441310.2:c.2441C>T	p.Thr814Ile	p.T814I	ENST00000441310	NM_000534.4	814	aCa/aTa	11/13	1	2	FACETS	0.864	0.792	0.94	0.864	0.792	0.94	CLONAL	1	TRUE	1	0.36159286715404	2		611	1024	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257113	16257113	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	168	495	1	ENST00000375759.3:c.4378G>T	p.Glu1460Ter	p.E1460*	ENST00000375759	NM_015001.2	1460	Gaa/Taa	11/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.280957457487572	2		496	1071	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422703	49422703	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	139	477	1	ENST00000301067.7:c.14290G>T	p.Glu4764Ter	p.E4764*	ENST00000301067	NM_003482.3	4764	Gag/Tag	45/54	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.280957457487572	2		478	827	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701205	43701205	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0017946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	130	532	0	ENST00000382044.4:c.5490T>A	p.Cys1830Ter	p.C1830*	ENST00000382044	NM_001141980.1	1830	tgT/tgA	26/28	0.280957457487572	1	FACETS	0.956	0.867	1	0.956	0.867	1	CLONAL	1	TRUE	0	0.280957457487572	1		532	832	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293268	91293268	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	96	314	0	ENST00000355112.3:c.770C>G	p.Ser257Cys	p.S257C	ENST00000355112	NM_000057.2	257	tCt/tGt	3/22	0.280957457487572	1	FACETS	0.904	0.806	1	0.904	0.806	1	CLONAL	1	TRUE	0	0.280957457487572	1		314	650	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56378179	56378179	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	138	353	0	ENST00000348428.3:c.952A>T	p.Thr318Ser	p.T318S	ENST00000348428	NM_006785.3	318	Act/Tct	7/17	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.280957457487572	2		353	861	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375218	15375218	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	30	285	0	ENST00000263377.2:c.1209C>G	p.Ile403Met	p.I403M	ENST00000263377	NM_058243.2	403	atC/atG	6/20	1	2	FACETS	0.369	0.297	0.452	0.369	0.297	0.452	SUBCLONAL	1	TRUE	1	0.280957457487572	2		285	578	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198260836	198260836	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	84	494	0	ENST00000335508.6:c.3483G>T	p.Met1161Ile	p.M1161I	ENST00000335508	NM_012433.2	1161	atG/atT	23/25	1	2	FACETS	0.569	0.501	0.643	0.569	0.501	0.643	SUBCLONAL	1	TRUE	1	0.280957457487572	2		494	1050	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248768	212248768	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	53	219	0	ENST00000342788.4:c.3499G>T	p.Glu1167Ter	p.E1167*	ENST00000342788	NM_005235.2	1167	Gag/Tag	28/28	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.280957457487572	2		219	327	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164411	47164411	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1425320029	NA	P-0017946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	40	238	0	ENST00000409792.3:c.1715C>T	p.Ser572Phe	p.S572F	ENST00000409792	NM_014159.6	572	tCt/tTt	3/21	0.266404576503843	1	FACETS	0.465	0.386	0.554	0.465	0.386	0.554	SUBCLONAL	1	TRUE	0	0.280957457487572	1		238	526	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528544	89528544	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	A	novel	NA	P-0017946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	38	205	0	ENST00000336596.2:c.2847-3C>A		p.X949_splice	ENST00000336596	NM_005233.5	949			0.266404576503843	1	FACETS	0.571	0.473	0.681	0.571	0.473	0.681	SUBCLONAL	1	TRUE	0	0.280957457487572	1		205	407	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056591	26056591	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	23	153	0	ENST00000343677.2:c.66G>C	p.Lys22Asn	p.K22N	ENST00000343677	NM_005319.3	22	aaG/aaC	1/1	1	2	FACETS	0.581	0.453	0.727	0.581	0.453	0.727	SUBCLONAL	1	TRUE	1	0.280957457487572	2		153	282	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984066	2984066	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	85	356	0	ENST00000396946.4:c.464G>A	p.Arg155Lys	p.R155K	ENST00000396946	NM_032415.4	155	aGg/aAg	5/25	0.107642694980591	5	FACETS	1	0.966	1	0.419	0.37	0.471	INDETERMINATE	1	TRUE	2	0.280957457487572	5		356	685	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852044	128852044	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	59	545	0	ENST00000249373.3:c.2116C>G	p.Gln706Glu	p.Q706E	ENST00000249373	NM_005631.4	706	Cag/Gag	12/12	1	2	FACETS	0.556	0.478	0.642	0.556	0.478	0.642	SUBCLONAL	1	TRUE	1	0.280957457487572	2		545	755	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874991	151874991	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	32	216	0	ENST00000262189.6:c.7547G>C	p.Arg2516Thr	p.R2516T	ENST00000262189	NM_170606.2	2516	aGa/aCa	38/59	1	2	FACETS	0.577	0.468	0.699	0.577	0.468	0.699	SUBCLONAL	1	TRUE	1	0.280957457487572	2		216	395	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934334	68934334	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1366	84	671	0	ENST00000288368.4:c.400C>G	p.Leu134Val	p.L134V	ENST00000288368	NM_024870.2	134	Ctt/Gtt	4/40	1	2	FACETS	0.412	0.362	0.466	0.412	0.362	0.466	SUBCLONAL	1	TRUE	1	0.280957457487572	2		671	1450	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591247	67591247	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0017957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	301	456	0	ENST00000274335.5:c.1746-1G>C		p.X582_splice	ENST00000274335		582			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		456	778	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	226	918	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.871	0.813	0.931	0.871	0.813	0.931	CLONAL	1	TRUE	1	0.622954780819924	2		918	833	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0017958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	222	366	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.853	0.795	0.912	0.853	0.795	0.912	CLONAL	1	TRUE	1	0.622954780819924	2		366	836	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577564	7577564	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	349	402	0	ENST00000269305.4:c.717C>A	p.Asn239Lys	p.N239K	ENST00000269305	NM_001126112.2	239	aaC/aaA	7/11	1	2	FACETS	0.994	0.942	1	0.994	0.942	1	CLONAL	1	TRUE	1	0.622954780819924	2		402	1127	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696425	47696425	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519967	NA	P-0017960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	89	552	0	ENST00000347630.2:c.398T>C	p.Phe133Ser	p.F133S	ENST00000347630	NM_001007230.1	133	tTc/tCc	6/11	1	2	FACETS	0.291	0.257	0.328	0.291	0.257	0.328	SUBCLONAL	1	TRUE	1	0.494359507929569	2		552	1236	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182139	11182142	+	frameshift_variant	Frame_Shift_Del	DEL	AGGC	AGGC	GG	novel	NA	P-0017960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	194	509	1	ENST00000361445.4:c.6704_6707delinsCC	p.Gly2235AlafsTer9	p.G2235Afs*9	ENST00000361445	NM_004958.3	2235	gGCCTc/gCCc	48/58	1	2	FACETS	0.73	0.675	0.788	0.73	0.675	0.788	SUBCLONAL	1	TRUE	1	0.494359507929569	2		510	1075	SUCCESS
APC	324	MSKCC	GRCh37	5	112162875	112162875	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0017960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	100	476	0	ENST00000257430.4:c.1479C>G	p.Tyr493Ter	p.Y493*	ENST00000257430	NM_000038.5	493	taC/taG	12/16	0.318662696556103	1	FACETS	0.363	0.324	0.405	0.363	0.324	0.405	SUBCLONAL	1	TRUE	0	0.494359507929569	1		476	839	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836301	151836301	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	180	443	0	ENST00000262189.6:c.14504T>C	p.Ile4835Thr	p.I4835T	ENST00000262189	NM_170606.2	4835	aTt/aCt	57/59	0.111706994517881	4	FACETS	0.972	0.895	1	0.486	0.447	0.526	INDETERMINATE	1	TRUE	2	0.494359507929569	4		443	1120	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921450	39921451	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	139	214	0	ENST00000378444.4:c.4369dup	p.Ile1457AsnfsTer4	p.I1457Nfs*4	ENST00000378444	NM_001123385.1	1457	att/aAtt	10/15	1	1	FACETS	0.93	0.854	1	0.93	0.854	1	CLONAL	1	TRUE	0	0.494359507929569	1		214	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578400	7578400	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs751477326	NA	P-0017961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	240	442	0	ENST00000269305.4:c.530C>G	p.Pro177Arg	p.P177R	ENST00000269305	NM_001126112.2	177	cCc/cGc	5/11	0.334812472898809	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.346100847225637	2		442	675	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120457	70120457	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	174	680	0	ENST00000245479.2:c.1459C>G	p.Pro487Ala	p.P487A	ENST00000245479	NM_000346.3	487	Cct/Gct	3/3	0.334812472898809	2	FACETS	0.876	0.805	0.95	0.438	0.402	0.475	CLONAL	1	TRUE	0	0.346100847225637	2		680	1148	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0017963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	570	584	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	2	TRUE	NA	0.624298239218526	2		585	891	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602767	10602767	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	587	659	0	ENST00000171111.5:c.811G>T	p.Val271Leu	p.V271L	ENST00000171111	NM_203500.1	271	Gtg/Ttg	3/6	0.624298239218526	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.624298239218526	2		659	898	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098409	11098409	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	313	447	0	ENST00000358026.2:c.928del	p.Arg310AlafsTer16	p.R310Afs*16	ENST00000358026	NM_001128849.1	309	ggC/gg	6/36	0.624298239218526	2	FACETS	0.937	0.896	0.978	0.937	0.896	0.978	CLONAL	2	TRUE	0	0.624298239218526	2		447	535	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333158	70333158	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	536	648	0	ENST00000373644.4:c.1063C>G	p.Gln355Glu	p.Q355E	ENST00000373644	NM_030625.2	355	Caa/Gaa	2/12	0.624298239218526	2	FACETS	0.995	0.963	1	0.995	0.963	1	CLONAL	2	TRUE	0	0.624298239218526	2		648	863	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136199	64136199	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	433	574	0	ENST00000334205.4:c.1358A>T	p.Glu453Val	p.E453V	ENST00000334205	NM_003942.2	453	gAa/gTa	12/17	0.618429480633564	4	FACETS	0.973	0.929	1	0.973	0.929	1	CLONAL	2	TRUE	2	0.624298239218526	4		574	1158	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226451	133226451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	133	360	0	ENST00000320574.5:c.3607G>A	p.Asp1203Asn	p.D1203N	ENST00000320574	NM_006231.2	1203	Gac/Aac	30/49	0.624298239218526	2	FACETS	0.938	0.859	1	0.469	0.429	0.511	CLONAL	1	TRUE	0	0.624298239218526	2		360	454	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527817	103527817	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	56	404	0	ENST00000355739.4:c.3125A>G	p.Glu1042Gly	p.E1042G	ENST00000355739	NM_000123.3	1042	gAg/gGg	15/15	0.624298239218526	2	FACETS	0.254	0.217	0.295	0.127	0.108	0.148	SUBCLONAL	1	TRUE	0	0.624298239218526	2		404	705	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061184	38061184	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	109	266	0	ENST00000250448.2:c.805G>C	p.Glu269Gln	p.E269Q	ENST00000250448	NM_004496.3	269	Gag/Cag	2/2	0.618429480633564	4	FACETS	0.908	0.817	1	0.454	0.408	0.502	CLONAL	1	TRUE	2	0.624298239218526	4		266	625	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110152	3110152	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	142	282	0	ENST00000078429.4:c.142G>A	p.Gly48Ser	p.G48S	ENST00000078429	NM_002067.2	48	Ggc/Agc	2/7	0.624298239218526	2	FACETS	0.978	0.899	1	0.489	0.449	0.531	CLONAL	1	TRUE	0	0.624298239218526	2		282	465	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280076	66280076	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	75	329	0	ENST00000273854.3:c.1613T>C	p.Phe538Ser	p.F538S	ENST00000273854	NM_004439.5	538	tTc/tCc	7/18	0.618429480633564	4	FACETS	0.429	0.375	0.488	0.215	0.187	0.244	SUBCLONAL	1	TRUE	2	0.624298239218526	4		329	909	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	256470	256470	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1388	252	396	0	ENST00000264932.6:c.1930G>T	p.Val644Leu	p.V644L	ENST00000264932	NM_004168.2	644	Gtg/Ttg	15/15	0.624298239218526	7	FACETS	1	0.988	1	0.252	0.235	0.27	CLONAL	1	TRUE	2	0.624298239218526	7		396	1640	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979258	93979259	+	stop_gained	Nonsense_Mutation	DNP	CA	CA	AT	novel	NA	P-0017963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	314	443	0	ENST00000369303.4:c.1569_1570delinsAT	p.Tyr523_Gly524delinsTer	p.Y523_G524delins*	ENST00000369303	NM_004440.3	523	taTGga/taATga	7/17	0.624298239218526	2	FACETS	0.89	0.85	0.93	0.89	0.85	0.93	CLONAL	2	TRUE	0	0.624298239218526	2		443	565	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978461	2978461	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	381	455	1	ENST00000396946.4:c.869G>T	p.Gly290Val	p.G290V	ENST00000396946	NM_032415.4	290	gGg/gTg	7/25	0.323025605292707	5	FACETS	1	0.993	1	0.812	0.774	0.851	INDETERMINATE	2	TRUE	2	0.624298239218526	5		456	970	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850226	128850226	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	409	512	0	ENST00000249373.3:c.1491del	p.Leu498CysfsTer35	p.L498Cfs*35	ENST00000249373	NM_005631.4	497	Ggg/gg	9/12	0.618429480633564	4	FACETS	0.93	0.887	0.974	0.93	0.887	0.974	CLONAL	2	TRUE	2	0.624298239218526	4		512	1144	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151946996	151946996	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0017963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	380	426	0	ENST00000262189.6:c.1778C>G	p.Ser593Ter	p.S593*	ENST00000262189	NM_170606.2	593	tCa/tGa	13/59	0.509077651623667	4	FACETS	0.977	0.93	1			1	CLONAL	2	TRUE	NA	0.624298239218526	4		426	1012	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346044	152346044	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1311575845	NA	P-0017963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	213	516	0	ENST00000359321.1:c.526T>C	p.Cys176Arg	p.C176R	ENST00000359321	NM_005431.1	176	Tgt/Cgt	3/3	0.509077651623667	4	FACETS	0.941	0.873	1			1	CLONAL	1	TRUE	NA	0.624298239218526	4		516	1178	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928900	44928900	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	111	254	0	ENST00000377967.4:c.2000del	p.Gln667ArgfsTer24	p.Q667Rfs*24	ENST00000377967	NM_021140.2	667	cAg/cg	17/29	1	1	FACETS	1	0.917	1	1	0.989	1	CLONAL	2	TRUE	0	0.25067005099892	1		254	383	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	267	184	0				ENST00000310581	NM_198253.2	-/1132			0.265338242876642	1	FACETS	0.544	0.512	0.576	0.544	0.512	0.576	INDETERMINATE	1	TRUE	0	0.804908152992975	1		184	729	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692991	89692991	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786202688	NA	P-0017965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	150	364	0	ENST00000371953.3:c.475A>G	p.Arg159Gly	p.R159G	ENST00000371953	NM_000314.4	159	Agg/Ggg	5/9	0.677680014474906	1	FACETS	0.354	0.324	0.384	0.354	0.324	0.384	SUBCLONAL	1	TRUE	0	0.804908152992975	1		364	630	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200963	108200971	+	inframe_deletion	In_Frame_Del	DEL	GAGCTGGAG	GAGCTGGAG	-	novel	NA	P-0017965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	35	311	0	ENST00000278616.4:c.7330_7338del	p.Glu2444_Glu2446del	p.E2444_E2446del	ENST00000278616	NM_000051.3	2444	GAGCTGGAG/-	50/63	0.804908152992975	1	FACETS	0.093	0.076	0.113	0.093	0.076	0.113	SUBCLONAL	1	TRUE	0	0.804908152992975	1		311	557	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007591	62007596	+	inframe_deletion	In_Frame_Del	DEL	CAGCTT	CAGCTT	-	novel	NA	P-0017965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1295	85	466	0	ENST00000392795.3:c.271_276del	p.Lys91_Leu92del	p.K91_L92del	ENST00000392795	NM_001039933.1	91	AAGCTG/-	3/6	1	2	FACETS	0.153	0.134	0.173	0.153	0.134	0.173	SUBCLONAL	1	TRUE	1	0.804908152992975	2		466	1380	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973168	25973169	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0017965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	49	322	0	ENST00000435504.4:c.1256_1257del	p.Leu419HisfsTer13	p.L419Hfs*13	ENST00000435504		419	cTT/c	12/13	0.804908152992975	1	FACETS	0.134	0.113	0.157	0.134	0.113	0.157	SUBCLONAL	1	TRUE	0	0.804908152992975	1		322	543	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747075	40747075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199637632	NA	P-0017965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1271	78	446	1	ENST00000373198.4:c.3007G>A	p.Val1003Ile	p.V1003I	ENST00000373198	NM_133170.3	1003	Gtc/Atc	22/32	1	2	FACETS	0.144	0.125	0.164	0.144	0.125	0.164	SUBCLONAL	1	TRUE	1	0.804908152992975	2		447	1349	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129729	47129732	+	frameshift_variant	Frame_Shift_Del	DEL	TCCA	TCCA	-	novel	NA	P-0017965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	131	346	0	ENST00000409792.3:c.5148_5151del	p.Asp1716GlufsTer3	p.D1716Efs*3	ENST00000409792	NM_014159.6	1716	gaTGGA/ga	10/21	0.804908152992975	1	FACETS	0.324	0.295	0.355	0.324	0.295	0.355	SUBCLONAL	1	TRUE	0	0.804908152992975	1		346	600	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	90	184	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.842	0.754	0.934	0.842	0.754	0.934	CLONAL	1	TRUE	1	0.641852527019827	2		184	333	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133561	55133561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs958381664	NA	P-0017966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	129	523	0	ENST00000257290.5:c.865G>A	p.Glu289Lys	p.E289K	ENST00000257290	NM_006206.4	289	Gaa/Aaa	6/23	1	2	FACETS	0.781	0.711	0.852	0.781	0.711	0.852	SUBCLONAL	1	TRUE	1	0.641852527019827	2		523	515	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827732	72827732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241554729	NA	P-0017966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	170	453	1	ENST00000268489.5:c.8849G>A	p.Arg2950His	p.R2950H	ENST00000268489	NM_006885.3	2950	cGc/cAc	9/10	1	2	FACETS	0.985	0.912	1	0.985	0.912	1	CLONAL	1	TRUE	1	0.641852527019827	2		454	538	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164873	47164873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867368102	NA	P-0017966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	87	336	0	ENST00000409792.3:c.1253C>T	p.Ser418Phe	p.S418F	ENST00000409792	NM_014159.6	418	tCc/tTc	3/21	1	2	FACETS	0.783	0.7	0.872	0.783	0.7	0.872	SUBCLONAL	1	TRUE	1	0.641852527019827	2		336	346	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	CT	rs121913227	NA	P-0017966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	200	554	2	ENST00000288602.6:c.1798_1799delinsAG	p.Val600Arg	p.V600R	ENST00000288602	NM_004333.4	600	GTg/AGg	15/18	0.298992227812323	4	FACETS	0.848	0.791	0.907			1	INDETERMINATE	2	TRUE	NA	0.641852527019827	4		556	603	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858461	27858461	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	103	253	0	ENST00000359303.2:c.110A>T	p.Lys37Met	p.K37M	ENST00000359303	NM_003535.2	37	aAg/aTg	1/1	0.365187745540062	3	FACETS	1	0.976	1	0.631	0.571	0.693	INDETERMINATE	1	TRUE	1	0.641852527019827	3		253	336	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111429	56111429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1311577375	NA	P-0017966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	92	288	0	ENST00000399503.3:c.29C>T	p.Ser10Leu	p.S10L	ENST00000399503	NM_005921.1	10	tCg/tTg	1/20	1	2	FACETS	0.879	0.789	0.973	0.879	0.789	0.973	CLONAL	1	TRUE	1	0.641852527019827	2		288	326	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100418	8100418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	152	738	0	ENST00000346208.3:c.392C>T	p.Ser131Phe	p.S131F	ENST00000346208		131	tCc/tTc	3/6	1	2	FACETS	0.918	0.845	0.993	0.918	0.845	0.993	CLONAL	1	TRUE	1	0.641852527019827	2		738	516	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653829	89653831	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0017966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	35	495	0	ENST00000371953.3:c.128_130del	p.Glu43del	p.E43del	ENST00000371953	NM_000314.4	43	GAA/-	2/9	0.641852527019827	1	FACETS	0.361	0.298	0.43	0.361	0.298	0.43	SUBCLONAL	1	TRUE	0	0.641852527019827	1		495	205	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125533	7125533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867354196	NA	P-0017966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	127	472	0	ENST00000302850.5:c.3019C>T	p.Pro1007Ser	p.P1007S	ENST00000302850	NM_000208.2	1007	Cca/Tca	17/22	1	2	FACETS	0.838	0.764	0.915	0.838	0.764	0.915	CLONAL	1	TRUE	1	0.641852527019827	2		472	472	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546872	9546872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	107	314	0	ENST00000353224.5:c.1150C>T	p.His384Tyr	p.H384Y	ENST00000353224	NM_177990.2	384	Cat/Tat	5/10	NA	2	FACETS	0.911	0.825	1			1	INDETERMINATE	1	TRUE	NA	0.641852527019827	2		314	366	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561211	9561211	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	119	424	1	ENST00000353224.5:c.571G>A	p.Asp191Asn	p.D191N	ENST00000353224	NM_177990.2	191	Gat/Aat	4/10	NA	2	FACETS	0.845	0.768	0.924			1	INDETERMINATE	1	TRUE	NA	0.641852527019827	2		425	439	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031733	36031733	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	158	591	0	ENST00000358208.4:c.1562A>G	p.Asp521Gly	p.D521G	ENST00000358208		521	gAc/gGc	12/12	0.641852527019827	3	FACETS	0.971	0.892	1	0.485	0.446	0.526	CLONAL	1	TRUE	1	0.641852527019827	3		591	670	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755558	39755558	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756534988	NA	P-0017966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	123	359	1	ENST00000288319.7:c.1207C>T	p.Pro403Ser	p.P403S	ENST00000288319	NM_182918.3	403	Ccc/Tcc	10/10	1	2	FACETS	0.904	0.824	0.987	0.904	0.824	0.987	CLONAL	1	TRUE	1	0.641852527019827	2		360	424	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526161	189526161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	182	594	0	ENST00000264731.3:c.425G>A	p.Ser142Asn	p.S142N	ENST00000264731	NM_003722.4	142	aGc/aAc	4/14	1	2	FACETS	0.96	0.89	1	0.96	0.89	1	CLONAL	1	TRUE	1	0.641852527019827	2		594	591	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156493	55156493	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	117	393	0	ENST00000257290.5:c.2894T>A	p.Ile965Asn	p.I965N	ENST00000257290	NM_006206.4	965	aTt/aAt	22/23	1	2	FACETS	0.803	0.729	0.88	0.803	0.729	0.88	CLONAL	1	TRUE	1	0.641852527019827	2		393	454	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750603	57750603	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0017966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	83	393	0	ENST00000274289.3:c.1867-2A>G		p.X623_splice	ENST00000274289	NM_006622.3	623			1	2	FACETS	0.781	0.696	0.871	0.781	0.696	0.871	SUBCLONAL	1	TRUE	1	0.641852527019827	2		393	331	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402494	20402494	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	144	628	0	ENST00000346618.3:c.31C>T	p.Gln11Ter	p.Q11*	ENST00000346618	NM_001949.4	11	Cag/Tag	1/7	0.365187745540062	3	FACETS	1	0.98	1	0.609	0.559	0.66	INDETERMINATE	1	TRUE	1	0.641852527019827	3		628	487	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553668	106553668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1261004652	NA	P-0017966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	152	466	0	ENST00000369096.4:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000369096	NM_001198.3	545	Gaa/Aaa	5/7	1	2	FACETS	0.951	0.876	1	0.951	0.876	1	CLONAL	1	TRUE	1	0.641852527019827	2		466	498	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878073	151878073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	154	354	0	ENST00000262189.6:c.6872C>T	p.Ser2291Phe	p.S2291F	ENST00000262189	NM_170606.2	2291	tCc/tTc	36/59	0.641852527019827	4	FACETS	1	0.977	1	0.59	0.541	0.64	CLONAL	1	TRUE	2	0.641852527019827	4		354	668	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0017967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	355	583	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	0.665193252291819	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.665193252291819	1		583	681	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259064	153259064	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	168	261	0	ENST00000281708.4:c.751C>T	p.Leu251Phe	p.L251F	ENST00000281708	NM_033632.3	251	Ctt/Ttt	5/12	1	2	FACETS	0.968	0.896	1	0.968	0.896	1	CLONAL	1	TRUE	1	0.665193252291819	2		261	522	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443695	29443695	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs863225281	NA	P-0121605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	130	494	0	ENST00000389048.3:c.3522C>G	p.Phe1174Leu	p.F1174L	ENST00000389048	NM_004304.4	1174	ttC/ttG	23/29	0.463535634418361	3	FACETS	0.769	0.697	0.844	0.384	0.348	0.422	SUBCLONAL	1	NA	1	0.486651433443122	3		494	864	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0017970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	240	523	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.265939562309128	1	FACETS	1	0.969	1	1	0.995	1	CLONAL	2	FALSE	0	0.265939562309128	1		523	742	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161148	56161190	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTCTTTTTAACTCTTTAGAACTGCAGCTGTGCACGTGGAACA	TTTCTTTTTAACTCTTTAGAACTGCAGCTGTGCACGTGGAACA	-	novel	NA	P-0017970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	163	224	0	ENST00000399503.3:c.1036-17_1061del		p.X346_splice	ENST00000399503	NM_005921.1	346		5/20	1	2	FACETS	1	0.976	1	1	0.993	1	CLONAL	2	FALSE	1	0.265939562309128	2		224	537	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170909	56170910	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0017970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	118	278	0	ENST00000399503.3:c.1743_1744del	p.Glu581AspfsTer9	p.E581Dfs*9	ENST00000399503	NM_005921.1	579	gtGAga/gtga	10/20	1	2	FACETS	0.808	0.732	0.888	1	0.986	1	CLONAL	2	FALSE	1	0.265939562309128	2		278	549	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220649	1220649	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	49	813	1	ENST00000326873.7:c.667G>T	p.Glu223Ter	p.E223*	ENST00000326873	NM_000455.4	223	Gag/Tag	5/10	1	2	FACETS	0.865	0.731	1	0.865	0.731	1	CLONAL	1	TRUE	1	0.15	2		814	755	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0017973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	52	847	1	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	1	2	FACETS	0.794	0.674	0.927	0.794	0.674	0.927	CLONAL	1	TRUE	1	0.15	2		848	873	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711876	89711899	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GAGTAACTATTCCCAGTCAGAGGC	GAGTAACTATTCCCAGTCAGAGGC	-	novel	NA	P-0017973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	32	514	0	ENST00000371953.3:c.495_518del	p.Val166_Arg173del	p.V166_R173del	ENST00000371953	NM_000314.4	165	gGAGTAACTATTCCCAGTCAGAGGCgc/ggc	6/9	1	2	FACETS	0.942	0.764	1	0.942	0.764	1	CLONAL	1	TRUE	1	0.15	2		514	453	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931472	131931472	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28903092	NA	P-0017973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	36	531	0	ENST00000265335.6:c.2177G>T	p.Arg726Leu	p.R726L	ENST00000265335		726	cGt/cTt	13/25	1	2	FACETS	0.859	0.705	1	0.859	0.705	1	CLONAL	1	TRUE	1	0.15	2		531	559	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041107	112041107	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	56	569	0	ENST00000368678.4:c.148T>A	p.Tyr50Asn	p.Y50N	ENST00000368678		50	Tac/Aac	3/13	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.15	2		569	550	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	3734	930	0	ENST00000397752.3:c.3028G>C	p.Asp1010His	p.D1010H	ENST00000397752	NM_000245.2	1010	Gat/Cat	14/21	0.407484710492895	25	FACETS	0.984	0.977	0.991			1	CLONAL	25	TRUE	NA	0.407484710492895	25		930	4236	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577144	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	295	673	0	ENST00000269305.4:c.794T>G	p.Leu265Arg	p.L265R	ENST00000269305	NM_001126112.2	265	cTg/cGg	8/11	0.303871353192218	3	FACETS	1	0.98	1	0.716	0.677	0.756	CLONAL	2	TRUE	0	0.407484710492895	3		673	811	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098794	178098817	+	inframe_deletion	In_Frame_Del	DEL	AGAAATTCACCTGTCTCTTCATCT	AGAAATTCACCTGTCTCTTCATCT	-	novel	NA	P-0017974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	252	722	0	ENST00000397062.3:c.228_251del	p.Asp77_Leu84del	p.D77_L84del	ENST00000397062	NM_006164.4	76	ctAGATGAAGAGACAGGTGAATTTCTc/ctc	2/5	0.140203763513548	3	FACETS	1	0.953	1	0.677	0.636	0.719	INDETERMINATE	2	TRUE	0	0.407484710492895	3		722	733	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0017976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	210	427	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.200855583067057	3	FACETS	0.912	0.848	0.978	1	0.99	1	CLONAL	3	TRUE	1	0.200855583067057	3		427	841	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17354353	17354353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	54	602	0	ENST00000375499.3:c.431G>A	p.Ser144Asn	p.S144N	ENST00000375499	NM_003000.2	144	aGc/aAc	5/8	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.200855583067057	2		602	525	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0017977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4251	234	929	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.630017345481041	25	FACETS	1	0.989	1			1	CLONAL	1	TRUE	NA	0.630017345481041	25		929	4485	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098816	178098816	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	213	944	0	ENST00000397062.3:c.229G>C	p.Asp77His	p.D77H	ENST00000397062	NM_006164.4	77	Gat/Cat	2/5	0.630017345481041	3	FACETS	1	0.989	1	0.642	0.599	0.687	CLONAL	1	TRUE	1	0.630017345481041	3		944	692	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577101	7577101	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	174	1091	3	ENST00000269305.4:c.837del	p.Arg280GlufsTer65	p.R280Efs*65	ENST00000269305	NM_001126112.2	279	ggG/gg	8/11	0.579193554363863	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.630017345481041	1		1094	360	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749964	162749964	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	175	969	0	ENST00000367921.3:c.2496G>C	p.Trp832Cys	p.W832C	ENST00000367921	NM_006182.2	832	tgG/tgC	18/18	0.630017345481041	3	FACETS	1	0.956	1	0.525	0.485	0.566	CLONAL	1	TRUE	1	0.630017345481041	3		969	696	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713543	30713543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	135	742	0	ENST00000295754.5:c.868G>A	p.Glu290Lys	p.E290K	ENST00000295754	NM_003242.5	290	Gag/Aag	4/7	0.630017345481041	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.630017345481041	1		742	289	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250047	53250047	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	170	971	0	ENST00000375401.3:c.202C>T	p.Arg68Ter	p.R68*	ENST00000375401	NM_004187.3	68	Cga/Tga	2/26	0.630017345481041	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.630017345481041	1		971	342	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514257	69514257	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	50	753	0	ENST00000294312.3:c.424C>G	p.Pro142Ala	p.P142A	ENST00000294312	NM_005117.2	142	Ccg/Gcg	3/3	0.259348433929366	3	FACETS	0.561	0.475	0.656	0.281	0.237	0.328	SUBCLONAL	1	TRUE	1	0.31	3		753	664	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221737	36221737	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	64	965	0	ENST00000222270.7:c.5406G>C	p.Gln1802His	p.Q1802H	ENST00000222270	NM_014727.1	1802	caG/caC	26/37	1	2	FACETS	0.65	0.563	0.745	0.65	0.563	0.745	SUBCLONAL	1	TRUE	1	0.31	2		965	635	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561376	9561376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774715756	NA	P-0017978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	38	475	0	ENST00000353224.5:c.406G>A	p.Asp136Asn	p.D136N	ENST00000353224	NM_177990.2	136	Gat/Aat	4/10	1	2	FACETS	0.575	0.476	0.687	0.575	0.476	0.687	SUBCLONAL	1	TRUE	1	0.31	2		475	426	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561376	9561376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774715756	NA	P-0017978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	46	475	0	ENST00000353224.5:c.406G>A	p.Asp136Asn	p.D136N	ENST00000353224	NM_177990.2	136	Gat/Aat	4/10	0.260091854323356	0	FACETS	0.212	0.179	0.248			1	INDETERMINATE	1	TRUE	0	0.563486528137913	0		475	336	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514257	69514257	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017978-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	82	753	0	ENST00000294312.3:c.424C>G	p.Pro142Ala	p.P142A	ENST00000294312	NM_005117.2	142	Ccg/Gcg	3/3	1	2	FACETS	0.447	0.393	0.505	0.447	0.393	0.505	SUBCLONAL	1	TRUE	1	0.359249043404093	2		753	1022	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221737	36221737	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017978-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	98	965	0	ENST00000222270.7:c.5406G>C	p.Gln1802His	p.Q1802H	ENST00000222270	NM_014727.1	1802	caG/caC	26/37	1	2	FACETS	0.453	0.403	0.507	0.453	0.403	0.507	SUBCLONAL	1	TRUE	1	0.359249043404093	2		965	1204	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561376	9561376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774715756	NA	P-0017978-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	44	475	0	ENST00000353224.5:c.406G>A	p.Asp136Asn	p.D136N	ENST00000353224	NM_177990.2	136	Gat/Aat	4/10	0.323933270381805	1	FACETS	0.335	0.28	0.396	0.335	0.28	0.396	SUBCLONAL	1	TRUE	0	0.359249043404093	1		475	600	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926885	112926885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507544	NA	P-0017978-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	72	646	0	ENST00000351677.2:c.1505C>T	p.Ser502Leu	p.S502L	ENST00000351677	NM_002834.3	502	tCa/tTa	13/16	0.323933270381805	1	FACETS	0.434	0.378	0.494	0.434	0.378	0.494	SUBCLONAL	1	TRUE	0	0.359249043404093	1		646	758	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033844	49033844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853294	NA	P-0017980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	263	641	1	ENST00000267163.4:c.1981C>T	p.Arg661Trp	p.R661W	ENST00000267163	NM_000321.2	661	Cgg/Tgg	20/27	0.83247925232247	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.83247925232247	1		642	342	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434711	128434711	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	332	978	0	ENST00000265960.3:c.143G>C	p.Gly48Ala	p.G48A	ENST00000265960	NM_001006617.1	48	gGa/gCa	2/12	0.83247925232247	3	FACETS	0.939	0.887	0.992	0.47	0.443	0.496	CLONAL	1	TRUE	1	0.83247925232247	3		978	1203	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	177	918	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.186007463003325	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.186007463003325	3		918	898	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0017981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	67	710	5	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.186007463003325	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.186007463003325	1		715	471	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971153	21971153	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913383	NA	P-0017981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	43	478	0	ENST00000304494.5:c.205G>T	p.Glu69Ter	p.E69*	ENST00000304494	NM_000077.4	69	Gag/Tag	2/3	0.186007463003325	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.186007463003325	1		478	325	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220000	5220000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369971329	NA	P-0017981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	40	791	0	ENST00000357368.4:c.3715G>A	p.Gly1239Ser	p.G1239S	ENST00000357368	NM_002850.3	1239	Ggc/Agc	22/38	1	2	FACETS	0.759	0.629	0.903	0.759	0.629	0.903	CLONAL	1	TRUE	1	0.186007463003325	2		791	567	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219240	133219240	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774541167	NA	P-0017981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	31	868	0	ENST00000320574.5:c.4804G>A	p.Val1602Ile	p.V1602I	ENST00000320574	NM_006231.2	1602	Gtc/Atc	37/49	1	2	FACETS	0.556	0.449	0.679	0.556	0.449	0.679	SUBCLONAL	1	TRUE	1	0.186007463003325	2		868	599	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131775	2131777	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-	rs876658759	NA	P-0017981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	42	751	0	ENST00000219476.3:c.3794_3796del	p.Pro1265del	p.P1265del	ENST00000219476	NM_000548.3	1264	CCT/-	31/42	1	2	FACETS	0.796	0.664	0.944	0.796	0.664	0.944	CLONAL	1	TRUE	1	0.186007463003325	2		751	567	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101199	41101199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368237025	NA	P-0017981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	31	707	2	ENST00000373198.4:c.1157C>T	p.Pro386Leu	p.P386L	ENST00000373198	NM_133170.3	386	cCg/cTg	8/32	1	2	FACETS	0.615	0.496	0.75	0.615	0.496	0.75	SUBCLONAL	1	TRUE	1	0.186007463003325	2		709	542	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599341	55599341	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519761	NA	P-0017982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	180	902	0	ENST00000288135.5:c.2467T>G	p.Tyr823Asp	p.Y823D	ENST00000288135	NM_000222.2	823	Tat/Gat	17/21	0.142685559437839	4	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.793997408129832	4		902	586	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593587	55593604	+	inframe_deletion	In_Frame_Del	DEL	CATGTATGAAGTACAGTG	CATGTATGAAGTACAGTG	-	novel	NA	P-0017982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	177	697	0	ENST00000288135.5:c.1653_1670del	p.Met552_Trp557del	p.M552_W557del	ENST00000288135	NM_000222.2	551	ccCATGTATGAAGTACAGTGg/ccg	11/21	0.142685559437839	4	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.793997408129832	4		697	544	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9928080	9928080	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	137	664	0	ENST00000330684.3:c.1659C>G	p.Phe553Leu	p.F553L	ENST00000330684	NM_001134407.1	553	ttC/ttG	8/13	1	2	FACETS	0.885	0.814	0.958	0.885	0.814	0.958	CLONAL	1	TRUE	1	0.793997408129832	2		664	390	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0017983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	104	294	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.535701369935059	2		294	336	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419986	41419986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372989163	NA	P-0017983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	109	643	1	ENST00000373198.4:c.335G>A	p.Arg112His	p.R112H	ENST00000373198	NM_133170.3	112	cGt/cAt	3/32	0.532512663272682	3	FACETS	0.801	0.721	0.886	0.401	0.36	0.443	CLONAL	1	TRUE	1	0.535701369935059	3		644	644	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117888	70117888	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs886043537	NA	P-0017983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	260	507	0	ENST00000245479.2:c.356C>A	p.Ala119Glu	p.A119E	ENST00000245479	NM_000346.3	119	gCg/gAg	1/3	0.525361100319992	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.535701369935059	2		507	444	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604790	48604790	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1568211615	NA	P-0017983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	117	566	1	ENST00000342988.3:c.1612G>T	p.Glu538Ter	p.E538*	ENST00000342988	NM_005359.5	538	Gaa/Taa	12/12	1	2	FACETS	0.91	0.825	0.998	0.91	0.825	0.998	CLONAL	1	TRUE	1	0.535701369935059	2		567	480	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274704	123274704	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	129	794	0	ENST00000358487.5:c.1214A>G	p.Lys405Arg	p.K405R	ENST00000358487	NM_000141.4	405	aAg/aGg	9/18	1	2	FACETS	0.83	0.756	0.908	0.83	0.756	0.908	CLONAL	1	TRUE	1	0.535701369935059	2		794	580	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809254	243809254	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	91	769	1	ENST00000263826.5:c.370C>A	p.Gln124Lys	p.Q124K	ENST00000263826	NM_005465.4	124	Caa/Aaa	4/13	1	2	FACETS	0.734	0.654	0.818	0.734	0.654	0.818	SUBCLONAL	1	TRUE	1	0.535701369935059	2		770	463	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778355	3778355	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	123	559	0	ENST00000262367.5:c.6693C>G	p.Phe2231Leu	p.F2231L	ENST00000262367	NM_004380.2	2231	ttC/ttG	31/31	1	2	FACETS	0.922	0.838	1	0.922	0.838	1	CLONAL	1	TRUE	1	0.535701369935059	2		559	498	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573623	48573624	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0017983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	113	626	1	ENST00000342988.3:c.209_210dup	p.Cys71AsnfsTer24	p.C71Nfs*24	ENST00000342988	NM_005359.5	69	-/AA	2/12	1	2	FACETS	0.9	0.814	0.989	0.9	0.814	0.989	CLONAL	1	TRUE	1	0.535701369935059	2		627	469	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046378	69046378	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375506738	NA	P-0017984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	196	559	1	ENST00000288368.4:c.3851C>T	p.Ala1284Val	p.A1284V	ENST00000288368	NM_024870.2	1284	gCg/gTg	32/40	1	2	FACETS	0.902	0.838	0.967	0.902	0.838	0.967	CLONAL	1	TRUE	1	0.625631193451397	2		560	695	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249013	55249014	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACCCCC	novel	NA	P-0017985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	462	646	0	ENST00000275493.2:c.2314_2319dup	p.Pro772_His773dup	p.P772_H773dup	ENST00000275493	NM_005228.3	772	aac/aACCCCCac	20/28	0.578882803079992	6	FACETS	0.88	0.844	0.915	0.88	0.844	0.915	CLONAL	4	TRUE	2	0.578882803079992	6		646	979	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0017985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	244	707	0	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	0.556883491530194	2	FACETS	0.951	0.903	1	0.951	0.903	1	CLONAL	2	TRUE	0	0.578882803079992	2		707	443	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174875	11174875	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	305	871	0	ENST00000361445.4:c.7159A>G	p.Met2387Val	p.M2387V	ENST00000361445	NM_004958.3	2387	Atg/Gtg	52/58	0.566453805181469	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	2	0.578882803079992	4		871	810	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37865627	37865627	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	151	961	0	ENST00000269571.5:c.496A>G	p.Thr166Ala	p.T166A	ENST00000269571		166	Acg/Gcg	4/27	0.556883491530194	2	FACETS	0.851	0.781	0.924	0.426	0.39	0.462	CLONAL	1	TRUE	0	0.578882803079992	2		961	613	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562990	176562990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	148	742	1	ENST00000439151.2:c.886C>T	p.Pro296Ser	p.P296S	ENST00000439151	NM_022455.4	296	Cct/Tct	2/23	0.556883491530194	2	FACETS	0.937	0.86	1	0.468	0.43	0.508	CLONAL	1	TRUE	0	0.578882803079992	2		743	546	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434231	49434232	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	333	1236	0	ENST00000301067.7:c.7321dup	p.Thr2441AsnfsTer8	p.T2441Nfs*8	ENST00000301067	NM_003482.3	2441	acc/aAcc	31/54	1	2	FACETS	0.934	0.882	0.987	0.934	0.882	0.987	CLONAL	1	TRUE	1	0.533479514500992	2		1236	1337	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805694	46805694	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	218	978	0	ENST00000290295.7:c.262T>G	p.Tyr88Asp	p.Y88D	ENST00000290295	NM_006361.5	88	Tac/Gac	1/2	1	2	FACETS	0.862	0.802	0.924	0.862	0.802	0.924	CLONAL	1	TRUE	1	0.533479514500992	2		978	948	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0017990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	121	523	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.547	0.495	0.601	0.547	0.495	0.601	SUBCLONAL	1	TRUE	1	0.705821622518812	2		523	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0017990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	96	958	2	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.48134992221442	1	FACETS	0.244	0.217	0.273	0.244	0.217	0.273	SUBCLONAL	1	TRUE	0	0.705821622518812	1		960	721	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177011	56177014	+	frameshift_variant	Frame_Shift_Del	DEL	ATAG	ATAG	-	novel	NA	P-0017990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	140	578	0	ENST00000399503.3:c.2286_2289del	p.Arg763CysfsTer35	p.R763Cfs*35	ENST00000399503	NM_005921.1	761	ATAGat/at	13/20	1	2	FACETS	0.672	0.615	0.732	0.672	0.615	0.732	SUBCLONAL	1	TRUE	1	0.705821622518812	2		578	590	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059204	27059204	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0017990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	143	824	0	ENST00000324856.7:c.1841C>G	p.Ser614Ter	p.S614*	ENST00000324856	NM_006015.4	614	tCa/tGa	4/20	1	2	FACETS	0.521	0.475	0.569	0.521	0.475	0.569	SUBCLONAL	1	TRUE	1	0.705821622518812	2		824	778	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218983	193218983	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	83	462	0	ENST00000367435.3:c.1541T>G	p.Phe514Cys	p.F514C	ENST00000367435	NM_024529.4	514	tTt/tGt	16/17	1	2	FACETS	0.595	0.528	0.666	0.595	0.528	0.666	SUBCLONAL	1	TRUE	1	0.705821622518812	2		462	395	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177827	56177828	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	127	547	0	ENST00000399503.3:c.2803dup	p.Ser935PhefsTer6	p.S935Ffs*6	ENST00000399503	NM_005921.1	934	att/aTtt	14/20	1	2	FACETS	0.652	0.593	0.713	0.652	0.593	0.713	SUBCLONAL	1	TRUE	1	0.705821622518812	2		547	552	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123837	46123837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	50	396	0	ENST00000334344.6:c.109del	p.Ile37SerfsTer21	p.I37Sfs*21	ENST00000334344	NM_152641.2	35	Aaa/aa	2/21	1	2	FACETS	0.636	0.541	0.74	0.636	0.541	0.74	SUBCLONAL	1	TRUE	1	0.404128355162624	2		396	389	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231791	36231791	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	72	959	0	ENST00000300305.3:c.593A>G	p.Asp198Gly	p.D198G	ENST00000300305		198	gAt/gGt	5/8	1	2	FACETS	0.4	0.349	0.456	0.4	0.349	0.456	SUBCLONAL	1	TRUE	1	0.404128355162624	2		959	890	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456321	32456321	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	107	1129	2	ENST00000332351.3:c.571G>T	p.Gly191Cys	p.G191C	ENST00000332351	NM_024426.4	191	Ggc/Tgc	1/10	1	2	FACETS	0.591	0.529	0.657	0.591	0.529	0.657	SUBCLONAL	1	TRUE	1	0.404128355162624	2		1131	896	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562192	21562192	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	152	1424	0	ENST00000382592.4:c.1727C>G	p.Ser576Cys	p.S576C	ENST00000382592	NM_014572.2	576	tCt/tGt	4/8	1	2	FACETS	0.544	0.495	0.594	0.544	0.495	0.594	SUBCLONAL	1	TRUE	1	0.404128355162624	2		1424	1384	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220634	1220635	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	T	novel	NA	P-0017991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	101	812	0	ENST00000326873.7:c.652_653delinsT	p.Ala218PhefsTer69	p.A218Ffs*69	ENST00000326873	NM_000455.4	218	GCt/Tt	5/10	1	2	FACETS	0.729	0.652	0.81	0.729	0.652	0.81	SUBCLONAL	1	TRUE	1	0.404128355162624	2		812	686	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0017992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	40	571	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.993	0.829	1	0.993	0.829	1	CLONAL	1	TRUE	1	0.264208049920176	2		571	305	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0017992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	89	588	2	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.232210170419875	1	FACETS	0.945	0.839	1	0.945	0.839	1	CLONAL	1	TRUE	0	0.264208049920176	1		590	619	SUCCESS
APC	324	MSKCC	GRCh37	5	112175198	112175198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	73	289	1	ENST00000257430.4:c.3907C>T	p.Gln1303Ter	p.Q1303*	ENST00000257430	NM_000038.5	1303	Caa/Taa	16/16	0.264208049920176	2	FACETS	0.937	0.827	1	0.937	0.827	1	CLONAL	2	TRUE	0	0.264208049920176	2		290	295	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922294	100922294	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1315135533	NA	P-0017992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	40	650	3	ENST00000325455.5:c.2218C>T	p.Arg740Ter	p.R740*	ENST00000325455	NM_001202474.3	740	Cga/Tga	5/8	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.264208049920176	2		653	282	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263258	115263258	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	43	905	0	ENST00000438362.2:c.2092G>C	p.Val698Leu	p.V698L	ENST00000438362	NM_001242891.1	698	Gtc/Ctc	17/20	0.159921214876641	3	FACETS	0.438	0.365	0.52	0.219	0.182	0.26	SUBCLONAL	1	TRUE	1	0.264208049920176	3		905	841	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046663	30046663	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0017992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	47	619	0	ENST00000331968.5:c.2521-1G>T		p.X841_splice	ENST00000331968	NM_002742.2	841			1	2	FACETS	0.729	0.615	0.854	0.729	0.615	0.854	SUBCLONAL	1	TRUE	1	0.264208049920176	2		619	488	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371810	45371810	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	49	562	1	ENST00000262160.6:c.1181T>C	p.Leu394Pro	p.L394P	ENST00000262160	NM_005901.5	394	cTg/cCg	10/11	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.264208049920176	2		563	316	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606006	47606147	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAATATTCTGATTCTCAATTAATGTTATTTTCAAATGATTTTGATTATATTAGTATTAATTTGTATTATTCAATTTTTTTCCCCAGTATGAGAATAATGTTATCACTATTGATCTGGTTCAAAATTCTTCTCAAAAAACTCA	GAATATTCTGATTCTCAATTAATGTTATTTTCAAATGATTTTGATTATATTAGTATTAATTTGTATTATTCAATTTTTTTCCCCAGTATGAGAATAATGTTATCACTATTGATCTGGTTCAAAATTCTTCTCAAAAAACTCA	-	novel	NA	P-0017992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	16	99	0	ENST00000263735.4:c.556-82_615del		p.X186_splice	ENST00000263735	NM_002354.2	186		6/9	1	2	FACETS	0.878	0.665	1	1	0.919	1	CLONAL	2	TRUE	1	0.264208049920176	2		99	69	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606183	47606183	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	22	479	0	ENST00000263735.4:c.647T>G	p.Phe216Cys	p.F216C	ENST00000263735	NM_002354.2	216	tTt/tGt	6/9	1	2	FACETS	0.534	0.414	0.673	0.534	0.414	0.673	SUBCLONAL	1	TRUE	1	0.264208049920176	2		479	312	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265516	152265517	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0017992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	60	691	0	ENST00000206249.3:c.974dup	p.Ile326AspfsTer7	p.I326Dfs*7	ENST00000206249	NM_000125.3	323	-/C	4/8	0.159921214876641	3	FACETS	0.945	0.815	1	0.473	0.407	0.544	CLONAL	1	TRUE	1	0.264208049920176	3		691	544	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456467	99456467	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56248469	NA	P-0017993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	55	658	0	ENST00000268035.6:c.1784G>A	p.Arg595His	p.R595H	ENST00000268035	NM_000875.3	595	cGt/cAt	8/21	1	2	FACETS	0.843	0.72	0.977	0.843	0.72	0.977	CLONAL	1	TRUE	1	0.19	2		658	687	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56363618	56363618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	36	520	1	ENST00000348428.3:c.397C>T	p.Pro133Ser	p.P133S	ENST00000348428	NM_006785.3	133	Cca/Tca	3/17	1	2	FACETS	0.846	0.695	1	0.846	0.695	1	CLONAL	1	TRUE	1	0.19	2		521	448	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984408	201984409	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	110	1094	1	ENST00000359651.3:c.1075dup	p.Ser359LysfsTer112	p.S359Kfs*112	ENST00000359651		358	tca/tcAa	8/8	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.19	2		1095	1124	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008324	29008324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770377283	NA	P-0017993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	35	445	0	ENST00000282397.4:c.547C>T	p.Arg183Cys	p.R183C	ENST00000282397	NM_002019.4	183	Cgc/Tgc	5/30	0.170314861879666	3	FACETS	0.822	0.673	0.989	0.411	0.336	0.495	CLONAL	1	TRUE	1	0.19	3		445	491	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647248	23647248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374090568	NA	P-0017993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	70	831	0	ENST00000261584.4:c.619C>T	p.Pro207Ser	p.P207S	ENST00000261584	NM_024675.3	207	Cca/Tca	4/13	1	2	FACETS	0.925	0.805	1	0.925	0.805	1	CLONAL	1	TRUE	1	0.19	2		831	797	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916935	+	inframe_deletion	In_Frame_Del	DEL	GCAACC	GCAACC	-	novel	NA	P-0017993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	58	823	0	ENST00000263967.3:c.318_323del	p.Asn107_Arg108del	p.N107_R108del	ENST00000263967	NM_006218.2	106	gGCAACCgt/ggt	2/21	1	2	FACETS	0.788	0.675	0.911	0.788	0.675	0.911	CLONAL	1	TRUE	1	0.19	2		823	775	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046361	180046361	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	64	638	0	ENST00000261937.6:c.2653G>A	p.Ala885Thr	p.A885T	ENST00000261937	NM_182925.4	885	Gcc/Acc	19/30	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.19	2		638	612	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188365	32188365	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	67	859	0	ENST00000375023.3:c.976T>A	p.Cys326Ser	p.C326S	ENST00000375023	NM_004557.3	326	Tgc/Agc	6/30	1	2	FACETS	0.907	0.787	1	0.907	0.787	1	CLONAL	1	TRUE	1	0.19	2		859	778	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561417	141561417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1487711892	NA	P-0017993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	38	453	0	ENST00000220592.5:c.1388C>T	p.Thr463Met	p.T463M	ENST00000220592	NM_012154.3	463	aCg/aTg	11/19	0.170314861879666	3	FACETS	0.814	0.672	0.973	0.407	0.336	0.487	CLONAL	1	TRUE	1	0.19	3		453	538	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0017994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	164	548	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.317402383446207	2		548	785	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0017994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	93	833	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.867	0.771	0.969	0.867	0.771	0.969	CLONAL	1	TRUE	1	0.317402383446207	2		833	676	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0017994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	61	710	5	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.583	0.503	0.671	0.583	0.503	0.671	SUBCLONAL	1	TRUE	1	0.317402383446207	2		715	659	SUCCESS
APC	324	MSKCC	GRCh37	5	112174112	112174112	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	88	503	0	ENST00000257430.4:c.2821G>T	p.Glu941Ter	p.E941*	ENST00000257430	NM_000038.5	941	Gaa/Taa	16/16	0.317402383446207	1	FACETS	0.976	0.868	1	0.976	0.868	1	CLONAL	1	TRUE	0	0.317402383446207	1		503	478	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38978730	38978730	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	78	467	0	ENST00000357387.3:c.776A>G	p.Asp259Gly	p.D259G	ENST00000357387	NM_152756.3	259	gAt/gGt	9/38	0.317402383446207	5	FACETS	0.935	0.821	1	0.234	0.205	0.265	CLONAL	1	TRUE	1	0.317402383446207	5		467	776	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506176	103506176	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs771721463	NA	P-0017994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	241	774	0	ENST00000355739.4:c.334A>G	p.Thr112Ala	p.T112A	ENST00000355739	NM_000123.3	112	Aca/Gca	3/15	0.317402383446207	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.317402383446207	3		774	833	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89833645	89833645	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	106	512	1	ENST00000389301.3:c.2505A>T	p.Lys835Asn	p.K835N	ENST00000389301	NM_000135.2	835	aaA/aaT	27/43	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.317402383446207	2		513	567	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754866	29754866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	63	412	1	ENST00000389048.3:c.1069C>T	p.Pro357Ser	p.P357S	ENST00000389048	NM_004304.4	357	Ccc/Tcc	4/29	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.317402383446207	2		413	329	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80171592	80171592	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	92	766	0	ENST00000265081.6:c.3325A>G	p.Lys1109Glu	p.K1109E	ENST00000265081	NM_002439.4	1109	Aag/Gag	24/24	0.317402383446207	1	FACETS	0.814	0.725	0.909	0.814	0.725	0.909	CLONAL	1	TRUE	0	0.317402383446207	1		766	599	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	302	741	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.578963863016652	3	FACETS	0.941	0.892	0.99	0.941	0.892	0.99	CLONAL	2	TRUE	1	0.578963863016652	3		741	715	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	166	555	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.578963863016652	2		558	547	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	121	689	0	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	1	2	FACETS	0.686	0.622	0.754	0.686	0.622	0.754	SUBCLONAL	1	TRUE	1	0.578963863016652	2		689	609	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	245	865	8	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.996	0.933	1	0.996	0.933	1	CLONAL	1	TRUE	1	0.578963863016652	2		873	850	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562577	21562577	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1395329857	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	37	91	0	ENST00000382592.4:c.1342C>T	p.Arg448Cys	p.R448C	ENST00000382592	NM_014572.2	448	Cgt/Tgt	4/8	1	2	FACETS	0.779	0.669	0.892	1	0.964	1	SUBCLONAL	2	TRUE	1	0.578963863016652	2		91	82	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353819	15353819	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	115	752	2	ENST00000263377.2:c.3061del	p.His1021IlefsTer47	p.H1021Ifs*47	ENST00000263377	NM_058243.2	1021	Cat/at	14/20	1	2	FACETS	0.713	0.645	0.785	0.713	0.645	0.785	SUBCLONAL	1	TRUE	1	0.578963863016652	2		754	557	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38616977	38616977	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	164	644	0	ENST00000299084.4:c.395del	p.Asn132MetfsTer20	p.N132Mfs*20	ENST00000299084	NM_152594.2	130	tcA/tc	4/7	0.578963863016652	2	FACETS	1	0.941	1	0.511	0.472	0.552	CLONAL	1	TRUE	0	0.578963863016652	2		644	554	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161907	47161907	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	130	705	2	ENST00000409792.3:c.4219del	p.Arg1407GlyfsTer5	p.R1407Gfs*5	ENST00000409792	NM_014159.6	1407	Agg/gg	3/21	1	2	FACETS	0.717	0.652	0.785	0.717	0.652	0.785	SUBCLONAL	1	TRUE	1	0.578963863016652	2		707	626	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952006	178952006	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	124	706	1	ENST00000263967.3:c.3061T>C	p.Tyr1021His	p.Y1021H	ENST00000263967	NM_006218.2	1021	Tac/Cac	21/21	1	2	FACETS	0.853	0.776	0.934	0.853	0.776	0.934	CLONAL	1	TRUE	1	0.578963863016652	2		707	502	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	192	951	1	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	0.965	0.896	1	0.965	0.896	1	CLONAL	1	TRUE	1	0.578963863016652	2		952	687	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962804	2962804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772900135	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	495	884	2	ENST00000396946.4:c.2104G>A	p.Glu702Lys	p.E702K	ENST00000396946	NM_032415.4	702	Gag/Aag	16/25	0.578963863016652	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.578963863016652	3		886	984	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70441157	70441157	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	rs764225020	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	181	672	1	ENST00000373644.4:c.4832del	p.Asn1611ThrfsTer13	p.N1611Tfs*13	ENST00000373644	NM_030625.2	1609	gAa/ga	9/12	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.578963863016652	2		673	595	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339111	65339111	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	115	715	6	ENST00000342505.4:c.425del	p.Lys142ArgfsTer26	p.K142Rfs*26	ENST00000342505	NM_002227.2	142	aAg/ag	5/25	1	2	FACETS	0.648	0.585	0.714	0.648	0.585	0.714	SUBCLONAL	1	TRUE	1	0.578963863016652	2		721	613	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	150	423	1	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.578963863016652	2		424	412	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	127	792	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.847	0.771	0.926	0.847	0.771	0.926	CLONAL	1	TRUE	1	0.578963863016652	2		792	518	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	71	330	2	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	1	2	FACETS	0.929	0.82	1	0.929	0.82	1	CLONAL	1	TRUE	1	0.578963863016652	2		332	264	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438316	110438317	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	rs532810290	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	38	231	0	ENST00000375856.3:c.82_84dup	p.Asn28dup	p.N28dup	ENST00000375856	NM_003749.2	28	-/AAC	1/2	1	2	FACETS	0.534	0.444	0.632	0.534	0.444	0.632	SUBCLONAL	1	TRUE	1	0.578963863016652	2		231	246	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	236	846	1	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	1	2	FACETS	0.932	0.871	0.994	0.932	0.871	0.994	CLONAL	1	TRUE	1	0.578963863016652	2		847	875	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	211	683	0	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.578963863016652	2		683	670	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	308	1089	7	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.578963863016652	2		1096	1056	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	151	537	3	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.578963863016652	2		540	474	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	177	612	6	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	NA	2	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.578963863016652	2		618	567	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008521	70008521	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876657699	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	199	839	1	ENST00000394351.3:c.808C>T	p.Arg270Ter	p.R270*	ENST00000394351	NM_000248.3	270	Cga/Tga	8/9	1	2	FACETS	0.786	0.729	0.845	0.786	0.729	0.845	SUBCLONAL	1	TRUE	1	0.578963863016652	2		840	875	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437230	220437230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs960266462	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	380	1295	1	ENST00000243786.2:c.134C>T	p.Ala45Val	p.A45V	ENST00000243786	NM_002191.3	45	gCg/gTg	1/2	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.578963863016652	2		1296	1153	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862850	9862850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751455326	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	216	929	0	ENST00000330684.3:c.2453C>T	p.Ala818Val	p.A818V	ENST00000330684	NM_001134407.1	818	gCg/gTg	12/13	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.578963863016652	2		929	743	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372193	55372193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753081636	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	97	264	0	ENST00000297316.4:c.883G>A	p.Val295Met	p.V295M	ENST00000297316	NM_022454.3	295	Gtg/Atg	2/2	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.578963863016652	2		264	294	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264357	30264357	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	38	191	0	ENST00000322652.5:c.92T>C	p.Val31Ala	p.V31A	ENST00000322652	NM_015355.2	31	gTg/gCg	1/16	1	2	FACETS	0.721	0.603	0.849	0.721	0.603	0.849	SUBCLONAL	1	TRUE	1	0.578963863016652	2		191	182	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026911	48026912	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587780670	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	133	534	0	ENST00000234420.5:c.1794dup	p.Gly599ArgfsTer8	p.G599Rfs*8	ENST00000234420	NM_000179.2	597	gaa/gAaa	4/10	1	2	FACETS	0.959	0.877	1	0.959	0.877	1	CLONAL	1	TRUE	1	0.578963863016652	2		534	479	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424178	49424178	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs886040960	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	154	625	2	ENST00000301067.7:c.13884del	p.Thr4629ProfsTer11	p.T4629Pfs*11	ENST00000301067	NM_003482.3	4628	ccC/cc	42/54	1	2	FACETS	0.89	0.818	0.964	0.89	0.818	0.964	CLONAL	1	TRUE	1	0.578963863016652	2		627	598	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518587	69518587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs114327249	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	220	479	2	ENST00000294312.3:c.58G>A	p.Val20Met	p.V20M	ENST00000294312	NM_005117.2	20	Gtg/Atg	1/3	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.578963863016652	2		481	538	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780702	9780702	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	46	673	0	ENST00000377346.4:c.1504C>T	p.His502Tyr	p.H502Y	ENST00000377346	NM_005026.3	502	Cat/Tat	12/24	1	2	FACETS	0.26	0.218	0.306	0.26	0.218	0.306	SUBCLONAL	1	TRUE	1	0.578963863016652	2		673	611	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567718	226567719	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	390	704	0	ENST00000366794.5:c.1447dup	p.Ala483GlyfsTer9	p.A483Gfs*9	ENST00000366794	NM_001618.3	483	gca/gGca	10/23	0.578963863016652	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.578963863016652	3		704	861	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623652	43623652	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1171787901	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	125	930	0	ENST00000355710.3:c.3280A>G	p.Ser1094Gly	p.S1094G	ENST00000355710	NM_020975.4	1094	Agt/Ggt	20/20	1	2	FACETS	0.57	0.516	0.627	0.57	0.516	0.627	SUBCLONAL	1	TRUE	1	0.578963863016652	2		930	757	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572272	64572272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372468697	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	147	614	3	ENST00000312049.6:c.1367G>A	p.Arg456His	p.R456H	ENST00000312049	NM_130799.2	456	cGc/cAc	10/10	1	2	FACETS	0.923	0.847	1	0.923	0.847	1	CLONAL	1	TRUE	1	0.578963863016652	2		617	550	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200086	67200086	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	180	628	0	ENST00000312629.5:c.473del	p.Thr158SerfsTer53	p.T158Sfs*53	ENST00000312629	NM_003952.2	158	aCg/ag	6/15	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.578963863016652	2		628	599	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200877	67200877	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	291	1157	3	ENST00000312629.5:c.870del	p.Tyr291ThrfsTer14	p.Y291Tfs*14	ENST00000312629	NM_003952.2	289	Ccc/cc	10/15	1	2	FACETS	0.993	0.936	1	0.993	0.936	1	CLONAL	1	TRUE	1	0.578963863016652	2		1160	1012	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514694	103514694	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs4150315	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	148	488	2	ENST00000355739.4:c.1195G>A	p.Glu399Lys	p.E399K	ENST00000355739	NM_000123.3	399	Gaa/Aaa	8/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.578963863016652	2		490	451	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003374	42003374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372252914	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	181	690	5	ENST00000219905.7:c.2911C>T	p.Arg971Trp	p.R971W	ENST00000219905	NM_001164273.1	971	Cgg/Tgg	8/24	0.578963863016652	2	FACETS	0.977	0.905	1	0.488	0.452	0.526	CLONAL	1	TRUE	0	0.578963863016652	2		695	640	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50811838	50811838	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	130	861	0	ENST00000398568.2:c.1115G>A	p.Trp372Ter	p.W372*	ENST00000398568	NM_001042412.1	372	tGg/tAg	7/18	1	2	FACETS	0.724	0.659	0.793	0.724	0.659	0.793	SUBCLONAL	1	TRUE	1	0.578963863016652	2		861	620	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619315	37619315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774190421	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	165	501	1	ENST00000447079.4:c.991C>T	p.Arg331Trp	p.R331W	ENST00000447079	NM_015083.1	331	Cgg/Tgg	1/14	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.578963863016652	2		502	458	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40855817	40855817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	213	848	0	ENST00000428826.2:c.2039G>A	p.Arg680Gln	p.R680Q	ENST00000428826		680	cGg/cAg	19/21	1	2	FACETS	0.913	0.85	0.977	0.913	0.85	0.977	CLONAL	1	TRUE	1	0.578963863016652	2		848	806	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492739	56492739	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	226	1071	0	ENST00000407977.2:c.200G>A	p.Gly67Asp	p.G67D	ENST00000407977		67	gGt/gAt	2/10	1	2	FACETS	0.972	0.908	1	0.972	0.908	1	CLONAL	1	TRUE	1	0.578963863016652	2		1071	803	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740377	58740377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	157	795	0	ENST00000305921.3:c.1282C>T	p.Pro428Ser	p.P428S	ENST00000305921	NM_003620.3	428	Cca/Tca	6/6	1	2	FACETS	0.948	0.873	1	0.948	0.873	1	CLONAL	1	TRUE	1	0.578963863016652	2		795	572	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593548	48593549	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	64	262	0	ENST00000342988.3:c.1304_1305del	p.Ile435LysfsTer4	p.I435Kfs*4	ENST00000342988	NM_005359.5	433	gcATat/gcat	10/12	1	2	FACETS	0.895	0.784	1	0.895	0.784	1	CLONAL	1	TRUE	1	0.578963863016652	2		262	247	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622111	1622111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573267242	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	252	872	2	ENST00000344749.5:c.764C>T	p.Pro255Leu	p.P255L	ENST00000344749	NM_001136139.2	255	cCg/cTg	10/19	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.578963863016652	2		874	734	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4123856	4123856	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	82	288	0	ENST00000262948.5:c.17A>C	p.Lys6Thr	p.K6T	ENST00000262948	NM_030662.3	6	aAg/aCg	1/11	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.578963863016652	2		288	273	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610072	10610073	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	233	921	0	ENST00000171111.5:c.637dup	p.Glu213GlyfsTer137	p.E213Gfs*137	ENST00000171111	NM_203500.1	213	gag/gGag	2/6	1	2	FACETS	0.835	0.779	0.892	0.835	0.779	0.892	CLONAL	1	TRUE	1	0.578963863016652	2		921	964	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223328	36223328	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	371	1393	5	ENST00000222270.7:c.5882del	p.Pro1961LeufsTer26	p.P1961Lfs*26	ENST00000222270	NM_014727.1	1960	Ccc/cc	28/37	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.578963863016652	2		1398	1272	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416374	29416374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	273	1008	2	ENST00000389048.3:c.4579C>T	p.Pro1527Ser	p.P1527S	ENST00000389048	NM_004304.4	1527	Cca/Tca	29/29	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.578963863016652	2		1010	877	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262541	39262541	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	76	780	0	ENST00000402219.2:c.965T>C	p.Leu322Pro	p.L322P	ENST00000402219	NM_005633.3	322	cTt/cCt	7/23	1	2	FACETS	0.478	0.42	0.541	0.478	0.42	0.541	SUBCLONAL	1	TRUE	1	0.578963863016652	2		780	549	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39721180	39721180	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	198	816	0	ENST00000361337.2:c.686del	p.Pro229HisfsTer19	p.P229Hfs*19	ENST00000361337	NM_003286.2	228	gCc/gc	9/21	0.578963863016652	3	FACETS	0.993	0.921	1	0.497	0.46	0.534	CLONAL	1	TRUE	1	0.578963863016652	3		816	888	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026114	71026114	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	175	600	0	ENST00000318789.4:c.1508G>T	p.Arg503Leu	p.R503L	ENST00000318789	NM_032682.5	503	cGa/cTa	17/21	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.578963863016652	2		600	581	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444543	187444543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs77733730	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	182	675	2	ENST00000232014.4:c.1684G>A	p.Ala562Thr	p.A562T	ENST00000232014	NM_001130845.1	562	Gcc/Acc	7/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.578963863016652	2		677	601	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803419	1803419	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	263	807	0	ENST00000260795.2:c.688G>A	p.Val230Met	p.V230M	ENST00000260795		230	Gtg/Atg	5/17	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.578963863016652	2		807	888	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201760	66201760	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	41	869	0	ENST00000273854.3:c.2742C>A	p.Cys914Ter	p.C914*	ENST00000273854	NM_004439.5	914	tgC/tgA	16/18	1	2	FACETS	0.203	0.168	0.242	0.203	0.168	0.242	SUBCLONAL	1	TRUE	1	0.578963863016652	2		869	697	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557846	187557848	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs764081811	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	149	621	0	ENST00000441802.2:c.3863_3865del	p.Ser1288del	p.S1288del	ENST00000441802	NM_005245.3	1288	tCCTac/tac	5/27	1	2	FACETS	0.916	0.841	0.993	0.916	0.841	0.993	CLONAL	1	TRUE	1	0.578963863016652	2		621	562	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294672	1294672	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	66	246	4	ENST00000310581.5:c.329G>C	p.Gly110Ala	p.G110A	ENST00000310581	NM_198253.2	110	gGc/gCc	2/16	1	2	FACETS	0.87	0.764	0.983	0.87	0.764	0.983	CLONAL	1	TRUE	1	0.578963863016652	2		250	262	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79974797	79974797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1355464585	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	106	837	1	ENST00000265081.6:c.1225G>A	p.Ala409Thr	p.A409T	ENST00000265081	NM_002439.4	409	Gct/Act	8/24	1	2	FACETS	0.465	0.417	0.517	0.465	0.417	0.517	SUBCLONAL	1	TRUE	1	0.578963863016652	2		838	787	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564506	86564506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1352395584	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	124	419	0	ENST00000274376.6:c.238G>A	p.Ala80Thr	p.A80T	ENST00000274376	NM_002890.2	80	Gca/Aca	1/25	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.578963863016652	2		419	368	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911503	131911503	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751320530	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	110	677	0	ENST00000265335.6:c.248G>A	p.Arg83His	p.R83H	ENST00000265335		83	cGt/cAt	3/25	1	2	FACETS	0.918	0.831	1	0.918	0.831	1	CLONAL	1	TRUE	1	0.578963863016652	2		677	414	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522424	176522424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	246	943	2	ENST00000292408.4:c.1613G>T	p.Gly538Val	p.G538V	ENST00000292408	NM_213647.1	538	gGt/gTt	12/18	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.578963863016652	2		945	815	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759377	133759377	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs982716836	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	226	950	0	ENST00000318560.5:c.1700C>T	p.Ala567Val	p.A567V	ENST00000318560	NM_005157.4	567	gCc/gTc	11/11	1	2	FACETS	0.905	0.844	0.967	0.905	0.844	0.967	CLONAL	1	TRUE	1	0.578963863016652	2		950	863	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400074	139400074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	296	1147	0	ENST00000277541.6:c.4274G>A	p.Cys1425Tyr	p.C1425Y	ENST00000277541	NM_017617.3	1425	tGc/tAc	25/34	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.578963863016652	2		1147	987	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405141	139405141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1448345366	NA	P-0017995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	239	851	2	ENST00000277541.6:c.2704C>T	p.Arg902Cys	p.R902C	ENST00000277541	NM_017617.3	902	Cgc/Tgc	17/34	1	2	FACETS	0.965	0.902	1	0.965	0.902	1	CLONAL	1	TRUE	1	0.578963863016652	2		853	856	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050657	30050657	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0017997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	70	700	0	ENST00000338641.4:c.459C>G	p.Tyr153Ter	p.Y153*	ENST00000338641	NM_000268.3	153	taC/taG	5/16	0.403617857595984	1	FACETS	0.702	0.616	0.794	0.702	0.616	0.794	SUBCLONAL	1	TRUE	0	0.441310056672775	1		700	352	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578412	7578412	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519747	NA	P-0017998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	359	711	0	ENST00000269305.4:c.518T>G	p.Val173Gly	p.V173G	ENST00000269305	NM_001126112.2	173	gTg/gGg	5/11	0.368114409944615	3	FACETS	0.966	0.922	1	0.966	0.922	1	CLONAL	3	TRUE	0	0.376911533769891	3		711	781	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428511	78428511	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	39	756	0	ENST00000370768.2:c.1288C>A	p.Arg430Ser	p.R430S	ENST00000370768	NM_003902.3	430	Cgt/Agt	14/20	0.274130303897466	4	FACETS	0.382	0.315	0.457	0.191	0.157	0.229	SUBCLONAL	1	TRUE	2	0.376911533769891	4		756	746	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372091	45372091	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	40	1010	0	ENST00000262160.6:c.1078C>T	p.Pro360Ser	p.P360S	ENST00000262160	NM_005901.5	360	Ccc/Tcc	9/11	0.376160028248614	3	FACETS	0.327	0.271	0.39	0.109	0.09	0.13	SUBCLONAL	1	TRUE	0	0.376911533769891	3		1010	771	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0017999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	600	548	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.865200946383515	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.889084387294968	1		548	730	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664534	29664535	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0017999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	532	753	0	ENST00000356175.3:c.6522_6523dup	p.Thr2175ArgfsTer5	p.T2175Rfs*5	ENST00000356175	NM_000267.3	2171	-/GA	42/57	0.865200946383515	1	FACETS	0.859	0.834	0.884	0.859	0.834	0.884	CLONAL	1	TRUE	0	0.889084387294968	1		753	774	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881440	111881440	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	238	634	0	ENST00000393256.3:c.118C>A	p.Pro40Thr	p.P40T	ENST00000393256	NM_006538.4	40	Cca/Aca	2/4	0.460543930633508	3	FACETS	0.588	0.547	0.629	0.294	0.273	0.315	INDETERMINATE	1	TRUE	1	0.889084387294968	3		634	1316	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796214	45796214	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	282	774	0	ENST00000450313.1:c.1492C>G	p.Gln498Glu	p.Q498E	ENST00000450313	NM_012222.2	498	Cag/Gag	15/16	0.445080833024791	1	FACETS	0.349	0.328	0.371	0.349	0.328	0.371	INDETERMINATE	1	TRUE	0	0.889084387294968	1		774	1009	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974273	18974274	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0017999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	301	764	0	ENST00000262803.5:c.2628dup	p.Lys877GlufsTer17	p.K877Efs*17	ENST00000262803	NM_002911.3	876	ccg/ccGg	19/24	0.889084387294968	2	FACETS	0.483	0.454	0.513	0.242	0.227	0.257	SUBCLONAL	1	TRUE	0	0.889084387294968	2		764	1401	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599333	55599333	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913682	NA	P-0018001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	406	690	0	ENST00000288135.5:c.2459A>G	p.Asp820Gly	p.D820G	ENST00000288135	NM_000222.2	820	gAt/gGt	17/21	0.837675306244096	5	FACETS	1	0.955	1	0.667	0.636	0.699	CLONAL	2	TRUE	2	0.84726649586895	5		690	1087	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016169	31016169	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	503	856	2	ENST00000375687.4:c.415del	p.Glu139AsnfsTer29	p.E139Nfs*29	ENST00000375687	NM_015338.5	139	Gaa/aa	6/13	0.801374184659794	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.84726649586895	4		858	1029	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593607	55593610	+	protein_altering_variant	In_Frame_Del	DEL	AGGT	AGGT	G	novel	NA	P-0018001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	476	665	0	ENST00000288135.5:c.1673_1676delinsG	p.Lys558_Val559delinsSer	p.K558_V559delinsS	ENST00000288135	NM_000222.2	558	aAGGTt/aGt	11/21	0.837675306244096	5	FACETS	0.847	0.814	0.881	0.847	0.814	0.881	CLONAL	3	TRUE	2	0.84726649586895	5		665	1004	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	94	184	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.484860878236909	2		184	369	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0018002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	175	741	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.928	0.856	1	0.928	0.856	1	CLONAL	1	TRUE	1	0.484860878236909	2		741	778	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0018003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	315	294	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.407829735390719	4	FACETS	0.914	0.869	0.961	0.914	0.869	0.961	CLONAL	3	TRUE	1	0.464514051233847	4		294	724	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0018003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	339	801	17	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.388829539489813	2	FACETS	0.865	0.822	0.908	0.865	0.822	0.908	CLONAL	2	TRUE	0	0.464514051233847	2		818	844	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0018003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	150	181	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.464514051233847	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.464514051233847	2		181	278	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740665	58740665	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	337	1102	0	ENST00000305921.3:c.1570C>T	p.Gln524Ter	p.Q524*	ENST00000305921	NM_003620.3	524	Caa/Taa	6/6	0.427968217682012	2	FACETS	0.899	0.855	0.944	0.899	0.855	0.944	CLONAL	2	TRUE	0	0.464514051233847	2		1102	807	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106393	27106393	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	192	822	0	ENST00000324856.7:c.6004del	p.Ser2002ProfsTer13	p.S2002Pfs*13	ENST00000324856	NM_006015.4	2002	Tcc/cc	20/20	0.137531006920892	6	FACETS	1	0.974	1	0.738	0.685	0.793	INDETERMINATE	2	TRUE	3	0.464514051233847	6		822	720	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106988	27106992	+	frameshift_variant	Frame_Shift_Del	DEL	AGGAC	AGGAC	-	novel	NA	P-0018003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	147	680	0	ENST00000324856.7:c.6601_6605del	p.Asp2201ProfsTer22	p.D2201Pfs*22	ENST00000324856	NM_006015.4	2200	gAGGAC/g	20/20	0.137531006920892	6	FACETS	1	0.971	1	0.749	0.688	0.813	INDETERMINATE	2	TRUE	3	0.464514051233847	6		680	543	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129172	2129172	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs45517281	NA	P-0018003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	412	1176	0	ENST00000219476.3:c.3106T>C	p.Ser1036Pro	p.S1036P	ENST00000219476	NM_000548.3	1036	Tcc/Ccc	27/42	0.464514051233847	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.464514051233847	2		1176	802	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5534760	5534760	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1320163307	NA	P-0121590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	141	584	1	ENST00000397747.3:c.71C>T	p.Thr24Ile	p.T24I	ENST00000397747	NM_025239.3	24	aCa/aTa	3/7	1	2	FACETS	0.882	0.811	0.954	0.882	0.811	0.954	CLONAL	1	NA	1	0.772597825607722	2		585	414	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	28	281	2	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.79	0.64	0.955	0.79	0.64	0.955	CLONAL	1	TRUE	1	0.51	2		283	139	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	42	455	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.51	2		455	156	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654642	67654642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	42	805	1	ENST00000264010.4:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000264010	NM_006565.3	377	Cgt/Tgt	6/12	1	2	FACETS	0.92	0.779	1	0.92	0.779	1	CLONAL	1	TRUE	1	0.51	2		806	179	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	65	918	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.10352987285212	3	FACETS	1	0.973	1	0.72	0.634	0.811	INDETERMINATE	1	TRUE	1	0.51	3		918	222	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259893	16259893	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	67	825	0	ENST00000375759.3:c.7158G>C	p.Gln2386His	p.Q2386H	ENST00000375759	NM_015001.2	2386	caG/caC	11/15	1	2	FACETS	0.962	0.845	1	0.962	0.845	1	CLONAL	1	TRUE	1	0.51	2		825	273	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097751	27097751	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	55	485	1	ENST00000324856.7:c.3344del	p.Pro1115GlnfsTer46	p.P1115Qfs*46	ENST00000324856	NM_006015.4	1114	Ccc/cc	12/20	1	2	FACETS	0.989	0.857	1	0.989	0.857	1	CLONAL	1	TRUE	1	0.51	2		486	218	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101198	27101198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1553153231	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	78	743	0	ENST00000324856.7:c.4480C>T	p.Gln1494Ter	p.Q1494*	ENST00000324856	NM_006015.4	1494	Caa/Taa	18/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.51	2		743	275	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266569	115266569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	32	852	3	ENST00000438362.2:c.1946G>A	p.Arg649His	p.R649H	ENST00000438362	NM_001242891.1	649	cGc/cAc	16/20	1	2	FACETS	0.678	0.556	0.813	0.678	0.556	0.813	SUBCLONAL	1	TRUE	1	0.51	2		855	185	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275302	115275302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	62	881	0	ENST00000438362.2:c.1111C>T	p.Arg371Cys	p.R371C	ENST00000438362	NM_001242891.1	371	Cgt/Tgt	10/20	1	2	FACETS	0.992	0.867	1	0.992	0.867	1	CLONAL	1	TRUE	1	0.51	2		881	245	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459206	120459206	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	56	658	2	ENST00000256646.2:c.6139del	p.Arg2047GlyfsTer21	p.R2047Gfs*21	ENST00000256646	NM_024408.3	2047	Cgg/gg	34/34	1	2	FACETS	0.807	0.698	0.925	0.807	0.698	0.925	CLONAL	1	TRUE	1	0.51	2		660	272	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724632	162724632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767283136	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	35	486	0	ENST00000367921.3:c.404G>A	p.Arg135His	p.R135H	ENST00000367921	NM_006182.2	135	cGt/cAt	5/18	1	2	FACETS	0.66	0.546	0.786	0.66	0.546	0.786	SUBCLONAL	1	TRUE	1	0.51	2		486	208	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624251	89624251	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	16	276	0	ENST00000371953.3:c.25G>C	p.Val9Leu	p.V9L	ENST00000371953	NM_000314.4	9	Gtt/Ctt	1/9	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.51	2		276	53	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	39	680	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	1	2	FACETS	0.894	0.752	1	0.894	0.752	1	CLONAL	1	TRUE	1	0.51	2		680	171	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741925	17741925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765066996	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	112	332	1	ENST00000250003.3:c.596C>T	p.Ala199Val	p.A199V	ENST00000250003	NM_002478.4	199	gCg/gTg	1/3	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.51	2		333	387	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996755	100996757	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	58	759	0	ENST00000325455.5:c.1770_1772del	p.Phe591del	p.F591del	ENST00000325455	NM_001202474.3	590	ttCTTt/ttt	2/8	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.51	2		759	195	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998838	100998838	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	86	927	0	ENST00000325455.5:c.964C>T	p.Gln322Ter	p.Q322*	ENST00000325455	NM_001202474.3	322	Cag/Tag	1/8	1	2	FACETS	0.701	0.622	0.785	0.701	0.622	0.785	SUBCLONAL	1	TRUE	1	0.51	2		927	481	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025569	1025569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	139	845	0	ENST00000358495.3:c.806G>A	p.Arg269Gln	p.R269Q	ENST00000358495	NM_134424.2	269	cGg/cAg	9/12	0.10352987285212	3	FACETS	1	0.978	1	0.605	0.553	0.659	INDETERMINATE	1	TRUE	1	0.51	3		845	565	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433883	49433883	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs189888707	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	78	1025	1	ENST00000301067.7:c.7670C>T	p.Pro2557Leu	p.P2557L	ENST00000301067	NM_003482.3	2557	cCg/cTg	31/54	0.10352987285212	3	FACETS	0.946	0.835	1	0.473	0.417	0.532	INDETERMINATE	1	TRUE	1	0.51	3		1026	406	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	61	867	1	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	0.10352987285212	3	FACETS	0.994	0.864	1	0.497	0.432	0.567	INDETERMINATE	1	TRUE	1	0.51	3		868	302	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112398	115112398	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	141	670	0	ENST00000257566.3:c.1342G>A	p.Gly448Ser	p.G448S	ENST00000257566	NM_016569.3	448	Ggc/Agc	7/8	0.10352987285212	3	FACETS	1	0.981	1	0.626	0.573	0.681	INDETERMINATE	1	TRUE	1	0.51	3		670	554	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21553861	21553861	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	94	836	2	ENST00000382592.4:c.2741del	p.Leu914TrpfsTer10	p.L914Wfs*10	ENST00000382592	NM_014572.2	914	tTg/tg	7/8	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.51	2		838	337	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972575	32972575	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80359251	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	38	815	0	ENST00000380152.3:c.9925G>A	p.Glu3309Lys	p.E3309K	ENST00000380152		3309	Gaa/Aaa	27/27	1	2	FACETS	0.842	0.705	0.991	0.842	0.705	0.991	CLONAL	1	TRUE	1	0.51	2		815	177	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506135	103506135	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375404851	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	30	668	1	ENST00000355739.4:c.293C>T	p.Ala98Val	p.A98V	ENST00000355739	NM_000123.3	98	gCg/gTg	3/15	1	2	FACETS	0.98	0.805	1	0.98	0.805	1	CLONAL	1	TRUE	1	0.51	2		669	120	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68934938	68934938	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1048458329	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	27	645	1	ENST00000487270.1:c.1007C>T	p.Thr336Ile	p.T336I	ENST00000487270	NM_133509.3	336	aCc/aTc	10/11	1	2	FACETS	0.821	0.663	0.994	0.821	0.663	0.994	CLONAL	1	TRUE	1	0.51	2		646	129	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863593	68863593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777078601	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	106	871	0	ENST00000261769.5:c.2332G>A	p.Ala778Thr	p.A778T	ENST00000261769	NM_004360.3	778	Gct/Act	15/16	1	2	FACETS	0.741	0.666	0.82	0.741	0.666	0.82	SUBCLONAL	1	TRUE	1	0.51	2		871	561	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138729528	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	60	691	0	ENST00000269305.4:c.523C>T	p.Arg175Cys	p.R175C	ENST00000269305	NM_001126112.2	175	Cgc/Tgc	5/11	1	2	FACETS	0.676	0.586	0.773	0.676	0.586	0.773	SUBCLONAL	1	TRUE	1	0.51	2		691	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579580	7579580	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781866	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	45	696	1	ENST00000269305.4:c.107C>T	p.Pro36Leu	p.P36L	ENST00000269305	NM_001126112.2	36	cCg/cTg	4/11	1	2	FACETS	0.836	0.711	0.972	0.836	0.711	0.972	CLONAL	1	TRUE	1	0.51	2		697	211	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042434	16042434	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1568277803	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	72	899	1	ENST00000268712.3:c.1240C>T	p.Arg414Ter	p.R414*	ENST00000268712	NM_006311.3	414	Cga/Tga	12/46	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.51	2		900	223	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637978	39637978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1406322792	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	46	868	3	ENST00000262039.4:c.2395C>T	p.Arg799Cys	p.R799C	ENST00000262039	NM_002647.2	799	Cgt/Tgt	22/25	0.10352987285212	0	FACETS	0.46	0.393	0.533			1	INDETERMINATE	1	TRUE	0	0.51	0		871	192	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622138	1622138	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	120	749	0	ENST00000344749.5:c.737del	p.Pro246ArgfsTer38	p.P246Rfs*38	ENST00000344749	NM_001136139.2	246	cCg/cg	10/19	1	2	FACETS	0.96	0.872	1	0.96	0.872	1	CLONAL	1	TRUE	1	0.51	2		749	490	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094903	11094903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145867502	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	75	743	1	ENST00000358026.2:c.76G>A	p.Ala26Thr	p.A26T	ENST00000358026	NM_001128849.1	26	Gcc/Acc	2/36	1	2	FACETS	0.774	0.682	0.872	0.774	0.682	0.872	SUBCLONAL	1	TRUE	1	0.51	2		744	380	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273240	18273240	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	54	736	4	ENST00000222254.8:c.1033C>T	p.Arg345Trp	p.R345W	ENST00000222254	NM_005027.3	345	Cgg/Tgg	9/16	1	2	FACETS	0.713	0.613	0.821	0.713	0.613	0.821	SUBCLONAL	1	TRUE	1	0.51	2		740	297	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753107	42753107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1453098687	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	109	653	0	ENST00000222329.4:c.1157G>A	p.Arg386His	p.R386H	ENST00000222329	NM_006494.2	386	cGc/cAc	4/4	1	2	FACETS	0.906	0.818	0.998	0.906	0.818	0.998	CLONAL	1	TRUE	1	0.51	2		653	472	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917081	50917081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs541483366	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	36	816	2	ENST00000440232.2:c.2333C>T	p.Ala778Val	p.A778V	ENST00000440232	NM_002691.3	778	gCc/gTc	19/27	1	2	FACETS	0.219	0.179	0.263	0.219	0.179	0.263	SUBCLONAL	1	TRUE	1	0.51	2		818	646	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025913	48025913	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	30	559	0	ENST00000234420.5:c.792del	p.Glu264AspfsTer15	p.E264Dfs*15	ENST00000234420	NM_000179.2	264	gAa/ga	4/10	1	2	FACETS	0.834	0.682	1	0.834	0.682	1	CLONAL	1	TRUE	1	0.51	2		559	141	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	43	712	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.77	0.651	0.899	0.77	0.651	0.899	SUBCLONAL	1	TRUE	1	0.51	2		714	219	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150022	202150022	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	61	677	0	ENST00000358485.4:c.1463T>C	p.Leu488Pro	p.L488P	ENST00000358485	NM_001080125.1	488	cTg/cCg	8/9	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.51	2		677	238	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661474	227661474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760049423	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	32	594	0	ENST00000305123.5:c.1981G>A	p.Gly661Ser	p.G661S	ENST00000305123	NM_005544.2	661	Ggc/Agc	1/2	1	2	FACETS	0.592	0.484	0.712	0.592	0.484	0.712	SUBCLONAL	1	TRUE	1	0.51	2		594	212	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913396	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	37	456	0	ENST00000349496.5:c.95A>G	p.Asp32Gly	p.D32G	ENST00000349496	NM_001904.3	32	gAc/gGc	3/15	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.51	2		456	143	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125398	47125398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377115716	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	13	553	0	ENST00000409792.3:c.5872G>A	p.Ala1958Thr	p.A1958T	ENST00000409792	NM_014159.6	1958	Gct/Act	12/21	1	2	FACETS	0.548	0.396	0.728	0.548	0.396	0.728	SUBCLONAL	1	TRUE	1	0.51	2		553	93	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921339	178921339	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	24	608	0	ENST00000263967.3:c.821G>C	p.Arg274Thr	p.R274T	ENST00000263967	NM_006218.2	274	aGa/aCa	5/21	1	2	FACETS	0.84	0.67	1	0.84	0.67	1	CLONAL	1	TRUE	1	0.51	2		608	112	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921373	178921373	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	37	792	0	ENST00000263967.3:c.855G>C	p.Leu285Phe	p.L285F	ENST00000263967	NM_006218.2	285	ttG/ttC	5/21	1	2	FACETS	0.78	0.65	0.921	0.78	0.65	0.921	CLONAL	1	TRUE	1	0.51	2		792	186	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446324	187446324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs541016998	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	75	529	1	ENST00000232014.4:c.1364C>T	p.Thr455Met	p.T455M	ENST00000232014	NM_001130845.1	455	aCg/aTg	6/10	1	2	FACETS	0.931	0.823	1	0.931	0.823	1	CLONAL	1	TRUE	1	0.51	2		530	316	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155180	55155180	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600187	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	52	630	0	ENST00000257290.5:c.2779G>A	p.Glu927Lys	p.E927K	ENST00000257290	NM_006206.4	927	Gag/Aag	21/23	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.51	2		630	154	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589619	67589620	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	55	634	0	ENST00000274335.5:c.1384_1385del	p.Glu462IlefsTer2	p.E462Ifs*2	ENST00000274335		461	cGA/c	10/15	1	2	FACETS	0.846	0.731	0.969	0.846	0.731	0.969	CLONAL	1	TRUE	1	0.51	2		634	255	SUCCESS
APC	324	MSKCC	GRCh37	5	112175166	112175166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371113837	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	18	341	0	ENST00000257430.4:c.3875C>T	p.Thr1292Met	p.T1292M	ENST00000257430	NM_000038.5	1292	aCg/aTg	16/16	1	2	FACETS	1	0.791	1	1	0.791	1	CLONAL	1	TRUE	1	0.51	2		341	69	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038349	180038349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373742042	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	79	577	2	ENST00000261937.6:c.3668G>A	p.Arg1223His	p.R1223H	ENST00000261937	NM_182925.4	1223	cGc/cAc	27/30	1	2	FACETS	0.743	0.657	0.835	0.743	0.657	0.835	SUBCLONAL	1	TRUE	1	0.51	2		579	417	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502244	157502244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370283707	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	71	713	1	ENST00000346085.5:c.3277G>A	p.Val1093Met	p.V1093M	ENST00000346085	NM_020732.3	1093	Gtg/Atg	12/20	0.166015869347414	3	FACETS	1	0.956	1	0.594	0.524	0.669	INDETERMINATE	1	TRUE	1	0.51	3		714	294	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738828	145738828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201883228	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	118	926	1	ENST00000428558.2:c.2237C>T	p.Ala746Val	p.A746V	ENST00000428558	NM_004260.3	746	gCg/gTg	14/22	1	2	FACETS	0.757	0.685	0.833	0.757	0.685	0.833	SUBCLONAL	1	TRUE	1	0.51	2		927	611	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650071	93650071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1486347243	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	40	751	1	ENST00000375746.1:c.1622C>T	p.Pro541Leu	p.P541L	ENST00000375746	NM_001174167.1	541	cCg/cTg	12/14	1	2	FACETS	0.777	0.652	0.912	0.777	0.652	0.912	CLONAL	1	TRUE	1	0.51	2		752	202	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221945	98221945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756465236	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	51	586	1	ENST00000331920.6:c.2824C>T	p.Arg942Trp	p.R942W	ENST00000331920	NM_000264.3	942	Cgg/Tgg	17/24	1	2	FACETS	0.606	0.518	0.702	0.606	0.518	0.702	SUBCLONAL	1	TRUE	1	0.51	2		587	330	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771740	135771740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	52	946	1	ENST00000298552.3:c.3377G>A	p.Gly1126Asp	p.G1126D	ENST00000298552	NM_001162426.1	1126	gGt/gAt	23/23	1	2	FACETS	0.819	0.704	0.943	0.819	0.704	0.943	CLONAL	1	TRUE	1	0.51	2		947	249	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650778	48650778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104894809	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	80	834	0	ENST00000376670.3:c.647G>A	p.Arg216Gln	p.R216Q	ENST00000376670	NM_002049.3	216	cGg/cAg	4/6	1	2	FACETS	0.811	0.718	0.909	0.811	0.718	0.909	CLONAL	1	TRUE	1	0.51	2		834	387	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225997	53225997	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	32	893	1	ENST00000375401.3:c.2852G>T	p.Arg951Leu	p.R951L	ENST00000375401	NM_004187.3	951	cGa/cTa	19/26	1	2	FACETS	0.237	0.191	0.288	0.237	0.191	0.288	SUBCLONAL	1	TRUE	1	0.51	2		894	530	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410102	63410102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761242587	NA	P-0018005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	51	722	1	ENST00000330258.3:c.3065G>A	p.Arg1022His	p.R1022H	ENST00000330258	NM_152424.3	1022	cGt/cAt	2/2	1	2	FACETS	0.772	0.662	0.891	0.772	0.662	0.891	SUBCLONAL	1	TRUE	1	0.51	2		723	259	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0018006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	19	326	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.385	0.292	0.494	0.385	0.292	0.494	SUBCLONAL	1	TRUE	1	0.378143691743976	2		326	261	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99482586	99482586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	55	366	0	ENST00000268035.6:c.3454G>A	p.Gly1152Arg	p.G1152R	ENST00000268035	NM_000875.3	1152	Gga/Aga	18/21	1	2	FACETS	0.385	0.329	0.447	0.385	0.329	0.447	SUBCLONAL	1	TRUE	1	0.378143691743976	2		366	755	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740556	58740557	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0018006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	51	518	0	ENST00000305921.3:c.1462dup	p.Asp488GlyfsTer5	p.D488Gfs*5	ENST00000305921	NM_003620.3	487	-/G	6/6	1	2	FACETS	0.313	0.265	0.366	0.313	0.265	0.366	SUBCLONAL	1	TRUE	1	0.378143691743976	2		518	862	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591217	67591262	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AATGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGGTTGACTCAAAA	AATGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGGTTGACTCAAAA	-	novel	NA	P-0018006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	50	320	0	ENST00000274335.5:c.1746-30_1761del		p.X582_splice	ENST00000274335		582		13/15	1	2	FACETS	0.443	0.375	0.517	0.443	0.375	0.517	SUBCLONAL	1	TRUE	1	0.378143691743976	2		320	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0018007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	26	984	1	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.132036294168591	5	FACETS	0.246	0.194	0.307	0.082	0.064	0.103	INDETERMINATE	1	FALSE	2	0.354107993258386	5		985	913	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0018007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	45	573	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.354107993258386	1	FACETS	0.996	0.847	1	0.996	0.847	1	CLONAL	1	FALSE	0	0.354107993258386	1		573	210	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0018008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	501	527	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.333400988029089	4	FACETS	0.977	0.939	1			1	CLONAL	3	TRUE	NA	0.45896929687545	4		527	1087	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578493	7578493	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1206165503	NA	P-0018008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	323	972	1	ENST00000269305.4:c.437G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tGg/tAg	5/11	0.383433435216756	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.45896929687545	1		973	1061	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205157	61205157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144867876	NA	P-0018008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	195	574	0	ENST00000301761.2:c.97C>T	p.Arg33Cys	p.R33C	ENST00000301761	NM_017841.2	33	Cgc/Tgc	2/4	1	2	FACETS	0.752	0.695	0.811	0.752	0.695	0.811	SUBCLONAL	1	TRUE	1	0.45896929687545	2		574	1130	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0018009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	74	366	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.801	0.701	0.909	0.801	0.701	0.909	CLONAL	1	TRUE	1	0.262507716642685	2		366	704	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0018009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	29	181	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.262507716642685	3	FACETS	0.735	0.591	0.899	0.368	0.295	0.45	SUBCLONAL	1	TRUE	1	0.262507716642685	3		181	340	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0018009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	97	477	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	0.905	0.806	1	0.905	0.806	1	CLONAL	1	TRUE	1	0.262507716642685	2		477	817	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0018009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	66	224	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.262507716642685	2		224	463	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412638	63412638	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369902795	NA	P-0018009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	80	393	0	ENST00000330258.3:c.529C>T	p.Arg177Cys	p.R177C	ENST00000330258	NM_152424.3	177	Cgc/Tgc	2/2	1	2	FACETS	0.857	0.754	0.968	0.857	0.754	0.968	CLONAL	1	TRUE	1	0.262507716642685	2		393	711	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690802	89690802	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1114167621	NA	P-0018009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	137	307	0	ENST00000371953.3:c.210-1G>A		p.X70_splice	ENST00000371953	NM_000314.4	70			0.262507716642685	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	1	0.262507716642685	3		307	545	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100387	27100387	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	72	335	2	ENST00000324856.7:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000324856	NM_006015.4	1367	Cag/Tag	17/20	1	2	FACETS	0.854	0.747	0.971	0.854	0.747	0.971	CLONAL	1	TRUE	1	0.262507716642685	2		337	642	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609084	43609086	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs377767399	NA	P-0018009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	81	450	1	ENST00000355710.3:c.1846_1848del	p.Glu616del	p.E616del	ENST00000355710	NM_020975.4	614	GAG/-	10/20	0.262507716642685	3	FACETS	0.878	0.773	0.991	0.439	0.386	0.496	CLONAL	1	TRUE	1	0.262507716642685	3		451	795	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653849	89653851	+	inframe_deletion	In_Frame_Del	DEL	TAT	TAT	-	novel	NA	P-0018009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	60	328	0	ENST00000371953.3:c.148_150del	p.Ile50del	p.I50del	ENST00000371953	NM_000314.4	49	aaTATt/aat	2/9	0.262507716642685	3	FACETS	0.842	0.725	0.97	0.421	0.362	0.485	CLONAL	1	TRUE	1	0.262507716642685	3		328	614	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118905	70118906	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0018009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	94	393	0	ENST00000245479.2:c.478dup	p.Arg160ProfsTer92	p.R160Pfs*92	ENST00000245479	NM_000346.3	159	-/C	2/3	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.262507716642685	2		393	703	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119928	70119929	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0018009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	69	305	0	ENST00000245479.2:c.932dup	p.Gln312ProfsTer266	p.Q312Pfs*266	ENST00000245479	NM_000346.3	310	-/G	3/3	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.262507716642685	2		305	503	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	73	184	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.316203212197105	2		184	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0018010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	135	438	2	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.316203212197105	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.316203212197105	1		440	676	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759686	133759686	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs61746126	NA	P-0018010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	91	417	0	ENST00000318560.5:c.2009A>G	p.Asn670Ser	p.N670S	ENST00000318560	NM_005157.4	670	aAt/aGt	11/11	1	2	FACETS	0.959	0.853	1	0.959	0.853	1	CLONAL	1	TRUE	1	0.316203212197105	2		417	600	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287238	38287238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140382957	NA	P-0018010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	186	577	3	ENST00000425967.3:c.419C>T	p.Ser140Leu	p.S140L	ENST00000425967	NM_001174067.1	140	tCg/tTg	4/19	0.316203212197105	4	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.316203212197105	4		580	1375	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827689	72827689	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	78	402	1	ENST00000268489.5:c.8892C>A	p.Cys2964Ter	p.C2964*	ENST00000268489	NM_006885.3	2964	tgC/tgA	9/10	1	2	FACETS	0.869	0.764	0.98	0.869	0.764	0.98	CLONAL	1	TRUE	1	0.316203212197105	2		403	568	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696464	47696464	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	116	383	0	ENST00000347630.2:c.359A>T	p.Gln120Leu	p.Q120L	ENST00000347630	NM_001007230.1	120	cAa/cTa	6/11	0.316203212197105	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.316203212197105	1		383	545	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89444989	89444989	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	119	454	0	ENST00000336596.2:c.1309C>G	p.Pro437Ala	p.P437A	ENST00000336596	NM_005233.5	437	Cca/Gca	6/17	1	2	FACETS	0.96	0.867	1	0.96	0.867	1	CLONAL	1	TRUE	1	0.316203212197105	2		454	784	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0018012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	34	294	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	0.746	0.608	0.901	0.746	0.608	0.901	CLONAL	1	TRUE	1	0.15	2		294	608	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	69	918	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.15	2		918	831	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578530	7578530	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1184	83	640	0	ENST00000269305.4:c.400T>G	p.Phe134Val	p.F134V	ENST00000269305	NM_001126112.2	134	Ttt/Gtt	5/11	1	2	FACETS	0.873	0.768	0.987	0.873	0.768	0.987	CLONAL	1	TRUE	1	0.15	2		640	1267	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0018014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	368	843	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.228612687517752	4	FACETS	0.859	0.813	0.906			1	CLONAL	3	TRUE	NA	0.228612687517752	4		843	1535	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934575	NA	P-0018014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	200	438	0	ENST00000269305.4:c.733G>C	p.Gly245Arg	p.G245R	ENST00000269305	NM_001126112.2	245	Ggc/Cgc	7/11	NA	2	FACETS	1	0.929	1			1	INDETERMINATE	2	TRUE	NA	0.228612687517752	2		438	874	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154363	2154363	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs530101369	NA	P-0018014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	186	573	0	ENST00000434045.2:c.565C>G	p.Leu189Val	p.L189V	ENST00000434045	NM_001127598.1	189	Ctc/Gtc	5/5	0.228612687517752	3	FACETS	0.881	0.813	0.952			1	CLONAL	2	TRUE	NA	0.228612687517752	3		573	1029	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995347	15995347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	126	321	0	ENST00000268712.3:c.2846C>T	p.Pro949Leu	p.P949L	ENST00000268712	NM_006311.3	949	cCa/cTa	22/46	0.228612687517752	4	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.228612687517752	4		321	943	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220448	1220448	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	224	617	0	ENST00000326873.7:c.541A>T	p.Asn181Tyr	p.N181Y	ENST00000326873	NM_000455.4	181	Aac/Tac	4/10	0.221977803461346	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.228612687517752	2		617	960	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597437	52597437	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	195	487	0	ENST00000394830.3:c.3873del	p.Phe1291LeufsTer4	p.F1291Lfs*4	ENST00000394830	NM_018313.4	1291	ttT/tt	25/30	0.228612687517752	2	FACETS	0.803	0.743	0.866	0.803	0.743	0.866	CLONAL	2	TRUE	0	0.228612687517752	2		487	1062	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36826863	36826863	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	174	619	0	ENST00000373129.3:c.71T>C	p.Ile24Thr	p.I24T	ENST00000373129	NM_032017.1	24	aTt/aCt	3/12	0.224913389481892	2	FACETS	0.541	0.498	0.586	0.271	0.249	0.293	INDETERMINATE	1	TRUE	0	0.659541167408622	2		619	975	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631907	90631907	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	416	511	0	ENST00000330062.3:c.446G>C	p.Arg149Pro	p.R149P	ENST00000330062	NM_002168.2	149	cGg/cCg	4/11	0.659541167408622	3	FACETS	1	0.988	1	0.558	0.531	0.587	CLONAL	1	TRUE	1	0.659541167408622	3		511	1502	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873945	151873945	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1426616542	NA	P-0018016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	474	302	0	ENST00000262189.6:c.8593G>A	p.Gly2865Arg	p.G2865R	ENST00000262189	NM_170606.2	2865	Gga/Aga	38/59	0.57191134338554	2	FACETS	0.948	0.916	0.98	0.948	0.916	0.98	CLONAL	2	TRUE	0	0.659541167408622	2		302	758	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631907	90631907	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	113	511	0	ENST00000330062.3:c.446G>C	p.Arg149Pro	p.R149P	ENST00000330062	NM_002168.2	149	cGg/cCg	4/11	0.192596334858495	3	FACETS	0.599	0.538	0.664	0.2	0.179	0.222	INDETERMINATE	1	TRUE	0	0.414394279578452	3		511	1099	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873945	151873945	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1426616542	NA	P-0018016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	184	302	0	ENST00000262189.6:c.8593G>A	p.Gly2865Arg	p.G2865R	ENST00000262189	NM_170606.2	2865	Gga/Aga	38/59	NA	2	FACETS	0.782	0.726	0.839			1	INDETERMINATE	2	TRUE	NA	0.414394279578452	2		302	568	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123833	46123833	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	158	258	0	ENST00000334344.6:c.102del	p.Phe34LeufsTer24	p.F34Lfs*24	ENST00000334344	NM_152641.2	33	ccT/cc	2/21	0.502965574691857	3	FACETS	1	0.93	1	0.507	0.465	0.551	CLONAL	1	TRUE	1	0.502965574691857	3		258	775	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924790	49924790	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	235	543	0	ENST00000296474.3:c.4153G>C	p.Gly1385Arg	p.G1385R	ENST00000296474	NM_002447.2	1385	Ggg/Cgg	20/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.429757447574986	2		543	1089	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971023	21971023	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	107	296	0	ENST00000304494.5:c.335G>C	p.Arg112Pro	p.R112P	ENST00000304494	NM_000077.4	112	cGt/cCt	2/3	0.274301080794484	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.274301080794484	1		296	566	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519920	NA	P-0018019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	87	265	0	ENST00000397062.3:c.85G>C	p.Asp29His	p.D29H	ENST00000397062	NM_006164.4	29	Gat/Cat	2/5	1	2	FACETS	0.95	0.841	1	0.95	0.841	1	CLONAL	1	TRUE	1	0.274301080794484	2		265	668	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	187	561	0	ENST00000269305.4:c.377A>C	p.Tyr126Ser	p.Y126S	ENST00000269305	NM_001126112.2	126	tAc/tCc	5/11	0.274301080794484	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.274301080794484	1		561	1139	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321308	65321308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	148	469	0	ENST00000342505.4:c.1532G>A	p.Gly511Asp	p.G511D	ENST00000342505	NM_002227.2	511	gGt/gAt	11/25	0.274301080794484	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.274301080794484	1		469	833	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400776	72400776	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	68	231	0	ENST00000357731.5:c.395A>T	p.His132Leu	p.H132L	ENST00000357731	NM_173808.2	132	cAt/cTt	2/7	0.274301080794484	1	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	0	0.274301080794484	1		231	427	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724601	162724601	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	128	377	0	ENST00000367921.3:c.373G>C	p.Asp125His	p.D125H	ENST00000367921	NM_006182.2	125	Gat/Cat	5/18	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.274301080794484	2		377	785	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953643	32953643	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0018019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	60	391	1	ENST00000380152.3:c.8944A>T	p.Lys2982Ter	p.K2982*	ENST00000380152		2982	Aaa/Taa	22/27	1	2	FACETS	0.53	0.456	0.612	0.53	0.456	0.612	SUBCLONAL	1	TRUE	1	0.274301080794484	2		392	825	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346127	89346127	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs750990942	NA	P-0018019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	31	100	0	ENST00000301030.4:c.6823G>T	p.Ala2275Ser	p.A2275S	ENST00000301030	NM_001256183.1	2275	Gcc/Tcc	9/13	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.274301080794484	2		100	185	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654623	29654623	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	52	335	0	ENST00000356175.3:c.5312G>C	p.Cys1771Ser	p.C1771S	ENST00000356175	NM_000267.3	1771	tGc/tCc	37/57	1	2	FACETS	0.642	0.546	0.747	0.642	0.546	0.747	SUBCLONAL	1	TRUE	1	0.274301080794484	2		335	591	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609343	39609343	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	128	358	0	ENST00000262039.4:c.1645G>T	p.Val549Leu	p.V549L	ENST00000262039	NM_002647.2	549	Gta/Tta	15/25	0.231219768157805	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.274301080794484	1		358	748	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299941	15299941	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	140	416	0	ENST00000263388.2:c.1237G>T	p.Gly413Cys	p.G413C	ENST00000263388	NM_000435.2	413	Ggc/Tgc	8/33	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.274301080794484	2		416	886	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464457	25464457	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	124	389	0	ENST00000264709.3:c.2056del	p.Asp686ThrfsTer19	p.D686Tfs*19	ENST00000264709	NM_175629.2	686	Gac/ac	17/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.274301080794484	2		389	770	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790003	40790003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	100	349	1	ENST00000373198.4:c.2728G>A	p.Glu910Lys	p.E910K	ENST00000373198	NM_133170.3	910	Gag/Aag	18/32	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.274301080794484	2		350	671	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664968	138664968	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	86	323	2	ENST00000330315.3:c.597C>A	p.Phe199Leu	p.F199L	ENST00000330315	NM_023067.3	199	ttC/ttA	1/1	0.160346512340969	3	FACETS	1	0.919	1	0.524	0.464	0.589	INDETERMINATE	1	TRUE	1	0.274301080794484	3		325	680	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332874	152332874	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	77	336	0	ENST00000206249.3:c.1180C>G	p.Arg394Gly	p.R394G	ENST00000206249	NM_000125.3	394	Cgc/Ggc	5/8	0.274301080794484	1	FACETS	0.848	0.746	0.958	0.848	0.746	0.958	CLONAL	1	TRUE	0	0.274301080794484	1		336	571	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509542	106509542	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	45	461	0	ENST00000359195.3:c.1536C>G	p.Asn512Lys	p.N512K	ENST00000359195	NM_002649.2	512	aaC/aaG	2/11	0.274301080794484	1	FACETS	0.317	0.266	0.375	0.317	0.266	0.375	SUBCLONAL	1	TRUE	0	0.274301080794484	1		461	892	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151882675	151882675	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0018019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	122	325	0	ENST00000262189.6:c.5050A>T	p.Lys1684Ter	p.K1684*	ENST00000262189	NM_170606.2	1684	Aaa/Taa	34/59	0.274301080794484	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.274301080794484	1		325	625	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331692	8331692	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1192328434	NA	P-0018019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	123	366	0	ENST00000356435.5:c.5424G>T	p.Trp1808Cys	p.W1808C	ENST00000356435		1808	tgG/tgT	33/35	0.274301080794484	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.274301080794484	1		366	650	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	267	184	0				ENST00000310581	NM_198253.2	-/1132			0.665200621753753	3	FACETS	0.954	0.907	1	0.954	0.907	1	CLONAL	2	TRUE	1	0.799611224675071	3		184	490	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0018020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	251	523	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.481529431950146	4	FACETS	1	0.989	1	0.622	0.583	0.662	CLONAL	1	TRUE	2	0.799611224675071	4		523	908	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0018020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	2452	557	0	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.799611224675071	10	FACETS	1	0.997	1			1	CLONAL	7	TRUE	NA	0.799611224675071	10		557	3536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs967461896	NA	P-0018020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	276	427	1	ENST00000269305.4:c.526T>A	p.Cys176Ser	p.C176S	ENST00000269305	NM_001126112.2	176	Tgc/Agc	5/11	0.67148745153455	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.799611224675071	1		428	361	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66468010	66468010	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	139	279	0	ENST00000273854.3:c.259G>A	p.Gly87Ser	p.G87S	ENST00000273854	NM_004439.5	87	Ggt/Agt	3/18	0.286226065258459	3	FACETS	1	0.939	1	0.514	0.472	0.559	INDETERMINATE	1	TRUE	1	0.799611224675071	3		279	473	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66468016	66468016	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	133	270	0	ENST00000273854.3:c.253G>A	p.Glu85Lys	p.E85K	ENST00000273854	NM_004439.5	85	Gag/Aag	3/18	0.286226065258459	3	FACETS	1	0.957	1	0.535	0.49	0.582	INDETERMINATE	1	TRUE	1	0.799611224675071	3		270	435	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864340	162864340	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0018020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	197	398	0	ENST00000366898.1:c.171+2T>C		p.X57_splice	ENST00000366898	NM_004562.2	57			0.286226065258459	3	FACETS	1	0.989	1	0.656	0.612	0.7	INDETERMINATE	1	TRUE	1	0.799611224675071	3		398	526	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215240	123215241	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0018020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	288	155	0	ENST00000218089.9:c.2787_2788del	p.Glu929AspfsTer8	p.E929Dfs*8	ENST00000218089	NM_001042749.1	929	gAA/g	28/35	0.254964056357544	2	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.799611224675071	2		155	334	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602493	10602493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	146	310	0	ENST00000171111.5:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000171111	NM_203500.1	362	cGg/cAg	3/6	0.36684495932141	1	FACETS	0.923	0.844	1	0.923	0.844	1	CLONAL	1	TRUE	0	0.36684495932141	1		310	704	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207009	1207009	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	179	409	0	ENST00000326873.7:c.97G>T	p.Glu33Ter	p.E33*	ENST00000326873	NM_000455.4	33	Gag/Tag	1/10	0.36684495932141	1	FACETS	0.954	0.881	1	0.954	0.881	1	CLONAL	1	TRUE	0	0.36684495932141	1		409	835	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs878854073	NA	P-0018021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	252	343	0	ENST00000269305.4:c.673-1G>A		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.299023698858625	2	FACETS	0.829	0.777	0.881	0.829	0.777	0.881	CLONAL	2	TRUE	0	0.36684495932141	2		343	829	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260956	16260956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559925121	NA	P-0018021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	119	258	0	ENST00000375759.3:c.8221G>A	p.Val2741Ile	p.V2741I	ENST00000375759	NM_015001.2	2741	Gtc/Atc	11/15	1	2	FACETS	0.935	0.845	1	0.935	0.845	1	CLONAL	1	TRUE	1	0.36684495932141	2		258	694	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716051	243716051	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	87	443	0	ENST00000263826.5:c.1143G>C	p.Leu381Phe	p.L381F	ENST00000263826	NM_005465.4	381	ttG/ttC	10/13	1	2	FACETS	0.386	0.34	0.435	0.386	0.34	0.435	SUBCLONAL	1	TRUE	1	0.36684495932141	2		443	1229	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245076	46245076	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	388	422	0	ENST00000334344.6:c.3170C>A	p.Ser1057Ter	p.S1057*	ENST00000334344	NM_152641.2	1057	tCg/tAg	15/21	0.36684495932141	2	FACETS	0.932	0.887	0.978	0.932	0.887	0.978	CLONAL	2	TRUE	0	0.36684495932141	2		422	1135	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943751	9943751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	169	413	1	ENST00000330684.3:c.1190C>T	p.Ser397Phe	p.S397F	ENST00000330684	NM_001134407.1	397	tCc/tTc	5/13	1	2	FACETS	0.915	0.841	0.993	0.915	0.841	0.993	CLONAL	1	TRUE	1	0.36684495932141	2		414	1007	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014063	14014063	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	128	317	0	ENST00000311895.7:c.41C>A	p.Pro14Gln	p.P14Q	ENST00000311895	NM_005236.2	14	cCg/cAg	1/11	1	2	FACETS	0.838	0.759	0.921	0.838	0.759	0.921	CLONAL	1	TRUE	1	0.36684495932141	2		317	833	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119696	17119696	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0018021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	161	225	0	ENST00000285071.4:c.1298C>G	p.Ser433Ter	p.S433*	ENST00000285071	NM_144997.5	433	tCa/tGa	11/14	0.299023698858625	2	FACETS	0.816	0.753	0.881	0.816	0.753	0.881	CLONAL	2	TRUE	0	0.36684495932141	2		225	538	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656983	47656983	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	174	420	0	ENST00000233146.2:c.1179G>C	p.Lys393Asn	p.K393N	ENST00000233146	NM_000251.2	393	aaG/aaC	7/16	1	2	FACETS	0.85	0.781	0.922	0.85	0.781	0.922	CLONAL	1	TRUE	1	0.36684495932141	2		420	1116	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721094	61721094	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1198	105	508	0	ENST00000401558.2:c.1180C>G	p.Leu394Val	p.L394V	ENST00000401558	NM_003400.3	394	Ctt/Gtt	12/25	1	2	FACETS	0.439	0.392	0.49	0.439	0.392	0.49	SUBCLONAL	1	TRUE	1	0.36684495932141	2		508	1303	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017823	31017823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1300241784	NA	P-0018021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	114	470	1	ENST00000375687.4:c.685C>T	p.Pro229Ser	p.P229S	ENST00000375687	NM_015338.5	229	Ccg/Tcg	8/13	0.212895657160305	2	FACETS	0.552	0.496	0.612	0.276	0.248	0.306	INDETERMINATE	1	TRUE	0	0.36684495932141	2		471	1126	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687146	176687146	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	157	457	0	ENST00000439151.2:c.5123G>T	p.Ser1708Ile	p.S1708I	ENST00000439151	NM_022455.4	1708	aGc/aTc	14/23	0.194286376795299	1	FACETS	0.719	0.658	0.783	0.719	0.658	0.783	INDETERMINATE	1	TRUE	0	0.36684495932141	1		457	972	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048249	180048249	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	176	489	0	ENST00000261937.6:c.2024T>C	p.Leu675Pro	p.L675P	ENST00000261937	NM_182925.4	675	cTg/cCg	14/30	0.194286376795299	1	FACETS	0.7	0.643	0.758	0.7	0.643	0.758	INDETERMINATE	1	TRUE	0	0.36684495932141	1		489	1120	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331917	81331917	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	118	225	0	ENST00000222390.5:c.2167T>A	p.Tyr723Asn	p.Y723N	ENST00000222390	NM_000601.4	723	Tat/Aat	18/18	1	2	FACETS	0.978	0.884	1	0.978	0.884	1	CLONAL	1	TRUE	1	0.36684495932141	2		225	658	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508563	106508563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757016725	NA	P-0018021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	133	177	0	ENST00000359195.3:c.557C>T	p.Ala186Val	p.A186V	ENST00000359195	NM_002649.2	186	gCg/gTg	2/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.36684495932141	2		177	569	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939132	76939132	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	192	192	0	ENST00000373344.5:c.1616A>G	p.Gln539Arg	p.Q539R	ENST00000373344	NM_000489.3	539	cAg/cGg	9/35	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.36684495932141	1		192	641	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0018022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	536	668	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.50480825043748	4	FACETS	0.934	0.894	0.974			1	CLONAL	2	TRUE	NA	0.522361968449094	4		668	1673	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138384011	138384011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759151757	NA	P-0018022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	223	379	0	ENST00000289153.2:c.2539C>T	p.Arg847Cys	p.R847C	ENST00000289153	NM_006219.2	847	Cgc/Tgc	18/22	0.443366092619241	2	FACETS	0.876	0.816	0.938	0.438	0.408	0.469	CLONAL	1	TRUE	0	0.522361968449094	2		379	975	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104377179	104377179	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1239	127	554	0	ENST00000369902.3:c.1290G>C	p.Trp430Cys	p.W430C	ENST00000369902	NM_016169.3	430	tgG/tgC	10/12	0.436224115099402	2	FACETS	0.356	0.321	0.393	0.178	0.16	0.197	SUBCLONAL	1	TRUE	0	0.522361968449094	2		554	1366	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989202	41989202	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	248	393	0	ENST00000219905.7:c.1994T>G	p.Phe665Cys	p.F665C	ENST00000219905	NM_001164273.1	665	tTt/tGt	3/24	0.443366092619241	2	FACETS	0.857	0.801	0.915	0.428	0.4	0.458	CLONAL	1	TRUE	0	0.522361968449094	2		393	1108	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579894	7579894	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	89	417	0	ENST00000269305.4:c.19G>A	p.Asp7Asn	p.D7N	ENST00000269305	NM_001126112.2	7	Gat/Aat	2/11	0.522361968449094	1	FACETS	0.258	0.228	0.291	0.258	0.228	0.291	SUBCLONAL	1	TRUE	0	0.522361968449094	1		417	974	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688761	47688761	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1157	212	342	0	ENST00000347630.2:c.539A>C	p.Lys180Thr	p.K180T	ENST00000347630	NM_001007230.1	180	aAg/aCg	7/11	0.522361968449094	3	FACETS	0.748	0.693	0.805	0.374	0.346	0.403	SUBCLONAL	1	TRUE	1	0.522361968449094	3		342	1369	SUCCESS
APC	324	MSKCC	GRCh37	5	112175163	112175163	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	81	215	0	ENST00000257430.4:c.3872A>G	p.Gln1291Arg	p.Q1291R	ENST00000257430	NM_000038.5	1291	cAg/cGg	16/16	0.26428232561268	3	FACETS	0.602	0.53	0.678	0.201	0.176	0.226	INDETERMINATE	1	TRUE	0	0.522361968449094	3		215	650	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0018023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	92	455	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.470397628005649	4	FACETS	0.914	0.813	1	0.305	0.271	0.341	CLONAL	1	TRUE	1	0.470397628005649	4		455	629	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0018023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	237	419	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.470397628005649	2		419	967	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037969	49037969	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	rs587778868	NA	P-0018023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	85	397	0	ENST00000267163.4:c.2209G>T	p.Glu737Ter	p.E737*	ENST00000267163	NM_000321.2	737	Gag/Tag	21/27	1	2	FACETS	0.897	0.797	1	0.897	0.797	1	CLONAL	1	TRUE	1	0.470397628005649	2		397	403	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937134	76937134	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	83	433	0	ENST00000373344.5:c.3614C>A	p.Ser1205Tyr	p.S1205Y	ENST00000373344	NM_000489.3	1205	tCt/tAt	9/35	NA	2	FACETS	0.757	0.671	0.849			1	INDETERMINATE	1	TRUE	NA	0.470397628005649	2		433	466	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216125	7216125	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	100	164	0	ENST00000380728.2:c.934C>T	p.Arg312Trp	p.R312W	ENST00000380728		312	Cgg/Tgg	11/11	1	2	FACETS	0.932	0.837	1	0.932	0.837	1	CLONAL	1	TRUE	1	0.470397628005649	2		164	456	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133710877	133710877	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	102	428	0	ENST00000318560.5:c.44A>T	p.Lys15Met	p.K15M	ENST00000318560	NM_005157.4	15	aAg/aTg	1/11	1	2	FACETS	0.365	0.325	0.407	0.365	0.325	0.407	SUBCLONAL	1	TRUE	1	0.470397628005649	2		428	1189	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444726	49444726	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1411	461	691	1	ENST00000301067.7:c.2740G>T	p.Glu914Ter	p.E914*	ENST00000301067	NM_003482.3	914	Gag/Tag	10/54	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.470397628005649	2		692	1872	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967096	18967096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	245	482	0	ENST00000262803.5:c.1811G>A	p.Arg604Lys	p.R604K	ENST00000262803	NM_002911.3	604	aGa/aAa	13/24	1	2	FACETS	0.923	0.863	0.986	0.923	0.863	0.986	CLONAL	1	TRUE	1	0.470397628005649	2		482	1128	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712529	52712529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	332	461	0	ENST00000394830.3:c.223G>A	p.Ala75Thr	p.A75T	ENST00000394830	NM_018313.4	75	Gca/Aca	3/30	0.470397628005649	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.470397628005649	1		461	839	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839876	27839876	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1396834312	NA	P-0018023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	192	341	1	ENST00000328488.2:c.218G>A	p.Arg73Gln	p.R73Q	ENST00000328488	NM_003533.2	73	cGg/cAg	1/1	1	2	FACETS	0.864	0.799	0.931	0.864	0.799	0.931	CLONAL	1	TRUE	1	0.470397628005649	2		342	945	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0018024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	460	548	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.627663926541538	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.626348811441402	2		548	698	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910714	32910797	+	inframe_deletion	In_Frame_Del	DEL	TACAACATTCAAAAGTGGAATACAGTGATACTGACTTTCAATCCCAGAAAAGTCTTTTATATGATCATGAAAATGCCAGCACTC	TACAACATTCAAAAGTGGAATACAGTGATACTGACTTTCAATCCCAGAAAAGTCTTTTATATGATCATGAAAATGCCAGCACTC	-	novel	NA	P-0018024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	210	588	0	ENST00000380152.3:c.2223_2306del	p.Gln742_Leu769del	p.Q742_L769del	ENST00000380152		741	gTACAACATTCAAAAGTGGAATACAGTGATACTGACTTTCAATCCCAGAAAAGTCTTTTATATGATCATGAAAATGCCAGCACTCtt/gtt	11/27	0.627663926541538	2	FACETS	0.896	0.835	0.96	0.448	0.417	0.48	CLONAL	1	TRUE	0	0.626348811441402	2		588	748	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103510754	103510754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	196	526	0	ENST00000355739.4:c.658G>A	p.Glu220Lys	p.E220K	ENST00000355739	NM_000123.3	220	Gaa/Aaa	6/15	0.627663926541538	3	FACETS	0.84	0.778	0.905	0.28	0.259	0.302	CLONAL	1	TRUE	0	0.626348811441402	3		526	978	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42026786	42026786	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	435	423	0	ENST00000219905.7:c.3911del	p.Leu1304TyrfsTer32	p.L1304Yfs*32	ENST00000219905	NM_001164273.1	1304	Tta/ta	12/24	0.627663926541538	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.626348811441402	2		423	642	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727905	78727905	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	619	503	1	ENST00000306801.3:c.750G>T	p.Glu250Asp	p.E250D	ENST00000306801	NM_020761.2	250	gaG/gaT	6/34	0.627663926541538	3	FACETS	0.959	0.933	0.985	0.959	0.933	0.985	CLONAL	3	TRUE	0	0.626348811441402	3		504	902	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205172	128205172	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	149	386	0	ENST00000341105.2:c.269T>G	p.Leu90Trp	p.L90W	ENST00000341105	NM_032638.4	90	tTg/tGg	3/6	0.44958878418581	3	FACETS	0.9	0.824	0.979	0.45	0.412	0.49	CLONAL	1	TRUE	1	0.626348811441402	3		386	694	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032251	26032251	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	91	189	0	ENST00000244661.2:c.38G>T	p.Gly13Val	p.G13V	ENST00000244661	NM_003537.3	13	gGc/gTc	1/1	0.627663926541538	3	FACETS	1	0.979	1	0.689	0.62	0.76	CLONAL	1	TRUE	1	0.626348811441402	3		189	277	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878428	151878428	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1220479962	NA	P-0018024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	409	491	2	ENST00000262189.6:c.6517C>G	p.Pro2173Ala	p.P2173A	ENST00000262189	NM_170606.2	2173	Cca/Gca	36/59	0.564796065962687	4	FACETS	0.967	0.922	1			1	CLONAL	2	TRUE	NA	0.626348811441402	4		493	1098	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287306	38287306	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	272	515	0	ENST00000425967.3:c.351G>C	p.Glu117Asp	p.E117D	ENST00000425967	NM_001174067.1	117	gaG/gaC	4/19	0.627663926541538	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.626348811441402	1		515	568	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866488	117866488	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1574	130	349	0	ENST00000297338.2:c.1157T>G	p.Leu386Arg	p.L386R	ENST00000297338	NM_006265.2	386	cTg/cGg	9/14	0.626348811441402	8	FACETS	0.701	0.633	0.774			1	SUBCLONAL	1	TRUE	NA	0.626348811441402	8		349	1704	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776138	135776138	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	223	447	0	ENST00000298552.3:c.2589G>T	p.Leu863Phe	p.L863F	ENST00000298552	NM_001162426.1	863	ttG/ttT	20/23	0.627663926541538	2	FACETS	1	0.97	1	0.531	0.496	0.566	CLONAL	1	TRUE	0	0.626348811441402	2		447	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882019	NA	P-0018025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	29	663	3	ENST00000269305.4:c.455dup	p.Pro153AlafsTer28	p.P153Afs*28	ENST00000269305	NM_001126112.2	152	ccg/ccCg	5/11	0.766842066848032	1	FACETS	0.083	0.066	0.102	0.083	0.066	0.102	SUBCLONAL	1	TRUE	0	0.83651767474728	1		666	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577091	7577091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149633775	NA	P-0018025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	11	603	0	ENST00000269305.4:c.847C>T	p.Arg283Cys	p.R283C	ENST00000269305	NM_001126112.2	283	Cgc/Tgc	8/11	0.766842066848032	1	FACETS	0.033	0.022	0.046	0.033	0.022	0.046	SUBCLONAL	1	TRUE	0	0.83651767474728	1		603	469	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488717	212488717	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1269407579	NA	P-0018025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	8	573	0	ENST00000342788.4:c.2132G>A	p.Arg711His	p.R711H	ENST00000342788	NM_005235.2	711	cGt/cAt	18/28	1	2	FACETS	0.053	0.034	0.079	0.053	0.034	0.079	SUBCLONAL	1	TRUE	1	0.83651767474728	2		573	359	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465638	8465638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781067774	NA	P-0018027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	192	363	0	ENST00000356435.5:c.3542G>A	p.Arg1181His	p.R1181H	ENST00000356435		1181	cGt/cAt	21/35	1	2	FACETS	0.806	0.748	0.865	0.806	0.748	0.865	CLONAL	1	TRUE	1	0.702801990959364	2		363	678	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0018028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	180	306	0				ENST00000310581	NM_198253.2	-/1132			0.373618538539378	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.373758687984231	2		306	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0018028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	205	394	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	0.373758687984231	2	FACETS	0.907	0.846	0.968	0.907	0.846	0.968	CLONAL	2	TRUE	0	0.373758687984231	2		394	605	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199717	11199717	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0018028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	86	333	0	ENST00000361445.4:c.4873-2A>C		p.X1625_splice	ENST00000361445	NM_004958.3	1625			0.268887706891093	3	FACETS	0.93	0.824	1	0.465	0.412	0.522	CLONAL	1	TRUE	1	0.373758687984231	3		333	587	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981170	201981170	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	287	550	0	ENST00000359651.3:c.249del	p.Asn83LysfsTer72	p.N83Kfs*72	ENST00000359651		83	aaC/aa	2/8	0.219885253437068	4	FACETS	0.925	0.87	0.982	0.925	0.87	0.982	INDETERMINATE	2	TRUE	2	0.373758687984231	4		550	1140	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426520	49426520	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	245	521	0	ENST00000301067.7:c.11968C>T	p.Gln3990Ter	p.Q3990*	ENST00000301067	NM_003482.3	3990	Caa/Taa	39/54	0.219885253437068	4	FACETS	0.788	0.736	0.842	0.788	0.736	0.842	INDETERMINATE	2	TRUE	2	0.373758687984231	4		521	1143	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433834	49433837	+	frameshift_variant	Frame_Shift_Del	DEL	GCCC	GCCC	-	novel	NA	P-0018028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	252	590	0	ENST00000301067.7:c.7716_7719del	p.Gly2573SerfsTer9	p.G2573Sfs*9	ENST00000301067	NM_003482.3	2572	ttGGGC/tt	31/54	0.219885253437068	4	FACETS	0.837	0.783	0.893	0.837	0.783	0.893	INDETERMINATE	2	TRUE	2	0.373758687984231	4		590	1106	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2221310	2221310	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	250	503	0	ENST00000326181.6:c.394C>G	p.Gln132Glu	p.Q132E	ENST00000326181	NM_032271.2	132	Cag/Gag	6/21	0.219885253437068	4	FACETS	0.905	0.847	0.965	0.905	0.847	0.965	INDETERMINATE	2	TRUE	2	0.373758687984231	4		503	1015	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976487	18976487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	284	561	0	ENST00000262803.5:c.3137C>T	p.Ser1046Leu	p.S1046L	ENST00000262803	NM_002911.3	1046	tCa/tTa	22/24	0.268887706891093	3	FACETS	0.935	0.88	0.991	0.935	0.88	0.991	CLONAL	2	TRUE	1	0.373758687984231	3		561	965	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976499	18976499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	287	551	0	ENST00000262803.5:c.3149C>T	p.Ser1050Phe	p.S1050F	ENST00000262803	NM_002911.3	1050	tCt/tTt	22/24	0.268887706891093	3	FACETS	0.974	0.917	1	0.974	0.917	1	CLONAL	2	TRUE	1	0.373758687984231	3		551	936	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480460	89480460	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	85	228	0	ENST00000336596.2:c.2297G>A	p.Gly766Glu	p.G766E	ENST00000336596	NM_005233.5	766	gGa/gAa	13/17	0.339473276471386	4	FACETS	1	0.978	1	0.737	0.655	0.824	CLONAL	1	TRUE	2	0.373758687984231	4		228	424	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0018029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	197	395	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.153375895907986	3	FACETS	1	0.99	1	0.493	0.456	0.531	INDETERMINATE	1	TRUE	0	0.317529522265104	3		395	972	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925711	114925711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752060378	NA	P-0018029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	35	348	0	ENST00000543371.1:c.1789G>A	p.Val597Ile	p.V597I	ENST00000543371	NM_001198531.1	597	Gtc/Atc	14/14	1	2	FACETS	0.345	0.282	0.416	0.345	0.282	0.416	SUBCLONAL	1	TRUE	1	0.317529522265104	2		348	639	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205316	61205321	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CTTAGG	CTTAGG	-	novel	NA	P-0018029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	66	343	0	ENST00000301761.2:c.256_260+1del		p.X86_splice	ENST00000301761	NM_017841.2	86		2/4	1	2	FACETS	0.661	0.573	0.756	0.661	0.573	0.756	SUBCLONAL	1	TRUE	1	0.317529522265104	2		343	629	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0018030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	610	668	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.52560315829921	5	FACETS	0.962	0.927	0.998	0.962	0.927	0.998	CLONAL	3	TRUE	2	0.52560315829921	5		668	1438	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259442	55259442	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397517127	NA	P-0018030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	437	291	1	ENST00000275493.2:c.2500G>T	p.Val834Leu	p.V834L	ENST00000275493	NM_005228.3	834	Gtg/Ttg	21/28	0.52560315829921	5	FACETS	0.947	0.906	0.988	0.947	0.906	0.988	CLONAL	3	TRUE	2	0.52560315829921	5		292	1047	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176176022	176176023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	81	398	0	ENST00000367669.3:c.92dup	p.Leu31PhefsTer47	p.L31Ffs*47	ENST00000367669	NM_022457.5	31	tta/ttTa	1/20	0.272548510552434	2	FACETS	0.417	0.367	0.471	0.209	0.183	0.236	INDETERMINATE	1	TRUE	0	0.52560315829921	2		398	739	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121466	108121466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	47	207	0	ENST00000278616.4:c.1274C>T	p.Ala425Val	p.A425V	ENST00000278616	NM_000051.3	425	gCa/gTa	10/63	0.272548510552434	2	FACETS	0.379	0.32	0.444	0.189	0.16	0.222	INDETERMINATE	1	TRUE	0	0.52560315829921	2		207	472	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217443	7217450	+	frameshift_variant	Frame_Shift_Del	DEL	TGCTGGTA	TGCTGGTA	-	novel	NA	P-0018030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	117	320	0	ENST00000380728.2:c.346_353del	p.Tyr116GlufsTer30	p.Y116Efs*30	ENST00000380728		116	TACCAGCAg/g	5/11	0.52560315829921	2	FACETS	0.785	0.71	0.864	0.393	0.355	0.432	SUBCLONAL	1	TRUE	0	0.52560315829921	2		320	567	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576849	7576872	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTACCTGAAGGGTGAAATATTCTC	GTACCTGAAGGGTGAAATATTCTC	TT	novel	NA	P-0018030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	78	394	3	ENST00000269305.4:c.974_993+4delinsAA		p.X325_splice	ENST00000269305	NM_001126112.2	325		9/11	0.52560315829921	2	FACETS	0.504	0.443	0.569	0.252	0.221	0.285	SUBCLONAL	1	TRUE	0	0.52560315829921	2		397	589	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556347	29556347	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	271	383	0	ENST00000356175.3:c.2714A>C	p.Asn905Thr	p.N905T	ENST00000356175	NM_000267.3	905	aAc/aCc	21/57	0.52560315829921	2	FACETS	1	0.99	1	0.619	0.582	0.656	CLONAL	1	TRUE	0	0.52560315829921	2		383	833	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664430	29664430	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	130	368	0	ENST00000356175.3:c.6409T>A	p.Leu2137Ile	p.L2137I	ENST00000356175	NM_000267.3	2137	Tta/Ata	42/57	0.52560315829921	2	FACETS	0.634	0.575	0.696	0.317	0.287	0.348	SUBCLONAL	1	TRUE	0	0.52560315829921	2		368	780	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050254	128050254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	81	363	1	ENST00000285398.2:c.403G>A	p.Asp135Asn	p.D135N	ENST00000285398	NM_000122.1	135	Gac/Aac	3/15	0.515574554577909	2	FACETS	0.5	0.441	0.564	0.25	0.22	0.282	SUBCLONAL	1	TRUE	0	0.52560315829921	2		364	616	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259262	89259262	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	58	274	0	ENST00000336596.2:c.406C>G	p.Arg136Gly	p.R136G	ENST00000336596	NM_005233.5	136	Cga/Gga	3/17	1	2	FACETS	0.506	0.436	0.582	0.506	0.436	0.582	SUBCLONAL	1	TRUE	1	0.52560315829921	2		274	436	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417849	138417849	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	251	497	0	ENST00000289153.2:c.1670T>C	p.Leu557Pro	p.L557P	ENST00000289153	NM_006219.2	557	cTt/cCt	11/22	0.420117650611914	4	FACETS	1	0.98	1	0.374	0.349	0.4	CLONAL	1	TRUE	1	0.52560315829921	4		497	1299	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673530	30673530	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	94	497	0	ENST00000376406.3:c.3430C>T	p.Gln1144Ter	p.Q1144*	ENST00000376406	NM_014641.2	1144	Cag/Tag	10/15	0.290629953233799	4	FACETS	0.511	0.453	0.573	0.128	0.113	0.144	INDETERMINATE	1	TRUE	0	0.52560315829921	4		497	1068	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023257	150023257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	184	293	0	ENST00000253339.5:c.6G>C	p.Lys2Asn	p.K2N	ENST00000253339		2	aaG/aaC	1/7	0.250451612714149	2	FACETS	1	0.989	1	0.666	0.619	0.713	INDETERMINATE	1	TRUE	0	0.52560315829921	2		293	526	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0018032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	598	475	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.656578987258086	5	FACETS	0.949	0.92	0.976	0.949	0.92	0.976	CLONAL	4	TRUE	1	0.679103227259783	5		475	937	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0018032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	468	460	2	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.66633424962824	2	FACETS	0.993	0.961	1	0.993	0.961	1	CLONAL	2	TRUE	0	0.679103227259783	2		462	694	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878060	48878103	+	frameshift_variant	Frame_Shift_Del	DEL	AACCCCCCGAAAAACGGCCGCCACCGCCGCCGCTGCCGCCGCGG	AACCCCCCGAAAAACGGCCGCCACCGCCGCCGCTGCCGCCGCGG	-	novel	NA	P-0018032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	134	286	0	ENST00000267163.4:c.19_62del	p.Arg7GlyfsTer9	p.R7Gfs*9	ENST00000267163	NM_000321.2	4	aaAACCCCCCGAAAAACGGCCGCCACCGCCGCCGCTGCCGCCGCGGaa/aaaa	1/27	0.663858519744592	2	FACETS	1	0.988	1	0.71	0.657	0.762	CLONAL	1	TRUE	0	0.679103227259783	2		286	278	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753186	42753186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	379	339	0	ENST00000222329.4:c.1078G>A	p.Val360Ile	p.V360I	ENST00000222329	NM_006494.2	360	Gtc/Atc	4/4	0.668289341340239	3	FACETS	0.949	0.907	0.991	0.949	0.907	0.991	CLONAL	2	TRUE	1	0.679103227259783	3		339	788	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267385	198267385	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	198	384	0	ENST00000335508.6:c.1972T>G	p.Trp658Gly	p.W658G	ENST00000335508	NM_012433.2	658	Tgg/Ggg	14/25	0.668289341340239	3	FACETS	1	0.938	1	0.505	0.469	0.543	CLONAL	1	TRUE	1	0.679103227259783	3		384	773	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936046	178936046	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	113	127	0	ENST00000263967.3:c.1588C>A	p.Gln530Lys	p.Q530K	ENST00000263967	NM_006218.2	530	Cag/Aag	10/21	0.67119053349842	5	FACETS	1	0.921	1	1	0.921	1	CLONAL	3	TRUE	2	0.679103227259783	5		127	224	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8338979	8338979	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	385	423	0	ENST00000356435.5:c.5322G>T	p.Met1774Ile	p.M1774I	ENST00000356435		1774	atG/atT	32/35	0.586251125477955	5	FACETS	0.93	0.888	0.972	0.93	0.888	0.972	CLONAL	3	TRUE	2	0.609700045518988	5		423	867	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577084	7577084	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121912667	NA	P-0018033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	538	619	1	ENST00000269305.4:c.854A>T	p.Glu285Val	p.E285V	ENST00000269305	NM_001126112.2	285	gAg/gTg	8/11	0.594798214182893	2	FACETS	0.995	0.962	1	0.995	0.962	1	CLONAL	2	TRUE	0	0.609700045518988	2		620	887	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99823108	99823108	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757655058	NA	P-0018033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	90	301	0	ENST00000280892.6:c.104C>T	p.Pro35Leu	p.P35L	ENST00000280892	NM_001130678.1	35	cCg/cTg	2/7	0.586251125477955	5	FACETS	0.784	0.695	0.878	0.261	0.231	0.293	SUBCLONAL	1	TRUE	2	0.609700045518988	5		301	721	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582169	189582169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908836	NA	P-0018033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	148	392	1	ENST00000264731.3:c.728G>A	p.Arg243Gln	p.R243Q	ENST00000264731	NM_003722.4	243	cGg/cAg	5/14	0.609700045518988	6	FACETS	0.851	0.775	0.931	0.284	0.258	0.311	CLONAL	1	TRUE	3	0.609700045518988	6		393	1266	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923137	48923137	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	94	356	0	ENST00000267163.4:c.585G>C	p.Trp195Cys	p.W195C	ENST00000267163	NM_000321.2	195	tgG/tgC	6/27	0.594132170043006	3	FACETS	0.965	0.896	1	0.965	0.896	1	CLONAL	3	TRUE	0	0.609700045518988	3		356	139	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029375	14029375	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	125	328	0	ENST00000311895.7:c.1586T>A	p.Ile529Asn	p.I529N	ENST00000311895	NM_005236.2	529	aTt/aAt	8/11	0.606666804562175	3	FACETS	0.922	0.838	1	0.461	0.419	0.506	CLONAL	1	TRUE	1	0.609700045518988	3		328	580	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657409	29657409	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	394	583	1	ENST00000356175.3:c.5643del	p.Asn1882ThrfsTer22	p.N1882Tfs*22	ENST00000356175	NM_000267.3	1881	gCc/gc	38/57	0.609700045518988	7	FACETS	0.955	0.909	1	0.716	0.681	0.751	CLONAL	3	TRUE	3	0.609700045518988	7		584	1139	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805780	46805780	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	163	405	0	ENST00000290295.7:c.176C>G	p.Pro59Arg	p.P59R	ENST00000290295	NM_006361.5	59	cCg/cGg	1/2	0.609700045518988	5	FACETS	0.882	0.808	0.959	0.22	0.202	0.24	CLONAL	1	TRUE	1	0.609700045518988	5		405	1161	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222016	2222016	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	191	511	0	ENST00000398665.3:c.2848G>C	p.Ala950Pro	p.A950P	ENST00000398665	NM_032482.2	950	Gcg/Ccg	24/28	1	2	FACETS	0.903	0.838	0.97	0.903	0.838	0.97	CLONAL	1	TRUE	1	0.609700045518988	2		511	694	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152061	11152061	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	205	441	1	ENST00000358026.2:c.4345A>T	p.Ser1449Cys	p.S1449C	ENST00000358026	NM_001128849.1	1449	Agc/Tgc	31/36	1	2	FACETS	0.996	0.928	1	0.996	0.928	1	CLONAL	1	TRUE	1	0.609700045518988	2		442	675	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467132	25467132	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs769419803	NA	P-0018033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	165	470	0	ENST00000264709.3:c.1743G>A	p.Trp581Ter	p.W581*	ENST00000264709	NM_175629.2	581	tgG/tgA	15/23	0.606666804562175	3	FACETS	0.823	0.756	0.893	0.412	0.378	0.447	CLONAL	1	TRUE	1	0.609700045518988	3		470	858	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003334	143003334	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	470	455	0	ENST00000262992.4:c.2492G>T	p.Cys831Phe	p.C831F	ENST00000262992	NM_001101669.1	831	tGc/tTc	23/24	0.586251125477955	5	FACETS	0.912	0.874	0.95	0.912	0.874	0.95	CLONAL	3	TRUE	2	0.609700045518988	5		455	1079	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871231	35871231	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	233	401	0	ENST00000303115.3:c.453T>A	p.Asn151Lys	p.N151K	ENST00000303115	NM_002185.3	151	aaT/aaA	4/8	0.609700045518988	6	FACETS	0.789	0.736	0.844	0.394	0.368	0.422	SUBCLONAL	2	TRUE	2	0.609700045518988	6		401	1075	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250820	26250821	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCGTGCGTGCC	novel	NA	P-0018033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	61	135	0	ENST00000446824.2:c.3_13dup	p.Lys5ArgfsTer36	p.K5Rfs*36	ENST00000446824	NM_021018.2	5	aag/aGGCACGCACGAag	1/1	0.609700045518988	7	FACETS	0.913	0.788	1			1	CLONAL	1	TRUE	NA	0.609700045518988	7		135	553	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729756	41729756	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1431859332	NA	P-0018033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	201	274	1	ENST00000242208.4:c.773G>T	p.Gly258Val	p.G258V	ENST00000242208	NM_002192.2	258	gGc/gTc	3/3	0.609700045518988	5	FACETS	1	0.99	1	0.355	0.329	0.382	CLONAL	1	TRUE	1	0.609700045518988	5		275	888	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846021	128846021	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	371	454	0	ENST00000249373.3:c.951C>G	p.Ile317Met	p.I317M	ENST00000249373	NM_005631.4	317	atC/atG	5/12	0.609700045518988	6	FACETS	0.933	0.884	0.983	0.466	0.442	0.492	CLONAL	2	TRUE	2	0.609700045518988	6		454	1448	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848043	151848043	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	133	375	0	ENST00000262189.6:c.12716G>A	p.Ser4239Asn	p.S4239N	ENST00000262189	NM_170606.2	4239	aGt/aAt	51/59	0.609700045518988	6	FACETS	0.974	0.884	1	0.244	0.221	0.268	CLONAL	1	TRUE	2	0.609700045518988	6		375	994	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038760	47038760	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	181	265	0	ENST00000377604.3:c.767del	p.Gln256ArgfsTer10	p.Q256Rfs*10	ENST00000377604	NM_001204468.1	256	cAg/cg	9/24	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.609700045518988	1		265	347	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0018035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	206	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.966	1	1	0.995	1	CLONAL	3	FALSE	1	0.254501807658206	2		306	515	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552111	29552119	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGCAGGCAG	AGCAGGCAG	-	novel	NA	P-0018035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	10	219	1	ENST00000356175.3:c.1846-1_1853del		p.X616_splice	ENST00000356175	NM_000267.3	616		17/57	1	2	FACETS	0.471	0.319	0.66	0.471	0.319	0.66	SUBCLONAL	1	FALSE	1	0.254501807658206	2		220	167	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339232	87339232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1404514232	NA	P-0018035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	376	783	2	ENST00000277120.3:c.814G>A	p.Val272Ile	p.V272I	ENST00000277120		272	Gta/Ata	8/19	1	2	FACETS	1	0.987	1	1	0.997	1	CLONAL	3	FALSE	1	0.254501807658206	2		785	903	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	60	918	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.0986157181552606	3	FACETS	1	0.932	1	0.572	0.491	0.66	CLONAL	1	TRUE	1	0.14	3		918	802	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732996	30732996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893809	NA	P-0018036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	31	521	0	ENST00000295754.5:c.1609C>T	p.Arg537Cys	p.R537C	ENST00000295754	NM_003242.5	537	Cgc/Tgc	7/7	1	2	FACETS	0.919	0.742	1	0.919	0.742	1	CLONAL	1	TRUE	1	0.14	2		521	482	SUCCESS
AR	367	MSKCC	GRCh37	X	66766357	66766395	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	-	rs746853821	NA	P-0018036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	21	183	0	ENST00000374690.3:c.1382_1420del	p.Gly461_Gly473del	p.G461_G473del	ENST00000374690	NM_000044.3	457	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC/-	1/8	1	2	FACETS	1	0.882	1	1	0.95	1	CLONAL	2	TRUE	1	0.14	2		183	123	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013719	170013719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388201066	NA	P-0018036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	40	735	1	ENST00000295797.4:c.1438C>T	p.Arg480Cys	p.R480C	ENST00000295797	NM_002740.5	480	Cgc/Tgc	15/18	1	2	FACETS	0.819	0.679	0.976	0.819	0.679	0.976	CLONAL	1	TRUE	1	0.14	2		736	698	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024010	27024016	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGCTC	GCCGCTC	-	novel	NA	P-0018036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	10	156	0	ENST00000324856.7:c.1119_1125del	p.Leu374GlyfsTer15	p.L374Gfs*15	ENST00000324856	NM_006015.4	372	caGCCGCTC/ca	1/20	1	2	FACETS	1	0.814	1	1	0.814	1	CLONAL	1	TRUE	1	0.14	2		156	108	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022859	12022959	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTCCCCGCCTGAAGAGCACGCCATGCCCATTGGGAGAATAGCAGGTGAGTGAGTTCCCCTCTCGCCGCTCCAGCATCATGGGGACCTGACAAAGTCCCAC	TCTCCCCGCCTGAAGAGCACGCCATGCCCATTGGGAGAATAGCAGGTGAGTGAGTTCCCCTCTCGCCGCTCCAGCATCATGGGGACCTGACAAAGTCCCAC	-	novel	NA	P-0018036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	44	777	1	ENST00000396373.4:c.972_1009+63del		p.X324_splice	ENST00000396373	NM_001987.4	324		5/8	0.0986157181552606	3	FACETS	1	0.915	1	0.575	0.481	0.679	CLONAL	1	TRUE	1	0.14	3		778	585	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950385	15950386	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0018036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	36	820	0	ENST00000268712.3:c.6557_6558dup	p.Ser2187GlyfsTer3	p.S2187Gfs*3	ENST00000268712	NM_006311.3	2186	-/GG	42/46	1	2	FACETS	0.879	0.721	1	0.879	0.721	1	CLONAL	1	TRUE	1	0.14	2		820	585	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031215	36031215	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	27	755	0	ENST00000358208.4:c.1334A>T	p.Lys445Met	p.K445M	ENST00000358208		445	aAg/aTg	11/12	1	2	FACETS	0.79	0.628	0.977	0.79	0.628	0.977	CLONAL	1	TRUE	1	0.14	2		755	488	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729874	30729874	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0018036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	27	428	0	ENST00000295754.5:c.1397-2A>C		p.X466_splice	ENST00000295754	NM_003242.5	466			1	2	FACETS	0.901	0.716	1	0.901	0.716	1	CLONAL	1	TRUE	1	0.14	2		428	428	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045136	47045136	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	30	812	0	ENST00000377604.3:c.2377C>T	p.Arg793Ter	p.R793*	ENST00000377604	NM_001204468.1	793	Cga/Tga	21/24	1	2	FACETS	0.806	0.648	0.985	0.806	0.648	0.985	CLONAL	1	TRUE	1	0.14	2		812	532	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645977	67645977	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	53	933	0	ENST00000264010.4:c.905C>T	p.Ala302Val	p.A302V	ENST00000264010	NM_006565.3	302	gCa/gTa	4/12	1	2	FACETS	0.488	0.415	0.569	0.488	0.415	0.569	SUBCLONAL	1	TRUE	1	0.258421911406582	2		933	840	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584602	48584602	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	126	816	0	ENST00000342988.3:c.775A>T	p.Thr259Ser	p.T259S	ENST00000342988	NM_005359.5	259	Act/Tct	6/12	0.255750290109092	1	FACETS	0.853	0.776	0.932	1	0.988	1	CLONAL	2	TRUE	0	0.258421911406582	1		816	498	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61711146	61711146	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	72	1041	0	ENST00000401558.2:c.2603C>G	p.Pro868Arg	p.P868R	ENST00000401558	NM_003400.3	868	cCt/cGt	21/25	1	2	FACETS	0.93	0.83	1	0.93	0.83	1	CLONAL	1	FALSE	1	0.836630482730423	2		1041	185	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	166	654	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	0.984	0.907	1	0.984	0.907	1	CLONAL	1	TRUE	1	0.487458030425395	2		654	692	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61712974	61712974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	195	926	1	ENST00000401558.2:c.2437G>A	p.Gly813Arg	p.G813R	ENST00000401558	NM_003400.3	813	Gga/Aga	20/25	0.44697237598596	3	FACETS	0.957	0.885	1	0.478	0.442	0.516	CLONAL	1	TRUE	1	0.487458030425395	3		927	1040	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	76	184	0				ENST00000310581	NM_198253.2	-/1132			0.346780967611691	1	FACETS	0.946	0.835	1	0.946	0.835	1	CLONAL	1	TRUE	0	0.346780967611691	1		184	383	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894228	NA	P-0018042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	201	673	0	ENST00000451590.1:c.37G>C	p.Gly13Arg	p.G13R	ENST00000451590	NM_001130442.1	13	Ggt/Cgt	2/5	0.346780967611691	1	FACETS	0.789	0.736	0.844	1	0.992	1	SUBCLONAL	2	TRUE	0	0.346780967611691	1		673	607	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436127	56436127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138844366	NA	P-0018042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	123	822	0	ENST00000407977.2:c.1010G>A	p.Arg337Gln	p.R337Q	ENST00000407977		337	cGa/cAa	9/10	0.346780967611691	3	FACETS	0.842	0.76	0.928	0.421	0.38	0.464	CLONAL	1	TRUE	1	0.346780967611691	3		822	989	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812340	212812340	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	80	496	1	ENST00000342788.4:c.236C>T	p.Ser79Phe	p.S79F	ENST00000342788	NM_005235.2	79	tCt/tTt	3/28	1	2	FACETS	0.932	0.823	1	0.932	0.823	1	CLONAL	1	TRUE	1	0.346780967611691	2		497	495	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247617	123247617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	130	709	0	ENST00000358487.5:c.1874G>A	p.Arg625Gln	p.R625Q	ENST00000358487	NM_000141.4	625	cGa/cAa	14/18	1	2	FACETS	0.943	0.856	1	0.943	0.856	1	CLONAL	1	TRUE	1	0.346780967611691	2		709	795	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830184	72830184	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	74	437	0	ENST00000268489.5:c.6397C>T	p.Gln2133Ter	p.Q2133*	ENST00000268489	NM_006885.3	2133	Cag/Tag	9/10	0.346780967611691	1	FACETS	0.919	0.809	1	0.919	0.809	1	CLONAL	1	TRUE	0	0.346780967611691	1		437	384	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717711	89717712	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0018042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	115	751	1	ENST00000371953.3:c.736_737delinsTT	p.Pro246Leu	p.P246L	ENST00000371953	NM_000314.4	246	CCg/TTg	7/9	1	2	FACETS	0.953	0.859	1	0.953	0.859	1	CLONAL	1	TRUE	1	0.346780967611691	2		752	696	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939869	71939869	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs999276105	NA	P-0018042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	178	929	0	ENST00000298229.2:c.496C>T	p.Pro166Ser	p.P166S	ENST00000298229	NM_001567.3	166	Ccc/Tcc	4/28	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.346780967611691	2		929	1025	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175561	108175561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	132	726	0	ENST00000278616.4:c.5656C>T	p.Pro1886Ser	p.P1886S	ENST00000278616	NM_000051.3	1886	Cct/Tct	37/63	0.346780967611691	1	FACETS	0.881	0.801	0.965	0.881	0.801	0.965	CLONAL	1	TRUE	0	0.346780967611691	1		726	714	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562501	21562501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	14	62	0	ENST00000382592.4:c.1418C>T	p.Pro473Leu	p.P473L	ENST00000382592	NM_014572.2	473	cCc/cTc	4/8	0.346780967611691	1	FACETS	1	0.832	1	1	0.832	1	CLONAL	1	TRUE	0	0.346780967611691	1		62	57	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609954	81609954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	61	438	0	ENST00000298171.2:c.1552G>A	p.Glu518Lys	p.E518K	ENST00000298171	NM_000369.2	518	Gag/Aag	10/10	0.346780967611691	1	FACETS	0.9	0.782	1	0.9	0.782	1	CLONAL	1	TRUE	0	0.346780967611691	1		438	323	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423623	88423623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	103	628	0	ENST00000360948.2:c.2212C>T	p.Pro738Ser	p.P738S	ENST00000360948	NM_001012338.2	738	Cct/Tct	18/19	1	2	FACETS	0.949	0.851	1	0.949	0.851	1	CLONAL	1	TRUE	1	0.346780967611691	2		628	626	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40379600	40379600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	182	936	0	ENST00000293328.3:c.232G>A	p.Glu78Lys	p.E78K	ENST00000293328	NM_012448.3	78	Gaa/Aaa	3/19	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.346780967611691	2		936	975	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796256	42796256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	122	772	1	ENST00000575354.2:c.2905G>A	p.Val969Met	p.V969M	ENST00000575354	NM_015125.3	969	Gtg/Atg	12/20	1	2	FACETS	0.969	0.877	1	0.969	0.877	1	CLONAL	1	TRUE	1	0.346780967611691	2		773	726	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754971	29754971	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs538843723	NA	P-0018042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	101	629	0	ENST00000389048.3:c.964C>T	p.Leu322Phe	p.L322F	ENST00000389048	NM_004304.4	322	Ctt/Ttt	4/29	1	2	FACETS	0.949	0.85	1	0.949	0.85	1	CLONAL	1	TRUE	1	0.346780967611691	2		629	614	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872594	136872594	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	93	605	0	ENST00000241393.3:c.904T>C	p.Tyr302His	p.Y302H	ENST00000241393	NM_003467.2	302	Tat/Cat	2/2	1	2	FACETS	0.914	0.814	1	0.914	0.814	1	CLONAL	1	TRUE	1	0.346780967611691	2		605	587	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439905	220439905	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750272026	NA	P-0018042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	126	984	2	ENST00000243786.2:c.758C>T	p.Pro253Leu	p.P253L	ENST00000243786	NM_002191.3	253	cCg/cTg	2/2	1	2	FACETS	0.903	0.818	0.992	0.903	0.818	0.992	CLONAL	1	TRUE	1	0.346780967611691	2		986	805	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547028	9547028	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	34	267	0	ENST00000353224.5:c.994G>A	p.Asp332Asn	p.D332N	ENST00000353224	NM_177990.2	332	Gat/Aat	5/10	1	2	FACETS	0.879	0.724	1	0.879	0.724	1	CLONAL	1	TRUE	1	0.346780967611691	2		267	223	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076903	41076903	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	140	759	1	ENST00000373198.4:c.1517G>A	p.Trp506Ter	p.W506*	ENST00000373198	NM_133170.3	506	tGg/tAg	9/32	1	2	FACETS	0.937	0.853	1	0.937	0.853	1	CLONAL	1	TRUE	1	0.346780967611691	2		760	862	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928673	49928673	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	148	890	1	ENST00000296474.3:c.3601G>A	p.Glu1201Lys	p.E1201K	ENST00000296474	NM_002447.2	1201	Gag/Aag	17/20	1	2	FACETS	0.995	0.909	1	0.995	0.909	1	CLONAL	1	TRUE	1	0.346780967611691	2		891	858	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564311	86564311	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	48	437	0	ENST00000274376.6:c.43A>T	p.Thr15Ser	p.T15S	ENST00000274376	NM_002890.2	15	Aca/Tca	1/25	1	2	FACETS	0.839	0.712	0.977	0.839	0.712	0.977	CLONAL	1	TRUE	1	0.346780967611691	2		437	330	SUCCESS
APC	324	MSKCC	GRCh37	5	112176095	112176095	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1408572186	NA	P-0018042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	158	852	1	ENST00000257430.4:c.4804C>T	p.Pro1602Ser	p.P1602S	ENST00000257430	NM_000038.5	1602	Cct/Tct	16/16	1	2	FACETS	0.967	0.886	1	0.967	0.886	1	CLONAL	1	TRUE	1	0.346780967611691	2		853	942	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039534	180039534	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	155	977	0	ENST00000261937.6:c.3509G>A	p.Gly1170Glu	p.G1170E	ENST00000261937	NM_182925.4	1170	gGg/gAg	26/30	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.346780967611691	2		977	876	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271395	26271395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	82	565	1	ENST00000305910.3:c.218G>A	p.Arg73Gln	p.R73Q	ENST00000305910	NM_003534.2	73	cGa/cAa	1/1	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.346780967611691	2		566	469	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839775	27839775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	111	677	0	ENST00000328488.2:c.319G>A	p.Asp107Asn	p.D107N	ENST00000328488	NM_003533.2	107	Gat/Aat	1/1	1	2	FACETS	0.916	0.824	1	0.916	0.824	1	CLONAL	1	TRUE	1	0.346780967611691	2		677	699	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671558	30671558	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755871425	NA	P-0018042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	136	913	0	ENST00000376406.3:c.5402C>T	p.Pro1801Leu	p.P1801L	ENST00000376406	NM_014641.2	1801	cCg/cTg	10/15	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.346780967611691	2		913	743	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188886	32188887	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0018042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	104	756	2	ENST00000375023.3:c.667_668delinsTT	p.Pro223Phe	p.P223F	ENST00000375023	NM_004557.3	223	CCt/TTt	4/30	1	2	FACETS	0.952	0.854	1	0.952	0.854	1	CLONAL	1	TRUE	1	0.346780967611691	2		758	630	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964483	93964483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	107	718	1	ENST00000369303.4:c.2414C>T	p.Pro805Leu	p.P805L	ENST00000369303	NM_004440.3	805	cCc/cTc	14/17	1	2	FACETS	0.793	0.711	0.88	0.793	0.711	0.88	SUBCLONAL	1	TRUE	1	0.346780967611691	2		719	778	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444260	50444260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	69	431	0	ENST00000331340.3:c.190G>A	p.Asp64Asn	p.D64N	ENST00000331340	NM_006060.4	64	Gat/Aat	4/8	1	2	FACETS	0.833	0.727	0.946	0.833	0.727	0.946	CLONAL	1	TRUE	1	0.346780967611691	2		431	478	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211148	55211148	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1485016142	NA	P-0018042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	147	777	0	ENST00000275493.2:c.391G>A	p.Gly131Arg	p.G131R	ENST00000275493	NM_005228.3	131	Gga/Aga	3/28	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.346780967611691	2		777	814	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477853	140477853	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs180177036	NA	P-0018042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	136	787	0	ENST00000288602.6:c.1455G>T	p.Leu485Phe	p.L485F	ENST00000288602	NM_004333.4	485	ttG/ttT	12/18	1	2	FACETS	0.995	0.906	1	0.995	0.906	1	CLONAL	1	TRUE	1	0.346780967611691	2		787	788	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031678	69031678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	110	728	1	ENST00000288368.4:c.3433C>T	p.Pro1145Ser	p.P1145S	ENST00000288368	NM_024870.2	1145	Ccc/Tcc	28/40	0.346780967611691	3	FACETS	0.905	0.812	1	0.452	0.406	0.501	CLONAL	1	TRUE	1	0.346780967611691	3		729	823	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293511	137293511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	156	1007	1	ENST00000481739.1:c.62C>T	p.Ser21Phe	p.S21F	ENST00000481739	NM_002957.4	21	tCc/tTc	2/10	0.346780967611691	1	FACETS	0.913	0.836	0.992	0.913	0.836	0.992	CLONAL	1	TRUE	0	0.346780967611691	1		1008	815	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246444	53246444	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	132	772	0	ENST00000375401.3:c.538C>A	p.Pro180Thr	p.P180T	ENST00000375401	NM_004187.3	180	Cca/Aca	5/26	1	2	FACETS	0.77	0.698	0.846	0.77	0.698	0.846	SUBCLONAL	1	TRUE	1	0.346780967611691	2		772	989	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188932	11188932	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	160	940	0	ENST00000361445.4:c.5791C>T	p.Gln1931Ter	p.Q1931*	ENST00000361445	NM_004958.3	1931	Cag/Tag	41/58	0.346780967611691	3	FACETS	0.916	0.838	0.998	0.458	0.419	0.499	CLONAL	1	TRUE	1	0.346780967611691	3		940	1182	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984723	72984723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879236303	NA	P-0018043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	171	782	0	ENST00000268489.5:c.2861C>T	p.Thr954Met	p.T954M	ENST00000268489	NM_006885.3	954	aCg/aTg	3/10	1	2	FACETS	0.948	0.872	1	0.948	0.872	1	CLONAL	1	TRUE	1	0.371121609051029	2		782	972	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577523	7577523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	204	730	0	ENST00000269305.4:c.758C>T	p.Thr253Ile	p.T253I	ENST00000269305	NM_001126112.2	253	aCc/aTc	7/11	0.371121609051029	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.371121609051029	1		730	869	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530091	212530091	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	152	592	4	ENST00000342788.4:c.1828C>A	p.Pro610Thr	p.P610T	ENST00000342788	NM_005235.2	610	Cca/Aca	15/28	0.371121609051029	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.371121609051029	1		596	579	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549384	187549409	+	frameshift_variant	Frame_Shift_Del	DEL	GCCAACGGCTGCCGATTCATAAACCC	GCCAACGGCTGCCGATTCATAAACCC	-	novel	NA	P-0018043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	139	955	0	ENST00000441802.2:c.4709_4734del	p.Arg1570LeufsTer18	p.R1570Lfs*18	ENST00000441802	NM_005245.3	1570	cGGGTTTATGAATCGGCAGCCGTTGGC/c	9/27	0.371121609051029	1	FACETS	0.63	0.572	0.69	0.63	0.572	0.69	SUBCLONAL	1	TRUE	0	0.371121609051029	1		955	969	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873595	35873595	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	85	506	0	ENST00000303115.3:c.551C>A	p.Ser184Tyr	p.S184Y	ENST00000303115	NM_002185.3	184	tCc/tAc	5/8	1	2	FACETS	0.881	0.781	0.987	0.881	0.781	0.987	CLONAL	1	TRUE	1	0.371121609051029	2		506	520	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046172	69046440	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTTTTCACATGCGTGAGTTTAGTGAAAAGATGAAATGCTAGTGAATGTAGATGCTGAACGCATTGGTTTTCACCATCTGCAACATTTTTCGAAGCATTCTCTATGTTCTCTTTGATCACAGATAGTGAGACACAGCTCCGTAGAGACATGGTTTTCTGCCAGACTCTTGTGGCCACTGTCTGTGCCTTCTCTGAGCAGCTCATGGCGGCCTTGAACCAGATGTTTGACAACAGCAAGGAAAATGAGATGGAAACTTGGGAAGCCAGCA	ATTTTTCACATGCGTGAGTTTAGTGAAAAGATGAAATGCTAGTGAATGTAGATGCTGAACGCATTGGTTTTCACCATCTGCAACATTTTTCGAAGCATTCTCTATGTTCTCTTTGATCACAGATAGTGAGACACAGCTCCGTAGAGACATGGTTTTCTGCCAGACTCTTGTGGCCACTGTCTGTGCCTTCTCTGAGCAGCTCATGGCGGCCTTGAACCAGATGTTTGACAACAGCAAGGAAAATGAGATGGAAACTTGGGAAGCCAGCA	-	novel	NA	P-0018043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	47	55	0	ENST00000288368.4:c.3767-122_3913del		p.X1256_splice	ENST00000288368	NM_024870.2	1256		32/40	1	2	FACETS	1	0.942	1	1	0.982	1	CLONAL	3	TRUE	1	0.371121609051029	2		55	77	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974679	21974679	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs864622636	NA	P-0018043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	135	690	1	ENST00000304494.5:c.148C>A	p.Gln50Lys	p.Q50K	ENST00000304494	NM_000077.4	50	Cag/Aag	1/3	0.371121609051029	1	FACETS	0.869	0.791	0.95	0.869	0.791	0.95	CLONAL	1	TRUE	0	0.371121609051029	1		691	682	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994285	21994285	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	151	786	1	ENST00000579755.1:c.46G>T	p.Gly16Cys	p.G16C	ENST00000579755		16	Ggc/Tgc	1/3	0.371121609051029				0.842	1				CLONAL	1	TRUE	0	0.371121609051029	1		787	721	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0018044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	442	808	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	NA	2	FACETS	0.953	0.919	0.987			1	INDETERMINATE	2	TRUE	NA	0.644962631835062	2		808	719	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90995027	90995028	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs864622253	NA	P-0018044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1692	126	811	0	ENST00000265433.3:c.93_94del	p.Ala32HisfsTer4	p.A32Hfs*4	ENST00000265433	NM_002485.4	31	tgTGcc/tgcc	2/16	0.644962631835062	9	FACETS	0.7	0.631	0.774	0.14	0.126	0.155	SUBCLONAL	1	TRUE	4	0.644962631835062	9		811	1818	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803485	43803525	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	GGATGGGCTAAGGCAGGCACACAGTGGCGGAGAAGATGCCC	GGATGGGCTAAGGCAGGCACACAGTGGCGGAGAAGATGCCC	AGCCT	novel	NA	P-0018044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	44	792	4	ENST00000372470.3:c.-35_6delinsAGCCT		p.*12*	ENST00000372470	NM_005373.2	?-2/635		1/12	0.603443289663357	2	FACETS	0.253	0.211	0.298	0.126	0.105	0.149	SUBCLONAL	1	TRUE	0	0.644962631835062	2		796	540	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306961	65306983	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTTCAAAATGTGTGGGGTCCA	CTTTTCAAAATGTGTGGGGTCCA	-	novel	NA	P-0018044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	201	723	0	ENST00000342505.4:c.2594_2616del	p.Val865AlafsTer8	p.V865Afs*8	ENST00000342505	NM_002227.2	865	gTGGACCCCACACATTTTGAAAAG/g	19/25	0.603443289663357	2	FACETS	1	0.991	1	0.7	0.657	0.744	CLONAL	1	TRUE	0	0.644962631835062	2		723	445	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434329	121434358	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCTTCCCCTCGTAGGTCTCAGCAGCTGGG	GGCTTCCCCTCGTAGGTCTCAGCAGCTGGG	-	novel	NA	P-0018044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	227	735	0	ENST00000257555.6:c.1108-12_1125del		p.X370_splice	ENST00000257555		370		6/10	0.644962631835062	3	FACETS	1	0.989	1	0.426	0.398	0.455	CLONAL	1	TRUE	0	0.644962631835062	3		735	728	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602822	10602822	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	465	988	1	ENST00000171111.5:c.756G>T	p.Trp252Cys	p.W252C	ENST00000171111	NM_203500.1	252	tgG/tgT	3/6	0.593058908903523	2	FACETS	0.98	0.946	1	0.98	0.946	1	CLONAL	2	TRUE	0	0.644962631835062	2		989	736	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221267	36221267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	447	1021	0	ENST00000222270.7:c.5101G>A	p.Asp1701Asn	p.D1701N	ENST00000222270	NM_014727.1	1701	Gat/Aat	24/37	0.644962631835062	5	FACETS	0.891	0.849	0.934			1	CLONAL	2	TRUE	NA	0.644962631835062	5		1021	1530	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140354	50140354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	303	706	0	ENST00000246792.3:c.187G>A	p.Glu63Lys	p.E63K	ENST00000246792	NM_006270.3	63	Gag/Aag	2/6	0.481858697488882	4	FACETS	0.895	0.847	0.945			1	CLONAL	2	TRUE	NA	0.644962631835062	4		706	863	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36022681	36022681	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0018044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	258	648	4	ENST00000358208.4:c.553+1G>T		p.X185_splice	ENST00000358208		185			0.562157038553398	5	FACETS	0.951	0.893	1			1	CLONAL	2	TRUE	NA	0.644962631835062	5		652	828	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514587	44514587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1307687940	NA	P-0018044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	227	552	2	ENST00000291552.4:c.569G>A	p.Arg190His	p.R190H	ENST00000291552	NM_006758.2	190	cGc/cAc	7/8	0.544302222994657	4	FACETS	0.884	0.828	0.941	0.884	0.828	0.941	CLONAL	2	TRUE	2	0.644962631835062	4		554	655	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683497	182683497	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	401	823	1	ENST00000292782.4:c.48G>T	p.Met16Ile	p.M16I	ENST00000292782	NM_020640.2	16	atG/atT	2/7	0.603443289663357	2	FACETS	0.943	0.908	0.978	0.943	0.908	0.978	CLONAL	2	TRUE	0	0.644962631835062	2		824	659	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79968073	79968073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760032154	NA	P-0018044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	320	756	0	ENST00000265081.6:c.803G>A	p.Arg268Gln	p.R268Q	ENST00000265081	NM_002439.4	268	cGa/cAa	5/24	0.593058908903523	2	FACETS	0.917	0.878	0.956	0.917	0.878	0.956	CLONAL	2	TRUE	0	0.644962631835062	2		756	541	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948731	71948732	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	A	novel	NA	P-0018044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	307	818	0	ENST00000298229.2:c.3443_3444delinsA	p.Gly1148AspfsTer54	p.G1148Dfs*54	ENST00000298229	NM_001567.3	1148	gGC/gA	26/28	0.603443289663357	2	FACETS	0.881	0.842	0.921	0.881	0.842	0.921	CLONAL	2	TRUE	0	0.644962631835062	2		818	540	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015052	27015052	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs776697460	NA	P-0018047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	37	713	1	ENST00000335756.4:c.154C>T	p.Arg52Ter	p.R52*	ENST00000335756	NM_001809.3	52	Cga/Tga	2/5	1	2	FACETS	0.485	0.399	0.583	0.485	0.399	0.583	SUBCLONAL	1	FALSE	1	0.22386135385842	2		714	681	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220493	1220493	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	74	794	1	ENST00000326873.7:c.586G>T	p.Gly196Cys	p.G196C	ENST00000326873	NM_000455.4	196	Ggc/Tgc	4/10	0.22386135385842	1	FACETS	0.975	0.854	1	0.975	0.854	1	CLONAL	1	FALSE	0	0.22386135385842	1		795	602	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117448	115117448	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	47	587	1	ENST00000257566.3:c.726G>T	p.Leu242Phe	p.L242F	ENST00000257566	NM_016569.3	242	ttG/ttT	4/8	0.22386135385842	1	FACETS	0.834	0.705	0.977	0.834	0.705	0.977	CLONAL	1	FALSE	0	0.22386135385842	1		588	447	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891720	28891720	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	67	662	1	ENST00000282397.4:c.3301C>A	p.Pro1101Thr	p.P1101T	ENST00000282397	NM_002019.4	1101	Cca/Aca	25/30	0.22386135385842	1	FACETS	0.926	0.805	1	0.926	0.805	1	CLONAL	1	FALSE	0	0.22386135385842	1		663	574	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348143	89348143	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	35	845	1	ENST00000301030.4:c.4807G>A	p.Glu1603Lys	p.E1603K	ENST00000301030	NM_001256183.1	1603	Gag/Aag	9/13	0.22386135385842	1	FACETS	0.444	0.363	0.536	0.444	0.363	0.536	SUBCLONAL	1	FALSE	0	0.22386135385842	1		846	625	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356356	66356356	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1424484338	NA	P-0018047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	62	711	0	ENST00000273854.3:c.1141G>T	p.Ala381Ser	p.A381S	ENST00000273854	NM_004439.5	381	Gct/Tct	5/18	0.22386135385842	1	FACETS	0.786	0.678	0.903	0.786	0.678	0.903	CLONAL	1	FALSE	0	0.22386135385842	1		711	626	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951832	2951832	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	234	822	0	ENST00000396946.4:c.3118G>T	p.Ala1040Ser	p.A1040S	ENST00000396946	NM_032415.4	1040	Gcc/Tcc	23/25	0.22386135385842	4	FACETS	0.981	0.917	1	0.981	0.917	1	CLONAL	3	FALSE	1	0.22386135385842	4		822	869	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933376	39933376	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	41	776	2	ENST00000378444.4:c.1223G>T	p.Gly408Val	p.G408V	ENST00000378444	NM_001123385.1	408	gGg/gTg	4/15	0.22386135385842	1	FACETS	0.525	0.436	0.624	0.525	0.436	0.624	SUBCLONAL	1	FALSE	0	0.22386135385842	1		778	620	SUCCESS
AR	367	MSKCC	GRCh37	X	66766410	66766410	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	11	231	0	ENST00000374690.3:c.1422G>T	p.Glu474Asp	p.E474D	ENST00000374690	NM_000044.3	474	gaG/gaT	1/8	0.22386135385842	1	FACETS	0.651	0.452	0.896	0.651	0.452	0.896	SUBCLONAL	1	FALSE	0	0.22386135385842	1		231	134	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624467	140624467	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1563042573	NA	P-0018047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	14	246	1	ENST00000288602.6:c.37G>A	p.Glu13Lys	p.E13K	ENST00000288602	NM_004333.4	13	Gag/Aag	1/18	1	2	FACETS	0.498	0.36	0.666	0.498	0.36	0.666	SUBCLONAL	1	FALSE	1	0.22386135385842	2		247	251	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163720	32163720	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253487294	NA	P-0018049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	257	295	0	ENST00000375023.3:c.5506G>A	p.Glu1836Lys	p.E1836K	ENST00000375023	NM_004557.3	1836	Gag/Aag	30/30	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.886174250554477	2		295	519	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874287	155874287	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs869025194	NA	P-0018049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	181	387	0	ENST00000368323.3:c.244T>A	p.Phe82Ile	p.F82I	ENST00000368323	NM_006912.5	82	Ttt/Att	5/6	1	2	FACETS	0.517	0.478	0.558	0.517	0.478	0.558	SUBCLONAL	1	TRUE	1	0.886174250554477	2		387	790	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027149	49027150	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0018049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	330	420	0	ENST00000267163.4:c.1716_1717insTA	p.Ile573Ter	p.I573*	ENST00000267163	NM_000321.2	572	-/TA	18/27	0.886174250554477	1	FACETS	0.985	0.954	1	0.985	0.954	1	CLONAL	1	TRUE	0	0.886174250554477	1		420	421	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819225	3819225	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	170	410	0	ENST00000262367.5:c.3010G>C	p.Glu1004Gln	p.E1004Q	ENST00000262367	NM_004380.2	1004	Gag/Cag	15/31	0.443375579173411	1	FACETS	0.339	0.313	0.366	0.339	0.313	0.366	INDETERMINATE	1	TRUE	0	0.886174250554477	1		410	630	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259192	36259192	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	418	527	0	ENST00000300305.3:c.299C>G	p.Ser100Cys	p.S100C	ENST00000300305		100	tCc/tGc	3/8	1	2	FACETS	0.915	0.874	0.956	0.915	0.874	0.956	CLONAL	1	TRUE	1	0.886174250554477	2		527	1031	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0018050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	147	741	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.173507106237507	2	FACETS	0.829	0.757	0.904	0.829	0.757	0.904	CLONAL	2	TRUE	0	0.213115736646388	2		741	832	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0018050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	131	710	5	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.213115736646388	1	FACETS	0.762	0.692	0.835	1	0.986	1	SUBCLONAL	2	TRUE	0	0.213115736646388	1		715	721	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473722	67473722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs794727798	NA	P-0018050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	265	345	1	ENST00000327367.4:c.802C>T	p.Arg268Cys	p.R268C	ENST00000327367	NM_005902.3	268	Cgc/Tgc	6/9	0.201496699920119	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	3	TRUE	0	0.213115736646388	3		346	892	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052629	42052629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	132	349	1	ENST00000219905.7:c.7300C>T	p.Arg2434Trp	p.R2434W	ENST00000219905	NM_001164273.1	2434	Cgg/Tgg	20/24	0.213115736646388	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.213115736646388	1		350	755	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906330	50906330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370734242	NA	P-0018050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	39	321	0	ENST00000440232.2:c.991C>T	p.Arg331Trp	p.R331W	ENST00000440232	NM_002691.3	331	Cgg/Tgg	9/27	0.213115736646388	2	FACETS	0.487	0.402	0.582	0.243	0.201	0.291	SUBCLONAL	1	TRUE	0	0.213115736646388	2		321	752	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051658	30051658	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555993345	NA	P-0018051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	81	295	0	ENST00000338641.4:c.592C>T	p.Arg198Ter	p.R198*	ENST00000338641	NM_000268.3	198	Cga/Tga	6/16	0.24503449899592	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.24503449899592	1		295	432	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	99	598	1	ENST00000281708.4:c.1514G>C	p.Arg505Pro	p.R505P	ENST00000281708	NM_033632.3	505	cGc/cCc	10/12	1	2	FACETS	0.87	0.775	0.971	0.87	0.775	0.971	CLONAL	1	TRUE	1	0.24503449899592	2		599	929	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994243	21994282	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGCGGGATGTGAACCACGAAAACCCTCACTCGCGGCGG	GCCGCGGGATGTGAACCACGAAAACCCTCACTCGCGGCGG	-	novel	NA	P-0018051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	68	589	0	ENST00000579755.1:c.49_88del	p.Pro17SerfsTer18	p.P17Sfs*18	ENST00000579755		17	CCGCCGCGAGTGAGGGTTTTCGTGGTTCACATCCCGCGGCtc/tc	1/3	0.24503449899592		FACETS		0.576	0.758				SUBCLONAL	1	TRUE	0	0.24503449899592	1		589	734	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0018052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	155	447	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.228719699041657	1	FACETS	0.803	0.736	0.872	0.803	0.736	0.872	INDETERMINATE	1	TRUE	0	0.418874822590961	1		447	729	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115719	8115720	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0018052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	186	482	0	ENST00000346208.3:c.1066_1067del	p.Met356GlufsTer14	p.M356Efs*14	ENST00000346208		355	acTAtg/actg	6/6	1	2	FACETS	0.902	0.832	0.974	0.902	0.832	0.974	CLONAL	1	TRUE	1	0.418874822590961	2		482	985	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070644	67070645	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	81	231	0	ENST00000412916.2:c.268_269insT	p.Arg90MetfsTer26	p.R90Mfs*26	ENST00000412916		90	aga/aTga	3/6	0.418874822590961	1	FACETS	0.761	0.674	0.853	0.761	0.674	0.853	SUBCLONAL	1	TRUE	0	0.418874822590961	1		231	402	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216741	7216741	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	38	331	0	ENST00000380728.2:c.682C>T	p.Gln228Ter	p.Q228*	ENST00000380728		228	Cag/Tag	8/11	0.295526558432449	0	FACETS	0.269	0.222	0.321			1	SUBCLONAL	1	TRUE	0	0.418874822590961	0		331	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0018053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	127	492	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.423484608132332	1	FACETS	0.967	0.881	1	0.967	0.881	1	CLONAL	1	TRUE	0	0.423484608132332	1		492	489	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665213	138665213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	49	712	0	ENST00000330315.3:c.352G>A	p.Glu118Lys	p.E118K	ENST00000330315	NM_023067.3	118	Gag/Aag	1/1	0.162770091021617	5	FACETS	0.393	0.332	0.462			1	INDETERMINATE	1	TRUE	NA	0.423484608132332	5		712	962	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458718	120458766	+	frameshift_variant	Frame_Shift_Del	DEL	AGGCTGCATTTCATGAAGGTTAGAAAAAGATAGTGCATGCTGGGCATGG	AGGCTGCATTTCATGAAGGTTAGAAAAAGATAGTGCATGCTGGGCATGG	-	novel	NA	P-0018053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	104	333	0	ENST00000256646.2:c.6579_6627del	p.His2194TrpfsTer12	p.H2194Wfs*12	ENST00000256646	NM_024408.3	2193	gtCCATGCCCAGCATGCACTATCTTTTTCTAACCTTCATGAAATGCAGCCT/gt	34/34	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.423484608132332	2		333	422	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778218	3778231	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTGCCCCATCTG	GGCTGCCCCATCTG	-	novel	NA	P-0018053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	103	459	0	ENST00000262367.5:c.6817_6830del	p.Gln2273GlyfsTer63	p.Q2273Gfs*63	ENST00000262367	NM_004380.2	2273	CAGATGGGGCAGCCg/g	31/31	0.423484608132332	2	FACETS	0.886	0.795	0.982	0.443	0.397	0.491	CLONAL	1	TRUE	0	0.423484608132332	2		459	549	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130469	29130469	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	255	481	0	ENST00000328354.6:c.241G>T	p.Glu81Ter	p.E81*	ENST00000328354	NM_007194.3	81	Gag/Tag	2/15	0.423484608132332	3	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	1	0.423484608132332	3		481	730	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151927360	151927360	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	11	76	0	ENST00000262189.6:c.2816C>G	p.Ser939Cys	p.S939C	ENST00000262189	NM_170606.2	939	tCt/tGt	17/59	0.394324666655747	1	FACETS	0.487	0.341	0.664	0.487	0.341	0.664	SUBCLONAL	1	TRUE	0	0.423484608132332	1		76	84	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	48	184	0				ENST00000310581	NM_198253.2	-/1132			0.167371515437421	1	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	0	0.21	1		184	406	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965075	15965075	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	62	310	0	ENST00000268712.3:c.5521G>A	p.Glu1841Lys	p.E1841K	ENST00000268712	NM_006311.3	1841	Gag/Aag	37/46	1	2	FACETS	0.979	0.846	1	0.979	0.846	1	CLONAL	1	TRUE	1	0.21	2		310	603	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281167	15281167	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs971041880	NA	P-0018054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	120	628	2	ENST00000263388.2:c.5089G>A	p.Val1697Met	p.V1697M	ENST00000263388	NM_000435.2	1697	Gtg/Atg	27/33	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.21	2		630	1092	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805967	32805978	+	inframe_deletion	In_Frame_Del	DEL	ACCAGCAGCAGG	ACCAGCAGCAGG	-	novel	NA	P-0018056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	112	721	0	ENST00000374899.4:c.33_44del	p.Leu12_Val15del	p.L12_V15del	ENST00000374899	NM_018833.2	11	tcCCTGCTGCTGGTg/tcg	2/12	0.80582950013024	3	FACETS	0.362	0.325	0.402	0.181	0.162	0.201	SUBCLONAL	1	TRUE	1	0.812564512979154	3		721	1070	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227872	55227886	+	inframe_deletion	In_Frame_Del	DEL	TCCTTGGGATTACGC	TCCTTGGGATTACGC	-	novel	NA	P-0018056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	168	474	0	ENST00000275493.2:c.1342_1356del	p.Gly449_Leu453del	p.G449_L453del	ENST00000275493	NM_005228.3	447	TCCTTGGGATTACGC/-	12/28	0.80582950013024	3	FACETS	0.874	0.806	0.945	0.437	0.403	0.473	CLONAL	1	TRUE	1	0.812564512979154	3		474	665	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760519	133760519	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	158	821	0	ENST00000318560.5:c.2842C>G	p.Pro948Ala	p.P948A	ENST00000318560	NM_005157.4	948	Ccc/Gcc	11/11	0.80582950013024	3	FACETS	0.434	0.396	0.474	0.217	0.198	0.237	SUBCLONAL	1	TRUE	1	0.812564512979154	3		821	1260	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78599549	78599549	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	209	353	0	ENST00000306801.3:c.221A>G	p.Asp74Gly	p.D74G	ENST00000306801	NM_020761.2	74	gAt/gGt	2/34	0.719129602824822	4	FACETS	0.907	0.842	0.974	0.454	0.421	0.487	CLONAL	1	TRUE	2	0.845265299927504	4		353	1006	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100142	157100142	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	39	67	0	ENST00000346085.5:c.1079G>C	p.Gly360Ala	p.G360A	ENST00000346085	NM_020732.3	360	gGc/gCc	1/20	0.845265299927504	3	FACETS	0.899	0.759	1	0.45	0.379	0.525	CLONAL	1	TRUE	1	0.845265299927504	3		67	146	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0018058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	551	471	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.893148433204442	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.893148433204442	1		471	678	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1039264	1039264	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1262	94	553	0	ENST00000358495.3:c.233T>A	p.Met78Lys	p.M78K	ENST00000358495	NM_134424.2	78	aTg/aAg	4/12	1	2	FACETS	0.155	0.137	0.175	0.155	0.137	0.175	SUBCLONAL	1	TRUE	1	0.893148433204442	2		553	1356	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955417	48955418	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0018058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	563	340	0	ENST00000267163.4:c.1534_1535del	p.Leu512ValfsTer10	p.L512Vfs*10	ENST00000267163	NM_000321.2	511	gaTTtg/gatg	17/27	0.893148433204442	2	FACETS	0.983	0.965	1	0.983	0.965	1	CLONAL	2	TRUE	0	0.893148433204442	2		340	641	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028639	12028639	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	374	346	0	ENST00000353533.5:c.842del	p.Arg281HisfsTer37	p.R281Hfs*37	ENST00000353533	NM_003010.3	281	cGa/ca	8/11	0.893148433204442	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.893148433204442	1		346	456	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260271	10260271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	504	482	2	ENST00000340748.4:c.2396C>T	p.Ala799Val	p.A799V	ENST00000340748		799	gCt/gTt	25/40	1	2	FACETS	0.988	0.949	1	0.988	0.949	1	CLONAL	1	TRUE	1	0.893148433204442	2		484	1142	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281476	198281476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	324	335	0	ENST00000335508.6:c.655G>A	p.Asp219Asn	p.D219N	ENST00000335508	NM_012433.2	219	Gat/Aat	6/25	1	2	FACETS	0.902	0.857	0.949	0.902	0.857	0.949	CLONAL	1	TRUE	1	0.893148433204442	2		335	804	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038203	30038203	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	71	411	0	ENST00000338641.4:c.376A>C	p.Ile126Leu	p.I126L	ENST00000338641	NM_000268.3	126	Att/Ctt	4/16	0.449302671801254	1	FACETS	0.106	0.091	0.121	0.106	0.091	0.121	INDETERMINATE	1	TRUE	0	0.893148433204442	1		411	834	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139265	37139265	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	187	231	0	ENST00000373509.5:c.605A>G	p.Asp202Gly	p.D202G	ENST00000373509	NM_002648.3	202	gAt/gGt	4/6	0.407936742284158	1	FACETS	0.498	0.465	0.532	0.498	0.465	0.532	INDETERMINATE	1	TRUE	0	0.893148433204442	1		231	465	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538892	23538892	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	287	363	0	ENST00000380871.4:c.547C>A	p.Gln183Lys	p.Q183K	ENST00000380871	NM_006167.3	183	Cag/Aag	2/2	0.223519052710559	1	FACETS	0.48	0.454	0.507	0.48	0.454	0.507	INDETERMINATE	1	TRUE	0	0.893148433204442	1		363	741	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8339000	8339000	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	400	480	1	ENST00000356435.5:c.5301G>T	p.Gln1767His	p.Q1767H	ENST00000356435		1767	caG/caT	32/35	1	2	FACETS	0.944	0.901	0.987	0.944	0.901	0.987	CLONAL	1	TRUE	1	0.893148433204442	2		481	949	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426720	121426721	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	C	novel	NA	P-0018058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	691	687	0	ENST00000257555.6:c.411_412delinsC	p.Gly138AlafsTer17	p.G138Afs*17	ENST00000257555		137	acTGgc/acCgc	2/10	0.493687562305593	1	FACETS	0.694	0.673	0.715	0.694	0.673	0.715	INDETERMINATE	1	TRUE	0	0.893148433204442	1		687	1234	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0018060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	214	306	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		306	741	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0018062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	162	916	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.439	0.403	0.477	0.439	0.403	0.477	SUBCLONAL	1	TRUE	1	0.939333954333373	2		916	785	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0018062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	83	292	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	0.431	0.382	0.483	0.431	0.382	0.483	SUBCLONAL	1	TRUE	1	0.939333954333373	2		292	410	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0018062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	73	127	1	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.465	0.41	0.524	0.465	0.41	0.524	SUBCLONAL	1	TRUE	1	0.939333954333373	2		128	334	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981721	101981721	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555075353	NA	P-0018062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	84	258	0	ENST00000282441.5:c.147del	p.Ala50ProfsTer24	p.A50Pfs*24	ENST00000282441	NM_001130145.2	48	Ccc/cc	1/9	1	2	FACETS	0.367	0.325	0.412	0.367	0.325	0.412	SUBCLONAL	1	TRUE	1	0.939333954333373	2		258	487	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690821	89690821	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs1554897866	NA	P-0018062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	78	379	0	ENST00000371953.3:c.228T>G	p.Tyr76Ter	p.Y76*	ENST00000371953	NM_000314.4	76	taT/taG	4/9	1	2	FACETS	0.48	0.425	0.538	0.48	0.425	0.538	SUBCLONAL	1	TRUE	1	0.939333954333373	2		379	346	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743758	46743760	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	novel	NA	P-0018062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	93	515	0	ENST00000371975.4:c.2050_2052del	p.Cys684del	p.C684del	ENST00000371975	NM_003579.3	683	cGTTgt/cgt	18/18	1	2	FACETS	0.201	0.178	0.226	0.201	0.178	0.226	SUBCLONAL	1	TRUE	1	0.939333954333373	2		515	983	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624296	89624296	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786201995	NA	P-0018062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	167	490	0	ENST00000371953.3:c.70G>T	p.Asp24Tyr	p.D24Y	ENST00000371953	NM_000314.4	24	Gac/Tac	1/9	1	2	FACETS	0.454	0.417	0.491	0.454	0.417	0.491	SUBCLONAL	1	TRUE	1	0.939333954333373	2		490	784	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082361	16082361	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	293	670	1	ENST00000281043.3:c.175C>A	p.Pro59Thr	p.P59T	ENST00000281043	NM_005378.4	59	Ccc/Acc	2/3	1	2	FACETS	0.502	0.472	0.533	0.502	0.472	0.533	SUBCLONAL	1	TRUE	1	0.939333954333373	2		671	1243	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018245	48018245	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	149	359	0	ENST00000234420.5:c.440T>C	p.Leu147Pro	p.L147P	ENST00000234420	NM_000179.2	147	cTt/cCt	2/10	1	2	FACETS	0.418	0.382	0.455	0.418	0.382	0.455	SUBCLONAL	1	TRUE	1	0.939333954333373	2		359	759	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610468	215610468	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	70	431	0	ENST00000260947.4:c.1788del	p.Lys596AsnfsTer9	p.K596Nfs*9	ENST00000260947	NM_000465.2	596	aaA/aa	8/11	1	2	FACETS	0.272	0.238	0.31	0.272	0.238	0.31	SUBCLONAL	1	TRUE	1	0.939333954333373	2		431	547	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188386	142188386	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	72	346	0	ENST00000350721.4:c.6345G>A	p.Met2115Ile	p.M2115I	ENST00000350721	NM_001184.3	2115	atG/atA	38/47	1	2	FACETS	0.404	0.355	0.457	0.404	0.355	0.457	SUBCLONAL	1	TRUE	1	0.939333954333373	2		346	379	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161349	185161349	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	110	493	0	ENST00000265026.3:c.776G>A	p.Trp259Ter	p.W259*	ENST00000265026	NM_004721.4	259	tGg/tAg	4/14	1	2	FACETS	0.277	0.249	0.308	0.277	0.249	0.308	SUBCLONAL	1	TRUE	1	0.939333954333373	2		493	844	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576424	67576424	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	119	357	0	ENST00000274335.5:c.703C>T	p.Gln235Ter	p.Q235*	ENST00000274335		235	Cag/Tag	5/15	1	2	FACETS	0.499	0.452	0.547	0.499	0.452	0.547	SUBCLONAL	1	TRUE	1	0.939333954333373	2		357	508	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020413	69020413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264802668	NA	P-0018062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	188	537	0	ENST00000288368.4:c.2785C>T	p.His929Tyr	p.H929Y	ENST00000288368	NM_024870.2	929	Cac/Tac	24/40	1	2	FACETS	0.497	0.46	0.536	0.497	0.46	0.536	SUBCLONAL	1	TRUE	1	0.939333954333373	2		537	805	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080630	5080630	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs561801024	NA	P-0018062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	118	425	0	ENST00000381652.3:c.2381T>C	p.Phe794Ser	p.F794S	ENST00000381652	NM_004972.3	794	tTc/tCc	18/25	1	2	FACETS	0.494	0.447	0.542	0.494	0.447	0.542	SUBCLONAL	1	TRUE	1	0.939333954333373	2		425	509	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	201	685	0	ENST00000347630.2:c.399C>A	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttA	6/11	1	2	FACETS	0.871	0.812	0.931	0.871	0.812	0.931	CLONAL	1	TRUE	1	0.764301246697102	2		685	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577129	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519986	NA	P-0018068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	563	808	0	ENST00000269305.4:c.809T>C	p.Phe270Ser	p.F270S	ENST00000269305	NM_001126112.2	270	tTt/tCt	8/11	0.735276089547288	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.764301246697102	2		808	716	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264271	46264271	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	118	412	0	ENST00000371998.3:c.1318G>T	p.Ala440Ser	p.A440S	ENST00000371998		440	Gct/Tct	11/23	1	2	FACETS	0.983	0.9	1	0.983	0.9	1	CLONAL	1	TRUE	1	0.764301246697102	2		412	314	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411774	63411774	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	197	459	0	ENST00000330258.3:c.1393C>T	p.Pro465Ser	p.P465S	ENST00000330258	NM_152424.3	465	Ccc/Tcc	2/2	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.764301246697102	1		459	272	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579491	7579491	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	157	928	1	ENST00000269305.4:c.196del	p.Met66CysfsTer57	p.M66Cfs*57	ENST00000269305	NM_001126112.2	66	Atg/tg	4/11	0.313753885718428	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.328577302454264	1		929	760	SUCCESS
REL	5966	MSKCC	GRCh37	2	61128191	61128191	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	116	557	0	ENST00000295025.8:c.367A>G	p.Ile123Val	p.I123V	ENST00000295025	NM_002908.2	123	Ata/Gta	4/11	1	2	FACETS	0.979	0.883	1	0.979	0.883	1	CLONAL	1	TRUE	1	0.328577302454264	2		557	721	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147552	47147552	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	104	732	1	ENST00000409792.3:c.4774C>G	p.Arg1592Gly	p.R1592G	ENST00000409792	NM_014159.6	1592	Cga/Gga	6/21	0.313753885718428	1	FACETS	0.927	0.832	1	0.927	0.832	1	CLONAL	1	TRUE	0	0.328577302454264	1		733	571	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971307	13971307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771410991	NA	P-0018069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	92	557	1	ENST00000405192.2:c.622C>T	p.Arg208Cys	p.R208C	ENST00000405192	NM_001163147.1	208	Cgt/Tgt	8/12	0.328577302454264	3	FACETS	0.941	0.836	1	0.47	0.418	0.526	CLONAL	1	TRUE	1	0.328577302454264	3		558	693	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835596	68835596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587783047	NA	P-0018071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	207	599	0	ENST00000261769.5:c.187C>T	p.Arg63Ter	p.R63*	ENST00000261769	NM_004360.3	63	Cga/Tga	3/16	0.561166253466866	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	0	0.561166253466866	1		599	513	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913471	NA	P-0018071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	221	767	2	ENST00000269571.5:c.2329G>C	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ctg	20/27	1	2	FACETS	0.941	0.878	1	0.941	0.878	1	CLONAL	1	FALSE	1	0.561166253466866	2		769	837	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226549745	226549745	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767540769	NA	P-0018071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	282	656	0	ENST00000366794.5:c.2888G>A	p.Ser963Asn	p.S963N	ENST00000366794	NM_001618.3	963	aGt/aAt	22/23	0.205315859475959	2	FACETS	1	0.981	1	0.548	0.516	0.581	INDETERMINATE	1	FALSE	0	0.561166253466866	2		656	917	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120823	115120838	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCAGGGCGCCCGGC	GGCCAGGGCGCCCGGC	-	novel	NA	P-0018071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	139	393	0	ENST00000257566.3:c.168_183del	p.Pro57SerfsTer26	p.P57Sfs*26	ENST00000257566	NM_016569.3	56	ctGCCGGGCGCCCTGGCC/ct	1/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.561166253466866	2		393	426	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281463	142281463	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	281	857	0	ENST00000350721.4:c.781C>G	p.Leu261Val	p.L261V	ENST00000350721	NM_001184.3	261	Cta/Gta	4/47	0.561166253466866	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	0	0.561166253466866	1		857	712	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526210	31526210	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	242	841	0	ENST00000344624.3:c.830G>T	p.Arg277Leu	p.R277L	ENST00000344624		277	cGc/cTc	2/33	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	1	0.561166253466866	2		841	859	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0018073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	76	523	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.853	0.749	0.965	0.853	0.749	0.965	CLONAL	1	FALSE	1	0.3	2		523	594	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984744	11984745	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0018073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	56	387	0	ENST00000353533.5:c.292_293dup	p.Ala99LeufsTer5	p.A99Lfs*5	ENST00000353533	NM_003010.3	97	ttc/ttCAc	3/11	0.260780882261311	1	FACETS	0.826	0.711	0.952	0.826	0.711	0.952	CLONAL	1	FALSE	0	0.3	1		387	384	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983743	15983743	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	82	487	1	ENST00000268712.3:c.3379C>T	p.Gln1127Ter	p.Q1127*	ENST00000268712	NM_006311.3	1127	Caa/Taa	25/46	0.260780882261311	1	FACETS	0.966	0.855	1	0.966	0.855	1	CLONAL	1	FALSE	0	0.3	1		488	481	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069363	30069363	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1556000842	NA	P-0018074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	70	676	1	ENST00000338641.4:c.1228C>T	p.Gln410Ter	p.Q410*	ENST00000338641	NM_000268.3	410	Cag/Tag	12/16	0.350364512425806	1	FACETS	0.577	0.503	0.656	0.577	0.503	0.656	SUBCLONAL	1	TRUE	0	0.365395337683934	1		677	543	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058646	47058646	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	102	868	0	ENST00000409792.3:c.7632del	p.Lys2545ArgfsTer19	p.K2545Rfs*19	ENST00000409792	NM_014159.6	2544	atT/at	21/21	0.350364512425806	1	FACETS	0.617	0.552	0.687	0.617	0.552	0.687	SUBCLONAL	1	TRUE	0	0.365395337683934	1		868	739	SUCCESS
APC	324	MSKCC	GRCh37	5	112173525	112173525	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	68	546	2	ENST00000257430.4:c.2234C>A	p.Pro745His	p.P745H	ENST00000257430	NM_000038.5	745	cCt/cAt	16/16	1	2	FACETS	0.833	0.727	0.947	0.833	0.727	0.947	CLONAL	1	TRUE	1	0.365395337683934	2		548	447	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	431	918	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.731815940870069	3	FACETS	0.98	0.941	1	0.98	0.941	1	CLONAL	2	TRUE	1	0.731815940870069	3		918	821	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0018075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	224	640	0	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	1	2	FACETS	0.961	0.9	1	0.961	0.9	1	CLONAL	1	TRUE	1	0.731815940870069	2		640	637	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057520005	NA	P-0018075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	514	908	0	ENST00000269305.4:c.820G>T	p.Val274Phe	p.V274F	ENST00000269305	NM_001126112.2	274	Gtt/Ttt	8/11	0.712564141972079	2	FACETS	0.978	0.95	1	0.978	0.95	1	CLONAL	2	TRUE	0	0.731815940870069	2		908	718	SUCCESS
APC	324	MSKCC	GRCh37	5	112175438	112175439	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0018075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	165	371	0	ENST00000257430.4:c.4147_4148del	p.Met1383ValfsTer2	p.M1383Vfs*2	ENST00000257430	NM_000038.5	1383	ATg/g	16/16	0.151027510564409	1	FACETS	1	0.974	1	1	0.974	1	INDETERMINATE	1	TRUE	0	0.731815940870069	1		371	269	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259406	16259406	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs765138549	NA	P-0018075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	149	488	0	ENST00000375759.3:c.6671A>G	p.Asn2224Ser	p.N2224S	ENST00000375759	NM_015001.2	2224	aAt/aGt	11/15	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.731815940870069	2		488	405	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625105	69625105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs782612620	NA	P-0018075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	161	549	0	ENST00000334134.2:c.688C>G	p.Leu230Val	p.L230V	ENST00000334134	NM_005247.2	230	Ctg/Gtg	3/3	0.702520095946329	3	FACETS	0.969	0.893	1	0.323	0.297	0.35	CLONAL	1	TRUE	0	0.731815940870069	3		549	620	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001964	29001964	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	217	646	1	ENST00000282397.4:c.1201G>T	p.Gly401Trp	p.G401W	ENST00000282397	NM_002019.4	401	Ggg/Tgg	9/30	0.696776998477039	5	FACETS	1	0.963	1	0.264	0.245	0.284	CLONAL	1	TRUE	1	0.731815940870069	5		647	1177	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0018076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	154	756	1	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.458740285978723	1	FACETS	0.989	0.911	1	0.989	0.911	1	CLONAL	1	TRUE	0	0.458740285978723	1		757	523	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259460	11259460	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	133	531	0	ENST00000361445.4:c.4108G>T	p.Gly1370Cys	p.G1370C	ENST00000361445	NM_004958.3	1370	Ggc/Tgc	28/58	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.458740285978723	2		531	509	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16247389	16247389	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	83	378	1	ENST00000375759.3:c.1660A>G	p.Met554Val	p.M554V	ENST00000375759	NM_015001.2	554	Atg/Gtg	9/15	1	2	FACETS	0.991	0.881	1	0.991	0.881	1	CLONAL	1	TRUE	1	0.458740285978723	2		379	365	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100790	8100790	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	142	671	0	ENST00000346208.3:c.764C>T	p.Ala255Val	p.A255V	ENST00000346208		255	gCc/gTc	3/6	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.458740285978723	2		671	605	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999099	100999099	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	144	830	0	ENST00000325455.5:c.703C>G	p.Pro235Ala	p.P235A	ENST00000325455	NM_001202474.3	235	Ccg/Gcg	1/8	1	2	FACETS	0.979	0.896	1	0.979	0.896	1	CLONAL	1	TRUE	1	0.458740285978723	2		830	641	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961904	15961904	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	80	399	0	ENST00000268712.3:c.5891A>G	p.His1964Arg	p.H1964R	ENST00000268712	NM_006311.3	1964	cAc/cGc	38/46	0.458740285978723	1	FACETS	0.977	0.871	1	0.977	0.871	1	CLONAL	1	TRUE	0	0.458740285978723	1		399	275	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953903	17953903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs973863737	NA	P-0018076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	175	857	1	ENST00000458235.1:c.499G>A	p.Val167Met	p.V167M	ENST00000458235	NM_000215.3	167	Gtg/Atg	5/24	0.458740285978723	3	FACETS	1	0.966	1	0.542	0.499	0.587	CLONAL	1	TRUE	1	0.458740285978723	3		858	865	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172252	99172252	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	144	738	0	ENST00000074304.5:c.1818C>G	p.Cys606Trp	p.C606W	ENST00000074304	NM_001134224.1	606	tgC/tgG	17/26	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.458740285978723	2		738	604	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249512	153249518	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTGTA	ACCTGTA	-	novel	NA	P-0018076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	136	649	0	ENST00000281708.4:c.1260_1266del	p.His420GlnfsTer8	p.H420Qfs*8	ENST00000281708	NM_033632.3	420	caTACAGGT/ca	9/12	1	2	FACETS	0.822	0.749	0.899	0.822	0.749	0.899	CLONAL	1	TRUE	1	0.458740285978723	2		649	721	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524960	187524960	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	137	689	0	ENST00000441802.2:c.10720G>T	p.Val3574Leu	p.V3574L	ENST00000441802	NM_005245.3	3574	Gtg/Ttg	19/27	1	2	FACETS	0.982	0.897	1	0.982	0.897	1	CLONAL	1	TRUE	1	0.458740285978723	2		689	608	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642491	117642491	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	222	799	0	ENST00000368508.3:c.5708A>G	p.Asp1903Gly	p.D1903G	ENST00000368508	NM_002944.2	1903	gAc/gGc	35/43	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.458740285978723	2		799	765	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209421	98209421	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	81	548	3	ENST00000331920.6:c.4117G>C	p.Ala1373Pro	p.A1373P	ENST00000331920	NM_000264.3	1373	Gct/Cct	23/24	0.458740285978723	1	FACETS	0.895	0.797	0.998	0.895	0.797	0.998	CLONAL	1	TRUE	0	0.458740285978723	1		551	304	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0018077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	66	393	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.291265034946435	3	FACETS	1	0.964	1	0.65	0.569	0.737	CLONAL	1	TRUE	1	0.394618860078312	3		393	308	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0018077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	202	1080	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.264811825347522	2	FACETS	1	0.988	1	0.657	0.61	0.705	CLONAL	1	TRUE	0	0.394618860078312	2		1080	779	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720726	89720726	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs878853944	NA	P-0018077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	57	222	1	ENST00000371953.3:c.877G>T	p.Gly293Ter	p.G293*	ENST00000371953	NM_000314.4	293	Gga/Tga	8/9	0.394618860078312	3	FACETS	0.854	0.754	0.957	0.854	0.754	0.957	CLONAL	3	TRUE	0	0.394618860078312	3		223	135	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8111119	8111119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747826611	NA	P-0018077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	70	707	0	ENST00000585124.1:c.88C>T	p.Arg30Trp	p.R30W	ENST00000585124	NM_004217.3	30	Cgg/Tgg	3/9	0.264811825347522	2	FACETS	0.771	0.674	0.875	0.386	0.337	0.438	SUBCLONAL	1	TRUE	0	0.394618860078312	2		707	460	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743913	40743913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375441200	NA	P-0018077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	147	756	1	ENST00000373198.4:c.3082G>A	p.Gly1028Arg	p.G1028R	ENST00000373198	NM_133170.3	1028	Gga/Aga	23/32	0.226696391131073	4	FACETS	0.826	0.757	0.898	0.826	0.757	0.898	INDETERMINATE	2	TRUE	2	0.394618860078312	4		757	629	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591147	67591148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0018077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	92	514	0	ENST00000274335.5:c.1741_1742dup	p.Leu581PhefsTer2	p.L581Ffs*2	ENST00000274335		580	-/TT	12/15	0.264811825347522	2	FACETS	1	0.979	1	0.696	0.624	0.771	CLONAL	1	TRUE	0	0.394618860078312	2		514	335	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399398	139399398	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771357343	NA	P-0018077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	100	907	2	ENST00000277541.6:c.4745C>T	p.Pro1582Leu	p.P1582L	ENST00000277541	NM_017617.3	1582	cCg/cTg	26/34	1	2	FACETS	0.852	0.762	0.946	0.852	0.762	0.946	CLONAL	1	TRUE	1	0.394618860078312	2		909	595	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100923	27100946	+	frameshift_variant	Frame_Shift_Del	DEL	AGCAGCAGTTGCCCCCAGCCCAGC	AGCAGCAGTTGCCCCCAGCCCAGC	CCAGT	novel	NA	P-0018077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	139	682	0	ENST00000324856.7:c.4205_4228delinsCCAGT	p.Gln1402ProfsTer73	p.Q1402Pfs*73	ENST00000324856	NM_006015.4	1402	cAGCAGCAGTTGCCCCCAGCCCAGCcc/cCCAGTcc	18/20	0.2795896830111	3	FACETS	0.761	0.696	0.829	0.761	0.696	0.829	SUBCLONAL	2	TRUE	1	0.394618860078312	3		682	554	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0018078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	246	427	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.634859028189113	1	FACETS	0.972	0.918	1	0.972	0.918	1	CLONAL	1	TRUE	0	0.634859028189113	1		427	544	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0018078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	97	368	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.915	0.824	1	0.915	0.824	1	CLONAL	1	TRUE	1	0.634859028189113	2		368	334	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247373	153247373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	182	497	0	ENST00000281708.4:c.1429G>A	p.Gly477Ser	p.G477S	ENST00000281708	NM_033632.3	477	Ggt/Agt	10/12	1	2	FACETS	0.99	0.919	1	0.99	0.919	1	CLONAL	1	TRUE	1	0.634859028189113	2		497	579	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266182	41266182	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	102	452	0	ENST00000349496.5:c.179C>T	p.Ser60Phe	p.S60F	ENST00000349496	NM_001904.3	60	tCc/tTc	3/15	1	2	FACETS	0.754	0.679	0.833	0.754	0.679	0.833	SUBCLONAL	1	TRUE	1	0.634859028189113	2		452	426	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910798	114910798	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	217	652	0	ENST00000543371.1:c.917C>G	p.Thr306Arg	p.T306R	ENST00000543371	NM_001198531.1	306	aCg/aGg	9/14	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.634859028189113	2		652	678	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192630	94192630	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	282	854	0	ENST00000323929.3:c.1444C>T	p.Gln482Ter	p.Q482*	ENST00000323929	NM_005591.3	482	Cag/Tag	13/20	1	2	FACETS	0.966	0.909	1	0.966	0.909	1	CLONAL	1	TRUE	1	0.634859028189113	2		854	920	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749329	43749329	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	266	801	0	ENST00000382044.4:c.1477G>T	p.Glu493Ter	p.E493*	ENST00000382044	NM_001141980.1	493	Gag/Tag	12/28	1	2	FACETS	0.987	0.928	1	0.987	0.928	1	CLONAL	1	TRUE	1	0.634859028189113	2		801	849	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346015	152346025	+	frameshift_variant	Frame_Shift_Del	DEL	ATTTACAAGCT	ATTTACAAGCT	-	novel	NA	P-0018079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	210	617	1	ENST00000359321.1:c.545_555del	p.Lys182ArgfsTer33	p.K182Rfs*33	ENST00000359321	NM_005431.1	182	aAGCTTGTAAAT/a	3/3	1	2	FACETS	1	0.982	1	1	0.995	1	CLONAL	3	TRUE	1	0.2	2		618	614	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0018081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	99	667	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.323434266930883	1	FACETS	0.848	0.76	0.942	0.848	0.76	0.942	CLONAL	1	TRUE	0	0.360969320287986	1		668	530	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0018081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	476	455	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.360969320287986	5	FACETS	0.985	0.945	1	0.985	0.945	1	CLONAL	4	TRUE	1	0.360969320287986	5		455	1032	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0018081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	132	695	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.360969320287986	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.360969320287986	1		695	545	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258593	16258593	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	47	548	1	ENST00000375759.3:c.5858C>A	p.Pro1953His	p.P1953H	ENST00000375759	NM_015001.2	1953	cCt/cAt	11/15	0.259304288744964	3	FACETS	0.446	0.375	0.524	0.223	0.187	0.262	SUBCLONAL	1	TRUE	1	0.360969320287986	3		549	689	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528071	103528071	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	45	569	0	ENST00000355739.4:c.3379T>G	p.Ser1127Ala	p.S1127A	ENST00000355739	NM_000123.3	1127	Tca/Gca	15/15	0.360969320287986	1	FACETS	0.468	0.393	0.55	0.468	0.393	0.55	SUBCLONAL	1	TRUE	0	0.360969320287986	1		569	437	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467208	25467208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0018081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	187	526	0	ENST00000264709.3:c.1668-1G>T		p.X556_splice	ENST00000264709	NM_175629.2	556			0.360969320287986	3	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	1	0.360969320287986	3		526	595	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991524	72991524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	79	531	1	ENST00000268489.5:c.2521C>T	p.Gln841Ter	p.Q841*	ENST00000268489	NM_006885.3	841	Cag/Tag	2/10	1	2	FACETS	0.984	0.865	1	0.984	0.865	1	CLONAL	1	TRUE	1	0.22015668911719	2		532	729	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549104	21549105	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0018083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	58	367	0	ENST00000382592.4:c.3171dup	p.Pro1058AlafsTer10	p.P1058Afs*10	ENST00000382592	NM_014572.2	1057	-/G	8/8	0.184844756066774	1	FACETS	0.981	0.844	1	0.981	0.844	1	CLONAL	1	TRUE	0	0.22015668911719	1		367	478	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579369	7579369	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555526581	NA	P-0018084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	81	565	0	ENST00000269305.4:c.318C>G	p.Ser106Arg	p.S106R	ENST00000269305	NM_001126112.2	106	agC/agG	4/11	0.46638498743062	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.46638498743062	1		565	178	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160489	108160489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749770110	NA	P-0018084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	56	389	0	ENST00000278616.4:c.4397G>A	p.Arg1466Gln	p.R1466Q	ENST00000278616	NM_000051.3	1466	cGa/cAa	29/63	1	2	FACETS	0.934	0.808	1	0.934	0.808	1	CLONAL	1	TRUE	1	0.46638498743062	2		389	257	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727455	66727455	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs869025608	NA	P-0018084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	35	630	2	ENST00000307102.5:c.171G>T	p.Lys57Asn	p.K57N	ENST00000307102	NM_002755.3	57	aaG/aaT	2/11	1	2	FACETS	0.718	0.594	0.855	0.718	0.594	0.855	SUBCLONAL	1	TRUE	1	0.46638498743062	2		632	209	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214591	5214591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770889503	NA	P-0018084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	54	532	1	ENST00000357368.4:c.4475G>A	p.Arg1492Gln	p.R1492Q	ENST00000357368	NM_002850.3	1492	cGg/cAg	29/38	0.157194667064561	0	FACETS	0.679	0.59	0.773			1	INDETERMINATE	1	TRUE	0	0.46638498743062	0		533	182	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285221	198285221	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	40	503	0	ENST00000335508.6:c.346del	p.Glu116LysfsTer11	p.E116Kfs*11	ENST00000335508	NM_012433.2	116	Gaa/aa	4/25	1	2	FACETS	0.689	0.576	0.812	0.689	0.576	0.812	SUBCLONAL	1	TRUE	1	0.46638498743062	2		503	249	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149238642	149238642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	31	444	0	ENST00000360632.3:c.1153G>A	p.Asp385Asn	p.D385N	ENST00000360632	NM_015472.4	385	Gat/Aat	7/7	1	2	FACETS	0.624	0.508	0.753	0.624	0.508	0.753	SUBCLONAL	1	TRUE	1	0.46638498743062	2		444	213	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129096	152129096	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	56	632	0	ENST00000206249.3:c.49C>T	p.Gln17Ter	p.Q17*	ENST00000206249	NM_000125.3	17	Cag/Tag	1/8	0.107269937811727	4	FACETS	0.872	0.758	0.992	0.872	0.758	0.992	INDETERMINATE	2	TRUE	2	0.46638498743062	4		632	202	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303662	65303662	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	225	547	0	ENST00000342505.4:c.3093T>A	p.Asp1031Glu	p.D1031E	ENST00000342505	NM_002227.2	1031	gaT/gaA	22/25	0.252436751625164	0	FACETS	0.768	0.725	0.81			1	SUBCLONAL	4	FALSE	0	0.252906885108977	0		547	433	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339605	70339605	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	33	273	0	ENST00000374080.3:c.274A>G	p.Arg92Gly	p.R92G	ENST00000374080		92	Agg/Ggg	3/45	0.252436751625164	0	FACETS	0.73	0.597	0.878			1	SUBCLONAL	1	FALSE	NA	0.252906885108977	0		273	267	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0018087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	67	455	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.821	0.713	0.938	0.821	0.713	0.938	CLONAL	1	TRUE	1	0.232202608039727	2		455	703	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	384	918	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.646415005150244	3	FACETS	0.949	0.908	0.99	0.949	0.908	0.99	CLONAL	2	TRUE	1	0.697835094715915	3		918	782	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0018088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	110	271	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.911	0.828	0.997	0.911	0.828	0.997	CLONAL	1	TRUE	1	0.697835094715915	2		271	346	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961608	18961645	+	frameshift_variant	Frame_Shift_Del	DEL	CGAGCAGGAGCAGCTGCGGGCACGCCAGATCACGGCAC	CGAGCAGGAGCAGCTGCGGGCACGCCAGATCACGGCAC	AAGATCCCCTCCG	novel	NA	P-0018088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	84	449	3	ENST00000262803.5:c.741_778delinsAAGATCCCCTCCG	p.Glu248ArgfsTer65	p.E248Rfs*65	ENST00000262803	NM_002911.3	247	tcCGAGCAGGAGCAGCTGCGGGCACGCCAGATCACGGCACag/tcAAGATCCCCTCCGag	5/24	1	2	FACETS	0.521	0.462	0.584	0.521	0.462	0.584	SUBCLONAL	1	TRUE	1	0.697835094715915	2		452	462	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961652	18961698	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCAACAAGCTGGAGGAGCTGTGGAAGGTGGGGCTGCCCAGCGGGCCG	TCAACAAGCTGGAGGAGCTGTGGAAGGTGGGGCTGCCCAGCGGGCCG	-	novel	NA	P-0018088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	59	436	0	ENST00000262803.5:c.785_810+21del		p.X262_splice	ENST00000262803	NM_002911.3	262		5/24	1	2	FACETS	0.439	0.379	0.504	0.439	0.379	0.504	SUBCLONAL	1	TRUE	1	0.697835094715915	2		436	385	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0018089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	307	294	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.783099542080197	2		294	734	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750394	133750394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	231	517	1	ENST00000318560.5:c.1225G>A	p.Glu409Lys	p.E409K	ENST00000318560	NM_005157.4	409	Gag/Aag	7/11	0.390262891311216	1	FACETS	0.358	0.333	0.383	0.358	0.333	0.383	INDETERMINATE	1	TRUE	0	0.783099542080197	1		518	1003	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057947	27057947	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0018089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	216	524	0	ENST00000324856.7:c.1655C>G	p.Ser552Ter	p.S552*	ENST00000324856	NM_006015.4	552	tCa/tGa	3/20	0.783099542080197	1	FACETS	0.462	0.431	0.494	0.462	0.431	0.494	SUBCLONAL	1	TRUE	0	0.783099542080197	1		524	727	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476272	88476272	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	488	600	3	ENST00000360948.2:c.1860G>A	p.Met620Ile	p.M620I	ENST00000360948	NM_001012338.2	620	atG/atA	15/19	1	2	FACETS	0.946	0.906	0.987	0.946	0.906	0.987	CLONAL	1	TRUE	1	0.783099542080197	2		603	1317	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851710	63851710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	557	680	2	ENST00000279873.7:c.2488G>A	p.Asp830Asn	p.D830N	ENST00000279873	NM_032199.2	830	Gac/Aac	10/10	0.390262891311216	1	FACETS	0.76	0.732	0.788	0.76	0.732	0.788	INDETERMINATE	1	TRUE	0	0.783099542080197	1		682	1139	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046707	42046707	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	550	562	4	ENST00000219905.7:c.7081G>T	p.Glu2361Ter	p.E2361*	ENST00000219905	NM_001164273.1	2361	Gaa/Taa	18/24	0.783099542080197	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.783099542080197	1		566	835	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823848	3823854	+	frameshift_variant	Frame_Shift_Del	DEL	AGCGGGC	AGCGGGC	-	novel	NA	P-0018089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	410	442	0	ENST00000262367.5:c.2361_2367del	p.Pro788ArgfsTer17	p.P788Rfs*17	ENST00000262367	NM_004380.2	787	gcGCCCGCT/gc	13/31	1	2	FACETS	0.996	0.951	1	0.996	0.951	1	CLONAL	1	TRUE	1	0.783099542080197	2		442	1051	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828186	72828186	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	221	544	0	ENST00000268489.5:c.8395C>T	p.Leu2799Phe	p.L2799F	ENST00000268489	NM_006885.3	2799	Ctt/Ttt	9/10	1	2	FACETS	0.445	0.414	0.479	0.445	0.414	0.479	SUBCLONAL	1	TRUE	1	0.783099542080197	2		544	1267	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526209	63526209	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs768614505	NA	P-0018089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	217	499	0	ENST00000307078.5:c.2417A>G	p.Lys806Arg	p.K806R	ENST00000307078	NM_004655.3	806	aAa/aGa	11/11	1	2	FACETS	0.492	0.457	0.528	0.492	0.457	0.528	SUBCLONAL	1	TRUE	1	0.783099542080197	2		499	1127	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439480	220439480	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	177	439	0	ENST00000243786.2:c.333C>A	p.Phe111Leu	p.F111L	ENST00000243786	NM_002191.3	111	ttC/ttA	2/2	0.390262891311216	1	FACETS	0.386	0.356	0.416	0.386	0.356	0.416	INDETERMINATE	1	TRUE	0	0.783099542080197	1		439	713	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36024667	36024667	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	504	592	0	ENST00000358208.4:c.656C>T	p.Ser219Phe	p.S219F	ENST00000358208		219	tCc/tTc	6/12	1	2	FACETS	0.966	0.925	1	0.966	0.925	1	CLONAL	1	TRUE	1	0.783099542080197	2		592	1333	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808261	99808261	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	393	383	0	ENST00000280892.6:c.428G>A	p.Arg143Gln	p.R143Q	ENST00000280892	NM_001130678.1	143	cGa/cAa	5/7	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.783099542080197	2		383	991	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180915	106180915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	117	310	2	ENST00000380013.4:c.3943G>A	p.Asp1315Asn	p.D1315N	ENST00000380013	NM_001127208.2	1315	Gac/Aac	7/11	NA	2	FACETS	0.421	0.38	0.464			1	INDETERMINATE	1	TRUE	NA	0.783099542080197	2		312	710	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525910	148525910	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	242	608	0	ENST00000320356.2:c.547G>C	p.Asp183His	p.D183H	ENST00000320356	NM_004456.4	183	Gat/Cat	6/20	1	2	FACETS	0.439	0.409	0.471	0.439	0.409	0.471	SUBCLONAL	1	TRUE	1	0.783099542080197	2		608	1407	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828176	72828176	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	197	433	0	ENST00000268489.5:c.8405del	p.Pro2802LeufsTer22	p.P2802Lfs*22	ENST00000268489	NM_006885.3	2802	cCt/ct	9/10	0.663267845533984	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.64	1		433	394	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0018091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	22	281	2	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.53	0.409	0.673	0.53	0.409	0.673	SUBCLONAL	1	TRUE	1	0.09	2		283	922	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0018091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	26	315	0	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	0.833	0.657	1	0.833	0.657	1	CLONAL	1	TRUE	1	0.09	2		315	694	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0018091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	14	334	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	1	2	FACETS	0.474	0.34	0.637	0.474	0.34	0.637	SUBCLONAL	1	TRUE	1	0.09	2		334	657	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0018092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	609	499	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	0.95	0.915	0.985	0.95	0.915	0.985	CLONAL	1	TRUE	1	0.892189409788951	2		499	1437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579408	7579460	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTG	CAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTG	-	rs1555526610	NA	P-0018092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	1012	475	0	ENST00000269305.4:c.227_279del	p.Ala76ValfsTer55	p.A76Vfs*55	ENST00000269305	NM_001126112.2	76	gCACCAGCAGCTCCTACACCGGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTG/g	4/11	NA	2	FACETS	0.829	0.813	0.845			1	INDETERMINATE	2	TRUE	NA	0.892189409788951	2		475	1368	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509084	66509085	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	99	381	0	ENST00000273854.3:c.242dup	p.Asn81LysfsTer8	p.N81Kfs*8	ENST00000273854	NM_004439.5	81	aat/aaAt	2/18	0.474982734235148	1	FACETS	0.315	0.283	0.349	0.315	0.283	0.349	INDETERMINATE	1	TRUE	0	0.892189409788951	1		381	390	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023381	27023381	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	291	247	2	ENST00000324856.7:c.487del	p.Ala163ProfsTer69	p.A163Pfs*69	ENST00000324856	NM_006015.4	163	Gcc/cc	1/20	1	2	FACETS	0.933	0.884	0.983	0.933	0.884	0.983	CLONAL	1	TRUE	1	0.892189409788951	2		249	699	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861825	57861825	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1430036137	NA	P-0018092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	549	483	1	ENST00000228682.2:c.1126C>A	p.Pro376Thr	p.P376T	ENST00000228682	NM_005269.2	376	Cct/Act	10/12	1	2	FACETS	0.97	0.933	1	0.97	0.933	1	CLONAL	1	TRUE	1	0.892189409788951	2		484	1269	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158476	26158476	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs776467875	NA	P-0018093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	63	471	1	ENST00000289316.2:c.79G>T	p.Gly27Trp	p.G27W	ENST00000289316	NM_138720.2	27	Ggg/Tgg	1/2	0.114128022614191	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		472	753	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0018094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	33	710	5	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.357	0.289	0.434	0.357	0.289	0.434	SUBCLONAL	1	TRUE	1	0.2	2		715	925	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0018095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	193	1001	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.254921843408399	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.254921843408399	1		1001	1148	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0018095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	2215	668	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.254921843408399	21	FACETS	1	0.994	1			1	CLONAL	19	TRUE	NA	0.254921843408399	21		668	3088	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101909953	101909953	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	63	202	0	ENST00000374994.4:c.1273C>T	p.Gln425Ter	p.Q425*	ENST00000374994	NM_004612.2	425	Caa/Taa	8/9	0.254921843408399	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.254921843408399	1		202	394	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971053	21971053	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137854598	NA	P-0018095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	108	343	0	ENST00000304494.5:c.305C>T	p.Ala102Val	p.A102V	ENST00000304494	NM_000077.4	102	gCg/gTg	2/3	0.202500225970525	0	FACETS	1	0.953	1			1	CLONAL	1	TRUE	0	0.254921843408399	0		343	573	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117173	7117173	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764041031	NA	P-0018095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	41	466	0	ENST00000302850.5:c.4043C>T	p.Ser1348Leu	p.S1348L	ENST00000302850	NM_000208.2	1348	tCg/tTg	22/22	0.204134701842833	1	FACETS	0.35	0.29	0.417	0.35	0.29	0.417	SUBCLONAL	1	TRUE	0	0.254921843408399	1		466	802	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0018096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	109	294	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.391915752342742	3	FACETS	1	0.964	1	0.575	0.518	0.636	CLONAL	1	TRUE	1	0.391915752342742	3		294	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0018096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	501	801	17	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.391915752342742	2	FACETS	0.836	0.804	0.867	1	0.995	1	CLONAL	3	TRUE	0	0.391915752342742	2		818	1020	SUCCESS
APC	324	MSKCC	GRCh37	5	112174096	112174096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs137854575	NA	P-0018096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	200	310	0	ENST00000257430.4:c.2805C>A	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	taC/taA	16/16	0.391915752342742	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.391915752342742	2		310	447	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135247	2135247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769834772	NA	P-0018096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	172	564	1	ENST00000219476.3:c.4586G>A	p.Arg1529Gln	p.R1529Q	ENST00000219476	NM_000548.3	1529	cGg/cAg	36/42	0.391915752342742	2	FACETS	0.911	0.838	0.988	0.456	0.419	0.494	CLONAL	1	TRUE	0	0.391915752342742	2		565	963	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274794	123274794	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913478	NA	P-0018098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	322	647	0	ENST00000358487.5:c.1124A>G	p.Tyr375Cys	p.Y375C	ENST00000358487	NM_000141.4	375	tAc/tGc	9/18	0.298627153384	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.31	2		647	858	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712011	89712012	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0018098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	62	242	0	ENST00000371953.3:c.630_631dup	p.Cys211PhefsTer11	p.C211Ffs*11	ENST00000371953	NM_000314.4	210	act/acTTt	6/9	0.298627153384	2	FACETS	0.772	0.674	0.876	0.772	0.674	0.876	SUBCLONAL	2	TRUE	0	0.31	2		242	259	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253983	133253983	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	215	751	0	ENST00000320574.5:c.767A>G	p.Glu256Gly	p.E256G	ENST00000320574	NM_006231.2	256	gAa/gGa	8/49	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.31	2		751	1130	SUCCESS
APC	324	MSKCC	GRCh37	5	112175687	112175687	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	236	426	2	ENST00000257430.4:c.4396G>T	p.Gly1466Ter	p.G1466*	ENST00000257430	NM_000038.5	1466	Gga/Tga	16/16	0.545271596938339	2	FACETS	0.972	0.921	1	0.972	0.921	1	CLONAL	2	TRUE	0	0.570086529820919	2		428	426	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220476	1220476	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	582	719	0	ENST00000326873.7:c.569T>C	p.Leu190Pro	p.L190P	ENST00000326873	NM_000455.4	190	cTc/cCc	4/10	0.38396087797694	4	FACETS	1	0.995	1			1	CLONAL	3	TRUE	NA	0.570086529820919	4		719	949	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118361952	118361952	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	163	253	0	ENST00000534358.1:c.4738G>C	p.Asp1580His	p.D1580H	ENST00000534358	NM_005933.3	1580	Gac/Cac	14/36	0.573600015263715	4	FACETS	0.898	0.83	0.967	0.898	0.83	0.967	CLONAL	2	TRUE	2	0.570086529820919	4		253	500	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686994	37686994	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769197936	NA	P-0018099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	443	483	0	ENST00000447079.4:c.3898G>A	p.Ala1300Thr	p.A1300T	ENST00000447079	NM_015083.1	1300	Gcc/Acc	14/14	0.570086529820919	7	FACETS	0.982	0.941	1			1	CLONAL	4	TRUE	NA	0.570086529820919	7		483	960	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211104	2211104	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	193	772	1	ENST00000398665.3:c.1358A>T	p.Tyr453Phe	p.Y453F	ENST00000398665	NM_032482.2	453	tAc/tTc	15/28	0.38396087797694	4	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.570086529820919	4		773	807	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46587815	46587815	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1267730152	NA	P-0018099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	262	481	0	ENST00000263734.3:c.493G>C	p.Glu165Gln	p.E165Q	ENST00000263734	NM_001430.4	165	Gag/Cag	5/16	0.573600015263715	4	FACETS	0.88	0.827	0.934	0.44	0.413	0.467	CLONAL	2	TRUE	0	0.570086529820919	4		481	820	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520112	9520112	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	79	254	0	ENST00000353224.5:c.2157C>G	p.His719Gln	p.H719Q	ENST00000353224	NM_177990.2	719	caC/caG	10/10	0.16988669854923	5	FACETS	1	0.958	1			1	INDETERMINATE	2	TRUE	NA	0.570086529820919	5		254	225	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866314	42866328	+	inframe_deletion	In_Frame_Del	DEL	GGGCTGCGTGCAGAC	GGGCTGCGTGCAGAC	-	novel	NA	P-0018099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	114	510	0	ENST00000398585.3:c.304_318del	p.Val102_Pro106del	p.V102_P106del	ENST00000398585	NM_001135099.1	102	GTCTGCACGCAGCCC/-	3/14	0.573600015263715	3	FACETS	0.813	0.734	0.897	0.407	0.367	0.449	CLONAL	1	TRUE	1	0.570086529820919	3		510	632	SUCCESS
APC	324	MSKCC	GRCh37	5	112175139	112175139	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	137	232	0	ENST00000257430.4:c.3848C>T	p.Ala1283Val	p.A1283V	ENST00000257430	NM_000038.5	1283	gCt/gTt	16/16	0.545271596938339	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	0	0.570086529820919	2		232	238	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012257	152012257	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	119	412	0	ENST00000262189.6:c.556A>C	p.Asn186His	p.N186H	ENST00000262189	NM_170606.2	186	Aac/Cac	4/59	0.573600015263715	4	FACETS	0.87	0.786	0.959	0.29	0.262	0.32	CLONAL	1	TRUE	1	0.570086529820919	4		412	753	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932240	39932240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	192	885	1	ENST00000378444.4:c.2359C>T	p.Pro787Ser	p.P787S	ENST00000378444	NM_001123385.1	787	Ccg/Tcg	4/15	0.424421672729434	3	FACETS	1	0.932	1			1	CLONAL	1	TRUE	NA	0.570086529820919	3		886	860	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0018101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	103	464	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.975	0.874	1	0.975	0.874	1	CLONAL	1	TRUE	1	0.324441839440464	2		464	651	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0018101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	289	710	5	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.324441839440464	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.324441839440464	2		715	810	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0018101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	152	843	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.239239930155979	1	FACETS	0.816	0.746	0.89	0.816	0.746	0.89	CLONAL	1	TRUE	0	0.324441839440464	1		843	962	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143994	11143994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	195	466	0	ENST00000358026.2:c.3575G>A	p.Arg1192His	p.R1192H	ENST00000358026	NM_001128849.1	1192	cGc/cAc	26/36	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.324441839440464	2		466	910	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251907	153251907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	143	412	0	ENST00000281708.4:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000281708	NM_033632.3	367	Cga/Tga	7/12	0.17196243299415	3	FACETS	0.847	0.775	0.921			1	INDETERMINATE	2	TRUE	NA	0.324441839440464	3		412	605	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920404	114920404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	134	480	0	ENST00000543371.1:c.1345G>A	p.Ala449Thr	p.A449T	ENST00000543371	NM_001198531.1	449	Gca/Aca	13/14	0.239239930155979	1	FACETS	0.821	0.746	0.9	0.821	0.746	0.9	CLONAL	1	TRUE	0	0.324441839440464	1		480	843	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0018102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	608	741	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.496511670910885	3	FACETS	0.989	0.958	1	0.989	0.958	1	CLONAL	3	TRUE	0	0.496738927076599	3		741	1030	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0018102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	134	306	0				ENST00000310581	NM_198253.2	-/1132			0.426669060188855	3	FACETS	0.926	0.843	1			1	CLONAL	1	TRUE	NA	0.496738927076599	3		306	727	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339500	116339500	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	308	254	0	ENST00000397752.3:c.362T>G	p.Val121Gly	p.V121G	ENST00000397752	NM_000245.2	121	gTt/gGt	2/21	0.496511670910885	3	FACETS	0.972	0.929	1	0.972	0.929	1	CLONAL	3	TRUE	0	0.496738927076599	3		254	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	132	605	1	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.551966217594439	1	FACETS	0.914	0.839	0.991	0.914	0.839	0.991	CLONAL	1	TRUE	0	0.551966217594439	1		606	379	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0018103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	119	761	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.551966217594439	2	FACETS	0.984	0.912	1	0.984	0.912	1	CLONAL	2	TRUE	0	0.551966217594439	2		761	219	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249983	110249983	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	55	286	0	ENST00000374672.4:c.692T>A	p.Leu231Gln	p.L231Q	ENST00000374672	NM_004235.4	231	cTg/cAg	3/5	1	2	FACETS	0.326	0.278	0.378	0.326	0.278	0.378	SUBCLONAL	1	TRUE	1	0.551966217594439	2		286	612	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0018104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	87	833	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.245455314182867	3	FACETS	1	0.977	1	0.722	0.64	0.81	CLONAL	1	TRUE	1	0.22	3		833	608	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0018104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	57	523	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	0.22	2		523	418	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0018104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	58	447	2	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.807	0.693	0.932	0.807	0.693	0.932	CLONAL	1	TRUE	1	0.22	2		449	653	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925334	114925334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	96	623	0	ENST00000543371.1:c.1412G>A	p.Arg471His	p.R471H	ENST00000543371	NM_001198531.1	471	cGc/cAc	14/14	1	2	FACETS	0.993	0.884	1	0.993	0.884	1	CLONAL	1	TRUE	1	0.22	2		623	879	SUCCESS
APC	324	MSKCC	GRCh37	5	112174751	112174753	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs386833391	NA	P-0018104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	28	371	0	ENST00000257430.4:c.3468_3470del	p.Glu1157del	p.E1157del	ENST00000257430	NM_000038.5	1154	GAA/-	16/16	1	2	FACETS	0.816	0.653	1	0.816	0.653	1	CLONAL	1	TRUE	1	0.22	2		371	312	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903750	114903750	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	103	620	0	ENST00000543371.1:c.754C>T	p.Gln252Ter	p.Q252*	ENST00000543371	NM_001198531.1	252	Caa/Taa	7/14	1	2	FACETS	0.932	0.832	1	0.932	0.832	1	CLONAL	1	TRUE	1	0.22	2		620	1005	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417953	32417953	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	67	419	0	ENST00000332351.3:c.1099G>T	p.Asp367Tyr	p.D367Y	ENST00000332351	NM_024426.4	367	Gat/Tat	7/10	1	2	FACETS	0.77	0.668	0.881	0.77	0.668	0.881	SUBCLONAL	1	TRUE	1	0.22	2		419	791	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123832	46123832	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	60	309	0	ENST00000334344.6:c.98C>G	p.Pro33Arg	p.P33R	ENST00000334344	NM_152641.2	33	cCt/cGt	2/21	0.245455314182867	3	FACETS	1	0.882	1	0.513	0.442	0.591	CLONAL	1	TRUE	1	0.22	3		309	590	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212625	36212625	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	122	804	0	ENST00000222270.7:c.2376G>T	p.Met792Ile	p.M792I	ENST00000222270	NM_014727.1	792	atG/atT	3/37	1	2	FACETS	0.895	0.807	0.989	0.895	0.807	0.989	CLONAL	1	TRUE	1	0.22	2		804	1239	SUCCESS
APC	324	MSKCC	GRCh37	5	112173563	112173563	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0018104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	43	357	0	ENST00000257430.4:c.2272A>T	p.Lys758Ter	p.K758*	ENST00000257430	NM_000038.5	758	Aaa/Taa	16/16	1	2	FACETS	0.944	0.791	1	0.944	0.791	1	CLONAL	1	TRUE	1	0.22	2		357	414	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0018106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	259	941	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.968	0.909	1	0.968	0.909	1	CLONAL	1	TRUE	1	0.611395308775928	2		942	875	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0018106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	201	844	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.938	0.873	1	0.938	0.873	1	CLONAL	1	TRUE	1	0.611395308775928	2		844	701	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796883	42796883	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	333	1267	5	ENST00000575354.2:c.3347del	p.Pro1116GlnfsTer45	p.P1116Qfs*45	ENST00000575354	NM_015125.3	1114	gCc/gc	14/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.611395308775928	2		1272	1061	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736166	204736166	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	84	636	1	ENST00000302823.3:c.529del	p.Tyr177IlefsTer10	p.Y177Ifs*10	ENST00000302823	NM_005214.4	175	Ttt/tt	3/4	1	2	FACETS	0.449	0.397	0.505	0.449	0.397	0.505	SUBCLONAL	1	TRUE	1	0.611395308775928	2		637	612	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696802	176696802	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	86	387	0	ENST00000439151.2:c.5508del	p.Ala1837LeufsTer12	p.A1837Lfs*12	ENST00000439151	NM_022455.4	1835	Aaa/aa	16/23	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.611395308775928	2		387	281	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	206	608	1	ENST00000397062.3:c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	NM_006164.4	34	Cga/Gga	2/5	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.611395308775928	2		609	668	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830902	72830903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0018106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	123	595	0	ENST00000268489.5:c.5677_5678dup	p.Asp1894GlyfsTer21	p.D1894Gfs*21	ENST00000268489	NM_006885.3	1893	agg/agAGg	9/10	1	2	FACETS	0.746	0.678	0.818	0.746	0.678	0.818	SUBCLONAL	1	TRUE	1	0.611395308775928	2		595	539	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0018106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	278	876	0	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	0.946	0.89	1	0.946	0.89	1	CLONAL	1	TRUE	1	0.611395308775928	2		876	961	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572404	41572404	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs139310551	NA	P-0018106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	252	867	0	ENST00000263253.7:c.4933C>T	p.Arg1645Ter	p.R1645*	ENST00000263253	NM_001429.3	1645	Cga/Tga	30/31	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.611395308775928	2		867	736	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566524	41566525	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	208	738	1	ENST00000263253.7:c.4408dup	p.Met1470AsnfsTer3	p.M1470Nfs*3	ENST00000263253	NM_001429.3	1467	-/A	27/31	1	2	FACETS	0.979	0.913	1	0.979	0.913	1	CLONAL	1	TRUE	1	0.611395308775928	2		739	695	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647657	3647657	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs774532876	NA	P-0018106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	156	1237	8	ENST00000294008.3:c.1406del	p.Pro469HisfsTer4	p.P469Hfs*4	ENST00000294008	NM_032444.2	469	cCa/ca	7/15	1	2	FACETS	0.452	0.413	0.493	0.452	0.413	0.493	SUBCLONAL	1	TRUE	1	0.611395308775928	2		1245	1130	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780921	9780921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1297091785	NA	P-0018106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	154	785	1	ENST00000377346.4:c.1643G>A	p.Arg548Gln	p.R548Q	ENST00000377346	NM_005026.3	548	cGg/cAg	13/24	1	2	FACETS	0.8	0.734	0.867	0.8	0.734	0.867	SUBCLONAL	1	TRUE	1	0.611395308775928	2		786	630	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845638	63845638	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	182	539	0	ENST00000279873.7:c.1379del	p.Lys460SerfsTer19	p.K460Sfs*19	ENST00000279873	NM_032199.2	459	ccA/cc	9/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.611395308775928	2		539	517	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456497	32456497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	60	199	0	ENST00000332351.3:c.395C>T	p.Pro132Leu	p.P132L	ENST00000332351	NM_024426.4	132	cCg/cTg	1/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.611395308775928	2		199	155	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418618	49418618	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	250	833	0	ENST00000301067.7:c.15896A>G	p.His5299Arg	p.H5299R	ENST00000301067	NM_003482.3	5299	cAt/cGt	49/54	1	2	FACETS	0.938	0.879	0.998	0.938	0.879	0.998	CLONAL	1	TRUE	1	0.611395308775928	2		833	872	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644826	67644826	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	184	738	0	ENST00000264010.4:c.95del	p.Gly32AlafsTer30	p.G32Afs*30	ENST00000264010	NM_006565.3	31	Ggg/gg	3/12	1	2	FACETS	0.888	0.823	0.955	0.888	0.823	0.955	CLONAL	1	TRUE	1	0.611395308775928	2		738	678	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117379	7117379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	62	835	0	ENST00000302850.5:c.3837G>A	p.Met1279Ile	p.M1279I	ENST00000302850	NM_000208.2	1279	atG/atA	22/22	1	2	FACETS	0.304	0.262	0.35	0.304	0.262	0.35	SUBCLONAL	1	TRUE	1	0.611395308775928	2		835	667	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798155	42798155	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	69	881	0	ENST00000575354.2:c.4109T>C	p.Val1370Ala	p.V1370A	ENST00000575354	NM_015125.3	1370	gTg/gCg	17/20	1	2	FACETS	0.313	0.272	0.357	0.313	0.272	0.357	SUBCLONAL	1	TRUE	1	0.611395308775928	2		881	722	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389195	31389195	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	178	742	0	ENST00000328111.2:c.2108A>T	p.Lys703Met	p.K703M	ENST00000328111	NM_006892.3	703	aAg/aTg	19/23	1	2	FACETS	0.854	0.79	0.92	0.854	0.79	0.92	CLONAL	1	TRUE	1	0.611395308775928	2		742	682	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936093	178936093	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913275	NA	P-0018106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	244	1074	0	ENST00000263967.3:c.1635G>C	p.Glu545Asp	p.E545D	ENST00000263967	NM_006218.2	545	gaG/gaC	10/21	1	2	FACETS	0.982	0.92	1	0.982	0.92	1	CLONAL	1	TRUE	1	0.611395308775928	2		1074	813	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590693	189590693	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	311	926	0	ENST00000264731.3:c.1258T>C	p.Ser420Pro	p.S420P	ENST00000264731	NM_003722.4	420	Tcc/Ccc	10/14	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.611395308775928	2		926	950	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538961	187538961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	109	685	1	ENST00000441802.2:c.8779G>A	p.Val2927Met	p.V2927M	ENST00000441802	NM_005245.3	2927	Gtg/Atg	10/27	1	2	FACETS	0.49	0.44	0.543	0.49	0.44	0.543	SUBCLONAL	1	TRUE	1	0.611395308775928	2		686	727	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38966741	38966741	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0018106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	142	527	0	ENST00000357387.3:c.1299+2T>C		p.X433_splice	ENST00000357387	NM_152756.3	433			1	2	FACETS	0.865	0.793	0.94	0.865	0.793	0.94	CLONAL	1	TRUE	1	0.611395308775928	2		527	537	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286921	33286921	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	228	981	0	ENST00000374542.5:c.2016del	p.Leu673TrpfsTer22	p.L673Wfs*22	ENST00000374542	NM_001141970.1	672	ccC/cc	7/8	1	2	FACETS	0.957	0.895	1	0.957	0.895	1	CLONAL	1	TRUE	1	0.611395308775928	2		981	779	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401854	139401854	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	290	987	2	ENST00000277541.6:c.3546G>T	p.Glu1182Asp	p.E1182D	ENST00000277541	NM_017617.3	1182	gaG/gaT	22/34	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.611395308775928	2		989	870	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223787	53223788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0018106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	306	1254	0	ENST00000375401.3:c.3570_3571dup	p.Gly1191ValfsTer74	p.G1191Vfs*74	ENST00000375401	NM_004187.3	1191	ggg/gTGgg	23/26	1	2	FACETS	0.905	0.853	0.958	0.905	0.853	0.958	CLONAL	1	TRUE	1	0.611395308775928	2		1254	1106	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227036	53227036	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	73	811	1	ENST00000375401.3:c.2539C>T	p.Gln847Ter	p.Q847*	ENST00000375401	NM_004187.3	847	Cag/Tag	18/26	1	2	FACETS	0.324	0.282	0.368	0.324	0.282	0.368	SUBCLONAL	1	TRUE	1	0.611395308775928	2		812	738	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272308	38272308	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs869320694	NA	P-0018107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	88	671	0	ENST00000425967.3:c.2059A>G	p.Lys687Glu	p.K687E	ENST00000425967	NM_001174067.1	687	Aag/Gag	15/19	1	2	FACETS	0.492	0.436	0.551	0.492	0.436	0.551	SUBCLONAL	1	TRUE	1	0.585904921136362	2		671	611	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0018108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1421	218	455	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.353357236244026	11	FACETS	0.975	0.904	1	0.195	0.18	0.21	CLONAL	2	TRUE	1	0.353357236244026	11		455	1639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574000	7574000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	173	1303	1	ENST00000269305.4:c.1027G>T	p.Glu343Ter	p.E343*	ENST00000269305	NM_001126112.2	343	Gag/Tag	10/11	0.353357236244026	1	FACETS	0.988	0.911	1	0.988	0.911	1	CLONAL	1	TRUE	0	0.353357236244026	1		1304	816	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600446	10600446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	105	1265	3	ENST00000171111.5:c.1409G>A	p.Arg470His	p.R470H	ENST00000171111	NM_203500.1	470	cGt/cAt	4/6	1	2	FACETS	0.634	0.567	0.705	0.634	0.567	0.705	SUBCLONAL	1	TRUE	1	0.353357236244026	2		1268	938	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573290	55573290	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs143388949	NA	P-0018108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	98	787	0	ENST00000288135.5:c.952A>G	p.Met318Val	p.M318V	ENST00000288135	NM_000222.2	318	Atg/Gtg	6/21	1	2	FACETS	0.844	0.754	0.94	0.844	0.754	0.94	CLONAL	1	TRUE	1	0.353357236244026	2		787	657	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111855750	111856076	+	splice_acceptor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	GCCCCTTACAGAATGCCACTTGGTAGGGGAGTGCATGTTTCCCTGCATCTTCACCAGCACTGGGTGTTATGGTCGCGTTGGATTTCTGCTGTGGTGCCCGGTGTGTAATGGGGCCTACACCTGCTTGCCCACCTGCTTACTCCTTGTCGCCCCCCCACCCACGTGTCTTTCAGCCCGGCCGCACCACCTGGGTCTCCGCCATGAACGGGCCTGCCCTGCAGCCCTCCTCGCCCTCTTCCGCGCCCTCAGCCTCCCCGGCGGCGGCCCCGCGGGGCTGGAGCGAGTTCTGTGAGTTGCACGCCGTAGCGGCGGCCCGGGAGCTGGCCC	GCCCCTTACAGAATGCCACTTGGTAGGGGAGTGCATGTTTCCCTGCATCTTCACCAGCACTGGGTGTTATGGTCGCGTTGGATTTCTGCTGTGGTGCCCGGTGTGTAATGGGGCCTACACCTGCTTGCCCACCTGCTTACTCCTTGTCGCCCCCCCACCCACGTGTCTTTCAGCCCGGCCGCACCACCTGGGTCTCCGCCATGAACGGGCCTGCCCTGCAGCCCTCCTCGCCCTCTTCCGCGCCCTCAGCCTCCCCGGCGGCGGCCCCGCGGGGCTGGAGCGAGTTCTGTGAGTTGCACGCCGTAGCGGCGGCCCGGGAGCTGGCCC	-	novel	NA	P-0018108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	83	35	2	ENST00000341259.2:c.-27-170_130del		p.X9_splice	ENST00000341259	NM_005475.2	9		2/8	1	2	FACETS	0.969	0.917	1	1	0.991	1	CLONAL	5	TRUE	1	0.353357236244026	2		37	97	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830244	72830244	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	31	320	0	ENST00000268489.5:c.6337C>T	p.Gln2113Ter	p.Q2113*	ENST00000268489	NM_006885.3	2113	Cag/Tag	9/10	0.353357236244026	1	FACETS	0.87	0.712	1	0.87	0.712	1	CLONAL	1	TRUE	0	0.353357236244026	1		320	166	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231417	5231417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	139	1075	1	ENST00000357368.4:c.2059G>A	p.Glu687Lys	p.E687K	ENST00000357368	NM_002850.3	687	Gag/Aag	14/38	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.353357236244026	2		1076	769	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050882	13050882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	105	867	0	ENST00000316448.5:c.413G>A	p.Gly138Asp	p.G138D	ENST00000316448	NM_004343.3	138	gGc/gAc	4/9	1	2	FACETS	0.894	0.802	0.991	0.894	0.802	0.991	CLONAL	1	TRUE	1	0.353357236244026	2		867	665	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754796	29754796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	44	554	0	ENST00000389048.3:c.1139C>T	p.Thr380Ile	p.T380I	ENST00000389048	NM_004304.4	380	aCt/aTt	4/29	1	2	FACETS	0.716	0.602	0.84	0.716	0.602	0.84	SUBCLONAL	1	TRUE	1	0.353357236244026	2		554	348	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169988339	169988339	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1184	66	526	0	ENST00000295797.4:c.581C>G	p.Ser194Cys	p.S194C	ENST00000295797	NM_002740.5	194	tCt/tGt	6/18	0.353357236244026	11	FACETS	0.774	0.669	0.889	0.077	0.066	0.089	SUBCLONAL	1	TRUE	1	0.353357236244026	11		526	1250	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139862	55139862	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	81	586	0	ENST00000257290.5:c.1523G>C	p.Gly508Ala	p.G508A	ENST00000257290	NM_006206.4	508	gGa/gCa	10/23	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.353357236244026	2		586	423	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294993	1294993	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1004308241	NA	P-0018108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	20	91	0	ENST00000310581.5:c.112C>A	p.Leu38Met	p.L38M	ENST00000310581	NM_198253.2	38	Ctg/Atg	1/16	0.333708938657323	3	FACETS	1	0.899	1	0.659	0.513	0.824	CLONAL	1	TRUE	1	0.353357236244026	3		91	101	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729697	41729697	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	119	900	0	ENST00000242208.4:c.832G>T	p.Gly278Trp	p.G278W	ENST00000242208	NM_002192.2	278	Ggg/Tgg	3/3	1	2	FACETS	0.969	0.876	1	0.969	0.876	1	CLONAL	1	TRUE	1	0.353357236244026	2		900	695	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739894	41739894	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	117	705	0	ENST00000242208.4:c.79G>A	p.Glu27Lys	p.E27K	ENST00000242208	NM_002192.2	27	Gag/Aag	2/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.353357236244026	2		705	505	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0018108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1901	329	455	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.57057458769254	14	FACETS	1	0.986	1	0.176	0.165	0.187	CLONAL	2	TRUE	1	0.57057458769254	14		455	2230	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574000	7574000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	297	1303	1	ENST00000269305.4:c.1027G>T	p.Glu343Ter	p.E343*	ENST00000269305	NM_001126112.2	343	Gag/Tag	10/11	0.57057458769254	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.57057458769254	1		1304	653	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573290	55573290	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs143388949	NA	P-0018108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	105	787	0	ENST00000288135.5:c.952A>G	p.Met318Val	p.M318V	ENST00000288135	NM_000222.2	318	Atg/Gtg	6/21	1	2	FACETS	0.946	0.855	1	0.946	0.855	1	CLONAL	1	TRUE	1	0.57057458769254	2		787	389	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111855750	111856076	+	splice_acceptor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	GCCCCTTACAGAATGCCACTTGGTAGGGGAGTGCATGTTTCCCTGCATCTTCACCAGCACTGGGTGTTATGGTCGCGTTGGATTTCTGCTGTGGTGCCCGGTGTGTAATGGGGCCTACACCTGCTTGCCCACCTGCTTACTCCTTGTCGCCCCCCCACCCACGTGTCTTTCAGCCCGGCCGCACCACCTGGGTCTCCGCCATGAACGGGCCTGCCCTGCAGCCCTCCTCGCCCTCTTCCGCGCCCTCAGCCTCCCCGGCGGCGGCCCCGCGGGGCTGGAGCGAGTTCTGTGAGTTGCACGCCGTAGCGGCGGCCCGGGAGCTGGCCC	GCCCCTTACAGAATGCCACTTGGTAGGGGAGTGCATGTTTCCCTGCATCTTCACCAGCACTGGGTGTTATGGTCGCGTTGGATTTCTGCTGTGGTGCCCGGTGTGTAATGGGGCCTACACCTGCTTGCCCACCTGCTTACTCCTTGTCGCCCCCCCACCCACGTGTCTTTCAGCCCGGCCGCACCACCTGGGTCTCCGCCATGAACGGGCCTGCCCTGCAGCCCTCCTCGCCCTCTTCCGCGCCCTCAGCCTCCCCGGCGGCGGCCCCGCGGGGCTGGAGCGAGTTCTGTGAGTTGCACGCCGTAGCGGCGGCCCGGGAGCTGGCCC	-	novel	NA	P-0018108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2	107	35	2	ENST00000341259.2:c.-27-170_130del		p.X9_splice	ENST00000341259	NM_005475.2	9		2/8	0.240775165327714	3	FACETS	1	0.992	1	1	0.993	1	INDETERMINATE	4	TRUE	1	0.57057458769254	3		37	109	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830244	72830244	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	29	320	0	ENST00000268489.5:c.6337C>T	p.Gln2113Ter	p.Q2113*	ENST00000268489	NM_006885.3	2113	Cag/Tag	9/10	0.542975503511585	1	FACETS	0.734	0.604	0.874	0.734	0.604	0.874	SUBCLONAL	1	TRUE	0	0.57057458769254	1		320	99	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231417	5231417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	185	1075	1	ENST00000357368.4:c.2059G>A	p.Glu687Lys	p.E687K	ENST00000357368	NM_002850.3	687	Gag/Aag	14/38	1	2	FACETS	0.955	0.885	1	0.955	0.885	1	CLONAL	1	TRUE	1	0.57057458769254	2		1076	679	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050882	13050882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	136	867	0	ENST00000316448.5:c.413G>A	p.Gly138Asp	p.G138D	ENST00000316448	NM_004343.3	138	gGc/gAc	4/9	1	2	FACETS	0.833	0.761	0.909	0.833	0.761	0.909	CLONAL	1	TRUE	1	0.57057458769254	2		867	572	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754796	29754796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	90	554	0	ENST00000389048.3:c.1139C>T	p.Thr380Ile	p.T380I	ENST00000389048	NM_004304.4	380	aCt/aTt	4/29	1	2	FACETS	0.936	0.838	1	0.936	0.838	1	CLONAL	1	TRUE	1	0.57057458769254	2		554	337	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169988339	169988339	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1695	133	526	0	ENST00000295797.4:c.581C>G	p.Ser194Cys	p.S194C	ENST00000295797	NM_002740.5	194	tCt/tGt	6/18	0.57057458769254	14	FACETS	1	0.963	1	0.087	0.078	0.096	CLONAL	1	TRUE	1	0.57057458769254	14		526	1828	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139862	55139862	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	93	586	0	ENST00000257290.5:c.1523G>C	p.Gly508Ala	p.G508A	ENST00000257290	NM_006206.4	508	gGa/gCa	10/23	1	2	FACETS	0.817	0.731	0.907	0.817	0.731	0.907	CLONAL	1	TRUE	1	0.57057458769254	2		586	399	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294993	1294993	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1004308241	NA	P-0018108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	39	91	0	ENST00000310581.5:c.112C>A	p.Leu38Met	p.L38M	ENST00000310581	NM_198253.2	38	Ctg/Atg	1/16	0.544362097693412	3	FACETS	1	0.96	1	0.745	0.632	0.863	CLONAL	1	TRUE	1	0.57057458769254	3		91	118	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729697	41729697	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	186	900	0	ENST00000242208.4:c.832G>T	p.Gly278Trp	p.G278W	ENST00000242208	NM_002192.2	278	Ggg/Tgg	3/3	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.57057458769254	2		900	616	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739894	41739894	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	166	705	0	ENST00000242208.4:c.79G>A	p.Glu27Lys	p.E27K	ENST00000242208	NM_002192.2	27	Gag/Aag	2/3	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.57057458769254	2		705	474	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813907	50813907	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	31	967	0	ENST00000398568.2:c.1461G>T	p.Trp487Cys	p.W487C	ENST00000398568	NM_001042412.1	487	tgG/tgT	8/18	0.542975503511585	1	FACETS	0.157	0.126	0.192	0.157	0.126	0.192	SUBCLONAL	1	TRUE	0	0.57057458769254	1		967	495	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816216	89816216	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	48	946	0	ENST00000389301.3:c.3161G>A	p.Arg1054Lys	p.R1054K	ENST00000389301	NM_000135.2	1054	aGa/aAa	32/43	0.542975503511585	1	FACETS	0.266	0.225	0.311	0.266	0.225	0.311	SUBCLONAL	1	TRUE	0	0.57057458769254	1		946	452	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0018109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	119	741	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	0.392679336189687	2		741	569	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0018109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	69	553	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.392679336189687	1	FACETS	0.888	0.78	1	0.888	0.78	1	CLONAL	1	TRUE	0	0.392679336189687	1		553	318	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0018109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	216	916	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.392679336189687	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.392679336189687	1		916	771	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636100	28636100	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	145	874	0	ENST00000241453.7:c.272T>A	p.Leu91Gln	p.L91Q	ENST00000241453	NM_004119.2	91	cTg/cAg	3/24	1	2	FACETS	0.917	0.838	1	0.917	0.838	1	CLONAL	1	TRUE	1	0.392679336189687	2		874	805	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641487	23641487	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	174	956	28	ENST00000261584.4:c.1988G>C	p.Arg663Pro	p.R663P	ENST00000261584	NM_024675.3	663	cGc/cCc	5/13	0.392679336189687	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.392679336189687	1		984	580	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050343	13050343	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	172	751	0	ENST00000316448.5:c.295C>G	p.His99Asp	p.H99D	ENST00000316448	NM_004343.3	99	Cat/Gat	3/9	0.392679336189687	1	FACETS	0.949	0.875	1	0.949	0.875	1	CLONAL	1	TRUE	0	0.392679336189687	1		751	742	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200121	128200121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	201	929	1	ENST00000341105.2:c.1184C>T	p.Thr395Ile	p.T395I	ENST00000341105	NM_032638.4	395	aCt/aTt	6/6	0.392679336189687	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.392679336189687	1		930	781	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274908	38274954	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGACAAGTCTTTCTCTGTTGCGTCCGCTTTAAAGAACACGTTGAGA	CTGACAAGTCTTTCTCTGTTGCGTCCGCTTTAAAGAACACGTTGAGA	-	novel	NA	P-0018109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	58	1081	0	ENST00000425967.3:c.1646-20_1672del		p.X549_splice	ENST00000425967	NM_001174067.1	549		13/19	1	2	FACETS	0.344	0.295	0.399	0.344	0.295	0.399	SUBCLONAL	1	TRUE	1	0.392679336189687	2		1081	858	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737698	145737698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560476442	NA	P-0018109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	155	842	0	ENST00000428558.2:c.3065G>A	p.Arg1022His	p.R1022H	ENST00000428558	NM_004260.3	1022	cGt/cAt	19/22	0.392679336189687	4	FACETS	0.962	0.879	1	0.321	0.293	0.35	CLONAL	1	TRUE	1	0.392679336189687	4		842	1143	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135777017	135777017	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	175	769	0	ENST00000298552.3:c.2461G>T	p.Val821Leu	p.V821L	ENST00000298552	NM_001162426.1	821	Gtg/Ttg	19/23	0.371721306524762	3	FACETS	1	0.97	1	0.555	0.511	0.601	CLONAL	1	TRUE	1	0.392679336189687	3		769	961	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279556	123279594	+	inframe_deletion	In_Frame_Del	DEL	CTTGATCCACTGGATGTGGGGCTGGGCATCACTGTAAAC	CTTGATCCACTGGATGTGGGGCTGGGCATCACTGTAAAC	-	novel	NA	P-0018110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	218	815	0	ENST00000358487.5:c.838_876del	p.Val280_Lys292del	p.V280_K292del	ENST00000358487	NM_000141.4	280	GTTTACAGTGATGCCCAGCCCCACATCCAGTGGATCAAG/-	7/18	0.21955937530385	2	FACETS	1	0.989	1	0.664	0.618	0.712	CLONAL	1	TRUE	0	0.353036691344478	2		815	930	SUCCESS
AR	367	MSKCC	GRCh37	X	66766298	66766298	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	34	218	0	ENST00000374690.3:c.1310C>T	p.Thr437Ile	p.T437I	ENST00000374690	NM_000044.3	437	aCt/aTt	1/8	1	1	FACETS	0.443	0.362	0.534	0.443	0.362	0.534	SUBCLONAL	1	TRUE	0	0.353036691344478	1		218	358	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0018111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1285	36	1208	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.061	0.05	0.074	0.061	0.05	0.074	SUBCLONAL	1	TRUE	1	0.890748948345173	2		1208	1321	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0018111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	255	326	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.510620384373969	3	FACETS	0.796	0.753	0.838	0.53	0.502	0.559	INDETERMINATE	2	TRUE	0	0.890748948345173	3		326	520	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913399	NA	P-0018111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	104	480	0	ENST00000349496.5:c.100G>C	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Cga	3/15	1	2	FACETS	0.503	0.453	0.556	0.503	0.453	0.556	SUBCLONAL	1	TRUE	1	0.890748948345173	2		480	464	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101044	41101044	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143164081	NA	P-0018111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	126	749	1	ENST00000373198.4:c.1312G>A	p.Glu438Lys	p.E438K	ENST00000373198	NM_133170.3	438	Gag/Aag	8/32	1	2	FACETS	0.646	0.589	0.705	0.646	0.589	0.705	SUBCLONAL	1	TRUE	1	0.890748948345173	2		750	438	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100135	27100139	+	frameshift_variant	Frame_Shift_Del	DEL	CCTTC	CCTTC	-	novel	NA	P-0018111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	150	990	0	ENST00000324856.7:c.3932_3936del	p.Pro1311GlnfsTer10	p.P1311Qfs*10	ENST00000324856	NM_006015.4	1311	CCTTCc/c	16/20	1	2	FACETS	0.507	0.465	0.551	0.507	0.465	0.551	SUBCLONAL	1	TRUE	1	0.890748948345173	2		990	664	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106533	27106533	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	248	1259	2	ENST00000324856.7:c.6144G>A	p.Trp2048Ter	p.W2048*	ENST00000324856	NM_006015.4	2048	tgG/tgA	20/20	1	2	FACETS	0.562	0.526	0.6	0.562	0.526	0.6	SUBCLONAL	1	TRUE	1	0.890748948345173	2		1261	990	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465988	69465988	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	36	1109	2	ENST00000227507.2:c.826G>T	p.Glu276Ter	p.E276*	ENST00000227507	NM_053056.2	276	Gag/Tag	5/5	1	2	FACETS	0.148	0.121	0.179	0.148	0.121	0.179	SUBCLONAL	1	TRUE	1	0.890748948345173	2		1111	545	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106201	2106201	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	120	880	0	ENST00000219476.3:c.604A>G	p.Ile202Val	p.I202V	ENST00000219476	NM_000548.3	202	Atc/Gtc	7/42	1	2	FACETS	0.52	0.472	0.571	0.52	0.472	0.571	SUBCLONAL	1	TRUE	1	0.890748948345173	2		880	518	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117623	70117624	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0018111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	155	926	3	ENST00000245479.2:c.91_92delinsTT	p.Ala31Leu	p.A31L	ENST00000245479	NM_000346.3	31	GCg/TTg	1/3	1	2	FACETS	0.62	0.571	0.672	0.62	0.571	0.672	SUBCLONAL	1	TRUE	1	0.890748948345173	2		929	561	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562685	176562685	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs769401719	NA	P-0018111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	254	1093	0	ENST00000439151.2:c.581A>G	p.Asn194Ser	p.N194S	ENST00000439151	NM_022455.4	194	aAt/aGt	2/23	1	2	FACETS	0.572	0.536	0.61	0.572	0.536	0.61	SUBCLONAL	1	TRUE	1	0.890748948345173	2		1093	997	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932687	39932687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	250	1335	0	ENST00000378444.4:c.1912A>G	p.Ile638Val	p.I638V	ENST00000378444	NM_001123385.1	638	Ata/Gta	4/15	1	2	FACETS	0.576	0.539	0.614	0.576	0.539	0.614	SUBCLONAL	1	TRUE	1	0.890748948345173	2		1335	975	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0018112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	202	607	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.979	0.907	1	0.979	0.907	1	CLONAL	1	TRUE	1	0.372776920658715	2		607	1107	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0018112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	167	584	1	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.372776920658715	1	FACETS	0.945	0.87	1	0.945	0.87	1	CLONAL	1	TRUE	0	0.372776920658715	1		585	771	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200305	67200305	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	83	738	1	ENST00000312629.5:c.613C>A	p.Gln205Lys	p.Q205K	ENST00000312629	NM_003952.2	205	Cag/Aag	7/15	0.200544106394997	3	FACETS	0.531	0.468	0.6	0.266	0.234	0.3	INDETERMINATE	1	TRUE	1	0.372776920658715	3		739	994	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236109	108236109	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	66	855	0	ENST00000278616.4:c.9045G>C	p.Glu3015Asp	p.E3015D	ENST00000278616	NM_000051.3	3015	gaG/gaC	63/63	0.200544106394997	3	FACETS	0.44	0.381	0.505	0.22	0.19	0.253	INDETERMINATE	1	TRUE	1	0.372776920658715	3		855	955	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380320	25380320	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs904755552	NA	P-0018112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	127	734	0	ENST00000311936.3:c.138T>G	p.Ile46Met	p.I46M	ENST00000311936	NM_004985.3	46	atT/atG	3/5	1	2	FACETS	0.995	0.903	1	0.995	0.903	1	CLONAL	1	TRUE	1	0.372776920658715	2		734	685	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	303	576	0	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	NA	2	FACETS	0.662	0.624	0.7			1	INDETERMINATE	1	TRUE	NA	0.90411365861046	2		576	1013	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032371	42032371	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	59	821	0	ENST00000219905.7:c.4555A>C	p.Lys1519Gln	p.K1519Q	ENST00000219905	NM_001164273.1	1519	Aag/Cag	14/24	0.90411365861046	1	FACETS	0.158	0.135	0.181	0.158	0.135	0.181	SUBCLONAL	1	TRUE	0	0.90411365861046	1		821	454	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654570	29654571	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAAT	novel	NA	P-0018113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	405	475	1	ENST00000356175.3:c.5262_5265dup	p.Val1756IlefsTer6	p.V1756Ifs*6	ENST00000356175	NM_000267.3	1753	-/CAAT	37/57	0.734767193358023	1	FACETS	0.953	0.926	0.979	0.953	0.926	0.979	CLONAL	1	TRUE	0	0.90411365861046	1		476	515	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682552	37682553	+	missense_variant	Missense_Mutation	DNP	CA	CA	AC	novel	NA	P-0018113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1484	94	505	0	ENST00000447079.4:c.3743_3744delinsAC	p.Pro1248His	p.P1248H	ENST00000447079	NM_015083.1	1248	cCA/cAC	13/14	0.609434839580863	5	FACETS	0.31	0.275	0.349			1	SUBCLONAL	1	TRUE	NA	0.90411365861046	5		505	1578	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114255	73114266	+	inframe_deletion	In_Frame_Del	DEL	AGAAGAGGATGA	AGAAGAGGATGA	-	rs754988583	NA	P-0018113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	31	463	0	ENST00000356692.5:c.906_917del	p.Asp304_Glu307del	p.D304_E307del	ENST00000356692		297	acAGAAGAGGATGAa/aca	8/9	0.442281428874381	1	FACETS	0.088	0.071	0.108	0.088	0.071	0.108	INDETERMINATE	1	TRUE	0	0.90411365861046	1		463	427	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131283	17131283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746507528	NA	P-0018114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	63	1027	1	ENST00000285071.4:c.169C>T	p.Arg57Trp	p.R57W	ENST00000285071	NM_144997.5	57	Cgg/Tgg	4/14	0.54088571264722	1	FACETS	0.26	0.224	0.299	0.26	0.224	0.299	SUBCLONAL	1	TRUE	0	0.54088571264722	1		1028	654	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210773	2210773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745490701	NA	P-0018114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	49	886	0	ENST00000398665.3:c.1270C>T	p.Arg424Trp	p.R424W	ENST00000398665	NM_032482.2	424	Cgg/Tgg	14/28	1	2	FACETS	0.204	0.172	0.24	0.204	0.172	0.24	SUBCLONAL	1	TRUE	1	0.54088571264722	2		886	888	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0018117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	66	210	1	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.723	0.635	0.814	0.723	0.635	0.814	SUBCLONAL	1	TRUE	1	0.761101047488479	2		211	240	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0018117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	229	882	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	0.761101047488479	3	FACETS	0.846	0.789	0.905	0.423	0.394	0.453	CLONAL	1	TRUE	1	0.761101047488479	3		882	982	SUCCESS
AR	367	MSKCC	GRCh37	X	66765159	66765188	+	inframe_deletion	In_Frame_Del	DEL	GCAGCAGCAGCAGCAGCAGCAGCAGCAGCA	GCAGCAGCAGCAGCAGCAGCAGCAGCAGCA	-	rs3032358	NA	P-0018117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	82	184	0	ENST00000374690.3:c.210_239del	p.Gln71_Gln80del	p.Q71_Q80del	ENST00000374690	NM_000044.3	57	ctGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAg/ctg	1/8	0.657774702937453	2	FACETS	0.688	0.613	0.768			1	SUBCLONAL	1	TRUE	NA	0.761101047488479	2		184	313	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197413	106197413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	196	531	0	ENST00000380013.4:c.5746C>T	p.Leu1916Phe	p.L1916F	ENST00000380013	NM_001127208.2	1916	Ctt/Ttt	11/11	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.761101047488479	2		531	505	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467747	50467747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	250	762	0	ENST00000331340.3:c.982C>T	p.Arg328Cys	p.R328C	ENST00000331340	NM_006060.4	328	Cgc/Tgc	8/8	NA	2	FACETS	0.888	0.834	0.943			1	INDETERMINATE	1	TRUE	NA	0.761101047488479	2		762	740	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251725	212251725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144311212	NA	P-0018117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	159	419	0	ENST00000342788.4:c.3334C>T	p.Arg1112Cys	p.R1112C	ENST00000342788	NM_005235.2	1112	Cgc/Tgc	27/28	1	2	FACETS	0.895	0.827	0.964	0.895	0.827	0.964	CLONAL	1	TRUE	1	0.761101047488479	2		419	467	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441780	49441781	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0018117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	360	695	0	ENST00000301067.7:c.4203_4204del	p.Gln1402ValfsTer29	p.Q1402Vfs*29	ENST00000301067	NM_003482.3	1401	tcTCag/tcag	14/54	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.761101047488479	2		695	840	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061142	38061161	+	frameshift_variant	Frame_Shift_Del	DEL	CGCTTCCGCTCCCGCCCCCG	CGCTTCCGCTCCCGCCCCCG	-	novel	NA	P-0018117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	95	169	0	ENST00000250448.2:c.828_847del	p.Gly278GlnfsTer8	p.G278Qfs*8	ENST00000250448	NM_004496.3	276	ggCGGGGGCGGGAGCGGAAGCGgg/gggg	2/2	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.761101047488479	2		169	194	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576838	7576866	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCAAGACTTAGTACCTGAAGGGTGAAAT	CCCAAGACTTAGTACCTGAAGGGTGAAAT	GATAAGATGG	novel	NA	P-0018117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	176	812	2	ENST00000269305.4:c.980_993+15delinsCCATCTTATC		p.X327_splice	ENST00000269305	NM_001126112.2	327		9/11	0.761101047488479	1	FACETS	0.8	0.749	0.851	0.8	0.749	0.851	SUBCLONAL	1	TRUE	0	0.761101047488479	1		814	358	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281838	39281838	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	374	965	0	ENST00000402219.2:c.637del	p.Arg213AspfsTer4	p.R213Dfs*4	ENST00000402219	NM_005633.3	213	Cga/ga	5/23	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.761101047488479	2		965	927	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598148	52598148	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772970975	NA	P-0018117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	327	881	2	ENST00000394830.3:c.3718G>A	p.Asp1240Asn	p.D1240N	ENST00000394830	NM_018313.4	1240	Gac/Aac	24/30	1	2	FACETS	0.899	0.851	0.947	0.899	0.851	0.947	CLONAL	1	TRUE	1	0.761101047488479	2		883	956	SUCCESS
AR	367	MSKCC	GRCh37	X	66765188	66765188	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	10	137	0	ENST00000374690.3:c.200A>T	p.Gln67Leu	p.Q67L	ENST00000374690	NM_000044.3	67	cAg/cTg	1/8	0.657774702937453	2	FACETS	0.141	0.095	0.198			1	SUBCLONAL	1	TRUE	NA	0.761101047488479	2		137	187	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0018118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	742	1171	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.609673124088941	2	FACETS	0.962	0.935	0.989	0.962	0.935	0.989	CLONAL	2	TRUE	0	0.609673124088941	2		1171	1265	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0018118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	205	484	1	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	0.562508170747127	2	FACETS	0.793	0.746	0.84	0.793	0.746	0.84	SUBCLONAL	2	TRUE	0	0.609673124088941	2		485	424	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163762	72163762	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	475	1056	0	ENST00000357731.5:c.596G>T	p.Gly199Val	p.G199V	ENST00000357731	NM_173808.2	199	gGg/gTg	4/7	0.260487751103724	2	FACETS	1	0.996	1	0.741	0.711	0.771	INDETERMINATE	1	TRUE	0	0.609673124088941	2		1056	1052	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851345	156851345	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	482	879	0	ENST00000524377.1:c.2305del	p.Gln769SerfsTer?	p.Q769Sfs*?	ENST00000524377	NM_002529.3	768	Ccc/cc	17/17	0.310846370965812	3	FACETS	1	0.992	1	0.743	0.715	0.772	INDETERMINATE	2	TRUE	0	0.609673124088941	3		879	925	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73340171	73340171	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	306	612	0	ENST00000377767.4:c.1909G>T	p.Val637Phe	p.V637F	ENST00000377767	NM_014953.3	637	Gtt/Ttt	15/21	0.562508170747127	2	FACETS	0.942	0.9	0.983	0.942	0.9	0.983	CLONAL	2	TRUE	0	0.609673124088941	2		612	533	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437436	110437436	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	308	640	0	ENST00000375856.3:c.965C>T	p.Ala322Val	p.A322V	ENST00000375856	NM_003749.2	322	gCg/gTg	1/2	0.562508170747127	2	FACETS	0.882	0.841	0.922	0.882	0.841	0.922	CLONAL	2	TRUE	0	0.609673124088941	2		640	573	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2105422	2105422	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	296	854	1	ENST00000219476.3:c.501G>T	p.Trp167Cys	p.W167C	ENST00000219476	NM_000548.3	167	tgG/tgT	6/42	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.609673124088941	2		855	786	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725543	117725543	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	193	750	0	ENST00000368508.3:c.338A>G	p.His113Arg	p.H113R	ENST00000368508	NM_002944.2	113	cAc/cGc	5/43	1	2	FACETS	0.81	0.751	0.871	0.81	0.751	0.871	CLONAL	1	TRUE	1	0.609673124088941	2		750	782	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950478	68950478	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	251	707	0	ENST00000288368.4:c.790G>T	p.Val264Leu	p.V264L	ENST00000288368	NM_024870.2	264	Gtg/Ttg	7/40	0.219801173368265	3	FACETS	1	0.992	1	0.679	0.637	0.722	INDETERMINATE	1	TRUE	1	0.609673124088941	3		707	791	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410018	139410018	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	493	992	0	ENST00000277541.6:c.1820G>T	p.Cys607Phe	p.C607F	ENST00000277541	NM_017617.3	607	tGc/tTc	11/34	0.562508170747127	2	FACETS	0.91	0.877	0.942	0.91	0.877	0.942	CLONAL	2	TRUE	0	0.609673124088941	2		992	889	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0018119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	34	523	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.418	0.341	0.506	0.418	0.341	0.506	SUBCLONAL	1	TRUE	1	0.270415345027789	2		523	601	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111517	8111518	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	43	811	0	ENST00000346208.3:c.1004dup	p.Asp335GlufsTer17	p.D335Efs*17	ENST00000346208		335	gac/gAac	5/6	1	2	FACETS	0.393	0.328	0.466	0.393	0.328	0.466	SUBCLONAL	1	TRUE	1	0.270415345027789	2		811	809	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023123	31023123	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	115	655	0	ENST00000375687.4:c.2609del	p.Gly870AlafsTer6	p.G870Afs*6	ENST00000375687	NM_015338.5	870	Ggc/gc	13/13	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.270415345027789	2		655	813	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0018120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	12	447	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.179	0.125	0.247	0.179	0.125	0.247	SUBCLONAL	1	TRUE	1	0.309686170763746	2		447	432	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207162	1207162	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs137853076	NA	P-0018120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	62	1039	0	ENST00000326873.7:c.250A>T	p.Lys84Ter	p.K84*	ENST00000326873	NM_000455.4	84	Aag/Tag	1/10	1	2	FACETS	0.462	0.398	0.532	0.462	0.398	0.532	SUBCLONAL	1	TRUE	1	0.309686170763746	2		1039	867	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221977	1221977	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	45	809	0	ENST00000326873.7:c.893del	p.Phe298SerfsTer38	p.F298Sfs*38	ENST00000326873	NM_000455.4	298	Ttc/tc	7/10	1	2	FACETS	0.384	0.322	0.454	0.384	0.322	0.454	SUBCLONAL	1	TRUE	1	0.309686170763746	2		809	756	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0018121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	219	455	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.156809918195106	2	FACETS	1	0.991	1	0.683	0.642	0.726	INDETERMINATE	1	TRUE	0	0.61046741673378	2		455	525	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0018121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	367	1081	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.61046741673378	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.61046741673378	1		1082	719	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031973	26031973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	27	345	0	ENST00000244661.2:c.316G>C	p.Glu106Gln	p.E106Q	ENST00000244661	NM_003537.3	106	Gag/Cag	1/1	1	2	FACETS	0.244	0.194	0.301	0.244	0.194	0.301	SUBCLONAL	1	TRUE	1	0.61046741673378	2		345	363	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459972	99459972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	236	698	3	ENST00000268035.6:c.2068G>A	p.Glu690Lys	p.E690K	ENST00000268035	NM_000875.3	690	Gag/Aag	10/21	0.61046741673378	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.61046741673378	1		701	466	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532552	187532552	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs748152388	NA	P-0018121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	169	438	0	ENST00000441802.2:c.9841G>T	p.Asp3281Tyr	p.D3281Y	ENST00000441802	NM_005245.3	3281	Gat/Tat	14/27	0.61046741673378	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.61046741673378	1		438	320	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040955	42040955	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0018121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	307	825	0	ENST00000219905.7:c.5333C>G	p.Ser1778Ter	p.S1778*	ENST00000219905	NM_001164273.1	1778	tCa/tGa	16/24	0.61046741673378	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.61046741673378	1		825	560	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302673	15302673	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	351	1148	0	ENST00000263388.2:c.685G>C	p.Glu229Gln	p.E229Q	ENST00000263388	NM_000435.2	229	Gag/Cag	5/33	0.591193198906875	3	FACETS	1	0.994	1	0.466	0.442	0.491	CLONAL	1	TRUE	0	0.61046741673378	3		1148	1073	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120460379	120460379	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	111	626	0	ENST00000256646.2:c.5936C>G	p.Ser1979Cys	p.S1979C	ENST00000256646	NM_024408.3	1979	tCt/tGt	33/34	0.202259068401801	2	FACETS	0.694	0.626	0.765	0.347	0.313	0.383	INDETERMINATE	1	TRUE	0	0.61046741673378	2		626	524	SUCCESS
BLM	641	MSKCC	GRCh37	15	91298159	91298159	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	172	569	1	ENST00000355112.3:c.1078G>A	p.Asp360Asn	p.D360N	ENST00000355112	NM_000057.2	360	Gac/Aac	5/22	0.61046741673378	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.61046741673378	1		570	346	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274223	10274223	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	90	449	0	ENST00000330684.3:c.46C>G	p.Leu16Val	p.L16V	ENST00000330684	NM_001134407.1	16	Ctg/Gtg	2/13	0.447191626183054	3	FACETS	0.877	0.782	0.977	0.438	0.391	0.489	CLONAL	1	TRUE	1	0.61046741673378	3		449	439	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969908	81969908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	315	896	1	ENST00000359376.3:c.2977G>A	p.Asp993Asn	p.D993N	ENST00000359376	NM_002661.3	993	Gac/Aac	27/33	0.61046741673378	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.61046741673378	1		897	614	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068409	16068409	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	30	83	0	ENST00000268712.3:c.502G>C	p.Asp168His	p.D168H	ENST00000268712	NM_006311.3	168	Gat/Cat	5/46	0.61046741673378	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.61046741673378	1		83	52	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650804	37650804	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	317	960	0	ENST00000447079.4:c.2276G>C	p.Arg759Thr	p.R759T	ENST00000447079	NM_015083.1	759	aGa/aCa	5/14	0.530550806202414	4	FACETS	1	0.992	1	0.432	0.407	0.458	CLONAL	1	TRUE	1	0.61046741673378	4		960	1290	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395716	45395716	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	233	601	0	ENST00000262160.6:c.418C>T	p.His140Tyr	p.H140Y	ENST00000262160	NM_005901.5	140	Cat/Tat	4/11	0.61046741673378	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.61046741673378	1		601	404	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302865	15302865	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	340	976	0	ENST00000263388.2:c.585G>C	p.Glu195Asp	p.E195D	ENST00000263388	NM_000435.2	195	gaG/gaC	4/33	0.591193198906875	3	FACETS	1	0.995	1	0.485	0.46	0.511	CLONAL	1	TRUE	0	0.61046741673378	3		976	999	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182606	99182606	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs778111638	NA	P-0018121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	157	389	0	ENST00000074304.5:c.2409C>G	p.Ile803Met	p.I803M	ENST00000074304	NM_001134224.1	803	atC/atG	22/26	0.202259068401801	2	FACETS	1	0.989	1	0.71	0.66	0.761	INDETERMINATE	1	TRUE	0	0.61046741673378	2		389	362	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884831	134884831	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	155	456	2	ENST00000398015.3:c.1607G>A	p.Arg536Lys	p.R536K	ENST00000398015	NM_004441.4	536	aGg/aAg	8/16	0.156809918195106	2	FACETS	1	0.988	1	0.692	0.642	0.742	INDETERMINATE	1	TRUE	0	0.61046741673378	2		458	367	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665360	138665360	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	74	1066	1	ENST00000330315.3:c.205G>C	p.Glu69Gln	p.E69Q	ENST00000330315	NM_023067.3	69	Gag/Cag	1/1	0.156809918195106	2	FACETS	0.265	0.231	0.302	0.132	0.115	0.151	INDETERMINATE	1	TRUE	0	0.61046741673378	2		1067	915	SUCCESS
APC	324	MSKCC	GRCh37	5	112116502	112116502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	150	471	0	ENST00000257430.4:c.547G>A	p.Asp183Asn	p.D183N	ENST00000257430	NM_000038.5	183	Gat/Aat	6/16	0.202259068401801	2	FACETS	1	0.986	1	0.652	0.603	0.701	INDETERMINATE	1	TRUE	0	0.61046741673378	2		471	377	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555344	106555344	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	31	686	0	ENST00000369096.4:c.2461G>C	p.Glu821Gln	p.E821Q	ENST00000369096	NM_001198.3	821	Gaa/Caa	7/7	1	2	FACETS	0.175	0.141	0.214	0.175	0.141	0.214	SUBCLONAL	1	TRUE	1	0.61046741673378	2		686	580	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157470056	157470081	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGGCTGCTGCGAACTCAGCACAAA	GCAGGCTGCTGCGAACTCAGCACAAA	-	novel	NA	P-0018121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	70	369	0	ENST00000346085.5:c.2855_2879+1del		p.MQAAANSAQS950fs	ENST00000346085	NM_020732.3	950	atGCAGGCTGCTGCGAACTCAGCACAAAgc/atgc	9/20	1	2	FACETS	0.754	0.664	0.851	0.754	0.664	0.851	SUBCLONAL	1	TRUE	1	0.61046741673378	2		369	304	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058452	69058452	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	88	644	0	ENST00000288368.4:c.4096C>G	p.Leu1366Val	p.L1366V	ENST00000288368	NM_024870.2	1366	Ctt/Gtt	34/40	0.202259068401801	2	FACETS	0.677	0.603	0.755	0.338	0.301	0.378	INDETERMINATE	1	TRUE	0	0.61046741673378	2		644	426	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054737	5054999	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGCCTTCTACACAGAGAAATTTGAAGTAAAAGAACCTGGAAGTGGTCCTTCAGGTGAGGAGATTTTTGCAACCATTATAATAACTGGAAACGGTGGAATTCAGTGGTCAAGAGGGAAACATAAAGAAAGTGAGACACTGACAGAACAGGTAATCCTTAATGATATGTTCTTGTTCTTTGTTATTTTAAGTACAATGGAAATAAAAACAAAGTAATTTTAATCATTTGCAACATGGTATTGCACTTCTCCCATTTGATAGAAGT	TGCCTTCTACACAGAGAAATTTGAAGTAAAAGAACCTGGAAGTGGTCCTTCAGGTGAGGAGATTTTTGCAACCATTATAATAACTGGAAACGGTGGAATTCAGTGGTCAAGAGGGAAACATAAAGAAAGTGAGACACTGACAGAACAGGTAATCCTTAATGATATGTTCTTGTTCTTTGTTATTTTAAGTACAATGGAAATAAAAACAAAGTAATTTTAATCATTTGCAACATGGTATTGCACTTCTCCCATTTGATAGAAGT	-	novel	NA	P-0018121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	46	637	0	ENST00000381652.3:c.789_936+115del		p.X263_splice	ENST00000381652	NM_004972.3	263		7/25	0.61046741673378	1	FACETS	0.438	0.372	0.51	0.438	0.372	0.51	SUBCLONAL	1	TRUE	0	0.61046741673378	1		637	239	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771774	135771774	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	360	1155	0	ENST00000298552.3:c.3343G>C	p.Glu1115Gln	p.E1115Q	ENST00000298552	NM_001162426.1	1115	Gag/Cag	23/23	0.200083679451632	2	FACETS	1	0.994	1	0.643	0.612	0.675	INDETERMINATE	1	TRUE	0	0.61046741673378	2		1155	917	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0018122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	208	523	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	0.8284350733792	2		523	481	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0018122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	519	637	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.785862734427454	2	FACETS	0.998	0.975	1	0.998	0.975	1	CLONAL	2	TRUE	0	0.8284350733792	2		637	628	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983806	15983810	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	TGATG	TGATG	-	novel	NA	P-0018122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	391	626	1	ENST00000268712.3:c.3312_3316del	p.Tyr1104Ter	p.Y1104*	ENST00000268712	NM_006311.3	1104	taCATCAag/taag	25/46	0.785862734427454	2	FACETS	0.916	0.889	0.943	0.916	0.889	0.943	CLONAL	2	TRUE	0	0.8284350733792	2		627	515	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177011	56177015	+	frameshift_variant	Frame_Shift_Del	DEL	ATAGA	ATAGA	TATC	novel	NA	P-0018122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	172	444	1	ENST00000399503.3:c.2281_2285delinsTATC	p.Ile761TyrfsTer38	p.I761Yfs*38	ENST00000399503	NM_005921.1	761	ATAGAt/TATCt	13/20	1	2	FACETS	0.97	0.903	1	0.97	0.903	1	CLONAL	1	TRUE	1	0.8284350733792	2		445	428	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180541	56180558	+	inframe_deletion	In_Frame_Del	DEL	ACTAAGAGAAGAGATAAG	ACTAAGAGAAGAGATAAG	-	novel	NA	P-0018122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	146	503	0	ENST00000399503.3:c.3871_3888del	p.Leu1291_Arg1296del	p.L1291_R1296del	ENST00000399503	NM_005921.1	1290	gcACTAAGAGAAGAGATAAGa/gca	16/20	1	2	FACETS	0.892	0.824	0.963	0.892	0.824	0.963	CLONAL	1	TRUE	1	0.8284350733792	2		503	395	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963948	2963948	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	275	653	0	ENST00000396946.4:c.1859C>A	p.Ser620Tyr	p.S620Y	ENST00000396946	NM_032415.4	620	tCc/tAc	15/25	0.819585942126672	3	FACETS	1	0.975	1	0.532	0.501	0.564	CLONAL	1	TRUE	1	0.8284350733792	3		653	882	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0018123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	16	523	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.446	0.328	0.588	0.446	0.328	0.588	SUBCLONAL	1	TRUE	1	0.13	2		523	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579536	7579536	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567556930	NA	P-0018123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	61	996	2	ENST00000269305.4:c.151G>T	p.Glu51Ter	p.E51*	ENST00000269305	NM_001126112.2	51	Gaa/Taa	4/11	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.13	2		998	808	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0018124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	12	306	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.691	0.486	0.944	0.691	0.486	0.944	SUBCLONAL	1	TRUE	1	0.16	2		307	217	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578191	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs530941076	NA	P-0018124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	50	997	0	ENST00000269305.4:c.658T>C	p.Tyr220His	p.Y220H	ENST00000269305	NM_001126112.2	220	Tat/Cat	6/11	1	2	FACETS	0.93	0.788	1	0.93	0.788	1	CLONAL	1	TRUE	1	0.16	2		997	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578400	7578400	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	37	610	0	ENST00000269305.4:c.530C>A	p.Pro177His	p.P177H	ENST00000269305	NM_001126112.2	177	cCc/cAc	5/11	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.16	2		610	434	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890109	76890109	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	32	321	0	ENST00000373344.5:c.4785del	p.Cys1595Ter	p.C1595*	ENST00000373344	NM_000489.3	1595	tgT/tg	17/35	1	1	FACETS	0.829	0.677	0.997	1	0.952	1	CLONAL	2	TRUE	0	0.16	1		321	222	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0018125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	80	461	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.310628010801829	2		461	497	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856020	68856020	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	124	811	0	ENST00000261769.5:c.1828C>T	p.Gln610Ter	p.Q610*	ENST00000261769	NM_004360.3	610	Cag/Tag	12/16	0.310628010801829	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.310628010801829	1		811	658	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371409680	NA	P-0018126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	431	924	0	ENST00000269305.4:c.848G>C	p.Arg283Pro	p.R283P	ENST00000269305	NM_001126112.2	283	cGc/cCc	8/11	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.862863466547222	2		924	488	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425329	49425329	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	376	855	1	ENST00000301067.7:c.13159C>T	p.Gln4387Ter	p.Q4387*	ENST00000301067	NM_003482.3	4387	Cag/Tag	39/54	0.642544619052286	3	FACETS	0.979	0.94	1			1	CLONAL	2	TRUE	NA	0.862863466547222	3		856	637	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28599027	28599027	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	410	787	0	ENST00000241453.7:c.2261G>T	p.Gly754Val	p.G754V	ENST00000241453	NM_004119.2	754	gGg/gTg	18/24	0.862863466547222	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.862863466547222	2		787	463	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047494	49047494	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0018126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	229	471	1	ENST00000267163.4:c.2490-2A>T		p.X830_splice	ENST00000267163	NM_000321.2	830			0.8481289451454	3	FACETS	0.956	0.926	0.982	0.956	0.926	0.982	CLONAL	3	TRUE	0	0.862863466547222	3		472	265	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321616	30321616	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1195143657	NA	P-0018126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	349	603	0	ENST00000322652.5:c.1471A>G	p.Ile491Val	p.I491V	ENST00000322652	NM_015355.2	491	Atc/Gtc	13/16	0.862863466547222	4	FACETS	1	0.965	1			1	CLONAL	2	TRUE	NA	0.862863466547222	4		603	743	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589012	67589012	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	152	348	0	ENST00000274335.5:c.1103A>G	p.Tyr368Cys	p.Y368C	ENST00000274335		368	tAt/tGt	8/15	0.803677020099971	4	FACETS	0.957	0.888	1			1	CLONAL	2	TRUE	NA	0.862863466547222	4		348	343	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210024	55210024	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	281	598	0	ENST00000275493.2:c.134A>G	p.Glu45Gly	p.E45G	ENST00000275493	NM_005228.3	45	gAa/gGa	2/28	0.645121019783738	4	FACETS	1	0.966	1			1	CLONAL	2	TRUE	NA	0.862863466547222	4		598	593	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395021	139395021	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	178	423	0	ENST00000277541.6:c.5917G>T	p.Ala1973Ser	p.A1973S	ENST00000277541	NM_017617.3	1973	Gca/Tca	31/34	0.640894969519763	4	FACETS	0.956	0.893	1	0.956	0.893	1	CLONAL	2	TRUE	2	0.862863466547222	4		423	402	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442575	52442575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	73	599	2	ENST00000460680.1:c.170G>A	p.Arg57Gln	p.R57Q	ENST00000460680	NM_004656.3	57	cGg/cAg	4/17	1	2	FACETS	0.812	0.711	0.92	0.812	0.711	0.92	CLONAL	1	TRUE	1	0.33350831856642	2		601	539	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0018129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	50	642	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.902	0.765	1	0.902	0.765	1	CLONAL	1	TRUE	1	0.21	2		642	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0018129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	123	1001	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.21	2		1001	947	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0018129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	93	805	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.21	2		805	780	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793340	242793340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201540918	NA	P-0018129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	62	1070	1	ENST00000334409.5:c.737C>T	p.Thr246Met	p.T246M	ENST00000334409	NM_005018.2	246	aCg/aTg	5/5	1	2	FACETS	0.641	0.552	0.738	0.641	0.552	0.738	SUBCLONAL	1	TRUE	1	0.21	2		1071	921	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199948	108199948	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs876658715	NA	P-0018129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	55	466	0	ENST00000278616.4:c.7290T>G	p.His2430Gln	p.H2430Q	ENST00000278616	NM_000051.3	2430	caT/caG	49/63	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.21	2		466	517	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435279	49435279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs181521514	NA	P-0018129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	49	787	1	ENST00000301067.7:c.6274G>A	p.Asp2092Asn	p.D2092N	ENST00000301067	NM_003482.3	2092	Gac/Aac	31/54	1	2	FACETS	0.601	0.507	0.704	0.601	0.507	0.704	SUBCLONAL	1	TRUE	1	0.21	2		788	777	SUCCESS
APC	324	MSKCC	GRCh37	5	112173473	112173473	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	35	476	1	ENST00000257430.4:c.2182A>G	p.Asn728Asp	p.N728D	ENST00000257430	NM_000038.5	728	Aat/Gat	16/16	1	2	FACETS	0.864	0.709	1	0.864	0.709	1	CLONAL	1	TRUE	1	0.21	2		477	386	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	74	184	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.841	0.753	0.932	1	0.982	1	CLONAL	2	FALSE	1	0.472828184068598	2		184	186	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0018130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	254	728	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	0.446477825451032	1	FACETS	0.841	0.797	0.884	1	0.995	1	CLONAL	2	FALSE	0	0.472828184068598	1		728	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0018131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	213	584	1	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.393933561176124	3	FACETS	1	0.974	1	0.714	0.67	0.758	CLONAL	2	TRUE	0	0.504485664851094	3		585	494	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249002	55249003	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCGTGGA	rs397517109	NA	P-0018131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	280	523	0	ENST00000275493.2:c.2303_2311dup	p.Ser768_Asp770dup	p.S768_D770dup	ENST00000275493	NM_005228.3	768	gcc/gcCAGCGTGGAc	20/28	0.504485664851094	5	FACETS	0.949	0.897	1	0.712	0.673	0.751	CLONAL	3	TRUE	1	0.504485664851094	5		523	685	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750568	57750568	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	51	523	0	ENST00000274289.3:c.1900A>G	p.Ile634Val	p.I634V	ENST00000274289	NM_006622.3	634	Atc/Gtc	14/14	0.142916083815727	3	FACETS	1	0.862	1	0.335	0.287	0.386	INDETERMINATE	1	TRUE	0	0.504485664851094	3		523	252	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821343	32821343	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	259	849	0	ENST00000354258.4:c.251G>T	p.Gly84Val	p.G84V	ENST00000354258	NM_000593.5	84	gGg/gTg	1/11	0.274328314375938	5	FACETS	1	0.964	1	0.691	0.649	0.734	INDETERMINATE	2	TRUE	2	0.504485664851094	5		849	870	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0018132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	119	511	4				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.569697287748217	2		515	342	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622218	162622218	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	124	524	0	ENST00000366898.1:c.479G>A	p.Gly160Glu	p.G160E	ENST00000366898	NM_004562.2	160	gGa/gAa	4/12	0.569697287748217	1	FACETS	0.811	0.741	0.883	0.811	0.741	0.883	CLONAL	1	TRUE	0	0.569697287748217	1		524	384	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317148	11317148	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	246	797	0	ENST00000361445.4:c.346C>T	p.Pro116Ser	p.P116S	ENST00000361445	NM_004958.3	116	Ccc/Tcc	4/58	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.569697287748217	2		797	837	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256529	+	missense_variant	Missense_Mutation	DNP	TT	TT	AA	novel	NA	P-0018132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	235	848	1	ENST00000369535.4:c.182_183inv	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAA/cTT	3/7	1	2	FACETS	0.87	0.813	0.93	0.87	0.813	0.93	CLONAL	1	TRUE	1	0.569697287748217	2		849	948	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425896	49425896	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783685	NA	P-0018132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1496	216	631	0	ENST00000301067.7:c.12592C>T	p.Arg4198Ter	p.R4198*	ENST00000301067	NM_003482.3	4198	Cga/Tga	39/54	0.569697287748217	6	FACETS	0.948	0.878	1			1	CLONAL	1	TRUE	NA	0.569697287748217	6		631	1712	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218146	69218146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	2168	444	0	ENST00000462284.1:c.362C>T	p.Ser121Leu	p.S121L	ENST00000462284	NM_002392.5	121	tCa/tTa	6/11	0.569697287748217	16	FACETS	0.985	0.975	0.995			1	CLONAL	15	TRUE	NA	0.569697287748217	16		444	2569	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247224	153247224	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	224	682	0	ENST00000281708.4:c.1578G>A	p.Trp526Ter	p.W526*	ENST00000281708	NM_033632.3	526	tgG/tgA	10/12	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.569697287748217	2		682	749	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180359	32180359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	177	742	1	ENST00000375023.3:c.2572C>T	p.His858Tyr	p.H858Y	ENST00000375023	NM_004557.3	858	Cac/Tac	17/30	0.55119712453689	3	FACETS	0.828	0.763	0.896	0.414	0.381	0.448	CLONAL	1	TRUE	1	0.569697287748217	3		743	964	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104760	69104760	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs754115767	NA	P-0018132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	205	465	0	ENST00000288368.4:c.4604G>A	p.Arg1535Gln	p.R1535Q	ENST00000288368	NM_024870.2	1535	cGg/cAg	37/40	0.229625478756595	3	FACETS	0.845	0.79	0.901	0.845	0.79	0.901	INDETERMINATE	2	TRUE	1	0.569697287748217	3		465	547	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210044	55210044	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	172	632	1	ENST00000275493.2:c.154C>T	p.Gln52Ter	p.Q52*	ENST00000275493	NM_005228.3	52	Cag/Tag	2/28	1	2	FACETS	0.87	0.803	0.939	0.87	0.803	0.939	CLONAL	1	TRUE	1	0.569697287748217	2		633	694	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920463	50920463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1005672452	NA	P-0018133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	134	610	2	ENST00000440232.2:c.3155C>T	p.Ser1052Leu	p.S1052L	ENST00000440232	NM_002691.3	1052	tCg/tTg	26/27	1	2	FACETS	0.789	0.72	0.861	0.789	0.72	0.861	SUBCLONAL	1	TRUE	1	0.610588253342593	2		612	556	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482607	56482607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs993665271	NA	P-0018133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	257	932	0	ENST00000267101.3:c.1064C>T	p.Thr355Ile	p.T355I	ENST00000267101	NM_001982.3	355	aCc/aTc	9/28	1	2	FACETS	0.975	0.916	1	0.975	0.916	1	CLONAL	1	TRUE	1	0.610588253342593	2		932	863	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510644	38510644	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	249	894	3	ENST00000254066.5:c.898G>A	p.Ala300Thr	p.A300T	ENST00000254066	NM_000964.3	300	Gct/Act	7/9	NA	2	FACETS	1	0.96	1			1	INDETERMINATE	1	TRUE	NA	0.610588253342593	2		897	792	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851402	63851402	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	206	716	0	ENST00000279873.7:c.2180A>G	p.Asp727Gly	p.D727G	ENST00000279873	NM_032199.2	727	gAc/gGc	10/10	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.610588253342593	2		716	654	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114118	115114119	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	163	477	0	ENST00000257566.3:c.1098dup	p.Asp367ArgfsTer8	p.D367Rfs*8	ENST00000257566	NM_016569.3	366	-/A	6/8	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.610588253342593	2		477	519	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862094	68862094	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	177	528	0	ENST00000261769.5:c.2183del	p.Leu728CysfsTer42	p.L728Cfs*42	ENST00000261769	NM_004360.3	728	Ttg/tg	14/16	0.610588253342593	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.610588253342593	1		528	384	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581281	48581281	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1316902116	NA	P-0018133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	225	894	0	ENST00000342988.3:c.585C>G	p.Tyr195Ter	p.Y195*	ENST00000342988	NM_005359.5	195	taC/taG	5/12	0.610588253342593	1	FACETS	0.897	0.842	0.952	0.897	0.842	0.952	CLONAL	1	TRUE	0	0.610588253342593	1		894	571	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165234	32165234	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	251	774	1	ENST00000375023.3:c.4894G>T	p.Gly1632Cys	p.G1632C	ENST00000375023	NM_004557.3	1632	Ggc/Tgc	27/30	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.610588253342593	2		775	759	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907824	76907824	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	59	192	0	ENST00000373344.5:c.4337A>T	p.Glu1446Val	p.E1446V	ENST00000373344	NM_000489.3	1446	gAg/gTg	15/35	1	2	FACETS	0.961	0.84	1	0.961	0.84	1	CLONAL	1	TRUE	1	0.610588253342593	2		192	201	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0018134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	143	722	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.462792260378783	1	FACETS	0.818	0.749	0.89	0.818	0.749	0.89	CLONAL	1	TRUE	0	0.466294073001074	1		722	575	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336073	73336073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	46	313	0	ENST00000377767.4:c.2330C>T	p.Ser777Leu	p.S777L	ENST00000377767	NM_014953.3	777	tCa/tTa	17/21	0.466294073001074	1	FACETS	0.801	0.683	0.926	0.801	0.683	0.926	CLONAL	1	TRUE	0	0.466294073001074	1		313	189	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033833	49033833	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	91	502	0	ENST00000267163.4:c.1970T>C	p.Leu657Pro	p.L657P	ENST00000267163	NM_000321.2	657	cTa/cCa	20/27	0.466294073001074	1	FACETS	0.802	0.718	0.891	0.802	0.718	0.891	CLONAL	1	TRUE	0	0.466294073001074	1		502	373	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061024	38061024	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	44	181	0	ENST00000250448.2:c.965G>T	p.Gly322Val	p.G322V	ENST00000250448	NM_004496.3	322	gGc/gTc	2/2	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.466294073001074	2		181	154	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217677	7217700	+	inframe_deletion	In_Frame_Del	DEL	GCTTCTCTTCCTGTAGAGCCAAAA	GCTTCTCTTCCTGTAGAGCCAAAA	-	novel	NA	P-0018134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	88	473	0	ENST00000380728.2:c.227_250del	p.Leu76_Lys83del	p.L76_K83del	ENST00000380728		76	cTTTTGGCTCTACAGGAAGAGAAGCac/cac	4/11	0.462792260378783	1	FACETS	0.694	0.618	0.774	0.694	0.618	0.774	SUBCLONAL	1	TRUE	0	0.466294073001074	1		473	417	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31939981	31939981	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573446910	NA	P-0018134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	92	337	0	ENST00000375333.2:c.208G>A	p.Gly70Arg	p.G70R	ENST00000375333	NM_032454.1	70	Gga/Aga	1/8	0.466528064161371	3	FACETS	1	0.972	1	0.629	0.563	0.698	CLONAL	1	TRUE	1	0.466294073001074	3		337	387	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819187	3819188	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	G	novel	NA	P-0018134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	82	448	0	ENST00000262367.5:c.3047_3048delinsC	p.Glu1016AlafsTer6	p.E1016Afs*6	ENST00000262367	NM_004380.2	1016	gAG/gC	15/31	1	2	FACETS	0.868	0.77	0.973	0.868	0.77	0.973	CLONAL	1	TRUE	1	0.466294073001074	2		448	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0018136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	152	836	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.448099596258993	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.459435273956514	1		836	459	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219685	36219685	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	63	888	0	ENST00000222270.7:c.4582C>G	p.Pro1528Ala	p.P1528A	ENST00000222270	NM_014727.1	1528	Ccc/Gcc	20/37	0.459435273956514	3	FACETS	0.497	0.429	0.57			1	SUBCLONAL	1	TRUE	NA	0.459435273956514	3		888	679	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0018137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	258	963	1	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.278580573556188	3	FACETS	1	0.969	1	0.698	0.656	0.74	CLONAL	2	TRUE	0	0.391986266110242	3		964	752	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591931	48591931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	31	426	0	ENST00000342988.3:c.1094G>A	p.Gly365Asp	p.G365D	ENST00000342988	NM_005359.5	365	gGt/gAt	9/12	1	2	FACETS	0.841	0.687	1	0.841	0.687	1	CLONAL	1	TRUE	1	0.391986266110242	2		426	188	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209465	98209465	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	85	453	0	ENST00000331920.6:c.4073G>T	p.Gly1358Val	p.G1358V	ENST00000331920	NM_000264.3	1358	gGc/gTc	23/24	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.391986266110242	2		453	426	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184601	11184601	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	140	714	0	ENST00000361445.4:c.6616A>G	p.Asn2206Asp	p.N2206D	ENST00000361445	NM_004958.3	2206	Aac/Gac	47/58	0.313577343871932	4	FACETS	1	0.981	1	0.644	0.587	0.704	CLONAL	1	TRUE	2	0.391986266110242	4		714	772	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027156	49027159	+	frameshift_variant	Frame_Shift_Del	DEL	CAAT	CAAT	-	novel	NA	P-0018137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	11	581	0	ENST00000267163.4:c.1726_1729del	p.Ser576ArgfsTer34	p.S576Rfs*34	ENST00000267163	NM_000321.2	575	CAATca/ca	18/27	0.391986266110242	1	FACETS	0.237	0.164	0.329	0.237	0.164	0.329	SUBCLONAL	1	TRUE	0	0.391986266110242	1		581	190	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533290	29533291	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0018137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	66	354	0	ENST00000356175.3:c.1296_1297del	p.Tyr433LeufsTer5	p.Y433Lfs*5	ENST00000356175	NM_000267.3	431	gcTGtg/gctg	12/57	0.278580573556188	3	FACETS	0.945	0.834	1	0.63	0.556	0.708	CLONAL	2	TRUE	0	0.391986266110242	3		354	213	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231530	5231530	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	103	698	1	ENST00000357368.4:c.1946G>T	p.Gly649Val	p.G649V	ENST00000357368	NM_002850.3	649	gGg/gTg	14/38	1	2	FACETS	0.9	0.807	0.998	0.9	0.807	0.998	CLONAL	1	TRUE	1	0.391986266110242	2		699	584	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281592	198281592	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	80	543	1	ENST00000335508.6:c.539A>T	p.Glu180Val	p.E180V	ENST00000335508	NM_012433.2	180	gAa/gTa	6/25	0.240025335761323	3	FACETS	0.946	0.835	1	0.473	0.417	0.533	CLONAL	1	TRUE	1	0.391986266110242	3		544	516	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546039	41546039	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	66	1024	0	ENST00000263253.7:c.2654C>G	p.Thr885Arg	p.T885R	ENST00000263253	NM_001429.3	885	aCa/aGa	14/31	0.240025335761323	3	FACETS	0.372	0.322	0.427	0.186	0.161	0.214	SUBCLONAL	1	TRUE	1	0.391986266110242	3		1024	1082	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391034	89391034	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	78	737	2	ENST00000336596.2:c.1100G>T	p.Gly367Val	p.G367V	ENST00000336596	NM_005233.5	367	gGg/gTg	5/17	1	2	FACETS	0.761	0.67	0.858	0.761	0.67	0.858	SUBCLONAL	1	TRUE	1	0.391986266110242	2		739	523	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920240	1920240	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1560642259	NA	P-0018137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	149	766	0	ENST00000382891.5:c.1300G>C	p.Gly434Arg	p.G434R	ENST00000382891	NM_133335.3	434	Gga/Cga	5/22	0.391986266110242	4	FACETS	1	0.966	1	0.371	0.339	0.405	CLONAL	1	TRUE	1	0.391986266110242	4		766	950	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980328	55980328	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs758344832	NA	P-0018137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	81	725	0	ENST00000263923.4:c.763G>C	p.Gly255Arg	p.G255R	ENST00000263923	NM_002253.2	255	Ggg/Cgg	6/30	0.337275763765039	2	FACETS	1	0.959	1	0.589	0.523	0.659	CLONAL	1	TRUE	0	0.391986266110242	2		725	351	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081638	143081638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	79	427	0	ENST00000262992.4:c.1436G>A	p.Gly479Glu	p.G479E	ENST00000262992	NM_001101669.1	479	gGa/gAa	15/24	0.337275763765039	2	FACETS	1	0.905	1	0.513	0.453	0.576	CLONAL	1	TRUE	0	0.391986266110242	2		427	393	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345232	70345232	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	106	329	2	ENST00000374080.3:c.2258G>T	p.Arg753Leu	p.R753L	ENST00000374080		753	cGg/cTg	16/45	0.360110815534939	2	FACETS	1	0.97	1			1	CLONAL	1	TRUE	NA	0.391986266110242	2		331	453	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964925	55964925	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	119	638	0	ENST00000263923.4:c.2312C>G	p.Thr771Arg	p.T771R	ENST00000263923	NM_002253.2	771	aCg/aGg	16/30	0.190154612091486	2	FACETS	1	0.979	1	0.65	0.589	0.713	INDETERMINATE	1	TRUE	0	0.346305348673182	2		638	529	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591086	67591086	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	47	462	0	ENST00000274335.5:c.1679A>G	p.Asp560Gly	p.D560G	ENST00000274335		560	gAc/gGc	12/15	1	2	FACETS	0.762	0.646	0.89	0.762	0.646	0.89	SUBCLONAL	1	TRUE	1	0.346305348673182	2		462	356	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937713	44937714	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	50	786	0	ENST00000377967.4:c.2902dup	p.Thr968AsnfsTer11	p.T968Nfs*11	ENST00000377967	NM_021140.2	967	-/A	19/29	1	2	FACETS	0.589	0.5	0.687	0.589	0.5	0.687	SUBCLONAL	1	TRUE	1	0.346305348673182	2		786	490	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0018139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	139	427	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.467094052116374	2	FACETS	0.783	0.721	0.847	0.783	0.721	0.847	SUBCLONAL	2	TRUE	0	0.467094052116374	2		427	380	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0018139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	207	643	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.467094052116374	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	3	TRUE	0	0.467094052116374	3		643	359	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591115	67591116	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1561299903	NA	P-0018139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	56	442	0	ENST00000274335.5:c.1710dup	p.Ile571TyrfsTer31	p.I571Yfs*31	ENST00000274335		570	ctt/cTtt	12/15	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.467094052116374	2		442	234	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118924	70118926	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0018139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	239	948	0	ENST00000245479.2:c.499_501del	p.Lys167del	p.K167del	ENST00000245479	NM_000346.3	166	AAG/-	2/3	0.467094052116374	3	FACETS	0.931	0.874	0.989	0.931	0.874	0.989	CLONAL	2	TRUE	1	0.467094052116374	3		948	678	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466040	69466040	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	88	683	0	ENST00000227507.2:c.878T>G	p.Val293Gly	p.V293G	ENST00000227507	NM_053056.2	293	gTg/gGg	5/5	1	2	FACETS	0.926	0.825	1	0.926	0.825	1	CLONAL	1	TRUE	1	0.467094052116374	2		683	407	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257510	16257510	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370305920	NA	P-0018139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	68	487	0	ENST00000375759.3:c.4775G>A	p.Arg1592Gln	p.R1592Q	ENST00000375759	NM_015001.2	1592	cGg/cAg	11/15	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.467094052116374	2		487	284	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178689	108178689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	30	349	0	ENST00000278616.4:c.5740G>A	p.Asp1914Asn	p.D1914N	ENST00000278616	NM_000051.3	1914	Gac/Aac	38/63	1	2	FACETS	0.706	0.574	0.852	0.706	0.574	0.852	SUBCLONAL	1	TRUE	1	0.467094052116374	2		349	182	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120405	70120406	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	191	1149	2	ENST00000245479.2:c.1409dup	p.Asn470LysfsTer108	p.N470Kfs*108	ENST00000245479	NM_000346.3	469	-/A	3/3	0.467094052116374	3	FACETS	1	0.965	1	0.536	0.496	0.578	CLONAL	1	TRUE	1	0.467094052116374	3		1151	941	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076937	41076937	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	62	695	0	ENST00000373198.4:c.1483G>A	p.Gly495Arg	p.G495R	ENST00000373198	NM_133170.3	495	Ggg/Agg	9/32	1	2	FACETS	0.729	0.633	0.833	0.729	0.633	0.833	SUBCLONAL	1	TRUE	1	0.467094052116374	2		695	364	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588965	67588966	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0018139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	27	366	0	ENST00000274335.5:c.1059dup	p.Thr354AspfsTer10	p.T354Dfs*10	ENST00000274335		352	-/G	8/15	1	2	FACETS	0.575	0.461	0.704	0.575	0.461	0.704	SUBCLONAL	1	TRUE	1	0.467094052116374	2		366	201	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0018140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	211	741	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.358424509025041	3	FACETS	1	0.984	1	0.762	0.715	0.81	CLONAL	2	TRUE	0	0.449440552620112	3		741	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0018140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	303	722	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.449440552620112	2	FACETS	0.994	0.944	1	0.994	0.944	1	CLONAL	2	TRUE	0	0.449440552620112	2		722	678	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591901	48591901	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	82	436	0	ENST00000342988.3:c.1064A>T	p.Asp355Val	p.D355V	ENST00000342988	NM_005359.5	355	gAc/gTc	9/12	0.449440552620112	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.449440552620112	1		436	270	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264400	16264400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	43	812	0	ENST00000375759.3:c.10603C>T	p.His3535Tyr	p.H3535Y	ENST00000375759	NM_015001.2	3535	Cat/Tat	13/15	0.239244116983915	3	FACETS	0.352	0.294	0.417	0.117	0.098	0.139	INDETERMINATE	1	TRUE	0	0.449440552620112	3		812	666	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998124	169998124	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762380206	NA	P-0018140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	65	718	1	ENST00000295797.4:c.815G>A	p.Arg272Gln	p.R272Q	ENST00000295797	NM_002740.5	272	cGa/cAa	9/18	0.399974655352932	4	FACETS	0.441	0.381	0.507	0.221	0.19	0.254	SUBCLONAL	1	TRUE	2	0.449440552620112	4		719	950	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0018141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	151	941	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.793	0.725	0.865	1	0.989	1	SUBCLONAL	2	TRUE	1	0.215577746591491	2		942	883	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974715	21974732	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCCCCCGCCTCCA	GCAGCGCCCCCGCCTCCA	-	novel	NA	P-0018141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	32	395	0	ENST00000304494.5:c.95_112del	p.Leu32_Leu37del	p.L32_L37del	ENST00000304494	NM_000077.4	32	cTGGAGGCGGGGGCGCTGCcc/ccc	1/3	0.215577746591491	1	FACETS	0.659	0.535	0.799	0.659	0.535	0.799	SUBCLONAL	1	TRUE	0	0.215577746591491	1		395	402	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593466	48593466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064796102	NA	P-0018141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	52	403	2	ENST00000342988.3:c.1217C>T	p.Ala406Val	p.A406V	ENST00000342988	NM_005359.5	406	gCg/gTg	10/12	0.215577746591491	1	FACETS	0.944	0.805	1	0.944	0.805	1	CLONAL	1	TRUE	0	0.215577746591491	1		405	456	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729939	30729940	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0018141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	30	432	0	ENST00000295754.5:c.1460_1461del	p.Met487LysfsTer28	p.M487Kfs*28	ENST00000295754	NM_003242.5	487	aTG/a	6/7	0.215577746591491	1	FACETS	0.462	0.372	0.566	0.462	0.372	0.566	SUBCLONAL	1	TRUE	0	0.215577746591491	1		432	537	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015019	37015019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751431527	NA	P-0018141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	64	506	1	ENST00000358127.4:c.385G>A	p.Val129Met	p.V129M	ENST00000358127	NM_001280556.1	129	Gtg/Atg	3/10	1	2	FACETS	0.991	0.859	1	0.991	0.859	1	CLONAL	1	TRUE	1	0.215577746591491	2		507	599	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710594	117710594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768790336	NA	P-0018143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	124	355	1	ENST00000368508.3:c.1678C>T	p.Arg560Cys	p.R560C	ENST00000368508	NM_002944.2	560	Cgc/Tgc	12/43	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.5751715502839	2		356	386	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532819	187532819	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1307123924	NA	P-0018143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	202	633	1	ENST00000441802.2:c.9574C>T	p.Gln3192Ter	p.Q3192*	ENST00000441802	NM_005245.3	3192	Cag/Tag	14/27	0.5751715502839	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.5751715502839	1		634	491	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129394	2129403	+	frameshift_variant	Frame_Shift_Del	DEL	GGACTCGGGG	GGACTCGGGG	-	novel	NA	P-0018143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	36	715	1	ENST00000219476.3:c.3250_3259del	p.Asp1084SerfsTer16	p.D1084Sfs*16	ENST00000219476	NM_000548.3	1083	ctGGACTCGGGG/ct	28/42	0.5751715502839	1	FACETS	0.198	0.163	0.238	0.198	0.163	0.238	SUBCLONAL	1	TRUE	0	0.5751715502839	1		716	450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577516	7577517	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	360	558	0	ENST00000269305.4:c.764dup	p.Thr256HisfsTer8	p.T256Hfs*8	ENST00000269305	NM_001126112.2	255	atc/atTc	7/11	0.5751715502839	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.5751715502839	2		558	588	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912173	29912173	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	30	119	0	ENST00000376809.5:c.894G>A	p.Trp298Ter	p.W298*	ENST00000376809	NM_002116.7	298	tgG/tgA	4/8	1	2	FACETS	0.966	0.796	1	0.966	0.796	1	CLONAL	1	TRUE	1	0.5751715502839	2		119	108	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671977	30671977	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	293	685	0	ENST00000376406.3:c.4983G>C	p.Glu1661Asp	p.E1661D	ENST00000376406	NM_014641.2	1661	gaG/gaC	10/15	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.5751715502839	2		685	811	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0018145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	19	455	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.681	0.517	0.875	0.681	0.517	0.875	SUBCLONAL	1	TRUE	1	0.17	2		455	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0018145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	16	693	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.152360141547013	1	FACETS	0.293	0.215	0.387	0.293	0.215	0.387	SUBCLONAL	1	TRUE	0	0.17	1		693	588	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982143	201982143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	35	898	2	ENST00000359651.3:c.667G>A	p.Asp223Asn	p.D223N	ENST00000359651		223	Gat/Aat	5/8	1	2	FACETS	0.835	0.684	1	0.835	0.684	1	CLONAL	1	TRUE	1	0.17	2		900	493	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624287	89624288	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0018145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	30	644	0	ENST00000371953.3:c.61_62del	p.Phe21ArgfsTer22	p.F21Rfs*22	ENST00000371953	NM_000314.4	21	TTc/c	1/9	1	2	FACETS	0.802	0.646	0.98	0.802	0.646	0.98	CLONAL	1	TRUE	1	0.17	2		644	440	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118758	115118758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	28	670	1	ENST00000257566.3:c.583del	p.Glu195AsnfsTer13	p.E195Nfs*13	ENST00000257566	NM_016569.3	195	Gaa/aa	2/8	1	2	FACETS	0.718	0.573	0.883	0.718	0.573	0.883	SUBCLONAL	1	TRUE	1	0.17	2		671	459	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110803	2110803	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	27	790	0	ENST00000219476.3:c.1108C>T	p.Gln370Ter	p.Q370*	ENST00000219476	NM_000548.3	370	Cag/Tag	11/42	0.3	2	FACETS	0.727	0.578	0.898			1	SUBCLONAL	1	TRUE	NA	0.17	2		790	437	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857532	68857532	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	C	novel	NA	P-0018145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	12	440	0	ENST00000261769.5:c.2164+3A>C		p.X722_splice	ENST00000261769	NM_004360.3	722			0.152360141547013	1	FACETS	0.569	0.4	0.778	0.569	0.4	0.778	SUBCLONAL	1	TRUE	0	0.17	1		440	227	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101193	41101193	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	23	661	0	ENST00000373198.4:c.1163A>G	p.His388Arg	p.H388R	ENST00000373198	NM_133170.3	388	cAt/cGt	8/32	1	2	FACETS	0.817	0.637	1	0.817	0.637	1	CLONAL	1	TRUE	1	0.17	2		661	331	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059184	47059184	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	26	633	0	ENST00000409792.3:c.7477G>C	p.Asp2493His	p.D2493H	ENST00000409792	NM_014159.6	2493	Gac/Cac	20/21	1	2	FACETS	0.75	0.593	0.929	0.75	0.593	0.929	CLONAL	1	TRUE	1	0.17	2		633	408	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405978	49405978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	35	805	0	ENST00000418115.1:c.160G>A	p.Glu54Lys	p.E54K	ENST00000418115	NM_001664.2	54	Gag/Aag	3/5	1	2	FACETS	0.829	0.678	0.997	0.829	0.678	0.997	CLONAL	1	TRUE	1	0.17	2		805	497	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940013	49940013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	40	859	0	ENST00000296474.3:c.1030G>A	p.Glu344Lys	p.E344K	ENST00000296474	NM_002447.2	344	Gaa/Aaa	1/20	1	2	FACETS	0.908	0.754	1	0.908	0.754	1	CLONAL	1	TRUE	1	0.17	2		859	518	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503671	186503671	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0018145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	23	418	0	ENST00000323963.5:c.349-1G>C		p.X117_splice	ENST00000323963		117			1	2	FACETS	0.995	0.777	1	0.995	0.777	1	CLONAL	1	TRUE	1	0.17	2		418	272	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156155	106156155	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	30	524	0	ENST00000380013.4:c.1056C>G	p.Phe352Leu	p.F352L	ENST00000380013	NM_001127208.2	352	ttC/ttG	3/11	1	2	FACETS	0.989	0.797	1	0.989	0.797	1	CLONAL	1	TRUE	1	0.17	2		524	357	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514405	149514405	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs17853027	NA	P-0018145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	23	645	0	ENST00000261799.4:c.539C>G	p.Ser180Cys	p.S180C	ENST00000261799	NM_002609.3	180	tCt/tGt	4/23	1	2	FACETS	0.754	0.587	0.946	0.754	0.587	0.946	CLONAL	1	TRUE	1	0.17	2		645	359	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045670	26045670	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	12	194	0	ENST00000540144.1:c.32C>T	p.Ser11Phe	p.S11F	ENST00000540144	NM_003531.2	11	tCt/tTt	1/1	0.152360141547013	3	FACETS	0.842	0.593	1	0.421	0.296	0.574	CLONAL	1	TRUE	1	0.17	3		194	182	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888701	76888701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	22	647	0	ENST00000373344.5:c.5128G>A	p.Asp1710Asn	p.D1710N	ENST00000373344	NM_000489.3	1710	Gat/Aat	19/35	1	2	FACETS	0.784	0.608	0.989	0.784	0.608	0.989	CLONAL	1	TRUE	1	0.17	2		647	330	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0018146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	51	527	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.427079685798642	3	FACETS	1	0.965	1	0.721	0.621	0.827	CLONAL	1	TRUE	1	0.427079685798642	3		527	201	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457242	25457242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147001633	NA	P-0018146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	11	518	2	ENST00000264709.3:c.2645G>A	p.Arg882His	p.R882H	ENST00000264709	NM_175629.2	882	cGc/cAc	23/23	NA	2	FACETS	0.176	0.121	0.245			1	INDETERMINATE	1	TRUE	NA	0.427079685798642	2		520	292	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115729	8115730	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	34	567	0	ENST00000346208.3:c.1077dup	p.Gly360ArgfsTer11	p.G360Rfs*11	ENST00000346208		359	gaa/gAaa	6/6	1	2	FACETS	0.463	0.379	0.557	0.463	0.379	0.557	SUBCLONAL	1	TRUE	1	0.427079685798642	2		567	344	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332103	70332103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763123299	NA	P-0018146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	29	152	0	ENST00000373644.4:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000373644	NM_030625.2	3	cGa/cAa	2/12	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.427079685798642	2		152	108	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665721	29665721	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs1060500266	NA	P-0018146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	27	415	0	ENST00000356175.3:c.6757-1G>C		p.X2253_splice	ENST00000356175	NM_000267.3	2253			NA	2	FACETS	0.472	0.376	0.58			1	INDETERMINATE	1	TRUE	NA	0.427079685798642	2		415	268	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461452	138461452	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	88	505	1	ENST00000289153.2:c.569A>T	p.Asp190Val	p.D190V	ENST00000289153	NM_006219.2	190	gAt/gTt	3/22	0.427079685798642	3	FACETS	1	0.979	1	0.48	0.429	0.534	CLONAL	1	TRUE	0	0.427079685798642	3		506	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0018148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	380	745	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	0.881836537876469	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.915219698685902	2		745	410	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680968	30680968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2517560	NA	P-0018148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	300	672	1	ENST00000376406.3:c.751G>A	p.Glu251Lys	p.E251K	ENST00000376406	NM_014641.2	251	Gaa/Aaa	5/15	0.888499501958658	2	FACETS	0.942	0.917	0.965	0.942	0.917	0.965	CLONAL	2	TRUE	0	0.915219698685902	2		673	348	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566488	41566488	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	17	368	0	ENST00000263253.7:c.4365G>C	p.Gln1455His	p.Q1455H	ENST00000263253	NM_001429.3	1455	caG/caC	27/31	NA	2	FACETS	0.115	0.085	0.15			1	INDETERMINATE	1	TRUE	NA	0.915219698685902	2		368	323	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602496	10602496	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750532889	NA	P-0018148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	352	515	0	ENST00000171111.5:c.1082C>T	p.Pro361Leu	p.P361L	ENST00000171111	NM_203500.1	361	cCg/cTg	3/6	0.888076157528997	3	FACETS	0.978	0.96	0.995	0.978	0.96	0.995	CLONAL	3	TRUE	0	0.915219698685902	3		515	382	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637673	176637673	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	429	866	1	ENST00000439151.2:c.2273C>T	p.Ser758Leu	p.S758L	ENST00000439151	NM_022455.4	758	tCa/tTa	5/23	0.881836537876469	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.915219698685902	2		867	468	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912075	76912075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782228142	NA	P-0018148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	169	471	0	ENST00000373344.5:c.4189G>A	p.Glu1397Lys	p.E1397K	ENST00000373344	NM_000489.3	1397	Gaa/Aaa	13/35	0.690713359565192	3	FACETS	0.908	0.839	0.979			1	CLONAL	1	TRUE	NA	0.915219698685902	3		471	593	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874529	155874529	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	298	720	0	ENST00000368323.3:c.230C>G	p.Ala77Gly	p.A77G	ENST00000368323	NM_006912.5	77	gCt/gGt	4/6	0.780681740408244	6	FACETS	0.951	0.897	1	0.476	0.448	0.503	CLONAL	2	TRUE	2	0.915219698685902	6		720	969	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937091	48937091	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	150	306	0	ENST00000267163.4:c.859G>T	p.Glu287Ter	p.E287*	ENST00000267163	NM_000321.2	287	Gag/Tag	8/27	0.886275226144367	2	FACETS	0.942	0.906	0.974	0.942	0.906	0.974	CLONAL	2	TRUE	0	0.915219698685902	2		306	174	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191012	2191012	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	189	364	0	ENST00000398665.3:c.266G>A	p.Trp89Ter	p.W89*	ENST00000398665	NM_032482.2	89	tGg/tAg	5/28	0.888076157528997	3	FACETS	0.998	0.975	1	0.998	0.975	1	CLONAL	3	TRUE	0	0.915219698685902	3		364	201	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388028	31388028	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	191	455	1	ENST00000328111.2:c.1829C>A	p.Ser610Tyr	p.S610Y	ENST00000328111	NM_006892.3	610	tCc/tAc	17/23	0.744527152419801	4	FACETS	0.98	0.918	1	0.98	0.918	1	CLONAL	2	TRUE	2	0.915219698685902	4		456	408	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374880	149374880	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223849448	NA	P-0018148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	264	499	1	ENST00000360632.3:c.214G>A	p.Gly72Ser	p.G72S	ENST00000360632	NM_015472.4	72	Ggc/Agc	2/7	0.856279598398324	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.915219698685902	3		500	411	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549372	187549372	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	349	814	1	ENST00000441802.2:c.4746G>T	p.Leu1582Phe	p.L1582F	ENST00000441802	NM_005245.3	1582	ttG/ttT	9/27	0.888499501958658	2	FACETS	0.919	0.894	0.942	0.919	0.894	0.942	CLONAL	2	TRUE	0	0.915219698685902	2		815	415	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227679	53227679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	151	616	0	ENST00000375401.3:c.2509G>A	p.Glu837Lys	p.E837K	ENST00000375401	NM_004187.3	837	Gaa/Aaa	17/26	NA	2	FACETS	0.991	0.921	1			1	INDETERMINATE	1	TRUE	NA	0.915219698685902	2		616	333	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411961	63411961	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	22	595	0	ENST00000330258.3:c.1206A>C	p.Glu402Asp	p.E402D	ENST00000330258	NM_152424.3	402	gaA/gaC	2/2	NA	2	FACETS	0.12	0.092	0.152			1	INDETERMINATE	1	TRUE	NA	0.915219698685902	2		595	401	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346942	70346942	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	120	562	0	ENST00000374080.3:c.2809C>T	p.Leu937Phe	p.L937F	ENST00000374080		937	Ctc/Ttc	20/45	NA	2	FACETS	0.892	0.818	0.967			1	INDETERMINATE	1	TRUE	NA	0.915219698685902	2		562	294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0018148-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	746	745	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	0.891995422661513	2	FACETS	0.996	0.981	1	0.996	0.981	1	CLONAL	2	TRUE	0	0.902855316561177	2		745	830	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680968	30680968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2517560	NA	P-0018148-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	605	672	1	ENST00000376406.3:c.751G>A	p.Glu251Lys	p.E251K	ENST00000376406	NM_014641.2	251	Gaa/Aaa	5/15	0.890539112788452	2	FACETS	0.98	0.963	0.996	0.98	0.963	0.996	CLONAL	2	TRUE	0	0.902855316561177	2		673	684	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602496	10602496	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750532889	NA	P-0018148-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	846	515	0	ENST00000171111.5:c.1082C>T	p.Pro361Leu	p.P361L	ENST00000171111	NM_203500.1	361	cCg/cTg	3/6	0.902855316561177	3	FACETS	0.997	0.986	1	0.997	0.986	1	CLONAL	3	TRUE	0	0.902855316561177	3		515	909	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637673	176637673	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018148-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	588	866	1	ENST00000439151.2:c.2273C>T	p.Ser758Leu	p.S758L	ENST00000439151	NM_022455.4	758	tCa/tTa	5/23	0.872128747039133	2	FACETS	0.984	0.967	1	0.984	0.967	1	CLONAL	2	TRUE	0	0.902855316561177	2		867	662	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874529	155874529	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018148-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	599	720	0	ENST00000368323.3:c.230C>G	p.Ala77Gly	p.A77G	ENST00000368323	NM_006912.5	77	gCt/gGt	4/6	0.902855316561177	5	FACETS	0.956	0.919	0.993	0.637	0.613	0.662	CLONAL	2	TRUE	2	0.902855316561177	5		720	1634	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937091	48937091	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018148-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	151	306	0	ENST00000267163.4:c.859G>T	p.Glu287Ter	p.E287*	ENST00000267163	NM_000321.2	287	Gag/Tag	8/27	0.902855316561177	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.902855316561177	1		306	181	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191012	2191012	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018148-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	336	364	0	ENST00000398665.3:c.266G>A	p.Trp89Ter	p.W89*	ENST00000398665	NM_032482.2	89	tGg/tAg	5/28	0.891995422661513	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.902855316561177	2		364	370	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388028	31388028	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018148-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	449	455	1	ENST00000328111.2:c.1829C>A	p.Ser610Tyr	p.S610Y	ENST00000328111	NM_006892.3	610	tCc/tAc	17/23	0.344565629499835	6	FACETS	1	0.985	1	1	0.985	1	INDETERMINATE	3	TRUE	3	0.902855316561177	6		456	884	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374880	149374880	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223849448	NA	P-0018148-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	264	499	1	ENST00000360632.3:c.214G>A	p.Gly72Ser	p.G72S	ENST00000360632	NM_015472.4	72	Ggc/Agc	2/7	0.902855316561177	3	FACETS	1	0.969	1	0.523	0.491	0.555	CLONAL	1	TRUE	1	0.902855316561177	3		500	812	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549372	187549372	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018148-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	994	814	1	ENST00000441802.2:c.4746G>T	p.Leu1582Phe	p.L1582F	ENST00000441802	NM_005245.3	1582	ttG/ttT	9/27	0.902855316561177	3	FACETS	0.985	0.973	0.995	0.985	0.973	0.995	CLONAL	3	TRUE	0	0.902855316561177	3		815	1082	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227679	53227679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018148-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	271	616	0	ENST00000375401.3:c.2509G>A	p.Glu837Lys	p.E837K	ENST00000375401	NM_004187.3	837	Gaa/Aaa	17/26	NA	2	FACETS	0.962	0.91	1			1	INDETERMINATE	1	TRUE	NA	0.902855316561177	2		616	624	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346942	70346942	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018148-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	252	562	0	ENST00000374080.3:c.2809C>T	p.Leu937Phe	p.L937F	ENST00000374080		937	Ctc/Ttc	20/45	NA	2	FACETS	0.948	0.894	1			1	INDETERMINATE	1	TRUE	NA	0.902855316561177	2		562	589	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224321	55224321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018148-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	298	679	0	ENST00000275493.2:c.1102G>A	p.Asp368Asn	p.D368N	ENST00000275493	NM_005228.3	368	Gat/Aat	9/28	0.902855316561177	3	FACETS	0.987	0.931	1	0.493	0.465	0.522	CLONAL	1	TRUE	1	0.902855316561177	3		679	971	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417802	32417802	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0018148-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	164	398	0	ENST00000332351.3:c.1249+1G>A		p.X417_splice	ENST00000332351	NM_024426.4	417			0.900143428624779	2	FACETS	0.904	0.84	0.969	0.452	0.42	0.485	CLONAL	1	TRUE	0	0.902855316561177	2		398	402	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435364	18435364	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749307445	NA	P-0018148-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	51	486	0	ENST00000266497.5:c.349C>T	p.Pro117Ser	p.P117S	ENST00000266497		117	Cct/Tct	1/31	0.900143428624779	2	FACETS	0.227	0.193	0.265	0.114	0.096	0.133	SUBCLONAL	1	TRUE	0	0.902855316561177	2		486	497	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627624	14627624	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018148-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	293	569	0	ENST00000254322.2:c.446C>G	p.Ser149Cys	p.S149C	ENST00000254322	NM_006145.1	149	tCc/tGc	2/3	0.902855316561177	3	FACETS	0.975	0.919	1	0.325	0.306	0.344	CLONAL	1	TRUE	0	0.902855316561177	3		569	966	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149877	99149877	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018148-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	51	521	0	ENST00000074304.5:c.189G>T	p.Lys63Asn	p.K63N	ENST00000074304	NM_001134224.1	63	aaG/aaT	5/26	0.799056871103345	3	FACETS	0.203	0.171	0.237	0.101	0.085	0.119	SUBCLONAL	1	TRUE	1	0.902855316561177	3		521	809	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0018153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	190	427	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.766406006699764	3	FACETS	0.879	0.825	0.934	0.879	0.825	0.934	CLONAL	2	TRUE	1	0.766406006699764	3		427	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0018153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	135	775	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.766406006699764	1	FACETS	0.829	0.77	0.888	0.829	0.77	0.888	CLONAL	1	TRUE	0	0.766406006699764	1		777	262	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0018153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	104	267	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.711385889245505	2	FACETS	0.822	0.763	0.88	0.822	0.763	0.88	CLONAL	2	TRUE	0	0.766406006699764	2		267	165	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223230	5223230	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	130	651	1	ENST00000357368.4:c.2573C>G	p.Thr858Ser	p.T858S	ENST00000357368	NM_002850.3	858	aCc/aGc	18/38	1	2	FACETS	0.798	0.73	0.868	0.798	0.73	0.868	SUBCLONAL	1	TRUE	1	0.766406006699764	2		652	425	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206737	27206737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764254208	NA	P-0018153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	85	402	0	ENST00000380036.4:c.2522C>T	p.Ala841Val	p.A841V	ENST00000380036	NM_000459.3	841	gCg/gTg	15/23	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.766406006699764	2		402	219	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931589	NA	P-0018154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	108	257	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	0.849272498124802	2		257	234	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996418	100996792	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAAAGTACTATTAGAACAAAGCTGTTTCCTCAAAGCTAAGCAGTTAAGGAACAATAGTAGCACTGTCCTCAAGATTTTTATGACTTATGTCTAATACTGAAAGTGTTAGTCAAAGAGTATGCAATTATAGTACCCAACCACATTCCATTTTGAGTATCATAAATAAAAACATATTGTTAAAATGTCATCATATATTTTAAATTATATGGAAATATCACCATTTCTTATAAGAAACAAGGAATAATTGAAATCTATACAATATTAGATGGTCTCCATTTACAATTAAACCAATAATAAAGGATCAGGGGAAAGGAGCCTACCTTCCATTGCCCTCTTAAAGAAGACCTTACAGCTCCCACAGGTAAGGACACCATA	AAAAGTACTATTAGAACAAAGCTGTTTCCTCAAAGCTAAGCAGTTAAGGAACAATAGTAGCACTGTCCTCAAGATTTTTATGACTTATGTCTAATACTGAAAGTGTTAGTCAAAGAGTATGCAATTATAGTACCCAACCACATTCCATTTTGAGTATCATAAATAAAAACATATTGTTAAAATGTCATCATATATTTTAAATTATATGGAAATATCACCATTTCTTATAAGAAACAAGGAATAATTGAAATCTATACAATATTAGATGGTCTCCATTTACAATTAAACCAATAATAAAGGATCAGGGGAAAGGAGCCTACCTTCCATTGCCCTCTTAAAGAAGACCTTACAGCTCCCACAGGTAAGGACACCATA	-	novel	NA	P-0018154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3	72	2	0	ENST00000325455.5:c.1735_1789+320del		p.X579_splice	ENST00000325455	NM_001202474.3	579		2/8	0.8271131919423	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.849272498124802	1		2	75	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199818	108199841	+	inframe_deletion	In_Frame_Del	DEL	TTCTCTCATTAGCCCGGTTTTCAG	TTCTCTCATTAGCCCGGTTTTCAG	-	novel	NA	P-0018154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	104	379	0	ENST00000278616.4:c.7160_7183del	p.Phe2387_Asp2395delinsTyr	p.F2387_D2395delinsY	ENST00000278616	NM_000051.3	2387	tTTCTCTCATTAGCCCGGTTTTCAGat/tat	49/63	0.8271131919423	1	FACETS	0.965	0.903	1	0.965	0.903	1	CLONAL	1	TRUE	0	0.849272498124802	1		379	146	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440145	49440145	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	565	603	1	ENST00000301067.7:c.4481del	p.Ser1494IlefsTer12	p.S1494Ifs*12	ENST00000301067	NM_003482.3	1494	aGt/at	16/54	0.827338195802361	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	0	0.849272498124802	3		604	632	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510064	187510064	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	91	419	0	ENST00000441802.2:c.13449G>T	p.Arg4483Ser	p.R4483S	ENST00000441802	NM_005245.3	4483	agG/agT	27/27	0.84115292988528	1	FACETS	0.856	0.791	0.92	0.856	0.791	0.92	CLONAL	1	TRUE	0	0.849272498124802	1		419	144	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	136	918	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.170905613062042	2	FACETS	0.967	0.881	1	0.967	0.881	1	CLONAL	2	TRUE	0	0.202456007302209	2		918	695	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0018156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	115	509	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.170905613062042	2	FACETS	1	0.984	1	0.747	0.673	0.826	CLONAL	1	TRUE	0	0.202456007302209	2		509	760	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290270	15290270	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	62	724	0	ENST00000263388.2:c.3365A>G	p.Asp1122Gly	p.D1122G	ENST00000263388	NM_000435.2	1122	gAc/gGc	21/33	1	2	FACETS	0.728	0.628	0.838	0.728	0.628	0.838	SUBCLONAL	1	TRUE	1	0.202456007302209	2		724	841	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046359	69046359	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	45	382	0	ENST00000288368.4:c.3832T>G	p.Phe1278Val	p.F1278V	ENST00000288368	NM_024870.2	1278	Ttc/Gtc	32/40	1	2	FACETS	0.834	0.701	0.982	0.834	0.701	0.982	CLONAL	1	TRUE	1	0.202456007302209	2		382	533	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0018157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	34	294	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.239565423973621	1	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	0	0.239565423973621	1		294	225	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0018157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	56	607	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.792	0.679	0.917	0.792	0.679	0.917	CLONAL	1	TRUE	1	0.239565423973621	2		607	590	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097731	8097731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	73	420	3	ENST00000346208.3:c.113C>T	p.Ala38Val	p.A38V	ENST00000346208		38	gCg/gTg	2/6	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.239565423973621	2		423	455	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	463369	463369	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1199969646	NA	P-0018157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	35	478	0	ENST00000399788.2:c.902G>A	p.Arg301Gln	p.R301Q	ENST00000399788	NM_001042603.1	301	cGg/cAg	8/28	0.239565423973621	3	FACETS	0.588	0.481	0.709			1	SUBCLONAL	1	TRUE	NA	0.239565423973621	3		478	556	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145121	58145121	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	35	351	0	ENST00000257904.6:c.223A>T	p.Met75Leu	p.M75L	ENST00000257904	NM_000075.3	75	Atg/Ttg	3/8	1	2	FACETS	0.744	0.61	0.893	0.744	0.61	0.893	SUBCLONAL	1	TRUE	1	0.239565423973621	2		351	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577124	+	frameshift_variant	Frame_Shift_Del	DEL	CACGCAC	CACGCAC	-	novel	NA	P-0018157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	76	673	0	ENST00000269305.4:c.814_820del	p.Val272PhefsTer71	p.V272Ffs*71	ENST00000269305	NM_001126112.2	272	GTGCGTGtt/tt	8/11	0.239565423973621	1	FACETS	0.999	0.878	1	0.999	0.878	1	CLONAL	1	TRUE	0	0.239565423973621	1		673	559	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252965	36252966	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0018157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	63	444	0	ENST00000300305.3:c.395_396dup	p.Met133Ter	p.M133*	ENST00000300305		132	-/TG	4/8	0.239565423973621	1	FACETS	0.979	0.848	1	0.979	0.848	1	CLONAL	1	TRUE	0	0.239565423973621	1		444	473	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793614	89793614	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	75	396	0	ENST00000336032.3:c.683C>G	p.Ala228Gly	p.A228G	ENST00000336032	NM_006813.2	228	gCa/gGa	2/2	0.239565423973621	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.239565423973621	1		396	406	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0018168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	132	306	0				ENST00000310581	NM_198253.2	-/1132			0.215644260747258	1	FACETS	0.731	0.67	0.794	0.731	0.67	0.794	INDETERMINATE	1	TRUE	0	0.625137898510129	1		306	397	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099406	157099426	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAGCAA	CAGCAGCAGCAGCAGCAGCAA	-	rs762617219	NA	P-0018168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	59	274	0	ENST00000346085.5:c.363_383del	p.Gln125_Gln131del	p.Q125_Q131del	ENST00000346085	NM_020732.3	115	CAGCAGCAGCAGCAGCAGCAA/-	1/20	1	2	FACETS	0.56	0.485	0.641	0.56	0.485	0.641	SUBCLONAL	1	TRUE	1	0.625137898510129	2		274	337	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs149840192	NA	P-0018168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	548	784	1	ENST00000275493.2:c.866C>A	p.Ala289Asp	p.A289D	ENST00000275493	NM_005228.3	289	gCc/gAc	7/28	0.612572482234762	4	FACETS	0.985	0.945	1	0.656	0.63	0.683	CLONAL	2	TRUE	1	0.625137898510129	4		785	1447	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201885	102201885	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	60	677	0	ENST00000263464.3:c.1237G>C	p.Val413Leu	p.V413L	ENST00000263464	NM_001165.4	413	Gtc/Ctc	6/9	0.572782823376079	1	FACETS	0.787	0.69	0.888	0.787	0.69	0.888	SUBCLONAL	1	TRUE	0	0.572782823376079	1		677	190	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56854491	56854491	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	168	978	0	ENST00000519728.1:c.73C>G	p.Arg25Gly	p.R25G	ENST00000519728	NM_002350.3	25	Cgt/Ggt	2/13	0.572782823376079	5	FACETS	1	0.986	1	0.451	0.415	0.489	CLONAL	1	TRUE	2	0.572782823376079	5		978	806	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978622	70978622	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	93	917	0	ENST00000276594.2:c.1031G>C	p.Cys344Ser	p.C344S	ENST00000276594	NM_024504.3	344	tGt/tCt	5/8	0.572782823376079	5	FACETS	0.558	0.495	0.626	0.186	0.165	0.209	SUBCLONAL	1	TRUE	2	0.572782823376079	5		917	1082	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412023	116412023	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	137	886	0	ENST00000397752.3:c.3008A>T	p.Tyr1003Phe	p.Y1003F	ENST00000397752	NM_000245.2	1003	tAc/tTc	14/21	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.21	2		886	1281	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459437	50459437	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	39	421	0	ENST00000331340.3:c.726A>T	p.Glu242Asp	p.E242D	ENST00000331340	NM_006060.4	242	gaA/gaT	7/8	0.103482923593909	3	FACETS	0.797	0.66	0.95	0.398	0.33	0.475	INDETERMINATE	1	TRUE	1	0.21	3		421	515	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513218	106513218	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	49	416	0	ENST00000359195.3:c.2122C>A	p.His708Asn	p.H708N	ENST00000359195	NM_002649.2	708	Cac/Aac	4/11	1	2	FACETS	0.827	0.7	0.967	0.827	0.7	0.967	CLONAL	1	TRUE	1	0.21	2		416	564	SUCCESS
MET	4233	MSKCC	GRCh37	7	116417464	116417464	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913243	NA	P-0018171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	76	531	0	ENST00000397752.3:c.3281A>G	p.His1094Arg	p.H1094R	ENST00000397752	NM_000245.2	1094	cAt/cGt	16/21	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.21	2		531	673	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650815	48650815	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	47	909	2	ENST00000376670.3:c.684C>A	p.Cys228Ter	p.C228*	ENST00000376670	NM_002049.3	228	tgC/tgA	4/6	1	2	FACETS	0.541	0.455	0.636	0.541	0.455	0.636	SUBCLONAL	1	TRUE	1	0.21	2		911	828	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0018173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	270	569	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.719581129955047	2		569	750	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725043	89725043	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0018174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	39	321	1	ENST00000371953.3:c.1027del		p.X343_splice	ENST00000371953	NM_000314.4	343			0.280965619099979	1	FACETS	0.564	0.468	0.671	0.564	0.468	0.671	SUBCLONAL	1	TRUE	0	0.280965619099979	1		322	423	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061220	38061243	+	inframe_deletion	In_Frame_Del	DEL	CGTTCTCGAACATGTTGCCGGAGT	CGTTCTCGAACATGTTGCCGGAGT	-	novel	NA	P-0018174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	82	577	0	ENST00000250448.2:c.746_769del	p.Asp249_Asn256del	p.D249_N256del	ENST00000250448	NM_004496.3	249	gACTCCGGCAACATGTTCGAGAACGgc/ggc	2/2	1	2	FACETS	0.79	0.696	0.891	0.79	0.696	0.891	SUBCLONAL	1	TRUE	1	0.280965619099979	2		577	739	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0018176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	351	710	5	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.558847909821662	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.558847909821662	2		715	553	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119050	70119050	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	150	490	0	ENST00000245479.2:c.622C>T	p.Gln208Ter	p.Q208*	ENST00000245479	NM_000346.3	208	Cag/Tag	2/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.558847909821662	2		490	475	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056425	26056427	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	rs774779034	NA	P-0018176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	69	301	0	ENST00000343677.2:c.230_232del	p.Asn77del	p.N77del	ENST00000343677	NM_005319.3	77	aACAgc/agc	1/1	1	2	FACETS	0.76	0.667	0.859	0.76	0.667	0.859	SUBCLONAL	1	TRUE	1	0.558847909821662	2		301	325	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170283	119170283	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs144191570	NA	P-0018176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	123	416	0	ENST00000264033.4:c.2513G>T	p.Gly838Val	p.G838V	ENST00000264033	NM_005188.3	838	gGc/gTc	16/16	0.558847909821662	3	FACETS	1	0.939	1	0.521	0.473	0.572	CLONAL	1	TRUE	1	0.558847909821662	3		416	540	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729775	41729775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	181	317	1	ENST00000242208.4:c.754G>A	p.Ala252Thr	p.A252T	ENST00000242208	NM_002192.2	252	Gcc/Acc	3/3	0.558847909821662	7	FACETS	1	0.971	1	0.55	0.509	0.593	CLONAL	2	TRUE	3	0.558847909821662	7		318	706	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212130	5212130	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529643294	NA	P-0018176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	208	847	1	ENST00000357368.4:c.4901C>T	p.Thr1634Met	p.T1634M	ENST00000357368	NM_002850.3	1634	aCg/aTg	32/38	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.558847909821662	2		848	682	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163734	72163734	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	200	853	0	ENST00000357731.5:c.624T>A	p.Asp208Glu	p.D208E	ENST00000357731	NM_173808.2	208	gaT/gaA	4/7	0.558847909821662	3	FACETS	0.994	0.922	1	0.497	0.461	0.535	CLONAL	1	TRUE	1	0.558847909821662	3		853	921	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246537	46246537	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	78	305	0	ENST00000334344.6:c.4631C>T	p.Pro1544Leu	p.P1544L	ENST00000334344	NM_152641.2	1544	cCc/cTc	15/21	0.558847909821662	3	FACETS	0.804	0.71	0.905	0.402	0.355	0.453	CLONAL	1	TRUE	1	0.558847909821662	3		305	444	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217804	7217805	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	A	novel	NA	P-0018176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	440	849	0	ENST00000380728.2:c.204+2dup		p.X68_splice	ENST00000380728		68			0.558847909821662	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.558847909821662	2		849	754	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526426	66526426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	108	429	0	ENST00000358598.2:c.982G>A	p.Ala328Thr	p.A328T	ENST00000358598	NM_212471.2	328	Gca/Aca	11/11	1	2	FACETS	0.922	0.834	1	0.922	0.834	1	CLONAL	1	TRUE	1	0.558847909821662	2		429	419	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566857	212566857	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	29	307	0	ENST00000342788.4:c.1324A>T	p.Ile442Phe	p.I442F	ENST00000342788	NM_005235.2	442	Atc/Ttc	12/28	0.558847909821662	2	FACETS	0.384	0.309	0.469	0.192	0.154	0.235	SUBCLONAL	1	TRUE	0	0.558847909821662	2		307	270	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266046	41266046	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	92	294	0	ENST00000349496.5:c.43G>A	p.Glu15Lys	p.E15K	ENST00000349496	NM_001904.3	15	Gaa/Aaa	3/15	0.558847909821662	2	FACETS	0.86	0.769	0.954	0.43	0.384	0.477	CLONAL	1	TRUE	0	0.558847909821662	2		294	383	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467625	66467625	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	123	562	0	ENST00000273854.3:c.644A>C	p.Gln215Pro	p.Q215P	ENST00000273854	NM_004439.5	215	cAa/cCa	3/18	0.558847909821662	3	FACETS	0.884	0.801	0.971	0.442	0.4	0.486	CLONAL	1	TRUE	1	0.558847909821662	3		562	637	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225504	26225504	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	90	247	0	ENST00000360408.1:c.122G>A	p.Arg41His	p.R41H	ENST00000360408	NM_003532.2	41	cGc/cAc	1/1	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.558847909821662	2		247	314	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674209	117674209	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	228	748	0	ENST00000368508.3:c.4265A>G	p.Lys1422Arg	p.K1422R	ENST00000368508	NM_002944.2	1422	aAg/aGg	26/43	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.558847909821662	2		748	757	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692819	89692823	+	frameshift_variant	Frame_Shift_Del	DEL	CAAAC	CAAAC	-	novel	NA	P-0018178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	52	483	0	ENST00000371953.3:c.304_308del	p.Lys102LeufsTer3	p.K102Lfs*3	ENST00000371953	NM_000314.4	101	atCAAACcc/atcc	5/9	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.33	2		483	285	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0018179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	1300	843	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.341470871019484	7	FACETS	1	0.994	1			1	CLONAL	6	TRUE	NA	0.341470871019484	7		843	2246	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	184	930	0	ENST00000397752.3:c.3028G>C	p.Asp1010His	p.D1010H	ENST00000397752	NM_000245.2	1010	Gat/Cat	14/21	0.341470871019484	1	FACETS	0.802	0.739	0.867	0.802	0.739	0.867	CLONAL	1	TRUE	0	0.341470871019484	1		930	1115	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627439	14627440	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTT	novel	NA	P-0018179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	159	695	0	ENST00000254322.2:c.628_630dup	p.Lys210dup	p.K210dup	ENST00000254322	NM_006145.1	210	-/AAG	2/3	0.341470871019484	1	FACETS	0.822	0.753	0.894	0.822	0.753	0.894	CLONAL	1	TRUE	0	0.341470871019484	1		695	940	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	50	184	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.21886995996696	2		184	323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934571	NA	P-0018180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	91	681	0	ENST00000269305.4:c.747G>C	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agC	7/11	0.21886995996696	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.21886995996696	1		681	609	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118846	115118846	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	64	693	0	ENST00000257566.3:c.495T>G	p.Phe165Leu	p.F165L	ENST00000257566	NM_016569.3	165	ttT/ttG	2/8	1	2	FACETS	0.839	0.726	0.962	0.839	0.726	0.962	CLONAL	1	TRUE	1	0.21886995996696	2		693	697	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351388	89351388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	177	665	0	ENST00000301030.4:c.1562C>T	p.Ser521Phe	p.S521F	ENST00000301030	NM_001256183.1	521	tCc/tTc	9/13	0.21886995996696	5	FACETS	1	0.939	1	1	0.939	1	CLONAL	3	TRUE	2	0.21886995996696	5		665	703	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37048498	37048498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	73	570	0	ENST00000231790.2:c.397G>A	p.Gly133Arg	p.G133R	ENST00000231790	NM_000249.3	133	Gga/Aga	5/19	0.193047379064269	3	FACETS	0.96	0.838	1	0.48	0.419	0.546	CLONAL	1	TRUE	1	0.21886995996696	3		570	771	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965857	90965857	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	107	401	0	ENST00000265433.3:c.1460G>T	p.Cys487Phe	p.C487F	ENST00000265433	NM_002485.4	487	tGt/tTt	11/16	0.193047379064269	3	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	1	0.21886995996696	3		401	513	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737419	145737419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756401653	NA	P-0018180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	35	676	1	ENST00000428558.2:c.3268G>A	p.Glu1090Lys	p.E1090K	ENST00000428558	NM_004260.3	1090	Gag/Aag	20/22	0.193047379064269	3	FACETS	0.551	0.45	0.665	0.275	0.225	0.333	SUBCLONAL	1	TRUE	1	0.21886995996696	3		677	644	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267360	198267360	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs374250186	NA	P-0018181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	418	919	0	ENST00000335508.6:c.1997A>C	p.Lys666Thr	p.K666T	ENST00000335508	NM_012433.2	666	aAg/aCg	14/25	1	2	FACETS	0.916	0.874	0.959	0.916	0.874	0.959	CLONAL	1	TRUE	1	0.82272041009503	2		919	1109	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100312	27100312	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	851	972	4	ENST00000324856.7:c.4024C>T	p.Gln1342Ter	p.Q1342*	ENST00000324856	NM_006015.4	1342	Cag/Tag	17/20	NA	2	FACETS	0.987	0.969	1			1	INDETERMINATE	2	TRUE	NA	0.82272041009503	2		976	1048	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0018182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	207	710	5	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.311302082605057	2	FACETS	0.985	0.919	1	0.985	0.919	1	CLONAL	2	TRUE	0	0.326833601575862	2		715	643	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954325	48954327	+	missense_variant	Missense_Mutation	TNP	TCA	TCA	AAT	novel	NA	P-0018182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	46	584	1	ENST00000267163.4:c.1446_1448delinsAAT	p.Phe482_His483delinsLeuIle	p.F482_H483delinsLI	ENST00000267163	NM_000321.2	482	ttTCAt/ttAATt	16/27	0.326833601575862	1	FACETS	0.722	0.611	0.844	0.722	0.611	0.844	SUBCLONAL	1	TRUE	0	0.326833601575862	1		585	326	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967268	25967268	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	47	542	0	ENST00000435504.4:c.1938del	p.Thr647LeufsTer152	p.T647Lfs*152	ENST00000435504		646	atC/at	13/13	1	2	FACETS	0.543	0.458	0.637	0.543	0.458	0.637	SUBCLONAL	1	TRUE	1	0.326833601575862	2		542	530	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428478	72428478	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	98	795	0	ENST00000477973.2:c.526C>T	p.Gln176Ter	p.Q176*	ENST00000477973	NM_012234.5	176	Cag/Tag	2/4	1	2	FACETS	0.852	0.76	0.949	0.852	0.76	0.949	CLONAL	1	TRUE	1	0.326833601575862	2		795	704	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854976	76854976	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	98	1097	0	ENST00000373344.5:c.5860G>C	p.Val1954Leu	p.V1954L	ENST00000373344	NM_000489.3	1954	Gtg/Ctg	25/35	1	2	FACETS	0.851	0.759	0.948	0.851	0.759	0.948	CLONAL	1	TRUE	1	0.326833601575862	2		1097	705	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029493	14029493	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	155	659	0	ENST00000311895.7:c.1704G>C	p.Arg568Ser	p.R568S	ENST00000311895	NM_005236.2	568	agG/agC	8/11	0.538549155637471	3	FACETS	0.918	0.841	0.997	0.459	0.42	0.499	CLONAL	1	TRUE	1	0.541391146119702	3		659	793	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578522	7578522	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs758781593	NA	P-0018183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	312	1116	1	ENST00000269305.4:c.408A>T	p.Gln136His	p.Q136H	ENST00000269305	NM_001126112.2	136	caA/caT	5/11	0.538354841315745	1	FACETS	0.926	0.876	0.977	0.926	0.876	0.977	CLONAL	1	TRUE	0	0.541391146119702	1		1117	908	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	131	306	0				ENST00000310581	NM_198253.2	-/1132			0.602262730599011	3	FACETS	1	0.97	1	0.57	0.521	0.621	CLONAL	1	TRUE	1	0.658452182878748	3		306	464	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	163	887	1	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.634754128187295	3	FACETS	0.856	0.787	0.928	0.428	0.393	0.464	CLONAL	1	TRUE	1	0.658452182878748	3		888	769	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579346	7579348	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs764486868	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	507	980	0	ENST00000269305.4:c.339_341del	p.Phe113del	p.F113del	ENST00000269305	NM_001126112.2	113	ttCTTg/ttg	4/11	0.258375593046293	3	FACETS	0.916	0.888	0.943			1	INDETERMINATE	3	TRUE	NA	0.658452182878748	3		980	745	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105745	27105745	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	64	434	0	ENST00000324856.7:c.5356G>C	p.Glu1786Gln	p.E1786Q	ENST00000324856	NM_006015.4	1786	Gag/Cag	20/20	0.602262730599011	3	FACETS	0.818	0.713	0.929	0.409	0.356	0.465	CLONAL	1	TRUE	1	0.658452182878748	3		434	316	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157624	106157624	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	120	644	0	ENST00000380013.4:c.2525C>G	p.Ser842Ter	p.S842*	ENST00000380013	NM_001127208.2	842	tCa/tGa	3/11	0.602262730599011	3	FACETS	0.838	0.759	0.921	0.419	0.379	0.461	CLONAL	1	TRUE	1	0.658452182878748	3		644	578	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287398	38287398	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778531708	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	138	629	0	ENST00000425967.3:c.259C>T	p.Arg87Cys	p.R87C	ENST00000425967	NM_001174067.1	87	Cgc/Tgc	4/19	0.658452182878748	1	FACETS	0.956	0.886	1	0.956	0.886	1	CLONAL	1	TRUE	0	0.658452182878748	1		629	294	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262280	16262280	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	56	247	0	ENST00000375759.3:c.9545C>G	p.Ser3182Cys	p.S3182C	ENST00000375759	NM_015001.2	3182	tCt/tGt	11/15	0.602262730599011	3	FACETS	1	0.933	1	0.56	0.486	0.637	CLONAL	1	TRUE	1	0.658452182878748	3		247	202	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332680	65332680	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	143	772	0	ENST00000342505.4:c.859G>C	p.Glu287Gln	p.E287Q	ENST00000342505	NM_002227.2	287	Gag/Cag	7/25	0.602262730599011	3	FACETS	0.844	0.771	0.92	0.422	0.385	0.46	CLONAL	1	TRUE	1	0.658452182878748	3		772	684	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115252327	115252327	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	183	599	0	ENST00000369535.4:c.313G>C	p.Asp105His	p.D105H	ENST00000369535	NM_002524.4	105	Gac/Cac	4/7	0.634754128187295	3	FACETS	0.794	0.741	0.849	0.794	0.741	0.849	SUBCLONAL	2	TRUE	1	0.658452182878748	3		599	465	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95598909	95598909	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	109	818	1	ENST00000393063.1:c.250C>G	p.Gln84Glu	p.Q84E	ENST00000393063	NM_030621.3	84	Cag/Gag	4/28	0.456576467637388	4	FACETS	0.652	0.585	0.723	0.326	0.292	0.362	SUBCLONAL	1	TRUE	2	0.658452182878748	4		819	842	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817799	3817799	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	225	1044	0	ENST00000262367.5:c.3172G>C	p.Glu1058Gln	p.E1058Q	ENST00000262367	NM_004380.2	1058	Gaa/Caa	16/31	0.602262730599011	3	FACETS	0.916	0.853	0.98	0.458	0.426	0.49	CLONAL	1	TRUE	1	0.658452182878748	3		1044	992	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817871	3817871	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	173	933	0	ENST00000262367.5:c.3100G>T	p.Glu1034Ter	p.E1034*	ENST00000262367	NM_004380.2	1034	Gaa/Taa	16/31	0.602262730599011	3	FACETS	0.833	0.767	0.901	0.416	0.383	0.451	CLONAL	1	TRUE	1	0.658452182878748	3		933	839	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041572	14041572	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	162	674	0	ENST00000311895.7:c.2119G>C	p.Glu707Gln	p.E707Q	ENST00000311895	NM_005236.2	707	Gaa/Caa	11/11	0.602262730599011	3	FACETS	0.991	0.912	1	0.496	0.456	0.537	CLONAL	1	TRUE	1	0.658452182878748	3		674	660	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346511	89346511	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	124	713	2	ENST00000301030.4:c.6439G>T	p.Asp2147Tyr	p.D2147Y	ENST00000301030	NM_001256183.1	2147	Gat/Tat	9/13	0.121297414169598	3	FACETS	0.98	0.891	1	0.327	0.297	0.358	INDETERMINATE	1	TRUE	0	0.658452182878748	3		715	511	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37865697	37865697	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	180	795	0	ENST00000269571.5:c.566C>G	p.Ser189Cys	p.S189C	ENST00000269571		189	tCt/tGt	4/27	0.634754128187295	3	FACETS	1	0.95	1	0.517	0.478	0.557	CLONAL	1	TRUE	1	0.658452182878748	3		795	703	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375565	40375565	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	84	532	0	ENST00000293328.3:c.385C>G	p.Pro129Ala	p.P129A	ENST00000293328	NM_012448.3	129	Cca/Gca	5/19	0.634754128187295	3	FACETS	0.776	0.689	0.869	0.388	0.344	0.435	SUBCLONAL	1	TRUE	1	0.658452182878748	3		532	437	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41242986	41242986	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	162	867	0	ENST00000357654.3:c.4160C>T	p.Ser1387Phe	p.S1387F	ENST00000357654	NM_007294.3	1387	tCt/tTt	11/23	0.634754128187295	3	FACETS	0.866	0.796	0.939	0.433	0.398	0.47	CLONAL	1	TRUE	1	0.658452182878748	3		867	755	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677936	58677936	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	109	440	0	ENST00000305921.3:c.161C>A	p.Ser54Ter	p.S54*	ENST00000305921	NM_003620.3	54	tCg/tAg	1/6	0.202029103516473	3	FACETS	1	0.969	1	0.388	0.351	0.426	INDETERMINATE	1	TRUE	0	0.658452182878748	3		440	378	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774737	73774737	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	57	237	0	ENST00000254810.4:c.350G>C	p.Arg117Thr	p.R117T	ENST00000254810	NM_005324.3	117	aGa/aCa	4/4	0.202029103516473	3	FACETS	1	0.902	1	0.349	0.303	0.397	INDETERMINATE	1	TRUE	0	0.658452182878748	3		237	220	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39620667	39620667	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	97	598	0	ENST00000262039.4:c.2065C>G	p.Pro689Ala	p.P689A	ENST00000262039	NM_002647.2	689	Cct/Gct	19/25	0.55151904170388	3	FACETS	0.777	0.695	0.863	0.389	0.347	0.432	SUBCLONAL	1	TRUE	1	0.658452182878748	3		598	504	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130320	11130320	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	366	917	0	ENST00000358026.2:c.2559C>G	p.Phe853Leu	p.F853L	ENST00000358026	NM_001128849.1	853	ttC/ttG	18/36	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	1	TRUE	NA	0.658452182878748	2		917	804	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223994	36223994	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	165	1086	0	ENST00000222270.7:c.6544G>C	p.Glu2182Gln	p.E2182Q	ENST00000222270	NM_014727.1	2182	Gag/Cag	28/37	0.65352717912314	3	FACETS	0.687	0.63	0.746			1	SUBCLONAL	1	TRUE	NA	0.658452182878748	3		1086	970	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637445	47637445	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	444	721	0	ENST00000233146.2:c.579G>C	p.Gln193His	p.Q193H	ENST00000233146	NM_000251.2	193	caG/caC	3/16	0.566161203749409	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	1	0.658452182878748	4		721	711	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736181	204736181	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	114	536	0	ENST00000302823.3:c.538C>G	p.Leu180Val	p.L180V	ENST00000302823	NM_005214.4	180	Ctc/Gtc	3/4	1	2	FACETS	0.817	0.741	0.896	0.817	0.741	0.896	CLONAL	1	TRUE	1	0.658452182878748	2		536	424	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225360637	225360637	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	130	611	0	ENST00000264414.4:c.1754C>G	p.Ser585Cys	p.S585C	ENST00000264414	NM_003590.4	585	tCt/tGt	13/16	1	2	FACETS	0.823	0.751	0.897	0.823	0.751	0.897	CLONAL	1	TRUE	1	0.658452182878748	2		611	480	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44515836	44515836	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	159	1007	0	ENST00000291552.4:c.217G>C	p.Glu73Gln	p.E73Q	ENST00000291552	NM_006758.2	73	Gag/Cag	4/8	0.636964074696392	4	FACETS	0.834	0.764	0.908	0.278	0.254	0.303	CLONAL	1	TRUE	1	0.658452182878748	4		1007	960	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556686	41556686	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	132	692	0	ENST00000263253.7:c.3631G>A	p.Glu1211Lys	p.E1211K	ENST00000263253	NM_001429.3	1211	Gag/Aag	20/31	0.248420519134	1	FACETS	0.487	0.444	0.532	0.487	0.444	0.532	INDETERMINATE	1	TRUE	0	0.658452182878748	1		692	552	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52621413	52621413	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	345	932	0	ENST00000394830.3:c.3004C>T	p.Pro1002Ser	p.P1002S	ENST00000394830	NM_018313.4	1002	Cca/Tca	20/30	0.634754128187295	3	FACETS	0.851	0.81	0.893	0.851	0.81	0.893	CLONAL	2	TRUE	1	0.658452182878748	3		932	818	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72897378	72897378	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs768322266	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	145	711	0	ENST00000325599.8:c.114C>G	p.Phe38Leu	p.F38L	ENST00000325599	NM_018130.2	38	ttC/ttG	1/11	NA	2	FACETS	0.89	0.817	0.965			1	INDETERMINATE	1	TRUE	NA	0.658452182878748	2		711	495	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260177	149260177	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	106	643	0	ENST00000360632.3:c.716G>C	p.Arg239Thr	p.R239T	ENST00000360632	NM_015472.4	239	aGa/aCa	4/7	0.459977368458812	4	FACETS	0.929	0.835	1	0.464	0.417	0.514	CLONAL	1	TRUE	2	0.658452182878748	4		643	575	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182679095	182679095	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	130	931	0	ENST00000292782.4:c.439G>C	p.Glu147Gln	p.E147Q	ENST00000292782	NM_020640.2	147	Gaa/Caa	4/7	0.459977368458812	4	FACETS	0.75	0.68	0.824	0.375	0.34	0.412	SUBCLONAL	1	TRUE	2	0.658452182878748	4		931	873	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31483667	31483667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	105	626	0	ENST00000344624.3:c.2065C>T	p.Leu689Phe	p.L689F	ENST00000344624		689	Ctt/Ttt	13/33	0.602262730599011	3	FACETS	0.737	0.662	0.816	0.369	0.331	0.408	SUBCLONAL	1	TRUE	1	0.658452182878748	3		626	575	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958917	38958917	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	108	475	1	ENST00000357387.3:c.2195C>T	p.Ala732Val	p.A732V	ENST00000357387	NM_152756.3	732	gCa/gTa	23/38	0.602262730599011	3	FACETS	0.85	0.766	0.938	0.425	0.383	0.469	CLONAL	1	TRUE	1	0.658452182878748	3		476	513	SUCCESS
APC	324	MSKCC	GRCh37	5	112174893	112174893	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	137	615	0	ENST00000257430.4:c.3602C>T	p.Ser1201Leu	p.S1201L	ENST00000257430	NM_000038.5	1201	tCa/tTa	16/16	1	2	FACETS	0.961	0.882	1	0.961	0.882	1	CLONAL	1	TRUE	1	0.658452182878748	2		615	433	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	105	449	0	ENST00000257430.4:c.4099C>G	p.Gln1367Glu	p.Q1367E	ENST00000257430	NM_000038.5	1367	Cag/Gag	16/16	1	2	FACETS	0.903	0.818	0.993	0.903	0.818	0.993	CLONAL	1	TRUE	1	0.658452182878748	2		449	353	SUCCESS
APC	324	MSKCC	GRCh37	5	112176641	112176641	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1561599480	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	133	734	1	ENST00000257430.4:c.5350G>A	p.Glu1784Lys	p.E1784K	ENST00000257430	NM_000038.5	1784	Gaa/Aaa	16/16	1	2	FACETS	0.7	0.638	0.765	0.7	0.638	0.765	SUBCLONAL	1	TRUE	1	0.658452182878748	2		735	577	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973778	131973778	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	68	450	0	ENST00000265335.6:c.3481G>C	p.Glu1161Gln	p.E1161Q	ENST00000265335		1161	Gaa/Caa	23/25	0.55151904170388	3	FACETS	0.719	0.628	0.815	0.359	0.314	0.408	SUBCLONAL	1	TRUE	1	0.658452182878748	3		450	382	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407554	407554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	186	1041	0	ENST00000380956.4:c.1312G>A	p.Glu438Lys	p.E438K	ENST00000380956	NM_001195286.1	438	Gaa/Aaa	9/9	NA	2	FACETS	0.88	0.816	0.945			1	INDETERMINATE	1	TRUE	NA	0.658452182878748	2		1041	642	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675735	30675735	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	261	1199	0	ENST00000376406.3:c.2621C>G	p.Ser874Cys	p.S874C	ENST00000376406	NM_014641.2	874	tCt/tGt	8/15	0.624034914078755	2	FACETS	0.934	0.877	0.992	0.467	0.438	0.496	CLONAL	1	TRUE	0	0.658452182878748	2		1199	849	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026915	6026915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782602	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	32	119	0	ENST00000265849.7:c.1481C>T	p.Ser494Leu	p.S494L	ENST00000265849	NM_000535.5	494	tCg/tTg	11/15	0.566161203749409	4	FACETS	1	0.889	1	0.371	0.305	0.442	CLONAL	1	TRUE	1	0.658452182878748	4		119	145	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92247469	92247469	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	129	600	0	ENST00000265734.4:c.751A>T	p.Arg251Trp	p.R251W	ENST00000265734	NM_001259.6	251	Agg/Tgg	7/8	0.602262730599011	3	FACETS	0.883	0.803	0.966	0.441	0.401	0.483	CLONAL	1	TRUE	1	0.658452182878748	3		600	590	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566280	141566280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	99	540	0	ENST00000220592.5:c.1132G>A	p.Glu378Lys	p.E378K	ENST00000220592	NM_012154.3	378	Gag/Aag	9/19	0.61801837518531	3	FACETS	0.91	0.818	1	0.303	0.272	0.336	CLONAL	1	TRUE	0	0.658452182878748	3		540	439	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050746	5050746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	133	756	0	ENST00000381652.3:c.529G>A	p.Glu177Lys	p.E177K	ENST00000381652	NM_004972.3	177	Gaa/Aaa	6/25	0.624034914078755	2	FACETS	0.729	0.665	0.796	0.365	0.332	0.398	SUBCLONAL	1	TRUE	0	0.658452182878748	2		756	554	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27220139	27220139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762495403	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	146	683	0	ENST00000380036.4:c.3196G>A	p.Glu1066Lys	p.E1066K	ENST00000380036	NM_000459.3	1066	Gag/Aag	21/23	0.624034914078755	2	FACETS	0.96	0.883	1	0.48	0.441	0.52	CLONAL	1	TRUE	0	0.658452182878748	2		683	462	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399318	139399318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	218	1039	0	ENST00000277541.6:c.4825G>A	p.Asp1609Asn	p.D1609N	ENST00000277541	NM_017617.3	1609	Gac/Aac	26/34	0.658452182878748	3	FACETS	0.952	0.886	1	0.317	0.295	0.34	CLONAL	1	TRUE	0	0.658452182878748	3		1039	925	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412711	63412711	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	123	402	0	ENST00000330258.3:c.456G>C	p.Glu152Asp	p.E152D	ENST00000330258	NM_152424.3	152	gaG/gaC	2/2	0.658452182878748	2	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.658452182878748	2		402	320	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637885	39637885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200000040	NA	P-0018188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	56	746	0	ENST00000262039.4:c.2302C>T	p.Arg768Trp	p.R768W	ENST00000262039	NM_002647.2	768	Cgg/Tgg	22/25	0.388625709497888	1	FACETS	0.277	0.237	0.32	0.277	0.237	0.32	SUBCLONAL	1	TRUE	0	0.594739200233306	1		746	478	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974792	21974792	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs141798398	NA	P-0018188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	184	210	0	ENST00000304494.5:c.35C>A	p.Ser12Ter	p.S12*	ENST00000304494	NM_000077.4	12	tCg/tAg	1/3	0.587463378289444	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.594739200233306	2		210	271	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436414	52436414	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	200	520	0	ENST00000460680.1:c.2080C>T	p.Gln694Ter	p.Q694*	ENST00000460680	NM_004656.3	694	Cag/Tag	17/17	0.594739200233306	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.594739200233306	1		520	420	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098973	178098973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	82	462	0	ENST00000397062.3:c.72G>C	p.Trp24Cys	p.W24C	ENST00000397062	NM_006164.4	24	tgG/tgC	2/5	1	2	FACETS	0.7	0.621	0.784	0.7	0.621	0.784	SUBCLONAL	1	TRUE	1	0.594739200233306	2		462	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0018188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	490	646	0	ENST00000269305.4:c.375+1G>T		p.X125_splice	ENST00000269305	NM_001126112.2	125			NA	2	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.594739200233306	2		646	757	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050658	30050658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1330473001	NA	P-0018188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	110	604	1	ENST00000338641.4:c.460G>A	p.Asp154Asn	p.D154N	ENST00000338641	NM_000268.3	154	Gac/Aac	5/16	0.272597515814485	1	FACETS	0.523	0.472	0.576	0.523	0.472	0.576	INDETERMINATE	1	TRUE	0	0.594739200233306	1		605	497	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798123	32798123	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	341	773	2	ENST00000374899.4:c.1556T>A	p.Leu519Gln	p.L519Q	ENST00000374899	NM_018833.2	519	cTg/cAg	9/12	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.594739200233306	2		775	1046	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983007	111983007	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	289	843	2	ENST00000368678.4:c.1540C>A	p.Gln514Lys	p.Q514K	ENST00000368678		514	Cag/Aag	13/13	0.594739200233306	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.594739200233306	1		845	680	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519869	29519869	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	41	1025	2	ENST00000389048.3:c.1702C>A	p.Leu568Ile	p.L568I	ENST00000389048	NM_004304.4	568	Cta/Ata	9/29	0.171031526303753	3	FACETS	0.894	0.744	1	0.447	0.372	0.531	CLONAL	1	FALSE	1	0.171031526303753	3		1027	582	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435837	56435837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	165	405	0	ENST00000407977.2:c.1300C>T	p.Pro434Ser	p.P434S	ENST00000407977		434	Ccc/Tcc	9/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.720821781357726	2		405	413	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019275	31019275	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	224	626	0	ENST00000375687.4:c.870A>T	p.Glu290Asp	p.E290D	ENST00000375687	NM_015338.5	290	gaA/gaT	9/13	1	2	FACETS	0.93	0.871	0.991	0.93	0.871	0.991	CLONAL	1	TRUE	1	0.720821781357726	2		626	668	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0018191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	206	613	1	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			0.163514628428136	2	FACETS	1	0.99	1	0.679	0.633	0.725	INDETERMINATE	1	TRUE	0	0.484833224535162	2		614	626	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070577	67070578	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	170	433	1	ENST00000412916.2:c.207dup	p.Pro70SerfsTer13	p.P70Sfs*13	ENST00000412916		67	-/T	3/6	0.484833224535162	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.484833224535162	1		434	453	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138921	64138921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	46	711	3	ENST00000334205.4:c.2288G>A	p.Arg763His	p.R763H	ENST00000334205	NM_003942.2	763	cGc/cAc	17/17	1	2	FACETS	0.296	0.248	0.348	0.296	0.248	0.348	SUBCLONAL	1	TRUE	1	0.484833224535162	2		714	642	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359721	40359721	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	132	857	1	ENST00000293328.3:c.1932G>T	p.Met644Ile	p.M644I	ENST00000293328	NM_012448.3	644	atG/atT	16/19	0.163256089725814	4	FACETS	0.777	0.704	0.854	0.388	0.352	0.427	INDETERMINATE	1	TRUE	2	0.484833224535162	4		858	1041	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760249	133760264	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTCAGGTGCACCAG	GGCTCAGGTGCACCAG	-	novel	NA	P-0018191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	85	590	0	ENST00000318560.5:c.2574_2589del	p.Ser859AlafsTer12	p.S859Afs*12	ENST00000318560	NM_005157.4	858	GGCTCAGGTGCACCAGgg/gg	11/11	0.483406418158211	4	FACETS	0.633	0.559	0.713	0.158	0.139	0.179	SUBCLONAL	1	TRUE	0	0.484833224535162	4		590	822	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428547	78428547	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0121514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	226	774	0	ENST00000370768.2:c.1252C>G	p.Pro418Ala	p.P418A	ENST00000370768	NM_003902.3	418	Cca/Gca	14/20	1	2	FACETS	0.913	0.855	0.971	0.913	0.855	0.971	CLONAL	1	NA	1	0.771210238983044	2		774	642	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028565	42028565	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0121514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	200	1044	0	ENST00000219905.7:c.4103A>T	p.Lys1368Met	p.K1368M	ENST00000219905	NM_001164273.1	1368	aAg/aTg	13/24	1	2	FACETS	0.884	0.824	0.944	0.884	0.824	0.944	CLONAL	1	NA	1	0.771210238983044	2		1044	587	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39613876	39613876	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0121514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	228	828	0	ENST00000262039.4:c.1794A>T	p.Gln598His	p.Q598H	ENST00000262039	NM_002647.2	598	caA/caT	16/25	1	2	FACETS	0.939	0.88	0.998	0.939	0.88	0.998	CLONAL	1	NA	1	0.771210238983044	2		828	630	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913535	NA	P-0018193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	125	1005	0	ENST00000311936.3:c.37G>C	p.Gly13Arg	p.G13R	ENST00000311936	NM_004985.3	13	Ggc/Cgc	2/5	0.23829986381122	1	FACETS	0.795	0.722	0.872	1	0.987	1	SUBCLONAL	2	TRUE	0	0.23829986381122	1		1005	581	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576885	7576885	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0018193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	84	827	0	ENST00000269305.4:c.961A>T	p.Lys321Ter	p.K321*	ENST00000269305	NM_001126112.2	321	Aaa/Taa	9/11	0.23829986381122	1	FACETS	0.915	0.808	1	0.915	0.808	1	CLONAL	1	TRUE	0	0.23829986381122	1		827	679	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999147	100999147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	60	1144	0	ENST00000325455.5:c.655G>A	p.Val219Met	p.V219M	ENST00000325455	NM_001202474.3	219	Gtg/Atg	1/8	1	2	FACETS	0.778	0.67	0.896	0.778	0.67	0.896	SUBCLONAL	1	TRUE	1	0.23829986381122	2		1144	647	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287300	46287300	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0018193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	50	807	0	ENST00000334344.6:c.5245A>T	p.Arg1749Ter	p.R1749*	ENST00000334344	NM_152641.2	1749	Aga/Tga	19/21	1	2	FACETS	0.74	0.628	0.864	0.74	0.628	0.864	SUBCLONAL	1	TRUE	1	0.23829986381122	2		807	567	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820626	3820626	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	45	866	0	ENST00000262367.5:c.2825C>T	p.Pro942Leu	p.P942L	ENST00000262367	NM_004380.2	942	cCt/cTt	14/31	0.225086592573994	1	FACETS	0.484	0.405	0.57	0.484	0.405	0.57	SUBCLONAL	1	TRUE	0	0.23829986381122	1		866	688	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774729	73774729	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	29	163	0	ENST00000254810.4:c.358A>G	p.Ile120Val	p.I120V	ENST00000254810	NM_005324.3	120	Atc/Gtc	4/4	0.147181927222308	3	FACETS	0.867	0.705	1	0.867	0.705	1	CLONAL	2	TRUE	1	0.23829986381122	3		163	157	SUCCESS
ALK	238	MSKCC	GRCh37	2	29419642	29419642	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	122	846	1	ENST00000389048.3:c.4158C>A	p.Cys1386Ter	p.C1386*	ENST00000389048	NM_004304.4	1386	tgC/tgA	28/29	1	2	FACETS	0.81	0.734	0.89	1	0.987	1	CLONAL	2	TRUE	1	0.23829986381122	2		847	632	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467965	66467965	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	52	637	0	ENST00000273854.3:c.304T>A	p.Cys102Ser	p.C102S	ENST00000273854	NM_004439.5	102	Tgc/Agc	3/18	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.23829986381122	2		637	427	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524644	187524644	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs751497113	NA	P-0018193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	100	1039	0	ENST00000441802.2:c.11036A>T	p.Gln3679Leu	p.Q3679L	ENST00000441802	NM_005245.3	3679	cAg/cTg	19/27	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.23829986381122	2		1039	813	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131972893	131972893	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1443728958	NA	P-0018193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	47	632	0	ENST00000265335.6:c.3475+1G>T		p.X1159_splice	ENST00000265335		1159			0.147181927222308	3	FACETS	0.929	0.785	1	0.465	0.392	0.545	CLONAL	1	TRUE	1	0.23829986381122	3		632	475	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504352	149504352	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	72	877	2	ENST00000261799.4:c.1850C>T	p.Ala617Val	p.A617V	ENST00000261799	NM_002609.3	617	gCc/gTc	13/23	0.147181927222308	3	FACETS	0.925	0.808	1	0.463	0.404	0.526	CLONAL	1	TRUE	1	0.23829986381122	3		879	731	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508196	106508196	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	42	352	0	ENST00000359195.3:c.190C>A	p.His64Asn	p.H64N	ENST00000359195	NM_002649.2	64	Cac/Aac	2/11	0.147181927222308	3	FACETS	1	0.95	1	0.687	0.577	0.808	CLONAL	1	TRUE	1	0.23829986381122	3		352	287	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389360	8389360	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	28	792	0	ENST00000356435.5:c.4258A>T	p.Arg1420Trp	p.R1420W	ENST00000356435		1420	Agg/Tgg	26/35	0.191471214084373	0	FACETS	0.396	0.316	0.488			1	SUBCLONAL	1	TRUE	0	0.23829986381122	0		792	452	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934152	48934152	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0018195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	250	422	0	ENST00000267163.4:c.608-1G>A		p.X203_splice	ENST00000267163	NM_000321.2	203			0.276965426259445	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	1	0.276965426259445	4		422	679	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577524	7577524	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	135	756	0	ENST00000269305.4:c.757A>G	p.Thr253Ala	p.T253A	ENST00000269305	NM_001126112.2	253	Acc/Gcc	7/11	0.188922960141265	3	FACETS	1	0.982	1	0.445	0.404	0.488	CLONAL	1	TRUE	0	0.276965426259445	3		756	831	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098966	178098966	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	123	509	0	ENST00000397062.3:c.79G>T	p.Asp27Tyr	p.D27Y	ENST00000397062	NM_006164.4	27	Gat/Tat	2/5	0.234841683863466	4	FACETS	0.783	0.709	0.861	0.783	0.709	0.861	SUBCLONAL	2	TRUE	2	0.276965426259445	4		509	724	SUCCESS
FH	2271	MSKCC	GRCh37	1	241672063	241672063	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	77	497	0	ENST00000366560.3:c.578C>A	p.Thr193Lys	p.T193K	ENST00000366560	NM_000143.3	193	aCa/aAa	5/10	0.276965426259445	4	FACETS	0.772	0.676	0.875	0.386	0.338	0.438	SUBCLONAL	1	TRUE	2	0.276965426259445	4		497	920	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288470	15288470	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	67	305	0	ENST00000263388.2:c.4269C>A	p.Asp1423Glu	p.D1423E	ENST00000263388	NM_000435.2	1423	gaC/gaA	24/33	0.245080388746587	4	FACETS	1	0.969	1	0.697	0.608	0.794	CLONAL	1	TRUE	2	0.276965426259445	4		305	443	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560875	9560875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770875912	NA	P-0018195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	136	542	0	ENST00000353224.5:c.907G>A	p.Ala303Thr	p.A303T	ENST00000353224	NM_177990.2	303	Gca/Aca	4/10	0.276965426259445	3	FACETS	1	0.979	1	0.629	0.571	0.689	CLONAL	1	TRUE	1	0.276965426259445	3		542	889	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948511	31948511	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	63	380	0	ENST00000375333.2:c.994C>G	p.Pro332Ala	p.P332A	ENST00000375333	NM_032454.1	332	Cct/Gct	7/8	0.276965426259445	3	FACETS	1	0.907	1	0.53	0.459	0.606	CLONAL	1	TRUE	1	0.276965426259445	3		380	489	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523536	106523536	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	53	507	0	ENST00000359195.3:c.2690del	p.Gly897AlafsTer11	p.G897Afs*11	ENST00000359195	NM_002649.2	896	gtG/gt	8/11	0.276965426259445	5	FACETS	0.563	0.478	0.656			1	SUBCLONAL	1	TRUE	NA	0.276965426259445	5		507	963	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317149	87317262	+	splice_acceptor_variant,splice_donor_variant,intron_variant	Splice_Site	DEL	GTGAGTACTCAGGACCAGGGCACATTATCTCAGAGAATTTTCCTGTTGTCTGCTCTGGTCAGGCAGGCATTCACTGGTTCGTTCTAATGTGCATGAAATTATGTGTTTTCACAG	GTGAGTACTCAGGACCAGGGCACATTATCTCAGAGAATTTTCCTGTTGTCTGCTCTGGTCAGGCAGGCATTCACTGGTTCGTTCTAATGTGCATGAAATTATGTGTTTTCACAG	-	novel	NA	P-0018195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	87	607	0	ENST00000277120.3:c.287+2_288del		p.X96_splice	ENST00000277120		96			0.276965426259445	3	FACETS	0.672	0.593	0.756	0.336	0.296	0.378	SUBCLONAL	1	TRUE	1	0.276965426259445	3		607	1065	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87338624	87339137	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTAAGGCTTGTGTTTGGCTGTGTCTTAATAGAGAGACAAGAGTGTTTCAGAATGCGAGAATGTATTAAACCTAGTGATGATCATTTGATATTTTATAAGGCTACATATAGAAATTTACAAAGAGTTTTTGATGTACATTCACTTTCTACTTATTCTTAATTAATAAAGACTAATGCAGGCTTGCATTTTAGTTATGCATACCTAAGAGAGCGAGGAGTCTCTATATCCCTAGTGAGCTCTTTGTATCATCCTGAACAAAGCGAGTGACTTTCCCTGTGGTCTTCTCCCTTGGAGGGAATTCAGGGATCAAGTCAACCTCATGCACTTAGCAATTGAAACCTAGAGAAATAGAATAACTTCTGATTTACTTCTTCGCCTGAGCCCAGTTCAGGCAGAGAAGCTTTTCTAATGCTATATATACATATTTTCTCTAGTTAGGGGAAGAAACCCCAAATCTTGTCACTTTGGGATCAATCCTAATCAAGGTTATTTTTGTCTGTTAATTCATTTGTA	GGTAAGGCTTGTGTTTGGCTGTGTCTTAATAGAGAGACAAGAGTGTTTCAGAATGCGAGAATGTATTAAACCTAGTGATGATCATTTGATATTTTATAAGGCTACATATAGAAATTTACAAAGAGTTTTTGATGTACATTCACTTTCTACTTATTCTTAATTAATAAAGACTAATGCAGGCTTGCATTTTAGTTATGCATACCTAAGAGAGCGAGGAGTCTCTATATCCCTAGTGAGCTCTTTGTATCATCCTGAACAAAGCGAGTGACTTTCCCTGTGGTCTTCTCCCTTGGAGGGAATTCAGGGATCAAGTCAACCTCATGCACTTAGCAATTGAAACCTAGAGAAATAGAATAACTTCTGATTTACTTCTTCGCCTGAGCCCAGTTCAGGCAGAGAAGCTTTTCTAATGCTATATATACATATTTTCTCTAGTTAGGGGAAGAAACCCCAAATCTTGTCACTTTGGGATCAATCCTAATCAAGGTTATTTTTGTCTGTTAATTCATTTGTA	-	novel	NA	P-0018195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	139	589	0	ENST00000277120.3:c.720+1_721-1del		p.X240_splice	ENST00000277120		240		7/19	0.276965426259445	3	FACETS	1	0.98	1	0.641	0.583	0.701	CLONAL	1	TRUE	1	0.276965426259445	3		589	892	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87366899	87366899	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0018195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	67	728	0	ENST00000277120.3:c.1297-2A>C		p.X433_splice	ENST00000277120		433			0.276965426259445	3	FACETS	0.498	0.431	0.572	0.249	0.215	0.286	SUBCLONAL	1	TRUE	1	0.276965426259445	3		728	1105	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133729537	133729537	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1257	75	792	1	ENST00000318560.5:c.166G>T	p.Ala56Ser	p.A56S	ENST00000318560	NM_005157.4	56	Gct/Tct	2/11	0.276965426259445	4	FACETS	0.519	0.453	0.591			1	SUBCLONAL	1	TRUE	NA	0.276965426259445	4		793	1332	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798853	135798872	+	frameshift_variant	Frame_Shift_Del	DEL	TGTGAGGACAACGACGTCAG	TGTGAGGACAACGACGTCAG	-	novel	NA	P-0018195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	83	308	0	ENST00000298552.3:c.371_390del	p.Thr124AsnfsTer23	p.T124Nfs*23	ENST00000298552	NM_001162426.1	124	aCTGACGTCGTTGTCCTCACA/a	6/23	0.276965426259445	3	FACETS	1	0.966	1	0.42	0.371	0.472	CLONAL	1	TRUE	0	0.276965426259445	3		308	542	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941947	44941960	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTCTTTTTTAAGT	TCTCTTTTTTAAGT	-	novel	NA	P-0018195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	47	378	0	ENST00000377967.4:c.3210-10_3213del		p.X1070_splice	ENST00000377967	NM_021140.2	1070		22/29	0.220114003445493	2	FACETS	0.618	0.521	0.725			1	SUBCLONAL	1	TRUE	NA	0.276965426259445	2		378	549	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942845	44942845	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	53	362	0	ENST00000377967.4:c.3425G>T	p.Arg1142Ile	p.R1142I	ENST00000377967	NM_021140.2	1142	aGa/aTa	23/29	0.220114003445493	2	FACETS	0.606	0.516	0.704			1	SUBCLONAL	1	TRUE	NA	0.276965426259445	2		362	632	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650332	48650332	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	169	371	1	ENST00000376670.3:c.302C>A	p.Thr101Lys	p.T101K	ENST00000376670	NM_002049.3	101	aCg/aAg	3/6	0.220114003445493	2	FACETS	1	0.97	1			1	CLONAL	2	TRUE	NA	0.276965426259445	2		372	558	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410354	63410354	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	124	478	0	ENST00000330258.3:c.2813G>C	p.Gly938Ala	p.G938A	ENST00000330258	NM_152424.3	938	gGa/gCa	2/2	0.215696793689915	2	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.276965426259445	2		478	637	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0018196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	508	509	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.477909520299837	2	FACETS	0.756	0.727	0.785	0.756	0.727	0.785	SUBCLONAL	2	TRUE	0	0.629807437254674	2		509	1067	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0018196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	473	749	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.45802163349191	3	FACETS	1	0.985	1	0.698	0.671	0.725	CLONAL	2	TRUE	0	0.629807437254674	3		749	943	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056406	26056406	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	56	363	0	ENST00000343677.2:c.251T>C	p.Leu84Pro	p.L84P	ENST00000343677	NM_005319.3	84	cTc/cCc	1/1	0.335663706921246	4	FACETS	0.418	0.358	0.485	0.209	0.179	0.243	INDETERMINATE	1	TRUE	2	0.629807437254674	4		363	693	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50811826	50811826	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs886040872	NA	P-0018198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	146	750	0	ENST00000398568.2:c.1103C>A	p.Ser368Ter	p.S368*	ENST00000398568	NM_001042412.1	368	tCa/tAa	7/18	0.483846080583461	1	FACETS	0.809	0.744	0.876	0.809	0.744	0.876	CLONAL	1	TRUE	0	0.540740562332883	1		750	487	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144879	47144879	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	105	628	0	ENST00000409792.3:c.4874G>C	p.Arg1625Pro	p.R1625P	ENST00000409792	NM_014159.6	1625	cGt/cCt	7/21	1	2	FACETS	0.721	0.648	0.797	0.721	0.648	0.797	SUBCLONAL	1	TRUE	1	0.540740562332883	2		628	539	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864391	151864392	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	113	590	0	ENST00000262189.6:c.9589dup	p.Tyr3197LeufsTer3	p.Y3197Lfs*3	ENST00000262189	NM_170606.2	3197	tat/tTat	42/59	0.540740562332883	2	FACETS	0.796	0.719	0.877	0.398	0.359	0.439	SUBCLONAL	1	TRUE	0	0.540740562332883	2		590	525	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0018201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	249	668	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.234349761514971	3	FACETS	1	0.986	1	0.79	0.739	0.842	CLONAL	2	TRUE	0	0.234349761514971	3		668	1002	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253911	NA	P-0018201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	49	582	0	ENST00000269305.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000269305	NM_001126112.2	180	Gag/Aag	5/11	1	2	FACETS	0.756	0.64	0.884	0.756	0.64	0.884	SUBCLONAL	1	TRUE	1	0.234349761514971	2		582	553	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044550	47044550	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	82	846	1	ENST00000377604.3:c.2047G>T	p.Glu683Ter	p.E683*	ENST00000377604	NM_001204468.1	683	Gag/Tag	18/24	1	2	FACETS	0.882	0.777	0.996	0.882	0.777	0.996	CLONAL	1	TRUE	1	0.234349761514971	2		847	793	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439798	51439798	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	40	313	0	ENST00000262662.1:c.364del	p.Leu122TrpfsTer2	p.L122Wfs*2	ENST00000262662		121	ttC/tt	4/4	0.105855993686351	4	FACETS	0.912	0.758	1	0.456	0.379	0.542	INDETERMINATE	1	TRUE	2	0.234349761514971	4		313	462	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685312	86685312	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	30	196	0	ENST00000274376.6:c.3028C>T	p.Arg1010Ter	p.R1010*	ENST00000274376	NM_002890.2	1010	Cga/Tga	24/25	1	2	FACETS	0.705	0.569	0.86	0.705	0.569	0.86	SUBCLONAL	1	TRUE	1	0.234349761514971	2		196	363	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741901	162741901	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	51	454	0	ENST00000367921.3:c.1592G>T	p.Gly531Val	p.G531V	ENST00000367921	NM_006182.2	531	gGa/gTa	13/18	0.109444019804739	3	FACETS	0.868	0.738	1	0.434	0.369	0.506	INDETERMINATE	1	TRUE	1	0.234349761514971	3		454	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578380	7578380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs72661117	NA	P-0018201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	44	531	0	ENST00000269305.4:c.550G>A	p.Asp184Asn	p.D184N	ENST00000269305	NM_001126112.2	184	Gat/Aat	5/11	1	2	FACETS	0.75	0.628	0.884	0.75	0.628	0.884	SUBCLONAL	1	TRUE	1	0.234349761514971	2		531	501	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467933	66467934	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0018201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	51	534	0	ENST00000273854.3:c.335_336delinsTT	p.Trp112Phe	p.W112F	ENST00000273854	NM_004439.5	112	tGG/tTT	3/18	1	2	FACETS	0.626	0.531	0.731	0.626	0.531	0.731	SUBCLONAL	1	TRUE	1	0.234349761514971	2		534	695	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685339	86685339	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060503440	NA	P-0018201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	27	145	0	ENST00000274376.6:c.3055C>T	p.Gln1019Ter	p.Q1019*	ENST00000274376	NM_002890.2	1019	Cag/Tag	24/25	1	2	FACETS	1	0.801	1	1	0.801	1	CLONAL	1	TRUE	1	0.234349761514971	2		145	230	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109314097	109314097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	92	628	0	ENST00000436639.2:c.1126G>A	p.Glu376Lys	p.E376K	ENST00000436639	NM_014454.2	376	Gaa/Aaa	7/10	0.105855993686351	4	FACETS	0.995	0.882	1	0.498	0.441	0.558	INDETERMINATE	1	TRUE	2	0.234349761514971	4		628	974	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309018	137309018	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	107	769	0	ENST00000481739.1:c.625C>G	p.Arg209Gly	p.R209G	ENST00000481739	NM_002957.4	209	Cgg/Ggg	5/10	0.109444019804739	3	FACETS	1	0.972	1	0.62	0.555	0.688	INDETERMINATE	1	TRUE	1	0.234349761514971	3		769	823	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	211	479	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.944	0.881	1	1	0.994	1	CLONAL	2	TRUE	1	0.353215833701977	2		479	633	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799299	42799300	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1158987717	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	53	404	0	ENST00000575354.2:c.4790dup	p.Pro1598ThrfsTer16	p.P1598Tfs*16	ENST00000575354	NM_015125.3	1595	tcc/tCcc	20/20	1	2	FACETS	0.782	0.669	0.904	0.782	0.669	0.904	CLONAL	1	TRUE	1	0.353215833701977	2		404	384	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913252	39913253	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs797044647	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	101	668	0	ENST00000378444.4:c.4862dup	p.Gly1622ArgfsTer7	p.G1622Rfs*7	ENST00000378444	NM_001123385.1	1621	cca/ccCa	14/15	1	2	FACETS	0.742	0.663	0.826	0.742	0.663	0.826	SUBCLONAL	1	TRUE	1	0.353215833701977	2		668	771	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	108	657	2	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.822	0.738	0.911	0.822	0.738	0.911	CLONAL	1	TRUE	1	0.353215833701977	2		659	744	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532653	63532654	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1301294410	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	145	658	0	ENST00000307078.5:c.1925dup	p.Ala643GlyfsTer64	p.A643Gfs*64	ENST00000307078	NM_004655.3	642	aag/aaAg	8/11	1	2	FACETS	0.952	0.869	1	0.952	0.869	1	CLONAL	1	TRUE	1	0.353215833701977	2		658	862	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274172	10274173	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1555491538	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	108	475	0	ENST00000330684.3:c.96dup	p.Ala33ArgfsTer105	p.A33Rfs*105	ENST00000330684	NM_001134407.1	32	-/C	2/13	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.353215833701977	2		475	554	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	59	651	0	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.388	0.333	0.449	0.388	0.333	0.449	SUBCLONAL	1	TRUE	1	0.353215833701977	2		651	860	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	117	624	2	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	0.866	0.781	0.956	0.866	0.781	0.956	CLONAL	1	TRUE	1	0.353215833701977	2		626	765	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528825	157528825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	102	540	0	ENST00000346085.5:c.6554del	p.Pro2185ArgfsTer8	p.P2185Rfs*8	ENST00000346085	NM_020732.3	2184	Ccc/cc	20/20	1	2	FACETS	0.87	0.779	0.966	0.87	0.779	0.966	CLONAL	1	TRUE	1	0.353215833701977	2		540	664	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023769	27023769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	120	538	0	ENST00000324856.7:c.879del	p.Thr294ProfsTer69	p.T294Pfs*69	ENST00000324856	NM_006015.4	292	aCc/ac	1/20	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.353215833701977	2		538	655	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539105	23539105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	221	587	0	ENST00000380871.4:c.334G>A	p.Ala112Thr	p.A112T	ENST00000380871	NM_006167.3	112	Gcc/Acc	2/2	0.353215833701977	3	FACETS	0.906	0.845	0.968	0.906	0.845	0.968	CLONAL	2	TRUE	1	0.353215833701977	3		587	813	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1627375	1627375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368163858	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	156	755	1	ENST00000344749.5:c.349G>A	p.Val117Met	p.V117M	ENST00000344749	NM_001136139.2	117	Gtg/Atg	6/19	1	2	FACETS	0.97	0.888	1	0.97	0.888	1	CLONAL	1	TRUE	1	0.353215833701977	2		756	911	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918759	50918759	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555793039	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	181	794	0	ENST00000440232.2:c.2629G>A	p.Asp877Asn	p.D877N	ENST00000440232	NM_002691.3	877	Gat/Aat	21/27	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.353215833701977	2		794	888	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376726	31376726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867559860	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	29	377	2	ENST00000328111.2:c.721G>A	p.Ala241Thr	p.A241T	ENST00000328111	NM_006892.3	241	Gcc/Acc	7/23	1	2	FACETS	0.328	0.263	0.403	0.328	0.263	0.403	SUBCLONAL	1	TRUE	1	0.353215833701977	2		379	500	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058747	180058748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755445139	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	91	705	0	ENST00000261937.6:c.89dup	p.Thr31AspfsTer15	p.T31Dfs*15	ENST00000261937	NM_182925.4	30	ccg/ccCg	2/30	1	2	FACETS	0.614	0.545	0.689	0.614	0.545	0.689	SUBCLONAL	1	TRUE	1	0.353215833701977	2		705	839	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659789	88659789	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs762900005	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	50	576	0	ENST00000372037.3:c.441del	p.Phe147LeufsTer18	p.F147Lfs*18	ENST00000372037	NM_004329.2	146	Ttt/tt	7/13	1	2	FACETS	0.44	0.372	0.514	0.44	0.372	0.514	SUBCLONAL	1	TRUE	1	0.353215833701977	2		576	644	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088659	27088659	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	169	828	0	ENST00000324856.7:c.2272del	p.Gln758ArgfsTer75	p.Q758Rfs*75	ENST00000324856	NM_006015.4	756	aaC/aa	7/20	1	2	FACETS	0.978	0.899	1	0.978	0.899	1	CLONAL	1	TRUE	1	0.353215833701977	2		828	978	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196879	108196880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs773570504	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	100	528	1	ENST00000278616.4:c.6908dup	p.Glu2304GlyfsTer69	p.E2304Gfs*69	ENST00000278616	NM_000051.3	2301	gca/gcAa	47/63	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.353215833701977	2		529	542	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24134056	24134057	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	164	806	0	ENST00000263121.7:c.214dup	p.Thr72AsnfsTer4	p.T72Nfs*4	ENST00000263121	NM_003073.3	69	-/A	2/9	1	2	FACETS	0.879	0.806	0.955	0.879	0.806	0.955	CLONAL	1	TRUE	1	0.353215833701977	2		806	1057	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432071	121432073	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs1288094664	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	150	762	0	ENST00000257555.6:c.824_826del	p.Glu275del	p.E275del	ENST00000257555		273	aAAGaa/aaa	4/10	1	2	FACETS	0.879	0.803	0.959	0.879	0.803	0.959	CLONAL	1	TRUE	1	0.353215833701977	2		762	966	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800902	120800903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs748469666	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	208	1014	2	ENST00000257552.2:c.345dup	p.Leu116AlafsTer15	p.L116Afs*15	ENST00000257552	NM_002442.3	115	-/G	6/15	1	2	FACETS	0.995	0.922	1	0.995	0.922	1	CLONAL	1	TRUE	1	0.353215833701977	2		1016	1184	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193974	106193974	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	34	464	0	ENST00000380013.4:c.4436T>C	p.Leu1479Pro	p.L1479P	ENST00000380013	NM_001127208.2	1479	cTt/cCt	10/11	1	2	FACETS	0.345	0.281	0.417	0.345	0.281	0.417	SUBCLONAL	1	TRUE	1	0.353215833701977	2		464	558	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9786991	9786993	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	133	603	0	ENST00000377346.4:c.3029_3031del	p.Glu1010del	p.E1010del	ENST00000377346	NM_005026.3	1008	GAG/-	24/24	1	2	FACETS	0.951	0.864	1	0.951	0.864	1	CLONAL	1	TRUE	1	0.353215833701977	2		603	792	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259564	16259564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1557761062	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	38	646	0	ENST00000375759.3:c.6829G>A	p.Ala2277Thr	p.A2277T	ENST00000375759	NM_015001.2	2277	Gct/Act	11/15	1	2	FACETS	0.299	0.246	0.359	0.299	0.246	0.359	SUBCLONAL	1	TRUE	1	0.353215833701977	2		646	719	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261707	16261707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1366534863	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	140	679	2	ENST00000375759.3:c.8972C>T	p.Pro2991Leu	p.P2991L	ENST00000375759	NM_015001.2	2991	cCc/cTc	11/15	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.353215833701977	2		681	776	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480045	120480045	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	119	619	0	ENST00000256646.2:c.3382A>G	p.Asn1128Asp	p.N1128D	ENST00000256646	NM_024408.3	1128	Aat/Gat	21/34	1	2	FACETS	0.908	0.82	1	0.908	0.82	1	CLONAL	1	TRUE	1	0.353215833701977	2		619	742	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741879	162741879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	99	466	0	ENST00000367921.3:c.1570G>A	p.Ala524Thr	p.A524T	ENST00000367921	NM_006182.2	524	Gct/Act	13/18	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.353215833701977	2		466	514	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720866	89720866	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	190	459	0	ENST00000371953.3:c.1019del	p.Asn340IlefsTer4	p.N340Ifs*4	ENST00000371953	NM_000314.4	339	ccA/cc	8/9	0.353215833701977	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.353215833701977	2		459	511	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199944	108199944	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	79	448	0	ENST00000278616.4:c.7286A>G	p.Glu2429Gly	p.E2429G	ENST00000278616	NM_000051.3	2429	gAa/gGa	49/63	1	2	FACETS	0.906	0.799	1	0.906	0.799	1	CLONAL	1	TRUE	1	0.353215833701977	2		448	494	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006403	12006403	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	112	636	0	ENST00000396373.4:c.371G>T	p.Arg124Met	p.R124M	ENST00000396373	NM_001987.4	124	aGg/aTg	4/8	1	2	FACETS	0.951	0.856	1	0.951	0.856	1	CLONAL	1	TRUE	1	0.353215833701977	2		636	667	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21630786	21630786	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	143	721	0	ENST00000421138.2:c.818del	p.Lys273SerfsTer33	p.K273Sfs*33	ENST00000421138		273	aAg/ag	8/16	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.353215833701977	2		721	784	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445040	49445041	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	80	546	0	ENST00000301067.7:c.2425dup	p.Gln809ProfsTer3	p.Q809Pfs*3	ENST00000301067	NM_003482.3	809	cag/cCag	10/54	1	2	FACETS	0.704	0.62	0.795	0.704	0.62	0.795	SUBCLONAL	1	TRUE	1	0.353215833701977	2		546	643	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039504	49039504	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	101	551	0	ENST00000267163.4:c.2489G>T	p.Arg830Ile	p.R830I	ENST00000267163	NM_000321.2	830	aGa/aTa	23/27	1	2	FACETS	0.828	0.74	0.92	0.828	0.74	0.92	CLONAL	1	TRUE	1	0.353215833701977	2		551	691	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436003	110436003	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	81	813	1	ENST00000375856.3:c.2398G>T	p.Gly800Cys	p.G800C	ENST00000375856	NM_003749.2	800	Ggc/Tgc	1/2	1	2	FACETS	0.431	0.378	0.488	0.431	0.378	0.488	SUBCLONAL	1	TRUE	1	0.353215833701977	2		814	1064	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100133	30100133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370296777	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	90	786	0	ENST00000331968.5:c.1487C>T	p.Thr496Met	p.T496M	ENST00000331968	NM_002742.2	496	aCg/aTg	10/18	1	2	FACETS	0.688	0.61	0.771	0.688	0.61	0.771	SUBCLONAL	1	TRUE	1	0.353215833701977	2		786	741	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032268	42032268	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	146	741	1	ENST00000219905.7:c.4452G>T	p.Lys1484Asn	p.K1484N	ENST00000219905	NM_001164273.1	1484	aaG/aaT	14/24	1	2	FACETS	0.889	0.811	0.971	0.889	0.811	0.971	CLONAL	1	TRUE	1	0.353215833701977	2		742	930	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457611	67457611	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	119	653	0	ENST00000327367.4:c.421C>G	p.Pro141Ala	p.P141A	ENST00000327367	NM_005902.3	141	Cca/Gca	3/9	1	2	FACETS	0.752	0.678	0.83	0.752	0.678	0.83	SUBCLONAL	1	TRUE	1	0.353215833701977	2		653	896	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817889	3817889	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	143	638	1	ENST00000262367.5:c.3082G>T	p.Gly1028Ter	p.G1028*	ENST00000262367	NM_004380.2	1028	Gga/Tga	16/31	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.353215833701977	2		639	726	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976521	7976521	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	101	567	0	ENST00000319144.4:c.1871C>T	p.Thr624Ile	p.T624I	ENST00000319144	NM_001139.2	624	aCc/aTc	14/15	1	2	FACETS	0.83	0.742	0.923	0.83	0.742	0.923	CLONAL	1	TRUE	1	0.353215833701977	2		567	689	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40879741	40879742	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	54	748	0	ENST00000428826.2:c.157dup	p.Thr53AsnfsTer6	p.T53Nfs*6	ENST00000428826		53	acc/aAcc	4/21	1	2	FACETS	0.358	0.304	0.416	0.358	0.304	0.416	SUBCLONAL	1	TRUE	1	0.353215833701977	2		748	855	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56811478	56811478	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1567818502	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	89	461	0	ENST00000337432.4:c.1027-1G>A		p.X343_splice	ENST00000337432	NM_058216.2	343			1	2	FACETS	0.906	0.805	1	0.906	0.805	1	CLONAL	1	TRUE	1	0.353215833701977	2		461	556	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853840	59853840	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	43	696	0	ENST00000259008.2:c.2019A>T	p.Gln673His	p.Q673H	ENST00000259008	NM_032043.2	673	caA/caT	14/20	1	2	FACETS	0.296	0.246	0.351	0.296	0.246	0.351	SUBCLONAL	1	TRUE	1	0.353215833701977	2		696	823	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573625	48573625	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555685038	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	68	537	0	ENST00000342988.3:c.209A>C	p.Lys70Thr	p.K70T	ENST00000342988	NM_005359.5	70	aAa/aCa	2/12	1	2	FACETS	0.828	0.722	0.942	0.828	0.722	0.942	CLONAL	1	TRUE	1	0.353215833701977	2		537	465	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226625	2226625	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	153	677	0	ENST00000398665.3:c.4105A>G	p.Ser1369Gly	p.S1369G	ENST00000398665	NM_032482.2	1369	Agc/Ggc	27/28	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.353215833701977	2		677	808	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11032060	11032060	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	145	644	4	ENST00000327064.4:c.1625G>T	p.Gly542Val	p.G542V	ENST00000327064	NM_199141.1	542	gGg/gTg	15/16	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.353215833701977	2		648	776	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098561	11098561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555755289	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	208	736	2	ENST00000358026.2:c.1079G>A	p.Gly360Asp	p.G360D	ENST00000358026	NM_001128849.1	360	gGc/gAc	6/36	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.353215833701977	2		738	951	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213270	36213270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	129	650	0	ENST00000222270.7:c.2467G>A	p.Gly823Arg	p.G823R	ENST00000222270	NM_014727.1	823	Gga/Aga	4/37	1	2	FACETS	0.996	0.905	1	0.996	0.905	1	CLONAL	1	TRUE	1	0.353215833701977	2		650	733	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36217254	36217254	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	105	656	0	ENST00000222270.7:c.4003G>A	p.Gly1335Arg	p.G1335R	ENST00000222270	NM_014727.1	1335	Gga/Aga	14/37	1	2	FACETS	0.817	0.732	0.907	0.817	0.732	0.907	CLONAL	1	TRUE	1	0.353215833701977	2		656	728	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919865	50919866	+	splice_acceptor_variant	Splice_Site	INS	-	-	G	rs756872503	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	115	633	2	ENST00000440232.2:c.2959dup		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	0.835	0.752	0.922	0.835	0.752	0.922	CLONAL	1	TRUE	1	0.353215833701977	2		635	780	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994392	25994392	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	86	414	0	ENST00000435504.4:c.421C>T	p.Gln141Ter	p.Q141*	ENST00000435504		141	Cag/Tag	6/13	1	2	FACETS	0.862	0.764	0.966	0.862	0.764	0.966	CLONAL	1	TRUE	1	0.353215833701977	2		414	565	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241056	39241056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	122	685	1	ENST00000402219.2:c.2015C>T	p.Ala672Val	p.A672V	ENST00000402219	NM_005633.3	672	gCa/gTa	12/23	1	2	FACETS	0.959	0.868	1	0.959	0.868	1	CLONAL	1	TRUE	1	0.353215833701977	2		686	720	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630490	47630490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749212640	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	147	729	0	ENST00000233146.2:c.160G>A	p.Ala54Thr	p.A54T	ENST00000233146	NM_000251.2	54	Gcc/Acc	1/16	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.353215833701977	2		729	783	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033402	48033402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	78	656	2	ENST00000234420.5:c.3706G>A	p.Ala1236Thr	p.A1236T	ENST00000234420	NM_000179.2	1236	Gct/Act	8/10	1	2	FACETS	0.685	0.602	0.774	0.685	0.602	0.774	SUBCLONAL	1	TRUE	1	0.353215833701977	2		658	645	SUCCESS
REL	5966	MSKCC	GRCh37	2	61128157	61128158	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	96	551	0	ENST00000295025.8:c.339dup	p.Glu114ArgfsTer21	p.E114Rfs*21	ENST00000295025	NM_002908.2	111	-/A	4/11	1	2	FACETS	0.748	0.666	0.835	0.748	0.666	0.835	SUBCLONAL	1	TRUE	1	0.353215833701977	2		551	727	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99163099	99163099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	65	716	0	ENST00000074304.5:c.1105G>A	p.Gly369Ser	p.G369S	ENST00000074304	NM_001134224.1	369	Ggt/Agt	13/26	1	2	FACETS	0.385	0.333	0.442	0.385	0.333	0.442	SUBCLONAL	1	TRUE	1	0.353215833701977	2		716	956	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921712	111921713	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	78	379	0	ENST00000393256.3:c.506dup	p.Leu169PhefsTer3	p.L169Ffs*3	ENST00000393256	NM_006538.4	167	-/T	4/4	1	2	FACETS	0.938	0.827	1	0.938	0.827	1	CLONAL	1	TRUE	1	0.353215833701977	2		379	471	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266175	198266175	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	134	595	2	ENST00000335508.6:c.2445del	p.Phe815LeufsTer19	p.F815Lfs*19	ENST00000335508	NM_012433.2	815	ttT/tt	17/25	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.353215833701977	2		597	754	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131490	202131490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	115	593	1	ENST00000358485.4:c.458G>A	p.Gly153Asp	p.G153D	ENST00000358485	NM_001080125.1	153	gGc/gAc	2/9	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.353215833701977	2		594	615	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979269	40979269	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	70	466	0	ENST00000373198.4:c.1864A>G	p.Ser622Gly	p.S622G	ENST00000373198	NM_133170.3	622	Agt/Ggt	11/32	1	2	FACETS	0.67	0.584	0.762	0.67	0.584	0.762	SUBCLONAL	1	TRUE	1	0.353215833701977	2		466	592	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182626	38182626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781778676	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	58	305	0	ENST00000396334.3:c.779C>T	p.Ala260Val	p.A260V	ENST00000396334	NM_002468.4	260	gCc/gTc	5/5	1	2	FACETS	0.873	0.754	1	0.873	0.754	1	CLONAL	1	TRUE	1	0.353215833701977	2		305	376	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390218	89390218	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	81	418	0	ENST00000336596.2:c.967A>G	p.Thr323Ala	p.T323A	ENST00000336596	NM_005233.5	323	Acc/Gcc	4/17	1	2	FACETS	0.96	0.848	1	0.96	0.848	1	CLONAL	1	TRUE	1	0.353215833701977	2		418	478	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747835	41747835	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	127	430	0	ENST00000226382.2:c.934A>G	p.Ser312Gly	p.S312G	ENST00000226382	NM_003924.3	312	Agt/Ggt	3/3	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.353215833701977	2		430	640	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867409	35867409	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	27	485	0	ENST00000303115.3:c.226del	p.Ala76ProfsTer5	p.A76Pfs*5	ENST00000303115	NM_002185.3	75	Ggg/gg	3/8	1	2	FACETS	0.344	0.273	0.425	0.344	0.273	0.425	SUBCLONAL	1	TRUE	1	0.353215833701977	2		485	445	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589576	67589593	+	inframe_deletion	In_Frame_Del	DEL	AAAAAATTACATGAATAT	AAAAAATTACATGAATAT	-	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	60	471	0	ENST00000274335.5:c.1341_1358del	p.Lys447_Tyr452del	p.K447_Y452del	ENST00000274335		447	AAAAAATTACATGAATAT/-	10/15	1	2	FACETS	0.712	0.615	0.818	0.712	0.615	0.818	SUBCLONAL	1	TRUE	1	0.353215833701977	2		471	477	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86667958	86667959	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	84	468	0	ENST00000274376.6:c.1726dup	p.Cys576LeufsTer7	p.C576Lfs*7	ENST00000274376	NM_002890.2	574	-/T	13/25	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.353215833701977	2		468	475	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402586	20402586	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	83	391	0	ENST00000346618.3:c.126del	p.Gly43AlafsTer37	p.G43Afs*37	ENST00000346618	NM_001949.4	41	agC/ag	1/7	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.353215833701977	2		391	449	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140500161	140500161	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1250	69	872	1	ENST00000288602.6:c.980+1del		p.X327_splice	ENST00000288602	NM_004333.4	327			1	2	FACETS	0.296	0.257	0.339	0.296	0.257	0.339	SUBCLONAL	1	TRUE	1	0.353215833701977	2		873	1319	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853352	151853352	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	103	532	0	ENST00000262189.6:c.11750C>T	p.Ala3917Val	p.A3917V	ENST00000262189	NM_170606.2	3917	gCc/gTc	45/59	1	2	FACETS	0.992	0.89	1	0.992	0.89	1	CLONAL	1	TRUE	1	0.353215833701977	2		532	588	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207603	29207603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	62	653	1	ENST00000240100.2:c.193G>A	p.Val65Ile	p.V65I	ENST00000240100	NM_001394.6	65	Gtc/Atc	1/4	0.353215833701977	3	FACETS	0.489	0.422	0.563	0.245	0.211	0.282	SUBCLONAL	1	TRUE	1	0.353215833701977	3		654	844	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772950	135772951	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	rs118203724	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	63	551	0	ENST00000298552.3:c.2671_2672dup	p.Asn891LysfsTer41	p.N891Kfs*41	ENST00000298552	NM_001162426.1	891	aac/aaAAc	21/23	1	2	FACETS	0.615	0.532	0.705	0.615	0.532	0.705	SUBCLONAL	1	TRUE	1	0.353215833701977	2		551	580	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929539	44929539	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	53	639	0	ENST00000377967.4:c.2639A>G	p.Gln880Arg	p.Q880R	ENST00000377967	NM_021140.2	880	cAg/cGg	17/29	1	2	FACETS	0.376	0.319	0.438	0.376	0.319	0.438	SUBCLONAL	1	TRUE	1	0.353215833701977	2		639	799	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949995	44949995	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	27	586	0	ENST00000377967.4:c.3764G>T	p.Arg1255Leu	p.R1255L	ENST00000377967	NM_021140.2	1255	cGg/cTg	26/29	1	2	FACETS	0.296	0.235	0.367	0.296	0.235	0.367	SUBCLONAL	1	TRUE	1	0.353215833701977	2		586	516	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs104886003	NA	P-0018205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	32	673	0	ENST00000263967.3:c.1633G>C	p.Glu545Gln	p.E545Q	ENST00000263967	NM_006218.2	545	Gag/Cag	10/21	1	2	FACETS	0.112	0.09	0.137	0.112	0.09	0.137	SUBCLONAL	1	TRUE	1	0.5927008938702	2		673	963	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0018205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	840	536	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.581598922255543	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.5927008938702	2		536	1380	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986625	36986629	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGC	CCTGC	-	novel	NA	P-0018205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	96	260	0	ENST00000354822.5:c.1060_1064del	p.Ala354ProfsTer83	p.A354Pfs*83	ENST00000354822	NM_001079668.2	354	GCAGGc/c	3/3	0.5927008938702	1	FACETS	0.942	0.855	1	0.942	0.855	1	CLONAL	1	TRUE	0	0.5927008938702	1		260	242	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127442	55127442	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553902417	NA	P-0018205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	147	775	0	ENST00000257290.5:c.230A>G	p.Asn77Ser	p.N77S	ENST00000257290	NM_006206.4	77	aAc/aGc	3/23	1	2	FACETS	0.379	0.345	0.415	0.379	0.345	0.415	SUBCLONAL	1	TRUE	1	0.5927008938702	2		775	1308	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882025	NA	P-0018207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	434	835	2	ENST00000269305.4:c.646G>T	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ttg	6/11	0.803405782291673	2	FACETS	0.948	0.922	0.973	0.948	0.922	0.973	CLONAL	2	TRUE	0	0.823441938382713	2		837	556	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916768	48916768	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	68	646	4	ENST00000267163.4:c.298G>T	p.Gly100Ter	p.G100*	ENST00000267163	NM_000321.2	100	Gga/Tga	3/27	0.823441938382713	1	FACETS	0.934	0.854	1	0.934	0.854	1	CLONAL	1	TRUE	0	0.823441938382713	1		650	104	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289955	15289955	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0018207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	249	771	2	ENST00000263388.2:c.3599T>A	p.Leu1200Ter	p.L1200*	ENST00000263388	NM_000435.2	1200	tTg/tAg	22/33	1	2	FACETS	0.926	0.872	0.981	0.926	0.872	0.981	CLONAL	1	TRUE	1	0.823441938382713	2		773	653	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508444	106508444	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	10	215	0	ENST00000359195.3:c.438G>T	p.Glu146Asp	p.E146D	ENST00000359195	NM_002649.2	146	gaG/gaT	2/11	1	2	FACETS	0.153	0.103	0.215	0.153	0.103	0.215	SUBCLONAL	1	TRUE	1	0.823441938382713	2		215	159	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104006	69104006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	74	501	1	ENST00000288368.4:c.4396G>A	p.Ala1466Thr	p.A1466T	ENST00000288368	NM_024870.2	1466	Gct/Act	36/40	1	2	FACETS	0.961	0.86	1	0.961	0.86	1	CLONAL	1	TRUE	1	0.823441938382713	2		502	187	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412683	63412683	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	140	648	0	ENST00000330258.3:c.484A>T	p.Met162Leu	p.M162L	ENST00000330258	NM_152424.3	162	Atg/Ttg	2/2	0.313425844577162	1	FACETS	0.617	0.571	0.664	0.617	0.571	0.664	INDETERMINATE	1	TRUE	0	0.823441938382713	1		648	324	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922695	44922695	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	265	514	0	ENST00000377967.4:c.1556del	p.Arg519HisfsTer29	p.R519Hfs*29	ENST00000377967	NM_021140.2	519	cGa/ca	16/29	0.832356730438274	1	FACETS	0.913	0.873	0.952	0.913	0.873	0.952	CLONAL	1	TRUE	0	0.832356730438274	1		514	407	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282115	38282115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554562012	NA	P-0018209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	507	838	1	ENST00000425967.3:c.941C>T	p.Pro314Leu	p.P314L	ENST00000425967	NM_001174067.1	314	cCg/cTg	8/19	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.832356730438274	2		839	1197	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720857	89720857	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	283	417	0	ENST00000371953.3:c.1008C>A	p.Tyr336Ter	p.Y336*	ENST00000371953	NM_000314.4	336	taC/taA	8/9	0.832356730438274	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.832356730438274	1		417	381	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896421	151896422	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATCC	novel	NA	P-0018209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	279	636	0	ENST00000262189.6:c.4212_4215dup	p.Pro1406GlyfsTer9	p.P1406Gfs*9	ENST00000262189	NM_170606.2	1405	-/GGAT	27/59	1	2	FACETS	0.956	0.904	1	0.956	0.904	1	CLONAL	1	TRUE	1	0.832356730438274	2		636	701	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549563	5549563	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1023826544	NA	P-0018209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	451	807	0	ENST00000397747.3:c.590C>G	p.Thr197Ser	p.T197S	ENST00000397747	NM_025239.3	197	aCt/aGt	4/7	1	2	FACETS	0.962	0.92	1	0.962	0.92	1	CLONAL	1	TRUE	1	0.832356730438274	2		807	1127	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	90	605	1	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.160932496063886	3	FACETS	0.829	0.738	0.925	0.553	0.492	0.617	CLONAL	2	TRUE	0	0.256893833256455	3		606	477	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	165	918	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.256893833256455	7	FACETS	1	0.962	1			1	CLONAL	5	TRUE	NA	0.256893833256455	7		918	401	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350291	15350291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1233820799	NA	P-0018210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	97	631	1	ENST00000263377.2:c.3488G>A	p.Arg1163Gln	p.R1163Q	ENST00000263377	NM_058243.2	1163	cGg/cAg	17/20	0.256893833256455	3	FACETS	1	0.897	1	1	0.897	1	CLONAL	2	TRUE	1	0.256893833256455	3		632	426	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52685769	52685769	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	80	707	0	ENST00000394830.3:c.703del	p.Gln235ArgfsTer18	p.Q235Rfs*18	ENST00000394830	NM_018313.4	235	Cag/ag	7/30	0.178679049375347	4	FACETS	1	0.916	1	1	0.916	1	CLONAL	2	TRUE	2	0.256893833256455	4		707	376	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094373	27094374	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTGGC	novel	NA	P-0018210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	78	537	0	ENST00000324856.7:c.3084_3088dup	p.Phe1030TrpfsTer11	p.F1030Wfs*11	ENST00000324856	NM_006015.4	1027	-/CTGGC	11/20	0.256893833256455	3	FACETS	0.812	0.717	0.913	0.812	0.717	0.913	CLONAL	2	TRUE	1	0.256893833256455	3		537	422	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612095	43612095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	76	607	1	ENST00000355710.3:c.2200G>A	p.Glu734Lys	p.E734K	ENST00000355710	NM_020975.4	734	Gaa/Aaa	12/20	0.237245204452391	3	FACETS	0.959	0.848	1	0.959	0.848	1	CLONAL	2	TRUE	1	0.256893833256455	3		608	348	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041696	42041696	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	40	600	0	ENST00000219905.7:c.5891C>A	p.Ala1964Asp	p.A1964D	ENST00000219905	NM_001164273.1	1964	gCt/gAt	17/24	0.220915314378284	4	FACETS	0.95	0.79	1	0.475	0.395	0.564	CLONAL	1	TRUE	2	0.256893833256455	4		600	412	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678584	88678584	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	32	330	0	ENST00000360948.2:c.952G>A	p.Glu318Lys	p.E318K	ENST00000360948	NM_001012338.2	318	Gag/Aag	9/19	0.256893833256455	8	FACETS	1	0.911	1	0.203	0.165	0.246	CLONAL	1	TRUE	2	0.256893833256455	8		330	362	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970917	21970917	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	85	818	0	ENST00000304494.5:c.441del	p.Ala148ArgfsTer45	p.A148Rfs*45	ENST00000304494	NM_000077.4	147	gcC/gc	2/3	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.256893833256455	2		818	538	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0018213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	39	523	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.591	0.49	0.705	0.591	0.49	0.705	SUBCLONAL	1	FALSE	1	0.271434292400302	2		523	486	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	43	576	0	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	1	2	FACETS	0.586	0.49	0.692	0.586	0.49	0.692	SUBCLONAL	1	FALSE	1	0.271434292400302	2		576	541	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967255	134967255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751581569	NA	P-0018213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	39	666	1	ENST00000398015.3:c.2594G>A	p.Arg865Gln	p.R865Q	ENST00000398015	NM_004441.4	865	cGg/cAg	14/16	1	2	FACETS	0.57	0.472	0.68	0.57	0.472	0.68	SUBCLONAL	1	FALSE	1	0.271434292400302	2		667	504	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174871	56174872	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0018213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	67	653	0	ENST00000399503.3:c.2031dup	p.Arg678GlufsTer19	p.R678Efs*19	ENST00000399503	NM_005921.1	677	cag/caGg	11/20	0.187200073316491	3	FACETS	0.808	0.701	0.923	0.404	0.35	0.462	CLONAL	1	FALSE	1	0.271434292400302	3		653	694	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945451	151945451	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	71	942	0	ENST00000262189.6:c.2068G>T	p.Glu690Ter	p.E690*	ENST00000262189	NM_170606.2	690	Gaa/Taa	14/59	1	2	FACETS	0.588	0.512	0.671	0.588	0.512	0.671	SUBCLONAL	1	FALSE	1	0.271434292400302	2		942	889	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073739	8073739	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1361059014	NA	P-0018216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	64	346	0	ENST00000377482.5:c.920C>T	p.Ser307Leu	p.S307L	ENST00000377482	NM_018948.3	307	tCg/tTg	4/4	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.242075698535636	2		346	393	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982163	201982164	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0018216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	42	634	0	ENST00000359651.3:c.688+1dup		p.-229fs	ENST00000359651		229	-/G	5/8	0.125516784830587	0	FACETS	0.504	0.42	0.597			1	INDETERMINATE	1	FALSE	0	0.242075698535636	0		634	522	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100297	8100297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	61	705	1	ENST00000346208.3:c.271C>T	p.His91Tyr	p.H91Y	ENST00000346208		91	Cat/Tat	3/6	0.125516784830587	0	FACETS	0.578	0.498	0.665			1	INDETERMINATE	1	FALSE	0	0.242075698535636	0		706	661	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445179	49445179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	74	798	0	ENST00000301067.7:c.2287C>T	p.Pro763Ser	p.P763S	ENST00000301067	NM_003482.3	763	Ccg/Tcg	10/54	1	2	FACETS	0.925	0.81	1	0.925	0.81	1	CLONAL	1	FALSE	1	0.242075698535636	2		798	661	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445959	49445959	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	108	987	0	ENST00000301067.7:c.1507C>G	p.Leu503Val	p.L503V	ENST00000301067	NM_003482.3	503	Ctg/Gtg	10/54	1	2	FACETS	0.9	0.807	1	0.9	0.807	1	CLONAL	1	FALSE	1	0.242075698535636	2		987	991	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935668	15935668	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779863527	NA	P-0018216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	70	401	0	ENST00000268712.3:c.7265G>A	p.Arg2422Gln	p.R2422Q	ENST00000268712	NM_006311.3	2422	cGa/cAa	46/46	1	2	FACETS	0.769	0.674	0.87	1	0.975	1	SUBCLONAL	2	FALSE	1	0.242075698535636	2		401	376	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067138	37067138	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	71	330	0	ENST00000231790.2:c.1049C>T	p.Pro350Leu	p.P350L	ENST00000231790	NM_000249.3	350	cCa/cTa	12/19	0.198736535597358	3	FACETS	0.911	0.8	1	0.911	0.8	1	CLONAL	2	FALSE	1	0.242075698535636	3		330	361	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096153	71096153	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	48	396	3	ENST00000318789.4:c.604C>T	p.Gln202Ter	p.Q202*	ENST00000318789	NM_032682.5	202	Caa/Taa	10/21	1	2	FACETS	0.831	0.703	0.972	0.831	0.703	0.972	CLONAL	1	FALSE	1	0.242075698535636	2		399	477	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651963	36651963	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	104	588	2	ENST00000244741.5:c.85C>T	p.Gln29Ter	p.Q29*	ENST00000244741	NM_000389.4	29	Cag/Tag	2/3	1	2	FACETS	0.791	0.711	0.876	1	0.984	1	SUBCLONAL	2	FALSE	1	0.242075698535636	2		590	543	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902215	151902215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749943795	NA	P-0018216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	45	651	0	ENST00000262189.6:c.3937G>A	p.Glu1313Lys	p.E1313K	ENST00000262189	NM_170606.2	1313	Gag/Aag	25/59	0.198736535597358	3	FACETS	0.615	0.515	0.725	0.307	0.257	0.363	SUBCLONAL	1	FALSE	1	0.242075698535636	3		651	678	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0018217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	43	571	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.357	0.298	0.423	0.357	0.298	0.423	SUBCLONAL	1	TRUE	1	0.429011597181289	2		571	561	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727454	66727454	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519909	NA	P-0018217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	9	490	0	ENST00000307102.5:c.170A>C	p.Lys57Thr	p.K57T	ENST00000307102	NM_002755.3	57	aAg/aCg	2/11	1	2	FACETS	0.098	0.064	0.141	0.098	0.064	0.141	SUBCLONAL	1	TRUE	1	0.429011597181289	2		490	430	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984375	72984375	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0018217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	123	415	0	ENST00000268489.5:c.3209T>A	p.Leu1070Ter	p.L1070*	ENST00000268489	NM_006885.3	1070	tTg/tAg	3/10	0.365196626967186	0	FACETS	0.748	0.694	0.8			1	SUBCLONAL	2	TRUE	0	0.429011597181289	0		415	219	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0018219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	337	833	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.399092880586128	3	FACETS	0.9	0.852	0.947	0.9	0.852	0.947	CLONAL	2	TRUE	1	0.461006857082516	3		833	1000	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0018219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	312	775	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	NA	2	FACETS	0.952	0.904	1			1	INDETERMINATE	2	TRUE	NA	0.461006857082516	2		777	711	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0018219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	336	914	3	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.398926354100129	4	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	2	0.461006857082516	4		917	1051	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247243	153247243	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	341	827	0	ENST00000281708.4:c.1559A>G	p.Asp520Gly	p.D520G	ENST00000281708	NM_033632.3	520	gAt/gGt	10/12	0.399092880586128	3	FACETS	0.898	0.851	0.945	0.898	0.851	0.945	CLONAL	2	TRUE	1	0.461006857082516	3		827	1014	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175481	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0018219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	173	538	0	ENST00000257430.4:c.4192_4193del	p.Arg1399PhefsTer9	p.R1399Ffs*9	ENST00000257430	NM_000038.5	1397	GAg/g	16/16	0.398926354100129	4	FACETS	0.894	0.827	0.964	0.894	0.827	0.964	CLONAL	2	TRUE	2	0.461006857082516	4		538	613	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101179	41101179	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770753852	NA	P-0018219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	153	878	1	ENST00000373198.4:c.1177G>A	p.Val393Met	p.V393M	ENST00000373198	NM_133170.3	393	Gtg/Atg	8/32	0.398926354100129	4	FACETS	1	0.958	1	0.538	0.492	0.586	CLONAL	1	TRUE	2	0.461006857082516	4		879	902	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249507	153249507	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	171	921	0	ENST00000281708.4:c.1271del	p.Val424AspfsTer6	p.V424Dfs*6	ENST00000281708	NM_033632.3	424	gTa/ga	9/12	0.399092880586128	3	FACETS	0.895	0.823	0.971	0.447	0.411	0.486	CLONAL	1	TRUE	1	0.461006857082516	3		921	1020	SUCCESS
APC	324	MSKCC	GRCh37	5	112170747	112170747	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1561568632	NA	P-0018219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	301	830	0	ENST00000257430.4:c.1847del	p.Leu616TrpfsTer14	p.L616Wfs*14	ENST00000257430	NM_000038.5	615	Ttt/tt	15/16	0.398926354100129	4	FACETS	0.918	0.866	0.972	0.918	0.866	0.972	CLONAL	2	TRUE	2	0.461006857082516	4		830	1039	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956723	68956723	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs750933833	NA	P-0018219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	457	773	0	ENST00000288368.4:c.841C>T	p.Arg281Trp	p.R281W	ENST00000288368	NM_024870.2	281	Cgg/Tgg	8/40	0.426807079381057	5	FACETS	0.909	0.873	0.945	0.909	0.873	0.945	CLONAL	4	TRUE	1	0.461006857082516	5		773	922	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031730	69031730	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	185	946	0	ENST00000288368.4:c.3485T>G	p.Leu1162Arg	p.L1162R	ENST00000288368	NM_024870.2	1162	cTt/cGt	28/40	0.426807079381057	5	FACETS	0.992	0.914	1	0.248	0.228	0.269	CLONAL	1	TRUE	1	0.461006857082516	5		946	1368	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	144	184	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.958	1			1	INDETERMINATE	1	TRUE	NA	0.781523635411108	2		184	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0018220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	200	849	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.574625681568527	1	FACETS	0.823	0.775	0.87	0.823	0.775	0.87	CLONAL	1	TRUE	0	0.781523635411108	1		849	379	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165818	118165818	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	142	625	1	ENST00000369448.3:c.328G>T	p.Asp110Tyr	p.D110Y	ENST00000369448	NM_017709.3	110	Gat/Tat	2/2	1	2	FACETS	0.913	0.841	0.987	0.913	0.841	0.987	CLONAL	1	TRUE	1	0.781523635411108	2		626	398	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692883	89692883	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	173	528	3	ENST00000371953.3:c.367del	p.His123ThrfsTer11	p.H123Tfs*11	ENST00000371953	NM_000314.4	123	Cac/ac	5/9	0.781523635411108	1	FACETS	0.97	0.916	1	0.97	0.916	1	CLONAL	1	TRUE	0	0.781523635411108	1		531	278	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793489	18793489	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0018220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	198	592	0	ENST00000266497.5:c.4185+1G>T		p.X1395_splice	ENST00000266497		1395			1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.781523635411108	2		592	506	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355105	15355105	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	303	1260	0	ENST00000263377.2:c.2518C>A	p.Pro840Thr	p.P840T	ENST00000263377	NM_058243.2	840	Ccc/Acc	13/20	0.733332046523702	3	FACETS	1	0.976	1	0.532	0.501	0.563	CLONAL	1	TRUE	1	0.781523635411108	3		1260	1014	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498433	89498433	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369423490	NA	P-0018220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	147	445	2	ENST00000336596.2:c.2405C>T	p.Thr802Met	p.T802M	ENST00000336596	NM_005233.5	802	aCg/aTg	14/17	1	2	FACETS	0.927	0.855	1	0.927	0.855	1	CLONAL	1	TRUE	1	0.781523635411108	2		447	406	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189349345	189349345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	193	727	0	ENST00000264731.3:c.41G>A	p.Cys14Tyr	p.C14Y	ENST00000264731	NM_003722.4	14	tGc/tAc	1/14	1	2	FACETS	0.879	0.819	0.94	0.879	0.819	0.94	CLONAL	1	TRUE	1	0.781523635411108	2		727	562	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417386	139417386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754236791	NA	P-0018220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	305	1093	3	ENST00000277541.6:c.658G>A	p.Val220Met	p.V220M	ENST00000277541	NM_017617.3	220	Gtg/Atg	4/34	0.781523635411108	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.781523635411108	1		1096	456	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830864	72830864	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	225	706	0	ENST00000268489.5:c.5717del	p.Lys1906ArgfsTer8	p.K1906Rfs*8	ENST00000268489	NM_006885.3	1906	aAg/ag	9/10	1	2	FACETS	0.996	0.933	1	0.996	0.933	1	CLONAL	1	TRUE	1	0.69	2		706	655	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752679	128752681	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	novel	NA	P-0018221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	119	430	0	ENST00000377970.2:c.841_843del	p.Ser281del	p.S281del	ENST00000377970	NM_002467.4	280	gtTTCt/gtt	3/3	1	2	FACETS	0.922	0.841	1	0.922	0.841	1	CLONAL	1	TRUE	1	0.69	2		430	374	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099977	157099977	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	140	376	0	ENST00000346085.5:c.914G>A	p.Gly305Asp	p.G305D	ENST00000346085	NM_020732.3	305	gGc/gAc	1/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.425932453319906	2		376	546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0018223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	719	571	0	ENST00000269305.4:c.97-1G>A		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.779377690945668	4	FACETS	1	0.994	1	1	0.998	1	CLONAL	4	TRUE	2	0.864779687278708	4		571	767	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542597	141542597	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	388	592	0	ENST00000220592.5:c.2389G>T	p.Val797Leu	p.V797L	ENST00000220592	NM_012154.3	797	Gtg/Ttg	18/19	0.347774501395482	6	FACETS	0.917	0.876	0.959	0.917	0.876	0.959	INDETERMINATE	3	TRUE	3	0.864779687278708	6		592	890	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829764	76829764	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	318	891	0	ENST00000373344.5:c.6277C>T	p.Gln2093Ter	p.Q2093*	ENST00000373344	NM_000489.3	2093	Cag/Tag	28/35	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.864779687278708	2		891	352	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0018224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	234	594	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.774996590161963	2		594	552	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0018224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	209	555	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.986	0.923	1	0.986	0.923	1	CLONAL	1	TRUE	1	0.774996590161963	2		558	547	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	164	782	2	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.638	0.588	0.691	0.638	0.588	0.691	SUBCLONAL	1	TRUE	1	0.774996590161963	2		784	663	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	31	479	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.153	0.123	0.187	0.153	0.123	0.187	SUBCLONAL	1	TRUE	1	0.774996590161963	2		479	524	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0018224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	262	634	0	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.774996590161963	2		634	676	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716212	52716212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555791268	NA	P-0018224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	197	520	0	ENST00000322088.6:c.656C>T	p.Ser219Leu	p.S219L	ENST00000322088	NM_014225.5	219	tCg/tTg	6/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.774996590161963	2		520	465	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0018224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	145	622	1	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	1	2	FACETS	0.856	0.788	0.926	0.856	0.788	0.926	CLONAL	1	TRUE	1	0.774996590161963	2		623	437	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0018224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	173	465	2	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	0.867	0.804	0.931	0.867	0.804	0.931	CLONAL	1	TRUE	1	0.774996590161963	2		467	515	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591259	67591259	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	27	605	0	ENST00000274335.5:c.1761del	p.Gly588ValfsTer7	p.G588Vfs*7	ENST00000274335		586	cAa/ca	13/15	1	2	FACETS	0.133	0.105	0.165	0.133	0.105	0.165	SUBCLONAL	1	TRUE	1	0.774996590161963	2		605	524	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881488	48881489	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0018224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	279	425	0	ENST00000267163.4:c.219_220dup	p.Ala74GlufsTer4	p.A74Efs*4	ENST00000267163	NM_000321.2	70	-/AG	2/27	0.774996590161963	2	FACETS	0.945	0.909	0.979	0.945	0.909	0.979	CLONAL	2	TRUE	0	0.774996590161963	2		425	381	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100299	27100302	+	frameshift_variant	Frame_Shift_Del	DEL	TTCC	TTCC	-	novel	NA	P-0018224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	284	833	0	ENST00000324856.7:c.4012_4015del	p.Ser1338MetfsTer142	p.S1338Mfs*142	ENST00000324856	NM_006015.4	1337	gaTTCC/ga	17/20	1	2	FACETS	0.988	0.933	1	0.988	0.933	1	CLONAL	1	TRUE	1	0.774996590161963	2		833	742	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115272956	115272956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1178464540	NA	P-0018224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	255	823	0	ENST00000438362.2:c.1417C>T	p.Arg473Cys	p.R473C	ENST00000438362	NM_001242891.1	473	Cgt/Tgt	12/20	1	2	FACETS	0.933	0.878	0.989	0.933	0.878	0.989	CLONAL	1	TRUE	1	0.774996590161963	2		823	705	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846288	156846288	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121964866	NA	P-0018224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	284	762	1	ENST00000524377.1:c.1729G>A	p.Gly577Ser	p.G577S	ENST00000524377	NM_002529.3	577	Ggc/Agc	14/17	0.774996590161963	3	FACETS	1	0.967	1	0.519	0.489	0.551	CLONAL	1	TRUE	1	0.774996590161963	3		763	979	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711950	89711950	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	366	558	0	ENST00000371953.3:c.569del	p.Pro190GlnfsTer9	p.P190Qfs*9	ENST00000371953	NM_000314.4	190	Cca/ca	6/9	0.774996590161963	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.774996590161963	2		558	461	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006377	12006377	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	176	516	0	ENST00000396373.4:c.345A>T	p.Glu115Asp	p.E115D	ENST00000396373	NM_001987.4	115	gaA/gaT	4/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.774996590161963	2		516	407	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43773164	43773164	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	238	835	0	ENST00000382044.4:c.428A>G	p.Glu143Gly	p.E143G	ENST00000382044	NM_001141980.1	143	gAg/gGg	5/28	1	2	FACETS	0.938	0.881	0.996	0.938	0.881	0.996	CLONAL	1	TRUE	1	0.774996590161963	2		835	655	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729175	66729175	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	253	707	0	ENST00000307102.5:c.383G>C	p.Gly128Ala	p.G128A	ENST00000307102	NM_002755.3	128	gGc/gCc	3/11	1	2	FACETS	0.979	0.922	1	0.979	0.922	1	CLONAL	1	TRUE	1	0.774996590161963	2		707	667	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857476	68857476	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	124	684	0	ENST00000261769.5:c.2111G>T	p.Gly704Val	p.G704V	ENST00000261769	NM_004360.3	704	gGa/gTa	13/16	1	2	FACETS	0.484	0.439	0.532	0.484	0.439	0.532	SUBCLONAL	1	TRUE	1	0.774996590161963	2		684	661	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229011	36229011	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	297	711	2	ENST00000222270.7:c.7795del	p.Glu2599ArgfsTer15	p.E2599Rfs*15	ENST00000222270	NM_014727.1	2597	gcG/gc	36/37	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.774996590161963	2		713	717	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794617	42794617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	247	781	2	ENST00000575354.2:c.1697G>A	p.Ser566Asn	p.S566N	ENST00000575354	NM_015125.3	566	aGc/aAc	10/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.774996590161963	2		783	606	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50138997	50138998	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0018224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	389	888	0	ENST00000246792.3:c.565dup	p.Ala189GlyfsTer120	p.A189Gfs*120	ENST00000246792	NM_006270.3	189	gct/gGct	5/6	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.774996590161963	2		888	975	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713713	30713713	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	170	481	0	ENST00000295754.5:c.1038C>A	p.Asp346Glu	p.D346E	ENST00000295754	NM_003242.5	346	gaC/gaA	4/7	1	2	FACETS	0.973	0.904	1	0.973	0.904	1	CLONAL	1	TRUE	1	0.774996590161963	2		481	451	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157804	106157804	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	142	412	1	ENST00000380013.4:c.2705G>T	p.Arg902Ile	p.R902I	ENST00000380013	NM_001127208.2	902	aGa/aTa	3/11	1	2	FACETS	0.982	0.906	1	0.982	0.906	1	CLONAL	1	TRUE	1	0.774996590161963	2		413	373	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183297	56183297	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	191	655	2	ENST00000399503.3:c.4207G>T	p.Gly1403Ter	p.G1403*	ENST00000399503	NM_005921.1	1403	Gga/Tga	18/20	1	2	FACETS	0.95	0.886	1	0.95	0.886	1	CLONAL	1	TRUE	1	0.774996590161963	2		657	519	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0018225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	246	795	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	0.731172600492263	4	FACETS	0.909	0.855	0.963	0.909	0.855	0.963	CLONAL	2	TRUE	2	0.731172600492263	4		795	641	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395108	139395108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371414501	NA	P-0018225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	12	675	1	ENST00000277541.6:c.5830G>A	p.Ala1944Thr	p.A1944T	ENST00000277541	NM_017617.3	1944	Gcc/Acc	31/34	0.731172600492263	4	FACETS	0.126	0.088	0.173	0.063	0.044	0.087	SUBCLONAL	1	TRUE	2	0.731172600492263	4		676	451	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0018226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	94	941	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	1	0.962	1			1	INDETERMINATE	1	TRUE	NA	0.257673832477254	2		942	617	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0018226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	106	895	0	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.257673832477254	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.257673832477254	1		895	579	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602333	28602333	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	27	637	0	ENST00000241453.7:c.2035G>T	p.Gly679Trp	p.G679W	ENST00000241453	NM_004119.2	679	Ggg/Tgg	16/24	1	2	FACETS	0.481	0.382	0.594	0.481	0.382	0.594	SUBCLONAL	1	TRUE	1	0.257673832477254	2		637	436	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603147	48603147	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0018226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	68	619	0	ENST00000342988.3:c.1447+1G>T		p.X483_splice	ENST00000342988	NM_005359.5	483			0.257673832477254	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.257673832477254	1		619	412	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	157	654	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	TRUE	1	0.490594427836305	2		654	601	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032093	10032093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367543123	NA	P-0018227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	170	675	1	ENST00000330684.3:c.730C>T	p.Arg244Cys	p.R244C	ENST00000330684	NM_001134407.1	244	Cgc/Tgc	3/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.490594427836305	2		676	593	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115852	8115853	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	180	751	0	ENST00000346208.3:c.1199dup	p.Met400IlefsTer107	p.M400Ifs*107	ENST00000346208		400	atg/aTtg	6/6	1	2	FACETS	0.998	0.923	1	0.998	0.923	1	CLONAL	1	TRUE	1	0.490594427836305	2		751	735	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294405	1294405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	161	709	2	ENST00000310581.5:c.596G>A	p.Cys199Tyr	p.C199Y	ENST00000310581	NM_198253.2	199	tGc/tAc	2/16	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.260327285184792	2		711	922	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519563	137519563	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	45	449	0	ENST00000367739.4:c.1075del	p.Glu359LysfsTer13	p.E359Kfs*13	ENST00000367739	NM_000416.2	359	Gaa/aa	7/7	0.260327285184792	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.260327285184792	1		449	244	SUCCESS
AR	367	MSKCC	GRCh37	X	66765340	66765340	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	192	656	0	ENST00000374690.3:c.352C>G	p.Gln118Glu	p.Q118E	ENST00000374690	NM_000044.3	118	Cag/Gag	1/8	0.0635704705837947	4	FACETS	0.982	0.908	1	0.982	0.908	1	INDETERMINATE	2	TRUE	2	0.260327285184792	4		656	947	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357136	70357136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	146	868	0	ENST00000374080.3:c.5651G>A	p.Gly1884Asp	p.G1884D	ENST00000374080		1884	gGc/gAc	39/45	0.0635704705837947	4	FACETS	1	0.982	1	0.65	0.592	0.711	INDETERMINATE	1	TRUE	2	0.260327285184792	4		868	1087	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937897	76937897	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	88	794	0	ENST00000373344.5:c.2851A>G	p.Thr951Ala	p.T951A	ENST00000373344	NM_000489.3	951	Acc/Gcc	9/35	0.0635704705837947	4	FACETS	1	0.942	1	1	0.942	1	INDETERMINATE	2	TRUE	2	0.260327285184792	4		794	392	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0018230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	60	941	1	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	0.12	2		942	779	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106648	27106648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553153748	NA	P-0018230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	24	786	3	ENST00000324856.7:c.6259G>A	p.Gly2087Arg	p.G2087R	ENST00000324856	NM_006015.4	2087	Gga/Aga	20/20	1	2	FACETS	0.621	0.485	0.779	0.621	0.485	0.779	SUBCLONAL	1	TRUE	1	0.12	2		789	644	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0018230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	31	643	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.992	0.801	1	0.992	0.801	1	CLONAL	1	TRUE	1	0.12	2		643	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0018230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	40	509	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.737	0.61	0.879	0.737	0.61	0.879	SUBCLONAL	1	TRUE	1	0.12	2		509	905	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922363	178922363	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	23	625	0	ENST00000263967.3:c.1132T>C	p.Cys378Arg	p.C378R	ENST00000263967	NM_006218.2	378	Tgt/Cgt	6/21	1	2	FACETS	0.632	0.491	0.796	0.632	0.491	0.796	SUBCLONAL	1	TRUE	1	0.12	2		625	607	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41276092	41276092	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528902306	NA	P-0018230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	45	782	0	ENST00000357654.3:c.22G>A	p.Val8Ile	p.V8I	ENST00000357654	NM_007294.3	8	Gtt/Att	2/23	1	2	FACETS	0.903	0.756	1	0.903	0.756	1	CLONAL	1	TRUE	1	0.12	2		782	831	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520171	176520171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs533751635	NA	P-0018230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	51	928	0	ENST00000292408.4:c.1090G>A	p.Glu364Lys	p.E364K	ENST00000292408	NM_213647.1	364	Gag/Aag	9/18	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.12	2		928	809	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692780	89692780	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0018232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	34	705	0	ENST00000371953.3:c.264T>G	p.Tyr88Ter	p.Y88*	ENST00000371953	NM_000314.4	88	taT/taG	5/9	0.686331992528783	1	FACETS	0.101	0.082	0.123	0.101	0.082	0.123	SUBCLONAL	1	TRUE	0	0.686331992528783	1		705	643	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104375135	104375135	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	107	816	1	ENST00000369902.3:c.1133G>A	p.Gly378Glu	p.G378E	ENST00000369902	NM_016169.3	378	gGa/gAa	9/12	0.686331992528783	1	FACETS	0.274	0.245	0.304	0.274	0.245	0.304	SUBCLONAL	1	TRUE	0	0.686331992528783	1		817	748	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999331	100999366	+	inframe_deletion	In_Frame_Del	DEL	GGTGGCGGGGGCAGCCGGTGGATCTTCGGGAAGTTC	GGTGGCGGGGGCAGCCGGTGGATCTTCGGGAAGTTC	-	novel	NA	P-0018232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	165	1082	0	ENST00000325455.5:c.436_471del	p.Glu146_Thr157del	p.E146_T157del	ENST00000325455	NM_001202474.3	146	GAACTTCCCGAAGATCCACCGGCTGCCCCCGCCACC/-	1/8	0.686331992528783	1	FACETS	0.356	0.327	0.387	0.356	0.327	0.387	SUBCLONAL	1	TRUE	0	0.686331992528783	1		1082	886	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042496	42042496	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs749657565	NA	P-0018232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	81	867	1	ENST00000219905.7:c.6691A>G	p.Thr2231Ala	p.T2231A	ENST00000219905	NM_001164273.1	2231	Act/Gct	17/24	0.686331992528783	1	FACETS	0.241	0.212	0.273	0.241	0.212	0.273	SUBCLONAL	1	TRUE	0	0.686331992528783	1		868	642	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226278	2226278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	75	899	0	ENST00000326181.6:c.1891G>A	p.Asp631Asn	p.D631N	ENST00000326181	NM_032271.2	631	Gac/Aac	20/21	0.686331992528783	1	FACETS	0.213	0.186	0.242	0.213	0.186	0.242	SUBCLONAL	1	TRUE	0	0.686331992528783	1		899	673	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647379	3647379	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0018232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	56	517	0	ENST00000294008.3:c.1683+1G>A		p.X561_splice	ENST00000294008	NM_032444.2	561			0.686331992528783	1	FACETS	0.254	0.218	0.293	0.254	0.218	0.293	SUBCLONAL	1	TRUE	0	0.686331992528783	1		517	422	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822225	72822225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	119	970	1	ENST00000268489.5:c.9950C>T	p.Pro3317Leu	p.P3317L	ENST00000268489	NM_006885.3	3317	cCt/cTt	10/10	0.686331992528783	1	FACETS	0.293	0.264	0.324	0.293	0.264	0.324	SUBCLONAL	1	TRUE	0	0.686331992528783	1		971	777	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983805	15983805	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1259464371	NA	P-0018232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	141	775	0	ENST00000268712.3:c.3317A>G	p.Lys1106Arg	p.K1106R	ENST00000268712	NM_006311.3	1106	aAg/aGg	25/46	1	2	FACETS	0.396	0.36	0.434	0.396	0.36	0.434	SUBCLONAL	1	TRUE	1	0.686331992528783	2		775	1038	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448312	56448312	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	122	868	0	ENST00000407977.2:c.335C>T	p.Pro112Leu	p.P112L	ENST00000407977		112	cCt/cTt	3/10	1	2	FACETS	0.317	0.285	0.35	0.317	0.285	0.35	SUBCLONAL	1	TRUE	1	0.686331992528783	2		868	1122	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945794	17945794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	105	804	0	ENST00000458235.1:c.2066C>T	p.Pro689Leu	p.P689L	ENST00000458235	NM_000215.3	689	cCc/cTc	16/24	1	2	FACETS	0.32	0.286	0.357	0.32	0.286	0.357	SUBCLONAL	1	TRUE	1	0.686331992528783	2		804	955	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058698	47058698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	106	881	1	ENST00000409792.3:c.7580C>T	p.Pro2527Leu	p.P2527L	ENST00000409792	NM_014159.6	2527	cCt/cTt	21/21	0.686331992528783	1	FACETS	0.322	0.289	0.357	0.322	0.289	0.357	SUBCLONAL	1	TRUE	0	0.686331992528783	1		882	630	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045922	180045922	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs757807375	NA	P-0018232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	65	506	0	ENST00000261937.6:c.2851-2A>G		p.X951_splice	ENST00000261937	NM_182925.4	951			0.358972204570484	1	FACETS	0.212	0.183	0.242	0.212	0.183	0.242	INDETERMINATE	1	TRUE	0	0.686331992528783	1		506	588	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287542	33287542	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	137	887	0	ENST00000374542.5:c.1555G>A	p.Gly519Arg	p.G519R	ENST00000374542	NM_001141970.1	519	Ggg/Agg	6/8	0.686331992528783	1	FACETS	0.327	0.297	0.358	0.327	0.297	0.358	SUBCLONAL	1	TRUE	0	0.686331992528783	1		887	803	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288630	33288630	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	215	537	0	ENST00000374542.5:c.922C>T	p.Gln308Ter	p.Q308*	ENST00000374542	NM_001141970.1	308	Cag/Tag	3/8	0.686331992528783	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.686331992528783	1		537	365	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004754	150004754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	96	655	0	ENST00000253339.5:c.1471C>T	p.Pro491Ser	p.P491S	ENST00000253339		491	Cca/Tca	3/7	0.686331992528783	1	FACETS	0.35	0.313	0.39	0.35	0.313	0.39	SUBCLONAL	1	TRUE	0	0.686331992528783	1		655	525	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574483	64574498	+	protein_altering_variant,splice_region_variant	In_Frame_Del	DEL	CTTGTGGTAGAGGGTG	CTTGTGGTAGAGGGTG	A	novel	NA	P-0018232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	319	782	0	ENST00000312049.6:c.897_912delinsT	p.Thr300_Lys304del	p.T300_K304del	ENST00000312049	NM_130799.2	299	ctCACCCTCTACCACAAG/ctT	6/10	0.686331992528783	1	FACETS	0.934	0.889	0.978	0.934	0.889	0.978	CLONAL	1	TRUE	0	0.686331992528783	1		782	654	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0018233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	656	916	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.387803232185459	6	FACETS	0.998	0.966	1	0.998	0.966	1	CLONAL	5	TRUE	1	0.387803232185459	6		916	1204	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0018233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	187	511	4				ENST00000310581	NM_198253.2	-/1132			0.378881018564402	5	FACETS	0.846	0.786	0.908	0.846	0.786	0.908	CLONAL	3	TRUE	2	0.387803232185459	5		515	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0018233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	166	678	1	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.307677929091745	2	FACETS	0.751	0.694	0.81	0.751	0.694	0.81	SUBCLONAL	2	TRUE	0	0.387803232185459	2		679	570	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716344	18716344	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778895247	NA	P-0018233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	169	678	3	ENST00000266497.5:c.3691G>A	p.Glu1231Lys	p.E1231K	ENST00000266497		1231	Gaa/Aaa	26/31	0.340654655669366	4	FACETS	0.839	0.773	0.907	0.839	0.773	0.907	CLONAL	2	TRUE	2	0.387803232185459	4		681	721	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166268	118166268	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	67	486	0	ENST00000369448.3:c.778C>T	p.Gln260Ter	p.Q260*	ENST00000369448	NM_017709.3	260	Cag/Tag	2/2	0.387803232185459	6	FACETS	0.739	0.641	0.846	0.148	0.128	0.17	SUBCLONAL	1	TRUE	1	0.387803232185459	6		486	830	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276442	115276442	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	88	664	2	ENST00000438362.2:c.886C>T	p.Gln296Ter	p.Q296*	ENST00000438362	NM_001242891.1	296	Caa/Taa	9/20	0.387803232185459	6	FACETS	0.716	0.632	0.806	0.143	0.126	0.162	SUBCLONAL	1	TRUE	1	0.387803232185459	6		666	1126	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584482	39584482	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	61	392	0	ENST00000262039.4:c.1147C>G	p.Arg383Gly	p.R383G	ENST00000262039	NM_002647.2	383	Cgg/Ggg	10/25	0.340654655669366	4	FACETS	0.871	0.753	1	0.436	0.376	0.5	CLONAL	1	TRUE	2	0.387803232185459	4		392	501	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097983	178097983	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	211	581	0	ENST00000397062.3:c.397A>T	p.Asn133Tyr	p.N133Y	ENST00000397062	NM_006164.4	133	Aat/Tat	3/5	0.272984185338214	5	FACETS	1	0.979	1	0.75	0.698	0.803	CLONAL	2	TRUE	2	0.387803232185459	5		581	765	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719245	190719245	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	137	476	0	ENST00000441310.2:c.1247T>G	p.Phe416Cys	p.F416C	ENST00000441310	NM_000534.4	416	tTt/tGt	9/13	0.272984185338214	5	FACETS	0.93	0.849	1	0.62	0.566	0.676	CLONAL	2	TRUE	2	0.387803232185459	5		476	601	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157380	106157380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	114	613	1	ENST00000380013.4:c.2281C>T	p.Pro761Ser	p.P761S	ENST00000380013	NM_001127208.2	761	Cct/Tct	3/11	0.207829825469616	4	FACETS	1	0.978	1	0.653	0.589	0.72	INDETERMINATE	1	TRUE	2	0.387803232185459	4		614	625	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141570521	141570521	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	237	884	0	ENST00000220592.5:c.607C>T	p.His203Tyr	p.H203Y	ENST00000220592	NM_012154.3	203	Cat/Tat	5/19	0.29478099002501	4	FACETS	0.939	0.878	1	0.939	0.878	1	CLONAL	2	TRUE	2	0.387803232185459	4		884	903	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223006	53223006	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	206	364	0	ENST00000375401.3:c.4066A>T	p.Ser1356Cys	p.S1356C	ENST00000375401	NM_004187.3	1356	Agt/Tgt	24/26	0.31322069549803	2	FACETS	1	0.983	1			1	CLONAL	2	TRUE	NA	0.387803232185459	2		364	468	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0018234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	108	527	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.454647922218947	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.454647922218947	1		527	324	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188164	11188164	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587777893	NA	P-0018234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	144	629	0	ENST00000361445.4:c.5930C>A	p.Thr1977Lys	p.T1977K	ENST00000361445	NM_004958.3	1977	aCa/aAa	43/58	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.454647922218947	2		629	596	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182146	11182146	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	150	788	0	ENST00000361445.4:c.6700T>C	p.Ser2234Pro	p.S2234P	ENST00000361445	NM_004958.3	2234	Tcg/Ccg	48/58	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	FALSE	1	0.446737056231335	2		788	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs967461896	NA	P-0018236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	494	701	0	ENST00000269305.4:c.526T>C	p.Cys176Arg	p.C176R	ENST00000269305	NM_001126112.2	176	Tgc/Cgc	5/11	0.533673214616035	4	FACETS	0.993	0.963	1	0.993	0.963	1	CLONAL	4	TRUE	0	0.533158325593321	4		701	715	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841306	15841306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1196200389	NA	P-0018236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	161	778	2	ENST00000307771.7:c.1390C>T	p.Arg464Cys	p.R464C	ENST00000307771	NM_005089.3	464	Cgt/Tgt	11/11	NA	2	FACETS	0.973	0.896	1			1	INDETERMINATE	1	TRUE	NA	0.533158325593321	2		780	621	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462090	120462090	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2644	148	643	0	ENST00000256646.2:c.5626A>G	p.Thr1876Ala	p.T1876A	ENST00000256646	NM_024408.3	1876	Act/Gct	31/34	0.533158325593321	19	FACETS	1	0.959	1			1	CLONAL	1	TRUE	NA	0.533158325593321	19		643	2792	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36014528	36014529	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0018236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	163	793	0	ENST00000358208.4:c.302_303del	p.Thr101ArgfsTer48	p.T101Rfs*48	ENST00000358208		101	ACa/a	3/12	0.533673214616035	3	FACETS	0.995	0.915	1	0.498	0.457	0.54	CLONAL	1	TRUE	1	0.533158325593321	3		793	778	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932696	39932696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	184	1090	0	ENST00000378444.4:c.1903C>T	p.Pro635Ser	p.P635S	ENST00000378444	NM_001123385.1	635	Cca/Tca	4/15	0.516447789904741	3	FACETS	0.869	0.802	0.939			1	CLONAL	1	TRUE	NA	0.533158325593321	3		1090	1006	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0018238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	244	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.83944750941756	2		306	541	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0018238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	198	306	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.975	0.912	1	0.975	0.912	1	CLONAL	1	TRUE	1	0.83944750941756	2		307	484	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861119	57861119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	57	620	0	ENST00000228682.2:c.916G>A	p.Glu306Lys	p.E306K	ENST00000228682	NM_005269.2	306	Gaa/Aaa	9/12	1	2	FACETS	0.154	0.131	0.179	0.154	0.131	0.179	SUBCLONAL	1	TRUE	1	0.83944750941756	2		620	883	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858549	27858549	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	21	310	0	ENST00000359303.2:c.22G>A	p.Ala8Thr	p.A8T	ENST00000359303	NM_003535.2	8	Gct/Act	1/1	1	2	FACETS	0.135	0.103	0.172	0.135	0.103	0.172	SUBCLONAL	1	TRUE	1	0.83944750941756	2		310	371	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2493147	2493147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	22	587	0	ENST00000355716.4:c.587C>T	p.Thr196Ile	p.T196I	ENST00000355716	NM_003820.2	196	aCc/aTc	6/8	0.83944750941756	1	FACETS	0.072	0.056	0.092	0.072	0.056	0.092	SUBCLONAL	1	TRUE	0	0.83944750941756	1		587	420	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784430	9784430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	66	694	0	ENST00000377346.4:c.2815G>A	p.Val939Ile	p.V939I	ENST00000377346	NM_005026.3	939	Gtc/Atc	22/24	0.83944750941756	1	FACETS	0.165	0.143	0.188	0.165	0.143	0.188	SUBCLONAL	1	TRUE	0	0.83944750941756	1		694	554	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932073	36932073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	52	527	1	ENST00000361632.4:c.2396C>T	p.Thr799Ile	p.T799I	ENST00000361632		799	aCc/aTc	16/16	0.83944750941756	1	FACETS	0.175	0.149	0.203	0.175	0.149	0.203	SUBCLONAL	1	TRUE	0	0.83944750941756	1		528	411	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511675	46511675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	44	736	1	ENST00000262741.5:c.1102G>A	p.Ala368Thr	p.A368T	ENST00000262741	NM_003629.3	368	Gca/Aca	9/10	0.83944750941756	1	FACETS	0.091	0.076	0.109	0.091	0.076	0.109	SUBCLONAL	1	TRUE	0	0.83944750941756	1		737	665	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46725737	46725737	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	20	546	0	ENST00000371975.4:c.373C>T	p.Pro125Ser	p.P125S	ENST00000371975	NM_003579.3	125	Ccg/Tcg	5/18	0.83944750941756	1	FACETS	0.071	0.054	0.092	0.071	0.054	0.092	SUBCLONAL	1	TRUE	0	0.83944750941756	1		546	387	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430411	78430412	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	351	654	0	ENST00000370768.2:c.756dup	p.Glu253ArgfsTer5	p.E253Rfs*5	ENST00000370768	NM_003902.3	252	-/A	10/20	0.83944750941756	1	FACETS	0.95	0.915	0.983	0.95	0.915	0.983	CLONAL	1	TRUE	0	0.83944750941756	1		654	511	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128026	64128026	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	60	723	1	ENST00000334205.4:c.424G>A	p.Gly142Arg	p.G142R	ENST00000334205	NM_003942.2	142	Ggg/Agg	4/17	1	2	FACETS	0.138	0.118	0.159	0.138	0.118	0.159	SUBCLONAL	1	TRUE	1	0.83944750941756	2		724	1039	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94153347	94153347	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs576011802	NA	P-0018238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	28	254	0	ENST00000323929.3:c.2071G>A	p.Asp691Asn	p.D691N	ENST00000323929	NM_005591.3	691	Gat/Aat	20/20	1	2	FACETS	0.176	0.14	0.216	0.176	0.14	0.216	SUBCLONAL	1	TRUE	1	0.83944750941756	2		254	380	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492527	50492527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	61	625	0	ENST00000394963.4:c.1423G>A	p.Glu475Lys	p.E475K	ENST00000394963	NM_003076.4	475	Gag/Aag	12/13	1	2	FACETS	0.184	0.158	0.213	0.184	0.158	0.213	SUBCLONAL	1	TRUE	1	0.83944750941756	2		625	788	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562939	95562939	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	35	470	0	ENST00000393063.1:c.4318G>A	p.Asp1440Asn	p.D1440N	ENST00000393063	NM_030621.3	1440	Gat/Aat	24/28	1	2	FACETS	0.136	0.111	0.164	0.136	0.111	0.164	SUBCLONAL	1	TRUE	1	0.83944750941756	2		470	614	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058574	42058574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	34	490	0	ENST00000219905.7:c.8294G>A	p.Gly2765Glu	p.G2765E	ENST00000219905	NM_001164273.1	2765	gGg/gAg	24/24	1	2	FACETS	0.137	0.111	0.166	0.137	0.111	0.166	SUBCLONAL	1	TRUE	1	0.83944750941756	2		490	591	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396401	396401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1345953002	NA	P-0018238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	53	719	1	ENST00000262320.3:c.625G>A	p.Glu209Lys	p.E209K	ENST00000262320	NM_003502.3	209	Gaa/Aaa	2/11	1	2	FACETS	0.128	0.109	0.15	0.128	0.109	0.15	SUBCLONAL	1	TRUE	1	0.83944750941756	2		720	984	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56409189	56409189	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	52	588	1	ENST00000348428.3:c.1696G>A	p.Gly566Arg	p.G566R	ENST00000348428	NM_006785.3	566	Gga/Aga	14/17	1	2	FACETS	0.156	0.132	0.183	0.156	0.132	0.183	SUBCLONAL	1	TRUE	1	0.83944750941756	2		589	792	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220002	5220002	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	67	803	0	ENST00000357368.4:c.3713C>T	p.Pro1238Leu	p.P1238L	ENST00000357368	NM_002850.3	1238	cCc/cTc	22/38	1	2	FACETS	0.167	0.144	0.192	0.167	0.144	0.192	SUBCLONAL	1	TRUE	1	0.83944750941756	2		803	956	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117294	7117294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	77	786	2	ENST00000302850.5:c.3922G>A	p.Glu1308Lys	p.E1308K	ENST00000302850	NM_000208.2	1308	Gag/Aag	22/22	1	2	FACETS	0.187	0.163	0.213	0.187	0.163	0.213	SUBCLONAL	1	TRUE	1	0.83944750941756	2		788	981	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211679	36211679	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1486583393	NA	P-0018238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	42	480	1	ENST00000222270.7:c.1430G>A	p.Ser477Asn	p.S477N	ENST00000222270	NM_014727.1	477	aGc/aAc	3/37	0.83944750941756	1	FACETS	0.174	0.146	0.206	0.174	0.146	0.206	SUBCLONAL	1	TRUE	0	0.83944750941756	1		481	333	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40771150	40771150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748173515	NA	P-0018238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	66	677	1	ENST00000392038.2:c.25G>A	p.Glu9Lys	p.E9K	ENST00000392038	NM_001626.4	9	Gaa/Aaa	2/14	0.83944750941756	1	FACETS	0.166	0.144	0.19	0.166	0.144	0.19	SUBCLONAL	1	TRUE	0	0.83944750941756	1		678	550	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791551	42791551	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	31	679	1	ENST00000575354.2:c.534del	p.Lys179ArgfsTer26	p.K179Rfs*26	ENST00000575354	NM_015125.3	178	Ccc/cc	4/20	0.83944750941756	1	FACETS	0.082	0.066	0.101	0.082	0.066	0.101	SUBCLONAL	1	TRUE	0	0.83944750941756	1		680	521	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791602	42791602	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0018238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	277	529	0	ENST00000575354.2:c.582+1G>T		p.X194_splice	ENST00000575354	NM_015125.3	194			0.83944750941756	1	FACETS	0.859	0.82	0.896	0.859	0.82	0.896	CLONAL	1	TRUE	0	0.83944750941756	1		529	446	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505310	25505310	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs367552590	NA	P-0018238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	47	568	0	ENST00000264709.3:c.448G>A	p.Gly150Ser	p.G150S	ENST00000264709	NM_175629.2	150	Ggc/Agc	4/23	1	2	FACETS	0.157	0.132	0.185	0.157	0.132	0.185	SUBCLONAL	1	TRUE	1	0.83944750941756	2		568	711	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693806	47693806	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	45	415	0	ENST00000233146.2:c.1520C>T	p.Pro507Leu	p.P507L	ENST00000233146	NM_000251.2	507	cCt/cTt	10/16	1	2	FACETS	0.16	0.134	0.189	0.16	0.134	0.189	SUBCLONAL	1	TRUE	1	0.83944750941756	2		415	669	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033349	48033349	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	52	581	0	ENST00000234420.5:c.3653G>A	p.Gly1218Asp	p.G1218D	ENST00000234420	NM_000179.2	1218	gGt/gAt	8/10	1	2	FACETS	0.155	0.132	0.182	0.155	0.132	0.182	SUBCLONAL	1	TRUE	1	0.83944750941756	2		581	797	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790872	89790872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	56	672	0	ENST00000336032.3:c.259G>A	p.Gly87Arg	p.G87R	ENST00000336032	NM_006813.2	87	Gga/Aga	1/2	1	2	FACETS	0.157	0.134	0.183	0.157	0.134	0.183	SUBCLONAL	1	TRUE	1	0.83944750941756	2		672	849	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024195	112024195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	46	476	1	ENST00000368678.4:c.590G>A	p.Gly197Glu	p.G197E	ENST00000368678		197	gGa/gAa	7/13	1	2	FACETS	0.153	0.128	0.18	0.153	0.128	0.18	SUBCLONAL	1	TRUE	1	0.83944750941756	2		477	718	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527294	137527294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	63	729	0	ENST00000367739.4:c.352G>A	p.Glu118Lys	p.E118K	ENST00000367739	NM_000416.2	118	Gaa/Aaa	3/7	1	2	FACETS	0.14	0.12	0.162	0.14	0.12	0.162	SUBCLONAL	1	TRUE	1	0.83944750941756	2		729	1072	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38186930	38186930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757691230	NA	P-0018238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	91	907	1	ENST00000317025.8:c.1547G>A	p.Gly516Glu	p.G516E	ENST00000317025	NM_023034.1	516	gGg/gAg	6/24	1	2	FACETS	0.181	0.16	0.203	0.181	0.16	0.203	SUBCLONAL	1	TRUE	1	0.83944750941756	2		908	1200	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750695	128750695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	45	612	0	ENST00000377970.2:c.232C>T	p.Pro78Ser	p.P78S	ENST00000377970	NM_002467.4	78	Cct/Tct	2/3	1	2	FACETS	0.157	0.131	0.185	0.157	0.131	0.185	SUBCLONAL	1	TRUE	1	0.83944750941756	2		612	684	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971354	15971354	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	171	625	0	ENST00000268712.3:c.4595A>T	p.Lys1532Met	p.K1532M	ENST00000268712	NM_006311.3	1532	aAg/aTg	32/46	1	2	FACETS	0.982	0.907	1	0.982	0.907	1	CLONAL	1	TRUE	1	0.513578574341105	2		625	678	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191487	10191496	+	frameshift_variant	Frame_Shift_Del	DEL	GCGATGCCTC	GCGATGCCTC	-	novel	NA	P-0018239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	90	464	0	ENST00000256474.2:c.480_489del	p.Glu160AspfsTer7	p.E160Dfs*7	ENST00000256474	NM_000551.3	160	gaGCGATGCCTC/ga	3/3	0.513578574341105	1	FACETS	0.749	0.67	0.831	0.749	0.67	0.831	SUBCLONAL	1	TRUE	0	0.513578574341105	1		464	348	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098310	47098310	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0018239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	65	407	0	ENST00000409792.3:c.6963+1G>C		p.X2321_splice	ENST00000409792	NM_014159.6	2321			0.513578574341105	1	FACETS	0.927	0.817	1	0.927	0.817	1	CLONAL	1	TRUE	0	0.513578574341105	1		407	203	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623240	52623247	+	frameshift_variant	Frame_Shift_Del	DEL	AGCACCAG	AGCACCAG	-	novel	NA	P-0018239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	54	413	0	ENST00000394830.3:c.2804_2811del	p.Ser935CysfsTer15	p.S935Cfs*15	ENST00000394830	NM_018313.4	935	tCTGGTGCT/t	19/30	0.513578574341105	1	FACETS	0.873	0.759	0.993	0.873	0.759	0.993	CLONAL	1	TRUE	0	0.513578574341105	1		413	179	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15818021	15818021	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	98	324	0	ENST00000307771.7:c.148G>C	p.Asp50His	p.D50H	ENST00000307771	NM_005089.3	50	Gac/Cac	3/11	1	1	FACETS	0.834	0.769	0.899	1	0.988	1	CLONAL	2	TRUE	0	0.513578574341105	1		324	170	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0018241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	141	833	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.17323026983794	3	FACETS	0.806	0.734	0.881	0.806	0.734	0.881	CLONAL	2	TRUE	1	0.228251917228146	3		833	854	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0018241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	156	588	2	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.174444136669268	3	FACETS	1	0.972	1			1	CLONAL	2	TRUE	NA	0.228251917228146	3		590	673	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435202	18435203	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0018241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	37	465	0	ENST00000266497.5:c.187_188insC	p.Phe63SerfsTer18	p.F63Sfs*18	ENST00000266497		63	ttt/tCtt	1/31	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.228251917228146	NA		465	504	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182509	99182509	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	55	544	0	ENST00000074304.5:c.2312G>A	p.Arg771Gln	p.R771Q	ENST00000074304	NM_001134224.1	771	cGg/cAg	22/26	0.201307270129806	3	FACETS	0.777	0.664	0.901	0.389	0.332	0.451	CLONAL	1	TRUE	1	0.228251917228146	3		544	691	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191299	185191299	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	28	462	0	ENST00000265026.3:c.2180A>C	p.Asp727Ala	p.D727A	ENST00000265026	NM_004721.4	727	gAc/gCc	11/14	0.17323026983794	3	FACETS	0.534	0.426	0.658	0.267	0.213	0.329	SUBCLONAL	1	TRUE	1	0.228251917228146	3		462	512	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27213507	27213507	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	43	547	0	ENST00000380036.4:c.2903G>C	p.Arg968Thr	p.R968T	ENST00000380036	NM_000459.3	968	aGa/aCa	18/23	0.17323026983794	3	FACETS	0.65	0.543	0.769	0.325	0.271	0.385	SUBCLONAL	1	TRUE	1	0.228251917228146	3		547	646	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691025	NA	P-0018242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	238	586	0	ENST00000269305.4:c.785G>T	p.Gly262Val	p.G262V	ENST00000269305	NM_001126112.2	262	gGt/gTt	8/11	0.480612449191874	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.480612449191874	1		586	718	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443613	29443613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519783	NA	P-0018242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	307	696	0	ENST00000389048.3:c.3604G>A	p.Gly1202Arg	p.G1202R	ENST00000389048	NM_004304.4	1202	Gga/Aga	23/29	0.227905459661301	3	FACETS	1	0.994	1	0.747	0.705	0.791	INDETERMINATE	1	TRUE	1	0.480612449191874	3		696	1060	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662428	227662428	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375415559	NA	P-0018242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	207	459	0	ENST00000305123.5:c.1027G>A	p.Asp343Asn	p.D343N	ENST00000305123	NM_005544.2	343	Gac/Aac	1/2	0.227905459661301	3	FACETS	1	0.988	1	0.652	0.606	0.7	INDETERMINATE	1	TRUE	1	0.480612449191874	3		459	819	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509111	106509111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	207	605	0	ENST00000359195.3:c.1105G>A	p.Asp369Asn	p.D369N	ENST00000359195	NM_002649.2	369	Gat/Aat	2/11	1	2	FACETS	0.928	0.862	0.997	0.928	0.862	0.997	CLONAL	1	TRUE	1	0.480612449191874	2		605	928	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0018243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	67	759	0	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	1	2	FACETS	0.981	0.85	1	0.981	0.85	1	CLONAL	1	TRUE	1	0.14	2		759	976	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0018244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	52	294	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.236753999893158	5	FACETS	0.888	0.755	1	0.296	0.251	0.345	CLONAL	1	TRUE	2	0.236753999893158	5		294	670	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0018244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	150	843	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.236753999893158	2		843	963	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951171	48951171	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587778846	NA	P-0018244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	317	548	0	ENST00000267163.4:c.1332+1G>A		p.X444_splice	ENST00000267163	NM_000321.2	444			0.236753999893158	5	FACETS	0.95	0.902	0.999	0.95	0.902	0.999	CLONAL	5	TRUE	0	0.236753999893158	5		548	764	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0018244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	234	808	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	0.995	1	CLONAL	2	TRUE	1	0.236753999893158	2		808	875	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928225	178928225	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	70	525	0	ENST00000263967.3:c.1411C>G	p.Pro471Ala	p.P471A	ENST00000263967	NM_006218.2	471	Cca/Gca	9/21	0.236753999893158	5	FACETS	1	0.948	1	0.392	0.341	0.446	CLONAL	1	TRUE	2	0.236753999893158	5		525	682	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740365	58740365	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs780886952	NA	P-0018244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	87	597	2	ENST00000305921.3:c.1270G>T	p.Glu424Ter	p.E424*	ENST00000305921	NM_003620.3	424	Gag/Tag	6/6	0.232205648197177	3	FACETS	1	0.957	1	0.585	0.517	0.656	CLONAL	1	TRUE	1	0.236753999893158	3		599	703	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468309	50468309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1159541845	NA	P-0018244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	80	681	2	ENST00000331340.3:c.1544G>A	p.Arg515His	p.R515H	ENST00000331340	NM_006060.4	515	cGc/cAc	8/8	0.236753999893158	8	FACETS	0.954	0.837	1	0.159	0.139	0.18	CLONAL	1	TRUE	2	0.236753999893158	8		683	1212	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17371347	17371347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761180960	NA	P-0018244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	88	658	1	ENST00000375499.3:c.109C>T	p.Pro37Ser	p.P37S	ENST00000375499	NM_003000.2	37	Ccc/Tcc	2/8	0.232205648197177	3	FACETS	1	0.955	1	0.578	0.512	0.649	CLONAL	1	TRUE	1	0.236753999893158	3		659	719	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166638	118166638	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	96	429	0	ENST00000369448.3:c.1148C>G	p.Pro383Arg	p.P383R	ENST00000369448	NM_017709.3	383	cCt/cGt	2/2	0.232205648197177	3	FACETS	0.933	0.835	1	0.933	0.835	1	CLONAL	2	TRUE	1	0.236753999893158	3		429	486	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666432	206666432	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs541558948	NA	P-0018244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	38	609	0	ENST00000367120.3:c.1912G>T	p.Val638Phe	p.V638F	ENST00000367120	NM_014002.3	638	Gtc/Ttc	19/22	0.222594282245196	4	FACETS	0.586	0.483	0.701	0.293	0.241	0.351	SUBCLONAL	1	TRUE	2	0.236753999893158	4		609	678	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885238	111885238	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	64	648	0	ENST00000341259.2:c.1126C>G	p.Gln376Glu	p.Q376E	ENST00000341259	NM_005475.2	376	Cag/Gag	6/8	1	2	FACETS	0.883	0.765	1	0.883	0.765	1	CLONAL	1	TRUE	1	0.236753999893158	2		648	612	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526171	63526171	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	62	934	0	ENST00000307078.5:c.2455G>C	p.Glu819Gln	p.E819Q	ENST00000307078	NM_004655.3	819	Gag/Cag	11/11	0.232205648197177	3	FACETS	0.528	0.454	0.608	0.264	0.227	0.304	SUBCLONAL	1	TRUE	1	0.236753999893158	3		934	1110	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257844	19257844	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0018244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	158	755	0	ENST00000162023.5:c.541+1G>A		p.X181_splice	ENST00000162023		181			0.136879474631713	3	FACETS	1	0.93	1	0.676	0.621	0.734	INDETERMINATE	2	TRUE	0	0.236753999893158	3		755	736	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211246	36211246	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1557	143	1119	0	ENST00000222270.7:c.997G>C	p.Glu333Gln	p.E333Q	ENST00000222270	NM_014727.1	333	Gag/Cag	3/37	0.236753999893158	5	FACETS	0.963	0.874	1	0.321	0.291	0.353	CLONAL	1	TRUE	2	0.236753999893158	5		1119	1700	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211363	36211363	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1358301425	NA	P-0018244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	132	802	0	ENST00000222270.7:c.1114G>C	p.Glu372Gln	p.E372Q	ENST00000222270	NM_014727.1	372	Gaa/Caa	3/37	0.236753999893158	5	FACETS	1	0.963	1	0.376	0.34	0.414	CLONAL	1	TRUE	2	0.236753999893158	5		802	1340	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033714	48033720	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGAGG	CCAGAGG	-	novel	NA	P-0018244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	78	697	0	ENST00000234420.5:c.3925_3931del	p.Pro1309LysfsTer16	p.P1309Kfs*16	ENST00000234420	NM_000179.2	1309	CCAGAGGaa/aa	9/10	0.232205648197177	3	FACETS	0.864	0.758	0.978	0.432	0.379	0.489	CLONAL	1	TRUE	1	0.236753999893158	3		697	853	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790168	40790168	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	109	556	0	ENST00000373198.4:c.2563G>T	p.Gly855Trp	p.G855W	ENST00000373198	NM_133170.3	855	Ggg/Tgg	18/32	0.142235083028867	4	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	2	0.236753999893158	4		556	553	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513282	44513293	+	inframe_deletion	In_Frame_Del	DEL	CCACCGCCACCG	CCACCGCCACCG	-	rs745888281	NA	P-0018244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	81	856	0	ENST00000291552.4:c.642_653del	p.Gly220_Gly223del	p.G220_G223del	ENST00000291552	NM_006758.2	214	ggCGGTGGCGGTGGt/ggt	8/8	0.142235083028867	4	FACETS	0.791	0.695	0.895	0.395	0.347	0.448	SUBCLONAL	1	TRUE	2	0.236753999893158	4		856	1070	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439855	52439855	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	111	625	0	ENST00000460680.1:c.857A>T	p.Lys286Met	p.K286M	ENST00000460680	NM_004656.3	286	aAg/aTg	10/17	0.172658936132941	4	FACETS	0.795	0.715	0.88	0.795	0.715	0.88	SUBCLONAL	2	TRUE	2	0.236753999893158	4		625	729	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531098	187531098	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	105	592	0	ENST00000441802.2:c.9925G>A	p.Asp3309Asn	p.D3309N	ENST00000441802	NM_005245.3	3309	Gat/Aat	15/27	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.236753999893158	2		592	749	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225734	26225734	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	238	615	0	ENST00000360408.1:c.352G>T	p.Val118Leu	p.V118L	ENST00000360408	NM_003532.2	118	Gtg/Ttg	1/1	0.236753999893158	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	TRUE	1	0.236753999893158	4		615	787	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039349	47039349	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	96	880	0	ENST00000377604.3:c.973del	p.Val325CysfsTer10	p.V325Cfs*10	ENST00000377604	NM_001204468.1	324	gcG/gc	10/24	NA	2	FACETS	0.899	0.8	1			1	INDETERMINATE	1	TRUE	NA	0.236753999893158	2		880	902	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342440	70342440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	43	646	0	ENST00000374080.3:c.1331G>A	p.Cys444Tyr	p.C444Y	ENST00000374080		444	tGc/tAc	9/45	1	2	FACETS	0.552	0.461	0.654	0.552	0.461	0.654	SUBCLONAL	1	TRUE	1	0.236753999893158	2		646	658	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814203	76814203	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	83	728	0	ENST00000373344.5:c.6441T>A	p.Ser2147Arg	p.S2147R	ENST00000373344	NM_000489.3	2147	agT/agA	29/35	1	2	FACETS	0.865	0.762	0.975	0.865	0.762	0.975	CLONAL	1	TRUE	1	0.236753999893158	2		728	811	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184087	123184087	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	115	555	0	ENST00000218089.9:c.945G>T	p.Trp315Cys	p.W315C	ENST00000218089	NM_001042749.1	315	tgG/tgT	11/35	1	2	FACETS	0.78	0.704	0.859	1	0.985	1	SUBCLONAL	2	TRUE	1	0.236753999893158	2		555	623	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018246-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	111	918	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.461491947963742	2		918	373	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044850	47044850	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018246-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	207	969	0	ENST00000377604.3:c.2176C>T	p.Arg726Ter	p.R726*	ENST00000377604	NM_001204468.1	726	Cga/Tga	20/24	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.461491947963742	2		969	797	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575152	48575152	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018246-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	62	523	0	ENST00000342988.3:c.346C>T	p.Gln116Ter	p.Q116*	ENST00000342988	NM_005359.5	116	Cag/Tag	3/12	0.461491947963742	1	FACETS	0.961	0.843	1	0.961	0.843	1	CLONAL	1	TRUE	0	0.461491947963742	1		523	215	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440700	56440726	+	inframe_deletion	In_Frame_Del	DEL	ATCAGCTTCTCAGCGTCATTACCCCAG	ATCAGCTTCTCAGCGTCATTACCCCAG	-	novel	NA	P-0018246-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	164	809	0	ENST00000407977.2:c.492_518del	p.Ile164_Leu172del	p.I164_L172del	ENST00000407977		164	atCTGGGGTAATGACGCTGAGAAGCTGATg/atg	5/10	1	2	FACETS	0.955	0.879	1	0.955	0.879	1	CLONAL	1	TRUE	1	0.461491947963742	2		809	744	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0018247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	268	941	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.567081123036255	2		942	925	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259262	89259262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770780950	NA	P-0018247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	168	441	2	ENST00000336596.2:c.406C>T	p.Arg136Ter	p.R136*	ENST00000336596	NM_005233.5	136	Cga/Tga	3/17	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.567081123036255	2		443	501	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519886	NA	P-0018247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	122	420	0	ENST00000349496.5:c.97T>G	p.Ser33Ala	p.S33A	ENST00000349496	NM_001904.3	33	Tct/Gct	3/15	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.567081123036255	2		420	410	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914723	39914723	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	167	638	0	ENST00000378444.4:c.4639C>T	p.Arg1547Ter	p.R1547*	ENST00000378444	NM_001123385.1	1547	Cga/Tga	12/15	NA	2	FACETS	0.91	0.84	0.983			1	INDETERMINATE	1	TRUE	NA	0.567081123036255	2		638	647	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206661272	206661272	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0018247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	186	687	0	ENST00000367120.3:c.1638T>A	p.Cys546Ter	p.C546*	ENST00000367120	NM_014002.3	546	tgT/tgA	16/22	0.514501638084838	4	FACETS	0.879	0.81	0.95	0.439	0.405	0.475	CLONAL	1	TRUE	2	0.567081123036255	4		687	1170	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870966	12870966	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	133	425	0	ENST00000228872.4:c.193C>T	p.Gln65Ter	p.Q65*	ENST00000228872	NM_004064.3	65	Cag/Tag	1/3	1	2	FACETS	0.977	0.893	1	0.977	0.893	1	CLONAL	1	TRUE	1	0.567081123036255	2		425	480	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554335	81554335	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	226	816	3	ENST00000298171.2:c.355C>T	p.Pro119Ser	p.P119S	ENST00000298171	NM_000369.2	119	Cct/Tct	4/10	1	2	FACETS	0.995	0.929	1	0.995	0.929	1	CLONAL	1	TRUE	1	0.567081123036255	2		819	801	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351899	89351899	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	316	967	1	ENST00000301030.4:c.1051G>T	p.Glu351Ter	p.E351*	ENST00000301030	NM_001256183.1	351	Gag/Tag	9/13	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.567081123036255	2		968	1087	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781129	161781129	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	137	628	0	ENST00000366898.1:c.1276del	p.Glu426LysfsTer9	p.E426Kfs*9	ENST00000366898	NM_004562.2	426	Gaa/aa	11/12	0.567081123036255	1	FACETS	0.865	0.795	0.937	0.865	0.795	0.937	CLONAL	1	TRUE	0	0.567081123036255	1		628	400	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945034	151945034	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	29	299	0	ENST00000262189.6:c.2485G>T	p.Ala829Ser	p.A829S	ENST00000262189	NM_170606.2	829	Gct/Tct	14/59	1	2	FACETS	0.272	0.218	0.333	0.272	0.218	0.333	SUBCLONAL	1	TRUE	1	0.567081123036255	2		299	376	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507419	8507419	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1287521671	NA	P-0018247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	46	377	0	ENST00000356435.5:c.1559T>C	p.Leu520Pro	p.L520P	ENST00000356435		520	cTa/cCa	11/35	1	2	FACETS	0.453	0.383	0.53	0.453	0.383	0.53	SUBCLONAL	1	TRUE	1	0.567081123036255	2		377	358	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855019	76855022	+	frameshift_variant	Frame_Shift_Del	DEL	TTTT	TTTT	-	novel	NA	P-0018247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	61	657	0	ENST00000373344.5:c.5814_5817del	p.Lys1939IlefsTer15	p.K1939Ifs*15	ENST00000373344	NM_000489.3	1938	aaAAAA/aa	25/35	0.243335428059591	1	FACETS	0.189	0.162	0.218	0.189	0.162	0.218	INDETERMINATE	1	TRUE	0	0.567081123036255	1		657	815	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0018248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	412	527	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.632926778113123	3	FACETS	0.966	0.925	1	0.966	0.925	1	CLONAL	2	TRUE	1	0.642344296760391	3		527	877	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	180	918	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.965	0.895	1	0.965	0.895	1	CLONAL	1	TRUE	1	0.642344296760391	2		918	581	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0018248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	224	761	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.642344296760391	2		761	671	SUCCESS
APC	324	MSKCC	GRCh37	5	112175411	112175411	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	158	333	0	ENST00000257430.4:c.4120G>T	p.Glu1374Ter	p.E1374*	ENST00000257430	NM_000038.5	1374	Gaa/Taa	16/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.642344296760391	2		333	443	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204643	108204643	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	183	550	0	ENST00000278616.4:c.7958T>G	p.Ile2653Ser	p.I2653S	ENST00000278616	NM_000051.3	2653	aTt/aGt	54/63	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.642344296760391	2		550	508	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816217	89816217	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs749912440	NA	P-0018248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	583	777	1	ENST00000389301.3:c.3160A>T	p.Arg1054Ter	p.R1054*	ENST00000389301	NM_000135.2	1054	Aga/Tga	32/43	0.639358138542642	4	FACETS	0.968	0.93	1	0.968	0.93	1	CLONAL	2	TRUE	2	0.642344296760391	4		778	1540	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554689	63554689	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	191	459	0	ENST00000307078.5:c.50T>G	p.Phe17Cys	p.F17C	ENST00000307078	NM_004655.3	17	tTc/tGc	2/11	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.642344296760391	2		459	593	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050902	13050902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	289	674	0	ENST00000316448.5:c.433C>T	p.His145Tyr	p.H145Y	ENST00000316448	NM_004343.3	145	Cat/Tat	4/9	1	2	FACETS	0.996	0.94	1	0.996	0.94	1	CLONAL	1	TRUE	1	0.642344296760391	2		674	903	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987147	69987147	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760770591	NA	P-0018248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	250	565	2	ENST00000394351.3:c.208G>A	p.Ala70Thr	p.A70T	ENST00000394351	NM_000248.3	70	Gca/Aca	2/9	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.642344296760391	2		567	756	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0018264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	211	801	17	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.327114414551046	1	FACETS	0.982	0.911	1	0.982	0.911	1	CLONAL	1	TRUE	0	0.327114414551046	1		818	1099	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916947	178916952	+	inframe_deletion	In_Frame_Del	DEL	ATCCTC	ATCCTC	-	novel	NA	P-0018264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	156	564	0	ENST00000263967.3:c.335_340del	p.Ile112_Leu113del	p.I112_L113del	ENST00000263967	NM_006218.2	112	ATCCTC/-	2/21	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.327114414551046	2		564	689	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577201	64577201	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	147	734	0	ENST00000312049.6:c.381C>G	p.Asn127Lys	p.N127K	ENST00000312049	NM_130799.2	127	aaC/aaG	2/10	0.281378308479719	1	FACETS	0.648	0.59	0.709	0.648	0.59	0.709	SUBCLONAL	1	TRUE	0	0.327114414551046	1		734	1160	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144443	58144443	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	45	366	0	ENST00000257904.6:c.628C>T	p.Arg210Ter	p.R210*	ENST00000257904	NM_000075.3	210	Cga/Tga	5/8	0.289935517253205	2	FACETS	0.466	0.391	0.549	0.233	0.195	0.275	SUBCLONAL	1	TRUE	0	0.327114414551046	2		366	591	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662785	227662785	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	215	640	0	ENST00000305123.5:c.670G>C	p.Glu224Gln	p.E224Q	ENST00000305123	NM_005544.2	224	Gag/Cag	1/2	0.327114414551046	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.327114414551046	1		640	1041	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672258	86672261	+	frameshift_variant	Frame_Shift_Del	DEL	ATGA	ATGA	-	novel	NA	P-0018264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	92	490	0	ENST00000274376.6:c.2063_2066del	p.Glu688GlyfsTer10	p.E688Gfs*10	ENST00000274376	NM_002890.2	687	gATGAa/ga	16/25	0.327114414551046	1	FACETS	0.919	0.819	1	0.919	0.819	1	CLONAL	1	TRUE	0	0.327114414551046	1		490	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573999	7573999	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	638	558	1	ENST00000269305.4:c.1028del	p.Glu343GlyfsTer2	p.E343Gfs*2	ENST00000269305	NM_001126112.2	343	gAg/gg	10/11	0.437332920689519	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	TRUE	0	0.437332920689519	3		559	1183	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716327	52716327	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	334	381	0	ENST00000322088.6:c.771G>T	p.Trp257Cys	p.W257C	ENST00000322088	NM_014225.5	257	tgG/tgT	6/15	0.404705115809032	4	FACETS	0.954	0.908	1	0.954	0.908	1	CLONAL	3	TRUE	1	0.437332920689519	4		381	767	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0018267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	275	630	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.888	0.833	0.945	0.888	0.833	0.945	CLONAL	1	TRUE	1	0.507435549776879	2		630	1220	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0018267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	261	536	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.965	0.904	1	0.965	0.904	1	CLONAL	1	TRUE	1	0.507435549776879	2		536	1066	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578523	7578523	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1567554216	NA	P-0018267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	241	756	0	ENST00000269305.4:c.407A>C	p.Gln136Pro	p.Q136P	ENST00000269305	NM_001126112.2	136	cAa/cCa	5/11	0.507435549776879	1	FACETS	0.794	0.743	0.846	0.794	0.743	0.846	SUBCLONAL	1	TRUE	0	0.507435549776879	1		756	893	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0018269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	349	523	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.467776591218576	2		523	1026	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097751	27097751	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	397	485	1	ENST00000324856.7:c.3344del	p.Pro1115GlnfsTer46	p.P1115Qfs*46	ENST00000324856	NM_006015.4	1114	Ccc/cc	12/20	0.415590720432028	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.467776591218576	1		486	926	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0018269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	232	559	1	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	1	2	FACETS	0.856	0.797	0.917	0.856	0.797	0.917	CLONAL	1	TRUE	1	0.467776591218576	2		560	1159	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247515	123247515	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	196	441	0	ENST00000358487.5:c.1976A>T	p.Lys659Met	p.K659M	ENST00000358487	NM_000141.4	659	aAg/aTg	14/18	1	2	FACETS	0.74	0.684	0.799	0.74	0.684	0.799	SUBCLONAL	1	TRUE	1	0.467776591218576	2		441	1132	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870985	12870986	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0018269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	464	272	0	ENST00000228872.4:c.214_215dup	p.Lys73AlafsTer47	p.K73Afs*47	ENST00000228872	NM_004064.3	71	gag/gaGGg	1/3	0.467776591218576	2	FACETS	0.97	0.939	1	1	0.997	1	CLONAL	3	TRUE	0	0.467776591218576	2		272	682	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911501	101911501	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	152	361	0	ENST00000374994.4:c.1426T>A	p.Tyr476Asn	p.Y476N	ENST00000374994	NM_004612.2	476	Tat/Aat	9/9	0.373561389643688	1	FACETS	0.647	0.593	0.704	0.647	0.593	0.704	SUBCLONAL	1	TRUE	0	0.467776591218576	1		361	769	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983060	201983060	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	85	820	1	ENST00000359651.3:c.909C>A	p.Phe303Leu	p.F303L	ENST00000359651		303	ttC/ttA	7/8	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		821	833	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739392	145739392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035926081	NA	P-0018270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	52	568	0	ENST00000428558.2:c.1978G>A	p.Glu660Lys	p.E660K	ENST00000428558	NM_004260.3	660	Gaa/Aaa	12/22	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		568	590	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0018271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	234	539	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.567412704880446	3	FACETS	0.993	0.926	1	0.497	0.463	0.531	CLONAL	1	TRUE	1	0.567412704880446	3		540	1066	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0018271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	391	674	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.567412704880446	3	FACETS	0.767	0.729	0.804	0.767	0.729	0.804	SUBCLONAL	2	TRUE	1	0.567412704880446	3		674	1154	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603148	48603148	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1060500740	NA	P-0018271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	371	346	0	ENST00000342988.3:c.1447+2T>C		p.X483_splice	ENST00000342988	NM_005359.5	483			0.567133481754635	2	FACETS	0.97	0.93	1	0.97	0.93	1	CLONAL	2	TRUE	0	0.567412704880446	2		346	674	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130234	2130234	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1393	262	649	0	ENST00000219476.3:c.3466C>T	p.Pro1156Ser	p.P1156S	ENST00000219476	NM_000548.3	1156	Cca/Tca	30/42	0.565456217276778	4	FACETS	0.875	0.817	0.935	0.437	0.408	0.468	CLONAL	1	TRUE	2	0.567412704880446	4		649	1655	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778645	3778645	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	175	447	0	ENST00000262367.5:c.6403C>T	p.Gln2135Ter	p.Q2135*	ENST00000262367	NM_004380.2	2135	Cag/Tag	31/31	0.565456217276778	4	FACETS	0.945	0.87	1	0.473	0.435	0.512	CLONAL	1	TRUE	2	0.567412704880446	4		447	1023	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944247	81944247	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	608	632	0	ENST00000359376.3:c.1856A>T	p.Glu619Val	p.E619V	ENST00000359376	NM_002661.3	619	gAg/gTg	18/33	0.350638873479278	5	FACETS	0.84	0.808	0.872	0.84	0.808	0.872	CLONAL	3	TRUE	2	0.567412704880446	5		632	1574	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145607	24145608	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	TGGT	novel	NA	P-0018271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	423	373	0	ENST00000263121.7:c.627_628+2dup		p.N209fs	ENST00000263121	NM_003073.3	209	aat/aaTGGTt	5/9	0.567412704880446	3	FACETS	0.958	0.916	1	0.958	0.916	1	CLONAL	2	TRUE	1	0.567412704880446	3		373	999	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678722	52678722	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	212	584	0	ENST00000394830.3:c.897G>C	p.Met299Ile	p.M299I	ENST00000394830	NM_018313.4	299	atG/atC	9/30	0.567412704880446	2	FACETS	0.87	0.809	0.932	0.435	0.404	0.466	CLONAL	1	TRUE	0	0.567412704880446	2		584	859	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249091	55249091	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519861	NA	P-0018271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	253	574	0	ENST00000275493.2:c.2389T>A	p.Cys797Ser	p.C797S	ENST00000275493	NM_005228.3	797	Tgc/Agc	20/28	0.567412704880446	3	FACETS	0.978	0.914	1	0.489	0.457	0.522	CLONAL	1	TRUE	1	0.567412704880446	3		574	1171	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045476	47045476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	516	329	0	ENST00000377604.3:c.2443C>T	p.Arg815Trp	p.R815W	ENST00000377604	NM_001204468.1	815	Cgg/Tgg	22/24	0.359357077938505	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.567412704880446	2		329	733	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821278	32821278	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	190	806	0	ENST00000354258.4:c.316C>G	p.Leu106Val	p.L106V	ENST00000354258	NM_000593.5	106	Ctg/Gtg	1/11	0.394073955538004	1	FACETS	0.878	0.814	0.945	0.878	0.814	0.945	CLONAL	1	TRUE	0	0.432439127874877	1		806	784	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589631	67589632	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATTATATGAAGA	novel	NA	P-0018273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	229	373	0	ENST00000274335.5:c.1397_1408dup	p.Leu466_Glu469dup	p.L466_E469dup	ENST00000274335		466	aga/agATTATATGAAGAa	10/15	0.618976794188582	3	FACETS	0.847	0.79	0.906	0.424	0.395	0.453	CLONAL	1	TRUE	1	0.804956933165284	3		373	942	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942593	17942593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	200	418	2	ENST00000458235.1:c.2695C>T	p.Arg899Trp	p.R899W	ENST00000458235	NM_000215.3	899	Cgg/Tgg	20/24	1	2	FACETS	0.628	0.583	0.675	0.628	0.583	0.675	SUBCLONAL	1	TRUE	1	0.804956933165284	2		420	791	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160671	56160679	+	inframe_deletion	In_Frame_Del	DEL	ACTGTACTT	ACTGTACTT	-	novel	NA	P-0018273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	362	435	0	ENST00000399503.3:c.949_957del	p.Tyr317_Leu319del	p.Y317_L319del	ENST00000399503	NM_005921.1	315	agACTGTACTTa/aga	4/20	0.618976794188582	3	FACETS	1	0.992	1	0.617	0.586	0.649	CLONAL	1	TRUE	1	0.804956933165284	3		435	1022	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178663	56178664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGAGAAG	novel	NA	P-0018273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	104	219	0	ENST00000399503.3:c.3637_3643dup	p.Asp1215GlyfsTer26	p.D1215Gfs*26	ENST00000399503	NM_005921.1	1212	-/GGAGAAG	14/20	0.618976794188582	3	FACETS	0.585	0.525	0.649	0.293	0.262	0.325	SUBCLONAL	1	TRUE	1	0.804956933165284	3		219	619	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916850	48916850	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1131690843	NA	P-0018274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	237	321	0	ENST00000267163.4:c.380G>A	p.Ser127Asn	p.S127N	ENST00000267163	NM_000321.2	127	aGt/aAt	3/27	0.790508865458523	1	FACETS	0.936	0.892	0.979	0.936	0.892	0.979	CLONAL	1	TRUE	0	0.814008268968459	1		321	369	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023056	27023059	+	frameshift_variant	Frame_Shift_Del	DEL	CGGG	CGGG	-	novel	NA	P-0018274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	60	55	0	ENST00000324856.7:c.163_166del	p.Gly55ArgfsTer45	p.G55Rfs*45	ENST00000324856	NM_006015.4	54	gcCGGG/gc	1/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.814008268968459	2		55	132	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533048	533458	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCCCGTGTCCCCAGTAGCCCCACTAAGACTCAGAACCAACAGGTGCCCGTGGGACACTCTGGGGACAAGAGGGGCCGGGCCCCAGGGTCACCGCTCCGGCCTGGCTCAGGGCAGCTCTCCCCAAGGACCTCCGCCTTCCCCGGAGCTGTGTCGGCCCAGGACTGCAGGGCGTGAGCCCAGACCCCGGCCCTCGCCTCCCTCACTGCCCTGCCGTCCCGGGAGACTTACAGCGCGAGGGGCCGCTGGGTCACATGGGTCCCGGGGGGTCCCAGAGGGTCCCGGAGCTGGAGCTAGAGCCAGAGCGGCTGCCCTGTGTCAAGGGAGAGGGTCAGTGAGTGCTGCTCCCTGGCTGGGGCGGGGCGGGGCGGGTCCCTGGCTAGCTGTGGGGTGGAGAGCTGCCTCACCTGCCG	GGCCCGTGTCCCCAGTAGCCCCACTAAGACTCAGAACCAACAGGTGCCCGTGGGACACTCTGGGGACAAGAGGGGCCGGGCCCCAGGGTCACCGCTCCGGCCTGGCTCAGGGCAGCTCTCCCCAAGGACCTCCGCCTTCCCCGGAGCTGTGTCGGCCCAGGACTGCAGGGCGTGAGCCCAGACCCCGGCCCTCGCCTCCCTCACTGCCCTGCCGTCCCGGGAGACTTACAGCGCGAGGGGCCGCTGGGTCACATGGGTCCCGGGGGGTCCCAGAGGGTCCCGGAGCTGGAGCTAGAGCCAGAGCGGCTGCCCTGTGTCAAGGGAGAGGGTCAGTGAGTGCTGCTCCCTGGCTGGGGCGGGGCGGGGCGGGTCCCTGGCTAGCTGTGGGGTGGAGAGCTGCCTCACCTGCCG	-	novel	NA	P-0018274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	396	10	0	ENST00000451590.1:c.445_451-293del		p.X149_splice	ENST00000451590	NM_001130442.1	149		4/5	0.799201655666161	2	FACETS	0.93	0.902	0.957	0.93	0.902	0.957	CLONAL	2	TRUE	0	0.814008268968459	2		10	523	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823921	3823921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	282	480	0	ENST00000262367.5:c.2294C>T	p.Ser765Phe	p.S765F	ENST00000262367	NM_004380.2	765	tCt/tTt	13/31	1	2	FACETS	0.93	0.879	0.982	0.93	0.879	0.982	CLONAL	1	TRUE	1	0.814008268968459	2		480	745	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027160	49027160	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0018275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	90	334	0	ENST00000267163.4:c.1727C>G	p.Ser576Ter	p.S576*	ENST00000267163	NM_000321.2	576	tCa/tGa	18/27	0.169121200495436	2	FACETS	0.828	0.735	0.926	0.828	0.735	0.926	CLONAL	2	TRUE	0	0.169121200495436	2		334	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0018275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1276	221	1008	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	1	2	FACETS	0.873	0.81	0.939	1	0.993	1	CLONAL	2	TRUE	1	0.169121200495436	2		1008	1497	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858956	45858956	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753317794	NA	P-0018275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	174	883	0	ENST00000391945.4:c.1510A>G	p.Ile504Val	p.I504V	ENST00000391945	NM_000400.3	504	Atc/Gtc	16/23	1	2	FACETS	0.9	0.827	0.976	1	0.991	1	CLONAL	2	TRUE	1	0.169121200495436	2		883	1143	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133883	55133883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	113	353	0	ENST00000257290.5:c.1096G>A	p.Asp366Asn	p.D366N	ENST00000257290	NM_006206.4	366	Gat/Aat	7/23	0.15410860355589	2	FACETS	0.966	0.87	1	0.966	0.87	1	CLONAL	2	TRUE	0	0.169121200495436	2		353	692	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156087	106156087	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	39	427	1	ENST00000380013.4:c.988G>A	p.Glu330Lys	p.E330K	ENST00000380013	NM_001127208.2	330	Gag/Aag	3/11	0.15410860355589	2	FACETS	0.693	0.573	0.827	0.346	0.286	0.414	SUBCLONAL	1	TRUE	0	0.169121200495436	2		428	666	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242481	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAGCAA	TTAAGAGAAGCAA	CCAG	novel	NA	P-0018275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	100	602	3	ENST00000275493.2:c.2239_2251delinsCCAG	p.Leu747_Thr751delinsProAla	p.L747_T751delinsPA	ENST00000275493	NM_005228.3	747	TTAAGAGAAGCAAca/CCAGca	19/28	0.169121200495436	3	FACETS	1	0.97	1	0.624	0.556	0.697	CLONAL	1	TRUE	1	0.169121200495436	3		605	1027	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339589	70339630	+	inframe_deletion	In_Frame_Del	DEL	TCCTGACACTGGTCGCAGGAAGCCCCAAGTGAACCAGAAGGA	TCCTGACACTGGTCGCAGGAAGCCCCAAGTGAACCAGAAGGA	-	novel	NA	P-0018275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	147	588	0	ENST00000374080.3:c.259_300del	p.Pro87_Asp100del	p.P87_D100del	ENST00000374080		86	ctTCCTGACACTGGTCGCAGGAAGCCCCAAGTGAACCAGAAGGAt/ctt	3/45	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.169121200495436	2		588	1191	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	169	184	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.96	0.888	1			1	INDETERMINATE	1	TRUE	NA	0.626395442847642	2		184	562	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0018276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19967	950	823	1	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.626395442847642	24	FACETS	1	0.994	1			1	CLONAL	1	TRUE	NA	0.626395442847642	24		824	20917	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0018277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	65	294	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.849	0.736	0.972	0.849	0.736	0.972	CLONAL	1	TRUE	1	0.237329478996084	2		294	645	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412095	63412095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852217	NA	P-0018277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	339	351	0	ENST00000330258.3:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000330258	NM_152424.3	358	Cga/Tga	2/2	0.213270109859941	2	FACETS	1	0.987	1			1	CLONAL	3	TRUE	NA	0.237329478996084	2		351	860	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0018277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	59	380	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	0.907	0.781	1	0.907	0.781	1	CLONAL	1	TRUE	1	0.237329478996084	2		380	548	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0018277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	49	267	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	0.769	0.651	0.899	0.769	0.651	0.899	SUBCLONAL	1	TRUE	1	0.237329478996084	2		267	537	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0018277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	62	289	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.943	0.815	1	0.943	0.815	1	CLONAL	1	TRUE	1	0.237329478996084	2		289	554	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604789	48604789	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	106	351	0	ENST00000342988.3:c.1611C>G	p.Asp537Glu	p.D537E	ENST00000342988	NM_005359.5	537	gaC/gaG	12/12	1	2	FACETS	0.996	0.892	1	0.996	0.892	1	CLONAL	1	TRUE	1	0.237329478996084	2		351	897	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0018277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	205	338	1	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.237329478996084	2	FACETS	0.904	0.839	0.972	0.904	0.839	0.972	CLONAL	2	TRUE	0	0.237329478996084	2		339	955	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627250	12627250	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	106	395	0	ENST00000251849.4:c.1466T>C	p.Leu489Ser	p.L489S	ENST00000251849	NM_002880.3	489	tTg/tCg	14/17	1	2	FACETS	0.942	0.843	1	0.942	0.843	1	CLONAL	1	TRUE	1	0.237329478996084	2		395	948	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271193	153271193	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0018277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	85	208	0	ENST00000281708.4:c.584+1G>A		p.X195_splice	ENST00000281708	NM_033632.3	195			0.237329478996084	2	FACETS	0.916	0.815	1	0.916	0.815	1	CLONAL	2	TRUE	0	0.237329478996084	2		208	391	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879673	151879673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	29	109	0	ENST00000262189.6:c.5272C>T	p.Arg1758Cys	p.R1758C	ENST00000262189	NM_170606.2	1758	Cgt/Tgt	36/59	0.237329478996084	3	FACETS	0.959	0.772	1	0.48	0.386	0.586	CLONAL	1	TRUE	1	0.237329478996084	3		109	285	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0018277-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	98	294	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.991	0.885	1	0.991	0.885	1	CLONAL	1	TRUE	1	0.29	2		294	682	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412095	63412095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852217	NA	P-0018277-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	402	351	0	ENST00000330258.3:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000330258	NM_152424.3	358	Cga/Tga	2/2	0.262188911279648	2	FACETS	0.967	0.923	1			1	CLONAL	3	TRUE	NA	0.29	2		351	956	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0018277-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	120	380	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.298016540431444	3	FACETS	1	0.916	1	0.508	0.458	0.561	CLONAL	1	TRUE	1	0.29	3		380	932	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0018277-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	94	267	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	0.877	0.78	0.98	0.877	0.78	0.98	CLONAL	1	TRUE	1	0.29	2		267	739	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0018277-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	195	289	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.298016540431444	3	FACETS	0.904	0.837	0.972	0.904	0.837	0.972	CLONAL	2	TRUE	1	0.29	3		289	852	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604789	48604789	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018277-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	104	351	0	ENST00000342988.3:c.1611C>G	p.Asp537Glu	p.D537E	ENST00000342988	NM_005359.5	537	gaC/gaG	12/12	1	2	FACETS	0.799	0.714	0.889	0.799	0.714	0.889	SUBCLONAL	1	TRUE	1	0.29	2		351	898	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0018277-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	269	338	1	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.298016540431444	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.29	2		339	904	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627250	12627250	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018277-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	156	395	0	ENST00000251849.4:c.1466T>C	p.Leu489Ser	p.L489S	ENST00000251849	NM_002880.3	489	tTg/tCg	14/17	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.29	2		395	1058	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271193	153271193	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0018277-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	137	208	0	ENST00000281708.4:c.584+1G>A		p.X195_splice	ENST00000281708	NM_033632.3	195			0.298016540431444	2	FACETS	0.945	0.865	1	0.945	0.865	1	CLONAL	2	TRUE	0	0.29	2		208	500	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879673	151879673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018277-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	52	109	0	ENST00000262189.6:c.5272C>T	p.Arg1758Cys	p.R1758C	ENST00000262189	NM_170606.2	1758	Cgt/Tgt	36/59	0.298016540431444	3	FACETS	0.966	0.824	1	0.483	0.412	0.561	CLONAL	1	TRUE	1	0.29	3		109	425	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	1156	918	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.483326239454892	4	FACETS	0.901	0.881	0.922			1	CLONAL	4	TRUE	NA	0.483326239454892	4		918	1968	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332868	152332868	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745723014	NA	P-0018278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	230	318	0	ENST00000206249.3:c.1174G>A	p.Val392Ile	p.V392I	ENST00000206249	NM_000125.3	392	Gtc/Atc	5/8	0.311290671922733	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.483326239454892	1		318	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0018278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	463	627	3	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.483326239454892	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.483326239454892	1		630	1224	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741349	17741349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	380	531	2	ENST00000250003.3:c.20C>T	p.Pro7Leu	p.P7L	ENST00000250003	NM_002478.4	7	cCg/cTg	1/3	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.483326239454892	2		533	1467	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022914	27022948	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCCGCCGCCAGCAGCCTGGGCAACCCGCCGCCG	CCGCCGCCGCCAGCAGCCTGGGCAACCCGCCGCCG	-	novel	NA	P-0018278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	70	41	0	ENST00000324856.7:c.28_62del	p.Ala10LeufsTer89	p.A10Lfs*89	ENST00000324856	NM_006015.4	7	cCCGCCGCCGCCAGCAGCCTGGGCAACCCGCCGCCG/c	1/20	0.483326239454892	2	FACETS	0.779	0.693	0.867	0.779	0.693	0.867	SUBCLONAL	2	TRUE	0	0.483326239454892	2		41	186	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39283859	39283860	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCA	novel	NA	P-0018278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	201	504	0	ENST00000402219.2:c.491_493dup	p.Val164dup	p.V164dup	ENST00000402219	NM_005633.3	164	gca/gTGGca	4/23	0.221441358277332	1	FACETS	0.714	0.662	0.767	0.714	0.662	0.767	INDETERMINATE	1	TRUE	0	0.483326239454892	1		504	884	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974709	21974727	+	frameshift_variant	Frame_Shift_Del	DEL	CGTTGGGCAGCGCCCCCGC	CGTTGGGCAGCGCCCCCGC	-	novel	NA	P-0018278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	149	352	0	ENST00000304494.5:c.100_118del	p.Ala34HisfsTer13	p.A34Hfs*13	ENST00000304494	NM_000077.4	34	GCGGGGGCGCTGCCCAACGca/ca	1/3	0.483326239454892	1	FACETS	0.75	0.688	0.815	0.75	0.688	0.815	SUBCLONAL	1	TRUE	0	0.483326239454892	1		352	623	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	337	918	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.908	0.858	0.959	0.908	0.858	0.959	CLONAL	1	TRUE	1	0.60846159520941	2		918	1220	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0018279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	502	801	17	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.60846159520941	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.60846159520941	1		818	1095	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457272	67457289	+	inframe_deletion	In_Frame_Del	DEL	GCTCCCTCATGTCATCTA	GCTCCCTCATGTCATCTA	-	novel	NA	P-0018279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	323	401	0	ENST00000327367.4:c.246_263del	p.Leu83_Tyr88del	p.L83_Y88del	ENST00000327367	NM_005902.3	82	ggGCTCCCTCATGTCATCTAc/ggc	2/9	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.60846159520941	2		401	946	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634429	23634429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555459584	NA	P-0018279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	293	464	0	ENST00000261584.4:c.2857G>A	p.Asp953Asn	p.D953N	ENST00000261584	NM_024675.3	953	Gat/Aat	9/13	1	2	FACETS	0.884	0.833	0.938	0.884	0.833	0.938	CLONAL	1	TRUE	1	0.60846159520941	2		464	1089	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs863224451	NA	P-0018280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	60	823	0	ENST00000269305.4:c.824G>C	p.Cys275Ser	p.C275S	ENST00000269305	NM_001126112.2	275	tGt/tCt	8/11	0.134574226994869	1	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	0	0.176678551707023	1		823	585	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644835	67644835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	33	378	0	ENST00000264010.4:c.100G>A	p.Glu34Lys	p.E34K	ENST00000264010	NM_006565.3	34	Gaa/Aaa	3/12	0.176678551707023	3	FACETS	0.899	0.732	1	0.45	0.366	0.544	CLONAL	1	TRUE	1	0.176678551707023	3		378	452	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0018281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	42	455	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.729	0.607	0.866	0.729	0.607	0.866	SUBCLONAL	1	TRUE	1	0.152180823973132	2		455	757	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0018281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	58	483	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	0.757	0.648	0.876	0.757	0.648	0.876	SUBCLONAL	1	TRUE	1	0.152180823973132	2		483	1007	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0018283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	145	941	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.974	0.888	1	0.974	0.888	1	CLONAL	1	TRUE	1	0.3	2		942	992	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660469	67660469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	88	289	4	ENST00000264010.4:c.1369C>T	p.Arg457Ter	p.R457*	ENST00000264010	NM_006565.3	457	Cga/Tga	8/12	1	2	FACETS	0.994	0.882	1	0.994	0.882	1	CLONAL	1	TRUE	1	0.3	2		293	590	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717731	89717732	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1114167661	NA	P-0018283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	114	399	0	ENST00000371953.3:c.757dup	p.Ile253AsnfsTer45	p.I253Nfs*45	ENST00000371953	NM_000314.4	252	-/A	7/9	1	2	FACETS	0.933	0.839	1	0.933	0.839	1	CLONAL	1	TRUE	1	0.3	2		399	815	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023727	27023728	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0018283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	93	574	0	ENST00000324856.7:c.837dup	p.Ser280LeufsTer120	p.S280Lfs*120	ENST00000324856	NM_006015.4	278	ggc/ggCc	1/20	1	2	FACETS	0.82	0.729	0.917	0.82	0.729	0.917	CLONAL	1	TRUE	1	0.3	2		574	756	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624230	89624231	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0018283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	28	95	0	ENST00000371953.3:c.5_6del	p.Thr2SerfsTer8	p.T2Sfs*8	ENST00000371953	NM_000314.4	2	ACa/a	1/9	1	2	FACETS	0.837	0.673	1	0.837	0.673	1	CLONAL	1	TRUE	1	0.3	2		95	223	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589579	67589580	+	inframe_insertion	In_Frame_Ins	INS	-	-	AATTACATG	novel	NA	P-0018283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	93	325	0	ENST00000274335.5:c.1346_1354dup	p.Leu449_Glu451dup	p.L449_E451dup	ENST00000274335		449	aaa/aAATTACATGaa	10/15	1	2	FACETS	0.928	0.826	1	0.928	0.826	1	CLONAL	1	TRUE	1	0.3	2		325	668	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591109	67591109	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	102	311	0	ENST00000274335.5:c.1702C>G	p.Pro568Ala	p.P568A	ENST00000274335		568	Cca/Gca	12/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.3	2		311	587	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0018284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	106	427	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	0.15	2		427	1215	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0018284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	88	378	0	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	1	2	FACETS	0.947	0.836	1	0.947	0.836	1	CLONAL	1	TRUE	1	0.15	2		378	1239	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679243	88679243	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs377057727	NA	P-0018284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	80	425	0	ENST00000360948.2:c.794C>A	p.Ala265Asp	p.A265D	ENST00000360948	NM_001012338.2	265	gCc/gAc	8/19	1	2	FACETS	0.845	0.741	0.957	0.845	0.741	0.957	CLONAL	1	TRUE	1	0.15	2		425	1263	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204578	128204578	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	55	286	0	ENST00000341105.2:c.863C>A	p.Ser288Tyr	p.S288Y	ENST00000341105	NM_032638.4	288	tCc/tAc	3/6	1	2	FACETS	0.719	0.613	0.836	0.719	0.613	0.836	SUBCLONAL	1	TRUE	1	0.15	2		286	1020	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523672	176523672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1337	115	449	1	ENST00000292408.4:c.2083G>A	p.Val695Met	p.V695M	ENST00000292408	NM_213647.1	695	Gtg/Atg	16/18	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.15	2		450	1452	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956799	68956799	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	74	333	0	ENST00000288368.4:c.917A>T	p.Glu306Val	p.E306V	ENST00000288368	NM_024870.2	306	gAa/gTa	8/40	1	2	FACETS	0.909	0.794	1	0.909	0.794	1	CLONAL	1	TRUE	1	0.15	2		333	1085	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411402	63411402	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	59	377	0	ENST00000330258.3:c.1765C>A	p.His589Asn	p.H589N	ENST00000330258	NM_152424.3	589	Cat/Aat	2/2	1	2	FACETS	0.862	0.739	0.996	0.862	0.739	0.996	CLONAL	1	TRUE	1	0.15	2		377	913	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584787	48584787	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	224	451	0	ENST00000342988.3:c.865C>T	p.Gln289Ter	p.Q289*	ENST00000342988	NM_005359.5	289	Cag/Tag	7/12	0.465099438982716	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.465099438982716	1		451	705	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913255	NA	P-0018285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	205	549	1	ENST00000369535.4:c.183A>T	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caT	3/7	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.465099438982716	2		550	830	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920413	114920413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767830105	NA	P-0018285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	181	332	0	ENST00000543371.1:c.1354G>A	p.Gly452Arg	p.G452R	ENST00000543371	NM_001198531.1	452	Ggg/Agg	13/14	0.206249998011266	1	FACETS	0.822	0.76	0.885	0.822	0.76	0.885	INDETERMINATE	1	TRUE	0	0.465099438982716	1		332	727	SUCCESS
APC	324	MSKCC	GRCh37	5	112175378	112175378	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0018285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	174	239	0	ENST00000257430.4:c.4087A>T	p.Lys1363Ter	p.K1363*	ENST00000257430	NM_000038.5	1363	Aaa/Taa	16/16	0.43607932024196	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	0	0.465099438982716	2		239	374	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874521	155874521	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0018285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	47	466	0	ENST00000368323.3:c.237+1G>T		p.X79_splice	ENST00000368323	NM_006912.5	79			1	2	FACETS	0.277	0.233	0.326	0.277	0.233	0.326	SUBCLONAL	1	TRUE	1	0.465099438982716	2		466	730	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363790	118363790	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	66	385	0	ENST00000534358.1:c.5023T>G	p.Leu1675Val	p.L1675V	ENST00000534358	NM_005933.3	1675	Tta/Gta	16/36	1	2	FACETS	0.431	0.374	0.494	0.431	0.374	0.494	SUBCLONAL	1	TRUE	1	0.465099438982716	2		385	658	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994896	73994896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780694082	NA	P-0018285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	11	23	0	ENST00000318443.5:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000318443	NM_001024736.1	127	cGg/cAg	3/10	0.292162024156009	1	FACETS	0.981	0.708	1	0.981	0.708	1	CLONAL	1	TRUE	0	0.465099438982716	1		23	37	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900611	3900611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757321118	NA	P-0018285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	187	336	3	ENST00000262367.5:c.485C>T	p.Ala162Val	p.A162V	ENST00000262367	NM_004380.2	162	gCg/gTg	2/31	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.465099438982716	2		339	750	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579362	7579367	+	inframe_deletion	In_Frame_Del	DEL	AACCGT	AACCGT	-	novel	NA	P-0018285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	225	546	0	ENST00000269305.4:c.320_325del	p.Tyr107_Gly108del	p.Y107_G108del	ENST00000269305	NM_001126112.2	107	tACGGTTtc/ttc	4/11	0.465099438982716	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.465099438982716	1		546	703	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681669	30681669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	42	344	1	ENST00000376406.3:c.428G>A	p.Gly143Asp	p.G143D	ENST00000376406	NM_014641.2	143	gGc/gAc	3/15	0.425097347489714	3	FACETS	0.281	0.234	0.334	0.094	0.078	0.112	SUBCLONAL	1	TRUE	0	0.465099438982716	3		345	792	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88651937	88651937	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	112	436	1	ENST00000372037.3:c.284C>A	p.Thr95Lys	p.T95K	ENST00000372037	NM_004329.2	95	aCa/aAa	5/13	0.80103374571363	1	FACETS	0.407	0.369	0.447	0.407	0.369	0.447	SUBCLONAL	1	TRUE	0	0.80103374571363	1		437	412	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28644737	28644737	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	85	258	0	ENST00000241453.7:c.56C>G	p.Ala19Gly	p.A19G	ENST00000241453	NM_004119.2	19	gCa/gGa	2/24	1	2	FACETS	0.367	0.324	0.412	0.367	0.324	0.412	SUBCLONAL	1	TRUE	1	0.80103374571363	2		258	579	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549413	21549413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764574613	NA	P-0018287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	148	184	0	ENST00000382592.4:c.2863G>A	p.Ala955Thr	p.A955T	ENST00000382592	NM_014572.2	955	Gca/Aca	8/8	0.178331409282993	1	FACETS	0.611	0.563	0.66	0.611	0.563	0.66	INDETERMINATE	1	TRUE	0	0.713568507240575	1		184	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578376	7578379	+	frameshift_variant	Frame_Shift_Del	DEL	CTAT	CTAT	-	novel	NA	P-0018288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	98	361	0	ENST00000269305.4:c.551_554del	p.Asp184AlafsTer62	p.D184Afs*62	ENST00000269305	NM_001126112.2	184	gATAGc/gc	5/11	0.286209058543924	1	FACETS	0.983	0.879	1	0.983	0.879	1	CLONAL	1	TRUE	0	0.286209058543924	1		361	597	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094386	27094386	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	95	327	1	ENST00000324856.7:c.3094G>T	p.Glu1032Ter	p.E1032*	ENST00000324856	NM_006015.4	1032	Gag/Tag	11/20	1	2	FACETS	0.852	0.758	0.952	0.852	0.758	0.952	CLONAL	1	TRUE	1	0.286209058543924	2		328	779	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254713	16254713	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	108	454	1	ENST00000375759.3:c.1978G>C	p.Glu660Gln	p.E660Q	ENST00000375759	NM_015001.2	660	Gaa/Caa	11/15	1	2	FACETS	0.722	0.646	0.802	0.722	0.646	0.802	SUBCLONAL	1	TRUE	1	0.286209058543924	2		455	1046	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754574	42754574	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768322408	NA	P-0018288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	184	579	1	ENST00000222329.4:c.166G>A	p.Val56Ile	p.V56I	ENST00000222329	NM_006494.2	56	Gtc/Atc	2/4	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.286209058543924	2		580	1233	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149506162	149506162	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	132	392	0	ENST00000261799.4:c.1595T>C	p.Val532Ala	p.V532A	ENST00000261799	NM_002609.3	532	gTg/gCg	11/23	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.286209058543924	2		392	845	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873749	151873749	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0018288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	74	306	0	ENST00000262189.6:c.8789C>G	p.Ser2930Ter	p.S2930*	ENST00000262189	NM_170606.2	2930	tCa/tGa	38/59	1	2	FACETS	0.738	0.645	0.837	0.738	0.645	0.837	SUBCLONAL	1	TRUE	1	0.286209058543924	2		306	701	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873782	151873782	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0018288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	59	266	0	ENST00000262189.6:c.8756C>G	p.Ser2919Ter	p.S2919*	ENST00000262189	NM_170606.2	2919	tCa/tGa	38/59	1	2	FACETS	0.65	0.559	0.75	0.65	0.559	0.75	SUBCLONAL	1	TRUE	1	0.286209058543924	2		266	634	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68982089	68982089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376775544	NA	P-0018288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	118	529	0	ENST00000288368.4:c.1463G>A	p.Arg488His	p.R488H	ENST00000288368	NM_024870.2	488	cGt/cAt	13/40	0.286209058543924	3	FACETS	0.874	0.787	0.967	0.437	0.393	0.484	CLONAL	1	TRUE	1	0.286209058543924	3		529	1078	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0018289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	129	453	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	0.214964055503422	1	FACETS	0.369	0.334	0.407	0.369	0.334	0.407	INDETERMINATE	1	TRUE	0	0.522756092820509	1		453	987	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705534	43705534	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0018289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	182	413	0	ENST00000382044.4:c.5090-2A>T		p.X1697_splice	ENST00000382044	NM_001141980.1	1697			1	2	FACETS	0.713	0.657	0.77	0.713	0.657	0.77	SUBCLONAL	1	TRUE	1	0.522756092820509	2		413	977	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511598	38511598	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	118	442	2	ENST00000254066.5:c.1096C>T	p.Arg366Trp	p.R366W	ENST00000254066	NM_000964.3	366	Cgg/Tgg	8/9	0.214964055503422	1	FACETS	0.343	0.309	0.38	0.343	0.309	0.38	INDETERMINATE	1	TRUE	0	0.522756092820509	1		444	971	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591925	48591925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660556	NA	P-0018289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	114	271	0	ENST00000342988.3:c.1088G>A	p.Cys363Tyr	p.C363Y	ENST00000342988	NM_005359.5	363	tGt/tAt	9/12	0.41241152381419	1	FACETS	0.659	0.596	0.724	0.659	0.596	0.724	SUBCLONAL	1	TRUE	0	0.522756092820509	1		271	489	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467357	66467357	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0018289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	45	108	0	ENST00000273854.3:c.910+2T>C		p.X304_splice	ENST00000273854	NM_004439.5	304			0.41241152381419	1	FACETS	0.703	0.599	0.813	0.703	0.599	0.813	SUBCLONAL	1	TRUE	0	0.522756092820509	1		108	181	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611791	100611791	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	176	355	0	ENST00000308731.7:c.1330G>A	p.Glu444Lys	p.E444K	ENST00000308731	NM_000061.2	444	Gaa/Aaa	14/19	1	2	FACETS	0.76	0.7	0.822	0.76	0.7	0.822	SUBCLONAL	1	TRUE	1	0.522756092820509	2		355	886	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0018294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	724	693	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.544601820231449	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.544601820231449	2		693	1321	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518425	204518425	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761828808	NA	P-0018294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	300	431	0	ENST00000367182.3:c.1088G>A	p.Arg363Gln	p.R363Q	ENST00000367182	NM_001278516.1	363	cGa/cAa	11/11	0.540297071400656	3	FACETS	0.886	0.838	0.934	0.886	0.838	0.934	CLONAL	2	TRUE	1	0.544601820231449	3		431	791	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670355	246670355	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0018294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	155	376	0	ENST00000388985.4:c.164+1G>A		p.X55_splice	ENST00000388985		55			0.540297071400656	3	FACETS	0.943	0.865	1	0.471	0.432	0.513	CLONAL	1	TRUE	1	0.544601820231449	3		376	768	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871637	35871648	+	inframe_deletion	In_Frame_Del	DEL	TCATAGCTCTCC	TCATAGCTCTCC	-	novel	NA	P-0018294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	93	230	0	ENST00000216797.5:c.858_869del	p.Glu286_Tyr289del	p.E286_Y289del	ENST00000216797	NM_020529.2	286	gaGGAGAGCTATGAc/gac	5/6	0.544601820231449	2	FACETS	0.782	0.699	0.869	0.391	0.349	0.435	SUBCLONAL	1	TRUE	0	0.544601820231449	2		230	437	SUCCESS
APC	324	MSKCC	GRCh37	5	112174920	112174921	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs1554085190	NA	P-0018294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	288	289	0	ENST00000257430.4:c.3631_3632del	p.Met1211ValfsTer5	p.M1211Vfs*5	ENST00000257430	NM_000038.5	1210	cAT/c	16/16	0.544601820231449	2	FACETS	0.963	0.917	1	0.963	0.917	1	CLONAL	2	TRUE	0	0.544601820231449	2		289	549	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992699	68992699	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	131	615	1	ENST00000288368.4:c.1664A>T	p.Lys555Ile	p.K555I	ENST00000288368	NM_024870.2	555	aAa/aTa	16/40	0.540297071400656	3	FACETS	0.584	0.529	0.642	0.292	0.264	0.321	SUBCLONAL	1	TRUE	1	0.544601820231449	3		616	1048	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933361	39933361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	801	221	1	ENST00000378444.4:c.1238C>T	p.Thr413Ile	p.T413I	ENST00000378444	NM_001123385.1	413	aCa/aTa	4/15	0.544601820231449	3	FACETS	0.89	0.871	0.909			1	CLONAL	4	TRUE	NA	0.544601820231449	3		222	1051	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630173	100630173	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141488935	NA	P-0018294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	419	206	0	ENST00000308731.7:c.100G>A	p.Val34Met	p.V34M	ENST00000308731	NM_000061.2	34	Gtg/Atg	2/19	0.544601820231449	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.544601820231449	2		206	625	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	97	184	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.804	0.717	0.895	0.804	0.717	0.895	CLONAL	1	TRUE	1	0.376607403614885	2		184	641	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664584	29664584	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0018295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	154	343	0	ENST00000356175.3:c.6563T>A	p.Leu2188Ter	p.L2188*	ENST00000356175	NM_000267.3	2188	tTg/tAg	42/57	1	2	FACETS	0.997	0.913	1	0.997	0.913	1	CLONAL	1	TRUE	1	0.376607403614885	2		343	820	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684109	29684109	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0018295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	114	298	0	ENST00000356175.3:c.7806+1G>T		p.X2602_splice	ENST00000356175	NM_000267.3	2602			1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.376607403614885	2		298	593	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667856	37667856	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1467	94	418	0	ENST00000447079.4:c.2741C>A	p.Thr914Lys	p.T914K	ENST00000447079	NM_015083.1	914	aCa/aAa	8/14	0.575289685773749	5	FACETS	0.341	0.302	0.383			1	SUBCLONAL	1	NA	NA	0.749958083596084	5		418	1561	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572005	64572005	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	154	633	0	ENST00000312049.6:c.1634C>T	p.Pro545Leu	p.P545L	ENST00000312049	NM_130799.2	545	cCg/cTg	10/10	1	2	FACETS	0.971	0.887	1	0.971	0.887	1	CLONAL	1	TRUE	1	0.28	2		633	1133	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895692	28895692	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	127	602	0	ENST00000282397.4:c.3082A>G	p.Ile1028Val	p.I1028V	ENST00000282397	NM_002019.4	1028	Att/Gtt	23/30	0.3	1	FACETS	0.646	0.583	0.712	0.646	0.583	0.712	SUBCLONAL	1	TRUE	0	0.28	1		602	1208	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0018298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	904	518	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.431064690821121	8	FACETS	1	0.993	1			1	CLONAL	6	TRUE	NA	0.431064690821121	8		518	1531	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74002009	74002009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	317	509	0	ENST00000318443.5:c.1525G>A	p.Glu509Lys	p.E509K	ENST00000318443	NM_001024736.1	509	Gag/Aag	8/10	0.220080372259509	5	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.431064690821121	5		509	970	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120572	2120572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934872	NA	P-0018298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	530	625	2	ENST00000219476.3:c.1832G>A	p.Arg611Gln	p.R611Q	ENST00000219476	NM_000548.3	611	cGg/cAg	17/42	0.431064690821121	3	FACETS	0.945	0.911	0.98	0.945	0.911	0.98	CLONAL	3	TRUE	0	0.431064690821121	3		627	1054	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217181	66217181	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	261	421	0	ENST00000273854.3:c.2434C>T	p.Leu812Phe	p.L812F	ENST00000273854	NM_004439.5	812	Ctt/Ttt	14/18	0.248116599762934	5	FACETS	1	0.969	1	0.7	0.657	0.745	INDETERMINATE	2	TRUE	2	0.431064690821121	5		421	949	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002844	69002844	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	72	242	0	ENST00000288368.4:c.2144C>G	p.Pro715Arg	p.P715R	ENST00000288368	NM_024870.2	715	cCt/cGt	20/40	0.431064690821121	7	FACETS	0.877	0.765	0.999			1	CLONAL	1	TRUE	NA	0.431064690821121	7		242	791	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0018301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	168	916	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.805	0.74	0.873	1	0.99	1	CLONAL	2	TRUE	1	0.239318087369161	2		916	872	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777666	9777666	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28730670	NA	P-0018301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	50	469	0	ENST00000377346.4:c.1002C>A	p.Asn334Lys	p.N334K	ENST00000377346	NM_005026.3	334	aaC/aaA	8/24	1	2	FACETS	0.562	0.475	0.657	0.562	0.475	0.657	SUBCLONAL	1	TRUE	1	0.239318087369161	2		469	744	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380350	14380350	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	153	358	0	ENST00000256196.4:c.67G>T	p.Gly23Cys	p.G23C	ENST00000256196		23	Ggc/Tgc	1/6	0.239318087369161	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.239318087369161	2		358	514	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0018304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	219	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.922	0.864	0.982	0.922	0.864	0.982	CLONAL	1	TRUE	1	0.768344985997751	2		306	618	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0018304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	291	507	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.927	0.876	0.979	0.927	0.876	0.979	CLONAL	1	TRUE	1	0.768344985997751	2		508	817	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20153932	20153932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	215	400	0	ENST00000379607.5:c.128G>A	p.Gly43Glu	p.G43E	ENST00000379607	NM_001412.3	43	gGa/gAa	3/7	0.768401734446434	1	FACETS	0.963	0.913	1	0.963	0.913	1	CLONAL	1	TRUE	0	0.768344985997751	1		400	358	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244626	46244626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770423384	NA	P-0018304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	383	506	0	ENST00000334344.6:c.2720C>T	p.Ser907Leu	p.S907L	ENST00000334344	NM_152641.2	907	tCa/tTa	15/21	1	2	FACETS	0.996	0.949	1	0.996	0.949	1	CLONAL	1	TRUE	1	0.768344985997751	2		506	1001	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557767	21557768	+	missense_variant	Missense_Mutation	DNP	AG	AG	GT	novel	NA	P-0018304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	335	524	0	ENST00000382592.4:c.2077_2078delinsAC	p.Leu693Thr	p.L693T	ENST00000382592	NM_014572.2	693	CTg/ACg	5/8	1	2	FACETS	0.913	0.866	0.961	0.913	0.866	0.961	CLONAL	1	TRUE	1	0.768344985997751	2		524	955	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627404	37627404	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0018304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	370	608	0	ENST00000447079.4:c.1319C>G	p.Ser440Ter	p.S440*	ENST00000447079	NM_015083.1	440	tCa/tGa	2/14	1	2	FACETS	0.901	0.856	0.946	0.901	0.856	0.946	CLONAL	1	TRUE	1	0.768344985997751	2		608	1069	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913492	NA	P-0018304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	202	477	0	ENST00000286548.4:c.626A>G	p.Gln209Arg	p.Q209R	ENST00000286548	NM_002072.3	209	cAa/cGa	5/7	1	2	FACETS	0.941	0.878	1	0.941	0.878	1	CLONAL	1	TRUE	1	0.768344985997751	2		477	559	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0018305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	49	355	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	FALSE	1	0.141644291392988	2		355	643	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107041	27107042	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCAGAACCCACCCTTTGAGCCAACTAGTGTGGACATGATGCGGCGGGC	novel	NA	P-0018305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	52	352	0	ENST00000324856.7:c.6656_6704dup	p.Arg2236GlufsTer5	p.R2236Efs*5	ENST00000324856	NM_006015.4	2218	atg/aTGCAGAACCCACCCTTTGAGCCAACTAGTGTGGACATGATGCGGCGGGCtg	20/20	1	2	FACETS	0.831	0.705	0.969	0.831	0.705	0.969	CLONAL	1	FALSE	1	0.141644291392988	2		352	884	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770103	56770103	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	71	408	0	ENST00000337432.4:c.99G>T	p.Gln33His	p.Q33H	ENST00000337432	NM_058216.2	33	caG/caT	1/9	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	FALSE	1	0.141644291392988	2		408	922	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0018306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	318	509	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.287415551223053	2	FACETS	0.898	0.847	0.95	0.898	0.847	0.95	CLONAL	2	TRUE	0	0.287415551223053	2		509	1232	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104006	69104006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	161	501	1	ENST00000288368.4:c.4396G>A	p.Ala1466Thr	p.A1466T	ENST00000288368	NM_024870.2	1466	Gct/Act	36/40	0.287415551223053	3	FACETS	1	0.988	1	0.725	0.665	0.787	CLONAL	1	TRUE	1	0.287415551223053	3		502	884	SUCCESS
RET	5979	MSKCC	GRCh37	10	43572708	43572708	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0018306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	11	61	0	ENST00000355710.3:c.2T>C	p.Met1?	p.M1?	ENST00000355710	NM_020975.4	1	aTg/aCg	1/20	0.285820586065058	1	FACETS	0.455	0.315	0.627	0.455	0.315	0.627	SUBCLONAL	1	TRUE	0	0.287415551223053	1		61	144	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112884118	112884118	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	144	304	0	ENST00000351677.2:c.53A>C	p.Asn18Thr	p.N18T	ENST00000351677	NM_002834.3	18	aAc/aCc	2/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.287415551223053	2		304	754	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817829	3817829	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1210983463	NA	P-0018306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	56	482	0	ENST00000262367.5:c.3142G>C	p.Val1048Leu	p.V1048L	ENST00000262367	NM_004380.2	1048	Gtg/Ctg	16/31	1	2	FACETS	0.414	0.353	0.481	0.414	0.353	0.481	SUBCLONAL	1	TRUE	1	0.287415551223053	2		482	941	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222263	53222263	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	128	315	0	ENST00000375401.3:c.4569G>T	p.Gln1523His	p.Q1523H	ENST00000375401	NM_004187.3	1523	caG/caT	26/26	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.287415551223053	1		315	582	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0018307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	144	420	1	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.95	0.874	1	0.95	0.874	1	CLONAL	1	TRUE	1	0.681611957265342	2		421	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0018307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	474	1204	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.681611957265342	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.681611957265342	1		1204	870	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437801	52437802	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	256	783	0	ENST00000460680.1:c.1359dup	p.Glu454ArgfsTer15	p.E454Rfs*15	ENST00000460680	NM_004656.3	453	-/A	13/17	0.681611957265342	1	FACETS	0.912	0.863	0.961	0.912	0.863	0.961	CLONAL	1	TRUE	0	0.681611957265342	1		783	543	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589609	67589617	+	inframe_deletion	In_Frame_Del	DEL	GAAAAAAGT	GAAAAAAGT	-	novel	NA	P-0018307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	196	670	0	ENST00000274335.5:c.1372_1380del	p.Glu458_Ser460del	p.E458_S460del	ENST00000274335		458	GAAAAAAGT/-	10/15	1	2	FACETS	0.909	0.845	0.973	0.909	0.845	0.973	CLONAL	1	TRUE	1	0.681611957265342	2		670	633	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0018309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	232	527	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.485896940983799	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.48679194922696	2		527	467	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	154	654	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.48679194922696	2		654	567	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016218	31016218	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	92	451	0	ENST00000375687.4:c.464C>T	p.Ser155Phe	p.S155F	ENST00000375687	NM_015338.5	155	tCc/tTc	6/13	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.48679194922696	2		451	356	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860346	151860346	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	142	698	0	ENST00000262189.6:c.10316C>G	p.Ser3439Cys	p.S3439C	ENST00000262189	NM_170606.2	3439	tCt/tGt	43/59	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.48679194922696	2		698	558	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6414397	6414397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	37	330	0	ENST00000356142.4:c.31G>A	p.Asp11Asn	p.D11N	ENST00000356142	NM_018890.3	11	Gac/Aac	1/7	0.241101802319095	2	FACETS	0.623	0.519	0.737	0.312	0.259	0.369	INDETERMINATE	1	TRUE	0	0.582209149679379	2		330	204	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577555	7577574	+	protein_altering_variant	In_Frame_Del	DEL	GCAGGAACTGTTACACATGT	GCAGGAACTGTTACACATGT	ACAGG	novel	NA	P-0018311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	200	641	3	ENST00000269305.4:c.707_726delinsCCTGT	p.Tyr236_Ser240del	p.Y236_S240del	ENST00000269305	NM_001126112.2	236	tACATGTGTAACAGTTCCTGC/tCCTGT	7/11	0.497922398825408	2	FACETS	1	0.992	1	0.727	0.681	0.773	CLONAL	1	TRUE	0	0.604696243019099	2		644	455	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967984	93967984	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs769370190	NA	P-0018311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	67	540	1	ENST00000369303.4:c.1943G>T	p.Cys648Phe	p.C648F	ENST00000369303	NM_004440.3	648	tGc/tTc	11/17	0.604696243019099	3	FACETS	0.697	0.608	0.793	0.349	0.304	0.397	SUBCLONAL	1	TRUE	1	0.604696243019099	3		541	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0018313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	49	801	17	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.258797881771419	3	FACETS	0.415	0.35	0.486	0.208	0.175	0.243	SUBCLONAL	1	TRUE	1	0.376609357194288	3		818	745	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0018313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	84	620	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	0.213762483733642	4	FACETS	0.961	0.849	1	0.481	0.424	0.54	INDETERMINATE	1	TRUE	2	0.376609357194288	4		620	639	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102067	27102067	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0018313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	167	535	0	ENST00000324856.7:c.4994-1G>T		p.X1665_splice	ENST00000324856	NM_006015.4	1665			0.299139210533899	4	FACETS	1	0.969	1			1	CLONAL	2	TRUE	NA	0.376609357194288	4		535	560	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534285	534285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894226	NA	P-0018314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	383	761	2	ENST00000451590.1:c.38G>T	p.Gly13Val	p.G13V	ENST00000451590	NM_001130442.1	13	gGt/gTt	2/5	0.779326502199253	4	FACETS	1	0.988	1			1	CLONAL	3	TRUE	NA	0.779326502199253	4		763	554	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091459	193091459	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	98	462	1	ENST00000367435.3:c.129G>T	p.Trp43Cys	p.W43C	ENST00000367435	NM_024529.4	43	tgG/tgT	1/17	0.779326502199253	4	FACETS	1	0.916	1	0.341	0.306	0.378	CLONAL	1	TRUE	1	0.779326502199253	4		463	437	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475451	12475451	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	171	885	2	ENST00000287820.6:c.1325T>C	p.Leu442Pro	p.L442P	ENST00000287820	NM_015869.4	442	cTa/cCa	7/7	0.779326502199253	3	FACETS	0.916	0.845	0.988	0.458	0.422	0.494	CLONAL	1	TRUE	1	0.779326502199253	3		887	666	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922646	56922646	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	282	876	0	ENST00000519728.1:c.1516G>A	p.Gly506Arg	p.G506R	ENST00000519728	NM_002350.3	506	Ggg/Agg	13/13	0.779326502199253	8	FACETS	0.815	0.764	0.868	0.233	0.218	0.248	CLONAL	2	TRUE	1	0.779326502199253	8		876	1482	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553496	29553499	+	missense_variant	Missense_Mutation	ONP	AAGC	AAGC	GAGA	novel	NA	P-0018314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	173	843	0	ENST00000356175.3:c.2045_2048delinsGAGA	p.Gln682_Ala683delinsArgAsp	p.Q682_A683delinsRD	ENST00000356175	NM_000267.3	682	cAAGCc/cGAGAc	18/57	0.758935732917822	2	FACETS	0.914	0.848	0.98	0.457	0.424	0.49	CLONAL	1	TRUE	0	0.779326502199253	2		843	486	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971153	21971153	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913383	NA	P-0018316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	84	478	0	ENST00000304494.5:c.205G>T	p.Glu69Ter	p.E69*	ENST00000304494	NM_000077.4	69	Gag/Tag	2/3	0.409496705601559	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.409496705601559	1		478	290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578538	7578538	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1131691037	NA	P-0018316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	326	1197	1	ENST00000269305.4:c.392A>T	p.Asn131Ile	p.N131I	ENST00000269305	NM_001126112.2	131	aAc/aTc	5/11	0.331788215443058	2	FACETS	0.905	0.858	0.952	0.905	0.858	0.952	CLONAL	2	TRUE	0	0.409496705601559	2		1198	880	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526608	106526608	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	118	635	0	ENST00000359195.3:c.2901C>A	p.His967Gln	p.H967Q	ENST00000359195	NM_002649.2	967	caC/caA	10/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.409496705601559	2		635	502	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546390	46546390	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	40	717	0	ENST00000262741.5:c.139T>C	p.Ser47Pro	p.S47P	ENST00000262741	NM_003629.3	47	Tca/Cca	2/10	1	2	FACETS	0.433	0.36	0.515	0.433	0.36	0.515	SUBCLONAL	1	TRUE	1	0.409496705601559	2		717	451	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313285	65313285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	44	777	0	ENST00000342505.4:c.1829G>A	p.Gly610Glu	p.G610E	ENST00000342505	NM_002227.2	610	gGa/gAa	13/25	1	2	FACETS	0.488	0.41	0.575	0.488	0.41	0.575	SUBCLONAL	1	TRUE	1	0.409496705601559	2		777	440	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409043	4409043	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	97	464	0	ENST00000261254.3:c.738C>A	p.Cys246Ter	p.C246*	ENST00000261254	NM_001759.3	246	tgC/tgA	5/5	0.270136139645374	3	FACETS	0.802	0.721	0.886	0.802	0.721	0.886	CLONAL	2	TRUE	1	0.409496705601559	3		464	356	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428394	49428394	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	328	913	1	ENST00000301067.7:c.10411C>T	p.Gln3471Ter	p.Q3471*	ENST00000301067	NM_003482.3	3471	Cag/Tag	36/54	0.248142290568867	5	FACETS	0.919	0.871	0.968			1	CLONAL	3	TRUE	NA	0.409496705601559	5		914	938	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879854	37879854	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	1903	831	0	ENST00000269571.5:c.2149G>A	p.Glu717Lys	p.E717K	ENST00000269571		717	Gag/Aag	18/27	0.409496705601559	19	FACETS	0.992	0.98	1			1	CLONAL	18	TRUE	NA	0.409496705601559	19		831	2332	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744021	41744021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	48	936	0	ENST00000301178.4:c.956C>T	p.Ser319Phe	p.S319F	ENST00000301178	NM_021913.4	319	tCc/tTc	7/20	1	2	FACETS	0.387	0.326	0.454	0.387	0.326	0.454	SUBCLONAL	1	TRUE	1	0.409496705601559	2		936	606	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858925	45858925	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs762741848	NA	P-0018316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	78	965	0	ENST00000391945.4:c.1541T>C	p.Ile514Thr	p.I514T	ENST00000391945	NM_000400.3	514	aTt/aCt	16/23	1	2	FACETS	0.518	0.454	0.586	0.518	0.454	0.586	SUBCLONAL	1	TRUE	1	0.409496705601559	2		965	736	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163814	152163814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	93	579	2	ENST00000206249.3:c.535G>A	p.Ala179Thr	p.A179T	ENST00000206249	NM_000125.3	179	Gcc/Acc	2/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.409496705601559	2		581	368	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468081	50468081	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	22	405	0	ENST00000331340.3:c.1316G>T	p.Arg439Leu	p.R439L	ENST00000331340	NM_006060.4	439	cGc/cTc	8/8	1	2	FACETS	0.43	0.334	0.541	0.43	0.334	0.541	SUBCLONAL	1	TRUE	1	0.409496705601559	2		405	250	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738406	145738406	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	62	776	0	ENST00000428558.2:c.2579C>A	p.Pro860Gln	p.P860Q	ENST00000428558	NM_004260.3	860	cCg/cAg	16/22	0.409496705601559	3	FACETS	0.507	0.437	0.583	0.253	0.218	0.292	SUBCLONAL	1	TRUE	1	0.409496705601559	3		776	720	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952128	76952128	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	128	413	0	ENST00000373344.5:c.307G>T	p.Val103Leu	p.V103L	ENST00000373344	NM_000489.3	103	Gta/Tta	5/35	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.409496705601559	1		413	336	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0018317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	29	306	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.888	0.731	1	1	0.956	1	CLONAL	2	TRUE	1	0.333350170143061	2		307	98	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs863224451	NA	P-0018317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	186	823	0	ENST00000269305.4:c.824G>C	p.Cys275Ser	p.C275S	ENST00000269305	NM_001126112.2	275	tGt/tCt	8/11	1	2	FACETS	1	0.985	1	1	0.994	1	CLONAL	2	TRUE	1	0.333350170143061	2		823	463	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578528	7578528	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	175	999	0	ENST00000269305.4:c.402T>G	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	ttT/ttG	5/11	1	2	FACETS	1	0.975	1	1	0.994	1	CLONAL	2	TRUE	1	0.333350170143061	2		999	474	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100350	27100350	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	64	764	2	ENST00000324856.7:c.4065del	p.Ser1356AlafsTer125	p.S1356Afs*125	ENST00000324856	NM_006015.4	1354	ttC/tt	17/20	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.333350170143061	2		766	340	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539780	187539780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779677759	NA	P-0018317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	10	445	0	ENST00000441802.2:c.7960G>A	p.Val2654Ile	p.V2654I	ENST00000441802	NM_005245.3	2654	Gta/Ata	10/27	1	2	FACETS	0.337	0.228	0.473	0.337	0.228	0.473	SUBCLONAL	1	TRUE	1	0.333350170143061	2		445	178	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938358	76938358	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	111	364	0	ENST00000373344.5:c.2390del	p.Ser797Ter	p.S797*	ENST00000373344	NM_000489.3	797	tCa/ta	9/35	1	1	FACETS	1	0.981	1	1	0.992	1	CLONAL	3	TRUE	0	0.333350170143061	1		364	161	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0018327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	80	741	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.134094068865921	3	FACETS	0.972	0.859	1	0.972	0.859	1	CLONAL	2	TRUE	1	0.193711392266501	3		741	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0018327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	59	738	0	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.193711392266501	2		738	605	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508536	106508536	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	22	211	0	ENST00000359195.3:c.530G>T	p.Arg177Leu	p.R177L	ENST00000359195	NM_002649.2	177	cGc/cTc	2/11	0.134094068865921	3	FACETS	1	0.922	1	0.746	0.583	0.932	CLONAL	1	TRUE	1	0.193711392266501	3		211	167	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866581	117866581	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057524012	NA	P-0018327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	47	567	0	ENST00000297338.2:c.1064C>T	p.Pro355Leu	p.P355L	ENST00000297338	NM_006265.2	355	cCg/cTg	9/14	0.134094068865921	3	FACETS	1	0.934	1	0.603	0.51	0.707	CLONAL	1	TRUE	1	0.193711392266501	3		567	441	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463532	25463532	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	38	464	0	ENST00000264709.3:c.2150A>G	p.Asn717Ser	p.N717S	ENST00000264709	NM_175629.2	717	aAc/aGc	18/23	1	2	FACETS	0.908	0.751	1	0.908	0.751	1	CLONAL	1	TRUE	1	0.193711392266501	2		464	432	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81957189	81957189	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	37	426	1	ENST00000359376.3:c.2407C>A	p.Pro803Thr	p.P803T	ENST00000359376	NM_002661.3	803	Ccc/Acc	22/33	1	2	FACETS	0.955	0.788	1	0.955	0.788	1	CLONAL	1	TRUE	1	0.193711392266501	2		427	400	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508624	38508650	+	inframe_deletion	In_Frame_Del	DEL	CTGGGACAAGTTCAGTGAACTCTCCAC	CTGGGACAAGTTCAGTGAACTCTCCAC	-	novel	NA	P-0018327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	82	732	0	ENST00000254066.5:c.673_699del	p.Trp225_Thr233del	p.W225_T233del	ENST00000254066	NM_000964.3	224	ctCTGGGACAAGTTCAGTGAACTCTCCACc/ctc	6/9	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.193711392266501	2		732	649	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123707	11123707	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	41	596	0	ENST00000358026.2:c.2357C>A	p.Thr786Asn	p.T786N	ENST00000358026	NM_001128849.1	786	aCc/aAc	16/36	1	2	FACETS	0.687	0.571	0.817	0.687	0.571	0.817	SUBCLONAL	1	TRUE	1	0.193711392266501	2		596	616	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464450	25464450	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	25	382	0	ENST00000264709.3:c.2063G>T	p.Arg688Leu	p.R688L	ENST00000264709	NM_175629.2	688	cGc/cTc	17/23	1	2	FACETS	0.662	0.521	0.824	0.662	0.521	0.824	SUBCLONAL	1	TRUE	1	0.193711392266501	2		382	390	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47604161	47604161	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	28	477	1	ENST00000263735.4:c.500A>T	p.Gln167Leu	p.Q167L	ENST00000263735	NM_002354.2	167	cAg/cTg	5/9	1	2	FACETS	0.642	0.513	0.791	0.642	0.513	0.791	SUBCLONAL	1	TRUE	1	0.193711392266501	2		478	450	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573264	41573264	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	56	808	0	ENST00000263253.7:c.5549C>T	p.Pro1850Leu	p.P1850L	ENST00000263253	NM_001429.3	1850	cCc/cTc	31/31	1	2	FACETS	0.791	0.676	0.917	0.791	0.676	0.917	CLONAL	1	TRUE	1	0.193711392266501	2		808	731	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936542	49936542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746538889	NA	P-0018327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	33	622	0	ENST00000296474.3:c.1385C>T	p.Ala462Val	p.A462V	ENST00000296474	NM_002447.2	462	gCa/gTa	2/20	1	2	FACETS	0.663	0.539	0.803	0.663	0.539	0.803	SUBCLONAL	1	TRUE	1	0.193711392266501	2		622	514	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446989	187446989	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769386051	NA	P-0018327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	40	537	0	ENST00000232014.4:c.1204C>T	p.Arg402Cys	p.R402C	ENST00000232014	NM_001130845.1	402	Cgc/Tgc	5/10	1	2	FACETS	0.816	0.678	0.97	0.816	0.678	0.97	CLONAL	1	TRUE	1	0.193711392266501	2		537	506	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545755	106545758	+	stop_gained	Nonsense_Mutation	ONP	AAAG	AAAG	CAAT	novel	NA	P-0018327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	68	643	0	ENST00000359195.3:c.3232_3235delinsCAAT	p.Lys1078_Gly1079delinsGlnTer	p.K1078_G1079delinsQ*	ENST00000359195	NM_002649.2	1078	AAAGga/CAATga	11/11	0.134094068865921	3	FACETS	0.846	0.738	0.962	0.846	0.738	0.962	CLONAL	2	TRUE	1	0.193711392266501	3		643	455	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0018328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	62	523	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.150844768224951	2	FACETS	0.771	0.667	0.884	0.771	0.667	0.884	SUBCLONAL	2	FALSE	0	0.150844768224951	2		523	533	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0018328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	30	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.812	0.657	0.985	1	0.947	1	CLONAL	2	FALSE	1	0.150844768224951	2		306	245	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425896	49425896	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783685	NA	P-0018328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	32	631	0	ENST00000301067.7:c.12592C>T	p.Arg4198Ter	p.R4198*	ENST00000301067	NM_003482.3	4198	Cga/Tga	39/54	0.14921247017947	3	FACETS	0.781	0.633	0.95	0.391	0.316	0.475	CLONAL	1	FALSE	1	0.150844768224951	3		631	584	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0018328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	40	526	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.150844768224951	2	FACETS	1	0.856	1	0.517	0.429	0.615	CLONAL	1	FALSE	0	0.150844768224951	2		526	513	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927381	245927381	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1260469748	NA	P-0018328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	33	643	0	ENST00000388985.4:c.1147C>G	p.Gln383Glu	p.Q383E	ENST00000388985		383	Caa/Gaa	11/12	1	2	FACETS	0.81	0.659	0.982	0.81	0.659	0.982	CLONAL	1	FALSE	1	0.150844768224951	2		643	540	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102056770	102056770	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	34	527	0	ENST00000282441.5:c.710A>G	p.Glu237Gly	p.E237G	ENST00000282441	NM_001130145.2	237	gAa/gGa	4/9	1	2	FACETS	0.785	0.64	0.949	0.785	0.64	0.949	CLONAL	1	FALSE	1	0.150844768224951	2		527	574	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989511	7989511	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	32	512	0	ENST00000319144.4:c.175C>T	p.Gln59Ter	p.Q59*	ENST00000319144	NM_001139.2	59	Cag/Tag	2/15	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	FALSE	1	0.150844768224951	2		512	400	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299139	15299139	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	39	769	2	ENST00000263388.2:c.1399G>A	p.Glu467Lys	p.E467K	ENST00000263388	NM_000435.2	467	Gag/Aag	9/33	1	2	FACETS	0.842	0.697	1	0.842	0.697	1	CLONAL	1	FALSE	1	0.150844768224951	2		771	614	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537050	41537050	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0018328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	23	410	0	ENST00000263253.7:c.1879-2A>G		p.X627_splice	ENST00000263253	NM_001429.3	627			1	2	FACETS	0.78	0.607	0.98	0.78	0.607	0.98	CLONAL	1	FALSE	1	0.150844768224951	2		410	391	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41558725	41558725	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0018328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	43	583	0	ENST00000263253.7:c.3672-2A>C		p.X1224_splice	ENST00000263253	NM_001429.3	1224			1	2	FACETS	0.939	0.785	1	0.939	0.785	1	CLONAL	1	FALSE	1	0.150844768224951	2		583	607	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879136	151879136	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	70	521	1	ENST00000262189.6:c.5809C>T	p.Gln1937Ter	p.Q1937*	ENST00000262189	NM_170606.2	1937	Caa/Taa	36/59	0.150844768224951	4	FACETS	0.883	0.77	1			1	CLONAL	2	FALSE	NA	0.150844768224951	4		522	605	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277120	38277120	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	92	650	0	ENST00000425967.3:c.1308G>C	p.Lys436Asn	p.K436N	ENST00000425967	NM_001174067.1	436	aaG/aaC	10/19	0.14921247017947	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	FALSE	1	0.150844768224951	3		650	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0018329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	141	775	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.231433261208575	3	FACETS	0.853	0.783	0.926	0.853	0.783	0.926	CLONAL	3	TRUE	0	0.261190322715719	3		777	477	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0018329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	19	352	2	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	1	2	FACETS	0.56	0.425	0.717	0.56	0.425	0.717	SUBCLONAL	1	TRUE	1	0.261190322715719	2		354	260	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28929495	NA	P-0018330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	265	640	8	ENST00000275493.2:c.2155G>T	p.Gly719Cys	p.G719C	ENST00000275493	NM_005228.3	719	Ggc/Tgc	18/28	0.647921502049845	3	FACETS	0.934	0.886	0.982	0.934	0.886	0.982	CLONAL	2	TRUE	1	0.740243183942549	3		648	525	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0018330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	186	492	4	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.647921502049845	3	FACETS	0.897	0.841	0.953	0.897	0.841	0.953	CLONAL	2	TRUE	1	0.740243183942549	3		496	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578525	7578525	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519976	NA	P-0018330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	928	898	4	ENST00000269305.4:c.405C>G	p.Cys135Trp	p.C135W	ENST00000269305	NM_001126112.2	135	tgC/tgG	5/11	0.67371455102509	4	FACETS	0.947	0.93	0.963	0.947	0.93	0.963	CLONAL	4	TRUE	0	0.740243183942549	4		902	1152	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450763	70450763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755857428	NA	P-0018330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	51	542	0	ENST00000373644.4:c.5603C>T	p.Ala1868Val	p.A1868V	ENST00000373644	NM_030625.2	1868	gCc/gTc	12/12	0.676686646818978	2	FACETS	0.429	0.367	0.497	0.215	0.183	0.249	SUBCLONAL	1	TRUE	0	0.740243183942549	2		542	321	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878186	48878186	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0018330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	98	114	0	ENST00000267163.4:c.137+1G>A		p.X46_splice	ENST00000267163	NM_000321.2	46			0.67371455102509	4	FACETS	0.922	0.868	0.97	0.922	0.868	0.97	CLONAL	4	TRUE	0	0.740243183942549	4		114	125	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163485	32163485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	289	573	2	ENST00000375023.3:c.5741G>A	p.Arg1914His	p.R1914H	ENST00000375023	NM_004557.3	1914	cGt/cAt	30/30	0.595532539102772	5	FACETS	1	0.96	1	0.68	0.642	0.718	CLONAL	2	TRUE	2	0.740243183942549	5		575	808	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578493	7578493	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1206165503	NA	P-0018331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	306	972	1	ENST00000269305.4:c.437G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tGg/tAg	5/11	0.662393425699979	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.662393425699979	1		973	571	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804360	46804360	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	471	413	0	ENST00000290295.7:c.647G>T	p.Gly216Val	p.G216V	ENST00000290295	NM_006361.5	216	gGc/gTc	2/2	0.560016543237137	4	FACETS	1	0.991	1			1	CLONAL	4	TRUE	NA	0.662393425699979	4		413	572	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101649	27101649	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	274	803	0	ENST00000324856.7:c.4931G>T	p.Gly1644Val	p.G1644V	ENST00000324856	NM_006015.4	1644	gGc/gTc	18/20	1	2	FACETS	0.992	0.934	1	0.992	0.934	1	CLONAL	1	TRUE	1	0.662393425699979	2		803	834	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937626	32937626	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	102	555	0	ENST00000380152.3:c.8287G>T	p.Asp2763Tyr	p.D2763Y	ENST00000380152		2763	Gat/Tat	18/27	0.658719865395232	2	FACETS	0.888	0.802	0.977	0.444	0.401	0.489	CLONAL	1	TRUE	0	0.662393425699979	2		555	347	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941645	48941645	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0018331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	138	286	1	ENST00000267163.4:c.955A>T	p.Lys319Ter	p.K319*	ENST00000267163	NM_000321.2	319	Aaa/Taa	10/27	0.658719865395232	2	FACETS	0.947	0.888	1	0.947	0.888	1	CLONAL	2	TRUE	0	0.662393425699979	2		287	220	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988417	36988417	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	115	264	0	ENST00000354822.5:c.236C>T	p.Pro79Leu	p.P79L	ENST00000354822	NM_001079668.2	79	cCa/cTa	2/3	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.662393425699979	2		264	259	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222290	2222290	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	263	846	0	ENST00000398665.3:c.3122C>G	p.Ala1041Gly	p.A1041G	ENST00000398665	NM_032482.2	1041	gCc/gGc	24/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.662393425699979	2		846	740	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211150	36211150	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	609	1007	1	ENST00000222270.7:c.901C>A	p.Leu301Ile	p.L301I	ENST00000222270	NM_014727.1	301	Ctc/Atc	3/37	0.662393425699979	3	FACETS	0.947	0.914	0.981			1	CLONAL	2	TRUE	NA	0.662393425699979	3		1008	1292	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31527010	31527010	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	131	555	0	ENST00000344624.3:c.30G>T	p.Met10Ile	p.M10I	ENST00000344624		10	atG/atT	2/33	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.662393425699979	2		555	377	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476743	140476743	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	84	393	0	ENST00000288602.6:c.1663G>C	p.Asp555His	p.D555H	ENST00000288602	NM_004333.4	555	Gat/Cat	13/18	1	2	FACETS	0.843	0.752	0.937	0.843	0.752	0.937	CLONAL	1	TRUE	1	0.662393425699979	2		393	301	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809500	36809500	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	ACGGGCGA	novel	NA	P-0018331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	188	668	0	ENST00000373129.3:c.965delinsTCGCCCGT	p.Ala322ValfsTer31	p.A322Vfs*31	ENST00000373129	NM_032017.1	322	gCc/gTCGCCCGTc	10/12	1	2	FACETS	0.938	0.872	1	0.938	0.872	1	CLONAL	1	TRUE	1	0.662393425699979	2		668	605	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556104	29556125	+	frameshift_variant	Frame_Shift_Del	DEL	GATCCATAGATTTGTCTGACAC	GATCCATAGATTTGTCTGACAC	-	novel	NA	P-0018332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	102	180	0	ENST00000356175.3:c.2471_2492del	p.Gly824GlufsTer10	p.G824Efs*10	ENST00000356175	NM_000267.3	824	gGATCCATAGATTTGTCTGACACa/ga	21/57	0.906714552803552	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.906714552803552	2		180	109	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322696	30322700	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGC	CCTGC	-	novel	NA	P-0018332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	491	731	0	ENST00000322652.5:c.1709_1713del	p.Thr570IlefsTer12	p.T570Ifs*12	ENST00000322652	NM_015355.2	570	aCCTGC/a	14/16	0.906714552803552	2	FACETS	0.972	0.953	0.99	0.972	0.953	0.99	CLONAL	2	TRUE	0	0.906714552803552	2		731	557	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902307	50902307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	146	716	0	ENST00000440232.2:c.199G>A	p.Asp67Asn	p.D67N	ENST00000440232	NM_002691.3	67	Gac/Aac	2/27	0.629059200827427	3	FACETS	0.936	0.86	1			1	CLONAL	1	TRUE	NA	0.906714552803552	3		716	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519999	NA	P-0018333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	42	559	1	ENST00000269305.4:c.716A>G	p.Asn239Ser	p.N239S	ENST00000269305	NM_001126112.2	239	aAc/aGc	7/11	1	2	FACETS	0.565	0.47	0.67	0.565	0.47	0.67	SUBCLONAL	1	TRUE	1	0.19	2		560	783	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740488	58740488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	104	803	1	ENST00000305921.3:c.1393G>A	p.Val465Ile	p.V465I	ENST00000305921	NM_003620.3	465	Gtc/Atc	6/6	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.19	2		804	1095	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645091	86645091	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	33	436	0	ENST00000274376.6:c.1163T>G	p.Leu388Arg	p.L388R	ENST00000274376	NM_002890.2	388	cTt/cGt	8/25	1	2	FACETS	0.608	0.494	0.737	0.608	0.494	0.737	SUBCLONAL	1	TRUE	1	0.19	2		436	571	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0018336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	211	492	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.38113630017945	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.38113630017945	2		492	527	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0018336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	172	607	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.203588729961965	5	FACETS	0.922	0.855	0.99	0.922	0.855	0.99	INDETERMINATE	3	TRUE	2	0.38113630017945	5		607	513	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058033	27058033	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	208	467	0	ENST00000324856.7:c.1741C>T	p.Gln581Ter	p.Q581*	ENST00000324856	NM_006015.4	581	Cag/Tag	3/20	0.321490834545356	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	1	0.369693587531154	4		467	444	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683924	117683924	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	22	539	0	ENST00000368508.3:c.3223G>A	p.Glu1075Lys	p.E1075K	ENST00000368508	NM_002944.2	1075	Gaa/Aaa	21/43	0.210067876737329	0	FACETS	0.419	0.327	0.525			1	INDETERMINATE	1	TRUE	0	0.369693587531154	0		539	179	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0018338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	230	532	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.423561886302237	2	FACETS	0.94	0.885	0.996	0.94	0.885	0.996	CLONAL	2	TRUE	0	0.459788167840036	2		532	532	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912482	32912482	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	139	501	0	ENST00000380152.3:c.3990T>A	p.Asn1330Lys	p.N1330K	ENST00000380152		1330	aaT/aaA	11/27	0.422330384979408	2	FACETS	1	0.973	1	0.576	0.527	0.627	CLONAL	1	TRUE	0	0.459788167840036	2		501	525	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983373	15983373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200574326	NA	P-0018338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	19	393	0	ENST00000268712.3:c.3406G>A	p.Ala1136Thr	p.A1136T	ENST00000268712	NM_006311.3	1136	Gca/Aca	26/46	0.423561886302237	2	FACETS	0.22	0.166	0.283	0.11	0.083	0.142	SUBCLONAL	1	TRUE	0	0.459788167840036	2		393	376	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813537	32813537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1199567167	NA	P-0018338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	32	339	0	ENST00000354258.4:c.2246C>T	p.Pro749Leu	p.P749L	ENST00000354258	NM_000593.5	749	cCt/cTt	11/11	0.193035167153126	5	FACETS	0.468	0.379	0.568	0.156	0.126	0.19	INDETERMINATE	1	TRUE	2	0.459788167840036	5		339	503	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919330	48919355	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGAAAGGTAAAGTAAACATTTTATTA	GGAAAGGTAAAGTAAACATTTTATTA	-	novel	NA	P-0018338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	61	245	0	ENST00000267163.4:c.497_500+22del		p.X166_splice	ENST00000267163	NM_000321.2	166		4/27	0.431439616724171	1	FACETS	0.933	0.816	1	0.933	0.816	1	CLONAL	1	TRUE	0	0.459788167840036	1		245	219	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0018339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	240	801	17	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.408355566704564	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.430113348325744	1		818	635	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0018340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	158	548	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.274883828538037	2	FACETS	0.834	0.77	0.901	0.834	0.77	0.901	CLONAL	2	TRUE	0	0.362040318968566	2		548	523	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117888	70117888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	116	388	0	ENST00000245479.2:c.356C>T	p.Ala119Val	p.A119V	ENST00000245479	NM_000346.3	119	gCg/gTg	1/3	0.245145987260546	4	FACETS	0.947	0.859	1	0.947	0.859	1	CLONAL	2	TRUE	2	0.362040318968566	4		388	461	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272526	11272526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	158	468	0	ENST00000361445.4:c.3404C>T	p.Ala1135Val	p.A1135V	ENST00000361445	NM_004958.3	1135	gCg/gTg	23/58	0.357437769009356	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.362040318968566	4		468	554	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533869	63533869	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773119996	NA	P-0018340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	74	414	0	ENST00000307078.5:c.1285G>A	p.Gly429Ser	p.G429S	ENST00000307078	NM_004655.3	429	Ggc/Agc	6/11	0.245145987260546	4	FACETS	1	0.957	1	0.603	0.529	0.681	CLONAL	1	TRUE	2	0.362040318968566	4		414	462	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755545	39755545	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	60	311	0	ENST00000288319.7:c.1220C>A	p.Ser407Tyr	p.S407Y	ENST00000288319	NM_182918.3	407	tCt/tAt	10/10	0.160547197383126	3	FACETS	1	0.942	1	0.583	0.505	0.666	INDETERMINATE	1	TRUE	1	0.362040318968566	3		311	336	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0018341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	430	833	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.969	0.926	1	0.969	0.926	1	CLONAL	1	TRUE	1	0.835748766482592	2		833	1062	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0018341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	370	734	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.835748766482592	2		734	884	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577520	7577520	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	290	607	1	ENST00000269305.4:c.761T>A	p.Ile254Asn	p.I254N	ENST00000269305	NM_001126112.2	254	aTc/aAc	7/11	1	2	FACETS	0.973	0.921	1	0.973	0.921	1	CLONAL	1	TRUE	1	0.835748766482592	2		608	713	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121173	11121173	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	367	850	0	ENST00000358026.2:c.2240C>G	p.Ala747Gly	p.A747G	ENST00000358026	NM_001128849.1	747	gCg/gGg	15/36	0.819155098275581	1	FACETS	0.935	0.901	0.968	0.935	0.901	0.968	CLONAL	1	TRUE	0	0.835748766482592	1		850	547	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789646	3789646	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	67	947	2	ENST00000262367.5:c.4213G>T	p.Val1405Leu	p.V1405L	ENST00000262367	NM_004380.2	1405	Gtg/Ttg	25/31	0.380704321442247	3	FACETS	0.565	0.49	0.646	0.282	0.245	0.323	SUBCLONAL	1	TRUE	1	0.380704321442247	3		949	742	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168785	56168785	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	66	687	1	ENST00000399503.3:c.1639C>T	p.Gln547Ter	p.Q547*	ENST00000399503	NM_005921.1	547	Cag/Tag	9/20	1	2	FACETS	0.724	0.63	0.825	0.724	0.63	0.825	SUBCLONAL	1	TRUE	1	0.380704321442247	2		688	479	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177054	56177055	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs1311306052	NA	P-0018342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	41	384	0	ENST00000399503.3:c.2326_2327del	p.Ile776CysfsTer4	p.I776Cfs*4	ENST00000399503	NM_005921.1	775	cAT/c	13/20	1	2	FACETS	0.686	0.574	0.81	0.686	0.574	0.81	SUBCLONAL	1	TRUE	1	0.380704321442247	2		384	314	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	42	184	0				ENST00000310581	NM_198253.2	-/1132			0.57585256664429	3	FACETS	1	0.895	1	0.537	0.454	0.625	CLONAL	1	TRUE	1	0.57585256664429	3		184	175	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0018343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	40	326	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.57585256664429	2	FACETS	1	0.934	1	0.594	0.506	0.686	CLONAL	1	TRUE	0	0.57585256664429	2		326	117	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226573373	226573373	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	207	645	0	ENST00000366794.5:c.843C>G	p.Asp281Glu	p.D281E	ENST00000366794	NM_001618.3	281	gaC/gaG	7/23	0.488405248483317	4	FACETS	0.806	0.751	0.862	0.806	0.751	0.862	CLONAL	2	TRUE	2	0.57585256664429	4		645	703	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574013	7574013	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	353	913	2	ENST00000269305.4:c.1014del	p.Phe338LeufsTer7	p.F338Lfs*7	ENST00000269305	NM_001126112.2	338	ttC/tt	10/11	0.572587214496082	2	FACETS	0.842	0.804	0.88	0.842	0.804	0.88	CLONAL	2	TRUE	0	0.57585256664429	2		915	728	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577025	7577025	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0018343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	29	730	0	ENST00000269305.4:c.913A>T	p.Lys305Ter	p.K305*	ENST00000269305	NM_001126112.2	305	Aag/Tag	8/11	0.572587214496082	2	FACETS	0.183	0.146	0.225	0.092	0.073	0.113	SUBCLONAL	1	TRUE	0	0.57585256664429	2		730	550	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587514	29587514	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060500242	NA	P-0018343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	179	640	0	ENST00000356175.3:c.4495C>T	p.Gln1499Ter	p.Q1499*	ENST00000356175	NM_000267.3	1499	Cag/Tag	33/57	0.572587214496082	2	FACETS	0.965	0.908	1	0.965	0.908	1	CLONAL	2	TRUE	0	0.57585256664429	2		640	322	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515163	106515163	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	272	793	0	ENST00000359195.3:c.2306A>C	p.Gln769Pro	p.Q769P	ENST00000359195	NM_002649.2	769	cAa/cCa	5/11	0.488405248483317	4	FACETS	0.908	0.855	0.962	0.908	0.855	0.962	CLONAL	2	TRUE	2	0.57585256664429	4		793	820	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0018344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	38	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.383745003327122	2		306	181	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624272	89624272	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1064796078	NA	P-0018344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	93	575	0	ENST00000371953.3:c.46T>G	p.Tyr16Asp	p.Y16D	ENST00000371953	NM_000314.4	16	Tat/Gat	1/9	0.383745003327122	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.383745003327122	1		575	335	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663898	29663899	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1567617129	NA	P-0018344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	70	567	0	ENST00000356175.3:c.6334_6335del	p.Leu2112ValfsTer9	p.L2112Vfs*9	ENST00000356175	NM_000267.3	2110	caCTct/cact	41/57	1	2	FACETS	0.818	0.716	0.928	0.818	0.716	0.928	CLONAL	1	TRUE	1	0.383745003327122	2		567	446	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923064	44923064	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0018344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	114	743	0	ENST00000377967.4:c.1923+2T>C		p.X641_splice	ENST00000377967	NM_021140.2	641			1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.383745003327122	2		743	550	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	227	775	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.544676001257454	2		777	683	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143993	11143993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568509370	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	113	724	0	ENST00000358026.2:c.3574C>T	p.Arg1192Cys	p.R1192C	ENST00000358026	NM_001128849.1	1192	Cgc/Tgc	26/36	0.544676001257454	4	FACETS	0.663	0.595	0.734	0.221	0.198	0.245	SUBCLONAL	1	TRUE	1	0.544676001257454	4		724	967	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023002	27023003	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6	19	8	0	ENST00000324856.7:c.108_109delinsAA	p.Gly37Ser	p.G37S	ENST00000324856	NM_006015.4	36	ggGGgc/ggAAgc	1/20	0.544676001257454	3	FACETS	0.888	0.76	0.993	1	0.953	1	CLONAL	4	TRUE	1	0.544676001257454	3		8	25	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246498692	246498692	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	246	649	0	ENST00000388985.4:c.313C>T	p.Leu105Phe	p.L105F	ENST00000388985		105	Ctt/Ttt	3/12	0.386280368863933	3	FACETS	0.813	0.764	0.863	0.813	0.764	0.863	CLONAL	2	TRUE	1	0.544676001257454	3		649	707	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332628	70332628	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457729740	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	222	866	1	ENST00000373644.4:c.533C>T	p.Pro178Leu	p.P178L	ENST00000373644	NM_030625.2	178	cCc/cTc	2/12	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.544676001257454	2		867	687	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903702	114903702	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	289	941	1	ENST00000543371.1:c.706C>A	p.Pro236Thr	p.P236T	ENST00000543371	NM_001198531.1	236	Cct/Act	7/14	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.544676001257454	2		942	938	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949199	71949200	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	208	933	2	ENST00000298229.2:c.3666_3667delinsAA	p.Trp1222_Asp1223delinsTer	p.W1222_D1223delins*	ENST00000298229	NM_001567.3	1222	tgGGac/tgAAac	27/28	0.293903135710769	3	FACETS	1	0.982	1	0.584	0.543	0.626	INDETERMINATE	1	TRUE	1	0.544676001257454	3		935	832	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870777	12870777	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	54	147	0	ENST00000228872.4:c.4del	p.Ser2GlnfsTer40	p.S2Qfs*40	ENST00000228872	NM_004064.3	2	Tca/ca	1/3	0.38215409109346	3	FACETS	0.809	0.706	0.916	0.809	0.706	0.916	CLONAL	2	TRUE	1	0.544676001257454	3		147	156	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870996	12870996	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	112	476	0	ENST00000228872.4:c.223G>T	p.Glu75Ter	p.E75*	ENST00000228872	NM_004064.3	75	Gag/Tag	1/3	0.38215409109346	3	FACETS	1	0.97	1	0.589	0.533	0.648	CLONAL	1	TRUE	1	0.544676001257454	3		476	444	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125020	46125020	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	68	270	0	ENST00000334344.6:c.207G>A	p.Trp69Ter	p.W69*	ENST00000334344	NM_152641.2	69	tgG/tgA	3/21	0.38215409109346	3	FACETS	1	0.882	1	0.503	0.441	0.569	CLONAL	1	TRUE	1	0.544676001257454	3		270	316	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861209	57861209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	217	844	1	ENST00000228682.2:c.1006G>A	p.Glu336Lys	p.E336K	ENST00000228682	NM_005269.2	336	Gag/Aag	9/12	0.38215409109346	3	FACETS	1	0.987	1	0.625	0.582	0.669	CLONAL	1	TRUE	1	0.544676001257454	3		845	811	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955427	48955428	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TA	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	101	552	0	ENST00000267163.4:c.1543_1544delinsTA	p.Pro515Ter	p.P515*	ENST00000267163	NM_000321.2	515	CCa/TAa	17/27	0.47220797319616	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.544676001257454	1		552	242	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988381	41988381	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	295	757	0	ENST00000219905.7:c.1173C>G	p.Tyr391Ter	p.Y391*	ENST00000219905	NM_001164273.1	391	taC/taG	3/24	0.386280368863933	3	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	1	0.544676001257454	3		757	687	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2132506	2132506	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	209	910	0	ENST00000219476.3:c.3883+1G>A		p.X1295_splice	ENST00000219476	NM_000548.3	1295			0.386280368863933	3	FACETS	1	0.98	1	0.572	0.532	0.614	CLONAL	1	TRUE	1	0.544676001257454	3		910	853	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632408	3632409	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	435	1118	3	ENST00000294008.3:c.5439_5440delinsTT	p.Arg1814Cys	p.R1814C	ENST00000294008	NM_032444.2	1813	acCCgc/acTTgc	15/15	0.386280368863933	3	FACETS	0.961	0.919	1	0.961	0.919	1	CLONAL	2	TRUE	1	0.544676001257454	3		1121	1057	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857679	9857679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886042648	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	109	352	0	ENST00000330684.3:c.3722G>A	p.Arg1241Gln	p.R1241Q	ENST00000330684	NM_001134407.1	1241	cGg/cAg	13/13	0.386280368863933	3	FACETS	0.762	0.692	0.834	0.762	0.692	0.834	SUBCLONAL	2	TRUE	1	0.544676001257454	3		352	334	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923423	9923423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	321	863	1	ENST00000330684.3:c.1864C>T	p.Pro622Ser	p.P622S	ENST00000330684	NM_001134407.1	622	Cct/Tct	9/13	0.386280368863933	3	FACETS	0.968	0.919	1	0.968	0.919	1	CLONAL	2	TRUE	1	0.544676001257454	3		864	775	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56878475	56878475	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	218	685	0	ENST00000308159.5:c.2414G>A	p.Gly805Glu	p.G805E	ENST00000308159	NM_014669.4	805	gGg/gAg	22/22	0.386280368863933	3	FACETS	1	0.992	1	0.74	0.691	0.79	CLONAL	1	TRUE	1	0.544676001257454	3		685	688	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670717	67670719	+	frameshift_variant	Frame_Shift_Del	DEL	ACC	ACC	TT	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	367	1006	2	ENST00000264010.4:c.1962_1964delinsTT	p.Pro655SerfsTer31	p.P655Sfs*31	ENST00000264010	NM_006565.3	654	cgACCc/cgTTc	11/12	0.386280368863933	3	FACETS	0.902	0.859	0.947	0.902	0.859	0.947	CLONAL	2	TRUE	1	0.544676001257454	3		1008	950	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827693	72827693	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	242	615	1	ENST00000268489.5:c.8888C>T	p.Ser2963Leu	p.S2963L	ENST00000268489	NM_006885.3	2963	tCa/tTa	9/10	0.386280368863933	3	FACETS	0.916	0.862	0.971	0.916	0.862	0.971	CLONAL	2	TRUE	1	0.544676001257454	3		616	617	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579433	7579433	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1064793279	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	241	866	0	ENST00000269305.4:c.254del	p.Pro85LeufsTer38	p.P85Lfs*38	ENST00000269305	NM_001126112.2	85	cCt/ct	4/11	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.544676001257454	2		866	682	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579890	7579890	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659415	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	279	829	0	ENST00000269305.4:c.23C>T	p.Pro8Leu	p.P8L	ENST00000269305	NM_001126112.2	8	cCt/cTt	2/11	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.544676001257454	2		829	831	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56409204	56409204	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	126	612	1	ENST00000348428.3:c.1711G>T	p.Ala571Ser	p.A571S	ENST00000348428	NM_006785.3	571	Gct/Tct	14/17	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.544676001257454	2		613	443	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622327	1622327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	730	932	2	ENST00000344749.5:c.637C>T	p.Pro213Ser	p.P213S	ENST00000344749	NM_001136139.2	213	Ccc/Tcc	9/19	0.544676001257454	4	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	1	0.544676001257454	4		934	1199	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298691	15298691	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	239	1133	0	ENST00000263388.2:c.1606+1G>T		p.X536_splice	ENST00000263388	NM_000435.2	536			0.544676001257454	4	FACETS	1	0.968	1	0.354	0.33	0.38	CLONAL	1	TRUE	1	0.544676001257454	4		1133	1275	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085650	16085650	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	266	949	1	ENST00000281043.3:c.826G>A	p.Glu276Lys	p.E276K	ENST00000281043	NM_005378.4	276	Gaa/Aaa	3/3	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.544676001257454	2		950	750	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288940	212288940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147624110	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	105	664	0	ENST00000342788.4:c.2806G>A	p.Gly936Arg	p.G936R	ENST00000342788	NM_005235.2	936	Gga/Aga	23/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.544676001257454	2		664	313	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022772	31022772	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	203	723	1	ENST00000375687.4:c.2257C>T	p.Pro753Ser	p.P753S	ENST00000375687	NM_015338.5	753	Ccc/Tcc	13/13	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.544676001257454	2		724	548	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513279	44513279	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	305	1102	0	ENST00000291552.4:c.656G>T	p.Gly219Val	p.G219V	ENST00000291552	NM_006758.2	219	gGa/gTa	8/8	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.544676001257454	2		1102	917	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143146	24143146	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	275	883	1	ENST00000263121.7:c.378G>T	p.Lys126Asn	p.K126N	ENST00000263121	NM_003073.3	126	aaG/aaT	4/9	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.544676001257454	2		884	732	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176352	24176353	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	266	1100	4	ENST00000263121.7:c.1143_1144delinsAA	p.Ala382Thr	p.A382T	ENST00000263121	NM_003073.3	381	acGGcc/acAAcc	9/9	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.544676001257454	2		1104	800	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936310	49936310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	161	664	0	ENST00000296474.3:c.1538C>T	p.Ser513Phe	p.S513F	ENST00000296474	NM_002447.2	513	tCt/tTt	3/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.544676001257454	2		664	498	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52649473	52649473	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	137	583	0	ENST00000394830.3:c.1819-1G>T		p.X607_splice	ENST00000394830	NM_018313.4	607			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.544676001257454	2		583	473	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127340	55127340	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	222	799	1	ENST00000257290.5:c.128C>T	p.Ser43Leu	p.S43L	ENST00000257290	NM_006206.4	43	tCa/tTa	3/23	0.386280368863933	3	FACETS	0.757	0.708	0.807	0.757	0.708	0.807	SUBCLONAL	2	TRUE	1	0.544676001257454	3		800	685	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573270	55573270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	147	470	0	ENST00000288135.5:c.932G>A	p.Gly311Glu	p.G311E	ENST00000288135	NM_000222.2	311	gGa/gAa	6/21	0.386280368863933	3	FACETS	0.869	0.803	0.937	0.869	0.803	0.937	CLONAL	2	TRUE	1	0.544676001257454	3		470	395	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197761	66197761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	221	810	0	ENST00000273854.3:c.2938G>A	p.Gly980Ser	p.G980S	ENST00000273854	NM_004439.5	980	Ggc/Agc	17/18	0.386280368863933	3	FACETS	0.753	0.704	0.803	0.753	0.704	0.803	SUBCLONAL	2	TRUE	1	0.544676001257454	3		810	686	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457763	149457764	+	missense_variant	Missense_Mutation	DNP	CG	CG	TT	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	170	694	4	ENST00000286301.3:c.640_641delinsAA	p.Arg214Lys	p.R214K	ENST00000286301	NM_005211.3	214	CGg/AAg	5/22	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.544676001257454	2		698	570	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514450	149514451	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	74	766	2	ENST00000261799.4:c.493_494delinsAA	p.Gly165Lys	p.G165K	ENST00000261799	NM_002609.3	165	GGg/AAg	4/23	1	2	FACETS	0.438	0.384	0.497	0.438	0.384	0.497	SUBCLONAL	1	TRUE	1	0.544676001257454	2		768	620	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675436	30675436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	169	616	0	ENST00000376406.3:c.2920G>A	p.Gly974Arg	p.G974R	ENST00000376406	NM_014641.2	974	Ggg/Agg	8/15	0.386280368863933	3	FACETS	1	0.988	1	0.685	0.633	0.739	CLONAL	1	TRUE	1	0.544676001257454	3		616	576	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341237	8341237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1195779630	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	79	433	0	ENST00000356435.5:c.4979G>A	p.Arg1660Lys	p.R1660K	ENST00000356435		1660	aGg/aAg	30/35	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.544676001257454	2		433	249	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396248	139396249	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	229	897	2	ENST00000277541.6:c.5589_5590delinsTT	p.Gln1864Ter	p.Q1864*	ENST00000277541	NM_017617.3	1863	ccCCag/ccTTag	30/34	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.544676001257454	2		899	782	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401001	139401002	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TA	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	182	810	1	ENST00000277541.6:c.3991_3992delinsTA	p.Gly1331Ter	p.G1331*	ENST00000277541	NM_017617.3	1331	GGg/TAg	24/34	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.544676001257454	2		811	583	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401302	139401303	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	309	1166	6	ENST00000277541.6:c.3766_3767delinsTT	p.Pro1256Leu	p.P1256L	ENST00000277541	NM_017617.3	1256	CCg/TTg	23/34	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.544676001257454	2		1172	930	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626628	100626628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	57	380	1	ENST00000308731.7:c.302C>T	p.Pro101Leu	p.P101L	ENST00000308731	NM_000061.2	101	cCc/cTc	4/19	0.544676001257454	2	FACETS	0.544	0.468	0.625			1	SUBCLONAL	1	TRUE	NA	0.544676001257454	2		381	385	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0018347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	208	833	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.290517556921919	4	FACETS	0.868	0.808	0.928	0.868	0.808	0.928	CLONAL	3	TRUE	1	0.290517556921919	4		833	710	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481417	140481417	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913348	NA	P-0018347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	101	693	0	ENST00000288602.6:c.1391G>T	p.Gly464Val	p.G464V	ENST00000288602	NM_004333.4	464	gGa/gTa	11/18	0.150829462847707	4	FACETS	0.759	0.68	0.843	0.759	0.68	0.843	INDETERMINATE	2	TRUE	2	0.290517556921919	4		693	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577093	7577093	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882008	NA	P-0018347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	157	988	1	ENST00000269305.4:c.845G>C	p.Arg282Pro	p.R282P	ENST00000269305	NM_001126112.2	282	cGg/cCg	8/11	0.195000856740578	2	FACETS	1	0.984	1	0.658	0.603	0.716	CLONAL	1	TRUE	0	0.290517556921919	2		989	821	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279540	123279540	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779566502	NA	P-0018347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	91	759	0	ENST00000358487.5:c.892G>A	p.Gly298Ser	p.G298S	ENST00000358487	NM_000141.4	298	Ggc/Agc	7/18	0.215573886132015	3	FACETS	1	0.935	1	0.537	0.477	0.601	CLONAL	1	TRUE	1	0.290517556921919	3		759	668	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007641	62007641	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	114	632	1	ENST00000392795.3:c.226A>T	p.Ser76Cys	p.S76C	ENST00000392795	NM_001039933.1	76	Agc/Tgc	3/6	0.150829462847707	4	FACETS	0.797	0.719	0.88	0.797	0.719	0.88	INDETERMINATE	2	TRUE	2	0.290517556921919	4		633	635	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170559	11170559	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	113	674	0	ENST00000358026.2:c.4863del	p.Glu1621AspfsTer7	p.E1621Dfs*7	ENST00000358026	NM_001128849.1	1621	gAa/ga	34/36	0.195000856740578	2	FACETS	1	0.983	1	0.726	0.656	0.799	CLONAL	1	TRUE	0	0.290517556921919	2		674	536	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69032461	69032461	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	219	1024	1	ENST00000288368.4:c.3535C>T	p.Gln1179Ter	p.Q1179*	ENST00000288368	NM_024870.2	1179	Cag/Tag	29/40	0.232374183667901	4	FACETS	1	0.979	1	0.747	0.696	0.8	CLONAL	2	TRUE	1	0.290517556921919	4		1025	868	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217311	123217311	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	170	951	3	ENST00000218089.9:c.2965G>T	p.Gly989Trp	p.G989W	ENST00000218089	NM_001042749.1	989	Ggg/Tgg	29/35	0.150829462847707	4	FACETS	0.999	0.92	1	0.999	0.92	1	INDETERMINATE	2	TRUE	2	0.290517556921919	4		954	756	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207034	1207034	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	TTTTT	novel	NA	P-0018347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	124	761	0	ENST00000326873.7:c.122delinsTTTTT	p.Lys41IlefsTer123	p.K41Ifs*123	ENST00000326873	NM_000455.4	41	aAg/aTTTTTg	1/10	0.195000856740578	2	FACETS	1	0.982	1	0.681	0.617	0.747	CLONAL	1	TRUE	0	0.290517556921919	2		761	627	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032354	42032354	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	47	863	2	ENST00000219905.7:c.4538G>T	p.Arg1513Leu	p.R1513L	ENST00000219905	NM_001164273.1	1513	cGc/cTc	14/24	1	2	FACETS	0.317	0.266	0.372	0.317	0.266	0.372	SUBCLONAL	1	TRUE	1	0.41	2		865	724	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578546	7578547	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0018348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	62	1391	0	ENST00000269305.4:c.383dup	p.Ala129CysfsTer20	p.A129Cfs*20	ENST00000269305	NM_001126112.2	128	cct/ccCt	5/11	1	2	FACETS	0.265	0.228	0.306	0.265	0.228	0.306	SUBCLONAL	1	TRUE	1	0.41	2		1391	1140	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665062	29665062	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	66	695	0	ENST00000356175.3:c.6662del	p.Pro2221HisfsTer23	p.P2221Hfs*23	ENST00000356175	NM_000267.3	2221	Cca/ca	44/57	1	2	FACETS	0.454	0.394	0.52	0.454	0.394	0.52	SUBCLONAL	1	TRUE	1	0.41	2		695	709	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0018351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	80	941	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.945	0.831	1	0.945	0.831	1	CLONAL	1	TRUE	1	0.211825563760923	2		942	799	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971177	21971177	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913382	NA	P-0018351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	44	460	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	0.211825563760923	2		461	335	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656878	45656878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1306205252	NA	P-0018351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	58	804	1	ENST00000407780.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000407780	NM_001283052.1	93	cGg/cAg	3/7	0.211825563760923	1	FACETS	0.844	0.725	0.974	0.844	0.725	0.974	CLONAL	1	TRUE	0	0.211825563760923	1		805	580	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973835	131973835	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1333645178	NA	P-0018351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	51	606	0	ENST00000265335.6:c.3538C>T	p.Arg1180Trp	p.R1180W	ENST00000265335		1180	Cgg/Tgg	23/25	0.211825563760923	1	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	0	0.211825563760923	1		606	395	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	33	918	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	0.547	0.445	0.663			1	INDETERMINATE	1	TRUE	NA	0.249740697809844	2		918	483	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0018352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	25	418	2	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	1	2	FACETS	0.628	0.495	0.78	0.628	0.495	0.78	SUBCLONAL	1	TRUE	1	0.249740697809844	2		420	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577579	7577579	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	69	725	0	ENST00000269305.4:c.702C>A	p.Tyr234Ter	p.Y234*	ENST00000269305	NM_001126112.2	234	taC/taA	7/11	1	2	FACETS	0.867	0.755	0.989	0.867	0.755	0.989	CLONAL	1	TRUE	1	0.249740697809844	2		725	637	SUCCESS
APC	324	MSKCC	GRCh37	5	112175351	112175351	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	25	400	0	ENST00000257430.4:c.4063del	p.Ser1355LeufsTer60	p.S1355Lfs*60	ENST00000257430	NM_000038.5	1354	Ttt/tt	16/16	1	2	FACETS	0.63	0.497	0.782	0.63	0.497	0.782	SUBCLONAL	1	TRUE	1	0.249740697809844	2		400	318	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	210	555	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.832	0.782	0.882	1	0.994	1	CLONAL	2	TRUE	1	0.557059204599014	2		558	453	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	98	579	4	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	0.773	0.693	0.857	0.773	0.693	0.857	SUBCLONAL	1	TRUE	1	0.557059204599014	2		583	455	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	155	865	8	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.658	0.602	0.716	0.658	0.602	0.716	SUBCLONAL	1	TRUE	1	0.557059204599014	2		873	846	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	100	710	5	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.696	0.624	0.772	0.696	0.624	0.772	SUBCLONAL	1	TRUE	1	0.557059204599014	2		715	516	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624530	21624530	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	51	922	0	ENST00000421138.2:c.1499T>C	p.Leu500Pro	p.L500P	ENST00000421138		500	cTg/cCg	14/16	1	2	FACETS	0.263	0.223	0.308	0.263	0.223	0.308	SUBCLONAL	1	TRUE	1	0.557059204599014	2		922	695	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	75	657	2	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.489	0.429	0.553	0.489	0.429	0.553	SUBCLONAL	1	TRUE	1	0.557059204599014	2		659	551	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	79	770	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	0.456611519088677	2	FACETS	0.48	0.422	0.542	0.24	0.211	0.271	SUBCLONAL	1	TRUE	0	0.557059204599014	2		770	591	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	38	398	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	0.502	0.417	0.595	0.502	0.417	0.595	SUBCLONAL	1	TRUE	1	0.557059204599014	2		398	272	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867443	35867443	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1020619032	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	27	615	1	ENST00000303115.3:c.257G>A	p.Arg86Lys	p.R86K	ENST00000303115	NM_002185.3	86	aGg/aAg	3/8	1	2	FACETS	0.229	0.181	0.283	0.229	0.181	0.283	SUBCLONAL	1	TRUE	1	0.557059204599014	2		616	424	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589149	67589151	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	novel	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	36	403	0	ENST00000274335.5:c.1138_1140del	p.Leu380del	p.L380del	ENST00000274335		379	aaATTa/aaa	9/15	1	2	FACETS	0.44	0.363	0.525	0.44	0.363	0.525	SUBCLONAL	1	TRUE	1	0.557059204599014	2		403	294	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863319	57863319	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	199	801	0	ENST00000228682.2:c.1418del	p.Gly473AlafsTer40	p.G473Afs*40	ENST00000228682	NM_005269.2	472	Ggg/gg	11/12	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.557059204599014	2		801	700	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	459909	459909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	161	1060	3	ENST00000399788.2:c.1186C>T	p.Arg396Trp	p.R396W	ENST00000399788	NM_001042603.1	396	Cgg/Tgg	10/28	NA	2	FACETS	0.729	0.669	0.791			1	INDETERMINATE	1	TRUE	NA	0.557059204599014	2		1063	793	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33433425	33433425	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs387906843	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	157	920	2	ENST00000345365.6:c.556C>T	p.Arg186Ter	p.R186*	ENST00000345365	NM_002878.3	186	Cga/Tga	6/10	1	2	FACETS	0.759	0.696	0.824	0.759	0.696	0.824	SUBCLONAL	1	TRUE	1	0.557059204599014	2		922	743	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551952	150551952	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	141	560	0	ENST00000369026.2:c.55del	p.Ala19ProfsTer30	p.A19Pfs*30	ENST00000369026	NM_021960.4	19	Gcc/cc	1/3	0.557059204599014	3	FACETS	1	0.934	1	0.513	0.468	0.559	CLONAL	1	TRUE	1	0.557059204599014	3		560	631	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021232	31021232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148964601	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	59	685	2	ENST00000375687.4:c.1231C>T	p.Arg411Cys	p.R411C	ENST00000375687	NM_015338.5	411	Cgc/Tgc	12/13	1	2	FACETS	0.374	0.321	0.431	0.374	0.321	0.431	SUBCLONAL	1	TRUE	1	0.557059204599014	2		687	567	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371810	55371831	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGCCCCGAGGGCGGCCGCGT	TGGGCCCCGAGGGCGGCCGCGT	-	novel	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	12	54	0	ENST00000297316.4:c.500_521del	p.Leu167ArgfsTer213	p.L167Rfs*213	ENST00000297316	NM_022454.3	167	cTGGGCCCCGAGGGCGGCCGCGTg/cg	2/2	1	2	FACETS	0.783	0.565	1	0.783	0.565	1	CLONAL	1	TRUE	1	0.557059204599014	2		54	55	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512370	38512370	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567767560	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	29	684	3	ENST00000254066.5:c.1286del	p.Gly429ValfsTer214	p.G429Vfs*214	ENST00000254066	NM_000964.3	427	ccG/cc	9/9	1	2	FACETS	0.222	0.177	0.272	0.222	0.177	0.272	SUBCLONAL	1	TRUE	1	0.557059204599014	2		687	470	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	64	1199	8	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.241	0.208	0.277	0.241	0.208	0.277	SUBCLONAL	1	TRUE	1	0.557059204599014	2		1207	954	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023852	27023852	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	26	231	1	ENST00000324856.7:c.961del	p.Gln321ArgfsTer42	p.Q321Rfs*42	ENST00000324856	NM_006015.4	320	Ccc/cc	1/20	1	2	FACETS	0.424	0.338	0.523	0.424	0.338	0.523	SUBCLONAL	1	TRUE	1	0.557059204599014	2		232	220	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843676	156843676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866261145	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	121	1137	0	ENST00000524377.1:c.1102G>A	p.Gly368Ser	p.G368S	ENST00000524377	NM_002529.3	368	Ggc/Agc	8/17	0.557059204599014	3	FACETS	0.444	0.399	0.491	0.222	0.199	0.246	SUBCLONAL	1	TRUE	1	0.557059204599014	3		1137	1252	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925523	114925523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780741000	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	79	818	3	ENST00000543371.1:c.1601C>T	p.Pro534Leu	p.P534L	ENST00000543371	NM_001198531.1	534	cCg/cTg	14/14	0.456611519088677	2	FACETS	0.546	0.482	0.616	0.273	0.241	0.308	SUBCLONAL	1	TRUE	0	0.557059204599014	2		821	519	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562756	21562756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs12867400	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	63	257	1	ENST00000382592.4:c.1163C>T	p.Ala388Val	p.A388V	ENST00000382592	NM_014572.2	388	gCg/gTg	4/8	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.557059204599014	2		258	215	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972651	32972651	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	34	730	0	ENST00000380152.3:c.10001T>A	p.Leu3334Ter	p.L3334*	ENST00000380152		3334	tTg/tAg	27/27	1	2	FACETS	0.207	0.169	0.251	0.207	0.169	0.251	SUBCLONAL	1	TRUE	1	0.557059204599014	2		730	589	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435202	110435202	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	54	871	1	ENST00000375856.3:c.3199G>T	p.Gly1067Trp	p.G1067W	ENST00000375856	NM_003749.2	1067	Ggg/Tgg	1/2	1	2	FACETS	0.247	0.21	0.287	0.247	0.21	0.287	SUBCLONAL	1	TRUE	1	0.557059204599014	2		872	785	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436833	110436833	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	80	896	0	ENST00000375856.3:c.1568C>A	p.Ser523Tyr	p.S523Y	ENST00000375856	NM_003749.2	523	tCc/tAc	1/2	1	2	FACETS	0.356	0.313	0.403	0.356	0.313	0.403	SUBCLONAL	1	TRUE	1	0.557059204599014	2		896	806	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414976	56414976	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	81	686	0	ENST00000348428.3:c.2377C>T	p.His793Tyr	p.H793Y	ENST00000348428	NM_006785.3	793	Cat/Tat	17/17	1	2	FACETS	0.631	0.558	0.709	0.631	0.558	0.709	SUBCLONAL	1	TRUE	1	0.557059204599014	2		686	461	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228997	36228997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	93	718	1	ENST00000222270.7:c.7777C>T	p.Arg2593Cys	p.R2593C	ENST00000222270	NM_014727.1	2593	Cgc/Tgc	36/37	1	2	FACETS	0.482	0.428	0.539	0.482	0.428	0.539	SUBCLONAL	1	TRUE	1	0.557059204599014	2		719	693	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794917	42794917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199751904	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	47	685	1	ENST00000575354.2:c.1997G>A	p.Arg666His	p.R666H	ENST00000575354	NM_015125.3	666	cGt/cAt	10/20	1	2	FACETS	0.31	0.261	0.364	0.31	0.261	0.364	SUBCLONAL	1	TRUE	1	0.557059204599014	2		686	544	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662527	227662527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1428460249	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	36	386	1	ENST00000305123.5:c.928G>A	p.Ala310Thr	p.A310T	ENST00000305123	NM_005544.2	310	Gcc/Acc	1/2	1	2	FACETS	0.523	0.433	0.623	0.523	0.433	0.623	SUBCLONAL	1	TRUE	1	0.557059204599014	2		387	247	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513304	44513304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196323575	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	125	1066	4	ENST00000291552.4:c.631C>T	p.Arg211Cys	p.R211C	ENST00000291552	NM_006758.2	211	Cgt/Tgt	8/8	1	2	FACETS	0.482	0.435	0.531	0.482	0.435	0.531	SUBCLONAL	1	TRUE	1	0.557059204599014	2		1070	932	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092944	29092944	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	143	873	0	ENST00000328354.6:c.1040A>G	p.Asp347Gly	p.D347G	ENST00000328354	NM_007194.3	347	gAc/gGc	10/15	1	2	FACETS	0.781	0.714	0.851	0.781	0.714	0.851	SUBCLONAL	1	TRUE	1	0.557059204599014	2		873	657	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164038	106164038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457913481	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	88	496	0	ENST00000380013.4:c.3548C>T	p.Thr1183Ile	p.T1183I	ENST00000380013	NM_001127208.2	1183	aCt/aTt	5/11	1	2	FACETS	0.782	0.697	0.872	0.782	0.697	0.872	SUBCLONAL	1	TRUE	1	0.557059204599014	2		496	404	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197096	106197096	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	41	415	2	ENST00000380013.4:c.5429C>T	p.Ala1810Val	p.A1810V	ENST00000380013	NM_001127208.2	1810	gCt/gTt	11/11	1	2	FACETS	0.478	0.4	0.564	0.478	0.4	0.564	SUBCLONAL	1	TRUE	1	0.557059204599014	2		417	308	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170832387	170832387	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	21	202	0	ENST00000296930.5:c.751A>G	p.Met251Val	p.M251V	ENST00000296930	NM_002520.6	251	Atg/Gtg	9/11	1	2	FACETS	0.389	0.301	0.49	0.389	0.301	0.49	SUBCLONAL	1	TRUE	1	0.557059204599014	2		202	194	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20483062	20483062	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	88	563	0	ENST00000346618.3:c.795G>T	p.Glu265Asp	p.E265D	ENST00000346618	NM_001949.4	265	gaG/gaT	4/7	1	2	FACETS	0.649	0.577	0.725	0.649	0.577	0.725	SUBCLONAL	1	TRUE	1	0.557059204599014	2		563	487	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858526	27858527	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	49	293	0	ENST00000359303.2:c.44dup	p.Ala16GlyfsTer36	p.A16Gfs*36	ENST00000359303	NM_003535.2	15	aag/aaAg	1/1	1	2	FACETS	0.838	0.718	0.966	0.838	0.718	0.966	CLONAL	1	TRUE	1	0.557059204599014	2		293	210	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97934381	97934381	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	142	831	1	ENST00000289081.3:c.394G>T	p.Ala132Ser	p.A132S	ENST00000289081	NM_000136.2	132	Gct/Tct	5/15	1	2	FACETS	0.783	0.716	0.853	0.783	0.716	0.853	SUBCLONAL	1	TRUE	1	0.557059204599014	2		832	651	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630250	100630250	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	73	478	1	ENST00000308731.7:c.23G>A	p.Ser8Asn	p.S8N	ENST00000308731	NM_000061.2	8	aGc/aAc	2/19	1	2	FACETS	0.667	0.586	0.753	0.667	0.586	0.753	SUBCLONAL	1	TRUE	1	0.557059204599014	2		479	393	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0018354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	36	642	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.561168268918738	1	FACETS	0.15	0.123	0.181	0.15	0.123	0.181	SUBCLONAL	1	TRUE	0	0.561168268918738	1		642	615	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	218	918	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.98	0.914	1	0.98	0.914	1	CLONAL	1	TRUE	1	0.561168268918738	2		918	793	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899079	40899079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs951719751	NA	P-0018354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	286	691	2	ENST00000373198.4:c.2191G>A	p.Ala731Thr	p.A731T	ENST00000373198	NM_133170.3	731	Gcc/Acc	14/32	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.561168268918738	2		693	951	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518250	8518250	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	144	377	0	ENST00000356435.5:c.1141G>A	p.Ala381Thr	p.A381T	ENST00000356435		381	Gct/Act	10/35	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.561168268918738	2		377	487	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981773	201981774	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0018354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	881	902	0	ENST00000359651.3:c.485_486dup	p.Ser163AlafsTer92	p.S163Afs*92	ENST00000359651		162	ggc/gGCgc	4/8	0.527485307970764	4	FACETS	0.931	0.904	0.958	0.931	0.904	0.958	CLONAL	3	TRUE	1	0.561168268918738	4		902	1755	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038932	12038932	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	279	794	0	ENST00000396373.4:c.1225A>G	p.Lys409Glu	p.K409E	ENST00000396373	NM_001987.4	409	Aag/Gag	7/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.561168268918738	2		794	937	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579310	7579310	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1555526469	NA	P-0018354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	286	697	0	ENST00000269305.4:c.375+2T>C		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.561168268918738	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.561168268918738	1		697	725	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727455	66727455	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs869025608	NA	P-0018366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	62	630	2	ENST00000307102.5:c.171G>T	p.Lys57Asn	p.K57N	ENST00000307102	NM_002755.3	57	aaG/aaT	2/11	0.230209876102644	2	FACETS	0.834	0.725	0.95	0.834	0.725	0.95	CLONAL	2	TRUE	0	0.230209876102644	2		632	323	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	52	1351	3	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	0.215564867266948	3	FACETS	0.827	0.704	0.963	0.414	0.352	0.482	CLONAL	1	TRUE	1	0.230209876102644	3		1354	609	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610227	10610227	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	80	1168	0	ENST00000171111.5:c.483G>T	p.Met161Ile	p.M161I	ENST00000171111	NM_203500.1	161	atG/atT	2/6	0.213836332544178	2	FACETS	1	0.97	1	0.663	0.585	0.747	CLONAL	1	TRUE	0	0.230209876102644	2		1168	524	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076932	41076932	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	46	910	0	ENST00000373198.4:c.1488del	p.Phe498LeufsTer103	p.F498Lfs*103	ENST00000373198	NM_133170.3	496	ggG/gg	9/32	0.230209876102644	3	FACETS	1	0.907	1	0.554	0.468	0.65	CLONAL	1	TRUE	1	0.230209876102644	3		910	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0018366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	67	858	0	ENST00000269305.4:c.560-1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.153295235546127	2	FACETS	0.818	0.715	0.927	0.818	0.715	0.927	CLONAL	2	TRUE	0	0.230209876102644	2		858	356	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120457936	120457936	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	43	635	0	ENST00000256646.2:c.7409A>T	p.Tyr2470Phe	p.Y2470F	ENST00000256646	NM_024408.3	2470	tAt/tTt	34/34	0.215564867266948	3	FACETS	1	0.951	1	0.69	0.58	0.81	CLONAL	1	TRUE	1	0.230209876102644	3		635	302	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742846	17742846	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	58	1083	2	ENST00000250003.3:c.754C>A	p.Leu252Met	p.L252M	ENST00000250003	NM_002478.4	252	Ctg/Atg	3/3	0.230209876102644	3	FACETS	1	0.926	1	0.56	0.481	0.645	CLONAL	1	TRUE	1	0.230209876102644	3		1085	502	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835678	68835678	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	55	1119	0	ENST00000261769.5:c.269G>T	p.Arg90Leu	p.R90L	ENST00000261769	NM_004360.3	90	cGg/cTg	3/16	0.215564867266948	3	FACETS	0.987	0.844	1	0.493	0.422	0.571	CLONAL	1	TRUE	1	0.230209876102644	3		1119	540	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985802	60985802	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	49	616	0	ENST00000333681.4:c.98del	p.Gly33GlufsTer63	p.G33Efs*63	ENST00000333681		33	gGa/ga	2/3	0.153295235546127	2	FACETS	1	0.925	1	0.574	0.487	0.668	CLONAL	1	TRUE	0	0.230209876102644	2		616	371	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7168056	7168056	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	47	1164	0	ENST00000302850.5:c.1533G>C	p.Lys511Asn	p.K511N	ENST00000302850	NM_000208.2	511	aaG/aaC	7/22	0.213836332544178	2	FACETS	0.791	0.668	0.928	0.396	0.334	0.464	CLONAL	1	TRUE	0	0.230209876102644	2		1164	516	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31422927	31422927	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	101	1189	1	ENST00000344624.3:c.3386C>T	p.Thr1129Ile	p.T1129I	ENST00000344624		1129	aCa/aTa	26/33	0.0656141859446175	4	FACETS	0.906	0.811	1	0.906	0.811	1	INDETERMINATE	2	TRUE	2	0.230209876102644	4		1190	596	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367323	50367323	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	44	648	0	ENST00000331340.3:c.130C>T	p.Gln44Ter	p.Q44*	ENST00000331340	NM_006060.4	44	Cag/Tag	3/8	0.230209876102644	2	FACETS	0.937	0.787	1	0.468	0.393	0.551	CLONAL	1	TRUE	0	0.230209876102644	2		648	408	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80343543	80343543	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	26	881	0	ENST00000286548.4:c.776T>C	p.Ile259Thr	p.I259T	ENST00000286548	NM_002072.3	259	aTc/aCc	6/7	1	2	FACETS	0.693	0.549	0.857	0.693	0.549	0.857	SUBCLONAL	1	TRUE	1	0.230209876102644	2		881	326	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937724	76937724	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	65	442	0	ENST00000373344.5:c.3024G>T	p.Gln1008His	p.Q1008H	ENST00000373344	NM_000489.3	1008	caG/caT	9/35	0.121688345640551	2	FACETS	0.927	0.818	1			1	INDETERMINATE	3	TRUE	NA	0.230209876102644	2		442	203	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0018367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	252	916	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.574965597552493	2		916	732	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374998	118374998	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	155	719	0	ENST00000534358.1:c.8391A>C	p.Gln2797His	p.Q2797H	ENST00000534358	NM_005933.3	2797	caA/caC	27/36	0.201325613500513	3	FACETS	1	0.987	1	0.683	0.63	0.738	INDETERMINATE	1	TRUE	1	0.574965597552493	3		719	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0018368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	26	710	5	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.647	0.511	0.805	0.647	0.511	0.805	SUBCLONAL	1	TRUE	1	0.13	2		715	618	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0018368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	19	609	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.991	0.752	1	0.991	0.752	1	CLONAL	1	TRUE	1	0.13	2		609	295	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096126	71096126	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	21	363	0	ENST00000318789.4:c.631C>T	p.Gln211Ter	p.Q211*	ENST00000318789	NM_032682.5	211	Cag/Tag	10/21	1	2	FACETS	0.95	0.731	1	0.95	0.731	1	CLONAL	1	TRUE	1	0.13	2		363	340	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346154	152346154	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	74	817	0	ENST00000359321.1:c.416G>T	p.Ser139Ile	p.S139I	ENST00000359321	NM_005431.1	139	aGt/aTt	3/3	1	2	FACETS	1	0.939	1	1	0.984	1	CLONAL	2	TRUE	1	0.13	2		817	510	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781371	NA	P-0018369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	8	982	0	ENST00000269305.4:c.328C>T	p.Arg110Cys	p.R110C	ENST00000269305	NM_001126112.2	110	Cgt/Tgt	4/11	0.27942991982504	3	FACETS	0.096	0.061	0.142	0.048	0.03	0.071	INDETERMINATE	1	TRUE	1	0.536929758272496	3		982	393	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115918	8115919	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	67	686	0	ENST00000346208.3:c.1265dup	p.Met422IlefsTer85	p.M422Ifs*85	ENST00000346208		422	atg/aTtg	6/6	0.337994490536242	0	FACETS	0.478	0.42	0.538			1	SUBCLONAL	1	TRUE	0	0.536929758272496	0		686	242	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348818	89348818	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	22	1270	2	ENST00000301030.4:c.4132del	p.Glu1378LysfsTer31	p.E1378Kfs*31	ENST00000301030	NM_001256183.1	1378	Gaa/aa	9/13	0.536929758272496	1	FACETS	0.222	0.172	0.28	0.222	0.172	0.28	SUBCLONAL	1	TRUE	0	0.536929758272496	1		1272	270	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193121549	193121549	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	342	511	0	ENST00000367435.3:c.947A>T	p.His316Leu	p.H316L	ENST00000367435	NM_024529.4	316	cAt/cTt	10/17	0.818609239104941	4	FACETS	0.952	0.906	0.999	0.635	0.604	0.666	CLONAL	2	TRUE	1	0.82375281867537	4		511	795	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445716	49445716	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	544	1681	0	ENST00000301067.7:c.1750C>G	p.Pro584Ala	p.P584A	ENST00000301067	NM_003482.3	584	Cca/Gca	10/54	1	2	FACETS	0.989	0.95	1	0.989	0.95	1	CLONAL	1	TRUE	1	0.82375281867537	2		1681	1336	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138382783	138382783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	276	775	2	ENST00000289153.2:c.2761C>T	p.His921Tyr	p.H921Y	ENST00000289153	NM_006219.2	921	Cat/Tat	19/22	1	2	FACETS	0.988	0.934	1	0.988	0.934	1	CLONAL	1	TRUE	1	0.82375281867537	2		777	678	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057520005	NA	P-0018371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	516	1023	0	ENST00000269305.4:c.820G>C	p.Val274Leu	p.V274L	ENST00000269305	NM_001126112.2	274	Gtt/Ctt	8/11	NA	2	FACETS	0.964	0.929	0.999			1	INDETERMINATE	2	TRUE	NA	0.551875382471731	2		1023	970	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098944	178098944	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	98	541	0	ENST00000397062.3:c.101G>C	p.Arg34Pro	p.R34P	ENST00000397062	NM_006164.4	34	cGa/cCa	2/5	1	2	FACETS	0.981	0.883	1	0.981	0.883	1	CLONAL	1	TRUE	1	0.551875382471731	2		541	362	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941709	48941710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0018371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	60	438	0	ENST00000267163.4:c.1019_1020insG	p.Asp340GlufsTer2	p.D340Efs*2	ENST00000267163	NM_000321.2	340	gat/gaGt	10/27	0.551875382471731	1	FACETS	0.915	0.805	1	0.915	0.805	1	CLONAL	1	TRUE	0	0.551875382471731	1		438	172	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095826	29095840	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CTGCACAGCCAAGAG	CTGCACAGCCAAGAG	-	novel	NA	P-0018371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	148	831	0	ENST00000328354.6:c.994_1008del	p.Leu332_Gln336del	p.L332_Q336del	ENST00000328354	NM_007194.3	332	CTCTTGGCTGTGCAG/-	9/15	1	2	FACETS	0.835	0.765	0.908	0.835	0.765	0.908	CLONAL	1	TRUE	1	0.551875382471731	2		831	642	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133310	38133310	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2296	201	775	0	ENST00000317025.8:c.4163A>T	p.Asp1388Val	p.D1388V	ENST00000317025	NM_023034.1	1388	gAt/gTt	24/24	0.551875382471731	10	FACETS	0.936	0.862	1			1	CLONAL	1	TRUE	NA	0.551875382471731	10		775	2497	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577460	64577460	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	180	854	0	ENST00000312049.6:c.122T>C	p.Leu41Pro	p.L41P	ENST00000312049	NM_130799.2	41	cTg/cCg	2/10	1	2	FACETS	0.873	0.81	0.937	0.873	0.81	0.937	CLONAL	1	TRUE	1	0.73	2		854	565	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577513	64577513	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	158	528	0	ENST00000312049.6:c.69del	p.Phe23LeufsTer96	p.F23Lfs*96	ENST00000312049	NM_130799.2	23	ttT/tt	2/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.73	2		528	386	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440209	49440209	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0018373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	78	718	0	ENST00000301067.7:c.4419-2A>C		p.X1473_splice	ENST00000301067	NM_003482.3	1473			1	2	FACETS	0.678	0.597	0.765	0.678	0.597	0.765	SUBCLONAL	1	TRUE	1	0.42	2		718	548	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779470	3779470	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	114	951	1	ENST00000262367.5:c.5578C>T	p.Gln1860Ter	p.Q1860*	ENST00000262367	NM_004380.2	1860	Cag/Tag	31/31	1	2	FACETS	0.664	0.597	0.734	0.664	0.597	0.734	SUBCLONAL	1	TRUE	1	0.42	2		952	818	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	152	741	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.862	0.792	0.934	0.862	0.792	0.934	CLONAL	1	TRUE	1	0.613443885034683	2		741	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	143	536	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	1	2	FACETS	0.721	0.659	0.785	0.721	0.659	0.785	SUBCLONAL	1	TRUE	1	0.613443885034683	2		536	647	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	362	555	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.898	0.86	0.936	1	0.997	1	CLONAL	2	TRUE	1	0.613443885034683	2		558	657	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	211	645	3	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	1	2	FACETS	0.886	0.826	0.949	0.886	0.826	0.949	CLONAL	1	TRUE	1	0.613443885034683	2		648	776	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825519	50825519	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	318	614	0	ENST00000398568.2:c.2156del	p.Asn719MetfsTer13	p.N719Mfs*13	ENST00000398568	NM_001042412.1	717	gAa/ga	14/18	1	2	FACETS	0.995	0.953	1	1	0.996	1	CLONAL	2	TRUE	1	0.613443885034683	2		614	521	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	228	716	6	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.882	0.823	0.942	0.882	0.823	0.942	CLONAL	1	TRUE	1	0.613443885034683	2		722	843	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	270	865	8	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.858	0.805	0.912	0.858	0.805	0.912	CLONAL	1	TRUE	1	0.613443885034683	2		873	1026	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	280	859	0	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.937	0.882	0.994	0.937	0.882	0.994	CLONAL	1	TRUE	1	0.613443885034683	2		859	974	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347983	347983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760961378	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	278	878	2	ENST00000262320.3:c.1523del	p.Gly508ValfsTer197	p.G508Vfs*197	ENST00000262320	NM_003502.3	508	gGt/gt	6/11	1	2	FACETS	0.881	0.828	0.935	0.881	0.828	0.935	CLONAL	1	TRUE	1	0.613443885034683	2		880	1029	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800902	120800903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs748469666	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	331	1014	2	ENST00000257552.2:c.345dup	p.Leu116AlafsTer15	p.L116Afs*15	ENST00000257552	NM_002442.3	115	-/G	6/15	1	2	FACETS	0.883	0.834	0.933	0.883	0.834	0.933	CLONAL	1	TRUE	1	0.613443885034683	2		1016	1222	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11175503	11175503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	179	632	0	ENST00000361445.4:c.7039G>A	p.Asp2347Asn	p.D2347N	ENST00000361445	NM_004958.3	2347	Gac/Aac	51/58	1	2	FACETS	0.896	0.83	0.965	0.896	0.83	0.965	CLONAL	1	TRUE	1	0.613443885034683	2		632	651	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	139	504	0	ENST00000324856.7:c.5547_5548dup	p.Asp1850GlyfsTer34	p.D1850Gfs*34	ENST00000324856	NM_006015.4	1847	-/GG	20/20	1	2	FACETS	0.764	0.698	0.833	0.764	0.698	0.833	SUBCLONAL	1	TRUE	1	0.613443885034683	2		504	593	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248391	59248391	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	103	246	0	ENST00000371222.2:c.352C>A	p.Leu118Met	p.L118M	ENST00000371222	NM_002228.3	118	Ctg/Atg	1/1	1	2	FACETS	0.938	0.848	1	0.938	0.848	1	CLONAL	1	TRUE	1	0.613443885034683	2		246	358	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851324	156851324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759637817	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	249	776	0	ENST00000524377.1:c.2281C>T	p.Arg761Trp	p.R761W	ENST00000524377	NM_002529.3	761	Cgg/Tgg	17/17	1	2	FACETS	0.99	0.929	1	0.99	0.929	1	CLONAL	1	TRUE	1	0.613443885034683	2		776	820	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720666	89720666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	100	419	0	ENST00000371953.3:c.820del	p.Trp274GlyfsTer2	p.W274Gfs*2	ENST00000371953	NM_000314.4	273	Ttt/tt	8/9	1	2	FACETS	0.874	0.787	0.964	0.874	0.787	0.964	CLONAL	1	TRUE	1	0.613443885034683	2		419	373	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154242	2154242	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755455183	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	215	735	3	ENST00000434045.2:c.686del	p.Pro229GlnfsTer27	p.P229Qfs*27	ENST00000434045	NM_001127598.1	229	cCa/ca	5/5	1	2	FACETS	0.856	0.797	0.916	0.856	0.797	0.916	CLONAL	1	TRUE	1	0.613443885034683	2		738	819	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999713	100999713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	287	957	0	ENST00000325455.5:c.89G>A	p.Arg30His	p.R30H	ENST00000325455	NM_001202474.3	30	cGc/cAc	1/8	1	2	FACETS	0.919	0.865	0.974	0.919	0.865	0.974	CLONAL	1	TRUE	1	0.613443885034683	2		957	1018	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431874	49431874	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	275	843	7	ENST00000301067.7:c.9265del	p.Val3089TrpfsTer30	p.V3089Wfs*30	ENST00000301067	NM_003482.3	3089	Gtg/tg	34/54	1	2	FACETS	0.893	0.839	0.948	0.893	0.839	0.948	CLONAL	1	TRUE	1	0.613443885034683	2		850	1004	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	267	749	9	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	0.166712496375742	6	FACETS	0.81	0.759	0.863			1	INDETERMINATE	2	TRUE	NA	0.613443885034683	6		758	1196	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32971082	32971082	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	39	719	0	ENST00000380152.3:c.9549A>G	p.Ile3183Met	p.I3183M	ENST00000380152		3183	atA/atG	26/27	1	2	FACETS	0.223	0.185	0.267	0.223	0.185	0.267	SUBCLONAL	1	TRUE	1	0.613443885034683	2		719	569	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43730569	43730569	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	61	775	0	ENST00000382044.4:c.3144G>T	p.Arg1048Ser	p.R1048S	ENST00000382044	NM_001141980.1	1048	agG/agT	16/28	1	2	FACETS	0.211	0.181	0.244	0.211	0.181	0.244	SUBCLONAL	1	TRUE	1	0.613443885034683	2		775	941	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99452055	99452055	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	188	556	0	ENST00000268035.6:c.1389G>T	p.Glu463Asp	p.E463D	ENST00000268035	NM_000875.3	463	gaG/gaT	6/21	1	2	FACETS	0.882	0.818	0.948	0.882	0.818	0.948	CLONAL	1	TRUE	1	0.613443885034683	2		556	695	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396590	396590	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	254	664	1	ENST00000262320.3:c.436C>T	p.Arg146Ter	p.R146*	ENST00000262320	NM_003502.3	146	Cga/Tga	2/11	1	2	FACETS	0.999	0.938	1	0.999	0.938	1	CLONAL	1	TRUE	1	0.613443885034683	2		665	829	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274214	10274214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768469157	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	115	360	1	ENST00000330684.3:c.55C>T	p.Arg19Cys	p.R19C	ENST00000330684	NM_001134407.1	19	Cgc/Tgc	2/13	1	2	FACETS	0.862	0.782	0.945	0.862	0.782	0.945	CLONAL	1	TRUE	1	0.613443885034683	2		361	435	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979022	7979022	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	286	695	2	ENST00000319144.4:c.1545G>T	p.Glu515Asp	p.E515D	ENST00000319144	NM_001139.2	515	gaG/gaT	12/15	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.613443885034683	2		697	929	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989613	15989613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	89	282	0	ENST00000268712.3:c.3160G>A	p.Gly1054Arg	p.G1054R	ENST00000268712	NM_006311.3	1054	Gga/Aga	23/46	1	2	FACETS	0.915	0.82	1	0.915	0.82	1	CLONAL	1	TRUE	1	0.613443885034683	2		282	317	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	137	471	14	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	1	2	FACETS	0.83	0.759	0.904	0.83	0.759	0.904	CLONAL	1	TRUE	1	0.613443885034683	2		485	538	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663368	29663370	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	160	521	0	ENST00000356175.3:c.5964_5966del	p.Val1989del	p.V1989del	ENST00000356175	NM_000267.3	1987	gaTGTt/gat	40/57	1	2	FACETS	0.957	0.883	1	0.957	0.883	1	CLONAL	1	TRUE	1	0.613443885034683	2		521	545	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33430316	33430316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28363283	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	293	804	1	ENST00000345365.6:c.695G>A	p.Arg232Gln	p.R232Q	ENST00000345365	NM_002878.3	232	cGa/cAa	8/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.613443885034683	2		805	943	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873699	37873699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766029214	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	301	796	1	ENST00000269571.5:c.1864G>A	p.Ala622Thr	p.A622T	ENST00000269571		622	Gca/Aca	15/27	1	2	FACETS	0.912	0.86	0.966	0.912	0.86	0.966	CLONAL	1	TRUE	1	0.613443885034683	2		797	1076	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244787	41244787	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs80357377	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	262	892	2	ENST00000357654.3:c.2761C>T	p.Gln921Ter	p.Q921*	ENST00000357654	NM_007294.3	921	Cag/Tag	10/23	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.613443885034683	2		894	833	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245587	41245587	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357522	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	233	794	2	ENST00000357654.3:c.1961del	p.Lys654SerfsTer47	p.K654Sfs*47	ENST00000357654	NM_007294.3	654	aAg/ag	10/23	1	2	FACETS	0.863	0.806	0.922	0.863	0.806	0.922	CLONAL	1	TRUE	1	0.613443885034683	2		796	880	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805588	46805588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201428095	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	325	1002	0	ENST00000290295.7:c.368G>A	p.Arg123His	p.R123H	ENST00000290295	NM_006361.5	123	cGc/cAc	1/2	1	2	FACETS	0.868	0.819	0.917	0.868	0.819	0.917	CLONAL	1	TRUE	1	0.613443885034683	2		1002	1221	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609380	39609380	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1370548557	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	136	526	0	ENST00000262039.4:c.1682G>A	p.Arg561His	p.R561H	ENST00000262039	NM_002647.2	561	cGc/cAc	15/25	1	2	FACETS	0.687	0.627	0.751	0.687	0.627	0.751	SUBCLONAL	1	TRUE	1	0.613443885034683	2		526	645	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245976	5245976	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	249	732	0	ENST00000357368.4:c.799G>A	p.Val267Met	p.V267M	ENST00000357368	NM_002850.3	267	Gtg/Atg	10/38	1	2	FACETS	0.927	0.868	0.986	0.927	0.868	0.986	CLONAL	1	TRUE	1	0.613443885034683	2		732	876	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123790	11123790	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	233	596	0	ENST00000358026.2:c.2438+2T>C		p.X813_splice	ENST00000358026	NM_001128849.1	813			1	2	FACETS	0.933	0.873	0.995	0.933	0.873	0.995	CLONAL	1	TRUE	1	0.613443885034683	2		596	814	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132635	11132635	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	286	851	2	ENST00000358026.2:c.2854del	p.Glu952LysfsTer5	p.E952Kfs*5	ENST00000358026	NM_001128849.1	951	Ggg/gg	19/36	1	2	FACETS	0.913	0.859	0.968	0.913	0.859	0.968	CLONAL	1	TRUE	1	0.613443885034683	2		853	1021	SUCCESS
CALR	811	MSKCC	GRCh37	19	13049552	13049552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	248	628	0	ENST00000316448.5:c.59C>T	p.Ala20Val	p.A20V	ENST00000316448	NM_004343.3	20	gCc/gTc	1/9	1	2	FACETS	0.938	0.879	0.998	0.938	0.879	0.998	CLONAL	1	TRUE	1	0.613443885034683	2		628	862	SUCCESS
AXL	558	MSKCC	GRCh37	19	41737136	41737136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761251235	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	89	996	6	ENST00000301178.4:c.716C>T	p.Thr239Met	p.T239M	ENST00000301178	NM_021913.4	239	aCg/aTg	6/20	1	2	FACETS	0.239	0.211	0.269	0.239	0.211	0.269	SUBCLONAL	1	TRUE	1	0.613443885034683	2		1002	1215	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39214651	39214651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	176	663	0	ENST00000402219.2:c.3473G>A	p.Arg1158Gln	p.R1158Q	ENST00000402219	NM_005633.3	1158	cGa/cAa	22/23	1	2	FACETS	0.761	0.702	0.822	0.761	0.702	0.822	SUBCLONAL	1	TRUE	1	0.613443885034683	2		663	754	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646085	215646085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	197	694	1	ENST00000260947.4:c.513del	p.Asp172MetfsTer40	p.D172Mfs*40	ENST00000260947	NM_000465.2	171	aaA/aa	4/11	1	2	FACETS	0.855	0.794	0.918	0.855	0.794	0.918	CLONAL	1	TRUE	1	0.613443885034683	2		695	751	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24129373	24129373	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	200	409	0	ENST00000263121.7:c.17T>C	p.Leu6Pro	p.L6P	ENST00000263121	NM_003073.3	6	cTg/cCg	1/9	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.613443885034683	2		409	582	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091740	29091740	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200649225	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	139	347	0	ENST00000328354.6:c.1217G>A	p.Arg406His	p.R406H	ENST00000328354	NM_007194.3	406	cGt/cAt	11/15	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.613443885034683	2		347	444	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665096	138665096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758370933	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	24	414	0	ENST00000330315.3:c.469C>T	p.Pro157Ser	p.P157S	ENST00000330315	NM_023067.3	157	Ccc/Tcc	1/1	1	2	FACETS	0.186	0.145	0.233	0.186	0.145	0.233	SUBCLONAL	1	TRUE	1	0.613443885034683	2		414	420	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803121	1803121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745863884	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	291	889	1	ENST00000260795.2:c.473G>A	p.Arg158Gln	p.R158Q	ENST00000260795		158	cGg/cAg	4/17	1	2	FACETS	0.942	0.887	0.998	0.942	0.887	0.998	CLONAL	1	TRUE	1	0.613443885034683	2		890	1007	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55597561	55597561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751005114	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	137	588	1	ENST00000288135.5:c.2209G>A	p.Asp737Asn	p.D737N	ENST00000288135	NM_000222.2	737	Gac/Aac	15/21	1	2	FACETS	0.777	0.71	0.847	0.777	0.71	0.847	SUBCLONAL	1	TRUE	1	0.613443885034683	2		589	575	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	231	630	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.912	0.852	0.973	0.912	0.852	0.973	CLONAL	1	TRUE	1	0.613443885034683	2		631	826	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294664	1294665	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1060502990	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	57	331	2	ENST00000310581.5:c.336dup	p.Glu113ArgfsTer79	p.E113Rfs*79	ENST00000310581	NM_198253.2	112	-/C	2/16	1	2	FACETS	0.506	0.436	0.582	0.506	0.436	0.582	SUBCLONAL	1	TRUE	1	0.613443885034683	2		333	367	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589576	67589576	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1289537429	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	100	542	1	ENST00000274335.5:c.1344del	p.Lys448AsnfsTer32	p.K448Nfs*32	ENST00000274335		447	Aaa/aa	10/15	1	2	FACETS	0.863	0.777	0.952	0.863	0.777	0.952	CLONAL	1	TRUE	1	0.613443885034683	2		543	378	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170814986	170814986	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	128	363	0	ENST00000296930.5:c.34C>A	p.Leu12Met	p.L12M	ENST00000296930	NM_002520.6	12	Ctg/Atg	1/11	1	2	FACETS	0.864	0.788	0.943	0.864	0.788	0.943	CLONAL	1	TRUE	1	0.613443885034683	2		363	483	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047941	180047941	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs184409663	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	303	926	0	ENST00000261937.6:c.2234G>A	p.Arg745His	p.R745H	ENST00000261937	NM_182925.4	745	cGc/cAc	15/30	1	2	FACETS	0.943	0.889	0.997	0.943	0.889	0.997	CLONAL	1	TRUE	1	0.613443885034683	2		926	1048	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057641	180057641	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	291	934	0	ENST00000261937.6:c.314A>G	p.Asp105Gly	p.D105G	ENST00000261937	NM_182925.4	105	gAc/gGc	3/30	1	2	FACETS	0.865	0.814	0.917	0.865	0.814	0.917	CLONAL	1	TRUE	1	0.613443885034683	2		934	1097	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015839	112015839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1364706330	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	236	667	0	ENST00000368678.4:c.1102G>A	p.Ala368Thr	p.A368T	ENST00000368678		368	Gca/Aca	10/13	1	2	FACETS	0.943	0.882	1	0.943	0.882	1	CLONAL	1	TRUE	1	0.613443885034683	2		667	816	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559284	141559284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	256	728	1	ENST00000220592.5:c.1517G>A	p.Arg506Gln	p.R506Q	ENST00000220592	NM_012154.3	506	cGg/cAg	12/19	0.583215619156719	1	FACETS	0.939	0.886	0.993	0.939	0.886	0.993	CLONAL	1	TRUE	0	0.613443885034683	1		729	616	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396277	139396277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878855028	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	79	915	3	ENST00000277541.6:c.5561G>A	p.Arg1854His	p.R1854H	ENST00000277541	NM_017617.3	1854	cGc/cAc	30/34	1	2	FACETS	0.245	0.215	0.278	0.245	0.215	0.278	SUBCLONAL	1	TRUE	1	0.613443885034683	2		918	1051	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399278	139399278	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778271353	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	70	852	3	ENST00000277541.6:c.4865G>A	p.Arg1622His	p.R1622H	ENST00000277541	NM_017617.3	1622	cGc/cAc	26/34	1	2	FACETS	0.218	0.189	0.249	0.218	0.189	0.249	SUBCLONAL	1	TRUE	1	0.613443885034683	2		855	1048	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139818403	139818403	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	63	732	0	ENST00000247668.2:c.1238T>C	p.Val413Ala	p.V413A	ENST00000247668	NM_021138.3	413	gTg/gCg	10/11	1	2	FACETS	0.212	0.182	0.244	0.212	0.182	0.244	SUBCLONAL	1	TRUE	1	0.613443885034683	2		732	969	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410472	63410472	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	229	610	3	ENST00000330258.3:c.2695G>A	p.Ala899Thr	p.A899T	ENST00000330258	NM_152424.3	899	Gca/Aca	2/2	1	2	FACETS	0.997	0.932	1	0.997	0.932	1	CLONAL	1	TRUE	1	0.613443885034683	2		613	749	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720648	89720649	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TA	TA	-	novel	NA	P-0018374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	46	463	0	ENST00000371953.3:c.802-3_802-2del		p.X268_splice	ENST00000371953	NM_000314.4	268			1	2	FACETS	0.386	0.325	0.452	0.386	0.325	0.452	SUBCLONAL	1	TRUE	1	0.613443885034683	2		463	389	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0018377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	11	823	1	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	1	2	FACETS	0.308	0.212	0.427	0.308	0.212	0.427	SUBCLONAL	1	TRUE	1	0.258025657810558	2		824	277	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490291	29490291	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	18	567	2	ENST00000356175.3:c.376G>T	p.Glu126Ter	p.E126*	ENST00000356175	NM_000267.3	126	Gaa/Taa	4/57	0.258025657810558	1	FACETS	0.459	0.345	0.592	0.459	0.345	0.592	SUBCLONAL	1	TRUE	0	0.258025657810558	1		569	265	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727847	41727847	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	43	912	0	ENST00000301178.4:c.472C>G	p.Leu158Val	p.L158V	ENST00000301178	NM_021913.4	158	Ctg/Gtg	4/20	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.258025657810558	2		912	301	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984911	55984911	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	36	660	0	ENST00000263923.4:c.218G>T	p.Arg73Met	p.R73M	ENST00000263923	NM_002253.2	73	aGg/aTg	3/30	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.258025657810558	2		660	243	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840002	27840002	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	11	364	0	ENST00000328488.2:c.92C>G	p.Pro31Arg	p.P31R	ENST00000328488	NM_003533.2	31	cCg/cGg	1/1	0.215734512025749	4	FACETS	0.777	0.539	1	0.259	0.179	0.357	CLONAL	1	TRUE	1	0.258025657810558	4		364	138	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974696	21974697	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	90	498	0	ENST00000304494.5:c.130dup	p.Tyr44LeufsTer76	p.Y44Lfs*76	ENST00000304494	NM_000077.4	44	tac/tTac	1/3	0.207773930243268	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.234755756355877	2		498	336	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477837	140477851	+	inframe_deletion	In_Frame_Del	DEL	TAGGTGCTGTCACAT	TAGGTGCTGTCACAT	-	novel	NA	P-0018378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	69	701	0	ENST00000288602.6:c.1457_1471del	p.Asn486_Pro490del	p.N486_P490del	ENST00000288602	NM_004333.4	486	aATGTGACAGCACCTAca/aca	12/18	0.178954846513801	4	FACETS	1	0.957	1	0.618	0.539	0.704	CLONAL	1	TRUE	2	0.234755756355877	4		701	587	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400932	72400932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	47	665	0	ENST00000357731.5:c.239C>T	p.Ala80Val	p.A80V	ENST00000357731	NM_173808.2	80	gCg/gTg	2/7	0.211663937276712	3	FACETS	0.781	0.658	0.916	0.39	0.329	0.458	CLONAL	1	TRUE	1	0.234755756355877	3		665	573	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248525	59248525	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	49	598	0	ENST00000371222.2:c.218C>A	p.Ser73Ter	p.S73*	ENST00000371222	NM_002228.3	73	tCg/tAg	1/1	0.211663937276712	3	FACETS	0.997	0.845	1	0.498	0.422	0.582	CLONAL	1	TRUE	1	0.234755756355877	3		598	468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576926	7576927	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GC	GC	AA	novel	NA	P-0018378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	80	573	1	ENST00000269305.4:c.920-1_920delinsTT		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	0.207773930243268	2	FACETS	0.798	0.706	0.896	0.798	0.706	0.896	SUBCLONAL	2	TRUE	0	0.234755756355877	2		574	427	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256677	19256677	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	72	702	0	ENST00000162023.5:c.1036T>G	p.Ser346Ala	p.S346A	ENST00000162023		346	Tcc/Gcc	13/13	1	2	FACETS	0.954	0.833	1	0.954	0.833	1	CLONAL	1	TRUE	1	0.234755756355877	2		702	643	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293800	1293800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370887827	NA	P-0018378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	102	953	4	ENST00000310581.5:c.1201G>A	p.Ala401Thr	p.A401T	ENST00000310581	NM_198253.2	401	Gcg/Acg	2/16	0.211663937276712	3	FACETS	1	0.927	1	0.524	0.468	0.584	CLONAL	1	TRUE	1	0.234755756355877	3		957	926	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0018380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	352	777	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.416094011944949	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.416094011944949	1		777	916	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	116	407	0	ENST00000397062.3:c.92G>A	p.Gly31Glu	p.G31E	ENST00000397062	NM_006164.4	31	gGa/gAa	2/5	0.214965552770888	1	FACETS	0.745	0.673	0.82	0.745	0.673	0.82	INDETERMINATE	1	TRUE	0	0.416094011944949	1		407	593	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825358	134825358	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	125	508	0	ENST00000398015.3:c.874C>G	p.Arg292Gly	p.R292G	ENST00000398015	NM_004441.4	292	Cgc/Ggc	4/16	0.416094011944949	1	FACETS	0.983	0.895	1	0.983	0.895	1	CLONAL	1	TRUE	0	0.416094011944949	1		508	484	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373700	118373700	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1414055420	NA	P-0018380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	54	604	0	ENST00000534358.1:c.7093A>G	p.Lys2365Glu	p.K2365E	ENST00000534358	NM_005933.3	2365	Aaa/Gaa	27/36	0.216745540437759	2	FACETS	0.303	0.257	0.352	0.151	0.128	0.176	INDETERMINATE	1	TRUE	0	0.416094011944949	2		604	858	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488222	56488222	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	243	576	0	ENST00000267101.3:c.1741G>C	p.Asp581His	p.D581H	ENST00000267101	NM_001982.3	581	Gat/Cat	15/28	0.341914600445478	2	FACETS	0.846	0.795	0.899	0.846	0.795	0.899	CLONAL	2	TRUE	0	0.416094011944949	2		576	690	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493482	56493482	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	256	583	0	ENST00000267101.3:c.2890G>C	p.Glu964Gln	p.E964Q	ENST00000267101	NM_001982.3	964	Gag/Cag	24/28	0.341914600445478	2	FACETS	0.797	0.749	0.846	0.797	0.749	0.846	SUBCLONAL	2	TRUE	0	0.416094011944949	2		583	772	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982365	25982365	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	94	261	0	ENST00000435504.4:c.925G>C	p.Glu309Gln	p.E309Q	ENST00000435504		309	Gag/Cag	9/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.416094011944949	2		261	401	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273282	198273282	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	74	628	0	ENST00000335508.6:c.928T>C	p.Trp310Arg	p.W310R	ENST00000335508	NM_012433.2	310	Tgg/Cgg	8/25	0.214965552770888	1	FACETS	0.386	0.337	0.438	0.386	0.337	0.438	INDETERMINATE	1	TRUE	0	0.416094011944949	1		628	730	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163671	32163671	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1257471825	NA	P-0018380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	123	378	0	ENST00000375023.3:c.5555del	p.Pro1852ArgfsTer33	p.P1852Rfs*33	ENST00000375023	NM_004557.3	1852	cCg/cg	30/30	NA	2	FACETS	0.968	0.878	1			1	INDETERMINATE	1	TRUE	NA	0.416094011944949	2		378	611	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37141760	37141760	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	70	731	0	ENST00000373509.5:c.835C>A	p.Pro279Thr	p.P279T	ENST00000373509	NM_002648.3	279	Cca/Aca	6/6	NA	2	FACETS	0.364	0.316	0.415			1	INDETERMINATE	1	TRUE	NA	0.416094011944949	2		731	925	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877127	151877127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs13231116	NA	P-0018380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	123	393	0	ENST00000262189.6:c.7234C>T	p.Pro2412Ser	p.P2412S	ENST00000262189	NM_170606.2	2412	Ccc/Tcc	37/59	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.416094011944949	2		393	551	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410079	63410079	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	134	593	0	ENST00000330258.3:c.3088A>T	p.Met1030Leu	p.M1030L	ENST00000330258	NM_152424.3	1030	Atg/Ttg	2/2	0.416094011944949	1	FACETS	0.787	0.717	0.861	0.787	0.717	0.861	SUBCLONAL	1	TRUE	0	0.416094011944949	1		593	648	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0018381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	126	744	2	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.185656529753848	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.187816536026365	2		746	554	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0018381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	67	715	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.175889177518037	4	FACETS	0.898	0.782	1	0.898	0.782	1	CLONAL	2	TRUE	2	0.187816536026365	4		717	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0018381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	82	1017	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.185742706649165	2	FACETS	0.957	0.848	1	0.957	0.848	1	CLONAL	2	TRUE	0	0.187816536026365	2		1018	456	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981888	201981888	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1340293456	NA	P-0018381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	105	960	0	ENST00000359651.3:c.598+1G>A		p.X200_splice	ENST00000359651		200			0.175889177518037	4	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	2	0.187816536026365	4		960	632	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940516	71940516	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	43	618	0	ENST00000298229.2:c.667G>A	p.Asp223Asn	p.D223N	ENST00000298229	NM_001567.3	223	Gac/Aac	6/28	0.187816536026365	3	FACETS	1	0.904	1	0.558	0.467	0.658	CLONAL	1	TRUE	1	0.187816536026365	3		618	449	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961187	41961187	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	34	538	1	ENST00000219905.7:c.95G>T	p.Gly32Val	p.G32V	ENST00000219905	NM_001164273.1	32	gGa/gTa	2/24	1	2	FACETS	0.921	0.753	1	0.921	0.753	1	CLONAL	1	TRUE	1	0.187816536026365	2		539	393	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799242	88799242	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	46	812	0	ENST00000360948.2:c.143C>T	p.Pro48Leu	p.P48L	ENST00000360948	NM_001012338.2	48	cCg/cTg	2/19	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.187816536026365	2		812	443	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30302682	30302682	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	24	806	0	ENST00000322652.5:c.773G>T	p.Gly258Val	p.G258V	ENST00000322652	NM_015355.2	258	gGa/gTa	7/16	0.187816536026365	3	FACETS	0.638	0.499	0.799	0.319	0.249	0.4	SUBCLONAL	1	TRUE	1	0.187816536026365	3		806	438	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223081	41223081	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	52	785	0	ENST00000357654.3:c.4850C>G	p.Ala1617Gly	p.A1617G	ENST00000357654	NM_007294.3	1617	gCt/gGt	15/23	0.187816536026365	3	FACETS	1	0.856	1	0.503	0.428	0.586	CLONAL	1	TRUE	1	0.187816536026365	3		785	602	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223270	5223270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759604875	NA	P-0018381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	44	743	1	ENST00000357368.4:c.2533G>A	p.Glu845Lys	p.E845K	ENST00000357368	NM_002850.3	845	Gag/Aag	18/38	0.185742706649165	2	FACETS	1	0.921	1	0.581	0.488	0.684	CLONAL	1	TRUE	0	0.187816536026365	2		744	403	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858976	45858976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757432268	NA	P-0018381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	66	775	0	ENST00000391945.4:c.1490G>A	p.Arg497His	p.R497H	ENST00000391945	NM_000400.3	497	cGt/cAt	16/23	0.187816536026365	3	FACETS	0.818	0.712	0.932	0.818	0.712	0.932	CLONAL	2	TRUE	1	0.187816536026365	3		775	470	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39751920	39751920	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	23	601	0	ENST00000361337.2:c.2281G>T	p.Glu761Ter	p.E761*	ENST00000361337	NM_003286.2	761	Gaa/Taa	21/21	0.175889177518037	4	FACETS	0.72	0.561	0.905	0.36	0.28	0.453	CLONAL	1	TRUE	2	0.187816536026365	4		601	404	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288119	21288119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148491827	NA	P-0018381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	29	681	0	ENST00000354336.3:c.364G>A	p.Glu122Lys	p.E122K	ENST00000354336	NM_005207.3	122	Gaa/Aaa	2/3	0.187816536026365	3	FACETS	0.746	0.598	0.914	0.373	0.299	0.457	CLONAL	1	TRUE	1	0.187816536026365	3		681	453	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447785	187447785	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	47	448	0	ENST00000232014.4:c.408C>G	p.Ile136Met	p.I136M	ENST00000232014	NM_001130845.1	136	atC/atG	5/10	0.175889177518037	4	FACETS	0.774	0.655	0.905	0.774	0.655	0.905	CLONAL	2	TRUE	2	0.187816536026365	4		448	384	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538900	187538901	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	48	422	0	ENST00000441802.2:c.8839dup	p.Ser2947PhefsTer2	p.S2947Ffs*2	ENST00000441802	NM_005245.3	2947	tct/tTct	10/27	0.185656529753848	2	FACETS	0.801	0.681	0.932	0.801	0.681	0.932	CLONAL	2	TRUE	0	0.187816536026365	2		422	319	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913212	39913212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367883774	NA	P-0018381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	39	730	1	ENST00000378444.4:c.4903G>A	p.Asp1635Asn	p.D1635N	ENST00000378444	NM_001123385.1	1635	Gat/Aat	14/15	1	2	FACETS	0.871	0.721	1	0.871	0.721	1	CLONAL	1	TRUE	1	0.187816536026365	2		731	477	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429978	78429978	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	28	607	3	ENST00000370768.2:c.901del	p.Ile301TyrfsTer22	p.I301Yfs*22	ENST00000370768	NM_003902.3	301	Ata/ta	11/20	1	2	FACETS	0.192	0.153	0.237	0.192	0.153	0.237	SUBCLONAL	1	TRUE	1	0.597577842553938	2		610	487	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	127	566	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.597577842553938	2		566	397	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738411	145738416	+	inframe_deletion	In_Frame_Del	DEL	GGTGCA	GGTGCA	-	rs548804317	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	30	658	0	ENST00000428558.2:c.2569_2574del	p.Cys857_Thr858del	p.C857_T858del	ENST00000428558	NM_004260.3	857	TGCACC/-	16/22	0.580916732282809	3	FACETS	0.265	0.212	0.324	0.132	0.106	0.162	SUBCLONAL	1	TRUE	1	0.597577842553938	3		658	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	212	949	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.963	0.897	1	0.963	0.897	1	CLONAL	1	TRUE	1	0.597577842553938	2		949	737	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	165	468	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.597577842553938	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.597577842553938	1		468	296	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	163	699	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	0.597577842553938	2		699	436	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	208	877	2	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.597577842553938	2		879	682	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141426	11141426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	126	754	0	ENST00000358026.2:c.3403C>T	p.Arg1135Trp	p.R1135W	ENST00000358026	NM_001128849.1	1135	Cgg/Tgg	25/36	1	2	FACETS	0.919	0.838	1	0.919	0.838	1	CLONAL	1	TRUE	1	0.597577842553938	2		754	459	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	329	810	4	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	0.597577842553938	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.597577842553938	1		814	535	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	192	574	3	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.597577842553938	2		577	522	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	192	797	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.597577842553938	2		797	614	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	121	858	13	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.967	0.88	1	0.967	0.88	1	CLONAL	1	TRUE	1	0.597577842553938	2		871	419	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278099	15278099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139983430	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	126	740	1	ENST00000263388.2:c.5323G>A	p.Ala1775Thr	p.A1775T	ENST00000263388	NM_000435.2	1775	Gca/Aca	29/33	1	2	FACETS	0.988	0.902	1	0.988	0.902	1	CLONAL	1	TRUE	1	0.597577842553938	2		741	427	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	133	583	11	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.597577842553938	2		594	436	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722927	49722927	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776261411	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	58	373	0	ENST00000449682.2:c.1400C>T	p.Pro467Leu	p.P467L	ENST00000449682	NM_020998.3	467	cCg/cTg	12/18	1	2	FACETS	0.87	0.758	0.99	0.87	0.758	0.99	CLONAL	1	TRUE	1	0.597577842553938	2		373	223	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276860	15276861	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs753725730	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	126	701	2	ENST00000263388.2:c.5404dup	p.Ala1802GlyfsTer8	p.A1802Gfs*8	ENST00000263388	NM_000435.2	1802	gct/gGct	30/33	1	2	FACETS	0.935	0.853	1	0.935	0.853	1	CLONAL	1	TRUE	1	0.597577842553938	2		703	451	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749400	41749400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1302196737	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	51	363	0	ENST00000226382.2:c.395C>T	p.Ala132Val	p.A132V	ENST00000226382	NM_003924.3	132	gCc/gTc	2/3	1	2	FACETS	0.841	0.724	0.965	0.841	0.724	0.965	CLONAL	1	TRUE	1	0.597577842553938	2		363	203	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830441	72830441	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	21	348	0	ENST00000268489.5:c.6140del	p.Pro2047LeufsTer54	p.P2047Lfs*54	ENST00000268489	NM_006885.3	2047	cCt/ct	9/10	1	2	FACETS	0.451	0.35	0.566	0.451	0.35	0.566	SUBCLONAL	1	TRUE	1	0.597577842553938	2		348	156	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280068	66280068	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	59	388	0	ENST00000273854.3:c.1621C>T	p.Arg541Ter	p.R541*	ENST00000273854	NM_004439.5	541	Cga/Tga	7/18	1	2	FACETS	0.898	0.783	1	0.898	0.783	1	CLONAL	1	TRUE	1	0.597577842553938	2		388	220	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332471	70332471	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	155	812	0	ENST00000373644.4:c.380del	p.Lys127ArgfsTer8	p.K127Rfs*8	ENST00000373644	NM_030625.2	126	Aaa/aa	2/12	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.597577842553938	2		812	516	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155778	106155779	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs759055581	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	31	508	0	ENST00000380013.4:c.685dup	p.Thr229AsnfsTer25	p.T229Nfs*25	ENST00000380013	NM_001127208.2	227	gaa/gAaa	3/11	1	2	FACETS	0.324	0.262	0.394	0.324	0.262	0.394	SUBCLONAL	1	TRUE	1	0.597577842553938	2		508	320	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403254	213403254	+	frameshift_variant,start_lost,start_retained_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	130	627	0	ENST00000342788.4:c.1del	p.Met1?	p.M1?	ENST00000342788	NM_005235.2	1	Atg/tg	1/28	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.597577842553938	2		627	401	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288550	15288550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	16	83	0	ENST00000263388.2:c.4189G>A	p.Gly1397Arg	p.G1397R	ENST00000263388	NM_000435.2	1397	Ggg/Agg	24/33	1	2	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	TRUE	1	0.597577842553938	2		83	47	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	203	874	2	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	0.580916732282809	3	FACETS	0.964	0.895	1	0.482	0.447	0.518	CLONAL	1	TRUE	1	0.597577842553938	3		876	915	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794917	42794917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199751904	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	110	650	1	ENST00000575354.2:c.1997G>A	p.Arg666His	p.R666H	ENST00000575354	NM_015125.3	666	cGt/cAt	10/20	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.597577842553938	2		651	356	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11318590	11318590	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	135	673	0	ENST00000361445.4:c.223G>A	p.Val75Ile	p.V75I	ENST00000361445	NM_004958.3	75	Gtt/Att	3/58	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.597577842553938	2		673	424	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245461	16245461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465789087	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	95	553	1	ENST00000375759.3:c.1436C>T	p.Ala479Val	p.A479V	ENST00000375759	NM_015001.2	479	gCg/gTg	7/15	1	2	FACETS	0.961	0.864	1	0.961	0.864	1	CLONAL	1	TRUE	1	0.597577842553938	2		554	331	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531733	46531733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	52	524	0	ENST00000262741.5:c.614C>T	p.Thr205Ile	p.T205I	ENST00000262741	NM_003629.3	205	aCa/aTa	5/10	1	2	FACETS	0.487	0.417	0.565	0.487	0.417	0.565	SUBCLONAL	1	TRUE	1	0.597577842553938	2		524	357	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201924	67201924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1275806945	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	34	552	2	ENST00000312629.5:c.1124C>T	p.Ala375Val	p.A375V	ENST00000312629	NM_003952.2	375	gCc/gTc	13/15	1	2	FACETS	0.283	0.231	0.341	0.283	0.231	0.341	SUBCLONAL	1	TRUE	1	0.597577842553938	2		554	402	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939413	71939413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148394356	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	40	808	0	ENST00000298229.2:c.268C>T	p.Arg90Cys	p.R90C	ENST00000298229	NM_001567.3	90	Cgc/Tgc	3/28	1	2	FACETS	0.272	0.225	0.323	0.272	0.225	0.323	SUBCLONAL	1	TRUE	1	0.597577842553938	2		808	493	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870845	12870846	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	35	234	0	ENST00000228872.4:c.74dup	p.Pro26AlafsTer99	p.P26Afs*99	ENST00000228872	NM_004064.3	24	-/A	1/3	1	2	FACETS	0.756	0.629	0.894	0.756	0.629	0.894	SUBCLONAL	1	TRUE	1	0.597577842553938	2		234	155	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378660	25378660	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	76	561	0	ENST00000311936.3:c.338T>G	p.Leu113Arg	p.L113R	ENST00000311936	NM_004985.3	113	cTa/cGa	4/5	1	2	FACETS	0.686	0.605	0.771	0.686	0.605	0.771	SUBCLONAL	1	TRUE	1	0.597577842553938	2		561	371	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432374	49432374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757791539	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	132	732	2	ENST00000301067.7:c.8765G>A	p.Arg2922Gln	p.R2922Q	ENST00000301067	NM_003482.3	2922	cGg/cAg	34/54	1	2	FACETS	0.958	0.876	1	0.958	0.876	1	CLONAL	1	TRUE	1	0.597577842553938	2		734	461	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440127	49440127	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	156	698	2	ENST00000301067.7:c.4499C>A	p.Pro1500His	p.P1500H	ENST00000301067	NM_003482.3	1500	cCc/cAc	16/54	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.597577842553938	2		700	457	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912770	32912771	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs80359439	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	107	673	0	ENST00000380152.3:c.4284dup	p.Gln1429SerfsTer9	p.Q1429Sfs*9	ENST00000380152		1426	-/T	11/27	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.597577842553938	2		673	348	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504578	103504578	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	80	500	0	ENST00000355739.4:c.199T>A	p.Phe67Ile	p.F67I	ENST00000355739	NM_000123.3	67	Ttt/Att	2/15	1	2	FACETS	0.834	0.741	0.932	0.834	0.741	0.932	CLONAL	1	TRUE	1	0.597577842553938	2		500	321	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105238752	105238752	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	162	775	0	ENST00000349310.3:c.1210C>G	p.Gln404Glu	p.Q404E	ENST00000349310	NM_001014432.1	404	Cag/Gag	13/15	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.597577842553938	2		775	538	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041650	42041650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	114	641	0	ENST00000219905.7:c.5845C>T	p.Leu1949Phe	p.L1949F	ENST00000219905	NM_001164273.1	1949	Ctc/Ttc	17/24	1	2	FACETS	0.991	0.901	1	0.991	0.901	1	CLONAL	1	TRUE	1	0.597577842553938	2		641	385	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350488	89350488	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	245	1004	0	ENST00000301030.4:c.2462del	p.Asn821IlefsTer42	p.N821Ifs*42	ENST00000301030	NM_001256183.1	821	aAt/at	9/13	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.597577842553938	2		1004	716	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007551	62007551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751548429	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	151	740	0	ENST00000392795.3:c.316G>A	p.Ala106Thr	p.A106T	ENST00000392795	NM_001039933.1	106	Gcc/Acc	3/6	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.597577842553938	2		740	467	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39550298	39550298	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749558522	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	62	406	2	ENST00000262039.4:c.409C>T	p.Arg137Cys	p.R137C	ENST00000262039	NM_002647.2	137	Cgc/Tgc	4/25	1	2	FACETS	0.956	0.838	1	0.956	0.838	1	CLONAL	1	TRUE	1	0.597577842553938	2		408	217	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39613908	39613908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1159943667	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	99	603	0	ENST00000262039.4:c.1826C>T	p.Ala609Val	p.A609V	ENST00000262039	NM_002647.2	609	gCt/gTt	16/25	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.597577842553938	2		603	328	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222467	2222467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	140	696	0	ENST00000398665.3:c.3299G>A	p.Ser1100Asn	p.S1100N	ENST00000398665	NM_032482.2	1100	aGc/aAc	24/28	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.597577842553938	2		696	419	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881515	111881516	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	107	632	1	ENST00000393256.3:c.197dup	p.Pro67ThrfsTer34	p.P67Tfs*34	ENST00000393256	NM_006538.4	65	gcc/gCcc	2/4	1	2	FACETS	0.958	0.867	1	0.958	0.867	1	CLONAL	1	TRUE	1	0.597577842553938	2		633	374	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718716	190718716	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	88	676	0	ENST00000441310.2:c.874T>C	p.Tyr292His	p.Y292H	ENST00000441310	NM_000534.4	292	Tat/Cat	8/13	1	2	FACETS	0.713	0.635	0.795	0.713	0.635	0.795	SUBCLONAL	1	TRUE	1	0.597577842553938	2		676	413	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-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	87	353	0	ENST00000349496.5:c.53_448del		p.X18_splice	ENST00000349496	NM_001904.3	18	gaCAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCAAGATGATGCAGAACTTGCc/gac	3-4/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.597577842553938	2		353	219	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184615	185184615	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs151275315	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	103	401	2	ENST00000265026.3:c.1507C>T	p.Arg503Cys	p.R503C	ENST00000265026	NM_004721.4	503	Cgt/Tgt	10/14	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.597577842553938	2		403	331	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155402	106155403	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	101	569	0	ENST00000380013.4:c.311_312dup	p.Gly105LeufsTer9	p.G105Lfs*9	ENST00000380013	NM_001127208.2	101	-/TC	3/11	1	2	FACETS	0.924	0.833	1	0.924	0.833	1	CLONAL	1	TRUE	1	0.597577842553938	2		569	366	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637963	176637963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752093886	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	134	833	2	ENST00000439151.2:c.2563G>A	p.Ala855Thr	p.A855T	ENST00000439151	NM_022455.4	855	Gca/Aca	5/23	1	2	FACETS	0.956	0.875	1	0.956	0.875	1	CLONAL	1	TRUE	1	0.597577842553938	2		835	469	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124440	94124440	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	29	599	0	ENST00000369303.4:c.143T>G	p.Ile48Ser	p.I48S	ENST00000369303	NM_004440.3	48	aTt/aGt	2/17	1	2	FACETS	0.277	0.222	0.339	0.277	0.222	0.339	SUBCLONAL	1	TRUE	1	0.597577842553938	2		599	351	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864800	117864800	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs905123790	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	52	450	0	ENST00000297338.2:c.1309C>T	p.Arg437Cys	p.R437C	ENST00000297338	NM_006265.2	437	Cgt/Tgt	10/14	0.580916732282809	3	FACETS	0.621	0.531	0.719	0.31	0.265	0.36	SUBCLONAL	1	TRUE	1	0.597577842553938	3		450	364	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5465511	5465511	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747218330	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	45	277	1	ENST00000381577.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000381577	NM_014143.3	232	gCa/gTa	5/7	1	2	FACETS	0.765	0.651	0.887	0.765	0.651	0.887	SUBCLONAL	1	TRUE	1	0.597577842553938	2		278	197	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158026	27158026	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	175	872	0	ENST00000380036.4:c.255del	p.Val86LeufsTer31	p.V86Lfs*31	ENST00000380036	NM_000459.3	84	Aaa/aa	2/23	1	2	FACETS	0.914	0.845	0.985	0.914	0.845	0.985	CLONAL	1	TRUE	1	0.597577842553938	2		872	641	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750371	133750372	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	123	629	0	ENST00000318560.5:c.1206dup	p.Ile403HisfsTer42	p.I403Hfs*42	ENST00000318560	NM_005157.4	401	ttc/ttCc	7/11	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.597577842553938	2		629	410	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399348	139399348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543770603	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	175	801	0	ENST00000277541.6:c.4795G>A	p.Val1599Met	p.V1599M	ENST00000277541	NM_017617.3	1599	Gtg/Atg	26/34	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.597577842553938	2		801	476	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564734	139564735	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	154	1003	0	ENST00000308874.7:c.525_526del	p.Val177AlafsTer106	p.V177Afs*106	ENST00000308874		175	CTc/c	7/10	1	2	FACETS	0.972	0.896	1	0.972	0.896	1	CLONAL	1	TRUE	1	0.597577842553938	2		1003	530	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932867	39932867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747939351	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	39	475	0	ENST00000378444.4:c.1732G>A	p.Ala578Thr	p.A578T	ENST00000378444	NM_001123385.1	578	Gca/Aca	4/15	1	2	FACETS	0.441	0.367	0.523	0.441	0.367	0.523	SUBCLONAL	1	TRUE	1	0.597577842553938	2		475	296	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222487	53222487	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	26	747	0	ENST00000375401.3:c.4345C>T	p.Arg1449Trp	p.R1449W	ENST00000375401	NM_004187.3	1449	Cgg/Tgg	26/26	1	2	FACETS	0.192	0.151	0.238	0.192	0.151	0.238	SUBCLONAL	1	TRUE	1	0.597577842553938	2		747	454	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410921	63410921	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	117	808	2	ENST00000330258.3:c.2246C>A	p.Ser749Ter	p.S749*	ENST00000330258	NM_152424.3	749	tCa/tAa	2/2	1	2	FACETS	0.926	0.841	1	0.926	0.841	1	CLONAL	1	TRUE	1	0.597577842553938	2		810	423	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860003	152860003	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0018382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	58	403	0	ENST00000406277.2:c.423+2T>C		p.X141_splice	ENST00000406277	NM_152274.4	141			1		FACETS		0.931	1				CLONAL	1	TRUE	1	0.597577842553938	2		403	177	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACT	novel	NA	P-0018383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	118	607	0	ENST00000275493.2:c.2310_2311insTAC	p.Asp770_Asn771insTyr	p.D770_N771insY	ENST00000275493	NM_005228.3	770	gac/gACTac	20/28	0.27641325482395	3	FACETS	0.827	0.748	0.909	0.827	0.748	0.909	CLONAL	2	TRUE	1	0.280690730151117	3		607	580	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923494	9923494	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	39	631	0	ENST00000330684.3:c.1793del	p.Ser598PhefsTer56	p.S598Ffs*56	ENST00000330684	NM_001134407.1	598	tCt/tt	9/13	1	2	FACETS	0.489	0.405	0.584	0.489	0.405	0.584	SUBCLONAL	1	TRUE	1	0.280690730151117	2		631	568	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822058	72822058	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	16	300	0	ENST00000268489.5:c.10117G>C	p.Glu3373Gln	p.E3373Q	ENST00000268489	NM_006885.3	3373	Gag/Cag	10/10	1	2	FACETS	0.418	0.308	0.548	0.418	0.308	0.548	SUBCLONAL	1	TRUE	1	0.280690730151117	2		300	273	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634813	158634813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	33	491	1	ENST00000263640.3:c.373G>A	p.Gly125Ser	p.G125S	ENST00000263640	NM_001105.4	125	Ggc/Agc	5/11	0.0835197579643934	3	FACETS	0.481	0.391	0.584	0.241	0.195	0.292	INDETERMINATE	1	TRUE	1	0.280690730151117	3		492	557	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575468	67575468	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs143572224	NA	P-0018383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	48	471	1	ENST00000274335.5:c.541G>T	p.Val181Phe	p.V181F	ENST00000274335		181	Gtt/Ttt	4/15	1	2	FACETS	0.698	0.59	0.817	0.698	0.59	0.817	SUBCLONAL	1	TRUE	1	0.280690730151117	2		472	490	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0018385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	103	574	9	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.985	0.888	1	1	0.988	1	CLONAL	2	TRUE	1	0.258169603388786	2		583	405	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0018385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	15	779	2	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	0.258169603388786	2	FACETS	0.197	0.143	0.262	0.098	0.071	0.131	SUBCLONAL	1	TRUE	0	0.258169603388786	2		781	590	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850704	63850705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	117	594	0	ENST00000279873.7:c.1489dup	p.Ile497AsnfsTer31	p.I497Nfs*31	ENST00000279873	NM_032199.2	494	-/A	10/10	0.258169603388786	2	FACETS	1	0.983	1	0.723	0.653	0.796	CLONAL	1	TRUE	0	0.258169603388786	2		594	627	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247516	123247516	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519795	NA	P-0018385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	104	722	0	ENST00000358487.5:c.1975A>G	p.Lys659Glu	p.K659E	ENST00000358487	NM_000141.4	659	Aag/Gag	14/18	0.258169603388786	2	FACETS	1	0.94	1	0.536	0.48	0.595	CLONAL	1	TRUE	0	0.258169603388786	2		722	752	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088800	27088800	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0018385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	106	512	0	ENST00000324856.7:c.2409T>G	p.Tyr803Ter	p.Y803*	ENST00000324856	NM_006015.4	803	taT/taG	7/20	0.111675858097143	4	FACETS	0.988	0.889	1	0.988	0.889	1	INDETERMINATE	2	TRUE	2	0.258169603388786	4		512	523	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692818	89692820	+	frameshift_variant	Frame_Shift_Del	DEL	TCA	TCA	CC	novel	NA	P-0018385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	135	382	2	ENST00000371953.3:c.302_304delinsCC	p.Ile101ThrfsTer12	p.I101Tfs*12	ENST00000371953	NM_000314.4	101	aTCAaa/aCCaa	5/9	0.258169603388786	2	FACETS	0.886	0.82	0.953	1	0.991	1	CLONAL	4	TRUE	0	0.258169603388786	2		384	295	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349179	11349179	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	21	150	0	ENST00000332029.2:c.157A>T	p.Thr53Ser	p.T53S	ENST00000332029	NM_003745.1	53	Acg/Tcg	2/2	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.258169603388786	2		150	126	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250162	39250162	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	155	912	0	ENST00000402219.2:c.1407T>G	p.Ile469Met	p.I469M	ENST00000402219	NM_005633.3	469	atT/atG	10/23	1	2	FACETS	1	0.948	1	1	0.992	1	CLONAL	2	TRUE	1	0.258169603388786	2		912	577	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278407	39278407	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	102	818	0	ENST00000402219.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000402219	NM_005633.3	248	Cgc/Tgc	6/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.258169603388786	2		818	594	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0018386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	216	894	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.21657399004267	5	FACETS	1	0.98	1	0.847	0.79	0.906	CLONAL	3	TRUE	1	0.217241515248851	5		894	778	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259554	55259554	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs397517134	NA	P-0018386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	206	802	0	ENST00000275493.2:c.2612C>G	p.Ala871Gly	p.A871G	ENST00000275493	NM_005228.3	871	gCa/gGa	21/28	0.21657399004267	5	FACETS	0.878	0.818	0.94	0.878	0.818	0.94	CLONAL	4	TRUE	1	0.217241515248851	5		802	716	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578234	7578234	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0018386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	99	965	0	ENST00000269305.4:c.615T>G	p.Tyr205Ter	p.Y205*	ENST00000269305	NM_001126112.2	205	taT/taG	6/11	0.217241515248851	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.217241515248851	1		965	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0018387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	672	949	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.695604650320695	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.695604650320695	2		949	886	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0018387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	56	752	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.695604650320695	2	FACETS	0.29	0.248	0.335	0.145	0.124	0.168	SUBCLONAL	1	TRUE	0	0.695604650320695	2		754	556	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0018387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	124	393	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	0.695604650320695	2		393	350	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719199	61719199	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	44	699	0	ENST00000401558.2:c.1858A>T	p.Thr620Ser	p.T620S	ENST00000401558	NM_003400.3	620	Act/Tct	16/25	1	2	FACETS	0.228	0.191	0.269	0.228	0.191	0.269	SUBCLONAL	1	TRUE	1	0.695604650320695	2		699	555	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872182	76872183	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0018387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	141	373	0	ENST00000373344.5:c.5463_5464dup	p.Ala1822GlufsTer3	p.A1822Efs*3	ENST00000373344	NM_000489.3	1822	gca/gAGca	22/35	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.695604650320695	1		373	214	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939904	76939904	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	41	476	0	ENST00000373344.5:c.844del	p.Ser282AlafsTer6	p.S282Afs*6	ENST00000373344	NM_000489.3	282	Agc/gc	9/35	1	1	FACETS	0.206	0.171	0.244	0.206	0.171	0.244	SUBCLONAL	1	TRUE	0	0.695604650320695	1		476	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0018391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	191	745	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.384352795644828	2	FACETS	0.897	0.837	0.958	0.897	0.837	0.958	CLONAL	2	TRUE	0	0.423221628260544	2		746	503	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459340	99459340	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs45451896	NA	P-0018391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	46	370	0	ENST00000268035.6:c.1976G>C	p.Arg659Pro	p.R659P	ENST00000268035	NM_000875.3	659	cGg/cCg	9/21	0.423221628260544	3	FACETS	0.759	0.641	0.888	0.38	0.32	0.444	SUBCLONAL	1	TRUE	1	0.423221628260544	3		370	347	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0018392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	192	446	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.657974605887997	1	FACETS	0.928	0.87	0.987	0.928	0.87	0.987	CLONAL	1	TRUE	0	0.657974605887997	1		446	422	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0018392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	101	283	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	0.657974605887997	1	FACETS	0.949	0.868	1	0.949	0.868	1	CLONAL	1	TRUE	0	0.657974605887997	1		283	217	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577128	7577128	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519987	NA	P-0018392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	372	466	0	ENST00000269305.4:c.810T>G	p.Phe270Leu	p.F270L	ENST00000269305	NM_001126112.2	270	ttT/ttG	8/11	0.606733479781229	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.657974605887997	1		466	730	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557891	29557892	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	46	80	0	ENST00000356175.3:c.3147dup	p.Met1050TyrfsTer10	p.M1050Yfs*10	ENST00000356175	NM_000267.3	1049	gtt/gTtt	24/57	0.657974605887997	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.657974605887997	1		80	83	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0018393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	185	745	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.91	0.844	0.979	1	0.993	1	CLONAL	2	TRUE	1	0.312138496378278	2		746	651	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	235	364	1				ENST00000310581	NM_198253.2	-/1132			0.312138496378278	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	TRUE	1	0.312138496378278	4		365	626	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873200	71873200	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	122	375	0	ENST00000357731.5:c.994T>A	p.Cys332Ser	p.C332S	ENST00000357731	NM_173808.2	332	Tgc/Agc	7/7	0.312138496378278	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.312138496378278	1		375	522	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161293444	161293444	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	69	317	0	ENST00000367975.2:c.61C>T	p.Gln21Ter	p.Q21*	ENST00000367975	NM_003001.3	21	Cag/Tag	2/6	0.251828840268766	1	FACETS	0.68	0.592	0.774	0.68	0.592	0.774	SUBCLONAL	1	TRUE	0	0.312138496378278	1		317	549	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121530	2121530	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	128	541	0	ENST00000219476.3:c.1859T>A	p.Leu620Gln	p.L620Q	ENST00000219476	NM_000548.3	620	cTg/cAg	18/42	NA	2	FACETS	0.82	0.742	0.903			1	INDETERMINATE	1	TRUE	NA	0.312138496378278	2		541	1000	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527466	157527466	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	109	296	0	ENST00000346085.5:c.5191G>C	p.Glu1731Gln	p.E1731Q	ENST00000346085	NM_020732.3	1731	Gag/Cag	20/20	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.312138496378278	2		296	634	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931796	39931796	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	61	452	0	ENST00000378444.4:c.2803G>A	p.Val935Met	p.V935M	ENST00000378444	NM_001123385.1	935	Gtg/Atg	4/15	0.216858162306786	0	FACETS	0.376	0.324	0.433			1	SUBCLONAL	1	TRUE	0	0.312138496378278	0		452	715	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70353037	70353037	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	71	379	1	ENST00000374080.3:c.4592A>T	p.Glu1531Val	p.E1531V	ENST00000374080		1531	gAg/gTg	33/45	0.216858162306786	0	FACETS	0.481	0.419	0.547			1	SUBCLONAL	1	TRUE	0	0.312138496378278	0		380	651	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0018394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	249	574	9	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.923	0.867	0.981	0.923	0.867	0.981	CLONAL	1	TRUE	1	0.706256895946452	2		583	764	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733044	74733044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	265	334	0	ENST00000359995.5:c.199G>A	p.Asp67Asn	p.D67N	ENST00000359995	NM_001195427.1	67	Gac/Aac	1/3	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.706256895946452	2		334	698	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248555	59248555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	139	371	0	ENST00000371222.2:c.188C>T	p.Ser63Leu	p.S63L	ENST00000371222	NM_002228.3	63	tCg/tTg	1/1	1	2	FACETS	0.542	0.494	0.592	0.542	0.494	0.592	SUBCLONAL	1	TRUE	1	0.706256895946452	2		371	726	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842745	68842751	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	ATACACT	ATACACT	-	novel	NA	P-0018394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	202	348	0	ENST00000261769.5:c.681_687del	p.Tyr228SerfsTer20	p.Y228Sfs*20	ENST00000261769	NM_004360.3	227	acATACACT/ac	5/16	0.675998842799145	1	FACETS	0.942	0.887	0.996	0.942	0.887	0.996	CLONAL	1	TRUE	0	0.706256895946452	1		348	393	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821857	72821857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	234	298	1	ENST00000268489.5:c.10318G>A	p.Glu3440Lys	p.E3440K	ENST00000268489	NM_006885.3	3440	Gaa/Aaa	10/10	0.675998842799145	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.706256895946452	1		299	402	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40872387	40872387	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	327	620	0	ENST00000428826.2:c.568G>A	p.Glu190Lys	p.E190K	ENST00000428826		190	Gag/Aag	7/21	1	2	FACETS	0.916	0.867	0.966	0.916	0.867	0.966	CLONAL	1	TRUE	1	0.706256895946452	2		620	1011	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910350	29910350	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1562680966	NA	P-0018394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	105	519	0	ENST00000376809.5:c.20G>C	p.Arg7Pro	p.R7P	ENST00000376809	NM_002116.7	7	cGa/cCa	1/8	1	2	FACETS	0.3	0.268	0.334	0.3	0.268	0.334	SUBCLONAL	1	TRUE	1	0.706256895946452	2		519	992	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14027754	14027754	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	219	331	0	ENST00000405192.2:c.90G>C	p.Arg30Ser	p.R30S	ENST00000405192	NM_001163147.1	30	agG/agC	3/12	1	2	FACETS	0.887	0.829	0.947	0.887	0.829	0.947	CLONAL	1	TRUE	1	0.706256895946452	2		331	699	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101151	27101151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	198	558	0	ENST00000324856.7:c.4433C>T	p.Pro1478Leu	p.P1478L	ENST00000324856	NM_006015.4	1478	cCa/cTa	18/20	1	2	FACETS	0.954	0.884	1	0.954	0.884	1	CLONAL	1	TRUE	1	0.41043476709949	2		558	1011	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206941993	206941993	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	36	220	0	ENST00000423557.1:c.525G>T	p.Lys175Asn	p.K175N	ENST00000423557	NM_000572.2	175	aaG/aaT	5/5	1	2	FACETS	0.348	0.286	0.418	0.348	0.286	0.418	SUBCLONAL	1	TRUE	1	0.41043476709949	2		220	504	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711907	89711908	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	169	473	0	ENST00000371953.3:c.526dup	p.Tyr176LeufsTer4	p.Y176Lfs*4	ENST00000371953	NM_000314.4	175	-/T	6/9	0.41043476709949	1	FACETS	0.874	0.805	0.945	0.874	0.805	0.945	CLONAL	1	TRUE	0	0.41043476709949	1		473	749	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114249	115114250	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	109	414	0	ENST00000257566.3:c.967dup	p.Arg323LysfsTer4	p.R323Kfs*4	ENST00000257566	NM_016569.3	323	agg/aAgg	6/8	1	2	FACETS	0.559	0.501	0.621	0.559	0.501	0.621	SUBCLONAL	1	TRUE	1	0.41043476709949	2		414	950	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474476	40474476	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	36	350	0	ENST00000264657.5:c.1925A>C	p.Lys642Thr	p.K642T	ENST00000264657	NM_139276.2	642	aAg/aCg	21/24	0.368166063132022	1	FACETS	0.242	0.199	0.292	0.242	0.199	0.292	SUBCLONAL	1	TRUE	0	0.41043476709949	1		350	575	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609379	39609379	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749775725	NA	P-0018395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	168	354	0	ENST00000262039.4:c.1681C>T	p.Arg561Cys	p.R561C	ENST00000262039	NM_002647.2	561	Cgc/Tgc	15/25	0.41043476709949	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.41043476709949	1		354	572	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643296	38643296	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1331443136	NA	P-0018396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	67	409	0	ENST00000299084.4:c.766C>T	p.Arg256Cys	p.R256C	ENST00000299084	NM_152594.2	256	Cgt/Tgt	7/7	1	2	FACETS	0.814	0.706	0.93	0.814	0.706	0.93	CLONAL	1	TRUE	1	0.23	2		409	716	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556908	29556908	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	22	183	0	ENST00000356175.3:c.2906A>G	p.Lys969Arg	p.K969R	ENST00000356175	NM_000267.3	969	aAg/aGg	22/57	1	2	FACETS	0.642	0.498	0.809	0.642	0.498	0.809	SUBCLONAL	1	TRUE	1	0.23	2		183	298	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243753	41243753	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	73	402	0	ENST00000357654.3:c.3795T>G	p.Asn1265Lys	p.N1265K	ENST00000357654	NM_007294.3	1265	aaT/aaG	10/23	1	2	FACETS	0.854	0.746	0.971	0.854	0.746	0.971	CLONAL	1	TRUE	1	0.23	2		402	743	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0018397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	64	715	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.975	0.861	1	0.975	0.861	1	CLONAL	1	TRUE	1	0.721359999144001	2		717	182	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0018397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	298	807	3	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.944	0.892	0.997	0.944	0.892	0.997	CLONAL	1	TRUE	1	0.721359999144001	2		810	875	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675571	30675571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772732783	NA	P-0018397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	50	529	0	ENST00000376406.3:c.2785G>A	p.Asp929Asn	p.D929N	ENST00000376406	NM_014641.2	929	Gat/Aat	8/15	1	2	FACETS	0.168	0.141	0.197	0.168	0.141	0.197	SUBCLONAL	1	TRUE	1	0.721359999144001	2		529	827	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054254	30054254	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1555994854	NA	P-0018397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	78	310	0	ENST00000338641.4:c.675+1G>A		p.X225_splice	ENST00000338641	NM_000268.3	225			0.693362133513995	1	FACETS	0.385	0.341	0.432	0.385	0.341	0.432	SUBCLONAL	1	TRUE	0	0.721359999144001	1		310	359	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439738	49439738	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	283	429	0	ENST00000301067.7:c.4706C>T	p.Pro1569Leu	p.P1569L	ENST00000301067	NM_003482.3	1569	cCt/cTt	18/54	1	2	FACETS	0.984	0.929	1	0.984	0.929	1	CLONAL	1	TRUE	1	0.721359999144001	2		429	797	SUCCESS
BLM	641	MSKCC	GRCh37	15	91328186	91328186	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	175	306	0	ENST00000355112.3:c.2698G>C	p.Glu900Gln	p.E900Q	ENST00000355112	NM_000057.2	900	Gaa/Caa	14/22	0.674687021812794	3	FACETS	0.842	0.777	0.91	0.421	0.388	0.455	CLONAL	1	TRUE	1	0.721359999144001	3		306	784	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163216	32163217	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	193	548	0	ENST00000375023.3:c.6009dup	p.Ter2004IlefsTer33	p.*2004Ifs*33	ENST00000375023	NM_004557.3	2003	-/A	30/30	1	2	FACETS	0.876	0.815	0.938	0.876	0.815	0.938	CLONAL	1	TRUE	1	0.721359999144001	2		548	611	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528449	157528449	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	218	381	0	ENST00000346085.5:c.6176del	p.Pro2059ArgfsTer40	p.P2059Rfs*40	ENST00000346085	NM_020732.3	2058	tgC/tg	20/20	0.693362133513995	1	FACETS	0.911	0.86	0.962	0.911	0.86	0.962	CLONAL	1	TRUE	0	0.721359999144001	1		381	424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0018398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	329	779	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.273917981500368	4	FACETS	1	0.983	1	0.814	0.772	0.857	CLONAL	3	TRUE	0	0.291689009622704	4		781	895	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0018398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	96	584	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.131045716976357	5	FACETS	0.871	0.779	0.969	0.581	0.519	0.646	INDETERMINATE	2	TRUE	2	0.291689009622704	5		584	543	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0018398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	246	339	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.273917981500368	4	FACETS	0.891	0.84	0.944	0.891	0.84	0.944	CLONAL	4	TRUE	0	0.291689009622704	4		339	611	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599332	55599332	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519710	NA	P-0018398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	15	537	0	ENST00000288135.5:c.2458G>T	p.Asp820Tyr	p.D820Y	ENST00000288135	NM_000222.2	820	Gat/Tat	17/21	0.25640539415363	4	FACETS	0.246	0.179	0.328	0.123	0.089	0.164	SUBCLONAL	1	TRUE	2	0.291689009622704	4		537	540	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023156	27023172	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGGCAGCGGCGGCGG	GCCGGCAGCGGCGGCGG	-	novel	NA	P-0018398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	102	63	0	ENST00000324856.7:c.265_281del	p.Gly89ArgfsTer16	p.G89Rfs*16	ENST00000324856	NM_006015.4	88	GCCGGCAGCGGCGGCGGg/g	1/20	0.131045716976357	5	FACETS	1	0.963	1	1	0.989	1	INDETERMINATE	5	TRUE	2	0.291689009622704	5		63	186	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041743	42041743	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	117	265	2	ENST00000219905.7:c.5938del	p.Glu1980LysfsTer5	p.E1980Kfs*5	ENST00000219905	NM_001164273.1	1980	Gaa/aa	17/24	0.19031184776834	4	FACETS	0.834	0.758	0.913	0.834	0.758	0.913	CLONAL	3	TRUE	1	0.291689009622704	4		267	414	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584593	48584593	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	139	347	0	ENST00000342988.3:c.766del	p.Gln256SerfsTer80	p.Q256Sfs*80	ENST00000342988	NM_005359.5	256	Cag/ag	6/12	0.242104865465715	3	FACETS	0.835	0.767	0.905	0.835	0.767	0.905	CLONAL	3	TRUE	0	0.291689009622704	3		347	436	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201869	67201869	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	106	395	0	ENST00000312629.5:c.1069C>G	p.Gln357Glu	p.Q357E	ENST00000312629	NM_003952.2	357	Cag/Gag	13/15	0.465899376810049	3	FACETS	0.692	0.62	0.768	0.346	0.31	0.384	SUBCLONAL	1	TRUE	1	0.465899376810049	3		395	811	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579401	7579401	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	129	468	0	ENST00000269305.4:c.286del	p.Ser96LeufsTer27	p.S96Lfs*27	ENST00000269305	NM_001126112.2	96	Tct/ct	4/11	0.465899376810049	1	FACETS	0.761	0.693	0.832	0.761	0.693	0.832	SUBCLONAL	1	TRUE	0	0.465899376810049	1		468	558	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342124	70342131	+	frameshift_variant	Frame_Shift_Del	DEL	ACCACTTG	ACCACTTG	-	novel	NA	P-0018401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	115	427	0	ENST00000374080.3:c.1184_1191del	p.Asp395AlafsTer13	p.D395Afs*13	ENST00000374080		392	tcACCACTTGac/tcac	8/45	NA	2	FACETS	0.644	0.581	0.712			1	INDETERMINATE	1	TRUE	NA	0.465899376810049	2		427	766	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0018402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	245	446	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.96	0.9	1	0.96	0.9	1	CLONAL	1	TRUE	1	0.632173590964184	2		446	807	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0018402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	219	894	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.866	0.808	0.926	0.866	0.808	0.926	CLONAL	1	TRUE	1	0.632173590964184	2		895	800	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411678	63411678	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	359	324	0	ENST00000330258.3:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000330258	NM_152424.3	497	Cga/Tga	2/2	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.632173590964184	1		324	533	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591148	67591149	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGA	novel	NA	P-0018402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	128	280	0	ENST00000274335.5:c.1744_1745+1dup		p.L582_M583dup	ENST00000274335		582	ttg/tTGAtg	12/15	1	2	FACETS	0.837	0.763	0.913	0.837	0.763	0.913	CLONAL	1	TRUE	1	0.632173590964184	2		280	484	SUCCESS
APC	324	MSKCC	GRCh37	5	112175108	112175108	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0018402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	118	227	0	ENST00000257430.4:c.3817A>T	p.Arg1273Ter	p.R1273*	ENST00000257430	NM_000038.5	1273	Aga/Tga	16/16	1	2	FACETS	0.957	0.872	1	0.957	0.872	1	CLONAL	1	TRUE	1	0.632173590964184	2		227	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0018403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	397	383	1	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	0.872229986256001	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.872229986256001	1		384	422	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557642	95557642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	475	533	0	ENST00000393063.1:c.5425G>A	p.Gly1809Arg	p.G1809R	ENST00000393063	NM_030621.3	1809	Ggg/Agg	26/28	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.872229986256001	2		533	1009	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784440	9784440	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	237	380	0	ENST00000377346.4:c.2825T>C	p.Ile942Thr	p.I942T	ENST00000377346	NM_005026.3	942	aTt/aCt	22/24	0.46844199651485	1	FACETS	0.428	0.401	0.456	0.428	0.401	0.456	INDETERMINATE	1	TRUE	0	0.872229986256001	1		380	716	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226573273	226573273	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	407	439	0	ENST00000366794.5:c.943G>T	p.Val315Phe	p.V315F	ENST00000366794	NM_001618.3	315	Gtc/Ttc	7/23	0.51977917729904	1	FACETS	0.789	0.76	0.818	0.789	0.76	0.818	INDETERMINATE	1	TRUE	0	0.872229986256001	1		439	667	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104375131	104375131	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	454	409	0	ENST00000369902.3:c.1129T>C	p.Ser377Pro	p.S377P	ENST00000369902	NM_016169.3	377	Tcc/Ccc	9/12	NA	2	FACETS	1	0.997	1			1	INDETERMINATE	1	TRUE	NA	0.872229986256001	2		409	732	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201860	67201860	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	217	340	0	ENST00000312629.5:c.1060G>A	p.Asp354Asn	p.D354N	ENST00000312629	NM_003952.2	354	Gac/Aac	13/15	0.581816408038612	1	FACETS	0.509	0.477	0.542	0.509	0.477	0.542	SUBCLONAL	1	TRUE	0	0.872229986256001	1		340	551	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936803	32936803	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	160	348	0	ENST00000380152.3:c.7949A>G	p.Glu2650Gly	p.E2650G	ENST00000380152		2650	gAa/gGa	17/27	0.51977917729904	1	FACETS	0.393	0.363	0.425	0.393	0.363	0.425	INDETERMINATE	1	TRUE	0	0.872229986256001	1		348	526	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557538	95557538	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0018403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	215	298	0	ENST00000393063.1:c.5527+2T>C		p.X1843_splice	ENST00000393063	NM_030621.3	1843			1	2	FACETS	0.965	0.906	1	0.965	0.906	1	CLONAL	1	TRUE	1	0.872229986256001	2		298	511	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90634864	90634864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	385	406	0	ENST00000330062.3:c.128G>A	p.Arg43Lys	p.R43K	ENST00000330062	NM_002168.2	43	aGg/aAg	2/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.872229986256001	2		406	820	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223509	36223509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867769309	NA	P-0018403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	392	482	0	ENST00000222270.7:c.6059C>T	p.Pro2020Leu	p.P2020L	ENST00000222270	NM_014727.1	2020	cCg/cTg	28/37	0.51977917729904	1	FACETS	0.771	0.742	0.801	0.771	0.742	0.801	INDETERMINATE	1	TRUE	0	0.872229986256001	1		482	657	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799261	42799261	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	205	347	0	ENST00000575354.2:c.4745G>A	p.Gly1582Glu	p.G1582E	ENST00000575354	NM_015125.3	1582	gGg/gAg	20/20	0.51977917729904	1	FACETS	0.465	0.434	0.496	0.465	0.434	0.496	INDETERMINATE	1	TRUE	0	0.872229986256001	1		347	570	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191065	185191065	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	218	506	1	ENST00000265026.3:c.1946C>T	p.Ser649Phe	p.S649F	ENST00000265026	NM_004721.4	649	tCc/tTc	11/14	0.47078570067818	1	FACETS	0.36	0.335	0.385	0.36	0.335	0.385	INDETERMINATE	1	TRUE	0	0.872229986256001	1		507	783	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446181	187446181	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1488877472	NA	P-0018403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	245	577	0	ENST00000232014.4:c.1507G>A	p.Glu503Lys	p.E503K	ENST00000232014	NM_001130845.1	503	Gag/Aag	6/10	0.47078570067818	1	FACETS	0.384	0.359	0.408	0.384	0.359	0.408	INDETERMINATE	1	TRUE	0	0.872229986256001	1		577	826	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637423	176637423	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	461	369	0	ENST00000439151.2:c.2023A>G	p.Met675Val	p.M675V	ENST00000439151	NM_022455.4	675	Atg/Gtg	5/23	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.872229986256001	2		369	869	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169251	32169251	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	344	405	0	ENST00000375023.3:c.3782A>G	p.Asp1261Gly	p.D1261G	ENST00000375023	NM_004557.3	1261	gAt/gGt	22/30	1	2	FACETS	0.967	0.92	1	0.967	0.92	1	CLONAL	1	TRUE	1	0.872229986256001	2		405	816	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226039	53226039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	379	473	0	ENST00000375401.3:c.2810C>T	p.Thr937Ile	p.T937I	ENST00000375401	NM_004187.3	937	aCa/aTa	19/26	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.872229986256001	2		473	861	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	118	364	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.944	0.86	1	0.944	0.86	1	CLONAL	1	TRUE	1	0.663140059339247	2		365	377	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692871	89692871	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139767111	NA	P-0018404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	53	176	0	ENST00000371953.3:c.355G>T	p.Val119Phe	p.V119F	ENST00000371953	NM_000314.4	119	Gtt/Ttt	5/9	0.663140059339247	1	FACETS	0.921	0.812	1	0.921	0.812	1	CLONAL	1	TRUE	0	0.663140059339247	1		176	116	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278352	39278352	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs137852812	NA	P-0018404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	187	515	0	ENST00000402219.2:c.797C>A	p.Thr266Lys	p.T266K	ENST00000402219	NM_005633.3	266	aCa/aAa	6/23	1	2	FACETS	0.901	0.836	0.967	0.901	0.836	0.967	CLONAL	1	TRUE	1	0.663140059339247	2		515	626	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710628	40710628	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	227	471	0	ENST00000373198.4:c.4223G>A	p.Cys1408Tyr	p.C1408Y	ENST00000373198	NM_133170.3	1408	tGt/tAt	31/32	1	2	FACETS	0.934	0.874	0.996	0.934	0.874	0.996	CLONAL	1	TRUE	1	0.663140059339247	2		471	733	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018410-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	154	917	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	0.511679085119913	2		917	555	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129867	55129867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373126818	NA	P-0018410-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	106	604	0	ENST00000257290.5:c.401C>T	p.Thr134Met	p.T134M	ENST00000257290	NM_006206.4	134	aCg/aTg	4/23	0.362215394223925	1	FACETS	0.48	0.431	0.532	0.48	0.431	0.532	SUBCLONAL	1	TRUE	0	0.511679085119913	1		604	642	SUCCESS
APC	324	MSKCC	GRCh37	5	112175751	112175752	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1114167577	NA	P-0018410-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	124	365	0	ENST00000257430.4:c.4463dup	p.Leu1488PhefsTer26	p.L1488Ffs*26	ENST00000257430	NM_000038.5	1487	act/acTt	16/16	0.511679085119913	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.511679085119913	1		365	318	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174419	11174419	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018410-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	199	789	0	ENST00000361445.4:c.7256A>C	p.Glu2419Ala	p.E2419A	ENST00000361445	NM_004958.3	2419	gAa/gCa	53/58	0.362215394223925	1	FACETS	0.679	0.629	0.73	0.679	0.629	0.73	SUBCLONAL	1	TRUE	0	0.511679085119913	1		789	853	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458452	120458452	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140832430	NA	P-0018410-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	30	465	2	ENST00000256646.2:c.6893G>A	p.Arg2298Gln	p.R2298Q	ENST00000256646	NM_024408.3	2298	cGg/cAg	34/34	0.362215394223925	1	FACETS	0.175	0.14	0.214	0.175	0.14	0.214	SUBCLONAL	1	TRUE	0	0.511679085119913	1		467	499	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422077	81422077	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018410-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	50	451	0	ENST00000298171.2:c.53A>C	p.Asp18Ala	p.D18A	ENST00000298171	NM_000369.2	18	gAc/gCc	1/10	NA	2	FACETS	0.417	0.354	0.486			1	INDETERMINATE	1	TRUE	NA	0.511679085119913	2		451	469	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41521991	41521991	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs761504502	NA	P-0018410-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	56	638	0	ENST00000263253.7:c.853T>C	p.Ser285Pro	p.S285P	ENST00000263253	NM_001429.3	285	Tct/Cct	3/31	NA	2	FACETS	0.301	0.258	0.35			1	INDETERMINATE	1	TRUE	NA	0.511679085119913	2		638	726	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639155	176639155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018410-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	227	642	0	ENST00000439151.2:c.3755G>T	p.Gly1252Val	p.G1252V	ENST00000439151	NM_022455.4	1252	gGa/gTa	5/23	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.511679085119913	2		642	773	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737573	145737573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781751586	NA	P-0018410-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	204	702	1	ENST00000428558.2:c.3190C>T	p.Arg1064Cys	p.R1064C	ENST00000428558	NM_004260.3	1064	Cgc/Tgc	19/22	1	2	FACETS	0.86	0.798	0.924	0.86	0.798	0.924	CLONAL	1	TRUE	1	0.511679085119913	2		703	927	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0018411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	188	715	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.99	0.924	1	0.99	0.924	1	CLONAL	1	TRUE	1	0.822220285717369	2		717	462	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0018411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	304	807	3	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.822220285717369	2		810	713	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0018411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	206	515	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.822220285717369	2		515	482	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1042197	1042197	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	304	650	0	ENST00000358495.3:c.28G>C	p.Gly10Arg	p.G10R	ENST00000358495	NM_134424.2	10	Gga/Cga	2/12	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.822220285717369	2		650	729	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853188	68853188	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	207	461	0	ENST00000261769.5:c.1572del	p.Ile525PhefsTer32	p.I525Ffs*32	ENST00000261769	NM_004360.3	524	cGg/cg	11/16	0.822226540515662	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.822220285717369	1		461	280	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656949	47656949	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	235	509	0	ENST00000233146.2:c.1145G>C	p.Arg382Pro	p.R382P	ENST00000233146	NM_000251.2	382	cGt/cCt	7/16	1	2	FACETS	0.992	0.934	1	0.992	0.934	1	CLONAL	1	TRUE	1	0.822220285717369	2		509	576	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0018412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	85	446	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.587684507912921	1	FACETS	0.916	0.825	1	0.916	0.825	1	CLONAL	1	TRUE	0	0.587684507912921	1		446	223	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0018412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	182	894	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.587684507912921	5	FACETS	1	0.98	1	0.765	0.711	0.819	CLONAL	2	TRUE	2	0.587684507912921	5		895	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0018412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	324	410	1	ENST00000269305.4:c.673-2A>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.587684507912921	3	FACETS	1	0.99	1			1	CLONAL	3	TRUE	NA	0.587684507912921	3		411	443	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906446	50906446	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	141	609	0	ENST00000440232.2:c.1107G>T	p.Gln369His	p.Q369H	ENST00000440232	NM_002691.3	369	caG/caT	9/27	0.587684507912921	3	FACETS	0.985	0.901	1	0.493	0.45	0.537	CLONAL	1	TRUE	1	0.587684507912921	3		609	630	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32182003	32182003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780829867	NA	P-0018412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	122	646	0	ENST00000375023.3:c.2051C>T	p.Thr684Met	p.T684M	ENST00000375023	NM_004557.3	684	aCg/aTg	13/30	0.587684507912921	3	FACETS	0.775	0.702	0.853	0.388	0.351	0.427	SUBCLONAL	1	TRUE	1	0.587684507912921	3		646	693	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0018414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	142	574	9	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.997	0.912	1	0.997	0.912	1	CLONAL	1	TRUE	1	0.463801333022073	2		583	614	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0018414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	248	730	1	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	0.463801333022073	2		731	1025	SUCCESS
EED	8726	MSKCC	GRCh37	11	85979599	85979599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	135	343	0	ENST00000263360.6:c.962C>T	p.Ser321Phe	p.S321F	ENST00000263360	NM_003797.3	321	tCt/tTt	9/12	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.463801333022073	2		343	575	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856129	68856129	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0018414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	135	525	0	ENST00000261769.5:c.1936+1G>T		p.X646_splice	ENST00000261769	NM_004360.3	646			0.463801333022073	1	FACETS	0.933	0.854	1	0.933	0.854	1	CLONAL	1	TRUE	0	0.463801333022073	1		525	479	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913220	39913221	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0018414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	147	528	2	ENST00000378444.4:c.4894_4895delinsTT	p.Ala1632Phe	p.A1632F	ENST00000378444	NM_001123385.1	1632	GCc/TTc	14/15	1	2	FACETS	0.785	0.718	0.857	0.785	0.718	0.857	SUBCLONAL	1	TRUE	1	0.463801333022073	2		530	807	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577123	7577123	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876660333	NA	P-0018416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	494	750	0	ENST00000269305.4:c.815T>A	p.Val272Glu	p.V272E	ENST00000269305	NM_001126112.2	272	gTg/gAg	8/11	0.564733371716787	2	FACETS	0.99	0.954	1	0.99	0.954	1	CLONAL	2	TRUE	0	0.564733371716787	2		750	884	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420976	49421030	+	frameshift_variant	Frame_Shift_Del	DEL	GAGAAGGTGCCAAGGGGGAAGGGGGCGGGGAGGGTTCTTCAGGAGGTGGGGCCGA	GAGAAGGTGCCAAGGGGGAAGGGGGCGGGGAGGGTTCTTCAGGAGGTGGGGCCGA	-	novel	NA	P-0018416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	145	364	0	ENST00000301067.7:c.14719_14773del	p.Ser4907LeufsTer70	p.S4907Lfs*70	ENST00000301067	NM_003482.3	4907	TCGGCCCCACCTCCTGAAGAACCCTCCCCGCCCCCTTCCCCCTTGGCACCTTCTCct/ct	48/54	0.564733371716787	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.564733371716787	1		364	336	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219404	1219430	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCCCACGGGTGCGTGCGCGGGGCAGG	GGCCCACGGGTGCGTGCGCGGGGCAGG	-	novel	NA	P-0018416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	143	472	1	ENST00000326873.7:c.460_464+22del		p.X154_splice	ENST00000326873	NM_000455.4	154		3/10	0.564733371716787	1	FACETS	0.837	0.77	0.906	0.837	0.77	0.906	CLONAL	1	TRUE	0	0.564733371716787	1		473	434	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220598	1220598	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1555738357	NA	P-0018416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	210	524	2	ENST00000326873.7:c.616G>T	p.Ala206Ser	p.A206S	ENST00000326873	NM_000455.4	206	Gcg/Tcg	5/10	0.564733371716787	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.564733371716787	1		526	499	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157520000	157520003	+	frameshift_variant	Frame_Shift_Ins	INS	CCGT	CCGT	AGGGCACC	novel	NA	P-0018416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	128	522	0	ENST00000346085.5:c.4069_4072delinsAGGGCACC	p.Pro1357ArgfsTer103	p.P1357Rfs*103	ENST00000346085	NM_020732.3	1357	CCGTat/AGGGCACCat	17/20	NA	2	FACETS	0.78	0.71	0.854			1	INDETERMINATE	1	TRUE	NA	0.564733371716787	2		522	581	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939786	71939797	+	frameshift_variant	Frame_Shift_Del	DEL	AGCCCCCGCTGC	AGCCCCCGCTGC	G	novel	NA	P-0018416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	208	735	0	ENST00000298229.2:c.413_424delinsG	p.Lys138SerfsTer23	p.K138Sfs*23	ENST00000298229	NM_001567.3	138	aAGCCCCCGCTGCcc/aGcc	4/28	1	2	FACETS	0.927	0.862	0.993	0.927	0.862	0.993	CLONAL	1	TRUE	1	0.564733371716787	2		735	795	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0018418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	40	1014	3	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.3	1	FACETS	0.986	0.821	1	0.986	0.821	1	CLONAL	1	TRUE	0	0.2	1		1017	365	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0018418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	139	708	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.892	0.813	0.975	1	0.989	1	CLONAL	2	TRUE	1	0.2	2		709	779	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0018419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	140	715	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.516885034944685	4	FACETS	1	0.978	1	0.303	0.277	0.331	CLONAL	1	TRUE	0	0.516885034944685	4		717	677	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	164	201	0	ENST00000397062.3:c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	NM_006164.4	34	Cga/Gga	2/5	0.172087632837356	3	FACETS	0.78	0.721	0.84	0.78	0.721	0.84	INDETERMINATE	2	TRUE	1	0.516885034944685	3		201	512	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285327	212285327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143134749	NA	P-0018419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	100	267	2	ENST00000342788.4:c.2974C>T	p.Arg992Cys	p.R992C	ENST00000342788	NM_005235.2	992	Cgt/Tgt	25/28	0.516885034944685	1	FACETS	0.92	0.832	1	0.92	0.832	1	CLONAL	1	TRUE	0	0.516885034944685	1		269	312	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522573	187522581	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	TGAACTCCC	TGAACTCCC	-	novel	NA	P-0018419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	54	186	0	ENST00000441802.2:c.11483-1_11490del		p.X3828_splice	ENST00000441802	NM_005245.3	3828		21/27	1	2	FACETS	0.595	0.511	0.687	0.595	0.511	0.687	SUBCLONAL	1	TRUE	1	0.516885034944685	2		186	351	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426058	49426058	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398123712	NA	P-0018419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	180	282	0	ENST00000301067.7:c.12430C>T	p.Gln4144Ter	p.Q4144*	ENST00000301067	NM_003482.3	4144	Cag/Tag	39/54	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.516885034944685	2		282	597	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379674	17379674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766735279	NA	P-0018419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	169	194	0	ENST00000359435.4:c.59C>T	p.Ser20Leu	p.S20L	ENST00000359435	NM_001033549.1	20	tCg/tTg	2/9	0.294178452821733	3	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.516885034944685	3		194	605	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250846	153250846	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	155	301	0	ENST00000281708.4:c.1214T>A	p.Val405Asp	p.V405D	ENST00000281708	NM_033632.3	405	gTt/gAt	8/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.516885034944685	2		301	492	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27217701	27217701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772600804	NA	P-0018419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	148	285	0	ENST00000380036.4:c.3007C>T	p.Arg1003Cys	p.R1003C	ENST00000380036	NM_000459.3	1003	Cgc/Tgc	19/23	1	2	FACETS	0.857	0.785	0.932	0.857	0.785	0.932	CLONAL	1	TRUE	1	0.516885034944685	2		285	668	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599332	55599332	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519710	NA	P-0018422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	3779	537	0	ENST00000288135.5:c.2458G>T	p.Asp820Tyr	p.D820Y	ENST00000288135	NM_000222.2	820	Gat/Tat	17/21	0.803937581302356	28	FACETS	1	0.996	1			1	CLONAL	22	TRUE	NA	0.803937581302356	28		537	4843	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0018434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	271	970	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.243231072670285	3	FACETS	1	0.964	1	0.689	0.648	0.731	CLONAL	2	TRUE	0	0.363216108079948	3		970	853	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004451	150004451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	59	578	0	ENST00000253339.5:c.1774G>A	p.Glu592Lys	p.E592K	ENST00000253339		592	Gag/Aag	3/7	0.295867498049528	2	FACETS	0.768	0.663	0.882	0.384	0.331	0.441	SUBCLONAL	1	TRUE	0	0.363216108079948	2		578	423	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251860	212251860	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764544368	NA	P-0018434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	27	360	0	ENST00000342788.4:c.3199C>T	p.Arg1067Ter	p.R1067*	ENST00000342788	NM_005235.2	1067	Cga/Tga	27/28	0.347057367421345	4	FACETS	0.494	0.393	0.61	0.165	0.131	0.204	SUBCLONAL	1	TRUE	1	0.363216108079948	4		360	410	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992206	11992206	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	286	606	0	ENST00000396373.4:c.296A>T	p.Lys99Ile	p.K99I	ENST00000396373	NM_001987.4	99	aAa/aTa	3/8	0.363216108079948	3	FACETS	0.874	0.826	0.921	0.874	0.826	0.921	CLONAL	3	TRUE	0	0.363216108079948	3		606	710	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0018434-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	428	970	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.219429521063729	3	FACETS	1	0.992	1	0.796	0.758	0.835	CLONAL	2	TRUE	0	0.29	3		970	1415	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004451	150004451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018434-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	149	578	0	ENST00000253339.5:c.1774G>A	p.Glu592Lys	p.E592K	ENST00000253339		592	Gag/Aag	3/7	0.248351164416749	2	FACETS	1	0.976	1	0.593	0.541	0.646	CLONAL	1	TRUE	0	0.29	2		578	867	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251860	212251860	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764544368	NA	P-0018434-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	40	360	0	ENST00000342788.4:c.3199C>T	p.Arg1067Ter	p.R1067*	ENST00000342788	NM_005235.2	1067	Cga/Tga	27/28	0.219429521063729	3	FACETS	0.481	0.398	0.573	0.16	0.132	0.191	SUBCLONAL	1	TRUE	0	0.29	3		360	657	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992206	11992206	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018434-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	436	606	0	ENST00000396373.4:c.296A>T	p.Lys99Ile	p.K99I	ENST00000396373	NM_001987.4	99	aAa/aTa	3/8	0.296554383322898	4	FACETS	0.903	0.863	0.943	0.903	0.863	0.943	CLONAL	4	TRUE	0	0.29	4		606	1074	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0018435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	385	416	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	0.859551714333865	2		416	831	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437846	52437846	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	436	433	1	ENST00000460680.1:c.1315G>A	p.Val439Met	p.V439M	ENST00000460680	NM_004656.3	439	Gtg/Atg	13/17	0.859551714333865	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.859551714333865	1		434	548	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52675969	52675978	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CCAGCTAAAG	CCAGCTAAAG	-	novel	NA	P-0018435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	30	375	0	ENST00000394830.3:c.1079_1087+1del		p.X360_splice	ENST00000394830	NM_018313.4	360		11/30	0.859551714333865	1	FACETS	0.11	0.088	0.135	0.11	0.088	0.135	SUBCLONAL	1	TRUE	0	0.859551714333865	1		375	361	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117874084	117874087	+	frameshift_variant	Frame_Shift_Del	DEL	AGTC	AGTC	-	novel	NA	P-0018435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	109	239	0	ENST00000297338.2:c.367_370del	p.Asp123Ter	p.D123*	ENST00000297338	NM_006265.2	123	GACTta/ta	4/14	0.859551714333865	4	FACETS	0.875	0.789	0.966	0.292	0.263	0.322	CLONAL	1	TRUE	1	0.859551714333865	4		239	539	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045754	47045754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	60	248	1	ENST00000377604.3:c.2635C>T	p.Arg879Cys	p.R879C	ENST00000377604	NM_001204468.1	879	Cgc/Tgc	23/24	1	1	FACETS	0.138	0.119	0.16	0.138	0.119	0.16	SUBCLONAL	1	TRUE	0	0.859551714333865	1		249	575	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0018436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	62	900	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.89	0.772	1	0.89	0.772	1	CLONAL	1	TRUE	1	0.374737596123458	2		901	372	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	116	272	2	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.374737596123458	2		274	483	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0018436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	231	486	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	TRUE	1	0.374737596123458	2		488	520	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0018436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	57	282	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.897	0.774	1	0.897	0.774	1	CLONAL	1	TRUE	1	0.374737596123458	2		282	339	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149728	202149728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	101	395	0	ENST00000358485.4:c.1173del	p.Ile392SerfsTer4	p.I392Sfs*4	ENST00000358485	NM_001080125.1	390	gCc/gc	8/9	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.374737596123458	2		395	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	146	370	0	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.374737596123458	2		370	607	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	119	392	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.374737596123458	2		392	448	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867540	35867541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs869312857	NA	P-0018436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	55	319	2	ENST00000303115.3:c.361dup	p.Ile121AsnfsTer8	p.I121Nfs*8	ENST00000303115	NM_002185.3	118	-/A	3/8	1	2	FACETS	0.874	0.751	1	0.874	0.751	1	CLONAL	1	TRUE	1	0.374737596123458	2		321	336	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40486032	40486032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	138	387	0	ENST00000264657.5:c.833G>A	p.Arg278His	p.R278H	ENST00000264657	NM_139276.2	278	cGt/cAt	9/24	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.374737596123458	2		387	618	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606304	93606304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	151	402	0	ENST00000375746.1:c.124C>T	p.Arg42Cys	p.R42C	ENST00000375746	NM_001174167.1	42	Cgc/Tgc	2/14	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.374737596123458	2		402	735	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	148	328	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.374737596123458	2		328	630	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434959	49434959	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555192751	NA	P-0018436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	179	252	0	ENST00000301067.7:c.6594del	p.Tyr2199IlefsTer65	p.Y2199Ifs*65	ENST00000301067	NM_003482.3	2198	ccC/cc	31/54	0.373457833636565	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.374737596123458	3		252	457	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427611	49427611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561903173	NA	P-0018436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	147	204	0	ENST00000301067.7:c.10877G>A	p.Arg3626Gln	p.R3626Q	ENST00000301067	NM_003482.3	3626	cGg/cAg	39/54	0.373457833636565	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.374737596123458	3		204	435	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432420	49432420	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	197	438	0	ENST00000301067.7:c.8719del	p.Tyr2907ThrfsTer3	p.Y2907Tfs*3	ENST00000301067	NM_003482.3	2907	Tac/ac	34/54	0.373457833636565	3	FACETS	1	0.98	1	0.583	0.54	0.629	CLONAL	1	TRUE	1	0.374737596123458	3		438	1070	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103513899	103513899	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	58	329	0	ENST00000355739.4:c.719del	p.Lys240ArgfsTer4	p.K240Rfs*4	ENST00000355739	NM_000123.3	239	Aaa/aa	7/15	1	2	FACETS	0.808	0.697	0.928	0.808	0.697	0.928	CLONAL	1	TRUE	1	0.374737596123458	2		329	383	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349024	89349024	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779550492	NA	P-0018436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	184	481	2	ENST00000301030.4:c.3926C>T	p.Thr1309Met	p.T1309M	ENST00000301030	NM_001256183.1	1309	aCg/aTg	9/13	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.374737596123458	2		483	773	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16005005	16005005	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767510556	NA	P-0018436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	155	419	1	ENST00000268712.3:c.2249C>T	p.Ala750Val	p.A750V	ENST00000268712	NM_006311.3	750	gCg/gTg	20/46	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.374737596123458	2		420	678	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78914339	78914339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147686617	NA	P-0018436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	166	418	0	ENST00000306801.3:c.2963G>A	p.Arg988Gln	p.R988Q	ENST00000306801	NM_020761.2	988	cGg/cAg	25/34	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.374737596123458	2		418	867	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719437	190719437	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	38	257	0	ENST00000441310.2:c.1442del	p.Asn481MetfsTer35	p.N481Mfs*35	ENST00000441310	NM_000534.4	480	gAa/ga	9/13	1	2	FACETS	0.994	0.83	1	0.994	0.83	1	CLONAL	1	TRUE	1	0.374737596123458	2		257	204	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30733031	30733031	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	116	318	0	ENST00000295754.5:c.1647del	p.Arg550GlyfsTer14	p.R550Gfs*14	ENST00000295754	NM_003242.5	548	tcG/tc	7/7	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.374737596123458	2		318	527	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499477	89499477	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752560194	NA	P-0018436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	89	313	1	ENST00000336596.2:c.2647C>T	p.Arg883Trp	p.R883W	ENST00000336596	NM_005233.5	883	Cgg/Tgg	15/17	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.374737596123458	2		314	462	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807536	1807536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	133	382	0	ENST00000260795.2:c.1705G>A	p.Ala569Thr	p.A569T	ENST00000260795		569	Gcg/Acg	12/17	1	2	FACETS	0.894	0.812	0.98	0.894	0.812	0.98	CLONAL	1	TRUE	1	0.374737596123458	2		382	794	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1918615	1918615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	109	338	0	ENST00000382891.5:c.778C>T	p.Arg260Cys	p.R260C	ENST00000382891	NM_133335.3	260	Cgc/Tgc	4/22	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.374737596123458	2		338	549	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391358	84391358	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1560574509	NA	P-0018436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	44	308	0	ENST00000321945.7:c.474del	p.Gly159AspfsTer8	p.G159Dfs*8	ENST00000321945	NM_139076.2	158	aaA/aa	5/9	1	2	FACETS	0.801	0.676	0.939	0.801	0.676	0.939	CLONAL	1	TRUE	1	0.374737596123458	2		308	293	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048145	180048145	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758234191	NA	P-0018436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	325	428	1	ENST00000261937.6:c.2128G>A	p.Val710Met	p.V710M	ENST00000261937	NM_182925.4	710	Gtg/Atg	14/30	0.373457833636565	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.374737596123458	3		429	1005	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818266	32818266	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	164	365	0	ENST00000354258.4:c.1259T>C	p.Leu420Pro	p.L420P	ENST00000354258	NM_000593.5	420	cTg/cCg	5/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.374737596123458	2		365	744	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820202	32820202	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	134	403	0	ENST00000354258.4:c.856C>T	p.Arg286Ter	p.R286*	ENST00000354258	NM_000593.5	286	Cga/Tga	2/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.374737596123458	2		403	655	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821277	32821278	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0018436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	165	474	0	ENST00000354258.4:c.316dup	p.Leu106ProfsTer82	p.L106Pfs*82	ENST00000354258	NM_000593.5	106	ctg/cCtg	1/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.374737596123458	2		474	766	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288636	33288636	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs776342399	NA	P-0018436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	89	191	0	ENST00000374542.5:c.916C>T	p.Arg306Ter	p.R306*	ENST00000374542	NM_001141970.1	306	Cga/Tga	3/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.374737596123458	2		191	394	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341970	8341970	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	40	238	0	ENST00000356435.5:c.4670T>A	p.Val1557Asp	p.V1557D	ENST00000356435		1557	gTt/gAt	29/35	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.374737596123458	2		238	207	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97888841	97888841	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777732881	NA	P-0018436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	86	422	1	ENST00000289081.3:c.866C>T	p.Ala289Val	p.A289V	ENST00000289081	NM_000136.2	289	gCc/gTc	9/15	1	2	FACETS	0.922	0.818	1	0.922	0.818	1	CLONAL	1	TRUE	1	0.374737596123458	2		423	498	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0018438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	134	446	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.442191198707876	3	FACETS	0.859	0.781	0.941	0.43	0.39	0.471	CLONAL	1	TRUE	1	0.51200187615208	3		446	765	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0018438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	118	836	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.991	0.9	1	0.991	0.9	1	CLONAL	1	TRUE	1	0.51200187615208	2		836	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912655	NA	P-0018438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	202	289	0	ENST00000269305.4:c.725G>C	p.Cys242Ser	p.C242S	ENST00000269305	NM_001126112.2	242	tGc/tCc	7/11	0.485615461623949	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.51200187615208	1		289	584	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120226	70120226	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	262	518	1	ENST00000245479.2:c.1228C>T	p.Gln410Ter	p.Q410*	ENST00000245479	NM_000346.3	410	Cag/Tag	3/3	1	2	FACETS	0.957	0.897	1	0.957	0.897	1	CLONAL	1	TRUE	1	0.51200187615208	2		519	1069	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602329	28602329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372303125	NA	P-0018438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	60	302	2	ENST00000241453.7:c.2039C>T	p.Ala680Val	p.A680V	ENST00000241453	NM_004119.2	680	gCg/gTg	16/24	0.36609299475681	3	FACETS	0.311	0.266	0.359	0.104	0.088	0.12	SUBCLONAL	1	TRUE	0	0.51200187615208	3		304	948	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412095	63412095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852217	NA	P-0018438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	317	372	6	ENST00000330258.3:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000330258	NM_152424.3	358	Cga/Tga	2/2	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.51200187615208	2		378	1166	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606334	93606334	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs796052158	NA	P-0018438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	215	369	1	ENST00000375746.1:c.154G>A	p.Ala52Thr	p.A52T	ENST00000375746	NM_001174167.1	52	Gcc/Acc	2/14	1	2	FACETS	0.908	0.845	0.973	0.908	0.845	0.973	CLONAL	1	TRUE	1	0.51200187615208	2		370	925	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999304	100999304	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	246	449	0	ENST00000325455.5:c.498C>G	p.Ser166Arg	p.S166R	ENST00000325455	NM_001202474.3	166	agC/agG	1/8	1	2	FACETS	0.997	0.933	1	0.997	0.933	1	CLONAL	1	TRUE	1	0.51200187615208	2		449	964	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482828	67482828	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	389	336	0	ENST00000327367.4:c.1232T>A	p.Leu411His	p.L411H	ENST00000327367	NM_005902.3	411	cTc/cAc	9/9	0.497494392644343	2	FACETS	0.957	0.916	0.998	0.957	0.916	0.998	CLONAL	2	TRUE	0	0.51200187615208	2		336	794	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830778	72830778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781579217	NA	P-0018438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	174	332	2	ENST00000268489.5:c.5803C>T	p.Arg1935Cys	p.R1935C	ENST00000268489	NM_006885.3	1935	Cgc/Tgc	9/10	0.51200187615208	3	FACETS	0.865	0.796	0.937	0.432	0.398	0.469	CLONAL	1	TRUE	1	0.51200187615208	3		334	987	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923762	72923762	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	177	325	0	ENST00000268489.5:c.3316C>T	p.His1106Tyr	p.H1106Y	ENST00000268489	NM_006885.3	1106	Cat/Tat	4/10	0.51200187615208	3	FACETS	0.987	0.91	1	0.493	0.455	0.534	CLONAL	1	TRUE	1	0.51200187615208	3		325	880	SUCCESS
APC	324	MSKCC	GRCh37	5	112170679	112170679	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0018438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	190	226	0	ENST00000257430.4:c.1775T>G	p.Leu592Ter	p.L592*	ENST00000257430	NM_000038.5	592	tTa/tGa	15/16	0.442191198707876	3	FACETS	0.809	0.753	0.867	0.809	0.753	0.867	CLONAL	2	TRUE	1	0.51200187615208	3		226	576	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519466	137519466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	104	195	0	ENST00000367739.4:c.1172G>A	p.Ser391Asn	p.S391N	ENST00000367739	NM_000416.2	391	aGc/aAc	7/7	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.51200187615208	2		195	390	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	44	364	1				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		365	125	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	82	364	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.270008524938149	2		365	521	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0018444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	116	562	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.864	0.778	0.956	0.864	0.778	0.956	CLONAL	1	TRUE	1	0.270008524938149	2		562	994	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636794	8636794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	100	421	1	ENST00000356435.5:c.115G>A	p.Gly39Arg	p.G39R	ENST00000356435		39	Gga/Aga	2/35	1	2	FACETS	0.945	0.844	1	0.945	0.844	1	CLONAL	1	TRUE	1	0.270008524938149	2		422	784	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230691	46230691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424958105	NA	P-0018444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	80	391	1	ENST00000334344.6:c.940C>T	p.Arg314Cys	p.R314C	ENST00000334344	NM_152641.2	314	Cgt/Tgt	8/21	1	2	FACETS	0.984	0.867	1	0.984	0.867	1	CLONAL	1	TRUE	1	0.270008524938149	2		392	602	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127920559	127920559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	123	523	0	ENST00000373547.4:c.340C>T	p.His114Tyr	p.H114Y	ENST00000373547	NM_002721.4	114	Cat/Tat	4/7	0.270008524938149	1	FACETS	0.967	0.874	1	0.967	0.874	1	CLONAL	1	TRUE	0	0.270008524938149	1		523	815	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307158	65307158	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	71	298	0	ENST00000342505.4:c.2530G>A	p.Asp844Asn	p.D844N	ENST00000342505	NM_002227.2	844	Gac/Aac	18/25	1	2	FACETS	0.888	0.776	1	0.888	0.776	1	CLONAL	1	TRUE	1	0.270008524938149	2		298	592	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281926	49281926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	108	479	0	ENST00000282018.3:c.973C>T	p.Pro325Ser	p.P325S	ENST00000282018	NM_020377.2	325	Cca/Tca	1/1	1	2	FACETS	0.748	0.67	0.832	0.748	0.67	0.832	SUBCLONAL	1	TRUE	1	0.270008524938149	2		479	1069	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799233	88799233	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141393833	NA	P-0018444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	221	515	0	ENST00000360948.2:c.152G>A	p.Gly51Glu	p.G51E	ENST00000360948	NM_001012338.2	51	gGg/gAg	2/19	0.270008524938149	3	FACETS	0.885	0.823	0.949	0.885	0.823	0.949	CLONAL	2	TRUE	1	0.270008524938149	3		515	1050	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639204	3639204	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs758409623	NA	P-0018444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	95	527	0	ENST00000294008.3:c.4435C>T	p.Arg1479Ter	p.R1479*	ENST00000294008	NM_032444.2	1479	Cga/Tga	12/15	1	2	FACETS	0.723	0.643	0.81	0.723	0.643	0.81	SUBCLONAL	1	TRUE	1	0.270008524938149	2		527	973	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346117	89346117	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	17	104	0	ENST00000301030.4:c.6833C>T	p.Thr2278Ile	p.T2278I	ENST00000301030	NM_001256183.1	2278	aCt/aTt	9/13	1	2	FACETS	0.754	0.566	0.975	0.754	0.566	0.975	CLONAL	1	TRUE	1	0.270008524938149	2		104	167	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245271	41245271	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	106	583	0	ENST00000357654.3:c.2277A>C	p.Gln759His	p.Q759H	ENST00000357654	NM_007294.3	759	caA/caC	10/23	1	2	FACETS	0.779	0.697	0.866	0.779	0.697	0.866	SUBCLONAL	1	TRUE	1	0.270008524938149	2		583	1008	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794872	42794872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	87	399	1	ENST00000575354.2:c.1952C>T	p.Pro651Leu	p.P651L	ENST00000575354	NM_015125.3	651	cCc/cTc	10/20	1	2	FACETS	0.877	0.776	0.985	0.877	0.776	0.985	CLONAL	1	TRUE	1	0.270008524938149	2		400	735	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498082	29498082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	95	426	0	ENST00000389048.3:c.1924G>A	p.Asp642Asn	p.D642N	ENST00000389048	NM_004304.4	642	Gac/Aac	11/29	1	2	FACETS	0.845	0.751	0.944	0.845	0.751	0.944	CLONAL	1	TRUE	1	0.270008524938149	2		426	833	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46583308	46583308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374243090	NA	P-0018444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	81	371	0	ENST00000263734.3:c.236C>T	p.Ser79Phe	p.S79F	ENST00000263734	NM_001430.4	79	tCc/tTc	3/16	1	2	FACETS	0.917	0.809	1	0.917	0.809	1	CLONAL	1	TRUE	1	0.270008524938149	2		371	654	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033968	48033968	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	97	346	2	ENST00000234420.5:c.4052A>T	p.His1351Leu	p.H1351L	ENST00000234420	NM_000179.2	1351	cAt/cTt	10/10	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.270008524938149	2		348	676	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523313	9523313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866291709	NA	P-0018444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	129	452	2	ENST00000353224.5:c.1924C>T	p.Pro642Ser	p.P642S	ENST00000353224	NM_177990.2	642	Ccc/Tcc	9/10	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.270008524938149	2		454	893	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713329	40713329	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	114	487	0	ENST00000373198.4:c.4186C>T	p.His1396Tyr	p.H1396Y	ENST00000373198	NM_133170.3	1396	Cac/Tac	30/32	1	2	FACETS	0.953	0.857	1	0.953	0.857	1	CLONAL	1	TRUE	1	0.270008524938149	2		487	886	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680659	30680659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	98	376	0	ENST00000376406.3:c.1060C>T	p.His354Tyr	p.H354Y	ENST00000376406	NM_014641.2	354	Cat/Tat	5/15	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.270008524938149	2		376	716	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741653	145741653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	123	476	0	ENST00000428558.2:c.850C>T	p.Pro284Ser	p.P284S	ENST00000428558	NM_004260.3	284	Ccc/Tcc	5/22	1	2	FACETS	0.959	0.866	1	0.959	0.866	1	CLONAL	1	TRUE	1	0.270008524938149	2		476	950	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939730	76939730	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	126	519	0	ENST00000373344.5:c.1018A>G	p.Thr340Ala	p.T340A	ENST00000373344	NM_000489.3	340	Acc/Gcc	9/35	1	2	FACETS	0.93	0.84	1	0.93	0.84	1	CLONAL	1	TRUE	1	0.270008524938149	2		519	1004	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	91	364	1				ENST00000310581	NM_198253.2	-/1132			0.118572135950808	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.767396130245244	0		365	267	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720679	89720679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123329	NA	P-0018445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	99	123	0	ENST00000371953.3:c.830C>T	p.Thr277Ile	p.T277I	ENST00000371953	NM_000314.4	277	aCa/aTa	8/9	0.767396130245244	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.767396130245244	1		123	144	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226584	2226898	+	inframe_deletion	In_Frame_Del	DEL	CGCAGCGCGGCAAGGAGGGCTCGGACGCCAACCCTTTCCTGAGCAAGAGGCAGCTGGACGGCCTGGCTGGGCTGAAGGGCGAGGGCAGCCGCGGCAAGGAGGCAGGGGAGGGCGGCCTACCGCTGTGCGGGCCCACGGACAAGACCCCACTGCTGAGCGGCAAGGCCGCCAAGGCCCGGGACCGCGAGGTCGACCTCAAGAATGGCCACAACCTCTTCATCTCTGCGGCGGCCGTGCCTCCCGGAAGCCTCCTCAGCGGCCCCGGCCTGGCCCCGGCGGCGTCCTCCGCAGGCGGCGCGGCGTCCTCCGCCCAGA	CGCAGCGCGGCAAGGAGGGCTCGGACGCCAACCCTTTCCTGAGCAAGAGGCAGCTGGACGGCCTGGCTGGGCTGAAGGGCGAGGGCAGCCGCGGCAAGGAGGCAGGGGAGGGCGGCCTACCGCTGTGCGGGCCCACGGACAAGACCCCACTGCTGAGCGGCAAGGCCGCCAAGGCCCGGGACCGCGAGGTCGACCTCAAGAATGGCCACAACCTCTTCATCTCTGCGGCGGCCGTGCCTCCCGGAAGCCTCCTCAGCGGCCCCGGCCTGGCCCCGGCGGCGTCCTCCGCAGGCGGCGCGGCGTCCTCCGCCCAGA	-	novel	NA	P-0018445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	228	439	1	ENST00000398665.3:c.4068_4382del	p.Gln1356_Thr1460del	p.Q1356_T1460del	ENST00000398665	NM_032482.2	1355	tCGCAGCGCGGCAAGGAGGGCTCGGACGCCAACCCTTTCCTGAGCAAGAGGCAGCTGGACGGCCTGGCTGGGCTGAAGGGCGAGGGCAGCCGCGGCAAGGAGGCAGGGGAGGGCGGCCTACCGCTGTGCGGGCCCACGGACAAGACCCCACTGCTGAGCGGCAAGGCCGCCAAGGCCCGGGACCGCGAGGTCGACCTCAAGAATGGCCACAACCTCTTCATCTCTGCGGCGGCCGTGCCTCCCGGAAGCCTCCTCAGCGGCCCCGGCCTGGCCCCGGCGGCGTCCTCCGCAGGCGGCGCGGCGTCCTCCGCCCAGAcg/tcg	27/28	1	2	FACETS	0.946	0.887	1	0.946	0.887	1	CLONAL	1	TRUE	1	0.767396130245244	2		440	628	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0018446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	160	755	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	0.275485454791415	1	FACETS	0.878	0.806	0.953	1	0.991	1	CLONAL	2	TRUE	0	0.2	1		755	820	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30099969	30099969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375956203	NA	P-0018446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	59	322	0	ENST00000331968.5:c.1651G>A	p.Gly551Ser	p.G551S	ENST00000331968	NM_002742.2	551	Ggt/Agt	10/18	1	2	FACETS	0.86	0.739	0.992	0.86	0.739	0.992	CLONAL	1	TRUE	1	0.2	2		322	686	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632648	3632648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	165	490	0	ENST00000294008.3:c.5200G>A	p.Glu1734Lys	p.E1734K	ENST00000294008	NM_032444.2	1734	Gag/Aag	15/15	1	2	FACETS	0.755	0.693	0.821	1	0.988	1	SUBCLONAL	2	TRUE	1	0.2	2		490	1092	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573157	41573161	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGC	GCAGC	-	novel	NA	P-0018446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	70	374	1	ENST00000263253.7:c.5442_5446del	p.Gln1815ThrfsTer66	p.Q1815Tfs*66	ENST00000263253	NM_001429.3	1814	cgGCAGCaa/cgaa	31/31	0.166010235892648	1	FACETS	0.798	0.695	0.911	0.798	0.695	0.911	CLONAL	1	TRUE	0	0.2	1		375	789	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211008	55211008	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	194	306	1	ENST00000275493.2:c.251A>T	p.Glu84Val	p.E84V	ENST00000275493	NM_005228.3	84	gAg/gTg	3/28	0.3	3	FACETS	0.947	0.879	1	1	0.99	1	CLONAL	3	TRUE	1	0.2	3		307	751	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579559	7579559	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	122	523	0	ENST00000269305.4:c.128del	p.Leu43Ter	p.L43*	ENST00000269305	NM_001126112.2	43	tTg/tg	4/11	0.181368308722949	2	FACETS	0.866	0.785	0.951	0.866	0.785	0.951	CLONAL	2	TRUE	0	0.228350544210237	2		523	617	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776636	9776643	+	frameshift_variant	Frame_Shift_Del	DEL	CATGAGTA	CATGAGTA	-	novel	NA	P-0018447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	41	517	0	ENST00000377346.4:c.740_747del	p.His247ProfsTer39	p.H247Pfs*39	ENST00000377346	NM_005026.3	247	CATGAGTAc/c	6/24	1	2	FACETS	0.628	0.522	0.746	0.628	0.522	0.746	SUBCLONAL	1	TRUE	1	0.228350544210237	2		517	572	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281226	142281226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	93	472	1	ENST00000350721.4:c.1018G>A	p.Asp340Asn	p.D340N	ENST00000350721	NM_001184.3	340	Gat/Aat	4/47	0.228350544210237	5	FACETS	1	0.978	1	0.486	0.432	0.544	CLONAL	1	TRUE	2	0.228350544210237	5		473	750	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983031	149983031	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	86	561	0	ENST00000253339.5:c.3227A>G	p.Tyr1076Cys	p.Y1076C	ENST00000253339		1076	tAt/tGt	7/7	0.228350544210237	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.228350544210237	1		561	529	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142985	30143000	+	protein_altering_variant	In_Frame_Del	DEL	CTTGGCGAATCCACCA	CTTGGCGAATCCACCA	G	novel	NA	P-0018447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	58	756	0	ENST00000389048.3:c.526_541delinsC	p.Trp176_Gly181delinsArg	p.W176_G181delinsR	ENST00000389048	NM_004304.4	176	TGGTGGATTCGCCAAGgc/Cgc	1/29	0.228350544210237	3	FACETS	0.759	0.651	0.877	0.379	0.325	0.439	SUBCLONAL	1	TRUE	1	0.228350544210237	3		756	746	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	860	917	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.688291541296991	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.688291541296991	3		917	1077	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274772	123274772	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	253	586	1	ENST00000358487.5:c.1146C>A	p.Cys382Ter	p.C382*	ENST00000358487	NM_000141.4	382	tgC/tgA	9/18	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.688291541296991	2		587	720	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245229	133245229	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	579	627	1	ENST00000320574.5:c.2018G>T	p.Gly673Val	p.G673V	ENST00000320574	NM_006231.2	673	gGc/gTc	18/49	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	2	TRUE	NA	0.688291541296991	2		628	778	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052629	42052629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	254	512	2	ENST00000219905.7:c.7300C>T	p.Arg2434Trp	p.R2434W	ENST00000219905	NM_001164273.1	2434	Cgg/Tgg	20/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.688291541296991	2		514	656	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578551	7578551	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	333	744	1	ENST00000269305.4:c.379T>A	p.Ser127Thr	p.S127T	ENST00000269305	NM_001126112.2	127	Tcc/Acc	5/11	0.688291541296991	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.688291541296991	1		745	572	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604773	48604773	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	453	476	0	ENST00000342988.3:c.1595C>A	p.Ala532Asp	p.A532D	ENST00000342988	NM_005359.5	532	gCc/gAc	12/12	0.688291541296991	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.688291541296991	2		476	600	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131415	202131415	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	360	562	0	ENST00000358485.4:c.383T>G	p.Ile128Ser	p.I128S	ENST00000358485	NM_001080125.1	128	aTt/aGt	2/9	0.369169563279949	3	FACETS	0.909	0.868	0.951	0.909	0.868	0.951	INDETERMINATE	2	TRUE	1	0.688291541296991	3		562	773	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646177	215646177	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	251	540	0	ENST00000260947.4:c.421A>G	p.Asn141Asp	p.N141D	ENST00000260947	NM_000465.2	141	Aat/Gat	4/11	0.369169563279949	3	FACETS	1	0.986	1	0.589	0.553	0.627	INDETERMINATE	1	TRUE	1	0.688291541296991	3		540	832	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264292	46264292	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	160	392	0	ENST00000371998.3:c.1339G>A	p.Gly447Ser	p.G447S	ENST00000371998		447	Ggc/Agc	11/23	0.657770394329168	4	FACETS	0.873	0.801	0.949	0.437	0.4	0.475	CLONAL	1	TRUE	2	0.688291541296991	4		392	899	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436674	52436674	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	221	595	0	ENST00000460680.1:c.2000G>C	p.Arg667Thr	p.R667T	ENST00000460680	NM_004656.3	667	aGg/aCg	16/17	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.688291541296991	2		595	622	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437647	52437647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1322319973	NA	P-0018448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	239	489	0	ENST00000460680.1:c.1514C>T	p.Ser505Leu	p.S505L	ENST00000460680	NM_004656.3	505	tCg/tTg	13/17	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.688291541296991	2		489	602	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873105	134873105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749312347	NA	P-0018448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	232	551	0	ENST00000398015.3:c.1409G>A	p.Arg470Gln	p.R470Q	ENST00000398015	NM_004441.4	470	cGg/cAg	6/16	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.688291541296991	2		551	674	SUCCESS
APC	324	MSKCC	GRCh37	5	112176008	112176008	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	183	452	0	ENST00000257430.4:c.4717G>T	p.Glu1573Ter	p.E1573*	ENST00000257430	NM_000038.5	1573	Gaa/Taa	16/16	0.688291541296991	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.688291541296991	1		452	327	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923614	131923614	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0018448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	156	386	0	ENST00000265335.6:c.886-2A>T		p.X296_splice	ENST00000265335		296			1	2	FACETS	0.944	0.872	1	0.944	0.872	1	CLONAL	1	TRUE	1	0.688291541296991	2		386	480	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225129	53225129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs967652938	NA	P-0018448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	199	591	5	ENST00000375401.3:c.3089G>A	p.Arg1030Gln	p.R1030Q	ENST00000375401	NM_004187.3	1030	cGg/cAg	20/26	0.688291541296991	4	FACETS	0.833	0.77	0.898	0.278	0.256	0.3	CLONAL	1	TRUE	1	0.688291541296991	4		596	1172	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412209	63412210	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0018448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	934	810	0	ENST00000330258.3:c.956_957dup	p.Lys320Ter	p.K320*	ENST00000330258	NM_152424.3	319	-/TG	2/2	0.688291541296991	4	FACETS	0.965	0.941	0.99	0.965	0.941	0.99	CLONAL	3	TRUE	1	0.688291541296991	4		810	1582	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0018449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	117	343	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.997	0.908	1	0.997	0.908	1	CLONAL	1	TRUE	1	0.612803950389473	2		344	383	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412664	139412664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	173	727	0	ENST00000277541.6:c.1180G>A	p.Gly394Ser	p.G394S	ENST00000277541	NM_017617.3	394	Ggc/Agc	7/34	1	2	FACETS	0.939	0.869	1	0.939	0.869	1	CLONAL	1	TRUE	1	0.612803950389473	2		727	601	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443643	49443643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1361420677	NA	P-0018449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	158	653	0	ENST00000301067.7:c.3728G>A	p.Gly1243Glu	p.G1243E	ENST00000301067	NM_003482.3	1243	gGg/gAg	11/54	1	2	FACETS	0.969	0.894	1	0.969	0.894	1	CLONAL	1	TRUE	1	0.612803950389473	2		653	532	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096886	11096886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	214	837	4	ENST00000358026.2:c.377G>A	p.Gly126Asp	p.G126D	ENST00000358026	NM_001128849.1	126	gGc/gAc	4/36	0.452876236458144	3	FACETS	0.968	0.9	1	0.484	0.45	0.519	CLONAL	1	TRUE	1	0.612803950389473	3		841	943	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0018450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	445	573	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.570233740153601	2	FACETS	0.877	0.843	0.911	0.877	0.843	0.911	CLONAL	2	TRUE	0	0.59684108856533	2		573	850	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0018450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	401	457	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.530860654439697	3	FACETS	0.839	0.8	0.878	0.839	0.8	0.878	CLONAL	2	TRUE	1	0.59684108856533	3		457	1040	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	403	393	0	ENST00000256196.4:c.68G>T	p.Gly23Val	p.G23V	ENST00000256196		23	gGc/gTc	1/6	0.580401448995969	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.59684108856533	2		393	656	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0018451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	528	752	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	2	TRUE	NA	0.865174445018261	2		754	582	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	579	917	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.86108465680401	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.865174445018261	2		917	664	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0018451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	461	343	1				ENST00000310581	NM_198253.2	-/1132			0.843593114082848	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.865174445018261	3		344	738	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456725	32456725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	247	518	0	ENST00000332351.3:c.167G>A	p.Arg56Gln	p.R56Q	ENST00000332351	NM_024426.4	56	cGg/cAg	1/10	0.739009508475831	4	FACETS	1	0.962	1	0.521	0.487	0.555	CLONAL	1	TRUE	2	0.865174445018261	4		518	1023	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919281	48919281	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	333	352	0	ENST00000267163.4:c.446del	p.Ser149Ter	p.S149*	ENST00000267163	NM_000321.2	149	tCa/ta	4/27	0.865174445018261	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.865174445018261	2		352	375	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449562	149449562	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	593	611	0	ENST00000286301.3:c.1384C>A	p.Pro462Thr	p.P462T	ENST00000286301	NM_005211.3	462	Ccc/Acc	10/22	0.865174445018261	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.865174445018261	2		611	678	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553485	106553485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	120	310	0	ENST00000369096.4:c.1450C>T	p.Pro484Ser	p.P484S	ENST00000369096	NM_001198.3	484	Ccc/Tcc	5/7	0.739009508475831	4	FACETS	0.922	0.836	1	0.461	0.418	0.507	CLONAL	1	TRUE	2	0.865174445018261	4		310	561	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200329	138200329	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	215	406	2	ENST00000237289.4:c.1747G>C	p.Gly583Arg	p.G583R	ENST00000237289	NM_001270507.1	583	Gga/Cga	7/9	0.864557177171852	3	FACETS	1	0.979	1	0.556	0.52	0.594	CLONAL	1	TRUE	1	0.865174445018261	3		408	640	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861870	57861870	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	158	577	0	ENST00000228682.2:c.1171G>C	p.Ala391Pro	p.A391P	ENST00000228682	NM_005269.2	391	Gcc/Ccc	10/12	0.217685303600011	3	FACETS	1	0.983	1	0.639	0.586	0.694	INDETERMINATE	1	TRUE	1	0.388485078189963	3		577	760	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514905	103514905	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	65	370	0	ENST00000355739.4:c.1406A>G	p.Asp469Gly	p.D469G	ENST00000355739	NM_000123.3	469	gAc/gGc	8/15	0.231291874554753	1	FACETS	0.702	0.612	0.799	0.702	0.612	0.799	INDETERMINATE	1	TRUE	0	0.388485078189963	1		370	384	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2089939	2089939	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	73	402	0	ENST00000219066.1:c.925G>T	p.Ala309Ser	p.A309S	ENST00000219066	NM_002528.5	309	Gcc/Tcc	6/6	0.29721422772931	2	FACETS	0.959	0.843	1	0.479	0.421	0.541	CLONAL	1	TRUE	0	0.388485078189963	2		402	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577539	+	missense_variant	Missense_Mutation	DNP	CG	CG	AA	novel	NA	P-0018452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	236	582	0	ENST00000269305.4:c.742_743delinsTT	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	CGg/TTg	7/11	0.216168543076452	3	FACETS	1	0.972	1	0.707	0.663	0.752	INDETERMINATE	2	TRUE	0	0.388485078189963	3		582	684	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248598	10248598	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	88	579	1	ENST00000340748.4:c.4155G>T	p.Glu1385Asp	p.E1385D	ENST00000340748		1385	gaG/gaT	35/40	0.335452942740794	3	FACETS	0.831	0.737	0.932	0.416	0.368	0.466	CLONAL	1	TRUE	1	0.388485078189963	3		580	651	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266934	18266934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	62	464	1	ENST00000222254.8:c.245C>T	p.Ala82Val	p.A82V	ENST00000222254	NM_005027.3	82	gCc/gTc	2/16	0.288730581919695	4	FACETS	0.709	0.612	0.814	0.355	0.306	0.407	SUBCLONAL	1	TRUE	2	0.388485078189963	4		465	625	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747127	40747127	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	267	494	1	ENST00000373198.4:c.2955G>T	p.Glu985Asp	p.E985D	ENST00000373198	NM_133170.3	985	gaG/gaT	22/32	0.310713198443264	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.388485078189963	4		495	828	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670648	134670648	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	367	624	0	ENST00000398015.3:c.559C>G	p.Leu187Val	p.L187V	ENST00000398015	NM_004441.4	187	Ctt/Gtt	3/16	0.388485078189963	5	FACETS	0.856	0.812	0.9	0.513	0.487	0.54	CLONAL	3	TRUE	0	0.388485078189963	5		624	1165	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169981211	169981211	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	79	566	0	ENST00000295797.4:c.358G>C	p.Glu120Gln	p.E120Q	ENST00000295797	NM_002740.5	120	Gaa/Caa	4/18	0.388485078189963	7	FACETS	0.668	0.585	0.758			1	SUBCLONAL	1	TRUE	NA	0.388485078189963	7		566	1200	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0018452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	309	824	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.388485078189963	7	FACETS	0.919	0.866	0.972	0.459	0.433	0.486	CLONAL	3	TRUE	1	0.388485078189963	7		824	1138	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250464	26250464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	62	517	0	ENST00000446824.2:c.370G>A	p.Asp124Asn	p.D124N	ENST00000446824	NM_021018.2	124	Gac/Aac	1/1	0.217685303600011	3	FACETS	0.734	0.635	0.842	0.367	0.317	0.421	INDETERMINATE	1	TRUE	1	0.388485078189963	3		517	519	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687241	117687241	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	48	308	0	ENST00000368508.3:c.2810C>T	p.Pro937Leu	p.P937L	ENST00000368508	NM_002944.2	937	cCa/cTa	18/43	1	2	FACETS	0.644	0.545	0.751	0.644	0.545	0.751	SUBCLONAL	1	TRUE	1	0.388485078189963	2		308	384	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227991	55227991	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	419	504	0	ENST00000275493.2:c.1458G>C	p.Gln486His	p.Q486H	ENST00000275493	NM_005228.3	486	caG/caC	12/28	0.388485078189963	6	FACETS	1	0.965	1	0.808	0.773	0.843	CLONAL	4	TRUE	1	0.388485078189963	6		504	949	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896363	151896363	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0018452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	152	362	0	ENST00000262189.6:c.4273+1G>T		p.X1425_splice	ENST00000262189	NM_170606.2	1425			0.388485078189963	3	FACETS	0.793	0.729	0.86	0.793	0.729	0.86	SUBCLONAL	2	TRUE	1	0.388485078189963	3		362	589	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343538	70343538	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	61	660	2	ENST00000374080.3:c.1712T>A	p.Leu571Gln	p.L571Q	ENST00000374080		571	cTg/cAg	12/45	0.217685303600011	3	FACETS	0.46	0.396	0.53	0.23	0.198	0.265	INDETERMINATE	1	TRUE	1	0.388485078189963	3		662	815	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191804	123191804	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	46	446	0	ENST00000218089.9:c.1393G>T	p.Val465Phe	p.V465F	ENST00000218089	NM_001042749.1	465	Gtt/Ttt	15/35	0.217685303600011	3	FACETS	0.364	0.305	0.428	0.182	0.152	0.214	INDETERMINATE	1	TRUE	1	0.388485078189963	3		446	778	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162735807	162735807	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	132	731	0	ENST00000367921.3:c.1116C>G	p.Asn372Lys	p.N372K	ENST00000367921	NM_006182.2	372	aaC/aaG	10/18	0.509317107354963	6	FACETS	1	0.929	1	0.257	0.233	0.283	CLONAL	1	TRUE	2	0.509317107354963	6		731	1017	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138627	11138627	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0018453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	86	499	0	ENST00000358026.2:c.3382+1G>A		p.X1128_splice	ENST00000358026	NM_001128849.1	1128			0.383314845870427	4	FACETS	1	0.961	1	0.591	0.526	0.661	CLONAL	1	TRUE	2	0.509317107354963	4		499	431	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497323	149497323	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1561984776	NA	P-0018453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	216	578	0	ENST00000261799.4:c.2995C>T	p.Arg999Ter	p.R999*	ENST00000261799	NM_002609.3	999	Cga/Tga	22/23	0.509522506727734	4	FACETS	0.924	0.863	0.986			1	CLONAL	2	TRUE	NA	0.509317107354963	4		578	693	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242486	+	protein_altering_variant	In_Frame_Del	DEL	ATTAAGAGAAGCAACATCT	ATTAAGAGAAGCAACATCT	GCAA	novel	NA	P-0018453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	268	703	2	ENST00000275493.2:c.2238_2256delinsGCAA	p.Leu747_Ser752delinsGln	p.L747_S752delinsQ	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACATCT/gaGCAA	19/28	0.509317107354963	6	FACETS	1	0.95	1	0.755	0.713	0.799	CLONAL	3	TRUE	2	0.509317107354963	6		705	703	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0018455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	384	900	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.275942568663025	3	FACETS	0.856	0.814	0.898	0.856	0.814	0.898	INDETERMINATE	2	TRUE	1	0.50948866209263	3		901	1105	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0018455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	220	595	3	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.50948866209263	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.50948866209263	1		598	586	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039372	47039372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	372	660	0	ENST00000377604.3:c.995G>A	p.Arg332His	p.R332H	ENST00000377604	NM_001204468.1	332	cGc/cAc	10/24	0.281625105115784	2	FACETS	0.773	0.736	0.811	0.773	0.736	0.811	INDETERMINATE	2	TRUE	0	0.50948866209263	2		660	944	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934874	NA	P-0018456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	223	661	0	ENST00000269305.4:c.451C>G	p.Pro151Ala	p.P151A	ENST00000269305	NM_001126112.2	151	Ccc/Gcc	5/11	0.468387142706217	1	FACETS	0.952	0.889	1	0.952	0.889	1	CLONAL	1	TRUE	0	0.468387142706217	1		661	766	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222986	1222986	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs864622488	NA	P-0018456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	181	498	0	ENST00000326873.7:c.923G>T	p.Trp308Leu	p.W308L	ENST00000326873	NM_000455.4	308	tGg/tTg	8/10	0.468387142706217	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.468387142706217	1		498	549	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748739	43748739	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	241	725	0	ENST00000382044.4:c.2067G>A	p.Met689Ile	p.M689I	ENST00000382044	NM_001141980.1	689	atG/atA	12/28	NA	2	FACETS	0.785	0.732	0.84			1	INDETERMINATE	1	TRUE	NA	0.468387142706217	2		725	1311	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748795	43748795	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	217	750	0	ENST00000382044.4:c.2011G>T	p.Glu671Ter	p.E671*	ENST00000382044	NM_001141980.1	671	Gaa/Taa	12/28	NA	2	FACETS	0.731	0.678	0.785			1	INDETERMINATE	1	TRUE	NA	0.468387142706217	2		750	1268	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796945	78796945	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	207	512	0	ENST00000306801.3:c.1058C>A	p.Ala353Glu	p.A353E	ENST00000306801	NM_020761.2	353	gCg/gAg	9/34	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.468387142706217	2		512	849	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866394	42866394	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	191	599	1	ENST00000398585.3:c.238C>G	p.Gln80Glu	p.Q80E	ENST00000398585	NM_001135099.1	80	Cag/Gag	3/14	0.451640762907281	3	FACETS	0.96	0.887	1	0.48	0.443	0.518	CLONAL	1	TRUE	1	0.468387142706217	3		600	1048	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2111996	2111996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374936223	NA	P-0018458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	36	632	1	ENST00000219476.3:c.1244C>T	p.Ala415Val	p.A415V	ENST00000219476	NM_000548.3	415	gCg/gTg	12/42	1	2	FACETS	0.427	0.35	0.513	0.427	0.35	0.513	SUBCLONAL	1	TRUE	1	0.292216474799924	2		633	577	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213590	36213590	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	131	614	0	ENST00000222270.7:c.2692C>T	p.Leu898Phe	p.L898F	ENST00000222270	NM_014727.1	898	Ctc/Ttc	5/37	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.292216474799924	2		614	848	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0018459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	28	613	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.43	0.343	0.53	0.43	0.343	0.53	SUBCLONAL	1	TRUE	1	0.264988840038245	2		613	491	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0018459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	16	220	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.422	0.312	0.554	0.422	0.312	0.554	SUBCLONAL	1	TRUE	1	0.264988840038245	2		220	286	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690847	89690847	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776667	NA	P-0018459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	64	396	0	ENST00000371953.3:c.253+1G>A		p.X85_splice	ENST00000371953	NM_000314.4	85			1	2	FACETS	0.994	0.862	1	0.994	0.862	1	CLONAL	1	TRUE	1	0.264988840038245	2		396	486	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121909229	NA	P-0018459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	76	413	4	ENST00000371953.3:c.389G>T	p.Arg130Leu	p.R130L	ENST00000371953	NM_000314.4	130	cGa/cTa	5/9	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.264988840038245	2		417	489	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057947	27057948	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	83	647	0	ENST00000324856.7:c.1656dup	p.Gln553ThrfsTer70	p.Q553Tfs*70	ENST00000324856	NM_006015.4	552	tca/tcAa	3/20	1	2	FACETS	0.793	0.699	0.894	0.793	0.699	0.894	SUBCLONAL	1	TRUE	1	0.264988840038245	2		647	790	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339328	70339328	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0018459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	97	378	1	ENST00000374080.3:c.204+1G>T		p.X68_splice	ENST00000374080		68			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.264988840038245	2		379	494	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138473	11138473	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	78	530	0	ENST00000358026.2:c.3229C>T	p.Arg1077Ter	p.R1077*	ENST00000358026	NM_001128849.1	1077	Cga/Tga	24/36	1	2	FACETS	0.848	0.745	0.959	0.848	0.745	0.959	CLONAL	1	TRUE	1	0.264988840038245	2		530	694	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916913	178916915	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0018459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	60	531	0	ENST00000263967.3:c.301_303del	p.Val101del	p.V101del	ENST00000263967	NM_006218.2	100	aaAGTa/aaa	2/21	1	2	FACETS	0.584	0.502	0.673	0.584	0.502	0.673	SUBCLONAL	1	TRUE	1	0.264988840038245	2		531	776	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468052	50468052	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	45	356	0	ENST00000331340.3:c.1287G>C	p.Lys429Asn	p.K429N	ENST00000331340	NM_006060.4	429	aaG/aaC	8/8	1	2	FACETS	0.839	0.706	0.985	0.839	0.706	0.985	CLONAL	1	TRUE	1	0.264988840038245	2		356	405	SUCCESS
AR	367	MSKCC	GRCh37	X	66765325	66765325	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	72	612	1	ENST00000374690.3:c.337G>T	p.Glu113Ter	p.E113*	ENST00000374690	NM_000044.3	113	Gaa/Taa	1/8	1	2	FACETS	0.741	0.647	0.843	0.741	0.647	0.843	SUBCLONAL	1	TRUE	1	0.264988840038245	2		613	733	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0018460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	42	691	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	0.511	0.726	0.613	0.511	0.726	SUBCLONAL	1	TRUE	1	0.23	2		691	596	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640924	3640924	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	170	735	0	ENST00000294008.3:c.2715G>C	p.Glu905Asp	p.E905D	ENST00000294008	NM_032444.2	905	gaG/gaC	12/15	0.267000201473845	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.23	3		735	756	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271877	18271877	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	80	575	0	ENST00000222254.8:c.480C>G	p.Ser160Arg	p.S160R	ENST00000222254	NM_005027.3	160	agC/agG	5/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.23	2		575	565	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289895	15289895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370233852	NA	P-0018461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	156	756	0	ENST00000263388.2:c.3659G>A	p.Arg1220Gln	p.R1220Q	ENST00000263388	NM_000435.2	1220	cGg/cAg	22/33	0.405914701579289	3	FACETS	0.879	0.805	0.957	0.44	0.402	0.479	CLONAL	1	TRUE	1	0.495285306676387	3		756	894	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0018461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	136	480	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.479537389176349	2	FACETS	0.988	0.902	1	0.494	0.451	0.539	CLONAL	1	TRUE	0	0.495285306676387	2		481	556	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188397	142188397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1169255490	NA	P-0018461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	24	432	2	ENST00000350721.4:c.6334C>T	p.Arg2112Cys	p.R2112C	ENST00000350721	NM_001184.3	2112	Cgt/Tgt	38/47	0.457567103501801	3	FACETS	0.285	0.222	0.356	0.095	0.074	0.119	SUBCLONAL	1	TRUE	0	0.495285306676387	3		434	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0018461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	289	647	1	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	0.448723821988279	2	FACETS	0.846	0.801	0.891	0.846	0.801	0.891	CLONAL	2	TRUE	0	0.495285306676387	2		648	690	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354314	354314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368340732	NA	P-0018461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	124	534	1	ENST00000262320.3:c.1244G>A	p.Arg415His	p.R415H	ENST00000262320	NM_003502.3	415	cGc/cAc	5/11	0.479537389176349	2	FACETS	0.764	0.693	0.839	0.382	0.346	0.42	SUBCLONAL	1	TRUE	0	0.495285306676387	2		535	655	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858738	9858738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149698593	NA	P-0018461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	118	244	0	ENST00000330684.3:c.2663C>T	p.Thr888Met	p.T888M	ENST00000330684	NM_001134407.1	888	aCg/aTg	13/13	0.479537389176349	2	FACETS	0.86	0.79	0.932	0.86	0.79	0.932	CLONAL	2	TRUE	0	0.495285306676387	2		244	277	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023957	31023957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139435094	NA	P-0018461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	133	638	1	ENST00000375687.4:c.3442C>T	p.Arg1148Cys	p.R1148C	ENST00000375687	NM_015338.5	1148	Cgc/Tgc	13/13	0.479537389176349	2	FACETS	0.793	0.722	0.868	0.397	0.361	0.434	SUBCLONAL	1	TRUE	0	0.495285306676387	2		639	677	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158626924	158626924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760152551	NA	P-0018461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	289	609	1	ENST00000263640.3:c.746C>T	p.Thr249Met	p.T249M	ENST00000263640	NM_001105.4	249	aCg/aTg	7/11	0.479537389176349	2	FACETS	0.854	0.809	0.9	0.854	0.809	0.9	CLONAL	2	TRUE	0	0.495285306676387	2		610	683	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115252203	115252203	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	158	360	0	ENST00000369535.4:c.437C>T	p.Ala146Val	p.A146V	ENST00000369535	NM_002524.4	146	gCc/gTc	4/7	0.430558808662706	3	FACETS	0.894	0.827	0.963	0.596	0.551	0.642	CLONAL	2	TRUE	0	0.495285306676387	3		360	445	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391716	139391716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371742334	NA	P-0018461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	293	563	0	ENST00000277541.6:c.6475C>T	p.Arg2159Cys	p.R2159C	ENST00000277541	NM_017617.3	2159	Cgc/Tgc	34/34	0.471842388110566	4	FACETS	0.878	0.827	0.929	0.439	0.413	0.465	CLONAL	2	TRUE	0	0.495285306676387	4		563	1008	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980581	1980581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370127436	NA	P-0018461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	271	567	0	ENST00000382891.5:c.4043C>T	p.Pro1348Leu	p.P1348L	ENST00000382891	NM_133335.3	1348	cCg/cTg	22/22	0.448723821988279	2	FACETS	0.913	0.865	0.962	0.913	0.865	0.962	CLONAL	2	TRUE	0	0.495285306676387	2		567	599	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22412956	22412956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553196096	NA	P-0018461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	34	177	1	ENST00000344548.3:c.203G>A	p.Arg68Gln	p.R68Q	ENST00000344548	NM_001039802.1	68	cGa/cAa	5/7	0.430558808662706	3	FACETS	0.735	0.605	0.88	0.245	0.201	0.294	SUBCLONAL	1	TRUE	0	0.495285306676387	3		178	233	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104269023	104269023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	341	581	2	ENST00000369902.3:c.280G>A	p.Gly94Ser	p.G94S	ENST00000369902	NM_016169.3	94	Ggc/Agc	2/12	0.479537389176349	2	FACETS	0.984	0.938	1	0.984	0.938	1	CLONAL	2	TRUE	0	0.495285306676387	2		583	700	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436467	110436467	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	445	940	2	ENST00000375856.3:c.1934G>A	p.Ser645Asn	p.S645N	ENST00000375856	NM_003749.2	645	aGc/aAc	1/2	0.479537389176349	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.495285306676387	2		942	878	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543265	65543265	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	20	308	0	ENST00000358664.4:c.412T>G	p.Ser138Ala	p.S138A	ENST00000358664	NM_002382.4	138	Tcg/Gcg	5/5	0.448955038726514	2	FACETS	0.214	0.163	0.274	0.107	0.081	0.137	SUBCLONAL	1	TRUE	0	0.495285306676387	2		308	377	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557618	95557618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	76	696	0	ENST00000393063.1:c.5449G>A	p.Gly1817Ser	p.G1817S	ENST00000393063	NM_030621.3	1817	Ggt/Agt	26/28	0.448955038726514	2	FACETS	0.402	0.352	0.456	0.201	0.176	0.228	SUBCLONAL	1	TRUE	0	0.495285306676387	2		696	764	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350438	89350438	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	466	805	2	ENST00000301030.4:c.2512C>T	p.Arg838Ter	p.R838*	ENST00000301030	NM_001256183.1	838	Cga/Tga	9/13	0.479537389176349	2	FACETS	0.995	0.955	1	0.995	0.955	1	CLONAL	2	TRUE	0	0.495285306676387	2		807	946	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015267	128015267	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	231	497	0	ENST00000285398.2:c.2254G>A	p.Gly752Arg	p.G752R	ENST00000285398	NM_000122.1	752	Ggg/Agg	15/15	0.479537389176349	2	FACETS	0.9	0.848	0.953	0.9	0.848	0.953	CLONAL	2	TRUE	0	0.495285306676387	2		497	518	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62294212	62294212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866785110	NA	P-0018461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	385	729	1	ENST00000360203.5:c.508C>T	p.Arg170Cys	p.R170C	ENST00000360203	NM_001283009.1	170	Cgc/Tgc	6/35	0.479537389176349	2	FACETS	0.95	0.908	0.992	0.95	0.908	0.992	CLONAL	2	TRUE	0	0.495285306676387	2		730	818	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518921	187518921	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs748249672	NA	P-0018461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	157	605	1	ENST00000441802.2:c.12283G>T	p.Asp4095Tyr	p.D4095Y	ENST00000441802	NM_005245.3	4095	Gat/Tat	24/27	0.448723821988279	2	FACETS	0.874	0.803	0.949	0.437	0.401	0.475	CLONAL	1	TRUE	0	0.495285306676387	2		606	725	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562721	176562721	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	353	676	0	ENST00000439151.2:c.617C>T	p.Ala206Val	p.A206V	ENST00000439151	NM_022455.4	206	gCc/gTc	2/23	0.479537389176349	2	FACETS	0.898	0.855	0.94	0.898	0.855	0.94	CLONAL	2	TRUE	0	0.495285306676387	2		676	794	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174441	11174441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	97	698	1	ENST00000361445.4:c.7234G>A	p.Asp2412Asn	p.D2412N	ENST00000361445	NM_004958.3	2412	Gac/Aac	53/58	1	2	FACETS	0.817	0.727	0.914	0.817	0.727	0.914	CLONAL	1	TRUE	1	0.233605323742756	2		699	1016	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692836	89692836	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs786204858	NA	P-0018462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	87	206	0	ENST00000371953.3:c.320A>T	p.Asp107Val	p.D107V	ENST00000371953	NM_000314.4	107	gAt/gTt	5/9	0.233605323742756	3	FACETS	0.994	0.891	1	1	0.981	1	CLONAL	3	TRUE	1	0.233605323742756	3		206	279	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0018462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	496	1181	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.233605323742756	6	FACETS	1	0.976	1			1	CLONAL	5	TRUE	NA	0.233605323742756	6		1182	1216	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444938	49444938	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	82	464	1	ENST00000301067.7:c.2528C>T	p.Ser843Phe	p.S843F	ENST00000301067	NM_003482.3	843	tCc/tTc	10/54	0.233605323742756	3	FACETS	1	0.915	1	0.524	0.462	0.591	CLONAL	1	TRUE	1	0.233605323742756	3		465	748	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445318	49445318	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	91	788	0	ENST00000301067.7:c.2148G>T	p.Met716Ile	p.M716I	ENST00000301067	NM_003482.3	716	atG/atT	10/54	0.233605323742756	3	FACETS	0.738	0.653	0.829	0.369	0.326	0.415	SUBCLONAL	1	TRUE	1	0.233605323742756	3		788	1179	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122934	7122934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	76	692	3	ENST00000302850.5:c.3325G>A	p.Gly1109Arg	p.G1109R	ENST00000302850	NM_000208.2	1109	Gga/Aga	18/22	0.21772717581578	1	FACETS	0.652	0.57	0.739	0.652	0.57	0.739	SUBCLONAL	1	TRUE	0	0.233605323742756	1		695	882	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213784	66213784	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	61	667	0	ENST00000273854.3:c.2646G>C	p.Met882Ile	p.M882I	ENST00000273854	NM_004439.5	882	atG/atC	15/18	1	2	FACETS	0.726	0.626	0.836	0.726	0.626	0.836	SUBCLONAL	1	TRUE	1	0.233605323742756	2		667	719	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467388	66467388	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	20	256	0	ENST00000273854.3:c.881G>T	p.Gly294Val	p.G294V	ENST00000273854	NM_004439.5	294	gGa/gTa	3/18	1	2	FACETS	0.493	0.377	0.63	0.493	0.377	0.63	SUBCLONAL	1	TRUE	1	0.233605323742756	2		256	347	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509282	106509282	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	108	529	0	ENST00000359195.3:c.1276G>T	p.Gly426Trp	p.G426W	ENST00000359195	NM_002649.2	426	Ggg/Tgg	2/11	1	2	FACETS	0.964	0.864	1	0.964	0.864	1	CLONAL	1	TRUE	1	0.233605323742756	2		529	959	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139563068	139563068	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs374275228	NA	P-0018462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	65	728	0	ENST00000308874.7:c.140G>T	p.Arg47Leu	p.R47L	ENST00000308874		47	cGt/cTt	4/10	1	2	FACETS	0.552	0.477	0.634	0.552	0.477	0.634	SUBCLONAL	1	TRUE	1	0.233605323742756	2		728	1008	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041648	47041648	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	83	338	0	ENST00000377604.3:c.1873G>T	p.Gly625Ter	p.G625*	ENST00000377604	NM_001204468.1	625	Gga/Tga	17/24	1	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.233605323742756	1		338	538	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829818	76829818	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	146	332	0	ENST00000373344.5:c.6223G>T	p.Gly2075Trp	p.G2075W	ENST00000373344	NM_000489.3	2075	Ggg/Tgg	28/35	0.233605323742756	2	FACETS	0.928	0.854	1			1	CLONAL	3	TRUE	NA	0.233605323742756	2		332	449	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0018463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	47	708	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.646	0.545	0.759	0.646	0.545	0.759	SUBCLONAL	1	TRUE	1	0.24	2		709	606	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226859	2226879	+	inframe_deletion	In_Frame_Del	DEL	GCGGCGTCCTCCGCAGGCGGC	GCGGCGTCCTCCGCAGGCGGC	-	rs748637415	NA	P-0018463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	27	331	0	ENST00000398665.3:c.4353_4373del	p.Gly1452_Ala1458del	p.G1452_A1458del	ENST00000398665	NM_032482.2	1447	GCGGCGTCCTCCGCAGGCGGC/-	27/28	1	2	FACETS	0.627	0.499	0.773	0.627	0.499	0.773	SUBCLONAL	1	TRUE	1	0.24	2		331	359	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023149	48023149	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	44	458	1	ENST00000234420.5:c.574G>T	p.Glu192Ter	p.E192*	ENST00000234420	NM_000179.2	192	Gaa/Taa	3/10	1	2	FACETS	0.63	0.528	0.744	0.63	0.528	0.744	SUBCLONAL	1	TRUE	1	0.24	2		459	582	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948200	55948200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	28	507	0	ENST00000263923.4:c.3771G>T	p.Gln1257His	p.Q1257H	ENST00000263923	NM_002253.2	1257	caG/caT	29/30	1	2	FACETS	0.478	0.381	0.589	0.478	0.381	0.589	SUBCLONAL	1	TRUE	1	0.24	2		507	488	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873597	35873597	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519759	NA	P-0018463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	35	269	0	ENST00000303115.3:c.553A>T	p.Ser185Cys	p.S185C	ENST00000303115	NM_002185.3	185	Agc/Tgc	5/8	0.168602287138636	3	FACETS	1	0.84	1	0.512	0.421	0.614	CLONAL	1	TRUE	1	0.24	3		269	319	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589275	67589275	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	24	467	0	ENST00000274335.5:c.1263T>A	p.Asp421Glu	p.D421E	ENST00000274335		421	gaT/gaA	9/15	1	2	FACETS	0.435	0.34	0.545	0.435	0.34	0.545	SUBCLONAL	1	TRUE	1	0.24	2		467	460	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962588	100962588	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0018464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	101	443	0	ENST00000325455.5:c.1809T>A	p.Cys603Ter	p.C603*	ENST00000325455	NM_001202474.3	603	tgT/tgA	3/8	0.283087912665368	3	FACETS	1	0.954	1	0.562	0.502	0.625	CLONAL	1	TRUE	1	0.283087912665368	3		443	725	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263856	133263856	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	49	280	0	ENST00000320574.5:c.46G>T	p.Asp16Tyr	p.D16Y	ENST00000320574	NM_006231.2	16	Gat/Tat	1/49	0.260754903632355	4	FACETS	0.859	0.728	1	0.43	0.364	0.502	CLONAL	1	TRUE	2	0.283087912665368	4		280	517	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103513931	103513931	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	94	539	0	ENST00000355739.4:c.747T>A	p.His249Gln	p.H249Q	ENST00000355739	NM_000123.3	249	caT/caA	7/15	0.283087912665368	5	FACETS	0.951	0.844	1	0.19	0.168	0.213	CLONAL	1	TRUE	0	0.283087912665368	5		539	995	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	216	510	0	ENST00000269305.4:c.772del	p.Glu258LysfsTer87	p.E258Kfs*87	ENST00000269305	NM_001126112.2	258	Gaa/aa	7/11	0.275473319141998	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.283087912665368	2		510	647	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251845	212251845	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	150	353	0	ENST00000342788.4:c.3214G>T	p.Ala1072Ser	p.A1072S	ENST00000342788	NM_005235.2	1072	Gct/Tct	27/28	0.272668272208017	4	FACETS	0.838	0.77	0.908	0.838	0.77	0.908	CLONAL	3	TRUE	1	0.283087912665368	4		353	541	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426735	212426735	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	99	503	0	ENST00000342788.4:c.2380C>G	p.Leu794Val	p.L794V	ENST00000342788	NM_005235.2	794	Ctg/Gtg	20/28	0.272668272208017	4	FACETS	1	0.945	1	0.365	0.325	0.407	CLONAL	1	TRUE	1	0.283087912665368	4		503	820	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505037	149505037	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	62	409	0	ENST00000261799.4:c.1778G>A	p.Trp593Ter	p.W593*	ENST00000261799	NM_002609.3	593	tGg/tAg	12/23	0.267452160564057	3	FACETS	0.899	0.777	1	0.45	0.388	0.516	CLONAL	1	TRUE	1	0.283087912665368	3		409	556	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578260	7578260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204041	NA	P-0018465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	389	494	0	ENST00000269305.4:c.589G>A	p.Val197Met	p.V197M	ENST00000269305	NM_001126112.2	197	Gtg/Atg	6/11	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	2	TRUE	NA	0.540066975654522	2		494	684	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712000	89712000	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	137	184	0	ENST00000371953.3:c.618del	p.Phe206LeufsTer15	p.F206Lfs*15	ENST00000371953	NM_000314.4	206	ttC/tt	6/9	0.500587844289181	2	FACETS	0.903	0.837	0.968	0.903	0.837	0.968	CLONAL	2	TRUE	0	0.540066975654522	2		184	281	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578502	7578502	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555526241	NA	P-0018467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	1016	660	2	ENST00000269305.4:c.428T>G	p.Val143Gly	p.V143G	ENST00000269305	NM_001126112.2	143	gTg/gGg	5/11	0.852546829175168	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	4	TRUE	0	0.852546829175168	4		662	1104	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0018467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	83	124	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	0.852546829175168	6	FACETS	1	0.956	1	1	0.956	1	CLONAL	4	TRUE	2	0.852546829175168	6		124	125	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141067	55141074	+	protein_altering_variant	In_Frame_Del	DEL	ATATATTT	ATATATTT	TA	novel	NA	P-0018467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	1796	388	0	ENST00000257290.5:c.1713_1720delinsTA	p.Glu571_Tyr574delinsAspAsn	p.E571_Y574delinsDN	ENST00000257290	NM_006206.4	571	gaATATATTTat/gaTAat	12/23	0.852546829175168	17	FACETS	0.975	0.964	0.986	0.975	0.964	0.986	CLONAL	15	TRUE	2	0.852546829175168	17		388	2130	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0018468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	203	745	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.439188608712923	1	FACETS	0.855	0.794	0.918	0.855	0.794	0.918	CLONAL	1	TRUE	0	0.439188608712923	1		746	844	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0018468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	303	745	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.383696650969177	2	FACETS	0.934	0.885	0.983	0.934	0.885	0.983	CLONAL	2	TRUE	0	0.439188608712923	2		745	739	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974727	21974744	+	inframe_deletion	In_Frame_Del	DEL	CCTCCAGCAGCGCCCGCA	CCTCCAGCAGCGCCCGCA	-	novel	NA	P-0018468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	225	637	0	ENST00000304494.5:c.83_100del	p.Val28_Glu33del	p.V28_E33del	ENST00000304494	NM_000077.4	28	gTGCGGGCGCTGCTGGAGGcg/gcg	1/3	0.439188608712923	2	FACETS	0.752	0.704	0.802	0.752	0.704	0.802	SUBCLONAL	2	TRUE	0	0.439188608712923	2		637	681	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691801	30691801	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	233	558	0	ENST00000295754.5:c.303C>A	p.Cys101Ter	p.C101*	ENST00000295754	NM_003242.5	101	tgC/tgA	3/7	0.439188608712923	1	FACETS	0.94	0.878	1	0.94	0.878	1	CLONAL	1	TRUE	0	0.439188608712923	1		558	881	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0018470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1413	135	921	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	0.644682927586351	10	FACETS	0.968	0.877	1	0.121	0.109	0.134	CLONAL	1	TRUE	2	0.644682927586351	10		921	1548	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519896	NA	P-0018470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	442	581	1	ENST00000281708.4:c.1514G>T	p.Arg505Leu	p.R505L	ENST00000281708	NM_033632.3	505	cGc/cTc	10/12	0.579383670022082	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.644682927586351	3		582	890	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944380	40944380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	107	431	0	ENST00000373198.4:c.2122C>T	p.Leu708Phe	p.L708F	ENST00000373198	NM_133170.3	708	Ctc/Ttc	12/32	1	2	FACETS	0.92	0.833	1	0.92	0.833	1	CLONAL	1	TRUE	1	0.644682927586351	2		431	361	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272386	11272386	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	173	480	0	ENST00000361445.4:c.3544T>C	p.Phe1182Leu	p.F1182L	ENST00000361445	NM_004958.3	1182	Ttt/Ctt	23/58	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.644682927586351	2		480	524	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619319	37619319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	126	385	0	ENST00000447079.4:c.995C>T	p.Ser332Phe	p.S332F	ENST00000447079	NM_015083.1	332	tCc/tTc	1/14	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.644682927586351	2		385	371	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627724	37627724	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	322	906	0	ENST00000447079.4:c.1639C>T	p.Gln547Ter	p.Q547*	ENST00000447079	NM_015083.1	547	Cag/Tag	2/14	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.644682927586351	2		906	972	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36014523	36014523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	196	579	2	ENST00000358208.4:c.296C>T	p.Thr99Met	p.T99M	ENST00000358208		99	aCg/aTg	3/12	1	2	FACETS	0.937	0.871	1	0.937	0.871	1	CLONAL	1	TRUE	1	0.644682927586351	2		581	649	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149440497	149440497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs281860269	NA	P-0018470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	145	609	0	ENST00000286301.3:c.1897G>A	p.Glu633Lys	p.E633K	ENST00000286301	NM_005211.3	633	Gag/Aag	14/22	1	2	FACETS	0.736	0.674	0.801	0.736	0.674	0.801	SUBCLONAL	1	TRUE	1	0.644682927586351	2		609	611	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048737	180048737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144803521	NA	P-0018470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	211	591	0	ENST00000261937.6:c.1825G>A	p.Asp609Asn	p.D609N	ENST00000261937	NM_182925.4	609	Gac/Aac	13/30	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.644682927586351	2		591	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0018471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	113	752	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.318373713648736	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.318373713648736	1		754	530	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0018471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	77	900	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.991	0.873	1	0.991	0.873	1	CLONAL	1	TRUE	1	0.318373713648736	2		901	488	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102056845	102056845	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	41	614	0	ENST00000282441.5:c.785G>A	p.Arg262Lys	p.R262K	ENST00000282441	NM_001130145.2	262	aGg/aAg	4/9	0.201553954959672	1	FACETS	0.51	0.425	0.604	0.51	0.425	0.604	SUBCLONAL	1	TRUE	0	0.318373713648736	1		614	425	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022642	12022642	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370744157	NA	P-0018471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	125	477	0	ENST00000396373.4:c.748G>A	p.Glu250Lys	p.E250K	ENST00000396373	NM_001987.4	250	Gag/Aag	5/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.318373713648736	2		477	618	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741861	40741861	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745550650	NA	P-0018471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	91	471	2	ENST00000392038.2:c.1111C>T	p.Arg371Cys	p.R371C	ENST00000392038	NM_001626.4	371	Cgc/Tgc	11/14	1	2	FACETS	0.931	0.828	1	0.931	0.828	1	CLONAL	1	TRUE	1	0.318373713648736	2		473	614	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62305351	62305351	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	58	626	1	ENST00000360203.5:c.824G>T	p.Gly275Val	p.G275V	ENST00000360203	NM_001283009.1	275	gGa/gTa	10/35	0.318373713648736	3	FACETS	0.464	0.397	0.537	0.232	0.198	0.269	SUBCLONAL	1	TRUE	1	0.318373713648736	3		627	911	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259335	89259335	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750779844	NA	P-0018471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	78	438	0	ENST00000336596.2:c.479G>A	p.Arg160His	p.R160H	ENST00000336596	NM_005233.5	160	cGt/cAt	3/17	0.290418546017294	3	FACETS	1	0.965	1			1	CLONAL	1	TRUE	NA	0.318373713648736	3		438	451	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448472	89448472	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1463190446	NA	P-0018471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	20	343	0	ENST00000336596.2:c.1436A>G	p.Glu479Gly	p.E479G	ENST00000336596	NM_005233.5	479	gAa/gGa	7/17	0.290418546017294	3	FACETS	0.458	0.35	0.584			1	SUBCLONAL	1	TRUE	NA	0.318373713648736	3		343	318	SUCCESS
APC	324	MSKCC	GRCh37	5	112179229	112179229	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	64	420	2	ENST00000257430.4:c.7938A>T	p.Gln2646His	p.Q2646H	ENST00000257430	NM_000038.5	2646	caA/caT	16/16	0.318373713648736	1	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	0	0.318373713648736	1		422	327	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404404	139404404	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	55	554	0	ENST00000277541.6:c.2750A>G	p.His917Arg	p.H917R	ENST00000277541	NM_017617.3	917	cAc/cGc	18/34	0.167293569550164	0	FACETS	0.402	0.343	0.466			1	INDETERMINATE	1	TRUE	0	0.318373713648736	0		554	586	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0018472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	291	812	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.68652683498208	1	FACETS	0.956	0.909	1	0.956	0.909	1	CLONAL	1	TRUE	0	0.693225615755503	1		812	574	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952086	178952086	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	195	493	1	ENST00000263967.3:c.3141T>A	p.His1047Gln	p.H1047Q	ENST00000263967	NM_006218.2	1047	caT/caA	21/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.693225615755503	2		494	539	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471084	8471084	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	42	363	0	ENST00000356435.5:c.3415G>A	p.Gly1139Ser	p.G1139S	ENST00000356435		1139	Ggt/Agt	20/35	0.266813440331228	3	FACETS	0.338	0.282	0.4	0.169	0.141	0.2	INDETERMINATE	1	TRUE	1	0.693225615755503	3		363	483	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033906	49033906	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	247	694	0	ENST00000267163.4:c.2043G>A	p.Trp681Ter	p.W681*	ENST00000267163	NM_000321.2	681	tgG/tgA	20/27	0.68652683498208	1	FACETS	0.958	0.907	1	0.958	0.907	1	CLONAL	1	TRUE	0	0.693225615755503	1		694	486	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380347	14380347	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	181	374	0	ENST00000256196.4:c.70G>C	p.Gly24Arg	p.G24R	ENST00000256196		24	Ggc/Cgc	1/6	1	2	FACETS	0.995	0.925	1	0.995	0.925	1	CLONAL	1	TRUE	1	0.693225615755503	2		374	525	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716326	52716326	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	247	579	0	ENST00000322088.6:c.770G>C	p.Trp257Ser	p.W257S	ENST00000322088	NM_014225.5	257	tGg/tCg	6/15	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.693225615755503	2		579	702	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260247	149260247	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753225952	NA	P-0018472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	173	681	1	ENST00000360632.3:c.646G>A	p.Ala216Thr	p.A216T	ENST00000360632	NM_015472.4	216	Gca/Aca	4/7	1	2	FACETS	0.486	0.447	0.528	0.486	0.447	0.528	SUBCLONAL	1	TRUE	1	0.693225615755503	2		682	1026	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519757	NA	P-0018472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	126	335	0	ENST00000274335.5:c.1126G>C	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Cga	9/15	1	2	FACETS	0.991	0.907	1	0.991	0.907	1	CLONAL	1	TRUE	1	0.693225615755503	2		335	367	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949758	151949758	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	228	529	2	ENST00000262189.6:c.1342C>T	p.Gln448Ter	p.Q448*	ENST00000262189	NM_170606.2	448	Cag/Tag	10/59	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.693225615755503	2		531	599	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0018485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	648	792	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.738341400606882	2	FACETS	0.993	0.968	1	0.993	0.968	1	CLONAL	2	TRUE	0	0.738341400606882	2		792	884	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248499	59248499	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	615	408	4	ENST00000371222.2:c.244C>T	p.Gln82Ter	p.Q82*	ENST00000371222	NM_002228.3	82	Cag/Tag	1/1	0.738341400606882	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.738341400606882	3		412	748	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551690	150551690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1190469700	NA	P-0018485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	141	267	4	ENST00000369026.2:c.317C>T	p.Ala106Val	p.A106V	ENST00000369026	NM_021960.4	106	gCg/gTg	1/3	0.738341400606882	3	FACETS	1	0.934	1	0.511	0.468	0.555	CLONAL	1	TRUE	1	0.738341400606882	3		271	512	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981176	201981176	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	376	647	2	ENST00000359651.3:c.255C>A	p.Tyr85Ter	p.Y85*	ENST00000359651		85	taC/taA	2/8	0.738341400606882	3	FACETS	1	0.988	1	0.565	0.537	0.595	CLONAL	1	TRUE	1	0.738341400606882	3		649	1233	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982334	201982343	+	frameshift_variant	Frame_Shift_Del	DEL	GGGATCCCAA	GGGATCCCAA	ACT	novel	NA	P-0018485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	518	691	5	ENST00000359651.3:c.713_722delinsACT	p.Gly238AspfsTer14	p.G238Dfs*14	ENST00000359651		238	gGGGATCCCAAg/gACTg	6/8	0.738341400606882	3	FACETS	0.81	0.778	0.842	0.81	0.778	0.842	CLONAL	2	TRUE	1	0.738341400606882	3		696	1186	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858492	9858492	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148669437	NA	P-0018485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	161	401	0	ENST00000330684.3:c.2909G>A	p.Arg970Gln	p.R970Q	ENST00000330684	NM_001134407.1	970	cGg/cAg	13/13	0.259386950548511	5	FACETS	1	0.98	1	0.243	0.223	0.264	INDETERMINATE	1	TRUE	0	0.738341400606882	5		401	757	SUCCESS
APC	324	MSKCC	GRCh37	5	112173848	112173848	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	171	345	3	ENST00000257430.4:c.2557G>T	p.Glu853Ter	p.E853*	ENST00000257430	NM_000038.5	853	Gag/Tag	16/16	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.738341400606882	2		348	453	SUCCESS
APC	324	MSKCC	GRCh37	5	112175178	112175179	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	106	225	0	ENST00000257430.4:c.3888dup	p.Asp1297ArgfsTer4	p.D1297Rfs*4	ENST00000257430	NM_000038.5	1296	gca/gcAa	16/16	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.738341400606882	2		225	280	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553770	106553770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	54	424	1	ENST00000369096.4:c.1735G>A	p.Val579Ile	p.V579I	ENST00000369096	NM_001198.3	579	Gtt/Att	5/7	0.738341400606882	3	FACETS	0.217	0.185	0.253	0.109	0.092	0.127	SUBCLONAL	1	TRUE	1	0.738341400606882	3		425	922	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230691	46230691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424958105	NA	P-0018487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	80	391	1	ENST00000334344.6:c.940C>T	p.Arg314Cys	p.R314C	ENST00000334344	NM_152641.2	314	Cgt/Tgt	8/21	1	2	FACETS	0.818	0.72	0.925	0.818	0.72	0.925	CLONAL	1	TRUE	1	0.246845381751995	2		392	792	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205238	46205238	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	107	446	0	ENST00000334344.6:c.322G>T	p.Glu108Ter	p.E108*	ENST00000334344	NM_152641.2	108	Gag/Tag	4/21	1	2	FACETS	0.823	0.736	0.915	0.823	0.736	0.915	CLONAL	1	TRUE	1	0.246845381751995	2		446	1054	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045430	47045607	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCCCAACATTCACATACACATACAAACTTTCAGCAAATGAAGTACCGGGACCGTGCAGCTGAACGCAGAGAAAAGTATGGCATCCCCGAGCCGCCAGAGCCCAAGAGGAGGAAGTACGGCGGCATATCCACAGCCTCTGTGTGAGTGGCTGGGCCAGGTGAGGGGGTCTGGAGCCCG	TCCCCAACATTCACATACACATACAAACTTTCAGCAAATGAAGTACCGGGACCGTGCAGCTGAACGCAGAGAAAAGTATGGCATCCCCGAGCCGCCAGAGCCCAAGAGGAGGAAGTACGGCGGCATATCCACAGCCTCTGTGTGAGTGGCTGGGCCAGGTGAGGGGGTCTGGAGCCCG	-	novel	NA	P-0018487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	43	323	0	ENST00000377604.3:c.2431-34_2537+37del		p.X811_splice	ENST00000377604	NM_001204468.1	811		22/24	0.246845381751995	1	FACETS	0.379	0.316	0.45	0.379	0.316	0.45	SUBCLONAL	1	TRUE	0	0.246845381751995	1		323	805	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0018488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	420	949	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.324398621550339	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.324398621550339	2		949	1186	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0018488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	251	1181	1	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	0.324398621550339	NA		1182	921	SUCCESS
APC	324	MSKCC	GRCh37	5	112175328	112175328	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	164	226	0	ENST00000257430.4:c.4037C>A	p.Ser1346Ter	p.S1346*	ENST00000257430	NM_000038.5	1346	tCa/tAa	16/16	0.324398621550339	3	FACETS	0.892	0.828	0.958	0.892	0.828	0.958	CLONAL	3	TRUE	0	0.324398621550339	3		226	439	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857680	9857680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303700994	NA	P-0018488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	48	259	1	ENST00000330684.3:c.3721C>T	p.Arg1241Trp	p.R1241W	ENST00000330684	NM_001134407.1	1241	Cgg/Tgg	13/13	0.324398621550339	3	FACETS	0.93	0.788	1	0.465	0.394	0.542	CLONAL	1	TRUE	1	0.324398621550339	3		260	370	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593395	48593395	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	16	198	0	ENST00000342988.3:c.1146C>G	p.His382Gln	p.H382Q	ENST00000342988	NM_005359.5	382	caC/caG	10/12	0.324398621550339	1	FACETS	0.292	0.215	0.384	0.292	0.215	0.384	SUBCLONAL	1	TRUE	0	0.324398621550339	1		198	283	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054423	13054423	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750961102	NA	P-0018488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	141	578	1	ENST00000316448.5:c.1033G>A	p.Glu345Lys	p.E345K	ENST00000316448	NM_004343.3	345	Gag/Aag	8/9	0.318643814496572	3	FACETS	0.981	0.892	1	0.49	0.446	0.537	CLONAL	1	TRUE	1	0.324398621550339	3		579	1030	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024380	31024380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201302084	NA	P-0018488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	263	504	3	ENST00000375687.4:c.3865C>T	p.Arg1289Trp	p.R1289W	ENST00000375687	NM_015338.5	1289	Cgg/Tgg	13/13	0.324398621550339	6	FACETS	1	0.947	1	0.507	0.474	0.541	CLONAL	2	TRUE	2	0.324398621550339	6		507	1318	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127414	55127414	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501504	NA	P-0018488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	51	597	0	ENST00000257290.5:c.202G>A	p.Asp68Asn	p.D68N	ENST00000257290	NM_006206.4	68	Gat/Aat	3/23	0.324398621550339	2	FACETS	0.329	0.279	0.385	0.165	0.139	0.193	SUBCLONAL	1	TRUE	0	0.324398621550339	2		597	955	SUCCESS
AR	367	MSKCC	GRCh37	X	66931504	66931504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1340026226	NA	P-0018489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	70	312	0	ENST00000374690.3:c.2146G>A	p.Val716Met	p.V716M	ENST00000374690	NM_000044.3	716	Gtg/Atg	4/8	0.227093493128844	2	FACETS	0.868	0.761	0.983			1	CLONAL	2	TRUE	NA	0.21	2		312	384	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933217	36933217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1287134931	NA	P-0018489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	111	639	1	ENST00000361632.4:c.1900G>A	p.Gly634Ser	p.G634S	ENST00000361632		634	Ggc/Agc	14/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.21	2		640	746	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248619	59248619	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs770768081	NA	P-0018489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	95	749	0	ENST00000371222.2:c.124C>G	p.Leu42Val	p.L42V	ENST00000371222	NM_002228.3	42	Ctg/Gtg	1/1	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.21	2		749	834	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136237	64136237	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1347144121	NA	P-0018489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	194	790	0	ENST00000334205.4:c.1396G>A	p.Val466Met	p.V466M	ENST00000334205	NM_003942.2	466	Gtg/Atg	12/17	0.227045129239871	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.21	4		790	1010	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2229783	2229783	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0018489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	99	693	0	ENST00000398665.3:c.4607-1G>A		p.X1536_splice	ENST00000398665	NM_032482.2	1536			0.253947934242482	3	FACETS	1	0.958	1	0.576	0.514	0.643	CLONAL	1	TRUE	1	0.21	3		693	904	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500852	149500852	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs768833854	NA	P-0018489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	154	624	0	ENST00000261799.4:c.2378A>G	p.Asn793Ser	p.N793S	ENST00000261799	NM_002609.3	793	aAc/aGc	17/23	0.2546652121575	3	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	1	0.21	3		624	795	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352259	70352259	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	83	313	0	ENST00000374080.3:c.4286C>A	p.Ala1429Asp	p.A1429D	ENST00000374080		1429	gCc/gAc	31/45	0.227093493128844	2	FACETS	0.892	0.791	1			1	CLONAL	2	TRUE	NA	0.21	2		313	443	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0018490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	31	715	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.171567858844808	3	FACETS	0.384	0.308	0.469	0.192	0.154	0.235	SUBCLONAL	1	TRUE	1	0.171567858844808	3		717	1023	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	85	364	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.171567858844808	2		365	942	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	263	917	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.171567858844808	3	FACETS	0.849	0.794	0.905	1	0.989	1	CLONAL	3	TRUE	1	0.171567858844808	3		917	1307	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158296	106158296	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs774246302	NA	P-0018490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	74	375	0	ENST00000380013.4:c.3197C>G	p.Thr1066Ser	p.T1066S	ENST00000380013	NM_001127208.2	1066	aCt/aGt	3/11	1	2	FACETS	0.952	0.832	1	0.952	0.832	1	CLONAL	1	TRUE	1	0.171567858844808	2		375	906	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963985	2963985	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200736339	NA	P-0018490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	122	434	0	ENST00000396946.4:c.1822C>T	p.Arg608Cys	p.R608C	ENST00000396946	NM_032415.4	608	Cgc/Tgc	15/25	0.171567858844808	3	FACETS	1	0.982	1	0.704	0.635	0.778	CLONAL	1	TRUE	1	0.171567858844808	3		434	1096	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	91	364	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.974	0.871	1	0.974	0.871	1	CLONAL	1	TRUE	1	0.471858168223812	2		365	396	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0018491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	116	365	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	1	2	FACETS	0.942	0.853	1	0.942	0.853	1	CLONAL	1	TRUE	1	0.471858168223812	2		365	522	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366680	40366680	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	57	375	0	ENST00000397332.2:c.517G>T	p.Ala173Ser	p.A173S	ENST00000397332	NM_001033082.2	173	Gcc/Tcc	2/3	1	2	FACETS	0.46	0.395	0.531	0.46	0.395	0.531	SUBCLONAL	1	TRUE	1	0.471858168223812	2		375	525	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67459152	67459152	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	195	509	0	ENST00000327367.4:c.568G>C	p.Glu190Gln	p.E190Q	ENST00000327367	NM_005902.3	190	Gaa/Caa	4/9	1	2	FACETS	0.982	0.91	1	0.982	0.91	1	CLONAL	1	TRUE	1	0.471858168223812	2		509	842	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952197	17952197	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0018491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	45	398	0	ENST00000458235.1:c.1142+1G>C		p.X381_splice	ENST00000458235	NM_000215.3	381			1	2	FACETS	0.312	0.262	0.368	0.312	0.262	0.368	SUBCLONAL	1	TRUE	1	0.471858168223812	2		398	611	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156043	106156043	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	137	388	0	ENST00000380013.4:c.944C>G	p.Ser315Cys	p.S315C	ENST00000380013	NM_001127208.2	315	tCc/tGc	3/11	1	2	FACETS	0.969	0.885	1	0.969	0.885	1	CLONAL	1	TRUE	1	0.471858168223812	2		388	599	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0018494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	373	601	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.388693488997735	3	FACETS	0.927	0.88	0.975	0.927	0.88	0.975	CLONAL	2	TRUE	1	0.388693488997735	3		602	1236	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591891	48591891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912581	NA	P-0018494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	153	368	0	ENST00000342988.3:c.1054G>A	p.Gly352Arg	p.G352R	ENST00000342988	NM_005359.5	352	Gga/Aga	9/12	0.344778590997636	2	FACETS	0.813	0.75	0.879	0.813	0.75	0.879	CLONAL	2	TRUE	0	0.388693488997735	2		368	484	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714462	40714462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167887381	NA	P-0018494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	252	427	0	ENST00000373198.4:c.3935C>T	p.Ser1312Phe	p.S1312F	ENST00000373198	NM_133170.3	1312	tCc/tTc	29/32	NA	2	FACETS	0.847	0.796	0.9			1	INDETERMINATE	2	TRUE	NA	0.388693488997735	2		427	765	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	264	582	0	ENST00000267101.3:c.850G>C	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Cga	7/28	0.388693488997735	6	FACETS	0.854	0.799	0.912			1	CLONAL	2	TRUE	NA	0.388693488997735	6		582	1413	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486841	56486842	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0018494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	430	482	1	ENST00000267101.3:c.1255_1256delinsAT	p.Gly419Ile	p.G419I	ENST00000267101	NM_001982.3	419	GGa/ATa	11/28	0.388693488997735	6	FACETS	1	0.992	1			1	CLONAL	3	TRUE	NA	0.388693488997735	6		483	1124	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799380	88799380	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	79	407	0	ENST00000360948.2:c.5A>T	p.Asp2Val	p.D2V	ENST00000360948	NM_001012338.2	2	gAt/gTt	2/19	1	2	FACETS	0.818	0.721	0.921	0.818	0.721	0.921	CLONAL	1	TRUE	1	0.388693488997735	2		407	497	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	364542	364542	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0018494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	333	519	0	ENST00000262320.3:c.1019+1G>T		p.X340_splice	ENST00000262320	NM_003502.3	340			0.376319110538889	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.388693488997735	2		519	803	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577098	7577106	+	inframe_deletion	In_Frame_Del	DEL	TCTCCCAGG	TCTCCCAGG	-	novel	NA	P-0018494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	423	736	0	ENST00000269305.4:c.832_840del	p.Pro278_Arg280del	p.P278_R280del	ENST00000269305	NM_001126112.2	278	CCTGGGAGA/-	8/11	0.344778590997636	2	FACETS	0.981	0.937	1	0.981	0.937	1	CLONAL	2	TRUE	0	0.388693488997735	2		736	1109	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699430	47699430	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0018494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	56	290	0	ENST00000347630.2:c.79-1G>T		p.X27_splice	ENST00000347630	NM_001007230.1	27			0.388693488997735	3	FACETS	0.705	0.605	0.815	0.353	0.302	0.408	SUBCLONAL	1	TRUE	1	0.388693488997735	3		290	488	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602518	10602518	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	128	430	1	ENST00000171111.5:c.1060C>T	p.Arg354Trp	p.R354W	ENST00000171111	NM_203500.1	354	Cgg/Tgg	3/6	0.376319110538889	2	FACETS	0.955	0.867	1	0.477	0.433	0.524	CLONAL	1	TRUE	0	0.388693488997735	2		431	690	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753186	42753186	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	301	524	1	ENST00000222329.4:c.1078G>T	p.Val360Phe	p.V360F	ENST00000222329	NM_006494.2	360	Gtc/Ttc	4/4	0.376319110538889	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	0	0.388693488997735	2		525	774	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024767	31024767	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	113	465	0	ENST00000375687.4:c.4252G>A	p.Gly1418Arg	p.G1418R	ENST00000375687	NM_015338.5	1418	Ggg/Agg	13/13	0.288047139235847	4	FACETS	0.979	0.88	1	0.489	0.44	0.542	CLONAL	1	TRUE	2	0.388693488997735	4		465	825	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059200	47059200	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	237	380	1	ENST00000409792.3:c.7461C>A	p.Asn2487Lys	p.N2487K	ENST00000409792	NM_014159.6	2487	aaC/aaA	20/21	0.388693488997735	3	FACETS	0.932	0.873	0.993	0.932	0.873	0.993	CLONAL	2	TRUE	1	0.388693488997735	3		381	781	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924471	131924471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	89	424	0	ENST00000265335.6:c.1144G>A	p.Gly382Ser	p.G382S	ENST00000265335		382	Ggc/Agc	8/25	1	2	FACETS	0.756	0.671	0.846	0.756	0.671	0.846	SUBCLONAL	1	TRUE	1	0.388693488997735	2		424	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691025	NA	P-0018495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	95	475	0	ENST00000269305.4:c.785G>T	p.Gly262Val	p.G262V	ENST00000269305	NM_001126112.2	262	gGt/gTt	8/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.22	2		475	760	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793008	33793010	+	inframe_deletion	In_Frame_Del	DEL	CGC	CGC	-	rs780345232	NA	P-0018495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	10	78	0	ENST00000498907.2:c.311_313del	p.Gly104del	p.G104del	ENST00000498907	NM_004364.3	104	gGCGac/gac	1/1	1	2	FACETS	0.514	0.348	0.721	0.514	0.348	0.721	SUBCLONAL	1	TRUE	1	0.22	2		78	177	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562298	21562298	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	62	519	0	ENST00000382592.4:c.1621G>T	p.Glu541Ter	p.E541*	ENST00000382592	NM_014572.2	541	Gag/Tag	4/8	0.195928045961703	1	FACETS	0.664	0.572	0.763	0.664	0.572	0.763	SUBCLONAL	1	TRUE	0	0.22	1		519	756	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113810	11113810	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	74	459	0	ENST00000358026.2:c.1918G>C	p.Glu640Gln	p.E640Q	ENST00000358026	NM_001128849.1	640	Gag/Cag	12/36	1	2	FACETS	0.992	0.868	1	0.992	0.868	1	CLONAL	1	TRUE	1	0.22	2		459	678	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899094	40899094	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0018495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	41	354	0	ENST00000373198.4:c.2177-1G>T		p.X726_splice	ENST00000373198	NM_133170.3	726			1	2	FACETS	0.586	0.487	0.697	0.586	0.487	0.697	SUBCLONAL	1	TRUE	1	0.22	2		354	636	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38153399	38153399	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1358	225	500	0	ENST00000317025.8:c.2830G>C	p.Glu944Gln	p.E944Q	ENST00000317025	NM_023034.1	944	Gaa/Caa	16/24	0.3	7	FACETS	1	0.93	1			1	CLONAL	2	TRUE	NA	0.22	7		500	1583	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38153464	38153464	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	214	411	0	ENST00000317025.8:c.2765G>C	p.Arg922Thr	p.R922T	ENST00000317025	NM_023034.1	922	aGa/aCa	16/24	0.3	7	FACETS	1	0.976	1			1	CLONAL	2	TRUE	NA	0.22	7		411	1351	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945109	44945109	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0018495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	14	104	0	ENST00000377967.4:c.3434-1G>A		p.X1145_splice	ENST00000377967	NM_021140.2	1145			1	1	FACETS	0.449	0.325	0.601	0.449	0.325	0.601	SUBCLONAL	1	TRUE	0	0.22	1		104	252	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0018496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	463	700	1	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	NA	2	FACETS	1	0.961	1			1	INDETERMINATE	1	TRUE	NA	0.714694287182505	2		701	1289	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0018496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	222	683	1	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	1	2	FACETS	0.871	0.814	0.93	0.871	0.814	0.93	CLONAL	1	TRUE	1	0.714694287182505	2		684	713	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508318	38508385	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTACGGTATGGCTTTCCCCCGGCCTGCAGGGTGGGATTTGCCCAGGGCCACAGGGCCAGGATGGGCCC	CTACGGTATGGCTTTCCCCCGGCCTGCAGGGTGGGATTTGCCCAGGGCCACAGGGCCAGGATGGGCCC	-	novel	NA	P-0018497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	45	475	0	ENST00000254066.5:c.628_630+65del		p.X210_splice	ENST00000254066	NM_000964.3	210		5/9	1	2	FACETS	0.6	0.504	0.707	0.6	0.504	0.707	SUBCLONAL	1	TRUE	1	0.293329236983695	2		475	511	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266745	18266745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754693011	NA	P-0018497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	26	586	1	ENST00000222254.8:c.56G>A	p.Arg19Gln	p.R19Q	ENST00000222254	NM_005027.3	19	cGg/cAg	2/16	0.124936496798196	0	FACETS	0.242	0.191	0.301			1	INDETERMINATE	1	TRUE	0	0.293329236983695	0		587	518	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188050	151188050	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	29	372	0	ENST00000262187.5:c.103T>C	p.Tyr35His	p.Y35H	ENST00000262187	NM_005614.3	35	Tac/Cac	2/8	1	2	FACETS	0.38	0.304	0.466	0.38	0.304	0.466	SUBCLONAL	1	TRUE	1	0.293329236983695	2		372	521	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188048	151188053	+	missense_variant	Missense_Mutation	ONP	GTAGGA	GTAGGA	TTGGGG	novel	NA	P-0018497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	31	357	1	ENST00000262187.5:c.100_105delinsCCCCAA	p.Ser34_Tyr35delinsProGln	p.S34_Y35delinsPQ	ENST00000262187	NM_005614.3	34	TCCTAC/CCCCAA	2/8	1	2	FACETS	0.419	0.338	0.511	0.419	0.338	0.511	SUBCLONAL	1	TRUE	1	0.293329236983695	2		358	504	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131228	202131228	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	197	308	0	ENST00000358485.4:c.196C>G	p.Leu66Val	p.L66V	ENST00000358485	NM_001080125.1	66	Ctt/Gtt	2/9	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.487043016256309	2		308	763	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0018498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	382	365	0	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.348929497480331	2	FACETS	0.871	0.831	0.912	0.871	0.831	0.912	CLONAL	2	TRUE	0	0.487043016256309	2		365	900	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665015	138665015	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	103	167	0	ENST00000330315.3:c.550G>A	p.Asp184Asn	p.D184N	ENST00000330315	NM_023067.3	184	Gac/Aac	1/1	0.487043016256309	3	FACETS	0.881	0.79	0.977	0.294	0.263	0.326	CLONAL	1	TRUE	0	0.487043016256309	3		167	597	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17371368	17371369	+	missense_variant	Missense_Mutation	DNP	GG	GG	TA	novel	NA	P-0018498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	72	277	0	ENST00000375499.3:c.87_88delinsTA	p.Gln30Lys	p.Q30K	ENST00000375499	NM_003000.2	29	gcCCag/gcTAag	2/8	1	2	FACETS	0.412	0.36	0.469	0.412	0.36	0.469	SUBCLONAL	1	TRUE	1	0.487043016256309	2		277	717	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441807	49441807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	246	478	0	ENST00000301067.7:c.4177C>A	p.His1393Asn	p.H1393N	ENST00000301067	NM_003482.3	1393	Cac/Aac	14/54	1	2	FACETS	0.813	0.759	0.869	0.813	0.759	0.869	CLONAL	1	TRUE	1	0.487043016256309	2		478	1242	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436095	56436095	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	175	317	0	ENST00000407977.2:c.1042C>A	p.His348Asn	p.H348N	ENST00000407977		348	Cat/Aat	9/10	1	2	FACETS	0.822	0.758	0.889	0.822	0.758	0.889	CLONAL	1	TRUE	1	0.487043016256309	2		317	874	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56809874	56809874	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	47	427	0	ENST00000337432.4:c.995A>C	p.Gln332Pro	p.Q332P	ENST00000337432	NM_058216.2	332	cAg/cCg	8/9	1	2	FACETS	0.231	0.194	0.272	0.231	0.194	0.272	SUBCLONAL	1	TRUE	1	0.487043016256309	2		427	835	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183633	185183633	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	53	255	0	ENST00000265026.3:c.1489del	p.Glu497ArgfsTer37	p.E497Rfs*37	ENST00000265026	NM_004721.4	496	cGg/cg	9/14	0.487043016256309	3	FACETS	0.266	0.226	0.31	0.089	0.075	0.104	SUBCLONAL	1	TRUE	0	0.487043016256309	3		255	1018	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067106	143067106	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1482695993	NA	P-0018498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	148	404	0	ENST00000262992.4:c.1607T>C	p.Ile536Thr	p.I536T	ENST00000262992	NM_001101669.1	536	aTt/aCt	16/24	1	2	FACETS	0.677	0.618	0.739	0.677	0.618	0.739	SUBCLONAL	1	TRUE	1	0.487043016256309	2		404	898	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1253949	1253949	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	T	novel	NA	P-0018498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	132	322	0	ENST00000310581.5:c.3296-3C>A		p.X1099_splice	ENST00000310581	NM_198253.2	1099			0.26810481934386	3	FACETS	0.73	0.662	0.802			1	INDETERMINATE	1	TRUE	NA	0.487043016256309	3		322	923	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31423041	31423041	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	154	404	1	ENST00000344624.3:c.3272C>A	p.Pro1091Gln	p.P1091Q	ENST00000344624		1091	cCa/cAa	26/33	1	2	FACETS	0.759	0.695	0.826	0.759	0.695	0.826	SUBCLONAL	1	TRUE	1	0.487043016256309	2		405	833	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647546	117647546	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	108	456	0	ENST00000368508.3:c.5398A>C	p.Asn1800His	p.N1800H	ENST00000368508	NM_002944.2	1800	Aat/Cat	33/43	1	2	FACETS	0.472	0.423	0.524	0.472	0.423	0.524	SUBCLONAL	1	TRUE	1	0.487043016256309	2		456	940	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101699	71101699	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	20	168	0	ENST00000318789.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000318789	NM_032682.5	167	Cag/Tag	9/21	0.418775552321558	1	FACETS	0.167	0.127	0.213	0.167	0.127	0.213	SUBCLONAL	1	TRUE	0	0.487043016256309	1		168	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0018508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1596	40	1017	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.211	0.174	0.253	0.211	0.174	0.253	SUBCLONAL	1	TRUE	1	0.231601436337028	2		1018	1636	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445040	49445041	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0018510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	95	521	0	ENST00000301067.7:c.2425dup	p.Gln809ProfsTer3	p.Q809Pfs*3	ENST00000301067	NM_003482.3	809	cag/cCag	10/54	0.337658200328751	3	FACETS	0.697	0.619	0.78	0.348	0.309	0.39	SUBCLONAL	1	TRUE	1	0.337658200328751	3		521	944	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057928	27057928	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	170	563	1	ENST00000324856.7:c.1636C>T	p.Gln546Ter	p.Q546*	ENST00000324856	NM_006015.4	546	Cag/Tag	3/20	0.152668669141633	2	FACETS	0.861	0.79	0.935	0.43	0.395	0.468	INDETERMINATE	1	TRUE	0	0.337658200328751	2		564	1170	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922221	100922221	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	145	413	1	ENST00000325455.5:c.2291G>A	p.Gly764Glu	p.G764E	ENST00000325455	NM_001202474.3	764	gGa/gAa	5/8	0.337658200328751	3	FACETS	1	0.968	1			1	CLONAL	1	TRUE	NA	0.337658200328751	3		414	891	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562051	21562051	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs990247058	NA	P-0018510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1343	187	787	0	ENST00000382592.4:c.1868G>A	p.Arg623Gln	p.R623Q	ENST00000382592	NM_014572.2	623	cGg/cAg	4/8	0.337658200328751	3	FACETS	0.846	0.779	0.916			1	CLONAL	1	TRUE	NA	0.337658200328751	3		787	1530	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941670	48941670	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	58	262	0	ENST00000267163.4:c.980A>C	p.Lys327Thr	p.K327T	ENST00000267163	NM_000321.2	327	aAa/aCa	10/27	NA	2	FACETS	0.667	0.574	0.769			1	INDETERMINATE	1	TRUE	NA	0.337658200328751	2		262	515	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577092	+	inframe_deletion	In_Frame_Del	DEL	CGC	CGC	-	novel	NA	P-0018510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	456	548	0	ENST00000269305.4:c.846_848del	p.Arg283del	p.R283del	ENST00000269305	NM_001126112.2	282	cgGCGc/cgc	8/11	0.281514677445586	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.337658200328751	2		548	1344	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431029	181431029	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1371	134	560	0	ENST00000325404.1:c.881T>C	p.Met294Thr	p.M294T	ENST00000325404	NM_003106.3	294	aTg/aCg	1/1	0.337658200328751	5	FACETS	0.794	0.719	0.874	0.159	0.143	0.175	SUBCLONAL	1	TRUE	0	0.337658200328751	5		560	1505	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92404083	92404083	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	106	367	0	ENST00000265734.4:c.296A>C	p.Glu99Ala	p.E99A	ENST00000265734	NM_001259.6	99	gAa/gCa	3/8	0.337658200328751	4	FACETS	0.97	0.869	1			1	CLONAL	1	TRUE	NA	0.337658200328751	4		367	866	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992796	68992796	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1445	444	499	0	ENST00000288368.4:c.1761A>C	p.Glu587Asp	p.E587D	ENST00000288368	NM_024870.2	587	gaA/gaC	16/40	0.337658200328751	8	FACETS	0.934	0.889	0.981	0.467	0.444	0.491	CLONAL	3	TRUE	2	0.337658200328751	8		499	1889	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0018511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	464	1181	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.647823672726641	3	FACETS	0.928	0.9	0.956	0.928	0.9	0.956	CLONAL	3	TRUE	0	0.676658560329318	3		1182	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0018511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	529	431	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	NA	2	FACETS	0.959	0.929	0.989			1	INDETERMINATE	2	TRUE	NA	0.676658560329318	2		431	815	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0018511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	242	428	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	0.265914342972854	2	FACETS	0.811	0.759	0.864	0.405	0.379	0.432	INDETERMINATE	1	TRUE	0	0.676658560329318	2		428	882	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400777	72400777	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	57	181	0	ENST00000357731.5:c.394C>A	p.His132Asn	p.H132N	ENST00000357731	NM_173808.2	132	Cat/Aat	2/7	1	2	FACETS	0.658	0.57	0.752	0.658	0.57	0.752	SUBCLONAL	1	TRUE	1	0.676658560329318	2		181	256	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050852	49050852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1231557654	NA	P-0018511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	131	282	0	ENST00000267163.4:c.2536C>T	p.Gln846Ter	p.Q846*	ENST00000267163	NM_000321.2	846	Cag/Tag	25/27	0.676658560329318	1	FACETS	0.537	0.49	0.585	0.537	0.49	0.585	SUBCLONAL	1	TRUE	0	0.676658560329318	1		282	477	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535418	66535418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	329	426	0	ENST00000273854.3:c.43C>T	p.Pro15Ser	p.P15S	ENST00000273854	NM_004439.5	15	Cca/Tca	1/18	0.228030993638705	4	FACETS	0.874	0.828	0.92	0.874	0.828	0.92	INDETERMINATE	2	TRUE	2	0.676658560329318	4		426	933	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510282	187510282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	296	302	0	ENST00000441802.2:c.13231C>T	p.Pro4411Ser	p.P4411S	ENST00000441802	NM_005245.3	4411	Ccc/Tcc	27/27	0.228030993638705	4	FACETS	0.931	0.88	0.982	0.931	0.88	0.982	INDETERMINATE	2	TRUE	2	0.676658560329318	4		302	788	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170884	56170884	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	74	148	2	ENST00000399503.3:c.1712G>T	p.Cys571Phe	p.C571F	ENST00000399503	NM_005921.1	571	tGc/tTc	10/20	0.219547396557416	2	FACETS	0.564	0.496	0.636	0.282	0.248	0.318	INDETERMINATE	1	TRUE	0	0.676658560329318	2		150	388	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423407	116423407	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913671	NA	P-0018511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	88	223	0	ENST00000397752.3:c.3682G>C	p.Asp1228His	p.D1228H	ENST00000397752	NM_000245.2	1228	Gac/Cac	19/21	0.334557844540565	6	FACETS	0.992	0.88	1	0.331	0.293	0.371	INDETERMINATE	1	TRUE	3	0.676658560329318	6		223	617	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974693	21974693	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	489	313	0	ENST00000304494.5:c.134del	p.Gly45ValfsTer8	p.G45Vfs*8	ENST00000304494	NM_000077.4	45	gGt/gt	1/3	0.613730691808016	2	FACETS	0.953	0.922	0.984	0.953	0.922	0.984	CLONAL	2	TRUE	0	0.676658560329318	2		313	758	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812200	212812200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	201	263	0	ENST00000342788.4:c.376G>T	p.Asp126Tyr	p.D126Y	ENST00000342788	NM_005235.2	126	Gat/Tat	3/28	0.351358458595232	2	FACETS	0.848	0.79	0.908	0.848	0.79	0.908	CLONAL	2	TRUE	0	0.365048860336254	2		263	649	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661545	227661545	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	91	413	0	ENST00000305123.5:c.1910C>A	p.Pro637His	p.P637H	ENST00000305123	NM_005544.2	637	cCc/cAc	1/2	1	2	FACETS	0.376	0.332	0.422	0.376	0.332	0.422	SUBCLONAL	1	TRUE	1	0.446249637752687	2		413	1086	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164438	36164438	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	62	122	0	ENST00000300305.3:c.1437del	p.Tyr480ThrfsTer114	p.Y480Tfs*114	ENST00000300305		479	ccC/cc	8/8	1	2	FACETS	0.688	0.596	0.786	0.688	0.596	0.786	SUBCLONAL	1	TRUE	1	0.446249637752687	2		122	404	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598087	52598087	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs111483865	NA	P-0018513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	48	424	0	ENST00000394830.3:c.3779A>G	p.Asp1260Gly	p.D1260G	ENST00000394830	NM_018313.4	1260	gAt/gGt	24/30	0.184619530445736	1	FACETS	0.178	0.149	0.209	0.178	0.149	0.209	INDETERMINATE	1	TRUE	0	0.446249637752687	1		424	940	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098393	11098393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	380	545	0	ENST00000358026.2:c.911C>T	p.Pro304Leu	p.P304L	ENST00000358026	NM_001128849.1	304	cCc/cTc	6/36	0.929604050994732	3	FACETS	1	0.979	1	0.527	0.501	0.554	CLONAL	1	TRUE	1	0.929604050994732	3		545	1136	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817382	39817382	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	201	293	0	ENST00000288319.7:c.181C>T	p.Pro61Ser	p.P61S	ENST00000288319	NM_182918.3	61	Cca/Tca	2/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.929604050994732	2		293	422	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955632	55955632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	204	349	0	ENST00000263923.4:c.3313C>T	p.Pro1105Ser	p.P1105S	ENST00000263923	NM_002253.2	1105	Cca/Tca	25/30	0.863146702312561	3	FACETS	1	0.945	1	0.508	0.473	0.543	CLONAL	1	TRUE	1	0.929604050994732	3		349	633	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500868	149500868	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1320275282	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	259	399	1	ENST00000261799.4:c.2362C>T	p.Arg788Ter	p.R788*	ENST00000261799	NM_002609.3	788	Cga/Tga	17/23	0.919068810421477	4	FACETS	1	0.939	1	0.334	0.313	0.356	CLONAL	1	TRUE	1	0.929604050994732	4		400	1073	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295254	1295254	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	778	372	0				ENST00000310581	NM_198253.2	-/1132			0.919068810421477	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	1	0.929604050994732	4		372	1065	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416732	121416732	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1338145634	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	670	622	2	ENST00000257555.6:c.161G>A	p.Arg54Gln	p.R54Q	ENST00000257555		54	cGa/cAa	1/10	0.863146702312561	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.929604050994732	3		624	1044	SUCCESS
BLM	641	MSKCC	GRCh37	15	91308637	91308637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866243946	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	344	274	0	ENST00000355112.3:c.2186C>T	p.Ser729Phe	p.S729F	ENST00000355112	NM_000057.2	729	tCc/tTc	9/22	0.884724784772892	4	FACETS	0.952	0.907	0.997	0.952	0.907	0.997	CLONAL	2	TRUE	2	0.929604050994732	4		274	750	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066482	94066482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542602078	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	322	290	2	ENST00000369303.4:c.1277G>A	p.Arg426Gln	p.R426Q	ENST00000369303	NM_004440.3	426	cGa/cAa	5/17	0.863146702312561	3	FACETS	0.954	0.914	0.993	0.954	0.914	0.993	CLONAL	2	TRUE	1	0.929604050994732	3		292	532	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729961	41729961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867739441	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1269	289	444	0	ENST00000242208.4:c.568G>A	p.Glu190Lys	p.E190K	ENST00000242208	NM_002192.2	190	Gaa/Aaa	3/3	0.906708203522327	5	FACETS	0.956	0.896	1	0.239	0.224	0.255	CLONAL	1	TRUE	1	0.929604050994732	5		444	1558	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56811537	56811537	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	537	467	0	ENST00000337432.4:c.1085C>T	p.Ser362Phe	p.S362F	ENST00000337432	NM_058216.2	362	tCc/tTc	9/9	0.884724784772892	4	FACETS	0.861	0.828	0.896	0.861	0.828	0.896	CLONAL	2	TRUE	2	0.929604050994732	4		467	1294	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444318	50444318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1427077431	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	282	215	0	ENST00000331340.3:c.248G>A	p.Arg83Gln	p.R83Q	ENST00000331340	NM_006060.4	83	cGa/cAa	4/8	0.929604050994732	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.929604050994732	3		215	442	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858687	9858687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	132	233	0	ENST00000330684.3:c.2714C>T	p.Ser905Phe	p.S905F	ENST00000330684	NM_001134407.1	905	tCc/tTc	13/13	0.929604050994732	3	FACETS	0.856	0.782	0.933	0.428	0.391	0.467	CLONAL	1	TRUE	1	0.929604050994732	3		233	486	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242871	98242871	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	307	289	0	ENST00000331920.6:c.747-1G>A		p.X249_splice	ENST00000331920	NM_000264.3	249			0.929604050994732	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.929604050994732	2		289	319	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100177	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	183	345	0	ENST00000324856.7:c.3972_3973delinsTT	p.Pro1325Ser	p.P1325S	ENST00000324856	NM_006015.4	1324	taCCcc/taTTcc	16/20	0.863146702312561	3	FACETS	0.871	0.807	0.937	0.436	0.403	0.469	CLONAL	1	TRUE	1	0.929604050994732	3		345	662	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439937	51439937	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	141	118	0	ENST00000262662.1:c.502C>T	p.Gln168Ter	p.Q168*	ENST00000262662		168	Caa/Taa	4/4	0.863146702312561	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	1	0.929604050994732	3		118	220	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94906450	94906450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	229	342	0	ENST00000536441.1:c.1448C>T	p.Ala483Val	p.A483V	ENST00000536441	NM_144665.3	483	gCt/gTt	10/10	0.863146702312561	3	FACETS	1	0.948	1	0.507	0.474	0.54	CLONAL	1	TRUE	1	0.929604050994732	3		342	712	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143056	58143056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	696	477	1	ENST00000257904.6:c.728C>T	p.Ser243Phe	p.S243F	ENST00000257904	NM_000075.3	243	tCc/tTc	7/8	0.863146702312561	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.929604050994732	3		478	1077	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102874155	102874155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3730195	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	173	272	0	ENST00000307046.8:c.5G>A	p.Gly2Glu	p.G2E	ENST00000307046	NM_001111285.1	2	gGa/gAa	1/4	0.863146702312561	3	FACETS	0.951	0.881	1	0.476	0.44	0.512	CLONAL	1	TRUE	1	0.929604050994732	3		272	573	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961583	41961583	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	442	314	0	ENST00000219905.7:c.491C>T	p.Ser164Phe	p.S164F	ENST00000219905	NM_001164273.1	164	tCc/tTc	2/24	0.884724784772892	4	FACETS	0.997	0.957	1	0.997	0.957	1	CLONAL	2	TRUE	2	0.929604050994732	4		314	920	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857940	9857940	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1412461359	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	224	362	0	ENST00000330684.3:c.3461C>T	p.Pro1154Leu	p.P1154L	ENST00000330684	NM_001134407.1	1154	cCc/cTc	13/13	0.929604050994732	3	FACETS	0.942	0.881	1	0.471	0.44	0.503	CLONAL	1	TRUE	1	0.929604050994732	3		362	749	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56792504	56792505	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	263	371	0	ENST00000308159.5:c.234_235delinsAA	p.Glu79Lys	p.E79K	ENST00000308159	NM_014669.4	78	ttGGag/ttAAag	3/22	0.929604050994732	3	FACETS	1	0.967	1	0.52	0.489	0.552	CLONAL	1	TRUE	1	0.929604050994732	3		371	797	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857304	68857304	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	176	266	0	ENST00000261769.5:c.1939C>T	p.Gln647Ter	p.Q647*	ENST00000261769	NM_004360.3	647	Caa/Taa	13/16	0.929604050994732	3	FACETS	0.975	0.903	1	0.487	0.451	0.524	CLONAL	1	TRUE	1	0.929604050994732	3		266	569	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828098	72828098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	317	473	0	ENST00000268489.5:c.8483C>T	p.Thr2828Ile	p.T2828I	ENST00000268489	NM_006885.3	2828	aCt/aTt	9/10	0.929604050994732	3	FACETS	1	0.945	1	0.5	0.472	0.528	CLONAL	1	TRUE	1	0.929604050994732	3		473	999	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347270	89347270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	473	330	0	ENST00000301030.4:c.5680C>T	p.Pro1894Ser	p.P1894S	ENST00000301030	NM_001256183.1	1894	Ccc/Tcc	9/13	0.929604050994732	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.929604050994732	3		330	713	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579486	7579490	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCA	TGGCA	-	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	1070	514	0	ENST00000269305.4:c.197_201del	p.Met66ArgfsTer81	p.M66Rfs*81	ENST00000269305	NM_001126112.2	66	aTGCCA/a	4/11	0.929604050994732	4	FACETS	1	0.995	1	1	0.995	1	CLONAL	4	TRUE	0	0.929604050994732	4		514	1106	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989501	7989502	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	399	374	1	ENST00000319144.4:c.184_185delinsAA	p.Gly62Asn	p.G62N	ENST00000319144	NM_001139.2	62	GGt/AAt	2/15	0.929604050994732	4	FACETS	0.998	0.955	1	0.499	0.477	0.521	CLONAL	2	TRUE	0	0.929604050994732	4		375	830	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661915	29661915	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	594	434	1	ENST00000356175.3:c.5809C>T	p.Arg1937Cys	p.R1937C	ENST00000356175	NM_000267.3	1937	Cgt/Tgt	39/57	0.884724784772892	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.929604050994732	4		435	1195	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40874825	40874825	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	288	484	0	ENST00000428826.2:c.475C>T	p.His159Tyr	p.H159Y	ENST00000428826		159	Cat/Tat	6/21	0.884724784772892	4	FACETS	0.898	0.843	0.954	0.449	0.421	0.477	CLONAL	1	TRUE	2	0.929604050994732	4		484	1332	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805757	46805757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780161	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	437	412	0	ENST00000290295.7:c.199C>T	p.Pro67Ser	p.P67S	ENST00000290295	NM_006361.5	67	Cct/Tct	1/2	0.884724784772892	4	FACETS	0.916	0.877	0.955	0.916	0.877	0.955	CLONAL	2	TRUE	2	0.929604050994732	4		412	990	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78617527	78617527	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	317	271	0	ENST00000306801.3:c.266-1G>A		p.X89_splice	ENST00000306801	NM_020761.2	89			0.820927085960019	4	FACETS	0.899	0.854	0.944	0.899	0.854	0.944	CLONAL	2	TRUE	2	0.929604050994732	4		271	732	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281185	15281185	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	801	653	1	ENST00000263388.2:c.5071A>T	p.Lys1691Ter	p.K1691*	ENST00000263388	NM_000435.2	1691	Aag/Tag	27/33	0.929604050994732	3	FACETS	0.963	0.938	0.989	0.963	0.938	0.989	CLONAL	2	TRUE	1	0.929604050994732	3		654	1310	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291545	15291545	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	618	514	0	ENST00000263388.2:c.3089G>A	p.Gly1030Glu	p.G1030E	ENST00000263388	NM_000435.2	1030	gGa/gAa	19/33	0.929604050994732	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.929604050994732	3		514	930	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212561	36212561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	401	654	0	ENST00000222270.7:c.2312C>T	p.Pro771Leu	p.P771L	ENST00000222270	NM_014727.1	771	cCc/cTc	3/37	0.929604050994732	3	FACETS	1	0.974	1	0.517	0.492	0.543	CLONAL	1	TRUE	1	0.929604050994732	3		654	1221	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902691	50902691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	387	603	0	ENST00000440232.2:c.266C>T	p.Pro89Leu	p.P89L	ENST00000440232	NM_002691.3	89	cCc/cTc	3/27	0.929604050994732	3	FACETS	0.881	0.836	0.926	0.44	0.418	0.463	CLONAL	1	TRUE	1	0.929604050994732	3		603	1385	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714604	52714604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	246	409	0	ENST00000322088.6:c.362C>T	p.Pro121Leu	p.P121L	ENST00000322088	NM_014225.5	121	cCc/cTc	4/15	0.929604050994732	3	FACETS	0.914	0.857	0.973	0.457	0.428	0.487	CLONAL	1	TRUE	1	0.929604050994732	3		409	848	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265097	46265097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1383691008	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	652	269	0	ENST00000371998.3:c.1967C>T	p.Pro656Leu	p.P656L	ENST00000371998		656	cCc/cTc	12/23	0.692451854705946	5	FACETS	0.954	0.931	0.977	0.954	0.931	0.977	CLONAL	4	TRUE	1	0.929604050994732	5		269	880	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134959991	134959991	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	276	234	0	ENST00000398015.3:c.2348G>A	p.Gly783Glu	p.G783E	ENST00000398015	NM_004441.4	783	gGa/gAa	13/16	0.863146702312561	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.929604050994732	3		234	434	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542070	187542070	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	172	249	0	ENST00000441802.2:c.5670A>T	p.Leu1890Phe	p.L1890F	ENST00000441802	NM_005245.3	1890	ttA/ttT	10/27	0.863146702312561	3	FACETS	1	0.962	1	0.529	0.491	0.569	CLONAL	1	TRUE	1	0.929604050994732	3		249	512	SUCCESS
APC	324	MSKCC	GRCh37	5	112175355	112175355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	406	205	0	ENST00000257430.4:c.4064C>T	p.Ser1355Phe	p.S1355F	ENST00000257430	NM_000038.5	1355	tCt/tTt	16/16	0.919068810421477	4	FACETS	0.962	0.93	0.993	0.962	0.93	0.993	CLONAL	3	TRUE	1	0.929604050994732	4		205	584	SUCCESS
APC	324	MSKCC	GRCh37	5	112178711	112178711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	229	370	0	ENST00000257430.4:c.7420C>T	p.Pro2474Ser	p.P2474S	ENST00000257430	NM_000038.5	2474	Ccc/Tcc	16/16	0.919068810421477	4	FACETS	0.983	0.917	1	0.328	0.305	0.351	CLONAL	1	TRUE	1	0.929604050994732	4		370	967	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176666801	176666801	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	291	448	1	ENST00000439151.2:c.4237C>T	p.Leu1413Phe	p.L1413F	ENST00000439151	NM_022455.4	1413	Ctt/Ttt	8/23	0.919068810421477	4	FACETS	0.913	0.858	0.97	0.304	0.286	0.324	CLONAL	1	TRUE	1	0.929604050994732	4		449	1323	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188893	32188893	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144962111	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	241	402	0	ENST00000375023.3:c.661C>T	p.Leu221Phe	p.L221F	ENST00000375023	NM_004557.3	221	Ctc/Ttc	4/30	0.919068810421477	4	FACETS	0.938	0.876	1	0.313	0.292	0.334	CLONAL	1	TRUE	1	0.929604050994732	4		402	1067	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112035550	112035550	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	207	248	0	ENST00000368678.4:c.344C>G	p.Ser115Trp	p.S115W	ENST00000368678		115	tCg/tGg	4/13	0.863146702312561	3	FACETS	0.993	0.926	1	0.496	0.463	0.531	CLONAL	1	TRUE	1	0.929604050994732	3		248	657	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265560	152265560	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	207	345	0	ENST00000206249.3:c.1013G>A	p.Ser338Asn	p.S338N	ENST00000206249	NM_000125.3	338	aGt/aAt	4/8	1	2	FACETS	0.946	0.887	1	0.946	0.887	1	CLONAL	1	TRUE	1	0.929604050994732	2		345	471	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946159	13946159	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	1177	497	0	ENST00000405192.2:c.937C>T	p.Gln313Ter	p.Q313*	ENST00000405192	NM_001163147.1	313	Cag/Tag	10/12	0.906708203522327	5	FACETS	0.996	0.979	1	0.996	0.979	1	CLONAL	4	TRUE	1	0.929604050994732	5		497	1522	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367264	50367264	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	175	239	0	ENST00000331340.3:c.71C>T	p.Pro24Leu	p.P24L	ENST00000331340	NM_006060.4	24	cCa/cTa	3/8	0.929604050994732	3	FACETS	1	0.931	1	0.502	0.465	0.54	CLONAL	1	TRUE	1	0.929604050994732	3		239	549	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221843	55221843	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	708	523	0	ENST00000275493.2:c.887C>T	p.Pro296Leu	p.P296L	ENST00000275493	NM_005228.3	296	cCc/cTc	7/28	0.929604050994732	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.929604050994732	3		523	1106	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0018516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	220	708	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.347818307719052	3	FACETS	0.896	0.835	0.958	0.597	0.557	0.639	CLONAL	2	TRUE	0	0.347818307719052	3		709	829	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695719	117695720	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	218	393	0	ENST00000369458.3:c.717dup	p.Val240SerfsTer72	p.V240Sfs*72	ENST00000369458	NM_024626.3	239	-/A	4/6	0.32707710233704	2	FACETS	0.933	0.872	0.995	0.933	0.872	0.995	CLONAL	2	TRUE	0	0.347818307719052	2		393	672	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243675707	243675707	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	55	200	0	ENST00000263826.5:c.1273C>T	p.Gln425Ter	p.Q425*	ENST00000263826	NM_005465.4	425	Caa/Taa	12/13	0.347818307719052	10	FACETS	0.766	0.653	0.891	0.128	0.108	0.149	SUBCLONAL	1	TRUE	4	0.347818307719052	10		200	987	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948663	71948663	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs929070901	NA	P-0018516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	110	525	0	ENST00000298229.2:c.3375G>C	p.Gln1125His	p.Q1125H	ENST00000298229	NM_001567.3	1125	caG/caC	26/28	0.347818307719052	3	FACETS	0.871	0.782	0.966	0.436	0.391	0.483	CLONAL	1	TRUE	1	0.347818307719052	3		525	852	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856313	111856313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747913408	NA	P-0018516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	28	67	0	ENST00000341259.2:c.364G>A	p.Glu122Lys	p.E122K	ENST00000341259	NM_005475.2	122	Gag/Aag	2/8	0.347818307719052	2	FACETS	1	0.833	1	0.516	0.417	0.626	CLONAL	1	TRUE	0	0.347818307719052	2		67	156	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061517	38061517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771653601	NA	P-0018516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	51	246	0	ENST00000250448.2:c.472G>A	p.Asp158Asn	p.D158N	ENST00000250448	NM_004496.3	158	Gac/Aac	2/2	0.347818307719052	3	FACETS	0.632	0.537	0.736	0.316	0.268	0.368	SUBCLONAL	1	TRUE	1	0.347818307719052	3		246	545	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720264	43720264	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	145	467	0	ENST00000382044.4:c.3778A>G	p.Thr1260Ala	p.T1260A	ENST00000382044	NM_001141980.1	1260	Aca/Gca	18/28	0.347818307719052	3	FACETS	0.882	0.803	0.965			1	CLONAL	1	TRUE	NA	0.347818307719052	3		467	1110	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070577	67070578	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	154	211	0	ENST00000412916.2:c.207dup	p.Pro70SerfsTer13	p.P70Sfs*13	ENST00000412916		67	-/T	3/6	0.347818307719052	2	FACETS	0.926	0.854	1	0.926	0.854	1	CLONAL	2	TRUE	0	0.347818307719052	2		211	478	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	343	858	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.347818307719052	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.347818307719052	2		858	946	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100942	41100942	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568909948	NA	P-0018516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	108	416	0	ENST00000373198.4:c.1414G>A	p.Glu472Lys	p.E472K	ENST00000373198	NM_133170.3	472	Gag/Aag	8/32	0.347818307719052	3	FACETS	0.973	0.874	1	0.487	0.437	0.54	CLONAL	1	TRUE	1	0.347818307719052	3		416	749	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70971009	70971009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	150	655	3	ENST00000276594.2:c.1252C>T	p.His418Tyr	p.H418Y	ENST00000276594	NM_024504.3	418	Cac/Tac	6/8	1	2	FACETS	0.907	0.828	0.989	0.907	0.828	0.989	CLONAL	1	TRUE	1	0.347818307719052	2		658	951	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0018516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	126	431	0	ENST00000374080.3:c.3670C>T	p.Leu1224Phe	p.L1224F	ENST00000374080		1224	Ctc/Ttc	26/45	1	2	FACETS	0.872	0.789	0.959	0.872	0.789	0.959	CLONAL	1	TRUE	1	0.347818307719052	2		431	831	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182858	123182858	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	98	280	0	ENST00000218089.9:c.823C>T	p.Gln275Ter	p.Q275*	ENST00000218089	NM_001042749.1	275	Cag/Tag	10/35	0.347818307719052	3	FACETS	0.946	0.845	1			1	CLONAL	1	TRUE	NA	0.347818307719052	3		280	699	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0018517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	164	1181	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.995	0.913	1	0.995	0.913	1	CLONAL	1	TRUE	1	0.337107872650162	2		1182	978	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221243	1221243	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1057520606	NA	P-0018517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	208	635	1	ENST00000326873.7:c.766G>T	p.Glu256Ter	p.E256*	ENST00000326873	NM_000455.4	256	Gaa/Taa	6/10	0.337107872650162	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.337107872650162	1		636	964	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518614	69518614	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	174	642	0	ENST00000294312.3:c.31T>C	p.Trp11Arg	p.W11R	ENST00000294312	NM_005117.2	11	Tgg/Cgg	1/3	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.337107872650162	2		642	983	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636427	21636427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	145	507	0	ENST00000421138.2:c.583G>A	p.Ala195Thr	p.A195T	ENST00000421138		195	Gca/Aca	7/16	1	2	FACETS	0.86	0.784	0.94	0.86	0.784	0.94	CLONAL	1	TRUE	1	0.337107872650162	2		507	1000	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100121	11100121	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0018517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	127	386	0	ENST00000358026.2:c.1245+2T>C		p.X415_splice	ENST00000358026	NM_001128849.1	415			0.337107872650162	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.337107872650162	1		386	592	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162770	47162771	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTTCA	novel	NA	P-0018517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	107	330	0	ENST00000409792.3:c.3351_3355dup	p.Ser1119MetfsTer4	p.S1119Mfs*4	ENST00000409792	NM_014159.6	1119	agt/aTGAAAgt	3/21	1	2	FACETS	0.861	0.773	0.955	0.861	0.773	0.955	CLONAL	1	TRUE	1	0.337107872650162	2		330	737	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557984	187557987	+	frameshift_variant	Frame_Shift_Del	DEL	GTTT	GTTT	-	novel	NA	P-0018517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	32	210	0	ENST00000441802.2:c.3724_3727del	p.Lys1242LeufsTer33	p.K1242Lfs*33	ENST00000441802	NM_005245.3	1242	AAACct/ct	5/27	1	2	FACETS	0.335	0.271	0.408	0.335	0.271	0.408	SUBCLONAL	1	TRUE	1	0.337107872650162	2		210	566	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129039	2129039	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	67	383	0	ENST00000219476.3:c.2973A>G	p.Ile991Met	p.I991M	ENST00000219476	NM_000548.3	991	atA/atG	27/42	0.255731512481459	4	FACETS	0.643	0.557	0.736	0.214	0.185	0.246	SUBCLONAL	1	TRUE	1	0.33699147473193	4		383	827	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619281	37619281	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0018518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	112	329	0	ENST00000447079.4:c.957C>G	p.Tyr319Ter	p.Y319*	ENST00000447079	NM_015083.1	319	taC/taG	1/14	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.33699147473193	2		329	540	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667781	37667781	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0018518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	86	393	1	ENST00000447079.4:c.2667-1G>T		p.X889_splice	ENST00000447079	NM_015083.1	889			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.33699147473193	2		394	405	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050781	5050781	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	98	589	0	ENST00000381652.3:c.564A>C	p.Arg188Ser	p.R188S	ENST00000381652	NM_004972.3	188	agA/agC	6/25	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.33699147473193	2		589	444	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457414	5457414	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	34	103	0	ENST00000381577.3:c.388G>A	p.Val130Ile	p.V130I	ENST00000381577	NM_014143.3	130	Gtc/Atc	3/7	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.33699147473193	2		103	160	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90971041	90971041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200297914	NA	P-0018519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	288	190	0	ENST00000265433.3:c.1036G>A	p.Val346Met	p.V346M	ENST00000265433	NM_002485.4	346	Gtg/Atg	9/16	0.646526727413195	4	FACETS	0.937	0.893	0.981	0.703	0.669	0.736	CLONAL	3	TRUE	0	0.638208878967366	4		190	526	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231131	53231131	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	125	329	0	ENST00000375401.3:c.1771G>C	p.Gly591Arg	p.G591R	ENST00000375401	NM_004187.3	591	Gga/Cga	13/26	0.646526727413195	4	FACETS	0.548	0.495	0.605			1	SUBCLONAL	1	TRUE	NA	0.638208878967366	4		329	1171	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938705	76938706	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0018519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	470	475	0	ENST00000373344.5:c.2042_2043del	p.Cys681Ter	p.C681*	ENST00000373344	NM_000489.3	681	tGT/t	9/35	0.646526727413195	3	FACETS	1	0.99	1			1	CLONAL	2	TRUE	NA	0.638208878967366	3		475	901	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123040886	123040886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	154	541	1	ENST00000355640.3:c.1349G>A	p.Cys450Tyr	p.C450Y	ENST00000355640		450	tGc/tAc	7/7	0.345179077227044	3	FACETS	0.652	0.596	0.711	0.217	0.198	0.237	INDETERMINATE	1	TRUE	0	0.638208878967366	3		542	976	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267383	198267383	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	294	391	0	ENST00000335508.6:c.1974G>C	p.Trp658Cys	p.W658C	ENST00000335508	NM_012433.2	658	tgG/tgC	14/25	1	2	FACETS	0.891	0.84	0.944	0.891	0.84	0.944	CLONAL	1	TRUE	1	0.651382720552116	2		391	1013	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659981	227659982	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0018520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	236	450	0	ENST00000305123.5:c.3473dup	p.Ala1159SerfsTer20	p.A1159Sfs*20	ENST00000305123	NM_005544.2	1158	gga/ggGa	1/2	1	2	FACETS	0.825	0.771	0.881	0.825	0.771	0.881	CLONAL	1	TRUE	1	0.651382720552116	2		450	878	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535426	187535426	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370628880	NA	P-0018520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	265	348	0	ENST00000441802.2:c.9148G>A	p.Ala3050Thr	p.A3050T	ENST00000441802	NM_005245.3	3050	Gca/Aca	12/27	0.651382720552116	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.651382720552116	1		348	532	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0018521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	207	515	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.57	0.531	0.611	0.57	0.531	0.611	SUBCLONAL	1	TRUE	1	0.988796905068005	2		515	734	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0018521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	89	629	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.266	0.235	0.298	0.266	0.235	0.298	SUBCLONAL	1	TRUE	1	0.988796905068005	2		630	677	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913283	NA	P-0018521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	15	387	0	ENST00000263967.3:c.3129G>T	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atT	21/21	1	2	FACETS	0.047	0.034	0.063	0.047	0.034	0.063	SUBCLONAL	1	TRUE	1	0.988796905068005	2		387	648	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063717	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0018521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	111	236	0	ENST00000412916.2:c.165+1G>C		p.X55_splice	ENST00000412916		55			0.538589450882718	1	FACETS	0.375	0.341	0.409	0.375	0.341	0.409	INDETERMINATE	1	TRUE	0	0.988796905068005	1		236	303	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0018522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	16	223	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.580157559188392	1	FACETS	0.979	0.763	1	0.979	0.763	1	CLONAL	1	TRUE	0	0.580157559188392	1		223	40	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772228	68772262	+	frameshift_variant	Frame_Shift_Del	DEL	AGCCCTGCCACCCTGGCTTTGACGCCGAGAGCTAC	AGCCCTGCCACCCTGGCTTTGACGCCGAGAGCTAC	-	novel	NA	P-0018522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	217	610	0	ENST00000261769.5:c.78_112del	p.Glu26AspfsTer21	p.E26Dfs*21	ENST00000261769	NM_004360.3	26	gAGCCCTGCCACCCTGGCTTTGACGCCGAGAGCTAC/g	2/16	0.556810842669057	1	FACETS	0.932	0.873	0.991	0.932	0.873	0.991	CLONAL	1	TRUE	0	0.580157559188392	1		610	570	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906321	50906321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	78	435	0	ENST00000440232.2:c.982G>A	p.Glu328Lys	p.E328K	ENST00000440232	NM_002691.3	328	Gag/Aag	9/27	1	2	FACETS	0.472	0.415	0.533	0.472	0.415	0.533	SUBCLONAL	1	TRUE	1	0.580157559188392	2		435	570	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0018523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	332	836	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	NA	2	FACETS	0.947	0.896	0.999			1	INDETERMINATE	2	FALSE	NA	0.321802542317819	2		836	1089	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579559	7579559	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1555526777	NA	P-0018523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	152	533	1	ENST00000269305.4:c.128T>A	p.Leu43Ter	p.L43*	ENST00000269305	NM_001126112.2	43	tTg/tAg	4/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.321802542317819	2		534	799	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207201	1207201	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0018523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	137	382	0	ENST00000326873.7:c.289A>T	p.Lys97Ter	p.K97*	ENST00000326873	NM_000455.4	97	Aag/Tag	1/10	0.300537895517188	1	FACETS	0.881	0.802	0.964	0.881	0.802	0.964	CLONAL	1	FALSE	0	0.321802542317819	1		382	811	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825530	50825530	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	58	405	0	ENST00000398568.2:c.2161A>G	p.Lys721Glu	p.K721E	ENST00000398568	NM_001042412.1	721	Aaa/Gaa	14/18	0.177056817970112	3	FACETS	0.45	0.386	0.522			1	INDETERMINATE	1	FALSE	NA	0.321802542317819	3		405	929	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59878836	59878836	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0018523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	64	222	0	ENST00000259008.2:c.919-1G>T		p.X307_splice	ENST00000259008	NM_032043.2	307			1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	FALSE	1	0.321802542317819	2		222	393	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602293	10602293	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	154	478	0	ENST00000171111.5:c.1285G>T	p.Gly429Cys	p.G429C	ENST00000171111	NM_203500.1	429	Ggc/Tgc	3/6	0.300537895517188	1	FACETS	0.931	0.852	1	0.931	0.852	1	CLONAL	1	FALSE	0	0.321802542317819	1		478	863	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279425	1279425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	72	470	0	ENST00000310581.5:c.2111C>T	p.Pro704Leu	p.P704L	ENST00000310581	NM_198253.2	704	cCt/cTt	5/16	1	2	FACETS	0.434	0.377	0.495	0.434	0.377	0.495	SUBCLONAL	1	FALSE	1	0.321802542317819	2		470	1032	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509451	149509451	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	84	555	0	ENST00000261799.4:c.1448G>T	p.Trp483Leu	p.W483L	ENST00000261799	NM_002609.3	483	tGg/tTg	10/23	1	2	FACETS	0.527	0.464	0.594	0.527	0.464	0.594	SUBCLONAL	1	FALSE	1	0.321802542317819	2		555	991	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434862	110434862	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	253	563	0	ENST00000375856.3:c.3539T>A	p.Val1180Asp	p.V1180D	ENST00000375856	NM_003749.2	1180	gTc/gAc	1/2	0.256587772101519	3	FACETS		NA	1			1	NA	NA	TRUE	1	NA	3		563	915	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023994	31023994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	52	379	0	ENST00000375687.4:c.3479G>A	p.Gly1160Asp	p.G1160D	ENST00000375687	NM_015338.5	1160	gGc/gAc	13/13	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		379	318	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699376	117699376	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	281	485	0	ENST00000369458.3:c.265G>T	p.Glu89Ter	p.E89*	ENST00000369458	NM_024626.3	89	Gag/Tag	3/6	0.424215995568674	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.424215995568674	1		485	904	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112745520	112745520	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	126	403	0	ENST00000369452.4:c.838A>G	p.Ile280Val	p.I280V	ENST00000369452	NM_007373.3	280	Ata/Gta	3/9	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.424215995568674	2		403	486	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137713	64137713	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	340	612	0	ENST00000334205.4:c.1814G>C	p.Gly605Ala	p.G605A	ENST00000334205	NM_003942.2	605	gGg/gCg	15/17	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.424215995568674	2		612	1274	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202205	108202205	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	139	444	0	ENST00000278616.4:c.7550T>G	p.Leu2517Trp	p.L2517W	ENST00000278616	NM_000051.3	2517	tTg/tGg	51/63	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.424215995568674	2		444	565	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420223	49420223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	255	541	1	ENST00000301067.7:c.15526C>T	p.His5176Tyr	p.H5176Y	ENST00000301067	NM_003482.3	5176	Cac/Tac	48/54	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.424215995568674	2		542	1078	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549482	21549482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	99	355	0	ENST00000382592.4:c.2794C>T	p.Leu932Phe	p.L932F	ENST00000382592	NM_014572.2	932	Ctc/Ttc	8/8	0.143690075161761	0	FACETS	0.467	0.417	0.519			1	INDETERMINATE	1	TRUE	0	0.424215995568674	0		355	576	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678589	88678589	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	128	223	0	ENST00000360948.2:c.947G>T	p.Arg316Leu	p.R316L	ENST00000360948	NM_001012338.2	316	cGc/cTc	9/19	0.424215995568674	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.424215995568674	1		223	407	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934629	9934629	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	149	418	0	ENST00000330684.3:c.1526T>C	p.Val509Ala	p.V509A	ENST00000330684	NM_001134407.1	509	gTt/gCt	7/13	1	2	FACETS	0.894	0.817	0.974	0.894	0.817	0.974	CLONAL	1	TRUE	1	0.424215995568674	2		418	786	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519990	NA	P-0018525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	345	575	0	ENST00000269305.4:c.796G>C	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Cga	8/11	0.424215995568674	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.424215995568674	1		575	1041	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78921093	78921093	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	305	504	1	ENST00000306801.3:c.3207G>T	p.Arg1069Ser	p.R1069S	ENST00000306801	NM_020761.2	1069	agG/agT	27/34	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.424215995568674	2		505	1009	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221339	1221339	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	201	382	0	ENST00000326873.7:c.862G>T	p.Gly288Trp	p.G288W	ENST00000326873	NM_000455.4	288	Ggg/Tgg	6/10	0.424215995568674	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.424215995568674	1		382	684	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610316	10610316	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	301	682	1	ENST00000171111.5:c.394G>T	p.Val132Phe	p.V132F	ENST00000171111	NM_203500.1	132	Gtc/Ttc	2/6	0.424215995568674	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.424215995568674	1		683	1011	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138550	11138550	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	59	671	1	ENST00000358026.2:c.3306C>A	p.Phe1102Leu	p.F1102L	ENST00000358026	NM_001128849.1	1102	ttC/ttA	24/36	0.424215995568674	1	FACETS	0.197	0.169	0.229	0.197	0.169	0.229	SUBCLONAL	1	TRUE	0	0.424215995568674	1		672	1111	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440066	220440066	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1398984162	NA	P-0018525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	237	684	0	ENST00000243786.2:c.919G>T	p.Val307Phe	p.V307F	ENST00000243786	NM_002191.3	307	Gtc/Ttc	2/2	1	2	FACETS	0.878	0.818	0.94	0.878	0.818	0.94	CLONAL	1	TRUE	1	0.424215995568674	2		684	1273	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225367693	225367693	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	43	325	0	ENST00000264414.4:c.1474C>T	p.Gln492Ter	p.Q492*	ENST00000264414	NM_003590.4	492	Cag/Tag	10/16	NA	2	FACETS	0.337	0.282	0.399			1	INDETERMINATE	1	TRUE	NA	0.424215995568674	2		325	601	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730882	40730882	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	569	504	0	ENST00000373198.4:c.3653T>C	p.Leu1218Pro	p.L1218P	ENST00000373198	NM_133170.3	1218	cTg/cCg	27/32	0.424215995568674	3	FACETS	0.954	0.92	0.988	0.954	0.92	0.988	CLONAL	3	TRUE	0	0.424215995568674	3		504	1136	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499422	89499422	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	195	381	0	ENST00000336596.2:c.2592C>A	p.Asp864Glu	p.D864E	ENST00000336596	NM_005233.5	864	gaC/gaA	15/17	0.195136999032414	1	FACETS	0.999	0.928	1	0.999	0.928	1	INDETERMINATE	1	TRUE	0	0.424215995568674	1		381	725	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979632	55979632	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	322	388	0	ENST00000263923.4:c.815T>A	p.Leu272His	p.L272H	ENST00000263923	NM_002253.2	272	cTt/cAt	7/30	NA	2	FACETS	0.951	0.903	1			1	INDETERMINATE	2	TRUE	NA	0.424215995568674	2		388	798	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1253872	1253872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	209	411	1	ENST00000310581.5:c.3370C>T	p.Pro1124Ser	p.P1124S	ENST00000310581	NM_198253.2	1124	Ccc/Tcc	16/16	0.424215995568674	3	FACETS	1	0.954	1	0.519	0.481	0.558	CLONAL	1	TRUE	1	0.424215995568674	3		412	1151	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197135	26197135	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	265	304	0	ENST00000356476.2:c.344C>A	p.Ala115Asp	p.A115D	ENST00000356476		115	gCc/gAc	1/1	0.424215995568674	2	FACETS	0.9	0.849	0.952	0.9	0.849	0.952	CLONAL	2	TRUE	0	0.424215995568674	2		304	694	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522485	157522485	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777745107	NA	P-0018525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	181	709	0	ENST00000346085.5:c.4757C>T	p.Thr1586Met	p.T1586M	ENST00000346085	NM_020732.3	1586	aCg/aTg	18/20	0.424215995568674	1	FACETS	0.612	0.564	0.663	0.612	0.564	0.663	SUBCLONAL	1	TRUE	0	0.424215995568674	1		709	1098	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372744	81372744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1168082930	NA	P-0018525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	194	324	0	ENST00000222390.5:c.790G>A	p.Asp264Asn	p.D264N	ENST00000222390	NM_000601.4	264	Gat/Aat	7/18	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.424215995568674	2		324	714	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930152	68930152	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	161	386	2	ENST00000288368.4:c.213G>T	p.Lys71Asn	p.K71N	ENST00000288368	NM_024870.2	71	aaG/aaT	2/40	0.424215995568674	4	FACETS	0.964	0.883	1	0.321	0.294	0.35	CLONAL	1	TRUE	1	0.424215995568674	4		388	1121	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69000034	69000035	+	missense_variant	Missense_Mutation	DNP	TG	TG	AT	novel	NA	P-0018525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	463	462	2	ENST00000288368.4:c.2103_2104delinsAT	p.Val702Leu	p.V702L	ENST00000288368	NM_024870.2	701	gcTGta/gcATta	19/40	0.424215995568674	4	FACETS	0.935	0.896	0.975	0.935	0.896	0.975	CLONAL	3	TRUE	1	0.424215995568674	4		464	1108	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220430	123220430	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	90	462	0	ENST00000218089.9:c.3087G>T	p.Gln1029His	p.Q1029H	ENST00000218089	NM_001042749.1	1029	caG/caT	30/35	0.272291546069372	1	FACETS	0.421	0.373	0.472	0.421	0.373	0.472	SUBCLONAL	1	TRUE	0	0.424215995568674	1		462	794	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	88	917	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		917	1092	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	77	631	0	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		631	1204	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0018531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	221	715	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.334670460243864	4	FACETS	1	0.986	1	0.589	0.551	0.626	CLONAL	2	TRUE	0	0.462194106028209	4		717	594	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0018531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	377	642	3	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.344609703278175	3	FACETS	1	0.989	1	0.748	0.713	0.783	CLONAL	2	TRUE	0	0.462194106028209	3		645	895	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28931588	NA	P-0018531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	44	233	0	ENST00000349496.5:c.94G>C	p.Asp32His	p.D32H	ENST00000349496	NM_001904.3	32	Gac/Cac	3/15	0.349816874050736	3	FACETS	0.681	0.573	0.8	0.227	0.191	0.267	SUBCLONAL	1	TRUE	0	0.462194106028209	3		233	344	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242483	55242506	+	inframe_deletion	In_Frame_Del	DEL	ATCTCCGAAAGCCAACAAGGAAAT	ATCTCCGAAAGCCAACAAGGAAAT	-	rs727504232	NA	P-0018531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	158	516	0	ENST00000275493.2:c.2253_2276del	p.Ser752_Ile759del	p.S752_I759del	ENST00000275493	NM_005228.3	751	acATCTCCGAAAGCCAACAAGGAAATc/acc	19/28	0.462194106028209	6	FACETS	1	0.981	1	0.314	0.287	0.342	CLONAL	1	TRUE	2	0.462194106028209	6		516	1048	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813004	89813004	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	116	523	0	ENST00000389301.3:c.3501G>T	p.Leu1167Phe	p.L1167F	ENST00000389301	NM_000135.2	1167	ttG/ttT	35/43	0.344899504755679	2	FACETS	0.757	0.683	0.835	0.379	0.341	0.418	SUBCLONAL	1	TRUE	0	0.462194106028209	2		523	663	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	441056	441056	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766684341	NA	P-0018531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	102	427	0	ENST00000399788.2:c.1702C>T	p.Arg568Cys	p.R568C	ENST00000399788	NM_001042603.1	568	Cgt/Tgt	13/28	0.371406293894394	3	FACETS	0.815	0.729	0.905	0.407	0.364	0.453	CLONAL	1	TRUE	1	0.462194106028209	3		427	667	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832547	72832547	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	33	281	1	ENST00000268489.5:c.4034A>T	p.Lys1345Ile	p.K1345I	ENST00000268489	NM_006885.3	1345	aAa/aTa	9/10	0.349816874050736	3	FACETS	0.434	0.353	0.525	0.145	0.117	0.175	SUBCLONAL	1	TRUE	0	0.462194106028209	3		282	405	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8339010	8339010	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	137	334	2	ENST00000356435.5:c.5291C>A	p.Ala1764Glu	p.A1764E	ENST00000356435		1764	gCa/gAa	32/35	0.344899504755679	2	FACETS	0.793	0.729	0.857	0.793	0.729	0.857	SUBCLONAL	2	TRUE	0	0.462194106028209	2		336	374	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0018533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	155	636	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.819	0.751	0.889	0.819	0.751	0.889	CLONAL	1	TRUE	1	0.544726303415015	2		636	695	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094347	27094347	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	177	351	2	ENST00000324856.7:c.3055del	p.Glu1019ArgfsTer20	p.E1019Rfs*20	ENST00000324856	NM_006015.4	1019	Gag/ag	11/20	1	2	FACETS	0.841	0.776	0.908	0.841	0.776	0.908	CLONAL	1	TRUE	1	0.544726303415015	2		353	773	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473672	67473672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	199	377	1	ENST00000327367.4:c.752C>T	p.Ser251Leu	p.S251L	ENST00000327367	NM_005902.3	251	tCg/tTg	6/9	1	2	FACETS	0.889	0.825	0.955	0.889	0.825	0.955	CLONAL	1	TRUE	1	0.544726303415015	2		378	822	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71050160	71050160	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	172	292	0	ENST00000318789.4:c.1025G>C	p.Arg342Thr	p.R342T	ENST00000318789	NM_032682.5	342	aGa/aCa	13/21	1	2	FACETS	0.729	0.671	0.789	0.729	0.671	0.789	SUBCLONAL	1	TRUE	1	0.544726303415015	2		292	866	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579409	7579409	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1567556114	NA	P-0018534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	366	454	0	ENST00000269305.4:c.278del	p.Leu93ArgfsTer30	p.L93Rfs*30	ENST00000269305	NM_001126112.2	93	cTg/cg	4/11	0.652225007551774	2	FACETS	0.971	0.934	1	0.971	0.934	1	CLONAL	2	TRUE	0	0.652225007551774	2		454	578	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	106	366	0	ENST00000397062.3:c.92G>A	p.Gly31Glu	p.G31E	ENST00000397062	NM_006164.4	31	gGa/gAa	2/5	0.279695878583112	3	FACETS	1	0.965	1	0.587	0.526	0.651	CLONAL	1	TRUE	1	0.279695878583112	3		366	736	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0018535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1432	186	652	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.224227453416263	3	FACETS	0.937	0.862	1	0.468	0.431	0.508	CLONAL	1	TRUE	1	0.279695878583112	3		652	1618	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037969	49037969	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	rs587778868	NA	P-0018535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	231	413	0	ENST00000267163.4:c.2209G>T	p.Glu737Ter	p.E737*	ENST00000267163	NM_000321.2	737	Gag/Tag	21/27	0.279695878583112	3	FACETS	1	0.934	1	0.667	0.622	0.713	CLONAL	2	TRUE	0	0.279695878583112	3		413	941	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781288	NA	P-0018535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1682	141	817	1	ENST00000269305.4:c.422G>T	p.Cys141Phe	p.C141F	ENST00000269305	NM_001126112.2	141	tGc/tTc	5/11	0.224227453416263	3	FACETS	0.63	0.572	0.693	0.315	0.286	0.347	SUBCLONAL	1	TRUE	1	0.279695878583112	3		818	1823	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792426	33792426	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1471	116	715	0	ENST00000498907.2:c.895A>G	p.Ser299Gly	p.S299G	ENST00000498907	NM_004364.3	299	Agc/Ggc	1/1	0.279695878583112	3	FACETS	0.596	0.535	0.661			1	SUBCLONAL	1	TRUE	NA	0.279695878583112	3		715	1587	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949116	71949116	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs757863805	NA	P-0018535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	67	357	0	ENST00000298229.2:c.3583G>C	p.Gly1195Arg	p.G1195R	ENST00000298229	NM_001567.3	1195	Ggg/Cgg	27/28	1	2	FACETS	0.542	0.47	0.621	0.542	0.47	0.621	SUBCLONAL	1	TRUE	1	0.279695878583112	2		357	884	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431385	49431385	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	149	435	1	ENST00000301067.7:c.9754C>A	p.Leu3252Met	p.L3252M	ENST00000301067	NM_003482.3	3252	Ctg/Atg	34/54	0.150618558289855	2	FACETS	1	0.97	1	0.567	0.518	0.619	INDETERMINATE	1	TRUE	0	0.279695878583112	2		436	939	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022994	33022994	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	140	461	0	ENST00000300177.4:c.103C>A	p.Pro35Thr	p.P35T	ENST00000300177	NM_001191322.1	35	Ccg/Acg	2/2	0.193890143672988	4	FACETS	1	0.972	1	0.586	0.533	0.642	CLONAL	1	TRUE	2	0.279695878583112	4		461	1093	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56878460	56878460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	130	439	0	ENST00000308159.5:c.2399C>T	p.Pro800Leu	p.P800L	ENST00000308159	NM_014669.4	800	cCa/cTa	22/22	0.150618558289855	2	FACETS	0.899	0.814	0.989	0.45	0.407	0.495	INDETERMINATE	1	TRUE	0	0.279695878583112	2		439	1034	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359681	40359681	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148568485	NA	P-0018535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1209	113	649	1	ENST00000293328.3:c.1972G>A	p.Asp658Asn	p.D658N	ENST00000293328	NM_012448.3	658	Gac/Aac	16/19	1	2	FACETS	0.611	0.548	0.679	0.611	0.548	0.679	SUBCLONAL	1	TRUE	1	0.279695878583112	2		650	1322	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774215	56774215	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	54	276	0	ENST00000337432.4:c.566G>T	p.Gly189Val	p.G189V	ENST00000337432	NM_058216.2	189	gGa/gTa	3/9	1	2	FACETS	0.628	0.536	0.729	0.628	0.536	0.729	SUBCLONAL	1	TRUE	1	0.279695878583112	2		276	615	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7152938	7152938	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	116	342	0	ENST00000302850.5:c.2030G>T	p.Gly677Val	p.G677V	ENST00000302850	NM_000208.2	677	gGg/gTg	10/22	0.224227453416263	3	FACETS	1	0.978	1	0.651	0.587	0.719	CLONAL	1	TRUE	1	0.279695878583112	3		342	726	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085842	16085842	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	201	463	0	ENST00000281043.3:c.1018G>T	p.Glu340Ter	p.E340*	ENST00000281043	NM_005378.4	340	Gag/Tag	3/3	0.279695878583112	3	FACETS	1	0.99	1	0.737	0.682	0.794	CLONAL	1	TRUE	1	0.279695878583112	3		463	1111	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339036	225339037	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	169	542	0	ENST00000264414.4:c.2232dup	p.Ile745TyrfsTer2	p.I745Yfs*2	ENST00000264414	NM_003590.4	744	-/T	16/16	0.138948500150429	3	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.279695878583112	3		542	1181	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665549	138665549	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	66	363	0	ENST00000330315.3:c.16C>T	p.Pro6Ser	p.P6S	ENST00000330315	NM_023067.3	6	Ccc/Tcc	1/1	0.279695878583112	3	FACETS	0.628	0.544	0.72			1	SUBCLONAL	1	TRUE	NA	0.279695878583112	3		363	856	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526312	189526312	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	107	337	2	ENST00000264731.3:c.576G>T	p.Trp192Cys	p.W192C	ENST00000264731	NM_003722.4	192	tgG/tgT	4/14	0.279695878583112	7	FACETS	1	0.946	1			1	CLONAL	1	TRUE	NA	0.279695878583112	7		339	1190	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777855	27777855	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	18	111	0	ENST00000369163.2:c.4G>C	p.Ala2Pro	p.A2P	ENST00000369163	NM_003536.2	2	Gcg/Ccg	1/1	0.138948500150429	3	FACETS	0.545	0.411	0.704			1	INDETERMINATE	1	TRUE	NA	0.279695878583112	3		111	269	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566298	141566298	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	64	320	0	ENST00000220592.5:c.1114G>C	p.Ala372Pro	p.A372P	ENST00000220592	NM_012154.3	372	Gcg/Ccg	9/19	0.224227453416263	3	FACETS	0.61	0.527	0.701	0.305	0.263	0.351	SUBCLONAL	1	TRUE	1	0.279695878583112	3		320	855	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409422	80409422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	56	395	1	ENST00000286548.4:c.692C>T	p.Ala231Val	p.A231V	ENST00000286548	NM_002072.3	231	gCg/gTg	5/7	0.15602740185003	5	FACETS	0.7	0.598	0.812	0.175	0.149	0.203	INDETERMINATE	1	TRUE	1	0.279695878583112	5		396	812	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879810	37879810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	264	277	0	ENST00000269571.5:c.2105C>T	p.Pro702Leu	p.P702L	ENST00000269571		702	cCt/cTt	18/27	0.549498334332021	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.549498334332021	2		277	476	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118930	115118930	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	256	252	0	ENST00000257566.3:c.411del	p.Val138Ter	p.V138*	ENST00000257566	NM_016569.3	137	aaA/aa	2/8	0.520354566776235	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	2	0.549498334332021	4		252	678	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42050032	42050032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	213	285	0	ENST00000219905.7:c.7186C>T	p.Arg2396Ter	p.R2396*	ENST00000219905	NM_001164273.1	2396	Cga/Tga	19/24	0.549498334332021	2	FACETS	0.991	0.937	1	0.991	0.937	1	CLONAL	2	TRUE	0	0.549498334332021	2		285	391	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591116	67591151	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TTATCCAGCTGAGAAAGACGAGAGACCAATACTTGA	TTATCCAGCTGAGAAAGACGAGAGACCAATACTTGA	-	novel	NA	P-0018536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	143	255	0	ENST00000274335.5:c.1710_1745del	p.Ile571_Met582del	p.I571_M582del	ENST00000274335		570	cTTATCCAGCTGAGAAAGACGAGAGACCAATACTTGAtg/ctg	12/15	0.549498334332021	2	FACETS	0.784	0.726	0.843	0.784	0.726	0.843	SUBCLONAL	2	TRUE	0	0.549498334332021	2		255	332	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645923	67645923	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	430	505	0	ENST00000264010.4:c.851A>T	p.His284Leu	p.H284L	ENST00000264010	NM_006565.3	284	cAc/cTc	4/12	0.549498334332021	2	FACETS	0.97	0.931	1	0.97	0.931	1	CLONAL	2	TRUE	0	0.549498334332021	2		505	807	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215583	36215583	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	306	668	0	ENST00000222270.7:c.3380C>G	p.Pro1127Arg	p.P1127R	ENST00000222270	NM_014727.1	1127	cCt/cGt	9/37	0.549498334332021	3	FACETS	1	0.983	1	0.557	0.524	0.591	CLONAL	1	TRUE	1	0.549498334332021	3		668	1274	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1222	146	917	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	0.202773377004433	2		917	1368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0018537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1209	133	710	0	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.198826616744228	1	FACETS	0.878	0.795	0.966	0.878	0.795	0.966	CLONAL	1	TRUE	0	0.202773377004433	1		710	1342	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0018539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	1009	708	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.792544589375437	4	FACETS	0.985	0.964	1	0.985	0.964	1	CLONAL	3	TRUE	1	0.885737992146398	4		709	1454	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0018539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	282	636	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.995	0.942	1	0.995	0.942	1	CLONAL	1	TRUE	1	0.885737992146398	2		636	640	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057937	27057955	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCCCTACTCACAGCCAC	CCCCCCTACTCACAGCCAC	-	novel	NA	P-0018539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	358	584	0	ENST00000324856.7:c.1645_1663del	p.Pro549ArgfsTer64	p.P549Rfs*64	ENST00000324856	NM_006015.4	549	CCCCCCTACTCACAGCCACag/ag	3/20	1	2	FACETS	0.972	0.926	1	0.972	0.926	1	CLONAL	1	TRUE	1	0.885737992146398	2		584	832	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560476	95560476	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	300	355	0	ENST00000393063.1:c.5113G>C	p.Glu1705Gln	p.E1705Q	ENST00000393063	NM_030621.3	1705	Gaa/Caa	25/28	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.885737992146398	2		355	665	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572558	95572558	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	156	202	0	ENST00000393063.1:c.2807A>G	p.Tyr936Cys	p.Y936C	ENST00000393063	NM_030621.3	936	tAt/tGt	19/28	1	2	FACETS	0.992	0.922	1	0.992	0.922	1	CLONAL	1	TRUE	1	0.885737992146398	2		202	355	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2114332	2114351	+	frameshift_variant	Frame_Shift_Del	DEL	CCACCAGGTCCGAAAGCTGG	CCACCAGGTCCGAAAGCTGG	-	novel	NA	P-0018539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	86	646	0	ENST00000219476.3:c.1508_1527del	p.Gln503ProfsTer79	p.Q503Pfs*79	ENST00000219476	NM_000548.3	501	gaCCACCAGGTCCGAAAGCTGGcc/gacc	15/42	1	2	FACETS	0.2	0.176	0.226	0.2	0.176	0.226	SUBCLONAL	1	TRUE	1	0.885737992146398	2		646	971	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779762	3779763	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	297	407	0	ENST00000262367.5:c.5285dup	p.Ser1763GlufsTer203	p.S1763Efs*203	ENST00000262367	NM_004380.2	1762	aag/aaAg	31/31	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.885737992146398	2		407	644	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136243	202136243	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	1069	360	0	ENST00000358485.4:c.487A>G	p.Met163Val	p.M163V	ENST00000358485	NM_001080125.1	163	Atg/Gtg	3/9	0.885737992146398	4	FACETS	1	0.998	1	1	0.998	1	CLONAL	4	TRUE	0	0.885737992146398	4		360	1096	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434191	12434191	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	332	464	0	ENST00000287820.6:c.559A>G	p.Arg187Gly	p.R187G	ENST00000287820	NM_015869.4	187	Aga/Gga	4/7	1	2	FACETS	0.941	0.894	0.988	0.941	0.894	0.988	CLONAL	1	TRUE	1	0.885737992146398	2		464	797	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403633	138403633	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	316	394	0	ENST00000289153.2:c.2149A>C	p.Asn717His	p.N717H	ENST00000289153	NM_006219.2	717	Aat/Cat	15/22	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.885737992146398	2		394	672	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	379	364	1				ENST00000310581	NM_198253.2	-/1132			0.218712691089982	7	FACETS	1	0.987	1	1	0.987	1	CLONAL	5	TRUE	2	0.218712691089982	7		365	976	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0018541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1285	981	732	1	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.218712691089982	9	FACETS	0.998	0.97	1			1	CLONAL	7	TRUE	NA	0.218712691089982	9		733	2266	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878061	48878062	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1131690852	NA	P-0018541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	57	228	0	ENST00000267163.4:c.19dup	p.Arg7ProfsTer24	p.R7Pfs*24	ENST00000267163	NM_000321.2	5	acc/aCcc	1/27	0.218712691089982	3	FACETS	0.614	0.525	0.712	0.307	0.262	0.356	SUBCLONAL	1	TRUE	1	0.218712691089982	3		228	941	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857925	9857925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs534440095	NA	P-0018541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	181	441	0	ENST00000330684.3:c.3476G>A	p.Arg1159His	p.R1159H	ENST00000330684	NM_001134407.1	1159	cGc/cAc	13/13	0.164055457238456	4	FACETS	0.999	0.921	1	0.999	0.921	1	CLONAL	2	TRUE	2	0.218712691089982	4		441	1010	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523588	41523588	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	125	501	0	ENST00000263253.7:c.1004G>A	p.Arg335His	p.R335H	ENST00000263253	NM_001429.3	335	cGc/cAc	4/31	0.203445689393946	3	FACETS	1	0.906	1	0.502	0.453	0.554	CLONAL	1	TRUE	1	0.218712691089982	3		501	1263	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047305	77047305	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	63	413	0	ENST00000356341.3:c.1239G>C	p.Gln413His	p.Q413H	ENST00000356341	NM_002576.4	413	caG/caC	13/15	0.218712691089982	3	FACETS	0.841	0.726	0.966	0.42	0.363	0.483	CLONAL	1	TRUE	1	0.218712691089982	3		413	760	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879855	37879855	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	876	530	0	ENST00000269571.5:c.2150A>T	p.Glu717Val	p.E717V	ENST00000269571		717	gAg/gTg	18/27	0.218712691089982	9	FACETS	1	0.99	1			1	CLONAL	7	TRUE	NA	0.218712691089982	9		530	1934	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47168147	47168147	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	117	566	0	ENST00000409792.3:c.78A>T	p.Glu26Asp	p.E26D	ENST00000409792	NM_014159.6	26	gaA/gaT	2/21	0.218712691089982	4	FACETS	0.82	0.739	0.905	0.82	0.739	0.905	CLONAL	2	TRUE	2	0.218712691089982	4		566	795	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197077	26197077	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs373554594	NA	P-0018541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	56	215	0	ENST00000356476.2:c.402G>C	p.Glu134Asp	p.E134D	ENST00000356476		134	gaG/gaC	1/1	0.218712691089982	5	FACETS	0.86	0.735	0.997	0.287	0.245	0.333	CLONAL	1	TRUE	2	0.218712691089982	5		215	791	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652056	36652056	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1328	357	620	0	ENST00000244741.5:c.178G>T	p.Glu60Ter	p.E60*	ENST00000244741	NM_000389.4	60	Gag/Tag	2/3	0.218712691089982	5	FACETS	0.858	0.81	0.906	0.858	0.81	0.906	CLONAL	3	TRUE	2	0.218712691089982	5		620	1685	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	54	486	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.181	0.154	0.211	0.181	0.154	0.211	SUBCLONAL	1	TRUE	1	0.81323991204935	2		488	733	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	66	189	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.721	0.635	0.812	0.721	0.635	0.812	SUBCLONAL	1	TRUE	1	0.81323991204935	2		189	225	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	198	418	1	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.706	0.656	0.757	0.706	0.656	0.757	SUBCLONAL	1	TRUE	1	0.81323991204935	2		419	690	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	159	640	5	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.513	0.471	0.557	0.513	0.471	0.557	SUBCLONAL	1	TRUE	1	0.81323991204935	2		645	762	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	111	527	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.596	0.539	0.656	0.596	0.539	0.656	SUBCLONAL	1	TRUE	1	0.81323991204935	2		528	458	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	245	861	4	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	0.81323991204935	3	FACETS	0.784	0.732	0.837	0.392	0.366	0.419	SUBCLONAL	1	TRUE	1	0.81323991204935	3		865	1081	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465943	69465943	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	411	534	0	ENST00000227507.2:c.781C>T	p.Gln261Ter	p.Q261*	ENST00000227507	NM_053056.2	261	Cag/Tag	5/5	1	2	FACETS	0.96	0.916	1	0.96	0.916	1	CLONAL	1	TRUE	1	0.81323991204935	2		534	1053	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653796	89653798	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs1554893765	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	84	335	0	ENST00000371953.3:c.97_99del	p.Ile33del	p.I33del	ENST00000371953	NM_000314.4	32	ATT/-	2/9	0.573443879895898	3	FACETS	0.674	0.598	0.755	0.337	0.299	0.378	SUBCLONAL	1	TRUE	1	0.81323991204935	3		335	431	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	292	385	0	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.924	0.874	0.975	0.924	0.874	0.975	CLONAL	1	TRUE	1	0.81323991204935	2		385	777	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415537	152415537	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519714	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	257	537	0	ENST00000206249.3:c.1387T>C	p.Ser463Pro	p.S463P	ENST00000206249	NM_000125.3	463	Tcc/Ccc	7/8	1	2	FACETS	0.785	0.738	0.834	0.785	0.738	0.834	SUBCLONAL	1	TRUE	1	0.81323991204935	2		537	805	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	80	472	0	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.23	0.201	0.26	0.23	0.201	0.26	SUBCLONAL	1	TRUE	1	0.81323991204935	2		472	857	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	331	422	2	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.81323991204935	2		424	790	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851754	134851754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56396912	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	321	625	2	ENST00000398015.3:c.1160C>T	p.Thr387Met	p.T387M	ENST00000398015	NM_004441.4	387	aCg/aTg	5/16	1	2	FACETS	0.944	0.895	0.994	0.944	0.895	0.994	CLONAL	1	TRUE	1	0.81323991204935	2		627	836	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617589	158617589	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121912679	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	187	283	0	ENST00000263640.3:c.1067G>A	p.Gly356Asp	p.G356D	ENST00000263640	NM_001105.4	356	gGc/gAc	9/11	1	2	FACETS	0.86	0.8	0.92	0.86	0.8	0.92	CLONAL	1	TRUE	1	0.81323991204935	2		283	535	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	45	64	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	1	2	FACETS	0.838	0.721	0.961	0.838	0.721	0.961	CLONAL	1	TRUE	1	0.81323991204935	2		64	132	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256067	123256067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	225	486	1	ENST00000358487.5:c.1842G>A	p.Met614Ile	p.M614I	ENST00000358487	NM_000141.4	614	atG/atA	13/18	0.81323991204935	3	FACETS	0.72	0.67	0.772	0.36	0.335	0.386	SUBCLONAL	1	TRUE	1	0.81323991204935	3		487	1081	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155673	106155673	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs200585520	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	69	316	0	ENST00000380013.4:c.574T>C	p.Tyr192His	p.Y192H	ENST00000380013	NM_001127208.2	192	Tac/Cac	3/11	1	2	FACETS	0.375	0.327	0.426	0.375	0.327	0.426	SUBCLONAL	1	TRUE	1	0.81323991204935	2		316	453	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154241	2154242	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755455183	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	47	457	1	ENST00000434045.2:c.686dup	p.Glu230ArgfsTer50	p.E230Rfs*50	ENST00000434045	NM_001127598.1	229	cca/ccCa	5/5	1	2	FACETS	0.129	0.108	0.152	0.129	0.108	0.152	SUBCLONAL	1	TRUE	1	0.81323991204935	2		458	899	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720964	176720964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	51	349	0	ENST00000439151.2:c.6595C>T	p.Arg2199Cys	p.R2199C	ENST00000439151	NM_022455.4	2199	Cgt/Tgt	23/23	1	2	FACETS	0.199	0.168	0.232	0.199	0.168	0.232	SUBCLONAL	1	TRUE	1	0.81323991204935	2		349	631	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955112	17955112	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755706305	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1229	77	731	9	ENST00000458235.1:c.115del	p.Gln39SerfsTer108	p.Q39Sfs*108	ENST00000458235	NM_000215.3	39	Cag/ag	2/24	1	2	FACETS	0.145	0.126	0.165	0.145	0.126	0.165	SUBCLONAL	1	TRUE	1	0.81323991204935	2		740	1306	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582407	119582407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199730714	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	142	218	0	ENST00000316626.5:c.994C>T	p.Arg332Cys	p.R332C	ENST00000316626		332	Cgt/Tgt	10/12	1	2	FACETS	0.762	0.7	0.826	0.762	0.7	0.826	SUBCLONAL	1	TRUE	1	0.81323991204935	2		218	458	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924269	11924269	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	86	87	0	ENST00000353533.5:c.69del	p.Val24Ter	p.V24*	ENST00000353533	NM_003010.3	22	ggC/gg	1/11	NA	2	FACETS	0.843	0.757	0.931			1	INDETERMINATE	1	TRUE	NA	0.81323991204935	2		87	251	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166547	118166547	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs74114325	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	69	359	0	ENST00000369448.3:c.1057G>A	p.Val353Ile	p.V353I	ENST00000369448	NM_017709.3	353	Gtc/Atc	2/2	1	2	FACETS	0.198	0.171	0.226	0.198	0.171	0.226	SUBCLONAL	1	TRUE	1	0.81323991204935	2		359	859	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339566	116339566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35469582	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	139	207	2	ENST00000397752.3:c.428G>A	p.Arg143Gln	p.R143Q	ENST00000397752	NM_000245.2	143	cGa/cAa	2/21	1	2	FACETS	0.789	0.725	0.856	0.789	0.725	0.856	SUBCLONAL	1	TRUE	1	0.81323991204935	2		209	433	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420460	49420460	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	217	570	1	ENST00000301067.7:c.15289C>T	p.Arg5097Ter	p.R5097*	ENST00000301067	NM_003482.3	5097	Cga/Tga	48/54	1	2	FACETS	0.614	0.572	0.658	0.614	0.572	0.658	SUBCLONAL	1	TRUE	1	0.81323991204935	2		571	869	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459194	120459194	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1479580345	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	279	402	0	ENST00000256646.2:c.6151C>T	p.Arg2051Trp	p.R2051W	ENST00000256646	NM_024408.3	2051	Cgg/Tgg	34/34	1	2	FACETS	0.934	0.882	0.986	0.934	0.882	0.986	CLONAL	1	TRUE	1	0.81323991204935	2		402	735	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097734	8097734	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1348071008	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1495	292	487	0	ENST00000346208.3:c.116C>T	p.Ala39Val	p.A39V	ENST00000346208		39	gCg/gTg	2/6	0.81323991204935	3	FACETS	0.565	0.53	0.602	0.283	0.265	0.301	SUBCLONAL	1	TRUE	1	0.81323991204935	3		487	1787	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724659	112724660	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	136	407	0	ENST00000369452.4:c.547_548del	p.Glu183AsnfsTer7	p.E183Nfs*7	ENST00000369452	NM_007373.3	181	ctGAga/ctga	2/9	0.573443879895898	3	FACETS	0.639	0.582	0.699	0.32	0.291	0.35	SUBCLONAL	1	TRUE	1	0.81323991204935	3		407	736	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156620	2156620	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	300	524	0	ENST00000434045.2:c.302G>C	p.Cys101Ser	p.C101S	ENST00000434045	NM_001127598.1	101	tGt/tCt	3/5	1	2	FACETS	0.794	0.75	0.84	0.794	0.75	0.84	SUBCLONAL	1	TRUE	1	0.81323991204935	2		524	929	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871008	12871009	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	163	279	0	ENST00000228872.4:c.236_237del	p.Val79GlyfsTer45	p.V79Gfs*45	ENST00000228872	NM_004064.3	79	GTg/g	1/3	1	2	FACETS	0.775	0.717	0.836	0.775	0.717	0.836	SUBCLONAL	1	TRUE	1	0.81323991204935	2		279	517	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003760	45003760	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	70	354	0	ENST00000558401.1:c.16G>T	p.Ala6Ser	p.A6S	ENST00000558401	NM_004048.2	6	Gcc/Tcc	1/4	1	2	FACETS	0.323	0.282	0.367	0.323	0.282	0.367	SUBCLONAL	1	TRUE	1	0.81323991204935	2		354	533	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473783	67473783	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	228	387	0	ENST00000327367.4:c.863G>C	p.Arg288Thr	p.R288T	ENST00000327367	NM_005902.3	288	aGa/aCa	6/9	1	2	FACETS	0.799	0.748	0.851	0.799	0.748	0.851	SUBCLONAL	1	TRUE	1	0.81323991204935	2		387	702	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020606	14020606	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	114	292	0	ENST00000311895.7:c.577T>C	p.Trp193Arg	p.W193R	ENST00000311895	NM_005236.2	193	Tgg/Cgg	3/11	1	2	FACETS	0.762	0.693	0.833	0.762	0.693	0.833	SUBCLONAL	1	TRUE	1	0.81323991204935	2		292	368	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831045	72831045	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	156	197	0	ENST00000268489.5:c.5536del	p.His1846IlefsTer15	p.H1846Ifs*15	ENST00000268489	NM_006885.3	1846	Cat/at	9/10	1	2	FACETS	0.905	0.837	0.974	0.905	0.837	0.974	CLONAL	1	TRUE	1	0.81323991204935	2		197	424	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836384	89836384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771698195	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	281	464	0	ENST00000389301.3:c.2365G>A	p.Val789Met	p.V789M	ENST00000389301	NM_000135.2	789	Gtg/Atg	26/43	1	2	FACETS	0.867	0.818	0.917	0.867	0.818	0.917	CLONAL	1	TRUE	1	0.81323991204935	2		464	797	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368217	45368217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773849578	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	62	312	0	ENST00000262160.6:c.1385G>A	p.Arg462His	p.R462H	ENST00000262160	NM_005901.5	462	cGt/cAt	11/11	1	2	FACETS	0.355	0.308	0.407	0.355	0.308	0.407	SUBCLONAL	1	TRUE	1	0.81323991204935	2		312	429	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226943	2226943	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150855728	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	421	456	2	ENST00000398665.3:c.4423G>A	p.Ala1475Thr	p.A1475T	ENST00000398665	NM_032482.2	1475	Gcg/Acg	27/28	1	2	FACETS	0.997	0.952	1	0.997	0.952	1	CLONAL	1	TRUE	1	0.81323991204935	2		458	1039	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964944	25964944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	220	306	1	ENST00000435504.4:c.4262G>A	p.Cys1421Tyr	p.C1421Y	ENST00000435504		1421	tGc/tAc	13/13	1	2	FACETS	0.902	0.845	0.96	0.902	0.845	0.96	CLONAL	1	TRUE	1	0.81323991204935	2		307	600	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536238	41536238	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	36	434	0	ENST00000263253.7:c.1855A>G	p.Met619Val	p.M619V	ENST00000263253	NM_001429.3	619	Atg/Gtg	9/31	1	2	FACETS	0.137	0.112	0.165	0.137	0.112	0.165	SUBCLONAL	1	TRUE	1	0.81323991204935	2		434	647	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267002	41267002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	130	291	0	ENST00000349496.5:c.673C>T	p.Arg225Cys	p.R225C	ENST00000349496	NM_001904.3	225	Cgt/Tgt	5/15	1	2	FACETS	0.669	0.611	0.729	0.669	0.611	0.729	SUBCLONAL	1	TRUE	1	0.81323991204935	2		291	478	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169977749	169977749	+	splice_region_variant,intron_variant	Splice_Region	DEL	T	T	-	rs1444840805	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	161	420	0	ENST00000295797.4:c.224-3del		p.X75_splice	ENST00000295797	NM_002740.5	75			1	2	FACETS	0.66	0.608	0.714	0.66	0.608	0.714	SUBCLONAL	1	TRUE	1	0.81323991204935	2		420	600	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948098	178948098	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	71	271	0	ENST00000263967.3:c.2870C>T	p.Thr957Ile	p.T957I	ENST00000263967	NM_006218.2	957	aCa/aTa	20/21	1	2	FACETS	0.532	0.468	0.601	0.532	0.468	0.601	SUBCLONAL	1	TRUE	1	0.81323991204935	2		271	328	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1956932	1956932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1190376594	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	236	544	1	ENST00000382891.5:c.2383G>A	p.Gly795Arg	p.G795R	ENST00000382891	NM_133335.3	795	Ggg/Agg	13/22	1	2	FACETS	0.537	0.501	0.575	0.537	0.501	0.575	SUBCLONAL	1	TRUE	1	0.81323991204935	2		545	1080	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539981	187539981	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1299762699	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	29	319	0	ENST00000441802.2:c.7759A>G	p.Thr2587Ala	p.T2587A	ENST00000441802	NM_005245.3	2587	Aca/Gca	10/27	1	2	FACETS	0.137	0.109	0.168	0.137	0.109	0.168	SUBCLONAL	1	TRUE	1	0.81323991204935	2		319	521	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540655	187540655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	53	305	0	ENST00000441802.2:c.7085C>T	p.Ala2362Val	p.A2362V	ENST00000441802	NM_005245.3	2362	gCa/gTa	10/27	1	2	FACETS	0.205	0.174	0.238	0.205	0.174	0.238	SUBCLONAL	1	TRUE	1	0.81323991204935	2		305	637	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541552	187541552	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1344941217	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	88	323	0	ENST00000441802.2:c.6188C>T	p.Ala2063Val	p.A2063V	ENST00000441802	NM_005245.3	2063	gCc/gTc	10/27	1	2	FACETS	0.376	0.333	0.421	0.376	0.333	0.421	SUBCLONAL	1	TRUE	1	0.81323991204935	2		323	576	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589168	67589168	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	57	298	0	ENST00000274335.5:c.1156C>G	p.Arg386Gly	p.R386G	ENST00000274335		386	Cga/Gga	9/15	1	2	FACETS	0.466	0.402	0.534	0.466	0.402	0.534	SUBCLONAL	1	TRUE	1	0.81323991204935	2		298	301	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721975	176721975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	38	410	0	ENST00000439151.2:c.7606G>A	p.Ala2536Thr	p.A2536T	ENST00000439151	NM_022455.4	2536	Gcc/Acc	23/23	1	2	FACETS	0.124	0.102	0.149	0.124	0.102	0.149	SUBCLONAL	1	TRUE	1	0.81323991204935	2		410	755	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271207	26271208	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	25	245	0	ENST00000305910.3:c.405_406del	p.Arg135SerfsTer8	p.R135Sfs*8	ENST00000305910	NM_003534.2	135	agAGcg/agcg	1/1	1	2	FACETS	0.147	0.115	0.184	0.147	0.115	0.184	SUBCLONAL	1	TRUE	1	0.81323991204935	2		245	418	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911107	29911107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45542135	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	298	271	1	ENST00000376809.5:c.406G>A	p.Gly136Arg	p.G136R	ENST00000376809	NM_002116.7	136	Ggg/Agg	3/8	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.81323991204935	2		272	581	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178715	32178715	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	392	493	0	ENST00000375023.3:c.2681-2A>G		p.X894_splice	ENST00000375023	NM_004557.3	894			1	2	FACETS	0.891	0.848	0.934	0.891	0.848	0.934	CLONAL	1	TRUE	1	0.81323991204935	2		493	1082	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41904398	41904398	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	351	467	2	ENST00000372991.4:c.610G>A	p.Ala204Thr	p.A204T	ENST00000372991	NM_001760.3	204	Gcc/Acc	4/5	1	2	FACETS	0.895	0.85	0.941	0.895	0.85	0.941	CLONAL	1	TRUE	1	0.81323991204935	2		469	964	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793535	89793535	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	157	362	1	ENST00000336032.3:c.604G>T	p.Gly202Cys	p.G202C	ENST00000336032	NM_006813.2	202	Ggt/Tgt	2/2	1	2	FACETS	0.816	0.754	0.88	0.816	0.754	0.88	CLONAL	1	TRUE	1	0.81323991204935	2		363	473	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552979	106552979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	390	609	2	ENST00000369096.4:c.944C>T	p.Ala315Val	p.A315V	ENST00000369096	NM_001198.3	315	gCc/gTc	5/7	1	2	FACETS	0.797	0.758	0.837	0.797	0.758	0.837	SUBCLONAL	1	TRUE	1	0.81323991204935	2		611	1203	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370900	55370900	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	388	612	0	ENST00000297316.4:c.202A>T	p.Ile68Phe	p.I68F	ENST00000297316	NM_022454.3	68	Atc/Ttc	1/2	1	2	FACETS	0.888	0.845	0.931	0.888	0.845	0.931	CLONAL	1	TRUE	1	0.81323991204935	2		612	1075	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328444	137328444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780219731	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	377	606	0	ENST00000481739.1:c.1373C>T	p.Pro458Leu	p.P458L	ENST00000481739	NM_002957.4	458	cCg/cTg	10/10	1	2	FACETS	0.851	0.809	0.893	0.851	0.809	0.893	CLONAL	1	TRUE	1	0.81323991204935	2		606	1090	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15833861	15833863	+	inframe_deletion	In_Frame_Del	DEL	ACG	ACG	-	novel	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	81	349	0	ENST00000307771.7:c.622_624del	p.Thr208del	p.T208del	ENST00000307771	NM_005089.3	207	ACG/-	8/11	1	2	FACETS	0.484	0.428	0.542	0.484	0.428	0.542	SUBCLONAL	1	TRUE	1	0.81323991204935	2		349	412	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937962	76937962	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	32	469	0	ENST00000373344.5:c.2786A>G	p.Gln929Arg	p.Q929R	ENST00000373344	NM_000489.3	929	cAg/cGg	9/35	1	2	FACETS	0.131	0.105	0.159	0.131	0.105	0.159	SUBCLONAL	1	TRUE	1	0.81323991204935	2		469	602	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11554273	NA	P-0018543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	54	415	0	ENST00000371085.3:c.601C>A	p.Arg201Ser	p.R201S	ENST00000371085	NM_000516.4	201	Cgt/Agt	8/13	1	2	FACETS	0.177	0.15	0.206	0.177	0.15	0.206	SUBCLONAL	1	TRUE	1	0.822382962954054	2		415	743	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	58	364	1				ENST00000310581	NM_198253.2	-/1132			0.122666438237872	3	FACETS	0.725	0.625	0.833	0.242	0.208	0.278	INDETERMINATE	1	TRUE	0	0.529753797856433	3		365	382	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0018544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	621	559	2	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.519363692203098	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	1	0.529753797856433	3		561	1220	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856499	111856499	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1347353602	NA	P-0018544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	100	381	0	ENST00000341259.2:c.550C>T	p.Pro184Ser	p.P184S	ENST00000341259	NM_005475.2	184	Ccc/Tcc	2/8	1	2	FACETS	0.684	0.613	0.759	0.684	0.613	0.759	SUBCLONAL	1	TRUE	1	0.529753797856433	2		381	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572935	7572938	+	frameshift_variant	Frame_Shift_Del	DEL	AGTC	AGTC	-	novel	NA	P-0018544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	202	399	0	ENST00000269305.4:c.1171_1174del	p.Asp391GlnfsTer30	p.D391Qfs*30	ENST00000269305	NM_001126112.2	391	GACTca/ca	11/11	0.519363692203098	3	FACETS	0.991	0.919	1	0.496	0.459	0.533	CLONAL	1	TRUE	1	0.529753797856433	3		399	973	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575507	67575507	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	170	358	0	ENST00000274335.5:c.581del	p.Pro194GlnfsTer13	p.P194Qfs*13	ENST00000274335		194	Cca/ca	4/15	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.529753797856433	2		358	434	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0018545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	347	897	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.974	0.925	1	0.974	0.925	1	CLONAL	1	TRUE	1	0.784775474459253	2		897	908	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0018547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	263	894	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.363966967001997	2		895	1314	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0018547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	170	636	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.363966967001997	2		636	930	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0018547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	104	457	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	0.363966967001997	1	FACETS	0.817	0.734	0.905	0.817	0.734	0.905	CLONAL	1	TRUE	0	0.363966967001997	1		457	572	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842405	68842405	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	282	664	0	ENST00000261769.5:c.466T>A	p.Trp156Arg	p.W156R	ENST00000261769	NM_004360.3	156	Tgg/Agg	4/16	0.363966967001997	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.363966967001997	1		664	1234	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110083	115110098	+	frameshift_variant	Frame_Shift_Del	DEL	TTCCGAAAGGGGACAT	TTCCGAAAGGGGACAT	CATGTC	novel	NA	P-0018547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1179	200	763	5	ENST00000257566.3:c.1780_1795delinsGACATG	p.Met594AspfsTer35	p.M594Dfs*35	ENST00000257566	NM_016569.3	594	ATGTCCCCTTTCGGAAgc/GACATGgc	8/8	1	2	FACETS	0.797	0.736	0.86	0.797	0.736	0.86	SUBCLONAL	1	TRUE	1	0.363966967001997	2		768	1379	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070659	67070659	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0018547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	94	213	0	ENST00000412916.2:c.282+1G>T		p.X94_splice	ENST00000412916		94			0.363966967001997	1	FACETS	0.935	0.836	1	0.935	0.836	1	CLONAL	1	TRUE	0	0.363966967001997	1		213	452	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950386	15950386	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	170	516	0	ENST00000268712.3:c.6558del	p.Ser2187ValfsTer2	p.S2187Vfs*2	ENST00000268712	NM_006311.3	2186	ggG/gg	42/46	0.251524906918798	1	FACETS	0.88	0.81	0.954	0.88	0.81	0.954	CLONAL	1	TRUE	0	0.363966967001997	1		516	868	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676136	29676136	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs772348111	NA	P-0018547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	143	340	0	ENST00000356175.3:c.7127-2A>G		p.X2376_splice	ENST00000356175	NM_000267.3	2376			0.363966967001997	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.363966967001997	1		340	563	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969459	44969459	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	184	603	0	ENST00000377967.4:c.4141G>T	p.Glu1381Ter	p.E1381*	ENST00000377967	NM_021140.2	1381	Gag/Tag	28/29	1	2	FACETS	0.882	0.812	0.954	0.882	0.812	0.954	CLONAL	1	TRUE	1	0.363966967001997	2		603	1147	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888736	76888736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	43	290	1	ENST00000373344.5:c.5093G>A	p.Arg1698Gln	p.R1698Q	ENST00000373344	NM_000489.3	1698	cGg/cAg	19/35	0.237358459186413	2	FACETS	0.74	0.621	0.87			1	SUBCLONAL	1	TRUE	NA	0.356709059541902	2		291	326	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598302	28598302	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1189397969	NA	P-0018549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	152	652	0	ENST00000253063.3:c.274A>G	p.Ser92Gly	p.S92G	ENST00000253063	NM_031459.4	92	Agc/Ggc	3/10	1	2	FACETS	0.711	0.653	0.772	0.711	0.653	0.772	SUBCLONAL	1	TRUE	1	0.682840651592339	2		652	626	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0018551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	93	559	2	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.384722134830995	1	FACETS	0.836	0.747	0.929	0.836	0.747	0.929	CLONAL	1	TRUE	0	0.402979290345585	1		561	441	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273231	18273231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1260910794	NA	P-0018551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	44	547	2	ENST00000222254.8:c.1024G>A	p.Glu342Lys	p.E342K	ENST00000222254	NM_005027.3	342	Gag/Aag	9/16	0.402979290345585	1	FACETS	0.36	0.302	0.425	0.36	0.302	0.425	SUBCLONAL	1	TRUE	0	0.402979290345585	1		549	484	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635577	47635577	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	126	453	0	ENST00000233146.2:c.249G>C	p.Met83Ile	p.M83I	ENST00000233146	NM_000251.2	83	atG/atC	2/16	1	2	FACETS	0.902	0.818	0.991	0.902	0.818	0.991	CLONAL	1	TRUE	1	0.402979290345585	2		453	693	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511337	157511337	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	62	315	0	ENST00000346085.5:c.3855G>C	p.Met1285Ile	p.M1285I	ENST00000346085	NM_020732.3	1285	atG/atC	15/20	1	2	FACETS	0.882	0.766	1	0.882	0.766	1	CLONAL	1	TRUE	1	0.402979290345585	2		315	349	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0018552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	459	715	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.456540681217035	4	FACETS	0.999	0.959	1	0.999	0.959	1	CLONAL	3	TRUE	1	0.456540681217035	4		717	977	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0018552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	185	807	3	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.334463609177053	3	FACETS	0.847	0.781	0.916	0.424	0.39	0.458	CLONAL	1	TRUE	1	0.456540681217035	3		810	1175	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577144	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs879253942	NA	P-0018552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	287	576	0	ENST00000269305.4:c.794T>C	p.Leu265Pro	p.L265P	ENST00000269305	NM_001126112.2	265	cTg/cCg	8/11	0.363768803535224	2	FACETS	1	0.994	1	0.73	0.689	0.772	CLONAL	1	TRUE	0	0.456540681217035	2		576	861	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	117	917	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	0.19	2		917	1177	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982405	201982405	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779747541	NA	P-0018553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	66	590	1	ENST00000359651.3:c.784G>A	p.Glu262Lys	p.E262K	ENST00000359651		262	Gag/Aag	6/8	0.292966344127468	3	FACETS	0.63	0.545	0.724	0.315	0.272	0.362	SUBCLONAL	1	TRUE	1	0.19	3		591	1207	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112767364	112767364	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	50	481	0	ENST00000369452.4:c.1237C>T	p.Gln413Ter	p.Q413*	ENST00000369452	NM_007373.3	413	Cag/Tag	6/9	1	2	FACETS	0.605	0.512	0.708	0.605	0.512	0.708	SUBCLONAL	1	TRUE	1	0.19	2		481	870	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142950051	142950051	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1276763932	NA	P-0018553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	33	349	0	ENST00000262992.4:c.2659G>C	p.Glu887Gln	p.E887Q	ENST00000262992	NM_001101669.1	887	Gag/Cag	24/24	0.183630369457963	2	FACETS	0.53	0.43	0.643	0.265	0.215	0.322	SUBCLONAL	1	TRUE	0	0.19	2		349	656	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295024	1295024	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	11	78	0	ENST00000310581.5:c.81C>A	p.Phe27Leu	p.F27L	ENST00000310581	NM_198253.2	27	ttC/ttA	1/16	0.3	4	FACETS	0.686	0.474	0.948	0.229	0.158	0.316	SUBCLONAL	1	TRUE	1	0.19	4		78	201	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591312	67591312	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	38	310	0	ENST00000274335.5:c.1810G>A	p.Glu604Lys	p.E604K	ENST00000274335		604	Gaa/Aaa	13/15	1	2	FACETS	0.582	0.48	0.697	0.582	0.48	0.697	SUBCLONAL	1	TRUE	1	0.19	2		310	687	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524946	8524946	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	36	286	0	ENST00000356435.5:c.658C>G	p.Pro220Ala	p.P220A	ENST00000356435		220	Cct/Gct	7/35	0.183630369457963	2	FACETS	0.756	0.621	0.908	0.378	0.31	0.454	CLONAL	1	TRUE	0	0.19	2		286	501	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344871	70344871	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	55	476	0	ENST00000374080.3:c.2101C>A	p.Pro701Thr	p.P701T	ENST00000374080		701	Cct/Act	15/45	1	2	FACETS	0.551	0.469	0.641	0.551	0.469	0.641	SUBCLONAL	1	TRUE	1	0.19	2		476	1051	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0018553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	140	1079	5	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.341672927700714	3	FACETS	1	0.933	1	0.515	0.468	0.564	CLONAL	1	TRUE	1	0.341672927700714	3		1084	932	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431036	49431036	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	119	443	0	ENST00000301067.7:c.10103del	p.Val3368AspfsTer24	p.V3368Dfs*24	ENST00000301067	NM_003482.3	3368	gTa/ga	34/54	0.341672927700714	3	FACETS	1	0.954	1	0.548	0.495	0.604	CLONAL	1	TRUE	1	0.341672927700714	3		443	744	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740376	58740376	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1064797099	NA	P-0018553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	162	494	0	ENST00000305921.3:c.1281G>A	p.Trp427Ter	p.W427*	ENST00000305921	NM_003620.3	427	tgG/tgA	6/6	0.184774898629037	5	FACETS	1	0.97	1	0.74	0.681	0.801	INDETERMINATE	2	TRUE	2	0.341672927700714	5		494	646	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25459811	25459811	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	269	488	0	ENST00000264709.3:c.2472del	p.Ile824MetfsTer7	p.I824Mfs*7	ENST00000264709	NM_175629.2	824	atA/at	21/23	0.239717856815517	3	FACETS	1	0.987	1	0.778	0.732	0.824	CLONAL	2	TRUE	0	0.341672927700714	3		488	790	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	68	917	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.732	0.635	0.837	0.732	0.635	0.837	SUBCLONAL	1	TRUE	1	0.217605652186443	2		917	854	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0018554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	548	1034	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.217605652186443	4	FACETS	0.953	0.914	0.993			1	CLONAL	4	TRUE	NA	0.217605652186443	4		1035	1609	SUCCESS
APC	324	MSKCC	GRCh37	5	112175766	112175766	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	174	187	0	ENST00000257430.4:c.4476del	p.Thr1493ArgfsTer14	p.T1493Rfs*14	ENST00000257430	NM_000038.5	1492	gCc/gc	16/16	0.217605652186443	4	FACETS	0.97	0.896	1			1	CLONAL	3	TRUE	NA	0.217605652186443	4		187	669	SUCCESS
APC	324	MSKCC	GRCh37	5	112174268	112174268	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0018554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	63	271	0	ENST00000257430.4:c.2977A>T	p.Lys993Ter	p.K993*	ENST00000257430	NM_000038.5	993	Aag/Tag	16/16	0.217605652186443	4	FACETS	1	0.881	1			1	CLONAL	1	TRUE	NA	0.217605652186443	4		271	690	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435347	18435347	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	68	386	0	ENST00000266497.5:c.332C>A	p.Pro111His	p.P111H	ENST00000266497		111	cCt/cAt	1/31	1	2	FACETS	0.82	0.713	0.937	0.82	0.713	0.937	CLONAL	1	TRUE	1	0.217605652186443	2		386	762	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254230	133254230	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	104	426	0	ENST00000320574.5:c.654T>G	p.Ile218Met	p.I218M	ENST00000320574	NM_006231.2	218	atT/atG	7/49	0.16073724499438	3	FACETS	0.98	0.876	1	0.49	0.438	0.546	CLONAL	1	TRUE	1	0.217605652186443	3		426	1081	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026008	48026022	+	inframe_deletion	In_Frame_Del	DEL	GTTGCTCGAAAGCGG	GTTGCTCGAAAGCGG	-	novel	NA	P-0018554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	64	234	0	ENST00000234420.5:c.886_900del	p.Val296_Arg300del	p.V296_R300del	ENST00000234420	NM_000179.2	296	GTTGCTCGAAAGCGG/-	4/10	0.217605652186443	3	FACETS	0.903	0.781	1	0.452	0.39	0.518	CLONAL	1	TRUE	1	0.217605652186443	3		234	722	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064395	30064395	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	100	353	0	ENST00000338641.4:c.959A>T	p.Gln320Leu	p.Q320L	ENST00000338641	NM_000268.3	320	cAg/cTg	10/16	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.217605652186443	2		353	884	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923640	131923640	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	62	333	0	ENST00000265335.6:c.910C>G	p.Leu304Val	p.L304V	ENST00000265335		304	Cta/Gta	7/25	NA	2	FACETS	0.823	0.711	0.946			1	INDETERMINATE	1	TRUE	NA	0.217605652186443	2		333	692	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273432	38273432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1412996644	NA	P-0018554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	127	563	0	ENST00000425967.3:c.1903G>A	p.Ala635Thr	p.A635T	ENST00000425967	NM_001174067.1	635	Gcc/Acc	14/19	0.16826154029008	1	FACETS	0.901	0.814	0.992	0.901	0.814	0.992	CLONAL	1	TRUE	0	0.217605652186443	1		563	1155	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006855	47006855	+	5_prime_UTR_variant	5'UTR	SNP	G	G	A	novel	NA	P-0018554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	91	445	0	ENST00000377604.3:c.-26G>A		p.*9*	ENST00000377604	NM_001204468.1	-/852		2/24	1	2	FACETS	0.867	0.768	0.973	0.867	0.768	0.973	CLONAL	1	TRUE	1	0.217605652186443	2		445	965	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	67	364	1				ENST00000310581	NM_198253.2	-/1132			0.36486982610414	3	FACETS	0.86	0.758	0.966	0.86	0.758	0.966	CLONAL	2	TRUE	1	0.414565249221163	3		365	227	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74858968	74858968	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	99	345	0	ENST00000284811.8:c.236A>G	p.Tyr79Cys	p.Y79C	ENST00000284811		79	tAc/tGc	4/4	0.414565249221163	3	FACETS	1	0.977	1	0.828	0.754	0.904	CLONAL	2	TRUE	0	0.414565249221163	3		345	232	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676171	29676171	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	53	436	0	ENST00000356175.3:c.7160G>C	p.Arg2387Thr	p.R2387T	ENST00000356175	NM_000267.3	2387	aGa/aCa	48/57	0.129149924141064	3	FACETS	0.83	0.71	0.96	0.277	0.236	0.32	INDETERMINATE	1	TRUE	0	0.414565249221163	3		436	372	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035185	6035185	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	121	382	0	ENST00000265849.7:c.883C>G	p.Arg295Gly	p.R295G	ENST00000265849	NM_000535.5	295	Cgg/Ggg	8/15	0.278103426526924	4	FACETS	0.924	0.84	1	0.924	0.84	1	CLONAL	2	TRUE	2	0.414565249221163	4		382	447	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967264	134967264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748426868	NA	P-0018556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	92	463	1	ENST00000398015.3:c.2603G>A	p.Arg868Gln	p.R868Q	ENST00000398015	NM_004441.4	868	cGg/cAg	14/16	0.175105129748094	4	FACETS	1	0.925	1	0.529	0.469	0.594	CLONAL	1	TRUE	2	0.194496351822132	4		464	1068	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186501406	186501406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	42	192	1	ENST00000323963.5:c.7G>A	p.Gly3Ser	p.G3S	ENST00000323963		3	Ggt/Agt	1/11	0.194496351822132	5	FACETS	1	0.933	1	0.414	0.346	0.49	CLONAL	1	TRUE	2	0.194496351822132	5		193	449	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056424	26056424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs556238695	NA	P-0018556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	41	197	0	ENST00000343677.2:c.233G>A	p.Ser78Asn	p.S78N	ENST00000343677	NM_005319.3	78	aGc/aAc	1/1	0.175105129748094	4	FACETS	1	0.851	1	0.512	0.426	0.607	CLONAL	1	TRUE	2	0.194496351822132	4		197	492	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797310	135797313	+	frameshift_variant	Frame_Shift_Del	DEL	GTGC	GTGC	AT	novel	NA	P-0018556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	125	291	2	ENST00000298552.3:c.556_559delinsAT	p.Ala186IlefsTer31	p.A186Ifs*31	ENST00000298552	NM_001162426.1	186	GCACtc/ATtc	7/23	0.190885729389417	2	FACETS	0.996	0.904	1	0.996	0.904	1	CLONAL	2	TRUE	0	0.194496351822132	2		293	645	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0018557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	277	752	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.235526362457457	3	FACETS	1	0.988	1			1	CLONAL	3	TRUE	NA	0.235526362457457	3		754	755	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0018557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	354	1181	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.235526362457457	5	FACETS	0.956	0.907	1	0.956	0.907	1	CLONAL	4	TRUE	1	0.235526362457457	5		1182	1064	SUCCESS
APC	324	MSKCC	GRCh37	5	112176150	112176150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	96	513	0	ENST00000257430.4:c.4859C>T	p.Ser1620Leu	p.S1620L	ENST00000257430	NM_000038.5	1620	tCa/tTa	16/16	1	2	FACETS	0.976	0.869	1	0.976	0.869	1	CLONAL	1	TRUE	1	0.235526362457457	2		513	835	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579433	7579433	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1064793279	NA	P-0018557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	262	548	0	ENST00000269305.4:c.254del	p.Pro85LeufsTer38	p.P85Lfs*38	ENST00000269305	NM_001126112.2	85	cCt/ct	4/11	0.235526362457457	3	FACETS	1	0.96	1			1	CLONAL	3	TRUE	NA	0.235526362457457	3		548	807	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49423199	49423199	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	89	559	0	ENST00000301067.7:c.14060A>G	p.Gln4687Arg	p.Q4687R	ENST00000301067	NM_003482.3	4687	cAg/cGg	43/54	0.227126479384441	3	FACETS	0.826	0.73	0.928			1	CLONAL	1	TRUE	NA	0.235526362457457	3		559	1023	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349415	89349415	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	149	668	0	ENST00000301030.4:c.3535A>C	p.Lys1179Gln	p.K1179Q	ENST00000301030	NM_001256183.1	1179	Aag/Cag	9/13	0.235526362457457	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.235526362457457	1		668	855	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265117	5265117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs724159891	NA	P-0018557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	213	635	2	ENST00000357368.4:c.470C>T	p.Ala157Val	p.A157V	ENST00000357368	NM_002850.3	157	gCa/gTa	5/38	0.231976619113089	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.235526362457457	4		637	1006	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610572	215610579	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	TGTTCATC	TGTTCATC	-	rs1559387297	NA	P-0018557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	47	468	0	ENST00000260947.4:c.1678-1_1684del		p.X560_splice	ENST00000260947	NM_000465.2	560		8/11	0.235526362457457	3	FACETS	0.672	0.566	0.789	0.336	0.283	0.395	SUBCLONAL	1	TRUE	1	0.235526362457457	3		468	664	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855249	76855249	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	89	616	1	ENST00000373344.5:c.5738C>T	p.Ser1913Leu	p.S1913L	ENST00000373344	NM_000489.3	1913	tCa/tTa	24/35	0.235526362457457	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.235526362457457	1		617	584	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508988	106508988	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	110	309	2	ENST00000359195.3:c.982G>T	p.Asp328Tyr	p.D328Y	ENST00000359195	NM_002649.2	328	Gac/Tac	2/11	0.235526362457457	3	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	1	0.235526362457457	3		311	506	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0018560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1311	115	807	3	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.474	0.426	0.526	0.474	0.426	0.526	SUBCLONAL	1	TRUE	1	0.34	2		810	1426	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0018560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	104	547	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	0.462	0.412	0.516	0.462	0.412	0.516	SUBCLONAL	1	TRUE	1	0.34	2		547	1323	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076911	41076911	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1348	83	505	0	ENST00000373198.4:c.1509C>A	p.Tyr503Ter	p.Y503*	ENST00000373198	NM_133170.3	503	taC/taA	9/32	0.20368024323739	3	FACETS	0.399	0.351	0.452			1	INDETERMINATE	1	TRUE	NA	0.34	3		505	1431	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246498755	246498755	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	62	438	0	ENST00000388985.4:c.250A>G	p.Lys84Glu	p.K84E	ENST00000388985		84	Aag/Gag	3/12	0.155868433975889	3	FACETS	0.374	0.322	0.431	0.187	0.161	0.216	INDETERMINATE	1	TRUE	1	0.34	3		438	1141	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953149	17953149	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1182	116	561	0	ENST00000458235.1:c.837C>G	p.Ile279Met	p.I279M	ENST00000458235	NM_000215.3	279	atC/atG	6/24	1	2	FACETS	0.526	0.472	0.583	0.526	0.472	0.583	SUBCLONAL	1	TRUE	1	0.34	2		561	1298	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031278	36031278	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	71	345	0	ENST00000358208.4:c.1397A>G	p.Tyr466Cys	p.Y466C	ENST00000358208		466	tAc/tGc	11/12	1	2	FACETS	0.467	0.406	0.532	0.467	0.406	0.532	SUBCLONAL	1	TRUE	1	0.34	2		345	895	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420030	41420030	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	79	348	0	ENST00000373198.4:c.291G>T	p.Glu97Asp	p.E97D	ENST00000373198	NM_133170.3	97	gaG/gaT	3/32	0.20368024323739	3	FACETS	0.605	0.531	0.685			1	INDETERMINATE	1	TRUE	NA	0.34	3		348	898	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331713	8331713	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	68	385	0	ENST00000356435.5:c.5403G>T	p.Arg1801Ser	p.R1801S	ENST00000356435		1801	agG/agT	33/35	1	2	FACETS	0.511	0.444	0.584	0.511	0.444	0.584	SUBCLONAL	1	TRUE	1	0.34	2		385	783	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578509	7578509	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519978	NA	P-0018563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1543	308	692	0	ENST00000269305.4:c.421T>G	p.Cys141Gly	p.C141G	ENST00000269305	NM_001126112.2	141	Tgc/Ggc	5/11	0.230017514969261	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.230017514969261	1		692	1851	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879580	37879580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	94	433	3	ENST00000269571.5:c.1955C>T	p.Thr652Met	p.T652M	ENST00000269571		652	aCg/aTg	17/27	1	2	FACETS	0.673	0.597	0.754	0.673	0.597	0.754	SUBCLONAL	1	TRUE	1	0.230017514969261	2		436	1215	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944469	40944469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	76	428	1	ENST00000373198.4:c.2033C>T	p.Pro678Leu	p.P678L	ENST00000373198	NM_133170.3	678	cCa/cTa	12/32	0.230017514969261	3	FACETS	0.624	0.546	0.71	0.312	0.273	0.355	SUBCLONAL	1	TRUE	1	0.230017514969261	3		429	1180	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400966	72400967	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0018563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	165	390	0	ENST00000357731.5:c.204_205delinsTT	p.Lys68_Gly69delinsAsnCys	p.K68_G69delinsNC	ENST00000357731	NM_173808.2	68	aaGGgt/aaTTgt	2/7	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.230017514969261	2		390	1184	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589548	69589548	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	30	159	0	ENST00000168712.1:c.305del	p.Gly102AlafsTer25	p.G102Afs*25	ENST00000168712	NM_002007.2	102	gGc/gc	1/3	1	2	FACETS	0.581	0.468	0.71	0.581	0.468	0.71	SUBCLONAL	1	TRUE	1	0.230017514969261	2		159	449	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115741	108115741	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1340517984	NA	P-0018563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	38	229	0	ENST00000278616.4:c.889A>G	p.Thr297Ala	p.T297A	ENST00000278616	NM_000051.3	297	Acc/Gcc	7/63	1	2	FACETS	0.582	0.48	0.696	0.582	0.48	0.696	SUBCLONAL	1	TRUE	1	0.230017514969261	2		229	568	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342539	118342539	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	80	332	0	ENST00000534358.1:c.665G>C	p.Arg222Thr	p.R222T	ENST00000534358	NM_005933.3	222	aGa/aCa	3/36	NA	2	FACETS	0.694	0.609	0.785			1	INDETERMINATE	1	TRUE	NA	0.230017514969261	2		332	1003	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432572	49432572	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1254	211	418	0	ENST00000301067.7:c.8567del	p.Gly2856GlufsTer54	p.G2856Efs*54	ENST00000301067	NM_003482.3	2856	gGa/ga	34/54	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.230017514969261	2		418	1465	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39550299	39550299	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374012011	NA	P-0018563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	70	247	0	ENST00000262039.4:c.410G>A	p.Arg137His	p.R137H	ENST00000262039	NM_002647.2	137	cGc/cAc	4/25	1	2	FACETS	0.794	0.691	0.905	0.794	0.691	0.905	CLONAL	1	TRUE	1	0.230017514969261	2		247	767	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152199	11152199	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0018563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1388	232	715	0	ENST00000358026.2:c.4483A>T	p.Lys1495Ter	p.K1495*	ENST00000358026	NM_001128849.1	1495	Aag/Tag	31/36	0.230017514969261	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.230017514969261	1		715	1620	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272495	15272495	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	211	567	2	ENST00000263388.2:c.5944G>T	p.Glu1982Ter	p.E1982*	ENST00000263388	NM_000435.2	1982	Gag/Tag	33/33	0.230017514969261	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.230017514969261	1		569	1371	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209263	36209263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	184	445	1	ENST00000222270.7:c.343G>A	p.Asp115Asn	p.D115N	ENST00000222270	NM_014727.1	115	Gac/Aac	1/37	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.230017514969261	2		446	1345	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641517	47641517	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	144	366	0	ENST00000233146.2:c.902A>G	p.Lys301Arg	p.K301R	ENST00000233146	NM_000251.2	301	aAa/aGa	5/16	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.230017514969261	2		366	1036	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158594104	158594104	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554387941	NA	P-0018563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	126	277	0	ENST00000263640.3:c.1469G>A	p.Arg490His	p.R490H	ENST00000263640	NM_001105.4	490	cGt/cAt	11/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.230017514969261	2		277	902	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934809	49934809	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs148694532	NA	P-0018563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1205	299	490	0	ENST00000296474.3:c.2087G>C	p.Arg696Pro	p.R696P	ENST00000296474	NM_002447.2	696	cGg/cCg	7/20	0.213583952677096	2	FACETS	0.864	0.812	0.918	0.864	0.812	0.918	CLONAL	2	TRUE	0	0.230017514969261	2		490	1504	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839936	27839936	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	136	435	0	ENST00000328488.2:c.158G>T	p.Arg53Leu	p.R53L	ENST00000328488	NM_003533.2	53	cGc/cTc	1/1	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.230017514969261	2		435	1024	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971013	21971014	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	163	329	0	ENST00000304494.5:c.344dup	p.Asp116GlyfsTer4	p.D116Gfs*4	ENST00000304494	NM_000077.4	115	gtg/gtTg	2/3	0.230017514969261	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.230017514969261	1		329	976	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	332	917	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.522339137076573	1	FACETS	0.974	0.924	1	0.974	0.924	1	CLONAL	1	TRUE	0	0.526292976882781	1		917	954	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577599	7577600	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1567550002	NA	P-0018564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	238	487	0	ENST00000269305.4:c.681dup	p.Asp228Ter	p.D228*	ENST00000269305	NM_001126112.2	227	-/T	7/11	0.476379392700573	1	FACETS	0.859	0.804	0.915	0.859	0.804	0.915	CLONAL	1	TRUE	0	0.526292976882781	1		487	776	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971170	21971170	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	190	333	0	ENST00000304494.5:c.188T>A	p.Leu63Gln	p.L63Q	ENST00000304494	NM_000077.4	63	cTg/cAg	2/3	0.526292976882781	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.526292976882781	1		333	523	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0018566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	208	836	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.27205755108371	4	FACETS	0.941	0.873	1	0.941	0.873	1	CLONAL	2	TRUE	2	0.277251325165233	4		836	1018	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207064	1207065	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1131690917	NA	P-0018566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	456	528	0	ENST00000326873.7:c.157dup	p.Asp53GlyfsTer110	p.D53Gfs*110	ENST00000326873	NM_000455.4	51	atg/atGg	1/10	0.233036076765087	4	FACETS	0.892	0.853	0.931	0.892	0.853	0.931	CLONAL	4	TRUE	0	0.277251325165233	4		528	1178	SUCCESS
ATM	472	MSKCC	GRCh37	11	108183190	108183191	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	269	401	0	ENST00000278616.4:c.5977dup	p.Ser1993LysfsTer2	p.S1993Kfs*2	ENST00000278616	NM_000051.3	1991	gaa/gAaa	40/63	0.259257038213377	3	FACETS	0.935	0.88	0.99	0.935	0.88	0.99	CLONAL	3	TRUE	0	0.277251325165233	3		401	788	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576110	88576110	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	251	516	0	ENST00000360948.2:c.1563C>A	p.His521Gln	p.H521Q	ENST00000360948	NM_001012338.2	521	caC/caA	13/19	0.277251325165233	2	FACETS	0.972	0.911	1	0.972	0.911	1	CLONAL	2	TRUE	0	0.277251325165233	2		516	931	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217784	2217785	+	missense_variant	Missense_Mutation	DNP	GC	GC	CT	novel	NA	P-0018566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	92	549	1	ENST00000398665.3:c.2558_2559delinsCT	p.Arg853Pro	p.R853P	ENST00000398665	NM_032482.2	853	cGC/cCT	22/28	0.233036076765087	4	FACETS	0.774	0.686	0.869	0.194	0.171	0.218	SUBCLONAL	1	TRUE	0	0.277251325165233	4		550	1095	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458359	12458359	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	120	570	0	ENST00000287820.6:c.976G>C	p.Glu326Gln	p.E326Q	ENST00000287820	NM_015869.4	326	Gag/Cag	6/7	NA	2	FACETS	0.929	0.838	1			1	INDETERMINATE	1	TRUE	NA	0.277251325165233	2		570	932	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233693	233693	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	39	310	0	ENST00000264932.6:c.997G>T	p.Val333Phe	p.V333F	ENST00000264932	NM_004168.2	333	Gtc/Ttc	8/15	0.277251325165233	3	FACETS	0.608	0.503	0.725	0.304	0.251	0.363	SUBCLONAL	1	TRUE	1	0.277251325165233	3		310	527	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672787	86672787	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	163	277	2	ENST00000274376.6:c.2274G>T	p.Arg758Ser	p.R758S	ENST00000274376	NM_002890.2	758	agG/agT	17/25	0.277251325165233	3	FACETS	0.982	0.904	1	0.982	0.904	1	CLONAL	2	TRUE	1	0.277251325165233	3		279	682	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509421	106509421	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	162	502	0	ENST00000359195.3:c.1415G>T	p.Arg472Leu	p.R472L	ENST00000359195	NM_002649.2	472	cGt/cTt	2/11	0.27205755108371	4	FACETS	0.762	0.699	0.829	0.762	0.699	0.829	SUBCLONAL	2	TRUE	2	0.277251325165233	4		502	979	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911143	40911143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370795038	NA	P-0018568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	195	387	1	ENST00000373198.4:c.2162G>A	p.Arg721His	p.R721H	ENST00000373198	NM_133170.3	721	cGt/cAt	13/32	0.482805200068473	3	FACETS	0.891	0.824	0.962			1	CLONAL	1	TRUE	NA	0.482805200068473	3		388	1125	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347183	347183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	256	445	0	ENST00000262320.3:c.1828G>A	p.Glu610Lys	p.E610K	ENST00000262320	NM_003502.3	610	Gag/Aag	7/11	0.482805200068473	2	FACETS	0.984	0.921	1	0.492	0.46	0.524	CLONAL	1	TRUE	0	0.482805200068473	2		445	1078	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917056	50917056	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	270	447	0	ENST00000440232.2:c.2308G>C	p.Glu770Gln	p.E770Q	ENST00000440232	NM_002691.3	770	Gag/Cag	19/27	0.482805200068473	2	FACETS	1	0.986	1	0.578	0.543	0.614	CLONAL	1	TRUE	0	0.482805200068473	2		447	967	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368160	31368160	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	238	442	0	ENST00000328111.2:c.31G>C	p.Glu11Gln	p.E11Q	ENST00000328111	NM_006892.3	11	Gag/Cag	2/23	0.482805200068473	3	FACETS	0.97	0.904	1	0.485	0.452	0.519	CLONAL	1	TRUE	1	0.482805200068473	3		442	1262	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1940200	1940200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	81	146	0	ENST00000382891.5:c.1697C>T	p.Thr566Met	p.T566M	ENST00000382891	NM_133335.3	566	aCg/aTg	8/22	0.244144011235221	1	FACETS	0.832	0.74	0.928	0.832	0.74	0.928	INDETERMINATE	1	TRUE	0	0.482805200068473	1		146	306	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117874084	117874084	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	138	308	0	ENST00000297338.2:c.370T>G	p.Leu124Val	p.L124V	ENST00000297338	NM_006265.2	124	Tta/Gta	4/14	0.482805200068473	3	FACETS	0.935	0.852	1	0.467	0.426	0.511	CLONAL	1	TRUE	1	0.482805200068473	3		308	759	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174395	11174395	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	356	468	0	ENST00000361445.4:c.7280T>G	p.Leu2427Arg	p.L2427R	ENST00000361445	NM_004958.3	2427	cTg/cGg	53/58	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		468	1270	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	158	364	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.343550282807492	2		365	693	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158225	47158227	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	novel	NA	P-0018572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	93	414	0	ENST00000409792.3:c.4472_4474del	p.His1491del	p.H1491del	ENST00000409792	NM_014159.6	1491	cATCga/cga	4/21	1	2	FACETS	0.773	0.688	0.865	0.773	0.688	0.865	SUBCLONAL	1	TRUE	1	0.343550282807492	2		414	700	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240690	55240690	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs772046081	NA	P-0018572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1679	6644	846	0	ENST00000275493.2:c.1934C>G	p.Ser645Cys	p.S645C	ENST00000275493	NM_005228.3	645	tCc/tGc	17/28	0.343550282807492	23	FACETS	1	0.998	1			1	CLONAL	21	TRUE	NA	0.343550282807492	23		846	8323	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028638	12028638	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	215	269	3	ENST00000353533.5:c.841C>T	p.Arg281Ter	p.R281*	ENST00000353533	NM_003010.3	281	Cga/Tga	8/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.517373131666124	2		272	776	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779647	3779663	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGCTTCATCTTCTGG	CCCGCTTCATCTTCTGG	-	novel	NA	P-0018573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	424	383	0	ENST00000262367.5:c.5385_5401del	p.Gln1796GlyfsTer164	p.Q1796Gfs*164	ENST00000262367	NM_004380.2	1795	tgCCAGAAGATGAAGCGGGtg/tgtg	31/31	0.517373131666124	2	FACETS	0.97	0.93	1	0.97	0.93	1	CLONAL	2	TRUE	0	0.517373131666124	2		383	845	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457866	69457866	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1328	77	496	0	ENST00000227507.2:c.266T>A	p.Leu89Gln	p.L89Q	ENST00000227507	NM_053056.2	89	cTg/cAg	2/5	1	2	FACETS	0.645	0.564	0.733	0.645	0.564	0.733	SUBCLONAL	1	TRUE	1	0.17	2		496	1405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578269	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATCC	novel	NA	P-0018574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1404	96	468	0	ENST00000269305.4:c.580_581insGGAT	p.Leu194ArgfsTer16	p.L194Rfs*16	ENST00000269305	NM_001126112.2	194	ctt/cGGATtt	6/11	1	2	FACETS	0.753	0.668	0.844	0.753	0.668	0.844	SUBCLONAL	1	TRUE	1	0.17	2		468	1500	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543608	9543608	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776769814	NA	P-0018575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	281	552	2	ENST00000353224.5:c.1546G>A	p.Gly516Ser	p.G516S	ENST00000353224	NM_177990.2	516	Ggc/Agc	6/10	0.122748572254036	3	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.587368191852546	3		554	1166	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443487	49443487	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	193	298	0	ENST00000301067.7:c.3884C>T	p.Pro1295Leu	p.P1295L	ENST00000301067	NM_003482.3	1295	cCa/cTa	11/54	0.539356336896059	3	FACETS	1	0.949	1	0.515	0.477	0.555	CLONAL	1	TRUE	1	0.587368191852546	3		298	825	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864666	56864666	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1404	312	560	0	ENST00000519728.1:c.629A>T	p.His210Leu	p.H210L	ENST00000519728	NM_002350.3	210	cAt/cTt	7/13	0.444425081671162	4	FACETS	0.983	0.924	1			1	CLONAL	1	TRUE	NA	0.587368191852546	4		560	1716	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0018576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	131	574	9	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.346520430976144	3	FACETS	1	0.943	1	1	0.943	1	CLONAL	3	TRUE	0	0.448058947414053	3		583	235	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577072	7577090	+	frameshift_variant	Frame_Shift_Del	DEL	AGATTCTCTTCCTCTGTGC	AGATTCTCTTCCTCTGTGC	-	novel	NA	P-0018576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	162	607	2	ENST00000269305.4:c.848_866del	p.Arg283ProfsTer56	p.R283Pfs*56	ENST00000269305	NM_001126112.2	283	cGCACAGAGGAAGAGAATCTc/cc	8/11	0.452698991942817	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.448058947414053	3		609	261	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0018577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	87	573	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.190700213081129	1	FACETS	0.76	0.672	0.854	0.76	0.672	0.854	SUBCLONAL	1	TRUE	0	0.26	1		573	766	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0018577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	86	636	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.711	0.628	0.801	0.711	0.628	0.801	SUBCLONAL	1	TRUE	1	0.26	2		636	930	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500593	99500593	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	113	416	0	ENST00000268035.6:c.4026G>C	p.Glu1342Asp	p.E1342D	ENST00000268035	NM_000875.3	1342	gaG/gaC	21/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.26	2		416	695	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238941	5238941	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs913402227	NA	P-0018578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	43	246	0	ENST00000357368.4:c.1838C>T	p.Thr613Met	p.T613M	ENST00000357368	NM_002850.3	613	aCg/aTg	13/38	0.30560892905474	3	FACETS	0.984	0.826	1	0.492	0.413	0.578	CLONAL	1	TRUE	1	0.306500814594527	3		246	329	SUCCESS
APC	324	MSKCC	GRCh37	5	112174484	112174484	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	23	307	0	ENST00000257430.4:c.3193C>T	p.Gln1065Ter	p.Q1065*	ENST00000257430	NM_000038.5	1065	Caa/Taa	16/16	1	2	FACETS	0.417	0.325	0.524	0.417	0.325	0.524	SUBCLONAL	1	TRUE	1	0.306500814594527	2		307	360	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239457	123239457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756718577	NA	P-0018578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	46	415	0	ENST00000358487.5:c.2380G>A	p.Asp794Asn	p.D794N	ENST00000358487	NM_000141.4	794	Gat/Aat	18/18	1	2	FACETS	0.596	0.501	0.699	0.596	0.501	0.699	SUBCLONAL	1	TRUE	1	0.306500814594527	2		415	504	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405962	49405962	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	99	504	1	ENST00000418115.1:c.176A>G	p.Asp59Gly	p.D59G	ENST00000418115	NM_001664.2	59	gAc/gGc	3/5	1	2	FACETS	0.862	0.77	0.961	0.862	0.77	0.961	CLONAL	1	TRUE	1	0.306500814594527	2		505	749	SUCCESS
APC	324	MSKCC	GRCh37	5	112175532	112175532	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1554085659	NA	P-0018578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	40	277	0	ENST00000257430.4:c.4241del	p.Val1414GlufsTer5	p.V1414Efs*5	ENST00000257430	NM_000038.5	1414	gTa/ga	16/16	1	2	FACETS	0.793	0.661	0.939	0.793	0.661	0.939	CLONAL	1	TRUE	1	0.306500814594527	2		277	329	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577155	7577163	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTACTCAG	ACTACTCAG	-	novel	NA	P-0018580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	375	533	2	ENST00000269305.4:c.783-8_783del		p.X261_splice	ENST00000269305	NM_001126112.2	261		8/11	0.266101039049234	4	FACETS	0.996	0.949	1	0.996	0.949	1	CLONAL	4	TRUE	0	0.266101039049234	4		535	896	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210817	5210817	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0018580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	71	348	0	ENST00000357368.4:c.5235-1G>A		p.X1745_splice	ENST00000357368	NM_002850.3	1745			0.266101039049234	3	FACETS	1	0.942	1	0.569	0.498	0.647	CLONAL	1	TRUE	1	0.266101039049234	3		348	531	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265569	41265569	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	141	418	0	ENST00000349496.5:c.10C>T	p.Gln4Ter	p.Q4*	ENST00000349496	NM_001904.3	4	Caa/Taa	2/15	0.266101039049234	3	FACETS	0.935	0.855	1	0.935	0.855	1	CLONAL	2	TRUE	1	0.266101039049234	3		418	642	SUCCESS
APC	324	MSKCC	GRCh37	5	112170670	112170670	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0018580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	85	333	0	ENST00000257430.4:c.1766T>A	p.Leu589Ter	p.L589*	ENST00000257430	NM_000038.5	589	tTg/tAg	15/16	0.226821332746628	4	FACETS	1	0.972	1	0.448	0.396	0.503	CLONAL	1	TRUE	1	0.266101039049234	4		333	602	SUCCESS
APC	324	MSKCC	GRCh37	5	112175482	112175486	+	frameshift_variant	Frame_Shift_Del	DEL	GAGTC	GAGTC	-	novel	NA	P-0018580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	135	285	0	ENST00000257430.4:c.4192_4196del	p.Ser1398PhefsTer9	p.S1398Ffs*9	ENST00000257430	NM_000038.5	1397	gaGAGTCgt/gagt	16/16	0.226821332746628	4	FACETS	0.856	0.783	0.932	0.856	0.783	0.932	CLONAL	3	TRUE	1	0.266101039049234	4		285	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0018581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	317	850	2	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	0.871577132366762	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.871577132366762	1		852	393	SUCCESS
APC	324	MSKCC	GRCh37	5	112175952	112175952	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587783031	NA	P-0018581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	197	295	0	ENST00000257430.4:c.4666del	p.Thr1556LeufsTer9	p.T1556Lfs*9	ENST00000257430	NM_000038.5	1554	gAa/ga	16/16	0.871577132366762	1	FACETS	0.785	0.743	0.826	0.785	0.743	0.826	SUBCLONAL	1	TRUE	0	0.871577132366762	1		295	325	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470920	25470920	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773312511	NA	P-0018581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	276	421	1	ENST00000264709.3:c.841G>A	p.Glu281Lys	p.E281K	ENST00000264709	NM_175629.2	281	Gag/Aag	7/23	NA	2	FACETS	0.985	0.932	1			1	INDETERMINATE	1	TRUE	NA	0.871577132366762	2		422	643	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012397	176012397	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	378	439	0	ENST00000367669.3:c.1537G>T	p.Glu513Ter	p.E513*	ENST00000367669	NM_022457.5	513	Gag/Tag	14/20	0.741427939789904	3	FACETS	0.957	0.907	1	0.479	0.453	0.504	CLONAL	1	TRUE	1	0.741427939789904	3		439	1460	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533919	533919	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1564789700	NA	P-0018582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	461	493	0	ENST00000451590.1:c.137T>C	p.Ile46Thr	p.I46T	ENST00000451590	NM_001130442.1	46	aTt/aCt	3/5	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.741427939789904	2		493	1176	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909864	100909864	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	180	235	0	ENST00000325455.5:c.2785C>T	p.Leu929Phe	p.L929F	ENST00000325455	NM_001202474.3	929	Ctc/Ttc	8/8	0.741427939789904	3	FACETS	1	0.964	1	0.532	0.493	0.573	CLONAL	1	TRUE	1	0.741427939789904	3		235	625	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552781	18552781	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	273	303	0	ENST00000266497.5:c.2192G>T	p.Ser731Ile	p.S731I	ENST00000266497		731	aGt/aTt	14/31	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.741427939789904	2		303	704	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28931751	28931751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	369	299	1	ENST00000282397.4:c.2188C>T	p.His730Tyr	p.H730Y	ENST00000282397	NM_002019.4	730	Cac/Tac	15/30	0.741427939789904	1	FACETS	0.958	0.918	0.997	0.958	0.918	0.997	CLONAL	1	TRUE	0	0.741427939789904	1		300	654	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873733	35873733	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	1057	460	0	ENST00000216797.5:c.118G>T	p.Glu40Ter	p.E40*	ENST00000216797	NM_020529.2	40	Gag/Tag	1/6	0.740316304801634	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.741427939789904	2		460	1400	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108555	8108555	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	451	471	0	ENST00000585124.1:c.840G>C	p.Glu280Asp	p.E280D	ENST00000585124	NM_004217.3	280	gaG/gaC	8/9	0.741427939789904	1	FACETS	0.979	0.943	1	0.979	0.943	1	CLONAL	1	TRUE	0	0.741427939789904	1		471	782	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667577	29667577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	480	503	0	ENST00000356175.3:c.6913G>A	p.Asp2305Asn	p.D2305N	ENST00000356175	NM_000267.3	2305	Gat/Aat	46/57	1	2	FACETS	0.967	0.925	1	0.967	0.925	1	CLONAL	1	TRUE	1	0.741427939789904	2		503	1339	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985718	60985718	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	135	83	0	ENST00000333681.4:c.182C>T	p.Ala61Val	p.A61V	ENST00000333681		61	gCa/gTa	2/3	0.741427939789904	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.741427939789904	1		83	217	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033438	48033438	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs63750882	NA	P-0018582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	366	438	0	ENST00000234420.5:c.3742C>G	p.His1248Asp	p.H1248D	ENST00000234420	NM_000179.2	1248	Cac/Gac	8/10	1	2	FACETS	0.997	0.948	1	0.997	0.948	1	CLONAL	1	TRUE	1	0.741427939789904	2		438	990	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622669	158622669	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	165	323	0	ENST00000263640.3:c.830C>G	p.Thr277Ser	p.T277S	ENST00000263640	NM_001105.4	277	aCc/aGc	8/11	0.741427939789904	1	FACETS	0.561	0.519	0.604	0.561	0.519	0.604	SUBCLONAL	1	TRUE	0	0.741427939789904	1		323	499	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0018582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	342	401	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	1	2	FACETS	0.99	0.94	1	0.99	0.94	1	CLONAL	1	TRUE	1	0.741427939789904	2		401	932	SUCCESS
ATR	545	MSKCC	GRCh37	3	142254038	142254038	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1232235665	NA	P-0018582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	244	302	0	ENST00000350721.4:c.3829G>C	p.Glu1277Gln	p.E1277Q	ENST00000350721	NM_001184.3	1277	Gag/Cag	21/47	0.741427939789904	3	FACETS	0.965	0.903	1	0.482	0.451	0.515	CLONAL	1	TRUE	1	0.741427939789904	3		302	935	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0018583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	247	921	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	1	2	FACETS	0.885	0.833	0.939	0.885	0.833	0.939	CLONAL	1	TRUE	1	0.827722238000328	2		921	674	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0018586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	52	574	9	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.858	0.73	0.999	0.858	0.73	0.999	CLONAL	1	TRUE	1	0.2	2		583	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0018588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	337	949	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.374776085217865	2	FACETS	0.96	0.911	1	0.96	0.911	1	CLONAL	2	TRUE	0	0.388013703408078	2		949	905	SUCCESS
APC	324	MSKCC	GRCh37	5	112175193	112175193	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1064794042	NA	P-0018588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	129	204	0	ENST00000257430.4:c.3904del	p.Leu1302CysfsTer3	p.L1302Cfs*3	ENST00000257430	NM_000038.5	1301	aCc/ac	16/16	0.374776085217865	2	FACETS	0.931	0.855	1	0.931	0.855	1	CLONAL	2	TRUE	0	0.388013703408078	2		204	357	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912173	114912173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	147	486	0	ENST00000543371.1:c.1243C>T	p.Pro415Ser	p.P415S	ENST00000543371	NM_001198531.1	415	Ccc/Tcc	11/14	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.388013703408078	2		486	706	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004609	16004609	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	122	399	0	ENST00000268712.3:c.2645C>T	p.Thr882Met	p.T882M	ENST00000268712	NM_006311.3	882	aCg/aTg	20/46	0.374776085217865	2	FACETS	1	0.963	1	0.559	0.507	0.614	CLONAL	1	TRUE	0	0.388013703408078	2		399	562	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807913	3807913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	375	493	0	ENST00000262367.5:c.3506G>A	p.Arg1169His	p.R1169H	ENST00000262367	NM_004380.2	1169	cGc/cAc	18/31	0.388013703408078	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	3	TRUE	1	0.388013703408078	4		493	893	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274846	41274846	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	137	433	0	ENST00000349496.5:c.1096T>A	p.Leu366Ile	p.L366I	ENST00000349496	NM_001904.3	366	Tta/Ata	8/15	0.374776085217865	2	FACETS	1	0.977	1	0.6	0.548	0.655	CLONAL	1	TRUE	0	0.388013703408078	2		433	588	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5463005	5463005	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	139	445	0	ENST00000381577.3:c.566A>C	p.Lys189Thr	p.K189T	ENST00000381577	NM_014143.3	189	aAg/aCg	4/7	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.388013703408078	2		445	612	SUCCESS
AR	367	MSKCC	GRCh37	X	66765733	66765733	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	160	411	0	ENST00000374690.3:c.745C>A	p.Leu249Met	p.L249M	ENST00000374690	NM_000044.3	249	Ctg/Atg	1/8	1	1	FACETS	0.801	0.743	0.86	1	0.991	1	CLONAL	2	TRUE	0	0.388013703408078	1		411	415	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526287	189526287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	95	334	0	ENST00000264731.3:c.551C>T	p.Ser184Leu	p.S184L	ENST00000264731	NM_003722.4	184	tCg/tTg	4/14	0.18099556757786	2	FACETS	0.755	0.69	0.82	0.755	0.69	0.82	INDETERMINATE	2	TRUE	0	0.662400060746083	2		334	190	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0018589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	105	749	1	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.187748901075737	3	FACETS	0.977	0.916	1	1	0.989	1	INDETERMINATE	3	TRUE	1	0.662400060746083	3		750	144	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0018590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	551	568	1	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		569	1181	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0018591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	33	715	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.698	0.567	0.848	0.698	0.567	0.848	SUBCLONAL	1	TRUE	1	0.11	2		717	859	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	31	917	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.521	0.419	0.638	0.521	0.419	0.638	SUBCLONAL	1	TRUE	1	0.11	2		917	1081	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163746	32163746	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1184162510	NA	P-0018591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	43	351	0	ENST00000375023.3:c.5480C>T	p.Ala1827Val	p.A1827V	ENST00000375023	NM_004557.3	1827	gCc/gTc	30/30	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.11	2		351	758	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0018592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	402	629	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.776024983544838	2	FACETS	0.998	0.969	1	0.998	0.969	1	CLONAL	2	TRUE	0	0.776024983544838	2		630	519	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178169	56178169	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	270	479	1	ENST00000399503.3:c.3142C>T	p.Gln1048Ter	p.Q1048*	ENST00000399503	NM_005921.1	1048	Cag/Tag	14/20	0.776024983544838	3	FACETS	1	0.948	1	0.505	0.474	0.536	CLONAL	1	TRUE	1	0.776024983544838	3		480	957	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522040	157522040	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	225	390	1	ENST00000346085.5:c.4312A>T	p.Ile1438Phe	p.I1438F	ENST00000346085	NM_020732.3	1438	Atc/Ttc	18/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.776024983544838	2		391	525	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859843	151859847	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTT	TTCTT	-	novel	NA	P-0018592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	231	221	0	ENST00000262189.6:c.10815_10819del	p.Lys3605AsnfsTer8	p.K3605Nfs*8	ENST00000262189	NM_170606.2	3605	aaAAGAAca/aaca	43/59	0.762697841955816	4	FACETS	0.82	0.769	0.871	0.82	0.769	0.871	CLONAL	2	TRUE	2	0.776024983544838	4		221	645	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0018593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	204	752	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.53118030528902	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.53118030528902	1		754	428	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs770248150	NA	P-0018593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	108	393	0	ENST00000311936.3:c.351A>C	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaC	4/5	1	2	FACETS	0.81	0.73	0.894	0.81	0.73	0.894	CLONAL	1	TRUE	1	0.53118030528902	2		393	502	SUCCESS
APC	324	MSKCC	GRCh37	5	112175606	112175606	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	160	370	0	ENST00000257430.4:c.4316del	p.Pro1439LeufsTer34	p.P1439Lfs*34	ENST00000257430	NM_000038.5	1439	Cct/ct	16/16	0.53118030528902	1	FACETS	0.916	0.847	0.987	0.916	0.847	0.987	CLONAL	1	TRUE	0	0.53118030528902	1		370	483	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968633	55968633	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200338299	NA	P-0018593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	140	462	0	ENST00000263923.4:c.2030C>T	p.Thr677Met	p.T677M	ENST00000263923	NM_002253.2	677	aCg/aTg	14/30	0.53118030528902	1	FACETS	0.942	0.866	1	0.942	0.866	1	CLONAL	1	TRUE	0	0.53118030528902	1		462	411	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225408	26225408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	56	124	0	ENST00000360408.1:c.26G>A	p.Arg9His	p.R9H	ENST00000360408	NM_003532.2	9	cGt/cAt	1/1	1	2	FACETS	0.737	0.637	0.845	0.737	0.637	0.845	SUBCLONAL	1	TRUE	1	0.53118030528902	2		124	286	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944325	81944325	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs781621510	NA	P-0018593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	179	383	0	ENST00000359376.3:c.1934C>T	p.Pro645Leu	p.P645L	ENST00000359376	NM_002661.3	645	cCg/cTg	18/33	0.141139450390298	3	FACETS	1	0.988	1	0.671	0.621	0.722	INDETERMINATE	1	TRUE	1	0.53118030528902	3		383	636	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548348	41548349	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0018593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	142	358	0	ENST00000263253.7:c.3139_3140del	p.Lys1047AspfsTer41	p.K1047Dfs*41	ENST00000263253	NM_001429.3	1046	AAa/a	16/31	0.466764327787026	1	FACETS	0.837	0.769	0.908	0.837	0.769	0.908	CLONAL	1	TRUE	0	0.53118030528902	1		358	469	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521478	187521478	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	131	400	0	ENST00000441802.2:c.11677G>C	p.Gly3893Arg	p.G3893R	ENST00000441802	NM_005245.3	3893	Gga/Cga	22/27	0.53118030528902	1	FACETS	0.987	0.906	1	0.987	0.906	1	CLONAL	1	TRUE	0	0.53118030528902	1		400	367	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959240	2959240	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148354898	NA	P-0018593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	132	436	0	ENST00000396946.4:c.2276G>A	p.Arg759Gln	p.R759Q	ENST00000396946	NM_032415.4	759	cGg/cAg	18/25	0.53118030528902	3	FACETS	0.887	0.807	0.972	0.444	0.403	0.486	CLONAL	1	TRUE	1	0.53118030528902	3		436	709	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540123	23540123	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	52	113	0	ENST00000380871.4:c.280G>T	p.Glu94Ter	p.E94*	ENST00000380871	NM_006167.3	94	Gag/Tag	1/2	0.53118030528902	1	FACETS	0.817	0.708	0.932	0.817	0.708	0.932	CLONAL	1	TRUE	0	0.53118030528902	1		113	176	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68982088	68982088	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754632853	NA	P-0018593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	166	519	1	ENST00000288368.4:c.1462C>T	p.Arg488Cys	p.R488C	ENST00000288368	NM_024870.2	488	Cgt/Tgt	13/40	1	2	FACETS	0.864	0.796	0.936	0.864	0.796	0.936	CLONAL	1	TRUE	1	0.53118030528902	2		520	723	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183742	10183742	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	177	475	0	ENST00000256474.2:c.213del	p.Ser72ProfsTer87	p.S72Pfs*87	ENST00000256474	NM_000551.3	71	Ccc/cc	1/3	0.511410286408885	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.511410286408885	1		475	487	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324674	31324674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11546719	NA	P-0018595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	19	68	2	ENST00000412585.2:c.134G>A	p.Arg45His	p.R45H	ENST00000412585	NM_005514.6	45	cGc/cAc	2/8	1	2	FACETS	0.604	0.464	0.765	0.604	0.464	0.765	SUBCLONAL	1	TRUE	1	0.511410286408885	2		70	123	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713606	52713607	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0018595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	156	418	0	ENST00000394830.3:c.121_122del	p.Leu41SerfsTer11	p.L41Sfs*11	ENST00000394830	NM_018313.4	41	CTt/t	2/30	0.511410286408885	1	FACETS	0.914	0.843	0.986	0.914	0.843	0.986	CLONAL	1	TRUE	0	0.511410286408885	1		418	497	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980496	70980496	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	289	758	0	ENST00000276594.2:c.881A>G	p.Lys294Arg	p.K294R	ENST00000276594	NM_024504.3	294	aAg/aGg	4/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.511410286408885	2		758	1068	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0018596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	400	949	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.429290913784893	2	FACETS	0.849	0.811	0.887	0.849	0.811	0.887	CLONAL	2	TRUE	0	0.516808871232747	2		949	912	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125067	46125067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	51	201	0	ENST00000334344.6:c.254C>T	p.Ala85Val	p.A85V	ENST00000334344	NM_152641.2	85	gCt/gTt	3/21	0.329374521458351	3	FACETS	0.686	0.585	0.796	0.343	0.292	0.398	SUBCLONAL	1	TRUE	1	0.516808871232747	3		201	362	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214422	5214422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	216	489	0	ENST00000357368.4:c.4564G>A	p.Asp1522Asn	p.D1522N	ENST00000357368	NM_002850.3	1522	Gat/Aat	30/38	0.332075058803009	4	FACETS	0.765	0.712	0.819			1	SUBCLONAL	2	TRUE	NA	0.516808871232747	4		489	829	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455286	29455286	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	61	444	0	ENST00000389048.3:c.2516T>C	p.Ile839Thr	p.I839T	ENST00000389048	NM_004304.4	839	aTc/aCc	15/29	0.509649199776633	4	FACETS	0.394	0.339	0.455	0.131	0.113	0.152	SUBCLONAL	1	TRUE	1	0.516808871232747	4		444	908	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39239394	39239394	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	75	503	0	ENST00000402219.2:c.2263C>T	p.Gln755Ter	p.Q755*	ENST00000402219	NM_005633.3	755	Cag/Tag	14/23	0.509649199776633	4	FACETS	0.37	0.323	0.421	0.123	0.107	0.141	SUBCLONAL	1	TRUE	1	0.516808871232747	4		503	1189	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163139	47163139	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0018596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	125	303	0	ENST00000409792.3:c.2987C>G	p.Ser996Ter	p.S996*	ENST00000409792	NM_014159.6	996	tCa/tGa	3/21	0.329374521458351	3	FACETS	0.897	0.813	0.984	0.448	0.406	0.492	CLONAL	1	TRUE	1	0.516808871232747	3		303	679	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578277	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs1555525902	NA	P-0018597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	358	482	0	ENST00000269305.4:c.572_574del	p.Pro191del	p.P191del	ENST00000269305	NM_001126112.2	191	cCTCag/cag	6/11	NA	2	FACETS	0.762	0.732	0.792			1	INDETERMINATE	2	TRUE	NA	0.792118565932033	2		482	593	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953760	48953760	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913302	NA	P-0018597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	340	326	0	ENST00000267163.4:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000267163	NM_000321.2	455	Cga/Tga	14/27	0.725233549017509	2	FACETS	0.872	0.841	0.903	0.872	0.841	0.903	CLONAL	2	TRUE	0	0.792118565932033	2		326	492	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99154429	99154429	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	377	388	0	ENST00000074304.5:c.571A>G	p.Asn191Asp	p.N191D	ENST00000074304	NM_001134224.1	191	Aat/Gat	8/26	0.766360388726033	3	FACETS	0.825	0.788	0.862	0.55	0.525	0.575	CLONAL	2	TRUE	0	0.792118565932033	3		388	805	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271512	26271512	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	71	168	1	ENST00000305910.3:c.101G>T	p.Gly34Val	p.G34V	ENST00000305910	NM_003534.2	34	gGc/gTc	1/1	0.704086068117438	4	FACETS	0.913	0.802	1	0.304	0.267	0.344	CLONAL	1	TRUE	1	0.792118565932033	4		169	352	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0018598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	141	1181	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.861	0.783	0.945	0.861	0.783	0.945	CLONAL	1	TRUE	1	0.26	2		1182	1259	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220717	1220717	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587782018	NA	P-0018598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	124	441	0	ENST00000326873.7:c.734+1G>T		p.X245_splice	ENST00000326873	NM_000455.4	245			0.256226092239952	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.26	1		441	739	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602340	10602340	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	161	620	3	ENST00000171111.5:c.1238G>T	p.Arg413Leu	p.R413L	ENST00000171111	NM_203500.1	413	cGt/cTt	3/6	0.256226092239952	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.26	1		623	1060	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791271	42791271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773819902	NA	P-0018598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1152	163	658	0	ENST00000575354.2:c.331C>T	p.Pro111Ser	p.P111S	ENST00000575354	NM_015125.3	111	Cca/Tca	3/20	0.3	2	FACETS	0.953	0.873	1			1	CLONAL	1	TRUE	NA	0.26	2		658	1315	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791714	42791714	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	118	458	0	ENST00000575354.2:c.600C>G	p.Ile200Met	p.I200M	ENST00000575354	NM_015125.3	200	atC/atG	5/20	0.3	2	FACETS	0.834	0.75	0.922			1	CLONAL	1	TRUE	NA	0.26	2		458	1089	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794838	42794838	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	118	471	1	ENST00000575354.2:c.1918C>T	p.Gln640Ter	p.Q640*	ENST00000575354	NM_015125.3	640	Caa/Taa	10/20	0.3	2	FACETS	0.987	0.889	1			1	CLONAL	1	TRUE	NA	0.26	2		472	920	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795832	42795832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	109	548	1	ENST00000575354.2:c.2821C>T	p.Pro941Ser	p.P941S	ENST00000575354	NM_015125.3	941	Cca/Tca	11/20	0.3	2	FACETS	0.739	0.662	0.821			1	SUBCLONAL	1	TRUE	NA	0.26	2		549	1135	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729951	30729954	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	novel	NA	P-0018598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	107	437	0	ENST00000295754.5:c.1472_1475del	p.Val491GlyfsTer26	p.V491Gfs*26	ENST00000295754	NM_003242.5	491	gTGTTg/gg	6/7	0.256226092239952	1	FACETS	0.917	0.822	1	0.917	0.822	1	CLONAL	1	TRUE	0	0.26	1		437	781	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0018598-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	85	815	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.844	0.746	0.95	0.844	0.746	0.95	CLONAL	1	TRUE	1	0.277342137943619	2		815	726	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519920	NA	P-0018598-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	25	358	0	ENST00000397062.3:c.85G>C	p.Asp29His	p.D29H	ENST00000397062	NM_006164.4	29	Gat/Cat	2/5	1	2	FACETS	0.426	0.335	0.531	0.426	0.335	0.531	SUBCLONAL	1	TRUE	1	0.277342137943619	2		358	423	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141874	108141874	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587781558	NA	P-0018598-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	43	524	1	ENST00000278616.4:c.2921+1G>A		p.X974_splice	ENST00000278616	NM_000051.3	974			1	2	FACETS	0.623	0.521	0.736	0.623	0.521	0.736	SUBCLONAL	1	TRUE	1	0.277342137943619	2		525	498	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102056769	102056769	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018598-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	37	511	1	ENST00000282441.5:c.709G>T	p.Glu237Ter	p.E237*	ENST00000282441	NM_001130145.2	237	Gaa/Taa	4/9	1	2	FACETS	0.559	0.461	0.67	0.559	0.461	0.67	SUBCLONAL	1	TRUE	1	0.277342137943619	2		512	477	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223056	1223057	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018598-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	139	589	1	ENST00000326873.7:c.994dup	p.Trp332LeufsTer28	p.W332Lfs*28	ENST00000326873	NM_000455.4	331	-/T	8/10	1	2	FACETS	0.873	0.793	0.958	0.873	0.793	0.958	CLONAL	1	TRUE	1	0.277342137943619	2		590	1148	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730771	40730771	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018598-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	97	483	0	ENST00000373198.4:c.3764T>C	p.Leu1255Pro	p.L1255P	ENST00000373198	NM_133170.3	1255	cTg/cCg	27/32	1	2	FACETS	0.766	0.682	0.856	0.766	0.682	0.856	SUBCLONAL	1	TRUE	1	0.277342137943619	2		483	913	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100974	41100974	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018598-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	100	506	0	ENST00000373198.4:c.1382G>T	p.Arg461Leu	p.R461L	ENST00000373198	NM_133170.3	461	cGa/cTa	8/32	1	2	FACETS	0.749	0.668	0.836	0.749	0.668	0.836	SUBCLONAL	1	TRUE	1	0.277342137943619	2		506	963	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156687	55156687	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018598-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	93	334	0	ENST00000257290.5:c.3088G>C	p.Glu1030Gln	p.E1030Q	ENST00000257290	NM_006206.4	1030	Gag/Cag	22/23	1	2	FACETS	0.801	0.712	0.897	0.801	0.712	0.897	CLONAL	1	TRUE	1	0.277342137943619	2		334	837	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143129578	143129578	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018598-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	44	351	0	ENST00000262992.4:c.1072G>C	p.Asp358His	p.D358H	ENST00000262992	NM_001101669.1	358	Gat/Cat	12/24	1	2	FACETS	0.824	0.693	0.969	0.824	0.693	0.969	CLONAL	1	TRUE	1	0.277342137943619	2		351	385	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524351	187524351	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018598-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	60	393	0	ENST00000441802.2:c.11329del	p.Ala3777GlnfsTer56	p.A3777Qfs*56	ENST00000441802	NM_005245.3	3777	Gca/ca	19/27	1	2	FACETS	0.502	0.431	0.579	0.502	0.431	0.579	SUBCLONAL	1	TRUE	1	0.277342137943619	2		393	862	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131972870	131972870	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018598-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	34	484	0	ENST00000265335.6:c.3453G>T	p.Trp1151Cys	p.W1151C	ENST00000265335		1151	tgG/tgT	22/25	1	2	FACETS	0.435	0.354	0.526	0.435	0.354	0.526	SUBCLONAL	1	TRUE	1	0.277342137943619	2		484	564	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790704	89790704	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018598-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1248	131	746	3	ENST00000336032.3:c.91G>T	p.Ala31Ser	p.A31S	ENST00000336032	NM_006813.2	31	Gcc/Tcc	1/2	1	2	FACETS	0.685	0.619	0.755	0.685	0.619	0.755	SUBCLONAL	1	TRUE	1	0.277342137943619	2		749	1379	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	209	385	0	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.934	0.868	1	0.934	0.868	1	CLONAL	1	TRUE	1	0.501429824785288	2		385	893	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	194	308	2	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.911	0.844	0.981	0.911	0.844	0.981	CLONAL	1	TRUE	1	0.501429824785288	2		310	849	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760106	133760106	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2229071	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	366	845	1	ENST00000318560.5:c.2429C>T	p.Pro810Leu	p.P810L	ENST00000318560	NM_005157.4	810	cCg/cTg	11/11	0.501429824785288	2	FACETS	1	0.991	1	0.592	0.562	0.624	CLONAL	1	TRUE	0	0.501429824785288	2		846	1232	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	226	485	4	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.847	0.789	0.908	0.847	0.789	0.908	CLONAL	1	TRUE	1	0.501429824785288	2		489	1064	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	240	848	1	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.955	0.893	1	0.955	0.893	1	CLONAL	1	TRUE	1	0.501429824785288	2		849	1002	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190891	185190891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777869754	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1903	400	680	2	ENST00000265026.3:c.1772G>A	p.Arg591His	p.R591H	ENST00000265026	NM_004721.4	591	cGc/cAc	11/14	0.501429824785288	4	FACETS	1	0.972	1	0.347	0.328	0.366	CLONAL	1	TRUE	1	0.501429824785288	4		682	2303	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913384	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	126	203	0	ENST00000304494.5:c.262G>T	p.Glu88Ter	p.E88*	ENST00000304494	NM_000077.4	88	Gag/Tag	2/3	0.501429824785288	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.501429824785288	1		203	294	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776561	9776561	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772233114	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	68	552	0	ENST00000377346.4:c.664C>T	p.Arg222Trp	p.R222W	ENST00000377346	NM_005026.3	222	Cgg/Tgg	6/24	1	2	FACETS	0.254	0.22	0.291	0.254	0.22	0.291	SUBCLONAL	1	TRUE	1	0.501429824785288	2		552	1068	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	163	362	8	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	0.819	0.752	0.888	0.819	0.752	0.888	CLONAL	1	TRUE	1	0.501429824785288	2		370	794	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602620	10602620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	646	435	1	ENST00000171111.5:c.958C>T	p.Arg320Trp	p.R320W	ENST00000171111	NM_203500.1	320	Cgg/Tgg	3/6	0.195875230402666	6	FACETS	0.902	0.871	0.934			1	INDETERMINATE	4	TRUE	NA	0.501429824785288	6		436	1430	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612735	228612735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	76	467	1	ENST00000366696.1:c.292G>A	p.Glu98Lys	p.E98K	ENST00000366696	NM_003493.2	98	Gag/Aag	1/1	1	2	FACETS	0.279	0.244	0.317	0.279	0.244	0.317	SUBCLONAL	1	TRUE	1	0.501429824785288	2		468	1086	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628340	187628340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536104649	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	80	503	2	ENST00000441802.2:c.2642G>A	p.Arg881His	p.R881H	ENST00000441802	NM_005245.3	881	cGc/cAc	2/27	1	2	FACETS	0.285	0.249	0.323	0.285	0.249	0.323	SUBCLONAL	1	TRUE	1	0.501429824785288	2		505	1121	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55124955	55124955	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764472307	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	326	594	2	ENST00000257290.5:c.20C>T	p.Ala7Val	p.A7V	ENST00000257290	NM_006206.4	7	gCg/gTg	2/23	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.501429824785288	2		596	1263	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	60	479	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	0.228	0.196	0.264	0.228	0.196	0.264	SUBCLONAL	1	TRUE	1	0.501429824785288	2		479	1048	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	296	491	0	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	0.501429824785288	2		491	1084	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431874	49431874	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	82	613	1	ENST00000301067.7:c.9265del	p.Val3089TrpfsTer30	p.V3089Wfs*30	ENST00000301067	NM_003482.3	3089	Gtg/tg	34/54	1	2	FACETS	0.289	0.254	0.328	0.289	0.254	0.328	SUBCLONAL	1	TRUE	1	0.501429824785288	2		614	1130	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205004	128205004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	277	419	0	ENST00000341105.2:c.437del	p.Gly146ValfsTer72	p.G146Vfs*72	ENST00000341105	NM_032638.4	146	gGt/gt	3/6	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.501429824785288	2		419	877	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196180	108196180	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1154	69	582	0	ENST00000278616.4:c.6716T>A	p.Met2239Lys	p.M2239K	ENST00000278616	NM_000051.3	2239	aTg/aAg	46/63	1	2	FACETS	0.225	0.195	0.258	0.225	0.195	0.258	SUBCLONAL	1	TRUE	1	0.501429824785288	2		582	1223	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374702	118374702	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587783680	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	122	373	0	ENST00000534358.1:c.8095C>T	p.Arg2699Ter	p.R2699*	ENST00000534358	NM_005933.3	2699	Cga/Tga	27/36	1	2	FACETS	0.599	0.541	0.66	0.599	0.541	0.66	SUBCLONAL	1	TRUE	1	0.501429824785288	2		373	812	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715821	18715821	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	144	377	0	ENST00000266497.5:c.3652A>G	p.Ser1218Gly	p.S1218G	ENST00000266497		1218	Agt/Ggt	25/31	1	2	FACETS	0.838	0.766	0.914	0.838	0.766	0.914	CLONAL	1	TRUE	1	0.501429824785288	2		377	685	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254614	46254614	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	280	429	0	ENST00000334344.6:c.4804C>T	p.Gln1602Ter	p.Q1602*	ENST00000334344	NM_152641.2	1602	Caa/Taa	16/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.501429824785288	2		429	1059	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416531	49416531	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768695414	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	157	366	0	ENST00000301067.7:c.16180G>A	p.Glu5394Lys	p.E5394K	ENST00000301067	NM_003482.3	5394	Gaa/Aaa	51/54	1	2	FACETS	0.706	0.647	0.768	0.706	0.647	0.768	SUBCLONAL	1	TRUE	1	0.501429824785288	2		366	887	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444960	49444960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	191	288	2	ENST00000301067.7:c.2506del	p.Gln836SerfsTer94	p.Q836Sfs*94	ENST00000301067	NM_003482.3	836	Cag/ag	10/54	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.501429824785288	2		290	726	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99473479	99473479	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555463008	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	39	309	0	ENST00000268035.6:c.2904del	p.Asn969MetfsTer8	p.N969Mfs*8	ENST00000268035	NM_000875.3	967	ctG/ct	15/21	1	2	FACETS	0.225	0.185	0.269	0.225	0.185	0.269	SUBCLONAL	1	TRUE	1	0.501429824785288	2		309	692	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777966	3777966	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	354	752	4	ENST00000262367.5:c.7082C>A	p.Ser2361Tyr	p.S2361Y	ENST00000262367	NM_004380.2	2361	tCc/tAc	31/31	1	2	FACETS	0.922	0.871	0.973	0.922	0.871	0.973	CLONAL	1	TRUE	1	0.501429824785288	2		756	1532	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3827627	3827627	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	255	480	0	ENST00000262367.5:c.2145G>T	p.Met715Ile	p.M715I	ENST00000262367	NM_004380.2	715	atG/atT	11/31	1	2	FACETS	0.89	0.832	0.949	0.89	0.832	0.949	CLONAL	1	TRUE	1	0.501429824785288	2		480	1143	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634300	23634300	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786203775	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	233	571	0	ENST00000261584.4:c.2986G>T	p.Glu996Ter	p.E996*	ENST00000261584	NM_024675.3	996	Gaa/Taa	9/13	1	2	FACETS	0.668	0.621	0.717	0.668	0.621	0.717	SUBCLONAL	1	TRUE	1	0.501429824785288	2		571	1391	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831446	72831446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143025874	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	58	380	2	ENST00000268489.5:c.5135G>A	p.Arg1712Gln	p.R1712Q	ENST00000268489	NM_006885.3	1712	cGg/cAg	9/10	1	2	FACETS	0.297	0.254	0.344	0.297	0.254	0.344	SUBCLONAL	1	TRUE	1	0.501429824785288	2		382	779	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578200	7578200	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	364	710	0	ENST00000269305.4:c.649del	p.Val217TrpfsTer30	p.V217Wfs*30	ENST00000269305	NM_001126112.2	217	Gtg/tg	6/11	0.501429824785288	1	FACETS	0.933	0.885	0.982	0.933	0.885	0.982	CLONAL	1	TRUE	0	0.501429824785288	1		710	1166	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586140	29586140	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	209	474	0	ENST00000356175.3:c.4360G>T	p.Ala1454Ser	p.A1454S	ENST00000356175	NM_000267.3	1454	Gca/Tca	32/57	1	2	FACETS	0.958	0.891	1	0.958	0.891	1	CLONAL	1	TRUE	1	0.501429824785288	2		474	870	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320308	30320308	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	269	558	0	ENST00000322652.5:c.1249G>C	p.Asp417His	p.D417H	ENST00000322652	NM_015355.2	417	Gat/Cat	11/16	1	2	FACETS	0.732	0.685	0.781	0.732	0.685	0.781	SUBCLONAL	1	TRUE	1	0.501429824785288	2		558	1465	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510684	38510684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762374504	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	287	422	0	ENST00000254066.5:c.938C>T	p.Ala313Val	p.A313V	ENST00000254066	NM_000964.3	313	gCc/gTc	7/9	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.501429824785288	2		422	1037	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59820497	59820497	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	216	417	0	ENST00000259008.2:c.2258-2A>G		p.X753_splice	ENST00000259008	NM_032043.2	753			1	2	FACETS	0.89	0.828	0.954	0.89	0.828	0.954	CLONAL	1	TRUE	1	0.501429824785288	2		417	968	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78831615	78831615	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	70	430	0	ENST00000306801.3:c.1424A>G	p.Tyr475Cys	p.Y475C	ENST00000306801	NM_020761.2	475	tAc/tGc	13/34	0.501429824785288	1	FACETS	0.267	0.232	0.305	0.267	0.232	0.305	SUBCLONAL	1	TRUE	0	0.501429824785288	1		430	783	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101259	4101259	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	241	487	0	ENST00000262948.5:c.548A>G	p.Tyr183Cys	p.Y183C	ENST00000262948	NM_030662.3	183	tAc/tGc	5/11	0.446804271408299	3	FACETS	0.94	0.876	1	0.47	0.438	0.503	CLONAL	1	TRUE	1	0.501429824785288	3		487	1279	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366981	15366981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	136	408	0	ENST00000263377.2:c.1645G>A	p.Glu549Lys	p.E549K	ENST00000263377	NM_058243.2	549	Gaa/Aaa	9/20	1	2	FACETS	0.49	0.445	0.539	0.49	0.445	0.539	SUBCLONAL	1	TRUE	1	0.501429824785288	2		408	1106	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37059090	37059090	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs63750144	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	293	492	0	ENST00000231790.2:c.884G>A	p.Ser295Asn	p.S295N	ENST00000231790	NM_000249.3	295	aGt/aAt	10/19	0.501429824785288	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.501429824785288	1		492	837	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671005	30671005	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1344945241	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	254	571	2	ENST00000376406.3:c.5741del	p.Gly1914GlufsTer57	p.G1914Efs*57	ENST00000376406	NM_014641.2	1914	gGa/ga	12/15	1	2	FACETS	0.888	0.83	0.947	0.888	0.83	0.947	CLONAL	1	TRUE	1	0.501429824785288	2		573	1141	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821440	32821440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	186	458	1	ENST00000354258.4:c.154C>T	p.Arg52Trp	p.R52W	ENST00000354258	NM_000593.5	52	Cgg/Tgg	1/11	1	2	FACETS	0.849	0.785	0.916	0.849	0.785	0.916	CLONAL	1	TRUE	1	0.501429824785288	2		459	874	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141549464	141549464	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	123	273	0	ENST00000220592.5:c.2124G>C	p.Gln708His	p.Q708H	ENST00000220592	NM_012154.3	708	caG/caC	16/19	1	2	FACETS	0.706	0.639	0.776	0.706	0.639	0.776	SUBCLONAL	1	TRUE	1	0.501429824785288	2		273	695	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738725	145738725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369488194	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	260	622	1	ENST00000428558.2:c.2339G>A	p.Arg780Gln	p.R780Q	ENST00000428558	NM_004260.3	780	cGg/cAg	15/22	1	2	FACETS	0.783	0.732	0.835	0.783	0.732	0.835	SUBCLONAL	1	TRUE	1	0.501429824785288	2		623	1325	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504384	8504384	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	209	424	0	ENST00000356435.5:c.1699G>T	p.Gly567Trp	p.G567W	ENST00000356435		567	Ggg/Tgg	12/35	0.501429824785288	1	FACETS	0.973	0.908	1	0.973	0.908	1	CLONAL	1	TRUE	0	0.501429824785288	1		424	642	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528659	8528659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	187	293	0	ENST00000356435.5:c.473C>T	p.Thr158Ile	p.T158I	ENST00000356435		158	aCt/aTt	4/35	0.501429824785288	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.501429824785288	1		293	524	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	82	364	1				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.954	1			1	INDETERMINATE	1	TRUE	NA	0.815980723679604	2		365	183	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026708	6026708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750668	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	188	644	0	ENST00000265849.7:c.1688G>A	p.Arg563Gln	p.R563Q	ENST00000265849	NM_000535.5	563	cGa/cAa	11/15	0.142713808206753	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.815980723679604	0		644	532	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552630	18552630	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200787716	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	235	499	0	ENST00000266497.5:c.2041C>T	p.Arg681Cys	p.R681C	ENST00000266497		681	Cgc/Tgc	14/31	1	2	FACETS	0.889	0.834	0.944	0.889	0.834	0.944	CLONAL	1	TRUE	1	0.815980723679604	2		499	648	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306689	41306689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868376470	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	190	520	0	ENST00000373198.4:c.970G>A	p.Glu324Lys	p.E324K	ENST00000373198	NM_133170.3	324	Gaa/Aaa	7/32	1	2	FACETS	0.919	0.857	0.982	0.919	0.857	0.982	CLONAL	1	TRUE	1	0.815980723679604	2		520	507	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092959	29092959	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	257	523	0	ENST00000328354.6:c.1025G>A	p.Gly342Asp	p.G342D	ENST00000328354	NM_007194.3	342	gGt/gAt	10/15	1	2	FACETS	0.922	0.869	0.977	0.922	0.869	0.977	CLONAL	1	TRUE	1	0.815980723679604	2		523	683	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141492	11141492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	170	654	0	ENST00000358026.2:c.3469C>T	p.Arg1157Trp	p.R1157W	ENST00000358026	NM_001128849.1	1157	Cgg/Tgg	25/36	0.142713808206753	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.815980723679604	0		654	419	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004278	29004278	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	181	356	0	ENST00000282397.4:c.1015C>T	p.Arg339Ter	p.R339*	ENST00000282397	NM_002019.4	339	Cga/Tga	8/30	NA	2	FACETS	0.94	0.875	1			1	INDETERMINATE	1	TRUE	NA	0.815980723679604	2		356	472	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120845	94120845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465346253	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	310	522	0	ENST00000369303.4:c.206G>A	p.Arg69Gln	p.R69Q	ENST00000369303	NM_004440.3	69	cGa/cAa	3/17	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.815980723679604	2		522	745	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557285	29557285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367684252	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	154	318	1	ENST00000356175.3:c.2998C>T	p.Arg1000Cys	p.R1000C	ENST00000356175	NM_000267.3	1000	Cgt/Tgt	23/57	1	2	FACETS	0.918	0.85	0.988	0.918	0.85	0.988	CLONAL	1	TRUE	1	0.815980723679604	2		319	411	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381466	81381466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	178	309	0	ENST00000222390.5:c.595G>A	p.Glu199Lys	p.E199K	ENST00000222390	NM_000601.4	199	Gaa/Aaa	5/18	0.779569592287106	3	FACETS	0.796	0.735	0.859	0.398	0.367	0.43	SUBCLONAL	1	TRUE	1	0.815980723679604	3		309	772	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388032	81388032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	654	521	0	ENST00000222390.5:c.343G>A	p.Glu115Lys	p.E115K	ENST00000222390	NM_000601.4	115	Gaa/Aaa	3/18	0.779569592287106	3	FACETS	0.992	0.961	1	0.992	0.961	1	CLONAL	2	TRUE	1	0.815980723679604	3		521	1138	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435658	18435658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143896492	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	179	296	0	ENST00000266497.5:c.643G>A	p.Gly215Arg	p.G215R	ENST00000266497		215	Gga/Aga	1/31	1	2	FACETS	0.958	0.892	1	0.958	0.892	1	CLONAL	1	TRUE	1	0.815980723679604	2		296	458	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120729	94120729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	253	395	0	ENST00000369303.4:c.322G>A	p.Asp108Asn	p.D108N	ENST00000369303	NM_004440.3	108	Gat/Aat	3/17	1	2	FACETS	0.981	0.925	1	0.981	0.925	1	CLONAL	1	TRUE	1	0.815980723679604	2		395	632	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944581	40944581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs900462377	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	196	413	0	ENST00000373198.4:c.1921G>A	p.Asp641Asn	p.D641N	ENST00000373198	NM_133170.3	641	Gac/Aac	12/32	1	2	FACETS	0.986	0.922	1	0.986	0.922	1	CLONAL	1	TRUE	1	0.815980723679604	2		413	487	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099518	157099518	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	100	211	0	ENST00000346085.5:c.455C>T	p.Pro152Leu	p.P152L	ENST00000346085	NM_020732.3	152	cCc/cTc	1/20	1	2	FACETS	0.973	0.884	1	0.973	0.884	1	CLONAL	1	TRUE	1	0.815980723679604	2		211	252	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149242	119149242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779039234	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	264	479	0	ENST00000264033.4:c.1250C>T	p.Pro417Leu	p.P417L	ENST00000264033	NM_005188.3	417	cCt/cTt	9/16	0.815980723679604	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.815980723679604	1		479	365	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945669	17945669	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201236217	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	162	572	0	ENST00000458235.1:c.2191C>T	p.Pro731Ser	p.P731S	ENST00000458235	NM_000215.3	731	Cct/Tct	16/24	0.142713808206753	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.815980723679604	0		572	405	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991682	25991682	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	204	334	0	ENST00000435504.4:c.560C>T	p.Ser187Phe	p.S187F	ENST00000435504		187	tCc/tTc	7/13	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.815980723679604	2		334	496	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185011	32185011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769158159	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	204	546	0	ENST00000375023.3:c.1657G>A	p.Asp553Asn	p.D553N	ENST00000375023	NM_004557.3	553	Gat/Aat	10/30	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.815980723679604	2		546	477	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950309	17950309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	199	596	0	ENST00000458235.1:c.1418C>T	p.Ser473Phe	p.S473F	ENST00000458235	NM_000215.3	473	tCc/tTc	10/24	0.142713808206753	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.815980723679604	0		596	503	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551730	150551730	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	52	125	0	ENST00000369026.2:c.277C>T	p.Pro93Ser	p.P93S	ENST00000369026	NM_021960.4	93	Ccc/Tcc	1/3	1	2	FACETS	0.973	0.851	1	0.973	0.851	1	CLONAL	1	TRUE	1	0.815980723679604	2		125	131	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206647698	206647698	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	110	433	1	ENST00000367120.3:c.112A>T	p.Lys38Ter	p.K38*	ENST00000367120	NM_014002.3	38	Aag/Tag	4/22	1	2	FACETS	0.788	0.716	0.863	0.788	0.716	0.863	SUBCLONAL	1	TRUE	1	0.815980723679604	2		434	342	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612719	228612719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	177	558	1	ENST00000366696.1:c.308G>A	p.Gly103Glu	p.G103E	ENST00000366696	NM_003493.2	103	gGg/gAg	1/1	1	2	FACETS	0.923	0.859	0.989	0.923	0.859	0.989	CLONAL	1	TRUE	1	0.815980723679604	2		559	470	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850834	63850834	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	622	475	0	ENST00000279873.7:c.1612C>T	p.Pro538Ser	p.P538S	ENST00000279873	NM_032199.2	538	Ccc/Tcc	10/10	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.815980723679604	2		475	750	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942225	71942225	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	144	376	0	ENST00000298229.2:c.1489T>C	p.Tyr497His	p.Y497H	ENST00000298229	NM_001567.3	497	Tac/Cac	12/28	1	2	FACETS	0.914	0.844	0.987	0.914	0.844	0.987	CLONAL	1	TRUE	1	0.815980723679604	2		376	386	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77054919	77054919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	242	471	0	ENST00000356341.3:c.943G>A	p.Glu315Lys	p.E315K	ENST00000356341	NM_002576.4	315	Gag/Aag	10/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.815980723679604	2		471	550	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219124	94219124	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	348	552	0	ENST00000323929.3:c.280C>T	p.Leu94Phe	p.L94F	ENST00000323929	NM_005591.3	94	Ctc/Ttc	4/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.815980723679604	2		552	839	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699346	18699346	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	231	490	0	ENST00000266497.5:c.3447A>C	p.Glu1149Asp	p.E1149D	ENST00000266497		1149	gaA/gaC	24/31	1	2	FACETS	0.927	0.87	0.984	0.927	0.87	0.984	CLONAL	1	TRUE	1	0.815980723679604	2		490	611	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699356	18699356	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	213	479	0	ENST00000266497.5:c.3457C>A	p.His1153Asn	p.H1153N	ENST00000266497		1153	Cat/Aat	24/31	1	2	FACETS	0.919	0.861	0.979	0.919	0.861	0.979	CLONAL	1	TRUE	1	0.815980723679604	2		479	568	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608048	28608048	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	198	546	0	ENST00000241453.7:c.1918C>T	p.Gln640Ter	p.Q640*	ENST00000241453	NM_004119.2	640	Cag/Tag	15/24	NA	2	FACETS	0.965	0.902	1			1	INDETERMINATE	1	TRUE	NA	0.815980723679604	2		546	503	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99482535	99482535	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	209	541	0	ENST00000268035.6:c.3403G>A	p.Asp1135Asn	p.D1135N	ENST00000268035	NM_000875.3	1135	Gac/Aac	18/21	1	2	FACETS	0.844	0.788	0.901	0.844	0.788	0.901	CLONAL	1	TRUE	1	0.815980723679604	2		541	607	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857890	9857890	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768174483	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	144	465	0	ENST00000330684.3:c.3511C>T	p.Pro1171Ser	p.P1171S	ENST00000330684	NM_001134407.1	1171	Ccc/Tcc	13/13	0.142713808206753	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.815980723679604	0		465	395	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858804	9858804	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	47	114	0	ENST00000330684.3:c.2597G>A	p.Gly866Asp	p.G866D	ENST00000330684	NM_001134407.1	866	gGc/gAc	13/13	0.142713808206753	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.815980723679604	0		114	117	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916163	9916163	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	221	479	2	ENST00000330684.3:c.2126A>T	p.Asn709Ile	p.N709I	ENST00000330684	NM_001134407.1	709	aAt/aTt	10/13	0.142713808206753	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.815980723679604	0		481	578	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15938124	15938124	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	151	279	0	ENST00000268712.3:c.7090A>T	p.Arg2364Trp	p.R2364W	ENST00000268712	NM_006311.3	2364	Agg/Tgg	45/46	1	2	FACETS	0.947	0.876	1	0.947	0.876	1	CLONAL	1	TRUE	1	0.815980723679604	2		279	391	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973617	15973617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	172	340	0	ENST00000268712.3:c.4375C>T	p.Leu1459Phe	p.L1459F	ENST00000268712	NM_006311.3	1459	Ctt/Ttt	31/46	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.815980723679604	2		340	418	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533389	29533390	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	129	248	1	ENST00000356175.3:c.1392_1392+1delinsAA		p.X464_splice	ENST00000356175	NM_000267.3	464		12/57	1	2	FACETS	0.891	0.817	0.966	0.891	0.817	0.966	CLONAL	1	TRUE	1	0.815980723679604	2		249	355	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654858	29654858	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1131691117	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	114	203	0	ENST00000356175.3:c.5546+1G>A		p.X1849_splice	ENST00000356175	NM_000267.3	1849			1	2	FACETS	0.89	0.812	0.97	0.89	0.812	0.97	CLONAL	1	TRUE	1	0.815980723679604	2		203	314	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627626	37627626	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	242	682	0	ENST00000447079.4:c.1541C>G	p.Thr514Ser	p.T514S	ENST00000447079	NM_015083.1	514	aCt/aGt	2/14	1	2	FACETS	0.931	0.876	0.988	0.931	0.876	0.988	CLONAL	1	TRUE	1	0.815980723679604	2		682	637	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530033	63530033	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	146	425	0	ENST00000307078.5:c.2402A>G	p.Tyr801Cys	p.Y801C	ENST00000307078	NM_004655.3	801	tAt/tGt	10/11	1	2	FACETS	0.983	0.909	1	0.983	0.909	1	CLONAL	1	TRUE	1	0.815980723679604	2		425	364	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152053	11152055	+	stop_gained	Nonsense_Mutation	TNP	AGC	AGC	CAT	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	125	473	3	ENST00000358026.2:c.4337_4339delinsCAT	p.Lys1446_Arg1447delinsThrTer	p.K1446_R1447delinsT*	ENST00000358026	NM_001128849.1	1446	aAGCga/aCATga	31/36	0.142713808206753	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.815980723679604	0		476	340	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355251	15355252	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	122	351	1	ENST00000263377.2:c.2371_2372delinsTT	p.Pro791Leu	p.P791L	ENST00000263377	NM_058243.2	791	CCg/TTg	13/20	0.142713808206753	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.815980723679604	0		352	329	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215909	36215909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	196	653	0	ENST00000222270.7:c.3449C>T	p.Pro1150Leu	p.P1150L	ENST00000222270	NM_014727.1	1150	cCc/cTc	10/37	0.142713808206753	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.815980723679604	0		653	491	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912133	50912133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768773535	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	220	648	0	ENST00000440232.2:c.1867C>T	p.Arg623Trp	p.R623W	ENST00000440232	NM_002691.3	623	Cgg/Tgg	15/27	0.20208201024449	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.815980723679604	0		648	549	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967018	25967018	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	279	619	1	ENST00000435504.4:c.2188G>A	p.Glu730Lys	p.E730K	ENST00000435504		730	Gaa/Aaa	13/13	1	2	FACETS	0.913	0.862	0.965	0.913	0.862	0.965	CLONAL	1	TRUE	1	0.815980723679604	2		620	749	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39239427	39239427	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	396	589	0	ENST00000402219.2:c.2230A>G	p.Arg744Gly	p.R744G	ENST00000402219	NM_005633.3	744	Aga/Gga	14/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.815980723679604	2		589	945	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47602375	47602375	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	245	461	1	ENST00000263735.4:c.428G>A	p.Trp143Ter	p.W143*	ENST00000263735	NM_002354.2	143	tGg/tAg	4/9	1	2	FACETS	0.972	0.915	1	0.972	0.915	1	CLONAL	1	TRUE	1	0.815980723679604	2		462	618	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61708384	61708384	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	237	460	0	ENST00000401558.2:c.3005T>C	p.Phe1002Ser	p.F1002S	ENST00000401558	NM_003400.3	1002	tTc/tCc	24/25	1	2	FACETS	0.886	0.831	0.941	0.886	0.831	0.941	CLONAL	1	TRUE	1	0.815980723679604	2		460	656	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715385	61715385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	245	463	0	ENST00000401558.2:c.2228C>T	p.Pro743Leu	p.P743L	ENST00000401558	NM_003400.3	743	cCa/cTa	19/25	1	2	FACETS	0.947	0.891	1	0.947	0.891	1	CLONAL	1	TRUE	1	0.815980723679604	2		463	634	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209106839	209106839	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	260	561	0	ENST00000345146.2:c.729G>T	p.Lys243Asn	p.K243N	ENST00000345146	NM_005896.2	243	aaG/aaT	7/10	1	2	FACETS	0.982	0.926	1	0.982	0.926	1	CLONAL	1	TRUE	1	0.815980723679604	2		561	649	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248717	212248717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	216	344	0	ENST00000342788.4:c.3550G>A	p.Asp1184Asn	p.D1184N	ENST00000342788	NM_005235.2	1184	Gat/Aat	28/28	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.815980723679604	2		344	505	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520138	9520138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	165	322	0	ENST00000353224.5:c.2131C>T	p.Pro711Ser	p.P711S	ENST00000353224	NM_177990.2	711	Ccc/Tcc	10/10	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.815980723679604	2		322	399	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256388	46256388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	266	579	0	ENST00000371998.3:c.616G>A	p.Asp206Asn	p.D206N	ENST00000371998		206	Gat/Aat	7/23	1	2	FACETS	0.966	0.911	1	0.966	0.911	1	CLONAL	1	TRUE	1	0.815980723679604	2		579	675	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755621	39755621	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	183	418	2	ENST00000288319.7:c.1144C>A	p.His382Asn	p.H382N	ENST00000288319	NM_182918.3	382	Cat/Aat	10/10	0.142713808206753	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.815980723679604	0		420	463	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39762946	39762946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	241	520	0	ENST00000288319.7:c.890G>A	p.Gly297Glu	p.G297E	ENST00000288319	NM_182918.3	297	gGa/gAa	9/10	0.142713808206753	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.815980723679604	0		520	600	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42842601	42842601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	201	608	1	ENST00000398585.3:c.1256C>T	p.Ser419Phe	p.S419F	ENST00000398585	NM_001135099.1	419	tCc/tTc	11/14	0.142713808206753	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.815980723679604	0		609	483	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458273	12458273	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	250	525	0	ENST00000287820.6:c.890C>T	p.Pro297Leu	p.P297L	ENST00000287820	NM_015869.4	297	cCc/cTc	6/7	0.731997395812195	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.815980723679604	1		525	362	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713544	30713544	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	241	364	1	ENST00000295754.5:c.869A>T	p.Glu290Val	p.E290V	ENST00000295754	NM_003242.5	290	gAg/gTg	4/7	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.815980723679604	2		365	563	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939812	49939812	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	223	560	0	ENST00000296474.3:c.1230+1G>C		p.X410_splice	ENST00000296474	NM_002447.2	410			1	2	FACETS	0.976	0.916	1	0.976	0.916	1	CLONAL	1	TRUE	1	0.815980723679604	2		560	560	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119634982	119634982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	194	335	0	ENST00000316626.5:c.517C>T	p.His173Tyr	p.H173Y	ENST00000316626		173	Cat/Tat	5/12	1	2	FACETS	0.978	0.914	1	0.978	0.914	1	CLONAL	1	TRUE	1	0.815980723679604	2		335	486	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155399	185155399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	174	390	1	ENST00000265026.3:c.640C>T	p.Pro214Ser	p.P214S	ENST00000265026	NM_004721.4	214	Cct/Tct	3/14	1	2	FACETS	0.965	0.898	1	0.965	0.898	1	CLONAL	1	TRUE	1	0.815980723679604	2		391	442	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573320	55573320	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	300	507	0	ENST00000288135.5:c.982G>A	p.Gly328Arg	p.G328R	ENST00000288135	NM_000222.2	328	Gga/Aga	6/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.815980723679604	2		507	731	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156334	106156334	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	217	396	0	ENST00000380013.4:c.1235T>A	p.Leu412His	p.L412H	ENST00000380013	NM_001127208.2	412	cTt/cAt	3/11	0.17410012599369	3	FACETS	1	0.991	1	0.676	0.634	0.719	INDETERMINATE	1	TRUE	1	0.815980723679604	3		396	554	SUCCESS
APC	324	MSKCC	GRCh37	5	112174002	112174002	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	199	405	0	ENST00000257430.4:c.2711G>A	p.Arg904Lys	p.R904K	ENST00000257430	NM_000038.5	904	aGa/aAa	16/16	0.815980723679604	1	FACETS	0.982	0.934	1	0.982	0.934	1	CLONAL	1	TRUE	0	0.815980723679604	1		405	294	SUCCESS
APC	324	MSKCC	GRCh37	5	112175780	112175781	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	146	301	0	ENST00000257430.4:c.4489_4490delinsTT	p.Pro1497Leu	p.P1497L	ENST00000257430	NM_000038.5	1497	CCa/TTa	16/16	0.815980723679604	1	FACETS	0.937	0.882	0.991	0.937	0.882	0.991	CLONAL	1	TRUE	0	0.815980723679604	1		301	226	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499658	149499658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	203	458	1	ENST00000261799.4:c.2615C>T	p.Pro872Leu	p.P872L	ENST00000261799	NM_002609.3	872	cCg/cTg	19/23	0.815980723679604	1	FACETS	0.912	0.865	0.958	0.912	0.865	0.958	CLONAL	1	TRUE	0	0.815980723679604	1		459	323	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637685	176637685	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	367	673	1	ENST00000439151.2:c.2285C>T	p.Ser762Phe	p.S762F	ENST00000439151	NM_022455.4	762	tCc/tTc	5/23	0.815980723679604	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.815980723679604	1		674	490	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816538	32816538	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1198262227	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	273	651	0	ENST00000354258.4:c.1637C>T	p.Pro546Leu	p.P546L	ENST00000354258	NM_000593.5	546	cCt/cTt	7/11	1	2	FACETS	0.964	0.911	1	0.964	0.911	1	CLONAL	1	TRUE	1	0.815980723679604	2		651	694	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93968002	93968002	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs766856886	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	253	410	0	ENST00000369303.4:c.1925G>A	p.Gly642Glu	p.G642E	ENST00000369303	NM_004440.3	642	gGa/gAa	11/17	1	2	FACETS	0.917	0.864	0.972	0.917	0.864	0.972	CLONAL	1	TRUE	1	0.815980723679604	2		410	676	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553476	106553476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747914409	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	120	269	0	ENST00000369096.4:c.1441C>T	p.Pro481Ser	p.P481S	ENST00000369096	NM_001198.3	481	Ccg/Tcg	5/7	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.815980723679604	2		269	267	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715410	117715410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	292	539	0	ENST00000368508.3:c.1079G>A	p.Arg360Lys	p.R360K	ENST00000368508	NM_002944.2	360	aGa/aAa	10/43	1	2	FACETS	0.94	0.889	0.992	0.94	0.889	0.992	CLONAL	1	TRUE	1	0.815980723679604	2		539	761	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978414	2978414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	206	511	0	ENST00000396946.4:c.916G>A	p.Glu306Lys	p.E306K	ENST00000396946	NM_032415.4	306	Gaa/Aaa	7/25	0.142713808206753	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.815980723679604	0		511	485	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450319	50450320	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	187	497	1	ENST00000331340.3:c.503_504delinsTT	p.Ser168Phe	p.S168F	ENST00000331340	NM_006060.4	168	tCC/tTT	5/8	1	2	FACETS	0.883	0.822	0.945	0.883	0.822	0.945	CLONAL	1	TRUE	1	0.815980723679604	2		498	519	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381519	81381519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs946485173	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	205	367	0	ENST00000222390.5:c.542G>A	p.Arg181Gln	p.R181Q	ENST00000222390	NM_000601.4	181	cGa/cAa	5/18	0.779569592287106	3	FACETS	0.809	0.752	0.869	0.405	0.376	0.435	CLONAL	1	TRUE	1	0.815980723679604	3		367	874	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339295	116339295	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	269	447	0	ENST00000397752.3:c.157C>T	p.Gln53Ter	p.Q53*	ENST00000397752	NM_000245.2	53	Cag/Tag	2/21	0.788959185111721	5	FACETS	1	0.948	1	0.254	0.237	0.271	CLONAL	1	TRUE	1	0.815980723679604	5		447	1446	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866486	56866486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	241	521	1	ENST00000519728.1:c.733G>A	p.Glu245Lys	p.E245K	ENST00000519728	NM_002350.3	245	Gag/Aag	8/13	NA	2	FACETS	0.965	0.908	1			1	INDETERMINATE	1	TRUE	NA	0.815980723679604	2		522	612	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542588	141542588	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	161	468	0	ENST00000220592.5:c.2398C>T	p.Pro800Ser	p.P800S	ENST00000220592	NM_012154.3	800	Cca/Tca	18/19	1	2	FACETS	0.871	0.806	0.937	0.871	0.806	0.937	CLONAL	1	TRUE	1	0.815980723679604	2		468	453	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504362	8504362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	278	448	0	ENST00000356435.5:c.1721G>A	p.Gly574Glu	p.G574E	ENST00000356435		574	gGa/gAa	12/35	0.815980723679604	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.815980723679604	1		448	385	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537205	80537205	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	155	346	0	ENST00000286548.4:c.193T>C	p.Ser65Pro	p.S65P	ENST00000286548	NM_002072.3	65	Tca/Cca	2/7	1	2	FACETS	0.869	0.804	0.937	0.869	0.804	0.937	CLONAL	1	TRUE	1	0.815980723679604	2		346	437	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641221	93641221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	176	347	2	ENST00000375746.1:c.1567G>A	p.Glu523Lys	p.E523K	ENST00000375746	NM_001174167.1	523	Gaa/Aaa	11/14	1	2	FACETS	0.978	0.911	1	0.978	0.911	1	CLONAL	1	TRUE	1	0.815980723679604	2		349	441	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351431	70351431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	239	335	0	ENST00000374080.3:c.4079C>T	p.Ser1360Phe	p.S1360F	ENST00000374080		1360	tCc/tTc	29/45	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.815980723679604	1		335	302	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56801449	56801451	+	stop_gained	Nonsense_Mutation	TNP	ACC	ACC	CCT	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	209	538	0	ENST00000337432.4:c.953_955delinsCCT	p.Asp318_Arg319delinsAlaTer	p.D318_R319delinsA*	ENST00000337432	NM_058216.2	318	gACCga/gCCTga	7/9	1	2	FACETS	0.851	0.795	0.908	0.851	0.795	0.908	CLONAL	1	TRUE	1	0.815980723679604	2		538	602	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627623	37627626	+	missense_variant	Missense_Mutation	ONP	TTAC	TTAC	GTAG	novel	NA	P-0018600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	241	673	0	ENST00000447079.4:c.1538_1541delinsGTAG	p.Val513_Thr514delinsGlySer	p.V513_T514delinsGS	ENST00000447079	NM_015083.1	513	gTTACt/gGTAGt	2/14	1	2	FACETS	0.919	0.864	0.975	0.919	0.864	0.975	CLONAL	1	TRUE	1	0.815980723679604	2		673	643	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567776	226567785	+	frameshift_variant	Frame_Shift_Del	DEL	CGGAGACGTC	CGGAGACGTC	-	novel	NA	P-0018601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	586	613	0	ENST00000366794.5:c.1381_1390del	p.Asp461ProfsTer11	p.D461Pfs*11	ENST00000366794	NM_001618.3	461	GACGTCTCCGcc/cc	10/23	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.736913154472006	2		613	1587	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942548	71942548	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs996859031	NA	P-0018601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	747	395	0	ENST00000298229.2:c.1504A>G	p.Met502Val	p.M502V	ENST00000298229	NM_001567.3	502	Atg/Gtg	13/28	0.258353762091536	4	FACETS	1	0.997	1			1	INDETERMINATE	2	TRUE	NA	0.736913154472006	4		395	1417	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444066	49444067	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	802	441	0	ENST00000301067.7:c.3304dup	p.Ser1102PhefsTer13	p.S1102Ffs*13	ENST00000301067	NM_003482.3	1102	tcc/tTcc	11/54	0.736913154472006	2	FACETS	0.962	0.94	0.984	0.962	0.94	0.984	CLONAL	2	TRUE	0	0.736913154472006	2		441	1131	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579391	7579392	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	559	654	0	ENST00000269305.4:c.295dup	p.Ser99PhefsTer50	p.S99Ffs*50	ENST00000269305	NM_001126112.2	99	tcc/tTcc	4/11	0.736913154472006	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.736913154472006	1		654	920	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139079	50139079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs925989732	NA	P-0018601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	397	503	0	ENST00000246792.3:c.484G>A	p.Ala162Thr	p.A162T	ENST00000246792	NM_006270.3	162	Gcc/Acc	5/6	0.312658908530282	1	FACETS	0.606	0.577	0.635	0.606	0.577	0.635	INDETERMINATE	1	TRUE	0	0.736913154472006	1		503	1123	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131514	202131515	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	TT	novel	NA	P-0018601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	308	362	0	ENST00000358485.4:c.482_482+1delinsTT		p.X161_splice	ENST00000358485	NM_001080125.1	161		2/9	0.736913154472006	1	FACETS	0.965	0.922	1	0.965	0.922	1	CLONAL	1	TRUE	0	0.736913154472006	1		362	547	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188002	32188002	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	592	642	0	ENST00000375023.3:c.1219T>C	p.Cys407Arg	p.C407R	ENST00000375023	NM_004557.3	407	Tgc/Cgc	7/30	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.736913154472006	2		642	1562	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881392	37881392	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	1885	593	0	ENST00000269571.5:c.2584A>G	p.Thr862Ala	p.T862A	ENST00000269571		862	Aca/Gca	21/27	0.225709455600077	22	FACETS	0.99	0.974	1			1	CLONAL	20	TRUE	NA	0.225709455600077	22		593	2749	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163310156	163310156	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	63	551	0	ENST00000271452.3:c.609A>G	p.Ile203Met	p.I203M	ENST00000271452	NM_145697.2	203	atA/atG	9/14	0.225709455600077	5	FACETS	0.659	0.568	0.759	0.22	0.189	0.253	SUBCLONAL	1	TRUE	2	0.225709455600077	5		551	1134	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612638	228612638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146830002	NA	P-0018602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	38	442	1	ENST00000366696.1:c.389G>A	p.Arg130His	p.R130H	ENST00000366696	NM_003493.2	130	cGt/cAt	1/1	0.175859457108166	3	FACETS	0.525	0.432	0.629	0.175	0.144	0.21	SUBCLONAL	1	TRUE	0	0.225709455600077	3		443	714	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577027	7577028	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0018602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	178	558	0	ENST00000269305.4:c.910_911del	p.Thr304Ter	p.T304*	ENST00000269305	NM_001126112.2	304	ACt/t	8/11	0.225709455600077	3	FACETS	1	0.962	1	0.713	0.658	0.77	CLONAL	2	TRUE	0	0.225709455600077	3		558	821	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228225	53228225	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	132	503	0	ENST00000375401.3:c.2177A>G	p.Asp726Gly	p.D726G	ENST00000375401	NM_004187.3	726	gAc/gGc	15/26	0.182142455528119	4	FACETS	0.834	0.756	0.915	0.556	0.504	0.61	CLONAL	2	TRUE	1	0.225709455600077	4		503	860	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0018603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	295	708	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.488689830846439	3	FACETS	0.921	0.872	0.971	0.921	0.872	0.971	CLONAL	2	TRUE	1	0.568934898071678	3		709	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0018603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	479	792	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	NA	2	FACETS	0.903	0.869	0.938			1	INDETERMINATE	2	TRUE	NA	0.568934898071678	2		792	932	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	336	441	0	ENST00000267101.3:c.889G>C	p.Asp297His	p.D297H	ENST00000267101	NM_001982.3	297	Gat/Cat	8/28	0.488689830846439	3	FACETS	0.869	0.825	0.913	0.869	0.825	0.913	CLONAL	2	TRUE	1	0.568934898071678	3		441	873	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593405	48593405	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519962	NA	P-0018603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	86	263	0	ENST00000342988.3:c.1156G>A	p.Gly386Ser	p.G386S	ENST00000342988	NM_005359.5	386	Ggt/Agt	10/12	0.568934898071678	1	FACETS	0.829	0.744	0.917	0.829	0.744	0.917	CLONAL	1	TRUE	0	0.568934898071678	1		263	261	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267186	41267186	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553630452	NA	P-0018603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	131	358	0	ENST00000349496.5:c.770C>T	p.Thr257Ile	p.T257I	ENST00000349496	NM_001904.3	257	aCa/aTa	6/15	0.488689830846439	3	FACETS	0.917	0.834	1	0.459	0.417	0.502	CLONAL	1	TRUE	1	0.568934898071678	3		358	645	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0018604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	436	565	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.331391230650591	5	FACETS	1	0.987	1	0.728	0.694	0.762	INDETERMINATE	2	TRUE	2	0.599950461510499	5		565	1265	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578207	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0018604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	518	671	0	ENST00000269305.4:c.642_643del	p.His214GlnfsTer7	p.H214Qfs*7	ENST00000269305	NM_001126112.2	214	caTAgt/cagt	6/11	0.331391230650591	5	FACETS	1	0.991	1	0.75	0.718	0.781	INDETERMINATE	2	TRUE	2	0.599950461510499	5		671	1459	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096967	11096967	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs539710314	NA	P-0018604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	535	636	1	ENST00000358026.2:c.458C>T	p.Pro153Leu	p.P153L	ENST00000358026	NM_001128849.1	153	cCg/cTg	4/36	0.554580511915107	4	FACETS	0.93	0.892	0.969	0.93	0.892	0.969	CLONAL	2	TRUE	2	0.599950461510499	4		637	1534	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981586	101981586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1319669560	NA	P-0018604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	142	159	2	ENST00000282441.5:c.7C>T	p.Pro3Ser	p.P3S	ENST00000282441	NM_001130145.2	3	Ccc/Tcc	1/9	0.599950461510499	3	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	1	0.599950461510499	3		161	306	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409102	4409102	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778716956	NA	P-0018604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	155	431	0	ENST00000261254.3:c.797G>A	p.Arg266His	p.R266H	ENST00000261254	NM_001759.3	266	cGt/cAt	5/5	0.554580511915107	4	FACETS	0.911	0.834	0.992	0.456	0.417	0.496	CLONAL	1	TRUE	2	0.599950461510499	4		431	907	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523532	106523532	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	294	407	0	ENST00000359195.3:c.2684C>A	p.Thr895Lys	p.T895K	ENST00000359195	NM_002649.2	895	aCa/aAa	8/11	0.554580511915107	4	FACETS	0.824	0.777	0.872	0.824	0.777	0.872	CLONAL	2	TRUE	2	0.599950461510499	4		407	951	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974798	21974798	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	48	75	0	ENST00000304494.5:c.29del	p.Glu10GlyfsTer16	p.E10Gfs*16	ENST00000304494	NM_000077.4	10	gAg/gg	1/3	0.571043909592579	2	FACETS	0.842	0.741	0.943	0.842	0.741	0.943	CLONAL	2	TRUE	0	0.599950461510499	2		75	95	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002716	37002716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1220180482	NA	P-0018604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	663	458	1	ENST00000358127.4:c.533C>T	p.Ser178Leu	p.S178L	ENST00000358127	NM_001280556.1	178	tCg/tTg	5/10	0.599950461510499	5	FACETS	1	0.995	1			1	CLONAL	3	TRUE	NA	0.599950461510499	5		459	1242	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182032	38182032	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	98	368	0	ENST00000396334.3:c.656C>G	p.Ser219Cys	p.S219C	ENST00000396334	NM_002468.4	219	tCt/tGt	3/5	0.718621746412801	1	FACETS	0.386	0.346	0.428	0.386	0.346	0.428	SUBCLONAL	1	TRUE	0	0.718621746412801	1		368	453	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436928	49436934	+	frameshift_variant	Frame_Shift_Del	DEL	CACTGGG	CACTGGG	-	novel	NA	P-0018608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	425	573	0	ENST00000301067.7:c.5569_5575del	p.Pro1857ThrfsTer17	p.P1857Tfs*17	ENST00000301067	NM_003482.3	1857	CCCAGTGac/ac	25/54	0.219160334821367	3	FACETS	1	0.995	1	0.697	0.665	0.729	INDETERMINATE	1	TRUE	1	0.718621746412801	3		573	1154	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742653	39742653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	76	298	1	ENST00000361337.2:c.1496C>T	p.Ala499Val	p.A499V	ENST00000361337	NM_003286.2	499	gCg/gTg	15/21	1	2	FACETS	0.35	0.307	0.396	0.35	0.307	0.396	SUBCLONAL	1	TRUE	1	0.718621746412801	2		299	604	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591233	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAACCAGACCTTATCCAGCTGAGAAAGACGAGAGACCAATACTTGATGTAAGTATTTGAAATGGAATCCTATACATGAATAATTGGTGATTGCTACAATTCAGGATGAGTTAATGCGTTCTCTTTTCA	AAACCAGACCTTATCCAGCTGAGAAAGACGAGAGACCAATACTTGATGTAAGTATTTGAAATGGAATCCTATACATGAATAATTGGTGATTGCTACAATTCAGGATGAGTTAATGCGTTCTCTTTTCA	-	novel	NA	P-0018608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	53	381	0	ENST00000274335.5:c.1703_1746-11del		p.X568_splice	ENST00000274335		568		12/15	1	2	FACETS	0.313	0.267	0.363	0.313	0.267	0.363	SUBCLONAL	1	TRUE	1	0.718621746412801	2		381	471	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	60	364	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.809	0.701	0.926	0.809	0.701	0.926	CLONAL	1	TRUE	1	0.419026992999996	2		365	354	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0018609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	59	900	1	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	TRUE	1	0.419026992999996	2		901	214	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0018610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	98	574	9	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	0.209773449272533	2		583	778	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647662	2647662	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	290	551	0	ENST00000342085.4:c.1565C>A	p.Thr522Lys	p.T522K	ENST00000342085	NM_002613.4	522	aCg/aAg	14/14	0.209773449272533	4	FACETS	0.944	0.888	1			1	CLONAL	3	TRUE	NA	0.209773449272533	4		551	1181	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41249264	41249264	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1288	150	648	1	ENST00000357654.3:c.590G>A	p.Cys197Tyr	p.C197Y	ENST00000357654	NM_007294.3	197	tGc/tAc	8/23	0.209773449272533	1	FACETS	0.89	0.811	0.974	0.89	0.811	0.974	CLONAL	1	TRUE	0	0.209773449272533	1		649	1438	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0018611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	786	568	1	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	1	TRUE	NA	0.735851909872491	2		569	1743	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555611	21555611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573724179	NA	P-0018611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	257	396	0	ENST00000382592.4:c.2659C>T	p.Arg887Cys	p.R887C	ENST00000382592	NM_014572.2	887	Cgc/Tgc	6/8	0.735851909872491	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.735851909872491	1		396	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138729528	NA	P-0018612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	276	396	0	ENST00000269305.4:c.523C>G	p.Arg175Gly	p.R175G	ENST00000269305	NM_001126112.2	175	Cgc/Ggc	5/11	0.545116647479865	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.545116647479865	1		396	695	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024223	112024223	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	152	286	0	ENST00000368678.4:c.562T>G	p.Ser188Ala	p.S188A	ENST00000368678		188	Tct/Gct	7/13	1	2	FACETS	0.95	0.873	1	0.95	0.873	1	CLONAL	1	TRUE	1	0.545116647479865	2		286	587	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955112	17955112	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755706305	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	171	731	9	ENST00000458235.1:c.115del	p.Gln39SerfsTer108	p.Q39Sfs*108	ENST00000458235	NM_000215.3	39	Cag/ag	2/24	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.34	2		740	979	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894899	101894899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs539413187	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	130	356	0	ENST00000374994.4:c.452G>A	p.Arg151His	p.R151H	ENST00000374994	NM_004612.2	151	cGc/cAc	3/9	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.34	2		356	740	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321697	30321697	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	114	579	0	ENST00000322652.5:c.1552G>A	p.Gly518Arg	p.G518R	ENST00000322652	NM_015355.2	518	Gga/Aga	13/16	1	2	FACETS	0.619	0.556	0.686	0.619	0.556	0.686	SUBCLONAL	1	TRUE	1	0.34	2		579	1083	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366939	15366939	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1266	117	666	1	ENST00000263377.2:c.1687del	p.Ser563AlafsTer21	p.S563Afs*21	ENST00000263377	NM_058243.2	563	Agc/gc	9/20	1	2	FACETS	0.498	0.447	0.552	0.498	0.447	0.552	SUBCLONAL	1	TRUE	1	0.34	2		667	1383	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342421	70342421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771266719	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	103	452	1	ENST00000374080.3:c.1312C>T	p.Arg438Cys	p.R438C	ENST00000374080		438	Cgc/Tgc	9/45	1	2	FACETS	0.7	0.625	0.779	0.7	0.625	0.779	SUBCLONAL	1	TRUE	1	0.34	2		453	866	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56787293	56787293	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881926	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	129	559	0	ENST00000337432.4:c.779G>A	p.Arg260Gln	p.R260Q	ENST00000337432	NM_058216.2	260	cGg/cAg	5/9	1	2	FACETS	0.761	0.689	0.837	0.761	0.689	0.837	SUBCLONAL	1	TRUE	1	0.34	2		559	997	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649922	88649922	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786201038	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	95	433	0	ENST00000372037.3:c.176del	p.Leu59Ter	p.L59*	ENST00000372037	NM_004329.2	57	ccT/cc	4/13	1	2	FACETS	0.749	0.667	0.837	0.749	0.667	0.837	SUBCLONAL	1	TRUE	1	0.34	2		433	746	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777792	3777792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200566758	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	247	717	0	ENST00000262367.5:c.7256C>T	p.Ala2419Val	p.A2419V	ENST00000262367	NM_004380.2	2419	gCg/gTg	31/31	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.34	2		717	1298	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132438	11132438	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794284	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	177	594	1	ENST00000358026.2:c.2654G>A	p.Arg885His	p.R885H	ENST00000358026	NM_001128849.1	885	cGc/cAc	19/36	1	2	FACETS	0.985	0.907	1	0.985	0.907	1	CLONAL	1	TRUE	1	0.34	2		595	1057	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7163084	7163084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201034510	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	200	676	2	ENST00000302850.5:c.1988C>T	p.Ala663Val	p.A663V	ENST00000302850	NM_000208.2	663	gCg/gTg	9/22	1	2	FACETS	0.987	0.913	1	0.987	0.913	1	CLONAL	1	TRUE	1	0.34	2		678	1192	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636182	28636182	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376895552	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	115	392	0	ENST00000241453.7:c.190G>A	p.Gly64Arg	p.G64R	ENST00000241453	NM_004119.2	64	Ggg/Agg	3/24	1	2	FACETS	0.795	0.716	0.879	0.795	0.716	0.879	SUBCLONAL	1	TRUE	1	0.34	2		392	851	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155200	108155200	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	97	332	0	ENST00000278616.4:c.3993G>T	p.Gln1331His	p.Q1331H	ENST00000278616	NM_000051.3	1331	caG/caT	26/63	1	2	FACETS	0.923	0.824	1	0.923	0.824	1	CLONAL	1	TRUE	1	0.34	2		332	618	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807543	1807543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	114	527	1	ENST00000260795.2:c.1712G>A	p.Arg571Gln	p.R571Q	ENST00000260795		571	cGg/cAg	12/17	1	2	FACETS	0.781	0.702	0.864	0.781	0.702	0.864	SUBCLONAL	1	TRUE	1	0.34	2		528	859	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021785	71021785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs112795301	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	101	330	1	ENST00000318789.4:c.1573C>T	p.Arg525Ter	p.R525*	ENST00000318789	NM_032682.5	525	Cga/Tga	18/21	1	2	FACETS	0.883	0.79	0.981	0.883	0.79	0.981	CLONAL	1	TRUE	1	0.34	2		331	673	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971195	13971195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777866452	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	74	267	4	ENST00000405192.2:c.734C>T	p.Ala245Val	p.A245V	ENST00000405192	NM_001163147.1	245	gCg/gTg	8/12	1	2	FACETS	0.847	0.743	0.958	0.847	0.743	0.958	CLONAL	1	TRUE	1	0.34	2		271	514	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42057138	42057138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780211238	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	293	610	0	ENST00000219905.7:c.7799C>T	p.Pro2600Leu	p.P2600L	ENST00000219905	NM_001164273.1	2600	cCg/cTg	23/24	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.34	2		610	1370	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499514	89499514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141716319	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	36	337	0	ENST00000336596.2:c.2684C>T	p.Ala895Val	p.A895V	ENST00000336596	NM_005233.5	895	gCc/gTc	15/17	1	2	FACETS	0.325	0.266	0.391	0.325	0.266	0.391	SUBCLONAL	1	TRUE	1	0.34	2		337	652	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990402	69990402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765051386	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	121	341	0	ENST00000394351.3:c.361G>A	p.Asp121Asn	p.D121N	ENST00000394351	NM_000248.3	121	Gat/Aat	4/9	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.34	2		341	597	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156639	55156639	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768291477	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	137	445	1	ENST00000257290.5:c.3040G>A	p.Ala1014Thr	p.A1014T	ENST00000257290	NM_006206.4	1014	Gct/Act	22/23	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.34	2		446	790	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410486	63410486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779325879	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	94	502	0	ENST00000330258.3:c.2681G>A	p.Arg894His	p.R894H	ENST00000330258	NM_152424.3	894	cGc/cAc	2/2	1	2	FACETS	0.754	0.671	0.843	0.754	0.671	0.843	SUBCLONAL	1	TRUE	1	0.34	2		502	733	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646085	215646085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	103	505	0	ENST00000260947.4:c.513del	p.Asp172MetfsTer40	p.D172Mfs*40	ENST00000260947	NM_000465.2	171	aaA/aa	4/11	1	2	FACETS	0.63	0.563	0.702	0.63	0.563	0.702	SUBCLONAL	1	TRUE	1	0.34	2		505	961	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436097	56436097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	137	411	0	ENST00000407977.2:c.1040G>A	p.Gly347Asp	p.G347D	ENST00000407977		347	gGc/gAc	9/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.34	2		411	750	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492862	8492862	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	68	329	0	ENST00000356435.5:c.2467G>T	p.Val823Phe	p.V823F	ENST00000356435		823	Gtt/Ttt	16/35	1	2	FACETS	0.599	0.521	0.684	0.599	0.521	0.684	SUBCLONAL	1	TRUE	1	0.34	2		329	668	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915943	127915943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781486938	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	177	489	0	ENST00000373547.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000373547	NM_002721.4	180	Gaa/Aaa	6/7	1	2	FACETS	0.992	0.913	1	0.992	0.913	1	CLONAL	1	TRUE	1	0.34	2		489	1050	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827964	72827964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768307205	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	234	635	2	ENST00000268489.5:c.8617G>A	p.Glu2873Lys	p.E2873K	ENST00000268489	NM_006885.3	2873	Gaa/Aaa	9/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.34	2		637	1194	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40476757	40476757	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	121	536	0	ENST00000264657.5:c.1572G>T	p.Gln524His	p.Q524H	ENST00000264657	NM_139276.2	524	caG/caT	17/24	1	2	FACETS	0.693	0.625	0.765	0.693	0.625	0.765	SUBCLONAL	1	TRUE	1	0.34	2		536	1027	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645069	67645069	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	211	639	3	ENST00000264010.4:c.334G>T	p.Glu112Ter	p.E112*	ENST00000264010	NM_006565.3	112	Gaa/Taa	3/12	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.34	2		642	1191	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141587	202141587	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771150445	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	125	530	1	ENST00000358485.4:c.875G>A	p.Arg292Gln	p.R292Q	ENST00000358485	NM_001080125.1	292	cGg/cAg	7/9	1	2	FACETS	0.715	0.646	0.788	0.715	0.646	0.788	SUBCLONAL	1	TRUE	1	0.34	2		531	1029	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70442623	70442623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867702783	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	77	418	1	ENST00000373644.4:c.4945C>T	p.Arg1649Trp	p.R1649W	ENST00000373644	NM_030625.2	1649	Cgg/Tgg	10/12	1	2	FACETS	0.528	0.462	0.599	0.528	0.462	0.599	SUBCLONAL	1	TRUE	1	0.34	2		419	858	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914478	32914478	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358833	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	124	554	1	ENST00000380152.3:c.5986G>A	p.Ala1996Thr	p.A1996T	ENST00000380152		1996	Gca/Aca	11/27	1	2	FACETS	0.846	0.765	0.932	0.846	0.765	0.932	CLONAL	1	TRUE	1	0.34	2		555	862	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692792	89692792	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs779530981	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	99	357	1	ENST00000371953.3:c.276C>A	p.Asp92Glu	p.D92E	ENST00000371953	NM_000314.4	92	gaC/gaA	5/9	1	2	FACETS	0.854	0.763	0.951	0.854	0.763	0.951	CLONAL	1	TRUE	1	0.34	2		358	682	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861837	57861837	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs759838377	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	213	547	0	ENST00000228682.2:c.1138C>T	p.Arg380Ter	p.R380*	ENST00000228682	NM_005269.2	380	Cga/Tga	10/12	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.34	2		547	1050	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012877	176012877	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	130	567	0	ENST00000367669.3:c.1499G>A	p.Gly500Glu	p.G500E	ENST00000367669	NM_022457.5	500	gGa/gAa	13/20	1	2	FACETS	0.742	0.672	0.816	0.742	0.672	0.816	SUBCLONAL	1	TRUE	1	0.34	2		567	1031	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71050150	71050150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	121	416	0	ENST00000318789.4:c.1035G>A	p.Met345Ile	p.M345I	ENST00000318789	NM_032682.5	345	atG/atA	13/21	1	2	FACETS	0.853	0.771	0.941	0.853	0.771	0.941	CLONAL	1	TRUE	1	0.34	2		416	834	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698180	47698180	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63751411	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	314	418	0	ENST00000233146.2:c.1738G>T	p.Glu580Ter	p.E580*	ENST00000233146	NM_000251.2	580	Gaa/Taa	11/16	1	2	FACETS	1	0.985	1	1	0.996	1	CLONAL	2	TRUE	1	0.34	2		418	836	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003184	143003184	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	53	322	0	ENST00000262992.4:c.2642G>T	p.Arg881Ile	p.R881I	ENST00000262992	NM_001101669.1	881	aGa/aTa	23/24	1	2	FACETS	0.524	0.446	0.609	0.524	0.446	0.609	SUBCLONAL	1	TRUE	1	0.34	2		322	595	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715678	30715678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039551	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	99	244	0	ENST00000295754.5:c.1336G>A	p.Asp446Asn	p.D446N	ENST00000295754	NM_003242.5	446	Gat/Aat	5/7	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.34	2		244	567	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900371	101900371	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1564162124	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	60	223	0	ENST00000374994.4:c.805G>A	p.Asp269Asn	p.D269N	ENST00000374994	NM_004612.2	269	Gac/Aac	4/9	1	2	FACETS	0.781	0.674	0.896	0.781	0.674	0.896	SUBCLONAL	1	TRUE	1	0.34	2		223	452	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450397	50450397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	80	321	0	ENST00000331340.3:c.581C>T	p.Thr194Met	p.T194M	ENST00000331340	NM_006060.4	194	aCg/aTg	5/8	1	2	FACETS	0.792	0.698	0.893	0.792	0.698	0.893	SUBCLONAL	1	TRUE	1	0.34	2		321	594	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412109	63412109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1157288902	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	190	712	1	ENST00000330258.3:c.1058G>A	p.Arg353Gln	p.R353Q	ENST00000330258	NM_152424.3	353	cGa/cAa	2/2	1	2	FACETS	0.918	0.847	0.992	0.918	0.847	0.992	CLONAL	1	TRUE	1	0.34	2		713	1217	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480083	20480083	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	40	340	2	ENST00000346618.3:c.400C>T	p.Arg134Ter	p.R134*	ENST00000346618	NM_001949.4	134	Cga/Tga	2/7	1	2	FACETS	0.33	0.273	0.393	0.33	0.273	0.393	SUBCLONAL	1	TRUE	1	0.34	2		342	714	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962529	100962529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767360879	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	196	491	1	ENST00000325455.5:c.1868G>A	p.Arg623His	p.R623H	ENST00000325455	NM_001202474.3	623	cGc/cAc	3/8	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.34	2		492	1069	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40993338	40993338	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145617142	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	108	459	0	ENST00000267868.3:c.164C>T	p.Ala55Val	p.A55V	ENST00000267868	NM_002875.4	55	gCg/gTg	3/10	1	2	FACETS	0.755	0.677	0.837	0.755	0.677	0.837	SUBCLONAL	1	TRUE	1	0.34	2		459	842	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840613	36840613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756710542	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	97	525	0	ENST00000358127.4:c.1120G>A	p.Ala374Thr	p.A374T	ENST00000358127	NM_001280556.1	374	Gct/Act	10/10	1	2	FACETS	0.692	0.616	0.772	0.692	0.616	0.772	SUBCLONAL	1	TRUE	1	0.34	2		525	825	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	158	516	2	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	1	2	FACETS	0.999	0.916	1	0.999	0.916	1	CLONAL	1	TRUE	1	0.34	2		518	930	SUCCESS
APC	324	MSKCC	GRCh37	5	112128198	112128198	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	80	470	0	ENST00000257430.4:c.704del	p.Leu235TyrfsTer58	p.L235Yfs*58	ENST00000257430	NM_000038.5	234	cTt/ct	7/16	1	2	FACETS	0.439	0.385	0.497	0.439	0.385	0.497	SUBCLONAL	1	TRUE	1	0.34	2		470	1073	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526163	189526163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	92	660	0	ENST00000264731.3:c.427G>A	p.Val143Ile	p.V143I	ENST00000264731	NM_003722.4	143	Gtc/Atc	4/14	1	2	FACETS	0.441	0.39	0.496	0.441	0.39	0.496	SUBCLONAL	1	TRUE	1	0.34	2		660	1227	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	209	630	1	ENST00000267101.3:c.273G>T	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atT	3/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.34	2		631	1135	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163557	47163557	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767694898	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	118	284	2	ENST00000409792.3:c.2569G>A	p.Gly857Ser	p.G857S	ENST00000409792	NM_014159.6	857	Ggt/Agt	3/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.34	2		286	576	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467747	50467747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	86	471	0	ENST00000331340.3:c.982C>T	p.Arg328Cys	p.R328C	ENST00000331340	NM_006060.4	328	Cgc/Tgc	8/8	1	2	FACETS	0.568	0.501	0.639	0.568	0.501	0.639	SUBCLONAL	1	TRUE	1	0.34	2		471	891	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650096	93650096	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	141	464	0	ENST00000375746.1:c.1647C>A	p.Phe549Leu	p.F549L	ENST00000375746	NM_001174167.1	549	ttC/ttA	12/14	1	2	FACETS	0.837	0.762	0.916	0.837	0.762	0.916	CLONAL	1	TRUE	1	0.34	2		464	991	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5207965	5207965	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	153	703	2	ENST00000357368.4:c.5746C>T	p.Arg1916Ter	p.R1916*	ENST00000357368	NM_002850.3	1916	Cga/Tga	37/38	1	2	FACETS	0.804	0.734	0.878	0.804	0.734	0.878	CLONAL	1	TRUE	1	0.34	2		705	1119	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296445	15296445	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1297	100	744	1	ENST00000263388.2:c.1997G>A	p.Cys666Tyr	p.C666Y	ENST00000263388	NM_000435.2	666	tGc/tAc	13/33	1	2	FACETS	0.421	0.374	0.471	0.421	0.374	0.471	SUBCLONAL	1	TRUE	1	0.34	2		745	1397	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319442	11319442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769877976	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	46	449	0	ENST00000361445.4:c.25G>A	p.Ala9Thr	p.A9T	ENST00000361445	NM_004958.3	9	Gcc/Acc	2/58	1	2	FACETS	0.305	0.256	0.36	0.305	0.256	0.36	SUBCLONAL	1	TRUE	1	0.34	2		449	886	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225789	26225789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	93	258	0	ENST00000360408.1:c.407C>T	p.Ala136Val	p.A136V	ENST00000360408	NM_003532.2	136	gCg/gTg	1/1	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.34	2		258	515	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937521	76937521	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	137	500	2	ENST00000373344.5:c.3227C>A	p.Ser1076Tyr	p.S1076Y	ENST00000373344	NM_000489.3	1076	tCt/tAt	9/35	1	2	FACETS	0.971	0.883	1	0.971	0.883	1	CLONAL	1	TRUE	1	0.34	2		502	830	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745623	162745623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs572243397	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	94	492	1	ENST00000367921.3:c.2038C>T	p.Arg680Cys	p.R680C	ENST00000367921	NM_006182.2	680	Cgc/Tgc	15/18	1	2	FACETS	0.601	0.534	0.673	0.601	0.534	0.673	SUBCLONAL	1	TRUE	1	0.34	2		493	920	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714724	52714724	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs557584612	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	132	500	1	ENST00000322088.6:c.482C>T	p.Ala161Val	p.A161V	ENST00000322088	NM_014225.5	161	gCt/gTt	4/15	1	2	FACETS	0.987	0.896	1	0.987	0.896	1	CLONAL	1	TRUE	1	0.34	2		501	787	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	245	565	6	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	0.982	1	CLONAL	1	TRUE	1	0.34	2		571	1265	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4388073	4388073	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	40	195	1	ENST00000261254.3:c.559C>A	p.Leu187Met	p.L187M	ENST00000261254	NM_001759.3	187	Ctg/Atg	3/5	1	2	FACETS	0.618	0.514	0.732	0.618	0.514	0.732	SUBCLONAL	1	TRUE	1	0.34	2		196	381	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582133	95582133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752424727	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	124	377	1	ENST00000393063.1:c.1778C>T	p.Ser593Leu	p.S593L	ENST00000393063	NM_030621.3	593	tCg/tTg	12/28	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.34	2		378	720	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868072	56868072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771065608	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	93	367	1	ENST00000308159.5:c.1570C>T	p.Arg524Trp	p.R524W	ENST00000308159	NM_014669.4	524	Cgg/Tgg	14/22	1	2	FACETS	0.775	0.689	0.866	0.775	0.689	0.866	SUBCLONAL	1	TRUE	1	0.34	2		368	706	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336276	73336276	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	48	212	1	ENST00000377767.4:c.2128-1G>T		p.X710_splice	ENST00000377767	NM_014953.3	710			1	2	FACETS	0.612	0.518	0.716	0.612	0.518	0.716	SUBCLONAL	1	TRUE	1	0.34	2		213	461	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104303	2104303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1256047792	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	142	430	2	ENST00000219476.3:c.343C>T	p.Arg115Cys	p.R115C	ENST00000219476	NM_000548.3	115	Cgt/Tgt	5/42	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.34	2		432	760	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602329	10602329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	115	593	1	ENST00000171111.5:c.1249G>A	p.Gly417Arg	p.G417R	ENST00000171111	NM_203500.1	417	Ggg/Agg	3/6	1	2	FACETS	0.652	0.586	0.722	0.652	0.586	0.722	SUBCLONAL	1	TRUE	1	0.34	2		594	1038	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412226	63412226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	192	695	0	ENST00000330258.3:c.941G>A	p.Gly314Glu	p.G314E	ENST00000330258	NM_152424.3	314	gGg/gAg	2/2	1	2	FACETS	0.847	0.781	0.915	0.847	0.781	0.915	CLONAL	1	TRUE	1	0.34	2		695	1334	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020225	123020225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	178	493	1	ENST00000355640.3:c.713G>A	p.Arg238Gln	p.R238Q	ENST00000355640		238	cGa/cAa	2/7	1	2	FACETS	0.999	0.92	1	0.999	0.92	1	CLONAL	1	TRUE	1	0.34	2		494	1048	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839705	42839705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1346752687	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	200	684	2	ENST00000398585.3:c.1534G>A	p.Gly512Arg	p.G512R	ENST00000398585	NM_001135099.1	512	Ggg/Agg	13/14	1	2	FACETS	0.95	0.879	1	0.95	0.879	1	CLONAL	1	TRUE	1	0.34	2		686	1238	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127731	64127731	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1455628289	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	40	439	1	ENST00000334205.4:c.224G>A	p.Arg75His	p.R75H	ENST00000334205	NM_003942.2	75	cGc/cAc	3/17	1	2	FACETS	0.332	0.275	0.396	0.332	0.275	0.396	SUBCLONAL	1	TRUE	1	0.34	2		440	709	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383645	15383645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	62	312	0	ENST00000263377.2:c.266C>T	p.Ala89Val	p.A89V	ENST00000263377	NM_058243.2	89	gCc/gTc	2/20	1	2	FACETS	0.59	0.509	0.678	0.59	0.509	0.678	SUBCLONAL	1	TRUE	1	0.34	2		312	618	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164799	36164799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	153	517	0	ENST00000300305.3:c.1076C>T	p.Pro359Leu	p.P359L	ENST00000300305		359	cCg/cTg	8/8	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.34	2		517	861	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998124	169998124	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762380206	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	214	595	1	ENST00000295797.4:c.815G>A	p.Arg272Gln	p.R272Q	ENST00000295797	NM_002740.5	272	cGa/cAa	9/18	1	2	FACETS	0.999	0.927	1	0.999	0.927	1	CLONAL	1	TRUE	1	0.34	2		596	1260	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491322	2491322	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	149	636	1	ENST00000355716.4:c.365G>A	p.Ser122Asn	p.S122N	ENST00000355716	NM_003820.2	122	aGc/aAc	4/8	1	2	FACETS	0.804	0.733	0.878	0.804	0.733	0.878	CLONAL	1	TRUE	1	0.34	2		637	1090	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11193169	11193169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753286555	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	191	493	3	ENST00000361445.4:c.5332G>A	p.Ala1778Thr	p.A1778T	ENST00000361445	NM_004958.3	1778	Gcc/Acc	38/58	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.34	2		496	925	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237650	16237650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	116	496	0	ENST00000375759.3:c.1097C>T	p.Thr366Ile	p.T366I	ENST00000375759	NM_015001.2	366	aCt/aTt	5/15	1	2	FACETS	0.705	0.634	0.78	0.705	0.634	0.78	SUBCLONAL	1	TRUE	1	0.34	2		496	968	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245986	16245986	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	41	287	0	ENST00000375759.3:c.1609T>G	p.Phe537Val	p.F537V	ENST00000375759	NM_015001.2	537	Ttc/Gtc	8/15	1	2	FACETS	0.354	0.294	0.421	0.354	0.294	0.421	SUBCLONAL	1	TRUE	1	0.34	2		287	681	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255275	16255275	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	162	550	2	ENST00000375759.3:c.2540G>T	p.Ser847Ile	p.S847I	ENST00000375759	NM_015001.2	847	aGc/aTc	11/15	1	2	FACETS	0.873	0.8	0.95	0.873	0.8	0.95	CLONAL	1	TRUE	1	0.34	2		552	1091	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262493	16262493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	24	225	0	ENST00000375759.3:c.9758C>A	p.Pro3253His	p.P3253H	ENST00000375759	NM_015001.2	3253	cCt/cAt	11/15	1	2	FACETS	0.381	0.298	0.476	0.381	0.298	0.476	SUBCLONAL	1	TRUE	1	0.34	2		225	371	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263859	16263859	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	113	583	0	ENST00000375759.3:c.10228A>G	p.Asn3410Asp	p.N3410D	ENST00000375759	NM_015001.2	3410	Aac/Gac	12/15	1	2	FACETS	0.682	0.612	0.755	0.682	0.612	0.755	SUBCLONAL	1	TRUE	1	0.34	2		583	975	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056323	27056323	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	69	259	0	ENST00000324856.7:c.1319G>A	p.Ser440Asn	p.S440N	ENST00000324856	NM_006015.4	440	aGt/aAt	2/20	1	2	FACETS	0.741	0.646	0.843	0.741	0.646	0.843	SUBCLONAL	1	TRUE	1	0.34	2		259	548	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057821	27057821	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1288	180	877	0	ENST00000324856.7:c.1529A>G	p.Gln510Arg	p.Q510R	ENST00000324856	NM_006015.4	510	cAg/cGg	3/20	1	2	FACETS	0.721	0.663	0.782	0.721	0.663	0.782	SUBCLONAL	1	TRUE	1	0.34	2		877	1468	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059251	27059251	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	88	509	1	ENST00000324856.7:c.1888C>A	p.Leu630Met	p.L630M	ENST00000324856	NM_006015.4	630	Ctg/Atg	4/20	1	2	FACETS	0.553	0.489	0.622	0.553	0.489	0.622	SUBCLONAL	1	TRUE	1	0.34	2		510	936	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101646	27101646	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	129	668	0	ENST00000324856.7:c.4928C>A	p.Pro1643His	p.P1643H	ENST00000324856	NM_006015.4	1643	cCt/cAt	18/20	1	2	FACETS	0.621	0.562	0.685	0.621	0.562	0.685	SUBCLONAL	1	TRUE	1	0.34	2		668	1221	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102154	27102154	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	87	482	1	ENST00000324856.7:c.5080C>A	p.Leu1694Met	p.L1694M	ENST00000324856	NM_006015.4	1694	Ctg/Atg	19/20	1	2	FACETS	0.591	0.522	0.665	0.591	0.522	0.665	SUBCLONAL	1	TRUE	1	0.34	2		483	866	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106142	27106142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369532498	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	125	488	0	ENST00000324856.7:c.5753G>A	p.Arg1918Gln	p.R1918Q	ENST00000324856	NM_006015.4	1918	cGg/cAg	20/20	1	2	FACETS	0.838	0.758	0.923	0.838	0.758	0.923	CLONAL	1	TRUE	1	0.34	2		488	877	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106364	27106364	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	148	454	0	ENST00000324856.7:c.5975C>A	p.Ser1992Ter	p.S1992*	ENST00000324856	NM_006015.4	1992	tCa/tAa	20/20	1	2	FACETS	0.932	0.851	1	0.932	0.851	1	CLONAL	1	TRUE	1	0.34	2		454	934	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107113	27107113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	139	410	0	ENST00000324856.7:c.6724G>A	p.Ala2242Thr	p.A2242T	ENST00000324856	NM_006015.4	2242	Gcc/Acc	20/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.34	2		410	747	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599125	28599125	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	148	723	2	ENST00000253063.3:c.571C>A	p.Leu191Met	p.L191M	ENST00000253063	NM_031459.4	191	Ctg/Atg	5/10	1	2	FACETS	0.766	0.698	0.838	0.766	0.698	0.838	SUBCLONAL	1	TRUE	1	0.34	2		725	1136	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937968	36937968	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	190	596	1	ENST00000361632.4:c.868C>A	p.Leu290Ile	p.L290I	ENST00000361632		290	Ctt/Att	7/16	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.34	2		597	1088	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46736409	46736409	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	122	431	0	ENST00000371975.4:c.1121G>T	p.Arg374Met	p.R374M	ENST00000371975	NM_003579.3	374	aGg/aTg	10/18	1	2	FACETS	0.913	0.825	1	0.913	0.825	1	CLONAL	1	TRUE	1	0.34	2		431	786	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432631	78432631	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	80	335	0	ENST00000370768.2:c.352A>G	p.Arg118Gly	p.R118G	ENST00000370768	NM_003902.3	118	Aga/Gga	6/20	1	2	FACETS	0.611	0.537	0.691	0.611	0.537	0.691	SUBCLONAL	1	TRUE	1	0.34	2		335	770	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433876	78433876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	74	397	0	ENST00000370768.2:c.223G>A	p.Ala75Thr	p.A75T	ENST00000370768	NM_003902.3	75	Gct/Act	3/20	1	2	FACETS	0.541	0.472	0.615	0.541	0.472	0.615	SUBCLONAL	1	TRUE	1	0.34	2		397	805	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736471	85736471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	85	385	1	ENST00000370580.1:c.176C>T	p.Thr59Ile	p.T59I	ENST00000370580	NM_003921.4	59	aCa/aTa	2/3	1	2	FACETS	0.559	0.493	0.629	0.559	0.493	0.629	SUBCLONAL	1	TRUE	1	0.34	2		386	895	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273130	115273130	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	50	479	0	ENST00000438362.2:c.1328C>A	p.Pro443His	p.P443H	ENST00000438362	NM_001242891.1	443	cCt/cAt	11/20	1	2	FACETS	0.304	0.257	0.356	0.304	0.257	0.356	SUBCLONAL	1	TRUE	1	0.34	2		479	968	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280175	115280175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142641678	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	105	327	0	ENST00000438362.2:c.457G>A	p.Ala153Thr	p.A153T	ENST00000438362	NM_001242891.1	153	Gct/Act	5/20	1	2	FACETS	0.991	0.89	1	0.991	0.89	1	CLONAL	1	TRUE	1	0.34	2		327	623	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483219	120483219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782077143	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	80	422	1	ENST00000256646.2:c.3142C>T	p.Arg1048Cys	p.R1048C	ENST00000256646	NM_024408.3	1048	Cgc/Tgc	19/34	1	2	FACETS	0.655	0.577	0.74	0.655	0.577	0.74	SUBCLONAL	1	TRUE	1	0.34	2		423	718	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731179	162731179	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	112	358	2	ENST00000367921.3:c.1034C>T	p.Ala345Val	p.A345V	ENST00000367921	NM_006182.2	345	gCc/gTc	9/18	1	2	FACETS	0.995	0.897	1	0.995	0.897	1	CLONAL	1	TRUE	1	0.34	2		360	662	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740255	162740255	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	158	428	0	ENST00000367921.3:c.1457G>T	p.Arg486Met	p.R486M	ENST00000367921	NM_006182.2	486	aGg/aTg	12/18	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.34	2		428	818	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163298093	163298093	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs766162853	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	44	435	1	ENST00000271452.3:c.274C>A	p.Leu92Met	p.L92M	ENST00000271452	NM_145697.2	92	Ctg/Atg	4/14	1	2	FACETS	0.32	0.267	0.379	0.32	0.267	0.379	SUBCLONAL	1	TRUE	1	0.34	2		436	809	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176176035	176176035	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	74	452	1	ENST00000367669.3:c.80C>T	p.Ala27Val	p.A27V	ENST00000367669	NM_022457.5	27	gCc/gTc	1/20	1	2	FACETS	0.542	0.474	0.616	0.542	0.474	0.616	SUBCLONAL	1	TRUE	1	0.34	2		453	803	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107240	193107240	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs71639185	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	58	278	0	ENST00000367435.3:c.449A>G	p.Lys150Arg	p.K150R	ENST00000367435	NM_024529.4	150	aAa/aGa	6/17	1	2	FACETS	0.82	0.707	0.943	0.82	0.707	0.943	CLONAL	1	TRUE	1	0.34	2		278	416	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193116996	193116996	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	139	381	0	ENST00000367435.3:c.730-1G>T		p.X244_splice	ENST00000367435	NM_024529.4	244			1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.34	2		381	785	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218967	193218967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	61	354	0	ENST00000367435.3:c.1525C>T	p.Pro509Ser	p.P509S	ENST00000367435	NM_024529.4	509	Cca/Tca	16/17	1	2	FACETS	0.56	0.482	0.644	0.56	0.482	0.644	SUBCLONAL	1	TRUE	1	0.34	2		354	641	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648208	206648208	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	43	240	0	ENST00000367120.3:c.229G>A	p.Gly77Ser	p.G77S	ENST00000367120	NM_014002.3	77	Ggc/Agc	5/22	1	2	FACETS	0.652	0.547	0.768	0.652	0.547	0.768	SUBCLONAL	1	TRUE	1	0.34	2		240	388	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649542	206649542	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	118	412	0	ENST00000367120.3:c.377T>C	p.Leu126Pro	p.L126P	ENST00000367120	NM_014002.3	126	cTg/cCg	6/22	1	2	FACETS	0.932	0.841	1	0.932	0.841	1	CLONAL	1	TRUE	1	0.34	2		412	745	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567728	226567728	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	106	484	0	ENST00000366794.5:c.1438C>A	p.Pro480Thr	p.P480T	ENST00000366794	NM_001618.3	480	Cct/Act	10/23	1	2	FACETS	0.763	0.684	0.848	0.763	0.684	0.848	SUBCLONAL	1	TRUE	1	0.34	2		484	817	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578123	226578123	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs372733683	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	86	437	0	ENST00000366794.5:c.605T>C	p.Val202Ala	p.V202A	ENST00000366794	NM_001618.3	202	gTc/gCc	4/23	1	2	FACETS	0.762	0.674	0.856	0.762	0.674	0.856	SUBCLONAL	1	TRUE	1	0.34	2		437	664	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612966	228612966	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	47	233	1	ENST00000366696.1:c.61C>A	p.Leu21Met	p.L21M	ENST00000366696	NM_003493.2	21	Ctg/Atg	1/1	1	2	FACETS	0.641	0.542	0.751	0.641	0.542	0.751	SUBCLONAL	1	TRUE	1	0.34	2		234	431	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667530	241667530	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	64	294	0	ENST00000366560.3:c.920C>T	p.Thr307Ile	p.T307I	ENST00000366560	NM_000143.3	307	aCt/aTt	7/10	1	2	FACETS	0.671	0.581	0.768	0.671	0.581	0.768	SUBCLONAL	1	TRUE	1	0.34	2		294	561	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851550	63851550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	193	561	0	ENST00000279873.7:c.2328G>T	p.Glu776Asp	p.E776D	ENST00000279873	NM_032199.2	776	gaG/gaT	10/10	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.34	2		561	1126	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852018	63852018	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	92	485	2	ENST00000279873.7:c.2796G>T	p.Gln932His	p.Q932H	ENST00000279873	NM_032199.2	932	caG/caT	10/10	1	2	FACETS	0.616	0.547	0.691	0.616	0.547	0.691	SUBCLONAL	1	TRUE	1	0.34	2		487	878	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405487	70405487	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	198	606	0	ENST00000373644.4:c.3001A>C	p.Asn1001His	p.N1001H	ENST00000373644	NM_030625.2	1001	Aat/Cat	4/12	1	2	FACETS	0.936	0.865	1	0.936	0.865	1	CLONAL	1	TRUE	1	0.34	2		606	1245	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406163	70406163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773912826	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	222	617	0	ENST00000373644.4:c.3677C>T	p.Thr1226Met	p.T1226M	ENST00000373644	NM_030625.2	1226	aCg/aTg	4/12	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.34	2		617	1258	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711964	89711970	+	frameshift_variant	Frame_Shift_Del	DEL	GTTTCAC	GTTTCAC	-	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	130	382	1	ENST00000371953.3:c.582_588del	p.Phe195ArgfsTer2	p.F195Rfs*2	ENST00000371953	NM_000314.4	194	ttGTTTCAC/tt	6/9	1	2	FACETS	0.987	0.896	1	0.987	0.896	1	CLONAL	1	TRUE	1	0.34	2		383	775	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741490	17741490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	145	575	1	ENST00000250003.3:c.161G>A	p.Gly54Asp	p.G54D	ENST00000250003	NM_002478.4	54	gGc/gAc	1/3	1	2	FACETS	0.888	0.81	0.971	0.888	0.81	0.971	CLONAL	1	TRUE	1	0.34	2		576	960	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456365	32456365	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	124	601	1	ENST00000332351.3:c.527G>A	p.Arg176His	p.R176H	ENST00000332351	NM_024426.4	176	cGc/cAc	1/10	1	2	FACETS	0.704	0.636	0.776	0.704	0.636	0.776	SUBCLONAL	1	TRUE	1	0.34	2		602	1036	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69458690	69458690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1261290754	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	195	604	0	ENST00000227507.2:c.505C>T	p.Pro169Ser	p.P169S	ENST00000227507	NM_053056.2	169	Cca/Tca	3/5	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.34	2		604	1102	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514146	69514146	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	142	521	0	ENST00000294312.3:c.535C>A	p.Leu179Ile	p.L179I	ENST00000294312	NM_005117.2	179	Ctc/Atc	3/3	1	2	FACETS	0.963	0.878	1	0.963	0.878	1	CLONAL	1	TRUE	1	0.34	2		521	867	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588160	69588160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	85	582	1	ENST00000168712.1:c.538G>A	p.Ala180Thr	p.A180T	ENST00000168712	NM_002007.2	180	Gcc/Acc	3/3	1	2	FACETS	0.51	0.45	0.575	0.51	0.45	0.575	SUBCLONAL	1	TRUE	1	0.34	2		583	980	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941475	71941475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200043222	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	185	643	1	ENST00000298229.2:c.1160G>A	p.Arg387Gln	p.R387Q	ENST00000298229	NM_001567.3	387	cGg/cAg	10/28	1	2	FACETS	0.912	0.841	0.987	0.912	0.841	0.987	CLONAL	1	TRUE	1	0.34	2		644	1193	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944152	71944152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757172795	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	116	609	1	ENST00000298229.2:c.1985G>A	p.Arg662His	p.R662H	ENST00000298229	NM_001567.3	662	cGc/cAc	17/28	1	2	FACETS	0.592	0.532	0.656	0.592	0.532	0.656	SUBCLONAL	1	TRUE	1	0.34	2		610	1152	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949306	71949306	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	72	509	1	ENST00000298229.2:c.3687-1G>T		p.X1229_splice	ENST00000298229	NM_001567.3	1229			1	2	FACETS	0.537	0.468	0.611	0.537	0.468	0.611	SUBCLONAL	1	TRUE	1	0.34	2		510	789	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988973	85988973	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	97	318	0	ENST00000263360.6:c.1139G>A	p.Gly380Asp	p.G380D	ENST00000263360	NM_003797.3	380	gGc/gAc	11/12	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.34	2		318	567	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098557	108098557	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	65	345	0	ENST00000278616.4:c.127C>A	p.Leu43Ile	p.L43I	ENST00000278616	NM_000051.3	43	Cta/Ata	3/63	1	2	FACETS	0.529	0.458	0.606	0.529	0.458	0.606	SUBCLONAL	1	TRUE	1	0.34	2		345	723	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119720	108119720	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1555069657	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	121	287	0	ENST00000278616.4:c.1126G>T	p.Glu376Ter	p.E376*	ENST00000278616	NM_000051.3	376	Gaa/Taa	9/63	1	2	FACETS	0.983	0.889	1	0.983	0.889	1	CLONAL	1	TRUE	1	0.34	2		287	724	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196144	108196144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879254132	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	151	497	2	ENST00000278616.4:c.6680G>A	p.Arg2227His	p.R2227H	ENST00000278616	NM_000051.3	2227	cGc/cAc	46/63	1	2	FACETS	0.975	0.891	1	0.975	0.891	1	CLONAL	1	TRUE	1	0.34	2		499	911	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352729	118352729	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	140	605	0	ENST00000534358.1:c.3934A>G	p.Thr1312Ala	p.T1312A	ENST00000534358	NM_005933.3	1312	Aca/Gca	7/36	1	2	FACETS	0.735	0.668	0.806	0.735	0.668	0.806	SUBCLONAL	1	TRUE	1	0.34	2		605	1120	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369150	118369150	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	78	392	0	ENST00000534358.1:c.5868C>A	p.Asn1956Lys	p.N1956K	ENST00000534358	NM_005933.3	1956	aaC/aaA	22/36	1	2	FACETS	0.573	0.502	0.649	0.573	0.502	0.649	SUBCLONAL	1	TRUE	1	0.34	2		392	801	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118370621	118370621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	98	297	1	ENST00000534358.1:c.6151G>A	p.Gly2051Arg	p.G2051R	ENST00000534358	NM_005933.3	2051	Gga/Aga	24/36	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.34	2		298	550	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374312	118374312	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	108	588	1	ENST00000534358.1:c.7705G>T	p.Gly2569Ter	p.G2569*	ENST00000534358	NM_005933.3	2569	Gga/Tga	27/36	1	2	FACETS	0.623	0.558	0.693	0.623	0.558	0.693	SUBCLONAL	1	TRUE	1	0.34	2		589	1019	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432480	49432480	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	77	544	0	ENST00000301067.7:c.8659G>T	p.Gly2887Ter	p.G2887*	ENST00000301067	NM_003482.3	2887	Gga/Tga	34/54	1	2	FACETS	0.488	0.427	0.553	0.488	0.427	0.553	SUBCLONAL	1	TRUE	1	0.34	2		544	929	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436942	49436942	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	188	568	1	ENST00000301067.7:c.5561C>T	p.Ser1854Phe	p.S1854F	ENST00000301067	NM_003482.3	1854	tCc/tTc	25/54	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.34	2		569	1026	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437212	49437212	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	104	521	0	ENST00000301067.7:c.5468-1G>T		p.X1823_splice	ENST00000301067	NM_003482.3	1823			1	2	FACETS	0.643	0.575	0.716	0.643	0.575	0.716	SUBCLONAL	1	TRUE	1	0.34	2		521	951	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445384	49445384	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1449494133	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	144	706	0	ENST00000301067.7:c.2082G>T	p.Glu694Asp	p.E694D	ENST00000301067	NM_003482.3	694	gaG/gaT	10/54	1	2	FACETS	0.702	0.639	0.769	0.702	0.639	0.769	SUBCLONAL	1	TRUE	1	0.34	2		706	1206	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56474128	56474128	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1441975473	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	173	482	1	ENST00000267101.3:c.44G>A	p.Ser15Asn	p.S15N	ENST00000267101	NM_001982.3	15	aGc/aAc	1/28	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.34	2		483	925	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495430	56495430	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	123	563	0	ENST00000267101.3:c.3620G>T	p.Ser1207Ile	p.S1207I	ENST00000267101	NM_001982.3	1207	aGt/aTt	28/28	1	2	FACETS	0.654	0.59	0.722	0.654	0.59	0.722	SUBCLONAL	1	TRUE	1	0.34	2		563	1106	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856154	111856154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	144	318	1	ENST00000341259.2:c.205G>A	p.Asp69Asn	p.D69N	ENST00000341259	NM_005475.2	69	Gac/Aac	2/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.34	2		319	713	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891012	112891012	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1053009990	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	57	274	0	ENST00000351677.2:c.346C>T	p.His116Tyr	p.H116Y	ENST00000351677	NM_002834.3	116	Cat/Tat	4/16	1	2	FACETS	0.555	0.476	0.642	0.555	0.476	0.642	SUBCLONAL	1	TRUE	1	0.34	2		274	604	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109668	115109668	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	218	700	0	ENST00000257566.3:c.2210G>T	p.Arg737Met	p.R737M	ENST00000257566	NM_016569.3	737	aGg/aTg	8/8	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.34	2		700	1235	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120535178	120535178	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	66	224	0	ENST00000229340.5:c.478-1G>A		p.X160_splice	ENST00000229340	NM_006861.6	160			1	2	FACETS	0.794	0.691	0.905	0.794	0.691	0.905	CLONAL	1	TRUE	1	0.34	2		224	489	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426820	121426820	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520291	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	112	483	0	ENST00000257555.6:c.511C>T	p.Arg171Ter	p.R171*	ENST00000257555		171	Cga/Tga	2/10	1	2	FACETS	0.826	0.742	0.914	0.826	0.742	0.914	CLONAL	1	TRUE	1	0.34	2		483	798	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244948	133244948	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	145	705	3	ENST00000320574.5:c.2167C>A	p.Leu723Met	p.L723M	ENST00000320574	NM_006231.2	723	Ctg/Atg	19/49	1	2	FACETS	0.778	0.709	0.851	0.778	0.709	0.851	SUBCLONAL	1	TRUE	1	0.34	2		708	1096	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253208	133253208	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	203	584	3	ENST00000320574.5:c.833C>A	p.Thr278Lys	p.T278K	ENST00000320574	NM_006231.2	278	aCg/aAg	9/49	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.34	2		587	997	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975718	26975718	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	131	447	0	ENST00000381527.3:c.1226C>A	p.Pro409His	p.P409H	ENST00000381527	NM_001260.1	409	cCt/cAt	12/13	1	2	FACETS	0.857	0.777	0.941	0.857	0.777	0.941	CLONAL	1	TRUE	1	0.34	2		447	899	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592727	28592727	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	139	480	0	ENST00000241453.7:c.2419-1G>T		p.X807_splice	ENST00000241453	NM_004119.2	807			1	2	FACETS	0.95	0.864	1	0.95	0.864	1	CLONAL	1	TRUE	1	0.34	2		480	861	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623892	28623892	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	31	381	0	ENST00000241453.7:c.762G>T	p.Gln254His	p.Q254H	ENST00000241453	NM_004119.2	254	caG/caT	7/24	1	2	FACETS	0.313	0.252	0.382	0.313	0.252	0.382	SUBCLONAL	1	TRUE	1	0.34	2		381	582	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895703	28895703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	206	563	0	ENST00000282397.4:c.3071C>T	p.Ala1024Val	p.A1024V	ENST00000282397	NM_002019.4	1024	gCa/gTa	23/30	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.34	2		563	1154	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896488	28896488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376257265	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	165	464	0	ENST00000282397.4:c.2962G>A	p.Gly988Ser	p.G988S	ENST00000282397	NM_002019.4	988	Ggt/Agt	22/30	1	2	FACETS	0.972	0.892	1	0.972	0.892	1	CLONAL	1	TRUE	1	0.34	2		464	999	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28897046	28897047	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	123	418	0	ENST00000282397.4:c.2833dup	p.Met945AsnfsTer15	p.M945Nfs*15	ENST00000282397	NM_002019.4	945	atg/aAtg	21/30	1	2	FACETS	0.931	0.842	1	0.931	0.842	1	CLONAL	1	TRUE	1	0.34	2		418	777	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906888	32906889	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	153	448	0	ENST00000380152.3:c.1278dup	p.Asp427ArgfsTer25	p.D427Rfs*25	ENST00000380152		425	gaa/gAaa	10/27	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.34	2		448	847	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912959	32912959	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	102	501	0	ENST00000380152.3:c.4467A>C	p.Lys1489Asn	p.K1489N	ENST00000380152		1489	aaA/aaC	11/27	1	2	FACETS	0.584	0.521	0.651	0.584	0.521	0.651	SUBCLONAL	1	TRUE	1	0.34	2		501	1028	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944642	32944642	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	59	523	2	ENST00000380152.3:c.8435G>T	p.Gly2812Val	p.G2812V	ENST00000380152		2812	gGa/gTa	19/27	1	2	FACETS	0.36	0.308	0.416	0.36	0.308	0.416	SUBCLONAL	1	TRUE	1	0.34	2		525	965	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134924	41134924	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	109	294	1	ENST00000379561.5:c.704C>A	p.Ser235Tyr	p.S235Y	ENST00000379561	NM_002015.3	235	tCt/tAt	2/3	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.34	2		295	611	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919264	48919264	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	69	214	0	ENST00000267163.4:c.429A>C	p.Lys143Asn	p.K143N	ENST00000267163	NM_000321.2	143	aaA/aaC	4/27	1	2	FACETS	0.711	0.619	0.809	0.711	0.619	0.809	SUBCLONAL	1	TRUE	1	0.34	2		214	571	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434920	110434920	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	226	681	2	ENST00000375856.3:c.3481G>A	p.Val1161Met	p.V1161M	ENST00000375856	NM_003749.2	1161	Gtg/Atg	1/2	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.34	2		683	1292	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436111	110436111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	252	695	0	ENST00000375856.3:c.2290G>A	p.Gly764Arg	p.G764R	ENST00000375856	NM_003749.2	764	Ggg/Agg	1/2	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.34	2		695	1262	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30103740	30103740	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	109	346	0	ENST00000331968.5:c.1198A>G	p.Thr400Ala	p.T400A	ENST00000331968	NM_002742.2	400	Aca/Gca	8/18	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.34	2		346	628	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988201	36988201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	85	395	0	ENST00000354822.5:c.452G>A	p.Arg151His	p.R151H	ENST00000354822	NM_001079668.2	151	cGc/cAc	2/3	1	2	FACETS	0.772	0.682	0.867	0.772	0.682	0.867	SUBCLONAL	1	TRUE	1	0.34	2		395	648	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060649	38060649	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	121	599	0	ENST00000250448.2:c.1340G>T	p.Arg447Met	p.R447M	ENST00000250448	NM_004496.3	447	aGg/aTg	2/2	1	2	FACETS	0.678	0.611	0.749	0.678	0.611	0.749	SUBCLONAL	1	TRUE	1	0.34	2		599	1050	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562256	95562256	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	126	322	0	ENST00000393063.1:c.5001A>C	p.Glu1667Asp	p.E1667D	ENST00000393063	NM_030621.3	1667	gaA/gaC	24/28	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.34	2		322	702	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41020914	41020914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs913824562	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	106	481	0	ENST00000267868.3:c.536G>A	p.Gly179Asp	p.G179D	ENST00000267868	NM_002875.4	179	gGt/gAt	7/10	1	2	FACETS	0.662	0.592	0.736	0.662	0.592	0.736	SUBCLONAL	1	TRUE	1	0.34	2		481	942	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748642	43748642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	132	689	0	ENST00000382044.4:c.2164G>A	p.Glu722Lys	p.E722K	ENST00000382044	NM_001141980.1	722	Gaa/Aaa	12/28	1	2	FACETS	0.63	0.57	0.693	0.63	0.57	0.693	SUBCLONAL	1	TRUE	1	0.34	2		689	1233	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631623	90631623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370851685	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	167	543	1	ENST00000330062.3:c.646G>A	p.Gly216Ser	p.G216S	ENST00000330062	NM_002168.2	216	Ggc/Agc	5/11	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.34	2		544	980	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343593	343593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	93	512	1	ENST00000262320.3:c.2081C>T	p.Thr694Ile	p.T694I	ENST00000262320	NM_003502.3	694	aCc/aTc	8/11	1	2	FACETS	0.638	0.566	0.714	0.638	0.566	0.714	SUBCLONAL	1	TRUE	1	0.34	2		513	858	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094798	2094798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370228590	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	161	462	1	ENST00000219066.1:c.382C>T	p.Arg128Cys	p.R128C	ENST00000219066	NM_002528.5	128	Cgc/Tgc	3/6	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.34	2		463	800	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2115519	2115519	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	114	550	1	ENST00000219476.3:c.1600-1G>T		p.X534_splice	ENST00000219476	NM_000548.3	534			1	2	FACETS	0.714	0.642	0.791	0.714	0.642	0.791	SUBCLONAL	1	TRUE	1	0.34	2		551	939	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226176	2226176	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	121	566	1	ENST00000326181.6:c.1873C>A	p.Leu625Ile	p.L625I	ENST00000326181	NM_032271.2	625	Ctc/Atc	19/21	1	2	FACETS	0.705	0.636	0.778	0.705	0.636	0.778	SUBCLONAL	1	TRUE	1	0.34	2		567	1010	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633344	3633344	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748624984	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	140	625	1	ENST00000294008.3:c.4907C>T	p.Pro1636Leu	p.P1636L	ENST00000294008	NM_032444.2	1636	cCt/cTt	14/15	1	2	FACETS	0.756	0.687	0.829	0.756	0.687	0.829	SUBCLONAL	1	TRUE	1	0.34	2		626	1089	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633420	3633420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766110479	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	197	684	0	ENST00000294008.3:c.4831G>A	p.Glu1611Lys	p.E1611K	ENST00000294008	NM_032444.2	1611	Gag/Aag	14/15	1	2	FACETS	0.94	0.869	1	0.94	0.869	1	CLONAL	1	TRUE	1	0.34	2		684	1233	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639720	3639720	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	175	742	0	ENST00000294008.3:c.3919A>C	p.Lys1307Gln	p.K1307Q	ENST00000294008	NM_032444.2	1307	Aag/Cag	12/15	1	2	FACETS	0.802	0.736	0.87	0.802	0.736	0.87	CLONAL	1	TRUE	1	0.34	2		742	1284	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641132	3641132	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1322	292	846	0	ENST00000294008.3:c.2507C>T	p.Ser836Phe	p.S836F	ENST00000294008	NM_032444.2	836	tCc/tTc	12/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.34	2		846	1614	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923485	9923485	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1404462639	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	75	456	0	ENST00000330684.3:c.1802T>C	p.Ile601Thr	p.I601T	ENST00000330684	NM_001134407.1	601	aTt/aCt	9/13	1	2	FACETS	0.528	0.462	0.6	0.528	0.462	0.6	SUBCLONAL	1	TRUE	1	0.34	2		456	835	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348869	11348869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	29	138	0	ENST00000332029.2:c.467C>T	p.Ala156Val	p.A156V	ENST00000332029	NM_003745.1	156	gCg/gTg	2/2	1	2	FACETS	0.586	0.472	0.716	0.586	0.472	0.716	SUBCLONAL	1	TRUE	1	0.34	2		138	291	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50810093	50810093	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	71	410	0	ENST00000398568.2:c.917G>A	p.Ser306Asn	p.S306N	ENST00000398568	NM_001042412.1	306	aGt/aAt	6/18	1	2	FACETS	0.581	0.506	0.661	0.581	0.506	0.661	SUBCLONAL	1	TRUE	1	0.34	2		410	719	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50816304	50816304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760703224	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	110	460	0	ENST00000398568.2:c.1744G>A	p.Glu582Lys	p.E582K	ENST00000398568	NM_001042412.1	582	Gag/Aag	10/18	1	2	FACETS	0.597	0.535	0.663	0.597	0.535	0.663	SUBCLONAL	1	TRUE	1	0.34	2		460	1084	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50827470	50827470	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	153	419	0	ENST00000398568.2:c.2355C>G	p.Cys785Trp	p.C785W	ENST00000398568	NM_001042412.1	785	tgC/tgG	16/18	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.34	2		419	843	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670706	67670706	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762060506	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	145	629	1	ENST00000264010.4:c.1951C>T	p.Arg651Trp	p.R651W	ENST00000264010	NM_006565.3	651	Cgg/Tgg	11/12	1	2	FACETS	0.732	0.666	0.801	0.732	0.666	0.801	SUBCLONAL	1	TRUE	1	0.34	2		630	1166	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991984	72991984	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	81	398	0	ENST00000268489.5:c.2061G>T	p.Glu687Asp	p.E687D	ENST00000268489	NM_006885.3	687	gaG/gaT	2/10	1	2	FACETS	0.678	0.597	0.765	0.678	0.597	0.765	SUBCLONAL	1	TRUE	1	0.34	2		398	703	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965124	81965124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691537	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	94	514	0	ENST00000359376.3:c.2604C>A	p.Asn868Lys	p.N868K	ENST00000359376	NM_002661.3	868	aaC/aaA	25/33	1	2	FACETS	0.588	0.522	0.658	0.588	0.522	0.658	SUBCLONAL	1	TRUE	1	0.34	2		514	941	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990439	81990439	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	195	549	0	ENST00000359376.3:c.3710T>C	p.Val1237Ala	p.V1237A	ENST00000359376	NM_002661.3	1237	gTt/gCt	32/33	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.34	2		549	1093	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348836	89348836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146474985	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1518	82	811	0	ENST00000301030.4:c.4114G>A	p.Glu1372Lys	p.E1372K	ENST00000301030	NM_001256183.1	1372	Gag/Aag	9/13	1	2	FACETS	0.301	0.264	0.342	0.301	0.264	0.342	SUBCLONAL	1	TRUE	1	0.34	2		811	1600	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350105	89350105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368593056	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	212	597	1	ENST00000301030.4:c.2845C>T	p.Arg949Trp	p.R949W	ENST00000301030	NM_001256183.1	949	Cgg/Tgg	9/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.34	2		598	1083	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8111056	8111056	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs548042738	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	102	476	1	ENST00000585124.1:c.151G>A	p.Ala51Thr	p.A51T	ENST00000585124	NM_004217.3	51	Gct/Act	3/9	1	2	FACETS	0.687	0.614	0.765	0.687	0.614	0.765	SUBCLONAL	1	TRUE	1	0.34	2		477	873	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965201	15965201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745388092	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	61	250	0	ENST00000268712.3:c.5395C>T	p.Pro1799Ser	p.P1799S	ENST00000268712	NM_006311.3	1799	Cct/Tct	37/46	1	2	FACETS	0.775	0.67	0.889	0.775	0.67	0.889	SUBCLONAL	1	TRUE	1	0.34	2		250	463	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983728	15983728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	123	342	0	ENST00000268712.3:c.3394G>A	p.Val1132Ile	p.V1132I	ENST00000268712	NM_006311.3	1132	Gtc/Atc	25/46	1	2	FACETS	0.995	0.901	1	0.995	0.901	1	CLONAL	1	TRUE	1	0.34	2		342	727	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989757	15989757	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	34	119	0	ENST00000268712.3:c.3017-1G>A		p.X1006_splice	ENST00000268712	NM_006311.3	1006			1	2	FACETS	0.662	0.543	0.796	0.662	0.543	0.796	SUBCLONAL	1	TRUE	1	0.34	2		119	302	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16022737	16022738	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	114	469	0	ENST00000268712.3:c.1914dup	p.Gly639ArgfsTer8	p.G639Rfs*8	ENST00000268712	NM_006311.3	638	-/A	17/46	1	2	FACETS	0.597	0.536	0.662	0.597	0.536	0.662	SUBCLONAL	1	TRUE	1	0.34	2		469	1123	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588787	29588787	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	114	394	0	ENST00000356175.3:c.4573C>A	p.Leu1525Met	p.L1525M	ENST00000356175	NM_000267.3	1525	Ctg/Atg	34/57	1	2	FACETS	0.953	0.859	1	0.953	0.859	1	CLONAL	1	TRUE	1	0.34	2		394	704	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883946	37883946	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	141	528	0	ENST00000269571.5:c.3417T>G	p.Tyr1139Ter	p.Y1139*	ENST00000269571		1139	taT/taG	27/27	1	2	FACETS	0.94	0.857	1	0.94	0.857	1	CLONAL	1	TRUE	1	0.34	2		528	882	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884010	37884010	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1210088528	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	54	569	1	ENST00000269571.5:c.3481C>T	p.Arg1161Ter	p.R1161*	ENST00000269571		1161	Cga/Tga	27/27	1	2	FACETS	0.316	0.269	0.368	0.316	0.269	0.368	SUBCLONAL	1	TRUE	1	0.34	2		570	1005	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245603	41245603	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs80356907	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	187	542	1	ENST00000357654.3:c.1945G>T	p.Glu649Ter	p.E649*	ENST00000357654	NM_007294.3	649	Gag/Tag	10/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.34	2		543	941	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804181	46804181	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs191886930	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	144	596	0	ENST00000290295.7:c.826G>A	p.Ala276Thr	p.A276T	ENST00000290295	NM_006361.5	276	Gcc/Acc	2/2	1	2	FACETS	0.862	0.785	0.942	0.862	0.785	0.942	CLONAL	1	TRUE	1	0.34	2		596	983	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804205	46804205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	129	597	1	ENST00000290295.7:c.802C>T	p.Arg268Trp	p.R268W	ENST00000290295	NM_006361.5	268	Cgg/Tgg	2/2	1	2	FACETS	0.751	0.679	0.826	0.751	0.679	0.826	SUBCLONAL	1	TRUE	1	0.34	2		598	1011	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696740	47696740	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	107	312	3	ENST00000347630.2:c.208C>T	p.Arg70Ter	p.R70*	ENST00000347630	NM_001007230.1	70	Cga/Tga	5/11	1	2	FACETS	0.965	0.867	1	0.965	0.867	1	CLONAL	1	TRUE	1	0.34	2		315	652	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55674262	55674262	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	140	424	0	ENST00000284073.2:c.488T>G	p.Val163Gly	p.V163G	ENST00000284073	NM_138962.2	163	gTt/gGt	8/14	1	2	FACETS	0.903	0.822	0.988	0.903	0.822	0.988	CLONAL	1	TRUE	1	0.34	2		424	912	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58725348	58725348	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	114	424	0	ENST00000305921.3:c.922T>C	p.Tyr308His	p.Y308H	ENST00000305921	NM_003620.3	308	Tat/Cat	4/6	1	2	FACETS	0.777	0.699	0.86	0.777	0.699	0.86	SUBCLONAL	1	TRUE	1	0.34	2		424	863	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740593	58740593	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	233	584	0	ENST00000305921.3:c.1498C>T	p.Pro500Ser	p.P500S	ENST00000305921	NM_003620.3	500	Cct/Tct	6/6	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.34	2		584	1172	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554728	63554728	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	59	279	1	ENST00000307078.5:c.11C>A	p.Ala4Asp	p.A4D	ENST00000307078	NM_004655.3	4	gCt/gAt	2/11	1	2	FACETS	0.588	0.506	0.678	0.588	0.506	0.678	SUBCLONAL	1	TRUE	1	0.34	2		280	590	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78923344	78923344	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	87	297	0	ENST00000306801.3:c.3367C>T	p.Arg1123Ter	p.R1123*	ENST00000306801	NM_020761.2	1123	Cga/Tga	28/34	1	2	FACETS	0.906	0.803	1	0.906	0.803	1	CLONAL	1	TRUE	1	0.34	2		297	565	SUCCESS
YES1	7525	MSKCC	GRCh37	18	751751	751751	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	131	450	0	ENST00000314574.4:c.325G>T	p.Asp109Tyr	p.D109Y	ENST00000314574	NM_005433.3	109	Gac/Tac	3/12	1	2	FACETS	0.749	0.678	0.823	0.749	0.678	0.823	SUBCLONAL	1	TRUE	1	0.34	2		450	1029	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39537553	39537553	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	50	322	0	ENST00000262039.4:c.87G>T	p.Lys29Asn	p.K29N	ENST00000262039	NM_002647.2	29	aaG/aaT	2/25	1	2	FACETS	0.535	0.453	0.624	0.535	0.453	0.624	SUBCLONAL	1	TRUE	1	0.34	2		322	550	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39623722	39623722	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	129	378	1	ENST00000262039.4:c.2129G>T	p.Ser710Ile	p.S710I	ENST00000262039	NM_002647.2	710	aGt/aTt	20/25	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.34	2		379	734	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637963	39637963	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	105	529	3	ENST00000262039.4:c.2380C>T	p.Gln794Ter	p.Q794*	ENST00000262039	NM_002647.2	794	Cag/Tag	22/25	1	2	FACETS	0.604	0.54	0.672	0.604	0.54	0.672	SUBCLONAL	1	TRUE	1	0.34	2		532	1023	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39647368	39647368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1045177250	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	99	302	0	ENST00000262039.4:c.2540G>A	p.Arg847His	p.R847H	ENST00000262039	NM_002647.2	847	cGc/cAc	24/25	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.34	2		302	572	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371756	45371756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	100	496	0	ENST00000262160.6:c.1235G>A	p.Cys412Tyr	p.C412Y	ENST00000262160	NM_005901.5	412	tGc/tAc	10/11	1	2	FACETS	0.671	0.598	0.748	0.671	0.598	0.748	SUBCLONAL	1	TRUE	1	0.34	2		496	877	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400634	56400634	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	49	273	0	ENST00000348428.3:c.1228T>G	p.Leu410Val	p.L410V	ENST00000348428	NM_006785.3	410	Tta/Gta	11/17	1	2	FACETS	0.608	0.515	0.71	0.608	0.515	0.71	SUBCLONAL	1	TRUE	1	0.34	2		273	474	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217796	2217796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	197	569	0	ENST00000398665.3:c.2570G>A	p.Ser857Asn	p.S857N	ENST00000398665	NM_032482.2	857	aGc/aAc	22/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.34	2		569	999	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226684	2226684	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	168	523	0	ENST00000398665.3:c.4164G>T	p.Glu1388Asp	p.E1388D	ENST00000398665	NM_032482.2	1388	gaG/gaT	27/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.34	2		523	865	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3114967	3114967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	135	568	2	ENST00000078429.4:c.502G>A	p.Ala168Thr	p.A168T	ENST00000078429	NM_002067.2	168	Gcc/Acc	4/7	1	2	FACETS	0.793	0.72	0.871	0.793	0.72	0.871	SUBCLONAL	1	TRUE	1	0.34	2		570	1001	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101118	4101118	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769471250	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	34	399	0	ENST00000262948.5:c.604G>A	p.Val202Met	p.V202M	ENST00000262948	NM_030662.3	202	Gtg/Atg	6/11	1	2	FACETS	0.302	0.245	0.365	0.302	0.245	0.365	SUBCLONAL	1	TRUE	1	0.34	2		399	663	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5225848	5225848	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1302269744	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	159	481	0	ENST00000357368.4:c.2384T>C	p.Val795Ala	p.V795A	ENST00000357368	NM_002850.3	795	gTc/gCc	17/38	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.34	2		481	823	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248546	10248546	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374047326	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	155	535	0	ENST00000340748.4:c.4207G>A	p.Ala1403Thr	p.A1403T	ENST00000340748		1403	Gca/Aca	35/40	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.34	2		535	912	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11027404	11027404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868638712	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	201	580	2	ENST00000327064.4:c.971C>T	p.Ser324Leu	p.S324L	ENST00000327064	NM_199141.1	324	tCg/tTg	8/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.34	2		582	1037	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144027	11144027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770680174	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	98	574	1	ENST00000358026.2:c.3608G>A	p.Arg1203His	p.R1203H	ENST00000358026	NM_001128849.1	1203	cGc/cAc	26/36	1	2	FACETS	0.576	0.513	0.644	0.576	0.513	0.644	SUBCLONAL	1	TRUE	1	0.34	2		575	1000	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15280969	15280969	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	119	625	2	ENST00000263388.2:c.5127G>T	p.Lys1709Asn	p.K1709N	ENST00000263388	NM_000435.2	1709	aaG/aaT	28/33	1	2	FACETS	0.719	0.648	0.795	0.719	0.648	0.795	SUBCLONAL	1	TRUE	1	0.34	2		627	973	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292387	15292387	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1161152977	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	72	392	0	ENST00000263388.2:c.2792G>T	p.Ser931Ile	p.S931I	ENST00000263388	NM_000435.2	931	aGc/aTc	17/33	1	2	FACETS	0.597	0.521	0.679	0.597	0.521	0.679	SUBCLONAL	1	TRUE	1	0.34	2		392	709	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303052	15303052	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151016108	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	195	634	1	ENST00000263388.2:c.398G>A	p.Arg133His	p.R133H	ENST00000263388	NM_000435.2	133	cGc/cAc	4/33	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.34	2		635	1076	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349757	15349757	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	145	479	0	ENST00000263377.2:c.3817C>T	p.Arg1273Trp	p.R1273W	ENST00000263377	NM_058243.2	1273	Cgg/Tgg	19/20	1	2	FACETS	0.996	0.909	1	0.996	0.909	1	CLONAL	1	TRUE	1	0.34	2		479	856	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366889	15366889	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	125	531	0	ENST00000263377.2:c.1737C>A	p.Ser579Arg	p.S579R	ENST00000263377	NM_058243.2	579	agC/agA	9/20	1	2	FACETS	0.683	0.617	0.753	0.683	0.617	0.753	SUBCLONAL	1	TRUE	1	0.34	2		531	1077	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387681	17387681	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	129	581	1	ENST00000359435.4:c.749A>C	p.Asn250Thr	p.N250T	ENST00000359435	NM_001033549.1	250	aAt/aCt	8/9	1	2	FACETS	0.691	0.625	0.761	0.691	0.625	0.761	SUBCLONAL	1	TRUE	1	0.34	2		582	1098	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274104	18274104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	111	521	2	ENST00000222254.8:c.1322C>T	p.Ala441Val	p.A441V	ENST00000222254	NM_005027.3	441	gCa/gTa	11/16	1	2	FACETS	0.704	0.632	0.781	0.704	0.632	0.781	SUBCLONAL	1	TRUE	1	0.34	2		523	927	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257571	19257571	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	134	542	1	ENST00000162023.5:c.655C>T	p.Arg219Ter	p.R219*	ENST00000162023		219	Cga/Tga	10/13	1	2	FACETS	0.81	0.735	0.889	0.81	0.735	0.889	CLONAL	1	TRUE	1	0.34	2		543	973	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260173	19260173	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	102	598	2	ENST00000162023.5:c.120C>A	p.Asp40Glu	p.D40E	ENST00000162023		40	gaC/gaA	7/13	1	2	FACETS	0.517	0.461	0.577	0.517	0.461	0.577	SUBCLONAL	1	TRUE	1	0.34	2		600	1160	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228979	36228979	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555734923	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	155	496	0	ENST00000222270.7:c.7759C>T	p.Arg2587Ter	p.R2587*	ENST00000222270	NM_014727.1	2587	Cga/Tga	36/37	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.34	2		496	878	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763533	41763533	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	56	281	1	ENST00000301178.4:c.2332C>A	p.Leu778Met	p.L778M	ENST00000301178	NM_021913.4	778	Ctg/Atg	19/20	1	2	FACETS	0.659	0.565	0.761	0.659	0.565	0.761	SUBCLONAL	1	TRUE	1	0.34	2		282	500	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753098	42753098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs923763445	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	82	500	1	ENST00000222329.4:c.1166G>A	p.Arg389Gln	p.R389Q	ENST00000222329	NM_006494.2	389	cGg/cAg	4/4	1	2	FACETS	0.675	0.595	0.761	0.675	0.595	0.761	SUBCLONAL	1	TRUE	1	0.34	2		501	715	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753428	42753428	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	133	495	2	ENST00000222329.4:c.836C>A	p.Pro279His	p.P279H	ENST00000222329	NM_006494.2	279	cCc/cAc	4/4	1	2	FACETS	0.978	0.889	1	0.978	0.889	1	CLONAL	1	TRUE	1	0.34	2		497	800	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729829	47729829	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	103	469	0	ENST00000449228.1:c.560G>T	p.Arg187Leu	p.R187L	ENST00000449228	NM_001127240.2	187	cGa/cTa	3/4	1	2	FACETS	0.708	0.633	0.788	0.708	0.633	0.788	SUBCLONAL	1	TRUE	1	0.34	2		469	856	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729965	47729965	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	48	205	1	ENST00000449228.1:c.424C>T	p.Arg142Cys	p.R142C	ENST00000449228	NM_001127240.2	142	Cgt/Tgt	3/4	1	2	FACETS	0.774	0.656	0.902	0.774	0.656	0.902	CLONAL	1	TRUE	1	0.34	2		206	365	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902725	50902725	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	202	626	1	ENST00000440232.2:c.300G>T	p.Glu100Asp	p.E100D	ENST00000440232	NM_002691.3	100	gaG/gaT	3/27	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.34	2		627	1179	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716267	52716267	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	106	449	2	ENST00000322088.6:c.711G>T	p.Gln237His	p.Q237H	ENST00000322088	NM_014225.5	237	caG/caT	6/15	1	2	FACETS	0.806	0.722	0.894	0.806	0.722	0.894	CLONAL	1	TRUE	1	0.34	2		451	774	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469145	25469145	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1558669435	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	103	552	0	ENST00000264709.3:c.1313A>G	p.Asp438Gly	p.D438G	ENST00000264709	NM_175629.2	438	gAc/gGc	11/23	1	2	FACETS	0.606	0.541	0.675	0.606	0.541	0.675	SUBCLONAL	1	TRUE	1	0.34	2		552	1000	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25536826	25536826	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs752093845	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	142	410	0	ENST00000264709.3:c.28G>C	p.Gly10Arg	p.G10R	ENST00000264709	NM_175629.2	10	Ggg/Cgg	2/23	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.34	2		410	742	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101060	26101060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	91	536	0	ENST00000435504.4:c.32G>A	p.Arg11Lys	p.R11K	ENST00000435504		11	aGg/aAg	1/13	1	2	FACETS	0.597	0.529	0.669	0.597	0.529	0.669	SUBCLONAL	1	TRUE	1	0.34	2		536	897	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754913	29754913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1279941719	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	33	374	0	ENST00000389048.3:c.1022G>A	p.Ser341Asn	p.S341N	ENST00000389048	NM_004304.4	341	aGc/aAc	4/29	1	2	FACETS	0.302	0.245	0.366	0.302	0.245	0.366	SUBCLONAL	1	TRUE	1	0.34	2		374	643	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940531	29940531	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1060500209	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	148	446	2	ENST00000389048.3:c.700C>A	p.Pro234Thr	p.P234T	ENST00000389048	NM_004304.4	234	Cct/Act	2/29	1	2	FACETS	0.88	0.803	0.961	0.88	0.803	0.961	CLONAL	1	TRUE	1	0.34	2		448	989	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705460	47705460	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	58	295	0	ENST00000233146.2:c.2260A>C	p.Thr754Pro	p.T754P	ENST00000233146	NM_000251.2	754	Act/Cct	14/16	1	2	FACETS	0.56	0.481	0.647	0.56	0.481	0.647	SUBCLONAL	1	TRUE	1	0.34	2		295	609	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707835	47707835	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	82	272	0	ENST00000233146.2:c.2459G>T	p.Gly820Val	p.G820V	ENST00000233146	NM_000251.2	820	gGt/gTt	15/16	1	2	FACETS	0.942	0.833	1	0.942	0.833	1	CLONAL	1	TRUE	1	0.34	2		272	512	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027712	48027712	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	103	301	1	ENST00000234420.5:c.2590G>T	p.Gly864Ter	p.G864*	ENST00000234420	NM_000179.2	864	Gga/Tga	4/10	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.34	2		302	582	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033385	48033385	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782117	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	78	520	0	ENST00000234420.5:c.3689C>T	p.Ala1230Val	p.A1230V	ENST00000234420	NM_000179.2	1230	gCa/gTa	8/10	1	2	FACETS	0.507	0.444	0.575	0.507	0.444	0.575	SUBCLONAL	1	TRUE	1	0.34	2		520	905	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147212	61147212	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	109	443	0	ENST00000295025.8:c.890C>T	p.Thr297Ile	p.T297I	ENST00000295025	NM_002908.2	297	aCt/aTt	8/11	1	2	FACETS	0.536	0.479	0.596	0.536	0.479	0.596	SUBCLONAL	1	TRUE	1	0.34	2		443	1197	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044322	128044322	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	79	486	0	ENST00000285398.2:c.1299G>T	p.Gln433His	p.Q433H	ENST00000285398	NM_000122.1	433	caG/caT	8/15	1	2	FACETS	0.577	0.507	0.653	0.577	0.507	0.653	SUBCLONAL	1	TRUE	1	0.34	2		486	805	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728483	190728483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	97	356	1	ENST00000441310.2:c.1871C>T	p.Ala624Val	p.A624V	ENST00000441310	NM_000534.4	624	gCt/gTt	10/13	1	2	FACETS	0.805	0.718	0.897	0.805	0.718	0.897	CLONAL	1	TRUE	1	0.34	2		357	709	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274548	198274548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778869024	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	172	358	1	ENST00000335508.6:c.850G>A	p.Ala284Thr	p.A284T	ENST00000335508	NM_012433.2	284	Gca/Aca	7/25	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.34	2		359	835	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274722	198274722	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	43	307	1	ENST00000335508.6:c.676C>T	p.His226Tyr	p.H226Y	ENST00000335508	NM_012433.2	226	Cat/Tat	7/25	1	2	FACETS	0.472	0.394	0.558	0.472	0.394	0.558	SUBCLONAL	1	TRUE	1	0.34	2		308	536	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131421	202131421	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	82	469	0	ENST00000358485.4:c.389G>T	p.Arg130Ile	p.R130I	ENST00000358485	NM_001080125.1	130	aGa/aTa	2/9	1	2	FACETS	0.544	0.478	0.614	0.544	0.478	0.614	SUBCLONAL	1	TRUE	1	0.34	2		469	887	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736158	204736158	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs963824682	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	140	360	0	ENST00000302823.3:c.515C>T	p.Ser172Leu	p.S172L	ENST00000302823	NM_005214.4	172	tCg/tTg	3/4	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.34	2		360	793	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204737476	204737476	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1559592490	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	161	563	0	ENST00000302823.3:c.617del	p.Pro206GlnfsTer23	p.P206Qfs*23	ENST00000302823	NM_005214.4	205	Ccc/cc	4/4	1	2	FACETS	0.903	0.827	0.982	0.903	0.827	0.982	CLONAL	1	TRUE	1	0.34	2		563	1049	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543903	212543903	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	86	430	0	ENST00000342788.4:c.1496A>C	p.Glu499Ala	p.E499A	ENST00000342788	NM_005235.2	499	gAa/gCa	13/28	1	2	FACETS	0.626	0.553	0.704	0.626	0.553	0.704	SUBCLONAL	1	TRUE	1	0.34	2		430	808	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661068	227661068	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	159	372	0	ENST00000305123.5:c.2387G>T	p.Gly796Val	p.G796V	ENST00000305123	NM_005544.2	796	gGt/gTt	1/2	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.34	2		372	660	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794497	242794497	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	105	520	0	ENST00000334409.5:c.445G>A	p.Ala149Thr	p.A149T	ENST00000334409	NM_005018.2	149	Gca/Aca	3/5	1	2	FACETS	0.644	0.576	0.717	0.644	0.576	0.717	SUBCLONAL	1	TRUE	1	0.34	2		520	959	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538311	9538311	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	156	430	0	ENST00000353224.5:c.1687G>T	p.Gly563Ter	p.G563*	ENST00000353224	NM_177990.2	563	Gga/Tga	7/10	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.34	2		430	916	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016182	31016182	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144437064	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	60	424	2	ENST00000375687.4:c.428G>A	p.Arg143Gln	p.R143Q	ENST00000375687	NM_015338.5	143	cGa/cAa	6/13	1	2	FACETS	0.387	0.332	0.446	0.387	0.332	0.446	SUBCLONAL	1	TRUE	1	0.34	2		426	913	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375077	31375077	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	200	645	0	ENST00000328111.2:c.474G>A	p.Trp158Ter	p.W158*	ENST00000328111	NM_006892.3	158	tgG/tgA	6/23	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.34	2		645	1155	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36014554	36014554	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	119	575	1	ENST00000358208.4:c.327G>T	p.Glu109Asp	p.E109D	ENST00000358208		109	gaG/gaT	3/12	1	2	FACETS	0.666	0.6	0.736	0.666	0.6	0.736	SUBCLONAL	1	TRUE	1	0.34	2		576	1051	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39726940	39726940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757344214	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	129	384	0	ENST00000361337.2:c.938C>T	p.Thr313Met	p.T313M	ENST00000361337	NM_003286.2	313	aCg/aTg	11/21	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.34	2		384	743	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100908	41100908	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	63	495	0	ENST00000373198.4:c.1448A>T	p.Asp483Val	p.D483V	ENST00000373198	NM_133170.3	483	gAc/gTc	8/32	1	2	FACETS	0.432	0.372	0.497	0.432	0.372	0.497	SUBCLONAL	1	TRUE	1	0.34	2		495	858	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268399	46268399	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	175	403	0	ENST00000371998.3:c.2786G>T	p.Arg929Ile	p.R929I	ENST00000371998		929	aGa/aTa	15/23	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.34	2		403	829	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46275889	46275889	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	205	585	0	ENST00000371998.3:c.3325G>T	p.Gly1109Ter	p.G1109*	ENST00000371998		1109	Gga/Tga	18/23	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.34	2		585	1060	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279790	46279790	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776910504	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	138	407	2	ENST00000371998.3:c.3716G>A	p.Arg1239Gln	p.R1239Q	ENST00000371998		1239	cGa/cAa	20/23	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.34	2		409	772	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62309678	62309678	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	66	394	0	ENST00000360203.5:c.1016G>T	p.Ser339Ile	p.S339I	ENST00000360203	NM_001283009.1	339	aGc/aTc	12/35	1	2	FACETS	0.53	0.46	0.607	0.53	0.46	0.607	SUBCLONAL	1	TRUE	1	0.34	2		394	732	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62323173	62323173	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142877871	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	74	373	0	ENST00000360203.5:c.2635C>T	p.Arg879Trp	p.R879W	ENST00000360203	NM_001283009.1	879	Cgg/Tgg	28/35	1	2	FACETS	0.77	0.675	0.873	0.77	0.675	0.873	SUBCLONAL	1	TRUE	1	0.34	2		373	565	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326255	62326255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559104198	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	168	684	0	ENST00000360203.5:c.3271G>A	p.Asp1091Asn	p.D1091N	ENST00000360203	NM_001283009.1	1091	Gac/Aac	32/35	1	2	FACETS	0.855	0.784	0.929	0.855	0.784	0.929	CLONAL	1	TRUE	1	0.34	2		684	1156	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397719	49397719	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	151	590	0	ENST00000418115.1:c.505G>T	p.Glu169Ter	p.E169*	ENST00000418115	NM_001664.2	169	Gag/Tag	5/5	1	2	FACETS	0.691	0.63	0.756	0.691	0.63	0.756	SUBCLONAL	1	TRUE	1	0.34	2		590	1285	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405878	49405878	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	118	582	0	ENST00000418115.1:c.260A>G	p.Asp87Gly	p.D87G	ENST00000418115	NM_001664.2	87	gAc/gGc	3/5	1	2	FACETS	0.602	0.542	0.666	0.602	0.542	0.666	SUBCLONAL	1	TRUE	1	0.34	2		582	1153	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799860	72799860	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	75	333	0	ENST00000325599.8:c.1309A>C	p.Lys437Gln	p.K437Q	ENST00000325599	NM_018130.2	437	Aaa/Caa	11/11	1	2	FACETS	0.639	0.56	0.725	0.639	0.56	0.725	SUBCLONAL	1	TRUE	1	0.34	2		333	690	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259658	89259658	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs754184476	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	25	222	0	ENST00000336596.2:c.802T>C	p.Phe268Leu	p.F268L	ENST00000336596	NM_005233.5	268	Ttt/Ctt	3/17	1	2	FACETS	0.455	0.359	0.566	0.455	0.359	0.566	SUBCLONAL	1	TRUE	1	0.34	2		222	323	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468354	89468354	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	59	203	0	ENST00000336596.2:c.1889-1G>T		p.X630_splice	ENST00000336596	NM_005233.5	630			1	2	FACETS	0.98	0.848	1	0.98	0.848	1	CLONAL	1	TRUE	1	0.34	2		203	354	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528549	89528549	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	40	267	0	ENST00000336596.2:c.2849A>G	p.Asp950Gly	p.D950G	ENST00000336596	NM_005233.5	950	gAc/gGc	17/17	1	2	FACETS	0.458	0.38	0.545	0.458	0.38	0.545	SUBCLONAL	1	TRUE	1	0.34	2		267	514	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200151	128200151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	94	517	0	ENST00000341105.2:c.1154C>T	p.Pro385Leu	p.P385L	ENST00000341105	NM_032638.4	385	cCa/cTa	6/6	1	2	FACETS	0.58	0.515	0.649	0.58	0.515	0.649	SUBCLONAL	1	TRUE	1	0.34	2		517	954	SUCCESS
ATR	545	MSKCC	GRCh37	3	142241664	142241664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	82	507	0	ENST00000350721.4:c.4172G>A	p.Ser1391Asn	p.S1391N	ENST00000350721	NM_001184.3	1391	aGc/aAc	23/47	1	2	FACETS	0.569	0.501	0.643	0.569	0.501	0.643	SUBCLONAL	1	TRUE	1	0.34	2		507	847	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278228	142278228	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1248870932	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	106	477	0	ENST00000350721.4:c.1597A>G	p.Thr533Ala	p.T533A	ENST00000350721	NM_001184.3	533	Act/Gct	7/47	1	2	FACETS	0.612	0.547	0.681	0.612	0.547	0.681	SUBCLONAL	1	TRUE	1	0.34	2		477	1019	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916935	178916935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	40	454	0	ENST00000263967.3:c.322C>T	p.Arg108Cys	p.R108C	ENST00000263967	NM_006218.2	108	Cgt/Tgt	2/21	1	2	FACETS	0.253	0.209	0.303	0.253	0.209	0.303	SUBCLONAL	1	TRUE	1	0.34	2		454	929	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178941908	178941908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	131	394	0	ENST00000263967.3:c.2227G>A	p.Asp743Asn	p.D743N	ENST00000263967	NM_006218.2	743	Gat/Aat	15/21	1	2	FACETS	0.988	0.897	1	0.988	0.897	1	CLONAL	1	TRUE	1	0.34	2		394	780	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665064	182665064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777859787	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	127	520	0	ENST00000292782.4:c.662C>T	p.Thr221Met	p.T221M	ENST00000292782	NM_020640.2	221	aCg/aTg	6/7	1	2	FACETS	0.645	0.582	0.71	0.645	0.582	0.71	SUBCLONAL	1	TRUE	1	0.34	2		520	1159	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146640	185146640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369957279	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	161	464	1	ENST00000265026.3:c.271G>A	p.Asp91Asn	p.D91N	ENST00000265026	NM_004721.4	91	Gat/Aat	2/14	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.34	2		465	914	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505049	186505049	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	52	208	0	ENST00000323963.5:c.905C>A	p.Ala302Asp	p.A302D	ENST00000323963		302	gCt/gAt	8/11	1	2	FACETS	0.639	0.544	0.742	0.639	0.544	0.742	SUBCLONAL	1	TRUE	1	0.34	2		208	479	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807119	1807119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	149	591	1	ENST00000260795.2:c.1450G>A	p.Gly484Ser	p.G484S	ENST00000260795		484	Ggc/Agc	10/17	1	2	FACETS	0.928	0.848	1	0.928	0.848	1	CLONAL	1	TRUE	1	0.34	2		592	944	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133465	55133465	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	133	514	1	ENST00000257290.5:c.769G>T	p.Gly257Cys	p.G257C	ENST00000257290	NM_006206.4	257	Ggc/Tgc	6/23	1	2	FACETS	0.901	0.818	0.989	0.901	0.818	0.989	CLONAL	1	TRUE	1	0.34	2		515	868	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197758	66197758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755988244	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	135	483	1	ENST00000273854.3:c.2941C>T	p.Arg981Trp	p.R981W	ENST00000273854	NM_004439.5	981	Cgg/Tgg	17/18	1	2	FACETS	0.87	0.79	0.954	0.87	0.79	0.954	CLONAL	1	TRUE	1	0.34	2		484	913	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218779	66218779	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	110	455	0	ENST00000273854.3:c.2279C>A	p.Ser760Tyr	p.S760Y	ENST00000273854	NM_004439.5	760	tCt/tAt	13/18	1	2	FACETS	0.776	0.697	0.86	0.776	0.697	0.86	SUBCLONAL	1	TRUE	1	0.34	2		455	834	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535376	66535376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	149	382	0	ENST00000273854.3:c.85G>A	p.Ala29Thr	p.A29T	ENST00000273854	NM_004439.5	29	Gcc/Acc	1/18	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.34	2		382	670	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509892	187509892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	48	288	3	ENST00000441802.2:c.13621G>A	p.Ala4541Thr	p.A4541T	ENST00000441802	NM_005245.3	4541	Gcc/Acc	27/27	1	2	FACETS	0.643	0.544	0.752	0.643	0.544	0.752	SUBCLONAL	1	TRUE	1	0.34	2		291	439	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875658	35875658	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	117	507	1	ENST00000303115.3:c.845C>A	p.Thr282Asn	p.T282N	ENST00000303115	NM_002185.3	282	aCt/aAt	7/8	1	2	FACETS	0.704	0.633	0.778	0.704	0.633	0.778	SUBCLONAL	1	TRUE	1	0.34	2		508	978	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876487	35876487	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	136	484	0	ENST00000303115.3:c.1279A>G	p.Thr427Ala	p.T427A	ENST00000303115	NM_002185.3	427	Aca/Gca	8/8	1	2	FACETS	0.732	0.664	0.803	0.732	0.664	0.803	SUBCLONAL	1	TRUE	1	0.34	2		484	1093	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967474	38967474	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	117	395	0	ENST00000357387.3:c.1116G>T	p.Glu372Asp	p.E372D	ENST00000357387	NM_152756.3	372	gaG/gaT	13/38	1	2	FACETS	0.868	0.783	0.958	0.868	0.783	0.958	CLONAL	1	TRUE	1	0.34	2		395	793	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750567	57750567	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	46	415	0	ENST00000274289.3:c.1901T>C	p.Ile634Thr	p.I634T	ENST00000274289	NM_006622.3	634	aTc/aCc	14/14	1	2	FACETS	0.34	0.285	0.4	0.34	0.285	0.4	SUBCLONAL	1	TRUE	1	0.34	2		415	797	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588949	67588949	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	105	231	0	ENST00000274335.5:c.1040T>G	p.Leu347Arg	p.L347R	ENST00000274335		347	cTt/cGt	8/15	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.34	2		231	581	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590397	67590397	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	69	269	0	ENST00000274335.5:c.1461del	p.Phe487LeufsTer5	p.F487Lfs*5	ENST00000274335		487	Ttt/tt	11/15	1	2	FACETS	0.615	0.535	0.701	0.615	0.535	0.701	SUBCLONAL	1	TRUE	1	0.34	2		269	660	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86676376	86676376	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	67	322	0	ENST00000274376.6:c.2654G>A	p.Trp885Ter	p.W885*	ENST00000274376	NM_002890.2	885	tGg/tAg	20/25	1	2	FACETS	0.833	0.726	0.949	0.833	0.726	0.949	CLONAL	1	TRUE	1	0.34	2		322	473	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923279	131923279	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	55	298	0	ENST00000265335.6:c.782A>C	p.Asn261Thr	p.N261T	ENST00000265335		261	aAt/aCt	6/25	1	2	FACETS	0.523	0.447	0.606	0.523	0.447	0.606	SUBCLONAL	1	TRUE	1	0.34	2		298	619	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924522	131924522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876659920	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	70	428	0	ENST00000265335.6:c.1195C>T	p.Leu399Phe	p.L399F	ENST00000265335		399	Ctt/Ttt	8/25	1	2	FACETS	0.503	0.438	0.574	0.503	0.438	0.574	SUBCLONAL	1	TRUE	1	0.34	2		428	818	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131976482	131976482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370560173	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	123	420	0	ENST00000265335.6:c.3737C>T	p.Ala1246Val	p.A1246V	ENST00000265335		1246	gCa/gTa	24/25	1	2	FACETS	0.825	0.746	0.909	0.825	0.746	0.909	CLONAL	1	TRUE	1	0.34	2		420	877	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562658	176562658	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	184	529	0	ENST00000439151.2:c.554A>C	p.Glu185Ala	p.E185A	ENST00000439151	NM_022455.4	185	gAg/gCg	2/23	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.34	2		529	996	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176619012	176619012	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	47	386	0	ENST00000439151.2:c.1055A>G	p.Lys352Arg	p.K352R	ENST00000439151	NM_022455.4	352	aAa/aGa	3/23	1	2	FACETS	0.335	0.281	0.394	0.335	0.281	0.394	SUBCLONAL	1	TRUE	1	0.34	2		386	826	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912367	29912367	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	99	298	0	ENST00000376809.5:c.986C>A	p.Ala329Asp	p.A329D	ENST00000376809	NM_002116.7	329	gCc/gAc	5/8	1	2	FACETS	0.967	0.865	1	0.967	0.865	1	CLONAL	1	TRUE	1	0.34	2		298	602	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323370	31323370	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	79	509	0	ENST00000412585.2:c.620-1G>T		p.X207_splice	ENST00000412585	NM_005514.6	207			1	2	FACETS	0.487	0.427	0.552	0.487	0.427	0.552	SUBCLONAL	1	TRUE	1	0.34	2		509	954	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166275	32166275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs967436228	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	142	497	0	ENST00000375023.3:c.4679C>T	p.Ala1560Val	p.A1560V	ENST00000375023	NM_004557.3	1560	gCg/gTg	26/30	1	2	FACETS	0.861	0.784	0.942	0.861	0.784	0.942	CLONAL	1	TRUE	1	0.34	2		497	970	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798511	32798511	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs765335850	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	256	579	1	ENST00000374899.4:c.1345C>T	p.Arg449Ter	p.R449*	ENST00000374899	NM_018833.2	449	Cga/Tga	8/12	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.34	2		580	1098	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800532	32800532	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	176	726	0	ENST00000374899.4:c.1015C>A	p.Leu339Met	p.L339M	ENST00000374899	NM_018833.2	339	Ctg/Atg	6/12	1	2	FACETS	0.86	0.79	0.932	0.86	0.79	0.932	CLONAL	1	TRUE	1	0.34	2		726	1204	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803059	32803059	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs61736923	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	180	558	1	ENST00000374899.4:c.817C>T	p.Arg273Ter	p.R273*	ENST00000374899	NM_018833.2	273	Cga/Tga	5/12	1	2	FACETS	0.915	0.842	0.991	0.915	0.842	0.991	CLONAL	1	TRUE	1	0.34	2		559	1157	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651876	36651876	+	splice_region_variant,5_prime_UTR_variant	Splice_Region	SNP	G	G	A	rs181964284	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	128	428	0	ENST00000244741.5:c.-3G>A		p.X1_splice	ENST00000244741	NM_000389.4	1		2/3	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.34	2		428	714	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908263	41908263	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs889367305	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	175	626	0	ENST00000372991.4:c.259C>T	p.Arg87Cys	p.R87C	ENST00000372991	NM_001760.3	87	Cgc/Tgc	2/5	1	2	FACETS	0.958	0.882	1	0.958	0.882	1	CLONAL	1	TRUE	1	0.34	2		626	1074	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790702	89790702	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	157	716	1	ENST00000336032.3:c.89G>T	p.Gly30Val	p.G30V	ENST00000336032	NM_006813.2	30	gGg/gTg	1/2	1	2	FACETS	0.741	0.677	0.808	0.741	0.677	0.808	SUBCLONAL	1	TRUE	1	0.34	2		717	1246	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662683	117662683	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	57	385	0	ENST00000368508.3:c.4782G>T	p.Gln1594His	p.Q1594H	ENST00000368508	NM_002944.2	1594	caG/caT	29/43	1	2	FACETS	0.485	0.416	0.561	0.485	0.416	0.561	SUBCLONAL	1	TRUE	1	0.34	2		385	691	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528187	157528187	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	144	397	0	ENST00000346085.5:c.5912T>C	p.Leu1971Pro	p.L1971P	ENST00000346085	NM_020732.3	1971	cTg/cCg	20/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.34	2		397	785	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977584	2977584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746318779	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	217	612	1	ENST00000396946.4:c.1100C>T	p.Thr367Met	p.T367M	ENST00000396946	NM_032415.4	367	aCg/aTg	8/25	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.34	2		613	1115	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6442013	6442013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	55	223	0	ENST00000356142.4:c.572C>T	p.Ala191Val	p.A191V	ENST00000356142	NM_018890.3	191	gCg/gTg	7/7	1	2	FACETS	0.783	0.672	0.904	0.783	0.672	0.904	CLONAL	1	TRUE	1	0.34	2		223	413	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940364	13940364	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	37	295	0	ENST00000405192.2:c.1142A>T	p.Lys381Met	p.K381M	ENST00000405192	NM_001163147.1	381	aAg/aTg	11/12	1	2	FACETS	0.415	0.341	0.497	0.415	0.341	0.497	SUBCLONAL	1	TRUE	1	0.34	2		295	525	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729711	41729711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	157	472	0	ENST00000242208.4:c.818G>A	p.Gly273Asp	p.G273D	ENST00000242208	NM_002192.2	273	gGc/gAc	3/3	1	2	FACETS	0.998	0.914	1	0.998	0.914	1	CLONAL	1	TRUE	1	0.34	2		472	925	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367280	50367280	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	115	365	0	ENST00000331340.3:c.87G>T	p.Glu29Asp	p.E29D	ENST00000331340	NM_006060.4	29	gaG/gaT	3/8	1	2	FACETS	0.92	0.83	1	0.92	0.83	1	CLONAL	1	TRUE	1	0.34	2		365	735	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508408	106508408	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	62	192	0	ENST00000359195.3:c.402G>T	p.Gln134His	p.Q134H	ENST00000359195	NM_002649.2	134	caG/caT	2/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.34	2		192	279	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509138	106509138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753981231	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	172	475	2	ENST00000359195.3:c.1132G>A	p.Asp378Asn	p.D378N	ENST00000359195	NM_002649.2	378	Gac/Aac	2/11	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.34	2		477	996	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128848602	128848602	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs781646841	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	113	564	0	ENST00000249373.3:c.1267G>T	p.Val423Phe	p.V423F	ENST00000249373	NM_005631.4	423	Gtc/Ttc	7/12	1	2	FACETS	0.657	0.59	0.728	0.657	0.59	0.728	SUBCLONAL	1	TRUE	1	0.34	2		564	1012	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524275	148524275	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	67	434	0	ENST00000320356.2:c.709G>T	p.Ala237Ser	p.A237S	ENST00000320356	NM_004456.4	237	Gca/Tca	7/20	1	2	FACETS	0.531	0.461	0.608	0.531	0.461	0.608	SUBCLONAL	1	TRUE	1	0.34	2		434	742	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132860	152132860	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	110	401	1	ENST00000262189.6:c.12G>T	p.Glu4Asp	p.E4D	ENST00000262189	NM_170606.2	4	gaG/gaT	1/59	1	2	FACETS	0.833	0.748	0.922	0.833	0.748	0.922	CLONAL	1	TRUE	1	0.34	2		402	777	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38184289	38184289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149768452	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	51	527	2	ENST00000317025.8:c.1667C>T	p.Thr556Met	p.T556M	ENST00000317025	NM_023034.1	556	aCg/aTg	7/24	1	2	FACETS	0.313	0.265	0.366	0.313	0.265	0.366	SUBCLONAL	1	TRUE	1	0.34	2		529	959	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187234	38187234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1430504174	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	259	699	1	ENST00000317025.8:c.1243G>A	p.Glu415Lys	p.E415K	ENST00000317025	NM_023034.1	415	Gaa/Aaa	6/24	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.34	2		700	1286	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277191	38277191	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	188	534	0	ENST00000425967.3:c.1237A>G	p.Thr413Ala	p.T413A	ENST00000425967	NM_001174067.1	413	Aca/Gca	10/19	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.34	2		534	1060	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38314904	38314904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1383262590	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	139	421	1	ENST00000425967.3:c.160G>A	p.Ala54Thr	p.A54T	ENST00000425967	NM_001174067.1	54	Gct/Act	3/19	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.34	2		422	749	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38315016	38315016	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs760118068	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	72	624	0	ENST00000425967.3:c.48G>T	p.Glu16Asp	p.E16D	ENST00000425967	NM_001174067.1	16	gaG/gaT	3/19	1	2	FACETS	0.373	0.324	0.425	0.373	0.324	0.425	SUBCLONAL	1	TRUE	1	0.34	2		624	1136	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866473	56866473	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	147	541	0	ENST00000519728.1:c.720G>T	p.Trp240Cys	p.W240C	ENST00000519728	NM_002350.3	240	tgG/tgT	8/13	1	2	FACETS	0.87	0.793	0.95	0.87	0.793	0.95	CLONAL	1	TRUE	1	0.34	2		541	994	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009253	69009253	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	88	323	0	ENST00000288368.4:c.2370G>T	p.Glu790Asp	p.E790D	ENST00000288368	NM_024870.2	790	gaG/gaT	22/40	1	2	FACETS	0.879	0.78	0.984	0.879	0.78	0.984	CLONAL	1	TRUE	1	0.34	2		323	589	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980735	70980735	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	106	557	0	ENST00000276594.2:c.733G>T	p.Asp245Tyr	p.D245Y	ENST00000276594	NM_024504.3	245	Gac/Tac	3/8	1	2	FACETS	0.558	0.499	0.621	0.558	0.499	0.621	SUBCLONAL	1	TRUE	1	0.34	2		557	1117	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551367	141551367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769158913	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	181	574	0	ENST00000220592.5:c.1930G>A	p.Ala644Thr	p.A644T	ENST00000220592	NM_012154.3	644	Gcc/Acc	15/19	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.34	2		574	1017	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566033	141566033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	124	480	2	ENST00000220592.5:c.1231C>T	p.Arg411Trp	p.R411W	ENST00000220592	NM_012154.3	411	Cgg/Tgg	10/19	1	2	FACETS	0.878	0.794	0.966	0.878	0.794	0.966	CLONAL	1	TRUE	1	0.34	2		482	831	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740820	145740820	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	165	619	2	ENST00000428558.2:c.1280C>A	p.Ala427Asp	p.A427D	ENST00000428558	NM_004260.3	427	gCt/gAt	7/22	1	2	FACETS	0.917	0.841	0.997	0.917	0.841	0.997	CLONAL	1	TRUE	1	0.34	2		621	1058	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741719	145741719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781314533	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	62	541	0	ENST00000428558.2:c.784C>T	p.Arg262Trp	p.R262W	ENST00000428558	NM_004260.3	262	Cgg/Tgg	5/22	1	2	FACETS	0.429	0.369	0.493	0.429	0.369	0.493	SUBCLONAL	1	TRUE	1	0.34	2		541	851	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126397	5126397	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	58	369	0	ENST00000381652.3:c.3242T>G	p.Leu1081Arg	p.L1081R	ENST00000381652	NM_004972.3	1081	cTt/cGt	24/25	1	2	FACETS	0.652	0.561	0.752	0.652	0.561	0.752	SUBCLONAL	1	TRUE	1	0.34	2		369	523	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499804	8499804	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	150	516	0	ENST00000356435.5:c.2165C>T	p.Ala722Val	p.A722V	ENST00000356435		722	gCt/gTt	14/35	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.34	2		516	877	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504363	8504363	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	112	420	0	ENST00000356435.5:c.1720G>T	p.Gly574Ter	p.G574*	ENST00000356435		574	Gga/Tga	12/35	1	2	FACETS	0.865	0.778	0.956	0.865	0.778	0.956	CLONAL	1	TRUE	1	0.34	2		420	762	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636724	8636724	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	55	235	0	ENST00000356435.5:c.185A>T	p.Lys62Met	p.K62M	ENST00000356435		62	aAg/aTg	2/35	1	2	FACETS	0.598	0.512	0.692	0.598	0.512	0.692	SUBCLONAL	1	TRUE	1	0.34	2		235	541	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971139	21971139	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730881679	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	37	291	0	ENST00000579755.1:c.262C>T	p.Arg88Ter	p.R88*	ENST00000579755		88	Cga/Tga	2/3	1	2	FACETS	0.491	0.405	0.588	0.491	0.405	0.588	SUBCLONAL	1	TRUE	1	0.34	2		291	443	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482163	87482163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	200	559	0	ENST00000277120.3:c.1450G>A	p.Ala484Thr	p.A484T	ENST00000277120		484	Gcc/Acc	14/19	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.34	2		559	1121	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232209	98232209	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs960630296	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	71	516	2	ENST00000331920.6:c.1733C>T	p.Ala578Val	p.A578V	ENST00000331920	NM_000264.3	578	gCg/gTg	13/24	1	2	FACETS	0.528	0.46	0.602	0.528	0.46	0.602	SUBCLONAL	1	TRUE	1	0.34	2		518	791	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908813	101908813	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	120	341	0	ENST00000374994.4:c.1177T>G	p.Phe393Val	p.F393V	ENST00000374994	NM_004612.2	393	Ttt/Gtt	7/9	1	2	FACETS	0.958	0.866	1	0.958	0.866	1	CLONAL	1	TRUE	1	0.34	2		341	737	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786397	135786397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1158970076	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	95	404	0	ENST00000298552.3:c.1133G>A	p.Gly378Asp	p.G378D	ENST00000298552	NM_001162426.1	378	gGt/gAt	11/23	1	2	FACETS	0.656	0.583	0.734	0.656	0.583	0.734	SUBCLONAL	1	TRUE	1	0.34	2		404	852	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137321059	137321059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781468867	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	89	468	2	ENST00000481739.1:c.1016G>A	p.Ser339Asn	p.S339N	ENST00000481739	NM_002957.4	339	aGc/aAc	7/10	1	2	FACETS	0.684	0.606	0.768	0.684	0.606	0.768	SUBCLONAL	1	TRUE	1	0.34	2		470	765	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391361	139391361	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	155	619	0	ENST00000277541.6:c.6830C>A	p.Pro2277His	p.P2277H	ENST00000277541	NM_017617.3	2277	cCt/cAt	34/34	1	2	FACETS	0.92	0.842	1	0.92	0.842	1	CLONAL	1	TRUE	1	0.34	2		619	991	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407471	139407471	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	118	366	0	ENST00000277541.6:c.2467+2T>C		p.X823_splice	ENST00000277541	NM_017617.3	823			1	2	FACETS	0.9	0.812	0.993	0.9	0.812	0.993	CLONAL	1	TRUE	1	0.34	2		366	771	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413140	139413140	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs754934469	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	181	630	1	ENST00000277541.6:c.1002G>T	p.Glu334Asp	p.E334D	ENST00000277541	NM_017617.3	334	gaG/gaT	6/34	1	2	FACETS	0.835	0.768	0.905	0.835	0.768	0.905	CLONAL	1	TRUE	1	0.34	2		631	1275	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930273	39930273	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769721734	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	125	599	1	ENST00000378444.4:c.3191C>T	p.Ser1064Leu	p.S1064L	ENST00000378444	NM_001123385.1	1064	tCg/tTg	6/15	1	2	FACETS	0.632	0.57	0.697	0.632	0.57	0.697	SUBCLONAL	1	TRUE	1	0.34	2		600	1164	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922698	44922698	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	101	406	0	ENST00000377967.4:c.1559C>A	p.Ser520Tyr	p.S520Y	ENST00000377967	NM_021140.2	520	tCt/tAt	16/29	1	2	FACETS	0.85	0.76	0.945	0.85	0.76	0.945	CLONAL	1	TRUE	1	0.34	2		406	699	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950052	44950052	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	82	481	0	ENST00000377967.4:c.3821C>T	p.Ser1274Phe	p.S1274F	ENST00000377967	NM_021140.2	1274	tCc/tTc	26/29	1	2	FACETS	0.577	0.508	0.651	0.577	0.508	0.651	SUBCLONAL	1	TRUE	1	0.34	2		481	836	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426781	47426781	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	91	314	0	ENST00000377045.4:c.1026G>T	p.Gln342His	p.Q342H	ENST00000377045	NM_001654.4	342	caG/caT	10/16	1	2	FACETS	0.931	0.828	1	0.931	0.828	1	CLONAL	1	TRUE	1	0.34	2		314	575	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429032	47429032	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	108	356	0	ENST00000377045.4:c.1395G>T	p.Gln465His	p.Q465H	ENST00000377045	NM_001654.4	465	caG/caT	13/16	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.34	2		356	601	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650577	48650577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	184	650	3	ENST00000376670.3:c.547G>A	p.Ala183Thr	p.A183T	ENST00000376670	NM_002049.3	183	Gca/Aca	3/6	1	2	FACETS	0.924	0.851	0.999	0.924	0.851	0.999	CLONAL	1	TRUE	1	0.34	2		653	1172	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227690	53227690	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	45	467	0	ENST00000375401.3:c.2498T>C	p.Val833Ala	p.V833A	ENST00000375401	NM_004187.3	833	gTc/gCc	17/26	1	2	FACETS	0.328	0.274	0.387	0.328	0.274	0.387	SUBCLONAL	1	TRUE	1	0.34	2		467	808	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411572	63411572	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	137	676	0	ENST00000330258.3:c.1595del	p.Ser532ThrfsTer9	p.S532Tfs*9	ENST00000330258	NM_152424.3	532	aGc/ac	2/2	1	2	FACETS	0.755	0.685	0.828	0.755	0.685	0.828	SUBCLONAL	1	TRUE	1	0.34	2		676	1068	SUCCESS
AR	367	MSKCC	GRCh37	X	66766152	66766152	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	66	378	0	ENST00000374690.3:c.1164G>T	p.Lys388Asn	p.K388N	ENST00000374690	NM_000044.3	388	aaG/aaT	1/8	1	2	FACETS	0.667	0.579	0.762	0.667	0.579	0.762	SUBCLONAL	1	TRUE	1	0.34	2		378	582	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937553	76937553	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	102	452	1	ENST00000373344.5:c.3195G>T	p.Glu1065Asp	p.E1065D	ENST00000373344	NM_000489.3	1065	gaG/gaT	9/35	1	2	FACETS	0.825	0.738	0.918	0.825	0.738	0.918	CLONAL	1	TRUE	1	0.34	2		453	727	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937744	76937745	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	146	456	0	ENST00000373344.5:c.3003dup	p.Val1002SerfsTer3	p.V1002Sfs*3	ENST00000373344	NM_000489.3	1001	-/A	9/35	1	2	FACETS	0.995	0.908	1	0.995	0.908	1	CLONAL	1	TRUE	1	0.34	2		456	863	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617189	100617189	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	89	517	1	ENST00000308731.7:c.560C>A	p.Pro187His	p.P187H	ENST00000308731	NM_000061.2	187	cCt/cAt	7/19	1	2	FACETS	0.506	0.448	0.569	0.506	0.448	0.569	SUBCLONAL	1	TRUE	1	0.34	2		518	1034	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020189	123020189	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	192	515	0	ENST00000355640.3:c.677A>T	p.Asn226Ile	p.N226I	ENST00000355640		226	aAt/aTt	2/7	1	2	FACETS	0.998	0.922	1	0.998	0.922	1	CLONAL	1	TRUE	1	0.34	2		515	1132	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224482	123224482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	92	684	0	ENST00000218089.9:c.3335C>T	p.Thr1112Ile	p.T1112I	ENST00000218089	NM_001042749.1	1112	aCc/aTc	31/35	1	2	FACETS	0.476	0.422	0.535	0.476	0.422	0.535	SUBCLONAL	1	TRUE	1	0.34	2		684	1136	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504047	123504047	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	102	399	0	ENST00000371139.4:c.223A>G	p.Arg75Gly	p.R75G	ENST00000371139	NM_001114937.2	75	Aga/Gga	3/4	1	2	FACETS	0.819	0.732	0.91	0.819	0.732	0.91	CLONAL	1	TRUE	1	0.34	2		399	733	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152853850	152853850	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	78	239	0	ENST00000406277.2:c.714T>G	p.Ile238Met	p.I238M	ENST00000406277	NM_152274.4	238	atT/atG	7/7	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.34	2		239	450	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861487	152861487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1188961308	NA	P-0018616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	77	302	0	ENST00000406277.2:c.265C>T	p.Arg89Cys	p.R89C	ENST00000406277	NM_152274.4	89	Cgt/Tgt	4/7	1		FACETS		0.864	1				CLONAL	1	TRUE	1	0.34	2		302	462	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8497255	8497255	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	54	530	0	ENST00000356435.5:c.2336A>G	p.Asp779Gly	p.D779G	ENST00000356435		779	gAt/gGt	15/35	1	2	FACETS	0.84	0.714	0.978	0.84	0.714	0.978	CLONAL	1	TRUE	1	0.12	2		530	1072	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339182	87339182	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	68	537	0	ENST00000277120.3:c.766del	p.Ser256HisfsTer17	p.S256Hfs*17	ENST00000277120		255	aTt/at	8/19	1	2	FACETS	0.985	0.854	1	0.985	0.854	1	CLONAL	1	TRUE	1	0.12	2		537	1151	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692844	89692845	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0018626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	151	172	0	ENST00000371953.3:c.328_329del	p.Gln110MetfsTer4	p.Q110Mfs*4	ENST00000371953	NM_000314.4	110	CAa/a	5/9	0.850654622462248	1	FACETS	0.981	0.93	1	0.981	0.93	1	CLONAL	1	TRUE	0	0.850819042310246	1		172	208	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41905096	41905096	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	320	367	0	ENST00000372991.4:c.451G>C	p.Asp151His	p.D151H	ENST00000372991	NM_001760.3	151	Gac/Cac	3/5	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.850819042310246	2		367	738	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0018627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	237	753	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.575441999940275	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.575441999940275	2		753	400	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0018627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	276	705	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	0.575441999940275	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.575441999940275	3		705	529	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060780	38060797	+	inframe_deletion	In_Frame_Del	DEL	GTTGATGGAGAACGGGTG	GTTGATGGAGAACGGGTG	-	novel	NA	P-0018627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	189	999	1	ENST00000250448.2:c.1192_1209del	p.His398_Asn403del	p.H398_N403del	ENST00000250448	NM_004496.3	398	CACCCGTTCTCCATCAAC/-	2/2	0.575441999940275	4	FACETS	0.908	0.845	0.973	0.908	0.845	0.973	CLONAL	2	TRUE	2	0.575441999940275	4		1000	570	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123875243	123875243	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	25	143	1	ENST00000330479.4:c.199C>T	p.Arg67Cys	p.R67C	ENST00000330479	NM_020382.3	67	Cgt/Tgt	3/9	0.575441999940275	3	FACETS	0.902	0.742	1	0.902	0.742	1	CLONAL	2	TRUE	1	0.575441999940275	3		144	62	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015171	71015179	+	frameshift_variant	Frame_Shift_Del	DEL	TAGTGTATA	TAGTGTATA	AT	novel	NA	P-0018627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	45	296	1	ENST00000318789.4:c.1751_1759delinsAT	p.Leu584HisfsTer13	p.L584Hfs*13	ENST00000318789	NM_032682.5	584	cTATACACTAcc/cATcc	20/21	0.545595817253031	1	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	0	0.575441999940275	1		297	106	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588956	67588967	+	inframe_deletion	In_Frame_Del	DEL	TACAGCAGACGG	TACAGCAGACGG	-	novel	NA	P-0018627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	58	308	0	ENST00000274335.5:c.1047_1058del	p.Asp349_Gly353delinsGlu	p.D349_G353delinsE	ENST00000274335		349	gaTACAGCAGACGGg/gag	8/15	0.550125103964915	2	FACETS	0.833	0.74	0.926	0.833	0.74	0.926	CLONAL	2	TRUE	0	0.575441999940275	2		308	121	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142966	47142966	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1559720382	NA	P-0018628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	238	639	0	ENST00000409792.3:c.4997A>G	p.Tyr1666Cys	p.Y1666C	ENST00000409792	NM_014159.6	1666	tAt/tGt	8/21	0.323801110338358	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.335776050858842	2		639	697	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191506	10191506	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs5030820	NA	P-0018628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	224	481	0	ENST00000256474.2:c.499C>G	p.Arg167Gly	p.R167G	ENST00000256474	NM_000551.3	167	Cgg/Ggg	3/3	0.323801110338358	2	FACETS	0.892	0.833	0.952	0.892	0.833	0.952	CLONAL	2	TRUE	0	0.335776050858842	2		481	748	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888166	81888166	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	142	507	0	ENST00000359376.3:c.311T>C	p.Phe104Ser	p.F104S	ENST00000359376	NM_002661.3	104	tTc/tCc	3/33	0.182716303174332	4	FACETS	1	0.93	1	0.513	0.467	0.562	INDETERMINATE	1	TRUE	2	0.335776050858842	4		507	1101	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731527	47731527	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	11	27	0	ENST00000449228.1:c.265G>T	p.Ala89Ser	p.A89S	ENST00000449228	NM_001127240.2	89	Gcc/Tcc	2/4	0.244383647495368	3	FACETS	1	0.781	1	0.571	0.402	0.772	CLONAL	1	TRUE	1	0.335776050858842	3		27	67	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620618	52620618	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	253	537	0	ENST00000394830.3:c.3135del	p.Phe1045LeufsTer89	p.F1045Lfs*89	ENST00000394830	NM_018313.4	1045	ttT/tt	21/30	0.323801110338358	2	FACETS	0.931	0.874	0.99	0.931	0.874	0.99	CLONAL	2	TRUE	0	0.335776050858842	2		537	809	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549832	187549832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371598532	NA	P-0018629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	59	421	0	ENST00000441802.2:c.4409C>T	p.Ala1470Val	p.A1470V	ENST00000441802	NM_005245.3	1470	gCg/gTg	8/27	0.43966781752014	1	FACETS	0.296	0.255	0.342	0.296	0.255	0.342	SUBCLONAL	1	TRUE	0	0.530080041616324	1		421	552	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444177	49444177	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0018629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	401	718	0	ENST00000301067.7:c.3194C>G	p.Ser1065Ter	p.S1065*	ENST00000301067	NM_003482.3	1065	tCa/tGa	11/54	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.530080041616324	2		718	1397	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222001	1222001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	251	449	0	ENST00000326873.7:c.916C>T	p.His306Tyr	p.H306Y	ENST00000326873	NM_000455.4	306	Cac/Tac	7/10	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.530080041616324	2		449	677	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3123	118	684	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.664826816380209	8	FACETS	0.328	0.294	0.365			1	SUBCLONAL	1	TRUE	NA	0.664826816380209	8		684	3241	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0018630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	508	667	1	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	NA	2	FACETS	0.943	0.913	0.974			1	INDETERMINATE	2	TRUE	NA	0.664826816380209	2		668	810	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545897	41545897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1215000818	NA	P-0018630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	511	841	2	ENST00000263253.7:c.2512C>T	p.Arg838Cys	p.R838C	ENST00000263253	NM_001429.3	838	Cgt/Tgt	14/31	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.664826816380209	2		843	1469	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695885	117695885	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	227	610	0	ENST00000369458.3:c.552A>C	p.Gln184His	p.Q184H	ENST00000369458	NM_024626.3	184	caA/caC	4/6	1	2	FACETS	0.694	0.647	0.743	0.694	0.647	0.743	SUBCLONAL	1	TRUE	1	0.664826816380209	2		610	984	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554615	29554616	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GATG	novel	NA	P-0018630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	784	503	0	ENST00000356175.3:c.2402_2405dup	p.Gln803TrpfsTer5	p.Q803Wfs*5	ENST00000356175	NM_000267.3	800	-/GATG	20/57	0.665507760837224	3	FACETS	0.915	0.893	0.937	0.915	0.893	0.937	CLONAL	3	TRUE	0	0.664826816380209	3		503	1145	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209117	36209117	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	21	34	0	ENST00000222270.7:c.197C>G	p.Ala66Gly	p.A66G	ENST00000222270	NM_014727.1	66	gCc/gGc	1/37	0.255474014142001	5	FACETS	1	0.811	1			1	INDETERMINATE	1	TRUE	NA	0.664826816380209	5		34	121	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200060	128200060	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	100	744	1	ENST00000341105.2:c.1245G>T	p.Glu415Asp	p.E415D	ENST00000341105	NM_032638.4	415	gaG/gaT	6/6	NA	2	FACETS	0.251	0.223	0.281			1	INDETERMINATE	1	TRUE	NA	0.664826816380209	2		745	1198	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957826	1957826	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767627490	NA	P-0018630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1182	226	583	0	ENST00000382891.5:c.2792C>T	p.Thr931Met	p.T931M	ENST00000382891	NM_133335.3	931	aCg/aTg	15/22	0.310029470278469	4	FACETS	0.804	0.747	0.863			1	INDETERMINATE	1	TRUE	NA	0.664826816380209	4		583	1408	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460411	8460411	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	165	332	0	ENST00000356435.5:c.3875G>T	p.Arg1292Met	p.R1292M	ENST00000356435		1292	aGg/aTg	22/35	0.651132606129476	2	FACETS	0.956	0.885	1	0.478	0.442	0.515	CLONAL	1	TRUE	0	0.664826816380209	2		332	519	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1319	155	797	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.876	0.799	0.957	0.876	0.799	0.957	CLONAL	1	TRUE	1	0.24	2		797	1474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	149	752	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.24	2		754	1202	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955112	17955112	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755706305	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1242	173	731	9	ENST00000458235.1:c.115del	p.Gln39SerfsTer108	p.Q39Sfs*108	ENST00000458235	NM_000215.3	39	Cag/ag	2/24	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.24	2		740	1415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1627	221	1034	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.997	0.924	1	0.997	0.924	1	CLONAL	1	TRUE	1	0.24	2		1035	1848	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263914	16263914	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369292765	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1531	212	912	3	ENST00000375759.3:c.10283C>T	p.Pro3428Leu	p.P3428L	ENST00000375759	NM_015001.2	3428	cCg/cTg	12/15	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.24	2		915	1743	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087503	27087503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1321	228	733	0	ENST00000324856.7:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000324856	NM_006015.4	693	Cga/Tga	5/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.24	2		733	1549	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163313649	163313649	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1231937327	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	37	323	0	ENST00000271452.3:c.800del	p.Asn267MetfsTer44	p.N267Mfs*44	ENST00000271452	NM_145697.2	266	Aaa/aa	10/14	1	2	FACETS	0.45	0.37	0.54	0.45	0.37	0.54	SUBCLONAL	1	TRUE	1	0.24	2		323	685	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	146	661	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.994	0.905	1	0.994	0.905	1	CLONAL	1	TRUE	1	0.24	2		661	1224	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161406	2161406	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1279	189	647	0	ENST00000434045.2:c.121G>T	p.Gly41Cys	p.G41C	ENST00000434045	NM_001127598.1	41	Ggc/Tgc	2/5	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.24	2		647	1468	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572284	64572284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775922507	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	139	481	1	ENST00000312049.6:c.1355G>A	p.Arg452Gln	p.R452Q	ENST00000312049	NM_130799.2	452	cGg/cAg	10/10	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.24	2		482	1118	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577250	64577250	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	70	584	0	ENST00000312049.6:c.332del	p.Gly111ValfsTer8	p.G111Vfs*8	ENST00000312049	NM_130799.2	111	gGt/gt	2/10	1	2	FACETS	0.47	0.408	0.537	0.47	0.408	0.537	SUBCLONAL	1	TRUE	1	0.24	2		584	1242	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939414	71939414	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762663532	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1357	75	678	1	ENST00000298229.2:c.269G>A	p.Arg90His	p.R90H	ENST00000298229	NM_001567.3	90	cGc/cAc	3/28	1	2	FACETS	0.436	0.381	0.497	0.436	0.381	0.497	SUBCLONAL	1	TRUE	1	0.24	2		679	1432	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940983	71940983	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1470	225	876	3	ENST00000298229.2:c.859C>T	p.Gln287Ter	p.Q287*	ENST00000298229	NM_001567.3	287	Cag/Tag	8/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.24	2		879	1695	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	81	863	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.53	0.465	0.6	0.53	0.465	0.6	SUBCLONAL	1	TRUE	1	0.24	2		865	1274	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360946	118360946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1388016179	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	54	507	0	ENST00000534358.1:c.4678G>A	p.Ala1560Thr	p.A1560T	ENST00000534358	NM_005933.3	1560	Gcc/Acc	13/36	1	2	FACETS	0.479	0.407	0.557	0.479	0.407	0.557	SUBCLONAL	1	TRUE	1	0.24	2		507	940	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155710	119155710	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	59	603	0	ENST00000264033.4:c.1466del	p.Pro489HisfsTer126	p.P489Hfs*126	ENST00000264033	NM_005188.3	488	gCc/gc	10/16	1	2	FACETS	0.424	0.363	0.491	0.424	0.363	0.491	SUBCLONAL	1	TRUE	1	0.24	2		603	1159	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420075	49420075	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	111	495	1	ENST00000301067.7:c.15674G>A	p.Arg5225His	p.R5225H	ENST00000301067	NM_003482.3	5225	cGc/cAc	48/54	1	2	FACETS	0.799	0.716	0.887	0.799	0.716	0.887	SUBCLONAL	1	TRUE	1	0.24	2		496	1158	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1306	116	843	0	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	1	2	FACETS	0.68	0.61	0.754	0.68	0.61	0.754	SUBCLONAL	1	TRUE	1	0.24	2		843	1422	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233239	69233240	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	101	347	0	ENST00000462284.1:c.1111dup	p.Thr371AsnfsTer5	p.T371Nfs*5	ENST00000462284	NM_002392.5	368	-/A	11/11	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.24	2		347	819	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244132	133244132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746774432	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	146	520	0	ENST00000320574.5:c.2276G>A	p.Arg759His	p.R759H	ENST00000320574	NM_006231.2	759	cGt/cAt	20/49	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.24	2		520	1027	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110684	2110684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140910086	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1339	175	690	1	ENST00000219476.3:c.989C>T	p.Pro330Leu	p.P330L	ENST00000219476	NM_000548.3	330	cCg/cTg	11/42	1	2	FACETS	0.963	0.884	1	0.963	0.884	1	CLONAL	1	TRUE	1	0.24	2		691	1514	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632413	3632413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1312542823	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1381	164	787	0	ENST00000294008.3:c.5435C>T	p.Ala1812Val	p.A1812V	ENST00000294008	NM_032444.2	1812	gCc/gTc	15/15	1	2	FACETS	0.885	0.809	0.964	0.885	0.809	0.964	CLONAL	1	TRUE	1	0.24	2		787	1545	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826512	50826512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	109	444	1	ENST00000398568.2:c.2237C>T	p.Pro746Leu	p.P746L	ENST00000398568	NM_001042412.1	746	cCa/cTa	15/18	1	2	FACETS	0.885	0.793	0.983	0.885	0.793	0.983	CLONAL	1	TRUE	1	0.24	2		445	1026	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984559	72984559	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770062973	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	171	664	4	ENST00000268489.5:c.3025G>A	p.Val1009Met	p.V1009M	ENST00000268489	NM_006885.3	1009	Gtg/Atg	3/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.24	2		668	1217	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127444	17127444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1289872207	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1343	170	568	2	ENST00000285071.4:c.410G>A	p.Arg137His	p.R137H	ENST00000285071	NM_144997.5	137	cGt/cAt	6/14	0.3	3	FACETS	1	0.949	1			1	CLONAL	1	TRUE	NA	0.24	3		570	1513	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29497004	29497004	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781670	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	79	305	1	ENST00000356175.3:c.575G>A	p.Arg192Gln	p.R192Q	ENST00000356175	NM_000267.3	192	cGa/cAa	5/57	1	2	FACETS	0.967	0.85	1	0.967	0.85	1	CLONAL	1	TRUE	1	0.24	2		306	681	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686962	37686962	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	129	528	0	ENST00000447079.4:c.3871del	p.Gln1291ArgfsTer3	p.Q1291Rfs*3	ENST00000447079	NM_015083.1	1289	gCc/gc	14/14	1	2	FACETS	0.926	0.838	1	0.926	0.838	1	CLONAL	1	TRUE	1	0.24	2		528	1161	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	149	779	2	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.915	0.833	1	0.915	0.833	1	CLONAL	1	TRUE	1	0.24	2		781	1357	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40458293	40458293	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	78	678	0	ENST00000345506.4:c.1508T>G	p.Leu503Arg	p.L503R	ENST00000345506	NM_003152.3	503	cTg/cGg	14/20	1	2	FACETS	0.52	0.455	0.59	0.52	0.455	0.59	SUBCLONAL	1	TRUE	1	0.24	2		678	1250	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134230	11134230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1227826852	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1221	196	694	1	ENST00000358026.2:c.2896C>T	p.Arg966Trp	p.R966W	ENST00000358026	NM_001128849.1	966	Cgg/Tgg	20/36	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.24	2		695	1417	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18960907	18960907	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	95	619	0	ENST00000262803.5:c.485G>T	p.Arg162Met	p.R162M	ENST00000262803	NM_002911.3	162	aGg/aTg	4/24	1	2	FACETS	0.611	0.542	0.685	0.611	0.542	0.685	SUBCLONAL	1	TRUE	1	0.24	2		619	1295	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	116	449	0	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.24	2		449	835	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037144	71037144	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	97	314	0	ENST00000318789.4:c.1146+1G>A		p.X382_splice	ENST00000318789	NM_032682.5	382			1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.24	2		314	737	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282704	1282704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760352197	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1307	144	651	2	ENST00000310581.5:c.1609C>T	p.Arg537Cys	p.R537C	ENST00000310581	NM_198253.2	537	Cgt/Tgt	3/16	1	2	FACETS	0.827	0.752	0.907	0.827	0.752	0.907	CLONAL	1	TRUE	1	0.24	2		653	1451	SUCCESS
APC	324	MSKCC	GRCh37	5	112179453	112179453	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780606	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	114	471	1	ENST00000257430.4:c.8162G>A	p.Arg2721His	p.R2721H	ENST00000257430	NM_000038.5	2721	cGc/cAc	16/16	1	2	FACETS	0.925	0.831	1	0.925	0.831	1	CLONAL	1	TRUE	1	0.24	2		472	1027	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6438342	6438342	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764885567	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1392	165	677	0	ENST00000356142.4:c.275C>T	p.Pro92Leu	p.P92L	ENST00000356142	NM_018890.3	92	cCg/cTg	4/7	1	2	FACETS	0.883	0.808	0.962	0.883	0.808	0.962	CLONAL	1	TRUE	1	0.24	2		677	1557	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729843	41729843	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138819536	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	71	361	0	ENST00000242208.4:c.686G>A	p.Arg229Gln	p.R229Q	ENST00000242208	NM_002192.2	229	cGg/cAg	3/3	1	2	FACETS	0.892	0.779	1	0.892	0.779	1	CLONAL	1	TRUE	1	0.24	2		361	663	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508835	106508835	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	82	411	0	ENST00000359195.3:c.829C>T	p.Arg277Trp	p.R277W	ENST00000359195	NM_002649.2	277	Cgg/Tgg	2/11	1	2	FACETS	0.823	0.725	0.929	0.823	0.725	0.929	CLONAL	1	TRUE	1	0.24	2		411	830	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863054	56863054	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1266824391	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1473	174	1009	1	ENST00000519728.1:c.327del	p.Glu110LysfsTer15	p.E110Kfs*15	ENST00000519728	NM_002350.3	107	acA/ac	5/13	1	2	FACETS	0.88	0.807	0.957	0.88	0.807	0.957	CLONAL	1	TRUE	1	0.24	2		1010	1647	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5066768	5066768	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	55	308	0	ENST00000381652.3:c.1310del	p.Leu437Ter	p.L437*	ENST00000381652	NM_004972.3	435	taT/ta	10/25	0.3	2	FACETS	1	0.9	1			1	CLONAL	1	TRUE	NA	0.24	2		308	431	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249393	110249393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747114701	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1646	244	953	2	ENST00000374672.4:c.1180G>A	p.Ala394Thr	p.A394T	ENST00000374672	NM_004235.4	394	Gcc/Acc	4/5	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.24	2		955	1890	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	140	337	0	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	1	FACETS	0.75	0.685	0.819	1	0.987	1	SUBCLONAL	2	TRUE	0	0.24	1		337	684	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652396	48652397	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	180	415	0	ENST00000376670.3:c.1073dup	p.Gly359ArgfsTer19	p.G359Rfs*19	ENST00000376670	NM_002049.3	356	ggc/ggCc	6/6	1	1	FACETS	0.752	0.694	0.812	1	0.99	1	SUBCLONAL	2	TRUE	0	0.24	1		415	878	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	129	310	2	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	1	1	FACETS	0.768	0.698	0.841	1	0.986	1	SUBCLONAL	2	TRUE	0	0.24	1		312	616	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356452	70356454	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0018631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	212	444	0	ENST00000374080.3:c.5353_5355del	p.Lys1785del	p.K1785del	ENST00000374080		1783	AAG/-	37/45	1	1	FACETS	0.78	0.724	0.837	1	0.992	1	SUBCLONAL	2	TRUE	0	0.24	1		444	997	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0018632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	148	708	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.271084533061482	5	FACETS	0.925	0.845	1	0.463	0.422	0.505	CLONAL	2	FALSE	1	0.271084533061482	5		709	830	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091797	29091797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780168	NA	P-0018632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	62	586	0	ENST00000328354.6:c.1160C>T	p.Thr387Ile	p.T387I	ENST00000328354	NM_007194.3	387	aCc/aTc	11/15	1	2	FACETS	0.55	0.474	0.634	0.55	0.474	0.634	SUBCLONAL	1	FALSE	1	0.271084533061482	2		586	831	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855010	76855010	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	35	297	0	ENST00000373344.5:c.5826C>G	p.Ser1942Arg	p.S1942R	ENST00000373344	NM_000489.3	1942	agC/agG	25/35	1	1	FACETS	0.681	0.559	0.816	0.681	0.559	0.816	SUBCLONAL	1	FALSE	0	0.271084533061482	1		297	328	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0018633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	508	583	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.794302509505937	2		583	1238	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0018633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	246	627	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	0.499	0.466	0.534	0.499	0.466	0.534	SUBCLONAL	1	TRUE	1	0.794302509505937	2		627	1241	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438542	52438542	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	490	562	0	ENST00000460680.1:c.1177C>T	p.Gln393Ter	p.Q393*	ENST00000460680	NM_004656.3	393	Cag/Tag	12/17	0.794302509505937	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.794302509505937	1		562	741	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29422354	29422354	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018635-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	338	748	0	ENST00000356175.3:c.27G>A	p.Trp9Ter	p.W9*	ENST00000356175	NM_000267.3	9	tgG/tgA	1/57	0.613244265366142	1	FACETS	0.917	0.872	0.962	0.917	0.872	0.962	CLONAL	1	TRUE	0	0.627167328914745	1		748	807	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685229	86685245	+	frameshift_variant	Frame_Shift_Del	DEL	ACACTACAGAGCATTCT	ACACTACAGAGCATTCT	-	novel	NA	P-0018635-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	115	396	0	ENST00000274376.6:c.2946_2962del	p.Asp982GlufsTer7	p.D982Efs*7	ENST00000274376	NM_002890.2	982	gACACTACAGAGCATTCT/g	24/25	1	2	FACETS	0.581	0.524	0.641	0.581	0.524	0.641	SUBCLONAL	1	TRUE	1	0.627167328914745	2		396	631	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0018638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	44	815	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.61	0.511	0.721	0.61	0.511	0.721	SUBCLONAL	1	TRUE	1	0.248983566530134	2		815	579	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0018638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	61	441	0	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	1	2	FACETS	0.855	0.738	0.983	0.855	0.738	0.983	CLONAL	1	TRUE	1	0.248983566530134	2		441	573	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732969	30732969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893810	NA	P-0018638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	82	235	0	ENST00000295754.5:c.1582C>T	p.Arg528Cys	p.R528C	ENST00000295754	NM_003242.5	528	Cgt/Tgt	7/7	0.212639548893039	2	FACETS	0.75	0.664	0.841	0.75	0.664	0.841	SUBCLONAL	2	TRUE	0	0.248983566530134	2		235	439	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958295	11958295	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	32	370	0	ENST00000353533.5:c.205C>T	p.Gln69Ter	p.Q69*	ENST00000353533	NM_003010.3	69	Caa/Taa	2/11	1	2	FACETS	0.772	0.628	0.934	0.772	0.628	0.934	CLONAL	1	TRUE	1	0.248983566530134	2		370	333	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986743	36986743	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	11	70	0	ENST00000354822.5:c.946G>A	p.Ala316Thr	p.A316T	ENST00000354822	NM_001079668.2	316	Gcg/Acg	3/3	1	2	FACETS	0.755	0.525	1	0.755	0.525	1	CLONAL	1	TRUE	1	0.248983566530134	2		70	117	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0018639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	81	636	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.218295157654212	1	FACETS	0.926	0.816	1	0.926	0.816	1	CLONAL	1	TRUE	0	0.229088195772724	1		636	676	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311619	15311621	+	inframe_deletion	In_Frame_Del	DEL	AGC	AGC	-	rs746497955	NA	P-0018639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	10	64	0	ENST00000263388.2:c.96_98del	p.Leu33del	p.L33del	ENST00000263388	NM_000435.2	32	ctGCTa/cta	1/33	1	2	FACETS	0.517	0.35	0.725	0.517	0.35	0.725	SUBCLONAL	1	TRUE	1	0.229088195772724	2		64	169	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453138	140453139	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTA	rs727502902	NA	P-0018639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	81	410	0	ENST00000288602.6:c.1794_1796dup	p.Thr599dup	p.T599dup	ENST00000288602	NM_004333.4	599	aca/acTACa	15/18	1	2	FACETS	0.703	0.618	0.795	0.703	0.618	0.795	SUBCLONAL	1	TRUE	1	0.229088195772724	2		410	1006	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983126	201983127	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	94	458	0	ENST00000359651.3:c.976dup	p.Tyr326LeufsTer145	p.Y326Lfs*145	ENST00000359651		325	-/T	7/8	1	2	FACETS	0.766	0.68	0.859	0.766	0.68	0.859	SUBCLONAL	1	TRUE	1	0.229088195772724	2		458	1071	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90992961	90992961	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs780470185	NA	P-0018639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	87	296	0	ENST00000265433.3:c.480+1G>A		p.X160_splice	ENST00000265433	NM_002485.4	160			1	2	FACETS	0.951	0.841	1	0.951	0.841	1	CLONAL	1	TRUE	1	0.229088195772724	2		296	799	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0018640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	19	715	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.103	0.078	0.134	0.103	0.078	0.134	SUBCLONAL	1	TRUE	1	0.423129521342996	2		717	869	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100402	8100403	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0018640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	211	587	1	ENST00000346208.3:c.380dup	p.Pro129AlafsTer174	p.P129Afs*174	ENST00000346208		126	tcc/tCcc	3/6	1	2	FACETS	0.969	0.9	1	0.969	0.9	1	CLONAL	1	TRUE	1	0.423129521342996	2		588	1029	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168741	56168744	+	frameshift_variant	Frame_Shift_Del	DEL	GAAG	GAAG	-	novel	NA	P-0018640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	166	363	0	ENST00000399503.3:c.1598_1601del	p.Arg533IlefsTer23	p.R533Ifs*23	ENST00000399503	NM_005921.1	532	cGAAGg/cg	9/20	1	2	FACETS	0.913	0.84	0.99	0.913	0.84	0.99	CLONAL	1	TRUE	1	0.423129521342996	2		363	859	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155733	56155734	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	A	novel	NA	P-0018640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	117	282	0	ENST00000399503.3:c.825_826delinsA	p.Pro276GlnfsTer36	p.P276Qfs*36	ENST00000399503	NM_005921.1	275	tcCCca/tcAca	3/20	1	2	FACETS	0.91	0.822	1	0.91	0.822	1	CLONAL	1	TRUE	1	0.423129521342996	2		282	608	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0018641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	108	636	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.103412890307815	3	FACETS	1	0.978	1	0.668	0.599	0.74	INDETERMINATE	1	TRUE	1	0.25	3		636	728	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0018641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	48	749	1	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	0.48	0.404	0.564	0.48	0.404	0.564	SUBCLONAL	1	TRUE	1	0.25	2		750	800	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359692	40359692	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201246187	NA	P-0018641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	48	561	0	ENST00000293328.3:c.1961G>A	p.Arg654Gln	p.R654Q	ENST00000293328	NM_012448.3	654	cGg/cAg	16/19	1	2	FACETS	0.462	0.389	0.543	0.462	0.389	0.543	SUBCLONAL	1	TRUE	1	0.25	2		561	831	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164901	123164901	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	30	312	1	ENST00000218089.9:c.214G>T	p.Gly72Cys	p.G72C	ENST00000218089	NM_001042749.1	72	Ggt/Tgt	5/35	1	2	FACETS	0.559	0.45	0.683	0.559	0.45	0.683	SUBCLONAL	1	TRUE	1	0.25	2		313	429	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	483	917	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.528778595607185	3	FACETS	0.889	0.851	0.927	0.889	0.851	0.927	CLONAL	2	TRUE	1	0.558994126307	3		917	1244	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610243	10610243	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	286	665	0	ENST00000171111.5:c.467T>C	p.Met156Thr	p.M156T	ENST00000171111	NM_203500.1	156	aTg/aCg	2/6	0.503069162087868	1	FACETS	0.783	0.737	0.829	0.783	0.737	0.829	SUBCLONAL	1	TRUE	0	0.558994126307	1		665	942	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11552822	NA	P-0018643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	176	278	0	ENST00000304494.5:c.250G>T	p.Asp84Tyr	p.D84Y	ENST00000304494	NM_000077.4	84	Gac/Tac	2/3	0.52007630711059	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.558994126307	1		278	428	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575209	48575209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767326	NA	P-0018643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	122	386	0	ENST00000342988.3:c.403C>T	p.Arg135Ter	p.R135*	ENST00000342988	NM_005359.5	135	Cga/Tga	3/12	0.558994126307	1	FACETS	0.567	0.514	0.622	0.567	0.514	0.622	SUBCLONAL	1	TRUE	0	0.558994126307	1		386	555	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs11575997	NA	P-0018643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	437	434	0	ENST00000269305.4:c.993+1G>T		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.520703511801365	2	FACETS	0.949	0.912	0.986	0.949	0.912	0.986	CLONAL	2	TRUE	0	0.558994126307	2		434	824	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210575	5210575	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1477121983	NA	P-0018643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	183	479	1	ENST00000357368.4:c.5392C>T	p.Arg1798Cys	p.R1798C	ENST00000357368	NM_002850.3	1798	Cgc/Tgc	35/38	0.501556620640447	2	FACETS	0.823	0.76	0.887	0.411	0.38	0.444	CLONAL	1	TRUE	0	0.558994126307	2		480	796	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121311	29121311	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	286	623	0	ENST00000328354.6:c.364G>C	p.Glu122Gln	p.E122Q	ENST00000328354	NM_007194.3	122	Gaa/Caa	3/15	0.520703511801365	2	FACETS	0.757	0.71	0.805	0.378	0.355	0.403	SUBCLONAL	1	TRUE	0	0.558994126307	2		623	1352	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982138	93982138	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	130	292	0	ENST00000369303.4:c.1327C>G	p.Pro443Ala	p.P443A	ENST00000369303	NM_004440.3	443	Ccc/Gcc	6/17	0.257596873471953	3	FACETS	0.918	0.835	1	0.306	0.278	0.336	INDETERMINATE	1	TRUE	0	0.558994126307	3		292	648	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0018644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	186	1181	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.944	0.871	1	0.944	0.871	1	CLONAL	1	TRUE	1	0.402266254060793	2		1182	980	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0018644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	250	1047	1	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.363054228645349	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.402266254060793	1		1048	930	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584763	48584763	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	102	565	0	ENST00000342988.3:c.842del	p.Pro281LeufsTer55	p.P281Lfs*55	ENST00000342988	NM_005359.5	281	Cct/ct	7/12	1	2	FACETS	0.45	0.401	0.502	0.45	0.401	0.502	SUBCLONAL	1	TRUE	1	0.402266254060793	2		565	1127	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368203	31368203	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	191	561	0	ENST00000328111.2:c.74G>A	p.Gly25Glu	p.G25E	ENST00000328111	NM_006892.3	25	gGg/gAg	2/23	0.402266254060793	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.402266254060793	1		561	713	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101693	71101693	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1220590443	NA	P-0018644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	35	208	0	ENST00000318789.4:c.505A>G	p.Lys169Glu	p.K169E	ENST00000318789	NM_032682.5	169	Aaa/Gaa	9/21	1	2	FACETS	0.364	0.298	0.438	0.364	0.298	0.438	SUBCLONAL	1	TRUE	1	0.402266254060793	2		208	478	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032564	47032564	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	222	554	0	ENST00000377604.3:c.472del	p.Glu158ArgfsTer4	p.E158Rfs*4	ENST00000377604	NM_001204468.1	157	cGg/cg	5/24	0.402266254060793	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.402266254060793	1		554	839	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0018645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	149	846	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.593378174098236	4	FACETS	1	0.984	1	0.662	0.607	0.718	CLONAL	1	TRUE	2	0.59464748350672	4		846	604	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619232	43619232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1384605415	NA	P-0018645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	151	560	0	ENST00000355710.3:c.2915G>A	p.Arg972Lys	p.R972K	ENST00000355710	NM_020975.4	972	aGg/aAg	17/20	0.484745676732558	4	FACETS	0.948	0.876	1			1	CLONAL	2	TRUE	NA	0.59464748350672	4		560	427	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446287	70446291	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	novel	NA	P-0018645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	119	744	0	ENST00000373644.4:c.5229_5233del	p.Lys1743AsnfsTer25	p.K1743Nfs*25	ENST00000373644	NM_030625.2	1743	AAAAGa/a	11/12	0.559463746719865	2	FACETS	0.92	0.837	1	0.46	0.418	0.504	CLONAL	1	TRUE	0	0.59464748350672	2		744	435	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426832	47426833	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0018645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	49	266	0	ENST00000377045.4:c.1076+2dup		p.X359_splice	ENST00000377045	NM_001654.4	359			0.436259896295919	4	FACETS	1	0.959	1	0.677	0.582	0.779	CLONAL	1	TRUE	2	0.59464748350672	4		266	194	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0018646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	85	393	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.832	0.746	0.923	0.832	0.746	0.923	CLONAL	1	FALSE	1	0.748073630991493	2		393	273	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	136	364	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	FALSE	1	0.748073630991493	2		365	359	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791828	42791828	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	34	698	0	ENST00000575354.2:c.714G>C	p.Trp238Cys	p.W238C	ENST00000575354	NM_015125.3	238	tgG/tgC	5/20	0.748073630991493	1	FACETS	0.106	0.086	0.128	0.106	0.086	0.128	SUBCLONAL	1	FALSE	0	0.748073630991493	1		698	538	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794052	42794061	+	frameshift_variant	Frame_Shift_Del	DEL	GACCGACAGC	GACCGACAGC	-	novel	NA	P-0018646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	40	546	0	ENST00000575354.2:c.1415_1424del	p.Thr472ArgfsTer24	p.T472Rfs*24	ENST00000575354	NM_015125.3	471	gtGACCGACAGC/gt	9/20	0.748073630991493	1	FACETS	0.126	0.104	0.15	0.126	0.104	0.15	SUBCLONAL	1	FALSE	0	0.748073630991493	1		546	533	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448276	56448276	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018646-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	44	680	2	ENST00000407977.2:c.371G>T	p.Ser124Ile	p.S124I	ENST00000407977		124	aGc/aTc	3/10	1	2	FACETS	0.193	0.161	0.228	0.193	0.161	0.228	SUBCLONAL	1	TRUE	1	0.572824352962802	2		682	797	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7132166	7132167	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	A	novel	NA	P-0018646-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	217	804	0	ENST00000302850.5:c.2842+2dup		p.X948_splice	ENST00000302850	NM_000208.2	948			1	2	FACETS	0.871	0.811	0.933	0.871	0.811	0.933	CLONAL	1	TRUE	1	0.572824352962802	2		804	870	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118633	11118635	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs765524239	NA	P-0018646-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	54	921	0	ENST00000358026.2:c.2066_2068del	p.Lys689del	p.K689del	ENST00000358026	NM_001128849.1	686	gAGAag/gag	14/36	1	2	FACETS	0.214	0.182	0.25	0.214	0.182	0.25	SUBCLONAL	1	TRUE	1	0.572824352962802	2		921	880	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141104	55141115	+	inframe_deletion	In_Frame_Del	DEL	TCAAGATGGGAG	TCAAGATGGGAG	-	novel	NA	P-0018646-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3203	178	464	0	ENST00000257290.5:c.1751_1762del	p.Ser584_Glu587del	p.S584_E587del	ENST00000257290	NM_006206.4	584	TCAAGATGGGAG/-	12/23	0.572824352962802	18	FACETS	1	0.936	1	0.06	0.055	0.066	CLONAL	1	TRUE	1	0.572824352962802	18		464	3381	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112767362	112767362	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	117	413	0	ENST00000369452.4:c.1235A>G	p.Asn412Ser	p.N412S	ENST00000369452	NM_007373.3	412	aAt/aGt	6/9	1	2	FACETS	0.478	0.432	0.527	0.478	0.432	0.527	SUBCLONAL	1	TRUE	1	0.774626983968212	2		413	632	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911168	32911168	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs879254111	NA	P-0018647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	255	418	0	ENST00000380152.3:c.2677del	p.Gln893LysfsTer2	p.Q893Kfs*2	ENST00000380152		892	ttC/tt	11/27	0.774626983968212	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.774626983968212	1		418	399	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916840	48916841	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs1566186125	NA	P-0018647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	200	306	0	ENST00000267163.4:c.371_372del	p.Ile124ArgfsTer6	p.I124Rfs*6	ENST00000267163	NM_000321.2	124	ATa/a	3/27	0.774626983968212	1	FACETS	0.881	0.832	0.93	0.881	0.832	0.93	CLONAL	1	TRUE	0	0.774626983968212	1		306	359	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031361	11031361	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	714	589	0	ENST00000327064.4:c.1363del	p.Gln455ArgfsTer15	p.Q455Rfs*15	ENST00000327064	NM_199141.1	454	gCc/gc	12/16	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.774626983968212	2		589	1731	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538322	9538332	+	frameshift_variant	Frame_Shift_Del	DEL	AGGTAGGAGAG	AGGTAGGAGAG	-	novel	NA	P-0018647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	229	353	0	ENST00000353224.5:c.1666_1676del	p.Leu556SerfsTer2	p.L556Sfs*2	ENST00000353224	NM_177990.2	556	CTCTCCTACCTt/t	7/10	1	2	FACETS	0.823	0.771	0.877	0.823	0.771	0.877	CLONAL	1	TRUE	1	0.774626983968212	2		353	718	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960107	134960107	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	380	438	0	ENST00000398015.3:c.2464G>C	p.Glu822Gln	p.E822Q	ENST00000398015	NM_004441.4	822	Gag/Cag	13/16	1	2	FACETS	0.937	0.892	0.983	0.937	0.892	0.983	CLONAL	1	TRUE	1	0.774626983968212	2		438	1047	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403480	138403480	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	131	319	0	ENST00000289153.2:c.2302C>G	p.Leu768Val	p.L768V	ENST00000289153	NM_006219.2	768	Ctc/Gtc	15/22	1	2	FACETS	0.483	0.439	0.53	0.483	0.439	0.53	SUBCLONAL	1	TRUE	1	0.774626983968212	2		319	700	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589620	67589640	+	inframe_deletion	In_Frame_Del	DEL	AGAATATGATAGATTATATGA	AGAATATGATAGATTATATGA	-	novel	NA	P-0018647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	72	342	0	ENST00000274335.5:c.1390_1410del	p.Asp464_Tyr470del	p.D464_Y470del	ENST00000274335		461	cgAGAATATGATAGATTATATGAa/cga	10/15	0.774626983968212	1	FACETS	0.292	0.256	0.33	0.292	0.256	0.33	SUBCLONAL	1	TRUE	0	0.774626983968212	1		342	390	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117645532	117645538	+	frameshift_variant	Frame_Shift_Del	DEL	AACTATA	AACTATA	-	novel	NA	P-0018647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	233	419	0	ENST00000368508.3:c.5598_5604del	p.Ile1866MetfsTer11	p.I1866Mfs*11	ENST00000368508	NM_002944.2	1866	atTATAGTT/at	34/43	1	2	FACETS	0.94	0.882	0.999	0.94	0.882	0.999	CLONAL	1	TRUE	1	0.774626983968212	2		419	640	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211880	123211880	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	144	470	0	ENST00000218089.9:c.2747C>G	p.Ala916Gly	p.A916G	ENST00000218089	NM_001042749.1	916	gCt/gGt	27/35	NA	2	FACETS	0.377	0.343	0.413			1	INDETERMINATE	1	TRUE	NA	0.774626983968212	2		470	986	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579473	7579477	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGA	GGGGA	AGG	novel	NA	P-0018647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	502	503	0	ENST00000269305.4:c.210_214delinsCCT	p.Pro71LeufsTer77	p.P71Lfs*77	ENST00000269305	NM_001126112.2	70	gcTCCCCcc/gcCCTcc	4/11	0.774626983968212	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.774626983968212	1		503	750	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0018648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	167	708	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.183560457623209	3	FACETS	0.861	0.789	0.935	0.861	0.789	0.935	CLONAL	2	TRUE	1	0.183560457623209	3		709	1154	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1241	104	609	0	ENST00000269305.4:c.380C>A	p.Ser127Tyr	p.S127Y	ENST00000269305	NM_001126112.2	127	tCc/tAc	5/11	0.183560457623209	1	FACETS	0.765	0.683	0.853	0.765	0.683	0.853	SUBCLONAL	1	TRUE	0	0.183560457623209	1		609	1345	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165518	47165519	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0018648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	38	255	0	ENST00000409792.3:c.607_608del	p.Ser203IlefsTer33	p.S203Ifs*33	ENST00000409792	NM_014159.6	203	TCa/a	3/21	1	2	FACETS	0.729	0.602	0.872	0.729	0.602	0.872	SUBCLONAL	1	TRUE	1	0.183560457623209	2		255	568	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650278	48650278	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	210	541	0	ENST00000376670.3:c.248G>C	p.Cys83Ser	p.C83S	ENST00000376670	NM_002049.3	83	tGt/tCt	3/6	0.183560457623209	4	FACETS	1	0.962	1			1	CLONAL	2	TRUE	NA	0.183560457623209	4		541	1278	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	24	609	0	ENST00000269305.4:c.380C>A	p.Ser127Tyr	p.S127Y	ENST00000269305	NM_001126112.2	127	tCc/tAc	5/11	0.208075565520155	3	FACETS	0.227	0.177	0.285	0.113	0.088	0.143	SUBCLONAL	1	TRUE	1	0.31	3		609	788	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870966	12870966	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	80	416	0	ENST00000228872.4:c.193C>T	p.Gln65Ter	p.Q65*	ENST00000228872	NM_004064.3	65	Cag/Tag	1/3	0.334875299131059	3	FACETS	0.793	0.698	0.896	0.397	0.349	0.448	SUBCLONAL	1	TRUE	1	0.334875299131059	3		416	703	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0018650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	406	574	9	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.552202005264662	4	FACETS	0.854	0.819	0.888	0.854	0.819	0.888	CLONAL	3	TRUE	1	0.695460972998108	4		583	773	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	203	681	0	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	0.695460972998108	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.695460972998108	1		681	355	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0018651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	311	715	2	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	0.587460254624294	2		717	1003	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0018651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	325	900	1	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	TRUE	1	0.587460254624294	2		901	1081	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0018651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	357	761	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.587460254624294	1	FACETS	0.996	0.948	1	0.996	0.948	1	CLONAL	1	TRUE	0	0.587460254624294	1		762	862	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800850	120800850	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1216	526	1028	0	ENST00000257552.2:c.398G>T	p.Gly133Val	p.G133V	ENST00000257552	NM_002442.3	133	gGg/gTg	6/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.587460254624294	2		1028	1742	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438267	56438268	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0018651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	301	602	0	ENST00000407977.2:c.725_726del	p.Gln242ProfsTer16	p.Q242Pfs*16	ENST00000407977		242	cAG/c	7/10	0.587460254624294	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.587460254624294	1		602	623	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0018652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	1350	862	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.601974665484886	2		862	2159	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662482	227662482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	250	372	0	ENST00000305123.5:c.973C>T	p.Arg325Cys	p.R325C	ENST00000305123	NM_005544.2	325	Cgt/Tgt	1/2	NA	2	FACETS	1	0.957	1			1	INDETERMINATE	1	TRUE	NA	0.601974665484886	2		372	811	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420314	49420314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	452	601	0	ENST00000301067.7:c.15435del	p.Glu5145AspfsTer2	p.E5145Dfs*2	ENST00000301067	NM_003482.3	5145	gaG/ga	48/54	1	2	FACETS	0.966	0.921	1	0.966	0.921	1	CLONAL	1	TRUE	1	0.601974665484886	2		601	1554	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022509	31022509	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	202	306	0	ENST00000375687.4:c.1994del	p.Ser665MetfsTer38	p.S665Mfs*38	ENST00000375687	NM_015338.5	665	aGt/at	13/13	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.601974665484886	2		306	664	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960098	151960099	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	A	novel	NA	P-0018652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	388	550	0	ENST00000262189.6:c.1299+2dup		p.X433_splice	ENST00000262189	NM_170606.2	433			1	2	FACETS	0.884	0.839	0.93	0.884	0.839	0.93	CLONAL	1	TRUE	1	0.601974665484886	2		550	1458	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023008	27023010	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs587779737	NA	P-0018654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	10	103	0	ENST00000324856.7:c.126_128del	p.Ala45del	p.A45del	ENST00000324856	NM_006015.4	38	gaGGCg/gag	1/20	1	2	FACETS	0.44	0.3	0.614	0.44	0.3	0.614	SUBCLONAL	1	TRUE	1	0.388313743435602	2		103	117	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578226	7578226	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1464727668	NA	P-0018654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	155	676	0	ENST00000269305.4:c.623A>T	p.Asp208Val	p.D208V	ENST00000269305	NM_001126112.2	208	gAc/gTc	6/11	0.388313743435602	1	FACETS	0.813	0.745	0.884	0.813	0.745	0.884	CLONAL	1	TRUE	0	0.388313743435602	1		676	791	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154836	2154836	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	166	656	0	ENST00000434045.2:c.385C>A	p.Arg129Ser	p.R129S	ENST00000434045	NM_001127598.1	129	Cgc/Agc	4/5	0.388313743435602	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.388313743435602	1		656	648	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491385	18491385	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	79	460	0	ENST00000266497.5:c.1298A>C	p.Glu433Ala	p.E433A	ENST00000266497		433	gAa/gCa	8/31	1	2	FACETS	0.592	0.521	0.669	0.592	0.521	0.669	SUBCLONAL	1	TRUE	1	0.388313743435602	2		460	687	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989108	41989108	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0018654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	112	601	0	ENST00000219905.7:c.1900A>T	p.Lys634Ter	p.K634*	ENST00000219905	NM_001164273.1	634	Aag/Tag	3/24	0.388313743435602	1	FACETS	0.646	0.581	0.714	0.646	0.581	0.714	SUBCLONAL	1	TRUE	0	0.388313743435602	1		601	720	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007496	45007646	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAATGGAATTGGGAGAAATCGATGACCAAATGTAAACACTTGGTGCCTGATATAGCTTGACACCAAGTTAGCCCCAAGTGAAATACCCTGGCAATATTAATGTGTCTTTTCCCGATATTCCTCAGGTACTCCAAAGATTCAGGTTTACTCA	AAATGGAATTGGGAGAAATCGATGACCAAATGTAAACACTTGGTGCCTGATATAGCTTGACACCAAGTTAGCCCCAAGTGAAATACCCTGGCAATATTAATGTGTCTTTTCCCGATATTCCTCAGGTACTCCAAAGATTCAGGTTTACTCA	-	novel	NA	P-0018654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	10	24	0	ENST00000558401.1:c.68-125_93del		p.X23_splice	ENST00000558401	NM_004048.2	23		2/4	0.388313743435602	1	FACETS	1	0.787	1	1	0.787	1	CLONAL	1	TRUE	0	0.388313743435602	1		24	36	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670457	88670457	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	83	375	0	ENST00000360948.2:c.1229T>A	p.Phe410Tyr	p.F410Y	ENST00000360948	NM_001012338.2	410	tTt/tAt	11/19	0.388313743435602	1	FACETS	0.757	0.671	0.849	0.757	0.671	0.849	SUBCLONAL	1	TRUE	0	0.388313743435602	1		375	455	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934504	9934504	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	rs1555494671	NA	P-0018654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	100	484	0	ENST00000330684.3:c.1651G>T	p.Glu551Ter	p.E551*	ENST00000330684	NM_001134407.1	551	Gaa/Taa	7/13	0.309430846825892	1	FACETS	0.717	0.642	0.796	0.717	0.642	0.796	SUBCLONAL	1	TRUE	0	0.388313743435602	1		484	579	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128306	30128306	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	106	604	2	ENST00000263025.4:c.926G>C	p.Arg309Pro	p.R309P	ENST00000263025	NM_002746.2	309	cGg/cCg	7/9	0.368522158033363	1	FACETS	0.595	0.534	0.661	0.595	0.534	0.661	SUBCLONAL	1	TRUE	0	0.388313743435602	1		606	739	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007659	62007659	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	141	514	0	ENST00000392795.3:c.208A>T	p.Ser70Cys	p.S70C	ENST00000392795	NM_001039933.1	70	Agc/Tgc	3/6	0.180835766375927	5	FACETS	0.796	0.726	0.869	0.531	0.484	0.579	INDETERMINATE	2	TRUE	2	0.388313743435602	5		514	722	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133787	55133787	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	141	544	0	ENST00000257290.5:c.1000C>A	p.His334Asn	p.H334N	ENST00000257290	NM_006206.4	334	Cat/Aat	7/23	0.388313743435602	1	FACETS	0.867	0.792	0.946	0.867	0.792	0.946	CLONAL	1	TRUE	0	0.388313743435602	1		544	675	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542692	187542692	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	123	472	3	ENST00000441802.2:c.5048G>A	p.Gly1683Glu	p.G1683E	ENST00000441802	NM_005245.3	1683	gGg/gAg	10/27	1	2	FACETS	0.84	0.76	0.924	0.84	0.76	0.924	CLONAL	1	TRUE	1	0.388313743435602	2		475	754	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629874	187629874	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	190	690	0	ENST00000441802.2:c.1108G>T	p.Asp370Tyr	p.D370Y	ENST00000441802	NM_005245.3	370	Gat/Tat	2/27	1	2	FACETS	0.884	0.816	0.955	0.884	0.816	0.955	CLONAL	1	TRUE	1	0.388313743435602	2		690	1107	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30668376	30668376	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	123	579	0	ENST00000376406.3:c.6136T>A	p.Phe2046Ile	p.F2046I	ENST00000376406	NM_014641.2	2046	Ttc/Atc	15/15	0.295261531920273	3	FACETS	0.827	0.747	0.911	0.276	0.249	0.304	CLONAL	1	TRUE	0	0.388313743435602	3		579	915	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066636	94066636	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	353	572	1	ENST00000369303.4:c.1123G>T	p.Glu375Ter	p.E375*	ENST00000369303	NM_004440.3	375	Gag/Tag	5/17	0.295261531920273	3	FACETS	1	0.992	1	0.8	0.76	0.84	CLONAL	2	TRUE	0	0.388313743435602	3		573	905	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346560	81346560	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	171	462	1	ENST00000222390.5:c.1393C>A	p.Pro465Thr	p.P465T	ENST00000222390	NM_000601.4	465	Cct/Act	11/18	0.18428460648231	5	FACETS	0.884	0.815	0.957	0.59	0.543	0.638	INDETERMINATE	2	TRUE	2	0.388313743435602	5		463	788	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172948	38172948	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	54	559	1	ENST00000317025.8:c.2101G>T	p.Asp701Tyr	p.D701Y	ENST00000317025	NM_023034.1	701	Gac/Tac	11/24	0.388313743435602	1	FACETS	0.265	0.226	0.309	0.265	0.226	0.309	SUBCLONAL	1	TRUE	0	0.388313743435602	1		560	845	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27192514	27192514	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	56	541	0	ENST00000380036.4:c.1517A>C	p.Tyr506Ser	p.Y506S	ENST00000380036	NM_000459.3	506	tAt/tCt	11/23	1	2	FACETS	0.327	0.279	0.38	0.327	0.279	0.38	SUBCLONAL	1	TRUE	1	0.388313743435602	2		541	882	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229656	98229656	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	74	364	0	ENST00000331920.6:c.2302A>G	p.Thr768Ala	p.T768A	ENST00000331920	NM_000264.3	768	Acc/Gcc	15/24	1	2	FACETS	0.663	0.581	0.751	0.663	0.581	0.751	SUBCLONAL	1	TRUE	1	0.388313743435602	2		364	575	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626618	100626618	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	A	novel	NA	P-0018654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	140	215	0	ENST00000308731.7:c.309+3G>T		p.X103_splice	ENST00000308731	NM_000061.2	103			1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.388313743435602	1		215	405	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115717	8115718	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTATG	novel	NA	P-0018655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	370	635	0	ENST00000346208.3:c.1064_1068dup	p.Lys357LeufsTer2	p.K357Lfs*2	ENST00000346208		355	act/aCTATGct	6/6	1	2	FACETS	0.745	0.707	0.785	0.745	0.707	0.785	SUBCLONAL	1	TRUE	1	0.801172259604353	2		635	1239	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070611	67070612	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	286	333	0	ENST00000412916.2:c.238dup	p.Thr80AsnfsTer3	p.T80Nfs*3	ENST00000412916		79	caa/cAaa	3/6	0.801172259604353	1	FACETS	0.955	0.914	0.995	0.955	0.914	0.995	CLONAL	1	TRUE	0	0.801172259604353	1		333	448	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069333	30069333	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	318	645	1	ENST00000338641.4:c.1198C>T	p.Gln400Ter	p.Q400*	ENST00000338641	NM_000268.3	400	Cag/Tag	12/16	0.719584176406674	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.718368149365827	1		646	425	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17380450	17380450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141230910	NA	P-0018659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	91	668	2	ENST00000375499.3:c.65G>A	p.Cys22Tyr	p.C22Y	ENST00000375499	NM_003000.2	22	tGc/tAc	1/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.24	2		670	550	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828359	72828359	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1165213811	NA	P-0018659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	33	527	0	ENST00000268489.5:c.8222C>G	p.Ala2741Gly	p.A2741G	ENST00000268489	NM_006885.3	2741	gCt/gGt	9/10	1	2	FACETS	0.908	0.741	1	0.908	0.741	1	CLONAL	1	TRUE	1	0.24	2		527	303	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349146	89349146	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	98	1055	1	ENST00000301030.4:c.3804del	p.Lys1269SerfsTer49	p.K1269Sfs*49	ENST00000301030	NM_001256183.1	1268	agG/ag	9/13	0.142038540445542	0	FACETS	1	0.956	1			1	INDETERMINATE	1	TRUE	0	0.24	0		1056	550	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226238	2226243	+	inframe_deletion	In_Frame_Del	DEL	AAGTGG	AAGTGG	-	novel	NA	P-0018659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	77	890	0	ENST00000398665.3:c.3722_3727del	p.Trp1241_Lys1242del	p.W1241_K1242del	ENST00000398665	NM_032482.2	1240	AAGTGG/-	27/28	0.3	0	FACETS	1	0.96	1			1	CLONAL	1	TRUE	0	0.24	0		890	403	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677840	117677840	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	41	343	0	ENST00000368508.3:c.4093C>A	p.Leu1365Met	p.L1365M	ENST00000368508	NM_002944.2	1365	Ctg/Atg	25/43	0.227539149085605	0	FACETS	0.822	0.687	0.97			1	CLONAL	1	TRUE	0	0.24	0		343	316	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624399	140624422	+	inframe_deletion	In_Frame_Del	DEL	GGCCGCGGCGCCGGCGCCGGCGCC	GGCCGCGGCGCCGGCGCCGGCGCC	-	novel	NA	P-0018659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	107	258	0	ENST00000288602.6:c.82_105del	p.Gly28_Ala35del	p.G28_A35del	ENST00000288602	NM_004333.4	28	GGCGCCGGCGCCGGCGCCGCGGCC/-	1/18	0.26915691053111	3	FACETS	1	0.97	1	1	0.99	1	CLONAL	4	TRUE	1	0.24	3		258	222	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624403	140624403	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	12	95	0	ENST00000288602.6:c.101C>A	p.Ala34Glu	p.A34E	ENST00000288602	NM_004333.4	34	gCg/gAg	1/18	0.26915691053111	3	FACETS	0.549	0.386	0.749	0.275	0.193	0.375	SUBCLONAL	1	TRUE	1	0.24	3		95	204	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17380450	17380450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141230910	NA	P-0018659-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	225	668	2	ENST00000375499.3:c.65G>A	p.Cys22Tyr	p.C22Y	ENST00000375499	NM_003000.2	22	tGc/tAc	1/8	0.422591991993553	1	FACETS	0.678	0.635	0.722	0.678	0.635	0.722	SUBCLONAL	1	TRUE	0	0.676594826326241	1		670	649	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828359	72828359	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1165213811	NA	P-0018659-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	151	527	0	ENST00000268489.5:c.8222C>G	p.Ala2741Gly	p.A2741G	ENST00000268489	NM_006885.3	2741	gCt/gGt	9/10	1	2	FACETS	0.817	0.752	0.886	0.817	0.752	0.886	CLONAL	1	TRUE	1	0.676594826326241	2		527	546	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349146	89349146	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018659-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	349	1055	1	ENST00000301030.4:c.3804del	p.Lys1269SerfsTer49	p.K1269Sfs*49	ENST00000301030	NM_001256183.1	1268	agG/ag	9/13	1	2	FACETS	0.874	0.827	0.921	0.874	0.827	0.921	CLONAL	1	TRUE	1	0.676594826326241	2		1056	1181	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226238	2226243	+	inframe_deletion	In_Frame_Del	DEL	AAGTGG	AAGTGG	-	novel	NA	P-0018659-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	319	890	0	ENST00000398665.3:c.3722_3727del	p.Trp1241_Lys1242del	p.W1241_K1242del	ENST00000398665	NM_032482.2	1240	AAGTGG/-	27/28	0.676594826326241	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.676594826326241	1		890	618	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677840	117677840	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018659-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	135	343	0	ENST00000368508.3:c.4093C>A	p.Leu1365Met	p.L1365M	ENST00000368508	NM_002944.2	1365	Ctg/Atg	25/43	1	2	FACETS	0.998	0.916	1	0.998	0.916	1	CLONAL	1	TRUE	1	0.676594826326241	2		343	400	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624399	140624422	+	inframe_deletion	In_Frame_Del	DEL	GGCCGCGGCGCCGGCGCCGGCGCC	GGCCGCGGCGCCGGCGCCGGCGCC	-	novel	NA	P-0018659-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	403	258	0	ENST00000288602.6:c.82_105del	p.Gly28_Ala35del	p.G28_A35del	ENST00000288602	NM_004333.4	28	GGCGCCGGCGCCGGCGCCGCGGCC/-	1/18	0.676594826326241	3	FACETS	0.863	0.832	0.893	1	0.996	1	CLONAL	3	TRUE	1	0.676594826326241	3		258	616	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0018660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	128	610	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.484250930385073	2	FACETS	0.911	0.829	0.998	0.456	0.414	0.499	CLONAL	1	TRUE	0	0.484250930385073	2		610	580	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0018660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	517	1047	1	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.484250930385073	2		1048	953	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0018660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	101	192	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.172237731944607	3	FACETS	0.952	0.854	1	0.317	0.284	0.352	INDETERMINATE	1	TRUE	0	0.484250930385073	3		192	544	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602619	10602619	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1239985410	NA	P-0018660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	209	575	0	ENST00000171111.5:c.959G>T	p.Arg320Leu	p.R320L	ENST00000171111	NM_203500.1	320	cGg/cTg	3/6	0.484645106609272	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.484250930385073	1		575	512	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578181	226578181	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	94	534	0	ENST00000366794.5:c.547G>A	p.Gly183Ser	p.G183S	ENST00000366794	NM_001618.3	183	Ggc/Agc	4/23	0.172237731944607	3	FACETS	0.661	0.588	0.739	0.22	0.196	0.247	INDETERMINATE	1	TRUE	0	0.484250930385073	3		534	729	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711350	114711350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243981730	NA	P-0018660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	81	337	0	ENST00000543371.1:c.365C>T	p.Ser122Leu	p.S122L	ENST00000543371	NM_001198531.1	122	tCg/tTg	3/14	0.484645106609272	3	FACETS	0.757	0.668	0.852	0.378	0.334	0.426	SUBCLONAL	1	TRUE	1	0.484250930385073	3		337	549	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942761	44942761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	155	389	0	ENST00000377967.4:c.3341C>T	p.Ser1114Leu	p.S1114L	ENST00000377967	NM_021140.2	1114	tCa/tTa	23/29	0.414010112854627	2	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.484250930385073	2		389	518	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361152	66361152	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	126	381	1	ENST00000273854.3:c.1020G>T	p.Lys340Asn	p.K340N	ENST00000273854	NM_004439.5	340	aaG/aaT	4/18	0.484250930385073	2	FACETS	1	0.962	1	0.551	0.502	0.602	CLONAL	1	TRUE	0	0.484250930385073	2		382	472	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682982	241682982	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553342163	NA	P-0018660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	210	345	0	ENST00000366560.3:c.41T>C	p.Leu14Pro	p.L14P	ENST00000366560	NM_000143.3	14	cTc/cCc	1/10	0.172237731944607	3	FACETS	1	0.97	1	0.706	0.661	0.75	INDETERMINATE	2	TRUE	0	0.484250930385073	3		345	509	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484313	50484313	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	323	737	0	ENST00000394963.4:c.1073C>G	p.Pro358Arg	p.P358R	ENST00000394963	NM_003076.4	358	cCt/cGt	9/13	0.403421044592003	4	FACETS	0.818	0.772	0.865	0.818	0.772	0.865	CLONAL	2	TRUE	2	0.484250930385073	4		737	1210	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554344	81554344	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	281	756	0	ENST00000298171.2:c.364C>A	p.Leu122Ile	p.L122I	ENST00000298171	NM_000369.2	122	Ctc/Atc	4/10	0.208825858364879	4	FACETS	0.87	0.818	0.923	0.87	0.818	0.923	INDETERMINATE	2	TRUE	2	0.484250930385073	4		756	990	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843423	3843423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	119	436	0	ENST00000262367.5:c.1180C>T	p.His394Tyr	p.H394Y	ENST00000262367	NM_004380.2	394	Cac/Tac	4/31	0.484250930385073	2	FACETS	1	0.917	1	0.506	0.459	0.555	CLONAL	1	TRUE	0	0.484250930385073	2		436	486	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014188	14014220	+	inframe_deletion	In_Frame_Del	DEL	GCCTGCCTGGTGCTGGTGCTCAACACGCAGCCG	GCCTGCCTGGTGCTGGTGCTCAACACGCAGCCG	-	novel	NA	P-0018660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	70	336	0	ENST00000311895.7:c.169_201del	p.Cys57_Ala67del	p.C57_A67del	ENST00000311895	NM_005236.2	56	GCCTGCCTGGTGCTGGTGCTCAACACGCAGCCG/-	1/11	0.484250930385073	2	FACETS	0.755	0.662	0.854	0.377	0.331	0.427	SUBCLONAL	1	TRUE	0	0.484250930385073	2		336	383	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853836	59853836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	163	731	0	ENST00000259008.2:c.2023G>A	p.Glu675Lys	p.E675K	ENST00000259008	NM_032043.2	675	Gaa/Aaa	14/20	0.484645106609272	3	FACETS	0.76	0.697	0.827	0.38	0.348	0.414	SUBCLONAL	1	TRUE	1	0.484250930385073	3		731	1100	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39573270	39573270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	130	576	0	ENST00000262039.4:c.751G>A	p.Glu251Lys	p.E251K	ENST00000262039	NM_002647.2	251	Gaa/Aaa	7/25	0.484645106609272	4	FACETS	0.777	0.703	0.854	0.388	0.351	0.427	SUBCLONAL	1	TRUE	2	0.484250930385073	4		576	1026	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207059	1207059	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0018660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	256	760	1	ENST00000326873.7:c.147C>G	p.Tyr49Ter	p.Y49*	ENST00000326873	NM_000455.4	49	taC/taG	1/10	0.484645106609272	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.484250930385073	1		761	633	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308346	30308346	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	170	762	0	ENST00000262643.3:c.360G>C	p.Met120Ile	p.M120I	ENST00000262643	NM_001238.2	120	atG/atC	6/12	0.172237731944607	3	FACETS	0.902	0.829	0.978	0.301	0.276	0.326	INDETERMINATE	1	TRUE	0	0.484250930385073	3		762	967	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705659	47705659	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs267608010	NA	P-0018660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	129	393	0	ENST00000233146.2:c.2458+1G>A		p.X820_splice	ENST00000233146	NM_000251.2	820			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.484250930385073	2		393	481	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198269824	198269824	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	300	685	0	ENST00000335508.6:c.1515G>T	p.Lys505Asn	p.K505N	ENST00000335508	NM_012433.2	505	aaG/aaT	11/25	0.204392291119328	2	FACETS	1	0.993	1	0.698	0.66	0.738	INDETERMINATE	1	TRUE	0	0.484250930385073	2		685	887	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149940	202149940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	184	666	0	ENST00000358485.4:c.1381G>A	p.Gly461Arg	p.G461R	ENST00000358485	NM_001080125.1	461	Ggg/Agg	8/9	0.204392291119328	2	FACETS	0.815	0.752	0.88	0.407	0.376	0.44	INDETERMINATE	1	TRUE	0	0.484250930385073	2		666	933	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440096	220440096	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	193	881	0	ENST00000243786.2:c.949C>T	p.Pro317Ser	p.P317S	ENST00000243786	NM_002191.3	317	Ccc/Tcc	2/2	0.204392291119328	2	FACETS	0.832	0.77	0.897	0.416	0.385	0.449	INDETERMINATE	1	TRUE	0	0.484250930385073	2		881	958	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556650	41556650	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	66	552	0	ENST00000263253.7:c.3595C>G	p.His1199Asp	p.H1199D	ENST00000263253	NM_001429.3	1199	Cat/Gat	20/31	0.484645106609272	1	FACETS	0.356	0.308	0.407	0.356	0.308	0.407	SUBCLONAL	1	TRUE	0	0.484250930385073	1		552	581	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502828	186502828	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	170	602	0	ENST00000323963.5:c.286G>C	p.Glu96Gln	p.E96Q	ENST00000323963		96	Gag/Cag	4/11	0.172237731944607	3	FACETS	1	0.94	1	0.342	0.314	0.371	INDETERMINATE	1	TRUE	0	0.484250930385073	3		602	850	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876479	35876479	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	163	625	0	ENST00000303115.3:c.1271G>T	p.Gly424Val	p.G424V	ENST00000303115	NM_002185.3	424	gGa/gTa	8/8	0.484645106609272	5	FACETS	1	0.918	1	0.25	0.229	0.273	CLONAL	1	TRUE	1	0.484250930385073	5		625	1160	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37141754	37141754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1181689554	NA	P-0018660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	156	667	0	ENST00000373509.5:c.829G>A	p.Asp277Asn	p.D277N	ENST00000373509	NM_002648.3	277	Gat/Aat	6/6	NA	2	FACETS	0.665	0.608	0.724			1	INDETERMINATE	1	TRUE	NA	0.484250930385073	2		667	969	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642434	117642434	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	235	726	0	ENST00000368508.3:c.5765G>T	p.Cys1922Phe	p.C1922F	ENST00000368508	NM_002944.2	1922	tGc/tTc	35/43	0.264514059763987	1	FACETS	0.973	0.911	1	0.973	0.911	1	INDETERMINATE	1	TRUE	0	0.484250930385073	1		726	756	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519619	137519619	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	99	390	0	ENST00000367739.4:c.1019C>T	p.Pro340Leu	p.P340L	ENST00000367739	NM_000416.2	340	cCa/cTa	7/7	0.264514059763987	1	FACETS	0.609	0.545	0.676	0.609	0.545	0.676	INDETERMINATE	1	TRUE	0	0.484250930385073	1		390	509	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069158	5069158	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	83	663	0	ENST00000381652.3:c.1463C>T	p.Ser488Leu	p.S488L	ENST00000381652	NM_004972.3	488	tCa/tTa	11/25	0.484645106609272	1	FACETS	0.434	0.383	0.488	0.434	0.383	0.488	SUBCLONAL	1	TRUE	0	0.484250930385073	1		663	599	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223484	53223485	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0018660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	220	243	0	ENST00000375401.3:c.3874_3875del	p.Ala1292GlnfsTer7	p.A1292Qfs*7	ENST00000375401	NM_004187.3	1292	GCc/c	23/26	0.414010112854627	2	FACETS	1	0.983	1			1	CLONAL	2	TRUE	NA	0.484250930385073	2		243	413	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0018661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	15452	757	1	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.276778346275214	51	FACETS	0.992	0.989	0.995			1	CLONAL	53	TRUE	NA	0.276778346275214	51		758	16531	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228980	36228980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780852805	NA	P-0018661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	147	570	0	ENST00000222270.7:c.7760G>A	p.Arg2587Gln	p.R2587Q	ENST00000222270	NM_014727.1	2587	cGa/cAa	36/37	0.276778346275214	2	FACETS	0.956	0.871	1	0.478	0.435	0.523	CLONAL	1	TRUE	0	0.276778346275214	2		570	1111	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578551	7578558	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTACTGT	AGTACTGT	-	novel	NA	P-0018661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1330	443	877	0	ENST00000269305.4:c.376-4_379del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	0.245600768821081	2	FACETS	0.903	0.859	0.947	0.903	0.859	0.947	CLONAL	2	TRUE	0	0.276778346275214	2		877	1773	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031530	11031530	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2145	253	885	0	ENST00000327064.4:c.1445C>T	p.Ser482Leu	p.S482L	ENST00000327064	NM_199141.1	482	tCa/tTa	13/16	0.276778346275214	5	FACETS	1	0.971	1	0.36	0.334	0.386	CLONAL	1	TRUE	2	0.276778346275214	5		885	2398	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928073	178928074	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0018661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	14996	606	3	ENST00000263967.3:c.1351_1352delinsAA	p.Gly451Lys	p.G451K	ENST00000263967	NM_006218.2	451	GGa/AAa	8/21	0.276778346275214	51	FACETS	1	0.999	1			1	CLONAL	52	TRUE	NA	0.276778346275214	51		609	16099	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486087	8486087	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1205	137	609	0	ENST00000356435.5:c.2730G>T	p.Glu910Asp	p.E910D	ENST00000356435		910	gaG/gaT	17/35	0.269964683899014	3	FACETS	0.84	0.761	0.923	0.42	0.38	0.462	CLONAL	1	TRUE	1	0.276778346275214	3		609	1342	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482577	56482577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762035321	NA	P-0018663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	198	530	1	ENST00000267101.3:c.1034C>T	p.Ser345Leu	p.S345L	ENST00000267101	NM_001982.3	345	tCg/tTg	9/28	0.706407901581394	2	FACETS	0.774	0.719	0.83			1	SUBCLONAL	1	TRUE	NA	0.71	2		531	721	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0018664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	250	900	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.2398592252297	4	FACETS	0.929	0.869	0.99	0.929	0.869	0.99	CLONAL	2	TRUE	2	0.360503402032555	4		901	1016	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0018664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	42	633	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.360503402032555	1	FACETS	0.18	0.149	0.214	0.18	0.149	0.214	SUBCLONAL	1	TRUE	0	0.360503402032555	1		633	1061	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551332	29551332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1275	115	523	1	ENST00000389048.3:c.1298C>T	p.Ser433Phe	p.S433F	ENST00000389048	NM_004304.4	433	tCc/tTc	6/29	0.327269303121284	2	FACETS	0.459	0.412	0.509	0.229	0.206	0.255	SUBCLONAL	1	TRUE	0	0.360503402032555	2		524	1390	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	279	917	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.695032542773361	2		917	803	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0018665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	136	304	0	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	0.695032542773361	1	FACETS	0.935	0.868	1	0.935	0.868	1	CLONAL	1	FALSE	0	0.695032542773361	1		304	273	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277275	41277275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	217	384	0	ENST00000349496.5:c.1744C>T	p.Arg582Trp	p.R582W	ENST00000349496	NM_001904.3	582	Cgg/Tgg	11/15	1	2	FACETS	0.997	0.933	1	0.997	0.933	1	CLONAL	1	FALSE	1	0.695032542773361	2		384	626	SUCCESS
AR	367	MSKCC	GRCh37	X	66766357	66766383	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGCGGCGGCGGCGGCGGCGGC	GGCGGCGGCGGCGGCGGCGGCGGCGGC	-	rs746853821	NA	P-0018665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	60	73	0	ENST00000374690.3:c.1394_1420del	p.Gly465_Gly473del	p.G465_G473del	ENST00000374690	NM_000044.3	457	GGCGGCGGCGGCGGCGGCGGCGGCGGC/-	1/8	1	1	FACETS	0.572	0.501	0.646	0.572	0.501	0.646	SUBCLONAL	1	FALSE	0	0.695032542773361	1		73	197	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518437	204518437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201947927	NA	P-0018665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	223	420	1	ENST00000367182.3:c.1100C>T	p.Ser367Leu	p.S367L	ENST00000367182	NM_001278516.1	367	tCg/tTg	11/11	1	2	FACETS	0.952	0.891	1	0.952	0.891	1	CLONAL	1	FALSE	1	0.695032542773361	2		421	674	SUCCESS
APC	324	MSKCC	GRCh37	5	112174096	112174096	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs137854575	NA	P-0018665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	176	385	0	ENST00000257430.4:c.2805C>G	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	taC/taG	16/16	1	2	FACETS	0.843	0.78	0.907	0.843	0.78	0.907	CLONAL	1	FALSE	1	0.695032542773361	2		385	601	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375325	15375325	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	242	491	0	ENST00000263377.2:c.1102A>G	p.Lys368Glu	p.K368E	ENST00000263377	NM_058243.2	368	Aag/Gag	6/20	0.579533988939952	3	FACETS	0.951	0.889	1	0.475	0.444	0.508	CLONAL	1	FALSE	1	0.695032542773361	3		491	987	SUCCESS
APC	324	MSKCC	GRCh37	5	112175959	112175960	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	rs786201118	NA	P-0018665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	194	293	0	ENST00000257430.4:c.4669_4670del	p.Ile1557Ter	p.I1557*	ENST00000257430	NM_000038.5	1556	acTAtt/actt	16/16	1	2	FACETS	0.999	0.931	1	0.999	0.931	1	CLONAL	1	FALSE	1	0.695032542773361	2		293	559	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32819898	32819898	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	168	602	0	ENST00000354258.4:c.1012C>G	p.Gln338Glu	p.Q338E	ENST00000354258	NM_000593.5	338	Cag/Gag	3/11	1	2	FACETS	0.459	0.421	0.499	0.459	0.421	0.499	SUBCLONAL	1	FALSE	1	0.695032542773361	2		602	1053	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0018666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	320	900	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.386224670465678	1	FACETS	0.71	0.675	0.746	0.71	0.675	0.746	INDETERMINATE	1	TRUE	0	0.767137835190375	1		901	724	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117870639	117870639	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1360712011	NA	P-0018666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	319	554	0	ENST00000297338.2:c.433A>C	p.Met145Leu	p.M145L	ENST00000297338	NM_006265.2	145	Atg/Ctg	5/14	1	2	FACETS	0.977	0.926	1	0.977	0.926	1	CLONAL	1	TRUE	1	0.767137835190375	2		554	851	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0018666-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	103	900	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		901	459	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0018667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	254	444	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.396053810977785	2	FACETS	1	0.99	1	0.625	0.588	0.661	CLONAL	1	TRUE	0	0.633490913868054	2		444	642	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024001	27024002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0018667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	67	124	0	ENST00000324856.7:c.1113dup	p.Gln372AlafsTer28	p.Q372Afs*28	ENST00000324856	NM_006015.4	369	-/G	1/20	0.276438813262541	1	FACETS	0.679	0.599	0.761	0.679	0.599	0.761	INDETERMINATE	1	TRUE	0	0.633490913868054	1		124	213	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878859	117878859	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	271	443	2	ENST00000297338.2:c.110T>C	p.Leu37Ser	p.L37S	ENST00000297338	NM_006265.2	37	tTa/tCa	2/14	0.143993340088442	3	FACETS	0.801	0.756	0.847	0.801	0.756	0.847	INDETERMINATE	2	TRUE	1	0.633490913868054	3		445	703	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578497	7578499	+	frameshift_variant	Frame_Shift_Del	DEL	GCT	GCT	C	novel	NA	P-0018667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	708	844	0	ENST00000269305.4:c.431_433delinsG	p.Gln144ArgfsTer4	p.Q144Rfs*4	ENST00000269305	NM_001126112.2	144	cAGCtg/cGtg	5/11	0.564827600853225	2	FACETS	0.785	0.76	0.81	0.785	0.76	0.81	SUBCLONAL	2	TRUE	0	0.633490913868054	2		844	1424	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0018668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	134	745	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.972	0.886	1	0.972	0.886	1	CLONAL	1	TRUE	1	0.461981424381918	2		745	597	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523292	176523292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1172824038	NA	P-0018668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	187	607	0	ENST00000292408.4:c.1949G>A	p.Arg650His	p.R650H	ENST00000292408	NM_213647.1	650	cGc/cAc	15/18	0.238054060708491	3	FACETS	1	0.983	1	0.607	0.561	0.654	INDETERMINATE	1	TRUE	1	0.461981424381918	3		607	821	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618666	37618666	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	366	734	0	ENST00000447079.4:c.343del	p.Gln115SerfsTer9	p.Q115Sfs*9	ENST00000447079	NM_015083.1	114	caC/ca	1/14	0.404361589286305	3	FACETS	0.87	0.826	0.915	0.87	0.826	0.915	CLONAL	2	TRUE	1	0.461981424381918	3		734	1121	SUCCESS
APC	324	MSKCC	GRCh37	5	112102099	112102099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750503329	NA	P-0018668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	61	309	0	ENST00000257430.4:c.212G>A	p.Arg71His	p.R71H	ENST00000257430	NM_000038.5	71	cGt/cAt	3/16	1	2	FACETS	0.936	0.815	1	0.936	0.815	1	CLONAL	1	TRUE	1	0.461981424381918	2		309	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0018670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	1109	518	1	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.821612903086546	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.821612903086546	2		519	1338	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332480	70332480	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	620	637	1	ENST00000373644.4:c.385C>A	p.Pro129Thr	p.P129T	ENST00000373644	NM_030625.2	129	Cca/Aca	2/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.821612903086546	2		638	1489	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28885788	28885788	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1256173877	NA	P-0018671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	321	489	1	ENST00000282397.4:c.3574G>T	p.Asp1192Tyr	p.D1192Y	ENST00000282397	NM_002019.4	1192	Gac/Tac	27/30	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.588246570603836	2		490	987	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309117	137309117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1383908613	NA	P-0018671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1240	556	836	6	ENST00000481739.1:c.724G>A	p.Val242Met	p.V242M	ENST00000481739	NM_002957.4	242	Gtg/Atg	5/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.588246570603836	2		842	1796	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0018672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	37	636	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.798	0.661	0.95	0.798	0.661	0.95	CLONAL	1	FALSE	1	0.324044610370046	2		636	286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577575	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587782289	NA	P-0018672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	109	481	0	ENST00000269305.4:c.706T>G	p.Tyr236Asp	p.Y236D	ENST00000269305	NM_001126112.2	236	Tac/Gac	7/11	0.324044610370046	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	0	0.324044610370046	1		481	397	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112767384	112767384	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	95	396	0	ENST00000369452.4:c.1258del	p.Asp420MetfsTer18	p.D420Mfs*18	ENST00000369452	NM_007373.3	419	gaG/ga	6/9	0.287111061460233	4	FACETS	1	0.955	1	0.741	0.666	0.82	CLONAL	2	FALSE	1	0.324044610370046	4		396	349	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732482	74732482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	184	136	0	ENST00000359995.5:c.427C>T	p.Arg143Cys	p.R143C	ENST00000359995	NM_001195427.1	143	Cgc/Tgc	2/3	0.324044610370046	5	FACETS	1	0.945	1	1	0.989	1	CLONAL	5	FALSE	1	0.324044610370046	5		136	336	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039374	49039374	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853293	NA	P-0018673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	187	683	1	ENST00000267163.4:c.2359C>T	p.Arg787Ter	p.R787*	ENST00000267163	NM_000321.2	787	Cga/Tga	23/27	0.536112494173238	1	FACETS	0.913	0.85	0.979	0.913	0.85	0.979	CLONAL	1	TRUE	0	0.536112494173238	1		684	559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0018673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	565	898	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.502201922292214	2	FACETS	0.89	0.858	0.923	0.89	0.858	0.923	CLONAL	2	TRUE	0	0.536112494173238	2		898	1184	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808962	3808962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	46	448	0	ENST00000262367.5:c.3262G>A	p.Glu1088Lys	p.E1088K	ENST00000262367	NM_004380.2	1088	Gag/Aag	17/31	0.247838145211567	3	FACETS	0.26	0.218	0.307	0.13	0.109	0.154	INDETERMINATE	1	TRUE	1	0.536112494173238	3		448	837	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	139	272	0	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	0.247838145211567	3	FACETS	1	0.966	1	0.555	0.507	0.605	INDETERMINATE	1	TRUE	1	0.536112494173238	3		272	592	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231689	66231689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	125	419	1	ENST00000273854.3:c.2011G>A	p.Glu671Lys	p.E671K	ENST00000273854	NM_004439.5	671	Gaa/Aaa	11/18	0.502201922292214	2	FACETS	0.79	0.727	0.854	0.79	0.727	0.854	SUBCLONAL	2	TRUE	0	0.536112494173238	2		420	295	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972633	25972633	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	130	251	0	ENST00000435504.4:c.1792C>T	p.Gln598Ter	p.Q598*	ENST00000435504		598	Cag/Tag	12/13	0.536112494173238	6	FACETS	0.931	0.842	1	0.186	0.168	0.205	CLONAL	1	TRUE	1	0.536112494173238	6		251	1080	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257200	133257200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	324	485	0	ENST00000320574.5:c.278G>A	p.Arg93Lys	p.R93K	ENST00000320574	NM_006231.2	93	aGa/aAa	3/49	0.518080481063384	2	FACETS	0.912	0.868	0.955	0.912	0.868	0.955	CLONAL	2	TRUE	0	0.536112494173238	2		485	663	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163313637	163313637	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	62	296	0	ENST00000271452.3:c.784G>T	p.Val262Phe	p.V262F	ENST00000271452	NM_145697.2	262	Gtc/Ttc	10/14	0.323956734057204	6	FACETS	0.853	0.737	0.979	0.284	0.245	0.327	CLONAL	1	TRUE	3	0.536112494173238	6		296	562	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666707	206666707	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1484	218	519	0	ENST00000367120.3:c.2041C>T	p.Leu681Phe	p.L681F	ENST00000367120	NM_014002.3	681	Ctc/Ttc	20/22	0.323956734057204	6	FACETS	0.99	0.918	1	0.33	0.306	0.356	CLONAL	1	TRUE	3	0.536112494173238	6		519	1702	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371781	118371781	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	191	387	0	ENST00000534358.1:c.6238C>G	p.Pro2080Ala	p.P2080A	ENST00000534358	NM_005933.3	2080	Cca/Gca	25/36	1	2	FACETS	0.975	0.904	1	0.975	0.904	1	CLONAL	1	TRUE	1	0.536112494173238	2		387	731	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497704	125497704	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	86	400	0	ENST00000428830.2:c.268G>A	p.Gly90Arg	p.G90R	ENST00000428830	NM_001114121.2	90	Gga/Aga	3/14	1	2	FACETS	0.919	0.82	1	0.919	0.82	1	CLONAL	1	TRUE	1	0.536112494173238	2		400	349	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448499	49448499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	514	456	0	ENST00000301067.7:c.212G>A	p.Cys71Tyr	p.C71Y	ENST00000301067	NM_003482.3	71	tGc/tAc	3/54	0.536112494173238	3	FACETS	0.95	0.911	0.989	0.95	0.911	0.989	CLONAL	2	TRUE	1	0.536112494173238	3		456	1280	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748314	43748314	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	268	675	0	ENST00000382044.4:c.2492T>G	p.Val831Gly	p.V831G	ENST00000382044	NM_001141980.1	831	gTa/gGa	12/28	0.195598298143644	5	FACETS	0.8	0.75	0.851	0.533	0.5	0.567	INDETERMINATE	2	TRUE	2	0.536112494173238	5		675	1128	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315387	30315387	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	396	522	0	ENST00000322652.5:c.1072A>C	p.Thr358Pro	p.T358P	ENST00000322652	NM_015355.2	358	Act/Cct	10/16	0.502201922292214	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.536112494173238	2		522	738	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602473	10602473	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	390	422	0	ENST00000171111.5:c.1105G>T	p.Val369Leu	p.V369L	ENST00000171111	NM_203500.1	369	Gtg/Ttg	3/6	0.485812127701137	3	FACETS	0.922	0.879	0.966			1	CLONAL	2	TRUE	NA	0.536112494173238	3		422	1000	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982532	10982532	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	102	195	0	ENST00000327064.4:c.154G>A	p.Glu52Lys	p.E52K	ENST00000327064	NM_199141.1	52	Gag/Aag	1/16	0.427463775603055	4	FACETS	0.789	0.706	0.877	0.394	0.353	0.439	SUBCLONAL	1	TRUE	2	0.536112494173238	4		195	741	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982553	10982553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	103	182	0	ENST00000327064.4:c.175G>A	p.Glu59Lys	p.E59K	ENST00000327064	NM_199141.1	59	Gag/Aag	1/16	0.427463775603055	4	FACETS	0.828	0.741	0.92	0.414	0.37	0.46	CLONAL	1	TRUE	2	0.536112494173238	4		182	713	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973155	25973155	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	126	281	0	ENST00000435504.4:c.1270C>T	p.Pro424Ser	p.P424S	ENST00000435504		424	Cca/Tca	12/13	0.536112494173238	6	FACETS	0.971	0.878	1	0.194	0.175	0.214	CLONAL	1	TRUE	1	0.536112494173238	6		281	1003	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374828	149374828	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	428	319	0	ENST00000360632.3:c.266C>G	p.Ser89Trp	p.S89W	ENST00000360632	NM_015472.4	89	tCg/tGg	2/7	0.536112494173238	6	FACETS	0.98	0.936	1	0.735	0.702	0.769	CLONAL	3	TRUE	2	0.536112494173238	6		319	1125	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170020871	170020871	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	38	175	0	ENST00000295797.4:c.1747G>C	p.Glu583Gln	p.E583Q	ENST00000295797	NM_002740.5	583	Gag/Cag	18/18	0.536112494173238	6	FACETS	0.718	0.594	0.856	0.18	0.148	0.215	SUBCLONAL	1	TRUE	2	0.536112494173238	6		175	409	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193954	106193954	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	239	320	0	ENST00000380013.4:c.4416G>C	p.Lys1472Asn	p.K1472N	ENST00000380013	NM_001127208.2	1472	aaG/aaC	10/11	0.502201922292214	2	FACETS	0.949	0.897	1	0.949	0.897	1	CLONAL	2	TRUE	0	0.536112494173238	2		320	470	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513537	149513537	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	408	407	0	ENST00000261799.4:c.666G>C	p.Gln222His	p.Q222H	ENST00000261799	NM_002609.3	222	caG/caC	5/23	0.518080481063384	2	FACETS	0.897	0.859	0.936	0.897	0.859	0.936	CLONAL	2	TRUE	0	0.536112494173238	2		407	848	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673701	30673701	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	190	452	0	ENST00000376406.3:c.3259C>T	p.Gln1087Ter	p.Q1087*	ENST00000376406	NM_014641.2	1087	Cag/Tag	10/15	0.536112494173238	4	FACETS	0.924	0.853	0.999	0.308	0.284	0.333	CLONAL	1	TRUE	1	0.536112494173238	4		452	1178	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609863	117609863	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	175	622	2	ENST00000368508.3:c.6836C>A	p.Thr2279Lys	p.T2279K	ENST00000368508	NM_002944.2	2279	aCa/aAa	43/43	0.348339141914126	3	FACETS	0.923	0.85	0.999	0.461	0.425	0.5	CLONAL	1	TRUE	1	0.536112494173238	3		624	897	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724433	117724433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	99	424	0	ENST00000368508.3:c.446C>T	p.Ser149Phe	p.S149F	ENST00000368508	NM_002944.2	149	tCc/tTc	6/43	0.348339141914126	3	FACETS	0.58	0.518	0.647	0.29	0.259	0.324	SUBCLONAL	1	TRUE	1	0.536112494173238	3		424	807	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945058	151945058	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs748010370	NA	P-0018673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	67	581	0	ENST00000262189.6:c.2461C>G	p.Pro821Ala	p.P821A	ENST00000262189	NM_170606.2	821	Cca/Gca	14/59	0.536112494173238	3	FACETS	0.277	0.239	0.317	0.138	0.119	0.159	SUBCLONAL	1	TRUE	1	0.536112494173238	3		581	1146	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868516	117868516	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	396	234	0	ENST00000297338.2:c.826G>C	p.Asp276His	p.D276H	ENST00000297338	NM_006265.2	276	Gat/Cat	8/14	0.536112494173238	7	FACETS	1	0.975	1			1	CLONAL	5	TRUE	NA	0.536112494173238	7		234	678	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123048	5123048	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0018673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	75	385	0	ENST00000381652.3:c.3104C>G	p.Ser1035Ter	p.S1035*	ENST00000381652	NM_004972.3	1035	tCa/tGa	23/25	0.40642352450684	1	FACETS	0.604	0.533	0.679	0.604	0.533	0.679	SUBCLONAL	1	TRUE	0	0.536112494173238	1		385	339	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27190632	27190632	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	433	583	0	ENST00000380036.4:c.1433C>A	p.Ser478Tyr	p.S478Y	ENST00000380036	NM_000459.3	478	tCc/tAc	10/23	0.518080481063384	2	FACETS	0.886	0.849	0.922	0.886	0.849	0.922	CLONAL	2	TRUE	0	0.536112494173238	2		583	912	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245054	53245054	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	499	530	0	ENST00000375401.3:c.886G>C	p.Glu296Gln	p.E296Q	ENST00000375401	NM_004187.3	296	Gag/Cag	7/26	0.20770875883935	3	FACETS	0.931	0.892	0.97			1	INDETERMINATE	2	TRUE	NA	0.536112494173238	3		530	1268	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361149	70361149	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	494	735	1	ENST00000374080.3:c.6337C>T	p.Gln2113Ter	p.Q2113*	ENST00000374080		2113	Caa/Taa	43/45	0.134318965831596	5	FACETS	1	0.973	1			1	INDETERMINATE	2	TRUE	NA	0.536112494173238	5		736	1622	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939111	76939111	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	106	492	0	ENST00000373344.5:c.1637G>T	p.Gly546Val	p.G546V	ENST00000373344	NM_000489.3	546	gGg/gTg	9/35	0.20253404894669	2	FACETS	0.674	0.605	0.746	0.337	0.302	0.373	INDETERMINATE	1	TRUE	0	0.536112494173238	2		492	587	SUCCESS
ATR	545	MSKCC	GRCh37	3	142297533	142297535	+	missense_variant	Missense_Mutation	TNP	CCA	CCA	TCT	novel	NA	P-0018673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1677	194	433	0	ENST00000350721.4:c.12_14delinsAGA	p.His4_Gly5delinsGlnAsp	p.H4_G5delinsQD	ENST00000350721	NM_001184.3	4	caTGGc/caAGAc	1/47	0.536112494173238	6	FACETS	0.802	0.738	0.868	0.2	0.184	0.217	CLONAL	1	TRUE	2	0.536112494173238	6		433	1871	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0018674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	84	343	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.372844638495848	2		344	442	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913355	NA	P-0018674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	34	434	0	ENST00000288602.6:c.1406G>T	p.Gly469Val	p.G469V	ENST00000288602	NM_004333.4	469	gGa/gTa	11/18	0.372844638495848	3	FACETS	0.478	0.39	0.576	0.239	0.195	0.288	SUBCLONAL	1	TRUE	1	0.372844638495848	3		434	453	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692793	89692793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	38	363	0	ENST00000371953.3:c.277C>T	p.His93Tyr	p.H93Y	ENST00000371953	NM_000314.4	93	Cat/Tat	5/9	0.372844638495848	1	FACETS	0.721	0.601	0.853	0.721	0.601	0.853	SUBCLONAL	1	TRUE	0	0.372844638495848	1		363	230	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858210	9858210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756930722	NA	P-0018674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	74	314	3	ENST00000330684.3:c.3191C>T	p.Thr1064Met	p.T1064M	ENST00000330684	NM_001134407.1	1064	aCg/aTg	13/13	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.372844638495848	2		317	382	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855972	68855972	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	113	591	0	ENST00000261769.5:c.1780A>C	p.Ile594Leu	p.I594L	ENST00000261769	NM_004360.3	594	Ata/Cta	12/16	1	2	FACETS	0.772	0.695	0.854	0.772	0.695	0.854	SUBCLONAL	1	TRUE	1	0.372844638495848	2		591	785	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0018675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	21	1014	3	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.303455927951544	1	FACETS	0.134	0.103	0.172	0.134	0.103	0.172	SUBCLONAL	1	TRUE	0	0.31	1		1017	852	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0018675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	21	636	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.303455927951544	1	FACETS	0.226	0.173	0.288	0.226	0.173	0.288	SUBCLONAL	1	TRUE	0	0.31	1		636	506	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0018675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	57	337	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	0.303455927951544	1	FACETS	0.833	0.718	0.958	0.833	0.718	0.958	CLONAL	1	TRUE	0	0.31	1		338	373	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0018675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	124	779	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	1	2	FACETS	0.893	0.807	0.983	0.893	0.807	0.983	CLONAL	1	TRUE	1	0.31	2		779	896	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0018675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	29	521	0	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.303455927951544	1	FACETS	0.254	0.203	0.313	0.254	0.203	0.313	SUBCLONAL	1	TRUE	0	0.31	1		521	622	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	53	491	1	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.474	0.403	0.552	0.474	0.403	0.552	SUBCLONAL	1	TRUE	1	0.31	2		492	721	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845623	128845623	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs201012381	NA	P-0018675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	40	251	0	ENST00000249373.3:c.920C>T	p.Thr307Ile	p.T307I	ENST00000249373	NM_005631.4	307	aCc/aTc	4/12	1	2	FACETS	0.784	0.654	0.929	0.784	0.654	0.929	CLONAL	1	TRUE	1	0.31	2		251	329	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255882	16255883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	48	453	2	ENST00000375759.3:c.3154dup	p.Ile1052AsnfsTer7	p.I1052Nfs*7	ENST00000375759	NM_015001.2	1049	-/A	11/15	1	2	FACETS	0.452	0.381	0.53	0.452	0.381	0.53	SUBCLONAL	1	TRUE	1	0.31	2		455	685	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	53	702	1	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	0.337	0.286	0.393	0.337	0.286	0.393	SUBCLONAL	1	TRUE	1	0.31	2		703	1014	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257254	16257254	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	139	647	2	ENST00000375759.3:c.4522del	p.Met1508TrpfsTer39	p.M1508Wfs*39	ENST00000375759	NM_015001.2	1507	Aaa/aa	11/15	1	2	FACETS	0.999	0.909	1	0.999	0.909	1	CLONAL	1	TRUE	1	0.31	2		649	898	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013737	12013738	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0018675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	27	415	0	ENST00000353533.5:c.681_682del	p.His227GlnfsTer17	p.H227Qfs*17	ENST00000353533	NM_003010.3	227	CAc/c	6/11	0.303455927951544	1	FACETS	0.282	0.224	0.349	0.282	0.224	0.349	SUBCLONAL	1	TRUE	0	0.31	1		415	522	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248737	212248737	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	20	305	0	ENST00000342788.4:c.3530del	p.Asn1177MetfsTer27	p.N1177Mfs*27	ENST00000342788	NM_005235.2	1177	aAt/at	28/28	1	2	FACETS	0.381	0.291	0.486	0.381	0.291	0.486	SUBCLONAL	1	TRUE	1	0.31	2		305	339	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36024634	36024634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867236697	NA	P-0018675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	181	816	1	ENST00000358208.4:c.623G>A	p.Arg208His	p.R208H	ENST00000358208		208	cGc/cAc	6/12	0.225043659255293	3	FACETS	1	0.932	1			1	CLONAL	1	TRUE	NA	0.31	3		817	1330	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042545	37042545	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs267607734	NA	P-0018675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	49	417	1	ENST00000231790.2:c.306+1G>A		p.X102_splice	ENST00000231790	NM_000249.3	102			0.303455927951544	1	FACETS	0.688	0.585	0.802	0.688	0.585	0.802	SUBCLONAL	1	TRUE	0	0.31	1		418	388	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849901	151849901	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	72	385	1	ENST00000262189.6:c.12415C>T	p.Arg4139Ter	p.R4139*	ENST00000262189	NM_170606.2	4139	Cga/Tga	49/59	1	2	FACETS	0.832	0.728	0.945	0.832	0.728	0.945	CLONAL	1	TRUE	1	0.31	2		386	558	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101895016	101895016	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	20	241	0	ENST00000374994.4:c.569G>A	p.Gly190Asp	p.G190D	ENST00000374994	NM_004612.2	190	gGc/gAc	3/9	1	2	FACETS	0.354	0.27	0.453	0.354	0.27	0.453	SUBCLONAL	1	TRUE	1	0.31	2		241	364	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399216	139399216	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs566680728	NA	P-0018675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	59	621	0	ENST00000277541.6:c.4927G>A	p.Ala1643Thr	p.A1643T	ENST00000277541	NM_017617.3	1643	Gcc/Acc	26/34	1	2	FACETS	0.481	0.413	0.556	0.481	0.413	0.556	SUBCLONAL	1	TRUE	1	0.31	2		621	791	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0018675-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	74	636	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.497	0.436	0.563	0.497	0.436	0.563	SUBCLONAL	1	TRUE	1	0.560504456318591	2		636	531	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155706	56155730	+	frameshift_variant	Frame_Shift_Del	DEL	TCCAGGAGTAAGGAGAAAAAGAGTT	TCCAGGAGTAAGGAGAAAAAGAGTT	-	novel	NA	P-0018675-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	50	464	0	ENST00000399503.3:c.801_825del	p.Gly268GlnfsTer36	p.G268Qfs*36	ENST00000399503	NM_005921.1	266	tcTCCAGGAGTAAGGAGAAAAAGAGTT/tc	3/20	1	2	FACETS	0.325	0.275	0.38	0.325	0.275	0.38	SUBCLONAL	1	TRUE	1	0.560504456318591	2		464	549	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161710	56161710	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018675-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	117	713	0	ENST00000399503.3:c.1208del	p.Pro403HisfsTer33	p.P403Hfs*33	ENST00000399503	NM_005921.1	403	Cca/ca	6/20	1	2	FACETS	0.505	0.455	0.558	0.505	0.455	0.558	SUBCLONAL	1	TRUE	1	0.560504456318591	2		713	826	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552876	106552876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1003783236	NA	P-0018675-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	170	1003	1	ENST00000369096.4:c.841G>A	p.Asp281Asn	p.D281N	ENST00000369096	NM_001198.3	281	Gat/Aat	5/7	1	2	FACETS	0.542	0.498	0.589	0.542	0.498	0.589	SUBCLONAL	1	TRUE	1	0.560504456318591	2		1004	1119	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	119	364	1				ENST00000310581	NM_198253.2	-/1132			0.423897552554067	3	FACETS	0.875	0.791	0.965	0.438	0.395	0.483	CLONAL	1	TRUE	1	0.457669589069079	3		365	730	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747342068	NA	P-0018676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	317	687	1	ENST00000269305.4:c.394A>G	p.Lys132Glu	p.K132E	ENST00000269305	NM_001126112.2	132	Aag/Gag	5/11	0.418936286323758	1	FACETS	0.902	0.851	0.954	0.902	0.851	0.954	CLONAL	1	TRUE	0	0.457669589069079	1		688	1185	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202246	108202267	+	frameshift_variant	Frame_Shift_Del	DEL	ATGATGGGAGGCCTAGGATTTC	ATGATGGGAGGCCTAGGATTTC	-	novel	NA	P-0018676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	65	438	0	ENST00000278616.4:c.7595_7616del	p.Met2532LysfsTer6	p.M2532Kfs*6	ENST00000278616	NM_000051.3	2531	ATGATGGGAGGCCTAGGATTTCat/at	51/63	1	2	FACETS	0.535	0.464	0.611	0.535	0.464	0.611	SUBCLONAL	1	TRUE	1	0.457669589069079	2		438	531	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650651	67650651	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	150	263	0	ENST00000264010.4:c.956C>G	p.Thr319Ser	p.T319S	ENST00000264010	NM_006565.3	319	aCt/aGt	5/12	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.457669589069079	2		263	631	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993351	72993351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752231847	NA	P-0018676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	201	471	1	ENST00000268489.5:c.694C>T	p.Arg232Cys	p.R232C	ENST00000268489	NM_006885.3	232	Cgc/Tgc	2/10	1	2	FACETS	0.853	0.79	0.918	0.853	0.79	0.918	CLONAL	1	TRUE	1	0.457669589069079	2		472	1030	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17129503	17129503	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	139	397	1	ENST00000285071.4:c.383G>T	p.Ser128Ile	p.S128I	ENST00000285071	NM_144997.5	128	aGc/aTc	5/14	0.418936286323758	1	FACETS	0.803	0.734	0.875	0.803	0.734	0.875	CLONAL	1	TRUE	0	0.457669589069079	1		398	583	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	85	364	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.841	0.746	0.941	0.841	0.746	0.941	CLONAL	1	TRUE	1	0.440533273269735	2		365	459	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221710	55221710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	5605	397	0	ENST00000275493.2:c.754C>T	p.Arg252Cys	p.R252C	ENST00000275493	NM_005228.3	252	Cgc/Tgc	7/28	0.440533273269735	37	FACETS	1	0.997	1			1	CLONAL	34	TRUE	NA	0.440533273269735	37		397	6486	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417868	138417868	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	133	512	0	ENST00000289153.2:c.1651T>C	p.Cys551Arg	p.C551R	ENST00000289153	NM_006219.2	551	Tgt/Cgt	11/22	1	2	FACETS	0.965	0.879	1	0.965	0.879	1	CLONAL	1	TRUE	1	0.440533273269735	2		512	626	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828212	72828212	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	137	504	0	ENST00000268489.5:c.8369A>G	p.Lys2790Arg	p.K2790R	ENST00000268489	NM_006885.3	2790	aAa/aGa	9/10	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.440533273269735	2		504	612	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987289	2987289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765680532	NA	P-0018678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	110	439	1	ENST00000396946.4:c.140G>A	p.Arg47His	p.R47H	ENST00000396946	NM_032415.4	47	cGt/cAt	3/25	NA	2	FACETS	0.572	0.513	0.634			1	INDETERMINATE	1	TRUE	NA	0.440533273269735	2		440	873	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0018680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	131	393	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.902	0.825	0.982	0.902	0.825	0.982	CLONAL	1	TRUE	1	0.655419200354791	2		393	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578505	7578516	+	inframe_deletion	In_Frame_Del	DEL	GGGCAGGTCTTG	GGGCAGGTCTTG	-	rs1482894608	NA	P-0018680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	518	624	0	ENST00000269305.4:c.414_425del	p.Lys139_Pro142del	p.K139_P142del	ENST00000269305	NM_001126112.2	138	gcCAAGACCTGCCCt/gct	5/11	0.655419200354791	2	FACETS	0.756	0.728	0.785	0.756	0.728	0.785	SUBCLONAL	2	TRUE	0	0.655419200354791	2		624	1045	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	45	609	0	ENST00000269305.4:c.380C>A	p.Ser127Tyr	p.S127Y	ENST00000269305	NM_001126112.2	127	tCc/tAc	5/11	0.235238033492754	3	FACETS	1	0.872	1	0.52	0.438	0.611	CLONAL	1	TRUE	1	0.235238033492754	3		609	411	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950724	79950725	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCGCAGCGC	rs1554066076	NA	P-0018682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	10	133	2	ENST00000265081.6:c.181_189dup	p.Ala61_Pro63dup	p.A61_P63dup	ENST00000265081	NM_002439.4	61	gcc/gCCGCAGCGCcc	1/24	1	2	FACETS	0.649	0.441	0.907	0.649	0.441	0.907	SUBCLONAL	1	TRUE	1	0.235238033492754	2		135	131	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557699	21557699	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	25	487	1	ENST00000382592.4:c.2146G>T	p.Glu716Ter	p.E716*	ENST00000382592	NM_014572.2	716	Gag/Tag	5/8	0.235238033492754	1	FACETS	0.805	0.637	0.996	0.805	0.637	0.996	CLONAL	1	TRUE	0	0.235238033492754	1		488	233	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151871223	151871223	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	13	380	0	ENST00000262189.6:c.9367A>T	p.Met3123Leu	p.M3123L	ENST00000262189	NM_170606.2	3123	Atg/Ttg	39/59	1	2	FACETS	0.807	0.579	1	0.807	0.579	1	CLONAL	1	TRUE	1	0.235238033492754	2		380	137	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913351	NA	P-0018682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	328	568	0	ENST00000288602.6:c.1397G>C	p.Gly466Ala	p.G466A	ENST00000288602	NM_004333.4	466	gGa/gCa	11/18	0.580356707561768	4	FACETS	0.895	0.856	0.934	0.895	0.856	0.934	CLONAL	3	TRUE	1	0.715159315205191	4		568	586	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602446	10602446	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	583	709	0	ENST00000171111.5:c.1132G>T	p.Gly378Cys	p.G378C	ENST00000171111	NM_203500.1	378	Ggc/Tgc	3/6	0.715159315205191	3	FACETS	0.879	0.855	0.903	0.879	0.855	0.903	CLONAL	3	TRUE	0	0.715159315205191	3		709	839	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332586	153332586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768666009	NA	P-0018682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	239	354	0	ENST00000281708.4:c.370G>A	p.Asp124Asn	p.D124N	ENST00000281708	NM_033632.3	124	Gat/Aat	2/12	0.5920502988922	3	FACETS	0.877	0.839	0.914	0.877	0.839	0.914	CLONAL	3	TRUE	0	0.715159315205191	3		354	345	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645687	12645687	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397516828	NA	P-0018682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	226	252	1	ENST00000251849.4:c.782C>T	p.Pro261Leu	p.P261L	ENST00000251849	NM_002880.3	261	cCt/cTt	7/17	0.18632338286604	6	FACETS	0.991	0.949	1			1	INDETERMINATE	5	TRUE	NA	0.715159315205191	6		253	310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0018682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	259	524	0	ENST00000269305.4:c.97-1G>T		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.5920502988922	3	FACETS	1	0.984	1	0.719	0.684	0.754	CLONAL	2	TRUE	0	0.715159315205191	3		524	456	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551595	150551595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	183	516	1	ENST00000369026.2:c.412C>T	p.Pro138Ser	p.P138S	ENST00000369026	NM_021960.4	138	Ccg/Tcg	1/3	0.715159315205191	3	FACETS	0.811	0.749	0.875	0.405	0.374	0.438	CLONAL	1	TRUE	1	0.715159315205191	3		517	857	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557425	95557425	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	184	516	1	ENST00000393063.1:c.5549C>A	p.Pro1850His	p.P1850H	ENST00000393063	NM_030621.3	1850	cCc/cAc	27/28	0.715159315205191	3	FACETS	0.893	0.837	0.95	0.893	0.837	0.95	CLONAL	2	TRUE	1	0.715159315205191	3		517	391	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784504	43784504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs900018235	NA	P-0018682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	138	654	0	ENST00000382044.4:c.170C>T	p.Thr57Met	p.T57M	ENST00000382044	NM_001141980.1	57	aCg/aTg	2/28	0.492904047282337	3	FACETS	1	0.944	1	0.347	0.317	0.377	CLONAL	1	TRUE	0	0.715159315205191	3		654	504	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612407	1612407	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	592	824	0	ENST00000344749.5:c.1612G>T	p.Glu538Ter	p.E538*	ENST00000344749	NM_001136139.2	538	Gag/Tag	18/19	0.715159315205191	3	FACETS	1	0.997	1	0.832	0.808	0.856	CLONAL	2	TRUE	0	0.715159315205191	3		824	900	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098419	11098419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	489	565	0	ENST00000358026.2:c.937C>T	p.Pro313Ser	p.P313S	ENST00000358026	NM_001128849.1	313	Ccc/Tcc	6/36	0.715159315205191	3	FACETS	0.91	0.884	0.936	0.91	0.884	0.936	CLONAL	3	TRUE	0	0.715159315205191	3		565	680	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289901	15289901	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	634	880	0	ENST00000263388.2:c.3653A>G	p.His1218Arg	p.H1218R	ENST00000263388	NM_000435.2	1218	cAc/cGc	22/33	0.715159315205191	3	FACETS	0.881	0.857	0.904	0.881	0.857	0.904	CLONAL	3	TRUE	0	0.715159315205191	3		880	911	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605134	46605134	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	352	687	0	ENST00000263734.3:c.1351G>T	p.Ala451Ser	p.A451S	ENST00000263734	NM_001430.4	451	Gct/Tct	10/16	0.713904957577411	3	FACETS	0.867	0.826	0.907	0.867	0.826	0.907	CLONAL	2	TRUE	1	0.715159315205191	3		687	771	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430757	181430757	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	353	807	0	ENST00000325404.1:c.609C>A	p.Ser203Arg	p.S203R	ENST00000325404	NM_003106.3	203	agC/agA	1/1	0.666283017804734	3	FACETS	0.823	0.784	0.863	0.823	0.784	0.863	CLONAL	2	TRUE	1	0.715159315205191	3		807	814	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235318	235318	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	338	544	1	ENST00000264932.6:c.1124A>T	p.Gln375Leu	p.Q375L	ENST00000264932	NM_004168.2	375	cAg/cTg	9/15	NA	2	FACETS	0.878	0.843	0.913			1	INDETERMINATE	2	TRUE	NA	0.715159315205191	2		545	538	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117746715	117746715	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	171	502	0	ENST00000368508.3:c.105G>T	p.Lys35Asn	p.K35N	ENST00000368508	NM_002944.2	35	aaG/aaT	1/43	0.587792172466659	2	FACETS	0.93	0.881	0.978	0.93	0.881	0.978	CLONAL	2	TRUE	0	0.715159315205191	2		502	257	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009331	69009331	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	227	637	0	ENST00000288368.4:c.2449del	p.Leu817TrpfsTer23	p.L817Wfs*23	ENST00000288368	NM_024870.2	816	caC/ca	22/40	0.288784128993953	4	FACETS	0.857	0.804	0.912	0.857	0.804	0.912	INDETERMINATE	2	TRUE	2	0.715159315205191	4		637	635	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375990	8375990	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs142960593	NA	P-0018682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	263	432	0	ENST00000356435.5:c.4607G>T	p.Arg1536Leu	p.R1536L	ENST00000356435		1536	cGt/cTt	28/35	0.715159315205191	3	FACETS	0.955	0.905	1	0.955	0.905	1	CLONAL	2	TRUE	1	0.715159315205191	3		432	523	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0018683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	116	708	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.270221717604105	2	FACETS	0.686	0.617	0.759	0.343	0.308	0.38	SUBCLONAL	1	TRUE	0	0.335151754355694	2		709	1009	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999009	100999009	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	81	423	0	ENST00000325455.5:c.793G>A	p.Val265Ile	p.V265I	ENST00000325455	NM_001202474.3	265	Gtc/Atc	1/8	1	2	FACETS	0.741	0.653	0.836	0.741	0.653	0.836	SUBCLONAL	1	TRUE	1	0.335151754355694	2		423	652	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136193	2136193	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs45517358	NA	P-0018683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	60	269	1	ENST00000219476.3:c.4663-1G>A		p.X1555_splice	ENST00000219476	NM_000548.3	1555			0.335151754355694	1	FACETS	0.635	0.548	0.73	0.635	0.548	0.73	SUBCLONAL	1	TRUE	0	0.335151754355694	1		270	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578284	7578284	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	175	434	0	ENST00000269305.4:c.565G>C	p.Ala189Pro	p.A189P	ENST00000269305	NM_001126112.2	189	Gcc/Ccc	6/11	0.335151754355694	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.335151754355694	1		434	712	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24129412	24129412	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	105	332	0	ENST00000263121.7:c.56T>C	p.Leu19Pro	p.L19P	ENST00000263121	NM_003073.3	19	cTg/cCg	1/9	0.314339742316394	1	FACETS	0.881	0.791	0.976	0.881	0.791	0.976	CLONAL	1	TRUE	0	0.335151754355694	1		332	592	SUCCESS
APC	324	MSKCC	GRCh37	5	112179446	112179446	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	43	312	0	ENST00000257430.4:c.8155G>T	p.Glu2719Ter	p.E2719*	ENST00000257430	NM_000038.5	2719	Gaa/Taa	16/16	0.335151754355694	1	FACETS	0.343	0.286	0.406	0.343	0.286	0.406	SUBCLONAL	1	TRUE	0	0.335151754355694	1		312	623	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459562	50459562	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0018683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	48	242	1	ENST00000331340.3:c.850+1G>A		p.X284_splice	ENST00000331340	NM_006060.4	284			1	2	FACETS	0.527	0.445	0.617	0.527	0.445	0.617	SUBCLONAL	1	TRUE	1	0.335151754355694	2		243	544	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0018684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	75	807	3	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.983	0.859	1	0.983	0.859	1	CLONAL	1	TRUE	1	0.16	2		810	954	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980345	55980345	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	61	482	0	ENST00000263923.4:c.746G>T	p.Arg249Ile	p.R249I	ENST00000263923	NM_002253.2	249	aGa/aTa	6/30	1	2	FACETS	0.92	0.792	1	0.92	0.792	1	CLONAL	1	TRUE	1	0.16	2		482	829	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405902	49405909	+	frameshift_variant	Frame_Shift_Del	DEL	ACATCGGT	ACATCGGT	-	novel	NA	P-0018684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	50	521	0	ENST00000418115.1:c.229_236del	p.Thr77TyrfsTer11	p.T77Yfs*11	ENST00000418115	NM_001664.2	77	ACCGATGTt/t	3/5	1	2	FACETS	0.671	0.568	0.786	0.671	0.568	0.786	SUBCLONAL	1	TRUE	1	0.16	2		521	931	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434682	110434682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	269	676	4	ENST00000375856.3:c.3719G>A	p.Arg1240His	p.R1240H	ENST00000375856	NM_003749.2	1240	cGc/cAc	1/2	1	2	FACETS	0.791	0.742	0.841	0.791	0.742	0.841	SUBCLONAL	1	TRUE	1	0.6463269095469	2		680	1052	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575484	64575484	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	275	544	0	ENST00000312049.6:c.533C>G	p.Ser178Cys	p.S178C	ENST00000312049	NM_130799.2	178	tCt/tGt	3/10	0.6463269095469	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.6463269095469	1		544	514	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115853	8115854	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0018685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	252	573	0	ENST00000346208.3:c.1200_1201del	p.Met400IlefsTer106	p.M400Ifs*106	ENST00000346208		400	aTG/a	6/6	1	2	FACETS	0.891	0.836	0.948	0.891	0.836	0.948	CLONAL	1	TRUE	1	0.6463269095469	2		573	875	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0018686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	270	883	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.449943654134413	1	FACETS	0.943	0.886	1	0.943	0.886	1	CLONAL	1	TRUE	0	0.449943654134413	1		885	986	SUCCESS
APC	324	MSKCC	GRCh37	5	112162804	112162804	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs863225313	NA	P-0018686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	68	282	0	ENST00000257430.4:c.1409-1G>A		p.X470_splice	ENST00000257430	NM_000038.5	470			0.227108641554002	1	FACETS	0.458	0.399	0.521	0.458	0.399	0.521	INDETERMINATE	1	TRUE	0	0.449943654134413	1		282	512	SUCCESS
APC	324	MSKCC	GRCh37	5	112151291	112151291	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs876660765	NA	P-0018686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	95	226	0	ENST00000257430.4:c.933+1G>A		p.X311_splice	ENST00000257430	NM_000038.5	311			0.227108641554002	1	FACETS	0.887	0.796	0.982	0.887	0.796	0.982	INDETERMINATE	1	TRUE	0	0.449943654134413	1		226	369	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971020	21971021	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0018686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	177	388	0	ENST00000304494.5:c.337_338del	p.Leu113AlafsTer6	p.L113Afs*6	ENST00000304494	NM_000077.4	113	CTg/g	2/3	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.449943654134413	2		388	740	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258943	16258944	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1322	182	853	0	ENST00000375759.3:c.6215dup	p.Asn2072LysfsTer51	p.N2072Kfs*51	ENST00000375759	NM_015001.2	2070	gaa/gAaa	11/15	0.247251777419253	3	FACETS	1	0.968	1	0.55	0.505	0.596	CLONAL	1	TRUE	1	0.247251777419253	3		853	1504	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163325188	163325188	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	70	504	0	ENST00000271452.3:c.1324G>T	p.Glu442Ter	p.E442*	ENST00000271452	NM_145697.2	442	Gag/Tag	14/14	1	2	FACETS	0.836	0.729	0.953	0.836	0.729	0.953	CLONAL	1	TRUE	1	0.247251777419253	2		504	677	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332801	70332801	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	151	615	0	ENST00000373644.4:c.706A>G	p.Thr236Ala	p.T236A	ENST00000373644	NM_030625.2	236	Acc/Gcc	2/12	0.247251777419253	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.247251777419253	1		615	820	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047519	49047519	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1131690908	NA	P-0018688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	76	305	0	ENST00000267163.4:c.2513C>G	p.Ser838Ter	p.S838*	ENST00000267163	NM_000321.2	838	tCa/tGa	24/27	0.247251777419253	1	FACETS	0.989	0.869	1	0.989	0.869	1	CLONAL	1	TRUE	0	0.247251777419253	1		305	545	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355766	73355766	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	115	460	0	ENST00000377767.4:c.205G>T	p.Asp69Tyr	p.D69Y	ENST00000377767	NM_014953.3	69	Gac/Tac	1/21	0.247251777419253	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.247251777419253	1		460	600	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609522	81609522	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	86	426	0	ENST00000298171.2:c.1120C>A	p.Gln374Lys	p.Q374K	ENST00000298171	NM_000369.2	374	Cag/Aag	10/10	1	2	FACETS	0.946	0.837	1	0.946	0.837	1	CLONAL	1	TRUE	1	0.247251777419253	2		426	735	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832871	3832871	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	190	405	1	ENST00000262367.5:c.1387G>A	p.Gly463Arg	p.G463R	ENST00000262367	NM_004380.2	463	Ggg/Agg	6/31	0.247251777419253	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.247251777419253	3		406	794	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993922	72993922	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	86	508	0	ENST00000268489.5:c.123G>T	p.Gln41His	p.Q41H	ENST00000268489	NM_006885.3	41	caG/caT	2/10	0.247251777419253	1	FACETS	0.918	0.813	1	0.918	0.813	1	CLONAL	1	TRUE	0	0.247251777419253	1		508	664	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550507	29550516	+	frameshift_variant	Frame_Shift_Del	DEL	AATGCTTAGT	AATGCTTAGT	-	novel	NA	P-0018688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	165	412	0	ENST00000356175.3:c.1768_1777del	p.Met590AlafsTer12	p.M590Afs*12	ENST00000356175	NM_000267.3	589	caAATGCTTAGT/ca	16/57	0.209873101895437	3	FACETS	1	0.967	1	0.73	0.672	0.79	CLONAL	2	TRUE	0	0.247251777419253	3		412	685	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414677	56414677	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	72	325	0	ENST00000348428.3:c.2078C>T	p.Ser693Leu	p.S693L	ENST00000348428	NM_006785.3	693	tCa/tTa	17/17	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.247251777419253	2		325	571	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214056	36214056	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1299829029	NA	P-0018688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	193	705	0	ENST00000222270.7:c.2882T>C	p.Met961Thr	p.M961T	ENST00000222270	NM_014727.1	961	aTg/aCg	6/37	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.247251777419253	2		705	1281	SUCCESS
AXL	558	MSKCC	GRCh37	19	41749586	41749586	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1172631104	NA	P-0018688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	117	669	1	ENST00000301178.4:c.1511A>G	p.Tyr504Cys	p.Y504C	ENST00000301178	NM_021913.4	504	tAc/tGc	12/20	1	2	FACETS	0.887	0.798	0.981	0.887	0.798	0.981	CLONAL	1	TRUE	1	0.247251777419253	2		670	1067	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447165	187447165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	91	472	0	ENST00000232014.4:c.1028C>T	p.Ser343Leu	p.S343L	ENST00000232014	NM_001130845.1	343	tCg/tTg	5/10	1	2	FACETS	0.929	0.825	1	0.929	0.825	1	CLONAL	1	TRUE	1	0.247251777419253	2		472	792	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99809059	99809059	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	86	440	0	ENST00000280892.6:c.326G>C	p.Cys109Ser	p.C109S	ENST00000280892	NM_001130678.1	109	tGt/tCt	4/7	1	2	FACETS	0.948	0.838	1	0.948	0.838	1	CLONAL	1	TRUE	1	0.247251777419253	2		440	734	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638344	176638344	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	153	699	3	ENST00000439151.2:c.2944G>T	p.Gly982Trp	p.G982W	ENST00000439151	NM_022455.4	982	Ggg/Tgg	5/23	0.210837546900315	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.247251777419253	1		702	957	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069121	5069121	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	86	529	0	ENST00000381652.3:c.1426G>T	p.Asp476Tyr	p.D476Y	ENST00000381652	NM_004972.3	476	Gat/Tat	11/25	1	2	FACETS	0.836	0.739	0.941	0.836	0.739	0.941	CLONAL	1	TRUE	1	0.247251777419253	2		529	832	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1331451	1331451	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	100	665	1	ENST00000400841.2:c.77C>A	p.Ala26Glu	p.A26E	ENST00000400841		26	gCa/gAa	1/6	0.210837546900315	1	FACETS	0.729	0.649	0.813	0.729	0.649	0.813	SUBCLONAL	1	TRUE	0	0.247251777419253	1		666	973	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424658	47424658	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	104	579	0	ENST00000377045.4:c.466C>A	p.His156Asn	p.H156N	ENST00000377045	NM_001654.4	156	Cac/Aac	6/16	0.210837546900315	1	FACETS	0.714	0.638	0.795	0.714	0.638	0.795	SUBCLONAL	1	TRUE	0	0.247251777419253	1		579	1033	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480539	123480539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	55	424	0	ENST00000371139.4:c.47G>T	p.Gly16Val	p.G16V	ENST00000371139	NM_001114937.2	16	gGc/gTc	1/4	0.210837546900315	1	FACETS	0.616	0.526	0.714	0.616	0.526	0.714	SUBCLONAL	1	TRUE	0	0.247251777419253	1		424	633	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576851	7576851	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0018689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	127	430	0	ENST00000269305.4:c.993+2T>C		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.160933723392468	2	FACETS	0.898	0.813	0.987	0.898	0.813	0.987	CLONAL	2	TRUE	0	0.160933723392468	2		430	879	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874031	123874031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1447464550	NA	P-0018689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	11	32	1	ENST00000330479.4:c.62C>T	p.Ala21Val	p.A21V	ENST00000330479	NM_020382.3	21	gCg/gTg	2/9	1	2	FACETS	1	0.782	1	1	0.904	1	CLONAL	2	TRUE	1	0.160933723392468	2		33	60	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218796	66218796	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	32	379	0	ENST00000273854.3:c.2262G>C	p.Glu754Asp	p.E754D	ENST00000273854	NM_004439.5	754	gaG/gaC	13/18	0.160933723392468	1	FACETS	0.739	0.599	0.897	0.739	0.599	0.897	SUBCLONAL	1	TRUE	0	0.160933723392468	1		379	495	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161807855	161807855	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1801582	NA	P-0018689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	126	417	2	ENST00000366898.1:c.1138G>A	p.Val380Ile	p.V380I	ENST00000366898	NM_004562.2	380	Gta/Ata	10/12	1	2	FACETS	0.885	0.801	0.973	1	0.988	1	CLONAL	2	TRUE	1	0.160933723392468	2		419	885	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0018690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	305	574	9	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.548349281551421	5	FACETS	0.902	0.855	0.95	0.902	0.855	0.95	CLONAL	3	FALSE	2	0.548349281551421	5		583	749	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0018690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	146	807	3	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.548349281551421	3	FACETS	0.795	0.726	0.868	0.398	0.363	0.434	SUBCLONAL	1	FALSE	1	0.548349281551421	3		810	853	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0018690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	206	868	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.380992907767994	3	FACETS	1	0.98	1	0.73	0.686	0.774	CLONAL	2	FALSE	0	0.548349281551421	3		868	437	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131772	2131772	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	100	625	1	ENST00000219476.3:c.3787C>G	p.Pro1263Ala	p.P1263A	ENST00000219476	NM_000548.3	1263	Ccc/Gcc	31/42	0.548349281551421	5	FACETS	0.678	0.604	0.756			1	SUBCLONAL	1	FALSE	NA	0.548349281551421	5		626	981	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022347	26022347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	86	535	0	ENST00000435504.4:c.310G>A	p.Gly104Ser	p.G104S	ENST00000435504		104	Ggt/Agt	5/13	0.155052366892232	5	FACETS	0.984	0.872	1			1	INDETERMINATE	1	FALSE	NA	0.548349281551421	5		535	581	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0018691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	119	393	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.976	0.889	1	0.976	0.889	1	CLONAL	1	TRUE	1	0.606619664479239	2		393	402	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0018691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	123	343	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.945	0.862	1	0.945	0.862	1	CLONAL	1	TRUE	1	0.606619664479239	2		344	429	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947865	178947865	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776932	NA	P-0018691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	140	250	0	ENST00000263967.3:c.2740G>A	p.Gly914Arg	p.G914R	ENST00000263967	NM_006218.2	914	Gga/Aga	19/21	1	2	FACETS	0.902	0.826	0.98	0.902	0.826	0.98	CLONAL	1	TRUE	1	0.606619664479239	2		250	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0018691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	256	528	0	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.606619664479239	2		528	832	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921551	178921551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	151	304	0	ENST00000263967.3:c.1033A>G	p.Asn345Asp	p.N345D	ENST00000263967	NM_006218.2	345	Aat/Gat	5/21	1	2	FACETS	0.786	0.722	0.854	0.786	0.722	0.854	SUBCLONAL	1	TRUE	1	0.606619664479239	2		304	633	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021211	31021211	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs373145711	NA	P-0018691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	180	419	0	ENST00000375687.4:c.1210C>T	p.Arg404Ter	p.R404*	ENST00000375687	NM_015338.5	404	Cga/Tga	12/13	1	2	FACETS	0.978	0.906	1	0.978	0.906	1	CLONAL	1	TRUE	1	0.606619664479239	2		419	607	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433324	78433325	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CATC	novel	NA	P-0018691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	208	361	0	ENST00000370768.2:c.273_276dup	p.His93AspfsTer30	p.H93Dfs*30	ENST00000370768	NM_003902.3	92	-/GATG	4/20	0.606619664479239	1	FACETS	0.905	0.847	0.963	0.905	0.847	0.963	CLONAL	1	TRUE	0	0.606619664479239	1		361	528	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418643	49418643	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	189	484	0	ENST00000301067.7:c.15871G>T	p.Glu5291Ter	p.E5291*	ENST00000301067	NM_003482.3	5291	Gag/Tag	49/54	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.606619664479239	2		484	606	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681715	78681716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	172	491	0	ENST00000306801.3:c.425dup	p.Glu143GlyfsTer39	p.E143Gfs*39	ENST00000306801	NM_020761.2	141	-/A	4/34	1	2	FACETS	0.93	0.86	1	0.93	0.86	1	CLONAL	1	TRUE	1	0.606619664479239	2		491	610	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803114	1803114	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	213	475	0	ENST00000260795.2:c.466C>A	p.Pro156Thr	p.P156T	ENST00000260795		156	Ccc/Acc	4/17	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.606619664479239	2		475	626	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651700	48651700	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	148	238	0	ENST00000376670.3:c.866A>G	p.His289Arg	p.H289R	ENST00000376670	NM_002049.3	289	cAc/cGc	5/6	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.606619664479239	1		238	287	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0018692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	263	1181	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.333038550226393	2	FACETS	0.983	0.925	1	0.983	0.925	1	CLONAL	2	TRUE	0	0.341165344493873	2		1182	784	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087936	27087936	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	122	591	2	ENST00000324856.7:c.2223G>T	p.Met741Ile	p.M741I	ENST00000324856	NM_006015.4	741	atG/atT	6/20	1	2	FACETS	0.785	0.709	0.866	0.785	0.709	0.866	SUBCLONAL	1	TRUE	1	0.341165344493873	2		593	911	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667504	241667504	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	80	294	0	ENST00000366560.3:c.946G>A	p.Ala316Thr	p.A316T	ENST00000366560	NM_000143.3	316	Gct/Act	7/10	0.341165344493873	3	FACETS	0.945	0.833	1	0.472	0.416	0.533	CLONAL	1	TRUE	1	0.341165344493873	3		294	581	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141839	108141839	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs374353016	NA	P-0018692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	97	459	0	ENST00000278616.4:c.2887A>G	p.Met963Val	p.M963V	ENST00000278616	NM_000051.3	963	Atg/Gtg	19/63	0.341165344493873	2	FACETS	0.768	0.685	0.857	0.384	0.342	0.429	SUBCLONAL	1	TRUE	0	0.341165344493873	2		459	740	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351048	89351054	+	frameshift_variant	Frame_Shift_Del	DEL	TGTTTTA	TGTTTTA	-	novel	NA	P-0018692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	74	577	0	ENST00000301030.4:c.1896_1902del	p.His632GlnfsTer19	p.H632Qfs*19	ENST00000301030	NM_001256183.1	632	caTAAAACA/ca	9/13	0.228295520379746	1	FACETS	0.371	0.324	0.422	0.371	0.324	0.422	SUBCLONAL	1	TRUE	0	0.341165344493873	1		577	970	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989414	7989414	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	62	597	1	ENST00000319144.4:c.272C>A	p.Ala91Asp	p.A91D	ENST00000319144	NM_001139.2	91	gCc/gAc	2/15	0.228295520379746	1	FACETS	0.425	0.366	0.488	0.425	0.366	0.488	SUBCLONAL	1	TRUE	0	0.341165344493873	1		598	710	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287239	33287239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1159355247	NA	P-0018692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	66	455	0	ENST00000374542.5:c.1858C>T	p.His620Tyr	p.H620Y	ENST00000374542	NM_001141970.1	620	Cac/Tac	6/8	0.175991920065775	3	FACETS	0.566	0.49	0.649	0.189	0.163	0.217	INDETERMINATE	1	TRUE	0	0.341165344493873	3		455	800	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034479	47034479	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	45	582	0	ENST00000377604.3:c.564G>C	p.Met188Ile	p.M188I	ENST00000377604	NM_001204468.1	188	atG/atC	6/24	0.269651384362478	0	FACETS	0.218	0.182	0.258			1	SUBCLONAL	1	TRUE	0	0.341165344493873	0		582	797	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	154	1297	1	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.198299172031916	3	FACETS	0.944	0.871	1	0.629	0.581	0.679	INDETERMINATE	2	TRUE	0	0.440665070636349	3		1298	452	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724560	162724560	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	29	411	0	ENST00000367921.3:c.332G>A	p.Gly111Asp	p.G111D	ENST00000367921	NM_006182.2	111	gGc/gAc	5/18	0.440665070636349	3	FACETS	0.484	0.389	0.592	0.242	0.194	0.296	SUBCLONAL	1	TRUE	1	0.440665070636349	3		411	332	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095680	178095680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	39	348	0	ENST00000397062.3:c.1651C>T	p.His551Tyr	p.H551Y	ENST00000397062	NM_006164.4	551	Cac/Tac	5/5	0.440665070636349	3	FACETS	0.628	0.522	0.746	0.314	0.261	0.373	SUBCLONAL	1	TRUE	1	0.440665070636349	3		348	344	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851815	134851815	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	51	631	0	ENST00000398015.3:c.1221G>T	p.Gln407His	p.Q407H	ENST00000398015	NM_004441.4	407	caG/caT	5/16	0.440665070636349	3	FACETS	0.789	0.673	0.915	0.395	0.336	0.458	CLONAL	1	TRUE	1	0.440665070636349	3		631	358	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106097	27106097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	23	436	2	ENST00000324856.7:c.5708C>T	p.Pro1903Leu	p.P1903L	ENST00000324856	NM_006015.4	1903	cCa/cTa	20/20	0.372017426375926	3	FACETS	0.342	0.266	0.43	0.171	0.133	0.215	SUBCLONAL	1	TRUE	1	0.440665070636349	3		438	372	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941167	36941167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	20	453	1	ENST00000361632.4:c.172G>A	p.Glu58Lys	p.E58K	ENST00000361632		58	Gag/Aag	3/16	0.372017426375926	3	FACETS	0.412	0.315	0.525	0.206	0.157	0.263	SUBCLONAL	1	TRUE	1	0.440665070636349	3		454	269	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400918	72400918	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	33	465	1	ENST00000357731.5:c.253T>A	p.Trp85Arg	p.W85R	ENST00000357731	NM_173808.2	85	Tgg/Agg	2/7	0.372017426375926	3	FACETS	0.653	0.534	0.786	0.326	0.267	0.393	SUBCLONAL	1	TRUE	1	0.440665070636349	3		466	280	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844801	156844801	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs764771898	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	22	441	0	ENST00000524377.1:c.1354+1G>T		p.X452_splice	ENST00000524377	NM_002529.3	452			0.440665070636349	3	FACETS	0.394	0.305	0.497	0.197	0.152	0.249	SUBCLONAL	1	TRUE	1	0.440665070636349	3		441	309	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246490507	246490507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	25	430	0	ENST00000388985.4:c.527C>T	p.Ala176Val	p.A176V	ENST00000388985		176	gCa/gTa	5/12	0.440665070636349	3	FACETS	0.669	0.53	0.826	0.334	0.265	0.413	SUBCLONAL	1	TRUE	1	0.440665070636349	3		430	207	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406258	70406258	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	52	653	1	ENST00000373644.4:c.3772G>T	p.Glu1258Ter	p.E1258*	ENST00000373644	NM_030625.2	1258	Gaa/Taa	4/12	0.198299172031916	3	FACETS	0.709	0.605	0.823	0.236	0.201	0.275	INDETERMINATE	1	TRUE	0	0.440665070636349	3		654	406	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624290	89624290	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660420	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	175	470	2	ENST00000371953.3:c.64G>T	p.Asp22Tyr	p.D22Y	ENST00000371953	NM_000314.4	22	Gac/Tac	1/9	0.198299172031916	3	FACETS	1	0.99	1	0.493	0.456	0.532	INDETERMINATE	1	TRUE	0	0.440665070636349	3		472	655	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123324988	123324988	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	40	466	0	ENST00000358487.5:c.340G>T	p.Asp114Tyr	p.D114Y	ENST00000358487	NM_000141.4	114	Gac/Tac	3/18	0.198299172031916	3	FACETS	0.715	0.596	0.845	0.238	0.198	0.282	INDETERMINATE	1	TRUE	0	0.440665070636349	3		466	310	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132784	64132784	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	194	470	0	ENST00000334205.4:c.918G>T	p.Trp306Cys	p.W306C	ENST00000334205	NM_003942.2	306	tgG/tgT	9/17	0.345897113427285	3	FACETS	0.923	0.867	0.979	0.923	0.867	0.979	CLONAL	3	TRUE	0	0.440665070636349	3		470	388	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514085	69514085	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	288	566	0	ENST00000294312.3:c.596C>A	p.Pro199Gln	p.P199Q	ENST00000294312	NM_005117.2	199	cCa/cAa	3/3	NA	2	FACETS	0.912	0.871	0.952			1	INDETERMINATE	3	TRUE	NA	0.440665070636349	2		566	478	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170456	108170456	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	98	351	0	ENST00000278616.4:c.5021G>T	p.Cys1674Phe	p.C1674F	ENST00000278616	NM_000051.3	1674	tGc/tTc	34/63	0.440665070636349	5	FACETS	1	0.965	1	0.462	0.416	0.509	CLONAL	2	TRUE	0	0.440665070636349	5		351	320	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374117	118374117	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	213	430	0	ENST00000534358.1:c.7510C>G	p.Pro2504Ala	p.P2504A	ENST00000534358	NM_005933.3	2504	Cca/Gca	27/36	0.440665070636349	5	FACETS	0.88	0.828	0.933	0.704	0.662	0.746	CLONAL	4	TRUE	0	0.440665070636349	5		430	456	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142480	119142480	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	175	587	0	ENST00000264033.4:c.479A>T	p.His160Leu	p.H160L	ENST00000264033	NM_005188.3	160	cAc/cTc	3/16	0.440665070636349	5	FACETS	0.844	0.783	0.906	0.506	0.47	0.544	CLONAL	3	TRUE	0	0.440665070636349	5		587	521	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022368	12022368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	297	659	3	ENST00000396373.4:c.475del	p.Gln159ArgfsTer50	p.Q159Rfs*50	ENST00000396373	NM_001987.4	158	gtC/gt	5/8	0.440665070636349	5	FACETS	1	0.961	1	0.764	0.723	0.805	CLONAL	3	TRUE	1	0.440665070636349	5		662	733	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524114	18524114	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1056319997	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	11	239	1	ENST00000266497.5:c.1626G>T	p.Arg542Ser	p.R542S	ENST00000266497		542	agG/agT	11/31	NA	2	FACETS	0.406	0.282	0.558			1	INDETERMINATE	1	TRUE	NA	0.440665070636349	2		240	123	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644567	21644567	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	80	487	0	ENST00000421138.2:c.100G>T	p.Glu34Ter	p.E34*	ENST00000421138		34	Gag/Tag	4/16	0.309214877878144	3	FACETS	0.797	0.71	0.888	0.531	0.473	0.592	SUBCLONAL	2	TRUE	0	0.440665070636349	3		487	278	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120785255	120785255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	87	472	0	ENST00000257552.2:c.853G>T	p.Gly285Trp	p.G285W	ENST00000257552	NM_002442.3	285	Ggg/Tgg	12/15	0.440665070636349	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.440665070636349	1		472	294	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619822	21619822	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	34	230	0	ENST00000382592.4:c.342+2T>A		p.X114_splice	ENST00000382592	NM_014572.2	114			NA	2	FACETS	0.787	0.649	0.939			1	INDETERMINATE	1	TRUE	NA	0.440665070636349	2		230	196	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008359	29008359	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	11	179	0	ENST00000282397.4:c.514-2A>T		p.X172_splice	ENST00000282397	NM_002019.4	172			0.326402462643098	0	FACETS	0.473	0.334	0.637			1	SUBCLONAL	1	TRUE	0	0.440665070636349	0		179	59	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929017	32929017	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	16	580	4	ENST00000380152.3:c.7027G>T	p.Glu2343Ter	p.E2343*	ENST00000380152		2343	Gag/Tag	14/27	NA	2	FACETS	0.335	0.248	0.438			1	INDETERMINATE	1	TRUE	NA	0.440665070636349	2		584	217	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068985	30068985	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1435203998	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	26	668	0	ENST00000331968.5:c.1944G>T	p.Met648Ile	p.M648I	ENST00000331968	NM_002742.2	648	atG/atT	14/18	0.100871071912297	3	FACETS	0.465	0.368	0.575			1	INDETERMINATE	1	TRUE	NA	0.440665070636349	3		668	310	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135354	30135354	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	53	526	0	ENST00000331968.5:c.464G>C	p.Arg155Thr	p.R155T	ENST00000331968	NM_002742.2	155	aGa/aCa	3/18	0.100871071912297	3	FACETS	0.747	0.639	0.864			1	INDETERMINATE	1	TRUE	NA	0.440665070636349	3		526	393	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988498	36988498	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	105	705	0	ENST00000354822.5:c.155A>C	p.Glu52Ala	p.E52A	ENST00000354822	NM_001079668.2	52	gAa/gCa	2/3	0.440665070636349	5	FACETS	1	0.943	1			1	CLONAL	1	TRUE	NA	0.440665070636349	5		705	734	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590564	95590564	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	31	415	0	ENST00000393063.1:c.1345G>T	p.Glu449Ter	p.E449*	ENST00000393063	NM_030621.3	449	Gaa/Taa	9/28	0.440665070636349	3	FACETS	0.477	0.386	0.58	0.238	0.193	0.29	SUBCLONAL	1	TRUE	1	0.440665070636349	3		415	360	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678594	88678594	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	26	301	0	ENST00000360948.2:c.942G>T	p.Glu314Asp	p.E314D	ENST00000360948	NM_001012338.2	314	gaG/gaT	9/19	1	2	FACETS	0.611	0.488	0.751	0.611	0.488	0.751	SUBCLONAL	1	TRUE	1	0.440665070636349	2		301	193	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679770	88679770	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	21	471	2	ENST00000360948.2:c.693C>A	p.Cys231Ter	p.C231*	ENST00000360948	NM_001012338.2	231	tgC/tgA	7/19	1	2	FACETS	0.479	0.37	0.604	0.479	0.37	0.604	SUBCLONAL	1	TRUE	1	0.440665070636349	2		473	199	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680764	88680764	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	53	586	0	ENST00000360948.2:c.493A>T	p.Ser165Cys	p.S165C	ENST00000360948	NM_001012338.2	165	Agc/Tgc	6/19	1	2	FACETS	0.888	0.763	1	0.888	0.763	1	CLONAL	1	TRUE	1	0.440665070636349	2		586	271	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292788	91292788	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	38	563	1	ENST00000355112.3:c.290A>T	p.Gln97Leu	p.Q97L	ENST00000355112	NM_000057.2	97	cAg/cTg	3/22	1	2	FACETS	0.524	0.434	0.624	0.524	0.434	0.624	SUBCLONAL	1	TRUE	1	0.440665070636349	2		564	329	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828059	3828059	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	72	530	0	ENST00000262367.5:c.2066G>T	p.Gly689Val	p.G689V	ENST00000262367	NM_004380.2	689	gGg/gTg	10/31	0.440665070636349	1	FACETS	0.698	0.614	0.788	0.698	0.614	0.788	SUBCLONAL	1	TRUE	0	0.440665070636349	1		530	365	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858433	9858433	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1555482795	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	22	361	0	ENST00000330684.3:c.2968G>T	p.Glu990Ter	p.E990*	ENST00000330684	NM_001134407.1	990	Gag/Tag	13/13	0.440665070636349	1	FACETS	0.484	0.378	0.604	0.484	0.378	0.604	SUBCLONAL	1	TRUE	0	0.440665070636349	1		361	161	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993588	72993588	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	80	441	0	ENST00000268489.5:c.457G>T	p.Gly153Cys	p.G153C	ENST00000268489	NM_006885.3	153	Ggc/Tgc	2/10	0.309214877878144	3	FACETS	1	0.978	1	0.489	0.435	0.546	CLONAL	1	TRUE	0	0.440665070636349	3		441	302	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59770869	59770869	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199831248	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	21	469	0	ENST00000259008.2:c.2497A>G	p.Ile833Val	p.I833V	ENST00000259008	NM_032043.2	833	Att/Gtt	18/20	0.183300613080141	3	FACETS	0.473	0.365	0.598	0.158	0.121	0.2	INDETERMINATE	1	TRUE	0	0.440665070636349	3		469	246	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775034	73775034	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	50	334	0	ENST00000254810.4:c.139G>T	p.Val47Leu	p.V47L	ENST00000254810	NM_005324.3	47	Gtg/Ttg	3/4	0.440665070636349	5	FACETS	0.71	0.602	0.828			1	SUBCLONAL	1	TRUE	NA	0.440665070636349	5		334	531	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78914380	78914380	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	53	482	1	ENST00000306801.3:c.3004G>T	p.Ala1002Ser	p.A1002S	ENST00000306801	NM_020761.2	1002	Gcc/Tcc	25/34	0.183300613080141	3	FACETS	0.844	0.723	0.975	0.281	0.241	0.325	INDETERMINATE	1	TRUE	0	0.440665070636349	3		483	348	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756587	756587	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	80	539	0	ENST00000314574.4:c.241G>T	p.Val81Leu	p.V81L	ENST00000314574	NM_005433.3	81	Gtg/Ttg	2/12	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.440665070636349	2		539	293	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39629506	39629506	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	31	461	1	ENST00000262039.4:c.2200G>T	p.Val734Leu	p.V734L	ENST00000262039	NM_002647.2	734	Gtg/Ttg	21/25	1	2	FACETS	0.529	0.429	0.641	0.529	0.429	0.641	SUBCLONAL	1	TRUE	1	0.440665070636349	2		462	266	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291956	15291956	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	72	647	0	ENST00000263388.2:c.2810G>T	p.Gly937Val	p.G937V	ENST00000263388	NM_000435.2	937	gGg/gTg	18/33	0.420913452710689	2	FACETS	0.847	0.744	0.956	0.423	0.372	0.478	CLONAL	1	TRUE	0	0.440665070636349	2		647	386	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213348	36213348	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	38	654	1	ENST00000222270.7:c.2545G>T	p.Val849Leu	p.V849L	ENST00000222270	NM_014727.1	849	Gtg/Ttg	4/37	0.372017426375926	3	FACETS	0.378	0.312	0.452	0.189	0.156	0.226	SUBCLONAL	1	TRUE	1	0.440665070636349	3		655	557	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918141	50918141	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs753609023	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	46	675	1	ENST00000440232.2:c.2458G>T	p.Ala820Ser	p.A820S	ENST00000440232	NM_002691.3	820	Gcc/Tcc	20/27	0.372017426375926	3	FACETS	0.47	0.395	0.553	0.235	0.197	0.277	SUBCLONAL	1	TRUE	1	0.440665070636349	3		676	542	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470534	25470534	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	72	653	0	ENST00000264709.3:c.940T>G	p.Trp314Gly	p.W314G	ENST00000264709	NM_175629.2	314	Tgg/Ggg	8/23	0.183300613080141	3	FACETS	0.841	0.737	0.953	0.28	0.245	0.318	INDETERMINATE	1	TRUE	0	0.440665070636349	3		653	474	SUCCESS
ALK	238	MSKCC	GRCh37	2	29497991	29497991	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	15	422	0	ENST00000389048.3:c.2015G>T	p.Arg672Ile	p.R672I	ENST00000389048	NM_004304.4	672	aGa/aTa	11/29	0.183300613080141	3	FACETS	0.371	0.271	0.49	0.124	0.09	0.164	INDETERMINATE	1	TRUE	0	0.440665070636349	3		422	224	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213383	39213383	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs368708238	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	35	539	0	ENST00000402219.2:c.3584G>T	p.Arg1195Leu	p.R1195L	ENST00000402219	NM_005633.3	1195	cGa/cTa	23/23	0.183300613080141	3	FACETS	0.486	0.398	0.584	0.162	0.132	0.195	INDETERMINATE	1	TRUE	0	0.440665070636349	3		539	399	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630442	47630442	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	45	533	0	ENST00000233146.2:c.112G>C	p.Asp38His	p.D38H	ENST00000233146	NM_000251.2	38	Gac/Cac	1/16	0.183300613080141	3	FACETS	0.442	0.371	0.521	0.147	0.123	0.174	INDETERMINATE	1	TRUE	0	0.440665070636349	3		533	564	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116253	209116253	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	32	449	0	ENST00000345146.2:c.23G>T	p.Gly8Val	p.G8V	ENST00000345146	NM_005896.2	8	gGt/gTt	3/10	0.440665070636349	3	FACETS	0.499	0.406	0.605	0.25	0.203	0.303	SUBCLONAL	1	TRUE	1	0.440665070636349	3		449	355	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593633	215593633	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	14	326	0	ENST00000260947.4:c.2101C>T	p.Gln701Ter	p.Q701*	ENST00000260947	NM_000465.2	701	Cag/Tag	11/11	0.440665070636349	3	FACETS	0.28	0.202	0.375	0.14	0.101	0.188	SUBCLONAL	1	TRUE	1	0.440665070636349	3		326	277	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790012	40790012	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	55	369	1	ENST00000373198.4:c.2719G>T	p.Gly907Trp	p.G907W	ENST00000373198	NM_133170.3	907	Ggg/Tgg	18/32	NA	2	FACETS	0.835	0.719	0.959			1	INDETERMINATE	1	TRUE	NA	0.440665070636349	2		370	299	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000075	30000075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	142	519	2	ENST00000338641.4:c.88G>A	p.Asp30Asn	p.D30N	ENST00000338641	NM_000268.3	30	Gac/Aac	1/16	0.198299172031916	3	FACETS	1	0.979	1	0.412	0.376	0.449	INDETERMINATE	1	TRUE	0	0.440665070636349	3		521	637	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413743	138413743	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	29	372	0	ENST00000289153.2:c.1777G>A	p.Ala593Thr	p.A593T	ENST00000289153	NM_006219.2	593	Gcg/Acg	12/22	0.440665070636349	3	FACETS	0.393	0.315	0.481	0.196	0.157	0.241	SUBCLONAL	1	TRUE	1	0.440665070636349	3		372	409	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584506	189584506	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	49	412	0	ENST00000264731.3:c.802G>T	p.Glu268Ter	p.E268*	ENST00000264731	NM_003722.4	268	Gag/Tag	6/14	0.440665070636349	3	FACETS	1	0.943	1	0.609	0.521	0.703	CLONAL	1	TRUE	1	0.440665070636349	3		412	223	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902396	1902396	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	21	502	0	ENST00000382891.5:c.15C>G	p.Ile5Met	p.I5M	ENST00000382891	NM_133335.3	5	atC/atG	2/22	0.440665070636349	1	FACETS	0.245	0.189	0.311	0.245	0.189	0.311	SUBCLONAL	1	TRUE	0	0.440665070636349	1		502	303	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133459	55133459	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	19	473	0	ENST00000257290.5:c.763G>C	p.Gly255Arg	p.G255R	ENST00000257290	NM_006206.4	255	Ggc/Cgc	6/23	1	2	FACETS	0.372	0.283	0.476	0.372	0.283	0.476	SUBCLONAL	1	TRUE	1	0.440665070636349	2		473	232	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161422	55161422	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	28	429	0	ENST00000257290.5:c.3253G>T	p.Glu1085Ter	p.E1085*	ENST00000257290	NM_006206.4	1085	Gaa/Taa	23/23	1	2	FACETS	0.424	0.339	0.52	0.424	0.339	0.52	SUBCLONAL	1	TRUE	1	0.440665070636349	2		429	300	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561894	55561894	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	24	284	0	ENST00000288135.5:c.284A>G	p.Tyr95Cys	p.Y95C	ENST00000288135	NM_000222.2	95	tAc/tGc	2/21	1	2	FACETS	0.482	0.379	0.599	0.482	0.379	0.599	SUBCLONAL	1	TRUE	1	0.440665070636349	2		284	226	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521440	187521440	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	48	393	0	ENST00000441802.2:c.11715G>T	p.Gln3905His	p.Q3905H	ENST00000441802	NM_005245.3	3905	caG/caT	22/27	1	2	FACETS	0.828	0.706	0.961	0.828	0.706	0.961	CLONAL	1	TRUE	1	0.440665070636349	2		393	263	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235339	235339	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	52	585	2	ENST00000264932.6:c.1145G>T	p.Gly382Val	p.G382V	ENST00000264932	NM_004168.2	382	gGc/gTc	9/15	NA	2	FACETS	0.661	0.565	0.765			1	INDETERMINATE	1	TRUE	NA	0.440665070636349	2		587	357	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754277	57754277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	22	436	1	ENST00000274289.3:c.574G>A	p.Gly192Arg	p.G192R	ENST00000274289	NM_006622.3	192	Gga/Aga	4/14	0.372017426375926	3	FACETS	0.4	0.31	0.504	0.2	0.155	0.252	SUBCLONAL	1	TRUE	1	0.440665070636349	3		437	305	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170834711	170834711	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	53	370	0	ENST00000296930.5:c.779C>G	p.Ser260Cys	p.S260C	ENST00000296930	NM_002520.6	260	tCt/tGt	10/11	0.440665070636349	6	FACETS	1	0.88	1	0.172	0.147	0.2	CLONAL	1	TRUE	0	0.440665070636349	6		370	438	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518737	176518737	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	241	581	0	ENST00000292408.4:c.655C>A	p.Arg219Ser	p.R219S	ENST00000292408	NM_213647.1	219	Cgc/Agc	6/18	0.440665070636349	6	FACETS	1	0.973	1	0.699	0.66	0.737	CLONAL	4	TRUE	0	0.440665070636349	6		581	491	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039516	180039516	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	185	699	0	ENST00000261937.6:c.3527G>C	p.Arg1176Thr	p.R1176T	ENST00000261937	NM_182925.4	1176	aGg/aCg	26/30	0.440665070636349	1	FACETS	0.759	0.71	0.81	1	0.992	1	SUBCLONAL	2	TRUE	0	0.440665070636349	1		699	431	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528372	157528373	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	74	494	2	ENST00000346085.5:c.6097_6098delinsTT	p.Gly2033Leu	p.G2033L	ENST00000346085	NM_020732.3	2033	GGg/TTg	20/20	0.440665070636349	3	FACETS	1	0.955	1	0.589	0.519	0.663	CLONAL	1	TRUE	1	0.440665070636349	3		496	348	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444338	50444338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	91	251	0	ENST00000331340.3:c.268G>A	p.Glu90Lys	p.E90K	ENST00000331340	NM_006060.4	90	Gag/Aag	4/8	0.440665070636349	4	FACETS	1	0.949	1	0.724	0.652	0.799	CLONAL	2	TRUE	1	0.440665070636349	4		251	274	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459468	50459468	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	62	343	0	ENST00000331340.3:c.757C>A	p.Leu253Met	p.L253M	ENST00000331340	NM_006060.4	253	Ctg/Atg	7/8	0.440665070636349	4	FACETS	1	0.967	1	0.461	0.401	0.525	CLONAL	1	TRUE	1	0.440665070636349	4		343	293	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346277	152346277	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	17	498	0	ENST00000359321.1:c.293A>G	p.His98Arg	p.H98R	ENST00000359321	NM_005431.1	98	cAc/cGc	3/3	0.309214877878144	3	FACETS	0.434	0.324	0.563	0.145	0.108	0.188	SUBCLONAL	1	TRUE	0	0.440665070636349	3		498	217	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372233	55372233	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	56	366	0	ENST00000297316.4:c.923G>C	p.Gly308Ala	p.G308A	ENST00000297316	NM_022454.3	308	gGg/gCg	2/2	0.440665070636349	1	FACETS	0.78	0.675	0.893	0.78	0.675	0.893	SUBCLONAL	1	TRUE	0	0.440665070636349	1		366	254	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376672	8376672	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	23	514	0	ENST00000356435.5:c.4441C>T	p.Gln1481Ter	p.Q1481*	ENST00000356435		1481	Caa/Taa	27/35	0.440665070636349	1	FACETS	0.286	0.223	0.358	0.286	0.223	0.358	SUBCLONAL	1	TRUE	0	0.440665070636349	1		514	285	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971110	21971110	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	37	386	0	ENST00000304494.5:c.248A>T	p.His83Leu	p.H83L	ENST00000304494	NM_000077.4	83	cAc/cTc	2/3	0.440665070636349	1	FACETS	0.552	0.459	0.656	0.552	0.459	0.656	SUBCLONAL	1	TRUE	0	0.440665070636349	1		386	237	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238339	98238339	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	19	282	0	ENST00000331920.6:c.1705G>T	p.Ala569Ser	p.A569S	ENST00000331920	NM_000264.3	569	Gct/Tct	12/24	1	2	FACETS	0.456	0.348	0.582	0.456	0.348	0.582	SUBCLONAL	1	TRUE	1	0.440665070636349	2		282	189	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045696	47045697	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	81	313	0	ENST00000377604.3:c.2578_2579dup	p.Asn860LysfsTer27	p.N860Kfs*27	ENST00000377604	NM_001204468.1	859	-/AA	23/24	0.412557831771308	2	FACETS	0.789	0.707	0.874			1	SUBCLONAL	2	TRUE	NA	0.440665070636349	2		313	233	SUCCESS
BTK	695	MSKCC	GRCh37	X	100614281	100614281	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	64	231	0	ENST00000308731.7:c.894G>C	p.Glu298Asp	p.E298D	ENST00000308731	NM_000061.2	298	gaG/gaC	10/19	0.412557831771308	2	FACETS	0.76	0.671	0.854			1	SUBCLONAL	2	TRUE	NA	0.440665070636349	2		231	191	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123499609	123499609	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0018693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	29	248	0	ENST00000371139.4:c.138-2A>T		p.X46_splice	ENST00000371139	NM_001114937.2	46			0.412557831771308	2	FACETS	1	0.838	1			1	CLONAL	1	TRUE	NA	0.440665070636349	2		248	128	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	457	588	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	0.909491326078318	1	FACETS	0.989	0.965	1	0.989	0.965	1	CLONAL	1	TRUE	0	0.909491326078318	1		588	554	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038261	30038261	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	346	439	0	ENST00000338641.4:c.435del	p.Val146SerfsTer28	p.V146Sfs*28	ENST00000338641	NM_000268.3	145	gCc/gc	4/16	0.909491326078318	1	FACETS	0.754	0.724	0.784	0.754	0.724	0.784	SUBCLONAL	1	TRUE	0	0.909491326078318	1		439	550	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440052	49440052	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	120	512	0	ENST00000301067.7:c.4574del	p.His1525ProfsTer37	p.H1525Pfs*37	ENST00000301067	NM_003482.3	1525	cAc/cc	16/54	0.174204532487351	3	FACETS	1	0.965	1	0.578	0.52	0.639	CLONAL	1	TRUE	1	0.174204532487351	3		512	1296	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	15	364	1				ENST00000310581	NM_198253.2	-/1132			0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		365	223	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0018697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	26	900	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		901	386	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0018698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	101	745	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.18	2		745	918	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604653	48604653	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	21	230	0	ENST00000342988.3:c.1475T>G	p.Val492Gly	p.V492G	ENST00000342988	NM_005359.5	492	gTt/gGt	12/12	1	2	FACETS	0.667	0.513	0.846	0.667	0.513	0.846	SUBCLONAL	1	TRUE	1	0.18	2		230	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579557	7579557	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	79	477	0	ENST00000269305.4:c.130del	p.Met44CysfsTer79	p.M44Cfs*79	ENST00000269305	NM_001126112.2	44	Atg/tg	4/11	0.195219467836116	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.18	1		477	754	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0018701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	79	708	1	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	0.169391767037736	2		709	860	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0018701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	73	459	1	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.169391767037736	3	FACETS	1	0.969	1	0.685	0.599	0.779	CLONAL	1	TRUE	1	0.169391767037736	3		460	682	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412110	63412110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852216	NA	P-0018701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	84	290	0	ENST00000330258.3:c.1057C>T	p.Arg353Ter	p.R353*	ENST00000330258	NM_152424.3	353	Cga/Tga	2/2	1	1	FACETS	0.844	0.747	0.947	1	0.982	1	CLONAL	2	TRUE	0	0.169391767037736	1		290	538	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0018701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	64	242	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	0.169391767037736	3	FACETS	1	0.939	1	0.576	0.498	0.661	CLONAL	1	TRUE	1	0.169391767037736	3		242	711	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501260	140501260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730880413	NA	P-0018701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	120	338	0	ENST00000288602.6:c.812G>A	p.Arg271His	p.R271H	ENST00000288602	NM_004333.4	271	cGt/cAt	6/18	0.142425818635617	4	FACETS	0.949	0.856	1	0.949	0.856	1	CLONAL	2	TRUE	2	0.169391767037736	4		338	873	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692920	89692921	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs398123323	NA	P-0018701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	91	363	0	ENST00000371953.3:c.405dup	p.Cys136MetfsTer44	p.C136Mfs*44	ENST00000371953	NM_000314.4	135	ata/atAa	5/9	0.167499982418716	2	FACETS	0.781	0.693	0.874	0.781	0.693	0.874	SUBCLONAL	2	TRUE	0	0.169391767037736	2		363	688	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573485	48573485	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	37	210	0	ENST00000342988.3:c.69G>T	p.Leu23Phe	p.L23F	ENST00000342988	NM_005359.5	23	ttG/ttT	2/12	0.169391767037736	1	FACETS	1	0.833	1	1	0.833	1	CLONAL	1	TRUE	0	0.169391767037736	1		210	396	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054254	30054254	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1555994854	NA	P-0018702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	146	310	0	ENST00000338641.4:c.675+1G>A		p.X225_splice	ENST00000338641	NM_000268.3	225			1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		310	701	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057273	30057309	+	frameshift_variant	Frame_Shift_Del	DEL	CCAAGATCTCCTTCCCGTGGAATGAAATCCGAAACAT	CCAAGATCTCCTTCCCGTGGAATGAAATCCGAAACAT	-	novel	NA	P-0018702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	134	498	0	ENST00000338641.4:c.756_792del	p.Lys253ArgfsTer31	p.K253Rfs*31	ENST00000338641	NM_000268.3	252	cCCAAGATCTCCTTCCCGTGGAATGAAATCCGAAACATc/cc	8/16	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		498	824	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0018704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	241	431	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.324246352789958	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.324246352789958	2		431	687	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0018705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	68	613	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.164559451459483	8	FACETS	1	0.964	1	0.224	0.194	0.257	CLONAL	1	TRUE	2	0.164559451459483	8		613	918	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0018705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	156	630	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	1	2	FACETS	1	0.926	1	1	0.993	1	CLONAL	3	TRUE	1	0.164559451459483	2		630	627	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597883	43597883	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs551142665	NA	P-0018705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	89	622	1	ENST00000355710.3:c.431G>A	p.Arg144His	p.R144H	ENST00000355710	NM_020975.4	144	cGc/cAc	3/20	1	2	FACETS	1	0.889	1	1	0.985	1	CLONAL	2	TRUE	1	0.164559451459483	2		623	541	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776910	76776910	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	100	575	0	ENST00000373344.5:c.7042C>T	p.Gln2348Ter	p.Q2348*	ENST00000373344	NM_000489.3	2348	Caa/Taa	33/35	0.164559451459483	3	FACETS	1	0.958	1	0.578	0.515	0.646	CLONAL	1	TRUE	1	0.164559451459483	3		575	1138	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0018706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	205	1181	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.268522592136298	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.268522592136298	3		1182	823	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0018706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	204	431	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.268522592136298	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.268522592136298	2		431	713	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877349	40877349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747289224	NA	P-0018706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	139	358	0	ENST00000373198.4:c.2347G>A	p.Val783Met	p.V783M	ENST00000373198	NM_133170.3	783	Gtg/Atg	15/32	0.268522592136298	3	FACETS	1	0.919	1	1	0.919	1	CLONAL	2	TRUE	1	0.268522592136298	3		358	584	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643348	52643348	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	203	541	1	ENST00000394830.3:c.2548C>T	p.Arg850Ter	p.R850*	ENST00000394830	NM_018313.4	850	Cga/Tga	17/30	0.268522592136298	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.268522592136298	2		542	698	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001317	150001317	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	185	641	0	ENST00000253339.5:c.2287G>T	p.Glu763Ter	p.E763*	ENST00000253339		763	Gaa/Taa	4/7	0.268522592136298	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.268522592136298	2		641	635	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090491	5090491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	80	478	0	ENST00000381652.3:c.2807G>A	p.Ser936Asn	p.S936N	ENST00000381652	NM_004972.3	936	aGt/aAt	21/25	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.268522592136298	2		478	537	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	396	364	1				ENST00000310581	NM_198253.2	-/1132			0.595223391033254	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	1	0.595223391033254	4		365	676	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0018707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	555	679	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.551492371428924	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.595223391033254	2		679	888	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105592	27105592	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	61	397	0	ENST00000324856.7:c.5203G>T	p.Glu1735Ter	p.E1735*	ENST00000324856	NM_006015.4	1735	Gag/Tag	20/20	0.583523178596909	3	FACETS	0.477	0.411	0.548	0.238	0.205	0.274	SUBCLONAL	1	TRUE	1	0.595223391033254	3		397	558	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490547	56490547	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	98	434	0	ENST00000267101.3:c.2191G>C	p.Glu731Gln	p.E731Q	ENST00000267101	NM_001982.3	731	Gag/Cag	19/28	0.594748168081535	2	FACETS	0.834	0.749	0.922	0.417	0.374	0.461	CLONAL	1	TRUE	0	0.595223391033254	2		434	395	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161458	2161467	+	frameshift_variant	Frame_Shift_Del	DEL	TTGGACTTGC	TTGGACTTGC	-	novel	NA	P-0018707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	172	600	0	ENST00000434045.2:c.60_69del	p.Met20IlefsTer7	p.M20Ifs*7	ENST00000434045	NM_001127598.1	20	atGCAAGTCCAA/at	2/5	1	2	FACETS	0.782	0.721	0.845	0.782	0.721	0.845	SUBCLONAL	1	TRUE	1	0.595223391033254	2		600	739	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954199	48954199	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	182	326	0	ENST00000267163.4:c.1400G>A	p.Arg467Gln	p.R467Q	ENST00000267163	NM_000321.2	467	cGa/cAa	15/27	NA	2	FACETS	0.759	0.709	0.808			1	INDETERMINATE	2	TRUE	NA	0.595223391033254	2		326	403	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039158	49039158	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	175	288	1	ENST00000267163.4:c.2236G>T	p.Glu746Ter	p.E746*	ENST00000267163	NM_000321.2	746	Gaa/Taa	22/27	NA	2	FACETS	0.948	0.892	1			1	INDETERMINATE	2	TRUE	NA	0.595223391033254	2		289	310	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643348	38643348	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs946203764	NA	P-0018707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	138	446	0	ENST00000299084.4:c.818G>C	p.Arg273Thr	p.R273T	ENST00000299084	NM_152594.2	273	aGa/aCa	7/7	0.425148811653304	2	FACETS	0.97	0.889	1	0.485	0.444	0.527	CLONAL	1	TRUE	0	0.595223391033254	2		446	478	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639653	3639653	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	284	796	0	ENST00000294008.3:c.3986C>G	p.Ser1329Cys	p.S1329C	ENST00000294008	NM_032444.2	1329	tCt/tGt	12/15	1	2	FACETS	0.999	0.941	1	0.999	0.941	1	CLONAL	1	TRUE	1	0.595223391033254	2		796	955	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646348	3646348	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0018707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	202	658	0	ENST00000294008.3:c.1730C>G	p.Ser577Ter	p.S577*	ENST00000294008	NM_032444.2	577	tCa/tGa	8/15	1	2	FACETS	0.93	0.865	0.997	0.93	0.865	0.997	CLONAL	1	TRUE	1	0.595223391033254	2		658	730	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719526	61719526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	105	544	0	ENST00000401558.2:c.1657C>T	p.Arg553Cys	p.R553C	ENST00000401558	NM_003400.3	553	Cgt/Tgt	15/25	0.543317193491289	2	FACETS	0.789	0.711	0.871	0.395	0.355	0.436	SUBCLONAL	1	TRUE	0	0.595223391033254	2		544	447	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568503	41568503	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	53	342	0	ENST00000263253.7:c.4453G>C	p.Asp1485His	p.D1485H	ENST00000263253	NM_001429.3	1485	Gat/Cat	28/31	0.595223391033254	2	FACETS	0.576	0.494	0.665	0.288	0.247	0.333	SUBCLONAL	1	TRUE	0	0.595223391033254	2		342	309	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021828	71021828	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0018707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	53	188	0	ENST00000318789.4:c.1531-1G>A		p.X511_splice	ENST00000318789	NM_032682.5	511			0.583523178596909	3	FACETS	0.843	0.725	0.971	0.422	0.362	0.486	CLONAL	1	TRUE	1	0.595223391033254	3		188	274	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508787	31508787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370207689	NA	P-0018707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	216	624	2	ENST00000344624.3:c.1528C>T	p.Arg510Cys	p.R510C	ENST00000344624		510	Cgc/Tgc	7/33	0.595223391033254	4	FACETS	0.863	0.8	0.928	0.288	0.266	0.31	CLONAL	1	TRUE	1	0.595223391033254	4		626	1342	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38964976	38964976	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1378946096	NA	P-0018707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	41	203	0	ENST00000357387.3:c.1318C>T	p.His440Tyr	p.H440Y	ENST00000357387	NM_152756.3	440	Cat/Tat	16/38	0.595223391033254	4	FACETS	0.633	0.529	0.749	0.211	0.176	0.25	SUBCLONAL	1	TRUE	1	0.595223391033254	4		203	347	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109415138	109415138	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	198	703	0	ENST00000436639.2:c.139C>G	p.His47Asp	p.H47D	ENST00000436639	NM_014454.2	47	Cat/Gat	1/10	0.424615362323426	3	FACETS	0.896	0.83	0.965	0.299	0.276	0.322	CLONAL	1	TRUE	0	0.595223391033254	3		703	963	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157256700	157256700	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0018707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	72	366	0	ENST00000346085.5:c.2027C>G	p.Ser676Ter	p.S676*	ENST00000346085	NM_020732.3	676	tCa/tGa	5/20	0.424615362323426	3	FACETS	0.851	0.748	0.96	0.284	0.249	0.32	CLONAL	1	TRUE	0	0.595223391033254	3		366	369	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815544	139815544	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	207	583	0	ENST00000247668.2:c.1015G>A	p.Glu339Lys	p.E339K	ENST00000247668	NM_021138.3	339	Gag/Aag	9/11	1	2	FACETS	0.981	0.914	1	0.981	0.914	1	CLONAL	1	TRUE	1	0.595223391033254	2		583	709	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0018708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	19	752	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.0886657250469529	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		754	341	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0018708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	19	745	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		745	412	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272302	15272302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	22	584	1	ENST00000263388.2:c.6137C>T	p.Pro2046Leu	p.P2046L	ENST00000263388	NM_000435.2	2046	cCa/cTa	33/33	0.0886657250469529	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		585	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0018709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	180	419	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	0.327668365464663	2	FACETS	0.974	0.904	1	0.974	0.904	1	CLONAL	2	TRUE	0	0.327668365464663	2		419	564	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0018709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	49	199	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	0.327668365464663	1	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	0	0.327668365464663	1		199	243	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023848	27023849	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGGCCCCAGGACGGGGGCGCCGGCAA	novel	NA	P-0018709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	33	270	0	ENST00000324856.7:c.961_986dup	p.Ala330ArgfsTer42	p.A330Rfs*42	ENST00000324856	NM_006015.4	318	-/GGGCCCCAGGACGGGGGCGCCGGCAA	1/20	0.327668365464663	1	FACETS	0.431	0.351	0.521	0.431	0.351	0.521	SUBCLONAL	1	TRUE	0	0.327668365464663	1		270	391	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672758	86672758	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1204340475	NA	P-0018710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	87	298	0	ENST00000274376.6:c.2245C>T	p.Arg749Ter	p.R749*	ENST00000274376	NM_002890.2	749	Cga/Tga	17/25	0.283782301410535	1	FACETS	0.782	0.692	0.877	0.782	0.692	0.877	SUBCLONAL	1	TRUE	0	0.283782301410535	1		298	673	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990399	81990399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199530350	NA	P-0018710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	198	603	0	ENST00000359376.3:c.3670C>T	p.Arg1224Cys	p.R1224C	ENST00000359376	NM_002661.3	1224	Cgc/Tgc	32/33	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.283782301410535	2		603	1166	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180653	56180653	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	95	261	0	ENST00000399503.3:c.3982G>A	p.Gly1328Arg	p.G1328R	ENST00000399503	NM_005921.1	1328	Ggg/Agg	16/20	0.283782301410535	1	FACETS	0.964	0.86	1	0.964	0.86	1	CLONAL	1	TRUE	0	0.283782301410535	1		261	596	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0018711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	526	1034	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.442019741297232	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.442019741297232	2		1035	1098	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528078	103528078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368829739	NA	P-0018711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	131	324	1	ENST00000355739.4:c.3386C>T	p.Ser1129Leu	p.S1129L	ENST00000355739	NM_000123.3	1129	tCg/tTg	15/15	0.442019741297232	2	FACETS	0.981	0.894	1	0.491	0.447	0.537	CLONAL	1	TRUE	0	0.442019741297232	2		325	604	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354324	354324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200716081	NA	P-0018711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	196	513	1	ENST00000262320.3:c.1234C>T	p.Arg412Trp	p.R412W	ENST00000262320	NM_003502.3	412	Cgg/Tgg	5/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.442019741297232	2		514	815	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274856	38274857	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0018711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	191	435	0	ENST00000425967.3:c.1723_1724del	p.Ile575HisfsTer111	p.I575Hfs*111	ENST00000425967	NM_001174067.1	575	ATc/c	13/19	0.442019741297232	5	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.442019741297232	5		435	1287	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27203000	27203000	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	188	538	0	ENST00000380036.4:c.2092C>T	p.Gln698Ter	p.Q698*	ENST00000380036	NM_000459.3	698	Cag/Tag	13/23	0.413197442903396	4	FACETS	0.939	0.865	1	0.469	0.432	0.508	CLONAL	1	TRUE	2	0.442019741297232	4		538	1307	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577070	7577070	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	252	554	0	ENST00000269305.4:c.868del	p.Arg290AlafsTer55	p.R290Afs*55	ENST00000269305	NM_001126112.2	290	Cgc/gc	8/11	0.534963441120368	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.534963441120368	1		554	652	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282378	115282378	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	26	413	0	ENST00000438362.2:c.272G>C	p.Arg91Pro	p.R91P	ENST00000438362	NM_001242891.1	91	cGt/cCt	3/20	0.534963441120368	1	FACETS	0.139	0.109	0.172	0.139	0.109	0.172	SUBCLONAL	1	TRUE	0	0.534963441120368	1		413	514	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348044	89348044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	276	663	0	ENST00000301030.4:c.4906G>A	p.Asp1636Asn	p.D1636N	ENST00000301030	NM_001256183.1	1636	Gac/Aac	9/13	1	2	FACETS	0.992	0.932	1	0.992	0.932	1	CLONAL	1	TRUE	1	0.534963441120368	2		663	1040	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212512	36212512	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	226	566	0	ENST00000222270.7:c.2263C>G	p.Pro755Ala	p.P755A	ENST00000222270	NM_014727.1	755	Cca/Gca	3/37	1	2	FACETS	0.911	0.85	0.975	0.911	0.85	0.975	CLONAL	1	TRUE	1	0.534963441120368	2		566	927	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054207	30054207	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	161	334	0	ENST00000338641.4:c.629T>A	p.Ile210Lys	p.I210K	ENST00000338641	NM_000268.3	210	aTa/aAa	7/16	0.428727305553037	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.534963441120368	1		334	440	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295293	1295293	+	upstream_gene_variant	5'Flank	SNP	T	T	C	novel	NA	P-0018712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	188	493	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.955	0.885	1	0.955	0.885	1	CLONAL	1	TRUE	1	0.534963441120368	2		493	736	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437912	52437912	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0018713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	182	767	0	ENST00000460680.1:c.1251-2A>T		p.X417_splice	ENST00000460680	NM_004656.3	417			0.352403033283448	1	FACETS	0.747	0.688	0.809	0.747	0.688	0.809	SUBCLONAL	1	TRUE	0	0.352403033283448	1		767	1139	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69986985	69986985	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	244	652	0	ENST00000394351.3:c.46C>T	p.Leu16Phe	p.L16F	ENST00000394351	NM_000248.3	16	Ctc/Ttc	2/9	0.352403033283448	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.352403033283448	1		652	938	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0018714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1194	115	730	1	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	0.205572850340951	1	FACETS	0.404	0.362	0.448	0.404	0.362	0.448	INDETERMINATE	1	TRUE	0	0.3575325981289	1		731	1309	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023857	27023863	+	frameshift_variant	Frame_Shift_Del	DEL	GGACGGG	GGACGGG	-	novel	NA	P-0018714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	156	228	0	ENST00000324856.7:c.965_971del	p.Asp322AlafsTer39	p.D322Afs*39	ENST00000324856	NM_006015.4	321	caGGACGGG/ca	1/20	0.342231710156856	2	FACETS	0.849	0.783	0.917	0.849	0.783	0.917	CLONAL	2	TRUE	0	0.3575325981289	2		228	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578446	7578458	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCCATGGCGCG	TGGCCATGGCGCG	-	novel	NA	P-0018714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	216	596	0	ENST00000269305.4:c.472_484del	p.Arg158SerfsTer8	p.R158Sfs*8	ENST00000269305	NM_001126112.2	158	CGCGCCATGGCCAtc/tc	5/11	0.3575325981289	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.3575325981289	1		596	884	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732974	30732975	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	92	267	0	ENST00000295754.5:c.1588dup	p.Thr530AsnfsTer11	p.T530Nfs*11	ENST00000295754	NM_003242.5	529	-/A	7/7	0.205572850340951	1	FACETS	0.753	0.671	0.841	0.753	0.671	0.841	INDETERMINATE	1	TRUE	0	0.3575325981289	1		267	561	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577560	7577560	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520002	NA	P-0018718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	451	565	0	ENST00000269305.4:c.721T>C	p.Ser241Pro	p.S241P	ENST00000269305	NM_001126112.2	241	Tcc/Ccc	7/11	0.675299787459494	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.731599275906589	1		565	696	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	125	684	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.244559505730204	4	FACETS	1	0.976	1	0.629	0.568	0.693	CLONAL	1	TRUE	2	0.244559505730204	4		684	1011	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs967461896	NA	P-0018719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	192	420	0	ENST00000269305.4:c.526T>C	p.Cys176Arg	p.C176R	ENST00000269305	NM_001126112.2	176	Tgc/Cgc	5/11	NA	2	FACETS	0.991	0.919	1			1	INDETERMINATE	2	TRUE	NA	0.244559505730204	2		420	792	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117642	70117642	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	123	514	0	ENST00000245479.2:c.110C>A	p.Ser37Ter	p.S37*	ENST00000245479	NM_000346.3	37	tCg/tAg	1/3	0.240550947467924	2	FACETS	1	0.947	1	0.537	0.485	0.592	CLONAL	1	TRUE	0	0.244559505730204	2		514	937	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917835	29917835	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	157	702	1	ENST00000389048.3:c.833C>A	p.Pro278His	p.P278H	ENST00000389048	NM_004304.4	278	cCt/cAt	3/29	0.240550947467924	2	FACETS	1	0.927	1	0.508	0.464	0.555	CLONAL	1	TRUE	0	0.244559505730204	2		703	1263	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165175	47165175	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	92	230	0	ENST00000409792.3:c.951C>G	p.Ile317Met	p.I317M	ENST00000409792	NM_014159.6	317	atC/atG	3/21	0.244559505730204	3	FACETS	0.869	0.775	0.968	0.869	0.775	0.968	CLONAL	2	TRUE	1	0.244559505730204	3		230	486	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165290	47165290	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0018719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	134	246	0	ENST00000409792.3:c.836C>G	p.Ser279Ter	p.S279*	ENST00000409792	NM_014159.6	279	tCa/tGa	3/21	0.244559505730204	3	FACETS	1	0.923	1	1	0.923	1	CLONAL	2	TRUE	1	0.244559505730204	3		246	607	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139213	37139213	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	71	368	1	ENST00000373509.5:c.553A>G	p.Ile185Val	p.I185V	ENST00000373509	NM_002648.3	185	Atc/Gtc	4/6	0.244559505730204	5	FACETS	0.703	0.611	0.803	0.234	0.203	0.268	SUBCLONAL	1	TRUE	2	0.244559505730204	5		369	1129	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522571	157522571	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1563	164	803	2	ENST00000346085.5:c.4843G>T	p.Ala1615Ser	p.A1615S	ENST00000346085	NM_020732.3	1615	Gca/Tca	18/20	0.117834523014421	3	FACETS	0.872	0.797	0.95			1	INDETERMINATE	1	TRUE	NA	0.244559505730204	3		805	1727	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215809	98215809	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	98	507	0	ENST00000331920.6:c.3400C>G	p.Leu1134Val	p.L1134V	ENST00000331920	NM_000264.3	1134	Ctg/Gtg	20/24	0.237616421695021	3	FACETS	0.857	0.762	0.957	0.286	0.254	0.319	CLONAL	1	TRUE	0	0.244559505730204	3		507	1050	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0018720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	212	629	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.373691592118628	2	FACETS	0.901	0.843	0.961	0.901	0.843	0.961	CLONAL	2	TRUE	0	0.396030432860193	2		630	594	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0018720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	90	192	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.396030432860193	2		192	391	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246472	105246472	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	179	408	0	ENST00000349310.3:c.128A>G	p.Gln43Arg	p.Q43R	ENST00000349310	NM_001014432.1	43	cAg/cGg	4/15	0.373691592118628	2	FACETS	1	0.94	1	0.511	0.471	0.552	CLONAL	1	TRUE	0	0.396030432860193	2		408	885	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210432	36210432	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	158	368	2	ENST00000222270.7:c.425G>A	p.Arg142Gln	p.R142Q	ENST00000222270	NM_014727.1	142	cGa/cAa	2/37	1	2	FACETS	0.929	0.852	1	0.929	0.852	1	CLONAL	1	TRUE	1	0.396030432860193	2		370	859	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0018723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	34	548	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	0.531	0.431	0.643	0.531	0.431	0.643	SUBCLONAL	1	TRUE	1	0.12	2		548	1068	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692818	89692818	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	9	221	0	ENST00000371953.3:c.302T>G	p.Ile101Ser	p.I101S	ENST00000371953	NM_000314.4	101	aTc/aGc	5/9	1	2	FACETS	0.38	0.25	0.547	0.38	0.25	0.547	SUBCLONAL	1	TRUE	1	0.12	2		221	395	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	194	917	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.428205655569158	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.428205655569158	1		917	582	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0018726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	100	636	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.284	0.253	0.317	0.284	0.253	0.317	SUBCLONAL	1	TRUE	1	0.742570676354285	2		636	949	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	95	401	1	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	1	2	FACETS	0.289	0.257	0.324	0.289	0.257	0.324	SUBCLONAL	1	TRUE	1	0.742570676354285	2		402	885	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654718	67654718	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	96	389	0	ENST00000264010.4:c.1205C>T	p.Ser402Leu	p.S402L	ENST00000264010	NM_006565.3	402	tCa/tTa	6/12	0.249186239951136	1	FACETS	0.213	0.189	0.238	0.213	0.189	0.238	INDETERMINATE	1	TRUE	0	0.742570676354285	1		389	763	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177010	56177011	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	96	293	0	ENST00000399503.3:c.2281dup	p.Ile761AsnfsTer3	p.I761Nfs*3	ENST00000399503	NM_005921.1	760	-/A	13/20	1	2	FACETS	0.355	0.316	0.397	0.355	0.316	0.397	SUBCLONAL	1	TRUE	1	0.742570676354285	2		293	728	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177907	56177908	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0018726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	143	414	0	ENST00000399503.3:c.2882_2883dup	p.Pro962AspfsTer7	p.P962Dfs*7	ENST00000399503	NM_005921.1	960	-/AG	14/20	1	2	FACETS	0.378	0.344	0.414	0.378	0.344	0.414	SUBCLONAL	1	TRUE	1	0.742570676354285	2		414	1018	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0018727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	158	636	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.198126505797149	4	FACETS	0.834	0.765	0.907	0.834	0.765	0.907	CLONAL	2	TRUE	2	0.287162487068138	4		636	849	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624269	89624269	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0018727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	274	274	1	ENST00000371953.3:c.43A>T	p.Arg15Ter	p.R15*	ENST00000371953	NM_000314.4	15	Aga/Tga	1/9	0.287162487068138	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	TRUE	0	0.287162487068138	3		275	697	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554175	63554175	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	183	442	0	ENST00000307078.5:c.564G>T	p.Gln188His	p.Q188H	ENST00000307078	NM_004655.3	188	caG/caT	2/11	0.198126505797149	4	FACETS	0.819	0.755	0.885	0.819	0.755	0.885	CLONAL	2	TRUE	2	0.287162487068138	4		442	1002	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0018728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	159	574	9	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.949	0.87	1	0.949	0.87	1	CLONAL	1	TRUE	1	0.41385207157297	2		583	810	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0018728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	158	515	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.41385207157297	2		515	748	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842748	68842748	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	171	336	0	ENST00000261769.5:c.684C>A	p.Tyr228Ter	p.Y228*	ENST00000261769	NM_004360.3	228	taC/taA	5/16	0.41385207157297	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.41385207157297	1		336	644	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0018729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	201	600	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.280288075824023	1	FACETS	1	0.956	1	1	0.956	1	INDETERMINATE	1	TRUE	0	0.477144266548241	1		600	620	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591931	48591931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	176	233	1	ENST00000342988.3:c.1094G>A	p.Gly365Asp	p.G365D	ENST00000342988	NM_005359.5	365	gGt/gAt	9/12	0.477144266548241	2	FACETS	0.936	0.874	0.999	0.936	0.874	0.999	CLONAL	2	TRUE	0	0.477144266548241	2		234	394	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663034	227663034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779847464	NA	P-0018729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	121	241	0	ENST00000305123.5:c.421G>A	p.Gly141Ser	p.G141S	ENST00000305123	NM_005544.2	141	Ggc/Agc	1/2	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.477144266548241	2		241	487	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971120	55971120	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	159	385	0	ENST00000263923.4:c.1677G>T	p.Met559Ile	p.M559I	ENST00000263923	NM_002253.2	559	atG/atT	13/30	1	2	FACETS	0.979	0.9	1	0.979	0.9	1	CLONAL	1	TRUE	1	0.477144266548241	2		385	681	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243896	46243897	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0018729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	124	325	1	ENST00000334344.6:c.1990_1991delinsTT	p.Ala664Leu	p.A664L	ENST00000334344	NM_152641.2	664	GCa/TTa	15/21	1	2	FACETS	0.861	0.781	0.944	0.861	0.781	0.944	CLONAL	1	TRUE	1	0.477144266548241	2		326	604	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108674	8108674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1461095881	NA	P-0018729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	233	405	2	ENST00000585124.1:c.721C>T	p.Pro241Ser	p.P241S	ENST00000585124	NM_004217.3	241	Ccc/Tcc	8/9	NA	2	FACETS	1	0.955	1			1	INDETERMINATE	1	TRUE	NA	0.477144266548241	2		407	949	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884852	134884852	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	116	268	0	ENST00000398015.3:c.1628C>G	p.Ala543Gly	p.A543G	ENST00000398015	NM_004441.4	543	gCt/gGt	8/16	NA	2	FACETS	1	0.96	1			1	INDETERMINATE	1	TRUE	NA	0.477144266548241	2		268	439	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295425	1295425	+	upstream_gene_variant	5'Flank	SNP	C	C	T	rs981523698	NA	P-0018729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	28	54	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.793	0.657	0.935	1	0.951	1	CLONAL	2	TRUE	1	0.477144266548241	2		54	74	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	145	364	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.924069616262112	2		365	309	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0018750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	322	683	1	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	1	2	FACETS	0.949	0.902	0.997	0.949	0.902	0.997	CLONAL	1	TRUE	1	0.924069616262112	2		684	734	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744408	41744408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374067962	NA	P-0018750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	317	607	2	ENST00000301178.4:c.1028C>T	p.Thr343Met	p.T343M	ENST00000301178	NM_021913.4	343	aCg/aTg	8/20	1	2	FACETS	0.911	0.865	0.958	0.911	0.865	0.958	CLONAL	1	TRUE	1	0.924069616262112	2		609	753	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0018750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	564	335	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.924069616262112	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.924069616262112	2		335	594	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170011279	170011279	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	98	520	0	ENST00000295797.4:c.1400A>G	p.Glu467Gly	p.E467G	ENST00000295797	NM_002740.5	467	gAg/gGg	14/18	0.924069616262112	3	FACETS	0.263	0.234	0.295	0.132	0.117	0.148	SUBCLONAL	1	TRUE	1	0.924069616262112	3		520	1179	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651598	48651598	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	53	358	0	ENST00000376670.3:c.764G>C	p.Gly255Ala	p.G255A	ENST00000376670	NM_002049.3	255	gGt/gCt	5/6	1	1	FACETS	0.132	0.112	0.153	0.132	0.112	0.153	SUBCLONAL	1	TRUE	0	0.924069616262112	1		358	469	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0018751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	303	636	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.784337268866757	2		636	701	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357181	70357181	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867804014	NA	P-0018751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	248	685	4	ENST00000374080.3:c.5696G>A	p.Arg1899Gln	p.R1899Q	ENST00000374080		1899	cGg/cAg	39/45	0.380977370520675	2	FACETS	0.485	0.452	0.519	0.242	0.226	0.26	INDETERMINATE	1	TRUE	0	0.784337268866757	2		689	1304	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18964097	18964097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770535477	NA	P-0018751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	684	675	0	ENST00000262803.5:c.1094G>A	p.Arg365Gln	p.R365Q	ENST00000262803	NM_002911.3	365	cGg/cAg	8/24	0.319594364284665	4	FACETS	0.942	0.909	0.975	0.942	0.909	0.975	INDETERMINATE	2	TRUE	2	0.784337268866757	4		675	1652	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584497	187584497	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	161	475	0	ENST00000441802.2:c.3536del	p.Thr1179LysfsTer25	p.T1179Kfs*25	ENST00000441802	NM_005245.3	1179	aCa/aa	3/27	NA	2	FACETS	0.534	0.49	0.579			1	INDETERMINATE	1	TRUE	NA	0.784337268866757	2		475	769	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934578	NA	P-0018753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	199	468	0	ENST00000269305.4:c.524G>T	p.Arg175Leu	p.R175L	ENST00000269305	NM_001126112.2	175	cGc/cTc	5/11	0.382514562182133	2	FACETS	0.955	0.893	1	0.955	0.893	1	CLONAL	2	TRUE	0	0.416792057831381	2		468	500	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0018753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	204	410	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.382514562182133	2	FACETS	0.85	0.794	0.907	0.85	0.794	0.907	CLONAL	2	TRUE	0	0.416792057831381	2		411	576	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115727	108115727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747727055	NA	P-0018753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	82	354	0	ENST00000278616.4:c.875C>T	p.Pro292Leu	p.P292L	ENST00000278616	NM_000051.3	292	cCg/cTg	7/63	0.180683524896043	5	FACETS	0.935	0.824	1	0.312	0.274	0.351	INDETERMINATE	1	TRUE	2	0.416792057831381	5		354	684	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699363	117699363	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	166	486	0	ENST00000369458.3:c.278A>T	p.Gln93Leu	p.Q93L	ENST00000369458	NM_024626.3	93	cAg/cTg	3/6	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.416792057831381	2		486	720	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117872	70117872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	145	347	0	ENST00000245479.2:c.340G>A	p.Val114Met	p.V114M	ENST00000245479	NM_000346.3	114	Gtg/Atg	1/3	0.135470896324495	4	FACETS	0.948	0.87	1	0.948	0.87	1	INDETERMINATE	2	TRUE	2	0.416792057831381	4		347	520	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265495	198265495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	124	622	1	ENST00000335508.6:c.2662C>T	p.Leu888Phe	p.L888F	ENST00000335508	NM_012433.2	888	Ctt/Ttt	18/25	0.398473111448367	3	FACETS	0.817	0.739	0.9	0.409	0.369	0.45	CLONAL	1	TRUE	1	0.416792057831381	3		623	880	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584581	52584581	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	128	499	0	ENST00000394830.3:c.4432G>T	p.Val1478Phe	p.V1478F	ENST00000394830	NM_018313.4	1478	Gtc/Ttc	29/30	0.398473111448367	3	FACETS	0.958	0.868	1	0.479	0.434	0.526	CLONAL	1	TRUE	1	0.416792057831381	3		499	775	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638326	117638326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752085591	NA	P-0018753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	89	486	2	ENST00000368508.3:c.6115C>T	p.Arg2039Cys	p.R2039C	ENST00000368508	NM_002944.2	2039	Cgt/Tgt	38/43	0.398473111448367	3	FACETS	0.728	0.645	0.816	0.364	0.322	0.408	SUBCLONAL	1	TRUE	1	0.416792057831381	3		488	709	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752729	128752729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	178	289	0	ENST00000377970.2:c.890C>T	p.Pro297Leu	p.P297L	ENST00000377970	NM_002467.4	297	cCt/cTt	3/3	0.416792057831381	4	FACETS	0.845	0.781	0.911	0.423	0.39	0.456	CLONAL	2	TRUE	0	0.416792057831381	4		289	716	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435357	110435357	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	95	442	1	ENST00000375856.3:c.3044C>T	p.Pro1015Leu	p.P1015L	ENST00000375856	NM_003749.2	1015	cCg/cTg	1/2	0.243536284220613	3	FACETS	0.422	0.375	0.472	0.211	0.187	0.236	INDETERMINATE	1	TRUE	1	0.745810340982108	3		443	829	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577026	7577026	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	679	588	2	ENST00000269305.4:c.912del	p.Lys305SerfsTer40	p.K305Sfs*40	ENST00000269305	NM_001126112.2	304	acT/ac	8/11	0.698244933720477	2	FACETS	0.954	0.93	0.978	0.954	0.93	0.978	CLONAL	2	TRUE	0	0.745810340982108	2		590	954	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253798	30253798	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1435	199	578	1	ENST00000307677.4:c.656C>A	p.Thr219Asn	p.T219N	ENST00000307677	NM_138578.1	219	aCt/aAt	3/3	0.417970552587284	5	FACETS	0.692	0.639	0.748	0.231	0.213	0.25	INDETERMINATE	1	TRUE	2	0.745810340982108	5		579	1634	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619057	37619057	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	93	643	0	ENST00000447079.4:c.733G>A	p.Asp245Asn	p.D245N	ENST00000447079	NM_015083.1	245	Gat/Aat	1/14	0.47445836062939	4	FACETS	0.718	0.638	0.803	0.359	0.319	0.402	SUBCLONAL	1	TRUE	2	0.502027653870966	4		643	775	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602748	10602748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	894	655	0	ENST00000171111.5:c.830C>T	p.Thr277Met	p.T277M	ENST00000171111	NM_203500.1	277	aCg/aTg	3/6	0.433274684369264	3	FACETS	1	0.997	1	0.823	0.799	0.846	CLONAL	2	TRUE	0	0.502027653870966	3		655	1805	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261910	16261910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	185	493	0	ENST00000375759.3:c.9175G>A	p.Ala3059Thr	p.A3059T	ENST00000375759	NM_015001.2	3059	Gct/Act	11/15	1	2	FACETS	0.578	0.532	0.625	0.578	0.532	0.625	SUBCLONAL	1	TRUE	1	0.502027653870966	2		493	1276	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982336	201982336	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2294	299	696	1	ENST00000359651.3:c.715G>T	p.Asp239Tyr	p.D239Y	ENST00000359651		239	Gat/Tat	6/8	0.436035474225849	3	FACETS	0.575	0.538	0.613	0.192	0.179	0.205	SUBCLONAL	1	TRUE	0	0.502027653870966	3		697	2593	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423505	88423505	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754383313	NA	P-0018756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	64	539	0	ENST00000360948.2:c.2330C>T	p.Thr777Met	p.T777M	ENST00000360948	NM_001012338.2	777	aCg/aTg	18/19	0.502027653870966	3	FACETS	0.767	0.666	0.875	0.383	0.333	0.438	SUBCLONAL	1	TRUE	1	0.502027653870966	3		539	416	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808896	3808896	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	188	541	1	ENST00000262367.5:c.3328C>A	p.Pro1110Thr	p.P1110T	ENST00000262367	NM_004380.2	1110	Cct/Act	17/31	0.502027653870966	2	FACETS	0.859	0.803	0.915	0.859	0.803	0.915	CLONAL	2	TRUE	0	0.502027653870966	2		542	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572996	7572996	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	109	331	0	ENST00000269305.4:c.1113del	p.Lys373ArgfsTer49	p.K373Rfs*49	ENST00000269305	NM_001126112.2	371	tcC/tc	11/11	0.497503070304691	2	FACETS	0.908	0.833	0.985	0.908	0.833	0.985	CLONAL	2	TRUE	0	0.502027653870966	2		331	239	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924223	11924225	+	inframe_deletion	In_Frame_Del	DEL	GCG	GCG	-	rs1002526348	NA	P-0018756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	10	9	0	ENST00000353533.5:c.31_33del	p.Gly11del	p.G11del	ENST00000353533	NM_003010.3	7	aGCGgc/agc	1/11	0.497503070304691	2	FACETS	0.383	0.261	0.533	0.192	0.13	0.267	SUBCLONAL	1	TRUE	0	0.502027653870966	2		9	104	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667556	29667556	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	189	550	3	ENST00000356175.3:c.6892G>T	p.Ala2298Ser	p.A2298S	ENST00000356175	NM_000267.3	2298	Gct/Tct	46/57	0.47445836062939	4	FACETS	1	0.988	1	0.671	0.621	0.723	CLONAL	1	TRUE	2	0.502027653870966	4		553	843	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207153	1207153	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0018756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	641	759	1	ENST00000326873.7:c.241A>T	p.Lys81Ter	p.K81*	ENST00000326873	NM_000455.4	81	Aag/Tag	1/10	0.433274684369264	3	FACETS	1	0.996	1	0.832	0.804	0.86	CLONAL	2	TRUE	0	0.502027653870966	3		760	1280	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251629	212251629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	118	398	1	ENST00000342788.4:c.3430G>A	p.Glu1144Lys	p.E1144K	ENST00000342788	NM_005235.2	1144	Gag/Aag	27/28	0.160621576111548	3	FACETS	0.821	0.742	0.905	0.274	0.247	0.302	INDETERMINATE	1	TRUE	0	0.502027653870966	3		399	716	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37622802	37622802	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1764	392	693	0	ENST00000249071.6:c.490G>T	p.Gly164Cys	p.G164C	ENST00000249071	NM_002872.4	164	Ggc/Tgc	6/7	0.160621576111548	3	FACETS	0.906	0.858	0.956	0.302	0.286	0.319	INDETERMINATE	1	TRUE	0	0.502027653870966	3		693	2156	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806194	1806194	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2046	421	735	0	ENST00000260795.2:c.1213G>C	p.Gly405Arg	p.G405R	ENST00000260795		405	Ggc/Cgc	8/17	0.160621576111548	3	FACETS	0.851	0.806	0.896	0.284	0.268	0.299	INDETERMINATE	1	TRUE	0	0.502027653870966	3		735	2467	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094936	143094936	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	33	434	0	ENST00000262992.4:c.1208C>A	p.Ser403Ter	p.S403*	ENST00000262992	NM_001101669.1	403	tCa/tAa	14/24	0.160621576111548	3	FACETS	1	0.95	1	0.489	0.408	0.577	INDETERMINATE	1	TRUE	0	0.502027653870966	3		434	112	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521851	157521851	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	163	422	0	ENST00000346085.5:c.4123C>T	p.His1375Tyr	p.H1375Y	ENST00000346085	NM_020732.3	1375	Cat/Tat	18/20	0.502027653870966	2	FACETS	0.896	0.824	0.97	0.448	0.412	0.485	CLONAL	1	TRUE	0	0.502027653870966	2		422	725	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945627	151945627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	20	518	0	ENST00000262189.6:c.1892C>T	p.Ser631Phe	p.S631F	ENST00000262189	NM_170606.2	631	tCt/tTt	14/59	0.22051935454325	5	FACETS	0.831	0.64	1	0.277	0.213	0.351	INDETERMINATE	1	TRUE	2	0.502027653870966	5		518	168	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907816	76907816	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	13	190	0	ENST00000373344.5:c.4345A>G	p.Lys1449Glu	p.K1449E	ENST00000373344	NM_000489.3	1449	Aaa/Gaa	15/35	0.160621576111548	3	FACETS	0.354	0.253	0.477	0.118	0.084	0.159	INDETERMINATE	1	TRUE	0	0.502027653870966	3		190	183	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0018760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	68	633	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.254391262749499	4	FACETS	1	0.898	1	0.519	0.451	0.592	CLONAL	1	TRUE	2	0.254391262749499	4		633	646	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0018760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	33	459	1	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.254391262749499	3	FACETS	1	0.947	1	0.742	0.61	0.888	CLONAL	1	TRUE	1	0.254391262749499	3		460	197	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577579	7577579	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0018760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	159	590	0	ENST00000269305.4:c.702C>G	p.Tyr234Ter	p.Y234*	ENST00000269305	NM_001126112.2	234	taC/taG	7/11	0.254391262749499	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.254391262749499	4		590	638	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223237	5223237	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	102	666	1	ENST00000357368.4:c.2566G>T	p.Ala856Ser	p.A856S	ENST00000357368	NM_002850.3	856	Gct/Tct	18/38	0.155979340586839	4	FACETS	0.878	0.787	0.974	0.878	0.787	0.974	CLONAL	2	TRUE	2	0.254391262749499	4		667	573	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587165	212587165	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	18	454	0	ENST00000342788.4:c.836T>G	p.Phe279Cys	p.F279C	ENST00000342788	NM_005235.2	279	tTc/tGc	7/28	0.236024469443209	1	FACETS	0.521	0.393	0.672	0.521	0.393	0.672	SUBCLONAL	1	TRUE	0	0.254391262749499	1		454	237	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0018761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	213	566	1	ENST00000311936.3:c.34_35delinsTT	p.Gly12Phe	p.G12F	ENST00000311936	NM_004985.3	12	GGt/TTt	2/5	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.343078411284663	2		567	1218	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446899	18446899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	166	426	1	ENST00000266497.5:c.987del	p.Asp331IlefsTer4	p.D331Ifs*4	ENST00000266497		328	ctC/ct	4/31	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.343078411284663	2		427	871	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246158	46246158	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	160	382	0	ENST00000334344.6:c.4252G>T	p.Gly1418Ter	p.G1418*	ENST00000334344	NM_152641.2	1418	Gga/Tga	15/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.343078411284663	2		382	841	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279975	18279975	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs751527809	NA	P-0018761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	244	505	0	ENST00000222254.8:c.2058C>G	p.Tyr686Ter	p.Y686*	ENST00000222254	NM_005027.3	686	taC/taG	16/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.343078411284663	2		505	1300	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944586	40944586	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	169	409	0	ENST00000373198.4:c.1916C>A	p.Ala639Glu	p.A639E	ENST00000373198	NM_133170.3	639	gCa/gAa	12/32	0.343078411284663	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.343078411284663	1		409	757	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803610	1803610	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1457537911	NA	P-0018761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	199	489	0	ENST00000260795.2:c.788A>G	p.Gln263Arg	p.Q263R	ENST00000260795		263	cAg/cGg	6/17	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.343078411284663	2		489	1062	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876229	35876229	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs766254348	NA	P-0018761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	153	449	0	ENST00000303115.3:c.1021G>T	p.Gly341Ter	p.G341*	ENST00000303115	NM_002185.3	341	Gga/Tga	8/8	0.343078411284663	3	FACETS	1	0.915	1	0.5	0.457	0.546	CLONAL	1	TRUE	1	0.343078411284663	3		449	1044	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271290	26271290	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	158	409	0	ENST00000305910.3:c.323C>A	p.Thr108Asn	p.T108N	ENST00000305910	NM_003534.2	108	aCc/aAc	1/1	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.343078411284663	2		409	874	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034491	47034491	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	266	569	0	ENST00000377604.3:c.576G>T	p.Gln192His	p.Q192H	ENST00000377604	NM_001204468.1	192	caG/caT	6/24	0.223961533339337	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.343078411284663	1		569	1176	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840564	36840564	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771002648	NA	P-0018770-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	135	905	3	ENST00000358127.4:c.1169G>A	p.Arg390His	p.R390H	ENST00000358127	NM_001280556.1	390	cGt/cAt	10/10	1	2	FACETS	0.511	0.466	0.558	0.511	0.466	0.558	SUBCLONAL	1	TRUE	1	0.889017990407194	2		908	594	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974727	21974744	+	inframe_deletion	In_Frame_Del	DEL	CCTCCAGCAGCGCCCGCA	CCTCCAGCAGCGCCCGCA	-	novel	NA	P-0018771-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	66	637	0	ENST00000304494.5:c.83_100del	p.Val28_Glu33del	p.V28_E33del	ENST00000304494	NM_000077.4	28	gTGCGGGCGCTGCTGGAGGcg/gcg	1/3	1	2	FACETS	0.599	0.522	0.681	0.599	0.522	0.681	SUBCLONAL	1	FALSE	1	0.571282096125852	2		637	386	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0018771-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	507	1374	1	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.489810596023827	4	FACETS	1	0.993	1	0.824	0.796	0.852	CLONAL	3	FALSE	0	0.571282096125852	4		1375	846	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462032	120462032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201996575	NA	P-0018771-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	130	747	1	ENST00000256646.2:c.5684G>A	p.Arg1895His	p.R1895H	ENST00000256646	NM_024408.3	1895	cGt/cAt	31/34	0.314248278440137	5	FACETS	1	0.985	1			1	INDETERMINATE	1	FALSE	NA	0.571282096125852	5		748	593	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885889	23885889	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018771-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	57	513	0	ENST00000374561.5:c.29G>T	p.Cys10Phe	p.C10F	ENST00000374561	NM_002167.4	10	tGc/tTc	1/3	0.540887801547897	5	FACETS	0.682	0.586	0.788			1	SUBCLONAL	1	FALSE	NA	0.571282096125852	5		513	543	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120783942	120783942	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018771-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	196	925	0	ENST00000257552.2:c.1043T>G	p.Leu348Arg	p.L348R	ENST00000257552	NM_002442.3	348	cTt/cGt	13/15	0.571282096125852	2	FACETS	0.975	0.919	1	0.975	0.919	1	CLONAL	2	FALSE	0	0.571282096125852	2		925	352	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437600	56437600	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018771-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	242	598	0	ENST00000407977.2:c.862A>T	p.Ile288Phe	p.I288F	ENST00000407977		288	Att/Ttt	8/10	0.480373211990893	3	FACETS	0.958	0.913	1	0.958	0.913	1	CLONAL	3	FALSE	0	0.571282096125852	3		598	379	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876220	35876220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018771-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	49	452	0	ENST00000303115.3:c.1012C>A	p.Gln338Lys	p.Q338K	ENST00000303115	NM_002185.3	338	Cag/Aag	8/8	0.433477224098767	4	FACETS	0.65	0.551	0.757	0.325	0.275	0.379	SUBCLONAL	1	FALSE	2	0.571282096125852	4		452	415	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840034	27840034	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018771-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	32	276	0	ENST00000328488.2:c.60G>C	p.Gln20His	p.Q20H	ENST00000328488	NM_003533.2	20	caG/caC	1/1	0.571282096125852	6	FACETS	0.797	0.649	0.964	0.266	0.216	0.322	CLONAL	1	FALSE	3	0.571282096125852	6		276	301	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506182	148506182	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018771-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	31	571	0	ENST00000320356.2:c.2176G>C	p.Glu726Gln	p.E726Q	ENST00000320356	NM_004456.4	726	Gag/Cag	19/20	0.435435875103452	3	FACETS	0.324	0.261	0.394	0.108	0.087	0.132	SUBCLONAL	1	FALSE	0	0.571282096125852	3		571	431	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0018777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	60	699	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	0.237250165156994	3	FACETS	1	0.943	1	0.591	0.51	0.678	CLONAL	1	TRUE	1	0.237250165156994	3		699	479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0018777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	386	941	1	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.237250165156994	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	0	0.237250165156994	3		942	1135	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0018777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	45	452	1	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.237250165156994	3	FACETS	0.84	0.706	0.989	0.42	0.353	0.495	CLONAL	1	TRUE	1	0.237250165156994	3		453	505	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928651	49928651	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	73	753	0	ENST00000296474.3:c.3623A>G	p.Asp1208Gly	p.D1208G	ENST00000296474	NM_002447.2	1208	gAc/gGc	17/20	0.237250165156994	3	FACETS	0.79	0.69	0.899	0.395	0.345	0.45	SUBCLONAL	1	TRUE	1	0.237250165156994	3		753	871	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670397	134670397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	101	510	0	ENST00000398015.3:c.308C>T	p.Pro103Leu	p.P103L	ENST00000398015	NM_004441.4	103	cCa/cTa	3/16	0.237250165156994	3	FACETS	0.947	0.85	1	0.947	0.85	1	CLONAL	2	TRUE	1	0.237250165156994	3		510	503	SUCCESS
APC	324	MSKCC	GRCh37	5	112128216	112128216	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	100	533	0	ENST00000257430.4:c.719del	p.Thr240LysfsTer53	p.T240Kfs*53	ENST00000257430	NM_000038.5	240	aCa/aa	7/16	0.237250165156994	3	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	1	0.237250165156994	3		533	441	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180931	32180931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771147216	NA	P-0018777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	96	513	0	ENST00000375023.3:c.2419C>T	p.Arg807Cys	p.R807C	ENST00000375023	NM_004557.3	807	Cgc/Tgc	15/30	0.166093367967367	4	FACETS	0.952	0.851	1	0.952	0.851	1	CLONAL	2	TRUE	2	0.237250165156994	4		513	526	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0018778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	63	894	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.19	2		895	654	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	29	527	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.612	0.49	0.751	0.612	0.49	0.751	SUBCLONAL	1	TRUE	1	0.19	2		528	499	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0018778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	56	661	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.97	0.83	1	0.97	0.83	1	CLONAL	1	TRUE	1	0.19	2		661	608	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0018778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	19	550	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	1	2	FACETS	0.433	0.327	0.558	0.433	0.327	0.558	SUBCLONAL	1	TRUE	1	0.19	2		550	462	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0018778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	54	580	0	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	0.656	0.559	0.764	0.656	0.559	0.764	SUBCLONAL	1	TRUE	1	0.19	2		580	866	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916957	178916957	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	28	482	0	ENST00000263967.3:c.344G>C	p.Arg115Pro	p.R115P	ENST00000263967	NM_006218.2	115	cGa/cCa	2/21	1	2	FACETS	0.642	0.512	0.79	0.642	0.512	0.79	SUBCLONAL	1	TRUE	1	0.19	2		482	459	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692883	89692883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204931	NA	P-0018778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	29	428	0	ENST00000371953.3:c.367C>T	p.His123Tyr	p.H123Y	ENST00000371953	NM_000314.4	123	Cac/Tac	5/9	1	2	FACETS	0.939	0.755	1	0.939	0.755	1	CLONAL	1	TRUE	1	0.19	2		428	325	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466019	69466019	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	117	786	0	ENST00000227507.2:c.857C>A	p.Thr286Lys	p.T286K	ENST00000227507	NM_053056.2	286	aCa/aAa	5/5	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.19	2		786	1064	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099449	27099450	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TAAG	novel	NA	P-0018778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	35	487	0	ENST00000324856.7:c.3687_3690dup	p.Asp1231Ter	p.D1231*	ENST00000324856	NM_006015.4	1229	aat/aaTAAGt	14/20	1	2	FACETS	0.849	0.696	1	0.849	0.696	1	CLONAL	1	TRUE	1	0.19	2		487	434	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650711	67650711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567610917	NA	P-0018778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	77	704	0	ENST00000264010.4:c.1016G>A	p.Arg339Gln	p.R339Q	ENST00000264010	NM_006565.3	339	cGg/cAg	5/12	1	2	FACETS	0.802	0.702	0.91	0.802	0.702	0.91	CLONAL	1	TRUE	1	0.19	2		704	1011	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181765	56181765	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	36	344	0	ENST00000399503.3:c.3989del	p.Ser1330TrpfsTer6	p.S1330Wfs*6	ENST00000399503	NM_005921.1	1330	tCg/tg	17/20	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.19	2		344	366	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32439195	32439195	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs907964605	NA	P-0018779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	46	562	0	ENST00000332351.3:c.878A>G	p.Asn293Ser	p.N293S	ENST00000332351	NM_024426.4	293	aAt/aGt	4/10	0.506970810215004	1	FACETS	0.545	0.469	0.625	0.545	0.469	0.625	SUBCLONAL	1	TRUE	0	0.748525645306463	1		562	141	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117756	108117756	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587781511	NA	P-0018779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	65	410	0	ENST00000278616.4:c.967A>G	p.Ile323Val	p.I323V	ENST00000278616	NM_000051.3	323	Ata/Gta	8/63	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.748525645306463	2		410	169	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061521	38061538	+	inframe_deletion	In_Frame_Del	DEL	GCCGCCGCCCGCGCGGCT	GCCGCCGCCCGCGCGGCT	-	novel	NA	P-0018779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	11	209	0	ENST00000250448.2:c.451_468del	p.Ser151_Gly156del	p.S151_G156del	ENST00000250448	NM_004496.3	151	AGCCGCGCGGGCGGCGGC/-	2/2	NA	2	FACETS	0.179	0.124	0.248			1	INDETERMINATE	1	TRUE	NA	0.748525645306463	2		209	164	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39550380	39550380	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	89	515	0	ENST00000262039.4:c.491G>C	p.Ser164Thr	p.S164T	ENST00000262039	NM_002647.2	164	aGt/aCt	4/25	0.525695978377003	1	FACETS	0.722	0.655	0.791	0.722	0.655	0.791	SUBCLONAL	1	TRUE	0	0.748525645306463	1		515	206	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760358	133760358	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064160	NA	P-0018779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	92	714	1	ENST00000318560.5:c.2681G>A	p.Arg894Lys	p.R894K	ENST00000318560	NM_005157.4	894	aGg/aAg	11/11	0.137793686993416	3	FACETS	0.862	0.785	0.939	0.575	0.523	0.626	INDETERMINATE	2	TRUE	0	0.748525645306463	3		715	196	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431623	6431623	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	33	449	0	ENST00000356142.4:c.176C>G	p.Ala59Gly	p.A59G	ENST00000356142	NM_018890.3	59	gCt/gGt	3/7	0.450009552615973	4	FACETS	0.396	0.322	0.48	0.198	0.161	0.24	SUBCLONAL	1	TRUE	2	0.538711673147494	4		449	476	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151871316	151871316	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1237156948	NA	P-0018780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	32	543	0	ENST00000262189.6:c.9274A>G	p.Ile3092Val	p.I3092V	ENST00000262189	NM_170606.2	3092	Att/Gtt	39/59	0.538711673147494	3	FACETS	0.34	0.275	0.412	0.17	0.137	0.206	SUBCLONAL	1	TRUE	1	0.538711673147494	3		543	444	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0018781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	330	797	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.94	0.889	0.991	0.94	0.889	0.991	CLONAL	1	TRUE	1	0.66	2		797	1064	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0018781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	288	708	1	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	0.66	2		709	864	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0018781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	581	863	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.922	0.893	0.95	1	0.998	1	CLONAL	2	TRUE	1	0.66	2		865	955	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	165	491	1	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.923	0.853	0.995	0.923	0.853	0.995	CLONAL	1	TRUE	1	0.66	2		492	542	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0018781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	196	500	1	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	1	2	FACETS	0.934	0.869	1	0.934	0.869	1	CLONAL	1	TRUE	1	0.66	2		501	636	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129329	152129329	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	187	549	2	ENST00000206249.3:c.287del	p.Gly96ValfsTer13	p.G96Vfs*13	ENST00000206249	NM_000125.3	94	ctG/ct	1/8	1	2	FACETS	0.885	0.822	0.951	0.885	0.822	0.951	CLONAL	1	TRUE	1	0.66	2		551	640	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661664	227661664	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs761880048	NA	P-0018781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	163	346	7	ENST00000305123.5:c.1791del	p.His598ThrfsTer38	p.H598Tfs*38	ENST00000305123	NM_005544.2	597	ggG/gg	1/2	1	2	FACETS	0.95	0.878	1	0.95	0.878	1	CLONAL	1	TRUE	1	0.66	2		353	520	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	293	676	4	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	1	2	FACETS	0.905	0.853	0.958	0.905	0.853	0.958	CLONAL	1	TRUE	1	0.66	2		680	981	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785964	135785964	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs118203506	NA	P-0018781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	268	469	0	ENST00000298552.3:c.1257del	p.Arg420GlyfsTer20	p.R420Gfs*20	ENST00000298552	NM_001162426.1	419	ccC/cc	12/23	1	2	FACETS	0.996	0.938	1	0.996	0.938	1	CLONAL	1	TRUE	1	0.66	2		469	815	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100871	27100871	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	244	509	0	ENST00000324856.7:c.4153G>T	p.Glu1385Ter	p.E1385*	ENST00000324856	NM_006015.4	1385	Gaa/Taa	18/20	1	2	FACETS	0.903	0.846	0.961	0.903	0.846	0.961	CLONAL	1	TRUE	1	0.66	2		509	819	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681120	117681120	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs748436511	NA	P-0018781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	254	601	0	ENST00000368508.3:c.3500del	p.Leu1167Ter	p.L1167*	ENST00000368508	NM_002944.2	1167	tTa/ta	23/43	1	2	FACETS	0.928	0.872	0.987	0.928	0.872	0.987	CLONAL	1	TRUE	1	0.66	2		601	829	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466040	69466040	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	262	711	0	ENST00000227507.2:c.878T>G	p.Val293Gly	p.V293G	ENST00000227507	NM_053056.2	293	gTg/gGg	5/5	1	2	FACETS	0.825	0.774	0.878	0.825	0.774	0.878	CLONAL	1	TRUE	1	0.66	2		711	962	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78921143	78921143	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	201	433	0	ENST00000306801.3:c.3257C>T	p.Thr1086Met	p.T1086M	ENST00000306801	NM_020761.2	1086	aCg/aTg	27/34	1	2	FACETS	0.94	0.875	1	0.94	0.875	1	CLONAL	1	TRUE	1	0.66	2		433	648	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928067	178928067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	246	634	0	ENST00000263967.3:c.1345C>T	p.Pro449Ser	p.P449S	ENST00000263967	NM_006218.2	449	Cct/Tct	8/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.66	2		634	728	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784909	9784909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	377	725	1	ENST00000377346.4:c.2912G>A	p.Gly971Glu	p.G971E	ENST00000377346	NM_005026.3	971	gGg/gAg	23/24	1	2	FACETS	0.945	0.897	0.993	0.945	0.897	0.993	CLONAL	1	TRUE	1	0.66	2		726	1209	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739340	46739340	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	212	682	0	ENST00000371975.4:c.1531C>G	p.Arg511Gly	p.R511G	ENST00000371975	NM_003579.3	511	Cgt/Ggt	14/18	1	2	FACETS	0.531	0.492	0.571	0.531	0.492	0.571	SUBCLONAL	1	TRUE	1	0.66	2		682	1210	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303738	65303738	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	311	592	2	ENST00000342505.4:c.3017C>T	p.Ala1006Val	p.A1006V	ENST00000342505	NM_002227.2	1006	gCa/gTa	22/25	1	2	FACETS	0.952	0.899	1	0.952	0.899	1	CLONAL	1	TRUE	1	0.66	2		594	990	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692879	89692879	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	150	368	0	ENST00000371953.3:c.364del	p.Ile122PhefsTer12	p.I122Ffs*12	ENST00000371953	NM_000314.4	121	gcA/gc	5/9	1	2	FACETS	0.933	0.859	1	0.933	0.859	1	CLONAL	1	TRUE	1	0.66	2		368	487	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725045	89725045	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	125	261	0	ENST00000371953.3:c.1028T>A	p.Val343Glu	p.V343E	ENST00000371953	NM_000314.4	343	gTg/gAg	9/9	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.66	2		261	342	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49430962	49430962	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	183	326	0	ENST00000301067.7:c.10177C>T	p.Pro3393Ser	p.P3393S	ENST00000301067	NM_003482.3	3393	Ccg/Tcg	34/54	1	2	FACETS	0.987	0.917	1	0.987	0.917	1	CLONAL	1	TRUE	1	0.66	2		326	562	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494958	56494958	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	259	488	1	ENST00000267101.3:c.3315G>T	p.Glu1105Asp	p.E1105D	ENST00000267101	NM_001982.3	1105	gaG/gaT	27/28	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.66	2		489	777	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819239	3819239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772991403	NA	P-0018781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	171	519	4	ENST00000262367.5:c.2996C>T	p.Thr999Met	p.T999M	ENST00000262367	NM_004380.2	999	aCg/aTg	15/31	1	2	FACETS	0.6	0.552	0.65	0.6	0.552	0.65	SUBCLONAL	1	TRUE	1	0.66	2		523	864	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303208	15303208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779797350	NA	P-0018781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	413	882	1	ENST00000263388.2:c.320G>A	p.Arg107Gln	p.R107Q	ENST00000263388	NM_000435.2	107	cGg/cAg	3/33	1	2	FACETS	0.969	0.923	1	0.969	0.923	1	CLONAL	1	TRUE	1	0.66	2		883	1291	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228986	36228986	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	298	701	0	ENST00000222270.7:c.7766T>C	p.Leu2589Pro	p.L2589P	ENST00000222270	NM_014727.1	2589	cTg/cCg	36/37	1	2	FACETS	0.877	0.826	0.928	0.877	0.826	0.928	CLONAL	1	TRUE	1	0.66	2		701	1030	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604682	55604682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766845123	NA	P-0018781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	278	469	1	ENST00000288135.5:c.2890G>A	p.Ala964Thr	p.A964T	ENST00000288135	NM_000222.2	964	Gct/Act	21/21	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.66	2		470	824	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542445	187542445	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	267	378	0	ENST00000441802.2:c.5295del	p.Phe1765LeufsTer21	p.F1765Lfs*21	ENST00000441802	NM_005245.3	1765	ttT/tt	10/27	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.66	2		378	797	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527472	157527472	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554237126	NA	P-0018781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	221	492	1	ENST00000346085.5:c.5197G>T	p.Glu1733Ter	p.E1733*	ENST00000346085	NM_020732.3	1733	Gaa/Taa	20/20	1	2	FACETS	0.881	0.823	0.941	0.881	0.823	0.941	CLONAL	1	TRUE	1	0.66	2		493	760	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978447	2978447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	261	566	0	ENST00000396946.4:c.883C>T	p.Pro295Ser	p.P295S	ENST00000396946	NM_032415.4	295	Cca/Tca	7/25	1	2	FACETS	0.979	0.92	1	0.979	0.92	1	CLONAL	1	TRUE	1	0.66	2		566	808	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422634	47422634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	257	496	1	ENST00000377045.4:c.106C>T	p.Arg36Trp	p.R36W	ENST00000377045	NM_001654.4	36	Cgg/Tgg	3/16	1	2	FACETS	0.945	0.888	1	0.945	0.888	1	CLONAL	1	TRUE	1	0.66	2		497	824	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0018782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	124	752	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.230982979486818	2	FACETS	0.82	0.745	0.898	0.82	0.745	0.898	CLONAL	2	TRUE	0	0.276942671345723	2		754	546	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251635	212251635	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1211840752	NA	P-0018782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	26	371	1	ENST00000342788.4:c.3424C>T	p.Arg1142Ter	p.R1142*	ENST00000342788	NM_005235.2	1142	Cga/Tga	27/28	0.276942671345723	1	FACETS	0.384	0.304	0.477	0.384	0.304	0.477	SUBCLONAL	1	TRUE	0	0.276942671345723	1		372	421	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0018784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	380	861	4	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.646099454146094	2		865	947	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437625	52437626	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0018784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	254	627	0	ENST00000460680.1:c.1535_1536del	p.Arg512LeufsTer24	p.R512Lfs*24	ENST00000460680	NM_004656.3	512	cGC/c	13/17	0.646099454146094	1	FACETS	0.924	0.873	0.976	0.924	0.873	0.976	CLONAL	1	TRUE	0	0.646099454146094	1		627	576	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0018785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	279	715	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.351055769348803	4	FACETS	0.852	0.803	0.902	0.852	0.803	0.902	CLONAL	3	TRUE	1	0.365770518569077	4		717	815	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0018785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	145	850	2	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.365770518569077	2		852	576	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446412	70446412	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	324	672	0	ENST00000373644.4:c.5352G>C	p.Lys1784Asn	p.K1784N	ENST00000373644	NM_030625.2	1784	aaG/aaC	11/12	0.36405601986012	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.365770518569077	2		672	865	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0018785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	94	317	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	0.36405601986012	2	FACETS	1	0.981	1	0.728	0.654	0.806	CLONAL	1	TRUE	0	0.365770518569077	2		317	353	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81902829	81902829	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	116	569	0	ENST00000359376.3:c.490C>T	p.Arg164Ter	p.R164*	ENST00000359376	NM_002661.3	164	Cga/Tga	6/33	0.346712417040698	4	FACETS	0.816	0.734	0.904	0.408	0.367	0.452	CLONAL	1	TRUE	2	0.365770518569077	4		569	1061	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663735	29663745	+	frameshift_variant	Frame_Shift_Del	DEL	ATATTGCTATT	ATATTGCTATT	-	novel	NA	P-0018785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	267	608	0	ENST00000356175.3:c.6167_6177del	p.Asp2056ValfsTer15	p.D2056Vfs*15	ENST00000356175	NM_000267.3	2056	gATATTGCTATT/g	41/57	0.36405601986012	2	FACETS	0.958	0.902	1	0.958	0.902	1	CLONAL	2	TRUE	0	0.365770518569077	2		608	762	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971116	21971116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552823	NA	P-0018785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	198	437	0	ENST00000304494.5:c.242C>T	p.Pro81Leu	p.P81L	ENST00000304494	NM_000077.4	81	cCc/cTc	2/3	0.347056068473796	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.365770518569077	2		437	489	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417370	139417370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs553542677	NA	P-0018785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	168	731	1	ENST00000277541.6:c.674C>T	p.Ser225Leu	p.S225L	ENST00000277541	NM_017617.3	225	tCg/tTg	4/34	0.345904500405378	3	FACETS	0.933	0.856	1	0.466	0.428	0.507	CLONAL	1	TRUE	1	0.365770518569077	3		732	1165	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0018786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	294	610	2	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.194742385551344	4	FACETS	0.901	0.849	0.953	0.901	0.849	0.953	CLONAL	4	TRUE	0	0.204534533743224	4		612	961	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201885	152201885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778449608	NA	P-0018786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	48	449	2	ENST00000206249.3:c.739G>A	p.Glu247Lys	p.E247K	ENST00000206249	NM_000125.3	247	Gaa/Aaa	3/8	1	2	FACETS	0.926	0.783	1	0.926	0.783	1	CLONAL	1	TRUE	1	0.204534533743224	2		451	507	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186589	108186589	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	30	297	0	ENST00000278616.4:c.6046G>C	p.Asp2016His	p.D2016H	ENST00000278616	NM_000051.3	2016	Gat/Cat	41/63	0.204534533743224	1	FACETS	0.742	0.598	0.904	0.742	0.598	0.904	CLONAL	1	TRUE	0	0.204534533743224	1		297	355	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570058	95570058	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs184830847	NA	P-0018786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	44	346	0	ENST00000393063.1:c.3675C>G	p.Tyr1225Ter	p.Y1225*	ENST00000393063	NM_030621.3	1225	taC/taG	22/28	1	2	FACETS	0.963	0.808	1	0.963	0.808	1	CLONAL	1	TRUE	1	0.204534533743224	2		346	447	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789623	3789623	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	83	685	0	ENST00000262367.5:c.4236G>T	p.Met1412Ile	p.M1412I	ENST00000262367	NM_004380.2	1412	atG/atT	25/31	1	2	FACETS	0.942	0.83	1	0.942	0.83	1	CLONAL	1	TRUE	1	0.204534533743224	2		685	862	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573642	48573642	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	40	399	0	ENST00000342988.3:c.226A>G	p.Arg76Gly	p.R76G	ENST00000342988	NM_005359.5	76	Aga/Gga	2/12	0.204534533743224	1	FACETS	0.744	0.618	0.884	0.744	0.618	0.884	SUBCLONAL	1	TRUE	0	0.204534533743224	1		399	472	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793286	242793286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757334336	NA	P-0018786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	64	842	0	ENST00000334409.5:c.791G>A	p.Arg264His	p.R264H	ENST00000334409	NM_005018.2	264	cGc/cAc	5/5	1	2	FACETS	0.599	0.517	0.689	0.599	0.517	0.689	SUBCLONAL	1	TRUE	1	0.204534533743224	2		842	1044	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0018787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	23	779	2	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.572	0.444	0.722	0.572	0.444	0.722	SUBCLONAL	1	TRUE	1	0.12	2		781	670	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0018787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	41	801	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	0.912	0.758	1	0.912	0.758	1	CLONAL	1	TRUE	1	0.12	2		801	749	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929412	44929415	+	frameshift_variant	Frame_Shift_Del	DEL	ACAA	ACAA	-	rs786205676	NA	P-0018787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	52	1057	0	ENST00000377967.4:c.2515_2518del	p.Asn839ValfsTer27	p.N839Vfs*27	ENST00000377967	NM_021140.2	838	ACAAac/ac	17/29	0.3	2	FACETS	0.913	0.775	1			1	CLONAL	1	TRUE	NA	0.12	2		1057	949	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11018810	11018810	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	56	956	0	ENST00000327064.4:c.442C>T	p.Gln148Ter	p.Q148*	ENST00000327064	NM_199141.1	148	Cag/Tag	3/16	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.12	2		956	793	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	116	364	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.517820616305142	2		365	353	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258028	16258028	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0018788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	24	401	0	ENST00000375759.3:c.5293A>T	p.Lys1765Ter	p.K1765*	ENST00000375759	NM_015001.2	1765	Aag/Tag	11/15	1	2	FACETS	0.196	0.153	0.246	0.196	0.153	0.246	SUBCLONAL	1	TRUE	1	0.517820616305142	2		401	472	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057661	27057661	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	63	703	2	ENST00000324856.7:c.1369C>T	p.Gln457Ter	p.Q457*	ENST00000324856	NM_006015.4	457	Caa/Taa	3/20	1	2	FACETS	0.395	0.341	0.453	0.395	0.341	0.453	SUBCLONAL	1	TRUE	1	0.517820616305142	2		705	616	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915280	32915280	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	64	764	0	ENST00000380152.3:c.6788T>G	p.Val2263Gly	p.V2263G	ENST00000380152		2263	gTt/gGt	11/27	0.168304240355596	0	FACETS	0.542	0.476	0.611			1	INDETERMINATE	1	TRUE	0	0.517820616305142	0		764	220	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609481	81609481	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	60	507	0	ENST00000298171.2:c.1079A>C	p.Glu360Ala	p.E360A	ENST00000298171	NM_000369.2	360	gAg/gCg	10/10	1	2	FACETS	0.855	0.744	0.974	0.855	0.744	0.974	CLONAL	1	TRUE	1	0.517820616305142	2		507	271	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271795	15271795	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1352746556	NA	P-0018788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	245	791	0	ENST00000263388.2:c.6644C>G	p.Pro2215Arg	p.P2215R	ENST00000263388	NM_000435.2	2215	cCa/cGa	33/33	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.517820616305142	2		791	856	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266095	41266095	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	82	334	0	ENST00000349496.5:c.92T>G	p.Leu31Arg	p.L31R	ENST00000349496	NM_001904.3	31	cTg/cGg	3/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.517820616305142	2		334	270	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266112	41266112	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913228	NA	P-0018788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	88	329	0	ENST00000349496.5:c.109T>G	p.Ser37Ala	p.S37A	ENST00000349496	NM_001904.3	37	Tct/Gct	3/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.517820616305142	2		329	275	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47168140	47168140	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	49	625	0	ENST00000409792.3:c.85G>A	p.Glu29Lys	p.E29K	ENST00000409792	NM_014159.6	29	Gag/Aag	2/21	1	2	FACETS	0.976	0.838	1	0.976	0.838	1	CLONAL	1	TRUE	1	0.517820616305142	2		625	194	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748233	41748233	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	267	904	1	ENST00000226382.2:c.536C>T	p.Ser179Phe	p.S179F	ENST00000226382	NM_003924.3	179	tCc/tTc	3/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.517820616305142	2		905	941	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835781	68835781	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060501215	NA	P-0018789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	89	679	6	ENST00000261769.5:c.377del	p.Pro126ArgfsTer89	p.P126Rfs*89	ENST00000261769	NM_004360.3	124	cgC/cg	3/16	0.3	1	FACETS	0.889	0.79	0.995	0.889	0.79	0.995	CLONAL	1	FALSE	0	0.3	1		685	567	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0018790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	67	574	9	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	0.214384419521229	2		583	476	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0018790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	68	486	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.214384419521229	2		488	459	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0018790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	48	577	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	1	0.214384419521229	2		577	447	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	85	729	0	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.214384419521229	2		729	722	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422384	47422384	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	34	495	0	ENST00000377045.4:c.23del	p.Pro8LeufsTer26	p.P8Lfs*26	ENST00000377045	NM_001654.4	6	ggC/gg	2/16	1	2	FACETS	0.664	0.542	0.801	0.664	0.542	0.801	SUBCLONAL	1	TRUE	1	0.214384419521229	2		495	478	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720877	89720877	+	splice_donor_variant	Splice_Site	SNP	T	T	G	rs1114167624	NA	P-0018790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	31	350	0	ENST00000371953.3:c.1026+2T>G		p.X342_splice	ENST00000371953	NM_000314.4	342			1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.214384419521229	2		350	271	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885145	111885145	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs892433462	NA	P-0018790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	63	518	0	ENST00000341259.2:c.1038del	p.Leu347CysfsTer26	p.L347Cfs*26	ENST00000341259	NM_005475.2	345	Ggg/gg	6/8	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.214384419521229	2		518	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577563	7577563	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1567549584	NA	P-0018790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	49	576	0	ENST00000269305.4:c.718A>G	p.Ser240Gly	p.S240G	ENST00000269305	NM_001126112.2	240	Agt/Ggt	7/11	1	2	FACETS	0.869	0.736	1	0.869	0.736	1	CLONAL	1	TRUE	1	0.214384419521229	2		576	526	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692900	89692900	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	89	478	2	ENST00000371953.3:c.384G>T	p.Lys128Asn	p.K128N	ENST00000371953	NM_000314.4	128	aaG/aaT	5/9	1	2	FACETS	0.986	0.879	1	1	0.986	1	CLONAL	2	TRUE	1	0.214384419521229	2		480	421	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741931	17741931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	33	207	0	ENST00000250003.3:c.602G>A	p.Ser201Asn	p.S201N	ENST00000250003	NM_002478.4	201	aGc/aAc	1/3	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.214384419521229	2		207	257	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102199668	102199668	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	45	586	0	ENST00000263464.3:c.1073A>G	p.Glu358Gly	p.E358G	ENST00000263464	NM_001165.4	358	gAg/gGg	5/9	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.214384419521229	2		586	400	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022433	12022433	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	111	1000	0	ENST00000396373.4:c.539A>G	p.His180Arg	p.H180R	ENST00000396373	NM_001987.4	180	cAc/cGc	5/8	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.214384419521229	2		1000	1017	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436386	110436386	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	56	577	1	ENST00000375856.3:c.2015G>A	p.Ser672Asn	p.S672N	ENST00000375856	NM_003749.2	672	aGc/aAc	1/2	1	2	FACETS	0.967	0.829	1	0.967	0.829	1	CLONAL	1	TRUE	1	0.214384419521229	2		578	540	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78923347	78923347	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	27	382	1	ENST00000306801.3:c.3370G>T	p.Gly1124Ter	p.G1124*	ENST00000306801	NM_020761.2	1124	Gga/Tga	28/34	1	2	FACETS	0.773	0.615	0.952	0.773	0.615	0.952	CLONAL	1	TRUE	1	0.214384419521229	2		383	326	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293751	1293751	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1440396485	NA	P-0018790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	67	791	2	ENST00000310581.5:c.1250C>T	p.Ala417Val	p.A417V	ENST00000310581	NM_198253.2	417	gCt/gTt	2/16	1	2	FACETS	0.847	0.735	0.968	0.847	0.735	0.968	CLONAL	1	TRUE	1	0.214384419521229	2		793	738	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931483	131931483	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	22	332	0	ENST00000265335.6:c.2188C>A	p.Leu730Met	p.L730M	ENST00000265335		730	Ctg/Atg	13/25	1	2	FACETS	0.477	0.369	0.604	0.477	0.369	0.604	SUBCLONAL	1	TRUE	1	0.214384419521229	2		332	430	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909246	41909246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	154	729	0	ENST00000372991.4:c.142G>A	p.Val48Met	p.V48M	ENST00000372991	NM_001760.3	48	Gtg/Atg	1/5	0.206556584167105	2	FACETS	0.988	0.906	1	0.988	0.906	1	CLONAL	2	TRUE	0	0.214384419521229	2		729	727	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405958	157405958	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	49	563	0	ENST00000346085.5:c.2200G>A	p.Gly734Ser	p.G734S	ENST00000346085	NM_020732.3	734	Ggc/Agc	6/20	1	2	FACETS	0.833	0.705	0.973	0.833	0.705	0.973	CLONAL	1	TRUE	1	0.214384419521229	2		563	549	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739878	41739878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	64	469	0	ENST00000242208.4:c.95C>T	p.Ala32Val	p.A32V	ENST00000242208	NM_002192.2	32	gCc/gTc	2/3	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.214384419521229	2		469	435	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341267	8341267	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs201344661	NA	P-0018790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	16	219	0	ENST00000356435.5:c.4949G>A	p.Arg1650His	p.R1650H	ENST00000356435		1650	cGt/cAt	30/35	1	2	FACETS	0.82	0.609	1	0.82	0.609	1	CLONAL	1	TRUE	1	0.214384419521229	2		219	182	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882025	NA	P-0018791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	655	876	0	ENST00000269305.4:c.646G>C	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ctg	6/11	NA	2	FACETS	0.964	0.94	0.988			1	INDETERMINATE	2	TRUE	NA	0.752262236685368	2		876	903	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560514	65560514	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	424	367	0	ENST00000358664.4:c.83A>G	p.His28Arg	p.H28R	ENST00000358664	NM_002382.4	28	cAt/cGt	3/5	0.752262236685368	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.752262236685368	2		367	526	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941645	48941645	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0018791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	120	315	0	ENST00000267163.4:c.955A>T	p.Lys319Ter	p.K319*	ENST00000267163	NM_000321.2	319	Aaa/Taa	10/27	0.752262236685368	1	FACETS	0.905	0.838	0.97	0.905	0.838	0.97	CLONAL	1	TRUE	0	0.752262236685368	1		315	220	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200029	128200029	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	373	695	0	ENST00000341105.2:c.1276T>G	p.Ser426Ala	p.S426A	ENST00000341105	NM_032638.4	426	Tcc/Gcc	6/6	0.500179275421593	4	FACETS	0.768	0.729	0.807	0.768	0.729	0.807	SUBCLONAL	2	TRUE	2	0.752262236685368	4		695	1132	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979482	55979482	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	167	462	0	ENST00000263923.4:c.965T>G	p.Val322Gly	p.V322G	ENST00000263923	NM_002253.2	322	gTc/gGc	7/30	1	2	FACETS	0.941	0.872	1	0.941	0.872	1	CLONAL	1	TRUE	1	0.752262236685368	2		462	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578497	7578498	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0018792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	416	924	0	ENST00000269305.4:c.432dup	p.Leu145AlafsTer4	p.L145Afs*4	ENST00000269305	NM_001126112.2	144	-/G	5/11	0.451513198107278	2	FACETS	0.933	0.892	0.975	0.933	0.892	0.975	CLONAL	2	TRUE	0	0.451513198107278	2		924	987	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068006	94068006	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	82	378	3	ENST00000369303.4:c.956C>A	p.Ala319Asp	p.A319D	ENST00000369303	NM_004440.3	319	gCt/gAt	4/17	NA	2	FACETS	0.641	0.566	0.721			1	INDETERMINATE	1	TRUE	NA	0.451513198107278	2		381	567	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	89	364	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.632387571830567	2		365	259	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221710	55221710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9193	1124	397	0	ENST00000275493.2:c.754C>T	p.Arg252Cys	p.R252C	ENST00000275493	NM_005228.3	252	Cgc/Tgc	7/28	0.632387571830567	34	FACETS	0.958	0.926	0.99			1	CLONAL	4	TRUE	NA	0.632387571830567	34		397	10317	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0018793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12296	4108	754	0	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.632387571830567	34	FACETS	0.978	0.962	0.995			1	CLONAL	9	TRUE	NA	0.632387571830567	34		754	16404	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458579	12458579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	36	561	2	ENST00000287820.6:c.1196C>T	p.Ala399Val	p.A399V	ENST00000287820	NM_015869.4	399	gCt/gTt	6/7	1	2	FACETS	0.178	0.145	0.214	0.178	0.145	0.214	SUBCLONAL	1	TRUE	1	0.632387571830567	2		563	640	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725042	89725042	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	rs1085308041	NA	P-0018793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	69	273	0	ENST00000371953.3:c.1027-2A>C		p.X343_splice	ENST00000371953	NM_000314.4	343			0.632387571830567	1	FACETS	0.975	0.873	1	0.975	0.873	1	CLONAL	1	TRUE	0	0.632387571830567	1		273	153	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975463	13975463	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	109	254	0	ENST00000405192.2:c.424A>G	p.Ser142Gly	p.S142G	ENST00000405192	NM_001163147.1	142	Agc/Ggc	7/12	0.632387571830567	3	FACETS	1	0.97	1	0.588	0.532	0.645	CLONAL	1	TRUE	1	0.632387571830567	3		254	386	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347920	70347920	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	167	600	0	ENST00000374080.3:c.3159T>A	p.Phe1053Leu	p.F1053L	ENST00000374080		1053	ttT/ttA	22/45	1	2	FACETS	0.84	0.775	0.907	0.84	0.775	0.907	CLONAL	1	TRUE	1	0.632387571830567	2		600	629	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526126	63526126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854728	NA	P-0018795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	198	745	1	ENST00000307078.5:c.2500C>T	p.Arg834Trp	p.R834W	ENST00000307078	NM_004655.3	834	Cgg/Tgg	11/11	1	2	FACETS	0.896	0.829	0.966	0.896	0.829	0.966	CLONAL	1	TRUE	1	0.38965444193026	2		746	1134	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096157	178096157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778015424	NA	P-0018795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	77	355	0	ENST00000397062.3:c.1174G>A	p.Gly392Ser	p.G392S	ENST00000397062	NM_006164.4	392	Ggt/Agt	5/5	1	2	FACETS	0.767	0.675	0.866	0.767	0.675	0.866	SUBCLONAL	1	TRUE	1	0.38965444193026	2		355	515	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436853	52436853	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	182	744	0	ENST00000460680.1:c.1925del	p.Glu642GlyfsTer13	p.E642Gfs*13	ENST00000460680	NM_004656.3	642	gAg/gg	15/17	0.38965444193026	1	FACETS	0.931	0.86	1	0.931	0.86	1	CLONAL	1	TRUE	0	0.38965444193026	1		744	808	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030585	47030585	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs377667483	NA	P-0018797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	31	303	0	ENST00000377604.3:c.360T>G	p.Asp120Glu	p.D120E	ENST00000377604	NM_001204468.1	120	gaT/gaG	4/24	1	1	FACETS	0.591	0.476	0.72	0.591	0.476	0.72	SUBCLONAL	1	TRUE	0	0.17	1		303	565	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992630	72992630	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1189486286	NA	P-0018797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	30	367	0	ENST00000268489.5:c.1415C>A	p.Ala472Glu	p.A472E	ENST00000268489	NM_006885.3	472	gCg/gAg	2/10	0.231997122096084	3	FACETS	0.907	0.731	1	0.454	0.365	0.554	CLONAL	1	TRUE	1	0.17	3		367	422	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750398	41750398	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	54	296	0	ENST00000226382.2:c.230C>T	p.Pro77Leu	p.P77L	ENST00000226382	NM_003924.3	77	cCg/cTg	1/3	1	2	FACETS	0.709	0.608	0.818	0.709	0.608	0.818	SUBCLONAL	1	TRUE	1	0.429342112620318	2		296	355	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578451	7578451	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	187	703	2	ENST00000269305.4:c.479T>A	p.Met160Lys	p.M160K	ENST00000269305	NM_001126112.2	160	aTg/aAg	5/11	0.370357581899667	1	FACETS	0.946	0.877	1	0.946	0.877	1	CLONAL	1	TRUE	0	0.429342112620318	1		705	723	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949985	44949985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	63	226	0	ENST00000377967.4:c.3754G>A	p.Ala1252Thr	p.A1252T	ENST00000377967	NM_021140.2	1252	Gca/Aca	26/29	1	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.429342112620318	1		226	160	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	197	858	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.45151731834317	1	FACETS	0.991	0.921	1	0.991	0.921	1	CLONAL	1	TRUE	0	0.45151731834317	1		858	682	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239617	105239617	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	64	701	0	ENST00000349310.3:c.928del	p.Cys310AlafsTer33	p.C310Afs*33	ENST00000349310	NM_001014432.1	310	Tgc/gc	11/15	1	2	FACETS	0.378	0.327	0.434	0.378	0.327	0.434	SUBCLONAL	1	TRUE	1	0.45151731834317	2		701	750	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873929	151873929	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	120	501	0	ENST00000262189.6:c.8609del	p.Leu2870CysfsTer36	p.L2870Cfs*36	ENST00000262189	NM_170606.2	2870	tTg/tg	38/59	1	2	FACETS	0.864	0.783	0.95	0.864	0.783	0.95	CLONAL	1	TRUE	1	0.45151731834317	2		501	615	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0018800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	27	574	9	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.418	0.332	0.516	0.418	0.332	0.516	SUBCLONAL	1	TRUE	1	0.320068335090843	2		583	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0018800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	162	883	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.300957976850017	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.320068335090843	1		885	768	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0018800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	40	599	1	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.300957976850017	1	FACETS	0.747	0.624	0.883	0.747	0.624	0.883	SUBCLONAL	1	TRUE	0	0.320068335090843	1		600	281	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88635834	88635834	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	42	403	0	ENST00000372037.3:c.59G>C	p.Arg20Pro	p.R20P	ENST00000372037	NM_004329.2	20	cGt/cCt	3/13	0.198101680949711	1	FACETS	0.758	0.636	0.891	0.758	0.636	0.891	SUBCLONAL	1	TRUE	0	0.320068335090843	1		403	291	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94923061	94923061	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	104	670	0	ENST00000536441.1:c.407G>C	p.Gly136Ala	p.G136A	ENST00000536441	NM_144665.3	136	gGa/gCa	4/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.320068335090843	2		670	466	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435477	18435478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	12	251	0	ENST00000266497.5:c.464dup	p.Asn155LysfsTer9	p.N155Kfs*9	ENST00000266497		154	-/A	1/31	1	2	FACETS	0.354	0.248	0.483	0.354	0.248	0.483	SUBCLONAL	1	TRUE	1	0.320068335090843	2		251	212	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972578	32972578	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	90	558	0	ENST00000380152.3:c.9928A>G	p.Thr3310Ala	p.T3310A	ENST00000380152		3310	Aca/Gca	27/27	0.320068335090843	7	FACETS	1	0.904	1			1	CLONAL	1	TRUE	NA	0.320068335090843	7		558	989	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819671	81819671	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs189301790	NA	P-0018800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	144	477	3	ENST00000359376.3:c.77C>T	p.Thr26Met	p.T26M	ENST00000359376	NM_002661.3	26	aCg/aTg	2/33	0.19028541109543	3	FACETS	0.895	0.82	0.973	0.895	0.82	0.973	INDETERMINATE	2	TRUE	1	0.320068335090843	3		480	583	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346763	89346763	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	26	319	0	ENST00000301030.4:c.6187G>C	p.Glu2063Gln	p.E2063Q	ENST00000301030	NM_001256183.1	2063	Gag/Cag	9/13	0.19028541109543	3	FACETS	0.519	0.411	0.643	0.26	0.205	0.322	INDETERMINATE	1	TRUE	1	0.320068335090843	3		319	363	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447464	12447464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	29	491	0	ENST00000287820.6:c.703G>A	p.Glu235Lys	p.E235K	ENST00000287820	NM_015869.4	235	Gag/Aag	5/7	1	2	FACETS	0.314	0.251	0.386	0.314	0.251	0.386	SUBCLONAL	1	TRUE	1	0.320068335090843	2		491	577	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	74	364	1				ENST00000310581	NM_198253.2	-/1132			0.147726004794297	4	FACETS	0.975	0.863	1	0.975	0.863	1	INDETERMINATE	2	FALSE	2	0.36455176145569	4		365	284	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0018801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	117	487	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.304697774101675	2	FACETS	0.86	0.784	0.94	0.86	0.784	0.94	CLONAL	2	FALSE	0	0.36455176145569	2		487	373	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562738	29562739	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555615472	NA	P-0018801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	105	432	0	ENST00000356175.3:c.3822_3823del	p.Phe1275ProfsTer8	p.F1275Pfs*8	ENST00000356175	NM_000267.3	1273	aCT/a	28/57	0.27442904243231	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	0	0.36455176145569	1		432	372	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217652	7217654	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	novel	NA	P-0018801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	95	392	1	ENST00000380728.2:c.273_275del	p.Lys92del	p.K92del	ENST00000380728		91	aaGAAa/aaa	4/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.36455176145569	2		393	449	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061185	38061202	+	inframe_deletion	In_Frame_Del	DEL	GCACTTGAAGCGCTTCTG	GCACTTGAAGCGCTTCTG	-	novel	NA	P-0018812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	97	386	0	ENST00000250448.2:c.787_804del	p.Gln263_Cys268del	p.Q263_C268del	ENST00000250448	NM_004496.3	263	CAGAAGCGCTTCAAGTGC/-	2/2	0.149609415903771	5	FACETS	0.944	0.856	1	0.708	0.642	0.775	INDETERMINATE	3	FALSE	1	0.46229528089361	5		386	251	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578429	7578429	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1567553148	NA	P-0018812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	235	755	0	ENST00000269305.4:c.501del	p.Gln167HisfsTer3	p.Q167Hfs*3	ENST00000269305	NM_001126112.2	167	caG/ca	5/11	0.433542112377876	1	FACETS	0.975	0.926	1	1	0.995	1	CLONAL	2	FALSE	0	0.46229528089361	1		755	401	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80021269	80021269	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0018812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	76	518	0	ENST00000265081.6:c.1341-3C>T		p.X447_splice	ENST00000265081	NM_002439.4	447			0.453561897672833	1	FACETS	0.687	0.606	0.772	0.687	0.606	0.772	SUBCLONAL	1	FALSE	0	0.46229528089361	1		518	368	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836815	151836815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	468	797	0	ENST00000262189.6:c.14405G>A	p.Gly4802Glu	p.G4802E	ENST00000262189	NM_170606.2	4802	gGg/gAg	56/59	0.46229528089361	4	FACETS	0.915	0.882	0.948	1	0.997	1	CLONAL	4	FALSE	2	0.46229528089361	4		797	809	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143999	11143999	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	51	498	0	ENST00000358026.2:c.3580G>C	p.Gly1194Arg	p.G1194R	ENST00000358026	NM_001128849.1	1194	Ggg/Cgg	26/36	1	2	FACETS	0.068	0.057	0.08	0.068	0.057	0.08	SUBCLONAL	1	TRUE	1	1.66	2		498	900	SUCCESS
NF2	4771	MSKCC	GRCh37	22	29999905	30000015	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	GCCTGTGCAGCAACTCCAGGGGGGCTAAAGGGCTCAGAGTGCAGGCCGTGGGGCGCGAGGGTCCCGGGCCTGAGCCCCGCGCCATGGCCGGGGCCATCGCTTCCCGCATGA	GCCTGTGCAGCAACTCCAGGGGGGCTAAAGGGCTCAGAGTGCAGGCCGTGGGGCGCGAGGGTCCCGGGCCTGAGCCCCGCGCCATGGCCGGGGCCATCGCTTCCCGCATGA	-	novel	NA	P-0018813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	114	44	0	ENST00000338641.4:c.-81_30del		p.*27*	ENST00000338641	NM_000268.3	?-10/595		1/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	1.66	2		44	137	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069320	30069320	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	163	604	0	ENST00000338641.4:c.1188del	p.Lys396AsnfsTer30	p.K396Nfs*30	ENST00000338641	NM_000268.3	395	gcA/gc	12/16	1	2	FACETS	0.241	0.221	0.262	0.241	0.221	0.262	SUBCLONAL	1	TRUE	1	1.66	2		604	815	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670335	30670335	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	89	377	0	ENST00000376406.3:c.6097T>C	p.Tyr2033His	p.Y2033H	ENST00000376406	NM_014641.2	2033	Tat/Cat	14/15	0.139573554107998	3	FACETS	0.449	0.4	0.501	0.225	0.2	0.251	INDETERMINATE	1	TRUE	1	1.66	3		377	437	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	116	574	3	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.496	0.446	0.549	0.496	0.446	0.549	SUBCLONAL	1	TRUE	1	0.46	2		577	1017	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	148	574	9	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	0.46	2		583	491	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	200	486	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.97	0.9	1	0.97	0.9	1	CLONAL	1	TRUE	1	0.46	2		488	896	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	194	392	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.46	2		392	757	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431874	49431874	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1169	148	613	1	ENST00000301067.7:c.9265del	p.Val3089TrpfsTer30	p.V3089Wfs*30	ENST00000301067	NM_003482.3	3089	Gtg/tg	34/54	1	2	FACETS	0.489	0.445	0.535	0.489	0.445	0.535	SUBCLONAL	1	TRUE	1	0.46	2		614	1317	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	125	584	4	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	1	2	FACETS	0.939	0.853	1	0.939	0.853	1	CLONAL	1	TRUE	1	0.46	2		588	579	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	96	698	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.492	0.437	0.55	0.492	0.437	0.55	SUBCLONAL	1	TRUE	1	0.46	2		699	849	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809239	243809239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	84	541	1	ENST00000263826.5:c.385G>T	p.Gly129Ter	p.G129*	ENST00000263826	NM_005465.4	129	Gga/Tga	4/13	1	2	FACETS	0.808	0.717	0.905	0.808	0.717	0.905	CLONAL	1	TRUE	1	0.46	2		542	452	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556463	29556463	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1567849208	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	125	441	1	ENST00000356175.3:c.2835del	p.Phe945LeufsTer9	p.F945Lfs*9	ENST00000356175	NM_000267.3	944	Ttt/tt	21/57	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.46	2		442	484	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106696	27106696	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	249	558	0	ENST00000324856.7:c.6310del	p.Ser2104ProfsTer31	p.S2104Pfs*31	ENST00000324856	NM_006015.4	2103	Ttt/tt	20/20	1	2	FACETS	0.941	0.88	1	0.941	0.88	1	CLONAL	1	TRUE	1	0.46	2		558	1150	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	262	544	6	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	1	2	FACETS	0.991	0.928	1	0.991	0.928	1	CLONAL	1	TRUE	1	0.46	2		550	1150	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672318	86672318	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	161	572	0	ENST00000274376.6:c.2120G>A	p.Arg707His	p.R707H	ENST00000274376	NM_002890.2	707	cGt/cAt	16/25	1	2	FACETS	0.963	0.885	1	0.963	0.885	1	CLONAL	1	TRUE	1	0.46	2		572	727	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646981	23646981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	140	591	1	ENST00000261584.4:c.886del	p.Met296Ter	p.M296*	ENST00000261584	NM_024675.3	296	Atg/tg	4/13	1	2	FACETS	0.96	0.877	1	0.96	0.877	1	CLONAL	1	TRUE	1	0.46	2		592	634	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934243	49934243	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1407832113	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	292	613	4	ENST00000296474.3:c.2264del	p.Gly755ValfsTer19	p.G755Vfs*19	ENST00000296474	NM_002447.2	755	gGt/gt	8/20	1	2	FACETS	0.995	0.935	1	0.995	0.935	1	CLONAL	1	TRUE	1	0.46	2		617	1276	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249457	153249457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	114	610	0	ENST00000281708.4:c.1321C>T	p.Arg441Trp	p.R441W	ENST00000281708	NM_033632.3	441	Cgg/Tgg	9/12	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.46	2		610	473	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575089	64575089	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs868087064	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	308	605	1	ENST00000312049.6:c.718G>T	p.Val240Leu	p.V240L	ENST00000312049	NM_130799.2	240	Gtg/Ttg	4/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.46	2		606	1312	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570064	212570064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55671017	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	47	507	0	ENST00000342788.4:c.1177C>T	p.Arg393Trp	p.R393W	ENST00000342788	NM_005235.2	393	Cgg/Tgg	10/28	1	2	FACETS	0.316	0.266	0.372	0.316	0.266	0.372	SUBCLONAL	1	TRUE	1	0.46	2		507	646	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405954	157405954	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	131	461	2	ENST00000346085.5:c.2201del	p.Gly734AlafsTer11	p.G734Afs*11	ENST00000346085	NM_020732.3	732	ccG/cc	6/20	1	2	FACETS	0.53	0.48	0.583	0.53	0.48	0.583	SUBCLONAL	1	TRUE	1	0.46	2		463	1075	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047959	180047959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs933223149	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	294	609	1	ENST00000261937.6:c.2216G>A	p.Arg739His	p.R739H	ENST00000261937	NM_182925.4	739	cGc/cAc	15/30	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.46	2		610	1269	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631128	69631128	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558206333	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	302	726	0	ENST00000334134.2:c.284G>A	p.Arg95Gln	p.R95Q	ENST00000334134	NM_005247.2	95	cGg/cAg	2/3	1	2	FACETS	0.965	0.908	1	0.965	0.908	1	CLONAL	1	TRUE	1	0.46	2		726	1360	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256832	16256832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs887977680	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	238	656	0	ENST00000375759.3:c.4097G>A	p.Arg1366Gln	p.R1366Q	ENST00000375759	NM_015001.2	1366	cGa/cAa	11/15	1	2	FACETS	0.973	0.909	1	0.973	0.909	1	CLONAL	1	TRUE	1	0.46	2		656	1063	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466018	69466018	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	255	659	0	ENST00000227507.2:c.856A>G	p.Thr286Ala	p.T286A	ENST00000227507	NM_053056.2	286	Aca/Gca	5/5	1	2	FACETS	0.902	0.843	0.963	0.902	0.843	0.963	CLONAL	1	TRUE	1	0.46	2		659	1229	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281517	15281517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	307	612	1	ENST00000263388.2:c.4856G>A	p.Arg1619His	p.R1619H	ENST00000263388	NM_000435.2	1619	cGc/cAc	26/33	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.46	2		613	1262	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278079	41278079	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1031583127	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	172	360	0	ENST00000349496.5:c.1955C>T	p.Ala652Val	p.A652V	ENST00000349496	NM_001904.3	652	gCg/gTg	13/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.46	2		360	665	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980394	7980394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs562084711	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1202	179	602	1	ENST00000319144.4:c.1189G>A	p.Ala397Thr	p.A397T	ENST00000319144	NM_001139.2	397	Gcc/Acc	9/15	1	2	FACETS	0.564	0.518	0.611	0.564	0.518	0.611	SUBCLONAL	1	TRUE	1	0.46	2		603	1381	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200107	138200107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746331032	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	133	471	0	ENST00000237289.4:c.1525G>A	p.Ala509Thr	p.A509T	ENST00000237289	NM_001270507.1	509	Gcc/Acc	7/9	1	2	FACETS	0.639	0.58	0.701	0.639	0.58	0.701	SUBCLONAL	1	TRUE	1	0.46	2		471	905	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589605	67589616	+	inframe_deletion	In_Frame_Del	DEL	TCAAGAAAAAAG	TCAAGAAAAAAG	-	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	64	481	0	ENST00000274335.5:c.1370_1381del	p.Gln457_Ser460del	p.Q457_S460del	ENST00000274335		456	ttTCAAGAAAAAAGt/ttt	10/15	1	2	FACETS	0.846	0.737	0.962	0.846	0.737	0.962	CLONAL	1	TRUE	1	0.46	2		481	329	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800902	120800903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs748469666	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1222	304	726	6	ENST00000257552.2:c.345dup	p.Leu116AlafsTer15	p.L116Afs*15	ENST00000257552	NM_002442.3	115	-/G	6/15	1	2	FACETS	0.866	0.814	0.92	0.866	0.814	0.92	CLONAL	1	TRUE	1	0.46	2		732	1526	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780277	9780277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	251	537	0	ENST00000377346.4:c.1447G>A	p.Val483Met	p.V483M	ENST00000377346	NM_005026.3	483	Gtg/Atg	11/24	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.46	2		537	1056	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262097	16262097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1481024603	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	160	313	2	ENST00000375759.3:c.9362G>A	p.Arg3121Gln	p.R3121Q	ENST00000375759	NM_015001.2	3121	cGg/cAg	11/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.46	2		315	641	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023083	27023083	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	45	77	0	ENST00000324856.7:c.192del	p.Pro65ArgfsTer36	p.P65Rfs*36	ENST00000324856	NM_006015.4	63	gtG/gt	1/20	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.46	2		77	193	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405651	70405652	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	113	557	1	ENST00000373644.4:c.3171dup	p.Leu1058IlefsTer5	p.L1058Ifs*5	ENST00000373644	NM_030625.2	1055	-/A	4/12	1	2	FACETS	0.91	0.822	1	0.91	0.822	1	CLONAL	1	TRUE	1	0.46	2		558	540	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363877	118363877	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	113	544	0	ENST00000534358.1:c.5110G>C	p.Asp1704His	p.D1704H	ENST00000534358	NM_005933.3	1704	Gat/Cat	16/36	1	2	FACETS	0.488	0.438	0.541	0.488	0.438	0.541	SUBCLONAL	1	TRUE	1	0.46	2		544	1006	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443832	18443832	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	32	520	0	ENST00000266497.5:c.805G>A	p.Gly269Arg	p.G269R	ENST00000266497		269	Ggg/Agg	3/31	1	2	FACETS	0.495	0.403	0.598	0.495	0.403	0.598	SUBCLONAL	1	TRUE	1	0.46	2		520	281	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443856	18443856	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	35	570	0	ENST00000266497.5:c.829G>A	p.Ala277Thr	p.A277T	ENST00000266497		277	Gca/Aca	3/31	1	2	FACETS	0.44	0.361	0.528	0.44	0.361	0.528	SUBCLONAL	1	TRUE	1	0.46	2		570	346	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491476	18491476	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	27	491	0	ENST00000266497.5:c.1389A>T	p.Lys463Asn	p.K463N	ENST00000266497		463	aaA/aaT	8/31	1	2	FACETS	0.331	0.263	0.408	0.331	0.263	0.408	SUBCLONAL	1	TRUE	1	0.46	2		491	355	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30099972	30099972	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755213384	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	191	443	2	ENST00000331968.5:c.1648G>A	p.Val550Met	p.V550M	ENST00000331968	NM_002742.2	550	Gtg/Atg	10/18	1	2	FACETS	0.955	0.883	1	0.955	0.883	1	CLONAL	1	TRUE	1	0.46	2		445	870	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652236	3652236	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201192909	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	325	698	1	ENST00000294008.3:c.833G>A	p.Arg278Gln	p.R278Q	ENST00000294008	NM_032444.2	278	cGg/cAg	4/15	1	2	FACETS	0.98	0.924	1	0.98	0.924	1	CLONAL	1	TRUE	1	0.46	2		699	1442	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991688	72991688	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	44	224	0	ENST00000268489.5:c.2357T>C	p.Ile786Thr	p.I786T	ENST00000268489	NM_006885.3	786	aTc/aCc	2/10	1	2	FACETS	0.429	0.36	0.505	0.429	0.36	0.505	SUBCLONAL	1	TRUE	1	0.46	2		224	446	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592336	29592336	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs876658492	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	62	492	0	ENST00000356175.3:c.4756del	p.Tyr1586IlefsTer17	p.Y1586Ifs*17	ENST00000356175	NM_000267.3	1584	aTt/at	35/57	1	2	FACETS	0.824	0.717	0.94	0.824	0.717	0.94	CLONAL	1	TRUE	1	0.46	2		492	327	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687093	37687093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142347393	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	157	601	1	ENST00000447079.4:c.3997C>T	p.Arg1333Cys	p.R1333C	ENST00000447079	NM_015083.1	1333	Cgt/Tgt	14/14	1	2	FACETS	0.571	0.522	0.623	0.571	0.522	0.623	SUBCLONAL	1	TRUE	1	0.46	2		602	1195	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267386	7267386	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	250	508	0	ENST00000302850.5:c.622C>T	p.Arg208Ter	p.R208*	ENST00000302850	NM_000208.2	208	Cga/Tga	2/22	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.46	2		508	974	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141559	11141559	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	135	619	0	ENST00000358026.2:c.3536A>T	p.Asn1179Ile	p.N1179I	ENST00000358026	NM_001128849.1	1179	aAt/aTt	25/36	1	2	FACETS	0.5	0.453	0.549	0.5	0.453	0.549	SUBCLONAL	1	TRUE	1	0.46	2		619	1174	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211090	36211090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776595230	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	164	714	2	ENST00000222270.7:c.841C>T	p.Arg281Cys	p.R281C	ENST00000222270	NM_014727.1	281	Cgt/Tgt	3/37	1	2	FACETS	0.519	0.474	0.565	0.519	0.474	0.565	SUBCLONAL	1	TRUE	1	0.46	2		716	1375	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214371	36214371	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1338	144	709	0	ENST00000222270.7:c.3025G>C	p.Glu1009Gln	p.E1009Q	ENST00000222270	NM_014727.1	1009	Gag/Cag	7/37	1	2	FACETS	0.422	0.384	0.463	0.422	0.384	0.463	SUBCLONAL	1	TRUE	1	0.46	2		709	1482	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798239	42798239	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1472569077	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	265	593	0	ENST00000575354.2:c.4193C>T	p.Thr1398Met	p.T1398M	ENST00000575354	NM_015125.3	1398	aCg/aTg	17/20	1	2	FACETS	0.988	0.926	1	0.988	0.926	1	CLONAL	1	TRUE	1	0.46	2		593	1166	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905629	50905629	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs776204287	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	285	638	0	ENST00000440232.2:c.757C>T	p.Arg253Trp	p.R253W	ENST00000440232	NM_002691.3	253	Cgg/Tgg	6/27	1	2	FACETS	0.937	0.879	0.996	0.937	0.879	0.996	CLONAL	1	TRUE	1	0.46	2		638	1323	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015652	27015652	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1443808231	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	138	657	1	ENST00000335756.4:c.239G>A	p.Arg80His	p.R80H	ENST00000335756	NM_001809.3	80	cGt/cAt	3/5	1	2	FACETS	0.487	0.442	0.535	0.487	0.442	0.535	SUBCLONAL	1	TRUE	1	0.46	2		658	1232	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47672741	47672741	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs557339938	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	97	588	0	ENST00000233146.2:c.1331G>A	p.Arg444His	p.R444H	ENST00000233146	NM_000251.2	444	cGt/cAt	8/16	1	2	FACETS	0.931	0.834	1	0.931	0.834	1	CLONAL	1	TRUE	1	0.46	2		588	453	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702393	47702393	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1558518588	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	90	320	0	ENST00000233146.2:c.1989del	p.Met663IlefsTer22	p.M663Ifs*22	ENST00000233146	NM_000251.2	663	atG/at	12/16	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.46	2		320	351	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99154399	99154399	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	65	532	2	ENST00000074304.5:c.545del	p.Pro182LeufsTer2	p.P182Lfs*2	ENST00000074304	NM_001134224.1	181	Ccc/cc	8/26	1	2	FACETS	0.262	0.226	0.302	0.262	0.226	0.302	SUBCLONAL	1	TRUE	1	0.46	2		534	1077	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661288	227661288	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	82	568	1	ENST00000305123.5:c.2167G>T	p.Gly723Cys	p.G723C	ENST00000305123	NM_005544.2	723	Ggt/Tgt	1/2	1	2	FACETS	0.365	0.32	0.412	0.365	0.32	0.412	SUBCLONAL	1	TRUE	1	0.46	2		569	978	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793427	242793427	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	241	665	0	ENST00000334409.5:c.650C>A	p.Pro217His	p.P217H	ENST00000334409	NM_005018.2	217	cCt/cAt	5/5	1	2	FACETS	0.887	0.828	0.949	0.887	0.828	0.949	CLONAL	1	TRUE	1	0.46	2		665	1181	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573522	41573522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1301825643	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	289	643	4	ENST00000263253.7:c.5807C>T	p.Ala1936Val	p.A1936V	ENST00000263253	NM_001429.3	1936	gCg/gTg	31/31	1	2	FACETS	0.976	0.916	1	0.976	0.916	1	CLONAL	1	TRUE	1	0.46	2		647	1288	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127295	55127295	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	93	571	0	ENST00000257290.5:c.83C>A	p.Pro28His	p.P28H	ENST00000257290	NM_006206.4	28	cCc/cAc	3/23	1	2	FACETS	0.434	0.385	0.486	0.434	0.385	0.486	SUBCLONAL	1	TRUE	1	0.46	2		571	932	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189868	66189868	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	84	516	0	ENST00000273854.3:c.3078G>A	p.Met1026Ile	p.M1026I	ENST00000273854	NM_004439.5	1026	atG/atA	18/18	1	2	FACETS	0.479	0.423	0.54	0.479	0.423	0.54	SUBCLONAL	1	TRUE	1	0.46	2		516	762	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233140	66233140	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs769393148	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	107	519	0	ENST00000273854.3:c.1859G>A	p.Arg620Gln	p.R620Q	ENST00000273854	NM_004439.5	620	cGg/cAg	10/18	1	2	FACETS	0.81	0.729	0.896	0.81	0.729	0.896	CLONAL	1	TRUE	1	0.46	2		519	574	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180792	106180792	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	80	253	0	ENST00000380013.4:c.3820C>T	p.Gln1274Ter	p.Q1274*	ENST00000380013	NM_001127208.2	1274	Cag/Tag	7/11	1	2	FACETS	0.938	0.831	1	0.938	0.831	1	CLONAL	1	TRUE	1	0.46	2		253	371	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564511	86564511	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	43	331	0	ENST00000274376.6:c.248del	p.Gly83GlufsTer4	p.G83Efs*4	ENST00000274376	NM_002890.2	81	ctG/ct	1/25	1	2	FACETS	0.349	0.291	0.413	0.349	0.291	0.413	SUBCLONAL	1	TRUE	1	0.46	2		331	536	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510165	149510165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs904740973	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	248	553	1	ENST00000261799.4:c.1304G>A	p.Arg435His	p.R435H	ENST00000261799	NM_002609.3	435	cGc/cAc	9/23	1	2	FACETS	0.967	0.904	1	0.967	0.904	1	CLONAL	1	TRUE	1	0.46	2		554	1115	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858236	27858236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	91	460	2	ENST00000359303.2:c.335C>T	p.Ala112Val	p.A112V	ENST00000359303	NM_003535.2	112	gCt/gTt	1/1	1	2	FACETS	0.435	0.385	0.488	0.435	0.385	0.488	SUBCLONAL	1	TRUE	1	0.46	2		462	910	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903746	41903746	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	226	503	0	ENST00000372991.4:c.811del	p.Arg271GlyfsTer33	p.R271Gfs*33	ENST00000372991	NM_001760.3	271	Cgg/gg	5/5	1	2	FACETS	0.961	0.896	1	0.961	0.896	1	CLONAL	1	TRUE	1	0.46	2		503	1022	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004447	150004448	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	79	484	0	ENST00000253339.5:c.1777_1778del	p.Ser593Ter	p.S593*	ENST00000253339		593	AGt/t	3/7	1	2	FACETS	0.52	0.458	0.588	0.52	0.458	0.588	SUBCLONAL	1	TRUE	1	0.46	2		484	660	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525010	157525010	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	65	347	0	ENST00000346085.5:c.4905G>T	p.Glu1635Asp	p.E1635D	ENST00000346085	NM_020732.3	1635	gaG/gaT	19/20	1	2	FACETS	0.486	0.422	0.557	0.486	0.422	0.557	SUBCLONAL	1	TRUE	1	0.46	2		347	581	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527398	157527398	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	200	481	0	ENST00000346085.5:c.5127del	p.Ala1710HisfsTer56	p.A1710Hfs*56	ENST00000346085	NM_020732.3	1708	cAa/ca	20/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.46	2		481	827	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340099	116340099	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	45	279	0	ENST00000397752.3:c.961T>C	p.Tyr321His	p.Y321H	ENST00000397752	NM_000245.2	321	Tat/Cat	2/21	1	2	FACETS	0.475	0.4	0.558	0.475	0.4	0.558	SUBCLONAL	1	TRUE	1	0.46	2		279	412	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845215	151845215	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	195	400	0	ENST00000262189.6:c.13797del	p.Cys4600AlafsTer26	p.C4600Afs*26	ENST00000262189	NM_170606.2	4599	ctG/ct	52/59	1	2	FACETS	0.949	0.879	1	0.949	0.879	1	CLONAL	1	TRUE	1	0.46	2		400	893	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194790	29194790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773054971	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	320	732	1	ENST00000240100.2:c.938G>A	p.Arg313His	p.R313H	ENST00000240100	NM_001394.6	313	cGc/cAc	4/4	1	2	FACETS	0.926	0.872	0.981	0.926	0.872	0.981	CLONAL	1	TRUE	1	0.46	2		733	1503	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239934	98239934	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	98	420	0	ENST00000331920.6:c.1398G>T	p.Gln466His	p.Q466H	ENST00000331920	NM_000264.3	466	caG/caT	10/24	1	2	FACETS	0.521	0.464	0.581	0.521	0.464	0.581	SUBCLONAL	1	TRUE	1	0.46	2		420	818	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137323821	137323821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769209021	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1229	168	657	2	ENST00000481739.1:c.1114G>A	p.Ala372Thr	p.A372T	ENST00000481739	NM_002957.4	372	Gcc/Acc	8/10	1	2	FACETS	0.523	0.479	0.569	0.523	0.479	0.569	SUBCLONAL	1	TRUE	1	0.46	2		659	1397	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391932	139391932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373806373	NA	P-0018815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	393	771	1	ENST00000277541.6:c.6259C>T	p.Arg2087Trp	p.R2087W	ENST00000277541	NM_017617.3	2087	Cgg/Tgg	34/34	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.46	2		772	1580	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0018816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	661	779	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.64900749171999	2	FACETS	0.95	0.922	0.977	0.95	0.922	0.977	CLONAL	2	TRUE	0	0.64900749171999	2		781	1072	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033906	49033906	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	300	694	0	ENST00000267163.4:c.2043G>A	p.Trp681Ter	p.W681*	ENST00000267163	NM_000321.2	681	tgG/tgA	20/27	0.64900749171999	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.64900749171999	1		694	604	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337281	89337281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150393722	NA	P-0018816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	52	556	2	ENST00000301030.4:c.7750G>A	p.Ala2584Thr	p.A2584T	ENST00000301030	NM_001256183.1	2584	Gcc/Acc	12/13	0.64900749171999	2	FACETS	0.229	0.194	0.267	0.114	0.097	0.134	SUBCLONAL	1	TRUE	0	0.64900749171999	2		558	701	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951086	17951086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1257606008	NA	P-0018816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	321	736	1	ENST00000458235.1:c.1207C>T	p.Arg403Cys	p.R403C	ENST00000458235	NM_000215.3	403	Cgc/Tgc	9/24	0.59031284778552	4	FACETS	1	0.986	1	0.57	0.537	0.604	CLONAL	1	TRUE	2	0.64900749171999	4		737	1430	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262593	39262593	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	251	721	0	ENST00000402219.2:c.913C>G	p.Pro305Ala	p.P305A	ENST00000402219	NM_005633.3	305	Cct/Gct	7/23	0.64900749171999	3	FACETS	0.815	0.761	0.871	0.408	0.38	0.436	CLONAL	1	TRUE	1	0.64900749171999	3		721	1257	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553348	41553348	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	538	697	0	ENST00000263253.7:c.3437C>G	p.Ser1146Cys	p.S1146C	ENST00000263253	NM_001429.3	1146	tCt/tGt	18/31	0.64900749171999	3	FACETS	0.869	0.836	0.903	0.869	0.836	0.903	CLONAL	2	TRUE	1	0.64900749171999	3		697	1263	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289492	33289494	+	splice_donor_variant,intron_variant	Splice_Site	TNP	TCA	TCA	AAC	novel	NA	P-0018816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	488	848	0	ENST00000374542.5:c.207+2_207+4delinsGTT		p.X69_splice	ENST00000374542	NM_001141970.1	69			0.536256866784334	4	FACETS	0.841	0.804	0.878	0.841	0.804	0.878	CLONAL	2	TRUE	2	0.64900749171999	4		848	1475	SUCCESS
AR	367	MSKCC	GRCh37	X	66863162	66863162	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	67	642	0	ENST00000374690.3:c.1681C>G	p.Leu561Val	p.L561V	ENST00000374690	NM_000044.3	561	Ctg/Gtg	2/8	0.64900749171999	1	FACETS	0.267	0.232	0.304	0.267	0.232	0.304	SUBCLONAL	1	TRUE	0	0.64900749171999	1		642	523	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0018817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	62	715	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.209643546350004	2	FACETS	0.527	0.453	0.607	0.263	0.226	0.304	SUBCLONAL	1	TRUE	0	0.209643546350004	2		717	1123	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276755	15276755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138265894	NA	P-0018817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	92	619	2	ENST00000263388.2:c.5510G>A	p.Arg1837His	p.R1837H	ENST00000263388	NM_000435.2	1837	cGt/cAt	30/33	1	2	FACETS	0.779	0.691	0.875	0.779	0.691	0.875	SUBCLONAL	1	TRUE	1	0.209643546350004	2		621	1126	SUCCESS
EED	8726	MSKCC	GRCh37	11	85975225	85975225	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	38	188	0	ENST00000263360.6:c.646C>T	p.Arg216Ter	p.R216*	ENST00000263360	NM_003797.3	216	Cga/Tga	7/12	0.13516728516406	1	FACETS	0.843	0.698	1	0.843	0.698	1	CLONAL	1	TRUE	0	0.209643546350004	1		188	385	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135025	2135025	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	61	576	0	ENST00000219476.3:c.4567G>A	p.Glu1523Lys	p.E1523K	ENST00000219476	NM_000548.3	1523	Gag/Aag	35/42	1	2	FACETS	0.527	0.453	0.608	0.527	0.453	0.608	SUBCLONAL	1	TRUE	1	0.209643546350004	2		576	1105	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628401	187628401	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199600336	NA	P-0018817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1227	103	656	0	ENST00000441802.2:c.2581A>G	p.Ile861Val	p.I861V	ENST00000441802	NM_005245.3	861	Att/Gtt	2/27	1	2	FACETS	0.739	0.659	0.824	0.739	0.659	0.824	SUBCLONAL	1	TRUE	1	0.209643546350004	2		656	1330	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031903	26031903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	28	211	0	ENST00000244661.2:c.386G>A	p.Arg129His	p.R129H	ENST00000244661	NM_003537.3	129	cGc/cAc	1/1	1	2	FACETS	0.6	0.479	0.739	0.6	0.479	0.739	SUBCLONAL	1	TRUE	1	0.209643546350004	2		211	445	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	157	917	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	0.966	1	CLONAL	1	TRUE	1	0.25	2		917	1130	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0018818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	84	440	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	1	2	FACETS	0.916	0.808	1	0.916	0.808	1	CLONAL	1	TRUE	1	0.25	2		440	734	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913385	NA	P-0018818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	121	399	0	ENST00000304494.5:c.247C>G	p.His83Asp	p.H83D	ENST00000304494	NM_000077.4	83	Cac/Gac	2/3	0.274288201761302	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.25	1		399	652	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0018818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	180	1104	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.274288201761302	1	FACETS	0.984	0.905	1	0.984	0.905	1	CLONAL	1	TRUE	0	0.25	1		1104	1281	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581286	48581286	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	167	669	0	ENST00000342988.3:c.593del	p.Pro198GlnfsTer4	p.P198Qfs*4	ENST00000342988	NM_005359.5	197	aCc/ac	5/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.25	2		669	1082	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264200	46264200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	74	286	0	ENST00000371998.3:c.1247C>T	p.Ala416Val	p.A416V	ENST00000371998		416	gCc/gTc	11/23	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.25	2		286	539	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0018819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	561	343	1				ENST00000310581	NM_198253.2	-/1132			0.80233497918148	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	1	0.80233497918148	3		344	841	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0018819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	513	897	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.977	0.937	1	0.977	0.937	1	CLONAL	1	TRUE	1	0.80233497918148	2		897	1309	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0018819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	222	341	3	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.997	0.936	1	0.997	0.936	1	CLONAL	1	TRUE	1	0.80233497918148	2		344	555	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521487	8521487	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758577045	NA	P-0018819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	400	640	2	ENST00000356435.5:c.751G>A	p.Gly251Arg	p.G251R	ENST00000356435		251	Gga/Aga	9/35	1	2	FACETS	0.989	0.944	1	0.989	0.944	1	CLONAL	1	TRUE	1	0.80233497918148	2		642	1008	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435247	18435247	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs775419502	NA	P-0018819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	302	466	0	ENST00000266497.5:c.232T>A	p.Leu78Ile	p.L78I	ENST00000266497		78	Tta/Ata	1/31	NA	2	FACETS	0.976	0.925	1			1	INDETERMINATE	1	TRUE	NA	0.80233497918148	2		466	771	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435040	18435040	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	374	605	0	ENST00000266497.5:c.25C>T	p.Pro9Ser	p.P9S	ENST00000266497		9	Cca/Tca	1/31	NA	2	FACETS	1	0.972	1			1	INDETERMINATE	1	TRUE	NA	0.80233497918148	2		605	908	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112034	115112034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1361474297	NA	P-0018819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	463	717	0	ENST00000257566.3:c.1706G>A	p.Gly569Glu	p.G569E	ENST00000257566	NM_016569.3	569	gGa/gAa	7/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.80233497918148	2		717	1142	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232165	98232165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	474	762	0	ENST00000331920.6:c.1777C>T	p.Pro593Ser	p.P593S	ENST00000331920	NM_000264.3	593	Cct/Tct	13/24	1	2	FACETS	0.973	0.932	1	0.973	0.932	1	CLONAL	1	TRUE	1	0.80233497918148	2		762	1214	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0018820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	432	1181	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.436539061278128	3	FACETS	0.935	0.892	0.979	0.935	0.892	0.979	CLONAL	2	TRUE	1	0.436499699434319	3		1182	1289	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	302	603	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.436499699434319	2	FACETS	0.97	0.92	1	0.97	0.92	1	CLONAL	2	TRUE	0	0.436499699434319	2		603	713	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276409	115276409	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	327	665	0	ENST00000438362.2:c.919G>T	p.Glu307Ter	p.E307*	ENST00000438362	NM_001242891.1	307	Gaa/Taa	9/20	0.393099171690828	4	FACETS	0.873	0.825	0.923	0.873	0.825	0.923	CLONAL	2	TRUE	2	0.436499699434319	4		665	1232	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656246	18656247	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0018820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	341	660	1	ENST00000266497.5:c.2925_2926delinsAG	p.Leu976Val	p.L976V	ENST00000266497		975	acCCta/acAGta	21/31	0.436539061278128	3	FACETS	0.978	0.928	1	0.978	0.928	1	CLONAL	2	TRUE	1	0.436499699434319	3		661	973	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244889	46244889	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	237	839	1	ENST00000334344.6:c.2983C>T	p.Gln995Ter	p.Q995*	ENST00000334344	NM_152641.2	995	Caa/Taa	15/21	0.436539061278128	3	FACETS	0.968	0.901	1	0.484	0.45	0.519	CLONAL	1	TRUE	1	0.436499699434319	3		840	1367	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210904	133210904	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	389	904	1	ENST00000320574.5:c.5872G>T	p.Glu1958Ter	p.E1958*	ENST00000320574	NM_006231.2	1958	Gaa/Taa	43/49	0.436539061278128	3	FACETS	0.99	0.942	1	0.99	0.942	1	CLONAL	2	TRUE	1	0.436499699434319	3		905	1097	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434717	110434717	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	369	811	0	ENST00000375856.3:c.3684G>T	p.Leu1228Phe	p.L1228F	ENST00000375856	NM_003749.2	1228	ttG/ttT	1/2	0.393099171690828	4	FACETS	0.928	0.88	0.978	0.928	0.88	0.978	CLONAL	2	TRUE	2	0.436499699434319	4		811	1308	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667637	29667637	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	337	692	0	ENST00000356175.3:c.6973G>T	p.Asp2325Tyr	p.D2325Y	ENST00000356175	NM_000267.3	2325	Gat/Tat	46/57	0.435901751688502	4	FACETS	0.862	0.814	0.91	0.862	0.814	0.91	CLONAL	2	TRUE	2	0.436499699434319	4		692	1287	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41562627	41562627	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	384	656	0	ENST00000263253.7:c.3831G>T	p.Lys1277Asn	p.K1277N	ENST00000263253	NM_001429.3	1277	aaG/aaT	23/31	0.435901751688502	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.436499699434319	4		656	1178	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422897	12422897	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	205	807	0	ENST00000287820.6:c.387G>T	p.Glu129Asp	p.E129D	ENST00000287820	NM_015869.4	129	gaG/gaT	3/7	0.355419323467185	3	FACETS	1	0.929	1	0.501	0.464	0.54	CLONAL	1	TRUE	1	0.436499699434319	3		807	1141	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270108	66270108	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	302	682	1	ENST00000273854.3:c.1774G>T	p.Val592Phe	p.V592F	ENST00000273854	NM_004439.5	592	Gtc/Ttc	8/18	0.436539061278128	3	FACETS	0.884	0.835	0.935	0.884	0.835	0.935	CLONAL	2	TRUE	1	0.436499699434319	3		683	953	SUCCESS
APC	324	MSKCC	GRCh37	5	112162862	112162862	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	319	651	0	ENST00000257430.4:c.1466C>T	p.Thr489Ile	p.T489I	ENST00000257430	NM_000038.5	489	aCt/aTt	12/16	0.436499699434319	2	FACETS	0.953	0.905	1	0.953	0.905	1	CLONAL	2	TRUE	0	0.436499699434319	2		651	767	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5557645	5557645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	165	718	0	ENST00000397747.3:c.659C>T	p.Thr220Ile	p.T220I	ENST00000397747	NM_025239.3	220	aCt/aTt	5/7	0.393099171690828	4	FACETS	0.881	0.807	0.958	0.44	0.403	0.479	CLONAL	1	TRUE	2	0.436499699434319	4		718	1233	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0018820-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	114	1181	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.928	0.835	1	0.928	0.835	1	CLONAL	1	TRUE	1	0.275510448306689	2		1182	892	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018820-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	103	603	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.19158542218369	1	FACETS	0.904	0.81	1	0.904	0.81	1	CLONAL	1	TRUE	0	0.275510448306689	1		603	713	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276409	115276409	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018820-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	121	665	0	ENST00000438362.2:c.919G>T	p.Glu307Ter	p.E307*	ENST00000438362	NM_001242891.1	307	Gaa/Taa	9/20	1	2	FACETS	0.995	0.898	1	0.995	0.898	1	CLONAL	1	TRUE	1	0.275510448306689	2		665	883	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656246	18656247	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0018820-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	102	660	1	ENST00000266497.5:c.2925_2926delinsAG	p.Leu976Val	p.L976V	ENST00000266497		975	acCCta/acAGta	21/31	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.275510448306689	2		661	721	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244889	46244889	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018820-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	63	839	1	ENST00000334344.6:c.2983C>T	p.Gln995Ter	p.Q995*	ENST00000334344	NM_152641.2	995	Caa/Taa	15/21	1	2	FACETS	0.399	0.344	0.46	0.399	0.344	0.46	SUBCLONAL	1	TRUE	1	0.275510448306689	2		840	1145	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210904	133210904	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018820-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	155	904	1	ENST00000320574.5:c.5872G>T	p.Glu1958Ter	p.E1958*	ENST00000320574	NM_006231.2	1958	Gaa/Taa	43/49	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.275510448306689	2		905	1033	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434717	110434717	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018820-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	138	811	0	ENST00000375856.3:c.3684G>T	p.Leu1228Phe	p.L1228F	ENST00000375856	NM_003749.2	1228	ttG/ttT	1/2	1	2	FACETS	0.953	0.866	1	0.953	0.866	1	CLONAL	1	TRUE	1	0.275510448306689	2		811	1051	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667637	29667637	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018820-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	100	692	0	ENST00000356175.3:c.6973G>T	p.Asp2325Tyr	p.D2325Y	ENST00000356175	NM_000267.3	2325	Gat/Tat	46/57	1	2	FACETS	0.81	0.723	0.903	0.81	0.723	0.903	CLONAL	1	TRUE	1	0.275510448306689	2		692	896	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41562627	41562627	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018820-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	88	656	0	ENST00000263253.7:c.3831G>T	p.Lys1277Asn	p.K1277N	ENST00000263253	NM_001429.3	1277	aaG/aaT	23/31	1	2	FACETS	0.752	0.665	0.844	0.752	0.665	0.844	SUBCLONAL	1	TRUE	1	0.275510448306689	2		656	850	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422897	12422897	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018820-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	67	807	0	ENST00000287820.6:c.387G>T	p.Glu129Asp	p.E129D	ENST00000287820	NM_015869.4	129	gaG/gaT	3/7	1	2	FACETS	0.519	0.45	0.595	0.519	0.45	0.595	SUBCLONAL	1	TRUE	1	0.275510448306689	2		807	937	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270108	66270108	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018820-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	127	682	1	ENST00000273854.3:c.1774G>T	p.Val592Phe	p.V592F	ENST00000273854	NM_004439.5	592	Gtc/Ttc	8/18	0.190895605852032	2	FACETS	1	0.96	1	0.556	0.504	0.611	CLONAL	1	TRUE	0	0.275510448306689	2		683	829	SUCCESS
APC	324	MSKCC	GRCh37	5	112162862	112162862	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018820-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	95	651	0	ENST00000257430.4:c.1466C>T	p.Thr489Ile	p.T489I	ENST00000257430	NM_000038.5	489	aCt/aTt	12/16	0.275510448306689	1	FACETS	0.994	0.887	1	0.994	0.887	1	CLONAL	1	TRUE	0	0.275510448306689	1		651	598	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5557645	5557645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018820-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	55	718	0	ENST00000397747.3:c.659C>T	p.Thr220Ile	p.T220I	ENST00000397747	NM_025239.3	220	aCt/aTt	5/7	1	2	FACETS	0.453	0.386	0.527	0.453	0.386	0.527	SUBCLONAL	1	TRUE	1	0.275510448306689	2		718	881	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0018821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	1828	691	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.854754273616469	6	FACETS	0.951	0.942	0.96	0.951	0.942	0.96	CLONAL	6	TRUE	0	0.854754273616469	6		691	2031	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380347	14380347	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	608	446	0	ENST00000256196.4:c.70G>T	p.Gly24Cys	p.G24C	ENST00000256196		24	Ggc/Tgc	1/6	0.500485080596118	2	FACETS	0.841	0.819	0.862	0.841	0.819	0.862	INDETERMINATE	2	TRUE	0	0.854754273616469	2		446	846	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89865632	89865632	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	138	578	0	ENST00000389301.3:c.835G>C	p.Asp279His	p.D279H	ENST00000389301	NM_000135.2	279	Gac/Cac	10/43	0.487338211106124	2	FACETS	0.348	0.316	0.382	0.174	0.158	0.191	INDETERMINATE	1	TRUE	0	0.854754273616469	2		578	927	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574026	7574027	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0018821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	692	732	0	ENST00000269305.4:c.1000_1001delinsTT	p.Gly334Leu	p.G334L	ENST00000269305	NM_001126112.2	334	GGg/TTg	10/11	0.854754273616469	2	FACETS	0.957	0.938	0.975	0.957	0.938	0.975	CLONAL	2	TRUE	0	0.854754273616469	2		732	846	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761336	59761336	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781744	NA	P-0018821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	1035	659	2	ENST00000259008.2:c.3071G>T	p.Gly1024Val	p.G1024V	ENST00000259008	NM_032043.2	1024	gGg/gTg	20/20	0.854754273616469	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.854754273616469	3		661	1140	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457246	89457246	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	337	490	0	ENST00000336596.2:c.1727C>A	p.Ala576Glu	p.A576E	ENST00000336596	NM_005233.5	576	gCa/gAa	9/17	0.854754273616469	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.854754273616469	1		490	418	SUCCESS
APC	324	MSKCC	GRCh37	5	112178928	112178928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	298	553	0	ENST00000257430.4:c.7637C>T	p.Thr2546Ile	p.T2546I	ENST00000257430	NM_000038.5	2546	aCc/aTc	16/16	1	2	FACETS	0.936	0.886	0.986	0.936	0.886	0.986	CLONAL	1	TRUE	1	0.854754273616469	2		553	745	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371818	55371818	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	119	131	0	ENST00000297316.4:c.508G>T	p.Glu170Ter	p.E170*	ENST00000297316	NM_022454.3	170	Gag/Tag	2/2	0.854754273616469	2	FACETS	1	0.984	1	0.633	0.586	0.679	CLONAL	1	TRUE	0	0.854754273616469	2		131	220	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68982089	68982089	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	196	757	0	ENST00000288368.4:c.1463G>C	p.Arg488Pro	p.R488P	ENST00000288368	NM_024870.2	488	cGt/cCt	13/40	0.854754273616469	2	FACETS	0.348	0.321	0.376	0.174	0.16	0.188	SUBCLONAL	1	TRUE	0	0.854754273616469	2		757	1318	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380276	+	missense_variant	Missense_Mutation	DNP	TT	TT	CA	novel	NA	P-0018822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	139	641	1	ENST00000311936.3:c.182_183delinsTG	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAA/cTG	3/5	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.254613302442013	2		642	946	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645138	67645138	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	169	607	1	ENST00000264010.4:c.403C>T	p.Gln135Ter	p.Q135*	ENST00000264010	NM_006565.3	135	Cag/Tag	3/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.254613302442013	2		608	1062	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256783	16256783	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1265317050	NA	P-0018822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	132	515	0	ENST00000375759.3:c.4048A>G	p.Arg1350Gly	p.R1350G	ENST00000375759	NM_015001.2	1350	Aga/Gga	11/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.254613302442013	2		515	884	SUCCESS
ATM	472	MSKCC	GRCh37	11	108225566	108225566	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	89	495	0	ENST00000278616.4:c.8815A>G	p.Arg2939Gly	p.R2939G	ENST00000278616	NM_000051.3	2939	Aga/Gga	61/63	1	2	FACETS	0.883	0.782	0.991	0.883	0.782	0.991	CLONAL	1	TRUE	1	0.254613302442013	2		495	792	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219341	1219341	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs760399253	NA	P-0018822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	270	626	0	ENST00000326873.7:c.393C>G	p.Tyr131Ter	p.Y131*	ENST00000326873	NM_000455.4	131	taC/taG	3/10	0.254613302442013	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.254613302442013	2		626	932	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447006	187447006	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	112	513	0	ENST00000232014.4:c.1187A>C	p.Glu396Ala	p.E396A	ENST00000232014	NM_001130845.1	396	gAg/gCg	5/10	0.113694186447902	3	FACETS	1	0.979	1	0.677	0.61	0.749	INDETERMINATE	1	TRUE	1	0.254613302442013	3		513	732	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434631	128434631	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	138	587	0	ENST00000265960.3:c.223A>G	p.Ser75Gly	p.S75G	ENST00000265960	NM_001006617.1	75	Agt/Ggt	2/12	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.254613302442013	2		587	903	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395053	139395053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1484525055	NA	P-0018822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	79	446	1	ENST00000277541.6:c.5885G>A	p.Arg1962His	p.R1962H	ENST00000277541	NM_017617.3	1962	cGc/cAc	31/34	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.254613302442013	2		447	601	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922860	44922872	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGCCATGTTCC	CAGGCCATGTTCC	-	novel	NA	P-0018822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	98	206	0	ENST00000377967.4:c.1722_1734del	p.Gly575ValfsTer14	p.G575Vfs*14	ENST00000377967	NM_021140.2	574	gCAGGCCATGTTCCc/gc	16/29	0.0634427524013272	2	FACETS	1	0.94	1			1	INDETERMINATE	2	TRUE	NA	0.254613302442013	2		206	362	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0018823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	961	1034	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.877656218806902	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.877656218806902	3		1035	1028	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591246	67591246	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0018823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	145	374	0	ENST00000274335.5:c.1746-2A>T		p.X582_splice	ENST00000274335		582			0.877656218806902	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.877656218806902	1		374	171	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772246	68772246	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	49	758	0	ENST00000261769.5:c.95T>G	p.Phe32Cys	p.F32C	ENST00000261769	NM_004360.3	32	tTt/tGt	2/16	0.877656218806902	3	FACETS	0.166	0.14	0.196	0.083	0.07	0.098	SUBCLONAL	1	TRUE	1	0.877656218806902	3		758	965	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881136	37881136	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	290	662	0	ENST00000269571.5:c.2465T>G	p.Leu822Arg	p.L822R	ENST00000269571		822	cTg/cGg	20/27	0.877656218806902	2	FACETS	0.992	0.94	1	0.496	0.47	0.522	CLONAL	1	TRUE	0	0.877656218806902	2		662	666	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43749811	43749811	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1540	178	426	1	ENST00000523873.1:c.664G>A	p.Glu222Lys	p.E222K	ENST00000523873		222	Gaa/Aaa	7/8	0.877656218806902	8	FACETS	0.858	0.787	0.932			1	CLONAL	1	TRUE	NA	0.877656218806902	8		427	1718	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860284	151860288	+	frameshift_variant	Frame_Shift_Del	DEL	AAGGT	AAGGT	-	novel	NA	P-0018823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	202	487	0	ENST00000262189.6:c.10374_10378del	p.Pro3459Ter	p.P3459*	ENST00000262189	NM_170606.2	3458	ttACCTTgt/ttgt	43/59	0.839311773593537	5	FACETS	0.896	0.829	0.966	0.299	0.276	0.322	CLONAL	1	TRUE	2	0.877656218806902	5		487	1190	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573174	64573174	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	329	519	0	ENST00000312049.6:c.1118C>G	p.Pro373Arg	p.P373R	ENST00000312049	NM_130799.2	373	cCc/cGc	8/10	0.520417329054155	1	FACETS	0.923	0.874	0.974	0.923	0.874	0.974	CLONAL	1	TRUE	0	0.520417329054155	1		519	1013	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814238	76814238	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	244	452	0	ENST00000373344.5:c.6406G>T	p.Asp2136Tyr	p.D2136Y	ENST00000373344	NM_000489.3	2136	Gac/Tac	29/35	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.520417329054155	2		452	862	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0018830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	172	894	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.897	0.826	0.971	0.897	0.826	0.971	CLONAL	1	TRUE	1	0.466482303540636	2		895	822	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0018830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	417	883	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.466482303540636	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.466482303540636	1		885	1212	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023568	27023568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1488298195	NA	P-0018830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	398	792	0	ENST00000324856.7:c.674C>T	p.Pro225Leu	p.P225L	ENST00000324856	NM_006015.4	225	cCc/cTc	1/20	0.244509468227275	1	FACETS	1	0.986	1	1	0.986	1	INDETERMINATE	1	TRUE	0	0.466482303540636	1		792	1198	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456738	32456738	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	294	604	0	ENST00000332351.3:c.154C>T	p.Arg52Cys	p.R52C	ENST00000332351	NM_024426.4	52	Cgt/Tgt	1/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.466482303540636	2		604	1151	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0018830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	2826	670	1	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.466482303540636	11	FACETS	1	0.994	1			1	CLONAL	10	TRUE	NA	0.466482303540636	11		671	3721	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280136	142280136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369434236	NA	P-0018830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	66	482	1	ENST00000350721.4:c.1298G>A	p.Arg433His	p.R433H	ENST00000350721	NM_001184.3	433	cGt/cAt	5/47	0.244509468227275	1	FACETS	0.349	0.303	0.4	0.349	0.303	0.4	INDETERMINATE	1	TRUE	0	0.466482303540636	1		483	621	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0018830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	68	527	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.244509468227275	1	FACETS	0.34	0.296	0.389	0.34	0.296	0.389	INDETERMINATE	1	TRUE	0	0.466482303540636	1		527	657	SUCCESS
APC	324	MSKCC	GRCh37	5	112175521	112175521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	132	331	0	ENST00000257430.4:c.4230C>A	p.Cys1410Ter	p.C1410*	ENST00000257430	NM_000038.5	1410	tgC/tgA	16/16	0.244509468227275	1	FACETS	0.895	0.817	0.975	0.895	0.817	0.975	INDETERMINATE	1	TRUE	0	0.466482303540636	1		331	485	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971099	21971099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749714198	NA	P-0018830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	207	419	0	ENST00000304494.5:c.259C>T	p.Arg87Trp	p.R87W	ENST00000304494	NM_000077.4	87	Cgg/Tgg	2/3	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.466482303540636	2		419	715	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0018831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	267	446	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.417321641051682	2	FACETS	1	0.994	1	0.693	0.657	0.729	INDETERMINATE	1	TRUE	0	0.714369423955965	2		446	539	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412095	63412095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852217	NA	P-0018831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	528	372	6	ENST00000330258.3:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000330258	NM_152424.3	358	Cga/Tga	2/2	0.714369423955965	2	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.714369423955965	2		378	701	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0018831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	356	562	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.633857783070292	2	FACETS	0.944	0.909	0.977	0.944	0.909	0.977	CLONAL	2	TRUE	0	0.714369423955965	2		562	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0018831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	529	695	3	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.633857783070292	2	FACETS	0.809	0.782	0.837	0.809	0.782	0.837	CLONAL	2	TRUE	0	0.714369423955965	2		698	915	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0018831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	187	567	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	1	2	FACETS	0.637	0.589	0.686	0.637	0.589	0.686	SUBCLONAL	1	TRUE	1	0.714369423955965	2		567	822	SUCCESS
APC	324	MSKCC	GRCh37	5	112154991	112154991	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs559510809	NA	P-0018831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	67	537	3	ENST00000257430.4:c.1262G>A	p.Trp421Ter	p.W421*	ENST00000257430	NM_000038.5	421	tGg/tAg	10/16	0.417321641051682	2	FACETS	0.259	0.225	0.297	0.13	0.112	0.149	INDETERMINATE	1	TRUE	0	0.714369423955965	2		540	723	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591852	48591852	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	118	345	2	ENST00000342988.3:c.1017del	p.Phe339LeufsTer45	p.F339Lfs*45	ENST00000342988	NM_005359.5	339	Ttt/tt	9/12	0.374606956361923	1	FACETS	0.775	0.712	0.839	0.775	0.712	0.839	INDETERMINATE	1	TRUE	0	0.714369423955965	1		347	274	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593494	48593494	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	53	246	0	ENST00000342988.3:c.1245C>G	p.Asp415Glu	p.D415E	ENST00000342988	NM_005359.5	415	gaC/gaG	10/12	0.374606956361923	1	FACETS	0.357	0.307	0.411	0.357	0.307	0.411	INDETERMINATE	1	TRUE	0	0.714369423955965	1		246	267	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0018833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	66	546	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	0.36204379740859	1	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	0	0.473253802459194	1		546	209	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537086	41537086	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs376635222	NA	P-0018833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	65	381	0	ENST00000263253.7:c.1913A>G	p.Tyr638Cys	p.Y638C	ENST00000263253	NM_001429.3	638	tAt/tGt	10/31	1	2	FACETS	0.904	0.79	1	0.904	0.79	1	CLONAL	1	TRUE	1	0.473253802459194	2		381	304	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195427	102195427	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	22	260	0	ENST00000263464.3:c.187A>C	p.Lys63Gln	p.K63Q	ENST00000263464	NM_001165.4	63	Aag/Cag	2/9	1	2	FACETS	0.458	0.357	0.575	0.458	0.357	0.575	SUBCLONAL	1	TRUE	1	0.473253802459194	2		260	203	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702235	47702235	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	200	505	1	ENST00000233146.2:c.1831G>T	p.Val611Leu	p.V611L	ENST00000233146	NM_000251.2	611	Gtg/Ttg	12/16	0.304095755469425	6	FACETS	1	0.976	1			1	CLONAL	3	TRUE	NA	0.473253802459194	6		506	502	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971047	21971060	+	frameshift_variant	Frame_Shift_Del	DEL	AGCCGCGCCCCGGC	AGCCGCGCCCCGGC	GGG	novel	NA	P-0018833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	71	434	3	ENST00000304494.5:c.298_311delinsCCC	p.Ala100ProfsTer16	p.A100Pfs*16	ENST00000304494	NM_000077.4	100	GCCGGGGCGCGGCTg/CCCg	2/3	0.473253802459194	1	FACETS	0.898	0.794	1	0.898	0.794	1	CLONAL	1	TRUE	0	0.473253802459194	1		437	255	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611108	100611108	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	52	283	0	ENST00000308731.7:c.1498G>A	p.Glu500Lys	p.E500K	ENST00000308731	NM_000061.2	500	Gag/Aag	15/19	1	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.473253802459194	1		283	141	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0018835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	111	708	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	0.21	2		709	992	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0018836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	307	343	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.581080387347696	2		344	971	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717714	89717714	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167662	NA	P-0018836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	269	446	0	ENST00000371953.3:c.740del	p.Leu247TyrfsTer9	p.L247Yfs*9	ENST00000371953	NM_000314.4	247	Tta/ta	7/9	0.581080387347696	1	FACETS	0.881	0.83	0.932	0.881	0.83	0.932	CLONAL	1	TRUE	0	0.581080387347696	1		446	746	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0018837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	261	752	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.257399537120024	3	FACETS	1	0.979	1	0.726	0.683	0.771	CLONAL	2	TRUE	0	0.351777671965657	3		754	801	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	265	225	0	ENST00000257430.4:c.4199del	p.Ser1400Ter	p.S1400*	ENST00000257430	NM_000038.5	1400	tCg/tg	16/16	0.351777671965657	4	FACETS	0.9	0.852	0.948	0.9	0.852	0.948	CLONAL	4	TRUE	0	0.351777671965657	4		225	566	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903727	114903727	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	467	683	0	ENST00000543371.1:c.731C>T	p.Pro244Leu	p.P244L	ENST00000543371	NM_001198531.1	244	cCa/cTa	7/14	0.334383381344443	2	FACETS	0.998	0.954	1	0.998	0.954	1	CLONAL	2	TRUE	0	0.351777671965657	2		683	1330	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473758	67473758	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	290	413	1	ENST00000327367.4:c.838A>T	p.Asn280Tyr	p.N280Y	ENST00000327367	NM_005902.3	280	Aat/Tat	6/9	NA	2	FACETS	0.974	0.92	1			1	INDETERMINATE	2	TRUE	NA	0.351777671965657	2		414	846	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117912	70117913	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0018837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	208	346	0	ENST00000245479.2:c.380_381del	p.Tyr127SerfsTer124	p.Y127Sfs*124	ENST00000245479	NM_000346.3	127	tAC/t	1/3	0.351777671965657	4	FACETS	0.971	0.903	1	0.971	0.903	1	CLONAL	2	TRUE	2	0.351777671965657	4		346	823	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781466	135781466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs118203538	NA	P-0018837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	225	255	0	ENST00000298552.3:c.1499G>A	p.Arg500Gln	p.R500Q	ENST00000298552	NM_001162426.1	500	cGa/cAa	15/23	0.351777671965657	5	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	3	0.351777671965657	5		255	858	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0018840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	195	715	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.856	0.792	0.924	0.856	0.792	0.924	CLONAL	1	TRUE	1	0.41329581158016	2		717	1102	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115745	8115745	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	236	569	0	ENST00000346208.3:c.1091G>T	p.Arg364Ile	p.R364I	ENST00000346208		364	aGa/aTa	6/6	1	2	FACETS	0.845	0.786	0.905	0.845	0.786	0.905	CLONAL	1	TRUE	1	0.41329581158016	2		569	1352	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845590	151845591	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0018840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	133	504	2	ENST00000262189.6:c.13421_13422delinsTT	p.Cys4474Phe	p.C4474F	ENST00000262189	NM_170606.2	4474	tGC/tTT	52/59	1	2	FACETS	0.693	0.629	0.76	0.693	0.629	0.76	SUBCLONAL	1	TRUE	1	0.41329581158016	2		506	929	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0018843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	258	343	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.837320981807452	2		344	605	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780226	9780226	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	521	700	0	ENST00000377346.4:c.1396G>A	p.Asp466Asn	p.D466N	ENST00000377346	NM_005026.3	466	Gat/Aat	11/24	1	2	FACETS	0.983	0.944	1	0.983	0.944	1	CLONAL	1	TRUE	1	0.837320981807452	2		700	1266	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941127	36941127	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	310	498	3	ENST00000361632.4:c.212C>T	p.Pro71Leu	p.P71L	ENST00000361632		71	cCc/cTc	3/16	1	2	FACETS	0.919	0.87	0.968	0.919	0.87	0.968	CLONAL	1	TRUE	1	0.837320981807452	2		501	806	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344760	65344760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768706312	NA	P-0018843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	247	338	0	ENST00000342505.4:c.277C>T	p.Arg93Cys	p.R93C	ENST00000342505	NM_002227.2	93	Cgc/Tgc	4/25	1	2	FACETS	0.897	0.843	0.951	0.897	0.843	0.951	CLONAL	1	TRUE	1	0.837320981807452	2		338	658	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115251269	115251269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866005906	NA	P-0018843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	302	413	0	ENST00000369535.4:c.457G>A	p.Glu153Lys	p.E153K	ENST00000369535	NM_002524.4	153	Gaa/Aaa	5/7	1	2	FACETS	0.991	0.939	1	0.991	0.939	1	CLONAL	1	TRUE	1	0.837320981807452	2		413	728	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913250	NA	P-0018843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	377	492	0	ENST00000369535.4:c.34G>C	p.Gly12Arg	p.G12R	ENST00000369535	NM_002524.4	12	Ggt/Cgt	2/7	1	2	FACETS	0.966	0.921	1	0.966	0.921	1	CLONAL	1	TRUE	1	0.837320981807452	2		492	932	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622074	43622074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200989078	NA	P-0018843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	322	418	0	ENST00000355710.3:c.3091G>A	p.Asp1031Asn	p.D1031N	ENST00000355710	NM_020975.4	1031	Gac/Aac	19/20	0.837320981807452	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.837320981807452	1		418	428	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068942	30068942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868560423	NA	P-0018843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	531	791	0	ENST00000331968.5:c.1987C>T	p.His663Tyr	p.H663Y	ENST00000331968	NM_002742.2	663	Cat/Tat	14/18	0.837320981807452	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.837320981807452	1		791	699	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0018843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	280	434	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	1	2	FACETS	0.903	0.852	0.953	0.903	0.852	0.953	CLONAL	1	TRUE	1	0.837320981807452	2		434	741	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858732	9858732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	178	323	1	ENST00000330684.3:c.2669C>T	p.Ser890Phe	p.S890F	ENST00000330684	NM_001134407.1	890	tCc/tTc	13/13	1	2	FACETS	0.91	0.847	0.975	0.91	0.847	0.975	CLONAL	1	TRUE	1	0.837320981807452	2		324	467	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984848	9984848	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	480	577	1	ENST00000330684.3:c.1117G>A	p.Glu373Lys	p.E373K	ENST00000330684	NM_001134407.1	373	Gaa/Aaa	4/13	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.837320981807452	2		578	1110	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585405	29585405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	441	611	1	ENST00000356175.3:c.4154G>A	p.Gly1385Glu	p.G1385E	ENST00000356175	NM_000267.3	1385	gGa/gAa	31/57	1	2	FACETS	0.931	0.889	0.972	0.931	0.889	0.972	CLONAL	1	TRUE	1	0.837320981807452	2		612	1132	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223160	41223160	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782825	NA	P-0018843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	352	468	0	ENST00000357654.3:c.4771G>A	p.Gly1591Ser	p.G1591S	ENST00000357654	NM_007294.3	1591	Ggc/Agc	15/23	1	2	FACETS	0.97	0.923	1	0.97	0.923	1	CLONAL	1	TRUE	1	0.837320981807452	2		468	867	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226242	2226242	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	585	778	0	ENST00000398665.3:c.3722G>A	p.Trp1241Ter	p.W1241*	ENST00000398665	NM_032482.2	1241	tGg/tAg	27/28	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.837320981807452	2		778	1383	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144026	11144026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	459	630	1	ENST00000358026.2:c.3607C>T	p.Arg1203Cys	p.R1203C	ENST00000358026	NM_001128849.1	1203	Cgc/Tgc	26/36	1	2	FACETS	0.975	0.933	1	0.975	0.933	1	CLONAL	1	TRUE	1	0.837320981807452	2		631	1125	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40743950	40743950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781527200	NA	P-0018843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	541	628	2	ENST00000392038.2:c.757C>T	p.Arg253Trp	p.R253W	ENST00000392038	NM_001626.4	253	Cgg/Tgg	9/14	1	2	FACETS	0.987	0.949	1	0.987	0.949	1	CLONAL	1	TRUE	1	0.837320981807452	2		630	1309	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044362	128044362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	405	544	0	ENST00000285398.2:c.1259C>T	p.Ser420Phe	p.S420F	ENST00000285398	NM_000122.1	420	tCc/tTc	8/15	1	2	FACETS	0.963	0.919	1	0.963	0.919	1	CLONAL	1	TRUE	1	0.837320981807452	2		544	1005	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131228	202131228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	335	436	0	ENST00000358485.4:c.196C>T	p.Leu66Phe	p.L66F	ENST00000358485	NM_001080125.1	66	Ctt/Ttt	2/9	1	2	FACETS	0.909	0.863	0.956	0.909	0.863	0.956	CLONAL	1	TRUE	1	0.837320981807452	2		436	880	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531825	41531825	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	433	553	1	ENST00000263253.7:c.1537C>T	p.Pro513Ser	p.P513S	ENST00000263253	NM_001429.3	513	Cct/Tct	7/31	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.837320981807452	2		554	985	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427585	72427585	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	148	229	0	ENST00000477973.2:c.905C>T	p.Ser302Phe	p.S302F	ENST00000477973	NM_012234.5	302	tCc/tTc	4/4	1	2	FACETS	0.902	0.833	0.972	0.902	0.833	0.972	CLONAL	1	TRUE	1	0.837320981807452	2		229	392	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79966117	79966117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773879116	NA	P-0018843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	261	450	2	ENST00000265081.6:c.781G>A	p.Glu261Lys	p.E261K	ENST00000265081	NM_002439.4	261	Gaa/Aaa	4/24	1	2	FACETS	0.896	0.844	0.948	0.896	0.844	0.948	CLONAL	1	TRUE	1	0.837320981807452	2		452	696	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680014	30680014	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	777	509	0	ENST00000376406.3:c.1705G>A	p.Glu569Lys	p.E569K	ENST00000376406	NM_014641.2	569	Gaa/Aaa	5/15	0.834500054581191	3	FACETS	0.985	0.957	1	0.985	0.957	1	CLONAL	2	TRUE	1	0.837320981807452	3		509	1337	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663602	117663602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	422	628	2	ENST00000368508.3:c.4630C>T	p.Pro1544Ser	p.P1544S	ENST00000368508	NM_002944.2	1544	Cca/Tca	28/43	0.837320981807452	1	FACETS	0.964	0.932	0.994	0.964	0.932	0.994	CLONAL	1	TRUE	0	0.837320981807452	1		630	608	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959121	2959121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778152	NA	P-0018843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	434	635	1	ENST00000396946.4:c.2395G>A	p.Asp799Asn	p.D799N	ENST00000396946	NM_032415.4	799	Gat/Aat	18/25	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.837320981807452	2		636	970	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970979	70970979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	582	805	0	ENST00000276594.2:c.1282G>A	p.Gly428Ser	p.G428S	ENST00000276594	NM_024504.3	428	Ggc/Agc	6/8	1	2	FACETS	0.979	0.942	1	0.979	0.942	1	CLONAL	1	TRUE	1	0.837320981807452	2		805	1420	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0018843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	316	412	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.837320981807452	1	FACETS	0.938	0.901	0.973	0.938	0.901	0.973	CLONAL	1	TRUE	0	0.837320981807452	1		412	468	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115923	8115923	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	84	590	0	ENST00000346208.3:c.1271del	p.Pro424ArgfsTer51	p.P424Rfs*51	ENST00000346208		423	caC/ca	6/6	1	2	FACETS	0.876	0.773	0.986	0.876	0.773	0.986	CLONAL	1	TRUE	1	0.256127573129561	2		590	749	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0018845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	119	1181	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.206454661604036	4	FACETS	0.761	0.689	0.836			1	INDETERMINATE	2	TRUE	NA	0.38	4		1182	568	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199352	16199352	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	45	410	0	ENST00000375759.3:c.125G>C	p.Gly42Ala	p.G42A	ENST00000375759	NM_015001.2	42	gGa/gCa	2/15	0.278519904109574	1	FACETS	0.571	0.482	0.669	0.571	0.482	0.669	SUBCLONAL	1	TRUE	0	0.38	1		410	336	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612162	43612162	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	28	247	1	ENST00000355710.3:c.2267C>A	p.Ala756Asp	p.A756D	ENST00000355710	NM_020975.4	756	gCc/gAc	12/20	0.213573899066416	3	FACETS	0.918	0.74	1	0.459	0.37	0.559	INDETERMINATE	1	TRUE	1	0.38	3		248	191	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310923	123310923	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	59	392	0	ENST00000358487.5:c.505G>T	p.Val169Leu	p.V169L	ENST00000358487	NM_000141.4	169	Gtg/Ttg	5/18	1	2	FACETS	0.908	0.786	1	0.908	0.786	1	CLONAL	1	TRUE	1	0.38	2		392	342	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443731	49443731	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	42	665	0	ENST00000301067.7:c.3640G>T	p.Gly1214Cys	p.G1214C	ENST00000301067	NM_003482.3	1214	Ggt/Tgt	11/54	1	2	FACETS	0.531	0.444	0.628	0.531	0.444	0.628	SUBCLONAL	1	TRUE	1	0.38	2		665	416	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811768	102811768	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	51	591	0	ENST00000307046.8:c.416C>A	p.Ser139Tyr	p.S139Y	ENST00000307046	NM_001111285.1	139	tCt/tAt	4/4	1	2	FACETS	0.645	0.55	0.75	0.645	0.55	0.75	SUBCLONAL	1	TRUE	1	0.38	2		591	416	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610436	10610436	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	84	628	0	ENST00000171111.5:c.274C>T	p.Gln92Ter	p.Q92*	ENST00000171111	NM_203500.1	92	Cag/Tag	2/6	0.3	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.38	1		628	338	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11172459	11172459	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0018845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	98	723	2	ENST00000358026.2:c.5008-1G>T		p.X1670_splice	ENST00000358026	NM_001128849.1	1670			0.3	1	FACETS	0.912	0.818	1	0.912	0.818	1	CLONAL	1	TRUE	0	0.38	1		725	458	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736158	204736158	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	116	393	0	ENST00000302823.3:c.515C>A	p.Ser172Ter	p.S172*	ENST00000302823	NM_005214.4	172	tCg/tAg	3/4	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.38	2		393	430	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662460	227662460	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	56	430	0	ENST00000305123.5:c.995G>T	p.Gly332Val	p.G332V	ENST00000305123	NM_005544.2	332	gGc/gTc	1/2	1	2	FACETS	0.899	0.774	1	0.899	0.774	1	CLONAL	1	TRUE	1	0.38	2		430	328	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285903	38285905	+	stop_gained	Nonsense_Mutation	TNP	CTG	CTG	ATA	novel	NA	P-0018845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	136	545	1	ENST00000425967.3:c.506_508delinsTAT	p.Ser169_Glu170delinsLeuTer	p.S169_E170delinsL*	ENST00000425967	NM_001174067.1	169	tCAGag/tTATag	5/19	0.224636045831348	3	FACETS	1	0.964	1			1	INDETERMINATE	2	TRUE	NA	0.38	3		546	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0018846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1370	189	949	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.495	0.456	0.536	0.495	0.456	0.536	SUBCLONAL	1	TRUE	1	0.49	2		949	1559	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0018846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	212	894	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.49	2		895	703	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481417	140481417	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913348	NA	P-0018846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	193	515	0	ENST00000288602.6:c.1391G>T	p.Gly464Val	p.G464V	ENST00000288602	NM_004333.4	464	gGa/gTa	11/18	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.49	2		515	711	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0018846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	103	286	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.49	2		286	359	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993828	72993828	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371922710	NA	P-0018846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	128	336	0	ENST00000268489.5:c.217G>A	p.Glu73Lys	p.E73K	ENST00000268489	NM_006885.3	73	Gag/Aag	2/10	1	2	FACETS	0.91	0.828	0.996	0.91	0.828	0.996	CLONAL	1	TRUE	1	0.49	2		336	574	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117872	70117872	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	118	479	0	ENST00000245479.2:c.340G>C	p.Val114Leu	p.V114L	ENST00000245479	NM_000346.3	114	Gtg/Ctg	1/3	1	2	FACETS	0.552	0.497	0.609	0.552	0.497	0.609	SUBCLONAL	1	TRUE	1	0.49	2		479	873	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670729	134670729	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	72	512	0	ENST00000398015.3:c.640G>T	p.Glu214Ter	p.E214*	ENST00000398015	NM_004441.4	214	Gag/Tag	3/16	1	2	FACETS	0.294	0.255	0.335	0.294	0.255	0.335	SUBCLONAL	1	TRUE	1	0.49	2		512	1001	SUCCESS
APC	324	MSKCC	GRCh37	5	112175559	112175560	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0018846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	206	456	0	ENST00000257430.4:c.4268_4269del	p.Leu1423ProfsTer3	p.L1423Pfs*3	ENST00000257430	NM_000038.5	1423	cTT/c	16/16	1	2	FACETS	0.995	0.925	1	0.995	0.925	1	CLONAL	1	TRUE	1	0.49	2		456	845	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392165	81392165	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	28	274	0	ENST00000222390.5:c.112A>G	p.Thr38Ala	p.T38A	ENST00000222390	NM_000601.4	38	Aca/Gca	2/18	1	2	FACETS	0.414	0.332	0.507	0.414	0.332	0.507	SUBCLONAL	1	TRUE	1	0.49	2		274	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203436	NA	P-0018847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	44	676	0	ENST00000269305.4:c.487T>C	p.Tyr163His	p.Y163H	ENST00000269305	NM_001126112.2	163	Tac/Cac	5/11	1	2	FACETS	0.262	0.219	0.311	0.262	0.219	0.311	SUBCLONAL	1	FALSE	1	0.3	2		676	1118	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249002	55249003	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCGTGGA	rs397517109	NA	P-0018847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	77	586	0	ENST00000275493.2:c.2303_2311dup	p.Ser768_Asp770dup	p.S768_D770dup	ENST00000275493	NM_005228.3	768	gcc/gcCAGCGTGGAc	20/28	0.192955727717408	3	FACETS	0.611	0.535	0.693	0.306	0.267	0.347	SUBCLONAL	1	FALSE	1	0.3	3		586	966	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034420	47034420	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	43	377	0	ENST00000377604.3:c.505C>T	p.Gln169Ter	p.Q169*	ENST00000377604	NM_001204468.1	169	Cag/Tag	6/24	1	1	FACETS	0.445	0.372	0.526	0.445	0.372	0.526	SUBCLONAL	1	FALSE	0	0.3	1		377	548	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0018848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	73	708	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.851	0.743	0.967	0.851	0.743	0.967	CLONAL	1	TRUE	1	0.223211432790429	2		709	769	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0018848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	188	1034	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.178666299762038	2	FACETS	1	0.98	1	0.593	0.546	0.642	CLONAL	1	TRUE	0	0.223211432790429	2		1035	1420	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77034326	77034326	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1321832144	NA	P-0018850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	90	591	0	ENST00000356341.3:c.1631A>G	p.Asn544Ser	p.N544S	ENST00000356341	NM_002576.4	544	aAt/aGt	15/15	1	2	FACETS	0.946	0.846	1	0.946	0.846	1	CLONAL	1	TRUE	1	0.508629142927446	2		591	374	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	120	364	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.79	0.718	0.864	0.79	0.718	0.864	SUBCLONAL	1	TRUE	1	0.689144460633452	2		365	441	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0018851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12415	9605	534	2	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.689144460633452	36	FACETS	1	0.995	1			1	CLONAL	16	TRUE	NA	0.689144460633452	36		536	22020	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307316	118307316	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs9332745	NA	P-0018851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	12	6	0	ENST00000534358.1:c.89C>G	p.Ala30Gly	p.A30G	ENST00000534358	NM_005933.3	30	gCc/gGc	1/36	1	2	FACETS	1	0.83	1	1	0.83	1	CLONAL	1	TRUE	1	0.689144460633452	2		6	30	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717739	89717740	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	120	506	0	ENST00000371953.3:c.765dup	p.Glu256ArgfsTer42	p.E256Rfs*42	ENST00000371953	NM_000314.4	255	gta/gtAa	7/9	0.689144460633452	1	FACETS	0.951	0.878	1	0.951	0.878	1	CLONAL	1	TRUE	0	0.689144460633452	1		506	240	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0018852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	330	715	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.485502357221046	7	FACETS	0.95	0.899	1	0.57	0.539	0.601	CLONAL	3	TRUE	2	0.485502357221046	7		717	1056	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445040	49445041	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0018852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	301	521	0	ENST00000301067.7:c.2425dup	p.Gln809ProfsTer3	p.Q809Pfs*3	ENST00000301067	NM_003482.3	809	cag/cCag	10/54	NA	2	FACETS	0.845	0.8	0.889			1	INDETERMINATE	2	TRUE	NA	0.485502357221046	2		521	734	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0018852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	1123	868	5	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	0.485502357221046	4	FACETS	1	0.992	1			1	CLONAL	4	TRUE	NA	0.485502357221046	4		873	1676	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472569	88472569	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	244	598	0	ENST00000360948.2:c.1986G>T	p.Gln662His	p.Q662H	ENST00000360948	NM_001012338.2	662	caG/caT	16/19	0.460553500911904	3	FACETS	0.824	0.773	0.876	0.824	0.773	0.876	CLONAL	2	TRUE	1	0.485502357221046	3		598	758	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519920	NA	P-0018852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	269	406	1	ENST00000397062.3:c.85G>T	p.Asp29Tyr	p.D29Y	ENST00000397062	NM_006164.4	29	Gat/Tat	2/5	0.460553500911904	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	1	0.485502357221046	3		407	681	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241923	72241923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	118	471	0	ENST00000357731.5:c.467T>C	p.Val156Ala	p.V156A	ENST00000357731	NM_173808.2	156	gTc/gCc	3/7	0.483876727802754	3	FACETS	1	0.909	1	0.503	0.454	0.553	CLONAL	1	TRUE	1	0.485502357221046	3		471	601	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104357035	104357035	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	446	579	0	ENST00000369902.3:c.895C>T	p.Arg299Ter	p.R299*	ENST00000369902	NM_016169.3	299	Cga/Tga	7/12	0.485502357221046	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.485502357221046	2		579	867	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281275	49281275	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	234	800	0	ENST00000282018.3:c.322G>T	p.Asp108Tyr	p.D108Y	ENST00000282018	NM_020377.2	108	Gac/Tac	1/1	0.485502357221046	4	FACETS	1	0.976	1	0.368	0.343	0.395	CLONAL	1	TRUE	1	0.485502357221046	4		800	1296	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654848	29654848	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	82	301	2	ENST00000356175.3:c.5537C>A	p.Pro1846Gln	p.P1846Q	ENST00000356175	NM_000267.3	1846	cCg/cAg	37/57	0.483419011983428	4	FACETS	0.807	0.712	0.908	0.403	0.356	0.454	CLONAL	1	TRUE	2	0.485502357221046	4		303	622	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566814	212566814	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	153	341	0	ENST00000342788.4:c.1367G>C	p.Gly456Ala	p.G456A	ENST00000342788	NM_005235.2	456	gGa/gCa	12/28	0.460553500911904	3	FACETS	0.832	0.767	0.898	0.832	0.767	0.898	CLONAL	2	TRUE	1	0.485502357221046	3		341	471	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573941	41573941	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	554	819	0	ENST00000263253.7:c.6226G>T	p.Ala2076Ser	p.A2076S	ENST00000263253	NM_001429.3	2076	Gcc/Tcc	31/31	0.485502357221046	2	FACETS	0.992	0.956	1	0.992	0.956	1	CLONAL	2	TRUE	0	0.485502357221046	2		819	1150	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884884	134884884	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536013299	NA	P-0018852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	341	597	1	ENST00000398015.3:c.1660G>A	p.Val554Met	p.V554M	ENST00000398015	NM_004441.4	554	Gtg/Atg	8/16	0.485502357221046	2	FACETS	0.982	0.937	1	0.982	0.937	1	CLONAL	2	TRUE	0	0.485502357221046	2		598	715	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86676363	86676363	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	203	400	0	ENST00000274376.6:c.2641G>C	p.Val881Leu	p.V881L	ENST00000274376	NM_002890.2	881	Gtt/Ctt	20/25	0.481177032965398	3	FACETS	0.957	0.904	1	0.957	0.904	1	CLONAL	3	TRUE	0	0.485502357221046	3		400	362	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449780	149449780	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	536	657	1	ENST00000286301.3:c.1284C>G	p.Asn428Lys	p.N428K	ENST00000286301	NM_005211.3	428	aaC/aaG	9/22	0.481177032965398	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	TRUE	0	0.485502357221046	3		658	911	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829820	76829820	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	242	425	0	ENST00000373344.5:c.6221A>T	p.Glu2074Val	p.E2074V	ENST00000373344	NM_000489.3	2074	gAg/gTg	28/35	0.387540800480226	2	FACETS	0.87	0.829	0.91			1	CLONAL	3	TRUE	NA	0.485502357221046	2		425	382	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	85	364	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.597354307399172	2		365	268	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0018854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	405	900	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.589481408485101	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	TRUE	1	0.597354307399172	4		901	709	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962804	2962804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772900135	NA	P-0018854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	152	426	1	ENST00000396946.4:c.2104G>A	p.Glu702Lys	p.E702K	ENST00000396946	NM_032415.4	702	Gag/Aag	16/25	0.589481408485101	4	FACETS	1	0.951	1	0.352	0.322	0.383	CLONAL	1	TRUE	1	0.597354307399172	4		427	770	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266134	41266136	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs587776850	NA	P-0018854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	82	240	0	ENST00000349496.5:c.133_135del	p.Ser45del	p.S45del	ENST00000349496	NM_001904.3	44	cCTTct/cct	3/15	1	2	FACETS	0.853	0.759	0.951	0.853	0.759	0.951	CLONAL	1	TRUE	1	0.597354307399172	2		240	322	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539951	187539951	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs777631605	NA	P-0018854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	79	263	0	ENST00000441802.2:c.7789C>T	p.Arg2597Ter	p.R2597*	ENST00000441802	NM_005245.3	2597	Cga/Tga	10/27	1	2	FACETS	0.762	0.676	0.854	0.762	0.676	0.854	SUBCLONAL	1	TRUE	1	0.597354307399172	2		263	347	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827988	40827988	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	105	337	0	ENST00000373198.4:c.2440C>T	p.Gln814Ter	p.Q814*	ENST00000373198	NM_133170.3	814	Cag/Tag	17/32	1	2	FACETS	0.881	0.796	0.97	0.881	0.796	0.97	CLONAL	1	TRUE	1	0.597354307399172	2		337	399	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965706	93965706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	122	345	0	ENST00000369303.4:c.2222G>A	p.Gly741Glu	p.G741E	ENST00000369303	NM_004440.3	741	gGa/gAa	13/17	0.597354307399172	1	FACETS	0.974	0.895	1	0.974	0.895	1	CLONAL	1	TRUE	0	0.597354307399172	1		345	294	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342931	118342931	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	63	391	0	ENST00000534358.1:c.1057C>T	p.Arg353Ter	p.R353*	ENST00000534358	NM_005933.3	353	Cga/Tga	3/36	0.295665774944133	1	FACETS	0.364	0.316	0.416	0.364	0.316	0.416	INDETERMINATE	1	TRUE	0	0.597354307399172	1		391	406	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133238161	133238161	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772307459	NA	P-0018854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	146	422	0	ENST00000320574.5:c.2816C>T	p.Ala939Val	p.A939V	ENST00000320574	NM_006231.2	939	gCc/gTc	24/49	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.597354307399172	2		422	481	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777972	3777972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	193	625	0	ENST00000262367.5:c.7076C>T	p.Pro2359Leu	p.P2359L	ENST00000262367	NM_004380.2	2359	cCa/cTa	31/31	1	2	FACETS	0.987	0.917	1	0.987	0.917	1	CLONAL	1	TRUE	1	0.597354307399172	2		625	655	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129707	30129707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	122	343	2	ENST00000263025.4:c.506C>T	p.Pro169Leu	p.P169L	ENST00000263025	NM_002746.2	169	cCc/cTc	3/9	1	2	FACETS	0.989	0.902	1	0.989	0.902	1	CLONAL	1	TRUE	1	0.597354307399172	2		345	413	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755561	39755561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	111	258	0	ENST00000288319.7:c.1204C>T	p.His402Tyr	p.H402Y	ENST00000288319	NM_182918.3	402	Cac/Tac	10/10	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.597354307399172	2		258	351	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051646	30051646	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	114	269	0	ENST00000338641.4:c.580G>A	p.Glu194Lys	p.E194K	ENST00000338641	NM_000268.3	194	Gag/Aag	6/16	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.597354307399172	2		269	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0018855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	332	1017	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.269587000919349	3	FACETS	1	0.968	1	0.688	0.651	0.726	CLONAL	2	TRUE	0	0.351978201788941	3		1018	1075	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0018855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	96	702	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.156880136741075	3	FACETS	0.97	0.866	1	0.485	0.433	0.541	INDETERMINATE	1	TRUE	1	0.351978201788941	3		702	661	SUCCESS
APC	324	MSKCC	GRCh37	5	112175136	112175136	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	45	221	0	ENST00000257430.4:c.3845C>A	p.Ser1282Ter	p.S1282*	ENST00000257430	NM_000038.5	1282	tCa/tAa	16/16	0.156880136741075	3	FACETS	0.806	0.679	0.946	0.403	0.339	0.473	INDETERMINATE	1	TRUE	1	0.351978201788941	3		221	373	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982980	201982985	+	inframe_deletion	In_Frame_Del	DEL	GAGTTC	GAGTTC	-	novel	NA	P-0018855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	232	663	1	ENST00000359651.3:c.829_834del	p.Glu277_Phe278del	p.E277_F278del	ENST00000359651		277	GAGTTC/-	7/8	0.233699654913218	4	FACETS	1	0.988	1	0.637	0.593	0.684	CLONAL	1	TRUE	2	0.351978201788941	4		664	1398	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710932	117710932	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	193	374	0	ENST00000368508.3:c.1340T>A	p.Val447Glu	p.V447E	ENST00000368508	NM_002944.2	447	gTg/gAg	12/43	NA	2	FACETS	0.882	0.82	0.945			1	INDETERMINATE	2	TRUE	NA	0.351978201788941	2		374	622	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0018856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	91	807	3	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.88	0.779	0.989	0.88	0.779	0.989	CLONAL	1	TRUE	1	0.17	2		810	1216	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	94	917	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.17	2		917	1058	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0018856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	46	301	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	1	2	FACETS	0.855	0.719	1	0.855	0.719	1	CLONAL	1	TRUE	1	0.17	2		301	633	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs730881677	NA	P-0018856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	90	345	0	ENST00000304494.5:c.151-1G>C		p.X51_splice	ENST00000304494	NM_000077.4	51			1	2	FACETS	0.822	0.73	0.92	1	0.982	1	CLONAL	2	TRUE	1	0.17	2		345	644	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	364679	364679	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	70	600	1	ENST00000262320.3:c.883G>T	p.Gly295Ter	p.G295*	ENST00000262320	NM_003502.3	295	Gga/Tga	3/11	0.13071183497185	1	FACETS	0.804	0.699	0.918	0.804	0.699	0.918	CLONAL	1	TRUE	0	0.17	1		601	937	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591108	67591108	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	15	404	0	ENST00000274335.5:c.1701A>C	p.Lys567Asn	p.K567N	ENST00000274335		567	aaA/aaC	12/15	1	2	FACETS	0.263	0.191	0.35	0.263	0.191	0.35	SUBCLONAL	1	TRUE	1	0.17	2		404	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0018857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	387	595	3	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.354957366212297	2	FACETS	0.936	0.89	0.982	0.936	0.89	0.982	CLONAL	2	FALSE	0	0.354957366212297	2		598	1165	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851754	134851754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56396912	NA	P-0018857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	227	625	2	ENST00000398015.3:c.1160C>T	p.Thr387Met	p.T387M	ENST00000398015	NM_004441.4	387	aCg/aTg	5/16	0.205557681732176	2	FACETS	1	0.988	1	0.643	0.599	0.688	INDETERMINATE	1	FALSE	0	0.354957366212297	2		627	995	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0018857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	210	341	3	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.204658538861057	3	FACETS	1	0.983	1	0.77	0.72	0.822	INDETERMINATE	2	FALSE	0	0.354957366212297	3		344	603	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741637	17741637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	98	371	0	ENST00000250003.3:c.308G>A	p.Arg103His	p.R103H	ENST00000250003	NM_002478.4	103	cGc/cAc	1/3	0.207533595874115	3	FACETS	0.901	0.804	1	0.45	0.402	0.502	INDETERMINATE	1	FALSE	1	0.354957366212297	3		371	722	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	130	603	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.31	2		603	662	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871245	12871245	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	28	209	0	ENST00000228872.4:c.472G>A	p.Asp158Asn	p.D158N	ENST00000228872	NM_004064.3	158	Gac/Aac	1/3	1	2	FACETS	0.684	0.549	0.838	0.684	0.549	0.838	SUBCLONAL	1	TRUE	1	0.31	2		209	264	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929053	32929053	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200078639	NA	P-0018858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	67	895	0	ENST00000380152.3:c.7063G>A	p.Glu2355Lys	p.E2355K	ENST00000380152		2355	Gaa/Aaa	14/27	0.221722025394261	2	FACETS	0.638	0.554	0.729	0.319	0.277	0.365	SUBCLONAL	1	TRUE	0	0.31	2		895	678	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772279	68772279	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	247	816	0	ENST00000261769.5:c.128G>T	p.Arg43Leu	p.R43L	ENST00000261769	NM_004360.3	43	cGg/cTg	2/16	0.221041377054333	3	FACETS	1	0.987	1	0.795	0.746	0.845	CLONAL	2	TRUE	0	0.31	3		816	772	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191155	2191155	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	109	978	0	ENST00000398665.3:c.409G>A	p.Gly137Arg	p.G137R	ENST00000398665	NM_032482.2	137	Ggg/Agg	5/28	0.221722025394261	2	FACETS	0.744	0.667	0.826	0.372	0.333	0.413	SUBCLONAL	1	TRUE	0	0.31	2		978	945	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961787	55961787	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	183	657	1	ENST00000263923.4:c.2774C>A	p.Ser925Tyr	p.S925Y	ENST00000263923	NM_002253.2	925	tCc/tAc	20/30	0.28927952039452	2	FACETS	0.945	0.876	1	0.945	0.876	1	CLONAL	2	TRUE	0	0.31	2		658	625	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249007	+	missense_variant	Missense_Mutation	TNP	GCG	GCG	TCT	novel	NA	P-0018858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2188	207	615	0	ENST00000275493.2:c.2303_2305delinsTCT	p.Ser768_Val769delinsIleLeu	p.S768_V769delinsIL	ENST00000275493	NM_005228.3	768	aGCGtg/aTCTtg	20/28	0.300967408279649	22	FACETS	1	0.977	1			1	CLONAL	2	TRUE	NA	0.31	22		615	2395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0018860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	333	546	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	0.450899388719284	3	FACETS	0.887	0.847	0.927	0.887	0.847	0.927	CLONAL	3	TRUE	0	0.490864918643054	3		546	635	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069059	5069060	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	209	457	0	ENST00000381652.3:c.1370dup	p.Asn457LysfsTer2	p.N457Kfs*2	ENST00000381652	NM_004972.3	455	aca/acAa	11/25	0.490864918643054	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.490864918643054	1		457	533	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589019	67589020	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	236	310	0	ENST00000274335.5:c.1111dup	p.Thr371AsnfsTer8	p.T371Nfs*8	ENST00000274335		370	-/A	8/15	0.490864918643054	3	FACETS	0.893	0.845	0.94	0.893	0.845	0.94	CLONAL	3	TRUE	0	0.490864918643054	3		310	447	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555761	21555761	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	137	748	2	ENST00000382592.4:c.2509G>T	p.Glu837Ter	p.E837*	ENST00000382592	NM_014572.2	837	Gag/Tag	6/8	0.183940247300656	2	FACETS	0.827	0.753	0.904	0.827	0.753	0.904	CLONAL	2	TRUE	0	0.224883455054651	2		750	737	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244290	153244290	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	67	297	0	ENST00000281708.4:c.1867del	p.His623IlefsTer5	p.H623Ifs*5	ENST00000281708	NM_033632.3	623	Cat/at	12/12	0.126538440164518	3	FACETS	0.923	0.807	1	0.615	0.538	0.698	INDETERMINATE	2	TRUE	0	0.224883455054651	3		297	359	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0018862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	337	461	0	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	0.388750142705792	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.389535269751955	2		461	762	SUCCESS
APC	324	MSKCC	GRCh37	5	112175162	112175162	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561588104	NA	P-0018862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	243	447	1	ENST00000257430.4:c.3871C>T	p.Gln1291Ter	p.Q1291*	ENST00000257430	NM_000038.5	1291	Cag/Tag	16/16	0.389535269751955	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	0	0.389535269751955	3		448	458	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936046	178936046	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	42	184	0	ENST00000263967.3:c.1588C>A	p.Gln530Lys	p.Q530K	ENST00000263967	NM_006218.2	530	Cag/Aag	10/21	0.389535269751955	4	FACETS	0.869	0.727	1	0.434	0.363	0.512	CLONAL	1	TRUE	2	0.389535269751955	4		184	345	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156920	89156933	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCTCCTTCTCAG	CTCCTCCTTCTCAG	-	novel	NA	P-0018862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	104	670	0	ENST00000336596.2:c.24_37del	p.Leu10CysfsTer15	p.L10Cfs*15	ENST00000336596	NM_005233.5	8	CTCCTCCTTCTCAGc/c	1/17	0.389535269751955	3	FACETS	0.55	0.491	0.614			1	SUBCLONAL	1	TRUE	NA	0.389535269751955	3		670	1159	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149453003	149453003	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756763314	NA	P-0018862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	83	471	0	ENST00000286301.3:c.943G>A	p.Val315Met	p.V315M	ENST00000286301	NM_005211.3	315	Gtg/Atg	7/22	0.389535269751955	3	FACETS	0.585	0.515	0.66	0.195	0.171	0.22	SUBCLONAL	1	TRUE	0	0.389535269751955	3		471	870	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5081841	5081841	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	196	290	0	ENST00000381652.3:c.2553del	p.Leu852TyrfsTer30	p.L852Yfs*30	ENST00000381652	NM_004972.3	851	Ttt/tt	19/25	0.389535269751955	5	FACETS	1	0.966	1	0.711	0.66	0.764	CLONAL	2	TRUE	2	0.389535269751955	5		290	747	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	113	364	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.3116257354742	2		365	493	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711350	114711350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243981730	NA	P-0018863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	52	337	0	ENST00000543371.1:c.365C>T	p.Ser122Leu	p.S122L	ENST00000543371	NM_001198531.1	122	tCg/tTg	3/14	1	2	FACETS	0.591	0.503	0.687	0.591	0.503	0.687	SUBCLONAL	1	TRUE	1	0.3116257354742	2		337	565	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220382	1220382	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	131	529	0	ENST00000326873.7:c.475C>T	p.Gln159Ter	p.Q159*	ENST00000326873	NM_000455.4	159	Cag/Tag	4/10	0.3116257354742	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.3116257354742	1		529	565	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953827	131953827	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104895051	NA	P-0018863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	50	542	0	ENST00000265335.6:c.3230G>A	p.Arg1077Gln	p.R1077Q	ENST00000265335		1077	cGa/cAa	21/25	1	2	FACETS	0.674	0.572	0.786	0.674	0.572	0.786	SUBCLONAL	1	TRUE	1	0.3116257354742	2		542	476	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118378263	118378263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	48	439	0	ENST00000534358.1:c.10774G>A	p.Glu3592Lys	p.E3592K	ENST00000534358	NM_005933.3	3592	Gag/Aag	28/36	0.3116257354742	1	FACETS	0.388	0.327	0.455	0.388	0.327	0.455	SUBCLONAL	1	TRUE	0	0.3116257354742	1		439	670	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479288	50479288	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	74	557	1	ENST00000394963.4:c.136C>T	p.Gln46Ter	p.Q46*	ENST00000394963	NM_003076.4	46	Caa/Taa	1/13	1	2	FACETS	0.643	0.562	0.73	0.643	0.562	0.73	SUBCLONAL	1	TRUE	1	0.3116257354742	2		558	739	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845816	72845816	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs199992763	NA	P-0018863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	50	515	0	ENST00000268489.5:c.3651C>G	p.Ile1217Met	p.I1217M	ENST00000268489	NM_006885.3	1217	atC/atG	6/10	1	2	FACETS	0.442	0.374	0.517	0.442	0.374	0.517	SUBCLONAL	1	TRUE	1	0.3116257354742	2		515	726	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791992	42791992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1294	79	708	0	ENST00000575354.2:c.796G>A	p.Asp266Asn	p.D266N	ENST00000575354	NM_015125.3	266	Gat/Aat	6/20	0.171927474848614	5	FACETS	0.542	0.474	0.615	0.181	0.158	0.205	INDETERMINATE	1	TRUE	2	0.3116257354742	5		708	1373	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682877	190682877	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	46	590	0	ENST00000441310.2:c.553G>C	p.Asp185His	p.D185H	ENST00000441310	NM_000534.4	185	Gac/Cac	5/13	0.3116257354742	1	FACETS	0.558	0.47	0.654	0.558	0.47	0.654	SUBCLONAL	1	TRUE	0	0.3116257354742	1		590	447	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089788	5089788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1431982074	NA	P-0018863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	48	408	0	ENST00000381652.3:c.2686G>A	p.Glu896Lys	p.E896K	ENST00000381652	NM_004972.3	896	Gaa/Aaa	20/25	1	2	FACETS	0.755	0.64	0.882	0.755	0.64	0.882	SUBCLONAL	1	TRUE	1	0.3116257354742	2		408	408	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0018864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	100	843	0	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	1	2	FACETS	0.754	0.672	0.84	0.754	0.672	0.84	SUBCLONAL	1	TRUE	1	0.310362657479095	2		843	855	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0018864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	80	600	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.310362657479095	2		600	500	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0018864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	49	427	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	0.88	0.748	1	0.88	0.748	1	CLONAL	1	TRUE	1	0.310362657479095	2		427	359	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692869	89692869	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	41	372	0	ENST00000371953.3:c.353A>T	p.His118Leu	p.H118L	ENST00000371953	NM_000314.4	118	cAt/cTt	5/9	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.310362657479095	2		372	231	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105917	27105917	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	221	502	0	ENST00000324856.7:c.5528del	p.His1843ProfsTer40	p.H1843Pfs*40	ENST00000324856	NM_006015.4	1843	cAc/cc	20/20	0.310362657479095	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.310362657479095	2		502	594	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633465	3633465	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	283	964	0	ENST00000294008.3:c.4786A>C	p.Lys1596Gln	p.K1596Q	ENST00000294008	NM_032444.2	1596	Aag/Cag	14/15	0.429533783481641	5	FACETS	1	0.958	1			1	CLONAL	2	TRUE	NA	0.632325993722514	5		964	855	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939554	76939554	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	271	689	0	ENST00000373344.5:c.1194del	p.Leu399TrpfsTer15	p.L399Wfs*15	ENST00000373344	NM_000489.3	398	gtG/gt	9/35	0.632325993722514	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.632325993722514	3		689	486	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0018869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	215	715	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.301305732457882	3	FACETS	1	0.978	1	0.558	0.52	0.598	INDETERMINATE	1	TRUE	1	0.592261181094493	3		717	843	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275842	38275842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367715495	NA	P-0018869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	263	690	0	ENST00000425967.3:c.1427G>A	p.Arg476Gln	p.R476Q	ENST00000425967	NM_001174067.1	476	cGg/cAg	11/19	0.592261181094493	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.592261181094493	1		690	550	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456600	32456600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	45	174	0	ENST00000332351.3:c.292G>A	p.Gly98Ser	p.G98S	ENST00000332351	NM_024426.4	98	Ggc/Agc	1/10	0.428704874491934	1	FACETS	0.493	0.418	0.573	0.493	0.418	0.573	SUBCLONAL	1	TRUE	0	0.592261181094493	1		174	217	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112287	115112287	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	113	149	2	ENST00000257566.3:c.1453C>T	p.Gln485Ter	p.Q485*	ENST00000257566	NM_016569.3	485	Cag/Tag	7/8	0.249323799621306	3	FACETS	1	0.968	1	1	0.968	1	INDETERMINATE	2	TRUE	1	0.592261181094493	3		151	225	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849628	68849628	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690810	NA	P-0018869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	252	709	0	ENST00000261769.5:c.1531C>T	p.Gln511Ter	p.Q511*	ENST00000261769	NM_004360.3	511	Cag/Tag	10/16	0.592261181094493	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.592261181094493	1		709	556	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0018879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	531	868	5	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	0.380141271660988	2	FACETS	0.971	0.931	1	0.971	0.931	1	CLONAL	2	TRUE	0	0.37536858996647	2		873	1457	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226590008	226590008	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377491451	NA	P-0018879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1721	284	941	2	ENST00000366794.5:c.193C>T	p.Arg65Trp	p.R65W	ENST00000366794	NM_001618.3	65	Cgg/Tgg	2/23	0.37536858996647	5	FACETS	1	0.986	1	0.295	0.276	0.315	CLONAL	1	TRUE	1	0.37536858996647	5		943	2005	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910625	32910625	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs535547513	NA	P-0018879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	196	745	1	ENST00000380152.3:c.2133C>A	p.Cys711Ter	p.C711*	ENST00000380152		711	tgC/tgA	11/27	0.381644872525072	3	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.37536858996647	3		746	1065	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73334713	73334713	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	68	471	0	ENST00000377767.4:c.2747C>G	p.Ser916Cys	p.S916C	ENST00000377767	NM_014953.3	916	tCt/tGt	20/21	0.381644872525072	3	FACETS	0.723	0.629	0.825			1	SUBCLONAL	1	TRUE	NA	0.37536858996647	3		471	595	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649185	23649185	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	130	563	2	ENST00000261584.4:c.197A>G	p.Gln66Arg	p.Q66R	ENST00000261584	NM_024675.3	66	cAg/cGg	3/13	0.381644872525072	3	FACETS	0.882	0.799	0.969			1	CLONAL	1	TRUE	NA	0.37536858996647	3		565	933	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383350	42383350	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	175	600	1	ENST00000221972.3:c.370C>G	p.Arg124Gly	p.R124G	ENST00000221972	NM_021601.3	124	Cgc/Ggc	2/5	0.380141271660988	2	FACETS	0.964	0.888	1	0.482	0.444	0.522	CLONAL	1	TRUE	0	0.37536858996647	2		601	967	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972949	25972949	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	119	399	0	ENST00000435504.4:c.1476G>T	p.Lys492Asn	p.K492N	ENST00000435504		492	aaG/aaT	12/13	0.37536858996647	5	FACETS	1	0.955	1			1	CLONAL	1	TRUE	NA	0.37536858996647	5		399	900	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196092	138196092	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	153	504	0	ENST00000237289.4:c.406C>G	p.Arg136Gly	p.R136G	ENST00000237289	NM_001270507.1	136	Cgc/Ggc	3/9	NA	2	FACETS	1	0.928	1			1	INDETERMINATE	1	TRUE	NA	0.37536858996647	2		504	803	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641084	93641084	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	201	737	3	ENST00000375746.1:c.1430A>T	p.Gln477Leu	p.Q477L	ENST00000375746	NM_001174167.1	477	cAg/cTg	11/14	0.271264412988998	5	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.37536858996647	5		740	1313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0018880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	19	850	2	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	1	2	FACETS	0.121	0.091	0.157	0.121	0.091	0.157	SUBCLONAL	1	FALSE	1	0.40427808573158	2		852	777	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676267	37676267	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	380	1000	3	ENST00000447079.4:c.3022C>T	p.Arg1008Trp	p.R1008W	ENST00000447079	NM_015083.1	1008	Cgg/Tgg	11/14	0.294943875959548	4	FACETS	0.986	0.935	1			1	CLONAL	2	FALSE	NA	0.40427808573158	4		1003	1339	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	216	917	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	0.36856752953626	2		917	1099	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	151	615	0	ENST00000269305.4:c.772G>C	p.Glu258Gln	p.E258Q	ENST00000269305	NM_001126112.2	258	Gaa/Caa	7/11	0.36856752953626	1	FACETS	0.984	0.902	1	0.984	0.902	1	CLONAL	1	TRUE	0	0.36856752953626	1		615	679	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939031	48939031	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	84	430	0	ENST00000267163.4:c.863T>A	p.Val288Glu	p.V288E	ENST00000267163	NM_000321.2	288	gTg/gAg	9/27	0.36856752953626	1	FACETS	0.739	0.655	0.829	0.739	0.655	0.829	SUBCLONAL	1	TRUE	0	0.36856752953626	1		430	503	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194876	30194876	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	141	629	0	ENST00000331968.5:c.269C>G	p.Pro90Arg	p.P90R	ENST00000331968	NM_002742.2	90	cCt/cGt	2/18	0.191821033322998	3	FACETS	0.981	0.893	1	0.49	0.446	0.537	INDETERMINATE	1	TRUE	1	0.36856752953626	3		629	924	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134277	11134277	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	208	784	0	ENST00000358026.2:c.2943G>C	p.Lys981Asn	p.K981N	ENST00000358026	NM_001128849.1	981	aaG/aaC	20/36	0.231973174085065	1	FACETS	0.932	0.865	1	0.932	0.865	1	CLONAL	1	TRUE	0	0.36856752953626	1		784	988	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098988	178098988	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	89	397	0	ENST00000397062.3:c.57G>C	p.Leu19Phe	p.L19F	ENST00000397062	NM_006164.4	19	ttG/ttC	2/5	1	2	FACETS	0.881	0.783	0.986	0.881	0.783	0.986	CLONAL	1	TRUE	1	0.36856752953626	2		397	548	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197020	123197020	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	93	797	0	ENST00000218089.9:c.1786G>C	p.Asp596His	p.D596H	ENST00000218089	NM_001042749.1	596	Gat/Cat	19/35	NA	2	FACETS	0.518	0.459	0.58			1	INDETERMINATE	1	TRUE	NA	0.36856752953626	2		797	975	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0018882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	209	584	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.861	0.8	0.923	0.861	0.8	0.923	CLONAL	1	TRUE	1	0.584540876029001	2		584	831	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0018882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	259	613	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.949	0.89	1	0.949	0.89	1	CLONAL	1	TRUE	1	0.584540876029001	2		613	934	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835596	68835596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587783047	NA	P-0018882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	277	621	2	ENST00000261769.5:c.187C>T	p.Arg63Ter	p.R63*	ENST00000261769	NM_004360.3	63	Cga/Tga	3/16	0.584540876029001	1	FACETS	0.954	0.901	1	0.954	0.901	1	CLONAL	1	TRUE	0	0.584540876029001	1		623	703	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409944	63409944	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	164	442	0	ENST00000330258.3:c.3223G>C	p.Ala1075Pro	p.A1075P	ENST00000330258	NM_152424.3	1075	Gcc/Ccc	2/2	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.584540876029001	2		442	526	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974722	15974722	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0018882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	204	467	0	ENST00000268712.3:c.4152+1del		p.X1384_splice	ENST00000268712	NM_006311.3	1384			0.584540876029001	1	FACETS	0.92	0.86	0.981	0.92	0.86	0.981	CLONAL	1	TRUE	0	0.584540876029001	1		467	537	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206728	36206728	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	255	655	0	ENST00000300305.3:c.784C>T	p.Gln262Ter	p.Q262*	ENST00000300305		262	Cag/Tag	6/8	1	2	FACETS	0.932	0.874	0.992	0.932	0.874	0.992	CLONAL	1	TRUE	1	0.584540876029001	2		655	936	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0018883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	41	824	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.235967279810039	3	FACETS	0.476	0.395	0.568	0.238	0.197	0.284	SUBCLONAL	1	TRUE	1	0.16	3		824	1162	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602314	10602314	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	54	1059	0	ENST00000171111.5:c.1264G>T	p.Asp422Tyr	p.D422Y	ENST00000171111	NM_203500.1	422	Gat/Tat	3/6	0.235967279810039	3	FACETS	0.739	0.629	0.86	0.369	0.314	0.43	SUBCLONAL	1	TRUE	1	0.16	3		1059	987	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332805	70332805	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	55	1048	0	ENST00000373644.4:c.710G>C	p.Ser237Thr	p.S237T	ENST00000373644	NM_030625.2	237	aGt/aCt	2/12	0.3	2	FACETS	0.788	0.672	0.915			1	CLONAL	1	TRUE	NA	0.16	2		1048	873	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445043	49445043	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	55	758	1	ENST00000301067.7:c.2423C>T	p.Pro808Leu	p.P808L	ENST00000301067	NM_003482.3	808	cCc/cTc	10/54	0.235967279810039	4	FACETS	0.914	0.779	1	0.457	0.389	0.531	CLONAL	1	TRUE	2	0.16	4		759	873	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42053955	42053955	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	42	743	1	ENST00000219905.7:c.7417G>T	p.Gly2473Ter	p.G2473*	ENST00000219905	NM_001164273.1	2473	Gga/Tga	21/24	0.235967279810039	3	FACETS	0.729	0.607	0.865	0.364	0.303	0.433	SUBCLONAL	1	TRUE	1	0.16	3		744	778	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610198	10610198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	113	1000	0	ENST00000171111.5:c.512G>A	p.Cys171Tyr	p.C171Y	ENST00000171111	NM_203500.1	171	tGc/tAc	2/6	0.235967279810039	3	FACETS	1	0.98	1	0.696	0.625	0.772	CLONAL	1	TRUE	1	0.16	3		1000	1096	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502704	149502704	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	72	683	0	ENST00000261799.4:c.2084G>T	p.Arg695Leu	p.R695L	ENST00000261799	NM_002609.3	695	cGc/cTc	15/23	0.3	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.16	1		683	621	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513451	149513452	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0018883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	81	794	1	ENST00000261799.4:c.751dup	p.Arg251ProfsTer13	p.R251Pfs*13	ENST00000261799	NM_002609.3	251	cgc/cCgc	5/23	0.3	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.16	1		795	690	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965605	93965605	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	68	887	0	ENST00000369303.4:c.2323T>A	p.Ser775Thr	p.S775T	ENST00000369303	NM_004440.3	775	Tca/Aca	13/17	0.153873193113272	3	FACETS	0.93	0.807	1	0.465	0.403	0.532	CLONAL	1	TRUE	1	0.16	3		887	987	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507405	8507405	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	31	527	0	ENST00000356435.5:c.1573G>T	p.Glu525Ter	p.E525*	ENST00000356435		525	Gaa/Taa	11/35	0.153873193113272	1	FACETS	0.751	0.606	0.914	0.751	0.606	0.914	CLONAL	1	TRUE	0	0.16	1		527	475	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	197	364	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.931	0.869	0.995	0.931	0.869	0.995	CLONAL	1	TRUE	1	0.775079170329572	2		365	546	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552118	29552121	+	frameshift_variant	Frame_Shift_Del	DEL	AGAT	AGAT	-	novel	NA	P-0018884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	58	281	0	ENST00000356175.3:c.1854_1857del	p.Asp618GlufsTer12	p.D618Efs*12	ENST00000356175	NM_000267.3	617	gcAGAT/gc	17/57	0.602268416438247	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.775079170329572	1		281	90	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41276049	41276381	+	splice_acceptor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	AAGATTTTCTGCATAGCATTAATGACATTTTGTACTTCTTCAACGCGAAGAGCAGATAAATCCATTTCTTTCTGTTCCAATGAACTTTAACACATTAGAAAAACATATATATATATCTTTTTAAAAGGTTTATAAAATGACAACTTCATTTTATCATTTTAAAATAAAGTAAATTTAAGATTTGGAAGGTTTTAGAATAATACAAACCAAAGAACTAATGACAACGTCCTTTATTTTTAAAGATTCTAGAAGTTGCTTTTTGTAATTAGACAACATAAATTCTGAATTTTTTCACATATTGCTGCCAACCCCTTGGGTCTTTTCCTTTCTCCA	AAGATTTTCTGCATAGCATTAATGACATTTTGTACTTCTTCAACGCGAAGAGCAGATAAATCCATTTCTTTCTGTTCCAATGAACTTTAACACATTAGAAAAACATATATATATATCTTTTTAAAAGGTTTATAAAATGACAACTTCATTTTATCATTTTAAAATAAAGTAAATTTAAGATTTGGAAGGTTTTAGAATAATACAAACCAAAGAACTAATGACAACGTCCTTTATTTTTAAAGATTCTAGAAGTTGCTTTTTGTAATTAGACAACATAAATTCTGAATTTTTTCACATATTGCTGCCAACCCCTTGGGTCTTTTCCTTTCTCCA	-	novel	NA	P-0018884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	121	935	0	ENST00000357654.3:c.-19-249_65del		p.X7_splice	ENST00000357654	NM_007294.3	7		2/23	0.581229106745494	1	FACETS	0.301	0.272	0.331	0.301	0.272	0.331	SUBCLONAL	1	TRUE	0	0.775079170329572	1		935	635	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911445	134911445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571583026	NA	P-0018884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	296	747	0	ENST00000398015.3:c.1910G>A	p.Arg637His	p.R637H	ENST00000398015	NM_004441.4	637	cGt/cAt	11/16	1	2	FACETS	0.903	0.853	0.954	0.903	0.853	0.954	CLONAL	1	TRUE	1	0.775079170329572	2		747	846	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0018885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	402	1104	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.666121322176374	1	FACETS	0.989	0.947	1	0.989	0.947	1	CLONAL	1	TRUE	0	0.666121322176374	1		1104	814	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426893	6426893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519948	NA	P-0018885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	286	618	0	ENST00000356142.4:c.86C>T	p.Pro29Leu	p.P29L	ENST00000356142	NM_018890.3	29	cCt/cTt	2/7	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.666121322176374	2		618	823	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	247	646	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	1	2	FACETS	0.945	0.886	1	0.945	0.886	1	CLONAL	1	TRUE	1	0.666121322176374	2		646	785	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007475	62007475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1389559363	NA	P-0018885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	210	616	0	ENST00000392795.3:c.392C>T	p.Ser131Leu	p.S131L	ENST00000392795	NM_001039933.1	131	tCg/tTg	3/6	1	2	FACETS	0.942	0.879	1	0.942	0.879	1	CLONAL	1	TRUE	1	0.666121322176374	2		616	669	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056533	26056533	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1332170864	NA	P-0018885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	110	300	0	ENST00000343677.2:c.124G>C	p.Glu42Gln	p.E42Q	ENST00000343677	NM_005319.3	42	Gag/Cag	1/1	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.666121322176374	2		300	325	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427588	49427588	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	137	448	0	ENST00000301067.7:c.10900C>T	p.Gln3634Ter	p.Q3634*	ENST00000301067	NM_003482.3	3634	Cag/Tag	39/54	1	2	FACETS	0.998	0.917	1	0.998	0.917	1	CLONAL	1	TRUE	1	0.666121322176374	2		448	412	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584479	187584479	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs951472406	NA	P-0018885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	188	451	0	ENST00000441802.2:c.3554G>A	p.Gly1185Glu	p.G1185E	ENST00000441802	NM_005245.3	1185	gGa/gAa	3/27	NA	2	FACETS	0.952	0.885	1			1	INDETERMINATE	1	TRUE	NA	0.666121322176374	2		451	593	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589550	67589552	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs1131692242	NA	P-0018885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	131	390	0	ENST00000274335.5:c.1317_1319del	p.Glu439del	p.E439del	ENST00000274335		438	aAAGaa/aaa	10/15	1	2	FACETS	0.993	0.91	1	0.993	0.91	1	CLONAL	1	TRUE	1	0.666121322176374	2		390	396	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	94	364	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.36932220367513	2		365	426	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0018887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	316	900	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.281845215576279	2	FACETS	0.904	0.856	0.954	0.904	0.856	0.954	CLONAL	2	TRUE	0	0.36932220367513	2		901	946	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699360	47699360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	131	626	0	ENST00000347630.2:c.148G>A	p.Glu50Lys	p.E50K	ENST00000347630	NM_001007230.1	50	Gaa/Aaa	4/11	1	2	FACETS	0.874	0.793	0.959	0.874	0.793	0.959	CLONAL	1	TRUE	1	0.36932220367513	2		626	812	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6439807	6439807	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	108	408	1	ENST00000356142.4:c.333T>A	p.Asn111Lys	p.N111K	ENST00000356142	NM_018890.3	111	aaT/aaA	5/7	0.233505623713432	1	FACETS	0.877	0.789	0.968	0.877	0.789	0.968	CLONAL	1	TRUE	0	0.36932220367513	1		409	544	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285666	46285666	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	81	490	0	ENST00000334344.6:c.5026C>T	p.Gln1676Ter	p.Q1676*	ENST00000334344	NM_152641.2	1676	Cag/Tag	17/21	1	2	FACETS	0.626	0.551	0.706	0.626	0.551	0.706	SUBCLONAL	1	TRUE	1	0.36932220367513	2		490	701	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518499	204518499	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61754765	NA	P-0018887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	88	403	0	ENST00000367182.3:c.1162C>T	p.Pro388Ser	p.P388S	ENST00000367182	NM_001278516.1	388	Ccc/Tcc	11/11	1	2	FACETS	0.816	0.724	0.914	0.816	0.724	0.914	CLONAL	1	TRUE	1	0.36932220367513	2		403	584	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245376	46245376	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0018887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	186	637	0	ENST00000334344.6:c.3470C>G	p.Ser1157Ter	p.S1157*	ENST00000334344	NM_152641.2	1157	tCa/tGa	15/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.36932220367513	2		637	800	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639245	3639245	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757128699	NA	P-0018887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	175	772	2	ENST00000294008.3:c.4394G>A	p.Arg1465His	p.R1465H	ENST00000294008	NM_032444.2	1465	cGt/cAt	12/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.36932220367513	2		774	804	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576870	7576870	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	122	607	0	ENST00000269305.4:c.976del	p.Glu326AsnfsTer19	p.E326Nfs*19	ENST00000269305	NM_001126112.2	326	Gaa/aa	9/11	0.36932220367513	1	FACETS	0.89	0.807	0.978	0.89	0.807	0.978	CLONAL	1	TRUE	0	0.36932220367513	1		607	605	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502624	149502624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142689325	NA	P-0018887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	66	269	2	ENST00000261799.4:c.2164G>A	p.Val722Ile	p.V722I	ENST00000261799	NM_002609.3	722	Gtt/Att	15/23	1	2	FACETS	0.977	0.852	1	0.977	0.852	1	CLONAL	1	TRUE	1	0.36932220367513	2		271	366	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860254	151860254	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	69	570	0	ENST00000262189.6:c.10408C>T	p.Gln3470Ter	p.Q3470*	ENST00000262189	NM_170606.2	3470	Cag/Tag	43/59	0.249406966308568	3	FACETS	0.544	0.473	0.622	0.181	0.157	0.208	SUBCLONAL	1	TRUE	0	0.36932220367513	3		570	813	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878785	151878785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	203	546	0	ENST00000262189.6:c.6160C>T	p.Gln2054Ter	p.Q2054*	ENST00000262189	NM_170606.2	2054	Cag/Tag	36/59	0.249406966308568	3	FACETS	0.982	0.915	1	0.655	0.61	0.701	CLONAL	2	TRUE	0	0.36932220367513	3		546	663	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0018888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	285	868	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.229439982025104	3	FACETS	0.979	0.924	1	0.979	0.924	1	CLONAL	3	TRUE	0	0.260458671974643	3		868	842	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94201025	94201025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780133	NA	P-0018888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	41	487	1	ENST00000323929.3:c.1052G>A	p.Arg351His	p.R351H	ENST00000323929	NM_005591.3	351	cGt/cAt	10/20	0.229439982025104	3	FACETS	0.565	0.469	0.671	0.188	0.156	0.224	SUBCLONAL	1	TRUE	0	0.260458671974643	3		488	630	SUCCESS
ALK	238	MSKCC	GRCh37	2	29450538	29450538	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	63	607	0	ENST00000389048.3:c.2816G>C	p.Gly939Ala	p.G939A	ENST00000389048	NM_004304.4	939	gGc/gCc	17/29	0.0559219138375915	4	FACETS	0.842	0.727	0.967	0.421	0.363	0.484	INDETERMINATE	1	TRUE	2	0.260458671974643	4		607	724	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944324	206944324	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	169	790	0	ENST00000423557.1:c.306C>G	p.Asp102Glu	p.D102E	ENST00000423557	NM_000572.2	102	gaC/gaG	3/5	0.379586172188918	3	FACETS	0.902	0.827	0.979	0.451	0.413	0.49	CLONAL	1	TRUE	1	0.379586172188918	3		790	1175	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050913	13050914	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AACT	novel	NA	P-0018889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	161	773	0	ENST00000316448.5:c.446_449dup	p.Tyr150Ter	p.Y150*	ENST00000316448	NM_004343.3	148	-/AACT	4/9	1	2	FACETS	0.808	0.74	0.879	0.808	0.74	0.879	CLONAL	1	TRUE	1	0.379586172188918	2		773	1050	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845397	151845397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779339485	NA	P-0018889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	198	754	1	ENST00000262189.6:c.13615G>A	p.Val4539Met	p.V4539M	ENST00000262189	NM_170606.2	4539	Gtg/Atg	52/59	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.379586172188918	2		755	1030	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	428	917	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.312747019231725	4	FACETS	1	0.987	1			1	CLONAL	3	TRUE	NA	0.327863440453473	4		917	1066	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0018890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	191	749	1	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.304175855343502	2	FACETS	0.913	0.848	0.98	0.913	0.848	0.98	CLONAL	2	TRUE	0	0.327863440453473	2		750	638	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023202	27023202	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	89	470	0	ENST00000324856.7:c.308C>A	p.Ser103Ter	p.S103*	ENST00000324856	NM_006015.4	103	tCg/tAg	1/20	0.2574106167059	4	FACETS	0.842	0.751	0.939	0.842	0.751	0.939	CLONAL	2	TRUE	2	0.327863440453473	4		470	428	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515193	103515193	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs370456073	NA	P-0018890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	75	502	0	ENST00000355739.4:c.1694A>G	p.Asp565Gly	p.D565G	ENST00000355739	NM_000123.3	565	gAt/gGt	8/15	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.327863440453473	2		502	456	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241453	105241453	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	214	894	0	ENST00000349310.3:c.527A>T	p.Tyr176Phe	p.Y176F	ENST00000349310	NM_001014432.1	176	tAc/tTc	7/15	0.2574106167059	4	FACETS	0.987	0.919	1	0.987	0.919	1	CLONAL	2	TRUE	2	0.327863440453473	4		894	878	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657349	29657349	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	137	837	0	ENST00000356175.3:c.5582G>T	p.Cys1861Phe	p.C1861F	ENST00000356175	NM_000267.3	1861	tGt/tTt	38/57	0.284176359688254	3	FACETS	1	0.91	1	0.501	0.455	0.549	CLONAL	1	TRUE	1	0.327863440453473	3		837	971	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25536834	25536834	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	158	753	1	ENST00000264709.3:c.20G>T	p.Ser7Ile	p.S7I	ENST00000264709	NM_175629.2	7	aGc/aTc	2/23	0.298041546696818	3	FACETS	0.97	0.894	1	0.97	0.894	1	CLONAL	2	TRUE	1	0.327863440453473	3		754	578	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546698	9546698	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	78	374	0	ENST00000353224.5:c.1324C>A	p.Pro442Thr	p.P442T	ENST00000353224	NM_177990.2	442	Cca/Aca	5/10	0.200957768590849	4	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	2	0.327863440453473	4		374	291	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664486	138664486	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	70	739	0	ENST00000330315.3:c.1079A>C	p.Tyr360Ser	p.Y360S	ENST00000330315	NM_023067.3	360	tAc/tCc	1/1	0.298041546696818	3	FACETS	0.866	0.756	0.985	0.433	0.378	0.493	CLONAL	1	TRUE	1	0.327863440453473	3		739	574	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143044448	143044448	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	120	457	0	ENST00000262992.4:c.2014T>A	p.Tyr672Asn	p.Y672N	ENST00000262992	NM_001101669.1	672	Tac/Aac	18/24	0.298041546696818	3	FACETS	0.878	0.798	0.962	0.878	0.798	0.962	CLONAL	2	TRUE	1	0.327863440453473	3		457	485	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045788	143045788	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1181059444	NA	P-0018890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	173	709	0	ENST00000262992.4:c.1846C>T	p.Gln616Ter	p.Q616*	ENST00000262992	NM_001101669.1	616	Cag/Tag	17/24	0.298041546696818	3	FACETS	0.915	0.845	0.988	0.915	0.845	0.988	CLONAL	2	TRUE	1	0.327863440453473	3		709	671	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969912	161969912	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	83	711	0	ENST00000366898.1:c.1057G>T	p.Glu353Ter	p.E353*	ENST00000366898	NM_004562.2	353	Gaa/Taa	9/12	0.327863440453473	2	FACETS	0.952	0.842	1	0.476	0.421	0.535	CLONAL	1	TRUE	0	0.327863440453473	2		711	532	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444486	50444486	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	59	351	0	ENST00000331340.3:c.416A>G	p.His139Arg	p.H139R	ENST00000331340	NM_006060.4	139	cAc/cGc	4/8	0.327863440453473	5	FACETS	1	0.883	1	0.343	0.295	0.395	CLONAL	1	TRUE	2	0.327863440453473	5		351	522	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046489	69046489	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	93	776	0	ENST00000288368.4:c.3962A>G	p.Gln1321Arg	p.Q1321R	ENST00000288368	NM_024870.2	1321	cAg/cGg	32/40	0.237417572011214	3	FACETS	0.758	0.673	0.849			1	SUBCLONAL	1	TRUE	NA	0.327863440453473	3		776	871	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840597	36840597	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	102	864	0	ENST00000358127.4:c.1136C>A	p.Ala379Asp	p.A379D	ENST00000358127	NM_001280556.1	379	gCc/gAc	10/10	0.284176359688254	3	FACETS	1	0.909	1	0.509	0.455	0.566	CLONAL	1	TRUE	1	0.327863440453473	3		864	712	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0018891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	230	574	9	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	0.602689799051316	2		583	684	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0018891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	149	457	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	1	2	FACETS	0.926	0.851	1	0.926	0.851	1	CLONAL	1	TRUE	1	0.602689799051316	2		457	534	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061240	38061240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	224	797	0	ENST00000250448.2:c.749C>T	p.Ser250Phe	p.S250F	ENST00000250448	NM_004496.3	250	tCc/tTc	2/2	1	2	FACETS	0.936	0.874	1	0.936	0.874	1	CLONAL	1	TRUE	1	0.602689799051316	2		797	794	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106058	8106058	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	223	634	0	ENST00000346208.3:c.878T>A	p.Met293Lys	p.M293K	ENST00000346208		293	aTg/aAg	4/6	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.602689799051316	2		634	739	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137033	64137033	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759826654	NA	P-0018891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	268	816	0	ENST00000334205.4:c.1544C>T	p.Ser515Leu	p.S515L	ENST00000334205	NM_003942.2	515	tCg/tTg	13/17	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.602689799051316	2		816	855	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644597	21644597	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	236	655	0	ENST00000421138.2:c.70C>G	p.Gln24Glu	p.Q24E	ENST00000421138		24	Caa/Gaa	4/16	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.602689799051316	2		655	776	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916932	178916932	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	235	655	0	ENST00000263967.3:c.319A>T	p.Asn107Tyr	p.N107Y	ENST00000263967	NM_006218.2	107	Aac/Tac	2/21	1	2	FACETS	0.88	0.823	0.939	0.88	0.823	0.939	CLONAL	1	TRUE	1	0.602689799051316	2		655	886	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs747342068	NA	P-0018892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1349	119	1278	0	ENST00000269305.4:c.394A>C	p.Lys132Gln	p.K132Q	ENST00000269305	NM_001126112.2	132	Aag/Cag	5/11	1	2	FACETS	0.669	0.601	0.741	0.669	0.601	0.741	SUBCLONAL	1	FALSE	1	0.242389379288153	2		1278	1468	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971029	21971029	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519852	NA	P-0018892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	40	684	0	ENST00000304494.5:c.329G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tGg/tAg	2/3	0.242389379288153	1	FACETS	0.405	0.335	0.482	0.405	0.335	0.482	SUBCLONAL	1	FALSE	0	0.242389379288153	1		684	717	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735470	40735470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761910971	NA	P-0018892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	57	1046	1	ENST00000373198.4:c.3403G>A	p.Val1135Met	p.V1135M	ENST00000373198	NM_133170.3	1135	Gtg/Atg	25/32	NA	2	FACETS	0.442	0.378	0.513			1	INDETERMINATE	1	FALSE	NA	0.242389379288153	2		1047	1063	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199469672	NA	P-0018892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	89	534	0	ENST00000374080.3:c.131G>T	p.Gly44Val	p.G44V	ENST00000374080		44	gGt/gTt	2/45	1	1	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	FALSE	0	0.242389379288153	1		534	645	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413085	139413085	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1300110216	NA	P-0018892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	51	875	0	ENST00000277541.6:c.1057C>T	p.Arg353Cys	p.R353C	ENST00000277541	NM_017617.3	353	Cgt/Tgt	6/34	1	2	FACETS	0.43	0.364	0.503	0.43	0.364	0.503	SUBCLONAL	1	FALSE	1	0.242389379288153	2		875	978	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670106	29670106	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs878853912	NA	P-0018892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	61	916	0	ENST00000356175.3:c.7079A>G	p.Asn2360Ser	p.N2360S	ENST00000356175	NM_000267.3	2360	aAt/aGt	47/57	1	2	FACETS	0.428	0.368	0.494	0.428	0.368	0.494	SUBCLONAL	1	FALSE	1	0.242389379288153	2		916	1176	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971051	21971065	+	inframe_deletion	In_Frame_Del	DEL	GCGCCCCGGCCCGGT	GCGCCCCGGCCCGGT	-	novel	NA	P-0018892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	103	647	0	ENST00000304494.5:c.293_307del	p.His98_Ala102del	p.H98_A102del	ENST00000304494	NM_000077.4	98	cACCGGGCCGGGGCGCgg/cgg	2/3	0.242389379288153				0.951	1				CLONAL	1	FALSE	0	0.242389379288153	1		647	675	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139440177	139440177	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0018892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	23	200	1	ENST00000277541.6:c.61+1G>A		p.X21_splice	ENST00000277541	NM_017617.3	21			1	2	FACETS	0.705	0.551	0.883	0.705	0.551	0.883	SUBCLONAL	1	FALSE	1	0.242389379288153	2		201	269	SUCCESS
AR	367	MSKCC	GRCh37	X	66942669	66942669	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	37	391	0	ENST00000374690.3:c.2450T>C	p.Ile817Thr	p.I817T	ENST00000374690	NM_000044.3	817	aTt/aCt	7/8	1	1	FACETS	0.791	0.654	0.944	0.791	0.654	0.944	CLONAL	1	FALSE	0	0.242389379288153	1		391	339	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953837	55953837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	52	548	1	ENST00000263923.4:c.3599C>T	p.Ser1200Phe	p.S1200F	ENST00000263923	NM_002253.2	1200	tCc/tTc	27/30	1	2	FACETS	0.348	0.295	0.406	0.348	0.295	0.406	SUBCLONAL	1	TRUE	1	0.315391916595573	2		549	948	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011144	12011144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	108	423	0	ENST00000353533.5:c.551C>T	p.Ser184Leu	p.S184L	ENST00000353533	NM_003010.3	184	tCg/tTg	5/11	0.315391916595573	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.315391916595573	1		423	546	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591135	67591137	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0018893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	108	351	0	ENST00000274335.5:c.1728_1730del	p.Arg577del	p.R577del	ENST00000274335		576	acGAGa/aca	12/15	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.315391916595573	2		351	651	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653835	89653841	+	frameshift_variant	Frame_Shift_Del	DEL	GTATACA	GTATACA	-	novel	NA	P-0018893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	106	460	0	ENST00000371953.3:c.134_140del	p.Val45GlyfsTer7	p.V45Gfs*7	ENST00000371953	NM_000314.4	45	GTATACAgg/gg	2/9	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.315391916595573	2		460	613	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145064	58145064	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	185	562	0	ENST00000257904.6:c.280G>C	p.Glu94Gln	p.E94Q	ENST00000257904	NM_000075.3	94	Gag/Cag	3/8	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.315391916595573	2		562	1120	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457707	67457707	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	186	602	0	ENST00000327367.4:c.517C>G	p.Gln173Glu	p.Q173E	ENST00000327367	NM_005902.3	173	Cag/Gag	3/9	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.315391916595573	2		602	1131	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465381	99465381	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	132	471	0	ENST00000268035.6:c.2206G>A	p.Glu736Lys	p.E736K	ENST00000268035	NM_000875.3	736	Gaa/Aaa	11/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.315391916595573	2		471	697	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856130	68856130	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0018893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	155	530	0	ENST00000261769.5:c.1936+2T>A		p.X646_splice	ENST00000261769	NM_004360.3	646			0.315391916595573	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.315391916595573	1		530	731	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030588	11030588	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	207	659	0	ENST00000327064.4:c.1142C>T	p.Ser381Leu	p.S381L	ENST00000327064	NM_199141.1	381	tCa/tTa	10/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.315391916595573	2		659	1152	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218500	36218500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	101	459	0	ENST00000222270.7:c.4279G>A	p.Gly1427Ser	p.G1427S	ENST00000222270	NM_014727.1	1427	Ggc/Agc	16/37	1	2	FACETS	0.902	0.807	1	0.902	0.807	1	CLONAL	1	TRUE	1	0.315391916595573	2		459	710	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36253005	36253006	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	141	517	1	ENST00000300305.3:c.356dup	p.Ala120GlyfsTer18	p.A120Gfs*18	ENST00000300305		119	gtg/gtTg	4/8	1	2	FACETS	0.865	0.787	0.947	0.865	0.787	0.947	CLONAL	1	TRUE	1	0.315391916595573	2		518	1034	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940022	49940022	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760389915	NA	P-0018893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	211	734	3	ENST00000296474.3:c.1021G>A	p.Glu341Lys	p.E341K	ENST00000296474	NM_002447.2	341	Gag/Aag	1/20	0.315391916595573	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.315391916595573	1		737	1082	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250442	110250442	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	116	552	0	ENST00000374672.4:c.233G>C	p.Gly78Ala	p.G78A	ENST00000374672	NM_004235.4	78	gGa/gCa	3/5	1	2	FACETS	0.948	0.855	1	0.948	0.855	1	CLONAL	1	TRUE	1	0.315391916595573	2		552	776	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0018894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	162	515	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.526	0.483	0.57	0.526	0.483	0.57	SUBCLONAL	1	TRUE	1	0.839112674352863	2		515	734	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063321	67063322	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	135	401	0	ENST00000412916.2:c.11_12insA	p.Val5ArgfsTer15	p.V5Rfs*15	ENST00000412916		4	gtc/gtAc	1/6	0.512149749314826	1	FACETS	0.419	0.383	0.455	0.419	0.383	0.455	SUBCLONAL	1	TRUE	0	0.839112674352863	1		401	446	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0018895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	61	629	1	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		630	754	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0018895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	87	779	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		779	936	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576862	7576862	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	188	710	1	ENST00000269305.4:c.984del	p.Phe328LeufsTer17	p.F328Lfs*17	ENST00000269305	NM_001126112.2	328	ttC/tt	9/11	0.325770776214254	2	FACETS	1	0.989	1	0.704	0.652	0.758	CLONAL	1	TRUE	0	0.345560921790361	2		711	773	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961459	54961459	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	53	333	0	ENST00000312783.6:c.173C>G	p.Pro58Arg	p.P58R	ENST00000312783	NM_198436.1	58	cCt/cGt	4/10	0.345560921790361	5	FACETS	0.802	0.683	0.931	0.267	0.227	0.311	CLONAL	1	TRUE	2	0.345560921790361	5		333	581	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164829	36164829	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	103	904	0	ENST00000300305.3:c.1046A>G	p.Tyr349Cys	p.Y349C	ENST00000300305		349	tAt/tGt	8/8	0.33260290801724	3	FACETS	0.683	0.61	0.761	0.341	0.305	0.381	SUBCLONAL	1	TRUE	1	0.345560921790361	3		904	1024	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161421	55161421	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	95	556	0	ENST00000257290.5:c.3253del	p.Glu1085LysfsTer40	p.E1085Kfs*40	ENST00000257290	NM_006206.4	1084	gtG/gt	23/23	0.345560921790361	7	FACETS	0.919	0.816	1	0.153	0.136	0.172	CLONAL	1	TRUE	1	0.345560921790361	7		556	1115	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662481	227662481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	68	446	2	ENST00000305123.5:c.974G>A	p.Arg325His	p.R325H	ENST00000305123	NM_005544.2	325	cGt/cAt	1/2	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.199815620042599	2		448	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934571	NA	P-0018897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	162	755	0	ENST00000269305.4:c.747G>C	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agC	7/11	0.190310580791398	2	FACETS	0.989	0.908	1	0.989	0.908	1	CLONAL	2	FALSE	0	0.199815620042599	2		755	820	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88651985	88651988	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	AAGT	AAGT	-	novel	NA	P-0018897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	44	507	0	ENST00000372037.3:c.333+2_333+5del		p.X111_splice	ENST00000372037	NM_004329.2	111		5/13	0.199815620042599	3	FACETS	0.75	0.628	0.886	0.25	0.209	0.296	SUBCLONAL	1	FALSE	0	0.199815620042599	3		507	646	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672764	30672764	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758481782	NA	P-0018897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	66	760	0	ENST00000376406.3:c.4196C>T	p.Ser1399Phe	p.S1399F	ENST00000376406	NM_014641.2	1399	tCc/tTc	10/15	0.199815620042599	4	FACETS	0.772	0.668	0.885	0.193	0.167	0.222	SUBCLONAL	1	FALSE	0	0.199815620042599	4		760	1027	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510861	157510862	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0018897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	115	876	0	ENST00000346085.5:c.3638dup	p.Thr1214TyrfsTer32	p.T1214Yfs*32	ENST00000346085	NM_020732.3	1212	-/C	14/20	0.190310580791398	2	FACETS	1	0.911	1	0.508	0.456	0.562	CLONAL	1	FALSE	0	0.199815620042599	2		876	1134	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242494	+	protein_altering_variant	In_Frame_Del	DEL	TAAGAGAAGCAACATCTCCGAAAGC	TAAGAGAAGCAACATCTCCGAAAGC	CGAAAGA	novel	NA	P-0018897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	148	889	0	ENST00000275493.2:c.2240_2264delinsCGAAAGA	p.Leu747_Ala755delinsSerLysAsp	p.L747_A755delinsSKD	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCCGAAAGCc/tCGAAAGAc	19/28	0.199815620042599	6	FACETS	0.826	0.752	0.904	0.33	0.301	0.362	CLONAL	2	FALSE	1	0.199815620042599	6		889	1255	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0018898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	107	824	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	TRUE	1	NA	2		824	802	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0018899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	120	124	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	0.515401606409457	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.78430050548181	3		124	205	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952093	178952093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs2108429932	NA	P-0018899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	385	604	0	ENST00000263967.3:c.3148G>A	p.Gly1050Ser	p.G1050S	ENST00000263967	NM_006218.2	1050	Ggc/Agc	21/21	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.78430050548181	2		604	900	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734181	58734187	+	frameshift_variant	Frame_Shift_Del	DEL	ATGTTCT	ATGTTCT	GA	novel	NA	P-0018899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	414	751	3	ENST00000305921.3:c.1239_1245delinsGA	p.Cys414AsnfsTer18	p.C414Nfs*18	ENST00000305921	NM_003620.3	413	ccATGTTCT/ccGA	5/6	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.78430050548181	2		754	993	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778824	76778824	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	429	381	0	ENST00000373344.5:c.6755A>G	p.His2252Arg	p.H2252R	ENST00000373344	NM_000489.3	2252	cAt/cGt	31/35	1	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.78430050548181	1		381	446	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0018900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	18	898	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	1	2	FACETS	0.366	0.274	0.474	0.366	0.274	0.474	SUBCLONAL	1	TRUE	1	0.23	2		898	428	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495306	212495306	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	22	727	0	ENST00000342788.4:c.1960G>T	p.Ala654Ser	p.A654S	ENST00000342788	NM_005235.2	654	Gca/Tca	17/28	1	2	FACETS	0.469	0.363	0.593	0.469	0.363	0.593	SUBCLONAL	1	TRUE	1	0.23	2		727	408	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360630	70360630	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	14	283	0	ENST00000374080.3:c.6190C>T	p.Gln2064Ter	p.Q2064*	ENST00000374080		2064	Cag/Tag	42/45	1	1	FACETS	0.686	0.498	0.911	0.686	0.498	0.911	SUBCLONAL	1	TRUE	0	0.23	1		283	157	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0018900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	110	898	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.465247810304965	2	FACETS	0.979	0.899	1	0.979	0.899	1	CLONAL	2	TRUE	0	0.482145793410934	2		898	233	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495306	212495306	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	74	727	0	ENST00000342788.4:c.1960G>T	p.Ala654Ser	p.A654S	ENST00000342788	NM_005235.2	654	Gca/Tca	17/28	0.409518083268606	4	FACETS	1	0.97	1	0.443	0.391	0.499	CLONAL	1	TRUE	1	0.482145793410934	4		727	342	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140165	50140165	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	179	608	1	ENST00000246792.3:c.260A>T	p.Gln87Leu	p.Q87L	ENST00000246792	NM_006270.3	87	cAg/cTg	3/6	0.482145793410934	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.482145793410934	3		609	266	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954379	48954379	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0018900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	97	375	0	ENST00000267163.4:c.1498+2T>G		p.X500_splice	ENST00000267163	NM_000321.2	500			0.465247810304965	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.482145793410934	2		375	172	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745477	162745477	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779963287	NA	P-0018900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	42	496	1	ENST00000367921.3:c.1892G>T	p.Arg631Leu	p.R631L	ENST00000367921	NM_006182.2	631	cGg/cTg	15/18	0.482145793410934	4	FACETS	0.906	0.761	1	0.453	0.38	0.533	CLONAL	1	TRUE	2	0.482145793410934	4		497	285	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445248	49445248	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	77	834	0	ENST00000301067.7:c.2218G>T	p.Gly740Trp	p.G740W	ENST00000301067	NM_003482.3	740	Ggg/Tgg	10/54	0.465247810304965	2	FACETS	0.913	0.821	1	0.913	0.821	1	CLONAL	2	TRUE	0	0.482145793410934	2		834	175	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343522	343522	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	26	779	1	ENST00000262320.3:c.2152G>T	p.Glu718Ter	p.E718*	ENST00000262320	NM_003502.3	718	Gaa/Taa	8/11	0.370026695103552	3	FACETS	0.72	0.574	0.883	0.36	0.287	0.442	SUBCLONAL	1	TRUE	1	0.482145793410934	3		780	186	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857148	9857148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	14	419	2	ENST00000330684.3:c.4253G>A	p.Gly1418Asp	p.G1418D	ENST00000330684	NM_001134407.1	1418	gGc/gAc	13/13	0.370026695103552	3	FACETS	0.348	0.252	0.464	0.174	0.126	0.232	SUBCLONAL	1	TRUE	1	0.482145793410934	3		421	207	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554616	63554626	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCACCCCTG	GCCCACCCCTG	-	novel	NA	P-0018900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	33	512	0	ENST00000307078.5:c.113_123del	p.Pro38GlnfsTer99	p.P38Qfs*99	ENST00000307078	NM_004655.3	38	cCAGGGGTGGGC/c	2/11	0.409518083268606	4	FACETS	1	0.914	1	0.398	0.328	0.475	CLONAL	1	TRUE	1	0.482145793410934	4		512	170	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735642	204735642	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	47	381	0	ENST00000302823.3:c.443A>T	p.Gln148Leu	p.Q148L	ENST00000302823	NM_005214.4	148	cAg/cTg	2/4	0.409518083268606	4	FACETS	0.826	0.708	0.951	0.55	0.472	0.634	CLONAL	2	TRUE	1	0.482145793410934	4		381	175	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624901	9624901	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	54	548	0	ENST00000353224.5:c.76G>C	p.Asp26His	p.D26H	ENST00000353224	NM_177990.2	26	Gat/Cat	3/10	0.412436448762427	5	FACETS	1	0.914	1	0.364	0.312	0.421	CLONAL	1	TRUE	2	0.482145793410934	5		548	353	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264982	46264982	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	43	598	0	ENST00000371998.3:c.1852C>A	p.His618Asn	p.H618N	ENST00000371998		618	Cat/Aat	12/23	0.482145793410934	3	FACETS	0.889	0.75	1	0.445	0.375	0.521	CLONAL	1	TRUE	1	0.482145793410934	3		598	249	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540041	187540041	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	42	481	0	ENST00000441802.2:c.7699C>A	p.Arg2567Ser	p.R2567S	ENST00000441802	NM_005245.3	2567	Cgt/Agt	10/27	0.424068957988587	4	FACETS	1	0.924	1	0.292	0.246	0.342	CLONAL	1	TRUE	0	0.482145793410934	4		481	221	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627873	187627873	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	66	750	1	ENST00000441802.2:c.3109T>A	p.Phe1037Ile	p.F1037I	ENST00000441802	NM_005245.3	1037	Ttt/Att	2/27	0.424068957988587	4	FACETS	0.763	0.669	0.862	0.381	0.334	0.431	SUBCLONAL	2	TRUE	0	0.482145793410934	4		751	266	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638257	176638257	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	69	781	0	ENST00000439151.2:c.2857T>C	p.Ser953Pro	p.S953P	ENST00000439151	NM_022455.4	953	Tct/Cct	5/23	0.482145793410934	2	FACETS	1	0.951	1	0.577	0.509	0.649	CLONAL	1	TRUE	0	0.482145793410934	2		781	248	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345759	152345759	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	30	474	1	ENST00000359321.1:c.811A>T	p.Ile271Phe	p.I271F	ENST00000359321	NM_005431.1	271	Att/Ttt	3/3	0.239541878590451	5	FACETS	1	0.828	1			1	INDETERMINATE	1	TRUE	NA	0.482145793410934	5		475	210	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98244282	98244282	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	53	813	0	ENST00000331920.6:c.695T>C	p.Leu232Ser	p.L232S	ENST00000331920	NM_000264.3	232	tTg/tCg	5/24	0.482145793410934	2	FACETS	0.92	0.793	1	0.46	0.396	0.528	CLONAL	1	TRUE	0	0.482145793410934	2		813	239	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797301	135797301	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	77	394	0	ENST00000298552.3:c.568del	p.Arg190AlafsTer20	p.R190Afs*20	ENST00000298552	NM_001162426.1	190	Cgc/gc	7/23	0.35801360342436	1	FACETS	0.883	0.779	0.993	0.883	0.779	0.993	CLONAL	1	TRUE	0	0.35801360342436	1		394	400	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664868	29664868	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1193716348	NA	P-0018902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	307	518	1	ENST00000356175.3:c.6611G>A	p.Trp2204Ter	p.W2204*	ENST00000356175	NM_000267.3	2204	tGg/tAg	43/57	0.543487690460181	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.596893233196155	4		519	798	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981797	201981797	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	303	960	1	ENST00000359651.3:c.508C>A	p.Leu170Met	p.L170M	ENST00000359651		170	Ctg/Atg	4/8	0.246322992546507	4	FACETS	0.799	0.754	0.846	0.799	0.754	0.846	INDETERMINATE	2	TRUE	2	0.596893233196155	4		961	1014	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679247	88679247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867521873	NA	P-0018902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	74	921	0	ENST00000360948.2:c.790C>T	p.His264Tyr	p.H264Y	ENST00000360948	NM_001012338.2	264	Cat/Tat	8/19	0.246322992546507	4	FACETS	0.392	0.342	0.446	0.196	0.171	0.223	INDETERMINATE	1	TRUE	2	0.596893233196155	4		921	1011	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573995	7573996	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	470	1051	3	ENST00000269305.4:c.1031dup	p.Asn345GlufsTer2	p.N345Efs*2	ENST00000269305	NM_001126112.2	344	ctg/ctTg	10/11	0.596893233196155	2	FACETS	0.989	0.954	1	0.989	0.954	1	CLONAL	2	TRUE	0	0.596893233196155	2		1054	796	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562114	21562157	+	frameshift_variant	Frame_Shift_Del	DEL	AAGGCGTATGGCGAGTAGCTCTTGATGCGTGACTCTCTCTTCTC	AAGGCGTATGGCGAGTAGCTCTTGATGCGTGACTCTCTCTTCTC	GAG	novel	NA	P-0018903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1664	336	1288	6	ENST00000382592.4:c.1762_1805delinsCTC	p.Glu588LeufsTer2	p.E588Lfs*2	ENST00000382592	NM_014572.2	588	GAGAAGAGAGAGTCACGCATCAAGAGCTACTCGCCATACGCCTTt/CTCt	4/8	0.514101819936851	1	FACETS	0.486	0.457	0.515	0.486	0.457	0.515	SUBCLONAL	1	TRUE	0	0.514101819936851	1		1294	2000	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219412	1219412	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1555737830	NA	P-0018903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	105	443	0	ENST00000326873.7:c.464G>A	p.Gly155Glu	p.G155E	ENST00000326873	NM_000455.4	155	gGg/gAg	3/10	0.514101819936851	1	FACETS	0.434	0.388	0.481	0.434	0.388	0.481	SUBCLONAL	1	TRUE	0	0.514101819936851	1		443	700	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057270	30057270	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	376	690	0	ENST00000338641.4:c.756del	p.Lys253ArgfsTer43	p.K253Rfs*43	ENST00000338641	NM_000268.3	251	aCc/ac	8/16	0.514101819936851	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.514101819936851	1		690	1038	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033844	49033844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853294	NA	P-0018908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	233	353	0	ENST00000267163.4:c.1981C>T	p.Arg661Trp	p.R661W	ENST00000267163	NM_000321.2	661	Cgg/Tgg	20/27	0.49796941745495	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.49796941745495	1		353	663	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678541	88678541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145157285	NA	P-0018908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	200	212	0	ENST00000360948.2:c.995C>T	p.Thr332Met	p.T332M	ENST00000360948	NM_001012338.2	332	aCg/aTg	9/19	0.391469766790373	2	FACETS	0.823	0.77	0.876	0.823	0.77	0.876	CLONAL	2	TRUE	0	0.49796941745495	2		212	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574035	7574035	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs867389695	NA	P-0018908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	593	499	0	ENST00000269305.4:c.994-2A>G		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.384856527276421	3	FACETS	0.868	0.838	0.897	0.868	0.838	0.897	CLONAL	3	TRUE	0	0.49796941745495	3		499	1143	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673482	30673482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775535131	NA	P-0018908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	41	406	0	ENST00000376406.3:c.3478C>T	p.Pro1160Ser	p.P1160S	ENST00000376406	NM_014641.2	1160	Cca/Tca	10/15	0.46458544964337	2	FACETS	0.245	0.203	0.291	0.122	0.101	0.146	SUBCLONAL	1	TRUE	0	0.49796941745495	2		406	673	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93626916	93626916	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	358	506	0	ENST00000375746.1:c.763C>A	p.Leu255Ile	p.L255I	ENST00000375746	NM_001174167.1	255	Ctt/Att	5/14	0.441847750561416	3	FACETS	0.754	0.715	0.794	0.754	0.715	0.794	SUBCLONAL	2	TRUE	1	0.49796941745495	3		506	1191	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0018909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	23	897	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.412	0.32	0.518	0.412	0.32	0.518	SUBCLONAL	1	TRUE	1	0.23	2		897	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577088	7577088	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1204379654	NA	P-0018909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1235	59	778	0	ENST00000269305.4:c.850A>C	p.Thr284Pro	p.T284P	ENST00000269305	NM_001126112.2	284	Aca/Cca	8/11	1	2	FACETS	0.396	0.339	0.459	0.396	0.339	0.459	SUBCLONAL	1	TRUE	1	0.23	2		778	1294	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148727	20148727	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0018909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	13	269	0	ENST00000379607.5:c.338-2A>C		p.X113_splice	ENST00000379607	NM_001412.3	113			1	1	FACETS	0.447	0.318	0.603	0.447	0.318	0.603	SUBCLONAL	1	TRUE	0	0.23	1		269	224	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0018911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	206	393	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.938	0.878	0.998	1	0.994	1	CLONAL	2	TRUE	1	0.436769423652706	2		393	503	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	1201	364	1				ENST00000310581	NM_198253.2	-/1132			0.436769423652706	14	FACETS	1	0.996	1			1	CLONAL	14	TRUE	NA	0.436769423652706	14		365	1388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577017	7577017	+	splice_donor_variant	Splice_Site	SNP	A	A	C	rs1131691016	NA	P-0018911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	413	481	0	ENST00000269305.4:c.919+2T>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			1	2	FACETS	0.901	0.86	0.942	1	0.997	1	CLONAL	2	TRUE	1	0.436769423652706	2		481	1050	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876660825	NA	P-0018911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	417	502	0	ENST00000269305.4:c.569C>G	p.Pro190Arg	p.P190R	ENST00000269305	NM_001126112.2	190	cCt/cGt	6/11	1	2	FACETS	0.837	0.798	0.876	1	0.996	1	CLONAL	2	TRUE	1	0.436769423652706	2		502	1141	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791861	42791861	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0018911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	158	489	0	ENST00000575354.2:c.747C>G	p.Tyr249Ter	p.Y249*	ENST00000575354	NM_015125.3	249	taC/taG	5/20	0.436769423652706	1	FACETS	0.66	0.605	0.717	0.66	0.605	0.717	SUBCLONAL	1	TRUE	0	0.436769423652706	1		489	857	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434872	110434872	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	100	675	0	ENST00000375856.3:c.3529G>C	p.Val1177Leu	p.V1177L	ENST00000375856	NM_003749.2	1177	Gtg/Ctg	1/2	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.436769423652706	NA		675	810	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578371	7578371	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs776167460	NA	P-0018912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	336	358	0	ENST00000269305.4:c.559G>A	p.Gly187Ser	p.G187S	ENST00000269305	NM_001126112.2	187	Ggt/Agt	5/11	0.603188931230061	2	FACETS	0.895	0.856	0.933	0.895	0.856	0.933	CLONAL	2	TRUE	0	0.6258624597998	2		358	600	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430635	78430635	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	531	517	0	ENST00000370768.2:c.655del	p.Met219TrpfsTer3	p.M219Wfs*3	ENST00000370768	NM_003902.3	219	Atg/tg	9/20	0.603188931230061	2	FACETS	0.909	0.878	0.94	0.909	0.878	0.94	CLONAL	2	TRUE	0	0.6258624597998	2		517	933	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0018913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	712	921	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	0.800035039883851	2	FACETS	0.836	0.815	0.858	0.836	0.815	0.858	CLONAL	2	TRUE	0	0.800035039883851	2		921	1064	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951099	48951100	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0018913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	210	301	0	ENST00000267163.4:c.1265_1266dup	p.Gly423Ter	p.G423*	ENST00000267163	NM_000321.2	421	gat/gATat	13/27	0.800035039883851	1	FACETS	0.937	0.89	0.984	0.937	0.89	0.984	CLONAL	1	TRUE	0	0.800035039883851	1		301	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0018914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	60	752	2	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		754	761	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0018914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	95	547	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.123035307114183	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		547	913	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0018915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	63	708	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.953	0.824	1	0.953	0.824	1	CLONAL	1	TRUE	1	0.218289455455823	2		709	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0018915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	114	792	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	TRUE	1	0.218289455455823	2		792	906	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240233	5240233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202189767	NA	P-0018915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	74	708	1	ENST00000357368.4:c.1681C>T	p.Arg561Trp	p.R561W	ENST00000357368	NM_002850.3	561	Cgg/Tgg	12/38	1	2	FACETS	0.85	0.743	0.965	0.85	0.743	0.965	CLONAL	1	TRUE	1	0.218289455455823	2		709	798	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852659	63852659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1349220963	NA	P-0018917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	91	489	1	ENST00000279873.7:c.3437C>T	p.Ala1146Val	p.A1146V	ENST00000279873	NM_032199.2	1146	gCg/gTg	10/10	1	2	FACETS	0.782	0.692	0.878	0.782	0.692	0.878	SUBCLONAL	1	FALSE	1	0.209257992442998	2		490	1112	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011192	12011192	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	76	342	0	ENST00000353533.5:c.600del	p.Pro201GlnfsTer5	p.P201Qfs*5	ENST00000353533	NM_003010.3	200	aTt/at	5/11	1	2	FACETS	0.986	0.864	1	0.986	0.864	1	CLONAL	1	FALSE	1	0.209257992442998	2		342	737	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219432	5219432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1351608223	NA	P-0018917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	59	584	2	ENST00000357368.4:c.3812C>T	p.Pro1271Leu	p.P1271L	ENST00000357368	NM_002850.3	1271	cCg/cTg	23/38	1	2	FACETS	0.492	0.422	0.569	0.492	0.422	0.569	SUBCLONAL	1	FALSE	1	0.209257992442998	2		586	1146	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224024	36224024	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1537	167	825	0	ENST00000222270.7:c.6574A>G	p.Ile2192Val	p.I2192V	ENST00000222270	NM_014727.1	2192	Ata/Gta	28/37	1	2	FACETS	0.937	0.857	1	0.937	0.857	1	CLONAL	1	FALSE	1	0.209257992442998	2		825	1704	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69230468	69230468	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	39	417	0	ENST00000462284.1:c.857T>C	p.Val286Ala	p.V286A	ENST00000462284	NM_002392.5	286	gTg/gCg	10/11	1	2	FACETS	0.241	0.199	0.288	0.241	0.199	0.288	SUBCLONAL	1	TRUE	1	0.657673216873991	2		417	492	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133923	38133923	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1296	117	857	0	ENST00000317025.8:c.3963A>C	p.Glu1321Asp	p.E1321D	ENST00000317025	NM_023034.1	1321	gaA/gaC	23/24	1	2	FACETS	0.252	0.226	0.279	0.252	0.226	0.279	SUBCLONAL	1	TRUE	1	0.657673216873991	2		857	1413	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099950	27099950	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	249	511	0	ENST00000324856.7:c.3829C>T	p.Gln1277Ter	p.Q1277*	ENST00000324856	NM_006015.4	1277	Cag/Tag	15/20	0.409072825539976	4	FACETS	0.892	0.836	0.949	0.892	0.836	0.949	CLONAL	2	TRUE	2	0.482098951946865	4		511	858	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549228	21549228	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	396	645	0	ENST00000382592.4:c.3048A>T	p.Glu1016Asp	p.E1016D	ENST00000382592	NM_014572.2	1016	gaA/gaT	8/8	0.482098951946865	2	FACETS	0.98	0.938	1	0.98	0.938	1	CLONAL	2	TRUE	0	0.482098951946865	2		645	838	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961814	41961814	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	161	315	0	ENST00000219905.7:c.722A>C	p.Asn241Thr	p.N241T	ENST00000219905	NM_001164273.1	241	aAc/aCc	2/24	0.240035588594029	5	FACETS	0.841	0.779	0.905	0.841	0.779	0.905	INDETERMINATE	3	TRUE	2	0.482098951946865	5		315	456	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437198	52437198	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	443	547	0	ENST00000460680.1:c.1846del	p.Val616Ter	p.V616*	ENST00000460680	NM_004656.3	616	Gtg/tg	14/17	0.474596159900029	3	FACETS	0.859	0.825	0.894	0.859	0.825	0.894	CLONAL	3	TRUE	0	0.482098951946865	3		547	885	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0018921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	444	543	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.498800444579584	2	FACETS	0.992	0.952	1	0.992	0.952	1	CLONAL	2	TRUE	0	0.498800444579584	2		543	897	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371633	55371633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs931390946	NA	P-0018921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	207	492	0	ENST00000297316.4:c.323C>T	p.Ala108Val	p.A108V	ENST00000297316	NM_022454.3	108	gCg/gTg	2/2	0.498800444579584	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.498800444579584	1		492	590	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675463	30675463	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	190	519	0	ENST00000376406.3:c.2893C>T	p.Pro965Ser	p.P965S	ENST00000376406	NM_014641.2	965	Cca/Tca	8/15	0.453022655411029	3	FACETS	0.973	0.9	1	0.487	0.45	0.525	CLONAL	1	TRUE	1	0.498800444579584	3		519	978	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0018923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	87	708	1	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	0.2	2		709	778	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438204	49438204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761386159	NA	P-0018923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	150	644	2	ENST00000301067.7:c.5065C>T	p.Arg1689Cys	p.R1689C	ENST00000301067	NM_003482.3	1689	Cgt/Tgt	20/54	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.2	2		646	1034	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986603	36986652	+	frameshift_variant	Frame_Shift_Del	DEL	GTGCGCCAGGTCCGGAGACTGGCCTGCGCTGCCTGGCTGGTGGCCCGGGT	GTGCGCCAGGTCCGGAGACTGGCCTGCGCTGCCTGGCTGGTGGCCCGGGT	-	novel	NA	P-0018923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	45	356	1	ENST00000354822.5:c.1037_1086del	p.His346ProfsTer76	p.H346Pfs*76	ENST00000354822	NM_001079668.2	346	cACCCGGGCCACCAGCCAGGCAGCGCAGGCCAGTCTCCGGACCTGGCGCAC/c	3/3	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.2	2		357	403	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986805	36986808	+	frameshift_variant	Frame_Shift_Del	DEL	TTCA	TTCA	-	novel	NA	P-0018923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	55	288	0	ENST00000354822.5:c.881_884del	p.Val294GlufsTer86	p.V294Efs*86	ENST00000354822	NM_001079668.2	294	gTGAAa/ga	3/3	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.2	2		288	442	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609305	39609305	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	56	365	0	ENST00000262039.4:c.1607G>C	p.Arg536Thr	p.R536T	ENST00000262039	NM_002647.2	536	aGa/aCa	15/25	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.2	2		365	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0018924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	358	667	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	NA	2	FACETS	0.798	0.764	0.832			1	INDETERMINATE	2	TRUE	NA	0.684732253988851	2		667	655	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918614	94918614	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	275	696	0	ENST00000536441.1:c.568C>A	p.Leu190Met	p.L190M	ENST00000536441	NM_144665.3	190	Ctg/Atg	5/10	0.588057186452027	3	FACETS	0.832	0.787	0.877	0.832	0.787	0.877	CLONAL	2	TRUE	1	0.684732253988851	3		696	648	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937879	76937880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	102	785	0	ENST00000373344.5:c.2868dup	p.Val957SerfsTer7	p.V957Sfs*7	ENST00000373344	NM_000489.3	956	-/A	9/35	1	2	FACETS	0.478	0.428	0.531	0.478	0.428	0.531	SUBCLONAL	1	TRUE	1	0.684732253988851	2		785	623	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141498	11141498	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	163	822	5	ENST00000358026.2:c.3480del	p.Leu1161SerfsTer3	p.L1161Sfs*3	ENST00000358026	NM_001128849.1	1159	Ggg/gg	25/36	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.284451705558665	2		827	839	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638491	176638491	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784096	NA	P-0018925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	74	841	0	ENST00000439151.2:c.3091C>T	p.Arg1031Ter	p.R1031*	ENST00000439151	NM_022455.4	1031	Cga/Tga	5/23	0.284451705558665	1	FACETS	0.491	0.429	0.558	0.491	0.429	0.558	SUBCLONAL	1	TRUE	0	0.284451705558665	1		841	909	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132428	11132428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	70	782	0	ENST00000358026.2:c.2644G>A	p.Glu882Lys	p.E882K	ENST00000358026	NM_001128849.1	882	Gaa/Aaa	19/36	1	2	FACETS	0.577	0.502	0.658	0.577	0.502	0.658	SUBCLONAL	1	TRUE	1	0.284451705558665	2		782	853	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214706	133214706	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1193081581	NA	P-0018925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	45	521	0	ENST00000320574.5:c.5572C>T	p.Arg1858Cys	p.R1858C	ENST00000320574	NM_006231.2	1858	Cgc/Tgc	41/49	1	2	FACETS	0.544	0.456	0.641	0.544	0.456	0.641	SUBCLONAL	1	TRUE	1	0.284451705558665	2		521	582	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035147	37035147	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs63751012	NA	P-0018925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	67	438	0	ENST00000231790.2:c.109G>C	p.Glu37Gln	p.E37Q	ENST00000231790	NM_000249.3	37	Gag/Cag	1/19	0.284451705558665	1	FACETS	0.933	0.814	1	0.933	0.814	1	CLONAL	1	TRUE	0	0.284451705558665	1		438	433	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508273	38508273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779485530	NA	P-0018925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	79	770	2	ENST00000254066.5:c.581C>T	p.Ala194Val	p.A194V	ENST00000254066	NM_000964.3	194	gCg/gTg	5/9	1	2	FACETS	0.644	0.565	0.728	0.644	0.565	0.728	SUBCLONAL	1	TRUE	1	0.284451705558665	2		772	863	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421039	49421039	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398123721	NA	P-0018925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	104	448	0	ENST00000301067.7:c.14710C>T	p.Arg4904Ter	p.R4904*	ENST00000301067	NM_003482.3	4904	Cga/Tga	48/54	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.284451705558665	2		448	578	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280669	115280671	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	novel	NA	P-0018925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	52	774	1	ENST00000438362.2:c.360_362del	p.Ser121del	p.S121del	ENST00000438362	NM_001242891.1	120	tcATCg/tcg	4/20	1	2	FACETS	0.444	0.377	0.518	0.444	0.377	0.518	SUBCLONAL	1	TRUE	1	0.284451705558665	2		775	823	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118354911	118354911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550235275	NA	P-0018925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	51	746	0	ENST00000534358.1:c.4100C>T	p.Pro1367Leu	p.P1367L	ENST00000534358	NM_005933.3	1367	cCg/cTg	9/36	1	2	FACETS	0.423	0.358	0.494	0.423	0.358	0.494	SUBCLONAL	1	TRUE	1	0.284451705558665	2		746	848	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376683	118376683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149340870	NA	P-0018925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	67	757	1	ENST00000534358.1:c.10076C>T	p.Ala3359Val	p.A3359V	ENST00000534358	NM_005933.3	3359	gCg/gTg	27/36	1	2	FACETS	0.543	0.471	0.622	0.543	0.471	0.622	SUBCLONAL	1	TRUE	1	0.284451705558665	2		758	867	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109968	115109968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	64	813	0	ENST00000257566.3:c.1910G>A	p.Arg637Gln	p.R637Q	ENST00000257566	NM_016569.3	637	cGg/cAg	8/8	1	2	FACETS	0.54	0.466	0.62	0.54	0.466	0.62	SUBCLONAL	1	TRUE	1	0.284451705558665	2		813	834	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129400	2129400	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs137854302	NA	P-0018925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	44	634	1	ENST00000219476.3:c.3259del	p.Glu1087SerfsTer16	p.E1087Sfs*16	ENST00000219476	NM_000548.3	1085	tcG/tc	28/42	1	2	FACETS	0.424	0.354	0.501	0.424	0.354	0.501	SUBCLONAL	1	TRUE	1	0.284451705558665	2		635	730	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390435	56390435	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757096789	NA	P-0018925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	47	451	1	ENST00000348428.3:c.1174C>T	p.Arg392Cys	p.R392C	ENST00000348428	NM_006785.3	392	Cgt/Tgt	10/17	1	2	FACETS	0.615	0.519	0.722	0.615	0.519	0.722	SUBCLONAL	1	TRUE	1	0.284451705558665	2		452	537	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966816	18966816	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	106	872	2	ENST00000262803.5:c.1627C>T	p.Arg543Cys	p.R543C	ENST00000262803	NM_002911.3	543	Cgc/Tgc	12/24	1	2	FACETS	0.813	0.728	0.903	0.813	0.728	0.903	CLONAL	1	TRUE	1	0.284451705558665	2		874	917	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593489	55593489	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	71	478	0	ENST00000288135.5:c.1646A>G	p.Gln549Arg	p.Q549R	ENST00000288135	NM_000222.2	549	cAg/cGg	10/21	1	2	FACETS	0.998	0.873	1	0.998	0.873	1	CLONAL	1	TRUE	1	0.284451705558665	2		478	500	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687407	117687407	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	78	555	0	ENST00000368508.3:c.2644G>A	p.Glu882Lys	p.E882K	ENST00000368508	NM_002944.2	882	Gaa/Aaa	18/43	1	2	FACETS	0.93	0.818	1	0.93	0.818	1	CLONAL	1	TRUE	1	0.284451705558665	2		555	590	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962391	2962391	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	50	632	0	ENST00000396946.4:c.2146G>T	p.Glu716Ter	p.E716*	ENST00000396946	NM_032415.4	716	Gaa/Taa	17/25	1	2	FACETS	0.502	0.424	0.586	0.502	0.424	0.586	SUBCLONAL	1	TRUE	1	0.284451705558665	2		632	701	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151947949	151947949	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	49	654	0	ENST00000262189.6:c.1724T>A	p.Ile575Asn	p.I575N	ENST00000262189	NM_170606.2	575	aTt/aAt	12/59	1	2	FACETS	0.518	0.438	0.607	0.518	0.438	0.607	SUBCLONAL	1	TRUE	1	0.284451705558665	2		654	665	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572610	141572610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764426394	NA	P-0018925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	67	691	0	ENST00000220592.5:c.460G>A	p.Val154Ile	p.V154I	ENST00000220592	NM_012154.3	154	Gtc/Atc	4/19	0.284451705558665	4	FACETS	0.57	0.493	0.653	0.19	0.164	0.218	SUBCLONAL	1	TRUE	1	0.284451705558665	4		691	1062	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223862	53223862	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	89	527	1	ENST00000375401.3:c.3497G>A	p.Arg1166His	p.R1166H	ENST00000375401	NM_004187.3	1166	cGc/cAc	23/26	1	1	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	0	0.284451705558665	1		528	535	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054241	30054241	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0018930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	90	498	0	ENST00000338641.4:c.663C>G	p.Tyr221Ter	p.Y221*	ENST00000338641	NM_000268.3	221	taC/taG	7/16	0.281180838953653	1	FACETS	0.707	0.627	0.793	0.707	0.627	0.793	SUBCLONAL	1	FALSE	0	0.3	1		498	721	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391192	89391192	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	113	489	0	ENST00000336596.2:c.1258T>C	p.Ser420Pro	p.S420P	ENST00000336596	NM_005233.5	420	Tcc/Ccc	5/17	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.3	2		489	638	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005417	150005417	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	81	461	1	ENST00000253339.5:c.808C>A	p.Pro270Thr	p.P270T	ENST00000253339		270	Cca/Aca	3/7	0.3	1	FACETS	0.721	0.635	0.812	0.721	0.635	0.812	SUBCLONAL	1	FALSE	0	0.3	1		462	637	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0018931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	340	667	1	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.719759862625193	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.719759862625193	1		668	591	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0018931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	492	444	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.719759862625193	5	FACETS	0.903	0.867	0.938	0.903	0.867	0.938	CLONAL	3	TRUE	2	0.719759862625193	5		444	1050	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236628	236628	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201139275	NA	P-0018931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	144	457	18	ENST00000264932.6:c.1346C>T	p.Ala449Val	p.A449V	ENST00000264932	NM_004168.2	449	gCc/gTc	10/15	1	2	FACETS	0.582	0.532	0.635	0.582	0.532	0.635	SUBCLONAL	1	TRUE	1	0.719759862625193	2		475	687	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527531	29527532	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs1555610893	NA	P-0018931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	475	660	0	ENST00000356175.3:c.983_984del	p.Cys328Ter	p.C328*	ENST00000356175	NM_000267.3	327	cTG/c	9/57	0.719759862625193	2	FACETS	0.907	0.877	0.936	0.907	0.877	0.936	CLONAL	2	TRUE	0	0.719759862625193	2		660	728	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589600	67589601	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0018931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	180	489	0	ENST00000274335.5:c.1363_1364del	p.Gln455ValfsTer9	p.Q455Vfs*9	ENST00000274335		455	CAg/g	10/15	0.719759862625193	1	FACETS	0.87	0.815	0.925	0.87	0.815	0.925	CLONAL	1	TRUE	0	0.719759862625193	1		489	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	480	1017	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.914525691154309	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.914525691154309	2		1018	500	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	43	917	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.914525691154309	2	FACETS	0.26	0.218	0.307	0.13	0.109	0.154	SUBCLONAL	1	TRUE	0	0.914525691154309	2		917	361	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259628	16259628	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1216	85	716	1	ENST00000375759.3:c.6893C>T	p.Thr2298Ile	p.T2298I	ENST00000375759	NM_015001.2	2298	aCc/aTc	11/15	0.861893515197451	4	FACETS	0.274	0.241	0.309	0.137	0.12	0.155	SUBCLONAL	1	TRUE	2	0.914525691154309	4		717	1301	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261880	16261880	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	74	537	0	ENST00000375759.3:c.9145G>A	p.Ala3049Thr	p.A3049T	ENST00000375759	NM_015001.2	3049	Gcg/Acg	11/15	0.861893515197451	4	FACETS	0.299	0.261	0.341	0.15	0.13	0.171	SUBCLONAL	1	TRUE	2	0.914525691154309	4		537	1035	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532582	46532582	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	29	356	0	ENST00000262741.5:c.495+1G>A		p.X165_splice	ENST00000262741	NM_003629.3	165			0.861893515197451	4	FACETS	0.298	0.238	0.365	0.149	0.119	0.183	SUBCLONAL	1	TRUE	2	0.914525691154309	4		356	408	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439570	51439570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	43	431	1	ENST00000262662.1:c.135G>A	p.Met45Ile	p.M45I	ENST00000262662		45	atG/atA	4/4	0.861893515197451	4	FACETS	0.31	0.259	0.367	0.155	0.129	0.184	SUBCLONAL	1	TRUE	2	0.914525691154309	4		432	581	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248288	59248288	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	11	91	0	ENST00000371222.2:c.455G>A	p.Gly152Glu	p.G152E	ENST00000371222	NM_002228.3	152	gGg/gAg	1/1	0.861893515197451	4	FACETS	0.288	0.199	0.397	0.144	0.099	0.199	SUBCLONAL	1	TRUE	2	0.914525691154309	4		91	160	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226566961	226566961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200485374	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	44	489	0	ENST00000366794.5:c.1627G>A	p.Ala543Thr	p.A543T	ENST00000366794	NM_001618.3	543	Gcg/Acg	12/23	0.861893515197451	4	FACETS	0.278	0.233	0.329	0.139	0.116	0.165	SUBCLONAL	1	TRUE	2	0.914525691154309	4		489	662	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675413	241675413	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	25	477	0	ENST00000366560.3:c.409C>T	p.Pro137Ser	p.P137S	ENST00000366560	NM_000143.3	137	Cct/Tct	4/10	0.861893515197451	4	FACETS	0.229	0.18	0.286	0.115	0.09	0.143	SUBCLONAL	1	TRUE	2	0.914525691154309	4		477	457	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852351	63852352	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	419	579	3	ENST00000279873.7:c.3129_3130delinsAA	p.Glu1044Lys	p.E1044K	ENST00000279873	NM_032199.2	1043	aaGGag/aaAAag	10/10	0.914525691154309	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.914525691154309	2		582	447	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925496	114925496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1356807409	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	540	723	0	ENST00000543371.1:c.1574C>T	p.Pro525Leu	p.P525L	ENST00000543371	NM_001198531.1	525	cCc/cTc	14/14	0.914525691154309	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.914525691154309	2		723	579	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363946	118363946	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	19	398	0	ENST00000534358.1:c.5178+1G>A		p.X1726_splice	ENST00000534358	NM_005933.3	1726			0.914525691154309	2	FACETS	0.157	0.119	0.201	0.078	0.059	0.101	SUBCLONAL	1	TRUE	0	0.914525691154309	2		398	265	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404774	404774	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	75	565	0	ENST00000399788.2:c.4420C>T	p.Pro1474Ser	p.P1474S	ENST00000399788	NM_001042603.1	1474	Cca/Tca	26/28	0.914525691154309	2	FACETS	0.343	0.301	0.388	0.172	0.15	0.194	SUBCLONAL	1	TRUE	0	0.914525691154309	2		565	478	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1036311	1036311	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	31	552	1	ENST00000358495.3:c.467G>T	p.Arg156Met	p.R156M	ENST00000358495	NM_134424.2	156	aGg/aTg	6/12	0.914525691154309	2	FACETS	0.146	0.118	0.178	0.073	0.059	0.089	SUBCLONAL	1	TRUE	0	0.914525691154309	2		553	464	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433401	49433401	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	63	833	0	ENST00000301067.7:c.8047-1G>A		p.X2683_splice	ENST00000301067	NM_003482.3	2683			0.914525691154309	2	FACETS	0.177	0.152	0.204	0.088	0.076	0.102	SUBCLONAL	1	TRUE	0	0.914525691154309	2		833	779	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910932	32910932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	204	733	1	ENST00000380152.3:c.2440C>T	p.Pro814Ser	p.P814S	ENST00000380152		814	Ccc/Tcc	11/27	0.862489260526681	3	FACETS	0.929	0.879	0.978	0.929	0.879	0.978	CLONAL	2	TRUE	1	0.914525691154309	3		734	350	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134820	41134820	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	13	452	0	ENST00000379561.5:c.808G>A	p.Ala270Thr	p.A270T	ENST00000379561	NM_002015.3	270	Gct/Act	2/3	0.914525691154309	1	FACETS	0.076	0.054	0.103	0.076	0.054	0.103	SUBCLONAL	1	TRUE	0	0.914525691154309	1		452	203	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027167	49027168	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	103	634	5	ENST00000267163.4:c.1734_1735delinsTT	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	578	gaCCga/gaTTga	18/27	0.914525691154309	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.914525691154309	1		639	122	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871677	35871677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	51	484	0	ENST00000216797.5:c.829C>T	p.Leu277Phe	p.L277F	ENST00000216797	NM_020529.2	277	Ctt/Ttt	5/6	0.914525691154309	3	FACETS	0.271	0.23	0.316	0.135	0.115	0.158	SUBCLONAL	1	TRUE	1	0.914525691154309	3		484	600	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348050	348050	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	51	658	0	ENST00000262320.3:c.1456T>C	p.Ser486Pro	p.S486P	ENST00000262320	NM_003502.3	486	Tcg/Ccg	6/11	0.786885946958719	3	FACETS	0.199	0.168	0.233	0.1	0.084	0.117	SUBCLONAL	1	TRUE	1	0.914525691154309	3		658	816	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662307	67662308	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	171	511	3	ENST00000264010.4:c.1553_1554delinsTT	p.Thr518Ile	p.T518I	ENST00000264010	NM_006565.3	518	aCC/aTT	9/12	1	2	FACETS	0.856	0.796	0.917	0.856	0.796	0.917	CLONAL	1	TRUE	1	0.914525691154309	2		514	437	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827301	72827301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	104	622	1	ENST00000268489.5:c.9280G>A	p.Ala3094Thr	p.A3094T	ENST00000268489	NM_006885.3	3094	Gca/Aca	9/10	1	2	FACETS	0.437	0.393	0.484	0.437	0.393	0.484	SUBCLONAL	1	TRUE	1	0.914525691154309	2		623	520	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56338931	56338931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	10	59	0	ENST00000348428.3:c.56G>A	p.Gly19Glu	p.G19E	ENST00000348428	NM_006785.3	19	gGg/gAg	1/17	NA	2	FACETS	0.421	0.292	0.573			1	INDETERMINATE	1	TRUE	NA	0.914525691154309	2		59	52	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615794	1615794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	58	655	2	ENST00000344749.5:c.1477G>A	p.Ala493Thr	p.A493T	ENST00000344749	NM_001136139.2	493	Gcc/Acc	17/19	0.558487740025564	4	FACETS	0.224	0.192	0.26	0.112	0.096	0.13	SUBCLONAL	1	TRUE	2	0.914525691154309	4		657	1083	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231522	5231522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	514	659	0	ENST00000357368.4:c.1954G>A	p.Val652Met	p.V652M	ENST00000357368	NM_002850.3	652	Gtg/Atg	14/38	0.750174163016789	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.914525691154309	4		659	1047	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291068	10291068	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769726219	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	68	648	0	ENST00000340748.4:c.403C>T	p.Pro135Ser	p.P135S	ENST00000340748		135	Cct/Tct	4/40	0.750174163016789	4	FACETS	0.267	0.231	0.306	0.133	0.115	0.153	SUBCLONAL	1	TRUE	2	0.914525691154309	4		648	1068	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276643	15276644	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTGC	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	510	611	0	ENST00000263388.2:c.5618_5621dup	p.Pro1875HisfsTer58	p.P1875Hfs*58	ENST00000263388	NM_000435.2	1874	act/acGCACt	30/33	0.750174163016789	4	FACETS	0.924	0.887	0.96	0.924	0.887	0.96	CLONAL	2	TRUE	2	0.914525691154309	4		611	1156	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027328	48027328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	20	455	0	ENST00000234420.5:c.2206G>A	p.Asp736Asn	p.D736N	ENST00000234420	NM_000179.2	736	Gat/Aat	4/10	0.914525691154309	2	FACETS	0.148	0.113	0.189	0.074	0.056	0.095	SUBCLONAL	1	TRUE	0	0.914525691154309	2		455	296	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028031	48028031	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	42	437	1	ENST00000234420.5:c.2909G>A	p.Trp970Ter	p.W970*	ENST00000234420	NM_000179.2	970	tGg/tAg	4/10	0.914525691154309	2	FACETS	0.286	0.24	0.337	0.143	0.12	0.169	SUBCLONAL	1	TRUE	0	0.914525691154309	2		438	321	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033352	48033352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750949	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	108	522	1	ENST00000234420.5:c.3656C>T	p.Thr1219Ile	p.T1219I	ENST00000234420	NM_000179.2	1219	aCt/aTt	8/10	0.914525691154309	2	FACETS	0.785	0.714	0.857	0.392	0.357	0.429	SUBCLONAL	1	TRUE	0	0.914525691154309	2		523	301	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273092	198273092	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	48	443	0	ENST00000335508.6:c.1117+1G>A		p.X373_splice	ENST00000335508	NM_012433.2	373			NA	2	FACETS	0.291	0.246	0.339			1	INDETERMINATE	1	TRUE	NA	0.914525691154309	2		443	361	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538361	9538361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	586	473	2	ENST00000353224.5:c.1637C>T	p.Ala546Val	p.A546V	ENST00000353224	NM_177990.2	546	gCt/gTt	7/10	0.844287058044604	4	FACETS	1	0.995	1			1	CLONAL	4	TRUE	NA	0.914525691154309	4		475	607	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023300	31023300	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	871	566	2	ENST00000375687.4:c.2785G>T	p.Glu929Ter	p.E929*	ENST00000375687	NM_015338.5	929	Gag/Tag	13/13	0.844287058044604	4	FACETS	1	0.997	1			1	CLONAL	4	TRUE	NA	0.914525691154309	4		568	900	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655194	45655195	+	missense_variant	Missense_Mutation	DNP	CG	CG	AT	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	423	513	1	ENST00000407780.3:c.657_658delinsAT	p.Asn219_Val220delinsLysLeu	p.N219_V220delinsKL	ENST00000407780	NM_001283052.1	219	aaCGtg/aaATtg	4/7	0.914525691154309	3	FACETS	0.935	0.9	0.97	0.935	0.9	0.97	CLONAL	2	TRUE	1	0.914525691154309	3		514	721	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655359	45655359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1205	83	959	1	ENST00000407780.3:c.493C>T	p.Pro165Ser	p.P165S	ENST00000407780	NM_001283052.1	165	Ccc/Tcc	4/7	0.914525691154309	3	FACETS	0.205	0.18	0.233	0.103	0.09	0.117	SUBCLONAL	1	TRUE	1	0.914525691154309	3		960	1288	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226793	142226793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	20	442	0	ENST00000350721.4:c.5011G>A	p.Glu1671Lys	p.E1671K	ENST00000350721	NM_001184.3	1671	Gaa/Aaa	28/47	1	2	FACETS	0.162	0.124	0.207	0.162	0.124	0.207	SUBCLONAL	1	TRUE	1	0.914525691154309	2		442	270	SUCCESS
ATR	545	MSKCC	GRCh37	3	142234253	142234253	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	22	685	0	ENST00000350721.4:c.4487G>A	p.Gly1496Asp	p.G1496D	ENST00000350721	NM_001184.3	1496	gGt/gAt	25/47	1	2	FACETS	0.149	0.115	0.189	0.149	0.115	0.189	SUBCLONAL	1	TRUE	1	0.914525691154309	2		685	322	SUCCESS
ATR	545	MSKCC	GRCh37	3	142241638	142241638	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	161	668	0	ENST00000350721.4:c.4198C>G	p.Leu1400Val	p.L1400V	ENST00000350721	NM_001184.3	1400	Cta/Gta	23/47	1	2	FACETS	0.995	0.926	1	0.995	0.926	1	CLONAL	1	TRUE	1	0.914525691154309	2		668	354	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803115	1803116	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	288	688	1	ENST00000260795.2:c.467_468delinsTT	p.Pro156Leu	p.P156L	ENST00000260795		156	cCC/cTT	4/17	1	2	FACETS	0.973	0.923	1	0.973	0.923	1	CLONAL	1	TRUE	1	0.914525691154309	2		689	647	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190797	106190797	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs759658003	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	184	540	0	ENST00000380013.4:c.4075C>G	p.Arg1359Gly	p.R1359G	ENST00000380013	NM_001127208.2	1359	Cgt/Ggt	9/11	1	2	FACETS	0.998	0.934	1	0.998	0.934	1	CLONAL	1	TRUE	1	0.914525691154309	2		540	403	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518859	187518859	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	245	678	0	ENST00000441802.2:c.12345T>G	p.Cys4115Trp	p.C4115W	ENST00000441802	NM_005245.3	4115	tgT/tgG	24/27	1	2	FACETS	0.989	0.933	1	0.989	0.933	1	CLONAL	1	TRUE	1	0.914525691154309	2		678	542	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530475	187530475	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	23	344	0	ENST00000441802.2:c.10069-1G>A		p.X3357_splice	ENST00000441802	NM_005245.3	3357			1	2	FACETS	0.179	0.139	0.225	0.179	0.139	0.225	SUBCLONAL	1	TRUE	1	0.914525691154309	2		344	281	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708051	117708051	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	59	563	0	ENST00000368508.3:c.2125+1G>A		p.X709_splice	ENST00000368508	NM_002944.2	709			0.914525691154309	1	FACETS	0.593	0.529	0.658	0.593	0.529	0.658	SUBCLONAL	1	TRUE	0	0.914525691154309	1		563	118	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222541	157222541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	144	716	0	ENST00000346085.5:c.1808G>A	p.Ser603Asn	p.S603N	ENST00000346085	NM_020732.3	603	aGt/aAt	4/20	0.914525691154309	2	FACETS	0.549	0.502	0.597	0.274	0.251	0.299	SUBCLONAL	1	TRUE	0	0.914525691154309	2		716	574	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963901	2963901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	71	821	0	ENST00000396946.4:c.1906G>A	p.Val636Ile	p.V636I	ENST00000396946	NM_032415.4	636	Gtc/Atc	15/25	0.861893515197451	4	FACETS	0.25	0.217	0.286	0.125	0.108	0.143	SUBCLONAL	1	TRUE	2	0.914525691154309	4		821	1189	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935508	13935508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536563766	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	226	377	2	ENST00000405192.2:c.1348G>A	p.Glu450Lys	p.E450K	ENST00000405192	NM_001163147.1	450	Gaa/Aaa	12/12	0.861893515197451	4	FACETS	0.95	0.895	1	0.95	0.895	1	CLONAL	2	TRUE	2	0.914525691154309	4		379	498	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856045	151856045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	69	664	0	ENST00000262189.6:c.11573G>A	p.Gly3858Asp	p.G3858D	ENST00000262189	NM_170606.2	3858	gGt/gAt	44/59	0.914525691154309	4	FACETS	0.244	0.211	0.28	0.122	0.105	0.14	SUBCLONAL	1	TRUE	2	0.914525691154309	4		664	1184	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56879351	56879351	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	546	715	0	ENST00000519728.1:c.868G>A	p.Glu290Lys	p.E290K	ENST00000519728	NM_002350.3	290	Gaa/Aaa	9/13	0.914525691154309	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.914525691154309	3		715	843	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046357	69046357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	36	552	1	ENST00000288368.4:c.3830C>T	p.Ala1277Val	p.A1277V	ENST00000288368	NM_024870.2	1277	gCc/gTc	32/40	0.914525691154309	3	FACETS	0.175	0.143	0.211	0.088	0.071	0.106	SUBCLONAL	1	TRUE	1	0.914525691154309	3		553	654	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215856	98215856	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	57	572	2	ENST00000331920.6:c.3353C>T	p.Ala1118Val	p.A1118V	ENST00000331920	NM_000264.3	1118	gCc/gTc	20/24	0.914525691154309	4	FACETS	0.211	0.18	0.245	0.07	0.06	0.082	SUBCLONAL	1	TRUE	1	0.914525691154309	4		574	1130	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247466	53247466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	237	671	0	ENST00000375401.3:c.343C>T	p.Leu115Phe	p.L115F	ENST00000375401	NM_004187.3	115	Ctc/Ttc	3/26	0.914525691154309	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.914525691154309	1		671	259	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0018933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	519	1034	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.591069229289941	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.591069229289941	2		1035	857	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508176	106508176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752039271	NA	P-0018933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	104	207	0	ENST00000359195.3:c.170C>T	p.Ala57Val	p.A57V	ENST00000359195	NM_002649.2	57	gCg/gTg	2/11	0.495314386816835	4	FACETS	0.927	0.841	1	0.927	0.841	1	CLONAL	2	TRUE	2	0.591069229289941	4		207	302	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0018933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	263	738	1	ENST00000311936.3:c.180_181delinsAA	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggAAaa	3/5	0.495314386816835	4	FACETS	0.843	0.792	0.895	0.843	0.792	0.895	CLONAL	2	TRUE	2	0.591069229289941	4		739	840	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277104	18277104	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	141	465	0	ENST00000222254.8:c.1551G>C	p.Glu517Asp	p.E517D	ENST00000222254	NM_005027.3	517	gaG/gaC	12/16	0.591069229289941	4	FACETS	0.85	0.774	0.93	0.283	0.258	0.31	CLONAL	1	TRUE	1	0.591069229289941	4		465	893	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279579	18279579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1403656005	NA	P-0018933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	666	752	2	ENST00000222254.8:c.1852G>A	p.Glu618Lys	p.E618K	ENST00000222254	NM_005027.3	618	Gag/Aag	15/16	0.591069229289941	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	1	0.591069229289941	4		754	1145	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606727	29606727	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0018933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	92	516	0	ENST00000389048.3:c.1155-2A>T		p.X385_splice	ENST00000389048	NM_004304.4	385			0.348366472485489	3	FACETS	0.564	0.501	0.631			1	INDETERMINATE	1	TRUE	NA	0.591069229289941	3		516	715	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634645	158634645	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	112	323	0	ENST00000263640.3:c.541G>T	p.Ala181Ser	p.A181S	ENST00000263640	NM_001105.4	181	Gca/Tca	5/11	0.583621013195774	3	FACETS	1	0.951	1	0.54	0.488	0.593	CLONAL	1	TRUE	1	0.591069229289941	3		323	455	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990439	69990439	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	83	551	1	ENST00000394351.3:c.398A>T	p.Glu133Val	p.E133V	ENST00000394351	NM_000248.3	133	gAa/gTa	4/9	0.591069229289941	2	FACETS	0.765	0.68	0.855	0.383	0.34	0.428	SUBCLONAL	1	TRUE	0	0.591069229289941	2		552	367	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056646	26056646	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766308934	NA	P-0018933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	13	242	1	ENST00000343677.2:c.11C>T	p.Thr4Ile	p.T4I	ENST00000343677	NM_005319.3	4	aCt/aTt	1/1	1	2	FACETS	0.175	0.124	0.236	0.175	0.124	0.236	SUBCLONAL	1	TRUE	1	0.591069229289941	2		243	252	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76777824	76777824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	265	811	0	ENST00000373344.5:c.6892C>T	p.Pro2298Ser	p.P2298S	ENST00000373344	NM_000489.3	2298	Ccc/Tcc	32/35	0.43825014043446	4	FACETS	0.889	0.837	0.943	0.889	0.837	0.943	CLONAL	2	TRUE	2	0.591069229289941	4		811	802	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	61	364	1				ENST00000310581	NM_198253.2	-/1132			0.180606872322715	3	FACETS	1	0.96	1	0.656	0.567	0.751	CLONAL	1	TRUE	1	0.247033597362594	3		365	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0018934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	131	801	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.247033597362594	2		801	964	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0018934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	57	548	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	1	2	FACETS	0.938	0.806	1	0.938	0.806	1	CLONAL	1	TRUE	1	0.247033597362594	2		548	492	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41276047	41276047	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs372047427	NA	P-0018934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	41	611	0	ENST00000357654.3:c.67G>C	p.Glu23Gln	p.E23Q	ENST00000357654	NM_007294.3	23	Gag/Cag	2/23	1	2	FACETS	0.484	0.402	0.575	0.484	0.402	0.575	SUBCLONAL	1	TRUE	1	0.247033597362594	2		611	686	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877391	40877391	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372713520	NA	P-0018934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	129	616	0	ENST00000373198.4:c.2305G>A	p.Val769Met	p.V769M	ENST00000373198	NM_133170.3	769	Gtg/Atg	15/32	0.180606872322715	3	FACETS	1	0.983	1	0.704	0.638	0.774	CLONAL	1	TRUE	1	0.247033597362594	3		616	833	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099442	27099442	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs875989849	NA	P-0018934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	102	530	0	ENST00000324856.7:c.3679G>T	p.Glu1227Ter	p.E1227*	ENST00000324856	NM_006015.4	1227	Gag/Tag	14/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.247033597362594	2		530	589	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186556	108186556	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	16	285	0	ENST00000278616.4:c.6013C>G	p.Leu2005Val	p.L2005V	ENST00000278616	NM_000051.3	2005	Ctc/Gtc	41/63	1	2	FACETS	0.602	0.446	0.788	0.602	0.446	0.788	SUBCLONAL	1	TRUE	1	0.247033597362594	2		285	215	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435626	18435626	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	19	517	0	ENST00000266497.5:c.611C>G	p.Ser204Cys	p.S204C	ENST00000266497		204	tCt/tGt	1/31	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.247033597362594	NA		517	366	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436007	49436007	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	43	507	0	ENST00000301067.7:c.5974G>T	p.Glu1992Ter	p.E1992*	ENST00000301067	NM_003482.3	1992	Gag/Tag	28/54	1	2	FACETS	0.579	0.484	0.685	0.579	0.484	0.685	SUBCLONAL	1	TRUE	1	0.247033597362594	2		507	601	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445035	49445035	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	36	530	0	ENST00000301067.7:c.2431G>C	p.Glu811Gln	p.E811Q	ENST00000301067	NM_003482.3	811	Gag/Cag	10/54	1	2	FACETS	0.478	0.392	0.575	0.478	0.392	0.575	SUBCLONAL	1	TRUE	1	0.247033597362594	2		530	610	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445891	49445891	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	107	912	0	ENST00000301067.7:c.1575G>C	p.Glu525Asp	p.E525D	ENST00000301067	NM_003482.3	525	gaG/gaC	10/54	1	2	FACETS	0.703	0.629	0.783	0.703	0.629	0.783	SUBCLONAL	1	TRUE	1	0.247033597362594	2		912	1232	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446133	49446133	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	68	778	0	ENST00000301067.7:c.1333G>A	p.Glu445Lys	p.E445K	ENST00000301067	NM_003482.3	445	Gag/Aag	10/54	1	2	FACETS	0.597	0.518	0.683	0.597	0.518	0.683	SUBCLONAL	1	TRUE	1	0.247033597362594	2		778	922	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95584069	95584069	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	37	536	0	ENST00000393063.1:c.1399C>G	p.Gln467Glu	p.Q467E	ENST00000393063	NM_030621.3	467	Caa/Gaa	10/28	1	2	FACETS	0.703	0.58	0.841	0.703	0.58	0.841	SUBCLONAL	1	TRUE	1	0.247033597362594	2		536	426	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000395	42000395	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs758732584	NA	P-0018934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	49	432	0	ENST00000219905.7:c.2414C>G	p.Ser805Cys	p.S805C	ENST00000219905	NM_001164273.1	805	tCt/tGt	7/24	1	2	FACETS	0.947	0.804	1	0.947	0.804	1	CLONAL	1	TRUE	1	0.247033597362594	2		432	419	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712637	43712637	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	87	798	1	ENST00000382044.4:c.4547G>A	p.Gly1516Glu	p.G1516E	ENST00000382044	NM_001141980.1	1516	gGa/gAa	21/28	1	2	FACETS	0.65	0.574	0.733	0.65	0.574	0.733	SUBCLONAL	1	TRUE	1	0.247033597362594	2		799	1083	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144089	11144089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	68	741	2	ENST00000358026.2:c.3670G>A	p.Val1224Met	p.V1224M	ENST00000358026	NM_001128849.1	1224	Gtg/Atg	26/36	1	2	FACETS	0.623	0.54	0.712	0.623	0.54	0.712	SUBCLONAL	1	TRUE	1	0.247033597362594	2		743	884	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387689	17387689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	61	620	0	ENST00000359435.4:c.757G>A	p.Glu253Lys	p.E253K	ENST00000359435	NM_001033549.1	253	Gag/Aag	8/9	1	2	FACETS	0.704	0.606	0.81	0.704	0.606	0.81	SUBCLONAL	1	TRUE	1	0.247033597362594	2		620	702	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683491	182683491	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	32	697	0	ENST00000292782.4:c.54C>G	p.Phe18Leu	p.F18L	ENST00000292782	NM_020640.2	18	ttC/ttG	2/7	1	2	FACETS	0.412	0.333	0.501	0.412	0.333	0.501	SUBCLONAL	1	TRUE	1	0.247033597362594	2		697	629	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271242	153271242	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	26	492	0	ENST00000281708.4:c.536G>T	p.Arg179Leu	p.R179L	ENST00000281708	NM_033632.3	179	cGc/cTc	3/12	1	2	FACETS	0.569	0.45	0.705	0.569	0.45	0.705	SUBCLONAL	1	TRUE	1	0.247033597362594	2		492	370	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876479	35876479	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	78	667	0	ENST00000303115.3:c.1271G>A	p.Gly424Glu	p.G424E	ENST00000303115	NM_002185.3	424	gGa/gAa	8/8	0.180606872322715	3	FACETS	0.753	0.66	0.854	0.377	0.33	0.427	SUBCLONAL	1	TRUE	1	0.247033597362594	3		667	942	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393194	393194	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	39	509	0	ENST00000380956.4:c.42G>C	p.Met14Ile	p.M14I	ENST00000380956	NM_001195286.1	14	atG/atC	2/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.247033597362594	NA		509	475	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874781	151874781	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs762665429	NA	P-0018934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	94	352	0	ENST00000262189.6:c.7757C>G	p.Ser2586Cys	p.S2586C	ENST00000262189	NM_170606.2	2586	tCt/tGt	38/59	0.207067370013102	2	FACETS	0.785	0.701	0.873	0.785	0.701	0.873	SUBCLONAL	2	TRUE	0	0.247033597362594	2		352	485	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876936	151876936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	33	456	0	ENST00000262189.6:c.7425G>A	p.Met2475Ile	p.M2475I	ENST00000262189	NM_170606.2	2475	atG/atA	37/59	0.207067370013102	2	FACETS	0.539	0.438	0.652	0.269	0.219	0.326	SUBCLONAL	1	TRUE	0	0.247033597362594	2		456	496	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80343433	80343433	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	30	357	0	ENST00000286548.4:c.886G>C	p.Asp296His	p.D296H	ENST00000286548	NM_002072.3	296	Gat/Cat	6/7	1	2	FACETS	0.747	0.603	0.91	0.747	0.603	0.91	CLONAL	1	TRUE	1	0.247033597362594	2		357	325	SUCCESS
AR	367	MSKCC	GRCh37	X	66765746	66765746	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs769445750	NA	P-0018934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	45	446	0	ENST00000374690.3:c.758C>G	p.Ala253Gly	p.A253G	ENST00000374690	NM_000044.3	253	gCg/gGg	1/8	0.122582425876538	2	FACETS	0.621	0.521	0.731			1	INDETERMINATE	1	TRUE	NA	0.247033597362594	2		446	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0018938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	125	633	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.255663114613226	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.255663114613226	1		633	697	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391023	139391023	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	116	875	0	ENST00000277541.6:c.7168T>G	p.Leu2390Val	p.L2390V	ENST00000277541	NM_017617.3	2390	Tta/Gta	34/34	1	2	FACETS	0.923	0.831	1	0.923	0.831	1	CLONAL	1	TRUE	1	0.255663114613226	2		875	983	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0018939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	99	752	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.279131462026647	1	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	0	0.288029611025241	1		754	585	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0018939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	646	629	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.288029611025241	8	FACETS	0.955	0.926	0.984			1	CLONAL	8	TRUE	NA	0.288029611025241	8		630	1094	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934573	NA	P-0018939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	41	652	3	ENST00000269305.4:c.722C>A	p.Ser241Tyr	p.S241Y	ENST00000269305	NM_001126112.2	241	tCc/tAc	7/11	0.279131462026647	1	FACETS	0.343	0.285	0.408	0.343	0.285	0.408	SUBCLONAL	1	TRUE	0	0.288029611025241	1		655	710	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740797	145740797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769553486	NA	P-0018939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	208	884	2	ENST00000428558.2:c.1303C>T	p.Pro435Ser	p.P435S	ENST00000428558	NM_004260.3	435	Cct/Tct	7/22	0.265439493362166	3	FACETS	0.834	0.775	0.897	0.834	0.775	0.897	CLONAL	2	TRUE	1	0.288029611025241	3		886	990	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158611	26158611	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	51	381	0	ENST00000289316.2:c.214G>C	p.Glu72Gln	p.E72Q	ENST00000289316	NM_138720.2	72	Gag/Cag	1/2	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.288029611025241	2		381	329	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346926	89346926	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs375589721	NA	P-0018939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	29	291	0	ENST00000301030.4:c.6024C>G	p.Phe2008Leu	p.F2008L	ENST00000301030	NM_001256183.1	2008	ttC/ttG	9/13	1	2	FACETS	0.712	0.573	0.868	0.712	0.573	0.868	SUBCLONAL	1	TRUE	1	0.288029611025241	2		291	283	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958204	11958204	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0018939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	70	596	0	ENST00000353533.5:c.116-2A>T		p.X39_splice	ENST00000353533	NM_003010.3	39			0.279131462026647	1	FACETS	0.788	0.688	0.896	0.788	0.688	0.896	SUBCLONAL	1	TRUE	0	0.288029611025241	1		596	528	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470507	25470507	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	109	874	0	ENST00000264709.3:c.967G>A	p.Glu323Lys	p.E323K	ENST00000264709	NM_175629.2	323	Gaa/Aaa	8/23	0.286394127042435	1	FACETS	0.76	0.681	0.842	0.76	0.681	0.842	SUBCLONAL	1	TRUE	0	0.288029611025241	1		874	853	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703527	47703527	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	60	607	0	ENST00000233146.2:c.2027C>A	p.Ser676Ter	p.S676*	ENST00000233146	NM_000251.2	676	tCa/tAa	13/16	0.288575628468818	4	FACETS	0.651	0.56	0.751			1	SUBCLONAL	1	TRUE	NA	0.288029611025241	4		607	824	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543870	41543870	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	67	671	0	ENST00000263253.7:c.2161G>C	p.Ala721Pro	p.A721P	ENST00000263253	NM_001429.3	721	Gcc/Ccc	12/31	0.288575628468818	3	FACETS	0.603	0.522	0.69	0.301	0.261	0.345	SUBCLONAL	1	TRUE	1	0.288029611025241	3		671	883	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593269	67593269	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	54	534	0	ENST00000274335.5:c.2015T>A	p.Ile672Lys	p.I672K	ENST00000274335		672	aTa/aAa	15/15	1	2	FACETS	0.761	0.65	0.881	0.761	0.65	0.881	SUBCLONAL	1	TRUE	1	0.288029611025241	2		534	493	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250551	26250551	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	67	622	0	ENST00000446824.2:c.283G>C	p.Glu95Gln	p.E95Q	ENST00000446824	NM_021018.2	95	Gag/Cag	1/1	1	2	FACETS	0.794	0.69	0.906	0.794	0.69	0.906	CLONAL	1	TRUE	1	0.288029611025241	2		622	586	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741524	145741524	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	215	795	0	ENST00000428558.2:c.979C>G	p.Gln327Glu	p.Q327E	ENST00000428558	NM_004260.3	327	Caa/Gaa	5/22	0.265439493362166	3	FACETS	0.946	0.88	1	0.946	0.88	1	CLONAL	2	TRUE	1	0.288029611025241	3		795	903	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0018940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	183	485	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.885	0.82	0.953	0.885	0.82	0.953	CLONAL	1	TRUE	1	0.59562426000226	2		485	694	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577524	7577524	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	416	594	2	ENST00000269305.4:c.757A>C	p.Thr253Pro	p.T253P	ENST00000269305	NM_001126112.2	253	Acc/Ccc	7/11	NA	2	FACETS	0.957	0.92	0.993			1	INDETERMINATE	2	TRUE	NA	0.59562426000226	2		596	730	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126094	2126094	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397515054	NA	P-0018940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	340	810	0	ENST00000219476.3:c.2665G>C	p.Ala889Pro	p.A889P	ENST00000219476	NM_000548.3	889	Gcc/Ccc	24/42	0.59562426000226	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.59562426000226	1		810	692	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42384751	42384751	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	167	485	0	ENST00000221972.3:c.513C>G	p.Asn171Lys	p.N171K	ENST00000221972	NM_021601.3	171	aaC/aaG	4/5	1	2	FACETS	0.889	0.82	0.96	0.889	0.82	0.96	CLONAL	1	TRUE	1	0.59562426000226	2		485	631	SUCCESS
MET	4233	MSKCC	GRCh37	7	116422063	116422063	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	172	526	0	ENST00000397752.3:c.3544A>G	p.Ile1182Val	p.I1182V	ENST00000397752	NM_000245.2	1182	Att/Gtt	18/21	1	2	FACETS	0.806	0.743	0.87	0.806	0.743	0.87	CLONAL	1	TRUE	1	0.59562426000226	2		526	717	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371963	55371963	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs201018397	NA	P-0018940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	206	643	0	ENST00000297316.4:c.653C>G	p.Pro218Arg	p.P218R	ENST00000297316	NM_022454.3	218	cCg/cGg	2/2	1	2	FACETS	0.994	0.926	1	0.994	0.926	1	CLONAL	1	TRUE	1	0.59562426000226	2		643	696	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420460	49420460	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	286	570	1	ENST00000301067.7:c.15289C>T	p.Arg5097Ter	p.R5097*	ENST00000301067	NM_003482.3	5097	Cga/Tga	48/54	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.859275514018534	2		571	602	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141492	11141492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	338	654	0	ENST00000358026.2:c.3469C>T	p.Arg1157Trp	p.R1157W	ENST00000358026	NM_001128849.1	1157	Cgg/Tgg	25/36	1	2	FACETS	0.997	0.949	1	0.997	0.949	1	CLONAL	1	TRUE	1	0.859275514018534	2		654	789	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0018941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	239	501	1	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.859275514018534	2		502	528	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549458	187549458	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	258	535	0	ENST00000441802.2:c.4660G>C	p.Asp1554His	p.D1554H	ENST00000441802	NM_005245.3	1554	Gac/Cac	9/27	1	2	FACETS	0.972	0.917	1	0.972	0.917	1	CLONAL	1	TRUE	1	0.859275514018534	2		535	618	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456342	32456342	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	335	751	0	ENST00000332351.3:c.550C>G	p.Pro184Ala	p.P184A	ENST00000332351	NM_024426.4	184	Ccg/Gcg	1/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.859275514018534	2		751	779	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422906	49422906	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555186527	NA	P-0018941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	322	665	1	ENST00000301067.7:c.14189G>A	p.Trp4730Ter	p.W4730*	ENST00000301067	NM_003482.3	4730	tGg/tAg	44/54	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.859275514018534	2		666	711	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859199	151859200	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	A	novel	NA	P-0018941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	163	384	0	ENST00000262189.6:c.11460+2dup		p.X3820_splice	ENST00000262189	NM_170606.2	3820			1	2	FACETS	0.868	0.805	0.933	0.868	0.805	0.933	CLONAL	1	TRUE	1	0.859275514018534	2		384	437	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	229	917	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.274218534931432	4	FACETS	0.941	0.88	1	0.941	0.88	1	CLONAL	3	TRUE	1	0.274218534931432	4		917	754	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023559	27023560	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0018943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	144	743	1	ENST00000324856.7:c.671dup	p.Pro225AlafsTer175	p.P225Afs*175	ENST00000324856	NM_006015.4	222	tac/taCc	1/20	0.238374290247327	3	FACETS	1	0.985	1	0.696	0.635	0.76	CLONAL	1	TRUE	1	0.274218534931432	3		744	858	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060694	38060694	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	172	971	0	ENST00000250448.2:c.1295C>T	p.Thr432Met	p.T432M	ENST00000250448	NM_004496.3	432	aCg/aTg	2/2	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.274218534931432	2		971	892	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106696	2106696	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs397515018	NA	P-0018943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	70	786	1	ENST00000219476.3:c.700G>T	p.Glu234Ter	p.E234*	ENST00000219476	NM_000548.3	234	Gag/Tag	8/42	0.115557030635266	3	FACETS	0.604	0.525	0.69	0.302	0.262	0.345	INDETERMINATE	1	TRUE	1	0.274218534931432	3		787	961	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572831	41572831	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	74	887	0	ENST00000263253.7:c.5116G>T	p.Glu1706Ter	p.E1706*	ENST00000263253	NM_001429.3	1706	Gag/Tag	31/31	1	2	FACETS	0.569	0.496	0.647	0.569	0.496	0.647	SUBCLONAL	1	TRUE	1	0.274218534931432	2		887	949	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247868	59247868	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1471048562	NA	P-0018943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	83	990	2	ENST00000371222.2:c.875C>T	p.Ser292Leu	p.S292L	ENST00000371222	NM_002228.3	292	tCg/tTg	1/1	0.238374290247327	3	FACETS	0.605	0.532	0.684	0.302	0.266	0.342	SUBCLONAL	1	TRUE	1	0.274218534931432	3		992	1138	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907102	32907102	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	32	715	0	ENST00000380152.3:c.1487C>G	p.Ser496Cys	p.S496C	ENST00000380152		496	tCt/tGt	10/27	1	2	FACETS	0.379	0.306	0.461	0.379	0.306	0.461	SUBCLONAL	1	TRUE	1	0.274218534931432	2		715	616	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576905	7576906	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0018943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	181	754	0	ENST00000269305.4:c.940_941del	p.Ser314LeufsTer22	p.S314Lfs*22	ENST00000269305	NM_001126112.2	314	TCc/c	9/11	NA	2	FACETS	0.935	0.865	1			1	INDETERMINATE	2	TRUE	NA	0.274218534931432	2		754	706	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139977	50139977	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs533583599	NA	P-0018943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	73	783	0	ENST00000246792.3:c.352G>A	p.Glu118Lys	p.E118K	ENST00000246792	NM_006270.3	118	Gag/Aag	4/6	0.274218534931432	5	FACETS	0.602	0.524	0.686	0.201	0.174	0.229	SUBCLONAL	1	TRUE	2	0.274218534931432	5		783	1248	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295755	212295755	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	80	924	0	ENST00000342788.4:c.2558C>G	p.Ser853Cys	p.S853C	ENST00000342788	NM_005235.2	853	tCt/tGt	21/28	1	2	FACETS	0.771	0.678	0.871	0.771	0.678	0.871	SUBCLONAL	1	TRUE	1	0.274218534931432	2		924	757	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662244	227662244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1395337787	NA	P-0018943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	70	893	1	ENST00000305123.5:c.1211C>T	p.Ser404Leu	p.S404L	ENST00000305123	NM_005544.2	404	tCg/tTg	1/2	1	2	FACETS	0.633	0.551	0.722	0.633	0.551	0.722	SUBCLONAL	1	TRUE	1	0.274218534931432	2		894	807	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326136	62326136	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	71	621	0	ENST00000360203.5:c.3152G>T	p.Arg1051Ile	p.R1051I	ENST00000360203	NM_001283009.1	1051	aGa/aTa	32/35	0.134296886450346	4	FACETS	0.854	0.744	0.972	0.427	0.372	0.486	INDETERMINATE	1	TRUE	2	0.274218534931432	4		621	773	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326738	62326738	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	88	811	1	ENST00000360203.5:c.3557G>T	p.Arg1186Ile	p.R1186I	ENST00000360203	NM_001283009.1	1186	aGa/aTa	34/35	0.134296886450346	4	FACETS	0.842	0.745	0.947	0.421	0.372	0.474	INDETERMINATE	1	TRUE	2	0.274218534931432	4		812	971	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171624	36171624	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	26	343	0	ENST00000300305.3:c.941C>G	p.Ser314Cys	p.S314C	ENST00000300305		314	tCt/tGt	7/8	1	2	FACETS	0.433	0.342	0.537	0.433	0.342	0.537	SUBCLONAL	1	TRUE	1	0.274218534931432	2		343	438	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572858	41572858	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	59	845	3	ENST00000263253.7:c.5143G>T	p.Glu1715Ter	p.E1715*	ENST00000263253	NM_001429.3	1715	Gag/Tag	31/31	1	2	FACETS	0.469	0.402	0.542	0.469	0.402	0.542	SUBCLONAL	1	TRUE	1	0.274218534931432	2		848	918	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593398	67593398	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	42	524	0	ENST00000274335.5:c.2144C>A	p.Ala715Asp	p.A715D	ENST00000274335		715	gCc/gAc	15/15	0.134296886450346	4	FACETS	0.614	0.511	0.728	0.307	0.255	0.364	INDETERMINATE	1	TRUE	2	0.274218534931432	4		524	636	SUCCESS
APC	324	MSKCC	GRCh37	5	112173504	112173504	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	112	577	0	ENST00000257430.4:c.2213A>C	p.Lys738Thr	p.K738T	ENST00000257430	NM_000038.5	738	aAg/aCg	16/16	0.134296886450346	4	FACETS	0.766	0.69	0.847	0.766	0.69	0.847	INDETERMINATE	2	TRUE	2	0.274218534931432	4		577	679	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739392	145739392	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	124	676	0	ENST00000428558.2:c.1978G>C	p.Glu660Gln	p.E660Q	ENST00000428558	NM_004260.3	660	Gaa/Caa	12/22	0.274218534931432	5	FACETS	1	0.971	1	0.399	0.36	0.44	CLONAL	1	TRUE	2	0.274218534931432	5		676	1066	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0018944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	591	696	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.76254708836537	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.76254708836537	1		696	869	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32968886	32968886	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs80359205	NA	P-0018944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	697	536	1	ENST00000380152.3:c.9317G>A	p.Trp3106Ter	p.W3106*	ENST00000380152		3106	tGg/tAg	25/27	0.76254708836537	2	FACETS	0.999	0.976	1	0.999	0.976	1	CLONAL	2	TRUE	0	0.76254708836537	2		537	915	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487646	38487646	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	164	634	0	ENST00000254066.5:c.176C>A	p.Ala59Asp	p.A59D	ENST00000254066	NM_000964.3	59	gCc/gAc	2/9	0.76254708836537	1	FACETS	0.419	0.386	0.453	0.419	0.386	0.453	SUBCLONAL	1	TRUE	0	0.76254708836537	1		634	635	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55339452	55339574	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATCATATATTTTTTCCTTAAAGTACTTTATTGACTCCTGCTTTTCTATTTTTTTTCCCAGATTGACCCCAAAGTTGCATTTCCTCGTCGAGCGCAACCCAAGGTAAGTAGGAGAATAAACAGT	ATCATATATTTTTTCCTTAAAGTACTTTATTGACTCCTGCTTTTCTATTTTTTTTCCCAGATTGACCCCAAAGTTGCATTTCCTCGTCGAGCGCAACCCAAGGTAAGTAGGAGAATAAACAGT	-	novel	NA	P-0018944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	45	318	0	ENST00000284073.2:c.271-59_312+22del		p.X91_splice	ENST00000284073	NM_138962.2	91		5/14	0.76254708836537	2	FACETS	0.297	0.249	0.348	0.148	0.124	0.174	SUBCLONAL	1	TRUE	0	0.76254708836537	2		318	398	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50143208	50143208	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	236	764	0	ENST00000246792.3:c.148A>G	p.Ile50Val	p.I50V	ENST00000246792	NM_006270.3	50	Atc/Gtc	1/6	0.76254708836537	1	FACETS	0.546	0.511	0.58	0.546	0.511	0.58	SUBCLONAL	1	TRUE	0	0.76254708836537	1		764	702	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012305	152012326	+	frameshift_variant	Frame_Shift_Del	DEL	TGTTAGAAGGTTGGTTTCTCCA	TGTTAGAAGGTTGGTTTCTCCA	-	novel	NA	P-0018944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	436	616	0	ENST00000262189.6:c.487_508del	p.Trp163ArgfsTer36	p.W163Rfs*36	ENST00000262189	NM_170606.2	163	TGGAGAAACCAACCTTCTAACAag/ag	4/59	0.513731217682749	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.76254708836537	1		616	675	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012348	152012348	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	479	643	1	ENST00000262189.6:c.465A>G	p.Ile155Met	p.I155M	ENST00000262189	NM_170606.2	155	atA/atG	4/59	0.513731217682749	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.76254708836537	1		644	707	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32968887	32968888	+	stop_gained	Nonsense_Mutation	DNP	GA	GA	AC	novel	NA	P-0018944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	539	273	1	ENST00000380152.3:c.9318_9319delinsAC	p.Trp3106_Ile3107delinsTer	p.W3106_I3107delins*	ENST00000380152		3106	tgGAta/tgACta	25/27	0.76254708836537	2	FACETS	1	0.995	1	0.595	0.573	0.618	CLONAL	1	TRUE	0	0.76254708836537	2		274	1187	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578484	7578485	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1064793929	NA	P-0018945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	107	821	0	ENST00000269305.4:c.445dup	p.Ser149PhefsTer32	p.S149Ffs*32	ENST00000269305	NM_001126112.2	149	tcc/tTcc	5/11	0.303660814783908	1	FACETS	0.831	0.746	0.921	0.831	0.746	0.921	CLONAL	1	TRUE	0	0.308926516192087	1		821	705	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509532	106509532	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	86	777	0	ENST00000359195.3:c.1526A>G	p.Asp509Gly	p.D509G	ENST00000359195	NM_002649.2	509	gAc/gGc	2/11	0.269865588735429	3	FACETS	0.697	0.615	0.785	0.349	0.307	0.393	SUBCLONAL	1	TRUE	1	0.308926516192087	3		777	922	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0018946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	437	761	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.709075188740325	2	FACETS	0.926	0.898	0.953	0.926	0.898	0.953	CLONAL	2	TRUE	0	0.784021954663875	2		762	602	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0018946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	242	400	1	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.709075188740325	2	FACETS	0.884	0.846	0.921	0.884	0.846	0.921	CLONAL	2	TRUE	0	0.784021954663875	2		401	349	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101138	27101138	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1476360310	NA	P-0018946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	254	881	1	ENST00000324856.7:c.4420C>T	p.Gln1474Ter	p.Q1474*	ENST00000324856	NM_006015.4	1474	Caa/Taa	18/20	0.767493434790212	3	FACETS	0.96	0.899	1	0.48	0.449	0.511	CLONAL	1	TRUE	1	0.784021954663875	3		882	940	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910883	114910883	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1477809102	NA	P-0018946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	156	510	2	ENST00000543371.1:c.1001+1G>A		p.X334_splice	ENST00000543371	NM_001198531.1	334			1	2	FACETS	0.936	0.866	1	0.936	0.866	1	CLONAL	1	TRUE	1	0.784021954663875	2		512	425	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186554	108186554	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1064795932	NA	P-0018946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	83	354	0	ENST00000278616.4:c.6011T>G	p.Leu2004Arg	p.L2004R	ENST00000278616	NM_000051.3	2004	cTt/cGt	41/63	0.69112092342332	4	FACETS	0.853	0.756	0.955	0.426	0.378	0.478	CLONAL	1	TRUE	2	0.784021954663875	4		354	443	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701204	43701204	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	230	778	0	ENST00000382044.4:c.5491G>T	p.Val1831Leu	p.V1831L	ENST00000382044	NM_001141980.1	1831	Gtg/Ttg	26/28	1	2	FACETS	0.847	0.793	0.901	0.847	0.793	0.901	CLONAL	1	TRUE	1	0.784021954663875	2		778	693	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459975	99459975	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	143	656	0	ENST00000268035.6:c.2071G>C	p.Val691Leu	p.V691L	ENST00000268035	NM_000875.3	691	Gtg/Ctg	10/21	1	2	FACETS	0.763	0.701	0.828	0.763	0.701	0.828	SUBCLONAL	1	TRUE	1	0.784021954663875	2		656	478	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223103	1223103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782058	NA	P-0018946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	234	787	0	ENST00000326873.7:c.1040C>T	p.Ala347Val	p.A347V	ENST00000326873	NM_000455.4	347	gCg/gTg	8/10	0.767493434790212	3	FACETS	0.925	0.864	0.988	0.463	0.432	0.494	CLONAL	1	TRUE	1	0.784021954663875	3		787	898	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658490	117658490	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	197	753	0	ENST00000368508.3:c.5093A>G	p.Glu1698Gly	p.E1698G	ENST00000368508	NM_002944.2	1698	gAg/gGg	31/43	0.69112092342332	4	FACETS	0.942	0.872	1	0.471	0.436	0.507	CLONAL	1	TRUE	2	0.784021954663875	4		753	952	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683741	162683741	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	198	681	0	ENST00000366898.1:c.228del	p.Gly77ValfsTer4	p.G77Vfs*4	ENST00000366898	NM_004562.2	76	aaA/aa	3/12	0.69112092342332	4	FACETS	0.842	0.786	0.899	0.842	0.786	0.899	CLONAL	2	TRUE	2	0.784021954663875	4		681	535	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509250	106509250	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	223	737	0	ENST00000359195.3:c.1244A>C	p.Glu415Ala	p.E415A	ENST00000359195	NM_002649.2	415	gAg/gCg	2/11	0.708567478968893	5	FACETS	0.982	0.913	1	0.327	0.304	0.352	CLONAL	1	TRUE	2	0.784021954663875	5		737	1260	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145736935	145736936	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1373	196	714	0	ENST00000428558.2:c.3505dup	p.Ser1169LysfsTer58	p.S1169Kfs*58	ENST00000428558	NM_004260.3	1169	agc/aAgc	22/22	0.784021954663875	7	FACETS	0.943	0.87	1	0.236	0.217	0.255	CLONAL	1	TRUE	3	0.784021954663875	7		714	1569	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518393	8518393	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	69	304	0	ENST00000356435.5:c.998A>T	p.Glu333Val	p.E333V	ENST00000356435		333	gAg/gTg	10/35	0.713241430397532	3	FACETS	0.725	0.636	0.82	0.362	0.318	0.41	SUBCLONAL	1	TRUE	1	0.784021954663875	3		304	338	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570385	87570385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	231	835	1	ENST00000277120.3:c.2125G>A	p.Gly709Arg	p.G709R	ENST00000277120		709	Ggg/Agg	17/19	0.713241430397532	3	FACETS	0.963	0.899	1	0.481	0.449	0.514	CLONAL	1	TRUE	1	0.784021954663875	3		836	852	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0018949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	174	708	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.869	0.802	0.938	0.869	0.802	0.938	CLONAL	1	TRUE	1	0.537683007889948	2		709	745	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141874	108141874	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587781558	NA	P-0018949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	116	524	1	ENST00000278616.4:c.2921+1G>A		p.X974_splice	ENST00000278616	NM_000051.3	974			1	2	FACETS	0.839	0.76	0.923	0.839	0.76	0.923	CLONAL	1	TRUE	1	0.537683007889948	2		525	514	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0018949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	91	400	1	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	1	2	FACETS	0.877	0.784	0.974	0.877	0.784	0.974	CLONAL	1	TRUE	1	0.537683007889948	2		401	386	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910883	114910883	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1477809102	NA	P-0018949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	121	510	2	ENST00000543371.1:c.1001+1G>A		p.X334_splice	ENST00000543371	NM_001198531.1	334			1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.537683007889948	2		512	441	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0018949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	348	683	1	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.459754554159123	3	FACETS	0.979	0.931	1	0.979	0.931	1	CLONAL	2	TRUE	1	0.537683007889948	3		684	839	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0018949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	182	793	1	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.834	0.77	0.899	0.834	0.77	0.899	CLONAL	1	TRUE	1	0.537683007889948	2		794	812	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	215	734	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	0.135528323666519	3	FACETS	1	0.99	1	0.685	0.639	0.732	INDETERMINATE	1	TRUE	1	0.537683007889948	3		734	741	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249453	153249453	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	166	814	1	ENST00000281708.4:c.1325C>T	p.Thr442Ile	p.T442I	ENST00000281708	NM_033632.3	442	aCa/aTa	9/12	0.135528323666519	3	FACETS	1	0.967	1	0.546	0.502	0.591	INDETERMINATE	1	TRUE	1	0.537683007889948	3		815	718	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903733	114903733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	201	848	2	ENST00000543371.1:c.737C>T	p.Ser246Leu	p.S246L	ENST00000543371	NM_001198531.1	246	tCg/tTg	7/14	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.537683007889948	2		850	748	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604790	48605164	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	GAAGTACTTCATACCATGCCGATTGCAGACCCACAACCTTTAGACTGAGGTCTTTTACCGTTGGGGCCCTTAACCTTATCAGGATGGTGGACTACAAAATACAATCCTGTTTATAATCTGAAGATATATTTCACTTTTGTTCTGCTTTATCTTTTCATAAAGGGTTGAAAATGTGTTTGCTGCCTTGCTCCTAGCAGACAGAAACTGGATTAAAACAATTTTTTTTTTCCTCTTCAGAACTTGTCAGGCATGGCTCAGAGCTTGAAGATTAGGAGAAACACATTCTTATTAATTCTTCACCTGTTATGTATGAAGGAATCATTCCAGTGCTAGAAAATTTAGCCCTTTAAAACGTCTTAGAGCCTTTTATCTGCA	GAAGTACTTCATACCATGCCGATTGCAGACCCACAACCTTTAGACTGAGGTCTTTTACCGTTGGGGCCCTTAACCTTATCAGGATGGTGGACTACAAAATACAATCCTGTTTATAATCTGAAGATATATTTCACTTTTGTTCTGCTTTATCTTTTCATAAAGGGTTGAAAATGTGTTTGCTGCCTTGCTCCTAGCAGACAGAAACTGGATTAAAACAATTTTTTTTTTCCTCTTCAGAACTTGTCAGGCATGGCTCAGAGCTTGAAGATTAGGAGAAACACATTCTTATTAATTCTTCACCTGTTATGTATGAAGGAATCATTCCAGTGCTAGAAAATTTAGCCCTTTAAAACGTCTTAGAGCCTTTTATCTGCA	-	novel	NA	P-0018949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	113	639	0	ENST00000342988.3:c.1615_*330del		p.*539*	ENST00000342988	NM_005359.5	538		12/12	0.526712561973628	1	FACETS	0.883	0.804	0.965	0.883	0.804	0.965	CLONAL	1	TRUE	0	0.537683007889948	1		639	348	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0018950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	111	745	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.964	0.867	1	0.964	0.867	1	CLONAL	1	TRUE	1	0.287819620679432	2		745	800	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0018950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	78	868	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.287819620679432	1	FACETS	0.807	0.71	0.911	0.807	0.71	0.911	CLONAL	1	TRUE	0	0.287819620679432	1		868	575	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	58	364	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.290554420889516	2		365	382	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969932	81969932	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024473204	NA	P-0018951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	95	636	0	ENST00000359376.3:c.3001C>T	p.Arg1001Cys	p.R1001C	ENST00000359376	NM_002661.3	1001	Cgc/Tgc	27/33	1	2	FACETS	0.962	0.857	1	0.962	0.857	1	CLONAL	1	TRUE	1	0.290554420889516	2		636	680	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692785	89692785	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	79	439	0	ENST00000371953.3:c.269T>C	p.Phe90Ser	p.F90S	ENST00000371953	NM_000314.4	90	tTt/tCt	5/9	0.290554420889516	1	FACETS	0.941	0.83	1	0.941	0.83	1	CLONAL	1	TRUE	0	0.290554420889516	1		439	494	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041676	29041676	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	78	528	0	ENST00000282397.4:c.143C>T	p.Thr48Ile	p.T48I	ENST00000282397	NM_002019.4	48	aCa/aTa	2/30	1	2	FACETS	0.926	0.814	1	0.926	0.814	1	CLONAL	1	TRUE	1	0.290554420889516	2		528	580	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524890	187524890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749669840	NA	P-0018951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	103	518	2	ENST00000441802.2:c.10790G>A	p.Gly3597Asp	p.G3597D	ENST00000441802	NM_005245.3	3597	gGc/gAc	19/27	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.290554420889516	2		520	632	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0018952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	66	715	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.435892863391853	7	FACETS	0.975	0.846	1	0.244	0.211	0.279	CLONAL	1	TRUE	3	0.435892863391853	7		717	649	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665274	176665274	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121908070	NA	P-0018952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	191	529	1	ENST00000439151.2:c.3958C>T	p.Arg1320Ter	p.R1320*	ENST00000439151	NM_022455.4	1320	Cga/Tga	7/23	0.413354653796763	2	FACETS	0.907	0.847	0.968	0.907	0.847	0.968	CLONAL	2	TRUE	0	0.435892863391853	2		530	483	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690847	89690847	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587776667	NA	P-0018952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	71	533	0	ENST00000371953.3:c.253+1G>T		p.X85_splice	ENST00000371953	NM_000314.4	85			1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.435892863391853	2		533	299	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448177	49448177	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555198640	NA	P-0018952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	142	735	0	ENST00000301067.7:c.423G>A	p.Trp141Ter	p.W141*	ENST00000301067	NM_003482.3	141	tgG/tgA	4/54	1	2	FACETS	0.951	0.869	1	0.951	0.869	1	CLONAL	1	TRUE	1	0.435892863391853	2		735	685	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063320	67063329	+	frameshift_variant	Frame_Shift_Del	DEL	GTCGTGCCCG	GTCGTGCCCG	-	novel	NA	P-0018952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	59	358	0	ENST00000412916.2:c.10_19del	p.Val4ThrfsTer15	p.V4Tfs*15	ENST00000412916		4	GTCGTGCCCGac/ac	1/6	1	2	FACETS	0.705	0.609	0.809	0.705	0.609	0.809	SUBCLONAL	1	TRUE	1	0.435892863391853	2		358	384	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523485	106523485	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	69	433	0	ENST00000359195.3:c.2637C>G	p.Ile879Met	p.I879M	ENST00000359195	NM_002649.2	879	atC/atG	8/11	1	2	FACETS	0.78	0.682	0.884	0.78	0.682	0.884	SUBCLONAL	1	TRUE	1	0.435892863391853	2		433	406	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891271	101891271	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	104	735	0	ENST00000374994.4:c.232A>T	p.Ile78Phe	p.I78F	ENST00000374994	NM_004612.2	78	Att/Ttt	2/9	1	2	FACETS	0.782	0.702	0.867	0.782	0.702	0.867	SUBCLONAL	1	TRUE	1	0.435892863391853	2		735	610	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	247	588	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.984	0.927	1	0.984	0.927	1	CLONAL	1	TRUE	1	0.814905961370047	2		588	616	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0018953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	230	684	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	0.814905961370047	4	FACETS	1	0.935	1	0.334	0.311	0.358	CLONAL	1	TRUE	1	0.814905961370047	4		684	1022	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880257	37880257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	337	801	0	ENST00000269571.5:c.2301C>G	p.Ile767Met	p.I767M	ENST00000269571		767	atC/atG	19/27	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.814905961370047	2		801	823	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519934	NA	P-0018953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	238	623	0	ENST00000263967.3:c.333G>C	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaC	2/21	0.814905961370047	4	FACETS	1	0.969	1	0.354	0.33	0.379	CLONAL	1	TRUE	1	0.814905961370047	4		623	998	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832751	3832751	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	180	555	0	ENST00000262367.5:c.1507C>T	p.Gln503Ter	p.Q503*	ENST00000262367	NM_004380.2	503	Cag/Tag	6/31	1	2	FACETS	0.817	0.758	0.876	0.817	0.758	0.876	CLONAL	1	TRUE	1	0.814905961370047	2		555	541	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508682	106508682	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760803722	NA	P-0018953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	368	759	0	ENST00000359195.3:c.676C>T	p.Arg226Cys	p.R226C	ENST00000359195	NM_002649.2	226	Cgc/Tgc	2/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.814905961370047	2		759	859	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944636	38944636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746712836	NA	P-0018953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	186	585	2	ENST00000357387.3:c.4825C>T	p.Arg1609Cys	p.R1609C	ENST00000357387	NM_152756.3	1609	Cgt/Tgt	36/38	1	2	FACETS	0.844	0.785	0.904	0.844	0.785	0.904	CLONAL	1	TRUE	1	0.814905961370047	2		587	541	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519220	187519220	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	322	866	0	ENST00000441802.2:c.12163C>T	p.Pro4055Ser	p.P4055S	ENST00000441802	NM_005245.3	4055	Ccg/Tcg	23/27	1	2	FACETS	0.949	0.9	0.998	0.949	0.9	0.998	CLONAL	1	TRUE	1	0.814905961370047	2		866	833	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076826	72076826	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	167	454	0	ENST00000357731.5:c.671C>A	p.Ala224Asp	p.A224D	ENST00000357731	NM_173808.2	224	gCt/gAt	5/7	1	2	FACETS	0.872	0.808	0.937	0.872	0.808	0.937	CLONAL	1	TRUE	1	0.814905961370047	2		454	470	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306609	163306609	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	202	587	1	ENST00000271452.3:c.406G>A	p.Glu136Lys	p.E136K	ENST00000271452	NM_145697.2	136	Gaa/Aaa	6/14	0.802572830025347	3	FACETS	1	0.964	1	0.526	0.49	0.564	CLONAL	1	TRUE	1	0.814905961370047	3		588	663	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945006	31945006	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	234	821	0	ENST00000340398.3:c.95C>G	p.Ser32Cys	p.S32C	ENST00000340398	NM_001013699.2	32	tCt/tGt	1/1	0.706448490486701	1	FACETS	0.574	0.539	0.609	0.574	0.539	0.609	SUBCLONAL	1	TRUE	0	0.814905961370047	1		821	593	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425503	49425503	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555187758	NA	P-0018953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	210	736	1	ENST00000301067.7:c.12985C>T	p.Gln4329Ter	p.Q4329*	ENST00000301067	NM_003482.3	4329	Cag/Tag	39/54	0.58227261416603	3	FACETS	0.77	0.715	0.827	0.385	0.357	0.414	SUBCLONAL	1	TRUE	1	0.814905961370047	3		737	942	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427647	49427647	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0018953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	310	475	0	ENST00000301067.7:c.10841C>G	p.Ser3614Ter	p.S3614*	ENST00000301067	NM_003482.3	3614	tCa/tGa	39/54	0.58227261416603	3	FACETS	0.884	0.842	0.925	0.884	0.842	0.925	CLONAL	2	TRUE	1	0.814905961370047	3		475	606	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440512	49440512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1236	86	942	2	ENST00000301067.7:c.4298G>A	p.Cys1433Tyr	p.C1433Y	ENST00000301067	NM_003482.3	1433	tGt/tAt	15/54	0.58227261416603	3	FACETS	0.225	0.198	0.254	0.112	0.099	0.127	SUBCLONAL	1	TRUE	1	0.814905961370047	3		944	1322	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906424	32906424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs276174902	NA	P-0018953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	1432	616	1	ENST00000380152.3:c.809C>T	p.Ser270Leu	p.S270L	ENST00000380152		270	tCa/tTa	10/27	0.814905961370047	10	FACETS	1	0.991	1			1	CLONAL	7	TRUE	NA	0.814905961370047	10		617	2108	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562303	95562303	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1372597986	NA	P-0018953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	227	603	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	0.814905961370047	2		603	539	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562918	95562918	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	181	585	0	ENST00000393063.1:c.4339C>T	p.Gln1447Ter	p.Q1447*	ENST00000393063	NM_030621.3	1447	Cag/Tag	24/28	1	2	FACETS	0.864	0.804	0.926	0.864	0.804	0.926	CLONAL	1	TRUE	1	0.814905961370047	2		585	514	SUCCESS
BLM	641	MSKCC	GRCh37	15	91326125	91326125	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	235	645	0	ENST00000355112.3:c.2629G>A	p.Asp877Asn	p.D877N	ENST00000355112	NM_000057.2	877	Gat/Aat	13/22	0.802572830025347	3	FACETS	0.934	0.873	0.997	0.467	0.436	0.499	CLONAL	1	TRUE	1	0.814905961370047	3		645	869	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883621	37883621	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	368	871	0	ENST00000269571.5:c.3233C>A	p.Ser1078Tyr	p.S1078Y	ENST00000269571		1078	tCc/tAc	26/27	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.814905961370047	2		871	881	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288096	21288096	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753427288	NA	P-0018953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	212	588	1	ENST00000354336.3:c.341C>T	p.Ser114Leu	p.S114L	ENST00000354336	NM_005207.3	114	tCa/tTa	2/3	1	2	FACETS	0.863	0.807	0.92	0.863	0.807	0.92	CLONAL	1	TRUE	1	0.814905961370047	2		589	603	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923761	131923761	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0018953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	183	658	0	ENST00000265335.6:c.1031C>G	p.Ser344Ter	p.S344*	ENST00000265335		344	tCa/tGa	7/25	1	2	FACETS	0.926	0.863	0.991	0.926	0.863	0.991	CLONAL	1	TRUE	1	0.814905961370047	2		658	485	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924441	131924441	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	178	659	3	ENST00000265335.6:c.1114C>A	p.Gln372Lys	p.Q372K	ENST00000265335		372	Cag/Aag	8/25	1	2	FACETS	0.821	0.762	0.881	0.821	0.762	0.881	CLONAL	1	TRUE	1	0.814905961370047	2		662	532	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522590	176522590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765924274	NA	P-0018953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	363	836	2	ENST00000292408.4:c.1687C>T	p.Arg563Trp	p.R563W	ENST00000292408	NM_213647.1	563	Cgg/Tgg	13/18	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.814905961370047	2		838	836	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254192	133254192	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500835	NA	P-0018955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	110	695	1	ENST00000320574.5:c.692G>A	p.Arg231His	p.R231H	ENST00000320574	NM_006231.2	231	cGc/cAc	7/49	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.265267902191453	2		696	710	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40476776	40476776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765182656	NA	P-0018955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	166	896	0	ENST00000264657.5:c.1553G>A	p.Arg518Gln	p.R518Q	ENST00000264657	NM_139276.2	518	cGa/cAa	17/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.265267902191453	2		896	963	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851406	156851406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	135	961	0	ENST00000524377.1:c.2363C>T	p.Pro788Leu	p.P788L	ENST00000524377	NM_002529.3	788	cCt/cTt	17/17	0.265267902191453	3	FACETS	1	0.975	1	0.607	0.551	0.666	CLONAL	1	TRUE	1	0.265267902191453	3		961	950	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653808	89653808	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs786204854	NA	P-0018955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	56	634	1	ENST00000371953.3:c.106G>T	p.Gly36Ter	p.G36*	ENST00000371953	NM_000314.4	36	Gga/Tga	2/9	0.265267902191453	1	FACETS	0.688	0.59	0.796	0.688	0.59	0.796	SUBCLONAL	1	TRUE	0	0.265267902191453	1		635	532	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42870093	42870093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	145	901	0	ENST00000398585.3:c.79del	p.Leu27TyrfsTer14	p.L27Yfs*14	ENST00000398585	NM_001135099.1	27	Cta/ta	2/14	0.218834988810165	3	FACETS	1	0.975	1	0.596	0.543	0.652	CLONAL	1	TRUE	1	0.265267902191453	3		901	1039	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778100	27778100	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	50	699	1	ENST00000369163.2:c.249G>T	p.Leu83Phe	p.L83F	ENST00000369163	NM_003536.2	83	ttG/ttT	1/1	0.218834988810165	3	FACETS	0.615	0.521	0.719	0.308	0.26	0.36	SUBCLONAL	1	TRUE	1	0.265267902191453	3		700	694	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576868	7576868	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	166	695	0	ENST00000269305.4:c.978del	p.Glu326AspfsTer19	p.E326Dfs*19	ENST00000269305	NM_001126112.2	326	gaA/ga	9/11	0.285650315917244	2	FACETS	0.893	0.823	0.965	0.893	0.823	0.965	CLONAL	2	TRUE	0	0.285650315917244	2		695	651	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073667	8073667	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	49	439	1	ENST00000377482.5:c.992G>T	p.Arg331Leu	p.R331L	ENST00000377482	NM_018948.3	331	cGc/cTc	4/4	0.285650315917244	5	FACETS	0.775	0.656	0.907	0.258	0.218	0.303	CLONAL	1	TRUE	2	0.285650315917244	5		440	632	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828208	72828220	+	frameshift_variant	Frame_Shift_Del	DEL	GGTTTTACTCACA	GGTTTTACTCACA	-	novel	NA	P-0018956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	160	881	1	ENST00000268489.5:c.8361_8373del	p.Val2788TrpfsTer9	p.V2788Wfs*9	ENST00000268489	NM_006885.3	2787	ccTGTGAGTAAAACC/cc	9/10	0.285650315917244	2	FACETS	0.83	0.763	0.899	0.83	0.763	0.899	CLONAL	2	TRUE	0	0.285650315917244	2		882	675	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715335	61715335	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	117	979	0	ENST00000401558.2:c.2278T>C	p.Ser760Pro	p.S760P	ENST00000401558	NM_003400.3	760	Tct/Cct	19/25	0.285650315917244	3	FACETS	0.996	0.897	1	0.498	0.448	0.551	CLONAL	1	TRUE	1	0.285650315917244	3		979	940	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393220	393220	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	182	655	0	ENST00000380956.4:c.68A>T	p.Lys23Met	p.K23M	ENST00000380956	NM_001195286.1	23	aAg/aTg	2/9	0.285650315917244	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.285650315917244	4		655	703	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376719	8376719	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	73	618	0	ENST00000356435.5:c.4394G>T	p.Cys1465Phe	p.C1465F	ENST00000356435		1465	tGt/tTt	27/35	0.285650315917244	7	FACETS	0.902	0.787	1	0.226	0.196	0.257	CLONAL	1	TRUE	3	0.285650315917244	7		618	971	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0018958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	1271	629	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.584706107471863	9	FACETS	1	0.997	1			1	CLONAL	9	TRUE	NA	0.584706107471863	9		630	1431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs863224499	NA	P-0018958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	535	963	1	ENST00000269305.4:c.672+1G>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			NA	2	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.584706107471863	2		964	874	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111553	8111554	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	374	625	0	ENST00000346208.3:c.1041dup	p.His348SerfsTer4	p.H348Sfs*4	ENST00000346208		347	ctt/cTtt	5/6	0.316647229029986	5	FACETS	1	0.992	1	0.809	0.769	0.848	INDETERMINATE	2	TRUE	2	0.584706107471863	5		625	990	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123575	108123575	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs747242300	NA	P-0018958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	184	533	1	ENST00000278616.4:c.1834C>A	p.Leu612Ile	p.L612I	ENST00000278616	NM_000051.3	612	Ctt/Att	12/63	0.584706107471863	3	FACETS	1	0.929	1	0.503	0.465	0.542	CLONAL	1	TRUE	1	0.584706107471863	3		534	809	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173738	108173738	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	146	514	1	ENST00000278616.4:c.5478A>T	p.Leu1826Phe	p.L1826F	ENST00000278616	NM_000051.3	1826	ttA/ttT	36/63	0.584706107471863	3	FACETS	1	0.964	1	0.548	0.502	0.596	CLONAL	1	TRUE	1	0.584706107471863	3		515	589	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016565	12016565	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	241	396	0	ENST00000353533.5:c.701A>G	p.Asn234Ser	p.N234S	ENST00000353533	NM_003010.3	234	aAt/aGt	7/11	0.584706107471863	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.584706107471863	2		396	334	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227117	2227117	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	181	639	1	ENST00000398665.3:c.4597A>T	p.Thr1533Ser	p.T1533S	ENST00000398665	NM_032482.2	1533	Aca/Tca	27/28	0.584706107471863	3	FACETS	1	0.971	1	0.55	0.509	0.593	CLONAL	1	TRUE	1	0.584706107471863	3		640	727	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1331474	1331474	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	111	798	1	ENST00000400841.2:c.54G>A	p.Trp18Ter	p.W18*	ENST00000400841		18	tgG/tgA	1/6	0.417146347355705	4	FACETS	0.559	0.501	0.62			1	SUBCLONAL	1	TRUE	NA	0.584706107471863	4		799	1077	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0018959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	288	1014	3	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.336110211285069	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.34157644033122	2		1017	772	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120173	70120173	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	193	464	1	ENST00000245479.2:c.1177del	p.Gln393SerfsTer10	p.Q393Sfs*10	ENST00000245479	NM_000346.3	392	tCc/tc	3/3	0.336110211285069	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.34157644033122	2		465	480	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0018959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	62	376	1	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	1	2	FACETS	0.926	0.803	1	0.926	0.803	1	CLONAL	1	TRUE	1	0.34157644033122	2		377	392	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918553	94918553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	132	691	1	ENST00000536441.1:c.629G>A	p.Ser210Asn	p.S210N	ENST00000536441	NM_144665.3	210	aGt/aAt	5/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.34157644033122	2		692	703	SUCCESS
APC	324	MSKCC	GRCh37	5	112174266	112174267	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	89	493	0	ENST00000257430.4:c.2976dup	p.Lys993Ter	p.K993*	ENST00000257430	NM_000038.5	992	agt/agTt	16/16	1	2	FACETS	0.863	0.766	0.966	0.863	0.766	0.966	CLONAL	1	TRUE	1	0.34157644033122	2		493	604	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	101	364	1				ENST00000310581	NM_198253.2	-/1132			0.320712426454864	2	FACETS	0.797	0.718	0.88	0.797	0.718	0.88	SUBCLONAL	2	TRUE	0	0.320712426454864	2		365	395	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735470	40735470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761910971	NA	P-0018961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	288	1046	1	ENST00000373198.4:c.3403G>A	p.Val1135Met	p.V1135M	ENST00000373198	NM_133170.3	1135	Gtg/Atg	25/32	0.320712426454864	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.320712426454864	3		1047	969	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916759	48916759	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	105	674	1	ENST00000267163.4:c.289G>T	p.Glu97Ter	p.E97*	ENST00000267163	NM_000321.2	97	Gaa/Taa	3/27	0.320712426454864	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.320712426454864	1		675	478	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0018961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	243	1048	1	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.320712426454864	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.320712426454864	1		1049	965	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564739	86564740	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs797044451	NA	P-0018961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	178	773	0	ENST00000274376.6:c.475_476del	p.Leu159GlyfsTer20	p.L159Gfs*20	ENST00000274376	NM_002890.2	157	gaCTct/gact	1/25	0.320712426454864	2	FACETS	0.884	0.818	0.951	0.884	0.818	0.951	CLONAL	2	TRUE	0	0.320712426454864	2		773	628	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056469	26056469	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	90	318	0	ENST00000343677.2:c.188A>G	p.Lys63Arg	p.K63R	ENST00000343677	NM_005319.3	63	aAa/aGa	1/1	0.288907421196172	3	FACETS	0.892	0.798	0.991	0.892	0.798	0.991	CLONAL	2	TRUE	1	0.320712426454864	3		318	365	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673220	30673220	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	63	377	0	ENST00000376406.3:c.3740C>T	p.Ala1247Val	p.A1247V	ENST00000376406	NM_014641.2	1247	gCc/gTc	10/15	1	2	FACETS	0.897	0.778	1	0.897	0.778	1	CLONAL	1	TRUE	1	0.320712426454864	2		377	438	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0018962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	218	708	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.282296055953633	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.282296055953633	4		709	858	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579355	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519997	NA	P-0018962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	232	793	0	ENST00000269305.4:c.332T>G	p.Leu111Arg	p.L111R	ENST00000269305	NM_001126112.2	111	cTg/cGg	4/11	0.231107196312556	3	FACETS	1	0.986	1	0.793	0.742	0.846	CLONAL	2	TRUE	0	0.282296055953633	3		793	788	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027074	48027086	+	frameshift_variant	Frame_Shift_Del	DEL	TTGGGGTGATGTT	TTGGGGTGATGTT	-	novel	NA	P-0018962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	81	536	0	ENST00000234420.5:c.1952_1964del	p.Ile651AsnfsTer8	p.I651Nfs*8	ENST00000234420	NM_000179.2	651	aTTGGGGTGATGTTa/aa	4/10	0.221834263919179	4	FACETS	1	0.977	1	0.742	0.655	0.834	CLONAL	1	TRUE	2	0.282296055953633	4		536	496	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867457	35867457	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	90	612	0	ENST00000303115.3:c.271A>G	p.Ile91Val	p.I91V	ENST00000303115	NM_002185.3	91	Ata/Gta	3/8	0.254292667895117	4	FACETS	1	0.965	1	0.609	0.541	0.682	CLONAL	1	TRUE	2	0.282296055953633	4		612	671	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974676	21974676	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0018962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	80	650	1	ENST00000304494.5:c.150+1G>A		p.X50_splice	ENST00000304494	NM_000077.4	50			0.282296055953633	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.282296055953633	1		651	410	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0018963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	161	629	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.282620212648278	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.3057414162871	2		630	506	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992390	72992390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1583	132	1373	1	ENST00000268489.5:c.1655C>T	p.Ser552Phe	p.S552F	ENST00000268489	NM_006885.3	552	tCt/tTt	2/10	1	2	FACETS	0.398	0.36	0.439	0.398	0.36	0.439	SUBCLONAL	1	TRUE	1	0.386743572499247	2		1374	1715	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668757	52668757	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	34	559	0	ENST00000394830.3:c.1162C>T	p.Gln388Ter	p.Q388*	ENST00000394830	NM_018313.4	388	Cag/Tag	12/30	1	2	FACETS	0.284	0.231	0.343	0.284	0.231	0.343	SUBCLONAL	1	TRUE	1	0.386743572499247	2		559	620	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201021	108201022	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	46	469	0	ENST00000278616.4:c.7389dup	p.Cys2464MetfsTer2	p.C2464Mfs*2	ENST00000278616	NM_000051.3	2463	tta/ttAa	50/63	1	2	FACETS	0.403	0.339	0.474	0.403	0.339	0.474	SUBCLONAL	1	TRUE	1	0.386743572499247	2		469	590	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214658	5214658	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1794	135	1711	2	ENST00000357368.4:c.4408G>C	p.Glu1470Gln	p.E1470Q	ENST00000357368	NM_002850.3	1470	Gag/Cag	29/38	1	2	FACETS	0.362	0.327	0.399	0.362	0.327	0.399	SUBCLONAL	1	TRUE	1	0.386743572499247	2		1713	1929	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602494	10602494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1239	126	1092	3	ENST00000171111.5:c.1084C>T	p.Arg362Trp	p.R362W	ENST00000171111	NM_203500.1	362	Cgg/Tgg	3/6	1	2	FACETS	0.477	0.431	0.527	0.477	0.431	0.527	SUBCLONAL	1	TRUE	1	0.386743572499247	2		1095	1365	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135804201	135804201	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	66	752	1	ENST00000298552.3:c.59G>T	p.Gly20Val	p.G20V	ENST00000298552	NM_001162426.1	20	gGt/gTt	3/23	1	2	FACETS	0.402	0.348	0.461	0.402	0.348	0.461	SUBCLONAL	1	TRUE	1	0.386743572499247	2		753	849	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938505	76938505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	24	243	0	ENST00000373344.5:c.2243C>T	p.Ser748Phe	p.S748F	ENST00000373344	NM_000489.3	748	tCt/tTt	9/35	1	1	FACETS	0.419	0.329	0.521	0.419	0.329	0.521	SUBCLONAL	1	TRUE	0	0.386743572499247	1		243	239	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0018967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	192	1181	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.261227163108652	2	FACETS	0.784	0.726	0.844	0.784	0.726	0.844	SUBCLONAL	2	TRUE	0	0.275191287269022	2		1182	890	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775720	9775720	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	99	1541	0	ENST00000377346.4:c.263G>T	p.Arg88Leu	p.R88L	ENST00000377346	NM_005026.3	88	cGt/cTt	4/24	0.14838085160281	0	FACETS	0.569	0.507	0.636			1	INDETERMINATE	1	TRUE	0	0.275191287269022	0		1541	916	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779065	3779065	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1371453440	NA	P-0018967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	68	1064	0	ENST00000262367.5:c.5983A>G	p.Met1995Val	p.M1995V	ENST00000262367	NM_004380.2	1995	Atg/Gtg	31/31	1	2	FACETS	0.899	0.783	1	0.899	0.783	1	CLONAL	1	TRUE	1	0.275191287269022	2		1064	550	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553530	29553530	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	111	1104	0	ENST00000356175.3:c.2079G>T	p.Met693Ile	p.M693I	ENST00000356175	NM_000267.3	693	atG/atT	18/57	1	2	FACETS	0.803	0.72	0.89	0.803	0.72	0.89	CLONAL	1	TRUE	1	0.275191287269022	2		1104	1005	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015035	27015035	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	154	827	0	ENST00000335756.4:c.137G>T	p.Gly46Val	p.G46V	ENST00000335756	NM_001809.3	46	gGt/gTt	2/5	1	2	FACETS	0.797	0.731	0.866	1	0.989	1	SUBCLONAL	2	TRUE	1	0.275191287269022	2		827	702	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440068	220440068	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	128	2050	0	ENST00000243786.2:c.923del	p.Pro308LeufsTer28	p.P308Lfs*28	ENST00000243786	NM_002191.3	307	gtC/gt	2/2	1	2	FACETS	0.892	0.807	0.982	0.892	0.807	0.982	CLONAL	1	TRUE	1	0.275191287269022	2		2050	1043	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55603390	55603390	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1453023259	NA	P-0018967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	78	693	0	ENST00000288135.5:c.2746A>G	p.Thr916Ala	p.T916A	ENST00000288135	NM_000222.2	916	Aca/Gca	20/21	1	2	FACETS	0.873	0.768	0.987	0.873	0.768	0.987	CLONAL	1	TRUE	1	0.275191287269022	2		693	649	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629232	187629232	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	73	807	0	ENST00000441802.2:c.1750G>T	p.Val584Leu	p.V584L	ENST00000441802	NM_005245.3	584	Gtg/Ttg	2/27	1	2	FACETS	0.824	0.72	0.935	0.824	0.72	0.935	CLONAL	1	TRUE	1	0.275191287269022	2		807	644	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953899	131953899	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs756702059	NA	P-0018967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	37	334	0	ENST00000265335.6:c.3302A>T	p.Glu1101Val	p.E1101V	ENST00000265335		1101	gAg/gTg	21/25	0.142362996427911	3	FACETS	0.744	0.614	0.89	0.372	0.307	0.445	INDETERMINATE	1	TRUE	1	0.275191287269022	3		334	411	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426427	47426427	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1175260065	NA	P-0018967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	70	1175	2	ENST00000377045.4:c.770G>T	p.Ser257Ile	p.S257I	ENST00000377045	NM_001654.4	257	aGc/aTc	9/16	1	2	FACETS	0.666	0.58	0.759	0.666	0.58	0.759	SUBCLONAL	1	TRUE	1	0.275191287269022	2		1177	764	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0018968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1191	167	752	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.55	0.504	0.598	0.55	0.504	0.598	SUBCLONAL	1	TRUE	1	0.447370899834921	2		754	1358	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0018968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	48	900	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.389	0.328	0.455	0.389	0.328	0.455	SUBCLONAL	1	TRUE	1	0.447370899834921	2		901	552	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0018968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	61	848	1	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.565	0.488	0.648	0.565	0.488	0.648	SUBCLONAL	1	TRUE	1	0.447370899834921	2		849	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0018968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	68	1355	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	1	2	FACETS	0.234	0.202	0.268	0.234	0.202	0.268	SUBCLONAL	1	TRUE	1	0.447370899834921	2		1355	1300	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101099	27101099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1739	130	1968	3	ENST00000324856.7:c.4381C>T	p.Arg1461Ter	p.R1461*	ENST00000324856	NM_006015.4	1461	Cga/Tga	18/20	1	2	FACETS	0.311	0.28	0.343	0.311	0.28	0.343	SUBCLONAL	1	TRUE	1	0.447370899834921	2		1971	1869	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152038	55152038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370600501	NA	P-0018968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	101	1038	1	ENST00000257290.5:c.2470G>A	p.Val824Ile	p.V824I	ENST00000257290	NM_006206.4	824	Gtc/Atc	18/23	1	2	FACETS	0.471	0.42	0.526	0.471	0.42	0.526	SUBCLONAL	1	TRUE	1	0.447370899834921	2		1039	958	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948208	71948209	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs749079348	NA	P-0018968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2272	252	2631	8	ENST00000298229.2:c.2927dup	p.Pro977ThrfsTer7	p.P977Tfs*7	ENST00000298229	NM_001567.3	974	gcc/gCcc	26/28	1	2	FACETS	0.446	0.415	0.479	0.446	0.415	0.479	SUBCLONAL	1	TRUE	1	0.447370899834921	2		2639	2524	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099225	4099225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200371894	NA	P-0018968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1387	142	1479	1	ENST00000262948.5:c.893C>T	p.Pro298Leu	p.P298L	ENST00000262948	NM_030662.3	298	cCg/cTg	7/11	1	2	FACETS	0.415	0.377	0.456	0.415	0.377	0.456	SUBCLONAL	1	TRUE	1	0.447370899834921	2		1480	1529	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137325963	137325963	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1006838045	NA	P-0018968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	126	1410	5	ENST00000481739.1:c.1151C>T	p.Ser384Leu	p.S384L	ENST00000481739	NM_002957.4	384	tCg/tTg	9/10	1	2	FACETS	0.441	0.398	0.487	0.441	0.398	0.487	SUBCLONAL	1	TRUE	1	0.447370899834921	2		1415	1276	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060983	38060983	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	32	867	0	ENST00000250448.2:c.1006G>T	p.Asp336Tyr	p.D336Y	ENST00000250448	NM_004496.3	336	Gac/Tac	2/2	1	2	FACETS	0.508	0.411	0.616	0.508	0.411	0.616	SUBCLONAL	1	FALSE	1	0.270584040138785	2		867	466	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130180	143130180	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0018969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	30	557	0	ENST00000262992.4:c.837-1G>C		p.X279_splice	ENST00000262992	NM_001101669.1	279			0.253125158661828	3	FACETS	0.659	0.531	0.804	0.33	0.265	0.402	SUBCLONAL	1	FALSE	1	0.270584040138785	3		557	382	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139563068	139563068	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374275228	NA	P-0018969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	33	1876	3	ENST00000308874.7:c.140G>A	p.Arg47His	p.R47H	ENST00000308874		47	cGt/cAt	4/10	0.270584040138785	1	FACETS	0.357	0.29	0.433	0.357	0.29	0.433	SUBCLONAL	1	FALSE	0	0.270584040138785	1		1879	591	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	849	364	1				ENST00000310581	NM_198253.2	-/1132			0.318068725253575	8	FACETS	1	0.989	1	1	0.989	1	CLONAL	6	FALSE	2	0.318068725253575	8		365	1676	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782620	NA	P-0018970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1378	452	1068	2	ENST00000269305.4:c.427G>A	p.Val143Met	p.V143M	ENST00000269305	NM_001126112.2	143	Gtg/Atg	5/11	0.189861703394123	3	FACETS	0.9	0.857	0.944	0.9	0.857	0.944	INDETERMINATE	2	FALSE	1	0.318068725253575	3		1070	1830	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257557	16257557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	93	671	0	ENST00000375759.3:c.4822G>A	p.Glu1608Lys	p.E1608K	ENST00000375759	NM_015001.2	1608	Gag/Aag	11/15	1	2	FACETS	0.883	0.786	0.987	0.883	0.786	0.987	CLONAL	1	FALSE	1	0.318068725253575	2		671	662	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46740253	46740253	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	69	467	2	ENST00000371975.4:c.1733G>T	p.Cys578Phe	p.C578F	ENST00000371975	NM_003579.3	578	tGt/tTt	16/18	0.302570288498352	4	FACETS	0.629	0.546	0.719			1	SUBCLONAL	1	FALSE	NA	0.318068725253575	4		469	909	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458521	120458521	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	88	534	0	ENST00000256646.2:c.6824C>T	p.Ala2275Val	p.A2275V	ENST00000256646	NM_024408.3	2275	gCt/gTt	34/34	0.187893813417837	4	FACETS	0.612	0.541	0.69	0.306	0.27	0.345	INDETERMINATE	1	FALSE	2	0.318068725253575	4		534	1191	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163315571	163315571	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	46	285	0	ENST00000271452.3:c.911C>T	p.Ser304Leu	p.S304L	ENST00000271452	NM_145697.2	304	tCa/tTa	11/14	0.318068725253575	11	FACETS	0.944	0.793	1			1	CLONAL	1	FALSE	NA	0.318068725253575	11		285	745	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226564942	226564942	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1314689313	NA	P-0018970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	101	605	0	ENST00000366794.5:c.1808A>G	p.Gln603Arg	p.Q603R	ENST00000366794	NM_001618.3	603	cAg/cGg	13/23	0.318068725253575	3	FACETS	0.731	0.652	0.815	0.365	0.326	0.408	SUBCLONAL	1	FALSE	1	0.318068725253575	3		605	1007	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050894	49050895	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0018970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	153	686	0	ENST00000267163.4:c.2580_2581del	p.Arg861LysfsTer3	p.R861Kfs*3	ENST00000267163	NM_000321.2	860	AAa/a	25/27	0.300403117191091	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	0	0.318068725253575	1		686	748	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40490749	40490749	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	34	425	1	ENST00000264657.5:c.550G>A	p.Asp184Asn	p.D184N	ENST00000264657	NM_139276.2	184	Gac/Aac	6/24	0.318068725253575	3	FACETS	0.607	0.496	0.732	0.304	0.248	0.366	SUBCLONAL	1	FALSE	1	0.318068725253575	3		426	408	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251556	10251556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	120	558	0	ENST00000340748.4:c.3376G>A	p.Glu1126Lys	p.E1126K	ENST00000340748		1126	Gag/Aag	31/40	0.318068725253575	3	FACETS	0.895	0.807	0.988	0.448	0.403	0.494	CLONAL	1	FALSE	1	0.318068725253575	3		558	977	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273877	18273877	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1336	138	773	0	ENST00000222254.8:c.1210C>T	p.His404Tyr	p.H404Y	ENST00000222254	NM_005027.3	404	Cac/Tac	10/16	0.318068725253575	3	FACETS	0.682	0.619	0.75	0.341	0.309	0.375	SUBCLONAL	1	FALSE	1	0.318068725253575	3		773	1474	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753501	42753501	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771103636	NA	P-0018970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1702	101	765	0	ENST00000222329.4:c.763G>A	p.Gly255Ser	p.G255S	ENST00000222329	NM_006494.2	255	Ggt/Agt	4/4	0.318068725253575	4	FACETS	0.464	0.413	0.52			1	SUBCLONAL	1	FALSE	NA	0.318068725253575	4		765	1803	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574307	41574307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370216095	NA	P-0018970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1171	164	801	0	ENST00000263253.7:c.6592G>A	p.Gly2198Arg	p.G2198R	ENST00000263253	NM_001429.3	2198	Ggg/Agg	31/31	0.318068725253575	3	FACETS	0.895	0.82	0.975	0.448	0.41	0.488	CLONAL	1	FALSE	1	0.318068725253575	3		801	1335	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217163	66217163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	97	637	0	ENST00000273854.3:c.2452G>A	p.Asp818Asn	p.D818N	ENST00000273854	NM_004439.5	818	Gac/Aac	14/18	0.295652916509294	3	FACETS	0.777	0.691	0.868	0.388	0.345	0.434	SUBCLONAL	1	FALSE	1	0.318068725253575	3		637	910	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235278	235278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1448	104	395	0	ENST00000264932.6:c.1084G>A	p.Asp362Asn	p.D362N	ENST00000264932	NM_004168.2	362	Gat/Aat	9/15	0.318068725253575	8	FACETS	0.823	0.734	0.919	0.137	0.122	0.154	CLONAL	1	FALSE	2	0.318068725253575	8		395	1552	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562555	176562555	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	156	645	0	ENST00000439151.2:c.451C>G	p.Leu151Val	p.L151V	ENST00000439151	NM_022455.4	151	Ctg/Gtg	2/23	0.318068725253575	3	FACETS	1	0.981	1	0.623	0.57	0.678	CLONAL	1	FALSE	1	0.318068725253575	3		645	913	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675175	30675175	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1292425270	NA	P-0018970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	122	644	0	ENST00000376406.3:c.3070G>T	p.Glu1024Ter	p.E1024*	ENST00000376406	NM_014641.2	1024	Gag/Tag	9/15	0.318068725253575	6	FACETS	1	0.923	1			1	CLONAL	1	FALSE	NA	0.318068725253575	6		644	1222	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31939817	31939817	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1223885755	NA	P-0018970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2147	156	987	0	ENST00000375333.2:c.44G>A	p.Arg15Gln	p.R15Q	ENST00000375333	NM_032454.1	15	cGa/cAa	1/8	0.318068725253575	4	FACETS	0.561	0.511	0.614	0.281	0.255	0.307	SUBCLONAL	1	FALSE	2	0.318068725253575	4		987	2303	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652031	36652031	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1295	239	857	0	ENST00000244741.5:c.153C>A	p.Phe51Leu	p.F51L	ENST00000244741	NM_000389.4	51	ttC/ttA	2/3	0.189861703394123	3	FACETS	1	0.98	1	0.568	0.528	0.609	INDETERMINATE	1	FALSE	1	0.318068725253575	3		857	1534	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864237	117864237	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	62	441	2	ENST00000297338.2:c.1420C>T	p.Gln474Ter	p.Q474*	ENST00000297338	NM_006265.2	474	Cag/Tag	11/14	0.295652916509294	3	FACETS	0.701	0.605	0.805	0.35	0.302	0.403	SUBCLONAL	1	FALSE	1	0.318068725253575	3		443	645	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044473	5044473	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	64	630	0	ENST00000381652.3:c.421G>A	p.Glu141Lys	p.E141K	ENST00000381652	NM_004972.3	141	Gaa/Aaa	5/25	0.187893813417837	4	FACETS	0.677	0.585	0.778	0.339	0.292	0.389	INDETERMINATE	1	FALSE	2	0.318068725253575	4		630	783	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409801	139409801	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758837712	NA	P-0018970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1347	198	860	1	ENST00000277541.6:c.1955C>T	p.Ser652Leu	p.S652L	ENST00000277541	NM_017617.3	652	tCg/tTg	12/34	1	2	FACETS	0.806	0.744	0.871	0.806	0.744	0.871	CLONAL	1	FALSE	1	0.318068725253575	2		861	1545	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879874	44879874	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	51	273	0	ENST00000377967.4:c.463G>T	p.Glu155Ter	p.E155*	ENST00000377967	NM_021140.2	155	Gag/Tag	6/29	0.196456123889216	2	FACETS	1	0.953	1			1	CLONAL	1	FALSE	NA	0.318068725253575	2		273	249	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179194	123179194	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	118	239	0	ENST00000218089.9:c.643T>A	p.Phe215Ile	p.F215I	ENST00000218089	NM_001042749.1	215	Ttt/Att	8/35	0.302570288498352	2	FACETS	1	0.963	1			1	CLONAL	2	FALSE	NA	0.318068725253575	2		239	337	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018970-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	477	364	1				ENST00000310581	NM_198253.2	-/1132			0.39923750985127	6	FACETS	0.946	0.91	0.981	0.946	0.91	0.981	CLONAL	5	TRUE	1	0.39923750985127	6		365	909	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782620	NA	P-0018970-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	306	1068	2	ENST00000269305.4:c.427G>A	p.Val143Met	p.V143M	ENST00000269305	NM_001126112.2	143	Gtg/Atg	5/11	0.159570851574713	2	FACETS	1	0.99	1	0.616	0.58	0.653	INDETERMINATE	1	TRUE	0	0.39923750985127	2		1070	1245	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257557	16257557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018970-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	121	671	0	ENST00000375759.3:c.4822G>A	p.Glu1608Lys	p.E1608K	ENST00000375759	NM_015001.2	1608	Gag/Aag	11/15	0.147736985592255	1	FACETS	0.693	0.627	0.763	0.693	0.627	0.763	INDETERMINATE	1	TRUE	0	0.39923750985127	1		671	700	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46740253	46740253	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018970-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	61	467	2	ENST00000371975.4:c.1733G>T	p.Cys578Phe	p.C578F	ENST00000371975	NM_003579.3	578	tGt/tTt	16/18	0.358969323569149	3	FACETS	0.575	0.495	0.661	0.287	0.247	0.331	SUBCLONAL	1	TRUE	1	0.39923750985127	3		469	638	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458521	120458521	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018970-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	81	534	0	ENST00000256646.2:c.6824C>T	p.Ala2275Val	p.A2275V	ENST00000256646	NM_024408.3	2275	gCt/gTt	34/34	0.358969323569149	3	FACETS	0.715	0.63	0.806	0.357	0.315	0.403	SUBCLONAL	1	TRUE	1	0.39923750985127	3		534	681	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226564942	226564942	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1314689313	NA	P-0018970-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	104	605	0	ENST00000366794.5:c.1808A>G	p.Gln603Arg	p.Q603R	ENST00000366794	NM_001618.3	603	cAg/cGg	13/23	0.159570851574713	2	FACETS	0.642	0.575	0.714	0.321	0.287	0.357	INDETERMINATE	1	TRUE	0	0.39923750985127	2		605	811	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050894	49050895	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0018970-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	119	686	0	ENST00000267163.4:c.2580_2581del	p.Arg861LysfsTer3	p.R861Kfs*3	ENST00000267163	NM_000321.2	860	AAa/a	25/27	0.358969323569149	3	FACETS	1	0.966	1	0.575	0.52	0.633	CLONAL	1	TRUE	1	0.39923750985127	3		686	622	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40490749	40490749	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018970-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	84	425	1	ENST00000264657.5:c.550G>A	p.Asp184Asn	p.D184N	ENST00000264657	NM_139276.2	184	Gac/Aac	6/24	0.159570851574713	2	FACETS	0.59	0.521	0.664	0.295	0.26	0.332	INDETERMINATE	1	TRUE	0	0.39923750985127	2		426	713	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251556	10251556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018970-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	98	558	0	ENST00000340748.4:c.3376G>A	p.Glu1126Lys	p.E1126K	ENST00000340748		1126	Gag/Aag	31/40	0.159570851574713	2	FACETS	0.68	0.607	0.758	0.34	0.303	0.379	INDETERMINATE	1	TRUE	0	0.39923750985127	2		558	722	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273877	18273877	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018970-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	130	773	0	ENST00000222254.8:c.1210C>T	p.His404Tyr	p.H404Y	ENST00000222254	NM_005027.3	404	Cac/Tac	10/16	0.159570851574713	2	FACETS	0.709	0.642	0.779	0.354	0.321	0.39	INDETERMINATE	1	TRUE	0	0.39923750985127	2		773	919	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753501	42753501	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771103636	NA	P-0018970-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	92	765	0	ENST00000222329.4:c.763G>A	p.Gly255Ser	p.G255S	ENST00000222329	NM_006494.2	255	Ggt/Agt	4/4	0.325751125063072	3	FACETS	0.574	0.508	0.643			1	SUBCLONAL	1	TRUE	NA	0.39923750985127	3		765	964	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574307	41574307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370216095	NA	P-0018970-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	118	801	0	ENST00000263253.7:c.6592G>A	p.Gly2198Arg	p.G2198R	ENST00000263253	NM_001429.3	2198	Ggg/Agg	31/31	0.39923750985127	3	FACETS	0.784	0.707	0.866	0.392	0.353	0.433	SUBCLONAL	1	TRUE	1	0.39923750985127	3		801	904	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217163	66217163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018970-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	104	637	0	ENST00000273854.3:c.2452G>A	p.Asp818Asn	p.D818N	ENST00000273854	NM_004439.5	818	Gac/Aac	14/18	0.147736985592255	1	FACETS	0.546	0.489	0.607	0.546	0.489	0.607	INDETERMINATE	1	TRUE	0	0.39923750985127	1		637	764	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235278	235278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018970-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	101	395	0	ENST00000264932.6:c.1084G>A	p.Asp362Asn	p.D362N	ENST00000264932	NM_004168.2	362	Gat/Aat	9/15	0.39923750985127	6	FACETS	0.941	0.84	1	0.188	0.168	0.21	CLONAL	1	TRUE	1	0.39923750985127	6		395	967	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562555	176562555	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018970-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	276	645	0	ENST00000439151.2:c.451C>G	p.Leu151Val	p.L151V	ENST00000439151	NM_022455.4	151	Ctg/Gtg	2/23	0.39923750985127	3	FACETS	0.901	0.848	0.956	0.901	0.848	0.956	CLONAL	2	TRUE	1	0.39923750985127	3		645	920	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675175	30675175	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1292425270	NA	P-0018970-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	122	644	0	ENST00000376406.3:c.3070G>T	p.Glu1024Ter	p.E1024*	ENST00000376406	NM_014641.2	1024	Gag/Tag	9/15	0.39923750985127	6	FACETS	0.942	0.849	1			1	CLONAL	1	TRUE	NA	0.39923750985127	6		644	1167	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31939817	31939817	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1223885755	NA	P-0018970-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	179	987	0	ENST00000375333.2:c.44G>A	p.Arg15Gln	p.R15Q	ENST00000375333	NM_032454.1	15	cGa/cAa	1/8	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.39923750985127	NA		987	1354	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652031	36652031	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018970-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	134	857	0	ENST00000244741.5:c.153C>A	p.Phe51Leu	p.F51L	ENST00000244741	NM_000389.4	51	ttC/ttA	2/3	0.39923750985127	3	FACETS	0.849	0.771	0.932	0.425	0.385	0.466	CLONAL	1	TRUE	1	0.39923750985127	3		857	948	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864237	117864237	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018970-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	65	441	2	ENST00000297338.2:c.1420C>T	p.Gln474Ter	p.Q474*	ENST00000297338	NM_006265.2	474	Cag/Tag	11/14	0.39923750985127	3	FACETS	0.609	0.528	0.698	0.305	0.264	0.349	SUBCLONAL	1	TRUE	1	0.39923750985127	3		443	641	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044473	5044473	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018970-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	82	630	0	ENST00000381652.3:c.421G>A	p.Glu141Lys	p.E141K	ENST00000381652	NM_004972.3	141	Gaa/Aaa	5/25	0.358969323569149	3	FACETS	0.563	0.496	0.636	0.282	0.248	0.318	SUBCLONAL	1	TRUE	1	0.39923750985127	3		630	875	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409801	139409801	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758837712	NA	P-0018970-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	82	860	1	ENST00000277541.6:c.1955C>T	p.Ser652Leu	p.S652L	ENST00000277541	NM_017617.3	652	tCg/tTg	12/34	1	2	FACETS	0.455	0.4	0.514	0.455	0.4	0.514	SUBCLONAL	1	TRUE	1	0.39923750985127	2		861	903	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879874	44879874	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018970-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	68	273	0	ENST00000377967.4:c.463G>T	p.Glu155Ter	p.E155*	ENST00000377967	NM_021140.2	155	Gag/Tag	6/29	1	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.39923750985127	1		273	235	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179194	123179194	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018970-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	162	239	0	ENST00000218089.9:c.643T>A	p.Phe215Ile	p.F215I	ENST00000218089	NM_001042749.1	215	Ttt/Att	8/35	0.39923750985127	2	FACETS	0.845	0.79	0.901			1	CLONAL	3	TRUE	NA	0.39923750985127	2		239	320	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173667	108173667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018970-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	52	549	1	ENST00000278616.4:c.5407G>A	p.Asp1803Asn	p.D1803N	ENST00000278616	NM_000051.3	1803	Gac/Aac	36/63	0.39923750985127	3	FACETS	0.473	0.402	0.552	0.237	0.201	0.276	SUBCLONAL	1	TRUE	1	0.39923750985127	3		550	660	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898803	134898803	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018970-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	34	405	0	ENST00000398015.3:c.1861A>C	p.Ile621Leu	p.I621L	ENST00000398015	NM_004441.4	621	Att/Ctt	10/16	0.39923750985127	3	FACETS	0.391	0.318	0.472	0.195	0.159	0.236	SUBCLONAL	1	TRUE	1	0.39923750985127	3		405	523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576865	7576865	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	rs879254077	NA	P-0018971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	191	546	2	ENST00000269305.4:c.981T>G	p.Tyr327Ter	p.Y327*	ENST00000269305	NM_001126112.2	327	taT/taG	9/11	0.641987465667494	2	FACETS	0.936	0.884	0.986	0.936	0.884	0.986	CLONAL	2	TRUE	0	0.641987465667494	2		548	318	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455222	29455222	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	90	758	0	ENST00000389048.3:c.2580A>C	p.Arg860Ser	p.R860S	ENST00000389048	NM_004304.4	860	agA/agC	15/29	0.543741298535597	3	FACETS	0.478	0.424	0.536	0.239	0.212	0.268	SUBCLONAL	1	TRUE	1	0.641987465667494	3		758	775	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947162	178947162	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	96	446	0	ENST00000263967.3:c.2598G>T	p.Leu866Phe	p.L866F	ENST00000263967	NM_006218.2	866	ttG/ttT	18/21	1	2	FACETS	0.872	0.784	0.963	0.872	0.784	0.963	CLONAL	1	TRUE	1	0.641987465667494	2		446	343	SUCCESS
APC	324	MSKCC	GRCh37	5	112157646	112157647	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	174	468	0	ENST00000257430.4:c.1369dup	p.Ser457PhefsTer3	p.S457Ffs*3	ENST00000257430	NM_000038.5	456	ctt/cTtt	11/16	0.626630638324233	3	FACETS	1	0.987	1	0.798	0.751	0.844	CLONAL	2	TRUE	0	0.641987465667494	3		468	299	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637110	93637110	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	89	841	2	ENST00000375746.1:c.1160A>G	p.Lys387Arg	p.K387R	ENST00000375746	NM_001174167.1	387	aAg/aGg	9/14	0.32816282849281	2	FACETS	0.455	0.404	0.51	0.228	0.202	0.255	INDETERMINATE	1	TRUE	0	0.641987465667494	2		843	609	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209370	98209370	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	106	796	0	ENST00000331920.6:c.4168G>T	p.Gly1390Trp	p.G1390W	ENST00000331920	NM_000264.3	1390	Ggg/Tgg	23/24	0.32816282849281	2	FACETS	0.579	0.521	0.641	0.29	0.26	0.321	INDETERMINATE	1	TRUE	0	0.641987465667494	2		796	570	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411221	63411222	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0018971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	322	930	0	ENST00000330258.3:c.1945_1946del	p.Lys649AlafsTer57	p.K649Afs*57	ENST00000330258	NM_152424.3	649	AAg/g	2/2	0.353021539587078	3	FACETS	1	0.975	1	0.69	0.658	0.723	INDETERMINATE	2	TRUE	0	0.641987465667494	3		930	640	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594221	55594221	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913512	NA	P-0018973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	269	867	0	ENST00000288135.5:c.1924A>G	p.Lys642Glu	p.K642E	ENST00000288135	NM_000222.2	642	Aaa/Gaa	13/21	0.236949200319242	3	FACETS	0.759	0.714	0.805	0.759	0.714	0.805	INDETERMINATE	2	TRUE	1	0.526652952577345	3		867	850	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0018974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	549	1737	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	1	2	FACETS	0.968	0.931	1	1	0.998	1	CLONAL	5	FALSE	1	0.169479567954359	2		1737	1338	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437657	49437658	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0018974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	185	1381	0	ENST00000301067.7:c.5312_5313del	p.Tyr1771PhefsTer16	p.Y1771Ffs*16	ENST00000301067	NM_003482.3	1771	tAC/t	22/54	0.136357780566573	3	FACETS	1	0.973	1	1	0.994	1	CLONAL	4	FALSE	1	0.169479567954359	3		1381	543	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588751	29588751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760703505	NA	P-0018975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	62	368	2	ENST00000356175.3:c.4537C>T	p.Arg1513Ter	p.R1513*	ENST00000356175	NM_000267.3	1513	Cga/Tga	34/57	0.625577371725833	2	FACETS	0.819	0.733	0.905	0.819	0.733	0.905	CLONAL	2	TRUE	0	0.625577371725833	2		370	121	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271746	15271747	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs773656789	NA	P-0018975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	427	1553	0	ENST00000263388.2:c.6692dup	p.Ala2233GlyfsTer9	p.A2233Gfs*9	ENST00000263388	NM_000435.2	2231	cca/ccCa	33/33	0.507410078349872	5	FACETS	1	0.991	1	0.762	0.728	0.798	CLONAL	2	TRUE	2	0.625577371725833	5		1553	1157	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652819	212652819	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	31	454	0	ENST00000342788.4:c.487T>G	p.Trp163Gly	p.W163G	ENST00000342788	NM_005235.2	163	Tgg/Ggg	4/28	0.625577371725833	3	FACETS	0.873	0.716	1	0.291	0.238	0.349	CLONAL	1	TRUE	0	0.625577371725833	3		454	149	SUCCESS
APC	324	MSKCC	GRCh37	5	112173348	112173348	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	21	288	0	ENST00000257430.4:c.2057A>C	p.Asn686Thr	p.N686T	ENST00000257430	NM_000038.5	686	aAt/aCt	16/16	0.625577371725833	3	FACETS	0.76	0.594	0.947	0.253	0.198	0.316	CLONAL	1	TRUE	0	0.625577371725833	3		288	116	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0018977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	247	521	0	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.536216346966966	2	FACETS	0.845	0.799	0.891	0.845	0.799	0.891	CLONAL	2	TRUE	0	0.569935930703237	2		521	513	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592681	28592681	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	327	956	0	ENST00000241453.7:c.2464G>C	p.Gly822Arg	p.G822R	ENST00000241453	NM_004119.2	822	Ggg/Cgg	20/24	0.511370063983722	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.569935930703237	1		956	700	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041690	42041691	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0018977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	252	765	0	ENST00000219905.7:c.5885_5886del	p.His1962ArgfsTer18	p.H1962Rfs*18	ENST00000219905	NM_001164273.1	1962	cAT/c	17/24	0.522217267345863	2	FACETS	0.965	0.917	1	0.965	0.917	1	CLONAL	2	TRUE	0	0.569935930703237	2		765	458	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101910	11101910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550815250	NA	P-0018977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	402	927	3	ENST00000358026.2:c.1330C>T	p.Arg444Cys	p.R444C	ENST00000358026	NM_001128849.1	444	Cgc/Tgc	8/36	0.569935930703237	5	FACETS	0.846	0.803	0.889	0.423	0.401	0.445	CLONAL	2	TRUE	1	0.569935930703237	5		930	1547	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371409680	NA	P-0018978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	451	1035	0	ENST00000269305.4:c.848G>C	p.Arg283Pro	p.R283P	ENST00000269305	NM_001126112.2	283	cGc/cCc	8/11	0.438134447302619	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.438134447302619	1		1035	1197	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771828	135771828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779599439	NA	P-0018978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	106	926	0	ENST00000298552.3:c.3289C>T	p.Arg1097Cys	p.R1097C	ENST00000298552	NM_001162426.1	1097	Cgt/Tgt	23/23	0.438134447302619	1	FACETS	0.345	0.308	0.384	0.345	0.308	0.384	SUBCLONAL	1	TRUE	0	0.438134447302619	1		926	1095	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797867	45797867	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs760889663	NA	P-0018978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	190	784	0	ENST00000450313.1:c.904G>T	p.Val302Leu	p.V302L	ENST00000450313	NM_012222.2	302	Gtg/Ttg	10/16	1	2	FACETS	0.908	0.84	0.979	0.908	0.84	0.979	CLONAL	1	TRUE	1	0.438134447302619	2		784	955	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211462	46211462	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	84	357	0	ENST00000334344.6:c.428G>C	p.Arg143Pro	p.R143P	ENST00000334344	NM_152641.2	143	cGt/cCt	5/21	0.258807509352925	1	FACETS	0.75	0.667	0.839	0.75	0.667	0.839	INDETERMINATE	1	TRUE	0	0.438134447302619	1		357	399	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941661	48941661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	304	400	2	ENST00000267163.4:c.973del	p.Tyr325IlefsTer7	p.Y325Ifs*7	ENST00000267163	NM_000321.2	324	aTt/at	10/27	0.438134447302619	3	FACETS	0.953	0.907	0.998	0.953	0.907	0.998	CLONAL	3	TRUE	0	0.438134447302619	3		402	592	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434967	110434967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	1095	1034	4	ENST00000375856.3:c.3434G>A	p.Arg1145His	p.R1145H	ENST00000375856	NM_003749.2	1145	cGc/cAc	1/2	0.438134447302619	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.438134447302619	3		1038	1767	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655372	67655372	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	87	833	0	ENST00000264010.4:c.1235G>T	p.Cys412Phe	p.C412F	ENST00000264010	NM_006565.3	412	tGt/tTt	7/12	NA	2	FACETS	0.478	0.423	0.538			1	INDETERMINATE	1	TRUE	NA	0.438134447302619	2		833	830	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176678804	176678804	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	84	658	0	ENST00000439151.2:c.4715G>C	p.Gly1572Ala	p.G1572A	ENST00000439151	NM_022455.4	1572	gGa/gCa	12/23	0.438134447302619	1	FACETS	0.409	0.361	0.461	0.409	0.361	0.461	SUBCLONAL	1	TRUE	0	0.438134447302619	1		658	732	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0018979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	46	812	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	1	2	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	TRUE	1	0.1	2		812	911	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0018979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	33	806	1	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	1	2	FACETS	0.765	0.62	0.929	0.765	0.62	0.929	CLONAL	1	TRUE	1	0.1	2		807	863	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986749	36986749	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	11	172	0	ENST00000354822.5:c.940G>C	p.Gly314Arg	p.G314R	ENST00000354822	NM_001079668.2	314	Ggc/Cgc	3/3	1	2	FACETS	1	0.794	1	1	0.794	1	CLONAL	1	TRUE	1	0.1	2		172	182	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0018980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	56	846	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	1	2	FACETS	0.377	0.322	0.437	0.377	0.322	0.437	SUBCLONAL	1	TRUE	1	0.403580428882954	2		846	737	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0018981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	18	752	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.898	0.676	1	0.898	0.676	1	CLONAL	1	TRUE	1	0.12	2		754	334	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	42	917	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.105832310200019	3	FACETS	0.866	0.72	1	0.433	0.36	0.514	CLONAL	1	TRUE	1	0.12	3		917	857	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017784	31017784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs957851818	NA	P-0018981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	33	654	0	ENST00000375687.4:c.646G>A	p.Ala216Thr	p.A216T	ENST00000375687	NM_015338.5	216	Gct/Act	8/13	0.105832310200019	0	FACETS	1	0.87	1			1	CLONAL	1	TRUE	0	0.12	0		654	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0018982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	567	923	0	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.739227058288891	3	FACETS	0.91	0.887	0.932	0.91	0.887	0.932	CLONAL	3	FALSE	0	0.770139407221025	3		923	747	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425577	49425577	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760819349	NA	P-0018982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	512	915	1	ENST00000301067.7:c.12911C>T	p.Pro4304Leu	p.P4304L	ENST00000301067	NM_003482.3	4304	cCt/cTt	39/54	0.770139407221025	3	FACETS	0.949	0.925	0.971	0.949	0.925	0.971	CLONAL	3	FALSE	0	0.770139407221025	3		916	647	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584552	48584552	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0018982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	257	689	0	ENST00000342988.3:c.725C>G	p.Ser242Ter	p.S242*	ENST00000342988	NM_005359.5	242	tCa/tGa	6/12	0.707815651884036	2	FACETS	0.895	0.857	0.931	0.895	0.857	0.931	CLONAL	2	FALSE	0	0.770139407221025	2		689	373	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296214	15296214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781574783	NA	P-0018982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	297	827	1	ENST00000263388.2:c.2150G>A	p.Arg717His	p.R717H	ENST00000263388	NM_000435.2	717	cGc/cAc	14/33	0.658127343312602	4	FACETS	0.942	0.892	0.992	0.942	0.892	0.992	CLONAL	2	FALSE	2	0.770139407221025	4		828	725	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480484	57480484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11554274	NA	P-0018982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	243	573	2	ENST00000371085.3:c.479G>A	p.Arg160His	p.R160H	ENST00000371085	NM_000516.4	160	cGt/cAt	6/13	0.733592860524261	4	FACETS	0.884	0.831	0.937	0.884	0.831	0.937	CLONAL	2	FALSE	2	0.770139407221025	4		575	632	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206888	36206888	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	106	379	0	ENST00000300305.3:c.624G>T	p.Gln208His	p.Q208H	ENST00000300305		208	caG/caT	6/8	0.387651836759543	3	FACETS	0.832	0.763	0.903	0.832	0.763	0.903	INDETERMINATE	2	FALSE	1	0.770139407221025	3		379	229	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755740	39755740	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747083136	NA	P-0018982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	87	606	0	ENST00000288319.7:c.1025C>T	p.Thr342Met	p.T342M	ENST00000288319	NM_182918.3	342	aCg/aTg	10/10	0.387651836759543	3	FACETS	0.879	0.785	0.978	0.44	0.392	0.489	INDETERMINATE	1	FALSE	1	0.770139407221025	3		606	356	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665383	117665383	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	240	427	0	ENST00000368508.3:c.4364C>G	p.Thr1455Ser	p.T1455S	ENST00000368508	NM_002944.2	1455	aCt/aGt	27/43	0.739227058288891	3	FACETS	0.869	0.833	0.904	0.869	0.833	0.904	CLONAL	3	FALSE	0	0.770139407221025	3		427	331	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100910	27100910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1209091196	NA	P-0018983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	47	624	1	ENST00000324856.7:c.4192G>A	p.Gly1398Arg	p.G1398R	ENST00000324856	NM_006015.4	1398	Ggg/Agg	18/20	1	2	FACETS	0.557	0.469	0.654	0.557	0.469	0.654	SUBCLONAL	1	TRUE	1	0.266181631338289	2		625	634	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480571	120480571	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	44	712	0	ENST00000256646.2:c.3246A>T	p.Lys1082Asn	p.K1082N	ENST00000256646	NM_024408.3	1082	aaA/aaT	20/34	1	2	FACETS	0.429	0.358	0.507	0.429	0.358	0.507	SUBCLONAL	1	TRUE	1	0.266181631338289	2		712	771	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15364981	15364982	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0018983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	146	760	0	ENST00000263377.2:c.2139_2140del	p.Asp713GlufsTer105	p.D713Efs*105	ENST00000263377	NM_058243.2	713	gaCAgc/gagc	11/20	0.17242504034374	3	FACETS	0.78	0.712	0.851	0.78	0.712	0.851	SUBCLONAL	2	TRUE	1	0.266181631338289	3		760	797	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716209	52716209	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	122	526	1	ENST00000322088.6:c.653A>T	p.Asp218Val	p.D218V	ENST00000322088	NM_014225.5	218	gAc/gTc	6/15	0.17242504034374	3	FACETS	0.798	0.723	0.877	0.798	0.723	0.877	SUBCLONAL	2	TRUE	1	0.266181631338289	3		527	651	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546816	9546816	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	22	356	0	ENST00000353224.5:c.1206C>A	p.Ser402Arg	p.S402R	ENST00000353224	NM_177990.2	402	agC/agA	5/10	0.17242504034374	3	FACETS	0.505	0.391	0.638	0.252	0.195	0.319	SUBCLONAL	1	TRUE	1	0.266181631338289	3		356	371	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170015146	170015146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	64	822	0	ENST00000295797.4:c.1552G>A	p.Gly518Arg	p.G518R	ENST00000295797	NM_002740.5	518	Gga/Aga	16/18	1	2	FACETS	0.519	0.448	0.597	0.519	0.448	0.597	SUBCLONAL	1	TRUE	1	0.266181631338289	2		822	926	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590991	67590991	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	27	287	0	ENST00000274335.5:c.1584del	p.Tyr528Ter	p.Y528*	ENST00000274335		528	taT/ta	12/15	1	2	FACETS	0.768	0.613	0.944	0.768	0.613	0.944	CLONAL	1	TRUE	1	0.266181631338289	2		287	264	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981442	70981442	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs148902231	NA	P-0018983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1202	68	1084	2	ENST00000276594.2:c.654C>A	p.Ser218Arg	p.S218R	ENST00000276594	NM_024504.3	218	agC/agA	2/8	0.266181631338289	4	FACETS	0.509	0.441	0.584	0.17	0.147	0.195	SUBCLONAL	1	TRUE	1	0.266181631338289	4		1086	1270	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411387	63411387	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	64	767	0	ENST00000330258.3:c.1780C>A	p.His594Asn	p.H594N	ENST00000330258	NM_152424.3	594	Cac/Aac	2/2	0.154762438366716	1	FACETS	0.622	0.538	0.713	0.622	0.538	0.713	INDETERMINATE	1	TRUE	0	0.266181631338289	1		767	670	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164929	123164929	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	40	534	0	ENST00000218089.9:c.242A>C	p.Asn81Thr	p.N81T	ENST00000218089	NM_001042749.1	81	aAc/aCc	5/35	0.154762438366716	1	FACETS	0.504	0.418	0.599	0.504	0.418	0.599	INDETERMINATE	1	TRUE	0	0.266181631338289	1		534	517	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589558	67589588	+	protein_altering_variant	In_Frame_Del	DEL	AATATTGAAGCTGTAGGGAAAAAATTACATG	AATATTGAAGCTGTAGGGAAAAAATTACATG	C	novel	NA	P-0018983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	46	475	0	ENST00000274335.5:c.1321_1351delinsC	p.Asn441_Glu451delinsGln	p.N441_E451delinsQ	ENST00000274335		441	AATATTGAAGCTGTAGGGAAAAAATTACATGaa/Caa	10/15	1	2	FACETS	0.787	0.664	0.923	0.787	0.664	0.923	CLONAL	1	TRUE	1	0.266181631338289	2		475	439	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0018984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	744	815	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.358101639654115	3	FACETS	0.857	0.83	0.883	1	0.997	1	CLONAL	3	TRUE	1	0.495157471522789	3		815	1459	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0018984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	207	884	1	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.495157471522789	1	FACETS	0.895	0.834	0.958	0.895	0.834	0.958	CLONAL	1	TRUE	0	0.495157471522789	1		885	703	SUCCESS
BTK	695	MSKCC	GRCh37	X	100625010	100625010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	129	421	1	ENST00000308731.7:c.367C>T	p.Arg123Trp	p.R123W	ENST00000308731	NM_000061.2	123	Cgg/Tgg	5/19	0.495157471522789	0	FACETS	0.739	0.678	0.801			1	SUBCLONAL	1	TRUE	NA	0.495157471522789	0		422	356	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272902	11272902	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	238	692	1	ENST00000361445.4:c.3349C>T	p.Pro1117Ser	p.P1117S	ENST00000361445	NM_004958.3	1117	Cct/Tct	22/58	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.495157471522789	2		693	891	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250211	133250211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs115047349	NA	P-0018984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	202	769	0	ENST00000320574.5:c.1309G>T	p.Val437Leu	p.V437L	ENST00000320574	NM_006231.2	437	Gtg/Ttg	13/49	1	2	FACETS	0.976	0.906	1	0.976	0.906	1	CLONAL	1	TRUE	1	0.495157471522789	2		769	836	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891675	28891675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	230	857	1	ENST00000282397.4:c.3346G>A	p.Gly1116Ser	p.G1116S	ENST00000282397	NM_002019.4	1116	Ggc/Agc	25/30	0.495157471522789	1	FACETS	0.887	0.829	0.946	0.887	0.829	0.946	CLONAL	1	TRUE	0	0.495157471522789	1		858	788	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793176	33793176	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	46	345	0	ENST00000498907.2:c.145C>G	p.Pro49Ala	p.P49A	ENST00000498907	NM_004364.3	49	Ccg/Gcg	1/1	NA	2	FACETS	0.443	0.374	0.52			1	INDETERMINATE	1	TRUE	NA	0.495157471522789	2		345	419	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635555	47635555	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1281311713	NA	P-0018984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	144	532	0	ENST00000233146.2:c.227A>C	p.Gln76Pro	p.Q76P	ENST00000233146	NM_000251.2	76	cAg/cCg	2/16	1	2	FACETS	0.952	0.871	1	0.952	0.871	1	CLONAL	1	TRUE	1	0.495157471522789	2		532	611	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285261	212285261	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	166	785	0	ENST00000342788.4:c.3040G>T	p.Glu1014Ter	p.E1014*	ENST00000342788	NM_005235.2	1014	Gaa/Taa	25/28	1	2	FACETS	0.906	0.834	0.981	0.906	0.834	0.981	CLONAL	1	TRUE	1	0.495157471522789	2		785	740	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050645	30050645	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0018984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	164	606	0	ENST00000338641.4:c.448-1G>A		p.X150_splice	ENST00000338641	NM_000268.3	150			0.495157471522789	1	FACETS	0.955	0.883	1	0.955	0.883	1	CLONAL	1	TRUE	0	0.495157471522789	1		606	522	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204887	128204887	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	649	915	0	ENST00000341105.2:c.554del	p.Pro185LeufsTer33	p.P185Lfs*33	ENST00000341105	NM_032638.4	185	cCt/ct	3/6	0.477265358874643	3	FACETS	0.904	0.875	0.933	0.904	0.875	0.933	CLONAL	3	TRUE	0	0.495157471522789	3		915	1206	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280331	1280331	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199422294	NA	P-0018984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	269	933	1	ENST00000310581.5:c.1892G>A	p.Arg631Gln	p.R631Q	ENST00000310581	NM_198253.2	631	cGg/cAg	4/16	0.199265852577776	3	FACETS	1	0.98	1	0.552	0.517	0.588	INDETERMINATE	1	TRUE	1	0.495157471522789	3		934	1228	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675633	86675640	+	frameshift_variant	Frame_Shift_Del	DEL	GAGAAAAT	GAGAAAAT	-	novel	NA	P-0018984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	110	640	0	ENST00000274376.6:c.2569_2576del	p.Glu857IlefsTer25	p.E857Ifs*25	ENST00000274376	NM_002890.2	857	GAGAAAATa/a	19/25	1	2	FACETS	0.704	0.634	0.778	0.704	0.634	0.778	SUBCLONAL	1	TRUE	1	0.495157471522789	2		640	631	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335715	81335715	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	187	648	1	ENST00000222390.5:c.1645G>T	p.Gly549Ter	p.G549*	ENST00000222390	NM_000601.4	549	Gga/Tga	15/18	0.288646527505079	1	FACETS	0.881	0.818	0.946	0.881	0.818	0.946	INDETERMINATE	1	TRUE	0	0.495157471522789	1		649	645	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971068	21971068	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	165	604	0	ENST00000304494.5:c.290T>C	p.Leu97Pro	p.L97P	ENST00000304494	NM_000077.4	97	cTg/cCg	2/3	0.495157471522789	1	FACETS	0.997	0.923	1	0.997	0.923	1	CLONAL	1	TRUE	0	0.495157471522789	1		604	503	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971070	21971070	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs557319056	NA	P-0018984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	168	600	0	ENST00000579755.1:c.331G>A	p.Ala111Thr	p.A111T	ENST00000579755		111	Gct/Act	2/3	0.495157471522789				0.952	1				CLONAL	1	TRUE	0	0.495157471522789	1		600	493	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105923	27105923	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	238	618	3	ENST00000324856.7:c.5534G>T	p.Arg1845Leu	p.R1845L	ENST00000324856	NM_006015.4	1845	cGg/cTg	20/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.775632895022314	2		621	565	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717776	89717776	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1554825266	NA	P-0018985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	70	437	0	ENST00000371953.3:c.801G>T	p.Lys267Asn	p.K267N	ENST00000371953	NM_000314.4	267	aaG/aaT	7/9	0.775632895022314	1	FACETS	0.493	0.437	0.552	0.493	0.437	0.552	SUBCLONAL	1	TRUE	0	0.775632895022314	1		437	224	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118365075	118365075	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs886041896	NA	P-0018985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	250	759	0	ENST00000534358.1:c.5251A>T	p.Lys1751Ter	p.K1751*	ENST00000534358	NM_005933.3	1751	Aaa/Taa	17/36	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.775632895022314	2		759	610	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934174	48934189	+	frameshift_variant	Frame_Shift_Del	DEL	ATGATCTGGTGATTTC	ATGATCTGGTGATTTC	-	novel	NA	P-0018985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	119	487	0	ENST00000267163.4:c.631_646del	p.Asp211PhefsTer3	p.D211Ffs*3	ENST00000267163	NM_000321.2	210	gATGATCTGGTGATTTCa/ga	7/27	0.775632895022314	1	FACETS	0.862	0.798	0.924	0.862	0.798	0.924	CLONAL	1	TRUE	0	0.775632895022314	1		487	218	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTGTCATCCAAATACTCCACACGCAAATTTCCTTCCACTCGGATAAGATGCTGAGGAGGGGCA	novel	NA	P-0018985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	129	901	0	ENST00000269305.4:c.626_627insTGCCCCTCCTCAGCATCTTATCCGAGTGGAAGGAAATTTGCGTGTGGAGTATTTGGATGACAG	p.Asp208_Arg209insSerAlaProProGlnHisLeuIleArgValGluGlyAsnLeuArgValGluTyrLeuAspAsp	p.D208_R209insSAPPQHLIRVEGNLRVEYLDD	ENST00000269305	NM_001126112.2	209	aga/agTGCCCCTCCTCAGCATCTTATCCGAGTGGAAGGAAATTTGCGTGTGGAGTATTTGGATGACAGa	6/11	0.775632895022314	1	FACETS	0.249	0.225	0.273	0.249	0.225	0.273	SUBCLONAL	1	TRUE	0	0.775632895022314	1		901	819	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190708753	190708753	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	227	716	0	ENST00000441310.2:c.646A>T	p.Thr216Ser	p.T216S	ENST00000441310	NM_000534.4	216	Act/Tct	6/13	1	2	FACETS	0.999	0.938	1	0.999	0.938	1	CLONAL	1	TRUE	1	0.775632895022314	2		716	586	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201737	66201737	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	294	669	0	ENST00000273854.3:c.2765G>T	p.Arg922Met	p.R922M	ENST00000273854	NM_004439.5	922	aGg/aTg	16/18	0.775632895022314	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.775632895022314	1		669	414	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659197	86659238	+	inframe_deletion	In_Frame_Del	DEL	ATCTTAGAGGGTAGTGATGCCCAACTTATTTATTTTGAAAGC	ATCTTAGAGGGTAGTGATGCCCAACTTATTTATTTTGAAAGC	-	novel	NA	P-0018985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	68	416	0	ENST00000274376.6:c.1486_1527del	p.Ile496_Ser509del	p.I496_S509del	ENST00000274376	NM_002890.2	496	ATCTTAGAGGGTAGTGATGCCCAACTTATTTATTTTGAAAGC/-	11/25	0.775632895022314	1	FACETS	0.767	0.688	0.846	0.767	0.688	0.846	SUBCLONAL	1	TRUE	0	0.775632895022314	1		416	140	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0018986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	159	752	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.367966694459944	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.374423305094524	1		754	623	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405953	157405954	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1554294674	NA	P-0018986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	135	628	0	ENST00000346085.5:c.2201dup	p.Ser736IlefsTer27	p.S736Ifs*27	ENST00000346085	NM_020732.3	732	ccg/ccGg	6/20	1	2	FACETS	0.898	0.817	0.984	0.898	0.817	0.984	CLONAL	1	TRUE	1	0.374423305094524	2		628	803	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489571	56489571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	84	546	0	ENST00000267101.3:c.2036G>A	p.Arg679Gln	p.R679Q	ENST00000267101	NM_001982.3	679	cGa/cAa	17/28	1	2	FACETS	0.726	0.642	0.816	0.726	0.642	0.816	SUBCLONAL	1	TRUE	1	0.374423305094524	2		546	618	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088681	27088682	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0018986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	182	893	0	ENST00000324856.7:c.2296dup	p.Gln766ProfsTer51	p.Q766Pfs*51	ENST00000324856	NM_006015.4	764	tcc/tCcc	7/20	1	2	FACETS	0.881	0.811	0.953	0.881	0.811	0.953	CLONAL	1	TRUE	1	0.374423305094524	2		893	1104	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917782	29917782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56077855	NA	P-0018986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	62	809	1	ENST00000389048.3:c.886G>A	p.Glu296Lys	p.E296K	ENST00000389048	NM_004304.4	296	Gag/Aag	3/29	1	2	FACETS	0.414	0.357	0.477	0.414	0.357	0.477	SUBCLONAL	1	TRUE	1	0.374423305094524	2		810	799	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057712	27057712	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	244	1074	2	ENST00000324856.7:c.1420C>T	p.Gln474Ter	p.Q474*	ENST00000324856	NM_006015.4	474	Caa/Taa	3/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.374423305094524	2		1076	1232	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359423	118359425	+	inframe_deletion	In_Frame_Del	DEL	GTC	GTC	-	novel	NA	P-0018986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	111	591	0	ENST00000534358.1:c.4432_4434del	p.Arg1478del	p.R1478del	ENST00000534358	NM_005933.3	1476	tGTCgt/tgt	11/36	1	2	FACETS	0.916	0.825	1	0.916	0.825	1	CLONAL	1	TRUE	1	0.374423305094524	2		591	647	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813823	50813823	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	73	852	0	ENST00000398568.2:c.1377G>A	p.Met459Ile	p.M459I	ENST00000398568	NM_001042412.1	459	atG/atA	8/18	1	2	FACETS	0.381	0.332	0.434	0.381	0.332	0.434	SUBCLONAL	1	TRUE	1	0.374423305094524	2		852	1024	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627844	14627844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766997470	NA	P-0018986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	81	802	0	ENST00000254322.2:c.226G>A	p.Gly76Ser	p.G76S	ENST00000254322	NM_006145.1	76	Ggc/Agc	2/3	1	2	FACETS	0.43	0.378	0.487	0.43	0.378	0.487	SUBCLONAL	1	TRUE	1	0.374423305094524	2		802	1006	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591109	67591114	+	inframe_deletion	In_Frame_Del	DEL	CCAGAC	CCAGAC	-	novel	NA	P-0018986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	24	440	0	ENST00000274335.5:c.1703_1708del	p.Pro568_Asp569del	p.P568_D569del	ENST00000274335		568	CCAGAC/-	12/15	0.374423305094524	1	FACETS	0.254	0.199	0.318	0.254	0.199	0.318	SUBCLONAL	1	TRUE	0	0.374423305094524	1		440	410	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459891	149459891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143025739	NA	P-0018986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	152	689	6	ENST00000286301.3:c.316C>T	p.Arg106Trp	p.R106W	ENST00000286301	NM_005211.3	106	Cgg/Tgg	4/22	1	2	FACETS	0.967	0.884	1	0.967	0.884	1	CLONAL	1	TRUE	1	0.374423305094524	2		695	840	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021826	69021826	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	109	614	0	ENST00000288368.4:c.3114A>C	p.Lys1038Asn	p.K1038N	ENST00000288368	NM_024870.2	1038	aaA/aaC	25/40	1	2	FACETS	0.838	0.753	0.927	0.838	0.753	0.927	CLONAL	1	TRUE	1	0.374423305094524	2		614	695	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807477	36807477	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139437228	NA	P-0018987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	245	692	3	ENST00000373129.3:c.1187G>A	p.Arg396Gln	p.R396Q	ENST00000373129	NM_032017.1	396	cGg/cAg	12/12	0.22130893950502	5	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.680033001358786	5		695	618	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653825	89653826	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0018987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	176	456	0	ENST00000371953.3:c.124dup	p.Leu42ProfsTer2	p.L42Pfs*2	ENST00000371953	NM_000314.4	41	-/C	2/9	0.680033001358786	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.680033001358786	1		456	307	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578411	7578416	+	frameshift_variant	Frame_Shift_Del	DEL	CACAAC	CACAAC	AACAA	novel	NA	P-0018987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	214	685	3	ENST00000269305.4:c.514_519delinsTTGTT	p.Val172LeufsTer75	p.V172Lfs*75	ENST00000269305	NM_001126112.2	172	GTTGTG/TTGTT	5/11	0.680033001358786	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.680033001358786	1		688	387	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0018988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	506	894	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.59165982020958	3	FACETS	0.987	0.948	1	0.987	0.948	1	CLONAL	2	TRUE	1	0.59165982020958	3		895	1123	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0018988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	238	884	1	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.59165982020958	1	FACETS	0.994	0.936	1	0.994	0.936	1	CLONAL	1	TRUE	0	0.59165982020958	1		885	570	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860064	57860064	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	236	1025	1	ENST00000228682.2:c.804C>A	p.Phe268Leu	p.F268L	ENST00000228682	NM_005269.2	268	ttC/ttA	8/12	1	2	FACETS	0.885	0.827	0.945	0.885	0.827	0.945	CLONAL	1	TRUE	1	0.59165982020958	2		1026	901	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602328	10602329	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0018988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	238	901	2	ENST00000171111.5:c.1249_1250delinsTT	p.Gly417Leu	p.G417L	ENST00000171111	NM_203500.1	417	GGg/TTg	3/6	0.59165982020958	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.59165982020958	1		903	565	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6439806	6439806	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	140	524	0	ENST00000356142.4:c.332A>C	p.Asn111Thr	p.N111T	ENST00000356142	NM_018890.3	111	aAt/aCt	5/7	0.59165982020958	3	FACETS	0.901	0.822	0.983	0.45	0.411	0.492	CLONAL	1	TRUE	1	0.59165982020958	3		524	681	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0018991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	78	600	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	0.31	2		600	476	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466022	69466022	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	108	849	2	ENST00000227507.2:c.860C>A	p.Pro287His	p.P287H	ENST00000227507	NM_053056.2	287	cCc/cAc	5/5	1	2	FACETS	0.958	0.861	1	0.958	0.861	1	CLONAL	1	TRUE	1	0.31	2		851	727	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023644	27023645	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCGCCTCCCTCCTCCAGCGCCT	novel	NA	P-0018991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	55	707	0	ENST00000324856.7:c.759_780dup	p.Ser261LeufsTer146	p.S261Lfs*146	ENST00000324856	NM_006015.4	250	-/CCGCCTCCCTCCTCCAGCGCCT	1/20	1	2	FACETS	0.615	0.526	0.713	0.615	0.526	0.713	SUBCLONAL	1	TRUE	1	0.31	2		707	577	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105581	27105582	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	92	662	1	ENST00000324856.7:c.5195dup	p.Glu1733GlyfsTer3	p.E1733Gfs*3	ENST00000324856	NM_006015.4	1731	tta/ttAa	20/20	1	2	FACETS	0.912	0.811	1	0.912	0.811	1	CLONAL	1	TRUE	1	0.31	2		663	651	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717687	89717688	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	93	720	0	ENST00000371953.3:c.712_713insA	p.Phe238TyrfsTer5	p.F238Yfs*5	ENST00000371953	NM_000314.4	238	ttc/tAtc	7/9	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.31	2		720	584	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487153	56487153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	107	653	0	ENST00000267101.3:c.1299G>A	p.Met433Ile	p.M433I	ENST00000267101	NM_001982.3	433	atG/atA	12/28	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.31	2		653	602	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67646020	67646021	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	83	581	0	ENST00000264010.4:c.949dup	p.Thr317AsnfsTer92	p.T317Nfs*92	ENST00000264010	NM_006565.3	316	-/A	4/12	1	2	FACETS	0.878	0.775	0.987	0.878	0.775	0.987	CLONAL	1	TRUE	1	0.31	2		581	610	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589563	67589619	+	inframe_deletion	In_Frame_Del	DEL	TGAAGCTGTAGGGAAAAAATTACATGAATATAACACTCAGTTTCAAGAAAAAAGTCG	TGAAGCTGTAGGGAAAAAATTACATGAATATAACACTCAGTTTCAAGAAAAAAGTCG	-	novel	NA	P-0018991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	32	517	0	ENST00000274335.5:c.1326_1382del	p.Ala444_Glu462del	p.A444_E462del	ENST00000274335		442	atTGAAGCTGTAGGGAAAAAATTACATGAATATAACACTCAGTTTCAAGAAAAAAGTCGa/ata	10/15	1	2	FACETS	0.475	0.385	0.576	0.475	0.385	0.576	SUBCLONAL	1	TRUE	1	0.31	2		517	435	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248148	110248148	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	85	662	0	ENST00000374672.4:c.1324G>C	p.Glu442Gln	p.E442Q	ENST00000374672	NM_004235.4	442	Gaa/Caa	5/5	1	2	FACETS	0.822	0.727	0.924	0.822	0.727	0.924	CLONAL	1	TRUE	1	0.31	2		662	667	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434208	121434208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	124	781	0	ENST00000257555.6:c.1099G>A	p.Ala367Thr	p.A367T	ENST00000257555		367	Gcc/Acc	5/10	0.16184816538868	3	FACETS	1	0.936	1	0.348	0.314	0.383	INDETERMINATE	1	TRUE	0	0.372051008684568	3		781	758	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906651	32906651	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	185	721	0	ENST00000380152.3:c.1036A>G	p.Asn346Asp	p.N346D	ENST00000380152		346	Aac/Gac	10/27	NA	2	FACETS	0.935	0.87	1			1	INDETERMINATE	2	TRUE	NA	0.372051008684568	2		721	532	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954246	32954246	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	189	740	0	ENST00000380152.3:c.9220C>G	p.Leu3074Val	p.L3074V	ENST00000380152		3074	Cta/Gta	24/27	0.372051008684568	2	FACETS	0.865	0.805	0.928	0.865	0.805	0.928	CLONAL	2	TRUE	0	0.372051008684568	2		740	587	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212745	27212745	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	108	1005	1	ENST00000380036.4:c.2727C>A	p.Asn909Lys	p.N909K	ENST00000380036	NM_000459.3	909	aaC/aaA	17/23	0.349309785685368	2	FACETS	0.833	0.748	0.923	0.416	0.374	0.462	CLONAL	1	TRUE	0	0.372051008684568	2		1006	697	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066748	77066748	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	178	620	4	ENST00000356341.3:c.737C>A	p.Pro246His	p.P246H	ENST00000356341	NM_002576.4	246	cCt/cAt	7/15	0.439097543035552	1	FACETS	0.495	0.461	0.53	0.495	0.461	0.53	INDETERMINATE	1	TRUE	0	0.886770607158345	1		624	451	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608529	28608529	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	333	859	0	ENST00000241453.7:c.1613T>C	p.Ile538Thr	p.I538T	ENST00000241453	NM_004119.2	538	aTc/aCc	13/24	0.886770607158345	3	FACETS	1	0.967	1	0.514	0.487	0.542	CLONAL	1	TRUE	1	0.886770607158345	3		859	1054	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0018997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	66	853	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.203407649943188	2		853	489	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929253	32929254	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0018997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	39	774	0	ENST00000380152.3:c.7267_7268del	p.Val2423Ter	p.V2423*	ENST00000380152		2421	caGTgt/cagt	14/27	0.203407649943188	3	FACETS	0.853	0.707	1	0.427	0.353	0.509	CLONAL	1	TRUE	1	0.203407649943188	3		774	495	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146555	185146555	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	45	661	1	ENST00000265026.3:c.186C>A	p.Ser62Arg	p.S62R	ENST00000265026	NM_004721.4	62	agC/agA	2/14	0.123174460028491	3	FACETS	1	0.935	1	0.612	0.516	0.719	CLONAL	1	TRUE	1	0.203407649943188	3		662	398	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607270	189607270	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	58	741	0	ENST00000264731.3:c.1649T>G	p.Val550Gly	p.V550G	ENST00000264731	NM_003722.4	550	gTc/gGc	12/14	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.203407649943188	2		741	434	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637027	176637027	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	40	830	0	ENST00000439151.2:c.1627T>C	p.Ser543Pro	p.S543P	ENST00000439151	NM_022455.4	543	Tct/Cct	5/23	0.203407649943188	3	FACETS	0.836	0.695	0.995	0.418	0.347	0.498	CLONAL	1	TRUE	1	0.203407649943188	3		830	518	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976564	7976581	+	frameshift_variant	Frame_Shift_Del	DEL	TCAGCCCCTTAGTCTGAA	TCAGCCCCTTAGTCTGAA	ACCT	novel	NA	P-0018997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	16	670	0	ENST00000319144.4:c.1811_1828delinsAGGT	p.Ile604LysfsTer32	p.I604Kfs*32	ENST00000319144	NM_001139.2	604	aTTCAGACTAAGGGGCTGAcc/aAGGTcc	14/15	1	2	FACETS	0.493	0.364	0.648	0.493	0.364	0.648	SUBCLONAL	1	TRUE	1	0.203407649943188	2		670	319	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0018999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	335	683	1	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	0.309272031423238	3	FACETS	1	0.988	1	0.736	0.702	0.771	INDETERMINATE	2	TRUE	0	0.554213402805261	3		684	699	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654566	29654566	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	155	523	0	ENST00000356175.3:c.5255T>C	p.Leu1752Pro	p.L1752P	ENST00000356175	NM_000267.3	1752	cTa/cCa	37/57	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.554213402805261	2		523	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0019000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	428	949	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	NA	2	FACETS	0.963	0.924	1			1	INDETERMINATE	2	TRUE	NA	0.536841714509825	2		949	828	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0019000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	66	702	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.747	0.653	0.848	0.747	0.653	0.848	SUBCLONAL	1	TRUE	1	0.536841714509825	2		702	329	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117888	70117888	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs886043537	NA	P-0019000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	253	593	0	ENST00000245479.2:c.356C>A	p.Ala119Glu	p.A119E	ENST00000245479	NM_000346.3	119	gCg/gAg	1/3	0.536841714509825	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.536841714509825	2		593	451	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152115	11152115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs796506759	NA	P-0019000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	235	807	1	ENST00000358026.2:c.4399G>A	p.Asp1467Asn	p.D1467N	ENST00000358026	NM_001128849.1	1467	Gac/Aac	31/36	1	2	FACETS	0.985	0.92	1	0.985	0.92	1	CLONAL	1	TRUE	1	0.536841714509825	2		808	889	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911607	134911607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1384145752	NA	P-0019000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	107	707	1	ENST00000398015.3:c.2072G>A	p.Arg691Gln	p.R691Q	ENST00000398015	NM_004441.4	691	cGg/cAg	11/16	1	2	FACETS	0.807	0.727	0.891	0.807	0.727	0.891	CLONAL	1	TRUE	1	0.536841714509825	2		708	494	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749527	41749527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528408156	NA	P-0019000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	187	654	1	ENST00000226382.2:c.268G>A	p.Gly90Ser	p.G90S	ENST00000226382	NM_003924.3	90	Ggc/Agc	2/3	0.510656138685107	2	FACETS	1	0.97	1	0.543	0.503	0.583	CLONAL	1	TRUE	0	0.536841714509825	2		655	642	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0019002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	183	715	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.237328707601639	4	FACETS	0.893	0.829	0.958	0.893	0.829	0.958	CLONAL	3	TRUE	1	0.327462561380661	4		717	554	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0019002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	26	648	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.29795714124954	1	FACETS	0.332	0.262	0.412	0.332	0.262	0.412	SUBCLONAL	1	TRUE	0	0.327462561380661	1		648	400	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230772	46230772	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	19	417	0	ENST00000334344.6:c.1021G>C	p.Glu341Gln	p.E341Q	ENST00000334344	NM_152641.2	341	Gag/Cag	8/21	1	2	FACETS	0.359	0.272	0.462	0.359	0.272	0.462	SUBCLONAL	1	TRUE	1	0.327462561380661	2		417	323	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141821	108141821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	31	780	1	ENST00000278616.4:c.2869G>A	p.Glu957Lys	p.E957K	ENST00000278616	NM_000051.3	957	Gaa/Aaa	19/63	0.264999736878645	1	FACETS	0.263	0.212	0.322	0.263	0.212	0.322	SUBCLONAL	1	TRUE	0	0.327462561380661	1		781	601	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59861733	59861733	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555603567	NA	P-0019002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	130	775	0	ENST00000259008.2:c.1526G>A	p.Gly509Asp	p.G509D	ENST00000259008	NM_032043.2	509	gGt/gAt	11/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.327462561380661	2		775	664	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053541	37053541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	161	919	2	ENST00000231790.2:c.628G>A	p.Ala210Thr	p.A210T	ENST00000231790	NM_000249.3	210	Gcc/Acc	8/19	0.327462561380661	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.327462561380661	1		921	732	SUCCESS
AR	367	MSKCC	GRCh37	X	66943569	66943569	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	38	710	0	ENST00000374690.3:c.2649C>G	p.Ile883Met	p.I883M	ENST00000374690	NM_000044.3	883	atC/atG	8/8	1	2	FACETS	0.354	0.292	0.424	0.354	0.292	0.424	SUBCLONAL	1	TRUE	1	0.327462561380661	2		710	655	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0019003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	567	898	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.501020947620701	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.545126872455254	2		898	990	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508199	106508199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749364940	NA	P-0019003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	67	283	0	ENST00000359195.3:c.193G>A	p.Gly65Ser	p.G65S	ENST00000359195	NM_002649.2	65	Ggc/Agc	2/11	0.463465371746037	1	FACETS	0.843	0.745	0.946	0.843	0.745	0.946	CLONAL	1	TRUE	0	0.545126872455254	1		283	212	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936959	48936960	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	220	530	0	ENST00000267163.4:c.729dup	p.Ile244TyrfsTer4	p.I244Yfs*4	ENST00000267163	NM_000321.2	243	gtt/gTtt	8/27	0.408896387051255	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.545126872455254	1		530	503	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480329	89480329	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	54	297	0	ENST00000336596.2:c.2166G>C	p.Gln722His	p.Q722H	ENST00000336596	NM_005233.5	722	caG/caC	13/17	0.545126872455254	3	FACETS	0.706	0.606	0.815	0.353	0.303	0.408	SUBCLONAL	1	TRUE	1	0.545126872455254	3		297	357	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915853	127915853	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	216	702	2	ENST00000373547.4:c.628C>T	p.Arg210Ter	p.R210*	ENST00000373547	NM_002721.4	210	Cga/Tga	6/7	0.474145344058615	3	FACETS	1	0.974	1	0.547	0.509	0.587	CLONAL	1	TRUE	1	0.545126872455254	3		704	921	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0019004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	669	832	1	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	0.882962686334652	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.882962686334652	3		833	707	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595519	55595519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913516	NA	P-0019004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	148	610	0	ENST00000288135.5:c.2009C>T	p.Thr670Ile	p.T670I	ENST00000288135	NM_000222.2	670	aCa/aTa	14/21	0.882962686334652	3	FACETS	0.929	0.854	1	0.31	0.284	0.336	CLONAL	1	TRUE	0	0.882962686334652	3		610	520	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161938	47161939	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	93	240	0	ENST00000409792.3:c.4187dup	p.Asn1396LysfsTer2	p.N1396Kfs*2	ENST00000409792	NM_014159.6	1396	aat/aaAt	3/21	0.466902217178277	1	FACETS	0.584	0.532	0.636	0.584	0.532	0.636	INDETERMINATE	1	TRUE	0	0.901937484988137	1		240	194	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593609	55593629	+	inframe_deletion	In_Frame_Del	DEL	GTTGTTGAGGAGATAAATGGA	GTTGTTGAGGAGATAAATGGA	-	novel	NA	P-0019006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	114	251	0	ENST00000288135.5:c.1675_1695del	p.Val559_Gly565del	p.V559_G565del	ENST00000288135	NM_000222.2	559	GTTGTTGAGGAGATAAATGGA/-	11/21	0.478042070007973	1	FACETS	0.652	0.602	0.701	0.652	0.602	0.701	INDETERMINATE	1	TRUE	0	0.901937484988137	1		251	213	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5534743	5534743	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0019006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	15	220	0	ENST00000397747.3:c.56-2A>T		p.X19_splice	ENST00000397747	NM_025239.3	19			0.536806648797655	1	FACETS	0.086	0.062	0.114	0.086	0.062	0.114	INDETERMINATE	1	TRUE	0	0.901937484988137	1		220	213	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938283	76938283	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	80	322	0	ENST00000373344.5:c.2465A>G	p.Glu822Gly	p.E822G	ENST00000373344	NM_000489.3	822	gAa/gGa	9/35	1	2	FACETS	0.522	0.463	0.584	0.522	0.463	0.584	SUBCLONAL	1	TRUE	1	0.901937484988137	2		322	340	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861577	152861577	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	461	1045	0	ENST00000406277.2:c.175G>T	p.Glu59Ter	p.E59*	ENST00000406277	NM_152274.4	59	Gag/Tag	4/7	1		FACETS		0.854	0.93				CLONAL	1	TRUE	1	0.901937484988137	2		1045	1146	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633560	69633560	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	234	625	0	ENST00000334134.2:c.142C>G	p.Leu48Val	p.L48V	ENST00000334134	NM_005247.2	48	Ctc/Gtc	1/3	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.802576767727738	NA		625	750	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136340	2136340	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	634	1177	0	ENST00000219476.3:c.4809C>G	p.Asp1603Glu	p.D1603E	ENST00000219476	NM_000548.3	1603	gaC/gaG	37/42	0.802576767727738	1	FACETS	0.998	0.97	1	0.998	0.97	1	CLONAL	1	TRUE	0	0.802576767727738	1		1177	948	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578294	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CTAAG	CTAAG	-	novel	NA	P-0019008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	359	717	0	ENST00000269305.4:c.560-5_560-1del		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.802576767727738	1	FACETS	0.958	0.922	0.994	0.958	0.922	0.994	CLONAL	1	TRUE	0	0.802576767727738	1		717	559	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955550	48955550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913304	NA	P-0019009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	109	304	0	ENST00000267163.4:c.1666C>T	p.Arg556Ter	p.R556*	ENST00000267163	NM_000321.2	556	Cga/Tga	17/27	0.814775527909167	2	FACETS	0.89	0.837	0.94	0.89	0.837	0.94	CLONAL	2	TRUE	0	0.833237032141814	2		304	147	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0019009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	496	1158	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.830614577283108	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.833237032141814	2		1158	579	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512221	120512221	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	421	749	0	ENST00000256646.2:c.1021G>C	p.Asp341His	p.D341H	ENST00000256646	NM_024408.3	341	Gat/Cat	6/34	0.534328762672304	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	2	0.833237032141814	4		749	805	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871044	12871044	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769828807	NA	P-0019009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	304	577	0	ENST00000228872.4:c.271C>T	p.Pro91Ser	p.P91S	ENST00000228872	NM_004064.3	91	Ccc/Tcc	1/3	0.586601581809412	6	FACETS	1	0.984	1	0.736	0.696	0.777	CLONAL	2	TRUE	3	0.833237032141814	6		577	881	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439959	49439959	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0019009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	380	884	0	ENST00000301067.7:c.4584-2A>T		p.X1528_splice	ENST00000301067	NM_003482.3	1528			0.817557840476912	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	2	0.833237032141814	4		884	813	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158594077	158594077	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	49	258	0	ENST00000263640.3:c.1496A>G	p.Asp499Gly	p.D499G	ENST00000263640	NM_001105.4	499	gAt/gGt	11/11	0.642938201611642	4	FACETS	0.971	0.832	1	0.324	0.277	0.374	CLONAL	1	TRUE	1	0.833237032141814	4		258	222	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660910	227660910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	348	936	0	ENST00000305123.5:c.2545G>A	p.Ala849Thr	p.A849T	ENST00000305123	NM_005544.2	849	Gct/Act	1/2	0.463423298438501	4	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.833237032141814	4		936	653	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499520	89499520	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	210	412	0	ENST00000336596.2:c.2690G>A	p.Arg897Lys	p.R897K	ENST00000336596	NM_005233.5	897	aGg/aAg	15/17	0.833237032141814	2	FACETS	0.944	0.907	0.979	0.944	0.907	0.979	CLONAL	2	TRUE	0	0.833237032141814	2		412	267	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205658	128205658	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	191	779	1	ENST00000341105.2:c.217A>T	p.Ser73Cys	p.S73C	ENST00000341105	NM_032638.4	73	Agc/Tgc	2/6	0.833237032141814	3	FACETS	0.977	0.907	1	0.488	0.453	0.524	CLONAL	1	TRUE	1	0.833237032141814	3		780	665	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169991071	169991071	+	splice_region_variant,intron_variant	Splice_Region	SNP	T	T	C	novel	NA	P-0019009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	167	479	0	ENST00000295797.4:c.592-3T>C		p.X198_splice	ENST00000295797	NM_002740.5	198			0.833237032141814	3	FACETS	0.825	0.771	0.88	0.825	0.771	0.88	CLONAL	2	TRUE	1	0.833237032141814	3		479	344	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356432	66356433	+	splice_acceptor_variant,intron_variant	Splice_Site	DNP	TG	TG	GT	novel	NA	P-0019009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	24	269	2	ENST00000273854.3:c.1067-3_1067-2delinsAC		p.X356_splice	ENST00000273854	NM_004439.5	356			0.833237032141814	3	FACETS	0.296	0.232	0.369	0.148	0.116	0.185	SUBCLONAL	1	TRUE	1	0.833237032141814	3		271	276	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361213	66361213	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	117	314	0	ENST00000273854.3:c.959G>C	p.Gly320Ala	p.G320A	ENST00000273854	NM_004439.5	320	gGc/gCc	4/18	0.833237032141814	3	FACETS	1	0.922	1	0.507	0.462	0.555	CLONAL	1	TRUE	1	0.833237032141814	3		314	392	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622239	162622239	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	213	526	0	ENST00000366898.1:c.458C>A	p.Pro153His	p.P153H	ENST00000366898	NM_004562.2	153	cCc/cAc	4/12	0.534328762672304	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.833237032141814	4		526	401	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386592	81386592	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs758097772	NA	P-0019009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	172	386	0	ENST00000222390.5:c.395A>G	p.Lys132Arg	p.K132R	ENST00000222390	NM_000601.4	132	aAa/aGa	4/18	0.750050093436232	4	FACETS	0.817	0.759	0.877	0.817	0.759	0.877	CLONAL	2	TRUE	2	0.833237032141814	4		386	463	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0019010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	32	836	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.702	0.568	0.854	0.702	0.568	0.854	SUBCLONAL	1	TRUE	1	0.14	2		836	651	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251554	251554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906780	NA	P-0019010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	65	1009	2	ENST00000264932.6:c.1765C>T	p.Arg589Trp	p.R589W	ENST00000264932	NM_004168.2	589	Cgg/Tgg	13/15	1	2	FACETS	0.84	0.725	0.964	0.84	0.725	0.964	CLONAL	1	TRUE	1	0.14	2		1011	1106	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578496	7578496	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587782197	NA	P-0019010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1654	79	1512	0	ENST00000269305.4:c.434T>A	p.Leu145Gln	p.L145Q	ENST00000269305	NM_001126112.2	145	cTg/cAg	5/11	1	2	FACETS	0.651	0.57	0.739	0.651	0.57	0.739	SUBCLONAL	1	TRUE	1	0.14	2		1512	1733	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0019011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	35	485	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.506	0.414	0.61	0.506	0.414	0.61	SUBCLONAL	1	TRUE	1	0.243899410950737	2		485	567	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070892	30070892	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	240	1194	0	ENST00000338641.4:c.1408C>T	p.Gln470Ter	p.Q470*	ENST00000338641	NM_000268.3	470	Cag/Tag	13/16	0.236913967078866	2	FACETS	0.803	0.749	0.859	0.803	0.749	0.859	CLONAL	2	TRUE	0	0.243899410950737	2		1194	1225	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873814	151873815	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0019011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	147	340	0	ENST00000262189.6:c.8723_8724del	p.Ser2908LeufsTer16	p.S2908Lfs*16	ENST00000262189	NM_170606.2	2908	tCT/t	38/59	0.243899410950737	4	FACETS	1	0.951	1	0.784	0.721	0.849	CLONAL	3	TRUE	0	0.243899410950737	4		340	478	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981735	70981735	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1412	340	1611	1	ENST00000276594.2:c.361T>A	p.Tyr121Asn	p.Y121N	ENST00000276594	NM_024504.3	121	Tac/Aac	2/8	0.243899410950737	3	FACETS	0.893	0.842	0.945	0.893	0.842	0.945	CLONAL	2	TRUE	1	0.243899410950737	3		1612	1752	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753886	133753886	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	172	641	0	ENST00000318560.5:c.1355T>C	p.Leu452Pro	p.L452P	ENST00000318560	NM_005157.4	452	cTa/cCa	8/11	0.236913967078866	2	FACETS	0.948	0.874	1	0.948	0.874	1	CLONAL	2	TRUE	0	0.243899410950737	2		641	744	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351298	89351298	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	162	951	0	ENST00000301030.4:c.1652G>C	p.Trp551Ser	p.W551S	ENST00000301030	NM_001256183.1	551	tGg/tCg	9/13	0.427822572273058	1	FACETS	0.994	0.916	1	0.994	0.916	1	CLONAL	1	TRUE	0	0.427822572273058	1		951	599	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621882	1621884	+	inframe_deletion	In_Frame_Del	DEL	CGC	CGC	-	novel	NA	P-0019012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	157	1136	0	ENST00000344749.5:c.908_910del	p.Gly303del	p.G303del	ENST00000344749	NM_001136139.2	303	gGCGtc/gtc	11/19	0.316831521689152	1	FACETS	0.851	0.782	0.923	0.851	0.782	0.923	CLONAL	1	TRUE	0	0.427822572273058	1		1136	678	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426035	49426035	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1565774857	NA	P-0019022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	122	813	0	ENST00000301067.7:c.12453C>A	p.Asn4151Lys	p.N4151K	ENST00000301067	NM_003482.3	4151	aaC/aaA	39/54	0.663935464173819	2	FACETS	0.765	0.696	0.837	0.383	0.348	0.419	SUBCLONAL	1	TRUE	0	0.664472951771736	2		813	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578506	7578507	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCAGGTCTTGGCCAGTTGGCAAAACATCTT	novel	NA	P-0019022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	428	1013	0	ENST00000269305.4:c.394_423dup	p.Lys132_Cys141dup	p.K132_C141dup	ENST00000269305	NM_001126112.2	132	-/AAGATGTTTTGCCAACTGGCCAAGACCTGC	5/11	0.663935464173819	2	FACETS	1	0.994	1	0.628	0.6	0.656	CLONAL	1	TRUE	0	0.664472951771736	2		1013	1026	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919736	96919736	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	140	704	0	ENST00000258439.3:c.527G>T	p.Ser176Ile	p.S176I	ENST00000258439	NM_001193304.2	176	aGc/aTc	4/4	0.663935464173819	3	FACETS	0.862	0.787	0.94			1	CLONAL	1	TRUE	NA	0.664472951771736	3		704	651	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439537	220439537	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	353	753	0	ENST00000243786.2:c.390G>C	p.Gln130His	p.Q130H	ENST00000243786	NM_002191.3	130	caG/caC	2/2	0.663935464173819	2	FACETS	0.875	0.839	0.911	0.875	0.839	0.911	CLONAL	2	TRUE	0	0.664472951771736	2		753	607	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609722	28609722	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	204	839	0	ENST00000241453.7:c.1507A>T	p.Met503Leu	p.M503L	ENST00000241453	NM_004119.2	503	Atg/Ttg	12/24	1	2	FACETS	0.475	0.44	0.512	0.475	0.44	0.512	SUBCLONAL	1	TRUE	1	0.793360351622651	2		839	1082	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569849	95569849	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	154	480	0	ENST00000393063.1:c.3884G>T	p.Gly1295Val	p.G1295V	ENST00000393063	NM_030621.3	1295	gGa/gTa	22/28	1	2	FACETS	0.778	0.717	0.841	0.778	0.717	0.841	SUBCLONAL	1	TRUE	1	0.793360351622651	2		480	499	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46276064	46276064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370656650	NA	P-0019023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	470	795	0	ENST00000371998.3:c.3500C>T	p.Pro1167Leu	p.P1167L	ENST00000371998		1167	cCc/cTc	18/23	0.36785758602567	3	FACETS	1	0.996	1	0.713	0.682	0.743	INDETERMINATE	1	TRUE	1	0.793360351622651	3		795	1161	SUCCESS
APC	324	MSKCC	GRCh37	5	112179225	112179225	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	192	495	0	ENST00000257430.4:c.7934A>T	p.Tyr2645Phe	p.Y2645F	ENST00000257430	NM_000038.5	2645	tAt/tTt	16/16	0.793360351622651	1	FACETS	0.99	0.939	1	0.99	0.939	1	CLONAL	1	TRUE	0	0.793360351622651	1		495	295	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0019024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	490	715	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.699585985361284	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.71324120077421	3		717	898	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0019024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	360	807	3	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.71324120077421	3	FACETS	0.888	0.839	0.937	0.444	0.419	0.469	CLONAL	1	TRUE	1	0.71324120077421	3		810	1543	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578419	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587781845	NA	P-0019024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	279	621	0	ENST00000269305.4:c.511G>T	p.Glu171Ter	p.E171*	ENST00000269305	NM_001126112.2	171	Gag/Tag	5/11	0.702115556824394	1	FACETS	0.9	0.855	0.946	0.9	0.855	0.946	CLONAL	1	TRUE	0	0.71324120077421	1		621	559	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9787044	9787044	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	341	662	0	ENST00000377346.4:c.3075G>C	p.Glu1025Asp	p.E1025D	ENST00000377346	NM_005026.3	1025	gaG/gaC	24/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.71324120077421	2		662	932	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256552	16256552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	367	758	0	ENST00000375759.3:c.3817G>A	p.Glu1273Lys	p.E1273K	ENST00000375759	NM_015001.2	1273	Gag/Aag	11/15	1	2	FACETS	0.994	0.945	1	0.994	0.945	1	CLONAL	1	TRUE	1	0.71324120077421	2		758	1035	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818343	43818343	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	379	834	0	ENST00000372470.3:c.1808C>G	p.Pro603Arg	p.P603R	ENST00000372470	NM_005373.2	603	cCc/cGc	12/12	1	2	FACETS	0.957	0.91	1	0.957	0.91	1	CLONAL	1	TRUE	1	0.71324120077421	2		834	1110	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058627	42058627	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs762434957	NA	P-0019024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	209	413	0	ENST00000219905.7:c.8347C>G	p.Leu2783Val	p.L2783V	ENST00000219905	NM_001164273.1	2783	Ctc/Gtc	24/24	1	2	FACETS	0.987	0.922	1	0.987	0.922	1	CLONAL	1	TRUE	1	0.71324120077421	2		413	594	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016549	12016549	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0019024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	149	347	0	ENST00000353533.5:c.686-1G>A		p.X229_splice	ENST00000353533	NM_003010.3	229			0.702115556824394	1	FACETS	0.97	0.906	1	0.97	0.906	1	CLONAL	1	TRUE	0	0.71324120077421	1		347	277	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629005	14629005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	293	682	1	ENST00000254322.2:c.157G>A	p.Asp53Asn	p.D53N	ENST00000254322	NM_006145.1	53	Gac/Aac	1/3	1	2	FACETS	0.817	0.769	0.865	0.817	0.769	0.865	CLONAL	1	TRUE	1	0.71324120077421	2		683	1006	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99185125	99185125	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	165	368	0	ENST00000074304.5:c.2527G>C	p.Glu843Gln	p.E843Q	ENST00000074304	NM_001134224.1	843	Gag/Cag	23/26	1	2	FACETS	0.94	0.871	1	0.94	0.871	1	CLONAL	1	TRUE	1	0.71324120077421	2		368	492	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443736	52443736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	327	754	0	ENST00000460680.1:c.61G>A	p.Asp21Asn	p.D21N	ENST00000460680	NM_004656.3	21	Gat/Aat	2/17	0.702115556824394	1	FACETS	0.922	0.879	0.964	0.922	0.879	0.964	CLONAL	1	TRUE	0	0.71324120077421	1		754	640	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916640	178916666	+	inframe_deletion	In_Frame_Del	DEL	ACTGTGGGGCATCCACTTGATGCCCCC	ACTGTGGGGCATCCACTTGATGCCCCC	-	novel	NA	P-0019024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	190	574	0	ENST00000263967.3:c.28_54del	p.Leu10_Pro18del	p.L10_P18del	ENST00000263967	NM_006218.2	9	gaACTGTGGGGCATCCACTTGATGCCCCCa/gaa	2/21	0.699585985361284	3	FACETS	0.812	0.751	0.875	0.406	0.375	0.438	CLONAL	1	TRUE	1	0.71324120077421	3		574	890	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	297	651	1	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.918	0.869	0.967	0.918	0.869	0.967	CLONAL	1	TRUE	1	0.873339133983341	2		652	741	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	358	829	0	ENST00000346208.3:c.1220_1221insA	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcAg	6/6	1	2	FACETS	0.935	0.89	0.98	0.935	0.89	0.98	CLONAL	1	TRUE	1	0.873339133983341	2		829	877	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552831	226552838	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCTTCA	CGCCTTCA	-	novel	NA	P-0019025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	541	604	0	ENST00000366794.5:c.2523_2530del	p.Glu842MetfsTer8	p.E842Mfs*8	ENST00000366794	NM_001618.3	841	cgTGAAGGCGaa/cgaa	19/23	0.864235393451397	3	FACETS	0.885	0.854	0.916	0.885	0.854	0.916	CLONAL	2	TRUE	1	0.873339133983341	3		604	1006	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944121	71944123	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0019025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	344	700	2	ENST00000298229.2:c.1960_1962del	p.Glu654del	p.E654del	ENST00000298229	NM_001567.3	652	GAG/-	17/28	0.873339133983341	1	FACETS	0.971	0.939	1	0.971	0.939	1	CLONAL	1	TRUE	0	0.873339133983341	1		702	457	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039430	49039430	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0019025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	362	699	0	ENST00000267163.4:c.2415T>G	p.Tyr805Ter	p.Y805*	ENST00000267163	NM_000321.2	805	taT/taG	23/27	0.873339133983341	1	FACETS	0.979	0.948	1	0.979	0.948	1	CLONAL	1	TRUE	0	0.873339133983341	1		699	477	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779590	3779590	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0019025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	454	870	0	ENST00000262367.5:c.5458A>T	p.Lys1820Ter	p.K1820*	ENST00000262367	NM_004380.2	1820	Aag/Tag	31/31	0.864235393451397	3	FACETS	0.962	0.917	1	0.481	0.458	0.504	CLONAL	1	TRUE	1	0.873339133983341	3		870	1553	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795109	42795109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752503838	NA	P-0019025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	457	850	1	ENST00000575354.2:c.2189C>T	p.Ser730Leu	p.S730L	ENST00000575354	NM_015125.3	730	tCg/tTg	10/20	1	2	FACETS	0.974	0.933	1	0.974	0.933	1	CLONAL	1	TRUE	1	0.873339133983341	2		851	1075	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0019026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	756	897	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.116706771147405	6	FACETS	0.919	0.893	0.946			1	INDETERMINATE	4	TRUE	NA	0.788236156790041	6		897	1344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0019027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	421	824	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.381563976728449	2	FACETS	0.949	0.907	0.992	0.949	0.907	0.992	CLONAL	2	TRUE	0	0.419278036111276	2		824	1058	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998559	100998559	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	111	572	0	ENST00000325455.5:c.1243C>A	p.Pro415Thr	p.P415T	ENST00000325455	NM_001202474.3	415	Ccg/Acg	1/8	0.381563976728449	2	FACETS	0.84	0.757	0.928	0.42	0.378	0.464	CLONAL	1	TRUE	0	0.419278036111276	2		572	630	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	219	513	0	ENST00000308159.5:c.40G>C	p.Glu14Gln	p.E14Q	ENST00000308159	NM_014669.4	14	Gaa/Caa	2/22	0.420280885531861	3	FACETS	1	0.956	1			1	CLONAL	2	TRUE	NA	0.419278036111276	3		513	616	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56409135	56409135	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	79	483	0	ENST00000348428.3:c.1642C>G	p.Leu548Val	p.L548V	ENST00000348428	NM_006785.3	548	Cta/Gta	14/17	0.418510758781419	3	FACETS	0.793	0.698	0.894	0.396	0.349	0.447	SUBCLONAL	1	TRUE	1	0.419278036111276	3		483	575	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29197737	29197737	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	169	877	0	ENST00000240100.2:c.457G>C	p.Glu153Gln	p.E153Q	ENST00000240100	NM_001394.6	153	Gag/Cag	2/4	1	2	FACETS	0.771	0.708	0.837	0.771	0.708	0.837	SUBCLONAL	1	TRUE	1	0.419278036111276	2		877	1046	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127164	22127164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057519911	NA	P-0019029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	8	459	0	ENST00000215832.6:c.964G>A	p.Glu322Lys	p.E322K	ENST00000215832	NM_002745.4	322	Gag/Aag	7/9	0.348127093703798	1	FACETS	0.148	0.095	0.217	0.148	0.095	0.217	SUBCLONAL	1	FALSE	0	0.35431508793095	1		459	251	SUCCESS
APC	324	MSKCC	GRCh37	5	112176278	112176278	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758987855	NA	P-0019029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	10	504	3	ENST00000257430.4:c.4987G>A	p.Glu1663Lys	p.E1663K	ENST00000257430	NM_000038.5	1663	Gaa/Aaa	16/16	0.202120911861896	1	FACETS	0.288	0.195	0.405	0.288	0.195	0.405	INDETERMINATE	1	FALSE	0	0.35431508793095	1		507	161	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579542	7579542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780728	NA	P-0019029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	11	736	2	ENST00000269305.4:c.145G>A	p.Asp49Asn	p.D49N	ENST00000269305	NM_001126112.2	49	Gat/Aat	4/11	1	2	FACETS	0.129	0.089	0.181	0.129	0.089	0.181	SUBCLONAL	1	FALSE	1	0.35431508793095	2		738	480	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871044	12871044	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	145	565	0	ENST00000228872.4:c.275del	p.Pro92ArgfsTer27	p.P92Rfs*27	ENST00000228872	NM_004064.3	91	Ccc/cc	1/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.442327687465528	2		565	576	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999429	100999429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs191163476	NA	P-0019030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	267	1119	0	ENST00000325455.5:c.373G>A	p.Gly125Arg	p.G125R	ENST00000325455	NM_001202474.3	125	Ggg/Agg	1/8	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.442327687465528	2		1119	1196	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26978189	26978189	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	181	920	0	ENST00000381527.3:c.1366C>T	p.Gln456Ter	p.Q456*	ENST00000381527	NM_001260.1	456	Cag/Tag	13/13	1	2	FACETS	0.941	0.868	1	0.941	0.868	1	CLONAL	1	TRUE	1	0.442327687465528	2		920	870	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0019031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	21	629	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.118	0.09	0.15	0.118	0.09	0.15	SUBCLONAL	1	TRUE	1	0.674055017979039	2		630	530	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0019031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	91	600	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.674055017979039	2		600	269	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0019031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	124	362	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.674055017979039	2		362	328	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685305	89685305	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	89	441	0	ENST00000371953.3:c.200T>C	p.Ile67Thr	p.I67T	ENST00000371953	NM_000314.4	67	aTa/aCa	3/9	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.674055017979039	2		441	255	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779129	135779129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	180	474	1	ENST00000298552.3:c.2117G>A	p.Arg706His	p.R706H	ENST00000298552	NM_001162426.1	706	cGt/cAt	17/23	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.674055017979039	2		475	533	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591135	67591149	+	inframe_deletion	In_Frame_Del	DEL	GAGAGACCAATACTT	GAGAGACCAATACTT	-	novel	NA	P-0019031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	53	369	0	ENST00000274335.5:c.1730_1744del	p.Arg577_Leu581del	p.R577_L581del	ENST00000274335		576	acGAGAGACCAATACTTg/acg	12/15	1	2	FACETS	0.79	0.684	0.903	0.79	0.684	0.903	CLONAL	1	TRUE	1	0.674055017979039	2		369	199	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720732	89720733	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs587780006	NA	P-0019031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	10	100	0	ENST00000371953.3:c.884dup	p.Cys296MetfsTer2	p.C296Mfs*2	ENST00000371953	NM_000314.4	295	cta/cTta	8/9	1	2	FACETS	0.549	0.381	0.75	0.549	0.381	0.75	SUBCLONAL	1	TRUE	1	0.674055017979039	2		100	54	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117852	108117852	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1555068615	NA	P-0019031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	53	399	0	ENST00000278616.4:c.1063C>T	p.Gln355Ter	p.Q355*	ENST00000278616	NM_000051.3	355	Cag/Tag	8/63	1	2	FACETS	0.823	0.713	0.94	0.823	0.713	0.94	CLONAL	1	TRUE	1	0.674055017979039	2		399	191	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647129	2647129	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	23	485	0	ENST00000342085.4:c.1407A>T	p.Leu469Phe	p.L469F	ENST00000342085	NM_002613.4	469	ttA/ttT	13/14	1	2	FACETS	0.149	0.116	0.188	0.149	0.116	0.188	SUBCLONAL	1	TRUE	1	0.674055017979039	2		485	458	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752401	55752401	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1221930442	NA	P-0019031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	282	903	1	ENST00000284073.2:c.859G>A	p.Gly287Ser	p.G287S	ENST00000284073	NM_138962.2	287	Ggc/Agc	12/14	1	2	FACETS	0.951	0.896	1	0.951	0.896	1	CLONAL	1	TRUE	1	0.674055017979039	2		904	880	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162072	47162072	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs752627883	NA	P-0019032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	179	571	1	ENST00000409792.3:c.4054C>T	p.Gln1352Ter	p.Q1352*	ENST00000409792	NM_014159.6	1352	Cag/Tag	3/21	1	2	FACETS	1	0.969	1	1	0.994	1	CLONAL	2	TRUE	1	0.378427343808223	2		572	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0019033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	278	1140	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.430854340469409	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.430854340469409	1		1140	973	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591555	48591945	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAAAAAAAAAAATTAGTGTTTTAAGAACAGTGCTAAGTACTGAGCTAGAAAATAGAAGACATGGAAATTCCTACCTTTTAATGCATTATGTTATTTTAATCCAGTTGTTTTGGGTGCATTACATTTCCATCTCCCCTCCCTTTACCCTTTCTTTTAGGAAAAACTGTGTTGTGGAGTGCAAGTGAAAGCCTTATATCTTTCTCATGGGAGGATGTTCTTTCCCATTTATTTCCTATAGCTCCTGAGTATTGGTGTTCCATTGCTTACTTTGAAATGGATGTTCAGGTAGGAGAGACATTTAAGGTTCCTTCAAGCTGCCCTATTGTTACTGTTGATGGATACGTGGACCCTTCTGGAGGAGATCGCTTTTGTTTGGGTCAACTCTCCAATG	TAAAAAAAAAAATTAGTGTTTTAAGAACAGTGCTAAGTACTGAGCTAGAAAATAGAAGACATGGAAATTCCTACCTTTTAATGCATTATGTTATTTTAATCCAGTTGTTTTGGGTGCATTACATTTCCATCTCCCCTCCCTTTACCCTTTCTTTTAGGAAAAACTGTGTTGTGGAGTGCAAGTGAAAGCCTTATATCTTTCTCATGGGAGGATGTTCTTTCCCATTTATTTCCTATAGCTCCTGAGTATTGGTGTTCCATTGCTTACTTTGAAATGGATGTTCAGGTAGGAGAGACATTTAAGGTTCCTTCAAGCTGCCCTATTGTTACTGTTGATGGATACGTGGACCCTTCTGGAGGAGATCGCTTTTGTTTGGGTCAACTCTCCAATG	-	novel	NA	P-0019033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	27	4	0	ENST00000342988.3:c.956-237_1109del		p.X319_splice	ENST00000342988	NM_005359.5	319		9/12	0.429496650188326	2	FACETS	0.503	0.402	0.618	0.252	0.201	0.309	SUBCLONAL	1	TRUE	0	0.430854340469409	2		4	249	SUCCESS
APC	324	MSKCC	GRCh37	5	112174658	112174658	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	94	493	0	ENST00000257430.4:c.3367C>T	p.Gln1123Ter	p.Q1123*	ENST00000257430	NM_000038.5	1123	Caa/Taa	16/16	0.305761541503132	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.305761541503132	1		493	503	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120620	115120620	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	183	1009	0	ENST00000257566.3:c.386G>T	p.Gly129Val	p.G129V	ENST00000257566	NM_016569.3	129	gGa/gTa	1/8	1	2	FACETS	0.954	0.878	1	0.954	0.878	1	CLONAL	1	TRUE	1	0.305761541503132	2		1009	1255	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794801	120794801	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	91	1037	2	ENST00000257552.2:c.556C>A	p.Pro186Thr	p.P186T	ENST00000257552	NM_002442.3	186	Cca/Aca	9/15	1	2	FACETS	0.472	0.417	0.531	0.472	0.417	0.531	SUBCLONAL	1	TRUE	1	0.305761541503132	2		1039	1261	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557692	21557692	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	193	768	0	ENST00000382592.4:c.2153del	p.Asp718AlafsTer27	p.D718Afs*27	ENST00000382592	NM_014572.2	718	gAc/gc	5/8	0.305761541503132	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.305761541503132	1		768	955	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610427	10610427	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	162	709	0	ENST00000171111.5:c.283G>T	p.Ala95Ser	p.A95S	ENST00000171111	NM_203500.1	95	Gcc/Tcc	2/6	0.305761541503132	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.305761541503132	1		709	863	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762511	41762511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200253980	NA	P-0019035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	57	363	0	ENST00000301178.4:c.2191G>A	p.Asp731Asn	p.D731N	ENST00000301178	NM_021913.4	731	Gat/Aat	18/20	1	2	FACETS	0.74	0.635	0.854	0.74	0.635	0.854	SUBCLONAL	1	TRUE	1	0.305761541503132	2		363	504	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793442	42793442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	125	565	0	ENST00000575354.2:c.1245del	p.Pro417ArgfsTer18	p.P417Rfs*18	ENST00000575354	NM_015125.3	415	cGg/cg	8/20	1	2	FACETS	0.957	0.866	1	0.957	0.866	1	CLONAL	1	TRUE	1	0.305761541503132	2		565	854	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133854	55133854	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	119	560	0	ENST00000257290.5:c.1067T>A	p.Leu356Gln	p.L356Q	ENST00000257290	NM_006206.4	356	cTg/cAg	7/23	0.305761541503132	1	FACETS	0.992	0.897	1	0.992	0.897	1	CLONAL	1	TRUE	0	0.305761541503132	1		560	665	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751864	57751864	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	95	496	1	ENST00000274289.3:c.1373G>T	p.Ser458Ile	p.S458I	ENST00000274289	NM_006622.3	458	aGc/aTc	10/14	0.305761541503132	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.305761541503132	1		497	507	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983028	111983028	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	83	878	0	ENST00000368678.4:c.1519C>A	p.Arg507Ser	p.R507S	ENST00000368678		507	Cgc/Agc	13/13	0.305761541503132	1	FACETS	0.513	0.451	0.579	0.513	0.451	0.579	SUBCLONAL	1	TRUE	0	0.305761541503132	1		878	897	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513299	106513299	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	113	526	1	ENST00000359195.3:c.2203C>A	p.Gln735Lys	p.Q735K	ENST00000359195	NM_002649.2	735	Caa/Aaa	4/11	1	2	FACETS	0.995	0.896	1	0.995	0.896	1	CLONAL	1	TRUE	1	0.305761541503132	2		527	743	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239616	53239616	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	133	344	0	ENST00000375401.3:c.1726del	p.Leu576SerfsTer83	p.L576Sfs*83	ENST00000375401	NM_004187.3	576	Ctc/tc	12/26	1	1	FACETS	0.792	0.725	0.862	1	0.988	1	SUBCLONAL	2	TRUE	0	0.305761541503132	1		344	465	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	136	364	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.78588605111146	2		365	299	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797314	135797314	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	113	474	0	ENST00000298552.3:c.555C>A	p.Tyr185Ter	p.Y185*	ENST00000298552	NM_001162426.1	185	taC/taA	7/23	0.78588605111146	1	FACETS	0.852	0.788	0.915	0.852	0.788	0.915	CLONAL	1	TRUE	0	0.78588605111146	1		474	205	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871143	12871143	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	106	344	0	ENST00000228872.4:c.371del	p.Asn124ThrfsTer21	p.N124Tfs*21	ENST00000228872	NM_004064.3	124	Aac/ac	1/3	0.115700560612167	3	FACETS	0.758	0.692	0.824	0.758	0.692	0.824	INDETERMINATE	2	TRUE	1	0.78588605111146	3		344	248	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555716	21555716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	246	1013	1	ENST00000382592.4:c.2554G>A	p.Asp852Asn	p.D852N	ENST00000382592	NM_014572.2	852	Gac/Aac	6/8	0.776329914595113	3	FACETS	0.97	0.908	1	0.485	0.454	0.517	CLONAL	1	TRUE	1	0.78588605111146	3		1014	899	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144124	11144124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs767509978	NA	P-0019036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	257	947	0	ENST00000358026.2:c.3705C>A	p.Asp1235Glu	p.D1235E	ENST00000358026	NM_001128849.1	1235	gaC/gaA	26/36	0.78588605111146	1	FACETS	0.943	0.899	0.986	0.943	0.899	0.986	CLONAL	1	TRUE	0	0.78588605111146	1		947	421	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69988248	69988248	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0019036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	122	447	0	ENST00000394351.3:c.262-1G>A		p.X88_splice	ENST00000394351	NM_000248.3	88			0.115700560612167	3	FACETS	1	0.976	1	0.599	0.547	0.652	INDETERMINATE	1	TRUE	1	0.78588605111146	3		447	361	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035972	47035985	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GGCTGTGCAATAAG	GGCTGTGCAATAAG	-	novel	NA	P-0019036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	233	515	0	ENST00000377604.3:c.651_663+1del		p.WLCNK217fs	ENST00000377604	NM_001204468.1	217	tGGCTGTGCAATAAG/t	7/24	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.78588605111146	1		515	321	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0019037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	217	824	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.262229272809529	3	FACETS	0.852	0.796	0.911	1	0.989	1	CLONAL	3	TRUE	1	0.262229272809529	3		824	732	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063718	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0019037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	76	426	0	ENST00000412916.2:c.165+2dup		p.X55_splice	ENST00000412916		55			0.210634893409948	1	FACETS	0.991	0.881	1	1	0.984	1	CLONAL	2	TRUE	0	0.262229272809529	1		426	254	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0019038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	328	1224	2	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	0.751641977793975	1	FACETS	0.89	0.85	0.93	0.89	0.85	0.93	CLONAL	1	TRUE	0	0.751641977793975	1		1226	612	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867241	68867241	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	308	864	0	ENST00000261769.5:c.2488C>G	p.Leu830Val	p.L830V	ENST00000261769	NM_004360.3	830	Ctg/Gtg	16/16	1	2	FACETS	0.724	0.683	0.766	0.724	0.683	0.766	SUBCLONAL	1	TRUE	1	0.751641977793975	2		864	1132	SUCCESS
ALK	238	MSKCC	GRCh37	2	29448381	29448381	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763143588	NA	P-0019038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	358	1287	2	ENST00000389048.3:c.3118G>A	p.Val1040Met	p.V1040M	ENST00000389048	NM_004304.4	1040	Gtg/Atg	19/29	0.722467217439963	3	FACETS	0.952	0.902	1	0.476	0.451	0.503	CLONAL	1	TRUE	1	0.751641977793975	3		1289	1376	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467810	66467810	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	112	486	1	ENST00000273854.3:c.459G>T	p.Met153Ile	p.M153I	ENST00000273854	NM_004439.5	153	atG/atT	3/18	1	2	FACETS	0.934	0.851	1	0.934	0.851	1	CLONAL	1	TRUE	1	0.751641977793975	2		487	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0019039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	662	949	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.55890947264317	3	FACETS	0.881	0.863	0.899			1	CLONAL	4	TRUE	NA	0.596860039415854	3		949	817	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0019039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	109	393	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.596860039415854	2		393	321	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889088	76889088	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	211	438	1	ENST00000373344.5:c.4922G>A	p.Trp1641Ter	p.W1641*	ENST00000373344	NM_000489.3	1641	tGg/tAg	18/35	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.596860039415854	1		439	375	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244799	46244799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	173	945	0	ENST00000334344.6:c.2893C>A	p.Gln965Lys	p.Q965K	ENST00000334344	NM_152641.2	965	Caa/Aaa	15/21	NA	2	FACETS	0.902	0.833	0.972			1	INDETERMINATE	1	TRUE	NA	0.596860039415854	2		945	643	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	166	574	9	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.89	0.821	0.962	0.89	0.821	0.962	CLONAL	1	TRUE	1	0.589077414519069	2		583	633	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0019040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	93	286	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	1	2	FACETS	0.905	0.812	1	0.905	0.812	1	CLONAL	1	TRUE	1	0.589077414519069	2		286	349	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793663	NA	P-0019040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	248	891	2	ENST00000263967.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000263967	NM_006218.2	93	cGg/cAg	2/21	1	2	FACETS	0.825	0.772	0.88	0.825	0.772	0.88	CLONAL	1	TRUE	1	0.589077414519069	2		893	1020	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645412	67645412	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	161	616	0	ENST00000264010.4:c.677A>G	p.Tyr226Cys	p.Y226C	ENST00000264010	NM_006565.3	226	tAc/tGc	3/12	0.579925579209893	1	FACETS	0.88	0.816	0.946	0.88	0.816	0.946	CLONAL	1	TRUE	0	0.589077414519069	1		616	438	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021828	71021828	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0019040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	76	338	0	ENST00000318789.4:c.1531-1G>C		p.X511_splice	ENST00000318789	NM_032682.5	511			1	2	FACETS	0.878	0.778	0.983	0.878	0.778	0.983	CLONAL	1	TRUE	1	0.589077414519069	2		338	294	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160646	56160656	+	frameshift_variant	Frame_Shift_Del	DEL	GTGTTAACAAA	GTGTTAACAAA	-	novel	NA	P-0019040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	124	584	0	ENST00000399503.3:c.923_933del	p.Val308AspfsTer14	p.V308Dfs*14	ENST00000399503	NM_005921.1	307	cGTGTTAACAAA/c	4/20	1	2	FACETS	0.678	0.615	0.744	0.678	0.615	0.744	SUBCLONAL	1	TRUE	1	0.589077414519069	2		584	621	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328454	137328454	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	206	793	0	ENST00000481739.1:c.1383G>C	p.Met461Ile	p.M461I	ENST00000481739	NM_002957.4	461	atG/atC	10/10	1	2	FACETS	0.786	0.73	0.844	0.786	0.73	0.844	SUBCLONAL	1	TRUE	1	0.589077414519069	2		793	890	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929252	44929252	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	214	948	0	ENST00000377967.4:c.2352G>C	p.Leu784Phe	p.L784F	ENST00000377967	NM_021140.2	784	ttG/ttC	17/29	1	2	FACETS	0.742	0.69	0.796	0.742	0.69	0.796	SUBCLONAL	1	TRUE	1	0.589077414519069	2		948	979	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177830	56177831	+	frameshift_variant	Frame_Shift_Ins	INS	TC	TC	GAA	novel	NA	P-0019040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	105	524	0	ENST00000399503.3:c.2803_2804delinsGAA	p.Ser935GlufsTer6	p.S935Efs*6	ENST00000399503	NM_005921.1	935	TCa/GAAa	14/20	1	2	FACETS	0.744	0.67	0.822	0.744	0.67	0.822	SUBCLONAL	1	TRUE	1	0.589077414519069	2		524	479	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	124	708	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.809	0.731	0.892	0.809	0.731	0.892	CLONAL	1	TRUE	1	0.29	2		709	1057	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0019041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	186	1104	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.296583228826447	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.29	1		1104	1073	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101300	27101300	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	176	810	1	ENST00000324856.7:c.4582C>T	p.Arg1528Ter	p.R1528*	ENST00000324856	NM_006015.4	1528	Cga/Tga	18/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.29	2		811	1000	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713430	30713450	+	inframe_deletion	In_Frame_Del	DEL	AAGGTCGCTTTGCTGAGGTCT	AAGGTCGCTTTGCTGAGGTCT	-	novel	NA	P-0019041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	139	603	0	ENST00000295754.5:c.756_776del	p.Lys252_Tyr259delinsAsn	p.K252_Y259delinsN	ENST00000295754	NM_003242.5	252	aAAGGTCGCTTTGCTGAGGTCTat/aat	4/7	0.23558839961353	2	FACETS	1	0.986	1	0.72	0.657	0.785	CLONAL	1	TRUE	0	0.29	2		603	666	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156521	55156521	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	110	599	1	ENST00000257290.5:c.2922T>A	p.His974Gln	p.H974Q	ENST00000257290	NM_006206.4	974	caT/caA	22/23	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.29	2		600	744	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0019042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	341	921	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	1	2	FACETS	0.797	0.755	0.84	0.797	0.755	0.84	SUBCLONAL	1	TRUE	1	0.792850456017906	2		921	1079	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125222	47125222	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	243	633	0	ENST00000409792.3:c.6048G>A	p.Trp2016Ter	p.W2016*	ENST00000409792	NM_014159.6	2016	tgG/tgA	12/21	1	2	FACETS	0.959	0.902	1	0.959	0.902	1	CLONAL	1	TRUE	1	0.792850456017906	2		633	639	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155996	106155996	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	31	578	0	ENST00000380013.4:c.897T>A	p.Asp299Glu	p.D299E	ENST00000380013	NM_001127208.2	299	gaT/gaA	3/11	1	2	FACETS	0.133	0.107	0.163	0.133	0.107	0.163	SUBCLONAL	1	TRUE	1	0.792850456017906	2		578	587	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061221	38061232	+	inframe_deletion	In_Frame_Del	DEL	GTTCTCGAACAT	GTTCTCGAACAT	-	novel	NA	P-0019043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	58	645	0	ENST00000250448.2:c.757_768del	p.Met253_Asn256del	p.M253_N256del	ENST00000250448	NM_004496.3	253	ATGTTCGAGAAC/-	2/2	1	2	FACETS	0.637	0.546	0.736	0.637	0.546	0.736	SUBCLONAL	1	FALSE	1	0.234708720879767	2		645	776	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425869	49425869	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0019043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	37	678	0	ENST00000301067.7:c.12619A>T	p.Lys4207Ter	p.K4207*	ENST00000301067	NM_003482.3	4207	Aaa/Taa	39/54	0.153949308383771	4	FACETS	1	0.933	1	0.64	0.53	0.763	CLONAL	1	FALSE	2	0.234708720879767	4		678	304	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	94	917	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.911	0.81	1	0.911	0.81	1	CLONAL	1	TRUE	1	0.240395446276499	2		917	858	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0019044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	20	599	1	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.240395446276499	1	FACETS	0.357	0.272	0.457	0.357	0.272	0.457	SUBCLONAL	1	TRUE	0	0.240395446276499	1		600	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0019044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	92	1087	0	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.240395446276499	2		1087	754	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918992	50918992	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568638496	NA	P-0019044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	50	902	0	ENST00000440232.2:c.2729G>A	p.Arg910Gln	p.R910Q	ENST00000440232	NM_002691.3	910	cGg/cAg	22/27	1	2	FACETS	0.704	0.597	0.822	0.704	0.597	0.822	SUBCLONAL	1	TRUE	1	0.240395446276499	2		902	591	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948520	71948520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777553838	NA	P-0019044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	37	1267	1	ENST00000298229.2:c.3232C>T	p.Arg1078Trp	p.R1078W	ENST00000298229	NM_001567.3	1078	Cgg/Tgg	26/28	1	2	FACETS	0.428	0.352	0.514	0.428	0.352	0.514	SUBCLONAL	1	TRUE	1	0.240395446276499	2		1268	719	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922954	44922954	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	46	1114	0	ENST00000377967.4:c.1817del	p.Asn606ThrfsTer19	p.N606Tfs*19	ENST00000377967	NM_021140.2	605	ggA/gg	16/29	1	2	FACETS	0.452	0.38	0.533	0.452	0.38	0.533	SUBCLONAL	1	TRUE	1	0.240395446276499	2		1114	846	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0019051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	15	696	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	1	2	FACETS	0.26	0.189	0.346	0.26	0.189	0.346	SUBCLONAL	1	TRUE	1	0.188550188214745	2		696	613	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097721	27097721	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	194	912	1	ENST00000324856.7:c.3310G>T	p.Glu1104Ter	p.E1104*	ENST00000324856	NM_006015.4	1104	Gaa/Taa	12/20	0.188550188214745	2	FACETS	0.86	0.797	0.924	1	0.987	1	CLONAL	3	TRUE	0	0.188550188214745	2		913	798	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856448	111856448	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1445323886	NA	P-0019051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	47	505	1	ENST00000341259.2:c.499G>A	p.Gly167Arg	p.G167R	ENST00000341259	NM_005475.2	167	Gga/Aga	2/8	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.188550188214745	2		506	450	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440957	56440957	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	47	671	0	ENST00000407977.2:c.380G>C	p.Arg127Pro	p.R127P	ENST00000407977		127	cGg/cCg	4/10	1	2	FACETS	0.983	0.83	1	0.983	0.83	1	CLONAL	1	TRUE	1	0.188550188214745	2		671	507	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900180	101900180	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	46	412	1	ENST00000374994.4:c.614T>A	p.Ile205Asn	p.I205N	ENST00000374994	NM_004612.2	205	aTt/aAt	4/9	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.188550188214745	2		413	405	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0019052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	94	393	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.725217345302448	4	FACETS	1	0.981	1	0.706	0.637	0.777	CLONAL	1	FALSE	2	0.958504772248213	4		393	272	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0019052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	534	1034	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.831511356445902	4	FACETS	1	0.997	1			1	CLONAL	3	FALSE	NA	0.958504772248213	4		1035	634	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589149	67589151	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	novel	NA	P-0019052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	48	474	0	ENST00000274335.5:c.1138_1140del	p.Leu380del	p.L380del	ENST00000274335		379	aaATTa/aaa	9/15	0.634633153350778	4	FACETS	0.88	0.752	1	0.293	0.25	0.339	CLONAL	1	FALSE	1	0.958504772248213	4		474	223	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890157	76890158	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0019052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	184	1000	0	ENST00000373344.5:c.4736_4737del	p.Val1579GlufsTer21	p.V1579Efs*21	ENST00000373344	NM_000489.3	1579	gTG/g	17/35	0.543685918732624	3	FACETS	1	0.992	1	0.73	0.684	0.777	INDETERMINATE	1	FALSE	1	0.958504772248213	3		1000	389	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260198	16260198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	43	700	3	ENST00000375759.3:c.7463G>A	p.Gly2488Glu	p.G2488E	ENST00000375759	NM_015001.2	2488	gGg/gAg	11/15	0.876007880173924	5	FACETS	0.443	0.37	0.523	0.148	0.123	0.175	SUBCLONAL	1	FALSE	2	0.958504772248213	5		703	494	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661951	29661952	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0019052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	23	943	0	ENST00000356175.3:c.5847_5848del	p.Arg1949SerfsTer6	p.R1949Sfs*6	ENST00000356175	NM_000267.3	1949	AGa/a	39/57	0.831511356445902	4	FACETS	0.212	0.164	0.267			1	SUBCLONAL	1	FALSE	NA	0.958504772248213	4		943	444	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39709868	39709870	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs748165145	NA	P-0019052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	30	544	1	ENST00000361337.2:c.504_506del	p.Glu169del	p.E169del	ENST00000361337	NM_003286.2	165	ctAGAa/cta	7/21	0.958504772248213	4	FACETS	0.269	0.217	0.33			1	SUBCLONAL	1	FALSE	NA	0.958504772248213	4		545	455	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404330	139404331	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0019052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	36	935	0	ENST00000277541.6:c.2823_2824del	p.Phe941LeufsTer2	p.F941Lfs*2	ENST00000277541	NM_017617.3	941	ttCTgt/ttgt	18/34	0.433436442667705	6	FACETS	0.351	0.288	0.423	0.117	0.096	0.141	INDETERMINATE	1	FALSE	3	0.958504772248213	6		935	624	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0019054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	79	715	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.862	0.757	0.975	0.862	0.757	0.975	CLONAL	1	TRUE	1	0.23	2		717	797	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855984	68855984	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121964877	NA	P-0019054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	108	887	1	ENST00000261769.5:c.1792C>T	p.Arg598Ter	p.R598*	ENST00000261769	NM_004360.3	598	Cga/Tga	12/16	0.3	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.23	1		888	729	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100663	67100663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	66	603	0	ENST00000412916.2:c.361G>A	p.Gly121Ser	p.G121S	ENST00000412916		121	Ggt/Agt	4/6	0.3	1	FACETS	0.91	0.791	1	0.91	0.791	1	CLONAL	1	TRUE	0	0.23	1		603	558	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679396	29679396	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	49	699	1	ENST00000356175.3:c.7516G>A	p.Gly2506Arg	p.G2506R	ENST00000356175	NM_000267.3	2506	Ggg/Agg	50/57	1	2	FACETS	0.2	0.169	0.234	0.2	0.169	0.234	SUBCLONAL	1	TRUE	1	0.815379801611609	2		700	601	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323231	31323232	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGGTGTCCTGAGTTTGGTCCTCGCCATC	novel	NA	P-0019055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	130	596	0	ENST00000412585.2:c.757_758insGATGGCGAGGACCAAACTCAGGACACCG	p.Glu253GlyfsTer20	p.E253Gfs*20	ENST00000412585	NM_005514.6	253	gag/gGATGGCGAGGACCAAACTCAGGACACCGag	4/8	0.815379801611609	1	FACETS	0.609	0.561	0.658	0.609	0.561	0.658	SUBCLONAL	1	TRUE	0	0.815379801611609	1		596	310	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	261	364	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.877368173226572	2		365	545	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027168	49027168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913305	NA	P-0019056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	438	688	2	ENST00000267163.4:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	579	Cga/Tga	18/27	0.877519748493915	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.877368173226572	2		690	499	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591076	67591076	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	186	494	0	ENST00000274335.5:c.1669C>G	p.Arg557Gly	p.R557G	ENST00000274335		557	Cga/Gga	12/15	1	2	FACETS	0.908	0.847	0.97	0.908	0.847	0.97	CLONAL	1	TRUE	1	0.877368173226572	2		494	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577612	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CTAG	CTAG	-	novel	NA	P-0019056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	312	567	0	ENST00000269305.4:c.673-4_673-1del		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.877519748493915	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.877368173226572	1		567	391	SUCCESS
AR	367	MSKCC	GRCh37	X	66765305	66765305	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	63	463	0	ENST00000374690.3:c.317G>A	p.Gly106Asp	p.G106D	ENST00000374690	NM_000044.3	106	gGc/gAc	1/8	0.629232237972832	2	FACETS	0.196	0.169	0.225			1	SUBCLONAL	1	TRUE	NA	0.877368173226572	2		463	733	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992354	72992354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770703902	NA	P-0019057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	259	1071	3	ENST00000268489.5:c.1691C>T	p.Ala564Val	p.A564V	ENST00000268489	NM_006885.3	564	gCg/gTg	2/10	0.248462967514953	1	FACETS	0.885	0.83	0.943	1	0.994	1	CLONAL	2	TRUE	0	0.248462967514953	1		1074	1031	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30034825	30035147	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGCCTTAATCCTAGCTCTGCTCACTTCTTGGGGCTATTGATTAATTTGTTTCAGAAACACCATAGGAAGTGAATATTACCTCTTGCTATAGGTGACTTTGTGAATACTTCAAACTGTAAAATCACAACTTTCAGGAAATGTGATAAATTTAGTGGGAAAAAAATTTAATGCACGCCTTGCAAAGGCTTCTTTGAGGGTAGCACAGGAGGAAGTGCCAATATAGTGTGTTTGTCTTTTGCTCTGCAATTCTGCAGGTACTGGATCATGATGTTTCAAAGGAAGAACCAGTCACCTTTCACTTCTTGGCCAAATTTTATCCTGAG	TGCCTTAATCCTAGCTCTGCTCACTTCTTGGGGCTATTGATTAATTTGTTTCAGAAACACCATAGGAAGTGAATATTACCTCTTGCTATAGGTGACTTTGTGAATACTTCAAACTGTAAAATCACAACTTTCAGGAAATGTGATAAATTTAGTGGGAAAAAAATTTAATGCACGCCTTGCAAAGGCTTCTTTGAGGGTAGCACAGGAGGAAGTGCCAATATAGTGTGTTTGTCTTTTGCTCTGCAATTCTGCAGGTACTGGATCATGATGTTTCAAAGGAAGAACCAGTCACCTTTCACTTCTTGGCCAAATTTTATCCTGAG	-	novel	NA	P-0019057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	37	3	0	ENST00000338641.4:c.241-254_309del		p.X81_splice	ENST00000338641	NM_000268.3	81		3/16	0.248462967514953	0	FACETS	0.414	0.34	0.496			1	SUBCLONAL	1	TRUE	0	0.248462967514953	0		3	541	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	278	364	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.88588469273271	2		365	621	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439634	51439634	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	233	520	0	ENST00000262662.1:c.199G>C	p.Asp67His	p.D67H	ENST00000262662		67	Gac/Cac	4/4	0.817140388347322	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.88588469273271	1		520	292	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433904	49433904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	510	1062	1	ENST00000301067.7:c.7649del	p.Pro2550LeufsTer33	p.P2550Lfs*33	ENST00000301067	NM_003482.3	2550	cCt/ct	31/54	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.88588469273271	2		1063	1108	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618892	37618892	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs771462646	NA	P-0019058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	422	1086	0	ENST00000447079.4:c.568C>G	p.Leu190Val	p.L190V	ENST00000447079	NM_015083.1	190	Ctg/Gtg	1/14	1	2	FACETS	0.893	0.853	0.933	0.893	0.853	0.933	CLONAL	1	TRUE	1	0.88588469273271	2		1086	1067	SUCCESS
APC	324	MSKCC	GRCh37	5	112178229	112178229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	296	745	0	ENST00000257430.4:c.6938C>T	p.Ala2313Val	p.A2313V	ENST00000257430	NM_000038.5	2313	gCc/gTc	16/16	1	2	FACETS	0.937	0.888	0.987	0.937	0.888	0.987	CLONAL	1	TRUE	1	0.88588469273271	2		745	713	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933238	39933238	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	591	575	0	ENST00000378444.4:c.1361A>C	p.Lys454Thr	p.K454T	ENST00000378444	NM_001123385.1	454	aAa/aCa	4/15	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.88588469273271	1		575	658	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061196	38061196	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	133	599	0	ENST00000250448.2:c.793del	p.Arg265AlafsTer56	p.R265Afs*56	ENST00000250448	NM_004496.3	265	Cgc/gc	2/2	1	2	FACETS	1	0.966	1	1	0.992	1	CLONAL	2	TRUE	1	0.35	2		599	348	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667816	37667816	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	120	771	0	ENST00000447079.4:c.2701T>G	p.Tyr901Asp	p.Y901D	ENST00000447079	NM_015083.1	901	Tac/Gac	8/14	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.35	2		771	488	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37672015	37672015	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	119	860	0	ENST00000447079.4:c.2801del	p.Pro934LeufsTer12	p.P934Lfs*12	ENST00000447079	NM_015083.1	934	Cct/ct	9/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.35	2		860	522	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	18	917	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.499	0.375	0.645	0.499	0.375	0.645	SUBCLONAL	1	FALSE	1	0.21746968376137	2		917	332	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603023	48603023	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555687378	NA	P-0019060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	14	370	0	ENST00000342988.3:c.1324C>T	p.Gln442Ter	p.Q442*	ENST00000342988	NM_005359.5	442	Cag/Tag	11/12	1	2	FACETS	0.79	0.573	1	0.79	0.573	1	CLONAL	1	FALSE	1	0.21746968376137	2		370	163	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578369	7578369	+	splice_donor_variant	Splice_Site	DEL	A	A	-	rs1567552459	NA	P-0019060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	18	582	1	ENST00000269305.4:c.559+2del		p.X187_splice	ENST00000269305	NM_001126112.2	187			1	2	FACETS	0.997	0.756	1	0.997	0.756	1	CLONAL	1	FALSE	1	0.21746968376137	2		583	166	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	59	669	2	ENST00000342988.3:c.1610A>T	p.Asp537Val	p.D537V	ENST00000342988	NM_005359.5	537	gAc/gTc	12/12	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.252982178640476	2		671	457	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022592	31022592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs373221034	NA	P-0019061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	46	888	1	ENST00000375687.4:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000375687	NM_015338.5	693	Cga/Tga	13/13	1	2	FACETS	0.54	0.453	0.635	0.54	0.453	0.635	SUBCLONAL	1	TRUE	1	0.252982178640476	2		889	674	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729984	41729984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	118	850	0	ENST00000242208.4:c.545C>T	p.Pro182Leu	p.P182L	ENST00000242208	NM_002192.2	182	cCg/cTg	3/3	0.185461010652805	3	FACETS	1	0.984	1	0.742	0.67	0.818	CLONAL	1	TRUE	1	0.252982178640476	3		850	708	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919637	50919665	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGCCATGTGGCCGCAGGACCCGCTGTTCG	TGCCATGTGGCCGCAGGACCCGCTGTTCG	-	novel	NA	P-0019061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	55	751	1	ENST00000440232.2:c.2821-13_2836del		p.X941_splice	ENST00000440232	NM_002691.3	941		23/27	1	2	FACETS	0.864	0.74	1	0.864	0.74	1	CLONAL	1	TRUE	1	0.252982178640476	2		752	503	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522566	187522566	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	54	633	0	ENST00000441802.2:c.11497A>C	p.Thr3833Pro	p.T3833P	ENST00000441802	NM_005245.3	3833	Aca/Cca	21/27	1	2	FACETS	0.684	0.584	0.794	0.684	0.584	0.794	SUBCLONAL	1	TRUE	1	0.252982178640476	2		633	624	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5078344	5078344	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	69	669	0	ENST00000381652.3:c.2031A>C	p.Lys677Asn	p.K677N	ENST00000381652	NM_004972.3	677	aaA/aaC	16/25	1	2	FACETS	0.82	0.714	0.935	0.82	0.714	0.935	CLONAL	1	TRUE	1	0.252982178640476	2		669	665	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400236	139400236	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	43	757	1	ENST00000277541.6:c.4112C>A	p.Thr1371Asn	p.T1371N	ENST00000277541	NM_017617.3	1371	aCc/aAc	25/34	1	2	FACETS	0.811	0.68	0.957	0.811	0.68	0.957	CLONAL	1	TRUE	1	0.252982178640476	2		758	419	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0019062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	107	527	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.433876043380606	1	FACETS	0.868	0.783	0.956	0.868	0.783	0.956	CLONAL	1	TRUE	0	0.433876043380606	1		527	445	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0019062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	98	643	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.754	0.674	0.839	0.754	0.674	0.839	SUBCLONAL	1	TRUE	1	0.433876043380606	2		643	599	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578214	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs864309495	NA	P-0019062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	440	1016	1	ENST00000269305.4:c.635_636del	p.Phe212SerfsTer3	p.F212Sfs*3	ENST00000269305	NM_001126112.2	212	tTT/t	6/11	0.383023069963079	2	FACETS	0.893	0.853	0.933	0.893	0.853	0.933	CLONAL	2	TRUE	0	0.433876043380606	2		1017	1136	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3794901	3794901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	128	611	0	ENST00000262367.5:c.3976G>A	p.Ala1326Thr	p.A1326T	ENST00000262367	NM_004380.2	1326	Gct/Act	23/31	0.433876043380606	1	FACETS	0.867	0.789	0.948	0.867	0.789	0.948	CLONAL	1	TRUE	0	0.433876043380606	1		611	533	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	158	917	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.206013416168461	3	FACETS	0.964	0.886	1	0.964	0.886	1	CLONAL	2	TRUE	1	0.26	3		917	712	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2111996	2111996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374936223	NA	P-0019063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	55	632	1	ENST00000219476.3:c.1244C>T	p.Ala415Val	p.A415V	ENST00000219476	NM_000548.3	415	gCg/gTg	12/42	0.242067039458196	4	FACETS	0.776	0.663	0.9	0.388	0.331	0.45	SUBCLONAL	1	TRUE	2	0.26	4		633	687	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579463	7579463	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	129	820	0	ENST00000269305.4:c.224del	p.Pro75LeufsTer48	p.P75Lfs*48	ENST00000269305	NM_001126112.2	75	cCt/ct	4/11	0.227531414165313	2	FACETS	0.91	0.829	0.995	0.91	0.829	0.995	CLONAL	2	TRUE	0	0.26	2		820	545	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562982	21562982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	67	678	2	ENST00000382592.4:c.937G>A	p.Val313Met	p.V313M	ENST00000382592	NM_014572.2	313	Gtg/Atg	4/8	0.258954448174838	4	FACETS	1	0.903	1	0.349	0.303	0.399	CLONAL	1	TRUE	1	0.26	4		680	620	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663307	67663307	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	40	518	0	ENST00000264010.4:c.1708A>G	p.Met570Val	p.M570V	ENST00000264010	NM_006565.3	570	Atg/Gtg	10/12	0.197221396072209	3	FACETS	0.7	0.581	0.832	0.35	0.29	0.416	SUBCLONAL	1	TRUE	1	0.26	3		518	497	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0019065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	180	815	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	NA	2	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.338239477785629	2		815	1001	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0019065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	67	459	1	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	0.693	0.602	0.79	0.693	0.602	0.79	SUBCLONAL	1	TRUE	1	0.338239477785629	2		460	572	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	81	385	0	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.338239477785629	2		385	448	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189847	11189847	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	107	631	0	ENST00000361445.4:c.5662T>A	p.Phe1888Ile	p.F1888I	ENST00000361445	NM_004958.3	1888	Ttc/Atc	40/58	0.338239477785629	1	FACETS	0.858	0.771	0.949	0.858	0.771	0.949	CLONAL	1	TRUE	0	0.338239477785629	1		631	613	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333889	70333889	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	98	544	2	ENST00000373644.4:c.1794G>T	p.Gln598His	p.Q598H	ENST00000373644	NM_030625.2	598	caG/caT	2/12	1	2	FACETS	0.985	0.881	1	0.985	0.881	1	CLONAL	1	TRUE	1	0.338239477785629	2		546	588	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028672	12028672	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	80	526	0	ENST00000353533.5:c.875G>C	p.Ser292Thr	p.S292T	ENST00000353533	NM_003010.3	292	aGt/aCt	8/11	0.320232558353645	1	FACETS	0.817	0.722	0.919	0.817	0.722	0.919	CLONAL	1	TRUE	0	0.338239477785629	1		526	481	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453387	40453387	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761867798	NA	P-0019065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	164	920	0	ENST00000345506.4:c.1084G>A	p.Val362Met	p.V362M	ENST00000345506	NM_003152.3	362	Gtg/Atg	10/20	0.338239477785629	3	FACETS	0.953	0.873	1	0.476	0.436	0.518	CLONAL	1	TRUE	1	0.338239477785629	3		920	1190	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119969	70119969	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	59	324	0	ENST00000245479.2:c.972del	p.Ala325ArgfsTer58	p.A325Rfs*58	ENST00000245479	NM_000346.3	324	aCc/ac	3/3	0.338239477785629	3	FACETS	1	0.875	1	0.507	0.438	0.582	CLONAL	1	TRUE	1	0.338239477785629	3		324	402	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120000	70120001	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGGA	novel	NA	P-0019065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	43	142	0	ENST00000245479.2:c.1005_1008dup	p.Ser337AspfsTer242	p.S337Dfs*242	ENST00000245479	NM_000346.3	334	-/TGGA	3/3	0.338239477785629	3	FACETS	0.751	0.636	0.875	0.751	0.636	0.875	SUBCLONAL	2	TRUE	1	0.338239477785629	3		142	198	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65569055	65569055	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0019067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	104	710	0	ENST00000358664.4:c.3G>A	p.Met1?	p.M1?	ENST00000358664	NM_002382.4	1	atG/atA	1/5	0.539204758900577	1	FACETS	0.694	0.626	0.765	0.694	0.626	0.765	SUBCLONAL	1	TRUE	0	0.539204758900577	1		710	406	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560530	65560530	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	85	463	0	ENST00000358664.4:c.67G>A	p.Asp23Asn	p.D23N	ENST00000358664	NM_002382.4	23	Gac/Aac	3/5	0.539204758900577	1	FACETS	0.872	0.782	0.966	0.872	0.782	0.966	CLONAL	1	TRUE	0	0.539204758900577	1		463	264	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65569036	65569036	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	104	754	0	ENST00000358664.4:c.22G>C	p.Glu8Gln	p.E8Q	ENST00000358664	NM_002382.4	8	Gag/Cag	1/5	0.539204758900577	1	FACETS	0.66	0.595	0.728	0.66	0.595	0.728	SUBCLONAL	1	TRUE	0	0.539204758900577	1		754	427	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684073	29684073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	270	733	1	ENST00000356175.3:c.7771G>A	p.Asp2591Asn	p.D2591N	ENST00000356175	NM_000267.3	2591	Gat/Aat	52/57	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.539204758900577	2		734	831	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264360	30264360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	79	277	1	ENST00000322652.5:c.95C>T	p.Ala32Val	p.A32V	ENST00000322652	NM_015355.2	32	gCg/gTg	1/16	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.539204758900577	2		278	277	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367825	15367825	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	233	904	0	ENST00000263377.2:c.1501G>C	p.Asp501His	p.D501H	ENST00000263377	NM_058243.2	501	Gat/Cat	8/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.539204758900577	2		904	814	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229256	36229256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	232	960	1	ENST00000222270.7:c.7946G>A	p.Arg2649His	p.R2649H	ENST00000222270	NM_014727.1	2649	cGc/cAc	37/37	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.539204758900577	2		961	850	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24158995	24158996	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0019067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	215	841	2	ENST00000263121.7:c.669_670del	p.Cys223Ter	p.C223*	ENST00000263121	NM_003073.3	223	TGt/t	6/9	0.539204758900577	1	FACETS	0.913	0.853	0.974	0.913	0.853	0.974	CLONAL	1	TRUE	0	0.539204758900577	1		843	638	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668807	52668807	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	170	515	1	ENST00000394830.3:c.1112C>T	p.Ser371Leu	p.S371L	ENST00000394830	NM_018313.4	371	tCa/tTa	12/30	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.539204758900577	2		516	599	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109415128	109415128	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1441272756	NA	P-0019067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	332	1281	0	ENST00000436639.2:c.149C>T	p.Ser50Leu	p.S50L	ENST00000436639	NM_014454.2	50	tCa/tTa	1/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.539204758900577	2		1281	1174	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65569028	65569030	+	missense_variant	Missense_Mutation	TNP	CTC	CTC	TTT	novel	NA	P-0019067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	105	761	0	ENST00000358664.4:c.28_30delinsAAA	p.Glu10Lys	p.E10K	ENST00000358664	NM_002382.4	10	GAG/AAA	1/5	0.539204758900577	1	FACETS	0.647	0.583	0.713	0.647	0.583	0.713	SUBCLONAL	1	TRUE	0	0.539204758900577	1		761	440	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	225	574	9	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.202000780112547	3	FACETS	1	0.974	1	1	0.993	1	CLONAL	3	TRUE	1	0.202000780112547	3		583	757	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111472	8111473	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0019068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	82	924	0	ENST00000346208.3:c.959_960del	p.Cys320SerfsTer31	p.C320Sfs*31	ENST00000346208		320	TGt/t	5/6	0.202000780112547	3	FACETS	1	0.922	1	0.531	0.468	0.6	CLONAL	1	TRUE	1	0.202000780112547	3		924	841	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434553	49434553	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196495584	NA	P-0019068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	70	760	1	ENST00000301067.7:c.7000C>T	p.Arg2334Trp	p.R2334W	ENST00000301067	NM_003482.3	2334	Cgg/Tgg	31/54	0.131138308572605	4	FACETS	1	0.93	1	0.552	0.481	0.63	CLONAL	1	TRUE	2	0.202000780112547	4		761	754	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845579	72845579	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	146	591	1	ENST00000268489.5:c.3761G>T	p.Cys1254Phe	p.C1254F	ENST00000268489	NM_006885.3	1254	tGc/tTc	7/10	0.202000780112547	2	FACETS	0.853	0.782	0.926	1	0.983	1	CLONAL	3	TRUE	0	0.202000780112547	2		592	565	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343198	118343198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	291	531	1	ENST00000534358.1:c.1324C>T	p.Arg442Ter	p.R442*	ENST00000534358	NM_005933.3	442	Cga/Tga	3/36	0.617196662746276	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.617196662746276	2		532	466	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102874156	102874156	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	148	594	0	ENST00000307046.8:c.4G>A	p.Gly2Arg	p.G2R	ENST00000307046	NM_001111285.1	2	Gga/Aga	1/4	0.617196662746276	4	FACETS	1	0.959	1	0.539	0.493	0.587	CLONAL	1	TRUE	2	0.617196662746276	4		594	719	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	211	858	13	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	0.224032369886997	3	FACETS	1	0.968	1	0.537	0.498	0.577	INDETERMINATE	1	TRUE	1	0.446215648402984	3		871	1077	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	70	584	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.404	0.351	0.461	0.404	0.351	0.461	SUBCLONAL	1	TRUE	1	0.446215648402984	2		584	777	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	186	894	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.224032369886997	3	FACETS	0.898	0.828	0.97	0.449	0.414	0.485	INDETERMINATE	1	TRUE	1	0.446215648402984	3		895	1136	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	66	527	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.507	0.44	0.579	0.507	0.44	0.579	SUBCLONAL	1	TRUE	1	0.446215648402984	2		528	584	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	208	863	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.971	0.902	1	0.971	0.902	1	CLONAL	1	TRUE	1	0.446215648402984	2		865	960	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863054	56863054	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1266824391	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	131	1009	1	ENST00000519728.1:c.327del	p.Glu110LysfsTer15	p.E110Kfs*15	ENST00000519728	NM_002350.3	107	acA/ac	5/13	1	2	FACETS	0.528	0.477	0.58	0.528	0.477	0.58	SUBCLONAL	1	TRUE	1	0.446215648402984	2		1010	1113	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	87	698	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.46	0.407	0.518	0.46	0.407	0.518	SUBCLONAL	1	TRUE	1	0.446215648402984	2		699	847	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261803	16261803	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	103	814	0	ENST00000375759.3:c.9068C>G	p.Ala3023Gly	p.A3023G	ENST00000375759	NM_015001.2	3023	gCt/gGt	11/15	1	2	FACETS	0.518	0.462	0.576	0.518	0.462	0.576	SUBCLONAL	1	TRUE	1	0.446215648402984	2		814	892	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105715	27105717	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs765246223	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	24	383	0	ENST00000324856.7:c.5334_5336del	p.Glu1780del	p.E1780del	ENST00000324856	NM_006015.4	1776	GAA/-	20/20	1	2	FACETS	0.282	0.22	0.352	0.282	0.22	0.352	SUBCLONAL	1	TRUE	1	0.446215648402984	2		383	382	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653859	89653861	+	inframe_deletion	In_Frame_Del	DEL	GTA	GTA	-	rs1554893831	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	84	671	0	ENST00000371953.3:c.160_162del	p.Val54del	p.V54del	ENST00000371953	NM_000314.4	53	GTA/-	2/9	1	2	FACETS	0.514	0.453	0.578	0.514	0.453	0.578	SUBCLONAL	1	TRUE	1	0.446215648402984	2		671	733	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712013	89712014	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1114167663	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	23	331	0	ENST00000371953.3:c.632dup	p.Cys211TrpfsTer32	p.C211Wfs*32	ENST00000371953	NM_000314.4	211	tgc/tGgc	6/9	1	2	FACETS	0.323	0.252	0.406	0.323	0.252	0.406	SUBCLONAL	1	TRUE	1	0.446215648402984	2		331	319	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022747	12022747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376242225	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	50	601	1	ENST00000396373.4:c.853G>A	p.Val285Met	p.V285M	ENST00000396373	NM_001987.4	285	Gtg/Atg	5/8	0.224032369886997	3	FACETS	0.363	0.307	0.424	0.181	0.153	0.212	INDETERMINATE	1	TRUE	1	0.446215648402984	3		602	756	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433089	49433089	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	123	887	0	ENST00000301067.7:c.8282T>C	p.Leu2761Pro	p.L2761P	ENST00000301067	NM_003482.3	2761	cTg/cCg	33/54	0.224032369886997	3	FACETS	0.589	0.532	0.651	0.295	0.266	0.326	INDETERMINATE	1	TRUE	1	0.446215648402984	3		887	1144	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	106	916	7	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	0.224032369886997	3	FACETS	0.468	0.418	0.521	0.234	0.209	0.261	INDETERMINATE	1	TRUE	1	0.446215648402984	3		923	1242	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636037	28636037	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	116	852	0	ENST00000241453.7:c.335T>C	p.Leu112Pro	p.L112P	ENST00000241453	NM_004119.2	112	cTg/cCg	3/24	1	2	FACETS	0.5	0.45	0.554	0.5	0.45	0.554	SUBCLONAL	1	TRUE	1	0.446215648402984	2		852	1039	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046674	42046674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780027483	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	92	795	1	ENST00000219905.7:c.7048G>A	p.Val2350Met	p.V2350M	ENST00000219905	NM_001164273.1	2350	Gtg/Atg	18/24	1	2	FACETS	0.465	0.413	0.522	0.465	0.413	0.522	SUBCLONAL	1	TRUE	1	0.446215648402984	2		796	886	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	39	374	3	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.453	0.376	0.539	0.453	0.376	0.539	SUBCLONAL	1	TRUE	1	0.446215648402984	2		377	386	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993137	72993137	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	142	1159	0	ENST00000268489.5:c.908A>C	p.His303Pro	p.H303P	ENST00000268489	NM_006885.3	303	cAt/cCt	2/10	1	2	FACETS	0.493	0.448	0.541	0.493	0.448	0.541	SUBCLONAL	1	TRUE	1	0.446215648402984	2		1159	1290	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435672	56435672	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	77	649	1	ENST00000407977.2:c.1465G>T	p.Gly489Trp	p.G489W	ENST00000407977		489	Ggg/Tgg	9/10	1	2	FACETS	0.447	0.392	0.507	0.447	0.392	0.507	SUBCLONAL	1	TRUE	1	0.446215648402984	2		650	772	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288789	15288789	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	17	108	0	ENST00000263388.2:c.3950del	p.Pro1317GlnfsTer103	p.P1317Qfs*103	ENST00000263388	NM_000435.2	1317	cCa/ca	24/33	1	2	FACETS	0.492	0.369	0.635	0.492	0.369	0.635	SUBCLONAL	1	TRUE	1	0.446215648402984	2		108	155	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298032	15298032	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371176740	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	126	1048	6	ENST00000263388.2:c.1724C>T	p.Thr575Met	p.T575M	ENST00000263388	NM_000435.2	575	aCg/aTg	11/33	1	2	FACETS	0.504	0.455	0.556	0.504	0.455	0.556	SUBCLONAL	1	TRUE	1	0.446215648402984	2		1054	1120	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383774	15383774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1229253526	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	89	755	1	ENST00000263377.2:c.137C>T	p.Pro46Leu	p.P46L	ENST00000263377	NM_058243.2	46	cCg/cTg	2/20	1	2	FACETS	0.481	0.426	0.54	0.481	0.426	0.54	SUBCLONAL	1	TRUE	1	0.446215648402984	2		756	829	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221481	36221481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	119	998	1	ENST00000222270.7:c.5240C>T	p.Ser1747Leu	p.S1747L	ENST00000222270	NM_014727.1	1747	tCg/tTg	25/37	1	2	FACETS	0.474	0.426	0.524	0.474	0.426	0.524	SUBCLONAL	1	TRUE	1	0.446215648402984	2		999	1126	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99163079	99163079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1403218618	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	77	806	2	ENST00000074304.5:c.1085C>T	p.Ala362Val	p.A362V	ENST00000074304	NM_001134224.1	362	gCg/gTg	13/26	1	2	FACETS	0.364	0.319	0.414	0.364	0.319	0.414	SUBCLONAL	1	TRUE	1	0.446215648402984	2		808	947	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265048	46265049	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	108	834	0	ENST00000371998.3:c.1924dup	p.Leu642ProfsTer6	p.L642Pfs*6	ENST00000371998		640	tcc/tCcc	12/23	1	2	FACETS	0.558	0.5	0.62	0.558	0.5	0.62	SUBCLONAL	1	TRUE	1	0.446215648402984	2		834	867	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513520	41513520	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	86	793	2	ENST00000263253.7:c.424G>T	p.Gly142Ter	p.G142*	ENST00000263253	NM_001429.3	142	Gga/Tga	2/31	1	2	FACETS	0.422	0.373	0.476	0.422	0.373	0.476	SUBCLONAL	1	TRUE	1	0.446215648402984	2		795	913	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582248	52582248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375268569	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	28	239	0	ENST00000394830.3:c.4580G>A	p.Arg1527Gln	p.R1527Q	ENST00000394830	NM_018313.4	1527	cGa/cAa	30/30	1	2	FACETS	0.483	0.387	0.591	0.483	0.387	0.591	SUBCLONAL	1	TRUE	1	0.446215648402984	2		239	260	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980601	1980601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201148179	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	81	643	2	ENST00000382891.5:c.4063C>T	p.Arg1355Trp	p.R1355W	ENST00000382891	NM_133335.3	1355	Cgg/Tgg	22/22	1	2	FACETS	0.55	0.485	0.62	0.55	0.485	0.62	SUBCLONAL	1	TRUE	1	0.446215648402984	2		645	660	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228442	228442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	69	402	1	ENST00000264932.6:c.764C>T	p.Ala255Val	p.A255V	ENST00000264932	NM_004168.2	255	gCc/gTc	6/15	NA	2	FACETS	0.64	0.559	0.728			1	INDETERMINATE	1	TRUE	NA	0.446215648402984	2		403	483	SUCCESS
APC	324	MSKCC	GRCh37	5	112170720	112170720	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1460191563	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	80	692	1	ENST00000257430.4:c.1816A>G	p.Ile606Val	p.I606V	ENST00000257430	NM_000038.5	606	Ata/Gta	15/16	1	2	FACETS	0.501	0.44	0.566	0.501	0.44	0.566	SUBCLONAL	1	TRUE	1	0.446215648402984	2		693	716	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778245	27778245	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	42	578	0	ENST00000369163.2:c.394C>A	p.Arg132Ser	p.R132S	ENST00000369163	NM_003536.2	132	Cgc/Agc	1/1	1	2	FACETS	0.293	0.244	0.347	0.293	0.244	0.347	SUBCLONAL	1	TRUE	1	0.446215648402984	2		578	643	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120732	94120732	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	90	637	0	ENST00000369303.4:c.319A>T	p.Arg107Trp	p.R107W	ENST00000369303	NM_004440.3	107	Agg/Tgg	3/17	1	2	FACETS	0.553	0.49	0.619	0.553	0.49	0.619	SUBCLONAL	1	TRUE	1	0.446215648402984	2		637	730	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969894	161969894	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	98	631	0	ENST00000366898.1:c.1075G>T	p.Gly359Cys	p.G359C	ENST00000366898	NM_004562.2	359	Ggc/Tgc	9/12	1	2	FACETS	0.584	0.521	0.651	0.584	0.521	0.651	SUBCLONAL	1	TRUE	1	0.446215648402984	2		631	752	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042177	6042177	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	94	873	2	ENST00000265849.7:c.444del	p.Tyr149ThrfsTer52	p.Y149Tfs*52	ENST00000265849	NM_000535.5	148	ccC/cc	5/15	1	2	FACETS	0.413	0.366	0.463	0.413	0.366	0.463	SUBCLONAL	1	TRUE	1	0.446215648402984	2		875	1020	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481397	140481397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913376	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	88	698	0	ENST00000288602.6:c.1411G>A	p.Val471Ile	p.V471I	ENST00000288602	NM_004333.4	471	Gtc/Atc	11/18	1	2	FACETS	0.49	0.433	0.551	0.49	0.433	0.551	SUBCLONAL	1	TRUE	1	0.446215648402984	2		698	805	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958469	90958469	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	62	703	0	ENST00000265433.3:c.1969A>G	p.Thr657Ala	p.T657A	ENST00000265433	NM_002485.4	657	Act/Gct	13/16	1	2	FACETS	0.364	0.314	0.419	0.364	0.314	0.419	SUBCLONAL	1	TRUE	1	0.446215648402984	2		703	763	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211533	98211533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs945517672	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	72	527	1	ENST00000331920.6:c.3622G>A	p.Ala1208Thr	p.A1208T	ENST00000331920	NM_000264.3	1208	Gcc/Acc	22/24	1	2	FACETS	0.486	0.424	0.553	0.486	0.424	0.553	SUBCLONAL	1	TRUE	1	0.446215648402984	2		528	664	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268793	98268793	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1554708751	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	120	955	2	ENST00000331920.6:c.290del	p.Asn97ThrfsTer20	p.N97Tfs*20	ENST00000331920	NM_000264.3	97	aAc/ac	2/24	1	2	FACETS	0.515	0.464	0.569	0.515	0.464	0.569	SUBCLONAL	1	TRUE	1	0.446215648402984	2		957	1044	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	84	605	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.583	0.515	0.656	0.583	0.515	0.656	SUBCLONAL	1	TRUE	1	0.446215648402984	2		605	646	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937602	76937603	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	74	536	0	ENST00000373344.5:c.3145dup	p.Ile1049AsnfsTer4	p.I1049Nfs*4	ENST00000373344	NM_000489.3	1049	ata/aAta	9/35	1	2	FACETS	0.536	0.469	0.608	0.536	0.469	0.608	SUBCLONAL	1	TRUE	1	0.446215648402984	2		536	619	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402776	139402776	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	635	1070	1	ENST00000277541.6:c.3233del	p.His1078ProfsTer101	p.H1078Pfs*101	ENST00000277541	NM_017617.3	1078	cAc/cc	20/34	0.777018529578936	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.777018529578936	2		1071	696	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52663015	52663015	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	95	522	0	ENST00000394830.3:c.1338T>A	p.Asp446Glu	p.D446E	ENST00000394830	NM_018313.4	446	gaT/gaA	13/30	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		522	599	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665752	29665755	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1555535032	NA	P-0019079-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	372	672	0	ENST00000356175.3:c.6789_6792del	p.Tyr2264ThrfsTer5	p.Y2264Tfs*5	ENST00000356175	NM_000267.3	2263	ACTTac/ac	45/57	0.728261865745902	4	FACETS	0.913	0.871	0.957	0.913	0.871	0.957	CLONAL	2	TRUE	2	0.852395405268679	4		672	885	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991902	72991902	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019079-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	184	776	1	ENST00000268489.5:c.2143C>T	p.Arg715Ter	p.R715*	ENST00000268489	NM_006885.3	715	Cga/Tga	2/10	0.767129900505831	3	FACETS	0.916	0.849	0.986	0.458	0.424	0.493	CLONAL	1	TRUE	1	0.852395405268679	3		777	672	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663442	29663442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019079-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	399	712	0	ENST00000356175.3:c.6035del	p.Asp2012ValfsTer4	p.D2012Vfs*4	ENST00000356175	NM_000267.3	2012	gAt/gt	40/57	0.728261865745902	4	FACETS	0.955	0.912	0.998	0.955	0.912	0.998	CLONAL	2	TRUE	2	0.852395405268679	4		712	908	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738201	133738202	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0019079-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	149	673	0	ENST00000318560.5:c.601_602del	p.His201SerfsTer96	p.H201Sfs*96	ENST00000318560	NM_005157.4	201	CAt/t	4/11	1	2	FACETS	0.915	0.846	0.985	0.915	0.846	0.985	CLONAL	1	TRUE	1	0.852395405268679	2		673	382	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771840	135771840	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1431256375	NA	P-0019080-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	236	767	0	ENST00000298552.3:c.3277C>T	p.Arg1093Ter	p.R1093*	ENST00000298552	NM_001162426.1	1093	Cga/Tga	23/23	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.833378828990733	2		767	549	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971124	21971125	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0019080-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	193	607	2	ENST00000304494.5:c.233_234del	p.Leu78HisfsTer41	p.L78Hfs*41	ENST00000304494	NM_000077.4	78	cTC/c	2/3	0.4463359553221	2	FACETS	1	0.971	1	0.532	0.498	0.567	INDETERMINATE	1	TRUE	0	0.833378828990733	2		609	435	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0019082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1246	878	1079	5	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.721548196347213	10	FACETS	1	0.995	1			1	CLONAL	4	TRUE	NA	0.721548196347213	10		1084	2124	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0019082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	642	1088	3	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	0.611777767532949	3	FACETS	0.943	0.92	0.965	0.943	0.92	0.965	CLONAL	3	TRUE	0	0.721548196347213	3		1091	856	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187483	32187483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1528	138	854	1	ENST00000375023.3:c.1396G>A	p.Gly466Ser	p.G466S	ENST00000375023	NM_004557.3	466	Ggc/Agc	8/30	0.721548196347213	8	FACETS	0.727	0.658	0.799	0.182	0.164	0.2	SUBCLONAL	1	TRUE	4	0.721548196347213	8		855	1666	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0019083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	105	1014	3	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.16	2		1017	1273	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0019084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	57	921	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	0.399	0.342	0.462	0.399	0.342	0.462	SUBCLONAL	1	FALSE	1	0.447714028226688	2		921	638	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412683	139412683	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	59	988	10	ENST00000277541.6:c.1161C>G	p.Cys387Trp	p.C387W	ENST00000277541	NM_017617.3	387	tgC/tgG	7/34	1	2	FACETS	0.313	0.268	0.362	0.313	0.268	0.362	SUBCLONAL	1	FALSE	1	0.447714028226688	2		998	842	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161326560	161326572	+	frameshift_variant	Frame_Shift_Del	DEL	TGATCCACACAGC	TGATCCACACAGC	AGA	novel	NA	P-0019084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	85	419	1	ENST00000367975.2:c.335_347delinsAGA	p.Leu112GlnfsTer21	p.L112Qfs*21	ENST00000367975	NM_003001.3	112	cTGATCCACACAGCt/cAGAt	5/6	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	1	0.447714028226688	2		420	350	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	352	708	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.327258154047988	3	FACETS	0.927	0.877	0.977	0.927	0.877	0.977	CLONAL	2	TRUE	1	0.348370502652198	3		709	1280	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0019085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	19	199	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	1	2	FACETS	0.527	0.401	0.674	0.527	0.401	0.674	SUBCLONAL	1	TRUE	1	0.348370502652198	2		199	207	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0019085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	503	1155	0	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	0.348370502652198	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.348370502652198	2		1155	1362	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323162	31323165	+	frameshift_variant	Frame_Shift_Del	DEL	CCAG	CCAG	-	novel	NA	P-0019085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	142	764	0	ENST00000412585.2:c.824_827del	p.Ser275Ter	p.S275*	ENST00000412585	NM_005514.6	275	tCTGGa/ta	4/8	1	2	FACETS	0.951	0.867	1	0.951	0.867	1	CLONAL	1	TRUE	1	0.348370502652198	2		764	857	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938259	76938259	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	160	463	0	ENST00000373344.5:c.2489A>T	p.Lys830Ile	p.K830I	ENST00000373344	NM_000489.3	830	aAa/aTa	9/35	0.306026764513488	2	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.348370502652198	2		463	676	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0019086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	271	1014	3	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.629554718697791	1	FACETS	0.928	0.878	0.978	0.928	0.878	0.978	CLONAL	1	TRUE	0	0.643953318307691	1		1017	615	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735470	40735470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761910971	NA	P-0019086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	198	1046	1	ENST00000373198.4:c.3403G>A	p.Val1135Met	p.V1135M	ENST00000373198	NM_133170.3	1135	Gtg/Atg	25/32	1	2	FACETS	0.885	0.823	0.949	0.885	0.823	0.949	CLONAL	1	TRUE	1	0.643953318307691	2		1047	695	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942685	48942685	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913301	NA	P-0019086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	310	707	0	ENST00000267163.4:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000267163	NM_000321.2	358	Cga/Tga	11/27	0.606302480509219	2	FACETS	0.83	0.792	0.868	0.83	0.792	0.868	CLONAL	2	TRUE	0	0.643953318307691	2		707	580	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933718	36933718	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	238	980	3	ENST00000361632.4:c.1681C>A	p.His561Asn	p.H561N	ENST00000361632		561	Cac/Aac	12/16	1	2	FACETS	0.986	0.924	1	0.986	0.924	1	CLONAL	1	TRUE	1	0.643953318307691	2		983	750	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506386	120506386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	227	873	1	ENST00000256646.2:c.1726C>T	p.Pro576Ser	p.P576S	ENST00000256646	NM_024408.3	576	Ccc/Tcc	11/34	1	2	FACETS	0.926	0.866	0.988	0.926	0.866	0.988	CLONAL	1	TRUE	1	0.643953318307691	2		874	761	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857593	9857593	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	116	541	0	ENST00000330684.3:c.3808G>T	p.Asp1270Tyr	p.D1270Y	ENST00000330684	NM_001134407.1	1270	Gac/Tac	13/13	1	2	FACETS	0.872	0.793	0.955	0.872	0.793	0.955	CLONAL	1	TRUE	1	0.643953318307691	2		541	413	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783709	50783709	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	199	1109	0	ENST00000398568.2:c.100C>T	p.Gln34Ter	p.Q34*	ENST00000398568	NM_001042412.1	34	Caa/Taa	3/18	0.629554718697791	1	FACETS	0.812	0.759	0.866	0.812	0.759	0.866	CLONAL	1	TRUE	0	0.643953318307691	1		1109	516	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948824	17948824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747854515	NA	P-0019086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	248	1094	0	ENST00000458235.1:c.1618C>T	p.Arg540Cys	p.R540C	ENST00000458235	NM_000215.3	540	Cgc/Tgc	12/24	1	2	FACETS	0.95	0.891	1	0.95	0.891	1	CLONAL	1	TRUE	1	0.643953318307691	2		1094	811	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954670	17954670	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	265	1134	5	ENST00000458235.1:c.224C>A	p.Thr75Lys	p.T75K	ENST00000458235	NM_000215.3	75	aCg/aAg	3/24	1	2	FACETS	0.996	0.937	1	0.996	0.937	1	CLONAL	1	TRUE	1	0.643953318307691	2		1139	826	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582379	119582379	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	126	454	0	ENST00000316626.5:c.1022G>C	p.Arg341Pro	p.R341P	ENST00000316626		341	cGa/cCa	10/12	NA	2	FACETS	0.667	0.606	0.731			1	INDETERMINATE	1	TRUE	NA	0.643953318307691	2		454	587	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638351	117638351	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	133	747	0	ENST00000368508.3:c.6090G>T	p.Glu2030Asp	p.E2030D	ENST00000368508	NM_002944.2	2030	gaG/gaT	38/43	1	2	FACETS	0.791	0.722	0.863	0.791	0.722	0.863	SUBCLONAL	1	TRUE	1	0.643953318307691	2		747	522	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877199	151877200	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	123	481	0	ENST00000262189.6:c.7161dup	p.Arg2388ThrfsTer2	p.R2388Tfs*2	ENST00000262189	NM_170606.2	2387	-/A	37/59	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.643953318307691	2		481	379	SUCCESS
AR	367	MSKCC	GRCh37	X	66943676	66943676	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	207	1048	0	ENST00000374690.3:c.2756C>A	p.Thr919Asn	p.T919N	ENST00000374690	NM_000044.3	919	aCc/aAc	8/8	0.260112896615213	1	FACETS	0.609	0.567	0.652	0.609	0.567	0.652	INDETERMINATE	1	TRUE	0	0.643953318307691	1		1048	716	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0019087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	520	894	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.337790600079607	5	FACETS	0.975	0.938	1			1	CLONAL	4	TRUE	NA	0.35722505703149	5		895	1146	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579871	7579872	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	103	1001	0	ENST00000269305.4:c.41dup	p.Ser15GlufsTer14	p.S15Efs*14	ENST00000269305	NM_001126112.2	14	ctg/ctTg	2/11	0.302258504396456	1	FACETS	0.811	0.728	0.899	0.811	0.728	0.899	CLONAL	1	TRUE	0	0.35722505703149	1		1001	584	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950760	38950760	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	60	370	0	ENST00000357387.3:c.3190A>G	p.Ile1064Val	p.I1064V	ENST00000357387	NM_152756.3	1064	Atc/Gtc	31/38	1	2	FACETS	0.855	0.739	0.979	0.855	0.739	0.979	CLONAL	1	TRUE	1	0.35722505703149	2		370	393	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0019087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	202	894	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.859	0.798	0.923	1	0.993	1	CLONAL	2	TRUE	1	0.28597373249815	2		895	822	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0019087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	62	1047	1	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.20752092081615	1	FACETS	0.466	0.402	0.537	0.466	0.402	0.537	SUBCLONAL	1	TRUE	0	0.28597373249815	1		1048	797	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950760	38950760	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	41	370	0	ENST00000357387.3:c.3190A>G	p.Ile1064Val	p.I1064V	ENST00000357387	NM_152756.3	1064	Atc/Gtc	31/38	1	2	FACETS	0.652	0.543	0.772	0.652	0.543	0.772	SUBCLONAL	1	TRUE	1	0.28597373249815	2		370	440	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069281	30069281	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	114	1114	0	ENST00000338641.4:c.1147del	p.Leu383CysfsTer43	p.L383Cfs*43	ENST00000338641	NM_000268.3	382	gaC/ga	12/16	0.3	1	FACETS	0.959	0.864	1	0.959	0.864	1	CLONAL	1	TRUE	0	0.29	1		1114	701	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436797	52436798	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0019088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	111	1292	0	ENST00000460680.1:c.1980_1981del	p.Phe660LeufsTer3	p.F660Lfs*3	ENST00000460680	NM_004656.3	660	ttCAag/ttag	15/17	1	2	FACETS	0.802	0.72	0.89	0.802	0.72	0.89	CLONAL	1	TRUE	1	0.29	2		1292	954	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443568	52443568	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0019088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	94	854	0	ENST00000460680.1:c.122+2T>C		p.X41_splice	ENST00000460680	NM_004656.3	41			1	2	FACETS	0.997	0.888	1	0.997	0.888	1	CLONAL	1	TRUE	1	0.29	2		854	650	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960133	134960133	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	131	1069	0	ENST00000398015.3:c.2490C>G	p.Asn830Lys	p.N830K	ENST00000398015	NM_004441.4	830	aaC/aaG	13/16	1	2	FACETS	0.996	0.903	1	0.996	0.903	1	CLONAL	1	TRUE	1	0.29	2		1069	907	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271218	153271240	+	frameshift_variant	Frame_Shift_Del	DEL	GGTTTCTTTCCCAAAGAAAAAGA	GGTTTCTTTCCCAAAGAAAAAGA	-	novel	NA	P-0019088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	54	707	0	ENST00000281708.4:c.538_560del	p.Ser180MetfsTer68	p.S180Mfs*68	ENST00000281708	NM_033632.3	180	TCTTTTTCTTTGGGAAAGAAACCa/a	3/12	1	2	FACETS	0.664	0.567	0.77	0.664	0.567	0.77	SUBCLONAL	1	TRUE	1	0.29	2		707	561	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0019089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	391	1297	1	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.88093188258896	2		1298	868	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913499	NA	P-0019089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	82	568	0	ENST00000345146.2:c.394C>A	p.Arg132Ser	p.R132S	ENST00000345146	NM_005896.2	132	Cgt/Agt	4/10	0.380418897196697	1	FACETS	0.347	0.309	0.387	0.347	0.309	0.387	INDETERMINATE	1	TRUE	0	0.88093188258896	1		568	300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0019089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	371	1214	2	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.88093188258896	2		1216	815	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524996	187524996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	284	1033	0	ENST00000441802.2:c.10684G>A	p.Gly3562Ser	p.G3562S	ENST00000441802	NM_005245.3	3562	Ggc/Agc	19/27	1	2	FACETS	0.88	0.831	0.929	0.88	0.831	0.929	CLONAL	1	TRUE	1	0.88093188258896	2		1033	733	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939340	76939343	+	frameshift_variant	Frame_Shift_Del	DEL	CTAC	CTAC	-	novel	NA	P-0019089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	294	580	0	ENST00000373344.5:c.1405_1408del	p.Val469IlefsTer44	p.V469Ifs*44	ENST00000373344	NM_000489.3	469	GTAGat/at	9/35	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.88093188258896	1		580	346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	303	966	0	ENST00000269305.4:c.472C>G	p.Arg158Gly	p.R158G	ENST00000269305	NM_001126112.2	158	Cgc/Ggc	5/11	0.519156468282116	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.519156468282116	1		966	839	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912177	114912177	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	210	643	1	ENST00000543371.1:c.1247G>T	p.Gly416Val	p.G416V	ENST00000543371	NM_001198531.1	416	gGc/gTc	11/14	0.519156468282116	1	FACETS	0.934	0.872	0.998	0.934	0.872	0.998	CLONAL	1	TRUE	0	0.519156468282116	1		644	641	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876545	59876545	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	179	680	0	ENST00000259008.2:c.1256G>T	p.Arg419Leu	p.R419L	ENST00000259008	NM_032043.2	419	cGg/cTg	9/20	1	2	FACETS	0.951	0.879	1	0.951	0.879	1	CLONAL	1	TRUE	1	0.519156468282116	2		680	725	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342998	225343000	+	inframe_deletion	In_Frame_Del	DEL	GTC	GTC	-	novel	NA	P-0019090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	217	883	0	ENST00000264414.4:c.2092_2094del	p.Asp698del	p.D698del	ENST00000264414	NM_003590.4	698	GAC/-	15/16	0.469782617586644	1	FACETS	0.949	0.888	1	0.949	0.888	1	CLONAL	1	TRUE	0	0.519156468282116	1		883	652	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151871304	151871304	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	189	615	0	ENST00000262189.6:c.9286A>G	p.Ile3096Val	p.I3096V	ENST00000262189	NM_170606.2	3096	Ata/Gta	39/59	1	2	FACETS	0.997	0.925	1	0.997	0.925	1	CLONAL	1	TRUE	1	0.519156468282116	2		615	730	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	200	574	9	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.362506103365759	3	FACETS	0.943	0.879	1	0.629	0.586	0.673	CLONAL	2	TRUE	0	0.405326069636594	3		583	629	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	254	640	5	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.694112124285773	2		645	662	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	666	861	4	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	0.694112124285773	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.694112124285773	2		865	856	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	256	698	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.949	0.892	1	0.949	0.892	1	CLONAL	1	TRUE	1	0.694112124285773	2		699	777	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216477	108216477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587782558	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	142	412	2	ENST00000278616.4:c.8432del	p.Lys2811SerfsTer46	p.K2811Sfs*46	ENST00000278616	NM_000051.3	2809	cAa/ca	58/63	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.694112124285773	2		414	406	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100195	27100195	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	233	597	0	ENST00000324856.7:c.3991C>T	p.Gln1331Ter	p.Q1331*	ENST00000324856	NM_006015.4	1331	Cag/Tag	16/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.694112124285773	2		597	610	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	366	1013	0	ENST00000227507.2:c.859C>T	p.Pro287Ser	p.P287S	ENST00000227507	NM_053056.2	287	Ccc/Tcc	5/5	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.694112124285773	2		1013	971	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468308	50468308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1270036178	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	318	808	2	ENST00000331340.3:c.1543C>T	p.Arg515Cys	p.R515C	ENST00000331340	NM_006060.4	515	Cgc/Tgc	8/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.694112124285773	2		810	865	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717715	89717716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587782341	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	584	738	0	ENST00000371953.3:c.741dup	p.Pro248ThrfsTer5	p.P248Tfs*5	ENST00000371953	NM_000314.4	247	tta/ttAa	7/9	0.694112124285773	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.694112124285773	2		738	784	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589147	67589147	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	179	489	0	ENST00000274335.5:c.1135A>G	p.Lys379Glu	p.K379E	ENST00000274335		379	Aaa/Gaa	9/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.694112124285773	2		489	442	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394349	162394349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137853054	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	439	497	0	ENST00000366898.1:c.719C>T	p.Thr240Met	p.T240M	ENST00000366898	NM_004562.2	240	aCg/aTg	6/12	0.694112124285773	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.694112124285773	3		497	778	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931589	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	153	466	0	ENST00000349496.5:c.101G>A	p.Gly34Glu	p.G34E	ENST00000349496	NM_001904.3	34	gGa/gAa	3/15	1	2	FACETS	0.928	0.856	1	0.928	0.856	1	CLONAL	1	TRUE	1	0.694112124285773	2		466	475	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351421	70351421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1474736821	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	359	949	4	ENST00000374080.3:c.4069C>T	p.Arg1357Cys	p.R1357C	ENST00000374080		1357	Cgc/Tgc	29/45	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.694112124285773	2		953	952	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101117	27101117	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	428	1014	0	ENST00000324856.7:c.4403del	p.Pro1468LeufsTer13	p.P1468Lfs*13	ENST00000324856	NM_006015.4	1467	Ccc/cc	18/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.694112124285773	2		1014	1129	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641058	23641058	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45464991	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	317	841	0	ENST00000261584.4:c.2417C>T	p.Pro806Leu	p.P806L	ENST00000261584	NM_024675.3	806	cCg/cTg	5/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.694112124285773	2		841	844	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	425	1185	8	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.941	0.896	0.985	0.941	0.896	0.985	CLONAL	1	TRUE	1	0.694112124285773	2		1193	1302	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045476	47045476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	390	872	2	ENST00000377604.3:c.2443C>T	p.Arg815Trp	p.R815W	ENST00000377604	NM_001204468.1	815	Cgg/Tgg	22/24	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.694112124285773	2		874	952	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784026	9784026	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	278	836	0	ENST00000377346.4:c.2595-1G>T		p.X865_splice	ENST00000377346	NM_005026.3	865			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.694112124285773	2		836	774	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111482	8111482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	368	970	0	ENST00000346208.3:c.968C>T	p.Thr323Ile	p.T323I	ENST00000346208		323	aCc/aTc	5/6	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.694112124285773	2		970	939	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850740	63850741	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	283	845	0	ENST00000279873.7:c.1522dup	p.Leu508ProfsTer20	p.L508Pfs*20	ENST00000279873	NM_032199.2	506	-/C	10/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.694112124285773	2		845	762	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70411693	70411693	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	282	730	5	ENST00000373644.4:c.4367G>T	p.Arg1456Met	p.R1456M	ENST00000373644	NM_030625.2	1456	aGg/aTg	5/12	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.694112124285773	2		735	762	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999467	100999467	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	360	1164	0	ENST00000325455.5:c.335A>G	p.Asp112Gly	p.D112G	ENST00000325455	NM_001202474.3	112	gAc/gGc	1/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.694112124285773	2		1164	994	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420376	49420376	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	298	851	2	ENST00000301067.7:c.15373T>A	p.Phe5125Ile	p.F5125I	ENST00000301067	NM_003482.3	5125	Ttc/Atc	48/54	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.694112124285773	2		853	827	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434759	49434759	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	139	1005	3	ENST00000301067.7:c.6794del	p.Gly2265GlufsTer21	p.G2265Efs*21	ENST00000301067	NM_003482.3	2265	gGa/ga	31/54	1	2	FACETS	0.416	0.378	0.456	0.416	0.378	0.456	SUBCLONAL	1	TRUE	1	0.694112124285773	2		1008	963	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222835	5222835	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	201	519	2	ENST00000357368.4:c.2968G>T	p.Gly990Cys	p.G990C	ENST00000357368	NM_002850.3	990	Ggc/Tgc	18/38	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.694112124285773	2		521	469	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291169	10291169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1401130665	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	402	978	2	ENST00000340748.4:c.302G>A	p.Arg101Gln	p.R101Q	ENST00000340748		101	cGg/cAg	4/40	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.694112124285773	2		980	1036	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211906	36211906	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	543	1326	2	ENST00000222270.7:c.1659del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	553	Aaa/aa	3/37	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.694112124285773	2		1328	1404	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221027	36221027	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	275	739	1	ENST00000222270.7:c.5076+1G>A		p.X1692_splice	ENST00000222270	NM_014727.1	1692			1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.694112124285773	2		740	685	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416485	29416485	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	332	936	0	ENST00000389048.3:c.4468C>T	p.His1490Tyr	p.H1490Y	ENST00000389048	NM_004304.4	1490	Cac/Tac	29/29	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.694112124285773	2		936	894	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376717	31376717	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	146	475	0	ENST00000328111.2:c.712T>A	p.Trp238Arg	p.W238R	ENST00000328111	NM_006892.3	238	Tgg/Agg	7/23	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.694112124285773	2		475	397	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188231	10188231	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs869025643	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	352	983	1	ENST00000256474.2:c.374A>C	p.His125Pro	p.H125P	ENST00000256474	NM_000551.3	125	cAc/cCc	2/3	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.694112124285773	2		984	987	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851874	134851874	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	335	962	1	ENST00000398015.3:c.1280T>C	p.Ile427Thr	p.I427T	ENST00000398015	NM_004441.4	427	aTc/aCc	5/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.694112124285773	2		963	898	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274893	142274893	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	316	881	2	ENST00000350721.4:c.2167del	p.Tyr723IlefsTer2	p.Y723Ifs*2	ENST00000350721	NM_001184.3	723	Tat/at	10/47	1	2	FACETS	0.998	0.945	1	0.998	0.945	1	CLONAL	1	TRUE	1	0.694112124285773	2		883	912	SUCCESS
APC	324	MSKCC	GRCh37	5	112176057	112176057	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374048423	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	314	704	0	ENST00000257430.4:c.4766G>A	p.Arg1589His	p.R1589H	ENST00000257430	NM_000038.5	1589	cGt/cAt	16/16	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.694112124285773	2		704	817	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099427	157099432	+	inframe_deletion	In_Frame_Del	DEL	CAGCAG	CAGCAG	-	rs587779744	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	93	539	1	ENST00000346085.5:c.381_386del	p.Gln130_Gln131del	p.Q130_Q131del	ENST00000346085	NM_020732.3	122	CAGCAG/-	1/20	0.694112124285773	3	FACETS	0.444	0.394	0.497	0.222	0.197	0.249	SUBCLONAL	1	TRUE	1	0.694112124285773	3		540	813	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527817	157527817	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	235	694	0	ENST00000346085.5:c.5547del	p.Leu1850Ter	p.L1850*	ENST00000346085	NM_020732.3	1848	Ccc/cc	20/20	0.694112124285773	3	FACETS	0.953	0.89	1	0.477	0.445	0.509	CLONAL	1	TRUE	1	0.694112124285773	3		694	957	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141549448	141549448	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866981753	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	171	432	0	ENST00000220592.5:c.2140C>T	p.Arg714Trp	p.R714W	ENST00000220592	NM_012154.3	714	Cgg/Tgg	16/19	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.694112124285773	2		432	429	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409891	63409892	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	141	444	0	ENST00000330258.3:c.3275dup	p.Glu1093Ter	p.E1093*	ENST00000330258	NM_152424.3	1092	cct/ccCt	2/2	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.694112124285773	2		444	354	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349701	70349701	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	179	530	0	ENST00000374080.3:c.3863A>G	p.Gln1288Arg	p.Q1288R	ENST00000374080		1288	cAa/cGa	27/45	1	2	FACETS	0.964	0.895	1	0.964	0.895	1	CLONAL	1	TRUE	1	0.694112124285773	2		530	535	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0019094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	156	1017	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.474433504580701	1	FACETS	0.934	0.861	1	0.934	0.861	1	CLONAL	1	TRUE	0	0.474433504580701	1		1018	537	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860581	45860581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531021258	NA	P-0019094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	132	1305	1	ENST00000391945.4:c.1426G>A	p.Val476Ile	p.V476I	ENST00000391945	NM_000400.3	476	Gtc/Atc	15/23	NA	2	FACETS	0.549	0.498	0.604			1	INDETERMINATE	1	TRUE	NA	0.474433504580701	2		1306	1013	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153607	108153607	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0019094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	40	326	0	ENST00000278616.4:c.3746+1G>C		p.X1249_splice	ENST00000278616	NM_000051.3	1249			0.443746159710042	3	FACETS	0.429	0.356	0.51	0.143	0.118	0.17	SUBCLONAL	1	TRUE	0	0.474433504580701	3		326	486	SUCCESS
APC	324	MSKCC	GRCh37	5	112174823	112174823	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	66	586	0	ENST00000257430.4:c.3532G>A	p.Asp1178Asn	p.D1178N	ENST00000257430	NM_000038.5	1178	Gat/Aat	16/16	0.257810327292794	1	FACETS	0.355	0.308	0.407	0.355	0.308	0.407	INDETERMINATE	1	TRUE	0	0.474433504580701	1		586	597	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92404120	92404120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	89	766	0	ENST00000265734.4:c.259C>T	p.Arg87Ter	p.R87*	ENST00000265734	NM_001259.6	87	Cga/Tga	3/8	0.457024545568622	2	FACETS	0.445	0.393	0.499	0.222	0.196	0.25	SUBCLONAL	1	TRUE	0	0.474433504580701	2		766	844	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738240	145738240	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	75	1063	0	ENST00000428558.2:c.2745G>C	p.Met915Ile	p.M915I	ENST00000428558	NM_004260.3	915	atG/atC	16/22	NA	2	FACETS	0.355	0.31	0.403			1	INDETERMINATE	1	TRUE	NA	0.474433504580701	2		1063	891	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27203097	27203097	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1353	112	1022	0	ENST00000380036.4:c.2189T>C	p.Val730Ala	p.V730A	ENST00000380036	NM_000459.3	730	gTg/gCg	13/23	0.474433504580701	3	FACETS	0.399	0.357	0.443	0.199	0.178	0.222	SUBCLONAL	1	TRUE	1	0.474433504580701	3		1022	1465	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357646	70357646	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1192	369	1278	0	ENST00000374080.3:c.5897C>A	p.Pro1966His	p.P1966H	ENST00000374080		1966	cCc/cAc	41/45	1	2	FACETS	0.536	0.507	0.565	0.536	0.507	0.565	SUBCLONAL	1	TRUE	1	0.882722088532121	2		1278	1561	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680538	241680538	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	516	869	0	ENST00000366560.3:c.211C>G	p.Gln71Glu	p.Q71E	ENST00000366560	NM_000143.3	71	Cag/Gag	2/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.882722088532121	2		869	1102	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936755	32936755	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786202102	NA	P-0019095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	274	748	0	ENST00000380152.3:c.7901T>C	p.Met2634Thr	p.M2634T	ENST00000380152		2634	aTg/aCg	17/27	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.882722088532121	2		748	588	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954218	48954239	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAGGTAAATTTTTTACTTTTAG	TAGGTAAATTTTTTACTTTTAG	-	novel	NA	P-0019095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	111	515	0	ENST00000267163.4:c.1421_1421+21del		p.X474_splice	ENST00000267163	NM_000321.2	474		15/27	0.882722088532121	1	FACETS	0.48	0.437	0.523	0.48	0.437	0.523	SUBCLONAL	1	TRUE	0	0.882722088532121	1		515	293	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992465	72992465	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	730	1104	1	ENST00000268489.5:c.1580del	p.Asn527ThrfsTer9	p.N527Tfs*9	ENST00000268489	NM_006885.3	527	aAc/ac	2/10	1	2	FACETS	0.983	0.95	1	0.983	0.95	1	CLONAL	1	TRUE	1	0.882722088532121	2		1105	1683	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533578	63533578	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	478	948	3	ENST00000307078.5:c.1576A>C	p.Lys526Gln	p.K526Q	ENST00000307078	NM_004655.3	526	Aag/Cag	6/11	1	2	FACETS	0.679	0.648	0.71	0.679	0.648	0.71	SUBCLONAL	1	TRUE	1	0.882722088532121	2		951	1596	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469973	25469973	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	557	841	1	ENST00000264709.3:c.1069G>T	p.Ala357Ser	p.A357S	ENST00000264709	NM_175629.2	357	Gcc/Tcc	9/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.882722088532121	2		842	1245	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224286	55224286	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	521	945	0	ENST00000275493.2:c.1067T>G	p.Ile356Ser	p.I356S	ENST00000275493	NM_005228.3	356	aTt/aGt	9/28	1	2	FACETS	0.988	0.949	1	0.988	0.949	1	CLONAL	1	TRUE	1	0.882722088532121	2		945	1195	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	137	708	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.166661639058154	4	FACETS	0.852	0.776	0.931	0.852	0.776	0.931	INDETERMINATE	2	FALSE	2	0.3	4		709	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0019096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	182	521	0	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.277581356454813	2	FACETS	0.96	0.89	1	0.96	0.89	1	CLONAL	2	FALSE	0	0.3	2		521	632	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873756	35873756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28933100	NA	P-0019096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	165	558	1	ENST00000216797.5:c.95G>A	p.Ser32Asn	p.S32N	ENST00000216797	NM_020529.2	32	aGc/aAc	1/6	0.237762473201338	3	FACETS	0.777	0.714	0.842	0.777	0.714	0.842	SUBCLONAL	2	FALSE	1	0.3	3		559	814	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521986	157521986	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554235614	NA	P-0019096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	196	502	0	ENST00000346085.5:c.4258C>T	p.Gln1420Ter	p.Q1420*	ENST00000346085	NM_020732.3	1420	Cag/Tag	18/20	0.237762473201338	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	FALSE	1	0.3	3		502	617	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942153	81942153	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	222	630	0	ENST00000359376.3:c.1690C>T	p.Arg564Trp	p.R564W	ENST00000359376	NM_002661.3	564	Cgg/Tgg	17/33	0.237762473201338	3	FACETS	0.977	0.911	1	0.977	0.911	1	CLONAL	2	FALSE	1	0.3	3		630	871	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280073	18280073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767770222	NA	P-0019096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	61	137	0	ENST00000222254.8:c.2156C>T	p.Pro719Leu	p.P719L	ENST00000222254	NM_005027.3	719	cCg/cTg	16/16	0.237762473201338	3	FACETS	0.838	0.736	0.944	1	0.962	1	CLONAL	3	FALSE	1	0.3	3		137	186	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912786	50912786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61751955	NA	P-0019096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	97	675	0	ENST00000440232.2:c.2017G>A	p.Glu673Lys	p.E673K	ENST00000440232	NM_002691.3	673	Gag/Aag	17/27	0.237762473201338	3	FACETS	0.853	0.759	0.953	0.426	0.379	0.477	CLONAL	1	FALSE	1	0.3	3		675	872	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55962423	55962423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	71	602	1	ENST00000263923.4:c.2701C>T	p.Leu901Phe	p.L901F	ENST00000263923	NM_002253.2	901	Ctt/Ttt	19/30	1	2	FACETS	0.647	0.564	0.736	0.647	0.564	0.736	SUBCLONAL	1	FALSE	1	0.3	2		603	732	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56171021	56171021	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	40	244	0	ENST00000399503.3:c.1849G>C	p.Gly617Arg	p.G617R	ENST00000399503	NM_005921.1	617	Gga/Cga	10/20	0.119599808338718	4	FACETS	0.996	0.83	1	0.498	0.415	0.59	INDETERMINATE	1	FALSE	2	0.3	4		244	348	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0019097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	126	715	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.228622958993455	1	FACETS	0.825	0.751	0.901	0.825	0.751	0.901	INDETERMINATE	1	TRUE	0	0.468154986874643	1		717	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0019097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	198	868	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.468154986874643	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.468154986874643	1		868	595	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032478	12032478	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	117	539	0	ENST00000353533.5:c.914T>G	p.Phe305Cys	p.F305C	ENST00000353533	NM_003010.3	305	tTt/tGt	9/11	0.468154986874643	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.468154986874643	1		539	352	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094972	11094972	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	167	972	0	ENST00000358026.2:c.146del	p.Pro49ArgfsTer45	p.P49Rfs*45	ENST00000358026	NM_001128849.1	49	Ccg/cg	2/36	1	2	FACETS	0.779	0.716	0.845	0.779	0.716	0.845	SUBCLONAL	1	TRUE	1	0.468154986874643	2		972	916	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528596	8528596	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	110	596	0	ENST00000356435.5:c.536G>T	p.Arg179Leu	p.R179L	ENST00000356435		179	cGa/cTa	4/35	0.468154986874643	1	FACETS	0.872	0.789	0.957	0.872	0.789	0.957	CLONAL	1	TRUE	0	0.468154986874643	1		596	413	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099480	27099480	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0019099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	235	374	0	ENST00000324856.7:c.3715+2T>C		p.X1239_splice	ENST00000324856	NM_006015.4	1239			0.201155105536528	5	FACETS	0.91	0.857	0.964	0.91	0.857	0.964	INDETERMINATE	3	TRUE	2	0.592193990320405	5		374	549	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205178	61205178	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	66	762	0	ENST00000301761.2:c.118C>G	p.Pro40Ala	p.P40A	ENST00000301761	NM_017841.2	40	Cca/Gca	2/4	0.215636000061683	2	FACETS	0.235	0.203	0.269	0.117	0.101	0.135	INDETERMINATE	1	TRUE	0	0.592193990320405	2		762	950	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979242	93979242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	211	547	0	ENST00000369303.4:c.1586G>A	p.Arg529Lys	p.R529K	ENST00000369303	NM_004440.3	529	aGa/aAa	7/17	0.592193990320405	3	FACETS	1	0.991	1	0.468	0.437	0.5	CLONAL	1	TRUE	0	0.592193990320405	3		547	658	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518187	8518187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	176	497	0	ENST00000356435.5:c.1204G>A	p.Gly402Arg	p.G402R	ENST00000356435		402	Ggg/Agg	10/35	0.155206501236307	5	FACETS	1	0.942	1	0.679	0.629	0.73	INDETERMINATE	2	TRUE	2	0.592193990320405	5		497	551	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849215	76849215	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	275	760	0	ENST00000373344.5:c.6061del	p.Val2021TyrfsTer29	p.V2021Yfs*29	ENST00000373344	NM_000489.3	2021	Gta/ta	26/35	0.178042661731109	4	FACETS	0.851	0.801	0.902	0.851	0.801	0.902	INDETERMINATE	2	TRUE	2	0.592193990320405	4		760	869	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0019100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	325	715	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.440569316166106	4	FACETS	0.948	0.901	0.995	0.948	0.901	0.995	CLONAL	3	TRUE	1	0.452196944553041	4		717	734	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0019100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	265	894	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.341381760357711	3	FACETS	0.823	0.773	0.874	0.823	0.773	0.874	CLONAL	2	TRUE	1	0.452196944553041	3		895	873	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0019100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	308	883	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.373223747411206	2	FACETS	0.807	0.764	0.851	0.807	0.764	0.851	CLONAL	2	TRUE	0	0.452196944553041	2		885	844	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047995	180047995	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762560832	NA	P-0019100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	269	684	3	ENST00000261937.6:c.2180C>T	p.Ala727Val	p.A727V	ENST00000261937	NM_182925.4	727	gCg/gTg	15/30	0.452196944553041	3	FACETS	0.95	0.895	1	0.633	0.596	0.671	CLONAL	2	TRUE	0	0.452196944553041	3		687	768	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	202	445	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	0.344198322093611	3	FACETS	0.874	0.821	0.926	1	0.991	1	CLONAL	3	TRUE	1	0.452196944553041	3		445	418	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274801	123274801	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	39	657	2	ENST00000358487.5:c.1117C>A	p.Pro373Thr	p.P373T	ENST00000358487	NM_000141.4	373	Cca/Aca	9/18	0.365847211224444	3	FACETS	0.279	0.23	0.333	0.139	0.115	0.167	SUBCLONAL	1	TRUE	1	0.452196944553041	3		659	759	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485827	8485827	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	123	372	0	ENST00000356435.5:c.2990A>G	p.His997Arg	p.H997R	ENST00000356435		997	cAt/cGt	17/35	0.431714737699913	5	FACETS	0.795	0.722	0.872	0.53	0.481	0.582	SUBCLONAL	2	TRUE	2	0.452196944553041	5		372	574	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921543	39921543	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	269	743	0	ENST00000378444.4:c.4277T>C	p.Leu1426Pro	p.L1426P	ENST00000378444	NM_001123385.1	1426	cTa/cCa	10/15	0.431714737699913	5	FACETS	0.913	0.857	0.972	0.609	0.571	0.648	CLONAL	2	TRUE	2	0.452196944553041	5		743	1093	SUCCESS
APC	324	MSKCC	GRCh37	5	112175191	112175191	+	synonymous_variant	Silent	SNP	T	T	C	novel	NA	P-0019100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	179	349	0	ENST00000257430.4:c.3900T>C	p.Asn1300=	p.N1300=	ENST00000257430	NM_000038.5	1300	aaT/aaC	16/16	0.452196944553041				0.984	1				CLONAL	2	TRUE	0	0.452196944553041	3		349	411	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	175	364	1				ENST00000310581	NM_198253.2	-/1132			0.277310350908141	4	FACETS	0.966	0.892	1	0.966	0.892	1	CLONAL	2	TRUE	2	0.353485876709129	4		365	694	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534285	534285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894226	NA	P-0019101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	134	710	0	ENST00000451590.1:c.38G>T	p.Gly13Val	p.G13V	ENST00000451590	NM_001130442.1	13	gGt/gTt	2/5	1	2	FACETS	0.75	0.68	0.823	0.75	0.68	0.823	SUBCLONAL	1	TRUE	1	0.353485876709129	2		710	1011	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0019101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	464	976	1	ENST00000269305.4:c.394A>T	p.Lys132Ter	p.K132*	ENST00000269305	NM_001126112.2	132	Aag/Tag	5/11	0.341895582470767	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.353485876709129	2		977	1308	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356170	70356170	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	578	975	0	ENST00000374080.3:c.5065G>A	p.Asp1689Asn	p.D1689N	ENST00000374080		1689	Gat/Aat	37/45	0.290203436647958	4	FACETS	0.866	0.831	0.901	0.866	0.831	0.901	CLONAL	3	TRUE	1	0.353485876709129	4		975	1704	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981167	201981168	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	107	905	0	ENST00000359651.3:c.248dup	p.Asn83LysfsTer9	p.N83Kfs*9	ENST00000359651		82	-/A	2/8	0.2163531382906	2	FACETS	0.467	0.417	0.52	0.234	0.208	0.26	SUBCLONAL	1	TRUE	0	0.353485876709129	2		905	1296	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446380	49446380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	307	799	1	ENST00000301067.7:c.1225C>T	p.Pro409Ser	p.P409S	ENST00000301067	NM_003482.3	409	Cca/Tca	9/54	0.31880943740548	4	FACETS	0.883	0.831	0.936	0.883	0.831	0.936	CLONAL	2	TRUE	2	0.353485876709129	4		800	1331	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336199	73336199	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	49	466	0	ENST00000377767.4:c.2204A>T	p.Tyr735Phe	p.Y735F	ENST00000377767	NM_014953.3	735	tAt/tTt	17/21	0.234766353156206	3	FACETS	0.456	0.385	0.535	0.152	0.128	0.179	SUBCLONAL	1	TRUE	0	0.353485876709129	3		466	715	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194826	30194826	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	291	969	0	ENST00000331968.5:c.319G>T	p.Asp107Tyr	p.D107Y	ENST00000331968	NM_002742.2	107	Gac/Tac	2/18	0.144352748049368	3	FACETS	0.811	0.763	0.861	0.811	0.763	0.861	INDETERMINATE	2	TRUE	1	0.353485876709129	3		969	1194	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042509	42042509	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	133	698	1	ENST00000219905.7:c.6704G>A	p.Arg2235Lys	p.R2235K	ENST00000219905	NM_001164273.1	2235	aGa/aAa	17/24	1	2	FACETS	0.902	0.819	0.989	0.902	0.819	0.989	CLONAL	1	TRUE	1	0.353485876709129	2		699	834	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632599	3632599	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745421287	NA	P-0019101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	87	860	2	ENST00000294008.3:c.5249C>T	p.Ala1750Val	p.A1750V	ENST00000294008	NM_032444.2	1750	gCg/gTg	15/15	NA	2	FACETS	0.494	0.436	0.556			1	INDETERMINATE	1	TRUE	NA	0.353485876709129	2		862	997	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143993	11143993	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	206	663	0	ENST00000358026.2:c.3574C>G	p.Arg1192Gly	p.R1192G	ENST00000358026	NM_001128849.1	1192	Cgc/Ggc	26/36	0.2163531382906	2	FACETS	1	0.99	1	0.715	0.665	0.767	CLONAL	1	TRUE	0	0.353485876709129	2		663	815	SUCCESS
CALR	811	MSKCC	GRCh37	19	13049951	13049951	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	280	681	2	ENST00000316448.5:c.95G>T	p.Gly32Val	p.G32V	ENST00000316448	NM_004343.3	32	gGg/gTg	2/9	0.2163531382906	2	FACETS	0.791	0.744	0.84	0.791	0.744	0.84	SUBCLONAL	2	TRUE	0	0.353485876709129	2		683	1001	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464568	25464568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	538	792	0	ENST00000264709.3:c.1945G>A	p.Val649Met	p.V649M	ENST00000264709	NM_175629.2	649	Gtg/Atg	17/23	0.35294645569995	4	FACETS	0.972	0.933	1	0.972	0.933	1	CLONAL	3	TRUE	1	0.353485876709129	4		792	1413	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754909	57754909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	145	459	0	ENST00000274289.3:c.281C>T	p.Ala94Val	p.A94V	ENST00000274289	NM_006622.3	94	gCa/gTa	2/14	0.18849209706355	2	FACETS	1	0.988	1	0.744	0.683	0.809	INDETERMINATE	1	TRUE	0	0.353485876709129	2		459	551	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681013	30681013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	260	733	1	ENST00000376406.3:c.706G>A	p.Ala236Thr	p.A236T	ENST00000376406	NM_014641.2	236	Gct/Act	5/15	0.258012523004871	3	FACETS	0.9	0.844	0.957	0.9	0.844	0.957	CLONAL	2	TRUE	1	0.353485876709129	3		734	962	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508129	106508129	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	63	287	0	ENST00000359195.3:c.123G>C	p.Glu41Asp	p.E41D	ENST00000359195	NM_002649.2	41	gaG/gaC	2/11	0.353485876709129	3	FACETS	1	0.946	1	0.586	0.509	0.668	CLONAL	1	TRUE	1	0.353485876709129	3		287	358	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786501	135786501	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs118203489	NA	P-0019101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	319	671	0	ENST00000298552.3:c.1030-1G>A		p.X344_splice	ENST00000298552	NM_001162426.1	344			0.289154023207913	3	FACETS	1	0.991	1	0.818	0.775	0.862	CLONAL	2	TRUE	0	0.353485876709129	3		671	865	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227763	53227763	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	475	821	0	ENST00000375401.3:c.2425A>T	p.Ser809Cys	p.S809C	ENST00000375401	NM_004187.3	809	Agt/Tgt	17/26	0.349919978702876	4	FACETS	0.861	0.823	0.9	1	0.995	1	CLONAL	3	TRUE	2	0.353485876709129	4		821	1408	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920209	76920209	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1174	67	810	0	ENST00000373344.5:c.3868G>T	p.Gly1290Ter	p.G1290*	ENST00000373344	NM_000489.3	1290	Gga/Tga	11/35	0.290203436647958	4	FACETS	0.413	0.358	0.474	0.138	0.119	0.158	SUBCLONAL	1	TRUE	1	0.353485876709129	4		810	1241	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0019102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	268	752	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.370490479847565	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.371174867789053	2		754	651	SUCCESS
APC	324	MSKCC	GRCh37	5	112175162	112175162	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561588104	NA	P-0019102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	108	447	1	ENST00000257430.4:c.3871C>T	p.Gln1291Ter	p.Q1291*	ENST00000257430	NM_000038.5	1291	Cag/Tag	16/16	0.371174867789053	3	FACETS	0.956	0.866	1	0.956	0.866	1	CLONAL	2	TRUE	1	0.371174867789053	3		448	361	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0019102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	85	608	1	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.371174867789053	3	FACETS	0.902	0.798	1	0.451	0.399	0.507	CLONAL	1	TRUE	1	0.371174867789053	3		609	602	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221987	1221987	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370222210	NA	P-0019102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	136	810	4	ENST00000326873.7:c.902G>A	p.Arg301Gln	p.R301Q	ENST00000326873	NM_000455.4	301	cGg/cAg	7/10	0.371174867789053	3	FACETS	1	0.952	1	0.535	0.486	0.586	CLONAL	1	TRUE	1	0.371174867789053	3		814	812	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911548	114911548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	205	776	0	ENST00000543371.1:c.1066G>A	p.Ala356Thr	p.A356T	ENST00000543371	NM_001198531.1	356	Gca/Aca	10/14	0.371174867789053	3	FACETS	0.96	0.894	1	0.96	0.894	1	CLONAL	2	TRUE	1	0.371174867789053	3		776	682	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859609	57859610	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	rs1566559797	NA	P-0019102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	160	646	0	ENST00000228682.2:c.671_672dup	p.Glu225ArgfsTer56	p.E225Rfs*56	ENST00000228682	NM_005269.2	221	-/GA	7/12	0.154776545639092	4	FACETS	0.869	0.799	0.942	0.869	0.799	0.942	INDETERMINATE	2	TRUE	2	0.371174867789053	4		646	680	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37680994	37680994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	290	817	1	ENST00000447079.4:c.3163G>A	p.Val1055Ile	p.V1055I	ENST00000447079	NM_015083.1	1055	Gtt/Att	12/14	0.371174867789053	6	FACETS	1	0.977	1	0.538	0.506	0.572	CLONAL	2	TRUE	2	0.371174867789053	6		818	1264	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40864884	40864884	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1197	108	837	1	ENST00000373198.4:c.2384C>A	p.Ser795Tyr	p.S795Y	ENST00000373198	NM_133170.3	795	tCc/tAc	16/32	0.371174867789053	6	FACETS	0.777	0.695	0.865			1	SUBCLONAL	1	TRUE	NA	0.371174867789053	6		838	1305	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120768	94120768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	38	718	1	ENST00000369303.4:c.283G>A	p.Ala95Thr	p.A95T	ENST00000369303	NM_004440.3	95	Gca/Aca	3/17	0.371174867789053	3	FACETS	0.352	0.29	0.422	0.176	0.145	0.211	SUBCLONAL	1	TRUE	1	0.371174867789053	3		719	689	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450345	50450345	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	120	797	0	ENST00000331340.3:c.529C>G	p.Leu177Val	p.L177V	ENST00000331340	NM_006060.4	177	Ctc/Gtc	5/8	0.334771016527937	5	FACETS	1	0.942	1	0.354	0.319	0.391	CLONAL	1	TRUE	2	0.371174867789053	5		797	948	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	720	574	9	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.636240591706711	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.636240591706711	3		583	985	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0019103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	381	807	3	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.636240591706711	2		810	1189	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	272	651	1	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	NA	2	FACETS	1	0.949	1			1	INDETERMINATE	1	TRUE	NA	0.636240591706711	2		652	848	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928089	178928089	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	426	697	9	ENST00000263967.3:c.1367T>G	p.Leu456Arg	p.L456R	ENST00000263967	NM_006218.2	456	cTg/cGg	8/21	0.636240591706711	3	FACETS	0.93	0.89	0.97	0.62	0.593	0.647	CLONAL	2	TRUE	0	0.636240591706711	3		706	949	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573703	64573703	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1114167489	NA	P-0019103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	179	410	6	ENST00000312049.6:c.1049+1G>A		p.X350_splice	ENST00000312049	NM_130799.2	350			1	2	FACETS	0.883	0.818	0.951	0.883	0.818	0.951	CLONAL	1	TRUE	1	0.636240591706711	2		416	637	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158637097	158637097	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	225	626	1	ENST00000263640.3:c.83T>A	p.Val28Asp	p.V28D	ENST00000263640	NM_001105.4	28	gTc/gAc	4/11	1	2	FACETS	0.995	0.93	1	0.995	0.93	1	CLONAL	1	TRUE	1	0.636240591706711	2		627	711	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0019104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	92	600	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.175696077823202	2	FACETS	0.957	0.853	1	0.957	0.853	1	CLONAL	2	FALSE	0	0.175696077823202	2		600	547	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338671	70338671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	85	825	1	ENST00000374080.3:c.67G>T	p.Asp23Tyr	p.D23Y	ENST00000374080		23	Gat/Tat	1/45	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	FALSE	1	0.175696077823202	2		826	939	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916948	178916950	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0019104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	45	693	0	ENST00000263967.3:c.337_339del	p.Leu113del	p.L113del	ENST00000263967	NM_006218.2	112	aTCCtc/atc	2/21	1	2	FACETS	0.822	0.69	0.969	0.822	0.69	0.969	CLONAL	1	FALSE	1	0.175696077823202	2		693	623	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696688	47696688	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519971	NA	P-0019105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	144	672	0	ENST00000347630.2:c.260A>G	p.Tyr87Cys	p.Y87C	ENST00000347630	NM_001007230.1	87	tAc/tGc	5/11	1	2	FACETS	0.947	0.867	1	0.947	0.867	1	CLONAL	1	TRUE	1	0.48036326252566	2		672	633	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932114	36932114	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	42	532	0	ENST00000361632.4:c.2355G>T	p.Lys785Asn	p.K785N	ENST00000361632		785	aaG/aaT	16/16	1	2	FACETS	0.313	0.261	0.372	0.313	0.261	0.372	SUBCLONAL	1	TRUE	1	0.48036326252566	2		532	558	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645784	215645792	+	inframe_deletion	In_Frame_Del	DEL	AACATTCAG	AACATTCAG	-	novel	NA	P-0019105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	129	672	0	ENST00000260947.4:c.806_814del	p.Ser269_Cys271del	p.S269_C271del	ENST00000260947	NM_000465.2	269	tCTGAATGTTtt/ttt	4/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.48036326252566	2		672	514	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112515	115112516	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0019106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	179	828	0	ENST00000257566.3:c.1223_1224dup	p.Ser409AlafsTer224	p.S409Afs*224	ENST00000257566	NM_016569.3	408	-/GC	7/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.391286835322781	2		828	816	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115443	115115443	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	174	766	0	ENST00000257566.3:c.883G>A	p.Asp295Asn	p.D295N	ENST00000257566	NM_016569.3	295	Gac/Aac	5/8	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.391286835322781	2		766	883	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098853	178098853	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	186	897	0	ENST00000397062.3:c.192G>T	p.Lys64Asn	p.K64N	ENST00000397062	NM_006164.4	64	aaG/aaT	2/5	1	2	FACETS	0.955	0.881	1	0.955	0.881	1	CLONAL	1	TRUE	1	0.391286835322781	2		897	996	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212867	27212867	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376285577	NA	P-0019106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	107	862	0	ENST00000380036.4:c.2849G>A	p.Arg950Gln	p.R950Q	ENST00000380036	NM_000459.3	950	cGg/cAg	17/23	0.345170000421182	3	FACETS	0.66	0.591	0.734	0.33	0.295	0.367	SUBCLONAL	1	TRUE	1	0.391286835322781	3		862	991	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0019108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	487	755	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.670797059074264	2		755	692	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748428	162748429	+	stop_gained	Nonsense_Mutation	DNP	TC	TC	AG	novel	NA	P-0019108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	206	549	2	ENST00000367921.3:c.2342_2343delinsAG	p.Phe781Ter	p.F781*	ENST00000367921	NM_006182.2	781	tTC/tAG	17/18	0.670797059074264	5	FACETS	0.763	0.71	0.819	0.382	0.355	0.41	SUBCLONAL	2	TRUE	1	0.670797059074264	5		551	807	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577093	7577093	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882008	NA	P-0019109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	160	1081	0	ENST00000269305.4:c.845G>C	p.Arg282Pro	p.R282P	ENST00000269305	NM_001126112.2	282	cGg/cCg	8/11	1	2	FACETS	0.893	0.818	0.971	1	0.991	1	CLONAL	2	TRUE	1	0.19	2		1081	943	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0019110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	140	629	1	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	0.27	2		630	796	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0019110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	69	610	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.702	0.611	0.801	0.702	0.611	0.801	SUBCLONAL	1	TRUE	1	0.27	2		610	728	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	112	684	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	0.768	0.689	0.852	0.768	0.689	0.852	SUBCLONAL	1	TRUE	1	0.27	2		684	1080	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0019110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	76	427	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	0.852	0.747	0.964	0.852	0.747	0.964	CLONAL	1	TRUE	1	0.27	2		427	661	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606697	29606697	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779282861	NA	P-0019111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	69	669	0	ENST00000389048.3:c.1183C>T	p.Arg395Cys	p.R395C	ENST00000389048	NM_004304.4	395	Cgt/Tgt	5/29	0.198146890720941	4	FACETS	0.745	0.648	0.851	0.373	0.324	0.426	SUBCLONAL	1	TRUE	2	0.308117953755688	4		669	786	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305278	39305278	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	222	770	1	ENST00000373001.3:c.1147G>T	p.Ala383Ser	p.A383S	ENST00000373001	NM_022157.3	383	Gcc/Tcc	7/7	0.308117953755688	3	FACETS	0.889	0.828	0.952	0.889	0.828	0.952	CLONAL	2	TRUE	1	0.308117953755688	3		771	935	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731083	162731083	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	76	621	1	ENST00000367921.3:c.940del	p.Glu314AsnfsTer44	p.E314Nfs*44	ENST00000367921	NM_006182.2	313	tGg/tg	9/18	0.308117953755688	6	FACETS	0.854	0.747	0.969			1	CLONAL	1	TRUE	NA	0.308117953755688	6		622	934	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445649	49445649	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	591	1042	0	ENST00000301067.7:c.1817C>G	p.Ser606Cys	p.S606C	ENST00000301067	NM_003482.3	606	tCt/tGt	10/54	0.308117953755688	7	FACETS	0.917	0.882	0.952	0.917	0.882	0.952	CLONAL	5	TRUE	2	0.308117953755688	7		1042	1481	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578420	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0019111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	192	673	0	ENST00000269305.4:c.510_511delinsTT	p.Glu171Ter	p.E171*	ENST00000269305	NM_001126112.2	170	acGGag/acTTag	5/11	0.306702466455399	2	FACETS	0.895	0.831	0.961	0.895	0.831	0.961	CLONAL	2	TRUE	0	0.308117953755688	2		673	696	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881620	37881620	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196082930	NA	P-0019111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	117	696	2	ENST00000269571.5:c.2690G>A	p.Arg897Gln	p.R897Q	ENST00000269571		897	cGg/cAg	22/27	0.271780049888261	3	FACETS	1	0.949	1	0.542	0.488	0.598	CLONAL	1	TRUE	1	0.308117953755688	3		698	809	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221282	1221282	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	194	815	0	ENST00000326873.7:c.806del	p.Lys269ArgfsTer18	p.K269Rfs*18	ENST00000326873	NM_000455.4	269	Aag/ag	6/10	0.293256534872096	2	FACETS	0.867	0.805	0.931	0.867	0.805	0.931	CLONAL	2	TRUE	0	0.308117953755688	2		815	726	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254614	10254614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	143	584	0	ENST00000340748.4:c.2896G>A	p.Glu966Lys	p.E966K	ENST00000340748		966	Gag/Aag	28/40	0.293256534872096	2	FACETS	0.848	0.778	0.922	0.848	0.778	0.922	CLONAL	2	TRUE	0	0.308117953755688	2		584	547	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383070	42383070	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	164	377	0	ENST00000221972.3:c.91del	p.Gln31ArgfsTer12	p.Q31Rfs*12	ENST00000221972	NM_021601.3	30	tgC/tg	2/5	0.308117953755688	5	FACETS	1	0.931	1	1	0.931	1	CLONAL	3	TRUE	2	0.308117953755688	5		377	515	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873092	136873092	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	85	406	1	ENST00000241393.3:c.406C>A	p.Leu136Met	p.L136M	ENST00000241393	NM_003467.2	136	Ctg/Atg	2/2	0.198146890720941	4	FACETS	0.83	0.737	0.928	0.83	0.737	0.928	CLONAL	2	TRUE	2	0.308117953755688	4		407	435	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419902	41419902	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	99	736	3	ENST00000373198.4:c.419G>T	p.Gly140Val	p.G140V	ENST00000373198	NM_133170.3	140	gGg/gTg	3/32	0.13911213815047	3	FACETS	0.984	0.878	1			1	INDETERMINATE	1	TRUE	NA	0.308117953755688	3		739	754	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963070	38963070	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	255	478	0	ENST00000357387.3:c.1474C>G	p.Leu492Val	p.L492V	ENST00000357387	NM_152756.3	492	Ctt/Gtt	17/38	0.300096761422721	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	4	TRUE	0	0.308117953755688	4		478	490	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504328	149504328	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	177	747	0	ENST00000261799.4:c.1874C>G	p.Ser625Cys	p.S625C	ENST00000261799	NM_002609.3	625	tCt/tGt	13/23	0.273118738049848	2	FACETS	0.927	0.858	0.997	0.927	0.858	0.997	CLONAL	2	TRUE	0	0.308117953755688	2		747	620	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045729	26045729	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	52	238	0	ENST00000540144.1:c.91C>G	p.Pro31Ala	p.P31A	ENST00000540144	NM_003531.2	31	Ccg/Gcg	1/1	0.306702466455399	2	FACETS	0.811	0.7	0.93	0.811	0.7	0.93	CLONAL	2	TRUE	0	0.308117953755688	2		238	208	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27168542	27168542	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	113	883	1	ENST00000380036.4:c.414C>A	p.Asn138Lys	p.N138K	ENST00000380036	NM_000459.3	138	aaC/aaA	3/23	0.308117953755688	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.308117953755688	1		884	558	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323234	31323234	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	199	560	0	ENST00000412585.2:c.755del	p.Thr252MetfsTer45	p.T252Mfs*45	ENST00000412585	NM_005514.6	252	aCt/at	4/8	0.308117953755688	5	FACETS	0.979	0.912	1	0.979	0.912	1	CLONAL	3	TRUE	2	0.308117953755688	5		560	643	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572627	64572627	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	287	794	1	ENST00000312049.6:c.1229del	p.Phe410SerfsTer35	p.F410Sfs*35	ENST00000312049	NM_130799.2	410	tTc/tc	9/10	0.82044086263379	1	FACETS	0.907	0.868	0.945	0.907	0.868	0.945	CLONAL	1	TRUE	0	0.82044086263379	1		795	455	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	107	364	1				ENST00000310581	NM_198253.2	-/1132			0.553611281255836	4	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.693696108191915	4		365	419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579575	7579575	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555526795	NA	P-0019113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	238	825	0	ENST00000269305.4:c.112del	p.Gln38LysfsTer6	p.Q38Kfs*6	ENST00000269305	NM_001126112.2	38	Caa/aa	4/11	0.693696108191915	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.693696108191915	1		825	432	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11172975	11172975	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1247005024	NA	P-0019113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	161	513	2	ENST00000361445.4:c.7301-1G>T		p.X2434_splice	ENST00000361445	NM_004958.3	2434			NA	2	FACETS	0.945	0.874	1			1	INDETERMINATE	1	TRUE	NA	0.693696108191915	2		515	491	SUCCESS
RET	5979	MSKCC	GRCh37	10	43595931	43595931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	203	907	0	ENST00000355710.3:c.98G>A	p.Arg33Lys	p.R33K	ENST00000355710	NM_020975.4	33	aGg/aAg	2/20	1	2	FACETS	0.888	0.827	0.95	0.888	0.827	0.95	CLONAL	1	TRUE	1	0.693696108191915	2		907	659	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039248	49039248	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1131690882	NA	P-0019113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	288	779	0	ENST00000267163.4:c.2325+1G>A		p.X775_splice	ENST00000267163	NM_000321.2	775			0.693696108191915	1	FACETS	0.984	0.937	1	0.984	0.937	1	CLONAL	1	TRUE	0	0.693696108191915	1		779	551	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113287	209113287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	211	646	0	ENST00000345146.2:c.220G>A	p.Ala74Thr	p.A74T	ENST00000345146	NM_005896.2	74	Gcc/Acc	4/10	0.693696108191915	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.693696108191915	1		646	371	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099080	157099080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057518648	NA	P-0019113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	120	257	0	ENST00000346085.5:c.17G>A	p.Gly6Asp	p.G6D	ENST00000346085	NM_020732.3	6	gGc/gAc	1/20	0.693696108191915	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.693696108191915	1		257	181	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132792	152132792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769792555	NA	P-0019113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	245	773	1	ENST00000262189.6:c.80C>T	p.Pro27Leu	p.P27L	ENST00000262189	NM_170606.2	27	cCg/cTg	1/59	0.693696108191915	3	FACETS	1	0.982	1	0.561	0.525	0.597	CLONAL	1	TRUE	1	0.693696108191915	3		774	848	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117824	108117824	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	133	608	1	ENST00000278616.4:c.1035del	p.Ile346LeufsTer3	p.I346Lfs*3	ENST00000278616	NM_000051.3	345	ttG/tt	8/63	0.785391805094515	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.785391805094515	1		609	199	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440074	49440074	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	589	828	1	ENST00000301067.7:c.4552G>C	p.Asp1518His	p.D1518H	ENST00000301067	NM_003482.3	1518	Gac/Cac	16/54	0.785391805094515	5	FACETS	0.94	0.907	0.972	0.94	0.907	0.972	CLONAL	3	TRUE	2	0.785391805094515	5		829	1159	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864145	57864145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426197874	NA	P-0019114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	190	671	2	ENST00000228682.2:c.1622G>A	p.Arg541His	p.R541H	ENST00000228682	NM_005269.2	541	cGc/cAc	12/12	0.785391805094515	5	FACETS	0.956	0.883	1	0.319	0.294	0.345	CLONAL	1	TRUE	2	0.785391805094515	5		673	1102	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394333	162394333	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0019114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	128	454	0	ENST00000366898.1:c.734+1G>C		p.X245_splice	ENST00000366898	NM_004562.2	245			0.785391805094515	3	FACETS	1	0.917	1	0.502	0.458	0.548	CLONAL	1	TRUE	1	0.785391805094515	3		454	452	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372376	55372376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1428	275	901	1	ENST00000297316.4:c.1066G>A	p.Gly356Arg	p.G356R	ENST00000297316	NM_022454.3	356	Ggg/Agg	2/2	0.785391805094515	6	FACETS	1	0.969	1	0.264	0.247	0.282	CLONAL	1	TRUE	2	0.785391805094515	6		902	1703	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835596	68835596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587783047	NA	P-0019116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	337	621	2	ENST00000261769.5:c.187C>T	p.Arg63Ter	p.R63*	ENST00000261769	NM_004360.3	63	Cga/Tga	3/16	0.783506061268094	1	FACETS	0.982	0.944	1	0.982	0.944	1	CLONAL	1	TRUE	0	0.796199724393399	1		623	519	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916932	178916932	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	203	655	0	ENST00000263967.3:c.319A>T	p.Asn107Tyr	p.N107Y	ENST00000263967	NM_006218.2	107	Aac/Tac	2/21	1	2	FACETS	0.887	0.828	0.947	0.887	0.828	0.947	CLONAL	1	TRUE	1	0.796199724393399	2		655	575	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484280	120484280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	621	620	0	ENST00000256646.2:c.2850G>A	p.Met950Ile	p.M950I	ENST00000256646	NM_024408.3	950	atG/atA	18/34	0.796199724393399	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.796199724393399	3		620	1082	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180199	38180199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779461452	NA	P-0019116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	198	525	2	ENST00000396334.3:c.47C>T	p.Ala16Val	p.A16V	ENST00000396334	NM_002468.4	16	gCa/gTa	1/5	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.796199724393399	2		527	486	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0019117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	57	877	2	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.935	0.8	1	0.935	0.8	1	CLONAL	1	TRUE	1	0.15	2		879	813	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981240	201981241	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	62	814	0	ENST00000359651.3:c.321dup	p.Glu108Ter	p.E108*	ENST00000359651		107	ctt/cTtt	2/8	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.15	2		814	782	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	54	636	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.976	0.834	1	0.976	0.834	1	CLONAL	1	TRUE	1	0.220937431316918	2		636	501	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760106	133760106	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2229071	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	60	845	1	ENST00000318560.5:c.2429C>T	p.Pro810Leu	p.P810L	ENST00000318560	NM_005157.4	810	cCg/cTg	11/11	0.180266192308373	2	FACETS	0.718	0.618	0.828	0.359	0.309	0.414	SUBCLONAL	1	TRUE	0	0.220937431316918	2		846	756	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	109	681	0	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	0.180266192308373	2	FACETS	0.797	0.717	0.881	0.797	0.717	0.881	SUBCLONAL	2	TRUE	0	0.220937431316918	2		681	619	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	77	757	1	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.957	0.84	1	0.957	0.84	1	CLONAL	1	TRUE	1	0.220937431316918	2		758	728	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021828	71021828	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	23	338	0	ENST00000318789.4:c.1531-1G>C		p.X511_splice	ENST00000318789	NM_032682.5	511			0.220937431316918	1	FACETS	0.759	0.594	0.949	0.759	0.594	0.949	CLONAL	1	TRUE	0	0.220937431316918	1		338	244	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	60	684	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.180266192308373	2	FACETS	0.819	0.705	0.944	0.41	0.352	0.472	CLONAL	1	TRUE	0	0.220937431316918	2		684	663	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879888	37879888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	62	781	1	ENST00000269571.5:c.2183C>T	p.Ser728Phe	p.S728F	ENST00000269571		728	tCt/tTt	18/27	1	2	FACETS	0.648	0.558	0.746	0.648	0.558	0.746	SUBCLONAL	1	TRUE	1	0.220937431316918	2		782	866	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719140	190719140	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	33	510	0	ENST00000441310.2:c.1142C>G	p.Ser381Ter	p.S381*	ENST00000441310	NM_000534.4	381	tCa/tGa	9/13	1	2	FACETS	0.608	0.495	0.737	0.608	0.495	0.737	SUBCLONAL	1	TRUE	1	0.220937431316918	2		510	491	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612879	228612879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767647652	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	55	554	2	ENST00000366696.1:c.148C>T	p.Arg50Cys	p.R50C	ENST00000366696	NM_003493.2	50	Cgc/Tgc	1/1	0.221001675603868	3	FACETS	0.818	0.699	0.949	0.273	0.233	0.317	CLONAL	1	TRUE	0	0.220937431316918	3		556	676	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652140	3652140	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759447034	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	73	853	2	ENST00000294008.3:c.929G>A	p.Arg310Gln	p.R310Q	ENST00000294008	NM_032444.2	310	cGa/cAa	4/15	1	2	FACETS	0.62	0.54	0.706	0.62	0.54	0.706	SUBCLONAL	1	TRUE	1	0.220937431316918	2		855	1066	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874240	155874240	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	55	784	0	ENST00000368323.3:c.291C>G	p.Ile97Met	p.I97M	ENST00000368323	NM_006912.5	97	atC/atG	5/6	0.221001675603868	3	FACETS	0.577	0.491	0.67	0.288	0.245	0.335	SUBCLONAL	1	TRUE	1	0.220937431316918	3		784	959	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518634	204518634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	46	503	1	ENST00000367182.3:c.1297C>T	p.Leu433Phe	p.L433F	ENST00000367182	NM_001278516.1	433	Ctc/Ttc	11/11	0.221001675603868	3	FACETS	0.701	0.589	0.824	0.35	0.294	0.412	SUBCLONAL	1	TRUE	1	0.220937431316918	3		504	660	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	532680	532680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	71	903	2	ENST00000451590.1:c.526G>A	p.Glu176Lys	p.E176K	ENST00000451590	NM_001130442.1	176	Gag/Aag	5/5	1	2	FACETS	0.715	0.622	0.815	0.715	0.622	0.815	SUBCLONAL	1	TRUE	1	0.220937431316918	2		905	899	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242651	46242651	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1273082653	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	26	588	1	ENST00000334344.6:c.1613G>T	p.Cys538Phe	p.C538F	ENST00000334344	NM_152641.2	538	tGt/tTt	13/21	0.180266192308373	2	FACETS	0.466	0.368	0.579	0.233	0.184	0.29	SUBCLONAL	1	TRUE	0	0.220937431316918	2		589	505	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446161	49446161	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	67	775	1	ENST00000301067.7:c.1305C>A	p.Asn435Lys	p.N435K	ENST00000301067	NM_003482.3	435	aaC/aaA	10/54	0.180266192308373	2	FACETS	0.758	0.658	0.867	0.379	0.329	0.434	SUBCLONAL	1	TRUE	0	0.220937431316918	2		776	800	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609637	28609637	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1221770410	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	36	542	0	ENST00000241453.7:c.1592C>G	p.Ser531Cys	p.S531C	ENST00000241453	NM_004119.2	531	tCt/tGt	12/24	1	2	FACETS	0.527	0.432	0.634	0.527	0.432	0.634	SUBCLONAL	1	TRUE	1	0.220937431316918	2		542	618	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912763	32912763	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs80358664	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	48	686	0	ENST00000380152.3:c.4271C>G	p.Ser1424Cys	p.S1424C	ENST00000380152		1424	tCt/tGt	11/27	1	2	FACETS	0.55	0.464	0.646	0.55	0.464	0.646	SUBCLONAL	1	TRUE	1	0.220937431316918	2		686	790	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108602	8108602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	78	900	1	ENST00000585124.1:c.793G>A	p.Glu265Lys	p.E265K	ENST00000585124	NM_004217.3	265	Gag/Aag	8/9	1	2	FACETS	0.819	0.718	0.928	0.819	0.718	0.928	CLONAL	1	TRUE	1	0.220937431316918	2		901	862	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108641	8108641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	68	868	2	ENST00000585124.1:c.754G>A	p.Glu252Lys	p.E252K	ENST00000585124	NM_004217.3	252	Gag/Aag	8/9	1	2	FACETS	0.712	0.618	0.814	0.712	0.618	0.814	SUBCLONAL	1	TRUE	1	0.220937431316918	2		870	865	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016632	12016632	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	56	495	0	ENST00000353533.5:c.768C>G	p.Asp256Glu	p.D256E	ENST00000353533	NM_003010.3	256	gaC/gaG	7/11	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.220937431316918	2		495	481	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016649	12016649	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	47	457	0	ENST00000353533.5:c.785G>C	p.Arg262Thr	p.R262T	ENST00000353533	NM_003010.3	262	aGa/aCa	7/11	1	2	FACETS	0.945	0.799	1	0.945	0.799	1	CLONAL	1	TRUE	1	0.220937431316918	2		457	450	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40476788	40476788	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	59	825	0	ENST00000264657.5:c.1541C>A	p.Ser514Tyr	p.S514Y	ENST00000264657	NM_139276.2	514	tCc/tAc	17/24	1	2	FACETS	0.626	0.537	0.723	0.626	0.537	0.723	SUBCLONAL	1	TRUE	1	0.220937431316918	2		825	853	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756691	756691	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	63	707	0	ENST00000314574.4:c.137C>A	p.Ser46Ter	p.S46*	ENST00000314574	NM_005433.3	46	tCa/tAa	2/12	1	2	FACETS	0.801	0.692	0.92	0.801	0.692	0.92	CLONAL	1	TRUE	1	0.220937431316918	2		707	712	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132561	11132561	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555778797	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	97	791	0	ENST00000358026.2:c.2777A>G	p.Asn926Ser	p.N926S	ENST00000358026	NM_001128849.1	926	aAc/aGc	19/36	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.220937431316918	2		791	849	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652804	212652804	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138433638	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	54	743	0	ENST00000342788.4:c.502C>T	p.Arg168Trp	p.R168W	ENST00000342788	NM_005235.2	168	Cgg/Tgg	4/28	1	2	FACETS	0.876	0.748	1	0.876	0.748	1	CLONAL	1	TRUE	1	0.220937431316918	2		743	558	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395677	31395677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1267164985	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	63	610	1	ENST00000328111.2:c.2530G>A	p.Ala844Thr	p.A844T	ENST00000328111	NM_006892.3	844	Gcc/Acc	23/23	1	2	FACETS	0.775	0.669	0.89	0.775	0.669	0.89	SUBCLONAL	1	TRUE	1	0.220937431316918	2		611	736	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944503	40944503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	51	730	1	ENST00000373198.4:c.1999G>A	p.Glu667Lys	p.E667K	ENST00000373198	NM_133170.3	667	Gag/Aag	12/32	1	2	FACETS	0.721	0.612	0.841	0.721	0.612	0.841	SUBCLONAL	1	TRUE	1	0.220937431316918	2		731	640	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448615	89448615	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs755956785	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	74	725	0	ENST00000336596.2:c.1579G>C	p.Glu527Gln	p.E527Q	ENST00000336596	NM_005233.5	527	Gaa/Caa	7/17	0.220937431316918	1	FACETS	0.892	0.781	1	0.892	0.781	1	CLONAL	1	TRUE	0	0.220937431316918	1		725	668	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1936905	1936905	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	77	924	0	ENST00000382891.5:c.1590G>C	p.Lys530Asn	p.K530N	ENST00000382891	NM_133335.3	530	aaG/aaC	7/22	1	2	FACETS	0.733	0.642	0.831	0.733	0.642	0.831	SUBCLONAL	1	TRUE	1	0.220937431316918	2		924	951	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143191914	143191914	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	68	678	0	ENST00000262992.4:c.517G>T	p.Gly173Cys	p.G173C	ENST00000262992	NM_001101669.1	173	Ggc/Tgc	8/24	1	2	FACETS	0.891	0.774	1	0.891	0.774	1	CLONAL	1	TRUE	1	0.220937431316918	2		678	691	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177701	56177701	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	96	537	0	ENST00000399503.3:c.2675del	p.Asn892ThrfsTer17	p.N892Tfs*17	ENST00000399503	NM_005921.1	892	Aac/ac	14/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.220937431316918	2		537	587	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046023	180046023	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1396816704	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	38	197	3	ENST00000261937.6:c.2848G>A	p.Ala950Thr	p.A950T	ENST00000261937	NM_182925.4	950	Gcg/Acg	20/30	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.220937431316918	2		200	269	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197328	26197328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	39	405	0	ENST00000356476.2:c.151G>A	p.Glu51Lys	p.E51K	ENST00000356476		51	Gag/Aag	1/1	1	2	FACETS	0.771	0.639	0.918	0.771	0.639	0.918	CLONAL	1	TRUE	1	0.220937431316918	2		405	458	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519329	137519329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	46	503	0	ENST00000367739.4:c.1309G>A	p.Glu437Lys	p.E437K	ENST00000367739	NM_000416.2	437	Gaa/Aaa	7/7	0.145181848924085	1	FACETS	0.772	0.65	0.906	0.772	0.65	0.906	CLONAL	1	TRUE	0	0.220937431316918	1		503	480	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005093	150005093	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	121	552	0	ENST00000253339.5:c.1132C>G	p.Leu378Val	p.L378V	ENST00000253339		378	Ctg/Gtg	3/7	0.180266192308373	2	FACETS	0.981	0.89	1	0.981	0.89	1	CLONAL	2	TRUE	0	0.220937431316918	2		552	558	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896396	151896396	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1390364171	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	47	657	0	ENST00000262189.6:c.4241C>T	p.Ser1414Leu	p.S1414L	ENST00000262189	NM_170606.2	1414	tCa/tTa	27/59	1	2	FACETS	0.679	0.572	0.797	0.679	0.572	0.797	SUBCLONAL	1	TRUE	1	0.220937431316918	2		657	627	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896463	151896463	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	41	573	2	ENST00000262189.6:c.4174C>T	p.Gln1392Ter	p.Q1392*	ENST00000262189	NM_170606.2	1392	Cag/Tag	27/59	1	2	FACETS	0.672	0.559	0.798	0.672	0.559	0.798	SUBCLONAL	1	TRUE	1	0.220937431316918	2		575	552	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223811	53223811	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1391142009	NA	P-0019118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	77	1050	0	ENST00000375401.3:c.3548C>T	p.Ser1183Phe	p.S1183F	ENST00000375401	NM_004187.3	1183	tCt/tTt	23/26	1	2	FACETS	0.65	0.568	0.737	0.65	0.568	0.737	SUBCLONAL	1	TRUE	1	0.220937431316918	2		1050	1073	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112269	115112269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446220330	NA	P-0019119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	71	103	1	ENST00000257566.3:c.1471G>A	p.Ala491Thr	p.A491T	ENST00000257566	NM_016569.3	491	Gcg/Acg	7/8	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.547077820031568	2		104	220	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932255	39932255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1452619451	NA	P-0019119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	349	499	1	ENST00000378444.4:c.2344G>A	p.Asp782Asn	p.D782N	ENST00000378444	NM_001123385.1	782	Gac/Aac	4/15	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.547077820031568	1		500	654	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172485	108172485	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	89	596	0	ENST00000278616.4:c.5288A>C	p.Tyr1763Ser	p.Y1763S	ENST00000278616	NM_000051.3	1763	tAt/tCt	35/63	0.509354741522781	1	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	0	0.547077820031568	1		596	236	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790400	3790400	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs121434626	NA	P-0019119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	192	420	0	ENST00000262367.5:c.4133G>C	p.Arg1378Pro	p.R1378P	ENST00000262367	NM_004380.2	1378	cGg/cCg	24/31	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.547077820031568	2		420	615	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273944	10273944	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	322	873	0	ENST00000330684.3:c.325G>T	p.Val109Leu	p.V109L	ENST00000330684	NM_001134407.1	109	Gta/Tta	2/13	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.547077820031568	2		873	1149	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955541	55955541	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	155	783	0	ENST00000263923.4:c.3404T>G	p.Met1135Arg	p.M1135R	ENST00000263923	NM_002253.2	1135	aTg/aGg	25/30	1	2	FACETS	0.927	0.853	1	0.927	0.853	1	CLONAL	1	TRUE	1	0.547077820031568	2		783	611	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80160730	80160730	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	162	657	0	ENST00000265081.6:c.3099G>T	p.Leu1033Phe	p.L1033F	ENST00000265081	NM_002439.4	1033	ttG/ttT	22/24	0.547077820031568	1	FACETS	0.913	0.845	0.983	0.913	0.845	0.983	CLONAL	1	TRUE	0	0.547077820031568	1		657	471	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965566	93965566	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	163	626	1	ENST00000369303.4:c.2362G>T	p.Glu788Ter	p.E788*	ENST00000369303	NM_004440.3	788	Gaa/Taa	13/17	1	2	FACETS	0.891	0.82	0.964	0.891	0.82	0.964	CLONAL	1	TRUE	1	0.547077820031568	2		627	669	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570408	87570408	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	259	777	0	ENST00000277120.3:c.2148C>A	p.Asp716Glu	p.D716E	ENST00000277120		716	gaC/gaA	17/19	0.547077820031568	1	FACETS	0.945	0.889	1	0.945	0.889	1	CLONAL	1	TRUE	0	0.547077820031568	1		777	728	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	115	364	1				ENST00000310581	NM_198253.2	-/1132			0.198999585718655	1	FACETS	1	0.919	1	1	0.989	1	CLONAL	2	FALSE	0	0.247078420547646	1		365	403	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0019120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	544	800	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	0.247078420547646	3	FACETS	1	0.993	1			1	CLONAL	4	FALSE	NA	0.247078420547646	3		800	1107	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918622	44918622	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	240	677	2	ENST00000377967.4:c.1105C>T	p.Gln369Ter	p.Q369*	ENST00000377967	NM_021140.2	369	Cag/Tag	12/29	0.247078420547646	3	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	FALSE	1	0.247078420547646	3		679	1067	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14022087	14022087	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	140	405	0	ENST00000311895.7:c.787G>C	p.Asp263His	p.D263H	ENST00000311895	NM_005236.2	263	Gac/Cac	4/11	1	2	FACETS	1	0.968	1	1	0.992	1	CLONAL	2	FALSE	1	0.247078420547646	2		405	509	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097665	27097665	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0019120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	281	841	0	ENST00000324856.7:c.3254C>G	p.Ser1085Ter	p.S1085*	ENST00000324856	NM_006015.4	1085	tCa/tGa	12/20	0.198999585718655	1	FACETS	1	0.974	1	1	0.996	1	CLONAL	2	FALSE	0	0.247078420547646	1		841	939	SUCCESS
APC	324	MSKCC	GRCh37	5	112103077	112103077	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	116	335	0	ENST00000257430.4:c.412G>C	p.Glu138Gln	p.E138Q	ENST00000257430	NM_000038.5	138	Gag/Cag	4/16	1	2	FACETS	0.978	0.887	1	1	0.989	1	CLONAL	2	FALSE	1	0.247078420547646	2		335	480	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509898	106509898	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	90	589	0	ENST00000359195.3:c.1892T>C	p.Leu631Pro	p.L631P	ENST00000359195	NM_002649.2	631	cTg/cCg	2/11	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	FALSE	1	0.247078420547646	2		589	696	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054729	5054729	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	153	497	0	ENST00000381652.3:c.781C>G	p.Leu261Val	p.L261V	ENST00000381652	NM_004972.3	261	Ctg/Gtg	7/25	1	2	FACETS	1	0.92	1	1	0.992	1	CLONAL	2	FALSE	1	0.247078420547646	2		497	618	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5078343	5078343	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019121-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	178	395	0	ENST00000381652.3:c.2030A>G	p.Lys677Arg	p.K677R	ENST00000381652	NM_004972.3	677	aAa/aGa	16/25	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		395	525	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309894	30309894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145910874	NA	P-0019122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	84	579	2	ENST00000307677.4:c.128C>T	p.Ser43Leu	p.S43L	ENST00000307677	NM_138578.1	43	tCg/tTg	2/3	0.532693682141603	4	FACETS	0.403	0.354	0.455	0.134	0.118	0.152	SUBCLONAL	1	TRUE	1	0.702632308499408	4		581	1011	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	161	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.340980276634282	2	FACETS	0.887	0.82	0.955	0.887	0.82	0.955	CLONAL	2	TRUE	0	0.384769568194661	2		509	472	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473722	67473722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs794727798	NA	P-0019123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	152	484	2	ENST00000327367.4:c.802C>T	p.Arg268Cys	p.R268C	ENST00000327367	NM_005902.3	268	Cgc/Tgc	6/9	0.319986874785165	2	FACETS	1	0.987	1	0.695	0.639	0.754	CLONAL	1	TRUE	0	0.384769568194661	2		486	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578396	+	inframe_deletion	In_Frame_Del	DEL	TGG	TGG	-	novel	NA	P-0019123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	170	640	0	ENST00000269305.4:c.534_536del	p.His179del	p.H179del	ENST00000269305	NM_001126112.2	178	caCCAt/cat	5/11	0.319986874785165	2	FACETS	0.837	0.775	0.9	0.837	0.775	0.9	CLONAL	2	TRUE	0	0.384769568194661	2		640	528	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396635	396635	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	81	514	0	ENST00000262320.3:c.391G>T	p.Asp131Tyr	p.D131Y	ENST00000262320	NM_003502.3	131	Gac/Tac	2/11	NA	2	FACETS	0.629	0.554	0.71			1	INDETERMINATE	1	TRUE	NA	0.384769568194661	2		514	669	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745082	41745082	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1432876896	NA	P-0019123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	119	474	0	ENST00000301178.4:c.1148T>C	p.Ile383Thr	p.I383T	ENST00000301178	NM_021913.4	383	aTa/aCa	9/20	0.328675047710452	4	FACETS	1	0.935	1	0.349	0.315	0.385	CLONAL	1	TRUE	1	0.384769568194661	4		474	818	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713226	30713226	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs863223839	NA	P-0019123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	178	409	0	ENST00000295754.5:c.551T>A	p.Ile184Asn	p.I184N	ENST00000295754	NM_003242.5	184	aTc/aAc	4/7	0.32483588994003	2	FACETS	0.916	0.851	0.982	0.916	0.851	0.982	CLONAL	2	TRUE	0	0.384769568194661	2		409	505	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220539	123220539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	137	572	3	ENST00000218089.9:c.3196C>T	p.Arg1066Trp	p.R1066W	ENST00000218089	NM_001042749.1	1066	Cgg/Tgg	30/35	0.157345113217198	3	FACETS	1	0.956	1	0.361	0.328	0.395	INDETERMINATE	1	TRUE	0	0.384769568194661	3		575	785	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0019124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	143	741	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.20050656961545	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.20050656961545	3		742	686	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905411	11905411	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	100	529	0	ENST00000396373.4:c.61G>A	p.Glu21Lys	p.E21K	ENST00000396373	NM_001987.4	21	Gag/Aag	2/8	0.20050656961545	5	FACETS	0.862	0.77	0.959	0.574	0.513	0.64	CLONAL	2	TRUE	2	0.20050656961545	5		529	753	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135384	30135384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373748041	NA	P-0019124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	126	615	1	ENST00000331968.5:c.434G>A	p.Arg145His	p.R145H	ENST00000331968	NM_002742.2	145	cGt/cAt	3/18	0.156245411629868	4	FACETS	0.953	0.863	1	0.953	0.863	1	CLONAL	2	TRUE	2	0.20050656961545	4		616	792	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842369	68842373	+	frameshift_variant	Frame_Shift_Del	DEL	AACTC	AACTC	GAG	novel	NA	P-0019124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	192	806	2	ENST00000261769.5:c.430_434delinsGAG	p.Asn144GlufsTer23	p.N144Efs*23	ENST00000261769	NM_004360.3	144	AACTCc/GAGc	4/16	0.20050656961545	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.20050656961545	2		808	894	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231817	36231817	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	209	960	1	ENST00000300305.3:c.567C>A	p.Tyr189Ter	p.Y189*	ENST00000300305		189	taC/taA	5/8	0.156245411629868	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.20050656961545	4		961	1120	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0019125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	109	741	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	0.475175150181689	2		742	411	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0019125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	8	629	0	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	0.475175150181689	1	FACETS	0.077	0.049	0.113	0.077	0.049	0.113	SUBCLONAL	1	TRUE	0	0.475175150181689	1		629	335	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40789994	40789994	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs746391800	NA	P-0019125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	104	412	2	ENST00000373198.4:c.2737G>A	p.Glu913Lys	p.E913K	ENST00000373198	NM_133170.3	913	Gag/Aag	18/32	1	2	FACETS	0.933	0.84	1	0.933	0.84	1	CLONAL	1	TRUE	1	0.475175150181689	2		414	469	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317019	11317019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	116	492	0	ENST00000361445.4:c.475G>A	p.Asp159Asn	p.D159N	ENST00000361445	NM_004958.3	159	Gac/Aac	4/58	0.475175150181689	1	FACETS	0.801	0.726	0.878	0.801	0.726	0.878	CLONAL	1	TRUE	0	0.475175150181689	1		492	465	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451087	70451087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	45	579	0	ENST00000373644.4:c.5927C>T	p.Ser1976Phe	p.S1976F	ENST00000373644	NM_030625.2	1976	tCt/tTt	12/12	1	2	FACETS	0.253	0.212	0.299	0.253	0.212	0.299	SUBCLONAL	1	TRUE	1	0.475175150181689	2		579	749	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416820	416820	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	109	416	0	ENST00000399788.2:c.3730G>A	p.Glu1244Lys	p.E1244K	ENST00000399788	NM_001042603.1	1244	Gag/Aag	23/28	1	2	FACETS	0.874	0.788	0.964	0.874	0.788	0.964	CLONAL	1	TRUE	1	0.475175150181689	2		416	525	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626796	28626796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	125	399	1	ENST00000241453.7:c.500C>T	p.Thr167Ile	p.T167I	ENST00000241453	NM_004119.2	167	aCa/aTa	5/24	1	2	FACETS	0.875	0.795	0.96	0.875	0.795	0.96	CLONAL	1	TRUE	1	0.475175150181689	2		400	601	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438348	110438348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	47	157	0	ENST00000375856.3:c.53C>T	p.Pro18Leu	p.P18L	ENST00000375856	NM_003749.2	18	cCc/cTc	1/2	1	2	FACETS	0.856	0.73	0.993	0.856	0.73	0.993	CLONAL	1	TRUE	1	0.475175150181689	2		157	231	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781821	3781821	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	151	554	0	ENST00000262367.5:c.4846G>A	p.Asp1616Asn	p.D1616N	ENST00000262367	NM_004380.2	1616	Gac/Aac	29/31	0.475175150181689	3	FACETS	0.787	0.719	0.859	0.394	0.359	0.43	SUBCLONAL	1	TRUE	1	0.475175150181689	3		554	999	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831119	72831120	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0019125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	116	367	0	ENST00000268489.5:c.5461dup	p.Ala1821GlyfsTer108	p.A1821Gfs*108	ENST00000268489	NM_006885.3	1821	gca/gGca	9/10	0.475175150181689	3	FACETS	0.891	0.804	0.983	0.446	0.402	0.492	CLONAL	1	TRUE	1	0.475175150181689	3		367	678	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653126	29653126	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	99	395	0	ENST00000356175.3:c.5061C>A	p.Phe1687Leu	p.F1687L	ENST00000356175	NM_000267.3	1687	ttC/ttA	36/57	1	2	FACETS	0.762	0.682	0.846	0.762	0.682	0.846	SUBCLONAL	1	TRUE	1	0.475175150181689	2		395	547	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653244	29653244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	97	353	0	ENST00000356175.3:c.5179C>T	p.His1727Tyr	p.H1727Y	ENST00000356175	NM_000267.3	1727	Cac/Tac	36/57	1	2	FACETS	0.704	0.629	0.783	0.704	0.629	0.783	SUBCLONAL	1	TRUE	1	0.475175150181689	2		353	580	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951068	17951068	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	203	603	0	ENST00000458235.1:c.1225G>A	p.Asp409Asn	p.D409N	ENST00000458235	NM_000215.3	409	Gac/Aac	9/24	1	2	FACETS	0.969	0.899	1	0.969	0.899	1	CLONAL	1	TRUE	1	0.475175150181689	2		603	882	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572530	41572530	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	134	403	0	ENST00000263253.7:c.5059G>C	p.Glu1687Gln	p.E1687Q	ENST00000263253	NM_001429.3	1687	Gag/Cag	30/31	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.475175150181689	2		403	549	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956136	55956136	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	181	504	0	ENST00000263923.4:c.3179T>A	p.Val1060Asp	p.V1060D	ENST00000263923	NM_002253.2	1060	gTc/gAc	23/30	0.475175150181689	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.475175150181689	1		504	519	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539747	187539747	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	147	545	0	ENST00000441802.2:c.7993G>T	p.Glu2665Ter	p.E2665*	ENST00000441802	NM_005245.3	2665	Gaa/Taa	10/27	0.475175150181689	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.475175150181689	1		545	458	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180943	32180943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	104	435	0	ENST00000375023.3:c.2407G>A	p.Glu803Lys	p.E803K	ENST00000375023	NM_004557.3	803	Gag/Aag	15/30	1	2	FACETS	0.832	0.748	0.921	0.832	0.748	0.921	CLONAL	1	TRUE	1	0.475175150181689	2		435	526	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0019126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	218	680	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	0.610781498444289	2		680	673	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0019126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	195	583	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.853	0.791	0.916	0.853	0.791	0.916	CLONAL	1	TRUE	1	0.610781498444289	2		583	749	SUCCESS
APC	324	MSKCC	GRCh37	5	112173656	112173656	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123117	NA	P-0019126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	243	562	0	ENST00000257430.4:c.2365C>T	p.Gln789Ter	p.Q789*	ENST00000257430	NM_000038.5	789	Cag/Tag	16/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.610781498444289	2		562	754	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578493	7578493	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1206165503	NA	P-0019126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	681	889	3	ENST00000269305.4:c.437G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tGg/tAg	5/11	0.610781498444289	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.610781498444289	2		892	1078	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0019126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	267	810	3	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.919	0.863	0.977	0.919	0.863	0.977	CLONAL	1	TRUE	1	0.610781498444289	2		813	951	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249501	153249501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1316840275	NA	P-0019126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	332	870	0	ENST00000281708.4:c.1277C>T	p.Ser426Leu	p.S426L	ENST00000281708	NM_033632.3	426	tCa/tTa	9/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.610781498444289	2		870	1010	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028610	12028610	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0019126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	254	465	1	ENST00000353533.5:c.814-1G>T		p.X272_splice	ENST00000353533	NM_003010.3	272			0.610781498444289	2	FACETS	0.904	0.859	0.949	0.904	0.859	0.949	CLONAL	2	TRUE	0	0.610781498444289	2		466	460	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943623	9943623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758815434	NA	P-0019126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	680	721	1	ENST00000330684.3:c.1318G>A	p.Val440Ile	p.V440I	ENST00000330684	NM_001134407.1	440	Gtc/Atc	5/13	0.399041993800427	3	FACETS	0.975	0.949	1			1	CLONAL	3	TRUE	NA	0.610781498444289	3		722	994	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046638	30046638	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1419328188	NA	P-0019126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	243	803	2	ENST00000331968.5:c.2545C>T	p.Arg849Ter	p.R849*	ENST00000331968	NM_002742.2	849	Cga/Tga	18/18	1	2	FACETS	0.947	0.887	1	0.947	0.887	1	CLONAL	1	TRUE	1	0.610781498444289	2		805	840	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554408	63554408	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	643	906	1	ENST00000307078.5:c.331T>C	p.Trp111Arg	p.W111R	ENST00000307078	NM_004655.3	111	Tgg/Cgg	2/11	0.610781498444289	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.610781498444289	2		907	1047	SUCCESS
APC	324	MSKCC	GRCh37	5	112176015	112176015	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	204	565	0	ENST00000257430.4:c.4724del	p.Leu1575GlnfsTer75	p.L1575Qfs*75	ENST00000257430	NM_000038.5	1575	cTa/ca	16/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.610781498444289	2		565	641	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0019128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	87	832	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.15	2		832	859	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578509	7578509	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519978	NA	P-0019128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	62	1077	0	ENST00000269305.4:c.421T>C	p.Cys141Arg	p.C141R	ENST00000269305	NM_001126112.2	141	Tgc/Cgc	5/11	1	2	FACETS	0.685	0.59	0.79	0.685	0.59	0.79	SUBCLONAL	1	TRUE	1	0.15	2		1077	1206	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835952	151835952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	52	546	1	ENST00000262189.6:c.14572G>A	p.Glu4858Lys	p.E4858K	ENST00000262189	NM_170606.2	4858	Gaa/Aaa	58/59	1	2	FACETS	0.921	0.782	1	0.921	0.782	1	CLONAL	1	TRUE	1	0.15	2		547	753	SUCCESS
APC	324	MSKCC	GRCh37	5	112175760	112175761	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs398123122	NA	P-0019129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	232	496	1	ENST00000257430.4:c.4473dup	p.Ala1492CysfsTer22	p.A1492Cfs*22	ENST00000257430	NM_000038.5	1490	cat/caTt	16/16	0.611919839825874	3	FACETS	0.885	0.833	0.938	0.885	0.833	0.938	CLONAL	2	TRUE	1	0.622611268110391	3		497	552	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920402	114920402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs927089403	NA	P-0019129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	350	739	1	ENST00000543371.1:c.1343G>A	p.Arg448Gln	p.R448Q	ENST00000543371	NM_001198531.1	448	cGg/cAg	13/14	0.610911194885979	3	FACETS	0.949	0.904	0.994	0.949	0.904	0.994	CLONAL	2	TRUE	1	0.622611268110391	3		740	777	SUCCESS
APC	324	MSKCC	GRCh37	5	112173590	112173590	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561575998	NA	P-0019129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	151	611	0	ENST00000257430.4:c.2299C>T	p.Gln767Ter	p.Q767*	ENST00000257430	NM_000038.5	767	Cag/Tag	16/16	0.611919839825874	3	FACETS	0.964	0.884	1	0.482	0.442	0.524	CLONAL	1	TRUE	1	0.622611268110391	3		611	660	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223120	5223120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764560600	NA	P-0019129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	490	863	2	ENST00000357368.4:c.2683G>A	p.Val895Met	p.V895M	ENST00000357368	NM_002850.3	895	Gtg/Atg	18/38	0.610911194885979	3	FACETS	0.962	0.924	1	0.962	0.924	1	CLONAL	2	TRUE	1	0.622611268110391	3		865	1073	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593557	48593557	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	137	251	2	ENST00000342988.3:c.1308G>C	p.Lys436Asn	p.K436N	ENST00000342988	NM_005359.5	436	aaG/aaC	10/12	0.622611268110391	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.622611268110391	2		253	214	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0019130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	499	697	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	NA	2	FACETS	0.995	0.961	1			1	INDETERMINATE	2	TRUE	NA	0.611832198009579	2		697	820	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249022	55249022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567477136	NA	P-0019130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	426	704	1	ENST00000275493.2:c.2320G>A	p.Val774Met	p.V774M	ENST00000275493	NM_005228.3	774	Gtg/Atg	20/28	0.440271264059099	3	FACETS	1	0.993	1	0.764	0.734	0.795	CLONAL	2	TRUE	0	0.611832198009579	3		705	793	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0019130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	388	690	1	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.440271264059099	3	FACETS	1	0.991	1	0.747	0.716	0.778	CLONAL	2	TRUE	0	0.611832198009579	3		691	739	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241873	72241873	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1252345844	NA	P-0019130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	53	484	1	ENST00000357731.5:c.517C>T	p.Arg173Ter	p.R173*	ENST00000357731	NM_173808.2	173	Cga/Tga	3/7	0.501692666646428	3	FACETS	0.436	0.372	0.506	0.218	0.186	0.253	SUBCLONAL	1	TRUE	1	0.611832198009579	3		485	519	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944275	206944275	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	400	580	0	ENST00000423557.1:c.355C>G	p.Leu119Val	p.L119V	ENST00000423557	NM_000572.2	119	Ctc/Gtc	3/5	0.491866697481234	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.611832198009579	4		580	986	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78599594	78599594	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0019130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	260	315	1	ENST00000306801.3:c.265+1G>T		p.X89_splice	ENST00000306801	NM_020761.2	89			0.611832198009579	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.611832198009579	3		316	511	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861646	152861646	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0019131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	111	749	0	ENST00000406277.2:c.107-1G>A		p.X36_splice	ENST00000406277	NM_152274.4	36			1		FACETS		0.837	1				CLONAL	1	TRUE	1	0.40455031589991	2		749	591	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40865324	40865327	+	frameshift_variant	Frame_Shift_Del	DEL	ACTG	ACTG	-	novel	NA	P-0019131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	35	771	0	ENST00000428826.2:c.1104_1107del	p.Ser369LeufsTer55	p.S369Lfs*55	ENST00000428826		368	gtCAGT/gt	11/21	1	2	FACETS	0.257	0.21	0.311	0.257	0.21	0.311	SUBCLONAL	1	TRUE	1	0.40455031589991	2		771	672	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702167	47702182	+	frameshift_variant	Frame_Shift_Del	DEL	ATGTAGAACCAATGCA	ATGTAGAACCAATGCA	-	novel	NA	P-0019131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	65	481	0	ENST00000233146.2:c.1763_1778del	p.Tyr588Ter	p.Y588*	ENST00000233146	NM_000251.2	588	tATGTAGAACCAATGCAg/tg	12/16	1	2	FACETS	0.761	0.662	0.868	0.761	0.662	0.868	SUBCLONAL	1	TRUE	1	0.40455031589991	2		481	422	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242483	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACA	AATTAAGAGAAGCAACA	CT	novel	NA	P-0019131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	172	923	4	ENST00000275493.2:c.2237_2253delinsCT	p.Glu746_Thr751delinsAla	p.E746_T751delinsA	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACA/gCT	19/28	0.219501146358571	5	FACETS	1	0.986	1	0.445	0.409	0.483	INDETERMINATE	1	TRUE	2	0.40455031589991	5		927	1023	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039418	47039421	+	frameshift_variant	Frame_Shift_Del	DEL	CATC	CATC	-	novel	NA	P-0019131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	108	813	0	ENST00000377604.3:c.1043_1046del	p.Ile348SerfsTer136	p.I348Sfs*136	ENST00000377604	NM_001204468.1	347	ttCATC/tt	10/24	1	2	FACETS	0.776	0.697	0.86	0.776	0.697	0.86	SUBCLONAL	1	TRUE	1	0.40455031589991	2		813	688	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0019132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	16	706	0	ENST00000311936.3:c.34_35delinsAT	p.Gly12Ile	p.G12I	ENST00000311936	NM_004985.3	12	GGt/ATt	2/5	1	2	FACETS	0.079	0.057	0.104	0.079	0.057	0.104	SUBCLONAL	1	TRUE	1	0.47	2		706	865	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0019133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	357	538	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.569314461151863	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.569314461151863	3		538	717	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0019133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	237	594	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	0.569314461151863	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.569314461151863	3		594	511	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776006	9776006	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	82	415	0	ENST00000377346.4:c.470T>C	p.Leu157Pro	p.L157P	ENST00000377346	NM_005026.3	157	cTg/cCg	5/24	1	2	FACETS	0.502	0.443	0.565	0.502	0.443	0.565	SUBCLONAL	1	TRUE	1	0.569314461151863	2		415	574	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981836	101981836	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	659	504	0	ENST00000282441.5:c.257T>C	p.Met86Thr	p.M86T	ENST00000282441	NM_001130145.2	86	aTg/aCg	1/9	0.569314461151863	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.569314461151863	2		504	1053	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422052	81422052	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	223	152	0	ENST00000298171.2:c.28G>C	p.Val10Leu	p.V10L	ENST00000298171	NM_000369.2	10	Gtg/Ctg	1/10	0.296493329864958	3	FACETS	1	0.981	1	0.728	0.686	0.769	INDETERMINATE	2	TRUE	0	0.569314461151863	3		152	461	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054492	42054492	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	193	304	1	ENST00000219905.7:c.7676G>T	p.Gly2559Val	p.G2559V	ENST00000219905	NM_001164273.1	2559	gGa/gTa	22/24	0.18888830934794	4	FACETS	0.81	0.752	0.869	0.81	0.752	0.869	INDETERMINATE	2	TRUE	2	0.569314461151863	4		305	657	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88428927	88428927	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	87	239	0	ENST00000360948.2:c.2173G>C	p.Glu725Gln	p.E725Q	ENST00000360948	NM_001012338.2	725	Gag/Cag	17/19	0.569314461151863	1	FACETS	0.483	0.429	0.539	0.483	0.429	0.539	SUBCLONAL	1	TRUE	0	0.569314461151863	1		239	453	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2111957	2111957	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs777172185	NA	P-0019133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	305	611	0	ENST00000219476.3:c.1205G>T	p.Gly402Val	p.G402V	ENST00000219476	NM_000548.3	402	gGg/gTg	12/42	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.569314461151863	2		611	919	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126120	2126120	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	353	681	1	ENST00000219476.3:c.2691C>A	p.Phe897Leu	p.F897L	ENST00000219476	NM_000548.3	897	ttC/ttA	24/42	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.569314461151863	2		682	1139	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355054	15355054	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	191	785	0	ENST00000263377.2:c.2569G>C	p.Val857Leu	p.V857L	ENST00000263377	NM_058243.2	857	Gtc/Ctc	13/20	0.569314461151863	1	FACETS	0.772	0.717	0.828	0.772	0.717	0.828	SUBCLONAL	1	TRUE	0	0.569314461151863	1		785	622	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456889	149456889	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	72	511	0	ENST00000286301.3:c.839C>G	p.Ala280Gly	p.A280G	ENST00000286301	NM_005211.3	280	gCc/gGc	6/22	0.266784371112131	2	FACETS	0.296	0.258	0.338	0.148	0.129	0.169	INDETERMINATE	1	TRUE	0	0.569314461151863	2		511	854	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149511645	149511645	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	288	184	0	ENST00000261799.4:c.1140G>C	p.Glu380Asp	p.E380D	ENST00000261799	NM_002609.3	380	gaG/gaC	8/23	0.569314461151863	3	FACETS	0.991	0.939	1	0.991	0.939	1	CLONAL	2	TRUE	1	0.569314461151863	3		184	656	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750910	128751932	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTGGAGCGGCTTCTCGGCCGCCGCCAAGCTCGTCTCAGAGAAGCTGGCCTCCTACCAGGCTGCGCGCAAAGACAGCGGCAGCCCGAACCCCGCCCGCGGCCACAGCGTCTGCTCCACCTCCAGCTTGTACCTGCAGGATCTGAGCGCCGCCGCCTCAGAGTGCATCGACCCCTCGGTGGTCTTCCCCTACCCTCTCAACGACAGCAGCTCGCCCAAGTCCTGCGCCTCGCAAGACTCCAGCGCCTTCTCTCCGTCCTCGGATTCTCTGCTCTCCTCGACGGAGTCCTCCCCGCAGGGCAGCCCCGAGCCCCTGGTGCTCCATGAGGAGACACCGCCCACCACCAGCAGCGACTCTGGTAAGCGAAGCCCGCCCAGGCCTGTCAAAAGTGGGCGGCTGGATACCTTTCCCATTTTCATTGGCAGCTTATTTAACGGGCCACTCTTATTAGGAAGGAGAGATAGCAGATCTGGAGAGATTTGGGAGCTCATCACCTCTGAAACCTTGGGCTTTAGCGTTTCCTCCCATCCCTTCCCCTTAGACTGCCCATGTTTGCAGCCCCCCTCCCCGTTTGTCTCCCACCCCTCAGGAATTTCATTTAGGTTTTTAAACCTTCTGGCTTATCTTACAACTCAATCCACTTCTTCTTACCTCCCGTTAACATTTTAATTGCCCTGGGGCGGGGTGGCAGGGAGTGTATGAATGAGGATAAGAGAGGATTGATCTCTGAGAGTGAATGAATTGCTTCCCTCTTAACTTCCGAGAAGTGGTGGGATTTAATGAACTATCTACAAAAATGAGGGGCTGTGTTTAGAGGCTAGGCAGGGCCTGCCTGAGTGCGGGAGCCAGTGAACTGCCTCAAGAGTGGGTGGGCTGAGGAGCTGGGATCTTCTCAGCCTATTTTGAACACTGAAAAGCAAATCCTTGCCAAAGTTGGACTTTTTTTTTTCTTTTATTCCTTCCCCCGCCCTCTTGGACTTTTGGCAAAACTGCAATTTTTTTTTTTTTATTTTTCATTTCCAGTA	GTGGAGCGGCTTCTCGGCCGCCGCCAAGCTCGTCTCAGAGAAGCTGGCCTCCTACCAGGCTGCGCGCAAAGACAGCGGCAGCCCGAACCCCGCCCGCGGCCACAGCGTCTGCTCCACCTCCAGCTTGTACCTGCAGGATCTGAGCGCCGCCGCCTCAGAGTGCATCGACCCCTCGGTGGTCTTCCCCTACCCTCTCAACGACAGCAGCTCGCCCAAGTCCTGCGCCTCGCAAGACTCCAGCGCCTTCTCTCCGTCCTCGGATTCTCTGCTCTCCTCGACGGAGTCCTCCCCGCAGGGCAGCCCCGAGCCCCTGGTGCTCCATGAGGAGACACCGCCCACCACCAGCAGCGACTCTGGTAAGCGAAGCCCGCCCAGGCCTGTCAAAAGTGGGCGGCTGGATACCTTTCCCATTTTCATTGGCAGCTTATTTAACGGGCCACTCTTATTAGGAAGGAGAGATAGCAGATCTGGAGAGATTTGGGAGCTCATCACCTCTGAAACCTTGGGCTTTAGCGTTTCCTCCCATCCCTTCCCCTTAGACTGCCCATGTTTGCAGCCCCCCTCCCCGTTTGTCTCCCACCCCTCAGGAATTTCATTTAGGTTTTTAAACCTTCTGGCTTATCTTACAACTCAATCCACTTCTTCTTACCTCCCGTTAACATTTTAATTGCCCTGGGGCGGGGTGGCAGGGAGTGTATGAATGAGGATAAGAGAGGATTGATCTCTGAGAGTGAATGAATTGCTTCCCTCTTAACTTCCGAGAAGTGGTGGGATTTAATGAACTATCTACAAAAATGAGGGGCTGTGTTTAGAGGCTAGGCAGGGCCTGCCTGAGTGCGGGAGCCAGTGAACTGCCTCAAGAGTGGGTGGGCTGAGGAGCTGGGATCTTCTCAGCCTATTTTGAACACTGAAAAGCAAATCCTTGCCAAAGTTGGACTTTTTTTTTTCTTTTATTCCTTCCCCCGCCCTCTTGGACTTTTGGCAAAACTGCAATTTTTTTTTTTTTATTTTTCATTTCCAGTA	-	novel	NA	P-0019133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	75	306	0	ENST00000377970.2:c.447_802+667del		p.X149_splice	ENST00000377970	NM_002467.4	149		2/3	0.569314461151863	4	FACETS	0.335	0.292	0.382	0.112	0.097	0.128	SUBCLONAL	1	TRUE	1	0.569314461151863	4		306	1234	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	193	736	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.892410018062257	2		736	373	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0019134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	170	405	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	1	2	FACETS	0.948	0.883	1	0.948	0.883	1	CLONAL	1	TRUE	1	0.892410018062257	2		405	402	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0019134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5894	412	1035	6	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.892410018062257	15	FACETS	0.996	0.94	1			1	CLONAL	1	TRUE	NA	0.892410018062257	15		1041	6306	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508856	106508856	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376958957	NA	P-0019134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	222	601	0	ENST00000359195.3:c.850G>A	p.Glu284Lys	p.E284K	ENST00000359195	NM_002649.2	284	Gaa/Aaa	2/11	0.859368257870487	3	FACETS	1	0.947	1	0.507	0.474	0.542	CLONAL	1	TRUE	1	0.892410018062257	3		601	709	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048166	180048166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1369049878	NA	P-0019134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	339	993	1	ENST00000261937.6:c.2107G>A	p.Gly703Arg	p.G703R	ENST00000261937	NM_182925.4	703	Gga/Aga	14/30	0.239698819007579	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.892410018062257	0		994	668	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47607076	47607076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	311	749	0	ENST00000263735.4:c.826G>A	p.Val276Met	p.V276M	ENST00000263735	NM_002354.2	276	Gtg/Atg	7/9	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.892410018062257	2		749	692	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	52	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.801	0.684	0.928	0.801	0.684	0.928	CLONAL	1	TRUE	1	0.345410452490848	2		509	376	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230604	46230604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	31	562	0	ENST00000334344.6:c.853C>T	p.Arg285Trp	p.R285W	ENST00000334344	NM_152641.2	285	Cgg/Tgg	8/21	1	2	FACETS	0.65	0.528	0.788	0.65	0.528	0.788	SUBCLONAL	1	TRUE	1	0.345410452490848	2		562	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	54	719	0	ENST00000269305.4:c.503A>C	p.His168Pro	p.H168P	ENST00000269305	NM_001126112.2	168	cAc/cCc	5/11	NA	2	FACETS	0.544	0.464	0.631			1	INDETERMINATE	1	TRUE	NA	0.345410452490848	2		719	575	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250677	26250677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	38	507	1	ENST00000446824.2:c.157C>T	p.Arg53Cys	p.R53C	ENST00000446824	NM_021018.2	53	Cgc/Tgc	1/1	1	2	FACETS	0.481	0.398	0.575	0.481	0.398	0.575	SUBCLONAL	1	TRUE	1	0.345410452490848	2		508	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0019136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	247	1015	3	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	0.221491934048573	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.23	2		1018	1008	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669547	88669547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56394626	NA	P-0019136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	143	1024	0	ENST00000360948.2:c.1351G>A	p.Val451Ile	p.V451I	ENST00000360948	NM_001012338.2	451	Gtc/Atc	12/19	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.23	2		1024	947	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865684	57865684	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	181	1088	0	ENST00000228682.2:c.3161A>G	p.Asp1054Gly	p.D1054G	ENST00000228682	NM_005269.2	1054	gAt/gGt	12/12	0.3	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.23	1		1088	1154	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112497	2112497	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs397515182	NA	P-0019136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	196	985	0	ENST00000219476.3:c.1258-1G>A		p.X420_splice	ENST00000219476	NM_000548.3	420			0.3	1	FACETS	0.835	0.774	0.899	1	0.992	1	CLONAL	2	TRUE	0	0.23	1		985	903	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81973570	81973571	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0019136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	143	895	3	ENST00000359376.3:c.3387_3388delinsAA	p.Ala1130Thr	p.A1130T	ENST00000359376	NM_002661.3	1129	ctGGca/ctAAca	30/33	0.3	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.23	1		898	845	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158595067	158595067	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	72	614	0	ENST00000263640.3:c.1280A>G	p.Tyr427Cys	p.Y427C	ENST00000263640	NM_001105.4	427	tAc/tGc	10/11	0.220528023644702	1	FACETS	0.866	0.756	0.984	0.866	0.756	0.984	CLONAL	1	TRUE	0	0.23	1		614	640	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661648	227661648	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	67	649	0	ENST00000305123.5:c.1807A>T	p.Ser603Cys	p.S603C	ENST00000305123	NM_005544.2	603	Agc/Tgc	1/2	0.220528023644702	1	FACETS	0.755	0.655	0.863	0.755	0.655	0.863	SUBCLONAL	1	TRUE	0	0.23	1		649	683	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39708821	39709804	+	splice_donor_variant,splice_acceptor_variant,intron_variant	Splice_Site	DEL	GTGAGTATTTTCTTAAAACTTTGACTTTTGAAAACAAAAAGGAGGAGTTTAAAGAATAAATGTGATGTGTTTCTTTATAATACATATAGAAACTGCATTAATTGGCTTTTACTCATTTGGAATTTGTGATTAATGGACTGATTTCTCTGAACTATGAGAAGTAGAGTTTGCTAAACAAGTAGTATACCCAAGGCTTACATGAAGATTATATAAATTTTTATTACTGAAAAGGCAATAGATATTTATTGTAGAAATTTCAAATAATACAGAATTCATGAAGAATAAATTATTTAAGTTACTTAAAATTTCTTATTGCCTACCACAGATAACTTAAAGCAGTTTCTCTTAGACCTATTCCTGTCAGACATTCTAAGTGAAGTTTCAGTGTGTAAAAATAATAAAACTGCTCATAAAACGGTCGAGGCTTACATGTATCTCTTTCCCCAGATTCAATGAGATTAAATTATATTCATTATTTTCACTCTTATATAGCTTACTATGCTATTGTTATAGTAGAAATTGGATGGAAAGGGAGAAGGGAAATACTTAGTGAACTCATTTGTATTCATTCAATATAGAATTTCTTTCCTCCACATTCCAGTGAGTTACTGCTATGTGGTAGCTAGTGTGCTGTGTGTTTGGTTCCCAAACTTTCATCTTTTATTTTTATTTATTTTATTTTATTTTTTTTCCCAGACTTTCATCTGATAATGATATTTATTTCTGCATATATCCCCCCACCCTATTTTGCTTCCAGGCCGGTGTAAGTGGTTTGTTTTGTTCTATATAGGGCTATAACTATTACTCTTTGGTCTGACCTTCATTATTTTCTCTATTTCTGTTAGTCTTGACCGTAGAATGCCCAGCCAAGAATAACAGTGATTACTCTTGCCATGGAGGCATCCAAGAGTTTGTAGGTCTCCTATGAGTGAGAACTCCTGAATCATAATTATGTTAACTGTGTATTCATGTTCCCCTTTCTAG	GTGAGTATTTTCTTAAAACTTTGACTTTTGAAAACAAAAAGGAGGAGTTTAAAGAATAAATGTGATGTGTTTCTTTATAATACATATAGAAACTGCATTAATTGGCTTTTACTCATTTGGAATTTGTGATTAATGGACTGATTTCTCTGAACTATGAGAAGTAGAGTTTGCTAAACAAGTAGTATACCCAAGGCTTACATGAAGATTATATAAATTTTTATTACTGAAAAGGCAATAGATATTTATTGTAGAAATTTCAAATAATACAGAATTCATGAAGAATAAATTATTTAAGTTACTTAAAATTTCTTATTGCCTACCACAGATAACTTAAAGCAGTTTCTCTTAGACCTATTCCTGTCAGACATTCTAAGTGAAGTTTCAGTGTGTAAAAATAATAAAACTGCTCATAAAACGGTCGAGGCTTACATGTATCTCTTTCCCCAGATTCAATGAGATTAAATTATATTCATTATTTTCACTCTTATATAGCTTACTATGCTATTGTTATAGTAGAAATTGGATGGAAAGGGAGAAGGGAAATACTTAGTGAACTCATTTGTATTCATTCAATATAGAATTTCTTTCCTCCACATTCCAGTGAGTTACTGCTATGTGGTAGCTAGTGTGCTGTGTGTTTGGTTCCCAAACTTTCATCTTTTATTTTTATTTATTTTATTTTATTTTTTTTCCCAGACTTTCATCTGATAATGATATTTATTTCTGCATATATCCCCCCACCCTATTTTGCTTCCAGGCCGGTGTAAGTGGTTTGTTTTGTTCTATATAGGGCTATAACTATTACTCTTTGGTCTGACCTTCATTATTTTCTCTATTTCTGTTAGTCTTGACCGTAGAATGCCCAGCCAAGAATAACAGTGATTACTCTTGCCATGGAGGCATCCAAGAGTTTGTAGGTCTCCTATGAGTGAGAACTCCTGAATCATAATTATGTTAACTGTGTATTCATGTTCCCCTTTCTAG	-	novel	NA	P-0019136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	19	466	0	ENST00000361337.2:c.431+1_432-1del		p.X144_splice	ENST00000361337	NM_003286.2	144			1	2	FACETS	0.709	0.539	0.908	0.709	0.539	0.908	CLONAL	1	TRUE	1	0.23	2		466	233	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39725980	39726852	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTACTGTAGCCCATGTGTTAATATCCTAGTACCTTGCAAAACAATCAAGTACTAAGTAATAAATTATCATTTTGCAAAACATTTCCTGATGTAAAATTTGAGTTGTATGGATTTTGTTGTATTTAAACTTGCGTATTTTTTGTCTTCATTTACTATATTATGTAGGGTTTCTGTCCAACAAGAGTACTTGTATATCTTTGCTATTGGCTCTCATGTGATGGCAGGTAGGTGGGGGTTATCAGATTAGGCCAAACAGAAAACCTCAACTCCAGTTGCGCACAGGAAAGTTTGTCGCTGCAGGACTGCCCCGTGTCTGCTGTTGCAAAGAGAAATGTTAATCTGATGTCCCTCTCGCTGTTAATTCTTGCTCATTTATTTTAGGTACTTTCTACTCTTGAAACCACATATACTATATTTGCCTAGGTGATTTTTTAAAATCTCATTATTCTCAATTTGGATAATGTGGACAGAGGCAGCAGTAAAGTTTACTTCCTGAACTAGCTCAGAAAAAGCAGACTTAATAAATGAATAGAATAGGGGTAATGTTTCCAAGAGAGAATCAGTATGGGATTTCAAACTTGTATTCATAATGCCTGGGGGCTGTGTGCCACGGAGTCTAAGAAACCACATAAGAATTCATTTTTTTCCATGATAAGTCATTTTAAAACATTTTAATATTAGTAAGTACATATTTTATAATAAAGTAATACAACTGTATTTTTTTGTTTTTTCAAAATTCATTAATTGAGATTGGCTACTTCCAGAAACCTTTGACTGAAAAAATGGTGCTTGGGTGTATTTGCAAAGAAACCCAAGGACTTATTAGTGTATTTTCGTTGTTTTTCTTTCATCTCCCCATTTTCTTTTGACT	AGGTACTGTAGCCCATGTGTTAATATCCTAGTACCTTGCAAAACAATCAAGTACTAAGTAATAAATTATCATTTTGCAAAACATTTCCTGATGTAAAATTTGAGTTGTATGGATTTTGTTGTATTTAAACTTGCGTATTTTTTGTCTTCATTTACTATATTATGTAGGGTTTCTGTCCAACAAGAGTACTTGTATATCTTTGCTATTGGCTCTCATGTGATGGCAGGTAGGTGGGGGTTATCAGATTAGGCCAAACAGAAAACCTCAACTCCAGTTGCGCACAGGAAAGTTTGTCGCTGCAGGACTGCCCCGTGTCTGCTGTTGCAAAGAGAAATGTTAATCTGATGTCCCTCTCGCTGTTAATTCTTGCTCATTTATTTTAGGTACTTTCTACTCTTGAAACCACATATACTATATTTGCCTAGGTGATTTTTTAAAATCTCATTATTCTCAATTTGGATAATGTGGACAGAGGCAGCAGTAAAGTTTACTTCCTGAACTAGCTCAGAAAAAGCAGACTTAATAAATGAATAGAATAGGGGTAATGTTTCCAAGAGAGAATCAGTATGGGATTTCAAACTTGTATTCATAATGCCTGGGGGCTGTGTGCCACGGAGTCTAAGAAACCACATAAGAATTCATTTTTTTCCATGATAAGTCATTTTAAAACATTTTAATATTAGTAAGTACATATTTTATAATAAAGTAATACAACTGTATTTTTTTGTTTTTTCAAAATTCATTAATTGAGATTGGCTACTTCCAGAAACCTTTGACTGAAAAAATGGTGCTTGGGTGTATTTGCAAAGAAACCCAAGGACTTATTAGTGTATTTTCGTTGTTTTTCTTTCATCTCCCCATTTTCTTTTGACT	-	novel	NA	P-0019136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	32	558	0	ENST00000361337.2:c.852+2_853del		p.X284_splice	ENST00000361337	NM_003286.2	284		10/21	1	2	FACETS	0.598	0.485	0.727	0.598	0.485	0.727	SUBCLONAL	1	TRUE	1	0.23	2		558	465	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741564	39742586	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTGAGAGCATCTTCCCATCGGCATTGTCTAGTGTTGAGCTTAACAAAGGGAGTTTCTGCTCTGCCCCAGGCCCTGTGCCACATACTGTATATCACAACTCAACATACATATATTTGTATGTAAAACTGAATCAAAAGTTGCACAAAACAATGCTTAGCCTTACTGTGAGCAGTAGATTCTGATCTTTTTTTAACTCTATTTCATTCCTTTAGAAAGTTGGTTATAACTTATAAAATTGTTTAAATAAACCATGCAGGTATCACCATTATATAGTTTTAAAGACCACGCTCTAGAGGAGATCAATTTCTTGGTACTCACGAGAAGAAAAAAAAGTTCATGTTTTTCCCCCAGTCTTGTATTTTAACATAAGTTCTGAATTGTCTCAAAATTCACACTAGCTTTTTGAGTTTGATTGCCCAGAGTAGCAGCACTCCCTCATTTGCTGCCTTATTTAATTTTTTTTTTCCTTTTCTCCATCCCTATTTCAGAGGACAGAATAGAAAGAAAAGGAGCATGAATATTTAACATCCCTATAGATTTCATAGTGAGTGGGGGAGGAAGTAACACTGCAGAATCCAGAGTTCCCAGGCCATGCTGACTGATGCTGTGGCTTCAAACAGAATTGGGAGGCTTCTGTTTTGGATGCCTAGAAATTGCATAAGGGTCAAAAGGCTGGGCGCAGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGTGGAACACGAGGTCAAGAGACCATCCTGGCCAATGTGGTGAAACCCCATCTCTACTAAAAATACAAAAAAAAAAAAAAAAATAAAAATTGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTTCGGAGGCTGAGGCAGGAGAATGGCATGAACCCGGGAGACGGAGCTTGCAGTGAGCCAAAATTGCGCCATTGCACTCTAGCCTGGCGACAGAGCGAGACTGTCTCAAAAAAAAAAAAAAAAAAAACACAGAACGAAATTGTGTAAGGATCATGTCTCTTCCATTCATGCTCA	AGGTGAGAGCATCTTCCCATCGGCATTGTCTAGTGTTGAGCTTAACAAAGGGAGTTTCTGCTCTGCCCCAGGCCCTGTGCCACATACTGTATATCACAACTCAACATACATATATTTGTATGTAAAACTGAATCAAAAGTTGCACAAAACAATGCTTAGCCTTACTGTGAGCAGTAGATTCTGATCTTTTTTTAACTCTATTTCATTCCTTTAGAAAGTTGGTTATAACTTATAAAATTGTTTAAATAAACCATGCAGGTATCACCATTATATAGTTTTAAAGACCACGCTCTAGAGGAGATCAATTTCTTGGTACTCACGAGAAGAAAAAAAAGTTCATGTTTTTCCCCCAGTCTTGTATTTTAACATAAGTTCTGAATTGTCTCAAAATTCACACTAGCTTTTTGAGTTTGATTGCCCAGAGTAGCAGCACTCCCTCATTTGCTGCCTTATTTAATTTTTTTTTTCCTTTTCTCCATCCCTATTTCAGAGGACAGAATAGAAAGAAAAGGAGCATGAATATTTAACATCCCTATAGATTTCATAGTGAGTGGGGGAGGAAGTAACACTGCAGAATCCAGAGTTCCCAGGCCATGCTGACTGATGCTGTGGCTTCAAACAGAATTGGGAGGCTTCTGTTTTGGATGCCTAGAAATTGCATAAGGGTCAAAAGGCTGGGCGCAGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGTGGAACACGAGGTCAAGAGACCATCCTGGCCAATGTGGTGAAACCCCATCTCTACTAAAAATACAAAAAAAAAAAAAAAAATAAAAATTGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTTCGGAGGCTGAGGCAGGAGAATGGCATGAACCCGGGAGACGGAGCTTGCAGTGAGCCAAAATTGCGCCATTGCACTCTAGCCTGGCGACAGAGCGAGACTGTCTCAAAAAAAAAAAAAAAAAAAACACAGAACGAAATTGTGTAAGGATCATGTCTCTTCCATTCATGCTCA	-	novel	NA	P-0019136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	32	535	1	ENST00000361337.2:c.1451_1453-24del		p.X484_splice	ENST00000361337	NM_003286.2	484		14/21	1	2	FACETS	0.458	0.37	0.557	0.458	0.37	0.557	SUBCLONAL	1	TRUE	1	0.23	2		536	608	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979629	55979629	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	128	752	0	ENST00000263923.4:c.818T>C	p.Val273Ala	p.V273A	ENST00000263923	NM_002253.2	273	gTa/gCa	7/30	NA	2	FACETS	0.879	0.799	0.963			1	INDETERMINATE	2	TRUE	NA	0.23	2		752	633	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31437388	31437388	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1303485152	NA	P-0019136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	102	1138	1	ENST00000344624.3:c.2900G>T	p.Arg967Leu	p.R967L	ENST00000344624		967	cGg/cTg	21/33	1	2	FACETS	0.934	0.834	1	0.934	0.834	1	CLONAL	1	TRUE	1	0.23	2		1139	950	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878466	151878466	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	162	856	0	ENST00000262189.6:c.6479C>G	p.Ser2160Cys	p.S2160C	ENST00000262189	NM_170606.2	2160	tCt/tGt	36/59	1	2	FACETS	0.761	0.698	0.827	1	0.989	1	SUBCLONAL	2	TRUE	1	0.23	2		856	925	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143285	58143285	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	80	478	0	ENST00000257904.6:c.635C>T	p.Pro212Leu	p.P212L	ENST00000257904	NM_000075.3	212	cCt/cTt	6/8	0.769696306670943	1	FACETS	0.465	0.414	0.518	0.465	0.414	0.518	SUBCLONAL	1	TRUE	0	0.769696306670943	1		478	275	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577112	7577112	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1131691029	NA	P-0019137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	483	851	0	ENST00000269305.4:c.826G>C	p.Ala276Pro	p.A276P	ENST00000269305	NM_001126112.2	276	Gcc/Ccc	8/11	NA	2	FACETS	0.873	0.845	0.9			1	INDETERMINATE	2	TRUE	NA	0.769696306670943	2		851	719	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149453055	149453055	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	57	426	1	ENST00000286301.3:c.891G>T	p.Glu297Asp	p.E297D	ENST00000286301	NM_005211.3	297	gaG/gaT	7/22	0.408215343939534	1	FACETS	0.263	0.226	0.302	0.263	0.226	0.302	INDETERMINATE	1	TRUE	0	0.769696306670943	1		427	347	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0019138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	49	895	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.805	0.681	0.943	0.805	0.681	0.943	CLONAL	1	TRUE	1	0.18	2		895	676	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488657	212488657	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374970657	NA	P-0019138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	63	756	0	ENST00000342788.4:c.2192C>T	p.Thr731Met	p.T731M	ENST00000342788	NM_005235.2	731	aCg/aTg	18/28	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.18	2		756	618	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135409	30135409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780784905	NA	P-0019138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	39	650	0	ENST00000331968.5:c.409G>A	p.Ala137Thr	p.A137T	ENST00000331968	NM_002742.2	137	Gcc/Acc	3/18	1	2	FACETS	0.808	0.669	0.964	0.808	0.669	0.964	CLONAL	1	TRUE	1	0.18	2		650	536	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	43	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.875	0.73	1	0.875	0.73	1	CLONAL	1	TRUE	1	0.11	2		555	893	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0019139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	23	582	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	0.936	0.728	1	0.936	0.728	1	CLONAL	1	TRUE	1	0.11	2		582	447	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057073	180057073	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	96	957	1	ENST00000261937.6:c.546G>T	p.Glu182Asp	p.E182D	ENST00000261937	NM_182925.4	182	gaG/gaT	5/30	0.460112507134522	3	FACETS	0.709	0.632	0.791	0.354	0.316	0.396	SUBCLONAL	1	TRUE	1	0.501018884375213	3		958	676	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030874	69030874	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	126	507	0	ENST00000288368.4:c.3416A>T	p.Asp1139Val	p.D1139V	ENST00000288368	NM_024870.2	1139	gAc/gTc	27/40	0.501018884375213	6	FACETS	0.836	0.76	0.917	0.418	0.38	0.459	CLONAL	2	TRUE	2	0.501018884375213	6		507	602	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0019141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	90	558	1	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.989	0.879	1	0.989	0.879	1	CLONAL	1	TRUE	1	0.291699038785862	2		559	624	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0019141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	96	397	1	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.291699038785862	2		398	512	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870836	12870836	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	28	265	0	ENST00000228872.4:c.64del	p.Glu22SerfsTer20	p.E22Sfs*20	ENST00000228872	NM_004064.3	21	gcG/gc	1/3	1	2	FACETS	0.861	0.692	1	0.861	0.692	1	CLONAL	1	TRUE	1	0.291699038785862	2		265	223	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063673	67063674	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCACGCTTCCAGAACGCCT	novel	NA	P-0019141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	74	511	0	ENST00000412916.2:c.124_143dup	p.Cys48TrpfsTer48	p.C48Wfs*48	ENST00000412916		41	cag/caGGCACGCTTCCAGAACGCCTg	2/6	0.291699038785862	1	FACETS	0.978	0.86	1	0.978	0.86	1	CLONAL	1	TRUE	0	0.291699038785862	1		511	443	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527299	187527300	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0019141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	103	593	3	ENST00000441802.2:c.10274_10275delinsTT	p.Thr3425Ile	p.T3425I	ENST00000441802	NM_005245.3	3425	aCC/aTT	17/27	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.291699038785862	2		596	634	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	120	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.24761641691353	1	FACETS	0.717	0.647	0.791	0.717	0.647	0.791	SUBCLONAL	1	TRUE	0	0.314230406136138	1		555	898	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0019142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	78	697	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.627	0.55	0.71	0.627	0.55	0.71	SUBCLONAL	1	TRUE	1	0.314230406136138	2		697	792	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0019142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	141	933	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.314230406136138	1	FACETS	0.961	0.876	1	0.961	0.876	1	CLONAL	1	TRUE	0	0.314230406136138	1		933	787	SUCCESS
APC	324	MSKCC	GRCh37	5	112175096	112175097	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs786203760	NA	P-0019142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	57	398	0	ENST00000257430.4:c.3807_3808del	p.Ile1269MetfsTer6	p.I1269Mfs*6	ENST00000257430	NM_000038.5	1269	ATa/a	16/16	1	2	FACETS	0.894	0.769	1	0.894	0.769	1	CLONAL	1	TRUE	1	0.314230406136138	2		398	406	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118946	115118946	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	47	398	0	ENST00000257566.3:c.395T>A	p.Met132Lys	p.M132K	ENST00000257566	NM_016569.3	132	aTg/aAg	2/8	1	2	FACETS	0.591	0.499	0.692	0.591	0.499	0.692	SUBCLONAL	1	TRUE	1	0.358292091949328	2		398	444	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478106	99478106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	74	464	1	ENST00000268035.6:c.3010G>A	p.Glu1004Lys	p.E1004K	ENST00000268035	NM_000875.3	1004	Gaa/Aaa	16/21	1	2	FACETS	0.935	0.821	1	0.935	0.821	1	CLONAL	1	TRUE	1	0.358292091949328	2		465	442	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600336	10600336	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs751088754	NA	P-0019143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	78	733	0	ENST00000171111.5:c.1519C>T	p.Arg507Ter	p.R507*	ENST00000171111	NM_203500.1	507	Cga/Tga	4/6	1	2	FACETS	0.706	0.62	0.797	0.706	0.62	0.797	SUBCLONAL	1	TRUE	1	0.358292091949328	2		733	617	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577571	7577571	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs765848205	NA	P-0019145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	105	678	0	ENST00000269305.4:c.710T>A	p.Met237Lys	p.M237K	ENST00000269305	NM_001126112.2	237	aTg/aAg	7/11	0.228411470321338	2	FACETS	0.804	0.722	0.89	0.804	0.722	0.89	CLONAL	2	TRUE	0	0.23	2		678	568	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118350932	118350932	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs980656132	NA	P-0019145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	56	708	0	ENST00000534358.1:c.3613T>C	p.Tyr1205His	p.Y1205H	ENST00000534358	NM_005933.3	1205	Tac/Cac	6/36	0.199632637501602	3	FACETS	1	0.883	1	0.517	0.443	0.598	CLONAL	1	TRUE	1	0.23	3		708	525	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658869	3658869	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780117582	NA	P-0019145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	140	704	1	ENST00000294008.3:c.97G>A	p.Asp33Asn	p.D33N	ENST00000294008	NM_032444.2	33	Gac/Aac	2/15	0.164840391985498	4	FACETS	0.95	0.866	1	0.95	0.866	1	CLONAL	2	TRUE	2	0.23	4		705	788	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266827	198266827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	70	837	2	ENST00000335508.6:c.2105G>A	p.Arg702Gln	p.R702Q	ENST00000335508	NM_012433.2	702	cGg/cAg	15/25	0.199632637501602	3	FACETS	0.799	0.696	0.912	0.4	0.348	0.456	CLONAL	1	TRUE	1	0.23	3		839	849	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215661822	215661822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	54	668	0	ENST00000260947.4:c.178C>T	p.Pro60Ser	p.P60S	ENST00000260947	NM_000465.2	60	Cct/Tct	2/11	0.199632637501602	3	FACETS	1	0.86	1	0.503	0.43	0.584	CLONAL	1	TRUE	1	0.23	3		668	520	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221738	55221738	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	126	714	0	ENST00000275493.2:c.782A>G	p.Lys261Arg	p.K261R	ENST00000275493	NM_005228.3	261	aAg/aGg	7/28	0.164840391985498	4	FACETS	0.882	0.799	0.969	0.882	0.799	0.969	CLONAL	2	TRUE	2	0.23	4		714	764	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	222	463	0	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	0.45434423214614	2	FACETS	0.962	0.905	1	0.962	0.905	1	CLONAL	2	TRUE	0	0.45434423214614	2		463	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	247	804	1	ENST00000269305.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	336	Gag/Tag	10/11	0.45434423214614	1	FACETS	0.986	0.924	1	0.986	0.924	1	CLONAL	1	TRUE	0	0.45434423214614	1		805	852	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420825	49420825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757011865	NA	P-0019146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	69	550	0	ENST00000301067.7:c.14924G>A	p.Arg4975His	p.R4975H	ENST00000301067	NM_003482.3	4975	cGt/cAt	48/54	1	2	FACETS	0.466	0.405	0.531	0.466	0.405	0.531	SUBCLONAL	1	TRUE	1	0.45434423214614	2		550	652	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488199	56488199	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs758858051	NA	P-0019146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	80	507	0	ENST00000267101.3:c.1718G>C	p.Cys573Ser	p.C573S	ENST00000267101	NM_001982.3	573	tGt/tCt	15/28	1	2	FACETS	0.591	0.521	0.666	0.591	0.521	0.666	SUBCLONAL	1	TRUE	1	0.45434423214614	2		507	596	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602427	10602427	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1365381442	NA	P-0019146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	549	666	0	ENST00000171111.5:c.1151C>T	p.Pro384Leu	p.P384L	ENST00000171111	NM_203500.1	384	cCc/cTc	3/6	0.45434423214614	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.45434423214614	3		666	1319	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012632	36012632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	83	323	0	ENST00000358208.4:c.76G>A	p.Gly26Ser	p.G26S	ENST00000358208		26	Ggc/Agc	2/12	0.45434423214614	3	FACETS	0.682	0.602	0.768	0.341	0.301	0.384	SUBCLONAL	1	TRUE	1	0.45434423214614	3		323	657	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	29	736	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.666	0.536	0.813	0.666	0.536	0.813	SUBCLONAL	1	TRUE	1	0.308928191680527	2		736	282	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039190	49039190	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0019147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	91	519	0	ENST00000267163.4:c.2268T>G	p.Tyr756Ter	p.Y756*	ENST00000267163	NM_000321.2	756	taT/taG	22/27	0.308928191680527	1	FACETS	0.954	0.85	1	0.954	0.85	1	CLONAL	1	TRUE	0	0.308928191680527	1		519	522	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636706	176636706	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	91	477	0	ENST00000439151.2:c.1306G>A	p.Gly436Arg	p.G436R	ENST00000439151	NM_022455.4	436	Ggg/Agg	5/23	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.308928191680527	2		477	506	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720678	89720679	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CATTCTTC	novel	NA	P-0019147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	22	144	0	ENST00000371953.3:c.830_837dup	p.Ile280HisfsTer14	p.I280Hfs*14	ENST00000371953	NM_000314.4	277	aca/aCATTCTTCca	8/9	0.308928191680527	1	FACETS	0.587	0.457	0.737	0.587	0.457	0.737	SUBCLONAL	1	TRUE	0	0.308928191680527	1		144	205	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31521275	31521275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	91	624	0	ENST00000344624.3:c.902C>T	p.Pro301Leu	p.P301L	ENST00000344624		301	cCa/cTa	3/33	1	2	FACETS	0.754	0.669	0.845	0.754	0.669	0.845	SUBCLONAL	1	TRUE	1	0.308928191680527	2		624	781	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033970	49033970	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0019148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	1002	649	0	ENST00000267163.4:c.2106+1G>A		p.X702_splice	ENST00000267163	NM_000321.2	702			0.725049531843053	5	FACETS	1	0.992	1			1	CLONAL	5	TRUE	NA	0.720352061844503	5		649	1146	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939458	76939467	+	frameshift_variant	Frame_Shift_Del	DEL	TTTGGTATTT	TTTGGTATTT	-	novel	NA	P-0019148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	403	364	0	ENST00000373344.5:c.1281_1290del	p.Asn428SerfsTer5	p.N428Sfs*5	ENST00000373344	NM_000489.3	427	aaAAATACCAAA/aa	9/35	0.689705726691175	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.720352061844503	2		364	488	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	30	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.243958122849626	4	FACETS	1	0.93	1	0.67	0.545	0.808	CLONAL	1	TRUE	2	0.343789513564817	4		555	175	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0019149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	16	682	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.343789513564817	2		682	63	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0019149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	16	492	1	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	0.176626763469737	3	FACETS	0.909	0.693	1	0.909	0.693	1	INDETERMINATE	2	TRUE	1	0.343789513564817	3		493	60	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440268	52440268	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0019149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	19	593	0	ENST00000460680.1:c.783+1G>A		p.X261_splice	ENST00000460680	NM_004656.3	261			0.171777587767157	2	FACETS	1	0.912	1	0.718	0.558	0.895	INDETERMINATE	1	TRUE	0	0.343789513564817	2		593	77	SUCCESS
APC	324	MSKCC	GRCh37	5	112175551	112175552	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0019149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	20	604	0	ENST00000257430.4:c.4260_4261del	p.Ser1421Ter	p.S1421*	ENST00000257430	NM_000038.5	1420	ccCAgt/ccgt	16/16	0.176626763469737	3	FACETS	0.96	0.756	1	0.96	0.756	1	INDETERMINATE	2	TRUE	1	0.343789513564817	3		604	71	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0019150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	129	704	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.370440025616677	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.382637737497595	1		704	527	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293194	212293194	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	112	588	2	ENST00000342788.4:c.2658G>T	p.Trp886Cys	p.W886C	ENST00000342788	NM_005235.2	886	tgG/tgT	22/28	0.358215610573717	2	FACETS	0.905	0.815	0.999	0.452	0.407	0.5	CLONAL	1	TRUE	0	0.382637737497595	2		590	647	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102098261	102098261	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	197	698	0	ENST00000282441.5:c.1225G>A	p.Val409Ile	p.V409I	ENST00000282441	NM_001130145.2	409	Gtc/Atc	8/9	0.866077589518957	1	FACETS	0.472	0.441	0.505	0.472	0.441	0.505	SUBCLONAL	1	TRUE	0	0.866077589518957	1		698	546	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56873446	56873469	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	TGAAGCTGGTGCCCCTGAATCAGG	TGAAGCTGGTGCCCCTGAATCAGG	-	novel	NA	P-0019153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	257	704	2	ENST00000308159.5:c.2150_2173del	p.Leu717_Glu725delinsTer	p.L717_E725delins*	ENST00000308159	NM_014669.4	717	tTGAAGCTGGTGCCCCTGAATCAGGaa/taa	20/22	0.479339303565429	1	FACETS	0.558	0.527	0.59	0.558	0.527	0.59	INDETERMINATE	1	TRUE	0	0.866077589518957	1		706	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0019153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	1113	852	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.866077589518957	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.866077589518957	2		852	1242	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29701109	29701109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs934837854	NA	P-0019153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	208	659	2	ENST00000356175.3:c.8393G>A	p.Ser2798Asn	p.S2798N	ENST00000356175	NM_000267.3	2798	aGc/aAc	57/57	0.853272016278434	2	FACETS	0.652	0.607	0.698	0.326	0.303	0.349	SUBCLONAL	1	TRUE	0	0.866077589518957	2		661	737	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481554	40481576	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGAGCTCCTCCCACATACCAAGT	GGAGCTCCTCCCACATACCAAGT	-	novel	NA	P-0019153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	413	672	0	ENST00000264657.5:c.1229_1233+18del		p.X410_splice	ENST00000264657	NM_139276.2	410		13/24	0.866077589518957	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.866077589518957	1		672	516	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41219635	41219637	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	rs80358344	NA	P-0019153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	428	733	1	ENST00000357654.3:c.5062_5064del	p.Val1688del	p.V1688del	ENST00000357654	NM_007294.3	1688	GTT/-	16/23	0.866077589518957	1	FACETS	0.997	0.968	1	0.997	0.968	1	CLONAL	1	TRUE	0	0.866077589518957	1		734	562	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968085	68968085	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	560	725	0	ENST00000288368.4:c.1114C>A	p.Gln372Lys	p.Q372K	ENST00000288368	NM_024870.2	372	Caa/Aaa	10/40	0.736214644177096	3	FACETS	0.803	0.774	0.832	0.803	0.774	0.832	CLONAL	2	TRUE	1	0.866077589518957	3		725	1154	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0019161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	265	852	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.535331028048787	1	FACETS	0.809	0.761	0.857	0.809	0.761	0.857	CLONAL	1	TRUE	0	0.591162744492957	1		852	781	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0019161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	144	918	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.944	0.866	1	0.944	0.866	1	CLONAL	1	TRUE	1	0.591162744492957	2		918	516	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092809	27092809	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	321	808	2	ENST00000324856.7:c.2830C>T	p.Gln944Ter	p.Q944*	ENST00000324856	NM_006015.4	944	Cag/Tag	9/20	0.591162744492957	1	FACETS	0.976	0.926	1	0.976	0.926	1	CLONAL	1	TRUE	0	0.591162744492957	1		810	784	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581229	48581229	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs377767331	NA	P-0019161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	243	736	0	ENST00000342988.3:c.533C>G	p.Ser178Ter	p.S178*	ENST00000342988	NM_005359.5	178	tCa/tGa	5/12	0.535331028048787	1	FACETS	0.879	0.826	0.932	0.879	0.826	0.932	CLONAL	1	TRUE	0	0.591162744492957	1		736	659	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92355102	92355102	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	81	274	0	ENST00000265734.4:c.375G>C	p.Met125Ile	p.M125I	ENST00000265734	NM_001259.6	125	atG/atC	4/8	1	2	FACETS	0.77	0.683	0.861	0.77	0.683	0.861	SUBCLONAL	1	TRUE	1	0.591162744492957	2		274	356	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094488	27094488	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	150	369	0	ENST00000324856.7:c.3196C>T	p.Gln1066Ter	p.Q1066*	ENST00000324856	NM_006015.4	1066	Cag/Tag	11/20	0.591162744492957	1	FACETS	0.953	0.882	1	0.953	0.882	1	CLONAL	1	TRUE	0	0.591162744492957	1		369	375	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173586	108173586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555106321	NA	P-0019161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	49	486	0	ENST00000278616.4:c.5326G>A	p.Glu1776Lys	p.E1776K	ENST00000278616	NM_000051.3	1776	Gaa/Aaa	36/63	1	2	FACETS	0.906	0.779	1	0.906	0.779	1	CLONAL	1	TRUE	1	0.591162744492957	2		486	183	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705646	47705646	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	58	495	0	ENST00000233146.2:c.2446C>G	p.Gln816Glu	p.Q816E	ENST00000233146	NM_000251.2	816	Cag/Gag	14/16	0.297748607655766	1	FACETS	0.415	0.358	0.476	0.415	0.358	0.476	INDETERMINATE	1	TRUE	0	0.591162744492957	1		495	333	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098959	178098959	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519921	NA	P-0019161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	199	468	0	ENST00000397062.3:c.86A>G	p.Asp29Gly	p.D29G	ENST00000397062	NM_006164.4	29	gAt/gGt	2/5	0.308020219831906	3	FACETS	0.796	0.743	0.85	0.796	0.743	0.85	INDETERMINATE	2	TRUE	1	0.591162744492957	3		468	548	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183703	10183703	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757781272	NA	P-0019161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	274	779	3	ENST00000256474.2:c.172C>T	p.Arg58Trp	p.R58W	ENST00000256474	NM_000551.3	58	Cgg/Tgg	1/3	1	2	FACETS	0.939	0.883	0.997	0.939	0.883	0.997	CLONAL	1	TRUE	1	0.591162744492957	2		782	987	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158148	106158148	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	158	476	0	ENST00000380013.4:c.3049G>A	p.Asp1017Asn	p.D1017N	ENST00000380013	NM_001127208.2	1017	Gat/Aat	3/11	1	2	FACETS	0.914	0.841	0.989	0.914	0.841	0.989	CLONAL	1	TRUE	1	0.591162744492957	2		476	585	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367345	50367346	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0019161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	133	431	2	ENST00000331340.3:c.152_153delinsAT	p.Arg51Asn	p.R51N	ENST00000331340	NM_006060.4	51	aGA/aAT	3/8	1	2	FACETS	0.795	0.725	0.868	0.795	0.725	0.868	SUBCLONAL	1	TRUE	1	0.591162744492957	2		433	566	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509379	106509379	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	243	659	3	ENST00000359195.3:c.1373T>C	p.Val458Ala	p.V458A	ENST00000359195	NM_002649.2	458	gTt/gCt	2/11	1	2	FACETS	0.938	0.879	1	0.938	0.879	1	CLONAL	1	TRUE	1	0.591162744492957	2		662	876	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841218	15841218	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	221	297	0	ENST00000307771.7:c.1302C>G	p.Ser434Arg	p.S434R	ENST00000307771	NM_005089.3	434	agC/agG	11/11	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.591162744492957	1		297	395	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	142	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.340098471865234	1	FACETS	0.927	0.846	1	0.927	0.846	1	CLONAL	1	TRUE	0	0.340098471865234	1		555	748	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0019163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	132	582	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.340098471865234	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.340098471865234	1		582	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0019163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	203	970	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.340098471865234	1	FACETS	0.999	0.926	1	0.999	0.926	1	CLONAL	1	TRUE	0	0.340098471865234	1		970	992	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229534	5229534	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	44	250	1	ENST00000357368.4:c.2317C>T	p.Arg773Cys	p.R773C	ENST00000357368	NM_002850.3	773	Cgc/Tgc	15/38	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.340098471865234	2		251	238	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	284	736	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.98	0.929	1	0.98	0.929	1	CLONAL	1	TRUE	1	0.889990264430631	2		736	651	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222650	69222650	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	378	788	0	ENST00000462284.1:c.623T>C	p.Ile208Thr	p.I208T	ENST00000462284	NM_002392.5	208	aTa/aCa	8/11	1	2	FACETS	0.909	0.866	0.952	0.909	0.866	0.952	CLONAL	1	TRUE	1	0.889990264430631	2		788	935	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455051	50455051	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	204	558	0	ENST00000331340.3:c.598C>A	p.Pro200Thr	p.P200T	ENST00000331340	NM_006060.4	200	Cct/Act	6/8	0.884798334435352	3	FACETS	0.911	0.848	0.976	0.456	0.424	0.488	CLONAL	1	TRUE	1	0.889990264430631	3		558	727	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0019165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	139	741	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.954	0.87	1	0.954	0.87	1	CLONAL	1	TRUE	1	0.445767561874628	2		742	654	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0019165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	93	397	1	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.697	0.62	0.778	0.697	0.62	0.778	SUBCLONAL	1	TRUE	1	0.445767561874628	2		398	599	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249510	153249510	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1157879635	NA	P-0019165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	36	556	0	ENST00000281708.4:c.1268G>T	p.Gly423Val	p.G423V	ENST00000281708	NM_033632.3	423	gGa/gTa	9/12	1	2	FACETS	0.233	0.19	0.28	0.233	0.19	0.28	SUBCLONAL	1	TRUE	1	0.445767561874628	2		556	694	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984782	11984782	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1164096095	NA	P-0019165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	24	783	3	ENST00000353533.5:c.328C>T	p.Arg110Ter	p.R110*	ENST00000353533	NM_003010.3	110	Cga/Tga	3/11	0.445767561874628	1	FACETS	0.21	0.164	0.263	0.21	0.164	0.263	SUBCLONAL	1	TRUE	0	0.445767561874628	1		786	399	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112399	115112400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0019165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	172	801	0	ENST00000257566.3:c.1340dup	p.Gly448ArgfsTer244	p.G448Rfs*244	ENST00000257566	NM_016569.3	447	cgc/cgGc	7/8	0.365201047270782	3	FACETS	1	0.989	1	0.735	0.679	0.793	CLONAL	1	TRUE	1	0.445767561874628	3		801	642	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070659	67070659	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0019165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	63	339	0	ENST00000412916.2:c.282+1G>T		p.X94_splice	ENST00000412916		94			0.445767561874628	1	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	0	0.445767561874628	1		339	218	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0019166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	367	830	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.939	0.893	0.986	0.939	0.893	0.986	CLONAL	1	TRUE	1	0.798222536632316	2		830	979	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204864	NA	P-0019166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	231	564	0	ENST00000371953.3:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000371953	NM_000314.4	171	Cag/Tag	6/9	0.798222536632316	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.798222536632316	1		564	344	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	259	557	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	0.954	0.899	1	0.954	0.899	1	CLONAL	1	TRUE	1	0.798222536632316	2		557	680	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367275	50367275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778910457	NA	P-0019166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	183	404	0	ENST00000331340.3:c.82G>A	p.Asp28Asn	p.D28N	ENST00000331340	NM_006060.4	28	Gat/Aat	3/8	1	2	FACETS	0.921	0.857	0.986	0.921	0.857	0.986	CLONAL	1	TRUE	1	0.798222536632316	2		404	498	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600447	10600447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	423	864	2	ENST00000171111.5:c.1408C>T	p.Arg470Cys	p.R470C	ENST00000171111	NM_203500.1	470	Cgt/Tgt	4/6	1	2	FACETS	0.998	0.953	1	0.998	0.953	1	CLONAL	1	TRUE	1	0.798222536632316	2		866	1062	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146112	38146112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5189	296	750	1	ENST00000317025.8:c.3394G>A	p.Asp1132Asn	p.D1132N	ENST00000317025	NM_023034.1	1132	Gat/Aat	19/24	0.798222536632316	13	FACETS	0.729	0.681	0.779			1	SUBCLONAL	1	TRUE	NA	0.798222536632316	13		751	5485	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146952	38146952	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5351	321	974	0	ENST00000317025.8:c.3190G>C	p.Glu1064Gln	p.E1064Q	ENST00000317025	NM_023034.1	1064	Gaa/Caa	18/24	0.798222536632316	13	FACETS	0.764	0.716	0.815			1	SUBCLONAL	1	TRUE	NA	0.798222536632316	13		974	5672	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	103	682	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.314458259733828	2		682	649	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	116	640	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	0.314458259733828	2		640	692	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	126	740	6	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.314458259733828	2		746	759	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123837	46123837	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	82	569	0	ENST00000334344.6:c.103A>T	p.Lys35Ter	p.K35*	ENST00000334344	NM_152641.2	35	Aaa/Taa	2/21	1	2	FACETS	0.836	0.738	0.941	0.836	0.738	0.941	CLONAL	1	TRUE	1	0.314458259733828	2		569	624	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	315	683	12	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	0.314458259733828	2		695	895	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	47	457	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	0.768	0.65	0.898	0.768	0.65	0.898	SUBCLONAL	1	TRUE	1	0.314458259733828	2		457	389	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	193	876	18	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.314458259733828	2		894	1134	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	195	655	0	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	0.976	1	CLONAL	1	TRUE	1	0.314458259733828	2		655	1096	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577129	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519986	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1293	324	1235	0	ENST00000269305.4:c.809T>C	p.Phe270Ser	p.F270S	ENST00000269305	NM_001126112.2	270	tTt/tCt	8/11	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.314458259733828	2		1235	1617	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937659	17937659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144968714	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	205	853	0	ENST00000458235.1:c.3268G>A	p.Ala1090Thr	p.A1090T	ENST00000458235	NM_000215.3	1090	Gcc/Acc	24/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.314458259733828	2		853	1051	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057520005	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1648	84	1288	0	ENST00000269305.4:c.820G>T	p.Val274Phe	p.V274F	ENST00000269305	NM_001126112.2	274	Gtt/Ttt	8/11	1	2	FACETS	0.308	0.271	0.349	0.308	0.271	0.349	SUBCLONAL	1	TRUE	1	0.314458259733828	2		1288	1732	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1334	222	979	4	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.907	0.842	0.976	0.907	0.842	0.976	CLONAL	1	TRUE	1	0.314458259733828	2		983	1556	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	222	849	5	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.314458259733828	2		854	1231	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460476	149460476	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	195	989	1	ENST00000286301.3:c.161del	p.Pro54HisfsTer58	p.P54Hfs*58	ENST00000286301	NM_005211.3	54	cCa/ca	3/22	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.314458259733828	2		990	1053	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233090	69233090	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746910913	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	93	590	2	ENST00000462284.1:c.961del	p.Leu321PhefsTer52	p.L321Ffs*52	ENST00000462284	NM_002392.5	319	Ccc/cc	11/11	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.314458259733828	2		592	545	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610522	10610522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	179	785	2	ENST00000171111.5:c.188C>T	p.Ala63Val	p.A63V	ENST00000171111	NM_203500.1	63	gCc/gTc	2/6	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.314458259733828	2		787	1060	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048668	180048668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1158883745	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	139	816	0	ENST00000261937.6:c.1894C>T	p.Arg632Cys	p.R632C	ENST00000261937	NM_182925.4	632	Cgc/Tgc	13/30	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.314458259733828	2		816	763	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920173	76920173	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	129	1004	3	ENST00000373344.5:c.3904del	p.Arg1302GlufsTer44	p.R1302Efs*44	ENST00000373344	NM_000489.3	1302	Aga/ga	11/35	1	2	FACETS	0.879	0.797	0.967	0.879	0.797	0.967	CLONAL	1	TRUE	1	0.314458259733828	2		1007	933	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795608	42795609	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1555770200	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1302	275	835	0	ENST00000575354.2:c.2694dup	p.Lys899GlnfsTer32	p.K899Qfs*32	ENST00000575354	NM_015125.3	896	-/C	10/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.314458259733828	2		835	1577	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395186	139395186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	272	1134	3	ENST00000277541.6:c.5752G>A	p.Ala1918Thr	p.A1918T	ENST00000277541	NM_017617.3	1918	Gcc/Acc	31/34	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.314458259733828	2		1137	1422	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346220	152346220	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	163	964	7	ENST00000359321.1:c.350del	p.Leu117TrpfsTer17	p.L117Wfs*17	ENST00000359321	NM_005431.1	117	tTg/tg	3/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.314458259733828	2		971	855	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937673	17937673	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	175	757	0	ENST00000458235.1:c.3254G>A	p.Arg1085Gln	p.R1085Q	ENST00000458235	NM_000215.3	1085	cGg/cAg	24/24	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.314458259733828	2		757	925	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1586	331	1509	10	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.314458259733828	2		1519	1917	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	204	729	4	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	0.314458259733828	2		733	1091	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	189	894	7	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.314458259733828	2		901	1079	SUCCESS
YES1	7525	MSKCC	GRCh37	18	732914	732914	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1384930568	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	150	1102	3	ENST00000314574.4:c.1343G>A	p.Arg448Gln	p.R448Q	ENST00000314574	NM_005433.3	448	cGg/cAg	11/12	1	2	FACETS	0.998	0.911	1	0.998	0.911	1	CLONAL	1	TRUE	1	0.314458259733828	2		1105	956	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399278	139399278	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778271353	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1228	274	1092	4	ENST00000277541.6:c.4865G>A	p.Arg1622His	p.R1622H	ENST00000277541	NM_017617.3	1622	cGc/cAc	26/34	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.314458259733828	2		1096	1502	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432420	49432420	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	324	1140	2	ENST00000301067.7:c.8719del	p.Tyr2907ThrfsTer3	p.Y2907Tfs*3	ENST00000301067	NM_003482.3	2907	Tac/ac	34/54	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.314458259733828	2		1142	1527	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100120	27100120	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	174	986	1	ENST00000324856.7:c.3916C>T	p.Gln1306Ter	p.Q1306*	ENST00000324856	NM_006015.4	1306	Cag/Tag	16/20	1	2	FACETS	0.967	0.888	1	0.967	0.888	1	CLONAL	1	TRUE	1	0.314458259733828	2		987	1145	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36940986	36940986	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	172	675	0	ENST00000361632.4:c.353G>C	p.Arg118Pro	p.R118P	ENST00000361632		118	cGc/cCc	3/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.314458259733828	2		675	901	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097730	8097730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747477962	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	187	939	0	ENST00000346208.3:c.112G>A	p.Ala38Thr	p.A38T	ENST00000346208		38	Gcg/Acg	2/6	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.314458259733828	2		939	1064	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404591	70404591	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	210	1011	0	ENST00000373644.4:c.2105T>C	p.Met702Thr	p.M702T	ENST00000373644	NM_030625.2	702	aTg/aCg	4/12	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.314458259733828	2		1011	986	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441816	49441816	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	251	895	2	ENST00000301067.7:c.4168del	p.Ala1390GlnfsTer27	p.A1390Qfs*27	ENST00000301067	NM_003482.3	1390	Gca/ca	14/54	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.314458259733828	2		897	1358	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437751	110437751	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1387	234	1303	0	ENST00000375856.3:c.650A>G	p.Tyr217Cys	p.Y217C	ENST00000375856	NM_003749.2	217	tAc/tGc	1/2	1	2	FACETS	0.918	0.854	0.985	0.918	0.854	0.985	CLONAL	1	TRUE	1	0.314458259733828	2		1303	1621	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420285	88420285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199690201	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	181	926	0	ENST00000360948.2:c.2401G>A	p.Asp801Asn	p.D801N	ENST00000360948	NM_001012338.2	801	Gat/Aat	19/19	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.314458259733828	2		926	1089	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213967	2213967	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1188110300	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1236	228	1178	0	ENST00000326181.6:c.46C>G	p.Pro16Ala	p.P16A	ENST00000326181	NM_032271.2	16	Ccc/Gcc	2/21	1	2	FACETS	0.991	0.92	1	0.991	0.92	1	CLONAL	1	TRUE	1	0.314458259733828	2		1178	1464	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129821	30129821	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	116	639	0	ENST00000263025.4:c.392A>G	p.Lys131Arg	p.K131R	ENST00000263025	NM_002746.2	131	aAg/aGg	3/9	1	2	FACETS	0.94	0.847	1	0.94	0.847	1	CLONAL	1	TRUE	1	0.314458259733828	2		639	785	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821382	72821382	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs774585182	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	109	670	1	ENST00000268489.5:c.10793del	p.Pro3598LeufsTer96	p.P3598Lfs*96	ENST00000268489	NM_006885.3	3598	cCt/ct	10/10	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.314458259733828	2		671	642	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350044	89350044	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	194	1033	0	ENST00000301030.4:c.2906A>G	p.Glu969Gly	p.E969G	ENST00000301030	NM_001256183.1	969	gAg/gGg	9/13	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.314458259733828	2		1033	1230	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357502	89357502	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1181	283	1146	1	ENST00000301030.4:c.316C>T	p.Arg106Ter	p.R106*	ENST00000301030	NM_001256183.1	106	Cga/Tga	5/13	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.314458259733828	2		1147	1464	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858926	89858927	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	218	1025	0	ENST00000389301.3:c.1034_1035dup	p.Trp346SerfsTer20	p.W346Sfs*20	ENST00000389301	NM_000135.2	345	-/AG	12/43	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.314458259733828	2		1025	1223	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369448	40369448	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1276	294	1239	0	ENST00000293328.3:c.1204G>A	p.Val402Ile	p.V402I	ENST00000293328	NM_012448.3	402	Gtc/Atc	10/19	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.314458259733828	2		1239	1570	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734161	58734161	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	200	1094	1	ENST00000305921.3:c.1219T>A	p.Cys407Ser	p.C407S	ENST00000305921	NM_003620.3	407	Tgt/Agt	5/6	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.314458259733828	2		1095	1042	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39550377	39550377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	106	707	0	ENST00000262039.4:c.488C>T	p.Thr163Ile	p.T163I	ENST00000262039	NM_002647.2	163	aCa/aTa	4/25	1	2	FACETS	0.847	0.759	0.94	0.847	0.759	0.94	CLONAL	1	TRUE	1	0.314458259733828	2		707	796	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121133	11121133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	253	1118	0	ENST00000358026.2:c.2200G>A	p.Val734Met	p.V734M	ENST00000358026	NM_001128849.1	734	Gtg/Atg	15/36	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.314458259733828	2		1118	1389	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051211	13051211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200173883	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	187	869	0	ENST00000316448.5:c.647C>T	p.Pro216Leu	p.P216L	ENST00000316448	NM_004343.3	216	cCg/cTg	5/9	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.314458259733828	2		869	1048	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967800	18967800	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1318	269	1251	0	ENST00000262803.5:c.1939A>G	p.Met647Val	p.M647V	ENST00000262803	NM_002911.3	647	Atg/Gtg	14/24	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.314458259733828	2		1251	1587	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416583	29416583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs112657055	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	123	627	0	ENST00000389048.3:c.4370C>T	p.Thr1457Ile	p.T1457I	ENST00000389048	NM_004304.4	1457	aCa/aTa	29/29	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.314458259733828	2		627	691	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182677	38182678	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	208	870	0	ENST00000396334.3:c.834dup	p.Ser279GlnfsTer153	p.S279Qfs*153	ENST00000396334	NM_002468.4	277	ttc/ttCc	5/5	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.314458259733828	2		870	1073	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275661	41275661	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	140	689	0	ENST00000349496.5:c.1556T>C	p.Leu519Pro	p.L519P	ENST00000349496	NM_001904.3	519	cTt/cCt	10/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.314458259733828	2		689	797	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940484	49940484	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	270	1338	0	ENST00000296474.3:c.559A>G	p.Thr187Ala	p.T187A	ENST00000296474	NM_002447.2	187	Act/Gct	1/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.314458259733828	2		1338	1375	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286255	66286255	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	64	633	0	ENST00000273854.3:c.1431del	p.Ile480LeufsTer21	p.I480Lfs*21	ENST00000273854	NM_004439.5	477	aaA/aa	6/18	1	2	FACETS	0.986	0.857	1	0.986	0.857	1	CLONAL	1	TRUE	1	0.314458259733828	2		633	413	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196731	106196731	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	128	791	0	ENST00000380013.4:c.5067del	p.Phe1689LeufsTer6	p.F1689Lfs*6	ENST00000380013	NM_001127208.2	1688	agT/ag	11/11	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.314458259733828	2		791	776	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687113	176687113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	156	868	0	ENST00000439151.2:c.5090G>A	p.Arg1697Gln	p.R1697Q	ENST00000439151	NM_022455.4	1697	cGg/cAg	14/23	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.314458259733828	2		868	926	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323362	31323363	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748204482	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	124	788	1	ENST00000412585.2:c.626dup	p.Thr211AspfsTer10	p.T211Dfs*10	ENST00000412585	NM_005514.6	209	cca/ccCa	4/8	1	2	FACETS	0.766	0.691	0.844	0.766	0.691	0.844	SUBCLONAL	1	TRUE	1	0.314458259733828	2		789	1030	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739714	41739715	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	168	1214	1	ENST00000242208.4:c.258_259delinsTT	p.Ile87Phe	p.I87F	ENST00000242208	NM_002192.2	86	gcGAtc/gcTTtc	2/3	1	2	FACETS	0.802	0.735	0.872	0.802	0.735	0.872	CLONAL	1	TRUE	1	0.314458259733828	2		1215	1333	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008888	152008888	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	77	756	0	ENST00000262189.6:c.734C>G	p.Ser245Cys	p.S245C	ENST00000262189	NM_170606.2	245	tCt/tGt	5/59	1	2	FACETS	0.759	0.667	0.859	0.759	0.667	0.859	SUBCLONAL	1	TRUE	1	0.314458259733828	2		756	645	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372133	55372133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161016147	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	227	1123	2	ENST00000297316.4:c.823G>A	p.Gly275Ser	p.G275S	ENST00000297316	NM_022454.3	275	Ggc/Agc	2/2	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.314458259733828	2		1125	1165	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485280	8485280	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329600473	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	120	1082	3	ENST00000356435.5:c.3100G>A	p.Val1034Met	p.V1034M	ENST00000356435		1034	Gtg/Atg	18/35	1	2	FACETS	0.861	0.777	0.95	0.861	0.777	0.95	CLONAL	1	TRUE	1	0.314458259733828	2		1085	886	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002717	37002717	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	144	775	0	ENST00000358127.4:c.532T>C	p.Ser178Pro	p.S178P	ENST00000358127	NM_001280556.1	178	Tcg/Ccg	5/10	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.314458259733828	2		775	914	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015109	37015109	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1152	198	1127	0	ENST00000358127.4:c.295del	p.Ile99SerfsTer60	p.I99Sfs*60	ENST00000358127	NM_001280556.1	99	Atc/tc	3/10	1	2	FACETS	0.933	0.862	1	0.933	0.862	1	CLONAL	1	TRUE	1	0.314458259733828	2		1127	1350	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390984	139390984	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	289	1131	2	ENST00000277541.6:c.7207C>A	p.Gln2403Lys	p.Q2403K	ENST00000277541	NM_017617.3	2403	Cag/Aag	34/34	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.314458259733828	2		1133	1489	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841240	15841240	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746842789	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	145	662	0	ENST00000307771.7:c.1324C>T	p.Arg442Trp	p.R442W	ENST00000307771	NM_005089.3	442	Cgg/Tgg	11/11	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.314458259733828	2		662	874	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041170	47041170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1356	260	1293	1	ENST00000377604.3:c.1598C>T	p.Ala533Val	p.A533V	ENST00000377604	NM_001204468.1	533	gCt/gTt	15/24	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.314458259733828	2		1294	1616	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411852	63411852	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1226	259	1401	0	ENST00000330258.3:c.1315C>A	p.Leu439Ile	p.L439I	ENST00000330258	NM_152424.3	439	Ctt/Att	2/2	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.314458259733828	2		1401	1485	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982123	93982123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769773179	NA	P-0019168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	110	606	0	ENST00000369303.4:c.1342G>A	p.Gly448Arg	p.G448R	ENST00000369303	NM_004440.3	448	Gga/Aga	6/17	1	2	FACETS	0.902	0.81	0.999	0.902	0.81	0.999	CLONAL	1	TRUE	1	0.314458259733828	2		606	776	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	142	736	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		736	365	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0019172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	139	918	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.19191046500768	4	FACETS	0.939	0.857	1	0.939	0.857	1	CLONAL	2	TRUE	2	0.270593521949514	4		918	695	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519989	NA	P-0019172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	158	682	0	ENST00000269305.4:c.730G>C	p.Gly244Arg	p.G244R	ENST00000269305	NM_001126112.2	244	Ggc/Cgc	7/11	NA	2	FACETS	1	0.924	1			1	INDETERMINATE	2	TRUE	NA	0.270593521949514	2		682	582	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781918	9781918	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	110	650	0	ENST00000377346.4:c.2055G>T	p.Gln685His	p.Q685H	ENST00000377346	NM_005026.3	685	caG/caT	16/24	0.270593521949514	5	FACETS	0.934	0.841	1	0.623	0.56	0.688	CLONAL	2	TRUE	2	0.270593521949514	5		650	612	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106088	8106088	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	115	558	0	ENST00000346208.3:c.908C>G	p.Pro303Arg	p.P303R	ENST00000346208		303	cCc/cGc	4/6	0.19191046500768	4	FACETS	0.9	0.813	0.992	0.9	0.813	0.992	CLONAL	2	TRUE	2	0.270593521949514	4		558	600	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617463	43617463	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	98	442	0	ENST00000355710.3:c.2800G>A	p.Val934Ile	p.V934I	ENST00000355710	NM_020975.4	934	Gta/Ata	16/20	0.19191046500768	4	FACETS	0.829	0.742	0.922	0.829	0.742	0.922	CLONAL	2	TRUE	2	0.270593521949514	4		442	555	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944959	31944959	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	138	601	0	ENST00000340398.3:c.142C>A	p.Leu48Ile	p.L48I	ENST00000340398	NM_001013699.2	48	Ctt/Att	1/1	0.19191046500768	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.270593521949514	4		601	586	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857529	57857529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759777434	NA	P-0019172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	189	854	0	ENST00000228682.2:c.55C>T	p.Leu19Phe	p.L19F	ENST00000228682	NM_005269.2	19	Ctc/Ttc	2/12	0.19191046500768	4	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	2	0.270593521949514	4		854	864	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562181	21562181	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs769047956	NA	P-0019172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	447	1258	0	ENST00000382592.4:c.1738G>T	p.Val580Phe	p.V580F	ENST00000382592	NM_014572.2	580	Gtc/Ttc	4/8	0.270593521949514	5	FACETS	0.996	0.949	1	0.996	0.949	1	CLONAL	3	TRUE	2	0.270593521949514	5		1258	1554	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544637	65544637	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1167538050	NA	P-0019172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	143	555	0	ENST00000358664.4:c.289C>T	p.Gln97Ter	p.Q97*	ENST00000358664	NM_002382.4	97	Cag/Tag	4/5	0.270593521949514	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.270593521949514	2		555	490	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923477	9923477	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	128	607	0	ENST00000330684.3:c.1810G>A	p.Ala604Thr	p.A604T	ENST00000330684	NM_001134407.1	604	Gct/Act	9/13	0.208609049503372	4	FACETS	0.982	0.893	1	0.982	0.893	1	CLONAL	2	TRUE	2	0.270593521949514	4		607	612	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543748	29543748	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	88	449	1	ENST00000389048.3:c.1415G>T	p.Arg472Leu	p.R472L	ENST00000389048	NM_004304.4	472	cGg/cTg	7/29	0.19191046500768	4	FACETS	0.892	0.794	0.997	0.892	0.794	0.997	CLONAL	2	TRUE	2	0.270593521949514	4		450	463	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046966	128046966	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0019172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	187	684	0	ENST00000285398.2:c.769A>T	p.Lys257Ter	p.K257*	ENST00000285398	NM_000122.1	257	Aag/Tag	6/15	0.19191046500768	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	2	0.270593521949514	4		684	836	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091800	29091800	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	113	742	0	ENST00000328354.6:c.1157G>T	p.Gly386Val	p.G386V	ENST00000328354	NM_007194.3	386	gGa/gTa	11/15	0.160040394068513	3	FACETS	1	0.972	1	0.614	0.553	0.679	INDETERMINATE	1	TRUE	1	0.270593521949514	3		742	772	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648427	30648427	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	176	744	0	ENST00000295754.5:c.52A>G	p.Thr18Ala	p.T18A	ENST00000295754	NM_003242.5	18	Acg/Gcg	1/7	0.266623756458387	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.270593521949514	2		744	577	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513283	149513283	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs751085975	NA	P-0019172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	44	564	0	ENST00000261799.4:c.800A>T	p.Asp267Val	p.D267V	ENST00000261799	NM_002609.3	267	gAt/gTt	6/23	0.266623756458387	2	FACETS	0.805	0.676	0.947	0.402	0.338	0.474	CLONAL	1	TRUE	0	0.270593521949514	2		564	404	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514525	149514525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138830253	NA	P-0019172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	61	495	0	ENST00000261799.4:c.419C>T	p.Thr140Met	p.T140M	ENST00000261799	NM_002609.3	140	aCg/aTg	4/23	0.266623756458387	2	FACETS	1	0.911	1	0.534	0.462	0.612	CLONAL	1	TRUE	0	0.270593521949514	2		495	422	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983243	149983243	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	67	582	0	ENST00000253339.5:c.3015del	p.Ala1006LeufsTer14	p.A1006Lfs*14	ENST00000253339		1005	aaA/aa	7/7	0.19191046500768	4	FACETS	0.78	0.676	0.892	0.39	0.338	0.446	SUBCLONAL	1	TRUE	2	0.270593521949514	4		582	807	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937242	76937242	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	90	560	0	ENST00000373344.5:c.3506A>T	p.Lys1169Met	p.K1169M	ENST00000373344	NM_000489.3	1169	aAg/aTg	9/35	0.160040394068513	3	FACETS	1	0.972	1	0.652	0.58	0.729	INDETERMINATE	1	TRUE	1	0.270593521949514	3		560	579	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	31	736	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.834	0.676	1	0.834	0.676	1	CLONAL	1	TRUE	1	0.242892298454789	2		736	306	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562738	29562739	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555615472	NA	P-0019173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	72	652	0	ENST00000356175.3:c.3822_3823del	p.Phe1275ProfsTer8	p.F1275Pfs*8	ENST00000356175	NM_000267.3	1273	aCT/a	28/57	0.242892298454789	1	FACETS	0.912	0.798	1	0.912	0.798	1	CLONAL	1	TRUE	0	0.242892298454789	1		652	571	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115907	8115907	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769298101	NA	P-0019173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	62	731	1	ENST00000346208.3:c.1253C>T	p.Thr418Met	p.T418M	ENST00000346208		418	aCg/aTg	6/6	0.242892298454789	2	FACETS	1	0.866	1	0.501	0.433	0.574	CLONAL	1	TRUE	0	0.242892298454789	2		732	510	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692816	89692817	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554898084	NA	P-0019173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	90	442	0	ENST00000371953.3:c.301dup	p.Ile101AsnfsTer6	p.I101Nfs*6	ENST00000371953	NM_000314.4	100	-/A	5/9	0.242892298454789	2	FACETS	0.838	0.748	0.934	0.838	0.748	0.934	CLONAL	2	TRUE	0	0.242892298454789	2		442	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574006	7574009	+	frameshift_variant	Frame_Shift_Del	DEL	ACAT	ACAT	-	novel	NA	P-0019173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	111	1030	0	ENST00000269305.4:c.1018_1021del	p.Met340SerfsTer4	p.M340Sfs*4	ENST00000269305	NM_001126112.2	340	ATGTtc/tc	10/11	0.242892298454789	1	FACETS	0.993	0.892	1	0.993	0.892	1	CLONAL	1	TRUE	0	0.242892298454789	1		1030	809	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	45	736	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.906	0.765	1	0.906	0.765	1	CLONAL	1	TRUE	1	0.3	2		736	331	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591085	67591085	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519839	NA	P-0019175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	41	454	1	ENST00000274335.5:c.1678G>T	p.Asp560Tyr	p.D560Y	ENST00000274335		560	Gac/Tac	12/15	1	2	FACETS	0.48	0.399	0.57	0.48	0.399	0.57	SUBCLONAL	1	TRUE	1	0.3	2		455	570	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712007	89712007	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765433422	NA	P-0019175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	55	320	1	ENST00000371953.3:c.625G>A	p.Gly209Arg	p.G209R	ENST00000371953	NM_000314.4	209	Gga/Aga	6/9	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.3	2		321	317	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432522	49432522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	89	843	1	ENST00000301067.7:c.8617G>A	p.Gly2873Ser	p.G2873S	ENST00000301067	NM_003482.3	2873	Ggt/Agt	34/54	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.3	2		844	591	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082359	16082359	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	116	1331	2	ENST00000281043.3:c.173C>T	p.Thr58Met	p.T58M	ENST00000281043	NM_005378.4	58	aCg/aTg	2/3	1	2	FACETS	0.921	0.829	1	0.921	0.829	1	CLONAL	1	TRUE	1	0.3	2		1333	840	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457176	25457176	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149095705	NA	P-0019175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	131	926	1	ENST00000264709.3:c.2711C>T	p.Pro904Leu	p.P904L	ENST00000264709	NM_175629.2	904	cCg/cTg	23/23	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.3	2		927	731	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470959	25470960	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGACCCCACGGGCTCAG	novel	NA	P-0019175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	76	830	0	ENST00000264709.3:c.785_801dup	p.Asp268LeufsTer54	p.D268Lfs*54	ENST00000264709	NM_175629.2	267	-/CTGAGCCCGTGGGGTCC	7/23	1	2	FACETS	0.799	0.701	0.905	0.799	0.701	0.905	CLONAL	1	TRUE	1	0.3	2		830	634	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624966	9624966	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	22	294	0	ENST00000353224.5:c.11A>C	p.Lys4Thr	p.K4T	ENST00000353224	NM_177990.2	4	aAg/aCg	3/10	1	2	FACETS	0.484	0.375	0.61	0.484	0.375	0.61	SUBCLONAL	1	TRUE	1	0.3	2		294	303	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352506	89352506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751642003	NA	P-0019177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	273	781	3	ENST00000301030.4:c.833C>T	p.Thr278Met	p.T278M	ENST00000301030	NM_001256183.1	278	aCg/aTg	8/13	1	2	FACETS	0.924	0.869	0.98	0.924	0.869	0.98	CLONAL	1	TRUE	1	0.673762020599445	2		784	877	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458433	120458433	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	1080	466	0	ENST00000256646.2:c.6912del	p.Ile2304MetfsTer2	p.I2304Mfs*2	ENST00000256646	NM_024408.3	2304	atT/at	34/34	0.781868236840464	13	FACETS	1	0.997	1			1	CLONAL	11	TRUE	NA	0.781868236840464	13		466	1277	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465004	120465004	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1360	945	550	0	ENST00000256646.2:c.5068C>G	p.Leu1690Val	p.L1690V	ENST00000256646	NM_024408.3	1690	Ctg/Gtg	28/34	0.781868236840464	13	FACETS	0.926	0.899	0.954			1	CLONAL	6	TRUE	NA	0.781868236840464	13		550	2305	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207025	1207057	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGCCGCAAGCGGGCCAAGCTCATCGGCAAGT	CGCGCCGCAAGCGGGCCAAGCTCATCGGCAAGT	TTGGCCCG	novel	NA	P-0019179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	116	686	3	ENST00000326873.7:c.113_145delinsTTGGCCCG	p.Pro38LeufsTer5	p.P38Lfs*5	ENST00000326873	NM_000455.4	38	cCGCGCCGCAAGCGGGCCAAGCTCATCGGCAAGTac/cTTGGCCCGac	1/10	0.781868236840464	1	FACETS	0.648	0.594	0.703	0.648	0.594	0.703	SUBCLONAL	1	TRUE	0	0.781868236840464	1		689	279	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469995	25470003	+	inframe_deletion	In_Frame_Del	DEL	CGAGCTCAG	CGAGCTCAG	-	novel	NA	P-0019179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	174	534	0	ENST00000264709.3:c.1039_1047del	p.Leu347_Ser349del	p.L347_S349del	ENST00000264709	NM_175629.2	347	CTGAGCTCG/-	9/23	0.163718107655015	4	FACETS	0.826	0.767	0.886	0.826	0.767	0.886	INDETERMINATE	2	TRUE	2	0.781868236840464	4		534	480	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523645	41523645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	218	763	1	ENST00000263253.7:c.1061G>A	p.Arg354Gln	p.R354Q	ENST00000263253	NM_001429.3	354	cGg/cAg	4/31	0.257556961006444	4	FACETS	0.855	0.801	0.91			1	INDETERMINATE	2	TRUE	NA	0.781868236840464	4		764	581	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798109	32798109	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	263	757	0	ENST00000374899.4:c.1570G>A	p.Gly524Arg	p.G524R	ENST00000374899	NM_018833.2	524	Ggg/Agg	9/12	0.3412331711998	4	FACETS	0.843	0.794	0.892	0.843	0.794	0.892	INDETERMINATE	2	TRUE	2	0.781868236840464	4		757	711	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0019180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	318	760	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.611214420101194	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.611051172399905	2		761	449	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063628	67063628	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0019180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	219	665	0	ENST00000412916.2:c.79-2A>G		p.X27_splice	ENST00000412916		27			0.611051172399905	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.611051172399905	2		665	358	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218788	66218788	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	80	698	0	ENST00000273854.3:c.2270A>T	p.Glu757Val	p.E757V	ENST00000273854	NM_004439.5	757	gAg/gTg	13/18	0.405568074969673	4	FACETS	0.972	0.86	1	0.486	0.43	0.546	CLONAL	1	TRUE	2	0.611051172399905	4		698	434	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39317341	39317341	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	50	1208	0	ENST00000373001.3:c.845A>C	p.Tyr282Ser	p.Y282S	ENST00000373001	NM_022157.3	282	tAt/tCt	5/7	1	2	FACETS	0.909	0.769	1	0.909	0.769	1	CLONAL	1	TRUE	1	0.14	2		1208	786	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842668	68842669	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	84	1158	0	ENST00000261769.5:c.606dup	p.Gly203TrpfsTer6	p.G203Wfs*6	ENST00000261769	NM_004360.3	202	gtt/gTtt	5/16	1	2	FACETS	0.851	0.752	0.958	1	0.981	1	CLONAL	2	TRUE	1	0.14	2		1158	705	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412895	49412895	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	42	1213	1	ENST00000418115.1:c.128T>G	p.Val43Gly	p.V43G	ENST00000418115	NM_001664.2	43	gTg/gGg	2/5	1	2	FACETS	0.744	0.62	0.884	0.744	0.62	0.884	SUBCLONAL	1	TRUE	1	0.14	2		1214	806	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	12	751	0	ENST00000263967.3:c.3139C>G	p.His1047Asp	p.H1047D	ENST00000263967	NM_006218.2	1047	Cat/Gat	21/21	1	2	FACETS	0.306	0.214	0.421	0.306	0.214	0.421	SUBCLONAL	1	TRUE	1	0.14	2		751	560	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176684117	176684117	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	76	718	0	ENST00000439151.2:c.4931A>T	p.His1644Leu	p.H1644L	ENST00000439151	NM_022455.4	1644	cAt/cTt	13/23	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		718	636	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0019183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	115	640	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.194891766524747	3	FACETS	0.84	0.757	0.927	0.84	0.757	0.927	CLONAL	2	TRUE	1	0.22	3		640	691	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391024	89391024	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	54	628	0	ENST00000336596.2:c.1095del	p.Lys365AsnfsTer6	p.K365Nfs*6	ENST00000336596	NM_005233.5	364	Aaa/aa	5/17	1	2	FACETS	0.776	0.662	0.9	0.776	0.662	0.9	SUBCLONAL	1	TRUE	1	0.22	2		628	633	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0019183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	40	472	2	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.792	0.658	0.941	0.792	0.658	0.941	CLONAL	1	TRUE	1	0.22	2		474	459	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053022	180053023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750808726	NA	P-0019183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	60	726	2	ENST00000261937.6:c.1267dup	p.Gln423ProfsTer4	p.Q423Pfs*4	ENST00000261937	NM_182925.4	423	cag/cCag	10/30	1	2	FACETS	0.899	0.774	1	0.899	0.774	1	CLONAL	1	TRUE	1	0.22	2		728	607	SUCCESS
APC	324	MSKCC	GRCh37	5	112177091	112177091	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1131691253	NA	P-0019183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	55	737	0	ENST00000257430.4:c.5803del	p.Gln1935SerfsTer35	p.Q1935Sfs*35	ENST00000257430	NM_000038.5	1934	Ccc/cc	16/16	1	2	FACETS	0.745	0.637	0.864	0.745	0.637	0.864	SUBCLONAL	1	TRUE	1	0.22	2		737	671	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070577	67070578	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	32	287	0	ENST00000412916.2:c.207dup	p.Pro70SerfsTer13	p.P70Sfs*13	ENST00000412916		67	-/T	3/6	1	2	FACETS	0.75	0.609	0.909	0.75	0.609	0.909	CLONAL	1	TRUE	1	0.22	2		287	388	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827927	40827927	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536150112	NA	P-0019183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	60	550	2	ENST00000373198.4:c.2501G>A	p.Arg834His	p.R834H	ENST00000373198	NM_133170.3	834	cGc/cAc	17/32	1	2	FACETS	0.869	0.748	1	0.869	0.748	1	CLONAL	1	TRUE	1	0.22	2		552	628	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431874	49431874	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	71	670	6	ENST00000301067.7:c.9265del	p.Val3089TrpfsTer30	p.V3089Wfs*30	ENST00000301067	NM_003482.3	3089	Gtg/tg	34/54	1	2	FACETS	0.903	0.787	1	0.903	0.787	1	CLONAL	1	TRUE	1	0.22	2		676	715	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692958	89692958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660321	NA	P-0019183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	50	559	0	ENST00000371953.3:c.442G>A	p.Ala148Thr	p.A148T	ENST00000371953	NM_000314.4	148	Gca/Aca	5/9	1	2	FACETS	0.828	0.702	0.966	0.828	0.702	0.966	CLONAL	1	TRUE	1	0.22	2		559	549	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199950	108199950	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	50	368	0	ENST00000278616.4:c.7292A>C	p.Lys2431Thr	p.K2431T	ENST00000278616	NM_000051.3	2431	aAa/aCa	49/63	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.22	2		368	421	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923144	48923144	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	37	425	0	ENST00000267163.4:c.596del	p.Leu199TyrfsTer2	p.L199Yfs*2	ENST00000267163	NM_000321.2	198	Ttt/tt	6/27	1	2	FACETS	0.648	0.534	0.776	0.648	0.534	0.776	SUBCLONAL	1	TRUE	1	0.22	2		425	519	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679814	88679814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753910026	NA	P-0019183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	37	370	0	ENST00000360948.2:c.649G>A	p.Val217Ile	p.V217I	ENST00000360948	NM_001012338.2	217	Gtc/Atc	7/19	1	2	FACETS	0.805	0.664	0.962	0.805	0.664	0.962	CLONAL	1	TRUE	1	0.22	2		370	418	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103415	2103415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369314296	NA	P-0019183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	73	628	1	ENST00000219476.3:c.298G>A	p.Ala100Thr	p.A100T	ENST00000219476	NM_000548.3	100	Gcg/Acg	4/42	1	2	FACETS	0.914	0.799	1	0.914	0.799	1	CLONAL	1	TRUE	1	0.22	2		629	726	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372138	45372138	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	78	706	0	ENST00000262160.6:c.1031A>C	p.Glu344Ala	p.E344A	ENST00000262160	NM_005901.5	344	gAa/gCa	9/11	1	2	FACETS	0.979	0.86	1	0.979	0.86	1	CLONAL	1	TRUE	1	0.22	2		706	724	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291084	10291084	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	97	647	0	ENST00000340748.4:c.387del	p.Lys130AsnfsTer129	p.K130Nfs*129	ENST00000340748		129	ccC/cc	4/40	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.22	2		647	730	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945737	17945737	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	91	726	0	ENST00000458235.1:c.2123A>C	p.Lys708Thr	p.K708T	ENST00000458235	NM_000215.3	708	aAg/aCg	16/24	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.22	2		726	819	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635601	47635603	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs267607919	NA	P-0019183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	62	578	0	ENST00000233146.2:c.279_281del	p.Leu94del	p.L94del	ENST00000233146	NM_000251.2	91	gaTCTt/gat	2/16	1	2	FACETS	0.873	0.753	1	0.873	0.753	1	CLONAL	1	TRUE	1	0.22	2		578	646	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170146	32170147	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1554147090	NA	P-0019183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	53	659	0	ENST00000375023.3:c.3461dup	p.Gly1156ArgfsTer24	p.G1156Rfs*24	ENST00000375023	NM_004557.3	1154	ggc/ggGc	21/30	1	2	FACETS	0.737	0.627	0.857	0.737	0.627	0.857	SUBCLONAL	1	TRUE	1	0.22	2		659	654	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100390	27100390	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0019184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	319	673	0	ENST00000324856.7:c.4101+1G>A		p.X1367_splice	ENST00000324856	NM_006015.4	1367			0.472832077623857	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.475954100170148	3		673	755	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111488	8111488	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	184	908	0	ENST00000346208.3:c.974C>G	p.Thr325Ser	p.T325S	ENST00000346208		325	aCc/aGc	5/6	0.472832077623857	3	FACETS	0.975	0.9	1	0.487	0.45	0.527	CLONAL	1	TRUE	1	0.475954100170148	3		908	982	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0019185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	54	906	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.2	2		906	528	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0019185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	35	678	4	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	1	2	FACETS	0.677	0.554	0.815	0.677	0.554	0.815	SUBCLONAL	1	TRUE	1	0.2	2		682	517	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021828	71021828	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0019185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	20	319	0	ENST00000318789.4:c.1531-1G>A		p.X511_splice	ENST00000318789	NM_032682.5	511			1	2	FACETS	0.962	0.738	1	0.962	0.738	1	CLONAL	1	TRUE	1	0.2	2		319	208	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640796	3640796	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781462011	NA	P-0019185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	26	608	0	ENST00000294008.3:c.2843C>T	p.Ala948Val	p.A948V	ENST00000294008	NM_032444.2	948	gCg/gTg	12/15	0.110226411855189	0	FACETS	0.86	0.684	1			1	INDETERMINATE	1	TRUE	0	0.2	0		608	242	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	411	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.289130785555079	4	FACETS	0.931	0.886	0.977	0.931	0.886	0.977	CLONAL	3	TRUE	1	0.289130785555079	4		509	1312	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946355	2946355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372251654	NA	P-0019186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	145	1144	3	ENST00000396946.4:c.3382G>A	p.Val1128Ile	p.V1128I	ENST00000396946	NM_032415.4	1128	Gta/Ata	25/25	0.256906048685289	3	FACETS	0.895	0.814	0.98	0.447	0.407	0.49	CLONAL	1	TRUE	1	0.289130785555079	3		1147	1283	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845851	72845851	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	188	673	0	ENST00000268489.5:c.3616del	p.Leu1206SerfsTer38	p.L1206Sfs*38	ENST00000268489	NM_006885.3	1206	Ctc/tc	6/10	0.256906048685289	3	FACETS	0.856	0.792	0.923	0.856	0.792	0.923	CLONAL	2	TRUE	1	0.289130785555079	3		673	869	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341283	89341283	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	86	295	1	ENST00000301030.4:c.7652C>G	p.Pro2551Arg	p.P2551R	ENST00000301030	NM_001256183.1	2551	cCa/cGa	11/13	0.256906048685289	3	FACETS	0.984	0.878	1	0.984	0.878	1	CLONAL	2	TRUE	1	0.289130785555079	3		296	346	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967004	18967024	+	inframe_deletion	In_Frame_Del	DEL	GCTGCAGAAGCTGCAGCAGCT	GCTGCAGAAGCTGCAGCAGCT	-	novel	NA	P-0019186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	78	454	1	ENST00000262803.5:c.1720_1740del	p.Leu574_Leu580del	p.L574_L580del	ENST00000262803	NM_002911.3	573	gaGCTGCAGAAGCTGCAGCAGCTg/gag	13/24	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.289130785555079	2		455	525	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39251263	39251263	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	150	852	0	ENST00000402219.2:c.1090A>C	p.Ser364Arg	p.S364R	ENST00000402219	NM_005633.3	364	Agt/Cgt	9/23	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.289130785555079	2		852	950	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161670	47161688	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ACCTTTCTGTTAAATAAAC	ACCTTTCTGTTAAATAAAC	-	novel	NA	P-0019186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	26	326	0	ENST00000409792.3:c.4438_4454+2del		p.X1480_splice	ENST00000409792	NM_014159.6	1480		3/21	0.289130785555079	1	FACETS	0.508	0.403	0.628	0.508	0.403	0.628	SUBCLONAL	1	TRUE	0	0.289130785555079	1		326	303	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155478	106155478	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	113	608	0	ENST00000380013.4:c.379G>A	p.Val127Ile	p.V127I	ENST00000380013	NM_001127208.2	127	Gta/Ata	3/11	0.289130785555079	1	FACETS	0.946	0.852	1	0.946	0.852	1	CLONAL	1	TRUE	0	0.289130785555079	1		608	707	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	178	600	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	0.700982325174524	2		600	506	SUCCESS
EED	8726	MSKCC	GRCh37	11	85966294	85966294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	44	387	0	ENST00000263360.6:c.391G>A	p.Glu131Lys	p.E131K	ENST00000263360	NM_003797.3	131	Gaa/Aaa	4/12	1	2	FACETS	0.355	0.298	0.417	0.355	0.298	0.417	SUBCLONAL	1	TRUE	1	0.700982325174524	2		387	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0019187-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	175	663	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	NA	2	FACETS	0.915	0.848	0.983			1	INDETERMINATE	2	TRUE	NA	0.34965014252564	2		663	547	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0019187-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	209	569	0	ENST00000269305.4:c.673-1G>C		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.591568577176152	2	FACETS	0.96	0.909	1	0.96	0.909	1	CLONAL	2	TRUE	0	0.620540302593597	2		569	351	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231831	36231831	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019187-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	229	920	0	ENST00000300305.3:c.553C>T	p.Gln185Ter	p.Q185*	ENST00000300305		185	Caa/Taa	5/8	0.508299106390291	4	FACETS	1	0.981	1	0.381	0.355	0.408	CLONAL	1	TRUE	1	0.620540302593597	4		920	1047	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115435	115115437	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	rs1319662056	NA	P-0019188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	174	723	0	ENST00000257566.3:c.889_891del	p.Asn297del	p.N297del	ENST00000257566	NM_016569.3	297	AAC/-	5/8	1	2	FACETS	0.901	0.831	0.975	0.901	0.831	0.975	CLONAL	1	TRUE	1	0.465782138503533	2		723	829	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844139	68844139	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	219	697	1	ENST00000261769.5:c.727G>A	p.Glu243Lys	p.E243K	ENST00000261769	NM_004360.3	243	Gag/Aag	6/16	0.465782138503533	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.465782138503533	1		698	630	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1039231	1039231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144832155	NA	P-0019189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	113	771	0	ENST00000358495.3:c.266C>T	p.Thr89Met	p.T89M	ENST00000358495	NM_134424.2	89	aCg/aTg	4/12	0.448065381931399	4	FACETS	0.892	0.802	0.986	0.297	0.267	0.329	CLONAL	1	TRUE	1	0.447408867782565	4		771	820	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447774	187447774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536118071	NA	P-0019189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	92	487	0	ENST00000232014.4:c.419G>A	p.Arg140His	p.R140H	ENST00000232014	NM_001130845.1	140	cGt/cAt	5/10	0.447408867782565	5	FACETS	1	0.956	1	0.382	0.34	0.427	CLONAL	1	TRUE	2	0.447408867782565	5		487	599	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621172	1621172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239148792	NA	P-0019189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	140	807	1	ENST00000344749.5:c.974C>T	p.Ala325Val	p.A325V	ENST00000344749	NM_001136139.2	325	gCt/gTt	12/19	0.448065381931399	3	FACETS	1	0.928	1	0.51	0.465	0.557	CLONAL	1	TRUE	1	0.447408867782565	3		808	751	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916928	178916939	+	inframe_deletion	In_Frame_Del	DEL	AGGCAACCGTGA	AGGCAACCGTGA	-	novel	NA	P-0019189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	194	799	0	ENST00000263967.3:c.317_328del	p.Gly106_Glu109del	p.G106_E109del	ENST00000263967	NM_006218.2	105	gtAGGCAACCGTGAa/gta	2/21	0.447408867782565	5	FACETS	0.933	0.865	1	0.622	0.576	0.668	CLONAL	2	TRUE	2	0.447408867782565	5		799	777	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961013	55961013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	113	720	0	ENST00000263923.4:c.2927G>A	p.Gly976Glu	p.G976E	ENST00000263923	NM_002253.2	976	gGa/gAa	21/30	1	2	FACETS	0.93	0.84	1	0.93	0.84	1	CLONAL	1	TRUE	1	0.447408867782565	2		720	543	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245456	153245456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	212	756	2	ENST00000281708.4:c.1735G>A	p.Gly579Arg	p.G579R	ENST00000281708	NM_033632.3	579	Ggg/Agg	11/12	0.448065381931399	3	FACETS	0.909	0.849	0.97	0.909	0.849	0.97	CLONAL	2	TRUE	1	0.447408867782565	3		758	638	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521403	8521403	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	110	878	1	ENST00000356435.5:c.835G>T	p.Glu279Ter	p.E279*	ENST00000356435		279	Gaa/Taa	9/35	0.448065381931399	3	FACETS	0.813	0.731	0.9	0.271	0.243	0.3	CLONAL	1	TRUE	0	0.447408867782565	3		879	740	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0019190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	218	397	1	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			0.321763838295664	1	FACETS	0.84	0.788	0.893	0.84	0.788	0.893	INDETERMINATE	1	TRUE	0	0.635695264627671	1		398	557	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0019190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	106	614	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.733	0.661	0.809	0.733	0.661	0.809	SUBCLONAL	1	TRUE	1	0.635695264627671	2		614	455	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457242	25457242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147001633	NA	P-0019190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	15	741	1	ENST00000264709.3:c.2645G>A	p.Arg882His	p.R882H	ENST00000264709	NM_175629.2	882	cGc/cAc	23/23	NA	2	FACETS	0.074	0.054	0.099			1	INDETERMINATE	1	TRUE	NA	0.635695264627671	2		742	636	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518999	103518999	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	105	478	0	ENST00000355739.4:c.2337C>A	p.Phe779Leu	p.F779L	ENST00000355739	NM_000123.3	779	ttC/ttA	11/15	1	2	FACETS	0.974	0.883	1	0.974	0.883	1	CLONAL	1	TRUE	1	0.635695264627671	2		478	339	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116114	67116114	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0019190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	123	400	0	ENST00000412916.2:c.400-2A>G		p.X134_splice	ENST00000412916		134			0.635695264627671	1	FACETS	0.8	0.733	0.868	0.8	0.733	0.868	SUBCLONAL	1	TRUE	0	0.635695264627671	1		400	330	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265456	152265456	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	184	613	0	ENST00000206249.3:c.909G>C	p.Lys303Asn	p.K303N	ENST00000206249	NM_000125.3	303	aaG/aaC	4/8	NA	2	FACETS	1	0.932	1			1	INDETERMINATE	1	TRUE	NA	0.635695264627671	2		613	577	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0019191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	21	741	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.212	0.162	0.27	0.212	0.162	0.27	SUBCLONAL	1	TRUE	1	0.2868923356231	2		742	692	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	57	600	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.629	0.539	0.727	0.629	0.539	0.727	SUBCLONAL	1	TRUE	1	0.2868923356231	2		600	632	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100603	67100603	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	51	466	0	ENST00000412916.2:c.301A>G	p.Met101Val	p.M101V	ENST00000412916		101	Atg/Gtg	4/6	0.2868923356231	1	FACETS	0.781	0.666	0.907	0.781	0.666	0.907	CLONAL	1	TRUE	0	0.2868923356231	1		466	390	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11177124	11177124	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	94	816	0	ENST00000361445.4:c.6953C>G	p.Thr2318Ser	p.T2318S	ENST00000361445	NM_004958.3	2318	aCc/aGc	50/58	1	2	FACETS	0.904	0.804	1	0.904	0.804	1	CLONAL	1	TRUE	1	0.2868923356231	2		816	725	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163301	47163301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	46	638	0	ENST00000409792.3:c.2825G>A	p.Gly942Glu	p.G942E	ENST00000409792	NM_014159.6	942	gGa/gAa	3/21	1	2	FACETS	0.55	0.463	0.647	0.55	0.463	0.647	SUBCLONAL	1	TRUE	1	0.2868923356231	2		638	583	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	42	736	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.27	2		736	305	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0019193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	74	640	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	0.27	2		640	499	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244652	46244652	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	88	1161	0	ENST00000334344.6:c.2746C>T	p.Gln916Ter	p.Q916*	ENST00000334344	NM_152641.2	916	Caa/Taa	15/21	1	2	FACETS	0.782	0.692	0.878	0.782	0.692	0.878	SUBCLONAL	1	TRUE	1	0.27	2		1161	834	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46215240	46215240	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	27	477	0	ENST00000334344.6:c.675G>A	p.Trp225Ter	p.W225*	ENST00000334344	NM_152641.2	225	tgG/tgA	6/21	1	2	FACETS	0.676	0.539	0.832	0.676	0.539	0.832	SUBCLONAL	1	TRUE	1	0.27	2		477	296	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0019195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	612	1189	11	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	0.868542526568731	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.871672896367125	1		1200	725	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961169	41961169	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	271	658	1	ENST00000219905.7:c.77T>G	p.Val26Gly	p.V26G	ENST00000219905	NM_001164273.1	26	gTc/gGc	2/24	1	2	FACETS	0.975	0.922	1	0.975	0.922	1	CLONAL	1	TRUE	1	0.871672896367125	2		659	638	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048608	180048608	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	462	1099	1	ENST00000261937.6:c.1954G>T	p.Val652Leu	p.V652L	ENST00000261937	NM_182925.4	652	Gtg/Ttg	13/30	1	2	FACETS	0.929	0.889	0.969	0.929	0.889	0.969	CLONAL	1	TRUE	1	0.871672896367125	2		1100	1141	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128347955	128347955	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	112	890	0	ENST00000265960.3:c.550C>G	p.His184Asp	p.H184D	ENST00000265960	NM_001006617.1	184	Cac/Gac	5/12	1	2	FACETS	0.813	0.731	0.901	0.813	0.731	0.901	CLONAL	1	FALSE	1	0.3	2		890	918	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0019197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	202	564	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.159765789927702	2	FACETS	0.947	0.879	1	1	0.99	1	CLONAL	3	TRUE	0	0.159765789927702	2		564	890	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752920	42752920	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1319	283	1772	0	ENST00000222329.4:c.1344G>C	p.Glu448Asp	p.E448D	ENST00000222329	NM_006494.2	448	gaG/gaC	4/4	0.159765789927702	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.159765789927702	2		1772	1602	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405954	49405954	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	143	1320	0	ENST00000418115.1:c.184G>T	p.Gly62Trp	p.G62W	ENST00000418115	NM_001664.2	62	Ggg/Tgg	3/5	0.159765789927702	2	FACETS	0.756	0.688	0.828	0.756	0.688	0.828	SUBCLONAL	2	TRUE	0	0.159765789927702	2		1320	1184	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620674	52620674	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	29	607	0	ENST00000394830.3:c.3079C>T	p.Arg1027Ter	p.R1027*	ENST00000394830	NM_018313.4	1027	Cga/Tga	21/30	0.159765789927702	2	FACETS	0.643	0.514	0.789	0.321	0.257	0.395	SUBCLONAL	1	TRUE	0	0.159765789927702	2		607	565	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	56	683	12	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.392626661172151	1	FACETS	0.37	0.318	0.427	0.37	0.318	0.427	SUBCLONAL	1	TRUE	0	0.528862373137674	1		695	421	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	174	894	7	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.45224112775364	1	FACETS	0.765	0.707	0.824	0.765	0.707	0.824	SUBCLONAL	1	TRUE	0	0.528862373137674	1		901	633	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	136	1015	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.392626661172151	1	FACETS	0.571	0.521	0.625	0.571	0.521	0.625	SUBCLONAL	1	TRUE	0	0.528862373137674	1		1017	662	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366945	15366945	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	57	911	0	ENST00000263377.2:c.1681A>T	p.Lys561Ter	p.K561*	ENST00000263377	NM_058243.2	561	Aaa/Taa	9/20	1	2	FACETS	0.234	0.2	0.272	0.234	0.2	0.272	SUBCLONAL	1	TRUE	1	0.528862373137674	2		911	920	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861129	57861129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767216717	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	76	745	0	ENST00000228682.2:c.926G>A	p.Arg309Gln	p.R309Q	ENST00000228682	NM_005269.2	309	cGg/cAg	9/12	1	2	FACETS	0.347	0.303	0.394	0.347	0.303	0.394	SUBCLONAL	1	TRUE	1	0.528862373137674	2		745	829	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134687	41134687	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760747458	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	21	455	0	ENST00000379561.5:c.941G>A	p.Arg314His	p.R314H	ENST00000379561	NM_002015.3	314	cGc/cAc	2/3	0.392626661172151	1	FACETS	0.157	0.12	0.2	0.157	0.12	0.2	SUBCLONAL	1	TRUE	0	0.528862373137674	1		455	372	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636203	87636203	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	57	506	1	ENST00000277120.3:c.2368C>T	p.Arg790Ter	p.R790*	ENST00000277120		790	Cga/Tga	19/19	1	2	FACETS	0.49	0.421	0.565	0.49	0.421	0.565	SUBCLONAL	1	TRUE	1	0.528862373137674	2		507	440	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500579	99500579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34102392	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	77	603	0	ENST00000268035.6:c.4012G>A	p.Ala1338Thr	p.A1338T	ENST00000268035	NM_000875.3	1338	Gcc/Acc	21/21	0.528862373137674	1	FACETS	0.497	0.438	0.56	0.497	0.438	0.56	SUBCLONAL	1	TRUE	0	0.528862373137674	1		603	431	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909689	50909689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	282	1196	0	ENST00000440232.2:c.1409G>A	p.Arg470His	p.R470H	ENST00000440232	NM_002691.3	470	cGc/cAc	12/27	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.528862373137674	2		1196	1017	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280066	18280066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1387844256	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	22	314	0	ENST00000222254.8:c.2149C>T	p.Arg717Cys	p.R717C	ENST00000222254	NM_005027.3	717	Cgc/Tgc	16/16	1	2	FACETS	0.251	0.194	0.316	0.251	0.194	0.316	SUBCLONAL	1	TRUE	1	0.528862373137674	2		314	332	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259578	89259578	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	29	399	0	ENST00000336596.2:c.722G>T	p.Arg241Met	p.R241M	ENST00000336596	NM_005233.5	241	aGg/aTg	3/17	1	2	FACETS	0.406	0.327	0.496	0.406	0.327	0.496	SUBCLONAL	1	TRUE	1	0.528862373137674	2		399	270	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111855968	111855968	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	66	953	0	ENST00000341259.2:c.19C>T	p.Gln7Ter	p.Q7*	ENST00000341259	NM_005475.2	7	Cag/Tag	2/8	1	2	FACETS	0.27	0.234	0.31	0.27	0.234	0.31	SUBCLONAL	1	TRUE	1	0.528862373137674	2		953	924	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	71	1200	1	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	1	2	FACETS	0.235	0.204	0.269	0.235	0.204	0.269	SUBCLONAL	1	TRUE	1	0.528862373137674	2		1201	1143	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222730	5222731	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs756013055	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	86	927	0	ENST00000357368.4:c.3072dup	p.Val1025ArgfsTer34	p.V1025Rfs*34	ENST00000357368	NM_002850.3	1024	-/C	18/38	1	2	FACETS	0.455	0.402	0.511	0.455	0.402	0.511	SUBCLONAL	1	TRUE	1	0.528862373137674	2		927	715	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	276	934	2	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	0.528862373137674	2		936	846	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188143	11188143	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772288758	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	61	501	1	ENST00000361445.4:c.5951C>T	p.Thr1984Met	p.T1984M	ENST00000361445	NM_004958.3	1984	aCg/aTg	43/58	0.392626661172151	1	FACETS	0.354	0.306	0.407	0.354	0.306	0.407	SUBCLONAL	1	TRUE	0	0.528862373137674	1		502	479	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261314	115261314	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1405036214	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	76	636	0	ENST00000438362.2:c.2407T>G	p.Leu803Val	p.L803V	ENST00000438362	NM_001242891.1	803	Ttg/Gtg	19/20	1	2	FACETS	0.455	0.399	0.516	0.455	0.399	0.516	SUBCLONAL	1	TRUE	1	0.528862373137674	2		636	631	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716229	243716229	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	72	856	0	ENST00000263826.5:c.965A>G	p.Asp322Gly	p.D322G	ENST00000263826	NM_005465.4	322	gAc/gGc	10/13	1	2	FACETS	0.417	0.364	0.474	0.417	0.364	0.474	SUBCLONAL	1	TRUE	1	0.528862373137674	2		856	653	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104375123	104375123	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	45	907	0	ENST00000369902.3:c.1121A>T	p.Asn374Ile	p.N374I	ENST00000369902	NM_016169.3	374	aAc/aTc	9/12	1	2	FACETS	0.199	0.166	0.235	0.199	0.166	0.235	SUBCLONAL	1	TRUE	1	0.528862373137674	2		907	857	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360844	118360844	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	52	292	0	ENST00000534358.1:c.4576A>C	p.Ile1526Leu	p.I1526L	ENST00000534358	NM_005933.3	1526	Atc/Ctc	13/36	1	2	FACETS	0.777	0.668	0.895	0.777	0.668	0.895	SUBCLONAL	1	TRUE	1	0.528862373137674	2		292	253	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366515	118366515	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	173	854	0	ENST00000534358.1:c.5464T>G	p.Leu1822Val	p.L1822V	ENST00000534358	NM_005933.3	1822	Tta/Gta	19/36	1	2	FACETS	0.931	0.859	1	0.931	0.859	1	CLONAL	1	TRUE	1	0.528862373137674	2		854	703	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628427	21628427	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	45	845	2	ENST00000421138.2:c.1191T>A	p.Asn397Lys	p.N397K	ENST00000421138		397	aaT/aaA	11/16	1	2	FACETS	0.391	0.329	0.46	0.391	0.329	0.46	SUBCLONAL	1	TRUE	1	0.528862373137674	2		847	435	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218390	133218390	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs781481160	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	146	901	0	ENST00000320574.5:c.5221C>T	p.Gln1741Ter	p.Q1741*	ENST00000320574	NM_006231.2	1741	Cag/Tag	39/49	1	2	FACETS	0.645	0.589	0.704	0.645	0.589	0.704	SUBCLONAL	1	TRUE	1	0.528862373137674	2		901	856	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919682	28919682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs115085855	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	72	590	1	ENST00000282397.4:c.2255C>T	p.Ser752Leu	p.S752L	ENST00000282397	NM_002019.4	752	tCg/tTg	16/30	0.392626661172151	1	FACETS	0.506	0.444	0.572	0.506	0.444	0.572	SUBCLONAL	1	TRUE	0	0.528862373137674	1		591	396	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906708	32906708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	59	833	0	ENST00000380152.3:c.1093C>T	p.Pro365Ser	p.P365S	ENST00000380152		365	Cca/Tca	10/27	0.392626661172151	1	FACETS	0.398	0.344	0.458	0.398	0.344	0.458	SUBCLONAL	1	TRUE	0	0.528862373137674	1		833	412	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873751	35873751	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	152	1008	1	ENST00000216797.5:c.100C>A	p.Leu34Met	p.L34M	ENST00000216797	NM_020529.2	34	Ctg/Atg	1/6	0.392626661172151	1	FACETS	0.465	0.425	0.507	0.465	0.425	0.507	SUBCLONAL	1	TRUE	0	0.528862373137674	1		1009	909	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95579430	95579430	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	27	332	0	ENST00000393063.1:c.2039T>C	p.Val680Ala	p.V680A	ENST00000393063	NM_030621.3	680	gTt/gCt	13/28	0.392626661172151	1	FACETS	0.337	0.269	0.413	0.337	0.269	0.413	SUBCLONAL	1	TRUE	0	0.528862373137674	1		332	223	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031966	10031966	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	35	753	0	ENST00000330684.3:c.857A>G	p.Tyr286Cys	p.Y286C	ENST00000330684	NM_001134407.1	286	tAc/tGc	3/13	1	2	FACETS	0.212	0.173	0.256	0.212	0.173	0.256	SUBCLONAL	1	TRUE	1	0.528862373137674	2		753	624	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830807	72830807	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	104	746	1	ENST00000268489.5:c.5774del	p.Gly1925ValfsTer72	p.G1925Vfs*72	ENST00000268489	NM_006885.3	1925	gGt/gt	9/10	1	2	FACETS	0.552	0.494	0.613	0.552	0.494	0.613	SUBCLONAL	1	TRUE	1	0.528862373137674	2		747	713	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992061	72992061	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs749332649	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	28	594	0	ENST00000268489.5:c.1984A>G	p.Met662Val	p.M662V	ENST00000268489	NM_006885.3	662	Atg/Gtg	2/10	1	2	FACETS	0.203	0.162	0.251	0.203	0.162	0.251	SUBCLONAL	1	TRUE	1	0.528862373137674	2		594	521	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346769	89346769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1277765790	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	21	377	0	ENST00000301030.4:c.6181G>A	p.Gly2061Arg	p.G2061R	ENST00000301030	NM_001256183.1	2061	Ggg/Agg	9/13	1	2	FACETS	0.28	0.215	0.355	0.28	0.215	0.355	SUBCLONAL	1	TRUE	1	0.528862373137674	2		377	284	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352004	89352004	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs922151127	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	58	1057	2	ENST00000301030.4:c.946G>A	p.Gly316Ser	p.G316S	ENST00000301030	NM_001256183.1	316	Ggc/Agc	9/13	1	2	FACETS	0.205	0.175	0.237	0.205	0.175	0.237	SUBCLONAL	1	TRUE	1	0.528862373137674	2		1059	1072	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682249	37682249	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	89	824	1	ENST00000447079.4:c.3440A>T	p.Gln1147Leu	p.Q1147L	ENST00000447079	NM_015083.1	1147	cAg/cTg	13/14	0.392626661172151	1	FACETS	0.358	0.317	0.402	0.358	0.317	0.402	SUBCLONAL	1	TRUE	0	0.528862373137674	1		825	691	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533905	63533905	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	37	519	1	ENST00000307078.5:c.1249G>A	p.Ala417Thr	p.A417T	ENST00000307078	NM_004655.3	417	Gcg/Acg	6/11	0.392626661172151	1	FACETS	0.238	0.196	0.285	0.238	0.196	0.285	SUBCLONAL	1	TRUE	0	0.528862373137674	1		520	433	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211820	2211820	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	65	1026	0	ENST00000398665.3:c.1536G>T	p.Gln512His	p.Q512H	ENST00000398665	NM_032482.2	512	caG/caT	16/28	1	2	FACETS	0.257	0.222	0.296	0.257	0.222	0.296	SUBCLONAL	1	TRUE	1	0.528862373137674	2		1026	955	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7141686	7141686	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	37	853	0	ENST00000302850.5:c.2682+2T>C		p.X894_splice	ENST00000302850	NM_000208.2	894			1	2	FACETS	0.189	0.155	0.228	0.189	0.155	0.228	SUBCLONAL	1	TRUE	1	0.528862373137674	2		853	739	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17382427	17382427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	46	934	0	ENST00000359435.4:c.307G>A	p.Glu103Lys	p.E103K	ENST00000359435	NM_001033549.1	103	Gag/Aag	3/9	1	2	FACETS	0.248	0.208	0.292	0.248	0.208	0.292	SUBCLONAL	1	TRUE	1	0.528862373137674	2		934	701	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212173	36212173	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1237717780	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	154	852	3	ENST00000222270.7:c.1924C>T	p.Arg642Trp	p.R642W	ENST00000222270	NM_014727.1	642	Cgg/Tgg	3/37	1	2	FACETS	0.803	0.737	0.873	0.803	0.737	0.873	CLONAL	1	TRUE	1	0.528862373137674	2		855	725	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752817	42752817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	200	1035	1	ENST00000222329.4:c.1447C>T	p.Arg483Cys	p.R483C	ENST00000222329	NM_006494.2	483	Cgc/Tgc	4/4	1	2	FACETS	0.819	0.759	0.88	0.819	0.759	0.88	CLONAL	1	TRUE	1	0.528862373137674	2		1036	924	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753732	42753732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767011693	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	58	1025	2	ENST00000222329.4:c.532G>A	p.Ala178Thr	p.A178T	ENST00000222329	NM_006494.2	178	Gcc/Acc	4/4	1	2	FACETS	0.238	0.204	0.276	0.238	0.204	0.276	SUBCLONAL	1	TRUE	1	0.528862373137674	2		1027	921	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912486	50912486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	121	765	1	ENST00000440232.2:c.2000G>A	p.Arg667Gln	p.R667Q	ENST00000440232	NM_002691.3	667	cGg/cAg	16/27	1	2	FACETS	0.778	0.705	0.855	0.778	0.705	0.855	SUBCLONAL	1	TRUE	1	0.528862373137674	2		766	588	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912806	50912806	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1419624611	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	53	953	0	ENST00000440232.2:c.2041del	p.Leu681SerfsTer13	p.L681Sfs*13	ENST00000440232	NM_002691.3	679	gaC/ga	17/27	1	2	FACETS	0.25	0.213	0.292	0.25	0.213	0.292	SUBCLONAL	1	TRUE	1	0.528862373137674	2		953	801	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967200	25967200	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	38	365	0	ENST00000435504.4:c.2006C>T	p.Ala669Val	p.A669V	ENST00000435504		669	gCa/gTa	13/13	1	2	FACETS	0.53	0.441	0.629	0.53	0.441	0.629	SUBCLONAL	1	TRUE	1	0.528862373137674	2		365	271	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560946	9560946	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	43	463	0	ENST00000353224.5:c.836A>G	p.Gln279Arg	p.Q279R	ENST00000353224	NM_177990.2	279	cAg/cGg	4/10	1	2	FACETS	0.463	0.389	0.545	0.463	0.389	0.545	SUBCLONAL	1	TRUE	1	0.528862373137674	2		463	351	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030853	36030853	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	27	435	0	ENST00000358208.4:c.1132G>A	p.Ala378Thr	p.A378T	ENST00000358208		378	Gcg/Acg	10/12	1	2	FACETS	0.244	0.194	0.302	0.244	0.194	0.302	SUBCLONAL	1	TRUE	1	0.528862373137674	2		435	418	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521688	89521688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1410875132	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	105	597	0	ENST00000336596.2:c.2765G>A	p.Gly922Asp	p.G922D	ENST00000336596	NM_005233.5	922	gGt/gAt	16/17	1	2	FACETS	0.767	0.689	0.848	0.767	0.689	0.848	SUBCLONAL	1	TRUE	1	0.528862373137674	2		597	518	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670255	134670255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1426484610	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	39	756	0	ENST00000398015.3:c.166C>T	p.Arg56Cys	p.R56C	ENST00000398015	NM_004441.4	56	Cgc/Tgc	3/16	1	2	FACETS	0.211	0.174	0.253	0.211	0.174	0.253	SUBCLONAL	1	TRUE	1	0.528862373137674	2		756	698	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1962829	1962829	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	68	659	1	ENST00000382891.5:c.3323A>T	p.His1108Leu	p.H1108L	ENST00000382891	NM_133335.3	1108	cAc/cTc	18/22	1	2	FACETS	0.403	0.35	0.46	0.403	0.35	0.46	SUBCLONAL	1	TRUE	1	0.528862373137674	2		660	638	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523731	176523731	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	71	943	0	ENST00000292408.4:c.2147del	p.Pro716GlnfsTer6	p.P716Qfs*6	ENST00000292408	NM_213647.1	714	tgC/tg	16/18	1	2	FACETS	0.362	0.315	0.412	0.362	0.315	0.412	SUBCLONAL	1	TRUE	1	0.528862373137674	2		943	742	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043368	180043368	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	94	688	0	ENST00000261937.6:c.3218G>A	p.Ser1073Asn	p.S1073N	ENST00000261937	NM_182925.4	1073	aGt/aAt	23/30	1	2	FACETS	0.517	0.46	0.578	0.517	0.46	0.578	SUBCLONAL	1	TRUE	1	0.528862373137674	2		688	687	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112035595	112035595	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	60	728	0	ENST00000368678.4:c.299A>G	p.Asp100Gly	p.D100G	ENST00000368678		100	gAc/gGc	4/13	1	2	FACETS	0.402	0.346	0.462	0.402	0.346	0.462	SUBCLONAL	1	TRUE	1	0.528862373137674	2		728	565	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0019200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	166	708	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.271486858259519	2		708	992	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440860	52440869	+	frameshift_variant	Frame_Shift_Del	DEL	CCGATACGCT	CCGATACGCT	-	novel	NA	P-0019200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	99	805	0	ENST00000460680.1:c.635_644del	p.Glu212AlafsTer16	p.E212Afs*16	ENST00000460680	NM_004656.3	212	gAGCGTATCGGc/gc	8/17	0.271486858259519	1	FACETS	0.952	0.851	1	0.952	0.851	1	CLONAL	1	TRUE	0	0.271486858259519	1		805	662	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737064	145737064	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs781543298	NA	P-0019200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	106	621	0	ENST00000428558.2:c.3502G>C	p.Gly1168Arg	p.G1168R	ENST00000428558	NM_004260.3	1168	Gga/Cga	21/22	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.271486858259519	2		621	591	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0121509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	147	736	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	NA	1	0.666901983505352	2		736	426	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106071	27106071	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	204	680	0	ENST00000324856.7:c.5682G>T	p.Gln1894His	p.Q1894H	ENST00000324856	NM_006015.4	1894	caG/caT	20/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	NA	1	0.666901983505352	2		680	562	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209265	133209265	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	47	1021	0	ENST00000320574.5:c.6121G>T	p.Val2041Phe	p.V2041F	ENST00000320574	NM_006231.2	2041	Gtc/Ttc	44/49	1	2	FACETS	0.18	0.151	0.212	0.18	0.151	0.212	SUBCLONAL	1	NA	1	0.666901983505352	2		1021	782	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443697	29443697	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs281864719	NA	P-0121509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	220	696	0	ENST00000389048.3:c.3520T>G	p.Phe1174Val	p.F1174V	ENST00000389048	NM_004304.4	1174	Ttc/Gtc	23/29	0.64519662158502	3	FACETS	1	0.969	1	0.534	0.498	0.571	CLONAL	1	NA	1	0.666901983505352	3		696	824	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0019202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	29	642	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	1	2	FACETS	1	0.821	1	1	0.821	1	CLONAL	1	TRUE	1	0.13	2		642	435	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0019202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	18	1022	0	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	1	2	FACETS	0.615	0.462	0.798	0.615	0.462	0.798	SUBCLONAL	1	TRUE	1	0.13	2		1022	450	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159750	20159750	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	11	413	0	ENST00000379607.5:c.9G>C	p.Lys3Asn	p.K3N	ENST00000379607	NM_001412.3	3	aaG/aaC	1/7	1	1	FACETS	1	0.813	1	1	0.813	1	CLONAL	1	TRUE	0	0.13	1		413	125	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955457	48955457	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778640	NA	P-0019202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	18	617	0	ENST00000267163.4:c.1573G>A	p.Ala525Thr	p.A525T	ENST00000267163	NM_000321.2	525	Gcc/Acc	17/27	1	2	FACETS	0.929	0.7	1	0.929	0.7	1	CLONAL	1	TRUE	1	0.13	2		617	298	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172396	108172396	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	149	517	0	ENST00000278616.4:c.5199del	p.Val1734LeufsTer4	p.V1734Lfs*4	ENST00000278616	NM_000051.3	1733	gcT/gc	35/63	0.404991241265108	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	0	0.404991241265108	2		517	368	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219343	1219372	+	inframe_deletion	In_Frame_Del	DEL	GCGTGTGTGGCATGCAGGAAATGCTGGACA	GCGTGTGTGGCATGCAGGAAATGCTGGACA	-	novel	NA	P-0019203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	141	827	0	ENST00000326873.7:c.400_429del	p.Cys134_Val143del	p.C134_V143del	ENST00000326873	NM_000455.4	132	tGCGTGTGTGGCATGCAGGAAATGCTGGACAgc/tgc	3/10	0.404991241265108	2	FACETS	1	0.98	1	0.615	0.563	0.669	CLONAL	1	TRUE	0	0.404991241265108	2		827	566	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0019206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	241	918	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.594524370473503	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.594524370473503	2		918	388	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913396	NA	P-0019206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	94	445	0	ENST00000349496.5:c.95A>G	p.Asp32Gly	p.D32G	ENST00000349496	NM_001904.3	32	gAc/gGc	3/15	0.594524370473503	2	FACETS	0.95	0.854	1	0.475	0.427	0.525	CLONAL	1	TRUE	0	0.594524370473503	2		445	333	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207146	1207146	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	629	1292	0	ENST00000326873.7:c.234G>T	p.Lys78Asn	p.K78N	ENST00000326873	NM_000455.4	78	aaG/aaT	1/10	NA	2	FACETS	0.968	0.938	0.998			1	INDETERMINATE	2	TRUE	NA	0.594524370473503	2		1292	1093	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074115	8074115	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	93	419	0	ENST00000377482.5:c.544C>A	p.Leu182Ile	p.L182I	ENST00000377482	NM_018948.3	182	Ctt/Att	4/4	0.594524370473503	2	FACETS	0.984	0.884	1	0.492	0.442	0.544	CLONAL	1	TRUE	0	0.594524370473503	2		419	318	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137339	64137339	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	471	819	2	ENST00000334205.4:c.1771G>T	p.Asp591Tyr	p.D591Y	ENST00000334205	NM_003942.2	591	Gac/Tac	14/17	0.594524370473503	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.594524370473503	3		821	1013	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204739	94204739	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0019206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	60	432	0	ENST00000323929.3:c.845+1G>T		p.X282_splice	ENST00000323929	NM_005591.3	282			0.594524370473503	3	FACETS	1	0.945	1	0.579	0.506	0.657	CLONAL	1	TRUE	1	0.594524370473503	3		432	226	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134241	11134241	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	449	810	0	ENST00000358026.2:c.2907C>A	p.His969Gln	p.H969Q	ENST00000358026	NM_001128849.1	969	caC/caA	20/36	0.594524370473503	2	FACETS	0.999	0.963	1	0.999	0.963	1	CLONAL	2	TRUE	0	0.594524370473503	2		810	756	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753199	57753199	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	124	348	0	ENST00000274289.3:c.817A>T	p.Met273Leu	p.M273L	ENST00000274289	NM_006622.3	273	Atg/Ttg	7/14	0.594524370473503	3	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	1	0.594524370473503	3		348	262	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444428	50444428	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	239	521	0	ENST00000331340.3:c.358G>T	p.Asp120Tyr	p.D120Y	ENST00000331340	NM_006060.4	120	Gat/Tat	4/8	0.160565510328355	6	FACETS	0.87	0.817	0.925	0.87	0.817	0.925	INDETERMINATE	3	TRUE	3	0.594524370473503	6		521	674	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89883017	89883017	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1246636933	NA	P-0019212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	113	321	0	ENST00000389301.3:c.7G>C	p.Asp3His	p.D3H	ENST00000389301	NM_000135.2	3	Gac/Cac	1/43	0.00749027562022153	3	FACETS	1	0.971	1			1	INDETERMINATE	2	TRUE	NA	0.230092648465939	3		321	463	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877980	151877980	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs373237480	NA	P-0019212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	67	334	1	ENST00000262189.6:c.6965T>C	p.Val2322Ala	p.V2322A	ENST00000262189	NM_170606.2	2322	gTt/gCt	36/59	0.195421784874631	4	FACETS	0.918	0.802	1	0.918	0.802	1	CLONAL	2	TRUE	2	0.230092648465939	4		335	390	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89883017	89883017	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1246636933	NA	P-0019212-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	32	321	0	ENST00000389301.3:c.7G>C	p.Asp3His	p.D3H	ENST00000389301	NM_000135.2	3	Gac/Cac	1/43	0.3	1	FACETS	0.732	0.597	0.884	0.732	0.597	0.884	SUBCLONAL	1	TRUE	0	0.27	1		321	280	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877980	151877980	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs373237480	NA	P-0019212-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	24	334	1	ENST00000262189.6:c.6965T>C	p.Val2322Ala	p.V2322A	ENST00000262189	NM_170606.2	2322	gTt/gCt	36/59	1	2	FACETS	0.552	0.433	0.689	0.552	0.433	0.689	SUBCLONAL	1	TRUE	1	0.27	2		335	322	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374945	45374945	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019212-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	128	732	0	ENST00000262160.6:c.898G>C	p.Asp300His	p.D300H	ENST00000262160	NM_005901.5	300	Gat/Cat	8/11	0.465331799183674	1	FACETS	0.761	0.693	0.832	0.761	0.693	0.832	SUBCLONAL	1	TRUE	0	0.478293022467632	1		732	535	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105946	27105946	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019212-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	82	521	0	ENST00000324856.7:c.5557G>A	p.Glu1853Lys	p.E1853K	ENST00000324856	NM_006015.4	1853	Gag/Aag	20/20	1	2	FACETS	0.73	0.646	0.819	0.73	0.646	0.819	SUBCLONAL	1	TRUE	1	0.478293022467632	2		521	470	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458949	120458949	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019212-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	139	864	0	ENST00000256646.2:c.6396G>C	p.Lys2132Asn	p.K2132N	ENST00000256646	NM_024408.3	2132	aaG/aaC	34/34	0.469991249602304	1	FACETS	0.862	0.789	0.937	0.862	0.789	0.937	CLONAL	1	TRUE	0	0.478293022467632	1		864	513	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56871519	56871519	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0019212-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	101	468	0	ENST00000308159.5:c.1900-1G>C		p.X634_splice	ENST00000308159	NM_014669.4	634			1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.478293022467632	2		468	401	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271910	15271910	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1439092728	NA	P-0019212-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	122	1080	1	ENST00000263388.2:c.6529C>A	p.Pro2177Thr	p.P2177T	ENST00000263388	NM_000435.2	2177	Cca/Aca	33/33	1	2	FACETS	0.797	0.722	0.876	0.797	0.722	0.876	SUBCLONAL	1	TRUE	1	0.478293022467632	2		1081	640	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18276981	18276981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019212-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	94	444	0	ENST00000222254.8:c.1428G>A	p.Met476Ile	p.M476I	ENST00000222254	NM_005027.3	476	atG/atA	12/16	1	2	FACETS	0.985	0.883	1	0.985	0.883	1	CLONAL	1	TRUE	1	0.478293022467632	2		444	399	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098854	47098854	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019212-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	125	1003	0	ENST00000409792.3:c.6420G>C	p.Gln2140His	p.Q2140H	ENST00000409792	NM_014159.6	2140	caG/caC	15/21	1	2	FACETS	0.603	0.545	0.664	0.603	0.545	0.664	SUBCLONAL	1	TRUE	1	0.478293022467632	2		1003	867	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855028	76855028	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019212-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	109	343	0	ENST00000373344.5:c.5808G>C	p.Lys1936Asn	p.K1936N	ENST00000373344	NM_000489.3	1936	aaG/aaC	25/35	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.478293022467632	1		343	270	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443757	52443757	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1208026193	NA	P-0019213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	58	741	0	ENST00000460680.1:c.40C>T	p.Leu14Phe	p.L14F	ENST00000460680	NM_004656.3	14	Ctc/Ttc	2/17	0.277051460269967	1	FACETS	0.742	0.639	0.855	0.742	0.639	0.855	SUBCLONAL	1	TRUE	0	0.277051460269967	1		741	486	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601363	28601369	+	frameshift_variant	Frame_Shift_Del	DEL	ATCAAGT	ATCAAGT	-	novel	NA	P-0019213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	38	691	0	ENST00000241453.7:c.2063_2069del	p.Tyr688PhefsTer14	p.Y688Ffs*14	ENST00000241453	NM_004119.2	688	tACTTGATt/tt	17/24	1	2	FACETS	0.497	0.41	0.594	0.497	0.41	0.594	SUBCLONAL	1	TRUE	1	0.277051460269967	2		691	552	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682407	52682408	+	missense_variant	Missense_Mutation	DNP	CG	CG	GA	novel	NA	P-0019213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	91	626	4	ENST00000394830.3:c.765_766delinsTC	p.Ala256Pro	p.A256P	ENST00000394830	NM_018313.4	255	ctCGca/ctTCca	8/30	0.277051460269967	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.277051460269967	1		630	489	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772727	135772741	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTCCTCTGAAAGAT	TGTCCTCTGAAAGAT	GAAAGG	novel	NA	P-0019213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	94	600	2	ENST00000298552.3:c.2814-9_2819delinsCCTTTC		p.X938_splice	ENST00000298552	NM_001162426.1	938		22/23	0.277051460269967	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.277051460269967	1		602	521	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001524	150001524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	277	683	0	ENST00000253339.5:c.2080C>T	p.Arg694Cys	p.R694C	ENST00000253339		694	Cgt/Tgt	4/7	0.70496522635793	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.705552189835543	1		683	498	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984774	11984774	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	291	643	0	ENST00000353533.5:c.322del	p.Ile108LeufsTer20	p.I108Lfs*20	ENST00000353533	NM_003010.3	107	gAa/ga	3/11	0.705552189835543	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.705552189835543	1		643	528	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241679	55241681	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	rs397517086	NA	P-0019215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	312	733	0	ENST00000275493.2:c.2127_2129del	p.Glu709_Thr710delinsAsp	p.E709_T710delinsD	ENST00000275493	NM_005228.3	709	gaAACt/gat	18/28	0.354399552393754	3	FACETS	0.983	0.928	1	0.983	0.928	1	CLONAL	2	TRUE	1	0.354399552393754	3		733	1054	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935595	13935595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776609162	NA	P-0019215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	83	420	0	ENST00000405192.2:c.1261G>A	p.Glu421Lys	p.E421K	ENST00000405192	NM_001163147.1	421	Gag/Aag	12/12	0.354399552393754	3	FACETS	0.858	0.757	0.965	0.429	0.378	0.483	CLONAL	1	TRUE	1	0.354399552393754	3		420	643	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220546	1220578	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	GGCACTCCCTGAGGGCTGCACGGCACCGCCACA	GGCACTCCCTGAGGGCTGCACGGCACCGCCACA	-	novel	NA	P-0019215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	153	555	0	ENST00000326873.7:c.598-28_602del		p.X200_splice	ENST00000326873	NM_000455.4	200			0.354399552393754	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.354399552393754	1		555	620	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0019216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	388	918	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.260423349214704	3	FACETS	0.893	0.852	0.934			1	CLONAL	4	TRUE	NA	0.271068564551841	3		918	910	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0019216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	150	717	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.271068564551841	1	FACETS	0.841	0.772	0.912	1	0.99	1	CLONAL	2	TRUE	0	0.271068564551841	1		718	569	SUCCESS
APC	324	MSKCC	GRCh37	5	112174096	112174096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs137854575	NA	P-0019216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	87	493	0	ENST00000257430.4:c.2805C>A	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	taC/taA	16/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.271068564551841	2		493	560	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544155	18544155	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs774380325	NA	P-0019216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	318	719	0	ENST00000266497.5:c.1972G>T	p.Ala658Ser	p.A658S	ENST00000266497		658	Gcc/Tcc	13/31	0.271068564551841	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	4	TRUE	0	0.271068564551841	4		719	727	SUCCESS
APC	324	MSKCC	GRCh37	5	112175672	112175672	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	119	619	2	ENST00000257430.4:c.4381G>T	p.Glu1461Ter	p.E1461*	ENST00000257430	NM_000038.5	1461	Gaa/Taa	16/16	1	2	FACETS	0.75	0.679	0.825	1	0.985	1	SUBCLONAL	2	TRUE	1	0.271068564551841	2		621	585	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27228229	27228229	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757379347	NA	P-0019216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	270	835	0	ENST00000380036.4:c.3226C>T	p.Arg1076Trp	p.R1076W	ENST00000380036	NM_000459.3	1076	Cgg/Tgg	22/23	0.225513913493318	2	FACETS	0.851	0.802	0.902	1	0.991	1	CLONAL	3	TRUE	0	0.271068564551841	2		835	780	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0019217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	87	581	0	ENST00000269305.4:c.782+1G>C		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.330687194980665	0	FACETS	0.74	0.679	0.8			1	SUBCLONAL	3	TRUE	0	0.346106644945499	0		581	148	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198262738	198262738	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	109	725	2	ENST00000335508.6:c.3237C>A	p.Asn1079Lys	p.N1079K	ENST00000335508	NM_012433.2	1079	aaC/aaA	22/25	0.348991033343911	4	FACETS	1	0.956	1	0.28	0.251	0.311	CLONAL	1	TRUE	0	0.346106644945499	4		727	757	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713421	40713421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199947379	NA	P-0019217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	28	770	0	ENST00000373198.4:c.4094C>T	p.Thr1365Met	p.T1365M	ENST00000373198	NM_133170.3	1365	aCg/aTg	30/32	0.348991033343911	1	FACETS	0.408	0.326	0.501	0.408	0.326	0.501	SUBCLONAL	1	TRUE	0	0.346106644945499	1		770	328	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47061251	47061265	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TCTTTTCTGAATACT	TCTTTTCTGAATACT	-	novel	NA	P-0019217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	119	586	0	ENST00000409792.3:c.7416_7430del	p.Val2473_Glu2477del	p.V2473_E2477del	ENST00000409792	NM_014159.6	2472	gaAGTATTCAGAAAAGAg/gag	19/21	0.348991033343911	1	FACETS	1	0.958	1	1	0.991	1	CLONAL	2	TRUE	0	0.346106644945499	1		586	267	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623232	52623232	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	131	447	0	ENST00000394830.3:c.2819del	p.Leu940ProfsTer68	p.L940Pfs*68	ENST00000394830	NM_018313.4	940	cTc/cc	19/30	0.348991033343911	1	FACETS	0.944	0.881	1	1	0.993	1	CLONAL	3	TRUE	0	0.346106644945499	1		447	221	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0019222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	214	763	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.529803962909505	1	FACETS	0.905	0.846	0.966	0.905	0.846	0.966	CLONAL	1	TRUE	0	0.529803962909505	1		764	656	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0019222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	25	493	2	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	0.529803962909505	1	FACETS	0.175	0.137	0.218	0.175	0.137	0.218	SUBCLONAL	1	TRUE	0	0.529803962909505	1		495	397	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367257	50367257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1245618829	NA	P-0019222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	34	471	0	ENST00000331340.3:c.64G>A	p.Asp22Asn	p.D22N	ENST00000331340	NM_006060.4	22	Gat/Aat	3/8	1	2	FACETS	0.27	0.22	0.326	0.27	0.22	0.326	SUBCLONAL	1	TRUE	1	0.529803962909505	2		471	476	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073616	8073616	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	35	398	1	ENST00000377482.5:c.1043del	p.Pro348ArgfsTer104	p.P348Rfs*104	ENST00000377482	NM_018948.3	348	cCg/cg	4/4	1	2	FACETS	0.346	0.283	0.416	0.346	0.283	0.416	SUBCLONAL	1	TRUE	1	0.529803962909505	2		399	382	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211539	98211539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772537644	NA	P-0019222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	108	532	1	ENST00000331920.6:c.3616C>T	p.Arg1206Cys	p.R1206C	ENST00000331920	NM_000264.3	1206	Cgc/Tgc	22/24	1	2	FACETS	0.888	0.802	0.979	0.888	0.802	0.979	CLONAL	1	TRUE	1	0.529803962909505	2		533	459	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578235	226578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	58	727	0	ENST00000366794.5:c.493A>G	p.Lys165Glu	p.K165E	ENST00000366794	NM_001618.3	165	Aag/Gag	4/23	0.455152786305901	4	FACETS	0.341	0.292	0.395	0.114	0.097	0.132	SUBCLONAL	1	TRUE	1	0.529803962909505	4		727	982	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279386	38279386	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	80	1058	0	ENST00000425967.3:c.1103G>C	p.Gly368Ala	p.G368A	ENST00000425967	NM_001174067.1	368	gGg/gCg	9/19	0.487533680690026	3	FACETS	0.299	0.262	0.34			1	SUBCLONAL	1	TRUE	NA	0.529803962909505	3		1058	1276	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872129	76872129	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	93	744	0	ENST00000373344.5:c.5518A>T	p.Thr1840Ser	p.T1840S	ENST00000373344	NM_000489.3	1840	Act/Tct	22/35	1	2	FACETS	0.742	0.663	0.826	0.742	0.663	0.826	SUBCLONAL	1	TRUE	1	0.529803962909505	2		744	473	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0019226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	303	860	0				ENST00000310581	NM_198253.2	-/1132			0.516935104806784	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.516935104806784	3		860	704	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405045	405045	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377483798	NA	P-0019226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	171	547	1	ENST00000380956.4:c.1127G>A	p.Arg376His	p.R376H	ENST00000380956	NM_001195286.1	376	cGc/cAc	8/9	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.516935104806784	2		548	644	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0019226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	73	677	0	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	0.243684716796667	1	FACETS	0.332	0.29	0.378	0.332	0.29	0.378	INDETERMINATE	1	TRUE	0	0.516935104806784	1		677	630	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424714	47424714	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	263	434	0	ENST00000377045.4:c.526del	p.Leu176Ter	p.L176*	ENST00000377045	NM_001654.4	174	cgC/cg	6/16	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.516935104806784	1		434	538	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412575	63412575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774927630	NA	P-0019226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	179	272	0	ENST00000330258.3:c.592G>A	p.Glu198Lys	p.E198K	ENST00000330258	NM_152424.3	198	Gag/Aag	2/2	1	1	FACETS	0.785	0.738	0.832	1	0.993	1	SUBCLONAL	2	TRUE	0	0.516935104806784	1		272	327	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0019231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	37	729	4	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.403	0.331	0.484	0.403	0.331	0.484	SUBCLONAL	1	FALSE	1	0.274243549089728	2		733	670	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882019	NA	P-0019231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	60	836	0	ENST00000269305.4:c.455del	p.Pro152ArgfsTer18	p.P152Rfs*18	ENST00000269305	NM_001126112.2	152	cCg/cg	5/11	1	2	FACETS	0.444	0.381	0.513	0.444	0.381	0.513	SUBCLONAL	1	FALSE	1	0.274243549089728	2		836	986	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720709	89720709	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs863224909	NA	P-0019231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	21	165	0	ENST00000371953.3:c.860C>G	p.Ser287Ter	p.S287*	ENST00000371953	NM_000314.4	287	tCa/tGa	8/9	1	2	FACETS	0.754	0.584	0.952	0.754	0.584	0.952	CLONAL	1	FALSE	1	0.274243549089728	2		165	203	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164711	47164711	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201984344	NA	P-0019231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	19	299	1	ENST00000409792.3:c.1415G>A	p.Arg472His	p.R472H	ENST00000409792	NM_014159.6	472	cGt/cAt	3/21	1	2	FACETS	0.393	0.297	0.505	0.393	0.297	0.505	SUBCLONAL	1	FALSE	1	0.274243549089728	2		300	353	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098534	11098534	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1018881303	NA	P-0019231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	57	739	0	ENST00000358026.2:c.1052G>A	p.Arg351His	p.R351H	ENST00000358026	NM_001128849.1	351	cGc/cAc	6/36	1	2	FACETS	0.495	0.423	0.573	0.495	0.423	0.573	SUBCLONAL	1	FALSE	1	0.274243549089728	2		739	840	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675571	86675571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1561325048	NA	P-0019231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	29	466	2	ENST00000274376.6:c.2513del	p.Asn838MetfsTer4	p.N838Mfs*4	ENST00000274376	NM_002890.2	836	gAa/ga	19/25	1	2	FACETS	0.494	0.396	0.606	0.494	0.396	0.606	SUBCLONAL	1	FALSE	1	0.274243549089728	2		468	428	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273974	10273974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773569899	NA	P-0019231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	52	881	2	ENST00000330684.3:c.295G>A	p.Val99Met	p.V99M	ENST00000330684	NM_001134407.1	99	Gtg/Atg	2/13	1	2	FACETS	0.409	0.347	0.477	0.409	0.347	0.477	SUBCLONAL	1	FALSE	1	0.274243549089728	2		883	928	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692895	89692895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781255	NA	P-0019231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	42	494	0	ENST00000371953.3:c.379G>A	p.Gly127Arg	p.G127R	ENST00000371953	NM_000314.4	127	Gga/Aga	5/9	1	2	FACETS	0.648	0.541	0.766	0.648	0.541	0.766	SUBCLONAL	1	FALSE	1	0.274243549089728	2		494	473	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291062	15291062	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371525707	NA	P-0019231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	62	961	4	ENST00000263388.2:c.3148C>T	p.Arg1050Trp	p.R1050W	ENST00000263388	NM_000435.2	1050	Cgg/Tgg	20/33	1	2	FACETS	0.417	0.359	0.481	0.417	0.359	0.481	SUBCLONAL	1	FALSE	1	0.274243549089728	2		965	1084	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060912	38060912	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	24	390	0	ENST00000250448.2:c.1077del	p.Ile360Ter	p.I360*	ENST00000250448	NM_004496.3	359	ccC/cc	2/2	1	2	FACETS	0.516	0.405	0.645	0.516	0.405	0.645	SUBCLONAL	1	FALSE	1	0.274243549089728	2		390	339	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942053	71942053	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	74	938	0	ENST00000298229.2:c.1322del	p.Asn441ThrfsTer2	p.N441Tfs*2	ENST00000298229	NM_001567.3	439	ccA/cc	12/28	1	2	FACETS	0.548	0.479	0.624	0.548	0.479	0.624	SUBCLONAL	1	FALSE	1	0.274243549089728	2		938	984	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057887	27057896	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCATACCC	CTCCATACCC	-	novel	NA	P-0019231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	53	856	0	ENST00000324856.7:c.1599_1608del	p.Tyr534SerfsTer82	p.Y534Sfs*82	ENST00000324856	NM_006015.4	532	gCTCCATACCCc/gc	3/20	1	2	FACETS	0.415	0.353	0.484	0.415	0.353	0.484	SUBCLONAL	1	FALSE	1	0.274243549089728	2		856	931	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059207	27059207	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	51	608	0	ENST00000324856.7:c.1848del	p.Ser617GlnfsTer2	p.S617Qfs*2	ENST00000324856	NM_006015.4	615	gCc/gc	4/20	1	2	FACETS	0.549	0.466	0.641	0.549	0.466	0.641	SUBCLONAL	1	FALSE	1	0.274243549089728	2		608	677	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406573	70406573	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	77	820	0	ENST00000373644.4:c.4087G>T	p.Gly1363Ter	p.G1363*	ENST00000373644	NM_030625.2	1363	Gga/Tga	4/12	1	2	FACETS	0.63	0.551	0.714	0.63	0.551	0.714	SUBCLONAL	1	FALSE	1	0.274243549089728	2		820	892	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589675	69589675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	10	171	0	ENST00000168712.1:c.178G>A	p.Val60Met	p.V60M	ENST00000168712	NM_002007.2	60	Gtg/Atg	1/3	1	2	FACETS	0.483	0.328	0.677	0.483	0.328	0.677	SUBCLONAL	1	FALSE	1	0.274243549089728	2		171	151	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134476	2134476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369164761	NA	P-0019231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	51	1082	0	ENST00000219476.3:c.4253C>T	p.Ser1418Leu	p.S1418L	ENST00000219476	NM_000548.3	1418	tCa/tTa	34/42	1	2	FACETS	0.463	0.392	0.541	0.463	0.392	0.541	SUBCLONAL	1	FALSE	1	0.274243549089728	2		1082	803	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134473	30134473	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	44	581	0	ENST00000263025.4:c.58del	p.Val20SerfsTer12	p.V20Sfs*12	ENST00000263025	NM_002746.2	20	Gtc/tc	1/9	1	2	FACETS	0.507	0.424	0.599	0.507	0.424	0.599	SUBCLONAL	1	FALSE	1	0.274243549089728	2		581	633	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650767	67650767	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	45	569	0	ENST00000264010.4:c.1072T>G	p.Tyr358Asp	p.Y358D	ENST00000264010	NM_006565.3	358	Tac/Gac	5/12	1	2	FACETS	0.424	0.355	0.501	0.424	0.355	0.501	SUBCLONAL	1	FALSE	1	0.274243549089728	2		569	774	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993168	72993168	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1204366489	NA	P-0019231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	51	889	0	ENST00000268489.5:c.877T>C	p.Tyr293His	p.Y293H	ENST00000268489	NM_006885.3	293	Tac/Cac	2/10	1	2	FACETS	0.384	0.325	0.45	0.384	0.325	0.45	SUBCLONAL	1	FALSE	1	0.274243549089728	2		889	968	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793054	33793056	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs747773004	NA	P-0019231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	33	469	2	ENST00000498907.2:c.265_267del	p.Glu89del	p.E89del	ENST00000498907	NM_004364.3	89	GAG/-	1/1	1	2	FACETS	0.525	0.427	0.636	0.525	0.427	0.636	SUBCLONAL	1	FALSE	1	0.274243549089728	2		471	458	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211899	36211899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	74	1095	6	ENST00000222270.7:c.1656del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	550	gaC/ga	3/37	1	2	FACETS	0.43	0.375	0.49	0.43	0.375	0.49	SUBCLONAL	1	FALSE	1	0.274243549089728	2		1101	1254	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262581	39262581	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs397517180	NA	P-0019231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	65	852	0	ENST00000402219.2:c.925G>T	p.Asp309Tyr	p.D309Y	ENST00000402219	NM_005633.3	309	Gat/Tat	7/23	1	2	FACETS	0.61	0.528	0.699	0.61	0.528	0.699	SUBCLONAL	1	FALSE	1	0.274243549089728	2		852	777	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45649972	45649972	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	33	556	0	ENST00000407780.3:c.863G>A	p.Gly288Asp	p.G288D	ENST00000407780	NM_001283052.1	288	gGt/gAt	6/7	1	2	FACETS	0.459	0.373	0.557	0.459	0.373	0.557	SUBCLONAL	1	FALSE	1	0.274243549089728	2		556	524	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928630	49928630	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	34	542	0	ENST00000296474.3:c.3644T>C	p.Met1215Thr	p.M1215T	ENST00000296474	NM_002447.2	1215	aTg/aCg	17/20	1	2	FACETS	0.38	0.31	0.46	0.38	0.31	0.46	SUBCLONAL	1	FALSE	1	0.274243549089728	2		542	652	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753328	57753328	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	46	522	1	ENST00000274289.3:c.796C>A	p.Leu266Met	p.L266M	ENST00000274289	NM_006622.3	266	Ctg/Atg	6/14	1	2	FACETS	0.598	0.503	0.703	0.598	0.503	0.703	SUBCLONAL	1	FALSE	1	0.274243549089728	2		523	561	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410444	63410444	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	39	638	0	ENST00000330258.3:c.2723A>T	p.Asn908Ile	p.N908I	ENST00000330258	NM_152424.3	908	aAt/aTt	2/2	1	2	FACETS	0.49	0.406	0.585	0.49	0.406	0.585	SUBCLONAL	1	FALSE	1	0.274243549089728	2		638	580	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230746	46230746	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	117	463	0	ENST00000334344.6:c.996del	p.Asp333ThrfsTer3	p.D333Tfs*3	ENST00000334344	NM_152641.2	332	cTt/ct	8/21	1	2	FACETS	0.954	0.863	1	0.954	0.863	1	CLONAL	1	TRUE	1	0.424361310440789	2		463	578	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170351	119170351	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	115	527	0	ENST00000264033.4:c.2581A>T	p.Ile861Phe	p.I861F	ENST00000264033	NM_005188.3	861	Atc/Ttc	16/16	1	2	FACETS	0.943	0.852	1	0.943	0.852	1	CLONAL	1	TRUE	1	0.424361310440789	2		527	575	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40491424	40491424	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	178	811	0	ENST00000264657.5:c.376G>A	p.Gly126Arg	p.G126R	ENST00000264657	NM_139276.2	126	Ggg/Agg	5/24	1	2	FACETS	0.923	0.851	0.998	0.923	0.851	0.998	CLONAL	1	TRUE	1	0.424361310440789	2		811	909	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70001022	70001022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	66	577	0	ENST00000394351.3:c.619G>A	p.Asp207Asn	p.D207N	ENST00000394351	NM_000248.3	207	Gac/Aac	6/9	1	2	FACETS	0.928	0.808	1	0.928	0.808	1	CLONAL	1	TRUE	1	0.305835968327104	2		577	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0019234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	107	1015	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.206347340312714	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.206347340312714	1		1017	814	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374361	81374361	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1476385169	NA	P-0019234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	80	703	1	ENST00000222390.5:c.701G>A	p.Arg234His	p.R234H	ENST00000222390	NM_000601.4	234	cGc/cAc	6/18	0.194157871180771	3	FACETS	1	0.972	1	0.69	0.608	0.778	CLONAL	1	TRUE	1	0.206347340312714	3		704	620	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546122	29546122	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs894292181	NA	P-0019234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	64	582	0	ENST00000356175.3:c.1627C>T	p.Gln543Ter	p.Q543*	ENST00000356175	NM_000267.3	543	Cag/Tag	14/57	0.206347340312714	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.206347340312714	1		582	494	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796784	42796784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746217053	NA	P-0019234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	97	1099	3	ENST00000575354.2:c.3242C>T	p.Pro1081Leu	p.P1081L	ENST00000575354	NM_015125.3	1081	cCg/cTg	14/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.206347340312714	2		1102	851	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324164	62324164	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	38	764	0	ENST00000360203.5:c.2659C>A	p.Pro887Thr	p.P887T	ENST00000360203	NM_001283009.1	887	Ccc/Acc	29/35	0.206347340312714	5	FACETS	0.734	0.605	0.879	0.184	0.151	0.22	SUBCLONAL	1	TRUE	1	0.206347340312714	5		764	657	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983434	90983434	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	57	627	0	ENST00000265433.3:c.669del	p.Thr226HisfsTer5	p.T226Hfs*5	ENST00000265433	NM_002485.4	223	aaA/aa	6/16	0.206347340312714	5	FACETS	0.915	0.783	1	0.183	0.156	0.212	CLONAL	1	TRUE	0	0.206347340312714	5		627	791	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995575	68995575	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0019235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	132	579	0	ENST00000288368.4:c.1979T>A	p.Leu660Ter	p.L660*	ENST00000288368	NM_024870.2	660	tTa/tAa	18/40	0.506903917078223	3	FACETS	0.526	0.476	0.578	0.263	0.238	0.289	SUBCLONAL	1	TRUE	1	0.665847946176894	3		579	1005	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0019236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	169	860	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.895756726288912	2		860	358	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0019236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	78	290	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	0.895756726288912	2		291	168	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799059	42799059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	139	418	1	ENST00000575354.2:c.4543C>T	p.Arg1515Cys	p.R1515C	ENST00000575354	NM_015125.3	1515	Cgc/Tgc	20/20	0.895756726288912	1	FACETS	0.497	0.458	0.536	0.497	0.458	0.536	SUBCLONAL	1	TRUE	0	0.895756726288912	1		419	345	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0019238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	201	822	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.417356021624911	2		822	903	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0019238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	90	447	1	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	0.985	0.878	1	0.985	0.878	1	CLONAL	1	TRUE	1	0.417356021624911	2		448	438	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098803	178098803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	176	891	0	ENST00000397062.3:c.242G>A	p.Gly81Asp	p.G81D	ENST00000397062	NM_006164.4	81	gGt/gAt	2/5	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.417356021624911	2		891	807	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88672106	88672106	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1305429176	NA	P-0019238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	125	602	0	ENST00000372037.3:c.640C>A	p.Gln214Lys	p.Q214K	ENST00000372037	NM_004329.2	214	Caa/Aaa	8/13	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.417356021624911	2		602	545	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692971	89692971	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1554898197	NA	P-0019238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	163	784	0	ENST00000371953.3:c.455T>C	p.Leu152Pro	p.L152P	ENST00000371953	NM_000314.4	152	cTa/cCa	5/9	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.417356021624911	2		784	713	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717693	89717714	+	frameshift_variant	Frame_Shift_Del	DEL	TACTTTGAGTTCCCTCAGCCGT	TACTTTGAGTTCCCTCAGCCGT	-	novel	NA	P-0019238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	113	771	0	ENST00000371953.3:c.721_742del	p.Phe241LeufsTer8	p.F241Lfs*8	ENST00000371953	NM_000314.4	240	TACTTTGAGTTCCCTCAGCCGTta/ta	7/9	1	2	FACETS	0.768	0.692	0.849	0.768	0.692	0.849	SUBCLONAL	1	TRUE	1	0.417356021624911	2		771	705	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498230	498230	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	58	303	2	ENST00000399788.2:c.28G>T	p.Ala10Ser	p.A10S	ENST00000399788	NM_001042603.1	10	Gcg/Tcg	1/28	1	2	FACETS	0.942	0.816	1	0.942	0.816	1	CLONAL	1	TRUE	1	0.417356021624911	2		305	295	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872210	45872210	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	170	913	0	ENST00000391945.4:c.224G>A	p.Arg75Lys	p.R75K	ENST00000391945	NM_000400.3	75	aGa/aAa	4/23	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.417356021624911	2		913	803	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561414	9561414	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	117	608	0	ENST00000353224.5:c.368del	p.Asn123MetfsTer50	p.N123Mfs*50	ENST00000353224	NM_177990.2	123	aAt/at	4/10	1	2	FACETS	0.96	0.868	1	0.96	0.868	1	CLONAL	1	TRUE	1	0.417356021624911	2		608	584	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	112	941	0	ENST00000263967.3:c.278G>C	p.Arg93Pro	p.R93P	ENST00000263967	NM_006218.2	93	cGg/cCg	2/21	1	2	FACETS	0.626	0.562	0.693	0.626	0.562	0.693	SUBCLONAL	1	TRUE	1	0.417356021624911	2		941	858	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207389	29207389	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	73	375	0	ENST00000240100.2:c.407A>G	p.Glu136Gly	p.E136G	ENST00000240100	NM_001394.6	136	gAg/gGg	1/4	1	2	FACETS	0.974	0.858	1	0.974	0.858	1	CLONAL	1	TRUE	1	0.417356021624911	2		375	359	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760183	133760183	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	117	651	0	ENST00000318560.5:c.2506G>C	p.Ala836Pro	p.A836P	ENST00000318560	NM_005157.4	836	Gct/Cct	11/11	1	2	FACETS	0.962	0.87	1	0.962	0.87	1	CLONAL	1	TRUE	1	0.417356021624911	2		651	583	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0019239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	43	734	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	1	2	FACETS	0.737	0.614	0.873	0.737	0.614	0.873	SUBCLONAL	1	TRUE	1	0.14	2		734	834	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032279	10032279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	41	593	0	ENST00000330684.3:c.544G>A	p.Glu182Lys	p.E182K	ENST00000330684	NM_001134407.1	182	Gaa/Aaa	3/13	1	2	FACETS	0.865	0.719	1	0.865	0.719	1	CLONAL	1	TRUE	1	0.14	2		593	677	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294264	1294264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377315722	NA	P-0019239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	28	641	1	ENST00000310581.5:c.737C>T	p.Pro246Leu	p.P246L	ENST00000310581	NM_198253.2	246	cCg/cTg	2/16	1	2	FACETS	0.738	0.588	0.909	0.738	0.588	0.909	CLONAL	1	TRUE	1	0.14	2		642	542	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946828	17946828	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1490183415	NA	P-0019239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	39	750	0	ENST00000458235.1:c.1819G>A	p.Ala607Thr	p.A607T	ENST00000458235	NM_000215.3	607	Gcc/Acc	14/24	1	2	FACETS	0.759	0.627	0.907	0.759	0.627	0.907	CLONAL	1	TRUE	1	0.14	2		750	734	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560989	9560989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	24	443	0	ENST00000353224.5:c.793G>A	p.Asp265Asn	p.D265N	ENST00000353224	NM_177990.2	265	Gac/Aac	4/10	1	2	FACETS	0.76	0.595	0.952	0.76	0.595	0.952	CLONAL	1	TRUE	1	0.14	2		443	451	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169953	32169953	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202197092	NA	P-0019239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	49	876	0	ENST00000375023.3:c.3655C>T	p.Arg1219Trp	p.R1219W	ENST00000375023	NM_004557.3	1219	Cgg/Tgg	21/30	0.11817650945514	3	FACETS	0.81	0.683	0.95	0.405	0.341	0.475	CLONAL	1	TRUE	1	0.14	3		876	925	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436605	8436605	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201031030	NA	P-0019239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	40	766	0	ENST00000356435.5:c.4073C>T	p.Ser1358Phe	p.S1358F	ENST00000356435		1358	tCc/tTc	24/35	1	2	FACETS	0.719	0.595	0.857	0.719	0.595	0.857	SUBCLONAL	1	TRUE	1	0.14	2		766	795	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159743	20159743	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	30	301	0	ENST00000379607.5:c.16G>A	p.Gly6Ser	p.G6S	ENST00000379607	NM_001412.3	6	Ggt/Agt	1/7	1	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.14	1		301	295	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0019240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	353	860	0				ENST00000310581	NM_198253.2	-/1132			0.616389849461974	5	FACETS	0.977	0.934	1	0.977	0.934	1	CLONAL	3	TRUE	2	0.721151926745471	5		860	695	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577546	7577547	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0019240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	484	623	2	ENST00000269305.4:c.734_735delinsTT	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGC/gTT	7/11	0.721151926745471	3	FACETS	0.929	0.903	0.955			1	CLONAL	3	TRUE	NA	0.721151926745471	3		625	655	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0019241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	96	691	5	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	1	2	FACETS	0.773	0.688	0.863	0.773	0.688	0.863	SUBCLONAL	1	TRUE	1	0.33	2		696	753	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	325	736	0				ENST00000310581	NM_198253.2	-/1132			0.450495952030058	3	FACETS	1	0.981	1	1	0.981	1	INDETERMINATE	2	TRUE	1	0.869385201588996	3		736	516	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0019242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	809	754	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	1	0.995	1	1	0.999	1	CLONAL	2	TRUE	1	0.869385201588996	2		754	909	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942817	44942817	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	438	782	1	ENST00000377967.4:c.3397C>T	p.Gln1133Ter	p.Q1133*	ENST00000377967	NM_021140.2	1133	Caa/Taa	23/29	0.869385201588996	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.869385201588996	1		783	549	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316995	11316995	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	117	364	0	ENST00000361445.4:c.499G>T	p.Ala167Ser	p.A167S	ENST00000361445	NM_004958.3	167	Gca/Tca	4/58	1	2	FACETS	0.627	0.57	0.687	0.627	0.57	0.687	SUBCLONAL	1	TRUE	1	0.869385201588996	2		364	429	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003751	45003751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765817584	NA	P-0019242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	91	390	1	ENST00000558401.1:c.7C>T	p.Arg3Cys	p.R3C	ENST00000558401	NM_004048.2	3	Cgc/Tgc	1/4	1	2	FACETS	0.417	0.371	0.465	0.417	0.371	0.465	SUBCLONAL	1	TRUE	1	0.869385201588996	2		391	502	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420186	88420186	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	279	560	0	ENST00000360948.2:c.2500T>C	p.Tyr834His	p.Y834H	ENST00000360948	NM_001012338.2	834	Tac/Cac	19/19	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.869385201588996	2		560	634	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30956900	30956901	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0019242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	148	593	1	ENST00000375687.4:c.226_227delinsTT	p.Gly76Phe	p.G76F	ENST00000375687	NM_015338.5	76	GGc/TTc	4/13	1	2	FACETS	0.437	0.399	0.476	0.437	0.399	0.476	SUBCLONAL	1	TRUE	1	0.869385201588996	2		594	780	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715698	30715699	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0019242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	72	309	2	ENST00000295754.5:c.1356_1357delinsAT	p.Val453Leu	p.V453L	ENST00000295754	NM_003242.5	452	ctGGtg/ctATtg	5/7	1	2	FACETS	0.412	0.361	0.466	0.412	0.361	0.466	SUBCLONAL	1	TRUE	1	0.869385201588996	2		311	402	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928959	49928959	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	200	771	1	ENST00000296474.3:c.3407G>T	p.Arg1136Leu	p.R1136L	ENST00000296474	NM_002447.2	1136	cGt/cTt	16/20	1	2	FACETS	0.534	0.495	0.574	0.534	0.495	0.574	SUBCLONAL	1	TRUE	1	0.869385201588996	2		772	862	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497350	149497350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1361458551	NA	P-0019242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	314	596	2	ENST00000261799.4:c.2968G>A	p.Ala990Thr	p.A990T	ENST00000261799	NM_002609.3	990	Gcc/Acc	22/23	0.392104061332102	1	FACETS	0.683	0.651	0.715	0.683	0.651	0.715	INDETERMINATE	1	TRUE	0	0.869385201588996	1		598	598	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967761	90967761	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs772909239	NA	P-0019242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	39	181	0	ENST00000265433.3:c.1147G>C	p.Glu383Gln	p.E383Q	ENST00000265433	NM_002485.4	383	Gaa/Caa	10/16	0.510536068474957	1	FACETS	0.254	0.212	0.299	0.254	0.212	0.299	INDETERMINATE	1	TRUE	0	0.869385201588996	1		181	200	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0019243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	165	697	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.730777927942872	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.729582486516837	1		697	276	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458037	120458040	+	frameshift_variant	Frame_Shift_Del	DEL	CCAG	CCAG	-	novel	NA	P-0019243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	100	505	0	ENST00000256646.2:c.7305_7308del	p.Trp2436GlnfsTer3	p.W2436Qfs*3	ENST00000256646	NM_024408.3	2435	gaCTGG/ga	34/34	0.473167234050729	4	FACETS	1	0.978	1	0.443	0.399	0.488	CLONAL	1	TRUE	1	0.729582486516837	4		505	357	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	149	736	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.887	0.821	0.955	0.887	0.821	0.955	CLONAL	1	TRUE	1	0.881674188046408	2		736	381	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36421187	36421187	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	209	594	0	ENST00000300305.3:c.10G>T	p.Asp4Tyr	p.D4Y	ENST00000300305		4	Gac/Tac	1/8	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.881674188046408	2		594	470	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589313	67589313	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0019245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	177	526	0	ENST00000274335.5:c.1299+2T>C		p.X433_splice	ENST00000274335		433			0.753391349776614	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.881674188046408	1		526	223	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513037	106513037	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765837588	NA	P-0019245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	101	323	0	ENST00000359195.3:c.2051G>A	p.Arg684His	p.R684H	ENST00000359195	NM_002649.2	684	cGt/cAt	3/11	0.881674188046408	3	FACETS	0.968	0.874	1	0.484	0.437	0.533	CLONAL	1	TRUE	1	0.881674188046408	3		323	341	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196779	123196779	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	200	317	0	ENST00000218089.9:c.1666C>T	p.Gln556Ter	p.Q556*	ENST00000218089	NM_001042749.1	556	Cag/Tag	18/35	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.881674188046408	1		317	240	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039236	49039236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	230	762	0	ENST00000267163.4:c.2314G>A	p.Ala772Thr	p.A772T	ENST00000267163	NM_000321.2	772	Gct/Act	22/27	1	2	FACETS	0.922	0.863	0.981	0.922	0.863	0.981	CLONAL	1	TRUE	1	0.705001583525096	2		762	708	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063341	67063341	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	69	572	0	ENST00000412916.2:c.31A>G	p.Lys11Glu	p.K11E	ENST00000412916		11	Aag/Gag	1/6	1	2	FACETS	0.314	0.273	0.358	0.314	0.273	0.358	SUBCLONAL	1	TRUE	1	0.705001583525096	2		572	623	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610306	10610306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	386	756	1	ENST00000171111.5:c.404G>A	p.Arg135His	p.R135H	ENST00000171111	NM_203500.1	135	cGc/cAc	2/6	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.705001583525096	2		757	1069	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442545	52442545	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	284	737	0	ENST00000460680.1:c.200del	p.Asp67ValfsTer5	p.D67Vfs*5	ENST00000460680	NM_004656.3	67	gAt/gt	4/17	0.705001583525096	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.705001583525096	1		737	477	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0019248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	112	680	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.976	0.879	1	0.976	0.879	1	CLONAL	1	TRUE	1	0.349888902897842	2		680	656	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0019248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	102	609	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.196801223702301	1	FACETS	0.867	0.777	0.961	0.867	0.777	0.961	INDETERMINATE	1	TRUE	0	0.349888902897842	1		609	555	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0019248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	123	530	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.349888902897842	2		530	667	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	72	480	1	ENST00000342988.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000342988	NM_005359.5	356	cCt/cTt	9/12	0.349888902897842	1	FACETS	0.777	0.681	0.879	0.777	0.681	0.879	SUBCLONAL	1	TRUE	0	0.349888902897842	1		481	437	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717733	89717733	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1554825235	NA	P-0019248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	239	615	0	ENST00000371953.3:c.758T>A	p.Ile253Asn	p.I253N	ENST00000371953	NM_000314.4	253	aTc/aAc	7/9	0.349888902897842	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.349888902897842	2		615	648	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213899	66213899	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	97	534	0	ENST00000273854.3:c.2531G>T	p.Trp844Leu	p.W844L	ENST00000273854	NM_004439.5	844	tGg/tTg	15/18	0.196801223702301	1	FACETS	0.785	0.701	0.873	0.785	0.701	0.873	INDETERMINATE	1	TRUE	0	0.349888902897842	1		534	583	SUCCESS
APC	324	MSKCC	GRCh37	5	112136997	112136997	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	120	531	0	ENST00000257430.4:c.751G>T	p.Glu251Ter	p.E251*	ENST00000257430	NM_000038.5	251	Gaa/Taa	8/16	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.349888902897842	2		531	631	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	533	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.192444307248175	4	FACETS	0.919	0.887	0.95			1	INDETERMINATE	3	TRUE	NA	0.707058481150828	4		555	934	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0019249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	233	661	2	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.707058481150828	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.707058481150828	1		663	405	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619279	23619279	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587776527	NA	P-0019249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	324	883	4	ENST00000261584.4:c.3256C>T	p.Arg1086Ter	p.R1086*	ENST00000261584	NM_024675.3	1086	Cga/Tga	12/13	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.707058481150828	2		887	916	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578537	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs879254214	NA	P-0019250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	767	1461	1	ENST00000269305.4:c.393_395del	p.Asn131del	p.N131del	ENST00000269305	NM_001126112.2	131	aaCAAg/aag	5/11	0.409491267714725	4	FACETS	0.9	0.873	0.927			1	CLONAL	4	FALSE	NA	0.407999416704052	4		1462	1470	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948286	31948286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	168	1018	0	ENST00000375333.2:c.874G>A	p.Val292Met	p.V292M	ENST00000375333	NM_032454.1	292	Gtg/Atg	6/8	0.407999416704052	6	FACETS	1	0.983	1	0.319	0.292	0.347	CLONAL	1	FALSE	2	0.407999416704052	6		1018	1172	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	101	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.887	0.798	0.98	0.887	0.798	0.98	CLONAL	1	TRUE	1	0.526078244615213	2		509	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0019251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	222	1551	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.521504659755702	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.526078244615213	1		1551	579	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625348	69625348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1156753470	NA	P-0019251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	87	595	2	ENST00000334134.2:c.445G>A	p.Ala149Thr	p.A149T	ENST00000334134	NM_005247.2	149	Gcc/Acc	3/3	1	2	FACETS	0.551	0.489	0.618	0.551	0.489	0.618	SUBCLONAL	1	TRUE	1	0.526078244615213	2		597	600	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573484	48573484	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	51	290	0	ENST00000342988.3:c.68T>C	p.Leu23Ser	p.L23S	ENST00000342988	NM_005359.5	23	tTg/tCg	2/12	0.521504659755702	1	FACETS	0.959	0.833	1	0.959	0.833	1	CLONAL	1	TRUE	0	0.526078244615213	1		290	149	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626680	100626680	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	120	447	1	ENST00000308731.7:c.250G>T	p.Glu84Ter	p.E84*	ENST00000308731	NM_000061.2	84	Gaa/Taa	4/19	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.526078244615213	2		448	400	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578177	7578177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs267605076	NA	P-0019253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	363	1056	1	ENST00000269305.4:c.672G>T	p.Glu224Asp	p.E224D	ENST00000269305	NM_001126112.2	224	gaG/gaT	6/11	0.751226656871648	1	FACETS	0.996	0.956	1	0.996	0.956	1	CLONAL	1	TRUE	0	0.751226656871648	1		1057	606	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971077	21971077	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	341	600	0	ENST00000304494.5:c.281T>A	p.Leu94Gln	p.L94Q	ENST00000304494	NM_000077.4	94	cTg/cAg	2/3	0.751226656871648	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.751226656871648	2		600	454	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937091	48937091	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	65	347	0	ENST00000267163.4:c.859G>T	p.Glu287Ter	p.E287*	ENST00000267163	NM_000321.2	287	Gag/Tag	8/27	0.751226656871648	1	FACETS	0.735	0.655	0.816	0.735	0.655	0.816	SUBCLONAL	1	TRUE	0	0.751226656871648	1		347	147	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406186	70406186	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	282	954	0	ENST00000373644.4:c.3700A>G	p.Thr1234Ala	p.T1234A	ENST00000373644	NM_030625.2	1234	Aca/Gca	4/12	1	2	FACETS	0.864	0.814	0.915	0.864	0.814	0.915	CLONAL	1	TRUE	1	0.751226656871648	2		954	869	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497560	125497560	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1458791146	NA	P-0019253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	112	379	0	ENST00000428830.2:c.124A>G	p.Met42Val	p.M42V	ENST00000428830	NM_001114121.2	42	Atg/Gtg	3/14	1	2	FACETS	0.824	0.748	0.902	0.824	0.748	0.902	CLONAL	1	TRUE	1	0.751226656871648	2		379	362	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134500	30134500	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	134	418	0	ENST00000263025.4:c.31G>T	p.Gly11Cys	p.G11C	ENST00000263025	NM_002746.2	11	Ggc/Tgc	1/9	0.751226656871648	3	FACETS	0.917	0.838	1	0.459	0.419	0.5	CLONAL	1	TRUE	1	0.751226656871648	3		418	535	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228152	36228152	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	440	704	0	ENST00000222270.7:c.7538A>T	p.Glu2513Val	p.E2513V	ENST00000222270	NM_014727.1	2513	gAg/gTg	33/37	0.751226656871648	3	FACETS	0.945	0.907	0.982	0.945	0.907	0.982	CLONAL	2	TRUE	1	0.751226656871648	3		704	853	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99169319	99169319	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	227	742	0	ENST00000074304.5:c.1249C>T	p.Gln417Ter	p.Q417*	ENST00000074304	NM_001134224.1	417	Cag/Tag	15/26	1	2	FACETS	0.924	0.866	0.983	0.924	0.866	0.983	CLONAL	1	TRUE	1	0.751226656871648	2		742	654	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851636	134851636	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	397	599	0	ENST00000398015.3:c.1042A>G	p.Thr348Ala	p.T348A	ENST00000398015	NM_004441.4	348	Aca/Gca	5/16	0.751226656871648	6	FACETS	1	0.979	1	0.525	0.499	0.552	CLONAL	2	TRUE	2	0.751226656871648	6		599	1259	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374411	81374411	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	191	609	0	ENST00000222390.5:c.651G>C	p.Glu217Asp	p.E217D	ENST00000222390	NM_000601.4	217	gaG/gaC	6/18	0.751226656871648	3	FACETS	0.949	0.88	1	0.475	0.44	0.51	CLONAL	1	TRUE	1	0.751226656871648	3		609	737	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374422	81374422	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	184	604	0	ENST00000222390.5:c.640T>G	p.Cys214Gly	p.C214G	ENST00000222390	NM_000601.4	214	Tgc/Ggc	6/18	0.751226656871648	3	FACETS	0.923	0.854	0.994	0.462	0.427	0.497	CLONAL	1	TRUE	1	0.751226656871648	3		604	730	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0019255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	65	741	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.251520663512238	4	FACETS	1	0.913	1	0.534	0.463	0.61	CLONAL	1	TRUE	2	0.312249105483547	4		742	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0019255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	208	713	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.312249105483547	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.312249105483547	2		713	635	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551831	150551831	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	21	298	2	ENST00000369026.2:c.176G>A	p.Gly59Glu	p.G59E	ENST00000369026	NM_021960.4	59	gGa/gAa	1/3	0.188621531514765	4	FACETS	0.706	0.545	0.893	0.353	0.272	0.447	SUBCLONAL	1	TRUE	2	0.312249105483547	4		300	250	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998306	100998306	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1255934976	NA	P-0019255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	10	127	0	ENST00000325455.5:c.1496C>T	p.Ser499Phe	p.S499F	ENST00000325455	NM_001202474.3	499	tCc/tTc	1/8	0.26517581662634	3	FACETS	0.771	0.527	1	0.386	0.263	0.536	CLONAL	1	TRUE	1	0.312249105483547	3		127	96	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427906	49427906	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	72	835	0	ENST00000301067.7:c.10684G>T	p.Glu3562Ter	p.E3562*	ENST00000301067	NM_003482.3	3562	Gag/Tag	38/54	0.251520663512238	4	FACETS	0.795	0.694	0.905	0.398	0.347	0.453	CLONAL	1	TRUE	2	0.312249105483547	4		835	761	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435967	49435967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	123	945	0	ENST00000301067.7:c.6014G>A	p.Arg2005His	p.R2005H	ENST00000301067	NM_003482.3	2005	cGc/cAc	28/54	0.251520663512238	4	FACETS	1	0.968	1	0.582	0.526	0.642	CLONAL	1	TRUE	2	0.312249105483547	4		945	888	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114115	115114116	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	AC	novel	NA	P-0019255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	113	494	0	ENST00000257566.3:c.1099+1_1099+2dup		p.X367_splice	ENST00000257566	NM_016569.3	367			0.312249105483547	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	2	TRUE	0	0.312249105483547	2		494	360	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475322	40475322	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	39	871	0	ENST00000264657.5:c.1704C>G	p.Ile568Met	p.I568M	ENST00000264657	NM_139276.2	568	atC/atG	19/24	0.312249105483547	2	FACETS	0.378	0.313	0.452	0.189	0.156	0.226	SUBCLONAL	1	TRUE	0	0.312249105483547	2		871	660	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466878	57466878	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1342	83	709	0	ENST00000371085.3:c.97G>C	p.Asp33His	p.D33H	ENST00000371085	NM_000516.4	33	Gac/Cac	1/13	0.312249105483547	9	FACETS	0.781	0.686	0.883	0.098	0.085	0.111	SUBCLONAL	1	TRUE	1	0.312249105483547	9		709	1425	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114203	73114203	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	78	749	0	ENST00000356692.5:c.839C>G	p.Ser280Cys	p.S280C	ENST00000356692		280	tCt/tGt	8/9	0.232642797933693	4	FACETS	1	0.92	1			1	CLONAL	1	TRUE	NA	0.312249105483547	4		749	618	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976648	55976648	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	84	924	0	ENST00000263923.4:c.1177A>G	p.Thr393Ala	p.T393A	ENST00000263923	NM_002253.2	393	Aca/Gca	9/30	1	2	FACETS	0.841	0.743	0.945	0.841	0.743	0.945	CLONAL	1	TRUE	1	0.312249105483547	2		924	640	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225722	26225722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1426924061	NA	P-0019255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	80	727	3	ENST00000360408.1:c.340C>T	p.His114Tyr	p.H114Y	ENST00000360408	NM_003532.2	114	Cat/Tat	1/1	0.256484196389819	3	FACETS	0.991	0.873	1	0.495	0.436	0.559	CLONAL	1	TRUE	1	0.312249105483547	3		730	598	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117739636	117739636	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	66	629	0	ENST00000368508.3:c.157C>G	p.Leu53Val	p.L53V	ENST00000368508	NM_002944.2	53	Ctg/Gtg	2/43	0.251520663512238	4	FACETS	0.888	0.77	1	0.444	0.385	0.508	CLONAL	1	TRUE	2	0.312249105483547	4		629	625	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0019257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	220	741	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.632617214981638	2		742	598	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0019257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	291	1015	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.632617214981638	1	FACETS	0.994	0.943	1	0.994	0.943	1	CLONAL	1	TRUE	0	0.632617214981638	1		1017	633	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0019257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	297	822	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.632617214981638	2		822	929	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022592	31022592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs373221034	NA	P-0019257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	533	681	0	ENST00000375687.4:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000375687	NM_015338.5	693	Cga/Tga	13/13	0.587381322131028	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.632617214981638	3		681	1106	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176495	123176495	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	108	436	0	ENST00000218089.9:c.462G>C	p.Glu154Asp	p.E154D	ENST00000218089	NM_001042749.1	154	gaG/gaC	7/35	0.193808922198186	1	FACETS	0.553	0.5	0.609	0.553	0.5	0.609	INDETERMINATE	1	TRUE	0	0.632617214981638	1		436	422	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098816	178098816	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	269	772	1	ENST00000397062.3:c.229G>C	p.Asp77His	p.D77H	ENST00000397062	NM_006164.4	77	Gat/Cat	2/5	1	2	FACETS	0.915	0.861	0.971	0.915	0.861	0.971	CLONAL	1	TRUE	1	0.666507426228523	2		773	882	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	148	488	0	ENST00000308159.5:c.43C>G	p.Gln15Glu	p.Q15E	ENST00000308159	NM_014669.4	15	Cag/Gag	2/22	0.66620863123404	2	FACETS	0.888	0.817	0.962	0.444	0.408	0.481	CLONAL	1	TRUE	0	0.666507426228523	2		488	500	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588819	69588819	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	329	1027	0	ENST00000168712.1:c.417G>C	p.Met139Ile	p.M139I	ENST00000168712	NM_002007.2	139	atG/atC	2/3	1	2	FACETS	0.951	0.9	1	0.951	0.9	1	CLONAL	1	TRUE	1	0.666507426228523	2		1027	1038	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482550	56482550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	246	616	1	ENST00000267101.3:c.1007C>T	p.Ser336Phe	p.S336F	ENST00000267101	NM_001982.3	336	tCt/tTt	9/28	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.666507426228523	2		617	727	SUCCESS
BLM	641	MSKCC	GRCh37	15	91341433	91341433	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	197	501	0	ENST00000355112.3:c.3224G>C	p.Arg1075Thr	p.R1075T	ENST00000355112	NM_000057.2	1075	aGa/aCa	17/22	0.66620863123404	2	FACETS	1	0.938	1	0.504	0.469	0.539	CLONAL	1	TRUE	0	0.666507426228523	2		501	587	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249962	39249962	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1363908468	NA	P-0019258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	229	788	0	ENST00000402219.2:c.1607A>G	p.Asn536Ser	p.N536S	ENST00000402219	NM_005633.3	536	aAt/aGt	10/23	1	2	FACETS	0.839	0.784	0.896	0.839	0.784	0.896	CLONAL	1	TRUE	1	0.666507426228523	2		788	819	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280389	1280389	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	254	765	0	ENST00000310581.5:c.1834G>A	p.Ala612Thr	p.A612T	ENST00000310581	NM_198253.2	612	Gcc/Acc	4/16	0.365813395571378	3	FACETS	1	0.977	1	0.543	0.509	0.579	INDETERMINATE	1	TRUE	1	0.666507426228523	3		765	935	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376036	8376036	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	146	429	0	ENST00000356435.5:c.4561G>A	p.Asp1521Asn	p.D1521N	ENST00000356435		1521	Gat/Aat	28/35	1	2	FACETS	0.957	0.88	1	0.957	0.88	1	CLONAL	1	TRUE	1	0.666507426228523	2		429	458	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0019259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	113	810	3	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.226299747622678	3	FACETS	1	0.982	1	0.712	0.643	0.785	CLONAL	1	TRUE	1	0.318809423585128	3		813	577	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098352	108098352	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs730881359	NA	P-0019259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	46	648	0	ENST00000278616.4:c.1A>G	p.Met1?	p.M1?	ENST00000278616	NM_000051.3	1	Atg/Gtg	2/63	0.318809423585128	1	FACETS	0.845	0.716	0.986	0.845	0.716	0.986	CLONAL	1	TRUE	0	0.318809423585128	1		648	287	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827997	40827997	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	49	523	1	ENST00000373198.4:c.2431A>T	p.Ser811Cys	p.S811C	ENST00000373198	NM_133170.3	811	Agt/Tgt	17/32	1	2	FACETS	0.518	0.438	0.606	0.518	0.438	0.606	SUBCLONAL	1	TRUE	1	0.318809423585128	2		524	593	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	88	736	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		736	355	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	180	736	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.949	0.885	1	0.949	0.885	1	CLONAL	1	TRUE	1	0.870184119660012	2		736	436	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0019261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	19688	1035	6	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.870184119660012	22	FACETS	0.981	0.979	0.983			1	CLONAL	22	TRUE	NA	0.870184119660012	22		1041	20349	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29686010	29686010	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757391670	NA	P-0019261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	188	485	0	ENST00000356175.3:c.8074C>T	p.Arg2692Trp	p.R2692W	ENST00000356175	NM_000267.3	2692	Cgg/Tgg	55/57	1	2	FACETS	0.893	0.833	0.954	0.893	0.833	0.954	CLONAL	1	TRUE	1	0.870184119660012	2		485	484	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162722894	162722894	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	245	583	1	ENST00000367921.3:c.92G>T	p.Arg31Leu	p.R31L	ENST00000367921	NM_006182.2	31	cGc/cTc	4/18	0.33164154800572	6	FACETS	0.926	0.871	0.983	0.926	0.871	0.983	CLONAL	3	TRUE	3	0.552087900327492	6		584	672	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46740279	46740279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150315374	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	154	558	1	ENST00000371975.4:c.1759C>T	p.Arg587Trp	p.R587W	ENST00000371975	NM_003579.3	587	Cgg/Tgg	16/18	0.552087900327492	3	FACETS	1	0.954	1	0.529	0.485	0.574	CLONAL	1	TRUE	1	0.552087900327492	3		559	673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	317	798	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.505303089292797	2	FACETS	0.934	0.89	0.977	0.934	0.89	0.977	CLONAL	2	TRUE	0	0.552087900327492	2		798	615	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	259	693	0	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.536892281714137	2	FACETS	0.897	0.85	0.944	0.897	0.85	0.944	CLONAL	2	TRUE	0	0.552087900327492	2		693	523	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670219	134670219	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	60	656	2	ENST00000398015.3:c.130G>T	p.Glu44Ter	p.E44*	ENST00000398015	NM_004441.4	44	Gaa/Taa	3/16	0.552087900327492	3	FACETS	0.622	0.537	0.714	0.311	0.268	0.357	SUBCLONAL	1	TRUE	1	0.552087900327492	3		658	446	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120460341	120460341	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	312	794	0	ENST00000256646.2:c.5974G>C	p.Ala1992Pro	p.A1992P	ENST00000256646	NM_024408.3	1992	Gca/Cca	33/34	0.33164154800572	6	FACETS	0.891	0.848	0.935	1	0.991	1	CLONAL	4	TRUE	3	0.552087900327492	6		794	667	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471649	120471649	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	170	472	0	ENST00000256646.2:c.3842G>C	p.Cys1281Ser	p.C1281S	ENST00000256646	NM_024408.3	1281	tGt/tCt	23/34	0.33164154800572	6	FACETS	0.985	0.909	1	0.656	0.606	0.709	CLONAL	2	TRUE	3	0.552087900327492	6		472	658	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512341	120512341	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	118	511	1	ENST00000256646.2:c.901G>A	p.Glu301Lys	p.E301K	ENST00000256646	NM_024408.3	301	Gaa/Aaa	6/34	0.33164154800572	6	FACETS	0.806	0.73	0.886	0.537	0.486	0.591	CLONAL	2	TRUE	3	0.552087900327492	6		512	558	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741537	17741537	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	257	526	0	ENST00000250003.3:c.208C>G	p.His70Asp	p.H70D	ENST00000250003	NM_002478.4	70	Cac/Gac	1/3	0.373970040367071	3	FACETS	1	0.988	1	0.769	0.728	0.809	CLONAL	2	TRUE	0	0.552087900327492	3		526	515	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741742	17741742	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	84	734	0	ENST00000250003.3:c.413G>C	p.Ser138Thr	p.S138T	ENST00000250003	NM_002478.4	138	aGc/aCc	1/3	0.373970040367071	3	FACETS	0.596	0.526	0.67	0.199	0.175	0.224	SUBCLONAL	1	TRUE	0	0.552087900327492	3		734	652	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742477	17742477	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	30	678	0	ENST00000250003.3:c.659C>G	p.Ala220Gly	p.A220G	ENST00000250003	NM_002478.4	220	gCc/gGc	2/3	0.373970040367071	3	FACETS	0.239	0.192	0.293	0.08	0.064	0.098	SUBCLONAL	1	TRUE	0	0.552087900327492	3		678	580	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138852	64138852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	93	799	0	ENST00000334205.4:c.2219C>T	p.Ala740Val	p.A740V	ENST00000334205	NM_003942.2	740	gCc/gTc	17/17	0.373970040367071	3	FACETS	0.551	0.49	0.617	0.184	0.163	0.206	SUBCLONAL	1	TRUE	0	0.552087900327492	3		799	780	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625132	69625132	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	50	741	2	ENST00000334134.2:c.661G>T	p.Glu221Ter	p.E221*	ENST00000334134	NM_005247.2	221	Gag/Tag	3/3	0.373970040367071	3	FACETS	0.43	0.365	0.502	0.143	0.121	0.168	SUBCLONAL	1	TRUE	0	0.552087900327492	3		743	537	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180568	94180568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	49	593	1	ENST00000323929.3:c.1600G>A	p.Glu534Lys	p.E534K	ENST00000323929	NM_005591.3	534	Gag/Aag	15/20	0.373970040367071	3	FACETS	0.582	0.494	0.678	0.194	0.164	0.226	SUBCLONAL	1	TRUE	0	0.552087900327492	3		594	389	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489538	56489538	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	288	535	0	ENST00000267101.3:c.2003G>T	p.Gly668Val	p.G668V	ENST00000267101	NM_001982.3	668	gGg/gTg	17/28	0.552087900327492	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.552087900327492	3		535	594	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112910793	112910793	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397507527	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	341	735	3	ENST00000351677.2:c.802G>T	p.Gly268Cys	p.G268C	ENST00000351677	NM_002834.3	268	Ggt/Tgt	7/16	0.552087900327492	6	FACETS	1	0.989	1	0.841	0.8	0.881	CLONAL	3	TRUE	2	0.552087900327492	6		738	773	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563091	21563091	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	321	868	3	ENST00000382592.4:c.828G>T	p.Gln276His	p.Q276H	ENST00000382592	NM_014572.2	276	caG/caT	4/8	0.505303089292797	2	FACETS	0.98	0.936	1	0.98	0.936	1	CLONAL	2	TRUE	0	0.552087900327492	2		871	593	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986631	36986731	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCCTGGCTGGTGGCCCGGGTGTGCGCCAAGGCCGGCGCCACCGCTGCCCACGGAGATGGCCGCTGCCGCCGCCTGCGCGGCCTGCGCCTGGTGCTGCGC	CTGCCTGGCTGGTGGCCCGGGTGTGCGCCAAGGCCGGCGCCACCGCTGCCCACGGAGATGGCCGCTGCCGCCGCCTGCGCGGCCTGCGCCTGGTGCTGCGC	-	novel	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2756	1122	213	0	ENST00000354822.5:c.958_1058del	p.Ala320ArgfsTer85	p.A320Rfs*85	ENST00000354822	NM_001079668.2	320	GCGCAGCACCAGGCGCAGGCCGCGCAGGCGGCGGCAGCGGCCATCTCCGTGGGCAGCGGTGGCGCCGGCCTTGGCGCACACCCGGGCCACCAGCCAGGCAGc/c	3/3	0.552087900327492	37	FACETS	1	0.982	1			1	CLONAL	11	TRUE	NA	0.552087900327492	37		213	3878	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992733	72992733	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	257	695	2	ENST00000268489.5:c.1312G>T	p.Ala438Ser	p.A438S	ENST00000268489	NM_006885.3	438	Gcg/Tcg	2/10	0.221770445742193	3	FACETS	0.982	0.927	1	0.655	0.618	0.692	INDETERMINATE	2	TRUE	0	0.552087900327492	3		697	605	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246290	41246290	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	105	770	0	ENST00000357654.3:c.1258G>C	p.Asp420His	p.D420H	ENST00000357654	NM_007294.3	420	Gat/Cat	10/23	0.491289542882911	3	FACETS	0.937	0.843	1	0.469	0.421	0.518	CLONAL	1	TRUE	1	0.552087900327492	3		770	518	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805568	46805568	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	185	892	0	ENST00000290295.7:c.388T>G	p.Tyr130Asp	p.Y130D	ENST00000290295	NM_006361.5	130	Tat/Gat	1/2	0.491289542882911	3	FACETS	1	0.966	1	0.538	0.497	0.58	CLONAL	1	TRUE	1	0.552087900327492	3		892	795	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117864	70117864	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	41	448	0	ENST00000245479.2:c.332C>G	p.Ala111Gly	p.A111G	ENST00000245479	NM_000346.3	111	gCc/gGc	1/3	0.491289542882911	3	FACETS	0.465	0.387	0.55	0.232	0.193	0.275	SUBCLONAL	1	TRUE	1	0.552087900327492	3		448	408	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600429	10600429	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	346	1033	2	ENST00000171111.5:c.1426G>T	p.Gly476Trp	p.G476W	ENST00000171111	NM_203500.1	476	Ggg/Tgg	4/6	0.536892281714137	2	FACETS	0.963	0.92	1	0.963	0.92	1	CLONAL	2	TRUE	0	0.552087900327492	2		1035	651	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966881	18966881	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	227	913	0	ENST00000262803.5:c.1692G>C	p.Gln564His	p.Q564H	ENST00000262803	NM_002911.3	564	caG/caC	12/24	0.536892281714137	2	FACETS	1	0.991	1	0.681	0.639	0.724	CLONAL	1	TRUE	0	0.552087900327492	2		913	604	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753170	42753170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753965187	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	178	624	1	ENST00000222329.4:c.1094C>T	p.Ser365Leu	p.S365L	ENST00000222329	NM_006494.2	365	tCg/tTg	4/4	0.29316550360264	4	FACETS	0.772	0.715	0.832	0.772	0.715	0.832	INDETERMINATE	2	TRUE	2	0.552087900327492	4		625	648	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467177	25467177	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	530	591	0	ENST00000264709.3:c.1698G>C	p.Leu566Phe	p.L566F	ENST00000264709	NM_175629.2	566	ttG/ttC	15/23	0.552087900327492	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.552087900327492	3		591	758	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209108244	209108244	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	219	694	0	ENST00000345146.2:c.605C>G	p.Ser202Cys	p.S202C	ENST00000345146	NM_005896.2	202	tCt/tGt	6/10	0.521989217376537	5	FACETS	0.977	0.912	1	0.652	0.608	0.696	CLONAL	2	TRUE	2	0.552087900327492	5		694	742	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205786	128205786	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	275	700	0	ENST00000341105.2:c.89C>A	p.Ala30Glu	p.A30E	ENST00000341105	NM_032638.4	30	gCg/gAg	2/6	0.552087900327492	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.552087900327492	3		700	567	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155059	55155059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	51	441	1	ENST00000257290.5:c.2768G>A	p.Ser923Asn	p.S923N	ENST00000257290	NM_006206.4	923	aGt/aAt	20/23	0.283443219525272	4	FACETS	0.699	0.596	0.813	0.175	0.149	0.204	INDETERMINATE	1	TRUE	0	0.552087900327492	4		442	410	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280028	66280028	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1276862103	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	34	323	0	ENST00000273854.3:c.1661G>T	p.Arg554Ile	p.R554I	ENST00000273854	NM_004439.5	554	aGa/aTa	7/18	0.161003822694502	2	FACETS	0.536	0.44	0.641	0.268	0.22	0.321	INDETERMINATE	1	TRUE	0	0.552087900327492	2		323	230	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138201315	138201315	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	186	580	0	ENST00000237289.4:c.2014G>C	p.Gly672Arg	p.G672R	ENST00000237289	NM_001270507.1	672	Gga/Cga	8/9	0.33164154800572	6	FACETS	1	0.969	1	0.722	0.669	0.775	CLONAL	2	TRUE	3	0.552087900327492	6		580	655	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505469	157505469	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	275	522	1	ENST00000346085.5:c.3450T>A	p.Phe1150Leu	p.F1150L	ENST00000346085	NM_020732.3	1150	ttT/ttA	13/20	0.33164154800572	6	FACETS	1	0.948	1	1	0.948	1	CLONAL	3	TRUE	3	0.552087900327492	6		523	696	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136798	69136798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	401	609	0	ENST00000288368.4:c.4712C>T	p.Ala1571Val	p.A1571V	ENST00000288368	NM_024870.2	1571	gCa/gTa	39/40	0.48475056911617	5	FACETS	1	0.993	1			1	CLONAL	3	TRUE	NA	0.552087900327492	5		609	763	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317888	8317888	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	122	647	1	ENST00000356435.5:c.5725C>A	p.His1909Asn	p.H1909N	ENST00000356435		1909	Cac/Aac	35/35	0.453534902515337	2	FACETS	1	0.986	1	0.708	0.649	0.768	CLONAL	1	TRUE	0	0.552087900327492	2		648	312	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356384	70356384	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	296	837	0	ENST00000374080.3:c.5279A>T	p.Glu1760Val	p.E1760V	ENST00000374080		1760	gAg/gTg	37/45	0.52003118319222	2	FACETS	0.947	0.902	0.992	0.947	0.902	0.992	CLONAL	2	TRUE	0	0.552087900327492	2		837	566	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205861	128205861	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	108	301	0	ENST00000341105.2:c.14C>A	p.Pro5His	p.P5H	ENST00000341105	NM_032638.4	5	cCc/cAc	2/6	0.552087900327492	3	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	1	0.552087900327492	3		301	237	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	141	729	4	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.945	0.866	1	0.945	0.866	1	CLONAL	1	TRUE	1	0.59	2		733	506	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	132	472	2	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.9	0.822	0.981	0.9	0.822	0.981	CLONAL	1	TRUE	1	0.59	2		474	497	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	220	475	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.875	0.826	0.924	1	0.994	1	CLONAL	2	TRUE	1	0.59	2		475	426	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100375	27100375	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	197	738	0	ENST00000324856.7:c.4087C>T	p.Gln1363Ter	p.Q1363*	ENST00000324856	NM_006015.4	1363	Caa/Taa	17/20	1	2	FACETS	0.978	0.909	1	0.978	0.909	1	CLONAL	1	TRUE	1	0.59	2		738	683	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653805	89653805	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659443	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	118	613	0	ENST00000371953.3:c.103A>G	p.Met35Val	p.M35V	ENST00000371953	NM_000314.4	35	Atg/Gtg	2/9	1	2	FACETS	0.826	0.75	0.906	0.826	0.75	0.906	CLONAL	1	TRUE	1	0.59	2		613	484	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402765	139402765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1386494518	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	267	982	3	ENST00000277541.6:c.3244C>T	p.Arg1082Cys	p.R1082C	ENST00000277541	NM_017617.3	1082	Cgc/Tgc	20/34	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.59	2		985	775	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743932	41743933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs778012871	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	45	1229	7	ENST00000301178.4:c.874dup	p.His292ProfsTer47	p.H292Pfs*47	ENST00000301178	NM_021913.4	289	-/C	7/20	1	2	FACETS	0.186	0.155	0.22	0.186	0.155	0.22	SUBCLONAL	1	TRUE	1	0.59	2		1236	820	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	133	870	0	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.907	0.829	0.988	0.907	0.829	0.988	CLONAL	1	TRUE	1	0.59	2		870	497	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	72	505	4	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	1	2	FACETS	0.777	0.685	0.875	0.777	0.685	0.875	SUBCLONAL	1	TRUE	1	0.59	2		509	314	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675268	176675269	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	90	429	2	ENST00000439151.2:c.4591dup	p.Met1531AsnfsTer4	p.M1531Nfs*4	ENST00000439151	NM_022455.4	1528	-/A	11/23	1	2	FACETS	0.822	0.735	0.914	0.822	0.735	0.914	CLONAL	1	TRUE	1	0.59	2		431	371	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577146	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	192	997	2	ENST00000269305.4:c.792_794del	p.Leu265del	p.L265del	ENST00000269305	NM_001126112.2	264	ctACTg/ctg	8/11	1	2	FACETS	0.892	0.827	0.958	0.892	0.827	0.958	CLONAL	1	TRUE	1	0.59	2		999	730	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661664	227661664	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs761880048	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	87	518	13	ENST00000305123.5:c.1791del	p.His598ThrfsTer38	p.H598Tfs*38	ENST00000305123	NM_005544.2	597	ggG/gg	1/2	1	2	FACETS	0.996	0.892	1	0.996	0.892	1	CLONAL	1	TRUE	1	0.59	2		531	296	SUCCESS
APC	324	MSKCC	GRCh37	5	112173578	112173578	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	98	598	0	ENST00000257430.4:c.2287G>T	p.Glu763Ter	p.E763*	ENST00000257430	NM_000038.5	763	Gaa/Taa	16/16	1	2	FACETS	0.854	0.768	0.944	0.854	0.768	0.944	CLONAL	1	TRUE	1	0.59	2		598	389	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371799	55371820	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCCGCGCTGGGCCCCGAG	GGCGGCCGCGCTGGGCCCCGAG	-	novel	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	79	138	0	ENST00000297316.4:c.499_520del	p.Leu167TrpfsTer213	p.L167Wfs*213	ENST00000297316	NM_022454.3	163	caGGCGGCCGCGCTGGGCCCCGAG/ca	2/2	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.59	2		138	210	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405954	157405954	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	146	718	3	ENST00000346085.5:c.2201del	p.Gly734AlafsTer11	p.G734Afs*11	ENST00000346085	NM_020732.3	732	ccG/cc	6/20	1	2	FACETS	0.91	0.835	0.987	0.91	0.835	0.987	CLONAL	1	TRUE	1	0.59	2		721	544	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41521913	41521913	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	236	1126	0	ENST00000263253.7:c.775C>T	p.Gln259Ter	p.Q259*	ENST00000263253	NM_001429.3	259	Cag/Tag	3/31	1	2	FACETS	0.982	0.919	1	0.982	0.919	1	CLONAL	1	TRUE	1	0.59	2		1126	815	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466022	69466022	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	165	905	0	ENST00000227507.2:c.860C>A	p.Pro287His	p.P287H	ENST00000227507	NM_053056.2	287	cCc/cAc	5/5	1	2	FACETS	0.866	0.798	0.936	0.866	0.798	0.936	CLONAL	1	TRUE	1	0.59	2		905	646	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015443	176015443	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	133	669	1	ENST00000367669.3:c.1295A>T	p.Asp432Val	p.D432V	ENST00000367669	NM_022457.5	432	gAt/gTt	12/20	1	2	FACETS	0.957	0.875	1	0.957	0.875	1	CLONAL	1	TRUE	1	0.59	2		670	471	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911587	114911587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	186	837	2	ENST00000543371.1:c.1105G>A	p.Val369Ile	p.V369I	ENST00000543371	NM_001198531.1	369	Gta/Ata	10/14	1	2	FACETS	0.998	0.926	1	0.998	0.926	1	CLONAL	1	TRUE	1	0.59	2		839	632	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	459926	459926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	175	913	0	ENST00000399788.2:c.1169T>C	p.Val390Ala	p.V390A	ENST00000399788	NM_001042603.1	390	gTa/gCa	10/28	0.3	2	FACETS	0.869	0.803	0.937			1	INDETERMINATE	1	TRUE	NA	0.59	2		913	683	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436343	110436343	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	112	516	1	ENST00000375856.3:c.2058del	p.Lys687SerfsTer140	p.K687Sfs*140	ENST00000375856	NM_003749.2	686	ccC/cc	1/2	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.59	2		517	361	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060842	38060842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1285265540	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	216	930	0	ENST00000250448.2:c.1147G>A	p.Glu383Lys	p.E383K	ENST00000250448	NM_004496.3	383	Gag/Aag	2/2	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.59	2		930	666	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2089944	2089944	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367629024	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	139	745	0	ENST00000219066.1:c.920C>T	p.Pro307Leu	p.P307L	ENST00000219066	NM_002528.5	307	cCg/cTg	6/6	1	2	FACETS	0.98	0.898	1	0.98	0.898	1	CLONAL	1	TRUE	1	0.59	2		745	481	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650756	67650756	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	190	881	0	ENST00000264010.4:c.1062del	p.Met355CysfsTer7	p.M355Cfs*7	ENST00000264010	NM_006565.3	354	tCc/tc	5/12	1	2	FACETS	0.839	0.777	0.902	0.839	0.777	0.902	CLONAL	1	TRUE	1	0.59	2		881	768	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827931	72827931	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs915158684	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	135	915	2	ENST00000268489.5:c.8650T>C	p.Ser2884Pro	p.S2884P	ENST00000268489	NM_006885.3	2884	Tct/Cct	9/10	1	2	FACETS	0.6	0.545	0.657	0.6	0.545	0.657	SUBCLONAL	1	TRUE	1	0.59	2		917	763	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357543	89357543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143894223	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	137	946	2	ENST00000301030.4:c.275G>A	p.Arg92Gln	p.R92Q	ENST00000301030	NM_001256183.1	92	cGg/cAg	5/13	1	2	FACETS	0.673	0.613	0.736	0.673	0.613	0.736	SUBCLONAL	1	TRUE	1	0.59	2		948	690	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	279	1422	3	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	1	2	FACETS	0.978	0.92	1	0.978	0.92	1	CLONAL	1	TRUE	1	0.59	2		1425	967	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25468153	25468154	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	225	1093	0	ENST00000264709.3:c.1522dup	p.Leu508ProfsTer38	p.L508Pfs*38	ENST00000264709	NM_175629.2	508	ctc/cCtc	13/23	1	2	FACETS	0.943	0.88	1	0.943	0.88	1	CLONAL	1	TRUE	1	0.59	2		1093	809	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376267	225376267	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	98	492	0	ENST00000264414.4:c.687T>G	p.Ser229Arg	p.S229R	ENST00000264414	NM_003590.4	229	agT/agG	6/16	1	2	FACETS	0.886	0.797	0.979	0.886	0.797	0.979	CLONAL	1	TRUE	1	0.59	2		492	375	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024614	31024614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147456014	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	68	703	2	ENST00000375687.4:c.4099G>A	p.Val1367Ile	p.V1367I	ENST00000375687	NM_015338.5	1367	Gtc/Atc	13/13	1	2	FACETS	0.468	0.407	0.532	0.468	0.407	0.532	SUBCLONAL	1	TRUE	1	0.59	2		705	493	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39690094	39690096	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	149	761	0	ENST00000361337.2:c.121_123del	p.Glu41del	p.E41del	ENST00000361337	NM_003286.2	40	aAGGag/aag	3/21	1	2	FACETS	0.786	0.72	0.854	0.786	0.72	0.854	SUBCLONAL	1	TRUE	1	0.59	2		761	643	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321773	62321773	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	129	704	0	ENST00000360203.5:c.2392A>G	p.Ser798Gly	p.S798G	ENST00000360203	NM_001283009.1	798	Agc/Ggc	26/35	1	2	FACETS	0.873	0.796	0.953	0.873	0.796	0.953	CLONAL	1	TRUE	1	0.59	2		704	501	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24134057	24134057	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	205	895	1	ENST00000263121.7:c.214del	p.Thr72GlnfsTer13	p.T72Qfs*13	ENST00000263121	NM_003073.3	70	Aaa/aa	2/9	1	2	FACETS	0.799	0.742	0.858	0.799	0.742	0.858	SUBCLONAL	1	TRUE	1	0.59	2		896	870	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144873	47144873	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	155	834	0	ENST00000409792.3:c.4880T>C	p.Met1627Thr	p.M1627T	ENST00000409792	NM_014159.6	1627	aTg/aCg	7/21	1	2	FACETS	0.857	0.788	0.929	0.857	0.788	0.929	CLONAL	1	TRUE	1	0.59	2		834	613	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589629	67589631	+	inframe_deletion	In_Frame_Del	DEL	TAG	TAG	-	novel	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	106	676	0	ENST00000274335.5:c.1392_1394del	p.Asp464_Arg465delinsGlu	p.D464_R465delinsE	ENST00000274335		464	gaTAGa/gaa	10/15	1	2	FACETS	0.683	0.615	0.755	0.683	0.615	0.755	SUBCLONAL	1	TRUE	1	0.59	2		676	526	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665631	86665631	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs756634599	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	76	418	1	ENST00000274376.6:c.1612C>T	p.Pro538Ser	p.P538S	ENST00000274376	NM_002890.2	538	Cca/Tca	12/25	1	2	FACETS	0.732	0.646	0.822	0.732	0.646	0.822	SUBCLONAL	1	TRUE	1	0.59	2		419	352	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13949304	13949304	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	103	567	0	ENST00000405192.2:c.824C>A	p.Pro275His	p.P275H	ENST00000405192	NM_001163147.1	275	cCc/cAc	9/12	1	2	FACETS	0.858	0.773	0.946	0.858	0.773	0.946	CLONAL	1	TRUE	1	0.59	2		567	407	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239929	98239929	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	29	587	1	ENST00000331920.6:c.1403C>T	p.Ala468Val	p.A468V	ENST00000331920	NM_000264.3	468	gCc/gTc	10/24	1	2	FACETS	0.2	0.16	0.246	0.2	0.16	0.246	SUBCLONAL	1	TRUE	1	0.59	2		588	491	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268715	98268715	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	178	585	0	ENST00000331920.6:c.368C>G	p.Thr123Ser	p.T123S	ENST00000331920	NM_000264.3	123	aCc/aGc	2/24	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.59	2		585	562	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035932	47035932	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	192	953	0	ENST00000377604.3:c.610A>G	p.Met204Val	p.M204V	ENST00000377604	NM_001204468.1	204	Atg/Gtg	7/24	1	2	FACETS	0.863	0.8	0.928	0.863	0.8	0.928	CLONAL	1	TRUE	1	0.59	2		953	754	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429040	47429040	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	128	506	2	ENST00000377045.4:c.1403G>A	p.Gly468Glu	p.G468E	ENST00000377045	NM_001654.4	468	gGa/gAa	13/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.59	2		508	401	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231107	53231107	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	186	755	2	ENST00000375401.3:c.1795del	p.Arg599ValfsTer60	p.R599Vfs*60	ENST00000375401	NM_004187.3	599	Cgt/gt	13/26	1	2	FACETS	0.894	0.829	0.962	0.894	0.829	0.962	CLONAL	1	TRUE	1	0.59	2		757	705	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434958	49434958	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs398123753	NA	P-0019265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	32	539	1	ENST00000301067.7:c.6595del	p.Tyr2199IlefsTer65	p.Y2199Ifs*65	ENST00000301067	NM_003482.3	2199	Tat/at	31/54	1	2	FACETS	0.72	0.585	0.874	0.72	0.585	0.874	SUBCLONAL	1	TRUE	1	0.21	2		540	423	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821476	72821476	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	95	876	0	ENST00000268489.5:c.10699G>C	p.Glu3567Gln	p.E3567Q	ENST00000268489	NM_006885.3	3567	Gag/Cag	10/10	1	2	FACETS	0.894	0.794	1	0.894	0.794	1	CLONAL	1	TRUE	1	0.21	2		876	1012	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117662	70117662	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	92	810	1	ENST00000245479.2:c.130G>T	p.Glu44Ter	p.E44*	ENST00000245479	NM_000346.3	44	Gag/Tag	1/3	0.180403408558032	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.21	1		811	726	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469899	157469899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs988746594	NA	P-0019265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	56	698	1	ENST00000346085.5:c.2693G>A	p.Arg898Gln	p.R898Q	ENST00000346085	NM_020732.3	898	cGa/cAa	9/20	1	2	FACETS	0.727	0.621	0.842	0.727	0.621	0.842	SUBCLONAL	1	TRUE	1	0.21	2		699	734	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468053	50468053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	45	458	0	ENST00000331340.3:c.1288G>A	p.Glu430Lys	p.E430K	ENST00000331340	NM_006060.4	430	Gag/Aag	8/8	1	2	FACETS	0.895	0.752	1	0.895	0.752	1	CLONAL	1	TRUE	1	0.21	2		458	479	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848574	151848574	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	110	649	0	ENST00000262189.6:c.12619G>T	p.Gly4207Ter	p.G4207*	ENST00000262189	NM_170606.2	4207	Gga/Tga	50/59	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.21	2		649	761	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397653	139397653	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	87	720	2	ENST00000277541.6:c.5148C>A	p.Tyr1716Ter	p.Y1716*	ENST00000277541	NM_017617.3	1716	taC/taA	27/34	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.21	2		722	768	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564168	139564168	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	79	915	0	ENST00000308874.7:c.308G>C	p.Gly103Ala	p.G103A	ENST00000308874		103	gGa/gCa	5/10	1	2	FACETS	0.769	0.674	0.87	0.769	0.674	0.87	SUBCLONAL	1	TRUE	1	0.21	2		915	979	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246376	46246404	+	frameshift_variant	Frame_Shift_Del	DEL	ATCAAAAGTATCCCATTCTCCTGCCCTAT	ATCAAAAGTATCCCATTCTCCTGCCCTAT	G	novel	NA	P-0019265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	44	508	0	ENST00000334344.6:c.4470_4498delinsG	p.Ser1491HisfsTer16	p.S1491Hfs*16	ENST00000334344	NM_152641.2	1490	ggATCAAAAGTATCCCATTCTCCTGCCCTATca/ggGca	15/21	1	2	FACETS	0.713	0.597	0.841	0.713	0.597	0.841	SUBCLONAL	1	TRUE	1	0.21	2		508	588	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610463	10610463	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	241	729	0	ENST00000171111.5:c.247G>T	p.Val83Phe	p.V83F	ENST00000171111	NM_203500.1	83	Gtc/Ttc	2/6	0.384226903771162	4	FACETS	0.87	0.822	0.918	0.652	0.616	0.689	CLONAL	3	TRUE	0	0.589446138838644	4		729	498	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0019266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	346	563	0	ENST00000269305.4:c.559+1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.599042847442046	3	FACETS	0.889	0.853	0.924			1	CLONAL	3	TRUE	NA	0.589446138838644	3		563	570	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375476	118375476	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	42	466	0	ENST00000534358.1:c.8869G>C	p.Asp2957His	p.D2957H	ENST00000534358	NM_005933.3	2957	Gac/Cac	27/36	0.589446138838644	6	FACETS	0.995	0.858	1			1	CLONAL	3	TRUE	NA	0.589446138838644	6		466	104	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597537	28597537	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	139	1078	0	ENST00000241453.7:c.2368T>C	p.Cys790Arg	p.C790R	ENST00000241453	NM_004119.2	790	Tgc/Cgc	19/24	0.385130639395392	5	FACETS	0.984	0.912	1	0.59	0.547	0.634	CLONAL	3	TRUE	0	0.589446138838644	5		1078	301	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475028	40475028	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	31	736	0	ENST00000264657.5:c.1882A>T	p.Ile628Phe	p.I628F	ENST00000264657	NM_139276.2	628	Atc/Ttc	20/24	NA	2	FACETS	1	0.846	1			1	INDETERMINATE	1	TRUE	NA	0.589446138838644	2		736	103	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793298	242793298	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	420	1104	0	ENST00000334409.5:c.779C>T	p.Ser260Leu	p.S260L	ENST00000334409	NM_005018.2	260	tCa/tTa	5/5	0.439137775248702	5	FACETS	1	0.99	1	0.752	0.717	0.788	CLONAL	2	TRUE	2	0.589446138838644	5		1104	1190	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546695	9546695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	52	331	0	ENST00000353224.5:c.1327G>A	p.Gly443Arg	p.G443R	ENST00000353224	NM_177990.2	443	Gga/Aga	5/10	0.579164638613479	4	FACETS	0.899	0.781	1	0.899	0.781	1	CLONAL	2	TRUE	2	0.589446138838644	4		331	156	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031768	36031768	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	223	808	0	ENST00000358208.4:c.1600del	p.Glu534ArgfsTer110	p.E534Rfs*110	ENST00000358208		533	Ggg/gg	12/12	0.579164638613479	4	FACETS	1	0.988	1	0.632	0.589	0.677	CLONAL	1	TRUE	2	0.589446138838644	4		808	951	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980927	40980927	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0019266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	21	464	0	ENST00000373198.4:c.1561-2A>T		p.X521_splice	ENST00000373198	NM_133170.3	521			NA	2	FACETS	0.758	0.596	0.939			1	INDETERMINATE	1	TRUE	NA	0.589446138838644	2		464	94	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749551	41749551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	106	611	1	ENST00000226382.2:c.244C>A	p.Pro82Thr	p.P82T	ENST00000226382	NM_003924.3	82	Cct/Act	2/3	0.233537830638793	5	FACETS	0.853	0.771	0.939	0.569	0.514	0.626	INDETERMINATE	2	TRUE	2	0.589446138838644	5		612	397	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056648	26056648	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs755438887	NA	P-0019266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	84	232	0	ENST00000343677.2:c.9G>T	p.Glu3Asp	p.E3D	ENST00000343677	NM_005319.3	3	gaG/gaT	1/1	0.589446138838644	8	FACETS	0.881	0.792	0.972			1	CLONAL	4	TRUE	NA	0.589446138838644	8		232	224	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197388	26197388	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	127	339	0	ENST00000356476.2:c.91C>G	p.Pro31Ala	p.P31A	ENST00000356476		31	Cca/Gca	1/1	0.589446138838644	8	FACETS	0.837	0.763	0.914			1	CLONAL	3	TRUE	NA	0.589446138838644	8		339	475	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509826	106509826	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	40	847	0	ENST00000359195.3:c.1820C>G	p.Thr607Arg	p.T607R	ENST00000359195	NM_002649.2	607	aCa/aGa	2/11	0.573991987739077	3	FACETS	0.518	0.432	0.614	0.173	0.144	0.205	SUBCLONAL	1	TRUE	0	0.589446138838644	3		847	339	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409809	139409809	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	500	1051	0	ENST00000277541.6:c.1947del	p.Cys650AlafsTer122	p.C650Afs*122	ENST00000277541	NM_017617.3	649	ccC/cc	12/34	0.512373791073389	4	FACETS	1	0.966	1	0.752	0.725	0.778	CLONAL	3	TRUE	0	0.589446138838644	4		1051	897	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412125	63412125	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	149	1271	0	ENST00000330258.3:c.1042G>T	p.Gly348Cys	p.G348C	ENST00000330258	NM_152424.3	348	Ggc/Tgc	2/2	0.599042847442046	3	FACETS	0.968	0.887	1			1	CLONAL	1	TRUE	NA	0.589446138838644	3		1271	676	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0019268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	109	832	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.147965809610359	3	FACETS	0.863	0.775	0.957	0.863	0.775	0.957	CLONAL	2	FALSE	1	0.177874440451698	3		832	773	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195643	102195643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200590873	NA	P-0019268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	107	765	1	ENST00000263464.3:c.403C>T	p.Arg135Cys	p.R135C	ENST00000263464	NM_001165.4	135	Cgt/Tgt	2/9	0.142807919973863	2	FACETS	1	0.978	1	0.676	0.605	0.751	CLONAL	1	FALSE	0	0.177874440451698	2		766	890	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945095	32945095	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs587776351	NA	P-0019268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	27	470	0	ENST00000380152.3:c.8490G>A	p.Trp2830Ter	p.W2830*	ENST00000380152		2830	tgG/tgA	20/27	0.142807919973863	2	FACETS	0.816	0.649	1	0.408	0.324	0.504	CLONAL	1	FALSE	0	0.177874440451698	2		470	372	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61717804	61717804	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	49	869	0	ENST00000401558.2:c.1995G>T	p.Trp665Cys	p.W665C	ENST00000401558	NM_003400.3	665	tgG/tgT	17/25	1	2	FACETS	0.566	0.478	0.664	0.566	0.478	0.664	SUBCLONAL	1	FALSE	1	0.177874440451698	2		869	973	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964397	93964397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	46	877	1	ENST00000369303.4:c.2500G>A	p.Glu834Lys	p.E834K	ENST00000369303	NM_004440.3	834	Gaa/Aaa	14/17	1	2	FACETS	0.668	0.561	0.787	0.668	0.561	0.787	SUBCLONAL	1	FALSE	1	0.177874440451698	2		878	774	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0019272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	329	852	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.522066567005724	2	FACETS	0.933	0.889	0.976	0.933	0.889	0.976	CLONAL	2	TRUE	0	0.536122452566561	2		852	658	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132428	11132428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	328	788	1	ENST00000358026.2:c.2644G>A	p.Glu882Lys	p.E882K	ENST00000358026	NM_001128849.1	882	Gaa/Aaa	19/36	0.522066567005724	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.536122452566561	2		789	602	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486121	8486121	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	91	581	0	ENST00000356435.5:c.2696A>C	p.Asn899Thr	p.N899T	ENST00000356435		899	aAc/aCc	17/35	1	2	FACETS	0.797	0.712	0.887	0.797	0.712	0.887	SUBCLONAL	1	TRUE	1	0.536122452566561	2		581	426	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559882	29559882	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	70	339	0	ENST00000356175.3:c.3479G>C	p.Gly1160Ala	p.G1160A	ENST00000356175	NM_000267.3	1160	gGt/gCt	26/57	1	2	FACETS	0.985	0.869	1	0.985	0.869	1	CLONAL	1	TRUE	1	0.536122452566561	2		339	265	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59861775	59861775	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	108	534	0	ENST00000259008.2:c.1484C>A	p.Ser495Tyr	p.S495Y	ENST00000259008	NM_032043.2	495	tCt/tAt	11/20	1	2	FACETS	0.907	0.82	0.999	0.907	0.82	0.999	CLONAL	1	TRUE	1	0.536122452566561	2		534	444	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62323159	62323159	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	99	528	1	ENST00000360203.5:c.2621G>T	p.Gly874Val	p.G874V	ENST00000360203	NM_001283009.1	874	gGg/gTg	28/35	0.536122452566561	7	FACETS	0.841	0.749	0.939			1	CLONAL	1	TRUE	NA	0.536122452566561	7		529	1028	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326695	62326695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140411308	NA	P-0019272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	1055	882	0	ENST00000360203.5:c.3514G>A	p.Glu1172Lys	p.E1172K	ENST00000360203	NM_001283009.1	1172	Gag/Aag	34/35	0.536122452566561	7	FACETS	0.963	0.942	0.984			1	CLONAL	6	TRUE	NA	0.536122452566561	7		882	1594	SUCCESS
AR	367	MSKCC	GRCh37	X	66943593	66943593	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	279	640	1	ENST00000374690.3:c.2673C>A	p.Asp891Glu	p.D891E	ENST00000374690	NM_000044.3	891	gaC/gaA	8/8	0.475901436646357	3	FACETS	0.954	0.902	1	0.954	0.902	1	CLONAL	2	TRUE	1	0.536122452566561	3		641	692	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202456	123202457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	167	729	0	ENST00000218089.9:c.2309dup	p.Ile771AspfsTer14	p.I771Dfs*14	ENST00000218089	NM_001042749.1	770	cag/cAag	24/35	0.361309561581101	6	FACETS	1	0.946	1			1	CLONAL	1	TRUE	NA	0.536122452566561	6		729	1240	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0019272-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	289	852	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.389059734225367	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.389059734225367	2		852	714	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132428	11132428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019272-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	270	788	1	ENST00000358026.2:c.2644G>A	p.Glu882Lys	p.E882K	ENST00000358026	NM_001128849.1	882	Gaa/Aaa	19/36	0.389059734225367	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.389059734225367	2		789	691	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486121	8486121	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019272-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	80	581	0	ENST00000356435.5:c.2696A>C	p.Asn899Thr	p.N899T	ENST00000356435		899	aAc/aCc	17/35	1	2	FACETS	0.853	0.753	0.96	0.853	0.753	0.96	CLONAL	1	TRUE	1	0.389059734225367	2		581	482	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559882	29559882	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019272-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	64	339	0	ENST00000356175.3:c.3479G>C	p.Gly1160Ala	p.G1160A	ENST00000356175	NM_000267.3	1160	gGt/gCt	26/57	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.389059734225367	2		339	303	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59861775	59861775	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019272-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	57	534	0	ENST00000259008.2:c.1484C>A	p.Ser495Tyr	p.S495Y	ENST00000259008	NM_032043.2	495	tCt/tAt	11/20	1	2	FACETS	0.663	0.57	0.764	0.663	0.57	0.764	SUBCLONAL	1	TRUE	1	0.389059734225367	2		534	442	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62323159	62323159	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019272-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	115	528	1	ENST00000360203.5:c.2621G>T	p.Gly874Val	p.G874V	ENST00000360203	NM_001283009.1	874	gGg/gTg	28/35	0.389059734225367	7	FACETS	1	0.974	1			1	CLONAL	1	TRUE	NA	0.389059734225367	7		529	929	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326695	62326695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140411308	NA	P-0019272-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	815	882	0	ENST00000360203.5:c.3514G>A	p.Glu1172Lys	p.E1172K	ENST00000360203	NM_001283009.1	1172	Gag/Aag	34/35	0.389059734225367	7	FACETS	0.946	0.92	0.972			1	CLONAL	6	TRUE	NA	0.389059734225367	7		882	1456	SUCCESS
AR	367	MSKCC	GRCh37	X	66943593	66943593	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019272-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	205	640	1	ENST00000374690.3:c.2673C>A	p.Asp891Glu	p.D891E	ENST00000374690	NM_000044.3	891	gaC/gaA	8/8	0.373382196872432	3	FACETS	0.946	0.882	1	0.946	0.882	1	CLONAL	2	TRUE	1	0.389059734225367	3		641	665	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202456	123202457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019272-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	87	729	0	ENST00000218089.9:c.2309dup	p.Ile771AspfsTer14	p.I771Dfs*14	ENST00000218089	NM_001042749.1	770	cag/cAag	24/35	0.389059734225367	5	FACETS	0.788	0.696	0.886			1	SUBCLONAL	1	TRUE	NA	0.389059734225367	5		729	899	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884466	151884466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1435892915	NA	P-0019272-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	87	470	3	ENST00000262189.6:c.4889C>T	p.Ser1630Leu	p.S1630L	ENST00000262189	NM_170606.2	1630	tCg/tTg	33/59	1	2	FACETS	0.992	0.882	1	0.992	0.882	1	CLONAL	1	TRUE	1	0.389059734225367	2		473	451	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061232	38061234	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0019273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	246	765	0	ENST00000250448.2:c.755_757del	p.Asn252del	p.N252del	ENST00000250448	NM_004496.3	252	aACAtg/atg	2/2	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.594756252488308	2		765	615	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005443	150005443	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	35	712	1	ENST00000253339.5:c.782C>A	p.Thr261Lys	p.T261K	ENST00000253339		261	aCa/aAa	3/7	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		713	685	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70967542	70967542	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	42	828	0	ENST00000276594.2:c.1481G>A	p.Cys494Tyr	p.C494Y	ENST00000276594	NM_024504.3	494	tGt/tAt	7/8	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		828	838	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577136	64577136	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0019275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	225	747	0	ENST00000312049.6:c.445+1del		p.X149_splice	ENST00000312049	NM_130799.2	149			0.51054196452596	1	FACETS	0.998	0.934	1	0.998	0.934	1	CLONAL	1	TRUE	0	0.51054196452596	1		747	658	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2111865	2111871	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	ACTGCAG	ACTGCAG	-	novel	NA	P-0019275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	162	420	0	ENST00000219476.3:c.1120-5_1121del		p.X374_splice	ENST00000219476	NM_000548.3	374			0.51054196452596	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.51054196452596	1		420	435	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286993	33286994	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	TAGC	novel	NA	P-0019275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	177	525	0	ENST00000374542.5:c.1941-1_1943dup	p.Tyr648Ter	p.Y648*	ENST00000374542	NM_001141970.1	648	tat/taGCTAt	7/8	0.51054196452596	1	FACETS	0.995	0.924	1	0.995	0.924	1	CLONAL	1	TRUE	0	0.51054196452596	1		525	519	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	330	736	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.826507114596163	2		736	770	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78935270	78935270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147241989	NA	P-0019276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	340	751	1	ENST00000306801.3:c.3682G>A	p.Val1228Met	p.V1228M	ENST00000306801	NM_020761.2	1228	Gtg/Atg	31/34	1	2	FACETS	0.948	0.9	0.996	0.948	0.9	0.996	CLONAL	1	TRUE	1	0.826507114596163	2		752	868	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925403	131925403	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	254	599	0	ENST00000265335.6:c.1326A>G	p.Ile442Met	p.I442M	ENST00000265335		442	atA/atG	9/25	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.826507114596163	2		599	583	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17949096	17949096	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	35	896	0	ENST00000458235.1:c.1545G>T	p.Lys515Asn	p.K515N	ENST00000458235	NM_000215.3	515	aaG/aaT	11/24	1	2	FACETS	0.304	0.248	0.367	0.304	0.248	0.367	SUBCLONAL	1	TRUE	1	0.406159864297858	2		896	567	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457179	25457179	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	46	592	0	ENST00000264709.3:c.2708C>G	p.Ala903Gly	p.A903G	ENST00000264709	NM_175629.2	903	gCt/gGt	23/23	1	2	FACETS	0.483	0.407	0.567	0.483	0.407	0.567	SUBCLONAL	1	TRUE	1	0.406159864297858	2		592	469	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729767	41729767	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	44	323	0	ENST00000242208.4:c.762G>T	p.Leu254Phe	p.L254F	ENST00000242208	NM_002192.2	254	ttG/ttT	3/3	1	2	FACETS	0.899	0.76	1	0.899	0.76	1	CLONAL	1	TRUE	1	0.406159864297858	2		323	241	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17949096	17949096	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019278-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	154	896	0	ENST00000458235.1:c.1545G>T	p.Lys515Asn	p.K515N	ENST00000458235	NM_000215.3	515	aaG/aaT	11/24	1	2	FACETS	0.847	0.774	0.924	0.847	0.774	0.924	CLONAL	1	TRUE	1	0.32	2		896	1136	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729767	41729767	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019278-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	68	323	0	ENST00000242208.4:c.762G>T	p.Leu254Phe	p.L254F	ENST00000242208	NM_002192.2	254	ttG/ttT	3/3	1	2	FACETS	0.924	0.806	1	0.924	0.806	1	CLONAL	1	TRUE	1	0.32	2		323	460	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0019279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	176	608	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.758874804177313	2		608	425	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913492	NA	P-0019279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	180	738	0	ENST00000286548.4:c.626A>G	p.Gln209Arg	p.Q209R	ENST00000286548	NM_002072.3	209	cAa/cGa	5/7	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.758874804177313	2		738	404	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0019280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	199	860	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.931	0.866	0.996	0.931	0.866	0.996	CLONAL	1	TRUE	1	0.665113913651091	2		860	643	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152033	55152033	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763325080	NA	P-0019280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	169	605	0	ENST00000257290.5:c.2465G>A	p.Arg822His	p.R822H	ENST00000257290	NM_006206.4	822	cGc/cAc	18/23	1	2	FACETS	0.932	0.863	1	0.932	0.863	1	CLONAL	1	TRUE	1	0.665113913651091	2		605	545	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107047	11107047	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	122	461	0	ENST00000358026.2:c.1752G>T	p.Lys584Asn	p.K584N	ENST00000358026	NM_001128849.1	584	aaG/aaT	10/36	0.653775524188438	3	FACETS	1	0.92	1	0.506	0.46	0.554	CLONAL	1	TRUE	1	0.665113913651091	3		461	483	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0019281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	57	405	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.742892454357772	1	FACETS	0.778	0.689	0.868	0.778	0.689	0.868	SUBCLONAL	1	TRUE	0	0.742892454357772	1		405	124	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578214	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs864309495	NA	P-0019281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	299	697	0	ENST00000269305.4:c.635_636del	p.Phe212SerfsTer3	p.F212Sfs*3	ENST00000269305	NM_001126112.2	212	tTT/t	6/11	0.742892454357772	1	FACETS	0.886	0.844	0.928	0.886	0.844	0.928	CLONAL	1	TRUE	0	0.742892454357772	1		697	571	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577222	64577224	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs794728657	NA	P-0019281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	263	655	1	ENST00000312049.6:c.358_360del	p.Lys120del	p.K120del	ENST00000312049	NM_130799.2	120	AAG/-	2/10	0.742892454357772	1	FACETS	0.905	0.859	0.95	0.905	0.859	0.95	CLONAL	1	TRUE	0	0.742892454357772	1		656	492	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740898	58740901	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs745470366	NA	P-0019281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	136	545	0	ENST00000305921.3:c.1806_1809del	p.Cys603PhefsTer21	p.C603Ffs*21	ENST00000305921	NM_003620.3	601	acTGTT/ac	6/6	1	2	FACETS	0.632	0.577	0.69	0.632	0.577	0.69	SUBCLONAL	1	TRUE	1	0.742892454357772	2		545	579	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923680	39923681	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	rs1555915763	NA	P-0019281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	217	541	0	ENST00000378444.4:c.3410_3411del	p.Lys1137SerfsTer4	p.K1137Sfs*4	ENST00000378444	NM_001123385.1	1137	aAA/a	7/15	1	2	FACETS	0.995	0.932	1	0.995	0.932	1	CLONAL	1	TRUE	1	0.742892454357772	2		541	587	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104325	2104327	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs1342475885	NA	P-0019281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	255	544	0	ENST00000219476.3:c.369_371del	p.Phe124del	p.F124del	ENST00000219476	NM_000548.3	122	cTCTtc/ctc	5/42	0.742892454357772	1	FACETS	0.963	0.916	1	0.963	0.916	1	CLONAL	1	TRUE	0	0.742892454357772	1		544	448	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633289	12633291	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0019281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	201	510	0	ENST00000251849.4:c.1109_1111del	p.Gly370del	p.G370del	ENST00000251849	NM_002880.3	370	gGAGat/gat	11/17	0.742892454357772	1	FACETS	0.893	0.841	0.944	0.893	0.841	0.944	CLONAL	1	TRUE	0	0.742892454357772	1		510	381	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286872	33286873	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0019281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	245	575	0	ENST00000374542.5:c.2064_2065del	p.Pro689GlnfsTer51	p.P689Qfs*51	ENST00000374542	NM_001141970.1	688	tcTCcc/tccc	7/8	0.742892454357772	1	FACETS	0.892	0.845	0.938	0.892	0.845	0.938	CLONAL	1	TRUE	0	0.742892454357772	1		575	465	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	158	736	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.754315073213154	2		736	413	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795608	42795609	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1555770200	NA	P-0019282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	20	835	0	ENST00000575354.2:c.2694dup	p.Lys899GlnfsTer32	p.K899Qfs*32	ENST00000575354	NM_015125.3	896	-/C	10/20	0.754315073213154	1	FACETS	0.083	0.063	0.106	0.083	0.063	0.106	SUBCLONAL	1	TRUE	0	0.754315073213154	1		835	400	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0019282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	106	290	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.946	0.86	1	0.946	0.86	1	CLONAL	1	TRUE	1	0.754315073213154	2		291	297	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791757	42791757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568504941	NA	P-0019282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	23	681	0	ENST00000575354.2:c.643C>T	p.Arg215Trp	p.R215W	ENST00000575354	NM_015125.3	215	Cgg/Tgg	5/20	0.754315073213154	1	FACETS	0.133	0.103	0.167	0.133	0.103	0.167	SUBCLONAL	1	TRUE	0	0.754315073213154	1		681	286	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797278	42797278	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs968289754	NA	P-0019282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	27	804	0	ENST00000575354.2:c.3640C>T	p.Arg1214Ter	p.R1214*	ENST00000575354	NM_015125.3	1214	Cga/Tga	15/20	0.754315073213154	1	FACETS	0.132	0.105	0.163	0.132	0.105	0.163	SUBCLONAL	1	TRUE	0	0.754315073213154	1		804	337	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791715	42791715	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1157030312	NA	P-0019282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	23	644	1	ENST00000575354.2:c.601C>T	p.Arg201Trp	p.R201W	ENST00000575354	NM_015125.3	201	Cgg/Tgg	5/20	0.754315073213154	1	FACETS	0.146	0.114	0.183	0.146	0.114	0.183	SUBCLONAL	1	TRUE	0	0.754315073213154	1		645	260	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	47	736	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		736	583	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	248	736	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.937	0.882	0.992	0.937	0.882	0.992	CLONAL	1	TRUE	1	0.85542434979078	2		736	619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572928	7572929	+	frameshift_variant,stop_lost	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0019284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	299	557	0	ENST00000269305.4:c.1180_1181del	p.Ter394ThrfsTer76	p.*394Tfs*76	ENST00000269305	NM_001126112.2	394	TGa/a	11/11	0.85542434979078	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.85542434979078	1		557	377	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244392	5244392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377318412	NA	P-0019284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	382	866	0	ENST00000357368.4:c.1090G>A	p.Val364Ile	p.V364I	ENST00000357368	NM_002850.3	364	Gtc/Atc	11/38	0.845065687848775	3	FACETS	0.945	0.896	0.994	0.472	0.448	0.497	CLONAL	1	TRUE	1	0.85542434979078	3		866	1350	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954362	48954363	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0019284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	136	568	0	ENST00000267163.4:c.1483_1484del	p.Met495GlyfsTer4	p.M495Gfs*4	ENST00000267163	NM_000321.2	495	ATg/g	16/27	0.85542434979078	1	FACETS	0.933	0.88	0.984	0.933	0.88	0.984	CLONAL	1	TRUE	0	0.85542434979078	1		568	195	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170002305	170002305	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	79	203	0	ENST00000295797.4:c.1124T>A	p.Ile375Asn	p.I375N	ENST00000295797	NM_002740.5	375	aTt/aAt	12/18	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.85542434979078	2		203	129	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	87	736	0				ENST00000310581	NM_198253.2	-/1132			0.366573578727355	0	FACETS	0.415	0.37	0.462			1	SUBCLONAL	1	FALSE	0	0.536787910299643	0		736	362	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0019285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	155	716	1	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.451931449268272	1	FACETS	0.78	0.718	0.843	0.78	0.718	0.843	SUBCLONAL	1	FALSE	0	0.536787910299643	1		717	542	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21643178	21643178	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	169	845	0	ENST00000421138.2:c.349G>A	p.Gly117Ser	p.G117S	ENST00000421138		117	Ggt/Agt	5/16	1	2	FACETS	0.707	0.65	0.766	0.707	0.65	0.766	SUBCLONAL	1	FALSE	1	0.536787910299643	2		845	891	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56474118	56474118	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	161	817	0	ENST00000267101.3:c.34T>A	p.Leu12Met	p.L12M	ENST00000267101	NM_001982.3	12	Ttg/Atg	1/28	1	2	FACETS	0.777	0.714	0.843	0.777	0.714	0.843	SUBCLONAL	1	FALSE	1	0.536787910299643	2		817	772	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028511	42028511	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs754614435	NA	P-0019285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	97	642	0	ENST00000219905.7:c.4049A>C	p.Lys1350Thr	p.K1350T	ENST00000219905	NM_001164273.1	1350	aAg/aCg	13/24	1	2	FACETS	0.608	0.543	0.677	0.608	0.543	0.677	SUBCLONAL	1	FALSE	1	0.536787910299643	2		642	594	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39629549	39629549	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	94	581	0	ENST00000262039.4:c.2243A>G	p.Asn748Ser	p.N748S	ENST00000262039	NM_002647.2	748	aAc/aGc	21/25	1	2	FACETS	0.663	0.592	0.739	0.663	0.592	0.739	SUBCLONAL	1	FALSE	1	0.536787910299643	2		581	528	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156496	55156496	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs200042995	NA	P-0019285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	25	548	0	ENST00000257290.5:c.2897A>G	p.His966Arg	p.H966R	ENST00000257290	NM_006206.4	966	cAc/cGc	22/23	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.536787910299643	NA		548	371	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845678	151845678	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	44	644	0	ENST00000262189.6:c.13334G>C	p.Gly4445Ala	p.G4445A	ENST00000262189	NM_170606.2	4445	gGt/gCt	52/59	NA	2	FACETS	0.262	0.219	0.31			1	INDETERMINATE	1	FALSE	NA	0.536787910299643	2		644	626	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797330	135797330	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs118203396	NA	P-0019285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	99	395	0	ENST00000298552.3:c.539T>C	p.Leu180Pro	p.L180P	ENST00000298552	NM_001162426.1	180	cTc/cCc	7/23	0.451931449268272	1	FACETS	0.865	0.781	0.951	0.865	0.781	0.951	CLONAL	1	FALSE	0	0.536787910299643	1		395	312	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0019295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	78	473	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.922	0.815	1	0.922	0.815	1	CLONAL	1	TRUE	1	0.448918362124375	2		473	377	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771319	68771319	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1555509622	NA	P-0019295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	40	216	0	ENST00000261769.5:c.1A>G	p.Met1?	p.M1?	ENST00000261769	NM_004360.3	1	Atg/Gtg	1/16	0.448918362124375	1	FACETS	0.973	0.824	1	0.973	0.824	1	CLONAL	1	TRUE	0	0.448918362124375	1		216	142	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514203	69514203	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	73	822	0	ENST00000294312.3:c.478C>G	p.Leu160Val	p.L160V	ENST00000294312	NM_005117.2	160	Ctt/Gtt	3/3	0.1206680906374	6	FACETS	0.52	0.453	0.593			1	INDETERMINATE	1	TRUE	NA	0.448918362124375	6		822	1186	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514274	69514274	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	80	810	0	ENST00000294312.3:c.407C>T	p.Ser136Phe	p.S136F	ENST00000294312	NM_005117.2	136	tCc/tTc	3/3	0.1206680906374	6	FACETS	0.567	0.497	0.642			1	INDETERMINATE	1	TRUE	NA	0.448918362124375	6		810	1193	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67132595	67132621	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATGATTTTGTCATTGCAGGCAAGAAGA	ATGATTTTGTCATTGCAGGCAAGAAGA	-	novel	NA	P-0019295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	91	571	0	ENST00000412916.2:c.496-18_504del		p.X166_splice	ENST00000412916		166		6/6	0.448918362124375	1	FACETS	0.788	0.704	0.876	0.788	0.704	0.876	SUBCLONAL	1	TRUE	0	0.448918362124375	1		571	399	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645892	67645894	+	inframe_deletion	In_Frame_Del	DEL	ACG	ACG	-	novel	NA	P-0019295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	176	711	0	ENST00000264010.4:c.820_822del	p.Thr274del	p.T274del	ENST00000264010	NM_006565.3	274	ACG/-	4/12	0.448918362124375	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.448918362124375	1		711	605	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359617	40359617	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747470866	NA	P-0019295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	56	771	0	ENST00000293328.3:c.2036A>G	p.Tyr679Cys	p.Y679C	ENST00000293328	NM_012448.3	679	tAc/tGc	16/19	1	2	FACETS	0.263	0.224	0.305	0.263	0.224	0.305	SUBCLONAL	1	TRUE	1	0.448918362124375	2		771	950	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148529838	148529838	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1182369323	NA	P-0019295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	28	525	2	ENST00000320356.2:c.251C>T	p.Ser84Leu	p.S84L	ENST00000320356	NM_004456.4	84	tCg/tTg	4/20	1	2	FACETS	0.235	0.187	0.29	0.235	0.187	0.29	SUBCLONAL	1	TRUE	1	0.448918362124375	2		527	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	179	872	0	ENST00000269305.4:c.596del	p.Gly199GlufsTer48	p.G199Efs*48	ENST00000269305	NM_001126112.2	199	gGa/ga	6/11	0.354738225085197	1	FACETS	0.891	0.825	0.96	0.891	0.825	0.96	CLONAL	1	TRUE	0	0.461745025607958	1		872	669	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0019298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	307	918	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.329024492464574	6	FACETS	0.888	0.84	0.937			1	CLONAL	4	TRUE	NA	0.329024492464574	6		918	871	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0019298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	48	717	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.145728940979677	3	FACETS	0.56	0.472	0.656	0.187	0.157	0.219	INDETERMINATE	1	TRUE	0	0.329024492464574	3		718	607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	202	907	1	ENST00000269305.4:c.853G>T	p.Glu285Ter	p.E285*	ENST00000269305	NM_001126112.2	285	Gag/Tag	8/11	0.145728940979677	3	FACETS	0.897	0.833	0.963	0.598	0.555	0.642	INDETERMINATE	2	TRUE	0	0.329024492464574	3		908	797	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028850	47028850	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	123	796	0	ENST00000377604.3:c.154G>T	p.Glu52Ter	p.E52*	ENST00000377604	NM_001204468.1	52	Gag/Tag	3/24	0.329024492464574	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.329024492464574	1		796	575	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225449680	225449680	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	150	503	0	ENST00000264414.4:c.47T>C	p.Met16Thr	p.M16T	ENST00000264414	NM_003590.4	16	aTg/aCg	1/16	0.329024492464574	3	FACETS	0.994	0.914	1	0.994	0.914	1	CLONAL	2	TRUE	1	0.329024492464574	3		503	534	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406267	70406267	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	191	858	0	ENST00000373644.4:c.3781G>T	p.Asp1261Tyr	p.D1261Y	ENST00000373644	NM_030625.2	1261	Gat/Tat	4/12	0.280691944616104	3	FACETS	0.949	0.881	1	0.949	0.881	1	CLONAL	2	TRUE	1	0.329024492464574	3		858	712	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437034	110437034	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	39	107	0	ENST00000375856.3:c.1367C>T	p.Ser456Leu	p.S456L	ENST00000375856	NM_003749.2	456	tCg/tTg	1/2	0.188144323409305	5	FACETS	1	0.926	1	1	0.926	1	INDETERMINATE	3	TRUE	2	0.329024492464574	5		107	103	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223186	5223186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	237	993	0	ENST00000357368.4:c.2617G>A	p.Glu873Lys	p.E873K	ENST00000357368	NM_002850.3	873	Gag/Aag	18/38	0.287115003927932	2	FACETS	0.983	0.921	1	0.983	0.921	1	CLONAL	2	TRUE	0	0.329024492464574	2		993	733	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370851	225370851	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0019298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	40	442	0	ENST00000264414.4:c.1030-2A>G		p.X344_splice	ENST00000264414	NM_003590.4	344			0.329024492464574	3	FACETS	0.798	0.664	0.945	0.399	0.332	0.473	CLONAL	1	TRUE	1	0.329024492464574	3		442	355	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860401	42860401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	187	764	0	ENST00000398585.3:c.476C>T	p.Ser159Phe	p.S159F	ENST00000398585	NM_001135099.1	159	tCc/tTc	5/14	0.228902473061774	3	FACETS	0.905	0.839	0.974	0.905	0.839	0.974	CLONAL	2	TRUE	1	0.329024492464574	3		764	731	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539113	23539113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	82	569	0	ENST00000380871.4:c.326C>T	p.Thr109Ile	p.T109I	ENST00000380871	NM_006167.3	109	aCt/aTt	2/2	0.287115003927932	2	FACETS	1	0.953	1	0.573	0.507	0.642	CLONAL	1	TRUE	0	0.329024492464574	2		569	435	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900287	101900287	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	104	560	0	ENST00000374994.4:c.721T>A	p.Ser241Thr	p.S241T	ENST00000374994	NM_004612.2	241	Tcg/Acg	4/9	0.280691944616104	3	FACETS	1	0.978	1	0.677	0.608	0.749	CLONAL	1	TRUE	1	0.329024492464574	3		560	544	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855958	76855958	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	111	882	0	ENST00000373344.5:c.5642G>C	p.Arg1881Thr	p.R1881T	ENST00000373344	NM_000489.3	1881	aGa/aCa	23/35	0.329024492464574	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.329024492464574	1		882	532	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591115	67591123	+	inframe_deletion	In_Frame_Del	DEL	CTTATCCAG	CTTATCCAG	-	novel	NA	P-0019299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	23	465	0	ENST00000274335.5:c.1710_1718del	p.Ile571_Leu573del	p.I571_L573del	ENST00000274335		570	CTTATCCAG/-	12/15	0.281443685988541	1	FACETS	0.867	0.682	1	0.867	0.682	1	CLONAL	1	TRUE	0	0.281443685988541	1		465	162	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574007	7574008	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0019299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	38	902	0	ENST00000269305.4:c.1018_1019dup	p.Met340IlefsTer6	p.M340Ifs*6	ENST00000269305	NM_001126112.2	340	atg/atATg	10/11	0.281443685988541	1	FACETS	0.906	0.754	1	0.906	0.754	1	CLONAL	1	TRUE	0	0.281443685988541	1		902	256	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383628	42383628	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	22	610	0	ENST00000221972.3:c.403G>T	p.Asp135Tyr	p.D135Y	ENST00000221972	NM_021601.3	135	Gac/Tac	3/5	0.281443685988541	1	FACETS	0.742	0.579	0.929	0.742	0.579	0.929	CLONAL	1	TRUE	0	0.281443685988541	1		610	181	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0019300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	150	708	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	1	2	FACETS	0.917	0.841	0.995	0.917	0.841	0.995	CLONAL	1	TRUE	1	0.553835359589773	2		708	591	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0019300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	8	473	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.095	0.06	0.139	0.095	0.06	0.139	SUBCLONAL	1	TRUE	1	0.553835359589773	2		473	305	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	170	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.269531836621843	2	FACETS	0.837	0.775	0.9	0.837	0.775	0.9	CLONAL	2	TRUE	0	0.387591124399144	2		509	524	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164177	108164177	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0019301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	59	385	0	ENST00000278616.4:c.4749C>G	p.Tyr1583Ter	p.Y1583*	ENST00000278616	NM_000051.3	1583	taC/taG	31/63	0.387591124399144	3	FACETS	0.799	0.689	0.918	0.399	0.344	0.459	CLONAL	1	TRUE	1	0.387591124399144	3		385	455	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236110	108236110	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0019301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	329	724	0	ENST00000278616.4:c.9046A>T	p.Lys3016Ter	p.K3016*	ENST00000278616	NM_000051.3	3016	Aaa/Taa	63/63	0.387591124399144	3	FACETS	0.937	0.887	0.989	0.937	0.887	0.989	CLONAL	2	TRUE	1	0.387591124399144	3		724	1081	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	51	736	0				ENST00000310581	NM_198253.2	-/1132			0.134997451374846	0	FACETS	0.712	0.607	0.826			1	SUBCLONAL	2	TRUE	0	0.16	0		736	376	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37665992	37665992	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	41	648	5	ENST00000447079.4:c.2644C>T	p.Arg882Trp	p.R882W	ENST00000447079	NM_015083.1	882	Cgg/Tgg	7/14	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.16	2		653	484	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665247	176665247	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886060443	NA	P-0019302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	22	445	1	ENST00000439151.2:c.3931C>T	p.Arg1311Cys	p.R1311C	ENST00000439151	NM_022455.4	1311	Cgc/Tgc	7/23	1	2	FACETS	0.694	0.537	0.877	0.694	0.537	0.877	SUBCLONAL	1	TRUE	1	0.16	2		446	396	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0019302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	110	1133	1	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.16	2		1134	1209	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987076	36987076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	36	986	0	ENST00000354822.5:c.613G>A	p.Glu205Lys	p.E205K	ENST00000354822	NM_001079668.2	205	Gag/Aag	3/3	1	2	FACETS	0.745	0.611	0.896	0.745	0.611	0.896	SUBCLONAL	1	TRUE	1	0.16	2		986	604	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779057	3779058	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0019302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	49	733	2	ENST00000262367.5:c.5990_5991delinsTT	p.Pro1997Leu	p.P1997L	ENST00000262367	NM_004380.2	1997	cCC/cTT	31/31	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.16	2		735	467	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265285	46265285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1447875218	NA	P-0019302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	28	545	1	ENST00000371998.3:c.2155G>A	p.Gly719Arg	p.G719R	ENST00000371998		719	Gga/Aga	12/23	1	2	FACETS	0.788	0.629	0.97	0.788	0.629	0.97	CLONAL	1	TRUE	1	0.16	2		546	444	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974744	21974744	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs775176191	NA	P-0019302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	19	327	0	ENST00000304494.5:c.83T>G	p.Val28Gly	p.V28G	ENST00000304494	NM_000077.4	28	gTg/gGg	1/3	0.189774006293499	1	FACETS	0.867	0.659	1	0.867	0.659	1	CLONAL	1	TRUE	0	0.16	1		327	252	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328332	137328332	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	52	817	4	ENST00000481739.1:c.1261C>T	p.Arg421Cys	p.R421C	ENST00000481739	NM_002957.4	421	Cgc/Tgc	10/10	0.189774006293499	1	FACETS	0.858	0.729	1	0.858	0.729	1	CLONAL	1	TRUE	0	0.16	1		821	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0019304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	175	760	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.536087434923433	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.536087434923433	1		761	471	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0019304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	113	462	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.51570714668858	1	FACETS	0.721	0.653	0.791	0.721	0.653	0.791	SUBCLONAL	1	TRUE	0	0.536087434923433	1		462	428	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074242	8074246	+	frameshift_variant	Frame_Shift_Del	DEL	AAGGG	AAGGG	-	novel	NA	P-0019304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	142	742	0	ENST00000377482.5:c.413_417del	p.Ser138PhefsTer8	p.S138Ffs*8	ENST00000377482	NM_018948.3	138	tCCCTT/t	4/4	0.239229917300411	4	FACETS	0.758	0.694	0.824	0.758	0.694	0.824	INDETERMINATE	2	TRUE	2	0.536087434923433	4		742	537	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929479	81929479	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	119	676	0	ENST00000359376.3:c.1140C>G	p.Ile380Met	p.I380M	ENST00000359376	NM_002661.3	380	atC/atG	13/33	0.536087434923433	1	FACETS	0.893	0.814	0.973	0.893	0.814	0.973	CLONAL	1	TRUE	0	0.536087434923433	1		676	364	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952019	178952019	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	84	572	0	ENST00000263967.3:c.3074C>A	p.Thr1025Asn	p.T1025N	ENST00000263967	NM_006218.2	1025	aCc/aAc	21/21	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.536087434923433	2		572	274	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0019306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	169	918	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.277826514471983	4	FACETS	0.951	0.88	1	0.951	0.88	1	CLONAL	3	FALSE	1	0.277826514471983	4		918	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578467	7578467	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	210	996	0	ENST00000269305.4:c.463A>C	p.Thr155Pro	p.T155P	ENST00000269305	NM_001126112.2	155	Acc/Ccc	5/11	0.264476937254274	2	FACETS	0.95	0.884	1	0.95	0.884	1	CLONAL	2	FALSE	0	0.277826514471983	2		996	796	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220489	1220490	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0019306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	260	789	0	ENST00000326873.7:c.582_583delinsAA	p.Asp194_Leu195delinsGluMet	p.D194_L195delinsEM	ENST00000326873	NM_000455.4	194	gaCCtg/gaAAtg	4/10	0.264476937254274	2	FACETS	0.845	0.796	0.896	1	0.991	1	CLONAL	3	FALSE	0	0.277826514471983	2		789	738	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220592	1220671	+	frameshift_variant	Frame_Shift_Del	DEL	TTCGCGGCGGACGACACCTGCCGGACCAGCCAGGGCTCCCCGGCTTTCCAGCCGCCCGAGATTGCCAACGGCCTGGACAC	TTCGCGGCGGACGACACCTGCCGGACCAGCCAGGGCTCCCCGGCTTTCCAGCCGCCCGAGATTGCCAACGGCCTGGACAC	-	novel	NA	P-0019306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	243	631	0	ENST00000326873.7:c.610_689del	p.Phe204LeufsTer35	p.F204Lfs*35	ENST00000326873	NM_000455.4	204	TTCGCGGCGGACGACACCTGCCGGACCAGCCAGGGCTCCCCGGCTTTCCAGCCGCCCGAGATTGCCAACGGCCTGGACACc/c	5/10	0.264476937254274	2	FACETS	0.84	0.789	0.892	1	0.99	1	CLONAL	3	FALSE	0	0.277826514471983	2		631	694	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610611	10610611	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0019306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	186	744	0	ENST00000171111.5:c.99C>G	p.Tyr33Ter	p.Y33*	ENST00000171111	NM_203500.1	33	taC/taG	2/6	0.264476937254274	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	FALSE	0	0.277826514471983	2		744	632	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426736	212426736	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs142841164	NA	P-0019306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	142	720	1	ENST00000342788.4:c.2379G>T	p.Gln793His	p.Q793H	ENST00000342788	NM_005235.2	793	caG/caT	20/28	0.255542479727135	3	FACETS	0.855	0.781	0.932	0.855	0.781	0.932	CLONAL	2	FALSE	1	0.277826514471983	3		721	681	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6038764	6038764	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	75	853	0	ENST00000265849.7:c.680del	p.Ile227ThrfsTer31	p.I227Tfs*31	ENST00000265849	NM_000535.5	227	aTc/ac	6/15	0.255542479727135	3	FACETS	0.715	0.625	0.812	0.358	0.312	0.406	SUBCLONAL	1	FALSE	1	0.277826514471983	3		853	860	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249878	110249878	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	156	719	0	ENST00000374672.4:c.797A>G	p.Tyr266Cys	p.Y266C	ENST00000374672	NM_004235.4	266	tAc/tGc	3/5	0.276523366582395	2	FACETS	0.891	0.819	0.966	0.891	0.819	0.966	CLONAL	2	FALSE	0	0.277826514471983	2		719	630	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	272	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.499218485722001	3	FACETS	0.895	0.844	0.947	0.895	0.844	0.947	CLONAL	2	TRUE	1	0.511812498874016	3		555	746	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0019307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	170	812	1	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	0.511812498874016	1	FACETS	0.799	0.738	0.861	0.799	0.738	0.861	SUBCLONAL	1	TRUE	0	0.511812498874016	1		813	619	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2588121	2588121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	16	38	0	ENST00000342085.4:c.8G>A	p.Arg3Lys	p.R3K	ENST00000342085	NM_002613.4	3	aGg/aAg	1/14	NA	2	FACETS	0.544	0.406	0.704			1	INDETERMINATE	1	TRUE	NA	0.511812498874016	2		38	115	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163770	152163770	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	59	619	0	ENST00000206249.3:c.491G>C	p.Arg164Thr	p.R164T	ENST00000206249	NM_000125.3	164	aGa/aCa	2/8	0.161967566799782	2	FACETS	0.364	0.312	0.42	0.182	0.156	0.21	INDETERMINATE	1	TRUE	0	0.511812498874016	2		619	634	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0019316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	159	674	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.580492715796404	2		674	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577518	7577518	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519995	NA	P-0019316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	365	823	0	ENST00000269305.4:c.763A>T	p.Ile255Phe	p.I255F	ENST00000269305	NM_001126112.2	255	Atc/Ttc	7/11	0.361626948591252	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.580492715796404	1		823	665	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974799	21974799	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	34	201	0	ENST00000304494.5:c.28G>T	p.Glu10Ter	p.E10*	ENST00000304494	NM_000077.4	10	Gag/Tag	1/3	0.580492715796404	1	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	0	0.580492715796404	1		201	77	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250272	39250272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397517147	NA	P-0019316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	223	1112	3	ENST00000402219.2:c.1297G>A	p.Glu433Lys	p.E433K	ENST00000402219	NM_005633.3	433	Gag/Aag	10/23	1	2	FACETS	0.859	0.801	0.919	0.859	0.801	0.919	CLONAL	1	TRUE	1	0.580492715796404	2		1115	894	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433004	49433005	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AG	novel	NA	P-0019316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	362	689	1	ENST00000301067.7:c.8366_8366+1delinsCT		p.X2789_splice	ENST00000301067	NM_003482.3	2789		33/54	0.580492715796404	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.580492715796404	3		690	802	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135360	30135360	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	223	749	0	ENST00000331968.5:c.458C>T	p.Ser153Leu	p.S153L	ENST00000331968	NM_002742.2	153	tCa/tTa	3/18	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.580492715796404	2		749	755	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690618	88690619	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0019316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	125	562	2	ENST00000360948.2:c.411_412delinsAA	p.Asn137Lys	p.N137K	ENST00000360948	NM_001012338.2	137	aaCCgg/aaAAgg	5/19	0.250040880869308	1	FACETS	0.567	0.515	0.621	0.567	0.515	0.621	INDETERMINATE	1	TRUE	0	0.580492715796404	1		564	539	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873019	134873019	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	49	740	0	ENST00000398015.3:c.1323C>A	p.His441Gln	p.H441Q	ENST00000398015	NM_004441.4	441	caC/caA	6/16	0.340063740286133	3	FACETS	0.268	0.226	0.315	0.134	0.113	0.158	INDETERMINATE	1	TRUE	1	0.580492715796404	3		740	812	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163600	32163600	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	102	627	0	ENST00000375023.3:c.5626T>C	p.Cys1876Arg	p.C1876R	ENST00000375023	NM_004557.3	1876	Tgt/Cgt	30/30	0.250040880869308	1	FACETS	0.419	0.375	0.465	0.419	0.375	0.465	INDETERMINATE	1	TRUE	0	0.580492715796404	1		627	595	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0019317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	192	657	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.755107420218502	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.773146253607693	2		657	235	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243859016	243859016	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs397514606	NA	P-0019317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	13	359	0	ENST00000263826.5:c.49G>A	p.Glu17Lys	p.E17K	ENST00000263826	NM_005465.4	17	Gaa/Aaa	2/13	1	2	FACETS	0.647	0.476	0.84	0.647	0.476	0.84	SUBCLONAL	1	TRUE	1	0.773146253607693	2		359	52	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117753456	117753456	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	69	689	0	ENST00000369458.3:c.22C>T	p.Leu8Phe	p.L8F	ENST00000369458	NM_024626.3	8	Ctc/Ttc	1/6	1	2	FACETS	0.96	0.853	1	0.96	0.853	1	CLONAL	1	TRUE	1	0.773146253607693	2		689	186	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748117	72748117	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	85	587	0	ENST00000357731.5:c.61C>T	p.Leu21Phe	p.L21F	ENST00000357731	NM_173808.2	21	Ctc/Ttc	1/7	1	2	FACETS	0.894	0.803	0.988	0.894	0.803	0.988	CLONAL	1	TRUE	1	0.773146253607693	2		587	246	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176055007	176055007	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	72	660	1	ENST00000367669.3:c.1046A>T	p.Tyr349Phe	p.Y349F	ENST00000367669	NM_022457.5	349	tAt/tTt	10/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.773146253607693	2		661	155	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333608	70333608	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	32	496	0	ENST00000373644.4:c.1513A>G	p.Ile505Val	p.I505V	ENST00000373644	NM_030625.2	505	Ata/Gta	2/12	1	2	FACETS	0.853	0.712	1	0.853	0.712	1	CLONAL	1	TRUE	1	0.773146253607693	2		496	97	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435415	18435415	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	22	407	0	ENST00000266497.5:c.400C>A	p.His134Asn	p.H134N	ENST00000266497		134	Cat/Aat	1/31	1	2	FACETS	0.79	0.632	0.962	0.79	0.632	0.962	CLONAL	1	TRUE	1	0.773146253607693	2		407	72	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422091	81422091	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	75	641	0	ENST00000298171.2:c.67G>A	p.Gly23Arg	p.G23R	ENST00000298171	NM_000369.2	23	Ggg/Agg	1/10	1	2	FACETS	0.822	0.731	0.917	0.822	0.731	0.917	CLONAL	1	TRUE	1	0.773146253607693	2		641	236	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209110120	209110120	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	57	586	0	ENST00000345146.2:c.443G>T	p.Gly148Val	p.G148V	ENST00000345146	NM_005896.2	148	gGg/gTg	5/10	1	2	FACETS	0.793	0.692	0.899	0.793	0.692	0.899	SUBCLONAL	1	TRUE	1	0.773146253607693	2		586	186	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570089	212570089	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	91	568	0	ENST00000342788.4:c.1152A>G	p.Ile384Met	p.I384M	ENST00000342788	NM_005235.2	384	atA/atG	10/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.773146253607693	2		568	182	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442845	187442845	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	59	555	1	ENST00000232014.4:c.1861G>T	p.Val621Leu	p.V621L	ENST00000232014	NM_001130845.1	621	Gtg/Ttg	9/10	1	2	FACETS	0.551	0.478	0.629	0.551	0.478	0.629	SUBCLONAL	1	TRUE	1	0.773146253607693	2		556	277	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146500	55146500	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	22	325	0	ENST00000257290.5:c.2174T>C	p.Phe725Ser	p.F725S	ENST00000257290	NM_006206.4	725	tTt/tCt	16/23	1	2	FACETS	0.933	0.752	1	0.933	0.752	1	CLONAL	1	TRUE	1	0.773146253607693	2		325	61	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289079	33289079	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	145	774	0	ENST00000374542.5:c.473A>G	p.Asn158Ser	p.N158S	ENST00000374542	NM_001141970.1	158	aAt/aGt	3/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.773146253607693	2		774	332	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997807	149997807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	45	741	2	ENST00000253339.5:c.2660G>A	p.Cys887Tyr	p.C887Y	ENST00000253339		887	tGt/tAt	5/7	1	2	FACETS	0.82	0.704	0.942	0.82	0.704	0.942	CLONAL	1	TRUE	1	0.773146253607693	2		743	142	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249797	110249797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1040773971	NA	P-0019317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	182	868	0	ENST00000374672.4:c.878C>T	p.Pro293Leu	p.P293L	ENST00000374672	NM_004235.4	293	cCt/cTt	3/5	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.773146253607693	2		868	440	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732884	44732884	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	176	711	1	ENST00000377967.4:c.87A>T	p.Lys29Asn	p.K29N	ENST00000377967	NM_021140.2	29	aaA/aaT	1/29	0.486116583458668	5	FACETS	0.907	0.841	0.975			1	CLONAL	2	TRUE	NA	0.773146253607693	5		712	542	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829782	76829782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	49	735	0	ENST00000373344.5:c.6259G>A	p.Asp2087Asn	p.D2087N	ENST00000373344	NM_000489.3	2087	Gat/Aat	28/35	0.299160397417861	1	FACETS	0.627	0.546	0.711	0.627	0.546	0.711	INDETERMINATE	1	TRUE	0	0.773146253607693	1		735	124	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858135	152858135	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	565	1118	0	ENST00000406277.2:c.480G>C	p.Gln160His	p.Q160H	ENST00000406277	NM_152274.4	160	caG/caC	6/7	0.299160397417861	1	FACETS	1	0.983	1	1	0.983	1	INDETERMINATE	1	TRUE	0	0.773146253607693	1		1118	879	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878111	48878111	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	TT	novel	NA	P-0019317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	238	126	0	ENST00000267163.4:c.63delinsTT	p.Ala22CysfsTer9	p.A22Cfs*9	ENST00000267163	NM_000321.2	21	ccG/ccTT	1/27	0.773146253607693	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.773146253607693	2		126	266	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	95	640	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	0.31	2		640	517	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	82	740	6	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.31	2		746	488	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	77	849	5	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	0.659	0.578	0.746	0.659	0.578	0.746	SUBCLONAL	1	TRUE	1	0.31	2		854	754	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	370	894	7	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.0918674596195326	3	FACETS	0.94	0.894	0.986	1	0.995	1	INDETERMINATE	3	TRUE	1	0.31	3		901	978	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	174	646	1	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.856	0.791	0.923	1	0.991	1	CLONAL	2	TRUE	1	0.31	2		647	656	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	38	448	0	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	1	FACETS	0.651	0.54	0.775	0.651	0.54	0.775	SUBCLONAL	1	TRUE	0	0.31	1		448	318	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133242017	133242017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778288256	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	207	881	1	ENST00000320574.5:c.2339C>T	p.Ser780Leu	p.S780L	ENST00000320574	NM_006231.2	780	tCg/tTg	21/49	0.123137505638123	3	FACETS	1	0.934	1	0.669	0.623	0.717	INDETERMINATE	2	TRUE	0	0.31	3		882	768	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537053	41537053	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1280109939	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	78	454	1	ENST00000263253.7:c.1880C>T	p.Ala627Val	p.A627V	ENST00000263253	NM_001429.3	627	gCg/gTg	10/31	0.156222233782688	0	FACETS	1	0.926	1			1	INDETERMINATE	1	TRUE	0	0.31	0		455	328	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129385	152129385	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	40	620	0	ENST00000206249.3:c.338C>T	p.Pro113Leu	p.P113L	ENST00000206249	NM_000125.3	113	cCg/cTg	1/8	0.0918674596195326	3	FACETS	0.6	0.498	0.713	0.3	0.249	0.357	INDETERMINATE	1	TRUE	1	0.31	3		620	497	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67459125	67459125	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	134	955	1	ENST00000327367.4:c.545del	p.Pro182LeufsTer4	p.P182Lfs*4	ENST00000327367	NM_005902.3	181	Ccc/cc	4/9	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.31	2		956	750	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764347	39764347	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	131	787	0	ENST00000288319.7:c.765del	p.Arg256GlyfsTer35	p.R256Gfs*35	ENST00000288319	NM_182918.3	255	ccC/cc	7/10	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.31	2		787	779	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	49	410	3	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	0.152339016779465	3	FACETS	1	0.872	1			1	INDETERMINATE	1	TRUE	NA	0.31	3		413	355	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196880	108196880	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	115	684	2	ENST00000278616.4:c.6908del	p.Lys2303ArgfsTer7	p.K2303Rfs*7	ENST00000278616	NM_000051.3	2301	gcA/gc	47/63	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.31	2		686	677	SUCCESS
APC	324	MSKCC	GRCh37	5	112175687	112175687	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	96	480	0	ENST00000257430.4:c.4396G>T	p.Gly1466Ter	p.G1466*	ENST00000257430	NM_000038.5	1466	Gga/Tga	16/16	0.0918674596195326	3	FACETS	0.756	0.677	0.84	0.756	0.677	0.84	INDETERMINATE	2	TRUE	1	0.31	3		480	473	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843495	3843495	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	114	666	4	ENST00000262367.5:c.1108C>T	p.Arg370Ter	p.R370*	ENST00000262367	NM_004380.2	370	Cga/Tga	4/31	0.156222233782688	0	FACETS	0.924	0.835	1			1	INDETERMINATE	1	TRUE	0	0.31	0		670	549	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155454	47155454	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	70	701	0	ENST00000409792.3:c.4627C>T	p.Arg1543Trp	p.R1543W	ENST00000409792	NM_014159.6	1543	Cgg/Tgg	5/21	1	2	FACETS	0.959	0.838	1	0.959	0.838	1	CLONAL	1	TRUE	1	0.31	2		701	471	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918759	50918759	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555793039	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	128	979	1	ENST00000440232.2:c.2629G>A	p.Asp877Asn	p.D877N	ENST00000440232	NM_002691.3	877	Gat/Aat	21/27	0.156222233782688	0	FACETS	0.857	0.778	0.939			1	INDETERMINATE	1	TRUE	0	0.31	0		980	665	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862749	9862749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150316865	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	134	790	4	ENST00000330684.3:c.2554G>A	p.Val852Met	p.V852M	ENST00000330684	NM_001134407.1	852	Gtg/Atg	12/13	0.156222233782688	0	FACETS	0.901	0.821	0.985			1	INDETERMINATE	1	TRUE	0	0.31	0		794	662	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434413	140434413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775889922	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	123	643	0	ENST00000288602.6:c.2285C>T	p.Ala762Val	p.A762V	ENST00000288602	NM_004333.4	762	gCg/gTg	18/18	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.31	2		643	569	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073804	8073804	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1557463619	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	55	338	2	ENST00000377482.5:c.855del	p.Arg286GlufsTer9	p.R286Efs*9	ENST00000377482	NM_018948.3	285	ccC/cc	4/4	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.31	2		340	319	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	131	678	3	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.31	2		681	639	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807363	3807364	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	96	693	0	ENST00000262367.5:c.3623dup	p.Gln1209ThrfsTer25	p.Q1209Tfs*25	ENST00000262367	NM_004380.2	1208	cca/ccCa	19/31	0.156222233782688	0	FACETS	0.793	0.708	0.882			1	INDETERMINATE	1	TRUE	0	0.31	0		693	539	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989562	212989562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755026855	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	82	370	0	ENST00000342788.4:c.149G>A	p.Arg50His	p.R50H	ENST00000342788	NM_005235.2	50	cGc/cAc	2/28	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.31	2		370	448	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643942	52643943	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	86	627	0	ENST00000394830.3:c.1953dup	p.Ser652IlefsTer13	p.S652Ifs*13	ENST00000394830	NM_018313.4	651	-/A	17/30	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.31	2		627	514	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532710	187532710	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1010116749	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	148	812	0	ENST00000441802.2:c.9683del	p.Pro3228LeufsTer42	p.P3228Lfs*42	ENST00000441802	NM_005245.3	3228	cCt/ct	14/27	0.0918674596195326	3	FACETS	1	0.987	1	0.742	0.679	0.808	INDETERMINATE	1	TRUE	1	0.31	3		812	743	SUCCESS
APC	324	MSKCC	GRCh37	5	112174466	112174466	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	76	555	1	ENST00000257430.4:c.3175G>T	p.Glu1059Ter	p.E1059*	ENST00000257430	NM_000038.5	1059	Gaa/Taa	16/16	0.0918674596195326	3	FACETS	1	0.972	1	0.692	0.61	0.78	INDETERMINATE	1	TRUE	1	0.31	3		556	409	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206814	36206814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150042294	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	96	589	4	ENST00000300305.3:c.698G>A	p.Arg233His	p.R233H	ENST00000300305		233	cGc/cAc	6/8	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.31	2		593	525	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393357	393357	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	66	603	1	ENST00000380956.4:c.205G>A	p.Ala69Thr	p.A69T	ENST00000380956	NM_001195286.1	69	Gcg/Acg	2/9	NA	2	FACETS	0.981	0.855	1			1	INDETERMINATE	1	TRUE	NA	0.31	2		604	434	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999042	100999042	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241953281	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	96	654	2	ENST00000325455.5:c.760G>A	p.Ala254Thr	p.A254T	ENST00000325455	NM_001202474.3	254	Gcg/Acg	1/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.31	2		656	500	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437288	220437288	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1190141661	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	64	1280	6	ENST00000243786.2:c.197del	p.Gly66AlafsTer61	p.G66Afs*61	ENST00000243786	NM_002191.3	64	ctG/ct	1/2	1	2	FACETS	0.499	0.431	0.573	0.499	0.431	0.573	SUBCLONAL	1	TRUE	1	0.31	2		1286	827	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448468	89448468	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	57	420	0	ENST00000336596.2:c.1432C>A	p.Gln478Lys	p.Q478K	ENST00000336596	NM_005233.5	478	Cag/Aag	7/17	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.31	2		420	330	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905514	11905514	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	134	273	0	ENST00000396373.4:c.163+1G>A		p.X55_splice	ENST00000396373	NM_001987.4	55			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.31	NA		273	381	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212522509	212522509	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs532377012	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	72	502	1	ENST00000342788.4:c.1916C>T	p.Thr639Met	p.T639M	ENST00000342788	NM_005235.2	639	aCg/aTg	16/28	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.31	2		503	440	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937711	36937711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752325760	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	96	855	2	ENST00000361632.4:c.1027C>T	p.Arg343Trp	p.R343W	ENST00000361632		343	Cgg/Tgg	8/16	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.31	2		857	547	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984830	11984830	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	122	749	0	ENST00000353533.5:c.376C>T	p.Gln126Ter	p.Q126*	ENST00000353533	NM_003010.3	126	Caa/Taa	3/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.31	2		749	604	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46736381	46736381	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs559500678	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	49	762	1	ENST00000371975.4:c.1093C>T	p.Arg365Ter	p.R365*	ENST00000371975	NM_003579.3	365	Cga/Tga	10/18	1	2	FACETS	0.546	0.462	0.639	0.546	0.462	0.639	SUBCLONAL	1	TRUE	1	0.31	2		763	579	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662759	117662759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141448347	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	87	458	0	ENST00000368508.3:c.4706G>A	p.Arg1569Gln	p.R1569Q	ENST00000368508	NM_002944.2	1569	cGg/cAg	29/43	0.0918674596195326	3	FACETS	0.785	0.699	0.876	0.785	0.699	0.876	INDETERMINATE	2	TRUE	1	0.31	3		458	413	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42384741	42384741	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1355355628	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	88	637	0	ENST00000221972.3:c.503G>A	p.Arg168Gln	p.R168Q	ENST00000221972	NM_021601.3	168	cGa/cAa	4/5	0.156222233782688	0	FACETS	0.776	0.689	0.867			1	INDETERMINATE	1	TRUE	0	0.31	0		637	505	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468065	50468065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749084924	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	68	481	1	ENST00000331340.3:c.1300G>A	p.Ala434Thr	p.A434T	ENST00000331340	NM_006060.4	434	Gcc/Acc	8/8	0.0918674596195326	3	FACETS	1	0.97	1	0.704	0.616	0.798	INDETERMINATE	1	TRUE	1	0.31	3		482	360	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229556	98229556	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	28	617	0	ENST00000331920.6:c.2402A>G	p.Tyr801Cys	p.Y801C	ENST00000331920	NM_000264.3	801	tAc/tGc	15/24	1	2	FACETS	0.388	0.31	0.478	0.388	0.31	0.478	SUBCLONAL	1	TRUE	1	0.31	2		617	465	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440334	187440334	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	140	587	3	ENST00000232014.4:c.2033G>A	p.Arg678His	p.R678H	ENST00000232014	NM_001130845.1	678	cGc/cAc	10/10	1	2	FACETS	0.765	0.7	0.834	1	0.988	1	SUBCLONAL	2	TRUE	1	0.31	2		590	590	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784394	9784394	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	123	950	0	ENST00000377346.4:c.2779C>T	p.Arg927Cys	p.R927C	ENST00000377346	NM_005026.3	927	Cgc/Tgc	22/24	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.31	2		950	646	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190768	11190768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1258909652	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	102	830	2	ENST00000361445.4:c.5431C>T	p.Arg1811Cys	p.R1811C	ENST00000361445	NM_004958.3	1811	Cgc/Tgc	39/58	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.31	2		832	575	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322620	39322620	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	119	976	3	ENST00000373001.3:c.372del	p.Phe124LeufsTer9	p.F124Lfs*9	ENST00000373001	NM_022157.3	124	ttT/tt	2/7	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.31	2		979	729	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46597612	46597612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	116	762	1	ENST00000262741.5:c.13G>A	p.Val5Met	p.V5M	ENST00000262741	NM_003629.3	5	Gtg/Atg	1/10	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.31	2		763	720	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78422338	78422338	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1244295456	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	111	532	1	ENST00000370768.2:c.1624G>A	p.Ala542Thr	p.A542T	ENST00000370768	NM_003902.3	542	Gct/Act	17/20	0.0918674596195326	3	FACETS	1	0.982	1	0.719	0.648	0.794	INDETERMINATE	1	TRUE	1	0.31	3		533	575	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471658	120471658	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	99	629	0	ENST00000256646.2:c.3833G>T	p.Ser1278Ile	p.S1278I	ENST00000256646	NM_024408.3	1278	aGc/aTc	23/34	0.0918674596195326	3	FACETS	1	0.979	1	0.707	0.633	0.784	INDETERMINATE	1	TRUE	1	0.31	3		629	522	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845975	156845975	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	81	806	0	ENST00000524377.1:c.1605G>T	p.Glu535Asp	p.E535D	ENST00000524377	NM_002529.3	535	gaG/gaT	13/17	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.31	2		806	493	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771563	112771563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1185910534	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	51	608	2	ENST00000369452.4:c.1736G>A	p.Arg579His	p.R579H	ENST00000369452	NM_007373.3	579	cGt/cAt	9/9	1	2	FACETS	0.539	0.458	0.629	0.539	0.458	0.629	SUBCLONAL	1	TRUE	1	0.31	2		610	610	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939792	71939792	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1041030521	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	114	917	1	ENST00000298229.2:c.419C>T	p.Pro140Leu	p.P140L	ENST00000298229	NM_001567.3	140	cCg/cTg	4/28	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.31	2		918	681	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203740	94203740	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752483206	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	57	546	0	ENST00000323929.3:c.914G>A	p.Arg305Gln	p.R305Q	ENST00000323929	NM_005591.3	305	cGg/cAg	9/20	1	2	FACETS	0.838	0.72	0.965	0.838	0.72	0.965	CLONAL	1	TRUE	1	0.31	2		546	439	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122658	108122658	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659425	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	101	713	0	ENST00000278616.4:c.1702A>G	p.Arg568Gly	p.R568G	ENST00000278616	NM_000051.3	568	Aga/Gga	11/63	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.31	2		713	514	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374922	118374922	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	42	621	0	ENST00000534358.1:c.8315A>C	p.Lys2772Thr	p.K2772T	ENST00000534358	NM_005933.3	2772	aAg/aCg	27/36	1	2	FACETS	0.578	0.482	0.684	0.578	0.482	0.684	SUBCLONAL	1	TRUE	1	0.31	2		621	469	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699350	18699350	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	36	628	0	ENST00000266497.5:c.3451A>G	p.Thr1151Ala	p.T1151A	ENST00000266497		1151	Aca/Gca	24/31	0.3	3	FACETS	0.455	0.373	0.547	0.227	0.186	0.274	SUBCLONAL	1	TRUE	1	0.31	3		628	590	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424384	49424384	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	176	673	0	ENST00000301067.7:c.13839G>T	p.Lys4613Asn	p.K4613N	ENST00000301067	NM_003482.3	4613	aaG/aaT	41/54	0.3	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.31	3		673	579	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433099	49433099	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	37	901	1	ENST00000301067.7:c.8272G>T	p.Gly2758Cys	p.G2758C	ENST00000301067	NM_003482.3	2758	Ggc/Tgc	33/54	0.3	3	FACETS	0.401	0.33	0.482	0.201	0.165	0.241	SUBCLONAL	1	TRUE	1	0.31	3		902	687	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435320	49435320	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	192	779	0	ENST00000301067.7:c.6235-2A>G		p.X2079_splice	ENST00000301067	NM_003482.3	2079			0.3	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.31	3		779	629	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865389	57865389	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	94	1279	0	ENST00000228682.2:c.2866T>A	p.Leu956Met	p.L956M	ENST00000228682	NM_005269.2	956	Ttg/Atg	12/12	0.3	3	FACETS	0.713	0.633	0.798	0.356	0.316	0.399	SUBCLONAL	1	TRUE	1	0.31	3		1279	983	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885255	111885255	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	92	753	1	ENST00000341259.2:c.1143G>T	p.Gln381His	p.Q381H	ENST00000341259	NM_005475.2	381	caG/caT	6/8	0.3	3	FACETS	1	0.927	1	0.528	0.47	0.591	CLONAL	1	TRUE	1	0.31	3		754	649	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536884	120536884	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781362390	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	264	987	2	ENST00000229340.5:c.302G>A	p.Arg101Gln	p.R101Q	ENST00000229340	NM_006861.6	101	cGg/cAg	4/6	0.123137505638123	3	FACETS	1	0.975	1	0.715	0.671	0.76	INDETERMINATE	2	TRUE	0	0.31	3		989	917	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26927980	26927980	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	67	678	0	ENST00000381527.3:c.419A>G	p.His140Arg	p.H140R	ENST00000381527	NM_001260.1	140	cAc/cGc	4/13	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.31	2		678	412	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626682	28626682	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	112	586	0	ENST00000241453.7:c.614G>T	p.Ser205Ile	p.S205I	ENST00000241453	NM_004119.2	205	aGc/aTc	5/24	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.31	2		586	606	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001431	29001431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	90	474	0	ENST00000282397.4:c.1301C>T	p.Ala434Val	p.A434V	ENST00000282397	NM_002019.4	434	gCc/gTc	10/30	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.31	2		474	527	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060686	38060686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780579934	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	247	1040	2	ENST00000250448.2:c.1303G>A	p.Ala435Thr	p.A435T	ENST00000250448	NM_004496.3	435	Gcc/Acc	2/2	0.3	3	FACETS	0.808	0.755	0.863	0.808	0.755	0.863	CLONAL	2	TRUE	1	0.31	3		1042	1139	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630695	90630695	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	74	868	0	ENST00000330062.3:c.791A>G	p.Asp264Gly	p.D264G	ENST00000330062	NM_002168.2	264	gAc/gGc	6/11	1	2	FACETS	0.67	0.586	0.76	0.67	0.586	0.76	SUBCLONAL	1	TRUE	1	0.31	2		868	713	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99454619	99454619	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	112	764	0	ENST00000268035.6:c.1539del	p.Pro515LeufsTer57	p.P515Lfs*57	ENST00000268035	NM_000875.3	513	cGg/cg	7/21	1	2	FACETS	0.98	0.882	1	0.98	0.882	1	CLONAL	1	TRUE	1	0.31	2		764	737	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465423	99465423	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs932826302	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	77	709	0	ENST00000268035.6:c.2248A>G	p.Met750Val	p.M750V	ENST00000268035	NM_000875.3	750	Atg/Gtg	11/21	1	2	FACETS	0.966	0.851	1	0.966	0.851	1	CLONAL	1	TRUE	1	0.31	2		709	514	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467175	99467175	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	99	718	0	ENST00000268035.6:c.2556G>A	p.Trp852Ter	p.W852*	ENST00000268035	NM_000875.3	852	tgG/tgA	12/21	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.31	2		718	580	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467758	99467758	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	80	445	0	ENST00000268035.6:c.2627A>C	p.Gln876Pro	p.Q876P	ENST00000268035	NM_000875.3	876	cAg/cCg	13/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.31	2		445	379	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639767	3639767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754761366	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	139	1040	3	ENST00000294008.3:c.3872C>T	p.Thr1291Met	p.T1291M	ENST00000294008	NM_032444.2	1291	aCg/aTg	12/15	0.156222233782688	0	FACETS	0.907	0.828	0.99			1	INDETERMINATE	1	TRUE	0	0.31	0		1043	682	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29701087	29701087	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	53	615	0	ENST00000356175.3:c.8371C>T	p.Arg2791Ter	p.R2791*	ENST00000356175	NM_000267.3	2791	Cga/Tga	57/57	1	2	FACETS	0.581	0.495	0.675	0.581	0.495	0.675	SUBCLONAL	1	TRUE	1	0.31	2		615	589	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244219	41244219	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357575	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	49	768	0	ENST00000357654.3:c.3329del	p.Lys1110SerfsTer7	p.K1110Sfs*7	ENST00000357654	NM_007294.3	1110	aAg/ag	10/23	1	2	FACETS	0.607	0.514	0.709	0.607	0.514	0.709	SUBCLONAL	1	TRUE	1	0.31	2		768	521	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118943	70118943	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555629158	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	214	1151	0	ENST00000245479.2:c.515A>G	p.Tyr172Cys	p.Y172C	ENST00000245479	NM_000346.3	172	tAc/tGc	2/3	1	2	FACETS	0.793	0.738	0.85	1	0.992	1	SUBCLONAL	2	TRUE	1	0.31	2		1151	870	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120311	70120311	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	260	1343	0	ENST00000245479.2:c.1313C>G	p.Ser438Ter	p.S438*	ENST00000245479	NM_000346.3	438	tCa/tGa	3/3	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.31	2		1343	1139	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387635	17387635	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	59	1149	1	ENST00000359435.4:c.703A>T	p.Met235Leu	p.M235L	ENST00000359435	NM_001033549.1	235	Atg/Ttg	8/9	0.156222233782688	0	FACETS	0.327	0.28	0.378			1	INDETERMINATE	1	TRUE	0	0.31	0		1150	803	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910304	50910304	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	95	941	0	ENST00000440232.2:c.1559T>C	p.Leu520Pro	p.L520P	ENST00000440232	NM_002691.3	520	cTg/cCg	13/27	0.156222233782688	0	FACETS	0.743	0.663	0.828			1	INDETERMINATE	1	TRUE	0	0.31	0		941	569	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27016049	27016049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756721845	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	110	868	0	ENST00000335756.4:c.325G>A	p.Ala109Thr	p.A109T	ENST00000335756	NM_001809.3	109	Gcc/Acc	4/5	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.31	2		868	653	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128016900	128016900	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	53	773	1	ENST00000285398.2:c.2189C>T	p.Ala730Val	p.A730V	ENST00000285398	NM_000122.1	730	gCt/gTt	14/15	1	2	FACETS	0.593	0.505	0.689	0.593	0.505	0.689	SUBCLONAL	1	TRUE	1	0.31	2		774	577	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131357	202131358	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	101	671	0	ENST00000358485.4:c.329dup	p.Arg111GlufsTer19	p.R111Efs*19	ENST00000358485	NM_001080125.1	109	gaa/gAaa	2/9	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.31	2		671	584	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662195	227662195	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	204	995	2	ENST00000305123.5:c.1260del	p.Ser421AlafsTer42	p.S421Afs*42	ENST00000305123	NM_005544.2	420	ccC/cc	1/2	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.31	2		997	941	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39721229	39721229	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	85	591	1	ENST00000361337.2:c.730+2T>C		p.X244_splice	ENST00000361337	NM_003286.2	244			0.156222233782688	0	FACETS	0.751	0.666	0.841			1	INDETERMINATE	1	TRUE	0	0.31	0		592	504	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485388	57485388	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	21	323	0	ENST00000371085.3:c.971-1G>A		p.X324_splice	ENST00000371085	NM_000516.4	324			0.156222233782688	0	FACETS	0.305	0.234	0.386			1	INDETERMINATE	1	TRUE	0	0.31	0		323	307	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650828	12650828	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	27	569	0	ENST00000251849.4:c.327del	p.Ala110HisfsTer3	p.A110Hfs*3	ENST00000251849	NM_002880.3	109	aaA/aa	4/17	1	2	FACETS	0.41	0.326	0.506	0.41	0.326	0.506	SUBCLONAL	1	TRUE	1	0.31	2		569	425	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713762	30713762	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	50	615	0	ENST00000295754.5:c.1087A>G	p.Ser363Gly	p.S363G	ENST00000295754	NM_003242.5	363	Agt/Ggt	4/7	1	2	FACETS	0.703	0.597	0.819	0.703	0.597	0.819	SUBCLONAL	1	TRUE	1	0.31	2		615	459	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266925	41266925	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	88	588	0	ENST00000349496.5:c.596T>C	p.Val199Ala	p.V199A	ENST00000349496	NM_001904.3	199	gTa/gCa	5/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.31	2		588	433	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928047	49928048	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	110	811	0	ENST00000296474.3:c.3680_3681del	p.Phe1227TrpfsTer13	p.F1227Wfs*13	ENST00000296474	NM_002447.2	1227	tTT/t	18/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.31	2		811	583	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440377	52440377	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	29	570	1	ENST00000460680.1:c.675C>A	p.Asp225Glu	p.D225E	ENST00000460680	NM_004656.3	225	gaC/gaA	9/17	1	2	FACETS	0.482	0.387	0.591	0.482	0.387	0.591	SUBCLONAL	1	TRUE	1	0.31	2		571	388	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188325	142188325	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	118	849	0	ENST00000350721.4:c.6406T>C	p.Tyr2136His	p.Y2136H	ENST00000350721	NM_001184.3	2136	Tat/Cat	38/47	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.31	2		849	655	SUCCESS
ATR	545	MSKCC	GRCh37	3	142286937	142286937	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	107	727	0	ENST00000350721.4:c.119T>C	p.Phe40Ser	p.F40S	ENST00000350721	NM_001184.3	40	tTc/tCc	2/47	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.31	2		727	563	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806237	1806237	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	87	1007	0	ENST00000260795.2:c.1256T>G	p.Leu419Arg	p.L419R	ENST00000260795		419	cTc/cGc	8/17	0.156222233782688	0	FACETS	0.771	0.685	0.863			1	INDETERMINATE	1	TRUE	0	0.31	0		1007	502	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1932446	1932446	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	63	926	0	ENST00000382891.5:c.1504T>A	p.Tyr502Asn	p.Y502N	ENST00000382891	NM_133335.3	502	Tac/Aac	6/22	0.156222233782688	0	FACETS	0.412	0.356	0.474			1	INDETERMINATE	1	TRUE	0	0.31	0		926	680	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561762	55561762	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1404387908	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	33	469	0	ENST00000288135.5:c.152G>A	p.Gly51Asp	p.G51D	ENST00000288135	NM_000222.2	51	gGc/gAc	2/21	0.156222233782688	0	FACETS	0.315	0.256	0.381			1	INDETERMINATE	1	TRUE	0	0.31	0		469	467	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976575	55976575	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	32	613	0	ENST00000263923.4:c.1250T>C	p.Val417Ala	p.V417A	ENST00000263923	NM_002253.2	417	gTg/gCg	9/30	0.156222233782688	0	FACETS	0.301	0.243	0.365			1	INDETERMINATE	1	TRUE	0	0.31	0		613	474	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532540	187532540	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	75	474	0	ENST00000441802.2:c.9853G>A	p.Gly3285Arg	p.G3285R	ENST00000441802	NM_005245.3	3285	Ggg/Agg	14/27	0.0918674596195326	3	FACETS	1	0.972	1	0.69	0.608	0.778	INDETERMINATE	1	TRUE	1	0.31	3		474	405	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235410	235410	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1258201485	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	119	840	0	ENST00000264932.6:c.1216G>A	p.Val406Met	p.V406M	ENST00000264932	NM_004168.2	406	Gtg/Atg	9/15	0.156222233782688	0	FACETS	0.88	0.796	0.968			1	INDETERMINATE	1	TRUE	0	0.31	0		840	602	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167819	56167819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751905861	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	118	611	1	ENST00000399503.3:c.1384G>A	p.Gly462Ser	p.G462S	ENST00000399503	NM_005921.1	462	Ggc/Agc	7/20	0.0918674596195326	3	FACETS	1	0.984	1	0.727	0.657	0.8	INDETERMINATE	1	TRUE	1	0.31	3		612	605	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576486	67576487	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	83	642	0	ENST00000274335.5:c.770dup	p.Asn257LysfsTer10	p.N257Kfs*10	ENST00000274335		255	-/A	5/15	0.0918674596195326	3	FACETS	1	0.97	1	0.65	0.575	0.729	INDETERMINATE	1	TRUE	1	0.31	3		642	476	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591100	67591100	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	102	605	0	ENST00000274335.5:c.1693A>C	p.Ser565Arg	p.S565R	ENST00000274335		565	Agc/Cgc	12/15	0.0918674596195326	3	FACETS	1	0.981	1	0.732	0.657	0.811	INDETERMINATE	1	TRUE	1	0.31	3		605	519	SUCCESS
APC	324	MSKCC	GRCh37	5	112175786	112175786	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs756912930	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	62	395	0	ENST00000257430.4:c.4495G>T	p.Gly1499Ter	p.G1499*	ENST00000257430	NM_000038.5	1499	Gga/Tga	16/16	0.0918674596195326	3	FACETS	1	0.969	1	0.713	0.62	0.813	INDETERMINATE	1	TRUE	1	0.31	3		395	324	SUCCESS
APC	324	MSKCC	GRCh37	5	112179088	112179088	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs730881267	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	64	471	0	ENST00000257430.4:c.7797A>C	p.Lys2599Asn	p.K2599N	ENST00000257430	NM_000038.5	2599	aaA/aaC	16/16	0.0918674596195326	3	FACETS	1	0.934	1	0.561	0.487	0.64	INDETERMINATE	1	TRUE	1	0.31	3		471	425	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449805	149449805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	148	1021	0	ENST00000286301.3:c.1259C>T	p.Ala420Val	p.A420V	ENST00000286301	NM_005211.3	420	gCt/gTt	9/22	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.31	2		1021	795	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523700	176523700	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	116	1073	0	ENST00000292408.4:c.2111A>G	p.Glu704Gly	p.E704G	ENST00000292408	NM_213647.1	704	gAg/gGg	16/18	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.31	2		1073	621	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048787	180048787	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	140	1003	1	ENST00000261937.6:c.1775G>A	p.Arg592His	p.R592H	ENST00000261937	NM_182925.4	592	cGc/cAc	13/30	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.31	2		1004	693	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056487	26056487	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	24	267	0	ENST00000343677.2:c.170T>C	p.Val57Ala	p.V57A	ENST00000343677	NM_005319.3	57	gTt/gCt	1/1	0.155853405989615	5	FACETS	0.744	0.584	0.928			1	INDETERMINATE	1	TRUE	NA	0.31	5		267	305	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911290	29911290	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	17	211	0	ENST00000376809.5:c.589G>T	p.Glu197Ter	p.E197*	ENST00000376809	NM_002116.7	197	Gag/Tag	3/8	0.0918674596195326	3	FACETS	0.704	0.528	0.911	0.352	0.264	0.456	INDETERMINATE	1	TRUE	1	0.31	3		211	180	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323103	31323103	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	83	853	1	ENST00000412585.2:c.886C>A	p.Leu296Met	p.L296M	ENST00000412585	NM_005514.6	296	Ctg/Atg	4/8	0.0918674596195326	3	FACETS	0.943	0.832	1	0.471	0.416	0.531	INDETERMINATE	1	TRUE	1	0.31	3		854	656	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324525	31324526	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	rs750527298	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	179	424	0	ENST00000412585.2:c.282_283del	p.Gln94HisfsTer4	p.Q94Hfs*4	ENST00000412585	NM_005514.6	94	caGGca/caca	2/8	0.0918674596195326	3	FACETS	1	0.98	1	1	0.993	1	INDETERMINATE	3	TRUE	1	0.31	3		424	396	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169056	32169056	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	118	1037	0	ENST00000375023.3:c.3977G>A	p.Gly1326Glu	p.G1326E	ENST00000375023	NM_004557.3	1326	gGa/gAa	22/30	0.0918674596195326	3	FACETS	1	0.981	1	0.675	0.61	0.744	INDETERMINATE	1	TRUE	1	0.31	3		1037	651	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903746	41903746	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200046302	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	105	828	3	ENST00000372991.4:c.811C>T	p.Arg271Trp	p.R271W	ENST00000372991	NM_001760.3	271	Cgg/Tgg	5/5	0.0918674596195326	3	FACETS	1	0.973	1	0.624	0.56	0.692	INDETERMINATE	1	TRUE	1	0.31	3		831	627	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109415053	109415053	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	147	1046	0	ENST00000436639.2:c.224G>A	p.Arg75Lys	p.R75K	ENST00000436639	NM_014454.2	75	aGg/aAg	1/10	0.0918674596195326	3	FACETS	1	0.972	1	0.578	0.527	0.631	INDETERMINATE	1	TRUE	1	0.31	3		1046	948	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522557	157522557	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	190	1072	0	ENST00000346085.5:c.4829C>T	p.Pro1610Leu	p.P1610L	ENST00000346085	NM_020732.3	1610	cCt/cTt	18/20	0.0918674596195326	3	FACETS	1	0.99	1	0.744	0.688	0.803	INDETERMINATE	1	TRUE	1	0.31	3		1072	951	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441954	6441954	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	95	1156	1	ENST00000356142.4:c.516del	p.Lys172AsnfsTer30	p.K172Nfs*30	ENST00000356142	NM_018890.3	171	gtA/gt	7/7	0.156222233782688	0	FACETS	0.43	0.382	0.481			1	INDETERMINATE	1	TRUE	0	0.31	0		1157	984	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211049	55211049	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	111	839	1	ENST00000275493.2:c.292C>T	p.Arg98Ter	p.R98*	ENST00000275493	NM_005228.3	98	Cga/Tga	3/28	0.156222233782688	0	FACETS	0.836	0.754	0.923			1	INDETERMINATE	1	TRUE	0	0.31	0		840	591	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224304	55224304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	94	853	0	ENST00000275493.2:c.1085G>A	p.Cys362Tyr	p.C362Y	ENST00000275493	NM_005228.3	362	tGc/tAc	9/28	0.156222233782688	0	FACETS	0.764	0.681	0.851			1	INDETERMINATE	1	TRUE	0	0.31	0		853	548	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148529784	148529784	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs999855448	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	42	671	0	ENST00000320356.2:c.305A>G	p.Asn102Ser	p.N102S	ENST00000320356	NM_004456.4	102	aAt/aGt	4/20	1	2	FACETS	0.509	0.425	0.603	0.509	0.425	0.603	SUBCLONAL	1	TRUE	1	0.31	2		671	532	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874092	151874093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	118	820	0	ENST00000262189.6:c.8445dup	p.Ser2816IlefsTer6	p.S2816Ifs*6	ENST00000262189	NM_170606.2	2815	-/A	38/59	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.31	2		820	619	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538843	23538843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	99	577	0	ENST00000380871.4:c.596C>T	p.Ala199Val	p.A199V	ENST00000380871	NM_006167.3	199	gCc/gTc	2/2	1	2	FACETS	0.789	0.709	0.872	1	0.984	1	SUBCLONAL	2	TRUE	1	0.31	2		577	405	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982001	70982001	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	85	1224	0	ENST00000276594.2:c.95C>A	p.Pro32His	p.P32H	ENST00000276594	NM_024504.3	32	cCt/cAt	2/8	1	2	FACETS	0.622	0.549	0.7	0.622	0.549	0.7	SUBCLONAL	1	TRUE	1	0.31	2		1224	882	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554345	141554345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748399150	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	134	1232	5	ENST00000220592.5:c.1806del	p.Ala603ProfsTer92	p.A603Pfs*92	ENST00000220592	NM_012154.3	602	ccC/cc	14/19	1	2	FACETS	0.977	0.887	1	0.977	0.887	1	CLONAL	1	TRUE	1	0.31	2		1237	885	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741472	145741472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745874353	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	136	1077	1	ENST00000428558.2:c.1031G>A	p.Arg344Gln	p.R344Q	ENST00000428558	NM_004260.3	344	cGg/cAg	5/22	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.31	2		1078	732	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742798	145742798	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	49	472	0	ENST00000428558.2:c.213G>T	p.Glu71Asp	p.E71D	ENST00000428558	NM_004260.3	71	gaG/gaT	3/22	1	2	FACETS	0.952	0.81	1	0.952	0.81	1	CLONAL	1	TRUE	1	0.31	2		472	332	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742857	145742857	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1331238003	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	40	559	0	ENST00000428558.2:c.154A>G	p.Thr52Ala	p.T52A	ENST00000428558	NM_004260.3	52	Acg/Gcg	3/22	1	2	FACETS	0.523	0.435	0.622	0.523	0.435	0.622	SUBCLONAL	1	TRUE	1	0.31	2		559	493	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5065022	5065022	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	71	575	0	ENST00000381652.3:c.1196A>T	p.Asn399Ile	p.N399I	ENST00000381652	NM_004972.3	399	aAc/aTc	9/25	1	2	FACETS	0.998	0.874	1	0.998	0.874	1	CLONAL	1	TRUE	1	0.31	2		575	459	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994324	21994324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554659249	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	105	631	0	ENST00000579755.1:c.7C>T	p.Arg3Cys	p.R3C	ENST00000579755		3	Cgc/Tgc	1/3	1		FACETS		0.971	1				CLONAL	1	TRUE	1	0.31	2		631	555	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231239	98231239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs570441437	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	131	809	0	ENST00000331920.6:c.2044C>T	p.Arg682Cys	p.R682C	ENST00000331920	NM_000264.3	682	Cgc/Tgc	14/24	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.31	2		809	636	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753948	133753948	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	63	582	1	ENST00000318560.5:c.1417C>T	p.Arg473Ter	p.R473*	ENST00000318560	NM_005157.4	473	Cga/Tga	8/11	0.3	1	FACETS	0.869	0.755	0.993	0.869	0.755	0.993	CLONAL	1	TRUE	0	0.31	1		583	395	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133756012	133756012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs574660646	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	103	701	1	ENST00000318560.5:c.1639G>A	p.Val547Met	p.V547M	ENST00000318560	NM_005157.4	547	Gtg/Atg	10/11	0.3	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.31	1		702	479	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760729	133760729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	115	994	0	ENST00000318560.5:c.3052C>T	p.Pro1018Ser	p.P1018S	ENST00000318560	NM_005157.4	1018	Cct/Tct	11/11	0.3	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	0	0.31	1		994	625	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399413	139399413	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	48	1015	0	ENST00000277541.6:c.4730T>C	p.Val1577Ala	p.V1577A	ENST00000277541	NM_017617.3	1577	gTg/gCg	26/34	0.3	1	FACETS	0.446	0.376	0.522	0.446	0.376	0.522	SUBCLONAL	1	TRUE	0	0.31	1		1015	587	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930391	39930391	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	104	258	0	ENST00000378444.4:c.3073G>T	p.Glu1025Ter	p.E1025*	ENST00000378444	NM_001123385.1	1025	Gag/Tag	6/15	1	1	FACETS	0.84	0.769	0.912	1	0.991	1	CLONAL	3	TRUE	0	0.31	1		258	225	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649705	48649705	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	41	491	0	ENST00000376670.3:c.189del	p.Tyr63Ter	p.Y63*	ENST00000376670	NM_002049.3	63	taC/ta	2/6	1	1	FACETS	0.581	0.484	0.687	0.581	0.484	0.687	SUBCLONAL	1	TRUE	0	0.31	1		491	385	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357136	70357136	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	156	527	0	ENST00000374080.3:c.5651G>T	p.Gly1884Val	p.G1884V	ENST00000374080		1884	gGc/gTc	39/45	1	1	FACETS	1	0.969	1	1	0.993	1	CLONAL	2	TRUE	0	0.31	1		527	393	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357594	70357594	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	125	546	0	ENST00000374080.3:c.5845T>C	p.Ser1949Pro	p.S1949P	ENST00000374080		1949	Tct/Cct	41/45	1	1	FACETS	1	0.926	1	1	0.991	1	CLONAL	2	TRUE	0	0.31	1		546	337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	120	937	1	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	0.274310286652688	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	2	TRUE	0	0.274310286652688	2		938	436	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100285	8100285	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	50	811	0	ENST00000346208.3:c.259C>A	p.Pro87Thr	p.P87T	ENST00000346208		87	Ccg/Acg	3/6	0.274310286652688	6	FACETS	1	0.88	1	0.261	0.221	0.305	CLONAL	1	TRUE	2	0.274310286652688	6		811	541	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682455	37682455	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	76	639	0	ENST00000447079.4:c.3646C>T	p.Gln1216Ter	p.Q1216*	ENST00000447079	NM_015083.1	1216	Cag/Tag	13/14	0.274310286652688	8	FACETS	1	0.968	1			1	CLONAL	1	TRUE	NA	0.274310286652688	8		639	757	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213869	66213869	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	46	712	0	ENST00000273854.3:c.2561A>G	p.Lys854Arg	p.K854R	ENST00000273854	NM_004439.5	854	aAg/aGg	15/18	1	2	FACETS	0.747	0.63	0.876	0.747	0.63	0.876	SUBCLONAL	1	TRUE	1	0.274310286652688	2		712	449	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944326	206944326	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	52	764	0	ENST00000423557.1:c.304G>A	p.Asp102Asn	p.D102N	ENST00000423557	NM_000572.2	102	Gac/Aac	3/5	0.274310286652688	5	FACETS	1	0.887	1	0.262	0.223	0.305	CLONAL	1	TRUE	1	0.274310286652688	5		764	510	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163848	32163848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1210630301	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	41	672	0	ENST00000375023.3:c.5378G>A	p.Arg1793Gln	p.R1793Q	ENST00000375023	NM_004557.3	1793	cGa/cAa	30/30	0.204814488482078	4	FACETS	0.955	0.796	1	0.477	0.398	0.565	CLONAL	1	TRUE	2	0.274310286652688	4		672	399	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950455	68950455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	45	764	0	ENST00000288368.4:c.767C>T	p.Ser256Phe	p.S256F	ENST00000288368	NM_024870.2	256	tCt/tTt	7/40	0.274310286652688	6	FACETS	0.804	0.675	0.948	0.161	0.135	0.19	CLONAL	1	TRUE	1	0.274310286652688	6		764	632	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17350530	17350530	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	58	766	0	ENST00000375499.3:c.580A>T	p.Thr194Ser	p.T194S	ENST00000375499	NM_003000.2	194	Acc/Tcc	6/8	0.27206964530241	3	FACETS	1	0.923	1	0.554	0.477	0.637	CLONAL	1	TRUE	1	0.274310286652688	3		766	434	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120478123	120478123	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	66	725	0	ENST00000256646.2:c.3627C>G	p.Phe1209Leu	p.F1209L	ENST00000256646	NM_024408.3	1209	ttC/ttG	22/34	0.27206964530241	3	FACETS	1	0.951	1	0.599	0.521	0.682	CLONAL	1	TRUE	1	0.274310286652688	3		725	457	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596035	43596035	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	31	856	0	ENST00000355710.3:c.202C>A	p.Leu68Met	p.L68M	ENST00000355710	NM_020975.4	68	Ctg/Atg	2/20	NA	2	FACETS	0.873	0.709	1			1	INDETERMINATE	1	TRUE	NA	0.274310286652688	2		856	259	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414250	32414250	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	44	699	0	ENST00000332351.3:c.1301G>T	p.Arg434Leu	p.R434L	ENST00000332351	NM_024426.4	434	cGt/cTt	8/10	0.18807594729459	3	FACETS	0.945	0.794	1	0.473	0.397	0.556	CLONAL	1	TRUE	1	0.274310286652688	3		699	386	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421493	32421493	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	55	491	0	ENST00000332351.3:c.1098+1G>T		p.X366_splice	ENST00000332351	NM_024426.4	366			0.18807594729459	3	FACETS	0.773	0.666	0.888	0.773	0.666	0.888	SUBCLONAL	2	TRUE	1	0.274310286652688	3		491	295	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125499192	125499192	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	89	727	0	ENST00000428830.2:c.354+1G>T		p.X118_splice	ENST00000428830	NM_001114121.2	118			0.18807594729459	3	FACETS	0.856	0.763	0.954	0.856	0.763	0.954	CLONAL	2	TRUE	1	0.274310286652688	3		727	431	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448529	49448529	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	33	598	0	ENST00000301067.7:c.182del	p.Gly61ValfsTer69	p.G61Vfs*69	ENST00000301067	NM_003482.3	61	gGt/gt	3/54	0.274310286652688	2	FACETS	0.774	0.632	0.933	0.387	0.316	0.467	CLONAL	1	TRUE	0	0.274310286652688	2		598	311	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249841	133249841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	33	767	0	ENST00000320574.5:c.1382C>T	p.Ser461Leu	p.S461L	ENST00000320574	NM_006231.2	461	tCa/tTa	14/49	0.274310286652688	1	FACETS	0.802	0.656	0.964	0.802	0.656	0.964	CLONAL	1	TRUE	0	0.274310286652688	1		767	259	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675145	40675145	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	85	954	0	ENST00000249776.8:c.109G>C	p.Glu37Gln	p.E37Q	ENST00000249776	NM_033286.3	37	Gaa/Caa	1/9	0.204814488482078	4	FACETS	1	0.968	1	0.635	0.562	0.713	CLONAL	1	TRUE	2	0.274310286652688	4		954	622	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423636	88423637	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	20	571	2	ENST00000360948.2:c.2198_2199delinsAA	p.Pro733Gln	p.P733Q	ENST00000360948	NM_001012338.2	733	cCC/cAA	18/19	1	2	FACETS	0.54	0.413	0.688	0.54	0.413	0.688	SUBCLONAL	1	TRUE	1	0.274310286652688	2		573	270	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640124	3640124	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	68	1208	0	ENST00000294008.3:c.3515C>G	p.Ser1172Cys	p.S1172C	ENST00000294008	NM_032444.2	1172	tCt/tGt	12/15	NA	2	FACETS	1	0.891	1			1	INDETERMINATE	1	TRUE	NA	0.274310286652688	2		1208	484	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349314	11349314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	130	870	2	ENST00000332029.2:c.22G>A	p.Ala8Thr	p.A8T	ENST00000332029	NM_003745.1	8	Gca/Aca	2/2	0.274310286652688	18	FACETS	1	0.971	1			1	CLONAL	2	TRUE	NA	0.274310286652688	18		872	1280	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627398	37627398	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	98	1082	0	ENST00000447079.4:c.1313A>T	p.Lys438Met	p.K438M	ENST00000447079	NM_015083.1	438	aAg/aTg	2/14	0.274310286652688	8	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.274310286652688	8		1082	926	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41247864	41247864	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	74	716	0	ENST00000357654.3:c.669G>T	p.Lys223Asn	p.K223N	ENST00000357654	NM_007294.3	223	aaG/aaT	9/23	0.18807594729459	3	FACETS	0.829	0.73	0.934	0.829	0.73	0.934	CLONAL	2	TRUE	1	0.274310286652688	3		716	370	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63531788	63531788	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	90	832	0	ENST00000307078.5:c.2193G>C	p.Gln731His	p.Q731H	ENST00000307078	NM_004655.3	731	caG/caC	9/11	0.18807594729459	3	FACETS	0.757	0.674	0.845	0.757	0.674	0.845	SUBCLONAL	2	TRUE	1	0.274310286652688	3		832	493	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597486	10597486	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	130	878	1	ENST00000171111.5:c.1717G>T	p.Asp573Tyr	p.D573Y	ENST00000171111	NM_203500.1	573	Gat/Tat	6/6	0.274310286652688	2	FACETS	0.943	0.867	1	1	0.987	1	CLONAL	3	TRUE	0	0.274310286652688	2		879	335	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953357	17953357	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	28	975	0	ENST00000458235.1:c.629G>T	p.Arg210Leu	p.R210L	ENST00000458235	NM_000215.3	210	cGg/cTg	6/24	0.274310286652688	2	FACETS	0.534	0.427	0.657	0.267	0.213	0.329	SUBCLONAL	1	TRUE	0	0.274310286652688	2		975	382	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227674	36227674	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	37	935	0	ENST00000222270.7:c.7243C>T	p.Arg2415Cys	p.R2415C	ENST00000222270	NM_014727.1	2415	Cgc/Tgc	31/37	0.274310286652688	2	FACETS	0.656	0.541	0.785	0.328	0.27	0.393	SUBCLONAL	1	TRUE	0	0.274310286652688	2		935	411	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920466	50920466	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	83	717	0	ENST00000440232.2:c.3158G>T	p.Arg1053Leu	p.R1053L	ENST00000440232	NM_002691.3	1053	cGc/cTc	26/27	0.274310286652688	2	FACETS	0.93	0.836	1	1	0.979	1	CLONAL	3	TRUE	0	0.274310286652688	2		717	217	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497809	25497809	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	69	658	0	ENST00000264709.3:c.639+1G>T		p.X213_splice	ENST00000264709	NM_175629.2	213			0.210845709058327	2	FACETS	0.838	0.737	0.946	0.838	0.737	0.946	CLONAL	2	TRUE	0	0.274310286652688	2		658	300	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288640	198288640	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	51	953	1	ENST00000335508.6:c.87A>T	p.Gln29His	p.Q29H	ENST00000335508	NM_012433.2	29	caA/caT	2/25	0.188908739893525	5	FACETS	0.86	0.731	1	0.287	0.243	0.335	CLONAL	1	TRUE	2	0.274310286652688	5		954	610	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845304	42845304	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	75	973	1	ENST00000398585.3:c.958G>T	p.Gly320Cys	p.G320C	ENST00000398585	NM_001135099.1	320	Ggc/Tgc	9/14	0.18807594729459	3	FACETS	1	0.975	1	0.733	0.645	0.827	CLONAL	1	TRUE	1	0.274310286652688	3		974	424	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077545	30077545	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	56	903	2	ENST00000338641.4:c.1692G>T	p.Glu564Asp	p.E564D	ENST00000338641	NM_000268.3	564	gaG/gaT	15/16	0.274310286652688	2	FACETS	0.941	0.808	1	0.47	0.404	0.543	CLONAL	1	TRUE	0	0.274310286652688	2		905	434	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69988247	69988247	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	53	571	0	ENST00000394351.3:c.262-2A>T		p.X88_splice	ENST00000394351	NM_000248.3	88			0.274310286652688	2	FACETS	0.976	0.835	1	0.488	0.417	0.565	CLONAL	1	TRUE	0	0.274310286652688	2		571	396	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391011	89391011	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	67	862	1	ENST00000336596.2:c.1077C>G	p.Phe359Leu	p.F359L	ENST00000336596	NM_005233.5	359	ttC/ttG	5/17	0.274310286652688	2	FACETS	0.863	0.751	0.985	0.432	0.375	0.493	CLONAL	1	TRUE	0	0.274310286652688	2		863	566	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146752	185146752	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	122	1023	2	ENST00000265026.3:c.383G>T	p.Gly128Val	p.G128V	ENST00000265026	NM_004721.4	128	gGt/gTt	2/14	0.27206964530241	3	FACETS	0.793	0.718	0.871	0.793	0.718	0.871	SUBCLONAL	2	TRUE	1	0.274310286652688	3		1025	638	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286182	66286182	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	14	561	0	ENST00000273854.3:c.1504T>A	p.Tyr502Asn	p.Y502N	ENST00000273854	NM_004439.5	502	Tat/Aat	6/18	1	2	FACETS	0.405	0.292	0.541	0.405	0.292	0.541	SUBCLONAL	1	TRUE	1	0.274310286652688	2		561	252	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554927	187554927	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	56	612	0	ENST00000441802.2:c.4234A>T	p.Ile1412Phe	p.I1412F	ENST00000441802	NM_005245.3	1412	Att/Ttt	7/27	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.274310286652688	2		612	370	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873616	35873616	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	23	425	0	ENST00000303115.3:c.572T>G	p.Leu191Arg	p.L191R	ENST00000303115	NM_002185.3	191	cTg/cGg	5/8	0.274310286652688	5	FACETS	0.728	0.568	0.914	0.243	0.189	0.305	CLONAL	1	TRUE	2	0.274310286652688	5		425	325	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80071558	80071558	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	39	662	0	ENST00000265081.6:c.2299G>C	p.Asp767His	p.D767H	ENST00000265081	NM_002439.4	767	Gat/Cat	16/24	1	2	FACETS	0.713	0.591	0.848	0.713	0.591	0.848	SUBCLONAL	1	TRUE	1	0.274310286652688	2		662	399	SUCCESS
APC	324	MSKCC	GRCh37	5	112174134	112174134	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1064793776	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	68	643	0	ENST00000257430.4:c.2843C>G	p.Ser948Cys	p.S948C	ENST00000257430	NM_000038.5	948	tCt/tGt	16/16	0.227048448710305	4	FACETS	0.946	0.829	1			1	CLONAL	2	TRUE	NA	0.274310286652688	4		643	334	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120708	94120708	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	45	573	0	ENST00000369303.4:c.343G>T	p.Val115Leu	p.V115L	ENST00000369303	NM_004440.3	115	Gta/Tta	3/17	0.204814488482078	4	FACETS	0.935	0.787	1	0.468	0.393	0.55	CLONAL	1	TRUE	2	0.274310286652688	4		573	447	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331964	81331964	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	72	534	0	ENST00000222390.5:c.2120T>C	p.Val707Ala	p.V707A	ENST00000222390	NM_000601.4	707	gTc/gCc	18/18	0.27206964530241	3	FACETS	0.972	0.857	1	0.972	0.857	1	CLONAL	2	TRUE	1	0.274310286652688	3		534	307	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372707	81372707	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	44	536	0	ENST00000222390.5:c.827C>G	p.Pro276Arg	p.P276R	ENST00000222390	NM_000601.4	276	cCt/cGt	7/18	0.27206964530241	3	FACETS	0.746	0.626	0.879	0.373	0.313	0.44	SUBCLONAL	1	TRUE	1	0.274310286652688	3		536	489	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525858	148525858	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	52	670	0	ENST00000320356.2:c.599A>G	p.Gln200Arg	p.Q200R	ENST00000320356	NM_004456.4	200	cAg/cGg	6/20	0.27206964530241	3	FACETS	0.998	0.851	1	0.499	0.425	0.579	CLONAL	1	TRUE	1	0.274310286652688	3		670	432	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965431	68965431	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	99	1277	0	ENST00000288368.4:c.1043A>G	p.Glu348Gly	p.E348G	ENST00000288368	NM_024870.2	348	gAg/gGg	9/40	0.274310286652688	6	FACETS	1	0.971	1	0.252	0.224	0.281	CLONAL	1	TRUE	1	0.274310286652688	6		1277	888	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972915	68972915	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	113	643	0	ENST00000288368.4:c.1240G>T	p.Glu414Ter	p.E414*	ENST00000288368	NM_024870.2	414	Gaa/Taa	11/40	0.274310286652688	6	FACETS	0.973	0.882	1	0.584	0.529	0.641	CLONAL	3	TRUE	1	0.274310286652688	6		643	437	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70971020	70971020	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	75	1128	0	ENST00000276594.2:c.1241A>G	p.Tyr414Cys	p.Y414C	ENST00000276594	NM_024504.3	414	tAc/tGc	6/8	0.274310286652688	6	FACETS	0.957	0.837	1	0.191	0.167	0.218	CLONAL	1	TRUE	1	0.274310286652688	6		1128	885	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738058	145738058	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	32	1015	0	ENST00000428558.2:c.2852G>C	p.Gly951Ala	p.G951A	ENST00000428558	NM_004260.3	951	gGg/gCg	17/22	0.274310286652688	7	FACETS	0.826	0.67	1	0.207	0.167	0.251	CLONAL	1	TRUE	3	0.274310286652688	7		1015	476	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742988	145742988	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	48	182	0	ENST00000428558.2:c.116G>T	p.Arg39Leu	p.R39L	ENST00000428558	NM_004260.3	39	cGc/cTc	2/22	0.274310286652688	7	FACETS	1	0.925	1	0.843	0.724	0.969	CLONAL	3	TRUE	3	0.274310286652688	7		182	175	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633334	8633334	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	53	709	0	ENST00000356435.5:c.335G>T	p.Arg112Ile	p.R112I	ENST00000356435		112	aGa/aTa	3/35	0.274310286652688	2	FACETS	0.774	0.661	0.899	0.387	0.33	0.45	SUBCLONAL	1	TRUE	0	0.274310286652688	2		709	499	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410680	63410680	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1334005803	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	40	929	2	ENST00000330258.3:c.2487C>A	p.His829Gln	p.H829Q	ENST00000330258	NM_152424.3	829	caC/caA	2/2	0.274310286652688	2	FACETS	0.624	0.519	0.742	0.312	0.259	0.371	SUBCLONAL	1	TRUE	0	0.274310286652688	2		931	467	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412260	63412260	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	38	1106	0	ENST00000330258.3:c.907G>T	p.Gly303Cys	p.G303C	ENST00000330258	NM_152424.3	303	Ggc/Tgc	2/2	0.274310286652688	2	FACETS	0.62	0.512	0.74	0.31	0.256	0.37	SUBCLONAL	1	TRUE	0	0.274310286652688	2		1106	447	SUCCESS
AR	367	MSKCC	GRCh37	X	66931358	66931358	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770166641	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	42	811	0	ENST00000374690.3:c.2000G>A	p.Gly667Asp	p.G667D	ENST00000374690	NM_000044.3	667	gGc/gAc	4/8	0.274310286652688	3	FACETS	0.736	0.615	0.871	0.368	0.307	0.436	SUBCLONAL	1	TRUE	1	0.274310286652688	3		811	473	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776914	76776914	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	53	1017	1	ENST00000373344.5:c.7038G>T	p.Arg2346Ser	p.R2346S	ENST00000373344	NM_000489.3	2346	agG/agT	33/35	0.274310286652688	3	FACETS	0.782	0.667	0.908	0.391	0.333	0.454	CLONAL	1	TRUE	1	0.274310286652688	3		1018	562	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937183	76937183	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	44	876	0	ENST00000373344.5:c.3565C>A	p.Leu1189Ile	p.L1189I	ENST00000373344	NM_000489.3	1189	Cta/Ata	9/35	0.274310286652688	3	FACETS	0.755	0.633	0.89	0.378	0.316	0.445	SUBCLONAL	1	TRUE	1	0.274310286652688	3		876	483	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938655	76938655	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	38	900	0	ENST00000373344.5:c.2093A>G	p.Lys698Arg	p.K698R	ENST00000373344	NM_000489.3	698	aAg/aGg	9/35	0.274310286652688	3	FACETS	0.598	0.494	0.715	0.299	0.247	0.358	SUBCLONAL	1	TRUE	1	0.274310286652688	3		900	527	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019576	123019576	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	43	823	1	ENST00000355640.3:c.64G>T	p.Glu22Ter	p.E22*	ENST00000355640		22	Gaa/Taa	2/7	0.274310286652688	3	FACETS	0.691	0.578	0.816	0.345	0.289	0.408	SUBCLONAL	1	TRUE	1	0.274310286652688	3		824	516	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	129	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.278308452149995	3	FACETS	0.923	0.84	1	0.923	0.84	1	CLONAL	2	TRUE	1	0.278308452149995	3		509	572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577035	7577036	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0019322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	117	891	0	ENST00000269305.4:c.902dup	p.Gly302ArgfsTer4	p.G302Rfs*4	ENST00000269305	NM_001126112.2	301	cca/ccCa	8/11	0.278308452149995	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.278308452149995	1		891	696	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101552	27101552	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	144	924	0	ENST00000324856.7:c.4834A>C	p.Lys1612Gln	p.K1612Q	ENST00000324856	NM_006015.4	1612	Aaa/Caa	18/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.278308452149995	2		924	832	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101559	27101569	+	frameshift_variant	Frame_Shift_Del	DEL	AGAAGGCAGGT	AGAAGGCAGGT	-	novel	NA	P-0019322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	139	908	0	ENST00000324856.7:c.4841_4851del	p.Gln1614ProfsTer30	p.Q1614Pfs*30	ENST00000324856	NM_006015.4	1614	cAGAAGGCAGGT/c	18/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.278308452149995	2		908	828	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459268	99459268	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	104	833	0	ENST00000268035.6:c.1904C>G	p.Ser635Cys	p.S635C	ENST00000268035	NM_000875.3	635	tCt/tGt	9/21	1	2	FACETS	0.995	0.891	1	0.995	0.891	1	CLONAL	1	TRUE	1	0.278308452149995	2		833	751	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44733217	44733218	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0019322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	69	276	0	ENST00000377967.4:c.209_210del	p.Lys70SerfsTer11	p.K70Sfs*11	ENST00000377967	NM_021140.2	70	aAG/a	2/29	1	1	FACETS	0.818	0.721	0.92	1	0.978	1	CLONAL	2	TRUE	0	0.278308452149995	1		276	261	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035956	47035956	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	CT	novel	NA	P-0019322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	144	506	0	ENST00000377604.3:c.634delinsCT	p.Lys212LeufsTer4	p.K212Lfs*4	ENST00000377604	NM_001204468.1	212	Aag/CTag	7/24	1	1	FACETS	0.936	0.86	1	1	0.991	1	CLONAL	2	TRUE	0	0.278308452149995	1		506	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578439	7578439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	147	1162	1	ENST00000269305.4:c.491del	p.Lys164SerfsTer6	p.K164Sfs*6	ENST00000269305	NM_001126112.2	164	aAg/ag	5/11	1	2	FACETS	0.917	0.838	1	0.917	0.838	1	CLONAL	1	TRUE	1	0.393815381055286	2		1163	814	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913355	NA	P-0019323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	87	705	0	ENST00000288602.6:c.1406G>T	p.Gly469Val	p.G469V	ENST00000288602	NM_004333.4	469	gGa/gTa	11/18	0.298057519172003	3	FACETS	0.949	0.842	1	0.475	0.421	0.532	CLONAL	1	TRUE	1	0.393815381055286	3		705	557	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553591	106553591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376600972	NA	P-0019323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	20	553	4	ENST00000369096.4:c.1556C>T	p.Ala519Val	p.A519V	ENST00000369096	NM_001198.3	519	gCg/gTg	5/7	0.352211269856858	2	FACETS	0.291	0.222	0.372	0.146	0.111	0.186	SUBCLONAL	1	TRUE	0	0.393815381055286	2		557	349	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812317	212812317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143662416	NA	P-0019323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	52	536	0	ENST00000342788.4:c.259G>A	p.Val87Met	p.V87M	ENST00000342788	NM_005235.2	87	Gtg/Atg	3/28	1	2	FACETS	0.667	0.569	0.773	0.667	0.569	0.773	SUBCLONAL	1	TRUE	1	0.393815381055286	2		536	396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0019323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	114	749	1	ENST00000269305.4:c.673-2A>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			1	2	FACETS	0.959	0.865	1	0.959	0.865	1	CLONAL	1	TRUE	1	0.393815381055286	2		750	604	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280161	66280161	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	29	368	1	ENST00000273854.3:c.1528G>T	p.Asp510Tyr	p.D510Y	ENST00000273854	NM_004439.5	510	Gac/Tac	7/18	0.259696634012245	1	FACETS	0.445	0.358	0.542	0.445	0.358	0.542	SUBCLONAL	1	TRUE	0	0.393815381055286	1		369	266	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797759	45797759	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0019323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	198	896	0	ENST00000450313.1:c.934-1G>T		p.X312_splice	ENST00000450313	NM_012222.2	312			0.332040050504376	3	FACETS	0.796	0.739	0.855	0.531	0.493	0.57	SUBCLONAL	2	TRUE	0	0.393815381055286	3		896	756	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981641	101981641	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	32	258	1	ENST00000282441.5:c.62C>A	p.Ser21Ter	p.S21*	ENST00000282441	NM_001130145.2	21	tCg/tAg	1/9	0.213379383595648	2	FACETS	0.763	0.624	0.917	0.381	0.312	0.459	INDETERMINATE	1	TRUE	0	0.393815381055286	2		259	213	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352582	118352582	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	80	1002	2	ENST00000534358.1:c.3787C>A	p.Pro1263Thr	p.P1263T	ENST00000534358	NM_005933.3	1263	Cca/Aca	7/36	0.213379383595648	2	FACETS	0.532	0.468	0.602	0.266	0.234	0.301	INDETERMINATE	1	TRUE	0	0.393815381055286	2		1004	763	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729133	66729133	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	163	958	1	ENST00000307102.5:c.341A>T	p.Glu114Val	p.E114V	ENST00000307102	NM_002755.3	114	gAg/gTg	3/11	0.259696634012245	1	FACETS	0.885	0.814	0.959	0.885	0.814	0.959	CLONAL	1	TRUE	0	0.393815381055286	1		959	751	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654802	29654802	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	108	549	0	ENST00000356175.3:c.5493del	p.Thr1832HisfsTer10	p.T1832Hfs*10	ENST00000356175	NM_000267.3	1831	Ggg/gg	37/57	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.393815381055286	2		549	473	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663933	29663933	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0019323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	71	430	0	ENST00000356175.3:c.6364+1G>A		p.X2122_splice	ENST00000356175	NM_000267.3	2122			1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.393815381055286	2		430	348	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463594	25463594	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	153	811	1	ENST00000264709.3:c.2088G>T	p.Gln696His	p.Q696H	ENST00000264709	NM_175629.2	696	caG/caT	18/23	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.393815381055286	2		812	646	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451930	29451930	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	102	1028	1	ENST00000389048.3:c.2635G>T	p.Gly879Cys	p.G879C	ENST00000389048	NM_004304.4	879	Ggt/Tgt	16/29	1	2	FACETS	0.756	0.677	0.84	0.756	0.677	0.84	SUBCLONAL	1	TRUE	1	0.393815381055286	2		1029	685	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606988	47606988	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	147	887	1	ENST00000263735.4:c.738A>T	p.Gln246His	p.Q246H	ENST00000263735	NM_002354.2	246	caA/caT	7/9	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.393815381055286	2		888	697	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295820	212295820	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	106	780	3	ENST00000342788.4:c.2493G>T	p.Met831Ile	p.M831I	ENST00000342788	NM_005235.2	831	atG/atT	21/28	1	2	FACETS	0.92	0.827	1	0.92	0.827	1	CLONAL	1	TRUE	1	0.393815381055286	2		783	585	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812257	212812257	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	70	631	0	ENST00000342788.4:c.319G>T	p.Gly107Trp	p.G107W	ENST00000342788	NM_005235.2	107	Ggg/Tgg	3/28	1	2	FACETS	0.756	0.661	0.859	0.756	0.661	0.859	SUBCLONAL	1	TRUE	1	0.393815381055286	2		631	470	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281224	46281224	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1355776553	NA	P-0019323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	105	778	1	ENST00000371998.3:c.4021G>T	p.Gly1341Cys	p.G1341C	ENST00000371998		1341	Ggt/Tgt	21/23	0.162957989244608	4	FACETS	1	0.952	1	0.552	0.495	0.613	INDETERMINATE	1	TRUE	2	0.393815381055286	4		779	673	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537209	41537209	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	134	950	0	ENST00000263253.7:c.2036A>T	p.Gln679Leu	p.Q679L	ENST00000263253	NM_001429.3	679	cAa/cTa	10/31	1	2	FACETS	0.842	0.765	0.923	0.842	0.765	0.923	CLONAL	1	TRUE	1	0.393815381055286	2		950	808	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967261	134967261	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	88	973	0	ENST00000398015.3:c.2600G>C	p.Ser867Thr	p.S867T	ENST00000398015	NM_004441.4	867	aGc/aCc	14/16	0.259696634012245	1	FACETS	0.511	0.453	0.574	0.511	0.453	0.574	SUBCLONAL	1	TRUE	0	0.393815381055286	1		973	702	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1955056	1955056	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	31	962	0	ENST00000382891.5:c.2143C>T	p.His715Tyr	p.H715Y	ENST00000382891	NM_133335.3	715	Cac/Tac	12/22	0.393815381055286	1	FACETS	0.209	0.168	0.255	0.209	0.168	0.255	SUBCLONAL	1	TRUE	0	0.393815381055286	1		962	606	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541616	187541616	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	46	559	0	ENST00000441802.2:c.6124G>T	p.Glu2042Ter	p.E2042*	ENST00000441802	NM_005245.3	2042	Gag/Tag	10/27	0.259696634012245	1	FACETS	0.468	0.395	0.548	0.468	0.395	0.548	SUBCLONAL	1	TRUE	0	0.393815381055286	1		559	401	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20487034	20487034	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	154	718	0	ENST00000346618.3:c.999G>C	p.Glu333Asp	p.E333D	ENST00000346618	NM_001949.4	333	gaG/gaC	5/7	0.106185571053255	5	FACETS	0.989	0.908	1	0.659	0.605	0.715	INDETERMINATE	2	TRUE	2	0.393815381055286	5		718	629	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528337	157528338	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGATAACAC	novel	NA	P-0019323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	149	1131	0	ENST00000346085.5:c.6064_6072dup	p.Asp2022_Thr2024dup	p.D2022_T2024dup	ENST00000346085	NM_020732.3	2022	agg/agGGATAACACg	20/20	0.393815381055286	1	FACETS	0.831	0.761	0.905	0.831	0.761	0.905	CLONAL	1	TRUE	0	0.393815381055286	1		1131	731	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50358676	50358676	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	104	526	0	ENST00000331340.3:c.19C>G	p.Gln7Glu	p.Q7E	ENST00000331340	NM_006060.4	7	Caa/Gaa	2/8	0.298057519172003	3	FACETS	0.775	0.699	0.854	0.775	0.699	0.854	SUBCLONAL	2	TRUE	1	0.393815381055286	3		526	408	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467693	50467693	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	249	1075	0	ENST00000331340.3:c.928G>T	p.Val310Leu	p.V310L	ENST00000331340	NM_006060.4	310	Gtg/Ttg	8/8	0.298057519172003	3	FACETS	0.817	0.765	0.871	0.817	0.765	0.871	CLONAL	2	TRUE	1	0.393815381055286	3		1075	926	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972970	68972970	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	291	891	0	ENST00000288368.4:c.1295T>A	p.Val432Glu	p.V432E	ENST00000288368	NM_024870.2	432	gTg/gAg	11/40	0.393815381055286	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.393815381055286	3		891	779	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465632	8465632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	159	834	0	ENST00000356435.5:c.3548G>A	p.Gly1183Glu	p.G1183E	ENST00000356435		1183	gGg/gAg	21/35	0.393815381055286	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.393815381055286	1		834	489	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249393	110249393	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	498	1531	0	ENST00000374672.4:c.1180G>T	p.Ala394Ser	p.A394S	ENST00000374672	NM_004235.4	394	Gcc/Tcc	4/5	0.393815381055286	2	FACETS	0.994	0.953	1	0.994	0.953	1	CLONAL	2	TRUE	0	0.393815381055286	2		1531	1272	SUCCESS
ATR	545	MSKCC	GRCh37	3	142224136	142224138	+	missense_variant	Missense_Mutation	TNP	CAT	CAT	TAC	novel	NA	P-0019323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	51	412	0	ENST00000350721.4:c.5039_5041delinsGTA	p.Tyr1680_Ala1681delinsCysThr	p.Y1680_A1681delinsCT	ENST00000350721	NM_001184.3	1680	tATGct/tGTAct	29/47	0.259696634012245	1	FACETS	0.738	0.631	0.852	0.738	0.631	0.852	SUBCLONAL	1	TRUE	0	0.393815381055286	1		412	282	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435372	18435374	+	missense_variant	Missense_Mutation	TNP	TAC	TAC	AAA	novel	NA	P-0019323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	35	647	0	ENST00000266497.5:c.357_359delinsAAA	p.Asn119_Thr120delinsLysLys	p.N119_T120delinsKK	ENST00000266497		119	aaTACg/aaAAAg	1/31	0.259696634012245	1	FACETS	0.37	0.303	0.444	0.37	0.303	0.444	SUBCLONAL	1	TRUE	0	0.393815381055286	1		647	386	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0019324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	82	472	2	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.650582639991165	1	FACETS	0.442	0.392	0.494	0.442	0.392	0.494	SUBCLONAL	1	TRUE	0	0.682935434754646	1		474	358	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572925	41572925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1389352663	NA	P-0019324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	97	793	2	ENST00000263253.7:c.5210G>A	p.Arg1737His	p.R1737H	ENST00000263253	NM_001429.3	1737	cGc/cAc	31/31	1	2	FACETS	0.371	0.331	0.415	0.371	0.331	0.415	SUBCLONAL	1	TRUE	1	0.682935434754646	2		795	765	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	236	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.53562848737923	3	FACETS	0.945	0.898	0.991	0.945	0.898	0.991	CLONAL	3	TRUE	0	0.53562848737923	3		509	394	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955510	48955518	+	frameshift_variant	Frame_Shift_Del	DEL	GACAAGAGA	GACAAGAGA	AGAG	novel	NA	P-0019326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	167	552	0	ENST00000267163.4:c.1626_1634delinsAGAG	p.Thr543GlufsTer10	p.T543Efs*10	ENST00000267163	NM_000321.2	542	ttGACAAGAGAa/ttAGAGa	17/27	0.461861555670657	4	FACETS	1	0.986	1	0.831	0.774	0.889	CLONAL	2	TRUE	1	0.53562848737923	4		552	384	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992369	72992369	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	223	857	0	ENST00000268489.5:c.1676T>A	p.Val559Asp	p.V559D	ENST00000268489	NM_006885.3	559	gTt/gAt	2/10	1	2	FACETS	0.898	0.837	0.961	0.898	0.837	0.961	CLONAL	1	TRUE	1	0.53562848737923	2		857	927	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578180	7578181	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCGGCTCATAGGGCAGTCT	novel	NA	P-0019326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	358	717	0	ENST00000269305.4:c.668_669insAGACTGCCCTATGAGCCGCC	p.Glu224AspfsTer30	p.E224Dfs*30	ENST00000269305	NM_001126112.2	223	cct/ccAGACTGCCCTATGAGCCGCCt	6/11	0.357520930126254	3	FACETS	0.884	0.84	0.928			1	CLONAL	2	TRUE	NA	0.53562848737923	3		717	959	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805785	32805785	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1246	166	696	1	ENST00000374899.4:c.226A>G	p.Thr76Ala	p.T76A	ENST00000374899	NM_018833.2	76	Act/Gct	2/12	0.53562848737923	5	FACETS	0.792	0.725	0.862	0.264	0.241	0.288	SUBCLONAL	1	TRUE	2	0.53562848737923	5		697	1412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0019327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	119	657	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	NA	2	FACETS	0.831	0.755	0.91			1	INDETERMINATE	2	TRUE	NA	0.316284190860235	2		657	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0019328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	57	646	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	0.784	0.672	0.907	0.784	0.672	0.907	CLONAL	1	TRUE	1	0.211303862565514	2		646	688	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056286	27056286	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	54	511	0	ENST00000324856.7:c.1282C>T	p.Gln428Ter	p.Q428*	ENST00000324856	NM_006015.4	428	Cag/Tag	2/20	1	2	FACETS	0.966	0.826	1	0.966	0.826	1	CLONAL	1	TRUE	1	0.211303862565514	2		511	529	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16235836	16235836	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0019328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	62	552	0	ENST00000375759.3:c.902C>G	p.Ser301Ter	p.S301*	ENST00000375759	NM_015001.2	301	tCa/tGa	4/15	1	2	FACETS	0.993	0.858	1	0.993	0.858	1	CLONAL	1	TRUE	1	0.211303862565514	2		552	591	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658354	206658354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs52817862	NA	P-0019328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	85	566	0	ENST00000367120.3:c.1448C>T	p.Thr483Met	p.T483M	ENST00000367120	NM_014002.3	483	aCg/aTg	14/22	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.211303862565514	2		566	663	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492340	56492340	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	48	606	0	ENST00000267101.3:c.2673G>C	p.Gln891His	p.Q891H	ENST00000267101	NM_001982.3	891	caG/caC	22/28	1	2	FACETS	0.644	0.544	0.756	0.644	0.544	0.756	SUBCLONAL	1	TRUE	1	0.211303862565514	2		606	705	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495666	56495666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	57	575	0	ENST00000267101.3:c.3856G>A	p.Glu1286Lys	p.E1286K	ENST00000267101	NM_001982.3	1286	Gag/Aag	28/28	1	2	FACETS	0.835	0.716	0.966	0.835	0.716	0.966	CLONAL	1	TRUE	1	0.211303862565514	2		575	646	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495681	56495681	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	54	561	2	ENST00000267101.3:c.3871G>A	p.Glu1291Lys	p.E1291K	ENST00000267101	NM_001982.3	1291	Gag/Aag	28/28	1	2	FACETS	0.815	0.696	0.946	0.815	0.696	0.946	CLONAL	1	TRUE	1	0.211303862565514	2		563	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	100	883	0	ENST00000269305.4:c.461G>C	p.Gly154Ala	p.G154A	ENST00000269305	NM_001126112.2	154	gGc/gCc	5/11	1	2	FACETS	0.9	0.802	1	0.9	0.802	1	CLONAL	1	TRUE	1	0.211303862565514	2		883	1052	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578488	7578488	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	129	1021	0	ENST00000269305.4:c.442G>C	p.Asp148His	p.D148H	ENST00000269305	NM_001126112.2	148	Gat/Cat	5/11	1	2	FACETS	0.984	0.89	1	0.984	0.89	1	CLONAL	1	TRUE	1	0.211303862565514	2		1021	1241	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682826	190682826	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	46	736	0	ENST00000441310.2:c.502G>A	p.Glu168Lys	p.E168K	ENST00000441310	NM_000534.4	168	Gaa/Aaa	5/13	1	2	FACETS	0.837	0.705	0.983	0.837	0.705	0.983	CLONAL	1	TRUE	1	0.211303862565514	2		736	520	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186507047	186507047	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	24	285	0	ENST00000323963.5:c.1213G>A	p.Asp405Asn	p.D405N	ENST00000323963		405	Gac/Aac	11/11	1	2	FACETS	0.992	0.781	1	0.992	0.781	1	CLONAL	1	TRUE	1	0.211303862565514	2		285	229	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230828	66230828	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	20	591	1	ENST00000273854.3:c.2143G>A	p.Glu715Lys	p.E715K	ENST00000273854	NM_004439.5	715	Gaa/Aaa	12/18	NA	2	FACETS	0.714	0.547	0.91			1	INDETERMINATE	1	TRUE	NA	0.211303862565514	2		592	265	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005527	150005529	+	missense_variant	Missense_Mutation	TNP	CTC	CTC	TTA	novel	NA	P-0019328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	42	415	0	ENST00000253339.5:c.696_698delinsTAA	p.Gln232_Arg233delinsHisLys	p.Q232_R233delinsHK	ENST00000253339		232	caGAGa/caTAAa	3/7	1	2	FACETS	0.924	0.773	1	0.924	0.773	1	CLONAL	1	TRUE	1	0.211303862565514	2		415	430	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0019329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	93	898	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.190398803514035	3	FACETS	0.804	0.713	0.901	0.402	0.356	0.451	CLONAL	1	TRUE	1	0.28	3		898	942	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0019330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	70	558	1	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.983	0.858	1	0.983	0.858	1	CLONAL	1	TRUE	1	0.259432843062748	2		559	549	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249954	110249954	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	110	474	0	ENST00000374672.4:c.721G>A	p.Glu241Lys	p.E241K	ENST00000374672	NM_004235.4	241	Gag/Aag	3/5	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.259432843062748	2		474	643	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037966	49037966	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	208	532	2	ENST00000267163.4:c.2206C>T	p.Gln736Ter	p.Q736*	ENST00000267163	NM_000321.2	736	Cag/Tag	21/27	0.867266376436014	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.867266376436014	1		534	267	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0019331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	280	814	2	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	0.867266376436014	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.867266376436014	1		816	351	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37672015	37672015	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	431	592	0	ENST00000447079.4:c.2801del	p.Pro934LeufsTer12	p.P934Lfs*12	ENST00000447079	NM_015083.1	934	Cct/ct	9/14	0.569900925591246	3	FACETS	0.88	0.847	0.913			1	CLONAL	3	TRUE	NA	0.569900925591246	3		592	736	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781193	135781193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768985094	NA	P-0019334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	119	804	0	ENST00000298552.3:c.1772C>T	p.Pro591Leu	p.P591L	ENST00000298552	NM_001162426.1	591	cCg/cTg	15/23	1	2	FACETS	0.746	0.674	0.821	0.746	0.674	0.821	SUBCLONAL	1	TRUE	1	0.466018202243144	2		804	685	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574650	64574650	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1060499976	NA	P-0019334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	145	825	0	ENST00000312049.6:c.824+1G>T		p.X275_splice	ENST00000312049	NM_130799.2	275			0.44000801816453	1	FACETS	0.886	0.812	0.961	0.886	0.812	0.961	CLONAL	1	TRUE	0	0.466018202243144	1		825	539	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174386	11174386	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	147	754	0	ENST00000361445.4:c.7289G>T	p.Arg2430Met	p.R2430M	ENST00000361445	NM_004958.3	2430	aGg/aTg	53/58	0.446599312932899	2	FACETS	0.965	0.883	1	0.482	0.441	0.525	CLONAL	1	TRUE	0	0.466018202243144	2		754	654	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255934	16255934	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	320	726	1	ENST00000375759.3:c.3199C>T	p.Gln1067Ter	p.Q1067*	ENST00000375759	NM_015001.2	1067	Cag/Tag	11/15	0.446599312932899	2	FACETS	0.978	0.93	1	0.978	0.93	1	CLONAL	2	TRUE	0	0.466018202243144	2		727	702	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512151	120512151	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	63	398	1	ENST00000256646.2:c.1091G>C	p.Cys364Ser	p.C364S	ENST00000256646	NM_024408.3	364	tGc/tCc	6/34	1	2	FACETS	0.837	0.729	0.953	0.837	0.729	0.953	CLONAL	1	TRUE	1	0.46172796332528	2		399	326	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230662	46230662	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	109	578	0	ENST00000334344.6:c.911A>G	p.Lys304Arg	p.K304R	ENST00000334344	NM_152641.2	304	aAg/aGg	8/21	1	2	FACETS	0.998	0.901	1	0.998	0.901	1	CLONAL	1	TRUE	1	0.46172796332528	2		578	473	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696688	47696688	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519971	NA	P-0019336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	25	550	0	ENST00000347630.2:c.260A>G	p.Tyr87Cys	p.Y87C	ENST00000347630	NM_001007230.1	87	tAc/tGc	5/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		550	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576891	7576891	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0019337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	538	738	1	ENST00000269305.4:c.955A>T	p.Lys319Ter	p.K319*	ENST00000269305	NM_001126112.2	319	Aag/Tag	9/11	0.566011870720061	3	FACETS	0.912	0.887	0.937			1	CLONAL	3	TRUE	NA	0.718310080806979	3		739	744	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954215	48954248	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTAGGTAAATTTTTTACTTTTAGTAAAAAATT	TTTTAGGTAAATTTTTTACTTTTAGTAAAAAATT	-	novel	NA	P-0019337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	52	438	0	ENST00000267163.4:c.1420_1421+32del		p.X474_splice	ENST00000267163	NM_000321.2	474		15/27	0.655541969334971	2	FACETS	0.515	0.442	0.595	0.258	0.221	0.298	SUBCLONAL	1	TRUE	0	0.718310080806979	2		438	281	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0019338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	477	879	1	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	0.543636011895277	2	FACETS	0.959	0.923	0.995	0.959	0.923	0.995	CLONAL	2	FALSE	0	0.543636011895277	2		880	915	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023366	27023366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	160	569	0	ENST00000324856.7:c.472C>A	p.Pro158Thr	p.P158T	ENST00000324856	NM_006015.4	158	Ccg/Acg	1/20	0.507610099313302	3	FACETS	1	0.922	1	0.502	0.461	0.544	CLONAL	1	FALSE	1	0.543636011895277	3		569	746	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028466	42028469	+	frameshift_variant	Frame_Shift_Del	DEL	TGAT	TGAT	-	novel	NA	P-0019338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	102	599	0	ENST00000219905.7:c.4007_4010del	p.Ile1336ArgfsTer16	p.I1336Rfs*16	ENST00000219905	NM_001164273.1	1335	cTGATt/ct	13/24	0.522270333498454	3	FACETS	0.759	0.68	0.843	0.253	0.226	0.281	SUBCLONAL	1	FALSE	0	0.543636011895277	3		599	629	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039195	49039195	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	153	654	0	ENST00000267163.4:c.2273C>A	p.Ser758Ter	p.S758*	ENST00000267163	NM_000321.2	758	tCg/tAg	22/27	0.311332691985697	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.311332691985697	1		654	633	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268138	153268138	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1406877044	NA	P-0019339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	68	485	2	ENST00000281708.4:c.670C>T	p.Arg224Ter	p.R224*	ENST00000281708	NM_033632.3	224	Cga/Tga	4/12	0.311332691985697	1	FACETS	0.9	0.786	1	0.9	0.786	1	CLONAL	1	TRUE	0	0.311332691985697	1		487	410	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139873	55139873	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs866988382	NA	P-0019339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	75	480	0	ENST00000257290.5:c.1534C>T	p.Arg512Ter	p.R512*	ENST00000257290	NM_006206.4	512	Cga/Tga	10/23	1	2	FACETS	0.977	0.859	1	0.977	0.859	1	CLONAL	1	TRUE	1	0.311332691985697	2		480	493	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518542	69518542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559561285	NA	P-0019339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	136	842	4	ENST00000294312.3:c.103C>T	p.His35Tyr	p.H35Y	ENST00000294312	NM_005117.2	35	Cac/Tac	1/3	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.311332691985697	2		846	783	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025542	1025542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1023065435	NA	P-0019339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	108	822	1	ENST00000358495.3:c.833G>A	p.Arg278Gln	p.R278Q	ENST00000358495	NM_134424.2	278	cGa/cAa	9/12	1	2	FACETS	0.864	0.775	0.958	0.864	0.775	0.958	CLONAL	1	TRUE	1	0.311332691985697	2		823	803	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444135	49444135	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0019339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	109	976	0	ENST00000301067.7:c.3236C>G	p.Ser1079Ter	p.S1079*	ENST00000301067	NM_003482.3	1079	tCa/tGa	11/54	1	2	FACETS	0.911	0.818	1	0.911	0.818	1	CLONAL	1	TRUE	1	0.311332691985697	2		976	769	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098965	178098965	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	236	412	0	ENST00000397062.3:c.80A>G	p.Asp27Gly	p.D27G	ENST00000397062	NM_006164.4	27	gAt/gGt	2/5	1	2	FACETS	0.844	0.793	0.895	1	0.995	1	CLONAL	3	TRUE	1	0.311332691985697	2		412	599	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940481	31940481	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	106	804	0	ENST00000375333.2:c.514A>T	p.Arg172Trp	p.R172W	ENST00000375333	NM_032454.1	172	Agg/Tgg	3/8	1	2	FACETS	0.824	0.739	0.916	0.824	0.739	0.916	CLONAL	1	TRUE	1	0.311332691985697	2		804	826	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540256	23540256	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	56	632	0	ENST00000380871.4:c.147G>C	p.Gln49His	p.Q49H	ENST00000380871	NM_006167.3	49	caG/caC	1/2	0.105026218396531	0	FACETS	0.456	0.391	0.528			1	INDETERMINATE	1	TRUE	0	0.311332691985697	0		632	543	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649601	48649601	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1480822697	NA	P-0019339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	156	1096	0	ENST00000376670.3:c.85G>C	p.Glu29Gln	p.E29Q	ENST00000376670	NM_002049.3	29	Gaa/Caa	2/6	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.311332691985697	2		1096	941	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578493	7578493	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1206165503	NA	P-0019340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	206	889	3	ENST00000269305.4:c.437G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tGg/tAg	5/11	0.358183202102446	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.358183202102446	1		892	911	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0019340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	66	483	0	ENST00000262160.6:c.1391C>G	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tGa	11/11	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.358183202102446	2		483	364	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465606	99465606	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	95	512	2	ENST00000268035.6:c.2431G>A	p.Glu811Lys	p.E811K	ENST00000268035	NM_000875.3	811	Gag/Aag	11/21	1	2	FACETS	0.842	0.751	0.939	0.842	0.751	0.939	CLONAL	1	TRUE	1	0.358183202102446	2		514	630	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276683	115276683	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	87	690	0	ENST00000438362.2:c.776A>G	p.Tyr259Cys	p.Y259C	ENST00000438362	NM_001242891.1	259	tAt/tGt	8/20	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.358183202102446	2		690	472	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953811	55953811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	80	571	0	ENST00000263923.4:c.3625G>A	p.Asp1209Asn	p.D1209N	ENST00000263923	NM_002253.2	1209	Gac/Aac	27/30	1	2	FACETS	0.781	0.688	0.88	0.781	0.688	0.88	SUBCLONAL	1	TRUE	1	0.358183202102446	2		571	572	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527294	137527294	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	58	724	0	ENST00000367739.4:c.352G>T	p.Glu118Ter	p.E118*	ENST00000367739	NM_000416.2	118	Gaa/Taa	3/7	0.358183202102446	1	FACETS	0.665	0.573	0.764	0.665	0.573	0.764	SUBCLONAL	1	TRUE	0	0.358183202102446	1		724	400	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992750	68992750	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747373237	NA	P-0019340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	28	779	0	ENST00000288368.4:c.1715C>T	p.Ser572Leu	p.S572L	ENST00000288368	NM_024870.2	572	tCa/tTa	16/40	0.358183202102446	3	FACETS	0.342	0.272	0.422	0.171	0.136	0.211	SUBCLONAL	1	TRUE	1	0.358183202102446	3		779	539	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	26	509	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		509	351	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	64	600	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.775	0.672	0.886	0.775	0.672	0.886	SUBCLONAL	1	TRUE	1	0.31	2		600	533	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063640	67063640	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	77	676	1	ENST00000412916.2:c.89C>A	p.Thr30Lys	p.T30K	ENST00000412916		30	aCg/aAg	2/6	0.3	1	FACETS	0.897	0.79	1	0.897	0.79	1	CLONAL	1	TRUE	0	0.31	1		677	468	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	56	600	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.915	0.784	1	0.915	0.784	1	CLONAL	1	TRUE	1	0.206726071024695	2		600	592	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117383	115117383	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	43	734	0	ENST00000257566.3:c.791del	p.Pro264LeufsTer18	p.P264Lfs*18	ENST00000257566	NM_016569.3	264	cCt/ct	4/8	1	2	FACETS	0.578	0.482	0.684	0.578	0.482	0.684	SUBCLONAL	1	TRUE	1	0.206726071024695	2		734	720	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566848	212566848	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	45	387	0	ENST00000342788.4:c.1333C>G	p.Leu445Val	p.L445V	ENST00000342788	NM_005235.2	445	Cta/Gta	12/28	1	2	FACETS	1	0.842	1	1	0.842	1	CLONAL	1	TRUE	1	0.206726071024695	2		387	435	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0019350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	179	741	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.592401296765201	2		742	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0019350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	482	1015	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.585185373970513	2	FACETS	0.992	0.957	1	0.992	0.957	1	CLONAL	2	TRUE	0	0.592401296765201	2		1017	820	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870231	155870231	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1405	138	787	0	ENST00000368323.3:c.608T>C	p.Val203Ala	p.V203A	ENST00000368323	NM_006912.5	203	gTa/gCa	6/6	0.592401296765201	3	FACETS	0.391	0.355	0.43	0.13	0.118	0.144	SUBCLONAL	1	TRUE	0	0.592401296765201	3		787	1543	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380338	14380339	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCCCACGCC	novel	NA	P-0019350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	506	547	0	ENST00000256196.4:c.70_78dup	p.Gly24_Gly26dup	p.G24_G26dup	ENST00000256196		24	-/GGCGTGGGC	1/6	0.430841970268446	4	FACETS	1	0.992	1			1	CLONAL	3	TRUE	NA	0.592401296765201	4		547	836	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0019351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	44	741	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.141186344154784	4	FACETS	0.861	0.724	1	0.861	0.724	1	CLONAL	2	TRUE	2	0.176389644666728	4		742	341	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0019351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	209	800	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.176389644666728	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.176389644666728	3		801	1125	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857152	9857152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369508378	NA	P-0019351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	89	509	0	ENST00000330684.3:c.4249C>T	p.Arg1417Trp	p.R1417W	ENST00000330684	NM_001134407.1	1417	Cgg/Tgg	13/13	0.176389644666728	3	FACETS	0.896	0.795	1	0.896	0.795	1	CLONAL	2	TRUE	1	0.176389644666728	3		509	613	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610033	43610033	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	77	926	1	ENST00000355710.3:c.1985A>G	p.Lys662Arg	p.K662R	ENST00000355710	NM_020975.4	662	aAg/aGg	11/20	1	2	FACETS	0.831	0.727	0.943	0.831	0.727	0.943	CLONAL	1	TRUE	1	0.176389644666728	2		927	1051	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245755	41245755	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	55	842	0	ENST00000357654.3:c.1793T>C	p.Leu598Ser	p.L598S	ENST00000357654	NM_007294.3	598	tTa/tCa	10/23	0.176389644666728	3	FACETS	0.848	0.724	0.985	0.424	0.362	0.493	CLONAL	1	TRUE	1	0.176389644666728	3		842	800	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584825	48584825	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	G	rs746084369	NA	P-0019351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	35	395	0	ENST00000342988.3:c.903C>G	p.Tyr301Ter	p.Y301*	ENST00000342988	NM_005359.5	301	taC/taG	7/12	0.176389644666728	1	FACETS	0.654	0.535	0.788	0.654	0.535	0.788	SUBCLONAL	1	TRUE	0	0.176389644666728	1		395	553	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	177	736	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.893	0.829	0.959	0.893	0.829	0.959	CLONAL	1	TRUE	1	0.73248809653012	2		736	541	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692880	89692880	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	141	483	0	ENST00000371953.3:c.364A>C	p.Ile122Leu	p.I122L	ENST00000371953	NM_000314.4	122	Att/Ctt	5/9	0.726798573579163	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.73248809653012	1		483	234	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763508	59763508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781609846	NA	P-0019352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	147	604	1	ENST00000259008.2:c.2594G>A	p.Arg865Gln	p.R865Q	ENST00000259008	NM_032043.2	865	cGg/cAg	19/20	1	2	FACETS	0.854	0.786	0.924	0.854	0.786	0.924	CLONAL	1	TRUE	1	0.73248809653012	2		605	470	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131127	55131131	+	missense_variant	Missense_Mutation	ONP	GTGTA	GTGTA	CTGTG	novel	NA	P-0019352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7563	3683	840	0	ENST00000257290.5:c.670_674delinsCTGTG	p.Val224_Tyr225delinsLeuCys	p.V224_Y225delinsLC	ENST00000257290	NM_006206.4	224	GTGTAt/CTGTGt	5/23	0.73248809653012	49	FACETS	1	0.993	1			1	CLONAL	16	TRUE	NA	0.73248809653012	49		840	11246	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	66	457	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	0.78	0.679	0.887	0.78	0.679	0.887	SUBCLONAL	1	TRUE	1	0.41	2		457	413	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	124	876	18	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.882	0.799	0.969	0.882	0.799	0.969	CLONAL	1	TRUE	1	0.41	2		894	686	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	169	475	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.838	0.777	0.9	1	0.991	1	CLONAL	2	TRUE	1	0.41	2		475	492	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	29	405	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.5	0.402	0.61	0.5	0.402	0.61	SUBCLONAL	1	TRUE	1	0.41	2		405	283	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866439	42866439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61735791	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	225	1316	4	ENST00000398585.3:c.193G>A	p.Ala65Thr	p.A65T	ENST00000398585	NM_001135099.1	65	Gca/Aca	3/14	1	2	FACETS	0.912	0.848	0.978	0.912	0.848	0.978	CLONAL	1	TRUE	1	0.41	2		1320	1204	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659245	86659245	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554048066	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	57	471	1	ENST00000274376.6:c.1534C>T	p.Arg512Ter	p.R512*	ENST00000274376	NM_002890.2	512	Cga/Tga	11/25	1	2	FACETS	0.888	0.767	1	0.888	0.767	1	CLONAL	1	TRUE	1	0.41	2		472	313	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs767894241	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	136	788	0	ENST00000358127.4:c.76dup	p.Val26GlyfsTer49	p.V26Gfs*49	ENST00000358127	NM_001280556.1	26	gtt/gGtt	2/10	1	2	FACETS	0.887	0.807	0.97	0.887	0.807	0.97	CLONAL	1	TRUE	1	0.41	2		788	748	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	191	1043	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	0.41	2		1043	920	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	126	942	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.826	0.749	0.908	0.826	0.749	0.908	CLONAL	1	TRUE	1	0.41	2		943	744	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930634	32930634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56070345	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	149	669	0	ENST00000380152.3:c.7505G>A	p.Arg2502His	p.R2502H	ENST00000380152		2502	cGc/cAc	15/27	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.41	2		669	682	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	93	554	0	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	0.918	0.82	1	0.918	0.82	1	CLONAL	1	TRUE	1	0.41	2		554	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579442	7579442	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs534447939	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	150	834	2	ENST00000269305.4:c.245C>T	p.Pro82Leu	p.P82L	ENST00000269305	NM_001126112.2	82	cCg/cTg	4/11	1	2	FACETS	0.973	0.891	1	0.973	0.891	1	CLONAL	1	TRUE	1	0.41	2		836	752	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	128	759	3	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	1	2	FACETS	0.862	0.783	0.946	0.862	0.783	0.946	CLONAL	1	TRUE	1	0.41	2		762	724	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	125	657	2	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.976	0.885	1	0.976	0.885	1	CLONAL	1	TRUE	1	0.41	2		659	625	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184150	56184150	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	86	554	0	ENST00000399503.3:c.4359del	p.Lys1453AsnfsTer8	p.K1453Nfs*8	ENST00000399503	NM_005921.1	1452	gAa/ga	19/20	1	2	FACETS	0.945	0.84	1	0.945	0.84	1	CLONAL	1	TRUE	1	0.41	2		554	444	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	85	598	1	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.747	0.662	0.838	0.747	0.662	0.838	SUBCLONAL	1	TRUE	1	0.41	2		599	555	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760024	133760024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	225	941	0	ENST00000318560.5:c.2352del	p.Arg785GlyfsTer3	p.R785Gfs*3	ENST00000318560	NM_005157.4	783	Ccc/cc	11/11	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.41	2		941	1081	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940108	49940108	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	146	794	0	ENST00000296474.3:c.935del	p.Pro312GlnfsTer26	p.P312Qfs*26	ENST00000296474	NM_002447.2	312	cCa/ca	1/20	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.41	2		794	702	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518900	187518900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745695748	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	130	801	1	ENST00000441802.2:c.12304G>A	p.Gly4102Arg	p.G4102R	ENST00000441802	NM_005245.3	4102	Gga/Aga	24/27	1	2	FACETS	0.898	0.816	0.984	0.898	0.816	0.984	CLONAL	1	TRUE	1	0.41	2		802	706	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339603	70339603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	146	777	0	ENST00000374080.3:c.272G>A	p.Arg91His	p.R91H	ENST00000374080		91	cGc/cAc	3/45	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.41	2		777	707	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137321073	137321073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768721235	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	35	708	4	ENST00000481739.1:c.1030G>A	p.Ala344Thr	p.A344T	ENST00000481739	NM_002957.4	344	Gcc/Acc	7/10	1	2	FACETS	0.3	0.245	0.362	0.3	0.245	0.362	SUBCLONAL	1	TRUE	1	0.41	2		712	569	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316397	14316397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782457908	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	72	621	0	ENST00000256196.4:c.208G>A	p.Ala70Thr	p.A70T	ENST00000256196		70	Gca/Aca	3/6	1	2	FACETS	0.802	0.703	0.907	0.802	0.703	0.907	CLONAL	1	TRUE	1	0.41	2		621	438	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16174647	16174647	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	80	442	0	ENST00000375759.3:c.83+2T>C		p.X28_splice	ENST00000375759	NM_015001.2	28			1	2	FACETS	0.901	0.797	1	0.901	0.797	1	CLONAL	1	TRUE	1	0.41	2		442	433	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057642	27057642	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	110	644	2	ENST00000324856.7:c.1351-1G>T		p.X451_splice	ENST00000324856	NM_006015.4	451			1	2	FACETS	0.977	0.881	1	0.977	0.881	1	CLONAL	1	TRUE	1	0.41	2		646	549	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275350	115275350	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	41	860	0	ENST00000438362.2:c.1063A>G	p.Thr355Ala	p.T355A	ENST00000438362	NM_001242891.1	355	Acc/Gcc	10/20	1	2	FACETS	0.266	0.22	0.316	0.266	0.22	0.316	SUBCLONAL	1	TRUE	1	0.41	2		860	753	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998673	100998674	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	173	1084	0	ENST00000325455.5:c.1128_1129del	p.Tyr377Ter	p.Y377*	ENST00000325455	NM_001202474.3	376	ctCTat/ctat	1/8	1	2	FACETS	0.875	0.805	0.948	0.875	0.805	0.948	CLONAL	1	TRUE	1	0.41	2		1084	964	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891183	112891183	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs545138829	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	117	822	0	ENST00000351677.2:c.517C>T	p.Arg173Cys	p.R173C	ENST00000351677	NM_002834.3	173	Cgc/Tgc	4/16	1	2	FACETS	0.838	0.757	0.924	0.838	0.757	0.924	CLONAL	1	TRUE	1	0.41	2		822	681	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779258	3779258	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	76	461	1	ENST00000262367.5:c.5790del	p.Thr1931ProfsTer45	p.T1931Pfs*45	ENST00000262367	NM_004380.2	1930	ccC/cc	31/31	1	2	FACETS	0.895	0.789	1	0.895	0.789	1	CLONAL	1	TRUE	1	0.41	2		462	414	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512470	38512471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	183	1305	0	ENST00000254066.5:c.1385dup	p.Ter463ValfsTer81	p.*463Vfs*81	ENST00000254066	NM_000964.3	461	tcc/tCcc	9/9	1	2	FACETS	0.762	0.702	0.824	0.762	0.702	0.824	SUBCLONAL	1	TRUE	1	0.41	2		1305	1172	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214866	36214866	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568372429	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	214	1127	1	ENST00000222270.7:c.3296del	p.Gly1099AlafsTer83	p.G1099Afs*83	ENST00000222270	NM_014727.1	1098	Ggg/gg	8/37	1	2	FACETS	0.989	0.918	1	0.989	0.918	1	CLONAL	1	TRUE	1	0.41	2		1128	1056	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443642	29443642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113994089	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	106	840	0	ENST00000389048.3:c.3575G>A	p.Arg1192Gln	p.R1192Q	ENST00000389048	NM_004304.4	1192	cGg/cAg	23/29	1	2	FACETS	0.626	0.561	0.695	0.626	0.561	0.695	SUBCLONAL	1	TRUE	1	0.41	2		840	826	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128036881	128036881	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	134	930	2	ENST00000285398.2:c.1598T>C	p.Leu533Pro	p.L533P	ENST00000285398	NM_000122.1	533	cTg/cCg	10/15	1	2	FACETS	0.857	0.779	0.938	0.857	0.779	0.938	CLONAL	1	TRUE	1	0.41	2		932	763	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36022377	36022377	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748389510	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	213	1109	0	ENST00000358208.4:c.430G>A	p.Asp144Asn	p.D144N	ENST00000358208		144	Gac/Aac	4/12	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.41	2		1109	1027	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042531	37042531	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863225382	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	91	688	1	ENST00000231790.2:c.293G>A	p.Gly98Asp	p.G98D	ENST00000231790	NM_000249.3	98	gGc/gAc	3/19	1	2	FACETS	0.83	0.739	0.926	0.83	0.739	0.926	CLONAL	1	TRUE	1	0.41	2		689	535	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067361	37067361	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	89	646	0	ENST00000231790.2:c.1272del	p.Arg425GlyfsTer66	p.R425Gfs*66	ENST00000231790	NM_000249.3	424	gcT/gc	12/19	1	2	FACETS	0.804	0.715	0.899	0.804	0.715	0.899	CLONAL	1	TRUE	1	0.41	2		646	540	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180344	38180346	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	rs878852993	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	150	909	0	ENST00000396334.3:c.196_198del	p.Glu66del	p.E66del	ENST00000396334	NM_002468.4	64	gcGGAg/gcg	1/5	1	2	FACETS	0.981	0.898	1	0.981	0.898	1	CLONAL	1	TRUE	1	0.41	2		909	746	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188981	142188981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1032148842	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	84	696	0	ENST00000350721.4:c.6266G>A	p.Arg2089Gln	p.R2089Q	ENST00000350721	NM_001184.3	2089	cGa/cAa	37/47	1	2	FACETS	0.796	0.705	0.893	0.796	0.705	0.893	SUBCLONAL	1	TRUE	1	0.41	2		696	515	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197847	66197847	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	36	316	0	ENST00000273854.3:c.2853-1G>A		p.X951_splice	ENST00000273854	NM_004439.5	951			1	2	FACETS	0.711	0.588	0.847	0.711	0.588	0.847	SUBCLONAL	1	TRUE	1	0.41	2		316	247	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630847	187630849	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	99	649	0	ENST00000441802.2:c.133_135del	p.Glu45del	p.E45del	ENST00000441802	NM_005245.3	45	GAG/-	2/27	1	2	FACETS	0.788	0.704	0.876	0.788	0.704	0.876	SUBCLONAL	1	TRUE	1	0.41	2		649	613	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	256531	256531	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	48	485	0	ENST00000264932.6:c.1991A>G	p.Tyr664Cys	p.Y664C	ENST00000264932	NM_004168.2	664	tAc/tGc	15/15	1	2	FACETS	0.525	0.444	0.614	0.525	0.444	0.614	SUBCLONAL	1	TRUE	1	0.41	2		485	446	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675594	86675594	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	77	545	0	ENST00000274376.6:c.2530A>G	p.Asn844Asp	p.N844D	ENST00000274376	NM_002890.2	844	Aat/Gat	19/25	1	2	FACETS	0.86	0.758	0.968	0.86	0.758	0.968	CLONAL	1	TRUE	1	0.41	2		545	437	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900093	151900093	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	127	645	0	ENST00000262189.6:c.4018A>C	p.Ser1340Arg	p.S1340R	ENST00000262189	NM_170606.2	1340	Agc/Cgc	26/59	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.41	2		645	560	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989671	68989671	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147538692	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	81	770	1	ENST00000288368.4:c.1609G>A	p.Val537Ile	p.V537I	ENST00000288368	NM_024870.2	537	Gtt/Att	15/40	1	2	FACETS	0.659	0.581	0.742	0.659	0.581	0.742	SUBCLONAL	1	TRUE	1	0.41	2		771	600	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738406	133738406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	66	571	0	ENST00000318560.5:c.806C>T	p.Ala269Val	p.A269V	ENST00000318560	NM_005157.4	269	gCc/gTc	4/11	1	2	FACETS	0.59	0.512	0.673	0.59	0.512	0.673	SUBCLONAL	1	TRUE	1	0.41	2		571	546	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032554	47032554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369088033	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	87	853	0	ENST00000377604.3:c.460G>A	p.Val154Met	p.V154M	ENST00000377604	NM_001204468.1	154	Gtg/Atg	5/24	1	2	FACETS	0.495	0.437	0.556	0.495	0.437	0.556	SUBCLONAL	1	TRUE	1	0.41	2		853	858	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342969	70342969	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	120	588	0	ENST00000374080.3:c.1510G>A	p.Val504Met	p.V504M	ENST00000374080		504	Gtg/Atg	11/45	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.41	2		588	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0019362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	470	758	1	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	0.812582078931662	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.812582078931662	1		759	650	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246062	41246062	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28897676	NA	P-0019362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	271	627	2	ENST00000357654.3:c.1486C>T	p.Arg496Cys	p.R496C	ENST00000357654	NM_007294.3	496	Cgt/Tgt	10/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.812582078931662	2		629	642	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333290	70333290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	147	692	1	ENST00000373644.4:c.1195C>T	p.Pro399Ser	p.P399S	ENST00000373644	NM_030625.2	399	Cct/Tct	2/12	1	2	FACETS	0.46	0.42	0.501	0.46	0.42	0.501	SUBCLONAL	1	TRUE	1	0.812582078931662	2		693	787	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864702	57864702	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	407	854	0	ENST00000228682.2:c.2179A>G	p.Thr727Ala	p.T727A	ENST00000228682	NM_005269.2	727	Act/Gct	12/12	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.812582078931662	2		854	993	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220025	133220025	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs113809231	NA	P-0019362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	279	648	0	ENST00000320574.5:c.4412G>T	p.Arg1471Leu	p.R1471L	ENST00000320574	NM_006231.2	1471	cGc/cTc	34/49	1	2	FACETS	0.955	0.902	1	0.955	0.902	1	CLONAL	1	TRUE	1	0.812582078931662	2		648	719	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953739	48953747	+	inframe_deletion	In_Frame_Del	DEL	CTTGGAGTT	CTTGGAGTT	-	novel	NA	P-0019362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	211	313	0	ENST00000267163.4:c.1343_1351del	p.Leu448_Val450del	p.L448_V450del	ENST00000267163	NM_000321.2	448	CTTGGAGTT/-	14/27	0.812582078931662	2	FACETS	0.902	0.862	0.939	0.902	0.862	0.939	CLONAL	2	TRUE	0	0.812582078931662	2		313	288	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90633771	90633771	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	171	605	0	ENST00000330062.3:c.313C>T	p.Gln105Ter	p.Q105*	ENST00000330062	NM_002168.2	105	Cag/Tag	3/11	0.263625852671495	1	FACETS	0.294	0.27	0.319	0.294	0.27	0.319	INDETERMINATE	1	TRUE	0	0.812582078931662	1		605	850	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356382	66356382	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	193	500	2	ENST00000273854.3:c.1115G>T	p.Ser372Ile	p.S372I	ENST00000273854	NM_004439.5	372	aGt/aTt	5/18	0.394925341795701	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.812582078931662	0		502	431	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325478	1325478	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	132	469	0	ENST00000400841.2:c.197A>G	p.Glu66Gly	p.E66G	ENST00000400841		66	gAg/gGg	3/6	1	1	FACETS	0.34	0.309	0.371	0.34	0.309	0.371	SUBCLONAL	1	TRUE	0	0.812582078931662	1		469	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0019363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	317	713	3	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	NA	2	FACETS	1	0.958	1			1	INDETERMINATE	2	TRUE	NA	0.471640580018985	2		716	667	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998901	11998902	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0019363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	116	278	0	ENST00000353533.5:c.404dup	p.Thr136AsnfsTer4	p.T136Nfs*4	ENST00000353533	NM_003010.3	135	tca/tCca	4/11	NA	2	FACETS	0.825	0.755	0.897			1	INDETERMINATE	2	TRUE	NA	0.471640580018985	2		278	298	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0019364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	230	830	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.988	0.926	1	0.988	0.926	1	CLONAL	1	TRUE	1	0.714136114612079	2		830	652	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252962	36252962	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs74315451	NA	P-0019364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	114	455	0	ENST00000300305.3:c.400G>C	p.Ala134Pro	p.A134P	ENST00000300305		134	Gct/Cct	4/8	0.549035846157771	1	FACETS	0.701	0.64	0.762	0.701	0.64	0.762	SUBCLONAL	1	TRUE	0	0.714136114612079	1		455	293	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257998	16257999	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0019364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	19	443	0	ENST00000375759.3:c.5263_5264del	p.Ser1755TyrfsTer12	p.S1755Yfs*12	ENST00000375759	NM_015001.2	1755	AGt/t	11/15	0.329956907688517	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.714136114612079	0		443	331	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259374	16259375	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0019364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	59	326	0	ENST00000375759.3:c.6641_6642del	p.Glu2214AlafsTer11	p.E2214Afs*11	ENST00000375759	NM_015001.2	2213	acAGag/acag	11/15	0.329956907688517	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.714136114612079	0		326	183	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259744	16259744	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	59	648	0	ENST00000375759.3:c.7009C>T	p.Arg2337Ter	p.R2337*	ENST00000375759	NM_015001.2	2337	Cga/Tga	11/15	0.329956907688517	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.714136114612079	0		648	410	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115710	8115711	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0019364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	317	584	0	ENST00000346208.3:c.1060dup	p.Leu354ProfsTer17	p.L354Pfs*17	ENST00000346208		352	-/C	6/6	0.276625810112192	6	FACETS	0.905	0.858	0.952			1	INDETERMINATE	3	TRUE	NA	0.714136114612079	6		584	794	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2206746	2206746	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	194	707	0	ENST00000398665.3:c.806C>G	p.Ser269Trp	p.S269W	ENST00000398665	NM_032482.2	269	tCg/tGg	10/28	1	2	FACETS	0.772	0.717	0.829	0.772	0.717	0.829	SUBCLONAL	1	TRUE	1	0.714136114612079	2		707	704	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135707	64135707	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	267	765	2	ENST00000334205.4:c.1175C>T	p.Ala392Val	p.A392V	ENST00000334205	NM_003942.2	392	gCg/gTg	10/17	0.359137786021716	5	FACETS	0.92	0.861	0.98	0.613	0.574	0.653	CLONAL	2	TRUE	2	0.359137786021716	5		767	1244	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831644	72831644	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	71	637	0	ENST00000268489.5:c.4937C>A	p.Ser1646Tyr	p.S1646Y	ENST00000268489	NM_006885.3	1646	tCc/tAc	9/10	0.265464092416142	3	FACETS	0.665	0.58	0.757	0.333	0.29	0.379	SUBCLONAL	1	TRUE	1	0.359137786021716	3		637	701	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208009	5208009	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1262	103	837	0	ENST00000357368.4:c.5702G>C	p.Arg1901Pro	p.R1901P	ENST00000357368	NM_002850.3	1901	cGg/cCg	37/38	0.359137786021716	5	FACETS	0.647	0.576	0.722			1	SUBCLONAL	1	TRUE	NA	0.359137786021716	5		837	1365	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383749	15383749	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1367	94	658	0	ENST00000263377.2:c.162C>G	p.Asn54Lys	p.N54K	ENST00000263377	NM_058243.2	54	aaC/aaG	2/20	0.359137786021716	7	FACETS	0.68	0.603	0.763			1	SUBCLONAL	1	TRUE	NA	0.359137786021716	7		658	1461	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273815	18273815	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1319	151	923	0	ENST00000222254.8:c.1148G>C	p.Arg383Pro	p.R383P	ENST00000222254	NM_005027.3	383	cGa/cCa	10/16	0.359137786021716	4	FACETS	0.777	0.708	0.85			1	SUBCLONAL	1	TRUE	NA	0.359137786021716	4		923	1470	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432728	29432728	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	82	548	1	ENST00000389048.3:c.3760A>T	p.Asn1254Tyr	p.N1254Y	ENST00000389048	NM_004304.4	1254	Aac/Tac	25/29	0.265464092416142	3	FACETS	0.848	0.748	0.955	0.424	0.374	0.478	CLONAL	1	TRUE	1	0.359137786021716	3		549	635	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566521	41566521	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	64	545	0	ENST00000263253.7:c.4398G>T	p.Trp1466Cys	p.W1466C	ENST00000263253	NM_001429.3	1466	tgG/tgT	27/31	0.359137786021716	3	FACETS	0.624	0.54	0.715			1	SUBCLONAL	1	TRUE	NA	0.359137786021716	3		545	674	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675706	30675706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1435	155	978	0	ENST00000376406.3:c.2650G>A	p.Glu884Lys	p.E884K	ENST00000376406	NM_014641.2	884	Gaa/Aaa	8/15	0.301620059440859	5	FACETS	0.835	0.762	0.913			1	CLONAL	1	TRUE	NA	0.359137786021716	5		978	1590	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340017	116340017	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	39	384	0	ENST00000397752.3:c.879A>C	p.Glu293Asp	p.E293D	ENST00000397752	NM_000245.2	293	gaA/gaC	2/21	0.359137786021716	5	FACETS	0.702	0.582	0.836	0.234	0.194	0.279	SUBCLONAL	1	TRUE	2	0.359137786021716	5		384	476	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398532	116398532	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	36	629	0	ENST00000397752.3:c.2122G>C	p.Glu708Gln	p.E708Q	ENST00000397752	NM_000245.2	708	Gaa/Caa	9/21	0.359137786021716	5	FACETS	0.618	0.508	0.742	0.206	0.169	0.248	SUBCLONAL	1	TRUE	2	0.359137786021716	5		629	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0019369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	480	970	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.458531779975878	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.458531779975878	2		970	984	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343545	343545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768565859	NA	P-0019369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	62	766	3	ENST00000262320.3:c.2129C>T	p.Ala710Val	p.A710V	ENST00000262320	NM_003502.3	710	gCg/gTg	8/11	1	2	FACETS	0.292	0.251	0.336	0.292	0.251	0.336	SUBCLONAL	1	TRUE	1	0.458531779975878	2		769	927	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510626	38510626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	422	765	1	ENST00000254066.5:c.880C>T	p.Arg294Trp	p.R294W	ENST00000254066	NM_000964.3	294	Cgg/Tgg	7/9	0.458531779975878	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.458531779975878	2		766	875	SUCCESS
APC	324	MSKCC	GRCh37	5	112128170	112128170	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	111	493	1	ENST00000257430.4:c.673G>T	p.Glu225Ter	p.E225*	ENST00000257430	NM_000038.5	225	Gaa/Taa	7/16	1	2	FACETS	0.816	0.736	0.901	0.816	0.736	0.901	CLONAL	1	TRUE	1	0.458531779975878	2		494	593	SUCCESS
APC	324	MSKCC	GRCh37	5	112174266	112174267	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0019369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	94	418	0	ENST00000257430.4:c.2975_2976del	p.Ser992LysfsTer15	p.S992Kfs*15	ENST00000257430	NM_000038.5	992	aGT/a	16/16	1	2	FACETS	0.943	0.843	1	0.943	0.843	1	CLONAL	1	TRUE	1	0.458531779975878	2		418	435	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163843	152163843	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	185	484	0	ENST00000206249.3:c.564C>A	p.Cys188Ter	p.C188*	ENST00000206249	NM_000125.3	188	tgC/tgA	2/8	0.141031021749866	5	FACETS	1	0.984	1	0.605	0.562	0.649	INDETERMINATE	2	TRUE	1	0.458531779975878	5		484	563	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121913370	NA	P-0019370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	204	302	1	ENST00000288602.6:c.1742A>G	p.Asn581Ser	p.N581S	ENST00000288602	NM_004333.4	581	aAt/aGt	15/18	0.457746205800428	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.711216281297357	4		303	462	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110558	4110558	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	149	697	0	ENST00000262948.5:c.399C>G	p.Phe133Leu	p.F133L	ENST00000262948	NM_030662.3	133	ttC/ttG	3/11	0.603305374337172	2	FACETS	0.736	0.676	0.799	0.368	0.338	0.4	SUBCLONAL	1	TRUE	0	0.711216281297357	2		697	569	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381466	81381466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	100	353	0	ENST00000222390.5:c.595G>A	p.Glu199Lys	p.E199K	ENST00000222390	NM_000601.4	199	Gaa/Aaa	5/18	0.457746205800428	4	FACETS	1	0.923	1	0.516	0.463	0.572	CLONAL	1	TRUE	2	0.711216281297357	4		353	466	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106364	27106364	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0019370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	297	507	1	ENST00000324856.7:c.5975C>G	p.Ser1992Ter	p.S1992*	ENST00000324856	NM_006015.4	1992	tCa/tGa	20/20	0.600681826140572	2	FACETS	0.84	0.803	0.877	0.84	0.803	0.877	CLONAL	2	TRUE	0	0.711216281297357	2		508	497	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955407	48955407	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	87	411	1	ENST00000267163.4:c.1523C>T	p.Ser508Phe	p.S508F	ENST00000267163	NM_000321.2	508	tCt/tTt	17/27	0.608301124785642	2	FACETS	0.709	0.633	0.789	0.355	0.316	0.395	SUBCLONAL	1	TRUE	0	0.711216281297357	2		412	345	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246538	105246538	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	157	583	2	ENST00000349310.3:c.62C>A	p.Thr21Asn	p.T21N	ENST00000349310	NM_001014432.1	21	aCc/aAc	4/15	0.704161805229609	3	FACETS	0.943	0.867	1	0.471	0.433	0.511	CLONAL	1	TRUE	1	0.711216281297357	3		585	635	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042175	42042175	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	194	753	0	ENST00000219905.7:c.6370G>C	p.Glu2124Gln	p.E2124Q	ENST00000219905	NM_001164273.1	2124	Gaa/Caa	17/24	0.608301124785642	2	FACETS	0.725	0.673	0.78	0.363	0.336	0.39	SUBCLONAL	1	TRUE	0	0.711216281297357	2		753	752	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782075	66782075	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	105	425	0	ENST00000307102.5:c.1042G>C	p.Glu348Gln	p.E348Q	ENST00000307102	NM_002755.3	348	Gag/Cag	10/11	0.608301124785642	2	FACETS	0.736	0.665	0.811	0.368	0.332	0.406	SUBCLONAL	1	TRUE	0	0.711216281297357	2		425	401	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843589	3843590	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0019370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	114	543	0	ENST00000262367.5:c.1012_1013dup	p.Gln338HisfsTer17	p.Q338Hfs*17	ENST00000262367	NM_004380.2	338	caa/caCAa	4/31	1	2	FACETS	0.58	0.524	0.639	0.58	0.524	0.639	SUBCLONAL	1	TRUE	1	0.711216281297357	2		543	553	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870080	40870080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	255	480	0	ENST00000428826.2:c.937C>T	p.His313Tyr	p.H313Y	ENST00000428826		313	Cat/Tat	10/21	0.711216281297357	3	FACETS	0.828	0.782	0.875	0.552	0.521	0.583	CLONAL	2	TRUE	0	0.711216281297357	3		480	587	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602939	10602939	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0019370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	446	856	0	ENST00000171111.5:c.640-1G>C		p.X214_splice	ENST00000171111	NM_203500.1	214			0.603305374337172	2	FACETS	0.876	0.845	0.906	0.876	0.845	0.906	CLONAL	2	TRUE	0	0.711216281297357	2		856	716	SUCCESS
APC	324	MSKCC	GRCh37	5	112174754	112174754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774847322	NA	P-0019370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	119	360	2	ENST00000257430.4:c.3463G>A	p.Glu1155Lys	p.E1155K	ENST00000257430	NM_000038.5	1155	Gaa/Aaa	16/16	1	2	FACETS	0.839	0.764	0.916	0.839	0.764	0.916	CLONAL	1	TRUE	1	0.711216281297357	2		362	399	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956563	93956563	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	96	362	0	ENST00000369303.4:c.2673C>A	p.Asp891Glu	p.D891E	ENST00000369303	NM_004440.3	891	gaC/gaA	15/17	0.64287221196266	1	FACETS	0.659	0.596	0.723	0.659	0.596	0.723	SUBCLONAL	1	TRUE	0	0.711216281297357	1		362	264	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509729	106509729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	134	600	2	ENST00000359195.3:c.1723C>T	p.Leu575Phe	p.L575F	ENST00000359195	NM_002649.2	575	Ctc/Ttc	2/11	0.457746205800428	4	FACETS	0.973	0.886	1	0.486	0.443	0.532	CLONAL	1	TRUE	2	0.711216281297357	4		602	663	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649634	48649634	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	208	493	0	ENST00000376670.3:c.118G>C	p.Gly40Arg	p.G40R	ENST00000376670	NM_002049.3	40	Ggc/Cgc	2/6	1	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.711216281297357	1		493	342	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223349	53223349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	184	353	1	ENST00000375401.3:c.4010G>A	p.Arg1337Lys	p.R1337K	ENST00000375401	NM_004187.3	1337	aGa/aAa	23/26	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.711216281297357	1		354	306	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225868	53225868	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	180	392	2	ENST00000375401.3:c.2981G>A	p.Arg994Lys	p.R994K	ENST00000375401	NM_004187.3	994	aGg/aAg	19/26	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.711216281297357	1		394	288	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626662	100626662	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	156	317	0	ENST00000308731.7:c.268G>C	p.Glu90Gln	p.E90Q	ENST00000308731	NM_000061.2	90	Gag/Cag	4/19	0.594529338544181	2	FACETS	0.99	0.916	1			1	CLONAL	1	TRUE	NA	0.711216281297357	2		317	443	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874286	155874286	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs868208063	NA	P-0019371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	110	409	0	ENST00000368323.3:c.245T>G	p.Phe82Cys	p.F82C	ENST00000368323	NM_006912.5	82	tTt/tGt	5/6	0.210005295779967	1	FACETS	0.793	0.715	0.876	0.793	0.715	0.876	INDETERMINATE	1	TRUE	0	0.400872458659112	1		409	553	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717634	89717647	+	frameshift_variant	Frame_Shift_Del	DEL	TAAAGGTGAAGATA	TAAAGGTGAAGATA	-	novel	NA	P-0019371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	108	495	0	ENST00000371953.3:c.661_674del	p.Lys221PhefsTer17	p.K221Ffs*17	ENST00000371953	NM_000314.4	220	cTAAAGGTGAAGATA/c	7/9	0.400872458659112	1	FACETS	0.929	0.838	1	0.929	0.838	1	CLONAL	1	TRUE	0	0.400872458659112	1		495	464	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134121	41134121	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	105	343	0	ENST00000379561.5:c.1507del	p.Val503SerfsTer14	p.V503Sfs*14	ENST00000379561	NM_002015.3	503	Gtc/tc	2/3	0.210005295779967	1	FACETS	1	0.936	1	1	0.936	1	INDETERMINATE	1	TRUE	0	0.400872458659112	1		343	400	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691003	NA	P-0019371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	136	720	0	ENST00000269305.4:c.96+1G>T		p.X32_splice	ENST00000269305	NM_001126112.2	32			0.367353754719212	1	FACETS	0.72	0.656	0.788	0.72	0.656	0.788	SUBCLONAL	1	TRUE	0	0.400872458659112	1		720	753	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098950	178098950	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	48	317	0	ENST00000397062.3:c.95T>G	p.Val32Gly	p.V32G	ENST00000397062	NM_006164.4	32	gTa/gGa	2/5	1	2	FACETS	0.649	0.55	0.757	0.649	0.55	0.757	SUBCLONAL	1	TRUE	1	0.400872458659112	2		317	369	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092922	29092922	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	132	500	0	ENST00000328354.6:c.1062A>C	p.Leu354Phe	p.L354F	ENST00000328354	NM_007194.3	354	ttA/ttC	10/15	1	2	FACETS	0.917	0.834	1	0.917	0.834	1	CLONAL	1	TRUE	1	0.400872458659112	2		500	718	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461563	138461563	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs558261053	NA	P-0019371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	97	456	0	ENST00000289153.2:c.458G>T	p.Arg153Leu	p.R153L	ENST00000289153	NM_006219.2	153	cGc/cTc	3/22	0.400872458659112	3	FACETS	0.927	0.827	1	0.463	0.413	0.516	CLONAL	1	TRUE	1	0.400872458659112	3		456	627	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281370	142281370	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	72	513	0	ENST00000350721.4:c.874G>A	p.Glu292Lys	p.E292K	ENST00000350721	NM_001184.3	292	Gaa/Aaa	4/47	0.400872458659112	3	FACETS	0.536	0.467	0.61	0.268	0.233	0.305	SUBCLONAL	1	TRUE	1	0.400872458659112	3		513	805	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193743	106193743	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	67	248	0	ENST00000380013.4:c.4205A>G	p.Asp1402Gly	p.D1402G	ENST00000380013	NM_001127208.2	1402	gAc/gGc	10/11	0.400872458659112	1	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	0	0.400872458659112	1		248	266	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538822	23538822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	102	353	1	ENST00000380871.4:c.617C>T	p.Ser206Phe	p.S206F	ENST00000380871	NM_006167.3	206	tCc/tTc	2/2	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.400872458659112	2		354	496	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0019372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	60	680	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.173430944866774	2		680	546	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0019372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	86	810	3	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.173430944866774	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	2	FALSE	0	0.173430944866774	2		813	496	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0019372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	35	493	2	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	FALSE	1	0.173430944866774	2		495	383	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0019372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	87	721	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.173430944866774	2		721	806	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0019372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	33	593	2	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.891	0.726	1	0.891	0.726	1	CLONAL	1	FALSE	1	0.173430944866774	2		595	427	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372098	55372098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs62642516	NA	P-0019372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	66	521	1	ENST00000297316.4:c.788C>T	p.Pro263Leu	p.P263L	ENST00000297316	NM_022454.3	263	cCg/cTg	2/2	0.101134240822178	3	FACETS	1	0.951	1	0.607	0.527	0.695	INDETERMINATE	1	FALSE	1	0.173430944866774	3		522	681	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740809	58740809	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs765769406	NA	P-0019372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	89	643	0	ENST00000305921.3:c.1714C>T	p.Arg572Ter	p.R572*	ENST00000305921	NM_003620.3	572	Cga/Tga	6/6	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.173430944866774	2		643	751	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841231	15841242	+	inframe_deletion	In_Frame_Del	DEL	AGCCGGAGCCGG	AGCCGGAGCCGG	-	rs752736259	NA	P-0019372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	30	115	0	ENST00000307771.7:c.1332_1343del	p.Ser445_Arg448del	p.S445_R448del	ENST00000307771	NM_005089.3	439	AGCCGGAGCCGG/-	11/11	1	1	FACETS	1	0.89	1	1	0.963	1	CLONAL	2	FALSE	0	0.173430944866774	1		115	140	SUCCESS
APC	324	MSKCC	GRCh37	5	112175825	112175825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778699501	NA	P-0019372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	20	254	1	ENST00000257430.4:c.4534G>A	p.Asp1512Asn	p.D1512N	ENST00000257430	NM_000038.5	1512	Gat/Aat	16/16	1	2	FACETS	0.934	0.716	1	0.934	0.716	1	CLONAL	1	FALSE	1	0.173430944866774	2		255	247	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981273	201981329	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGGACCAACTCCATGCCCAGCTGCGAGACCTCAGTGAGTCCAGGCCCCTGGAGGCT	GGGGACCAACTCCATGCCCAGCTGCGAGACCTCAGTGAGTCCAGGCCCCTGGAGGCT	-	novel	NA	P-0019372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	35	718	0	ENST00000359651.3:c.357_385+28del		p.X119_splice	ENST00000359651		119		2/8	1	2	FACETS	0.602	0.492	0.726	0.602	0.492	0.726	SUBCLONAL	1	FALSE	1	0.173430944866774	2		718	671	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713727	30713727	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs869025537	NA	P-0019372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	82	410	0	ENST00000295754.5:c.1052G>A	p.Gly351Asp	p.G351D	ENST00000295754	NM_003242.5	351	gGc/gAc	4/7	1	2	FACETS	1	0.964	1	1	0.987	1	CLONAL	2	FALSE	1	0.173430944866774	2		410	387	SUCCESS
ATR	545	MSKCC	GRCh37	3	142218559	142218559	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	22	365	0	ENST00000350721.4:c.5290T>C	p.Ser1764Pro	p.S1764P	ENST00000350721	NM_001184.3	1764	Tcc/Ccc	31/47	1	2	FACETS	0.669	0.518	0.845	0.669	0.518	0.845	SUBCLONAL	1	FALSE	1	0.173430944866774	2		365	379	SUCCESS
APC	324	MSKCC	GRCh37	5	112175954	112175954	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0019372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	24	323	0	ENST00000257430.4:c.4663A>T	p.Lys1555Ter	p.K1555*	ENST00000257430	NM_000038.5	1555	Aaa/Taa	16/16	1	2	FACETS	0.902	0.708	1	0.902	0.708	1	CLONAL	1	FALSE	1	0.173430944866774	2		323	307	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519666	137519666	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1276396064	NA	P-0019372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	25	314	0	ENST00000367739.4:c.972G>T	p.Glu324Asp	p.E324D	ENST00000367739	NM_000416.2	324	gaG/gaT	7/7	1	2	FACETS	0.868	0.685	1	0.868	0.685	1	CLONAL	1	FALSE	1	0.173430944866774	2		314	332	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843748	151843748	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778512	NA	P-0019372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	36	463	1	ENST00000262189.6:c.13967C>T	p.Ala4656Val	p.A4656V	ENST00000262189	NM_170606.2	4656	gCg/gTg	53/59	1	2	FACETS	0.808	0.663	0.97	0.808	0.663	0.97	CLONAL	1	FALSE	1	0.173430944866774	2		464	514	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0019373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	49	580	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.269759164589097	2		580	294	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59878797	59878797	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	58	382	0	ENST00000259008.2:c.957del	p.Ser320ValfsTer18	p.S320Vfs*18	ENST00000259008	NM_032043.2	319	atT/at	8/20	1	2	FACETS	1	0.894	1	1	0.98	1	CLONAL	2	TRUE	1	0.269759164589097	2		382	209	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922648	44922729	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCTTTGTTTTTTTGACAGATGAGACCAACAGGAGTTGCACAGGTACGATCTACTGGAATTCCTAATGGGCCAACAGCTGAC	TCCTTTGTTTTTTTGACAGATGAGACCAACAGGAGTTGCACAGGTACGATCTACTGGAATTCCTAATGGGCCAACAGCTGAC	-	novel	NA	P-0019373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	23	245	0	ENST00000377967.4:c.1528-17_1592del		p.X510_splice	ENST00000377967	NM_021140.2	510		16/29	0.269759164589097	1	FACETS	0.776	0.619	0.95	1	0.934	1	CLONAL	2	TRUE	0	0.269759164589097	1		245	95	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0019374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	16	918	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.514	0.378	0.678	0.514	0.378	0.678	SUBCLONAL	1	TRUE	1	0.11	2		918	566	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220488	1220488	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	42	855	0	ENST00000326873.7:c.581A>C	p.Asp194Ala	p.D194A	ENST00000326873	NM_000455.4	194	gAc/gCc	4/10	1	2	FACETS	0.841	0.7	0.999	0.841	0.7	0.999	CLONAL	1	TRUE	1	0.11	2		855	908	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	193	736	0				ENST00000310581	NM_198253.2	-/1132			0.397586877944351	3	FACETS	0.768	0.72	0.817	0.768	0.72	0.817	INDETERMINATE	2	TRUE	1	0.867763746339856	3		736	415	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725042	89725042	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1085308041	NA	P-0019375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	139	230	0	ENST00000371953.3:c.1027-2A>G		p.X343_splice	ENST00000371953	NM_000314.4	343			0.854824044168465	2	FACETS	0.995	0.955	1	0.995	0.955	1	CLONAL	2	TRUE	0	0.867763746339856	2		230	161	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0019375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32906	3957	846	1	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.867763746339856	32	FACETS	1	0.998	1			1	CLONAL	3	TRUE	NA	0.867763746339856	32		847	36863	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197697	123197697	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0019375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	234	421	0	ENST00000218089.9:c.1822-1G>A		p.X608_splice	ENST00000218089	NM_001042749.1	608			0.867763746339856	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.867763746339856	1		421	275	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0019376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	202	747	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	NA	2	FACETS	0.935	0.889	0.979			1	INDETERMINATE	2	TRUE	NA	0.717696102949346	2		747	301	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0019376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	140	659	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	2	TRUE	NA	0.717696102949346	2		659	186	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376726	31376726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867559860	NA	P-0019376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	42	528	4	ENST00000328111.2:c.721G>A	p.Ala241Thr	p.A241T	ENST00000328111	NM_006892.3	241	Gcc/Acc	7/23	0.441170529421548	6	FACETS	0.496	0.413	0.588	0.165	0.137	0.196	SUBCLONAL	1	TRUE	3	0.717696102949346	6		532	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578541	7578541	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	349	1510	2	ENST00000269305.4:c.389T>A	p.Leu130His	p.L130H	ENST00000269305	NM_001126112.2	130	cTc/cAc	5/11	0.710555508106691	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.717696102949346	1		1512	590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0019377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	370	1015	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.459288672421881	2	FACETS	0.998	0.953	1	0.998	0.953	1	CLONAL	2	TRUE	0	0.459288672421881	2		1017	807	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0019377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	167	605	1	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.459288672421881	3	FACETS	0.941	0.873	1	0.941	0.873	1	CLONAL	2	TRUE	1	0.459288672421881	3		606	475	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141874	108141874	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587781558	NA	P-0019377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	182	459	4	ENST00000278616.4:c.2921+1G>A		p.X974_splice	ENST00000278616	NM_000051.3	974			0.408414895685165	4	FACETS	0.965	0.896	1	0.965	0.896	1	CLONAL	2	TRUE	2	0.459288672421881	4		463	599	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426737	47426737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200106543	NA	P-0019377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	115	775	0	ENST00000377045.4:c.982C>T	p.Arg328Trp	p.R328W	ENST00000377045	NM_001654.4	328	Cgg/Tgg	10/16	0.346236741175967	4	FACETS	0.782	0.704	0.866			1	SUBCLONAL	1	TRUE	NA	0.459288672421881	4		775	934	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319346	11319346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	251	580	8	ENST00000361445.4:c.121G>A	p.Ala41Thr	p.A41T	ENST00000361445	NM_004958.3	41	Gcc/Acc	2/58	0.459288672421881	2	FACETS	0.96	0.907	1	0.96	0.907	1	CLONAL	2	TRUE	0	0.459288672421881	2		588	569	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924728	94924728	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	356	892	0	ENST00000536441.1:c.182T>A	p.Phe61Tyr	p.F61Y	ENST00000536441	NM_144665.3	61	tTt/tAt	3/10	0.408414895685165	4	FACETS	0.93	0.881	0.98	0.93	0.881	0.98	CLONAL	2	TRUE	2	0.459288672421881	4		892	1216	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236083	108236083	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs876660382	NA	P-0019377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	248	645	7	ENST00000278616.4:c.9019G>T	p.Glu3007Ter	p.E3007*	ENST00000278616	NM_000051.3	3007	Gaa/Taa	63/63	0.408414895685165	4	FACETS	0.938	0.879	0.998	0.938	0.879	0.998	CLONAL	2	TRUE	2	0.459288672421881	4		652	840	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120490	70120491	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0019377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	557	1311	1	ENST00000245479.2:c.1495dup	p.Glu499GlyfsTer79	p.E499Gfs*79	ENST00000245479	NM_000346.3	498	tgg/tGgg	3/3	0.459288672421881	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.459288672421881	3		1312	1428	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573661	48573711	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCAGGTTAGTCTTATAAGAGTTTTTCTATACCCTCTATGGTGGCAGATTT	TTCAGGTTAGTCTTATAAGAGTTTTTCTATACCCTCTATGGTGGCAGATTT	-	novel	NA	P-0019377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	34	408	2	ENST00000342988.3:c.245_249+46del		p.X82_splice	ENST00000342988	NM_005359.5	82		2/12	0.44573161589207	1	FACETS	0.473	0.389	0.567	0.473	0.389	0.567	SUBCLONAL	1	TRUE	0	0.459288672421881	1		410	241	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	252	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.199497610465097	5	FACETS	1	0.987	1	0.694	0.656	0.733	INDETERMINATE	3	TRUE	0	0.412093093270064	5		555	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0019378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	154	763	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.412093093270064	1	FACETS	0.973	0.894	1	0.973	0.894	1	CLONAL	1	TRUE	0	0.412093093270064	1		764	610	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371799	55371820	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCCGCGCTGGGCCCCGAG	GGCGGCCGCGCTGGGCCCCGAG	-	novel	NA	P-0019378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	67	138	0	ENST00000297316.4:c.499_520del	p.Leu167TrpfsTer213	p.L167Wfs*213	ENST00000297316	NM_022454.3	163	caGGCGGCCGCGCTGGGCCCCGAG/ca	2/2	0.412093093270064	6	FACETS	0.875	0.765	0.992	0.437	0.382	0.496	CLONAL	2	TRUE	2	0.412093093270064	6		138	339	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138402532	138402532	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0019378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	227	508	0	ENST00000289153.2:c.2413A>T	p.Lys805Ter	p.K805*	ENST00000289153	NM_006219.2	805	Aaa/Taa	16/22	0.373208268970756	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.412093093270064	4		508	724	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	166	736	0				ENST00000310581	NM_198253.2	-/1132			0.114855755884904	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.882821430606225	0		736	323	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561547	9561547	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	171	428	0	ENST00000353224.5:c.235G>A	p.Glu79Lys	p.E79K	ENST00000353224	NM_177990.2	79	Gaa/Aaa	4/10	0.882821430606225	3	FACETS	0.912	0.843	0.984	0.456	0.421	0.492	CLONAL	1	TRUE	1	0.882821430606225	3		428	612	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913250	NA	P-0019379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	157	370	0	ENST00000369535.4:c.34G>A	p.Gly12Ser	p.G12S	ENST00000369535	NM_002524.4	12	Ggt/Agt	2/7	1	2	FACETS	0.946	0.878	1	0.946	0.878	1	CLONAL	1	TRUE	1	0.882821430606225	2		370	376	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17124889	17124889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748031634	NA	P-0019379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	245	637	0	ENST00000285071.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000285071	NM_144997.5	278	cCg/cTg	8/14	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.882821430606225	2		637	516	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387101	31387101	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1226308460	NA	P-0019379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	274	680	0	ENST00000328111.2:c.1726C>T	p.Arg576Ter	p.R576*	ENST00000328111	NM_006892.3	576	Cga/Tga	16/23	0.882821430606225	3	FACETS	0.93	0.874	0.987	0.465	0.437	0.494	CLONAL	1	TRUE	1	0.882821430606225	3		680	962	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256562	115256562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267606921	NA	P-0019379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	243	551	0	ENST00000369535.4:c.149C>T	p.Thr50Ile	p.T50I	ENST00000369535	NM_002524.4	50	aCc/aTc	3/7	1	2	FACETS	0.99	0.934	1	0.99	0.934	1	CLONAL	1	TRUE	1	0.882821430606225	2		551	556	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683747	162683747	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	194	507	0	ENST00000366898.1:c.222G>A	p.Trp74Ter	p.W74*	ENST00000366898	NM_004562.2	74	tgG/tgA	3/12	0.882821430606225	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.882821430606225	1		507	242	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857334	9857334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	141	401	0	ENST00000330684.3:c.4067C>T	p.Ser1356Phe	p.S1356F	ENST00000330684	NM_001134407.1	1356	tCt/tTt	13/13	1	2	FACETS	0.945	0.874	1	0.945	0.874	1	CLONAL	1	TRUE	1	0.882821430606225	2		401	338	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857061	9857061	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	99	280	0	ENST00000330684.3:c.4340C>T	p.Ser1447Phe	p.S1447F	ENST00000330684	NM_001134407.1	1447	tCc/tTc	13/13	1	2	FACETS	0.958	0.873	1	0.958	0.873	1	CLONAL	1	TRUE	1	0.882821430606225	2		280	234	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2492117	2492117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs944782838	NA	P-0019379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	398	832	0	ENST00000355716.4:c.515C>T	p.Pro172Leu	p.P172L	ENST00000355716	NM_003820.2	172	cCc/cTc	5/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.882821430606225	2		832	854	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980370	201980370	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	333	851	1	ENST00000359651.3:c.106G>A	p.Gly36Arg	p.G36R	ENST00000359651		36	Ggg/Agg	1/8	0.882821430606225	3	FACETS	0.984	0.931	1	0.492	0.465	0.519	CLONAL	1	TRUE	1	0.882821430606225	3		852	1105	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945090	31945090	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	212	672	2	ENST00000340398.3:c.11C>T	p.Thr4Ile	p.T4I	ENST00000340398	NM_001013699.2	4	aCc/aTc	1/1	1	2	FACETS	0.888	0.832	0.945	0.888	0.832	0.945	CLONAL	1	TRUE	1	0.882821430606225	2		674	541	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434961	49434961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	259	522	0	ENST00000301067.7:c.6592C>T	p.Pro2198Ser	p.P2198S	ENST00000301067	NM_003482.3	2198	Ccc/Tcc	31/54	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.882821430606225	2		522	507	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916199	9916199	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	193	483	0	ENST00000330684.3:c.2090A>C	p.Asn697Thr	p.N697T	ENST00000330684	NM_001134407.1	697	aAc/aCc	10/13	1	2	FACETS	0.894	0.835	0.954	0.894	0.835	0.954	CLONAL	1	TRUE	1	0.882821430606225	2		483	489	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684326	29684326	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	32	440	0	ENST00000356175.3:c.7846del	p.Arg2616GlufsTer7	p.R2616Efs*7	ENST00000356175	NM_000267.3	2616	Cga/ga	53/57	1	2	FACETS	0.144	0.117	0.176	0.144	0.117	0.176	SUBCLONAL	1	TRUE	1	0.882821430606225	2		440	502	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740535	58740535	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	278	609	0	ENST00000305921.3:c.1440A>C	p.Lys480Asn	p.K480N	ENST00000305921	NM_003620.3	480	aaA/aaC	6/6	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.882821430606225	2		609	596	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265315	46265315	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	127	331	0	ENST00000371998.3:c.2185C>T	p.Pro729Ser	p.P729S	ENST00000371998		729	Cct/Tct	12/23	0.882821430606225	3	FACETS	0.967	0.883	1	0.483	0.441	0.527	CLONAL	1	TRUE	1	0.882821430606225	3		331	429	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54948572	54948572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373550419	NA	P-0019379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	174	395	0	ENST00000312783.6:c.746C>T	p.Ser249Leu	p.S249L	ENST00000312783	NM_198436.1	249	tCg/tTg	8/10	0.882821430606225	3	FACETS	0.881	0.814	0.95	0.44	0.407	0.475	CLONAL	1	TRUE	1	0.882821430606225	3		395	645	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928072	178928101	+	inframe_deletion	In_Frame_Del	DEL	TGGATTAGAAGATTTGCTGAACCCTATTGG	TGGATTAGAAGATTTGCTGAACCCTATTGG	-	novel	NA	P-0019379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	73	622	0	ENST00000263967.3:c.1352_1381del	p.Gly451_Gly460del	p.G451_G460del	ENST00000263967	NM_006218.2	450	caTGGATTAGAAGATTTGCTGAACCCTATTGGt/cat	8/21	1	2	FACETS	0.329	0.288	0.373	0.329	0.288	0.373	SUBCLONAL	1	TRUE	1	0.882821430606225	2		622	503	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680458	30680458	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	161	427	0	ENST00000376406.3:c.1261G>A	p.Glu421Lys	p.E421K	ENST00000376406	NM_014641.2	421	Gag/Aag	5/15	0.882821430606225	4	FACETS	0.877	0.806	0.952	0.292	0.268	0.318	CLONAL	1	TRUE	1	0.882821430606225	4		427	783	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395472	116395472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	256	513	0	ENST00000397752.3:c.1765G>A	p.Gly589Arg	p.G589R	ENST00000397752	NM_000245.2	589	Gga/Aga	6/21	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.882821430606225	2		513	579	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759803	133759803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	177	516	0	ENST00000318560.5:c.2126C>T	p.Ser709Phe	p.S709F	ENST00000318560	NM_005157.4	709	tCc/tTc	11/11	1	2	FACETS	0.993	0.927	1	0.993	0.927	1	CLONAL	1	TRUE	1	0.882821430606225	2		516	404	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932044	36932044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	254	624	0	ENST00000361632.4:c.2425G>A	p.Asp809Asn	p.D809N	ENST00000361632		809	Gac/Aac	16/16	1				0.919	1				CLONAL	1	TRUE	1	0.882821430606225	2		624	591	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0019380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	381	741	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.23588508256789	9	FACETS	1	0.98	1	0.787	0.75	0.824	CLONAL	6	TRUE	1	0.23588508256789	9		742	937	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs760043106	NA	P-0019380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	70	737	0	ENST00000269305.4:c.584T>A	p.Ile195Asn	p.I195N	ENST00000269305	NM_001126112.2	195	aTc/aAc	6/11	0.23588508256789	1	FACETS	0.954	0.832	1	0.954	0.832	1	CLONAL	1	TRUE	0	0.23588508256789	1		737	549	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772248	68772248	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	107	1024	2	ENST00000261769.5:c.97G>A	p.Asp33Asn	p.D33N	ENST00000261769	NM_004360.3	33	Gac/Aac	2/16	1	2	FACETS	0.991	0.888	1	0.991	0.888	1	CLONAL	1	TRUE	1	0.23588508256789	2		1026	915	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	117	600	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.572845824491582	3	FACETS	0.856	0.775	0.941	0.428	0.387	0.471	CLONAL	1	TRUE	1	0.67437864748873	3		600	542	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0019385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	444	518	0	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.67437864748873	3	FACETS	0.972	0.943	1	1	0.997	1	CLONAL	3	TRUE	1	0.67437864748873	3		518	604	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725041	89725046	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAGGTG	TAGGTG	-	novel	NA	P-0019385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	99	269	0	ENST00000371953.3:c.1027-3_1029del		p.X343_splice	ENST00000371953	NM_000314.4	343		9/9	0.67437864748873	2	FACETS	0.972	0.903	1	0.972	0.903	1	CLONAL	2	TRUE	0	0.67437864748873	2		269	151	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177707	56177708	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	162	327	0	ENST00000399503.3:c.2681dup	p.Glu895GlyfsTer9	p.E895Gfs*9	ENST00000399503	NM_005921.1	894	ctg/cTtg	14/20	0.524376075867974	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.67437864748873	1		327	277	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929090	44929090	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1250	199	589	0	ENST00000377967.4:c.2191del	p.Ser731AlafsTer24	p.S731Afs*24	ENST00000377967	NM_021140.2	730	acA/ac	17/29	0.67437864748873	5	FACETS	0.819	0.757	0.885			1	CLONAL	1	TRUE	NA	0.67437864748873	5		589	1449	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0019386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	406	729	4	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.634276141020198	2		733	951	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0019386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	277	764	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.468767301043411	2	FACETS	0.762	0.723	0.801	0.762	0.723	0.801	SUBCLONAL	2	TRUE	0	0.634276141020198	2		764	573	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0019386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	202	692	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.856	0.796	0.918	0.856	0.796	0.918	CLONAL	1	TRUE	1	0.634276141020198	2		692	744	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739064	40739064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780908301	NA	P-0019386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	138	773	1	ENST00000373198.4:c.3220G>A	p.Val1074Ile	p.V1074I	ENST00000373198	NM_133170.3	1074	Gtt/Att	24/32	1	2	FACETS	0.537	0.488	0.587	0.537	0.488	0.587	SUBCLONAL	1	TRUE	1	0.634276141020198	2		774	811	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426123	138426123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217537873	NA	P-0019386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	56	436	0	ENST00000289153.2:c.1408G>A	p.Glu470Lys	p.E470K	ENST00000289153	NM_006219.2	470	Gaa/Aaa	9/22	1	2	FACETS	0.516	0.444	0.594	0.516	0.444	0.594	SUBCLONAL	1	TRUE	1	0.634276141020198	2		436	342	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0019386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	201	526	0	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.634276141020198	2		526	531	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411489	63411489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200798538	NA	P-0019386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	183	1084	1	ENST00000330258.3:c.1678C>T	p.Arg560Trp	p.R560W	ENST00000330258	NM_152424.3	560	Cgg/Tgg	2/2	1	2	FACETS	0.481	0.443	0.521	0.481	0.443	0.521	SUBCLONAL	1	TRUE	1	0.634276141020198	2		1085	1200	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411717	63411717	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	269	1080	0	ENST00000330258.3:c.1450G>T	p.Gly484Cys	p.G484C	ENST00000330258	NM_152424.3	484	Ggt/Tgt	2/2	1	2	FACETS	0.738	0.691	0.785	0.738	0.691	0.785	SUBCLONAL	1	TRUE	1	0.634276141020198	2		1080	1150	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655413	45655413	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1194	77	1037	1	ENST00000407780.3:c.439del	p.His147ThrfsTer15	p.H147Tfs*15	ENST00000407780	NM_001283052.1	147	Cac/ac	4/7	1	2	FACETS	0.191	0.167	0.217	0.191	0.167	0.217	SUBCLONAL	1	TRUE	1	0.634276141020198	2		1038	1271	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513352	41513352	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	46	772	1	ENST00000263253.7:c.256C>T	p.Arg86Ter	p.R86*	ENST00000263253	NM_001429.3	86	Cga/Tga	2/31	1	2	FACETS	0.17	0.143	0.201	0.17	0.143	0.201	SUBCLONAL	1	TRUE	1	0.634276141020198	2		773	851	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459759	149459759	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374166176	NA	P-0019386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	176	865	3	ENST00000286301.3:c.448C>T	p.Arg150Cys	p.R150C	ENST00000286301	NM_005211.3	150	Cgc/Tgc	4/22	1	2	FACETS	0.601	0.554	0.651	0.601	0.554	0.651	SUBCLONAL	1	TRUE	1	0.634276141020198	2		868	923	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131411	202131411	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs777784105	NA	P-0019386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	67	663	0	ENST00000358485.4:c.379C>T	p.Arg127Ter	p.R127*	ENST00000358485	NM_001080125.1	127	Cga/Tga	2/9	1	2	FACETS	0.337	0.293	0.386	0.337	0.293	0.386	SUBCLONAL	1	TRUE	1	0.634276141020198	2		663	626	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959106	2959106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs895214237	NA	P-0019386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	243	819	0	ENST00000396946.4:c.2410C>T	p.Arg804Cys	p.R804C	ENST00000396946	NM_032415.4	804	Cgt/Tgt	18/25	1	2	FACETS	0.744	0.695	0.794	0.744	0.695	0.794	SUBCLONAL	1	TRUE	1	0.634276141020198	2		819	1030	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609084	43609086	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs377767399	NA	P-0019386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	121	1156	4	ENST00000355710.3:c.1846_1848del	p.Glu616del	p.E616del	ENST00000355710	NM_020975.4	614	GAG/-	10/20	1	2	FACETS	0.323	0.29	0.357	0.323	0.29	0.357	SUBCLONAL	1	TRUE	1	0.634276141020198	2		1160	1183	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100877	27100877	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	176	726	0	ENST00000324856.7:c.4159G>T	p.Glu1387Ter	p.E1387*	ENST00000324856	NM_006015.4	1387	Gag/Tag	18/20	1	2	FACETS	0.744	0.687	0.803	0.744	0.687	0.803	SUBCLONAL	1	TRUE	1	0.634276141020198	2		726	746	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154294	2154294	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1243657106	NA	P-0019386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1250	120	1233	1	ENST00000434045.2:c.634C>T	p.Arg212Cys	p.R212C	ENST00000434045	NM_001127598.1	212	Cgt/Tgt	5/5	1	2	FACETS	0.276	0.248	0.306	0.276	0.248	0.306	SUBCLONAL	1	TRUE	1	0.634276141020198	2		1234	1370	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425890	49425890	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	151	865	0	ENST00000301067.7:c.12598C>T	p.Gln4200Ter	p.Q4200*	ENST00000301067	NM_003482.3	4200	Cag/Tag	39/54	1	2	FACETS	0.52	0.475	0.567	0.52	0.475	0.567	SUBCLONAL	1	TRUE	1	0.634276141020198	2		865	915	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039436	49039437	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0019386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	95	838	0	ENST00000267163.4:c.2425dup	p.Leu809ProfsTer6	p.L809Pfs*6	ENST00000267163	NM_000321.2	807	-/C	23/27	1	2	FACETS	0.396	0.352	0.443	0.396	0.352	0.443	SUBCLONAL	1	TRUE	1	0.634276141020198	2		838	756	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872956	35872956	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	122	567	0	ENST00000216797.5:c.276A>T	p.Glu92Asp	p.E92D	ENST00000216797	NM_020529.2	92	gaA/gaT	2/6	1	2	FACETS	0.554	0.502	0.61	0.554	0.502	0.61	SUBCLONAL	1	TRUE	1	0.634276141020198	2		567	694	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762148	43762148	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1295099562	NA	P-0019386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	165	1008	0	ENST00000382044.4:c.1297G>A	p.Val433Ile	p.V433I	ENST00000382044	NM_001141980.1	433	Gta/Ata	11/28	1	2	FACETS	0.485	0.444	0.527	0.485	0.444	0.527	SUBCLONAL	1	TRUE	1	0.634276141020198	2		1008	1073	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916137	9916137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	93	524	0	ENST00000330684.3:c.2152G>A	p.Val718Ile	p.V718I	ENST00000330684	NM_001134407.1	718	Gtc/Atc	10/13	1	2	FACETS	0.456	0.406	0.51	0.456	0.406	0.51	SUBCLONAL	1	TRUE	1	0.634276141020198	2		524	643	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942031	81942031	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	119	590	0	ENST00000359376.3:c.1568C>A	p.Pro523His	p.P523H	ENST00000359376	NM_002661.3	523	cCt/cAt	17/33	1	2	FACETS	0.634	0.574	0.697	0.634	0.574	0.697	SUBCLONAL	1	TRUE	1	0.634276141020198	2		590	592	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15952178	15952178	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746349109	NA	P-0019386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	139	617	1	ENST00000268712.3:c.6517G>A	p.Ala2173Thr	p.A2173T	ENST00000268712	NM_006311.3	2173	Gca/Aca	41/46	1	2	FACETS	0.563	0.512	0.615	0.563	0.512	0.615	SUBCLONAL	1	TRUE	1	0.634276141020198	2		618	779	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663907	29663907	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1555534766	NA	P-0019386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	72	460	1	ENST00000356175.3:c.6339T>A	p.Cys2113Ter	p.C2113*	ENST00000356175	NM_000267.3	2113	tgT/tgA	41/57	1	2	FACETS	0.456	0.399	0.517	0.456	0.399	0.517	SUBCLONAL	1	TRUE	1	0.634276141020198	2		461	498	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274187	18274187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	168	918	0	ENST00000222254.8:c.1405C>T	p.Arg469Trp	p.R469W	ENST00000222254	NM_005027.3	469	Cgg/Tgg	11/16	1	2	FACETS	0.511	0.469	0.555	0.511	0.469	0.555	SUBCLONAL	1	TRUE	1	0.634276141020198	2		918	1036	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308412	30308412	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	48	826	2	ENST00000262643.3:c.430del	p.Met144CysfsTer9	p.M144Cfs*9	ENST00000262643	NM_001238.2	142	ccA/cc	6/12	1	2	FACETS	0.161	0.135	0.189	0.161	0.135	0.189	SUBCLONAL	1	TRUE	1	0.634276141020198	2		828	942	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921185	50921185	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	128	1126	1	ENST00000440232.2:c.3305C>A	p.Pro1102His	p.P1102H	ENST00000440232	NM_002691.3	1102	cCt/cAt	27/27	1	2	FACETS	0.319	0.288	0.351	0.319	0.288	0.351	SUBCLONAL	1	TRUE	1	0.634276141020198	2		1127	1267	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61722664	61722664	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	70	653	0	ENST00000401558.2:c.973T>C	p.Phe325Leu	p.F325L	ENST00000401558	NM_003400.3	325	Ttt/Ctt	11/25	1	2	FACETS	0.43	0.376	0.489	0.43	0.376	0.489	SUBCLONAL	1	TRUE	1	0.634276141020198	2		653	513	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628503	187628503	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1429904564	NA	P-0019386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	242	962	1	ENST00000441802.2:c.2479T>C	p.Tyr827His	p.Y827H	ENST00000441802	NM_005245.3	827	Tat/Cat	2/27	1	2	FACETS	0.744	0.695	0.795	0.744	0.695	0.795	SUBCLONAL	1	TRUE	1	0.634276141020198	2		963	1025	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591259	67591260	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0019386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	68	598	0	ENST00000274335.5:c.1760_1761del	p.Lys587ArgfsTer14	p.K587Rfs*14	ENST00000274335		586	cAA/c	13/15	1	2	FACETS	0.388	0.338	0.443	0.388	0.338	0.443	SUBCLONAL	1	TRUE	1	0.634276141020198	2		598	552	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288965	33288965	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774538403	NA	P-0019386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	94	434	0	ENST00000374542.5:c.587C>T	p.Ala196Val	p.A196V	ENST00000374542	NM_001141970.1	196	gCg/gTg	3/8	1	2	FACETS	0.571	0.51	0.636	0.571	0.51	0.636	SUBCLONAL	1	TRUE	1	0.634276141020198	2		434	519	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024114	112024114	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	95	692	0	ENST00000368678.4:c.671T>G	p.Leu224Arg	p.L224R	ENST00000368678		224	cTt/cGt	7/13	1	2	FACETS	0.423	0.376	0.472	0.423	0.376	0.472	SUBCLONAL	1	TRUE	1	0.634276141020198	2		692	709	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835940	151835940	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	162	634	0	ENST00000262189.6:c.14584T>G	p.Phe4862Val	p.F4862V	ENST00000262189	NM_170606.2	4862	Ttt/Gtt	58/59	1	2	FACETS	0.691	0.635	0.749	0.691	0.635	0.749	SUBCLONAL	1	TRUE	1	0.634276141020198	2		634	739	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248079	98248079	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs758656848	NA	P-0019386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	42	706	0	ENST00000331920.6:c.472A>G	p.Met158Val	p.M158V	ENST00000331920	NM_000264.3	158	Atg/Gtg	3/24	1	2	FACETS	0.171	0.142	0.203	0.171	0.142	0.203	SUBCLONAL	1	TRUE	1	0.634276141020198	2		706	776	SUCCESS
FH	2271	MSKCC	GRCh37	1	241672042	241672042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	83	557	2	ENST00000366560.3:c.599C>T	p.Ala200Val	p.A200V	ENST00000366560	NM_000143.3	200	gCa/gTa	5/10	1	2	FACETS	0.865	0.766	0.969	1	0.982	1	CLONAL	2	TRUE	1	0.206453167538179	2		559	465	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105702	30105702	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0019387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	20	388	0	ENST00000331968.5:c.986-2A>C		p.X329_splice	ENST00000331968	NM_002742.2	329			1	2	FACETS	0.546	0.417	0.697	0.546	0.417	0.697	SUBCLONAL	1	TRUE	1	0.206453167538179	2		388	355	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47643434	47643434	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs12476364	NA	P-0019387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	32	490	0	ENST00000233146.2:c.943-1G>A		p.X315_splice	ENST00000233146	NM_000251.2	315			0.206453167538179	3	FACETS	0.74	0.6	0.899			1	SUBCLONAL	1	TRUE	NA	0.206453167538179	3		490	462	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159124	24159166	+	splice_donor_variant,intron_variant	Splice_Site	DEL	GTAGGTGACTTCTCACCCAGCACTGGAGCCTTCCTGGCCCTCA	GTAGGTGACTTCTCACCCAGCACTGGAGCCTTCCTGGCCCTCA	-	novel	NA	P-0019387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	66	372	0	ENST00000263121.7:c.795+2_795+44del		p.X265_splice	ENST00000263121	NM_003073.3	265			0.206453167538179	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	0	0.206453167538179	2		372	287	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202346	138202346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780709741	NA	P-0019388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	43	747	1	ENST00000237289.4:c.2263G>A	p.Glu755Lys	p.E755K	ENST00000237289	NM_001270507.1	755	Gaa/Aaa	9/9	0.233480960913742	9	FACETS	0.867	0.727	1			1	CLONAL	2	FALSE	NA	0.233480960913742	9		748	386	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784112	9784112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	67	632	1	ENST00000377346.4:c.2680C>T	p.Arg894Trp	p.R894W	ENST00000377346	NM_005026.3	894	Cgg/Tgg	21/24	0.181045592313947	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	0	0.233480960913742	1		633	348	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961818	15961818	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs542449256	NA	P-0019388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	143	666	0	ENST00000268712.3:c.5977C>T	p.Gln1993Ter	p.Q1993*	ENST00000268712	NM_006311.3	1993	Cag/Tag	38/46	0.233480960913742	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	3	FALSE	0	0.233480960913742	3		666	430	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509830	187509830	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	25	308	0	ENST00000441802.2:c.13683G>C	p.Met4561Ile	p.M4561I	ENST00000441802	NM_005245.3	4561	atG/atC	27/27	NA	2	FACETS	1	0.917	1			1	INDETERMINATE	1	FALSE	NA	0.233480960913742	2		308	160	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841855	151841858	+	frameshift_variant	Frame_Shift_Del	DEL	GTAC	GTAC	CA	novel	NA	P-0019388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	51	376	0	ENST00000262189.6:c.14283_14286delinsTG	p.Gln4761HisfsTer7	p.Q4761Hfs*7	ENST00000262189	NM_170606.2	4761	caGTAC/caTG	55/59	0.233480960913742	5	FACETS	0.865	0.738	1			1	CLONAL	2	FALSE	NA	0.233480960913742	5		376	341	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	47	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.964	0.812	1	0.964	0.812	1	CLONAL	1	TRUE	1	0.13	2		555	750	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0019389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	71	970	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.984	0.856	1	0.984	0.856	1	CLONAL	1	TRUE	1	0.13	2		970	1110	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972458	81972458	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	44	603	0	ENST00000359376.3:c.3251T>C	p.Phe1084Ser	p.F1084S	ENST00000359376	NM_002661.3	1084	tTt/tCt	29/33	1	2	FACETS	0.98	0.82	1	0.98	0.82	1	CLONAL	1	TRUE	1	0.13	2		603	691	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600369	10600369	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	668	1306	0	ENST00000171111.5:c.1486G>T	p.Glu496Ter	p.E496*	ENST00000171111	NM_203500.1	496	Gag/Tag	4/6	0.515278415502244	2	FACETS	0.971	0.939	1	0.971	0.939	1	CLONAL	2	TRUE	0	0.515278415502244	2		1306	1335	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097703	27097703	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	477	939	0	ENST00000324856.7:c.3292C>T	p.Gln1098Ter	p.Q1098*	ENST00000324856	NM_006015.4	1098	Cag/Tag	12/20	0.515278415502244	3	FACETS	0.951	0.911	0.992	0.951	0.911	0.992	CLONAL	2	TRUE	1	0.515278415502244	3		939	1224	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1131691035	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	748	1008	4	ENST00000269305.4:c.592del	p.Glu198LysfsTer49	p.E198Kfs*49	ENST00000269305	NM_001126112.2	198	Gaa/aa	6/11	0.515278415502244	3	FACETS	0.931	0.904	0.957	0.931	0.904	0.957	CLONAL	3	TRUE	0	0.515278415502244	3		1012	1308	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246344	46246344	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	230	445	0	ENST00000334344.6:c.4438G>T	p.Gly1480Ter	p.G1480*	ENST00000334344	NM_152641.2	1480	Gga/Tga	15/21	0.515278415502244	3	FACETS	0.877	0.823	0.933	0.877	0.823	0.933	CLONAL	2	TRUE	1	0.515278415502244	3		445	640	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727138	40727138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375402843	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	228	799	2	ENST00000373198.4:c.3826G>A	p.Val1276Met	p.V1276M	ENST00000373198	NM_133170.3	1276	Gtg/Atg	28/32	1	2	FACETS	0.961	0.896	1	0.961	0.896	1	CLONAL	1	TRUE	1	0.515278415502244	2		801	921	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797731	45797731	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	536	1036	0	ENST00000450313.1:c.961G>T	p.Gly321Trp	p.G321W	ENST00000450313	NM_012222.2	321	Ggg/Tgg	11/16	0.515278415502244	3	FACETS	0.944	0.906	0.982	0.944	0.906	0.982	CLONAL	2	TRUE	1	0.515278415502244	3		1036	1386	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465304	120465304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	169	620	0	ENST00000256646.2:c.4957C>T	p.His1653Tyr	p.H1653Y	ENST00000256646	NM_024408.3	1653	Cac/Tac	27/34	0.508140087428418	3	FACETS	1	0.957	1	0.529	0.487	0.573	CLONAL	1	TRUE	1	0.515278415502244	3		620	779	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466420	120466420	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs552225415	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	163	782	0	ENST00000256646.2:c.4699C>T	p.Arg1567Trp	p.R1567W	ENST00000256646	NM_024408.3	1567	Cgg/Tgg	26/34	0.508140087428418	3	FACETS	0.868	0.796	0.942	0.434	0.398	0.471	CLONAL	1	TRUE	1	0.515278415502244	3		782	917	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612644	228612644	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	394	965	0	ENST00000366696.1:c.383C>A	p.Ala128Glu	p.A128E	ENST00000366696	NM_003493.2	128	gCa/gAa	1/1	0.497329009726304	4	FACETS	0.856	0.814	0.9	0.856	0.814	0.9	CLONAL	2	TRUE	2	0.515278415502244	4		965	1353	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17743028	17743028	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	572	1208	0	ENST00000250003.3:c.939del	p.Asn314ThrfsTer22	p.N314Tfs*22	ENST00000250003	NM_002478.4	312	aaC/aa	3/3	NA	2	FACETS	0.996	0.961	1			1	INDETERMINATE	2	TRUE	NA	0.515278415502244	2		1208	1115	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943789	71943789	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs773085707	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	257	913	1	ENST00000298229.2:c.1832G>T	p.Arg611Leu	p.R611L	ENST00000298229	NM_001567.3	611	cGc/cTc	15/28	0.508140087428418	3	FACETS	0.875	0.818	0.935	0.438	0.409	0.468	CLONAL	1	TRUE	1	0.515278415502244	3		914	1433	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307567	118307567	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	428	858	0	ENST00000534358.1:c.340G>C	p.Ala114Pro	p.A114P	ENST00000534358	NM_005933.3	114	Gcg/Ccg	1/36	0.508140087428418	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.515278415502244	3		858	1043	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244897	46244898	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	194	787	1	ENST00000334344.6:c.2991_2992delinsTT	p.Gln997_Gly998delinsHisTer	p.Q997_G998delinsH*	ENST00000334344	NM_152641.2	997	caGGga/caTTga	15/21	0.515278415502244	3	FACETS	0.902	0.834	0.973	0.451	0.417	0.487	CLONAL	1	TRUE	1	0.515278415502244	3		788	1050	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557489	21557489	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1170530046	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	594	731	0	ENST00000382592.4:c.2356G>T	p.Gly786Cys	p.G786C	ENST00000382592	NM_014572.2	786	Ggc/Tgc	5/8	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	2	TRUE	NA	0.515278415502244	2		731	1008	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434920	110434920	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs868225719	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	451	1735	1	ENST00000375856.3:c.3481G>T	p.Val1161Leu	p.V1161L	ENST00000375856	NM_003749.2	1161	Gtg/Ttg	1/2	0.510238140660678	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.515278415502244	1		1736	1261	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068922	30068922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1445	538	1158	2	ENST00000331968.5:c.2007G>A	p.Met669Ile	p.M669I	ENST00000331968	NM_002742.2	669	atG/atA	14/18	0.442607821188053	5	FACETS	0.933	0.893	0.975			1	CLONAL	2	TRUE	NA	0.515278415502244	5		1160	1983	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30102103	30102103	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	422	855	0	ENST00000331968.5:c.1364A>T	p.Gln455Leu	p.Q455L	ENST00000331968	NM_002742.2	455	cAg/cTg	9/18	0.442607821188053	5	FACETS	0.936	0.89	0.982			1	CLONAL	2	TRUE	NA	0.515278415502244	5		855	1552	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557417	95557417	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	3709	604	1	ENST00000393063.1:c.5557C>T	p.Pro1853Ser	p.P1853S	ENST00000393063	NM_030621.3	1853	Cct/Tct	27/28	0.515278415502244	23	FACETS	1	0.994	1			1	CLONAL	21	TRUE	NA	0.515278415502244	23		605	4381	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591732	38591732	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	250	603	0	ENST00000299084.4:c.191G>T	p.Arg64Leu	p.R64L	ENST00000299084	NM_152594.2	64	cGa/cTa	2/7	0.508140087428418	3	FACETS	0.801	0.752	0.851	0.801	0.752	0.851	CLONAL	2	TRUE	1	0.515278415502244	3		603	762	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42053936	42053936	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	335	450	0	ENST00000219905.7:c.7399-1G>T		p.X2467_splice	ENST00000219905	NM_001164273.1	2467			0.508140087428418	3	FACETS	0.922	0.883	0.962	1	0.995	1	CLONAL	3	TRUE	1	0.515278415502244	3		450	591	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273887	10273887	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	542	1191	2	ENST00000330684.3:c.382C>A	p.His128Asn	p.H128N	ENST00000330684	NM_001134407.1	128	Cat/Aat	2/13	0.515278415502244	2	FACETS	0.915	0.881	0.95	0.915	0.881	0.95	CLONAL	2	TRUE	0	0.515278415502244	2		1193	1149	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993917	72993917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772079187	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	180	726	1	ENST00000268489.5:c.128C>T	p.Thr43Ile	p.T43I	ENST00000268489	NM_006885.3	43	aCa/aTa	2/10	0.515278415502244	2	FACETS	0.889	0.821	0.959	0.444	0.41	0.48	CLONAL	1	TRUE	0	0.515278415502244	2		727	786	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16001772	16001772	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	225	884	0	ENST00000268712.3:c.2729C>G	p.Pro910Arg	p.P910R	ENST00000268712	NM_006311.3	910	cCc/cGc	21/46	0.515278415502244	3	FACETS	0.9	0.837	0.966	0.3	0.279	0.322	CLONAL	1	TRUE	0	0.515278415502244	3		884	1220	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509524	29509524	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs1555608924	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	147	629	2	ENST00000356175.3:c.731-2A>T		p.X244_splice	ENST00000356175	NM_000267.3	244			0.508140087428418	3	FACETS	0.901	0.824	0.983	0.451	0.412	0.492	CLONAL	1	TRUE	1	0.515278415502244	3		631	796	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550561	29550561	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	147	663	1	ENST00000356175.3:c.1821G>T	p.Arg607Ser	p.R607S	ENST00000356175	NM_000267.3	607	agG/agT	16/57	0.508140087428418	3	FACETS	0.8	0.73	0.873	0.4	0.365	0.437	SUBCLONAL	1	TRUE	1	0.515278415502244	3		664	897	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663795	29663795	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	452	721	0	ENST00000356175.3:c.6227del	p.Ala2076GlufsTer14	p.A2076Efs*14	ENST00000356175	NM_000267.3	2076	gCa/ga	41/57	0.508140087428418	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.515278415502244	3		721	1094	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676236	29676236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	319	675	0	ENST00000356175.3:c.7225G>A	p.Glu2409Lys	p.E2409K	ENST00000356175	NM_000267.3	2409	Gaa/Aaa	48/57	0.508140087428418	3	FACETS	0.867	0.821	0.914	0.867	0.821	0.914	CLONAL	2	TRUE	1	0.515278415502244	3		675	898	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354384	40354384	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1216	405	1638	1	ENST00000293328.3:c.2211G>T	p.Gln737His	p.Q737H	ENST00000293328	NM_012448.3	737	caG/caT	18/19	1	2	FACETS	0.97	0.921	1	0.97	0.921	1	CLONAL	1	TRUE	1	0.515278415502244	2		1639	1621	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117083	7117083	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs52826008	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	311	890	0	ENST00000302850.5:c.4133G>C	p.Arg1378Pro	p.R1378P	ENST00000302850	NM_000208.2	1378	cGg/cCg	22/22	0.515278415502244	2	FACETS	0.768	0.728	0.808	0.768	0.728	0.808	SUBCLONAL	2	TRUE	0	0.515278415502244	2		890	786	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795456	42795456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1360466120	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	161	684	0	ENST00000575354.2:c.2536C>T	p.Pro846Ser	p.P846S	ENST00000575354	NM_015125.3	846	Cct/Tct	10/20	0.515278415502244	3	FACETS	0.943	0.866	1			1	CLONAL	1	TRUE	NA	0.515278415502244	3		684	833	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25990466	25990466	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	323	624	0	ENST00000435504.4:c.761A>T	p.Glu254Val	p.E254V	ENST00000435504		254	gAg/gTg	8/13	0.465027784534232	4	FACETS	0.897	0.848	0.947	0.897	0.848	0.947	CLONAL	2	TRUE	2	0.515278415502244	4		624	1059	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142907	30142907	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1249	549	1424	0	ENST00000389048.3:c.619del	p.Ala207GlnfsTer42	p.A207Qfs*42	ENST00000389048	NM_004304.4	207	Gca/ca	1/29	0.465027784534232	4	FACETS	0.898	0.86	0.936	0.898	0.86	0.936	CLONAL	2	TRUE	2	0.515278415502244	4		1424	1798	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251632	212251632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	105	518	0	ENST00000342788.4:c.3427G>A	p.Gly1143Arg	p.G1143R	ENST00000342788	NM_005235.2	1143	Gga/Aga	27/28	0.508140087428418	3	FACETS	0.832	0.747	0.922	0.416	0.373	0.461	CLONAL	1	TRUE	1	0.515278415502244	3		518	616	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530141	212530141	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	230	553	0	ENST00000342788.4:c.1778G>A	p.Cys593Tyr	p.C593Y	ENST00000342788	NM_005235.2	593	tGt/tAt	15/28	0.508140087428418	3	FACETS	0.783	0.733	0.834	0.783	0.733	0.834	SUBCLONAL	2	TRUE	1	0.515278415502244	3		553	717	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652850	212652850	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	139	600	0	ENST00000342788.4:c.456C>G	p.Asn152Lys	p.N152K	ENST00000342788	NM_005235.2	152	aaC/aaG	4/28	0.508140087428418	3	FACETS	0.837	0.762	0.915	0.418	0.381	0.458	CLONAL	1	TRUE	1	0.515278415502244	3		600	811	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546689	9546689	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	109	418	0	ENST00000353224.5:c.1333C>A	p.Pro445Thr	p.P445T	ENST00000353224	NM_177990.2	445	Ccc/Acc	5/10	NA	2	FACETS	1	0.911	1			1	INDETERMINATE	1	TRUE	NA	0.515278415502244	2		418	420	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739028	40739029	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	186	840	1	ENST00000373198.4:c.3255_3256delinsAA	p.Arg1086Ser	p.R1086S	ENST00000373198	NM_133170.3	1085	gtCCgc/gtAAgc	24/32	1	2	FACETS	0.854	0.79	0.921	0.854	0.79	0.921	CLONAL	1	TRUE	1	0.515278415502244	2		841	845	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743933	40743933	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	174	678	0	ENST00000373198.4:c.3062C>G	p.Pro1021Arg	p.P1021R	ENST00000373198	NM_133170.3	1021	cCa/cGa	23/32	1	2	FACETS	0.861	0.794	0.931	0.861	0.794	0.931	CLONAL	1	TRUE	1	0.515278415502244	2		678	784	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408909	41408909	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	163	714	0	ENST00000373198.4:c.517C>A	p.His173Asn	p.H173N	ENST00000373198	NM_133170.3	173	Cat/Aat	4/32	1	2	FACETS	0.959	0.883	1	0.959	0.883	1	CLONAL	1	TRUE	1	0.515278415502244	2		714	660	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62294240	62294240	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	235	988	0	ENST00000360203.5:c.536A>G	p.Glu179Gly	p.E179G	ENST00000360203	NM_001283009.1	179	gAa/gGa	6/35	NA	2	FACETS	0.994	0.928	1			1	INDETERMINATE	1	TRUE	NA	0.515278415502244	2		988	918	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475489	12475489	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	515	994	3	ENST00000287820.6:c.1363G>T	p.Glu455Ter	p.E455*	ENST00000287820	NM_015869.4	455	Gag/Tag	7/7	0.508140087428418	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.515278415502244	3		997	1235	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480460	89480460	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1366099808	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	130	479	0	ENST00000336596.2:c.2297G>T	p.Gly766Val	p.G766V	ENST00000336596	NM_005233.5	766	gGa/gTa	13/17	0.508140087428418	3	FACETS	0.957	0.87	1	0.479	0.435	0.524	CLONAL	1	TRUE	1	0.515278415502244	3		479	663	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665062	138665062	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	89	262	0	ENST00000330315.3:c.503G>A	p.Gly168Glu	p.G168E	ENST00000330315	NM_023067.3	168	gGg/gAg	1/1	0.508140087428418	3	FACETS	1	0.977	1	0.675	0.604	0.748	CLONAL	1	TRUE	1	0.515278415502244	3		262	322	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957525	1957525	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	331	1022	0	ENST00000382891.5:c.2624G>T	p.Gly875Val	p.G875V	ENST00000382891	NM_133335.3	875	gGg/gTg	14/22	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.515278415502244	2		1022	1116	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127312	55127312	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	404	795	2	ENST00000257290.5:c.100G>T	p.Glu34Ter	p.E34*	ENST00000257290	NM_006206.4	34	Gaa/Taa	3/23	0.508140087428418	3	FACETS	0.956	0.912	1	0.956	0.912	1	CLONAL	2	TRUE	1	0.515278415502244	3		797	1031	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31472187	31472187	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1297095352	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	557	1119	0	ENST00000344624.3:c.2224G>C	p.Val742Leu	p.V742L	ENST00000344624		742	Gtt/Ctt	14/33	0.470711944119347	3	FACETS	0.911	0.875	0.948			1	CLONAL	2	TRUE	NA	0.515278415502244	3		1119	1492	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590996	67590996	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	78	269	0	ENST00000274335.5:c.1589A>G	p.Lys530Arg	p.K530R	ENST00000274335		530	aAg/aGg	12/15	0.515278415502244	2	FACETS	0.867	0.768	0.973	0.434	0.384	0.487	CLONAL	1	TRUE	0	0.515278415502244	2		269	349	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225758	26225758	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	242	578	1	ENST00000360408.1:c.376C>A	p.Gln126Lys	p.Q126K	ENST00000360408	NM_003532.2	126	Cag/Aag	1/1	0.515278415502244	3	FACETS	0.841	0.79	0.894	0.841	0.79	0.894	CLONAL	2	TRUE	1	0.515278415502244	3		579	702	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778236	27778236	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	142	637	0	ENST00000369163.2:c.385C>G	p.Arg129Gly	p.R129G	ENST00000369163	NM_003536.2	129	Cgt/Ggt	1/1	0.515278415502244	3	FACETS	0.906	0.827	0.989	0.453	0.413	0.495	CLONAL	1	TRUE	1	0.515278415502244	3		637	765	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180948	32180948	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	213	794	0	ENST00000375023.3:c.2402G>T	p.Arg801Leu	p.R801L	ENST00000375023	NM_004557.3	801	cGc/cTc	15/30	0.515278415502244	3	FACETS	0.896	0.832	0.963	0.448	0.416	0.482	CLONAL	1	TRUE	1	0.515278415502244	3		794	1160	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180997	32180997	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	283	1043	0	ENST00000375023.3:c.2353A>T	p.Arg785Trp	p.R785W	ENST00000375023	NM_004557.3	785	Agg/Tgg	15/30	0.515278415502244	3	FACETS	0.938	0.879	0.998	0.469	0.439	0.499	CLONAL	1	TRUE	1	0.515278415502244	3		1043	1473	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111995804	111995804	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	309	621	1	ENST00000368678.4:c.1294C>T	p.Pro432Ser	p.P432S	ENST00000368678		432	Ccc/Tcc	12/13	0.515278415502244	2	FACETS	0.972	0.925	1	0.972	0.925	1	CLONAL	2	TRUE	0	0.515278415502244	2		622	617	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622209	162622209	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	149	512	0	ENST00000366898.1:c.488G>T	p.Arg163Met	p.R163M	ENST00000366898	NM_004562.2	163	aGg/aTg	4/12	0.515278415502244	2	FACETS	1	0.956	1	0.531	0.487	0.575	CLONAL	1	TRUE	0	0.515278415502244	2		512	545	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540357	23540357	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	165	607	1	ENST00000380871.4:c.46G>T	p.Gly16Trp	p.G16W	ENST00000380871	NM_006167.3	16	Ggg/Tgg	1/2	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.515278415502244	2		608	605	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572599	141572599	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	259	932	1	ENST00000220592.5:c.471G>T	p.Glu157Asp	p.E157D	ENST00000220592	NM_012154.3	157	gaG/gaT	4/19	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.515278415502244	2		933	856	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484199	8484199	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	330	697	0	ENST00000356435.5:c.3333G>T	p.Lys1111Asn	p.K1111N	ENST00000356435		1111	aaG/aaT	19/35	0.515278415502244	2	FACETS	0.834	0.793	0.875	0.834	0.793	0.875	CLONAL	2	TRUE	0	0.515278415502244	2		697	768	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520008	NA	P-0019391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	395	892	0	ENST00000269305.4:c.613T>G	p.Tyr205Asp	p.Y205D	ENST00000269305	NM_001126112.2	205	Tat/Gat	6/11	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	2	TRUE	NA	0.78835774319677	2		892	464	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984797	72984797	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	108	730	0	ENST00000268489.5:c.2787C>G	p.Asn929Lys	p.N929K	ENST00000268489	NM_006885.3	929	aaC/aaG	3/10	0.235272517740102	3	FACETS	1	0.966	1	0.38	0.345	0.417	INDETERMINATE	1	TRUE	0	0.78835774319677	3		730	335	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244110	41244110	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0019391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	553	703	0	ENST00000357654.3:c.3438T>A	p.Cys1146Ter	p.C1146*	ENST00000357654	NM_007294.3	1146	tgT/tgA	10/23	0.78835774319677	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.78835774319677	3		703	637	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285333	212285333	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	439	471	0	ENST00000342788.4:c.2968G>A	p.Asp990Asn	p.D990N	ENST00000342788	NM_005235.2	990	Gat/Aat	25/28	0.78835774319677	4	FACETS	0.995	0.962	1	0.995	0.962	1	CLONAL	3	TRUE	1	0.78835774319677	4		471	667	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671637	30671637	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	91	715	0	ENST00000376406.3:c.5323T>C	p.Ser1775Pro	p.S1775P	ENST00000376406	NM_014641.2	1775	Tct/Cct	10/15	0.554757756309056	4	FACETS	0.705	0.627	0.787	0.352	0.313	0.394	SUBCLONAL	1	TRUE	2	0.78835774319677	4		715	586	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	254	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.175688596950705	2	FACETS	0.842	0.797	0.887	1	0.992	1	INDETERMINATE	3	TRUE	0	0.383202657250259	2		509	525	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578504	7578540	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTG	AGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTG	-	novel	NA	P-0019392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	223	1247	0	ENST00000269305.4:c.390_426del	p.Asn131CysfsTer27	p.N131Cfs*27	ENST00000269305	NM_001126112.2	130	ctCAACAAGATGTTTTGCCAACTGGCCAAGACCTGCCCT/ct	5/11	0.290038200843429	2	FACETS	0.931	0.865	0.999	0.466	0.432	0.5	CLONAL	1	TRUE	0	0.383202657250259	2		1247	1250	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111959704	111959704	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	182	631	0	ENST00000375549.3:c.283C>G	p.Leu95Val	p.L95V	ENST00000375549	NM_003002.3	95	Ctg/Gtg	3/4	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.383202657250259	2		631	686	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492739	56492739	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	139	770	0	ENST00000407977.2:c.200del	p.Gly67ValfsTer9	p.G67Vfs*9	ENST00000407977		67	gGt/gt	2/10	0.290038200843429	2	FACETS	1	0.981	1	0.633	0.579	0.69	CLONAL	1	TRUE	0	0.383202657250259	2		770	573	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248684	212248684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	29	444	0	ENST00000342788.4:c.3583C>T	p.Pro1195Ser	p.P1195S	ENST00000342788	NM_005235.2	1195	Cca/Tca	28/28	1	2	FACETS	0.357	0.286	0.438	0.357	0.286	0.438	SUBCLONAL	1	TRUE	1	0.383202657250259	2		444	424	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019400-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	94	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.374	0.332	0.419	0.374	0.332	0.419	SUBCLONAL	1	TRUE	1	0.555349765744669	2		555	906	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466522	120466522	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019400-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	246	873	0	ENST00000256646.2:c.4597G>C	p.Asp1533His	p.D1533H	ENST00000256646	NM_024408.3	1533	Gac/Cac	26/34	0.555349765744669	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.555349765744669	1		873	629	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971342	15971342	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	318	937	0	ENST00000268712.3:c.4607del	p.Pro1536LeufsTer7	p.P1536Lfs*7	ENST00000268712	NM_006311.3	1536	cCt/ct	32/46	0.423478931045683	2	FACETS	0.9	0.853	0.947	0.45	0.426	0.474	INDETERMINATE	1	TRUE	0	0.879359342141386	2		937	804	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300156	15300156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867723391	NA	P-0019405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	230	1186	1	ENST00000263388.2:c.1120C>T	p.Arg374Trp	p.R374W	ENST00000263388	NM_000435.2	374	Cgg/Tgg	7/33	0.45215920295216	2	FACETS	0.436	0.406	0.468	0.218	0.203	0.234	INDETERMINATE	1	TRUE	0	0.879359342141386	2		1187	1199	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670665	86670665	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	100	575	0	ENST00000274376.6:c.1943C>A	p.Pro648His	p.P648H	ENST00000274376	NM_002890.2	648	cCt/cAt	15/25	0.876000067551849	2	FACETS	0.779	0.705	0.855	0.389	0.352	0.428	SUBCLONAL	1	TRUE	0	0.879359342141386	2		575	292	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131976486	131976486	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	177	806	1	ENST00000265335.6:c.3741T>A	p.His1247Gln	p.H1247Q	ENST00000265335		1247	caT/caA	24/25	0.853580658718208	2	FACETS	0.616	0.57	0.664	0.308	0.285	0.332	SUBCLONAL	1	TRUE	0	0.879359342141386	2		807	653	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371750	55371750	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs772539708	NA	P-0019405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	226	815	1	ENST00000297316.4:c.440G>T	p.Arg147Leu	p.R147L	ENST00000297316	NM_022454.3	147	cGg/cTg	2/2	0.489605036270818	1	FACETS	0.403	0.377	0.43	0.403	0.377	0.43	INDETERMINATE	1	TRUE	0	0.879359342141386	1		816	715	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163155	47163155	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	128	513	0	ENST00000409792.3:c.2971del	p.His991IlefsTer15	p.H991Ifs*15	ENST00000409792	NM_014159.6	991	Cat/at	3/21	0.50484735664073	1	FACETS	0.958	0.883	1	0.958	0.883	1	CLONAL	1	TRUE	0	0.626294911825254	1		513	293	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0019407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	337	564	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.630984634896764	3	FACETS	0.955	0.909	1	0.955	0.909	1	CLONAL	2	FALSE	1	0.630984634896764	3		564	736	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0019407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	221	796	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.630984634896764	3	FACETS	0.912	0.849	0.978	0.456	0.424	0.489	CLONAL	1	FALSE	1	0.630984634896764	3		796	1010	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402586	20402586	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	669	666	0	ENST00000346618.3:c.126del	p.Gly43AlafsTer37	p.G43Afs*37	ENST00000346618	NM_001949.4	41	agC/ag	1/7	0.569303265024352	4	FACETS	0.916	0.893	0.939			1	CLONAL	4	FALSE	NA	0.630984634896764	4		666	944	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665383	117665383	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	180	391	0	ENST00000368508.3:c.4364C>G	p.Thr1455Ser	p.T1455S	ENST00000368508	NM_002944.2	1455	aCt/aGt	27/43	0.514625196638946	4	FACETS	0.816	0.757	0.877	0.816	0.757	0.877	CLONAL	2	FALSE	2	0.630984634896764	4		391	570	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402013	402013	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0019407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1620	227	443	0	ENST00000399788.2:c.4778C>G	p.Ser1593Ter	p.S1593*	ENST00000399788	NM_001042603.1	1593	tCa/tGa	27/28	0.630984634896764	11	FACETS	1	0.991	1	0.166	0.154	0.179	CLONAL	1	FALSE	2	0.630984634896764	11		443	1847	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913357	32913357	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	168	557	2	ENST00000380152.3:c.4865G>A	p.Arg1622Lys	p.R1622K	ENST00000380152		1622	aGa/aAa	11/27	0.510802165593085	5	FACETS	0.862	0.791	0.937			1	CLONAL	1	FALSE	NA	0.630984634896764	5		559	1202	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060976	38060977	+	missense_variant	Missense_Mutation	DNP	CT	CT	AA	novel	NA	P-0019407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	28	402	1	ENST00000250448.2:c.1012_1013delinsTT	p.Ser338Phe	p.S338F	ENST00000250448	NM_004496.3	338	AGt/TTt	2/2	1	2	FACETS	0.261	0.208	0.321	0.261	0.208	0.321	SUBCLONAL	1	FALSE	1	0.630984634896764	2		403	340	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56376637	56376637	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs149988025	NA	P-0019407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	53	568	0	ENST00000348428.3:c.677A>G	p.Lys226Arg	p.K226R	ENST00000348428	NM_006785.3	226	aAg/aGg	5/17	0.630984634896764	3	FACETS	0.287	0.244	0.335	0.144	0.122	0.168	SUBCLONAL	1	FALSE	1	0.630984634896764	3		568	769	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921758	111921758	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	164	541	0	ENST00000393256.3:c.547A>G	p.Ile183Val	p.I183V	ENST00000393256	NM_006538.4	183	Atc/Gtc	4/4	0.630984634896764	3	FACETS	1	0.922	1	0.501	0.461	0.542	CLONAL	1	FALSE	1	0.630984634896764	3		541	683	SUCCESS
APC	324	MSKCC	GRCh37	5	112177545	112177545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770637582	NA	P-0019407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	76	413	0	ENST00000257430.4:c.6254G>A	p.Arg2085Lys	p.R2085K	ENST00000257430	NM_000038.5	2085	aGa/aAa	16/16	0.173408470591312	2	FACETS	0.619	0.546	0.697	0.31	0.273	0.349	INDETERMINATE	1	FALSE	0	0.630984634896764	2		413	389	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372711	81372711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	168	448	0	ENST00000222390.5:c.823G>A	p.Asp275Asn	p.D275N	ENST00000222390	NM_000601.4	275	Gac/Aac	7/18	0.362790644680207	4	FACETS	0.832	0.77	0.895	0.832	0.77	0.895	INDETERMINATE	2	FALSE	2	0.630984634896764	4		448	522	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860842	151860843	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0019407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	84	444	0	ENST00000262189.6:c.9819_9820del	p.Ala3274AsnfsTer51	p.A3274Nfs*51	ENST00000262189	NM_170606.2	3273	tgTGca/tgca	43/59	0.330654803425357	3	FACETS	0.557	0.492	0.626			1	INDETERMINATE	1	FALSE	NA	0.630984634896764	3		444	629	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141567313	141567313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs905630231	NA	P-0019407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	47	561	0	ENST00000220592.5:c.901G>A	p.Gly301Arg	p.G301R	ENST00000220592	NM_012154.3	301	Ggg/Agg	8/19	0.630984634896764	3	FACETS	0.272	0.228	0.32	0.136	0.114	0.16	SUBCLONAL	1	FALSE	1	0.630984634896764	3		561	721	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739635	145739635	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs878854644	NA	P-0019407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	246	851	0	ENST00000428558.2:c.1816G>T	p.Glu606Ter	p.E606*	ENST00000428558	NM_004260.3	606	Gag/Tag	11/22	0.630984634896764	3	FACETS	0.897	0.837	0.958	0.448	0.418	0.479	CLONAL	1	FALSE	1	0.630984634896764	3		851	1144	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579317	7579317	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	177	610	1	ENST00000269305.4:c.370T>C	p.Cys124Arg	p.C124R	ENST00000269305	NM_001126112.2	124	Tgc/Cgc	4/11	0.501804676556395	1	FACETS	0.979	0.908	1	0.979	0.908	1	CLONAL	1	TRUE	0	0.501804676556395	1		611	540	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77085411	77085411	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0019410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	180	617	0	ENST00000356341.3:c.440-1G>C		p.X147_splice	ENST00000356341	NM_002576.4	147			1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.501804676556395	2		617	680	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716359	18716359	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	42	594	0	ENST00000266497.5:c.3706G>C	p.Glu1236Gln	p.E1236Q	ENST00000266497		1236	Gaa/Caa	26/31	0.501804676556395	1	FACETS	0.254	0.212	0.301	0.254	0.212	0.301	SUBCLONAL	1	TRUE	0	0.501804676556395	1		594	493	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906804	32906804	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760815829	NA	P-0019410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	55	851	2	ENST00000380152.3:c.1189C>T	p.Gln397Ter	p.Q397*	ENST00000380152		397	Caa/Taa	10/27	1	2	FACETS	0.283	0.241	0.329	0.283	0.241	0.329	SUBCLONAL	1	TRUE	1	0.501804676556395	2		853	775	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56862956	56862956	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	136	569	0	ENST00000308159.5:c.862G>C	p.Gly288Arg	p.G288R	ENST00000308159	NM_014669.4	288	Ggg/Cgg	9/22	0.501804676556395	1	FACETS	0.883	0.809	0.959	0.883	0.809	0.959	CLONAL	1	TRUE	0	0.501804676556395	1		569	460	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71050209	71050209	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	95	382	0	ENST00000318789.4:c.976C>A	p.His326Asn	p.H326N	ENST00000318789	NM_032682.5	326	Cat/Aat	13/21	1	2	FACETS	0.904	0.81	1	0.904	0.81	1	CLONAL	1	TRUE	1	0.501804676556395	2		382	419	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251526	251526	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	123	400	0	ENST00000264932.6:c.1737C>G	p.Ile579Met	p.I579M	ENST00000264932	NM_004168.2	579	atC/atG	13/15	0.434561513951923	3	FACETS	1	0.966	1			1	CLONAL	1	TRUE	NA	0.501804676556395	3		400	540	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143020	58143020	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	92	756	1	ENST00000257904.6:c.764G>T	p.Arg255Leu	p.R255L	ENST00000257904	NM_000075.3	255	cGc/cTc	7/8	0.256399681295152	3	FACETS	1	0.948	1	0.557	0.495	0.623	CLONAL	1	TRUE	1	0.256399681295152	3		757	727	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579191	7579367	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAAAACACTGACAGGAAGCCAAAGGGTGAAGAGGAATCCCAAAGTTCCAAACAAAAGAAATGCAGGGGGATACGGCCAGGCATTGAAGTCTCATGGAAGCCAGCCCCTCAGGGCAACTGACCGTGCAAGTCACAGACTTGGCTGTCCCAGAATGCAAGAAGCCCAGACGGAAACCGT	AAAAACACTGACAGGAAGCCAAAGGGTGAAGAGGAATCCCAAAGTTCCAAACAAAAGAAATGCAGGGGGATACGGCCAGGCATTGAAGTCTCATGGAAGCCAGCCCCTCAGGGCAACTGACCGTGCAAGTCACAGACTTGGCTGTCCCAGAATGCAAGAAGCCCAGACGGAAACCGT	-	novel	NA	P-0019411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	72	72	0	ENST00000269305.4:c.320_375+121del		p.X107_splice	ENST00000269305	NM_001126112.2	107		4/11	NA	2	FACETS	1	0.954	1			1	INDETERMINATE	5	TRUE	NA	0.256399681295152	2		72	106	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528151	29528151	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	190	761	0	ENST00000356175.3:c.1159A>T	p.Ser387Cys	p.S387C	ENST00000356175	NM_000267.3	387	Agc/Tgc	10/57	0.240648066472278	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	1	0.256399681295152	3		761	806	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27217702	27217702	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773518368	NA	P-0019411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	290	647	0	ENST00000380036.4:c.3008G>A	p.Arg1003His	p.R1003H	ENST00000380036	NM_000459.3	1003	cGc/cAc	19/23	0.233773051412802	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.256399681295152	3		647	754	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0019412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	72	930	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	0.819	0.717	0.929	0.819	0.717	0.929	CLONAL	1	TRUE	1	0.328618566858263	2		930	535	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299127	15299127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	51	1068	1	ENST00000263388.2:c.1411G>A	p.Asp471Asn	p.D471N	ENST00000263388	NM_000435.2	471	Gac/Aac	9/33	1	2	FACETS	0.531	0.45	0.619	0.531	0.45	0.619	SUBCLONAL	1	TRUE	1	0.328618566858263	2		1069	585	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	137	566	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	0.318041681745637	3	FACETS	0.923	0.844	1	0.923	0.844	1	CLONAL	2	TRUE	1	0.318041681745637	3		567	541	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0019413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	39	592	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	1	2	FACETS	0.674	0.56	0.801	0.674	0.56	0.801	SUBCLONAL	1	TRUE	1	0.318041681745637	2		592	364	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274911	41274911	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs868651538	NA	P-0019413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	104	563	1	ENST00000349496.5:c.1161T>A	p.Asn387Lys	p.N387K	ENST00000349496	NM_001904.3	387	aaT/aaA	8/15	0.297367778955794	3	FACETS	1	0.982	1	0.737	0.663	0.816	CLONAL	1	TRUE	1	0.318041681745637	3		564	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576851	7576851	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0019413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	98	607	0	ENST00000269305.4:c.993+2T>C		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.245855541150907	2	FACETS	1	0.978	1	0.685	0.614	0.759	CLONAL	1	TRUE	0	0.318041681745637	2		607	450	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143345	30143345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	26	884	1	ENST00000389048.3:c.181C>T	p.Pro61Ser	p.P61S	ENST00000389048	NM_004304.4	61	Ccc/Tcc	1/29	0.318041681745637	1	FACETS	0.318	0.251	0.395	0.318	0.251	0.395	SUBCLONAL	1	TRUE	0	0.318041681745637	1		885	432	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488711	212488711	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	48	674	0	ENST00000342788.4:c.2138T>C	p.Leu713Ser	p.L713S	ENST00000342788	NM_005235.2	713	tTg/tCg	18/28	1	2	FACETS	0.537	0.454	0.629	0.537	0.454	0.629	SUBCLONAL	1	TRUE	1	0.318041681745637	2		674	562	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0019414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	402	798	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.632506966165554	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.632506966165554	1		798	834	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134768	41134768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	194	372	1	ENST00000379561.5:c.860G>A	p.Ser287Asn	p.S287N	ENST00000379561	NM_002015.3	287	aGc/aAc	2/3	0.632506966165554	1	FACETS	0.912	0.853	0.971	0.912	0.853	0.971	CLONAL	1	TRUE	0	0.632506966165554	1		373	460	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082203	16082203	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	464	1061	0	ENST00000281043.3:c.17C>A	p.Thr6Lys	p.T6K	ENST00000281043	NM_005378.4	6	aCg/aAg	2/3	0.632506966165554	1	FACETS	0.896	0.858	0.934	0.896	0.858	0.934	CLONAL	1	TRUE	0	0.632506966165554	1		1061	1120	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702215	47702215	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	351	644	0	ENST00000233146.2:c.1811C>G	p.Ala604Gly	p.A604G	ENST00000233146	NM_000251.2	604	gCt/gGt	12/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.632506966165554	2		644	1021	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026894	48026894	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1558662903	NA	P-0019414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	194	384	0	ENST00000234420.5:c.1772C>A	p.Pro591Gln	p.P591Q	ENST00000234420	NM_000179.2	591	cCa/cAa	4/10	1	2	FACETS	0.899	0.836	0.965	0.899	0.836	0.965	CLONAL	1	TRUE	1	0.632506966165554	2		384	682	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794912	242794912	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	839	789	0	ENST00000334409.5:c.297A>T	p.Gln99His	p.Q99H	ENST00000334409	NM_005018.2	99	caA/caT	2/5	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	2	TRUE	NA	0.632506966165554	2		789	1311	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62290777	62290777	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	135	269	0	ENST00000360203.5:c.22G>T	p.Gly8Cys	p.G8C	ENST00000360203	NM_001283009.1	8	Ggt/Tgt	2/35	1	2	FACETS	0.849	0.776	0.924	0.849	0.776	0.924	CLONAL	1	TRUE	1	0.632506966165554	2		269	503	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86642539	86642539	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	66	387	0	ENST00000274376.6:c.1100C>A	p.Thr367Lys	p.T367K	ENST00000274376	NM_002890.2	367	aCa/aAa	7/25	0.632506966165554	1	FACETS	0.484	0.423	0.548	0.484	0.423	0.548	SUBCLONAL	1	TRUE	0	0.632506966165554	1		387	295	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637211	176637211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61744451	NA	P-0019414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	290	678	1	ENST00000439151.2:c.1811G>A	p.Arg604Gln	p.R604Q	ENST00000439151	NM_022455.4	604	cGa/cAa	5/23	NA	2	FACETS	1	0.96	1			1	INDETERMINATE	1	TRUE	NA	0.632506966165554	2		679	897	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273152	55273152	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1433524783	NA	P-0019414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	310	620	1	ENST00000275493.2:c.3475C>T	p.Gln1159Ter	p.Q1159*	ENST00000275493	NM_005228.3	1159	Cag/Tag	28/28	1	2	FACETS	0.948	0.895	1	0.948	0.895	1	CLONAL	1	TRUE	1	0.632506966165554	2		621	1034	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764346	39764348	+	frameshift_variant	Frame_Shift_Ins	INS	TGG	TGG	CGGA	novel	NA	P-0019414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	277	648	0	ENST00000288319.7:c.764_766delinsTCCG	p.Pro255LeufsTer30	p.P255Lfs*30	ENST00000288319	NM_182918.3	255	cCCAgg/cTCCGgg	7/10	1	2	FACETS	0.915	0.861	0.971	0.915	0.861	0.971	CLONAL	1	TRUE	1	0.632506966165554	2		648	957	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913517	NA	P-0019415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	232	323	0	ENST00000288135.5:c.1676T>A	p.Val559Asp	p.V559D	ENST00000288135	NM_000222.2	559	gTt/gAt	11/21	1	2	FACETS	0.902	0.848	0.957	0.902	0.848	0.957	CLONAL	1	TRUE	1	0.87759258424957	2		323	586	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	626	683	12	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.908	0.884	0.933	1	0.998	1	CLONAL	2	TRUE	1	0.756482913820899	2		695	911	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	472	979	4	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.943	0.901	0.984	0.943	0.901	0.984	CLONAL	1	TRUE	1	0.756482913820899	2		983	1324	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	762	729	4	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.984	0.962	1	1	0.998	1	CLONAL	2	TRUE	1	0.756482913820899	2		733	1024	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	176	646	1	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.687	0.635	0.741	0.687	0.635	0.741	SUBCLONAL	1	TRUE	1	0.756482913820899	2		647	677	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	265	503	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.903	0.85	0.957	0.903	0.85	0.957	CLONAL	1	TRUE	1	0.756482913820899	2		503	776	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741868	17741868	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1466899825	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	96	194	0	ENST00000250003.3:c.539C>T	p.Ala180Val	p.A180V	ENST00000250003	NM_002478.4	180	gCg/gTg	1/3	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.756482913820899	2		194	211	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	164	369	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.926	0.858	0.996	0.926	0.858	0.996	CLONAL	1	TRUE	1	0.756482913820899	2		369	468	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528825	157528825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	233	648	1	ENST00000346085.5:c.6554del	p.Pro2185ArgfsTer8	p.P2185Rfs*8	ENST00000346085	NM_020732.3	2184	Ccc/cc	20/20	1	2	FACETS	0.879	0.823	0.935	0.879	0.823	0.935	CLONAL	1	TRUE	1	0.756482913820899	2		649	701	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332459	70332459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751344073	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	297	786	4	ENST00000373644.4:c.364G>A	p.Val122Ile	p.V122I	ENST00000373644	NM_030625.2	122	Gta/Ata	2/12	0.75269052735692	2	FACETS	0.884	0.835	0.934	0.442	0.417	0.467	CLONAL	1	TRUE	0	0.756482913820899	2		790	888	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260214	16260214	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	215	486	0	ENST00000375759.3:c.7484del	p.Pro2495LeufsTer4	p.P2495Lfs*4	ENST00000375759	NM_015001.2	2493	agC/ag	11/15	1	2	FACETS	0.959	0.897	1	0.959	0.897	1	CLONAL	1	TRUE	1	0.756482913820899	2		486	593	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	236	668	7	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.75269052735692	2	FACETS	0.933	0.875	0.991	0.466	0.437	0.496	CLONAL	1	TRUE	0	0.756482913820899	2		675	669	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	59	151	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	1	2	FACETS	0.975	0.858	1	0.975	0.858	1	CLONAL	1	TRUE	1	0.756482913820899	2		151	160	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030692	48030692	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs267608092	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	126	403	0	ENST00000234420.5:c.3312del	p.Phe1104LeufsTer11	p.F1104Lfs*11	ENST00000234420	NM_000179.2	1102	acT/ac	5/10	1	2	FACETS	0.744	0.678	0.811	0.744	0.678	0.811	SUBCLONAL	1	TRUE	1	0.756482913820899	2		403	448	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991757	72991758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760959844	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	155	419	0	ENST00000268489.5:c.2287dup	p.Glu763GlyfsTer26	p.E763Gfs*26	ENST00000268489	NM_006885.3	763	gag/gGag	2/10	1	2	FACETS	0.907	0.838	0.977	0.907	0.838	0.977	CLONAL	1	TRUE	1	0.756482913820899	2		419	452	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	288	732	0	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	0.916	0.865	0.969	0.916	0.865	0.969	CLONAL	1	TRUE	1	0.756482913820899	2		732	831	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565535	41565535	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	136	520	2	ENST00000263253.7:c.4201G>T	p.Val1401Phe	p.V1401F	ENST00000263253	NM_001429.3	1401	Gtt/Ttt	26/31	1	2	FACETS	0.858	0.788	0.931	0.858	0.788	0.931	CLONAL	1	TRUE	1	0.756482913820899	2		522	419	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796991	45796993	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs747232389	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	244	667	0	ENST00000450313.1:c.1337_1339del	p.Phe446del	p.F446del	ENST00000450313	NM_012222.2	446	tTCTct/tct	14/16	1	2	FACETS	0.938	0.881	0.995	0.938	0.881	0.995	CLONAL	1	TRUE	1	0.756482913820899	2		667	688	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518698	204518698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1270135772	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	196	459	0	ENST00000367182.3:c.1361C>T	p.Thr454Met	p.T454M	ENST00000367182	NM_001278516.1	454	aCg/aTg	11/11	0.725538282127536	4	FACETS	1	0.947	1	0.342	0.317	0.369	CLONAL	1	TRUE	1	0.756482913820899	4		459	886	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685314	89685314	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	114	389	0	ENST00000371953.3:c.209T>G	p.Leu70Arg	p.L70R	ENST00000371953	NM_000314.4	70	cTt/cGt	3/9	0.75269052735692	2	FACETS	0.866	0.809	0.921	0.866	0.809	0.921	CLONAL	2	TRUE	0	0.756482913820899	2		389	174	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434697	49434697	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	419	1065	1	ENST00000301067.7:c.6856G>T	p.Glu2286Ter	p.E2286*	ENST00000301067	NM_003482.3	2286	Gag/Tag	31/54	1	2	FACETS	0.951	0.907	0.995	0.951	0.907	0.995	CLONAL	1	TRUE	1	0.756482913820899	2		1066	1165	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562177	21562177	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769433391	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1565	144	1461	5	ENST00000382592.4:c.1742G>A	p.Arg581His	p.R581H	ENST00000382592	NM_014572.2	581	cGc/cAc	4/8	1	2	FACETS	0.223	0.202	0.245	0.223	0.202	0.245	SUBCLONAL	1	TRUE	1	0.756482913820899	2		1466	1709	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988490	41988490	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	89	869	0	ENST00000219905.7:c.1282A>G	p.Lys428Glu	p.K428E	ENST00000219905	NM_001164273.1	428	Aag/Gag	3/24	1	2	FACETS	0.27	0.239	0.303	0.27	0.239	0.303	SUBCLONAL	1	TRUE	1	0.756482913820899	2		869	872	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42026741	42026741	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	111	634	0	ENST00000219905.7:c.3865C>T	p.Pro1289Ser	p.P1289S	ENST00000219905	NM_001164273.1	1289	Ccc/Tcc	12/24	1	2	FACETS	0.793	0.72	0.869	0.793	0.72	0.869	SUBCLONAL	1	TRUE	1	0.756482913820899	2		634	370	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641637	23641637	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	198	704	0	ENST00000261584.4:c.1838A>G	p.Gln613Arg	p.Q613R	ENST00000261584	NM_024675.3	613	cAg/cGg	5/13	1	2	FACETS	0.966	0.902	1	0.966	0.902	1	CLONAL	1	TRUE	1	0.756482913820899	2		704	542	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849655	68849655	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555516192	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	248	629	0	ENST00000261769.5:c.1558A>G	p.Lys520Glu	p.K520E	ENST00000261769	NM_004360.3	520	Aaa/Gaa	10/16	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.756482913820899	2		629	648	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831310	72831311	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCAGGTGAGCTTGAACTTGAGCCTGGGCCTGGGCCAGCGTTTGTGCTTGTTGTTGTTGTTG	novel	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	38	415	0	ENST00000268489.5:c.5209_5270dup	p.Gln1757HisfsTer31	p.Q1757Hfs*31	ENST00000268489	NM_006885.3	1757	cag/caCAACAACAACAACAAGCACAAACGCTGGCCCAGGCCCAGGCTCAAGTTCAAGCTCACCTGCAg	9/10	1	2	FACETS	0.212	0.175	0.253	0.212	0.175	0.253	SUBCLONAL	1	TRUE	1	0.756482913820899	2		415	474	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934267	81934267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774111706	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	330	860	0	ENST00000359376.3:c.1244G>A	p.Arg415His	p.R415H	ENST00000359376	NM_002661.3	415	cGt/cAt	14/33	1	2	FACETS	0.905	0.857	0.953	0.905	0.857	0.953	CLONAL	1	TRUE	1	0.756482913820899	2		860	964	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40476849	40476850	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	241	555	1	ENST00000264657.5:c.1479dup	p.Thr494TyrfsTer55	p.T494Yfs*55	ENST00000264657	NM_139276.2	493	-/T	17/24	1	2	FACETS	0.965	0.907	1	0.965	0.907	1	CLONAL	1	TRUE	1	0.756482913820899	2		556	660	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858268	59858268	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	190	682	0	ENST00000259008.2:c.1727del	p.Asn576IlefsTer14	p.N576Ifs*14	ENST00000259008	NM_032043.2	576	aAt/at	12/20	1	2	FACETS	0.9	0.838	0.964	0.9	0.838	0.964	CLONAL	1	TRUE	1	0.756482913820899	2		682	558	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117800	70117800	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	340	767	5	ENST00000245479.2:c.268C>T	p.Pro90Ser	p.P90S	ENST00000245479	NM_000346.3	90	Ccc/Tcc	1/3	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.756482913820899	2		772	898	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288799	15288799	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764992581	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	128	158	0	ENST00000263388.2:c.3940G>A	p.Ala1314Thr	p.A1314T	ENST00000263388	NM_000435.2	1314	Gcc/Acc	24/33	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.756482913820899	2		158	278	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355177	15355177	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760576705	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1274	110	1181	2	ENST00000263377.2:c.2446G>A	p.Val816Ile	p.V816I	ENST00000263377	NM_058243.2	816	Gtc/Atc	13/20	1	2	FACETS	0.21	0.188	0.234	0.21	0.188	0.234	SUBCLONAL	1	TRUE	1	0.756482913820899	2		1183	1384	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213956	36213956	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	411	1150	0	ENST00000222270.7:c.2782G>T	p.Glu928Ter	p.E928*	ENST00000222270	NM_014727.1	928	Gag/Tag	6/37	1	2	FACETS	0.89	0.848	0.933	0.89	0.848	0.933	CLONAL	1	TRUE	1	0.756482913820899	2		1150	1221	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224152	36224153	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	299	800	0	ENST00000222270.7:c.6707dup	p.Gly2237ArgfsTer66	p.G2237Rfs*66	ENST00000222270	NM_014727.1	2234	-/C	28/37	1	2	FACETS	0.825	0.779	0.873	0.825	0.779	0.873	CLONAL	1	TRUE	1	0.756482913820899	2		800	958	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505498	25505498	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	284	707	0	ENST00000264709.3:c.260T>C	p.Leu87Pro	p.L87P	ENST00000264709	NM_175629.2	87	cTa/cCa	4/23	1	2	FACETS	0.929	0.877	0.982	0.929	0.877	0.982	CLONAL	1	TRUE	1	0.756482913820899	2		707	808	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661132	227661132	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	66	851	0	ENST00000305123.5:c.2323del	p.Gln775SerfsTer168	p.Q775Sfs*168	ENST00000305123	NM_005544.2	775	Cag/ag	1/2	1	2	FACETS	0.197	0.17	0.226	0.197	0.17	0.226	SUBCLONAL	1	TRUE	1	0.756482913820899	2		851	887	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620572	52620572	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	257	596	0	ENST00000394830.3:c.3181G>T	p.Val1061Phe	p.V1061F	ENST00000394830	NM_018313.4	1061	Gtc/Ttc	21/30	1	2	FACETS	0.904	0.85	0.958	0.904	0.85	0.958	CLONAL	1	TRUE	1	0.756482913820899	2		596	752	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146555	185146555	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	67	569	0	ENST00000265026.3:c.189del	p.Val64SerfsTer6	p.V64Sfs*6	ENST00000265026	NM_004721.4	62	agC/ag	2/14	1	2	FACETS	0.238	0.206	0.273	0.238	0.206	0.273	SUBCLONAL	1	TRUE	1	0.756482913820899	2		569	744	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158269	106158269	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	175	425	0	ENST00000380013.4:c.3170A>G	p.Glu1057Gly	p.E1057G	ENST00000380013	NM_001127208.2	1057	gAa/gGa	3/11	1	2	FACETS	0.87	0.807	0.934	0.87	0.807	0.934	CLONAL	1	TRUE	1	0.756482913820899	2		425	532	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542009	187542009	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	196	495	0	ENST00000441802.2:c.5731T>G	p.Phe1911Val	p.F1911V	ENST00000441802	NM_005245.3	1911	Ttc/Gtc	10/27	1	2	FACETS	0.953	0.889	1	0.953	0.889	1	CLONAL	1	TRUE	1	0.756482913820899	2		495	544	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526755	31526755	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	69	972	0	ENST00000344624.3:c.285del	p.Cys96AlafsTer12	p.C96Afs*12	ENST00000344624		95	ccC/cc	2/33	1	2	FACETS	0.205	0.177	0.234	0.205	0.177	0.234	SUBCLONAL	1	TRUE	1	0.756482913820899	2		972	892	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512378	149512378	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	350	799	0	ENST00000261799.4:c.1062C>G	p.Asn354Lys	p.N354K	ENST00000261799	NM_002609.3	354	aaC/aaG	7/23	1	2	FACETS	0.925	0.878	0.973	0.925	0.878	0.973	CLONAL	1	TRUE	1	0.756482913820899	2		799	1000	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987265	2987265	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	85	618	0	ENST00000396946.4:c.164A>G	p.Gln55Arg	p.Q55R	ENST00000396946	NM_032415.4	55	cAg/cGg	3/25	1	2	FACETS	0.286	0.252	0.322	0.286	0.252	0.322	SUBCLONAL	1	TRUE	1	0.756482913820899	2		618	786	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975411	13975411	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	240	609	0	ENST00000405192.2:c.476C>G	p.Pro159Arg	p.P159R	ENST00000405192	NM_001163147.1	159	cCg/cGg	7/12	1	2	FACETS	0.928	0.871	0.985	0.928	0.871	0.985	CLONAL	1	TRUE	1	0.756482913820899	2		609	684	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90994969	90994969	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	127	520	1	ENST00000265433.3:c.152A>C	p.Asn51Thr	p.N51T	ENST00000265433	NM_002485.4	51	aAc/aCc	2/16	1	2	FACETS	0.941	0.862	1	0.941	0.862	1	CLONAL	1	TRUE	1	0.756482913820899	2		521	357	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970963	21970963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1413479756	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	511	923	2	ENST00000304494.5:c.395C>T	p.Ala132Val	p.A132V	ENST00000304494	NM_000077.4	132	gCg/gTg	2/3	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.756482913820899	2		925	1273	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426093	47426094	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1431646407	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	432	1116	0	ENST00000377045.4:c.619dup	p.Leu207ProfsTer36	p.L207Pfs*36	ENST00000377045	NM_001654.4	205	gcc/gCcc	7/16	1	2	FACETS	0.901	0.86	0.944	0.901	0.86	0.944	CLONAL	1	TRUE	1	0.756482913820899	2		1116	1267	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409806	63409806	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	237	578	0	ENST00000330258.3:c.3361G>A	p.Ala1121Thr	p.A1121T	ENST00000330258	NM_152424.3	1121	Gcc/Acc	2/2	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.756482913820899	2		578	589	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356311	70356311	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1042718707	NA	P-0019416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	228	701	3	ENST00000374080.3:c.5206G>A	p.Ala1736Thr	p.A1736T	ENST00000374080		1736	Gcc/Acc	37/45	1	2	FACETS	0.685	0.639	0.732	0.685	0.639	0.732	SUBCLONAL	1	TRUE	1	0.756482913820899	2		704	880	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0019417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	271	680	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.263214302802009	5	FACETS	1	0.982	1	1	0.982	1	CLONAL	4	TRUE	1	0.263214302802009	5		680	657	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	166	736	0				ENST00000310581	NM_198253.2	-/1132			0.293122900288346	3	FACETS	1	0.959	1	1	0.991	1	CLONAL	3	TRUE	1	0.263214302802009	3		736	453	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	116	770	0	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	0.293122900288346	3	FACETS	0.754	0.681	0.832			1	SUBCLONAL	2	TRUE	NA	0.263214302802009	3		770	661	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914851	32914851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507845	NA	P-0019417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	30	551	0	ENST00000380152.3:c.6359C>T	p.Ser2120Leu	p.S2120L	ENST00000380152		2120	tCa/tTa	11/27	0.263214302802009	5	FACETS	0.567	0.455	0.694			1	SUBCLONAL	1	TRUE	NA	0.263214302802009	5		551	561	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137524722	137524722	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	88	649	0	ENST00000367739.4:c.647C>T	p.Ser216Leu	p.S216L	ENST00000367739	NM_000416.2	216	tCa/tTa	5/7	0.263214302802009	7	FACETS	0.785	0.696	0.881			1	SUBCLONAL	2	TRUE	NA	0.263214302802009	7		649	706	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094409	27094409	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	84	593	0	ENST00000324856.7:c.3119del	p.Asn1040IlefsTer19	p.N1040Ifs*19	ENST00000324856	NM_006015.4	1039	acA/ac	11/20	0.293122900288346	3	FACETS	1	0.97	1	0.654	0.579	0.735	CLONAL	1	TRUE	1	0.263214302802009	3		593	552	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909918	100909918	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	39	553	0	ENST00000325455.5:c.2731G>A	p.Glu911Lys	p.E911K	ENST00000325455	NM_001202474.3	911	Gaa/Aaa	8/8	0.293122900288346	4	FACETS	0.654	0.541	0.781	0.218	0.18	0.261	SUBCLONAL	1	TRUE	1	0.263214302802009	4		553	572	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128222	30128222	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs527481960	NA	P-0019417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	66	634	1	ENST00000263025.4:c.1010C>T	p.Thr337Met	p.T337M	ENST00000263025	NM_002746.2	337	aCg/aTg	7/9	0.293122900288346	3	FACETS	0.907	0.787	1			1	CLONAL	1	TRUE	NA	0.263214302802009	3		635	626	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576114	29576114	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	33	533	0	ENST00000356175.3:c.4087A>C	p.Ser1363Arg	p.S1363R	ENST00000356175	NM_000267.3	1363	Agt/Cgt	30/57	0.293122900288346	3	FACETS	0.517	0.42	0.626	0.258	0.21	0.313	SUBCLONAL	1	TRUE	1	0.263214302802009	3		533	549	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684061	29684061	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	94	659	0	ENST00000356175.3:c.7759G>A	p.Glu2587Lys	p.E2587K	ENST00000356175	NM_000267.3	2587	Gaa/Aaa	52/57	0.293122900288346	3	FACETS	1	0.975	1	0.668	0.595	0.745	CLONAL	1	TRUE	1	0.263214302802009	3		659	605	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682206	37682206	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	91	661	0	ENST00000447079.4:c.3397C>T	p.Gln1133Ter	p.Q1133*	ENST00000447079	NM_015083.1	1133	Caa/Taa	13/14	0.263214302802009	5	FACETS	1	0.968	1			1	CLONAL	1	TRUE	NA	0.263214302802009	5		661	765	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215674142	215674142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766788652	NA	P-0019417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	85	565	0	ENST00000260947.4:c.152C>T	p.Ser51Leu	p.S51L	ENST00000260947	NM_000465.2	51	tCg/tTg	1/11	0.293122900288346	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.263214302802009	1		565	457	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662930	227662930	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	138	804	0	ENST00000305123.5:c.525G>T	p.Gln175His	p.Q175H	ENST00000305123	NM_005544.2	175	caG/caT	1/2	NA	2	FACETS	0.786	0.717	0.858			1	INDETERMINATE	2	TRUE	NA	0.263214302802009	2		804	667	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42870081	42870081	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	42	817	0	ENST00000398585.3:c.91G>C	p.Asp31His	p.D31H	ENST00000398585	NM_001135099.1	31	Gat/Cat	2/14	0.293122900288346	2	FACETS	0.52	0.433	0.616	0.26	0.216	0.308	SUBCLONAL	1	TRUE	0	0.263214302802009	2		817	614	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815326	32815326	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1430994238	NA	P-0019417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	161	967	0	ENST00000354258.4:c.2047A>G	p.Ser683Gly	p.S683G	ENST00000354258	NM_000593.5	683	Agt/Ggt	9/11	0.263214302802009	5	FACETS	0.808	0.74	0.879	0.539	0.493	0.586	CLONAL	2	TRUE	2	0.263214302802009	5		967	1056	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439629	140439629	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	70	601	1	ENST00000288602.6:c.2110A>G	p.Arg704Gly	p.R704G	ENST00000288602	NM_004333.4	704	Aga/Gga	17/18	0.293122900288346	3	FACETS	1	0.962	1	0.635	0.555	0.721	CLONAL	1	TRUE	1	0.263214302802009	3		602	474	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151168508	151168508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	90	615	0	ENST00000262187.5:c.352G>A	p.Gly118Arg	p.G118R	ENST00000262187	NM_005614.3	118	Ggg/Agg	6/8	0.293122900288346	3	FACETS	1	0.965	1	0.609	0.541	0.682	CLONAL	1	TRUE	1	0.263214302802009	3		615	635	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759583	133759583	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	123	876	1	ENST00000318560.5:c.1906G>T	p.Glu636Ter	p.E636*	ENST00000318560	NM_005157.4	636	Gaa/Taa	11/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.263214302802009	2		877	664	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403482	139403482	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	71	1059	0	ENST00000277541.6:c.3011C>G	p.Ser1004Trp	p.S1004W	ENST00000277541	NM_017617.3	1004	tCg/tGg	19/34	1	2	FACETS	0.709	0.618	0.807	0.709	0.618	0.807	SUBCLONAL	1	TRUE	1	0.263214302802009	2		1059	761	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44919370	44919371	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0019417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	42	257	3	ENST00000377967.4:c.1298_1299delinsTT	p.Ser433Phe	p.S433F	ENST00000377967	NM_021140.2	433	tCC/tTT	13/29	0.263214302802009	2	FACETS	1	0.915	1			1	CLONAL	1	TRUE	NA	0.263214302802009	2		260	279	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838320	156838320	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1210	91	1150	0	ENST00000524377.1:c.598G>T	p.Val200Leu	p.V200L	ENST00000524377	NM_002529.3	200	Gtg/Ttg	6/17	1	2	FACETS	0.164	0.145	0.185	0.164	0.145	0.185	SUBCLONAL	1	TRUE	1	0.851232197369195	2		1150	1301	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631881	90631881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	71	1096	0	ENST00000330062.3:c.472C>T	p.Pro158Ser	p.P158S	ENST00000330062	NM_002168.2	158	Cca/Tca	4/11	1	2	FACETS	0.147	0.127	0.168	0.147	0.127	0.168	SUBCLONAL	1	TRUE	1	0.851232197369195	2		1096	1137	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576103	29576104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	46	834	0	ENST00000356175.3:c.4077dup	p.Gln1360SerfsTer14	p.Q1360Sfs*14	ENST00000356175	NM_000267.3	1359	cct/ccTt	30/57	1	2	FACETS	0.129	0.108	0.153	0.129	0.108	0.153	SUBCLONAL	1	TRUE	1	0.851232197369195	2		834	836	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654566	29654566	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	48	458	0	ENST00000356175.3:c.5255del	p.Leu1752GlnfsTer7	p.L1752Qfs*7	ENST00000356175	NM_000267.3	1752	cTa/ca	37/57	1	2	FACETS	0.199	0.167	0.233	0.199	0.167	0.233	SUBCLONAL	1	TRUE	1	0.851232197369195	2		458	568	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945786	17945786	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	73	992	0	ENST00000458235.1:c.2074G>T	p.Ala692Ser	p.A692S	ENST00000458235	NM_000215.3	692	Gcc/Tcc	16/24	1	2	FACETS	0.152	0.132	0.174	0.152	0.132	0.174	SUBCLONAL	1	TRUE	1	0.851232197369195	2		992	1126	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325629	87325629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	48	689	1	ENST00000277120.3:c.506C>T	p.Pro169Leu	p.P169L	ENST00000277120		169	cCa/cTa	6/19	1	2	FACETS	0.148	0.124	0.174	0.148	0.124	0.174	SUBCLONAL	1	TRUE	1	0.851232197369195	2		690	762	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044469	47044469	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	76	1046	1	ENST00000377604.3:c.1966G>T	p.Glu656Ter	p.E656*	ENST00000377604	NM_001204468.1	656	Gaa/Taa	18/24	1	2	FACETS	0.145	0.126	0.165	0.145	0.126	0.165	SUBCLONAL	1	TRUE	1	0.851232197369195	2		1047	1235	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528097	29528097	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	86	492	0	ENST00000356175.3:c.1105C>T	p.Gln369Ter	p.Q369*	ENST00000356175	NM_000267.3	369	Cag/Tag	10/57	0.406229352569995	4	FACETS	1	0.919	1			1	CLONAL	1	TRUE	NA	0.405479423077455	4		492	570	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30326004	30326005	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs769517721	NA	P-0019419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	91	537	0	ENST00000322652.5:c.2208dup	p.Gln737ThrfsTer20	p.Q737Tfs*20	ENST00000322652	NM_015355.2	734	-/A	16/16	0.406229352569995	4	FACETS	0.89	0.79	0.996			1	CLONAL	1	TRUE	NA	0.405479423077455	4		537	709	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627487	37627487	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	126	800	0	ENST00000447079.4:c.1402C>G	p.Leu468Val	p.L468V	ENST00000447079	NM_015083.1	468	Cta/Gta	2/14	0.406229352569995	3	FACETS	0.859	0.778	0.945	0.43	0.389	0.473	CLONAL	1	TRUE	1	0.405479423077455	3		800	870	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921197	50921197	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	114	793	0	ENST00000440232.2:c.3317C>A	p.Ala1106Asp	p.A1106D	ENST00000440232	NM_002691.3	1106	gCc/gAc	27/27	0.300928811327386	4	FACETS	0.884	0.795	0.978	0.442	0.397	0.489	CLONAL	1	TRUE	2	0.405479423077455	4		793	894	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778050	27778050	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369791329	NA	P-0019419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	51	367	0	ENST00000369163.2:c.199C>T	p.Pro67Ser	p.P67S	ENST00000369163	NM_003536.2	67	Cct/Tct	1/1	0.375930832564874	4	FACETS	0.834	0.71	0.969	0.417	0.355	0.485	CLONAL	1	TRUE	2	0.405479423077455	4		367	424	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268993	55268993	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1273	251	851	0	ENST00000275493.2:c.3059A>G	p.Gln1020Arg	p.Q1020R	ENST00000275493	NM_005228.3	1020	cAg/cGg	25/28	0.405479423077455	9	FACETS	0.983	0.917	1			1	CLONAL	2	TRUE	NA	0.405479423077455	9		851	1524	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117874171	117874171	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	203	526	0	ENST00000297338.2:c.283G>C	p.Asp95His	p.D95H	ENST00000297338	NM_006265.2	95	Gac/Cac	4/14	0.406229352569995	4	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	2	0.405479423077455	4		526	701	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964356	70964357	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0019420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	211	450	0	ENST00000276594.2:c.1671_1672del	p.Asp557GlufsTer12	p.D557Efs*12	ENST00000276594	NM_024504.3	557	gaTCaa/gaaa	8/8	0.786088253006461	3	FACETS	0.975	0.908	1	0.488	0.454	0.522	CLONAL	1	TRUE	1	0.786088253006461	3		450	767	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460516	8460516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748838568	NA	P-0019420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	354	789	0	ENST00000356435.5:c.3770C>T	p.Pro1257Leu	p.P1257L	ENST00000356435		1257	cCg/cTg	22/35	1	2	FACETS	0.934	0.888	0.982	0.934	0.888	0.982	CLONAL	1	TRUE	1	0.786088253006461	2		789	964	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0019421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	64	766	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	1	2	FACETS	0.999	0.863	1	0.999	0.863	1	CLONAL	1	TRUE	1	0.17	2		766	754	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	28	791	0	ENST00000397062.3:c.246A>T	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaT	2/5	1	2	FACETS	0.409	0.325	0.506	0.409	0.325	0.506	SUBCLONAL	1	TRUE	1	0.17	2		791	805	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50810152	50810152	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	43	686	0	ENST00000398568.2:c.976A>G	p.Lys326Glu	p.K326E	ENST00000398568	NM_001042412.1	326	Aaa/Gaa	6/18	1	2	FACETS	0.758	0.633	0.898	0.758	0.633	0.898	SUBCLONAL	1	TRUE	1	0.17	2		686	667	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591084	67591086	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0019421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	41	517	0	ENST00000274335.5:c.1677_1679del	p.Asp560del	p.D560del	ENST00000274335		559	atTGAc/atc	12/15	1	2	FACETS	0.879	0.731	1	0.879	0.731	1	CLONAL	1	TRUE	1	0.17	2		517	549	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	142	736	0				ENST00000310581	NM_198253.2	-/1132			0.359863283244553	1	FACETS	0.636	0.582	0.691	0.636	0.582	0.691	SUBCLONAL	1	TRUE	0	0.582868428781855	1		736	543	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9770652	9770652	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	71	445	0	ENST00000377346.4:c.139C>T	p.Gln47Ter	p.Q47*	ENST00000377346	NM_005026.3	47	Cag/Tag	3/24	0.379084222856324	1	FACETS	0.358	0.313	0.406	0.358	0.313	0.406	SUBCLONAL	1	TRUE	0	0.582868428781855	1		445	482	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28979948	28979948	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1393872506	NA	P-0019422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	117	685	0	ENST00000282397.4:c.1520A>T	p.Gln507Leu	p.Q507L	ENST00000282397	NM_002019.4	507	cAg/cTg	11/30	0.582868428781855	1	FACETS	0.471	0.426	0.519	0.471	0.426	0.519	SUBCLONAL	1	TRUE	0	0.582868428781855	1		685	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0019422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	191	938	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.329717821237615	0	FACETS	0.509	0.474	0.545			1	INDETERMINATE	1	TRUE	0	0.582868428781855	0		938	537	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118859	70118859	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0019422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	149	509	0	ENST00000245479.2:c.432-1G>A		p.X144_splice	ENST00000245479	NM_000346.3	144			0.164523575636631	2	FACETS	1	0.93	1	0.506	0.465	0.548	INDETERMINATE	1	TRUE	0	0.582868428781855	2		509	505	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375011	45375011	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	76	498	1	ENST00000262160.6:c.832G>T	p.Ala278Ser	p.A278S	ENST00000262160	NM_005901.5	278	Gca/Tca	8/11	0.164523575636631	2	FACETS	0.434	0.381	0.491	0.217	0.19	0.246	INDETERMINATE	1	TRUE	0	0.582868428781855	2		499	601	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226305	2226305	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	107	982	0	ENST00000398665.3:c.3785A>T	p.Gln1262Leu	p.Q1262L	ENST00000398665	NM_032482.2	1262	cAg/cTg	27/28	0.3678820583102	0	FACETS	0.233	0.209	0.258			1	SUBCLONAL	1	TRUE	0	0.582868428781855	0		982	658	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47613726	47613726	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	75	520	0	ENST00000263735.4:c.919G>A	p.Glu307Lys	p.E307K	ENST00000263735	NM_002354.2	307	Gag/Aag	9/9	0.164523575636631	2	FACETS	0.359	0.314	0.407	0.179	0.157	0.204	INDETERMINATE	1	TRUE	0	0.582868428781855	2		520	717	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268334	198268334	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	98	540	0	ENST00000335508.6:c.1694A>G	p.Asp565Gly	p.D565G	ENST00000335508	NM_012433.2	565	gAc/gGc	12/25	0.156600590870291	3	FACETS	0.536	0.478	0.598	0.179	0.159	0.2	INDETERMINATE	1	TRUE	0	0.582868428781855	3		540	810	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1918645	1918645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	97	651	2	ENST00000382891.5:c.808G>T	p.Ala270Ser	p.A270S	ENST00000382891	NM_133335.3	270	Gcc/Tcc	4/22	0.459868123624	1	FACETS	0.341	0.304	0.381	0.341	0.304	0.381	SUBCLONAL	1	TRUE	0	0.582868428781855	1		653	691	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958846	55958846	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	94	579	0	ENST00000263923.4:c.3007G>A	p.Glu1003Lys	p.E1003K	ENST00000263923	NM_002253.2	1003	Gag/Aag	22/30	0.459868123624	1	FACETS	0.404	0.36	0.45	0.404	0.36	0.45	SUBCLONAL	1	TRUE	0	0.582868428781855	1		579	566	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397690	116397690	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0019422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	91	475	0	ENST00000397752.3:c.1966-2A>C		p.X656_splice	ENST00000397752	NM_000245.2	656			0.164523575636631	2	FACETS	0.483	0.429	0.541	0.242	0.214	0.271	INDETERMINATE	1	TRUE	0	0.582868428781855	2		475	646	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873482	151873482	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	73	486	0	ENST00000262189.6:c.9056A>G	p.Gln3019Arg	p.Q3019R	ENST00000262189	NM_170606.2	3019	cAg/cGg	38/59	0.139552752824048	3	FACETS	0.437	0.382	0.497			1	INDETERMINATE	1	TRUE	NA	0.582868428781855	3		486	740	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038815	47038815	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	116	772	1	ENST00000377604.3:c.822G>T	p.Gln274His	p.Q274H	ENST00000377604	NM_001204468.1	274	caG/caT	9/24	0.329717821237615	0	FACETS	0.287	0.259	0.316			1	INDETERMINATE	1	TRUE	0	0.582868428781855	0		773	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587781525	NA	P-0019424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	444	976	0	ENST00000269305.4:c.842A>T	p.Asp281Val	p.D281V	ENST00000269305	NM_001126112.2	281	gAc/gTc	8/11	0.772060820218983	1	FACETS	0.937	0.902	0.97	0.937	0.902	0.97	CLONAL	1	TRUE	0	0.772060820218983	1		976	754	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491471	18491471	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs754123698	NA	P-0019424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	40	617	0	ENST00000266497.5:c.1384A>G	p.Arg462Gly	p.R462G	ENST00000266497		462	Aga/Gga	8/31	0.403481534638584	1	FACETS	0.094	0.078	0.113	0.094	0.078	0.113	INDETERMINATE	1	TRUE	0	0.772060820218983	1		617	675	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43769902	43769902	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	198	664	0	ENST00000382044.4:c.844G>T	p.Glu282Ter	p.E282*	ENST00000382044	NM_001141980.1	282	Gaa/Taa	8/28	0.403481534638584	1	FACETS	0.393	0.365	0.423	0.393	0.365	0.423	INDETERMINATE	1	TRUE	0	0.772060820218983	1		664	801	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81954842	81954842	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	348	845	0	ENST00000359376.3:c.2275T>A	p.Tyr759Asn	p.Y759N	ENST00000359376	NM_002661.3	759	Tat/Aat	21/33	0.772060820218983	1	FACETS	0.94	0.901	0.978	0.94	0.901	0.978	CLONAL	1	TRUE	0	0.772060820218983	1		845	589	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983258	7983258	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	233	587	0	ENST00000319144.4:c.756G>C	p.Glu252Asp	p.E252D	ENST00000319144	NM_001139.2	252	gaG/gaC	7/15	0.772060820218983	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.772060820218983	1		587	354	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348496	56348496	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	71	415	0	ENST00000348428.3:c.304A>G	p.Thr102Ala	p.T102A	ENST00000348428	NM_006785.3	102	Aca/Gca	2/17	0.172128387140843	2	FACETS	0.286	0.25	0.326	0.143	0.125	0.163	INDETERMINATE	1	TRUE	0	0.772060820218983	2		415	642	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240756	55240756	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	234	1077	0	ENST00000275493.2:c.2000T>G	p.Phe667Cys	p.F667C	ENST00000275493	NM_005228.3	667	tTc/tGc	17/28	1	2	FACETS	0.454	0.422	0.487	0.454	0.422	0.487	SUBCLONAL	1	TRUE	1	0.772060820218983	2		1077	1335	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240779	55240779	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	252	1072	1	ENST00000275493.2:c.2023C>T	p.Arg675Trp	p.R675W	ENST00000275493	NM_005228.3	675	Cgg/Tgg	17/28	1	2	FACETS	0.493	0.46	0.527	0.493	0.46	0.527	SUBCLONAL	1	TRUE	1	0.772060820218983	2		1073	1325	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	216	600	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.941	0.876	1	0.941	0.876	1	CLONAL	1	TRUE	1	0.515323535400511	2		600	891	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100338	27100339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCAGCCCCTTCC	novel	NA	P-0019425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	245	759	0	ENST00000324856.7:c.4051_4063dup	p.Pro1355ArgfsTer94	p.P1355Rfs*94	ENST00000324856	NM_006015.4	1350	-/GGCAGCCCCTTCC	17/20	1	2	FACETS	0.737	0.687	0.788	0.737	0.687	0.788	SUBCLONAL	1	TRUE	1	0.515323535400511	2		759	1291	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354339	354339	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1283	309	891	0	ENST00000262320.3:c.1219G>A	p.Glu407Lys	p.E407K	ENST00000262320	NM_003502.3	407	Gag/Aag	5/11	0.507149692242068	3	FACETS	0.947	0.891	1	0.474	0.445	0.503	CLONAL	1	TRUE	1	0.515323535400511	3		891	1592	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259095	89259095	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	160	352	0	ENST00000336596.2:c.239A>G	p.Asn80Ser	p.N80S	ENST00000336596	NM_005233.5	80	aAt/aGt	3/17	1	2	FACETS	0.905	0.832	0.981	0.905	0.832	0.981	CLONAL	1	TRUE	1	0.515323535400511	2		352	686	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919285	178919285	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	102	337	0	ENST00000263967.3:c.770G>A	p.Cys257Tyr	p.C257Y	ENST00000263967	NM_006218.2	257	tGt/tAt	4/21	1	2	FACETS	0.818	0.735	0.905	0.818	0.735	0.905	CLONAL	1	TRUE	1	0.515323535400511	2		337	484	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845366	151845366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	103	640	1	ENST00000262189.6:c.13646G>A	p.Arg4549His	p.R4549H	ENST00000262189	NM_170606.2	4549	cGc/cAc	52/59	1	2	FACETS	0.344	0.306	0.384	0.344	0.306	0.384	SUBCLONAL	1	TRUE	1	0.515323535400511	2		641	1163	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0019426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	119	416	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.209409346000808	4	FACETS	1	0.984	1	0.736	0.665	0.81	CLONAL	1	FALSE	2	0.329989053352519	4		416	652	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0019426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	382	726	2	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.304308091475716	3	FACETS	0.895	0.853	0.939	0.895	0.853	0.939	CLONAL	3	FALSE	0	0.329989053352519	3		728	1004	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633229	12633229	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs368807126	NA	P-0019426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	113	720	0	ENST00000251849.4:c.1171A>T	p.Arg391Trp	p.R391W	ENST00000251849	NM_002880.3	391	Agg/Tgg	11/17	0.315908107883454	3	FACETS	0.859	0.772	0.951	0.429	0.386	0.476	CLONAL	1	FALSE	1	0.329989053352519	3		720	929	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28595728	28595728	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769967309	NA	P-0019426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1325	71	990	1	ENST00000253063.3:c.125G>A	p.Arg42Gln	p.R42Q	ENST00000253063	NM_031459.4	42	cGa/cAa	2/10	0.187042111186353	5	FACETS	0.461	0.4	0.527	0.154	0.133	0.176	INDETERMINATE	1	FALSE	2	0.329989053352519	5		991	1396	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073980	8073980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	40	476	0	ENST00000377482.5:c.679G>A	p.Asp227Asn	p.D227N	ENST00000377482	NM_018948.3	227	Gac/Aac	4/4	0.187042111186353	5	FACETS	0.516	0.427	0.615	0.172	0.142	0.205	INDETERMINATE	1	FALSE	2	0.329989053352519	5		476	703	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17359555	17359555	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	218	690	0	ENST00000375499.3:c.286G>T	p.Gly96Cys	p.G96C	ENST00000375499	NM_003000.2	96	Ggc/Tgc	3/8	0.187042111186353	5	FACETS	1	0.982	1	0.766	0.714	0.821	INDETERMINATE	2	FALSE	2	0.329989053352519	5		690	859	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741665	17741665	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	59	746	1	ENST00000250003.3:c.336G>T	p.Lys112Asn	p.K112N	ENST00000250003	NM_002478.4	112	aaG/aaT	1/3	0.159617944538857	3	FACETS	0.538	0.461	0.621	0.179	0.153	0.207	INDETERMINATE	1	FALSE	0	0.329989053352519	3		747	775	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943938	71943938	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	521	985	2	ENST00000298229.2:c.1871G>T	p.Ser624Ile	p.S624I	ENST00000298229	NM_001567.3	624	aGc/aTc	16/28	0.329989053352519	5	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	FALSE	2	0.329989053352519	5		987	1555	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230669	46230669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	69	553	0	ENST00000334344.6:c.918G>T	p.Leu306Phe	p.L306F	ENST00000334344	NM_152641.2	306	ttG/ttT	8/21	0.315908107883454	3	FACETS	0.808	0.704	0.92	0.404	0.352	0.46	CLONAL	1	FALSE	1	0.329989053352519	3		553	603	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246012	46246012	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	97	514	1	ENST00000334344.6:c.4106G>T	p.Gly1369Val	p.G1369V	ENST00000334344	NM_152641.2	1369	gGt/gTt	15/21	0.315908107883454	3	FACETS	0.766	0.687	0.85	0.766	0.687	0.85	SUBCLONAL	2	FALSE	1	0.329989053352519	3		515	447	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112893865	112893865	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	50	768	0	ENST00000351677.2:c.754G>A	p.Glu252Lys	p.E252K	ENST00000351677	NM_002834.3	252	Gag/Aag	6/16	0.315908107883454	3	FACETS	0.433	0.366	0.506	0.216	0.183	0.253	SUBCLONAL	1	FALSE	1	0.329989053352519	3		768	816	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549410	21549410	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	196	494	0	ENST00000382592.4:c.2866G>T	p.Asp956Tyr	p.D956Y	ENST00000382592	NM_014572.2	956	Gac/Tac	8/8	0.272692039616818	4	FACETS	1	0.971	1			1	CLONAL	2	FALSE	NA	0.329989053352519	4		494	727	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483882	88483882	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	101	925	1	ENST00000360948.2:c.1688C>A	p.Thr563Asn	p.T563N	ENST00000360948	NM_001012338.2	563	aCc/aAc	14/19	1	2	FACETS	0.713	0.636	0.794	0.713	0.636	0.794	SUBCLONAL	1	FALSE	1	0.329989053352519	2		926	859	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641320	23641320	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	114	901	0	ENST00000261584.4:c.2155C>T	p.Pro719Ser	p.P719S	ENST00000261584	NM_024675.3	719	Cct/Tct	5/13	0.329989053352519	3	FACETS	0.715	0.642	0.792	0.357	0.321	0.396	SUBCLONAL	1	FALSE	1	0.329989053352519	3		901	1126	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671683	67671683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	87	806	0	ENST00000264010.4:c.2092G>A	p.Glu698Lys	p.E698K	ENST00000264010	NM_006565.3	698	Gag/Aag	12/12	0.329989053352519	3	FACETS	0.607	0.536	0.683	0.304	0.268	0.342	SUBCLONAL	1	FALSE	1	0.329989053352519	3		806	1012	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17117121	17117121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	69	755	1	ENST00000285071.4:c.1588G>A	p.Glu530Lys	p.E530K	ENST00000285071	NM_144997.5	530	Gag/Aag	14/14	0.187042111186353	5	FACETS	0.677	0.588	0.773	0.226	0.196	0.258	INDETERMINATE	1	FALSE	2	0.329989053352519	5		756	924	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687037	37687037	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	79	746	2	ENST00000447079.4:c.3941G>T	p.Gly1314Val	p.G1314V	ENST00000447079	NM_015083.1	1314	gGc/gTc	14/14	0.187042111186353	5	FACETS	0.673	0.59	0.762	0.224	0.196	0.254	INDETERMINATE	1	FALSE	2	0.329989053352519	5		748	1064	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609292	39609292	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	45	419	0	ENST00000262039.4:c.1594G>C	p.Asp532His	p.D532H	ENST00000262039	NM_002647.2	532	Gat/Cat	15/25	0.196470033279442	3	FACETS	0.663	0.558	0.78	0.332	0.279	0.39	INDETERMINATE	1	FALSE	1	0.329989053352519	3		419	479	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379676	17379676	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	193	707	1	ENST00000359435.4:c.61G>A	p.Ala21Thr	p.A21T	ENST00000359435	NM_001033549.1	21	Gca/Aca	2/9	0.279307237916635	3	FACETS	0.78	0.723	0.84	0.78	0.723	0.84	SUBCLONAL	2	FALSE	1	0.329989053352519	3		708	873	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856065	45856065	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	150	879	0	ENST00000391945.4:c.1841A>C	p.Tyr614Ser	p.Y614S	ENST00000391945	NM_000400.3	614	tAc/tCc	20/23	0.315908107883454	3	FACETS	0.899	0.82	0.982	0.45	0.41	0.491	CLONAL	1	FALSE	1	0.329989053352519	3		879	1178	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578280	212578280	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	114	819	0	ENST00000342788.4:c.977G>T	p.Cys326Phe	p.C326F	ENST00000342788	NM_005235.2	326	tGc/tTc	8/28	0.187042111186353	5	FACETS	0.914	0.826	1	0.609	0.55	0.671	INDETERMINATE	2	FALSE	2	0.329989053352519	5		819	565	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31372576	31372576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868507905	NA	P-0019426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	71	741	0	ENST00000328111.2:c.217G>A	p.Asp73Asn	p.D73N	ENST00000328111	NM_006892.3	73	Gat/Aat	4/23	0.329989053352519	3	FACETS	0.534	0.465	0.609	0.267	0.232	0.305	SUBCLONAL	1	FALSE	1	0.329989053352519	3		741	939	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42861469	42861469	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1305373683	NA	P-0019426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	75	729	2	ENST00000398585.3:c.401G>A	p.Gly134Glu	p.G134E	ENST00000398585	NM_001135099.1	134	gGa/gAa	4/14	0.209409346000808	4	FACETS	0.542	0.473	0.616	0.271	0.236	0.308	SUBCLONAL	1	FALSE	2	0.329989053352519	4		731	1116	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748119	41748119	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	65	222	0	ENST00000226382.2:c.650G>T	p.Gly217Val	p.G217V	ENST00000226382	NM_003924.3	217	gGg/gTg	3/3	1	2	FACETS	0.895	0.788	1	1	0.98	1	CLONAL	2	FALSE	1	0.329989053352519	2		222	220	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599347	55599347	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	106	598	0	ENST00000288135.5:c.2473G>T	p.Val825Phe	p.V825F	ENST00000288135	NM_000222.2	825	Gtt/Ttt	17/21	0.329989053352519	3	FACETS	0.828	0.747	0.913	0.828	0.747	0.913	CLONAL	2	FALSE	1	0.329989053352519	3		598	452	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961058	55961058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199904772	NA	P-0019426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	142	1033	3	ENST00000263923.4:c.2882G>A	p.Arg961Gln	p.R961Q	ENST00000263923	NM_002253.2	961	cGg/cAg	21/30	0.329989053352519	3	FACETS	0.767	0.697	0.841	0.384	0.348	0.421	SUBCLONAL	1	FALSE	1	0.329989053352519	3		1036	1307	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576465	67576465	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	146	637	1	ENST00000274335.5:c.744C>A	p.Phe248Leu	p.F248L	ENST00000274335		248	ttC/ttA	5/15	0.329989053352519	2	FACETS	0.869	0.798	0.942	0.869	0.798	0.942	CLONAL	2	FALSE	0	0.329989053352519	2		638	509	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048237	180048237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754733831	NA	P-0019426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	403	1217	3	ENST00000261937.6:c.2036G>A	p.Arg679Gln	p.R679Q	ENST00000261937	NM_182925.4	679	cGg/cAg	14/30	0.329989053352519	2	FACETS	0.962	0.915	1	0.962	0.915	1	CLONAL	2	FALSE	0	0.329989053352519	2		1220	1270	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43742102	43742102	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	143	985	0	ENST00000523873.1:c.91G>C	p.Glu31Gln	p.E31Q	ENST00000523873		31	Gaa/Caa	2/8	0.187042111186353	5	FACETS	0.99	0.9	1	0.33	0.3	0.362	INDETERMINATE	1	FALSE	2	0.329989053352519	5		985	1309	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729399	41729399	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	189	747	0	ENST00000242208.4:c.1130G>C	p.Arg377Pro	p.R377P	ENST00000242208	NM_002192.2	377	cGc/cCc	3/3	0.187042111186353	5	FACETS	0.819	0.757	0.885	0.546	0.504	0.59	INDETERMINATE	2	FALSE	2	0.329989053352519	5		747	1045	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358967	81358967	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	122	699	0	ENST00000222390.5:c.994C>A	p.Gln332Lys	p.Q332K	ENST00000222390	NM_000601.4	332	Cag/Aag	8/18	0.187042111186353	5	FACETS	1	0.984	1	0.488	0.441	0.537	INDETERMINATE	1	FALSE	2	0.329989053352519	5		699	755	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863249	56863249	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	71	842	0	ENST00000519728.1:c.393C>G	p.Phe131Leu	p.F131L	ENST00000519728	NM_002350.3	131	ttC/ttG	6/13	0.290551569348009	4	FACETS	0.594	0.517	0.677	0.198	0.172	0.226	SUBCLONAL	1	FALSE	1	0.329989053352519	4		842	964	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	85	741	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	FALSE	1	0.449276642168679	2		742	376	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	132	640	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	FALSE	1	0.449276642168679	2		640	580	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	121	934	2	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.691	0.624	0.761	0.691	0.624	0.761	SUBCLONAL	1	FALSE	1	0.449276642168679	2		936	780	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	186	870	0	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.449276642168679	2		870	632	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	92	716	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.873	0.779	0.972	0.873	0.779	0.972	CLONAL	1	FALSE	1	0.449276642168679	2		717	469	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103755	47103756	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	44	586	4	ENST00000409792.3:c.6190_6191del	p.Asp2064ProfsTer8	p.D2064Pfs*8	ENST00000409792	NM_014159.6	2064	GAc/c	14/21	1	2	FACETS	0.333	0.278	0.393	0.333	0.278	0.393	SUBCLONAL	1	FALSE	1	0.449276642168679	2		590	589	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	35	418	0	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	1	2	FACETS	0.337	0.276	0.406	0.337	0.276	0.406	SUBCLONAL	1	FALSE	1	0.449276642168679	2		418	462	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795103	242795104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs768249210	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	42	1014	2	ENST00000334409.5:c.105dup	p.Thr36HisfsTer70	p.T36Hfs*70	ENST00000334409	NM_005018.2	35	-/C	2/5	1	2	FACETS	0.238	0.198	0.283	0.238	0.198	0.283	SUBCLONAL	1	FALSE	1	0.449276642168679	2		1016	785	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553478	29553478	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781807	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	186	922	7	ENST00000356175.3:c.2033del	p.Pro678ArgfsTer10	p.P678Rfs*10	ENST00000356175	NM_000267.3	676	aCc/ac	18/57	1	2	FACETS	0.963	0.89	1	0.963	0.89	1	CLONAL	1	FALSE	1	0.449276642168679	2		929	860	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919545	78919545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776174012	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	38	533	0	ENST00000306801.3:c.3104C>T	p.Thr1035Met	p.T1035M	ENST00000306801	NM_020761.2	1035	aCg/aTg	26/34	1	2	FACETS	0.31	0.255	0.371	0.31	0.255	0.371	SUBCLONAL	1	FALSE	1	0.449276642168679	2		533	546	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	167	736	6	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.449276642168679	2		742	678	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	194	720	14	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.449276642168679	2		734	649	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	159	809	8	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	1	2	FACETS	0.898	0.824	0.975	0.898	0.824	0.975	CLONAL	1	FALSE	1	0.449276642168679	2		817	788	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	45	729	0	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	0.361580400682002	1	FACETS	0.291	0.244	0.343	0.291	0.244	0.343	SUBCLONAL	1	FALSE	0	0.449276642168679	1		729	533	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736165	204736166	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	104	543	0	ENST00000302823.3:c.529dup	p.Tyr177LeufsTer2	p.Y177Lfs*2	ENST00000302823	NM_005214.4	174	-/T	3/4	1	2	FACETS	0.775	0.696	0.86	0.775	0.696	0.86	SUBCLONAL	1	FALSE	1	0.449276642168679	2		543	597	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169934	32169934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759022399	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	329	862	0	ENST00000375023.3:c.3674G>A	p.Arg1225Gln	p.R1225Q	ENST00000375023	NM_004557.3	1225	cGg/cAg	21/30	0.449276642168679	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	FALSE	0	0.449276642168679	2		862	695	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106917	27106917	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	63	501	0	ENST00000324856.7:c.6532del	p.Asp2178ThrfsTer22	p.D2178Tfs*22	ENST00000324856	NM_006015.4	2176	caG/ca	20/20	1	2	FACETS	0.558	0.483	0.638	0.558	0.483	0.638	SUBCLONAL	1	FALSE	1	0.449276642168679	2		501	503	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911172	29911172	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	197	446	0	ENST00000376809.5:c.471G>A	p.Trp157Ter	p.W157*	ENST00000376809	NM_002116.7	157	tgG/tgA	3/8	1	2	FACETS	1	0.945	1	1	0.994	1	CLONAL	2	FALSE	1	0.449276642168679	2		446	435	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225657	26225657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202067024	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	261	508	0	ENST00000360408.1:c.275C>T	p.Ala92Val	p.A92V	ENST00000360408	NM_003532.2	92	gCg/gTg	1/1	0.415788448555989	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	FALSE	0	0.449276642168679	2		508	506	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817720	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	59	538	0	ENST00000262367.5:c.3250dup	p.Ile1084AsnfsTer3	p.I1084Nfs*3	ENST00000262367	NM_004380.2	1084	atc/aAtc		1	2	FACETS	0.542	0.466	0.623	0.542	0.466	0.623	SUBCLONAL	1	FALSE	1	0.449276642168679	2		538	485	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275420	38275420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369356672	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	231	984	1	ENST00000425967.3:c.1613G>A	p.Arg538His	p.R538H	ENST00000425967	NM_001174067.1	538	cGt/cAt	12/19	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.449276642168679	2		985	902	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444685	78444685	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	148	496	2	ENST00000370768.2:c.4G>A	p.Ala2Thr	p.A2T	ENST00000370768	NM_003902.3	2	Gca/Aca	1/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.449276642168679	2		498	580	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161326623	161326623	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs386833414	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	147	869	0	ENST00000367975.2:c.398G>A	p.Arg133Gln	p.R133Q	ENST00000367975	NM_003001.3	133	cGa/cAa	5/6	1	2	FACETS	0.843	0.771	0.919	0.843	0.771	0.919	CLONAL	1	FALSE	1	0.449276642168679	2		869	776	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692803	89692803	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	82	488	0	ENST00000371953.3:c.287C>A	p.Pro96Gln	p.P96Q	ENST00000371953	NM_000314.4	96	cCa/cAa	5/9	1	2	FACETS	0.951	0.844	1	0.951	0.844	1	CLONAL	1	FALSE	1	0.449276642168679	2		488	384	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104353757	104353757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1457485957	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	124	637	0	ENST00000369902.3:c.691G>A	p.Gly231Ser	p.G231S	ENST00000369902	NM_016169.3	231	Ggc/Agc	6/12	1	2	FACETS	0.896	0.813	0.983	0.896	0.813	0.983	CLONAL	1	FALSE	1	0.449276642168679	2		637	616	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118365112	118365112	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs781944403	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	108	611	1	ENST00000534358.1:c.5288G>A	p.Arg1763Gln	p.R1763Q	ENST00000534358	NM_005933.3	1763	cGg/cAg	17/36	1	2	FACETS	0.918	0.827	1	0.918	0.827	1	CLONAL	1	FALSE	1	0.449276642168679	2		612	524	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425784	49425784	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	135	555	0	ENST00000301067.7:c.12704A>G	p.Gln4235Arg	p.Q4235R	ENST00000301067	NM_003482.3	4235	cAg/cGg	39/54	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.449276642168679	2		555	553	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446166	49446166	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs398123715	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	88	798	0	ENST00000301067.7:c.1300del	p.Leu434Ter	p.L434*	ENST00000301067	NM_003482.3	434	Cta/ta	10/54	1	2	FACETS	0.515	0.456	0.578	0.515	0.456	0.578	SUBCLONAL	1	FALSE	1	0.449276642168679	2		798	761	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28599048	28599048	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781675235	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	56	713	0	ENST00000241453.7:c.2240C>T	p.Pro747Leu	p.P747L	ENST00000241453	NM_004119.2	747	cCg/cTg	18/24	1	2	FACETS	0.443	0.379	0.512	0.443	0.379	0.512	SUBCLONAL	1	FALSE	1	0.449276642168679	2		713	563	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436792	110436792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	52	1093	2	ENST00000375856.3:c.1609G>A	p.Gly537Ser	p.G537S	ENST00000375856	NM_003749.2	537	Ggt/Agt	1/2	1	2	FACETS	0.274	0.232	0.32	0.274	0.232	0.32	SUBCLONAL	1	FALSE	1	0.449276642168679	2		1095	845	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639156	3639156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762565535	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	48	885	3	ENST00000294008.3:c.4483G>A	p.Ala1495Thr	p.A1495T	ENST00000294008	NM_032444.2	1495	Gcg/Acg	12/15	1	2	FACETS	0.271	0.228	0.319	0.271	0.228	0.319	SUBCLONAL	1	FALSE	1	0.449276642168679	2		888	788	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639540	3639540	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs17136464	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	88	920	2	ENST00000294008.3:c.4099G>A	p.Ala1367Thr	p.A1367T	ENST00000294008	NM_032444.2	1367	Gcc/Acc	12/15	1	2	FACETS	0.502	0.444	0.564	0.502	0.444	0.564	SUBCLONAL	1	FALSE	1	0.449276642168679	2		922	780	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004813	16004813	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	182	737	2	ENST00000268712.3:c.2441del	p.Pro814HisfsTer13	p.P814Hfs*13	ENST00000268712	NM_006311.3	814	cCa/ca	20/46	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.449276642168679	2		739	754	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245848	41245848	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357784	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	84	756	0	ENST00000357654.3:c.1700del	p.Asn567IlefsTer5	p.N567Ifs*5	ENST00000357654	NM_007294.3	567	aAt/at	10/23	1	2	FACETS	0.62	0.548	0.697	0.62	0.548	0.697	SUBCLONAL	1	FALSE	1	0.449276642168679	2		756	603	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982557	10982557	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	27	285	0	ENST00000327064.4:c.179T>C	p.Val60Ala	p.V60A	ENST00000327064	NM_199141.1	60	gTg/gCg	1/16	1	2	FACETS	0.384	0.306	0.473	0.384	0.306	0.473	SUBCLONAL	1	FALSE	1	0.449276642168679	2		285	313	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794440	42794440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776806622	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	124	1085	3	ENST00000575354.2:c.1520G>A	p.Arg507His	p.R507H	ENST00000575354	NM_015125.3	507	cGc/cAc	10/20	1	2	FACETS	0.584	0.527	0.643	0.584	0.527	0.643	SUBCLONAL	1	FALSE	1	0.449276642168679	2		1088	946	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609156	46609156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1462311206	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	159	922	4	ENST00000263734.3:c.2215C>T	p.Arg739Trp	p.R739W	ENST00000263734	NM_001430.4	739	Cgg/Tgg	14/16	1	2	FACETS	0.922	0.846	1	0.922	0.846	1	CLONAL	1	FALSE	1	0.449276642168679	2		926	768	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587222	212587222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	108	647	0	ENST00000342788.4:c.779C>T	p.Thr260Ile	p.T260I	ENST00000342788	NM_005235.2	260	aCt/aTt	7/28	1	2	FACETS	0.894	0.805	0.987	0.894	0.805	0.987	CLONAL	1	FALSE	1	0.449276642168679	2		647	538	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652834	212652834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375361752	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	81	636	0	ENST00000342788.4:c.472G>A	p.Ala158Thr	p.A158T	ENST00000342788	NM_005235.2	158	Gca/Aca	4/28	1	2	FACETS	0.937	0.83	1	0.937	0.83	1	CLONAL	1	FALSE	1	0.449276642168679	2		636	385	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242800938	242800938	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	116	873	2	ENST00000334409.5:c.53G>A	p.Gly18Asp	p.G18D	ENST00000334409	NM_005018.2	18	gGc/gAc	1/5	1	2	FACETS	0.715	0.645	0.789	0.715	0.645	0.789	SUBCLONAL	1	FALSE	1	0.449276642168679	2		875	722	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546066	41546066	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	97	799	0	ENST00000263253.7:c.2681C>T	p.Pro894Leu	p.P894L	ENST00000263253	NM_001429.3	894	cCc/cTc	14/31	1	2	FACETS	0.534	0.476	0.597	0.534	0.476	0.597	SUBCLONAL	1	FALSE	1	0.449276642168679	2		799	808	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38946623	38946623	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1554059320	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	31	568	0	ENST00000357387.3:c.4346del	p.Asn1449ThrfsTer28	p.N1449Tfs*28	ENST00000357387	NM_152756.3	1449	aAc/ac	33/38	1	2	FACETS	0.382	0.309	0.465	0.382	0.309	0.465	SUBCLONAL	1	FALSE	1	0.449276642168679	2		568	361	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80083386	80083386	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs150446804	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	56	703	0	ENST00000265081.6:c.2438A>G	p.Lys813Arg	p.K813R	ENST00000265081	NM_002439.4	813	aAa/aGa	18/24	1	2	FACETS	0.393	0.336	0.455	0.393	0.336	0.455	SUBCLONAL	1	FALSE	1	0.449276642168679	2		703	634	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840020	27840020	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	27	346	0	ENST00000328488.2:c.74C>T	p.Ala25Val	p.A25V	ENST00000328488	NM_003533.2	25	gCg/gTg	1/1	0.415788448555989	2	FACETS	0.374	0.298	0.461	0.187	0.149	0.231	SUBCLONAL	1	FALSE	0	0.449276642168679	2		346	321	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509177	106509177	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	75	642	2	ENST00000359195.3:c.1171C>T	p.Gln391Ter	p.Q391*	ENST00000359195	NM_002649.2	391	Caa/Taa	2/11	1	2	FACETS	0.461	0.404	0.523	0.461	0.404	0.523	SUBCLONAL	1	FALSE	1	0.449276642168679	2		644	724	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845240	128845240	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765318599	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	83	488	0	ENST00000249373.3:c.734C>T	p.Thr245Met	p.T245M	ENST00000249373	NM_005631.4	245	aCg/aTg	3/12	1	2	FACETS	0.869	0.771	0.974	0.869	0.771	0.974	CLONAL	1	FALSE	1	0.449276642168679	2		488	425	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994329	21994329	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs759736526	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	118	546	1	ENST00000579755.1:c.2T>C	p.Met1?	p.M1?	ENST00000579755		1	aTg/aCg	1/3	1		FACETS		0.84	1				CLONAL	1	FALSE	1	0.449276642168679	2		547	566	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760288	133760288	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756787093	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	99	566	0	ENST00000318560.5:c.2611G>A	p.Glu871Lys	p.E871K	ENST00000318560	NM_005157.4	871	Gag/Aag	11/11	1	2	FACETS	0.825	0.739	0.916	0.825	0.739	0.916	CLONAL	1	FALSE	1	0.449276642168679	2		566	534	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225198	53225198	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556836492	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	72	884	1	ENST00000375401.3:c.3020G>A	p.Arg1007His	p.R1007H	ENST00000375401	NM_004187.3	1007	cGt/cAt	20/26	0.361580400682002	1	FACETS	0.395	0.345	0.449	0.395	0.345	0.449	SUBCLONAL	1	FALSE	0	0.449276642168679	1		885	629	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53244010	53244010	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs945455521	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	169	784	1	ENST00000375401.3:c.983G>A	p.Arg328Gln	p.R328Q	ENST00000375401	NM_004187.3	328	cGg/cAg	8/26	0.361580400682002	1	FACETS	0.944	0.872	1	0.944	0.872	1	CLONAL	1	FALSE	0	0.449276642168679	1		785	618	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937992	76937992	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	50	613	0	ENST00000373344.5:c.2756A>C	p.Asp919Ala	p.D919A	ENST00000373344	NM_000489.3	919	gAt/gCt	9/35	0.361580400682002	1	FACETS	0.327	0.278	0.382	0.327	0.278	0.382	SUBCLONAL	1	FALSE	0	0.449276642168679	1		613	527	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938233	76938233	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	150	754	0	ENST00000373344.5:c.2515A>G	p.Lys839Glu	p.K839E	ENST00000373344	NM_000489.3	839	Aaa/Gaa	9/35	0.361580400682002	1	FACETS	0.891	0.818	0.967	0.891	0.818	0.967	CLONAL	1	FALSE	0	0.449276642168679	1		754	581	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0019429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	70	632	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.220223741654082	2		632	487	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945219	32945219	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	47	673	0	ENST00000380152.3:c.8614G>T	p.Glu2872Ter	p.E2872*	ENST00000380152		2872	Gaa/Taa	20/27	0.220223741654082	1	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	0	0.220223741654082	1		673	362	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914039	32914040	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	59	639	0	ENST00000380152.3:c.5551dup	p.Ile1851AsnfsTer7	p.I1851Nfs*7	ENST00000380152		1849	-/A	11/27	0.220223741654082	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.220223741654082	1		639	419	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108079	30108079	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs754654624	NA	P-0019429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	55	682	0	ENST00000331968.5:c.728G>T	p.Arg243Leu	p.R243L	ENST00000331968	NM_002742.2	243	cGa/cTa	5/18	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.220223741654082	2		682	432	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43771511	43771602	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTAAAAATGTTTTCATCTGGTAAAATGACATTAGTATAACCCTACAGCAAAACTCGTAAATCCTTTTTAGAAAGTTCGGCTTACCTTGCAGG	CTAAAAATGTTTTCATCTGGTAAAATGACATTAGTATAACCCTACAGCAAAACTCGTAAATCCTTTTTAGAAAGTTCGGCTTACCTTGCAGG	TTAATTTTAAAA	novel	NA	P-0019429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	32	586	3	ENST00000382044.4:c.781_788+84delinsTTTTAAAATTAA		p.X261_splice	ENST00000382044	NM_001141980.1	261		7/28	0.200329741500221	1	FACETS	0.739	0.601	0.895	0.739	0.601	0.895	SUBCLONAL	1	TRUE	0	0.220223741654082	1		589	350	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604665	48604665	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	21	461	0	ENST00000342988.3:c.1487G>C	p.Arg496Pro	p.R496P	ENST00000342988	NM_005359.5	496	cGt/cCt	12/12	0.220223741654082	1	FACETS	0.558	0.43	0.708	0.558	0.43	0.708	SUBCLONAL	1	TRUE	0	0.220223741654082	1		461	304	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634668	158634668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1199234423	NA	P-0019429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	34	387	0	ENST00000263640.3:c.518C>T	p.Thr173Ile	p.T173I	ENST00000263640	NM_001105.4	173	aCc/aTc	5/11	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.220223741654082	2		387	275	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918347	44918348	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0019429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	28	270	0	ENST00000377967.4:c.974+1dup		p.-324fs	ENST00000377967	NM_021140.2	324	-/G	11/29	1	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.220223741654082	1		270	153	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223529	53223604	+	frameshift_variant	Frame_Shift_Del	DEL	GCCTCGCCCTCGGGCAGCCGCACAGGCAGTCTCTGCAGGGCTACCAGCAGTGCCAGGATGGTCTCCAGGCGCGGGC	GCCTCGCCCTCGGGCAGCCGCACAGGCAGTCTCTGCAGGGCTACCAGCAGTGCCAGGATGGTCTCCAGGCGCGGGC	-	novel	NA	P-0019429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	39	235	0	ENST00000375401.3:c.3755_3830del	p.Arg1252ProfsTer25	p.R1252Pfs*25	ENST00000375401	NM_004187.3	1252	cGCCCGCGCCTGGAGACCATCCTGGCACTGCTGGTAGCCCTGCAGAGACTGCCTGTGCGGCTGCCCGAGGGCGAGGCc/cc	23/26	1	1	FACETS	1	0.913	1	1	0.972	1	CLONAL	2	TRUE	0	0.220223741654082	1		235	140	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436624	52436624	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs387906848	NA	P-0019430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	323	856	0	ENST00000460680.1:c.2050C>T	p.Gln684Ter	p.Q684*	ENST00000460680	NM_004656.3	684	Cag/Tag	16/17	0.571489710945163	1	FACETS	0.947	0.899	0.996	0.947	0.899	0.996	CLONAL	1	TRUE	0	0.594153885378477	1		856	807	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578471	7578471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	423	938	0	ENST00000269305.4:c.459del	p.Gly154AlafsTer16	p.G154Afs*16	ENST00000269305	NM_001126112.2	153	ccC/cc	5/11	0.571489710945163	1	FACETS	0.971	0.928	1	0.971	0.928	1	CLONAL	1	TRUE	0	0.594153885378477	1		938	1031	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027172	49027178	+	frameshift_variant	Frame_Shift_Del	DEL	AAGGACC	AAGGACC	-	novel	NA	P-0019430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	218	776	0	ENST00000267163.4:c.1741_1747del	p.Gly581LeufsTer28	p.G581Lfs*28	ENST00000267163	NM_000321.2	580	gAAGGACCa/ga	18/27	0.593357269671075	1	FACETS	0.72	0.673	0.769	0.72	0.673	0.769	SUBCLONAL	1	TRUE	0	0.594153885378477	1		776	716	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	50	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.275142619521566	5	FACETS	0.932	0.79	1	0.311	0.263	0.363	CLONAL	1	TRUE	2	0.275142619521566	5		555	551	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0019433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	43	555	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.208348662709665	5	FACETS	1	0.909	1	0.376	0.315	0.444	CLONAL	1	TRUE	2	0.275142619521566	5		556	391	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154449	2154449	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	19	776	0	ENST00000434045.2:c.479A>G	p.Asn160Ser	p.N160S	ENST00000434045	NM_001127598.1	160	aAc/aGc	5/5	1	2	FACETS	0.478	0.363	0.613	0.478	0.363	0.613	SUBCLONAL	1	TRUE	1	0.275142619521566	2		776	289	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578537	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTTGAGGGCAA	novel	NA	P-0019433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	31	1216	0	ENST00000269305.4:c.393_394insTTGCCCTCAAC	p.Lys132LeufsTer42	p.K132Lfs*42	ENST00000269305	NM_001126112.2	131	-/TTGCCCTCAAC	5/11	0.275142619521566	3	FACETS	0.415	0.335	0.507	0.208	0.167	0.254	SUBCLONAL	1	TRUE	1	0.275142619521566	3		1216	617	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213618	2213619	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	66	965	0	ENST00000398665.3:c.1641dup	p.Gln548SerfsTer6	p.Q548Sfs*6	ENST00000398665	NM_032482.2	546	-/T	17/28	0.275142619521566	3	FACETS	1	0.875	1	0.503	0.437	0.575	CLONAL	1	TRUE	1	0.275142619521566	3		965	542	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	61	600	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.951	0.821	1	0.951	0.821	1	CLONAL	1	TRUE	1	0.23	2		600	558	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506428	148506428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	77	667	1	ENST00000320356.2:c.2084C>T	p.Ser695Leu	p.S695L	ENST00000320356	NM_004456.4	695	tCg/tTg	18/20	1	2	FACETS	0.954	0.837	1	0.954	0.837	1	CLONAL	1	TRUE	1	0.23	2		668	702	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16203049	16203049	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	69	665	0	ENST00000375759.3:c.757C>T	p.Gln253Ter	p.Q253*	ENST00000375759	NM_015001.2	253	Cag/Tag	3/15	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.23	2		665	553	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919638	28919638	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	69	1034	1	ENST00000282397.4:c.2299G>T	p.Val767Leu	p.V767L	ENST00000282397	NM_002019.4	767	Gtg/Ttg	16/30	1	2	FACETS	0.913	0.794	1	0.913	0.794	1	CLONAL	1	FALSE	1	0.195772275065388	2		1035	772	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943794	9943794	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	39	565	0	ENST00000330684.3:c.1147C>A	p.Leu383Met	p.L383M	ENST00000330684	NM_001134407.1	383	Ctg/Atg	5/13	1	2	FACETS	0.951	0.789	1	0.951	0.789	1	CLONAL	1	FALSE	1	0.195772275065388	2		565	419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577098	7577098	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1567547687	NA	P-0019436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	73	1033	0	ENST00000269305.4:c.840A>C	p.Arg280Ser	p.R280S	ENST00000269305	NM_001126112.2	280	agA/agC	8/11	1	2	FACETS	0.855	0.746	0.973	0.855	0.746	0.973	CLONAL	1	FALSE	1	0.195772275065388	2		1033	872	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553668	29553669	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0019436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	47	830	1	ENST00000356175.3:c.2217_2218delinsTT	p.Met739_Glu740delinsIleTer	p.M739_E740delinsI*	ENST00000356175	NM_000267.3	739	atGGag/atTTag	18/57	1	2	FACETS	0.779	0.657	0.915	0.779	0.657	0.915	CLONAL	1	FALSE	1	0.195772275065388	2		831	616	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556281	29556281	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	30	718	0	ENST00000356175.3:c.2648C>A	p.Ser883Ter	p.S883*	ENST00000356175	NM_000267.3	883	tCa/tAa	21/57	1	2	FACETS	0.56	0.45	0.686	0.56	0.45	0.686	SUBCLONAL	1	FALSE	1	0.195772275065388	2		718	547	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569823	67569823	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1230037871	NA	P-0019436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	22	455	0	ENST00000274335.5:c.484C>T	p.Arg162Ter	p.R162*	ENST00000274335		162	Cga/Tga	3/15	1	2	FACETS	0.581	0.449	0.734	0.581	0.449	0.734	SUBCLONAL	1	FALSE	1	0.195772275065388	2		455	387	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314907	1314907	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1363162924	NA	P-0019436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	35	737	0	ENST00000400841.2:c.754T>C	p.Trp252Arg	p.W252R	ENST00000400841		252	Tgg/Cgg	6/6	1	2	FACETS	0.73	0.597	0.878	0.73	0.597	0.878	SUBCLONAL	1	FALSE	1	0.195772275065388	2		737	490	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239733	53239733	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	55	837	0	ENST00000375401.3:c.1609G>T	p.Val537Leu	p.V537L	ENST00000375401	NM_004187.3	537	Gtg/Ttg	12/26	0.195772275065388	1	FACETS	0.828	0.708	0.96	0.828	0.708	0.96	CLONAL	1	FALSE	0	0.195772275065388	1		837	612	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	82	655	0	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.958	0.845	1	0.958	0.845	1	CLONAL	1	TRUE	1	0.23	2		655	744	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	42	593	2	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.7	0.584	0.828	0.7	0.584	0.828	SUBCLONAL	1	TRUE	1	0.23	2		595	522	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	39	416	2	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.909	0.755	1	0.909	0.755	1	CLONAL	1	TRUE	1	0.23	2		418	373	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	42	427	1	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS	0.886	0.741	1	0.886	0.741	1	CLONAL	1	TRUE	1	0.23	2		428	412	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692893	89692893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1114167656	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	50	622	0	ENST00000371953.3:c.377C>T	p.Ala126Val	p.A126V	ENST00000371953	NM_000314.4	126	gCt/gTt	5/9	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.23	2		622	417	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850705	63850705	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs201178069	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	50	686	0	ENST00000279873.7:c.1489del	p.Ile497Ter	p.I497*	ENST00000279873	NM_032199.2	495	Aaa/aa	10/10	1	2	FACETS	0.636	0.538	0.743	0.636	0.538	0.743	SUBCLONAL	1	TRUE	1	0.23	2		686	684	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	67	857	1	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	1	2	FACETS	0.727	0.631	0.832	0.727	0.631	0.832	SUBCLONAL	1	TRUE	1	0.23	2		858	801	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	108	1008	3	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	1	2	FACETS	0.952	0.853	1	0.952	0.853	1	CLONAL	1	TRUE	1	0.23	2		1011	986	SUCCESS
BTK	695	MSKCC	GRCh37	X	100624988	100624988	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs864321664	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	77	802	2	ENST00000308731.7:c.389del	p.Asn130ThrfsTer2	p.N130Tfs*2	ENST00000308731	NM_000061.2	130	aAc/ac	5/19	1	2	FACETS	0.966	0.848	1	0.966	0.848	1	CLONAL	1	TRUE	1	0.23	2		804	693	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220275	55220275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751295137	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	125	1026	2	ENST00000275493.2:c.665G>A	p.Arg222His	p.R222H	ENST00000275493	NM_005228.3	222	cGc/cAc	6/28	1	2	FACETS	0.947	0.855	1	0.947	0.855	1	CLONAL	1	TRUE	1	0.23	2		1028	1148	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104356979	104356979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145704867	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	92	737	2	ENST00000369902.3:c.839G>A	p.Arg280Gln	p.R280Q	ENST00000369902	NM_016169.3	280	cGg/cAg	7/12	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.23	2		739	721	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601893	43601893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057521089	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	104	922	2	ENST00000355710.3:c.937C>T	p.Arg313Trp	p.R313W	ENST00000355710	NM_020975.4	313	Cgg/Tgg	5/20	1	2	FACETS	0.953	0.852	1	0.953	0.852	1	CLONAL	1	TRUE	1	0.23	2		924	949	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	97	944	0	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	0.897	0.799	1	0.897	0.799	1	CLONAL	1	TRUE	1	0.23	2		944	940	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	31	596	2	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	0.547	0.441	0.666	0.547	0.441	0.666	SUBCLONAL	1	TRUE	1	0.23	2		598	493	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855029	76855029	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1557085898	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	91	742	1	ENST00000373344.5:c.5807A>G	p.Lys1936Arg	p.K1936R	ENST00000373344	NM_000489.3	1936	aAg/aGg	25/35	1	2	FACETS	0.799	0.712	0.891	1	0.982	1	SUBCLONAL	2	TRUE	1	0.23	2		743	495	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788672	3788672	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1387351570	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	59	678	1	ENST00000262367.5:c.4282C>T	p.Arg1428Cys	p.R1428C	ENST00000262367	NM_004380.2	1428	Cgt/Tgt	26/31	1	2	FACETS	0.687	0.59	0.793	0.687	0.59	0.793	SUBCLONAL	1	TRUE	1	0.23	2		679	747	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412544	80412544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	42	445	1	ENST00000286548.4:c.497G>A	p.Arg166His	p.R166H	ENST00000286548	NM_002072.3	166	cGc/cAc	4/7	1	2	FACETS	0.849	0.71	1	0.849	0.71	1	CLONAL	1	TRUE	1	0.23	2		446	430	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812573	43812573	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs753018650	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	72	1038	2	ENST00000372470.3:c.1276C>T	p.Arg426Ter	p.R426*	ENST00000372470	NM_005373.2	426	Cga/Tga	8/12	1	2	FACETS	0.725	0.632	0.825	0.725	0.632	0.825	SUBCLONAL	1	TRUE	1	0.23	2		1040	864	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117690	108117690	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs1064793518	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	26	332	0	ENST00000278616.4:c.902-1G>T		p.X301_splice	ENST00000278616	NM_000051.3	301			1	2	FACETS	1	0.81	1	1	0.81	1	CLONAL	1	TRUE	1	0.23	2		332	222	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118361992	118361992	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782281385	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	60	569	1	ENST00000534358.1:c.4778G>A	p.Arg1593His	p.R1593H	ENST00000534358	NM_005933.3	1593	cGc/cAc	14/36	1	2	FACETS	0.942	0.812	1	0.942	0.812	1	CLONAL	1	TRUE	1	0.23	2		570	554	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493809	56493809	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759751183	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	39	559	2	ENST00000267101.3:c.3125G>A	p.Arg1042His	p.R1042H	ENST00000267101	NM_001982.3	1042	cGt/cAt	25/28	1	2	FACETS	0.585	0.484	0.698	0.585	0.484	0.698	SUBCLONAL	1	TRUE	1	0.23	2		561	580	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435099	110435099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	97	1076	1	ENST00000375856.3:c.3302C>T	p.Pro1101Leu	p.P1101L	ENST00000375856	NM_003749.2	1101	cCg/cTg	1/2	1	2	FACETS	0.794	0.706	0.888	0.794	0.706	0.888	SUBCLONAL	1	TRUE	1	0.23	2		1077	1062	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023064	33023064	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	46	551	0	ENST00000300177.4:c.177del	p.Arg60GlyfsTer24	p.R60Gfs*24	ENST00000300177	NM_001191322.1	58	cGg/cg	2/2	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.23	2		551	395	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226602	1226602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762482152	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	77	754	3	ENST00000326873.7:c.1258G>A	p.Ala420Thr	p.A420T	ENST00000326873	NM_000455.4	420	Gcc/Acc	9/10	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.23	2		757	669	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106976	11106976	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	101	1098	5	ENST00000358026.2:c.1681G>A	p.Val561Met	p.V561M	ENST00000358026	NM_001128849.1	561	Gtg/Atg	10/36	1	2	FACETS	0.852	0.76	0.95	0.852	0.76	0.95	CLONAL	1	TRUE	1	0.23	2		1103	1031	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113790	11113790	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	93	881	0	ENST00000358026.2:c.1902del	p.Ala636ProfsTer10	p.A636Pfs*10	ENST00000358026	NM_001128849.1	633	gCc/gc	12/36	1	2	FACETS	0.867	0.769	0.971	0.867	0.769	0.971	CLONAL	1	TRUE	1	0.23	2		881	933	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168992	11168992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	75	992	1	ENST00000358026.2:c.4582G>A	p.Glu1528Lys	p.E1528K	ENST00000358026	NM_001128849.1	1528	Gag/Aag	32/36	1	2	FACETS	0.678	0.592	0.77	0.678	0.592	0.77	SUBCLONAL	1	TRUE	1	0.23	2		993	962	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379691	17379691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	73	839	0	ENST00000359435.4:c.76C>T	p.Arg26Cys	p.R26C	ENST00000359435	NM_001033549.1	26	Cgc/Tgc	2/9	1	2	FACETS	0.742	0.648	0.845	0.742	0.648	0.845	SUBCLONAL	1	TRUE	1	0.23	2		839	855	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280081	18280081	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778796616	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	37	286	0	ENST00000222254.8:c.2164G>A	p.Gly722Ser	p.G722S	ENST00000222254	NM_005027.3	722	Ggc/Agc	16/16	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.23	2		286	273	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791751	42791751	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	100	856	2	ENST00000575354.2:c.637C>T	p.Arg213Trp	p.R213W	ENST00000575354	NM_015125.3	213	Cgg/Tgg	5/20	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.23	2		858	820	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794469	42794469	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	127	1227	3	ENST00000575354.2:c.1553del	p.Pro518ArgfsTer5	p.P518Rfs*5	ENST00000575354	NM_015125.3	517	Ccc/cc	10/20	1	2	FACETS	0.942	0.852	1	0.942	0.852	1	CLONAL	1	TRUE	1	0.23	2		1230	1172	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445397	29445397	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	87	1006	1	ENST00000389048.3:c.3436C>T	p.Gln1146Ter	p.Q1146*	ENST00000389048	NM_004304.4	1146	Caa/Taa	21/29	1	2	FACETS	0.76	0.671	0.856	0.76	0.671	0.856	SUBCLONAL	1	TRUE	1	0.23	2		1007	995	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606991	47606995	+	frameshift_variant	Frame_Shift_Del	DEL	TTTAA	TTTAA	-	novel	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	74	745	0	ENST00000263735.4:c.745_749del	p.Ile249LeufsTer3	p.I249Lfs*3	ENST00000263735	NM_002354.2	247	acTTTAAtt/actt	7/9	1	2	FACETS	0.979	0.857	1	0.979	0.857	1	CLONAL	1	TRUE	1	0.23	2		745	657	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635629	47635629	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63750318	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	104	900	3	ENST00000233146.2:c.301G>T	p.Glu101Ter	p.E101*	ENST00000233146	NM_000251.2	101	Gaa/Taa	2/16	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.23	2		903	831	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637291	47637291	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs63750910	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	93	906	0	ENST00000233146.2:c.425C>G	p.Ser142Ter	p.S142*	ENST00000233146	NM_000251.2	142	tCa/tGa	3/16	1	2	FACETS	0.971	0.862	1	0.971	0.862	1	CLONAL	1	TRUE	1	0.23	2		906	833	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018263	48018263	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	59	680	0	ENST00000234420.5:c.457+1G>A		p.X153_splice	ENST00000234420	NM_000179.2	153			1	2	FACETS	0.791	0.68	0.912	0.791	0.68	0.912	CLONAL	1	TRUE	1	0.23	2		680	649	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99185045	99185045	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778972642	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	45	492	1	ENST00000074304.5:c.2447C>T	p.Thr816Met	p.T816M	ENST00000074304	NM_001134224.1	816	aCg/aTg	23/26	1	2	FACETS	0.696	0.585	0.82	0.696	0.585	0.82	SUBCLONAL	1	TRUE	1	0.23	2		493	562	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478074	138478074	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	76	918	0	ENST00000289153.2:c.112A>G	p.Thr38Ala	p.T38A	ENST00000289153	NM_006219.2	38	Act/Gct	1/22	1	2	FACETS	0.915	0.802	1	0.915	0.802	1	CLONAL	1	TRUE	1	0.23	2		918	722	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294124	1294124	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	148	1312	4	ENST00000310581.5:c.877C>T	p.Arg293Cys	p.R293C	ENST00000310581	NM_198253.2	293	Cgc/Tgc	2/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.23	2		1316	1214	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460377	149460377	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	69	709	0	ENST00000286301.3:c.260C>A	p.Pro87His	p.P87H	ENST00000286301	NM_005211.3	87	cCt/cAt	3/22	1	2	FACETS	0.904	0.787	1	0.904	0.787	1	CLONAL	1	TRUE	1	0.23	2		709	664	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163608	32163608	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	54	793	1	ENST00000375023.3:c.5618del	p.Gly1873AlafsTer12	p.G1873Afs*12	ENST00000375023	NM_004557.3	1873	gGc/gc	30/30	1	2	FACETS	0.754	0.643	0.875	0.754	0.643	0.875	SUBCLONAL	1	TRUE	1	0.23	2		794	623	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932455	39932455	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	111	943	1	ENST00000378444.4:c.2144C>T	p.Thr715Ile	p.T715I	ENST00000378444	NM_001123385.1	715	aCc/aTc	4/15	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.23	2		944	901	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349634	70349634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060502168	NA	P-0019437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	69	911	0	ENST00000374080.3:c.3796C>T	p.Arg1266Cys	p.R1266C	ENST00000374080		1266	Cgc/Tgc	27/45	1	2	FACETS	0.643	0.559	0.735	0.643	0.559	0.735	SUBCLONAL	1	TRUE	1	0.23	2		911	933	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152093	55152093	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121908585	NA	P-0019438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	412	766	0	ENST00000257290.5:c.2525A>T	p.Asp842Val	p.D842V	ENST00000257290	NM_006206.4	842	gAc/gTc	18/23	1	2	FACETS	0.941	0.897	0.986	0.941	0.897	0.986	CLONAL	1	TRUE	1	0.750844366398539	2		766	1166	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0019440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	65	713	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	0.587	0.509	0.673	0.587	0.509	0.673	SUBCLONAL	1	TRUE	1	0.315317159056431	2		713	702	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31369182	31369182	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	117	632	0	ENST00000328111.2:c.166T>C	p.Ser56Pro	p.S56P	ENST00000328111	NM_006892.3	56	Tcc/Ccc	3/23	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.315317159056431	2		632	708	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170817107	170817107	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	17	572	0	ENST00000296930.5:c.111A>T	p.Glu37Asp	p.E37D	ENST00000296930	NM_002520.6	37	gaA/gaT	2/11	0.315317159056431	1	FACETS	0.365	0.272	0.474	0.365	0.272	0.474	SUBCLONAL	1	TRUE	0	0.315317159056431	1		572	249	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981515	70981515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745606576	NA	P-0019440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	63	1198	0	ENST00000276594.2:c.581G>A	p.Arg194Gln	p.R194Q	ENST00000276594	NM_024504.3	194	cGg/cAg	2/8	0.235993113775074	1	FACETS	0.295	0.254	0.34	0.295	0.254	0.34	SUBCLONAL	1	TRUE	0	0.315317159056431	1		1198	1140	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0019441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	458	822	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.697647691655366	2	FACETS	0.971	0.94	1	0.971	0.94	1	CLONAL	2	TRUE	0	0.697691240036483	2		822	676	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0019442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	201	713	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.215413915291619	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.215413915291619	2		713	871	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	105	892	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.215413915291619	3	FACETS	1	0.97	1	0.616	0.551	0.685	CLONAL	1	TRUE	1	0.215413915291619	3		892	876	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94209465	94209465	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	36	423	2	ENST00000323929.3:c.649C>A	p.His217Asn	p.H217N	ENST00000323929	NM_005591.3	217	Cat/Aat	7/20	0.16164526930664	4	FACETS	1	0.902	1			1	CLONAL	1	TRUE	NA	0.215413915291619	4		425	354	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487162	56487162	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs2229045	NA	P-0019442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	71	618	0	ENST00000267101.3:c.1308G>C	p.Leu436Phe	p.L436F	ENST00000267101	NM_001982.3	436	ttG/ttC	12/28	0.215413915291619	8	FACETS	0.928	0.807	1	0.155	0.134	0.177	CLONAL	1	TRUE	2	0.215413915291619	8		618	1169	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37882082	37882082	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	77	678	0	ENST00000269571.5:c.2848G>C	p.Asp950His	p.D950H	ENST00000269571		950	Gat/Cat	23/27	0.192691969252264	4	FACETS	0.872	0.764	0.99	0.436	0.382	0.495	CLONAL	1	TRUE	2	0.215413915291619	4		678	996	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0019443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	128	640	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.438037804712065	3	FACETS	0.856	0.783	0.932	0.856	0.783	0.932	CLONAL	2	TRUE	1	0.438037804712065	3		640	416	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435155	56435155	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	320	654	1	ENST00000407977.2:c.1982C>T	p.Ser661Phe	p.S661F	ENST00000407977		661	tCc/tTc	9/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.438037804712065	2		655	1381	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0019443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	114	409	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.438037804712065	1	FACETS	0.88	0.797	0.966	0.88	0.797	0.966	CLONAL	1	TRUE	0	0.438037804712065	1		409	462	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0019443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	182	634	1				ENST00000310581	NM_198253.2	-/1132			0.261961048372097	1	FACETS	1	0.974	1	1	0.974	1	INDETERMINATE	1	TRUE	0	0.438037804712065	1		635	586	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964947	55964947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	163	478	2	ENST00000263923.4:c.2290G>A	p.Glu764Lys	p.E764K	ENST00000263923	NM_002253.2	764	Gaa/Aaa	16/30	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.438037804712065	2		480	661	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40477072	40477072	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	163	501	0	ENST00000264657.5:c.1373C>T	p.Ser458Phe	p.S458F	ENST00000264657	NM_139276.2	458	tCc/tTc	16/24	1	2	FACETS	0.884	0.812	0.959	0.884	0.812	0.959	CLONAL	1	TRUE	1	0.438037804712065	2		501	842	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649173	23649173	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	36	477	0	ENST00000261584.4:c.209C>T	p.Ser70Leu	p.S70L	ENST00000261584	NM_024675.3	70	tCa/tTa	3/13	0.229148111355753	1	FACETS	0.283	0.233	0.34	0.283	0.233	0.34	INDETERMINATE	1	TRUE	0	0.438037804712065	1		477	453	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511593	38511594	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0019443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	242	764	4	ENST00000254066.5:c.1091_1092delinsAA	p.Arg364Gln	p.R364Q	ENST00000254066	NM_000964.3	364	cGG/cAA	8/9	1	2	FACETS	0.867	0.809	0.928	0.867	0.809	0.928	CLONAL	1	TRUE	1	0.438037804712065	2		768	1274	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024625	11024625	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	278	640	1	ENST00000327064.4:c.742C>T	p.Pro248Ser	p.P248S	ENST00000327064	NM_199141.1	248	Ccc/Tcc	6/16	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.438037804712065	2		641	1249	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852443	42852443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139092674	NA	P-0019443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	261	626	0	ENST00000398585.3:c.643G>A	p.Glu215Lys	p.E215K	ENST00000398585	NM_001135099.1	215	Gag/Aag	6/14	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.438037804712065	2		626	1148	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713361	30713361	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	115	431	0	ENST00000295754.5:c.686C>T	p.Ser229Phe	p.S229F	ENST00000295754	NM_003242.5	229	tCc/tTc	4/7	0.229148111355753	1	FACETS	0.471	0.424	0.521	0.471	0.424	0.521	INDETERMINATE	1	TRUE	0	0.438037804712065	1		431	871	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944636	38944636	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	59	498	0	ENST00000357387.3:c.4825C>G	p.Arg1609Gly	p.R1609G	ENST00000357387	NM_152756.3	1609	Cgt/Ggt	36/38	0.261961048372097	1	FACETS	0.685	0.594	0.783	0.685	0.594	0.783	INDETERMINATE	1	TRUE	0	0.438037804712065	1		498	307	SUCCESS
APC	324	MSKCC	GRCh37	5	112177341	112177341	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	95	360	0	ENST00000257430.4:c.6050C>T	p.Thr2017Ile	p.T2017I	ENST00000257430	NM_000038.5	2017	aCc/aTc	16/16	0.261961048372097	1	FACETS	0.788	0.705	0.874	0.788	0.705	0.874	INDETERMINATE	1	TRUE	0	0.438037804712065	1		360	430	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042511	42042512	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	A	novel	NA	P-0019443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	115	524	0	ENST00000219905.7:c.6706_6707delinsA	p.Val2236IlefsTer2	p.V2236Ifs*2	ENST00000219905	NM_001164273.1	2236	GTt/At	17/24	1	2	FACETS	0.75	0.676	0.828	0.75	0.676	0.828	SUBCLONAL	1	TRUE	1	0.438037804712065	2		524	700	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134476	2134476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369164761	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	104	1082	0	ENST00000219476.3:c.4253C>T	p.Ser1418Leu	p.S1418L	ENST00000219476	NM_000548.3	1418	tCa/tTa	34/42	1	2	FACETS	0.674	0.602	0.751	0.674	0.602	0.751	SUBCLONAL	1	TRUE	1	0.292235030064615	2		1082	1056	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298106	11298106	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	47	529	0	ENST00000361445.4:c.2003-1G>C		p.X668_splice	ENST00000361445	NM_004958.3	668			0.179178807019673	2	FACETS	0.587	0.495	0.689	0.293	0.247	0.345	SUBCLONAL	1	TRUE	0	0.292235030064615	2		529	548	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458258	120458258	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	49	749	0	ENST00000256646.2:c.7087G>T	p.Gly2363Trp	p.G2363W	ENST00000256646	NM_024408.3	2363	Ggg/Tgg	34/34	0.249864827876499	1	FACETS	0.476	0.403	0.558	0.476	0.403	0.558	SUBCLONAL	1	TRUE	0	0.292235030064615	1		749	601	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680489	241680489	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs200007371	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	85	560	0	ENST00000366560.3:c.260G>T	p.Arg87Leu	p.R87L	ENST00000366560	NM_000143.3	87	cGc/cTc	2/10	0.106974305957991	5	FACETS	1	0.973	1	0.455	0.402	0.511	INDETERMINATE	1	TRUE	2	0.292235030064615	5		560	613	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097641	8097641	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	19	243	0	ENST00000346208.3:c.23C>A	p.Pro8Gln	p.P8Q	ENST00000346208		8	cCg/cAg	2/6	0.292235030064615	3	FACETS	0.517	0.393	0.664	0.259	0.196	0.332	SUBCLONAL	1	TRUE	1	0.292235030064615	3		243	288	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716309	18716309	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	23	429	0	ENST00000266497.5:c.3658-2A>T		p.X1220_splice	ENST00000266497		1220			1	2	FACETS	0.483	0.376	0.606	0.483	0.376	0.606	SUBCLONAL	1	TRUE	1	0.292235030064615	2		429	326	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380229	25380229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	57	634	0	ENST00000311936.3:c.229G>A	p.Gly77Ser	p.G77S	ENST00000311936	NM_004985.3	77	Ggc/Agc	3/5	1	2	FACETS	0.645	0.553	0.745	0.645	0.553	0.745	SUBCLONAL	1	TRUE	1	0.292235030064615	2		634	605	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231176	46231176	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	30	488	0	ENST00000334344.6:c.1096A>T	p.Arg366Trp	p.R366W	ENST00000334344	NM_152641.2	366	Agg/Tgg	9/21	0.182013817115009	3	FACETS	0.777	0.627	0.945	0.259	0.209	0.315	CLONAL	1	TRUE	0	0.292235030064615	3		488	303	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244661	46244661	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	152	731	0	ENST00000334344.6:c.2755C>T	p.Gln919Ter	p.Q919*	ENST00000334344	NM_152641.2	919	Cag/Tag	15/21	0.182013817115009	3	FACETS	0.818	0.749	0.889	0.545	0.499	0.593	CLONAL	2	TRUE	0	0.292235030064615	3		731	729	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481938	56481938	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	89	809	1	ENST00000267101.3:c.866G>A	p.Ser289Asn	p.S289N	ENST00000267101	NM_001982.3	289	aGc/aAc	7/28	0.182013817115009	3	FACETS	0.833	0.738	0.935	0.278	0.246	0.312	CLONAL	1	TRUE	0	0.292235030064615	3		810	838	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039365	49039365	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	39	969	1	ENST00000267163.4:c.2350C>T	p.His784Tyr	p.H784Y	ENST00000267163	NM_000321.2	784	Cac/Tac	23/27	0.179178807019673	2	FACETS	0.44	0.364	0.526	0.22	0.182	0.263	SUBCLONAL	1	TRUE	0	0.292235030064615	2		970	606	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281476	49281476	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	96	670	1	ENST00000282018.3:c.523G>T	p.Asp175Tyr	p.D175Y	ENST00000282018	NM_020377.2	175	Gac/Tac	1/1	0.179178807019673	2	FACETS	1	0.959	1	0.576	0.515	0.642	CLONAL	1	TRUE	0	0.292235030064615	2		671	570	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281735	49281735	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	53	959	0	ENST00000282018.3:c.782T>A	p.Leu261Gln	p.L261Q	ENST00000282018	NM_020377.2	261	cTg/cAg	1/1	0.179178807019673	2	FACETS	0.399	0.339	0.465	0.199	0.169	0.233	SUBCLONAL	1	TRUE	0	0.292235030064615	2		959	910	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434677	99434677	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	133	853	1	ENST00000268035.6:c.764A>T	p.Tyr255Phe	p.Y255F	ENST00000268035	NM_000875.3	255	tAc/tTc	3/21	0.16450639206337	3	FACETS	0.968	0.877	1	0.484	0.438	0.532	INDETERMINATE	1	TRUE	1	0.292235030064615	3		854	1078	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892140	9892140	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	52	650	0	ENST00000330684.3:c.2350G>T	p.Gly784Cys	p.G784C	ENST00000330684	NM_001134407.1	784	Ggt/Tgt	11/13	0.210847922500996	4	FACETS	0.541	0.459	0.631			1	SUBCLONAL	1	TRUE	NA	0.292235030064615	4		650	850	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862127	68862127	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	110	698	0	ENST00000261769.5:c.2215G>C	p.Glu739Gln	p.E739Q	ENST00000261769	NM_004360.3	739	Gag/Cag	14/16	0.292235030064615	4	FACETS	0.999	0.896	1	0.333	0.298	0.37	CLONAL	1	TRUE	1	0.292235030064615	4		698	974	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992271	72992271	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1280	89	1040	3	ENST00000268489.5:c.1774G>T	p.Asp592Tyr	p.D592Y	ENST00000268489	NM_006885.3	592	Gac/Tac	2/10	0.292235030064615	4	FACETS	0.575	0.508	0.647	0.192	0.169	0.216	SUBCLONAL	1	TRUE	1	0.292235030064615	4		1043	1369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	193	898	1	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.292235030064615	3	FACETS	1	0.987	1	0.663	0.612	0.716	CLONAL	1	TRUE	1	0.292235030064615	3		899	1142	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15938084	15938084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	27	233	0	ENST00000268712.3:c.7130C>T	p.Ser2377Leu	p.S2377L	ENST00000268712	NM_006311.3	2377	tCa/tTa	45/46	0.292235030064615	3	FACETS	0.933	0.746	1	0.466	0.373	0.572	CLONAL	1	TRUE	1	0.292235030064615	3		233	227	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964961	15964961	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	38	725	2	ENST00000268712.3:c.5635C>T	p.Gln1879Ter	p.Q1879*	ENST00000268712	NM_006311.3	1879	Cag/Tag	37/46	0.292235030064615	3	FACETS	0.467	0.385	0.559	0.234	0.192	0.28	SUBCLONAL	1	TRUE	1	0.292235030064615	3		727	638	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117581	70117581	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	69	819	1	ENST00000245479.2:c.49G>T	p.Gly17Cys	p.G17C	ENST00000245479	NM_000346.3	17	Ggc/Tgc	1/3	0.284433388563336	4	FACETS	0.548	0.475	0.627	0.183	0.158	0.209	SUBCLONAL	1	TRUE	1	0.292235030064615	4		820	1114	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602864	10602864	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	508	1169	3	ENST00000171111.5:c.714C>A	p.Asn238Lys	p.N238K	ENST00000171111	NM_203500.1	238	aaC/aaA	3/6	0.182013817115009	3	FACETS	1	0.994	1	0.815	0.78	0.851	CLONAL	2	TRUE	0	0.292235030064615	3		1172	1629	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276741	15276741	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	77	877	0	ENST00000263388.2:c.5524G>C	p.Ala1842Pro	p.A1842P	ENST00000263388	NM_000435.2	1842	Gct/Cct	30/33	0.182013817115009	3	FACETS	0.634	0.555	0.719	0.211	0.185	0.24	SUBCLONAL	1	TRUE	0	0.292235030064615	3		877	953	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61717879	61717879	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	34	841	0	ENST00000401558.2:c.1920G>C	p.Met640Ile	p.M640I	ENST00000401558	NM_003400.3	640	atG/atC	17/25	0.292235030064615	3	FACETS	0.421	0.343	0.509	0.21	0.171	0.255	SUBCLONAL	1	TRUE	1	0.292235030064615	3		841	634	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288654	198288654	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	49	797	0	ENST00000335508.6:c.73C>G	p.Leu25Val	p.L25V	ENST00000335508	NM_012433.2	25	Ctt/Gtt	2/25	0.16450639206337	3	FACETS	0.51	0.431	0.597	0.255	0.215	0.299	INDETERMINATE	1	TRUE	1	0.292235030064615	3		797	754	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251707	212251707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	63	433	0	ENST00000342788.4:c.3352C>T	p.His1118Tyr	p.H1118Y	ENST00000342788	NM_005235.2	1118	Cat/Tat	27/28	0.16450639206337	3	FACETS	0.984	0.853	1	0.492	0.426	0.564	INDETERMINATE	1	TRUE	1	0.292235030064615	3		433	502	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743914	40743914	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	107	667	0	ENST00000373198.4:c.3081C>G	p.Tyr1027Ter	p.Y1027*	ENST00000373198	NM_133170.3	1027	taC/taG	23/32	0.292235030064615	3	FACETS	1	0.902	1	0.503	0.451	0.559	CLONAL	1	TRUE	1	0.292235030064615	3		667	834	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608630	189608630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	49	718	0	ENST00000264731.3:c.1705G>A	p.Gly569Arg	p.G569R	ENST00000264731	NM_003722.4	569	Ggg/Agg	13/14	0.187910521768584	2	FACETS	0.468	0.396	0.549	0.234	0.198	0.275	SUBCLONAL	1	TRUE	0	0.292235030064615	2		718	716	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807310	1807310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778356	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	55	819	2	ENST00000260795.2:c.1559C>T	p.Ser520Leu	p.S520L	ENST00000260795		520	tCg/tTg	11/17	0.292235030064615	3	FACETS	0.538	0.459	0.625	0.269	0.229	0.313	SUBCLONAL	1	TRUE	1	0.292235030064615	3		821	802	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750485	41750485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	104	629	1	ENST00000226382.2:c.143G>A	p.Arg48Lys	p.R48K	ENST00000226382	NM_003924.3	48	aGg/aAg	1/3	0.292235030064615	3	FACETS	1	0.97	1	0.613	0.55	0.681	CLONAL	1	TRUE	1	0.292235030064615	3		630	665	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144632	55144632	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	93	618	2	ENST00000257290.5:c.2106G>T	p.Lys702Asn	p.K702N	ENST00000257290	NM_006206.4	702	aaG/aaT	15/23	0.287844978705393	4	FACETS	1	0.947	1			1	CLONAL	1	TRUE	NA	0.292235030064615	4		620	741	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38972022	38972022	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	24	532	0	ENST00000357387.3:c.929A>T	p.Gln310Leu	p.Q310L	ENST00000357387	NM_152756.3	310	cAg/cTg	11/38	0.292235030064615	4	FACETS	0.566	0.443	0.708	0.189	0.147	0.236	SUBCLONAL	1	TRUE	1	0.292235030064615	4		532	375	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591054	67591054	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	55	519	0	ENST00000274335.5:c.1647del	p.Lys550ArgfsTer14	p.K550Rfs*14	ENST00000274335		549	ttG/tt	12/15	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.292235030064615	2		519	366	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562657	176562657	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	61	780	0	ENST00000439151.2:c.553G>C	p.Glu185Gln	p.E185Q	ENST00000439151	NM_022455.4	185	Gag/Cag	2/23	1	2	FACETS	0.663	0.571	0.762	0.663	0.571	0.762	SUBCLONAL	1	TRUE	1	0.292235030064615	2		780	630	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151947968	151947968	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	83	734	0	ENST00000262189.6:c.1705C>T	p.Gln569Ter	p.Q569*	ENST00000262189	NM_170606.2	569	Cag/Tag	12/59	0.292235030064615	3	FACETS	1	0.977	1	0.723	0.641	0.811	CLONAL	1	TRUE	1	0.292235030064615	3		734	450	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279365	38279365	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	95	1013	1	ENST00000425967.3:c.1124G>T	p.Gly375Val	p.G375V	ENST00000425967	NM_001174067.1	375	gGt/gTt	9/19	1	2	FACETS	0.723	0.643	0.809	0.723	0.643	0.809	SUBCLONAL	1	TRUE	1	0.292235030064615	2		1014	899	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56860200	56860200	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	98	730	0	ENST00000519728.1:c.202G>A	p.Val68Met	p.V68M	ENST00000519728	NM_002350.3	68	Gtg/Atg	4/13	1	2	FACETS	0.91	0.812	1	0.91	0.812	1	CLONAL	1	TRUE	1	0.292235030064615	2		730	737	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141568583	141568583	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	111	656	1	ENST00000220592.5:c.878+1G>A		p.X293_splice	ENST00000220592	NM_012154.3	293			1	2	FACETS	0.831	0.746	0.921	0.831	0.746	0.921	CLONAL	1	TRUE	1	0.292235030064615	2		657	914	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389308	8389308	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	100	830	0	ENST00000356435.5:c.4310G>T	p.Gly1437Val	p.G1437V	ENST00000356435		1437	gGg/gTg	26/35	0.292235030064615	3	FACETS	1	0.974	1	0.643	0.575	0.715	CLONAL	1	TRUE	1	0.292235030064615	3		830	610	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250337	110250337	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	218	958	1	ENST00000374672.4:c.338T>A	p.Leu113Gln	p.L113Q	ENST00000374672	NM_004235.4	113	cTg/cAg	3/5	0.292235030064615	3	FACETS	0.807	0.75	0.866	0.807	0.75	0.866	CLONAL	2	TRUE	1	0.292235030064615	3		959	1059	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15822269	15822269	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	46	365	0	ENST00000307771.7:c.348G>C	p.Arg116Ser	p.R116S	ENST00000307771	NM_005089.3	116	agG/agC	5/11	1	1	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	0	0.292235030064615	1		365	255	SUCCESS
AR	367	MSKCC	GRCh37	X	66942750	66942750	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	120	449	0	ENST00000374690.3:c.2531C>A	p.Ala844Glu	p.A844E	ENST00000374690	NM_000044.3	844	gCa/gAa	7/8	0.0500959011883522	2	FACETS	0.788	0.715	0.865			1	INDETERMINATE	2	TRUE	NA	0.292235030064615	2		449	521	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	49	736	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.243566898986698	2		736	368	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992224	11992224	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	65	444	1	ENST00000396373.4:c.314G>C	p.Arg105Pro	p.R105P	ENST00000396373	NM_001987.4	105	cGa/cCa	3/8	1	2	FACETS	0.851	0.738	0.974	0.851	0.738	0.974	CLONAL	1	TRUE	1	0.243566898986698	2		445	627	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015357	176015357	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	55	638	0	ENST00000367669.3:c.1381C>G	p.His461Asp	p.H461D	ENST00000367669	NM_022457.5	461	Cat/Gat	12/20	0.243566898986698	3	FACETS	0.812	0.694	0.941	0.406	0.347	0.471	CLONAL	1	TRUE	1	0.243566898986698	3		638	624	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858399	89858399	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	124	924	0	ENST00000389301.3:c.1161G>C	p.Gln387His	p.Q387H	ENST00000389301	NM_000135.2	387	caG/caC	13/43	1	2	FACETS	0.888	0.802	0.98	0.888	0.802	0.98	CLONAL	1	TRUE	1	0.243566898986698	2		924	1146	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740526	58740526	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747990992	NA	P-0019445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	99	849	0	ENST00000305921.3:c.1432del	p.Cys478AlafsTer5	p.C478Afs*5	ENST00000305921	NM_003620.3	477	aaT/aa	6/6	0.243566898986698	3	FACETS	0.791	0.704	0.884	0.395	0.352	0.442	SUBCLONAL	1	TRUE	1	0.243566898986698	3		849	1153	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728512	190728512	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	101	734	0	ENST00000441310.2:c.1900C>G	p.Gln634Glu	p.Q634E	ENST00000441310	NM_000534.4	634	Caa/Gaa	10/13	1	2	FACETS	0.919	0.821	1	0.919	0.821	1	CLONAL	1	TRUE	1	0.243566898986698	2		734	902	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324579	62324579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144034326	NA	P-0019445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	141	958	2	ENST00000360203.5:c.2935C>T	p.Arg979Trp	p.R979W	ENST00000360203	NM_001283009.1	979	Cgg/Tgg	30/35	0.2194521931531	3	FACETS	1	0.951	1	0.535	0.486	0.587	CLONAL	1	TRUE	1	0.243566898986698	3		960	1214	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839874	27839874	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	88	574	0	ENST00000328488.2:c.220G>C	p.Glu74Gln	p.E74Q	ENST00000328488	NM_003533.2	74	Gag/Cag	1/1	1	2	FACETS	0.978	0.866	1	0.978	0.866	1	CLONAL	1	TRUE	1	0.243566898986698	2		574	739	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779055	135779055	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	68	494	0	ENST00000298552.3:c.2191G>C	p.Glu731Gln	p.E731Q	ENST00000298552	NM_001162426.1	731	Gaa/Caa	17/23	0.243566898986698	1	FACETS	0.906	0.79	1	0.906	0.79	1	CLONAL	1	TRUE	0	0.243566898986698	1		494	541	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344925	70344925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	104	898	0	ENST00000374080.3:c.2155G>A	p.Glu719Lys	p.E719K	ENST00000374080		719	Gaa/Aaa	15/45	0.211302960103095	1	FACETS	0.705	0.63	0.785	0.705	0.63	0.785	SUBCLONAL	1	TRUE	0	0.243566898986698	1		898	1064	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	62	509	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	0.267482054849072	2		509	404	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	14	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.259	0.186	0.348	0.259	0.186	0.348	SUBCLONAL	1	TRUE	1	0.267482054849072	2		555	404	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0019446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	29	536	1	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.267482054849072	1	FACETS	0.639	0.514	0.78	0.639	0.514	0.78	SUBCLONAL	1	TRUE	0	0.267482054849072	1		537	294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0019446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	51	617	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	0.267482054849072	1	FACETS	0.694	0.59	0.808	0.694	0.59	0.808	SUBCLONAL	1	TRUE	0	0.267482054849072	1		617	476	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686374	30686374	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	64	404	2	ENST00000295754.5:c.230G>T	p.Cys77Phe	p.C77F	ENST00000295754	NM_003242.5	77	tGt/tTt	2/7	0.229522105247215	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.267482054849072	1		406	346	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410082	139410082	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	116	893	0	ENST00000277541.6:c.1756A>G	p.Thr586Ala	p.T586A	ENST00000277541	NM_017617.3	586	Acc/Gcc	11/34	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.267482054849072	2		893	805	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233037	55233037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1477025000	NA	P-0019447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	579	493	2	ENST00000275493.2:c.1787C>T	p.Pro596Leu	p.P596L	ENST00000275493	NM_005228.3	596	cCg/cTg	15/28	0.749154408456732	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.749154408456732	3		495	1035	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913444	NA	P-0019447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	154	595	0	ENST00000275493.2:c.2582T>G	p.Leu861Arg	p.L861R	ENST00000275493	NM_005228.3	861	cTg/cGg	21/28	0.749154408456732	3	FACETS	0.447	0.408	0.488	0.224	0.204	0.244	SUBCLONAL	1	TRUE	1	0.749154408456732	3		595	1264	SUCCESS
APC	324	MSKCC	GRCh37	5	112175246	112175246	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1057517558	NA	P-0019449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	249	397	0	ENST00000257430.4:c.3956del	p.Pro1319LeufsTer2	p.P1319Lfs*2	ENST00000257430	NM_000038.5	1319	Cct/ct	16/16	0.545386512584916	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.545386512584916	2		397	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0019449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	209	733	0	ENST00000269305.4:c.97-1G>A		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.545386512584916	1	FACETS	0.946	0.885	1	0.946	0.885	1	CLONAL	1	TRUE	0	0.545386512584916	1		733	589	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748660	43748661	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	164	1156	1	ENST00000382044.4:c.2145dup	p.Glu716ArgfsTer9	p.E716Rfs*9	ENST00000382044	NM_001141980.1	715	-/A	12/28	0.355909920702917	1	FACETS	0.41	0.375	0.445	0.41	0.375	0.445	SUBCLONAL	1	TRUE	0	0.545386512584916	1		1157	1068	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332102	70332102	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs750698861	NA	P-0019449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	68	270	0	ENST00000373644.4:c.7C>T	p.Arg3Ter	p.R3*	ENST00000373644	NM_030625.2	3	Cga/Tga	2/12	1	2	FACETS	0.878	0.771	0.991	0.878	0.771	0.991	CLONAL	1	TRUE	1	0.545386512584916	2		270	284	SUCCESS
CBL	867	MSKCC	GRCh37	11	119146766	119146766	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764199611	NA	P-0019449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	217	738	2	ENST00000264033.4:c.929C>T	p.Ala310Val	p.A310V	ENST00000264033	NM_005188.3	310	gCt/gTt	6/16	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.545386512584916	2		740	776	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806170	1806170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576428377	NA	P-0019449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	409	1278	1	ENST00000260795.2:c.1189C>T	p.Arg397Cys	p.R397C	ENST00000260795		397	Cgc/Tgc	8/17	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.545386512584916	2		1279	1258	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244214	153244214	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	191	663	0	ENST00000281708.4:c.1943T>G	p.Leu648Arg	p.L648R	ENST00000281708	NM_033632.3	648	cTa/cGa	12/12	1	2	FACETS	0.945	0.876	1	0.945	0.876	1	CLONAL	1	TRUE	1	0.545386512584916	2		663	741	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153252005	153252005	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0019449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	180	673	1	ENST00000281708.4:c.1001T>A	p.Leu334Ter	p.L334*	ENST00000281708	NM_033632.3	334	tTg/tAg	7/12	1	2	FACETS	0.968	0.896	1	0.968	0.896	1	CLONAL	1	TRUE	1	0.545386512584916	2		674	682	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0019450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	102	831	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.3	1	FACETS	0.714	0.638	0.794	0.714	0.638	0.794	SUBCLONAL	1	FALSE	0	0.3	1		831	810	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0019450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	19	807	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	0.186221060873864	2	FACETS	0.162	0.122	0.209	0.081	0.061	0.105	SUBCLONAL	1	FALSE	0	0.3	2		807	784	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0019450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	2344	614	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.3	36	FACETS	1	0.992	1			1	CLONAL	30	FALSE	NA	0.3	36		614	3159	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032057	26032057	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	29	322	0	ENST00000244661.2:c.232G>C	p.Asp78His	p.D78H	ENST00000244661	NM_003537.3	78	Gac/Cac	1/1	0.139646119903727	3	FACETS	0.603	0.484	0.738	0.201	0.161	0.246	INDETERMINATE	1	FALSE	0	0.3	3		322	369	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987257	2987257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	51	587	0	ENST00000396946.4:c.172G>C	p.Asp58His	p.D58H	ENST00000396946	NM_032415.4	58	Gat/Cat	3/25	0.221064993932999	3	FACETS	0.573	0.486	0.669	0.287	0.243	0.335	SUBCLONAL	1	FALSE	1	0.3	3		587	682	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0019451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	157	918	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.179386599958143	1	FACETS	0.947	0.868	1	0.947	0.868	1	INDETERMINATE	1	TRUE	0	0.314864133707513	1		918	887	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266713	198266713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776846119	NA	P-0019451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	49	543	0	ENST00000335508.6:c.2219G>A	p.Gly740Glu	p.G740E	ENST00000335508	NM_012433.2	740	gGa/gAa	15/25	1	2	FACETS	0.438	0.37	0.514	0.438	0.37	0.514	SUBCLONAL	1	TRUE	1	0.314864133707513	2		543	710	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843502	156843502	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1440909093	NA	P-0019451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	61	532	0	ENST00000524377.1:c.928G>A	p.Ala310Thr	p.A310T	ENST00000524377	NM_002529.3	310	Gca/Aca	8/17	0.314864133707513	3	FACETS	0.511	0.439	0.589	0.255	0.219	0.295	SUBCLONAL	1	TRUE	1	0.314864133707513	3		532	878	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012956	176012956	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0019451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	41	414	3	ENST00000367669.3:c.1422-2A>T		p.X474_splice	ENST00000367669	NM_022457.5	474			0.314864133707513	3	FACETS	0.426	0.354	0.507	0.213	0.177	0.254	SUBCLONAL	1	TRUE	1	0.314864133707513	3		417	707	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651135	206651135	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	169	864	0	ENST00000367120.3:c.745G>T	p.Ala249Ser	p.A249S	ENST00000367120	NM_014002.3	249	Gcc/Tcc	8/22	0.314864133707513	3	FACETS	1	0.953	1	0.527	0.484	0.573	CLONAL	1	TRUE	1	0.314864133707513	3		864	1178	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95578572	95578572	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	56	461	0	ENST00000393063.1:c.2053A>G	p.Ser685Gly	p.S685G	ENST00000393063	NM_030621.3	685	Agc/Ggc	14/28	1	2	FACETS	0.553	0.473	0.641	0.553	0.473	0.641	SUBCLONAL	1	TRUE	1	0.314864133707513	2		461	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578452	7578839	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGCGCGGACGCGGGTGCCGGGCGGGGGTGTGGAATCAACCCACAGCTGCACAGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAAGCAACTGGAAGACGGCAGCAAAGAAACAAACATGCGTAAGCACCTCCTGCAACCCACTAGCGAGCTAGAGAGAGTTGGCGTCTACACCTCAGGAGCTTTTCTTTTTTTTTTTTTTTTTTGAGATAGGGTCTTGCTCTGTCACTCAGGCTGGAGCACAGTGGTGTGATCACAGCTCACTGCAGCCTCCATCTCCTGGCCTCAAGTGATCTTCCCACCTCAGCCTCCTAAG	TGGCGCGGACGCGGGTGCCGGGCGGGGGTGTGGAATCAACCCACAGCTGCACAGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAAGCAACTGGAAGACGGCAGCAAAGAAACAAACATGCGTAAGCACCTCCTGCAACCCACTAGCGAGCTAGAGAGAGTTGGCGTCTACACCTCAGGAGCTTTTCTTTTTTTTTTTTTTTTTTGAGATAGGGTCTTGCTCTGTCACTCAGGCTGGAGCACAGTGGTGTGATCACAGCTCACTGCAGCCTCCATCTCCTGGCCTCAAGTGATCTTCCCACCTCAGCCTCCTAAG	-	novel	NA	P-0019451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	59	749	0	ENST00000269305.4:c.376-285_478del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	0.179386599958143	1	FACETS	0.352	0.301	0.407	0.352	0.301	0.407	INDETERMINATE	1	TRUE	0	0.314864133707513	1		749	898	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47672706	47672706	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	73	517	2	ENST00000233146.2:c.1296G>T	p.Leu432Phe	p.L432F	ENST00000233146	NM_000251.2	432	ttG/ttT	8/16	1	2	FACETS	0.564	0.492	0.642	0.564	0.492	0.642	SUBCLONAL	1	TRUE	1	0.314864133707513	2		519	822	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149434821	149434822	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0019451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	61	606	0	ENST00000286301.3:c.2632_2633delinsAA	p.Pro878Asn	p.P878N	ENST00000286301	NM_005211.3	878	CCt/AAt	20/22	1	2	FACETS	0.431	0.37	0.497	0.431	0.37	0.497	SUBCLONAL	1	TRUE	1	0.314864133707513	2		606	900	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798557	32798557	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	110	704	0	ENST00000374899.4:c.1299G>T	p.Met433Ile	p.M433I	ENST00000374899	NM_018833.2	433	atG/atT	8/12	1	2	FACETS	0.673	0.603	0.747	0.673	0.603	0.747	SUBCLONAL	1	TRUE	1	0.314864133707513	2		704	1038	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937145	39937145	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	62	822	0	ENST00000378444.4:c.38G>C	p.Ser13Thr	p.S13T	ENST00000378444	NM_001123385.1	13	aGc/aCc	2/15	1	2	FACETS	0.374	0.322	0.432	0.374	0.322	0.432	SUBCLONAL	1	TRUE	1	0.314864133707513	2		822	1052	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118705	115118715	+	frameshift_variant	Frame_Shift_Del	DEL	GTTGTTGGTGA	GTTGTTGGTGA	-	novel	NA	P-0019452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	269	805	0	ENST00000257566.3:c.626_636del	p.Leu209HisfsTer14	p.L209Hfs*14	ENST00000257566	NM_016569.3	209	cTCACCAACAAC/c	2/8	0.336135292332921	3	FACETS	0.887	0.832	0.943	0.887	0.832	0.943	CLONAL	2	TRUE	1	0.336135292332921	3		805	1054	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267361	198267361	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs754688962	NA	P-0019452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	352	841	0	ENST00000335508.6:c.1996A>G	p.Lys666Glu	p.K666E	ENST00000335508	NM_012433.2	666	Aag/Gag	14/25	0.309526553167268	4	FACETS	0.834	0.791	0.879			1	CLONAL	3	TRUE	NA	0.336135292332921	4		841	1118	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	60	553	2	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	0.1	2		555	855	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0019455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	14	440	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.46	0.33	0.618	0.46	0.33	0.618	SUBCLONAL	1	TRUE	1	0.1	2		441	609	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0019455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	17	555	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.559	0.415	0.732	0.559	0.415	0.732	SUBCLONAL	1	TRUE	1	0.1	2		556	608	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578419	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587781845	NA	P-0019456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	426	679	0	ENST00000269305.4:c.511G>T	p.Glu171Ter	p.E171*	ENST00000269305	NM_001126112.2	171	Gag/Tag	5/11	0.398386898221806	3	FACETS	0.846	0.812	0.88	0.846	0.812	0.88	CLONAL	3	TRUE	0	0.519712284801352	3		679	814	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571850	64571850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	199	980	2	ENST00000312049.6:c.1789G>A	p.Asp597Asn	p.D597N	ENST00000312049	NM_130799.2	597	Gac/Aac	10/10	0.463881988490939	3	FACETS	0.736	0.68	0.794			1	SUBCLONAL	1	TRUE	NA	0.519712284801352	3		982	1311	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245322	46245322	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	93	543	2	ENST00000334344.6:c.3416G>A	p.Gly1139Glu	p.G1139E	ENST00000334344	NM_152641.2	1139	gGa/gAa	15/21	0.307316991187679	3	FACETS	0.713	0.635	0.797	0.357	0.317	0.399	INDETERMINATE	1	TRUE	1	0.519712284801352	3		545	632	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420061	49420061	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	60	656	0	ENST00000301067.7:c.15688T>C	p.Cys5230Arg	p.C5230R	ENST00000301067	NM_003482.3	5230	Tgt/Cgt	48/54	0.307316991187679	3	FACETS	0.379	0.325	0.437	0.189	0.162	0.219	INDETERMINATE	1	TRUE	1	0.519712284801352	3		656	768	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589396	28589396	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	C	novel	NA	P-0019456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	201	543	0	ENST00000241453.7:c.2654-3C>G		p.X885_splice	ENST00000241453	NM_004119.2	885			0.519712284801352	3	FACETS	1	0.985	1	0.406	0.376	0.436	CLONAL	1	TRUE	0	0.519712284801352	3		543	801	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005660	42005660	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	56	404	0	ENST00000219905.7:c.3396G>C	p.Leu1132Phe	p.L1132F	ENST00000219905	NM_001164273.1	1132	ttG/ttC	9/24	0.327835819155907	2	FACETS	0.537	0.462	0.62	0.269	0.231	0.31	SUBCLONAL	1	TRUE	0	0.519712284801352	2		404	401	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661909	29661909	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs747678243	NA	P-0019456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	107	637	0	ENST00000356175.3:c.5803C>G	p.Leu1935Val	p.L1935V	ENST00000356175	NM_000267.3	1935	Cta/Gta	39/57	0.428127924721137	3	FACETS	0.68	0.61	0.754	0.34	0.305	0.377	SUBCLONAL	1	TRUE	1	0.519712284801352	3		637	763	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243523	41243523	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	155	797	0	ENST00000357654.3:c.4025C>A	p.Ser1342Ter	p.S1342*	ENST00000357654	NM_007294.3	1342	tCa/tAa	10/23	0.428127924721137	3	FACETS	0.813	0.744	0.886	0.407	0.372	0.443	CLONAL	1	TRUE	1	0.519712284801352	3		797	924	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218419	36218419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747829749	NA	P-0019456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	133	722	1	ENST00000222270.7:c.4198C>T	p.Arg1400Cys	p.R1400C	ENST00000222270	NM_014727.1	1400	Cgc/Tgc	16/37	0.387100527935228	4	FACETS	0.766	0.694	0.841	0.255	0.231	0.281	SUBCLONAL	1	TRUE	1	0.519712284801352	4		723	1016	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906843	50906843	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	89	620	0	ENST00000440232.2:c.1231C>T	p.Gln411Ter	p.Q411*	ENST00000440232	NM_002691.3	411	Cag/Tag	10/27	0.387100527935228	4	FACETS	0.691	0.612	0.775	0.23	0.204	0.259	SUBCLONAL	1	TRUE	1	0.519712284801352	4		620	753	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991682	25991682	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	98	540	0	ENST00000435504.4:c.560C>G	p.Ser187Cys	p.S187C	ENST00000435504		187	tCc/tGc	7/13	0.387100527935228	4	FACETS	0.784	0.699	0.874	0.261	0.233	0.292	SUBCLONAL	1	TRUE	1	0.519712284801352	4		540	731	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422464	225422464	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	188	713	0	ENST00000264414.4:c.176G>C	p.Arg59Thr	p.R59T	ENST00000264414	NM_003590.4	59	aGa/aCa	2/16	0.387100527935228	4	FACETS	1	0.99	1	0.497	0.46	0.535	CLONAL	1	TRUE	1	0.519712284801352	4		713	738	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62298822	62298822	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	295	793	1	ENST00000360203.5:c.615G>T	p.Arg205Ser	p.R205S	ENST00000360203	NM_001283009.1	205	agG/agT	8/35	0.352173043490961	5	FACETS	0.838	0.789	0.889			1	CLONAL	2	TRUE	NA	0.519712284801352	5		794	1205	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62320966	62320966	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	121	701	0	ENST00000360203.5:c.1990G>T	p.Asp664Tyr	p.D664Y	ENST00000360203	NM_001283009.1	664	Gat/Tat	23/35	0.352173043490961	5	FACETS	0.72	0.649	0.795			1	SUBCLONAL	1	TRUE	NA	0.519712284801352	5		701	1151	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553371	41553371	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	201	725	0	ENST00000263253.7:c.3460G>C	p.Asp1154His	p.D1154H	ENST00000263253	NM_001429.3	1154	Gac/Cac	18/31	0.519712284801352	5	FACETS	1	0.982	1	0.296	0.274	0.32	CLONAL	1	TRUE	1	0.519712284801352	5		725	1161	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52621383	52621383	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	135	712	0	ENST00000394830.3:c.3034G>C	p.Val1012Leu	p.V1012L	ENST00000394830	NM_018313.4	1012	Gtc/Ctc	20/30	0.390720730920873	2	FACETS	0.77	0.701	0.841	0.385	0.35	0.421	SUBCLONAL	1	TRUE	0	0.519712284801352	2		712	675	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72866509	72866509	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	58	526	0	ENST00000325599.8:c.754C>G	p.Gln252Glu	p.Q252E	ENST00000325599	NM_018130.2	252	Cag/Gag	7/11	0.390720730920873	2	FACETS	0.547	0.471	0.629	0.274	0.235	0.315	SUBCLONAL	1	TRUE	0	0.519712284801352	2		526	408	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138409969	138409969	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	78	627	0	ENST00000289153.2:c.1909C>G	p.Gln637Glu	p.Q637E	ENST00000289153	NM_006219.2	637	Caa/Gaa	13/22	0.295824441925126	5	FACETS	0.679	0.596	0.768			1	INDETERMINATE	1	TRUE	NA	0.519712284801352	5		627	787	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190777	185190777	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1400	116	611	0	ENST00000265026.3:c.1658G>C	p.Arg553Thr	p.R553T	ENST00000265026	NM_004721.4	553	aGa/aCa	11/14	0.519712284801352	8	FACETS	0.754	0.676	0.836			1	SUBCLONAL	1	TRUE	NA	0.519712284801352	8		611	1516	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001085	150001085	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	308	637	0	ENST00000253339.5:c.2519G>T	p.Gly840Val	p.G840V	ENST00000253339		840	gGt/gTt	4/7	0.427086429097034	3	FACETS	0.842	0.803	0.882	0.842	0.803	0.882	CLONAL	3	TRUE	0	0.519712284801352	3		637	591	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	92	600	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.918	0.816	1	0.918	0.816	1	CLONAL	1	TRUE	1	0.290926340899244	2		600	689	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0019458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	87	689	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.943	0.836	1	0.943	0.836	1	CLONAL	1	TRUE	1	0.290926340899244	2		689	634	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189412	56189412	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	106	598	0	ENST00000399503.3:c.4444C>T	p.Arg1482Ter	p.R1482*	ENST00000399503	NM_005921.1	1482	Cga/Tga	20/20	0.204765620952291	3	FACETS	0.899	0.804	0.999	0.449	0.402	0.5	CLONAL	1	TRUE	1	0.290926340899244	3		598	929	SUCCESS
AR	367	MSKCC	GRCh37	X	66943543	66943543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852581	NA	P-0019458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	99	463	0	ENST00000374690.3:c.2623C>T	p.His875Tyr	p.H875Y	ENST00000374690	NM_000044.3	875	Cat/Tat	8/8	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.290926340899244	2		463	667	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061463	38061463	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	90	614	0	ENST00000250448.2:c.526A>G	p.Ile176Val	p.I176V	ENST00000250448	NM_004496.3	176	Atc/Gtc	2/2	1	2	FACETS	0.856	0.759	0.959	0.856	0.759	0.959	CLONAL	1	TRUE	1	0.290926340899244	2		614	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0019460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	155	938	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.296515601829592	2	FACETS	1	0.987	1	0.705	0.649	0.764	CLONAL	1	TRUE	0	0.383461593647258	2		938	573	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948503	31948503	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	84	589	0	ENST00000375333.2:c.986G>T	p.Arg329Leu	p.R329L	ENST00000375333	NM_032454.1	329	cGg/cTg	7/8	0.383461593647258	4	FACETS	1	0.965	1	0.616	0.546	0.691	CLONAL	1	TRUE	2	0.383461593647258	4		589	492	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436075	49436075	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	40	506	0	ENST00000301067.7:c.5906C>A	p.Pro1969His	p.P1969H	ENST00000301067	NM_003482.3	1969	cCc/cAc	28/54	0.314915907159522	4	FACETS	0.943	0.787	1	0.472	0.393	0.558	CLONAL	1	TRUE	2	0.383461593647258	4		506	306	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31431786	31431786	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0019460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	39	638	0	ENST00000344624.3:c.3043-1G>C		p.X1015_splice	ENST00000344624		1015			0.383461593647258	4	FACETS	1	0.93	1	0.41	0.342	0.484	CLONAL	1	TRUE	1	0.383461593647258	4		638	229	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0019461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	161	594	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	0.143722166739637	5	FACETS	1	0.974	1	0.567	0.522	0.613	INDETERMINATE	2	TRUE	1	0.365337737876372	5		594	602	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0019461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	113	681	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.365337737876372	3	FACETS	0.833	0.749	0.922	0.417	0.374	0.461	CLONAL	1	TRUE	1	0.365337737876372	3		681	878	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225896	2225896	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1424	78	749	0	ENST00000326181.6:c.1688A>G	p.Tyr563Cys	p.Y563C	ENST00000326181	NM_032271.2	563	tAc/tGc	18/21	0.365337737876372	6	FACETS	0.492	0.43	0.559			1	SUBCLONAL	1	TRUE	NA	0.365337737876372	6		749	1502	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412639	139412639	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1037236860	NA	P-0019463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	45	874	3	ENST00000277541.6:c.1205C>T	p.Ser402Leu	p.S402L	ENST00000277541	NM_017617.3	402	tCg/tTg	7/34	0.380446406784301	3	FACETS	0.397	0.333	0.469	0.199	0.166	0.235	SUBCLONAL	1	TRUE	1	0.380446406784301	3		877	709	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711344	114711344	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	68	560	0	ENST00000543371.1:c.359C>T	p.Ser120Leu	p.S120L	ENST00000543371	NM_001198531.1	120	tCg/tTg	3/14	0.380446406784301	3	FACETS	1	0.892	1	0.511	0.446	0.581	CLONAL	1	TRUE	1	0.380446406784301	3		560	416	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248297	59248297	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	16	140	0	ENST00000371222.2:c.446C>A	p.Ser149Ter	p.S149*	ENST00000371222	NM_002228.3	149	tCg/tAg	1/1	1	2	FACETS	0.673	0.502	0.873	0.673	0.502	0.873	SUBCLONAL	1	TRUE	1	0.380446406784301	2		140	125	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666608	206666608	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	110	703	0	ENST00000367120.3:c.1942G>C	p.Glu648Gln	p.E648Q	ENST00000367120	NM_014002.3	648	Gag/Cag	20/22	0.380446406784301	6	FACETS	1	0.964	1	0.232	0.208	0.258	CLONAL	1	TRUE	1	0.380446406784301	6		703	877	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	495071	495071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	74	704	1	ENST00000399788.2:c.235G>A	p.Glu79Lys	p.E79K	ENST00000399788	NM_001042603.1	79	Gaa/Aaa	2/28	0.380446406784301	3	FACETS	0.971	0.852	1			1	CLONAL	1	TRUE	NA	0.380446406784301	3		705	477	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114246	115114247	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCT	novel	NA	P-0019463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	181	890	0	ENST00000257566.3:c.967_970dup	p.Val324GlufsTer4	p.V324Efs*4	ENST00000257566	NM_016569.3	324	gtg/gAGGGtg	6/8	0.380446406784301	2	FACETS	0.917	0.852	0.983	0.917	0.852	0.983	CLONAL	2	TRUE	0	0.380446406784301	2		890	519	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844098	68844099	+	splice_acceptor_variant	Splice_Site	DNP	AG	AG	CC	novel	NA	P-0019463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	111	610	0	ENST00000261769.5:c.688-2_688-1delinsCC		p.X230_splice	ENST00000261769	NM_004360.3	230			0.380446406784301	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.380446406784301	1		610	351	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11114044	11114044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	31	985	0	ENST00000358026.2:c.1972G>A	p.Glu658Lys	p.E658K	ENST00000358026	NM_001128849.1	658	Gaa/Aaa	13/36	1	2	FACETS	0.376	0.304	0.458	0.376	0.304	0.458	SUBCLONAL	1	TRUE	1	0.380446406784301	2		985	433	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748805	41748805	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs759103229	NA	P-0019463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	103	1067	0	ENST00000301178.4:c.1330C>G	p.Pro444Ala	p.P444A	ENST00000301178	NM_021913.4	444	Cct/Gct	11/20	1	2	FACETS	0.924	0.829	1	0.924	0.829	1	CLONAL	1	TRUE	1	0.380446406784301	2		1067	586	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023157	31023157	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	79	922	0	ENST00000375687.4:c.2642G>A	p.Arg881Lys	p.R881K	ENST00000375687	NM_015338.5	881	aGa/aAa	13/13	0.380446406784301	3	FACETS	0.895	0.789	1	0.448	0.394	0.505	CLONAL	1	TRUE	1	0.380446406784301	3		922	552	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191497	185191497	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	98	935	0	ENST00000265026.3:c.2378C>G	p.Ser793Cys	p.S793C	ENST00000265026	NM_004721.4	793	tCt/tGt	11/14	0.380446406784301	3	FACETS	0.866	0.773	0.965	0.433	0.386	0.483	CLONAL	1	TRUE	1	0.380446406784301	3		935	708	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970907	55970907	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	100	848	0	ENST00000263923.4:c.1890G>C	p.Lys630Asn	p.K630N	ENST00000263923	NM_002253.2	630	aaG/aaC	13/30	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.380446406784301	2		848	450	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032057	26032057	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561919033	NA	P-0019463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	110	499	0	ENST00000244661.2:c.232G>A	p.Asp78Asn	p.D78N	ENST00000244661	NM_003537.3	78	Gac/Aac	1/1	0.380446406784301	3	FACETS	0.889	0.806	0.976	0.889	0.806	0.976	CLONAL	2	TRUE	1	0.380446406784301	3		499	387	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962914	2962914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147823569	NA	P-0019463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	152	1070	2	ENST00000396946.4:c.1994C>T	p.Ser665Leu	p.S665L	ENST00000396946	NM_032415.4	665	tCg/tTg	16/25	0.380446406784301	3	FACETS	1	0.983	1	0.651	0.596	0.707	CLONAL	1	TRUE	1	0.380446406784301	3		1072	731	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984044	2984044	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	46	734	0	ENST00000396946.4:c.486G>C	p.Glu162Asp	p.E162D	ENST00000396946	NM_032415.4	162	gaG/gaC	5/25	0.380446406784301	3	FACETS	0.524	0.441	0.616	0.262	0.22	0.308	SUBCLONAL	1	TRUE	1	0.380446406784301	3		734	549	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860485	151860485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	84	840	0	ENST00000262189.6:c.10177G>A	p.Glu3393Lys	p.E3393K	ENST00000262189	NM_170606.2	3393	Gaa/Aaa	43/59	0.380446406784301	3	FACETS	0.919	0.813	1	0.459	0.406	0.516	CLONAL	1	TRUE	1	0.380446406784301	3		840	572	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860512	151860512	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	88	799	0	ENST00000262189.6:c.10150G>T	p.Glu3384Ter	p.E3384*	ENST00000262189	NM_170606.2	3384	Gaa/Taa	43/59	0.380446406784301	3	FACETS	0.983	0.873	1	0.492	0.436	0.551	CLONAL	1	TRUE	1	0.380446406784301	3		799	560	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151946966	151946967	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0019463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	57	646	0	ENST00000262189.6:c.1807_1808del	p.Ile603CysfsTer11	p.I603Cfs*11	ENST00000262189	NM_170606.2	603	ATt/t	13/59	0.380446406784301	3	FACETS	0.855	0.736	0.985	0.428	0.368	0.493	CLONAL	1	TRUE	1	0.380446406784301	3		646	417	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342625	87342625	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	89	756	0	ENST00000277120.3:c.910C>G	p.Pro304Ala	p.P304A	ENST00000277120		304	Cca/Gca	9/19	0.380446406784301	3	FACETS	1	0.927	1	0.528	0.47	0.591	CLONAL	1	TRUE	1	0.380446406784301	3		756	527	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	72	852	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.332	0.289	0.378	0.332	0.289	0.378	SUBCLONAL	1	TRUE	1	0.54	2		852	803	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	193	640	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.54	2		640	603	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	259	683	12	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.54	2		695	677	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	306	894	7	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	0.54	2		901	1030	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	49	678	4	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	1	2	FACETS	0.23	0.194	0.27	0.23	0.194	0.27	SUBCLONAL	1	TRUE	1	0.54	2		682	789	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	14	473	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.106	0.076	0.143	0.106	0.076	0.143	SUBCLONAL	1	TRUE	1	0.54	2		473	489	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	53	440	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.189773498978192	5	FACETS	0.473	0.402	0.551	0.158	0.134	0.184	INDETERMINATE	1	TRUE	2	0.54	5		441	751	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	119	448	0	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	2	FACETS	0.697	0.631	0.767	0.697	0.631	0.767	SUBCLONAL	1	TRUE	1	0.54	2		448	632	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	34	598	1	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.19	0.154	0.23	0.19	0.154	0.23	SUBCLONAL	1	TRUE	1	0.54	2		599	664	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760024	133760024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	272	941	0	ENST00000318560.5:c.2352del	p.Arg785GlyfsTer3	p.R785Gfs*3	ENST00000318560	NM_005157.4	783	Ccc/cc	11/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.54	2		941	949	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	302	668	7	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.971	0.925	1	1	0.996	1	CLONAL	2	TRUE	1	0.54	2		675	576	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	208	536	1	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.54	2		537	586	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188071	11188071	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	19	440	0	ENST00000361445.4:c.6023A>G	p.Gln2008Arg	p.Q2008R	ENST00000361445	NM_004958.3	2008	cAg/cGg	43/58	1	2	FACETS	0.193	0.146	0.249	0.193	0.146	0.249	SUBCLONAL	1	TRUE	1	0.54	2		440	364	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	71	757	4	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	0.343	0.299	0.391	0.343	0.299	0.391	SUBCLONAL	1	TRUE	1	0.54	2		761	767	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509485	46509485	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748855044	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	117	564	2	ENST00000262741.5:c.1246G>A	p.Ala416Thr	p.A416T	ENST00000262741	NM_003629.3	416	Gca/Aca	10/10	1	2	FACETS	0.778	0.704	0.855	0.778	0.704	0.855	SUBCLONAL	1	TRUE	1	0.54	2		566	557	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248285	59248285	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	12	93	1	ENST00000371222.2:c.458del	p.Gly153AlafsTer29	p.G153Afs*29	ENST00000371222	NM_002228.3	153	gGc/gc	1/1	1	2	FACETS	0.473	0.336	0.637	0.473	0.336	0.637	SUBCLONAL	1	TRUE	1	0.54	2		94	94	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175973	176175973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	29	277	1	ENST00000367669.3:c.142G>A	p.Val48Met	p.V48M	ENST00000367669	NM_022457.5	48	Gtg/Atg	1/20	1	2	FACETS	0.389	0.313	0.475	0.389	0.313	0.475	SUBCLONAL	1	TRUE	1	0.54	2		278	276	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206669462	206669462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	74	713	2	ENST00000367120.3:c.2135C>T	p.Ala712Val	p.A712V	ENST00000367120	NM_014002.3	712	gCa/gTa	22/22	1	2	FACETS	0.43	0.376	0.487	0.43	0.376	0.487	SUBCLONAL	1	TRUE	1	0.54	2		715	638	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615077	43615077	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	49	758	1	ENST00000355710.3:c.2491G>T	p.Gly831Cys	p.G831C	ENST00000355710	NM_020975.4	831	Ggc/Tgc	14/20	1	2	FACETS	0.323	0.274	0.378	0.323	0.274	0.378	SUBCLONAL	1	TRUE	1	0.54	2		759	561	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104353420	104353420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770678862	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	75	883	1	ENST00000369902.3:c.625C>T	p.His209Tyr	p.H209Y	ENST00000369902	NM_016169.3	209	Cac/Tac	5/12	1	2	FACETS	0.368	0.322	0.418	0.368	0.322	0.418	SUBCLONAL	1	TRUE	1	0.54	2		884	755	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518458	69518458	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	149	430	0	ENST00000294312.3:c.187C>T	p.Arg63Cys	p.R63C	ENST00000294312	NM_005117.2	63	Cgt/Tgt	1/3	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.54	2		430	457	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589692	69589692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs924238902	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	10	184	0	ENST00000168712.1:c.161C>T	p.Ser54Leu	p.S54L	ENST00000168712	NM_002007.2	54	tCg/tTg	1/3	1	2	FACETS	0.234	0.159	0.329	0.234	0.159	0.329	SUBCLONAL	1	TRUE	1	0.54	2		184	158	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633547	69633547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	163	513	4	ENST00000334134.2:c.155C>T	p.Thr52Met	p.T52M	ENST00000334134	NM_005247.2	52	aCg/aTg	1/3	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.54	2		517	522	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936141	71936141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543631142	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	23	376	0	ENST00000298229.2:c.113C>T	p.Ala38Val	p.A38V	ENST00000298229	NM_001567.3	38	gCg/gTg	1/28	1	2	FACETS	0.194	0.15	0.244	0.194	0.15	0.244	SUBCLONAL	1	TRUE	1	0.54	2		376	440	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998220	100998220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs534426691	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	179	594	1	ENST00000325455.5:c.1582G>A	p.Ala528Thr	p.A528T	ENST00000325455	NM_001202474.3	528	Gcc/Acc	1/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.54	2		595	551	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998289	100998289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	63	210	2	ENST00000325455.5:c.1513G>A	p.Ala505Thr	p.A505T	ENST00000325455	NM_001202474.3	505	Gcc/Acc	1/8	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.54	2		212	210	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216476	108216477	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587782558	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	14	279	0	ENST00000278616.4:c.8432dup	p.Ser2812ValfsTer3	p.S2812Vfs*3	ENST00000278616	NM_000051.3	2809	caa/cAaa	58/63	1	2	FACETS	0.192	0.138	0.257	0.192	0.138	0.257	SUBCLONAL	1	TRUE	1	0.54	2		279	270	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216609	108216609	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141534716	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	20	365	0	ENST00000278616.4:c.8558C>T	p.Thr2853Met	p.T2853M	ENST00000278616	NM_000051.3	2853	aCg/aTg	58/63	1	2	FACETS	0.209	0.159	0.267	0.209	0.159	0.267	SUBCLONAL	1	TRUE	1	0.54	2		365	355	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343356	118343356	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	103	387	0	ENST00000534358.1:c.1482G>T	p.Glu494Asp	p.E494D	ENST00000534358	NM_005933.3	494	gaG/gaT	3/36	1	2	FACETS	0.942	0.849	1	0.942	0.849	1	CLONAL	1	TRUE	1	0.54	2		387	405	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344146	118344146	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	190	607	0	ENST00000534358.1:c.2272A>G	p.Arg758Gly	p.R758G	ENST00000534358	NM_005933.3	758	Aga/Gga	3/36	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.54	2		607	700	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376016	118376016	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	43	591	0	ENST00000534358.1:c.9409G>T	p.Gly3137Ter	p.G3137*	ENST00000534358	NM_005933.3	3137	Gga/Tga	27/36	1	2	FACETS	0.289	0.241	0.342	0.289	0.241	0.342	SUBCLONAL	1	TRUE	1	0.54	2		591	551	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390420	118390420	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	79	724	0	ENST00000534358.1:c.11234A>G	p.Asn3745Ser	p.N3745S	ENST00000534358	NM_005933.3	3745	aAt/aGt	32/36	1	2	FACETS	0.428	0.376	0.483	0.428	0.376	0.483	SUBCLONAL	1	TRUE	1	0.54	2		724	684	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416219	416219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768337054	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	183	609	2	ENST00000399788.2:c.3967C>T	p.Arg1323Trp	p.R1323W	ENST00000399788	NM_001042603.1	1323	Cgg/Tgg	24/28	0.3	3	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.54	3		611	679	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435198	49435198	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1349513172	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	26	506	4	ENST00000301067.7:c.6355G>A	p.Ala2119Thr	p.A2119T	ENST00000301067	NM_003482.3	2119	Gct/Act	31/54	0.189773498978192	3	FACETS	0.256	0.202	0.318	0.128	0.101	0.159	INDETERMINATE	1	TRUE	1	0.54	3		510	478	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445614	49445614	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	383	1178	0	ENST00000301067.7:c.1852del	p.Ser618ProfsTer312	p.S618Pfs*312	ENST00000301067	NM_003482.3	618	Tcc/cc	10/54	0.189773498978192	3	FACETS	1	0.995	1	0.704	0.669	0.741	INDETERMINATE	1	TRUE	1	0.54	3		1178	1279	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480424	56480424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	47	712	0	ENST00000267101.3:c.531G>T	p.Lys177Asn	p.K177N	ENST00000267101	NM_001982.3	177	aaG/aaT	4/28	0.189773498978192	3	FACETS	0.257	0.216	0.303	0.129	0.108	0.152	INDETERMINATE	1	TRUE	1	0.54	3		712	859	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495715	56495715	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	71	560	0	ENST00000267101.3:c.3910del	p.His1304MetfsTer7	p.H1304Mfs*7	ENST00000267101	NM_001982.3	1302	gCc/gc	28/28	0.189773498978192	3	FACETS	0.637	0.557	0.724	0.319	0.278	0.362	INDETERMINATE	1	TRUE	1	0.54	3		560	524	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112190	115112190	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1450269147	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	246	635	0	ENST00000257566.3:c.1550C>T	p.Pro517Leu	p.P517L	ENST00000257566	NM_016569.3	517	cCg/cTg	7/8	0.189773498978192	3	FACETS	0.805	0.756	0.855	0.805	0.756	0.855	INDETERMINATE	2	TRUE	1	0.54	3		635	719	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112505	115112505	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	60	856	0	ENST00000257566.3:c.1235T>C	p.Val412Ala	p.V412A	ENST00000257566	NM_016569.3	412	gTc/gCc	7/8	0.189773498978192	3	FACETS	0.338	0.29	0.39	0.169	0.145	0.195	INDETERMINATE	1	TRUE	1	0.54	3		856	836	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120797	115120797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	55	527	0	ENST00000257566.3:c.209G>A	p.Gly70Glu	p.G70E	ENST00000257566	NM_016569.3	70	gGg/gAg	1/8	0.189773498978192	3	FACETS	0.515	0.441	0.596	0.258	0.22	0.298	INDETERMINATE	1	TRUE	1	0.54	3		527	502	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219487	133219487	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	147	868	4	ENST00000320574.5:c.4647del	p.Lys1550AsnfsTer12	p.K1550Nfs*12	ENST00000320574	NM_006231.2	1549	ccC/cc	36/49	0.189773498978192	3	FACETS	0.798	0.729	0.871	0.399	0.364	0.436	INDETERMINATE	1	TRUE	1	0.54	3		872	866	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245441	133245441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747929590	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	64	762	0	ENST00000320574.5:c.1879G>A	p.Val627Met	p.V627M	ENST00000320574	NM_006231.2	627	Gtg/Atg	17/49	0.189773498978192	3	FACETS	0.389	0.336	0.447	0.195	0.168	0.224	INDETERMINATE	1	TRUE	1	0.54	3		762	773	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	54	804	2	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	1	2	FACETS	0.235	0.2	0.274	0.235	0.2	0.274	SUBCLONAL	1	TRUE	1	0.54	2		806	851	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240333	41240333	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	108	532	0	ENST00000379561.5:c.17A>G	p.Gln6Arg	p.Q6R	ENST00000379561	NM_002015.3	6	cAg/cGg	1/3	1	2	FACETS	0.798	0.72	0.881	0.798	0.72	0.881	SUBCLONAL	1	TRUE	1	0.54	2		532	501	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438211	110438211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756734259	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	16	230	1	ENST00000375856.3:c.190G>A	p.Gly64Arg	p.G64R	ENST00000375856	NM_003749.2	64	Ggg/Agg	1/2	1	2	FACETS	0.236	0.174	0.31	0.236	0.174	0.31	SUBCLONAL	1	TRUE	1	0.54	2		231	251	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988327	36988327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	60	627	1	ENST00000354822.5:c.326C>T	p.Ser109Leu	p.S109L	ENST00000354822	NM_001079668.2	109	tCg/tTg	2/3	1	2	FACETS	0.408	0.351	0.469	0.408	0.351	0.469	SUBCLONAL	1	TRUE	1	0.54	2		628	545	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	57	547	2	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.304	0.26	0.352	0.304	0.26	0.352	SUBCLONAL	1	TRUE	1	0.54	2		549	695	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40679406	40679406	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	88	693	1	ENST00000249776.8:c.484G>A	p.Gly162Ser	p.G162S	ENST00000249776	NM_033286.3	162	Ggc/Agc	4/9	1	2	FACETS	0.433	0.384	0.487	0.433	0.384	0.487	SUBCLONAL	1	TRUE	1	0.54	2		694	752	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041422	42041424	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs775361103	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	174	666	0	ENST00000219905.7:c.5622_5624del	p.Ser1875del	p.S1875del	ENST00000219905	NM_001164273.1	1873	TCT/-	17/24	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.54	2		666	581	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396234	396234	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	63	674	4	ENST00000262320.3:c.792del	p.Gly265GlufsTer149	p.G265Efs*149	ENST00000262320	NM_003502.3	264	ccC/cc	2/11	1	2	FACETS	0.328	0.283	0.377	0.328	0.283	0.377	SUBCLONAL	1	TRUE	1	0.54	2		678	711	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134575	2134575	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142848358	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	40	816	3	ENST00000219476.3:c.4352G>A	p.Arg1451His	p.R1451H	ENST00000219476	NM_000548.3	1451	cGc/cAc	34/42	1	2	FACETS	0.201	0.166	0.24	0.201	0.166	0.24	SUBCLONAL	1	TRUE	1	0.54	2		819	737	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225955	2225955	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs756230613	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	31	665	2	ENST00000326181.6:c.1746+1G>A		p.X582_splice	ENST00000326181	NM_032271.2	582			1	2	FACETS	0.192	0.154	0.234	0.192	0.154	0.234	SUBCLONAL	1	TRUE	1	0.54	2		667	599	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858517	9858517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765370528	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	49	623	0	ENST00000330684.3:c.2884G>A	p.Glu962Lys	p.E962K	ENST00000330684	NM_001134407.1	962	Gaa/Aaa	13/13	1	2	FACETS	0.277	0.234	0.324	0.277	0.234	0.324	SUBCLONAL	1	TRUE	1	0.54	2		623	656	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133281	30133283	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	207	748	0	ENST00000263025.4:c.215_217del	p.Lys72del	p.K72del	ENST00000263025	NM_002746.2	72	aAGAtc/atc	2/9	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.54	2		748	719	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116167	67116167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	176	634	0	ENST00000412916.2:c.451C>T	p.Arg151Cys	p.R151C	ENST00000412916		151	Cgc/Tgc	5/6	1	2	FACETS	0.957	0.885	1	0.957	0.885	1	CLONAL	1	TRUE	1	0.54	2		634	681	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953228	81953228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369760877	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	90	348	0	ENST00000359376.3:c.2194C>T	p.Arg732Cys	p.R732C	ENST00000359376	NM_002661.3	732	Cgc/Tgc	20/33	1	2	FACETS	0.939	0.84	1	0.939	0.84	1	CLONAL	1	TRUE	1	0.54	2		348	355	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836659	89836659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	232	889	0	ENST00000389301.3:c.2231C>T	p.Pro744Leu	p.P744L	ENST00000389301	NM_000135.2	744	cCc/cTc	25/43	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.54	2		889	756	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574030	7574030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769934890	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	46	646	0	ENST00000269305.4:c.997C>T	p.Arg333Cys	p.R333C	ENST00000269305	NM_001126112.2	333	Cgt/Tgt	10/11	1	2	FACETS	0.218	0.183	0.257	0.218	0.183	0.257	SUBCLONAL	1	TRUE	1	0.54	2		646	782	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	79	908	0	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	1	2	FACETS	0.357	0.313	0.404	0.357	0.313	0.404	SUBCLONAL	1	TRUE	1	0.54	2		908	819	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032541	12032541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267604739	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	159	539	0	ENST00000353533.5:c.977C>T	p.Pro326Leu	p.P326L	ENST00000353533	NM_003010.3	326	cCg/cTg	9/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.54	2		539	490	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942857	15942857	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	33	664	1	ENST00000268712.3:c.6845A>G	p.His2282Arg	p.H2282R	ENST00000268712	NM_006311.3	2282	cAt/cGt	44/46	1	2	FACETS	0.195	0.158	0.236	0.195	0.158	0.236	SUBCLONAL	1	TRUE	1	0.54	2		665	628	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486049	29486050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	112	575	0	ENST00000356175.3:c.233dup	p.Asn78LysfsTer29	p.N78Kfs*29	ENST00000356175	NM_000267.3	76	gaa/gAaa	3/57	1	2	FACETS	0.75	0.677	0.827	0.75	0.677	0.827	SUBCLONAL	1	TRUE	1	0.54	2		575	553	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29579995	29579996	+	intron_variant	Intron	INS	-	-	A	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	33	619	0	ENST00000356175.3:c.4110+3865dup		p.*1370*	ENST00000356175	NM_000267.3	1384/2839			1	2	FACETS	0.201	0.163	0.244	0.201	0.163	0.244	SUBCLONAL	1	TRUE	1	0.54	2		619	608	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325864	30325864	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	33	666	0	ENST00000322652.5:c.2062T>A	p.Leu688Ile	p.L688I	ENST00000322652	NM_015355.2	688	Tta/Ata	16/16	1	2	FACETS	0.205	0.167	0.249	0.205	0.167	0.249	SUBCLONAL	1	TRUE	1	0.54	2		666	595	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	141	710	3	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	0.754	0.688	0.822	0.754	0.688	0.822	SUBCLONAL	1	TRUE	1	0.54	2		713	693	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78829286	78829286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	62	665	0	ENST00000306801.3:c.1337G>A	p.Arg446Gln	p.R446Q	ENST00000306801	NM_020761.2	446	cGg/cAg	12/34	1	2	FACETS	0.328	0.283	0.377	0.328	0.283	0.377	SUBCLONAL	1	TRUE	1	0.54	2		665	700	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619799	1619799	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs535113552	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	50	862	1	ENST00000344749.5:c.1147G>A	p.Asp383Asn	p.D383N	ENST00000344749	NM_001136139.2	383	Gac/Aac	14/19	1	2	FACETS	0.195	0.165	0.229	0.195	0.165	0.229	SUBCLONAL	1	TRUE	1	0.54	2		863	949	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2229782	2229782	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs754384597	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	141	754	0	ENST00000398665.3:c.4607-2A>G		p.X1536_splice	ENST00000398665	NM_032482.2	1536			1	2	FACETS	0.687	0.627	0.751	0.687	0.627	0.751	SUBCLONAL	1	TRUE	1	0.54	2		754	760	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210512	5210512	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	63	686	0	ENST00000357368.4:c.5455A>G	p.Ile1819Val	p.I1819V	ENST00000357368	NM_002850.3	1819	Atc/Gtc	35/38	1	2	FACETS	0.331	0.286	0.38	0.331	0.286	0.38	SUBCLONAL	1	TRUE	1	0.54	2		686	705	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229545	5229545	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	91	251	0	ENST00000357368.4:c.2306G>A	p.Arg769His	p.R769H	ENST00000357368	NM_002850.3	769	cGc/cAc	15/38	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.54	2		251	254	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272201	15272201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113178142	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	51	614	2	ENST00000263388.2:c.6238C>T	p.Arg2080Trp	p.R2080W	ENST00000263388	NM_000435.2	2080	Cgg/Tgg	33/33	1	2	FACETS	0.408	0.347	0.475	0.408	0.347	0.475	SUBCLONAL	1	TRUE	1	0.54	2		616	463	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353974	15353974	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	51	235	0	ENST00000263377.2:c.2906A>T	p.Gln969Leu	p.Q969L	ENST00000263377	NM_058243.2	969	cAg/cTg	14/20	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.54	2		235	187	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379880	17379880	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	58	1080	0	ENST00000359435.4:c.265G>A	p.Val89Ile	p.V89I	ENST00000359435	NM_001033549.1	89	Gtc/Atc	2/9	1	2	FACETS	0.202	0.173	0.235	0.202	0.173	0.235	SUBCLONAL	1	TRUE	1	0.54	2		1080	1062	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955187	17955187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs896064879	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	112	908	0	ENST00000458235.1:c.40C>T	p.Arg14Cys	p.R14C	ENST00000458235	NM_000215.3	14	Cgt/Tgt	2/24	1	2	FACETS	0.449	0.403	0.498	0.449	0.403	0.498	SUBCLONAL	1	TRUE	1	0.54	2		908	923	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966829	18966829	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	265	851	0	ENST00000262803.5:c.1640A>G	p.Lys547Arg	p.K547R	ENST00000262803	NM_002911.3	547	aAg/aGg	12/24	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.54	2		851	954	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212225	36212225	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1311247867	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	395	799	0	ENST00000222270.7:c.1976T>C	p.Leu659Pro	p.L659P	ENST00000222270	NM_014727.1	659	cTg/cCg	3/37	0.3	3	FACETS	0.953	0.909	0.997			1	INDETERMINATE	2	TRUE	NA	0.54	3		799	975	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919935	50919935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1044937882	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	139	795	0	ENST00000440232.2:c.3022C>T	p.Arg1008Cys	p.R1008C	ENST00000440232	NM_002691.3	1008	Cgc/Tgc	24/27	1	2	FACETS	0.686	0.625	0.749	0.686	0.625	0.749	SUBCLONAL	1	TRUE	1	0.54	2		795	751	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25458619	25458619	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs746967478	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	162	605	0	ENST00000264709.3:c.2554A>G	p.Met852Val	p.M852V	ENST00000264709	NM_175629.2	852	Atg/Gtg	22/23	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.54	2		605	583	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467482	25467484	+	inframe_deletion	In_Frame_Del	DEL	CGT	CGT	-	rs753742392	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	70	684	2	ENST00000264709.3:c.1592_1594del	p.Asp531del	p.D531del	ENST00000264709	NM_175629.2	531	gACGgc/ggc	14/23	1	2	FACETS	0.332	0.289	0.379	0.332	0.289	0.379	SUBCLONAL	1	TRUE	1	0.54	2		686	781	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607815	46607816	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	80	918	0	ENST00000263734.3:c.2009dup	p.Val671CysfsTer45	p.V671Cfs*45	ENST00000263734	NM_001430.4	668	-/C	12/16	1	2	FACETS	0.334	0.293	0.378	0.334	0.293	0.378	SUBCLONAL	1	TRUE	1	0.54	2		918	887	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147565	61147565	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	13	45	0	ENST00000295025.8:c.970A>G	p.Thr324Ala	p.T324A	ENST00000295025	NM_002908.2	324	Aca/Gca	9/11	1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	1	0.54	2		45	40	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660251	227660252	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	167	618	2	ENST00000305123.5:c.3203dup	p.Met1069HisfsTer12	p.M1069Hfs*12	ENST00000305123	NM_005544.2	1068	ggc/ggGc	1/2	1	2	FACETS	0.963	0.889	1	0.963	0.889	1	CLONAL	1	TRUE	1	0.54	2		620	642	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	71	970	2	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.344	0.299	0.392	0.344	0.299	0.392	SUBCLONAL	1	TRUE	1	0.54	2		972	765	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	55	195	2	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	0.189773498978192	5	FACETS	1	0.933	1	0.74	0.646	0.839	INDETERMINATE	2	TRUE	2	0.54	5		197	166	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012647	36012647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1437496392	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	172	319	0	ENST00000358208.4:c.91G>A	p.Ala31Thr	p.A31T	ENST00000358208		31	Gct/Act	2/12	0.189773498978192	5	FACETS	1	0.983	1	0.797	0.74	0.856	INDETERMINATE	2	TRUE	2	0.54	5		319	482	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728761	39728762	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	267	635	0	ENST00000361337.2:c.1045_1046del	p.Arg349AspfsTer3	p.R349Dfs*3	ENST00000361337	NM_003286.2	347	aaAGag/aaag	12/21	0.189773498978192	5	FACETS	0.956	0.898	1	0.637	0.599	0.677	INDETERMINATE	2	TRUE	2	0.54	5		635	936	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478633	57478633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1131691999	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	58	656	1	ENST00000371085.3:c.305C>T	p.Ala102Val	p.A102V	ENST00000371085	NM_000516.4	102	gCg/gTg	4/13	0.189773498978192	5	FACETS	0.369	0.315	0.427	0.123	0.105	0.143	INDETERMINATE	1	TRUE	2	0.54	5		657	1055	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564828	41564828	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	74	770	1	ENST00000263253.7:c.4129C>T	p.His1377Tyr	p.H1377Y	ENST00000263253	NM_001429.3	1377	Cat/Tat	25/31	1	2	FACETS	0.34	0.297	0.387	0.34	0.297	0.387	SUBCLONAL	1	TRUE	1	0.54	2		771	805	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12632347	12632347	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	53	667	0	ENST00000251849.4:c.1320del	p.Gln441ArgfsTer5	p.Q441Rfs*5	ENST00000251849	NM_002880.3	440	ttT/tt	12/17	1	2	FACETS	0.266	0.226	0.31	0.266	0.226	0.31	SUBCLONAL	1	TRUE	1	0.54	2		667	739	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934243	49934243	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1407832113	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	185	798	2	ENST00000296474.3:c.2264del	p.Gly755ValfsTer19	p.G755Vfs*19	ENST00000296474	NM_002447.2	755	gGt/gt	8/20	1	2	FACETS	0.941	0.872	1	0.941	0.872	1	CLONAL	1	TRUE	1	0.54	2		800	728	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438516	52438518	+	missense_variant	Missense_Mutation	TNP	ATA	ATA	CTC	rs1553645128	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	155	833	0	ENST00000460680.1:c.1201_1203delinsGAG	p.Tyr401Glu	p.Y401E	ENST00000460680	NM_004656.3	401	TAT/GAG	12/17	1	2	FACETS	0.866	0.795	0.939	0.866	0.795	0.939	CLONAL	1	TRUE	1	0.54	2		833	663	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134872997	134872997	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	86	562	0	ENST00000398015.3:c.1301C>A	p.Pro434His	p.P434H	ENST00000398015	NM_004441.4	434	cCc/cAc	6/16	1	2	FACETS	0.664	0.589	0.743	0.664	0.589	0.743	SUBCLONAL	1	TRUE	1	0.54	2		562	480	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	28	541	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	1	2	FACETS	0.204	0.162	0.251	0.204	0.162	0.251	SUBCLONAL	1	TRUE	1	0.54	2		541	509	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447436	187447436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886560305	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	148	652	0	ENST00000232014.4:c.757G>A	p.Val253Met	p.V253M	ENST00000232014	NM_001130845.1	253	Gtg/Atg	5/10	1	2	FACETS	0.774	0.709	0.843	0.774	0.709	0.843	SUBCLONAL	1	TRUE	1	0.54	2		652	708	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801053	1801053	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1480286871	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	95	987	2	ENST00000260795.2:c.182G>A	p.Cys61Tyr	p.C61Y	ENST00000260795		61	tGt/tAt	2/17	1	2	FACETS	0.413	0.367	0.462	0.413	0.367	0.462	SUBCLONAL	1	TRUE	1	0.54	2		989	852	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280032	66280032	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	20	364	0	ENST00000273854.3:c.1657C>T	p.Arg553Ter	p.R553*	ENST00000273854	NM_004439.5	553	Cga/Tga	7/18	1	2	FACETS	0.201	0.153	0.257	0.201	0.153	0.257	SUBCLONAL	1	TRUE	1	0.54	2		364	369	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532624	187532624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200112487	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	150	545	0	ENST00000441802.2:c.9769C>T	p.Arg3257Trp	p.R3257W	ENST00000441802	NM_005245.3	3257	Cgg/Tgg	14/27	0.3	3	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.54	3		545	568	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628340	187628340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536104649	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	112	667	1	ENST00000441802.2:c.2642G>A	p.Arg881His	p.R881H	ENST00000441802	NM_005245.3	881	cGc/cAc	2/27	0.3	3	FACETS	0.681	0.612	0.753			1	INDETERMINATE	1	TRUE	NA	0.54	3		668	774	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293871	1293871	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756954938	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	227	1069	1	ENST00000310581.5:c.1130G>A	p.Arg377His	p.R377H	ENST00000310581	NM_198253.2	377	cGc/cAc	2/16	1	2	FACETS	0.848	0.791	0.908	0.848	0.791	0.908	CLONAL	1	TRUE	1	0.54	2		1070	991	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409418	31409418	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	64	693	0	ENST00000344624.3:c.3689T>C	p.Ile1230Thr	p.I1230T	ENST00000344624		1230	aTt/aCt	29/33	1	2	FACETS	0.315	0.272	0.361	0.315	0.272	0.361	SUBCLONAL	1	TRUE	1	0.54	2		693	753	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876095	35876095	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	130	431	0	ENST00000303115.3:c.887T>C	p.Val296Ala	p.V296A	ENST00000303115	NM_002185.3	296	gTg/gCg	8/8	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.54	2		431	450	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673711	176673711	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs570278338	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	97	504	0	ENST00000439151.2:c.4411C>T	p.Arg1471Ter	p.R1471*	ENST00000439151	NM_022455.4	1471	Cga/Tga	10/23	1	2	FACETS	0.559	0.499	0.623	0.559	0.499	0.623	SUBCLONAL	1	TRUE	1	0.54	2		504	643	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056541	26056541	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	66	280	0	ENST00000343677.2:c.116del	p.Pro39ArgfsTer24	p.P39Rfs*24	ENST00000343677	NM_005319.3	39	cCg/cg	1/1	1	2	FACETS	0.889	0.779	1	0.889	0.779	1	CLONAL	1	TRUE	1	0.54	2		280	275	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324567	31324567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151341161	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	53	591	0	ENST00000412585.2:c.241C>T	p.Pro81Ser	p.P81S	ENST00000412585	NM_005514.6	81	Ccg/Tcg	2/8	1	2	FACETS	0.305	0.259	0.355	0.305	0.259	0.355	SUBCLONAL	1	TRUE	1	0.54	2		591	644	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163846	32163846	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	144	538	1	ENST00000375023.3:c.5380G>T	p.Glu1794Ter	p.E1794*	ENST00000375023	NM_004557.3	1794	Gag/Tag	30/30	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.54	2		539	498	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964420	93964420	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1422163923	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	35	690	0	ENST00000369303.4:c.2477T>C	p.Met826Thr	p.M826T	ENST00000369303	NM_004440.3	826	aTg/aCg	14/17	0.199700937872357	1	FACETS	0.161	0.131	0.195	0.161	0.131	0.195	INDETERMINATE	1	TRUE	0	0.54	1		690	587	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265394	152265394	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	113	560	4	ENST00000206249.3:c.847G>T	p.Ala283Ser	p.A283S	ENST00000206249	NM_000125.3	283	Gct/Tct	4/8	0.199700937872357	1	FACETS	0.601	0.544	0.662	0.601	0.544	0.662	INDETERMINATE	1	TRUE	0	0.54	1		564	508	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940395	13940395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1007679355	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	163	560	0	ENST00000405192.2:c.1111C>T	p.Arg371Cys	p.R371C	ENST00000405192	NM_001163147.1	371	Cgc/Tgc	11/12	1	2	FACETS	0.996	0.919	1	0.996	0.919	1	CLONAL	1	TRUE	1	0.54	2		560	606	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729844	41729844	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs908163566	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	90	362	0	ENST00000242208.4:c.685C>T	p.Arg229Trp	p.R229W	ENST00000242208	NM_002192.2	229	Cgg/Tgg	3/3	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.54	2		362	318	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509806	106509806	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	54	780	1	ENST00000359195.3:c.1800G>T	p.Gln600His	p.Q600H	ENST00000359195	NM_002649.2	600	caG/caT	2/11	1	2	FACETS	0.27	0.23	0.314	0.27	0.23	0.314	SUBCLONAL	1	TRUE	1	0.54	2		781	741	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339370	116339370	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	26	478	0	ENST00000397752.3:c.232C>A	p.Leu78Ile	p.L78I	ENST00000397752	NM_000245.2	78	Ctt/Att	2/21	1	2	FACETS	0.229	0.181	0.285	0.229	0.181	0.285	SUBCLONAL	1	TRUE	1	0.54	2		478	420	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151216593	151216593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	76	206	1	ENST00000262187.5:c.5C>T	p.Pro2Leu	p.P2L	ENST00000262187	NM_005614.3	2	cCg/cTg	1/8	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.54	2		207	229	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151866289	151866289	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	90	709	0	ENST00000262189.6:c.9499T>G	p.Phe3167Val	p.F3167V	ENST00000262189	NM_170606.2	3167	Ttt/Gtt	41/59	1	2	FACETS	0.426	0.377	0.478	0.426	0.377	0.478	SUBCLONAL	1	TRUE	1	0.54	2		709	783	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	370	630	24	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	1	2	FACETS	0.933	0.893	0.974	1	0.997	1	CLONAL	2	TRUE	1	0.54	2		654	734	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38173513	38173513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	92	610	2	ENST00000317025.8:c.1903C>T	p.Arg635Cys	p.R635C	ENST00000317025	NM_023034.1	635	Cgc/Tgc	10/24	1	2	FACETS	0.475	0.422	0.532	0.475	0.422	0.532	SUBCLONAL	1	TRUE	1	0.54	2		612	717	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371995	55371995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	38	673	2	ENST00000297316.4:c.685G>A	p.Gly229Ser	p.G229S	ENST00000297316	NM_022454.3	229	Ggc/Agc	2/2	1	2	FACETS	0.214	0.176	0.256	0.214	0.176	0.256	SUBCLONAL	1	TRUE	1	0.54	2		675	658	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340351	8340351	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	31	461	0	ENST00000356435.5:c.5245del	p.Met1749TrpfsTer23	p.M1749Wfs*23	ENST00000356435		1749	Atg/tg	31/35	1	2	FACETS	0.235	0.19	0.287	0.235	0.19	0.287	SUBCLONAL	1	TRUE	1	0.54	2		461	488	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499763	8499763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745717615	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	151	655	3	ENST00000356435.5:c.2206G>A	p.Val736Met	p.V736M	ENST00000356435		736	Gtg/Atg	14/35	1	2	FACETS	0.893	0.82	0.97	0.893	0.82	0.97	CLONAL	1	TRUE	1	0.54	2		658	626	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293628	137293628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	196	962	0	ENST00000481739.1:c.179G>A	p.Gly60Asp	p.G60D	ENST00000481739	NM_002957.4	60	gGc/gAc	2/10	1	2	FACETS	0.832	0.771	0.896	0.832	0.771	0.896	CLONAL	1	TRUE	1	0.54	2		962	872	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028845	47028845	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	42	800	2	ENST00000377604.3:c.149G>A	p.Ser50Asn	p.S50N	ENST00000377604	NM_001204468.1	50	aGc/aAc	3/24	1	2	FACETS	0.205	0.17	0.244	0.205	0.17	0.244	SUBCLONAL	1	TRUE	1	0.54	2		802	758	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040987	47040987	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	162	753	1	ENST00000377604.3:c.1517G>A	p.Gly506Asp	p.G506D	ENST00000377604	NM_001204468.1	506	gGc/gAc	14/24	1	2	FACETS	0.762	0.7	0.827	0.762	0.7	0.827	SUBCLONAL	1	TRUE	1	0.54	2		754	787	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650481	48650481	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	249	1030	0	ENST00000376670.3:c.451G>A	p.Ala151Thr	p.A151T	ENST00000376670	NM_002049.3	151	Gca/Aca	3/6	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.54	2		1030	841	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411678	63411678	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	218	889	0	ENST00000330258.3:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000330258	NM_152424.3	497	Cga/Tga	2/2	1	2	FACETS	0.969	0.903	1	0.969	0.903	1	CLONAL	1	TRUE	1	0.54	2		889	833	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344155	70344155	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	149	652	3	ENST00000374080.3:c.1894del	p.Arg632GlyfsTer79	p.R632Gfs*79	ENST00000374080		631	Ccc/cc	13/45	1	2	FACETS	0.903	0.828	0.981	0.903	0.828	0.981	CLONAL	1	TRUE	1	0.54	2		655	611	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357196	70357196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200663107	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	41	682	1	ENST00000374080.3:c.5711C>T	p.Ala1904Val	p.A1904V	ENST00000374080		1904	gCg/gTg	39/45	1	2	FACETS	0.23	0.191	0.274	0.23	0.191	0.274	SUBCLONAL	1	TRUE	1	0.54	2		683	659	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608214	100608214	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1193720975	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	169	674	0	ENST00000308731.7:c.1876G>T	p.Val626Leu	p.V626L	ENST00000308731	NM_000061.2	626	Gta/Tta	18/19	1	2	FACETS	0.961	0.887	1	0.961	0.887	1	CLONAL	1	TRUE	1	0.54	2		674	651	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52676062	52676062	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0019464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	132	348	1	ENST00000394830.3:c.996-1G>C		p.X332_splice	ENST00000394830	NM_018313.4	332			1	2	FACETS	0.986	0.9	1	0.986	0.9	1	CLONAL	1	TRUE	1	0.54	2		349	496	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0019466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	61	1185	3	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.728948324296203	1	FACETS	0.146	0.125	0.168	0.146	0.125	0.168	SUBCLONAL	1	TRUE	0	0.728948324296203	1		1188	729	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68878170	68878170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138522390	NA	P-0019466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	90	646	0	ENST00000487270.1:c.883G>A	p.Ala295Thr	p.A295T	ENST00000487270	NM_133509.3	295	Gca/Aca	9/11	1	2	FACETS	0.394	0.35	0.441	0.394	0.35	0.441	SUBCLONAL	1	TRUE	1	0.728948324296203	2		646	627	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670088	29670088	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	391	991	0	ENST00000356175.3:c.7061del	p.Asp2354ValfsTer21	p.D2354Vfs*21	ENST00000356175	NM_000267.3	2354	gAt/gt	47/57	0.728948324296203	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.728948324296203	1		991	640	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905989	50905989	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41554817	NA	P-0019466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	336	1094	1	ENST00000440232.2:c.961G>A	p.Gly321Ser	p.G321S	ENST00000440232	NM_002691.3	321	Ggc/Agc	8/27	0.728948324296203	1	FACETS	0.956	0.914	0.997	0.956	0.914	0.997	CLONAL	1	TRUE	0	0.728948324296203	1		1095	613	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293540	137293540	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	536	1546	0	ENST00000481739.1:c.91C>G	p.Pro31Ala	p.P31A	ENST00000481739	NM_002957.4	31	Ccc/Gcc	2/10	0.728948324296203	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.728948324296203	1		1546	923	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938619	76938619	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	306	1091	0	ENST00000373344.5:c.2129A>G	p.Asn710Ser	p.N710S	ENST00000373344	NM_000489.3	710	aAt/aGt	9/35	1	2	FACETS	0.859	0.811	0.908	0.859	0.811	0.908	CLONAL	1	TRUE	1	0.728948324296203	2		1091	977	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0019467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	76	918	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.347225703268593	2		918	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0019467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	119	938	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.347225703268593	2		938	516	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651537	206651537	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	134	678	1	ENST00000367120.3:c.847A>T	p.Asn283Tyr	p.N283Y	ENST00000367120	NM_014002.3	283	Aac/Tac	9/22	0.347225703268593	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.347225703268593	3		679	418	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220691	1220691	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs878853247	NA	P-0019467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	165	1079	2	ENST00000326873.7:c.709G>T	p.Asp237Tyr	p.D237Y	ENST00000326873	NM_000455.4	237	Gac/Tac	5/10	0.328846605096891	2	FACETS	0.773	0.713	0.835	0.773	0.713	0.835	SUBCLONAL	2	TRUE	0	0.347225703268593	2		1081	615	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113723	11113723	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1568455217	NA	P-0019467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	150	969	0	ENST00000358026.2:c.1831C>T	p.Gln611Ter	p.Q611*	ENST00000358026	NM_001128849.1	611	Cag/Tag	12/36	0.328846605096891	2	FACETS	0.801	0.737	0.868	0.801	0.737	0.868	CLONAL	2	TRUE	0	0.347225703268593	2		969	539	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950446	68950446	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	61	796	0	ENST00000288368.4:c.758T>A	p.Leu253Gln	p.L253Q	ENST00000288368	NM_024870.2	253	cTg/cAg	7/40	0.347225703268593	1	FACETS	0.844	0.732	0.964	0.844	0.732	0.964	CLONAL	1	TRUE	0	0.347225703268593	1		796	344	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412571	63412571	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	79	435	0	ENST00000330258.3:c.596G>T	p.Arg199Met	p.R199M	ENST00000330258	NM_152424.3	199	aGg/aTg	2/2	1	1	FACETS	0.855	0.765	0.947	1	0.983	1	CLONAL	2	TRUE	0	0.347225703268593	1		435	220	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0019469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	49	918	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.8	0.676	0.937	0.8	0.676	0.937	CLONAL	1	TRUE	1	0.16	2		918	766	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218020	108218020	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	66	523	0	ENST00000278616.4:c.8599G>A	p.Gly2867Arg	p.G2867R	ENST00000278616	NM_000051.3	2867	Gga/Aga	59/63	1	2	FACETS	0.796	0.692	0.909	1	0.974	1	CLONAL	2	TRUE	1	0.16	2		523	518	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813301	102813301	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	36	590	1	ENST00000307046.8:c.388C>A	p.Pro130Thr	p.P130T	ENST00000307046	NM_001111285.1	130	Ccc/Acc	3/4	1	2	FACETS	0.849	0.697	1	0.849	0.697	1	CLONAL	1	TRUE	1	0.16	2		591	530	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992287	72992287	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	70	1152	1	ENST00000268489.5:c.1758G>T	p.Arg586Ser	p.R586S	ENST00000268489	NM_006885.3	586	agG/agT	2/10	1	2	FACETS	0.848	0.737	0.968	0.848	0.737	0.968	CLONAL	1	TRUE	1	0.16	2		1153	1032	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790122	40790122	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs372056802	NA	P-0019469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	37	740	0	ENST00000373198.4:c.2609G>T	p.Arg870Leu	p.R870L	ENST00000373198	NM_133170.3	870	cGc/cTc	18/32	1	2	FACETS	0.715	0.588	0.858	0.715	0.588	0.858	SUBCLONAL	1	TRUE	1	0.16	2		740	647	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356258	66356258	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	47	755	0	ENST00000273854.3:c.1239G>C	p.Arg413Ser	p.R413S	ENST00000273854	NM_004439.5	413	agG/agC	5/18	1	2	FACETS	0.659	0.554	0.776	0.659	0.554	0.776	SUBCLONAL	1	TRUE	1	0.16	2		755	891	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610306	10610306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	121	756	1	ENST00000171111.5:c.404G>A	p.Arg135His	p.R135H	ENST00000171111	NM_203500.1	135	cGc/cAc	2/6	0.158497267763395	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	0	0.174184597108394	1		757	1259	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0019471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	174	462	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.174184597108394	3	FACETS	1	0.972	1			1	CLONAL	2	TRUE	NA	0.174184597108394	3		462	971	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0019471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	34	343	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.824	0.672	0.994	0.824	0.672	0.994	CLONAL	1	TRUE	1	0.174184597108394	2		343	474	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913283	NA	P-0019471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	97	342	2	ENST00000263967.3:c.3129G>T	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atT	21/21	0.174184597108394	3	FACETS	0.757	0.674	0.845	0.757	0.674	0.845	SUBCLONAL	2	TRUE	1	0.174184597108394	3		344	800	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225060	NA	P-0019471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	133	432	0	ENST00000263967.3:c.311C>T	p.Pro104Leu	p.P104L	ENST00000263967	NM_006218.2	104	cCa/cTa	2/21	0.174184597108394	3	FACETS	0.826	0.749	0.907	0.826	0.749	0.907	CLONAL	2	TRUE	1	0.174184597108394	3		432	1005	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579317	7579317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	164	477	1	ENST00000269305.4:c.370del	p.Cys124AlafsTer46	p.C124Afs*46	ENST00000269305	NM_001126112.2	124	Tgc/gc	4/11	0.172791283617997	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.174184597108394	2		478	834	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715995	52715995	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	186	524	0	ENST00000322088.6:c.560C>T	p.Ser187Phe	p.S187F	ENST00000322088	NM_014225.5	187	tCc/tTc	5/15	0.174184597108394	3	FACETS	1	0.974	1			1	CLONAL	2	TRUE	NA	0.174184597108394	3		524	1033	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249083	55249083	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	59	497	0	ENST00000275493.2:c.2381C>G	p.Pro794Arg	p.P794R	ENST00000275493	NM_005228.3	794	cCc/cGc	20/28	1	2	FACETS	0.706	0.605	0.816	0.706	0.605	0.816	SUBCLONAL	1	TRUE	1	0.174184597108394	2		497	960	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0019472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	390	822	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	0.997	1	CLONAL	3	FALSE	1	0.232716157154592	2		822	1022	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579323	7579324	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	80	813	0	ENST00000269305.4:c.363dup	p.Val122CysfsTer27	p.V122Cfs*27	ENST00000269305	NM_001126112.2	121	-/T	4/11	NA	2	FACETS	1	0.929	1			1	INDETERMINATE	1	TRUE	NA	0.393865177346652	2		813	381	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199471	11199471	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	59	723	0	ENST00000361445.4:c.5020G>T	p.Val1674Leu	p.V1674L	ENST00000361445	NM_004958.3	1674	Gtg/Ttg	36/58	0.393865177346652	1	FACETS	0.827	0.717	0.944	0.827	0.717	0.944	CLONAL	1	TRUE	0	0.393865177346652	1		723	291	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822201	72822201	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	45	843	0	ENST00000268489.5:c.9974G>T	p.Gly3325Val	p.G3325V	ENST00000268489	NM_006885.3	3325	gGc/gTc	10/10	0.393865177346652	1	FACETS	0.504	0.425	0.591	0.504	0.425	0.591	SUBCLONAL	1	TRUE	0	0.393865177346652	1		843	364	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59870975	59870975	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1190796460	NA	P-0019473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	89	656	0	ENST00000259008.2:c.1456A>G	p.Thr486Ala	p.T486A	ENST00000259008	NM_032043.2	486	Act/Gct	10/20	0.179454447511904	2	FACETS	0.811	0.721	0.908	0.406	0.36	0.454	INDETERMINATE	1	TRUE	0	0.393865177346652	2		656	557	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051166	13051166	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	72	756	0	ENST00000316448.5:c.602A>C	p.Asp201Ala	p.D201A	ENST00000316448	NM_004343.3	201	gAc/gCc	5/9	0.201848553414976	0	FACETS	0.364	0.318	0.414			1	INDETERMINATE	1	TRUE	0	0.393865177346652	0		756	608	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296409	15296409	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	50	1237	0	ENST00000263388.2:c.2033G>T	p.Gly678Val	p.G678V	ENST00000263388	NM_000435.2	678	gGc/gTc	13/33	0.201848553414976	0	FACETS	0.43	0.366	0.5			1	INDETERMINATE	1	TRUE	0	0.393865177346652	0		1237	358	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383136	42383136	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	54	871	0	ENST00000221972.3:c.156C>A	p.Phe52Leu	p.F52L	ENST00000221972	NM_021601.3	52	ttC/ttA	2/5	0.364132080460025	3	FACETS	0.458	0.39	0.532			1	SUBCLONAL	1	TRUE	NA	0.393865177346652	3		871	717	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961465	54961465	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	46	399	0	ENST00000312783.6:c.167G>T	p.Arg56Leu	p.R56L	ENST00000312783	NM_198436.1	56	cGc/cTc	4/10	0.179454447511904	2	FACETS	0.961	0.817	1	0.481	0.408	0.559	INDETERMINATE	1	TRUE	0	0.393865177346652	2		399	243	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	163148696	163148696	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	60	684	0	ENST00000366898.1:c.5T>G	p.Ile2Arg	p.I2R	ENST00000366898	NM_004562.2	2	aTa/aGa	1/12	0.281009313183344	2	FACETS	0.901	0.781	1	0.451	0.39	0.516	CLONAL	1	TRUE	0	0.393865177346652	2		684	338	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962906	2962906	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	81	1002	4	ENST00000396946.4:c.2002C>A	p.His668Asn	p.H668N	ENST00000396946	NM_032415.4	668	Cac/Aac	16/25	0.393865177346652	0	FACETS	0.997	0.892	1			1	CLONAL	1	TRUE	0	0.393865177346652	0		1006	250	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372755	81372755	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	58	633	0	ENST00000222390.5:c.779G>T	p.Cys260Phe	p.C260F	ENST00000222390	NM_000601.4	260	tGc/tTc	7/18	0.126783648764302	4	FACETS	0.855	0.736	0.985	0.428	0.368	0.493	INDETERMINATE	1	TRUE	2	0.393865177346652	4		633	480	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513284	106513284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1055978595	NA	P-0019473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	28	432	0	ENST00000359195.3:c.2188C>T	p.His730Tyr	p.H730Y	ENST00000359195	NM_002649.2	730	Cac/Tac	4/11	0.126783648764302	4	FACETS	0.407	0.324	0.501	0.203	0.162	0.251	INDETERMINATE	1	TRUE	2	0.393865177346652	4		432	487	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317454	1317454	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0019473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	26	887	0	ENST00000400841.2:c.611C>G	p.Ser204Ter	p.S204*	ENST00000400841		204	tCa/tGa	5/6	1	1	FACETS	0.39	0.309	0.481	0.39	0.309	0.481	SUBCLONAL	1	TRUE	0	0.393865177346652	1		887	272	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0019474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	131	741	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.231765000744789	2	FACETS	1	0.984	1	0.701	0.638	0.766	CLONAL	1	TRUE	0	0.31	2		742	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0019474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	195	1061	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.282902537006275	1	FACETS	0.909	0.84	0.98	0.909	0.84	0.98	CLONAL	1	TRUE	0	0.31	1		1061	1170	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242444	55242445	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAAATTCCCGTCGCTATC	rs397517090	NA	P-0019474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	591	683	0	ENST00000275493.2:c.2217_2234dup	p.Ile740_Lys745dup	p.I740_K745dup	ENST00000275493	NM_005228.3	740	-/AAAATTCCCGTCGCTATC	19/28	0.3	8	FACETS	1	0.986	1			1	CLONAL	4	TRUE	NA	0.31	8		683	1744	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093455	30093455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776034417	NA	P-0019474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	47	490	0	ENST00000331968.5:c.1808G>A	p.Arg603His	p.R603H	ENST00000331968	NM_002742.2	603	cGt/cAt	13/18	1	2	FACETS	0.576	0.486	0.676	0.576	0.486	0.676	SUBCLONAL	1	TRUE	1	0.31	2		490	526	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092809	27092809	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	68	749	0	ENST00000324856.7:c.2830C>G	p.Gln944Glu	p.Q944E	ENST00000324856	NM_006015.4	944	Cag/Gag	9/20	1	2	FACETS	0.453	0.393	0.519	0.453	0.393	0.519	SUBCLONAL	1	TRUE	1	0.31	2		749	968	SUCCESS
BLM	641	MSKCC	GRCh37	15	91328192	91328192	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	110	541	0	ENST00000355112.3:c.2704G>C	p.Asp902His	p.D902H	ENST00000355112	NM_000057.2	902	Gac/Cac	14/22	0.282902537006275	1	FACETS	0.862	0.775	0.953	0.862	0.775	0.953	CLONAL	1	TRUE	0	0.31	1		541	696	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	209	680	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.962	0.895	1	0.962	0.895	1	CLONAL	1	TRUE	1	0.542496073613611	2		680	801	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	388	683	12	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.916	0.876	0.955	1	0.997	1	CLONAL	2	TRUE	1	0.542496073613611	2		695	781	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	436	894	7	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.542496073613611	2		901	1144	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	244	448	0	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.542496073613611	1		448	482	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	387	668	7	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.972	0.931	1	1	0.997	1	CLONAL	2	TRUE	1	0.542496073613611	2		675	734	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526755	31526755	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	231	972	0	ENST00000344624.3:c.285del	p.Cys96AlafsTer12	p.C96Afs*12	ENST00000344624		95	ccC/cc	2/33	1	2	FACETS	0.938	0.876	1	0.938	0.876	1	CLONAL	1	TRUE	1	0.542496073613611	2		972	908	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	362	720	14	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	0.542496073613611	2	FACETS	0.864	0.825	0.904	0.864	0.825	0.904	CLONAL	2	TRUE	0	0.542496073613611	2		734	772	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024505	16024505	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	164	699	2	ENST00000268712.3:c.1713del	p.Arg572GlufsTer18	p.R572Efs*18	ENST00000268712	NM_006311.3	571	ggG/gg	16/46	1	2	FACETS	0.905	0.834	0.979	0.905	0.834	0.979	CLONAL	1	TRUE	1	0.542496073613611	2		701	668	SUCCESS
BLM	641	MSKCC	GRCh37	15	91306241	91306241	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs12720097	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	171	803	0	ENST00000355112.3:c.1928G>A	p.Arg643His	p.R643H	ENST00000355112	NM_000057.2	643	cGt/cAt	8/22	1	2	FACETS	0.889	0.82	0.961	0.889	0.82	0.961	CLONAL	1	TRUE	1	0.542496073613611	2		803	709	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	138	405	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.973	0.89	1	0.973	0.89	1	CLONAL	1	TRUE	1	0.542496073613611	2		405	523	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368208	45368208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	108	526	1	ENST00000262160.6:c.1394G>A	p.Ser465Asn	p.S465N	ENST00000262160	NM_005901.5	465	aGc/aAc	11/11	1	2	FACETS	0.796	0.718	0.879	0.796	0.718	0.879	SUBCLONAL	1	TRUE	1	0.542496073613611	2		527	500	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216477	108216477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587782558	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	75	238	0	ENST00000278616.4:c.8432del	p.Lys2811SerfsTer46	p.K2811Sfs*46	ENST00000278616	NM_000051.3	2809	cAa/ca	58/63	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.542496073613611	2		238	259	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180367	32180367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1382129029	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	228	980	2	ENST00000375023.3:c.2564G>A	p.Arg855His	p.R855H	ENST00000375023	NM_004557.3	855	cGc/cAc	17/30	1	2	FACETS	0.899	0.838	0.961	0.899	0.838	0.961	CLONAL	1	TRUE	1	0.542496073613611	2		982	935	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	245	1336	14	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	0.542496073613611	2	FACETS	0.647	0.603	0.692	0.324	0.301	0.347	SUBCLONAL	1	TRUE	0	0.542496073613611	2		1350	1396	SUCCESS
APC	324	MSKCC	GRCh37	5	112175651	112175651	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	143	598	0	ENST00000257430.4:c.4364del	p.Asn1455IlefsTer18	p.N1455Ifs*18	ENST00000257430	NM_000038.5	1454	Aaa/aa	16/16	1	2	FACETS	0.846	0.774	0.921	0.846	0.774	0.921	CLONAL	1	TRUE	1	0.542496073613611	2		598	623	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127447	55127447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1333247214	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	281	974	0	ENST00000257290.5:c.235G>A	p.Gly79Ser	p.G79S	ENST00000257290	NM_006206.4	79	Ggc/Agc	3/23	1	2	FACETS	0.916	0.86	0.973	0.916	0.86	0.973	CLONAL	1	TRUE	1	0.542496073613611	2		974	1131	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821594	72821596	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	rs374416547	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	11	158	2	ENST00000268489.5:c.10579_10581del	p.Gly3527del	p.G3527del	ENST00000268489	NM_006885.3	3527	GGC/-	10/10	1	2	FACETS	0.296	0.205	0.408	0.296	0.205	0.408	SUBCLONAL	1	TRUE	1	0.542496073613611	2		160	137	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629033	14629035	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs764800868	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	210	817	0	ENST00000254322.2:c.127_129del	p.Glu43del	p.E43del	ENST00000254322	NM_006145.1	43	GAG/-	1/3	1	2	FACETS	0.893	0.83	0.958	0.893	0.83	0.958	CLONAL	1	TRUE	1	0.542496073613611	2		817	867	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213912	66213912	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	126	600	1	ENST00000273854.3:c.2518del	p.Ile840PhefsTer11	p.I840Ffs*11	ENST00000273854	NM_004439.5	840	Att/tt	15/18	1	2	FACETS	0.952	0.867	1	0.952	0.867	1	CLONAL	1	TRUE	1	0.542496073613611	2		601	488	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245587	41245587	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357522	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	204	951	4	ENST00000357654.3:c.1961del	p.Lys654SerfsTer47	p.K654Sfs*47	ENST00000357654	NM_007294.3	654	aAg/ag	10/23	1	2	FACETS	0.897	0.834	0.963	0.897	0.834	0.963	CLONAL	1	TRUE	1	0.542496073613611	2		955	838	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149655	61149656	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	41	232	0	ENST00000295025.8:c.1851dup	p.Gln618SerfsTer8	p.Q618Sfs*8	ENST00000295025	NM_002908.2	615	-/T	11/11	0.542496073613611	2	FACETS	0.879	0.743	1	0.439	0.371	0.513	CLONAL	1	TRUE	0	0.542496073613611	2		232	172	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639588	47639588	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63749897	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	95	710	0	ENST00000233146.2:c.687del	p.Ala230LeufsTer16	p.A230Lfs*16	ENST00000233146	NM_000251.2	227	agA/ag	4/16	0.542496073613611	2	FACETS	0.49	0.436	0.547	0.245	0.218	0.274	SUBCLONAL	1	TRUE	0	0.542496073613611	2		710	715	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606273	93606273	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	251	1013	6	ENST00000375746.1:c.98del	p.Gly33AlafsTer2	p.G33Afs*2	ENST00000375746	NM_001174167.1	31	caG/ca	2/14	1	2	FACETS	0.847	0.792	0.904	0.847	0.792	0.904	CLONAL	1	TRUE	1	0.542496073613611	2		1019	1092	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042300	42042301	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs866465268	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	53	879	0	ENST00000219905.7:c.6499_6500del	p.Leu2167GlyfsTer27	p.L2167Gfs*27	ENST00000219905	NM_001164273.1	2165	gaCTct/gact	17/24	1	2	FACETS	0.235	0.199	0.274	0.235	0.199	0.274	SUBCLONAL	1	TRUE	1	0.542496073613611	2		879	833	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101117	27101117	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	260	1081	1	ENST00000324856.7:c.4403del	p.Pro1468LeufsTer13	p.P1468Lfs*13	ENST00000324856	NM_006015.4	1467	Ccc/cc	18/20	1	2	FACETS	0.928	0.87	0.988	0.928	0.87	0.988	CLONAL	1	TRUE	1	0.542496073613611	2		1082	1033	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574679	41574679	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	615	1149	2	ENST00000263253.7:c.6970del	p.His2324ThrfsTer29	p.H2324Tfs*29	ENST00000263253	NM_001429.3	2322	Ccc/cc	31/31	1	2	FACETS	0.978	0.946	1	1	0.998	1	CLONAL	2	TRUE	1	0.542496073613611	2		1151	1159	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201885	152201885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778449608	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	161	686	1	ENST00000206249.3:c.739G>A	p.Glu247Lys	p.E247K	ENST00000206249	NM_000125.3	247	Gaa/Aaa	3/8	1	2	FACETS	0.882	0.811	0.955	0.882	0.811	0.955	CLONAL	1	TRUE	1	0.542496073613611	2		687	673	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870961	12870962	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	139	550	0	ENST00000228872.4:c.192dup	p.Gln65SerfsTer60	p.Q65Sfs*60	ENST00000228872	NM_004064.3	63	gat/gaTt	1/3	1	2	FACETS	0.899	0.822	0.979	0.899	0.822	0.979	CLONAL	1	TRUE	1	0.542496073613611	2		550	570	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563349	21563349	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	750	1471	1	ENST00000382592.4:c.570del	p.Tyr191ThrfsTer49	p.Y191Tfs*49	ENST00000382592	NM_014572.2	190	ccC/cc	4/8	0.542496073613611	3	FACETS	0.979	0.946	1	0.979	0.946	1	CLONAL	2	TRUE	1	0.542496073613611	3		1472	1796	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190900	106190900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs977008842	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	105	436	0	ENST00000380013.4:c.4178C>T	p.Thr1393Ile	p.T1393I	ENST00000380013	NM_001127208.2	1393	aCa/aTa	9/11	1	2	FACETS	0.827	0.745	0.913	0.827	0.745	0.913	CLONAL	1	TRUE	1	0.542496073613611	2		436	468	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533939	63533942	+	frameshift_variant	Frame_Shift_Del	DEL	CTCT	CTCT	-	rs771001164	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	128	561	0	ENST00000307078.5:c.1212_1215del	p.Glu405AlafsTer52	p.E405Afs*52	ENST00000307078	NM_004655.3	404	agAGAG/ag	6/11	1	2	FACETS	0.822	0.748	0.9	0.822	0.748	0.9	CLONAL	1	TRUE	1	0.542496073613611	2		561	574	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212230	5212230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367918810	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	188	767	0	ENST00000357368.4:c.4801G>A	p.Val1601Ile	p.V1601I	ENST00000357368	NM_002850.3	1601	Gtc/Atc	32/38	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.542496073613611	2		767	663	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070324	37070324	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63749795	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	161	685	2	ENST00000231790.2:c.1459C>T	p.Arg487Ter	p.R487*	ENST00000231790	NM_000249.3	487	Cga/Tga	13/19	1	2	FACETS	0.855	0.787	0.927	0.855	0.787	0.927	CLONAL	1	TRUE	1	0.542496073613611	2		687	694	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413710	138413710	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	186	730	9	ENST00000289153.2:c.1810del	p.Arg604GlyfsTer4	p.R604Gfs*4	ENST00000289153	NM_006219.2	604	Cgg/gg	12/22	1	2	FACETS	0.812	0.75	0.875	0.812	0.75	0.875	CLONAL	1	TRUE	1	0.542496073613611	2		739	845	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186507012	186507012	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	116	385	0	ENST00000323963.5:c.1178A>G	p.Asn393Ser	p.N393S	ENST00000323963		393	aAt/aGt	11/11	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.542496073613611	2		385	410	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	217	897	11	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.857	0.797	0.918	0.857	0.797	0.918	CLONAL	1	TRUE	1	0.542496073613611	2		908	934	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609673	46609673	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	546	1223	3	ENST00000263734.3:c.2402del	p.Pro801HisfsTer39	p.P801Hfs*39	ENST00000263734	NM_001430.4	799	ttC/tt	15/16	0.542496073613611	2	FACETS	0.899	0.867	0.932	0.899	0.867	0.932	CLONAL	2	TRUE	0	0.542496073613611	2		1226	1119	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458270	12458270	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	204	856	0	ENST00000287820.6:c.892del	p.Leu298CysfsTer38	p.L298Cfs*38	ENST00000287820	NM_015869.4	296	aCc/ac	6/7	1	2	FACETS	0.883	0.82	0.948	0.883	0.82	0.948	CLONAL	1	TRUE	1	0.542496073613611	2		856	852	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825539	50825539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762650238	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	148	792	2	ENST00000398568.2:c.2170G>A	p.Val724Ile	p.V724I	ENST00000398568	NM_001042412.1	724	Gtt/Att	14/18	1	2	FACETS	0.867	0.795	0.943	0.867	0.795	0.943	CLONAL	1	TRUE	1	0.542496073613611	2		794	629	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007331	143007332	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs772784869	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	150	586	1	ENST00000262992.4:c.2452dup	p.Arg818LysfsTer26	p.R818Kfs*26	ENST00000262992	NM_001101669.1	818	aga/aAga	22/24	1	2	FACETS	0.876	0.804	0.952	0.876	0.804	0.952	CLONAL	1	TRUE	1	0.542496073613611	2		587	631	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782409	9782409	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	297	1172	1	ENST00000377346.4:c.2342G>A	p.Gly781Glu	p.G781E	ENST00000377346	NM_005026.3	781	gGg/gAg	18/24	1	2	FACETS	0.998	0.94	1	0.998	0.94	1	CLONAL	1	TRUE	1	0.542496073613611	2		1173	1097	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169741	11169741	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1228569453	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	224	819	0	ENST00000361445.4:c.7412C>T	p.Thr2471Met	p.T2471M	ENST00000361445	NM_004958.3	2471	aCg/aTg	55/58	1	2	FACETS	0.872	0.813	0.933	0.872	0.813	0.933	CLONAL	1	TRUE	1	0.542496073613611	2		819	947	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11297986	11297986	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	277	977	2	ENST00000361445.4:c.2122C>T	p.Arg708Trp	p.R708W	ENST00000361445	NM_004958.3	708	Cgg/Tgg	13/58	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.542496073613611	2		979	985	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258750	16258750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	205	856	0	ENST00000375759.3:c.6015G>T	p.Lys2005Asn	p.K2005N	ENST00000375759	NM_015001.2	2005	aaG/aaT	11/15	1	2	FACETS	0.895	0.832	0.961	0.895	0.832	0.961	CLONAL	1	TRUE	1	0.542496073613611	2		856	844	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933744	36933744	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	332	1200	0	ENST00000361632.4:c.1655C>T	p.Pro552Leu	p.P552L	ENST00000361632		552	cCt/cTt	12/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.542496073613611	2		1200	1152	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226568823	226568823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779381164	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	76	1100	1	ENST00000366794.5:c.1246G>A	p.Gly416Arg	p.G416R	ENST00000366794	NM_001618.3	416	Ggg/Agg	9/23	1	2	FACETS	0.235	0.205	0.268	0.235	0.205	0.268	SUBCLONAL	1	TRUE	1	0.542496073613611	2		1101	1191	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596095	43596095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs141679950	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	209	983	0	ENST00000355710.3:c.262A>G	p.Ile88Val	p.I88V	ENST00000355710	NM_020975.4	88	Atc/Gtc	2/20	1	2	FACETS	0.877	0.815	0.94	0.877	0.815	0.94	CLONAL	1	TRUE	1	0.542496073613611	2		983	879	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852117	63852118	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs375905946	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	173	846	0	ENST00000279873.7:c.2901dup	p.Tyr968IlefsTer3	p.Y968Ifs*3	ENST00000279873	NM_032199.2	965	-/A	10/10	1	2	FACETS	0.781	0.719	0.844	0.781	0.719	0.844	SUBCLONAL	1	TRUE	1	0.542496073613611	2		846	817	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276974	123276974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918504	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	122	452	0	ENST00000358487.5:c.943G>A	p.Ala315Thr	p.A315T	ENST00000358487	NM_000141.4	315	Gcc/Acc	8/18	1	2	FACETS	0.974	0.886	1	0.974	0.886	1	CLONAL	1	TRUE	1	0.542496073613611	2		452	462	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154792	2154792	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	191	1400	0	ENST00000434045.2:c.429del	p.Ala144ProfsTer71	p.A144Pfs*71	ENST00000434045	NM_001127598.1	143	ccC/cc	4/5	1	2	FACETS	0.574	0.529	0.62	0.574	0.529	0.62	SUBCLONAL	1	TRUE	1	0.542496073613611	2		1400	1227	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132906	64132907	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	262	947	0	ENST00000334205.4:c.1046dup	p.Pro350ThrfsTer20	p.P350Tfs*20	ENST00000334205	NM_003942.2	347	agc/agCc	9/17	1	2	FACETS	0.962	0.902	1	0.962	0.902	1	CLONAL	1	TRUE	1	0.542496073613611	2		947	1004	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377024	118377024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781919840	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	151	644	0	ENST00000534358.1:c.10417C>T	p.Arg3473Cys	p.R3473C	ENST00000534358	NM_005933.3	3473	Cgt/Tgt	27/36	1	2	FACETS	0.91	0.835	0.987	0.91	0.835	0.987	CLONAL	1	TRUE	1	0.542496073613611	2		644	612	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436042	49436042	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1164333482	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	43	678	0	ENST00000301067.7:c.5939C>T	p.Thr1980Met	p.T1980M	ENST00000301067	NM_003482.3	1980	aCg/aTg	28/54	1	2	FACETS	0.28	0.233	0.331	0.28	0.233	0.331	SUBCLONAL	1	TRUE	1	0.542496073613611	2		678	567	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858581	57858581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	267	1001	1	ENST00000228682.2:c.319G>A	p.Val107Ile	p.V107I	ENST00000228682	NM_005269.2	107	Gta/Ata	4/12	1	2	FACETS	0.977	0.917	1	0.977	0.917	1	CLONAL	1	TRUE	1	0.542496073613611	2		1002	1008	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856545	111856545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1157707616	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	91	452	0	ENST00000341259.2:c.596C>T	p.Ala199Val	p.A199V	ENST00000341259	NM_005475.2	199	gCg/gTg	2/8	1	2	FACETS	0.676	0.603	0.754	0.676	0.603	0.754	SUBCLONAL	1	TRUE	1	0.542496073613611	2		452	496	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225594	133225594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	251	946	2	ENST00000320574.5:c.4070G>A	p.Cys1357Tyr	p.C1357Y	ENST00000320574	NM_006231.2	1357	tGc/tAc	32/49	1	2	FACETS	0.956	0.895	1	0.956	0.895	1	CLONAL	1	TRUE	1	0.542496073613611	2		948	968	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953905	32953905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80359150	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	101	625	0	ENST00000380152.3:c.8972G>A	p.Arg2991His	p.R2991H	ENST00000380152		2991	cGt/cAt	23/27	0.542496073613611	3	FACETS	0.732	0.655	0.813	0.366	0.327	0.407	SUBCLONAL	1	TRUE	1	0.542496073613611	3		625	647	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937023	48937023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	70	726	0	ENST00000267163.4:c.791C>T	p.Ala264Val	p.A264V	ENST00000267163	NM_000321.2	264	gCa/gTa	8/27	0.542496073613611	3	FACETS	0.331	0.288	0.378	0.166	0.143	0.189	SUBCLONAL	1	TRUE	1	0.542496073613611	3		726	991	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335526	73335526	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	53	559	0	ENST00000377767.4:c.2645A>C	p.Asn882Thr	p.N882T	ENST00000377767	NM_014953.3	882	aAc/aCc	19/21	0.542496073613611	3	FACETS	0.343	0.292	0.4	0.172	0.146	0.2	SUBCLONAL	1	TRUE	1	0.542496073613611	3		559	724	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590812	95590812	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774693190	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	125	584	0	ENST00000393063.1:c.1097C>T	p.Ala366Val	p.A366V	ENST00000393063	NM_030621.3	366	gCc/gTc	9/28	1	2	FACETS	0.913	0.83	0.998	0.913	0.83	0.998	CLONAL	1	TRUE	1	0.542496073613611	2		584	505	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95593021	95593021	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	209	915	0	ENST00000393063.1:c.799T>C	p.Tyr267His	p.Y267H	ENST00000393063	NM_030621.3	267	Tat/Cat	8/28	1	2	FACETS	0.922	0.857	0.988	0.922	0.857	0.988	CLONAL	1	TRUE	1	0.542496073613611	2		915	836	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43772200	43772200	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	239	968	0	ENST00000382044.4:c.515A>G	p.Gln172Arg	p.Q172R	ENST00000382044	NM_001141980.1	172	cAg/cGg	6/28	1	2	FACETS	0.953	0.89	1	0.953	0.89	1	CLONAL	1	TRUE	1	0.542496073613611	2		968	925	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457615	67457615	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	223	909	0	ENST00000327367.4:c.425G>A	p.Arg142His	p.R142H	ENST00000327367	NM_005902.3	142	cGc/cAc	3/9	1	2	FACETS	0.877	0.817	0.939	0.877	0.817	0.939	CLONAL	1	TRUE	1	0.542496073613611	2		909	937	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250823	99250823	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	209	649	0	ENST00000268035.6:c.127T>C	p.Tyr43His	p.Y43H	ENST00000268035	NM_000875.3	43	Tat/Cat	2/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.542496073613611	2		649	699	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2111956	2111956	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	249	982	1	ENST00000219476.3:c.1204G>T	p.Gly402Trp	p.G402W	ENST00000219476	NM_000548.3	402	Ggg/Tgg	12/42	1	2	FACETS	0.899	0.841	0.959	0.899	0.841	0.959	CLONAL	1	TRUE	1	0.542496073613611	2		983	1021	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213997	2213997	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	51	1010	0	ENST00000326181.6:c.76A>G	p.Thr26Ala	p.T26A	ENST00000326181	NM_032271.2	26	Aca/Gca	2/21	1	2	FACETS	0.195	0.165	0.229	0.195	0.165	0.229	SUBCLONAL	1	TRUE	1	0.542496073613611	2		1010	962	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348740	11348740	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	305	1087	2	ENST00000332029.2:c.596T>C	p.Val199Ala	p.V199A	ENST00000332029	NM_003745.1	199	gTc/gCc	2/2	1	2	FACETS	0.92	0.867	0.975	0.92	0.867	0.975	CLONAL	1	TRUE	1	0.542496073613611	2		1089	1222	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134505	30134505	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	67	379	0	ENST00000263025.4:c.26del	p.Gly9AlafsTer23	p.G9Afs*23	ENST00000263025	NM_002746.2	9	gGc/gc	1/9	1	2	FACETS	0.74	0.647	0.838	0.74	0.647	0.838	SUBCLONAL	1	TRUE	1	0.542496073613611	2		379	334	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865798	56865798	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	131	471	0	ENST00000308159.5:c.1130G>T	p.Arg377Met	p.R377M	ENST00000308159	NM_014669.4	377	aGg/aTg	11/22	1	2	FACETS	0.869	0.792	0.949	0.869	0.792	0.949	CLONAL	1	TRUE	1	0.542496073613611	2		471	556	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827231	72827231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375039347	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	166	780	1	ENST00000268489.5:c.9350C>T	p.Ala3117Val	p.A3117V	ENST00000268489	NM_006885.3	3117	gCg/gTg	9/10	1	2	FACETS	0.826	0.76	0.894	0.826	0.76	0.894	CLONAL	1	TRUE	1	0.542496073613611	2		781	741	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944133	81944133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	176	729	1	ENST00000359376.3:c.1742G>A	p.Gly581Asp	p.G581D	ENST00000359376	NM_002661.3	581	gGc/gAc	18/33	1	2	FACETS	0.936	0.865	1	0.936	0.865	1	CLONAL	1	TRUE	1	0.542496073613611	2		730	693	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965104	15965104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1211353793	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	124	551	1	ENST00000268712.3:c.5492C>T	p.Ala1831Val	p.A1831V	ENST00000268712	NM_006311.3	1831	gCa/gTa	37/46	1	2	FACETS	0.909	0.827	0.994	0.909	0.827	0.994	CLONAL	1	TRUE	1	0.542496073613611	2		552	503	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548875	29548875	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs886052798	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	146	987	1	ENST00000356175.3:c.1649T>C	p.Leu550Pro	p.L550P	ENST00000356175	NM_000267.3	550	cTg/cCg	15/57	1	2	FACETS	0.564	0.514	0.617	0.564	0.514	0.617	SUBCLONAL	1	TRUE	1	0.542496073613611	2		988	954	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602901	10602901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	391	1264	0	ENST00000171111.5:c.677G>A	p.Cys226Tyr	p.C226Y	ENST00000171111	NM_203500.1	226	tGc/tAc	3/6	1	2	FACETS	0.986	0.936	1	0.986	0.936	1	CLONAL	1	TRUE	1	0.542496073613611	2		1264	1462	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169552	11169552	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	148	930	0	ENST00000358026.2:c.4718T>C	p.Leu1573Pro	p.L1573P	ENST00000358026	NM_001128849.1	1573	cTg/cCg	33/36	1	2	FACETS	0.618	0.564	0.674	0.618	0.564	0.674	SUBCLONAL	1	TRUE	1	0.542496073613611	2		930	883	SUCCESS
CALR	811	MSKCC	GRCh37	19	13049513	13049513	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	59	970	0	ENST00000316448.5:c.20T>C	p.Leu7Pro	p.L7P	ENST00000316448	NM_004343.3	7	cTg/cCg	1/9	1	2	FACETS	0.232	0.199	0.268	0.232	0.199	0.268	SUBCLONAL	1	TRUE	1	0.542496073613611	2		970	938	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967091	18967092	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1384543747	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	59	1039	2	ENST00000262803.5:c.1814_1815del	p.Glu605AlafsTer17	p.E605Afs*17	ENST00000262803	NM_002911.3	602	gcAGag/gcag	13/24	1	2	FACETS	0.199	0.17	0.23	0.199	0.17	0.23	SUBCLONAL	1	TRUE	1	0.542496073613611	2		1041	1094	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906476	50906476	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	253	1128	1	ENST00000440232.2:c.1137G>T	p.Gln379His	p.Q379H	ENST00000440232	NM_002691.3	379	caG/caT	9/27	1	2	FACETS	0.974	0.912	1	0.974	0.912	1	CLONAL	1	TRUE	1	0.542496073613611	2		1129	958	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	240	912	7	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.542496073613611	2		919	833	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085794	16085794	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	89	801	0	ENST00000281043.3:c.970C>A	p.Leu324Ile	p.L324I	ENST00000281043	NM_005378.4	324	Ctt/Att	3/3	0.542496073613611	2	FACETS	0.467	0.414	0.523	0.233	0.207	0.262	SUBCLONAL	1	TRUE	0	0.542496073613611	2		801	703	SUCCESS
ALK	238	MSKCC	GRCh37	2	29430040	29430040	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	199	908	0	ENST00000389048.3:c.3935C>T	p.Thr1312Ile	p.T1312I	ENST00000389048	NM_004304.4	1312	aCa/aTa	26/29	0.542496073613611	2	FACETS	0.851	0.789	0.915	0.426	0.394	0.458	CLONAL	1	TRUE	0	0.542496073613611	2		908	862	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606137	47606138	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	65	827	0	ENST00000263735.4:c.607dup	p.Thr203AsnfsTer4	p.T203Nfs*4	ENST00000263735	NM_002354.2	201	caa/cAaa	6/9	0.542496073613611	2	FACETS	0.342	0.296	0.392	0.171	0.148	0.196	SUBCLONAL	1	TRUE	0	0.542496073613611	2		827	701	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198264800	198264800	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	184	794	0	ENST00000335508.6:c.2992A>C	p.Lys998Gln	p.K998Q	ENST00000335508	NM_012433.2	998	Aag/Cag	20/25	0.542496073613611	2	FACETS	0.945	0.875	1	0.472	0.437	0.509	CLONAL	1	TRUE	0	0.542496073613611	2		794	718	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149674	202149674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1225512894	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	200	776	0	ENST00000358485.4:c.1115G>A	p.Cys372Tyr	p.C372Y	ENST00000358485	NM_001080125.1	372	tGt/tAt	8/9	0.542496073613611	2	FACETS	0.913	0.847	0.98	0.456	0.423	0.49	CLONAL	1	TRUE	0	0.542496073613611	2		776	808	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735507	204735507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	105	656	0	ENST00000302823.3:c.308G>A	p.Cys103Tyr	p.C103Y	ENST00000302823	NM_005214.4	103	tGc/tAc	2/4	0.542496073613611	2	FACETS	0.608	0.545	0.674	0.304	0.272	0.337	SUBCLONAL	1	TRUE	0	0.542496073613611	2		656	637	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741473	39741473	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	187	727	1	ENST00000361337.2:c.1360G>A	p.Val454Met	p.V454M	ENST00000361337	NM_003286.2	454	Gtg/Atg	14/21	1	2	FACETS	0.831	0.768	0.895	0.831	0.768	0.895	CLONAL	1	TRUE	1	0.542496073613611	2		728	830	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514602	44514602	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	206	713	0	ENST00000291552.4:c.554T>C	p.Leu185Pro	p.L185P	ENST00000291552	NM_006758.2	185	cTg/cCg	7/8	1	2	FACETS	0.997	0.927	1	0.997	0.927	1	CLONAL	1	TRUE	1	0.542496073613611	2		713	762	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050676	30050676	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150667239	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	182	618	1	ENST00000338641.4:c.478C>T	p.Arg160Trp	p.R160W	ENST00000338641	NM_000268.3	160	Cgg/Tgg	5/16	1	2	FACETS	0.967	0.895	1	0.967	0.895	1	CLONAL	1	TRUE	1	0.542496073613611	2		619	694	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626694	12626694	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	233	850	0	ENST00000251849.4:c.1595A>G	p.Tyr532Cys	p.Y532C	ENST00000251849	NM_002880.3	532	tAc/tGc	15/17	1	2	FACETS	0.987	0.923	1	0.987	0.923	1	CLONAL	1	TRUE	1	0.542496073613611	2		850	870	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732913	30732913	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	41	307	0	ENST00000295754.5:c.1526G>A	p.Gly509Asp	p.G509D	ENST00000295754	NM_003242.5	509	gGc/gAc	7/7	1	2	FACETS	0.494	0.413	0.583	0.494	0.413	0.583	SUBCLONAL	1	TRUE	1	0.542496073613611	2		307	306	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161834	47161834	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1226885899	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	184	603	0	ENST00000409792.3:c.4292T>C	p.Val1431Ala	p.V1431A	ENST00000409792	NM_014159.6	1431	gTa/gCa	3/21	1	2	FACETS	0.993	0.92	1	0.993	0.92	1	CLONAL	1	TRUE	1	0.542496073613611	2		603	683	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119721054	119721054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	240	735	0	ENST00000316626.5:c.121G>A	p.Val41Met	p.V41M	ENST00000316626		41	Gtg/Atg	2/12	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.542496073613611	2		735	876	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201768	66201768	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	184	804	0	ENST00000273854.3:c.2734C>G	p.Leu912Val	p.L912V	ENST00000273854	NM_004439.5	912	Ctg/Gtg	16/18	1	2	FACETS	0.844	0.78	0.91	0.844	0.78	0.91	CLONAL	1	TRUE	1	0.542496073613611	2		804	804	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31421438	31421438	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	167	894	0	ENST00000344624.3:c.3466C>A	p.Leu1156Met	p.L1156M	ENST00000344624		1156	Ctg/Atg	27/33	1	2	FACETS	0.83	0.764	0.898	0.83	0.764	0.898	CLONAL	1	TRUE	1	0.542496073613611	2		894	742	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111485	56111485	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	33	239	0	ENST00000399503.3:c.85G>T	p.Gly29Ter	p.G29*	ENST00000399503	NM_005921.1	29	Gga/Tga	1/20	1	2	FACETS	0.845	0.699	1	0.845	0.699	1	CLONAL	1	TRUE	1	0.542496073613611	2		239	144	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815757	32815757	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	295	1172	2	ENST00000354258.4:c.1859del	p.Gly620AspfsTer44	p.G620Dfs*44	ENST00000354258	NM_000593.5	620	gGa/ga	8/11	1	2	FACETS	0.919	0.865	0.975	0.919	0.865	0.975	CLONAL	1	TRUE	1	0.542496073613611	2		1174	1183	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967242	93967242	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs770896087	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	104	480	0	ENST00000369303.4:c.2111-1G>A		p.X704_splice	ENST00000369303	NM_004440.3	704			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.542496073613611	2		480	346	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963981	2963981	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	208	838	0	ENST00000396946.4:c.1826A>G	p.Tyr609Cys	p.Y609C	ENST00000396946	NM_032415.4	609	tAc/tGc	15/25	1	2	FACETS	0.951	0.885	1	0.951	0.885	1	CLONAL	1	TRUE	1	0.542496073613611	2		838	806	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971277	13971277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs971724465	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	40	701	0	ENST00000405192.2:c.652C>T	p.Pro218Ser	p.P218S	ENST00000405192	NM_001163147.1	218	Cca/Tca	8/12	1	2	FACETS	0.203	0.167	0.242	0.203	0.167	0.242	SUBCLONAL	1	TRUE	1	0.542496073613611	2		701	728	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509670	106509670	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	197	748	0	ENST00000359195.3:c.1664T>C	p.Leu555Ser	p.L555S	ENST00000359195	NM_002649.2	555	tTg/tCg	2/11	1	2	FACETS	0.911	0.846	0.979	0.911	0.846	0.979	CLONAL	1	TRUE	1	0.542496073613611	2		748	797	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046312	69046312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769708831	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	123	554	0	ENST00000288368.4:c.3785G>A	p.Arg1262His	p.R1262H	ENST00000288368	NM_024870.2	1262	cGt/cAt	32/40	1	2	FACETS	0.872	0.792	0.955	0.872	0.792	0.955	CLONAL	1	TRUE	1	0.542496073613611	2		554	520	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090509	5090509	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	145	760	0	ENST00000381652.3:c.2829del	p.Lys943AsnfsTer6	p.K943Nfs*6	ENST00000381652	NM_004972.3	942	cAa/ca	21/25	1	2	FACETS	0.865	0.792	0.941	0.865	0.792	0.941	CLONAL	1	TRUE	1	0.542496073613611	2		760	618	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090859	5090859	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	87	425	0	ENST00000381652.3:c.3007C>T	p.Gln1003Ter	p.Q1003*	ENST00000381652	NM_004972.3	1003	Caa/Taa	22/25	1	2	FACETS	0.914	0.816	1	0.914	0.816	1	CLONAL	1	TRUE	1	0.542496073613611	2		425	351	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402784	139402784	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	338	1196	0	ENST00000277541.6:c.3225G>A	p.Trp1075Ter	p.W1075*	ENST00000277541	NM_017617.3	1075	tgG/tgA	20/34	1	2	FACETS	0.994	0.94	1	0.994	0.94	1	CLONAL	1	TRUE	1	0.542496073613611	2		1196	1253	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040933	47040933	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1233279563	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	301	636	0	ENST00000377604.3:c.1463C>T	p.Ala488Val	p.A488V	ENST00000377604	NM_001204468.1	488	gCc/gTc	14/24	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.542496073613611	1		636	594	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412657	63412657	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	179	419	0	ENST00000330258.3:c.510del	p.Gly171AlafsTer38	p.G171Afs*38	ENST00000330258	NM_152424.3	170	aaA/aa	2/2	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.542496073613611	1		419	390	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0019484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	44	290	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.903	0.772	1	1	0.978	1	CLONAL	3	FALSE	1	0.216527653939607	2		291	150	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413070	139413072	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0019484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	214	754	0	ENST00000277541.6:c.1070_1072del	p.Phe357del	p.F357del	ENST00000277541	NM_017617.3	357	tTCTac/tac	6/34	0.216527653939607	1	FACETS	1	0.977	1	1	0.996	1	CLONAL	4	FALSE	0	0.216527653939607	1		754	412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577113	7577113	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555525279	NA	P-0019484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	519	953	0	ENST00000269305.4:c.825T>G	p.Cys275Trp	p.C275W	ENST00000269305	NM_001126112.2	275	tgT/tgG	8/11	NA	3	FACETS	0.962	0.937	0.987			1	INDETERMINATE	8	FALSE	NA	0.216527653939607	3		953	690	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175836	24175837	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555881563	NA	P-0019484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	92	679	0	ENST00000263121.7:c.1066_1067del	p.Leu356AspfsTer4	p.L356Dfs*4	ENST00000263121	NM_003073.3	355	aCT/a	8/9	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.216527653939607	2		679	577	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38955717	38955718	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0019484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	89	504	0	ENST00000357387.3:c.2588_2589del	p.Tyr863CysfsTer5	p.Y863Cfs*5	ENST00000357387	NM_152756.3	863	tAT/t	26/38	1	2	FACETS	1	0.943	1	1	0.989	1	CLONAL	3	FALSE	1	0.216527653939607	2		504	256	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324904	31324906	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0019484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	64	700	0	ENST00000412585.2:c.30_32del	p.Leu13del	p.L13del	ENST00000412585	NM_005514.6	10	ctCCTg/ctg	1/8	1	2	FACETS	0.78	0.679	0.889	1	0.974	1	SUBCLONAL	2	FALSE	1	0.216527653939607	2		700	379	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658333	117658333	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0019484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	233	1156	0	ENST00000368508.3:c.5248+2T>G		p.X1750_splice	ENST00000368508	NM_002944.2	1750			1	2	FACETS	0.882	0.828	0.936	1	0.996	1	CLONAL	4	FALSE	1	0.216527653939607	2		1156	610	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938326	76938326	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	142	343	2	ENST00000373344.5:c.2422C>T	p.Arg808Ter	p.R808*	ENST00000373344	NM_000489.3	808	Cga/Tga	9/35	1	1	FACETS	1	0.972	1	1	0.994	1	CLONAL	6	FALSE	0	0.216527653939607	1		345	188	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0019485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	283	819	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.3	5	FACETS	0.993	0.936	1	0.745	0.702	0.788	CLONAL	3	TRUE	1	0.33	5		819	861	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889108	76889108	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	59	879	2	ENST00000373344.5:c.4902G>T	p.Trp1634Cys	p.W1634C	ENST00000373344	NM_000489.3	1634	tgG/tgT	18/35	0.3	3	FACETS	0.588	0.505	0.678	0.294	0.252	0.339	SUBCLONAL	1	TRUE	1	0.33	3		881	709	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433273	49433273	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	83	966	1	ENST00000301067.7:c.8174G>T	p.Ser2725Ile	p.S2725I	ENST00000301067	NM_003482.3	2725	aGc/aTc	32/54	1	2	FACETS	0.796	0.703	0.896	0.796	0.703	0.896	SUBCLONAL	1	TRUE	1	0.33	2		967	632	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28897032	28897032	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	44	676	0	ENST00000282397.4:c.2848G>T	p.Glu950Ter	p.E950*	ENST00000282397	NM_002019.4	950	Gaa/Taa	21/30	0.234051319202811	2	FACETS	0.544	0.456	0.642	0.272	0.228	0.321	SUBCLONAL	1	TRUE	0	0.33	2		676	490	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911251	32911251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555282835	NA	P-0019485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	189	1020	1	ENST00000380152.3:c.2759C>T	p.Pro920Leu	p.P920L	ENST00000380152		920	cCc/cTc	11/27	0.234051319202811	2	FACETS	0.768	0.711	0.826	0.768	0.711	0.826	SUBCLONAL	2	TRUE	0	0.33	2		1021	746	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276327	15276327	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0019485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	180	925	0	ENST00000263388.2:c.5668-1G>T		p.X1890_splice	ENST00000263388	NM_000435.2	1890			0.3	3	FACETS	0.868	0.803	0.936	0.868	0.803	0.936	CLONAL	2	TRUE	1	0.33	3		925	732	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019286	31019286	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	52	509	0	ENST00000375687.4:c.881A>T	p.Gln294Leu	p.Q294L	ENST00000375687	NM_015338.5	294	cAg/cTg	9/13	0.3	3	FACETS	0.872	0.744	1	0.436	0.372	0.506	CLONAL	1	TRUE	1	0.33	3		509	421	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589014	67589014	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	35	438	0	ENST00000274335.5:c.1105A>T	p.Thr369Ser	p.T369S	ENST00000274335		369	Act/Tct	8/15	1	2	FACETS	0.663	0.545	0.795	0.663	0.545	0.795	SUBCLONAL	1	TRUE	1	0.33	2		438	320	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76953089	76953089	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs782198677	NA	P-0019485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	90	973	0	ENST00000373344.5:c.224G>T	p.Gly75Val	p.G75V	ENST00000373344	NM_000489.3	75	gGa/gTa	4/35	0.3	3	FACETS	0.783	0.694	0.878	0.391	0.347	0.439	SUBCLONAL	1	TRUE	1	0.33	3		973	812	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020030	123020030	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	107	974	1	ENST00000355640.3:c.518G>T	p.Trp173Leu	p.W173L	ENST00000355640		173	tGg/tTg	2/7	0.3	3	FACETS	0.946	0.848	1	0.473	0.424	0.525	CLONAL	1	TRUE	1	0.33	3		975	799	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671930	30671930	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	39	1003	1	ENST00000376406.3:c.5030A>T	p.Gln1677Leu	p.Q1677L	ENST00000376406	NM_014641.2	1677	cAg/cTg	10/15	0.234051319202811				0.288	0.416				SUBCLONAL	1	TRUE	0	0.33	2		1004	679	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692962	89692964	+	stop_gained	Nonsense_Mutation	TNP	AAG	AAG	CAT	novel	NA	P-0019485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	56	868	1	ENST00000371953.3:c.446_448delinsCAT	p.Gln149_Glu150delinsProTer	p.Q149_E150delinsP*	ENST00000371953	NM_000314.4	149	cAAGag/cCATag	5/9	1	2	FACETS	0.526	0.45	0.609	0.526	0.45	0.609	SUBCLONAL	1	TRUE	1	0.33	2		869	645	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	105	600	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.208873274313574	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.208873274313574	3		600	471	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881392	37881392	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	79	1015	1	ENST00000269571.5:c.2584A>G	p.Thr862Ala	p.T862A	ENST00000269571		862	Aca/Gca	21/27	1	2	FACETS	0.877	0.77	0.992	0.877	0.77	0.992	CLONAL	1	TRUE	1	0.208873274313574	2		1016	863	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579634	7579693	+	splice_region_variant,intron_variant	Splice_Region	DEL	CCCCCCAGCCCCCCAGCCCTCCAGGTCCCCAGCCCTCCAGGTCCCCAGCCCAACCCTTGT	CCCCCCAGCCCCCCAGCCCTCCAGGTCCCCAGCCCTCCAGGTCCCCAGCCCAACCCTTGT	-	novel	NA	P-0019486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	110	795	0	ENST00000269305.4:c.96+7_97-44del		p.X32_splice	ENST00000269305	NM_001126112.2	32			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.208873274313574	2		795	740	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587182	212587182	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	40	787	0	ENST00000342788.4:c.819del	p.Gln274AsnfsTer26	p.Q274Nfs*26	ENST00000342788	NM_005235.2	273	ttT/tt	7/28	0.208873274313574	1	FACETS	0.569	0.472	0.677	0.569	0.472	0.677	SUBCLONAL	1	TRUE	0	0.208873274313574	1		787	603	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0019487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	162	680	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.812	0.747	0.88	0.812	0.747	0.88	CLONAL	1	TRUE	1	0.558789076687122	2		680	714	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0019487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	228	887	1	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	0.546428335011713	1	FACETS	0.811	0.759	0.865	0.811	0.759	0.865	CLONAL	1	TRUE	0	0.558789076687122	1		888	725	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0019487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	148	483	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.481955562041502	1	FACETS	0.911	0.841	0.983	0.911	0.841	0.983	CLONAL	1	TRUE	0	0.558789076687122	1		483	419	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743948	41743948	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751738506	NA	P-0019487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	403	1244	0	ENST00000301178.4:c.883C>T	p.Arg295Trp	p.R295W	ENST00000301178	NM_021913.4	295	Cgg/Tgg	7/20	1	2	FACETS	0.982	0.933	1	0.982	0.933	1	CLONAL	1	TRUE	1	0.558789076687122	2		1244	1469	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981777	201981777	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	55	870	0	ENST00000359651.3:c.488del	p.Ser163ThrfsTer91	p.S163Tfs*91	ENST00000359651		163	aGc/ac	4/8	0.544276437308219	1	FACETS	0.206	0.175	0.239	0.206	0.175	0.239	SUBCLONAL	1	TRUE	0	0.558789076687122	1		870	689	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710600	114710601	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	271	764	2	ENST00000543371.1:c.86dup	p.Lys30GlufsTer14	p.K30Efs*14	ENST00000543371	NM_001198531.1	29	gag/gAag	1/14	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.558789076687122	2		766	876	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18962981	18962981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763818930	NA	P-0019487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	411	1351	2	ENST00000262803.5:c.848C>T	p.Pro283Leu	p.P283L	ENST00000262803	NM_002911.3	283	cCg/cTg	6/24	1	2	FACETS	0.953	0.906	1	0.953	0.906	1	CLONAL	1	TRUE	1	0.558789076687122	2		1353	1543	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022400	31022422	+	frameshift_variant	Frame_Shift_Del	DEL	GGTCACCACTGCCATAGAGAGGC	GGTCACCACTGCCATAGAGAGGC	-	novel	NA	P-0019487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	157	296	0	ENST00000375687.4:c.1887_1909del	p.Glu635ArgfsTer15	p.E635Rfs*15	ENST00000375687	NM_015338.5	629	GGTCACCACTGCCATAGAGAGGCg/g	13/13	0.540080629128484	3	FACETS	0.939	0.871	1	0.939	0.871	1	CLONAL	2	TRUE	1	0.558789076687122	3		296	383	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265614	41266221	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTCGTTGCCATTAAGCCAGTCTGGCTGAGATCCCCCTGCTTTCCTCTCTCCCTGCTTACTTGTCAGGCTACCTTTTGCTCCATTTTCTGCTCACTCCTCCTAATGGCTTGGTGAAATAGCAAACAAGCCACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTC	CTTCGTTGCCATTAAGCCAGTCTGGCTGAGATCCCCCTGCTTTCCTCTCTCCCTGCTTACTTGTCAGGCTACCTTTTGCTCCATTTTCTGCTCACTCCTCCTAATGGCTTGGTGAAATAGCAAACAAGCCACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTC	-	novel	NA	P-0019487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	218	478	0	ENST00000349496.5:c.13+46_222del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.540923171569171	2	FACETS	0.823	0.774	0.872	0.823	0.774	0.872	CLONAL	2	TRUE	0	0.558789076687122	2		478	474	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114222	73114222	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	195	521	0	ENST00000356692.5:c.858C>G	p.Asp286Glu	p.D286E	ENST00000356692		286	gaC/gaG	8/9	1	2	FACETS	0.963	0.894	1	0.963	0.894	1	CLONAL	1	TRUE	1	0.558789076687122	2		521	725	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81340836	81340836	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0019487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	60	394	0	ENST00000222390.5:c.1406-1G>A		p.X469_splice	ENST00000222390	NM_000601.4	469			1	2	FACETS	0.673	0.584	0.769	0.673	0.584	0.769	SUBCLONAL	1	TRUE	1	0.558789076687122	2		394	319	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246429	53246429	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	300	434	0	ENST00000375401.3:c.553G>T	p.Glu185Ter	p.E185*	ENST00000375401	NM_004187.3	185	Gag/Tag	5/26	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.558789076687122	1		434	547	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0019488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	157	741	1	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	TRUE	1	0.409627477287916	2		742	608	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115710	8115711	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0019488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	94	584	0	ENST00000346208.3:c.1060dup	p.Leu354ProfsTer17	p.L354Pfs*17	ENST00000346208		352	-/C	6/6	1	2	FACETS	0.755	0.673	0.842	0.755	0.673	0.842	SUBCLONAL	1	TRUE	1	0.409627477287916	2		584	608	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38968098	38968098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777143677	NA	P-0019488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	36	654	0	ENST00000357387.3:c.1007G>A	p.Arg336His	p.R336H	ENST00000357387	NM_152756.3	336	cGt/cAt	12/38	1	2	FACETS	0.29	0.237	0.348	0.29	0.237	0.348	SUBCLONAL	1	TRUE	1	0.409627477287916	2		654	607	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870993	12870994	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0019488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	83	382	0	ENST00000228872.4:c.221dup	p.Tyr74Ter	p.Y74*	ENST00000228872	NM_004064.3	74	tac/tAac	1/3	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.409627477287916	2		382	371	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063389	67063389	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0019488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	142	641	1	ENST00000412916.2:c.78+1G>A		p.X26_splice	ENST00000412916		26			0.409627477287916	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.409627477287916	1		642	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0019489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	107	852	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.175817663979428	2	FACETS	1	0.97	1	0.605	0.543	0.67	CLONAL	1	TRUE	0	0.28130923101146	2		852	629	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37672059	37672059	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs1489040904	NA	P-0019489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	58	587	0	ENST00000447079.4:c.2844C>G	p.Ile948Met	p.I948M	ENST00000447079	NM_015083.1	948	atC/atG	9/14	0.28130923101146	13	FACETS	1	0.905	1			1	CLONAL	1	TRUE	NA	0.28130923101146	13		587	978	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0019491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	177	704	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	1	2	FACETS	0.89	0.821	0.96	0.89	0.821	0.96	CLONAL	1	TRUE	1	0.52430211770608	2		704	759	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0019491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	211	949	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.52430211770608	2		950	803	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945351	151945352	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0019491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	34	271	0	ENST00000262189.6:c.2167_2168del	p.Glu723LysfsTer8	p.E723Kfs*8	ENST00000262189	NM_170606.2	723	GAa/a	14/59	1	2	FACETS	0.584	0.481	0.699	0.584	0.481	0.699	SUBCLONAL	1	TRUE	1	0.52430211770608	2		271	222	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945396	151945403	+	frameshift_variant	Frame_Shift_Del	DEL	GAAATACT	GAAATACT	CAAAACC	novel	NA	P-0019491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	98	905	0	ENST00000262189.6:c.2116_2123delinsGGTTTTG	p.Ser706GlyfsTer12	p.S706Gfs*12	ENST00000262189	NM_170606.2	706	AGTATTTCa/GGTTTTGa	14/59	1	2	FACETS	0.514	0.458	0.573	0.514	0.458	0.573	SUBCLONAL	1	TRUE	1	0.52430211770608	2		905	728	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720676	89720676	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	41	381	0	ENST00000371953.3:c.827A>C	p.Asn276Thr	p.N276T	ENST00000371953	NM_000314.4	276	aAt/aCt	8/9	0.52430211770608	1	FACETS	0.611	0.515	0.714	0.611	0.515	0.714	SUBCLONAL	1	TRUE	0	0.52430211770608	1		381	189	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115982	8115983	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	29	313	0	ENST00000346208.3:c.1330dup	p.Ter444LeufsTer63	p.*444Lfs*63	ENST00000346208		443	ggt/ggTt	6/6	0.174859419072445	2	FACETS	1	0.834	1	0.52	0.418	0.634	CLONAL	1	TRUE	0	0.202984509783102	2		313	275	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517201	NA	P-0019493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	121	884	1	ENST00000263967.3:c.1637A>C	p.Gln546Pro	p.Q546P	ENST00000263967	NM_006218.2	546	cAg/cCg	10/21	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.32706509040947	2		885	697	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551708	150551708	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	40	371	1	ENST00000369026.2:c.299C>T	p.Ala100Val	p.A100V	ENST00000369026	NM_021960.4	100	gCg/gTg	1/3	0.32706509040947	3	FACETS	0.813	0.677	0.963	0.407	0.338	0.482	CLONAL	1	TRUE	1	0.32706509040947	3		372	350	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844120	68844142	+	frameshift_variant	Frame_Shift_Del	DEL	ATCCAACGGGAATGCAGTTGAGG	ATCCAACGGGAATGCAGTTGAGG	-	novel	NA	P-0019493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	103	656	0	ENST00000261769.5:c.714_736del	p.Asn240AspfsTer10	p.N240Dfs*10	ENST00000261769	NM_004360.3	236	tcATCCAACGGGAATGCAGTTGAGGat/tcat	6/16	0.32706509040947	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.32706509040947	1		656	496	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41219665	41219665	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	111	643	0	ENST00000357654.3:c.5034T>G	p.Asn1678Lys	p.N1678K	ENST00000357654	NM_007294.3	1678	aaT/aaG	16/23	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.32706509040947	2		643	672	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133755	41133755	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	138	338	1	ENST00000379561.5:c.1873G>A	p.Gly625Arg	p.G625R	ENST00000379561	NM_002015.3	625	Gga/Aga	2/3	0.694604748858025	1	FACETS	0.953	0.886	1	0.953	0.886	1	CLONAL	1	TRUE	0	0.694604748858025	1		339	272	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	25	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.552	0.434	0.689	0.552	0.434	0.689	SUBCLONAL	1	TRUE	1	0.18	2		509	503	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0019495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	95	689	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.865	0.772	0.965	1	0.984	1	CLONAL	2	TRUE	1	0.18	2		689	610	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41021774	41021774	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	34	575	0	ENST00000267868.3:c.716C>T	p.Ser239Leu	p.S239L	ENST00000267868	NM_002875.4	239	tCa/tTa	8/10	1	2	FACETS	0.625	0.51	0.756	0.625	0.51	0.756	SUBCLONAL	1	TRUE	1	0.18	2		575	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0019495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	69	741	0	ENST00000269305.4:c.560-1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.18	2		741	591	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325189	123325189	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1367082521	NA	P-0019495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	58	620	0	ENST00000358487.5:c.139C>G	p.Pro47Ala	p.P47A	ENST00000358487	NM_000141.4	47	Cca/Gca	3/18	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.18	2		620	544	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420906	49420906	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs940178682	NA	P-0019495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	46	733	0	ENST00000301067.7:c.14843C>T	p.Ser4948Leu	p.S4948L	ENST00000301067	NM_003482.3	4948	tCa/tTa	48/54	1	2	FACETS	0.747	0.628	0.88	0.747	0.628	0.88	SUBCLONAL	1	TRUE	1	0.18	2		733	684	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243108	105243108	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0019495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	66	746	0	ENST00000349310.3:c.176-1G>A		p.X59_splice	ENST00000349310	NM_001014432.1	59			1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.18	2		746	618	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610225	10610225	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	57	936	0	ENST00000171111.5:c.485A>T	p.Tyr162Phe	p.Y162F	ENST00000171111	NM_203500.1	162	tAc/tTc	2/6	1	2	FACETS	0.748	0.64	0.866	0.748	0.64	0.866	SUBCLONAL	1	TRUE	1	0.18	2		936	847	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293191	212293191	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	29	564	1	ENST00000342788.4:c.2661G>T	p.Met887Ile	p.M887I	ENST00000342788	NM_005235.2	887	atG/atT	22/28	1	2	FACETS	0.864	0.694	1	0.864	0.694	1	CLONAL	1	TRUE	1	0.18	2		565	373	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067099	143067099	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	34	613	0	ENST00000262992.4:c.1614G>T	p.Met538Ile	p.M538I	ENST00000262992	NM_001101669.1	538	atG/atT	16/24	1	2	FACETS	0.853	0.697	1	0.853	0.697	1	CLONAL	1	TRUE	1	0.18	2		613	443	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527796	157527796	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	27	534	0	ENST00000346085.5:c.5522del	p.Pro1841LeufsTer10	p.P1841Lfs*10	ENST00000346085	NM_020732.3	1841	Cct/ct	20/20	1	2	FACETS	0.629	0.499	0.777	0.629	0.499	0.777	SUBCLONAL	1	TRUE	1	0.18	2		534	477	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979529	2979529	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	56	663	0	ENST00000396946.4:c.718G>T	p.Glu240Ter	p.E240*	ENST00000396946	NM_032415.4	240	Gag/Tag	6/25	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.18	2		663	570	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37006472	37006472	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1300663454	NA	P-0019495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	27	410	0	ENST00000358127.4:c.473T>C	p.Ile158Thr	p.I158T	ENST00000358127	NM_001280556.1	158	aTa/aCa	4/10	1	2	FACETS	0.875	0.696	1	0.875	0.696	1	CLONAL	1	TRUE	1	0.18	2		410	343	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914675	39914675	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	37	859	0	ENST00000378444.4:c.4687G>T	p.Gly1563Cys	p.G1563C	ENST00000378444	NM_001123385.1	1563	Ggt/Tgt	12/15	1	2	FACETS	0.568	0.467	0.682	0.568	0.467	0.682	SUBCLONAL	1	TRUE	1	0.18	2		859	724	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409824	63409824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	42	570	0	ENST00000330258.3:c.3343G>A	p.Glu1115Lys	p.E1115K	ENST00000330258	NM_152424.3	1115	Gag/Aag	2/2	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.18	2		570	424	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0019496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	243	558	1	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.244170775974063	3	FACETS	0.787	0.738	0.837	0.787	0.738	0.837	INDETERMINATE	2	TRUE	1	0.515016266970509	3		559	754	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440379	52440379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	174	446	0	ENST00000460680.1:c.673G>A	p.Asp225Asn	p.D225N	ENST00000460680	NM_004656.3	225	Gac/Aac	9/17	0.515016266970509	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.515016266970509	1		446	402	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575671	48575671	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0019496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	220	769	0	ENST00000342988.3:c.431C>G	p.Ser144Ter	p.S144*	ENST00000342988	NM_005359.5	144	tCa/tGa	4/12	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.515016266970509	2		769	616	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4387983	4387983	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	169	652	0	ENST00000261254.3:c.469C>G	p.His157Asp	p.H157D	ENST00000261254	NM_001759.3	157	Cat/Gat	3/5	0.515016266970509	1	FACETS	0.963	0.892	1	0.963	0.892	1	CLONAL	1	TRUE	0	0.515016266970509	1		652	506	SUCCESS
REL	5966	MSKCC	GRCh37	2	61148994	61148994	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0019496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	83	478	0	ENST00000295025.8:c.1184C>G	p.Ser395Ter	p.S395*	ENST00000295025	NM_002908.2	395	tCa/tGa	11/11	0.204571767887072	1	FACETS	0.404	0.357	0.455	0.404	0.357	0.455	INDETERMINATE	1	TRUE	0	0.515016266970509	1		478	592	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149237	61149237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1233682212	NA	P-0019496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	50	382	1	ENST00000295025.8:c.1427C>T	p.Ser476Phe	p.S476F	ENST00000295025	NM_002908.2	476	tCc/tTc	11/11	0.204571767887072	1	FACETS	0.375	0.319	0.437	0.375	0.319	0.437	INDETERMINATE	1	TRUE	0	0.515016266970509	1		383	384	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149285	61149285	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	46	373	0	ENST00000295025.8:c.1475C>G	p.Ser492Cys	p.S492C	ENST00000295025	NM_002908.2	492	tCt/tGt	11/11	0.204571767887072	1	FACETS	0.328	0.277	0.385	0.328	0.277	0.385	INDETERMINATE	1	TRUE	0	0.515016266970509	1		373	404	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149387	61149387	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	91	499	1	ENST00000295025.8:c.1577C>A	p.Ser526Ter	p.S526*	ENST00000295025	NM_002908.2	526	tCa/tAa	11/11	0.204571767887072	1	FACETS	0.498	0.443	0.556	0.498	0.443	0.556	INDETERMINATE	1	TRUE	0	0.515016266970509	1		500	527	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0019497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4756	5422	1035	6	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.5434049499676	29	FACETS	1	0.997	1			1	CLONAL	16	TRUE	NA	0.5434049499676	29		1041	10178	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0019497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	172	860	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.941	1			1	INDETERMINATE	1	TRUE	NA	0.5434049499676	2		860	620	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711928	89711931	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	rs1564837868	NA	P-0019497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	157	758	0	ENST00000371953.3:c.548_551del	p.Lys183IlefsTer15	p.K183Ifs*15	ENST00000371953	NM_000314.4	182	ttAAAG/tt	6/9	0.537612109591148	1	FACETS	0.967	0.895	1	0.967	0.895	1	CLONAL	1	TRUE	0	0.5434049499676	1		758	435	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273075	55273075	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2979	4303	738	3	ENST00000275493.2:c.3398T>C	p.Val1133Ala	p.V1133A	ENST00000275493	NM_005228.3	1133	gTg/gCg	28/28	0.5434049499676	29	FACETS	1	0.993	1			1	CLONAL	18	TRUE	NA	0.5434049499676	29		741	7282	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273200	55273579	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	GACTTCTTTCCCAAGGAAGCCAAGCCAAATGGCATCTTTAAGGGCTCCACAGCTGAAAATGCAGAATACCTAAGGGTCGCGCCACAAAGCAGTGAATTTATTGGAGCATGACCACGGAGGATAGTATGAGCCCTAAAAATCCAGACTCTTTCGATACCCAGGACCAAGCCACAGCAGGTCCTCCATCCCAACAGCCATGCCCGCATTAGCTCTTAGACCCACAGACTGGTTTTGCAACGTTTACACCGACTAGCCAGGAAGTACTTCCACCTCGGGCACATTTTGGGAAGTTGCATTCCTTTGTCTTCAAACTGTGAAGCATTTACAGAAACGCATCCAGCAAGAATATTGTCCCTTTGAGCAGAAATTTATCTTTCAAA	GACTTCTTTCCCAAGGAAGCCAAGCCAAATGGCATCTTTAAGGGCTCCACAGCTGAAAATGCAGAATACCTAAGGGTCGCGCCACAAAGCAGTGAATTTATTGGAGCATGACCACGGAGGATAGTATGAGCCCTAAAAATCCAGACTCTTTCGATACCCAGGACCAAGCCACAGCAGGTCCTCCATCCCAACAGCCATGCCCGCATTAGCTCTTAGACCCACAGACTGGTTTTGCAACGTTTACACCGACTAGCCAGGAAGTACTTCCACCTCGGGCACATTTTGGGAAGTTGCATTCCTTTGTCTTCAAACTGTGAAGCATTTACAGAAACGCATCCAGCAAGAATATTGTCCCTTTGAGCAGAAATTTATCTTTCAAA	-	novel	NA	P-0019497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7421	395	916	0	ENST00000275493.2:c.3525_*271del		p.*1175*	ENST00000275493	NM_005228.3	1175		28/28	0.5434049499676	29	FACETS	0.775	0.731	0.821			1	SUBCLONAL	2	TRUE	NA	0.5434049499676	29		916	7816	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0019499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	124	573	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	NA	2	FACETS	0.814	0.736	0.895			1	INDETERMINATE	1	TRUE	NA	0.386210488534882	2		573	789	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412898	49412898	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519954	NA	P-0019499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	106	845	0	ENST00000418115.1:c.125A>G	p.Tyr42Cys	p.Y42C	ENST00000418115	NM_001664.2	42	tAt/tGt	2/5	1	2	FACETS	0.577	0.516	0.642	0.577	0.516	0.642	SUBCLONAL	1	TRUE	1	0.386210488534882	2		845	951	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409117	4409117	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs776036883	NA	P-0019499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	72	518	1	ENST00000261254.3:c.812C>A	p.Ser271Ter	p.S271*	ENST00000261254	NM_001759.3	271	tCg/tAg	5/5	1	2	FACETS	0.576	0.503	0.655	0.576	0.503	0.655	SUBCLONAL	1	TRUE	1	0.386210488534882	2		519	647	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420700	49420703	+	frameshift_variant	Frame_Shift_Del	DEL	CAAG	CAAG	AAT	novel	NA	P-0019499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	87	675	2	ENST00000301067.7:c.15046_15049delinsATT	p.Leu5016IlefsTer35	p.L5016Ifs*35	ENST00000301067	NM_003482.3	5016	CTTGgc/ATTgc	48/54	1	2	FACETS	0.602	0.533	0.677	0.602	0.533	0.677	SUBCLONAL	1	TRUE	1	0.386210488534882	2		677	748	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15938117	15938117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769360451	NA	P-0019499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	23	302	1	ENST00000268712.3:c.7097C>T	p.Thr2366Met	p.T2366M	ENST00000268712	NM_006311.3	2366	aCg/aTg	45/46	NA	2	FACETS	0.338	0.263	0.425			1	INDETERMINATE	1	TRUE	NA	0.386210488534882	2		303	352	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685568	29685568	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	36	711	0	ENST00000356175.3:c.7978A>T	p.Ile2660Phe	p.I2660F	ENST00000356175	NM_000267.3	2660	Atc/Ttc	54/57	1	2	FACETS	0.347	0.285	0.417	0.347	0.285	0.417	SUBCLONAL	1	TRUE	1	0.386210488534882	2		711	537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0019500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	390	697	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.605783284961794	2	FACETS	0.986	0.949	1	0.986	0.949	1	CLONAL	2	TRUE	0	0.632744590115558	2		697	625	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435153	110435153	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776792996	NA	P-0019500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3877	268	823	1	ENST00000375856.3:c.3248C>T	p.Pro1083Leu	p.P1083L	ENST00000375856	NM_003749.2	1083	cCg/cTg	1/2	0.632744590115558	14	FACETS	0.98	0.913	1			1	CLONAL	1	TRUE	NA	0.632744590115558	14		824	4145	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771987	135771988	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs2234980	NA	P-0019500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	58	301	0	ENST00000298552.3:c.3127_3129dup	p.Ser1043dup	p.S1043dup	ENST00000298552	NM_001162426.1	1043	-/AGC	23/23	1	2	FACETS	0.687	0.595	0.784	0.687	0.595	0.784	SUBCLONAL	1	TRUE	1	0.632744590115558	2		301	267	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138110	64138110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	211	653	0	ENST00000334205.4:c.2033G>A	p.Ser678Asn	p.S678N	ENST00000334205	NM_003942.2	678	aGc/aAc	16/17	0.438725411369614	3	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.632744590115558	3		653	706	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662662	227662662	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1412312472	NA	P-0019500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	154	543	1	ENST00000305123.5:c.793C>T	p.Arg265Cys	p.R265C	ENST00000305123	NM_005544.2	265	Cgc/Tgc	1/2	0.616022439711639	3	FACETS	0.933	0.856	1	0.466	0.428	0.507	CLONAL	1	TRUE	1	0.632744590115558	3		544	687	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858566	27858566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761264569	NA	P-0019500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	41	185	0	ENST00000359303.2:c.5C>T	p.Ala2Val	p.A2V	ENST00000359303	NM_003535.2	2	gCc/gTc	1/1	0.631403102022079	4	FACETS	0.874	0.734	1	0.291	0.244	0.343	CLONAL	1	TRUE	1	0.632744590115558	4		185	242	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882019	NA	P-0019501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	510	1106	2	ENST00000269305.4:c.455dup	p.Pro153AlafsTer28	p.P153Afs*28	ENST00000269305	NM_001126112.2	152	ccg/ccCg	5/11	NA	2	FACETS	0.887	0.852	0.923			1	INDETERMINATE	2	TRUE	NA	0.47180951950267	2		1108	1218	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944983	31944983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1175067252	NA	P-0019501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	282	863	1	ENST00000340398.3:c.118C>T	p.Arg40Cys	p.R40C	ENST00000340398	NM_001013699.2	40	Cgc/Tgc	1/1	0.339466108801994	3	FACETS	0.838	0.79	0.888	0.838	0.79	0.888	CLONAL	2	TRUE	1	0.47180951950267	3		864	881	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778897	9778897	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1460280596	NA	P-0019501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	150	844	3	ENST00000377346.4:c.1166G>A	p.Arg389His	p.R389H	ENST00000377346	NM_005026.3	389	cGt/cAt	9/24	0.144022677929059	5	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.47180951950267	5		847	859	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56787349	56787349	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs587782507	NA	P-0019501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	31	442	0	ENST00000337432.4:c.835G>C	p.Ala279Pro	p.A279P	ENST00000337432	NM_058216.2	279	Gct/Cct	5/9	0.430386039316867	2	FACETS	0.282	0.228	0.344	0.141	0.114	0.172	SUBCLONAL	1	TRUE	0	0.47180951950267	2		442	466	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156298	106156303	+	inframe_deletion	In_Frame_Del	DEL	CACCAT	CACCAT	-	novel	NA	P-0019501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	37	411	0	ENST00000380013.4:c.1202_1207del	p.Pro401_Ser402del	p.P401_S402del	ENST00000380013	NM_001127208.2	400	cCACCATca/cca	3/11	0.398753624830914	2	FACETS	0.39	0.322	0.467	0.195	0.161	0.234	SUBCLONAL	1	TRUE	0	0.47180951950267	2		411	402	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815827	32815827	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	168	771	1	ENST00000354258.4:c.1789G>T	p.Val597Leu	p.V597L	ENST00000354258	NM_000593.5	597	Gtg/Ttg	8/11	0.25817824534732	2	FACETS	0.94	0.865	1	0.47	0.432	0.509	INDETERMINATE	1	TRUE	0	0.47180951950267	2		772	758	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739594	41739594	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	149	543	0	ENST00000242208.4:c.379G>T	p.Ala127Ser	p.A127S	ENST00000242208	NM_002192.2	127	Gcc/Tcc	2/3	0.43048842282256	3	FACETS	1	0.988	1	0.743	0.683	0.806	CLONAL	1	TRUE	1	0.47180951950267	3		543	525	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0019503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	222	860	0				ENST00000310581	NM_198253.2	-/1132			0.2164829719111	3	FACETS	1	0.989	1	0.643	0.601	0.686	INDETERMINATE	1	TRUE	1	0.642305378077257	3		860	710	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175793	24175793	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772804160	NA	P-0019503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	196	683	0	ENST00000263121.7:c.1021C>T	p.Arg341Trp	p.R341W	ENST00000263121	NM_003073.3	341	Cgg/Tgg	8/9	0.636470513337993	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.642305378077257	1		683	401	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008324	29008324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770377283	NA	P-0019503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	103	361	0	ENST00000282397.4:c.547C>T	p.Arg183Cys	p.R183C	ENST00000282397	NM_002019.4	183	Cgc/Tgc	5/30	0.609357399660388	2	FACETS	0.831	0.764	0.897	0.831	0.764	0.897	CLONAL	2	TRUE	0	0.642305378077257	2		361	193	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047524	49047525	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0019503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	141	489	0	ENST00000267163.4:c.2520_2520+1del		p.G840fs	ENST00000267163	NM_000321.2	840	GGg/g	24/27	0.609357399660388	2	FACETS	0.787	0.731	0.842	0.787	0.731	0.842	SUBCLONAL	2	TRUE	0	0.642305378077257	2		489	279	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653119	29653119	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	145	406	0	ENST00000356175.3:c.5054T>C	p.Leu1685Pro	p.L1685P	ENST00000356175	NM_000267.3	1685	cTt/cCt	36/57	0.2164829719111	3	FACETS	1	0.988	1	0.717	0.661	0.775	INDETERMINATE	1	TRUE	1	0.642305378077257	3		406	416	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0019505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	96	290	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	TRUE	1	0.628825534806674	2		291	300	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791758	42791758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1380826096	NA	P-0019505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	66	862	2	ENST00000575354.2:c.644G>A	p.Arg215Gln	p.R215Q	ENST00000575354	NM_015125.3	215	cGg/cAg	5/20	0.346846516419577	0	FACETS	0.16	0.139	0.183			1	INDETERMINATE	1	TRUE	0	0.628825534806674	0		864	487	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574675	64574675	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	247	667	0	ENST00000312049.6:c.800T>G	p.Leu267Arg	p.L267R	ENST00000312049	NM_130799.2	267	cTc/cGc	5/10	0.610675664200987	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.610675664200987	2		667	364	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	41	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.86	0.716	1	0.86	0.716	1	CLONAL	1	TRUE	1	0.172652700017917	2		509	552	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727454	66727454	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519909	NA	P-0019507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	24	445	0	ENST00000307102.5:c.170A>C	p.Lys57Thr	p.K57T	ENST00000307102	NM_002755.3	57	aAg/aCg	2/11	1	2	FACETS	0.563	0.44	0.705	0.563	0.44	0.705	SUBCLONAL	1	TRUE	1	0.172652700017917	2		445	494	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453148	140453148	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs397507483	NA	P-0019507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	39	462	0	ENST00000288602.6:c.1787G>T	p.Gly596Val	p.G596V	ENST00000288602	NM_004333.4	596	gGt/gTt	15/18	0.172652700017917	3	FACETS	0.972	0.805	1	0.486	0.402	0.579	CLONAL	1	TRUE	1	0.172652700017917	3		462	505	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219164	133219164	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1274894982	NA	P-0019507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	67	759	0	ENST00000320574.5:c.4880A>G	p.His1627Arg	p.H1627R	ENST00000320574	NM_006231.2	1627	cAt/cGt	37/49	1	2	FACETS	0.961	0.833	1	0.961	0.833	1	CLONAL	1	TRUE	1	0.172652700017917	2		759	808	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991332	72991332	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	47	463	0	ENST00000268489.5:c.2713G>C	p.Ala905Pro	p.A905P	ENST00000268489	NM_006885.3	905	Gct/Cct	2/10	1	2	FACETS	0.974	0.821	1	0.974	0.821	1	CLONAL	1	TRUE	1	0.172652700017917	2		463	559	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207642	2207642	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	89	760	0	ENST00000398665.3:c.926C>A	p.Pro309Gln	p.P309Q	ENST00000398665	NM_032482.2	309	cCa/cAa	11/28	NA	2	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.172652700017917	2		760	810	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152118	11152118	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	58	599	0	ENST00000358026.2:c.4402G>T	p.Glu1468Ter	p.E1468*	ENST00000358026	NM_001128849.1	1468	Gag/Tag	31/36	0.163018860861147	1	FACETS	0.946	0.812	1	0.946	0.812	1	CLONAL	1	TRUE	0	0.172652700017917	1		599	649	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372482	55372500	+	frameshift_variant	Frame_Shift_Del	DEL	GCCACGGGGCCATTTCCTC	GCCACGGGGCCATTTCCTC	-	novel	NA	P-0019507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	120	1227	0	ENST00000297316.4:c.1173_1191del	p.Ser391ArgfsTer57	p.S391Rfs*57	ENST00000297316	NM_022454.3	391	aGCCACGGGGCCATTTCCTCg/ag	2/2	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.172652700017917	2		1227	1181	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964431	70964431	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	44	490	0	ENST00000276594.2:c.1597G>T	p.Asp533Tyr	p.D533Y	ENST00000276594	NM_024504.3	533	Gac/Tac	8/8	1	2	FACETS	0.942	0.79	1	0.942	0.79	1	CLONAL	1	TRUE	1	0.172652700017917	2		490	541	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411175	63411175	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	77	499	0	ENST00000330258.3:c.1992G>T	p.Met664Ile	p.M664I	ENST00000330258	NM_152424.3	664	atG/atT	2/2	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.172652700017917	2		499	667	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229279	123229279	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	32	348	0	ENST00000218089.9:c.3763G>A	p.Ala1255Thr	p.A1255T	ENST00000218089	NM_001042749.1	1255	Gct/Act	34/35	1	2	FACETS	0.854	0.693	1	0.854	0.693	1	CLONAL	1	TRUE	1	0.172652700017917	2		348	434	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947395	38947395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	984	407	0	ENST00000357387.3:c.4285C>T	p.Leu1429Phe	p.L1429F	ENST00000357387	NM_152756.3	1429	Ctc/Ttc	32/38	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.670889177251773	NA		407	1972	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947491	38947491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	1091	426	1	ENST00000357387.3:c.4189C>T	p.Pro1397Ser	p.P1397S	ENST00000357387	NM_152756.3	1397	Cct/Tct	32/38	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.670889177251773	NA		427	2114	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024001	27024002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0019509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	46	188	1	ENST00000324856.7:c.1113dup	p.Gln372AlafsTer28	p.Q372Afs*28	ENST00000324856	NM_006015.4	369	-/G	1/20	0.780273100577858	1	FACETS	0.949	0.847	1	0.949	0.847	1	CLONAL	1	TRUE	0	0.797827972481391	1		189	73	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0019509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	121	413	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	0.797827972481391	1	FACETS	0.916	0.854	0.977	0.916	0.854	0.977	CLONAL	1	TRUE	0	0.797827972481391	1		413	199	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169209	119169209	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	177	452	0	ENST00000264033.4:c.2393C>G	p.Ser798Cys	p.S798C	ENST00000264033	NM_005188.3	798	tCc/tGc	15/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.797827972481391	2		452	414	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134269	11134269	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	228	716	0	ENST00000358026.2:c.2935C>G	p.Arg979Gly	p.R979G	ENST00000358026	NM_001128849.1	979	Cga/Gga	20/36	0.797827972481391	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.797827972481391	1		716	333	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000041	30000042	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0019509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	205	694	2	ENST00000338641.4:c.57dup	p.Lys20GlnfsTer29	p.K20Qfs*29	ENST00000338641	NM_000268.3	18	-/C	1/16	0.761277532766624	1	FACETS	0.971	0.923	1	0.971	0.923	1	CLONAL	1	TRUE	0	0.797827972481391	1		696	318	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97873816	97873816	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	202	831	0	ENST00000289081.3:c.1258A>C	p.Thr420Pro	p.T420P	ENST00000289081	NM_000136.2	420	Acg/Ccg	13/15	1	2	FACETS	0.917	0.857	0.979	0.917	0.857	0.979	CLONAL	1	TRUE	1	0.797827972481391	2		831	552	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156836730	156836730	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1449	288	869	0	ENST00000524377.1:c.388del	p.Leu130SerfsTer67	p.L130Sfs*67	ENST00000524377	NM_002529.3	130	Ctc/tc	4/17	0.646309875479591	4	FACETS	0.845	0.792	0.9			1	CLONAL	1	TRUE	NA	0.646309875479591	4		869	1737	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772262	68772325	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CACGTTCACGGTGCCCCGGCGCCACCTGGAGAGAGGCCGCGTCCTGGGCAGAGGTGAGGGCGCG	CACGTTCACGGTGCCCCGGCGCCACCTGGAGAGAGGCCGCGTCCTGGGCAGAGGTGAGGGCGCG	-	novel	NA	P-0019510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	229	1015	0	ENST00000261769.5:c.112_163+12del		p.X38_splice	ENST00000261769	NM_004360.3	38		2/16	0.646309875479591	1	FACETS	0.707	0.663	0.753	0.707	0.663	0.753	SUBCLONAL	1	TRUE	0	0.646309875479591	1		1015	678	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579710	7579710	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1555526931	NA	P-0019510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	310	847	0	ENST00000269305.4:c.86del	p.Asn29ThrfsTer15	p.N29Tfs*15	ENST00000269305	NM_001126112.2	29	aAc/ac	3/11	0.618434581614903	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.646309875479591	1		847	644	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273278	55273278	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369585356	NA	P-0019510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	210	751	0	ENST00000275493.2:c.3601G>A	p.Ala1201Thr	p.A1201T	ENST00000275493	NM_005228.3	1201	Gcg/Acg	28/28	1	2	FACETS	0.824	0.767	0.882	0.824	0.767	0.882	CLONAL	1	TRUE	1	0.646309875479591	2		751	789	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38184296	38184296	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	247	836	0	ENST00000317025.8:c.1660A>G	p.Lys554Glu	p.K554E	ENST00000317025	NM_023034.1	554	Aag/Gag	7/24	0.646309875479591	3	FACETS	1	0.958	1			1	CLONAL	1	TRUE	NA	0.646309875479591	3		836	980	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028781	47028789	+	inframe_deletion	In_Frame_Del	DEL	AACCGCAGC	AACCGCAGC	-	novel	NA	P-0019510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	310	1021	0	ENST00000377604.3:c.85_93del	p.Asn29_Ser31del	p.N29_S31del	ENST00000377604	NM_001204468.1	29	AACCGCAGC/-	3/24	1	2	FACETS	0.902	0.852	0.954	0.902	0.852	0.954	CLONAL	1	TRUE	1	0.646309875479591	2		1021	1063	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0019511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	310	831	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.361318040148024	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.361318040148024	2		831	788	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866429	37866429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376183465	NA	P-0019511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	37	919	0	ENST00000269571.5:c.734C>T	p.Thr245Met	p.T245M	ENST00000269571		245	aCg/aTg	6/27	0.361318040148024	2	FACETS	0.284	0.233	0.342	0.142	0.116	0.171	SUBCLONAL	1	TRUE	0	0.361318040148024	2		919	720	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58700901	58700901	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	43	480	3	ENST00000305921.3:c.492G>T	p.Met164Ile	p.M164I	ENST00000305921	NM_003620.3	164	atG/atT	2/6	0.288335417991384	4	FACETS	0.615	0.514	0.727	0.307	0.257	0.364	SUBCLONAL	1	TRUE	2	0.361318040148024	4		483	527	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371658	225371658	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	25	718	0	ENST00000264414.4:c.946T>C	p.Cys316Arg	p.C316R	ENST00000264414	NM_003590.4	316	Tgt/Cgt	7/16	0.322193221103887	2	FACETS	0.434	0.342	0.539	0.217	0.171	0.27	SUBCLONAL	1	TRUE	0	0.361318040148024	2		718	319	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	79	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.915	0.805	1	0.915	0.805	1	CLONAL	1	TRUE	1	0.26	2		555	664	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0019512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	54	338	0	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.26	2		338	293	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588869	69588869	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766381502	NA	P-0019512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	31	586	2	ENST00000168712.1:c.367C>T	p.Arg123Trp	p.R123W	ENST00000168712	NM_002007.2	123	Cgg/Tgg	2/3	1	2	FACETS	0.403	0.325	0.492	0.403	0.325	0.492	SUBCLONAL	1	TRUE	1	0.26	2		588	592	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152864420	152864420	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	21	271	0	ENST00000406277.2:c.106G>A	p.Gly36Ser	p.G36S	ENST00000406277	NM_152274.4	36	Ggt/Agt	3/7	NA		FACETS		NA	1				INDETERMINATE	NA	TRUE	NA	0.26	NA		271	331	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0019513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	331	906	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.722855816027574	2		906	854	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572988	7572988	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs878854063	NA	P-0019513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	159	565	0	ENST00000269305.4:c.1121del	p.Gly374ValfsTer48	p.G374Vfs*48	ENST00000269305	NM_001126112.2	374	gGt/gt	11/11	0.722855816027574	1	FACETS	0.839	0.781	0.896	0.839	0.781	0.896	CLONAL	1	TRUE	0	0.722855816027574	1		565	335	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443631	29443631	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519784	NA	P-0019513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	281	824	0	ENST00000389048.3:c.3586C>A	p.Leu1196Met	p.L1196M	ENST00000389048	NM_004304.4	1196	Ctg/Atg	23/29	0.70739988693075	3	FACETS	1	0.951	1	0.338	0.317	0.359	CLONAL	1	TRUE	0	0.722855816027574	3		824	1045	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39763610	39763610	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	160	560	0	ENST00000288319.7:c.842C>G	p.Pro281Arg	p.P281R	ENST00000288319	NM_182918.3	281	cCc/cGc	8/10	1	2	FACETS	0.993	0.919	1	0.993	0.919	1	CLONAL	1	TRUE	1	0.722855816027574	2		560	446	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509031	106509031	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	476	583	0	ENST00000359195.3:c.1025A>C	p.His342Pro	p.H342P	ENST00000359195	NM_002649.2	342	cAc/cCc	2/11	0.722855816027574	3	FACETS	0.956	0.93	0.981	0.956	0.93	0.981	CLONAL	3	TRUE	0	0.722855816027574	3		583	625	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391214	89391214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs530556931	NA	P-0019514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	30	382	0	ENST00000336596.2:c.1280C>T	p.Ala427Val	p.A427V	ENST00000336596	NM_005233.5	427	gCg/gTg	5/17	0.370457839760043	1	FACETS	0.345	0.278	0.419	0.345	0.278	0.419	SUBCLONAL	1	TRUE	0	0.47960324832071	1		382	276	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385222	41385222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	50	661	1	ENST00000373198.4:c.739C>T	p.Arg247Cys	p.R247C	ENST00000373198	NM_133170.3	247	Cgc/Tgc	6/32	0.427685315297677	5	FACETS	0.368	0.311	0.432	0.123	0.103	0.144	SUBCLONAL	1	TRUE	2	0.47960324832071	5		662	973	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970914	79970915	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587776701	NA	P-0019514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	227	1080	7	ENST00000265081.6:c.1148dup	p.Asn385GlnfsTer19	p.N385Qfs*19	ENST00000265081	NM_002439.4	380	-/A	7/24	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.47960324832071	2		1087	792	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46733212	46733212	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	146	779	0	ENST00000371975.4:c.973G>T	p.Gly325Ter	p.G325*	ENST00000371975	NM_003579.3	325	Gga/Tga	9/18	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.47960324832071	2		779	538	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380246	25380246	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	88	742	0	ENST00000311936.3:c.212A>G	p.Tyr71Cys	p.Y71C	ENST00000311936	NM_004985.3	71	tAc/tGc	3/5	NA	2	FACETS	0.629	0.558	0.705			1	INDETERMINATE	1	TRUE	NA	0.47960324832071	2		742	583	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107994	30107994	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	62	801	1	ENST00000331968.5:c.813C>A	p.His271Gln	p.H271Q	ENST00000331968	NM_002742.2	271	caC/caA	5/18	0.47960324832071	1	FACETS	0.381	0.329	0.437	0.381	0.329	0.437	SUBCLONAL	1	TRUE	0	0.47960324832071	1		802	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579348	7579349	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAGA	novel	NA	P-0019514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	263	845	0	ENST00000269305.4:c.338_339insTCTT	p.His115LeufsTer35	p.H115Lfs*35	ENST00000269305	NM_001126112.2	113	ttc/ttTCTTc	4/11	0.426512016994805	1	FACETS	0.842	0.8	0.884	1	0.995	1	CLONAL	2	TRUE	0	0.47960324832071	1		845	495	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867148	45867148	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs892942500	NA	P-0019514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	49	846	2	ENST00000391945.4:c.971G>A	p.Arg324His	p.R324H	ENST00000391945	NM_000400.3	324	cGc/cAc	11/23	0.45587565410315	2	FACETS	0.322	0.272	0.377	0.161	0.136	0.189	SUBCLONAL	1	TRUE	0	0.47960324832071	2		848	635	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163575	47163575	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	22	365	0	ENST00000409792.3:c.2551G>T	p.Glu851Ter	p.E851*	ENST00000409792	NM_014159.6	851	Gaa/Taa	3/21	0.370457839760043	1	FACETS	0.373	0.291	0.467	0.373	0.291	0.467	SUBCLONAL	1	TRUE	0	0.47960324832071	1		365	187	SUCCESS
APC	324	MSKCC	GRCh37	5	112162882	112162883	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0019514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	128	701	0	ENST00000257430.4:c.1488_1489del	p.Leu497LysfsTer39	p.L497Kfs*39	ENST00000257430	NM_000038.5	496	ACa/a	12/16	1	2	FACETS	0.881	0.811	0.951	1	0.99	1	CLONAL	2	TRUE	1	0.47960324832071	2		701	303	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	26	736	0				ENST00000310581	NM_198253.2	-/1132			0.111486920429764	5	FACETS	0.654	0.52	0.805			1	INDETERMINATE	1	FALSE	NA	0.752153545618327	5		736	225	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0019515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	130	715	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.325983969784744	3	FACETS	0.849	0.785	0.914	0.566	0.523	0.61	INDETERMINATE	2	FALSE	0	0.752153545618327	3		715	280	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151839	108151839	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	137	589	0	ENST00000278616.4:c.3520T>C	p.Phe1174Leu	p.F1174L	ENST00000278616	NM_000051.3	1174	Ttt/Ctt	24/63	0.766097947565081	3	FACETS	1	0.979	1	0.605	0.556	0.656	CLONAL	1	FALSE	1	0.752153545618327	3		589	414	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422663	49422663	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	212	765	0	ENST00000301067.7:c.14330del	p.Gly4777AlafsTer20	p.G4777Afs*20	ENST00000301067	NM_003482.3	4777	gGc/gc	45/54	0.496372290249356	6	FACETS	0.862	0.807	0.917	0.862	0.807	0.917	CLONAL	3	FALSE	3	0.752153545618327	6		765	546	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427950	49427950	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775632051	NA	P-0019515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	104	689	1	ENST00000301067.7:c.10640G>A	p.Arg3547His	p.R3547H	ENST00000301067	NM_003482.3	3547	cGc/cAc	38/54	0.496372290249356	6	FACETS	0.794	0.716	0.877	0.529	0.477	0.585	SUBCLONAL	2	FALSE	3	0.752153545618327	6		690	436	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923365	9923365	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	39	631	0	ENST00000330684.3:c.1922T>C	p.Phe641Ser	p.F641S	ENST00000330684	NM_001134407.1	641	tTc/tCc	9/13	1	2	FACETS	0.564	0.473	0.662	0.564	0.473	0.662	SUBCLONAL	1	FALSE	1	0.752153545618327	2		631	184	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577576	7577576	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	124	647	0	ENST00000269305.4:c.705C>G	p.Asn235Lys	p.N235K	ENST00000269305	NM_001126112.2	235	aaC/aaG	7/11	0.325983969784744	3	FACETS	0.859	0.793	0.926	0.573	0.528	0.618	INDETERMINATE	2	FALSE	0	0.752153545618327	3		647	264	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249890	39249890	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	180	656	0	ENST00000402219.2:c.1679A>C	p.Gln560Pro	p.Q560P	ENST00000402219	NM_005633.3	560	cAg/cCg	10/23	0.511617439844215	3	FACETS	1	0.986	1	0.627	0.583	0.673	CLONAL	1	FALSE	1	0.752153545618327	3		656	525	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171760	36171760	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0019515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	134	274	0	ENST00000300305.3:c.806-1G>C		p.X269_splice	ENST00000300305		269			0.766097947565081	3	FACETS	0.969	0.901	1	0.969	0.901	1	CLONAL	2	FALSE	1	0.752153545618327	3		274	253	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610715	52610715	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0019515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	70	431	0	ENST00000394830.3:c.3459-1G>A		p.X1153_splice	ENST00000394830	NM_018313.4	1153			0.766097947565081	4	FACETS	1	0.93	1	0.542	0.476	0.611	CLONAL	1	FALSE	2	0.752153545618327	4		431	301	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0019516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	98	685	1	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.308942542604758	1	FACETS	0.859	0.768	0.955	0.859	0.768	0.955	CLONAL	1	TRUE	0	0.337541230759451	1		686	562	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257434	16257434	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	41	774	0	ENST00000375759.3:c.4699G>A	p.Glu1567Lys	p.E1567K	ENST00000375759	NM_015001.2	1567	Gag/Aag	11/15	1	2	FACETS	0.359	0.298	0.427	0.359	0.298	0.427	SUBCLONAL	1	TRUE	1	0.337541230759451	2		774	677	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256882	16256882	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	52	956	0	ENST00000375759.3:c.4147G>C	p.Asp1383His	p.D1383H	ENST00000375759	NM_015001.2	1383	Gac/Cac	11/15	1	2	FACETS	0.422	0.358	0.492	0.422	0.358	0.492	SUBCLONAL	1	TRUE	1	0.337541230759451	2		956	730	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805724	32805725	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAGC	novel	NA	P-0019516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	85	768	0	ENST00000374899.4:c.283_286dup	p.Ser96CysfsTer72	p.S96Cfs*72	ENST00000374899	NM_018833.2	96	tca/tGCTTca	2/12	1	2	FACETS	0.752	0.665	0.845	0.752	0.665	0.845	SUBCLONAL	1	TRUE	1	0.337541230759451	2		768	670	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339211	87339211	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	56	820	0	ENST00000277120.3:c.793T>A	p.Ser265Thr	p.S265T	ENST00000277120		265	Tct/Act	8/19	0.199027079659593	1	FACETS	0.454	0.388	0.525	0.454	0.388	0.525	INDETERMINATE	1	TRUE	0	0.337541230759451	1		820	608	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0019517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	92	680	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.765	0.683	0.852	0.765	0.683	0.852	SUBCLONAL	1	TRUE	1	0.517264929555747	2		680	465	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	157	736	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.517264929555747	2		736	541	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0019517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	110	670	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.911	0.823	1	0.911	0.823	1	CLONAL	1	TRUE	1	0.517264929555747	2		670	467	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253212	133253212	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	139	746	0	ENST00000320574.5:c.829G>C	p.Glu277Gln	p.E277Q	ENST00000320574	NM_006231.2	277	Gag/Cag	9/49	1	2	FACETS	0.868	0.793	0.947	0.868	0.793	0.947	CLONAL	1	TRUE	1	0.517264929555747	2		746	619	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539690	187539690	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs748166431	NA	P-0019517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	71	430	0	ENST00000441802.2:c.8050G>T	p.Glu2684Ter	p.E2684*	ENST00000441802	NM_005245.3	2684	Gaa/Taa	10/27	1	2	FACETS	0.638	0.559	0.723	0.638	0.559	0.723	SUBCLONAL	1	TRUE	1	0.517264929555747	2		430	430	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243774	41243774	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs431825399	NA	P-0019517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	56	535	1	ENST00000357654.3:c.3774G>T	p.Glu1258Asp	p.E1258D	ENST00000357654	NM_007294.3	1258	gaG/gaT	10/23	1	2	FACETS	0.475	0.407	0.548	0.475	0.407	0.548	SUBCLONAL	1	TRUE	1	0.517264929555747	2		536	456	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094291	27094291	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	22	427	0	ENST00000324856.7:c.2999C>T	p.Ser1000Phe	p.S1000F	ENST00000324856	NM_006015.4	1000	tCt/tTt	11/20	1	2	FACETS	0.215	0.166	0.272	0.215	0.166	0.272	SUBCLONAL	1	TRUE	1	0.517264929555747	2		427	396	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112745487	112745487	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	82	721	0	ENST00000369452.4:c.805C>T	p.Gln269Ter	p.Q269*	ENST00000369452	NM_007373.3	269	Cag/Tag	3/9	1	2	FACETS	0.724	0.641	0.812	0.724	0.641	0.812	SUBCLONAL	1	TRUE	1	0.517264929555747	2		721	438	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972451	32972451	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	195	857	0	ENST00000380152.3:c.9801G>C	p.Lys3267Asn	p.K3267N	ENST00000380152		3267	aaG/aaC	27/27	1	2	FACETS	0.888	0.823	0.955	0.888	0.823	0.955	CLONAL	1	TRUE	1	0.517264929555747	2		857	849	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951166	48951166	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	72	432	1	ENST00000267163.4:c.1328C>T	p.Ser443Leu	p.S443L	ENST00000267163	NM_000321.2	443	tCa/tTa	13/27	1	2	FACETS	0.884	0.779	0.995	0.884	0.779	0.995	CLONAL	1	TRUE	1	0.517264929555747	2		433	315	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23652463	23652463	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	155	797	0	ENST00000261584.4:c.16G>C	p.Gly6Arg	p.G6R	ENST00000261584	NM_024675.3	6	Ggg/Cgg	1/13	1	2	FACETS	0.907	0.833	0.984	0.907	0.833	0.984	CLONAL	1	TRUE	1	0.517264929555747	2		797	661	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829971	72829971	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	54	720	0	ENST00000268489.5:c.6610A>G	p.Asn2204Asp	p.N2204D	ENST00000268489	NM_006885.3	2204	Aac/Gac	9/10	1	2	FACETS	0.321	0.273	0.373	0.321	0.273	0.373	SUBCLONAL	1	TRUE	1	0.517264929555747	2		720	651	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831318	72831318	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	49	338	0	ENST00000268489.5:c.5263C>T	p.His1755Tyr	p.H1755Y	ENST00000268489	NM_006885.3	1755	Cac/Tac	9/10	1	2	FACETS	0.686	0.585	0.796	0.686	0.585	0.796	SUBCLONAL	1	TRUE	1	0.517264929555747	2		338	276	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17941003	17941003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	133	965	0	ENST00000458235.1:c.3121G>A	p.Glu1041Lys	p.E1041K	ENST00000458235	NM_000215.3	1041	Gag/Aag	23/24	1	2	FACETS	0.585	0.531	0.642	0.585	0.531	0.642	SUBCLONAL	1	TRUE	1	0.517264929555747	2		965	879	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525047	187525054	+	frameshift_variant	Frame_Shift_Del	DEL	TCGCAGGC	TCGCAGGC	-	novel	NA	P-0019517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	73	520	0	ENST00000441802.2:c.10626_10633del	p.Pro3543PhefsTer31	p.P3543Ffs*31	ENST00000441802	NM_005245.3	3542	ccGCCTGCGAtt/cctt	19/27	1	2	FACETS	0.61	0.535	0.69	0.61	0.535	0.69	SUBCLONAL	1	TRUE	1	0.517264929555747	2		520	463	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638922	176638922	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	68	806	0	ENST00000439151.2:c.3522G>T	p.Met1174Ile	p.M1174I	ENST00000439151	NM_022455.4	1174	atG/atT	5/23	1	2	FACETS	0.381	0.331	0.435	0.381	0.331	0.435	SUBCLONAL	1	TRUE	1	0.517264929555747	2		806	690	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946057	13946057	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	22	383	0	ENST00000405192.2:c.1039G>A	p.Glu347Lys	p.E347K	ENST00000405192	NM_001163147.1	347	Gag/Aag	10/12	1	2	FACETS	0.202	0.156	0.255	0.202	0.156	0.255	SUBCLONAL	1	TRUE	1	0.517264929555747	2		383	422	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942761	44942761	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	124	746	0	ENST00000377967.4:c.3341C>A	p.Ser1114Ter	p.S1114*	ENST00000377967	NM_021140.2	1114	tCa/tAa	23/29	1	2	FACETS	0.811	0.736	0.89	0.811	0.736	0.89	CLONAL	1	TRUE	1	0.517264929555747	2		746	591	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949105	44949106	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0019517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	146	634	0	ENST00000377967.4:c.3668dup	p.Thr1224HisfsTer27	p.T1224Hfs*27	ENST00000377967	NM_021140.2	1222	-/G	25/29	1	2	FACETS	0.967	0.886	1	0.967	0.886	1	CLONAL	1	TRUE	1	0.517264929555747	2		634	584	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041400	47041400	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	49	1092	0	ENST00000377604.3:c.1744T>C	p.Tyr582His	p.Y582H	ENST00000377604	NM_001204468.1	582	Tat/Cat	16/24	1	2	FACETS	0.2	0.168	0.235	0.2	0.168	0.235	SUBCLONAL	1	TRUE	1	0.517264929555747	2		1092	947	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044872	47044872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	217	1070	2	ENST00000377604.3:c.2198G>A	p.Ser733Asn	p.S733N	ENST00000377604	NM_001204468.1	733	aGc/aAc	20/24	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.517264929555747	2		1072	799	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357083	70357083	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	213	1018	0	ENST00000374080.3:c.5598G>C	p.Gln1866His	p.Q1866H	ENST00000374080		1866	caG/caC	39/45	1	2	FACETS	0.95	0.884	1	0.95	0.884	1	CLONAL	1	TRUE	1	0.517264929555747	2		1018	867	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171442	123171442	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	25	720	0	ENST00000218089.9:c.354C>G	p.Ile118Met	p.I118M	ENST00000218089	NM_001042749.1	118	atC/atG	6/35	0.120068407261819	0	FACETS	0.104	0.082	0.13			1	INDETERMINATE	1	TRUE	0	0.517264929555747	0		720	448	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945071	151945071	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs202184064	NA	P-0019518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	108	831	1	ENST00000262189.6:c.2448C>A	p.Tyr816Ter	p.Y816*	ENST00000262189	NM_170606.2	816	taC/taA	14/59	1	2	FACETS	0.335	0.3	0.371	0.335	0.3	0.371	SUBCLONAL	1	TRUE	1	0.81946675196613	2		832	788	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115961	8115964	+	frameshift_variant	Frame_Shift_Del	DEL	CCAG	CCAG	-	novel	NA	P-0019518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	114	338	0	ENST00000346208.3:c.1308_1311del	p.Ser437TrpfsTer37	p.S437Wfs*37	ENST00000346208		436	tCCAGc/tc	6/6	1	2	FACETS	0.758	0.689	0.829	0.758	0.689	0.829	SUBCLONAL	1	TRUE	1	0.81946675196613	2		338	367	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350973	89350976	+	frameshift_variant	Frame_Shift_Del	DEL	GTAA	GTAA	-	novel	NA	P-0019518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	404	1228	0	ENST00000301030.4:c.1974_1977del	p.Tyr659AsnfsTer15	p.Y659Nfs*15	ENST00000301030	NM_001256183.1	658	acTTAC/ac	9/13	1	2	FACETS	0.836	0.796	0.877	0.836	0.796	0.877	CLONAL	1	TRUE	1	0.81946675196613	2		1228	1179	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968233	134968233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753895808	NA	P-0019518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	328	798	1	ENST00000398015.3:c.2746G>A	p.Val916Met	p.V916M	ENST00000398015	NM_004441.4	916	Gtg/Atg	15/16	1	2	FACETS	0.912	0.865	0.959	0.912	0.865	0.959	CLONAL	1	TRUE	1	0.81946675196613	2		799	878	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	175	736	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.893	0.827	0.96	0.893	0.827	0.96	CLONAL	1	TRUE	1	0.692482811774707	2		736	566	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936083	178936083	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519927	NA	P-0019519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	122	441	0	ENST00000263967.3:c.1625A>C	p.Glu542Ala	p.E542A	ENST00000263967	NM_006218.2	542	gAa/gCa	10/21	1	2	FACETS	0.806	0.734	0.881	0.806	0.734	0.881	CLONAL	1	TRUE	1	0.692482811774707	2		441	437	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661663	227661664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761880048	NA	P-0019519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	127	506	4	ENST00000305123.5:c.1791dup	p.His598AlafsTer13	p.H598Afs*13	ENST00000305123	NM_005544.2	597	-/G	1/2	1	2	FACETS	0.88	0.804	0.958	0.88	0.804	0.958	CLONAL	1	TRUE	1	0.692482811774707	2		510	417	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938922	178938922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	180	713	0	ENST00000263967.3:c.2164G>A	p.Glu722Lys	p.E722K	ENST00000263967	NM_006218.2	722	Gag/Aag	14/21	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.692482811774707	2		713	512	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134978	2134979	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0019519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	511	1210	0	ENST00000219476.3:c.4523_4524del	p.Pro1508LeufsTer15	p.P1508Lfs*15	ENST00000219476	NM_000548.3	1507	tCC/t	35/42	0.687454911732748	2	FACETS	0.927	0.897	0.956	0.927	0.897	0.956	CLONAL	2	TRUE	0	0.692482811774707	2		1210	796	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7977032	7977032	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	239	878	0	ENST00000319144.4:c.1698del	p.Tyr566Ter	p.Y566*	ENST00000319144	NM_001139.2	566	taT/ta	13/15	1	2	FACETS	0.917	0.859	0.975	0.917	0.859	0.975	CLONAL	1	TRUE	1	0.692482811774707	2		878	753	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974922	15974922	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	129	620	0	ENST00000268712.3:c.3953T>C	p.Ile1318Thr	p.I1318T	ENST00000268712	NM_006311.3	1318	aTt/aCt	30/46	1	2	FACETS	0.778	0.71	0.848	0.778	0.71	0.848	SUBCLONAL	1	TRUE	1	0.692482811774707	2		620	479	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921107	50921107	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	172	818	1	ENST00000440232.2:c.3227G>A	p.Cys1076Tyr	p.C1076Y	ENST00000440232	NM_002691.3	1076	tGc/tAc	27/27	1	2	FACETS	0.92	0.852	0.989	0.92	0.852	0.989	CLONAL	1	TRUE	1	0.692482811774707	2		819	540	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162852	47162852	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	123	494	0	ENST00000409792.3:c.3274C>T	p.Gln1092Ter	p.Q1092*	ENST00000409792	NM_014159.6	1092	Caa/Taa	3/21	1	2	FACETS	0.971	0.887	1	0.971	0.887	1	CLONAL	1	TRUE	1	0.692482811774707	2		494	366	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0019520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	110	691	5	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.43030784309473	2		696	435	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673792	30673792	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	81	703	4	ENST00000376406.3:c.3168G>C	p.Gln1056His	p.Q1056H	ENST00000376406	NM_014641.2	1056	caG/caC	10/15	1	2	FACETS	0.905	0.801	1	0.905	0.801	1	CLONAL	1	TRUE	1	0.43030784309473	2		707	416	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133528	55133529	+	protein_altering_variant	In_Frame_Ins	INS	-	-	TCG	novel	NA	P-0019521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	2020	838	0	ENST00000257290.5:c.832_833insTCG	p.Pro278delinsLeuAla	p.P278delinsLA	ENST00000257290	NM_006206.4	278	ccc/cTCGcc	6/23	0.656838899208154	11	FACETS	1	0.994	1			1	CLONAL	8	TRUE	NA	0.656838899208154	11		838	2989	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346751	91346751	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs753072653	NA	P-0019523-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	108	619	0	ENST00000355112.3:c.3359G>A	p.Gly1120Glu	p.G1120E	ENST00000355112	NM_000057.2	1120	gGg/gAg	18/22	0.79106805506129	3	FACETS	0.876	0.791	0.964	0.438	0.395	0.482	CLONAL	1	TRUE	1	0.79106805506129	3		619	435	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808875	3808878	+	frameshift_variant	Frame_Shift_Del	DEL	GATC	GATC	-	novel	NA	P-0019523-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	223	721	0	ENST00000262367.5:c.3346_3349del	p.Asp1116ProfsTer13	p.D1116Pfs*13	ENST00000262367	NM_004380.2	1116	GATCcc/cc	17/31	0.489997308381083	4	FACETS	1	0.986	1	0.4	0.373	0.428	CLONAL	1	TRUE	1	0.79106805506129	4		721	841	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677952	117677952	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0019523-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	158	628	0	ENST00000368508.3:c.3981T>A	p.Cys1327Ter	p.C1327*	ENST00000368508	NM_002944.2	1327	tgT/tgA	25/43	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.79106805506129	2		628	387	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934194	48934194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	167	634	1	ENST00000267163.4:c.649C>T	p.Gln217Ter	p.Q217*	ENST00000267163	NM_000321.2	217	Cag/Tag	7/27	0.689339132766415	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.689339132766415	1		635	293	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0019528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	180	521	0	ENST00000269305.4:c.673-2A>C		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.689339132766415	1	FACETS	0.983	0.923	1	0.983	0.923	1	CLONAL	1	TRUE	0	0.689339132766415	1		521	348	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263419	123263430	+	protein_altering_variant	In_Frame_Del	DEL	TGTTGGAGTTCA	TGTTGGAGTTCA	AGC	novel	NA	P-0019528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	101	457	1	ENST00000358487.5:c.1313_1324delinsGCT	p.Met438_Thr442delinsSerSer	p.M438_T442delinsSS	ENST00000358487	NM_000141.4	438	aTGAACTCCAACAcc/aGCTcc	10/18	0.689339132766415	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.689339132766415	1		458	190	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436575	110436575	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	295	1006	0	ENST00000375856.3:c.1826del	p.Ala609GlyfsTer48	p.A609Gfs*48	ENST00000375856	NM_003749.2	609	gCg/gg	1/2	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.689339132766415	2		1006	818	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640737	3640737	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs777514343	NA	P-0019528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	156	606	0	ENST00000294008.3:c.2902G>C	p.Glu968Gln	p.E968Q	ENST00000294008	NM_032444.2	968	Gag/Cag	12/15	1	2	FACETS	0.986	0.911	1	0.986	0.911	1	CLONAL	1	TRUE	1	0.689339132766415	2		606	459	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855909	68855932	+	inframe_deletion	In_Frame_Del	DEL	CCAGTTGCTACTGGAACAGGGACA	CCAGTTGCTACTGGAACAGGGACA	-	novel	NA	P-0019528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	419	396	1	ENST00000261769.5:c.1718_1741del	p.Pro573_Thr580del	p.P573_T580del	ENST00000261769	NM_004360.3	573	CCAGTTGCTACTGGAACAGGGACA/-	12/16	0.689339132766415	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.689339132766415	3		397	526	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474455	40474455	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	160	567	0	ENST00000264657.5:c.1946C>T	p.Ser649Leu	p.S649L	ENST00000264657	NM_139276.2	649	tCa/tTa	21/24	1	2	FACETS	0.91	0.841	0.982	0.91	0.841	0.982	CLONAL	1	TRUE	1	0.689339132766415	2		567	510	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678793	52678823	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTGAATTTGCATCCTGTCAAGATAAAATTAC	TTGAATTTGCATCCTGTCAAGATAAAATTAC	-	novel	NA	P-0019528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	120	357	0	ENST00000394830.3:c.814-18_826del		p.X272_splice	ENST00000394830	NM_018313.4	272		9/30	1	2	FACETS	0.924	0.842	1	0.924	0.842	1	CLONAL	1	TRUE	1	0.689339132766415	2		357	377	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149516600	149516600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144923639	NA	P-0019528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	215	825	1	ENST00000261799.4:c.11C>T	p.Pro4Leu	p.P4L	ENST00000261799	NM_002609.3	4	cCg/cTg	2/23	1	2	FACETS	0.879	0.82	0.939	0.879	0.82	0.939	CLONAL	1	TRUE	1	0.689339132766415	2		826	710	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44920623	44920623	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	213	651	0	ENST00000377967.4:c.1384C>G	p.Gln462Glu	p.Q462E	ENST00000377967	NM_021140.2	462	Caa/Gaa	14/29	NA	2	FACETS	0.943	0.881	1			1	INDETERMINATE	1	TRUE	NA	0.689339132766415	2		651	655	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0019529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	319	573	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.4065118930006	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.4065118930006	2		573	726	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126129	2126129	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs45517257	NA	P-0019529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	373	1005	0	ENST00000219476.3:c.2700C>A	p.Cys900Ter	p.C900*	ENST00000219476	NM_000548.3	900	tgC/tgA	24/42	0.4065118930006	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.4065118930006	2		1005	889	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61706083	61706083	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	274	731	1	ENST00000401558.2:c.3088A>T	p.Thr1030Ser	p.T1030S	ENST00000401558	NM_003400.3	1030	Act/Tct	25/25	0.32714805510354	4	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	2	0.4065118930006	4		732	916	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845361	42845361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	51	832	0	ENST00000398585.3:c.901C>T	p.Pro301Ser	p.P301S	ENST00000398585	NM_001135099.1	301	Ccg/Tcg	9/14	0.4065118930006	2	FACETS	0.328	0.278	0.383	0.164	0.139	0.192	SUBCLONAL	1	TRUE	0	0.4065118930006	2		832	765	SUCCESS
APC	324	MSKCC	GRCh37	5	112175456	112175457	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0019529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	232	318	0	ENST00000257430.4:c.4166_4167del	p.Ser1389CysfsTer5	p.S1389Cfs*5	ENST00000257430	NM_000038.5	1389	TCt/t	16/16	0.4065118930006	4	FACETS	0.904	0.855	0.953	0.904	0.855	0.953	CLONAL	4	TRUE	0	0.4065118930006	4		318	444	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265454	152265454	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	110	526	0	ENST00000206249.3:c.907A>G	p.Lys303Glu	p.K303E	ENST00000206249	NM_000125.3	303	Aag/Gag	4/8	0.4065118930006	3	FACETS	0.969	0.872	1	0.485	0.436	0.536	CLONAL	1	TRUE	1	0.4065118930006	3		526	672	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5522596	5522596	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs941236320	NA	P-0019529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	116	617	0	ENST00000397747.3:c.50T>C	p.Ile17Thr	p.I17T	ENST00000397747	NM_025239.3	17	aTa/aCa	2/7	0.12559277005136	5	FACETS	1	0.978	1	0.327	0.294	0.361	INDETERMINATE	1	TRUE	1	0.4065118930006	5		617	703	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317012	11317012	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs151205593	NA	P-0019530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	269	378	0	ENST00000361445.4:c.482A>G	p.Asn161Ser	p.N161S	ENST00000361445	NM_004958.3	161	aAt/aGt	4/58	1	2	FACETS	0.979	0.927	1	0.979	0.927	1	CLONAL	1	TRUE	1	0.93486474192639	2		378	588	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553456	106553456	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	179	240	0	ENST00000369096.4:c.1421G>T	p.Gly474Val	p.G474V	ENST00000369096	NM_001198.3	474	gGa/gTa	5/7	1	2	FACETS	0.995	0.93	1	0.995	0.93	1	CLONAL	1	TRUE	1	0.93486474192639	2		240	385	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	93	600	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.934	0.833	1	0.934	0.833	1	CLONAL	1	TRUE	1	0.38	2		600	524	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984846	11984846	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	114	513	0	ENST00000353533.5:c.392A>G	p.Lys131Arg	p.K131R	ENST00000353533	NM_003010.3	131	aAa/aGa	3/11	0.3	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.38	1		513	447	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25458627	25458627	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	232	741	0	ENST00000264709.3:c.2546C>A	p.Pro849His	p.P849H	ENST00000264709	NM_175629.2	849	cCt/cAt	22/23	0.357734431157131	2	FACETS	0.919	0.861	0.978	0.919	0.861	0.978	CLONAL	2	TRUE	0	0.357734431157131	2		741	706	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982403	25982403	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	208	464	0	ENST00000435504.4:c.887del	p.Pro296LeufsTer15	p.P296Lfs*15	ENST00000435504		296	cCt/ct	9/13	0.357734431157131	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.357734431157131	2		464	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579346	7579348	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs764486868	NA	P-0019534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	265	913	0	ENST00000269305.4:c.339_341del	p.Phe113del	p.F113del	ENST00000269305	NM_001126112.2	113	ttCTTg/ttg	4/11	0.620189152451431	3	FACETS	0.999	0.939	1	0.499	0.469	0.53	CLONAL	1	TRUE	1	0.878868876744512	3		913	869	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252155	226252155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553260624	NA	P-0019534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	84	145	0	ENST00000366813.1:c.103G>A	p.Gly35Arg	p.G35R	ENST00000366813		35	Ggg/Agg	1/3	0.548814190387658	3	FACETS	0.976	0.895	1	0.976	0.895	1	CLONAL	2	TRUE	1	0.878868876744512	3		145	141	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138295	2138295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45507199	NA	P-0019534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	68	1014	4	ENST00000219476.3:c.5228G>A	p.Arg1743Gln	p.R1743Q	ENST00000219476	NM_000548.3	1743	cGg/cAg	41/42	0.875864090175507	2	FACETS	0.234	0.203	0.267	0.117	0.101	0.134	SUBCLONAL	1	TRUE	0	0.878868876744512	2		1018	662	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139796	55139797	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCGTGTGACTTT	novel	NA	P-0019534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	638	647	0	ENST00000257290.5:c.1459_1470dup	p.Arg487_Phe490dup	p.R487_F490dup	ENST00000257290	NM_006206.4	487	ggc/ggCCGTGTGACTTTc	10/23	0.878868876744512	4	FACETS	1	0.982	1			1	CLONAL	2	TRUE	NA	0.878868876744512	4		647	1329	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755688	57755690	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs1416035156	NA	P-0019534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	311	983	0	ENST00000274289.3:c.97_99del	p.Lys33del	p.K33del	ENST00000274289	NM_006622.3	33	AAG/-	1/14	0.515919223463617	3	FACETS	0.975	0.92	1	0.487	0.46	0.515	INDETERMINATE	1	TRUE	1	0.878868876744512	3		983	1045	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849205	76849209	+	frameshift_variant	Frame_Shift_Del	DEL	AAGAG	AAGAG	-	novel	NA	P-0019534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	328	306	0	ENST00000373344.5:c.6067_6071del	p.Leu2023Ter	p.L2023*	ENST00000373344	NM_000489.3	2023	CTCTTt/t	26/35	0.495683172088552	2	FACETS	1	0.981	1			1	INDETERMINATE	2	TRUE	NA	0.878868876744512	2		306	371	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024351	31024352	+	frameshift_variant	Frame_Shift_Ins	INS	TG	TG	GTCC	novel	NA	P-0019534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	399	733	0	ENST00000375687.4:c.3836_3837delinsGTCC	p.Val1279GlyfsTer172	p.V1279Gfs*172	ENST00000375687	NM_015338.5	1279	gTG/gGTCC	13/13	0.518374306791734	4	FACETS	1	0.966	1	1	0.966	1	INDETERMINATE	2	TRUE	2	0.878868876744512	4		733	844	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22143071	22143071	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019535-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	41	628	0	ENST00000215832.6:c.636G>T	p.Trp212Cys	p.W212C	ENST00000215832	NM_002745.4	212	tgG/tgT	5/9	0.319196568346147	3	FACETS	0.525	0.437	0.624	0.263	0.218	0.312	SUBCLONAL	1	TRUE	1	0.32267119459468	3		628	562	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156906	89156906	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019535-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	74	744	1	ENST00000336596.2:c.8G>T	p.Cys3Phe	p.C3F	ENST00000336596	NM_005233.5	3	tGt/tTt	1/17	0.301320088468605	2	FACETS	0.854	0.749	0.967	0.427	0.374	0.484	CLONAL	1	TRUE	0	0.32267119459468	2		745	537	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190742156	190742156	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	87	311	0	ENST00000441310.2:c.2793del	p.Thr932HisfsTer3	p.T932Hfs*3	ENST00000441310	NM_000534.4	931	acT/ac	13/13	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.718325138147499	2		311	239	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038265	30038265	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	189	442	0	ENST00000338641.4:c.439del	p.Gln147ArgfsTer27	p.Q147Rfs*27	ENST00000338641	NM_000268.3	146	gtC/gt	4/16	0.718325138147499	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.718325138147499	1		442	336	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	64	553	2	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		555	547	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0019538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	58	717	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		718	721	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974813	21974813	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	13	157	0	ENST00000304494.5:c.14del	p.Ala5GlyfsTer21	p.A5Gfs*21	ENST00000304494	NM_000077.4	5	gCg/gg	1/3	0.157088101959714	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		157	126	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0019540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	279	697	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.36688160874779	2	FACETS	1	0.992	1	0.654	0.617	0.693	CLONAL	1	TRUE	0	0.526308440778049	2		697	810	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	206	736	0				ENST00000310581	NM_198253.2	-/1132			0.350085593438246	4	FACETS	1	0.99	1			1	CLONAL	1	TRUE	NA	0.526308440778049	4		736	859	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333551	70333551	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	105	593	0	ENST00000373644.4:c.1456A>C	p.Asn486His	p.N486H	ENST00000373644	NM_030625.2	486	Aat/Cat	2/12	0.365720188258011	3	FACETS	0.646	0.579	0.718	0.323	0.289	0.359	SUBCLONAL	1	TRUE	1	0.526308440778049	3		593	780	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81916879	81916879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	135	701	0	ENST00000359376.3:c.698C>T	p.Thr233Ile	p.T233I	ENST00000359376	NM_002661.3	233	aCt/aTt	9/33	0.365720188258011	3	FACETS	0.649	0.589	0.713	0.325	0.294	0.357	SUBCLONAL	1	TRUE	1	0.526308440778049	3		701	998	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530198	212530198	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	64	360	0	ENST00000342788.4:c.1721C>A	p.Pro574His	p.P574H	ENST00000342788	NM_005235.2	574	cCt/cAt	15/28	NA	2	FACETS	0.695	0.605	0.791			1	INDETERMINATE	1	TRUE	NA	0.526308440778049	2		360	350	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157573	106157573	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1193321482	NA	P-0019540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	167	398	0	ENST00000380013.4:c.2474C>G	p.Ser825Ter	p.S825*	ENST00000380013	NM_001127208.2	825	tCa/tGa	3/11	0.36688160874779	2	FACETS	1	0.986	1	0.646	0.599	0.695	CLONAL	1	TRUE	0	0.526308440778049	2		398	491	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665655	86665655	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	191	458	0	ENST00000274376.6:c.1636C>T	p.Gln546Ter	p.Q546*	ENST00000274376	NM_002890.2	546	Cag/Tag	12/25	0.36688160874779	2	FACETS	1	0.991	1	0.747	0.697	0.797	CLONAL	1	TRUE	0	0.526308440778049	2		458	486	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911064	29911064	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	GATGT	novel	NA	P-0019540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	288	818	0	ENST00000376809.5:c.363delinsGATGT	p.Ile121MetfsTer57	p.I121Mfs*57	ENST00000376809	NM_002116.7	121	atA/atGATGT	3/8	0.365720188258011	3	FACETS	1	0.987	1	0.585	0.55	0.622	CLONAL	1	TRUE	1	0.526308440778049	3		818	1181	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005391	29005391	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	17	587	0	ENST00000282397.4:c.870C>A	p.Asn290Lys	p.N290K	ENST00000282397	NM_002019.4	290	aaC/aaA	7/30	1	2	FACETS	0.313	0.233	0.409	0.313	0.233	0.409	SUBCLONAL	1	TRUE	1	0.32	2		587	339	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591247	67591249	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GGT	GGT	-	rs1131692243	NA	P-0019542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	92	406	0	ENST00000274335.5:c.1748_1750del		p.X583_splice	ENST00000274335		583		13/15	1	2	FACETS	0.705	0.629	0.786	0.705	0.629	0.786	SUBCLONAL	1	TRUE	1	0.539232134971585	2		406	484	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	164	568	1	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	1	2	FACETS	0.916	0.844	0.991	0.916	0.844	0.991	CLONAL	1	TRUE	1	0.539232134971585	2		569	664	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0019542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	103	323	3	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.539232134971585	2		326	318	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591104	67591115	+	inframe_deletion	In_Frame_Del	DEL	TTAAACCAGACC	TTAAACCAGACC	-	novel	NA	P-0019542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	80	645	0	ENST00000274335.5:c.1700_1711del	p.Lys567_Leu570del	p.K567_L570del	ENST00000274335		566	aTTAAACCAGACCtt/att	12/15	1	2	FACETS	0.753	0.667	0.845	0.753	0.667	0.845	SUBCLONAL	1	TRUE	1	0.539232134971585	2		645	394	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106983	27106983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	118	334	0	ENST00000324856.7:c.6595del	p.Leu2199Ter	p.L2199*	ENST00000324856	NM_006015.4	2198	ttC/tt	20/20	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.539232134971585	2		334	427	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624263	89624263	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	269	403	0	ENST00000371953.3:c.37A>G	p.Lys13Glu	p.K13E	ENST00000371953	NM_000314.4	13	Aaa/Gaa	1/9	0.528639859035793	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.539232134971585	2		403	468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0019544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	105	717	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.292995077104581	1	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	0	0.319334859279638	1		718	549	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	114	640	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.954	0.861	1	0.954	0.861	1	CLONAL	1	TRUE	1	0.41	2		640	583	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	289	683	12	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.931	0.88	0.983	1	0.995	1	CLONAL	2	TRUE	1	0.41	2		695	757	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	154	614	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.41	2		614	727	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790459	3790459	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	163	600	0	ENST00000262367.5:c.4074del	p.Phe1358LeufsTer18	p.F1358Lfs*18	ENST00000262367	NM_004380.2	1358	ttT/tt	24/31	1	2	FACETS	0.968	0.89	1	0.968	0.89	1	CLONAL	1	TRUE	1	0.41	2		600	821	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	35	560	1	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	0.25	0.204	0.302	0.25	0.204	0.302	SUBCLONAL	1	TRUE	1	0.41	2		561	682	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440713	56440713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779337229	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	144	689	1	ENST00000407977.2:c.505G>A	p.Ala169Thr	p.A169T	ENST00000407977		169	Gct/Act	5/10	1	2	FACETS	0.996	0.911	1	0.996	0.911	1	CLONAL	1	TRUE	1	0.41	2		690	705	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188296	32188296	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561687277	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	196	889	1	ENST00000375023.3:c.1045G>A	p.Gly349Ser	p.G349S	ENST00000375023	NM_004557.3	349	Ggc/Agc	6/30	1	2	FACETS	0.971	0.898	1	0.971	0.898	1	CLONAL	1	TRUE	1	0.41	2		890	985	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881489	48881490	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs587778862	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	76	399	1	ENST00000267163.4:c.219_220del	p.Arg73SerfsTer36	p.R73Sfs*36	ENST00000267163	NM_000321.2	71	AGa/a	2/27	1	2	FACETS	0.768	0.675	0.866	0.768	0.675	0.866	SUBCLONAL	1	TRUE	1	0.41	2		400	483	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696410	47696410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	135	660	0	ENST00000347630.2:c.413G>A	p.Arg138His	p.R138H	ENST00000347630	NM_001007230.1	138	cGt/cAt	6/11	1	2	FACETS	0.865	0.787	0.947	0.865	0.787	0.947	CLONAL	1	TRUE	1	0.41	2		660	761	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349214	11349230	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCGCGGGCGCGCGGG	GGCCGCGGGCGCGCGGG	-	novel	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	146	229	0	ENST00000332029.2:c.106_122del	p.Pro36ValfsTer75	p.P36Vfs*75	ENST00000332029	NM_003745.1	36	CCCGCGCGCCCGCGGCCg/g	2/2	1	2	FACETS	1	0.935	1	1	0.992	1	CLONAL	2	TRUE	1	0.41	2		229	352	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324917	31324917	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	87	372	0	ENST00000412585.2:c.19del	p.Arg7GlufsTer13	p.R7Efs*13	ENST00000412585	NM_005514.6	7	Cga/ga	1/8	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.41	2		372	389	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458579	12458579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	153	783	1	ENST00000287820.6:c.1196C>T	p.Ala399Val	p.A399V	ENST00000287820	NM_015869.4	399	gCt/gTt	6/7	1	2	FACETS	0.966	0.884	1	0.966	0.884	1	CLONAL	1	TRUE	1	0.41	2		784	773	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864769	68864769	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	120	559	2	ENST00000288368.4:c.140C>T	p.Ser47Leu	p.S47L	ENST00000288368	NM_024870.2	47	tCg/tTg	1/40	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.41	2		561	579	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65349020	65349020	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754991396	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	84	431	0	ENST00000342505.4:c.145C>T	p.Arg49Trp	p.R49W	ENST00000342505	NM_002227.2	49	Cgg/Tgg	3/25	1	2	FACETS	0.828	0.733	0.928	0.828	0.733	0.928	CLONAL	1	TRUE	1	0.41	2		431	495	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276425	115276425	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	113	609	2	ENST00000438362.2:c.903del	p.Phe301LeufsTer13	p.F301Lfs*13	ENST00000438362	NM_001242891.1	301	ttT/tt	9/20	1	2	FACETS	0.855	0.77	0.943	0.855	0.77	0.943	CLONAL	1	TRUE	1	0.41	2		611	645	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910841	114910841	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	137	646	0	ENST00000543371.1:c.960A>T	p.Lys320Asn	p.K320N	ENST00000543371	NM_001198531.1	320	aaA/aaT	9/14	1	2	FACETS	0.85	0.774	0.93	0.85	0.774	0.93	CLONAL	1	TRUE	1	0.41	2		646	786	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274749	123274749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	75	680	0	ENST00000358487.5:c.1169G>A	p.Cys390Tyr	p.C390Y	ENST00000358487	NM_000141.4	390	tGt/tAt	9/18	1	2	FACETS	0.464	0.406	0.527	0.464	0.406	0.527	SUBCLONAL	1	TRUE	1	0.41	2		680	788	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417925	32417925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1014605516	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	125	667	1	ENST00000332351.3:c.1127C>T	p.Pro376Leu	p.P376L	ENST00000332351	NM_024426.4	376	cCg/cTg	7/10	1	2	FACETS	0.826	0.748	0.908	0.826	0.748	0.908	CLONAL	1	TRUE	1	0.41	2		668	738	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186820	108186820	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778078	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	41	709	0	ENST00000278616.4:c.6178C>T	p.Arg2060Cys	p.R2060C	ENST00000278616	NM_000051.3	2060	Cgc/Tgc	42/63	1	2	FACETS	0.253	0.21	0.302	0.253	0.21	0.302	SUBCLONAL	1	TRUE	1	0.41	2		709	789	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202201	108202201	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	76	479	0	ENST00000278616.4:c.7550del	p.Leu2517CysfsTer15	p.L2517Cfs*15	ENST00000278616	NM_000051.3	2516	Ttt/tt	51/63	1	2	FACETS	0.818	0.72	0.923	0.818	0.72	0.923	CLONAL	1	TRUE	1	0.41	2		479	453	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937034	48937035	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	77	428	0	ENST00000267163.4:c.806dup	p.Asn269LysfsTer2	p.N269Kfs*2	ENST00000267163	NM_000321.2	268	gaa/gAaa	8/27	1	2	FACETS	0.751	0.661	0.848	0.751	0.661	0.848	SUBCLONAL	1	TRUE	1	0.41	2		428	500	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986703	36986703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	30	67	0	ENST00000354822.5:c.986C>T	p.Ala329Val	p.A329V	ENST00000354822	NM_001079668.2	329	gCg/gTg	3/3	1	2	FACETS	0.882	0.734	1	1	0.959	1	CLONAL	2	TRUE	1	0.41	2		67	83	SUCCESS
BLM	641	MSKCC	GRCh37	15	91333930	91333930	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs762354041	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	97	640	0	ENST00000355112.3:c.2875C>T	p.Arg959Ter	p.R959*	ENST00000355112	NM_000057.2	959	Cga/Tga	15/22	1	2	FACETS	0.682	0.608	0.76	0.682	0.608	0.76	SUBCLONAL	1	TRUE	1	0.41	2		640	694	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828498	72828498	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142218077	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	148	635	0	ENST00000268489.5:c.8083C>T	p.Arg2695Trp	p.R2695W	ENST00000268489	NM_006885.3	2695	Cgg/Tgg	9/10	1	2	FACETS	0.928	0.848	1	0.928	0.848	1	CLONAL	1	TRUE	1	0.41	2		635	778	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216419	7216419	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	172	793	0	ENST00000380728.2:c.829del	p.Gln277ArgfsTer68	p.Q277Rfs*68	ENST00000380728		277	Cag/ag	10/11	1	2	FACETS	0.95	0.875	1	0.95	0.875	1	CLONAL	1	TRUE	1	0.41	2		793	883	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120049	70120049	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	14	76	0	ENST00000245479.2:c.1051C>T	p.Gln351Ter	p.Q351*	ENST00000245479	NM_000346.3	351	Cag/Tag	3/3	1	2	FACETS	1	0.803	1	1	0.803	1	CLONAL	1	TRUE	1	0.41	2		76	62	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622084	1622084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748395369	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	211	1111	2	ENST00000344749.5:c.791C>T	p.Thr264Met	p.T264M	ENST00000344749	NM_001136139.2	264	aCg/aTg	10/19	1	2	FACETS	0.943	0.875	1	0.943	0.875	1	CLONAL	1	TRUE	1	0.41	2		1113	1092	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125509	7125509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147176789	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	62	655	0	ENST00000302850.5:c.3043G>A	p.Glu1015Lys	p.E1015K	ENST00000302850	NM_000208.2	1015	Gag/Aag	17/22	1	2	FACETS	0.407	0.351	0.468	0.407	0.351	0.468	SUBCLONAL	1	TRUE	1	0.41	2		655	743	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311640	15311640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1329279009	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	31	88	0	ENST00000263388.2:c.77C>T	p.Ala26Val	p.A26V	ENST00000263388	NM_000435.2	26	gCg/gTg	1/33	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.41	2		88	123	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350532	15350532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748633137	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	190	938	1	ENST00000263377.2:c.3383C>T	p.Ser1128Leu	p.S1128L	ENST00000263377	NM_058243.2	1128	tCg/tTg	16/20	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.41	2		939	922	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379692	17379692	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	56	826	0	ENST00000359435.4:c.77G>T	p.Arg26Leu	p.R26L	ENST00000359435	NM_001033549.1	26	cGc/cTc	2/9	1	2	FACETS	0.343	0.293	0.398	0.343	0.293	0.398	SUBCLONAL	1	TRUE	1	0.41	2		826	797	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228563	36228564	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	218	969	0	ENST00000222270.7:c.7579dup	p.Leu2527ProfsTer10	p.L2527Pfs*10	ENST00000222270	NM_014727.1	2526	ttc/ttCc	34/37	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.41	2		969	1039	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440022	220440022	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	257	1376	0	ENST00000243786.2:c.875A>G	p.His292Arg	p.H292R	ENST00000243786	NM_002191.3	292	cAt/cGt	2/2	1	2	FACETS	0.894	0.835	0.955	0.894	0.835	0.955	CLONAL	1	TRUE	1	0.41	2		1376	1402	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121329	29121329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	163	797	2	ENST00000328354.6:c.346G>A	p.Gly116Arg	p.G116R	ENST00000328354	NM_007194.3	116	Ggg/Agg	3/15	1	2	FACETS	0.979	0.9	1	0.979	0.9	1	CLONAL	1	TRUE	1	0.41	2		799	812	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1955176	1955176	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	168	702	1	ENST00000382891.5:c.2263C>T	p.Arg755Ter	p.R755*	ENST00000382891	NM_133335.3	755	Cga/Tga	12/22	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.41	2		703	797	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631129	176631129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	104	510	0	ENST00000439151.2:c.1072C>T	p.Arg358Trp	p.R358W	ENST00000439151	NM_022455.4	358	Cgg/Tgg	4/23	1	2	FACETS	0.936	0.841	1	0.936	0.841	1	CLONAL	1	TRUE	1	0.41	2		510	542	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665365	176665365	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	87	412	0	ENST00000439151.2:c.4049C>T	p.Pro1350Leu	p.P1350L	ENST00000439151	NM_022455.4	1350	cCg/cTg	7/23	1	2	FACETS	0.929	0.826	1	0.929	0.826	1	CLONAL	1	TRUE	1	0.41	2		412	457	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670391	30670391	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	56	690	0	ENST00000376406.3:c.6041T>C	p.Met2014Thr	p.M2014T	ENST00000376406	NM_014641.2	2014	aTg/aCg	14/15	1	2	FACETS	0.319	0.272	0.37	0.319	0.272	0.37	SUBCLONAL	1	TRUE	1	0.41	2		690	856	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797749	32797749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753393321	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	119	771	1	ENST00000374899.4:c.1753G>A	p.Ala585Thr	p.A585T	ENST00000374899	NM_018833.2	585	Gca/Aca	10/12	1	2	FACETS	0.704	0.635	0.776	0.704	0.635	0.776	SUBCLONAL	1	TRUE	1	0.41	2		772	825	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129219	152129219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1199270277	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	238	968	2	ENST00000206249.3:c.172G>A	p.Ala58Thr	p.A58T	ENST00000206249	NM_000125.3	58	Gcc/Acc	1/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.41	2		970	1063	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787753	135787753	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	132	642	1	ENST00000298552.3:c.829G>A	p.Val277Met	p.V277M	ENST00000298552	NM_001162426.1	277	Gtg/Atg	9/23	1	2	FACETS	0.793	0.72	0.87	0.793	0.72	0.87	SUBCLONAL	1	TRUE	1	0.41	2		643	812	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0019546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	24	721	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.273	0.213	0.344	0.273	0.213	0.344	SUBCLONAL	1	TRUE	1	0.15	2		721	1172	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948136	178948136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	39	269	0	ENST00000263967.3:c.2908G>A	p.Glu970Lys	p.E970K	ENST00000263967	NM_006218.2	970	Gaa/Aaa	20/21	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.15	2		269	480	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0019546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	35	358	1	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	1	2	FACETS	0.795	0.65	0.958	0.795	0.65	0.958	CLONAL	1	TRUE	1	0.15	2		359	587	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486842	56486842	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	69	687	0	ENST00000267101.3:c.1256G>C	p.Gly419Ala	p.G419A	ENST00000267101	NM_001982.3	419	gGa/gCa	11/28	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.15	2		687	844	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258808	16258808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	71	615	2	ENST00000375759.3:c.6073G>A	p.Glu2025Lys	p.E2025K	ENST00000375759	NM_015001.2	2025	Gag/Aag	11/15	1	2	FACETS	0.983	0.856	1	0.983	0.856	1	CLONAL	1	TRUE	1	0.15	2		617	963	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433784	49433784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760007799	NA	P-0019546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1418	92	1040	0	ENST00000301067.7:c.7769C>T	p.Ser2590Leu	p.S2590L	ENST00000301067	NM_003482.3	2590	tCg/tTg	31/54	1	2	FACETS	0.812	0.719	0.913	0.812	0.719	0.913	CLONAL	1	TRUE	1	0.15	2		1040	1510	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118784	115118787	+	frameshift_variant	Frame_Shift_Del	DEL	ATGT	ATGT	-	novel	NA	P-0019546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	46	487	0	ENST00000257566.3:c.554_557del	p.Tyr185PhefsTer22	p.Y185Ffs*22	ENST00000257566	NM_016569.3	185	tACATt/tt	2/8	1	2	FACETS	0.727	0.61	0.856	0.727	0.61	0.856	SUBCLONAL	1	TRUE	1	0.15	2		487	844	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579449	7579449	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501204	NA	P-0019546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	68	698	2	ENST00000269305.4:c.238C>T	p.Pro80Ser	p.P80S	ENST00000269305	NM_001126112.2	80	Cct/Tct	4/11	1	2	FACETS	0.855	0.741	0.978	0.855	0.741	0.978	CLONAL	1	TRUE	1	0.15	2		700	1061	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719598	190719598	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329105408	NA	P-0019546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	19	248	0	ENST00000441310.2:c.1600C>T	p.Pro534Ser	p.P534S	ENST00000441310	NM_000534.4	534	Cca/Tca	9/13	1	2	FACETS	0.85	0.645	1	0.85	0.645	1	CLONAL	1	TRUE	1	0.15	2		248	298	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842283	151842283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1162128184	NA	P-0019546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	29	365	0	ENST00000262189.6:c.14129G>A	p.Arg4710His	p.R4710H	ENST00000262189	NM_170606.2	4710	cGt/cAt	54/59	1	2	FACETS	0.704	0.564	0.865	0.704	0.564	0.865	SUBCLONAL	1	TRUE	1	0.15	2		365	549	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873855	151873855	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	53	368	0	ENST00000262189.6:c.8683C>T	p.Gln2895Ter	p.Q2895*	ENST00000262189	NM_170606.2	2895	Cag/Tag	38/59	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.15	2		368	634	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224164	98224164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753008328	NA	P-0019546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	24	234	1	ENST00000331920.6:c.2677C>T	p.Arg893Cys	p.R893C	ENST00000331920	NM_000264.3	893	Cgc/Tgc	16/24	1	2	FACETS	0.771	0.604	0.965	0.771	0.604	0.965	CLONAL	1	TRUE	1	0.15	2		235	415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0019547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	151	970	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.396044472871014	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.403675663649577	1		970	574	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962304	2962304	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs895009948	NA	P-0019547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	133	707	0	ENST00000396946.4:c.2233G>A	p.Gly745Ser	p.G745S	ENST00000396946	NM_032415.4	745	Ggc/Agc	17/25	0.346239839647473	3	FACETS	1	0.959	1	0.548	0.499	0.601	CLONAL	1	TRUE	1	0.403675663649577	3		707	722	SUCCESS
APC	324	MSKCC	GRCh37	5	112175300	112175301	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	92	239	0	ENST00000257430.4:c.4010dup	p.Gln1338AlafsTer4	p.Q1338Afs*4	ENST00000257430	NM_000038.5	1337	ctg/cTtg	16/16	0.403675663649577	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.403675663649577	2		239	215	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0019548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	104	741	1	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	0.277567299232964	2		742	716	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063718	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0019548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	56	428	0	ENST00000412916.2:c.165+2dup		p.X55_splice	ENST00000412916		55			0.277567299232964	1	FACETS	0.968	0.833	1	0.968	0.833	1	CLONAL	1	TRUE	0	0.277567299232964	1		428	359	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115750	8115750	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs104894164	NA	P-0019548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	47	618	1	ENST00000346208.3:c.1096C>T	p.Arg366Ter	p.R366*	ENST00000346208		366	Cga/Tga	6/6	1	2	FACETS	0.438	0.368	0.515	0.438	0.368	0.515	SUBCLONAL	1	TRUE	1	0.277567299232964	2		619	774	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505430	25505430	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	29	461	1	ENST00000264709.3:c.328C>T	p.Gln110Ter	p.Q110*	ENST00000264709	NM_175629.2	110	Cag/Tag	4/23	1	2	FACETS	0.483	0.387	0.592	0.483	0.387	0.592	SUBCLONAL	1	TRUE	1	0.277567299232964	2		462	433	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778781	3778786	+	inframe_deletion	In_Frame_Del	DEL	AATGTT	AATGTT	-	novel	NA	P-0019550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	241	1171	0	ENST00000262367.5:c.6262_6267del	p.Asn2088_Ile2089del	p.N2088_I2089del	ENST00000262367	NM_004380.2	2088	AACATT/-	31/31	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	1	0.323547996031704	2		1171	1069	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047022	128047022	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	45	704	0	ENST00000285398.2:c.713C>G	p.Pro238Arg	p.P238R	ENST00000285398	NM_000122.1	238	cCa/cGa	6/15	1	2	FACETS	0.35	0.293	0.414	0.35	0.293	0.414	SUBCLONAL	1	FALSE	1	0.323547996031704	2		704	794	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	277	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.811	0.763	0.86	0.811	0.763	0.86	CLONAL	1	TRUE	1	0.732580920030498	2		555	933	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0019551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	367	830	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.864	0.82	0.909	0.864	0.82	0.909	CLONAL	1	TRUE	1	0.732580920030498	2		830	1159	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0019551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	466	949	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.697492859137266	1	FACETS	0.929	0.894	0.964	0.929	0.894	0.964	CLONAL	1	TRUE	0	0.732580920030498	1		950	868	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584528	48584528	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	248	423	0	ENST00000342988.3:c.701del	p.Ser234MetfsTer7	p.S234Mfs*7	ENST00000342988	NM_005359.5	234	aGt/at	6/12	0.710602228613659	1	FACETS	0.919	0.871	0.966	0.919	0.871	0.966	CLONAL	1	TRUE	0	0.732580920030498	1		423	467	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974763	21974763	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	150	315	0	ENST00000304494.5:c.64del	p.Arg22GlyfsTer4	p.R22Gfs*4	ENST00000304494	NM_000077.4	22	Cgg/gg	1/3	0.732580920030498	1	FACETS	0.814	0.756	0.871	0.814	0.756	0.871	CLONAL	1	TRUE	0	0.732580920030498	1		315	319	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0019552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	485	680	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.520130143429476	3	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.520130143429476	3		680	1066	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0019552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	85	840	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.313089828106654	3	FACETS	0.708	0.626	0.794	0.354	0.313	0.397	SUBCLONAL	1	TRUE	1	0.520130143429476	3		840	582	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269009	142269009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369913351	NA	P-0019552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	113	706	1	ENST00000350721.4:c.2941G>A	p.Val981Ile	p.V981I	ENST00000350721	NM_001184.3	981	Gtt/Att	14/47	NA	2	FACETS	0.656	0.591	0.725			1	INDETERMINATE	1	TRUE	NA	0.520130143429476	2		707	662	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726619	41726619	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750804190	NA	P-0019552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	85	911	1	ENST00000301178.4:c.164G>A	p.Arg55Gln	p.R55Q	ENST00000301178	NM_021913.4	55	cGg/cAg	2/20	0.520130143429476	1	FACETS	0.331	0.292	0.372	0.331	0.292	0.372	SUBCLONAL	1	TRUE	0	0.520130143429476	1		912	731	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0019553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	62	726	2	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	1	2	FACETS	0.627	0.541	0.721	0.627	0.541	0.721	SUBCLONAL	1	TRUE	1	0.29	2		728	682	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411902	116411902	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0019553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	230	1091	0	ENST00000397752.3:c.2888-1G>A		p.X963_splice	ENST00000397752	NM_000245.2	963			0.216855723880274	2	FACETS	1	0.992	1	0.743	0.693	0.796	CLONAL	1	TRUE	0	0.29	2		1091	1067	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7128926	7128926	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	52	824	0	ENST00000302850.5:c.2882C>G	p.Pro961Arg	p.P961R	ENST00000302850	NM_000208.2	961	cCc/cGc	15/22	1	2	FACETS	0.445	0.378	0.52	0.445	0.378	0.52	SUBCLONAL	1	TRUE	1	0.29	2		824	805	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0019554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	204	908	0	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	0.450905452009282	2	FACETS	0.894	0.837	0.952	0.894	0.837	0.952	CLONAL	2	TRUE	0	0.450905452009282	2		908	506	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135370	30135370	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	94	698	0	ENST00000331968.5:c.448T>C	p.Phe150Leu	p.F150L	ENST00000331968	NM_002742.2	150	Ttt/Ctt	3/18	0.450187464544092	3	FACETS	0.884	0.788	0.986	0.442	0.394	0.493	CLONAL	1	TRUE	1	0.450905452009282	3		698	578	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245279	41245279	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs80357583	NA	P-0019554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	463	783	0	ENST00000357654.3:c.2269del	p.Val757PhefsTer8	p.V757Ffs*8	ENST00000357654	NM_007294.3	757	Gtt/tt	10/23	0.450905452009282	4	FACETS	0.961	0.927	0.995	0.961	0.927	0.995	CLONAL	4	TRUE	0	0.450905452009282	4		783	775	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149251	119149251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267606708	NA	P-0019556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	85	715	0	ENST00000264033.4:c.1259G>A	p.Arg420Gln	p.R420Q	ENST00000264033	NM_005188.3	420	cGa/cAa	9/16	0.865950873296653	1	FACETS	0.172	0.152	0.193	0.172	0.152	0.193	SUBCLONAL	1	TRUE	0	0.865950873296653	1		715	648	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0019556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	226	1190	2	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	0.865950873296653	1	FACETS	0.247	0.229	0.265	0.247	0.229	0.265	SUBCLONAL	1	TRUE	0	0.865950873296653	1		1192	1200	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780068	NA	P-0019556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	770	890	1	ENST00000269305.4:c.472C>T	p.Arg158Cys	p.R158C	ENST00000269305	NM_001126112.2	158	Cgc/Tgc	5/11	0.865950873296653	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.865950873296653	1		891	979	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76919037	76919038	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	153	303	0	ENST00000373344.5:c.3953dup	p.Asn1318LysfsTer6	p.N1318Kfs*6	ENST00000373344	NM_000489.3	1318	aat/aaAt	12/35	1	2	FACETS	0.739	0.682	0.799	0.739	0.682	0.799	SUBCLONAL	1	TRUE	1	0.865950873296653	2		303	478	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482926	140482927	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs777474487	NA	P-0019556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	240	824	3	ENST00000288602.6:c.1208dup	p.Ala404CysfsTer9	p.A404Cfs*9	ENST00000288602	NM_004333.4	403	cct/ccCt	10/18	1	2	FACETS	0.465	0.434	0.498	0.465	0.434	0.498	SUBCLONAL	1	TRUE	1	0.865950873296653	2		827	1191	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540654	NA	P-0019556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	599	1062	1	ENST00000269305.4:c.329G>A	p.Arg110His	p.R110H	ENST00000269305	NM_001126112.2	110	cGt/cAt	4/11	0.865950873296653	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.865950873296653	1		1063	775	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464537	25464537	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752434188	NA	P-0019556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	616	925	2	ENST00000264709.3:c.1976G>A	p.Arg659His	p.R659H	ENST00000264709	NM_175629.2	659	cGc/cAc	17/23	0.865950873296653	1	FACETS	0.981	0.957	1	0.981	0.957	1	CLONAL	1	TRUE	0	0.865950873296653	1		927	822	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692940	89692940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746152219	NA	P-0019556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	510	749	1	ENST00000371953.3:c.424C>T	p.Arg142Trp	p.R142W	ENST00000371953	NM_000314.4	142	Cgg/Tgg	5/9	0.865950873296653	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.865950873296653	1		750	659	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300837	137300837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	112	1179	1	ENST00000481739.1:c.482G>A	p.Arg161Gln	p.R161Q	ENST00000481739	NM_002957.4	161	cGg/cAg	4/10	0.762590888009569	1	FACETS	0.127	0.113	0.141	0.127	0.113	0.141	SUBCLONAL	1	TRUE	0	0.865950873296653	1		1180	1159	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059133	47059133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	387	523	0	ENST00000409792.3:c.7528C>T	p.Arg2510Cys	p.R2510C	ENST00000409792	NM_014159.6	2510	Cgc/Tgc	20/21	0.865950873296653	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.865950873296653	1		523	485	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294255	1294255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1174718400	NA	P-0019556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	60	1227	0	ENST00000310581.5:c.746C>T	p.Thr249Met	p.T249M	ENST00000310581	NM_198253.2	249	aCg/aTg	2/16	0.865950873296653	1	FACETS	0.086	0.074	0.1	0.086	0.074	0.1	SUBCLONAL	1	TRUE	0	0.865950873296653	1		1227	912	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395161	139395161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771407924	NA	P-0019556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	721	1214	4	ENST00000277541.6:c.5777G>A	p.Arg1926His	p.R1926H	ENST00000277541	NM_017617.3	1926	cGc/cAc	31/34	0.762590888009569	1	FACETS	0.903	0.88	0.925	0.903	0.88	0.925	CLONAL	1	TRUE	0	0.865950873296653	1		1218	1046	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185545	27185545	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1564083506	NA	P-0019556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	403	879	5	ENST00000380036.4:c.1250del	p.Pro417LeufsTer10	p.P417Lfs*10	ENST00000380036	NM_000459.3	415	ctC/ct	9/23	0.369108466849093	1	FACETS	0.46	0.438	0.482	0.46	0.438	0.482	INDETERMINATE	1	TRUE	0	0.865950873296653	1		884	1148	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257183	16257183	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	103	741	0	ENST00000375759.3:c.4448T>G	p.Val1483Gly	p.V1483G	ENST00000375759	NM_015001.2	1483	gTt/gGt	11/15	0.865950873296653	1	FACETS	0.205	0.183	0.228	0.205	0.183	0.228	SUBCLONAL	1	TRUE	0	0.865950873296653	1		741	659	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804367	43804367	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1443655691	NA	P-0019556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	426	514	0	ENST00000372470.3:c.367C>T	p.Arg123Ter	p.R123*	ENST00000372470	NM_005373.2	123	Cga/Tga	3/12	0.865950873296653	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.865950873296653	1		514	532	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464394	120464394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs923129064	NA	P-0019556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	116	693	2	ENST00000256646.2:c.5252G>A	p.Gly1751Asp	p.G1751D	ENST00000256646	NM_024408.3	1751	gGt/gAt	29/34	0.865950873296653	1	FACETS	0.235	0.212	0.259	0.235	0.212	0.259	SUBCLONAL	1	TRUE	0	0.865950873296653	1		695	647	SUCCESS
EED	8726	MSKCC	GRCh37	11	85966300	85966300	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745786094	NA	P-0019556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	181	340	0	ENST00000263360.6:c.397C>T	p.Arg133Trp	p.R133W	ENST00000263360	NM_003797.3	133	Cgg/Tgg	4/12	0.865950873296653	1	FACETS	0.905	0.859	0.948	0.905	0.859	0.948	CLONAL	1	TRUE	0	0.865950873296653	1		340	262	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243365	46243365	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs76994389	NA	P-0019556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	162	258	1	ENST00000334344.6:c.1718C>T	p.Thr573Met	p.T573M	ENST00000334344	NM_152641.2	573	aCg/aTg	14/21	0.865950873296653	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.865950873296653	1		259	201	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966765	18966765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	385	1269	2	ENST00000262803.5:c.1576G>A	p.Ala526Thr	p.A526T	ENST00000262803	NM_002911.3	526	Gcc/Acc	12/24	0.865950873296653	1	FACETS	0.508	0.484	0.532	0.508	0.484	0.532	SUBCLONAL	1	TRUE	0	0.865950873296653	1		1271	993	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702410	47702410	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs267607986	NA	P-0019556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	174	278	0	ENST00000233146.2:c.2005+1G>A		p.X669_splice	ENST00000233146	NM_000251.2	669			0.865950873296653	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.865950873296653	1		278	214	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514894	44514894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754274409	NA	P-0019556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	206	507	0	ENST00000291552.4:c.353G>A	p.Arg118His	p.R118H	ENST00000291552	NM_006758.2	118	cGc/cAc	6/8	0.865950873296653	1	FACETS	0.641	0.603	0.679	0.641	0.603	0.679	SUBCLONAL	1	TRUE	0	0.865950873296653	1		507	421	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651506	52651508	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	novel	NA	P-0019556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	403	580	0	ENST00000394830.3:c.1588_1590del	p.Val530del	p.V530del	ENST00000394830	NM_018313.4	530	GTT/-	15/30	0.865950873296653	1	FACETS	0.956	0.926	0.985	0.956	0.926	0.985	CLONAL	1	TRUE	0	0.865950873296653	1		580	552	SUCCESS
ATR	545	MSKCC	GRCh37	3	142168389	142168389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199948706	NA	P-0019556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	311	571	0	ENST00000350721.4:c.7817G>A	p.Arg2606Gln	p.R2606Q	ENST00000350721	NM_001184.3	2606	cGa/cAa	47/47	0.865950873296653	1	FACETS	0.956	0.922	0.989	0.956	0.922	0.989	CLONAL	1	TRUE	0	0.865950873296653	1		571	426	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201815	66201815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764665078	NA	P-0019556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	315	593	0	ENST00000273854.3:c.2687G>A	p.Arg896His	p.R896H	ENST00000273854	NM_004439.5	896	cGt/cAt	16/18	1	2	FACETS	0.823	0.779	0.868	0.823	0.779	0.868	CLONAL	1	TRUE	1	0.865950873296653	2		593	884	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396913	139396913	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768040014	NA	P-0019556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	510	794	2	ENST00000277541.6:c.5195C>T	p.Ala1732Val	p.A1732V	ENST00000277541	NM_017617.3	1732	gCg/gTg	28/34	0.762590888009569	1	FACETS	0.941	0.914	0.967	0.941	0.914	0.967	CLONAL	1	TRUE	0	0.865950873296653	1		796	710	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227777	53227777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556839568	NA	P-0019556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	646	962	1	ENST00000375401.3:c.2411G>A	p.Arg804Gln	p.R804Q	ENST00000375401	NM_004187.3	804	cGg/cAg	17/26	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.865950873296653	2		963	1441	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0019557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	206	860	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.902	0.84	0.965	0.902	0.84	0.965	CLONAL	1	TRUE	1	0.650018155396474	2		860	703	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0019557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	511	571	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.641150875506318	2	FACETS	0.943	0.911	0.973	0.943	0.911	0.973	CLONAL	2	TRUE	0	0.650018155396474	2		571	834	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310896	123310896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs974173968	NA	P-0019557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	177	416	1	ENST00000358487.5:c.532C>T	p.Arg178Cys	p.R178C	ENST00000358487	NM_000141.4	178	Cgc/Tgc	5/18	1	2	FACETS	0.999	0.927	1	0.999	0.927	1	CLONAL	1	TRUE	1	0.650018155396474	2		417	545	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057967	27057967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	411	524	0	ENST00000324856.7:c.1675C>T	p.Pro559Ser	p.P559S	ENST00000324856	NM_006015.4	559	Cct/Tct	3/20	0.641150875506318	2	FACETS	0.944	0.909	0.978	0.944	0.909	0.978	CLONAL	2	TRUE	0	0.650018155396474	2		524	670	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144627	119144627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	148	391	1	ENST00000264033.4:c.640C>T	p.Pro214Ser	p.P214S	ENST00000264033	NM_005188.3	214	Ccc/Tcc	4/16	1	2	FACETS	0.846	0.777	0.918	0.846	0.777	0.918	CLONAL	1	TRUE	1	0.650018155396474	2		392	538	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445469	49445469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	372	993	1	ENST00000301067.7:c.1997C>T	p.Pro666Leu	p.P666L	ENST00000301067	NM_003482.3	666	cCt/cTt	10/54	1	2	FACETS	0.971	0.922	1	0.971	0.922	1	CLONAL	1	TRUE	1	0.650018155396474	2		994	1179	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863226	57863226	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	136	428	0	ENST00000228682.2:c.1321A>G	p.Ser441Gly	p.S441G	ENST00000228682	NM_005269.2	441	Agc/Ggc	11/12	1	2	FACETS	0.824	0.753	0.897	0.824	0.753	0.897	CLONAL	1	TRUE	1	0.650018155396474	2		428	508	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557653	95557653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	233	564	0	ENST00000393063.1:c.5414C>T	p.Pro1805Leu	p.P1805L	ENST00000393063	NM_030621.3	1805	cCa/cTa	26/28	1	2	FACETS	0.946	0.885	1	0.946	0.885	1	CLONAL	1	TRUE	1	0.650018155396474	2		564	758	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678602	88678602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243717189	NA	P-0019557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	69	271	0	ENST00000360948.2:c.934G>A	p.Glu312Lys	p.E312K	ENST00000360948	NM_001012338.2	312	Gag/Aag	9/19	1	2	FACETS	0.742	0.653	0.837	0.742	0.653	0.837	SUBCLONAL	1	TRUE	1	0.650018155396474	2		271	286	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303994	91303994	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1303724070	NA	P-0019557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	264	613	1	ENST00000355112.3:c.1391C>T	p.Ser464Phe	p.S464F	ENST00000355112	NM_000057.2	464	tCt/tTt	7/22	1	2	FACETS	0.939	0.882	0.997	0.939	0.882	0.997	CLONAL	1	TRUE	1	0.650018155396474	2		614	865	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829866	72829866	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	258	612	0	ENST00000268489.5:c.6715T>A	p.Trp2239Arg	p.W2239R	ENST00000268489	NM_006885.3	2239	Tgg/Agg	9/10	1	2	FACETS	0.921	0.865	0.979	0.921	0.865	0.979	CLONAL	1	TRUE	1	0.650018155396474	2		612	862	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760818	59760818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	224	558	0	ENST00000259008.2:c.3589G>A	p.Gly1197Arg	p.G1197R	ENST00000259008	NM_032043.2	1197	Gga/Aga	20/20	1	2	FACETS	0.877	0.819	0.936	0.877	0.819	0.936	CLONAL	1	TRUE	1	0.650018155396474	2		558	786	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575119	48575119	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	155	338	1	ENST00000342988.3:c.313C>T	p.His105Tyr	p.H105Y	ENST00000342988	NM_005359.5	105	Cac/Tac	3/12	1	2	FACETS	0.873	0.804	0.945	0.873	0.804	0.945	CLONAL	1	TRUE	1	0.650018155396474	2		339	546	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141516	11141516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	242	707	1	ENST00000358026.2:c.3493C>T	p.Leu1165Phe	p.L1165F	ENST00000358026	NM_001128849.1	1165	Ctc/Ttc	25/36	1	2	FACETS	0.93	0.871	0.99	0.93	0.871	0.99	CLONAL	1	TRUE	1	0.650018155396474	2		708	801	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606675	29606675	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	211	575	0	ENST00000389048.3:c.1205T>G	p.Val402Gly	p.V402G	ENST00000389048	NM_004304.4	402	gTg/gGg	5/29	1	2	FACETS	0.958	0.893	1	0.958	0.893	1	CLONAL	1	TRUE	1	0.650018155396474	2		575	678	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437162	220437163	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0019557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	310	894	1	ENST00000243786.2:c.66_67delinsAA	p.Glu23Lys	p.E23K	ENST00000243786	NM_002191.3	22	ctGGag/ctAAag	1/2	1	2	FACETS	0.895	0.844	0.946	0.895	0.844	0.946	CLONAL	1	TRUE	1	0.650018155396474	2		895	1066	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631391	117631391	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1022614558	NA	P-0019557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	151	365	1	ENST00000368508.3:c.6287G>A	p.Arg2096Gln	p.R2096Q	ENST00000368508	NM_002944.2	2096	cGg/cAg	40/43	0.650018155396474	1	FACETS	0.942	0.875	1	0.942	0.875	1	CLONAL	1	TRUE	0	0.650018155396474	1		366	333	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527931	103527931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs4150388	NA	P-0019557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	172	390	0	ENST00000355739.4:c.3239G>A	p.Gly1080Glu	p.G1080E	ENST00000355739	NM_000123.3	1080	gGa/gAa	15/15	1	2	FACETS	0.964	0.893	1	0.964	0.893	1	CLONAL	1	TRUE	1	0.650018155396474	2		390	549	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0019558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	62	783	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.996	0.859	1	0.996	0.859	1	CLONAL	1	TRUE	1	0.18	2		783	692	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73342987	73342987	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	57	603	0	ENST00000377767.4:c.1819A>T	p.Thr607Ser	p.T607S	ENST00000377767	NM_014953.3	607	Acc/Tcc	14/21	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.18	2		603	610	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374385	81374385	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	72	613	0	ENST00000222390.5:c.677C>A	p.Thr226Lys	p.T226K	ENST00000222390	NM_000601.4	226	aCa/aAa	6/18	1	2	FACETS	0.791	0.692	0.896	1	0.976	1	SUBCLONAL	2	TRUE	1	0.18	2		613	506	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	593	600	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.389232999826066	6	FACETS	1	0.991	1	1	0.991	1	CLONAL	6	TRUE	0	0.389232999826066	6		600	863	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0019559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	345	646	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.351019477839189	3	FACETS	0.912	0.869	0.956	0.912	0.869	0.956	CLONAL	3	TRUE	0	0.389232999826066	3		646	774	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41011093	41011093	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	102	525	0	ENST00000267868.3:c.526G>A	p.Glu176Lys	p.E176K	ENST00000267868	NM_002875.4	176	Gag/Aag	6/10	1	2	FACETS	0.855	0.766	0.949	0.855	0.766	0.949	CLONAL	1	TRUE	1	0.389232999826066	2		525	613	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460389	149460389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761230419	NA	P-0019559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	92	558	1	ENST00000286301.3:c.248G>A	p.Arg83His	p.R83H	ENST00000286301	NM_005211.3	83	cGc/cAc	3/22	0.36767588299917	2	FACETS	0.889	0.792	0.991	0.444	0.396	0.496	CLONAL	1	TRUE	0	0.389232999826066	2		559	532	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512309	38512309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	441	977	0	ENST00000254066.5:c.1220C>T	p.Pro407Leu	p.P407L	ENST00000254066	NM_000964.3	407	cCg/cTg	9/9	NA	2	FACETS	0.998	0.954	1			1	INDETERMINATE	1	TRUE	NA	0.777098675725586	2		977	1137	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653841	89653850	+	frameshift_variant	Frame_Shift_Del	DEL	AGGAACAATA	AGGAACAATA	-	novel	NA	P-0019561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	187	631	0	ENST00000371953.3:c.139_148del	p.Arg47LeufsTer4	p.R47Lfs*4	ENST00000371953	NM_000314.4	47	AGGAACAATAtt/tt	2/9	1	2	FACETS	0.758	0.703	0.814	0.758	0.703	0.814	SUBCLONAL	1	TRUE	1	0.777098675725586	2		631	635	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711953	89711959	+	frameshift_variant	Frame_Shift_Del	DEL	GTGGCAC	GTGGCAC	-	novel	NA	P-0019561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	242	633	0	ENST00000371953.3:c.571_577del	p.Val191CysfsTer6	p.V191Cfs*6	ENST00000371953	NM_000314.4	191	GTGGCACtg/tg	6/9	1	2	FACETS	0.963	0.905	1	0.963	0.905	1	CLONAL	1	TRUE	1	0.777098675725586	2		633	647	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944143	71944143	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	329	787	0	ENST00000298229.2:c.1976C>G	p.Pro659Arg	p.P659R	ENST00000298229	NM_001567.3	659	cCc/cGc	17/28	0.777098675725586	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.777098675725586	1		787	502	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0019562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	199	681	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.90174312375835	3	FACETS	0.71	0.658	0.764	0.355	0.329	0.382	SUBCLONAL	1	TRUE	1	0.90174312375835	3		681	902	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579592	+	splice_acceptor_variant	Splice_Site	INS	-	-	G	novel	NA	P-0019562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	618	718	0	ENST00000269305.4:c.97-2_97-1insC		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.90174312375835	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.90174312375835	2		718	647	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322931	31322933	+	inframe_deletion	In_Frame_Del	DEL	ACC	ACC	-	novel	NA	P-0019562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1765	381	1044	0	ENST00000412585.2:c.963_965del	p.Val322del	p.V322del	ENST00000412585	NM_005514.6	321	gtGGTc/gtc	5/8	0.90174312375835	5	FACETS	0.926	0.876	0.978	0.309	0.292	0.326	CLONAL	1	TRUE	2	0.90174312375835	5		1044	2146	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980750	70980750	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1258679783	NA	P-0019562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	280	858	0	ENST00000276594.2:c.718C>G	p.Gln240Glu	p.Q240E	ENST00000276594	NM_024504.3	240	Caa/Gaa	3/8	0.90174312375835	3	FACETS	0.929	0.874	0.985	0.31	0.291	0.329	CLONAL	1	TRUE	0	0.90174312375835	3		858	970	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965780	90965780	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	121	379	0	ENST00000265433.3:c.1537C>G	p.Pro513Ala	p.P513A	ENST00000265433	NM_002485.4	513	Cct/Gct	11/16	0.90174312375835	3	FACETS	0.86	0.782	0.94	0.287	0.26	0.314	CLONAL	1	TRUE	0	0.90174312375835	3		379	453	SUCCESS
MET	4233	MSKCC	GRCh37	7	116422038	116422064	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCAGAATCCAACTGTAAAAGATCTTAT	GCAGAATCCAACTGTAAAAGATCTTAT	AG	novel	NA	P-0019562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	124	423	0	ENST00000397752.3:c.3523-4_3545delinsAG		p.X1175_splice	ENST00000397752	NM_000245.2	1175		18/21	0.90174312375835	3	FACETS	0.792	0.72	0.866	0.396	0.36	0.433	SUBCLONAL	1	TRUE	1	0.90174312375835	3		423	504	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411882	116411938	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTCTTTCTCTCTGTTTTAAGATCTGGGCAGTGAATTAGTTCGCTACGATGCAAGAG	TTTCTTTCTCTCTGTTTTAAGATCTGGGCAGTGAATTAGTTCGCTACGATGCAAGAG	-	novel	NA	P-0019564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	138	1182	0	ENST00000397752.3:c.2888-20_2924del		p.X963_splice	ENST00000397752	NM_000245.2	963		14/21	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		1182	982	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0019565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	102	614	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.951	1	1	0.991	1	CLONAL	4	TRUE	1	0.13	2		614	361	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226309	2226309	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	153	800	1	ENST00000326181.6:c.1922G>T	p.Arg641Leu	p.R641L	ENST00000326181	NM_032271.2	641	cGt/cTt	20/21	1	2	FACETS	0.919	0.849	0.99	1	0.994	1	CLONAL	6	TRUE	1	0.13	2		801	427	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201096	108201096	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	93	600	0	ENST00000278616.4:c.7463G>T	p.Cys2488Phe	p.C2488F	ENST00000278616	NM_000051.3	2488	tGt/tTt	50/63	0.475347436736863	1	FACETS	0.932	0.838	1	0.932	0.838	1	CLONAL	1	TRUE	0	0.475347436736863	1		600	320	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17941391	17941391	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	323	1165	3	ENST00000458235.1:c.3017G>A	p.Arg1006His	p.R1006H	ENST00000458235	NM_000215.3	1006	cGc/cAc	22/24	0.23685140704523	6	FACETS	0.907	0.855	0.961			1	INDETERMINATE	2	TRUE	NA	0.475347436736863	6		1168	1461	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115696	8115701	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	GTTTAG	GTTTAG	AC	novel	NA	P-0019566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	60	551	0	ENST00000346208.3:c.1048-6_1048-1delinsAC		p.X350_splice	ENST00000346208		350			1	2	FACETS	0.614	0.531	0.704	0.614	0.531	0.704	SUBCLONAL	1	TRUE	1	0.475347436736863	2		551	411	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0019567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	89	918	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.704	0.623	0.791	0.704	0.623	0.791	SUBCLONAL	1	FALSE	1	0.251318453569064	2		918	1006	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0019567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	104	987	2	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.20007996410165	1	FACETS	0.643	0.574	0.717	0.643	0.574	0.717	SUBCLONAL	1	FALSE	0	0.251318453569064	1		989	1125	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412038	63412038	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	88	411	0	ENST00000330258.3:c.1129G>A	p.Asp377Asn	p.D377N	ENST00000330258	NM_152424.3	377	Gat/Aat	2/2	1	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	0	0.251318453569064	1		411	484	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627752	187627752	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	73	548	0	ENST00000441802.2:c.3230C>G	p.Ser1077Cys	p.S1077C	ENST00000441802	NM_005245.3	1077	tCt/tGt	2/27	1	2	FACETS	0.745	0.65	0.847	0.745	0.65	0.847	SUBCLONAL	1	FALSE	1	0.251318453569064	2		548	780	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775698	9775698	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1253851300	NA	P-0019567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	79	919	0	ENST00000377346.4:c.241G>C	p.Glu81Gln	p.E81Q	ENST00000377346	NM_005026.3	81	Gag/Cag	4/24	1	2	FACETS	0.587	0.515	0.665	0.587	0.515	0.665	SUBCLONAL	1	FALSE	1	0.251318453569064	2		919	1071	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692918	89692918	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	51	604	0	ENST00000371953.3:c.402G>A	p.Met134Ile	p.M134I	ENST00000371953	NM_000314.4	134	atG/atA	5/9	0.251318453569064	1	FACETS	0.398	0.337	0.466	0.398	0.337	0.466	SUBCLONAL	1	FALSE	0	0.251318453569064	1		604	891	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863392	57863392	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759027001	NA	P-0019567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	118	956	2	ENST00000228682.2:c.1487G>A	p.Arg496His	p.R496H	ENST00000228682	NM_005269.2	496	cGc/cAc	11/12	1	2	FACETS	0.784	0.705	0.867	0.784	0.705	0.867	SUBCLONAL	1	FALSE	1	0.251318453569064	2		958	1198	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976422	25976422	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	69	716	0	ENST00000435504.4:c.1123G>C	p.Glu375Gln	p.E375Q	ENST00000435504		375	Gaa/Caa	11/13	1	2	FACETS	0.56	0.486	0.641	0.56	0.486	0.641	SUBCLONAL	1	FALSE	1	0.251318453569064	2		716	980	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142866	30142866	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	97	872	1	ENST00000389048.3:c.660C>A	p.Phe220Leu	p.F220L	ENST00000389048	NM_004304.4	220	ttC/ttA	1/29	1	2	FACETS	0.813	0.724	0.909	0.813	0.724	0.909	CLONAL	1	FALSE	1	0.251318453569064	2		873	949	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391455	84391455	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	57	474	0	ENST00000321945.7:c.377C>T	p.Ser126Leu	p.S126L	ENST00000321945	NM_139076.2	126	tCa/tTa	5/9	1	2	FACETS	0.768	0.658	0.887	0.768	0.658	0.887	SUBCLONAL	1	FALSE	1	0.251318453569064	2		474	591	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706949	117706949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779006477	NA	P-0019567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	54	757	2	ENST00000368508.3:c.2201C>T	p.Thr734Met	p.T734M	ENST00000368508	NM_002944.2	734	aCg/aTg	15/43	1	2	FACETS	0.414	0.352	0.483	0.414	0.352	0.483	SUBCLONAL	1	FALSE	1	0.251318453569064	2		759	1037	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	320	736	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.898	0.853	0.944	0.898	0.853	0.944	CLONAL	1	TRUE	1	0.912216320861755	2		736	781	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0019568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	199	290	1	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	0.912216320861755	2		291	426	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724541	162724541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759709680	NA	P-0019568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	47	528	1	ENST00000367921.3:c.313C>T	p.Arg105Cys	p.R105C	ENST00000367921	NM_006182.2	105	Cgc/Tgc	5/18	1	2	FACETS	0.145	0.122	0.171	0.145	0.122	0.171	SUBCLONAL	1	TRUE	1	0.912216320861755	2		529	711	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0019569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	96	860	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.991	0.886	1	0.991	0.886	1	CLONAL	1	TRUE	1	0.339148450806364	2		860	571	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029126	26029126	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	139	567	0	ENST00000435504.4:c.224C>T	p.Pro75Leu	p.P75L	ENST00000435504		75	cCa/cTa	4/13	0.217145499742262	2	FACETS	0.96	0.882	1	0.96	0.882	1	CLONAL	2	TRUE	0	0.339148450806364	2		567	427	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057627	180057627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756234174	NA	P-0019569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	127	1037	0	ENST00000261937.6:c.328G>A	p.Val110Ile	p.V110I	ENST00000261937	NM_182925.4	110	Gtc/Atc	3/30	1	2	FACETS	0.901	0.816	0.991	0.901	0.816	0.991	CLONAL	1	TRUE	1	0.339148450806364	2		1037	831	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455576	189455576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754361670	NA	P-0019569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	119	745	1	ENST00000264731.3:c.110G>A	p.Arg37Gln	p.R37Q	ENST00000264731	NM_003722.4	37	cGa/cAa	2/14	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.339148450806364	2		746	507	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453135	140453136	+	missense_variant	Missense_Mutation	DNP	CA	CA	TT	rs121913377	NA	P-0019569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	112	642	0	ENST00000288602.6:c.1799_1800delinsAA	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTG/gAA	15/18	1	2	FACETS	0.817	0.741	0.897	1	0.986	1	CLONAL	2	TRUE	1	0.339148450806364	2		642	404	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948523	31948523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756991872	NA	P-0019569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	17	350	1	ENST00000375333.2:c.1006C>T	p.Arg336Trp	p.R336W	ENST00000375333	NM_032454.1	336	Cgg/Tgg	7/8	1	2	FACETS	0.304	0.226	0.396	0.304	0.226	0.396	SUBCLONAL	1	TRUE	1	0.339148450806364	2		351	330	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826577	50826577	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	97	506	1	ENST00000398568.2:c.2302C>T	p.Pro768Ser	p.P768S	ENST00000398568	NM_001042412.1	768	Cct/Tct	15/18	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.339148450806364	2		507	445	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100298	27100301	+	frameshift_variant	Frame_Shift_Del	DEL	ATTC	ATTC	TTT	novel	NA	P-0019569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	106	851	1	ENST00000324856.7:c.4010_4013delinsTTT	p.Asp1337ValfsTer144	p.D1337Vfs*144	ENST00000324856	NM_006015.4	1337	gATTCc/gTTTc	17/20	1	2	FACETS	0.89	0.799	0.987	0.89	0.799	0.987	CLONAL	1	TRUE	1	0.339148450806364	2		852	702	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243777028	243777028	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	125	608	1	ENST00000263826.5:c.641C>T	p.Ser214Phe	p.S214F	ENST00000263826	NM_005465.4	214	tCc/tTc	7/13	1	2	FACETS	0.899	0.821	0.98	1	0.989	1	CLONAL	2	TRUE	1	0.339148450806364	2		609	410	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588617	28588617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	126	576	0	ENST00000241453.7:c.2831G>A	p.Gly944Glu	p.G944E	ENST00000241453	NM_004119.2	944	gGa/gAa	23/24	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.339148450806364	2		576	551	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16062159	16062159	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	171	701	0	ENST00000268712.3:c.647C>T	p.Pro216Leu	p.P216L	ENST00000268712	NM_006311.3	216	cCt/cTt	6/46	1	2	FACETS	0.849	0.785	0.915	1	0.991	1	CLONAL	2	TRUE	1	0.339148450806364	2		701	594	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868605	37868605	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775972596	NA	P-0019569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	75	643	0	ENST00000269571.5:c.1052G>A	p.Arg351Gln	p.R351Q	ENST00000269571		351	cGa/cAa	9/27	1	2	FACETS	0.866	0.76	0.978	0.866	0.76	0.978	CLONAL	1	TRUE	1	0.339148450806364	2		643	511	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7132319	7132319	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	111	446	0	ENST00000302850.5:c.2692C>T	p.Leu898Phe	p.L898F	ENST00000302850	NM_000208.2	898	Ctc/Ttc	14/22	1	2	FACETS	0.796	0.721	0.874	1	0.986	1	SUBCLONAL	2	TRUE	1	0.339148450806364	2		446	411	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272073	15272074	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0019569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	207	908	1	ENST00000263388.2:c.6365_6366delinsTT	p.Pro2122Leu	p.P2122L	ENST00000263388	NM_000435.2	2122	cCC/cTT	33/33	1	2	FACETS	0.926	0.864	0.99	1	0.993	1	CLONAL	2	TRUE	1	0.339148450806364	2		909	659	SUCCESS
APC	324	MSKCC	GRCh37	5	112179462	112179462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	119	549	0	ENST00000257430.4:c.8171C>T	p.Ser2724Phe	p.S2724F	ENST00000257430	NM_000038.5	2724	tCc/tTc	16/16	1	2	FACETS	0.81	0.737	0.887	1	0.987	1	CLONAL	2	TRUE	1	0.339148450806364	2		549	433	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509409	149509409	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	68	795	0	ENST00000261799.4:c.1490T>G	p.Leu497Arg	p.L497R	ENST00000261799	NM_002609.3	497	cTg/cGg	10/23	1	2	FACETS	0.615	0.535	0.702	0.615	0.535	0.702	SUBCLONAL	1	TRUE	1	0.339148450806364	2		795	652	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679654	30679654	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	113	747	0	ENST00000376406.3:c.2065G>T	p.Gly689Cys	p.G689C	ENST00000376406	NM_014641.2	689	Ggt/Tgt	5/15	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.339148450806364	2		747	646	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658482	117658482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	67	698	0	ENST00000368508.3:c.5101C>T	p.His1701Tyr	p.H1701Y	ENST00000368508	NM_002944.2	1701	Cat/Tat	31/43	1	2	FACETS	0.846	0.737	0.963	0.846	0.737	0.963	CLONAL	1	TRUE	1	0.339148450806364	2		698	467	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340297	116340297	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs757846126	NA	P-0019569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	93	477	0	ENST00000397752.3:c.1159C>T	p.Gln387Ter	p.Q387*	ENST00000397752	NM_000245.2	387	Cag/Tag	2/21	1	2	FACETS	0.839	0.753	0.927	1	0.984	1	CLONAL	2	TRUE	1	0.339148450806364	2		477	327	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275778	38275779	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0019569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	139	753	3	ENST00000425967.3:c.1490_1491delinsTT	p.Pro497Leu	p.P497L	ENST00000425967	NM_001174067.1	497	cCC/cTT	11/19	0.256840649327221	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.339148450806364	1		756	593	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561434	141561435	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0019569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	61	524	2	ENST00000220592.5:c.1370_1371delinsTT	p.Ala457Val	p.A457V	ENST00000220592	NM_012154.3	457	gCC/gTT	11/19	0.256840649327221	1	FACETS	0.727	0.629	0.832	0.727	0.629	0.832	SUBCLONAL	1	TRUE	0	0.339148450806364	1		526	411	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391529	139391529	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	357	1190	0	ENST00000277541.6:c.6662C>T	p.Ser2221Phe	p.S2221F	ENST00000277541	NM_017617.3	2221	tCc/tTc	34/34	0.217145499742262	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.339148450806364	2		1190	1003	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932584	39932584	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	113	600	0	ENST00000378444.4:c.2015C>A	p.Ser672Tyr	p.S672Y	ENST00000378444	NM_001123385.1	672	tCc/tAc	4/15	1	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.339148450806364	1		600	476	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0019570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	548	832	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.566698439647	4	FACETS	0.81	0.777	0.843	0.81	0.777	0.843	CLONAL	2	TRUE	2	0.766970156828811	4		832	1559	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602493	10602493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	530	641	0	ENST00000171111.5:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000171111	NM_203500.1	362	cGg/cAg	3/6	0.622906942842503	2	FACETS	0.819	0.793	0.845	0.819	0.793	0.845	CLONAL	2	TRUE	0	0.766970156828811	2		641	844	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438566	52438566	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1553645164	NA	P-0019570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	519	575	0	ENST00000460680.1:c.1153C>T	p.Arg385Ter	p.R385*	ENST00000460680	NM_004656.3	385	Cga/Tga	12/17	0.622906942842503	2	FACETS	0.832	0.806	0.858	0.832	0.806	0.858	CLONAL	2	TRUE	0	0.766970156828811	2		575	813	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11273567	11273567	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	244	660	0	ENST00000361445.4:c.3174A>C	p.Gln1058His	p.Q1058H	ENST00000361445	NM_004958.3	1058	caA/caC	21/58	0.618704201197737	3	FACETS	0.851	0.795	0.908	0.425	0.397	0.454	CLONAL	1	TRUE	1	0.766970156828811	3		660	1035	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17355147	17355147	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1557741456	NA	P-0019570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	459	659	0	ENST00000375499.3:c.371T>C	p.Val124Ala	p.V124A	ENST00000375499	NM_003000.2	124	gTc/gCc	4/8	0.618704201197737	3	FACETS	0.834	0.8	0.868	0.834	0.8	0.868	CLONAL	2	TRUE	1	0.766970156828811	3		659	993	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599149	28599149	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	758	1037	1	ENST00000253063.3:c.595G>A	p.Val199Ile	p.V199I	ENST00000253063	NM_031459.4	199	Gtc/Atc	5/10	0.618704201197737	3	FACETS	0.821	0.795	0.848	0.821	0.795	0.848	CLONAL	2	TRUE	1	0.766970156828811	3		1038	1665	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458000	120458000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	361	533	0	ENST00000256646.2:c.7345G>T	p.Gly2449Ter	p.G2449*	ENST00000256646	NM_024408.3	2449	Gga/Tga	34/34	0.618704201197737	3	FACETS	0.841	0.803	0.88	0.841	0.803	0.88	CLONAL	2	TRUE	1	0.766970156828811	3		533	774	SUCCESS
ATM	472	MSKCC	GRCh37	11	108183217	108183217	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	290	435	0	ENST00000278616.4:c.5998A>C	p.Ser2000Arg	p.S2000R	ENST00000278616	NM_000051.3	2000	Agt/Cgt	40/63	0.627254793581088	4	FACETS	1	0.993	1	0.854	0.823	0.884	CLONAL	3	TRUE	0	0.766970156828811	4		435	391	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923364	9923364	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	233	603	3	ENST00000330684.3:c.1923C>A	p.Phe641Leu	p.F641L	ENST00000330684	NM_001134407.1	641	ttC/ttA	9/13	0.618704201197737	3	FACETS	0.839	0.783	0.897	0.419	0.391	0.449	CLONAL	1	TRUE	1	0.766970156828811	3		606	1002	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560040	29560040	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500375	NA	P-0019570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	106	330	0	ENST00000356175.3:c.3517C>T	p.Leu1173Phe	p.L1173F	ENST00000356175	NM_000267.3	1173	Ctc/Ttc	27/57	0.619126856768721	4	FACETS	0.857	0.77	0.948	0.428	0.385	0.474	CLONAL	1	TRUE	2	0.766970156828811	4		330	570	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804307	46804307	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	562	687	0	ENST00000290295.7:c.700G>A	p.Glu234Lys	p.E234K	ENST00000290295	NM_006361.5	234	Gag/Aag	2/2	0.619126856768721	4	FACETS	0.834	0.801	0.868	0.834	0.801	0.868	CLONAL	2	TRUE	2	0.766970156828811	4		687	1552	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78914311	78914311	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	527	706	2	ENST00000306801.3:c.2935G>T	p.Asp979Tyr	p.D979Y	ENST00000306801	NM_020761.2	979	Gac/Tac	25/34	0.618704201197737	3	FACETS	0.825	0.794	0.857	0.825	0.794	0.857	CLONAL	2	TRUE	1	0.766970156828811	3		708	1152	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602622	10602622	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	595	702	0	ENST00000171111.5:c.956G>C	p.Cys319Ser	p.C319S	ENST00000171111	NM_203500.1	319	tGc/tCc	3/6	0.622906942842503	2	FACETS	0.794	0.769	0.818	0.794	0.769	0.818	SUBCLONAL	2	TRUE	0	0.766970156828811	2		702	977	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143043281	143043281	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	401	487	0	ENST00000262992.4:c.2135G>T	p.Arg712Leu	p.R712L	ENST00000262992	NM_001101669.1	712	cGa/cTa	19/24	0.766970156828811	4	FACETS	1	0.973	1			1	CLONAL	2	TRUE	NA	0.766970156828811	4		487	902	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457721	149457721	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	668	879	0	ENST00000286301.3:c.683G>T	p.Ser228Ile	p.S228I	ENST00000286301	NM_005211.3	228	aGc/aTc	5/22	0.566698439647	4	FACETS	0.845	0.814	0.876	0.845	0.814	0.876	CLONAL	2	TRUE	2	0.766970156828811	4		879	1821	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180040064	180040064	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2055	150	1050	1	ENST00000261937.6:c.3378G>T	p.Gln1126His	p.Q1126H	ENST00000261937	NM_182925.4	1126	caG/caT	25/30	0.566698439647	4	FACETS	0.313	0.285	0.344	0.157	0.142	0.172	SUBCLONAL	1	TRUE	2	0.766970156828811	4		1051	2205	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650050	93650050	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	406	522	3	ENST00000375746.1:c.1601G>T	p.Trp534Leu	p.W534L	ENST00000375746	NM_001174167.1	534	tGg/tTg	12/14	0.566698439647	4	FACETS	0.757	0.721	0.794	0.757	0.721	0.794	SUBCLONAL	2	TRUE	2	0.766970156828811	4		525	1235	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268719	98268719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374150356	NA	P-0019570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1191	398	547	1	ENST00000331920.6:c.364G>A	p.Glu122Lys	p.E122K	ENST00000331920	NM_000264.3	122	Gag/Aag	2/24	0.695241635776281	6	FACETS	0.828	0.785	0.871	0.414	0.392	0.436	CLONAL	2	TRUE	2	0.766970156828811	6		548	1589	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040904	47040904	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0019570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	669	416	1	ENST00000377604.3:c.1436-2A>G		p.X479_splice	ENST00000377604	NM_001204468.1	479			0.766970156828811	2	FACETS	0.977	0.954	0.999			1	CLONAL	2	TRUE	NA	0.766970156828811	2		417	893	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0019576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	264	680	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.476700522585979	2	FACETS	0.97	0.918	1	0.97	0.918	1	CLONAL	2	TRUE	0	0.476700522585979	2		680	571	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0019578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	14	640	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		640	244	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778764	3778764	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	28	981	0	ENST00000262367.5:c.6284A>C	p.Gln2095Pro	p.Q2095P	ENST00000262367	NM_004380.2	2095	cAg/cCg	31/31	1	2	FACETS	0.226	0.18	0.279	0.226	0.18	0.279	SUBCLONAL	1	TRUE	1	0.46	2		981	539	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490331	56490332	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0019581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	89	505	0	ENST00000267101.3:c.2100_2101del	p.Leu700PhefsTer13	p.L700Ffs*13	ENST00000267101	NM_001982.3	700	ttGGcc/ttcc	18/28	0.187609026710504	5	FACETS	1	0.978	1	0.478	0.426	0.532	INDETERMINATE	1	TRUE	2	0.56292012684182	5		505	407	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426491	49426506	+	protein_altering_variant	In_Frame_Del	DEL	AGGGCCAAGTGCCACT	AGGGCCAAGTGCCACT	G	novel	NA	P-0019581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	52	1030	0	ENST00000301067.7:c.11982_11997delinsC	p.Gln3994_Pro3999delinsHis	p.Q3994_P3999delinsH	ENST00000301067	NM_003482.3	3994	caAGTGGCACTTGGCCCT/caC	39/54	1	2	FACETS	0.348	0.296	0.405	0.348	0.296	0.405	SUBCLONAL	1	TRUE	1	0.56292012684182	2		1030	531	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0019582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	394	738	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	0.225438497815136	6	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.447510248062962	6		738	1414	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274195	10274195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542256226	NA	P-0019582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	130	480	1	ENST00000330684.3:c.74C>T	p.Ala25Val	p.A25V	ENST00000330684	NM_001134407.1	25	gCg/gTg	2/13	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.447510248062962	2		481	546	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871199	12871199	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	212	319	1	ENST00000228872.4:c.429del	p.Leu144Ter	p.L144*	ENST00000228872	NM_004064.3	142	acG/ac	1/3	1	2	FACETS	0.999	0.939	1	1	0.994	1	CLONAL	2	TRUE	1	0.447510248062962	2		320	474	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431298	49431298	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	116	437	0	ENST00000301067.7:c.9841C>T	p.Gln3281Ter	p.Q3281*	ENST00000301067	NM_003482.3	3281	Cag/Tag	34/54	NA	2	FACETS	0.949	0.859	1			1	INDETERMINATE	1	TRUE	NA	0.447510248062962	2		437	546	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060551	38060571	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	AACCCCCCAGTCCCGGGAGCT	AACCCCCCAGTCCCGGGAGCT	-	novel	NA	P-0019582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	513	841	0	ENST00000250448.2:c.1418_*19del		p.*473*	ENST00000250448	NM_004496.3	473		2/2	1	2	FACETS	1	0.969	1	1	0.997	1	CLONAL	2	TRUE	1	0.447510248062962	2		841	1136	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944238	81944238	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	487	791	0	ENST00000359376.3:c.1847A>C	p.His616Pro	p.H616P	ENST00000359376	NM_002661.3	616	cAc/cCc	18/33	0.447510248062962	0	FACETS		NA	1			1	NA	3	TRUE	0	0.447510248062962	0		791	561	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224535	36224535	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	320	1252	2	ENST00000222270.7:c.6997G>A	p.Gly2333Arg	p.G2333R	ENST00000222270	NM_014727.1	2333	Ggg/Agg	29/37	1	2	FACETS	0.969	0.913	1	0.969	0.913	1	CLONAL	1	TRUE	1	0.447510248062962	2		1254	1476	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45873458	45873458	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	379	784	0	ENST00000391945.4:c.38del	p.Pro13ArgfsTer43	p.P13Rfs*43	ENST00000391945	NM_000400.3	13	cCg/cg	2/23	1	2	FACETS	0.899	0.857	0.942	1	0.996	1	CLONAL	2	TRUE	1	0.447510248062962	2		784	942	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44527574	44527574	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	169	710	1	ENST00000291552.4:c.31A>T	p.Thr11Ser	p.T11S	ENST00000291552	NM_006758.2	11	Acc/Tcc	1/8	1	2	FACETS	0.922	0.849	0.999	0.922	0.849	0.999	CLONAL	1	TRUE	1	0.447510248062962	2		711	819	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553353	41553353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750777340	NA	P-0019582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	57	801	0	ENST00000263253.7:c.3442G>A	p.Val1148Ile	p.V1148I	ENST00000263253	NM_001429.3	1148	Gtc/Atc	18/31	0.275443451337305	1	FACETS	0.209	0.178	0.242	0.209	0.178	0.242	SUBCLONAL	1	TRUE	0	0.447510248062962	1		801	947	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474649	138474649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	187	795	1	ENST00000289153.2:c.344G>A	p.Ser115Asn	p.S115N	ENST00000289153	NM_006219.2	115	aGt/aAt	2/22	0.365964874233466	3	FACETS	0.854	0.787	0.923	0.427	0.393	0.462	CLONAL	1	TRUE	1	0.447510248062962	3		796	1198	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576482	67576482	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	233	601	0	ENST00000274335.5:c.761C>A	p.Ser254Tyr	p.S254Y	ENST00000274335		254	tCc/tAc	5/15	NA	2	FACETS	0.802	0.753	0.853			1	INDETERMINATE	2	TRUE	NA	0.447510248062962	2		601	649	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759951	133759968	+	inframe_deletion	In_Frame_Del	DEL	GAAGCCGGCTCTGCCTCG	GAAGCCGGCTCTGCCTCG	-	novel	NA	P-0019582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	502	1067	0	ENST00000318560.5:c.2278_2295del	p.Pro760_Lys765del	p.P760_K765del	ENST00000318560	NM_005157.4	758	gaGAAGCCGGCTCTGCCTCGg/gag	11/11	0.365964874233466	3	FACETS	0.964	0.923	1	0.964	0.923	1	CLONAL	2	TRUE	1	0.447510248062962	3		1067	1424	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0019584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	437	941	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.857343486843222	2		941	978	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966872	25966873	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0019584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	150	507	0	ENST00000435504.4:c.2333dup	p.Val779SerfsTer25	p.V779Sfs*25	ENST00000435504		778	cca/ccCa	13/13	0.728710503026196	1	FACETS	0.469	0.433	0.507	0.469	0.433	0.507	SUBCLONAL	1	TRUE	0	0.857343486843222	1		507	426	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061247	38061247	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	714	860	0	ENST00000250448.2:c.742C>G	p.Pro248Ala	p.P248A	ENST00000250448	NM_004496.3	248	Ccg/Gcg	2/2	0.322439686757947	5	FACETS	1	0.992	1			1	INDETERMINATE	3	TRUE	NA	0.857343486843222	5		860	1201	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879622	151879622	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	35	345	0	ENST00000262189.6:c.5323C>T	p.Gln1775Ter	p.Q1775*	ENST00000262189	NM_170606.2	1775	Cag/Tag	36/59	0.783686258471566	1	FACETS	0.199	0.163	0.237	0.199	0.163	0.237	SUBCLONAL	1	TRUE	0	0.857343486843222	1		345	235	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	250	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.294965874734906	1	FACETS	0.897	0.848	0.946	1	0.996	1	CLONAL	3	TRUE	0	0.294965874734906	1		509	537	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0019585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	40	492	1	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.294965874734906	2		493	199	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0019585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	43	472	2	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.294965874734906	2		474	279	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0019585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	107	717	1	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	0.989	1	CLONAL	2	TRUE	1	0.294965874734906	2		718	353	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953760	48953760	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913302	NA	P-0019585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	92	384	0	ENST00000267163.4:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000267163	NM_000321.2	455	Cga/Tga	14/27	1	2	FACETS	1	0.972	1	1	0.989	1	CLONAL	2	TRUE	1	0.294965874734906	2		384	256	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052632	42052632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779811318	NA	P-0019585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	145	631	0	ENST00000219905.7:c.7303C>T	p.Arg2435Trp	p.R2435W	ENST00000219905	NM_001164273.1	2435	Cgg/Tgg	20/24	1	2	FACETS	0.917	0.841	0.996	1	0.991	1	CLONAL	2	TRUE	1	0.294965874734906	2		631	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578429	7578429	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1567553148	NA	P-0019585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	135	790	0	ENST00000269305.4:c.501del	p.Gln167HisfsTer3	p.Q167Hfs*3	ENST00000269305	NM_001126112.2	167	caG/ca	5/11	1	2	FACETS	0.982	0.899	1	1	0.991	1	CLONAL	2	TRUE	1	0.294965874734906	2		790	466	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598336	28598336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769442139	NA	P-0019585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	138	829	0	ENST00000253063.3:c.308C>T	p.Thr103Met	p.T103M	ENST00000253063	NM_031459.4	103	aCg/aTg	3/10	1	2	FACETS	0.908	0.832	0.988	1	0.99	1	CLONAL	2	TRUE	1	0.294965874734906	2		829	515	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725042	162725042	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	94	432	0	ENST00000367921.3:c.514C>T	p.His172Tyr	p.H172Y	ENST00000367921	NM_006182.2	172	Cac/Tac	6/18	1	2	FACETS	1	0.955	1	1	0.988	1	CLONAL	2	TRUE	1	0.294965874734906	2		432	288	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741681	17741681	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	59	579	0	ENST00000250003.3:c.352G>A	p.Glu118Lys	p.E118K	ENST00000250003	NM_002478.4	118	Gag/Aag	1/3	0.294965874734906	1	FACETS	0.927	0.801	1	0.927	0.801	1	CLONAL	1	TRUE	0	0.294965874734906	1		579	368	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32905065	32905065	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	67	361	0	ENST00000380152.3:c.691A>C	p.Ser231Arg	p.S231R	ENST00000380152		231	Agc/Cgc	9/27	1	2	FACETS	1	0.949	1	1	0.984	1	CLONAL	2	TRUE	1	0.294965874734906	2		361	200	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655248	45655248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs533193731	NA	P-0019585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	107	707	1	ENST00000407780.3:c.604G>A	p.Val202Met	p.V202M	ENST00000407780	NM_001283052.1	202	Gtg/Atg	4/7	0.294965874734906	1	FACETS	0.976	0.886	1	1	0.989	1	CLONAL	2	TRUE	0	0.294965874734906	1		708	317	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540252	187540252	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	22	537	1	ENST00000441802.2:c.7488A>T	p.Glu2496Asp	p.E2496D	ENST00000441802	NM_005245.3	2496	gaA/gaT	10/27	0.294965874734906	1	FACETS	0.476	0.37	0.6	0.476	0.37	0.6	SUBCLONAL	1	TRUE	0	0.294965874734906	1		538	267	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111558	56111559	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCGG	novel	NA	P-0019585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	10	84	0	ENST00000399503.3:c.163_166dup	p.Asp56GlyfsTer21	p.D56Gfs*21	ENST00000399503	NM_005921.1	53	gag/gaGCGGg	1/20	1	2	FACETS	0.983	0.677	1	0.983	0.677	1	CLONAL	1	TRUE	1	0.294965874734906	2		84	69	SUCCESS
APC	324	MSKCC	GRCh37	5	112164574	112164574	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	50	377	0	ENST00000257430.4:c.1648A>G	p.Asn550Asp	p.N550D	ENST00000257430	NM_000038.5	550	Aat/Gat	14/16	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.294965874734906	2		377	273	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874641	151874649	+	inframe_deletion	In_Frame_Del	DEL	GTTGAGATG	GTTGAGATG	-	novel	NA	P-0019585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	36	463	0	ENST00000262189.6:c.7889_7897del	p.Pro2630_Gln2632del	p.P2630_Q2632del	ENST00000262189	NM_170606.2	2630	cCATCTCAACaa/caa	38/59	0.280403685670271	1	FACETS	0.897	0.743	1	0.897	0.743	1	CLONAL	1	TRUE	0	0.294965874734906	1		463	232	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	288	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	0.98	0.937	1			1	INDETERMINATE	2	TRUE	NA	0.631843066693291	2		555	465	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105920	27105920	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	92	620	2	ENST00000324856.7:c.5531G>A	p.Trp1844Ter	p.W1844*	ENST00000324856	NM_006015.4	1844	tGg/tAg	20/20	0.631843066693291	1	FACETS	0.893	0.81	0.979	0.893	0.81	0.979	CLONAL	1	TRUE	0	0.631843066693291	1		622	223	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375642	118375642	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	89	462	0	ENST00000534358.1:c.9035G>T	p.Cys3012Phe	p.C3012F	ENST00000534358	NM_005933.3	3012	tGt/tTt	27/36	0.631843066693291	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.631843066693291	1		462	161	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591085	67591085	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	102	474	0	ENST00000274335.5:c.1678G>C	p.Asp560His	p.D560H	ENST00000274335		560	Gac/Cac	12/15	1	2	FACETS	0.952	0.861	1	0.952	0.861	1	CLONAL	1	TRUE	1	0.631843066693291	2		474	339	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923643	39923643	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	174	385	0	ENST00000378444.4:c.3448G>T	p.Glu1150Ter	p.E1150*	ENST00000378444	NM_001123385.1	1150	Gag/Tag	7/15	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.631843066693291	1		385	255	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411868	116411883	+	intron_variant	Intron	DEL	TCTTTAACAAGCTCTT	TCTTTAACAAGCTCTT	-	novel	NA	P-0019588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	241	1058	0	ENST00000397752.3:c.2888-30_2888-15del		p.*963*	ENST00000397752	NM_000245.2	-/1390			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		1058	1198	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610715	52610715	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0019592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	39	321	0	ENST00000394830.3:c.3459-1G>T		p.X1153_splice	ENST00000394830	NM_018313.4	1153			0.243504395803746	1	FACETS	0.998	0.831	1	0.998	0.831	1	CLONAL	1	TRUE	0	0.243504395803746	1		321	282	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27093058	27093058	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs886042036	NA	P-0019592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	28	384	0	ENST00000324856.7:c.2988+1G>A		p.X996_splice	ENST00000324856	NM_006015.4	996			1	2	FACETS	0.505	0.403	0.622	0.505	0.403	0.622	SUBCLONAL	1	TRUE	1	0.243504395803746	2		384	455	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692917	89692917	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1085308046	NA	P-0019592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	29	657	0	ENST00000371953.3:c.401T>C	p.Met134Thr	p.M134T	ENST00000371953	NM_000314.4	134	aTg/aCg	5/9	0.243504395803746	1	FACETS	0.371	0.297	0.456	0.371	0.297	0.456	SUBCLONAL	1	TRUE	0	0.243504395803746	1		657	564	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086009	16086009	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	69	674	0	ENST00000281043.3:c.1185C>G	p.Asn395Lys	p.N395K	ENST00000281043	NM_005378.4	395	aaC/aaG	3/3	NA	2	FACETS	0.798	0.695	0.911			1	INDETERMINATE	1	TRUE	NA	0.243504395803746	2		674	710	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965485	25965485	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	86	724	0	ENST00000435504.4:c.3721A>G	p.Thr1241Ala	p.T1241A	ENST00000435504		1241	Acc/Gcc	13/13	NA	2	FACETS	0.982	0.869	1			1	INDETERMINATE	1	TRUE	NA	0.243504395803746	2		724	719	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183757	10183757	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	84	798	1	ENST00000256474.2:c.227del	p.Phe76SerfsTer83	p.F76Sfs*83	ENST00000256474	NM_000551.3	76	Ttc/tc	1/3	0.243504395803746	1	FACETS	0.89	0.786	1	0.89	0.786	1	CLONAL	1	TRUE	0	0.243504395803746	1		799	681	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0019593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	65	741	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	0.341646503304948	2		742	332	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0019593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	108	810	3	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.341646503304948	3	FACETS	0.83	0.749	0.914	0.83	0.749	0.914	CLONAL	2	TRUE	1	0.341646503304948	3		813	446	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0019593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	43	566	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.625	0.523	0.736	0.625	0.523	0.736	SUBCLONAL	1	TRUE	1	0.341646503304948	2		566	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs967461896	NA	P-0019593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	288	642	0	ENST00000269305.4:c.526T>A	p.Cys176Ser	p.C176S	ENST00000269305	NM_001126112.2	176	Tgc/Agc	5/11	0.321538660884197	3	FACETS	0.9	0.851	0.95	0.9	0.851	0.95	CLONAL	3	TRUE	0	0.341646503304948	3		642	731	SUCCESS
APC	324	MSKCC	GRCh37	5	112175531	112175532	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1554085654	NA	P-0019593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	62	362	0	ENST00000257430.4:c.4241dup	p.Ser1415LysfsTer8	p.S1415Kfs*8	ENST00000257430	NM_000038.5	1414	gta/gTta	16/16	0.341646503304948	1	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	0	0.341646503304948	1		362	293	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295226	1295226	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0019593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	93	438	0				ENST00000310581	NM_198253.2	-/1132			0.341646503304948	3	FACETS	1	0.969	1	0.62	0.553	0.691	CLONAL	1	TRUE	1	0.341646503304948	3		438	514	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114193	115114193	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	209	738	0	ENST00000257566.3:c.1024G>T	p.Glu342Ter	p.E342*	ENST00000257566	NM_016569.3	342	Gaa/Taa	6/8	0.341646503304948	3	FACETS	0.976	0.909	1	0.976	0.909	1	CLONAL	2	TRUE	1	0.341646503304948	3		738	734	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213503	36213503	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	217	1144	0	ENST00000222270.7:c.2605A>C	p.Lys869Gln	p.K869Q	ENST00000222270	NM_014727.1	869	Aaa/Caa	5/37	0.341646503304948	3	FACETS	1	0.98	1	0.573	0.531	0.616	CLONAL	1	TRUE	1	0.341646503304948	3		1144	1298	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190656573	190656573	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0019593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	38	254	0	ENST00000441310.2:c.38C>G	p.Ser13Ter	p.S13*	ENST00000441310	NM_000534.4	13	tCa/tGa	2/13	0.341646503304948	3	FACETS	0.883	0.733	1	0.441	0.366	0.525	CLONAL	1	TRUE	1	0.341646503304948	3		254	295	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665248	138665248	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	220	1065	0	ENST00000330315.3:c.317T>A	p.Leu106His	p.L106H	ENST00000330315	NM_023067.3	106	cTc/cAc	1/1	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.341646503304948	2		1065	1077	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0019595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	98	290	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	0.674508969970966	2		291	241	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0019595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	656	760	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	0.998	1	NA	3	TRUE	1	0.674508969970966	2		760	738	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	34	736	0				ENST00000310581	NM_198253.2	-/1132			0.151660210070758	4	FACETS	1	0.913	1	0.584	0.485	0.691	INDETERMINATE	1	TRUE	2	0.687222835219555	4		736	143	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0019596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	64	760	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.843	0.74	0.95	0.843	0.74	0.95	CLONAL	1	TRUE	1	0.687222835219555	2		761	221	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845619	68845619	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1255556757	NA	P-0019596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	71	647	0	ENST00000261769.5:c.865G>A	p.Ala289Thr	p.A289T	ENST00000261769	NM_004360.3	289	Gcg/Acg	7/16	1	2	FACETS	0.918	0.814	1	0.918	0.814	1	CLONAL	1	TRUE	1	0.687222835219555	2		647	225	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857556	57858030	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCAGTGTGGGGACAGAAGGTCAGTGTATATACCAATCCCTGGGCCTTGAGGATTTGGCAGATCTCCCACTTGGGCCCACCCCCACCCCATGCCAGTTTCCTATCTACAGGAGGATTTGAGGCCCCATGTCATATGGACCTGGAATCTGGGATCAGGTCATGTCTGGGGTTTTAAGGTGAGGTTTATGTATCCTCCATTCCCATTCCAGCTGTCTCTTTTTTCTAGGACTGTCTGGCCCGCCCTTCTGCCACCAAGCTAACCTCATGTCCGGCCCCCACAGTTATGGGCCAGCCAGAGAGACCAACAGCTGCACCGAGGGTGAGGGCTCAGGCAACACCTCTTCCCTTTCTGCCCCTCTCTGACTTGTTCTGAAAGAGAAAGTGGGAGGGCAGGGGATCTCACTTGGAGGAGGAGATGCTTGGAGATGTGAGGCGTCAGAGCACCATCAAGAAGTCACAGATGGGGCCGGGCGCG	CCCAGTGTGGGGACAGAAGGTCAGTGTATATACCAATCCCTGGGCCTTGAGGATTTGGCAGATCTCCCACTTGGGCCCACCCCCACCCCATGCCAGTTTCCTATCTACAGGAGGATTTGAGGCCCCATGTCATATGGACCTGGAATCTGGGATCAGGTCATGTCTGGGGTTTTAAGGTGAGGTTTATGTATCCTCCATTCCCATTCCAGCTGTCTCTTTTTTCTAGGACTGTCTGGCCCGCCCTTCTGCCACCAAGCTAACCTCATGTCCGGCCCCCACAGTTATGGGCCAGCCAGAGAGACCAACAGCTGCACCGAGGGTGAGGGCTCAGGCAACACCTCTTCCCTTTCTGCCCCTCTCTGACTTGTTCTGAAAGAGAAAGTGGGAGGGCAGGGGATCTCACTTGGAGGAGGAGATGCTTGGAGATGTGAGGCGTCAGAGCACCATCAAGAAGTCACAGATGGGGCCGGGCGCG	-	novel	NA	P-0019596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	47	532	0	ENST00000228682.2:c.82_193+156del		p.X28_splice	ENST00000228682	NM_005269.2	28		2-3/12	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.687222835219555	2		532	122	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579472	7579505	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGGAGCAGCCTCTGGCATTCTGGGAGCTTCAT	GGGGGAGCAGCCTCTGGCATTCTGGGAGCTTCAT	-	novel	NA	P-0019596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	78	754	0	ENST00000269305.4:c.182_215del	p.Asp61AlafsTer51	p.D61Afs*51	ENST00000269305	NM_001126112.2	61	gATGAAGCTCCCAGAATGCCAGAGGCTGCTCCCCCc/gc	4/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.687222835219555	2		754	196	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976720	2976720	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	18	666	0	ENST00000396946.4:c.1292T>A	p.Leu431Gln	p.L431Q	ENST00000396946	NM_032415.4	431	cTg/cAg	9/25	0.583922678232685	4	FACETS	0.257	0.193	0.333	0.086	0.064	0.111	SUBCLONAL	1	TRUE	1	0.687222835219555	4		666	344	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0019597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	77	895	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.829	0.728	0.938	0.829	0.728	0.938	CLONAL	1	TRUE	1	0.3	2		895	619	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	148	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.561	0.513	0.612	0.561	0.513	0.612	SUBCLONAL	1	TRUE	1	0.703081494450487	2		509	750	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	182	655	0	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.524	0.483	0.567	0.524	0.483	0.567	SUBCLONAL	1	TRUE	1	0.703081494450487	2		655	988	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0019598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	135	646	1	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.442	0.402	0.485	0.442	0.402	0.485	SUBCLONAL	1	TRUE	1	0.703081494450487	2		647	868	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0019598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	153	692	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.496	0.453	0.54	0.496	0.453	0.54	SUBCLONAL	1	TRUE	1	0.703081494450487	2		692	878	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186841	11186841	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	103	451	0	ENST00000361445.4:c.6364G>T	p.Glu2122Ter	p.E2122*	ENST00000361445	NM_004958.3	2122	Gag/Tag	46/58	1	2	FACETS	0.553	0.496	0.612	0.553	0.496	0.612	SUBCLONAL	1	TRUE	1	0.703081494450487	2		451	530	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0019598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	183	684	1	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	0.562	0.519	0.607	0.562	0.519	0.607	SUBCLONAL	1	TRUE	1	0.703081494450487	2		685	926	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305242	39305242	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	154	632	0	ENST00000373001.3:c.1183C>T	p.Pro395Ser	p.P395S	ENST00000373001	NM_022157.3	395	Cca/Tca	7/7	1	2	FACETS	0.5	0.457	0.545	0.5	0.457	0.545	SUBCLONAL	1	TRUE	1	0.703081494450487	2		632	876	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927443	245927443	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1171	183	717	2	ENST00000388985.4:c.1085del	p.Phe362SerfsTer12	p.F362Sfs*12	ENST00000388985		362	tTc/tc	11/12	0.703081494450487	3	FACETS	0.52	0.478	0.563	0.26	0.239	0.282	SUBCLONAL	1	TRUE	1	0.703081494450487	3		719	1354	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653830	89653836	+	frameshift_variant	Frame_Shift_Del	DEL	AAGGCGT	AAGGCGT	-	novel	NA	P-0019598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	89	648	0	ENST00000371953.3:c.129_135del	p.Glu43AspfsTer9	p.E43Dfs*9	ENST00000371953	NM_000314.4	43	gAAGGCGTa/ga	2/9	1	2	FACETS	0.41	0.364	0.46	0.41	0.364	0.46	SUBCLONAL	1	TRUE	1	0.703081494450487	2		648	617	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720733	89720734	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	rs1564568350	NA	P-0019598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	14	212	0	ENST00000371953.3:c.885_886del	p.Cys296Ter	p.C296*	ENST00000371953	NM_000314.4	295	cTA/c	8/9	1	2	FACETS	0.219	0.158	0.292	0.219	0.158	0.292	SUBCLONAL	1	TRUE	1	0.703081494450487	2		212	182	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941052	71941052	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	211	1071	0	ENST00000298229.2:c.928C>T	p.Gln310Ter	p.Q310*	ENST00000298229	NM_001567.3	310	Cag/Tag	8/28	1	2	FACETS	0.502	0.465	0.54	0.502	0.465	0.54	SUBCLONAL	1	TRUE	1	0.703081494450487	2		1071	1196	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943379	71943379	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1165709765	NA	P-0019598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	165	651	0	ENST00000298229.2:c.1711C>T	p.Arg571Trp	p.R571W	ENST00000298229	NM_001567.3	571	Cgg/Tgg	14/28	1	2	FACETS	0.562	0.516	0.61	0.562	0.516	0.61	SUBCLONAL	1	TRUE	1	0.703081494450487	2		651	835	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435262	110435263	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0019598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	32	437	0	ENST00000375856.3:c.3138dup	p.Ala1047ArgfsTer25	p.A1047Rfs*25	ENST00000375856	NM_003749.2	1046	-/C	1/2	1	2	FACETS	0.159	0.128	0.194	0.159	0.128	0.194	SUBCLONAL	1	TRUE	1	0.703081494450487	2		437	572	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569756	95569756	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	73	359	0	ENST00000393063.1:c.3977C>A	p.Ala1326Asp	p.A1326D	ENST00000393063	NM_030621.3	1326	gCc/gAc	22/28	1	2	FACETS	0.487	0.428	0.551	0.487	0.428	0.551	SUBCLONAL	1	TRUE	1	0.703081494450487	2		359	426	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645012	67645012	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	161	868	0	ENST00000264010.4:c.277A>G	p.Thr93Ala	p.T93A	ENST00000264010	NM_006565.3	93	Acc/Gcc	3/12	1	2	FACETS	0.444	0.407	0.483	0.444	0.407	0.483	SUBCLONAL	1	TRUE	1	0.703081494450487	2		868	1031	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831201	72831201	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	143	634	0	ENST00000268489.5:c.5380C>T	p.Gln1794Ter	p.Q1794*	ENST00000268489	NM_006885.3	1794	Cag/Tag	9/10	1	2	FACETS	0.519	0.473	0.567	0.519	0.473	0.567	SUBCLONAL	1	TRUE	1	0.703081494450487	2		634	784	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687471	37687472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs760014508	NA	P-0019598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	82	440	3	ENST00000447079.4:c.4382dup	p.Thr1463AsnfsTer50	p.T1463Nfs*50	ENST00000447079	NM_015083.1	1459	tgg/tGgg	14/14	1	2	FACETS	0.416	0.367	0.468	0.416	0.367	0.468	SUBCLONAL	1	TRUE	1	0.703081494450487	2		443	561	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38504656	38504659	+	frameshift_variant	Frame_Shift_Del	DEL	TGTC	TGTC	-	novel	NA	P-0019598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	192	911	1	ENST00000254066.5:c.271_274del	p.Cys91ArgfsTer44	p.C91Rfs*44	ENST00000254066	NM_000964.3	89	ttTGTC/tt	3/9	1	2	FACETS	0.493	0.456	0.533	0.493	0.456	0.533	SUBCLONAL	1	TRUE	1	0.703081494450487	2		912	1107	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510573	38510573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	152	713	0	ENST00000254066.5:c.827G>A	p.Arg276Gln	p.R276Q	ENST00000254066	NM_000964.3	276	cGg/cAg	7/9	1	2	FACETS	0.498	0.455	0.542	0.498	0.455	0.542	SUBCLONAL	1	TRUE	1	0.703081494450487	2		713	869	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11019824	11019824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745964402	NA	P-0019598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	204	894	0	ENST00000327064.4:c.499G>A	p.Val167Met	p.V167M	ENST00000327064	NM_199141.1	167	Gtg/Atg	4/16	1	2	FACETS	0.551	0.51	0.593	0.551	0.51	0.593	SUBCLONAL	1	TRUE	1	0.703081494450487	2		894	1054	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273797	18273797	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	199	947	0	ENST00000222254.8:c.1130T>G	p.Leu377Arg	p.L377R	ENST00000222254	NM_005027.3	377	cTg/cGg	10/16	1	2	FACETS	0.502	0.464	0.541	0.502	0.464	0.541	SUBCLONAL	1	TRUE	1	0.703081494450487	2		947	1128	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	134	579	2	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	0.498	0.453	0.546	0.498	0.453	0.546	SUBCLONAL	1	TRUE	1	0.703081494450487	2		581	765	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451444	187451444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	93	621	0	ENST00000232014.4:c.38G>A	p.Arg13His	p.R13H	ENST00000232014	NM_001130845.1	13	cGc/cAc	3/10	1	2	FACETS	0.303	0.268	0.339	0.303	0.268	0.339	SUBCLONAL	1	TRUE	1	0.703081494450487	2		621	874	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0019598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	189	971	7	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	1	2	FACETS	0.499	0.46	0.539	0.499	0.46	0.539	SUBCLONAL	1	TRUE	1	0.703081494450487	2		978	1078	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467646	66467646	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	128	436	0	ENST00000273854.3:c.623del	p.Lys208ArgfsTer60	p.K208Rfs*60	ENST00000273854	NM_004439.5	208	aAg/ag	3/18	1	2	FACETS	0.525	0.477	0.576	0.525	0.477	0.576	SUBCLONAL	1	TRUE	1	0.703081494450487	2		436	693	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629765	187629765	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	54	801	0	ENST00000441802.2:c.1217C>A	p.Pro406His	p.P406H	ENST00000441802	NM_005245.3	406	cCt/cAt	2/27	1	2	FACETS	0.159	0.135	0.185	0.159	0.135	0.185	SUBCLONAL	1	TRUE	1	0.703081494450487	2		801	969	SUCCESS
APC	324	MSKCC	GRCh37	5	112176921	112176921	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	33	602	0	ENST00000257430.4:c.5633del	p.Lys1878ArgfsTer4	p.K1878Rfs*4	ENST00000257430	NM_000038.5	1877	gAa/ga	16/16	1	2	FACETS	0.146	0.118	0.177	0.146	0.118	0.177	SUBCLONAL	1	TRUE	1	0.703081494450487	2		602	645	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287927	33287929	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs755745890	NA	P-0019598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	121	613	0	ENST00000374542.5:c.1324_1326del	p.Glu442del	p.E442del	ENST00000374542	NM_001141970.1	442	GAG/-	5/8	1	2	FACETS	0.467	0.422	0.514	0.467	0.422	0.514	SUBCLONAL	1	TRUE	1	0.703081494450487	2		613	737	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467916	50467916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1372604802	NA	P-0019598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	117	558	1	ENST00000331340.3:c.1151C>T	p.Ser384Leu	p.S384L	ENST00000331340	NM_006060.4	384	tCg/tTg	8/8	1	2	FACETS	0.502	0.453	0.553	0.502	0.453	0.553	SUBCLONAL	1	TRUE	1	0.703081494450487	2		559	663	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240798	55240798	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	228	1077	2	ENST00000275493.2:c.2042G>T	p.Arg681Met	p.R681M	ENST00000275493	NM_005228.3	681	aGg/aTg	17/28	1	2	FACETS	0.489	0.455	0.525	0.489	0.455	0.525	SUBCLONAL	1	TRUE	1	0.703081494450487	2		1079	1325	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	165	831	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	0.512	0.47	0.556	0.512	0.47	0.556	SUBCLONAL	1	TRUE	1	0.703081494450487	2		831	917	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38139044	38139044	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	127	858	1	ENST00000317025.8:c.3559C>T	p.Arg1187Ter	p.R1187*	ENST00000317025	NM_023034.1	1187	Cga/Tga	20/24	1	2	FACETS	0.416	0.377	0.458	0.416	0.377	0.458	SUBCLONAL	1	TRUE	1	0.703081494450487	2		859	868	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020120	123020122	+	inframe_deletion	In_Frame_Del	DEL	GTG	GTG	-	novel	NA	P-0019598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	178	1153	0	ENST00000355640.3:c.612_614del	p.Gly205del	p.G205del	ENST00000355640		203	tGTGgt/tgt	2/7	1	2	FACETS	0.395	0.363	0.428	0.395	0.363	0.428	SUBCLONAL	1	TRUE	1	0.703081494450487	2		1153	1283	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438316	110438317	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	rs532810290	NA	P-0019598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	46	420	0	ENST00000375856.3:c.82_84dup	p.Asn28dup	p.N28dup	ENST00000375856	NM_003749.2	28	-/AAC	1/2	1	2	FACETS	0.263	0.221	0.309	0.263	0.221	0.309	SUBCLONAL	1	TRUE	1	0.703081494450487	2		420	498	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	241	832	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.938	0.877	1	0.938	0.877	1	CLONAL	1	TRUE	1	0.536921620124907	2		832	957	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	537	683	12	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.535348026639806	3	FACETS	0.997	0.958	1	0.997	0.958	1	CLONAL	2	TRUE	1	0.536921620124907	3		695	1272	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	299	894	7	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.887	0.835	0.941	0.887	0.835	0.941	CLONAL	1	TRUE	1	0.536921620124907	2		901	1255	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	218	860	0				ENST00000310581	NM_198253.2	-/1132			0.525371663092008	5	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.536921620124907	5		860	1216	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1586	373	1422	3	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	0.462050616830026	3	FACETS	0.9	0.85	0.95			1	CLONAL	1	TRUE	NA	0.536921620124907	3		1425	1959	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577035	7577036	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	286	891	0	ENST00000269305.4:c.902dup	p.Gly302ArgfsTer4	p.G302Rfs*4	ENST00000269305	NM_001126112.2	301	cca/ccCa	8/11	0.536921620124907	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.536921620124907	1		891	774	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294124	1294124	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2155	353	1312	4	ENST00000310581.5:c.877C>T	p.Arg293Cys	p.R293C	ENST00000310581	NM_198253.2	293	Cgc/Tgc	2/16	0.525371663092008	5	FACETS	0.947	0.892	1			1	CLONAL	1	TRUE	NA	0.536921620124907	5		1316	2508	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551682	150551682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	175	478	0	ENST00000369026.2:c.325G>A	p.Glu109Lys	p.E109K	ENST00000369026	NM_021960.4	109	Gag/Aag	1/3	0.536921620124907	4	FACETS	1	0.96	1	0.356	0.328	0.386	CLONAL	1	TRUE	1	0.536921620124907	4		478	938	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	154	538	5	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.976	0.897	1	0.976	0.897	1	CLONAL	1	TRUE	1	0.536921620124907	2		543	588	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127164	22127164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057519911	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	183	556	2	ENST00000215832.6:c.964G>A	p.Glu322Lys	p.E322K	ENST00000215832	NM_002745.4	322	Gag/Aag	7/9	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.536921620124907	2		558	663	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879604	37879604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196929947	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	569	1056	2	ENST00000269571.5:c.1979G>A	p.Gly660Asp	p.G660D	ENST00000269571		660	gGc/gAc	17/27	0.535348026639806	3	FACETS	0.942	0.906	0.979	0.942	0.906	0.979	CLONAL	2	TRUE	1	0.536921620124907	3		1058	1427	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685313	86685313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886060844	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	74	250	0	ENST00000274376.6:c.3029G>A	p.Arg1010Gln	p.R1010Q	ENST00000274376	NM_002890.2	1010	cGa/cAa	24/25	1	2	FACETS	0.96	0.85	1	0.96	0.85	1	CLONAL	1	TRUE	1	0.536921620124907	2		250	287	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021182	31021182	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201899433	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	292	831	1	ENST00000375687.4:c.1181G>A	p.Arg394His	p.R394H	ENST00000375687	NM_015338.5	394	cGt/cAt	12/13	0.535348026639806	3	FACETS	1	0.984	1	0.565	0.531	0.599	CLONAL	1	TRUE	1	0.536921620124907	3		832	1222	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041373	47041373	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	315	560	1	ENST00000377604.3:c.1717C>T	p.Gln573Ter	p.Q573*	ENST00000377604	NM_001204468.1	573	Cag/Tag	16/24	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.536921620124907	1		561	662	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724361	52724361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	199	593	2	ENST00000322088.6:c.1493G>A	p.Arg498His	p.R498H	ENST00000322088	NM_014225.5	498	cGc/cAc	12/15	0.536921620124907	3	FACETS	1	0.937	1	0.506	0.469	0.545	CLONAL	1	TRUE	1	0.536921620124907	3		595	929	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134160	41134160	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374723626	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	19	457	0	ENST00000379561.5:c.1468C>T	p.Arg490Trp	p.R490W	ENST00000379561	NM_002015.3	490	Cgg/Tgg	2/3	0.536921620124907	1	FACETS	0.138	0.104	0.178	0.138	0.104	0.178	SUBCLONAL	1	TRUE	0	0.536921620124907	1		457	375	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521525	46521525	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	221	785	1	ENST00000262741.5:c.883del	p.Met295Ter	p.M295*	ENST00000262741	NM_003629.3	295	Atg/tg	7/10	1	2	FACETS	0.91	0.847	0.974	0.91	0.847	0.974	CLONAL	1	TRUE	1	0.536921620124907	2		786	905	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248106	59248106	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	63	233	0	ENST00000371222.2:c.637del	p.Gln213SerfsTer13	p.Q213Sfs*13	ENST00000371222	NM_002228.3	213	Cag/ag	1/1	0.535348026639806	3	FACETS	0.939	0.818	1	0.47	0.409	0.534	CLONAL	1	TRUE	1	0.536921620124907	3		233	317	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241963	72241963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	99	399	0	ENST00000357731.5:c.427G>A	p.Asp143Asn	p.D143N	ENST00000357731	NM_173808.2	143	Gac/Aac	3/7	0.535348026639806	3	FACETS	0.776	0.694	0.863	0.388	0.347	0.432	SUBCLONAL	1	TRUE	1	0.536921620124907	3		399	603	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333971	70333971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	385	625	0	ENST00000373644.4:c.1876G>A	p.Glu626Lys	p.E626K	ENST00000373644	NM_030625.2	626	Gag/Aag	2/12	0.536921620124907	2	FACETS	0.972	0.931	1	0.972	0.931	1	CLONAL	2	TRUE	0	0.536921620124907	2		625	738	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406108	70406108	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs746949364	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	243	777	0	ENST00000373644.4:c.3622A>G	p.Thr1208Ala	p.T1208A	ENST00000373644	NM_030625.2	1208	Act/Gct	4/12	0.536921620124907	2	FACETS	0.985	0.922	1	0.492	0.461	0.525	CLONAL	1	TRUE	0	0.536921620124907	2		777	919	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201939	102201942	+	frameshift_variant	Frame_Shift_Del	DEL	GAGA	GAGA	-	novel	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	122	404	0	ENST00000263464.3:c.1295_1298del	p.Arg432LysfsTer14	p.R432Kfs*14	ENST00000263464	NM_001165.4	431	GAGAga/ga	6/9	1	2	FACETS	0.814	0.739	0.893	0.814	0.739	0.893	CLONAL	1	TRUE	1	0.536921620124907	2		404	558	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416112	49416112	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	197	597	0	ENST00000301067.7:c.16363A>C	p.Ile5455Leu	p.I5455L	ENST00000301067	NM_003482.3	5455	Ata/Cta	52/54	1	2	FACETS	0.931	0.864	1	0.931	0.864	1	CLONAL	1	TRUE	1	0.536921620124907	2		597	788	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28599069	28599069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1462100311	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	182	651	2	ENST00000241453.7:c.2219C>T	p.Ser740Leu	p.S740L	ENST00000241453	NM_004119.2	740	tCa/tTa	18/24	0.536921620124907	1	FACETS	0.912	0.847	0.978	0.912	0.847	0.978	CLONAL	1	TRUE	0	0.536921620124907	1		653	544	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947622	48947622	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	125	470	0	ENST00000267163.4:c.1209T>G	p.Tyr403Ter	p.Y403*	ENST00000267163	NM_000321.2	403	taT/taG	12/27	0.536921620124907	1	FACETS	0.901	0.824	0.98	0.901	0.824	0.98	CLONAL	1	TRUE	0	0.536921620124907	1		470	378	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519037	103519037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434571	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	223	554	0	ENST00000355739.4:c.2375C>T	p.Ala792Val	p.A792V	ENST00000355739	NM_000123.3	792	gCg/gTg	11/15	0.536921620124907	3	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.536921620124907	3		554	866	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826565	50826565	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	153	512	0	ENST00000398568.2:c.2296del	p.Ile766PhefsTer7	p.I766Ffs*7	ENST00000398568	NM_001042412.1	764	Aaa/aa	15/18	0.536921620124907	1	FACETS	0.941	0.869	1	0.941	0.869	1	CLONAL	1	TRUE	0	0.536921620124907	1		512	443	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830616	72830616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149779567	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	238	885	0	ENST00000268489.5:c.5965G>A	p.Gly1989Ser	p.G1989S	ENST00000268489	NM_006885.3	1989	Ggc/Agc	9/10	0.536921620124907	1	FACETS	0.878	0.823	0.934	0.878	0.823	0.934	CLONAL	1	TRUE	0	0.536921620124907	1		885	739	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657587	37657587	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1164373930	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	257	810	1	ENST00000447079.4:c.2504A>G	p.His835Arg	p.H835R	ENST00000447079	NM_015083.1	835	cAt/cGt	6/14	0.535348026639806	3	FACETS	0.914	0.855	0.976	0.457	0.427	0.488	CLONAL	1	TRUE	1	0.536921620124907	3		811	1328	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40444050	40444050	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	230	798	0	ENST00000345506.4:c.346G>C	p.Glu116Gln	p.E116Q	ENST00000345506	NM_003152.3	116	Gaa/Caa	5/20	0.535348026639806	3	FACETS	0.888	0.826	0.952	0.444	0.413	0.476	CLONAL	1	TRUE	1	0.536921620124907	3		798	1224	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41197783	41197783	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs273902776	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	290	904	1	ENST00000357654.3:c.5504G>A	p.Arg1835Gln	p.R1835Q	ENST00000357654	NM_007294.3	1835	cGa/cAa	23/23	0.535348026639806	3	FACETS	0.999	0.938	1	0.499	0.469	0.531	CLONAL	1	TRUE	1	0.536921620124907	3		905	1372	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7132295	7132295	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs575954707	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	199	705	0	ENST00000302850.5:c.2716G>A	p.Ala906Thr	p.A906T	ENST00000302850	NM_000208.2	906	Gct/Act	14/22	1	2	FACETS	0.983	0.913	1	0.983	0.913	1	CLONAL	1	TRUE	1	0.536921620124907	2		705	754	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350204	15350204	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	311	967	4	ENST00000263377.2:c.3575del	p.Lys1192ArgfsTer3	p.K1192Rfs*3	ENST00000263377	NM_058243.2	1192	aAg/ag	17/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.536921620124907	2		971	1035	SUCCESS
AXL	558	MSKCC	GRCh37	19	41749571	41749571	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200850031	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	304	1075	2	ENST00000301178.4:c.1496G>A	p.Arg499His	p.R499H	ENST00000301178	NM_021913.4	499	cGc/cAc	12/20	0.462050616830026	3	FACETS	0.966	0.908	1			1	CLONAL	1	TRUE	NA	0.536921620124907	3		1077	1487	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39216450	39216450	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	172	747	0	ENST00000402219.2:c.3352G>C	p.Asp1118His	p.D1118H	ENST00000402219	NM_005633.3	1118	Gat/Cat	21/23	1	2	FACETS	0.88	0.812	0.951	0.88	0.812	0.951	CLONAL	1	TRUE	1	0.536921620124907	2		747	728	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027883	48027883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	150	449	0	ENST00000234420.5:c.2761G>A	p.Ala921Thr	p.A921T	ENST00000234420	NM_000179.2	921	Gct/Act	4/10	1	2	FACETS	0.958	0.88	1	0.958	0.88	1	CLONAL	1	TRUE	1	0.536921620124907	2		449	583	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288901	212288901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376298364	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	85	330	0	ENST00000342788.4:c.2845G>A	p.Val949Ile	p.V949I	ENST00000342788	NM_005235.2	949	Gtt/Att	23/28	1	2	FACETS	0.951	0.848	1	0.951	0.848	1	CLONAL	1	TRUE	1	0.536921620124907	2		330	333	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793363	242793363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	336	1211	0	ENST00000334409.5:c.714del	p.Val239CysfsTer39	p.V239Cfs*39	ENST00000334409	NM_005018.2	238	ccC/cc	5/5	1	2	FACETS	0.921	0.87	0.973	0.921	0.87	0.973	CLONAL	1	TRUE	1	0.536921620124907	2		1211	1359	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553359	41553359	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	221	784	0	ENST00000263253.7:c.3448G>C	p.Glu1150Gln	p.E1150Q	ENST00000263253	NM_001429.3	1150	Gaa/Caa	18/31	1	2	FACETS	0.839	0.781	0.899	0.839	0.781	0.899	CLONAL	1	TRUE	1	0.536921620124907	2		784	981	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070411	37070412	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGGG	novel	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	191	372	0	ENST00000231790.2:c.1546_1547insCGGG	p.Gln516ProfsTer5	p.Q516Pfs*5	ENST00000231790	NM_000249.3	516	cag/cCGGGag	13/19	0.536921620124907	2	FACETS	0.855	0.801	0.909	0.855	0.801	0.909	CLONAL	2	TRUE	0	0.536921620124907	2		372	416	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233748	233748	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	1053	879	0	ENST00000264932.6:c.1052T>A	p.Ile351Asn	p.I351N	ENST00000264932	NM_004168.2	351	aTc/aAc	8/15	0.525371663092008	5	FACETS	0.967	0.944	0.991			1	CLONAL	4	TRUE	NA	0.536921620124907	5		879	1830	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864422	162864422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	218	799	0	ENST00000366898.1:c.91G>A	p.Ala31Thr	p.A31T	ENST00000366898	NM_004562.2	31	Gct/Act	2/12	1	2	FACETS	0.924	0.86	0.989	0.924	0.86	0.989	CLONAL	1	TRUE	1	0.536921620124907	2		799	879	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026972	6026972	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587781827	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	109	421	0	ENST00000265849.7:c.1424T>C	p.Val475Ala	p.V475A	ENST00000265849	NM_000535.5	475	gTg/gCg	11/15	0.535348026639806	3	FACETS	0.888	0.8	0.981	0.444	0.4	0.491	CLONAL	1	TRUE	1	0.536921620124907	3		421	580	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729610	41729610	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	183	652	1	ENST00000242208.4:c.919C>T	p.Arg307Trp	p.R307W	ENST00000242208	NM_002192.2	307	Cgg/Tgg	3/3	0.535348026639806	3	FACETS	0.993	0.917	1	0.496	0.458	0.536	CLONAL	1	TRUE	1	0.536921620124907	3		653	871	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738644	145738644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs571684398	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	271	819	1	ENST00000428558.2:c.2420G>A	p.Arg807His	p.R807H	ENST00000428558	NM_004260.3	807	cGt/cAt	15/22	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.536921620124907	2		820	975	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413109	63413109	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	231	504	0	ENST00000330258.3:c.58A>G	p.Thr20Ala	p.T20A	ENST00000330258	NM_152424.3	20	Acc/Gcc	2/2	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.536921620124907	1		504	432	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070413	37070413	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	195	367	0	ENST00000231790.2:c.1548G>C	p.Gln516His	p.Q516H	ENST00000231790	NM_000249.3	516	caG/caC	13/19	0.536921620124907	2	FACETS	0.886	0.831	0.94	0.886	0.831	0.94	CLONAL	2	TRUE	0	0.536921620124907	2		367	410	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070412	37070412	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	25	372	0	ENST00000231790.2:c.1547A>C	p.Gln516Pro	p.Q516P	ENST00000231790	NM_000249.3	516	cAg/cCg	13/19	0.536921620124907	2	FACETS	0.224	0.176	0.279	0.112	0.088	0.14	SUBCLONAL	1	TRUE	0	0.536921620124907	2		372	416	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0019600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	36	741	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	NA	2	FACETS	0.323	0.265	0.389			1	INDETERMINATE	1	TRUE	NA	0.370336688276784	2		742	601	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0019600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	632	642	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.370336688276784	6	FACETS	0.906	0.872	0.94			1	CLONAL	4	TRUE	NA	0.370336688276784	6		642	1640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0019600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	107	779	1	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.370336688276784	1	FACETS	0.565	0.507	0.628	0.565	0.507	0.628	SUBCLONAL	1	TRUE	0	0.370336688276784	1		780	833	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756577	756577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	65	580	0	ENST00000314574.4:c.251C>T	p.Ser84Leu	p.S84L	ENST00000314574	NM_005433.3	84	tCa/tTa	2/12	1	2	FACETS	0.519	0.45	0.595	0.519	0.45	0.595	SUBCLONAL	1	TRUE	1	0.370336688276784	2		580	676	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409104	4409104	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	46	539	0	ENST00000261254.3:c.799G>A	p.Asp267Asn	p.D267N	ENST00000261254	NM_001759.3	267	Gac/Aac	5/5	1	2	FACETS	0.417	0.35	0.49	0.417	0.35	0.49	SUBCLONAL	1	TRUE	1	0.370336688276784	2		539	596	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246324	46246324	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	49	435	0	ENST00000334344.6:c.4418C>G	p.Ser1473Cys	p.S1473C	ENST00000334344	NM_152641.2	1473	tCt/tGt	15/21	1	2	FACETS	0.49	0.415	0.573	0.49	0.415	0.573	SUBCLONAL	1	TRUE	1	0.370336688276784	2		435	540	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46603687	46603687	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	67	593	0	ENST00000263734.3:c.1044G>C	p.Glu348Asp	p.E348D	ENST00000263734	NM_001430.4	348	gaG/gaC	9/16	1	2	FACETS	0.468	0.406	0.536	0.468	0.406	0.536	SUBCLONAL	1	TRUE	1	0.370336688276784	2		593	773	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252892	36252893	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	135	438	0	ENST00000300305.3:c.469dup	p.Arg157LysfsTer3	p.R157Kfs*3	ENST00000300305		157	aga/aAga	4/8	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.370336688276784	2		438	550	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069309	30069309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1026724985	NA	P-0019600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	58	777	2	ENST00000338641.4:c.1174G>A	p.Glu392Lys	p.E392K	ENST00000338641	NM_000268.3	392	Gag/Aag	12/16	1	2	FACETS	0.356	0.305	0.412	0.356	0.305	0.412	SUBCLONAL	1	TRUE	1	0.370336688276784	2		779	880	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37061805	37061805	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	42	600	0	ENST00000231790.2:c.889G>C	p.Glu297Gln	p.E297Q	ENST00000231790	NM_000249.3	297	Gaa/Caa	11/19	1	2	FACETS	0.366	0.305	0.435	0.366	0.305	0.435	SUBCLONAL	1	TRUE	1	0.370336688276784	2		600	619	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49399938	49399938	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	64	602	0	ENST00000418115.1:c.399G>C	p.Lys133Asn	p.K133N	ENST00000418115	NM_001664.2	133	aaG/aaC	4/5	1	2	FACETS	0.463	0.4	0.531	0.463	0.4	0.531	SUBCLONAL	1	TRUE	1	0.370336688276784	2		602	747	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324609	31324609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151341120	NA	P-0019600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	31	385	0	ENST00000412585.2:c.199C>T	p.Pro67Ser	p.P67S	ENST00000412585	NM_005514.6	67	Ccg/Tcg	2/8	1	2	FACETS	0.337	0.272	0.411	0.337	0.272	0.411	SUBCLONAL	1	TRUE	1	0.370336688276784	2		385	497	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242349	98242349	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	47	576	0	ENST00000331920.6:c.969G>C	p.Leu323Phe	p.L323F	ENST00000331920	NM_000264.3	323	ttG/ttC	7/24	0.155741282248984	2	FACETS	0.335	0.282	0.394	0.167	0.141	0.197	INDETERMINATE	1	TRUE	0	0.370336688276784	2		576	758	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907155	101907155	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	43	506	0	ENST00000374994.4:c.1115G>C	p.Arg372Thr	p.R372T	ENST00000374994	NM_004612.2	372	aGa/aCa	6/9	0.155741282248984	2	FACETS	0.385	0.322	0.456	0.193	0.161	0.228	INDETERMINATE	1	TRUE	0	0.370336688276784	2		506	603	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041164	47041164	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0019600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	89	851	0	ENST00000377604.3:c.1592C>G	p.Ser531Ter	p.S531*	ENST00000377604	NM_001204468.1	531	tCa/tGa	15/24	0.370336688276784	1	FACETS	0.493	0.437	0.554	0.493	0.437	0.554	SUBCLONAL	1	TRUE	0	0.370336688276784	1		851	794	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0019602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	57	741	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.372609554635286	2		742	249	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888198	112888198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121918453	NA	P-0019602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	83	747	0	ENST00000351677.2:c.214G>A	p.Ala72Thr	p.A72T	ENST00000351677	NM_002834.3	72	Gcc/Acc	3/16	1	2	FACETS	0.983	0.872	1	0.983	0.872	1	CLONAL	1	TRUE	1	0.372609554635286	2		747	453	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604785	48604785	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	145	543	0	ENST00000342988.3:c.1607T>C	p.Leu536Pro	p.L536P	ENST00000342988	NM_005359.5	536	cTa/cCa	12/12	0.177725109494133	2	FACETS	0.958	0.884	1	0.958	0.884	1	INDETERMINATE	2	TRUE	0	0.372609554635286	2		543	406	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267186	41267186	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553630452	NA	P-0019602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	64	451	1	ENST00000349496.5:c.770C>T	p.Thr257Ile	p.T257I	ENST00000349496	NM_001904.3	257	aCa/aTa	6/15	1	2	FACETS	0.899	0.782	1	0.899	0.782	1	CLONAL	1	TRUE	1	0.372609554635286	2		452	382	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174873	11174873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	84	704	1	ENST00000361445.4:c.7161G>A	p.Met2387Ile	p.M2387I	ENST00000361445	NM_004958.3	2387	atG/atA	52/58	1	2	FACETS	0.926	0.821	1	0.926	0.821	1	CLONAL	1	TRUE	1	0.372609554635286	2		705	487	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005422	29005422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141286646	NA	P-0019602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	33	351	0	ENST00000282397.4:c.839G>A	p.Arg280Gln	p.R280Q	ENST00000282397	NM_002019.4	280	cGa/cAa	7/30	0.372609554635286	3	FACETS	0.655	0.534	0.789	0.327	0.267	0.395	SUBCLONAL	1	TRUE	1	0.372609554635286	3		351	321	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486077	29486078	+	inframe_insertion	In_Frame_Ins	INS	-	-	TATATTGGA	novel	NA	P-0019602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	44	530	0	ENST00000356175.3:c.257_265dup	p.Ile86_Asp88dup	p.I86_D88dup	ENST00000356175	NM_000267.3	86	att/atTATATTGGAt	3/57	1	2	FACETS	0.837	0.707	0.98	0.837	0.707	0.98	CLONAL	1	TRUE	1	0.372609554635286	2		530	282	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653180	29653189	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTGCTGCC	ACCTGCTGCC	-	novel	NA	P-0019602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	46	387	1	ENST00000356175.3:c.5119_5128del	p.Ala1707TrpfsTer3	p.A1707Wfs*3	ENST00000356175	NM_000267.3	1705	ctACCTGCTGCC/ct	36/57	1	2	FACETS	0.823	0.697	0.961	0.823	0.697	0.961	CLONAL	1	TRUE	1	0.372609554635286	2		388	300	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118937	70118937	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	102	939	0	ENST00000245479.2:c.509C>G	p.Pro170Arg	p.P170R	ENST00000245479	NM_000346.3	170	cCg/cGg	2/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.372609554635286	2		939	444	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038894	47038897	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTG	AGTG	-	novel	NA	P-0019602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	62	390	0	ENST00000377604.3:c.901+3_901+6del		p.X301_splice	ENST00000377604	NM_001204468.1	301		9/24	1	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.372609554635286	1		390	207	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	93	736	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.626383572195386	2		736	244	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692918	89692918	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	187	604	0	ENST00000371953.3:c.402G>A	p.Met134Ile	p.M134I	ENST00000371953	NM_000314.4	134	atG/atA	5/9	0.626383572195386	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.626383572195386	1		604	402	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964186	28964186	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs747004871	NA	P-0019603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	21	363	0	ENST00000282397.4:c.1716C>A	p.Asp572Glu	p.D572E	ENST00000282397	NM_002019.4	572	gaC/gaA	13/30	1	2	FACETS	0.161	0.123	0.205	0.161	0.123	0.205	SUBCLONAL	1	TRUE	1	0.626383572195386	2		363	417	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566770	212566770	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	134	418	0	ENST00000342788.4:c.1411A>G	p.Thr471Ala	p.T471A	ENST00000342788	NM_005235.2	471	Acc/Gcc	12/28	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.626383572195386	2		418	408	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519989	NA	P-0019604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	338	682	0	ENST00000269305.4:c.730G>C	p.Gly244Arg	p.G244R	ENST00000269305	NM_001126112.2	244	Ggc/Cgc	7/11	0.707491421081004	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	0	0.707491421081004	1		682	580	SUCCESS
APC	324	MSKCC	GRCh37	5	112174040	112174040	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1561579402	NA	P-0019604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	215	399	0	ENST00000257430.4:c.2749G>A	p.Asp917Asn	p.D917N	ENST00000257430	NM_000038.5	917	Gat/Aat	16/16	0.707491421081004	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	0	0.707491421081004	1		399	382	SUCCESS
APC	324	MSKCC	GRCh37	5	112174823	112174823	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	190	332	0	ENST00000257430.4:c.3532G>A	p.Asp1178Asn	p.D1178N	ENST00000257430	NM_000038.5	1178	Gat/Aat	16/16	0.707491421081004	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	0	0.707491421081004	1		332	325	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73352361	73352361	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	217	522	0	ENST00000377767.4:c.544G>A	p.Glu182Lys	p.E182K	ENST00000377767	NM_014953.3	182	Gag/Aag	3/21	0.707491421081004	1	FACETS	0.547	0.51	0.584	0.547	0.51	0.584	SUBCLONAL	1	FALSE	0	0.707491421081004	1		522	725	SUCCESS
APC	324	MSKCC	GRCh37	5	112170717	112170717	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	259	567	1	ENST00000257430.4:c.1813G>T	p.Asp605Tyr	p.D605Y	ENST00000257430	NM_000038.5	605	Gat/Tat	15/16	0.707491421081004	1	FACETS	0.97	0.92	1	0.97	0.92	1	CLONAL	1	FALSE	0	0.707491421081004	1		568	488	SUCCESS
APC	324	MSKCC	GRCh37	5	112173396	112173396	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658289	NA	P-0019604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	156	455	0	ENST00000257430.4:c.2105G>A	p.Gly702Glu	p.G702E	ENST00000257430	NM_000038.5	702	gGg/gAg	16/16	0.707491421081004	1	FACETS	0.88	0.82	0.94	0.88	0.82	0.94	CLONAL	1	FALSE	0	0.707491421081004	1		455	324	SUCCESS
APC	324	MSKCC	GRCh37	5	112173830	112173830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	201	397	1	ENST00000257430.4:c.2539G>A	p.Glu847Lys	p.E847K	ENST00000257430	NM_000038.5	847	Gaa/Aaa	16/16	0.707491421081004	1	FACETS	0.984	0.928	1	0.984	0.928	1	CLONAL	1	FALSE	0	0.707491421081004	1		398	373	SUCCESS
APC	324	MSKCC	GRCh37	5	112173840	112173840	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	203	405	0	ENST00000257430.4:c.2549G>C	p.Arg850Thr	p.R850T	ENST00000257430	NM_000038.5	850	aGa/aCa	16/16	0.707491421081004	1	FACETS	0.958	0.903	1	0.958	0.903	1	CLONAL	1	FALSE	0	0.707491421081004	1		405	387	SUCCESS
APC	324	MSKCC	GRCh37	5	112174259	112174259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	236	409	0	ENST00000257430.4:c.2968G>A	p.Asp990Asn	p.D990N	ENST00000257430	NM_000038.5	990	Gat/Aat	16/16	0.707491421081004	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	0	0.707491421081004	1		409	418	SUCCESS
APC	324	MSKCC	GRCh37	5	112174406	112174406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	178	352	0	ENST00000257430.4:c.3115G>A	p.Gly1039Arg	p.G1039R	ENST00000257430	NM_000038.5	1039	Gga/Aga	16/16	0.707491421081004	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	0	0.707491421081004	1		352	322	SUCCESS
APC	324	MSKCC	GRCh37	5	112174466	112174466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253882360	NA	P-0019604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	230	406	0	ENST00000257430.4:c.3175G>A	p.Glu1059Lys	p.E1059K	ENST00000257430	NM_000038.5	1059	Gaa/Aaa	16/16	0.707491421081004	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	0	0.707491421081004	1		406	397	SUCCESS
APC	324	MSKCC	GRCh37	5	112175448	112175448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	127	297	0	ENST00000257430.4:c.4157G>A	p.Arg1386Lys	p.R1386K	ENST00000257430	NM_000038.5	1386	aGa/aAa	16/16	0.707491421081004	1	FACETS	0.987	0.917	1	0.987	0.917	1	CLONAL	1	FALSE	0	0.707491421081004	1		297	235	SUCCESS
APC	324	MSKCC	GRCh37	5	112175642	112175642	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1325458165	NA	P-0019604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	198	464	0	ENST00000257430.4:c.4351G>A	p.Glu1451Lys	p.E1451K	ENST00000257430	NM_000038.5	1451	Gaa/Aaa	16/16	0.707491421081004	1	FACETS	0.954	0.899	1	0.954	0.899	1	CLONAL	1	FALSE	0	0.707491421081004	1		464	379	SUCCESS
APC	324	MSKCC	GRCh37	5	112175672	112175672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	184	426	2	ENST00000257430.4:c.4381G>A	p.Glu1461Lys	p.E1461K	ENST00000257430	NM_000038.5	1461	Gaa/Aaa	16/16	0.707491421081004	1	FACETS	0.972	0.913	1	0.972	0.913	1	CLONAL	1	FALSE	0	0.707491421081004	1		428	346	SUCCESS
APC	324	MSKCC	GRCh37	5	112175842	112175842	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	176	309	0	ENST00000257430.4:c.4551G>C	p.Gln1517His	p.Q1517H	ENST00000257430	NM_000038.5	1517	caG/caC	16/16	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.707491421081004	NA		309	314	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0019605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	303	671	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.677031042196615	2		671	882	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0019605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	309	576	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	0.677031042196615	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.677031042196615	1		576	569	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971207	21971207	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	219	447	0	ENST00000304494.5:c.151del	p.Val51SerfsTer2	p.V51Sfs*2	ENST00000304494	NM_000077.4	51	Gtc/tc	2/3	0.677031042196615	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.677031042196615	1		447	382	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411447	63411447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754938624	NA	P-0019605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	30	404	0	ENST00000330258.3:c.1720C>T	p.Arg574Trp	p.R574W	ENST00000330258	NM_152424.3	574	Cgg/Tgg	2/2	1	1	FACETS	0.117	0.094	0.144	0.117	0.094	0.144	SUBCLONAL	1	TRUE	0	0.677031042196615	1		404	499	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740106	162740106	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	137	380	0	ENST00000367921.3:c.1308G>T	p.Met436Ile	p.M436I	ENST00000367921	NM_006182.2	436	atG/atT	12/18	0.618771400234418	3	FACETS	0.955	0.873	1	0.478	0.436	0.521	CLONAL	1	TRUE	1	0.677031042196615	3		380	567	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786142	3786142	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	64	704	0	ENST00000262367.5:c.4623A>T	p.Glu1541Asp	p.E1541D	ENST00000262367	NM_004380.2	1541	gaA/gaT	28/31	1	2	FACETS	0.173	0.149	0.199	0.173	0.149	0.199	SUBCLONAL	1	TRUE	1	0.677031042196615	2		704	1094	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224279	36224279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1166713872	NA	P-0019605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	352	834	0	ENST00000222270.7:c.6829C>T	p.Arg2277Cys	p.R2277C	ENST00000222270	NM_014727.1	2277	Cgc/Tgc	28/37	1	2	FACETS	0.934	0.886	0.984	0.934	0.886	0.984	CLONAL	1	TRUE	1	0.677031042196615	2		834	1113	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902125	50902125	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	228	467	0	ENST00000440232.2:c.17G>T	p.Arg6Leu	p.R6L	ENST00000440232	NM_002691.3	6	cGg/cTg	2/27	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.677031042196615	2		467	621	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713466	40713466	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	302	692	2	ENST00000373198.4:c.4049T>C	p.Ile1350Thr	p.I1350T	ENST00000373198	NM_133170.3	1350	aTa/aCa	30/32	1	2	FACETS	0.969	0.915	1	0.969	0.915	1	CLONAL	1	TRUE	1	0.677031042196615	2		694	921	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134885782	134885782	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0019605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	247	547	0	ENST00000398015.3:c.1695-2A>T		p.X565_splice	ENST00000398015	NM_004441.4	565			0.677031042196615	3	FACETS	0.942	0.881	1	0.471	0.44	0.503	CLONAL	1	TRUE	1	0.677031042196615	3		547	1037	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253750	153253751	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0019605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	168	326	0	ENST00000281708.4:c.982dup	p.Glu328GlyfsTer4	p.E328Gfs*4	ENST00000281708	NM_033632.3	328	gag/gGag	6/12	0.677031042196615	1	FACETS	0.899	0.839	0.96	0.899	0.839	0.96	CLONAL	1	TRUE	0	0.677031042196615	1		326	365	SUCCESS
APC	324	MSKCC	GRCh37	5	112174483	112174483	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	125	394	0	ENST00000257430.4:c.3192del	p.Glu1064AspfsTer62	p.E1064Dfs*62	ENST00000257430	NM_000038.5	1064	gaG/ga	16/16	0.677031042196615	1	FACETS	0.831	0.765	0.898	0.831	0.765	0.898	CLONAL	1	TRUE	0	0.677031042196615	1		394	294	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662588	117662588	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	200	389	0	ENST00000368508.3:c.4877C>A	p.Ser1626Tyr	p.S1626Y	ENST00000368508	NM_002944.2	1626	tCt/tAt	29/43	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.677031042196615	2		389	556	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163802	152163802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	246	464	0	ENST00000206249.3:c.523G>A	p.Ala175Thr	p.A175T	ENST00000206249	NM_000125.3	175	Gct/Act	2/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.677031042196615	2		464	687	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913396	NA	P-0019612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	60	445	0	ENST00000349496.5:c.95A>G	p.Asp32Gly	p.D32G	ENST00000349496	NM_001904.3	32	gAc/gGc	3/15	1	2	FACETS	0.706	0.61	0.81	0.706	0.61	0.81	SUBCLONAL	1	TRUE	1	0.410460512046103	2		445	414	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955382	48955382	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1485450031	NA	P-0019612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	42	367	0	ENST00000267163.4:c.1499-1G>A		p.X500_splice	ENST00000267163	NM_000321.2	500			1	2	FACETS	0.781	0.656	0.917	0.781	0.656	0.917	CLONAL	1	TRUE	1	0.410460512046103	2		367	262	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396315	396315	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	144	1139	3	ENST00000262320.3:c.711C>A	p.Tyr237Ter	p.Y237*	ENST00000262320	NM_003502.3	237	taC/taA	2/11	1	2	FACETS	0.984	0.899	1	0.984	0.899	1	CLONAL	1	TRUE	1	0.410460512046103	2		1142	713	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25468888	25468888	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs761608224	NA	P-0019612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	111	1086	0	ENST00000264709.3:c.1474+1G>A		p.X492_splice	ENST00000264709	NM_175629.2	492			1	2	FACETS	0.815	0.733	0.9	0.815	0.733	0.9	CLONAL	1	TRUE	1	0.410460512046103	2		1086	664	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913396	NA	P-0019612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	88	445	0	ENST00000349496.5:c.95A>G	p.Asp32Gly	p.D32G	ENST00000349496	NM_001904.3	32	gAc/gGc	3/15	1	2	FACETS	0.942	0.843	1	0.942	0.843	1	CLONAL	1	TRUE	1	0.571334721891916	2		445	327	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396315	396315	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	169	1139	3	ENST00000262320.3:c.711C>A	p.Tyr237Ter	p.Y237*	ENST00000262320	NM_003502.3	237	taC/taA	2/11	1	2	FACETS	0.899	0.83	0.971	0.899	0.83	0.971	CLONAL	1	TRUE	1	0.571334721891916	2		1142	658	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25468888	25468888	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs761608224	NA	P-0019612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	202	1086	0	ENST00000264709.3:c.1474+1G>A		p.X492_splice	ENST00000264709	NM_175629.2	492			1	2	FACETS	0.978	0.91	1	0.978	0.91	1	CLONAL	1	TRUE	1	0.571334721891916	2		1086	723	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463248	25463248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754613602	NA	P-0019612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	121	845	4	ENST00000264709.3:c.2245C>T	p.Arg749Cys	p.R749C	ENST00000264709	NM_175629.2	749	Cgc/Tgc	19/23	1	2	FACETS	0.734	0.665	0.806	0.734	0.665	0.806	SUBCLONAL	1	TRUE	1	0.571334721891916	2		849	577	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	128	736	0				ENST00000310581	NM_198253.2	-/1132			0.140089270353345	3	FACETS	0.996	0.906	1	0.996	0.906	1	INDETERMINATE	2	TRUE	1	0.244544475493078	3		736	590	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652927	29652927	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	20	538	0	ENST00000356175.3:c.4862T>C	p.Val1621Ala	p.V1621A	ENST00000356175	NM_000267.3	1621	gTa/gCa	36/57	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.244544475493078	2		538	132	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004361	150004362	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0019613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	15	656	0	ENST00000253339.5:c.1863_1864del	p.Lys622ArgfsTer2	p.K622Rfs*2	ENST00000253339		621	aaGAaa/aaaa	3/7	0.140089270353345	3	FACETS	0.983	0.724	1	0.492	0.362	0.645	INDETERMINATE	1	TRUE	1	0.244544475493078	3		656	140	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561516	141561516	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	76	575	1	ENST00000220592.5:c.1289C>T	p.Pro430Leu	p.P430L	ENST00000220592	NM_012154.3	430	cCt/cTt	11/19	0.244544475493078	6	FACETS	1	0.931	1	0.219	0.191	0.249	CLONAL	1	TRUE	1	0.244544475493078	6		576	845	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	55	736	0				ENST00000310581	NM_198253.2	-/1132			0.564414213013028	1	FACETS	0.736	0.64	0.838	0.736	0.64	0.838	SUBCLONAL	1	FALSE	0	0.564414213013028	1		736	190	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250820	99250820	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	64	550	0	ENST00000268035.6:c.124G>A	p.Asp42Asn	p.D42N	ENST00000268035	NM_000875.3	42	Gac/Aac	2/21	0.215601003799276	0	FACETS	0.359	0.314	0.407			1	INDETERMINATE	1	FALSE	0	0.564414213013028	0		550	275	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604683	48604683	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	149	641	0	ENST00000342988.3:c.1505G>C	p.Arg502Thr	p.R502T	ENST00000342988	NM_005359.5	502	aGg/aCg	12/12	1	2	FACETS	0.96	0.882	1	0.96	0.882	1	CLONAL	1	FALSE	1	0.564414213013028	2		641	550	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629121	14629121	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	103	538	0	ENST00000254322.2:c.41G>T	p.Gly14Val	p.G14V	ENST00000254322	NM_006145.1	14	gGc/gTc	1/3	0.125334371896071	1	FACETS	0.665	0.6	0.733	0.665	0.6	0.733	INDETERMINATE	1	FALSE	0	0.564414213013028	1		538	394	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033712	48033712	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	150	648	0	ENST00000234420.5:c.3923T>G	p.Leu1308Arg	p.L1308R	ENST00000234420	NM_000179.2	1308	cTc/cGc	9/10	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	FALSE	1	0.564414213013028	2		648	531	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266605	198266605	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs754077338	NA	P-0019614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	116	555	1	ENST00000335508.6:c.2231C>A	p.Ala744Asp	p.A744D	ENST00000335508	NM_012433.2	744	gCt/gAt	16/25	1	2	FACETS	0.878	0.796	0.964	0.878	0.796	0.964	CLONAL	1	FALSE	1	0.564414213013028	2		556	468	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	155	736	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.853	0.787	0.922	0.853	0.787	0.922	CLONAL	1	TRUE	1	0.732413277229881	2		736	496	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0019616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	162	460	1	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.732413277229881	2		461	409	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425277	49425277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	315	984	0	ENST00000301067.7:c.13211G>A	p.Gly4404Glu	p.G4404E	ENST00000301067	NM_003482.3	4404	gGa/gAa	39/54	1	2	FACETS	0.972	0.92	1	0.972	0.92	1	CLONAL	1	TRUE	1	0.732413277229881	2		984	885	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	75	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.223610042268253	5	FACETS	1	0.949	1	0.762	0.671	0.859	CLONAL	2	TRUE	2	0.224978624636253	5		555	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0019617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	153	831	0	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	0.992	1	CLONAL	2	TRUE	1	0.224978624636253	2		831	585	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552630	18552630	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200787716	NA	P-0019617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	25	602	3	ENST00000266497.5:c.2041C>T	p.Arg681Cys	p.R681C	ENST00000266497		681	Cgc/Tgc	14/31	0.223610042268253	5	FACETS	0.669	0.527	0.834	0.223	0.175	0.278	SUBCLONAL	1	TRUE	2	0.224978624636253	5		605	444	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891287	101891287	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757374917	NA	P-0019617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	61	683	0	ENST00000374994.4:c.248C>T	p.Pro83Leu	p.P83L	ENST00000374994	NM_004612.2	83	cCg/cTg	2/9	0.224978624636253	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	0	0.224978624636253	1		683	453	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456332	99456332	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	33	492	0	ENST00000268035.6:c.1649A>G	p.Asn550Ser	p.N550S	ENST00000268035	NM_000875.3	550	aAc/aGc	8/21	1	2	FACETS	0.737	0.601	0.891	0.737	0.601	0.891	SUBCLONAL	1	TRUE	1	0.224978624636253	2		492	398	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277082	18277082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs552434792	NA	P-0019617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	90	658	1	ENST00000222254.8:c.1529G>A	p.Arg510Gln	p.R510Q	ENST00000222254	NM_005027.3	510	cGg/cAg	12/16	0.224978624636253	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.224978624636253	1		659	584	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285804	198285805	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0019617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	48	708	0	ENST00000335508.6:c.248dup	p.Tyr84IlefsTer9	p.Y84Ifs*9	ENST00000335508	NM_012433.2	83	gga/ggGa	3/25	0.192294729083467	3	FACETS	0.979	0.828	1	0.489	0.414	0.573	CLONAL	1	TRUE	1	0.224978624636253	3		708	485	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	83	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.158705934824648	3	FACETS	0.78	0.688	0.878	0.39	0.344	0.439	INDETERMINATE	1	TRUE	1	0.37	3		555	682	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0019620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	84	1061	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	NA	2	FACETS	0.363	0.319	0.41			1	INDETERMINATE	1	TRUE	NA	0.37	2		1061	1251	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39744078	39744078	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs372925211	NA	P-0019620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	32	556	0	ENST00000361337.2:c.1706A>G	p.Asn569Ser	p.N569S	ENST00000361337	NM_003286.2	569	aAt/aGt	16/21	1	2	FACETS	0.323	0.262	0.393	0.323	0.262	0.393	SUBCLONAL	1	TRUE	1	0.37	2		556	535	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371661	55371662	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0019620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	47	789	0	ENST00000297316.4:c.353_354dup	p.Glu119TrpfsTer28	p.E119Wfs*28	ENST00000297316	NM_022454.3	117	-/GT	2/2	1	2	FACETS	0.326	0.274	0.383	0.326	0.274	0.383	SUBCLONAL	1	TRUE	1	0.37	2		789	780	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0019621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	60	717	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.216582641080122	1	FACETS	0.939	0.817	1	1	0.978	1	CLONAL	2	TRUE	0	0.216582641080122	1		718	263	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047888	180047888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	27	1048	0	ENST00000261937.6:c.2287G>A	p.Val763Met	p.V763M	ENST00000261937	NM_182925.4	763	Gtg/Atg	15/30	0.216582641080122	0	FACETS	0.695	0.554	0.855			1	SUBCLONAL	1	TRUE	0	0.216582641080122	0		1048	281	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213242	39213243	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1558454973	NA	P-0019621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	40	998	3	ENST00000402219.2:c.3724dup	p.Ser1242LysfsTer2	p.S1242Kfs*2	ENST00000402219	NM_005633.3	1242	agt/aAgt	23/23	1	2	FACETS	0.793	0.659	0.942	0.793	0.659	0.942	CLONAL	1	TRUE	1	0.216582641080122	2		1001	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577529	7577543	+	inframe_deletion	In_Frame_Del	DEL	ATGGGCCTCCGGTTC	ATGGGCCTCCGGTTC	-	novel	NA	P-0019622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	235	862	0	ENST00000269305.4:c.738_752del	p.Met246_Pro250del	p.M246_P250del	ENST00000269305	NM_001126112.2	246	atGAACCGGAGGCCCATc/atc	7/11	0.340122664683221	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.340122664683221	2		862	686	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162293	47162293	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs778158607	NA	P-0019622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	104	494	0	ENST00000409792.3:c.3833A>G	p.Tyr1278Cys	p.Y1278C	ENST00000409792	NM_014159.6	1278	tAt/tGt	3/21	0.336175311376746	3	FACETS	0.79	0.711	0.872	0.79	0.711	0.872	SUBCLONAL	2	TRUE	1	0.340122664683221	3		494	453	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197086	106197086	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	75	413	0	ENST00000380013.4:c.5419G>A	p.Asp1807Asn	p.D1807N	ENST00000380013	NM_001127208.2	1807	Gat/Aat	11/11	0.252844192485287	3	FACETS	1	0.962	1	0.619	0.545	0.698	CLONAL	1	TRUE	1	0.340122664683221	3		413	417	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0019624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	165	350	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	0.486462881058996	4	FACETS	1	0.976	1	0.749	0.694	0.804	CLONAL	2	TRUE	1	0.486462881058996	4		350	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057519990	NA	P-0019624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	292	705	0	ENST00000269305.4:c.796G>T	p.Gly266Ter	p.G266*	ENST00000269305	NM_001126112.2	266	Gga/Tga	8/11	0.438231922063385	0	FACETS		NA	1			1	NA	3	TRUE	0	0.486462881058996	0		705	323	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722327	176722328	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAGCAC	novel	NA	P-0019624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	60	550	0	ENST00000439151.2:c.7959_7964dup	p.Ser2654_Thr2655dup	p.S2654_T2655dup	ENST00000439151	NM_022455.4	2654	ggg/ggGAGCACg	23/23	0.450416678784311	2	FACETS	0.612	0.529	0.702	0.306	0.264	0.351	SUBCLONAL	1	TRUE	0	0.486462881058996	2		550	403	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658346	117658356	+	frameshift_variant	Frame_Shift_Del	DEL	AAGCTTTCTGG	AAGCTTTCTGG	-	novel	NA	P-0019624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	193	1064	0	ENST00000368508.3:c.5227_5237del	p.Pro1743Ter	p.P1743*	ENST00000368508	NM_002944.2	1743	CCAGAAAGCTTt/t	31/43	0.486462881058996	1	FACETS	0.805	0.757	0.853	1	0.993	1	CLONAL	2	TRUE	0	0.486462881058996	1		1064	373	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945129	32945129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80359104	NA	P-0019625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	61	642	2	ENST00000380152.3:c.8524C>T	p.Arg2842Cys	p.R2842C	ENST00000380152		2842	Cgc/Tgc	20/27	0.70138564762688	2	FACETS	0.344	0.297	0.395	0.172	0.148	0.198	SUBCLONAL	1	TRUE	0	0.70138564762688	2		644	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579359	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0019625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	681	848	0	ENST00000269305.4:c.327_328dup	p.Arg110ProfsTer14	p.R110Pfs*14	ENST00000269305	NM_001126112.2	110	cgt/cCCgt	4/11	0.3144921187021	4	FACETS	0.916	0.894	0.936	1	0.998	1	INDETERMINATE	4	TRUE	2	0.70138564762688	4		848	902	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220394	1220394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	173	844	1	ENST00000326873.7:c.487G>A	p.Gly163Ser	p.G163S	ENST00000326873	NM_000455.4	163	Ggc/Agc	4/10	NA	2	FACETS	0.782	0.723	0.843			1	INDETERMINATE	1	TRUE	NA	0.70138564762688	2		845	631	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373486	118373486	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	66	444	1	ENST00000534358.1:c.6879G>T	p.Gln2293His	p.Q2293H	ENST00000534358	NM_005933.3	2293	caG/caT	27/36	0.573698878167525	3	FACETS	0.494	0.429	0.563			1	SUBCLONAL	1	TRUE	NA	0.70138564762688	3		445	515	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285793	46285793	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0019625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	146	638	0	ENST00000334344.6:c.5062-1G>C		p.X1688_splice	ENST00000334344	NM_152641.2	1688			0.70138564762688	2	FACETS	0.946	0.871	1	0.473	0.435	0.512	CLONAL	1	TRUE	0	0.70138564762688	2		638	440	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637254	47637254	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	118	611	0	ENST00000233146.2:c.388C>G	p.Gln130Glu	p.Q130E	ENST00000233146	NM_000251.2	130	Cag/Gag	3/16	0.163306191830304	4	FACETS	1	0.939	1	0.524	0.475	0.576	INDETERMINATE	1	TRUE	2	0.70138564762688	4		611	546	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197129	26197129	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	59	488	0	ENST00000356476.2:c.350G>C	p.Arg117Pro	p.R117P	ENST00000356476		117	cGa/cCa	1/1	0.209538078450179	5	FACETS	0.832	0.718	0.955	0.208	0.179	0.239	INDETERMINATE	1	TRUE	1	0.70138564762688	5		488	415	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64288396	64288396	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	65	611	0	ENST00000370651.3:c.160G>A	p.Asp54Asn	p.D54N	ENST00000370651	NM_003463.4	54	Gac/Aac	3/6	0.512293298056628	5	FACETS	0.53	0.459	0.608			1	SUBCLONAL	1	TRUE	NA	0.70138564762688	5		611	717	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650296	48650296	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	83	841	4	ENST00000376670.3:c.266G>T	p.Gly89Val	p.G89V	ENST00000376670	NM_002049.3	89	gGg/gTg	3/6	1	2	FACETS	0.352	0.31	0.396	0.352	0.31	0.396	SUBCLONAL	1	TRUE	1	0.70138564762688	2		845	673	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	143	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.832	0.761	0.906	0.832	0.761	0.906	CLONAL	1	TRUE	1	0.552363739598151	2		555	622	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	189	903	1	ENST00000269305.4:c.517G>C	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ctg	5/11	0.541738915315247	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.552363739598151	1		904	457	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741886	17741886	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	51	184	0	ENST00000250003.3:c.557C>A	p.Pro186Gln	p.P186Q	ENST00000250003	NM_002478.4	186	cCg/cAg	1/3	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.552363739598151	2		184	167	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0019626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	216	546	5	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	0.541065089542453	2	FACETS	0.924	0.872	0.977	0.924	0.872	0.977	CLONAL	2	TRUE	0	0.552363739598151	2		551	423	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765474	41765474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763936923	NA	P-0019626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	137	891	0	ENST00000301178.4:c.2350C>T	p.Arg784Trp	p.R784W	ENST00000301178	NM_021913.4	784	Cgg/Tgg	20/20	0.21462057487372	2	FACETS	0.589	0.536	0.645	0.295	0.268	0.323	INDETERMINATE	1	TRUE	0	0.552363739598151	2		891	842	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920401	114920401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1422891742	NA	P-0019626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	394	724	0	ENST00000543371.1:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000543371	NM_001198531.1	448	Cgg/Tgg	13/14	0.552363739598151	2	FACETS	0.977	0.937	1	0.977	0.937	1	CLONAL	2	TRUE	0	0.552363739598151	2		724	730	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402217	402217	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	217	1013	1	ENST00000399788.2:c.4574A>C	p.Lys1525Thr	p.K1525T	ENST00000399788	NM_001042603.1	1525	aAg/aCg	27/28	1	2	FACETS	0.952	0.888	1	0.952	0.888	1	CLONAL	1	TRUE	1	0.552363739598151	2		1014	825	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994910	73994910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777380321	NA	P-0019626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	17	150	0	ENST00000318443.5:c.394G>A	p.Ala132Thr	p.A132T	ENST00000318443	NM_001024736.1	132	Gct/Act	3/10	1	2	FACETS	0.751	0.572	0.953	0.751	0.572	0.953	CLONAL	1	TRUE	1	0.552363739598151	2		150	82	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390162	89390162	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	131	524	4	ENST00000336596.2:c.911G>T	p.Cys304Phe	p.C304F	ENST00000336596	NM_005233.5	304	tGc/tTc	4/17	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.552363739598151	2		528	425	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934364	39934364	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1462787258	NA	P-0019626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	366	745	5	ENST00000378444.4:c.235C>T	p.Arg79Trp	p.R79W	ENST00000378444	NM_001123385.1	79	Cgg/Tgg	4/15	0.352305778925524	3	FACETS	0.913	0.869	0.958	0.913	0.869	0.958	CLONAL	2	TRUE	1	0.552363739598151	3		750	926	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115875	8115879	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCT	GCCCT	-	novel	NA	P-0019627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	138	802	0	ENST00000346208.3:c.1221_1225del	p.Pro408GlnfsTer97	p.P408Qfs*97	ENST00000346208		407	tcGCCCTtc/tctc	6/6	1	2	FACETS	0.773	0.706	0.842	0.773	0.706	0.842	SUBCLONAL	1	TRUE	1	0.62	2		802	576	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180390	38180390	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	201	853	1	ENST00000396334.3:c.238C>A	p.Gln80Lys	p.Q80K	ENST00000396334	NM_002468.4	80	Caa/Aaa	1/5	1	2	FACETS	0.937	0.872	1	0.937	0.872	1	CLONAL	1	TRUE	1	0.62	2		854	692	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	80	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.181187044262395	3	FACETS	1	0.962	1	0.613	0.54	0.691	CLONAL	1	TRUE	1	0.25	3		555	587	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584513	48584514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs377767334	NA	P-0019628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	78	442	0	ENST00000342988.3:c.692dup	p.Ser232GlnfsTer3	p.S232Qfs*3	ENST00000342988	NM_005359.5	229	ctg/ctGg	6/12	0.0959842261276955	3	FACETS	1	0.974	1	0.711	0.626	0.801	INDETERMINATE	1	TRUE	1	0.25	3		442	494	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573628	48573628	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	39	504	1	ENST00000342988.3:c.212G>T	p.Cys71Phe	p.C71F	ENST00000342988	NM_005359.5	71	tGt/tTt	2/12	0.0959842261276955	3	FACETS	0.891	0.739	1	0.445	0.369	0.53	INDETERMINATE	1	TRUE	1	0.25	3		505	394	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971192	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCGCT	GGGCGCT	-	novel	NA	P-0019628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	62	475	0	ENST00000304494.5:c.166_172del	p.Ser56GlufsTer88	p.S56Efs*88	ENST00000304494	NM_000077.4	56	AGCGCCCga/ga	2/3	1	2	FACETS	0.912	0.795	1	1	0.978	1	CLONAL	2	TRUE	1	0.25	2		475	272	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	23	736	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.658	0.513	0.825	0.658	0.513	0.825	SUBCLONAL	1	FALSE	1	0.229149581633544	2		736	305	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201506	67201506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	39	1007	1	ENST00000312629.5:c.947C>T	p.Pro316Leu	p.P316L	ENST00000312629	NM_003952.2	316	cCa/cTa	11/15	0.229149581633544	3	FACETS	0.583	0.482	0.696			1	SUBCLONAL	1	FALSE	NA	0.229149581633544	3		1008	651	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578187	7578187	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs878854071	NA	P-0019630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	142	1124	0	ENST00000269305.4:c.662del	p.Glu221GlyfsTer26	p.E221Gfs*26	ENST00000269305	NM_001126112.2	221	gAg/gg	6/11	1	2	FACETS	0.811	0.74	0.886	1	0.988	1	CLONAL	2	FALSE	1	0.229149581633544	2		1124	764	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295181	15295181	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	87	1282	1	ENST00000263388.2:c.2491G>T	p.Gly831Trp	p.G831W	ENST00000263388	NM_000435.2	831	Ggg/Tgg	16/33	1	2	FACETS	0.955	0.845	1	0.955	0.845	1	CLONAL	1	FALSE	1	0.229149581633544	2		1283	795	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0019632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	33	538	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	1	2	FACETS	0.798	0.648	0.967	0.798	0.648	0.967	CLONAL	1	TRUE	1	0.14	2		538	591	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0019632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	41	830	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.615	0.51	0.733	0.615	0.51	0.733	SUBCLONAL	1	TRUE	1	0.14	2		830	952	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087395	27087395	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	57	816	0	ENST00000324856.7:c.1969C>G	p.Leu657Val	p.L657V	ENST00000324856	NM_006015.4	657	Ctg/Gtg	5/20	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.14	2		816	778	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856053	151856054	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	44	589	0	ENST00000262189.6:c.11564dup	p.Arg3856GlufsTer4	p.R3856Efs*4	ENST00000262189	NM_170606.2	3855	cag/caAg	44/59	1	2	FACETS	0.996	0.834	1	0.996	0.834	1	CLONAL	1	TRUE	1	0.14	2		589	631	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859891	151859891	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	29	425	0	ENST00000262189.6:c.10771C>T	p.Gln3591Ter	p.Q3591*	ENST00000262189	NM_170606.2	3591	Cag/Tag	43/59	1	2	FACETS	0.923	0.74	1	0.923	0.74	1	CLONAL	1	TRUE	1	0.14	2		425	449	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961530	54961530	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs145616804	NA	P-0019634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	411	783	0	ENST00000312783.6:c.102G>C	p.Gln34His	p.Q34H	ENST00000312783	NM_198436.1	34	caG/caC	4/10	0.715703224139087	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	0	0.715703224139087	3		783	508	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55270219	55270219	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1277	193	1062	2	ENST00000275493.2:c.3172T>A	p.Cys1058Ser	p.C1058S	ENST00000275493	NM_005228.3	1058	Tgt/Agt	27/28	0.715703224139087	7	FACETS	1	0.941	1	0.256	0.236	0.277	CLONAL	1	TRUE	3	0.715703224139087	7		1064	1470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0019635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	653	1286	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.443781969404627	3	FACETS	0.915	0.885	0.944	0.915	0.885	0.944	CLONAL	3	TRUE	0	0.489715492641817	3		1286	1210	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938748	76938748	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61752457	NA	P-0019635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	146	866	0	ENST00000373344.5:c.2000C>T	p.Pro667Leu	p.P667L	ENST00000373344	NM_000489.3	667	cCg/cTg	9/35	0.489715492641817	6	FACETS	0.921	0.839	1	0.184	0.167	0.202	CLONAL	1	TRUE	1	0.489715492641817	6		866	1281	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023047	48023047	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	93	490	0	ENST00000234420.5:c.472G>T	p.Glu158Ter	p.E158*	ENST00000234420	NM_000179.2	158	Gaa/Taa	3/10	1	2	FACETS	0.924	0.827	1	0.924	0.827	1	CLONAL	1	TRUE	1	0.489715492641817	2		490	411	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820875	32820875	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1441	140	1095	1	ENST00000354258.4:c.719T>C	p.Leu240Pro	p.L240P	ENST00000354258	NM_000593.5	240	cTg/cCg	1/11	0.489715492641817	5	FACETS	0.627	0.569	0.689	0.125	0.113	0.138	SUBCLONAL	1	TRUE	0	0.489715492641817	5		1096	1581	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93636953	93636953	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0019635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	30	402	0	ENST00000375746.1:c.1004-1G>A		p.X335_splice	ENST00000375746	NM_001174167.1	335			1	2	FACETS	0.415	0.335	0.506	0.415	0.335	0.506	SUBCLONAL	1	TRUE	1	0.489715492641817	2		402	295	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0019636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	197	558	1	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.18891850471755	4	FACETS	0.982	0.916	1	0.982	0.916	1	INDETERMINATE	2	TRUE	2	0.563307325913595	4		559	557	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835629	68835629	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658932	NA	P-0019636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	283	720	1	ENST00000261769.5:c.220C>T	p.Arg74Ter	p.R74*	ENST00000261769	NM_004360.3	74	Cga/Tga	3/16	0.563307325913595	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.563307325913595	1		721	579	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577152	64577152	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	375	965	0	ENST00000312049.6:c.430T>A	p.Phe144Ile	p.F144I	ENST00000312049	NM_130799.2	144	Ttc/Atc	2/10	0.563307325913595	5	FACETS	1	0.989	1	0.755	0.717	0.793	CLONAL	2	TRUE	2	0.563307325913595	5		965	1085	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274100	18274100	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	63	790	0	ENST00000222254.8:c.1318G>C	p.Glu440Gln	p.E440Q	ENST00000222254	NM_005027.3	440	Gag/Cag	11/16	1	2	FACETS	0.192	0.165	0.221	0.192	0.165	0.221	SUBCLONAL	1	TRUE	1	0.563307325913595	2		790	1168	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662564	117662564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	15	426	0	ENST00000368508.3:c.4901A>C	p.Lys1634Thr	p.K1634T	ENST00000368508	NM_002944.2	1634	aAg/aCg	29/43	0.538245667668763	0	FACETS	0.167	0.123	0.22			1	SUBCLONAL	1	TRUE	0	0.563307325913595	0		426	139	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662588	117662588	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	23	508	0	ENST00000368508.3:c.4877C>G	p.Ser1626Cys	p.S1626C	ENST00000368508	NM_002944.2	1626	tCt/tGt	29/43	0.538245667668763	0	FACETS	0.199	0.156	0.248			1	SUBCLONAL	1	TRUE	0	0.563307325913595	0		508	179	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877802	151877802	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	22	286	0	ENST00000262189.6:c.7143G>C	p.Leu2381Phe	p.L2381F	ENST00000262189	NM_170606.2	2381	ttG/ttC	36/59	0.135226395585575	3	FACETS	0.323	0.25	0.407	0.161	0.125	0.204	INDETERMINATE	1	TRUE	1	0.563307325913595	3		286	310	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	218	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.804	0.75	0.859	0.804	0.75	0.859	CLONAL	1	TRUE	1	0.72801354248617	2		555	745	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0019637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	387	1015	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.724382635870039	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.72801354248617	1		1017	640	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0019637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	143	382	0	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.72801354248617	2		382	363	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247367	153247367	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747241612	NA	P-0019637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	172	519	0	ENST00000281708.4:c.1435C>G	p.Arg479Gly	p.R479G	ENST00000281708	NM_033632.3	479	Cga/Gga	10/12	1	2	FACETS	0.865	0.802	0.931	0.865	0.802	0.931	CLONAL	1	TRUE	1	0.72801354248617	2		519	546	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427027	49427027	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	205	678	0	ENST00000301067.7:c.11461del	p.Gln3821ArgfsTer9	p.Q3821Rfs*9	ENST00000301067	NM_003482.3	3821	Cag/ag	39/54	1	2	FACETS	0.956	0.893	1	0.956	0.893	1	CLONAL	1	TRUE	1	0.72801354248617	2		678	589	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727516	88727516	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	232	775	0	ENST00000360948.2:c.263G>A	p.Trp88Ter	p.W88*	ENST00000360948	NM_001012338.2	88	tGg/tAg	3/19	NA	2	FACETS	0.872	0.816	0.929			1	INDETERMINATE	1	TRUE	NA	0.72801354248617	2		775	731	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46602869	46602869	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769824544	NA	P-0019637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	348	1055	2	ENST00000263734.3:c.927G>A	p.Met309Ile	p.M309I	ENST00000263734	NM_001430.4	309	atG/atA	8/16	1	2	FACETS	0.923	0.875	0.971	0.923	0.875	0.971	CLONAL	1	TRUE	1	0.72801354248617	2		1057	1036	SUCCESS
APC	324	MSKCC	GRCh37	5	112162804	112162804	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0019637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	124	611	0	ENST00000257430.4:c.1412del		p.X471_splice	ENST00000257430	NM_000038.5	471			1	2	FACETS	0.759	0.691	0.829	0.759	0.691	0.829	SUBCLONAL	1	TRUE	1	0.72801354248617	2		611	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0019638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	288	938	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.134494701069608	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		938	666	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0019638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	110	395	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		395	284	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0019638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	277	834	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.134494701069608	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		834	548	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939606	76939606	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0019638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	288	408	0	ENST00000373344.5:c.1142C>G	p.Ser381Ter	p.S381*	ENST00000373344	NM_000489.3	381	tCa/tGa	9/35	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		408	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0019639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	133	760	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.211655921499433	2	FACETS	1	0.975	1	0.604	0.549	0.662	CLONAL	1	FALSE	0	0.28595928311169	2		761	770	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101138	27101138	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1476360310	NA	P-0019639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	75	832	1	ENST00000324856.7:c.4420C>T	p.Gln1474Ter	p.Q1474*	ENST00000324856	NM_006015.4	1474	Caa/Taa	18/20	0.208078653864976	1	FACETS	0.555	0.485	0.63	0.555	0.485	0.63	SUBCLONAL	1	FALSE	0	0.28595928311169	1		833	810	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100213	157100253	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCGGGGCCGCGAGCCTCAGCAAGGCGGCCGCCGGCTC	GGCGGCGGGGCCGCGAGCCTCAGCAAGGCGGCCGCCGGCTC	-	novel	NA	P-0019639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	61	47	0	ENST00000346085.5:c.1160_1200del	p.Ala387GlyfsTer134	p.A387Gfs*134	ENST00000346085	NM_020732.3	384	GGCGGCGGGGCCGCGAGCCTCAGCAAGGCGGCCGCCGGCTCg/g	1/20	1	2	FACETS	0.878	0.766	0.996	1	0.977	1	CLONAL	2	FALSE	1	0.28595928311169	2		47	243	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61760990	61760990	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	52	509	0	ENST00000401558.2:c.43C>G	p.Gln15Glu	p.Q15E	ENST00000401558	NM_003400.3	15	Cag/Gag	2/25	1	2	FACETS	0.523	0.444	0.609	0.523	0.444	0.609	SUBCLONAL	1	FALSE	1	0.28595928311169	2		509	696	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521129	187521129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	56	549	3	ENST00000441802.2:c.12026G>A	p.Cys4009Tyr	p.C4009Y	ENST00000441802	NM_005245.3	4009	tGc/tAc	22/27	0.208078653864976	1	FACETS	0.58	0.496	0.671	0.58	0.496	0.671	SUBCLONAL	1	FALSE	0	0.28595928311169	1		552	579	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797206	32797208	+	inframe_deletion	In_Frame_Del	DEL	TAG	TAG	-	novel	NA	P-0019639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	135	797	0	ENST00000374899.4:c.1901_1903del	p.Thr634del	p.T634del	ENST00000374899	NM_018833.2	634	aCTAgt/agt	11/12	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	FALSE	1	0.28595928311169	2		797	944	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	62	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.194559469665358	1	FACETS	0.781	0.674	0.898	0.781	0.674	0.898	SUBCLONAL	1	TRUE	0	0.197876141547516	1		509	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0019640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	80	1015	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.194559469665358	1	FACETS	0.899	0.791	1	0.899	0.791	1	CLONAL	1	TRUE	0	0.197876141547516	1		1015	810	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0019642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	188	860	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.910072138586062	2		860	362	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0019642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7574	6629	761	1	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.910072138586062	22	FACETS	1	0.998	1			1	CLONAL	10	TRUE	NA	0.910072138586062	22		762	14203	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39762931	39762931	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774038422	NA	P-0019642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	242	566	0	ENST00000288319.7:c.905G>A	p.Arg302His	p.R302H	ENST00000288319	NM_182918.3	302	cGc/cAc	9/10	1	2	FACETS	0.855	0.804	0.906	0.855	0.804	0.906	CLONAL	1	TRUE	1	0.910072138586062	2		566	622	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	87	736	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.906	0.807	1	0.906	0.807	1	CLONAL	1	TRUE	1	0.458252090701307	2		736	419	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021728	71021728	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1559602356	NA	P-0019643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	121	525	0	ENST00000318789.4:c.1630C>T	p.Arg544Ter	p.R544*	ENST00000318789	NM_032682.5	544	Cga/Tga	18/21	1	2	FACETS	0.761	0.688	0.837	0.761	0.688	0.837	SUBCLONAL	1	TRUE	1	0.458252090701307	2		525	694	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589599	67589604	+	inframe_deletion	In_Frame_Del	DEL	TCAGTT	TCAGTT	-	novel	NA	P-0019643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	107	508	0	ENST00000274335.5:c.1365_1370del	p.Phe456_Gln457del	p.F456_Q457del	ENST00000274335		454	acTCAGTTt/act	10/15	1	2	FACETS	0.746	0.67	0.826	0.746	0.67	0.826	SUBCLONAL	1	TRUE	1	0.458252090701307	2		508	626	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519941	NA	P-0019643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	99	464	0	ENST00000263967.3:c.1031T>C	p.Val344Ala	p.V344A	ENST00000263967	NM_006218.2	344	gTg/gCg	5/21	0.224683308218861	3	FACETS	0.807	0.721	0.898	0.404	0.36	0.449	INDETERMINATE	1	TRUE	1	0.458252090701307	3		464	658	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577562	7577563	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTT	novel	NA	P-0019643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	382	742	0	ENST00000269305.4:c.715_718dup	p.Ser240LysfsTer25	p.S240Kfs*25	ENST00000269305	NM_001126112.2	240	agt/aAACAgt	7/11	0.386508588253263	2	FACETS	0.789	0.751	0.828	0.789	0.751	0.828	SUBCLONAL	2	TRUE	0	0.458252090701307	2		742	1056	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375234	15375234	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	64	579	0	ENST00000263377.2:c.1193T>G	p.Met398Arg	p.M398R	ENST00000263377	NM_058243.2	398	aTg/aGg	6/20	1	2	FACETS	0.349	0.301	0.401	0.349	0.301	0.401	SUBCLONAL	1	TRUE	1	0.458252090701307	2		579	800	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163588	47163589	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0019643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	123	442	0	ENST00000409792.3:c.2537_2538del	p.Lys846IlefsTer4	p.K846Ifs*4	ENST00000409792	NM_014159.6	846	aAA/a	3/21	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.458252090701307	2		442	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577571	7577571	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs765848205	NA	P-0019644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	549	678	0	ENST00000269305.4:c.710T>A	p.Met237Lys	p.M237K	ENST00000269305	NM_001126112.2	237	aTg/aAg	7/11	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	2	TRUE	NA	0.640965782629944	2		678	831	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0019644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	108	290	1	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	0.640965782629944	2		291	331	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406252	406252	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	156	559	0	ENST00000399788.2:c.4189T>A	p.Cys1397Ser	p.C1397S	ENST00000399788	NM_001042603.1	1397	Tgt/Agt	25/28	0.521589624344673	4	FACETS	0.725	0.663	0.791	0.242	0.221	0.264	SUBCLONAL	1	TRUE	1	0.640965782629944	4		559	1101	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937039	76937039	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	166	270	0	ENST00000373344.5:c.3709del	p.Ser1237HisfsTer41	p.S1237Hfs*41	ENST00000373344	NM_000489.3	1237	Tca/ca	9/35	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.640965782629944	1		270	270	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591892	48591892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767345	NA	P-0019646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	406	526	0	ENST00000342988.3:c.1055G>A	p.Gly352Glu	p.G352E	ENST00000342988	NM_005359.5	352	gGa/gAa	9/12	0.622674689853066	2	FACETS	0.984	0.948	1	0.984	0.948	1	CLONAL	2	TRUE	0	0.635728953100097	2		526	649	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0019646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	203	507	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	1	2	FACETS	0.938	0.873	1	0.938	0.873	1	CLONAL	1	TRUE	1	0.635728953100097	2		507	681	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577296	64577296	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	588	828	0	ENST00000312049.6:c.286del	p.Gln96ArgfsTer23	p.Q96Rfs*23	ENST00000312049	NM_130799.2	96	Cag/ag	2/10	0.622674689853066	2	FACETS	0.987	0.957	1	0.987	0.957	1	CLONAL	2	TRUE	0	0.635728953100097	2		828	937	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	162	682	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.931	0.859	1	1	0.994	1	CLONAL	3	TRUE	1	0.2	2		682	580	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989562	212989562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755026855	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	40	370	0	ENST00000342788.4:c.149G>A	p.Arg50His	p.R50H	ENST00000342788	NM_005235.2	50	cGc/cAc	2/28	1	2	FACETS	0.733	0.608	0.872	0.733	0.608	0.872	SUBCLONAL	1	TRUE	1	0.2	2		370	546	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	50	416	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.852	0.722	0.994	0.852	0.722	0.994	CLONAL	1	TRUE	1	0.2	2		416	587	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	24	427	1	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS	0.559	0.438	0.7	0.559	0.438	0.7	SUBCLONAL	1	TRUE	1	0.2	2		428	429	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673711	176673711	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs570278338	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	51	504	0	ENST00000439151.2:c.4411C>T	p.Arg1471Ter	p.R1471*	ENST00000439151	NM_022455.4	1471	Cga/Tga	10/23	1	2	FACETS	0.781	0.663	0.911	0.781	0.663	0.911	CLONAL	1	TRUE	1	0.2	2		504	653	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804367	43804367	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1443655691	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	53	514	0	ENST00000372470.3:c.367C>T	p.Arg123Ter	p.R123*	ENST00000372470	NM_005373.2	123	Cga/Tga	3/12	1	2	FACETS	0.84	0.716	0.977	0.84	0.716	0.977	CLONAL	1	TRUE	1	0.2	2		514	631	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073692	8073692	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	61	475	0	ENST00000377482.5:c.967G>T	p.Glu323Ter	p.E323*	ENST00000377482	NM_018948.3	323	Gaa/Taa	4/4	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.2	2		475	549	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074357	8074369	+	frameshift_variant	Frame_Shift_Del	DEL	TCACTTGGGGGAA	TCACTTGGGGGAA	-	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	46	445	0	ENST00000377482.5:c.290_302del	p.Ile97LysfsTer20	p.I97Kfs*20	ENST00000377482	NM_018948.3	97	aTTCCCCCAAGTGAa/aa	4/4	1	2	FACETS	0.998	0.841	1	0.998	0.841	1	CLONAL	1	TRUE	1	0.2	2		445	461	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782057	9782057	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	50	865	1	ENST00000377346.4:c.2080G>A	p.Ala694Thr	p.A694T	ENST00000377346	NM_005026.3	694	Gcc/Acc	17/24	1	2	FACETS	0.632	0.535	0.74	0.632	0.535	0.74	SUBCLONAL	1	TRUE	1	0.2	2		866	791	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257581	16257581	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	53	682	0	ENST00000375759.3:c.4846C>A	p.His1616Asn	p.H1616N	ENST00000375759	NM_015001.2	1616	Cat/Aat	11/15	1	2	FACETS	0.602	0.511	0.701	0.602	0.511	0.701	SUBCLONAL	1	TRUE	1	0.2	2		682	881	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105786	27105786	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	46	553	1	ENST00000324856.7:c.5397G>T	p.Glu1799Asp	p.E1799D	ENST00000324856	NM_006015.4	1799	gaG/gaT	20/20	1	2	FACETS	0.778	0.655	0.915	0.778	0.655	0.915	CLONAL	1	TRUE	1	0.2	2		554	591	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106648	27106648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553153748	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	115	635	1	ENST00000324856.7:c.6259G>A	p.Gly2087Arg	p.G2087R	ENST00000324856	NM_006015.4	2087	Gga/Aga	20/20	1	2	FACETS	0.769	0.693	0.849	1	0.984	1	SUBCLONAL	2	TRUE	1	0.2	2		636	748	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321211	65321211	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	28	451	0	ENST00000342505.4:c.1629C>A	p.Cys543Ter	p.C543*	ENST00000342505	NM_002227.2	543	tgC/tgA	11/25	1	2	FACETS	0.508	0.405	0.626	0.508	0.405	0.626	SUBCLONAL	1	TRUE	1	0.2	2		451	551	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332884	65332884	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	20	234	0	ENST00000342505.4:c.655C>T	p.Arg219Ter	p.R219*	ENST00000342505	NM_002227.2	219	Cga/Tga	7/25	1	2	FACETS	0.733	0.561	0.933	0.733	0.561	0.933	CLONAL	1	TRUE	1	0.2	2		234	273	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429360	78429360	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	56	556	0	ENST00000370768.2:c.1082G>T	p.Arg361Ile	p.R361I	ENST00000370768	NM_003902.3	361	aGa/aTa	13/20	1	2	FACETS	0.76	0.65	0.881	0.76	0.65	0.881	SUBCLONAL	1	TRUE	1	0.2	2		556	737	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263192	115263192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	64	687	0	ENST00000438362.2:c.2158C>T	p.Arg720Cys	p.R720C	ENST00000438362	NM_001242891.1	720	Cgc/Tgc	17/20	1	2	FACETS	0.79	0.683	0.907	0.79	0.683	0.907	CLONAL	1	TRUE	1	0.2	2		687	810	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273000	115273000	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	78	675	0	ENST00000438362.2:c.1373A>C	p.Lys458Thr	p.K458T	ENST00000438362	NM_001242891.1	458	aAa/aCa	12/20	1	2	FACETS	0.905	0.794	1	0.905	0.794	1	CLONAL	1	TRUE	1	0.2	2		675	862	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276614	115276614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	54	622	1	ENST00000438362.2:c.845G>A	p.Arg282Lys	p.R282K	ENST00000438362	NM_001242891.1	282	aGa/aAa	8/20	1	2	FACETS	0.761	0.648	0.884	0.761	0.648	0.884	SUBCLONAL	1	TRUE	1	0.2	2		623	710	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462008	120462008	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	40	534	0	ENST00000256646.2:c.5708C>T	p.Ala1903Val	p.A1903V	ENST00000256646	NM_024408.3	1903	gCc/gTc	31/34	1	2	FACETS	0.645	0.535	0.768	0.645	0.535	0.768	SUBCLONAL	1	TRUE	1	0.2	2		534	620	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743290	162743290	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	68	391	0	ENST00000367921.3:c.1760A>C	p.Lys587Thr	p.K587T	ENST00000367921	NM_006182.2	587	aAa/aCa	14/18	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.2	2		391	499	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746018	162746018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	57	464	2	ENST00000367921.3:c.2141G>A	p.Arg714Gln	p.R714Q	ENST00000367921	NM_006182.2	714	cGa/cAa	16/18	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.2	2		466	495	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956236	175956236	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	52	353	0	ENST00000367669.3:c.1976G>C	p.Ser659Thr	p.S659T	ENST00000367669	NM_022457.5	659	aGt/aCt	18/20	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.2	2		353	459	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649698	206649698	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	47	572	0	ENST00000367120.3:c.533A>C	p.Glu178Ala	p.E178A	ENST00000367120	NM_014002.3	178	gAg/gCg	6/22	1	2	FACETS	0.74	0.624	0.869	0.74	0.624	0.869	SUBCLONAL	1	TRUE	1	0.2	2		572	635	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206941988	206941988	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376415487	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	36	321	0	ENST00000423557.1:c.530G>A	p.Arg177Gln	p.R177Q	ENST00000423557	NM_000572.2	177	cGa/cAa	5/5	1	2	FACETS	0.935	0.77	1	0.935	0.77	1	CLONAL	1	TRUE	1	0.2	2		321	385	SUCCESS
FH	2271	MSKCC	GRCh37	1	241669344	241669344	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	56	684	1	ENST00000366560.3:c.863G>A	p.Gly288Asp	p.G288D	ENST00000366560	NM_000143.3	288	gGc/gAc	6/10	1	2	FACETS	0.708	0.605	0.821	0.708	0.605	0.821	SUBCLONAL	1	TRUE	1	0.2	2		685	791	SUCCESS
FH	2271	MSKCC	GRCh37	1	241669404	241669404	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	50	551	0	ENST00000366560.3:c.803G>T	p.Arg268Ile	p.R268I	ENST00000366560	NM_000143.3	268	aGa/aTa	6/10	1	2	FACETS	0.745	0.631	0.871	0.745	0.631	0.871	SUBCLONAL	1	TRUE	1	0.2	2		551	671	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243668588	243668588	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	85	572	0	ENST00000263826.5:c.1403T>C	p.Phe468Ser	p.F468S	ENST00000263826	NM_005465.4	468	tTc/tCc	13/13	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.2	2		572	675	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333864	70333864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528233201	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	37	489	0	ENST00000373644.4:c.1769G>A	p.Arg590Gln	p.R590Q	ENST00000373644	NM_030625.2	590	cGa/cAa	2/12	1	2	FACETS	0.68	0.56	0.815	0.68	0.56	0.815	SUBCLONAL	1	TRUE	1	0.2	2		489	544	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681426	88681426	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	68	725	0	ENST00000372037.3:c.1316A>G	p.Glu439Gly	p.E439G	ENST00000372037	NM_004329.2	439	gAg/gGg	11/13	1	2	FACETS	0.918	0.797	1	0.918	0.797	1	CLONAL	1	TRUE	1	0.2	2		725	741	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724723	112724723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	65	603	1	ENST00000369452.4:c.607C>T	p.Arg203Cys	p.R203C	ENST00000369452	NM_007373.3	203	Cgt/Tgt	2/9	1	2	FACETS	0.931	0.807	1	0.931	0.807	1	CLONAL	1	TRUE	1	0.2	2		604	698	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741688	17741688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	68	536	0	ENST00000250003.3:c.359G>A	p.Arg120His	p.R120H	ENST00000250003	NM_002478.4	120	cGc/cAc	1/3	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.2	2		536	578	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180441	94180441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139461096	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	77	663	0	ENST00000323929.3:c.1727G>A	p.Arg576Gln	p.R576Q	ENST00000323929	NM_005591.3	576	cGa/cAa	15/20	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.2	2		663	723	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94201042	94201042	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	72	424	0	ENST00000323929.3:c.1035A>C	p.Glu345Asp	p.E345D	ENST00000323929	NM_005591.3	345	gaA/gaC	10/20	1	2	FACETS	0.8	0.701	0.906	1	0.977	1	CLONAL	2	TRUE	1	0.2	2		424	450	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212851	94212851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368403414	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	31	545	2	ENST00000323929.3:c.391G>A	p.Asp131Asn	p.D131N	ENST00000323929	NM_005591.3	131	Gat/Aat	5/20	1	2	FACETS	0.581	0.468	0.708	0.581	0.468	0.708	SUBCLONAL	1	TRUE	1	0.2	2		547	534	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933469	100933469	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	29	236	0	ENST00000325455.5:c.1921A>C	p.Lys641Gln	p.K641Q	ENST00000325455	NM_001202474.3	641	Aag/Cag	4/8	1	2	FACETS	0.836	0.671	1	0.836	0.671	1	CLONAL	1	TRUE	1	0.2	2		236	347	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076740	102076740	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	62	609	3	ENST00000282441.5:c.919C>T	p.Arg307Ter	p.R307*	ENST00000282441	NM_001130145.2	307	Cga/Tga	5/9	1	2	FACETS	0.701	0.604	0.807	0.701	0.604	0.807	SUBCLONAL	1	TRUE	1	0.2	2		612	884	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106403	108106403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876658324	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	19	225	1	ENST00000278616.4:c.338C>T	p.Pro113Leu	p.P113L	ENST00000278616	NM_000051.3	113	cCt/cTt	5/63	1	2	FACETS	0.905	0.689	1	0.905	0.689	1	CLONAL	1	TRUE	1	0.2	2		226	210	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106517	108106517	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	49	474	0	ENST00000278616.4:c.452C>A	p.Ser151Tyr	p.S151Y	ENST00000278616	NM_000051.3	151	tCt/tAt	5/63	1	2	FACETS	0.955	0.809	1	0.955	0.809	1	CLONAL	1	TRUE	1	0.2	2		474	513	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374486	118374486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555046878	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	47	486	0	ENST00000534358.1:c.7879C>T	p.Arg2627Cys	p.R2627C	ENST00000534358	NM_005933.3	2627	Cgt/Tgt	27/36	1	2	FACETS	0.808	0.681	0.948	0.808	0.681	0.948	CLONAL	1	TRUE	1	0.2	2		486	582	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375245	118375245	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	38	418	0	ENST00000534358.1:c.8638C>T	p.Leu2880Phe	p.L2880F	ENST00000534358	NM_005933.3	2880	Ctt/Ttt	27/36	1	2	FACETS	0.832	0.687	0.993	0.832	0.687	0.993	CLONAL	1	TRUE	1	0.2	2		418	457	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169179	119169179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150811339	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	91	489	0	ENST00000264033.4:c.2363G>A	p.Arg788Gln	p.R788Q	ENST00000264033	NM_005188.3	788	cGa/cAa	15/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.2	2		489	637	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402275	402275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751548422	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	80	702	1	ENST00000399788.2:c.4516C>T	p.Arg1506Trp	p.R1506W	ENST00000399788	NM_001042603.1	1506	Cgg/Tgg	27/28	1	2	FACETS	0.882	0.775	0.998	0.882	0.775	0.998	CLONAL	1	TRUE	1	0.2	2		703	907	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406231	406231	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	49	486	0	ENST00000399788.2:c.4210T>C	p.Ser1404Pro	p.S1404P	ENST00000399788	NM_001042603.1	1404	Tct/Cct	25/28	1	2	FACETS	0.893	0.756	1	0.893	0.756	1	CLONAL	1	TRUE	1	0.2	2		486	549	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544156	18544156	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	58	541	0	ENST00000266497.5:c.1973C>T	p.Ala658Val	p.A658V	ENST00000266497		658	gCc/gTc	13/31	1	2	FACETS	0.921	0.791	1	0.921	0.791	1	CLONAL	1	TRUE	1	0.2	2		541	630	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800901	18800901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767127006	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	36	566	0	ENST00000266497.5:c.4277G>A	p.Arg1426Gln	p.R1426Q	ENST00000266497		1426	cGa/cAa	31/31	1	2	FACETS	0.612	0.502	0.736	0.612	0.502	0.736	SUBCLONAL	1	TRUE	1	0.2	2		566	588	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244092	46244092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	54	514	0	ENST00000334344.6:c.2186C>T	p.Pro729Leu	p.P729L	ENST00000334344	NM_152641.2	729	cCt/cTt	15/21	1	2	FACETS	0.954	0.815	1	0.954	0.815	1	CLONAL	1	TRUE	1	0.2	2		514	566	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244925	46244925	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	52	614	0	ENST00000334344.6:c.3019T>G	p.Leu1007Val	p.L1007V	ENST00000334344	NM_152641.2	1007	Tta/Gta	15/21	1	2	FACETS	0.654	0.555	0.763	0.654	0.555	0.763	SUBCLONAL	1	TRUE	1	0.2	2		614	795	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254704	46254704	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	43	483	0	ENST00000334344.6:c.4894T>G	p.Phe1632Val	p.F1632V	ENST00000334344	NM_152641.2	1632	Ttc/Gtc	16/21	1	2	FACETS	0.83	0.694	0.981	0.83	0.694	0.981	CLONAL	1	TRUE	1	0.2	2		483	518	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427951	49427951	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	104	701	1	ENST00000301067.7:c.10639C>T	p.Arg3547Cys	p.R3547C	ENST00000301067	NM_003482.3	3547	Cgc/Tgc	38/54	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.2	2		702	839	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433722	49433722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572359740	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	65	954	2	ENST00000301067.7:c.7831C>T	p.Arg2611Cys	p.R2611C	ENST00000301067	NM_003482.3	2611	Cgc/Tgc	31/54	1	2	FACETS	0.615	0.531	0.706	0.615	0.531	0.706	SUBCLONAL	1	TRUE	1	0.2	2		956	1057	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487277	56487277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035001455	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	59	584	0	ENST00000267101.3:c.1423C>T	p.Arg475Trp	p.R475W	ENST00000267101	NM_001982.3	475	Cgg/Tgg	12/28	1	2	FACETS	0.809	0.695	0.934	0.809	0.695	0.934	CLONAL	1	TRUE	1	0.2	2		584	729	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864505	57864505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	38	664	0	ENST00000228682.2:c.1982G>A	p.Gly661Asp	p.G661D	ENST00000228682	NM_005269.2	661	gGc/gAc	12/12	1	2	FACETS	0.594	0.49	0.711	0.594	0.49	0.711	SUBCLONAL	1	TRUE	1	0.2	2		664	640	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115397	115115397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866796237	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	75	630	0	ENST00000257566.3:c.929G>A	p.Arg310Gln	p.R310Q	ENST00000257566	NM_016569.3	310	cGa/cAa	5/8	1	2	FACETS	0.897	0.785	1	0.897	0.785	1	CLONAL	1	TRUE	1	0.2	2		630	836	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120675	115120675	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	114	922	1	ENST00000257566.3:c.331G>T	p.Glu111Ter	p.E111*	ENST00000257566	NM_016569.3	111	Gaa/Taa	1/8	1	2	FACETS	0.983	0.883	1	0.983	0.883	1	CLONAL	1	TRUE	1	0.2	2		923	1160	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120717	115120717	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	54	790	0	ENST00000257566.3:c.289G>T	p.Glu97Ter	p.E97*	ENST00000257566	NM_016569.3	97	Gaa/Taa	1/8	1	2	FACETS	0.576	0.491	0.671	0.576	0.491	0.671	SUBCLONAL	1	TRUE	1	0.2	2		790	937	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426689	121426689	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	70	722	0	ENST00000257555.6:c.380A>G	p.Asn127Ser	p.N127S	ENST00000257555		127	aAc/aGc	2/10	1	2	FACETS	0.921	0.802	1	0.921	0.802	1	CLONAL	1	TRUE	1	0.2	2		722	760	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431482	121431482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057520779	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	65	620	0	ENST00000257555.6:c.686G>A	p.Arg229Gln	p.R229Q	ENST00000257555		229	cGa/cAa	3/10	1	2	FACETS	0.832	0.72	0.954	0.832	0.72	0.954	CLONAL	1	TRUE	1	0.2	2		620	781	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437163	121437163	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1421619915	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	94	1020	1	ENST00000257555.6:c.1594G>A	p.Ala532Thr	p.A532T	ENST00000257555		532	Gcc/Acc	8/10	1	2	FACETS	0.913	0.81	1	0.913	0.81	1	CLONAL	1	TRUE	1	0.2	2		1021	1030	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	66	492	0	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.2	2		492	484	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619894	21619894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55842804	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	71	478	0	ENST00000382592.4:c.272C>T	p.Ser91Leu	p.S91L	ENST00000382592	NM_014572.2	91	tCg/tTg	2/8	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.2	2		478	589	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597512	28597512	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	99	640	0	ENST00000241453.7:c.2393G>T	p.Gly798Val	p.G798V	ENST00000241453	NM_004119.2	798	gGa/gTa	19/24	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.2	2		640	755	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636162	28636162	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	78	589	0	ENST00000241453.7:c.210G>T	p.Gln70His	p.Q70H	ENST00000241453	NM_004119.2	70	caG/caT	3/24	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.2	2		589	640	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912588	32912588	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	59	639	0	ENST00000380152.3:c.4096C>A	p.Leu1366Ile	p.L1366I	ENST00000380152		1366	Ctt/Att	11/27	1	2	FACETS	0.859	0.738	0.991	0.859	0.738	0.991	CLONAL	1	TRUE	1	0.2	2		639	687	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915238	32915238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	63	715	1	ENST00000380152.3:c.6746C>T	p.Ala2249Val	p.A2249V	ENST00000380152		2249	gCc/gTc	11/27	1	2	FACETS	0.933	0.807	1	0.933	0.807	1	CLONAL	1	TRUE	1	0.2	2		716	675	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32920972	32920972	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	62	551	0	ENST00000380152.3:c.6946A>C	p.Lys2316Gln	p.K2316Q	ENST00000380152		2316	Aaa/Caa	13/27	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.2	2		551	588	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972616	32972616	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	79	520	0	ENST00000380152.3:c.9966G>T	p.Met3322Ile	p.M3322I	ENST00000380152		3322	atG/atT	27/27	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.2	2		520	605	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134288	41134288	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1005190964	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	43	434	0	ENST00000379561.5:c.1340C>T	p.Ser447Leu	p.S447L	ENST00000379561	NM_002015.3	447	tCg/tTg	2/3	1	2	FACETS	0.79	0.661	0.934	0.79	0.661	0.934	CLONAL	1	TRUE	1	0.2	2		434	544	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916735	48916735	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	25	389	1	ENST00000267163.4:c.265G>T	p.Gly89Ter	p.G89*	ENST00000267163	NM_000321.2	89	Gga/Tga	3/27	1	2	FACETS	0.541	0.426	0.675	0.541	0.426	0.675	SUBCLONAL	1	TRUE	1	0.2	2		390	462	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347916	73347916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139907646	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	15	337	0	ENST00000377767.4:c.1145G>A	p.Arg382Gln	p.R382Q	ENST00000377767	NM_014953.3	382	cGa/cAa	8/21	1	2	FACETS	0.432	0.315	0.574	0.432	0.315	0.574	SUBCLONAL	1	TRUE	1	0.2	2		337	347	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73350083	73350083	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373230191	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	31	439	1	ENST00000377767.4:c.802G>A	p.Asp268Asn	p.D268N	ENST00000377767	NM_014953.3	268	Gac/Aac	5/21	1	2	FACETS	0.681	0.55	0.83	0.681	0.55	0.83	SUBCLONAL	1	TRUE	1	0.2	2		440	455	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518233	103518233	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764873580	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	45	338	0	ENST00000355739.4:c.2171C>T	p.Ser724Leu	p.S724L	ENST00000355739	NM_000123.3	724	tCg/tTg	9/15	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.2	2		338	367	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435406	110435406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35927012	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	71	740	5	ENST00000375856.3:c.2995G>A	p.Val999Met	p.V999M	ENST00000375856	NM_003749.2	999	Gtg/Atg	1/2	1	2	FACETS	0.76	0.662	0.867	0.76	0.662	0.867	SUBCLONAL	1	TRUE	1	0.2	2		745	934	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435726	110435726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	46	330	1	ENST00000375856.3:c.2675G>A	p.Arg892His	p.R892H	ENST00000375856	NM_003749.2	892	cGc/cAc	1/2	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.2	2		331	439	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81574754	81574754	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	45	534	0	ENST00000298171.2:c.650A>G	p.Asp217Gly	p.D217G	ENST00000298171	NM_000369.2	217	gAc/gGc	8/10	1	2	FACETS	0.818	0.687	0.963	0.818	0.687	0.963	CLONAL	1	TRUE	1	0.2	2		534	550	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571504	95571504	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	45	517	0	ENST00000393063.1:c.3173T>G	p.Leu1058Arg	p.L1058R	ENST00000393063	NM_030621.3	1058	cTt/cGt	21/28	1	2	FACETS	0.672	0.563	0.792	0.672	0.563	0.792	SUBCLONAL	1	TRUE	1	0.2	2		517	670	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988691	41988691	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	38	552	0	ENST00000219905.7:c.1483C>T	p.Arg495Ter	p.R495*	ENST00000219905	NM_001164273.1	495	Cga/Tga	3/24	1	2	FACETS	0.606	0.5	0.725	0.606	0.5	0.725	SUBCLONAL	1	TRUE	1	0.2	2		552	627	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058845	42058845	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	40	330	1	ENST00000219905.7:c.8565C>A	p.Phe2855Leu	p.F2855L	ENST00000219905	NM_001164273.1	2855	ttC/ttA	24/24	1	2	FACETS	0.959	0.798	1	0.959	0.798	1	CLONAL	1	TRUE	1	0.2	2		331	417	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43700270	43700270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	76	736	0	ENST00000382044.4:c.5617C>T	p.Pro1873Ser	p.P1873S	ENST00000382044	NM_001141980.1	1873	Cct/Tct	27/28	1	2	FACETS	0.859	0.752	0.974	0.859	0.752	0.974	CLONAL	1	TRUE	1	0.2	2		736	885	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748182	43748182	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	66	714	0	ENST00000382044.4:c.2624C>A	p.Ala875Asp	p.A875D	ENST00000382044	NM_001141980.1	875	gCt/gAt	12/28	1	2	FACETS	0.843	0.73	0.965	0.843	0.73	0.965	CLONAL	1	TRUE	1	0.2	2		714	783	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749089	43749089	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	66	819	0	ENST00000382044.4:c.1717C>A	p.Leu573Met	p.L573M	ENST00000382044	NM_001141980.1	573	Ctg/Atg	12/28	1	2	FACETS	0.759	0.657	0.869	0.759	0.657	0.869	SUBCLONAL	1	TRUE	1	0.2	2		819	870	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749386	43749386	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	54	561	0	ENST00000382044.4:c.1420G>T	p.Glu474Ter	p.E474*	ENST00000382044	NM_001141980.1	474	Gaa/Taa	12/28	1	2	FACETS	0.902	0.77	1	0.902	0.77	1	CLONAL	1	TRUE	1	0.2	2		561	599	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007702	45007702	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	26	383	0	ENST00000558401.1:c.149T>G	p.Phe50Cys	p.F50C	ENST00000558401	NM_004048.2	50	tTt/tGt	2/4	1	2	FACETS	0.588	0.465	0.73	0.588	0.465	0.73	SUBCLONAL	1	TRUE	1	0.2	2		383	442	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994847	73994847	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs7173476	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	15	173	0	ENST00000318443.5:c.331C>T	p.Arg111Cys	p.R111C	ENST00000318443	NM_001024736.1	111	Cgc/Tgc	3/10	1	2	FACETS	0.882	0.648	1	0.882	0.648	1	CLONAL	1	TRUE	1	0.2	2		173	170	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103398	2103398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200045926	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	77	823	0	ENST00000219476.3:c.281C>T	p.Pro94Leu	p.P94L	ENST00000219476	NM_000548.3	94	cCg/cTg	4/42	1	2	FACETS	0.823	0.721	0.933	0.823	0.721	0.933	CLONAL	1	TRUE	1	0.2	2		823	936	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641150	3641150	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757069261	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1214	107	1210	0	ENST00000294008.3:c.2489C>T	p.Ala830Val	p.A830V	ENST00000294008	NM_032444.2	830	gCg/gTg	12/15	1	2	FACETS	0.81	0.724	0.902	0.81	0.724	0.902	CLONAL	1	TRUE	1	0.2	2		1210	1321	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644567	3644567	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115866745	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	91	785	0	ENST00000294008.3:c.2047G>A	p.Ala683Thr	p.A683T	ENST00000294008	NM_032444.2	683	Gcc/Acc	10/15	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.2	2		785	899	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778398	3778398	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	41	572	0	ENST00000262367.5:c.6650G>A	p.Gly2217Glu	p.G2217E	ENST00000262367	NM_004380.2	2217	gGg/gAg	31/31	1	2	FACETS	0.741	0.617	0.88	0.741	0.617	0.88	SUBCLONAL	1	TRUE	1	0.2	2		572	553	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828177	3828177	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	28	307	0	ENST00000262367.5:c.1948T>C	p.Tyr650His	p.Y650H	ENST00000262367	NM_004380.2	650	Tat/Cat	10/31	1	2	FACETS	0.731	0.584	0.898	0.731	0.584	0.898	SUBCLONAL	1	TRUE	1	0.2	2		307	383	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3842041	3842041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	52	525	3	ENST00000262367.5:c.1271G>A	p.Arg424Gln	p.R424Q	ENST00000262367	NM_004380.2	424	cGa/cAa	5/31	1	2	FACETS	0.758	0.644	0.883	0.758	0.644	0.883	SUBCLONAL	1	TRUE	1	0.2	2		528	686	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858227	9858227	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1064796658	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	30	462	1	ENST00000330684.3:c.3174C>A	p.His1058Gln	p.H1058Q	ENST00000330684	NM_001134407.1	1058	caC/caA	13/13	1	2	FACETS	0.673	0.541	0.822	0.673	0.541	0.822	SUBCLONAL	1	TRUE	1	0.2	2		463	446	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943680	9943680	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	63	649	0	ENST00000330684.3:c.1261G>T	p.Asp421Tyr	p.D421Y	ENST00000330684	NM_001134407.1	421	Gac/Tac	5/13	1	2	FACETS	0.839	0.724	0.964	0.839	0.724	0.964	CLONAL	1	TRUE	1	0.2	2		649	751	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041557	14041557	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180030515	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	41	480	0	ENST00000311895.7:c.2104C>T	p.Arg702Trp	p.R702W	ENST00000311895	NM_005236.2	702	Cgg/Tgg	11/11	1	2	FACETS	0.765	0.637	0.908	0.765	0.637	0.908	CLONAL	1	TRUE	1	0.2	2		480	536	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56862895	56862895	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	19	337	0	ENST00000308159.5:c.801G>T	p.Lys267Asn	p.K267N	ENST00000308159	NM_014669.4	267	aaG/aaT	9/22	1	2	FACETS	0.504	0.382	0.648	0.504	0.382	0.648	SUBCLONAL	1	TRUE	1	0.2	2		337	377	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845625	68845625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660645	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	66	695	0	ENST00000261769.5:c.871G>A	p.Asp291Asn	p.D291N	ENST00000261769	NM_004360.3	291	Gat/Aat	7/16	1	2	FACETS	0.704	0.61	0.808	0.704	0.61	0.808	SUBCLONAL	1	TRUE	1	0.2	2		695	937	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867391	68867391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34507583	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	55	379	0	ENST00000261769.5:c.2638G>A	p.Glu880Lys	p.E880K	ENST00000261769	NM_004360.3	880	Gag/Aag	16/16	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.2	2		379	492	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821926	72821926	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	22	284	1	ENST00000268489.5:c.10249G>T	p.Glu3417Ter	p.E3417*	ENST00000268489	NM_006885.3	3417	Gaa/Taa	10/10	1	2	FACETS	0.541	0.418	0.683	0.541	0.418	0.683	SUBCLONAL	1	TRUE	1	0.2	2		285	407	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831566	72831566	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1340237537	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	68	673	0	ENST00000268489.5:c.5015G>T	p.Gly1672Val	p.G1672V	ENST00000268489	NM_006885.3	1672	gGc/gTc	9/10	1	2	FACETS	0.863	0.75	0.986	0.863	0.75	0.986	CLONAL	1	TRUE	1	0.2	2		673	788	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929495	81929495	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769180169	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	58	592	0	ENST00000359376.3:c.1156G>A	p.Val386Met	p.V386M	ENST00000359376	NM_002661.3	386	Gtg/Atg	13/33	1	2	FACETS	0.763	0.654	0.882	0.763	0.654	0.882	SUBCLONAL	1	TRUE	1	0.2	2		592	760	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347959	89347959	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201160642	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	60	854	1	ENST00000301030.4:c.4991C>T	p.Ala1664Val	p.A1664V	ENST00000301030	NM_001256183.1	1664	gCg/gTg	9/13	1	2	FACETS	0.571	0.49	0.66	0.571	0.49	0.66	SUBCLONAL	1	TRUE	1	0.2	2		855	1051	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348857	89348857	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	81	972	1	ENST00000301030.4:c.4093C>T	p.Arg1365Ter	p.R1365*	ENST00000301030	NM_001256183.1	1365	Cga/Tga	9/13	1	2	FACETS	0.655	0.575	0.742	0.655	0.575	0.742	SUBCLONAL	1	TRUE	1	0.2	2		973	1236	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350281	89350281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200971432	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	91	820	1	ENST00000301030.4:c.2669G>A	p.Arg890Gln	p.R890Q	ENST00000301030	NM_001256183.1	890	cGg/cAg	9/13	1	2	FACETS	0.936	0.83	1	0.936	0.83	1	CLONAL	1	TRUE	1	0.2	2		821	972	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350635	89350635	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765315608	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1280	71	1149	2	ENST00000301030.4:c.2315G>A	p.Arg772Gln	p.R772Q	ENST00000301030	NM_001256183.1	772	cGg/cAg	9/13	1	2	FACETS	0.526	0.457	0.601	0.526	0.457	0.601	SUBCLONAL	1	TRUE	1	0.2	2		1151	1351	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976482	7976482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	44	462	3	ENST00000319144.4:c.1910G>A	p.Arg637Gln	p.R637Q	ENST00000319144	NM_001139.2	637	cGa/cAa	14/15	1	2	FACETS	0.835	0.7	0.985	0.835	0.7	0.985	CLONAL	1	TRUE	1	0.2	2		465	527	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982784	7982784	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	57	871	0	ENST00000319144.4:c.1001A>G	p.Gln334Arg	p.Q334R	ENST00000319144	NM_001139.2	334	cAg/cGg	8/15	1	2	FACETS	0.718	0.614	0.831	0.718	0.614	0.831	SUBCLONAL	1	TRUE	1	0.2	2		871	794	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984090	7984090	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	37	473	0	ENST00000319144.4:c.536G>A	p.Gly179Asp	p.G179D	ENST00000319144	NM_001139.2	179	gGc/gAc	5/15	1	2	FACETS	0.746	0.614	0.893	0.746	0.614	0.893	SUBCLONAL	1	TRUE	1	0.2	2		473	496	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998959	11998959	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1208900089	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	30	419	0	ENST00000353533.5:c.461G>A	p.Arg154Gln	p.R154Q	ENST00000353533	NM_003010.3	154	cGg/cAg	4/11	1	2	FACETS	0.674	0.543	0.824	0.674	0.543	0.824	SUBCLONAL	1	TRUE	1	0.2	2		419	445	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15960849	15960849	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	24	242	0	ENST00000268712.3:c.6371T>G	p.Leu2124Arg	p.L2124R	ENST00000268712	NM_006311.3	2124	cTt/cGt	40/46	1	2	FACETS	0.696	0.545	0.869	0.696	0.545	0.869	SUBCLONAL	1	TRUE	1	0.2	2		242	345	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995309	15995309	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1366875142	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	50	507	0	ENST00000268712.3:c.2884C>T	p.Arg962Ter	p.R962*	ENST00000268712	NM_006311.3	962	Cga/Tga	22/46	1	2	FACETS	0.821	0.696	0.959	0.821	0.696	0.959	CLONAL	1	TRUE	1	0.2	2		507	609	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556989	29556989	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	12	153	0	ENST00000356175.3:c.2987T>G	p.Val996Gly	p.V996G	ENST00000356175	NM_000267.3	996	gTc/gGc	22/57	1	2	FACETS	0.87	0.614	1	0.87	0.614	1	CLONAL	1	TRUE	1	0.2	2		153	138	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559807	29559807	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	48	336	0	ENST00000356175.3:c.3404C>A	p.Ser1135Tyr	p.S1135Y	ENST00000356175	NM_000267.3	1135	tCt/tAt	26/57	1	2	FACETS	0.887	0.75	1	0.887	0.75	1	CLONAL	1	TRUE	1	0.2	2		336	541	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665144	29665144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs562367786	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	49	641	1	ENST00000356175.3:c.6743G>A	p.Arg2248His	p.R2248H	ENST00000356175	NM_000267.3	2248	cGt/cAt	44/57	1	2	FACETS	0.645	0.545	0.755	0.645	0.545	0.755	SUBCLONAL	1	TRUE	1	0.2	2		642	760	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	31	414	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.615	0.497	0.75	0.615	0.497	0.75	SUBCLONAL	1	TRUE	1	0.2	2		414	504	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619098	37619098	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	48	638	0	ENST00000447079.4:c.774T>G	p.Asn258Lys	p.N258K	ENST00000447079	NM_015083.1	258	aaT/aaG	1/14	1	2	FACETS	0.652	0.55	0.765	0.652	0.55	0.765	SUBCLONAL	1	TRUE	1	0.2	2		638	736	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369467	40369467	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	45	602	2	ENST00000293328.3:c.1185G>T	p.Glu395Asp	p.E395D	ENST00000293328	NM_012448.3	395	gaG/gaT	10/19	1	2	FACETS	0.647	0.542	0.763	0.647	0.542	0.763	SUBCLONAL	1	TRUE	1	0.2	2		604	696	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474351	40474351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780466766	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	48	641	1	ENST00000264657.5:c.2050G>A	p.Gly684Arg	p.G684R	ENST00000264657	NM_139276.2	684	Gga/Aga	21/24	1	2	FACETS	0.62	0.523	0.728	0.62	0.523	0.728	SUBCLONAL	1	TRUE	1	0.2	2		642	774	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244824	41244824	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1350643283	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	85	602	0	ENST00000357654.3:c.2724A>C	p.Glu908Asp	p.E908D	ENST00000357654	NM_007294.3	908	gaA/gaC	10/23	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.2	2		602	675	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526198	63526198	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140344858	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	84	667	0	ENST00000307078.5:c.2428G>A	p.Asp810Asn	p.D810N	ENST00000307078	NM_004655.3	810	Gat/Aat	11/11	1	2	FACETS	0.912	0.804	1	0.912	0.804	1	CLONAL	1	TRUE	1	0.2	2		667	921	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532456	63532456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780123	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	48	764	0	ENST00000307078.5:c.2123C>T	p.Ser708Leu	p.S708L	ENST00000307078	NM_004655.3	708	tCg/tTg	8/11	1	2	FACETS	0.542	0.457	0.637	0.542	0.457	0.637	SUBCLONAL	1	TRUE	1	0.2	2		764	885	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532616	63532616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767111161	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	87	814	3	ENST00000307078.5:c.1963G>A	p.Glu655Lys	p.E655K	ENST00000307078	NM_004655.3	655	Gaa/Aaa	8/11	1	2	FACETS	0.815	0.719	0.917	0.815	0.719	0.917	CLONAL	1	TRUE	1	0.2	2		817	1068	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519878	66519878	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	42	570	0	ENST00000358598.2:c.361G>T	p.Asp121Tyr	p.D121Y	ENST00000358598	NM_212471.2	121	Gat/Tat	4/11	1	2	FACETS	0.728	0.607	0.863	0.728	0.607	0.863	SUBCLONAL	1	TRUE	1	0.2	2		570	577	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66522024	66522024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	47	358	0	ENST00000358598.2:c.679G>A	p.Asp227Asn	p.D227N	ENST00000358598	NM_212471.2	227	Gac/Aac	7/11	1	2	FACETS	0.933	0.787	1	0.933	0.787	1	CLONAL	1	TRUE	1	0.2	2		358	504	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78829330	78829330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	51	536	0	ENST00000306801.3:c.1381C>T	p.Pro461Ser	p.P461S	ENST00000306801	NM_020761.2	461	Ccc/Tcc	12/34	1	2	FACETS	0.774	0.657	0.903	0.774	0.657	0.903	CLONAL	1	TRUE	1	0.2	2		536	659	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78938071	78938071	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	64	775	0	ENST00000306801.3:c.3949G>A	p.Ala1317Thr	p.A1317T	ENST00000306801	NM_020761.2	1317	Gcc/Acc	34/34	1	2	FACETS	0.736	0.635	0.845	0.736	0.635	0.845	SUBCLONAL	1	TRUE	1	0.2	2		775	870	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39575891	39575891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	36	618	1	ENST00000262039.4:c.824G>A	p.Arg275Gln	p.R275Q	ENST00000262039	NM_002647.2	275	cGg/cAg	8/25	1	2	FACETS	0.542	0.444	0.652	0.542	0.444	0.652	SUBCLONAL	1	TRUE	1	0.2	2		619	664	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45396936	45396936	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	46	372	0	ENST00000262160.6:c.237-1G>A		p.X79_splice	ENST00000262160	NM_005901.5	79			1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.2	2		372	354	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348554	56348554	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	31	342	0	ENST00000348428.3:c.362T>G	p.Leu121Arg	p.L121R	ENST00000348428	NM_006785.3	121	cTt/cGt	2/17	1	2	FACETS	0.868	0.703	1	0.868	0.703	1	CLONAL	1	TRUE	1	0.2	2		342	357	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414988	56414988	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	77	620	0	ENST00000348428.3:c.2389C>A	p.His797Asn	p.H797N	ENST00000348428	NM_006785.3	797	Cat/Aat	17/17	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.2	2		620	684	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227079	2227079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	64	676	0	ENST00000398665.3:c.4559C>T	p.Ser1520Leu	p.S1520L	ENST00000398665	NM_032482.2	1520	tCg/tTg	27/28	1	2	FACETS	0.706	0.609	0.811	0.706	0.609	0.811	SUBCLONAL	1	TRUE	1	0.2	2		676	907	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4097279	4097279	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	55	729	0	ENST00000262948.5:c.982G>A	p.Glu328Lys	p.E328K	ENST00000262948	NM_030662.3	328	Gag/Aag	8/11	1	2	FACETS	0.631	0.538	0.733	0.631	0.538	0.733	SUBCLONAL	1	TRUE	1	0.2	2		729	872	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244274	5244274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750721878	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	87	799	1	ENST00000357368.4:c.1208C>T	p.Ser403Leu	p.S403L	ENST00000357368	NM_002850.3	403	tCg/tTg	11/38	1	2	FACETS	0.919	0.812	1	0.919	0.812	1	CLONAL	1	TRUE	1	0.2	2		800	947	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129655	11129655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	63	716	2	ENST00000358026.2:c.2461G>A	p.Glu821Lys	p.E821K	ENST00000358026	NM_001128849.1	821	Gag/Aag	17/36	1	2	FACETS	0.787	0.679	0.904	0.787	0.679	0.904	CLONAL	1	TRUE	1	0.2	2		718	801	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054435	13054435	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144233437	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	39	589	0	ENST00000316448.5:c.1045G>A	p.Val349Ile	p.V349I	ENST00000316448	NM_004343.3	349	Gta/Ata	8/9	1	2	FACETS	0.519	0.428	0.62	0.519	0.428	0.62	SUBCLONAL	1	TRUE	1	0.2	2		589	752	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271304	18271304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs553673157	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	76	820	0	ENST00000222254.8:c.346G>A	p.Glu116Lys	p.E116K	ENST00000222254	NM_005027.3	116	Gag/Aag	3/16	1	2	FACETS	0.844	0.739	0.958	0.844	0.739	0.958	CLONAL	1	TRUE	1	0.2	2		820	900	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221667	36221667	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779863547	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	76	993	1	ENST00000222270.7:c.5336G>A	p.Arg1779Gln	p.R1779Q	ENST00000222270	NM_014727.1	1779	cGa/cAa	26/37	1	2	FACETS	0.708	0.619	0.804	0.708	0.619	0.804	SUBCLONAL	1	TRUE	1	0.2	2		994	1074	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795382	42795382	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	29	551	0	ENST00000575354.2:c.2462G>A	p.Gly821Glu	p.G821E	ENST00000575354	NM_015125.3	821	gGa/gAa	10/20	1	2	FACETS	0.569	0.455	0.698	0.569	0.455	0.698	SUBCLONAL	1	TRUE	1	0.2	2		551	510	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799258	42799258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs530430600	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	62	649	1	ENST00000575354.2:c.4742C>T	p.Ser1581Leu	p.S1581L	ENST00000575354	NM_015125.3	1581	tCg/tTg	20/20	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.2	2		650	543	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905896	50905896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748657880	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	83	928	0	ENST00000440232.2:c.868G>A	p.Val290Met	p.V290M	ENST00000440232	NM_002691.3	290	Gtg/Atg	8/27	1	2	FACETS	0.81	0.713	0.914	0.81	0.713	0.914	CLONAL	1	TRUE	1	0.2	2		928	1025	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964903	25964903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561088610	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	37	333	0	ENST00000435504.4:c.4303C>T	p.Arg1435Trp	p.R1435W	ENST00000435504		1435	Cgg/Tgg	13/13	0.3	2	FACETS	0.76	0.626	0.91			1	CLONAL	1	TRUE	NA	0.2	2		333	487	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965136	25965136	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	36	533	0	ENST00000435504.4:c.4070T>C	p.Val1357Ala	p.V1357A	ENST00000435504		1357	gTc/gCc	13/13	0.3	2	FACETS	0.572	0.469	0.688			1	SUBCLONAL	1	TRUE	NA	0.2	2		533	629	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262387	39262387	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	55	918	0	ENST00000402219.2:c.1040T>C	p.Val347Ala	p.V347A	ENST00000402219	NM_005633.3	347	gTt/gCt	8/23	1	2	FACETS	0.643	0.548	0.746	0.643	0.548	0.746	SUBCLONAL	1	TRUE	1	0.2	2		918	856	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025814	48025814	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	25	415	0	ENST00000234420.5:c.692T>C	p.Val231Ala	p.V231A	ENST00000234420	NM_000179.2	231	gTa/gCa	4/10	1	2	FACETS	0.557	0.438	0.694	0.557	0.438	0.694	SUBCLONAL	1	TRUE	1	0.2	2		415	449	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026606	48026606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1358771617	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	77	432	0	ENST00000234420.5:c.1484G>A	p.Arg495Gln	p.R495Q	ENST00000234420	NM_000179.2	495	cGa/cAa	4/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.2	2		432	522	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033753	48033753	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1553333707	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	45	455	0	ENST00000234420.5:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000234420	NM_000179.2	1322	Gaa/Taa	9/10	1	2	FACETS	0.815	0.685	0.96	0.815	0.685	0.96	CLONAL	1	TRUE	1	0.2	2		455	552	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033781	48033781	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs184131049	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	42	429	0	ENST00000234420.5:c.3992G>A	p.Arg1331Gln	p.R1331Q	ENST00000234420	NM_000179.2	1331	cGa/cAa	9/10	1	2	FACETS	0.917	0.766	1	0.917	0.766	1	CLONAL	1	TRUE	1	0.2	2		429	458	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147184	61147184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752907267	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	45	472	0	ENST00000295025.8:c.862G>A	p.Gly288Ser	p.G288S	ENST00000295025	NM_002908.2	288	Ggc/Agc	8/11	1	2	FACETS	0.751	0.63	0.885	0.751	0.63	0.885	SUBCLONAL	1	TRUE	1	0.2	2		472	599	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726963	61726963	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	64	575	0	ENST00000401558.2:c.475A>G	p.Thr159Ala	p.T159A	ENST00000401558	NM_003400.3	159	Acc/Gcc	7/25	1	2	FACETS	0.87	0.752	0.998	0.87	0.752	0.998	CLONAL	1	TRUE	1	0.2	2		575	736	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152628	99152628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	73	610	0	ENST00000074304.5:c.424G>A	p.Asp142Asn	p.D142N	ENST00000074304	NM_001134224.1	142	Gat/Aat	7/26	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.2	2		610	615	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155420	99155420	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	63	573	0	ENST00000074304.5:c.646C>T	p.Arg216Ter	p.R216*	ENST00000074304	NM_001134224.1	216	Cga/Tga	9/26	1	2	FACETS	0.868	0.75	0.997	0.868	0.75	0.997	CLONAL	1	TRUE	1	0.2	2		573	726	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189323	99189323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173310435	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	93	628	0	ENST00000074304.5:c.2579G>A	p.Arg860Gln	p.R860Q	ENST00000074304	NM_001134224.1	860	cGg/cAg	24/26	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.2	2		628	688	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189373	99189373	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1187659012	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	60	730	1	ENST00000074304.5:c.2629C>A	p.Leu877Ile	p.L877I	ENST00000074304	NM_001134224.1	877	Ctc/Atc	24/26	1	2	FACETS	0.758	0.651	0.874	0.758	0.651	0.874	SUBCLONAL	1	TRUE	1	0.2	2		731	792	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190656563	190656563	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1367090018	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	23	233	0	ENST00000441310.2:c.28C>T	p.Arg10Ter	p.R10*	ENST00000441310	NM_000534.4	10	Cga/Tga	2/13	1	2	FACETS	0.714	0.557	0.896	0.714	0.557	0.896	SUBCLONAL	1	TRUE	1	0.2	2		233	322	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728891	190728891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	61	526	0	ENST00000441310.2:c.2279G>T	p.Arg760Ile	p.R760I	ENST00000441310	NM_000534.4	760	aGa/aTa	10/13	1	2	FACETS	0.982	0.847	1	0.982	0.847	1	CLONAL	1	TRUE	1	0.2	2		526	621	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732553	190732553	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781501975	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	35	546	0	ENST00000441310.2:c.2371G>A	p.Val791Ile	p.V791I	ENST00000441310	NM_000534.4	791	Gtt/Att	11/13	1	2	FACETS	0.731	0.598	0.879	0.731	0.598	0.879	SUBCLONAL	1	TRUE	1	0.2	2		546	479	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268455	198268455	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	54	602	0	ENST00000335508.6:c.1573G>T	p.Glu525Ter	p.E525*	ENST00000335508	NM_012433.2	525	Gaa/Taa	12/25	1	2	FACETS	0.795	0.678	0.924	0.795	0.678	0.924	CLONAL	1	TRUE	1	0.2	2		602	679	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662211	227662211	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	71	909	1	ENST00000305123.5:c.1244C>T	p.Ser415Leu	p.S415L	ENST00000305123	NM_005544.2	415	tCg/tTg	1/2	1	2	FACETS	0.647	0.563	0.739	0.647	0.563	0.739	SUBCLONAL	1	TRUE	1	0.2	2		910	1097	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39721144	39721144	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	49	677	0	ENST00000361337.2:c.647A>C	p.Lys216Thr	p.K216T	ENST00000361337	NM_003286.2	216	aAg/aCg	9/21	1	2	FACETS	0.727	0.615	0.851	0.727	0.615	0.851	SUBCLONAL	1	TRUE	1	0.2	2		677	674	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46251038	46251038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1348905384	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	38	501	3	ENST00000371998.3:c.47G>A	p.Arg16Gln	p.R16Q	ENST00000371998		16	cGa/cAa	3/23	1	2	FACETS	0.638	0.526	0.763	0.638	0.526	0.763	SUBCLONAL	1	TRUE	1	0.2	2		504	596	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36421192	36421192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	56	477	1	ENST00000300305.3:c.5C>T	p.Ala2Val	p.A2V	ENST00000300305		2	gCt/gTt	1/8	1	2	FACETS	0.889	0.761	1	0.889	0.761	1	CLONAL	1	TRUE	1	0.2	2		478	630	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162044	22162044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	46	577	0	ENST00000215832.6:c.211G>A	p.Glu71Lys	p.E71K	ENST00000215832	NM_002745.4	71	Gag/Aag	2/9	1	2	FACETS	0.638	0.536	0.751	0.638	0.536	0.751	SUBCLONAL	1	TRUE	1	0.2	2		577	721	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513220	41513220	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1430803896	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	59	623	1	ENST00000263253.7:c.124G>A	p.Asp42Asn	p.D42N	ENST00000263253	NM_001429.3	42	Gac/Aac	2/31	1	2	FACETS	0.792	0.68	0.914	0.792	0.68	0.914	CLONAL	1	TRUE	1	0.2	2		624	745	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565530	41565530	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	69	490	0	ENST00000263253.7:c.4196A>G	p.Asp1399Gly	p.D1399G	ENST00000263253	NM_001429.3	1399	gAt/gGt	26/31	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.2	2		490	628	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058735	47058735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	38	368	0	ENST00000409792.3:c.7543G>A	p.Gly2515Ser	p.G2515S	ENST00000409792	NM_014159.6	2515	Ggt/Agt	21/21	1	2	FACETS	0.814	0.673	0.971	0.814	0.673	0.971	CLONAL	1	TRUE	1	0.2	2		368	467	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47108598	47108598	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	33	527	0	ENST00000409792.3:c.6071G>A	p.Arg2024Gln	p.R2024Q	ENST00000409792	NM_014159.6	2024	cGa/cAa	13/21	1	2	FACETS	0.521	0.423	0.631	0.521	0.423	0.631	SUBCLONAL	1	TRUE	1	0.2	2		527	634	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165456	47165456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217051214	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	42	453	0	ENST00000409792.3:c.670G>A	p.Ala224Thr	p.A224T	ENST00000409792	NM_014159.6	224	Gca/Aca	3/21	1	2	FACETS	0.819	0.683	0.969	0.819	0.683	0.969	CLONAL	1	TRUE	1	0.2	2		453	513	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397700	49397700	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	86	627	0	ENST00000418115.1:c.524C>T	p.Thr175Met	p.T175M	ENST00000418115	NM_001664.2	175	aCg/aTg	5/5	1	2	FACETS	0.914	0.807	1	0.914	0.807	1	CLONAL	1	TRUE	1	0.2	2		627	941	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940079	49940079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778931500	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	46	699	2	ENST00000296474.3:c.964C>T	p.Arg322Trp	p.R322W	ENST00000296474	NM_002447.2	322	Cgg/Tgg	1/20	1	2	FACETS	0.608	0.51	0.716	0.608	0.51	0.716	SUBCLONAL	1	TRUE	1	0.2	2		701	757	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940529	49940529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778223436	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	94	839	0	ENST00000296474.3:c.514G>A	p.Asp172Asn	p.D172N	ENST00000296474	NM_002447.2	172	Gat/Aat	1/20	1	2	FACETS	0.958	0.851	1	0.958	0.851	1	CLONAL	1	TRUE	1	0.2	2		839	981	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70005639	70005639	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763119975	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	50	634	0	ENST00000394351.3:c.668G>A	p.Arg223His	p.R223H	ENST00000394351	NM_000248.3	223	cGc/cAc	7/9	1	2	FACETS	0.794	0.673	0.927	0.794	0.673	0.927	CLONAL	1	TRUE	1	0.2	2		634	630	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73096477	73096477	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	26	324	0	ENST00000356692.5:c.257G>T	p.Arg86Ile	p.R86I	ENST00000356692		86	aGa/aTa	3/9	1	2	FACETS	0.754	0.597	0.933	0.754	0.597	0.933	CLONAL	1	TRUE	1	0.2	2		324	345	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665131	138665131	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	46	582	4	ENST00000330315.3:c.434G>A	p.Arg145His	p.R145H	ENST00000330315	NM_023067.3	145	cGc/cAc	1/1	1	2	FACETS	0.682	0.574	0.803	0.682	0.574	0.803	SUBCLONAL	1	TRUE	1	0.2	2		586	674	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149290746	149290746	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775570561	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	72	604	0	ENST00000360632.3:c.473C>T	p.Ala158Val	p.A158V	ENST00000360632	NM_015472.4	158	gCg/gTg	3/7	1	2	FACETS	0.951	0.83	1	0.951	0.83	1	CLONAL	1	TRUE	1	0.2	2		604	757	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183551	185183551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	37	454	0	ENST00000265026.3:c.1405C>T	p.Arg469Cys	p.R469C	ENST00000265026	NM_004721.4	469	Cgt/Tgt	9/14	1	2	FACETS	0.731	0.602	0.876	0.731	0.602	0.876	SUBCLONAL	1	TRUE	1	0.2	2		454	506	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808635	1808635	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750501941	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	79	849	1	ENST00000260795.2:c.2248C>T	p.Arg750Cys	p.R750C	ENST00000260795		750	Cgt/Tgt	16/17	1	2	FACETS	0.96	0.843	1	0.96	0.843	1	CLONAL	1	TRUE	1	0.2	2		850	823	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129884	55129884	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs574683248	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	51	648	2	ENST00000257290.5:c.418G>A	p.Val140Met	p.V140M	ENST00000257290	NM_006206.4	140	Gtg/Atg	4/23	1	2	FACETS	0.692	0.587	0.808	0.692	0.587	0.808	SUBCLONAL	1	TRUE	1	0.2	2		650	737	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565858	55565858	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	74	725	0	ENST00000288135.5:c.682G>T	p.Glu228Ter	p.E228*	ENST00000288135	NM_000222.2	228	Gaa/Taa	4/21	1	2	FACETS	0.941	0.823	1	0.941	0.823	1	CLONAL	1	TRUE	1	0.2	2		725	786	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958788	55958788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780764266	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	77	686	0	ENST00000263923.4:c.3065G>A	p.Arg1022Gln	p.R1022Q	ENST00000263923	NM_002253.2	1022	cGa/cAa	22/30	1	2	FACETS	0.937	0.821	1	0.937	0.821	1	CLONAL	1	TRUE	1	0.2	2		686	822	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55962438	55962438	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	50	621	0	ENST00000263923.4:c.2686C>T	p.Leu896Phe	p.L896F	ENST00000263923	NM_002253.2	896	Ctc/Ttc	19/30	1	2	FACETS	0.806	0.683	0.942	0.806	0.683	0.942	CLONAL	1	TRUE	1	0.2	2		621	620	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217270	66217270	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	30	437	0	ENST00000273854.3:c.2345G>T	p.Arg782Ile	p.R782I	ENST00000273854	NM_004439.5	782	aGa/aTa	14/18	1	2	FACETS	0.75	0.604	0.915	0.75	0.604	0.915	CLONAL	1	TRUE	1	0.2	2		437	400	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217310	66217310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	30	278	0	ENST00000273854.3:c.2305G>A	p.Asp769Asn	p.D769N	ENST00000273854	NM_004439.5	769	Gat/Aat	14/18	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.2	2		278	276	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164772	106164772	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761811530	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	35	420	1	ENST00000380013.4:c.3640C>T	p.Arg1214Trp	p.R1214W	ENST00000380013	NM_001127208.2	1214	Cgg/Tgg	6/11	1	2	FACETS	0.676	0.553	0.814	0.676	0.553	0.814	SUBCLONAL	1	TRUE	1	0.2	2		421	518	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142950019	142950019	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	53	527	0	ENST00000262992.4:c.2691G>T	p.Lys897Asn	p.K897N	ENST00000262992	NM_001101669.1	897	aaG/aaT	24/24	1	2	FACETS	0.993	0.847	1	0.993	0.847	1	CLONAL	1	TRUE	1	0.2	2		527	534	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143235873	143235873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	34	394	0	ENST00000262992.4:c.415G>A	p.Glu139Lys	p.E139K	ENST00000262992	NM_001101669.1	139	Gaa/Aaa	6/24	1	2	FACETS	0.717	0.586	0.866	0.717	0.586	0.866	SUBCLONAL	1	TRUE	1	0.2	2		394	474	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253789	153253789	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	31	465	0	ENST00000281708.4:c.944C>A	p.Ala315Asp	p.A315D	ENST00000281708	NM_033632.3	315	gCt/gAt	6/12	1	2	FACETS	0.619	0.5	0.754	0.619	0.5	0.754	SUBCLONAL	1	TRUE	1	0.2	2		465	501	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628125	187628125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1196972484	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	53	761	0	ENST00000441802.2:c.2857G>A	p.Asp953Asn	p.D953N	ENST00000441802	NM_005245.3	953	Gat/Aat	2/27	1	2	FACETS	0.609	0.518	0.71	0.609	0.518	0.71	SUBCLONAL	1	TRUE	1	0.2	2		761	870	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228414	228414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	42	511	0	ENST00000264932.6:c.736C>T	p.Arg246Cys	p.R246C	ENST00000264932	NM_004168.2	246	Cgc/Tgc	6/15	1	2	FACETS	0.685	0.571	0.812	0.685	0.571	0.812	SUBCLONAL	1	TRUE	1	0.2	2		511	613	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233687	233687	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200526913	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	39	378	0	ENST00000264932.6:c.991G>A	p.Ala331Thr	p.A331T	ENST00000264932	NM_004168.2	331	Gcc/Acc	8/15	1	2	FACETS	0.813	0.673	0.968	0.813	0.673	0.968	CLONAL	1	TRUE	1	0.2	2		378	480	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294024	1294024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	68	1123	1	ENST00000310581.5:c.977C>T	p.Ala326Val	p.A326V	ENST00000310581	NM_198253.2	326	gCc/gTc	2/16	1	2	FACETS	0.614	0.532	0.703	0.614	0.532	0.703	SUBCLONAL	1	TRUE	1	0.2	2		1124	1108	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31431691	31431691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	41	477	0	ENST00000344624.3:c.3137C>T	p.Ala1046Val	p.A1046V	ENST00000344624		1046	gCg/gTg	23/33	1	2	FACETS	0.686	0.57	0.814	0.686	0.57	0.814	SUBCLONAL	1	TRUE	1	0.2	2		477	598	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31486610	31486610	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	43	521	0	ENST00000344624.3:c.1902G>T	p.Glu634Asp	p.E634D	ENST00000344624		634	gaG/gaT	11/33	1	2	FACETS	0.665	0.555	0.787	0.665	0.555	0.787	SUBCLONAL	1	TRUE	1	0.2	2		521	647	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876188	35876188	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536561203	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	48	664	2	ENST00000303115.3:c.980C>T	p.Thr327Met	p.T327M	ENST00000303115	NM_002185.3	327	aCg/aTg	8/8	1	2	FACETS	0.705	0.595	0.827	0.705	0.595	0.827	SUBCLONAL	1	TRUE	1	0.2	2		666	681	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39003721	39003721	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1050741127	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	29	491	0	ENST00000357387.3:c.199C>A	p.Leu67Ile	p.L67I	ENST00000357387	NM_152756.3	67	Ctt/Att	4/38	1	2	FACETS	0.572	0.458	0.702	0.572	0.458	0.702	SUBCLONAL	1	TRUE	1	0.2	2		491	507	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178095	56178095	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374455781	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	29	359	0	ENST00000399503.3:c.3068G>A	p.Arg1023His	p.R1023H	ENST00000399503	NM_005921.1	1023	cGc/cAc	14/20	1	2	FACETS	0.67	0.537	0.821	0.67	0.537	0.821	SUBCLONAL	1	TRUE	1	0.2	2		359	433	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576819	67576819	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs367669362	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	61	543	1	ENST00000274335.5:c.901C>T	p.Arg301Ter	p.R301*	ENST00000274335		301	Cga/Tga	6/15	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.2	2		544	600	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	52	400	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.2	2		400	421	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591132	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	rs1057519842	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	46	461	0	ENST00000274335.5:c.1727_1729del	p.Thr576del	p.T576del	ENST00000274335		575	aaGACg/aag	12/15	1	2	FACETS	0.852	0.717	1	0.852	0.717	1	CLONAL	1	TRUE	1	0.2	2		461	540	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79966007	79966007	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772141055	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	78	748	1	ENST00000265081.6:c.671G>A	p.Arg224Gln	p.R224Q	ENST00000265081	NM_002439.4	224	cGg/cAg	4/24	1	2	FACETS	0.869	0.762	0.984	0.869	0.762	0.984	CLONAL	1	TRUE	1	0.2	2		749	898	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80057372	80057372	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	44	392	0	ENST00000265081.6:c.1771A>C	p.Asn591His	p.N591H	ENST00000265081	NM_002439.4	591	Aat/Cat	13/24	1	2	FACETS	0.911	0.764	1	0.911	0.764	1	CLONAL	1	TRUE	1	0.2	2		392	483	SUCCESS
APC	324	MSKCC	GRCh37	5	112174554	112174554	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	34	487	0	ENST00000257430.4:c.3263A>C	p.Lys1088Thr	p.K1088T	ENST00000257430	NM_000038.5	1088	aAg/aCg	16/16	1	2	FACETS	0.634	0.517	0.766	0.634	0.517	0.766	SUBCLONAL	1	TRUE	1	0.2	2		487	536	SUCCESS
APC	324	MSKCC	GRCh37	5	112175793	112175793	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	32	270	0	ENST00000257430.4:c.4502C>A	p.Ser1501Tyr	p.S1501Y	ENST00000257430	NM_000038.5	1501	tCt/tAt	16/16	1	2	FACETS	0.853	0.693	1	0.853	0.693	1	CLONAL	1	TRUE	1	0.2	2		270	375	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977919	131977919	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	38	571	0	ENST00000265335.6:c.3802A>G	p.Thr1268Ala	p.T1268A	ENST00000265335		1268	Act/Gct	25/25	1	2	FACETS	0.742	0.613	0.887	0.742	0.613	0.887	SUBCLONAL	1	TRUE	1	0.2	2		571	512	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501544	149501544	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs537725629	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	75	633	1	ENST00000261799.4:c.2243C>T	p.Ser748Leu	p.S748L	ENST00000261799	NM_002609.3	748	tCg/tTg	16/23	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.2	2		634	730	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176678813	176678813	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	56	473	0	ENST00000439151.2:c.4724A>C	p.Glu1575Ala	p.E1575A	ENST00000439151	NM_022455.4	1575	gAg/gCg	12/23	1	2	FACETS	0.798	0.682	0.924	0.798	0.682	0.924	CLONAL	1	TRUE	1	0.2	2		473	702	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045919	26045919	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	66	455	0	ENST00000540144.1:c.281A>G	p.Gln94Arg	p.Q94R	ENST00000540144	NM_003531.2	94	cAg/cGg	1/1	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.2	2		455	478	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858492	27858492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	23	286	0	ENST00000359303.2:c.79C>T	p.Arg27Cys	p.R27C	ENST00000359303	NM_003535.2	27	Cgc/Tgc	1/1	1	2	FACETS	0.594	0.463	0.747	0.594	0.463	0.747	SUBCLONAL	1	TRUE	1	0.2	2		286	387	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324066	31324066	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1358750678	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	25	424	0	ENST00000412585.2:c.497T>C	p.Ile166Thr	p.I166T	ENST00000412585	NM_005514.6	166	aTc/aCc	3/8	1	2	FACETS	0.543	0.427	0.677	0.543	0.427	0.677	SUBCLONAL	1	TRUE	1	0.2	2		424	460	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821103	32821103	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	82	992	0	ENST00000354258.4:c.491G>A	p.Gly164Asp	p.G164D	ENST00000354258	NM_000593.5	164	gGc/gAc	1/11	1	2	FACETS	0.804	0.707	0.908	0.804	0.707	0.908	CLONAL	1	TRUE	1	0.2	2		992	1020	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956553	93956553	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1035177735	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	44	328	0	ENST00000369303.4:c.2683C>T	p.Arg895Ter	p.R895*	ENST00000369303	NM_004440.3	895	Cga/Tga	15/17	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.2	2		328	423	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109313997	109313997	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772956928	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	33	464	2	ENST00000436639.2:c.1226G>A	p.Arg409His	p.R409H	ENST00000436639	NM_014454.2	409	cGt/cAt	7/10	1	2	FACETS	0.645	0.524	0.781	0.645	0.524	0.781	SUBCLONAL	1	TRUE	1	0.2	2		466	512	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609954	117609954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369184938	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	48	432	0	ENST00000368508.3:c.6745G>A	p.Asp2249Asn	p.D2249N	ENST00000368508	NM_002944.2	2249	Gat/Aat	43/43	0.3	1	FACETS	0.882	0.746	1	0.882	0.746	1	CLONAL	1	TRUE	0	0.2	1		432	490	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686764	117686764	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	65	637	0	ENST00000368508.3:c.2953G>T	p.Glu985Ter	p.E985*	ENST00000368508	NM_002944.2	985	Gaa/Taa	19/43	0.3	1	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	0	0.2	1		637	574	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715885	117715885	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	27	485	0	ENST00000368508.3:c.873G>T	p.Gln291His	p.Q291H	ENST00000368508	NM_002944.2	291	caG/caT	9/43	0.3	1	FACETS	0.514	0.408	0.635	0.514	0.408	0.635	SUBCLONAL	1	TRUE	0	0.2	1		485	473	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005375	150005375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775410465	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	55	681	0	ENST00000253339.5:c.850G>A	p.Val284Ile	p.V284I	ENST00000253339		284	Gta/Ata	3/7	1	2	FACETS	0.775	0.662	0.899	0.775	0.662	0.899	SUBCLONAL	1	TRUE	1	0.2	2		681	710	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206827	162206827	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs56154308	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	40	629	0	ENST00000366898.1:c.848T>C	p.Leu283Pro	p.L283P	ENST00000366898	NM_004562.2	283	cTt/cCt	7/12	1	2	FACETS	0.505	0.418	0.602	0.505	0.418	0.602	SUBCLONAL	1	TRUE	1	0.2	2		629	792	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951847	2951847	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868687398	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	82	739	1	ENST00000396946.4:c.3103G>A	p.Glu1035Lys	p.E1035K	ENST00000396946	NM_032415.4	1035	Gaa/Aaa	23/25	1	2	FACETS	0.969	0.853	1	0.969	0.853	1	CLONAL	1	TRUE	1	0.2	2		740	846	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962888	2962888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1016457945	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	78	764	0	ENST00000396946.4:c.2020G>A	p.Asp674Asn	p.D674N	ENST00000396946	NM_032415.4	674	Gac/Aac	16/25	1	2	FACETS	0.891	0.782	1	0.891	0.782	1	CLONAL	1	TRUE	1	0.2	2		764	875	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035253	6035253	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	34	405	0	ENST00000265849.7:c.815T>G	p.Phe272Cys	p.F272C	ENST00000265849	NM_000535.5	272	tTc/tGc	8/15	1	2	FACETS	0.653	0.532	0.788	0.653	0.532	0.788	SUBCLONAL	1	TRUE	1	0.2	2		405	521	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14027746	14027746	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	50	467	0	ENST00000405192.2:c.98A>C	p.Lys33Thr	p.K33T	ENST00000405192	NM_001163147.1	33	aAa/aCa	3/12	1	2	FACETS	0.809	0.686	0.945	0.809	0.686	0.945	CLONAL	1	TRUE	1	0.2	2		467	618	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55229228	55229228	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	32	378	0	ENST00000275493.2:c.1535C>A	p.Pro512His	p.P512H	ENST00000275493	NM_005228.3	512	cCc/cAc	13/28	1	2	FACETS	0.904	0.735	1	0.904	0.735	1	CLONAL	1	TRUE	1	0.2	2		378	354	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380982	116380982	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	52	669	0	ENST00000397752.3:c.1604T>G	p.Phe535Cys	p.F535C	ENST00000397752	NM_000245.2	535	tTt/tGt	5/21	1	2	FACETS	0.672	0.571	0.783	0.672	0.571	0.783	SUBCLONAL	1	TRUE	1	0.2	2		669	774	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397538	116397538	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	62	614	0	ENST00000397752.3:c.1910C>T	p.Ser637Phe	p.S637F	ENST00000397752	NM_000245.2	637	tCc/tTc	7/21	1	2	FACETS	0.944	0.815	1	0.944	0.815	1	CLONAL	1	TRUE	1	0.2	2		614	657	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128848674	128848674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1006687669	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	80	744	1	ENST00000249373.3:c.1339G>A	p.Glu447Lys	p.E447K	ENST00000249373	NM_005631.4	447	Gag/Aag	7/12	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.2	2		745	777	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534596	140534596	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	67	533	2	ENST00000288602.6:c.317G>T	p.Gly106Val	p.G106V	ENST00000288602	NM_004333.4	106	gGa/gTa	3/18	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.2	2		535	647	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	66	506	0	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.2	2		506	616	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285450	38285450	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	78	670	0	ENST00000425967.3:c.703G>T	p.Gly235Ter	p.G235*	ENST00000425967	NM_001174067.1	235	Gga/Tga	6/19	1	2	FACETS	0.905	0.794	1	0.905	0.794	1	CLONAL	1	TRUE	1	0.2	2		670	862	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56859017	56859017	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	51	579	0	ENST00000519728.1:c.143C>A	p.Ser48Tyr	p.S48Y	ENST00000519728	NM_002350.3	48	tCt/tAt	3/13	1	2	FACETS	0.716	0.608	0.836	0.716	0.608	0.836	SUBCLONAL	1	TRUE	1	0.2	2		579	712	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931826	68931826	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs759461290	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	148	687	3	ENST00000288368.4:c.256G>T	p.Glu86Ter	p.E86*	ENST00000288368	NM_024870.2	86	Gaa/Taa	3/40	1	2	FACETS	0.893	0.816	0.973	1	0.99	1	CLONAL	2	TRUE	1	0.2	2		690	829	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020474	69020474	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	86	746	0	ENST00000288368.4:c.2846A>C	p.Lys949Thr	p.K949T	ENST00000288368	NM_024870.2	949	aAa/aCa	24/40	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.2	2		746	764	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080532	5080532	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	29	264	0	ENST00000381652.3:c.2284-1G>A		p.X762_splice	ENST00000381652	NM_004972.3	762			1	2	FACETS	0.871	0.7	1	0.871	0.7	1	CLONAL	1	TRUE	1	0.2	2		264	333	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319841	8319841	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	32	382	0	ENST00000356435.5:c.5660T>C	p.Val1887Ala	p.V1887A	ENST00000356435		1887	gTa/gCa	34/35	1	2	FACETS	0.847	0.688	1	0.847	0.688	1	CLONAL	1	TRUE	1	0.2	2		382	378	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340450	8340450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200354236	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	25	410	0	ENST00000356435.5:c.5146G>A	p.Ala1716Thr	p.A1716T	ENST00000356435		1716	Gct/Act	31/35	1	2	FACETS	0.567	0.446	0.706	0.567	0.446	0.706	SUBCLONAL	1	TRUE	1	0.2	2		410	441	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518231	8518231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750058892	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	31	356	1	ENST00000356435.5:c.1160C>T	p.Ser387Leu	p.S387L	ENST00000356435		387	tCg/tTg	10/35	1	2	FACETS	0.7	0.565	0.852	0.7	0.565	0.852	SUBCLONAL	1	TRUE	1	0.2	2		357	443	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169576	27169576	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	75	739	0	ENST00000380036.4:c.577T>C	p.Tyr193His	p.Y193H	ENST00000380036	NM_000459.3	193	Tat/Cat	4/23	1	2	FACETS	0.899	0.787	1	0.899	0.787	1	CLONAL	1	TRUE	1	0.2	2		739	834	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206773	27206773	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	78	601	0	ENST00000380036.4:c.2558C>T	p.Ala853Val	p.A853V	ENST00000380036	NM_000459.3	853	gCc/gTc	15/23	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.2	2		601	683	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27220064	27220064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780622660	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	48	598	0	ENST00000380036.4:c.3121G>A	p.Gly1041Arg	p.G1041R	ENST00000380036	NM_000459.3	1041	Ggg/Agg	21/23	1	2	FACETS	0.661	0.558	0.776	0.661	0.558	0.776	SUBCLONAL	1	TRUE	1	0.2	2		598	726	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325632	87325632	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	48	570	0	ENST00000277120.3:c.509A>G	p.Asp170Gly	p.D170G	ENST00000277120		170	gAc/gGc	6/19	1	2	FACETS	0.822	0.694	0.963	0.822	0.694	0.963	CLONAL	1	TRUE	1	0.2	2		570	584	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98003012	98003012	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	63	351	0	ENST00000289081.3:c.264A>C	p.Lys88Asn	p.K88N	ENST00000289081	NM_000136.2	88	aaA/aaC	4/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.2	2		351	421	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212188	98212188	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	81	495	0	ENST00000331920.6:c.3484C>A	p.Leu1162Ile	p.L1162I	ENST00000331920	NM_000264.3	1162	Ctc/Atc	21/24	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.2	2		495	664	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242365	98242365	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	58	502	1	ENST00000331920.6:c.953A>C	p.Asp318Ala	p.D318A	ENST00000331920	NM_000264.3	318	gAt/gCt	7/24	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.2	2		503	541	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128201272	128201272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779657195	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	86	632	2	ENST00000265960.3:c.1463C>T	p.Ser488Leu	p.S488L	ENST00000265960	NM_001006617.1	488	tCg/tTg	12/12	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.2	2		634	781	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128432172	128432172	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	44	550	2	ENST00000265960.3:c.274C>T	p.Arg92Ter	p.R92*	ENST00000265960	NM_001006617.1	92	Cga/Tga	3/12	1	2	FACETS	0.679	0.568	0.802	0.679	0.568	0.802	SUBCLONAL	1	TRUE	1	0.2	2		552	648	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391476	139391476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747504082	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	51	909	0	ENST00000277541.6:c.6715G>A	p.Asp2239Asn	p.D2239N	ENST00000277541	NM_017617.3	2239	Gac/Aac	34/34	1	2	FACETS	0.603	0.511	0.705	0.603	0.511	0.705	SUBCLONAL	1	TRUE	1	0.2	2		909	846	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410037	139410037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749381544	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	81	968	1	ENST00000277541.6:c.1801G>A	p.Glu601Lys	p.E601K	ENST00000277541	NM_017617.3	601	Gag/Aag	11/34	1	2	FACETS	0.723	0.635	0.818	0.723	0.635	0.818	SUBCLONAL	1	TRUE	1	0.2	2		969	1120	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814713	139814713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753016580	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	39	531	0	ENST00000247668.2:c.706G>A	p.Glu236Lys	p.E236K	ENST00000247668	NM_021138.3	236	Gag/Aag	8/11	1	2	FACETS	0.672	0.556	0.802	0.672	0.556	0.802	SUBCLONAL	1	TRUE	1	0.2	2		531	580	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911436	39911436	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	69	642	0	ENST00000378444.4:c.5194G>T	p.Glu1732Ter	p.E1732*	ENST00000378444	NM_001123385.1	1732	Gaa/Taa	15/15	0.3	2	FACETS	0.919	0.799	1			1	CLONAL	1	TRUE	NA	0.2	2		642	751	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913224	39913224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769982436	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	86	650	1	ENST00000378444.4:c.4891G>A	p.Asp1631Asn	p.D1631N	ENST00000378444	NM_001123385.1	1631	Gat/Aat	14/15	0.3	2	FACETS	1	0.954	1			1	CLONAL	1	TRUE	NA	0.2	2		651	741	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921447	39921447	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	78	636	0	ENST00000378444.4:c.4373T>C	p.Val1458Ala	p.V1458A	ENST00000378444	NM_001123385.1	1458	gTc/gCc	10/15	0.3	2	FACETS	1	0.945	1			1	CLONAL	1	TRUE	NA	0.2	2		636	686	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922070	39922070	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	61	878	0	ENST00000378444.4:c.4102T>G	p.Leu1368Val	p.L1368V	ENST00000378444	NM_001123385.1	1368	Ttg/Gtg	9/15	0.3	2	FACETS	0.562	0.483	0.648			1	SUBCLONAL	1	TRUE	NA	0.2	2		878	1086	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039665	47039665	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	86	856	0	ENST00000377604.3:c.1117G>A	p.Asp373Asn	p.D373N	ENST00000377604	NM_001204468.1	373	Gac/Aac	11/24	1	2	FACETS	0.924	0.816	1	0.924	0.816	1	CLONAL	1	TRUE	1	0.2	2		856	931	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652261	48652261	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	125	934	0	ENST00000376670.3:c.932G>A	p.Gly311Glu	p.G311E	ENST00000376670	NM_002049.3	311	gGa/gAa	6/6	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.2	2		934	938	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225199	53225199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781854324	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	91	768	2	ENST00000375401.3:c.3019C>T	p.Arg1007Cys	p.R1007C	ENST00000375401	NM_004187.3	1007	Cgt/Tgt	20/26	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.2	2		770	825	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412029	63412029	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754922124	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	49	695	0	ENST00000330258.3:c.1138G>A	p.Glu380Lys	p.E380K	ENST00000330258	NM_152424.3	380	Gag/Aag	2/2	1	2	FACETS	0.73	0.617	0.855	0.73	0.617	0.855	SUBCLONAL	1	TRUE	1	0.2	2		695	671	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412110	63412110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852216	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	56	986	1	ENST00000330258.3:c.1057C>T	p.Arg353Ter	p.R353*	ENST00000330258	NM_152424.3	353	Cga/Tga	2/2	1	2	FACETS	0.575	0.491	0.667	0.575	0.491	0.667	SUBCLONAL	1	TRUE	1	0.2	2		987	974	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412637	63412637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779222316	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	38	611	1	ENST00000330258.3:c.530G>A	p.Arg177His	p.R177H	ENST00000330258	NM_152424.3	177	cGc/cAc	2/2	1	2	FACETS	0.535	0.441	0.641	0.535	0.441	0.641	SUBCLONAL	1	TRUE	1	0.2	2		612	710	SUCCESS
AR	367	MSKCC	GRCh37	X	66765023	66765023	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	90	962	0	ENST00000374690.3:c.35C>A	p.Pro12His	p.P12H	ENST00000374690	NM_000044.3	12	cCt/cAt	1/8	1	2	FACETS	0.78	0.69	0.877	0.78	0.69	0.877	SUBCLONAL	1	TRUE	1	0.2	2		962	1154	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351421	70351421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1474736821	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	75	726	2	ENST00000374080.3:c.4069C>T	p.Arg1357Cys	p.R1357C	ENST00000374080		1357	Cgc/Tgc	29/45	1	2	FACETS	0.903	0.79	1	0.903	0.79	1	CLONAL	1	TRUE	1	0.2	2		728	831	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76812950	76812950	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	39	602	0	ENST00000373344.5:c.6671A>C	p.Lys2224Thr	p.K2224T	ENST00000373344	NM_000489.3	2224	aAg/aCg	30/35	1	2	FACETS	0.672	0.556	0.802	0.672	0.556	0.802	SUBCLONAL	1	TRUE	1	0.2	2		602	580	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849266	76849266	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	67	688	0	ENST00000373344.5:c.6010G>T	p.Asp2004Tyr	p.D2004Y	ENST00000373344	NM_000489.3	2004	Gat/Tat	26/35	1	2	FACETS	0.892	0.774	1	0.892	0.774	1	CLONAL	1	TRUE	1	0.2	2		688	751	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937744	76937744	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	57	516	0	ENST00000373344.5:c.3004G>T	p.Val1002Leu	p.V1002L	ENST00000373344	NM_000489.3	1002	Gta/Tta	9/35	1	2	FACETS	0.852	0.73	0.985	0.852	0.73	0.985	CLONAL	1	TRUE	1	0.2	2		516	669	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123025163	123025163	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	35	517	0	ENST00000355640.3:c.1053T>G	p.Cys351Trp	p.C351W	ENST00000355640		351	tgT/tgG	4/7	1	2	FACETS	0.673	0.551	0.811	0.673	0.551	0.811	SUBCLONAL	1	TRUE	1	0.2	2		517	520	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860058	152860058	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	97	749	0	ENST00000406277.2:c.370C>T	p.Leu124Phe	p.L124F	ENST00000406277	NM_152274.4	124	Ctt/Ttt	5/7	1		FACETS		0.964	1				CLONAL	1	TRUE	1	0.2	2		749	814	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	119	655	0	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.932	0.842	1	0.932	0.842	1	CLONAL	1	TRUE	1	0.376723390326436	2		655	678	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	57	729	4	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.434	0.372	0.502	0.434	0.372	0.502	SUBCLONAL	1	TRUE	1	0.376723390326436	2		733	697	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	134	970	2	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.798	0.724	0.875	0.798	0.724	0.875	SUBCLONAL	1	TRUE	1	0.376723390326436	2		972	892	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216477	108216477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587782558	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	56	238	0	ENST00000278616.4:c.8432del	p.Lys2811SerfsTer46	p.K2811Sfs*46	ENST00000278616	NM_000051.3	2809	cAa/ca	58/63	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.376723390326436	2		238	206	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175836	24175837	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555881563	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	107	679	0	ENST00000263121.7:c.1066_1067del	p.Leu356AspfsTer4	p.L356Dfs*4	ENST00000263121	NM_003073.3	355	aCT/a	8/9	1	2	FACETS	0.732	0.656	0.812	0.732	0.656	0.812	SUBCLONAL	1	TRUE	1	0.376723390326436	2		679	776	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	163	798	3	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.959	0.881	1	0.959	0.881	1	CLONAL	1	TRUE	1	0.376723390326436	2		801	902	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	82	505	0	ENST00000263967.3:c.333G>T	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaT	2/21	1	2	FACETS	0.918	0.813	1	0.918	0.813	1	CLONAL	1	TRUE	1	0.376723390326436	2		505	474	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310914	123310914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	125	479	0	ENST00000358487.5:c.514G>A	p.Ala172Thr	p.A172T	ENST00000358487	NM_000141.4	172	Gcc/Acc	5/18	NA	2	FACETS	1	0.963	1			1	INDETERMINATE	1	TRUE	NA	0.376723390326436	2		479	594	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785964	135785964	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs118203506	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	122	640	2	ENST00000298552.3:c.1257del	p.Arg420GlyfsTer20	p.R420Gfs*20	ENST00000298552	NM_001162426.1	419	ccC/cc	12/23	1	2	FACETS	0.927	0.839	1	0.927	0.839	1	CLONAL	1	TRUE	1	0.376723390326436	2		642	699	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523313	176523313	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	161	744	2	ENST00000292408.4:c.1970C>T	p.Ala657Val	p.A657V	ENST00000292408	NM_213647.1	657	gCg/gTg	15/18	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.376723390326436	2		746	820	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871053	12871053	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	66	349	0	ENST00000228872.4:c.285del	p.Gly97ValfsTer22	p.G97Vfs*22	ENST00000228872	NM_004064.3	94	Ccc/cc	1/3	NA	2	FACETS	0.932	0.813	1			1	INDETERMINATE	1	TRUE	NA	0.376723390326436	2		349	376	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430600	181430600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1372564199	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	109	362	0	ENST00000325404.1:c.452C>T	p.Ala151Val	p.A151V	ENST00000325404	NM_003106.3	151	gCg/gTg	1/1	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.376723390326436	2		362	404	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800902	120800903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs748469666	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	174	872	0	ENST00000257552.2:c.345dup	p.Leu116AlafsTer15	p.L116Afs*15	ENST00000257552	NM_002442.3	115	-/G	6/15	1	2	FACETS	0.882	0.811	0.956	0.882	0.811	0.956	CLONAL	1	TRUE	1	0.376723390326436	2		872	1047	SUCCESS
ALK	238	MSKCC	GRCh37	2	29497965	29497965	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	90	421	0	ENST00000389048.3:c.2041G>T	p.Val681Phe	p.V681F	ENST00000389048	NM_004304.4	681	Gtt/Ttt	11/29	1	2	FACETS	0.971	0.865	1	0.971	0.865	1	CLONAL	1	TRUE	1	0.376723390326436	2		421	492	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106128	27106144	+	frameshift_variant	Frame_Shift_Del	DEL	CATGTTGTCTACTCGGT	CATGTTGTCTACTCGGT	-	novel	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	122	579	0	ENST00000324856.7:c.5740_5756del	p.Met1914Ter	p.M1914*	ENST00000324856	NM_006015.4	1913	gaCATGTTGTCTACTCGGTct/gact	20/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.376723390326436	2		579	600	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106696	27106696	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	102	596	1	ENST00000324856.7:c.6307T>C	p.Phe2103Leu	p.F2103L	ENST00000324856	NM_006015.4	2103	Ttt/Ctt	20/20	1	2	FACETS	0.901	0.808	1	0.901	0.808	1	CLONAL	1	TRUE	1	0.376723390326436	2		597	601	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599271	28599271	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs770146088	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	162	882	0	ENST00000253063.3:c.722del	p.Pro241GlnfsTer6	p.P241Qfs*6	ENST00000253063	NM_031459.4	239	agC/ag	5/10	1	2	FACETS	0.852	0.781	0.926	0.852	0.781	0.926	CLONAL	1	TRUE	1	0.376723390326436	2		882	1010	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798971	45798971	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	127	772	0	ENST00000450313.1:c.374G>T	p.Arg125Met	p.R125M	ENST00000450313	NM_012222.2	125	aGg/aTg	4/16	1	2	FACETS	0.881	0.799	0.968	0.881	0.799	0.968	CLONAL	1	TRUE	1	0.376723390326436	2		772	765	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624271	89624272	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs786204883	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	203	458	0	ENST00000371953.3:c.46dup	p.Tyr16LeufsTer28	p.Y16Lfs*28	ENST00000371953	NM_000314.4	15	-/T	1/9	0.376723390326436	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.376723390326436	2		458	514	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173755	108173755	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	72	362	0	ENST00000278616.4:c.5495A>G	p.Glu1832Gly	p.E1832G	ENST00000278616	NM_000051.3	1832	gAa/gGa	36/63	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.376723390326436	2		362	310	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	464364	464364	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	147	665	0	ENST00000399788.2:c.830T>C	p.Met277Thr	p.M277T	ENST00000399788	NM_001042603.1	277	aTg/aCg	7/28	NA	2	FACETS	0.992	0.906	1			1	INDETERMINATE	1	TRUE	NA	0.376723390326436	2		665	787	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871130	12871131	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	54	267	1	ENST00000228872.4:c.361dup	p.Ala121GlyfsTer4	p.A121Gfs*4	ENST00000228872	NM_004064.3	119	-/G	1/3	NA	2	FACETS	0.949	0.816	1			1	INDETERMINATE	1	TRUE	NA	0.376723390326436	2		268	302	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495721	56495721	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	80	480	0	ENST00000267101.3:c.3911A>G	p.His1304Arg	p.H1304R	ENST00000267101	NM_001982.3	1304	cAt/cGt	28/28	1	2	FACETS	0.911	0.805	1	0.911	0.805	1	CLONAL	1	TRUE	1	0.376723390326436	2		480	466	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68292199	68292199	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	65	353	0	ENST00000487270.1:c.103C>A	p.Pro35Thr	p.P35T	ENST00000487270	NM_133509.3	35	Cca/Aca	3/11	1	2	FACETS	0.786	0.684	0.896	0.786	0.684	0.896	SUBCLONAL	1	TRUE	1	0.376723390326436	2		353	439	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67132659	67132659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	109	695	0	ENST00000412916.2:c.542G>A	p.Gly181Asp	p.G181D	ENST00000412916		181	gGt/gAt	6/6	1	2	FACETS	0.86	0.773	0.952	0.86	0.773	0.952	CLONAL	1	TRUE	1	0.376723390326436	2		695	673	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660554	67660554	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	150	803	0	ENST00000264010.4:c.1454del	p.His485LeufsTer26	p.H485Lfs*26	ENST00000264010	NM_006565.3	485	cAt/ct	8/12	1	2	FACETS	0.91	0.832	0.992	0.91	0.832	0.992	CLONAL	1	TRUE	1	0.376723390326436	2		803	875	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89839686	89839686	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	116	549	0	ENST00000389301.3:c.2007G>T	p.Gln669His	p.Q669H	ENST00000389301	NM_000135.2	669	caG/caT	22/43	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.376723390326436	2		549	595	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353965	15353965	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	28	253	0	ENST00000263377.2:c.2915A>T	p.Gln972Leu	p.Q972L	ENST00000263377	NM_058243.2	972	cAg/cTg	14/20	1	2	FACETS	0.688	0.553	0.84	0.688	0.553	0.84	SUBCLONAL	1	TRUE	1	0.376723390326436	2		253	216	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354052	15354052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753396296	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	78	587	0	ENST00000263377.2:c.2828C>T	p.Pro943Leu	p.P943L	ENST00000263377	NM_058243.2	943	cCg/cTg	14/20	1	2	FACETS	0.771	0.679	0.87	0.771	0.679	0.87	SUBCLONAL	1	TRUE	1	0.376723390326436	2		587	537	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273104	18273105	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	132	792	0	ENST00000222254.8:c.1000dup	p.Asp334GlyfsTer26	p.D334Gfs*26	ENST00000222254	NM_005027.3	332	tgg/tGgg	8/16	1	2	FACETS	0.868	0.789	0.952	0.868	0.789	0.952	CLONAL	1	TRUE	1	0.376723390326436	2		792	807	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026525	48026525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41295268	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	72	534	1	ENST00000234420.5:c.1403G>A	p.Arg468His	p.R468H	ENST00000234420	NM_000179.2	468	cGt/cAt	4/10	1	2	FACETS	0.729	0.638	0.827	0.729	0.638	0.827	SUBCLONAL	1	TRUE	1	0.376723390326436	2		535	524	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180427	38180427	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	75	546	0	ENST00000396334.3:c.275A>G	p.Gln92Arg	p.Q92R	ENST00000396334	NM_002468.4	92	cAg/cGg	1/5	1	2	FACETS	0.79	0.694	0.893	0.79	0.694	0.893	SUBCLONAL	1	TRUE	1	0.376723390326436	2		546	504	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664900	138664900	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	70	254	1	ENST00000330315.3:c.665C>T	p.Ala222Val	p.A222V	ENST00000330315	NM_023067.3	222	gCa/gTa	1/1	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.376723390326436	2		255	269	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590421	67590421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	49	373	0	ENST00000274335.5:c.1483G>A	p.Glu495Lys	p.E495K	ENST00000274335		495	Gaa/Aaa	11/15	1	2	FACETS	0.593	0.502	0.691	0.593	0.502	0.691	SUBCLONAL	1	TRUE	1	0.376723390326436	2		373	439	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771165	161771165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748955949	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	143	702	2	ENST00000366898.1:c.1364G>A	p.Arg455His	p.R455H	ENST00000366898	NM_004562.2	455	cGc/cAc	12/12	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.376723390326436	2		704	703	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878937	117878938	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	90	424	0	ENST00000297338.2:c.31dup	p.Arg11LysfsTer15	p.R11Kfs*15	ENST00000297338	NM_006265.2	11	aga/aAga	2/14	0.376723390326436	2	FACETS	0.983	0.876	1	0.492	0.438	0.549	CLONAL	1	TRUE	0	0.376723390326436	2		424	486	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141557684	141557684	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1382352330	NA	P-0019650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	137	786	0	ENST00000220592.5:c.1631C>T	p.Thr544Met	p.T544M	ENST00000220592	NM_012154.3	544	aCg/aTg	13/19	0.376723390326436	2	FACETS	0.803	0.73	0.88	0.401	0.365	0.44	CLONAL	1	TRUE	0	0.376723390326436	2		786	906	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226905	2226905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780394086	NA	P-0019653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	87	338	0	ENST00000398665.3:c.4385G>A	p.Arg1462Gln	p.R1462Q	ENST00000398665	NM_032482.2	1462	cGg/cAg	27/28	0.474381394686993	2	FACETS	0.698	0.622	0.777	0.349	0.311	0.389	SUBCLONAL	1	TRUE	0	0.681266557223832	2		338	366	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719573	61719573	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	133	601	0	ENST00000401558.2:c.1610A>G	p.Lys537Arg	p.K537R	ENST00000401558	NM_003400.3	537	aAa/aGa	15/25	0.239718921885276	3	FACETS	1	0.97	1	0.377	0.344	0.41	INDETERMINATE	1	TRUE	0	0.681266557223832	3		601	463	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277507	142277507	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	49	610	0	ENST00000350721.4:c.1844C>G	p.Ala615Gly	p.A615G	ENST00000350721	NM_001184.3	615	gCt/gGt	8/47	0.2909538306928	2	FACETS	0.338	0.287	0.395	0.169	0.143	0.198	INDETERMINATE	1	TRUE	0	0.681266557223832	2		610	425	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376062	8376062	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	159	382	0	ENST00000356435.5:c.4535G>A	p.Arg1512Lys	p.R1512K	ENST00000356435		1512	aGa/aAa	28/35	0.206952656086542	3	FACETS	0.817	0.759	0.876			1	INDETERMINATE	2	TRUE	NA	0.681266557223832	3		382	383	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0019654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	837	680	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.55137226714287	4	FACETS	0.95	0.926	0.973			1	CLONAL	3	TRUE	NA	0.810166307650584	4		680	1313	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249510	153249510	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1157879635	NA	P-0019654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	297	556	0	ENST00000281708.4:c.1268G>T	p.Gly423Val	p.G423V	ENST00000281708	NM_033632.3	423	gGa/gTa	9/12	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.810166307650584	2		556	729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576883	7576883	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	559	684	0	ENST00000269305.4:c.963del	p.Lys321AsnfsTer24	p.K321Nfs*24	ENST00000269305	NM_001126112.2	321	aaA/aa	9/11	0.794990539869657	2	FACETS	0.965	0.942	0.987	0.965	0.942	0.987	CLONAL	2	TRUE	0	0.810166307650584	2		684	715	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185169	123185169	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	194	524	0	ENST00000218089.9:c.1121G>A	p.Arg374Lys	p.R374K	ENST00000218089	NM_001042749.1	374	aGa/aAa	13/35	1	2	FACETS	0.754	0.701	0.808	0.754	0.701	0.808	SUBCLONAL	1	TRUE	1	0.810166307650584	2		524	635	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763453	41763453	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1444915408	NA	P-0019654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	509	777	3	ENST00000301178.4:c.2252C>T	p.Pro751Leu	p.P751L	ENST00000301178	NM_021913.4	751	cCg/cTg	19/20	0.361846945551932	3	FACETS	0.835	0.803	0.867	0.835	0.803	0.867	INDETERMINATE	2	TRUE	1	0.810166307650584	3		780	1057	SUCCESS
AR	367	MSKCC	GRCh37	X	66765992	66765992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	95	913	1	ENST00000374690.3:c.1004G>A	p.Ser335Asn	p.S335N	ENST00000374690	NM_000044.3	335	aGc/aAc	1/8	1	2	FACETS	0.199	0.176	0.223	0.199	0.176	0.223	SUBCLONAL	1	TRUE	1	0.810166307650584	2		914	1181	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0019656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	125	895	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.321161871458319	3	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.321161871458319	3		895	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578505	7578505	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	601	1213	0	ENST00000269305.4:c.425del	p.Pro142LeufsTer28	p.P142Lfs*28	ENST00000269305	NM_001126112.2	142	cCt/ct	5/11	0.307096906077302	3	FACETS	0.915	0.88	0.951	0.915	0.88	0.951	CLONAL	3	TRUE	0	0.321161871458319	3		1213	1582	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479720	67479720	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	164	628	0	ENST00000327367.4:c.1027T>C	p.Phe343Leu	p.F343L	ENST00000327367	NM_005902.3	343	Ttc/Ctc	8/9	0.280824780756477	2	FACETS	0.813	0.749	0.879	0.813	0.749	0.879	CLONAL	2	TRUE	0	0.321161871458319	2		628	628	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0019657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	299	1015	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.264262447408475	2	FACETS	0.766	0.722	0.811	0.766	0.722	0.811	SUBCLONAL	2	TRUE	0	0.382346252927381	2		1015	1021	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974696	21974697	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	273	551	0	ENST00000304494.5:c.130dup	p.Tyr44LeufsTer76	p.Y44Lfs*76	ENST00000304494	NM_000077.4	44	tac/tTac	1/3	0.289397074013153	3	FACETS	1	0.99	1	0.813	0.768	0.859	CLONAL	2	TRUE	0	0.382346252927381	3		551	697	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61724071	61724071	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	144	905	0	ENST00000401558.2:c.831C>A	p.Ser277Arg	p.S277R	ENST00000401558	NM_003400.3	277	agC/agA	10/25	0.262135971065021	3	FACETS	0.928	0.845	1	0.464	0.422	0.507	CLONAL	1	TRUE	1	0.382346252927381	3		905	967	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346058	152346058	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	105	843	0	ENST00000359321.1:c.512C>T	p.Ser171Phe	p.S171F	ENST00000359321	NM_005431.1	171	tCt/tTt	3/3	0.382346252927381	3	FACETS	0.562	0.502	0.626			1	SUBCLONAL	1	TRUE	NA	0.382346252927381	3		843	1164	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005863	69005863	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0019657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	80	783	0	ENST00000288368.4:c.2274T>G	p.Tyr758Ter	p.Y758*	ENST00000288368	NM_024870.2	758	taT/taG	21/40	0.208970565924802	4	FACETS	0.591	0.519	0.669	0.296	0.259	0.335	INDETERMINATE	1	TRUE	2	0.382346252927381	4		783	978	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	72	682	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.94	0.825	1	0.94	0.825	1	CLONAL	1	TRUE	1	0.37	2		682	414	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107047	11107047	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	60	461	0	ENST00000358026.2:c.1752G>T	p.Lys584Asn	p.K584N	ENST00000358026	NM_001128849.1	584	aaG/aaT	10/36	1	2	FACETS	0.785	0.679	0.9	0.785	0.679	0.9	SUBCLONAL	1	TRUE	1	0.37	2		461	413	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	111	942	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.877	0.789	0.97	0.877	0.789	0.97	CLONAL	1	TRUE	1	0.37	2		943	684	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149251	119149251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267606708	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	99	715	0	ENST00000264033.4:c.1259G>A	p.Arg420Gln	p.R420Q	ENST00000264033	NM_005188.3	420	cGa/cAa	9/16	1	2	FACETS	0.796	0.711	0.886	0.796	0.711	0.886	SUBCLONAL	1	TRUE	1	0.37	2		715	672	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692940	89692940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746152219	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	81	749	1	ENST00000371953.3:c.424C>T	p.Arg142Trp	p.R142W	ENST00000371953	NM_000314.4	142	Cgg/Tgg	5/9	1	2	FACETS	0.905	0.8	1	0.905	0.8	1	CLONAL	1	TRUE	1	0.37	2		750	484	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236086	108236086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782292	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	86	678	1	ENST00000278616.4:c.9022C>T	p.Arg3008Cys	p.R3008C	ENST00000278616	NM_000051.3	3008	Cgt/Tgt	63/63	1	2	FACETS	0.775	0.686	0.869	0.775	0.686	0.869	SUBCLONAL	1	TRUE	1	0.37	2		679	600	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	55	400	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.37	2		400	290	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	88	663	2	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.37	2		665	442	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	121	748	4	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	1	2	FACETS	0.878	0.794	0.967	0.878	0.794	0.967	CLONAL	1	TRUE	1	0.37	2		752	745	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	117	656	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.37	2		656	626	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547022	9547022	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs58486349	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	23	263	0	ENST00000353224.5:c.1000G>A	p.Asp334Asn	p.D334N	ENST00000353224	NM_177990.2	334	Gat/Aat	5/10	1	2	FACETS	0.606	0.475	0.757	0.606	0.475	0.757	SUBCLONAL	1	TRUE	1	0.37	2		263	205	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111958593	111958593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555186772	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	89	669	2	ENST00000375549.3:c.65G>A	p.Arg22Gln	p.R22Q	ENST00000375549	NM_003002.3	22	cGa/cAa	2/4	1	2	FACETS	0.825	0.733	0.923	0.825	0.733	0.923	CLONAL	1	TRUE	1	0.37	2		671	583	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171607	36171607	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1569008655	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	51	337	0	ENST00000300305.3:c.958C>T	p.Arg320Ter	p.R320*	ENST00000300305		320	Cga/Tga	7/8	1	2	FACETS	0.751	0.641	0.871	0.751	0.641	0.871	SUBCLONAL	1	TRUE	1	0.37	2		337	367	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941657	48941657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1060503077	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	59	527	0	ENST00000267163.4:c.967G>T	p.Glu323Ter	p.E323*	ENST00000267163	NM_000321.2	323	Gaa/Taa	10/27	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.37	2		527	299	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692919	89692919	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782360	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	82	747	0	ENST00000371953.3:c.403A>G	p.Ile135Val	p.I135V	ENST00000371953	NM_000314.4	135	Ata/Gta	5/9	1	2	FACETS	0.985	0.872	1	0.985	0.872	1	CLONAL	1	TRUE	1	0.37	2		747	450	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89815155	89815155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376089640	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	140	798	2	ENST00000389301.3:c.3260C>T	p.Ser1087Leu	p.S1087L	ENST00000389301	NM_000135.2	1087	tCg/tTg	33/43	1	2	FACETS	0.95	0.865	1	0.95	0.865	1	CLONAL	1	TRUE	1	0.37	2		800	797	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922301	178922301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	53	609	0	ENST00000263967.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000263967	NM_006218.2	357	cGa/cAa	6/21	1	2	FACETS	0.796	0.681	0.92	0.796	0.681	0.92	CLONAL	1	TRUE	1	0.37	2		609	360	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894916	101894916	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060502040	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	65	475	0	ENST00000374994.4:c.469C>T	p.Arg157Ter	p.R157*	ENST00000374994	NM_004612.2	157	Cga/Tga	3/9	1	2	FACETS	0.971	0.846	1	0.971	0.846	1	CLONAL	1	TRUE	1	0.37	2		475	362	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915943	127915943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781486938	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	99	742	2	ENST00000373547.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000373547	NM_002721.4	180	Gaa/Aaa	6/7	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.37	2		744	522	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246754	41246754	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	85	664	0	ENST00000357654.3:c.794C>A	p.Ser265Tyr	p.S265Y	ENST00000357654	NM_007294.3	265	tCt/tAt	10/23	1	2	FACETS	0.873	0.774	0.979	0.873	0.774	0.979	CLONAL	1	TRUE	1	0.37	2		664	526	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111048	193111048	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	48	430	0	ENST00000367435.3:c.581G>T	p.Arg194Ile	p.R194I	ENST00000367435	NM_024529.4	194	aGa/aTa	7/17	1	2	FACETS	0.937	0.797	1	0.937	0.797	1	CLONAL	1	TRUE	1	0.37	2		430	277	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494187	140494187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1158980679	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	117	1012	1	ENST00000288602.6:c.1061G>A	p.Arg354Gln	p.R354Q	ENST00000288602	NM_004333.4	354	cGa/cAa	8/18	1	2	FACETS	0.794	0.715	0.876	0.794	0.715	0.876	SUBCLONAL	1	TRUE	1	0.37	2		1013	797	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	84	723	0	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	1	2	FACETS	0.927	0.821	1	0.927	0.821	1	CLONAL	1	TRUE	1	0.37	2		723	490	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646884	23646884	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	102	808	1	ENST00000261584.4:c.983C>A	p.Ser328Tyr	p.S328Y	ENST00000261584	NM_024675.3	328	tCt/tAt	4/13	1	2	FACETS	0.922	0.826	1	0.922	0.826	1	CLONAL	1	TRUE	1	0.37	2		809	598	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259357	89259357	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	81	590	1	ENST00000336596.2:c.501G>T	p.Glu167Asp	p.E167D	ENST00000336596	NM_005233.5	167	gaG/gaT	3/17	1	2	FACETS	0.991	0.877	1	0.991	0.877	1	CLONAL	1	TRUE	1	0.37	2		591	442	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	93	708	1	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	1	2	FACETS	0.976	0.871	1	0.976	0.871	1	CLONAL	1	TRUE	1	0.37	2		709	515	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729551	41729551	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1356119994	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	91	794	0	ENST00000242208.4:c.978C>A	p.Phe326Leu	p.F326L	ENST00000242208	NM_002192.2	326	ttC/ttA	3/3	1	2	FACETS	0.776	0.69	0.868	0.776	0.69	0.868	SUBCLONAL	1	TRUE	1	0.37	2		794	634	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592269	29592269	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	44	273	2	ENST00000356175.3:c.4684G>T	p.Glu1562Ter	p.E1562*	ENST00000356175	NM_000267.3	1562	Gaa/Taa	35/57	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.37	2		275	183	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249857	133249857	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1565972665	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	74	535	0	ENST00000320574.5:c.1366G>C	p.Ala456Pro	p.A456P	ENST00000320574	NM_006231.2	456	Gcc/Ccc	14/49	1	2	FACETS	0.855	0.751	0.966	0.855	0.751	0.966	CLONAL	1	TRUE	1	0.37	2		535	468	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133729585	133729585	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	77	781	0	ENST00000318560.5:c.214T>G	p.Phe72Val	p.F72V	ENST00000318560	NM_005157.4	72	Ttt/Gtt	2/11	1	2	FACETS	0.679	0.596	0.768	0.679	0.596	0.768	SUBCLONAL	1	TRUE	1	0.37	2		781	613	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62309650	62309650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753838163	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	79	620	0	ENST00000360203.5:c.988G>A	p.Asp330Asn	p.D330N	ENST00000360203	NM_001283009.1	330	Gat/Aat	12/35	1	2	FACETS	0.723	0.636	0.815	0.723	0.636	0.815	SUBCLONAL	1	TRUE	1	0.37	2		620	591	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199821	138199821	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	81	723	0	ENST00000237289.4:c.1239G>T	p.Lys413Asn	p.K413N	ENST00000237289	NM_001270507.1	413	aaG/aaT	7/9	1	2	FACETS	0.677	0.596	0.763	0.677	0.596	0.763	SUBCLONAL	1	TRUE	1	0.37	2		723	647	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020225	123020225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	79	779	2	ENST00000355640.3:c.713G>A	p.Arg238Gln	p.R238Q	ENST00000355640		238	cGa/cAa	2/7	1	2	FACETS	0.776	0.684	0.875	0.776	0.684	0.875	SUBCLONAL	1	TRUE	1	0.37	2		781	550	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039158	49039158	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	37	470	0	ENST00000267163.4:c.2236G>T	p.Glu746Ter	p.E746*	ENST00000267163	NM_000321.2	746	Gaa/Taa	22/27	1	2	FACETS	0.576	0.476	0.688	0.576	0.476	0.688	SUBCLONAL	1	TRUE	1	0.37	2		470	347	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480484	57480484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11554274	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	39	421	1	ENST00000371085.3:c.479G>A	p.Arg160His	p.R160H	ENST00000371085	NM_000516.4	160	cGt/cAt	6/13	1	2	FACETS	0.502	0.416	0.597	0.502	0.416	0.597	SUBCLONAL	1	TRUE	1	0.37	2		422	420	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818219	43818219	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	86	674	2	ENST00000372470.3:c.1684G>T	p.Glu562Ter	p.E562*	ENST00000372470	NM_005373.2	562	Gaa/Taa	12/12	1	2	FACETS	0.858	0.76	0.961	0.858	0.76	0.961	CLONAL	1	TRUE	1	0.37	2		676	542	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741930	162741930	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	82	531	1	ENST00000367921.3:c.1621C>T	p.Pro541Ser	p.P541S	ENST00000367921	NM_006182.2	541	Cct/Tct	13/18	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.37	2		532	430	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663891	241663891	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	80	501	0	ENST00000366560.3:c.1237-1G>T		p.X413_splice	ENST00000366560	NM_000143.3	413			1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.37	2		501	381	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716178	243716178	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	64	1021	0	ENST00000263826.5:c.1016T>G	p.Met339Arg	p.M339R	ENST00000263826	NM_005465.4	339	aTg/aGg	10/13	1	2	FACETS	0.621	0.538	0.711	0.621	0.538	0.711	SUBCLONAL	1	TRUE	1	0.37	2		1021	557	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800939	243800939	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	63	661	1	ENST00000263826.5:c.535C>A	p.Leu179Met	p.L179M	ENST00000263826	NM_005465.4	179	Ctg/Atg	5/13	1	2	FACETS	0.788	0.684	0.901	0.788	0.684	0.901	CLONAL	1	TRUE	1	0.37	2		662	432	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246091297	246091297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758081490	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	66	685	1	ENST00000388985.4:c.638C>T	p.Ser213Leu	p.S213L	ENST00000388985		213	tCg/tTg	7/12	1	2	FACETS	0.518	0.449	0.593	0.518	0.449	0.593	SUBCLONAL	1	TRUE	1	0.37	2		686	689	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333555	70333555	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	86	639	0	ENST00000373644.4:c.1460C>A	p.Ser487Ter	p.S487*	ENST00000373644	NM_030625.2	487	tCa/tAa	2/12	1	2	FACETS	0.919	0.815	1	0.919	0.815	1	CLONAL	1	TRUE	1	0.37	2		639	506	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119731	108119731	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	46	408	0	ENST00000278616.4:c.1137T>G	p.Asp379Glu	p.D379E	ENST00000278616	NM_000051.3	379	gaT/gaG	9/63	1	2	FACETS	0.767	0.649	0.897	0.767	0.649	0.897	SUBCLONAL	1	TRUE	1	0.37	2		408	324	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123597	108123597	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	63	632	0	ENST00000278616.4:c.1856A>G	p.Asn619Ser	p.N619S	ENST00000278616	NM_000051.3	619	aAc/aGc	12/63	1	2	FACETS	0.847	0.736	0.967	0.847	0.736	0.967	CLONAL	1	TRUE	1	0.37	2		632	402	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170259	119170259	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs750959492	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	54	426	1	ENST00000264033.4:c.2489G>T	p.Arg830Ile	p.R830I	ENST00000264033	NM_005188.3	830	aGa/aTa	16/16	1	2	FACETS	0.75	0.643	0.867	0.75	0.643	0.867	SUBCLONAL	1	TRUE	1	0.37	2		427	389	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254700	46254700	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	66	600	2	ENST00000334344.6:c.4890G>T	p.Gln1630His	p.Q1630H	ENST00000334344	NM_152641.2	1630	caG/caT	16/21	1	2	FACETS	0.733	0.637	0.835	0.733	0.637	0.835	SUBCLONAL	1	TRUE	1	0.37	2		602	487	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428653	49428653	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	77	893	0	ENST00000301067.7:c.10297A>C	p.Lys3433Gln	p.K3433Q	ENST00000301067	NM_003482.3	3433	Aaa/Caa	35/54	1	2	FACETS	0.608	0.533	0.688	0.608	0.533	0.688	SUBCLONAL	1	TRUE	1	0.37	2		893	685	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144796	58144796	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	80	696	1	ENST00000257904.6:c.432G>T	p.Glu144Asp	p.E144D	ENST00000257904	NM_000075.3	144	gaG/gaT	4/8	1	2	FACETS	0.675	0.594	0.761	0.675	0.594	0.761	SUBCLONAL	1	TRUE	1	0.37	2		697	641	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220022	133220022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761610433	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	56	691	0	ENST00000320574.5:c.4415C>T	p.Ser1472Phe	p.S1472F	ENST00000320574	NM_006231.2	1472	tCt/tTt	34/49	1	2	FACETS	0.543	0.465	0.629	0.543	0.465	0.629	SUBCLONAL	1	TRUE	1	0.37	2		691	557	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245254	133245254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367902268	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	129	949	3	ENST00000320574.5:c.1993C>T	p.Arg665Trp	p.R665W	ENST00000320574	NM_006231.2	665	Cgg/Tgg	18/49	1	2	FACETS	0.841	0.763	0.924	0.841	0.763	0.924	CLONAL	1	TRUE	1	0.37	2		952	829	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26971331	26971331	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	74	598	0	ENST00000381527.3:c.902A>G	p.Lys301Arg	p.K301R	ENST00000381527	NM_001260.1	301	aAa/aGa	9/13	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.37	2		598	348	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622482	28622482	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	73	878	0	ENST00000241453.7:c.1135A>C	p.Ile379Leu	p.I379L	ENST00000241453	NM_004119.2	379	Atc/Ctc	9/24	1	2	FACETS	0.791	0.693	0.895	0.791	0.693	0.895	SUBCLONAL	1	TRUE	1	0.37	2		878	499	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913037	32913037	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1555283835	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	101	911	2	ENST00000380152.3:c.4545G>T	p.Lys1515Asn	p.K1515N	ENST00000380152		1515	aaG/aaT	11/27	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.37	2		913	540	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95593018	95593018	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	76	770	1	ENST00000393063.1:c.802G>T	p.Glu268Ter	p.E268*	ENST00000393063	NM_030621.3	268	Gaa/Taa	8/28	1	2	FACETS	0.851	0.748	0.96	0.851	0.748	0.96	CLONAL	1	TRUE	1	0.37	2		771	483	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95598897	95598897	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	74	651	2	ENST00000393063.1:c.262G>A	p.Asp88Asn	p.D88N	ENST00000393063	NM_030621.3	88	Gac/Aac	4/28	1	2	FACETS	0.924	0.812	1	0.924	0.812	1	CLONAL	1	TRUE	1	0.37	2		653	433	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857930	9857930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs749175723	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	102	746	1	ENST00000330684.3:c.3471C>A	p.Asn1157Lys	p.N1157K	ENST00000330684	NM_001134407.1	1157	aaC/aaA	13/13	1	2	FACETS	0.942	0.845	1	0.942	0.845	1	CLONAL	1	TRUE	1	0.37	2		747	585	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024666	14024666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	88	605	0	ENST00000311895.7:c.892C>T	p.Leu298Phe	p.L298F	ENST00000311895	NM_005236.2	298	Ctc/Ttc	5/11	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.37	2		605	467	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17117004	17117004	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	99	676	0	ENST00000285071.4:c.1705G>T	p.Val569Phe	p.V569F	ENST00000285071	NM_144997.5	569	Gtc/Ttc	14/14	1	2	FACETS	0.835	0.746	0.929	0.835	0.746	0.929	CLONAL	1	TRUE	1	0.37	2		676	641	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37671991	37671991	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	72	685	0	ENST00000447079.4:c.2776C>A	p.Leu926Ile	p.L926I	ENST00000447079	NM_015083.1	926	Ctt/Att	9/14	1	2	FACETS	0.796	0.697	0.902	0.796	0.697	0.902	CLONAL	1	TRUE	1	0.37	2		685	489	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220895	36220895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	37	254	0	ENST00000222270.7:c.4945G>A	p.Ala1649Thr	p.A1649T	ENST00000222270	NM_014727.1	1649	Gcc/Acc	23/37	1	2	FACETS	0.93	0.774	1	0.93	0.774	1	CLONAL	1	TRUE	1	0.37	2		254	215	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639587	47639587	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	86	626	1	ENST00000233146.2:c.680G>T	p.Arg227Ile	p.R227I	ENST00000233146	NM_000251.2	227	aGa/aTa	4/16	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.37	2		627	436	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149666	202149666	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	89	651	0	ENST00000358485.4:c.1107C>A	p.Phe369Leu	p.F369L	ENST00000358485	NM_001080125.1	369	ttC/ttA	8/9	1	2	FACETS	0.856	0.761	0.958	0.856	0.761	0.958	CLONAL	1	TRUE	1	0.37	2		651	562	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209106765	209106765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	120	707	0	ENST00000345146.2:c.803C>T	p.Ala268Val	p.A268V	ENST00000345146	NM_005896.2	268	gCc/gTc	7/10	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.37	2		707	628	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657050	215657050	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781591	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	88	648	1	ENST00000260947.4:c.335G>A	p.Arg112Gln	p.R112Q	ENST00000260947	NM_000465.2	112	cGa/cAa	3/11	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.37	2		649	440	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662932	227662932	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	111	943	3	ENST00000305123.5:c.523C>A	p.Gln175Lys	p.Q175K	ENST00000305123	NM_005544.2	175	Cag/Aag	1/2	1	2	FACETS	0.927	0.835	1	0.927	0.835	1	CLONAL	1	TRUE	1	0.37	2		946	647	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524475	44524475	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	49	459	2	ENST00000291552.4:c.82C>T	p.Arg28Cys	p.R28C	ENST00000291552	NM_006758.2	28	Cgt/Tgt	2/8	1	2	FACETS	0.683	0.58	0.795	0.683	0.58	0.795	SUBCLONAL	1	TRUE	1	0.37	2		461	388	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434118	12434118	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	41	539	0	ENST00000287820.6:c.486C>A	p.Phe162Leu	p.F162L	ENST00000287820	NM_015869.4	162	ttC/ttA	4/7	1	2	FACETS	0.66	0.551	0.779	0.66	0.551	0.779	SUBCLONAL	1	TRUE	1	0.37	2		539	336	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119595322	119595322	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	25	470	1	ENST00000316626.5:c.847G>T	p.Glu283Ter	p.E283*	ENST00000316626		283	Gaa/Taa	8/12	1	2	FACETS	0.408	0.322	0.508	0.408	0.322	0.508	SUBCLONAL	1	TRUE	1	0.37	2		471	331	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261510	142261510	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	76	562	0	ENST00000350721.4:c.3447A>C	p.Lys1149Asn	p.K1149N	ENST00000350721	NM_001184.3	1149	aaA/aaC	17/47	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.37	2		562	384	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139882	55139882	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	42	388	0	ENST00000257290.5:c.1543A>G	p.Lys515Glu	p.K515E	ENST00000257290	NM_006206.4	515	Aag/Gag	10/23	1	2	FACETS	0.599	0.501	0.707	0.599	0.501	0.707	SUBCLONAL	1	TRUE	1	0.37	2		388	379	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956149	55956149	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	79	641	1	ENST00000263923.4:c.3166G>T	p.Asp1056Tyr	p.D1056Y	ENST00000263923	NM_002253.2	1056	Gat/Tat	23/30	1	2	FACETS	0.801	0.706	0.903	0.801	0.706	0.903	CLONAL	1	TRUE	1	0.37	2		642	533	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361242	66361242	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	51	428	0	ENST00000273854.3:c.930C>A	p.Phe310Leu	p.F310L	ENST00000273854	NM_004439.5	310	ttC/ttA	4/18	1	2	FACETS	0.766	0.653	0.888	0.766	0.653	0.888	SUBCLONAL	1	TRUE	1	0.37	2		428	360	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540120	187540120	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	76	586	0	ENST00000441802.2:c.7620T>G	p.Phe2540Leu	p.F2540L	ENST00000441802	NM_005245.3	2540	ttT/ttG	10/27	1	2	FACETS	0.976	0.86	1	0.976	0.86	1	CLONAL	1	TRUE	1	0.37	2		586	421	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542915	187542915	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	70	377	0	ENST00000441802.2:c.4825T>G	p.Ser1609Ala	p.S1609A	ENST00000441802	NM_005245.3	1609	Tct/Gct	10/27	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.37	2		377	353	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043944	180043944	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	64	857	0	ENST00000261937.6:c.3052A>C	p.Ser1018Arg	p.S1018R	ENST00000261937	NM_182925.4	1018	Agc/Cgc	22/30	1	2	FACETS	0.523	0.452	0.599	0.523	0.452	0.599	SUBCLONAL	1	TRUE	1	0.37	2		857	662	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969191	93969191	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	39	491	0	ENST00000369303.4:c.1805T>G	p.Phe602Cys	p.F602C	ENST00000369303	NM_004440.3	602	tTt/tGt	10/17	1	2	FACETS	0.745	0.62	0.882	0.745	0.62	0.882	SUBCLONAL	1	TRUE	1	0.37	2		491	283	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609898	117609898	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	104	826	0	ENST00000368508.3:c.6801G>T	p.Lys2267Asn	p.K2267N	ENST00000368508	NM_002944.2	2267	aaG/aaT	43/43	0.3	1	FACETS	0.886	0.797	0.98	0.886	0.797	0.98	CLONAL	1	TRUE	0	0.37	1		826	517	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527318	137527318	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	103	809	0	ENST00000367739.4:c.328G>T	p.Glu110Ter	p.E110*	ENST00000367739	NM_000416.2	110	Gaa/Taa	3/7	1	2	FACETS	0.977	0.877	1	0.977	0.877	1	CLONAL	1	TRUE	1	0.37	2		809	570	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508759	106508759	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	89	669	0	ENST00000359195.3:c.753G>T	p.Lys251Asn	p.K251N	ENST00000359195	NM_002649.2	251	aaG/aaT	2/11	1	2	FACETS	0.854	0.759	0.956	0.854	0.759	0.956	CLONAL	1	TRUE	1	0.37	2		669	563	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339324	116339324	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	78	562	0	ENST00000397752.3:c.186T>G	p.Ile62Met	p.I62M	ENST00000397752	NM_000245.2	62	atT/atG	2/21	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.37	2		562	411	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90960111	90960111	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	49	330	0	ENST00000265433.3:c.1855G>T	p.Glu619Ter	p.E619*	ENST00000265433	NM_002485.4	619	Gaa/Taa	12/16	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.37	2		330	262	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965561	90965561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	61	608	0	ENST00000265433.3:c.1756G>A	p.Asp586Asn	p.D586N	ENST00000265433	NM_002485.4	586	Gat/Aat	11/16	1	2	FACETS	0.894	0.775	1	0.894	0.775	1	CLONAL	1	TRUE	1	0.37	2		608	369	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932000	39932000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	162	827	1	ENST00000378444.4:c.2599G>A	p.Glu867Lys	p.E867K	ENST00000378444	NM_001123385.1	867	Gaa/Aaa	4/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.37	2		828	723	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413077	63413077	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	152	1054	0	ENST00000330258.3:c.90G>T	p.Lys30Asn	p.K30N	ENST00000330258	NM_152424.3	30	aaG/aaT	2/2	1	2	FACETS	0.936	0.856	1	0.936	0.856	1	CLONAL	1	TRUE	1	0.37	2		1054	878	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70350059	70350059	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	61	538	1	ENST00000374080.3:c.4042C>A	p.Leu1348Ile	p.L1348I	ENST00000374080		1348	Ctc/Atc	28/45	1	2	FACETS	0.715	0.618	0.82	0.715	0.618	0.82	SUBCLONAL	1	TRUE	1	0.37	2		539	461	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352241	70352241	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	78	704	0	ENST00000374080.3:c.4268C>A	p.Ser1423Tyr	p.S1423Y	ENST00000374080		1423	tCt/tAt	31/45	1	2	FACETS	0.705	0.62	0.796	0.705	0.62	0.796	SUBCLONAL	1	TRUE	1	0.37	2		704	598	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890120	76890120	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	28	784	0	ENST00000373344.5:c.4774C>A	p.Leu1592Ile	p.L1592I	ENST00000373344	NM_000489.3	1592	Ctt/Att	17/35	1	2	FACETS	0.294	0.235	0.363	0.294	0.235	0.363	SUBCLONAL	1	TRUE	1	0.37	2		784	514	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938341	76938341	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	76	756	0	ENST00000373344.5:c.2407A>G	p.Ile803Val	p.I803V	ENST00000373344	NM_000489.3	803	Att/Gtt	9/35	1	2	FACETS	0.854	0.751	0.964	0.854	0.751	0.964	CLONAL	1	TRUE	1	0.37	2		756	481	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938460	76938460	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	74	650	1	ENST00000373344.5:c.2288C>T	p.Thr763Ile	p.T763I	ENST00000373344	NM_000489.3	763	aCt/aTt	9/35	1	2	FACETS	0.853	0.749	0.964	0.853	0.749	0.964	CLONAL	1	TRUE	1	0.37	2		651	469	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22405002	22405002	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	10	70	0	ENST00000344548.3:c.31G>A	p.Asp11Asn	p.D11N	ENST00000344548	NM_001039802.1	11	Gat/Aat	3/7	1	2	FACETS	1	0.796	1	1	0.796	1	CLONAL	1	TRUE	1	0.37	2		70	45	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0019659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	892	942	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.624792815975493	9	FACETS	1	0.991	1			1	CLONAL	5	TRUE	NA	0.624792815975493	9		943	1737	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	169	892	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.624792815975493	3	FACETS	1	0.964	1	0.538	0.496	0.581	CLONAL	1	TRUE	1	0.624792815975493	3		892	660	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0019659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	384	933	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.624792815975493	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.624792815975493	2		933	584	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916935	178916935	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	648	819	0	ENST00000263967.3:c.322C>A	p.Arg108Ser	p.R108S	ENST00000263967	NM_006218.2	108	Cgt/Agt	2/21	0.624792815975493	9	FACETS	1	0.991	1			1	CLONAL	5	TRUE	NA	0.624792815975493	9		819	1244	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31468149	31468149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	63	1024	0	ENST00000344624.3:c.2263G>A	p.Asp755Asn	p.D755N	ENST00000344624		755	Gat/Aat	15/33	0.624792815975493	4	FACETS	0.367	0.316	0.422	0.122	0.105	0.141	SUBCLONAL	1	TRUE	1	0.624792815975493	4		1024	893	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0019661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	128	800	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.554772292766188	3	FACETS	0.907	0.847	0.967	0.907	0.847	0.967	CLONAL	3	TRUE	0	0.563142057984133	3		800	214	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469551	25469551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	36	810	0	ENST00000264709.3:c.1217T>C	p.Met406Thr	p.M406T	ENST00000264709	NM_175629.2	406	aTg/aCg	10/23	0.281263178427759	6	FACETS	1	0.876	1	0.269	0.222	0.32	INDETERMINATE	1	TRUE	2	0.563142057984133	6		810	253	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622216	117622216	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	21	683	0	ENST00000368508.3:c.6654C>G	p.Phe2218Leu	p.F2218L	ENST00000368508	NM_002944.2	2218	ttC/ttG	42/43	0.350375075326791	2	FACETS	0.408	0.315	0.513	0.204	0.157	0.257	SUBCLONAL	1	TRUE	0	0.563142057984133	2		683	183	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332415	70332415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1419371452	NA	P-0019662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	213	884	0	ENST00000373644.4:c.320G>A	p.Arg107Gln	p.R107Q	ENST00000373644	NM_030625.2	107	cGa/cAa	2/12	1	2	FACETS	0.98	0.915	1	0.98	0.915	1	CLONAL	1	FALSE	1	0.652689226630902	2		884	666	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533859	533860	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGCTGT	novel	NA	P-0019662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	242	995	1	ENST00000451590.1:c.191_196dup	p.Ser65_Ala66insAspSer	p.S65_A66insDS	ENST00000451590	NM_001130442.1	66	gcc/gACAGCGcc	3/5	0.131681693934114	0	FACETS	0.333	0.312	0.355			1	INDETERMINATE	1	FALSE	0	0.652689226630902	0		996	773	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197177	26197180	+	frameshift_variant	Frame_Shift_Del	DEL	AGGT	AGGT	-	novel	NA	P-0019662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	159	478	0	ENST00000356476.2:c.299_302del	p.Tyr100TrpfsTer18	p.Y100Wfs*18	ENST00000356476		100	tACCTg/tg	1/1	0.54975437200628	4	FACETS	1	0.987	1			1	CLONAL	1	FALSE	NA	0.652689226630902	4		478	589	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836816	151836816	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	204	837	0	ENST00000262189.6:c.14404G>A	p.Gly4802Arg	p.G4802R	ENST00000262189	NM_170606.2	4802	Ggg/Agg	56/59	0.709717745424022	3	FACETS	0.95	0.883	1	0.475	0.441	0.51	CLONAL	1	TRUE	1	0.709717745424022	3		837	820	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28624235	28624235	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	507	743	0	ENST00000241453.7:c.739A>G	p.Ile247Val	p.I247V	ENST00000241453	NM_004119.2	247	Ata/Gta	6/24	0.540253538406988	4	FACETS	0.931	0.898	0.962	0.931	0.898	0.962	CLONAL	3	TRUE	1	0.709717745424022	4		743	875	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115916	8115916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771315353	NA	P-0019669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	101	485	1	ENST00000346208.3:c.1262C>T	p.Pro421Leu	p.P421L	ENST00000346208		421	cCg/cTg	6/6	0.274794263988063	4	FACETS	0.942	0.841	1			1	CLONAL	1	TRUE	NA	0.33677000338711	4		486	851	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498424	89498424	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1176464192	NA	P-0019669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	63	462	1	ENST00000336596.2:c.2396G>A	p.Arg799His	p.R799H	ENST00000336596	NM_005233.5	799	cGc/cAc	14/17	0.309521911651464	1	FACETS	0.761	0.66	0.869	0.761	0.66	0.869	SUBCLONAL	1	TRUE	0	0.33677000338711	1		463	409	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287229	46287229	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	75	537	0	ENST00000334344.6:c.5174C>A	p.Ser1725Ter	p.S1725*	ENST00000334344	NM_152641.2	1725	tCa/tAa	19/21	1	2	FACETS	0.749	0.656	0.848	0.749	0.656	0.848	SUBCLONAL	1	TRUE	1	0.33677000338711	2		537	595	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024001	27024002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0019675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	49	188	1	ENST00000324856.7:c.1113dup	p.Gln372AlafsTer28	p.Q372Afs*28	ENST00000324856	NM_006015.4	369	-/G	1/20	0.242361839510879	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	0	0.271471581270575	2		189	155	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0019675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	103	820	0	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.271471581270575	2		820	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0019675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	110	954	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	1	2	FACETS	0.782	0.701	0.868	0.782	0.701	0.868	SUBCLONAL	1	TRUE	1	0.271471581270575	2		954	1036	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117861187	117861187	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	45	570	0	ENST00000297338.2:c.1702C>T	p.Gln568Ter	p.Q568*	ENST00000297338	NM_006265.2	568	Cag/Tag	13/14	0.271471581270575	3	FACETS	0.77	0.647	0.906	0.385	0.323	0.453	CLONAL	1	TRUE	1	0.271471581270575	3		570	489	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983041	201983054	+	frameshift_variant	Frame_Shift_Del	DEL	ATCGGCATGAAGGC	ATCGGCATGAAGGC	-	novel	NA	P-0019675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	256	1076	0	ENST00000359651.3:c.890_903del	p.Asn297SerfsTer169	p.N297Sfs*169	ENST00000359651		297	aATCGGCATGAAGGC/a	7/8	0.271471581270575	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	0	0.271471581270575	2		1076	939	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298106	123298106	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	42	688	1	ENST00000358487.5:c.748G>A	p.Glu250Lys	p.E250K	ENST00000358487	NM_000141.4	250	Gag/Aag	6/18	0.271471581270575	3	FACETS	0.527	0.439	0.625	0.263	0.219	0.313	SUBCLONAL	1	TRUE	1	0.271471581270575	3		689	667	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248589	8248589	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	73	912	0	ENST00000335790.3:c.298A>G	p.Met100Val	p.M100V	ENST00000335790	NM_002315.2	100	Atg/Gtg	3/4	1	2	FACETS	0.632	0.552	0.719	0.632	0.552	0.719	SUBCLONAL	1	TRUE	1	0.271471581270575	2		912	851	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538978	187538978	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	34	627	0	ENST00000441802.2:c.8762A>T	p.Glu2921Val	p.E2921V	ENST00000441802	NM_005245.3	2921	gAg/gTg	10/27	1	2	FACETS	0.464	0.378	0.561	0.464	0.378	0.561	SUBCLONAL	1	TRUE	1	0.271471581270575	2		627	540	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187560881	187560890	+	frameshift_variant	Frame_Shift_Del	DEL	ATATGTGTTC	ATATGTGTTC	-	novel	NA	P-0019675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	26	605	0	ENST00000441802.2:c.3628_3637del	p.Glu1210Ter	p.E1210*	ENST00000441802	NM_005245.3	1210	GAACACATATta/ta	4/27	1	2	FACETS	0.593	0.47	0.734	0.593	0.47	0.734	SUBCLONAL	1	TRUE	1	0.271471581270575	2		605	323	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249013	55249014	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACCCCC	novel	NA	P-0019676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	139	429	0	ENST00000275493.2:c.2314_2319dup	p.Pro772_His773dup	p.P772_H773dup	ENST00000275493	NM_005228.3	772	aac/aACCCCCac	20/28	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.402385840691341	2		429	623	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981607	101981607	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	66	302	0	ENST00000282441.5:c.28C>T	p.Gln10Ter	p.Q10*	ENST00000282441	NM_001130145.2	10	Caa/Taa	1/9	1	2	FACETS	0.804	0.701	0.915	0.804	0.701	0.915	CLONAL	1	TRUE	1	0.402385840691341	2		302	408	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	137	629	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.832239959903152	1	FACETS	0.467	0.428	0.506	0.467	0.428	0.506	SUBCLONAL	1	TRUE	0	0.832239959903152	1		629	412	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100829	27100829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	234	570	1	ENST00000324856.7:c.4111C>T	p.Arg1371Trp	p.R1371W	ENST00000324856	NM_006015.4	1371	Cgg/Tgg	18/20	0.832239959903152	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.832239959903152	1		571	303	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0019679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	87	440	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.933	0.83	1	0.933	0.83	1	CLONAL	1	TRUE	1	0.402705940911879	2		441	463	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827958	40827958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200990749	NA	P-0019679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	135	512	0	ENST00000373198.4:c.2470G>A	p.Asp824Asn	p.D824N	ENST00000373198	NM_133170.3	824	Gac/Aac	17/32	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.402705940911879	2		512	621	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0019679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	138	804	2	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	1	2	FACETS	0.92	0.838	1	0.92	0.838	1	CLONAL	1	TRUE	1	0.402705940911879	2		806	745	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488222	56488222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	119	590	0	ENST00000267101.3:c.1741G>A	p.Asp581Asn	p.D581N	ENST00000267101	NM_001982.3	581	Gat/Aat	15/28	1	2	FACETS	0.974	0.881	1	0.974	0.881	1	CLONAL	1	TRUE	1	0.402705940911879	2		590	607	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105793	27105793	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	76	514	0	ENST00000324856.7:c.5404G>T	p.Glu1802Ter	p.E1802*	ENST00000324856	NM_006015.4	1802	Gag/Tag	20/20	1	2	FACETS	0.866	0.762	0.976	0.866	0.762	0.976	CLONAL	1	TRUE	1	0.402705940911879	2		514	436	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023176	27023188	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCGCGGAGCCG	CGGCGCGGAGCCG	-	novel	NA	P-0019679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	95	274	0	ENST00000324856.7:c.282_294del	p.Gly95ThrfsTer2	p.G95Tfs*2	ENST00000324856	NM_006015.4	94	ccCGGCGCGGAGCCG/cc	1/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.402705940911879	2		274	356	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88651967	88651967	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	55	570	2	ENST00000372037.3:c.314G>T	p.Gly105Val	p.G105V	ENST00000372037	NM_004329.2	105	gGa/gTa	5/13	1	2	FACETS	0.904	0.779	1	0.904	0.779	1	CLONAL	1	TRUE	1	0.402705940911879	2		572	302	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659609	88659609	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	84	756	0	ENST00000372037.3:c.392A>G	p.Asn131Ser	p.N131S	ENST00000372037	NM_004329.2	131	aAc/aGc	6/13	1	2	FACETS	0.897	0.796	1	0.897	0.796	1	CLONAL	1	TRUE	1	0.402705940911879	2		756	465	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243764	41243766	+	inframe_deletion	In_Frame_Del	DEL	ATA	ATA	-	rs1064793058	NA	P-0019679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	71	607	0	ENST00000357654.3:c.3782_3784del	p.Leu1261del	p.L1261del	ENST00000357654	NM_007294.3	1261	tTATca/tca	10/23	1	2	FACETS	0.966	0.848	1	0.966	0.848	1	CLONAL	1	TRUE	1	0.402705940911879	2		607	365	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271784	15271784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559474673	NA	P-0019679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	225	1044	0	ENST00000263388.2:c.6655G>A	p.Glu2219Lys	p.E2219K	ENST00000263388	NM_000435.2	2219	Gag/Aag	33/33	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.402705940911879	2		1044	1092	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713332	40713342	+	frameshift_variant	Frame_Shift_Del	DEL	CCACAGTACGT	CCACAGTACGT	-	novel	NA	P-0019679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	85	632	0	ENST00000373198.4:c.4173_4183del	p.Arg1392ProfsTer9	p.R1392Pfs*9	ENST00000373198	NM_133170.3	1391	ggACGTACTGTGGtc/ggtc	30/32	1	2	FACETS	0.66	0.583	0.741	0.66	0.583	0.741	SUBCLONAL	1	TRUE	1	0.402705940911879	2		632	640	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686283	117686283	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	59	525	0	ENST00000368508.3:c.3058C>A	p.Pro1020Thr	p.P1020T	ENST00000368508	NM_002944.2	1020	Cct/Act	20/43	1	2	FACETS	0.97	0.841	1	0.97	0.841	1	CLONAL	1	TRUE	1	0.402705940911879	2		525	302	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123022531	123022531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	74	415	0	ENST00000355640.3:c.940G>A	p.Glu314Lys	p.E314K	ENST00000355640		314	Gaa/Aaa	3/7	1	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.402705940911879	1		415	223	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144049	11144051	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0019680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	381	1062	2	ENST00000358026.2:c.3634_3636del	p.Glu1212del	p.E1212del	ENST00000358026	NM_001128849.1	1210	gtGGAg/gtg	26/36	0.284264799903536	1	FACETS	0.891	0.847	0.935	0.891	0.847	0.935	INDETERMINATE	1	TRUE	0	0.559461764236681	1		1064	1101	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094440	27094440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	233	662	1	ENST00000324856.7:c.3148G>A	p.Asp1050Asn	p.D1050N	ENST00000324856	NM_006015.4	1050	Gac/Aac	11/20	0.480993660065117	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.559461764236681	1		663	562	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482870	67482870	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	151	459	0	ENST00000327367.4:c.1274C>G	p.Ser425Cys	p.S425C	ENST00000327367	NM_005902.3	425	tCt/tGt	9/9	0.212717074269792	0	FACETS	0.51	0.47	0.552			1	INDETERMINATE	1	TRUE	0	0.559461764236681	0		459	466	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39607435	39607435	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	198	543	0	ENST00000262039.4:c.1513G>C	p.Asp505His	p.D505H	ENST00000262039	NM_002647.2	505	Gat/Cat	14/25	0.474233143643731	2	FACETS	0.843	0.791	0.894	0.843	0.791	0.894	CLONAL	2	TRUE	0	0.559461764236681	2		543	420	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332708	153332708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138203389	NA	P-0019680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	81	539	0	ENST00000281708.4:c.248G>A	p.Arg83Lys	p.R83K	ENST00000281708	NM_033632.3	83	aGa/aAa	2/12	0.317503493059707	1	FACETS	0.373	0.329	0.42	0.373	0.329	0.42	INDETERMINATE	1	TRUE	0	0.559461764236681	1		539	559	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015177	37015177	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	414	680	0	ENST00000358127.4:c.227G>A	p.Gly76Glu	p.G76E	ENST00000358127	NM_001280556.1	76	gGa/gAa	3/10	0.542642833257802	2	FACETS	0.936	0.898	0.973	0.936	0.898	0.973	CLONAL	2	TRUE	0	0.559461764236681	2		680	791	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	99	553	2	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	0.988	1	0.985	1	CLONAL	2	TRUE	1	0.162796553378001	2		555	685	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0019681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	27	555	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.577	0.458	0.714	0.577	0.458	0.714	SUBCLONAL	1	TRUE	1	0.162796553378001	2		556	575	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0019681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	38	499	2	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.150689527720157	2	FACETS	0.987	0.816	1	0.493	0.408	0.589	CLONAL	1	TRUE	0	0.162796553378001	2		501	473	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11552822	NA	P-0019681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	127	680	0	ENST00000304494.5:c.250G>T	p.Asp84Tyr	p.D84Y	ENST00000304494	NM_000077.4	84	Gac/Tac	2/3	0.150689527720157	2	FACETS	0.88	0.8	0.964	1	0.981	1	CLONAL	3	TRUE	0	0.162796553378001	2		680	591	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045514	47045514	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	58	407	1	ENST00000377604.3:c.2484del	p.Glu829SerfsTer18	p.E829Sfs*18	ENST00000377604	NM_001204468.1	827	atC/at	22/24	1	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.162796553378001	1		408	481	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492882	56492908	+	inframe_deletion	In_Frame_Del	DEL	AGCCATCAGCAGCCAGGGCCAGAGGGC	AGCCATCAGCAGCCAGGGCCAGAGGGC	-	novel	NA	P-0019681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	52	359	0	ENST00000407977.2:c.31_57del	p.Ala11_Ala19del	p.A11_A19del	ENST00000407977		11	GCCCTCTGGCCCTGGCTGCTGATGGCT/-	2/10	0.150689527720157	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	2	TRUE	0	0.162796553378001	2		359	314	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268400	142268400	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	42	696	1	ENST00000350721.4:c.3092A>G	p.Asn1031Ser	p.N1031S	ENST00000350721	NM_001184.3	1031	aAc/aGc	15/47	1	2	FACETS	0.814	0.678	0.965	0.814	0.678	0.965	CLONAL	1	TRUE	1	0.162796553378001	2		697	634	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0019683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	158	918	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.335913885217189	3	FACETS	0.808	0.742	0.876	0.808	0.742	0.876	CLONAL	2	TRUE	1	0.335913885217189	3		918	680	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222987	1222987	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	49	697	1	ENST00000326873.7:c.924G>T	p.Trp308Cys	p.W308C	ENST00000326873	NM_000455.4	308	tgG/tgT	8/10	1	2	FACETS	0.545	0.462	0.637	0.545	0.462	0.637	SUBCLONAL	1	TRUE	1	0.335913885217189	2		698	535	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682363	37682363	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	36	646	0	ENST00000447079.4:c.3554C>G	p.Ala1185Gly	p.A1185G	ENST00000447079	NM_015083.1	1185	gCc/gGc	13/14	1	2	FACETS	0.368	0.302	0.443	0.368	0.302	0.443	SUBCLONAL	1	TRUE	1	0.335913885217189	2		646	582	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748545	43748545	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	67	711	0	ENST00000523873.1:c.499G>T	p.Val167Phe	p.V167F	ENST00000523873		167	Gtt/Ttt	6/8	1	2	FACETS	0.559	0.486	0.64	0.559	0.486	0.64	SUBCLONAL	1	TRUE	1	0.335913885217189	2		711	713	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411558	63411558	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	114	538	0	ENST00000330258.3:c.1609G>C	p.Asp537His	p.D537H	ENST00000330258	NM_152424.3	537	Gac/Cac	2/2	1	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.335913885217189	1		538	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0019684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	87	726	2	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.15	2		728	862	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220698	1220698	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs730881975	NA	P-0019684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	120	875	0	ENST00000326873.7:c.716G>C	p.Trp239Ser	p.W239S	ENST00000326873	NM_000455.4	239	tGg/tCg	5/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.15	2		875	1103	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405382	70405382	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	105	954	0	ENST00000373644.4:c.2896A>T	p.Asn966Tyr	p.N966Y	ENST00000373644	NM_030625.2	966	Aac/Tac	4/12	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.15	2		954	1017	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749219	43749219	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	65	1017	0	ENST00000382044.4:c.1587G>T	p.Gln529His	p.Q529H	ENST00000382044	NM_001141980.1	529	caG/caT	12/28	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.15	2		1017	865	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245808	5245808	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	110	955	1	ENST00000357368.4:c.967G>A	p.Val323Ile	p.V323I	ENST00000357368	NM_002850.3	323	Gtt/Att	10/38	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.15	2		956	1100	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119642254	119642254	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	39	732	1	ENST00000316626.5:c.443G>T	p.Arg148Leu	p.R148L	ENST00000316626		148	cGa/cTa	4/12	1	2	FACETS	0.892	0.738	1	0.892	0.738	1	CLONAL	1	TRUE	1	0.15	2		733	583	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134959989	134959989	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0019684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	40	427	0	ENST00000398015.3:c.2347-1G>A		p.X783_splice	ENST00000398015	NM_004441.4	783			1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.15	2		427	482	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534397	187534397	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	60	637	0	ENST00000441802.2:c.9329G>T	p.Ser3110Ile	p.S3110I	ENST00000441802	NM_005245.3	3110	aGt/aTt	13/27	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.15	2		637	761	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508622	106508622	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	41	499	0	ENST00000359195.3:c.616C>A	p.Pro206Thr	p.P206T	ENST00000359195	NM_002649.2	206	Ccc/Acc	2/11	1	2	FACETS	0.916	0.762	1	0.916	0.762	1	CLONAL	1	TRUE	1	0.15	2		499	597	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829161	128829161	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	38	196	0	ENST00000249373.3:c.169C>A	p.Pro57Thr	p.P57T	ENST00000249373	NM_005631.4	57	Cct/Act	1/12	1	2	FACETS	0.974	0.81	1	1	0.966	1	CLONAL	2	TRUE	1	0.15	2		196	260	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986871	36986883	+	protein_altering_variant	In_Frame_Del	DEL	CCGGTGCCCCCGC	CCGGTGCCCCCGC	G	novel	NA	P-0019684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	212	457	0	ENST00000354822.5:c.806_818delinsC	p.Gly269_Gly273delinsAla	p.G269_G273delinsA	ENST00000354822	NM_001079668.2	269	gGCGGGGGCACCGGg/gCg	3/3	0.261030019574874	4	FACETS	1	0.96	1	1	0.99	1	CLONAL	4	TRUE	1	0.15	4		457	779	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0019685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	194	697	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.569287557258576	1	FACETS	0.999	0.934	1	0.999	0.934	1	CLONAL	1	TRUE	0	0.569287557258576	1		697	488	SUCCESS
APC	324	MSKCC	GRCh37	5	112175182	112175182	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	166	292	0	ENST00000257430.4:c.3892del	p.Ser1298LeufsTer7	p.S1298Lfs*7	ENST00000257430	NM_000038.5	1297	gaT/ga	16/16	0.569287557258576	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	0	0.569287557258576	2		292	289	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142901	30142901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1365924896	NA	P-0019685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	202	989	0	ENST00000389048.3:c.625C>T	p.Arg209Cys	p.R209C	ENST00000389048	NM_004304.4	209	Cgc/Tgc	1/29	1	2	FACETS	0.976	0.908	1	0.976	0.908	1	CLONAL	1	TRUE	1	0.569287557258576	2		989	727	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946453	2946453	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368574818	NA	P-0019685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	162	720	2	ENST00000396946.4:c.3284C>T	p.Thr1095Met	p.T1095M	ENST00000396946	NM_032415.4	1095	aCg/aTg	25/25	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.569287557258576	2		722	543	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508398	106508398	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs762519363	NA	P-0019685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	48	212	1	ENST00000359195.3:c.392G>T	p.Ser131Ile	p.S131I	ENST00000359195	NM_002649.2	131	aGc/aTc	2/11	1	2	FACETS	0.843	0.722	0.973	0.843	0.722	0.973	CLONAL	1	TRUE	1	0.569287557258576	2		213	200	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398278	25398282	+	missense_variant	Missense_Mutation	ONP	ACGCC	ACGCC	CCGCA	novel	NA	P-0019685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	183	718	0	ENST00000311936.3:c.37_41delinsTGCGG	p.Gly13_Val14delinsCysGly	p.G13_V14delinsCG	ENST00000311936	NM_004985.3	13	GGCGTa/TGCGGa	2/5	1	2	FACETS	0.903	0.836	0.972	0.903	0.836	0.972	CLONAL	1	TRUE	1	0.569287557258576	2		718	712	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307893	11307893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1161509979	NA	P-0019686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	28	811	0	ENST00000361445.4:c.1099G>A	p.Glu367Lys	p.E367K	ENST00000361445	NM_004958.3	367	Gag/Aag	7/58	NA	2	FACETS	0.124	0.098	0.153			1	INDETERMINATE	1	TRUE	NA	0.835629727816082	2		811	542	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46736438	46736438	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	188	665	2	ENST00000371975.4:c.1150C>G	p.Leu384Val	p.L384V	ENST00000371975	NM_003579.3	384	Ctc/Gtc	10/18	0.839743446526609	3	FACETS	0.922	0.855	0.991			1	CLONAL	1	TRUE	NA	0.835629727816082	3		667	692	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982421	201982421	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	327	1133	3	ENST00000359651.3:c.800A>G	p.Lys267Arg	p.K267R	ENST00000359651		267	aAg/aGg	6/8	0.664924667184486	5	FACETS	1	0.991	1	0.252	0.237	0.267	CLONAL	1	TRUE	0	0.835629727816082	5		1136	1399	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579363	7579364	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0019686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	1035	913	7	ENST00000269305.4:c.322_323dup	p.Phe109ValfsTer15	p.F109Vfs*15	ENST00000269305	NM_001126112.2	108	ggt/ggGGt	4/11	0.839743446526609	4	FACETS	0.998	0.986	1	0.998	0.986	1	CLONAL	4	TRUE	0	0.835629727816082	4		920	1139	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153693	55153693	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	182	633	2	ENST00000257290.5:c.2659G>T	p.Glu887Ter	p.E887*	ENST00000257290	NM_006206.4	887	Gag/Tag	19/23	0.839743446526609	5	FACETS	1	0.968	1	0.363	0.335	0.393	CLONAL	1	TRUE	2	0.835629727816082	5		635	901	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0019690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	79	852	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.404	0.355	0.458	0.404	0.355	0.458	SUBCLONAL	1	TRUE	1	0.43	2		852	909	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441816	49441816	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	269	895	2	ENST00000301067.7:c.4168del	p.Ala1390GlnfsTer27	p.A1390Qfs*27	ENST00000301067	NM_003482.3	1390	Gca/ca	14/54	0.204000345527002	5	FACETS	1	0.977	1	0.722	0.678	0.767	INDETERMINATE	2	TRUE	2	0.390380722262922	5		897	1009	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	350	870	0	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	0.360725143260824	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.390380722262922	4		870	1175	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088787	27088788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0019691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	219	790	0	ENST00000324856.7:c.2402dup	p.Gln802SerfsTer15	p.Q802Sfs*15	ENST00000324856	NM_006015.4	799	cag/caGg	7/20	0.360725143260824	4	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	2	0.390380722262922	4		790	761	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0019691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	121	425	0	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	0.360725143260824	4	FACETS	1	0.917	1	1	0.917	1	CLONAL	2	TRUE	2	0.390380722262922	4		425	428	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256141	133256141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1250780418	NA	P-0019691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	236	655	1	ENST00000320574.5:c.520G>A	p.Val174Met	p.V174M	ENST00000320574	NM_006231.2	174	Gtg/Atg	6/49	0.204000345527002	5	FACETS	1	0.988	1	0.827	0.774	0.881	INDETERMINATE	2	TRUE	2	0.390380722262922	5		656	773	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56875722	56875722	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768650810	NA	P-0019691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	115	767	0	ENST00000308159.5:c.2326C>T	p.Arg776Ter	p.R776*	ENST00000308159	NM_014669.4	776	Cga/Tga	21/22	0.333842780636024	5	FACETS	1	0.96	1			1	CLONAL	1	TRUE	NA	0.390380722262922	5		767	828	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32189003	32189003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751063545	NA	P-0019691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	153	898	2	ENST00000375023.3:c.551C>T	p.Pro184Leu	p.P184L	ENST00000375023	NM_004557.3	184	cCg/cTg	4/30	0.390380722262922	3	FACETS	1	0.971	1	0.566	0.518	0.617	CLONAL	1	TRUE	1	0.390380722262922	3		900	827	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825519	50825519	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	89	713	2	ENST00000398568.2:c.2156del	p.Asn719MetfsTer13	p.N719Mfs*13	ENST00000398568	NM_001042412.1	717	gAa/ga	14/18	0.333842780636024	5	FACETS	1	0.897	1			1	CLONAL	1	TRUE	NA	0.390380722262922	5		715	714	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223858	36223858	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1244	211	1496	7	ENST00000222270.7:c.6413del	p.Pro2138ArgfsTer15	p.P2138Rfs*15	ENST00000222270	NM_014727.1	2136	ctC/ct	28/37	0.390380722262922	3	FACETS	0.888	0.822	0.956			1	CLONAL	1	TRUE	NA	0.390380722262922	3		1503	1455	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6442013	6442013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	93	451	0	ENST00000356142.4:c.572C>T	p.Ala191Val	p.A191V	ENST00000356142	NM_018890.3	191	gCg/gTg	7/7	0.204000345527002	5	FACETS	0.944	0.845	1	0.63	0.563	0.699	INDETERMINATE	2	TRUE	2	0.390380722262922	5		451	400	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11308135	11308135	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	177	711	0	ENST00000361445.4:c.857T>C	p.Met286Thr	p.M286T	ENST00000361445	NM_004958.3	286	aTg/aCg	7/58	0.360725143260824	4	FACETS	0.91	0.841	0.981	0.91	0.841	0.981	CLONAL	2	TRUE	2	0.390380722262922	4		711	693	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17354273	17354293	+	inframe_deletion	In_Frame_Del	DEL	GATACTGCTGCTTGCCTTCCT	GATACTGCTGCTTGCCTTCCT	-	novel	NA	P-0019691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	98	652	0	ENST00000375499.3:c.491_511del	p.Gln164_Tyr170del	p.Q164_Y170del	ENST00000375499	NM_003000.2	164	cAGGAAGGCAAGCAGCAGTATCtg/ctg	5/8	0.360725143260824	4	FACETS	1	0.955	1	0.565	0.505	0.629	CLONAL	1	TRUE	2	0.390380722262922	4		652	618	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459274	120459274	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	85	594	0	ENST00000256646.2:c.6071A>G	p.Glu2024Gly	p.E2024G	ENST00000256646	NM_024408.3	2024	gAa/gGa	34/34	0.360725143260824	4	FACETS	0.963	0.852	1	0.481	0.426	0.541	CLONAL	1	TRUE	2	0.390380722262922	4		594	629	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120611990	120611990	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	10	100	0	ENST00000256646.2:c.31del	p.Ala11ArgfsTer26	p.A11Rfs*26	ENST00000256646	NM_024408.3	11	Gcg/cg	1/34	0.360725143260824	4	FACETS	0.52	0.353	0.727	0.26	0.176	0.364	SUBCLONAL	1	TRUE	2	0.390380722262922	4		100	137	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450838	70450838	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	85	507	1	ENST00000373644.4:c.5678C>T	p.Ala1893Val	p.A1893V	ENST00000373644	NM_030625.2	1893	gCa/gTa	12/12	0.387174044789998	3	FACETS	1	0.918	1	0.522	0.462	0.585	CLONAL	1	TRUE	1	0.390380722262922	3		508	499	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631120	69631120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	269	1081	0	ENST00000334134.2:c.292G>A	p.Ala98Thr	p.A98T	ENST00000334134	NM_005247.2	98	Gcc/Acc	2/3	0.360725143260824	4	FACETS	0.914	0.858	0.972	0.914	0.858	0.972	CLONAL	2	TRUE	2	0.390380722262922	4		1081	1048	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480402	50480402	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0019691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	101	807	0	ENST00000394963.4:c.366-2A>G		p.X122_splice	ENST00000394963	NM_003076.4	122			0.204000345527002	5	FACETS	1	0.931	1	0.352	0.314	0.392	INDETERMINATE	1	TRUE	2	0.390380722262922	5		807	778	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536878	120536878	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	149	1042	0	ENST00000229340.5:c.308T>G	p.Leu103Arg	p.L103R	ENST00000229340	NM_006861.6	103	cTt/cGt	4/6	0.204000345527002	5	FACETS	1	0.973	1	0.388	0.354	0.424	INDETERMINATE	1	TRUE	2	0.390380722262922	5		1042	1039	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068249	30068249	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	171	608	0	ENST00000331968.5:c.2150C>T	p.Ala717Val	p.A717V	ENST00000331968	NM_002742.2	717	gCt/gTt	15/18	0.390380722262922	4	FACETS	0.93	0.859	1	0.93	0.859	1	CLONAL	2	TRUE	2	0.390380722262922	4		608	655	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844173	68844173	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	407	956	0	ENST00000261769.5:c.761A>T	p.Asp254Val	p.D254V	ENST00000261769	NM_004360.3	254	gAt/gTt	6/16	0.36657739939999	3	FACETS	0.965	0.924	1	0.965	0.924	1	CLONAL	3	TRUE	0	0.390380722262922	3		956	861	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993075	72993075	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	319	1109	2	ENST00000268489.5:c.970G>A	p.Ala324Thr	p.A324T	ENST00000268489	NM_006885.3	324	Gct/Act	2/10	0.36657739939999	3	FACETS	0.972	0.919	1	0.648	0.612	0.684	CLONAL	2	TRUE	0	0.390380722262922	3		1111	1005	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486068	29486068	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	151	663	0	ENST00000356175.3:c.245C>G	p.Ser82Cys	p.S82C	ENST00000356175	NM_000267.3	82	tCt/tGt	3/57	0.390380722262922	5	FACETS	0.997	0.915	1			1	CLONAL	2	TRUE	NA	0.390380722262922	5		663	615	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46587791	46587791	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	77	616	0	ENST00000263734.3:c.475del	p.Ser159AlafsTer12	p.S159Afs*12	ENST00000263734	NM_001430.4	157	Aaa/aa	5/16	0.387174044789998	3	FACETS	0.777	0.682	0.878	0.388	0.341	0.439	SUBCLONAL	1	TRUE	1	0.390380722262922	3		616	607	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794967	242794967	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1380350073	NA	P-0019691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	380	1237	2	ENST00000334409.5:c.242C>T	p.Ala81Val	p.A81V	ENST00000334409	NM_005018.2	81	gCc/gTc	2/5	0.390380722262922	5	FACETS	1	0.981	1	0.714	0.676	0.751	CLONAL	2	TRUE	2	0.390380722262922	5		1239	1442	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292787	62292787	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	77	622	0	ENST00000360203.5:c.239T>C	p.Leu80Pro	p.L80P	ENST00000360203	NM_001283009.1	80	cTt/cCt	3/35	0.390380722262922	6	FACETS	0.861	0.755	0.976	0.215	0.188	0.244	CLONAL	1	TRUE	2	0.390380722262922	6		622	816	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722296	49722297	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs1559647379	NA	P-0019691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	67	283	0	ENST00000449682.2:c.1643_1644del	p.Tyr548Ter	p.Y548*	ENST00000449682	NM_020998.3	548	tAT/t	15/18	0.390380722262922	2	FACETS	1	0.973	1	0.718	0.632	0.808	CLONAL	1	TRUE	0	0.390380722262922	2		283	239	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620657	52620657	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	173	688	2	ENST00000394830.3:c.3096del	p.Phe1032LeufsTer102	p.F1032Lfs*102	ENST00000394830	NM_018313.4	1032	ttT/tt	21/30	0.390380722262922	2	FACETS	0.903	0.838	0.969	0.903	0.838	0.969	CLONAL	2	TRUE	0	0.390380722262922	2		690	491	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294259	1294259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	346	1119	1	ENST00000310581.5:c.742C>T	p.Arg248Trp	p.R248W	ENST00000310581	NM_198253.2	248	Cgg/Tgg	2/16	0.390380722262922	4	FACETS	1	0.985	1	0.549	0.52	0.579	CLONAL	2	TRUE	0	0.390380722262922	4		1120	1122	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554990	106554990	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	196	662	0	ENST00000369096.4:c.2107A>G	p.Lys703Glu	p.K703E	ENST00000369096	NM_001198.3	703	Aag/Gag	7/7	0.387174044789998	3	FACETS	0.941	0.875	1	0.941	0.875	1	CLONAL	2	TRUE	1	0.390380722262922	3		662	638	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873336	151873336	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	62	410	0	ENST00000262189.6:c.9202C>T	p.Gln3068Ter	p.Q3068*	ENST00000262189	NM_170606.2	3068	Cag/Tag	38/59	0.390380722262922	5	FACETS	0.972	0.841	1	0.324	0.28	0.372	CLONAL	1	TRUE	2	0.390380722262922	5		410	518	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737557	145737557	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752847936	NA	P-0019691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	166	968	2	ENST00000428558.2:c.3206G>A	p.Arg1069His	p.R1069H	ENST00000428558	NM_004260.3	1069	cGt/cAt	19/22	0.360725143260824	4	FACETS	1	0.978	1	0.594	0.545	0.645	CLONAL	1	TRUE	2	0.390380722262922	4		970	995	SUCCESS
AR	367	MSKCC	GRCh37	X	66765102	66765102	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	224	481	0	ENST00000374690.3:c.117del	p.Arg40GlyfsTer135	p.R40Gfs*135	ENST00000374690	NM_000044.3	38	ggC/gg	1/8	0.390380722262922	3	FACETS	1	0.986	1			1	CLONAL	2	TRUE	NA	0.390380722262922	3		481	583	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599122	28599122	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	99	1066	0	ENST00000253063.3:c.568T>C	p.Ser190Pro	p.S190P	ENST00000253063	NM_031459.4	190	Tcc/Ccc	5/10	1	2	FACETS	0.576	0.514	0.642	0.576	0.514	0.642	SUBCLONAL	1	TRUE	1	0.434987425365373	2		1066	790	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0019694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	245	918	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.3	6	FACETS	1	0.948	1	0.762	0.712	0.814	CLONAL	3	TRUE	2	0.22	6		918	1052	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031919	26031919	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1270004025	NA	P-0019695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	65	409	0	ENST00000244661.2:c.370G>C	p.Asp124His	p.D124H	ENST00000244661	NM_003537.3	124	Gac/Cac	1/1	0.288933959248878	9	FACETS	0.884	0.767	1			1	CLONAL	2	TRUE	NA	0.288933959248878	9		409	512	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061334	38061334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	49	1189	2	ENST00000250448.2:c.655C>T	p.Arg219Cys	p.R219C	ENST00000250448	NM_004496.3	219	Cgc/Tgc	2/2	0.165975497881877	4	FACETS	0.634	0.535	0.742	0.317	0.267	0.371	INDETERMINATE	1	TRUE	2	0.288933959248878	4		1191	690	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872045	37872045	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200497646	NA	P-0019695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	55	1259	0	ENST00000269571.5:c.1366C>T	p.Arg456Cys	p.R456C	ENST00000269571		456	Cgc/Tgc	12/27	0.232177542983447	3	FACETS	0.848	0.726	0.981	0.424	0.363	0.491	CLONAL	1	TRUE	1	0.288933959248878	3		1259	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0019696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	408	697	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.382619873795576	3	FACETS	0.902	0.864	0.94	0.902	0.864	0.94	CLONAL	3	TRUE	0	0.43705489624929	3		697	841	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0019696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	542	681	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.43705489624929	6	FACETS	1	0.99	1	0.856	0.825	0.887	CLONAL	4	TRUE	1	0.43705489624929	6		681	1086	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0019696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	244	873	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.43705489624929	6	FACETS	0.859	0.802	0.918	0.344	0.32	0.368	CLONAL	2	TRUE	1	0.43705489624929	6		873	1218	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820012	36820013	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	134	723	0	ENST00000373129.3:c.575dup	p.Asn192LysfsTer65	p.N192Kfs*65	ENST00000373129	NM_032017.1	192	aat/aaAt	7/12	0.194331084579984	5	FACETS	1	0.936	1	0.346	0.314	0.38	INDETERMINATE	1	TRUE	2	0.43705489624929	5		723	977	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120791129	120791129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375034852	NA	P-0019696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	173	952	0	ENST00000257552.2:c.706G>A	p.Ala236Thr	p.A236T	ENST00000257552	NM_002442.3	236	Gcc/Acc	10/15	NA	2	FACETS	0.836	0.769	0.906			1	INDETERMINATE	1	TRUE	NA	0.43705489624929	2		952	947	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	139	736	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.816	0.746	0.889	0.816	0.746	0.889	CLONAL	1	TRUE	1	0.58754230489327	2		736	580	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0019697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	692	640	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.58754230489327	5	FACETS	0.986	0.958	1			1	CLONAL	4	TRUE	NA	0.58754230489327	5		640	1124	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873660	35873660	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs201559094	NA	P-0019697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	114	460	1	ENST00000303115.3:c.616C>T	p.Arg206Ter	p.R206*	ENST00000303115	NM_002185.3	206	Cga/Tga	5/8	1	2	FACETS	0.946	0.859	1	0.946	0.859	1	CLONAL	1	TRUE	1	0.58754230489327	2		461	410	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0019697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	379	440	1	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	0.587041575292591	4	FACETS	0.955	0.915	0.995	0.955	0.915	0.995	CLONAL	3	TRUE	1	0.58754230489327	4		441	715	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138362	37138362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	493	1014	3	ENST00000373509.5:c.11C>T	p.Ser4Phe	p.S4F	ENST00000373509	NM_002648.3	4	tCc/tTc	1/6	0.498835333641533	4	FACETS	0.982	0.94	1	0.982	0.94	1	CLONAL	2	TRUE	2	0.58754230489327	4		1017	1357	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625110	69625110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782454437	NA	P-0019697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	398	926	0	ENST00000334134.2:c.683C>T	p.Ser228Leu	p.S228L	ENST00000334134	NM_005247.2	228	tCg/tTg	3/3	0.56767151968444	3	FACETS	0.986	0.942	1	0.986	0.942	1	CLONAL	2	TRUE	1	0.58754230489327	3		926	889	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118355576	118355576	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0019697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	123	609	0	ENST00000534358.1:c.4219-1G>A		p.X1407_splice	ENST00000534358	NM_005933.3	1407			0.56767151968444	3	FACETS	0.783	0.709	0.861	0.391	0.354	0.431	SUBCLONAL	1	TRUE	1	0.58754230489327	3		609	692	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18762516	18762516	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs777720648	NA	P-0019697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	258	755	0	ENST00000266497.5:c.4012T>C	p.Tyr1338His	p.Y1338H	ENST00000266497		1338	Tac/Cac	29/31	0.58754230489327	2	FACETS	0.848	0.803	0.892	0.848	0.803	0.892	CLONAL	2	TRUE	0	0.58754230489327	2		755	518	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857851	9857851	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	188	669	0	ENST00000330684.3:c.3550T>C	p.Tyr1184His	p.Y1184H	ENST00000330684	NM_001134407.1	1184	Tat/Cat	13/13	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.58754230489327	2		669	636	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101847	11101847	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	258	1049	1	ENST00000358026.2:c.1267T>G	p.Cys423Gly	p.C423G	ENST00000358026	NM_001128849.1	423	Tgc/Ggc	8/36	0.56767151968444	3	FACETS	0.925	0.865	0.986	0.462	0.432	0.493	CLONAL	1	TRUE	1	0.58754230489327	3		1050	1229	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39214627	39214627	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	366	788	0	ENST00000402219.2:c.3497C>A	p.Ser1166Tyr	p.S1166Y	ENST00000402219	NM_005633.3	1166	tCt/tAt	22/23	0.571040625180359	3	FACETS	0.851	0.81	0.893	0.567	0.54	0.595	CLONAL	2	TRUE	0	0.58754230489327	3		788	947	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807646	1807646	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	467	1124	1	ENST00000260795.2:c.1815G>A	p.Met605Ile	p.M605I	ENST00000260795		605	atG/atA	12/17	0.58754230489327	2	FACETS	0.923	0.889	0.958	0.923	0.889	0.958	CLONAL	2	TRUE	0	0.58754230489327	2		1125	861	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636916	176636916	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	224	769	0	ENST00000439151.2:c.1516C>T	p.Pro506Ser	p.P506S	ENST00000439151	NM_022455.4	506	Cca/Tca	5/23	1	2	FACETS	0.939	0.877	1	0.939	0.877	1	CLONAL	1	TRUE	1	0.58754230489327	2		769	812	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710789	117710789	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	151	478	0	ENST00000368508.3:c.1483C>T	p.Pro495Ser	p.P495S	ENST00000368508	NM_002944.2	495	Ccc/Tcc	12/43	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.58754230489327	2		478	489	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459478	50459478	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	125	538	0	ENST00000331340.3:c.767T>C	p.Ile256Thr	p.I256T	ENST00000331340	NM_006060.4	256	aTa/aCa	7/8	0.58754230489327	4	FACETS	0.801	0.725	0.882	0.267	0.241	0.294	CLONAL	1	TRUE	1	0.58754230489327	4		538	843	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0019700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	168	918	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.166892470667821	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.14	3		918	1109	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0019700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	19	1015	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.3	1	FACETS	0.31	0.234	0.401	0.31	0.234	0.401	SUBCLONAL	1	TRUE	0	0.14	1		1017	813	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483916	88483916	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	66	920	1	ENST00000360948.2:c.1654G>T	p.Val552Phe	p.V552F	ENST00000360948	NM_001012338.2	552	Gtc/Ttc	14/19	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.14	2		921	775	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998684	100998685	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0019700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	121	1339	1	ENST00000325455.5:c.1117_1118delinsAA	p.Ala373Lys	p.A373K	ENST00000325455	NM_001202474.3	373	GCg/AAg	1/8	0.166892470667821	3	FACETS	0.772	0.695	0.853	0.772	0.695	0.853	SUBCLONAL	2	TRUE	1	0.14	3		1340	1198	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186743	108186743	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	66	697	0	ENST00000278616.4:c.6101G>C	p.Arg2034Pro	p.R2034P	ENST00000278616	NM_000051.3	2034	cGa/cCa	42/63	0.166892470667821	3	FACETS	1	0.949	1	0.601	0.521	0.689	CLONAL	1	TRUE	1	0.14	3		697	839	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900750	32900750	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	90	601	0	ENST00000380152.3:c.631G>T	p.Val211Phe	p.V211F	ENST00000380152		211	Gtc/Ttc	7/27	0.166892470667821	3	FACETS	0.892	0.791	1	0.892	0.791	1	CLONAL	2	TRUE	1	0.14	3		601	771	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988957	41988957	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	116	878	0	ENST00000219905.7:c.1751del	p.Gly584AlafsTer16	p.G584Afs*16	ENST00000219905	NM_001164273.1	583	ttG/tt	3/24	0.3	1	FACETS	1	0.936	1	1	0.989	1	CLONAL	2	TRUE	0	0.14	1		878	734	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554705	63554705	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	83	527	0	ENST00000307078.5:c.34G>T	p.Asp12Tyr	p.D12Y	ENST00000307078	NM_004655.3	12	Gac/Tac	2/11	1	2	FACETS	0.966	0.858	1	1	0.988	1	CLONAL	3	TRUE	1	0.14	2		527	409	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905055	50905055	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	56	729	2	ENST00000440232.2:c.337G>T	p.Gly113Trp	p.G113W	ENST00000440232	NM_002691.3	113	Ggg/Tgg	4/27	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.14	2		731	543	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662617	227662617	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs374471017	NA	P-0019700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	35	628	0	ENST00000305123.5:c.838A>G	p.Ile280Val	p.I280V	ENST00000305123	NM_005544.2	280	Atc/Gtc	1/2	1	2	FACETS	0.873	0.714	1	0.873	0.714	1	CLONAL	1	TRUE	1	0.14	2		628	573	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012603	36012603	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	30	762	0	ENST00000358208.4:c.47G>T	p.Arg16Leu	p.R16L	ENST00000358208		16	cGc/cTc	2/12	1	2	FACETS	0.755	0.606	0.923	0.755	0.606	0.923	CLONAL	1	TRUE	1	0.14	2		762	568	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589831	55589831	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	88	608	0	ENST00000288135.5:c.1313T>G	p.Ile438Arg	p.I438R	ENST00000288135	NM_000222.2	438	aTa/aGa	8/21	1	2	FACETS	0.899	0.797	1	1	0.983	1	CLONAL	2	TRUE	1	0.14	2		608	699	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361262	66361262	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0019700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	27	346	0	ENST00000273854.3:c.911-1G>A		p.X304_splice	ENST00000273854	NM_004439.5	304			1	2	FACETS	0.95	0.756	1	0.95	0.756	1	CLONAL	1	TRUE	1	0.14	2		346	406	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143181675	143181675	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	104	860	0	ENST00000262992.4:c.658G>C	p.Gly220Arg	p.G220R	ENST00000262992	NM_001101669.1	220	Gga/Cga	9/24	0.166892470667821	3	FACETS	1	0.98	1	0.731	0.653	0.815	CLONAL	1	TRUE	1	0.14	3		860	1087	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629556	187629556	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	116	826	0	ENST00000441802.2:c.1426G>T	p.Val476Leu	p.V476L	ENST00000441802	NM_005245.3	476	Gtg/Ttg	2/27	NA	2	FACETS	0.975	0.878	1			1	INDETERMINATE	2	TRUE	NA	0.14	2		826	850	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218640	98218640	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	93	661	0	ENST00000331920.6:c.3224G>T	p.Gly1075Val	p.G1075V	ENST00000331920	NM_000264.3	1075	gGa/gTa	19/24	1	2	FACETS	1	0.903	1	1	0.986	1	CLONAL	2	TRUE	1	0.14	2		661	654	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855028	76855028	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	63	744	1	ENST00000373344.5:c.5808G>T	p.Lys1936Asn	p.K1936N	ENST00000373344	NM_000489.3	1936	aaG/aaT	25/35	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.14	2		745	839	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938796	76938796	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1557140502	NA	P-0019700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	89	887	0	ENST00000373344.5:c.1952C>G	p.Ser651Cys	p.S651C	ENST00000373344	NM_000489.3	651	tCt/tGt	9/35	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.14	2		887	1031	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023909	27023923	+	inframe_deletion	In_Frame_Del	DEL	GCTGCGGCGGCGGCA	GCTGCGGCGGCGGCA	-	rs751352361	NA	P-0019709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	22	204	0	ENST00000324856.7:c.1029_1043del	p.Ala345_Ala349del	p.A345_A349del	ENST00000324856	NM_006015.4	339	GCTGCGGCGGCGGCA/-	1/20	0.358823078859376	2	FACETS	0.604	0.471	0.756	0.302	0.235	0.378	SUBCLONAL	1	TRUE	0	0.416136031503235	2		204	175	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578217	7578217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	228	825	0	ENST00000269305.4:c.632C>T	p.Thr211Ile	p.T211I	ENST00000269305	NM_001126112.2	211	aCt/aTt	6/11	0.416136031503235	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.416136031503235	1		825	807	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106928	11106928	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0019709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	259	953	1	ENST00000358026.2:c.1633A>T	p.Lys545Ter	p.K545*	ENST00000358026	NM_001128849.1	545	Aag/Tag	10/36	0.416136031503235	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.416136031503235	1		954	863	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790791	89790791	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	250	919	0	ENST00000336032.3:c.178T>G	p.Phe60Val	p.F60V	ENST00000336032	NM_006813.2	60	Ttc/Gtc	1/2	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.416136031503235	2		919	1119	SUCCESS
APC	324	MSKCC	GRCh37	5	112173656	112173656	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123117	NA	P-0019710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	27	562	0	ENST00000257430.4:c.2365C>T	p.Gln789Ter	p.Q789*	ENST00000257430	NM_000038.5	789	Cag/Tag	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		562	387	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	24	553	2	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		555	539	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0019710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	28	405	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		405	406	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749415085	NA	P-0019710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	24	534	1	ENST00000263967.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000263967	NM_006218.2	38	Cgt/Tgt	2/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		535	373	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	T	rs1023835002	NA	P-0019710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	18	469	0	ENST00000558401.1:c.1A>T	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Ttg	1/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		469	354	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs371769427	NA	P-0019710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	33	485	0	ENST00000291552.4:c.101C>A	p.Ser34Tyr	p.S34Y	ENST00000291552	NM_006758.2	34	tCt/tAt	2/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		485	439	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977584	2977584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746318779	NA	P-0019710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	76	785	2	ENST00000396946.4:c.1100C>T	p.Thr367Met	p.T367M	ENST00000396946	NM_032415.4	367	aCg/aTg	8/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		787	703	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696293	52696293	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0019710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	50	490	0	ENST00000394830.3:c.385-1G>A		p.X129_splice	ENST00000394830	NM_018313.4	129			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		490	431	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	93	600	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.204935014307814	4	FACETS	0.927	0.83	1	0.927	0.83	1	INDETERMINATE	2	TRUE	2	0.346500722075908	4		600	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0019711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	173	717	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.336194508837354	2	FACETS	0.895	0.829	0.963	0.895	0.829	0.963	CLONAL	2	TRUE	0	0.346500722075908	2		718	558	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0019711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	83	369	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	0.336194508837354	2	FACETS	0.943	0.845	1	0.943	0.845	1	CLONAL	2	TRUE	0	0.346500722075908	2		369	254	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943806	9943806	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	102	439	0	ENST00000330684.3:c.1135G>A	p.Glu379Lys	p.E379K	ENST00000330684	NM_001134407.1	379	Gag/Aag	5/13	0.173250487848193	5	FACETS	0.996	0.896	1	0.664	0.597	0.734	INDETERMINATE	2	TRUE	2	0.346500722075908	5		439	449	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0019711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	196	762	0	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	0.343902048206541	2	FACETS	0.951	0.886	1	0.951	0.886	1	CLONAL	2	TRUE	0	0.346500722075908	2		762	595	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953214	81953214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369516453	NA	P-0019711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	100	457	0	ENST00000359376.3:c.2180G>A	p.Arg727Gln	p.R727Q	ENST00000359376	NM_002661.3	727	cGa/cAa	20/33	0.173250487848193	5	FACETS	1	0.926	1	0.691	0.621	0.765	INDETERMINATE	2	TRUE	2	0.346500722075908	5		457	423	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016634	12016634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	80	521	0	ENST00000353533.5:c.770C>T	p.Ser257Phe	p.S257F	ENST00000353533	NM_003010.3	257	tCt/tTt	7/11	0.336194508837354	2	FACETS	0.759	0.675	0.848	0.759	0.675	0.848	SUBCLONAL	2	TRUE	0	0.346500722075908	2		521	304	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650377	48650377	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1557020191	NA	P-0019711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	119	1040	0	ENST00000376670.3:c.347C>G	p.Ser116Cys	p.S116C	ENST00000376670	NM_002049.3	116	tCt/tGt	3/6	0.346500722075908	3	FACETS	1	0.902	1	0.5	0.451	0.552	CLONAL	1	TRUE	1	0.346500722075908	3		1040	806	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	128	736	0				ENST00000310581	NM_198253.2	-/1132			0.350644235771535	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	0	0.350644235771535	1		736	563	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	144	600	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	0.992	1	CLONAL	2	FALSE	1	0.350644235771535	2		600	400	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487153	56487153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	182	592	0	ENST00000267101.3:c.1299G>A	p.Met433Ile	p.M433I	ENST00000267101	NM_001982.3	433	atG/atA	12/28	1	2	FACETS	0.871	0.808	0.936	1	0.992	1	CLONAL	2	FALSE	1	0.350644235771535	2		592	596	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851304	156851304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	326	840	2	ENST00000524377.1:c.2261C>T	p.Pro754Leu	p.P754L	ENST00000524377	NM_002529.3	754	cCa/cTa	17/17	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	FALSE	1	0.350644235771535	2		842	828	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160450	108160451	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	209	644	0	ENST00000278616.4:c.4363dup	p.Ser1455LysfsTer36	p.S1455Kfs*36	ENST00000278616	NM_000051.3	1453	ata/atAa	29/63	1	2	FACETS	1	0.946	1	1	0.994	1	CLONAL	2	FALSE	1	0.350644235771535	2		644	588	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	472218	472218	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	68	538	0	ENST00000399788.2:c.583G>C	p.Glu195Gln	p.E195Q	ENST00000399788	NM_001042603.1	195	Gag/Cag	5/28	0.350644235771535	1	FACETS	0.711	0.62	0.808	0.711	0.62	0.808	SUBCLONAL	1	FALSE	0	0.350644235771535	1		538	450	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880937	134880937	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	272	659	0	ENST00000398015.3:c.1500G>A	p.Met500Ile	p.M500I	ENST00000398015	NM_004441.4	500	atG/atA	7/16	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	FALSE	1	0.350644235771535	2		659	669	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570426	87570426	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	321	904	0	ENST00000277120.3:c.2166C>A	p.Tyr722Ter	p.Y722*	ENST00000277120		722	taC/taA	17/19	1	2	FACETS	1	0.972	1	1	0.996	1	CLONAL	2	FALSE	1	0.350644235771535	2		904	881	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2202742	2202742	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	585	840	0	ENST00000398665.3:c.751C>T	p.His251Tyr	p.H251Y	ENST00000398665	NM_032482.2	251	Cac/Tac	9/28	0.449505643315903	3	FACETS	0.917	0.886	0.949	0.917	0.886	0.949	CLONAL	3	TRUE	0	0.463955790361412	3		840	1129	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127446	55127446	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	89	893	0	ENST00000257290.5:c.234C>A	p.Ser78Arg	p.S78R	ENST00000257290	NM_006206.4	78	agC/agA	3/23	0.428842301024714	3	FACETS	0.997	0.9	1			1	CLONAL	2	TRUE	NA	0.463955790361412	3		893	237	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325172	39325173	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCTGCC	rs772893914	NA	P-0019713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1871	429	1095	1	ENST00000373001.3:c.141_146dup	p.Ala48_Gly49dup	p.A48_G49dup	ENST00000373001	NM_022157.3	48	ggc/ggGGCAGGc	1/7	0.299685080757144	5	FACETS	1	0.994	1			1	CLONAL	1	TRUE	NA	0.463955790361412	5		1096	2300	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514178	69514178	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	168	819	0	ENST00000294312.3:c.503T>A	p.Met168Lys	p.M168K	ENST00000294312	NM_005117.2	168	aTg/aAg	3/3	0.339792092964424	3	FACETS	0.903	0.829	0.98	0.452	0.414	0.49	CLONAL	1	TRUE	1	0.463955790361412	3		819	988	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355083	73355083	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	132	684	0	ENST00000377767.4:c.287A>G	p.Gln96Arg	p.Q96R	ENST00000377767	NM_014953.3	96	cAa/cGa	2/21	0.462724459290696	2	FACETS	0.822	0.756	0.89	0.822	0.756	0.89	CLONAL	2	TRUE	0	0.463955790361412	2		684	346	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40742005	40742005	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	261	905	0	ENST00000392038.2:c.967G>C	p.Glu323Gln	p.E323Q	ENST00000392038	NM_001626.4	323	Gag/Cag	11/14	0.401093215905013	2	FACETS	0.957	0.896	1	0.478	0.448	0.51	CLONAL	1	TRUE	0	0.463955790361412	2		905	1176	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281889	39281889	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	96	693	0	ENST00000402219.2:c.586T>A	p.Ser196Thr	p.S196T	ENST00000402219	NM_005633.3	196	Tca/Aca	5/23	0.397604422471461	3	FACETS	1	0.945	1	0.544	0.486	0.604	CLONAL	1	TRUE	1	0.463955790361412	3		693	469	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547924	41547924	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	86	763	0	ENST00000263253.7:c.2905G>T	p.Glu969Ter	p.E969*	ENST00000263253	NM_001429.3	969	Gag/Tag	15/31	0.372195562382507	3	FACETS	1	0.958	1	0.386	0.344	0.431	CLONAL	1	TRUE	0	0.463955790361412	3		763	394	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547954	41547954	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	94	823	0	ENST00000263253.7:c.2935G>C	p.Glu979Gln	p.E979Q	ENST00000263253	NM_001429.3	979	Gag/Cag	15/31	0.372195562382507	3	FACETS	1	0.96	1	0.384	0.344	0.427	CLONAL	1	TRUE	0	0.463955790361412	3		823	433	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185169125	185169125	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	123	674	0	ENST00000265026.3:c.1220T>C	p.Leu407Ser	p.L407S	ENST00000265026	NM_004721.4	407	tTa/tCa	7/14	0.309937662576122	5	FACETS	1	0.962	1	0.375	0.339	0.413	CLONAL	1	TRUE	2	0.463955790361412	5		674	799	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526719	31526719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2274	192	1197	0	ENST00000344624.3:c.321G>A	p.Met107Ile	p.M107I	ENST00000344624		107	atG/atA	2/33	0.463955790361412	4	FACETS	0.491	0.452	0.533	0.164	0.15	0.178	SUBCLONAL	1	TRUE	1	0.463955790361412	4		1197	2466	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137313613	137313613	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	570	1051	0	ENST00000481739.1:c.872A>G	p.Glu291Gly	p.E291G	ENST00000481739	NM_002957.4	291	gAg/gGg	6/10	0.418298857058877	2	FACETS	0.879	0.845	0.913	0.879	0.845	0.913	CLONAL	2	TRUE	0	0.463955790361412	2		1051	1398	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239595	53239595	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0019713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	113	288	0	ENST00000375401.3:c.1746+1G>T		p.X582_splice	ENST00000375401	NM_004187.3	582			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.463955790361412	NA		288	180	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152864444	152864759	+	coding_sequence_variant,5_prime_UTR_variant	Frame_Shift_Del	DEL	CTCGGAAGTGCACCCTGGCTTCGGGCGCCGGCTGCCCTCCGGGCCCCGCGCTGCAGGCCCCCCTCCGCCGCCTCCGGGGCTTCCATGAGGCGCCGCGGCACCGGCGGAAGGAGAGGCGGCCCCGGCGCGCAGAAGCCGGCAGAACTGGAGGTGCTCGCGGCGGGCGTGCCGCCCCACCCGGCCGCGTCCGGCCCCGCCCCGCCCCGCCCCTCGCCGCCCCGCCCCGCCCCTCGCCGCCCCGCCCCGCCCCTCGCCGCCCCGCCGCTCCTCCGCCCCGCCCCGCCCCTCAGGGCCCTCGCCCAAGGGTGAGCGCGCG	CTCGGAAGTGCACCCTGGCTTCGGGCGCCGGCTGCCCTCCGGGCCCCGCGCTGCAGGCCCCCCTCCGCCGCCTCCGGGGCTTCCATGAGGCGCCGCGGCACCGGCGGAAGGAGAGGCGGCCCCGGCGCGCAGAAGCCGGCAGAACTGGAGGTGCTCGCGGCGGGCGTGCCGCCCCACCCGGCCGCGTCCGGCCCCGCCCCGCCCCGCCCCTCGCCGCCCCGCCCCGCCCCTCGCCGCCCCGCCCCGCCCCTCGCCGCCCCGCCGCTCCTCCGCCCCGCCCCGCCCCTCAGGGCCCTCGCCCAAGGGTGAGCGCGCG	-	novel	NA	P-0019713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	100	68	0				ENST00000406277	NM_152274.4	?-28/246		1-3/7	NA		FACETS		NA	1				INDETERMINATE	NA	TRUE	NA	0.463955790361412	NA		68	337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0019716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	151	697	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.280522695369773	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.280522695369773	1		697	775	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849798	151849888	+	frameshift_variant	Frame_Shift_Del	DEL	GTTGGAGGAAATGGTACATTAGGCTGCTTCAGCCGGTAAGAGCTCACTAATCTGGGAGGGTTTGCAGATCCTGGCGGAGGCCCACGGAGAA	GTTGGAGGAAATGGTACATTAGGCTGCTTCAGCCGGTAAGAGCTCACTAATCTGGGAGGGTTTGCAGATCCTGGCGGAGGCCCACGGAGAA	-	novel	NA	P-0019716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	26	315	0	ENST00000262189.6:c.12428_12518del	p.Leu4143GlnfsTer45	p.L4143Qfs*45	ENST00000262189	NM_170606.2	4143	cTTCTCCGTGGGCCTCCGCCAGGATCTGCAAACCCTCCCAGATTAGTGAGCTCTTACCGGCTGAAGCAGCCTAATGTACCATTTCCTCCAACa/ca	49/59	1	2	FACETS	0.576	0.456	0.712	0.576	0.456	0.712	SUBCLONAL	1	TRUE	1	0.280522695369773	2		315	322	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0019717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	117	860	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.25489541851906	2		860	861	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486842	56486842	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	89	687	0	ENST00000267101.3:c.1256G>C	p.Gly419Ala	p.G419A	ENST00000267101	NM_001982.3	419	gGa/gCa	11/28	1	2	FACETS	0.957	0.848	1	0.957	0.848	1	CLONAL	1	TRUE	1	0.25489541851906	2		687	730	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192065	108192065	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1317619286	NA	P-0019717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	64	620	0	ENST00000278616.4:c.6490G>C	p.Glu2164Gln	p.E2164Q	ENST00000278616	NM_000051.3	2164	Gag/Cag	45/63	1	2	FACETS	0.864	0.749	0.99	0.864	0.749	0.99	CLONAL	1	TRUE	1	0.25489541851906	2		620	581	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057947	27057947	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0019717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	110	772	0	ENST00000324856.7:c.1655C>G	p.Ser552Ter	p.S552*	ENST00000324856	NM_006015.4	552	tCa/tGa	3/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.25489541851906	2		772	754	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77070044	77070044	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	77	647	0	ENST00000356341.3:c.496G>C	p.Glu166Gln	p.E166Q	ENST00000356341	NM_002576.4	166	Gag/Cag	6/15	1	2	FACETS	0.823	0.722	0.932	0.823	0.722	0.932	CLONAL	1	TRUE	1	0.25489541851906	2		647	734	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0019717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	287	911	2	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.249590532290587	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.25489541851906	2		913	1069	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853836	59853836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	79	840	0	ENST00000259008.2:c.2023G>A	p.Glu675Lys	p.E675K	ENST00000259008	NM_032043.2	675	Gaa/Aaa	14/20	1	2	FACETS	0.787	0.691	0.89	0.787	0.691	0.89	SUBCLONAL	1	TRUE	1	0.25489541851906	2		840	788	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057793	27057793	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1212	171	1310	0	ENST00000324856.7:c.1501C>G	p.Gln501Glu	p.Q501E	ENST00000324856	NM_006015.4	501	Cag/Gag	3/20	1	2	FACETS	0.97	0.89	1	0.97	0.89	1	CLONAL	1	TRUE	1	0.25489541851906	2		1310	1383	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100334	27100335	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	110	899	0	ENST00000324856.7:c.4048dup	p.Ser1350PhefsTer95	p.S1350Ffs*95	ENST00000324856	NM_006015.4	1349	cct/ccTt	17/20	1	2	FACETS	0.881	0.79	0.977	0.881	0.79	0.977	CLONAL	1	TRUE	1	0.25489541851906	2		899	980	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451281	70451281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	113	1005	1	ENST00000373644.4:c.6121C>T	p.Pro2041Ser	p.P2041S	ENST00000373644	NM_030625.2	2041	Cca/Tca	12/12	1	2	FACETS	0.836	0.751	0.927	0.836	0.751	0.927	CLONAL	1	TRUE	1	0.25489541851906	2		1006	1060	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101985104	101985104	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	116	1081	1	ENST00000282441.5:c.551C>A	p.Ser184Tyr	p.S184Y	ENST00000282441	NM_001130145.2	184	tCt/tAt	2/9	1	2	FACETS	0.864	0.777	0.956	0.864	0.777	0.956	CLONAL	1	TRUE	1	0.25489541851906	2		1082	1054	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198371	108198371	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0019717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	62	568	0	ENST00000278616.4:c.6976-1G>A		p.X2326_splice	ENST00000278616	NM_000051.3	2326			1	2	FACETS	0.928	0.803	1	0.928	0.803	1	CLONAL	1	TRUE	1	0.25489541851906	2		568	524	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487326	56487326	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	61	350	0	ENST00000267101.3:c.1472G>A	p.Arg491Lys	p.R491K	ENST00000267101	NM_001982.3	491	aGa/aAa	12/28	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.25489541851906	2		350	431	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99175943	99175943	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	81	615	0	ENST00000074304.5:c.1855G>A	p.Glu619Lys	p.E619K	ENST00000074304	NM_001134224.1	619	Gaa/Aaa	18/26	1	2	FACETS	0.851	0.749	0.96	0.851	0.749	0.96	CLONAL	1	TRUE	1	0.25489541851906	2		615	747	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250840	153250840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1560763689	NA	P-0019717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	28	633	0	ENST00000281708.4:c.1220C>T	p.Ser407Leu	p.S407L	ENST00000281708	NM_033632.3	407	tCa/tTa	8/12	1	2	FACETS	0.537	0.429	0.661	0.537	0.429	0.661	SUBCLONAL	1	TRUE	1	0.25489541851906	2		633	409	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158101	27158101	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1236479837	NA	P-0019717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	89	848	0	ENST00000380036.4:c.325G>C	p.Glu109Gln	p.E109Q	ENST00000380036	NM_000459.3	109	Gag/Cag	2/23	1	2	FACETS	0.909	0.806	1	0.909	0.806	1	CLONAL	1	TRUE	1	0.25489541851906	2		848	768	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797295	135797296	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAGGCGATGAAAGAGTGCGTACACACTGGCATGGAGATGGACGAT	novel	NA	P-0019717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	20	388	0	ENST00000298552.3:c.573_574insATCGTCCATCTCCATGCCAGTGTGTACGCACTCTTTCATCGCCTT	p.Leu191_Tyr192insIleValHisLeuHisAlaSerValTyrAlaLeuPheHisArgLeu	p.L191_Y192insIVHLHASVYALFHRL	ENST00000298552	NM_001162426.1	191	-/ATCGTCCATCTCCATGCCAGTGTGTACGCACTCTTTCATCGCCTT	7/23	0.25489541851906	1	FACETS	0.352	0.268	0.45	0.352	0.268	0.45	SUBCLONAL	1	TRUE	0	0.25489541851906	1		388	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0019719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	19	697	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.378708118840409	1	FACETS	0.149	0.112	0.193	0.149	0.112	0.193	SUBCLONAL	1	TRUE	0	0.378708118840409	1		697	545	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	147	553	2	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	0.378708118840409	2		555	699	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028660	12028660	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1334746981	NA	P-0019719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	104	660	0	ENST00000353533.5:c.863C>G	p.Ser288Cys	p.S288C	ENST00000353533	NM_003010.3	288	tCt/tGt	8/11	0.378708118840409	1	FACETS	0.972	0.875	1	0.972	0.875	1	CLONAL	1	TRUE	0	0.378708118840409	1		660	458	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851295	156851295	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780170701	NA	P-0019719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	139	1007	0	ENST00000524377.1:c.2252C>T	p.Ala751Val	p.A751V	ENST00000524377	NM_002529.3	751	gCc/gTc	17/17	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.378708118840409	2		1007	630	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624298	89624298	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	211	932	0	ENST00000371953.3:c.72C>A	p.Asp24Glu	p.D24E	ENST00000371953	NM_000314.4	24	gaC/gaA	1/9	0.321663749502197	2	FACETS	0.751	0.7	0.804	0.751	0.7	0.804	SUBCLONAL	2	TRUE	0	0.378708118840409	2		932	742	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244816	41244816	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	137	876	0	ENST00000357654.3:c.2732G>C	p.Gly911Ala	p.G911A	ENST00000357654	NM_007294.3	911	gGa/gCa	10/23	0.378708118840409	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.378708118840409	1		876	569	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876199	35876199	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	106	773	1	ENST00000303115.3:c.991C>A	p.Gln331Lys	p.Q331K	ENST00000303115	NM_002185.3	331	Caa/Aaa	8/8	1	2	FACETS	0.897	0.806	0.994	0.897	0.806	0.994	CLONAL	1	TRUE	1	0.378708118840409	2		774	624	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931247	131931307	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTATTTTCTTAAAATAGCCATGCTGGCTGGAGCCACAGCAGTTTACTCCCAGTTCATTAC	TTTATTTTCTTAAAATAGCCATGCTGGCTGGAGCCACAGCAGTTTACTCCCAGTTCATTAC	-	novel	NA	P-0019719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	30	296	0	ENST00000265335.6:c.1970-17_2013del		p.X657_splice	ENST00000265335		657		13/25	1	2	FACETS	0.624	0.505	0.757	0.624	0.505	0.757	SUBCLONAL	1	TRUE	1	0.378708118840409	2		296	254	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	187	634	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.905	0.843	0.969	0.905	0.843	0.969	CLONAL	1	TRUE	1	0.791678647907098	2		635	522	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528489	29528489	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764079291	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	230	692	0	ENST00000356175.3:c.1246C>T	p.Arg416Ter	p.R416*	ENST00000356175	NM_000267.3	416	Cga/Tga	11/57	1	2	FACETS	0.886	0.83	0.942	0.886	0.83	0.942	CLONAL	1	TRUE	1	0.791678647907098	2		692	656	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477807	140477807	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs180177038	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	240	652	1	ENST00000288602.6:c.1501G>A	p.Glu501Lys	p.E501K	ENST00000288602	NM_004333.4	501	Gaa/Aaa	12/18	1	2	FACETS	0.913	0.858	0.97	0.913	0.858	0.97	CLONAL	1	TRUE	1	0.791678647907098	2		653	664	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369273	40369273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	282	655	0	ENST00000293328.3:c.1285C>T	p.Arg429Cys	p.R429C	ENST00000293328	NM_012448.3	429	Cgt/Tgt	11/19	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.791678647907098	2		655	695	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411267	63411267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866313799	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	302	397	2	ENST00000330258.3:c.1900C>T	p.Arg634Cys	p.R634C	ENST00000330258	NM_152424.3	634	Cgt/Tgt	2/2	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.791678647907098	1		399	384	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969779	81969779	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	198	506	0	ENST00000359376.3:c.2848C>T	p.Pro950Ser	p.P950S	ENST00000359376	NM_002661.3	950	Cct/Tct	27/33	1	2	FACETS	0.89	0.83	0.951	0.89	0.83	0.951	CLONAL	1	TRUE	1	0.791678647907098	2		506	562	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740479	58740479	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	251	705	3	ENST00000305921.3:c.1384C>T	p.Gln462Ter	p.Q462*	ENST00000305921	NM_003620.3	462	Caa/Taa	6/6	1	2	FACETS	0.879	0.827	0.933	0.879	0.827	0.933	CLONAL	1	TRUE	1	0.791678647907098	2		708	721	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105682	27105682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1164908440	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	128	356	0	ENST00000324856.7:c.5293G>A	p.Glu1765Lys	p.E1765K	ENST00000324856	NM_006015.4	1765	Gaa/Aaa	20/20	1	2	FACETS	0.948	0.871	1	0.948	0.871	1	CLONAL	1	TRUE	1	0.791678647907098	2		356	341	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820866	36820866	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	229	651	1	ENST00000373129.3:c.511G>A	p.Glu171Lys	p.E171K	ENST00000373129	NM_032017.1	171	Gag/Aag	6/12	1	2	FACETS	0.987	0.927	1	0.987	0.927	1	CLONAL	1	TRUE	1	0.791678647907098	2		652	586	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612807	228612807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	200	597	1	ENST00000366696.1:c.220G>A	p.Glu74Lys	p.E74K	ENST00000366696	NM_003493.2	74	Gag/Aag	1/1	0.36957731046563	3	FACETS	1	0.952	1	0.515	0.479	0.552	INDETERMINATE	1	TRUE	1	0.791678647907098	3		598	685	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609119	43609120	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	303	1027	2	ENST00000355710.3:c.1875_1876delinsTT	p.Gln626Ter	p.Q626*	ENST00000355710	NM_020975.4	625	atCCag/atTTag	10/20	1	2	FACETS	0.927	0.877	0.977	0.927	0.877	0.977	CLONAL	1	TRUE	1	0.791678647907098	2		1029	826	SUCCESS
ATM	472	MSKCC	GRCh37	11	108181018	108181018	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	176	431	0	ENST00000278616.4:c.5894A>G	p.Lys1965Arg	p.K1965R	ENST00000278616	NM_000051.3	1965	aAa/aGa	39/63	0.791678647907098	1	FACETS	0.966	0.913	1	0.966	0.913	1	CLONAL	1	TRUE	0	0.791678647907098	1		431	278	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344368	118344368	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	118	252	0	ENST00000534358.1:c.2494C>T	p.Pro832Ser	p.P832S	ENST00000534358	NM_005933.3	832	Cct/Tct	3/36	0.791678647907098	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.791678647907098	1		252	160	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243915	46243915	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	229	446	1	ENST00000334344.6:c.2009C>T	p.Pro670Leu	p.P670L	ENST00000334344	NM_152641.2	670	cCt/cTt	15/21	0.14850030749283	3	FACETS	0.769	0.724	0.815	0.769	0.724	0.815	INDETERMINATE	2	TRUE	1	0.791678647907098	3		447	525	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828872	26828872	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	184	553	0	ENST00000381527.3:c.94T>C	p.Tyr32His	p.Y32H	ENST00000381527	NM_001260.1	32	Tat/Cat	1/13	1	2	FACETS	0.935	0.871	1	0.935	0.871	1	CLONAL	1	TRUE	1	0.791678647907098	2		553	497	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578233	28578233	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	266	704	0	ENST00000241453.7:c.2938G>A	p.Asp980Asn	p.D980N	ENST00000241453	NM_004119.2	980	Gat/Aat	24/24	1	2	FACETS	0.923	0.87	0.977	0.923	0.87	0.977	CLONAL	1	TRUE	1	0.791678647907098	2		704	728	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225848	2225848	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs781270559	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	288	710	1	ENST00000326181.6:c.1640G>T	p.Arg547Leu	p.R547L	ENST00000326181	NM_032271.2	547	cGa/cTa	18/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.791678647907098	2		711	695	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862815	9862815	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	239	726	0	ENST00000330684.3:c.2488C>T	p.Leu830Phe	p.L830F	ENST00000330684	NM_001134407.1	830	Ctt/Ttt	12/13	1	2	FACETS	0.957	0.899	1	0.957	0.899	1	CLONAL	1	TRUE	1	0.791678647907098	2		726	631	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641356	23641356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	280	937	1	ENST00000261584.4:c.2119C>T	p.Pro707Ser	p.P707S	ENST00000261584	NM_024675.3	707	Cct/Tct	5/13	1	2	FACETS	0.809	0.762	0.857	0.809	0.762	0.857	CLONAL	1	TRUE	1	0.791678647907098	2		938	874	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490300	29490300	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	247	546	1	ENST00000356175.3:c.385C>T	p.Gln129Ter	p.Q129*	ENST00000356175	NM_000267.3	129	Cag/Tag	4/57	1	2	FACETS	0.947	0.891	1	0.947	0.891	1	CLONAL	1	TRUE	1	0.791678647907098	2		547	659	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321614	30321614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	196	619	0	ENST00000322652.5:c.1469C>T	p.Ser490Phe	p.S490F	ENST00000322652	NM_015355.2	490	tCt/tTt	13/16	1	2	FACETS	0.941	0.879	1	0.941	0.879	1	CLONAL	1	TRUE	1	0.791678647907098	2		619	526	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858042	40858042	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	258	707	0	ENST00000428826.2:c.1822C>T	p.Gln608Ter	p.Q608*	ENST00000428826		608	Cag/Tag	16/21	1	2	FACETS	0.909	0.856	0.963	0.909	0.856	0.963	CLONAL	1	TRUE	1	0.791678647907098	2		707	717	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59934445	59934446	+	missense_variant	Missense_Mutation	DNP	CT	CT	TC	novel	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	195	497	1	ENST00000259008.2:c.352_353delinsGA	p.Arg118Glu	p.R118E	ENST00000259008	NM_032043.2	118	AGa/GAa	4/20	1	2	FACETS	0.966	0.902	1	0.966	0.902	1	CLONAL	1	TRUE	1	0.791678647907098	2		498	510	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295785	15295785	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	416	1140	0	ENST00000263388.2:c.2342A>C	p.Glu781Ala	p.E781A	ENST00000263388	NM_000435.2	781	gAg/gCg	15/33	1	2	FACETS	0.979	0.934	1	0.979	0.934	1	CLONAL	1	TRUE	1	0.791678647907098	2		1140	1074	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383620	42383620	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201206281	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	201	540	1	ENST00000221972.3:c.395C>T	p.Pro132Leu	p.P132L	ENST00000221972	NM_021601.3	132	cCc/cTc	3/5	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.791678647907098	2		541	480	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719111	52719111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	254	640	1	ENST00000322088.6:c.887C>T	p.Ala296Val	p.A296V	ENST00000322088	NM_014225.5	296	gCc/gTc	7/15	1	2	FACETS	0.934	0.879	0.99	0.934	0.879	0.99	CLONAL	1	TRUE	1	0.791678647907098	2		641	687	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606158	47606158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	219	557	0	ENST00000263735.4:c.622G>A	p.Asp208Asn	p.D208N	ENST00000263735	NM_002354.2	208	Gac/Aac	6/9	1	2	FACETS	0.901	0.844	0.96	0.901	0.844	0.96	CLONAL	1	TRUE	1	0.791678647907098	2		557	614	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561016	9561016	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	152	387	0	ENST00000353224.5:c.766G>A	p.Glu256Lys	p.E256K	ENST00000353224	NM_177990.2	256	Gaa/Aaa	4/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.791678647907098	2		387	344	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266131	41266157	+	inframe_deletion	In_Frame_Del	DEL	CTCCTTCTCTGAGTGGTAAAGGCAATC	CTCCTTCTCTGAGTGGTAAAGGCAATC	-	novel	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	267	311	0	ENST00000349496.5:c.130_156del	p.Pro44_Pro52del	p.P44_P52del	ENST00000349496	NM_001904.3	43	gCTCCTTCTCTGAGTGGTAAAGGCAATCct/gct	3/15	0.682518803318313	3	FACETS	0.918	0.871	0.964			1	CLONAL	2	TRUE	NA	0.791678647907098	3		311	513	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127776	47127776	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	206	441	0	ENST00000409792.3:c.5306C>T	p.Ser1769Phe	p.S1769F	ENST00000409792	NM_014159.6	1769	tCc/tTc	11/21	1	2	FACETS	0.997	0.933	1	0.997	0.933	1	CLONAL	1	TRUE	1	0.791678647907098	2		441	522	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164174	47164177	+	frameshift_variant	Frame_Shift_Del	DEL	TCCT	TCCT	CCC	novel	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	184	399	1	ENST00000409792.3:c.1949_1952delinsGGG	p.Lys650ArgfsTer3	p.K650Rfs*3	ENST00000409792	NM_014159.6	650	aAGGAa/aGGGa	3/21	1	2	FACETS	0.939	0.875	1	0.939	0.875	1	CLONAL	1	TRUE	1	0.791678647907098	2		400	495	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204863	128204863	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	358	1015	1	ENST00000341105.2:c.578C>T	p.Pro193Leu	p.P193L	ENST00000341105	NM_032638.4	193	cCa/cTa	3/6	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.791678647907098	2		1016	897	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628425	187628425	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752504990	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	355	805	1	ENST00000441802.2:c.2557C>T	p.Pro853Ser	p.P853S	ENST00000441802	NM_005245.3	853	Ccc/Tcc	2/27	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.791678647907098	2		806	844	SUCCESS
APC	324	MSKCC	GRCh37	5	112173366	112173366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1322926033	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	143	424	0	ENST00000257430.4:c.2075C>T	p.Pro692Leu	p.P692L	ENST00000257430	NM_000038.5	692	cCt/cTt	16/16	1	2	FACETS	0.926	0.854	1	0.926	0.854	1	CLONAL	1	TRUE	1	0.791678647907098	2		424	390	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522621	176522621	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569707811	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	292	923	1	ENST00000292408.4:c.1718G>A	p.Ser573Asn	p.S573N	ENST00000292408	NM_213647.1	573	aGc/aAc	13/18	1	2	FACETS	0.957	0.905	1	0.957	0.905	1	CLONAL	1	TRUE	1	0.791678647907098	2		924	771	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955149	93955149	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	204	641	0	ENST00000369303.4:c.2749C>T	p.Gln917Ter	p.Q917*	ENST00000369303	NM_004440.3	917	Caa/Taa	16/17	0.791678647907098	1	FACETS	0.949	0.9	0.997	0.949	0.9	0.997	CLONAL	1	TRUE	0	0.791678647907098	1		641	328	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509446	106509446	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	206	630	0	ENST00000359195.3:c.1440C>G	p.Tyr480Ter	p.Y480*	ENST00000359195	NM_002649.2	480	taC/taG	2/11	1	2	FACETS	0.857	0.8	0.916	0.857	0.8	0.916	CLONAL	1	TRUE	1	0.791678647907098	2		630	607	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509642	106509642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	239	570	2	ENST00000359195.3:c.1636G>A	p.Glu546Lys	p.E546K	ENST00000359195	NM_002649.2	546	Gaa/Aaa	2/11	1	2	FACETS	0.954	0.897	1	0.954	0.897	1	CLONAL	1	TRUE	1	0.791678647907098	2		572	633	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939497	68939497	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	195	647	1	ENST00000288368.4:c.482C>T	p.Pro161Leu	p.P161L	ENST00000288368	NM_024870.2	161	cCc/cTc	5/40	0.71080829229696	3	FACETS	0.873	0.809	0.938	0.436	0.404	0.469	CLONAL	1	TRUE	1	0.791678647907098	3		648	788	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68993027	68993027	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	456	632	0	ENST00000288368.4:c.1832A>T	p.Asn611Ile	p.N611I	ENST00000288368	NM_024870.2	611	aAt/aTt	17/40	0.71080829229696	3	FACETS	0.909	0.874	0.945	0.909	0.874	0.945	CLONAL	2	TRUE	1	0.791678647907098	3		632	884	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409399	80409399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	246	625	0	ENST00000286548.4:c.715C>T	p.Leu239Phe	p.L239F	ENST00000286548	NM_002072.3	239	Ctc/Ttc	5/7	0.791678647907098	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.791678647907098	1		625	373	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6442036	6442040	+	missense_variant	Missense_Mutation	ONP	CCTCC	CCTCC	GCTCT	novel	NA	P-0019720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	41	52	0	ENST00000356142.4:c.595_599delinsGCTCT	p.Pro199_Pro200delinsAlaLeu	p.P199_P200delinsAL	ENST00000356142	NM_018890.3	199	CCTCCc/GCTCTc	7/7	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.791678647907098	2		52	79	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0019721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	171	970	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.506240534186583	2	FACETS	0.838	0.772	0.907	0.419	0.386	0.454	CLONAL	1	TRUE	0	0.506240534186583	2		970	806	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913499	NA	P-0019721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	95	318	2	ENST00000345146.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000345146	NM_005896.2	132	Cgt/Ggt	4/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.506240534186583	2		320	320	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577575	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587782289	NA	P-0019721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	250	775	0	ENST00000269305.4:c.706T>G	p.Tyr236Asp	p.Y236D	ENST00000269305	NM_001126112.2	236	Tac/Gac	7/11	0.506240534186583	2	FACETS	0.788	0.742	0.834	0.788	0.742	0.834	SUBCLONAL	2	TRUE	0	0.506240534186583	2		775	627	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859625	57859625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200097138	NA	P-0019721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	40	689	0	ENST00000228682.2:c.679C>T	p.Arg227Cys	p.R227C	ENST00000228682	NM_005269.2	227	Cgt/Tgt	7/12	1	2	FACETS	0.241	0.199	0.287	0.241	0.199	0.287	SUBCLONAL	1	TRUE	1	0.506240534186583	2		689	656	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872091	76872095	+	frameshift_variant	Frame_Shift_Del	DEL	ATCTA	ATCTA	-	novel	NA	P-0019721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	75	280	0	ENST00000373344.5:c.5552_5556del	p.Leu1851SerfsTer8	p.L1851Sfs*8	ENST00000373344	NM_000489.3	1851	tTAGAT/t	22/35	1	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.506240534186583	1		280	185	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	50	736	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.882	0.75	1	0.882	0.75	1	CLONAL	1	TRUE	1	0.27	2		736	420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253911	NA	P-0019722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	54	726	0	ENST00000269305.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000269305	NM_001126112.2	180	Gag/Aag	5/11	0.202012784879969	1	FACETS	0.66	0.564	0.765	0.66	0.564	0.765	SUBCLONAL	1	TRUE	0	0.27	1		726	524	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197187	26197187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	23	376	0	ENST00000356476.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000356476		98	Gag/Aag	1/1	1	2	FACETS	0.406	0.316	0.51	0.406	0.316	0.51	SUBCLONAL	1	TRUE	1	0.27	2		376	420	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434793	99434793	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201529410	NA	P-0019722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	47	627	2	ENST00000268035.6:c.880G>A	p.Glu294Lys	p.E294K	ENST00000268035	NM_000875.3	294	Gag/Aag	3/21	0.202012784879969	1	FACETS	0.605	0.51	0.709	0.605	0.51	0.709	SUBCLONAL	1	TRUE	0	0.27	1		629	498	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46251019	46251019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	48	475	0	ENST00000371998.3:c.28C>T	p.Pro10Ser	p.P10S	ENST00000371998		10	Cca/Tca	3/23	1	2	FACETS	0.623	0.526	0.729	0.623	0.526	0.729	SUBCLONAL	1	TRUE	1	0.27	2		475	571	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248679	59248679	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	81	1148	0	ENST00000371222.2:c.64G>C	p.Glu22Gln	p.E22Q	ENST00000371222	NM_002228.3	22	Gag/Cag	1/1	1	2	FACETS	0.564	0.495	0.638	0.564	0.495	0.638	SUBCLONAL	1	TRUE	1	0.27	2		1148	1064	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027216	49027216	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	113	676	1	ENST00000267163.4:c.1784del	p.Pro595LeufsTer16	p.P595Lfs*16	ENST00000267163	NM_000321.2	595	Cct/ct	18/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.27	2		677	613	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222935	36222935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	81	1326	1	ENST00000222270.7:c.5564C>T	p.Pro1855Leu	p.P1855L	ENST00000222270	NM_014727.1	1855	cCa/cTa	27/37	1	2	FACETS	0.589	0.517	0.666	0.589	0.517	0.666	SUBCLONAL	1	TRUE	1	0.27	2		1327	1019	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456514	29456514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	61	820	0	ENST00000389048.3:c.2404G>A	p.Glu802Lys	p.E802K	ENST00000389048	NM_004304.4	802	Gaa/Aaa	14/29	1	2	FACETS	0.583	0.502	0.672	0.583	0.502	0.672	SUBCLONAL	1	TRUE	1	0.27	2		820	775	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202771	128202788	+	inframe_deletion	In_Frame_Del	DEL	TGCACAGGTAGTGGCCGG	TGCACAGGTAGTGGCCGG	-	novel	NA	P-0019722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	95	798	0	ENST00000341105.2:c.932_949del	p.Thr311_Cys316del	p.T311_C316del	ENST00000341105	NM_032638.4	311	aCCGGCCACTACCTGTGCAat/aat	4/6	NA	2	FACETS	1	0.942	1			1	INDETERMINATE	1	TRUE	NA	0.27	2		798	647	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652054	36652055	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0019722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	109	993	0	ENST00000244741.5:c.177_178dup	p.Glu60GlyfsTer89	p.E60Gfs*89	ENST00000244741	NM_000389.4	59	ctg/ctGGg	2/3	1	2	FACETS	0.969	0.87	1	0.969	0.87	1	CLONAL	1	TRUE	1	0.27	2		993	833	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455153	50455153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	23	351	0	ENST00000331340.3:c.700G>A	p.Gly234Ser	p.G234S	ENST00000331340	NM_006060.4	234	Ggc/Agc	6/8	1	2	FACETS	0.467	0.363	0.586	0.467	0.363	0.586	SUBCLONAL	1	TRUE	1	0.27	2		351	365	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427612	49427612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766696812	NA	P-0019723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	272	480	0	ENST00000301067.7:c.10876C>T	p.Arg3626Trp	p.R3626W	ENST00000301067	NM_003482.3	3626	Cgg/Tgg	39/54	0.333185841313582	2	FACETS	1	0.994	1	0.722	0.683	0.76	INDETERMINATE	1	TRUE	0	0.62512885707594	2		480	603	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772252	68772252	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	427	1052	0	ENST00000261769.5:c.102del	p.Glu35ArgfsTer21	p.E35Rfs*21	ENST00000261769	NM_004360.3	34	gCc/gc	2/16	0.241741212209574	5	FACETS	0.838	0.797	0.879	0.558	0.531	0.586	INDETERMINATE	2	TRUE	2	0.62512885707594	5		1052	1580	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847385	68847399	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TGAAAACAGCAAAGG	TGAAAACAGCAAAGG	-	novel	NA	P-0019723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	387	782	0	ENST00000261769.5:c.1308_1320+2del		p.X436_splice	ENST00000261769	NM_004360.3	436		9/16	0.241741212209574	5	FACETS	1	0.989	1	0.754	0.718	0.791	INDETERMINATE	2	TRUE	2	0.62512885707594	5		782	1060	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	117	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.357848080100551	2		509	596	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984844	9984844	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	59	453	0	ENST00000330684.3:c.1121A>T	p.Lys374Met	p.K374M	ENST00000330684	NM_001134407.1	374	aAg/aTg	4/13	1	2	FACETS	0.776	0.669	0.891	0.776	0.669	0.891	SUBCLONAL	1	TRUE	1	0.357848080100551	2		453	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0019724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	74	451	0	ENST00000269305.4:c.375+1G>T		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.357848080100551	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.357848080100551	1		451	290	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244255	46244255	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	57	345	0	ENST00000334344.6:c.2351del	p.Pro784LeufsTer8	p.P784Lfs*8	ENST00000334344	NM_152641.2	783	atC/at	15/21	0.357848080100551	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.357848080100551	1		345	240	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424512	49424512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756908474	NA	P-0019724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	115	755	3	ENST00000301067.7:c.13711G>A	p.Ala4571Thr	p.A4571T	ENST00000301067	NM_003482.3	4571	Gcc/Acc	41/54	0.357848080100551	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.357848080100551	1		758	444	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	149	736	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.931	0.857	1	0.931	0.857	1	CLONAL	1	TRUE	1	0.632274755372429	2		736	506	SUCCESS
APC	324	MSKCC	GRCh37	5	112176798	112176798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1363066852	NA	P-0019725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	131	505	0	ENST00000257430.4:c.5507G>A	p.Gly1836Glu	p.G1836E	ENST00000257430	NM_000038.5	1836	gGa/gAa	16/16	NA	2	FACETS	0.839	0.766	0.915			1	INDETERMINATE	1	TRUE	NA	0.632274755372429	2		505	494	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500482	149500484	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	novel	NA	P-0019725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	298	738	0	ENST00000261799.4:c.2553_2555del	p.Ile851del	p.I851del	ENST00000261799	NM_002609.3	851	atCATg/atg	18/23	0.382314500647933	2	FACETS	1	0.994	1	0.697	0.661	0.733	CLONAL	1	TRUE	0	0.632274755372429	2		738	676	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503840	149503840	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs797044887	NA	P-0019725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	316	756	0	ENST00000261799.4:c.1996A>C	p.Asn666His	p.N666H	ENST00000261799	NM_002609.3	666	Aac/Cac	14/23	0.382314500647933	2	FACETS	0.775	0.738	0.812	0.775	0.738	0.812	SUBCLONAL	2	TRUE	0	0.632274755372429	2		756	645	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866528	117866528	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	132	619	0	ENST00000297338.2:c.1117T>C	p.Phe373Leu	p.F373L	ENST00000297338	NM_006265.2	373	Ttt/Ctt	9/14	0.632274755372429	3	FACETS	0.894	0.814	0.977	0.447	0.407	0.489	CLONAL	1	TRUE	1	0.632274755372429	3		619	615	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0019726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	247	800	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.226880720825846	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.226880720825846	2		801	1021	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0019726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	113	503	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.226880720825846	2	FACETS	0.848	0.766	0.936	0.848	0.766	0.936	CLONAL	2	TRUE	0	0.226880720825846	2		503	587	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0019726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	116	453	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	0.226880720825846	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	TRUE	0	0.226880720825846	2		453	497	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845465	151845465	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0019726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	169	682	0	ENST00000262189.6:c.13547T>G	p.Leu4516Ter	p.L4516*	ENST00000262189	NM_170606.2	4516	tTa/tGa	52/59	0.226880720825846	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	0	0.226880720825846	2		682	730	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0019727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	583	1097	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.403186683316579	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.403186683316579	2		1097	1293	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956565	93956565	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	118	445	0	ENST00000369303.4:c.2671G>C	p.Asp891His	p.D891H	ENST00000369303	NM_004440.3	891	Gac/Cac	15/17	0.403186683316579	3	FACETS	1	0.96	1	0.558	0.505	0.615	CLONAL	1	TRUE	1	0.403186683316579	3		445	630	SUCCESS
FH	2271	MSKCC	GRCh37	1	241676991	241676991	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	152	685	0	ENST00000366560.3:c.290G>T	p.Gly97Val	p.G97V	ENST00000366560	NM_000143.3	97	gGc/gTc	3/10	0.403186683316579	5	FACETS	0.985	0.899	1	0.328	0.299	0.359	CLONAL	1	TRUE	2	0.403186683316579	5		685	1228	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436369	110436369	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	674	896	1	ENST00000375856.3:c.2032A>G	p.Met678Val	p.M678V	ENST00000375856	NM_003749.2	678	Atg/Gtg	1/2	0.403186683316579	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.403186683316579	3		897	1254	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799175	88799175	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	665	1120	0	ENST00000360948.2:c.210T>A	p.Ser70Arg	p.S70R	ENST00000360948	NM_001012338.2	70	agT/agA	2/19	0.254499360628335	6	FACETS	0.892	0.86	0.924	0.892	0.86	0.924	CLONAL	4	TRUE	2	0.403186683316579	6		1120	1670	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934623	9934623	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	422	549	0	ENST00000330684.3:c.1532C>G	p.Ser511Trp	p.S511W	ENST00000330684	NM_001134407.1	511	tCg/tGg	7/13	0.403186683316579	5	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	2	0.403186683316579	5		549	1081	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348135	89348135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	239	868	0	ENST00000301030.4:c.4815G>A	p.Met1605Ile	p.M1605I	ENST00000301030	NM_001256183.1	1605	atG/atA	9/13	0.403186683316579	3	FACETS	0.982	0.915	1	0.491	0.457	0.527	CLONAL	1	TRUE	1	0.403186683316579	3		868	1450	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350087	89350087	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	225	803	0	ENST00000301030.4:c.2863C>G	p.Leu955Val	p.L955V	ENST00000301030	NM_001256183.1	955	Ctg/Gtg	9/13	0.403186683316579	3	FACETS	1	0.975	1	0.552	0.513	0.592	CLONAL	1	TRUE	1	0.403186683316579	3		803	1215	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980733	40980747	+	inframe_deletion	In_Frame_Del	DEL	TGGTGGCAATCCGAG	TGGTGGCAATCCGAG	-	novel	NA	P-0019727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	116	496	0	ENST00000373198.4:c.1739_1753del	p.Thr580_Thr584del	p.T580_T584del	ENST00000373198	NM_133170.3	580	aCTCGGATTGCCACCAaa/aaa	10/32	0.403186683316579	3	FACETS	1	0.922	1	0.512	0.462	0.565	CLONAL	1	TRUE	1	0.403186683316579	3		496	675	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980813	40980813	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	207	779	0	ENST00000373198.4:c.1673del	p.Pro558GlnfsTer43	p.P558Qfs*43	ENST00000373198	NM_133170.3	558	cCa/ca	10/32	0.403186683316579	3	FACETS	1	0.968	1	0.538	0.499	0.579	CLONAL	1	TRUE	1	0.403186683316579	3		779	1146	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164866	36164866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	606	1092	1	ENST00000300305.3:c.1009C>T	p.Pro337Ser	p.P337S	ENST00000300305		337	Ccc/Tcc	8/8	0.403186683316579	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.403186683316579	2		1093	1213	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405093	405093	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	363	736	0	ENST00000380956.4:c.1175C>A	p.Pro392Gln	p.P392Q	ENST00000380956	NM_001195286.1	392	cCa/cAa	8/9	0.403186683316579	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.403186683316579	2		736	778	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450283	50450283	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	294	637	0	ENST00000331340.3:c.467A>C	p.Gln156Pro	p.Q156P	ENST00000331340	NM_006060.4	156	cAg/cCg	5/8	0.403186683316579	5	FACETS	0.958	0.901	1	0.639	0.601	0.678	CLONAL	2	TRUE	2	0.403186683316579	5		637	1221	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346138	152346138	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	351	831	0	ENST00000359321.1:c.432C>G	p.Cys144Trp	p.C144W	ENST00000359321	NM_005431.1	144	tgC/tgG	3/3	0.403186683316579	5	FACETS	0.952	0.9	1	0.634	0.6	0.67	CLONAL	2	TRUE	2	0.403186683316579	5		831	1468	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046404	69046404	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	408	847	1	ENST00000288368.4:c.3877A>T	p.Ser1293Cys	p.S1293C	ENST00000288368	NM_024870.2	1293	Agc/Tgc	32/40	0.394861867133012	4	FACETS	0.973	0.925	1	0.973	0.925	1	CLONAL	2	TRUE	2	0.403186683316579	4		848	1459	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0019730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	78	860	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	0.991	0.871	1	0.991	0.871	1	CLONAL	1	TRUE	0	0.22	1		860	637	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653808	89653808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	57	562	0	ENST00000371953.3:c.106G>A	p.Gly36Arg	p.G36R	ENST00000371953	NM_000314.4	36	Gga/Aga	2/9	0.213016530325716	1	FACETS	0.818	0.702	0.944	0.818	0.702	0.944	CLONAL	1	TRUE	0	0.22	1		562	564	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000060	30000061	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0019730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	84	821	0	ENST00000338641.4:c.75dup	p.Ile26AspfsTer23	p.I26Dfs*23	ENST00000338641	NM_000268.3	25	agg/aGgg	1/16	0.213016530325716	1	FACETS	0.907	0.801	1	0.907	0.801	1	CLONAL	1	TRUE	0	0.22	1		821	749	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974207	2974207	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	66	844	0	ENST00000396946.4:c.1398C>A	p.Ser466Arg	p.S466R	ENST00000396946	NM_032415.4	466	agC/agA	10/25	0.3	2	FACETS	0.788	0.683	0.903			1	CLONAL	1	TRUE	NA	0.22	2		844	761	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745581	162745581	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	95	523	0	ENST00000367921.3:c.1996C>A	p.Leu666Ile	p.L666I	ENST00000367921	NM_006182.2	666	Ctt/Att	15/18	0.428673512626375	3	FACETS	0.697	0.621	0.779	0.349	0.31	0.39	SUBCLONAL	1	TRUE	1	0.438140549641636	3		523	758	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576900	7576901	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	316	736	0	ENST00000269305.4:c.945dup	p.Pro316SerfsTer21	p.P316Sfs*21	ENST00000269305	NM_001126112.2	315	-/T	9/11	0.360455376276125	2	FACETS	0.849	0.804	0.894	0.849	0.804	0.894	CLONAL	2	TRUE	0	0.438140549641636	2		736	850	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246559	41246560	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CATTA	novel	NA	P-0019731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	347	801	0	ENST00000357654.3:c.984_988dup	p.Asp330ValfsTer13	p.D330Vfs*13	ENST00000357654	NM_007294.3	330	gat/gTAATGat	10/23	0.360455376276125	2	FACETS	0.833	0.791	0.876	0.833	0.791	0.876	CLONAL	2	TRUE	0	0.438140549641636	2		801	951	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923760	39923938	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTGCCTCTCCACAAAGTACTTCTCCACAGGAAGATCTTTGTCCTCTGGGGCTTCAAAGGGATCACGGTGCTTGTTTCCAACACTATACTCGCCTGGGGGAGGGGAGACAAGAGGGCATTAATGAAGCCCGAAGGTCGCCATGAGAAGGCAGGATCTGGGGAGTGCGTGGGACCACCAT	GCTGCCTCTCCACAAAGTACTTCTCCACAGGAAGATCTTTGTCCTCTGGGGCTTCAAAGGGATCACGGTGCTTGTTTCCAACACTATACTCGCCTGGGGGAGGGGAGACAAGAGGGCATTAATGAAGCCCGAAGGTCGCCATGAGAAGGCAGGATCTGGGGAGTGCGTGGGACCACCAT	-	novel	NA	P-0019731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	104	853	0	ENST00000378444.4:c.3239-86_3331del		p.X1080_splice	ENST00000378444	NM_001123385.1	1080		7/15	1	2	FACETS	0.525	0.469	0.584	0.525	0.469	0.584	SUBCLONAL	1	TRUE	1	0.438140549641636	2		853	904	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932231	39932231	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	288	1147	0	ENST00000378444.4:c.2368A>T	p.Asn790Tyr	p.N790Y	ENST00000378444	NM_001123385.1	790	Aac/Tac	4/15	1	2	FACETS	0.936	0.878	0.995	0.936	0.878	0.995	CLONAL	1	TRUE	1	0.438140549641636	2		1147	1405	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0019733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	177	670	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.55695501514844	2		670	549	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0019733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	341	639	2	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.55695501514844	2		641	853	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195628	123195631	+	frameshift_variant	Frame_Shift_Del	DEL	AGAT	AGAT	-	novel	NA	P-0019733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	147	205	0	ENST00000218089.9:c.1544_1547del	p.Asp515GlyfsTer6	p.D515Gfs*6	ENST00000218089	NM_001042749.1	514	acAGAT/ac	17/35	1	1	FACETS	0.957	0.908	1	1	0.993	1	CLONAL	2	TRUE	0	0.55695501514844	1		205	199	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922763	44922763	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	280	203	0	ENST00000377967.4:c.1624C>T	p.Gln542Ter	p.Q542*	ENST00000377967	NM_021140.2	542	Cag/Tag	16/29	1	1	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	0	0.55695501514844	1		203	337	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983120	201983121	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	384	934	1	ENST00000359651.3:c.970dup	p.Met324AsnfsTer147	p.M324Nfs*147	ENST00000359651		323	-/A	7/8	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.55695501514844	2		935	966	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806564	1806564	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	290	804	1	ENST00000260795.2:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000260795		427	tCc/tTc	9/17	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.55695501514844	2		805	714	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989653	68989653	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	352	677	0	ENST00000288368.4:c.1591G>C	p.Glu531Gln	p.E531Q	ENST00000288368	NM_024870.2	531	Gag/Cag	15/40	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.55695501514844	2		677	853	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742459	145742459	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	378	960	0	ENST00000428558.2:c.329A>T	p.Lys110Met	p.K110M	ENST00000428558	NM_004260.3	110	aAg/aTg	4/22	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	1	TRUE	NA	0.55695501514844	2		960	917	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0019734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	196	918	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.488569891847903	1	FACETS	0.961	0.897	1	0.961	0.897	1	CLONAL	1	TRUE	0	0.563465921955074	1		918	520	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170303	119170303	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	165	357	0	ENST00000264033.4:c.2533G>T	p.Gly845Cys	p.G845C	ENST00000264033	NM_005188.3	845	Ggt/Tgt	16/16	NA	2	FACETS	1	0.949	1			1	INDETERMINATE	1	TRUE	NA	0.563465921955074	2		357	566	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99486157	99486157	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	211	479	1	ENST00000268035.6:c.3463G>T	p.Gly1155Cys	p.G1155C	ENST00000268035	NM_000875.3	1155	Ggt/Tgt	19/21	0.177661082308618	1	FACETS	0.762	0.71	0.815	0.762	0.71	0.815	INDETERMINATE	1	TRUE	0	0.563465921955074	1		480	706	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579544	7579545	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCGGGGA	novel	NA	P-0019734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	368	865	0	ENST00000269305.4:c.136_142dup	p.Asp48ValfsTer6	p.D48Vfs*6	ENST00000269305	NM_001126112.2	48	gac/gTCCCCGGac	4/11	0.53533793949394	1	FACETS	0.921	0.875	0.967	0.921	0.875	0.967	CLONAL	1	TRUE	0	0.563465921955074	1		865	1019	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602727	10602727	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	436	879	0	ENST00000171111.5:c.851A>C	p.Gln284Pro	p.Q284P	ENST00000171111	NM_203500.1	284	cAg/cCg	3/6	0.563465921955074	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.563465921955074	1		879	1027	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285863	39285863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	126	712	0	ENST00000402219.2:c.296G>A	p.Arg99Gln	p.R99Q	ENST00000402219	NM_005633.3	99	cGa/cAa	3/23	0.22175212127633	3	FACETS	0.941	0.855	1	0.471	0.427	0.516	INDETERMINATE	1	TRUE	1	0.563465921955074	3		712	609	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582437	119582437	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	138	221	0	ENST00000316626.5:c.964A>T	p.Thr322Ser	p.T322S	ENST00000316626		322	Act/Tct	10/12	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.563465921955074	2		221	456	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955890	55955890	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	248	720	0	ENST00000263923.4:c.3272T>C	p.Phe1091Ser	p.F1091S	ENST00000263923	NM_002253.2	1091	tTt/tCt	24/30	0.540296958515814	1	FACETS	0.881	0.827	0.935	0.881	0.827	0.935	CLONAL	1	TRUE	0	0.563465921955074	1		720	718	SUCCESS
APC	324	MSKCC	GRCh37	5	112175996	112175996	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	129	374	0	ENST00000257430.4:c.4705G>T	p.Asp1569Tyr	p.D1569Y	ENST00000257430	NM_000038.5	1569	Gat/Tat	16/16	1	2	FACETS	0.826	0.753	0.904	0.826	0.753	0.904	CLONAL	1	TRUE	1	0.563465921955074	2		374	554	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671417	30671437	+	inframe_deletion	In_Frame_Del	DEL	TCTGCAGTATCTTCTTCCTCT	TCTGCAGTATCTTCTTCCTCT	-	novel	NA	P-0019734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	516	762	0	ENST00000376406.3:c.5523_5543del	p.Glu1842_Glu1848del	p.E1842_E1848del	ENST00000376406	NM_014641.2	1841	gaAGAGGAAGAAGATACTGCAGAg/gag	10/15	0.548610965321257	3	FACETS	0.915	0.878	0.952	0.915	0.878	0.952	CLONAL	2	TRUE	1	0.563465921955074	3		762	1283	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450289	50450289	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	274	629	0	ENST00000331340.3:c.473G>T	p.Gly158Val	p.G158V	ENST00000331340	NM_006060.4	158	gGc/gTc	5/8	1	2	FACETS	0.996	0.937	1	0.996	0.937	1	CLONAL	1	TRUE	1	0.563465921955074	2		629	976	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509098	106509098	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	288	622	0	ENST00000359195.3:c.1092G>T	p.Lys364Asn	p.K364N	ENST00000359195	NM_002649.2	364	aaG/aaT	2/11	1	2	FACETS	0.984	0.926	1	0.984	0.926	1	CLONAL	1	TRUE	1	0.563465921955074	2		622	1039	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346895	70346895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767783777	NA	P-0019734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	291	685	0	ENST00000374080.3:c.2762G>A	p.Ser921Asn	p.S921N	ENST00000374080		921	aGc/aAc	20/45	1	2	FACETS	0.978	0.921	1	0.978	0.921	1	CLONAL	1	TRUE	1	0.563465921955074	2		685	1056	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100063	11100064	+	stop_gained,protein_altering_variant	Nonsense_Mutation	INS	-	-	TGGTCTTAAACTCCT	novel	NA	P-0019734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	182	923	0	ENST00000358026.2:c.1189_1190insTGGTCTTAAACTCCT	p.Arg397delinsLeuValLeuAsnSerTer	p.R397delinsLVLNS*	ENST00000358026	NM_001128849.1	397	cga/cTGGTCTTAAACTCCTga	7/36	0.563465921955074	1	FACETS	0.558	0.516	0.603	0.558	0.516	0.603	SUBCLONAL	1	TRUE	0	0.563465921955074	1		923	831	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	43	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.628	0.525	0.742	0.628	0.525	0.742	SUBCLONAL	1	TRUE	1	0.245528006793133	2		509	558	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971124	21971125	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0019735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	59	645	0	ENST00000304494.5:c.233_234del	p.Leu78HisfsTer41	p.L78Hfs*41	ENST00000304494	NM_000077.4	78	cTC/c	2/3	0.245528006793133	1	FACETS	0.828	0.713	0.953	0.828	0.713	0.953	CLONAL	1	TRUE	0	0.245528006793133	1		645	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577567	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1567549651	NA	P-0019735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	58	641	0	ENST00000269305.4:c.714dup	p.Asn239Ter	p.N239*	ENST00000269305	NM_001126112.2	238	-/T	7/11	0.245528006793133	1	FACETS	0.676	0.581	0.78	0.676	0.581	0.78	SUBCLONAL	1	TRUE	0	0.245528006793133	1		641	613	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358698	67358698	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	26	484	0	ENST00000327367.4:c.206G>T	p.Arg69Met	p.R69M	ENST00000327367	NM_005902.3	69	aGg/aTg	1/9	0.245528006793133	1	FACETS	0.555	0.439	0.686	0.555	0.439	0.686	SUBCLONAL	1	TRUE	0	0.245528006793133	1		484	335	SUCCESS
AR	367	MSKCC	GRCh37	X	66766603	66766603	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	67	468	0	ENST00000374690.3:c.1615C>T	p.Arg539Cys	p.R539C	ENST00000374690	NM_000044.3	539	Cgt/Tgt	1/8	1	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.245528006793133	1		468	398	SUCCESS
APC	324	MSKCC	GRCh37	5	112174096	112174096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs137854575	NA	P-0019737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	63	493	0	ENST00000257430.4:c.2805C>A	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	taC/taA	16/16	1	2	FACETS	0.718	0.62	0.824	0.718	0.62	0.824	SUBCLONAL	1	TRUE	1	0.27	2		493	650	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0019737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	178	609	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.118115646085203	3	FACETS	0.916	0.845	0.989			1	INDETERMINATE	2	TRUE	NA	0.27	3		609	817	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0019737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	101	756	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.248574754086706	1	FACETS	0.802	0.716	0.893	0.802	0.716	0.893	CLONAL	1	TRUE	0	0.27	1		756	807	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391761	139391761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776577038	NA	P-0019737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	64	765	0	ENST00000277541.6:c.6430G>A	p.Gly2144Ser	p.G2144S	ENST00000277541	NM_017617.3	2144	Ggc/Agc	34/34	1	2	FACETS	0.545	0.471	0.626	0.545	0.471	0.626	SUBCLONAL	1	TRUE	1	0.27	2		765	870	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118888	70118888	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	322	801	0	ENST00000245479.2:c.460T>G	p.Phe154Val	p.F154V	ENST00000245479	NM_000346.3	154	Ttc/Gtc	2/3	0.253812849922009	3	FACETS	0.866	0.819	0.914	0.866	0.819	0.914	CLONAL	3	TRUE	0	0.27	3		801	1042	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224469	55224471	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0019737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	94	700	0	ENST00000275493.2:c.1157_1159del	p.Pro386del	p.P386del	ENST00000275493	NM_005228.3	384	aCTCct/act	10/28	0.240634824641302	3	FACETS	0.822	0.73	0.92	0.411	0.365	0.46	CLONAL	1	TRUE	1	0.27	3		700	962	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042728	42042728	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	40	562	0	ENST00000219905.7:c.6923A>G	p.Asp2308Gly	p.D2308G	ENST00000219905	NM_001164273.1	2308	gAt/gGt	17/24	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		562	654	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	174	600	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.148817646488635	4	FACETS	0.944	0.874	1	1	0.992	1	CLONAL	4	TRUE	2	0.186629348897714	4		600	586	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380338	14380339	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCCCACGCC	novel	NA	P-0019739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	133	547	0	ENST00000256196.4:c.70_78dup	p.Gly24_Gly26dup	p.G24_G26dup	ENST00000256196		24	-/GGCGTGGGC	1/6	0.104580278293346	4	FACETS	1	0.967	1	1	0.967	1	INDETERMINATE	2	TRUE	2	0.186629348897714	4		547	744	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	121	566	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	0.148817646488635	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.186629348897714	4		567	618	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0019739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	75	350	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	0.148817646488635	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	2	0.186629348897714	4		350	407	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	165	688	1	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	0.148817646488635	4	FACETS	0.967	0.89	1	1	0.988	1	CLONAL	3	TRUE	2	0.186629348897714	4		689	723	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319934	8319934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764537367	NA	P-0019739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	39	320	1	ENST00000356435.5:c.5567C>T	p.Thr1856Met	p.T1856M	ENST00000356435		1856	aCg/aTg	34/35	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.186629348897714	2		321	374	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374828	149374828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	80	417	0	ENST00000360632.3:c.266C>T	p.Ser89Leu	p.S89L	ENST00000360632	NM_015472.4	89	tCg/tTg	2/7	0.148817646488635	4	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	2	0.186629348897714	4		417	456	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221206	5221206	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200191658	NA	P-0019740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	315	880	2	ENST00000357368.4:c.3260C>T	p.Thr1087Met	p.T1087M	ENST00000357368	NM_002850.3	1087	aCg/aTg	20/38	1	2	FACETS	0.937	0.891	0.984	0.937	0.891	0.984	CLONAL	1	TRUE	1	0.945310783819852	2		882	711	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352619	68352619	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	129	593	0	ENST00000487270.1:c.486A>C	p.Arg162Ser	p.R162S	ENST00000487270	NM_133509.3	162	agA/agC	6/11	1	2	FACETS	0.428	0.389	0.47	0.428	0.389	0.47	SUBCLONAL	1	TRUE	1	0.945310783819852	2		593	637	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413115	63413115	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	261	911	0	ENST00000330258.3:c.52G>T	p.Gly18Trp	p.G18W	ENST00000330258	NM_152424.3	18	Ggg/Tgg	2/2	1	2	FACETS	0.798	0.752	0.845	0.798	0.752	0.845	SUBCLONAL	1	TRUE	1	0.945310783819852	2		911	692	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339299	70339299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	84	630	0	ENST00000374080.3:c.176C>T	p.Ala59Val	p.A59V	ENST00000374080		59	gCc/gTc	2/45	1	2	FACETS	0.306	0.27	0.344	0.306	0.27	0.344	SUBCLONAL	1	TRUE	1	0.945310783819852	2		630	581	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	45	942	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.829	0.695	0.979	0.829	0.695	0.979	CLONAL	1	TRUE	1	0.14	2		943	775	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	17	593	2	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.525	0.39	0.685	0.525	0.39	0.685	SUBCLONAL	1	TRUE	1	0.14	2		595	463	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	27	716	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.712	0.565	0.88	0.712	0.565	0.88	SUBCLONAL	1	TRUE	1	0.14	2		717	542	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	35	541	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.14	2		541	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	61	949	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.914	0.787	1	0.914	0.787	1	CLONAL	1	TRUE	1	0.14	2		950	953	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720649	89720649	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs587782455	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	17	269	0	ENST00000371953.3:c.802-2A>T		p.X268_splice	ENST00000371953	NM_000314.4	268			1	2	FACETS	0.93	0.695	1	0.93	0.695	1	CLONAL	1	TRUE	1	0.14	2		269	261	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436867	110436867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367592112	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	69	984	2	ENST00000375856.3:c.1534G>A	p.Ala512Thr	p.A512T	ENST00000375856	NM_003749.2	512	Gcc/Acc	1/2	1	2	FACETS	0.929	0.807	1	0.929	0.807	1	CLONAL	1	TRUE	1	0.14	2		986	1061	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264491	16264491	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747375812	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	48	649	1	ENST00000375759.3:c.10694G>A	p.Arg3565Gln	p.R3565Q	ENST00000375759	NM_015001.2	3565	cGa/cAa	13/15	1	2	FACETS	0.918	0.774	1	0.918	0.774	1	CLONAL	1	TRUE	1	0.14	2		650	747	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240789	55240789	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138193597	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	48	997	1	ENST00000275493.2:c.2033C>T	p.Thr678Met	p.T678M	ENST00000275493	NM_005228.3	678	aCg/aTg	17/28	1	2	FACETS	0.757	0.638	0.889	0.757	0.638	0.889	SUBCLONAL	1	TRUE	1	0.14	2		998	906	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099080	157099080	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	21	309	0	ENST00000346085.5:c.17G>C	p.Gly6Ala	p.G6A	ENST00000346085	NM_020732.3	6	gGc/gCc	1/20	1	2	FACETS	0.798	0.614	1	0.798	0.614	1	CLONAL	1	TRUE	1	0.14	2		309	376	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781375	3781375	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	65	905	2	ENST00000262367.5:c.4990C>T	p.Arg1664Cys	p.R1664C	ENST00000262367	NM_004380.2	1664	Cgc/Tgc	30/31	1	2	FACETS	0.989	0.855	1	0.989	0.855	1	CLONAL	1	TRUE	1	0.14	2		907	939	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962930	2962930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1349831751	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	73	1026	3	ENST00000396946.4:c.1978C>T	p.Arg660Trp	p.R660W	ENST00000396946	NM_032415.4	660	Cgg/Tgg	16/25	1	2	FACETS	0.945	0.823	1	0.945	0.823	1	CLONAL	1	TRUE	1	0.14	2		1029	1104	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663356	67663356	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	44	788	3	ENST00000264010.4:c.1760del	p.Asn587MetfsTer44	p.N587Mfs*44	ENST00000264010	NM_006565.3	586	gAa/ga	10/12	1	2	FACETS	0.801	0.67	0.947	0.801	0.67	0.947	CLONAL	1	TRUE	1	0.14	2		791	785	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436057	110436057	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1204032443	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1337	87	1184	3	ENST00000375856.3:c.2344G>A	p.Asp782Asn	p.D782N	ENST00000375856	NM_003749.2	782	Gac/Aac	1/2	1	2	FACETS	0.873	0.77	0.984	0.873	0.77	0.984	CLONAL	1	TRUE	1	0.14	2		1187	1424	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188182	11188182	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	39	486	0	ENST00000361445.4:c.5912C>T	p.Ala1971Val	p.A1971V	ENST00000361445	NM_004958.3	1971	gCc/gTc	43/58	1	2	FACETS	0.984	0.815	1	0.984	0.815	1	CLONAL	1	TRUE	1	0.14	2		486	566	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348722	11348722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	95	1090	1	ENST00000332029.2:c.614G>A	p.Ser205Asn	p.S205N	ENST00000332029	NM_003745.1	205	aGc/aAc	2/2	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.14	2		1091	1314	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380346	14380346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	48	631	0	ENST00000256196.4:c.71G>A	p.Gly24Asp	p.G24D	ENST00000256196		24	gGc/gAc	1/6	1	2	FACETS	0.998	0.842	1	0.998	0.842	1	CLONAL	1	TRUE	1	0.14	2		631	687	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	73	1194	0	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.967	0.843	1	0.967	0.843	1	CLONAL	1	TRUE	1	0.14	2		1194	1078	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100507	8100507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1158297550	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	48	925	2	ENST00000346208.3:c.481G>A	p.Val161Ile	p.V161I	ENST00000346208		161	Gtc/Atc	3/6	1	2	FACETS	0.752	0.633	0.883	0.752	0.633	0.883	SUBCLONAL	1	TRUE	1	0.14	2		927	912	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059166	27059166	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	30	458	0	ENST00000324856.7:c.1804-1G>T		p.X602_splice	ENST00000324856	NM_006015.4	602			1	2	FACETS	0.95	0.765	1	0.95	0.765	1	CLONAL	1	TRUE	1	0.14	2		458	451	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100964	27100964	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	45	708	1	ENST00000324856.7:c.4246C>T	p.Gln1416Ter	p.Q1416*	ENST00000324856	NM_006015.4	1416	Caa/Taa	18/20	1	2	FACETS	0.925	0.776	1	0.925	0.776	1	CLONAL	1	TRUE	1	0.14	2		709	695	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101713	27101713	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	65	903	0	ENST00000324856.7:c.4993+2T>C		p.X1665_splice	ENST00000324856	NM_006015.4	1665			1	2	FACETS	0.984	0.851	1	0.984	0.851	1	CLONAL	1	TRUE	1	0.14	2		903	944	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982372	201982372	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1258691938	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	97	1132	1	ENST00000359651.3:c.751C>T	p.Arg251Ter	p.R251*	ENST00000359651		251	Cga/Tga	6/8	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.14	2		1133	1195	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211607	46211607	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	23	495	0	ENST00000334344.6:c.573G>A	p.Met191Ile	p.M191I	ENST00000334344	NM_152641.2	191	atG/atA	5/21	1	2	FACETS	0.99	0.772	1	0.99	0.772	1	CLONAL	1	TRUE	1	0.14	2		495	332	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445624	49445624	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1331	92	1442	0	ENST00000301067.7:c.1842G>C	p.Glu614Asp	p.E614D	ENST00000301067	NM_003482.3	614	gaG/gaC	10/54	1	2	FACETS	0.924	0.817	1	0.924	0.817	1	CLONAL	1	TRUE	1	0.14	2		1442	1423	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994848	73994848	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910584858	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	11	160	1	ENST00000318443.5:c.332G>A	p.Arg111His	p.R111H	ENST00000318443	NM_001024736.1	111	cGc/cAc	3/10	1	2	FACETS	1	0.759	1	1	0.759	1	CLONAL	1	TRUE	1	0.14	2		161	141	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778569	3778569	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779980394	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	46	791	3	ENST00000262367.5:c.6479C>T	p.Ala2160Val	p.A2160V	ENST00000262367	NM_004380.2	2160	gCg/gTg	31/31	1	2	FACETS	0.91	0.765	1	0.91	0.765	1	CLONAL	1	TRUE	1	0.14	2		794	722	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341523	89341523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1349086238	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	64	687	0	ENST00000301030.4:c.7547G>A	p.Arg2516His	p.R2516H	ENST00000301030	NM_001256183.1	2516	cGt/cAt	10/13	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.14	2		687	743	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983655	7983655	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	27	443	0	ENST00000319144.4:c.652G>A	p.Ala218Thr	p.A218T	ENST00000319144	NM_001139.2	218	Gca/Aca	6/15	1	2	FACETS	0.851	0.677	1	0.851	0.677	1	CLONAL	1	TRUE	1	0.14	2		443	453	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435401	56435401	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	54	786	1	ENST00000407977.2:c.1736G>T	p.Arg579Met	p.R579M	ENST00000407977		579	aGg/aTg	9/10	1	2	FACETS	0.952	0.811	1	0.952	0.811	1	CLONAL	1	TRUE	1	0.14	2		787	810	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017737	31017737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	38	558	1	ENST00000375687.4:c.599G>A	p.Gly200Asp	p.G200D	ENST00000375687	NM_015338.5	200	gGc/gAc	8/13	1	2	FACETS	0.964	0.796	1	0.964	0.796	1	CLONAL	1	TRUE	1	0.14	2		559	563	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790089	40790089	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759416965	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	36	595	0	ENST00000373198.4:c.2642G>A	p.Arg881Gln	p.R881Q	ENST00000373198	NM_133170.3	881	cGg/cAg	18/32	1	2	FACETS	0.756	0.62	0.91	0.756	0.62	0.91	CLONAL	1	TRUE	1	0.14	2		595	680	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980527	1980527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760185069	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	54	980	2	ENST00000382891.5:c.3989C>T	p.Ala1330Val	p.A1330V	ENST00000382891	NM_133335.3	1330	gCg/gTg	22/22	1	2	FACETS	0.854	0.727	0.994	0.854	0.727	0.994	CLONAL	1	TRUE	1	0.14	2		982	903	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200083	138200083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141614391	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	40	411	1	ENST00000237289.4:c.1501G>A	p.Ala501Thr	p.A501T	ENST00000237289	NM_001270507.1	501	Gcc/Acc	7/9	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.14	2		412	458	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467736	50467736	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	44	796	0	ENST00000331340.3:c.971C>G	p.Ala324Gly	p.A324G	ENST00000331340	NM_006060.4	324	gCc/gGc	8/8	1	2	FACETS	0.88	0.737	1	0.88	0.737	1	CLONAL	1	TRUE	1	0.14	2		796	714	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140487353	140487353	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	52	984	0	ENST00000288602.6:c.1172A>G	p.Asp391Gly	p.D391G	ENST00000288602	NM_004333.4	391	gAt/gGt	9/18	1	2	FACETS	0.77	0.653	0.899	0.77	0.653	0.899	SUBCLONAL	1	TRUE	1	0.14	2		984	965	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226043	53226043	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782308622	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	47	939	0	ENST00000375401.3:c.2806C>T	p.Arg936Cys	p.R936C	ENST00000375401	NM_004187.3	936	Cgc/Tgc	19/26	1	2	FACETS	0.756	0.636	0.89	0.756	0.636	0.89	SUBCLONAL	1	TRUE	1	0.14	2		939	888	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356270	70356270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	61	727	1	ENST00000374080.3:c.5165G>A	p.Arg1722Gln	p.R1722Q	ENST00000374080		1722	cGg/cAg	37/45	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.14	2		728	754	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238356	98238358	+	missense_variant	Missense_Mutation	TNP	GCG	GCG	ACA	novel	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	37	523	0	ENST00000331920.6:c.1686_1688delinsTGT	p.Ala563Val	p.A563V	ENST00000331920	NM_000264.3	562	gcCGCg/gcTGTg	12/24	1	2	FACETS	0.867	0.713	1	0.867	0.713	1	CLONAL	1	TRUE	1	0.14	2		523	610	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271771	15271775	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGG	GCCGG	ACCA	novel	NA	P-0019741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	1095	63	0	ENST00000263388.2:c.6664_6668delinsTGGT	p.Pro2222TrpfsTer24	p.P2222Wfs*24	ENST00000263388	NM_000435.2	2222	CCGGCg/TGGTg	33/33	1	2	FACETS	1	0.991	1			1	CLONAL	7	TRUE	1	0.14	2		63	2160	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0019742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	199	697	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.212082123978379	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.246713816261155	2		697	737	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0019742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	163	807	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	0.203484129321491	4	FACETS	0.957	0.878	1	0.957	0.878	1	CLONAL	2	TRUE	2	0.246713816261155	4		807	861	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0019743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	213	680	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.576348243562087	3	FACETS	0.925	0.859	0.993	0.463	0.429	0.497	CLONAL	1	TRUE	1	0.582272909840409	3		680	1021	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442542	52442542	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1194652468	NA	P-0019743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	188	697	0	ENST00000460680.1:c.203A>G	p.Asp68Gly	p.D68G	ENST00000460680	NM_004656.3	68	gAt/gGt	4/17	0.582272909840409	1	FACETS	0.914	0.852	0.977	0.914	0.852	0.977	CLONAL	1	TRUE	0	0.582272909840409	1		697	501	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843386	3843386	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0019743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	115	263	0	ENST00000262367.5:c.1216+1G>A		p.X406_splice	ENST00000262367	NM_004380.2	406			0.337736461769675	3	FACETS	0.777	0.709	0.848	0.777	0.709	0.848	INDETERMINATE	2	TRUE	1	0.582272909840409	3		263	328	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158246	47158246	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0019743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	113	315	0	ENST00000409792.3:c.4455-2A>C		p.X1485_splice	ENST00000409792	NM_014159.6	1485			0.582272909840409	1	FACETS	0.836	0.762	0.913	0.836	0.762	0.913	CLONAL	1	TRUE	0	0.582272909840409	1		315	329	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0019744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	183	852	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.390922445803704	1	FACETS	0.851	0.787	0.917	0.851	0.787	0.917	CLONAL	1	TRUE	0	0.434044649903087	1		852	776	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591238	67591251	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTTTTTCAGGTGG	TGTTTTTCAGGTGG	-	novel	NA	P-0019744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	73	510	0	ENST00000274335.5:c.1746-9_1750del		p.X582_splice	ENST00000274335		582		13/15	0.326828863220849	1	FACETS	0.506	0.443	0.573	0.506	0.443	0.573	SUBCLONAL	1	TRUE	0	0.434044649903087	1		510	521	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057654	180057654	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	195	1017	0	ENST00000261937.6:c.301G>C	p.Val101Leu	p.V101L	ENST00000261937	NM_182925.4	101	Gta/Cta	3/30	1	2	FACETS	0.867	0.802	0.935	0.867	0.802	0.935	CLONAL	1	TRUE	1	0.434044649903087	2		1017	1036	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411161	63411161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1206766799	NA	P-0019744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	125	336	0	ENST00000330258.3:c.2006G>A	p.Gly669Glu	p.G669E	ENST00000330258	NM_152424.3	669	gGg/gAg	2/2	1	1	FACETS	0.759	0.698	0.821	1	0.988	1	SUBCLONAL	2	TRUE	0	0.434044649903087	1		336	297	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293298	91293298	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0019745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	99	294	0	ENST00000355112.3:c.799+1G>C		p.X267_splice	ENST00000355112	NM_000057.2	267			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		294	382	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741694	17741694	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	817	783	0	ENST00000250003.3:c.365T>G	p.Leu122Arg	p.L122R	ENST00000250003	NM_002478.4	122	cTg/cGg	1/3	0.917693483167022	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.917693483167022	3		783	1287	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0019746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	406	842	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	0.983	0.94	1	0.983	0.94	1	CLONAL	1	TRUE	1	0.917693483167022	2		842	900	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	56	654	0	ENST00000256196.4:c.68G>A	p.Gly23Asp	p.G23D	ENST00000256196		23	gGc/gAc	1/6	1	2	FACETS	0.319	0.273	0.369	0.319	0.273	0.369	SUBCLONAL	1	TRUE	1	0.556695149375811	2		654	631	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17941354	17941354	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0019747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	54	988	1	ENST00000458235.1:c.3054C>G	p.Tyr1018Ter	p.Y1018*	ENST00000458235	NM_000215.3	1018	taC/taG	22/24	1	2	FACETS	0.245	0.208	0.285	0.245	0.208	0.285	SUBCLONAL	1	TRUE	1	0.556695149375811	2		989	792	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936083	178936083	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519927	NA	P-0019748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	58	441	0	ENST00000263967.3:c.1625A>C	p.Glu542Ala	p.E542A	ENST00000263967	NM_006218.2	542	gAa/gCa	10/21	1	2	FACETS	0.6	0.515	0.693	0.6	0.515	0.693	SUBCLONAL	1	TRUE	1	0.321646766555655	2		441	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0019748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	182	811	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.300657474395652	1	FACETS	0.928	0.856	1	0.928	0.856	1	CLONAL	1	TRUE	0	0.321646766555655	1		811	1023	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272804	142272804	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	62	422	0	ENST00000350721.4:c.2395G>A	p.Glu799Lys	p.E799K	ENST00000350721	NM_001184.3	799	Gaa/Aaa	11/47	1	2	FACETS	0.473	0.408	0.545	0.473	0.408	0.545	SUBCLONAL	1	TRUE	1	0.321646766555655	2		422	815	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057520000	NA	P-0019748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	40	685	0	ENST00000269305.4:c.452C>G	p.Pro151Arg	p.P151R	ENST00000269305	NM_001126112.2	151	cCc/cGc	5/11	0.300657474395652	1	FACETS	0.178	0.147	0.213	0.178	0.147	0.213	SUBCLONAL	1	TRUE	0	0.321646766555655	1		685	1173	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088646	27088647	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	381	552	0	ENST00000324856.7:c.2256dup	p.Met753TyrfsTer64	p.M753Yfs*64	ENST00000324856	NM_006015.4	752	tat/taTt	7/20	NA	2	FACETS	0.951	0.903	0.999			1	INDETERMINATE	2	TRUE	NA	0.321646766555655	2		552	1246	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61213517	61213517	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	122	385	0	ENST00000301761.2:c.475G>C	p.Glu159Gln	p.E159Q	ENST00000301761	NM_017841.2	159	Gag/Cag	4/4	1	2	FACETS	0.91	0.822	1	0.91	0.822	1	CLONAL	1	TRUE	1	0.321646766555655	2		385	834	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098638	2098638	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	118	465	0	ENST00000219476.3:c.22G>C	p.Asp8His	p.D8H	ENST00000219476	NM_000548.3	8	Gat/Cat	2/42	1	2	FACETS	0.825	0.744	0.912	0.825	0.744	0.912	CLONAL	1	TRUE	1	0.321646766555655	2		465	889	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0019749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	199	741	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.467123349670483	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.477335489394184	3		742	468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0019749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	304	760	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.468732371269381	2	FACETS	0.901	0.855	0.947	0.901	0.855	0.947	CLONAL	2	TRUE	0	0.477335489394184	2		761	707	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227896	123227896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	56	538	0	ENST00000218089.9:c.3607G>A	p.Asp1203Asn	p.D1203N	ENST00000218089	NM_001042749.1	1203	Gat/Aat	33/35	0.211867925073829	3	FACETS	0.716	0.615	0.825	0.239	0.205	0.275	INDETERMINATE	1	TRUE	0	0.477335489394184	3		538	406	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222406	2222406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755921261	NA	P-0019749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	171	617	0	ENST00000398665.3:c.3238G>A	p.Gly1080Arg	p.G1080R	ENST00000398665	NM_032482.2	1080	Ggg/Agg	24/28	0.467123349670483	3	FACETS	1	0.971	1	0.555	0.511	0.601	CLONAL	1	TRUE	1	0.477335489394184	3		617	799	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9787046	9787046	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	132	697	0	ENST00000377346.4:c.3077G>A	p.Ser1026Asn	p.S1026N	ENST00000377346	NM_005026.3	1026	aGc/aAc	24/24	0.430912703549796	3	FACETS	0.836	0.759	0.917			1	CLONAL	1	TRUE	NA	0.477335489394184	3		697	819	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624301	89624301	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	266	800	0	ENST00000371953.3:c.75del	p.Thr26ProfsTer28	p.T26Pfs*28	ENST00000371953	NM_000314.4	25	ttG/tt	1/9	0.477335489394184	2	FACETS	0.892	0.843	0.941	0.892	0.843	0.941	CLONAL	2	TRUE	0	0.477335489394184	2		800	625	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115385	115115386	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	97	655	0	ENST00000257566.3:c.940dup	p.Arg314LysfsTer13	p.R314Kfs*13	ENST00000257566	NM_016569.3	314	aga/aAga	5/8	1	2	FACETS	0.724	0.647	0.806	0.724	0.647	0.806	SUBCLONAL	1	TRUE	1	0.477335489394184	2		655	561	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506975	186506977	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	novel	NA	P-0019749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	66	334	0	ENST00000323963.5:c.1141_1143del	p.Asp381del	p.D381del	ENST00000323963		381	GAC/-	11/11	0.467123349670483	3	FACETS	0.881	0.768	1	0.44	0.384	0.501	CLONAL	1	TRUE	1	0.477335489394184	3		334	389	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859639	151859639	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	153	394	0	ENST00000262189.6:c.11023C>T	p.Gln3675Ter	p.Q3675*	ENST00000262189	NM_170606.2	3675	Cag/Tag	43/59	0.477335489394184	2	FACETS	0.898	0.833	0.963	0.898	0.833	0.963	CLONAL	2	TRUE	0	0.477335489394184	2		394	357	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798990	42798990	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368086483	NA	P-0019750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	440	1151	1	ENST00000575354.2:c.4474G>A	p.Ala1492Thr	p.A1492T	ENST00000575354	NM_015125.3	1492	Gcc/Acc	20/20	1	2	FACETS	0.959	0.914	1	0.959	0.914	1	CLONAL	1	TRUE	1	0.618258955076945	2		1152	1484	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941293	71941293	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	256	807	1	ENST00000298229.2:c.1068G>A	p.Trp356Ter	p.W356*	ENST00000298229	NM_001567.3	356	tgG/tgA	9/28	0.618258955076945	1	FACETS	0.767	0.721	0.814	0.767	0.721	0.814	SUBCLONAL	1	TRUE	0	0.618258955076945	1		808	746	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481599	56481599	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1481957883	NA	P-0019750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	93	598	1	ENST00000267101.3:c.634C>T	p.Pro212Ser	p.P212S	ENST00000267101	NM_001982.3	212	Cct/Tct	6/28	0.29900539215857	1	FACETS	0.305	0.271	0.341	0.305	0.271	0.341	INDETERMINATE	1	TRUE	0	0.618258955076945	1		599	681	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0019751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	43	741	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.16	2		742	503	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894230	NA	P-0019751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	30	671	0	ENST00000451590.1:c.35G>T	p.Gly12Val	p.G12V	ENST00000451590	NM_001130442.1	12	gGc/gTc	2/5	1	2	FACETS	0.812	0.653	0.992	0.812	0.653	0.992	CLONAL	1	TRUE	1	0.16	2		671	462	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489493	56489493	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	35	620	0	ENST00000267101.3:c.1958T>A	p.Val653Glu	p.V653E	ENST00000267101	NM_001982.3	653	gTa/gAa	17/28	1	2	FACETS	0.72	0.588	0.868	0.72	0.588	0.868	SUBCLONAL	1	TRUE	1	0.16	2		620	608	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127412	55127412	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	40	910	0	ENST00000257290.5:c.200C>G	p.Ser67Cys	p.S67C	ENST00000257290	NM_006206.4	67	tCc/tGc	3/23	1	2	FACETS	0.646	0.535	0.77	0.646	0.535	0.77	SUBCLONAL	1	TRUE	1	0.16	2		910	774	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197902	123197902	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0019751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	15	235	1	ENST00000218089.9:c.2025+1G>A		p.X675_splice	ENST00000218089	NM_001042749.1	675			1	1	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	0	0.16	1		236	130	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782144	NA	P-0019752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	341	877	0	ENST00000269305.4:c.473G>C	p.Arg158Pro	p.R158P	ENST00000269305	NM_001126112.2	158	cGc/cCc	5/11	0.561163597763502	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.561163597763502	1		877	765	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99185071	99185072	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0019752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	64	535	0	ENST00000074304.5:c.2476_2477del	p.Ser826PhefsTer9	p.S826Ffs*9	ENST00000074304	NM_001134224.1	825	GAg/g	23/26	1	2	FACETS	0.307	0.265	0.353	0.307	0.265	0.353	SUBCLONAL	1	TRUE	1	0.561163597763502	2		535	742	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55231463	55231463	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1488695603	NA	P-0019752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	251	652	0	ENST00000275493.2:c.1669C>T	p.Gln557Ter	p.Q557*	ENST00000275493	NM_005228.3	557	Cag/Tag	14/28	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.561163597763502	2		652	893	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850823	128850823	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	252	816	0	ENST00000249373.3:c.1670A>C	p.Asp557Ala	p.D557A	ENST00000249373	NM_005631.4	557	gAc/gCc	10/12	0.561163597763502	1	FACETS	0.976	0.919	1	0.976	0.919	1	CLONAL	1	TRUE	0	0.561163597763502	1		816	662	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223685	53223685	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	277	1017	0	ENST00000375401.3:c.3674C>A	p.Pro1225His	p.P1225H	ENST00000375401	NM_004187.3	1225	cCc/cAc	23/26	0.561163597763502	1	FACETS	0.786	0.739	0.833	0.786	0.739	0.833	SUBCLONAL	1	TRUE	0	0.561163597763502	1		1017	904	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0019753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	146	416	2	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	0.549832476347755	1	FACETS	0.975	0.9	1	0.975	0.9	1	CLONAL	1	TRUE	0	0.549832476347755	1		418	395	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575550	64575550	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs794728648	NA	P-0019753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	228	688	0	ENST00000312049.6:c.467G>T	p.Gly156Val	p.G156V	ENST00000312049	NM_130799.2	156	gGt/gTt	3/10	0.549832476347755	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.549832476347755	1		688	569	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569832	67569832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	118	418	0	ENST00000274335.5:c.493C>T	p.Leu165Phe	p.L165F	ENST00000274335		165	Ctt/Ttt	3/15	1	2	FACETS	0.931	0.845	1	0.931	0.845	1	CLONAL	1	TRUE	1	0.549832476347755	2		418	461	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0019754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	124	582	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.392462072518088	2		582	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0019754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	270	717	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.392462072518088	2	FACETS	0.984	0.929	1	0.984	0.929	1	CLONAL	2	TRUE	0	0.392462072518088	2		718	699	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439981	56439981	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	222	1005	1	ENST00000407977.2:c.611C>G	p.Thr204Arg	p.T204R	ENST00000407977		204	aCa/aGa	6/10	0.392462072518088	1	FACETS	0.976	0.909	1	0.976	0.909	1	CLONAL	1	TRUE	0	0.392462072518088	1		1006	932	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790042	40790042	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	132	638	0	ENST00000373198.4:c.2689A>G	p.Ile897Val	p.I897V	ENST00000373198	NM_133170.3	897	Atc/Gtc	18/32	0.327753247645031	4	FACETS	1	0.94	1	0.523	0.475	0.575	CLONAL	1	TRUE	2	0.392462072518088	4		638	895	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0019755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	73	949	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		950	708	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0019758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	120	680	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.330741871013299	2		680	717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0019758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	123	780	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.330741871013299	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.330741871013299	1		780	535	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849591	68849592	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	108	663	0	ENST00000261769.5:c.1497dup	p.Gly500TrpfsTer37	p.G500Wfs*37	ENST00000261769	NM_004360.3	498	-/T	10/16	0.330741871013299	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.330741871013299	1		663	530	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112892398	112892398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143433437	NA	P-0019758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	110	656	1	ENST00000351677.2:c.556C>T	p.Arg186Trp	p.R186W	ENST00000351677	NM_002834.3	186	Cgg/Tgg	5/16	1	2	FACETS	0.925	0.832	1	0.925	0.832	1	CLONAL	1	TRUE	1	0.330741871013299	2		657	719	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71161782	71161782	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	30	217	0	ENST00000318789.4:c.187C>T	p.Gln63Ter	p.Q63*	ENST00000318789	NM_032682.5	63	Cag/Tag	7/21	0.330741871013299	1	FACETS	0.977	0.797	1	0.977	0.797	1	CLONAL	1	TRUE	0	0.330741871013299	1		217	155	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157663	106157663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	62	374	0	ENST00000380013.4:c.2564C>T	p.Ala855Val	p.A855V	ENST00000380013	NM_001127208.2	855	gCa/gTa	3/11	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.330741871013299	2		374	359	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937744	44937744	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0019758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	103	590	0	ENST00000377967.4:c.2932A>T	p.Lys978Ter	p.K978*	ENST00000377967	NM_021140.2	978	Aag/Tag	19/29	1	2	FACETS	0.881	0.789	0.979	0.881	0.789	0.979	CLONAL	1	TRUE	1	0.330741871013299	2		590	707	SUCCESS
AR	367	MSKCC	GRCh37	X	66905889	66905889	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	71	501	0	ENST00000374690.3:c.1806C>A	p.Cys602Ter	p.C602*	ENST00000374690	NM_000044.3	602	tgC/tgA	3/8	1	2	FACETS	0.893	0.781	1	0.893	0.781	1	CLONAL	1	TRUE	1	0.330741871013299	2		501	481	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	164	600	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.517746133881199	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	1	0.517746133881199	3		600	386	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347581	89347581	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	28	604	0	ENST00000301030.4:c.5369C>A	p.Ser1790Ter	p.S1790*	ENST00000301030	NM_001256183.1	1790	tCg/tAg	9/13	0.517746133881199	2	FACETS	0.27	0.216	0.333	0.135	0.108	0.167	SUBCLONAL	1	TRUE	0	0.517746133881199	2		604	400	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593558	48593558	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587781618	NA	P-0019759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	17	185	1	ENST00000342988.3:c.1308+1G>T		p.X436_splice	ENST00000342988	NM_005359.5	436			0.499034002587388	1	FACETS	0.412	0.311	0.53	0.412	0.311	0.53	SUBCLONAL	1	TRUE	0	0.517746133881199	1		186	118	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427975	49427975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	137	599	1	ENST00000301067.7:c.10615C>T	p.Arg3539Trp	p.R3539W	ENST00000301067	NM_003482.3	3539	Cgg/Tgg	38/54	1	2	FACETS	0.843	0.768	0.921	0.843	0.768	0.921	CLONAL	1	TRUE	1	0.441148428369071	2		600	737	SUCCESS
RET	5979	MSKCC	GRCh37	10	43595978	43596009	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTTGCTGTACGTCCATGCCCTGCGGGACGC	CCCTTGCTGTACGTCCATGCCCTGCGGGACGC	-	novel	NA	P-0019760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	46	696	0	ENST00000355710.3:c.149_180del	p.Leu50Ter	p.L50*	ENST00000355710	NM_020975.4	49	CCCTTGCTGTACGTCCATGCCCTGCGGGACGCc/c	2/20	1	2	FACETS	0.244	0.205	0.288	0.244	0.205	0.288	SUBCLONAL	1	TRUE	1	0.441148428369071	2		696	853	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421848	49421848	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	183	677	0	ENST00000301067.7:c.14459del	p.Pro4820GlnfsTer38	p.P4820Qfs*38	ENST00000301067	NM_003482.3	4820	cCa/ca	46/54	1	2	FACETS	0.888	0.82	0.959	0.888	0.82	0.959	CLONAL	1	TRUE	1	0.441148428369071	2		677	934	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968600	55968600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	173	699	1	ENST00000263923.4:c.2063G>A	p.Cys688Tyr	p.C688Y	ENST00000263923	NM_002253.2	688	tGc/tAc	14/30	1	2	FACETS	0.942	0.868	1	0.942	0.868	1	CLONAL	1	TRUE	1	0.441148428369071	2		700	833	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502306	157502306	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	96	367	0	ENST00000346085.5:c.3339G>C	p.Leu1113Phe	p.L1113F	ENST00000346085	NM_020732.3	1113	ttG/ttC	12/20	1	2	FACETS	0.886	0.793	0.985	0.886	0.793	0.985	CLONAL	1	TRUE	1	0.441148428369071	2		367	491	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118370564	118370564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781795624	NA	P-0019761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	18	464	1	ENST00000534358.1:c.6094G>A	p.Asp2032Asn	p.D2032N	ENST00000534358	NM_005933.3	2032	Gac/Aac	24/36	0.201603346946697	2	FACETS	0.757	0.571	0.975	0.378	0.285	0.488	CLONAL	1	TRUE	0	0.215207763964441	2		465	221	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202322	138202322	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	11	576	0	ENST00000237289.4:c.2239G>A	p.Ala747Thr	p.A747T	ENST00000237289	NM_001270507.1	747	Gcc/Acc	9/9	1	2	FACETS	0.519	0.359	0.718	0.519	0.359	0.718	SUBCLONAL	1	TRUE	1	0.215207763964441	2		576	197	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0019762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	41	918	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.658	0.546	0.784	0.658	0.546	0.784	SUBCLONAL	1	TRUE	1	0.14	2		918	890	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0019762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	41	555	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.774	0.643	0.92	0.774	0.643	0.92	CLONAL	1	TRUE	1	0.14	2		556	757	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239420	105239420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	60	611	0	ENST00000349310.3:c.967G>A	p.Asp323Asn	p.D323N	ENST00000349310	NM_001014432.1	323	Gac/Aac	12/15	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.14	2		611	815	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946495	71946495	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs747360226	NA	P-0019762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	47	509	1	ENST00000298229.2:c.2659G>A	p.Glu887Lys	p.E887K	ENST00000298229	NM_001567.3	887	Gag/Aag	23/28	1	2	FACETS	0.823	0.692	0.968	0.823	0.692	0.968	CLONAL	1	TRUE	1	0.14	2		510	816	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246143	46246143	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	54	431	2	ENST00000334344.6:c.4237G>T	p.Glu1413Ter	p.E1413*	ENST00000334344	NM_152641.2	1413	Gaa/Taa	15/21	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.14	2		433	679	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912167	29912183	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGATGGGGTAAGGAGG	GAGATGGGGTAAGGAGG	-	novel	NA	P-0019762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	14	162	0	ENST00000376809.5:c.895+2_895+18del		p.X299_splice	ENST00000376809	NM_002116.7	299		4/8	1	2	FACETS	0.787	0.569	1	0.787	0.569	1	CLONAL	1	TRUE	1	0.14	2		162	254	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248151	110248151	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	54	446	0	ENST00000374672.4:c.1321G>C	p.Asp441His	p.D441H	ENST00000374672	NM_004235.4	441	Gat/Cat	5/5	1	2	FACETS	0.985	0.84	1	0.985	0.84	1	CLONAL	1	TRUE	1	0.14	2		446	783	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201059	NA	P-0019763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	215	764	0	ENST00000269305.4:c.856G>T	p.Glu286Ter	p.E286*	ENST00000269305	NM_001126112.2	286	Gaa/Taa	8/11	0.511926153377809	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.511926153377809	1		764	597	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257950	16257950	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	165	507	0	ENST00000375759.3:c.5218del	p.Ala1740ProfsTer10	p.A1740Pfs*10	ENST00000375759	NM_015001.2	1739	Ggg/gg	11/15	NA	2	FACETS	0.79	0.734	0.847			1	INDETERMINATE	2	TRUE	NA	0.511926153377809	2		507	408	SUCCESS
ATM	472	MSKCC	GRCh37	11	108225590	108225590	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	120	686	0	ENST00000278616.4:c.8839A>G	p.Thr2947Ala	p.T2947A	ENST00000278616	NM_000051.3	2947	Acc/Gcc	61/63	0.464513413130993	1	FACETS	0.979	0.892	1	0.979	0.892	1	CLONAL	1	TRUE	0	0.464513413130993	1		686	405	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934105	39934105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs538820529	NA	P-0019764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	115	856	1	ENST00000378444.4:c.494C>T	p.Ala165Val	p.A165V	ENST00000378444	NM_001123385.1	165	gCg/gTg	4/15	1	2	FACETS	0.952	0.862	1	0.952	0.862	1	CLONAL	1	TRUE	1	0.464513413130993	2		857	520	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974799	21974799	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	66	201	0	ENST00000304494.5:c.28G>T	p.Glu10Ter	p.E10*	ENST00000304494	NM_000077.4	10	Gag/Tag	1/3	0.400424975026457	2	FACETS	1	0.975	1	0.741	0.655	0.83	CLONAL	1	TRUE	0	0.459207229486844	2		201	194	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600464	10600464	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	525	847	0	ENST00000171111.5:c.1391G>T	p.Gly464Val	p.G464V	ENST00000171111	NM_203500.1	464	gGc/gTc	4/6	0.423019750926375	3	FACETS	0.964	0.93	0.998	0.964	0.93	0.998	CLONAL	3	TRUE	0	0.459207229486844	3		847	972	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677765	47677765	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	56	569	1	ENST00000347630.2:c.1100del	p.Pro367HisfsTer5	p.P367Hfs*5	ENST00000347630	NM_001007230.1	367	cCa/ca	11/11	0.203277745361386	2	FACETS	0.45	0.385	0.52	0.225	0.192	0.26	INDETERMINATE	1	TRUE	0	0.459207229486844	2		570	542	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258581	16258581	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	314	609	0	ENST00000375759.3:c.5846G>T	p.Arg1949Leu	p.R1949L	ENST00000375759	NM_015001.2	1949	cGg/cTg	11/15	0.459207229486844	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.459207229486844	2		609	634	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731181	162731181	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	227	404	0	ENST00000367921.3:c.1036A>T	p.Ile346Phe	p.I346F	ENST00000367921	NM_006182.2	346	Atc/Ttc	9/18	0.459207229486844	3	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	1	0.459207229486844	3		404	607	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944122	71944122	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	559	688	0	ENST00000298229.2:c.1955A>T	p.Glu652Val	p.E652V	ENST00000298229	NM_001567.3	652	gAg/gTg	17/28	0.382020041341096	4	FACETS	0.949	0.918	0.979			1	CLONAL	4	TRUE	NA	0.459207229486844	4		688	936	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117430	115117430	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0019765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	145	533	0	ENST00000257566.3:c.744C>G	p.Tyr248Ter	p.Y248*	ENST00000257566	NM_016569.3	248	taC/taG	4/8	0.459207229486844	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.459207229486844	1		533	419	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478604	99478604	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	228	544	0	ENST00000268035.6:c.3246G>T	p.Met1082Ile	p.M1082I	ENST00000268035	NM_000875.3	1082	atG/atT	17/21	0.271877591716752	2	FACETS	0.759	0.711	0.808	0.759	0.711	0.808	INDETERMINATE	2	TRUE	0	0.459207229486844	2		544	654	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577542	7577561	+	frameshift_variant	Frame_Shift_Del	DEL	TCATGCCGCCCATGCAGGAA	TCATGCCGCCCATGCAGGAA	-	novel	NA	P-0019765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	104	736	0	ENST00000269305.4:c.720_739del	p.Ser240ArgfsTer17	p.S240Rfs*17	ENST00000269305	NM_001126112.2	240	agTTCCTGCATGGGCGGCATGAac/agac	7/11	0.400424975026457	2	FACETS	0.908	0.816	1	0.454	0.408	0.502	CLONAL	1	TRUE	0	0.459207229486844	2		736	499	SUCCESS
YES1	7525	MSKCC	GRCh37	18	739749	739749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	664	796	1	ENST00000314574.4:c.1123G>A	p.Asp375Asn	p.D375N	ENST00000314574	NM_005433.3	375	Gat/Aat	9/12	0.459207229486844	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	4	TRUE	0	0.459207229486844	4		797	1010	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288740	15288741	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0019765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	119	163	1	ENST00000263388.2:c.3998_3999delinsTT	p.Gly1333Val	p.G1333V	ENST00000263388	NM_000435.2	1333	gGG/gTT	24/33	0.423019750926375	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	TRUE	0	0.459207229486844	3		164	196	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379718	17379718	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	493	994	0	ENST00000359435.4:c.103G>T	p.Glu35Ter	p.E35*	ENST00000359435	NM_001033549.1	35	Gag/Tag	2/9	0.423019750926375	3	FACETS	0.854	0.821	0.888	0.854	0.821	0.888	CLONAL	3	TRUE	0	0.459207229486844	3		994	1030	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36217207	36217207	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1309	74	930	0	ENST00000222270.7:c.3956C>G	p.Ser1319Cys	p.S1319C	ENST00000222270	NM_014727.1	1319	tCt/tGt	14/37	0.459207229486844	4	FACETS	0.34	0.296	0.388	0.113	0.098	0.13	SUBCLONAL	1	TRUE	1	0.459207229486844	4		930	1383	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047393	128047393	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	102	434	0	ENST00000285398.2:c.529G>T	p.Val177Phe	p.V177F	ENST00000285398	NM_000122.1	177	Gtt/Ttt	5/15	1	2	FACETS	0.92	0.826	1	0.92	0.826	1	CLONAL	1	TRUE	1	0.459207229486844	2		434	483	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39772532	39772532	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	188	591	0	ENST00000288319.7:c.709T>C	p.Tyr237His	p.Y237H	ENST00000288319	NM_182918.3	237	Tat/Cat	6/10	0.435040951051163	2	FACETS	0.775	0.722	0.83	0.775	0.722	0.83	SUBCLONAL	2	TRUE	0	0.459207229486844	2		591	528	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37622769	37622769	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	404	907	0	ENST00000249071.6:c.523G>T	p.Ala175Ser	p.A175S	ENST00000249071	NM_002872.4	175	Gcc/Tcc	6/7	0.450104098817212	2	FACETS	0.96	0.918	1	0.96	0.918	1	CLONAL	2	TRUE	0	0.459207229486844	2		907	916	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683507	182683507	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	55	690	0	ENST00000292782.4:c.38G>T	p.Arg13Leu	p.R13L	ENST00000292782	NM_020640.2	13	cGt/cTt	2/7	0.184640739333037	6	FACETS	0.61	0.521	0.708	0.102	0.086	0.118	INDETERMINATE	1	TRUE	0	0.459207229486844	6		690	753	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946270	55946270	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	206	349	0	ENST00000263923.4:c.3909C>G	p.Ser1303Arg	p.S1303R	ENST00000263923	NM_002253.2	1303	agC/agG	30/30	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.459207229486844	NA		349	405	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818363	170818363	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs11551576	NA	P-0019765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	136	484	0	ENST00000296930.5:c.193A>G	p.Met65Val	p.M65V	ENST00000296930	NM_002520.6	65	Atg/Gtg	3/11	0.459207229486844	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.459207229486844	1		484	361	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976825	2976825	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	128	802	0	ENST00000396946.4:c.1187G>T	p.Cys396Phe	p.C396F	ENST00000396946	NM_032415.4	396	tGc/tTc	9/25	0.459207229486844	3	FACETS	0.757	0.685	0.832	0.378	0.342	0.416	SUBCLONAL	1	TRUE	1	0.459207229486844	3		802	906	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381516	81381516	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	143	369	0	ENST00000222390.5:c.545G>T	p.Gly182Val	p.G182V	ENST00000222390	NM_000601.4	182	gGg/gTg	5/18	0.171080395504788	5	FACETS	1	0.94	1	0.686	0.629	0.745	INDETERMINATE	2	TRUE	2	0.459207229486844	5		369	511	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319966	8319966	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	37	219	0	ENST00000356435.5:c.5535C>A	p.Ser1845Arg	p.S1845R	ENST00000356435		1845	agC/agA	34/35	0.400424975026457	2	FACETS	0.822	0.685	0.972	0.411	0.342	0.486	CLONAL	1	TRUE	0	0.459207229486844	2		219	196	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650616	48650617	+	missense_variant	Missense_Mutation	DNP	CT	CT	AA	novel	NA	P-0019765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	63	739	0	ENST00000376670.3:c.586_587delinsAA	p.Leu196Lys	p.L196K	ENST00000376670	NM_002049.3	196	CTg/AAg	3/6	0.236793806330044	3	FACETS	0.383	0.33	0.44			1	INDETERMINATE	1	TRUE	NA	0.459207229486844	3		739	882	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652384	48652384	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	81	982	2	ENST00000376670.3:c.1055G>T	p.Gly352Val	p.G352V	ENST00000376670	NM_002049.3	352	gGc/gTc	6/6	0.236793806330044	3	FACETS	0.402	0.353	0.455			1	INDETERMINATE	1	TRUE	NA	0.459207229486844	3		984	1079	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0019771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	103	697	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.889	0.796	0.987	0.889	0.796	0.987	CLONAL	1	TRUE	1	0.328782917645863	2		697	705	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	166	736	0				ENST00000310581	NM_198253.2	-/1132			0.136583224650039	4	FACETS	1	0.97	1	1	0.97	1	INDETERMINATE	2	TRUE	2	0.328782917645863	4		736	609	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678029	58678029	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567962294	NA	P-0019771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	43	432	0	ENST00000305921.3:c.254C>T	p.Ser85Leu	p.S85L	ENST00000305921	NM_003620.3	85	tCg/tTg	1/6	1	2	FACETS	0.703	0.59	0.828	0.703	0.59	0.828	SUBCLONAL	1	TRUE	1	0.328782917645863	2		432	372	SUCCESS
ATM	472	MSKCC	GRCh37	11	108137989	108137989	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	84	735	1	ENST00000278616.4:c.2558C>A	p.Ser853Ter	p.S853*	ENST00000278616	NM_000051.3	853	tCa/tAa	17/63	0.195051059959349	2	FACETS	0.77	0.68	0.866	0.385	0.34	0.433	INDETERMINATE	1	TRUE	0	0.328782917645863	2		736	664	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030454	49030457	+	frameshift_variant	Frame_Shift_Del	DEL	ATCT	ATCT	-	novel	NA	P-0019771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	143	633	0	ENST00000267163.4:c.1930_1933del	p.Ser644ProfsTer13	p.S644Pfs*13	ENST00000267163	NM_000321.2	643	aaATCT/aa	19/27	0.328782917645863	1	FACETS	0.895	0.825	0.967	1	0.991	1	CLONAL	2	TRUE	0	0.328782917645863	1		633	406	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543716	29543716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	67	718	0	ENST00000389048.3:c.1447G>A	p.Glu483Lys	p.E483K	ENST00000389048	NM_004304.4	483	Gaa/Aaa	7/29	1	2	FACETS	0.538	0.467	0.616	0.538	0.467	0.616	SUBCLONAL	1	TRUE	1	0.328782917645863	2		718	757	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714481	40715408	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTGCATACAGAACTGAGATAAGGAAAGAGGTCACAGAAGGAGCTCAAAGGCAGGGGGCGGGTATCAAAGTCTCATTTATCAACAAGCTTTTCTTTTCTTTTTTTCTTTTTCTTTTTTTTTTTTGAGATGGAGCATCACTCTTGTTGCCCAGCCTGGAGTGCATTGGCACGATTTTGGCTCACTGCAACCTCTGCCTCCCAGGTTCAAGTGATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGATTATAGGCACCTGCCACCATGTCTGGCTATTTTTAGTAAAGATGGGGTTTCGCCGTGTTGGCCAGGCTAGTCTTGAACTCCTGACCTCGGGTGATCCACCTGTCCCAGCCTCCCAGAGTGCTAGGATTATAGGTGTGAGCCACTGTGCCCAGCCGTCACCAAGCTTTTTTTATGGCTGGAAGGACACATTGGCCAGAAAGGTAGAGTATTATGTAGGAAATTAGACTCAGTTTCCCCTTTAGGGAGCAGCCATCCACTTTTTCTGGTGTTGAAATATCAAGGCTTTGAGCACAGAAACACTGGGCTTGCAAATCTTTGCTATGTTGATTTCAAACCATTTGTTAGGTTTGCTTAACCTGAGTTTCCTCATCTGTAAAATGGGGAGAATAATATCTACCTCTAAGCCCCGCTGTCAGGATTAGATAGAACATGCTAAAGAAAGGGCAAGTACCATCTATTTTTCTTTTCACCACGCAAATCATCACAAGCTCTTCCTCATTCCAGGAAAACCTTCATAGTGTTCATTCATGATCAGATCAGAAGTAGTGTAAAAAATATAGGGGTTTCGGGAGGCGGAGCTTGCAGTGAGCTGAGATCGCGCCACTGCACTCCAGCCTGGGTGACACAGCGAGACTCCATCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAATATATATATATATG	ACTGCATACAGAACTGAGATAAGGAAAGAGGTCACAGAAGGAGCTCAAAGGCAGGGGGCGGGTATCAAAGTCTCATTTATCAACAAGCTTTTCTTTTCTTTTTTTCTTTTTCTTTTTTTTTTTTGAGATGGAGCATCACTCTTGTTGCCCAGCCTGGAGTGCATTGGCACGATTTTGGCTCACTGCAACCTCTGCCTCCCAGGTTCAAGTGATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGATTATAGGCACCTGCCACCATGTCTGGCTATTTTTAGTAAAGATGGGGTTTCGCCGTGTTGGCCAGGCTAGTCTTGAACTCCTGACCTCGGGTGATCCACCTGTCCCAGCCTCCCAGAGTGCTAGGATTATAGGTGTGAGCCACTGTGCCCAGCCGTCACCAAGCTTTTTTTATGGCTGGAAGGACACATTGGCCAGAAAGGTAGAGTATTATGTAGGAAATTAGACTCAGTTTCCCCTTTAGGGAGCAGCCATCCACTTTTTCTGGTGTTGAAATATCAAGGCTTTGAGCACAGAAACACTGGGCTTGCAAATCTTTGCTATGTTGATTTCAAACCATTTGTTAGGTTTGCTTAACCTGAGTTTCCTCATCTGTAAAATGGGGAGAATAATATCTACCTCTAAGCCCCGCTGTCAGGATTAGATAGAACATGCTAAAGAAAGGGCAAGTACCATCTATTTTTCTTTTCACCACGCAAATCATCACAAGCTCTTCCTCATTCCAGGAAAACCTTCATAGTGTTCATTCATGATCAGATCAGAAGTAGTGTAAAAAATATAGGGGTTTCGGGAGGCGGAGCTTGCAGTGAGCTGAGATCGCGCCACTGCACTCCAGCCTGGGTGACACAGCGAGACTCCATCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAATATATATATATATG	-	novel	NA	P-0019771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	56	565	0	ENST00000373198.4:c.3904-915_3916del		p.X1302_splice	ENST00000373198	NM_133170.3	1302		29/32	0.328782917645863	5	FACETS	0.561	0.479	0.652	0.14	0.119	0.163	SUBCLONAL	1	TRUE	1	0.328782917645863	5		565	906	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27204960	27204960	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	81	722	0	ENST00000380036.4:c.2261C>T	p.Ser754Phe	p.S754F	ENST00000380036	NM_000459.3	754	tCt/tTt	14/23	0.328782917645863	3	FACETS	0.763	0.672	0.861	0.381	0.336	0.431	SUBCLONAL	1	TRUE	1	0.328782917645863	3		722	752	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0019772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	196	749	1	ENST00000269305.4:c.673-2A>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.229974641607573	4	FACETS	0.903	0.843	0.964	0.903	0.843	0.964	CLONAL	4	TRUE	0	0.265103245241678	4		750	518	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0019772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	409	928	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.265103245241678	9	FACETS	1	0.964	1	1	0.964	1	CLONAL	5	TRUE	4	0.265103245241678	9		928	1173	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243969	46243969	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	63	749	0	ENST00000334344.6:c.2063C>G	p.Pro688Arg	p.P688R	ENST00000334344	NM_152641.2	688	cCt/cGt	15/21	0.246583433772888	3	FACETS	0.893	0.772	1	0.446	0.386	0.512	CLONAL	1	TRUE	1	0.265103245241678	3		749	603	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442738	99442738	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	51	911	0	ENST00000268035.6:c.1135G>A	p.Gly379Arg	p.G379R	ENST00000268035	NM_000875.3	379	Ggg/Agg	5/21	0.213451924159248	2	FACETS	0.554	0.47	0.647	0.277	0.235	0.324	SUBCLONAL	1	TRUE	0	0.265103245241678	2		911	694	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46252756	46252756	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	65	749	0	ENST00000371998.3:c.185T>C	p.Phe62Ser	p.F62S	ENST00000371998		62	tTc/tCc	4/23	0.240203596340958	3	FACETS	0.938	0.814	1	0.313	0.271	0.358	CLONAL	1	TRUE	0	0.265103245241678	3		749	592	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557316	187557330	+	inframe_deletion	In_Frame_Del	DEL	GGCTTGGAGATCCAT	GGCTTGGAGATCCAT	-	novel	NA	P-0019772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	34	751	0	ENST00000441802.2:c.4032_4046del	p.Glu1344_Pro1349delinsAsp	p.E1344_P1349delinsD	ENST00000441802	NM_005245.3	1344	gaATGGATCTCCAAGCCc/gac	6/27	1	2	FACETS	0.483	0.394	0.584	0.483	0.394	0.584	SUBCLONAL	1	TRUE	1	0.265103245241678	2		751	531	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	147	600	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.324435347347547	3	FACETS	1	0.985	1	0.68	0.622	0.742	CLONAL	1	TRUE	1	0.324435347347547	3		600	774	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0019773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	144	646	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	0.944	0.861	1	0.944	0.861	1	CLONAL	1	TRUE	1	0.324435347347547	2		646	940	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918843	50918843	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759530743	NA	P-0019773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	74	791	0	ENST00000440232.2:c.2713G>A	p.Glu905Lys	p.E905K	ENST00000440232	NM_002691.3	905	Gag/Aag	21/27	1	2	FACETS	0.4	0.349	0.456	0.4	0.349	0.456	SUBCLONAL	1	TRUE	1	0.324435347347547	2		791	1140	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346960	70346960	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	81	449	0	ENST00000374080.3:c.2827C>A	p.Gln943Lys	p.Q943K	ENST00000374080		943	Cag/Aag	20/45	1	2	FACETS	0.682	0.601	0.77	0.682	0.601	0.77	SUBCLONAL	1	TRUE	1	0.324435347347547	2		449	732	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907691	111907693	+	missense_variant	Missense_Mutation	TNP	TGG	TGG	CGA	novel	NA	P-0019773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	66	499	0	ENST00000393256.3:c.465_467delinsCGA	p.Gly156Glu	p.G156E	ENST00000393256	NM_006538.4	155	atTGGa/atCGAa	3/4	1	2	FACETS	0.513	0.444	0.588	0.513	0.444	0.588	SUBCLONAL	1	TRUE	1	0.324435347347547	2		499	793	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577523	7577524	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	227	641	0	ENST00000269305.4:c.757dup	p.Thr253AsnfsTer11	p.T253Nfs*11	ENST00000269305	NM_001126112.2	253	acc/aAcc	7/11	0.25615053470436	3	FACETS	1	0.975	1	0.721	0.675	0.768	CLONAL	2	TRUE	0	0.366828301831044	3		641	677	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164875	36164876	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0019776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	388	871	0	ENST00000300305.3:c.999dup	p.Arg334AlafsTer266	p.R334Afs*266	ENST00000300305		333	-/G	8/8	0.366828301831044	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.366828301831044	3		871	1011	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665332	176665332	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	58	474	1	ENST00000439151.2:c.4016A>T	p.Lys1339Ile	p.K1339I	ENST00000439151	NM_022455.4	1339	aAa/aTa	7/23	0.366828301831044	3	FACETS	0.701	0.602	0.808	0.35	0.301	0.404	SUBCLONAL	1	TRUE	1	0.366828301831044	3		475	534	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508336	106508336	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	89	348	0	ENST00000359195.3:c.330C>A	p.Tyr110Ter	p.Y110*	ENST00000359195	NM_002649.2	110	taC/taA	2/11	0.276781622211462	5	FACETS	0.998	0.891	1	0.665	0.594	0.74	CLONAL	2	TRUE	2	0.366828301831044	5		348	377	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137323830	137323830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	91	790	0	ENST00000481739.1:c.1123C>T	p.Leu375Phe	p.L375F	ENST00000481739	NM_002957.4	375	Ctc/Ttc	8/10	0.28946562368951	3	FACETS	0.7	0.621	0.785			1	SUBCLONAL	1	TRUE	NA	0.366828301831044	3		790	839	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696689	47696689	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519972	NA	P-0019777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	171	710	0	ENST00000347630.2:c.259T>A	p.Tyr87Asn	p.Y87N	ENST00000347630	NM_001007230.1	87	Tac/Aac	5/11	1	2	FACETS	0.757	0.697	0.819	1	0.989	1	SUBCLONAL	2	TRUE	1	0.29	2		710	779	SUCCESS
APC	324	MSKCC	GRCh37	5	112175940	112175943	+	frameshift_variant	Frame_Shift_Del	DEL	AGAA	AGAA	-	rs863225358	NA	P-0019777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	19	449	0	ENST00000257430.4:c.4652_4655del	p.Lys1551ArgfsTer13	p.K1551Rfs*13	ENST00000257430	NM_000038.5	1550	gAGAAa/ga	16/16	0.290034303282283	0	FACETS	0.247	0.187	0.318			1	SUBCLONAL	1	TRUE	0	0.29	0		449	377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0019778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	245	697	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.518732098657447	2	FACETS	0.977	0.926	1	0.977	0.926	1	CLONAL	2	TRUE	0	0.535625129560795	2		697	468	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0019778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	30	1097	0	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	0.328403312540772	3	FACETS	0.18	0.144	0.221	0.09	0.072	0.111	SUBCLONAL	1	TRUE	1	0.535625129560795	3		1097	790	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0019778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	154	498	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	0.5186224204076	2	FACETS	0.968	0.904	1	0.968	0.904	1	CLONAL	2	TRUE	0	0.535625129560795	2		498	297	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982965	201982966	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0019778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	264	939	0	ENST00000359651.3:c.815_816dup	p.Thr273AlafsTer22	p.T273Afs*22	ENST00000359651		272	ggc/gGCgc	7/8	0.45210091792653	3	FACETS	0.867	0.817	0.918	0.867	0.817	0.918	CLONAL	2	TRUE	1	0.535625129560795	3		939	721	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233133	46233133	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	83	362	0	ENST00000334344.6:c.1352del	p.Ser451LeufsTer12	p.S451Lfs*12	ENST00000334344	NM_152641.2	451	tCt/tt	11/21	0.535625129560795	2	FACETS	1	0.97	1	0.622	0.557	0.69	CLONAL	1	TRUE	0	0.535625129560795	2		362	249	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0019779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	67	918	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.964	0.835	1	0.964	0.835	1	CLONAL	1	TRUE	1	0.12	2		918	1158	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0019779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1759	42	1551	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	1	2	FACETS	0.389	0.322	0.463	0.389	0.322	0.463	SUBCLONAL	1	TRUE	1	0.12	2		1551	1801	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261077	16261077	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	96	776	0	ENST00000375759.3:c.8345del	p.Asn2782ThrfsTer11	p.N2782Tfs*11	ENST00000375759	NM_015001.2	2781	gAa/ga	11/15	0.198682993028349	3	FACETS	0.804	0.72	0.893	0.804	0.72	0.893	CLONAL	2	FALSE	1	0.286082343053359	3		776	477	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929426	32929426	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0019782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	170	772	0	ENST00000380152.3:c.7435+1G>A		p.X2479_splice	ENST00000380152		2479			0.227296345238392	3	FACETS	1	0.97	1	0.73	0.675	0.788	CLONAL	2	FALSE	0	0.286082343053359	3		772	620	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578497	7578497	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	232	1345	0	ENST00000269305.4:c.433del	p.Leu145CysfsTer25	p.L145Cfs*25	ENST00000269305	NM_001126112.2	145	Ctg/tg	5/11	0.227296345238392	3	FACETS	0.835	0.782	0.89	0.835	0.782	0.89	CLONAL	3	FALSE	0	0.286082343053359	3		1345	740	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983243	7983243	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	39	738	0	ENST00000319144.4:c.771C>G	p.His257Gln	p.H257Q	ENST00000319144	NM_001139.2	257	caC/caG	7/15	0.227296345238392	3	FACETS	0.746	0.618	0.887	0.249	0.206	0.296	SUBCLONAL	1	FALSE	0	0.286082343053359	3		738	418	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805940	46805940	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	64	496	0	ENST00000290295.7:c.16T>C	p.Tyr6His	p.Y6H	ENST00000290295	NM_006361.5	6	Tat/Cat	1/2	0.28630661668556	2	FACETS	0.822	0.719	0.932	0.822	0.719	0.932	CLONAL	2	FALSE	0	0.286082343053359	2		496	272	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17389808	17389808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	80	1312	0	ENST00000359435.4:c.941G>A	p.Ser314Asn	p.S314N	ENST00000359435	NM_001033549.1	314	aGc/aAc	9/9	NA	2	FACETS	0.675	0.594	0.764			1	INDETERMINATE	1	FALSE	NA	0.286082343053359	2		1312	828	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40744822	40744822	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs988297708	NA	P-0019782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	85	976	0	ENST00000392038.2:c.698A>G	p.Asn233Ser	p.N233S	ENST00000392038	NM_001626.4	233	aAc/aGc	8/14	0.198682993028349	3	FACETS	1	0.961	1	0.601	0.532	0.675	CLONAL	1	FALSE	1	0.286082343053359	3		976	565	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518270	8518270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556357771	NA	P-0019782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	20	410	2	ENST00000356435.5:c.1121C>T	p.Ala374Val	p.A374V	ENST00000356435		374	gCg/gTg	10/35	0.246503369726261	3	FACETS	0.522	0.399	0.666	0.174	0.133	0.222	SUBCLONAL	1	FALSE	0	0.286082343053359	3		412	306	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs879253911	NA	P-0019783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	150	474	0	ENST00000269305.4:c.538G>T	p.Glu180Ter	p.E180*	ENST00000269305	NM_001126112.2	180	Gag/Tag	5/11	0.581546885782909	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.581546885782909	1		474	354	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671286	30671286	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	149	367	0	ENST00000376406.3:c.5591G>C	p.Arg1864Thr	p.R1864T	ENST00000376406	NM_014641.2	1864	aGa/aCa	11/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.581546885782909	2		367	485	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670422	246670422	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	247	576	0	ENST00000388985.4:c.98C>G	p.Ser33Trp	p.S33W	ENST00000388985		33	tCg/tGg	1/12	0.317530638653435	6	FACETS	0.979	0.917	1	0.49	0.458	0.522	INDETERMINATE	2	TRUE	2	0.581546885782909	6		576	938	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433614	49433614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	239	790	0	ENST00000301067.7:c.7939G>A	p.Asp2647Asn	p.D2647N	ENST00000301067	NM_003482.3	2647	Gac/Aac	31/54	1	2	FACETS	0.987	0.924	1	0.987	0.924	1	CLONAL	1	TRUE	1	0.581546885782909	2		790	833	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434849	49434849	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	227	768	0	ENST00000301067.7:c.6704G>C	p.Arg2235Thr	p.R2235T	ENST00000301067	NM_003482.3	2235	aGa/aCa	31/54	1	2	FACETS	0.981	0.916	1	0.981	0.916	1	CLONAL	1	TRUE	1	0.581546885782909	2		768	796	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435312	49435312	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	157	508	0	ENST00000301067.7:c.6241G>A	p.Glu2081Lys	p.E2081K	ENST00000301067	NM_003482.3	2081	Gag/Aag	31/54	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.581546885782909	2		508	491	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436602	49436602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	181	553	2	ENST00000301067.7:c.5704G>A	p.Glu1902Lys	p.E1902K	ENST00000301067	NM_003482.3	1902	Gaa/Aaa	26/54	1	2	FACETS	0.967	0.895	1	0.967	0.895	1	CLONAL	1	TRUE	1	0.581546885782909	2		555	644	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436856	49436856	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0019783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	127	464	0	ENST00000301067.7:c.5644+3G>A		p.X1882_splice	ENST00000301067	NM_003482.3	1882			1	2	FACETS	0.939	0.857	1	0.939	0.857	1	CLONAL	1	TRUE	1	0.581546885782909	2		464	465	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41011054	41011054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	152	533	0	ENST00000267868.3:c.487G>A	p.Glu163Lys	p.E163K	ENST00000267868	NM_002875.4	163	Gag/Aag	6/10	1	2	FACETS	0.863	0.792	0.936	0.863	0.792	0.936	CLONAL	1	TRUE	1	0.581546885782909	2		533	606	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855969	68855969	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	145	461	2	ENST00000261769.5:c.1777C>A	p.Pro593Thr	p.P593T	ENST00000261769	NM_004360.3	593	Ccc/Acc	12/16	0.581546885782909	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.581546885782909	1		463	335	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004871	16004871	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	168	504	0	ENST00000268712.3:c.2383C>T	p.Gln795Ter	p.Q795*	ENST00000268712	NM_006311.3	795	Cag/Tag	20/46	0.373042727686494	1	FACETS	0.933	0.867	1	0.933	0.867	1	CLONAL	1	TRUE	0	0.581546885782909	1		504	439	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277027	18277027	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	136	554	0	ENST00000222254.8:c.1474G>C	p.Glu492Gln	p.E492Q	ENST00000222254	NM_005027.3	492	Gaa/Caa	12/16	0.373042727686494	1	FACETS	0.701	0.642	0.763	0.701	0.642	0.763	SUBCLONAL	1	TRUE	0	0.581546885782909	1		554	473	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	132	600	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.609	0.555	0.666	0.609	0.555	0.666	SUBCLONAL	1	TRUE	1	0.757682495034109	2		600	572	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169377	11169377	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519916	NA	P-0019784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	79	772	0	ENST00000361445.4:c.7498A>T	p.Ile2500Phe	p.I2500F	ENST00000361445	NM_004958.3	2500	Att/Ttt	56/58	1	2	FACETS	0.272	0.239	0.308	0.272	0.239	0.308	SUBCLONAL	1	TRUE	1	0.757682495034109	2		772	767	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115433	115115433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	164	788	0	ENST00000257566.3:c.893C>T	p.Pro298Leu	p.P298L	ENST00000257566	NM_016569.3	298	cCt/cTt	5/8	1	2	FACETS	0.478	0.439	0.519	0.478	0.439	0.519	SUBCLONAL	1	TRUE	1	0.757682495034109	2		788	905	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061184	38061184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778808721	NA	P-0019784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	79	574	0	ENST00000250448.2:c.805G>A	p.Glu269Lys	p.E269K	ENST00000250448	NM_004496.3	269	Gag/Aag	2/2	1	2	FACETS	0.376	0.331	0.424	0.376	0.331	0.424	SUBCLONAL	1	TRUE	1	0.757682495034109	2		574	555	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515117	31515117	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	93	940	1	ENST00000344624.3:c.1268C>G	p.Ser423Cys	p.S423C	ENST00000344624		423	tCc/tGc	5/33	1	2	FACETS	0.282	0.25	0.316	0.282	0.25	0.316	SUBCLONAL	1	TRUE	1	0.757682495034109	2		941	872	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177488	56177488	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	97	449	0	ENST00000399503.3:c.2462del	p.Leu821Ter	p.L821*	ENST00000399503	NM_005921.1	821	Ttg/tg	14/20	1	2	FACETS	0.523	0.468	0.58	0.523	0.468	0.58	SUBCLONAL	1	TRUE	1	0.757682495034109	2		449	490	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183331	56183331	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	144	644	0	ENST00000399503.3:c.4241del	p.Ala1414AspfsTer8	p.A1414Dfs*8	ENST00000399503	NM_005921.1	1414	gCa/ga	18/20	1	2	FACETS	0.6	0.549	0.654	0.6	0.549	0.654	SUBCLONAL	1	TRUE	1	0.757682495034109	2		644	633	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877878	151877878	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	AA	novel	NA	P-0019784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	108	431	0	ENST00000262189.6:c.7067delinsTT	p.Pro2356LeufsTer11	p.P2356Lfs*11	ENST00000262189	NM_170606.2	2356	cCt/cTTt	36/59	1	2	FACETS	0.59	0.532	0.651	0.59	0.532	0.651	SUBCLONAL	1	TRUE	1	0.757682495034109	2		431	483	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0019785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	223	810	3	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.468802839621376	2		813	935	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0019785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	176	530	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.468802839621376	2		530	632	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0019785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	72	327	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.751	0.659	0.849	0.751	0.659	0.849	SUBCLONAL	1	TRUE	1	0.468802839621376	2		327	409	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95598926	95598926	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	155	649	2	ENST00000393063.1:c.233C>A	p.Thr78Asn	p.T78N	ENST00000393063	NM_030621.3	78	aCt/aAt	4/28	0.468802839621376	1	FACETS	0.876	0.806	0.948	0.876	0.806	0.948	CLONAL	1	TRUE	0	0.468802839621376	1		651	578	SUCCESS
APC	324	MSKCC	GRCh37	5	112173552	112173552	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	141	477	0	ENST00000257430.4:c.2262del	p.Arg755GlyfsTer6	p.R755Gfs*6	ENST00000257430	NM_000038.5	754	gTt/gt	16/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.468802839621376	2		477	544	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449858	149449859	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0019785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	246	1068	0	ENST00000286301.3:c.1205dup	p.Glu403ArgfsTer37	p.E403Rfs*37	ENST00000286301	NM_005211.3	402	cca/ccCa	9/22	1	2	FACETS	0.925	0.864	0.988	0.925	0.864	0.988	CLONAL	1	TRUE	1	0.468802839621376	2		1068	1135	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579361	7579361	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	181	1059	0	ENST00000269305.4:c.326del	p.Phe109SerfsTer14	p.F109Sfs*14	ENST00000269305	NM_001126112.2	109	tTc/tc	4/11	0.30036798688806	1	FACETS	0.878	0.809	0.951	0.878	0.809	0.951	CLONAL	1	FALSE	0	0.30036798688806	1		1059	1166	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81916944	81916944	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	66	673	0	ENST00000359376.3:c.763C>A	p.Gln255Lys	p.Q255K	ENST00000359376	NM_002661.3	255	Cag/Aag	9/33	0.247612794053428	2	FACETS	0.491	0.425	0.563	0.246	0.212	0.282	SUBCLONAL	1	FALSE	0	0.30036798688806	2		673	895	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288347	15288347	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs186300168	NA	P-0019786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1546	218	1415	0	ENST00000263388.2:c.4392G>C	p.Glu1464Asp	p.E1464D	ENST00000263388	NM_000435.2	1464	gaG/gaC	24/33	1	2	FACETS	0.823	0.762	0.886	0.823	0.762	0.886	CLONAL	1	FALSE	1	0.30036798688806	2		1415	1764	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0019787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	295	614	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.469838869021567	3	FACETS	0.842	0.796	0.888	0.842	0.796	0.888	CLONAL	2	TRUE	1	0.565584173405327	3		614	795	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118831	115118831	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	179	586	0	ENST00000257566.3:c.510G>A	p.Trp170Ter	p.W170*	ENST00000257566	NM_016569.3	170	tgG/tgA	2/8	1	2	FACETS	0.975	0.903	1	0.975	0.903	1	CLONAL	1	TRUE	1	0.565584173405327	2		586	649	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645412	67645412	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	83	649	0	ENST00000264010.4:c.677A>T	p.Tyr226Phe	p.Y226F	ENST00000264010	NM_006565.3	226	tAc/tTc	3/12	0.530861855130071	2	FACETS	0.615	0.545	0.69	0.308	0.272	0.345	SUBCLONAL	1	TRUE	0	0.565584173405327	2		649	477	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660557	67660557	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	369	876	0	ENST00000264010.4:c.1457A>C	p.Gln486Pro	p.Q486P	ENST00000264010	NM_006565.3	486	cAg/cCg	8/12	0.530861855130071	2	FACETS	0.843	0.805	0.881	0.843	0.805	0.881	CLONAL	2	TRUE	0	0.565584173405327	2		876	774	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958307	11958308	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0019787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	124	612	0	ENST00000353533.5:c.217_218del	p.Ile73ArgfsTer9	p.I73Rfs*9	ENST00000353533	NM_003010.3	73	ATa/a	2/11	0.525845548627314	1	FACETS	0.98	0.899	1	0.98	0.899	1	CLONAL	1	TRUE	0	0.565584173405327	1		612	321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578396	+	inframe_deletion	In_Frame_Del	DEL	TGG	TGG	-	novel	NA	P-0019788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	39	640	0	ENST00000269305.4:c.534_536del	p.His179del	p.H179del	ENST00000269305	NM_001126112.2	178	caCCAt/cat	5/11	1	2	FACETS	0.997	0.825	1	0.997	0.825	1	CLONAL	1	TRUE	1	0.12	2		640	652	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635621	47635621	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	78	730	0	ENST00000233146.2:c.293A>C	p.Tyr98Ser	p.Y98S	ENST00000233146	NM_000251.2	98	tAt/tCt	2/16	0.3	2	FACETS	0.758	0.664	0.858			1	SUBCLONAL	2	TRUE	NA	0.12	2		730	858	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412336	139412336	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1060502238	NA	P-0019788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	48	798	0	ENST00000277541.6:c.1309G>T	p.Glu437Ter	p.E437*	ENST00000277541	NM_017617.3	437	Gag/Tag	8/34	1	2	FACETS	0.93	0.784	1	0.93	0.784	1	CLONAL	1	TRUE	1	0.12	2		798	860	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0019789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	694	1119	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	0.6233269334986	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.6233269334986	3		1119	1456	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0019790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	20	405	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.261	0.2	0.331	0.261	0.2	0.331	SUBCLONAL	1	TRUE	1	0.730349106267645	2		405	210	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720805	89720808	+	frameshift_variant	Frame_Shift_Del	DEL	CTTT	CTTT	-	rs398123330	NA	P-0019790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	33	444	0	ENST00000371953.3:c.956_959del	p.Thr319LysfsTer24	p.T319Kfs*24	ENST00000371953	NM_000314.4	319	aCTTTa/aa	8/9	1	2	FACETS	0.439	0.36	0.526	0.439	0.36	0.526	SUBCLONAL	1	TRUE	1	0.730349106267645	2		444	206	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0019791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	167	397	1	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.996	0.921	1	0.996	0.921	1	CLONAL	1	TRUE	1	0.610636243783	2		398	549	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654642	67654642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	293	514	0	ENST00000264010.4:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000264010	NM_006565.3	377	Cgt/Tgt	6/12	0.610636243783	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.610636243783	1		514	584	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	158	364	0	ENST00000263967.3:c.3132T>G	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaG	21/21	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.610636243783	2		364	509	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023612	27023613	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCTCCGGCGC	novel	NA	P-0019791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	44	474	0	ENST00000324856.7:c.720_729dup	p.Ala244LeufsTer159	p.A244Lfs*159	ENST00000324856	NM_006015.4	240	ggc/gGCTCCGGCGCgc	1/20	1	2	FACETS	0.278	0.233	0.328	0.278	0.233	0.328	SUBCLONAL	1	TRUE	1	0.610636243783	2		474	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0019792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	589	697	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.745641066764323	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.745641066764323	2		697	766	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50488314	50488314	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	177	676	0	ENST00000394963.4:c.1228T>C	p.Ser410Pro	p.S410P	ENST00000394963	NM_003076.4	410	Tcc/Ccc	10/13	0.745641066764323	3	FACETS	0.832	0.768	0.899	0.416	0.384	0.45	CLONAL	1	TRUE	1	0.745641066764323	3		676	783	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	59	736	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.78	0.671	0.897	0.78	0.671	0.897	SUBCLONAL	1	TRUE	1	0.287199714591363	2		736	527	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640644	3640644	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	136	1140	1	ENST00000294008.3:c.2995C>A	p.Gln999Lys	p.Q999K	ENST00000294008	NM_032444.2	999	Caa/Aaa	12/15	1	2	FACETS	0.895	0.813	0.982	0.895	0.813	0.982	CLONAL	1	TRUE	1	0.287199714591363	2		1141	1058	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989609	15989609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	27	347	0	ENST00000268712.3:c.3164G>A	p.Gly1055Asp	p.G1055D	ENST00000268712	NM_006311.3	1055	gGc/gAc	23/46	1	2	FACETS	0.555	0.442	0.684	0.555	0.442	0.684	SUBCLONAL	1	TRUE	1	0.287199714591363	2		347	339	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019407	31019407	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	111	579	0	ENST00000375687.4:c.904C>G	p.Arg302Gly	p.R302G	ENST00000375687	NM_015338.5	302	Cgt/Ggt	10/13	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.287199714591363	2		579	591	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191593	10191593	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs281860296	NA	P-0019793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	140	702	0	ENST00000256474.2:c.586A>T	p.Lys196Ter	p.K196*	ENST00000256474	NM_000551.3	196	Aaa/Taa	3/3	0.232902415631716	2	FACETS	1	0.985	1	0.709	0.647	0.773	CLONAL	1	TRUE	0	0.287199714591363	2		702	688	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440311	52440311	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	163	785	0	ENST00000460680.1:c.741del	p.Leu248Ter	p.L248*	ENST00000460680	NM_004656.3	247	gtG/gt	9/17	0.232902415631716	2	FACETS	0.796	0.732	0.862	0.796	0.732	0.862	SUBCLONAL	2	TRUE	0	0.287199714591363	2		785	713	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914679	39914679	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0019793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	53	892	0	ENST00000378444.4:c.4683C>G	p.Tyr1561Ter	p.Y1561*	ENST00000378444	NM_001123385.1	1561	taC/taG	12/15	1	2	FACETS	0.43	0.365	0.501	0.43	0.365	0.501	SUBCLONAL	1	TRUE	1	0.287199714591363	2		892	859	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591104	67591115	+	inframe_deletion	In_Frame_Del	DEL	TTAAACCAGACC	TTAAACCAGACC	-	novel	NA	P-0019794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	119	645	0	ENST00000274335.5:c.1700_1711del	p.Lys567_Leu570del	p.K567_L570del	ENST00000274335		566	aTTAAACCAGACCtt/att	12/15	0.210862662730084	3	FACETS	0.936	0.85	1	0.624	0.566	0.685	CLONAL	2	TRUE	0	0.293870290337067	3		645	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0019794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	83	861	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	0.293870290337067	1	FACETS	0.864	0.764	0.97	0.864	0.764	0.97	CLONAL	1	TRUE	0	0.293870290337067	1		861	558	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717615	89717666	+	frameshift_variant	Frame_Shift_Del	DEL	CAGTTTGTGGTCTGCCAGCTAAAGGTGAAGATATATTCCTCCAATTCAGGAC	CAGTTTGTGGTCTGCCAGCTAAAGGTGAAGATATATTCCTCCAATTCAGGAC	-	novel	NA	P-0019794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	117	629	1	ENST00000371953.3:c.641_692del	p.Gln214ProfsTer25	p.Q214Pfs*25	ENST00000371953	NM_000314.4	214	CAGTTTGTGGTCTGCCAGCTAAAGGTGAAGATATATTCCTCCAATTCAGGACcc/cc	7/9	1	2	FACETS	0.816	0.74	0.895	1	0.987	1	CLONAL	2	TRUE	1	0.293870290337067	2		630	488	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631165	69631165	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1381894272	NA	P-0019794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	80	1004	1	ENST00000334134.2:c.247G>T	p.Val83Leu	p.V83L	ENST00000334134	NM_005247.2	83	Gtg/Ttg	2/3	1	2	FACETS	0.909	0.801	1	0.909	0.801	1	CLONAL	1	TRUE	1	0.293870290337067	2		1005	599	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032538	12032539	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TAAA	novel	NA	P-0019794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	71	615	0	ENST00000353533.5:c.975_976insAAAT	p.Pro326LysfsTer6	p.P326Kfs*6	ENST00000353533	NM_003010.3	325	cct/ccTAAAt	9/11	0.293870290337067	1	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	0	0.293870290337067	1		615	402	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663069	227663069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745927014	NA	P-0019794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	62	614	2	ENST00000305123.5:c.386C>T	p.Ala129Val	p.A129V	ENST00000305123	NM_005544.2	129	gCg/gTg	1/2	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.293870290337067	2		616	372	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218787	66218787	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	25	623	0	ENST00000273854.3:c.2271G>T	p.Glu757Asp	p.E757D	ENST00000273854	NM_004439.5	757	gaG/gaT	13/18	0.293870290337067	1	FACETS	0.374	0.294	0.466	0.374	0.294	0.466	SUBCLONAL	1	TRUE	0	0.293870290337067	1		623	388	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987346	2987346	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	43	1007	0	ENST00000396946.4:c.83G>C	p.Cys28Ser	p.C28S	ENST00000396946	NM_032415.4	28	tGt/tCt	3/25	1	2	FACETS	0.489	0.409	0.579	0.489	0.409	0.579	SUBCLONAL	1	TRUE	1	0.293870290337067	2		1007	598	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391383	139391383	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	95	1136	3	ENST00000277541.6:c.6808C>T	p.Pro2270Ser	p.P2270S	ENST00000277541	NM_017617.3	2270	Cca/Tca	34/34	0.215073805915629	2	FACETS	0.921	0.82	1	0.461	0.41	0.514	CLONAL	1	TRUE	0	0.293870290337067	2		1139	702	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0019795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	218	281	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.883	0.828	0.939	0.883	0.828	0.939	CLONAL	1	TRUE	1	0.879667999916304	2		281	561	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981878	201981879	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0019796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	110	1250	0	ENST00000359651.3:c.591dup	p.Thr198HisfsTer19	p.T198Hfs*19	ENST00000359651		197	tcc/tCcc	4/8	1	2	FACETS	0.863	0.773	0.959	0.863	0.773	0.959	CLONAL	1	TRUE	1	0.206645992688287	2		1250	1234	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347106	347106	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1255	122	1321	2	ENST00000262320.3:c.1905G>A	p.Trp635Ter	p.W635*	ENST00000262320	NM_003502.3	635	tgG/tgA	7/11	1	2	FACETS	0.857	0.772	0.948	0.857	0.772	0.948	CLONAL	1	TRUE	1	0.206645992688287	2		1323	1377	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949994	44949994	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1450363794	NA	P-0019797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	236	337	1	ENST00000377967.4:c.3763C>T	p.Arg1255Trp	p.R1255W	ENST00000377967	NM_021140.2	1255	Cgg/Tgg	26/29	1	1	FACETS	0.993	0.951	1	1	0.996	1	CLONAL	3	FALSE	0	0.387116294998515	1		338	330	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951053	48951053	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0019797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	66	313	0	ENST00000267163.4:c.1216-1G>C		p.X406_splice	ENST00000267163	NM_000321.2	406			0.387116294998515	0	FACETS	0.657	0.585	0.731			1	SUBCLONAL	2	FALSE	0	0.387116294998515	0		313	159	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645519	215645519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	182	763	1	ENST00000260947.4:c.1079C>T	p.Pro360Leu	p.P360L	ENST00000260947	NM_000465.2	360	cCt/cTt	4/11	0.387116294998515	1	FACETS	0.889	0.821	0.96	0.889	0.821	0.96	CLONAL	1	FALSE	0	0.387116294998515	1		764	853	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0019798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	170	614	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.951	0.877	1	0.951	0.877	1	CLONAL	1	TRUE	1	0.482497207684999	2		614	741	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	192	629	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.961	0.89	1	0.961	0.89	1	CLONAL	1	TRUE	1	0.482497207684999	2		629	828	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855921	68855921	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	281	427	0	ENST00000261769.5:c.1729G>T	p.Gly577Ter	p.G577*	ENST00000261769	NM_004360.3	577	Gga/Tga	12/16	0.477578166504535	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.482497207684999	2		427	579	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0019802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	89	840	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.247463641574744	4	FACETS	1	0.968	1	0.629	0.558	0.706	CLONAL	1	TRUE	2	0.247463641574744	4		840	713	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447394	49447394	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	93	911	0	ENST00000301067.7:c.704C>G	p.Pro235Arg	p.P235R	ENST00000301067	NM_003482.3	235	cCa/cGa	6/54	0.247463641574744	3	FACETS	1	0.922	1	0.523	0.465	0.586	CLONAL	1	TRUE	1	0.247463641574744	3		911	807	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514892	44514892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	102	540	1	ENST00000291552.4:c.355C>T	p.Arg119Cys	p.R119C	ENST00000291552	NM_006758.2	119	Cgt/Tgt	6/8	0.247463641574744	4	FACETS	0.779	0.698	0.865	0.779	0.698	0.865	SUBCLONAL	2	TRUE	2	0.247463641574744	4		541	660	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244610	46244613	+	frameshift_variant	Frame_Shift_Del	DEL	CCTT	CCTT	-	novel	NA	P-0019803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	60	641	0	ENST00000334344.6:c.2705_2708del	p.Pro902LeufsTer24	p.P902Lfs*24	ENST00000334344	NM_152641.2	902	CCTTct/ct	15/21	1	2	FACETS	0.783	0.673	0.902	0.783	0.673	0.902	CLONAL	1	TRUE	1	0.219056692274685	2		641	700	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188222	10188222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	60	654	0	ENST00000256474.2:c.365C>T	p.Ala122Val	p.A122V	ENST00000256474	NM_000551.3	122	gCa/gTa	2/3	0.190979295800152	1	FACETS	0.723	0.622	0.833	0.723	0.622	0.833	SUBCLONAL	1	TRUE	0	0.219056692274685	1		654	675	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	112	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.245205595402735	2	FACETS	0.946	0.858	1	0.946	0.858	1	CLONAL	2	TRUE	0	0.293875715639564	2		509	403	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793131	33793131	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	145	713	0	ENST00000498907.2:c.190A>G	p.Ile64Val	p.I64V	ENST00000498907	NM_004364.3	64	Atc/Gtc	1/1	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.293875715639564	2		713	712	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435918	110435918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774519000	NA	P-0019804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	166	812	0	ENST00000375856.3:c.2483C>T	p.Ser828Phe	p.S828F	ENST00000375856	NM_003749.2	828	tCc/tTc	1/2	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.293875715639564	2		812	915	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226308	2226308	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	161	898	0	ENST00000326181.6:c.1921C>G	p.Arg641Gly	p.R641G	ENST00000326181	NM_032271.2	641	Cgt/Ggt	20/21	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.293875715639564	2		898	873	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259079	89259079	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	57	418	3	ENST00000336596.2:c.223G>T	p.Asp75Tyr	p.D75Y	ENST00000336596	NM_005233.5	75	Gac/Tac	3/17	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.293875715639564	2		421	331	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670870	134670870	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs752301410	NA	P-0019804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	70	403	0	ENST00000398015.3:c.781C>G	p.Pro261Ala	p.P261A	ENST00000398015	NM_004441.4	261	Cct/Gct	3/16	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.293875715639564	2		403	432	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250607	26250607	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	88	487	3	ENST00000446824.2:c.227C>A	p.Ala76Glu	p.A76E	ENST00000446824	NM_021018.2	76	gCg/gAg	1/1	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.293875715639564	2		490	484	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940102	31940102	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	173	948	0	ENST00000375333.2:c.244C>G	p.Arg82Gly	p.R82G	ENST00000375333	NM_032454.1	82	Cgt/Ggt	2/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.293875715639564	2		948	996	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0019805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	153	840	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.547636695820619	5	FACETS	1	0.922	1	0.337	0.307	0.367	CLONAL	1	TRUE	2	0.547636695820619	5		840	1008	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0019805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	170	873	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.547636695820619	5	FACETS	0.977	0.897	1	0.326	0.299	0.354	CLONAL	1	TRUE	2	0.547636695820619	5		873	1157	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242494	55242494	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	151	733	0	ENST00000275493.2:c.2264C>G	p.Ala755Gly	p.A755G	ENST00000275493	NM_005228.3	755	gCc/gGc	19/28	0.547636695820619	5	FACETS	1	0.969	1	0.376	0.343	0.41	CLONAL	1	TRUE	2	0.547636695820619	5		733	891	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1555525585	NA	P-0019805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	268	695	0	ENST00000269305.4:c.673-2A>G		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.547636695820619	2	FACETS	0.983	0.934	1	0.983	0.934	1	CLONAL	2	TRUE	0	0.547636695820619	2		695	498	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26974650	26974650	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	320	879	1	ENST00000381527.3:c.994G>A	p.Asp332Asn	p.D332N	ENST00000381527	NM_001260.1	332	Gac/Aac	10/13	0.547636695820619	2	FACETS	0.98	0.936	1	0.98	0.936	1	CLONAL	2	TRUE	0	0.547636695820619	2		880	596	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68292188	68292188	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	105	477	0	ENST00000487270.1:c.92T>C	p.Leu31Ser	p.L31S	ENST00000487270	NM_133509.3	31	tTa/tCa	3/11	0.547636695820619	3	FACETS	0.895	0.804	0.99	0.447	0.402	0.495	CLONAL	1	TRUE	1	0.547636695820619	3		477	546	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336639	81336639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	391	722	0	ENST00000222390.5:c.1583G>A	p.Trp528Ter	p.W528*	ENST00000222390	NM_000601.4	528	tGg/tAg	14/18	0.547636695820619	5	FACETS	0.948	0.905	0.991	0.948	0.905	0.991	CLONAL	3	TRUE	2	0.547636695820619	5		722	915	SUCCESS
APC	324	MSKCC	GRCh37	5	112174783	112174783	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	81	455	0	ENST00000257430.4:c.3495del	p.Lys1165AsnfsTer17	p.K1165Nfs*17	ENST00000257430	NM_000038.5	1164	atA/at	16/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.287820604411699	2		455	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579484	7579484	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	140	830	0	ENST00000269305.4:c.203del	p.Glu68GlyfsTer55	p.E68Gfs*55	ENST00000269305	NM_001126112.2	68	gAg/gg	4/11	0.287820604411699	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	0	0.287820604411699	1		830	593	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40500453	40500453	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	64	632	0	ENST00000264657.5:c.82A>G	p.Met28Val	p.M28V	ENST00000264657	NM_139276.2	28	Atg/Gtg	2/24	1	2	FACETS	0.705	0.61	0.808	0.705	0.61	0.808	SUBCLONAL	1	FALSE	1	0.287820604411699	2		632	631	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440934	56440934	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	63	912	0	ENST00000407977.2:c.403A>T	p.Ser135Cys	p.S135C	ENST00000407977		135	Agt/Tgt	4/10	1	2	FACETS	0.607	0.524	0.697	0.607	0.524	0.697	SUBCLONAL	1	FALSE	1	0.287820604411699	2		912	721	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575117	48575117	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	95	500	0	ENST00000342988.3:c.311T>G	p.Leu104Arg	p.L104R	ENST00000342988	NM_005359.5	104	cTt/cGt	3/12	0.287820604411699	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	0	0.287820604411699	1		500	433	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251888	153251888	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	26	542	0	ENST00000281708.4:c.1118del	p.Pro373LeufsTer4	p.P373Lfs*4	ENST00000281708	NM_033632.3	373	cCt/ct	7/12	0.185366142973691	0	FACETS	0.345	0.273	0.428			1	SUBCLONAL	1	FALSE	0	0.287820604411699	0		542	373	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739097	145739097	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs386833849	NA	P-0019806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	105	576	0	ENST00000428558.2:c.2059-1G>A		p.X687_splice	ENST00000428558	NM_004260.3	687			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.287820604411699	2		576	581	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0019808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	8	629	0	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	0.354450875573536	1	FACETS	0.1	0.064	0.147	0.1	0.064	0.147	SUBCLONAL	1	TRUE	0	0.354450875573536	1		629	371	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	203	600	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.110846822901998	3	FACETS	1	0.979	1	1	0.979	1	INDETERMINATE	2	TRUE	1	0.354450875573536	3		600	603	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0019808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	239	639	2	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	0.110846822901998	3	FACETS	0.973	0.911	1	0.973	0.911	1	INDETERMINATE	2	TRUE	1	0.354450875573536	3		641	816	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155725	56155726	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0019808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	249	513	0	ENST00000399503.3:c.819_820del	p.Arg273SerfsTer27	p.R273Sfs*27	ENST00000399503	NM_005921.1	273	AGa/a	3/20	0.354450875573536	7	FACETS	0.836	0.782	0.892	0.501	0.469	0.535	CLONAL	3	TRUE	2	0.354450875573536	7		513	1057	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178622	56178622	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	434	388	0	ENST00000399503.3:c.3595C>T	p.Gln1199Ter	p.Q1199*	ENST00000399503	NM_005921.1	1199	Cag/Tag	14/20	0.354450875573536	7	FACETS	0.933	0.896	0.97	1	0.992	1	CLONAL	6	TRUE	2	0.354450875573536	7		388	825	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867502	45867502	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161399233	NA	P-0019808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	261	918	0	ENST00000391945.4:c.806C>T	p.Thr269Met	p.T269M	ENST00000391945	NM_000400.3	269	aCg/aTg	9/23	0.110846822901998	3	FACETS	1	0.989	1	1	0.989	1	INDETERMINATE	2	TRUE	1	0.354450875573536	3		918	722	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832320	72832320	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	162	608	1	ENST00000268489.5:c.4261C>T	p.Gln1421Ter	p.Q1421*	ENST00000268489	NM_006885.3	1421	Cag/Tag	9/10	0.354903581929608	0	FACETS	0.681	0.638	0.723			1	SUBCLONAL	3	TRUE	0	0.354450875573536	0		609	289	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78921038	78921038	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	139	807	0	ENST00000306801.3:c.3152G>A	p.Trp1051Ter	p.W1051*	ENST00000306801	NM_020761.2	1051	tGg/tAg	27/34	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.354450875573536	2		807	589	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	151	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.278181880262137	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.278181880262137	2		555	498	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096651	178096651	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	166	520	1	ENST00000397062.3:c.680A>G	p.His227Arg	p.H227R	ENST00000397062	NM_006164.4	227	cAt/cGt	5/5	1	2	FACETS	0.872	0.804	0.944	1	0.991	1	CLONAL	2	TRUE	1	0.278181880262137	2		521	684	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433395	138433395	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	72	819	0	ENST00000289153.2:c.1217C>G	p.Ala406Gly	p.A406G	ENST00000289153	NM_006219.2	406	gCa/gGa	7/22	0.278181880262137	1	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	0	0.278181880262137	1		819	430	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0019810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	163	741	1	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	0.993	1	CLONAL	2	FALSE	1	0.225597385466253	2		742	668	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0019810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	27	756	0	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	1	2	FACETS	0.358	0.284	0.444	0.358	0.284	0.444	SUBCLONAL	1	FALSE	1	0.225597385466253	2		756	668	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902181	50902181	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426253750	NA	P-0019810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	155	878	0	ENST00000440232.2:c.73G>A	p.Asp25Asn	p.D25N	ENST00000440232	NM_002691.3	25	Gat/Aat	2/27	1	2	FACETS	1	0.923	1	1	0.992	1	CLONAL	2	FALSE	1	0.225597385466253	2		878	683	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781914	9781920	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	AGCAGGT	AGCAGGT	-	novel	NA	P-0019810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	57	667	0	ENST00000377346.4:c.2051_2055+2del		p.X684_splice	ENST00000377346	NM_005026.3	684		16/24	0.225597385466253	1	FACETS	0.759	0.651	0.876	0.759	0.651	0.876	SUBCLONAL	1	FALSE	0	0.225597385466253	1		667	591	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135349	30135349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756128592	NA	P-0019810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	71	717	0	ENST00000331968.5:c.469C>T	p.Pro157Ser	p.P157S	ENST00000331968	NM_002742.2	157	Cca/Tca	3/18	1	2	FACETS	0.777	0.677	0.885	0.777	0.677	0.885	SUBCLONAL	1	FALSE	1	0.225597385466253	2		717	810	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984834	11984835	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	138	641	0	ENST00000353533.5:c.382dup	p.Met128AsnfsTer4	p.M128Nfs*4	ENST00000353533	NM_003010.3	127	ata/atAa	3/11	0.225597385466253	0	FACETS	0.889	0.813	0.967			1	CLONAL	2	FALSE	0	0.225597385466253	0		641	533	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586148	29586148	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs773151680	NA	P-0019810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	97	538	0	ENST00000356175.3:c.4367+1G>C		p.X1456_splice	ENST00000356175	NM_000267.3	1456			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.225597385466253	2		538	582	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562462	95562462	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	186	231	1	ENST00000393063.1:c.4795del	p.Arg1599GlyfsTer21	p.R1599Gfs*21	ENST00000393063	NM_030621.3	1599	Cgg/gg	24/28	0.970147320054503	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.970147320054503	1		232	195	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519991	NA	P-0019813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	378	695	0	ENST00000269305.4:c.536A>C	p.His179Pro	p.H179P	ENST00000269305	NM_001126112.2	179	cAt/cCt	5/11	0.525092621920177	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.525092621920177	2		695	682	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586046	29586059	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTAGATACTTCAGA	GTAGATACTTCAGA	-	novel	NA	P-0019813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	221	402	1	ENST00000356175.3:c.4270-1_4282del		p.X1424_splice	ENST00000356175	NM_000267.3	1424		32/57	0.525092621920177	3	FACETS	1	0.988	1	0.793	0.747	0.838	CLONAL	2	TRUE	0	0.525092621920177	3		403	447	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113377	209113377	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	85	301	0	ENST00000345146.2:c.130T>G	p.Leu44Val	p.L44V	ENST00000345146	NM_005896.2	44	Tta/Gta	4/10	0.525092621920177	3	FACETS	0.969	0.861	1	0.484	0.43	0.542	CLONAL	1	TRUE	1	0.525092621920177	3		301	422	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542337	187542338	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0019813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	185	357	0	ENST00000441802.2:c.5402_5403del	p.Lys1801ArgfsTer12	p.K1801Rfs*12	ENST00000441802	NM_005245.3	1801	aAA/a	10/27	0.525092621920177	2	FACETS	0.95	0.891	1	0.95	0.891	1	CLONAL	2	TRUE	0	0.525092621920177	2		357	371	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064770	80064771	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	488	763	0	ENST00000265081.6:c.2206dup	p.Ile736AsnfsTer32	p.I736Nfs*32	ENST00000265081	NM_002439.4	734	cga/cgAa	15/24	0.525092621920177	3	FACETS	0.893	0.861	0.925	0.893	0.861	0.925	CLONAL	3	TRUE	0	0.525092621920177	3		763	876	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659287	86659290	+	frameshift_variant	Frame_Shift_Del	DEL	TCTG	TCTG	-	novel	NA	P-0019813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	245	445	0	ENST00000274376.6:c.1579_1582del	p.Val527MetfsTer16	p.V527Mfs*16	ENST00000274376	NM_002890.2	526	TCTGtc/tc	11/25	0.525092621920177	3	FACETS	0.836	0.792	0.879	0.836	0.792	0.879	CLONAL	3	TRUE	0	0.525092621920177	3		445	470	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045946	26045946	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	105	509	0	ENST00000540144.1:c.308G>C	p.Gly103Ala	p.G103A	ENST00000540144	NM_003531.2	103	gGa/gCa	1/1	0.525092621920177	3	FACETS	0.874	0.785	0.967	0.437	0.392	0.484	CLONAL	1	TRUE	1	0.525092621920177	3		509	578	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395048	139395053	+	inframe_deletion	In_Frame_Del	DEL	GGGTGC	GGGTGC	-	novel	NA	P-0019813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	480	666	0	ENST00000277541.6:c.5885_5890del	p.Arg1962_Thr1963del	p.R1962_T1963del	ENST00000277541	NM_017617.3	1962	cGCACCCcg/ccg	31/34	0.525092621920177	3	FACETS	0.968	0.934	1	0.968	0.934	1	CLONAL	3	TRUE	0	0.525092621920177	3		666	795	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0019814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	336	818	0	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	NA	2	FACETS	1	0.972	1			1	INDETERMINATE	2	TRUE	NA	0.759965811237953	2		818	440	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455592	189455592	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	149	947	0	ENST00000264731.3:c.126G>C	p.Gln42His	p.Q42H	ENST00000264731	NM_003722.4	42	caG/caC	2/14	0.684314390122383	5	FACETS	0.911	0.832	0.994	0.304	0.277	0.332	CLONAL	1	TRUE	2	0.759965811237953	5		947	921	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0019815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	121	861	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.385849715976405	1	FACETS	0.907	0.827	0.991	0.907	0.827	0.991	CLONAL	1	TRUE	0	0.491751919116786	1		861	409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0019818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	47	573	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.15	2		573	527	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231782	36231782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs74315450	NA	P-0019818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	41	603	2	ENST00000300305.3:c.602G>A	p.Arg201Gln	p.R201Q	ENST00000300305		201	cGa/cAa	5/8	1	2	FACETS	0.996	0.829	1	0.996	0.829	1	CLONAL	1	TRUE	1	0.15	2		605	549	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061149	38061193	+	inframe_deletion	In_Frame_Del	DEL	GCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAA	GCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAA	-	novel	NA	P-0019818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	12	222	0	ENST00000250448.2:c.796_840del	p.Phe266_Ser280del	p.F266_S280del	ENST00000250448	NM_004496.3	266	TTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGC/-	2/2	1	2	FACETS	0.816	0.574	1	0.816	0.574	1	CLONAL	1	TRUE	1	0.15	2		222	196	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177024	56177024	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	31	403	0	ENST00000399503.3:c.2294T>G	p.Leu765Trp	p.L765W	ENST00000399503	NM_005921.1	765	tTg/tGg	13/20	1	2	FACETS	0.931	0.752	1	0.931	0.752	1	CLONAL	1	TRUE	1	0.15	2		403	444	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916928	178916936	+	inframe_deletion	In_Frame_Del	DEL	AGGCAACCG	AGGCAACCG	-	novel	NA	P-0019818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	112	472	0	ENST00000263967.3:c.315_323del	p.Gly106_Arg108del	p.G106_R108del	ENST00000263967	NM_006218.2	105	gtAGGCAACCGt/gtt	2/21	0.3	4	FACETS	0.912	0.822	1			1	CLONAL	3	TRUE	NA	0.15	4		472	628	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061134	38061148	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGCCCCCGCTTCC	GCTGCCCCCGCTTCC	A	novel	NA	P-0019818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	13	215	0	ENST00000250448.2:c.841_855delinsT	p.Gly281TrpfsTer7	p.G281Wfs*7	ENST00000250448	NM_004496.3	281	GGAAGCGGGGGCAGC/T	2/2	1	2	FACETS	0.985	0.704	1	0.985	0.704	1	CLONAL	1	TRUE	1	0.15	2		215	176	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	17	736	0				ENST00000310581	NM_198253.2	-/1132			0.18810577657342	1	FACETS	0.58	0.44	0.74	0.58	0.44	0.74	INDETERMINATE	1	TRUE	0	0.475497864771916	1		736	94	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0019821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	30	860	1	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.475497864771916	2		861	96	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202644	108202647	+	frameshift_variant	Frame_Shift_Del	DEL	TTTG	TTTG	-	rs1555124506	NA	P-0019821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	10	608	1	ENST00000278616.4:c.7671_7674del	p.Phe2558LeufsTer5	p.F2558Lfs*5	ENST00000278616	NM_000051.3	2556	acTTTG/ac	52/63	1	2	FACETS	1	0.804	1	1	0.804	1	CLONAL	1	TRUE	1	0.475497864771916	2		609	35	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62316888	62316888	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	56	893	0	ENST00000360203.5:c.1204G>A	p.Val402Met	p.V402M	ENST00000360203	NM_001283009.1	402	Gtg/Atg	15/35	1	2	FACETS	0.86	0.757	0.965	1	0.977	1	CLONAL	2	TRUE	1	0.475497864771916	2		893	137	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0019822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	280	811	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.247350918611437	2	FACETS	0.885	0.831	0.94	0.885	0.831	0.94	CLONAL	2	TRUE	0	0.28309362562017	2		811	1118	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0019823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	79	632	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.121103770524318	3	FACETS	1	0.974	1	0.726	0.638	0.82	CLONAL	1	TRUE	1	0.170788580522909	3		632	692	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0019823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	85	860	1	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.148492839330536	1	FACETS	0.975	0.86	1	0.975	0.86	1	CLONAL	1	TRUE	0	0.170788580522909	1		861	934	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340309	116340309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778443	NA	P-0019823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	37	418	1	ENST00000397752.3:c.1171G>A	p.Gly391Arg	p.G391R	ENST00000397752	NM_000245.2	391	Gga/Aga	2/21	1	2	FACETS	0.91	0.75	1	0.91	0.75	1	CLONAL	1	TRUE	1	0.170788580522909	2		419	476	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273198	115273198	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	269	721	0	ENST00000438362.2:c.1260C>G	p.Phe420Leu	p.F420L	ENST00000438362	NM_001242891.1	420	ttC/ttG	11/20	0.315629005939411	5	FACETS	0.917	0.864	0.972			1	INDETERMINATE	2	TRUE	NA	0.82106985645155	5		721	797	SUCCESS
APC	324	MSKCC	GRCh37	5	112175958	112175958	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	78	416	0	ENST00000257430.4:c.4667C>G	p.Thr1556Ser	p.T1556S	ENST00000257430	NM_000038.5	1556	aCt/aGt	16/16	0.396191884626672	1	FACETS	0.362	0.321	0.406	0.362	0.321	0.406	INDETERMINATE	1	TRUE	0	0.82106985645155	1		416	309	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191570	10191570	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1559429824	NA	P-0019833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	156	567	1	ENST00000256474.2:c.563T>A	p.Leu188Gln	p.L188Q	ENST00000256474	NM_000551.3	188	cTg/cAg	3/3	0.56537146306202	1	FACETS	0.876	0.811	0.942	0.876	0.811	0.942	CLONAL	1	TRUE	0	0.610951380380225	1		568	405	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362264	40362264	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	71	550	0	ENST00000293328.3:c.1831C>A	p.Pro611Thr	p.P611T	ENST00000293328	NM_012448.3	611	Cca/Aca	15/19	1	2	FACETS	0.726	0.639	0.819	0.726	0.639	0.819	SUBCLONAL	1	TRUE	1	0.610951380380225	2		550	320	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627548	14627548	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1202117106	NA	P-0019833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	124	604	0	ENST00000254322.2:c.522G>C	p.Glu174Asp	p.E174D	ENST00000254322	NM_006145.1	174	gaG/gaC	2/3	1	2	FACETS	0.92	0.839	1	0.92	0.839	1	CLONAL	1	TRUE	1	0.610951380380225	2		604	441	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442605	52442605	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	88	389	0	ENST00000460680.1:c.140del	p.Ile47ThrfsTer25	p.I47Tfs*25	ENST00000460680	NM_004656.3	47	aTc/ac	4/17	0.56537146306202	1	FACETS	0.885	0.799	0.974	0.885	0.799	0.974	CLONAL	1	TRUE	0	0.610951380380225	1		389	226	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564771	139564771	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	227	789	2	ENST00000308874.7:c.560C>A	p.Pro187His	p.P187H	ENST00000308874		187	cCc/cAc	7/10	0.577478242410325	1	FACETS	0.928	0.872	0.985	0.928	0.872	0.985	CLONAL	1	TRUE	0	0.610951380380225	1		791	556	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	191	509	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	0.385738062956763	2		509	989	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0019834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	410	680	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.385738062956763	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.385738062956763	3		680	1143	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659675	NA	P-0019834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	197	772	1	ENST00000269305.4:c.764T>C	p.Ile255Thr	p.I255T	ENST00000269305	NM_001126112.2	255	aTc/aCc	7/11	0.385738062956763	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.385738062956763	1		773	822	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044524	12044525	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0019834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	196	669	0	ENST00000353533.5:c.1148_1149insCA	p.Lys383AsnfsTer31	p.K383Nfs*31	ENST00000353533	NM_003010.3	383	aaa/aACaa	11/11	0.385738062956763	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.385738062956763	1		669	763	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578433	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	48	704	0	ENST00000269305.4:c.497C>A	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	166	tCa/tAa	5/11	1	2	FACETS	0.534	0.45	0.626	0.534	0.45	0.626	SUBCLONAL	1	TRUE	1	0.26	2		704	692	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139264	108139279	+	frameshift_variant	Frame_Shift_Del	DEL	TATTCGGAGGAAATTG	TATTCGGAGGAAATTG	-	novel	NA	P-0019836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	48	787	0	ENST00000278616.4:c.2767_2782del	p.Ile923Ter	p.I923*	ENST00000278616	NM_000051.3	922	gaTATTCGGAGGAAATTG/ga	18/63	1	2	FACETS	0.424	0.357	0.499	0.424	0.357	0.499	SUBCLONAL	1	TRUE	1	0.26	2		787	870	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692830	89692853	+	inframe_deletion	In_Frame_Del	DEL	GTGAAGATCTTGACCAATGGCTAA	GTGAAGATCTTGACCAATGGCTAA	-	novel	NA	P-0019839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	45	247	0	ENST00000371953.3:c.322_345del	p.Leu108_Asp115del	p.L108_D115del	ENST00000371953	NM_000314.4	105	tGTGAAGATCTTGACCAATGGCTAAgt/tgt	5/9	0.546861810783302	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.546861810783302	1		247	108	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950156	38950156	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	39	616	0	ENST00000357387.3:c.3794A>C	p.Lys1265Thr	p.K1265T	ENST00000357387	NM_152756.3	1265	aAg/aCg	31/38	0.312243323930235	4	FACETS	0.799	0.666	0.946	0.4	0.333	0.473	INDETERMINATE	1	TRUE	2	0.546861810783302	4		616	276	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871870	12871888	+	stop_lost,splice_region_variant,3_prime_UTR_variant	Nonstop_Mutation	DEL	GTCAAACGTAAACAGCTCG	GTCAAACGTAAACAGCTCG	-	novel	NA	P-0019842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	68	365	0	ENST00000228872.4:c.589_*8+2del		p.*197*	ENST00000228872	NM_004064.3	196		2/3	0.501657144345914	1	FACETS	0.883	0.779	0.992	0.883	0.779	0.992	CLONAL	1	TRUE	0	0.501657144345914	1		365	230	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426778	49426778	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555188537	NA	P-0019842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	16	234	0	ENST00000301067.7:c.11710C>T	p.Gln3904Ter	p.Q3904*	ENST00000301067	NM_003482.3	3904	Cag/Tag	39/54	1	2	FACETS	0.329	0.244	0.43	0.329	0.244	0.43	SUBCLONAL	1	TRUE	1	0.501657144345914	2		234	194	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37665993	37665993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	23	592	0	ENST00000447079.4:c.2645G>A	p.Arg882Gln	p.R882Q	ENST00000447079	NM_015083.1	882	cGg/cAg	7/14	1	2	FACETS	0.207	0.16	0.26	0.207	0.16	0.26	SUBCLONAL	1	TRUE	1	0.501657144345914	2		592	444	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180557	56180557	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	72	694	0	ENST00000399503.3:c.3886A>G	p.Arg1296Gly	p.R1296G	ENST00000399503	NM_005921.1	1296	Aga/Gga	16/20	1	2	FACETS	0.911	0.803	1	0.911	0.803	1	CLONAL	1	TRUE	1	0.501657144345914	2		694	315	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900786	3900786	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	66	738	0	ENST00000262367.5:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000262367	NM_004380.2	104	Caa/Taa	2/31	1	2	FACETS	0.724	0.628	0.829	0.724	0.628	0.829	SUBCLONAL	1	FALSE	1	0.273608094088339	2		738	666	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	145	509	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.221258593922531	1	FACETS	1	0.954	1	1	0.954	1	INDETERMINATE	1	TRUE	0	0.501518056920723	1		509	413	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41962066	41962066	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	48	496	0	ENST00000219905.7:c.974C>T	p.Ser325Phe	p.S325F	ENST00000219905	NM_001164273.1	325	tCc/tTc	2/24	0.221258593922531	1	FACETS	0.346	0.292	0.404	0.346	0.292	0.404	INDETERMINATE	1	TRUE	0	0.501518056920723	1		496	415	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143031	47143031	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	105	600	0	ENST00000409792.3:c.4932del	p.Gln1645AsnfsTer2	p.Q1645Nfs*2	ENST00000409792	NM_014159.6	1644	ggA/gg	8/21	1	2	FACETS	0.77	0.692	0.852	0.77	0.692	0.852	SUBCLONAL	1	TRUE	1	0.501518056920723	2		600	544	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164103	47164103	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	76	387	0	ENST00000409792.3:c.2023G>T	p.Gly675Ter	p.G675*	ENST00000409792	NM_014159.6	675	Gga/Tga	3/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.501518056920723	2		387	261	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	73	640	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.31	2		640	463	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	113	683	12	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.31	2		695	643	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	127	894	7	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.31	2		901	810	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	50	593	2	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.781	0.664	0.909	0.781	0.664	0.909	CLONAL	1	TRUE	1	0.31	2		595	413	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	15	555	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.184	0.134	0.245	0.184	0.134	0.245	SUBCLONAL	1	TRUE	1	0.31	2		556	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780068	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	121	890	1	ENST00000269305.4:c.472C>T	p.Arg158Cys	p.R158C	ENST00000269305	NM_001126112.2	158	Cgc/Tgc	5/11	1	2	FACETS	0.93	0.84	1	0.93	0.84	1	CLONAL	1	TRUE	1	0.31	2		891	839	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	96	562	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.31	2		562	457	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	107	749	3	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.31	2		752	687	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577524	7577524	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	66	700	0	ENST00000269305.4:c.757A>G	p.Thr253Ala	p.T253A	ENST00000269305	NM_001126112.2	253	Acc/Gcc	7/11	1	2	FACETS	0.624	0.541	0.714	0.624	0.541	0.714	SUBCLONAL	1	TRUE	1	0.31	2		700	682	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781141	135781141	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs118203585	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	91	673	0	ENST00000298552.3:c.1824del	p.Phe608LeufsTer21	p.F608Lfs*21	ENST00000298552	NM_001162426.1	608	ttT/tt	15/23	1	2	FACETS	0.978	0.87	1	0.978	0.87	1	CLONAL	1	TRUE	1	0.31	2		673	600	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759443	133759443	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376925416	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	39	791	1	ENST00000318560.5:c.1766G>A	p.Arg589His	p.R589H	ENST00000318560	NM_005157.4	589	cGc/cAc	11/11	1	2	FACETS	0.372	0.307	0.444	0.372	0.307	0.444	SUBCLONAL	1	TRUE	1	0.31	2		792	677	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226412	133226412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200114024	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	112	712	0	ENST00000320574.5:c.3646G>A	p.Gly1216Ser	p.G1216S	ENST00000320574	NM_006231.2	1216	Ggc/Agc	30/49	0.3	3	FACETS	1	0.956	1	0.556	0.5	0.615	CLONAL	1	TRUE	1	0.31	3		712	751	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135800999	135800999	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs118203367	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	76	619	0	ENST00000298552.3:c.338del	p.Leu113CysfsTer5	p.L113Cfs*5	ENST00000298552	NM_001162426.1	113	tTg/tg	5/23	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.31	2		619	459	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258943	16258944	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	52	1125	0	ENST00000375759.3:c.6215dup	p.Asn2072LysfsTer51	p.N2072Kfs*51	ENST00000375759	NM_015001.2	2070	gaa/gAaa	11/15	1	2	FACETS	0.339	0.287	0.396	0.339	0.287	0.396	SUBCLONAL	1	TRUE	1	0.31	2		1125	991	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097792	27097792	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	29	558	0	ENST00000324856.7:c.3381G>T	p.Gln1127His	p.Q1127H	ENST00000324856	NM_006015.4	1127	caG/caT	12/20	1	2	FACETS	0.395	0.316	0.484	0.395	0.316	0.484	SUBCLONAL	1	TRUE	1	0.31	2		558	474	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803799	43803799	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	41	820	0	ENST00000372470.3:c.112del	p.Leu38Ter	p.L38*	ENST00000372470	NM_005373.2	37	Ccc/cc	2/12	1	2	FACETS	0.417	0.346	0.495	0.417	0.346	0.495	SUBCLONAL	1	TRUE	1	0.31	2		820	635	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076724	72076724	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	79	640	1	ENST00000357731.5:c.773A>G	p.Tyr258Cys	p.Y258C	ENST00000357731	NM_173808.2	258	tAc/tGc	5/7	1	2	FACETS	0.848	0.747	0.957	0.848	0.747	0.957	CLONAL	1	TRUE	1	0.31	2		641	601	SUCCESS
H3C13	653604	MSKCC	GRCh37	1	149784842	149784842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	32	258	0	ENST00000331491.1:c.395G>A	p.Arg132His	p.R132H	ENST00000331491	NM_001123375.2	132	cGc/cAc	1/1	1	2	FACETS	0.867	0.708	1	0.867	0.708	1	CLONAL	1	TRUE	1	0.31	2		258	238	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205836	108205836	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	64	511	0	ENST00000278616.4:c.8151G>T	p.Lys2717Asn	p.K2717N	ENST00000278616	NM_000051.3	2717	aaG/aaT	55/63	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.31	2		511	377	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492779	50492779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1215265267	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	191	715	0	ENST00000394963.4:c.1544C>T	p.Thr515Ile	p.T515I	ENST00000394963	NM_003076.4	515	aCa/aTa	13/13	0.3	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.31	3		715	654	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924295	112924295	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1193000800	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	231	852	0	ENST00000351677.2:c.1241C>T	p.Thr414Met	p.T414M	ENST00000351677	NM_002834.3	414	aCg/aTg	11/16	0.3	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.31	3		852	781	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120918	115120918	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1393790676	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	144	449	0	ENST00000257566.3:c.88A>G	p.Met30Val	p.M30V	ENST00000257566	NM_016569.3	30	Atg/Gtg	1/8	0.3	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.31	3		449	448	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436761	110436761	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	68	857	0	ENST00000375856.3:c.1640G>T	p.Arg547Met	p.R547M	ENST00000375856	NM_003749.2	547	aGg/aTg	1/2	0.3	3	FACETS	0.601	0.522	0.687	0.301	0.261	0.344	SUBCLONAL	1	TRUE	1	0.31	3		857	843	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132924	30132924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	25	670	0	ENST00000331968.5:c.677C>T	p.Ala226Val	p.A226V	ENST00000331968	NM_002742.2	226	gCc/gTc	4/18	1	2	FACETS	0.326	0.256	0.407	0.326	0.256	0.407	SUBCLONAL	1	TRUE	1	0.31	2		670	494	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396146	396146	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	30	496	0	ENST00000262320.3:c.878+2T>C		p.X293_splice	ENST00000262320	NM_003502.3	293			1	2	FACETS	0.456	0.367	0.558	0.456	0.367	0.558	SUBCLONAL	1	TRUE	1	0.31	2		496	424	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14015916	14015916	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	18	414	0	ENST00000311895.7:c.236A>G	p.Glu79Gly	p.E79G	ENST00000311895	NM_005236.2	79	gAa/gGa	2/11	1	2	FACETS	0.355	0.267	0.46	0.355	0.267	0.46	SUBCLONAL	1	TRUE	1	0.31	2		414	327	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822385	72822385	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	144	1015	0	ENST00000268489.5:c.9790G>C	p.Ala3264Pro	p.A3264P	ENST00000268489	NM_006885.3	3264	Gcc/Ccc	10/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.31	2		1015	814	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348443	89348443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537684815	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	124	865	0	ENST00000301030.4:c.4507G>A	p.Ala1503Thr	p.A1503T	ENST00000301030	NM_001256183.1	1503	Gcc/Acc	9/13	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.31	2		865	728	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578279	7578280	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	116	699	0	ENST00000269305.4:c.569_570insA	p.Pro191SerfsTer18	p.P191Sfs*18	ENST00000269305	NM_001126112.2	190	cct/ccAt	6/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.31	2		699	641	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492890	56492906	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGCCAGGGCCAGAGG	GCAGCCAGGGCCAGAGG	-	novel	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	47	373	0	ENST00000407977.2:c.33_49del	p.Leu12AspfsTer22	p.L12Dfs*22	ENST00000407977		11	gcCCTCTGGCCCTGGCTGCtg/gctg	2/10	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.31	2		373	287	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534372	63534377	+	inframe_deletion	In_Frame_Del	DEL	CAGCTT	CAGCTT	-	rs1459191371	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	129	881	0	ENST00000307078.5:c.1144_1149del	p.Lys382_Leu383del	p.K382_L383del	ENST00000307078	NM_004655.3	382	AAGCTG/-	5/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.31	2		881	753	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627583	14627583	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	101	518	1	ENST00000254322.2:c.487C>A	p.Pro163Thr	p.P163T	ENST00000254322	NM_006145.1	163	Cca/Aca	2/3	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.31	2		519	565	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349561	15349561	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772267056	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	158	939	3	ENST00000263377.2:c.4013G>A	p.Arg1338Gln	p.R1338Q	ENST00000263377	NM_058243.2	1338	cGg/cAg	19/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.31	2		942	792	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871986	45871986	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs748842373	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	120	736	0	ENST00000391945.4:c.262C>T	p.Arg88Ter	p.R88*	ENST00000391945	NM_000400.3	88	Cga/Tga	5/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.31	2		736	659	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149727	202149727	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	46	699	0	ENST00000358485.4:c.1168G>C	p.Ala390Pro	p.A390P	ENST00000358485	NM_001080125.1	390	Gcc/Ccc	8/9	0.170214820060155	3	FACETS	0.548	0.461	0.645	0.274	0.23	0.323	INDETERMINATE	1	TRUE	1	0.31	3		699	625	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659763	227659763	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	33	532	0	ENST00000305123.5:c.3692G>A	p.Ser1231Asn	p.S1231N	ENST00000305123	NM_005544.2	1231	aGc/aAc	1/2	0.170214820060155	3	FACETS	0.482	0.392	0.584	0.241	0.196	0.292	INDETERMINATE	1	TRUE	1	0.31	3		532	510	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795003	242795003	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764200391	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	167	1020	4	ENST00000334409.5:c.206G>A	p.Arg69His	p.R69H	ENST00000334409	NM_005018.2	69	cGc/cAc	2/5	0.170214820060155	3	FACETS	1	0.987	1	0.686	0.63	0.744	INDETERMINATE	1	TRUE	1	0.31	3		1024	907	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564491	41564491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555911073	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	38	502	0	ENST00000263253.7:c.3913C>T	p.Arg1305Cys	p.R1305C	ENST00000263253	NM_001429.3	1305	Cgt/Tgt	24/31	1	2	FACETS	0.621	0.514	0.74	0.621	0.514	0.74	SUBCLONAL	1	TRUE	1	0.31	2		502	395	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169985715	169985715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567380681	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	96	558	0	ENST00000295797.4:c.377G>A	p.Arg126His	p.R126H	ENST00000295797	NM_002740.5	126	cGt/cAt	5/18	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.31	2		558	567	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430993	181430993	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	116	821	1	ENST00000325404.1:c.845A>G	p.Glu282Gly	p.E282G	ENST00000325404	NM_003106.3	282	gAg/gGg	1/1	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.31	2		822	739	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541018	187541018	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	67	426	0	ENST00000441802.2:c.6722C>A	p.Pro2241His	p.P2241H	ENST00000441802	NM_005245.3	2241	cCt/cAt	10/27	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.31	2		426	349	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649045	86649046	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	51	499	0	ENST00000274376.6:c.1327dup	p.Met443AsnfsTer10	p.M443Nfs*10	ENST00000274376	NM_002890.2	442	cca/ccAa	9/25	1	2	FACETS	0.962	0.821	1	0.962	0.821	1	CLONAL	1	TRUE	1	0.31	2		499	342	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043364	180043365	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	novel	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	79	603	0	ENST00000261937.6:c.3219+2_3219+3del		p.X1073_splice	ENST00000261937	NM_182925.4	1073			1	2	FACETS	0.918	0.809	1	0.918	0.809	1	CLONAL	1	TRUE	1	0.31	2		603	555	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858216	27858216	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	119	613	0	ENST00000359303.2:c.355A>G	p.Thr119Ala	p.T119A	ENST00000359303	NM_003535.2	119	Act/Gct	1/1	0.170214820060155	3	FACETS	1	0.982	1	0.703	0.636	0.773	INDETERMINATE	1	TRUE	1	0.31	3		613	631	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675718	30675718	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	142	1048	0	ENST00000376406.3:c.2638del	p.Ser880ValfsTer11	p.S880Vfs*11	ENST00000376406	NM_014641.2	880	Agt/gt	8/15	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.31	2		1048	897	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324192	31324192	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	120	371	0	ENST00000412585.2:c.371G>A	p.Gly124Asp	p.G124D	ENST00000412585	NM_005514.6	124	gGc/gAc	3/8	1	2	FACETS	1	0.953	1	1	0.99	1	CLONAL	2	TRUE	1	0.31	2		371	363	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391260	139391260	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	70	975	0	ENST00000277541.6:c.6931C>A	p.Leu2311Met	p.L2311M	ENST00000277541	NM_017617.3	2311	Ctg/Atg	34/34	1	2	FACETS	0.51	0.444	0.583	0.51	0.444	0.583	SUBCLONAL	1	TRUE	1	0.31	2		975	885	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	181	816	0	ENST00000269305.4:c.613del	p.Tyr205IlefsTer42	p.Y205Ifs*42	ENST00000269305	NM_001126112.2	205	Tat/at	6/11	0.285538892803427	2	FACETS	0.942	0.872	1	0.942	0.872	1	CLONAL	2	TRUE	0	0.288531097928125	2		816	666	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	120	600	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.519992481092411	3	FACETS	0.828	0.749	0.911	0.414	0.374	0.456	CLONAL	1	TRUE	1	0.575889777838004	3		600	648	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917611	151917611	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs938655561	NA	P-0019848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	149	728	0	ENST00000262189.6:c.3709C>T	p.Arg1237Ter	p.R1237*	ENST00000262189	NM_170606.2	1237	Cga/Tga	23/59	1	2	FACETS	0.913	0.838	0.99	0.913	0.838	0.99	CLONAL	1	TRUE	1	0.575889777838004	2		728	567	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223482	53223492	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCGCGGCCT	TGGCGCGGCCT	-	novel	NA	P-0019848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	109	666	0	ENST00000375401.3:c.3867_3877del	p.Gly1290AlafsTer6	p.G1290Afs*6	ENST00000375401	NM_004187.3	1289	caAGGCCGCGCCAgg/cagg	23/26	1	2	FACETS	0.841	0.76	0.926	0.841	0.76	0.926	CLONAL	1	TRUE	1	0.575889777838004	2		666	450	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519851	29519851	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000322-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	123	446	0	ENST00000389048.3:c.1720G>T	p.Gly574Trp	p.G574W	ENST00000389048	NM_004304.4	574	Ggg/Tgg	9/29	NA	2	FACETS	0.6	0.544	0.66			1	INDETERMINATE	1	FALSE	NA	0.602570782087994	2		446	680	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499510	89499511	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0000322-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	19	198	0	ENST00000336596.2:c.2680_2681delinsTT	p.Ala894Leu	p.A894L	ENST00000336596	NM_005233.5	894	GCa/TTa	15/17	1	2	FACETS	0.203	0.154	0.262	0.203	0.154	0.262	SUBCLONAL	1	FALSE	1	0.602570782087994	2		198	310	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950808	38950808	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000322-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	45	180	0	ENST00000357387.3:c.3142G>A	p.Glu1048Lys	p.E1048K	ENST00000357387	NM_152756.3	1048	Gag/Aag	31/38	0.521804641019696	4	FACETS	0.531	0.446	0.624	0.133	0.111	0.156	SUBCLONAL	1	FALSE	0	0.602570782087994	4		180	451	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134508	2134508	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs45474795	NA	P-0000322-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	232	522	1	ENST00000219476.3:c.4285G>T	p.Ala1429Ser	p.A1429S	ENST00000219476	NM_000548.3	1429	Gcc/Tcc	34/42	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	FALSE	1	0.602570782087994	2		523	517	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849476	89849476	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000322-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	369	505	0	ENST00000389301.3:c.1505A>G	p.Lys502Arg	p.K502R	ENST00000389301	NM_000135.2	502	aAg/aGg	16/43	0.443611841769997	3	FACETS	0.912	0.869	0.955			1	CLONAL	2	FALSE	NA	0.602570782087994	3		505	874	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0000322-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	65	482	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	0.346	0.299	0.396	0.346	0.299	0.396	SUBCLONAL	1	FALSE	1	0.602570782087994	2		482	624	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344963	70344977	+	inframe_deletion	In_Frame_Del	DEL	CGTGCAGTACGCCAC	CGTGCAGTACGCCAC	-	novel	NA	P-0000322-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	96	784	0	ENST00000374080.3:c.2194_2208del	p.Val732_Thr736del	p.V732_T736del	ENST00000374080		731	caCGTGCAGTACGCCACc/cac	15/45	0.602570782087994	1	FACETS	0.333	0.297	0.372	0.333	0.297	0.372	SUBCLONAL	1	FALSE	0	0.602570782087994	1		784	668	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0004403-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	358	603	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.77186397901505	3	FACETS	0.827	0.791	0.864	0.827	0.791	0.864	CLONAL	2	TRUE	1	0.898629662413558	3		603	698	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0004403-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	397	860	0	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	0.768705843730011	2	FACETS	0.835	0.81	0.86	0.835	0.81	0.86	CLONAL	2	TRUE	0	0.898629662413558	2		860	529	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0004403-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	120	288	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.853372171760834	1	FACETS	0.813	0.76	0.863	0.813	0.76	0.863	CLONAL	1	TRUE	0	0.898629662413558	1		288	181	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685309	89685309	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs773176120	NA	P-0004403-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	136	477	0	ENST00000371953.3:c.204C>G	p.Tyr68Ter	p.Y68*	ENST00000371953	NM_000314.4	68	taC/taG	3/9	NA	2	FACETS	0.809	0.765	0.851			1	INDETERMINATE	2	TRUE	NA	0.898629662413558	2		477	187	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575096	48575096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555685159	NA	P-0004403-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	201	519	0	ENST00000342988.3:c.290G>A	p.Arg97His	p.R97H	ENST00000342988	NM_005359.5	97	cGt/cAt	3/12	0.768705843730011	2	FACETS	0.87	0.835	0.903	0.87	0.835	0.903	CLONAL	2	TRUE	0	0.898629662413558	2		519	257	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411164	63411164	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004403-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	294	683	0	ENST00000330258.3:c.2003del	p.Ala668GlufsTer51	p.A668Efs*51	ENST00000330258	NM_152424.3	668	gCa/ga	2/2	0.77186397901505	3	FACETS	0.886	0.845	0.927	0.886	0.845	0.927	CLONAL	2	TRUE	1	0.898629662413558	3		683	535	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300566	11300566	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004403-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	356	853	0	ENST00000361445.4:c.1580A>C	p.Gln527Pro	p.Q527P	ENST00000361445	NM_004958.3	527	cAg/cCg	11/58	0.767518306958148	3	FACETS	0.881	0.843	0.918	0.587	0.562	0.612	CLONAL	2	TRUE	0	0.898629662413558	3		853	652	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219287	133219287	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004403-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	161	711	0	ENST00000320574.5:c.4757C>A	p.Ala1586Asp	p.A1586D	ENST00000320574	NM_006231.2	1586	gCt/gAt	37/49	0.768705843730011	2	FACETS	0.805	0.746	0.866	0.403	0.373	0.433	CLONAL	1	TRUE	0	0.898629662413558	2		711	445	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89869681	89869681	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004403-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	61	855	0	ENST00000389301.3:c.778G>C	p.Glu260Gln	p.E260Q	ENST00000389301	NM_000135.2	260	Gaa/Caa	8/43	0.755396157096393	3	FACETS	0.263	0.226	0.303	0.131	0.113	0.152	SUBCLONAL	1	TRUE	1	0.898629662413558	3		855	749	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556353	29556353	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004403-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	147	661	0	ENST00000356175.3:c.2720A>G	p.Glu907Gly	p.E907G	ENST00000356175	NM_000267.3	907	gAg/gGg	21/57	0.768705843730011	2	FACETS	0.822	0.759	0.887	0.411	0.379	0.444	CLONAL	1	TRUE	0	0.898629662413558	2		661	398	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509562	106509562	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004403-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	46	718	0	ENST00000359195.3:c.1556T>C	p.Leu519Pro	p.L519P	ENST00000359195	NM_002649.2	519	cTt/cCt	2/11	0.768846386450981	4	FACETS	0.262	0.22	0.309	0.087	0.073	0.103	SUBCLONAL	1	TRUE	1	0.898629662413558	4		718	741	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0007874-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	347	552	0	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	0.380171288391377	2	FACETS	0.941	0.893	0.989	0.941	0.893	0.989	CLONAL	2	TRUE	0	0.389124828533403	2		552	948	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061213	38061213	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007874-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	264	478	0	ENST00000250448.2:c.776A>C	p.Tyr259Ser	p.Y259S	ENST00000250448	NM_004496.3	259	tAc/tCc	2/2	0.389124828533403	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	1	0.389124828533403	3		478	797	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434946	110434947	+	missense_variant	Missense_Mutation	DNP	AA	AA	GT	novel	NA	P-0007874-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	234	840	2	ENST00000375856.3:c.3454_3455delinsAC	p.Phe1152Thr	p.F1152T	ENST00000375856	NM_003749.2	1152	TTc/ACc	1/2	0.382580435809179	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.389124828533403	1		842	865	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117874161	117874169	+	inframe_deletion	In_Frame_Del	DEL	TCAGGCAGG	TCAGGCAGG	-	novel	NA	P-0007874-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	201	355	0	ENST00000297338.2:c.285_293del	p.Asp95_Pro97del	p.D95_P97del	ENST00000297338	NM_006265.2	95	gaCCTGCCTGAg/gag	4/14	0.389124828533403	5	FACETS	0.946	0.878	1	0.63	0.585	0.678	CLONAL	2	TRUE	2	0.389124828533403	5		355	865	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0008756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	72	554	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.59	0.514	0.672	0.59	0.514	0.672	SUBCLONAL	1	TRUE	1	0.253435953924963	2		554	963	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692896	89692896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123322	NA	P-0008756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	227	604	0	ENST00000371953.3:c.380G>A	p.Gly127Glu	p.G127E	ENST00000371953	NM_000314.4	127	gGa/gAa	5/9	0.241668738876357	2	FACETS	0.927	0.864	0.992	0.927	0.864	0.992	CLONAL	2	TRUE	0	0.253435953924963	2		604	966	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084094	47084094	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	255	665	0	ENST00000409792.3:c.7195C>T	p.Arg2399Ter	p.R2399*	ENST00000409792	NM_014159.6	2399	Cga/Tga	17/21	0.241668738876357	2	FACETS	0.836	0.782	0.892	0.836	0.782	0.892	CLONAL	2	TRUE	0	0.253435953924963	2		665	1203	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815562	139815562	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs748178503	NA	P-0008756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	150	659	0	ENST00000247668.2:c.1033A>T	p.Met345Leu	p.M345L	ENST00000247668	NM_021138.3	345	Atg/Ttg	9/11	1	2	FACETS	0.935	0.852	1	0.935	0.852	1	CLONAL	1	TRUE	1	0.253435953924963	2		659	1266	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142099	108142099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555085210	NA	P-0008756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	137	661	2	ENST00000278616.4:c.3043C>T	p.Gln1015Ter	p.Q1015*	ENST00000278616	NM_000051.3	1015	Caa/Taa	20/63	1	2	FACETS	0.948	0.861	1	0.948	0.861	1	CLONAL	1	TRUE	1	0.253435953924963	2		663	1140	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830911	72830911	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	82	450	0	ENST00000268489.5:c.5670G>C	p.Gln1890His	p.Q1890H	ENST00000268489	NM_006885.3	1890	caG/caC	9/10	1	2	FACETS	0.886	0.781	0.999	0.886	0.781	0.999	CLONAL	1	TRUE	1	0.253435953924963	2		450	730	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584586	48584608	+	frameshift_variant	Frame_Shift_Del	DEL	TACTGGTCAGCCAGCTACTTACC	TACTGGTCAGCCAGCTACTTACC	-	novel	NA	P-0008756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	50	467	0	ENST00000342988.3:c.759_781del	p.Phe253LeufsTer3	p.F253Lfs*3	ENST00000342988	NM_005359.5	253	ttTACTGGTCAGCCAGCTACTTACCat/ttat	6/12	0.246903511005501	1	FACETS	0.493	0.417	0.576	0.493	0.417	0.576	SUBCLONAL	1	TRUE	0	0.253435953924963	1		467	699	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945474	151945474	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0008756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1924	244	1435	0	ENST00000262189.6:c.2045C>G	p.Ser682Ter	p.S682*	ENST00000262189	NM_170606.2	682	tCa/tGa	14/59	1	2	FACETS	0.888	0.826	0.953	0.888	0.826	0.953	CLONAL	1	TRUE	1	0.253435953924963	2		1435	2168	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046315	69046315	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	65	449	0	ENST00000288368.4:c.3788G>C	p.Arg1263Thr	p.R1263T	ENST00000288368	NM_024870.2	1263	aGa/aCa	32/40	1	2	FACETS	0.741	0.642	0.849	0.741	0.642	0.849	SUBCLONAL	1	TRUE	1	0.253435953924963	2		449	692	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30061031	30061031	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0009896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	458	577	0	ENST00000338641.4:c.863C>G	p.Ser288Ter	p.S288*	ENST00000338641	NM_000268.3	288	tCa/tGa	9/16	0.752061175330936	1	FACETS	0.948	0.913	0.982	0.948	0.913	0.982	CLONAL	1	TRUE	0	0.752061175330936	1		577	802	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	98	122	0				ENST00000310581	NM_198253.2	-/1132			0.353468312134994	3	FACETS	0.955	0.862	1	0.478	0.431	0.526	INDETERMINATE	1	TRUE	1	0.922643502600625	3		122	325	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241722	55241722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1051753269	NA	P-0013305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	977	576	1	ENST00000275493.2:c.2170G>A	p.Gly724Ser	p.G724S	ENST00000275493	NM_005228.3	724	Ggc/Agc	18/28	0.582519045658833	6	FACETS	1	0.996	1	1	0.996	1	CLONAL	4	TRUE	2	0.922643502600625	6		577	1407	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510627	38510627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	666	592	1	ENST00000254066.5:c.881G>A	p.Arg294Gln	p.R294Q	ENST00000254066	NM_000964.3	294	cGg/cAg	7/9	0.922643502600625	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.922643502600625	3		593	691	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578537	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs879254214	NA	P-0013305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	506	763	2	ENST00000269305.4:c.393_395del	p.Asn131del	p.N131del	ENST00000269305	NM_001126112.2	131	aaCAAg/aag	5/11	0.353468312134994	3	FACETS	0.843	0.812	0.873	0.843	0.812	0.873	INDETERMINATE	2	TRUE	1	0.922643502600625	3		765	951	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437539	52437540	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0013305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	386	640	0	ENST00000460680.1:c.1621_1622del	p.Val541Ter	p.V541*	ENST00000460680	NM_004656.3	541	GTt/t	13/17	0.922643502600625	2	FACETS	0.957	0.936	0.977	0.957	0.936	0.977	CLONAL	2	TRUE	0	0.922643502600625	2		640	437	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152864343	152864418	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CCGGCCTGGCCAGCCGGGCCCGCTCCGCGAAGCGGGCCGCGGCGCCGCCTGTCCTGGCCTCCCCCGGCCGCGGTTA	CCGGCCTGGCCAGCCGGGCCCGCTCCGCGAAGCGGGCCGCGGCGCCGCCTGTCCTGGCCTCCCCCGGCCGCGGTTA	-	novel	NA	P-0013305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	31	71	0	ENST00000406277.2:c.106+2_106+77del		p.X36_splice	ENST00000406277	NM_152274.4	36			0.292125388270422		FACETS		0.857	1				INDETERMINATE	2	TRUE	2	0.922643502600625	4		71	64	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0014434-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	137	466	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.607046930659739	2		467	419	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793208	139793208	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561210418	NA	P-0014434-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	150	580	1	ENST00000247668.2:c.16G>A	p.Val6Met	p.V6M	ENST00000247668	NM_021138.3	6	Gtg/Atg	2/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.607046930659739	2		581	439	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916937	178916948	+	inframe_deletion	In_Frame_Del	DEL	TGAAGAAAAGAT	TGAAGAAAAGAT	-	novel	NA	P-0014434-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	44	490	0	ENST00000263967.3:c.324_335del	p.Glu109_Ile112del	p.E109_I112del	ENST00000263967	NM_006218.2	108	cgTGAAGAAAAGATc/cgc	2/21	1	2	FACETS	0.531	0.448	0.622	0.531	0.448	0.622	SUBCLONAL	1	TRUE	1	0.607046930659739	2		490	273	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015230-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	56	122	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.77	0.665	0.883	0.77	0.665	0.883	SUBCLONAL	1	TRUE	1	0.503425031280204	2		122	289	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508508	29508509	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0015230-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	131	397	0	ENST00000356175.3:c.654+2dup		p.X218_splice	ENST00000356175	NM_000267.3	218			0.498351957695395	1	FACETS	0.966	0.885	1	0.966	0.885	1	CLONAL	1	TRUE	0	0.503425031280204	1		397	403	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78426147	78426147	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015230-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	61	323	0	ENST00000370768.2:c.1378C>T	p.His460Tyr	p.H460Y	ENST00000370768	NM_003902.3	460	Cat/Tat	15/20	1	2	FACETS	0.824	0.717	0.939	0.824	0.717	0.939	CLONAL	1	TRUE	1	0.503425031280204	2		323	294	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480170	20480170	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015230-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	82	366	0	ENST00000346618.3:c.487A>G	p.Ser163Gly	p.S163G	ENST00000346618	NM_001949.4	163	Agt/Ggt	2/7	NA	2	FACETS	0.785	0.696	0.88			1	INDETERMINATE	1	TRUE	NA	0.503425031280204	2		366	415	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878529	151878529	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1400133609	NA	P-0015230-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	115	501	0	ENST00000262189.6:c.6416G>T	p.Arg2139Leu	p.R2139L	ENST00000262189	NM_170606.2	2139	cGa/cTa	36/59	0.503425031280204	3	FACETS	0.865	0.781	0.954	0.433	0.39	0.477	CLONAL	1	TRUE	1	0.503425031280204	3		501	661	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396530	139396530	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015230-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	73	485	1	ENST00000277541.6:c.5395A>G	p.Asn1799Asp	p.N1799D	ENST00000277541	NM_017617.3	1799	Aac/Gac	29/34	0.194611408818574	1	FACETS	0.512	0.449	0.579	0.512	0.449	0.579	INDETERMINATE	1	TRUE	0	0.503425031280204	1		486	424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	294	782	0	ENST00000269305.4:c.772G>C	p.Glu258Gln	p.E258Q	ENST00000269305	NM_001126112.2	258	Gaa/Caa	7/11	0.259397590418838	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.28	2		782	1028	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954172	32954172	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs200924727	NA	P-0121531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	266	506	0	ENST00000380152.3:c.9146A>G	p.Tyr3049Cys	p.Y3049C	ENST00000380152		3049	tAc/tGc	24/27	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	NA	1	0.919379540681951	2		506	576	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986928	36986928	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1422890661	NA	P-0121531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	226	552	1	ENST00000354822.5:c.761C>A	p.Ala254Glu	p.A254E	ENST00000354822	NM_001079668.2	254	gCg/gAg	3/3	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	NA	1	0.919379540681951	2		553	487	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857311	68857312	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	123	319	0	ENST00000261769.5:c.1947dup	p.Ile650TyrfsTer13	p.I650Yfs*13	ENST00000261769	NM_004360.3	649	tct/tcTt	13/16	NA	2	FACETS	0.784	0.714	0.856			1	INDETERMINATE	2	TRUE	NA	0.360786746813142	2		319	435	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490910	56490910	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018594-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	96	661	0	ENST00000267101.3:c.2356G>T	p.Val786Phe	p.V786F	ENST00000267101	NM_001982.3	786	Gtc/Ttc	20/28	1	2	FACETS	0.457	0.406	0.511	0.457	0.406	0.511	SUBCLONAL	1	TRUE	1	0.407230545302502	2		661	1032	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0019141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	17	501	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.171	0.126	0.224	0.171	0.126	0.224	SUBCLONAL	1	FALSE	1	0.31443709394431	2		501	634	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	16	352	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.204	0.149	0.269	0.204	0.149	0.269	SUBCLONAL	1	FALSE	1	0.31443709394431	2		352	500	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0019141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	35	425	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.31443709394431	3	FACETS	0.387	0.316	0.468			1	SUBCLONAL	1	FALSE	NA	0.31443709394431	3		425	665	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458941	120458942	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0019141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	87	671	0	ENST00000256646.2:c.6403_6404del	p.Leu2135GlufsTer2	p.L2135Efs*2	ENST00000256646	NM_024408.3	2135	CTg/g	34/34	1	2	FACETS	0.681	0.602	0.765	0.681	0.602	0.765	SUBCLONAL	1	FALSE	1	0.31443709394431	2		671	813	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11803063	11803063	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0019141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	36	350	0	ENST00000396373.4:c.2T>C	p.Met1?	p.M1?	ENST00000396373	NM_001987.4	1	aTg/aCg	1/8	NA	2	FACETS	0.408	0.335	0.491			1	INDETERMINATE	1	FALSE	NA	0.31443709394431	2		350	561	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528757	8528757	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs750992182	NA	P-0019141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	20	340	0	ENST00000356435.5:c.375C>G	p.Phe125Leu	p.F125L	ENST00000356435		125	ttC/ttG	4/35	1	2	FACETS	0.321	0.245	0.411	0.321	0.245	0.411	SUBCLONAL	1	FALSE	1	0.31443709394431	2		340	396	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019141-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	139	352	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.95	0.868	1	0.95	0.868	1	CLONAL	1	TRUE	1	0.468850835422295	2		352	624	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528757	8528757	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs750992182	NA	P-0019141-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	162	340	0	ENST00000356435.5:c.375C>G	p.Phe125Leu	p.F125L	ENST00000356435		125	ttC/ttG	4/35	0.284896541534137	3	FACETS	0.76	0.701	0.821	0.76	0.701	0.821	SUBCLONAL	2	TRUE	1	0.468850835422295	3		340	561	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845757	68845757	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587780784	NA	P-0019141-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	97	396	0	ENST00000261769.5:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000261769	NM_004360.3	335	Cga/Tga	7/16	0.468850835422295	1	FACETS	0.954	0.86	1	0.954	0.86	1	CLONAL	1	TRUE	0	0.468850835422295	1		396	332	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0019141-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	216	610	2	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	1	2	FACETS	0.926	0.861	0.993	0.926	0.861	0.993	CLONAL	1	TRUE	1	0.468850835422295	2		612	995	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139041	50139041	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019141-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	99	708	1	ENST00000246792.3:c.522A>T	p.Lys174Asn	p.K174N	ENST00000246792	NM_006270.3	174	aaA/aaT	5/6	1	2	FACETS	0.469	0.418	0.523	0.469	0.418	0.523	SUBCLONAL	1	TRUE	1	0.468850835422295	2		709	901	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0019623-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	134	532	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.908	0.825	0.995	0.908	0.825	0.995	CLONAL	1	TRUE	1	0.367482391678831	2		533	803	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0019623-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	140	595	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	1	2	FACETS	0.988	0.901	1	0.988	0.901	1	CLONAL	1	TRUE	1	0.367482391678831	2		595	771	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293158	91293158	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019623-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	114	531	0	ENST00000355112.3:c.660G>T	p.Leu220Phe	p.L220F	ENST00000355112	NM_000057.2	220	ttG/ttT	3/22	0.367482391678831	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.367482391678831	1		531	483	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720817	89720818	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	G	novel	NA	P-0019623-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	36	333	1	ENST00000371953.3:c.968_969delinsG	p.Asn323ArgfsTer21	p.N323Rfs*21	ENST00000371953	NM_000314.4	323	aAT/aG	8/9	0.367482391678831	1	FACETS	0.776	0.644	0.922	0.776	0.644	0.922	CLONAL	1	TRUE	0	0.367482391678831	1		334	206	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100624	8100624	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	349	964	0	ENST00000346208.3:c.598C>A	p.His200Asn	p.H200N	ENST00000346208		200	Cac/Aac	3/6	0.404198676778762	4	FACETS	0.911	0.863	0.96	0.911	0.863	0.96	CLONAL	2	TRUE	2	0.484445621124357	4		964	1174	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343425	118343425	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	145	515	0	ENST00000534358.1:c.1551G>C	p.Gln517His	p.Q517H	ENST00000534358	NM_005933.3	517	caG/caC	3/36	0.404198676778762	4	FACETS	0.752	0.689	0.817	0.752	0.689	0.817	SUBCLONAL	2	TRUE	2	0.484445621124357	4		515	591	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863370	57863370	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	256	912	0	ENST00000228682.2:c.1465G>T	p.Gly489Cys	p.G489C	ENST00000228682	NM_005269.2	489	Ggc/Tgc	11/12	0.229954286694373	4	FACETS	0.902	0.846	0.959	0.902	0.846	0.959	INDETERMINATE	2	TRUE	2	0.484445621124357	4		912	870	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112940056	112940056	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	129	893	3	ENST00000351677.2:c.1708G>T	p.Ala570Ser	p.A570S	ENST00000351677	NM_002834.3	570	Gca/Tca	14/16	0.229954286694373	4	FACETS	0.826	0.748	0.908	0.413	0.374	0.454	INDETERMINATE	1	TRUE	2	0.484445621124357	4		896	957	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842401	68842401	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	40	830	1	ENST00000261769.5:c.462A>T	p.Arg154Ser	p.R154S	ENST00000261769	NM_004360.3	154	agA/agT	4/16	0.433299805311379	2	FACETS	0.241	0.2	0.288	0.121	0.1	0.144	SUBCLONAL	1	TRUE	0	0.484445621124357	2		831	684	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577115	7577115	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	299	1008	1	ENST00000269305.4:c.823T>A	p.Cys275Ser	p.C275S	ENST00000269305	NM_001126112.2	275	Tgt/Agt	8/11	0.356678339500718	2	FACETS	0.88	0.835	0.927	0.88	0.835	0.927	CLONAL	2	TRUE	0	0.484445621124357	2		1009	701	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804374	46804374	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs760440566	NA	P-0019849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	211	510	3	ENST00000290295.7:c.633C>A	p.Cys211Ter	p.C211*	ENST00000290295	NM_006361.5	211	tgC/tgA	2/2	0.356678339500718	2	FACETS	0.909	0.854	0.965	0.909	0.854	0.965	CLONAL	2	TRUE	0	0.484445621124357	2		513	479	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207104	1207105	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0019849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	366	1102	2	ENST00000326873.7:c.192_193delinsTT	p.Lys64_Glu65delinsAsnTer	p.K64_E65delinsN*	ENST00000326873	NM_000455.4	64	aaGGag/aaTTag	1/10	0.456982345134907	2	FACETS	0.902	0.86	0.944	0.902	0.86	0.944	CLONAL	2	TRUE	0	0.484445621124357	2		1104	838	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599995	10600018	+	inframe_deletion	In_Frame_Del	DEL	ACCATCATAGCCCCCAGCAGCATA	ACCATCATAGCCCCCAGCAGCATA	-	novel	NA	P-0019849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	289	966	0	ENST00000171111.5:c.1558_1581del	p.Tyr520_Gly527del	p.Y520_G527del	ENST00000171111	NM_203500.1	520	TATGCTGCTGGGGGCTATGATGGT/-	5/6	0.456982345134907	2	FACETS	1	0.994	1	0.734	0.693	0.775	CLONAL	1	TRUE	0	0.484445621124357	2		966	813	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770633	40770633	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	139	465	0	ENST00000373198.4:c.2749G>T	p.Glu917Ter	p.E917*	ENST00000373198	NM_133170.3	917	Gag/Tag	19/32	0.433299805311379	2	FACETS	0.834	0.77	0.899	0.834	0.77	0.899	CLONAL	2	TRUE	0	0.484445621124357	2		465	344	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980804	40980804	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	234	769	2	ENST00000373198.4:c.1682C>A	p.Thr561Asn	p.T561N	ENST00000373198	NM_133170.3	561	aCc/aAc	10/32	0.433299805311379	2	FACETS	0.89	0.838	0.942	0.89	0.838	0.942	CLONAL	2	TRUE	0	0.484445621124357	2		771	543	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141027	55141027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761924292	NA	P-0019849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	43	439	0	ENST00000257290.5:c.1673G>A	p.Arg558His	p.R558H	ENST00000257290	NM_006206.4	558	cGc/cAc	12/23	0.433299805311379	2	FACETS	0.527	0.442	0.62	0.263	0.221	0.31	SUBCLONAL	1	TRUE	0	0.484445621124357	2		439	337	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324216	31324224	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GACCCTGGC	GACCCTGGC	-	novel	NA	P-0019849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	134	292	0	ENST00000412585.2:c.344-5_347del		p.X115_splice	ENST00000412585	NM_005514.6	115		3/8	0.300643716184317	4	FACETS	1	0.961	1	1	0.99	1	CLONAL	3	TRUE	2	0.484445621124357	4		292	260	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104673	69104673	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	156	673	0	ENST00000288368.4:c.4517C>A	p.Ser1506Tyr	p.S1506Y	ENST00000288368	NM_024870.2	1506	tCt/tAt	37/40	0.484445621124357	3	FACETS	1	0.935	1	0.512	0.469	0.556	CLONAL	1	TRUE	1	0.484445621124357	3		673	782	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342574	87342574	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	78	490	0	ENST00000277120.3:c.859C>A	p.Pro287Thr	p.P287T	ENST00000277120		287	Cca/Aca	9/19	0.363240474881873	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.363240474881873	1		490	327	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244642	46244642	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	125	817	0	ENST00000334344.6:c.2736G>T	p.Gln912His	p.Q912H	ENST00000334344	NM_152641.2	912	caG/caT	15/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.363240474881873	2		817	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578285	7578288	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CAGA	CAGA	AC	novel	NA	P-0019851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	276	722	2	ENST00000269305.4:c.561_564delinsGT	p.Leu188CysfsTer20	p.L188Cfs*20	ENST00000269305	NM_001126112.2	187	ggTCTG/ggGT	6/11	0.350461976809904	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.363240474881873	2		724	631	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296221	15296221	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0019851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	96	953	0	ENST00000263388.2:c.2145-2A>G		p.X715_splice	ENST00000263388	NM_000435.2	715			1	2	FACETS	0.823	0.734	0.918	0.823	0.734	0.918	CLONAL	1	TRUE	1	0.363240474881873	2		953	642	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880975	134880975	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	71	628	1	ENST00000398015.3:c.1538G>T	p.Gly513Val	p.G513V	ENST00000398015	NM_004441.4	513	gGc/gTc	7/16	1	2	FACETS	0.832	0.728	0.943	0.832	0.728	0.943	CLONAL	1	TRUE	1	0.363240474881873	2		629	470	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444545	187444545	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	74	747	2	ENST00000232014.4:c.1682T>A	p.Leu561His	p.L561H	ENST00000232014	NM_001130845.1	561	cTc/cAc	7/10	1	2	FACETS	0.75	0.658	0.85	0.75	0.658	0.85	SUBCLONAL	1	TRUE	1	0.363240474881873	2		749	543	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652153	36652153	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	113	736	0	ENST00000244741.5:c.275G>T	p.Gly92Val	p.G92V	ENST00000244741	NM_000389.4	92	gGc/gTc	2/3	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.363240474881873	2		736	589	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404599	8404599	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	46	436	0	ENST00000356435.5:c.4148A>C	p.Lys1383Thr	p.K1383T	ENST00000356435		1383	aAg/aCg	25/35	0.363240474881873	1	FACETS	0.807	0.684	0.939	0.807	0.684	0.939	CLONAL	1	TRUE	0	0.363240474881873	1		436	257	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0019852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	211	770	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.307410299851204	5	FACETS	1	0.956	1	0.692	0.643	0.742	CLONAL	2	TRUE	2	0.356759445570433	5		770	875	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123837	46123837	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0019852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	70	447	0	ENST00000334344.6:c.103A>T	p.Lys35Ter	p.K35*	ENST00000334344	NM_152641.2	35	Aaa/Taa	2/21	0.311031365836527	2	FACETS	1	0.966	1	0.648	0.57	0.73	CLONAL	1	TRUE	0	0.356759445570433	2		447	303	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691039	NA	P-0019852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	146	722	0	ENST00000269305.4:c.919+1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.356759445570433	2		722	604	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871861	12871861	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	144	477	2	ENST00000228872.4:c.578del	p.Leu193ProfsTer32	p.L193Pfs*32	ENST00000228872	NM_004064.3	193	cTc/cc	2/3	0.311031365836527	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.356759445570433	2		479	392	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39537702	39537702	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs770629565	NA	P-0019852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	27	422	0	ENST00000262039.4:c.236A>G	p.Lys79Arg	p.K79R	ENST00000262039	NM_002647.2	79	aAa/aGa	2/25	0.311031365836527	2	FACETS	0.408	0.324	0.503	0.204	0.162	0.252	SUBCLONAL	1	TRUE	0	0.356759445570433	2		422	371	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597412	52597412	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	97	728	0	ENST00000394830.3:c.3898G>C	p.Asp1300His	p.D1300H	ENST00000394830	NM_018313.4	1300	Gat/Cat	25/30	0.274804892344106	3	FACETS	0.923	0.824	1	0.308	0.274	0.343	CLONAL	1	TRUE	0	0.356759445570433	3		728	694	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155088	108155090	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	novel	NA	P-0019854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	501	654	0	ENST00000278616.4:c.3884_3886del	p.Leu1295del	p.L1295del	ENST00000278616	NM_000051.3	1294	aTTCtt/att	26/63	0.7811103992252	2	FACETS	0.942	0.917	0.968	0.942	0.917	0.968	CLONAL	2	TRUE	0	0.791020002955409	2		654	672	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196133	108196133	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	156	758	0	ENST00000278616.4:c.6669C>G	p.Ile2223Met	p.I2223M	ENST00000278616	NM_000051.3	2223	atC/atG	46/63	0.7811103992252	2	FACETS	0.529	0.485	0.574	0.264	0.242	0.287	SUBCLONAL	1	TRUE	0	0.791020002955409	2		758	746	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015185	128015185	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146427260	NA	P-0019854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	261	627	2	ENST00000285398.2:c.2336G>A	p.Arg779His	p.R779H	ENST00000285398	NM_000122.1	779	cGc/cAc	15/15	1	2	FACETS	0.954	0.899	1	0.954	0.899	1	CLONAL	1	TRUE	1	0.791020002955409	2		629	692	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0019855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	223	825	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.726035949284775	3	FACETS	0.96	0.895	1	0.48	0.447	0.514	CLONAL	1	TRUE	1	0.726035949284775	3		825	872	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424437	49424438	+	stop_gained	Nonsense_Mutation	DNP	CA	CA	AG	novel	NA	P-0019855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	322	706	4	ENST00000301067.7:c.13785_13786delinsCT	p.Gly4596Ter	p.G4596*	ENST00000301067	NM_003482.3	4595	ttTGga/ttCTga	41/54	0.726035949284775	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.726035949284775	1		710	550	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427251	49427268	+	inframe_deletion	In_Frame_Del	DEL	TGCTGCTGCTGCTGTTGC	TGCTGCTGCTGCTGTTGC	-	rs1328650739	NA	P-0019855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	35	532	0	ENST00000301067.7:c.11220_11237del	p.Gln3740_Gln3745del	p.Q3740_Q3745del	ENST00000301067	NM_003482.3	3740	caGCAACAGCAGCAGCAGCAc/cac	39/54	0.726035949284775	1	FACETS	0.137	0.112	0.165	0.137	0.112	0.165	SUBCLONAL	1	TRUE	0	0.726035949284775	1		532	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579368	7579368	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	369	890	0	ENST00000269305.4:c.319del	p.Tyr107ThrfsTer16	p.Y107Tfs*16	ENST00000269305	NM_001126112.2	107	Tac/ac	4/11	0.710501988647304	1	FACETS	0.954	0.913	0.993	0.954	0.913	0.993	CLONAL	1	TRUE	0	0.726035949284775	1		890	679	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984843	11984843	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs77267737	NA	P-0019855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	186	524	0	ENST00000353533.5:c.389T>G	p.Val130Gly	p.V130G	ENST00000353533	NM_003010.3	130	gTt/gGt	3/11	0.710501988647304	1	FACETS	0.941	0.885	0.996	0.941	0.885	0.996	CLONAL	1	TRUE	0	0.726035949284775	1		524	347	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021529	31021529	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	241	609	0	ENST00000375687.4:c.1528C>A	p.Leu510Met	p.L510M	ENST00000375687	NM_015338.5	510	Ctg/Atg	12/13	1	2	FACETS	0.931	0.874	0.99	0.931	0.874	0.99	CLONAL	1	TRUE	1	0.726035949284775	2		609	713	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs786202525	NA	P-0019856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	100	491	1	ENST00000269305.4:c.532del	p.His178ThrfsTer69	p.H178Tfs*69	ENST00000269305	NM_001126112.2	178	Cac/ac	5/11	0.397463002835665	2	FACETS	1	0.981	1	0.706	0.638	0.777	CLONAL	1	TRUE	0	0.426492073344432	2		492	332	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482926	140482927	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs777474487	NA	P-0019856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	70	483	1	ENST00000288602.6:c.1208dup	p.Ala404CysfsTer9	p.A404Cfs*9	ENST00000288602	NM_004333.4	403	cct/ccCt	10/18	0.427109839892777	5	FACETS	0.885	0.772	1	0.295	0.257	0.336	CLONAL	1	TRUE	2	0.426492073344432	5		484	608	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249007	+	missense_variant	Missense_Mutation	TNP	GCG	GCG	TCT	novel	NA	P-0019856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	515	411	1	ENST00000275493.2:c.2303_2305delinsTCT	p.Ser768_Val769delinsIleLeu	p.S768_V769delinsIL	ENST00000275493	NM_005228.3	768	aGCGtg/aTCTtg	20/28	0.426492073344432	8	FACETS	1	0.989	1	0.906	0.875	0.936	CLONAL	6	TRUE	1	0.426492073344432	8		412	868	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976733	55976733	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	54	387	0	ENST00000263923.4:c.1092G>C	p.Trp364Cys	p.W364C	ENST00000263923	NM_002253.2	364	tgG/tgC	9/30	0.39469058603467	3	FACETS	1	0.933	1	0.571	0.492	0.656	CLONAL	1	TRUE	1	0.426492073344432	3		387	269	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0019857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	242	770	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.332236104097039	3	FACETS	1	0.987	1	0.798	0.749	0.848	CLONAL	2	TRUE	0	0.332236104097039	3		770	710	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560982	9560982	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	24	468	1	ENST00000353224.5:c.800G>T	p.Arg267Met	p.R267M	ENST00000353224	NM_177990.2	267	aGg/aTg	4/10	0.222545742060462	4	FACETS	0.443	0.347	0.555	0.222	0.173	0.278	SUBCLONAL	1	TRUE	2	0.332236104097039	4		469	434	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067131	143067131	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	127	574	0	ENST00000262992.4:c.1582G>A	p.Val528Met	p.V528M	ENST00000262992	NM_001101669.1	528	Gtg/Atg	16/24	0.155706063722567	5	FACETS	1	0.974	1	0.791	0.721	0.863	INDETERMINATE	2	TRUE	2	0.332236104097039	5		574	483	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0019858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	159	786	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.595988133497218	2	FACETS	1	0.986	1	0.637	0.59	0.684	CLONAL	1	TRUE	0	0.595988133497218	2		786	419	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954272	32954273	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359752	NA	P-0019858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	101	596	0	ENST00000380152.3:c.9253dup	p.Thr3085AsnfsTer26	p.T3085Nfs*26	ENST00000380152		3082	-/A	24/27	0.595988133497218	1	FACETS	0.832	0.754	0.912	0.832	0.754	0.912	CLONAL	1	TRUE	0	0.595988133497218	1		596	286	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056283	26056283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1459637809	NA	P-0019858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	149	668	1	ENST00000343677.2:c.374G>A	p.Gly125Glu	p.G125E	ENST00000343677	NM_005319.3	125	gGa/gAa	1/1	1	2	FACETS	0.938	0.862	1	0.938	0.862	1	CLONAL	1	TRUE	1	0.595988133497218	2		669	533	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842613	68842614	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	233	908	0	ENST00000261769.5:c.552dup	p.Glu185ArgfsTer14	p.E185Rfs*14	ENST00000261769	NM_004360.3	183	-/A	5/16	0.595988133497218	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.595988133497218	1		908	530	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40872468	40872468	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0019858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	420	789	0	ENST00000428826.2:c.488-1G>T		p.X163_splice	ENST00000428826		163			0.595988133497218	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.595988133497218	3		789	885	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435363	56435363	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	58	936	0	ENST00000407977.2:c.1774C>A	p.Pro592Thr	p.P592T	ENST00000407977		592	Cct/Act	9/10	0.273889936410396	3	FACETS	0.285	0.244	0.33	0.143	0.122	0.165	INDETERMINATE	1	TRUE	1	0.595988133497218	3		936	886	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39234173	39234173	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs760457239	NA	P-0019858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	159	787	0	ENST00000402219.2:c.2672A>G	p.Glu891Gly	p.E891G	ENST00000402219	NM_005633.3	891	gAg/gGg	16/23	1	2	FACETS	0.999	0.922	1	0.999	0.922	1	CLONAL	1	TRUE	1	0.595988133497218	2		787	534	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520188	176520188	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	111	1159	0	ENST00000292408.4:c.1107C>A	p.Asp369Glu	p.D369E	ENST00000292408	NM_213647.1	369	gaC/gaA	9/18	1	2	FACETS	0.441	0.396	0.489	0.441	0.396	0.489	SUBCLONAL	1	TRUE	1	0.595988133497218	2		1159	844	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76764064	76764064	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	214	736	0	ENST00000373344.5:c.7244A>C	p.Gln2415Pro	p.Q2415P	ENST00000373344	NM_000489.3	2415	cAg/cCg	35/35	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.595988133497218	2		736	698	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983039	201983040	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	358	891	0	ENST00000359651.3:c.890dup	p.Asn297LysfsTer4	p.N297Kfs*4	ENST00000359651		296	-/A	7/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.654421588674833	2		891	1047	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171606	36171606	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	181	343	0	ENST00000300305.3:c.959G>C	p.Arg320Pro	p.R320P	ENST00000300305		320	cGa/cCa	7/8	1	2	FACETS	0.987	0.924	1	0.987	0.924	1	CLONAL	1	TRUE	1	0.928062771095018	2		343	395	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0019861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	78	554	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.151341088044539	3	FACETS	0.902	0.794	1	0.902	0.794	1	CLONAL	2	TRUE	1	0.17	3		554	552	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0019861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	116	146	0				ENST00000310581	NM_198253.2	-/1132			0.155256040343328	3	FACETS	1	0.955	1	0.734	0.663	0.81	CLONAL	2	TRUE	0	0.17	3		146	672	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374244	138374244	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	38	626	0	ENST00000289153.2:c.3200A>T	p.Asp1067Val	p.D1067V	ENST00000289153	NM_006219.2	1067	gAc/gTc	22/22	1	2	FACETS	0.771	0.636	0.922	0.771	0.636	0.922	CLONAL	1	TRUE	1	0.17	2		626	580	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123499615	123499615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	52	821	1	ENST00000371139.4:c.142C>T	p.His48Tyr	p.H48Y	ENST00000371139	NM_001114937.2	48	Cac/Tac	2/4	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.17	2		822	523	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40476813	40476813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	52	799	2	ENST00000264657.5:c.1516G>A	p.Glu506Lys	p.E506K	ENST00000264657	NM_139276.2	506	Gag/Aag	17/24	0.2952640768644	3	FACETS	0.768	0.652	0.896	0.384	0.326	0.448	SUBCLONAL	1	TRUE	1	0.17	3		801	864	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287264	46287264	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	42	669	2	ENST00000334344.6:c.5209C>A	p.Pro1737Thr	p.P1737T	ENST00000334344	NM_152641.2	1737	Ccc/Acc	19/21	1	2	FACETS	0.777	0.647	0.921	0.777	0.647	0.921	CLONAL	1	TRUE	1	0.17	2		671	636	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675119	40675119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766760890	NA	P-0019861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	72	966	3	ENST00000249776.8:c.83C>T	p.Pro28Leu	p.P28L	ENST00000249776	NM_033286.3	28	cCg/cTg	1/9	1	2	FACETS	0.945	0.824	1	0.945	0.824	1	CLONAL	1	TRUE	1	0.17	2		969	896	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902604	1902604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	73	884	0	ENST00000382891.5:c.223C>T	p.Pro75Ser	p.P75S	ENST00000382891	NM_133335.3	75	Cca/Tca	2/22	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.17	2		884	859	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874091	151874091	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	92	779	0	ENST00000262189.6:c.8447C>T	p.Ser2816Phe	p.S2816F	ENST00000262189	NM_170606.2	2816	tCc/tTc	38/59	0.151341088044539	3	FACETS	0.764	0.678	0.855	0.764	0.678	0.855	SUBCLONAL	2	TRUE	1	0.17	3		779	769	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182178	11182178	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	71	816	0	ENST00000361445.4:c.6668A>G	p.Gln2223Arg	p.Q2223R	ENST00000361445	NM_004958.3	2223	cAg/cGg	48/58	1	2	FACETS	0.911	0.793	1	0.911	0.793	1	CLONAL	1	TRUE	1	0.16	2		816	974	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560451	65560451	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0019862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	48	509	0	ENST00000358664.4:c.146C>G	p.Ser49Ter	p.S49*	ENST00000358664	NM_002382.4	49	tCa/tGa	3/5	1	2	FACETS	0.942	0.795	1	0.942	0.795	1	CLONAL	1	TRUE	1	0.16	2		509	637	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0019863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	402	874	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.64491633370375	5	FACETS	0.869	0.826	0.912			1	CLONAL	2	TRUE	NA	0.806332125487097	5		874	1268	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717713	89717713	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	353	625	0	ENST00000371953.3:c.738del	p.Leu247TyrfsTer9	p.L247Yfs*9	ENST00000371953	NM_000314.4	246	ccG/cc	7/9	0.696266118652743	2	FACETS	0.855	0.824	0.885	0.855	0.824	0.885	CLONAL	2	TRUE	0	0.806332125487097	2		625	512	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262325	115262325	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	117	681	0	ENST00000438362.2:c.2229G>T	p.Lys743Asn	p.K743N	ENST00000438362	NM_001242891.1	743	aaG/aaT	18/20	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.293080475002853	2		681	780	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465304	120465304	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	48	541	0	ENST00000256646.2:c.4957C>G	p.His1653Asp	p.H1653D	ENST00000256646	NM_024408.3	1653	Cac/Gac	27/34	1	2	FACETS	0.504	0.425	0.591	0.504	0.425	0.591	SUBCLONAL	1	TRUE	1	0.293080475002853	2		541	650	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469123	25469134	+	frameshift_variant	Frame_Shift_Del	DEL	TGCCTCAGGTTC	TGCCTCAGGTTC	GTAGG	novel	NA	P-0019864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	120	780	3	ENST00000264709.3:c.1324_1335delinsCCTAC	p.Glu442ProfsTer207	p.E442Pfs*207	ENST00000264709	NM_175629.2	442	GAACCTGAGGCA/CCTAC	11/23	1	2	FACETS	0.847	0.764	0.935	0.847	0.764	0.935	CLONAL	1	TRUE	1	0.293080475002853	2		783	967	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469174	25469174	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	38	590	0	ENST00000264709.3:c.1284G>C	p.Glu428Asp	p.E428D	ENST00000264709	NM_175629.2	428	gaG/gaC	11/23	1	2	FACETS	0.353	0.291	0.423	0.353	0.291	0.423	SUBCLONAL	1	TRUE	1	0.293080475002853	2		590	734	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270051	198270051	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	77	643	0	ENST00000335508.6:c.1385G>T	p.Gly462Val	p.G462V	ENST00000335508	NM_012433.2	462	gGa/gTa	10/25	1	2	FACETS	0.716	0.628	0.811	0.716	0.628	0.811	SUBCLONAL	1	TRUE	1	0.293080475002853	2		643	734	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748578	40748578	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	48	521	0	ENST00000373198.4:c.2938C>G	p.Gln980Glu	p.Q980E	ENST00000373198	NM_133170.3	980	Caa/Gaa	21/32	1	2	FACETS	0.517	0.436	0.606	0.517	0.436	0.606	SUBCLONAL	1	TRUE	1	0.293080475002853	2		521	634	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873943	151873948	+	frameshift_variant	Frame_Shift_Del	DEL	TCCATC	TCCATC	CCATT	novel	NA	P-0019864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	120	658	4	ENST00000262189.6:c.8590_8595delinsAATGG	p.Asp2864AsnfsTer42	p.D2864Nfs*42	ENST00000262189	NM_170606.2	2864	GATGGA/AATGG	38/59	0.245813459707745	4	FACETS	1	0.971	1	0.6	0.541	0.662	CLONAL	1	TRUE	2	0.293080475002853	4		662	882	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964486	70964486	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	121	777	0	ENST00000276594.2:c.1542G>T	p.Glu514Asp	p.E514D	ENST00000276594	NM_024504.3	514	gaG/gaT	8/8	1	2	FACETS	0.932	0.841	1	0.932	0.841	1	CLONAL	1	TRUE	1	0.293080475002853	2		777	886	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742462	145742462	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	264	824	0	ENST00000428558.2:c.326T>A	p.Leu109His	p.L109H	ENST00000428558	NM_004260.3	109	cTc/cAc	4/22	1	2	FACETS	0.806	0.756	0.859	1	0.994	1	CLONAL	2	TRUE	1	0.293080475002853	2		824	1117	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022183	5022183	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1183227511	NA	P-0019864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	59	709	0	ENST00000381652.3:c.196G>C	p.Glu66Gln	p.E66Q	ENST00000381652	NM_004972.3	66	Gaa/Caa	3/25	1	2	FACETS	0.581	0.499	0.67	0.581	0.499	0.67	SUBCLONAL	1	TRUE	1	0.293080475002853	2		709	693	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	406	424	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.620564088036438	4	FACETS	0.842	0.81	0.873	0.842	0.81	0.873	CLONAL	3	TRUE	1	0.930739399212904	4		424	667	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141874	108141874	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587781558	NA	P-0019865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	153	519	1	ENST00000278616.4:c.2921+1G>A		p.X974_splice	ENST00000278616	NM_000051.3	974			0.924390193151622	2	FACETS	0.945	0.877	1	0.472	0.438	0.507	CLONAL	1	TRUE	0	0.930739399212904	2		520	348	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16056646	16056652	+	splice_donor_variant,intron_variant	Splice_Site	DEL	TACTTAC	TACTTAC	-	novel	NA	P-0019865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	26	571	1	ENST00000268712.3:c.789+1_789+7del		p.X263_splice	ENST00000268712	NM_006311.3	263			1	2	FACETS	0.145	0.114	0.18	0.145	0.114	0.18	SUBCLONAL	1	TRUE	1	0.930739399212904	2		572	385	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	52	424	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.272847566642543	4	FACETS	0.55	0.466	0.642	0.275	0.233	0.321	SUBCLONAL	1	TRUE	2	0.274652144131943	4		424	878	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0019867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	22	860	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.258694723039852	3	FACETS	0.431	0.333	0.545	0.215	0.166	0.273	SUBCLONAL	1	TRUE	1	0.274652144131943	3		861	423	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0019867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	15	218	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	0.107119866745934	3	FACETS	0.618	0.453	0.816	0.309	0.226	0.408	INDETERMINATE	1	TRUE	1	0.274652144131943	3		218	201	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0019868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	217	501	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.611022878472859	2	FACETS	0.927	0.881	0.973	0.927	0.881	0.973	CLONAL	2	TRUE	0	0.678154751166122	2		501	345	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48921980	48921980	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	88	553	0	ENST00000267163.4:c.520T>G	p.Leu174Val	p.L174V	ENST00000267163	NM_000321.2	174	Ttg/Gtg	5/27	0.583271246563349	2	FACETS	0.934	0.838	1	0.467	0.419	0.517	CLONAL	1	TRUE	0	0.678154751166122	2		553	278	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591892	48591892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767345	NA	P-0019869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	191	681	0	ENST00000342988.3:c.1055G>A	p.Gly352Glu	p.G352E	ENST00000342988	NM_005359.5	352	gGa/gAa	9/12	0.537630023893423	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.537630023893423	1		681	462	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	38	301	0	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	0.0318442122849754	3	FACETS	0.473	0.392	0.564			1	INDETERMINATE	1	TRUE	NA	0.537630023893423	3		301	379	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0019869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	248	624	4	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.0318442122849754	3	FACETS	1	0.968	1			1	INDETERMINATE	2	TRUE	NA	0.537630023893423	3		628	565	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247516	123247516	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519795	NA	P-0019869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	152	731	2	ENST00000358487.5:c.1975A>G	p.Lys659Glu	p.K659E	ENST00000358487	NM_000141.4	659	Aag/Gag	14/18	1	2	FACETS	0.861	0.79	0.935	0.861	0.79	0.935	CLONAL	1	TRUE	1	0.537630023893423	2		733	657	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247527	123247527	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	168	789	1	ENST00000358487.5:c.1964A>G	p.Asp655Gly	p.D655G	ENST00000358487	NM_000141.4	655	gAc/gGc	14/18	1	2	FACETS	0.893	0.823	0.965	0.893	0.823	0.965	CLONAL	1	TRUE	1	0.537630023893423	2		790	700	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120373	70120374	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0019869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	791	1297	3	ENST00000245479.2:c.1376_1377dup	p.Thr460AlafsTer11	p.T460Afs*11	ENST00000245479	NM_000346.3	459	ggc/gGCgc	3/3	0.537630023893423	2	FACETS	0.892	0.864	0.919	0.892	0.864	0.919	CLONAL	2	TRUE	0	0.537630023893423	2		1300	1650	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098411	11098411	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	255	875	1	ENST00000358026.2:c.929G>T	p.Arg310Leu	p.R310L	ENST00000358026	NM_001128849.1	310	cGc/cTc	6/36	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.537630023893423	2		876	942	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579515	7579515	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	CC	novel	NA	P-0019869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	457	918	6	ENST00000269305.4:c.172delinsGG	p.Pro58GlyfsTer5	p.P58Gfs*5	ENST00000269305	NM_001126112.2	58	Cca/GGca	4/11	0.537630023893423	2	FACETS	0.899	0.863	0.935	0.899	0.863	0.935	CLONAL	2	TRUE	0	0.537630023893423	2		924	946	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0019870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	45	562	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	1	2	FACETS	0.466	0.395	0.543	0.466	0.395	0.543	SUBCLONAL	1	TRUE	1	0.836088208495718	2		562	231	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0019870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	115	416	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	0.836088208495718	3	FACETS	0.844	0.765	0.927	0.422	0.382	0.464	CLONAL	1	TRUE	1	0.836088208495718	3		416	462	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0019870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	495	856	0	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.836088208495718	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.836088208495718	3		856	833	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932110	39932111	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555918014	NA	P-0019870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	213	799	0	ENST00000378444.4:c.2488_2489del	p.Ser830CysfsTer6	p.S830Cfs*6	ENST00000378444	NM_001123385.1	830	AGt/t	4/15	0.225202367775901	3	FACETS	1	0.991	1	0.685	0.643	0.729	INDETERMINATE	1	TRUE	1	0.836088208495718	3		799	527	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319438	11319438	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	47	609	0	ENST00000361445.4:c.29C>G	p.Thr10Ser	p.T10S	ENST00000361445	NM_004958.3	10	aCc/aGc	2/58	1	2	FACETS	0.612	0.515	0.719	0.612	0.515	0.719	SUBCLONAL	1	TRUE	1	0.23	2		609	668	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22405051	22405051	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	30	327	0	ENST00000344548.3:c.80A>C	p.Lys27Thr	p.K27T	ENST00000344548	NM_001039802.1	27	aAa/aCa	3/7	1	2	FACETS	0.872	0.705	1	0.872	0.705	1	CLONAL	1	TRUE	1	0.23	2		327	299	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059183	27059183	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	38	521	0	ENST00000324856.7:c.1820C>A	p.Ser607Ter	p.S607*	ENST00000324856	NM_006015.4	607	tCa/tAa	4/20	1	2	FACETS	0.673	0.556	0.804	0.673	0.556	0.804	SUBCLONAL	1	TRUE	1	0.23	2		521	491	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099419	27099419	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	58	628	0	ENST00000324856.7:c.3656A>G	p.Asp1219Gly	p.D1219G	ENST00000324856	NM_006015.4	1219	gAc/gGc	14/20	1	2	FACETS	0.815	0.7	0.94	0.815	0.7	0.94	CLONAL	1	TRUE	1	0.23	2		628	619	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818219	43818219	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	59	596	0	ENST00000372470.3:c.1684G>T	p.Glu562Ter	p.E562*	ENST00000372470	NM_005373.2	562	Gaa/Taa	12/12	1	2	FACETS	0.832	0.715	0.958	0.832	0.715	0.958	CLONAL	1	TRUE	1	0.23	2		596	617	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509523	46509523	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1233591180	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	39	442	0	ENST00000262741.5:c.1208A>G	p.His403Arg	p.H403R	ENST00000262741	NM_003629.3	403	cAc/cGc	10/10	1	2	FACETS	0.677	0.561	0.807	0.677	0.561	0.807	SUBCLONAL	1	TRUE	1	0.23	2		442	501	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301869	65301869	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	53	419	0	ENST00000342505.4:c.3170A>G	p.Lys1057Arg	p.K1057R	ENST00000342505	NM_002227.2	1057	aAa/aGa	23/25	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.23	2		419	361	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276624	115276624	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs749198304	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	52	729	0	ENST00000438362.2:c.835A>G	p.Ile279Val	p.I279V	ENST00000438362	NM_001242891.1	279	Atc/Gtc	8/20	1	2	FACETS	0.772	0.656	0.898	0.772	0.656	0.898	SUBCLONAL	1	TRUE	1	0.23	2		729	586	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165657	118165657	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs565811357	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	31	381	0	ENST00000369448.3:c.167G>A	p.Arg56His	p.R56H	ENST00000369448	NM_017709.3	56	cGc/cAc	2/2	1	2	FACETS	0.729	0.59	0.886	0.729	0.59	0.886	SUBCLONAL	1	TRUE	1	0.23	2		381	370	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464967	120464967	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs999822357	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	59	592	0	ENST00000256646.2:c.5105G>A	p.Arg1702Gln	p.R1702Q	ENST00000256646	NM_024408.3	1702	cGa/cAa	28/34	1	2	FACETS	0.845	0.727	0.974	0.845	0.727	0.974	CLONAL	1	TRUE	1	0.23	2		592	607	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497849	120497849	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	43	493	0	ENST00000256646.2:c.2033G>T	p.Arg678Ile	p.R678I	ENST00000256646	NM_024408.3	678	aGa/aTa	13/34	1	2	FACETS	0.74	0.619	0.875	0.74	0.619	0.875	SUBCLONAL	1	TRUE	1	0.23	2		493	505	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120529630	120529630	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	59	643	2	ENST00000256646.2:c.827T>C	p.Val276Ala	p.V276A	ENST00000256646	NM_024408.3	276	gTg/gCg	5/34	1	2	FACETS	0.679	0.583	0.783	0.679	0.583	0.783	SUBCLONAL	1	TRUE	1	0.23	2		645	756	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737136	162737136	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	35	481	0	ENST00000367921.3:c.1280A>G	p.Lys427Arg	p.K427R	ENST00000367921	NM_006182.2	427	aAa/aGa	11/18	1	2	FACETS	0.735	0.603	0.884	0.735	0.603	0.884	SUBCLONAL	1	TRUE	1	0.23	2		481	414	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163313556	163313556	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	29	491	0	ENST00000271452.3:c.703G>T	p.Glu235Ter	p.E235*	ENST00000271452	NM_145697.2	235	Gaa/Taa	10/14	1	2	FACETS	0.552	0.442	0.677	0.552	0.442	0.677	SUBCLONAL	1	TRUE	1	0.23	2		491	457	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111048	193111048	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	39	364	0	ENST00000367435.3:c.581G>T	p.Arg194Ile	p.R194I	ENST00000367435	NM_024529.4	194	aGa/aTa	7/17	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.23	2		364	267	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658356	206658356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	51	621	0	ENST00000367120.3:c.1450C>T	p.Pro484Ser	p.P484S	ENST00000367120	NM_014002.3	484	Cct/Tct	14/22	1	2	FACETS	0.755	0.642	0.881	0.755	0.642	0.881	SUBCLONAL	1	TRUE	1	0.23	2		621	587	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945699	206945699	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	53	587	0	ENST00000423557.1:c.82A>C	p.Asn28His	p.N28H	ENST00000423557	NM_000572.2	28	Aac/Cac	1/5	1	2	FACETS	0.785	0.669	0.912	0.785	0.669	0.912	CLONAL	1	TRUE	1	0.23	2		587	587	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555974	226555974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766670559	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	38	586	1	ENST00000366794.5:c.2203C>T	p.Arg735Cys	p.R735C	ENST00000366794	NM_001618.3	735	Cgc/Tgc	16/23	1	2	FACETS	0.598	0.493	0.714	0.598	0.493	0.714	SUBCLONAL	1	TRUE	1	0.23	2		587	553	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243801017	243801017	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	40	601	0	ENST00000263826.5:c.457C>A	p.Leu153Ile	p.L153I	ENST00000263826	NM_005465.4	153	Cta/Ata	5/13	1	2	FACETS	0.656	0.545	0.781	0.656	0.545	0.781	SUBCLONAL	1	TRUE	1	0.23	2		601	530	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097733	8097733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	70	717	0	ENST00000346208.3:c.115G>A	p.Ala39Thr	p.A39T	ENST00000346208		39	Gcg/Acg	2/6	1	2	FACETS	0.998	0.87	1	0.998	0.87	1	CLONAL	1	TRUE	1	0.23	2		717	610	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851549	63851549	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	73	718	0	ENST00000279873.7:c.2327A>T	p.Glu776Val	p.E776V	ENST00000279873	NM_032199.2	776	gAg/gTg	10/10	1	2	FACETS	0.835	0.73	0.949	0.835	0.73	0.949	CLONAL	1	TRUE	1	0.23	2		718	760	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851560	63851560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	70	698	0	ENST00000279873.7:c.2338C>T	p.Arg780Ter	p.R780*	ENST00000279873	NM_032199.2	780	Cga/Tga	10/10	1	2	FACETS	0.817	0.711	0.931	0.817	0.711	0.931	CLONAL	1	TRUE	1	0.23	2		698	745	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446146	70446146	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	47	530	0	ENST00000373644.4:c.5086T>G	p.Leu1696Val	p.L1696V	ENST00000373644	NM_030625.2	1696	Ttg/Gtg	11/12	1	2	FACETS	0.832	0.703	0.975	0.832	0.703	0.975	CLONAL	1	TRUE	1	0.23	2		530	491	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446173	70446173	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138726459	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	46	541	0	ENST00000373644.4:c.5113C>T	p.Leu1705Phe	p.L1705F	ENST00000373644	NM_030625.2	1705	Ctc/Ttc	11/12	1	2	FACETS	0.794	0.668	0.932	0.794	0.668	0.932	CLONAL	1	TRUE	1	0.23	2		541	504	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624245	89624245	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554890335	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	31	258	0	ENST00000371953.3:c.19G>T	p.Glu7Ter	p.E7*	ENST00000371953	NM_000314.4	7	Gag/Tag	1/9	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.23	2		258	251	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692931	89692931	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	65	724	0	ENST00000371953.3:c.415T>G	p.Leu139Val	p.L139V	ENST00000371953	NM_000314.4	139	Tta/Gta	5/9	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.23	2		724	555	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720870	89720870	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1554825652	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	62	510	0	ENST00000371953.3:c.1021T>G	p.Phe341Val	p.F341V	ENST00000371953	NM_000314.4	341	Ttt/Gtt	8/9	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.23	2		510	457	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741366	17741366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	67	865	0	ENST00000250003.3:c.37C>A	p.Leu13Met	p.L13M	ENST00000250003	NM_002478.4	13	Ctg/Atg	1/3	1	2	FACETS	0.704	0.611	0.806	0.704	0.611	0.806	SUBCLONAL	1	TRUE	1	0.23	2		865	827	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417875	32417875	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	86	706	0	ENST00000332351.3:c.1177T>C	p.Cys393Arg	p.C393R	ENST00000332351	NM_024426.4	393	Tgt/Cgt	7/10	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.23	2		706	737	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417946	32417946	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772590420	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	62	612	0	ENST00000332351.3:c.1106G>A	p.Arg369Gln	p.R369Q	ENST00000332351	NM_024426.4	369	cGa/cAa	7/10	1	2	FACETS	0.8	0.69	0.919	0.8	0.69	0.919	CLONAL	1	TRUE	1	0.23	2		612	674	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939770	71939770	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	87	735	1	ENST00000298229.2:c.398-1G>T		p.X133_splice	ENST00000298229	NM_001567.3	133			1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.23	2		736	723	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946918	71946918	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	85	881	0	ENST00000298229.2:c.2767G>T	p.Glu923Ter	p.E923*	ENST00000298229	NM_001567.3	923	Gag/Tag	25/28	1	2	FACETS	0.882	0.779	0.993	0.882	0.779	0.993	CLONAL	1	TRUE	1	0.23	2		881	838	SUCCESS
EED	8726	MSKCC	GRCh37	11	85977228	85977228	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	45	466	0	ENST00000263360.6:c.830C>A	p.Ser277Tyr	p.S277Y	ENST00000263360	NM_003797.3	277	tCt/tAt	8/12	1	2	FACETS	0.834	0.702	0.981	0.834	0.702	0.981	CLONAL	1	TRUE	1	0.23	2		466	469	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94170371	94170371	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745614941	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	44	445	2	ENST00000323929.3:c.1898G>A	p.Arg633Gln	p.R633Q	ENST00000323929	NM_005591.3	633	cGa/cAa	17/20	1	2	FACETS	0.886	0.744	1	0.886	0.744	1	CLONAL	1	TRUE	1	0.23	2		447	432	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918489	94918489	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	56	689	0	ENST00000536441.1:c.693T>G	p.Asn231Lys	p.N231K	ENST00000536441	NM_144665.3	231	aaT/aaG	5/10	1	2	FACETS	0.848	0.727	0.981	0.848	0.727	0.981	CLONAL	1	TRUE	1	0.23	2		689	574	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195917	102195917	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	60	466	0	ENST00000263464.3:c.677T>G	p.Leu226Arg	p.L226R	ENST00000263464	NM_001165.4	226	cTg/cGg	2/9	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.23	2		466	519	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	49	588	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	0.864	0.732	1	0.864	0.732	1	CLONAL	1	TRUE	1	0.23	2		588	493	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119783	108119783	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	30	377	0	ENST00000278616.4:c.1189A>G	p.Lys397Glu	p.K397E	ENST00000278616	NM_000051.3	397	Aaa/Gaa	9/63	1	2	FACETS	0.721	0.581	0.879	0.721	0.581	0.879	SUBCLONAL	1	TRUE	1	0.23	2		377	362	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163396	108163396	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	47	602	0	ENST00000278616.4:c.4487A>G	p.Asp1496Gly	p.D1496G	ENST00000278616	NM_000051.3	1496	gAc/gGc	30/63	1	2	FACETS	0.789	0.666	0.925	0.789	0.666	0.925	CLONAL	1	TRUE	1	0.23	2		602	518	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342559	118342559	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	31	448	0	ENST00000534358.1:c.685C>T	p.Pro229Ser	p.P229S	ENST00000534358	NM_005933.3	229	Cct/Tct	3/36	1	2	FACETS	0.779	0.631	0.946	0.779	0.631	0.946	CLONAL	1	TRUE	1	0.23	2		448	346	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344107	118344107	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs727503777	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	45	513	1	ENST00000534358.1:c.2233C>T	p.Arg745Ter	p.R745*	ENST00000534358	NM_005933.3	745	Cga/Tga	3/36	1	2	FACETS	0.952	0.802	1	0.952	0.802	1	CLONAL	1	TRUE	1	0.23	2		514	411	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374726	118374726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437799270	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	49	489	1	ENST00000534358.1:c.8119C>T	p.Arg2707Trp	p.R2707W	ENST00000534358	NM_005933.3	2707	Cgg/Tgg	27/36	1	2	FACETS	0.936	0.794	1	0.936	0.794	1	CLONAL	1	TRUE	1	0.23	2		490	455	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409121	4409121	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	46	620	1	ENST00000261254.3:c.816G>T	p.Glu272Asp	p.E272D	ENST00000261254	NM_001759.3	272	gaG/gaT	5/5	0.3	2	FACETS	0.671	0.564	0.789			1	SUBCLONAL	1	TRUE	NA	0.23	2		621	596	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435466	18435466	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	34	386	0	ENST00000266497.5:c.451T>G	p.Leu151Val	p.L151V	ENST00000266497		151	Ttg/Gtg	1/31	1	2	FACETS	0.942	0.772	1	0.942	0.772	1	CLONAL	1	TRUE	1	0.23	2		386	314	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650568	18650568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368805708	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	35	589	0	ENST00000266497.5:c.2779C>T	p.Arg927Cys	p.R927C	ENST00000266497		927	Cgt/Tgt	20/31	1	2	FACETS	0.751	0.616	0.903	0.751	0.616	0.903	CLONAL	1	TRUE	1	0.23	2		589	405	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719980	18719980	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	54	471	2	ENST00000266497.5:c.3877G>T	p.Glu1293Ter	p.E1293*	ENST00000266497		1293	Gaa/Taa	27/31	1	2	FACETS	0.974	0.833	1	0.974	0.833	1	CLONAL	1	TRUE	1	0.23	2		473	482	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211500	46211500	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	35	376	0	ENST00000334344.6:c.466A>G	p.Asn156Asp	p.N156D	ENST00000334344	NM_152641.2	156	Aat/Gat	5/21	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.23	2		376	258	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431393	49431393	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	49	601	0	ENST00000301067.7:c.9746T>G	p.Ile3249Ser	p.I3249S	ENST00000301067	NM_003482.3	3249	aTt/aGt	34/54	0.178909931881574	3	FACETS	0.922	0.781	1	0.461	0.39	0.539	CLONAL	1	TRUE	1	0.23	3		601	515	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433059	49433059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	68	848	1	ENST00000301067.7:c.8312G>A	p.Arg2771Gln	p.R2771Q	ENST00000301067	NM_003482.3	2771	cGa/cAa	33/54	0.178909931881574	3	FACETS	0.903	0.785	1	0.452	0.392	0.516	CLONAL	1	TRUE	1	0.23	3		849	730	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811630	102811630	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	44	685	0	ENST00000307046.8:c.554G>T	p.Arg185Ile	p.R185I	ENST00000307046	NM_001111285.1	185	aGa/aTa	4/4	1	2	FACETS	0.618	0.517	0.73	0.618	0.517	0.73	SUBCLONAL	1	TRUE	1	0.23	2		685	619	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241895	133241895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1483635586	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	71	619	1	ENST00000320574.5:c.2461C>T	p.Arg821Cys	p.R821C	ENST00000320574	NM_006231.2	821	Cgc/Tgc	21/49	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.23	2		620	593	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252743	133252743	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	62	694	0	ENST00000320574.5:c.957T>G	p.Asp319Glu	p.D319E	ENST00000320574	NM_006231.2	319	gaT/gaG	10/49	1	2	FACETS	0.856	0.739	0.983	0.856	0.739	0.983	CLONAL	1	TRUE	1	0.23	2		694	630	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	88	684	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.23	2		684	744	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967567	26967567	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	65	718	0	ENST00000381527.3:c.710G>A	p.Arg237Gln	p.R237Q	ENST00000381527	NM_001260.1	237	cGa/cAa	7/13	1	2	FACETS	0.867	0.751	0.992	0.867	0.751	0.992	CLONAL	1	TRUE	1	0.23	2		718	652	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012465	29012465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373801409	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	36	556	0	ENST00000282397.4:c.406G>A	p.Val136Ile	p.V136I	ENST00000282397	NM_002019.4	136	Gta/Ata	4/30	1	2	FACETS	0.721	0.593	0.865	0.721	0.593	0.865	SUBCLONAL	1	TRUE	1	0.23	2		556	434	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893213	32893213	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs1060502376	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	26	279	2	ENST00000380152.3:c.68-1G>T		p.X23_splice	ENST00000380152		23			1	2	FACETS	0.729	0.578	0.902	0.729	0.578	0.902	CLONAL	1	TRUE	1	0.23	2		281	310	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912103	32912103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1566228843	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	73	764	0	ENST00000380152.3:c.3611C>T	p.Ala1204Val	p.A1204V	ENST00000380152		1204	gCt/gTt	11/27	1	2	FACETS	0.904	0.79	1	0.904	0.79	1	CLONAL	1	TRUE	1	0.23	2		764	702	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912670	32912670	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398122776	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	60	660	1	ENST00000380152.3:c.4178C>T	p.Ala1393Val	p.A1393V	ENST00000380152		1393	gCg/gTg	11/27	1	2	FACETS	0.889	0.766	1	0.889	0.766	1	CLONAL	1	TRUE	1	0.23	2		661	587	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913044	32913044	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs397507727	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	54	729	1	ENST00000380152.3:c.4552G>T	p.Glu1518Ter	p.E1518*	ENST00000380152		1518	Gaa/Taa	11/27	1	2	FACETS	0.702	0.599	0.815	0.702	0.599	0.815	SUBCLONAL	1	TRUE	1	0.23	2		730	669	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915295	32915295	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	68	804	2	ENST00000380152.3:c.6803G>T	p.Arg2268Ile	p.R2268I	ENST00000380152		2268	aGa/aTa	11/27	1	2	FACETS	0.908	0.79	1	0.908	0.79	1	CLONAL	1	TRUE	1	0.23	2		806	651	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941697	48941697	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	41	368	0	ENST00000267163.4:c.1007T>G	p.Phe336Cys	p.F336C	ENST00000267163	NM_000321.2	336	tTt/tGt	10/27	1	2	FACETS	0.9	0.751	1	0.9	0.751	1	CLONAL	1	TRUE	1	0.23	2		368	396	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515335	103515335	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	43	472	1	ENST00000355739.4:c.1836G>T	p.Glu612Asp	p.E612D	ENST00000355739	NM_000123.3	612	gaG/gaT	8/15	1	2	FACETS	0.912	0.764	1	0.912	0.764	1	CLONAL	1	TRUE	1	0.23	2		473	410	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103525656	103525656	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	42	482	0	ENST00000355739.4:c.2927C>A	p.Ser976Tyr	p.S976Y	ENST00000355739	NM_000123.3	976	tCt/tAt	14/15	1	2	FACETS	0.821	0.686	0.97	0.821	0.686	0.97	CLONAL	1	TRUE	1	0.23	2		482	445	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434391	110434391	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	74	895	0	ENST00000375856.3:c.4010A>C	p.Lys1337Thr	p.K1337T	ENST00000375856	NM_003749.2	1337	aAa/aCa	1/2	1	2	FACETS	0.702	0.613	0.798	0.702	0.613	0.798	SUBCLONAL	1	TRUE	1	0.23	2		895	917	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438064	110438064	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	106	823	2	ENST00000375856.3:c.337A>G	p.Ile113Val	p.I113V	ENST00000375856	NM_003749.2	113	Atc/Gtc	1/2	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.23	2		825	898	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590844	95590844	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	30	483	0	ENST00000393063.1:c.1065A>G	p.Ile355Met	p.I355M	ENST00000393063	NM_030621.3	355	atA/atG	9/28	1	2	FACETS	0.767	0.619	0.935	0.767	0.619	0.935	CLONAL	1	TRUE	1	0.23	2		483	340	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95598943	95598943	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	25	542	0	ENST00000393063.1:c.216T>G	p.Phe72Leu	p.F72L	ENST00000393063	NM_030621.3	72	ttT/ttG	4/28	1	2	FACETS	0.528	0.415	0.657	0.528	0.415	0.657	SUBCLONAL	1	TRUE	1	0.23	2		542	412	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43739596	43739596	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	36	605	0	ENST00000382044.4:c.2804A>C	p.Lys935Thr	p.K935T	ENST00000382044	NM_001141980.1	935	aAa/aCa	13/28	0.220728899968982	1	FACETS	0.653	0.537	0.784	0.653	0.537	0.784	SUBCLONAL	1	TRUE	0	0.23	1		605	424	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483961	88483961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	40	566	0	ENST00000360948.2:c.1609G>A	p.Asp537Asn	p.D537N	ENST00000360948	NM_001012338.2	537	Gac/Aac	14/19	1	2	FACETS	0.595	0.493	0.708	0.595	0.493	0.708	SUBCLONAL	1	TRUE	1	0.23	2		566	585	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347993	347993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1249674216	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	76	895	0	ENST00000262320.3:c.1513G>A	p.Ala505Thr	p.A505T	ENST00000262320	NM_003502.3	505	Gca/Aca	6/11	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.23	2		895	647	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781369	3781369	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1159046430	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	60	779	2	ENST00000262367.5:c.4996G>A	p.Ala1666Thr	p.A1666T	ENST00000262367	NM_004380.2	1666	Gcc/Acc	30/31	1	2	FACETS	0.704	0.606	0.812	0.704	0.606	0.812	SUBCLONAL	1	TRUE	1	0.23	2		781	741	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790534	3790534	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1567273064	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	57	648	0	ENST00000262367.5:c.3999A>C	p.Arg1333Ser	p.R1333S	ENST00000262367	NM_004380.2	1333	agA/agC	24/31	1	2	FACETS	0.77	0.66	0.89	0.77	0.66	0.89	SUBCLONAL	1	TRUE	1	0.23	2		648	644	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817868	3817868	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	64	728	0	ENST00000262367.5:c.3103G>T	p.Glu1035Ter	p.E1035*	ENST00000262367	NM_004380.2	1035	Gaa/Taa	16/31	1	2	FACETS	0.895	0.775	1	0.895	0.775	1	CLONAL	1	TRUE	1	0.23	2		728	622	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900948	3900948	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	103	796	0	ENST00000262367.5:c.148G>T	p.Glu50Ter	p.E50*	ENST00000262367	NM_004380.2	50	Gaa/Taa	2/31	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.23	2		796	895	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857127	9857127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs976259560	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	30	416	0	ENST00000330684.3:c.4274C>T	p.Ser1425Leu	p.S1425L	ENST00000330684	NM_001134407.1	1425	tCg/tTg	13/13	1	2	FACETS	0.723	0.583	0.881	0.723	0.583	0.881	SUBCLONAL	1	TRUE	1	0.23	2		416	361	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14015894	14015894	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	39	276	0	ENST00000311895.7:c.214T>C	p.Phe72Leu	p.F72L	ENST00000311895	NM_005236.2	72	Ttt/Ctt	2/11	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.23	2		276	262	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038660	14038660	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	64	526	0	ENST00000311895.7:c.1985C>A	p.Ser662Tyr	p.S662Y	ENST00000311895	NM_005236.2	662	tCt/tAt	10/11	1	2	FACETS	0.963	0.834	1	0.963	0.834	1	CLONAL	1	TRUE	1	0.23	2		526	578	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129087	30129087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	91	679	0	ENST00000263025.4:c.679G>A	p.Asp227Asn	p.D227N	ENST00000263025	NM_002746.2	227	Gac/Aac	5/9	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.23	2		679	716	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50784004	50784004	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	55	778	0	ENST00000398568.2:c.395A>C	p.Lys132Thr	p.K132T	ENST00000398568	NM_001042412.1	132	aAa/aCa	3/18	1	2	FACETS	0.736	0.629	0.853	0.736	0.629	0.853	SUBCLONAL	1	TRUE	1	0.23	2		778	650	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813584	50813584	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1325890438	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	44	531	2	ENST00000398568.2:c.1138G>T	p.Asp380Tyr	p.D380Y	ENST00000398568	NM_001042412.1	380	Gac/Tac	8/18	1	2	FACETS	0.75	0.629	0.885	0.75	0.629	0.885	SUBCLONAL	1	TRUE	1	0.23	2		533	510	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50818298	50818298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1467188617	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	44	574	1	ENST00000398568.2:c.1876G>A	p.Asp626Asn	p.D626N	ENST00000398568	NM_001042412.1	626	Gat/Aat	11/18	1	2	FACETS	0.797	0.669	0.939	0.797	0.669	0.939	CLONAL	1	TRUE	1	0.23	2		575	480	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56870616	56870616	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs757674160	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	54	597	0	ENST00000308159.5:c.1886A>G	p.Tyr629Cys	p.Y629C	ENST00000308159	NM_014669.4	629	tAt/tGt	17/22	1	2	FACETS	0.903	0.772	1	0.903	0.772	1	CLONAL	1	TRUE	1	0.23	2		597	520	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56873473	56873473	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	45	717	0	ENST00000308159.5:c.2177G>A	p.Ser726Asn	p.S726N	ENST00000308159	NM_014669.4	726	aGt/aAt	20/22	1	2	FACETS	0.632	0.53	0.745	0.632	0.53	0.745	SUBCLONAL	1	TRUE	1	0.23	2		717	619	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100605	67100605	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	55	533	1	ENST00000412916.2:c.303G>T	p.Met101Ile	p.M101I	ENST00000412916		101	atG/atT	4/6	1	2	FACETS	0.962	0.824	1	0.962	0.824	1	CLONAL	1	TRUE	1	0.23	2		534	497	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829580	72829593	+	frameshift_variant	Frame_Shift_Del	DEL	CTACATTTTTTGCA	CTACATTTTTTGCA	-	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	59	699	0	ENST00000268489.5:c.6988_7001del	p.Cys2330ProfsTer8	p.C2330Pfs*8	ENST00000268489	NM_006885.3	2330	TGCAAAAAATGTAGc/c	9/10	1	2	FACETS	0.791	0.68	0.912	0.791	0.68	0.912	CLONAL	1	TRUE	1	0.23	2		699	649	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81904463	81904463	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	48	477	0	ENST00000359376.3:c.571G>T	p.Gly191Ter	p.G191*	ENST00000359376	NM_002661.3	191	Gga/Tga	7/33	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.23	2		477	332	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81957097	81957097	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	45	506	2	ENST00000359376.3:c.2315G>T	p.Arg772Ile	p.R772I	ENST00000359376	NM_002661.3	772	aGa/aTa	22/33	1	2	FACETS	0.744	0.625	0.876	0.744	0.625	0.876	SUBCLONAL	1	TRUE	1	0.23	2		508	526	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805358	89805358	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	70	677	0	ENST00000389301.3:c.4192A>C	p.Lys1398Gln	p.K1398Q	ENST00000389301	NM_000135.2	1398	Aaa/Caa	42/43	1	2	FACETS	0.838	0.73	0.956	0.838	0.73	0.956	CLONAL	1	TRUE	1	0.23	2		677	726	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984773	11984773	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	53	569	2	ENST00000353533.5:c.319G>T	p.Glu107Ter	p.E107*	ENST00000353533	NM_003010.3	107	Gaa/Taa	3/11	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.23	2		571	443	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028639	12028639	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	43	587	1	ENST00000353533.5:c.842G>A	p.Arg281Gln	p.R281Q	ENST00000353533	NM_003010.3	281	cGa/cAa	8/11	1	2	FACETS	0.676	0.565	0.799	0.676	0.565	0.799	SUBCLONAL	1	TRUE	1	0.23	2		588	553	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044463	12044463	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	13	276	0	ENST00000353533.5:c.1087-1G>A		p.X363_splice	ENST00000353533	NM_003010.3	363			1	2	FACETS	0.445	0.317	0.601	0.445	0.317	0.601	SUBCLONAL	1	TRUE	1	0.23	2		276	254	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618711	37618711	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	82	762	0	ENST00000447079.4:c.387A>C	p.Glu129Asp	p.E129D	ENST00000447079	NM_015083.1	129	gaA/gaC	1/14	1	2	FACETS	0.915	0.806	1	0.915	0.806	1	CLONAL	1	TRUE	1	0.23	2		762	779	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37863258	37863258	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	51	658	0	ENST00000269571.5:c.89A>T	p.Asp30Val	p.D30V	ENST00000269571		30	gAc/gTc	2/27	1	2	FACETS	0.679	0.576	0.792	0.679	0.576	0.792	SUBCLONAL	1	TRUE	1	0.23	2		658	653	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370184	40370184	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	78	842	0	ENST00000293328.3:c.1154A>C	p.Asn385Thr	p.N385T	ENST00000293328	NM_012448.3	385	aAc/aCc	9/19	1	2	FACETS	0.795	0.697	0.901	0.795	0.697	0.901	CLONAL	1	TRUE	1	0.23	2		842	853	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40461070	40461070	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778121170	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	75	832	0	ENST00000345506.4:c.2068G>A	p.Ala690Thr	p.A690T	ENST00000345506	NM_003152.3	690	Gct/Act	18/20	1	2	FACETS	0.818	0.716	0.929	0.818	0.716	0.929	CLONAL	1	TRUE	1	0.23	2		832	797	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243531	41243531	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	68	822	0	ENST00000357654.3:c.4017A>C	p.Glu1339Asp	p.E1339D	ENST00000357654	NM_007294.3	1339	gaA/gaC	10/23	1	2	FACETS	0.881	0.766	1	0.881	0.766	1	CLONAL	1	TRUE	1	0.23	2		822	671	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245486	41245486	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	80	1004	0	ENST00000357654.3:c.2062A>G	p.Thr688Ala	p.T688A	ENST00000357654	NM_007294.3	688	Aca/Gca	10/23	1	2	FACETS	0.817	0.718	0.924	0.817	0.718	0.924	CLONAL	1	TRUE	1	0.23	2		1004	851	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245779	41245779	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	51	707	0	ENST00000357654.3:c.1769G>C	p.Ser590Thr	p.S590T	ENST00000357654	NM_007294.3	590	aGt/aCt	10/23	1	2	FACETS	0.759	0.645	0.885	0.759	0.645	0.885	SUBCLONAL	1	TRUE	1	0.23	2		707	584	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246636	41246636	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	70	645	0	ENST00000357654.3:c.912C>A	p.Phe304Leu	p.F304L	ENST00000357654	NM_007294.3	304	ttC/ttA	10/23	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.23	2		645	474	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761219	59761219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs575998972	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	67	893	1	ENST00000259008.2:c.3188C>T	p.Ser1063Leu	p.S1063L	ENST00000259008	NM_032043.2	1063	tCg/tTg	20/20	1	2	FACETS	0.883	0.767	1	0.883	0.767	1	CLONAL	1	TRUE	1	0.23	2		894	660	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724435	724435	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	146	726	0	ENST00000314574.4:c.1621G>T	p.Glu541Ter	p.E541*	ENST00000314574	NM_005433.3	541	Gaa/Taa	12/12	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.23	NA		726	660	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584497	39584497	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748472988	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	30	281	0	ENST00000262039.4:c.1162G>A	p.Asp388Asn	p.D388N	ENST00000262039	NM_002647.2	388	Gat/Aat	10/25	0.178909931881574	3	FACETS	0.776	0.625	0.946	0.388	0.312	0.473	CLONAL	1	TRUE	1	0.23	3		281	375	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56367674	56367674	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	54	287	0	ENST00000348428.3:c.500T>G	p.Ile167Ser	p.I167S	ENST00000348428	NM_006785.3	167	aTt/aGt	4/17	0.178909931881574	3	FACETS	0.97	0.835	1	0.97	0.835	1	CLONAL	2	TRUE	1	0.23	3		287	270	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56377292	56377292	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	29	401	0	ENST00000348428.3:c.913G>T	p.Glu305Ter	p.E305*	ENST00000348428	NM_006785.3	305	Gaa/Taa	6/17	0.178909931881574	3	FACETS	0.744	0.597	0.911	0.372	0.298	0.456	CLONAL	1	TRUE	1	0.23	3		401	378	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985718	60985718	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	20	207	0	ENST00000333681.4:c.182C>T	p.Ala61Val	p.A61V	ENST00000333681		61	gCa/gTa	2/3	0.178909931881574	3	FACETS	1	0.892	1	0.651	0.502	0.821	CLONAL	1	TRUE	1	0.23	3		207	149	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226668	2226668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	64	868	0	ENST00000398665.3:c.4148G>A	p.Gly1383Asp	p.G1383D	ENST00000398665	NM_032482.2	1383	gGc/gAc	27/28	1	2	FACETS	0.816	0.706	0.936	0.816	0.706	0.936	CLONAL	1	TRUE	1	0.23	2		868	682	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117503	4117503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs187018595	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	34	400	0	ENST00000262948.5:c.217G>A	p.Glu73Lys	p.E73K	ENST00000262948	NM_030662.3	73	Gaa/Aaa	2/11	1	2	FACETS	0.752	0.615	0.906	0.752	0.615	0.906	CLONAL	1	TRUE	1	0.23	2		400	393	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10273405	10273405	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200601847	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	68	685	1	ENST00000340748.4:c.898G>A	p.Glu300Lys	p.E300K	ENST00000340748		300	Gaa/Aaa	12/40	1	2	FACETS	0.816	0.709	0.931	0.816	0.709	0.931	CLONAL	1	TRUE	1	0.23	2		686	725	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130320	11130320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	85	781	1	ENST00000358026.2:c.2559C>A	p.Phe853Leu	p.F853L	ENST00000358026	NM_001128849.1	853	ttC/ttA	18/36	1	2	FACETS	0.95	0.839	1	0.95	0.839	1	CLONAL	1	TRUE	1	0.23	2		782	778	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367966	15367966	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	66	758	0	ENST00000263377.2:c.1360T>A	p.Phe454Ile	p.F454I	ENST00000263377	NM_058243.2	454	Ttt/Att	8/20	1	2	FACETS	0.753	0.653	0.862	0.753	0.653	0.862	SUBCLONAL	1	TRUE	1	0.23	2		758	762	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383903	15383903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324868843	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	43	394	1	ENST00000263377.2:c.8C>T	p.Ala3Val	p.A3V	ENST00000263377	NM_058243.2	3	gCg/gTg	2/20	1	2	FACETS	0.852	0.713	1	0.852	0.713	1	CLONAL	1	TRUE	1	0.23	2		395	439	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948867	17948867	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	52	653	2	ENST00000458235.1:c.1575G>T	p.Glu525Asp	p.E525D	ENST00000458235	NM_000215.3	525	gaG/gaT	12/24	1	2	FACETS	0.763	0.649	0.888	0.763	0.649	0.888	SUBCLONAL	1	TRUE	1	0.23	2		655	593	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277005	18277005	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	44	602	0	ENST00000222254.8:c.1452C>A	p.Phe484Leu	p.F484L	ENST00000222254	NM_005027.3	484	ttC/ttA	12/16	1	2	FACETS	0.683	0.572	0.806	0.683	0.572	0.806	SUBCLONAL	1	TRUE	1	0.23	2		602	560	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214101	36214101	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1287498488	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	59	1042	0	ENST00000222270.7:c.2927A>G	p.Gln976Arg	p.Q976R	ENST00000222270	NM_014727.1	976	cAg/cGg	6/37	1	2	FACETS	0.525	0.45	0.607	0.525	0.45	0.607	SUBCLONAL	1	TRUE	1	0.23	2		1042	978	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762511	41762511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200253980	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	32	330	0	ENST00000301178.4:c.2191G>A	p.Asp731Asn	p.D731N	ENST00000301178	NM_021913.4	731	Gat/Aat	18/20	1	2	FACETS	0.841	0.684	1	0.841	0.684	1	CLONAL	1	TRUE	1	0.23	2		330	331	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27016037	27016037	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1196363577	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	56	666	0	ENST00000335756.4:c.313C>A	p.Leu105Ile	p.L105I	ENST00000335756	NM_001809.3	105	Ctc/Atc	4/5	1	2	FACETS	0.716	0.613	0.829	0.716	0.613	0.829	SUBCLONAL	1	TRUE	1	0.23	2		666	680	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142910	30142910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141093002	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	60	899	1	ENST00000389048.3:c.616G>A	p.Ala206Thr	p.A206T	ENST00000389048	NM_004304.4	206	Gcg/Acg	1/29	1	2	FACETS	0.798	0.687	0.919	0.798	0.687	0.919	CLONAL	1	TRUE	1	0.23	2		900	654	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705472	47705472	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658254	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	30	454	0	ENST00000233146.2:c.2272G>A	p.Asp758Asn	p.D758N	ENST00000233146	NM_000251.2	758	Gat/Aat	14/16	1	2	FACETS	0.715	0.576	0.872	0.715	0.576	0.872	SUBCLONAL	1	TRUE	1	0.23	2		454	365	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025792	48025792	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	19	309	3	ENST00000234420.5:c.670G>T	p.Glu224Ter	p.E224*	ENST00000234420	NM_000179.2	224	Gaa/Taa	4/10	1	2	FACETS	0.574	0.435	0.736	0.574	0.435	0.736	SUBCLONAL	1	TRUE	1	0.23	2		312	288	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152241	99152241	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	49	577	0	ENST00000074304.5:c.320C>A	p.Ser107Tyr	p.S107Y	ENST00000074304	NM_001134224.1	107	tCt/tAt	6/26	1	2	FACETS	0.823	0.697	0.961	0.823	0.697	0.961	CLONAL	1	TRUE	1	0.23	2		577	518	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051285	128051285	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	63	585	0	ENST00000285398.2:c.38A>C	p.Lys13Thr	p.K13T	ENST00000285398	NM_000122.1	13	aAa/aCa	2/15	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.23	2		585	504	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137487	202137487	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	68	796	6	ENST00000358485.4:c.715G>T	p.Glu239Ter	p.E239*	ENST00000358485	NM_001080125.1	239	Gaa/Taa	4/9	1	2	FACETS	0.836	0.727	0.955	0.836	0.727	0.955	CLONAL	1	TRUE	1	0.23	2		802	707	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209106744	209106744	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	72	556	0	ENST00000345146.2:c.824A>T	p.Asp275Val	p.D275V	ENST00000345146	NM_005896.2	275	gAc/gTc	7/10	1	2	FACETS	0.968	0.845	1	0.968	0.845	1	CLONAL	1	TRUE	1	0.23	2		556	647	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225362541	225362541	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs767240461	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	39	552	1	ENST00000264414.4:c.1636C>T	p.Arg546Ter	p.R546*	ENST00000264414	NM_003590.4	546	Cga/Tga	12/16	1	2	FACETS	0.829	0.688	0.986	0.829	0.688	0.986	CLONAL	1	TRUE	1	0.23	2		553	409	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794494	242794494	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	68	766	1	ENST00000334409.5:c.448G>T	p.Glu150Ter	p.E150*	ENST00000334409	NM_005018.2	150	Gaa/Taa	3/5	1	2	FACETS	0.908	0.79	1	0.908	0.79	1	CLONAL	1	TRUE	1	0.23	2		767	651	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546916	9546916	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	39	545	0	ENST00000353224.5:c.1106G>T	p.Ser369Ile	p.S369I	ENST00000353224	NM_177990.2	369	aGc/aTc	5/10	0.178909931881574	3	FACETS	0.734	0.608	0.875	0.367	0.304	0.438	SUBCLONAL	1	TRUE	1	0.23	3		545	515	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383216	31383216	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	113	528	0	ENST00000328111.2:c.1128G>T	p.Glu376Asp	p.E376D	ENST00000328111	NM_006892.3	376	gaG/gaT	11/23	0.178909931881574	3	FACETS	0.861	0.777	0.951	0.861	0.777	0.951	CLONAL	2	TRUE	1	0.23	3		528	636	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39708807	39708807	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	98	380	0	ENST00000361337.2:c.418C>T	p.Arg140Ter	p.R140*	ENST00000361337	NM_003286.2	140	Cga/Tga	6/21	0.178909931881574	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.23	3		380	421	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757416	40757416	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	82	779	0	ENST00000373198.4:c.2882A>G	p.Tyr961Cys	p.Y961C	ENST00000373198	NM_133170.3	961	tAc/tGc	20/32	0.178909931881574	3	FACETS	0.972	0.856	1	0.486	0.428	0.549	CLONAL	1	TRUE	1	0.23	3		779	818	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944433	40944433	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	75	677	0	ENST00000373198.4:c.2069A>G	p.Tyr690Cys	p.Y690C	ENST00000373198	NM_133170.3	690	tAc/tGc	12/32	0.178909931881574	3	FACETS	1	0.938	1	0.558	0.488	0.632	CLONAL	1	TRUE	1	0.23	3		677	652	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064380	30064380	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	47	667	0	ENST00000338641.4:c.944C>A	p.Ser315Tyr	p.S315Y	ENST00000338641	NM_000268.3	315	tCt/tAt	10/16	1	2	FACETS	0.797	0.672	0.934	0.797	0.672	0.934	CLONAL	1	TRUE	1	0.23	2		667	513	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523498	41523498	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	48	424	0	ENST00000263253.7:c.914A>G	p.Gln305Arg	p.Q305R	ENST00000263253	NM_001429.3	305	cAg/cGg	4/31	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.23	2		424	395	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545121	41545121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	84	804	0	ENST00000263253.7:c.2321G>A	p.Gly774Glu	p.G774E	ENST00000263253	NM_001429.3	774	gGa/gAa	13/31	1	2	FACETS	0.997	0.88	1	0.997	0.88	1	CLONAL	1	TRUE	1	0.23	2		804	733	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564866	41564866	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	65	555	0	ENST00000263253.7:c.4167C>A	p.Asn1389Lys	p.N1389K	ENST00000263253	NM_001429.3	1389	aaC/aaA	25/31	1	2	FACETS	0.947	0.821	1	0.947	0.821	1	CLONAL	1	TRUE	1	0.23	2		555	597	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191526	10191526	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	50	522	0	ENST00000256474.2:c.519G>T	p.Glu173Asp	p.E173D	ENST00000256474	NM_000551.3	173	gaG/gaT	3/3	1	2	FACETS	0.772	0.655	0.901	0.772	0.655	0.901	CLONAL	1	TRUE	1	0.23	2		522	563	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182673	38182673	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	38	527	0	ENST00000396334.3:c.826G>T	p.Glu276Ter	p.E276*	ENST00000396334	NM_002468.4	276	Gag/Tag	5/5	1	2	FACETS	0.616	0.509	0.737	0.616	0.509	0.737	SUBCLONAL	1	TRUE	1	0.23	2		527	536	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47079187	47079187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	67	604	1	ENST00000409792.3:c.7319G>A	p.Gly2440Glu	p.G2440E	ENST00000409792	NM_014159.6	2440	gGa/gAa	18/21	1	2	FACETS	0.833	0.724	0.953	0.833	0.724	0.953	CLONAL	1	TRUE	1	0.23	2		605	699	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164223	47164223	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs147609782	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	38	446	0	ENST00000409792.3:c.1903A>G	p.Ile635Val	p.I635V	ENST00000409792	NM_014159.6	635	Att/Gtt	3/21	1	2	FACETS	0.798	0.66	0.952	0.798	0.66	0.952	CLONAL	1	TRUE	1	0.23	2		446	414	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008462	70008462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	60	543	1	ENST00000394351.3:c.749C>T	p.Ser250Phe	p.S250F	ENST00000394351	NM_000248.3	250	tCc/tTc	8/9	1	2	FACETS	0.809	0.696	0.932	0.809	0.696	0.932	CLONAL	1	TRUE	1	0.23	2		544	645	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73047227	73047227	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	38	464	0	ENST00000356692.5:c.35-1G>T		p.X12_splice	ENST00000356692		12			1	2	FACETS	0.9	0.746	1	0.9	0.746	1	CLONAL	1	TRUE	1	0.23	2		464	367	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119635008	119635008	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	26	300	0	ENST00000316626.5:c.491A>C	p.Gln164Pro	p.Q164P	ENST00000316626		164	cAg/cCg	5/12	1	2	FACETS	1	0.796	1	1	0.796	1	CLONAL	1	TRUE	1	0.23	2		300	226	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960039	134960039	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs533462328	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	65	641	3	ENST00000398015.3:c.2396G>A	p.Arg799His	p.R799H	ENST00000398015	NM_004441.4	799	cGc/cAc	13/16	1	2	FACETS	0.841	0.729	0.963	0.841	0.729	0.963	CLONAL	1	TRUE	1	0.23	2		644	672	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403622	138403622	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	54	517	0	ENST00000289153.2:c.2160A>C	p.Lys720Asn	p.K720N	ENST00000289153	NM_006219.2	720	aaA/aaC	15/22	1	2	FACETS	0.854	0.729	0.99	0.854	0.729	0.99	CLONAL	1	TRUE	1	0.23	2		517	550	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664745	138664745	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	52	493	0	ENST00000330315.3:c.820T>C	p.Tyr274His	p.Y274H	ENST00000330315	NM_023067.3	274	Tac/Cac	1/1	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.23	2		493	372	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188271	142188271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202193482	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	50	606	3	ENST00000350721.4:c.6460G>A	p.Asp2154Asn	p.D2154N	ENST00000350721	NM_001184.3	2154	Gat/Aat	38/47	1	2	FACETS	0.841	0.714	0.981	0.841	0.714	0.981	CLONAL	1	TRUE	1	0.23	2		609	517	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280130	142280130	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	64	652	1	ENST00000350721.4:c.1304G>A	p.Ser435Asn	p.S435N	ENST00000350721	NM_001184.3	435	aGc/aAc	5/47	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.23	2		653	541	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149238685	149238685	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	73	772	0	ENST00000360632.3:c.1110C>A	p.Asp370Glu	p.D370E	ENST00000360632	NM_015472.4	370	gaC/gaA	7/7	1	2	FACETS	0.876	0.765	0.995	0.876	0.765	0.995	CLONAL	1	TRUE	1	0.23	2		772	725	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260151	149260151	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1307297959	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	37	558	1	ENST00000360632.3:c.742C>T	p.Arg248Ter	p.R248*	ENST00000360632	NM_015472.4	248	Cga/Tga	4/7	1	2	FACETS	0.71	0.585	0.85	0.71	0.585	0.85	SUBCLONAL	1	TRUE	1	0.23	2		559	453	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169953016	169953016	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	50	503	0	ENST00000295797.4:c.102-2A>C		p.X34_splice	ENST00000295797	NM_002740.5	34			1	2	FACETS	0.904	0.768	1	0.904	0.768	1	CLONAL	1	TRUE	1	0.23	2		503	481	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013719	170013719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388201066	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	64	562	0	ENST00000295797.4:c.1438C>T	p.Arg480Cys	p.R480C	ENST00000295797	NM_002740.5	480	Cgc/Tgc	15/18	1	2	FACETS	0.856	0.741	0.981	0.856	0.741	0.981	CLONAL	1	TRUE	1	0.23	2		562	650	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916860	178916860	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	51	757	0	ENST00000263967.3:c.247T>A	p.Phe83Ile	p.F83I	ENST00000263967	NM_006218.2	83	Ttt/Att	2/21	1	2	FACETS	0.657	0.557	0.767	0.657	0.557	0.767	SUBCLONAL	1	TRUE	1	0.23	2		757	675	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	62	606	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.766	0.661	0.88	0.766	0.661	0.88	SUBCLONAL	1	TRUE	1	0.23	2		606	704	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928095	178928095	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	34	584	0	ENST00000263967.3:c.1373C>T	p.Pro458Leu	p.P458L	ENST00000263967	NM_006218.2	458	cCt/cTt	8/21	1	2	FACETS	0.653	0.533	0.787	0.653	0.533	0.787	SUBCLONAL	1	TRUE	1	0.23	2		584	453	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430288	181430288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1284559761	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	48	486	2	ENST00000325404.1:c.140C>T	p.Ala47Val	p.A47V	ENST00000325404	NM_003106.3	47	gCc/gTc	1/1	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.23	2		488	402	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505667	186505667	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	46	376	0	ENST00000323963.5:c.1075C>A	p.His359Asn	p.H359N	ENST00000323963		359	Cac/Aac	10/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.23	2		376	311	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612028	189612028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs900140738	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	69	544	0	ENST00000264731.3:c.1780C>T	p.Arg594Ter	p.R594*	ENST00000264731	NM_003722.4	594	Cga/Tga	14/14	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.23	2		544	565	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129833	55129833	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	39	501	2	ENST00000257290.5:c.368-1G>T		p.X123_splice	ENST00000257290	NM_006206.4	123			1	2	FACETS	0.802	0.665	0.954	0.802	0.665	0.954	CLONAL	1	TRUE	1	0.23	2		503	423	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565811	55565811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	56	623	0	ENST00000288135.5:c.635C>T	p.Pro212Leu	p.P212L	ENST00000288135	NM_000222.2	212	cCt/cTt	4/21	1	2	FACETS	0.785	0.672	0.909	0.785	0.672	0.909	CLONAL	1	TRUE	1	0.23	2		623	620	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565858	55565858	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	81	679	1	ENST00000288135.5:c.682G>T	p.Glu228Ter	p.E228*	ENST00000288135	NM_000222.2	228	Gaa/Taa	4/21	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.23	2		680	685	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599297	55599297	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	45	554	0	ENST00000288135.5:c.2423T>G	p.Ile808Ser	p.I808S	ENST00000288135	NM_000222.2	808	aTt/aGt	17/21	1	2	FACETS	0.851	0.715	1	0.851	0.715	1	CLONAL	1	TRUE	1	0.23	2		554	460	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946193	55946193	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	55	460	0	ENST00000263923.4:c.3986T>A	p.Leu1329Gln	p.L1329Q	ENST00000263923	NM_002253.2	1329	cTg/cAg	30/30	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.23	2		460	459	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231757	66231757	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	37	477	1	ENST00000273854.3:c.1943G>T	p.Arg648Ile	p.R648I	ENST00000273854	NM_004439.5	648	aGa/aTa	11/18	1	2	FACETS	0.933	0.771	1	0.933	0.771	1	CLONAL	1	TRUE	1	0.23	2		478	345	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155360	106155360	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	43	564	2	ENST00000380013.4:c.261G>T	p.Lys87Asn	p.K87N	ENST00000380013	NM_001127208.2	87	aaG/aaT	3/11	1	2	FACETS	0.696	0.582	0.823	0.696	0.582	0.823	SUBCLONAL	1	TRUE	1	0.23	2		566	537	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534467	187534467	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375998390	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	58	512	0	ENST00000441802.2:c.9259C>T	p.Arg3087Cys	p.R3087C	ENST00000441802	NM_005245.3	3087	Cgt/Tgt	13/27	1	2	FACETS	0.964	0.829	1	0.964	0.829	1	CLONAL	1	TRUE	1	0.23	2		512	523	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539690	187539690	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs748166431	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	59	479	0	ENST00000441802.2:c.8050G>T	p.Glu2684Ter	p.E2684*	ENST00000441802	NM_005245.3	2684	Gaa/Taa	10/27	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.23	2		479	392	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31504681	31504681	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	66	707	1	ENST00000344624.3:c.1649G>A	p.Ser550Asn	p.S550N	ENST00000344624		550	aGc/aAc	8/33	1	2	FACETS	0.709	0.615	0.813	0.709	0.615	0.813	SUBCLONAL	1	TRUE	1	0.23	2		708	809	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873660	35873660	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs201559094	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	29	530	1	ENST00000303115.3:c.616C>T	p.Arg206Ter	p.R206*	ENST00000303115	NM_002185.3	206	Cga/Tga	5/8	1	2	FACETS	0.796	0.64	0.972	0.796	0.64	0.972	CLONAL	1	TRUE	1	0.23	2		531	317	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874636	35874637	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1384901919	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	40	395	0	ENST00000303115.3:c.799dup	p.Arg267LysfsTer3	p.R267Kfs*3	ENST00000303115	NM_002185.3	264	-/A	6/8	1	2	FACETS	0.818	0.681	0.972	0.818	0.681	0.972	CLONAL	1	TRUE	1	0.23	2		395	425	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38957773	38957773	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	43	533	0	ENST00000357387.3:c.2480A>C	p.Gln827Pro	p.Q827P	ENST00000357387	NM_152756.3	827	cAa/cCa	25/38	1	2	FACETS	0.829	0.694	0.978	0.829	0.694	0.978	CLONAL	1	TRUE	1	0.23	2		533	451	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576546	67576546	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs377030014	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	30	400	0	ENST00000274335.5:c.825C>A	p.Phe275Leu	p.F275L	ENST00000274335		275	ttC/ttA	5/15	1	2	FACETS	0.729	0.588	0.888	0.729	0.588	0.888	SUBCLONAL	1	TRUE	1	0.23	2		400	358	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670704	86670704	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	33	349	0	ENST00000274376.6:c.1982A>C	p.Lys661Thr	p.K661T	ENST00000274376	NM_002890.2	661	aAa/aCa	15/25	1	2	FACETS	0.755	0.615	0.912	0.755	0.615	0.912	CLONAL	1	TRUE	1	0.23	2		349	380	SUCCESS
APC	324	MSKCC	GRCh37	5	112174655	112174655	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	37	509	0	ENST00000257430.4:c.3364A>G	p.Asn1122Asp	p.N1122D	ENST00000257430	NM_000038.5	1122	Aat/Gat	16/16	1	2	FACETS	0.914	0.755	1	0.914	0.755	1	CLONAL	1	TRUE	1	0.23	2		509	352	SUCCESS
APC	324	MSKCC	GRCh37	5	112178000	112178000	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768922431	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	50	575	3	ENST00000257430.4:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000257430	NM_000038.5	2237	Cga/Tga	16/16	1	2	FACETS	0.856	0.726	0.998	0.856	0.726	0.998	CLONAL	1	TRUE	1	0.23	2		578	508	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638731	176638731	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151165525	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	55	845	2	ENST00000439151.2:c.3331G>A	p.Asp1111Asn	p.D1111N	ENST00000439151	NM_022455.4	1111	Gat/Aat	5/23	1	2	FACETS	0.763	0.652	0.884	0.763	0.652	0.884	SUBCLONAL	1	TRUE	1	0.23	2		847	627	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721826	176721826	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	45	482	0	ENST00000439151.2:c.7457T>C	p.Leu2486Ser	p.L2486S	ENST00000439151	NM_022455.4	2486	tTg/tCg	23/23	1	2	FACETS	0.773	0.65	0.91	0.773	0.65	0.91	CLONAL	1	TRUE	1	0.23	2		482	506	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056806	180056806	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	74	781	2	ENST00000261937.6:c.706C>T	p.Pro236Ser	p.P236S	ENST00000261937	NM_182925.4	236	Ccc/Tcc	6/30	1	2	FACETS	0.837	0.732	0.95	0.837	0.732	0.95	CLONAL	1	TRUE	1	0.23	2		783	769	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020961	26020961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778917059	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	24	337	0	ENST00000357647.3:c.244G>A	p.Asp82Asn	p.D82N	ENST00000357647	NM_003529.2	82	Gac/Aac	1/1	1	2	FACETS	0.68	0.533	0.848	0.68	0.533	0.848	SUBCLONAL	1	TRUE	1	0.23	2		337	307	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289504	33289504	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	91	945	0	ENST00000374542.5:c.199T>C	p.Phe67Leu	p.F67L	ENST00000374542	NM_001141970.1	67	Ttc/Ctc	2/8	1	2	FACETS	0.723	0.64	0.812	0.723	0.64	0.812	SUBCLONAL	1	TRUE	1	0.23	2		945	1095	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793479	89793479	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	29	302	0	ENST00000336032.3:c.548A>C	p.Lys183Thr	p.K183T	ENST00000336032	NM_006813.2	183	aAa/aCa	2/2	1	2	FACETS	0.882	0.71	1	0.882	0.71	1	CLONAL	1	TRUE	1	0.23	2		302	286	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967904	93967904	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs201814256	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	62	657	1	ENST00000369303.4:c.2023C>A	p.Gln675Lys	p.Q675K	ENST00000369303	NM_004440.3	675	Caa/Aaa	11/17	1	2	FACETS	0.93	0.803	1	0.93	0.803	1	CLONAL	1	TRUE	1	0.23	2		658	580	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969087	93969087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1270476760	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	21	345	0	ENST00000369303.4:c.1909C>T	p.Arg637Cys	p.R637C	ENST00000369303	NM_004440.3	637	Cgt/Tgt	10/17	1	2	FACETS	0.52	0.4	0.66	0.52	0.4	0.66	SUBCLONAL	1	TRUE	1	0.23	2		345	351	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982095	93982095	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779416238	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	66	554	0	ENST00000369303.4:c.1370G>A	p.Arg457Gln	p.R457Q	ENST00000369303	NM_004440.3	457	cGg/cAg	6/17	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.23	2		554	564	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609759	117609759	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs771164515	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	48	551	0	ENST00000368508.3:c.6940G>T	p.Asp2314Tyr	p.D2314Y	ENST00000368508	NM_002944.2	2314	Gat/Tat	43/43	1	2	FACETS	0.873	0.739	1	0.873	0.739	1	CLONAL	1	TRUE	1	0.23	2		551	478	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117650517	117650517	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	80	818	0	ENST00000368508.3:c.5341A>C	p.Ile1781Leu	p.I1781L	ENST00000368508	NM_002944.2	1781	Att/Ctt	32/43	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.23	2		818	671	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662373	117662373	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	40	654	1	ENST00000368508.3:c.5004G>T	p.Glu1668Asp	p.E1668D	ENST00000368508	NM_002944.2	1668	gaG/gaT	30/43	1	2	FACETS	0.755	0.627	0.896	0.755	0.627	0.896	SUBCLONAL	1	TRUE	1	0.23	2		655	461	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715495	117715495	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	38	466	0	ENST00000368508.3:c.994G>A	p.Val332Ile	p.V332I	ENST00000368508	NM_002944.2	332	Gtc/Atc	10/43	1	2	FACETS	0.908	0.752	1	0.908	0.752	1	CLONAL	1	TRUE	1	0.23	2		466	364	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137528200	137528200	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	42	404	0	ENST00000367739.4:c.100A>C	p.Asn34His	p.N34H	ENST00000367739	NM_000416.2	34	Aat/Cat	2/7	1	2	FACETS	0.995	0.833	1	0.995	0.833	1	CLONAL	1	TRUE	1	0.23	2		404	367	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202251	138202251	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	45	540	0	ENST00000237289.4:c.2168A>C	p.Asn723Thr	p.N723T	ENST00000237289	NM_001270507.1	723	aAc/aCc	9/9	1	2	FACETS	0.631	0.529	0.744	0.631	0.529	0.744	SUBCLONAL	1	TRUE	1	0.23	2		540	620	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001285	150001285	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	31	634	0	ENST00000253339.5:c.2319A>C	p.Gln773His	p.Q773H	ENST00000253339		773	caA/caC	4/7	1	2	FACETS	0.589	0.475	0.717	0.589	0.475	0.717	SUBCLONAL	1	TRUE	1	0.23	2		634	458	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962294	2962294	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1003847451	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	152	778	0	ENST00000396946.4:c.2243C>T	p.Thr748Met	p.T748M	ENST00000396946	NM_032415.4	748	aCg/aTg	17/25	1	2	FACETS	0.814	0.745	0.886	1	0.989	1	CLONAL	2	TRUE	1	0.23	2		778	812	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729739	41729739	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	42	425	2	ENST00000242208.4:c.790G>T	p.Glu264Ter	p.E264*	ENST00000242208	NM_002192.2	264	Gaa/Taa	3/3	1	2	FACETS	0.732	0.611	0.866	0.732	0.611	0.866	SUBCLONAL	1	TRUE	1	0.23	2		427	499	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221719	55221719	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs776490661	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	36	504	1	ENST00000275493.2:c.763C>T	p.Arg255Ter	p.R255*	ENST00000275493	NM_005228.3	255	Cga/Tga	7/28	1	2	FACETS	0.684	0.562	0.82	0.684	0.562	0.82	SUBCLONAL	1	TRUE	1	0.23	2		505	458	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55269462	55269462	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs529174941	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	94	1040	0	ENST00000275493.2:c.3149T>G	p.Ile1050Ser	p.I1050S	ENST00000275493	NM_005228.3	1050	aTt/aGt	26/28	1	2	FACETS	0.853	0.758	0.955	0.853	0.758	0.955	CLONAL	1	TRUE	1	0.23	2		1040	958	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513345	106513345	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs767791735	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	49	438	0	ENST00000359195.3:c.2249A>C	p.Lys750Thr	p.K750T	ENST00000359195	NM_002649.2	750	aAa/aCa	4/11	1	2	FACETS	0.905	0.767	1	0.905	0.767	1	CLONAL	1	TRUE	1	0.23	2		438	471	SUCCESS
MET	4233	MSKCC	GRCh37	7	116422071	116422071	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs765771575	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	63	540	0	ENST00000397752.3:c.3552T>G	p.Phe1184Leu	p.F1184L	ENST00000397752	NM_000245.2	1184	ttT/ttG	18/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.23	2		540	470	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435796	116435796	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	91	790	0	ENST00000397752.3:c.3886T>G	p.Leu1296Val	p.L1296V	ENST00000397752	NM_000245.2	1296	Ttg/Gtg	20/21	1	2	FACETS	0.966	0.857	1	0.966	0.857	1	CLONAL	1	TRUE	1	0.23	2		790	819	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543671	148543671	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1333628386	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	42	410	0	ENST00000320356.2:c.137G>A	p.Arg46His	p.R46H	ENST00000320356	NM_004456.4	46	cGt/cAt	3/20	1	2	FACETS	0.785	0.656	0.929	0.785	0.656	0.929	CLONAL	1	TRUE	1	0.23	2		410	465	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836804	151836804	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	66	566	1	ENST00000262189.6:c.14416C>T	p.Arg4806Ter	p.R4806*	ENST00000262189	NM_170606.2	4806	Cga/Tga	56/59	1	2	FACETS	0.986	0.856	1	0.986	0.856	1	CLONAL	1	TRUE	1	0.23	2		567	582	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845300	151845300	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	42	487	0	ENST00000262189.6:c.13712C>A	p.Ser4571Tyr	p.S4571Y	ENST00000262189	NM_170606.2	4571	tCt/tAt	52/59	1	2	FACETS	0.733	0.612	0.868	0.733	0.612	0.868	SUBCLONAL	1	TRUE	1	0.23	2		487	498	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874945	151874945	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	37	383	0	ENST00000262189.6:c.7593G>T	p.Met2531Ile	p.M2531I	ENST00000262189	NM_170606.2	2531	atG/atT	38/59	1	2	FACETS	0.806	0.665	0.964	0.806	0.665	0.964	CLONAL	1	TRUE	1	0.23	2		383	399	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877806	151877806	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	33	223	0	ENST00000262189.6:c.7139A>C	p.Lys2380Thr	p.K2380T	ENST00000262189	NM_170606.2	2380	aAa/aCa	36/59	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.23	2		223	258	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345999	152345999	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	62	585	2	ENST00000359321.1:c.571C>A	p.Leu191Ile	p.L191I	ENST00000359321	NM_005431.1	191	Ctt/Att	3/3	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.23	2		587	537	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38148136	38148136	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	198	860	0	ENST00000317025.8:c.2975A>C	p.Lys992Thr	p.K992T	ENST00000317025	NM_023034.1	992	aAa/aCa	17/24	0.178909931881574	3	FACETS	0.979	0.907	1	0.979	0.907	1	CLONAL	2	TRUE	1	0.23	3		860	980	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38176445	38176464	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGAACTGTTTCAACCTGTTT	GGAACTGTTTCAACCTGTTT	-	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	32	591	0	ENST00000317025.8:c.1810-6_1823del		p.X604_splice	ENST00000317025	NM_023034.1	604		9/24	0.178909931881574	3	FACETS	0.511	0.414	0.622	0.256	0.207	0.311	SUBCLONAL	1	TRUE	1	0.23	3		591	607	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56854465	56854465	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1366782003	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	70	807	0	ENST00000519728.1:c.47G>A	p.Gly16Glu	p.G16E	ENST00000519728	NM_002350.3	16	gGa/gAa	2/13	0.178909931881574	3	FACETS	0.757	0.659	0.865	0.379	0.329	0.433	SUBCLONAL	1	TRUE	1	0.23	3		807	896	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958522	90958522	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	28	422	0	ENST00000265433.3:c.1916A>G	p.Asn639Ser	p.N639S	ENST00000265433	NM_002485.4	639	aAc/aGc	13/16	0.178909931881574	3	FACETS	0.611	0.488	0.752	0.306	0.244	0.376	SUBCLONAL	1	TRUE	1	0.23	3		422	444	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090868	5090868	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	20	364	0	ENST00000381652.3:c.3016G>T	p.Glu1006Ter	p.E1006*	ENST00000381652	NM_004972.3	1006	Gaa/Taa	22/25	0.220728899968982	1	FACETS	0.681	0.522	0.866	0.681	0.522	0.866	SUBCLONAL	1	TRUE	0	0.23	1		364	226	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485312	8485312	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	50	581	0	ENST00000356435.5:c.3068A>C	p.Asn1023Thr	p.N1023T	ENST00000356435		1023	aAt/aCt	18/35	0.220728899968982	1	FACETS	0.883	0.75	1	0.883	0.75	1	CLONAL	1	TRUE	0	0.23	1		581	436	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606395	93606395	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	43	703	3	ENST00000375746.1:c.215G>T	p.Gly72Val	p.G72V	ENST00000375746	NM_001174167.1	72	gGc/gTc	2/14	1	2	FACETS	0.636	0.531	0.752	0.636	0.531	0.752	SUBCLONAL	1	TRUE	1	0.23	2		706	588	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239054	98239054	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	50	531	0	ENST00000331920.6:c.1589G>T	p.Arg530Ile	p.R530I	ENST00000331920	NM_000264.3	530	aGa/aTa	11/24	1	2	FACETS	0.878	0.746	1	0.878	0.746	1	CLONAL	1	TRUE	1	0.23	2		531	495	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894974	101894974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745324433	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	36	358	0	ENST00000374994.4:c.527C>T	p.Thr176Met	p.T176M	ENST00000374994	NM_004612.2	176	aCg/aTg	3/9	1	2	FACETS	0.803	0.661	0.962	0.803	0.661	0.962	CLONAL	1	TRUE	1	0.23	2		358	390	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796804	135796804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223799508	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	29	439	0	ENST00000298552.3:c.683G>A	p.Arg228Gln	p.R228Q	ENST00000298552	NM_001162426.1	228	cGa/cAa	8/23	1	2	FACETS	0.729	0.585	0.892	0.729	0.585	0.892	SUBCLONAL	1	TRUE	1	0.23	2		439	346	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137323770	137323770	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	64	774	0	ENST00000481739.1:c.1063T>C	p.Ser355Pro	p.S355P	ENST00000481739	NM_002957.4	355	Tcc/Ccc	8/10	1	2	FACETS	0.728	0.63	0.836	0.728	0.63	0.836	SUBCLONAL	1	TRUE	1	0.23	2		774	764	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399976	139399976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200495793	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	84	897	1	ENST00000277541.6:c.4372G>A	p.Ala1458Thr	p.A1458T	ENST00000277541	NM_017617.3	1458	Gcg/Acg	25/34	1	2	FACETS	0.771	0.68	0.87	0.771	0.68	0.87	SUBCLONAL	1	TRUE	1	0.23	2		898	947	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20152109	20152109	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	84	684	0	ENST00000379607.5:c.221C>T	p.Ser74Leu	p.S74L	ENST00000379607	NM_001412.3	74	tCg/tTg	4/7	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.23	2		684	653	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44733190	44733190	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	71	684	1	ENST00000377967.4:c.182G>T	p.Arg61Ile	p.R61I	ENST00000377967	NM_021140.2	61	aGa/aTa	2/29	1	2	FACETS	0.8	0.697	0.911	0.8	0.697	0.911	CLONAL	1	TRUE	1	0.23	2		685	772	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969349	44969349	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	22	586	0	ENST00000377967.4:c.4031T>C	p.Val1344Ala	p.V1344A	ENST00000377967	NM_021140.2	1344	gTc/gCc	28/29	1	2	FACETS	0.447	0.346	0.565	0.447	0.346	0.565	SUBCLONAL	1	TRUE	1	0.23	2		586	428	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426397	47426397	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	55	615	1	ENST00000377045.4:c.740G>T	p.Arg247Ile	p.R247I	ENST00000377045	NM_001654.4	247	aGa/aTa	9/16	1	2	FACETS	0.816	0.698	0.946	0.816	0.698	0.946	CLONAL	1	TRUE	1	0.23	2		616	586	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410478	63410478	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749609920	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	52	656	0	ENST00000330258.3:c.2689G>A	p.Asp897Asn	p.D897N	ENST00000330258	NM_152424.3	897	Gac/Aac	2/2	1	2	FACETS	0.705	0.6	0.822	0.705	0.6	0.822	SUBCLONAL	1	TRUE	1	0.23	2		656	641	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412884	63412884	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	67	795	0	ENST00000330258.3:c.283A>G	p.Thr95Ala	p.T95A	ENST00000330258	NM_152424.3	95	Acc/Gcc	2/2	1	2	FACETS	0.76	0.659	0.869	0.76	0.659	0.869	SUBCLONAL	1	TRUE	1	0.23	2		795	767	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345313	70345313	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	78	781	0	ENST00000374080.3:c.2339A>C	p.Lys780Thr	p.K780T	ENST00000374080		780	aAg/aCg	16/45	1	2	FACETS	0.861	0.755	0.974	0.861	0.755	0.974	CLONAL	1	TRUE	1	0.23	2		781	788	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347294	70347294	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	49	648	4	ENST00000374080.3:c.2958G>T	p.Lys986Asn	p.K986N	ENST00000374080		986	aaG/aaT	21/45	1	2	FACETS	0.74	0.626	0.865	0.74	0.626	0.865	SUBCLONAL	1	TRUE	1	0.23	2		652	576	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347888	70347888	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	70	716	0	ENST00000374080.3:c.3127C>A	p.Leu1043Ile	p.L1043I	ENST00000374080		1043	Ctt/Att	22/45	1	2	FACETS	0.894	0.779	1	0.894	0.779	1	CLONAL	1	TRUE	1	0.23	2		716	681	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349928	70349928	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	52	907	6	ENST00000374080.3:c.3911G>T	p.Ser1304Ile	p.S1304I	ENST00000374080		1304	aGc/aTc	28/45	1	2	FACETS	0.486	0.412	0.567	0.486	0.412	0.567	SUBCLONAL	1	TRUE	1	0.23	2		913	931	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854897	76854897	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	77	832	2	ENST00000373344.5:c.5939C>A	p.Ser1980Tyr	p.S1980Y	ENST00000373344	NM_000489.3	1980	tCt/tAt	25/35	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.23	2		834	543	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872169	76872169	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	49	587	0	ENST00000373344.5:c.5478C>A	p.Phe1826Leu	p.F1826L	ENST00000373344	NM_000489.3	1826	ttC/ttA	22/35	1	2	FACETS	0.847	0.718	0.989	0.847	0.718	0.989	CLONAL	1	TRUE	1	0.23	2		587	503	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938401	76938401	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	63	754	0	ENST00000373344.5:c.2347A>C	p.Ser783Arg	p.S783R	ENST00000373344	NM_000489.3	783	Agt/Cgt	9/35	1	2	FACETS	0.875	0.757	1	0.875	0.757	1	CLONAL	1	TRUE	1	0.23	2		754	626	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938595	76938595	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	40	700	0	ENST00000373344.5:c.2153A>C	p.Lys718Thr	p.K718T	ENST00000373344	NM_000489.3	718	aAa/aCa	9/35	1	2	FACETS	0.686	0.57	0.816	0.686	0.57	0.816	SUBCLONAL	1	TRUE	1	0.23	2		700	507	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939561	76939561	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	40	690	0	ENST00000373344.5:c.1187A>C	p.Lys396Thr	p.K396T	ENST00000373344	NM_000489.3	396	aAg/aCg	9/35	1	2	FACETS	0.671	0.557	0.799	0.671	0.557	0.799	SUBCLONAL	1	TRUE	1	0.23	2		690	518	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611131	100611131	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782338603	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	64	709	0	ENST00000308731.7:c.1475G>A	p.Arg492His	p.R492H	ENST00000308731	NM_000061.2	492	cGc/cAc	15/19	1	2	FACETS	0.859	0.743	0.984	0.859	0.743	0.984	CLONAL	1	TRUE	1	0.23	2		709	648	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195113	123195113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	44	573	1	ENST00000218089.9:c.1456G>A	p.Asp486Asn	p.D486N	ENST00000218089	NM_001042749.1	486	Gac/Aac	16/35	1	2	FACETS	0.905	0.76	1	0.905	0.76	1	CLONAL	1	TRUE	1	0.23	2		574	423	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197758	123197758	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	49	716	0	ENST00000218089.9:c.1882G>T	p.Val628Phe	p.V628F	ENST00000218089	NM_001042749.1	628	Gtt/Ttt	20/35	1	2	FACETS	0.815	0.69	0.952	0.815	0.69	0.952	CLONAL	1	TRUE	1	0.23	2		716	523	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096196	71096196	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	101	467	0	ENST00000318789.4:c.561G>T	p.Gln187His	p.Q187H	ENST00000318789	NM_032682.5	187	caG/caT	10/21	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.413241575556666	2		467	397	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402719	20402719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	137	583	0	ENST00000346618.3:c.256C>T	p.Pro86Ser	p.P86S	ENST00000346618	NM_001949.4	86	Ccc/Tcc	1/7	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.413241575556666	2		583	557	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066571	94066571	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	116	683	0	ENST00000369303.4:c.1188G>T	p.Glu396Asp	p.E396D	ENST00000369303	NM_004440.3	396	gaG/gaT	5/17	0.142613349658972	0	FACETS	0.681	0.617	0.747			1	INDETERMINATE	1	TRUE	0	0.413241575556666	0		683	484	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920223	76920224	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	149	727	0	ENST00000373344.5:c.3853dup	p.Ser1285PhefsTer3	p.S1285Ffs*3	ENST00000373344	NM_000489.3	1285	tcc/tTcc	11/35	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.413241575556666	2		727	632	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	26	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.801	1	1	0.801	1	CLONAL	1	FALSE	1	0.248833246797922	2		555	208	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0019874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	73	1046	1	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	1	2	FACETS	0.805	0.703	0.915	0.805	0.703	0.915	CLONAL	1	FALSE	1	0.248833246797922	2		1047	729	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946174	13946174	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1176085263	NA	P-0019874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	50	866	3	ENST00000405192.2:c.922C>T	p.Arg308Trp	p.R308W	ENST00000405192	NM_001163147.1	308	Cgg/Tgg	10/12	1	2	FACETS	0.825	0.701	0.962	0.825	0.701	0.962	CLONAL	1	FALSE	1	0.248833246797922	2		869	487	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612221	1612221	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	33	543	0	ENST00000344749.5:c.1798G>C	p.Glu600Gln	p.E600Q	ENST00000344749	NM_001136139.2	600	Gag/Cag	18/19	0.248833246797922	1	FACETS	0.483	0.393	0.585	0.483	0.393	0.585	SUBCLONAL	1	FALSE	0	0.248833246797922	1		543	481	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612227	1612227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	35	566	0	ENST00000344749.5:c.1792G>A	p.Gly598Arg	p.G598R	ENST00000344749	NM_001136139.2	598	Ggg/Agg	18/19	0.248833246797922	1	FACETS	0.482	0.394	0.581	0.482	0.394	0.581	SUBCLONAL	1	FALSE	0	0.248833246797922	1		566	511	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612297	1612297	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	76	1001	0	ENST00000344749.5:c.1722G>C	p.Gln574His	p.Q574H	ENST00000344749	NM_001136139.2	574	caG/caC	18/19	0.248833246797922	1	FACETS	0.693	0.607	0.786	0.693	0.607	0.786	SUBCLONAL	1	FALSE	0	0.248833246797922	1		1001	772	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612356	1612356	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	81	990	0	ENST00000344749.5:c.1663G>C	p.Glu555Gln	p.E555Q	ENST00000344749	NM_001136139.2	555	Gag/Cag	18/19	0.248833246797922	1	FACETS	0.684	0.602	0.773	0.684	0.602	0.773	SUBCLONAL	1	FALSE	0	0.248833246797922	1		990	833	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0019875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	189	146	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.935186493349384	2		146	351	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0019875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	102	465	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.924	0.843	1	0.924	0.843	1	CLONAL	1	TRUE	1	0.935186493349384	2		465	236	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346337	73346337	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	153	602	0	ENST00000377767.4:c.1463A>G	p.Asp488Gly	p.D488G	ENST00000377767	NM_014953.3	488	gAt/gGt	10/21	1	2	FACETS	0.887	0.822	0.952	0.887	0.822	0.952	CLONAL	1	TRUE	1	0.935186493349384	2		602	369	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796236	42796236	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0019875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	272	808	0	ENST00000575354.2:c.2887-2A>G		p.X963_splice	ENST00000575354	NM_015125.3	963			0.935186493349384	1	FACETS	0.971	0.943	0.997	0.971	0.943	0.997	CLONAL	1	TRUE	0	0.935186493349384	1		808	319	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589575	67589583	+	inframe_deletion	In_Frame_Del	DEL	GAAAAAATT	GAAAAAATT	-	novel	NA	P-0019875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	163	483	0	ENST00000274335.5:c.1338_1346del	p.Lys447_Leu449del	p.K447_L449del	ENST00000274335		446	ggGAAAAAATTa/gga	10/15	1	2	FACETS	0.971	0.905	1	0.971	0.905	1	CLONAL	1	TRUE	1	0.935186493349384	2		483	359	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519513	176519513	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0019875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	70	974	1	ENST00000292408.4:c.918+1G>A		p.X306_splice	ENST00000292408	NM_213647.1	306			1	2	FACETS	0.171	0.148	0.196	0.171	0.148	0.196	SUBCLONAL	1	TRUE	1	0.935186493349384	2		975	875	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0019876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	220	146	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.806461128102052	2		146	470	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0019876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	37	408	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.366	0.303	0.435	0.366	0.303	0.435	SUBCLONAL	1	TRUE	1	0.806461128102052	2		408	251	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0019876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	165	603	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.89	0.825	0.956	0.89	0.825	0.956	CLONAL	1	TRUE	1	0.806461128102052	2		603	460	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346016	73346016	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	55	593	1	ENST00000377767.4:c.1522G>T	p.Asp508Tyr	p.D508Y	ENST00000377767	NM_014953.3	508	Gat/Tat	11/21	0.806461128102052	1	FACETS	0.754	0.67	0.838	0.754	0.67	0.838	SUBCLONAL	1	TRUE	0	0.806461128102052	1		594	108	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39570518	39570518	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	24	365	0	ENST00000262039.4:c.714+1del		p.K238fs	ENST00000262039	NM_002647.2	238	aaG/aa	6/25	1	2	FACETS	0.595	0.476	0.726	0.595	0.476	0.726	SUBCLONAL	1	TRUE	1	0.806461128102052	2		365	100	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	146	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.233308212720104	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.26285303000352	2		555	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0019877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	187	1120	2	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.233308212720104	2	FACETS	0.788	0.728	0.85	0.788	0.728	0.85	SUBCLONAL	2	TRUE	0	0.26285303000352	2		1122	903	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137499	202137499	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	212	937	2	ENST00000358485.4:c.727G>T	p.Glu243Ter	p.E243*	ENST00000358485	NM_001080125.1	243	Gag/Tag	4/9	0.229513585206979	2	FACETS	0.964	0.897	1	0.964	0.897	1	CLONAL	2	TRUE	0	0.26285303000352	2		939	837	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0019878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	71	631	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.771	0.676	0.872	0.771	0.676	0.872	SUBCLONAL	1	TRUE	1	0.474775428566801	2		631	388	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942171	71942171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762627344	NA	P-0019878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	138	1025	2	ENST00000298229.2:c.1435C>T	p.Arg479Cys	p.R479C	ENST00000298229	NM_001567.3	479	Cgc/Tgc	12/28	0.474775428566801	3	FACETS	0.646	0.587	0.709	0.323	0.293	0.355	SUBCLONAL	1	TRUE	1	0.474775428566801	3		1027	1113	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075163	16075163	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	137	507	0	ENST00000268712.3:c.389T>A	p.Val130Glu	p.V130E	ENST00000268712	NM_006311.3	130	gTg/gAg	4/46	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.474775428566801	2		507	548	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419871	152419897	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGGCATGGAGCATCTGTACAGCATG	AAAGGCATGGAGCATCTGTACAGCATG	CATGCTGTAC	novel	NA	P-0019878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	111	781	4	ENST00000206249.3:c.1558_1584delinsCATGCTGTAC	p.Lys520HisfsTer13	p.K520Hfs*13	ENST00000206249	NM_000125.3	520	AAAGGCATGGAGCATCTGTACAGCATG/CATGCTGTAC	8/8	1	2	FACETS	0.738	0.664	0.815	0.738	0.664	0.815	SUBCLONAL	1	TRUE	1	0.474775428566801	2		785	634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0019880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	41	860	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.152780898157766	1	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	0	0.14	1		861	490	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0019880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	14	705	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.372	0.267	0.5	0.372	0.267	0.5	SUBCLONAL	1	TRUE	1	0.14	2		705	538	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0019880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	62	453	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.801	0.692	0.919	1	0.973	1	CLONAL	2	TRUE	1	0.14	2		453	553	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741598	17741598	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	10	173	1	ENST00000250003.3:c.269C>T	p.Ala90Val	p.A90V	ENST00000250003	NM_002478.4	90	gCg/gTg	1/3	1	2	FACETS	1	0.684	1	1	0.684	1	CLONAL	1	TRUE	1	0.14	2		174	142	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937085	48937085	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	36	477	0	ENST00000267163.4:c.853A>G	p.Ile285Val	p.I285V	ENST00000267163	NM_000321.2	285	Ata/Gta	8/27	0.152780898157766	4	FACETS	1	0.946	1	0.727	0.598	0.872	CLONAL	1	TRUE	2	0.14	4		477	403	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211779	5211779	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs544687640	NA	P-0019880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	39	751	2	ENST00000357368.4:c.5056C>T	p.Arg1686Trp	p.R1686W	ENST00000357368	NM_002850.3	1686	Cgg/Tgg	33/38	0.152780898157766	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.14	1		753	405	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295792	15295792	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	33	1310	1	ENST00000263388.2:c.2335C>T	p.Pro779Ser	p.P779S	ENST00000263388	NM_000435.2	779	Ccc/Tcc	15/33	0.152780898157766	1	FACETS	0.684	0.555	0.83	0.684	0.555	0.83	SUBCLONAL	1	TRUE	0	0.14	1		1311	641	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324545	31324545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151341182	NA	P-0019880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	49	824	1	ENST00000412585.2:c.263C>T	p.Thr88Ile	p.T88I	ENST00000412585	NM_005514.6	88	aCa/aTa	2/8	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.14	2		825	488	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	123	122	0				ENST00000310581	NM_198253.2	-/1132			0.502413237648312	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.502413237648312	2		122	223	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832443	72832443	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	200	628	2	ENST00000268489.5:c.4138C>T	p.His1380Tyr	p.H1380Y	ENST00000268489	NM_006885.3	1380	Cat/Tat	9/10	0.502413237648312	2	FACETS	0.919	0.863	0.976	0.919	0.863	0.976	CLONAL	2	TRUE	0	0.502413237648312	2		630	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0019882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	323	604	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.693444668423903	1	FACETS	0.969	0.93	1	0.969	0.93	1	CLONAL	1	TRUE	0	0.791240321176495	1		606	509	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916926	+	inframe_deletion	In_Frame_Del	DEL	CAG	CAG	-	novel	NA	P-0019882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	231	744	0	ENST00000263967.3:c.311_313del	p.Pro104_Val105delinsLeu	p.P104_V105delinsL	ENST00000263967	NM_006218.2	104	cCAGta/cta	2/21	1	2	FACETS	0.927	0.87	0.985	0.927	0.87	0.985	CLONAL	1	TRUE	1	0.791240321176495	2		744	630	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244338	46244338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	248	609	0	ENST00000334344.6:c.2432G>A	p.Cys811Tyr	p.C811Y	ENST00000334344	NM_152641.2	811	tGt/tAt	15/21	0.780231398317405	1	FACETS	0.942	0.898	0.986	0.942	0.898	0.986	CLONAL	1	TRUE	0	0.791240321176495	1		609	402	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728757	39728757	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	84	749	0	ENST00000361337.2:c.1037A>G	p.His346Arg	p.H346R	ENST00000361337	NM_003286.2	346	cAc/cGc	12/21	1	2	FACETS	0.33	0.292	0.372	0.33	0.292	0.372	SUBCLONAL	1	TRUE	1	0.791240321176495	2		749	643	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513447	41513447	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	292	760	0	ENST00000263253.7:c.351G>C	p.Leu117Phe	p.L117F	ENST00000263253	NM_001429.3	117	ttG/ttC	2/31	1	2	FACETS	0.997	0.944	1	0.997	0.944	1	CLONAL	1	TRUE	1	0.791240321176495	2		760	740	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0019883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	426	532	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.586991651406657	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.586991651406657	2		533	712	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696461	47696461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	172	550	0	ENST00000347630.2:c.362G>A	p.Arg121Gln	p.R121Q	ENST00000347630	NM_001007230.1	121	cGg/cAg	6/11	0.586991651406657	2	FACETS	0.921	0.865	0.978	0.921	0.865	0.978	CLONAL	2	TRUE	0	0.586991651406657	2		550	318	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46740262	46740262	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs944371830	NA	P-0019883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	263	624	0	ENST00000371975.4:c.1742A>G	p.Asn581Ser	p.N581S	ENST00000371975	NM_003579.3	581	aAt/aGt	16/18	0.479105246645147	3	FACETS	1	0.99	1	0.785	0.746	0.825	CLONAL	2	TRUE	0	0.586991651406657	3		624	492	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007110	152007110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	121	875	0	ENST00000262189.6:c.790C>T	p.Gln264Ter	p.Q264*	ENST00000262189	NM_170606.2	264	Cag/Tag	6/59	1	2	FACETS	0.912	0.83	0.998	0.912	0.83	0.998	CLONAL	1	TRUE	1	0.586991651406657	2		875	452	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972594	32972594	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876659263	NA	P-0019895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	86	629	0	ENST00000380152.3:c.9944A>C	p.Lys3315Thr	p.K3315T	ENST00000380152		3315	aAa/aCa	27/27	1	2	FACETS	0.522	0.462	0.587	0.522	0.462	0.587	SUBCLONAL	1	TRUE	1	0.513614937737072	2		629	641	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135288	30135288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764900497	NA	P-0019895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	81	548	1	ENST00000331968.5:c.530G>A	p.Cys177Tyr	p.C177Y	ENST00000331968	NM_002742.2	177	tGt/tAt	3/18	0.422710620547853	1	FACETS	0.471	0.416	0.529	0.471	0.416	0.529	SUBCLONAL	1	TRUE	0	0.513614937737072	1		549	498	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215908	41215908	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	205	788	0	ENST00000357654.3:c.5135G>T	p.Trp1712Leu	p.W1712L	ENST00000357654	NM_007294.3	1712	tGg/tTg	17/23	0.513614937737072	3	FACETS	0.97	0.9	1	0.485	0.45	0.522	CLONAL	1	TRUE	1	0.513614937737072	3		788	1034	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084178	47084179	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	86	400	0	ENST00000409792.3:c.7110dup	p.Val2371CysfsTer4	p.V2371Cfs*4	ENST00000409792	NM_014159.6	2370	-/T	17/21	0.513614937737072	1	FACETS	0.832	0.745	0.924	0.832	0.745	0.924	CLONAL	1	TRUE	0	0.513614937737072	1		400	299	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233691	233691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	70	324	0	ENST00000264932.6:c.995C>T	p.Pro332Leu	p.P332L	ENST00000264932	NM_004168.2	332	cCt/cTt	8/15	0.513614937737072	3	FACETS	0.53	0.462	0.604	0.265	0.231	0.302	SUBCLONAL	1	TRUE	1	0.513614937737072	3		324	646	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937338	76937338	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	74	570	0	ENST00000373344.5:c.3410G>T	p.Arg1137Ile	p.R1137I	ENST00000373344	NM_000489.3	1137	aGa/aTa	9/35	1	2	FACETS	0.625	0.549	0.707	0.625	0.549	0.707	SUBCLONAL	1	TRUE	1	0.513614937737072	2		570	461	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111451	8111452	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0019896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	66	742	0	ENST00000346208.3:c.938dup	p.Gly314ArgfsTer38	p.G314Rfs*38	ENST00000346208		313	gca/gCca	5/6	1	2	FACETS	0.853	0.74	0.977	0.853	0.74	0.977	CLONAL	1	FALSE	1	0.21275218238659	2		742	727	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0019897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	51	812	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	1	2	FACETS	0.527	0.447	0.616	0.527	0.447	0.616	SUBCLONAL	1	TRUE	1	0.25	2		812	774	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041582	47041582	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	80	836	2	ENST00000377604.3:c.1807C>T	p.Gln603Ter	p.Q603*	ENST00000377604	NM_001204468.1	603	Cag/Tag	17/24	1	2	FACETS	0.716	0.629	0.81	0.716	0.629	0.81	SUBCLONAL	1	TRUE	1	0.25	2		838	894	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0019899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	122	146	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.895	0.822	0.97	0.895	0.822	0.97	CLONAL	1	TRUE	1	0.908553525611713	2		146	300	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0019899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	71	465	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.995	0.893	1	0.995	0.893	1	CLONAL	1	TRUE	1	0.908553525611713	2		465	157	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413129	139413131	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	novel	NA	P-0019899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	110	896	0	ENST00000277541.6:c.1011_1013del	p.Asp338del	p.D338del	ENST00000277541	NM_017617.3	337	gaTGAc/gac	6/34	1	2	FACETS	0.298	0.267	0.331	0.298	0.267	0.331	SUBCLONAL	1	TRUE	1	0.908553525611713	2		896	812	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791716	42791716	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	210	631	0	ENST00000575354.2:c.602G>A	p.Arg201Gln	p.R201Q	ENST00000575354	NM_015125.3	201	cGg/cAg	5/20	0.908553525611713	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.908553525611713	1		631	252	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114119	73114121	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0019899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	21	577	0	ENST00000356692.5:c.758_760del	p.Glu253del	p.E253del	ENST00000356692		252	aAAGaa/aaa	8/9	1	2	FACETS	0.115	0.088	0.147	0.115	0.088	0.147	SUBCLONAL	1	TRUE	1	0.908553525611713	2		577	401	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77060330	77060331	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	CACTGAA	novel	NA	P-0019900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	52	273	0	ENST00000356341.3:c.837-5_838dup	p.Ala280ValfsTer22	p.A280Vfs*22	ENST00000356341	NM_002576.4	280	gct/gTTCAGTGct	9/15	0.388536404151336	3	FACETS	0.805	0.687	0.934	0.403	0.343	0.467	CLONAL	1	TRUE	1	0.388536404151336	3		273	397	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520006	NA	P-0019900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	335	745	0	ENST00000269305.4:c.821T>C	p.Val274Ala	p.V274A	ENST00000269305	NM_001126112.2	274	gTt/gCt	8/11	0.36739388618718	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.388536404151336	2		745	758	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589610	67589612	+	inframe_deletion	In_Frame_Del	DEL	AAA	AAA	-	novel	NA	P-0019900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	199	473	0	ENST00000274335.5:c.1376_1378del	p.Lys459del	p.K459del	ENST00000274335		458	gAAAaa/gaa	10/15	0.388536404151336	2	FACETS	0.974	0.91	1	0.974	0.91	1	CLONAL	2	TRUE	0	0.388536404151336	2		473	526	SUCCESS
APC	324	MSKCC	GRCh37	5	112174182	112174182	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0019900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	220	470	0	ENST00000257430.4:c.2891T>G	p.Leu964Ter	p.L964*	ENST00000257430	NM_000038.5	964	tTa/tGa	16/16	0.388536404151336	3	FACETS	1	0.943	1			1	CLONAL	2	TRUE	NA	0.388536404151336	3		470	670	SUCCESS
APC	324	MSKCC	GRCh37	5	112175754	112175760	+	frameshift_variant	Frame_Shift_Del	DEL	TATTACA	TATTACA	-	novel	NA	P-0019900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	59	345	0	ENST00000257430.4:c.4464_4470del	p.Leu1488PhefsTer17	p.L1488Ffs*17	ENST00000257430	NM_000038.5	1488	tTATTACAt/tt	16/16	0.388536404151336	3	FACETS	0.801	0.69	0.92			1	CLONAL	1	TRUE	NA	0.388536404151336	3		345	453	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437496	52437496	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	106	659	0	ENST00000460680.1:c.1665del	p.Val556SerfsTer15	p.V556Sfs*15	ENST00000460680	NM_004656.3	555	ccT/cc	13/17	1	2	FACETS	0.978	0.88	1	0.978	0.88	1	CLONAL	1	TRUE	1	0.4	2		659	542	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439813	52439814	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0019901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	111	542	0	ENST00000460680.1:c.898_899del	p.Arg300GlyfsTer6	p.R300Gfs*6	ENST00000460680	NM_004656.3	300	AGg/g	10/17	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.4	2		542	543	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	63	352	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.563	0.486	0.646	0.563	0.486	0.646	SUBCLONAL	1	TRUE	1	0.327172514155987	2		352	684	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070644	67070645	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0019903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	21	259	0	ENST00000412916.2:c.268_269insCT	p.Arg90ThrfsTer9	p.R90Tfs*9	ENST00000412916		90	aga/aCTga	3/6	1	2	FACETS	0.346	0.266	0.44	0.346	0.266	0.44	SUBCLONAL	1	TRUE	1	0.327172514155987	2		259	371	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140767	55140767	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	69	646	0	ENST00000257290.5:c.1628T>A	p.Ile543Asn	p.I543N	ENST00000257290	NM_006206.4	543	aTt/aAt	11/23	1	2	FACETS	0.552	0.48	0.63	0.552	0.48	0.63	SUBCLONAL	1	TRUE	1	0.327172514155987	2		646	764	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177385	56177403	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTTCTTTCAGGTATAAG	TTTTTCTTTCAGGTATAAG	-	novel	NA	P-0019903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	18	280	0	ENST00000399503.3:c.2370-12_2376del		p.X790_splice	ENST00000399503	NM_005921.1	790		14/20	1	2	FACETS	0.317	0.238	0.411	0.317	0.238	0.411	SUBCLONAL	1	TRUE	1	0.327172514155987	2		280	347	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	262	531	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.286410337321574	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.29	2		531	814	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	170	733	1	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	0.3	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.29	1		734	845	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112138	115112138	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	261	833	0	ENST00000257566.3:c.1602G>T	p.Met534Ile	p.M534I	ENST00000257566	NM_016569.3	534	atG/atT	7/8	0.286410337321574	2	FACETS	0.904	0.847	0.961	0.904	0.847	0.961	CLONAL	2	TRUE	0	0.29	2		833	996	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345042	73345042	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	148	548	0	ENST00000377767.4:c.1755G>T	p.Lys585Asn	p.K585N	ENST00000377767	NM_014953.3	585	aaG/aaT	13/21	0.3	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.29	1		548	750	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013742	12013742	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	105	489	0	ENST00000353533.5:c.684A>T	p.Arg228Ser	p.R228S	ENST00000353533	NM_003010.3	228	agA/agT	6/11	0.3	1	FACETS	0.991	0.889	1	0.991	0.889	1	CLONAL	1	TRUE	0	0.29	1		489	625	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306761	41306761	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	187	458	0	ENST00000373198.4:c.898G>T	p.Val300Leu	p.V300L	ENST00000373198	NM_133170.3	300	Gtg/Ttg	7/32	0.240529434941422	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.29	3		458	684	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005391	29005391	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	133	465	0	ENST00000282397.4:c.870C>A	p.Asn290Lys	p.N290K	ENST00000282397	NM_002019.4	290	aaC/aaA	7/30	0.3	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.29	1		465	639	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937847	36937847	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	172	912	1	ENST00000361632.4:c.989C>A	p.Thr330Asn	p.T330N	ENST00000361632		330	aCc/aAc	7/16	1	2	FACETS	0.971	0.891	1	0.971	0.891	1	CLONAL	1	TRUE	1	0.29	2		913	1222	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462209	120462209	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	110	455	2	ENST00000256646.2:c.5507C>A	p.Ser1836Tyr	p.S1836Y	ENST00000256646	NM_024408.3	1836	tCt/tAt	31/34	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.29	2		457	748	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610170	43610170	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	211	769	0	ENST00000355710.3:c.2122G>T	p.Ala708Ser	p.A708S	ENST00000355710	NM_020975.4	708	Gcc/Tcc	11/20	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.29	2		769	976	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405593	70405593	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs766203888	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	223	690	0	ENST00000373644.4:c.3107A>G	p.His1036Arg	p.H1036R	ENST00000373644	NM_030625.2	1036	cAt/cGt	4/12	1	2	FACETS	0.783	0.729	0.839	1	0.992	1	SUBCLONAL	2	TRUE	1	0.29	2		690	982	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562433	21562433	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	132	505	0	ENST00000382592.4:c.1486G>C	p.Gly496Arg	p.G496R	ENST00000382592	NM_014572.2	496	Ggc/Cgc	4/8	0.3	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.29	1		505	619	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588675	28588675	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	108	487	0	ENST00000241453.7:c.2773T>C	p.Cys925Arg	p.C925R	ENST00000241453	NM_004119.2	925	Tgc/Cgc	23/24	0.3	1	FACETS	0.959	0.862	1	0.959	0.862	1	CLONAL	1	TRUE	0	0.29	1		487	664	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893589	28893590	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	142	579	3	ENST00000282397.4:c.3256_3257delinsTT	p.Gly1086Leu	p.G1086L	ENST00000282397	NM_002019.4	1086	GGa/TTa	24/30	0.3	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.29	1		582	695	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919214	48919214	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	84	199	0	ENST00000267163.4:c.381-2A>T		p.X127_splice	ENST00000267163	NM_000321.2	127			0.3	1	FACETS	0.848	0.758	0.942	1	0.983	1	CLONAL	2	TRUE	0	0.29	1		199	292	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95599663	95599663	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	58	389	0	ENST00000393063.1:c.133A>T	p.Arg45Ter	p.R45*	ENST00000393063	NM_030621.3	45	Aga/Tga	3/28	1	2	FACETS	0.632	0.542	0.73	0.632	0.542	0.73	SUBCLONAL	1	TRUE	1	0.29	2		389	633	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339451	339451	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	196	694	1	ENST00000262320.3:c.2451G>T	p.Lys817Asn	p.K817N	ENST00000262320	NM_003502.3	817	aaG/aaT	10/11	0.225812027516693	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.29	1		695	969	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813941	50813941	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	163	587	0	ENST00000398568.2:c.1495G>T	p.Ala499Ser	p.A499S	ENST00000398568	NM_001042412.1	499	Gct/Tct	8/18	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.29	2		587	844	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56867193	56867193	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	76	606	0	ENST00000308159.5:c.1412A>C	p.Gln471Pro	p.Q471P	ENST00000308159	NM_014669.4	471	cAg/cCg	13/22	1	2	FACETS	0.596	0.521	0.676	0.596	0.521	0.676	SUBCLONAL	1	TRUE	1	0.29	2		606	880	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991404	72991404	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	75	773	1	ENST00000268489.5:c.2641G>T	p.Ala881Ser	p.A881S	ENST00000268489	NM_006885.3	881	Gcc/Tcc	2/10	1	2	FACETS	0.482	0.421	0.548	0.482	0.421	0.548	SUBCLONAL	1	TRUE	1	0.29	2		774	1073	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991952	72991952	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	166	579	0	ENST00000268489.5:c.2093G>T	p.Gly698Val	p.G698V	ENST00000268489	NM_006885.3	698	gGg/gTg	2/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.29	2		579	768	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41251843	41251843	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	162	713	1	ENST00000357654.3:c.496A>T	p.Arg166Trp	p.R166W	ENST00000357654	NM_007294.3	166	Agg/Tgg	7/23	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.29	2		714	1096	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215326	5215326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064298	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	62	512	0	ENST00000357368.4:c.4292C>T	p.Ser1431Phe	p.S1431F	ENST00000357368	NM_002850.3	1431	tCc/tTc	28/38	1	2	FACETS	0.508	0.437	0.585	0.508	0.437	0.585	SUBCLONAL	1	TRUE	1	0.29	2		512	842	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950390	17950390	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	212	801	0	ENST00000458235.1:c.1337C>A	p.Pro446His	p.P446H	ENST00000458235	NM_000215.3	446	cCc/cAc	10/24	0.3	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.29	1		801	1007	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268766	46268766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	59	596	1	ENST00000371998.3:c.3051G>A	p.Met1017Ile	p.M1017I	ENST00000371998		1017	atG/atA	16/23	0.240529434941422	3	FACETS	0.41	0.351	0.474	0.205	0.175	0.237	SUBCLONAL	1	TRUE	1	0.29	3		597	1137	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839745	42839745	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	59	671	0	ENST00000398585.3:c.1494G>T	p.Trp498Cys	p.W498C	ENST00000398585	NM_001135099.1	498	tgG/tgT	13/14	0.291876793079031	1	FACETS	0.338	0.29	0.391	0.338	0.29	0.391	SUBCLONAL	1	TRUE	0	0.29	1		671	1029	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434112	12434112	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs1455092076	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	55	356	0	ENST00000287820.6:c.481-1G>T		p.X161_splice	ENST00000287820	NM_015869.4	161			0.3	1	FACETS	0.557	0.476	0.646	0.557	0.476	0.646	SUBCLONAL	1	TRUE	0	0.29	1		356	582	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670881	134670881	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	81	300	0	ENST00000398015.3:c.792C>G	p.Ser264Arg	p.S264R	ENST00000398015	NM_004441.4	264	agC/agG	3/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.29	2		300	405	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825295	134825295	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	51	341	0	ENST00000398015.3:c.811C>A	p.Pro271Thr	p.P271T	ENST00000398015	NM_004441.4	271	Cct/Act	4/16	1	2	FACETS	0.792	0.674	0.921	0.792	0.674	0.921	CLONAL	1	TRUE	1	0.29	2		341	444	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281604	142281604	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	186	652	0	ENST00000350721.4:c.640A>G	p.Thr214Ala	p.T214A	ENST00000350721	NM_001184.3	214	Act/Gct	4/47	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.29	2		652	950	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170011257	170011257	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	79	710	0	ENST00000295797.4:c.1378G>C	p.Asp460His	p.D460H	ENST00000295797	NM_002740.5	460	Gat/Cat	14/18	1	2	FACETS	0.538	0.472	0.609	0.538	0.472	0.609	SUBCLONAL	1	TRUE	1	0.29	2		710	1013	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957012	1957012	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	166	604	0	ENST00000382891.5:c.2463G>T	p.Lys821Asn	p.K821N	ENST00000382891	NM_133335.3	821	aaG/aaT	13/22	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.29	2		604	817	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187558046	187558046	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	38	286	0	ENST00000441802.2:c.3665G>T	p.Ser1222Ile	p.S1222I	ENST00000441802	NM_005245.3	1222	aGt/aTt	5/27	0.3	1	FACETS	0.737	0.612	0.876	0.737	0.612	0.876	SUBCLONAL	1	TRUE	0	0.29	1		286	304	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31521267	31521267	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	175	649	0	ENST00000344624.3:c.910G>T	p.Glu304Ter	p.E304*	ENST00000344624		304	Gaa/Taa	3/33	0.140390379288062	3	FACETS	1	0.988	1	0.699	0.643	0.757	INDETERMINATE	1	TRUE	1	0.29	3		649	989	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576527	67576527	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	122	468	0	ENST00000274335.5:c.806G>T	p.Ser269Ile	p.S269I	ENST00000274335		269	aGc/aTc	5/15	0.140390379288062	3	FACETS	1	0.975	1	0.617	0.557	0.679	INDETERMINATE	1	TRUE	1	0.29	3		468	781	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449444	149449444	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	125	411	1	ENST00000286301.3:c.1502T>A	p.Ile501Asn	p.I501N	ENST00000286301	NM_005211.3	501	aTc/aAc	10/22	0.3	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.29	1		412	591	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169917	32169917	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	243	818	3	ENST00000375023.3:c.3691C>A	p.Pro1231Thr	p.P1231T	ENST00000375023	NM_004557.3	1231	Cca/Aca	21/30	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.29	NA		821	1247	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729832	41729832	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	82	362	1	ENST00000242208.4:c.697C>A	p.Gln233Lys	p.Q233K	ENST00000242208	NM_002192.2	233	Cag/Aag	3/3	0.240529434941422	3	FACETS	1	0.964	1	0.618	0.546	0.695	CLONAL	1	TRUE	1	0.29	3		363	524	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350081	81350081	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	176	446	0	ENST00000222390.5:c.1251G>T	p.Lys417Asn	p.K417N	ENST00000222390	NM_000601.4	417	aaG/aaT	10/18	0.240529434941422	3	FACETS	0.894	0.825	0.966	0.894	0.825	0.966	CLONAL	2	TRUE	1	0.29	3		446	777	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524643	106524643	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1035403350	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	111	370	0	ENST00000359195.3:c.2804A>G	p.Tyr935Cys	p.Y935C	ENST00000359195	NM_002649.2	935	tAc/tGc	9/11	0.240529434941422	3	FACETS	1	0.973	1	0.622	0.559	0.688	CLONAL	1	TRUE	1	0.29	3		370	705	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339673	116339673	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs753697730	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	138	386	1	ENST00000397752.3:c.535G>T	p.Ala179Ser	p.A179S	ENST00000397752	NM_000245.2	179	Gcc/Tcc	2/21	0.240529434941422	3	FACETS	0.941	0.86	1	0.941	0.86	1	CLONAL	2	TRUE	1	0.29	3		387	579	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879121	151879121	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	249	560	0	ENST00000262189.6:c.5824A>T	p.Thr1942Ser	p.T1942S	ENST00000262189	NM_170606.2	1942	Aca/Tca	36/59	0.240529434941422	3	FACETS	0.948	0.887	1	0.948	0.887	1	CLONAL	2	TRUE	1	0.29	3		560	1037	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507318	8507318	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	39	402	0	ENST00000356435.5:c.1660G>T	p.Gly554Trp	p.G554W	ENST00000356435		554	Ggg/Tgg	11/35	0.278833701519392	0	FACETS	0.431	0.357	0.513			1	SUBCLONAL	1	TRUE	0	0.29	0		402	443	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636727	8636727	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	26	384	0	ENST00000356435.5:c.182G>T	p.Gly61Val	p.G61V	ENST00000356435		61	gGa/gTa	2/35	0.278833701519392	0	FACETS	0.315	0.249	0.391			1	SUBCLONAL	1	TRUE	0	0.29	0		384	404	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240450	98240450	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs370354759	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	58	410	0	ENST00000331920.6:c.1234G>T	p.Ala412Ser	p.A412S	ENST00000331920	NM_000264.3	412	Gca/Tca	9/24	1	2	FACETS	0.657	0.564	0.758	0.657	0.564	0.758	SUBCLONAL	1	TRUE	1	0.29	2		410	609	SUCCESS
AR	367	MSKCC	GRCh37	X	66765380	66765380	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	98	676	1	ENST00000374690.3:c.392G>T	p.Cys131Phe	p.C131F	ENST00000374690	NM_000044.3	131	tGc/tTc	1/8	NA	2	FACETS	0.749	0.667	0.837			1	INDETERMINATE	1	TRUE	NA	0.29	2		677	902	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0019905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	298	786	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.613282068690272	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.613282068690272	3		786	561	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	73	122	0				ENST00000310581	NM_198253.2	-/1132			0.181719973300143	1	FACETS	0.522	0.461	0.588	0.522	0.461	0.588	INDETERMINATE	1	TRUE	0	0.613282068690272	1		122	316	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0019905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	322	931	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.550174045964827	3	FACETS	0.902	0.866	0.938	0.902	0.866	0.938	CLONAL	3	TRUE	0	0.613282068690272	3		931	507	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0019905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	313	788	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.594733441408933	2	FACETS	0.899	0.858	0.939	0.899	0.858	0.939	CLONAL	2	TRUE	0	0.613282068690272	2		788	568	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376694	118376695	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0019905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	125	490	0	ENST00000534358.1:c.10087_10088delinsCT	p.Gly3363Leu	p.G3363L	ENST00000534358	NM_005933.3	3363	GGa/CTa	27/36	1	2	FACETS	0.759	0.69	0.831	0.759	0.69	0.831	SUBCLONAL	1	TRUE	1	0.613282068690272	2		490	537	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657361	29657361	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1555533853	NA	P-0019905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	84	786	1	ENST00000356175.3:c.5594T>A	p.Leu1865Ter	p.L1865*	ENST00000356175	NM_000267.3	1865	tTa/tAa	38/57	1	2	FACETS	0.51	0.451	0.573	0.51	0.451	0.573	SUBCLONAL	1	TRUE	1	0.613282068690272	2		787	537	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966753	18966753	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	182	832	1	ENST00000262803.5:c.1564C>T	p.Pro522Ser	p.P522S	ENST00000262803	NM_002911.3	522	Ccg/Tcg	12/24	1	2	FACETS	0.948	0.879	1	0.948	0.879	1	CLONAL	1	TRUE	1	0.613282068690272	2		833	626	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271291	1271291	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	111	494	2	ENST00000310581.5:c.2411G>A	p.Gly804Asp	p.G804D	ENST00000310581	NM_198253.2	804	gGc/gAc	8/16	0.181719973300143	1	FACETS	0.654	0.593	0.717	0.654	0.593	0.717	INDETERMINATE	1	TRUE	0	0.613282068690272	1		496	384	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562542	176562542	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	42	613	0	ENST00000439151.2:c.438C>G	p.Ile146Met	p.I146M	ENST00000439151	NM_022455.4	146	atC/atG	2/23	1	2	FACETS	0.249	0.207	0.295	0.249	0.207	0.295	SUBCLONAL	1	TRUE	1	0.613282068690272	2		613	550	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683940	117683941	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0019905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	132	647	1	ENST00000368508.3:c.3206_3207delinsTT	p.Trp1069Phe	p.W1069F	ENST00000368508	NM_002944.2	1069	tGG/tTT	21/43	1	2	FACETS	0.851	0.777	0.928	0.851	0.777	0.928	CLONAL	1	TRUE	1	0.613282068690272	2		648	506	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929147	44929148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0019905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	157	607	0	ENST00000377967.4:c.2248dup	p.His750ProfsTer14	p.H750Pfs*14	ENST00000377967	NM_021140.2	749	-/C	17/29	0.428382510662443	1	FACETS	0.843	0.781	0.907	0.843	0.781	0.907	CLONAL	1	TRUE	0	0.613282068690272	1		607	421	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034466	47034467	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	154	703	0	ENST00000377604.3:c.552dup	p.Thr185TyrfsTer24	p.T185Yfs*24	ENST00000377604	NM_001204468.1	184	gct/gcTt	6/24	0.428382510662443	1	FACETS	0.759	0.7	0.819	0.759	0.7	0.819	SUBCLONAL	1	TRUE	0	0.613282068690272	1		703	459	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855966	68855967	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs876661118	NA	P-0019907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	114	504	0	ENST00000261769.5:c.1779dup	p.Ile594HisfsTer11	p.I594Hfs*11	ENST00000261769	NM_004360.3	592	gcc/gCcc	12/16	0.211827174899824	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.211827174899824	1		504	687	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272204	15272219	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGGGGCCCCTGCGG	CCCGGGGCCCCTGCGG	-	novel	NA	P-0019907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	95	461	0	ENST00000263388.2:c.6220_6235del	p.Pro2074GlyfsTer6	p.P2074Gfs*6	ENST00000263388	NM_000435.2	2074	CCGCAGGGGCCCCGGGgg/gg	33/33	1	2	FACETS	0.811	0.724	0.903	1	0.983	1	CLONAL	2	TRUE	1	0.211827174899824	2		461	553	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2952980	2952980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376039195	NA	P-0019907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	92	498	3	ENST00000396946.4:c.2960C>T	p.Thr987Met	p.T987M	ENST00000396946	NM_032415.4	987	aCg/aTg	22/25	1	2	FACETS	0.984	0.873	1	0.984	0.873	1	CLONAL	1	TRUE	1	0.211827174899824	2		501	883	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0019914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	68	453	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.284341801772106	2	FACETS	0.916	0.806	1	0.916	0.806	1	CLONAL	2	TRUE	0	0.28	2		453	265	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597452	10597452	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	96	714	0	ENST00000171111.5:c.1751A>G	p.Tyr584Cys	p.Y584C	ENST00000171111	NM_203500.1	584	tAc/tGc	6/6	0.392199864068327	1	FACETS	0.835	0.751	0.923	1	0.985	1	CLONAL	2	TRUE	0	0.28	1		714	353	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688809	47688811	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0019914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	40	401	0	ENST00000347630.2:c.489_491del	p.Val164del	p.V164del	ENST00000347630	NM_001007230.1	163	gtTGTg/gtg	7/11	0.3	3	FACETS	0.915	0.762	1			1	CLONAL	1	TRUE	NA	0.28	3		401	356	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972051	55972051	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	73	484	1	ENST00000263923.4:c.1593A>T	p.Glu531Asp	p.E531D	ENST00000263923	NM_002253.2	531	gaA/gaT	12/30	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.28	2		485	350	SUCCESS
AR	367	MSKCC	GRCh37	X	66765667	66765667	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	29	830	0	ENST00000374690.3:c.679G>T	p.Gly227Trp	p.G227W	ENST00000374690	NM_000044.3	227	Ggg/Tgg	1/8	0.121262186717288	0	FACETS	0.469	0.377	0.573			1	INDETERMINATE	1	TRUE	0	0.28	0		830	318	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019914-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	328	553	2	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	0.476218691265092	2		555	1338	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059194	27059194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019914-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	208	843	1	ENST00000324856.7:c.1831C>T	p.Gln611Ter	p.Q611*	ENST00000324856	NM_006015.4	611	Cag/Tag	4/20	0.476218691265092	1	FACETS	0.972	0.906	1	0.972	0.906	1	CLONAL	1	TRUE	0	0.476218691265092	1		844	685	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839850	27839850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019914-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	255	918	0	ENST00000328488.2:c.244G>A	p.Asp82Asn	p.D82N	ENST00000328488	NM_003533.2	82	Gat/Aat	1/1	0.196500307146986	1	FACETS	0.772	0.723	0.823	0.772	0.723	0.823	INDETERMINATE	1	TRUE	0	0.476218691265092	1		918	1057	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691929	30691929	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019914-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	173	645	1	ENST00000295754.5:c.431A>G	p.Asn144Ser	p.N144S	ENST00000295754	NM_003242.5	144	aAt/aGt	3/7	0.476218691265092	1	FACETS	0.881	0.815	0.95	0.881	0.815	0.95	CLONAL	1	TRUE	0	0.476218691265092	1		646	628	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72866509	72866509	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019914-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	201	501	0	ENST00000325599.8:c.754C>G	p.Gln252Glu	p.Q252E	ENST00000325599	NM_018130.2	252	Cag/Gag	7/11	0.476218691265092	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.476218691265092	1		501	602	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805200	43805200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019914-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	297	1110	0	ENST00000372470.3:c.650C>A	p.Pro217His	p.P217H	ENST00000372470	NM_005373.2	217	cCc/cAc	4/12	1	2	FACETS	0.984	0.925	1	0.984	0.925	1	CLONAL	1	TRUE	1	0.476218691265092	2		1110	1268	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110408656	110408656	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0019914-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	135	438	0	ENST00000375856.3:c.4013-1G>C		p.X1338_splice	ENST00000375856	NM_003749.2	1338			1	2	FACETS	0.872	0.795	0.953	0.872	0.795	0.953	CLONAL	1	TRUE	1	0.476218691265092	2		438	650	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089999	16089999	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019914-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	91	429	0	ENST00000268712.3:c.111G>C	p.Glu37Asp	p.E37D	ENST00000268712	NM_006311.3	37	gaG/gaC	3/46	1	2	FACETS	0.751	0.669	0.838	0.751	0.669	0.838	SUBCLONAL	1	TRUE	1	0.476218691265092	2		429	509	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546098	29546098	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1567843917	NA	P-0019914-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	207	737	0	ENST00000356175.3:c.1603C>T	p.Gln535Ter	p.Q535*	ENST00000356175	NM_000267.3	535	Cag/Tag	14/57	1	2	FACETS	0.919	0.853	0.987	0.919	0.853	0.987	CLONAL	1	TRUE	1	0.476218691265092	2		737	946	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0019916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	108	834	0	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	0.293147488418223	1	FACETS	0.778	0.699	0.862	0.778	0.699	0.862	SUBCLONAL	1	TRUE	0	0.318389861809178	1		834	733	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405969	49405969	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	97	619	0	ENST00000418115.1:c.169T>G	p.Leu57Val	p.L57V	ENST00000418115	NM_001664.2	57	Ttg/Gtg	3/5	1	2	FACETS	0.707	0.629	0.79	0.707	0.629	0.79	SUBCLONAL	1	TRUE	1	0.318389861809178	2		619	862	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047151	77047151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	984	756	0	ENST00000356341.3:c.1393C>T	p.Leu465Phe	p.L465F	ENST00000356341	NM_002576.4	465	Ctc/Ttc	13/15	0.318389861809178	9	FACETS	0.982	0.958	1			1	CLONAL	8	TRUE	NA	0.318389861809178	9		756	1664	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400035	139400035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61751541	NA	P-0019916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	237	643	0	ENST00000277541.6:c.4313G>A	p.Arg1438His	p.R1438H	ENST00000277541	NM_017617.3	1438	cGc/cAc	25/34	0.290551695695766	2	FACETS	0.868	0.811	0.925	0.868	0.811	0.925	CLONAL	2	TRUE	0	0.318389861809178	2		643	858	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs786202525	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	96	491	1	ENST00000269305.4:c.532del	p.His178ThrfsTer69	p.H178Tfs*69	ENST00000269305	NM_001126112.2	178	Cac/ac	5/11	0.284119956883402	1	FACETS	0.952	0.85	1	0.952	0.85	1	CLONAL	1	FALSE	0	0.284119956883402	1		492	609	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	41	424	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.221206103917926	0	FACETS	0.551	0.46	0.652			1	SUBCLONAL	1	FALSE	0	0.284119956883402	0		424	375	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141499	11141499	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	183	658	2	ENST00000358026.2:c.3476G>T	p.Gly1159Val	p.G1159V	ENST00000358026	NM_001128849.1	1159	gGg/gTg	25/36	0.238390802621113	2	FACETS	0.846	0.783	0.912	0.846	0.783	0.912	CLONAL	2	FALSE	0	0.284119956883402	2		660	761	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597401	10597401	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	231	651	0	ENST00000171111.5:c.1802G>T	p.Arg601Leu	p.R601L	ENST00000171111	NM_203500.1	601	cGg/cTg	6/6	0.238390802621113	2	FACETS	0.9	0.841	0.962	0.9	0.841	0.962	CLONAL	2	FALSE	0	0.284119956883402	2		651	903	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625189	69625189	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	112	562	0	ENST00000334134.2:c.604C>A	p.Pro202Thr	p.P202T	ENST00000334134	NM_005247.2	202	Cct/Act	3/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.284119956883402	2		562	641	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414460	78414460	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	17	361	0	ENST00000370768.2:c.1927-1G>C		p.X643_splice	ENST00000370768	NM_003902.3	643			0.15165095751635	0	FACETS	0.317	0.237	0.413			1	INDETERMINATE	1	FALSE	0	0.284119956883402	0		361	270	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510235	120510235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs371046188	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	25	339	1	ENST00000256646.2:c.1274A>G	p.Asn425Ser	p.N425S	ENST00000256646	NM_024408.3	425	aAt/aGt	8/34	0.15165095751635	0	FACETS	0.293	0.23	0.365			1	INDETERMINATE	1	FALSE	0	0.284119956883402	0		340	430	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360883	118360883	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	43	407	0	ENST00000534358.1:c.4615A>T	p.Thr1539Ser	p.T1539S	ENST00000534358	NM_005933.3	1539	Aca/Tca	13/36	1	2	FACETS	0.671	0.562	0.792	0.671	0.562	0.792	SUBCLONAL	1	FALSE	1	0.284119956883402	2		407	451	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125097	46125097	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	32	145	0	ENST00000334344.6:c.284G>T	p.Arg95Leu	p.R95L	ENST00000334344	NM_152641.2	95	cGt/cTt	3/21	0.238390802621113	2	FACETS	0.756	0.622	0.902	0.756	0.622	0.902	CLONAL	2	FALSE	0	0.284119956883402	2		145	149	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424509	49424510	+	missense_variant	Missense_Mutation	DNP	TG	TG	AT	novel	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	133	632	0	ENST00000301067.7:c.13713_13714delinsAT	p.Asn4572Tyr	p.N4572Y	ENST00000301067	NM_003482.3	4571	gcCAat/gcATat	41/54	0.238390802621113	2	FACETS	1	0.983	1	0.68	0.619	0.745	CLONAL	1	FALSE	0	0.284119956883402	2		632	688	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068247	30068247	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	66	455	1	ENST00000331968.5:c.2152G>T	p.Asp718Tyr	p.D718Y	ENST00000331968	NM_002742.2	718	Gat/Tat	15/18	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	FALSE	1	0.284119956883402	2		456	449	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434598	99434598	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	47	480	0	ENST00000268035.6:c.685G>A	p.Glu229Lys	p.E229K	ENST00000268035	NM_000875.3	229	Gag/Aag	3/21	1	2	FACETS	0.497	0.418	0.584	0.497	0.418	0.584	SUBCLONAL	1	FALSE	1	0.284119956883402	2		480	666	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857673	9857673	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471308483	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	26	324	0	ENST00000330684.3:c.3728G>A	p.Gly1243Glu	p.G1243E	ENST00000330684	NM_001134407.1	1243	gGg/gAg	13/13	0.238390802621113	2	FACETS	0.504	0.399	0.625	0.252	0.199	0.313	SUBCLONAL	1	FALSE	0	0.284119956883402	2		324	363	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992251	72992251	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	138	682	0	ENST00000268489.5:c.1794C>A	p.Asp598Glu	p.D598E	ENST00000268489	NM_006885.3	598	gaC/gaA	2/10	0.284119956883402	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	0	0.284119956883402	1		682	771	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993840	72993840	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	83	427	0	ENST00000268489.5:c.205G>T	p.Gly69Trp	p.G69W	ENST00000268489	NM_006885.3	69	Ggg/Tgg	2/10	0.284119956883402	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	0	0.284119956883402	1		427	391	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119072	70119072	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	102	438	0	ENST00000245479.2:c.644C>A	p.Ser215Tyr	p.S215Y	ENST00000245479	NM_000346.3	215	tCc/tAc	2/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.284119956883402	2		438	512	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632392	1632392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368633375	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	62	676	0	ENST00000344749.5:c.158G>A	p.Arg53Gln	p.R53Q	ENST00000344749	NM_001136139.2	53	cGg/cAg	4/19	0.238390802621113	2	FACETS	0.614	0.529	0.706	0.307	0.264	0.353	SUBCLONAL	1	FALSE	0	0.284119956883402	2		676	711	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260071	19260071	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	206	681	0	ENST00000162023.5:c.222G>T	p.Glu74Asp	p.E74D	ENST00000162023		74	gaG/gaT	7/13	0.238390802621113	2	FACETS	0.816	0.758	0.877	0.816	0.758	0.877	CLONAL	2	FALSE	0	0.284119956883402	2		681	888	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082398	16082398	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	61	648	0	ENST00000281043.3:c.212G>T	p.Ser71Ile	p.S71I	ENST00000281043	NM_005378.4	71	aGc/aTc	2/3	1	2	FACETS	0.605	0.521	0.696	0.605	0.521	0.696	SUBCLONAL	1	FALSE	1	0.284119956883402	2		648	710	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251857	212251857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	38	322	0	ENST00000342788.4:c.3202G>A	p.Asp1068Asn	p.D1068N	ENST00000342788	NM_005235.2	1068	Gat/Aat	27/28	1	2	FACETS	0.733	0.607	0.873	0.733	0.607	0.873	SUBCLONAL	1	FALSE	1	0.284119956883402	2		322	365	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730826	40730826	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	110	682	1	ENST00000373198.4:c.3709C>A	p.Leu1237Met	p.L1237M	ENST00000373198	NM_133170.3	1237	Ctg/Atg	27/32	1	2	FACETS	0.898	0.806	0.996	0.898	0.806	0.996	CLONAL	1	FALSE	1	0.284119956883402	2		683	862	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259201	36259201	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	42	688	1	ENST00000300305.3:c.290T>A	p.Phe97Tyr	p.F97Y	ENST00000300305		97	tTc/tAc	3/8	1	2	FACETS	0.37	0.307	0.439	0.37	0.307	0.439	SUBCLONAL	1	FALSE	1	0.284119956883402	2		689	800	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259416	89259416	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	64	472	0	ENST00000336596.2:c.560G>T	p.Gly187Val	p.G187V	ENST00000336596	NM_005233.5	187	gGt/gTt	3/17	1	2	FACETS	0.775	0.672	0.888	0.775	0.672	0.888	SUBCLONAL	1	FALSE	1	0.284119956883402	2		472	581	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644675	134644675	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	97	440	0	ENST00000398015.3:c.76A>G	p.Arg26Gly	p.R26G	ENST00000398015	NM_004441.4	26	Aga/Gga	2/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.284119956883402	2		440	606	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138431080	138431080	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1468716826	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	83	521	0	ENST00000289153.2:c.1369A>G	p.Ile457Val	p.I457V	ENST00000289153	NM_006219.2	457	Ata/Gta	8/22	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	1	0.284119956883402	2		521	531	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198255	185198255	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs759993681	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	107	468	0	ENST00000265026.3:c.2737G>T	p.Val913Leu	p.V913L	ENST00000265026	NM_004721.4	913	Gtg/Ttg	13/14	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	FALSE	1	0.284119956883402	2		468	735	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156612	55156612	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	101	552	0	ENST00000257290.5:c.3013G>T	p.Gly1005Cys	p.G1005C	ENST00000257290	NM_006206.4	1005	Ggt/Tgt	22/23	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	FALSE	1	0.284119956883402	2		552	670	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964433	55964433	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	70	415	0	ENST00000263923.4:c.2380G>T	p.Gly794Ter	p.G794*	ENST00000263923	NM_002253.2	794	Gga/Tga	17/30	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	FALSE	1	0.284119956883402	2		415	460	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99802243	99802243	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	24	156	0	ENST00000280892.6:c.650A>G	p.Tyr217Cys	p.Y217C	ENST00000280892	NM_001130678.1	217	tAt/tGt	7/7	1	2	FACETS	0.899	0.709	1	0.899	0.709	1	CLONAL	1	FALSE	1	0.284119956883402	2		156	188	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193720	106193720	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	26	193	1	ENST00000380013.4:c.4183-1G>T		p.X1395_splice	ENST00000380013	NM_001127208.2	1395			1	2	FACETS	1	0.82	1	1	0.82	1	CLONAL	1	FALSE	1	0.284119956883402	2		194	178	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683635	162683635	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	90	450	3	ENST00000366898.1:c.334C>A	p.Leu112Ile	p.L112I	ENST00000366898	NM_004562.2	112	Ctc/Atc	3/12	0.284119956883402	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	0	0.284119956883402	1		453	480	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331965	81331965	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	45	373	0	ENST00000222390.5:c.2119G>T	p.Val707Phe	p.V707F	ENST00000222390	NM_000601.4	707	Gtc/Ttc	18/18	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	FALSE	1	0.284119956883402	2		373	265	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978664	70978664	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	123	665	0	ENST00000276594.2:c.989G>C	p.Cys330Ser	p.C330S	ENST00000276594	NM_024504.3	330	tGt/tCt	5/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.284119956883402	2		665	778	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319879	8319879	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	36	386	0	ENST00000356435.5:c.5622G>T	p.Gln1874His	p.Q1874H	ENST00000356435		1874	caG/caT	34/35	0.284119956883402	1	FACETS	0.528	0.434	0.633	0.528	0.434	0.633	SUBCLONAL	1	FALSE	0	0.284119956883402	1		386	412	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971054	21971054	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	81	430	0	ENST00000304494.5:c.304G>T	p.Ala102Ser	p.A102S	ENST00000304494	NM_000077.4	102	Gcg/Tcg	2/3	0.284119956883402	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	FALSE	0	0.284119956883402	1		430	458	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002741	37002741	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	99	445	0	ENST00000358127.4:c.508G>T	p.Val170Leu	p.V170L	ENST00000358127	NM_001280556.1	170	Gtg/Ttg	5/10	0.284119956883402	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	0	0.284119956883402	1		445	511	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914668	39914668	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	96	563	0	ENST00000378444.4:c.4694C>G	p.Thr1565Ser	p.T1565S	ENST00000378444	NM_001123385.1	1565	aCc/aGc	12/15	0.15165095751635	0	FACETS	0.801	0.715	0.892			1	INDETERMINATE	1	FALSE	0	0.284119956883402	0		563	604	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941974	44941974	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	38	490	0	ENST00000377967.4:c.3224G>T	p.Arg1075Met	p.R1075M	ENST00000377967	NM_021140.2	1075	aGg/aTg	22/29	0.15165095751635	0	FACETS	0.36	0.297	0.43			1	INDETERMINATE	1	FALSE	0	0.284119956883402	0		490	532	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123505237	123505237	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	33	565	0	ENST00000371139.4:c.383C>A	p.Pro128Gln	p.P128Q	ENST00000371139	NM_001114937.2	128	cCa/cAa	4/4	0.15165095751635	0	FACETS	0.523	0.427	0.631			1	INDETERMINATE	1	FALSE	0	0.284119956883402	0		565	318	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205774	108205774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555127177	NA	P-0019918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	17	510	0	ENST00000278616.4:c.8089A>G	p.Asn2697Asp	p.N2697D	ENST00000278616	NM_000051.3	2697	Aat/Gat	55/63	1	2	FACETS	0.999	0.754	1	0.999	0.754	1	CLONAL	1	TRUE	1	0.27	2		510	126	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169993015	169993015	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0019918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	12	314	0	ENST00000295797.4:c.647-2A>G		p.X216_splice	ENST00000295797	NM_002740.5	216			1	2	FACETS	0.916	0.651	1	0.916	0.651	1	CLONAL	1	TRUE	1	0.27	2		314	97	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141568614	141568614	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs755874332	NA	P-0019918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	55	596	0	ENST00000220592.5:c.848A>G	p.Asn283Ser	p.N283S	ENST00000220592	NM_012154.3	283	aAt/aGt	7/19	0.22492608203729	5	FACETS	1	0.959	1	0.452	0.388	0.522	CLONAL	1	TRUE	2	0.27	5		596	422	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173632	108173634	+	frameshift_variant	Frame_Shift_Del	DEL	ATA	ATA	G	novel	NA	P-0019918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	29	473	0	ENST00000278616.4:c.5372_5374delinsG	p.Asp1791GlyfsTer9	p.D1791Gfs*9	ENST00000278616	NM_000051.3	1791	gATAta/gGta	36/63	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.27	2		473	144	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0019919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	244	704	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.219163983625901	2	FACETS	0.91	0.85	0.971	0.91	0.85	0.971	CLONAL	2	TRUE	0	0.266902206189356	2		704	1005	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940241	71940241	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113909227	NA	P-0019919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	199	667	3	ENST00000298229.2:c.626G>A	p.Arg209His	p.R209H	ENST00000298229	NM_001567.3	209	cGt/cAt	5/28	0.266902206189356	3	FACETS	0.881	0.816	0.948	0.881	0.816	0.948	CLONAL	2	TRUE	1	0.266902206189356	3		670	959	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652882	212652882	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	52	279	0	ENST00000342788.4:c.424A>G	p.Ile142Val	p.I142V	ENST00000342788	NM_005235.2	142	Atc/Gtc	4/28	0.218548106324022	3	FACETS	1	0.872	1	0.512	0.437	0.595	CLONAL	1	TRUE	1	0.266902206189356	3		279	431	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250755	26250755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	49	291	0	ENST00000446824.2:c.79C>T	p.Arg27Cys	p.R27C	ENST00000446824	NM_021018.2	27	Cgc/Tgc	1/1	0.218548106324022	3	FACETS	0.829	0.702	0.968	0.415	0.351	0.484	CLONAL	1	TRUE	1	0.266902206189356	3		291	502	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974785	21974792	+	frameshift_variant	Frame_Shift_Del	DEL	GTCAGCCG	GTCAGCCG	-	novel	NA	P-0019919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	43	208	0	ENST00000304494.5:c.35_42del	p.Ser12LeufsTer29	p.S12Lfs*29	ENST00000304494	NM_000077.4	12	tCGGCTGAC/t	1/3	0.212652380673786	2	FACETS	1	0.952	1	0.688	0.581	0.805	CLONAL	1	TRUE	0	0.266902206189356	2		208	234	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0019920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	223	499	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.474444442862441	3	FACETS	0.929	0.871	0.988	0.929	0.871	0.988	CLONAL	2	TRUE	1	0.501183965462756	3		499	599	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101259	27101259	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	138	526	0	ENST00000324856.7:c.4541del	p.Thr1514ArgfsTer13	p.T1514Rfs*13	ENST00000324856	NM_006015.4	1514	aCg/ag	18/20	1	2	FACETS	0.888	0.811	0.969	0.888	0.811	0.969	CLONAL	1	TRUE	1	0.501183965462756	2		526	620	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	835	482	0	ENST00000256196.4:c.68G>A	p.Gly23Asp	p.G23D	ENST00000256196		23	gGc/gAc	1/6	0.501183965462756	7	FACETS	0.969	0.948	0.989			1	CLONAL	7	TRUE	NA	0.501183965462756	7		482	1107	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557610	21557610	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	81	645	0	ENST00000382592.4:c.2235G>A	p.Met745Ile	p.M745I	ENST00000382592	NM_014572.2	745	atG/atA	5/8	1	2	FACETS	0.443	0.39	0.501	0.443	0.39	0.501	SUBCLONAL	1	TRUE	1	0.501183965462756	2		645	729	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779521	3779522	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0019920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	231	885	1	ENST00000262367.5:c.5526_5527del	p.Phe1842LeufsTer123	p.F1842Lfs*123	ENST00000262367	NM_004380.2	1842	ttCTgc/ttgc	31/31	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.501183965462756	2		886	912	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223382	36223382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs930333173	NA	P-0019920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	161	789	0	ENST00000222270.7:c.5932G>A	p.Glu1978Lys	p.E1978K	ENST00000222270	NM_014727.1	1978	Gag/Aag	28/37	1	2	FACETS	0.769	0.705	0.834	0.769	0.705	0.834	SUBCLONAL	1	TRUE	1	0.501183965462756	2		789	836	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953597	38953597	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	108	309	0	ENST00000357387.3:c.2756A>C	p.Glu919Ala	p.E919A	ENST00000357387	NM_152756.3	919	gAa/gCa	28/38	1	2	FACETS	0.905	0.817	0.998	0.905	0.817	0.998	CLONAL	1	TRUE	1	0.501183965462756	2		309	476	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672291	86672291	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0019920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	105	521	0	ENST00000274376.6:c.2093T>G	p.Leu698Ter	p.L698*	ENST00000274376	NM_002890.2	698	tTa/tGa	16/25	1	2	FACETS	0.797	0.716	0.881	0.797	0.716	0.881	SUBCLONAL	1	TRUE	1	0.501183965462756	2		521	526	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43739021	43739021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	158	543	0	ENST00000523873.1:c.38C>T	p.Ala13Val	p.A13V	ENST00000523873		13	gCc/gTc	1/8	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.501183965462756	2		543	614	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997694	149997694	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	86	316	0	ENST00000253339.5:c.2773del	p.Thr925GlnfsTer32	p.T925Qfs*32	ENST00000253339		925	Aca/ca	5/7	1	2	FACETS	0.86	0.766	0.96	0.86	0.766	0.96	CLONAL	1	TRUE	1	0.501183965462756	2		316	399	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020777	37020777	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	58	545	0	ENST00000358127.4:c.68T>C	p.Leu23Pro	p.L23P	ENST00000358127	NM_001280556.1	23	cTt/cCt	2/10	1	2	FACETS	0.351	0.301	0.406	0.351	0.301	0.406	SUBCLONAL	1	TRUE	1	0.501183965462756	2		545	659	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050393	176050393	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs777025600	NA	P-0019921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	33	411	0	ENST00000367669.3:c.1172A>T	p.Glu391Val	p.E391V	ENST00000367669	NM_022457.5	391	gAa/gTa	11/20	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.236307192626964	2		411	239	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593654	55593655	+	inframe_insertion	In_Frame_Ins	INS	-	-	CACAACTTCCTTATGATCACAAATGGGAGTTTC	novel	NA	P-0019921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	46	543	0	ENST00000288135.5:c.1722_1754dup	p.Gln575_Pro585dup	p.Q575_P585dup	ENST00000288135	NM_000222.2	575	aca/aCACAACTTCCTTATGATCACAAATGGGAGTTTCca	11/21	0.236307192626964	3	FACETS	1	0.917	1	0.568	0.48	0.666	CLONAL	1	TRUE	1	0.236307192626964	3		543	383	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	121	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.25678911256528	3	FACETS	0.921	0.835	1	0.921	0.835	1	CLONAL	2	TRUE	1	0.26165577282345	3		555	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576873	7576873	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs863224500	NA	P-0019923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	201	601	0	ENST00000269305.4:c.973G>T	p.Gly325Ter	p.G325*	ENST00000269305	NM_001126112.2	325	Gga/Tga	9/11	0.26165577282345	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.26165577282345	2		601	667	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022883	31022883	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	248	498	3	ENST00000375687.4:c.2368G>T	p.Glu790Ter	p.E790*	ENST00000375687	NM_015338.5	790	Gag/Tag	13/13	0.26165577282345	5	FACETS	1	0.941	1	1	0.941	1	CLONAL	3	TRUE	2	0.26165577282345	5		501	876	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598065	52598065	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0019923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	129	382	0	ENST00000394830.3:c.3800+1G>A		p.X1267_splice	ENST00000394830	NM_018313.4	1267			0.186066507415512	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	0	0.26165577282345	2		382	485	SUCCESS
APC	324	MSKCC	GRCh37	5	112175891	112175892	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0019923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	35	302	0	ENST00000257430.4:c.4601_4602del	p.Gly1534GlufsTer2	p.G1534Efs*2	ENST00000257430	NM_000038.5	1534	GGg/g	16/16	1	2	FACETS	0.847	0.696	1	0.847	0.696	1	CLONAL	1	TRUE	1	0.26165577282345	2		302	316	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411333	63411333	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	194	626	0	ENST00000330258.3:c.1834G>T	p.Glu612Ter	p.E612*	ENST00000330258	NM_152424.3	612	Gag/Tag	2/2	0.151300596549403	3	FACETS	1	0.98	1	0.768	0.713	0.825	INDETERMINATE	2	TRUE	0	0.26165577282345	3		626	728	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0019924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	100	786	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.262933804509304	2		786	678	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	125	603	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.15966185039858	2	FACETS	1	0.981	1	0.674	0.611	0.741	CLONAL	1	TRUE	0	0.262933804509304	2		603	705	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941265	71941265	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144485030	NA	P-0019924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	115	783	0	ENST00000298229.2:c.1040G>A	p.Arg347Gln	p.R347Q	ENST00000298229	NM_001567.3	347	cGg/cAg	9/28	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.262933804509304	2		783	795	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0019925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	738	716	0	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	0.880936370458355	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	4	TRUE	0	0.880936370458355	4		716	784	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857869	9857869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	107	461	0	ENST00000330684.3:c.3532C>T	p.Leu1178Phe	p.L1178F	ENST00000330684	NM_001134407.1	1178	Ctt/Ttt	13/13	0.880936370458355	3	FACETS	1	0.931	1	0.516	0.468	0.566	CLONAL	1	TRUE	1	0.880936370458355	3		461	339	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131439	17131439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767235709	NA	P-0019925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	121	601	1	ENST00000285071.4:c.13G>A	p.Val5Met	p.V5M	ENST00000285071	NM_144997.5	5	Gtg/Atg	4/14	0.880936370458355	4	FACETS	0.957	0.868	1	0.239	0.217	0.263	CLONAL	1	TRUE	0	0.880936370458355	4		602	540	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467632	66467632	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	44	450	0	ENST00000273854.3:c.637G>T	p.Ala213Ser	p.A213S	ENST00000273854	NM_004439.5	213	Gct/Tct	3/18	0.880936370458355	2	FACETS	0.378	0.319	0.443	0.189	0.159	0.222	SUBCLONAL	1	TRUE	0	0.880936370458355	2		450	264	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31431707	31431707	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	250	557	0	ENST00000344624.3:c.3121G>A	p.Ala1041Thr	p.A1041T	ENST00000344624		1041	Gcc/Acc	23/33	0.880936370458355	6	FACETS	1	0.992	1	0.367	0.343	0.392	CLONAL	1	TRUE	2	0.880936370458355	6		557	1068	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131945085	131945085	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	383	448	0	ENST00000265335.6:c.3033G>C	p.Gln1011His	p.Q1011H	ENST00000265335		1011	caG/caC	19/25	0.880936370458355	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	0	0.880936370458355	3		448	417	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390899	139390899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753752321	NA	P-0019925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	141	669	0	ENST00000277541.6:c.7292G>A	p.Arg2431Gln	p.R2431Q	ENST00000277541	NM_017617.3	2431	cGg/cAg	34/34	0.752233883216049	4	FACETS	0.981	0.897	1	0.49	0.448	0.534	CLONAL	1	TRUE	2	0.880936370458355	4		669	614	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0019927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	333	831	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	0.473422333059806	4	FACETS	0.885	0.837	0.933	0.885	0.837	0.933	CLONAL	2	TRUE	2	0.538923109749432	4		831	1075	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996765	73996765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558691012	NA	P-0019927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	84	352	1	ENST00000318443.5:c.1321C>T	p.Arg441Cys	p.R441C	ENST00000318443	NM_001024736.1	441	Cgc/Tgc	6/10	0.216408704600908	2	FACETS	0.999	0.892	1	0.5	0.446	0.556	INDETERMINATE	1	TRUE	0	0.538923109749432	2		353	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576938	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TAGGAAAGAGG	TAGGAAAGAGG	-	novel	NA	P-0019927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	334	817	0	ENST00000269305.4:c.920-12_920-2del		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.538923109749432	2	FACETS	0.92	0.877	0.962	0.92	0.877	0.962	CLONAL	2	TRUE	0	0.538923109749432	2		817	674	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464480	25464481	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	179	814	0	ENST00000264709.3:c.2032_2033insT	p.Gln678LeufsTer35	p.Q678Lfs*35	ENST00000264709	NM_175629.2	678	cag/cTag	17/23	0.473422333059806	4	FACETS	0.919	0.846	0.996	0.46	0.423	0.498	CLONAL	1	TRUE	2	0.538923109749432	4		814	1112	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225770	26225770	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs966515186	NA	P-0019927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	111	687	0	ENST00000360408.1:c.388C>T	p.Arg130Cys	p.R130C	ENST00000360408	NM_003532.2	130	Cgc/Tgc	1/1	0.473422333059806	4	FACETS	0.779	0.7	0.863	0.389	0.35	0.432	SUBCLONAL	1	TRUE	2	0.538923109749432	4		687	814	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	323	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.394907283594999	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.394907283594999	3		555	921	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023290	27023290	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	52	321	1	ENST00000324856.7:c.400del	p.Ala134ArgfsTer98	p.A134Rfs*98	ENST00000324856	NM_006015.4	132	gtG/gt	1/20	0.394907283594999	1	FACETS	0.923	0.795	1	0.923	0.795	1	CLONAL	1	TRUE	0	0.394907283594999	1		322	229	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56477627	56477627	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	168	814	0	ENST00000267101.3:c.175G>C	p.Val59Leu	p.V59L	ENST00000267101	NM_001982.3	59	Gtg/Ctg	2/28	0.394907283594999	3	FACETS	0.999	0.917	1	0.499	0.458	0.542	CLONAL	1	TRUE	1	0.394907283594999	3		814	1020	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965154	15965154	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	75	459	0	ENST00000268712.3:c.5442C>A	p.Tyr1814Ter	p.Y1814*	ENST00000268712	NM_006311.3	1814	taC/taA	37/46	1	2	FACETS	0.92	0.81	1	0.92	0.81	1	CLONAL	1	TRUE	1	0.394907283594999	2		459	413	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584728	48584729	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	111	628	0	ENST00000342988.3:c.807dup	p.Gly270TrpfsTer3	p.G270Wfs*3	ENST00000342988	NM_005359.5	269	act/acTt	7/12	0.386777285503639	1	FACETS	0.826	0.745	0.911	0.826	0.745	0.911	CLONAL	1	TRUE	0	0.394907283594999	1		628	546	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066759	94066759	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	79	466	0	ENST00000369303.4:c.1000G>T	p.Ala334Ser	p.A334S	ENST00000369303	NM_004440.3	334	Gca/Tca	5/17	0.388696108872928	1	FACETS	0.747	0.66	0.839	0.747	0.66	0.839	SUBCLONAL	1	TRUE	0	0.394907283594999	1		466	430	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28624268	28624268	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	79	878	0	ENST00000241453.7:c.706G>C	p.Glu236Gln	p.E236Q	ENST00000241453	NM_004119.2	236	Gaa/Caa	6/24	1	2	FACETS	0.226	0.198	0.256	0.226	0.198	0.256	SUBCLONAL	1	TRUE	1	0.646059267189	2		878	1082	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178679	56178679	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	101	335	0	ENST00000399503.3:c.3652A>T	p.Ile1218Phe	p.I1218F	ENST00000399503	NM_005921.1	1218	Att/Ttt	14/20	1	2	FACETS	0.743	0.668	0.821	0.743	0.668	0.821	SUBCLONAL	1	TRUE	1	0.646059267189	2		335	421	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0019932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	103	333	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.154179547405544	5	FACETS	0.808	0.726	0.894			1	INDETERMINATE	2	TRUE	NA	0.408890127175333	5		333	503	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720877	89720877	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0019932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	61	396	0	ENST00000371953.3:c.1026+2T>A		p.X342_splice	ENST00000371953	NM_000314.4	342			0.154179547405544	5	FACETS	0.946	0.817	1			1	INDETERMINATE	1	TRUE	NA	0.408890127175333	5		396	509	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346671	225346671	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	67	521	0	ENST00000264414.4:c.1967del	p.Gly656ValfsTer40	p.G656Vfs*40	ENST00000264414	NM_003590.4	656	gGt/gt	14/16	NA	2	FACETS	0.708	0.617	0.806			1	INDETERMINATE	1	TRUE	NA	0.408890127175333	2		521	463	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439240	52439242	+	frameshift_variant	Frame_Shift_Del	DEL	TAG	TAG	AA	novel	NA	P-0019932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	106	762	0	ENST00000460680.1:c.1000_1002delinsTT	p.Val335TrpfsTer2	p.V335Wfs*2	ENST00000460680	NM_004656.3	334	CTA/TT	11/17	0.108944059103885	4	FACETS	1	0.955	1	0.558	0.5	0.618	INDETERMINATE	1	TRUE	2	0.408890127175333	4		762	655	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630365	187630365	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0019932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	39	726	0	ENST00000441802.2:c.617T>A	p.Leu206Ter	p.L206*	ENST00000441802	NM_005245.3	206	tTa/tAa	2/27	0.39919851502613	1	FACETS	0.259	0.214	0.309	0.259	0.214	0.309	SUBCLONAL	1	TRUE	0	0.408890127175333	1		726	587	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21968123	21968238	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	TACGAAAGCGGGGTGGGTTGTGGCGGGGGCAGTTGTGGCCCTGTAGGACCTTCGGTGACTGATGATCTAAGTTTCCCGAGGTTTCTCAGAGCCTCTCTGGTTCTTTCAATCGGGGA	TACGAAAGCGGGGTGGGTTGTGGCGGGGGCAGTTGTGGCCCTGTAGGACCTTCGGTGACTGATGATCTAAGTTTCCCGAGGTTTCTCAGAGCCTCTCTGGTTCTTTCAATCGGGGA	-	novel	NA	P-0019932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	19	165	0	ENST00000304494.5:c.461_*105del		p.*154*	ENST00000304494	NM_000077.4	154		3/3	0.321449998217061	1	FACETS	0.77	0.595	0.968	0.77	0.595	0.968	CLONAL	1	TRUE	0	0.408890127175333	1		165	96	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195091	123195098	+	frameshift_variant	Frame_Shift_Del	DEL	ATACCTTG	ATACCTTG	-	novel	NA	P-0019932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	72	458	0	ENST00000218089.9:c.1434_1441del	p.Tyr479GlyfsTer2	p.Y479Gfs*2	ENST00000218089	NM_001042749.1	478	gcATACCTTGtg/gctg	16/35	0.408890127175333	1	FACETS	0.745	0.655	0.841	0.745	0.655	0.841	SUBCLONAL	1	TRUE	0	0.408890127175333	1		458	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0019934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	733	1151	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.670945419351122	3	FACETS	1	0.987	1			1	CLONAL	3	TRUE	NA	0.670945419351122	3		1151	960	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459167	120459167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746551843	NA	P-0019934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	88	772	0	ENST00000256646.2:c.6178C>T	p.Arg2060Cys	p.R2060C	ENST00000256646	NM_024408.3	2060	Cgc/Tgc	34/34	0.303573434913014	6	FACETS	0.914	0.81	1	0.229	0.202	0.257	INDETERMINATE	1	TRUE	2	0.670945419351122	6		772	672	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742930	17742930	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	33	792	0	ENST00000250003.3:c.839del	p.Pro280ArgfsTer56	p.P280Rfs*56	ENST00000250003	NM_002478.4	280	Ccg/cg	3/3	0.670945419351122	4	FACETS	0.553	0.452	0.667	0.184	0.15	0.223	SUBCLONAL	1	TRUE	1	0.670945419351122	4		792	297	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561258	9561258	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1411277423	NA	P-0019934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	106	628	0	ENST00000353224.5:c.524T>C	p.Met175Thr	p.M175T	ENST00000353224	NM_177990.2	175	aTg/aCg	4/10	0.189170281995984	6	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.670945419351122	6		628	589	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739576	145739576	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1301085885	NA	P-0019934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	42	933	0	ENST00000428558.2:c.1875C>G	p.Cys625Trp	p.C625W	ENST00000428558	NM_004260.3	625	tgC/tgG	11/22	NA	2	FACETS	0.279	0.233	0.33			1	INDETERMINATE	1	TRUE	NA	0.670945419351122	2		933	449	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912113	127912113	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	102	553	1	ENST00000373547.4:c.757G>T	p.Val253Leu	p.V253L	ENST00000373547	NM_002721.4	253	Gtg/Ttg	7/7	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.670945419351122	2		554	272	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	234	352	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.209166077837706	5	FACETS	0.882	0.825	0.941	0.588	0.55	0.628	INDETERMINATE	2	TRUE	2	0.575320195026292	5		352	859	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948136	178948136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	32	486	0	ENST00000263967.3:c.2908G>A	p.Glu970Lys	p.E970K	ENST00000263967	NM_006218.2	970	Gaa/Aaa	20/21	0.209166077837706	5	FACETS	0.334	0.27	0.407	0.111	0.09	0.136	INDETERMINATE	1	TRUE	2	0.575320195026292	5		486	620	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251907	8251907	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773156387	NA	P-0019935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	285	828	6	ENST00000335790.3:c.170G>A	p.Arg57His	p.R57H	ENST00000335790	NM_002315.2	57	cGc/cAc	2/4	0.1314155598677	4	FACETS	0.885	0.834	0.937			1	INDETERMINATE	2	TRUE	NA	0.575320195026292	4		834	882	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577506	64577507	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0019935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	301	636	0	ENST00000312049.6:c.75dup	p.Glu26ArgfsTer91	p.E26Rfs*91	ENST00000312049	NM_130799.2	25	-/C	2/10	NA	2	FACETS	0.931	0.887	0.974			1	INDETERMINATE	2	TRUE	NA	0.575320195026292	2		636	562	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838145	89838145	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	305	774	2	ENST00000389301.3:c.2092G>A	p.Glu698Lys	p.E698K	ENST00000389301	NM_000135.2	698	Gag/Aag	23/43	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.575320195026292	2		776	984	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128028977	128028977	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	157	766	0	ENST00000285398.2:c.1880C>T	p.Ser627Leu	p.S627L	ENST00000285398	NM_000122.1	627	tCa/tTa	12/15	NA	2	FACETS	0.672	0.616	0.731			1	INDETERMINATE	1	TRUE	NA	0.575320195026292	2		766	812	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0019936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	42	549	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.525	0.437	0.624	0.525	0.437	0.624	SUBCLONAL	1	TRUE	1	0.18	2		549	889	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587781525	NA	P-0019936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	106	851	0	ENST00000269305.4:c.842A>T	p.Asp281Val	p.D281V	ENST00000269305	NM_001126112.2	281	gAc/gTc	8/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.18	2		851	903	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044839	47044839	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0019936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	74	815	0	ENST00000377604.3:c.2167-2A>G		p.X723_splice	ENST00000377604	NM_001204468.1	723			1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.18	2		815	752	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039519	180039519	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1426017403	NA	P-0019936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	46	848	0	ENST00000261937.6:c.3524G>T	p.Gly1175Val	p.G1175V	ENST00000261937	NM_182925.4	1175	gGc/gTc	26/30	1	2	FACETS	0.668	0.561	0.787	0.668	0.561	0.787	SUBCLONAL	1	TRUE	1	0.18	2		848	765	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612736	228612736	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	106	749	1	ENST00000366696.1:c.291C>A	p.Cys97Ter	p.C97*	ENST00000366696	NM_003493.2	97	tgC/tgA	1/1	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.18	2		750	886	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194173	94194173	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1186737287	NA	P-0019936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	34	663	0	ENST00000323929.3:c.1255A>G	p.Thr419Ala	p.T419A	ENST00000323929	NM_005591.3	419	Aca/Gca	12/20	1	2	FACETS	0.625	0.51	0.756	0.625	0.51	0.756	SUBCLONAL	1	TRUE	1	0.18	2		663	604	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934644	9934644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1331671132	NA	P-0019936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	42	426	0	ENST00000330684.3:c.1511G>A	p.Arg504Gln	p.R504Q	ENST00000330684	NM_001134407.1	504	cGg/cAg	7/13	1	2	FACETS	0.871	0.726	1	0.871	0.726	1	CLONAL	1	TRUE	1	0.18	2		426	536	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515587	31515588	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0019936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	34	552	1	ENST00000344624.3:c.1031_1032delinsTT	p.Trp344Phe	p.W344F	ENST00000344624		344	tGG/tTT	4/33	1	2	FACETS	0.827	0.675	0.997	0.827	0.675	0.997	CLONAL	1	TRUE	1	0.18	2		553	457	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763855	76763855	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	57	779	2	ENST00000373344.5:c.7453G>T	p.Gly2485Ter	p.G2485*	ENST00000373344	NM_000489.3	2485	Gga/Tga	35/35	1	2	FACETS	0.905	0.775	1	0.905	0.775	1	CLONAL	1	TRUE	1	0.18	2		781	700	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907777	76907777	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	67	451	1	ENST00000373344.5:c.4384G>T	p.Glu1462Ter	p.E1462*	ENST00000373344	NM_000489.3	1462	Gag/Tag	15/35	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.18	2		452	522	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	304	501	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.299039613703046	0	FACETS	0.577	0.548	0.607			1	INDETERMINATE	1	TRUE	0	0.6	0		501	702	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	186	482	0	ENST00000256196.4:c.68G>A	p.Gly23Asp	p.G23D	ENST00000256196		23	gGc/gAc	1/6	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.6	2		482	578	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16247407	16247407	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	49	489	0	ENST00000375759.3:c.1678A>G	p.Asn560Asp	p.N560D	ENST00000375759	NM_015001.2	560	Aat/Gat	9/15	0.284501164089216	1	FACETS	0.201	0.17	0.235	0.201	0.17	0.235	INDETERMINATE	1	TRUE	0	0.6	1		489	569	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258803	16258803	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	275	765	0	ENST00000375759.3:c.6068T>C	p.Val2023Ala	p.V2023A	ENST00000375759	NM_015001.2	2023	gTg/gCg	11/15	0.284501164089216	1	FACETS	0.815	0.769	0.863	0.815	0.769	0.863	INDETERMINATE	1	TRUE	0	0.6	1		765	787	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259043	16259043	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	258	725	0	ENST00000375759.3:c.6313del	p.Ala2105LeufsTer33	p.A2105Lfs*33	ENST00000375759	NM_015001.2	2103	aGg/ag	11/15	0.284501164089216	1	FACETS	0.786	0.739	0.834	0.786	0.739	0.834	INDETERMINATE	1	TRUE	0	0.6	1		725	766	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36824388	36824388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	263	717	0	ENST00000373129.3:c.148G>A	p.Val50Met	p.V50M	ENST00000373129	NM_032017.1	50	Gtg/Atg	4/12	1	2	FACETS	0.864	0.81	0.919	0.864	0.81	0.919	CLONAL	1	TRUE	1	0.6	2		717	1015	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	193	640	2	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.946	0.879	1	0.946	0.879	1	CLONAL	1	TRUE	1	0.6	2		642	680	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444659	78444659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs908264837	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	197	482	2	ENST00000370768.2:c.30del	p.Ser11LeufsTer43	p.S11Lfs*43	ENST00000370768	NM_003902.3	10	ccC/cc	1/20	1	2	FACETS	0.986	0.917	1	0.986	0.917	1	CLONAL	1	TRUE	1	0.6	2		484	666	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165717	118165718	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	166	390	1	ENST00000369448.3:c.228dup	p.Gly77TrpfsTer33	p.G77Wfs*33	ENST00000369448	NM_017709.3	76	gct/gcTt	2/2	1	2	FACETS	0.985	0.91	1	0.985	0.91	1	CLONAL	1	TRUE	1	0.6	2		391	562	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483219	120483219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782077143	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	102	558	2	ENST00000256646.2:c.3142C>T	p.Arg1048Cys	p.R1048C	ENST00000256646	NM_024408.3	1048	Cgc/Tgc	19/34	1	2	FACETS	0.482	0.431	0.536	0.482	0.431	0.536	SUBCLONAL	1	TRUE	1	0.6	2		560	705	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741813	162741813	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	183	391	1	ENST00000367921.3:c.1505-1G>T		p.X502_splice	ENST00000367921	NM_006182.2	502			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.6	2		392	526	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828126	243828126	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	300	671	3	ENST00000263826.5:c.232C>A	p.Gln78Lys	p.Q78K	ENST00000263826	NM_005465.4	78	Cag/Aag	3/13	1	2	FACETS	0.998	0.941	1	0.998	0.941	1	CLONAL	1	TRUE	1	0.6	2		674	1002	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596120	43596120	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	262	796	0	ENST00000355710.3:c.287A>G	p.Tyr96Cys	p.Y96C	ENST00000355710	NM_020975.4	96	tAc/tGc	2/20	1	2	FACETS	0.917	0.861	0.975	0.917	0.861	0.975	CLONAL	1	TRUE	1	0.6	2		796	952	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710595	114710597	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs754968616	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	206	718	0	ENST00000543371.1:c.85_87del	p.Glu29del	p.E29del	ENST00000543371	NM_001198531.1	27	cAGGag/cag	1/14	1	2	FACETS	0.787	0.731	0.844	0.787	0.731	0.844	SUBCLONAL	1	TRUE	1	0.6	2		718	873	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343660	118343660	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	44	543	0	ENST00000534358.1:c.1790del	p.Leu597CysfsTer26	p.L597Cfs*26	ENST00000534358	NM_005933.3	596	Ttt/tt	3/36	1	2	FACETS	0.207	0.173	0.246	0.207	0.173	0.246	SUBCLONAL	1	TRUE	1	0.6	2		543	707	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373430	118373430	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	183	539	0	ENST00000534358.1:c.6823A>G	p.Thr2275Ala	p.T2275A	ENST00000534358	NM_005933.3	2275	Act/Gct	27/36	1	2	FACETS	0.879	0.814	0.946	0.879	0.814	0.946	CLONAL	1	TRUE	1	0.6	2		539	694	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125523663	125523663	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	121	619	0	ENST00000428830.2:c.1256G>T	p.Arg419Met	p.R419M	ENST00000428830	NM_001114121.2	419	aGg/aTg	12/14	1	2	FACETS	0.485	0.438	0.535	0.485	0.438	0.535	SUBCLONAL	1	TRUE	1	0.6	2		619	831	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	209	473	7	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	0.973	1	CLONAL	1	TRUE	1	0.6	2		480	645	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	211	739	11	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.795	0.739	0.852	0.795	0.739	0.852	SUBCLONAL	1	TRUE	1	0.6	2		750	885	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420208	49420208	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	314	854	0	ENST00000301067.7:c.15541G>T	p.Gly5181Trp	p.G5181W	ENST00000301067	NM_003482.3	5181	Ggg/Tgg	48/54	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.6	2		854	966	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432243	49432243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs970105771	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	355	891	3	ENST00000301067.7:c.8896C>T	p.Arg2966Trp	p.R2966W	ENST00000301067	NM_003482.3	2966	Cgg/Tgg	34/54	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.6	2		894	1173	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443482	49443482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746084513	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	216	525	0	ENST00000301067.7:c.3889C>T	p.Arg1297Cys	p.R1297C	ENST00000301067	NM_003482.3	1297	Cgt/Tgt	11/54	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.6	2		525	694	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800902	120800903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs748469666	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	344	828	3	ENST00000257552.2:c.345dup	p.Leu116AlafsTer15	p.L116Afs*15	ENST00000257552	NM_002442.3	115	-/G	6/15	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.6	2		831	1142	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426790	121426790	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201095611	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	283	807	2	ENST00000257555.6:c.481G>A	p.Ala161Thr	p.A161T	ENST00000257555		161	Gcc/Acc	2/10	1	2	FACETS	0.984	0.926	1	0.984	0.926	1	CLONAL	1	TRUE	1	0.6	2		809	959	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202290	133202290	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752113614	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	321	839	0	ENST00000320574.5:c.6598G>A	p.Glu2200Lys	p.E2200K	ENST00000320574	NM_006231.2	2200	Gag/Aag	47/49	1	2	FACETS	0.985	0.931	1	0.985	0.931	1	CLONAL	1	TRUE	1	0.6	2		839	1086	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434967	110434967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	343	1007	4	ENST00000375856.3:c.3434G>A	p.Arg1145His	p.R1145H	ENST00000375856	NM_003749.2	1145	cGc/cAc	1/2	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.6	2		1011	1121	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435136	110435136	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs780127725	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	150	834	0	ENST00000375856.3:c.3265G>C	p.Ala1089Pro	p.A1089P	ENST00000375856	NM_003749.2	1089	Gcc/Ccc	1/2	1	2	FACETS	0.486	0.444	0.531	0.486	0.444	0.531	SUBCLONAL	1	TRUE	1	0.6	2		834	1028	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30098266	30098266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	148	760	2	ENST00000331968.5:c.1706G>A	p.Cys569Tyr	p.C569Y	ENST00000331968	NM_002742.2	569	tGc/tAc	11/18	1	2	FACETS	0.479	0.437	0.524	0.479	0.437	0.524	SUBCLONAL	1	TRUE	1	0.6	2		762	1029	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061249	38061249	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	283	801	0	ENST00000250448.2:c.740A>G	p.His247Arg	p.H247R	ENST00000250448	NM_004496.3	247	cAc/cGc	2/2	1	2	FACETS	0.846	0.795	0.898	0.846	0.795	0.898	CLONAL	1	TRUE	1	0.6	2		801	1115	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353890	68353890	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	282	637	0	ENST00000487270.1:c.725T>C	p.Leu242Ser	p.L242S	ENST00000487270	NM_133509.3	242	tTg/tCg	7/11	1	2	FACETS	0.986	0.929	1	0.986	0.929	1	CLONAL	1	TRUE	1	0.6	2		637	953	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609807	81609807	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	157	406	1	ENST00000298171.2:c.1405C>A	p.Leu469Ile	p.L469I	ENST00000298171	NM_000369.2	469	Ctc/Atc	10/10	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.6	2		407	498	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643578	38643578	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	270	719	2	ENST00000299084.4:c.1048G>T	p.Gly350Ter	p.G350*	ENST00000299084	NM_152594.2	350	Gga/Tga	7/7	1	2	FACETS	0.952	0.895	1	0.952	0.895	1	CLONAL	1	TRUE	1	0.6	2		721	945	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	316	1005	5	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	1	2	FACETS	0.83	0.783	0.879	0.83	0.783	0.879	CLONAL	1	TRUE	1	0.6	2		1010	1269	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122886	2122886	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs574205203	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	150	845	0	ENST00000219476.3:c.2257G>A	p.Ala753Thr	p.A753T	ENST00000219476	NM_000548.3	753	Gcc/Acc	21/42	1	2	FACETS	0.491	0.448	0.536	0.491	0.448	0.536	SUBCLONAL	1	TRUE	1	0.6	2		845	1019	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223214	2223214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1386833224	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	312	823	0	ENST00000326181.6:c.826G>A	p.Glu276Lys	p.E276K	ENST00000326181	NM_032271.2	276	Gag/Aag	10/21	1	2	FACETS	0.951	0.897	1	0.951	0.897	1	CLONAL	1	TRUE	1	0.6	2		823	1094	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3634851	3634853	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	rs760517738	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	292	826	0	ENST00000294008.3:c.4656_4658del	p.Lys1552del	p.K1552del	ENST00000294008	NM_032444.2	1552	aaGAAc/aac	13/15	1	2	FACETS	0.948	0.893	1	0.948	0.893	1	CLONAL	1	TRUE	1	0.6	2		826	1027	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639726	3639726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763524714	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	401	1095	3	ENST00000294008.3:c.3913G>A	p.Ala1305Thr	p.A1305T	ENST00000294008	NM_032444.2	1305	Gca/Aca	12/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.6	2		1098	1234	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828768	3828768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	309	752	1	ENST00000262367.5:c.1874G>A	p.Arg625His	p.R625H	ENST00000262367	NM_004380.2	625	cGc/cAc	9/31	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.6	2		753	1008	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671655	67671655	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1400980130	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	233	716	1	ENST00000264010.4:c.2070del	p.Glu691SerfsTer30	p.E691Sfs*30	ENST00000264010	NM_006565.3	688	gtA/gt	12/12	1	2	FACETS	0.839	0.783	0.896	0.839	0.783	0.896	CLONAL	1	TRUE	1	0.6	2		717	926	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821938	72821938	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	60	326	2	ENST00000268489.5:c.10237G>A	p.Asp3413Asn	p.D3413N	ENST00000268489	NM_006885.3	3413	Gac/Aac	10/10	0.228532481338425	3	FACETS	0.587	0.507	0.674			1	INDETERMINATE	1	TRUE	NA	0.6	3		328	443	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827702	72827702	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	317	581	1	ENST00000268489.5:c.8879T>A	p.Val2960Asp	p.V2960D	ENST00000268489	NM_006885.3	2960	gTc/gAc	9/10	0.228532481338425	3	FACETS	0.834	0.79	0.878			1	INDETERMINATE	2	TRUE	NA	0.6	3		582	824	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	175	482	4	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	0.228532481338425	3	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.6	3		486	667	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346157	89346158	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs878855327	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	25	275	0	ENST00000301030.4:c.6792dup	p.Ala2265ArgfsTer8	p.A2265Rfs*8	ENST00000301030	NM_001256183.1	2264	-/C	9/13	1	2	FACETS	0.244	0.192	0.303	0.244	0.192	0.303	SUBCLONAL	1	TRUE	1	0.6	2		275	342	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347752	89347752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148243995	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	55	678	0	ENST00000301030.4:c.5198C>T	p.Ala1733Val	p.A1733V	ENST00000301030	NM_001256183.1	1733	gCg/gTg	9/13	1	2	FACETS	0.236	0.201	0.275	0.236	0.201	0.275	SUBCLONAL	1	TRUE	1	0.6	2		678	776	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216380	7216380	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	262	725	1	ENST00000380728.2:c.868del	p.Gln290SerfsTer55	p.Q290Sfs*55	ENST00000380728		290	Cag/ag	10/11	0.299039613703046	0	FACETS	0.552	0.521	0.583			1	INDETERMINATE	1	TRUE	0	0.6	0		726	633	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	250	609	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	0.299039613703046	0	FACETS	0.613	0.579	0.647			1	INDETERMINATE	1	TRUE	0	0.6	0		609	544	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686901	37686901	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	128	588	0	ENST00000447079.4:c.3810del	p.Gly1271AspfsTer23	p.G1271Dfs*23	ENST00000447079	NM_015083.1	1269	Ccc/cc	14/14	1	2	FACETS	0.579	0.525	0.636	0.579	0.525	0.636	SUBCLONAL	1	TRUE	1	0.6	2		588	737	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244070	41244070	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	47	686	0	ENST00000357654.3:c.3478A>G	p.Lys1160Glu	p.K1160E	ENST00000357654	NM_007294.3	1160	Aag/Gag	10/23	1	2	FACETS	0.183	0.153	0.215	0.183	0.153	0.215	SUBCLONAL	1	TRUE	1	0.6	2		686	858	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	246	752	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.897	0.84	0.956	0.897	0.84	0.956	CLONAL	1	TRUE	1	0.6	2		755	914	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435233	56435234	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	263	753	0	ENST00000407977.2:c.1903dup	p.Ser635LysfsTer112	p.S635Kfs*112	ENST00000407977		635	agt/aAgt	9/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.6	2		753	850	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440757	56440757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774211426	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	211	533	0	ENST00000407977.2:c.461C>T	p.Pro154Leu	p.P154L	ENST00000407977		154	cCg/cTg	5/10	1	2	FACETS	0.995	0.928	1	0.995	0.928	1	CLONAL	1	TRUE	1	0.6	2		533	707	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62009590	62009590	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	179	859	0	ENST00000392795.3:c.32G>A	p.Ser11Asn	p.S11N	ENST00000392795	NM_001039933.1	11	aGc/aAc	1/6	1	2	FACETS	0.542	0.499	0.588	0.542	0.499	0.588	SUBCLONAL	1	TRUE	1	0.6	2		859	1100	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119010	70119010	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	309	914	0	ENST00000245479.2:c.582G>T	p.Glu194Asp	p.E194D	ENST00000245479	NM_000346.3	194	gaG/gaT	2/3	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.6	2		914	1022	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78931487	78931487	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	275	851	1	ENST00000306801.3:c.3434G>A	p.Arg1145Gln	p.R1145Q	ENST00000306801	NM_020761.2	1145	cGg/cAg	29/34	1	2	FACETS	0.962	0.904	1	0.962	0.904	1	CLONAL	1	TRUE	1	0.6	2		852	953	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619821	1619821	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	319	939	0	ENST00000344749.5:c.1125del	p.Gly376ValfsTer18	p.G376Vfs*18	ENST00000344749	NM_001136139.2	375	ccC/cc	14/19	1	2	FACETS	0.915	0.864	0.968	0.915	0.864	0.968	CLONAL	1	TRUE	1	0.6	2		939	1162	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226589	2226589	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760808115	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	159	891	4	ENST00000398665.3:c.4069C>T	p.Arg1357Cys	p.R1357C	ENST00000398665	NM_032482.2	1357	Cgc/Tgc	27/28	1	2	FACETS	0.497	0.454	0.541	0.497	0.454	0.541	SUBCLONAL	1	TRUE	1	0.6	2		895	1067	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210704	5210704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766174955	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	265	754	0	ENST00000357368.4:c.5347C>T	p.Arg1783Trp	p.R1783W	ENST00000357368	NM_002850.3	1783	Cgg/Tgg	34/38	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.6	2		754	869	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274304	5274304	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	305	775	6	ENST00000357368.4:c.143del	p.Gly48ValfsTer17	p.G48Vfs*17	ENST00000357368	NM_002850.3	48	gGt/gt	3/38	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.6	2		781	989	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599970	10599970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749651891	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	346	865	1	ENST00000171111.5:c.1606C>T	p.Arg536Cys	p.R536C	ENST00000171111	NM_203500.1	536	Cgc/Tgc	5/6	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.6	2		866	1134	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107001	11107001	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1050237	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	146	686	4	ENST00000358026.2:c.1706G>A	p.Arg569Gln	p.R569Q	ENST00000358026	NM_001128849.1	569	cGg/cAg	10/36	1	2	FACETS	0.537	0.489	0.586	0.537	0.489	0.586	SUBCLONAL	1	TRUE	1	0.6	2		690	907	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295828	15295828	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs532100840	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	329	964	1	ENST00000263388.2:c.2299C>T	p.Arg767Cys	p.R767C	ENST00000263388	NM_000435.2	767	Cgt/Tgt	15/33	1	2	FACETS	0.969	0.916	1	0.969	0.916	1	CLONAL	1	TRUE	1	0.6	2		965	1132	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303200	15303200	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775836288	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	311	989	1	ENST00000263388.2:c.328C>T	p.Arg110Cys	p.R110C	ENST00000263388	NM_000435.2	110	Cgt/Tgt	3/33	1	2	FACETS	0.961	0.907	1	0.961	0.907	1	CLONAL	1	TRUE	1	0.6	2		990	1079	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216189	36216189	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	125	760	2	ENST00000222270.7:c.3602del	p.Pro1201ArgfsTer154	p.P1201Rfs*154	ENST00000222270	NM_014727.1	1199	ggC/gg	11/37	1	2	FACETS	0.492	0.445	0.542	0.492	0.445	0.542	SUBCLONAL	1	TRUE	1	0.6	2		762	847	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40745977	40745977	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	294	797	0	ENST00000392038.2:c.614A>G	p.Gln205Arg	p.Q205R	ENST00000392038	NM_001626.4	205	cAg/cGg	7/14	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.6	2		797	963	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752788	42752789	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	282	960	0	ENST00000222329.4:c.1475_1476del	p.Cys492SerfsTer13	p.C492Sfs*13	ENST00000222329	NM_006494.2	492	tGT/t	4/4	1	2	FACETS	0.903	0.849	0.958	0.903	0.849	0.958	CLONAL	1	TRUE	1	0.6	2		960	1041	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	303	1043	2	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.88	0.829	0.932	0.88	0.829	0.932	CLONAL	1	TRUE	1	0.6	2		1045	1148	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753887	42753887	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	293	920	0	ENST00000222329.4:c.377del	p.Gly126ValfsTer145	p.G126Vfs*145	ENST00000222329	NM_006494.2	126	gGt/gt	4/4	1	2	FACETS	0.887	0.835	0.94	0.887	0.835	0.94	CLONAL	1	TRUE	1	0.6	2		920	1101	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716250	52716250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769334090	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	235	691	1	ENST00000322088.6:c.694G>A	p.Ala232Thr	p.A232T	ENST00000322088	NM_014225.5	232	Gcc/Acc	6/15	1	2	FACETS	0.928	0.868	0.99	0.928	0.868	0.99	CLONAL	1	TRUE	1	0.6	2		692	844	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086094	16086094	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	115	830	3	ENST00000281043.3:c.1274del	p.Lys425ArgfsTer31	p.K425Rfs*31	ENST00000281043	NM_005378.4	424	Aaa/aa	3/3	0.299039613703046	1	FACETS	0.32	0.288	0.354	0.32	0.288	0.354	INDETERMINATE	1	TRUE	0	0.6	1		833	839	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416200	29416200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	128	656	0	ENST00000389048.3:c.4753G>A	p.Gly1585Ser	p.G1585S	ENST00000389048	NM_004304.4	1585	Ggc/Agc	29/29	0.299039613703046	1	FACETS	0.413	0.374	0.453	0.413	0.374	0.453	INDETERMINATE	1	TRUE	0	0.6	1		656	724	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919691	96919691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200327514	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	99	554	0	ENST00000258439.3:c.572C>T	p.Thr191Met	p.T191M	ENST00000258439	NM_001193304.2	191	aCg/aTg	4/4	0.202767522361204	2	FACETS	0.549	0.491	0.611	0.275	0.245	0.306	INDETERMINATE	1	TRUE	0	0.6	2		554	601	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204737495	204737495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	126	698	3	ENST00000302823.3:c.632G>A	p.Cys211Tyr	p.C211Y	ENST00000302823	NM_005214.4	211	tGt/tAt	4/4	0.299039613703046	2	FACETS	0.456	0.412	0.502	0.228	0.206	0.251	INDETERMINATE	1	TRUE	0	0.6	2		701	922	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251644	212251644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368679346	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	285	494	0	ENST00000342788.4:c.3415C>T	p.Arg1139Trp	p.R1139W	ENST00000342788	NM_005235.2	1139	Cgg/Tgg	27/28	0.299039613703046	2	FACETS	0.788	0.747	0.828	0.788	0.747	0.828	INDETERMINATE	2	TRUE	0	0.6	2		494	603	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39745000	39745000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	144	740	0	ENST00000361337.2:c.1790C>T	p.Thr597Met	p.T597M	ENST00000361337	NM_003286.2	597	aCg/aTg	17/21	1	2	FACETS	0.472	0.43	0.517	0.472	0.43	0.517	SUBCLONAL	1	TRUE	1	0.6	2		740	1016	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265178	46265178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1202360619	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	205	448	1	ENST00000371998.3:c.2048G>A	p.Arg683Gln	p.R683Q	ENST00000371998		683	cGg/cAg	12/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.6	2		449	639	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852493	42852493	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	301	879	0	ENST00000398585.3:c.593A>G	p.Tyr198Cys	p.Y198C	ENST00000398585	NM_001135099.1	198	tAc/tGc	6/14	1	2	FACETS	0.951	0.897	1	0.951	0.897	1	CLONAL	1	TRUE	1	0.6	2		879	1055	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274897	41274897	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	106	628	0	ENST00000349496.5:c.1147T>C	p.Trp383Arg	p.W383R	ENST00000349496	NM_001904.3	383	Tgg/Cgg	8/15	1	2	FACETS	0.443	0.397	0.492	0.443	0.397	0.492	SUBCLONAL	1	TRUE	1	0.6	2		628	797	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058596	47058596	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	253	668	0	ENST00000409792.3:c.7682C>T	p.Thr2561Ile	p.T2561I	ENST00000409792	NM_014159.6	2561	aCt/aTt	21/21	1	2	FACETS	0.978	0.918	1	0.978	0.918	1	CLONAL	1	TRUE	1	0.6	2		668	862	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440912	52440912	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1205668341	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	284	686	0	ENST00000460680.1:c.592del	p.Glu198ArgfsTer33	p.E198Rfs*33	ENST00000460680	NM_004656.3	198	Gag/ag	8/17	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.6	2		686	911	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682399	52682400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	217	779	0	ENST00000394830.3:c.773dup	p.Asn258LysfsTer6	p.N258Kfs*6	ENST00000394830	NM_018313.4	258	aat/aaAt	8/30	1	2	FACETS	0.868	0.809	0.929	0.868	0.809	0.929	CLONAL	1	TRUE	1	0.6	2		779	833	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427721	72427721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1382885623	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	161	604	0	ENST00000477973.2:c.769G>A	p.Val257Ile	p.V257I	ENST00000477973	NM_012234.5	257	Gtc/Atc	4/4	1	2	FACETS	0.957	0.882	1	0.957	0.882	1	CLONAL	1	TRUE	1	0.6	2		604	561	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200004	128200004	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	146	786	0	ENST00000341105.2:c.1301C>T	p.Ala434Val	p.A434V	ENST00000341105	NM_032638.4	434	gCt/gTt	6/6	1	2	FACETS	0.495	0.451	0.541	0.495	0.451	0.541	SUBCLONAL	1	TRUE	1	0.6	2		786	983	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440320	187440320	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1230004461	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	132	599	0	ENST00000232014.4:c.2047G>A	p.Ala683Thr	p.A683T	ENST00000232014	NM_001130845.1	683	Gcc/Acc	10/10	0.284501164089216	1	FACETS	0.466	0.424	0.51	0.466	0.424	0.51	INDETERMINATE	1	TRUE	0	0.6	1		599	661	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1795713	1795713	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	139	314	0	ENST00000260795.2:c.52G>C	p.Ala18Pro	p.A18P	ENST00000260795		18	Gcc/Ccc	1/17	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.6	2		314	402	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383944	84383944	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	120	701	1	ENST00000321945.7:c.908del	p.Asn303IlefsTer17	p.N303Ifs*17	ENST00000321945	NM_139076.2	303	aAt/at	9/9	0.299039613703046	0	FACETS	0.247	0.223	0.272			1	INDETERMINATE	1	TRUE	0	0.6	0		702	647	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589576	67589576	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1289537429	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	163	523	0	ENST00000274335.5:c.1344del	p.Lys448AsnfsTer32	p.K448Nfs*32	ENST00000274335		447	Aaa/aa	10/15	1	2	FACETS	0.838	0.772	0.907	0.838	0.772	0.907	CLONAL	1	TRUE	1	0.6	2		523	648	SUCCESS
APC	324	MSKCC	GRCh37	5	112157674	112157674	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	93	521	0	ENST00000257430.4:c.1394C>T	p.Ala465Val	p.A465V	ENST00000257430	NM_000038.5	465	gCa/gTa	11/16	1	2	FACETS	0.452	0.402	0.505	0.452	0.402	0.505	SUBCLONAL	1	TRUE	1	0.6	2		521	686	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433707	149433707	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	269	702	1	ENST00000286301.3:c.2844T>A	p.Ser948Arg	p.S948R	ENST00000286301	NM_005211.3	948	agT/agA	22/22	1	2	FACETS	0.959	0.901	1	0.959	0.901	1	CLONAL	1	TRUE	1	0.6	2		703	935	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638357	176638357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	88	776	3	ENST00000439151.2:c.2957C>T	p.Ala986Val	p.A986V	ENST00000439151	NM_022455.4	986	gCa/gTa	5/23	1	2	FACETS	0.315	0.278	0.355	0.315	0.278	0.355	SUBCLONAL	1	TRUE	1	0.6	2		779	931	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675287	176675287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	97	482	2	ENST00000439151.2:c.4603C>T	p.Arg1535Cys	p.R1535C	ENST00000439151	NM_022455.4	1535	Cgc/Tgc	11/23	1	2	FACETS	0.508	0.454	0.567	0.508	0.454	0.567	SUBCLONAL	1	TRUE	1	0.6	2		484	636	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393366	393366	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	43	419	0	ENST00000380956.4:c.214A>G	p.Lys72Glu	p.K72E	ENST00000380956	NM_001195286.1	72	Aag/Gag	2/9	NA	2	FACETS	0.243	0.202	0.287			1	INDETERMINATE	1	TRUE	NA	0.6	2		419	591	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840030	27840030	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	164	493	1	ENST00000328488.2:c.64G>A	p.Ala22Thr	p.A22T	ENST00000328488	NM_003533.2	22	Gcc/Acc	1/1	1	2	FACETS	0.947	0.874	1	0.947	0.874	1	CLONAL	1	TRUE	1	0.6	2		494	577	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821580	32821582	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs1357362490	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	290	863	0	ENST00000354258.4:c.12_14del	p.Leu5del	p.L5del	ENST00000354258	NM_000593.5	4	ctTCTc/ctc	1/11	1	2	FACETS	0.931	0.877	0.987	0.931	0.877	0.987	CLONAL	1	TRUE	1	0.6	2		863	1038	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202351	138202351	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	105	729	0	ENST00000237289.4:c.2274del	p.Lys759SerfsTer57	p.K759Sfs*57	ENST00000237289	NM_001270507.1	756	gaC/ga	9/9	1	2	FACETS	0.436	0.391	0.485	0.436	0.391	0.485	SUBCLONAL	1	TRUE	1	0.6	2		729	802	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527705	157527705	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	232	672	1	ENST00000346085.5:c.5430G>T	p.Gln1810His	p.Q1810H	ENST00000346085	NM_020732.3	1810	caG/caT	20/20	1	2	FACETS	0.965	0.903	1	0.965	0.903	1	CLONAL	1	TRUE	1	0.6	2		673	801	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527931	157527931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	243	738	0	ENST00000346085.5:c.5659del	p.Ala1887HisfsTer87	p.A1887Hfs*87	ENST00000346085	NM_020732.3	1886	Ggg/gg	20/20	1	2	FACETS	0.965	0.904	1	0.965	0.904	1	CLONAL	1	TRUE	1	0.6	2		738	839	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683680	162683680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373593750	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	225	605	1	ENST00000366898.1:c.289C>T	p.Arg97Trp	p.R97W	ENST00000366898	NM_004562.2	97	Cgg/Tgg	3/12	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.6	2		606	733	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026652	6026653	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1345	214	1138	0	ENST00000265849.7:c.1743dup	p.Glu582ArgfsTer8	p.E582Rfs*8	ENST00000265849	NM_000535.5	581	-/A	11/15	1	2	FACETS	0.458	0.424	0.493	0.458	0.424	0.493	SUBCLONAL	1	TRUE	1	0.6	2		1138	1559	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13949307	13949307	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	75	407	0	ENST00000405192.2:c.821del	p.Gly274AlafsTer46	p.G274Afs*46	ENST00000405192	NM_001163147.1	274	gGc/gc	9/12	1	2	FACETS	0.455	0.399	0.514	0.455	0.399	0.514	SUBCLONAL	1	TRUE	1	0.6	2		407	550	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852282	128852282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1425442829	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	121	735	1	ENST00000249373.3:c.2354C>T	p.Ser785Leu	p.S785L	ENST00000249373	NM_005631.4	785	tCg/tTg	12/12	1	2	FACETS	0.448	0.404	0.494	0.448	0.404	0.494	SUBCLONAL	1	TRUE	1	0.6	2		736	901	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891109	151891109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269387429	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	172	425	2	ENST00000262189.6:c.4645C>T	p.Pro1549Ser	p.P1549S	ENST00000262189	NM_170606.2	1549	Cca/Tca	31/59	1	2	FACETS	0.982	0.908	1	0.982	0.908	1	CLONAL	1	TRUE	1	0.6	2		427	584	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74868172	74868172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1563677151	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	51	156	0	ENST00000284811.8:c.122C>T	p.Thr41Met	p.T41M	ENST00000284811		41	aCg/aTg	3/4	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.6	2		156	163	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542687	141542687	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1435049396	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	318	788	1	ENST00000220592.5:c.2299G>A	p.Val767Ile	p.V767I	ENST00000220592	NM_012154.3	767	Gtc/Atc	18/19	0.299039613703046	1	FACETS	0.806	0.762	0.85	0.806	0.762	0.85	INDETERMINATE	1	TRUE	0	0.6	1		789	921	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737551	145737551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773856131	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	328	746	1	ENST00000428558.2:c.3212G>A	p.Arg1071His	p.R1071H	ENST00000428558	NM_004260.3	1071	cGc/cAc	19/22	0.299039613703046	1	FACETS	0.909	0.863	0.956	0.909	0.863	0.956	INDETERMINATE	1	TRUE	0	0.6	1		747	842	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639911	93639911	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	79	421	0	ENST00000375746.1:c.1240A>G	p.Lys414Glu	p.K414E	ENST00000375746	NM_001174167.1	414	Aaa/Gaa	10/14	0.299039613703046	1	FACETS	0.389	0.343	0.438	0.389	0.343	0.438	INDETERMINATE	1	TRUE	0	0.6	1		421	474	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937164	39937164	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	174	444	1	ENST00000378444.4:c.19del	p.Leu7CysfsTer9	p.L7Cfs*9	ENST00000378444	NM_001123385.1	7	Ctg/tg	2/15	1	1	FACETS	0.643	0.595	0.694	0.643	0.595	0.694	SUBCLONAL	1	TRUE	0	0.6	1		445	631	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949134	44949134	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	40	342	0	ENST00000377967.4:c.3695G>A	p.Gly1232Asp	p.G1232D	ENST00000377967	NM_021140.2	1232	gGc/gAc	25/29	1	1	FACETS	0.225	0.187	0.268	0.225	0.187	0.268	SUBCLONAL	1	TRUE	0	0.6	1		342	414	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441499	6441499	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	41	290	0	ENST00000356142.4:c.346T>C	p.Trp116Arg	p.W116R	ENST00000356142	NM_018890.3	116	Tgg/Cgg	6/7	1	2	FACETS	0.432	0.361	0.511	0.432	0.361	0.511	SUBCLONAL	1	TRUE	1	0.6	2		290	316	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541542	29541542	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137854557	NA	P-0019940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	21	735	0	ENST00000356175.3:c.1466A>G	p.Tyr489Cys	p.Y489C	ENST00000356175	NM_000267.3	489	tAt/tGt	13/57	0.632147051391796	2	FACETS	0.266	0.205	0.337	0.133	0.102	0.169	SUBCLONAL	1	TRUE	0	0.641956128151774	2		735	246	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579310	7579310	+	splice_donor_variant	Splice_Site	SNP	A	A	T	rs1555526469	NA	P-0019940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	371	534	0	ENST00000269305.4:c.375+2T>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.632147051391796	2	FACETS	0.938	0.901	0.975	0.938	0.901	0.975	CLONAL	2	TRUE	0	0.641956128151774	2		534	616	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257881	19257881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	335	850	0	ENST00000162023.5:c.505C>T	p.Pro169Ser	p.P169S	ENST00000162023		169	Ccc/Tcc	9/13	0.641956128151774	3	FACETS	1	0.989	1	0.587	0.555	0.619	CLONAL	1	TRUE	1	0.641956128151774	3		850	1175	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650334	12650334	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876657969	NA	P-0019940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	382	676	0	ENST00000251849.4:c.512A>G	p.Lys171Arg	p.K171R	ENST00000251849	NM_002880.3	171	aAa/aGa	5/17	0.63902437155964	3	FACETS	0.905	0.863	0.946	0.905	0.863	0.946	CLONAL	2	TRUE	1	0.641956128151774	3		676	869	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957038	1957038	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019943-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	401	894	0	ENST00000382891.5:c.2489A>G	p.Asn830Ser	p.N830S	ENST00000382891	NM_133335.3	830	aAc/aGc	13/22	0.614905866004318	4	FACETS	0.953	0.908	0.998	0.953	0.908	0.998	CLONAL	2	TRUE	2	0.638200838100778	4		894	1080	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938805	76938805	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019943-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	397	1105	1	ENST00000373344.5:c.1943del	p.Leu648Ter	p.L648*	ENST00000373344	NM_000489.3	648	tTa/ta	9/35	0.605546896977591	3	FACETS	0.944	0.903	0.986	0.944	0.903	0.986	CLONAL	2	TRUE	1	0.638200838100778	3		1106	869	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	178	352	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	0.503172872381264	2		352	657	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0019945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	210	466	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.503172872381264	2		467	733	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865726	57865726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144893788	NA	P-0019945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	190	907	0	ENST00000228682.2:c.3203G>A	p.Arg1068Gln	p.R1068Q	ENST00000228682	NM_005269.2	1068	cGg/cAg	12/12	1	2	FACETS	0.835	0.773	0.9	0.835	0.773	0.9	CLONAL	1	TRUE	1	0.503172872381264	2		907	904	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182028	38182028	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	185	635	0	ENST00000396334.3:c.652T>G	p.Trp218Gly	p.W218G	ENST00000396334	NM_002468.4	218	Tgg/Ggg	3/5	0.503172872381264	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.503172872381264	1		635	547	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	56	553	2	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	0.234442025358869	2		555	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	66	872	0	ENST00000269305.4:c.380C>A	p.Ser127Tyr	p.S127Y	ENST00000269305	NM_001126112.2	127	tCc/tAc	5/11	0.234442025358869	1	FACETS	0.864	0.751	0.987	0.864	0.751	0.987	CLONAL	1	TRUE	0	0.234442025358869	1		872	575	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026297	48026297	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1064794625	NA	P-0019946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	30	460	0	ENST00000234420.5:c.1175A>T	p.Asp392Val	p.D392V	ENST00000234420	NM_000179.2	392	gAt/gTt	4/10	1	2	FACETS	0.694	0.559	0.846	0.694	0.559	0.846	SUBCLONAL	1	TRUE	1	0.234442025358869	2		460	369	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974751	21974752	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	A	novel	NA	P-0019946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	51	401	0	ENST00000304494.5:c.75_76delinsT	p.Glu26ArgfsTer27	p.E26Rfs*27	ENST00000304494	NM_000077.4	25	gtAGag/gtTag	1/3	0.234442025358869	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.234442025358869	1		401	336	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115956	8115956	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	125	518	0	ENST00000346208.3:c.1305del	p.Ser436ProfsTer39	p.S436Pfs*39	ENST00000346208		434	caC/ca	6/6	1	2	FACETS	0.866	0.787	0.949	0.866	0.787	0.949	CLONAL	1	TRUE	1	0.495167826371895	2		518	583	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575023	64575023	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs794728652	NA	P-0019947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	107	493	1	ENST00000312049.6:c.783+1G>A		p.X261_splice	ENST00000312049	NM_130799.2	261			0.448049399130804	1	FACETS	0.805	0.728	0.886	0.805	0.728	0.886	CLONAL	1	TRUE	0	0.495167826371895	1		494	404	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879331	151879331	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1563292120	NA	P-0019947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	499	624	0	ENST00000262189.6:c.5614C>T	p.Gln1872Ter	p.Q1872*	ENST00000262189	NM_170606.2	1872	Cag/Tag	36/59	0.495167826371895	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	3	TRUE	0	0.495167826371895	3		624	837	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0019948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	297	552	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	0.760256928631855	4	FACETS	0.827	0.783	0.872			1	CLONAL	2	TRUE	NA	0.927433445824446	4		552	746	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052601	42052601	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0019948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	461	623	0	ENST00000219905.7:c.7272T>G	p.Tyr2424Ter	p.Y2424*	ENST00000219905	NM_001164273.1	2424	taT/taG	20/24	0.927433445824446	2	FACETS	0.971	0.953	0.987	0.971	0.953	0.987	CLONAL	2	TRUE	0	0.927433445824446	2		623	512	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0019950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	98	146	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.798	0.718	0.882	0.798	0.718	0.882	SUBCLONAL	1	TRUE	1	0.641290553603626	2		146	383	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520456	176520456	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	192	756	1	ENST00000292408.4:c.1301G>T	p.Arg434Leu	p.R434L	ENST00000292408	NM_213647.1	434	cGa/cTa	10/18	1	2	FACETS	0.888	0.825	0.954	0.888	0.825	0.954	CLONAL	1	TRUE	1	0.641290553603626	2		757	674	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041636	47041636	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	202	910	1	ENST00000377604.3:c.1861C>T	p.Gln621Ter	p.Q621*	ENST00000377604	NM_001204468.1	621	Cag/Tag	17/24	1	2	FACETS	0.986	0.919	1	0.986	0.919	1	CLONAL	1	TRUE	1	0.641290553603626	2		911	639	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117439	4117439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202220799	NA	P-0019950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	105	655	1	ENST00000262948.5:c.281C>T	p.Ser94Leu	p.S94L	ENST00000262948	NM_030662.3	94	tCg/tTg	2/11	0.641290553603626	1	FACETS	0.615	0.556	0.676	0.615	0.556	0.676	SUBCLONAL	1	TRUE	0	0.641290553603626	1		656	362	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221228	1221228	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	225	786	0	ENST00000326873.7:c.751G>T	p.Gly251Cys	p.G251C	ENST00000326873	NM_000455.4	251	Ggt/Tgt	6/10	0.641290553603626	1	FACETS	0.894	0.841	0.949	0.894	0.841	0.949	CLONAL	1	TRUE	0	0.641290553603626	1		786	533	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780921	9780921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1297091785	NA	P-0019950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	186	807	1	ENST00000377346.4:c.1643G>A	p.Arg548Gln	p.R548Q	ENST00000377346	NM_005026.3	548	cGg/cAg	13/24	1	2	FACETS	0.99	0.92	1	0.99	0.92	1	CLONAL	1	TRUE	1	0.641290553603626	2		808	586	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518334	204518334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	175	639	0	ENST00000367182.3:c.997G>T	p.Asp333Tyr	p.D333Y	ENST00000367182	NM_001278516.1	333	Gat/Tat	11/11	0.641290553603626	3	FACETS	0.965	0.891	1	0.482	0.445	0.521	CLONAL	1	TRUE	1	0.641290553603626	3		639	747	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671614	67671614	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	104	640	0	ENST00000264010.4:c.2023G>A	p.Asp675Asn	p.D675N	ENST00000264010	NM_006565.3	675	Gac/Aac	12/12	1	2	FACETS	0.567	0.509	0.628	0.567	0.509	0.628	SUBCLONAL	1	TRUE	1	0.641290553603626	2		640	572	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233702	233702	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1553999038	NA	P-0019950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	179	602	2	ENST00000264932.6:c.1006G>T	p.Asp336Tyr	p.D336Y	ENST00000264932	NM_004168.2	336	Gac/Tac	8/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.641290553603626	2		604	494	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279436	1279436	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	200	841	0	ENST00000310581.5:c.2100G>T	p.Gln700His	p.Q700H	ENST00000310581	NM_198253.2	700	caG/caT	5/16	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.641290553603626	2		841	618	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453135	+	missense_variant	Missense_Mutation	DNP	TC	TC	CA	novel	NA	P-0019950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	215	766	1	ENST00000288602.6:c.1800_1801delinsTG	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	600	gtGAaa/gtTGaa	15/18	1	2	FACETS	0.912	0.851	0.975	0.912	0.851	0.975	CLONAL	1	TRUE	1	0.641290553603626	2		767	735	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370795	55370795	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	56	636	1	ENST00000297316.4:c.97G>T	p.Ala33Ser	p.A33S	ENST00000297316	NM_022454.3	33	Gcc/Tcc	1/2	1	2	FACETS	0.38	0.326	0.439	0.38	0.326	0.439	SUBCLONAL	1	TRUE	1	0.641290553603626	2		637	459	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813050	76813050	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	244	725	0	ENST00000373344.5:c.6571G>C	p.Asp2191His	p.D2191H	ENST00000373344	NM_000489.3	2191	Gat/Cat	30/35	1	2	FACETS	0.968	0.908	1	0.968	0.908	1	CLONAL	1	TRUE	1	0.641290553603626	2		725	786	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881489	48881490	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs587778862	NA	P-0019951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	291	495	0	ENST00000267163.4:c.219_220del	p.Arg73SerfsTer36	p.R73Sfs*36	ENST00000267163	NM_000321.2	71	AGa/a	2/27	0.709966950521024	2	FACETS	0.897	0.859	0.934	0.897	0.859	0.934	CLONAL	2	TRUE	0	0.709966950521024	2		495	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0019951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	524	914	4	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	0.709966950521024	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.709966950521024	2		918	708	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141453	11141453	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	567	889	1	ENST00000358026.2:c.3430G>T	p.Glu1144Ter	p.E1144*	ENST00000358026	NM_001128849.1	1144	Gag/Tag	25/36	0.709966950521024	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.709966950521024	2		890	786	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552773	18552773	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1295080808	NA	P-0019951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	273	628	0	ENST00000266497.5:c.2184G>T	p.Leu728Phe	p.L728F	ENST00000266497		728	ttG/ttT	14/31	0.601150752256258	3	FACETS	0.97	0.921	1	0.97	0.921	1	CLONAL	2	TRUE	1	0.709966950521024	3		628	537	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758871	41758871	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	418	807	1	ENST00000301178.4:c.1925T>A	p.Val642Glu	p.V642E	ENST00000301178	NM_021913.4	642	gTg/gAg	16/20	0.709966950521024	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.709966950521024	3		808	762	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390197	89390197	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	309	608	0	ENST00000336596.2:c.946G>T	p.Asp316Tyr	p.D316Y	ENST00000336596	NM_005233.5	316	Gac/Tac	4/17	0.709966950521024	2	FACETS	0.994	0.956	1	0.994	0.956	1	CLONAL	2	TRUE	0	0.709966950521024	2		608	438	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201736	66201736	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	191	752	0	ENST00000273854.3:c.2766G>T	p.Arg922Ser	p.R922S	ENST00000273854	NM_004439.5	922	agG/agT	16/18	0.709966950521024	3	FACETS	0.862	0.798	0.928	0.431	0.399	0.464	CLONAL	1	TRUE	1	0.709966950521024	3		752	846	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540703	187540703	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	334	637	2	ENST00000441802.2:c.7037G>C	p.Arg2346Thr	p.R2346T	ENST00000441802	NM_005245.3	2346	aGa/aCa	10/27	0.709966950521024	3	FACETS	0.969	0.924	1	0.969	0.924	1	CLONAL	2	TRUE	1	0.709966950521024	3		639	658	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005933	69005933	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	396	905	1	ENST00000288368.4:c.2344G>T	p.Asp782Tyr	p.D782Y	ENST00000288368	NM_024870.2	782	Gat/Tat	21/40	0.709966950521024	3	FACETS	0.932	0.892	0.972	0.932	0.892	0.972	CLONAL	2	TRUE	1	0.709966950521024	3		906	811	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508057	106508059	+	missense_variant	Missense_Mutation	TNP	CCG	CCG	TCT	novel	NA	P-0019951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	175	384	3	ENST00000359195.3:c.51_53delinsTCT	p.Arg18Leu	p.R18L	ENST00000359195	NM_002649.2	17	tgCCGa/tgTCTa	2/11	0.709966950521024	3	FACETS	0.928	0.868	0.987	0.928	0.868	0.987	CLONAL	2	TRUE	1	0.709966950521024	3		387	360	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0019952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	129	425	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.39249643605699	2		425	628	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252856	36252857	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	106	541	0	ENST00000300305.3:c.505dup	p.Arg169LysfsTer44	p.R169Kfs*44	ENST00000300305		169	aga/aAga	4/8	1	2	FACETS	0.917	0.824	1	0.917	0.824	1	CLONAL	1	TRUE	1	0.39249643605699	2		541	589	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061261	38061264	+	missense_variant	Missense_Mutation	ONP	TAGG	TAGG	GAGC	novel	NA	P-0019952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	141	815	0	ENST00000250448.2:c.725_728delinsGCTC	p.Ser242_Tyr243delinsCysSer	p.S242_Y243delinsCS	ENST00000250448	NM_004496.3	242	tCCTAc/tGCTCc	2/2	1	2	FACETS	0.937	0.854	1	0.937	0.854	1	CLONAL	1	TRUE	1	0.39249643605699	2		815	767	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486102	29486102	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0019952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	124	660	0	ENST00000356175.3:c.279T>A	p.Cys93Ter	p.C93*	ENST00000356175	NM_000267.3	93	tgT/tgA	3/57	0.39249643605699	1	FACETS	0.964	0.876	1	0.964	0.876	1	CLONAL	1	TRUE	0	0.39249643605699	1		660	527	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457335	67457337	+	missense_variant	Missense_Mutation	TNP	ACG	ACG	GCT	novel	NA	P-0019952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	145	693	2	ENST00000327367.4:c.309_311delinsGCT	p.Arg104Leu	p.R104L	ENST00000327367	NM_005902.3	103	ctACGg/ctGCTg	2/9	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.39249643605699	2		695	689	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912655	NA	P-0019953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	795	763	0	ENST00000269305.4:c.725G>C	p.Cys242Ser	p.C242S	ENST00000269305	NM_001126112.2	242	tGc/tCc	7/11	0.706930838061455	3	FACETS	0.991	0.971	1			1	CLONAL	3	TRUE	NA	0.706930838061455	3		763	1024	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718186	117718186	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs771923036	NA	P-0019953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	191	706	0	ENST00000368508.3:c.671C>A	p.Pro224His	p.P224H	ENST00000368508	NM_002944.2	224	cCt/cAt	7/43	0.69165688422086	2	FACETS	0.89	0.828	0.954	0.445	0.414	0.477	CLONAL	1	TRUE	0	0.706930838061455	2		706	607	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845744	68845771	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CACTGGGCTGGACCGAGAGGTCAGGGGT	CACTGGGCTGGACCGAGAGGTCAGGGGT	-	novel	NA	P-0019953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	155	573	0	ENST00000261769.5:c.992_1008+11del		p.X331_splice	ENST00000261769	NM_004360.3	331		7/16	0.706930838061455	1	FACETS	0.936	0.873	0.998	0.936	0.873	0.998	CLONAL	1	TRUE	0	0.706930838061455	1		573	303	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028638	12028638	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	245	729	1	ENST00000353533.5:c.841C>T	p.Arg281Ter	p.R281*	ENST00000353533	NM_003010.3	281	Cga/Tga	8/11	0.636250610579463	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.636250610579463	1		730	525	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277157	38277157	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369059499	NA	P-0019954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	6668	925	3	ENST00000425967.3:c.1271C>T	p.Ser424Leu	p.S424L	ENST00000425967	NM_001174067.1	424	tCg/tTg	10/19	0.636250610579463	21	FACETS	1	0.999	1			1	CLONAL	20	TRUE	NA	0.636250610579463	21		928	7273	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0019955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	66	146	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.582	0.504	0.667	0.582	0.504	0.667	SUBCLONAL	1	TRUE	1	0.29	2		146	782	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866987936	NA	P-0019955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	105	693	0	ENST00000281708.4:c.1436G>C	p.Arg479Pro	p.R479P	ENST00000281708	NM_033632.3	479	cGa/cCa	10/12	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.29	2		693	709	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023208	31023208	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	179	1113	0	ENST00000375687.4:c.2693G>A	p.Trp898Ter	p.W898*	ENST00000375687	NM_015338.5	898	tGg/tAg	13/13	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.29	2		1113	1227	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307881	11307881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	152	987	0	ENST00000361445.4:c.1111G>A	p.Asp371Asn	p.D371N	ENST00000361445	NM_004958.3	371	Gat/Aat	7/58	0.273686585741974	3	FACETS	1	0.95	1	0.53	0.483	0.578	CLONAL	1	TRUE	1	0.29	3		987	1133	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574797	95574797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	120	725	0	ENST00000393063.1:c.2300C>T	p.Pro767Leu	p.P767L	ENST00000393063	NM_030621.3	767	cCc/cTc	16/28	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.29	2		725	756	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646693	23646693	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	89	735	0	ENST00000261584.4:c.1174G>C	p.Glu392Gln	p.E392Q	ENST00000261584	NM_024675.3	392	Gaa/Caa	4/13	1	2	FACETS	0.715	0.633	0.802	0.715	0.633	0.802	SUBCLONAL	1	TRUE	1	0.29	2		735	859	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357113	89357113	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1258661652	NA	P-0019955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	180	942	0	ENST00000301030.4:c.521G>T	p.Arg174Leu	p.R174L	ENST00000301030	NM_001256183.1	174	cGa/cTa	6/13	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.29	2		942	1113	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118990	70118990	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	112	984	3	ENST00000245479.2:c.562G>T	p.Glu188Ter	p.E188*	ENST00000245479	NM_000346.3	188	Gag/Tag	2/3	0.295066093690898	2	FACETS	0.721	0.647	0.8	0.361	0.323	0.4	SUBCLONAL	1	TRUE	0	0.29	2		987	1071	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374857	45374857	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	103	837	0	ENST00000262160.6:c.986G>C	p.Arg329Thr	p.R329T	ENST00000262160	NM_005901.5	329	aGa/aCa	8/11	1	2	FACETS	0.783	0.7	0.872	0.783	0.7	0.872	SUBCLONAL	1	TRUE	1	0.29	2		837	907	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271771	18271771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770445875	NA	P-0019955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	170	941	2	ENST00000222254.8:c.458C>T	p.Pro153Leu	p.P153L	ENST00000222254	NM_005027.3	153	cCg/cTg	4/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.29	2		943	1087	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513220	41513220	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	59	844	2	ENST00000263253.7:c.124G>T	p.Asp42Tyr	p.D42Y	ENST00000263253	NM_001429.3	42	Gac/Tac	2/31	0.295066093690898	2	FACETS	0.424	0.364	0.491	0.212	0.182	0.246	SUBCLONAL	1	TRUE	0	0.29	2		846	959	SUCCESS
ATR	545	MSKCC	GRCh37	3	142184047	142184047	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	43	678	2	ENST00000350721.4:c.6933G>T	p.Lys2311Asn	p.K2311N	ENST00000350721	NM_001184.3	2311	aaG/aaT	41/47	0.290688770894585	4	FACETS	0.447	0.373	0.531	0.224	0.186	0.266	SUBCLONAL	1	TRUE	2	0.29	4		680	855	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264696	1264696	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	148	936	4	ENST00000310581.5:c.2666G>T	p.Arg889Leu	p.R889L	ENST00000310581	NM_198253.2	889	cGa/cTa	11/16	1	2	FACETS	0.992	0.905	1	0.992	0.905	1	CLONAL	1	TRUE	1	0.29	2		940	1029	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15808631	15808631	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	83	445	0	ENST00000307771.7:c.13G>A	p.Glu5Lys	p.E5K	ENST00000307771	NM_005089.3	5	Gag/Aag	1/11	1	1	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	0	0.29	1		445	485	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0019956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	45	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.888	0.746	1	0.888	0.746	1	CLONAL	1	TRUE	1	0.17	2		555	596	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0019956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	110	825	1	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.18901452577967	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.17	1		826	897	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0019957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	447	874	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.606427512809463	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.606427512809463	2		874	686	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363809	118363809	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	177	728	1	ENST00000534358.1:c.5042A>T	p.Glu1681Val	p.E1681V	ENST00000534358	NM_005933.3	1681	gAg/gTg	16/36	0.384320694225083	5	FACETS	1	0.96	1	0.356	0.327	0.385	CLONAL	1	TRUE	2	0.606427512809463	5		729	1045	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589732	28589732	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0019957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	219	708	0	ENST00000241453.7:c.2648C>G	p.Ser883Ter	p.S883*	ENST00000241453	NM_004119.2	883	tCa/tGa	21/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.606427512809463	2		708	676	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845842	72845842	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	192	815	1	ENST00000268489.5:c.3625A>G	p.Lys1209Glu	p.K1209E	ENST00000268489	NM_006885.3	1209	Aag/Gag	6/10	0.606427512809463	3	FACETS	0.946	0.876	1	0.315	0.292	0.34	CLONAL	1	TRUE	0	0.606427512809463	3		816	872	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750437	57750438	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	172	728	0	ENST00000274289.3:c.2030dup	p.Asn678GlufsTer8	p.N678Efs*8	ENST00000274289	NM_006622.3	677	ctg/ctTg	14/14	0.497214385035523	3	FACETS	0.937	0.864	1	0.468	0.432	0.507	CLONAL	1	TRUE	1	0.606427512809463	3		728	789	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821545	32821545	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	224	885	0	ENST00000354258.4:c.49C>G	p.Pro17Ala	p.P17A	ENST00000354258	NM_000593.5	17	Ccg/Gcg	1/11	0.606427512809463	3	FACETS	0.976	0.91	1	0.488	0.455	0.523	CLONAL	1	TRUE	1	0.606427512809463	3		885	986	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0019958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	181	591	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.232256167169119	2	FACETS	0.908	0.839	0.981	0.908	0.839	0.981	CLONAL	2	TRUE	0	0.232256167169119	2		591	858	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998273	100998273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	27	418	1	ENST00000325455.5:c.1529C>T	p.Ala510Val	p.A510V	ENST00000325455	NM_001202474.3	510	gCg/gTg	1/8	1	2	FACETS	0.965	0.771	1	0.965	0.771	1	CLONAL	1	TRUE	1	0.232256167169119	2		419	241	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440697	56440698	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0019958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	183	887	0	ENST00000407977.2:c.520dup	p.Glu174GlyfsTer14	p.E174Gfs*14	ENST00000407977		174	gag/gGag	5/10	0.232256167169119	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.232256167169119	2		887	755	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540481	187540481	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0019958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	50	561	0	ENST00000441802.2:c.7259C>G	p.Ser2420Ter	p.S2420*	ENST00000441802	NM_005245.3	2420	tCa/tGa	10/27	0.184480868174491	2	FACETS	0.957	0.813	1	0.478	0.406	0.557	CLONAL	1	TRUE	0	0.232256167169119	2		561	450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0019960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	105	773	1	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	FALSE	1	0.157237183379429	2		774	1187	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096688	178096688	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	42	590	0	ENST00000397062.3:c.643A>C	p.Ser215Arg	p.S215R	ENST00000397062	NM_006164.4	215	Agt/Cgt	5/5	1	2	FACETS	0.666	0.554	0.791	0.666	0.554	0.791	SUBCLONAL	1	FALSE	1	0.157237183379429	2		590	802	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	268	424	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.518198159476258	5	FACETS	1	0.979	1	0.724	0.682	0.768	CLONAL	2	TRUE	2	0.537178330472922	5		424	829	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219381	1219381	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	232	931	1	ENST00000326873.7:c.433G>T	p.Glu145Ter	p.E145*	ENST00000326873	NM_000455.4	145	Gag/Tag	3/10	0.559140880211376	4	FACETS	0.995	0.941	1			1	CLONAL	3	TRUE	NA	0.537178330472922	4		932	445	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239812	105239812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1390179436	NA	P-0019961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	42	792	1	ENST00000349310.3:c.808G>A	p.Val270Met	p.V270M	ENST00000349310	NM_001014432.1	270	Gtg/Atg	10/15	0.245980071778271	5	FACETS	0.804	0.674	0.949	0.268	0.224	0.317	INDETERMINATE	1	TRUE	2	0.537178330472922	5		793	351	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582249	52582249	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	40	263	0	ENST00000394830.3:c.4579C>T	p.Arg1527Ter	p.R1527*	ENST00000394830	NM_018313.4	1527	Cga/Tga	30/30	0.341678529935978	3	FACETS	0.891	0.748	1	0.297	0.249	0.349	CLONAL	1	TRUE	0	0.537178330472922	3		263	212	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623218	52623218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1402934247	NA	P-0019961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	55	571	1	ENST00000394830.3:c.2833C>T	p.Arg945Cys	p.R945C	ENST00000394830	NM_018313.4	945	Cgc/Tgc	19/30	0.341678529935978	3	FACETS	0.915	0.789	1	0.305	0.263	0.35	CLONAL	1	TRUE	0	0.537178330472922	3		572	284	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623229	52623229	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0019961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	41	513	0	ENST00000394830.3:c.2822C>G	p.Ser941Ter	p.S941*	ENST00000394830	NM_018313.4	941	tCa/tGa	19/30	0.341678529935978	3	FACETS	0.765	0.642	0.9	0.255	0.214	0.3	SUBCLONAL	1	TRUE	0	0.537178330472922	3		513	253	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15809088	15809088	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	141	637	0	ENST00000307771.7:c.73G>T	p.Glu25Ter	p.E25*	ENST00000307771	NM_005089.3	25	Gag/Tag	2/11	0.48626094287331	3	FACETS	1	0.92	1			1	CLONAL	1	TRUE	NA	0.537178330472922	3		637	661	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428185	47428185	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	39	820	0	ENST00000377045.4:c.1145C>T	p.Thr382Ile	p.T382I	ENST00000377045	NM_001654.4	382	aCa/aTa	11/16	1	2	FACETS	0.396	0.328	0.47	0.396	0.328	0.47	SUBCLONAL	1	TRUE	1	0.537178330472922	2		820	367	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019961-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	108	424	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	0.257097862225428	2		424	772	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0019961-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	155	856	0	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.257097862225428	3	FACETS	1	0.984	1	0.66	0.603	0.719	CLONAL	1	TRUE	1	0.257097862225428	3		856	1031	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219381	1219381	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019961-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	135	931	1	ENST00000326873.7:c.433G>T	p.Glu145Ter	p.E145*	ENST00000326873	NM_000455.4	145	Gag/Tag	3/10	0.257097862225428	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.257097862225428	1		932	705	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239812	105239812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1390179436	NA	P-0019961-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	119	792	1	ENST00000349310.3:c.808G>A	p.Val270Met	p.V270M	ENST00000349310	NM_001014432.1	270	Gtg/Atg	10/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.257097862225428	2		793	792	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623218	52623218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1402934247	NA	P-0019961-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	85	571	1	ENST00000394830.3:c.2833C>T	p.Arg945Cys	p.R945C	ENST00000394830	NM_018313.4	945	Cgc/Tgc	19/30	0.257097862225428	1	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	0	0.257097862225428	1		572	557	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623229	52623229	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0019961-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	72	513	0	ENST00000394830.3:c.2822C>G	p.Ser941Ter	p.S941*	ENST00000394830	NM_018313.4	941	tCa/tGa	19/30	0.257097862225428	1	FACETS	0.976	0.855	1	0.976	0.855	1	CLONAL	1	TRUE	0	0.257097862225428	1		513	500	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15809088	15809088	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019961-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	63	637	0	ENST00000307771.7:c.73G>T	p.Glu25Ter	p.E25*	ENST00000307771	NM_005089.3	25	Gag/Tag	2/11	1	2	FACETS	0.586	0.506	0.674	0.586	0.506	0.674	SUBCLONAL	1	TRUE	1	0.257097862225428	2		637	836	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428185	47428185	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019961-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	48	820	0	ENST00000377045.4:c.1145C>T	p.Thr382Ile	p.T382I	ENST00000377045	NM_001654.4	382	aCa/aTa	11/16	1	2	FACETS	0.409	0.344	0.481	0.409	0.344	0.481	SUBCLONAL	1	TRUE	1	0.257097862225428	2		820	913	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932819	39932819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764515953	NA	P-0019961-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	81	815	3	ENST00000378444.4:c.1780G>A	p.Val594Ile	p.V594I	ENST00000378444	NM_001123385.1	594	Gtt/Att	4/15	1	2	FACETS	0.731	0.643	0.826	0.731	0.643	0.826	SUBCLONAL	1	TRUE	1	0.257097862225428	2		818	862	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371409680	NA	P-0019962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	501	900	0	ENST00000269305.4:c.848G>C	p.Arg283Pro	p.R283P	ENST00000269305	NM_001126112.2	283	cGc/cCc	8/11	0.313111245183093	3	FACETS	1	0.994	1	0.793	0.76	0.826	CLONAL	2	TRUE	0	0.388199003940695	3		900	1296	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466022	69466022	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	251	953	0	ENST00000227507.2:c.860C>A	p.Pro287His	p.P287H	ENST00000227507	NM_053056.2	287	cCc/cAc	5/5	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.388199003940695	2		953	1199	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77043818	77043818	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	215	750	0	ENST00000356341.3:c.1508A>T	p.Glu503Val	p.E503V	ENST00000356341	NM_002576.4	503	gAg/gTg	14/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.388199003940695	2		750	1058	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438079	438080	+	missense_variant	Missense_Mutation	DNP	CC	CC	GA	novel	NA	P-0019962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	131	605	1	ENST00000399788.2:c.1889_1890delinsTC	p.Gly630Val	p.G630V	ENST00000399788	NM_001042603.1	630	gGG/gTC	14/28	0.332996277658328	3	FACETS	0.973	0.883	1	0.487	0.441	0.534	CLONAL	1	TRUE	1	0.388199003940695	3		606	828	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432603	49432616	+	frameshift_variant	Frame_Shift_Del	DEL	CAAGTTCAGGTCCA	CAAGTTCAGGTCCA	-	novel	NA	P-0019962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	388	927	1	ENST00000301067.7:c.8523_8536del	p.Gly2842ProfsTer20	p.G2842Pfs*20	ENST00000301067	NM_003482.3	2841	ccTGGACCTGAACTTGgc/ccgc	34/54	0.178281773842425	4	FACETS	0.998	0.948	1	0.998	0.948	1	INDETERMINATE	2	TRUE	2	0.388199003940695	4		928	1390	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336212	73336212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749936817	NA	P-0019962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	162	507	1	ENST00000377767.4:c.2191C>T	p.Pro731Ser	p.P731S	ENST00000377767	NM_014953.3	731	Cct/Tct	17/21	0.388199003940695	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.388199003940695	2		508	400	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909727	50909727	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	460	986	0	ENST00000440232.2:c.1447G>T	p.Gly483Cys	p.G483C	ENST00000440232	NM_002691.3	483	Ggc/Tgc	12/27	0.268725572087945	3	FACETS	0.925	0.882	0.968			1	CLONAL	2	TRUE	NA	0.388199003940695	3		986	1530	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265061	198265061	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	118	555	0	ENST00000335508.6:c.2816G>T	p.Arg939Leu	p.R939L	ENST00000335508	NM_012433.2	939	cGt/cTt	19/25	0.332996277658328	3	FACETS	0.926	0.835	1	0.463	0.417	0.511	CLONAL	1	TRUE	1	0.388199003940695	3		555	784	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019136	31019136	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	321	720	0	ENST00000375687.4:c.731G>T	p.Arg244Leu	p.R244L	ENST00000375687	NM_015338.5	244	cGc/cTc	9/13	0.388199003940695	3	FACETS	0.871	0.823	0.921	0.871	0.823	0.921	CLONAL	2	TRUE	1	0.388199003940695	3		720	1133	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971014	55971014	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	338	794	2	ENST00000263923.4:c.1783G>T	p.Val595Leu	p.V595L	ENST00000263923	NM_002253.2	595	Gtg/Ttg	13/30	0.388199003940695	2	FACETS	0.944	0.896	0.993	0.944	0.896	0.993	CLONAL	2	TRUE	0	0.388199003940695	2		796	922	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532867	187532867	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	293	673	0	ENST00000441802.2:c.9526del	p.Glu3176AsnfsTer8	p.E3176Nfs*8	ENST00000441802	NM_005245.3	3176	Gaa/aa	14/27	0.388199003940695	3	FACETS	0.989	0.933	1	0.989	0.933	1	CLONAL	2	TRUE	1	0.388199003940695	3		673	911	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323112	31323112	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1407	503	1154	0	ENST00000412585.2:c.877C>A	p.Pro293Thr	p.P293T	ENST00000412585	NM_005514.6	293	Ccc/Acc	4/8	0.388199003940695	3	FACETS	0.81	0.773	0.847	0.81	0.773	0.847	CLONAL	2	TRUE	1	0.388199003940695	3		1154	1910	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964409	93964409	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	119	800	0	ENST00000369303.4:c.2488A>T	p.Met830Leu	p.M830L	ENST00000369303	NM_004440.3	830	Atg/Ttg	14/17	0.388199003940695	3	FACETS	1	0.966	1	0.573	0.518	0.63	CLONAL	1	TRUE	1	0.388199003940695	3		800	639	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971158	21971158	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	242	565	0	ENST00000304494.5:c.200G>T	p.Gly67Val	p.G67V	ENST00000304494	NM_000077.4	67	gGc/gTc	2/3	0.388199003940695	2	FACETS	0.79	0.74	0.841	0.79	0.74	0.841	SUBCLONAL	2	TRUE	0	0.388199003940695	2		565	789	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0019963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	571	733	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.783344507315961	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.783344507315961	2		733	714	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041210	29041210	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	452	744	0	ENST00000282397.4:c.218G>T	p.Arg73Met	p.R73M	ENST00000282397	NM_002019.4	73	aGg/aTg	3/30	0.75402254215472	2	FACETS	0.975	0.947	1	0.975	0.947	1	CLONAL	2	TRUE	0	0.783344507315961	2		744	592	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857736	9857736	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	319	487	0	ENST00000330684.3:c.3665C>T	p.Pro1222Leu	p.P1222L	ENST00000330684	NM_001134407.1	1222	cCc/cTc	13/13	0.75402254215472	2	FACETS	0.988	0.956	1	0.988	0.956	1	CLONAL	2	TRUE	0	0.783344507315961	2		487	412	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275266	142275266	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	635	637	0	ENST00000350721.4:c.2037G>T	p.Leu679Phe	p.L679F	ENST00000350721	NM_001184.3	679	ttG/ttT	9/47	0.783344507315961	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.783344507315961	2		637	786	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779073	135779077	+	frameshift_variant	Frame_Shift_Del	DEL	TGATC	TGATC	-	novel	NA	P-0019963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	402	532	0	ENST00000298552.3:c.2169_2173del	p.Ile724SerfsTer8	p.I724Sfs*8	ENST00000298552	NM_001162426.1	723	gtGATCAaa/gtaa	17/23	0.783344507315961	2	FACETS	0.989	0.96	1	0.989	0.96	1	CLONAL	2	TRUE	0	0.783344507315961	2		532	519	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0019964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	179	532	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.388205529949253	2		533	884	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0019964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	426	453	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.388205529949253	3	FACETS	0.97	0.929	1	0.97	0.929	1	CLONAL	3	TRUE	0	0.388205529949253	3		453	901	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143994	11143994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	177	578	3	ENST00000358026.2:c.3575G>A	p.Arg1192His	p.R1192H	ENST00000358026	NM_001128849.1	1192	cGc/cAc	26/36	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.388205529949253	2		581	848	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0019964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	134	596	0	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	0.388205529949253	1	FACETS	0.893	0.814	0.976	0.893	0.814	0.976	CLONAL	1	TRUE	0	0.388205529949253	1		596	623	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553486	29553486	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1254780857	NA	P-0019964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	158	637	0	ENST00000356175.3:c.2035A>G	p.Ile679Val	p.I679V	ENST00000356175	NM_000267.3	679	Att/Gtt	18/57	1	2	FACETS	0.897	0.822	0.976	0.897	0.822	0.976	CLONAL	1	TRUE	1	0.388205529949253	2		637	907	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	578	424	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.45709328665935	5	FACETS	0.939	0.907	0.971	0.939	0.907	0.971	CLONAL	4	TRUE	1	0.476708450873398	5		424	1107	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0019965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	409	839	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.476708450873398	2		841	785	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373574	118373574	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	270	503	0	ENST00000534358.1:c.6967G>T	p.Ala2323Ser	p.A2323S	ENST00000534358	NM_005933.3	2323	Gca/Tca	27/36	0.476708450873398	4	FACETS	0.921	0.866	0.978	0.921	0.866	0.978	CLONAL	2	TRUE	2	0.476708450873398	4		503	908	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs104886003	NA	P-0019966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	23	616	0	ENST00000263967.3:c.1633G>C	p.Glu545Gln	p.E545Q	ENST00000263967	NM_006218.2	545	Gag/Cag	10/21	0.26807443984149	8	FACETS	0.271	0.21	0.342	0.054	0.042	0.069	SUBCLONAL	1	TRUE	3	0.26807443984149	8		616	1143	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	242	751	2	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	NA	2	FACETS	0.878	0.82	0.938			1	INDETERMINATE	2	TRUE	NA	0.26807443984149	2		753	1028	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0019966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	37	615	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	0.26807443984149	1	FACETS	0.336	0.276	0.403	0.336	0.276	0.403	SUBCLONAL	1	TRUE	0	0.26807443984149	1		615	712	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724988	162724988	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	137	566	0	ENST00000367921.3:c.460G>C	p.Asp154His	p.D154H	ENST00000367921	NM_006182.2	154	Gac/Cac	6/18	0.210951276271908	3	FACETS	1	0.985	1	0.724	0.659	0.793	CLONAL	1	TRUE	1	0.26807443984149	3		566	800	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	443562	443562	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	105	731	0	ENST00000399788.2:c.1335G>C	p.Leu445Phe	p.L445F	ENST00000399788	NM_001042603.1	445	ttG/ttC	11/28	0.26807443984149	4	FACETS	0.904	0.808	1			1	CLONAL	1	TRUE	NA	0.26807443984149	4		731	1099	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	493320	493320	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0019966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	87	489	1	ENST00000399788.2:c.244-1G>A		p.X82_splice	ENST00000399788	NM_001042603.1	82			0.26807443984149	4	FACETS	0.981	0.867	1			1	CLONAL	1	TRUE	NA	0.26807443984149	4		490	839	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434745	110434745	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	149	640	0	ENST00000375856.3:c.3656C>A	p.Pro1219Gln	p.P1219Q	ENST00000375856	NM_003749.2	1219	cCg/cAg	1/2	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.26807443984149	2		640	919	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781857	3781857	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	188	959	0	ENST00000262367.5:c.4810A>G	p.Asn1604Asp	p.N1604D	ENST00000262367	NM_004380.2	1604	Aac/Gac	29/31	0.18173574065691	2	FACETS	1	0.986	1	0.651	0.601	0.703	CLONAL	1	TRUE	0	0.26807443984149	2		959	1077	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45423027	45423027	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	82	426	0	ENST00000262160.6:c.101A>G	p.Asn34Ser	p.N34S	ENST00000262160	NM_005901.5	34	aAt/aGt	2/11	0.26807443984149	1	FACETS	0.915	0.808	1	0.915	0.808	1	CLONAL	1	TRUE	0	0.26807443984149	1		426	579	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449496	149449496	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1452088406	NA	P-0019966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	135	740	1	ENST00000286301.3:c.1450G>C	p.Glu484Gln	p.E484Q	ENST00000286301	NM_005211.3	484	Gag/Cag	10/22	0.26807443984149	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.26807443984149	1		741	770	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005035	150005035	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	77	576	0	ENST00000253339.5:c.1190C>T	p.Pro397Leu	p.P397L	ENST00000253339		397	cCt/cTt	3/7	1	2	FACETS	0.877	0.77	0.992	0.877	0.77	0.992	CLONAL	1	TRUE	1	0.26807443984149	2		576	655	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476740	140476740	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	142	509	0	ENST00000288602.6:c.1666A>T	p.Ile556Phe	p.I556F	ENST00000288602	NM_004333.4	556	Att/Ttt	13/18	0.210951276271908	3	FACETS	0.863	0.788	0.941	0.863	0.788	0.941	CLONAL	2	TRUE	1	0.26807443984149	3		509	696	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971209	21971209	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0019966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	50	566	0	ENST00000304494.5:c.151-2A>C		p.X51_splice	ENST00000304494	NM_000077.4	51			0.183286829558731	0	FACETS	0.509	0.432	0.594			1	SUBCLONAL	1	TRUE	0	0.26807443984149	0		566	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0019967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	196	604	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.258662161431899	2	FACETS	0.906	0.842	0.972	0.906	0.842	0.972	CLONAL	2	TRUE	0	0.31486401365264	2		606	687	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371984	55371984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	116	598	1	ENST00000297316.4:c.674C>T	p.Ser225Phe	p.S225F	ENST00000297316	NM_022454.3	225	tCc/tTc	2/2	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.31486401365264	2		599	672	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970878	70970878	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	36	626	0	ENST00000276594.2:c.1383C>G	p.His461Gln	p.H461Q	ENST00000276594	NM_024504.3	461	caC/caG	6/8	1	2	FACETS	0.353	0.29	0.425	0.353	0.29	0.425	SUBCLONAL	1	TRUE	1	0.31486401365264	2		626	647	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344057	70344057	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	60	1021	0	ENST00000374080.3:c.1793T>G	p.Leu598Arg	p.L598R	ENST00000374080		598	cTg/cGg	13/45	1	2	FACETS	0.492	0.423	0.567	0.492	0.423	0.567	SUBCLONAL	1	TRUE	1	0.31486401365264	2		1021	775	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0019969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	882	786	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.255778265274108	13	FACETS	0.972	0.948	0.996			1	CLONAL	12	TRUE	NA	0.255778265274108	13		786	1423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0019969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	128	604	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.255778265274108	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.255778265274108	1		606	698	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806092	1806092	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913484	NA	P-0019970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	152	777	0	ENST00000260795.2:c.1111A>T	p.Ser371Cys	p.S371C	ENST00000260795		371	Agt/Tgt	8/17	1	2	FACETS	0.469	0.428	0.512	0.469	0.428	0.512	SUBCLONAL	1	TRUE	1	0.53	2		777	1223	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0019970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	294	860	0	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	0.500077311269973	1	FACETS	0.972	0.918	1	0.972	0.918	1	CLONAL	1	TRUE	0	0.53	1		860	839	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948799	71948799	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	258	826	1	ENST00000298229.2:c.3514del	p.Arg1172AlafsTer30	p.R1172Afs*30	ENST00000298229	NM_001567.3	1171	Ccc/cc	26/28	1	2	FACETS	0.921	0.863	0.981	0.921	0.863	0.981	CLONAL	1	TRUE	1	0.53	2		827	1057	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436553	49436553	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778461	NA	P-0019970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	265	744	1	ENST00000301067.7:c.5753G>A	p.Arg1918His	p.R1918H	ENST00000301067	NM_003482.3	1918	cGt/cAt	26/54	1	2	FACETS	0.991	0.93	1	0.991	0.93	1	CLONAL	1	TRUE	1	0.53	2		745	1009	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444220	49444220	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	350	1045	0	ENST00000301067.7:c.3151G>C	p.Val1051Leu	p.V1051L	ENST00000301067	NM_003482.3	1051	Gtt/Ctt	11/54	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.53	2		1045	1314	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951086	48951086	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	189	517	0	ENST00000267163.4:c.1248del	p.Arg418GlufsTer2	p.R418Efs*2	ENST00000267163	NM_000321.2	416	ctG/ct	13/27	0.529267964091777	1	FACETS	0.984	0.916	1	0.984	0.916	1	CLONAL	1	TRUE	0	0.53	1		517	533	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569764	95569764	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	129	404	0	ENST00000393063.1:c.3969A>C	p.Leu1323Phe	p.L1323F	ENST00000393063	NM_030621.3	1323	ttA/ttC	22/28	1	2	FACETS	0.88	0.802	0.962	0.88	0.802	0.962	CLONAL	1	TRUE	1	0.53	2		404	553	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426713	212426714	+	missense_variant	Missense_Mutation	DNP	TG	TG	AT	novel	NA	P-0019970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	216	784	1	ENST00000342788.4:c.2401_2402delinsAT	p.His801Ile	p.H801I	ENST00000342788	NM_005235.2	801	CAt/ATt	20/28	0.529267964091777	1	FACETS	0.968	0.905	1	0.968	0.905	1	CLONAL	1	TRUE	0	0.53	1		785	619	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293556	1293556	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	600	894	0	ENST00000310581.5:c.1445A>G	p.His482Arg	p.H482R	ENST00000310581	NM_198253.2	482	cAc/cGc	2/16	0.529267964091777	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.53	3		894	1409	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981585	70981585	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	316	1055	0	ENST00000276594.2:c.511C>A	p.Pro171Thr	p.P171T	ENST00000276594	NM_024504.3	171	Cct/Act	2/8	1	2	FACETS	0.98	0.924	1	0.98	0.924	1	CLONAL	1	TRUE	1	0.53	2		1055	1217	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739455	145739455	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	251	775	0	ENST00000428558.2:c.1915G>C	p.Gly639Arg	p.G639R	ENST00000428558	NM_004260.3	639	Ggc/Cgc	12/22	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.53	2		775	924	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449786	8449786	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	231	890	0	ENST00000356435.5:c.3927G>T	p.Glu1309Asp	p.E1309D	ENST00000356435		1309	gaG/gaT	23/35	0.529267964091777	2	FACETS	0.915	0.853	0.978			1	CLONAL	1	TRUE	NA	0.53	2		890	953	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840615	36840615	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	282	635	0	ENST00000358127.4:c.1118G>C	p.Ser373Thr	p.S373T	ENST00000358127	NM_001280556.1	373	aGc/aCc	10/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.53	2		635	957	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434674	128434674	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	299	813	0	ENST00000265960.3:c.180G>T	p.Glu60Asp	p.E60D	ENST00000265960	NM_001006617.1	60	gaG/gaT	2/12	1	2	FACETS	0.999	0.941	1	0.999	0.941	1	CLONAL	1	TRUE	1	0.53	2		813	1129	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702564	52702565	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	T	novel	NA	P-0019970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	228	786	0	ENST00000394830.3:c.333_334delinsA	p.Leu112Ter	p.L112*	ENST00000394830	NM_018313.4	111	ttGCtg/ttAtg	4/30	0.529267964091777	1	FACETS	0.881	0.824	0.939	0.881	0.824	0.939	CLONAL	1	TRUE	0	0.53	1		786	718	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578440	7578440	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs879254249	NA	P-0019972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	377	929	0	ENST00000269305.4:c.490A>G	p.Lys164Glu	p.K164E	ENST00000269305	NM_001126112.2	164	Aag/Gag	5/11	0.651972635076357	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.651972635076357	1		929	731	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119699	70119699	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	353	941	0	ENST00000245479.2:c.701C>A	p.Pro234Gln	p.P234Q	ENST00000245479	NM_000346.3	234	cCa/cAa	3/3	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.526103583076868	2		941	1170	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941023	71941023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1237449594	NA	P-0019977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	128	1031	0	ENST00000298229.2:c.899C>T	p.Ser300Phe	p.S300F	ENST00000298229	NM_001567.3	300	tCc/tTc	8/28	0.277331665548882	3	FACETS	0.5	0.452	0.551	0.25	0.226	0.276	INDETERMINATE	1	TRUE	1	0.547649406421527	3		1031	1190	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164127	108164127	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	85	615	0	ENST00000278616.4:c.4699G>C	p.Asp1567His	p.D1567H	ENST00000278616	NM_000051.3	1567	Gac/Cac	31/63	0.277331665548882	3	FACETS	0.606	0.535	0.681	0.303	0.267	0.341	INDETERMINATE	1	TRUE	1	0.547649406421527	3		615	653	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380765	118380765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	97	721	0	ENST00000534358.1:c.11003C>T	p.Pro3668Leu	p.P3668L	ENST00000534358	NM_005933.3	3668	cCc/cTc	30/36	0.277331665548882	3	FACETS	0.526	0.468	0.588	0.263	0.234	0.294	INDETERMINATE	1	TRUE	1	0.547649406421527	3		721	858	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864417	57864417	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	528	861	0	ENST00000228682.2:c.1895del	p.Asn632MetfsTer87	p.N632Mfs*87	ENST00000228682	NM_005269.2	632	Aat/at	12/12	0.516367095225473	3	FACETS	0.9	0.869	0.93	0.9	0.869	0.93	CLONAL	3	TRUE	0	0.547649406421527	3		861	910	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872054	35872054	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	476	650	0	ENST00000216797.5:c.559C>G	p.Leu187Val	p.L187V	ENST00000216797	NM_020529.2	187	Cta/Gta	4/6	0.547649406421527	3	FACETS	0.951	0.911	0.991	0.951	0.911	0.991	CLONAL	2	TRUE	1	0.547649406421527	3		650	1164	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705453	43705453	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	140	856	0	ENST00000382044.4:c.5169G>C	p.Gln1723His	p.Q1723H	ENST00000382044	NM_001141980.1	1723	caG/caC	24/28	0.547649406421527	1	FACETS	0.507	0.462	0.554	0.507	0.462	0.554	SUBCLONAL	1	TRUE	0	0.547649406421527	1		856	732	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778575	3778575	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	289	762	0	ENST00000262367.5:c.6473A>T	p.Gln2158Leu	p.Q2158L	ENST00000262367	NM_004380.2	2158	cAg/cTg	31/31	0.270895046653589	2	FACETS	1	0.993	1	0.685	0.648	0.724	INDETERMINATE	1	TRUE	0	0.547649406421527	2		762	770	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632768	23632768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	93	761	0	ENST00000261584.4:c.3028G>A	p.Glu1010Lys	p.E1010K	ENST00000261584	NM_024675.3	1010	Gag/Aag	10/13	0.270895046653589	2	FACETS	0.444	0.394	0.497	0.222	0.197	0.249	INDETERMINATE	1	TRUE	0	0.547649406421527	2		761	765	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646626	23646626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749461008	NA	P-0019977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	105	646	1	ENST00000261584.4:c.1241G>A	p.Arg414Gln	p.R414Q	ENST00000261584	NM_024675.3	414	cGa/cAa	4/13	0.270895046653589	2	FACETS	0.521	0.467	0.579	0.261	0.233	0.29	INDETERMINATE	1	TRUE	0	0.547649406421527	2		647	736	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691025	NA	P-0019977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	547	579	0	ENST00000269305.4:c.785G>T	p.Gly262Val	p.G262V	ENST00000269305	NM_001126112.2	262	gGt/gTt	8/11	0.297810720097059	3	FACETS	0.962	0.931	0.992			1	INDETERMINATE	3	TRUE	NA	0.547649406421527	3		579	882	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761481	59761481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	63	541	0	ENST00000259008.2:c.2926G>A	p.Glu976Lys	p.E976K	ENST00000259008	NM_032043.2	976	Gaa/Aaa	20/20	0.268111248933326	5	FACETS	0.549	0.474	0.631	0.183	0.158	0.211	INDETERMINATE	1	TRUE	2	0.547649406421527	5		541	763	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266796	198266796	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	487	805	0	ENST00000335508.6:c.2136G>T	p.Leu712Phe	p.L712F	ENST00000335508	NM_012433.2	712	ttG/ttT	15/25	0.244591642816791	3	FACETS	1	0.993	1	0.767	0.738	0.797	INDETERMINATE	2	TRUE	0	0.547649406421527	3		805	984	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155457	47155457	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0019977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	240	654	0	ENST00000409792.3:c.4624A>T	p.Arg1542Ter	p.R1542*	ENST00000409792	NM_014159.6	1542	Aga/Tga	5/21	0.277331665548882	3	FACETS	0.764	0.716	0.812	0.764	0.716	0.812	INDETERMINATE	2	TRUE	1	0.547649406421527	3		654	731	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014360	70014360	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	388	753	0	ENST00000394351.3:c.1221G>C	p.Arg407Ser	p.R407S	ENST00000394351	NM_000248.3	407	agG/agC	9/9	0.277331665548882	3	FACETS	0.881	0.84	0.924	0.881	0.84	0.924	INDETERMINATE	2	TRUE	1	0.547649406421527	3		753	1024	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967290	134967290	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	221	826	1	ENST00000398015.3:c.2629A>T	p.Thr877Ser	p.T877S	ENST00000398015	NM_004441.4	877	Acc/Tcc	14/16	1	2	FACETS	0.953	0.888	1	0.953	0.888	1	CLONAL	1	TRUE	1	0.547649406421527	2		827	847	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149498409	149498409	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	181	757	0	ENST00000261799.4:c.2805G>C	p.Glu935Asp	p.E935D	ENST00000261799	NM_002609.3	935	gaG/gaC	21/23	1	2	FACETS	0.998	0.925	1	0.998	0.925	1	CLONAL	1	TRUE	1	0.547649406421527	2		757	662	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459484	50459484	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	267	570	0	ENST00000331340.3:c.773C>T	p.Ser258Leu	p.S258L	ENST00000331340	NM_006060.4	258	tCa/tTa	7/8	0.495390189926497	4	FACETS	1	0.991	1	0.448	0.42	0.477	CLONAL	1	TRUE	1	0.547649406421527	4		570	1123	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054762	5054762	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	88	571	0	ENST00000381652.3:c.814G>A	p.Val272Ile	p.V272I	ENST00000381652	NM_004972.3	272	Gta/Ata	7/25	0.547649406421527	2	FACETS	0.579	0.514	0.648	0.29	0.257	0.324	SUBCLONAL	1	TRUE	0	0.547649406421527	2		571	555	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971116	21971116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552823	NA	P-0019977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	437	641	0	ENST00000304494.5:c.242C>T	p.Pro81Leu	p.P81L	ENST00000304494	NM_000077.4	81	cCc/cTc	2/3	0.303701856775924	3	FACETS	0.894	0.861	0.927	0.894	0.861	0.927	INDETERMINATE	3	TRUE	0	0.547649406421527	3		641	758	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814758	139814758	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779694447	NA	P-0019977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	204	913	0	ENST00000247668.2:c.751G>T	p.Val251Leu	p.V251L	ENST00000247668	NM_021138.3	251	Gtg/Ttg	8/11	1	2	FACETS	0.893	0.83	0.959	0.893	0.83	0.959	CLONAL	1	TRUE	1	0.547649406421527	2		913	834	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352710	70352710	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	158	659	0	ENST00000374080.3:c.4431C>G	p.Ser1477Arg	p.S1477R	ENST00000374080		1477	agC/agG	32/45	1	2	FACETS	0.722	0.662	0.785	0.722	0.662	0.785	SUBCLONAL	1	TRUE	1	0.547649406421527	2		659	799	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219381	1219381	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	145	931	1	ENST00000326873.7:c.433G>T	p.Glu145Ter	p.E145*	ENST00000326873	NM_000455.4	145	Gag/Tag	3/10	0.283575731529128	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	FALSE	0	0.322551493481519	1		932	734	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882025	NA	P-0019978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	115	1046	1	ENST00000269305.4:c.646G>T	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ttg	6/11	1	2	FACETS	0.715	0.643	0.792	0.715	0.643	0.792	SUBCLONAL	1	FALSE	1	0.322551493481519	2		1047	997	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400147	139400147	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	60	935	3	ENST00000277541.6:c.4201G>T	p.Gly1401Trp	p.G1401W	ENST00000277541	NM_017617.3	1401	Ggg/Tgg	25/34	0.118629021606874	0	FACETS	0.33	0.284	0.381			1	INDETERMINATE	1	FALSE	0	0.322551493481519	0		938	763	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426876	70426877	+	missense_variant	Missense_Mutation	DNP	TG	TG	CT	novel	NA	P-0019978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	93	721	1	ENST00000373644.4:c.4536_4537delinsCT	p.Ala1513Ser	p.A1513S	ENST00000373644	NM_030625.2	1512	acTGct/acCTct	7/12	0.179042021700776	1	FACETS	0.673	0.598	0.752	0.673	0.598	0.752	INDETERMINATE	1	FALSE	0	0.322551493481519	1		722	719	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129804	108129804	+	splice_donor_variant	Splice_Site	SNP	T	T	G	rs878853495	NA	P-0019978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	85	527	0	ENST00000278616.4:c.2466+2T>G		p.X822_splice	ENST00000278616	NM_000051.3	822			1	2	FACETS	0.754	0.666	0.848	0.754	0.666	0.848	SUBCLONAL	1	FALSE	1	0.322551493481519	2		527	699	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896966	28896966	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	110	761	3	ENST00000282397.4:c.2914C>A	p.Gln972Lys	p.Q972K	ENST00000282397	NM_002019.4	972	Cag/Aag	21/30	0.276287296719321	1	FACETS	0.796	0.715	0.881	0.796	0.715	0.881	SUBCLONAL	1	FALSE	0	0.322551493481519	1		764	719	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29002027	29002027	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	122	672	0	ENST00000282397.4:c.1138T>C	p.Ser380Pro	p.S380P	ENST00000282397	NM_002019.4	380	Tct/Cct	9/30	0.276287296719321	1	FACETS	0.924	0.836	1	0.924	0.836	1	CLONAL	1	FALSE	0	0.322551493481519	1		672	687	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239723	41239723	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	61	942	0	ENST00000379561.5:c.627G>T	p.Trp209Cys	p.W209C	ENST00000379561	NM_002015.3	209	tgG/tgT	1/3	0.276287296719321	1	FACETS	0.42	0.361	0.483	0.42	0.361	0.483	SUBCLONAL	1	FALSE	0	0.322551493481519	1		942	756	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347853	73347853	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1310582067	NA	P-0019978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	73	520	0	ENST00000377767.4:c.1208A>T	p.Asp403Val	p.D403V	ENST00000377767	NM_014953.3	403	gAt/gTt	8/21	NA	2	FACETS	0.826	0.723	0.936			1	INDETERMINATE	1	FALSE	NA	0.322551493481519	2		520	548	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129797	30129797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	112	781	0	ENST00000263025.4:c.416G>A	p.Ser139Asn	p.S139N	ENST00000263025	NM_002746.2	139	aGc/aAc	3/9	0.283575731529128	1	FACETS	0.842	0.758	0.93	0.842	0.758	0.93	CLONAL	1	FALSE	0	0.322551493481519	1		781	692	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553570	29553570	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	40	266	0	ENST00000356175.3:c.2119A>T	p.Met707Leu	p.M707L	ENST00000356175	NM_000267.3	707	Atg/Ttg	18/57	1	2	FACETS	0.83	0.692	0.981	0.83	0.692	0.981	CLONAL	1	FALSE	1	0.322551493481519	2		266	299	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78921128	78921128	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	120	739	0	ENST00000306801.3:c.3242G>T	p.Cys1081Phe	p.C1081F	ENST00000306801	NM_020761.2	1081	tGc/tTc	27/34	1	2	FACETS	0.987	0.892	1	0.987	0.892	1	CLONAL	1	FALSE	1	0.322551493481519	2		739	754	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279691	18279691	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	95	651	0	ENST00000222254.8:c.1964A>T	p.Tyr655Phe	p.Y655F	ENST00000222254	NM_005027.3	655	tAc/tTc	15/16	0.283575731529128	1	FACETS	0.853	0.761	0.951	0.853	0.761	0.951	CLONAL	1	FALSE	0	0.322551493481519	1		651	579	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484768	57484768	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	79	822	0	ENST00000371085.3:c.748A>T	p.Ser250Cys	p.S250C	ENST00000371085	NM_000516.4	250	Agc/Tgc	10/13	0.283575731529128	1	FACETS	0.505	0.443	0.571	0.505	0.443	0.571	SUBCLONAL	1	FALSE	0	0.322551493481519	1		822	814	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825326	134825326	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	76	594	0	ENST00000398015.3:c.842C>G	p.Ala281Gly	p.A281G	ENST00000398015	NM_004441.4	281	gCt/gGt	4/16	0.283575731529128	1	FACETS	0.735	0.645	0.83	0.735	0.645	0.83	SUBCLONAL	1	FALSE	0	0.322551493481519	1		594	538	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982115	38982115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	73	578	0	ENST00000357387.3:c.607G>A	p.Ala203Thr	p.A203T	ENST00000357387	NM_152756.3	203	Gcc/Acc	8/38	0.322551493481519	6	FACETS	0.773	0.674	0.88			1	SUBCLONAL	1	FALSE	NA	0.322551493481519	6		578	963	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982018	93982018	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0019978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	66	442	0	ENST00000369303.4:c.1447A>T	p.Lys483Ter	p.K483*	ENST00000369303	NM_004440.3	483	Aaa/Taa	6/17	0.283575731529128	1	FACETS	0.992	0.867	1	0.992	0.867	1	CLONAL	1	FALSE	0	0.322551493481519	1		442	346	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5029906	5029906	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	48	642	0	ENST00000381652.3:c.350G>A	p.Arg117Lys	p.R117K	ENST00000381652	NM_004972.3	117	aGa/aAa	4/25	0.232388497675737	0	FACETS	0.375	0.316	0.439			1	SUBCLONAL	1	FALSE	0	0.322551493481519	0		642	538	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549130	87549130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	59	828	0	ENST00000277120.3:c.1687G>A	p.Gly563Arg	p.G563R	ENST00000277120		563	Gga/Aga	15/19	0.118629021606874	0	FACETS	0.336	0.289	0.388			1	INDETERMINATE	1	FALSE	0	0.322551493481519	0		828	737	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209591	98209591	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs147067171	NA	P-0019978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	59	688	0	ENST00000331920.6:c.3947A>G	p.Tyr1316Cys	p.Y1316C	ENST00000331920	NM_000264.3	1316	tAc/tGc	23/24	0.118629021606874	0	FACETS	0.417	0.359	0.481			1	INDETERMINATE	1	FALSE	0	0.322551493481519	0		688	594	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858125	152858125	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	125	501	2	ENST00000406277.2:c.490G>C	p.Val164Leu	p.V164L	ENST00000406277	NM_152274.4	164	Gtt/Ctt	6/7	1	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	0	0.322551493481519	1		503	472	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389363	8389364	+	missense_variant	Missense_Mutation	DNP	AC	AC	GG	novel	NA	P-0019978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	54	704	0	ENST00000356435.5:c.4254_4255delinsCC	p.Tyr1419His	p.Y1419H	ENST00000356435		1418	ggGTat/ggCCat	26/35	0.232388497675737	0	FACETS	0.384	0.327	0.446			1	SUBCLONAL	1	FALSE	0	0.322551493481519	0		704	591	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	85	424	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	0.25	2		424	644	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0019980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	173	709	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.231536410137635	3	FACETS	0.909	0.841	0.978	0.909	0.841	0.978	CLONAL	3	TRUE	0	0.25	3		709	571	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0019980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	135	891	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.219460454628682	2	FACETS	0.882	0.805	0.963	0.882	0.805	0.963	CLONAL	2	TRUE	0	0.25	2		891	612	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589581	67589583	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	novel	NA	P-0019980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	85	670	0	ENST00000274335.5:c.1345_1347del	p.Leu449del	p.L449del	ENST00000274335		448	aaATTa/aaa	10/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.25	2		670	572	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372036	55372037	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0019980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	37	766	0	ENST00000297316.4:c.730dup	p.Asp244GlyfsTer121	p.D244Gfs*121	ENST00000297316	NM_022454.3	242	-/G	2/2	1	2	FACETS	0.495	0.407	0.594	0.495	0.407	0.594	SUBCLONAL	1	TRUE	1	0.25	2		766	598	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249013	55249014	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACCCCC	novel	NA	P-0019981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	994	489	1	ENST00000275493.2:c.2314_2319dup	p.Pro772_His773dup	p.P772_H773dup	ENST00000275493	NM_005228.3	772	aac/aACCCCCac	20/28	0.805209265441267	4	FACETS	0.948	0.926	0.97	0.948	0.926	0.97	CLONAL	3	TRUE	1	0.805209265441267	4		490	1567	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0019981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	225	350	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	0.805209265441267	2		350	530	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012462	29012462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	277	740	0	ENST00000282397.4:c.409G>A	p.Glu137Lys	p.E137K	ENST00000282397	NM_002019.4	137	Gag/Aag	4/30	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.805209265441267	2		740	655	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118350	17118350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750535468	NA	P-0019981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1703	188	1064	1	ENST00000285071.4:c.1487C>T	p.Ser496Phe	p.S496F	ENST00000285071	NM_144997.5	496	tCt/tTt	13/14	0.422572820717676	5	FACETS	0.545	0.501	0.591	0.109	0.1	0.119	INDETERMINATE	1	TRUE	0	0.805209265441267	5		1065	1891	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453149	140453149	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913361	NA	P-0019982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	59	734	0	ENST00000288602.6:c.1786G>C	p.Gly596Arg	p.G596R	ENST00000288602	NM_004333.4	596	Ggt/Cgt	15/18	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	FALSE	1	0.196783430322915	2		734	586	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599303	28599303	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1345330241	NA	P-0019982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	58	868	0	ENST00000253063.3:c.749G>A	p.Gly250Glu	p.G250E	ENST00000253063	NM_031459.4	250	gGg/gAg	5/10	1	2	FACETS	0.674	0.577	0.78	0.674	0.577	0.78	SUBCLONAL	1	FALSE	1	0.196783430322915	2		868	875	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120479951	120479951	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	74	796	0	ENST00000256646.2:c.3476A>G	p.Gln1159Arg	p.Q1159R	ENST00000256646	NM_024408.3	1159	cAg/cGg	21/34	1	2	FACETS	0.877	0.766	0.996	0.877	0.766	0.996	CLONAL	1	FALSE	1	0.196783430322915	2		796	858	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658577	206658577	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	61	652	0	ENST00000367120.3:c.1550A>T	p.Gln517Leu	p.Q517L	ENST00000367120	NM_014002.3	517	cAg/cTg	15/22	0.156248030353225	3	FACETS	0.9	0.775	1	0.45	0.387	0.518	CLONAL	1	FALSE	1	0.196783430322915	3		652	757	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236085	108236085	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	61	757	0	ENST00000278616.4:c.9021A>T	p.Glu3007Asp	p.E3007D	ENST00000278616	NM_000051.3	3007	gaA/gaT	63/63	0.196783430322915	1	FACETS	0.812	0.7	0.935	0.812	0.7	0.935	CLONAL	1	FALSE	0	0.196783430322915	1		757	688	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544075	18544075	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	35	507	0	ENST00000266497.5:c.1892G>T	p.Gly631Val	p.G631V	ENST00000266497		631	gGg/gTg	13/31	1	2	FACETS	0.866	0.71	1	0.866	0.71	1	CLONAL	1	FALSE	1	0.196783430322915	2		507	411	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437356	110437356	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	29	163	0	ENST00000375856.3:c.1045G>C	p.Ala349Pro	p.A349P	ENST00000375856	NM_003749.2	349	Gcc/Ccc	1/2	1	2	FACETS	1	0.837	1	1	0.959	1	CLONAL	2	FALSE	1	0.196783430322915	2		163	143	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996248	73996248	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	16	198	0	ENST00000318443.5:c.982C>T	p.Gln328Ter	p.Q328*	ENST00000318443	NM_001024736.1	328	Cag/Tag	5/10	1	2	FACETS	0.789	0.585	1	0.789	0.585	1	CLONAL	1	FALSE	1	0.196783430322915	2		198	206	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394747	45394747	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	80	700	1	ENST00000262160.6:c.602del	p.Pro201GlnfsTer37	p.P201Qfs*37	ENST00000262160	NM_005901.5	201	cCa/ca	5/11	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	1	0.196783430322915	2		701	751	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165599	185165599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	38	620	0	ENST00000265026.3:c.874G>A	p.Ala292Thr	p.A292T	ENST00000265026	NM_004721.4	292	Gcg/Acg	5/14	0.196783430322915	1	FACETS	0.639	0.527	0.764	0.639	0.527	0.764	SUBCLONAL	1	FALSE	0	0.196783430322915	1		620	545	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554338	141554338	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	79	977	0	ENST00000220592.5:c.1813del	p.Asp605MetfsTer90	p.D605Mfs*90	ENST00000220592	NM_012154.3	605	Gat/at	14/19	0.196783430322915	3	FACETS	0.824	0.723	0.934	0.412	0.361	0.467	CLONAL	1	FALSE	1	0.196783430322915	3		977	1070	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504275	8504275	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	47	675	0	ENST00000356435.5:c.1808G>C	p.Arg603Thr	p.R603T	ENST00000356435		603	aGa/aCa	12/35	1	2	FACETS	0.777	0.654	0.912	0.777	0.654	0.912	CLONAL	1	FALSE	1	0.196783430322915	2		675	615	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045030	47045030	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0019982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	92	960	1	ENST00000377604.3:c.2355+1G>T		p.X785_splice	ENST00000377604	NM_001204468.1	785			1	2	FACETS	0.991	0.879	1	0.991	0.879	1	CLONAL	1	FALSE	1	0.196783430322915	2		961	944	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201059	NA	P-0019984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	137	889	0	ENST00000269305.4:c.856G>T	p.Glu286Ter	p.E286*	ENST00000269305	NM_001126112.2	286	Gaa/Taa	8/11	1	2	FACETS	0.775	0.704	0.851	0.775	0.704	0.851	SUBCLONAL	1	TRUE	1	0.3	2		889	1178	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557387	95557387	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	79	625	0	ENST00000393063.1:c.5587G>C	p.Glu1863Gln	p.E1863Q	ENST00000393063	NM_030621.3	1863	Gaa/Caa	27/28	1	2	FACETS	0.628	0.551	0.71	0.628	0.551	0.71	SUBCLONAL	1	TRUE	1	0.3	2		625	839	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938891	178938891	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	28	322	0	ENST00000263967.3:c.2133G>C	p.Lys711Asn	p.K711N	ENST00000263967	NM_006218.2	711	aaG/aaC	14/21	1	2	FACETS	0.495	0.396	0.609	0.495	0.396	0.609	SUBCLONAL	1	TRUE	1	0.3	2		322	377	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242482	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAGCAAC	TTAAGAGAAGCAAC	CCGAG	novel	NA	P-0019984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	193	782	2	ENST00000275493.2:c.2239_2252delinsCCGAG	p.Leu747_Thr751delinsProArg	p.L747_T751delinsPR	ENST00000275493	NM_005228.3	747	TTAAGAGAAGCAACa/CCGAGa	19/28	0.3	4	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.3	4		784	1209	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932116	39932123	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGCAAA	GCTGCAAA	-	novel	NA	P-0019984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	103	841	0	ENST00000378444.4:c.2476_2483del	p.Phe826ArgfsTer8	p.F826Rfs*8	ENST00000378444	NM_001123385.1	826	TTTGCAGCa/a	4/15	1	2	FACETS	0.603	0.538	0.673	0.603	0.538	0.673	SUBCLONAL	1	TRUE	1	0.3	2		841	1138	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	226	122	0				ENST00000310581	NM_198253.2	-/1132			0.381767761264497	5	FACETS	0.92	0.858	0.984	0.613	0.572	0.656	CLONAL	2	TRUE	2	0.446075971616914	5		122	919	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0019985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	369	839	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.446075971616914	2	FACETS	0.936	0.892	0.98	0.936	0.892	0.98	CLONAL	2	TRUE	0	0.446075971616914	2		841	884	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776783	NA	P-0019985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	180	318	0	ENST00000267163.4:c.1215+1G>A		p.X405_splice	ENST00000267163	NM_000321.2	405			0.446075971616914	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	0	0.446075971616914	2		318	403	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0019986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	63	606	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.821	0.708	0.945	0.821	0.708	0.945	CLONAL	1	TRUE	1	0.14	2		606	1096	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0019986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	56	531	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	0.14	2		531	676	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0019986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	68	440	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.974	0.845	1	0.974	0.845	1	CLONAL	1	TRUE	1	0.14	2		440	997	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979987	7979987	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746723399	NA	P-0019986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	65	885	1	ENST00000319144.4:c.1350del	p.Leu451SerfsTer16	p.L451Sfs*16	ENST00000319144	NM_001139.2	450	ggG/gg	10/15	1	2	FACETS	0.881	0.761	1	0.881	0.761	1	CLONAL	1	TRUE	1	0.14	2		886	1054	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463206	25463206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1369746569	NA	P-0019986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	61	803	0	ENST00000264709.3:c.2287G>A	p.Val763Ile	p.V763I	ENST00000264709	NM_175629.2	763	Gtt/Att	19/23	1	2	FACETS	0.81	0.696	0.934	0.81	0.696	0.934	CLONAL	1	TRUE	1	0.14	2		803	1076	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023949	31023949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777670355	NA	P-0019986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	57	811	1	ENST00000375687.4:c.3434G>A	p.Gly1145Asp	p.G1145D	ENST00000375687	NM_015338.5	1145	gGc/gAc	13/13	1	2	FACETS	0.734	0.627	0.851	0.734	0.627	0.851	SUBCLONAL	1	TRUE	1	0.14	2		812	1110	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936518	49936518	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867261592	NA	P-0019986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	76	899	3	ENST00000296474.3:c.1409G>A	p.Arg470His	p.R470H	ENST00000296474	NM_002447.2	470	cGt/cAt	2/20	1	2	FACETS	0.942	0.823	1	0.942	0.823	1	CLONAL	1	TRUE	1	0.14	2		902	1153	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101125	41101125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756719404	NA	P-0019986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	47	748	1	ENST00000373198.4:c.1231G>A	p.Gly411Ser	p.G411S	ENST00000373198	NM_133170.3	411	Ggc/Agc	8/32	1	2	FACETS	0.819	0.689	0.963	0.819	0.689	0.963	CLONAL	1	TRUE	1	0.14	2		749	820	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991757	72991758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760959844	NA	P-0019986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	37	473	0	ENST00000268489.5:c.2287dup	p.Glu763GlyfsTer26	p.E763Gfs*26	ENST00000268489	NM_006885.3	763	gag/gGag	2/10	1	2	FACETS	0.762	0.626	0.914	0.762	0.626	0.914	CLONAL	1	TRUE	1	0.14	2		473	694	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720649	89720649	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs587782455	NA	P-0019986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	42	327	0	ENST00000371953.3:c.802-2A>G		p.X268_splice	ENST00000371953	NM_000314.4	268			1	2	FACETS	0.89	0.746	1	1	0.966	1	CLONAL	2	TRUE	1	0.14	2		327	337	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214871	36214871	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1282	71	885	1	ENST00000222270.7:c.3302del	p.Pro1101LeufsTer81	p.P1101Lfs*81	ENST00000222270	NM_014727.1	1099	ggC/gg	8/37	1	2	FACETS	0.75	0.652	0.857	0.75	0.652	0.857	SUBCLONAL	1	TRUE	1	0.14	2		886	1353	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916935	178916935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	41	700	1	ENST00000263967.3:c.322C>T	p.Arg108Cys	p.R108C	ENST00000263967	NM_006218.2	108	Cgt/Tgt	2/21	1	2	FACETS	0.726	0.603	0.864	0.726	0.603	0.864	SUBCLONAL	1	TRUE	1	0.14	2		701	807	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432347	49432347	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	68	935	1	ENST00000301067.7:c.8792del	p.Pro2931HisfsTer12	p.P2931Hfs*12	ENST00000301067	NM_003482.3	2931	cCa/ca	34/54	1	2	FACETS	0.843	0.73	0.965	0.843	0.73	0.965	CLONAL	1	TRUE	1	0.14	2		936	1153	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639326	3639326	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs779769996	NA	P-0019986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	63	973	0	ENST00000294008.3:c.4313T>C	p.Ile1438Thr	p.I1438T	ENST00000294008	NM_032444.2	1438	aTt/aCt	12/15	1	2	FACETS	0.82	0.707	0.944	0.82	0.707	0.944	CLONAL	1	TRUE	1	0.14	2		973	1097	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857491	68857491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	49	782	0	ENST00000261769.5:c.2126C>T	p.Ala709Val	p.A709V	ENST00000261769	NM_004360.3	709	gCc/gTc	13/16	1	2	FACETS	0.742	0.626	0.87	0.742	0.626	0.87	SUBCLONAL	1	TRUE	1	0.14	2		782	944	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980052	7980052	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	67	786	0	ENST00000319144.4:c.1285C>A	p.Pro429Thr	p.P429T	ENST00000319144	NM_001139.2	429	Ccc/Acc	10/15	1	2	FACETS	0.988	0.856	1	0.988	0.856	1	CLONAL	1	TRUE	1	0.14	2		786	969	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376268	15376268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536634033	NA	P-0019986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	59	709	1	ENST00000263377.2:c.746C>T	p.Thr249Met	p.T249M	ENST00000263377	NM_058243.2	249	aCg/aTg	5/20	1	2	FACETS	0.958	0.822	1	0.958	0.822	1	CLONAL	1	TRUE	1	0.14	2		710	880	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40742204	40742204	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	74	900	0	ENST00000392038.2:c.920T>C	p.Met307Thr	p.M307T	ENST00000392038	NM_001626.4	307	aTg/aCg	10/14	1	2	FACETS	0.85	0.741	0.968	0.85	0.741	0.968	CLONAL	1	TRUE	1	0.14	2		900	1244	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031235	36031235	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	78	816	0	ENST00000358208.4:c.1356del	p.Ile453SerfsTer3	p.I453Sfs*3	ENST00000358208		452	Ggg/gg	11/12	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.14	2		816	1094	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664819	138664819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	35	271	3	ENST00000330315.3:c.746C>T	p.Ala249Val	p.A249V	ENST00000330315	NM_023067.3	249	gCg/gTg	1/1	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.14	2		274	415	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801218	1801218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569221269	NA	P-0019986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	58	857	0	ENST00000260795.2:c.347G>A	p.Arg116His	p.R116H	ENST00000260795		116	cGc/cAc	2/17	1	2	FACETS	0.719	0.615	0.833	0.719	0.615	0.833	SUBCLONAL	1	TRUE	1	0.14	2		857	1153	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750762	57750762	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	48	599	0	ENST00000274289.3:c.1842G>A	p.Met614Ile	p.M614I	ENST00000274289	NM_006622.3	614	atG/atA	13/14	1	2	FACETS	0.804	0.677	0.944	0.804	0.677	0.944	CLONAL	1	TRUE	1	0.14	2		599	853	SUCCESS
APC	324	MSKCC	GRCh37	5	112157626	112157626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554080697	NA	P-0019986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	50	754	0	ENST00000257430.4:c.1346C>T	p.Ala449Val	p.A449V	ENST00000257430	NM_000038.5	449	gCt/gTt	11/16	1	2	FACETS	0.871	0.737	1	0.871	0.737	1	CLONAL	1	TRUE	1	0.14	2		754	820	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030364	180030364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	61	807	2	ENST00000261937.6:c.3920C>T	p.Ala1307Val	p.A1307V	ENST00000261937	NM_182925.4	1307	gCt/gTt	30/30	1	2	FACETS	0.766	0.658	0.884	0.766	0.658	0.884	SUBCLONAL	1	TRUE	1	0.14	2		809	1138	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141582970	141582970	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1194	83	902	0	ENST00000220592.5:c.277del	p.Val93CysfsTer46	p.V93Cfs*46	ENST00000220592	NM_012154.3	93	Gtg/tg	3/19	1	2	FACETS	0.929	0.816	1	0.929	0.816	1	CLONAL	1	TRUE	1	0.14	2		902	1277	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922105	39922105	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1205	74	962	0	ENST00000378444.4:c.4067A>G	p.Lys1356Arg	p.K1356R	ENST00000378444	NM_001123385.1	1356	aAg/aGg	9/15	1	2	FACETS	0.827	0.721	0.941	0.827	0.721	0.941	CLONAL	1	TRUE	1	0.14	2		962	1279	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123159696	123159707	+	inframe_deletion	In_Frame_Del	DEL	AGAAACACATTT	AGAAACACATTT	-	novel	NA	P-0019986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	37	688	0	ENST00000218089.9:c.51_62del	p.Glu18_Phe21del	p.E18_F21del	ENST00000218089	NM_001042749.1	17	tcAGAAACACATTTt/tct	4/35	1	2	FACETS	0.798	0.657	0.958	0.798	0.657	0.958	CLONAL	1	TRUE	1	0.14	2		688	662	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576888	7576888	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0019987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	145	897	1	ENST00000269305.4:c.958A>T	p.Lys320Ter	p.K320*	ENST00000269305	NM_001126112.2	320	Aag/Tag	9/11	0.253746654495959	2	FACETS	1	0.983	1	0.649	0.594	0.707	CLONAL	1	FALSE	0	0.343117622564293	2		898	651	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539951	187539951	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs777631605	NA	P-0019987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	86	552	0	ENST00000441802.2:c.7789C>T	p.Arg2597Ter	p.R2597*	ENST00000441802	NM_005245.3	2597	Cga/Tga	10/27	1	2	FACETS	0.957	0.849	1	0.957	0.849	1	CLONAL	1	FALSE	1	0.343117622564293	2		552	524	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118368660	118368660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555044474	NA	P-0019987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	135	519	0	ENST00000534358.1:c.5674C>T	p.Arg1892Cys	p.R1892C	ENST00000534358	NM_005933.3	1892	Cgt/Tgt	21/36	0.209634286164397	4	FACETS	1	0.985	1	0.717	0.652	0.785	CLONAL	1	FALSE	2	0.343117622564293	4		519	737	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060903	38060904	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0019987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	106	554	0	ENST00000250448.2:c.1084_1085dup	p.Gly363ProfsTer27	p.G363Pfs*27	ENST00000250448	NM_004496.3	362	tcc/tcTCc	2/2	0.209634286164397	4	FACETS	0.815	0.734	0.901	0.815	0.734	0.901	CLONAL	2	FALSE	2	0.343117622564293	4		554	509	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131462	202131462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	58	758	0	ENST00000358485.4:c.430G>A	p.Glu144Lys	p.E144K	ENST00000358485	NM_001080125.1	144	Gag/Aag	2/9	0.179455482429969	3	FACETS	0.545	0.467	0.63	0.182	0.155	0.21	INDETERMINATE	1	FALSE	0	0.343117622564293	3		758	727	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960080	134960080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1042786	NA	P-0019988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	47	997	2	ENST00000398015.3:c.2437G>A	p.Val813Ile	p.V813I	ENST00000398015	NM_004441.4	813	Gtc/Atc	13/16	1	2	FACETS	0.865	0.729	1	0.865	0.729	1	CLONAL	1	TRUE	1	0.16	2		999	679	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239530	123239530	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	57	1153	2	ENST00000358487.5:c.2307C>A	p.Tyr769Ter	p.Y769*	ENST00000358487	NM_000141.4	769	taC/taA	18/18	1	2	FACETS	0.822	0.703	0.952	0.822	0.703	0.952	CLONAL	1	TRUE	1	0.16	2		1155	867	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	60	999	0	ENST00000267101.3:c.850G>C	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Cga	7/28	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.16	2		999	735	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243224	123243225	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0019988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	47	1093	0	ENST00000358487.5:c.2288_2289del	p.Leu763HisfsTer4	p.L763Hfs*4	ENST00000358487	NM_000141.4	763	cTC/c	17/18	1	2	FACETS	0.868	0.731	1	0.868	0.731	1	CLONAL	1	TRUE	1	0.16	2		1093	677	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999024	100999024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778694496	NA	P-0019988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	38	783	0	ENST00000325455.5:c.778G>A	p.Ala260Thr	p.A260T	ENST00000325455	NM_001202474.3	260	Gcg/Acg	1/8	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.16	2		783	365	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900206	101900206	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727503470	NA	P-0019988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	35	665	0	ENST00000374994.4:c.640G>A	p.Gly214Ser	p.G214S	ENST00000374994	NM_004612.2	214	Ggt/Agt	4/9	1	2	FACETS	0.882	0.722	1	0.882	0.722	1	CLONAL	1	TRUE	1	0.16	2		665	496	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929273	44929274	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0019988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	52	602	0	ENST00000377967.4:c.2375_2376del	p.Val792GlyfsTer6	p.V792Gfs*6	ENST00000377967	NM_021140.2	791	aaTGtg/aatg	17/29	1	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.16	1		602	432	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0019989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	206	763	2	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.484224522165956	2	FACETS	0.976	0.917	1	0.976	0.917	1	CLONAL	2	TRUE	0	0.484224522165956	2		765	436	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0019989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	268	926	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.484224522165956	NA		926	636	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976706	2976706	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1044557293	NA	P-0019989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	222	521	0	ENST00000396946.4:c.1306C>T	p.Arg436Trp	p.R436W	ENST00000396946	NM_032415.4	436	Cgg/Tgg	9/25	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.484224522165956	2		521	699	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468071	50468071	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770657999	NA	P-0019989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	36	460	0	ENST00000331340.3:c.1306G>A	p.Asp436Asn	p.D436N	ENST00000331340	NM_006060.4	436	Gac/Aac	8/8	0.170177458951239	4	FACETS	0.417	0.342	0.501	0.209	0.171	0.251	INDETERMINATE	1	TRUE	2	0.484224522165956	4		460	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579401	7579401	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	241	758	0	ENST00000269305.4:c.286del	p.Ser96LeufsTer27	p.S96Lfs*27	ENST00000269305	NM_001126112.2	96	Tct/ct	4/11	0.487473143448482	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.484224522165956	1		758	705	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612974	228612974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756810829	NA	P-0019989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	153	461	0	ENST00000366696.1:c.53G>A	p.Arg18His	p.R18H	ENST00000366696	NM_003493.2	18	cGc/cAc	1/1	0.275849037517224	3	FACETS	0.814	0.751	0.88	0.814	0.751	0.88	INDETERMINATE	2	TRUE	1	0.484224522165956	3		461	482	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121936	2121936	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0019989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	138	678	1	ENST00000219476.3:c.2097+1G>T		p.X699_splice	ENST00000219476	NM_000548.3	699			0.298272141404247	3	FACETS	0.947	0.862	1	0.473	0.431	0.518	CLONAL	1	TRUE	1	0.484224522165956	3		679	748	SUCCESS
APC	324	MSKCC	GRCh37	5	112175511	112175512	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0019989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	212	504	0	ENST00000257430.4:c.4221_4222del	p.Ser1407ArgfsTer15	p.S1407Rfs*15	ENST00000257430	NM_000038.5	1407	aGT/a	16/16	0.484224522165956	2	FACETS	0.975	0.917	1	0.975	0.917	1	CLONAL	2	TRUE	0	0.484224522165956	2		504	449	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725526	117725526	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	38	622	0	ENST00000368508.3:c.355T>G	p.Trp119Gly	p.W119G	ENST00000368508	NM_002944.2	119	Tgg/Ggg	5/43	1	2	FACETS	0.243	0.2	0.291	0.243	0.2	0.291	SUBCLONAL	1	TRUE	1	0.484224522165956	2		622	646	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128268639	128268639	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	277	757	1	ENST00000265960.3:c.1016G>A	p.Ser339Asn	p.S339N	ENST00000265960	NM_001006617.1	339	aGc/aAc	8/12	0.218500269390528	2	FACETS	1	0.992	1	0.674	0.635	0.714	INDETERMINATE	1	TRUE	0	0.484224522165956	2		758	849	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0019991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	491	895	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	0.512710725177405	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.512710725177405	2		895	893	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187799	11187799	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	187	801	0	ENST00000361445.4:c.6098A>G	p.Glu2033Gly	p.E2033G	ENST00000361445	NM_004958.3	2033	gAg/gGg	44/58	0.49117912715331	4	FACETS	0.879	0.81	0.95			1	CLONAL	1	TRUE	NA	0.512710725177405	4		801	1256	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325149	39325149	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1841	201	804	1	ENST00000373001.3:c.170C>T	p.Ala57Val	p.A57V	ENST00000373001	NM_022157.3	57	gCt/gTt	1/7	0.512710725177405	7	FACETS	0.876	0.808	0.947			1	CLONAL	1	TRUE	NA	0.512710725177405	7		805	2042	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349967	15349967	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1272	192	770	0	ENST00000263377.2:c.3685C>G	p.Arg1229Gly	p.R1229G	ENST00000263377	NM_058243.2	1229	Cgc/Ggc	18/20	0.476978804402067	5	FACETS	0.905	0.834	0.979	0.302	0.278	0.327	CLONAL	1	TRUE	2	0.512710725177405	5		770	1464	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170020843	170020844	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0019991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	172	440	0	ENST00000295797.4:c.1719_1720delinsTT	p.Lys573_Ile574delinsAsnPhe	p.K573_I574delinsNF	ENST00000295797	NM_002740.5	573	aaGAtt/aaTTtt	18/18	0.476978804402067	5	FACETS	0.935	0.864	1	0.623	0.576	0.672	CLONAL	2	TRUE	2	0.512710725177405	5		440	635	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0019993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	384	528	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.928620762841914	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.973406057811303	1		530	401	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720819	89720819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	189	279	0	ENST00000371953.3:c.970G>A	p.Asp324Asn	p.D324N	ENST00000371953	NM_000314.4	324	Gat/Aat	8/9	0.973019803731552	1	FACETS	0.992	0.968	1	0.992	0.968	1	CLONAL	1	TRUE	0	0.973406057811303	1		279	201	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720840	89720840	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	175	322	0	ENST00000371953.3:c.991G>A	p.Asp331Asn	p.D331N	ENST00000371953	NM_000314.4	331	Gac/Aac	8/9	0.973019803731552	1	FACETS	0.992	0.968	1	0.992	0.968	1	CLONAL	1	TRUE	0	0.973406057811303	1		322	186	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941630	48941630	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1566194312	NA	P-0019993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	308	370	0	ENST00000267163.4:c.940G>T	p.Val314Phe	p.V314F	ENST00000267163	NM_000321.2	314	Gtt/Ttt	10/27	0.966481024230337	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.973406057811303	1		370	320	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593597	55593602	+	inframe_deletion	In_Frame_Del	DEL	GTACAG	GTACAG	-	novel	NA	P-0019993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	646	635	0	ENST00000288135.5:c.1663_1668del	p.Val555_Gln556del	p.V555_Q556del	ENST00000288135	NM_000222.2	555	GTACAG/-	11/21	NA	2	FACETS	0.991	0.981	0.999			1	INDETERMINATE	2	TRUE	NA	0.973406057811303	2		635	670	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410313	63410313	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs768563880	NA	P-0019993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	402	419	1	ENST00000330258.3:c.2854C>A	p.Pro952Thr	p.P952T	ENST00000330258	NM_152424.3	952	Ccc/Acc	2/2	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.973406057811303	1		420	416	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725042	89725042	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1085308041	NA	P-0019994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	30	309	0	ENST00000371953.3:c.1027-2A>G		p.X343_splice	ENST00000371953	NM_000314.4	343			1	2	FACETS	0.796	0.644	0.968	0.796	0.644	0.968	CLONAL	1	TRUE	1	0.27	2		309	279	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0019994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	65	403	1	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	0.975	0.847	1	0.975	0.847	1	CLONAL	1	TRUE	1	0.27	2		404	494	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591140	67591141	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0019994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	56	501	0	ENST00000274335.5:c.1735dup	p.Gln579ProfsTer23	p.Q579Pfs*23	ENST00000274335		578	gac/gaCc	12/15	1	2	FACETS	0.883	0.757	1	0.883	0.757	1	CLONAL	1	TRUE	1	0.27	2		501	470	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105634	27105635	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0019994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	95	581	0	ENST00000324856.7:c.5246_5247dup	p.Phe1750GlyfsTer21	p.F1750Gfs*21	ENST00000324856	NM_006015.4	1749	agg/aGGgg	20/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.27	2		581	615	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624283	89624284	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0019994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	105	568	0	ENST00000371953.3:c.59dup	p.Phe21IlefsTer23	p.F21Ifs*23	ENST00000371953	NM_000314.4	19	-/G	1/9	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.27	2		568	722	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259259	89259259	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	31	521	0	ENST00000336596.2:c.403T>C	p.Phe135Leu	p.F135L	ENST00000336596	NM_005233.5	135	Ttt/Ctt	3/17	1	2	FACETS	0.419	0.338	0.511	0.419	0.338	0.511	SUBCLONAL	1	TRUE	1	0.27	2		521	548	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469820	157469820	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	104	725	0	ENST00000346085.5:c.2616del	p.Gly873ValfsTer41	p.G873Vfs*41	ENST00000346085	NM_020732.3	872	Ccc/cc	9/20	1	2	FACETS	0.99	0.887	1	0.99	0.887	1	CLONAL	1	TRUE	1	0.27	2		725	778	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0019998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	230	575	2	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	NA	2	FACETS	0.958	0.895	1			1	INDETERMINATE	1	TRUE	NA	0.576273977629544	2		577	833	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375194	31375194	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	34	826	2	ENST00000328111.2:c.596del	p.Gly199AlafsTer27	p.G199Afs*27	ENST00000328111	NM_006892.3	197	caG/ca	6/23	0.576273977629544	1	FACETS	0.145	0.117	0.175	0.145	0.117	0.175	SUBCLONAL	1	TRUE	0	0.576273977629544	1		828	581	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281435	142281435	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	192	878	0	ENST00000350721.4:c.809del	p.Phe270SerfsTer8	p.F270Sfs*8	ENST00000350721	NM_001184.3	270	tTc/tc	4/47	0.275411219182799	1	FACETS	0.46	0.425	0.496	0.46	0.425	0.496	INDETERMINATE	1	TRUE	0	0.576273977629544	1		878	1032	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050241	13050241	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0019998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	53	532	0	ENST00000316448.5:c.194-1G>T		p.X65_splice	ENST00000316448	NM_004343.3	65			0.576273977629544	1	FACETS	0.309	0.264	0.358	0.309	0.264	0.358	SUBCLONAL	1	TRUE	0	0.576273977629544	1		532	424	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11313982	11313982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	142	969	1	ENST00000361445.4:c.754G>A	p.Glu252Lys	p.E252K	ENST00000361445	NM_004958.3	252	Gag/Aag	6/58	0.304924731701258	1	FACETS	0.403	0.367	0.441	0.403	0.367	0.441	INDETERMINATE	1	TRUE	0	0.576273977629544	1		970	870	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420730	49420730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201855029	NA	P-0019998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	203	802	1	ENST00000301067.7:c.15019C>T	p.Arg5007Trp	p.R5007W	ENST00000301067	NM_003482.3	5007	Cgg/Tgg	48/54	0.576273977629544	1	FACETS	0.997	0.933	1	0.997	0.933	1	CLONAL	1	TRUE	0	0.576273977629544	1		803	503	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487975	56487975	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0019998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	74	618	0	ENST00000267101.3:c.1704+2T>C		p.X568_splice	ENST00000267101	NM_001982.3	568			0.576273977629544	1	FACETS	0.432	0.38	0.488	0.432	0.38	0.488	SUBCLONAL	1	TRUE	0	0.576273977629544	1		618	423	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541748	120541748	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	62	631	0	ENST00000229340.5:c.109T>C	p.Tyr37His	p.Y37H	ENST00000229340	NM_006861.6	37	Tac/Cac	3/6	0.576273977629544	1	FACETS	0.298	0.257	0.342	0.298	0.257	0.342	SUBCLONAL	1	TRUE	0	0.576273977629544	1		631	514	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661917	29661917	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	249	788	0	ENST00000356175.3:c.5815del	p.Cys1939AlafsTer19	p.C1939Afs*19	ENST00000356175	NM_000267.3	1937	cgT/cg	39/57	0.576273977629544	1	FACETS	0.909	0.855	0.964	0.909	0.855	0.964	CLONAL	1	TRUE	0	0.576273977629544	1		788	677	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226492	1226492	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881990	NA	P-0019998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	109	820	1	ENST00000326873.7:c.1148G>A	p.Arg383His	p.R383H	ENST00000326873	NM_000455.4	383	cGc/cAc	9/10	0.576273977629544	1	FACETS	0.444	0.4	0.491	0.444	0.4	0.491	SUBCLONAL	1	TRUE	0	0.576273977629544	1		821	606	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795417	42795417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	48	621	0	ENST00000575354.2:c.2497C>T	p.Pro833Ser	p.P833S	ENST00000575354	NM_015125.3	833	Ccc/Tcc	10/20	NA	2	FACETS	0.28	0.236	0.328			1	INDETERMINATE	1	TRUE	NA	0.576273977629544	2		621	596	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266180	198266180	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	113	849	0	ENST00000335508.6:c.2440T>G	p.Phe814Val	p.F814V	ENST00000335508	NM_012433.2	814	Ttt/Gtt	17/25	0.275411219182799	1	FACETS	0.273	0.245	0.303	0.273	0.245	0.303	INDETERMINATE	1	TRUE	0	0.576273977629544	1		849	1023	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130700	29130700	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	184	470	0	ENST00000328354.6:c.10G>T	p.Glu4Ter	p.E4*	ENST00000328354	NM_007194.3	4	Gag/Tag	2/15	0.576273977629544	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.576273977629544	1		470	373	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000023	30000024	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1418675250	NA	P-0019998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	120	572	1	ENST00000338641.4:c.41_42del	p.Leu14GlnfsTer34	p.L14Qfs*34	ENST00000338641	NM_000268.3	12	agCTct/agct	1/16	0.576273977629544	1	FACETS	0.924	0.846	1	0.924	0.846	1	CLONAL	1	TRUE	0	0.576273977629544	1		573	321	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55143620	55143620	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	25	516	0	ENST00000257290.5:c.1852T>C	p.Ser618Pro	p.S618P	ENST00000257290	NM_006206.4	618	Tcc/Ccc	13/23	0.576273977629544	1	FACETS	0.146	0.114	0.182	0.146	0.114	0.182	SUBCLONAL	1	TRUE	0	0.576273977629544	1		516	424	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152113	55152113	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	147	896	0	ENST00000257290.5:c.2545T>A	p.Tyr849Asn	p.Y849N	ENST00000257290	NM_006206.4	849	Tat/Aat	18/23	0.576273977629544	1	FACETS	0.511	0.467	0.556	0.511	0.467	0.556	SUBCLONAL	1	TRUE	0	0.576273977629544	1		896	711	SUCCESS
APC	324	MSKCC	GRCh37	5	112170735	112170735	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	131	846	0	ENST00000257430.4:c.1831G>A	p.Gly611Ser	p.G611S	ENST00000257430	NM_000038.5	611	Ggt/Agt	15/16	0.154845764283741	3	FACETS	0.555	0.503	0.611	0.278	0.251	0.306	INDETERMINATE	1	TRUE	1	0.576273977629544	3		846	1055	SUCCESS
APC	324	MSKCC	GRCh37	5	112174604	112174604	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768454793	NA	P-0019998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	226	653	3	ENST00000257430.4:c.3313C>T	p.Arg1105Trp	p.R1105W	ENST00000257430	NM_000038.5	1105	Cgg/Tgg	16/16	0.154845764283741	3	FACETS	1	0.988	1	0.62	0.579	0.662	INDETERMINATE	1	TRUE	1	0.576273977629544	3		656	815	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164200	32164200	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0019998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	62	464	0	ENST00000375023.3:c.5201-2A>G		p.X1734_splice	ENST00000375023	NM_004557.3	1734			0.576273977629544	1	FACETS	0.36	0.312	0.413	0.36	0.312	0.413	SUBCLONAL	1	TRUE	0	0.576273977629544	1		464	425	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539077	23539084	+	frameshift_variant	Frame_Shift_Del	DEL	TTAGGGGT	TTAGGGGT	-	novel	NA	P-0019998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	218	719	0	ENST00000380871.4:c.355_362del	p.Thr119AlafsTer32	p.T119Afs*32	ENST00000380871	NM_006167.3	119	ACCCCTAAg/g	2/2	0.576273977629544	1	FACETS	0.986	0.925	1	0.986	0.925	1	CLONAL	1	TRUE	0	0.576273977629544	1		719	546	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624613	93624613	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	165	590	0	ENST00000375746.1:c.704A>G	p.Asp235Gly	p.D235G	ENST00000375746	NM_001174167.1	235	gAc/gGc	4/14	1	2	FACETS	0.982	0.907	1	0.982	0.907	1	CLONAL	1	TRUE	1	0.576273977629544	2		590	583	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422646	47422646	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	104	671	2	ENST00000377045.4:c.118A>C	p.Ser40Arg	p.S40R	ENST00000377045	NM_001654.4	40	Agt/Cgt	3/16	0.44826760913411	0	FACETS	0.379	0.341	0.418			1	SUBCLONAL	1	TRUE	0	0.576273977629544	0		673	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0020007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	192	532	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.452776248384718	2	FACETS	0.843	0.787	0.9	0.843	0.787	0.9	CLONAL	2	TRUE	0	0.452776248384718	2		533	503	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0020008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	102	300	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.341619915337229	4	FACETS	0.881	0.793	0.973	0.881	0.793	0.973	CLONAL	2	TRUE	2	0.379455680697148	4		300	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0020008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	363	1028	6	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.341619915337229	4	FACETS	0.92	0.871	0.97	0.92	0.871	0.97	CLONAL	2	TRUE	2	0.379455680697148	4		1034	1434	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653814	89653814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780004	NA	P-0020008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	194	588	0	ENST00000371953.3:c.112C>T	p.Pro38Ser	p.P38S	ENST00000371953	NM_000314.4	38	Cct/Tct	2/9	0.363413420727589	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.379455680697148	2		588	464	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2105520	2105520	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	95	627	0	ENST00000219476.3:c.599A>C	p.Gln200Pro	p.Q200P	ENST00000219476	NM_000548.3	200	cAg/cCg	6/42	0.328954619474749	3	FACETS	0.832	0.741	0.929	0.416	0.37	0.465	CLONAL	1	TRUE	1	0.379455680697148	3		627	716	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574029	7574030	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	280	727	0	ENST00000269305.4:c.997dup	p.Arg333ProfsTer4	p.R333Pfs*4	ENST00000269305	NM_001126112.2	333	cgt/cCgt	10/11	0.341619915337229	4	FACETS	0.961	0.903	1	0.961	0.903	1	CLONAL	2	TRUE	2	0.379455680697148	4		727	1059	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39763608	39763609	+	missense_variant	Missense_Mutation	DNP	TG	TG	GT	novel	NA	P-0020008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	74	517	2	ENST00000288319.7:c.843_844delinsAC	p.Lys282Gln	p.K282Q	ENST00000288319	NM_182918.3	281	ccCAaa/ccACaa	8/10	0.328954619474749	3	FACETS	0.755	0.661	0.855	0.377	0.33	0.428	SUBCLONAL	1	TRUE	1	0.379455680697148	3		519	615	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52661299	52661299	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0020008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	159	557	1	ENST00000394830.3:c.1531A>T	p.Lys511Ter	p.K511*	ENST00000394830	NM_018313.4	511	Aaa/Taa	14/30	0.350497157165435	2	FACETS	0.82	0.757	0.885	0.82	0.757	0.885	CLONAL	2	TRUE	0	0.379455680697148	2		558	511	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	35	640	2	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.391	0.32	0.47	0.391	0.32	0.47	SUBCLONAL	1	TRUE	1	0.399807361889736	2		642	448	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0020009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	67	891	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.593	0.516	0.677	0.593	0.516	0.677	SUBCLONAL	1	TRUE	1	0.399807361889736	2		891	565	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0020009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	59	350	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.736	0.635	0.845	0.736	0.635	0.845	SUBCLONAL	1	TRUE	1	0.399807361889736	2		350	401	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0020009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	161	440	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.399807361889736	2		440	695	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	174	622	4	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	0.399807361889736	2		626	832	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911535	101911535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113605875	NA	P-0020009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	109	472	1	ENST00000374994.4:c.1460G>A	p.Arg487Gln	p.R487Q	ENST00000374994	NM_004612.2	487	cGg/cAg	9/9	0.399807361889736	2	FACETS	0.981	0.884	1	0.49	0.442	0.542	CLONAL	1	TRUE	0	0.399807361889736	2		473	556	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799098	42799098	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	166	722	1	ENST00000575354.2:c.4586del	p.Pro1529LeufsTer91	p.P1529Lfs*91	ENST00000575354	NM_015125.3	1528	Ccc/cc	20/20	1	2	FACETS	0.861	0.791	0.935	0.861	0.791	0.935	CLONAL	1	TRUE	1	0.399807361889736	2		723	964	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502466	186502468	+	inframe_deletion	In_Frame_Del	DEL	TAT	TAT	-	rs755185062	NA	P-0020009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	58	314	0	ENST00000323963.5:c.193_195del	p.Ile65del	p.I65del	ENST00000323963		63	gcTATt/gct	3/11	1	2	FACETS	0.915	0.792	1	0.915	0.792	1	CLONAL	1	TRUE	1	0.399807361889736	2		314	317	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630626	158630626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912678	NA	P-0020009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	80	384	0	ENST00000263640.3:c.617G>A	p.Arg206His	p.R206H	ENST00000263640	NM_001105.4	206	cGc/cAc	6/11	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.399807361889736	2		384	383	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088659	27088659	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	171	747	1	ENST00000324856.7:c.2272del	p.Gln758ArgfsTer75	p.Q758Rfs*75	ENST00000324856	NM_006015.4	756	aaC/aa	7/20	1	2	FACETS	0.945	0.87	1	0.945	0.87	1	CLONAL	1	TRUE	1	0.399807361889736	2		748	905	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196879	108196880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs773570504	NA	P-0020009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	74	462	0	ENST00000278616.4:c.6908dup	p.Glu2304GlyfsTer69	p.E2304Gfs*69	ENST00000278616	NM_000051.3	2301	gca/gcAa	47/63	0.399807361889736	2	FACETS	0.678	0.594	0.768	0.339	0.297	0.384	SUBCLONAL	1	TRUE	0	0.399807361889736	2		462	546	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348560	89348561	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0020009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	155	770	0	ENST00000301030.4:c.4389_4390del	p.Lys1464ThrfsTer89	p.K1464Tfs*89	ENST00000301030	NM_001256183.1	1463	gaGAaa/gaaa	9/13	1	2	FACETS	0.745	0.681	0.812	0.745	0.681	0.812	SUBCLONAL	1	TRUE	1	0.399807361889736	2		770	1041	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354393	354393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1488869543	NA	P-0020009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	47	601	0	ENST00000262320.3:c.1165G>A	p.Ala389Thr	p.A389T	ENST00000262320	NM_003502.3	389	Gcg/Acg	5/11	1	2	FACETS	0.258	0.216	0.303	0.258	0.216	0.303	SUBCLONAL	1	TRUE	1	0.399807361889736	2		601	913	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131403	17131403	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs758385503	NA	P-0020009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	135	556	0	ENST00000285071.4:c.49del	p.Arg17AlafsTer38	p.R17Afs*38	ENST00000285071	NM_144997.5	17	Cgc/gc	4/14	1	2	FACETS	0.963	0.877	1	0.963	0.877	1	CLONAL	1	TRUE	1	0.399807361889736	2		556	701	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989591	212989592	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1553563398	NA	P-0020009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	20	333	0	ENST00000342788.4:c.119_120del	p.Ser40Ter	p.S40*	ENST00000342788	NM_005235.2	40	tCT/t	2/28	1	2	FACETS	0.3	0.229	0.383	0.3	0.229	0.383	SUBCLONAL	1	TRUE	1	0.399807361889736	2		333	334	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776072	9776072	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	108	604	1	ENST00000377346.4:c.536G>T	p.Gly179Val	p.G179V	ENST00000377346	NM_005026.3	179	gGg/gTg	5/24	1	2	FACETS	0.714	0.641	0.791	0.714	0.641	0.791	SUBCLONAL	1	TRUE	1	0.399807361889736	2		605	757	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105551	27105551	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	112	427	0	ENST00000324856.7:c.5162G>C	p.Arg1721Pro	p.R1721P	ENST00000324856	NM_006015.4	1721	cGa/cCa	20/20	1	2	FACETS	0.969	0.874	1	0.969	0.874	1	CLONAL	1	TRUE	1	0.399807361889736	2		427	578	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692796	89692797	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACC	novel	NA	P-0020009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	113	372	0	ENST00000371953.3:c.281_283dup	p.Asn94_Pro95insHis	p.N94_P95insH	ENST00000371953	NM_000314.4	94	aac/aACCac	5/9	0.399807361889736	2	FACETS	0.88	0.803	0.96	0.88	0.803	0.96	CLONAL	2	TRUE	0	0.399807361889736	2		372	321	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424970	49424970	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783691	NA	P-0020009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	144	503	0	ENST00000301067.7:c.13518del	p.Ser4507AlafsTer12	p.S4507Afs*12	ENST00000301067	NM_003482.3	4506	ccC/cc	39/54	1	2	FACETS	0.975	0.89	1	0.975	0.89	1	CLONAL	1	TRUE	1	0.399807361889736	2		503	739	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504478	103504478	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	57	304	0	ENST00000355739.4:c.99T>G	p.Ile33Met	p.I33M	ENST00000355739	NM_000123.3	33	atT/atG	2/15	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.399807361889736	2		304	263	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663351	67663351	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	92	512	0	ENST00000264010.4:c.1756del	p.Glu586LysfsTer45	p.E586Kfs*45	ENST00000264010	NM_006565.3	584	gaG/ga	10/12	1	2	FACETS	0.788	0.702	0.88	0.788	0.702	0.88	SUBCLONAL	1	TRUE	1	0.399807361889736	2		512	584	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805669	89805669	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751928369	NA	P-0020009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	51	494	1	ENST00000389301.3:c.4039G>A	p.Ala1347Thr	p.A1347T	ENST00000389301	NM_000135.2	1347	Gcc/Acc	41/43	1	2	FACETS	0.357	0.303	0.417	0.357	0.303	0.417	SUBCLONAL	1	TRUE	1	0.399807361889736	2		495	714	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868196	37868196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1308928763	NA	P-0020009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	123	570	1	ENST00000269571.5:c.917C>T	p.Thr306Met	p.T306M	ENST00000269571		306	aCg/aTg	8/27	1	2	FACETS	0.79	0.714	0.869	0.79	0.714	0.869	SUBCLONAL	1	TRUE	1	0.399807361889736	2		571	779	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246955	10246955	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	143	461	0	ENST00000340748.4:c.4450G>A	p.Ala1484Thr	p.A1484T	ENST00000340748		1484	Gcc/Acc	37/40	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.399807361889736	2		461	706	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266865	18266865	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	79	637	2	ENST00000222254.8:c.176G>A	p.Gly59Asp	p.G59D	ENST00000222254	NM_005027.3	59	gGc/gAc	2/16	1	2	FACETS	0.5	0.439	0.565	0.5	0.439	0.565	SUBCLONAL	1	TRUE	1	0.399807361889736	2		639	791	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104629	209104629	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754290687	NA	P-0020009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	123	465	0	ENST00000345146.2:c.949C>T	p.Arg317Cys	p.R317C	ENST00000345146	NM_005896.2	317	Cgc/Tgc	8/10	1	2	FACETS	0.939	0.851	1	0.939	0.851	1	CLONAL	1	TRUE	1	0.399807361889736	2		465	655	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021205	31021205	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	84	544	0	ENST00000375687.4:c.1204C>T	p.Arg402Ter	p.R402*	ENST00000375687	NM_015338.5	402	Cga/Tga	12/13	1	2	FACETS	0.562	0.496	0.633	0.562	0.496	0.633	SUBCLONAL	1	TRUE	1	0.399807361889736	2		544	748	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146583	185146583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142468620	NA	P-0020009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	127	496	1	ENST00000265026.3:c.214G>A	p.Val72Ile	p.V72I	ENST00000265026	NM_004721.4	72	Gta/Ata	2/14	1	2	FACETS	0.896	0.813	0.983	0.896	0.813	0.983	CLONAL	1	TRUE	1	0.399807361889736	2		497	709	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589573	67589592	+	protein_altering_variant	In_Frame_Del	DEL	GGGAAAAAATTACATGAATA	GGGAAAAAATTACATGAATA	AATAT	novel	NA	P-0020009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	38	404	2	ENST00000274335.5:c.1336_1355delinsAATAT	p.Gly446_Tyr452delinsAsnIle	p.G446_Y452delinsNI	ENST00000274335		446	GGGAAAAAATTACATGAATAt/AATATt	10/15	1	2	FACETS	0.506	0.418	0.602	0.506	0.418	0.602	SUBCLONAL	1	TRUE	1	0.399807361889736	2		406	376	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593287	67593287	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	95	347	0	ENST00000274335.5:c.2033G>T	p.Gly678Val	p.G678V	ENST00000274335		678	gGc/gTc	15/15	1	2	FACETS	0.947	0.846	1	0.947	0.846	1	CLONAL	1	TRUE	1	0.399807361889736	2		347	502	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800475	32800475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	265	801	0	ENST00000374899.4:c.1072G>A	p.Ala358Thr	p.A358T	ENST00000374899	NM_018833.2	358	Gcc/Acc	6/12	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.399807361889736	2		801	1090	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141549487	141549487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	102	376	1	ENST00000220592.5:c.2101G>A	p.Gly701Arg	p.G701R	ENST00000220592	NM_012154.3	701	Ggg/Agg	16/19	1	2	FACETS	0.809	0.724	0.898	0.809	0.724	0.898	CLONAL	1	TRUE	1	0.399807361889736	2		377	631	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528665	8528665	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	101	378	0	ENST00000356435.5:c.467A>G	p.Glu156Gly	p.E156G	ENST00000356435		156	gAa/gGa	4/35	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.399807361889736	2		378	490	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226001	53226001	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	193	765	1	ENST00000375401.3:c.2848A>G	p.Met950Val	p.M950V	ENST00000375401	NM_004187.3	950	Atg/Gtg	19/26	0.32554038943965	3	FACETS	1	0.974	1			1	CLONAL	1	TRUE	NA	0.399807361889736	3		766	1035	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0020010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	113	825	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.330852299242355	2		825	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0020010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	132	802	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	0.315494296552447	1	FACETS	0.839	0.762	0.92	0.839	0.762	0.92	CLONAL	1	TRUE	0	0.330852299242355	1		802	794	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0020011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	229	453	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.413548134032022	2	FACETS	0.798	0.751	0.845	0.798	0.751	0.845	SUBCLONAL	2	TRUE	0	0.55097122166304	2		453	521	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559089	29559089	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1131691089	NA	P-0020011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	39	83	0	ENST00000356175.3:c.3198-2A>G		p.X1066_splice	ENST00000356175	NM_000267.3	1066			1	2	FACETS	0.848	0.713	0.993	0.848	0.713	0.993	CLONAL	1	TRUE	1	0.55097122166304	2		83	167	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045190	47045190	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0020011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	150	337	2	ENST00000377604.3:c.2430+1G>T		p.X810_splice	ENST00000377604	NM_001204468.1	810			1	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.55097122166304	1		339	374	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857344	9857344	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	205	447	0	ENST00000330684.3:c.4057A>G	p.Arg1353Gly	p.R1353G	ENST00000330684	NM_001134407.1	1353	Agg/Ggg	13/13	0.386538016395101	3	FACETS	0.769	0.718	0.822	0.769	0.718	0.822	SUBCLONAL	2	TRUE	1	0.55097122166304	3		447	617	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721109	61721109	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	463	703	0	ENST00000401558.2:c.1165T>G	p.Ser389Ala	p.S389A	ENST00000401558	NM_003400.3	389	Tct/Gct	12/25	0.414180424769426	3	FACETS	1	0.994	1	0.778	0.747	0.808	CLONAL	2	TRUE	0	0.55097122166304	3		703	919	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091121	29091121	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	346	722	0	ENST00000328354.6:c.1369G>T	p.Glu457Ter	p.E457*	ENST00000328354	NM_007194.3	457	Gag/Tag	12/15	0.405398689584762	4	FACETS	0.829	0.785	0.874	0.829	0.785	0.874	CLONAL	2	TRUE	2	0.55097122166304	4		722	1175	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509100	66509100	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs753467224	NA	P-0020011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	77	541	1	ENST00000273854.3:c.227T>A	p.Ile76Asn	p.I76N	ENST00000273854	NM_004439.5	76	aTt/aAt	2/18	0.386538016395101	3	FACETS	0.706	0.621	0.797	0.353	0.31	0.399	SUBCLONAL	1	TRUE	1	0.55097122166304	3		542	505	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910333	29910384	+	frameshift_variant,start_lost	Frame_Shift_Del	DEL	GGCCGTCATGGCGCCCCGAACCCTCCTCCTGCTACTCTCGGGGGCCCTGGCC	GGCCGTCATGGCGCCCCGAACCCTCCTCCTGCTACTCTCGGGGGCCCTGGCC	-	novel	NA	P-0020011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	217	752	0	ENST00000376809.5:c.3_54del	p.Met1_?18	p.M1_?18	ENST00000376809	NM_002116.7	1	atGGCCGTCATGGCGCCCCGAACCCTCCTCCTGCTACTCTCGGGGGCCCTGGCC/at	1/8	0.414180424769426	3	FACETS	1	0.99	1	0.45	0.419	0.481	CLONAL	1	TRUE	0	0.55097122166304	3		752	745	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180315	27180315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	131	542	1	ENST00000380036.4:c.979C>T	p.Gln327Ter	p.Q327*	ENST00000380036	NM_000459.3	327	Caa/Taa	7/23	0.405398689584762	4	FACETS	0.864	0.783	0.948	0.432	0.391	0.474	CLONAL	1	TRUE	2	0.55097122166304	4		543	854	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	229	540	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.447642365616685	2		540	973	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696462	47696462	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	346	448	0	ENST00000347630.2:c.361C>G	p.Arg121Gly	p.R121G	ENST00000347630	NM_001007230.1	121	Cgg/Ggg	6/11	0.439312756001099	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.447642365616685	2		448	752	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0020014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	20	531	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.513	0.391	0.656	0.513	0.391	0.656	SUBCLONAL	1	TRUE	1	0.17	2		531	459	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433848	78433848	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0020014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	40	362	0	ENST00000370768.2:c.250+1del		p.X84_splice	ENST00000370768	NM_003902.3	84			1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.17	2		362	405	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236153	108236153	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876658529	NA	P-0020014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	45	605	2	ENST00000278616.4:c.9089G>T	p.Gly3030Val	p.G3030V	ENST00000278616	NM_000051.3	3030	gGa/gTa	63/63	1	2	FACETS	0.758	0.636	0.895	0.758	0.636	0.895	SUBCLONAL	1	TRUE	1	0.17	2		607	698	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972589	32972590	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs431825381	NA	P-0020014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	43	464	0	ENST00000380152.3:c.9945dup	p.Glu3316ArgfsTer11	p.E3316Rfs*11	ENST00000380152		3313	-/A	27/27	1	2	FACETS	0.883	0.738	1	0.883	0.738	1	CLONAL	1	TRUE	1	0.17	2		464	573	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774943	73774943	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	29	364	0	ENST00000254810.4:c.230A>C	p.Gln77Pro	p.Q77P	ENST00000254810	NM_005324.3	77	cAg/cCg	3/4	1	2	FACETS	0.724	0.58	0.888	0.724	0.58	0.888	SUBCLONAL	1	TRUE	1	0.17	2		364	471	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600330	10600330	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	42	509	0	ENST00000171111.5:c.1525G>C	p.Gly509Arg	p.G509R	ENST00000171111	NM_203500.1	509	Ggg/Cgg	4/6	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.17	2		509	485	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384598	31384598	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	46	552	1	ENST00000328111.2:c.1300G>T	p.Gly434Cys	p.G434C	ENST00000328111	NM_006892.3	434	Ggc/Tgc	13/23	1	2	FACETS	0.887	0.746	1	0.887	0.746	1	CLONAL	1	TRUE	1	0.17	2		553	610	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964318	55964318	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	34	379	0	ENST00000263923.4:c.2495A>G	p.Asp832Gly	p.D832G	ENST00000263923	NM_002253.2	832	gAc/gGc	17/30	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.17	2		379	370	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874355	151874355	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	33	406	0	ENST00000262189.6:c.8183A>T	p.Lys2728Met	p.K2728M	ENST00000262189	NM_170606.2	2728	aAg/aTg	38/59	1	2	FACETS	0.791	0.643	0.957	0.791	0.643	0.957	CLONAL	1	TRUE	1	0.17	2		406	491	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372385	55372385	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs780951017	NA	P-0020014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	49	747	3	ENST00000297316.4:c.1075G>T	p.Asp359Tyr	p.D359Y	ENST00000297316	NM_022454.3	359	Gac/Tac	2/2	1	2	FACETS	0.793	0.67	0.929	0.793	0.67	0.929	CLONAL	1	TRUE	1	0.17	2		750	727	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0020016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	189	146	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.614672789796425	2		146	553	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0020016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	101	465	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.614672789796425	2		465	314	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978940	25978940	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs367567129	NA	P-0020016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	177	537	0	ENST00000435504.4:c.983A>G	p.Asn328Ser	p.N328S	ENST00000435504		328	aAc/aGc	10/13	1	2	FACETS	0.886	0.82	0.954	0.886	0.82	0.954	CLONAL	1	TRUE	1	0.614672789796425	2		537	650	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845391	151845391	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	186	627	3	ENST00000262189.6:c.13621C>T	p.Arg4541Ter	p.R4541*	ENST00000262189	NM_170606.2	4541	Cga/Tga	52/59	1	2	FACETS	0.866	0.802	0.931	0.866	0.802	0.931	CLONAL	1	TRUE	1	0.614672789796425	2		630	699	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0020017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	179	786	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.347093546294537	4	FACETS	0.926	0.861	0.993	0.926	0.861	0.993	CLONAL	3	TRUE	1	0.347093546294537	4		786	500	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581351	48581351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1368696589	NA	P-0020017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	130	461	2	ENST00000342988.3:c.655G>A	p.Val219Met	p.V219M	ENST00000342988	NM_005359.5	219	Gtg/Atg	5/12	0.170650793173881	2	FACETS	0.757	0.69	0.825	0.757	0.69	0.825	INDETERMINATE	2	TRUE	0	0.347093546294537	2		463	495	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0020017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	113	496	0				ENST00000310581	NM_198253.2	-/1132			0.347093546294537	3	FACETS	0.778	0.704	0.856	0.778	0.704	0.856	SUBCLONAL	2	TRUE	1	0.347093546294537	3		496	491	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412282	139412282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	416	944	0	ENST00000277541.6:c.1363G>A	p.Glu455Lys	p.E455K	ENST00000277541	NM_017617.3	455	Gag/Aag	8/34	0.301651566327432	3	FACETS	0.867	0.828	0.907	0.867	0.828	0.907	CLONAL	3	TRUE	0	0.347093546294537	3		944	1081	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	95	424	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.279342690378815	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.279342690378815	1		424	489	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0020018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	138	649	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.255793269483354	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.279342690378815	1		649	717	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	59	553	2	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	0.209166942294614	2		555	555	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912580	NA	P-0020019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	43	333	0	ENST00000342988.3:c.1157G>A	p.Gly386Asp	p.G386D	ENST00000342988	NM_005359.5	386	gGt/gAt	10/12	0.153847273967251	1	FACETS	0.92	0.772	1	0.92	0.772	1	CLONAL	1	TRUE	0	0.209166942294614	1		333	400	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088795	27088795	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	58	567	0	ENST00000324856.7:c.2404C>T	p.Gln802Ter	p.Q802*	ENST00000324856	NM_006015.4	802	Cag/Tag	7/20	0.209166942294614	1	FACETS	0.862	0.741	0.994	0.862	0.741	0.994	CLONAL	1	TRUE	0	0.209166942294614	1		567	576	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754670	42754670	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	45	426	0	ENST00000222329.4:c.70T>A	p.Ser24Thr	p.S24T	ENST00000222329	NM_006494.2	24	Tca/Aca	2/4	1	2	FACETS	0.91	0.765	1	0.91	0.765	1	CLONAL	1	TRUE	1	0.209166942294614	2		426	473	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936103	178936103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519699	NA	P-0020020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	212	684	0	ENST00000263967.3:c.1645G>A	p.Asp549Asn	p.D549N	ENST00000263967	NM_006218.2	549	Gat/Aat	10/21	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.479017793784707	2		684	692	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952152	178952159	+	stop_retained_variant,3_prime_UTR_variant	Silent	DEL	AAAAGATA	AAAAGATA	-	novel	NA	P-0020020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	79	305	0	ENST00000263967.3:c.*1_*8del			ENST00000263967	NM_006218.2	1069		21/21	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.479017793784707	2		305	288	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0020022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	119	499	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.372566319751831	2		499	549	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872214	45872214	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	66	563	0	ENST00000391945.4:c.220T>C	p.Ser74Pro	p.S74P	ENST00000391945	NM_000400.3	74	Tca/Cca	4/23	0.193361991549667	0	FACETS	0.378	0.328	0.432			1	INDETERMINATE	1	TRUE	0	0.372566319751831	0		563	588	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717695	89717696	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1060500115	NA	P-0020022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	67	488	0	ENST00000371953.3:c.723dup	p.Glu242Ter	p.E242*	ENST00000371953	NM_000314.4	240	-/T	7/9	0.181386326470485	1	FACETS	0.575	0.5	0.655	0.575	0.5	0.655	INDETERMINATE	1	TRUE	0	0.372566319751831	1		488	509	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859924	117859924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139935751	NA	P-0020022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	131	251	0	ENST00000297338.2:c.1711C>T	p.Leu571Phe	p.L571F	ENST00000297338	NM_006265.2	571	Ctt/Ttt	14/14	0.317940012041533	3	FACETS	0.998	0.914	1	0.998	0.914	1	CLONAL	2	TRUE	1	0.372566319751831	3		251	418	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72863714	72863716	+	inframe_deletion	In_Frame_Del	DEL	CAG	CAG	-	novel	NA	P-0020022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	144	561	0	ENST00000268489.5:c.3491_3493del	p.Ala1164del	p.A1164del	ENST00000268489	NM_006885.3	1164	gCTGat/gat	5/10	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.372566319751831	2		561	745	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351644	89351644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1307402586	NA	P-0020022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	87	666	0	ENST00000301030.4:c.1306G>A	p.Gly436Ser	p.G436S	ENST00000301030	NM_001256183.1	436	Ggt/Agt	9/13	1	2	FACETS	0.51	0.45	0.574	0.51	0.45	0.574	SUBCLONAL	1	TRUE	1	0.372566319751831	2		666	916	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577088	7577104	+	protein_altering_variant	In_Frame_Del	DEL	TGCGCCGGTCTCTCCCA	TGCGCCGGTCTCTCCCA	GG	novel	NA	P-0020022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	161	653	4	ENST00000269305.4:c.834_850delinsCC	p.Gly279_Thr284delinsPro	p.G279_T284delinsP	ENST00000269305	NM_001126112.2	278	ccTGGGAGAGACCGGCGCAca/ccCCca	8/11	0.372566319751831	1	FACETS	0.991	0.911	1	0.991	0.911	1	CLONAL	1	TRUE	0	0.372566319751831	1		657	710	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981911	70981911	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	73	636	1	ENST00000276594.2:c.185C>A	p.Ala62Asp	p.A62D	ENST00000276594	NM_024504.3	62	gCt/gAt	2/8	1	2	FACETS	0.548	0.479	0.623	0.548	0.479	0.623	SUBCLONAL	1	TRUE	1	0.372566319751831	2		637	715	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0020023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	97	288	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	0.30749885769417	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	FALSE	0	0.310070642897466	2		288	255	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519996	NA	P-0020023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	232	841	1	ENST00000269305.4:c.395A>T	p.Lys132Met	p.K132M	ENST00000269305	NM_001126112.2	132	aAg/aTg	5/11	0.246117812760119	3	FACETS	1	0.973	1	0.717	0.671	0.765	CLONAL	2	FALSE	0	0.310070642897466	3		842	803	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0020024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	104	600	3	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.1936037672959	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	2	0.263729954204605	4		603	451	SUCCESS
APC	324	MSKCC	GRCh37	5	112111384	112111384	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658325	NA	P-0020024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	108	526	0	ENST00000257430.4:c.481C>T	p.Gln161Ter	p.Q161*	ENST00000257430	NM_000038.5	161	Caa/Taa	5/16	0.211403116340201	3	FACETS	0.912	0.822	1	0.608	0.548	0.671	CLONAL	2	TRUE	0	0.263729954204605	3		526	508	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438108	110438108	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	146	701	0	ENST00000375856.3:c.293G>A	p.Cys98Tyr	p.C98Y	ENST00000375856	NM_003749.2	98	tGc/tAc	1/2	0.263729954204605	4	FACETS	1	0.972	1			1	CLONAL	2	TRUE	NA	0.263729954204605	4		701	612	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42026780	42026817	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GATAAATTACAAGGTCAGAATGAAAACTAGATCTTAAC	GATAAATTACAAGGTCAGAATGAAAACTAGATCTTAAC	-	novel	NA	P-0020024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	94	525	1	ENST00000219905.7:c.3904_3916+25del		p.X1302_splice	ENST00000219905	NM_001164273.1	1302		12/24	NA	2	FACETS	0.758	0.678	0.843			1	INDETERMINATE	2	TRUE	NA	0.263729954204605	2		526	470	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971324	13971324	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	117	506	2	ENST00000405192.2:c.605C>A	p.Thr202Lys	p.T202K	ENST00000405192	NM_001163147.1	202	aCg/aAg	8/12	0.263729954204605	6	FACETS	1	0.957	1	0.552	0.499	0.608	CLONAL	2	TRUE	2	0.263729954204605	6		508	614	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0020026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	125	408	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.209231314699621	3	FACETS	0.926	0.844	1	0.926	0.844	1	CLONAL	3	TRUE	0	0.209231314699621	3		408	475	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	183	673	0	ENST00000269305.4:c.377A>C	p.Tyr126Ser	p.Y126S	ENST00000269305	NM_001126112.2	126	tAc/tCc	5/11	1	2	FACETS	0.983	0.907	1	1	0.993	1	CLONAL	2	TRUE	1	0.209231314699621	2		673	890	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15365013	15365013	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1453756538	NA	P-0020026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	58	458	0	ENST00000263377.2:c.2108C>T	p.Ser703Leu	p.S703L	ENST00000263377	NM_058243.2	703	tCg/tTg	11/20	0.209231314699621	7	FACETS	0.871	0.746	1	0.174	0.149	0.202	CLONAL	1	TRUE	2	0.209231314699621	7		458	970	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0020027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	259	532	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.248837631250047	4	FACETS	1	0.985	1	0.841	0.793	0.889	CLONAL	3	TRUE	0	0.320196669766411	4		533	635	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	40	553	2	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	0.15	2		555	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0020028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	59	839	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.15	NA		841	600	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249348	110249348	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	43	886	0	ENST00000374672.4:c.1225A>C	p.Lys409Gln	p.K409Q	ENST00000374672	NM_004235.4	409	Aag/Cag	4/5	1	2	FACETS	0.748	0.624	0.886	0.748	0.624	0.886	SUBCLONAL	1	TRUE	1	0.15	2		886	767	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106497	27106498	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	42	714	0	ENST00000324856.7:c.6109dup	p.Gln2037ProfsTer62	p.Q2037Pfs*62	ENST00000324856	NM_006015.4	2036	-/C	20/20	1	2	FACETS	0.889	0.741	1	0.889	0.741	1	CLONAL	1	TRUE	1	0.15	2		714	630	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041704	47041705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	59	391	0	ENST00000377604.3:c.1931dup	p.Thr645AspfsTer28	p.T645Dfs*28	ENST00000377604	NM_001204468.1	643	-/A	17/24	1	1	FACETS	0.933	0.806	1	1	0.977	1	CLONAL	2	TRUE	0	0.15	1		391	390	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0020029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	104	465	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.961	0.875	1	0.961	0.875	1	CLONAL	1	TRUE	1	0.810537091235769	2		465	267	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577102	7577102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793881	NA	P-0020029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	336	1022	2	ENST00000269305.4:c.836G>A	p.Gly279Glu	p.G279E	ENST00000269305	NM_001126112.2	279	gGg/gAg	8/11	1	2	FACETS	0.979	0.93	1	0.979	0.93	1	CLONAL	1	TRUE	1	0.810537091235769	2		1024	847	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578430	7578431	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTGACTGCTTGTAGATGGCCATGGCG	novel	NA	P-0020029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	225	599	0	ENST00000269305.4:c.474_499dup	p.Gln167ProfsTer12	p.Q167Pfs*12	ENST00000269305	NM_001126112.2	167	cag/cCGCCATGGCCATCTACAAGCAGTCACag	5/11	1	2	FACETS	0.671	0.626	0.717	0.671	0.626	0.717	SUBCLONAL	1	TRUE	1	0.810537091235769	2		599	828	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940039	76940045	+	frameshift_variant	Frame_Shift_Del	DEL	TATGGCA	TATGGCA	-	novel	NA	P-0020029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	219	524	0	ENST00000373344.5:c.703_709del	p.Cys235MetfsTer20	p.C235Mfs*20	ENST00000373344	NM_000489.3	235	TGCCATAat/at	9/35	0.200793898243418	1	FACETS	0.604	0.567	0.642	0.604	0.567	0.642	INDETERMINATE	1	TRUE	0	0.810537091235769	1		524	532	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835596	68835596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587783047	NA	P-0020030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	123	447	2	ENST00000261769.5:c.187C>T	p.Arg63Ter	p.R63*	ENST00000261769	NM_004360.3	63	Cga/Tga	3/16	0.445676455285099	1	FACETS	0.482	0.437	0.529	0.482	0.437	0.529	SUBCLONAL	1	TRUE	0	0.621313970296284	1		449	566	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0020030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	171	550	1	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	1	2	FACETS	0.615	0.566	0.666	0.615	0.566	0.666	SUBCLONAL	1	TRUE	1	0.621313970296284	2		551	895	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099412	157099426	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAA	CAGCAGCAGCAGCAA	-	rs774668010	NA	P-0020030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	44	368	0	ENST00000346085.5:c.363_377del	p.Gln127_Gln131del	p.Q127_Q131del	ENST00000346085	NM_020732.3	117	CAGCAGCAGCAGCAA/-	1/20	1	2	FACETS	0.264	0.221	0.311	0.264	0.221	0.311	SUBCLONAL	1	TRUE	1	0.621313970296284	2		368	537	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070599	67070599	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	97	249	0	ENST00000412916.2:c.223G>T	p.Gly75Ter	p.G75*	ENST00000412916		75	Gga/Tga	3/6	0.445676455285099	1	FACETS	0.58	0.521	0.642	0.58	0.521	0.642	SUBCLONAL	1	TRUE	0	0.621313970296284	1		249	371	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500570	149500570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377442091	NA	P-0020030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	147	413	0	ENST00000261799.4:c.2467G>A	p.Val823Ile	p.V823I	ENST00000261799	NM_002609.3	823	Gtc/Atc	18/23	1	2	FACETS	0.71	0.65	0.773	0.71	0.65	0.773	SUBCLONAL	1	TRUE	1	0.621313970296284	2		413	666	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874908	151874908	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	85	283	1	ENST00000262189.6:c.7630C>T	p.Gln2544Ter	p.Q2544*	ENST00000262189	NM_170606.2	2544	Cag/Tag	38/59	1	2	FACETS	0.522	0.463	0.586	0.522	0.463	0.586	SUBCLONAL	1	TRUE	1	0.621313970296284	2		284	524	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	39	122	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.791	0.656	0.941	0.791	0.656	0.941	CLONAL	1	TRUE	1	0.233678042856835	2		122	422	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0020033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	62	748	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.233678042856835	3	FACETS	0.832	0.718	0.957	0.416	0.359	0.479	CLONAL	1	TRUE	1	0.233678042856835	3		748	712	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653799	89653799	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	58	510	0	ENST00000371953.3:c.97A>T	p.Ile33Phe	p.I33F	ENST00000371953	NM_000314.4	33	Att/Ttt	2/9	0.233678042856835	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.233678042856835	1		510	369	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216718	2216718	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	56	791	2	ENST00000398665.3:c.2362G>T	p.Asp788Tyr	p.D788Y	ENST00000398665	NM_032482.2	788	Gac/Tac	20/28	1	2	FACETS	0.781	0.668	0.903	0.781	0.668	0.903	CLONAL	1	TRUE	1	0.233678042856835	2		793	614	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0020036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	79	603	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.327273140747366	3	FACETS	0.415	0.365	0.47	0.208	0.182	0.235	INDETERMINATE	1	TRUE	1	0.622621774135344	3		603	801	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0020036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	334	532	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.622621774135344	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.622621774135344	1		533	594	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420591	49420591	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	78	706	0	ENST00000301067.7:c.15158A>T	p.Asp5053Val	p.D5053V	ENST00000301067	NM_003482.3	5053	gAc/gTc	48/54	0.193126679260639	2	FACETS	0.321	0.282	0.364	0.161	0.141	0.182	INDETERMINATE	1	TRUE	0	0.622621774135344	2		706	780	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133238	30133238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374549766	NA	P-0020036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	84	688	2	ENST00000263025.4:c.260G>A	p.Arg87Gln	p.R87Q	ENST00000263025	NM_002746.2	87	cGg/cAg	2/9	0.327273140747366	3	FACETS	0.373	0.329	0.421	0.187	0.164	0.211	INDETERMINATE	1	TRUE	1	0.622621774135344	3		690	948	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346085	89346085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1282116476	NA	P-0020036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	15	91	0	ENST00000301030.4:c.6865G>A	p.Gly2289Ser	p.G2289S	ENST00000301030	NM_001256183.1	2289	Ggc/Agc	9/13	0.327273140747366	3	FACETS	0.408	0.299	0.536	0.204	0.149	0.268	INDETERMINATE	1	TRUE	1	0.622621774135344	3		91	155	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968937	15968937	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	46	545	0	ENST00000268712.3:c.4813G>T	p.Ala1605Ser	p.A1605S	ENST00000268712	NM_006311.3	1605	Gca/Tca	33/46	NA	2	FACETS	0.309	0.26	0.363			1	INDETERMINATE	1	TRUE	NA	0.622621774135344	2		545	478	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7120639	7120641	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0020036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	57	699	0	ENST00000302850.5:c.3649_3651del	p.Ser1217del	p.S1217del	ENST00000302850	NM_000208.2	1217	TCT/-	20/22	0.360943802615957	3	FACETS	0.247	0.211	0.286	0.123	0.105	0.143	INDETERMINATE	1	TRUE	1	0.622621774135344	3		699	973	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031999	26031999	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1411351920	NA	P-0020036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	35	438	0	ENST00000244661.2:c.290G>C	p.Cys97Ser	p.C97S	ENST00000244661	NM_003537.3	97	tGt/tCt	1/1	0.360943802615957	3	FACETS	0.229	0.187	0.276	0.114	0.093	0.138	INDETERMINATE	1	TRUE	1	0.622621774135344	3		438	644	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793546	89793546	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	182	500	0	ENST00000336032.3:c.615G>C	p.Leu205Phe	p.L205F	ENST00000336032	NM_006813.2	205	ttG/ttC	2/2	0.171301611129695	3	FACETS	1	0.989	1	0.675	0.626	0.724	INDETERMINATE	1	TRUE	1	0.622621774135344	3		500	568	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709129	117709129	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	206	535	0	ENST00000368508.3:c.1828T>C	p.Tyr610His	p.Y610H	ENST00000368508	NM_002944.2	610	Tat/Cat	13/43	0.171301611129695	3	FACETS	1	0.988	1	0.647	0.603	0.692	INDETERMINATE	1	TRUE	1	0.622621774135344	3		535	671	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0020037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	37	825	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.561	0.461	0.675	0.561	0.461	0.675	SUBCLONAL	1	TRUE	1	0.15	2		825	879	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871116	12871116	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779986355	NA	P-0020037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	28	259	0	ENST00000228872.4:c.343G>T	p.Ala115Ser	p.A115S	ENST00000228872	NM_004064.3	115	Gcg/Tcg	1/3	0.3	3	FACETS	0.965	0.771	1			1	CLONAL	1	TRUE	NA	0.15	3		259	416	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18478007	18478007	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs747684196	NA	P-0020037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	54	635	0	ENST00000266497.5:c.1247A>T	p.His416Leu	p.H416L	ENST00000266497		416	cAc/cTc	7/31	0.3	1	FACETS	0.7	0.596	0.815	0.7	0.596	0.815	SUBCLONAL	1	TRUE	0	0.15	1		635	951	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207062	1207091	+	inframe_deletion	In_Frame_Del	DEL	GATGGGGGACCTGCTGGGGGAAGGCTCTTA	GATGGGGGACCTGCTGGGGGAAGGCTCTTA	-	novel	NA	P-0020037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	74	663	2	ENST00000326873.7:c.150_179del	p.Met51_Tyr60del	p.M51_Y60del	ENST00000326873	NM_000455.4	50	ctGATGGGGGACCTGCTGGGGGAAGGCTCTTAc/ctc	1/10	0.0999827905180736	0	FACETS	0.921	0.804	1			1	CLONAL	1	TRUE	0	0.15	0		665	911	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17941343	17941343	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	52	609	1	ENST00000458235.1:c.3065C>A	p.Thr1022Asn	p.T1022N	ENST00000458235	NM_000215.3	1022	aCc/aAc	22/24	0.0999827905180736	0	FACETS	0.745	0.633	0.869			1	SUBCLONAL	1	TRUE	0	0.15	0		610	791	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041349	47041349	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0020037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	54	627	1	ENST00000377604.3:c.1694-1G>T		p.X565_splice	ENST00000377604	NM_001204468.1	565			1	2	FACETS	0.854	0.728	0.993	0.854	0.728	0.993	CLONAL	1	TRUE	1	0.15	2		628	843	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0020038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	561	627	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.679824717736749	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.68337899439699	2		627	785	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213912	36213912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	560	644	1	ENST00000222270.7:c.2738C>T	p.Ser913Phe	p.S913F	ENST00000222270	NM_014727.1	913	tCc/tTc	6/37	0.305367082596556	5	FACETS	0.845	0.812	0.877	0.845	0.812	0.877	INDETERMINATE	3	TRUE	2	0.68337899439699	5		645	1310	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151855967	151855968	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	177	459	0	ENST00000262189.6:c.11650dup	p.Thr3884AsnfsTer10	p.T3884Nfs*10	ENST00000262189	NM_170606.2	3884	acg/aAcg	44/59	0.581179331368767	4	FACETS	0.923	0.85	0.998	0.461	0.425	0.499	CLONAL	1	TRUE	2	0.68337899439699	4		459	945	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	54	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.270927516585643	2		555	391	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0020039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	38	999	1	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	1	2	FACETS	0.693	0.573	0.826	0.693	0.573	0.826	SUBCLONAL	1	TRUE	1	0.270927516585643	2		1000	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587780070	NA	P-0020039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	122	1061	1	ENST00000269305.4:c.535C>A	p.His179Asn	p.H179N	ENST00000269305	NM_001126112.2	179	Cat/Aat	5/11	0.157240577535144	3	FACETS	0.978	0.888	1	0.652	0.592	0.714	INDETERMINATE	2	TRUE	0	0.270927516585643	3		1062	523	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4387995	4387995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	113	950	2	ENST00000261254.3:c.481G>A	p.Glu161Lys	p.E161K	ENST00000261254	NM_001759.3	161	Gag/Aag	3/5	0.270927516585643	8	FACETS	0.758	0.68	0.84			1	SUBCLONAL	2	TRUE	NA	0.270927516585643	8		952	998	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509579	29509579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754343223	NA	P-0020039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	42	1296	1	ENST00000356175.3:c.784C>T	p.Arg262Cys	p.R262C	ENST00000356175	NM_000267.3	262	Cgt/Tgt	8/57	0.111575706134275	4	FACETS	0.765	0.638	0.906	0.383	0.319	0.453	INDETERMINATE	1	TRUE	2	0.270927516585643	4		1297	515	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522336	176522336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1178604851	NA	P-0020039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	33	1059	0	ENST00000292408.4:c.1525G>A	p.Ala509Thr	p.A509T	ENST00000292408	NM_213647.1	509	Gcc/Acc	12/18	0.270927516585643	2	FACETS	0.43	0.35	0.522	0.215	0.175	0.261	SUBCLONAL	1	TRUE	0	0.270927516585643	2		1059	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0020040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	293	987	2	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.580013954349385	2		989	899	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578412	7578412	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519747	NA	P-0020040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	222	930	0	ENST00000269305.4:c.518T>C	p.Val173Ala	p.V173A	ENST00000269305	NM_001126112.2	173	gTg/gCg	5/11	1	2	FACETS	0.936	0.873	1	0.936	0.873	1	CLONAL	1	TRUE	1	0.580013954349385	2		930	818	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600446	10600446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	87	1116	1	ENST00000171111.5:c.1409G>A	p.Arg470His	p.R470H	ENST00000171111	NM_203500.1	470	cGt/cAt	4/6	0.580013954349385	1	FACETS	0.232	0.204	0.261	0.232	0.204	0.261	SUBCLONAL	1	TRUE	0	0.580013954349385	1		1117	920	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444219	49444222	+	frameshift_variant	Frame_Shift_Del	DEL	ACGG	ACGG	-	novel	NA	P-0020040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	309	1227	0	ENST00000301067.7:c.3149_3152del	p.Ser1050PhefsTer5	p.S1050Ffs*5	ENST00000301067	NM_003482.3	1050	tCCGTt/tt	11/54	1	2	FACETS	0.992	0.936	1	0.992	0.936	1	CLONAL	1	TRUE	1	0.580013954349385	2		1227	1074	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0020041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	193	408	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.715	0.665	0.766	0.715	0.665	0.766	SUBCLONAL	1	TRUE	1	0.890801035578017	2		408	606	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97887392	97887392	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	392	619	1	ENST00000289081.3:c.972A>C	p.Glu324Asp	p.E324D	ENST00000289081	NM_000136.2	324	gaA/gaC	10/15	1	2	FACETS	0.979	0.935	1	0.979	0.935	1	CLONAL	1	TRUE	1	0.890801035578017	2		620	899	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938931	178938931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	69	469	0	ENST00000263967.3:c.2173G>A	p.Asp725Asn	p.D725N	ENST00000263967	NM_006218.2	725	Gat/Aat	14/21	1	2	FACETS	0.771	0.681	0.865	1	0.977	1	SUBCLONAL	2	FALSE	1	0.385996770478575	2		469	232	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266711	198266711	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	75	557	0	ENST00000335508.6:c.2221A>G	p.Lys741Glu	p.K741E	ENST00000335508	NM_012433.2	741	Aag/Gag	15/25	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.385996770478575	2		557	290	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115637	8115791	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGCCTGTGCATTTCAGAGGCAGCAAAAAAGTAAAAAAAAAAAAAAAAAATTGATCTTTGTTTAGATTAACAGACCCCTGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCAT	GAGCCTGTGCATTTCAGAGGCAGCAAAAAAGTAAAAAAAAAAAAAAAAAATTGATCTTTGTTTAGATTAACAGACCCCTGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCAT	-	novel	NA	P-0020043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	58	106	0	ENST00000346208.3:c.1048-63_1139del		p.X350_splice	ENST00000346208		350		6/6	NA	2	FACETS	0.928	0.829	1			1	INDETERMINATE	3	FALSE	NA	0.385996770478575	2		106	108	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413566	32413566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121907900	NA	P-0020043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	9	483	0	ENST00000332351.3:c.1384C>T	p.Arg462Trp	p.R462W	ENST00000332351	NM_024426.4	462	Cgg/Tgg	9/10	1	2	FACETS	0.111	0.072	0.159	0.111	0.072	0.159	SUBCLONAL	1	FALSE	1	0.385996770478575	2		483	422	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928067	178928093	+	inframe_deletion	In_Frame_Del	DEL	CCTCATGGATTAGAAGATTTGCTGAAC	CCTCATGGATTAGAAGATTTGCTGAAC	-	novel	NA	P-0020043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	20	660	0	ENST00000263967.3:c.1348_1374del	p.His450_Pro458del	p.H450_P458del	ENST00000263967	NM_006218.2	449	CCTCATGGATTAGAAGATTTGCTGAAC/-	8/21	1	2	FACETS	0.589	0.453	0.746	0.589	0.453	0.746	SUBCLONAL	1	FALSE	1	0.385996770478575	2		660	176	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	274	122	0				ENST00000310581	NM_198253.2	-/1132			0.298534458366869	4	FACETS	0.936	0.88	0.993	1	0.993	1	CLONAL	3	TRUE	2	0.27	4		122	918	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0020044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	187	815	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.197084924482547	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.27	1		815	1002	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112221	115112221	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	170	491	0	ENST00000257566.3:c.1519C>A	p.Leu507Met	p.L507M	ENST00000257566	NM_016569.3	507	Ctg/Atg	7/8	0.192233360009531	3	FACETS	0.959	0.884	1	0.959	0.884	1	CLONAL	2	TRUE	1	0.27	3		491	745	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281778	39281778	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519963	NA	P-0020044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	137	450	1	ENST00000402219.2:c.697A>T	p.Asn233Tyr	p.N233Y	ENST00000402219	NM_005633.3	233	Aat/Tat	5/23	1	2	FACETS	0.8	0.73	0.874	1	0.988	1	SUBCLONAL	2	TRUE	1	0.27	2		451	634	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969797	81969797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759995209	NA	P-0020044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	114	605	0	ENST00000359376.3:c.2866C>T	p.Arg956Cys	p.R956C	ENST00000359376	NM_002661.3	956	Cgc/Tgc	27/33	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.27	2		605	794	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90645522	90645522	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	18	130	0	ENST00000330062.3:c.101A>T	p.Gln34Leu	p.Q34L	ENST00000330062	NM_002168.2	34	cAg/cTg	1/11	0.197084924482547	1	FACETS	0.769	0.583	0.984	0.769	0.583	0.984	CLONAL	1	TRUE	0	0.27	1		130	150	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170321	119170321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	105	358	0	ENST00000264033.4:c.2551G>A	p.Ala851Thr	p.A851T	ENST00000264033	NM_005188.3	851	Gcc/Acc	16/16	0.160578912266433	2	FACETS	1	0.981	1	0.723	0.65	0.8	INDETERMINATE	1	TRUE	0	0.27	2		358	538	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923632	72923632	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	39	511	0	ENST00000268489.5:c.3446C>A	p.Pro1149Gln	p.P1149Q	ENST00000268489	NM_006885.3	1149	cCa/cAa	4/10	1	2	FACETS	0.489	0.404	0.583	0.489	0.404	0.583	SUBCLONAL	1	TRUE	1	0.27	2		511	591	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489457	40489467	+	frameshift_variant	Frame_Shift_Del	DEL	TTTCTAGCCGA	TTTCTAGCCGA	-	novel	NA	P-0020044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	98	463	1	ENST00000264657.5:c.783_793del	p.Asp261GlufsTer18	p.D261Efs*18	ENST00000264657	NM_139276.2	261	gaTCGGCTAGAAAac/gaac	8/24	1	2	FACETS	0.997	0.89	1	0.997	0.89	1	CLONAL	1	TRUE	1	0.27	2		464	728	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144875	47144875	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	178	621	1	ENST00000409792.3:c.4878C>A	p.Phe1626Leu	p.F1626L	ENST00000409792	NM_014159.6	1626	ttC/ttA	7/21	1	2	FACETS	0.752	0.693	0.813	1	0.99	1	SUBCLONAL	2	TRUE	1	0.27	2		622	877	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526605	31526605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	139	554	1	ENST00000344624.3:c.435G>A	p.Met145Ile	p.M145I	ENST00000344624		145	atG/atA	2/33	0.298534458366869	4	FACETS	1	0.983	1	0.678	0.616	0.742	CLONAL	1	TRUE	2	0.27	4		555	965	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967841	93967841	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	108	610	3	ENST00000369303.4:c.2086C>A	p.His696Asn	p.H696N	ENST00000369303	NM_004440.3	696	Cat/Aat	11/17	0.197084924482547	1	FACETS	0.929	0.834	1	0.929	0.834	1	CLONAL	1	TRUE	0	0.27	1		613	745	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450282	50450282	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	137	619	0	ENST00000331340.3:c.466C>A	p.Gln156Lys	p.Q156K	ENST00000331340	NM_006060.4	156	Cag/Aag	5/8	0.191334004078662	4	FACETS	1	0.985	1	0.712	0.647	0.78	CLONAL	1	TRUE	2	0.27	4		619	905	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194611	29194611	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	54	839	0	ENST00000240100.2:c.1117G>A	p.Gly373Ser	p.G373S	ENST00000240100	NM_001394.6	373	Ggc/Agc	4/4	0.197084924482547	1	FACETS	0.365	0.31	0.425	0.365	0.31	0.425	SUBCLONAL	1	TRUE	0	0.27	1		839	949	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038562	47038562	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	123	391	0	ENST00000377604.3:c.724G>C	p.Glu242Gln	p.E242Q	ENST00000377604	NM_001204468.1	242	Gag/Cag	8/24	1	1	FACETS	0.814	0.741	0.891	1	0.987	1	CLONAL	2	TRUE	0	0.27	1		391	484	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622419	28622419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776699712	NA	P-0020045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	27	668	1	ENST00000241453.7:c.1198G>A	p.Gly400Arg	p.G400R	ENST00000241453	NM_004119.2	400	Gga/Aga	9/24	0.266766081101456	1	FACETS	0.433	0.344	0.535	0.433	0.344	0.535	SUBCLONAL	1	FALSE	0	0.266766081101456	1		669	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579547	7579557	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGACAGCAT	GGGGACAGCAT	-	novel	NA	P-0020045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	104	1017	0	ENST00000269305.4:c.130_140del	p.Met44GlyfsTer4	p.M44Gfs*4	ENST00000269305	NM_001126112.2	44	ATGCTGTCCCCg/g	4/11	0.266766081101456	1	FACETS	0.855	0.766	0.951	0.855	0.766	0.951	CLONAL	1	FALSE	0	0.266766081101456	1		1017	790	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293589	1293589	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	162	1096	2	ENST00000310581.5:c.1412G>A	p.Arg471Gln	p.R471Q	ENST00000310581	NM_198253.2	471	cGg/cAg	2/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.266766081101456	2		1098	929	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13949264	13949264	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	28	515	0	ENST00000405192.2:c.864del	p.Lys288AsnfsTer32	p.K288Nfs*32	ENST00000405192	NM_001163147.1	288	aaA/aa	9/12	0.266766081101456	1	FACETS	0.497	0.397	0.611	0.497	0.397	0.611	SUBCLONAL	1	FALSE	0	0.266766081101456	1		515	366	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412470	80412470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28764015	NA	P-0020045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	42	592	0	ENST00000286548.4:c.571G>A	p.Glu191Lys	p.E191K	ENST00000286548	NM_002072.3	191	Gaa/Aaa	4/7	0.266766081101456	1	FACETS	0.505	0.421	0.599	0.505	0.421	0.599	SUBCLONAL	1	FALSE	0	0.266766081101456	1		592	540	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0020046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	56	417	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.998	0.856	1	0.998	0.856	1	CLONAL	1	TRUE	1	0.22	2		417	510	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0020046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	78	554	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.89	0.781	1	0.89	0.781	1	CLONAL	1	TRUE	1	0.22	2		554	797	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257053	16257053	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs376552510	NA	P-0020046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	99	1006	0	ENST00000375759.3:c.4318A>G	p.Ile1440Val	p.I1440V	ENST00000375759	NM_015001.2	1440	Atc/Gtc	11/15	1	2	FACETS	0.84	0.748	0.938	0.84	0.748	0.938	CLONAL	1	TRUE	1	0.22	2		1006	1072	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433071	49433113	+	frameshift_variant	Frame_Shift_Del	DEL	GGGAAGGACCCTGGCCCCAGGATGGGGCCACTCAGCTTGCTTG	GGGAAGGACCCTGGCCCCAGGATGGGGCCACTCAGCTTGCTTG	-	novel	NA	P-0020046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	134	1166	0	ENST00000301067.7:c.8258_8300del	p.Pro2753LeufsTer20	p.P2753Lfs*20	ENST00000301067	NM_003482.3	2753	cCAAGCAAGCTGAGTGGCCCCATCCTGGGGCCAGGGTCCTTCCCt/ct	33/54	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.22	2		1166	1198	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969101	93969101	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	53	489	1	ENST00000369303.4:c.1895G>A	p.Cys632Tyr	p.C632Y	ENST00000369303	NM_004440.3	632	tGt/tAt	10/17	1	2	FACETS	0.86	0.734	0.999	0.86	0.734	0.999	CLONAL	1	TRUE	1	0.22	2		490	560	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0020048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	76	146	0				ENST00000310581	NM_198253.2	-/1132			0.517521212434067	1	FACETS	0.806	0.72	0.894	0.806	0.72	0.894	CLONAL	1	FALSE	0	0.625943218716548	1		146	207	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0020048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	92	465	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	FALSE	1	0.625943218716548	2		465	233	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0020048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	12	786	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.075	0.052	0.103	0.075	0.052	0.103	SUBCLONAL	1	FALSE	1	0.625943218716548	2		786	514	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339835	116339835	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	51	639	0	ENST00000397752.3:c.697T>C	p.Ser233Pro	p.S233P	ENST00000397752	NM_000245.2	233	Tcc/Ccc	2/21	1	2	FACETS	0.529	0.452	0.612	0.529	0.452	0.612	SUBCLONAL	1	FALSE	1	0.625943218716548	2		639	308	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795831	42795832	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0020048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	56	727	0	ENST00000575354.2:c.2820_2821insGC	p.Pro941AlafsTer6	p.P941Afs*6	ENST00000575354	NM_015125.3	940	-/GC	11/20	0.625943218716548	1	FACETS	0.428	0.37	0.491	0.428	0.37	0.491	SUBCLONAL	1	FALSE	0	0.625943218716548	1		727	287	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0020049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	73	786	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.543	0.474	0.618	0.543	0.474	0.618	SUBCLONAL	1	TRUE	1	0.351376445837569	2		786	765	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0020049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	27	352	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.242	0.191	0.3	0.242	0.191	0.3	SUBCLONAL	1	TRUE	1	0.351376445837569	2		352	636	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117321	115117321	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	119	474	0	ENST00000257566.3:c.853C>T	p.Gln285Ter	p.Q285*	ENST00000257566	NM_016569.3	285	Cag/Tag	4/8	1	2	FACETS	0.996	0.9	1	0.996	0.9	1	CLONAL	1	TRUE	1	0.351376445837569	2		474	680	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844171	68844172	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	185	798	1	ENST00000261769.5:c.759_760insA	p.Asp254ArgfsTer4	p.D254Rfs*4	ENST00000261769	NM_004360.3	253	-/A	6/16	0.351376445837569	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.351376445837569	1		799	804	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884933	151884933	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0020049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	24	368	0	ENST00000262189.6:c.4661-1G>A		p.X1554_splice	ENST00000262189	NM_170606.2	1554			1	2	FACETS	0.354	0.277	0.443	0.354	0.277	0.443	SUBCLONAL	1	TRUE	1	0.351376445837569	2		368	386	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0020050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	185	839	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.240064711934902	3	FACETS	0.901	0.832	0.973	0.901	0.832	0.973	CLONAL	2	TRUE	1	0.240064711934902	3		841	958	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021128	31021128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	183	745	0	ENST00000375687.4:c.1127G>A	p.Gly376Asp	p.G376D	ENST00000375687	NM_015338.5	376	gGc/gAc	12/13	0.303208518096609	5	FACETS	0.843	0.777	0.912	0.281	0.259	0.304	INDETERMINATE	1	TRUE	2	0.958267041108968	5		745	1104	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-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	32	113	0	ENST00000349496.5:c.13+126_153del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	1	2	FACETS	0.954	0.809	1	0.954	0.809	1	CLONAL	1	TRUE	1	0.958267041108968	2		113	70	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188760	32188760	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	101	777	0	ENST00000375023.3:c.794C>T	p.Pro265Leu	p.P265L	ENST00000375023	NM_004557.3	265	cCc/cTc	4/30	0.543916703559143	3	FACETS	0.516	0.462	0.573	0.258	0.231	0.287	INDETERMINATE	1	TRUE	1	0.958267041108968	3		777	604	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0020053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	250	146	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.93	0.877	0.983	0.93	0.877	0.983	CLONAL	1	TRUE	1	0.90097897503826	2		146	597	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0020053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	175	465	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.182955366241356	1	FACETS	0.556	0.519	0.593	0.556	0.519	0.593	INDETERMINATE	1	TRUE	0	0.90097897503826	1		465	384	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932510	39932510	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	350	927	1	ENST00000378444.4:c.2089G>T	p.Ala697Ser	p.A697S	ENST00000378444	NM_001123385.1	697	Gcc/Tcc	4/15	0.182955366241356	1	FACETS	0.465	0.442	0.489	0.465	0.442	0.489	INDETERMINATE	1	TRUE	0	0.90097897503826	1		928	918	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039374	47039374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	377	862	1	ENST00000377604.3:c.997G>A	p.Val333Ile	p.V333I	ENST00000377604	NM_001204468.1	333	Gtc/Atc	10/24	0.182955366241356	1	FACETS	0.484	0.461	0.507	0.484	0.461	0.507	INDETERMINATE	1	TRUE	0	0.90097897503826	1		863	950	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0020054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	125	631	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.796307024782916	2		631	299	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196653	67196653	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	158	117	0	ENST00000312629.5:c.182G>T	p.Arg61Leu	p.R61L	ENST00000312629	NM_003952.2	61	cGc/cTc	3/15	0.605658799877804	3	FACETS	1	0.988	1	0.673	0.624	0.724	CLONAL	1	TRUE	1	0.796307024782916	3		117	412	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845561	151845561	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	204	169	0	ENST00000262189.6:c.13451A>G	p.His4484Arg	p.H4484R	ENST00000262189	NM_170606.2	4484	cAc/cGc	52/59	1	2	FACETS	0.993	0.929	1	0.993	0.929	1	CLONAL	1	TRUE	1	0.796307024782916	2		169	516	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310909	123310929	+	inframe_deletion	In_Frame_Del	DEL	GTTGGCCGCAGGCACAGCATG	GTTGGCCGCAGGCACAGCATG	-	novel	NA	P-0020056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	147	622	0	ENST00000358487.5:c.499_519del	p.His167_Asn173del	p.H167_N173del	ENST00000358487	NM_000141.4	167	CATGCTGTGCCTGCGGCCAAC/-	5/18	0.334897212483466	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.334897212483466	1		622	622	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0020057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	66	549	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.623	0.54	0.713	0.623	0.54	0.713	SUBCLONAL	1	TRUE	1	0.293732202218112	2		549	721	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577128	7577128	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519987	NA	P-0020058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	418	817	0	ENST00000269305.4:c.810T>G	p.Phe270Leu	p.F270L	ENST00000269305	NM_001126112.2	270	ttT/ttG	8/11	0.532453104764334	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.532453104764334	2		817	770	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469527	25469527	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1258189576	NA	P-0020058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	295	888	0	ENST00000264709.3:c.1241T>C	p.Phe414Ser	p.F414S	ENST00000264709	NM_175629.2	414	tTc/tCc	10/23	0.410083667388331	4	FACETS	0.951	0.897	1	0.951	0.897	1	CLONAL	2	TRUE	2	0.532453104764334	4		888	893	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336664	81336664	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	152	583	0	ENST00000222390.5:c.1558G>T	p.Gly520Ter	p.G520*	ENST00000222390	NM_000601.4	520	Gga/Tga	14/18	0.493508827410202	4	FACETS	0.902	0.831	0.975	0.902	0.831	0.975	CLONAL	2	TRUE	2	0.532453104764334	4		583	485	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0020059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	197	786	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.919	0.852	0.988	0.919	0.852	0.988	CLONAL	1	TRUE	1	0.518365545738265	2		786	827	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0020059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	192	602	1	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.985	0.914	1	0.985	0.914	1	CLONAL	1	TRUE	1	0.518365545738265	2		603	752	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645875	67645875	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	211	745	2	ENST00000264010.4:c.803G>T	p.Cys268Phe	p.C268F	ENST00000264010	NM_006565.3	268	tGt/tTt	4/12	0.480475782767649	1	FACETS	0.839	0.782	0.897	0.839	0.782	0.897	CLONAL	1	TRUE	0	0.518365545738265	1		747	719	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443595	52443595	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	162	661	1	ENST00000460680.1:c.97T>C	p.Tyr33His	p.Y33H	ENST00000460680	NM_004656.3	33	Tac/Cac	3/17	1	2	FACETS	0.756	0.694	0.82	0.756	0.694	0.82	SUBCLONAL	1	TRUE	1	0.518365545738265	2		662	827	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032136	26032136	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	138	535	0	ENST00000244661.2:c.153G>C	p.Glu51Asp	p.E51D	ENST00000244661	NM_003537.3	51	gaG/gaC	1/1	1	2	FACETS	0.899	0.822	0.98	0.899	0.822	0.98	CLONAL	1	TRUE	1	0.518365545738265	2		535	592	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158407	26158407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757195477	NA	P-0020059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	265	1189	5	ENST00000289316.2:c.10C>T	p.Pro4Ser	p.P4S	ENST00000289316	NM_138720.2	4	Cct/Tct	1/2	1	2	FACETS	0.883	0.827	0.94	0.883	0.827	0.94	CLONAL	1	TRUE	1	0.518365545738265	2		1194	1158	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0020060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	765	786	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.652334708565982	4	FACETS	0.99	0.962	1	0.99	0.962	1	CLONAL	3	TRUE	1	0.652334708565982	4		786	1305	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	310	800	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.652334708565982	2		800	948	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097629	27097631	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	novel	NA	P-0020060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	179	872	2	ENST00000324856.7:c.3220_3222del	p.Arg1074del	p.R1074del	ENST00000324856	NM_006015.4	1073	tGGCgg/tgg	12/20	1	2	FACETS	0.529	0.487	0.572	0.529	0.487	0.572	SUBCLONAL	1	TRUE	1	0.652334708565982	2		874	1038	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15984036	15984048	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTTCCCTAAGAA	TGTTCCCTAAGAA	-	novel	NA	P-0020060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	122	338	0	ENST00000268712.3:c.3178-7_3183del		p.X1060_splice	ENST00000268712	NM_006311.3	1060		24/46	1	2	FACETS	0.822	0.748	0.899	0.822	0.748	0.899	CLONAL	1	TRUE	1	0.652334708565982	2		338	455	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46525053	46525053	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs1370202451	NA	P-0020060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	323	894	2	ENST00000263734.3:c.3G>A	p.Met1?	p.M1?	ENST00000263734	NM_001430.4	1	atG/atA	1/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.652334708565982	2		896	976	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361221	70361221	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0020060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	41	943	0	ENST00000374080.3:c.6408+1G>A		p.X2136_splice	ENST00000374080		2136			0.652334708565982	1	FACETS	0.131	0.109	0.156	0.131	0.109	0.156	SUBCLONAL	1	TRUE	0	0.652334708565982	1		943	646	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	238	122	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.867237759506168	2		122	508	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023307	27023307	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0020062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	180	332	0	ENST00000324856.7:c.413C>G	p.Ser138Ter	p.S138*	ENST00000324856	NM_006015.4	138	tCa/tGa	1/20	0.171943745462618	5	FACETS	1	0.982	1	0.763	0.713	0.815	INDETERMINATE	2	TRUE	2	0.867237759506168	5		332	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0020062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	525	804	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.172553880264239	3	FACETS	1	0.996	1	0.65	0.624	0.677	INDETERMINATE	1	TRUE	1	0.867237759506168	3		805	1335	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0020062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	42	533	0	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	NA	2	FACETS	0.088	0.073	0.105			1	INDETERMINATE	1	TRUE	NA	0.867237759506168	2		533	1097	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126343	5126343	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41316003	NA	P-0020062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	251	512	0	ENST00000381652.3:c.3188G>A	p.Arg1063His	p.R1063H	ENST00000381652	NM_004972.3	1063	cGt/cAt	24/25	1	2	FACETS	0.988	0.932	1	0.988	0.932	1	CLONAL	1	TRUE	1	0.867237759506168	2		512	586	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937001	48937001	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	406	677	0	ENST00000267163.4:c.769C>T	p.Gln257Ter	p.Q257*	ENST00000267163	NM_000321.2	257	Cag/Tag	8/27	0.867237759506168	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.867237759506168	1		677	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	657	1026	0	ENST00000269305.4:c.859G>C	p.Glu287Gln	p.E287Q	ENST00000269305	NM_001126112.2	287	Gag/Cag	8/11	0.172553880264239	3	FACETS	0.806	0.779	0.833	0.806	0.779	0.833	INDETERMINATE	2	TRUE	1	0.867237759506168	3		1026	1347	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969322	44969322	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0020062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	254	255	0	ENST00000377967.4:c.4006-2A>T		p.X1336_splice	ENST00000377967	NM_021140.2	1336			1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.867237759506168	1		255	284	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001124	150001124	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	427	830	0	ENST00000253339.5:c.2480G>C	p.Arg827Thr	p.R827T	ENST00000253339		827	aGa/aCa	4/7	0.172553880264239	3	FACETS	1	0.996	1	0.735	0.703	0.766	INDETERMINATE	1	TRUE	1	0.867237759506168	3		830	961	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519989	NA	P-0020062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	507	841	0	ENST00000269305.4:c.730G>C	p.Gly244Arg	p.G244R	ENST00000269305	NM_001126112.2	244	Ggc/Cgc	7/11	0.172553880264239	3	FACETS	0.773	0.743	0.803	0.773	0.743	0.803	INDETERMINATE	2	TRUE	1	0.867237759506168	3		841	1084	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252859	36252859	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	318	548	0	ENST00000300305.3:c.503G>A	p.Gly168Glu	p.G168E	ENST00000300305		168	gGa/gAa	4/8	0.276691309524759	1	FACETS	0.501	0.475	0.528	0.501	0.475	0.528	INDETERMINATE	1	TRUE	0	0.867237759506168	1		548	829	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057908	27057908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540644702	NA	P-0020062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	487	937	1	ENST00000324856.7:c.1616C>T	p.Ser539Leu	p.S539L	ENST00000324856	NM_006015.4	539	tCg/tTg	3/20	0.171943745462618	5	FACETS	1	0.992	1	0.757	0.726	0.788	INDETERMINATE	2	TRUE	2	0.867237759506168	5		938	1138	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442953	49442953	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	416	929	1	ENST00000301067.7:c.3955del	p.His1319MetfsTer11	p.H1319Mfs*11	ENST00000301067	NM_003482.3	1319	Cat/at	12/54	NA	2	FACETS	0.931	0.889	0.973			1	INDETERMINATE	1	TRUE	NA	0.867237759506168	2		930	1031	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123873984	123873984	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	69	85	1	ENST00000330479.4:c.15G>T	p.Arg5Ser	p.R5S	ENST00000330479	NM_020382.3	5	agG/agT	2/9	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.867237759506168	2		86	140	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190708762	190708762	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	504	891	0	ENST00000441310.2:c.655A>T	p.Met219Leu	p.M219L	ENST00000441310	NM_000534.4	219	Atg/Ttg	6/13	0.867237759506168	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.867237759506168	1		891	633	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681458	30681458	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	63	685	0	ENST00000376406.3:c.554G>T	p.Arg185Met	p.R185M	ENST00000376406	NM_014641.2	185	aGg/aTg	4/15	0.172553880264239	3	FACETS	0.211	0.182	0.244	0.106	0.091	0.122	INDETERMINATE	1	TRUE	1	0.867237759506168	3		685	985	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001436	150001436	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	521	995	0	ENST00000253339.5:c.2168G>C	p.Arg723Thr	p.R723T	ENST00000253339		723	aGa/aCa	4/7	0.172553880264239	3	FACETS	1	0.997	1	0.728	0.7	0.757	INDETERMINATE	1	TRUE	1	0.867237759506168	3		995	1183	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525053	157525053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	359	585	0	ENST00000346085.5:c.4948G>A	p.Glu1650Lys	p.E1650K	ENST00000346085	NM_020732.3	1650	Gag/Aag	19/20	0.172553880264239	3	FACETS	0.776	0.74	0.811	0.776	0.74	0.811	INDETERMINATE	2	TRUE	1	0.867237759506168	3		585	765	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371708	55371709	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0020062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	317	866	3	ENST00000297316.4:c.398_399delinsAA	p.Pro133Gln	p.P133Q	ENST00000297316	NM_022454.3	133	cCC/cAA	2/2	1	2	FACETS	0.898	0.852	0.945	0.898	0.852	0.945	CLONAL	1	TRUE	1	0.867237759506168	2		869	814	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339154	87339154	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	108	593	0	ENST00000277120.3:c.736A>G	p.Thr246Ala	p.T246A	ENST00000277120		246	Aca/Gca	8/19	1	2	FACETS	0.39	0.351	0.432	0.39	0.351	0.432	SUBCLONAL	1	TRUE	1	0.867237759506168	2		593	638	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349949	70349949	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	469	539	0	ENST00000374080.3:c.3932T>G	p.Val1311Gly	p.V1311G	ENST00000374080		1311	gTg/gGg	28/45	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.867237759506168	1		539	554	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	585	425	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.769091354285716	2	FACETS	0.979	0.954	1	0.979	0.954	1	CLONAL	2	TRUE	0	0.769091354285716	2		425	777	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918596	44918597	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	270	822	0	ENST00000377967.4:c.1083_1084del	p.Tyr362Ter	p.Y362*	ENST00000377967	NM_021140.2	360	aCT/a	12/29	1	2	FACETS	0.951	0.897	1	0.951	0.897	1	CLONAL	1	TRUE	1	0.769091354285716	2		822	738	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	275	753	3	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	0.892	0.84	0.944	0.892	0.84	0.944	CLONAL	1	TRUE	1	0.769091354285716	2		756	802	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653835	89653835	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1382752324	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	194	714	0	ENST00000371953.3:c.133G>A	p.Val45Ile	p.V45I	ENST00000371953	NM_000314.4	45	Gta/Ata	2/9	1	2	FACETS	0.933	0.87	0.997	0.933	0.87	0.997	CLONAL	1	TRUE	1	0.769091354285716	2		714	541	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	318	878	1	ENST00000206249.3:c.1607T>C	p.Leu536Pro	p.L536P	ENST00000206249	NM_000125.3	536	cTc/cCc	8/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.769091354285716	2		879	802	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608087	28608087	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs997265952	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	300	951	2	ENST00000241453.7:c.1879G>A	p.Ala627Thr	p.A627T	ENST00000241453	NM_004119.2	627	Gca/Aca	15/24	1	2	FACETS	0.937	0.886	0.988	0.937	0.886	0.988	CLONAL	1	TRUE	1	0.769091354285716	2		953	833	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057937	27057937	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	440	973	2	ENST00000324856.7:c.1650del	p.Tyr551ThrfsTer68	p.Y551Tfs*68	ENST00000324856	NM_006015.4	549	Ccc/cc	3/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.769091354285716	2		975	1073	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435128	110435129	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs772322568	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	367	1095	4	ENST00000375856.3:c.3272dup	p.Lys1092GlufsTer233	p.K1092Efs*233	ENST00000375856	NM_003749.2	1091	ccg/ccCg	1/2	1	2	FACETS	0.812	0.771	0.855	0.812	0.771	0.855	CLONAL	1	TRUE	1	0.769091354285716	2		1099	1175	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143999	11143999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1171822727	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	376	792	2	ENST00000358026.2:c.3580G>A	p.Gly1194Arg	p.G1194R	ENST00000358026	NM_001128849.1	1194	Ggg/Agg	26/36	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.769091354285716	2		794	855	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562994	95562994	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1219156713	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	218	649	0	ENST00000393063.1:c.4263T>G	p.Asp1421Glu	p.D1421E	ENST00000393063	NM_030621.3	1421	gaT/gaG	24/28	0.769091354285716	2	FACETS	0.887	0.83	0.946	0.444	0.415	0.473	CLONAL	1	TRUE	0	0.769091354285716	2		649	639	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811605	102811605	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1565968684	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	286	880	2	ENST00000307046.8:c.579del	p.Gly194GlufsTer8	p.G194Efs*8	ENST00000307046	NM_001111285.1	193	aaA/aa	4/4	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.769091354285716	2		882	731	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15821896	15821896	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	202	702	2	ENST00000307771.7:c.294del	p.Lys98AsnfsTer10	p.K98Nfs*10	ENST00000307771	NM_005089.3	97	Aaa/aa	4/11	1	2	FACETS	0.857	0.799	0.916	0.857	0.799	0.916	CLONAL	1	TRUE	1	0.769091354285716	2		704	613	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561914	55561914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769632130	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	43	412	1	ENST00000288135.5:c.304G>A	p.Gly102Ser	p.G102S	ENST00000288135	NM_000222.2	102	Ggc/Agc	2/21	1	2	FACETS	0.267	0.223	0.315	0.267	0.223	0.315	SUBCLONAL	1	TRUE	1	0.769091354285716	2		413	419	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741869	40741869	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768703735	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	400	900	4	ENST00000392038.2:c.1103G>A	p.Arg368His	p.R368H	ENST00000392038	NM_001626.4	368	cGc/cAc	11/14	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.769091354285716	2		904	984	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845397	151845397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779339485	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	52	1029	0	ENST00000262189.6:c.13615G>A	p.Val4539Met	p.V4539M	ENST00000262189	NM_170606.2	4539	Gtg/Atg	52/59	1	2	FACETS	0.132	0.112	0.155	0.132	0.112	0.155	SUBCLONAL	1	TRUE	1	0.769091354285716	2		1029	1024	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29068932	29068932	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	248	596	0	ENST00000282397.4:c.49T>A	p.Cys17Ser	p.C17S	ENST00000282397	NM_002019.4	17	Tgt/Agt	1/30	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.769091354285716	2		596	621	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	483	854	34	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	1	2	FACETS	0.851	0.823	0.878	1	0.997	1	CLONAL	2	TRUE	1	0.769091354285716	2		888	738	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11193219	11193219	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	380	912	0	ENST00000361445.4:c.5282T>A	p.Leu1761Gln	p.L1761Q	ENST00000361445	NM_004958.3	1761	cTa/cAa	38/58	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.769091354285716	2		912	965	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261578	16261578	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	294	850	1	ENST00000375759.3:c.8843T>C	p.Val2948Ala	p.V2948A	ENST00000375759	NM_015001.2	2948	gTc/gCc	11/15	1	2	FACETS	0.911	0.861	0.963	0.911	0.861	0.963	CLONAL	1	TRUE	1	0.769091354285716	2		851	839	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599914	28599914	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	353	920	2	ENST00000253063.3:c.796C>T	p.Gln266Ter	p.Q266*	ENST00000253063	NM_031459.4	266	Cag/Tag	6/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.769091354285716	2		922	882	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226564829	226564829	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1558236428	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	295	855	3	ENST00000366794.5:c.1921del	p.Leu641TrpfsTer12	p.L641Wfs*12	ENST00000366794	NM_001618.3	641	Ctg/tg	13/23	1	2	FACETS	0.99	0.936	1	0.99	0.936	1	CLONAL	1	TRUE	1	0.769091354285716	2		858	775	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041680	29041680	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	246	796	0	ENST00000282397.4:c.139C>A	p.Gln47Lys	p.Q47K	ENST00000282397	NM_002019.4	47	Cag/Aag	2/30	1	2	FACETS	0.854	0.802	0.908	0.854	0.802	0.908	CLONAL	1	TRUE	1	0.769091354285716	2		796	749	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779727	3779727	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	321	781	3	ENST00000262367.5:c.5321G>A	p.Arg1774His	p.R1774H	ENST00000262367	NM_004380.2	1774	cGc/cAc	31/31	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.769091354285716	2		784	793	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788671	3788671	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs778448390	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	259	664	0	ENST00000262367.5:c.4283G>A	p.Arg1428His	p.R1428H	ENST00000262367	NM_004380.2	1428	cGt/cAt	26/31	1	2	FACETS	0.961	0.905	1	0.961	0.905	1	CLONAL	1	TRUE	1	0.769091354285716	2		664	701	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864488	56864488	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1324927881	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	408	838	2	ENST00000308159.5:c.976A>G	p.Met326Val	p.M326V	ENST00000308159	NM_014669.4	326	Atg/Gtg	10/22	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.769091354285716	2		840	1000	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40856673	40856673	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	229	693	0	ENST00000428826.2:c.1964G>A	p.Arg655His	p.R655H	ENST00000428826		655	cGc/cAc	18/21	1	2	FACETS	0.918	0.86	0.976	0.918	0.86	0.976	CLONAL	1	TRUE	1	0.769091354285716	2		693	649	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212483	5212483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754177433	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	165	872	3	ENST00000357368.4:c.4634G>A	p.Arg1545His	p.R1545H	ENST00000357368	NM_002850.3	1545	cGc/cAc	31/38	1	2	FACETS	0.458	0.421	0.498	0.458	0.421	0.498	SUBCLONAL	1	TRUE	1	0.769091354285716	2		875	936	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213355	36213355	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	510	1218	0	ENST00000222270.7:c.2552C>G	p.Ala851Gly	p.A851G	ENST00000222270	NM_014727.1	851	gCt/gGt	4/37	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.769091354285716	2		1218	1305	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213973	36213986	+	frameshift_variant	Frame_Shift_Del	DEL	GGGAGAATCAGAGC	GGGAGAATCAGAGC	-	novel	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	413	1114	0	ENST00000222270.7:c.2799_2812del	p.Gly934HisfsTer56	p.G934Hfs*56	ENST00000222270	NM_014727.1	933	ggGGGAGAATCAGAGCcc/ggcc	6/37	1	2	FACETS	0.91	0.867	0.953	0.91	0.867	0.953	CLONAL	1	TRUE	1	0.769091354285716	2		1114	1180	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744453	41744453	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138219571	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	152	1045	4	ENST00000301178.4:c.1073C>T	p.Ala358Val	p.A358V	ENST00000301178	NM_021913.4	358	gCg/gTg	8/20	1	2	FACETS	0.377	0.344	0.412	0.377	0.344	0.412	SUBCLONAL	1	TRUE	1	0.769091354285716	2		1049	1048	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082784	16082784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	111	237	0	ENST00000281043.3:c.598C>T	p.Arg200Cys	p.R200C	ENST00000281043	NM_005378.4	200	Cgc/Tgc	2/3	1	2	FACETS	0.744	0.675	0.816	0.744	0.675	0.816	SUBCLONAL	1	TRUE	1	0.769091354285716	2		237	388	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661671	227661671	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369611716	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	195	725	1	ENST00000305123.5:c.1784G>A	p.Arg595Gln	p.R595Q	ENST00000305123	NM_005544.2	595	cGg/cAg	1/2	1	2	FACETS	0.936	0.873	1	0.936	0.873	1	CLONAL	1	TRUE	1	0.769091354285716	2		726	542	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721883	49721883	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs532706844	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	166	488	0	ENST00000449682.2:c.1880C>T	p.Thr627Met	p.T627M	ENST00000449682	NM_020998.3	627	aCg/aTg	17/18	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.769091354285716	2		488	421	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426032	138426032	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	280	773	0	ENST00000289153.2:c.1499A>G	p.Lys500Arg	p.K500R	ENST00000289153	NM_006219.2	500	aAa/aGa	9/22	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.769091354285716	2		773	719	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504375	186504375	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	118	591	0	ENST00000323963.5:c.716del	p.Lys239ArgfsTer4	p.K239Rfs*4	ENST00000323963		238	Aaa/aa	7/11	1	2	FACETS	0.651	0.591	0.714	0.651	0.591	0.714	SUBCLONAL	1	TRUE	1	0.769091354285716	2		591	471	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1962801	1962803	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	293	743	1	ENST00000382891.5:c.3301_3303del	p.Glu1101del	p.E1101del	ENST00000382891	NM_133335.3	1099	GAG/-	18/22	1	2	FACETS	0.971	0.918	1	0.971	0.918	1	CLONAL	1	TRUE	1	0.769091354285716	2		744	785	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968630	55968632	+	inframe_deletion	In_Frame_Del	DEL	GTC	GTC	-	novel	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	303	1008	0	ENST00000263923.4:c.2031_2033del	p.Thr678del	p.T678del	ENST00000263923	NM_002253.2	677	acGACa/aca	14/30	1	2	FACETS	0.872	0.824	0.921	0.872	0.824	0.921	CLONAL	1	TRUE	1	0.769091354285716	2		1008	904	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197760	66197760	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765103637	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	40	899	0	ENST00000273854.3:c.2939G>A	p.Gly980Asp	p.G980D	ENST00000273854	NM_004439.5	980	gGc/gAc	17/18	1	2	FACETS	0.146	0.121	0.175	0.146	0.121	0.175	SUBCLONAL	1	TRUE	1	0.769091354285716	2		899	712	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517607	176517607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	535	1247	4	ENST00000292408.4:c.308C>T	p.Ala103Val	p.A103V	ENST00000292408	NM_213647.1	103	gCa/gTa	3/18	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.769091354285716	2		1251	1278	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696801	176696802	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	116	320	1	ENST00000439151.2:c.5508dup	p.Ala1837SerfsTer10	p.A1837Sfs*10	ENST00000439151	NM_022455.4	1834	-/A	16/23	1	2	FACETS	0.898	0.819	0.979	0.898	0.819	0.979	CLONAL	1	TRUE	1	0.769091354285716	2		321	336	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176710899	176710899	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	307	644	1	ENST00000439151.2:c.6121G>T	p.Gly2041Cys	p.G2041C	ENST00000439151	NM_022455.4	2041	Ggc/Tgc	20/23	1	2	FACETS	0.977	0.925	1	0.977	0.925	1	CLONAL	1	TRUE	1	0.769091354285716	2		645	817	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528391	157528392	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	324	1030	0	ENST00000346085.5:c.6118dup	p.Tyr2040LeufsTer49	p.Y2040Lfs*49	ENST00000346085	NM_020732.3	2039	gct/gcTt	20/20	1	2	FACETS	0.92	0.871	0.969	0.92	0.871	0.969	CLONAL	1	TRUE	1	0.769091354285716	2		1030	916	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409995	139409995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764942073	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	541	1186	0	ENST00000277541.6:c.1843G>A	p.Gly615Arg	p.G615R	ENST00000277541	NM_017617.3	615	Ggg/Agg	11/34	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.769091354285716	2		1186	1323	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879925	44879925	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs189751539	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	262	982	3	ENST00000377967.4:c.514C>T	p.Arg172Ter	p.R172*	ENST00000377967	NM_021140.2	172	Cga/Tga	6/29	1	2	FACETS	0.987	0.931	1	0.987	0.931	1	CLONAL	1	TRUE	1	0.769091354285716	2		985	690	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44910996	44910999	+	frameshift_variant	Frame_Shift_Del	DEL	CAGA	CAGA	-	novel	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	216	816	0	ENST00000377967.4:c.701_704del	p.Thr234ArgfsTer7	p.T234Rfs*7	ENST00000377967	NM_021140.2	233	CAGAca/ca	9/29	1	2	FACETS	0.847	0.792	0.904	0.847	0.792	0.904	CLONAL	1	TRUE	1	0.769091354285716	2		816	663	SUCCESS
AR	367	MSKCC	GRCh37	X	66766405	66766405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	41	430	0	ENST00000374690.3:c.1417G>A	p.Gly473Ser	p.G473S	ENST00000374690	NM_000044.3	473	Ggc/Agc	1/8	1	2	FACETS	0.291	0.242	0.344	0.291	0.242	0.344	SUBCLONAL	1	TRUE	1	0.769091354285716	2		430	367	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456521	32456525	+	missense_variant	Missense_Mutation	ONP	GGCGC	GGCGC	AGCGT	novel	NA	P-0020064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	206	143	1	ENST00000332351.3:c.367_371delinsACGCT	p.Ala123_Pro124delinsThrLeu	p.A123_P124delinsTL	ENST00000332351	NM_024426.4	123	GCGCCg/ACGCTg	1/10	0.769091354285716	2	FACETS	0.804	0.763	0.845	0.804	0.763	0.845	CLONAL	2	TRUE	0	0.769091354285716	2		144	333	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0020066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	162	786	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	0.339676738602645	2		786	780	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0020066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	111	990	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.691	0.62	0.766	0.691	0.62	0.766	SUBCLONAL	1	TRUE	1	0.339676738602645	2		990	946	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0020068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	222	465	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.975	0.917	1	0.975	0.917	1	CLONAL	1	TRUE	1	0.925907087996881	2		465	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0020068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	1247	591	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.925907087996881	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.925907087996881	2		591	1331	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0020068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	9	763	2	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.925907087996881	1	FACETS	0.029	0.019	0.042	0.029	0.019	0.042	SUBCLONAL	1	TRUE	0	0.925907087996881	1		765	359	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133829	55133829	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3711	6865	460	2	ENST00000257290.5:c.1042T>C	p.Ser348Pro	p.S348P	ENST00000257290	NM_006206.4	348	Tcc/Ccc	7/23	0.925907087996881	12	FACETS	0.987	0.978	0.995			1	CLONAL	8	TRUE	NA	0.925907087996881	12		462	10576	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859852	117859852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1283070450	NA	P-0020068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	283	362	0	ENST00000297338.2:c.1783G>A	p.Ala595Thr	p.A595T	ENST00000297338	NM_006265.2	595	Gca/Aca	14/14	1	2	FACETS	0.997	0.946	1	0.997	0.946	1	CLONAL	1	TRUE	1	0.925907087996881	2		362	613	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015058	37015058	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	545	701	0	ENST00000358127.4:c.346G>A	p.Asp116Asn	p.D116N	ENST00000358127	NM_001280556.1	116	Gac/Aac	3/10	1	2	FACETS	0.983	0.946	1	0.983	0.946	1	CLONAL	1	TRUE	1	0.925907087996881	2		701	1198	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651669	48651669	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	550	844	0	ENST00000376670.3:c.835T>G	p.Cys279Gly	p.C279G	ENST00000376670	NM_002049.3	279	Tgc/Ggc	5/6	1	2	FACETS	0.896	0.861	0.931	0.896	0.861	0.931	CLONAL	1	TRUE	1	0.925907087996881	2		844	1326	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854932	76854933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	477	907	0	ENST00000373344.5:c.5903dup	p.Asn1969LysfsTer4	p.N1969Kfs*4	ENST00000373344	NM_000489.3	1968	gga/ggGa	25/35	1	2	FACETS	0.947	0.908	0.986	0.947	0.908	0.986	CLONAL	1	TRUE	1	0.925907087996881	2		907	1088	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	42	416	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	0.407	0.341	0.481	0.407	0.341	0.481	SUBCLONAL	1	TRUE	1	0.574742269927218	2		416	359	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	45	606	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.183	0.153	0.217	0.183	0.153	0.217	SUBCLONAL	1	TRUE	1	0.574742269927218	2		606	854	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	176	640	2	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.574742269927218	2		642	611	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	355	752	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.574742269927218	2		755	899	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881489	48881490	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs587778862	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	23	495	0	ENST00000267163.4:c.219_220del	p.Arg73SerfsTer36	p.R73Sfs*36	ENST00000267163	NM_000321.2	71	AGa/a	2/27	1	2	FACETS	0.182	0.141	0.229	0.182	0.141	0.229	SUBCLONAL	1	TRUE	1	0.574742269927218	2		495	440	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536164	41536164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750740148	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	167	713	2	ENST00000263253.7:c.1781C>T	p.Thr594Met	p.T594M	ENST00000263253	NM_001429.3	594	aCg/aTg	9/31	1	2	FACETS	0.953	0.879	1	0.953	0.879	1	CLONAL	1	TRUE	1	0.574742269927218	2		715	610	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	76	697	3	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	0.317506932105442	1	FACETS	0.208	0.182	0.237	0.208	0.182	0.237	INDETERMINATE	1	TRUE	0	0.574742269927218	1		700	904	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473780	67473780	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730880214	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	120	562	1	ENST00000327367.4:c.860G>A	p.Arg287Gln	p.R287Q	ENST00000327367	NM_005902.3	287	cGg/cAg	6/9	1	2	FACETS	0.625	0.565	0.688	0.625	0.565	0.688	SUBCLONAL	1	TRUE	1	0.574742269927218	2		563	668	SUCCESS
APC	324	MSKCC	GRCh37	5	112175166	112175166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371113837	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	16	301	0	ENST00000257430.4:c.3875C>T	p.Thr1292Met	p.T1292M	ENST00000257430	NM_000038.5	1292	aCg/aTg	16/16	1	2	FACETS	0.213	0.157	0.279	0.213	0.157	0.279	SUBCLONAL	1	TRUE	1	0.574742269927218	2		301	262	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115916	8115916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771315353	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	115	557	0	ENST00000346208.3:c.1262C>T	p.Pro421Leu	p.P421L	ENST00000346208		421	cCg/cTg	6/6	1	2	FACETS	0.474	0.427	0.524	0.474	0.427	0.524	SUBCLONAL	1	TRUE	1	0.574742269927218	2		557	844	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	217	965	6	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	1	2	FACETS	0.625	0.58	0.672	0.625	0.58	0.672	SUBCLONAL	1	TRUE	1	0.574742269927218	2		971	1208	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097200	11097205	+	inframe_deletion	In_Frame_Del	DEL	GGCCCT	GGCCCT	-	rs372601826	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	224	750	0	ENST00000358026.2:c.708_713del	p.Gly243_Pro244del	p.G243_P244del	ENST00000358026	NM_001128849.1	231	GGCCCT/-	4/36	1	2	FACETS	0.861	0.803	0.921	0.861	0.803	0.921	CLONAL	1	TRUE	1	0.574742269927218	2		750	905	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130120	143130120	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	118	833	0	ENST00000262992.4:c.896del	p.Asn299MetfsTer10	p.N299Mfs*10	ENST00000262992	NM_001101669.1	299	aAt/at	11/24	1	2	FACETS	0.573	0.517	0.631	0.573	0.517	0.631	SUBCLONAL	1	TRUE	1	0.574742269927218	2		833	717	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100425	8100425	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	127	836	1	ENST00000346208.3:c.404del	p.Pro135ArgfsTer60	p.P135Rfs*60	ENST00000346208		133	taC/ta	3/6	1	2	FACETS	0.395	0.357	0.435	0.395	0.357	0.435	SUBCLONAL	1	TRUE	1	0.574742269927218	2		837	1119	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	178	400	3	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.574742269927218	2		403	592	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794441	42794441	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1226	70	1068	1	ENST00000575354.2:c.1526del	p.Pro509HisfsTer14	p.P509Hfs*14	ENST00000575354	NM_015125.3	507	cgC/cg	10/20	1	2	FACETS	0.188	0.163	0.215	0.188	0.163	0.215	SUBCLONAL	1	TRUE	1	0.574742269927218	2		1069	1296	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	72	880	1	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	0.227	0.197	0.259	0.227	0.197	0.259	SUBCLONAL	1	TRUE	1	0.574742269927218	2		881	1106	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885145	111885145	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs892433462	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	134	608	0	ENST00000341259.2:c.1038del	p.Leu347CysfsTer26	p.L347Cfs*26	ENST00000341259	NM_005475.2	345	Ggg/gg	6/8	1	2	FACETS	0.651	0.592	0.713	0.651	0.592	0.713	SUBCLONAL	1	TRUE	1	0.574742269927218	2		608	716	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938499	76938501	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs1297294136	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	122	605	0	ENST00000373344.5:c.2247_2249del	p.Ser750del	p.S750del	ENST00000373344	NM_000489.3	749	tcTTCa/tca	9/35	0.317506932105442	1	FACETS	0.712	0.648	0.778	0.712	0.648	0.778	INDETERMINATE	1	TRUE	0	0.574742269927218	1		605	425	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745962	745963	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	41	801	0	ENST00000314574.4:c.559_560del	p.Ser187Ter	p.S187*	ENST00000314574	NM_005433.3	187	AGt/t	5/12	1	2	FACETS	0.222	0.184	0.264	0.222	0.184	0.264	SUBCLONAL	1	TRUE	1	0.574742269927218	2		801	644	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992581	72992582	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCTTCCTCCTCCTCT	rs376713069	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	49	671	0	ENST00000268489.5:c.1449_1463dup	p.Glu483_Glu487dup	p.E483_E487dup	ENST00000268489	NM_006885.3	483	gac/gaAGAGGAGGAGGAAGAc	2/10	0.574742269927218	1	FACETS	0.207	0.175	0.243	0.207	0.175	0.243	SUBCLONAL	1	TRUE	0	0.574742269927218	1		671	586	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	186	653	1	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.543	0.501	0.588	0.543	0.501	0.588	SUBCLONAL	1	TRUE	1	0.574742269927218	2		654	1191	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	47	474	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.186	0.156	0.219	0.186	0.156	0.219	SUBCLONAL	1	TRUE	1	0.574742269927218	2		477	880	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614463	38614463	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	53	764	2	ENST00000299084.4:c.234del	p.Asp79ThrfsTer42	p.D79Tfs*42	ENST00000299084	NM_152594.2	77	Aaa/aa	3/7	1	2	FACETS	0.342	0.292	0.398	0.342	0.292	0.398	SUBCLONAL	1	TRUE	1	0.574742269927218	2		766	539	SUCCESS
APC	324	MSKCC	GRCh37	5	112176555	112176555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771967537	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	18	385	2	ENST00000257430.4:c.5264C>T	p.Ala1755Val	p.A1755V	ENST00000257430	NM_000038.5	1755	gCg/gTg	16/16	1	2	FACETS	0.184	0.138	0.239	0.184	0.138	0.239	SUBCLONAL	1	TRUE	1	0.574742269927218	2		387	340	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43730536	43730536	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	161	662	0	ENST00000382044.4:c.3177del	p.Thr1060ProfsTer36	p.T1060Pfs*36	ENST00000382044	NM_001141980.1	1059	ccC/cc	16/28	1	2	FACETS	0.812	0.747	0.88	0.812	0.747	0.88	CLONAL	1	TRUE	1	0.574742269927218	2		662	690	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223858	36223858	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	185	966	6	ENST00000222270.7:c.6413del	p.Pro2138ArgfsTer15	p.P2138Rfs*15	ENST00000222270	NM_014727.1	2136	ctC/ct	28/37	1	2	FACETS	0.593	0.547	0.642	0.593	0.547	0.642	SUBCLONAL	1	TRUE	1	0.574742269927218	2		972	1085	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211899	36211899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	227	546	2	ENST00000222270.7:c.1656del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	550	gaC/ga	3/37	1	2	FACETS	0.58	0.539	0.623	0.58	0.539	0.623	SUBCLONAL	1	TRUE	1	0.574742269927218	2		548	1362	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255040	16255041	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	26	357	0	ENST00000375759.3:c.2308_2309del	p.Ser770ProfsTer5	p.S770Pfs*5	ENST00000375759	NM_015001.2	769	CTc/c	11/15	0.574742269927218	1	FACETS	0.194	0.153	0.24	0.194	0.153	0.24	SUBCLONAL	1	TRUE	0	0.574742269927218	1		357	333	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841484	156841484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201509717	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	186	847	0	ENST00000524377.1:c.787G>A	p.Val263Met	p.V263M	ENST00000524377	NM_002529.3	263	Gtg/Atg	7/17	1	2	FACETS	0.625	0.576	0.675	0.625	0.576	0.675	SUBCLONAL	1	TRUE	1	0.574742269927218	2		847	1036	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604478	43604478	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	58	752	1	ENST00000355710.3:c.1064-1G>T		p.X355_splice	ENST00000355710	NM_020975.4	355			NA	2	FACETS	0.237	0.203	0.275			1	INDETERMINATE	1	TRUE	NA	0.574742269927218	2		753	851	SUCCESS
EED	8726	MSKCC	GRCh37	11	85963269	85963269	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1565689787	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	32	513	0	ENST00000263360.6:c.347T>C	p.Val116Ala	p.V116A	ENST00000263360	NM_003797.3	116	gTa/gCa	3/12	1	2	FACETS	0.259	0.21	0.315	0.259	0.21	0.315	SUBCLONAL	1	TRUE	1	0.574742269927218	2		513	430	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100551	102100553	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	194	672	1	ENST00000282441.5:c.1397_1399del	p.Glu466del	p.E466del	ENST00000282441	NM_001130145.2	465	atAGAa/ata	9/9	1	2	FACETS	0.978	0.909	1	0.978	0.909	1	CLONAL	1	TRUE	1	0.574742269927218	2		673	690	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416188	416188	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201274262	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	51	606	2	ENST00000399788.2:c.3998G>A	p.Arg1333Gln	p.R1333Q	ENST00000399788	NM_001042603.1	1333	cGa/cAa	24/28	NA	2	FACETS	0.313	0.266	0.365			1	INDETERMINATE	1	TRUE	NA	0.574742269927218	2		608	567	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944928	31944928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	141	349	0	ENST00000340398.3:c.173C>T	p.Thr58Ile	p.T58I	ENST00000340398	NM_001013699.2	58	aCc/aTc	1/1	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.574742269927218	2		349	464	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864813	57864813	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	220	773	0	ENST00000228682.2:c.2290A>G	p.Asn764Asp	p.N764D	ENST00000228682	NM_005269.2	764	Aac/Gac	12/12	1	2	FACETS	0.955	0.89	1	0.955	0.89	1	CLONAL	1	TRUE	1	0.574742269927218	2		773	802	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120795647	120795647	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	126	624	1	ENST00000257552.2:c.506T>A	p.Ile169Asn	p.I169N	ENST00000257552	NM_002442.3	169	aTt/aAt	8/15	1	2	FACETS	0.553	0.501	0.608	0.553	0.501	0.608	SUBCLONAL	1	TRUE	1	0.574742269927218	2		625	793	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434471	121434471	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747433197	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	211	896	0	ENST00000257555.6:c.1235T>C	p.Met412Thr	p.M412T	ENST00000257555		412	aTg/aCg	6/10	1	2	FACETS	0.651	0.604	0.7	0.651	0.604	0.7	SUBCLONAL	1	TRUE	1	0.574742269927218	2		896	1128	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256160	133256160	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	103	704	1	ENST00000320574.5:c.501G>T	p.Arg167Ser	p.R167S	ENST00000320574	NM_006231.2	167	agG/agT	6/49	1	2	FACETS	0.388	0.346	0.432	0.388	0.346	0.432	SUBCLONAL	1	TRUE	1	0.574742269927218	2		705	924	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95556980	95556980	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	76	645	0	ENST00000393063.1:c.5624A>T	p.Asp1875Val	p.D1875V	ENST00000393063	NM_030621.3	1875	gAc/gTc	28/28	1	2	FACETS	0.361	0.316	0.41	0.361	0.316	0.41	SUBCLONAL	1	TRUE	1	0.574742269927218	2		645	732	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943779	9943779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1211198789	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	143	589	0	ENST00000330684.3:c.1162G>A	p.Ala388Thr	p.A388T	ENST00000330684	NM_001134407.1	388	Gcc/Acc	5/13	1	2	FACETS	0.664	0.606	0.725	0.664	0.606	0.725	SUBCLONAL	1	TRUE	1	0.574742269927218	2		589	749	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351685	89351685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	110	838	0	ENST00000301030.4:c.1265C>T	p.Thr422Ile	p.T422I	ENST00000301030	NM_001256183.1	422	aCa/aTa	9/13	0.574742269927218	1	FACETS	0.322	0.289	0.358	0.322	0.289	0.358	SUBCLONAL	1	TRUE	0	0.574742269927218	1		838	846	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924262	11924262	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	45	90	0	ENST00000353533.5:c.63del	p.Gly22AlafsTer3	p.G22Afs*3	ENST00000353533	NM_003010.3	20	aCc/ac	1/11	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.574742269927218	2		90	138	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117764	70117764	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	189	832	0	ENST00000245479.2:c.232A>G	p.Ser78Gly	p.S78G	ENST00000245479	NM_000346.3	78	Agc/Ggc	1/3	1	2	FACETS	0.622	0.574	0.671	0.622	0.574	0.671	SUBCLONAL	1	TRUE	1	0.574742269927218	2		832	1058	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267364	7267364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	38	524	0	ENST00000302850.5:c.644G>A	p.Cys215Tyr	p.C215Y	ENST00000302850	NM_000208.2	215	tGc/tAc	2/22	1	2	FACETS	0.199	0.164	0.238	0.199	0.164	0.238	SUBCLONAL	1	TRUE	1	0.574742269927218	2		524	665	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168951	11168951	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	49	569	1	ENST00000358026.2:c.4541G>A	p.Ser1514Asn	p.S1514N	ENST00000358026	NM_001128849.1	1514	aGc/aAc	32/36	1	2	FACETS	0.206	0.174	0.242	0.206	0.174	0.242	SUBCLONAL	1	TRUE	1	0.574742269927218	2		570	826	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289665	15289665	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781401262	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	135	1003	0	ENST00000263388.2:c.3806G>A	p.Gly1269Asp	p.G1269D	ENST00000263388	NM_000435.2	1269	gGt/gAt	23/33	1	2	FACETS	0.388	0.351	0.427	0.388	0.351	0.427	SUBCLONAL	1	TRUE	1	0.574742269927218	2		1003	1211	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18964076	18964076	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs771840537	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	66	609	0	ENST00000262803.5:c.1073A>G	p.Gln358Arg	p.Q358R	ENST00000262803	NM_002911.3	358	cAg/cGg	8/24	1	2	FACETS	0.282	0.244	0.324	0.282	0.244	0.324	SUBCLONAL	1	TRUE	1	0.574742269927218	2		609	814	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791471	42791471	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	90	689	3	ENST00000575354.2:c.453-1G>T		p.X151_splice	ENST00000575354	NM_015125.3	151			1	2	FACETS	0.378	0.335	0.424	0.378	0.335	0.424	SUBCLONAL	1	TRUE	1	0.574742269927218	2		692	829	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920639	96920639	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	63	469	0	ENST00000258439.3:c.341A>C	p.Asp114Ala	p.D114A	ENST00000258439	NM_001193304.2	114	gAt/gCt	3/4	1	2	FACETS	0.294	0.253	0.338	0.294	0.253	0.338	SUBCLONAL	1	TRUE	1	0.574742269927218	2		469	746	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225362540	225362540	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	50	632	0	ENST00000264414.4:c.1637del	p.Arg546HisfsTer37	p.R546Hfs*37	ENST00000264414	NM_003590.4	546	cGa/ca	12/16	1	2	FACETS	0.315	0.267	0.368	0.315	0.267	0.368	SUBCLONAL	1	TRUE	1	0.574742269927218	2		632	552	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370686	225370686	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1232071537	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	72	494	1	ENST00000264414.4:c.1193del	p.Lys398ArgfsTer6	p.K398Rfs*6	ENST00000264414	NM_003590.4	398	aAg/ag	8/16	1	2	FACETS	0.553	0.485	0.626	0.553	0.485	0.626	SUBCLONAL	1	TRUE	1	0.574742269927218	2		495	453	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940064	49940064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200757776	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	180	765	1	ENST00000296474.3:c.979G>A	p.Ala327Thr	p.A327T	ENST00000296474	NM_002447.2	327	Gct/Act	1/20	1	2	FACETS	0.676	0.623	0.73	0.676	0.623	0.73	SUBCLONAL	1	TRUE	1	0.574742269927218	2		766	927	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191226	185191226	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs759430612	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	25	487	0	ENST00000265026.3:c.2107A>G	p.Met703Val	p.M703V	ENST00000265026	NM_004721.4	703	Atg/Gtg	11/14	1	2	FACETS	0.175	0.137	0.219	0.175	0.137	0.219	SUBCLONAL	1	TRUE	1	0.574742269927218	2		487	497	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1953932	1953932	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	81	942	0	ENST00000382891.5:c.2111G>T	p.Arg704Met	p.R704M	ENST00000382891	NM_133335.3	704	aGg/aTg	11/22	1	2	FACETS	0.242	0.212	0.274	0.242	0.212	0.274	SUBCLONAL	1	TRUE	1	0.574742269927218	2		942	1165	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156652	106156652	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	57	432	0	ENST00000380013.4:c.1557del	p.Phe519LeufsTer14	p.F519Lfs*14	ENST00000380013	NM_001127208.2	518	aTt/at	3/11	1	2	FACETS	0.461	0.397	0.531	0.461	0.397	0.531	SUBCLONAL	1	TRUE	1	0.574742269927218	2		432	430	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721024	176721024	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	86	590	0	ENST00000439151.2:c.6655C>A	p.Arg2219Ser	p.R2219S	ENST00000439151	NM_022455.4	2219	Cgt/Agt	23/23	1	2	FACETS	0.415	0.367	0.467	0.415	0.367	0.467	SUBCLONAL	1	TRUE	1	0.574742269927218	2		590	721	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675764	30675764	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	318	1050	0	ENST00000376406.3:c.2592G>T	p.Leu864Phe	p.L864F	ENST00000376406	NM_014641.2	864	ttG/ttT	8/15	1	2	FACETS	0.953	0.9	1	0.953	0.9	1	CLONAL	1	TRUE	1	0.574742269927218	2		1050	1161	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940464	31940464	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	66	774	0	ENST00000375333.2:c.497T>C	p.Leu166Pro	p.L166P	ENST00000375333	NM_032454.1	166	cTg/cCg	3/8	1	2	FACETS	0.222	0.192	0.255	0.222	0.192	0.255	SUBCLONAL	1	TRUE	1	0.574742269927218	2		774	1033	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109319921	109319921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	209	734	3	ENST00000436639.2:c.767C>T	p.Ala256Val	p.A256V	ENST00000436639	NM_014454.2	256	gCg/gTg	5/10	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.574742269927218	2		737	719	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017498	112017498	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	32	481	0	ENST00000368678.4:c.1015A>G	p.Thr339Ala	p.T339A	ENST00000368678		339	Acc/Gcc	9/13	1	2	FACETS	0.175	0.141	0.213	0.175	0.141	0.213	SUBCLONAL	1	TRUE	1	0.574742269927218	2		481	636	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199747	138199747	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	169	620	0	ENST00000237289.4:c.1165A>G	p.Thr389Ala	p.T389A	ENST00000237289	NM_001270507.1	389	Acg/Gcg	7/9	1	2	FACETS	0.77	0.709	0.833	0.77	0.709	0.833	SUBCLONAL	1	TRUE	1	0.574742269927218	2		620	764	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81399266	81399266	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	48	710	2	ENST00000222390.5:c.22C>T	p.Pro8Ser	p.P8S	ENST00000222390	NM_000601.4	8	Cca/Tca	1/18	1	2	FACETS	0.183	0.154	0.215	0.183	0.154	0.215	SUBCLONAL	1	TRUE	1	0.574742269927218	2		712	914	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739075	145739075	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	251	625	1	ENST00000428558.2:c.2080G>T	p.Gly694Cys	p.G694C	ENST00000428558	NM_004260.3	694	Ggc/Tgc	13/22	0.0802024282895009	4	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.574742269927218	4		626	1148	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93607759	93607759	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	87	465	0	ENST00000375746.1:c.461T>C	p.Leu154Pro	p.L154P	ENST00000375746	NM_001174167.1	154	cTg/cCg	3/14	0.574742269927218	1	FACETS	0.644	0.575	0.716	0.644	0.575	0.716	SUBCLONAL	1	TRUE	0	0.574742269927218	1		465	335	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923847	39923847	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	142	698	0	ENST00000378444.4:c.3244T>A	p.Tyr1082Asn	p.Y1082N	ENST00000378444	NM_001123385.1	1082	Tat/Aat	7/15	0.317506932105442	1	FACETS	0.447	0.408	0.489	0.447	0.408	0.489	INDETERMINATE	1	TRUE	0	0.574742269927218	1		698	787	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412701	63412701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1371810064	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	119	661	0	ENST00000330258.3:c.466G>A	p.Ala156Thr	p.A156T	ENST00000330258	NM_152424.3	156	Gct/Act	2/2	0.317506932105442	1	FACETS	0.462	0.417	0.508	0.462	0.417	0.508	INDETERMINATE	1	TRUE	0	0.574742269927218	1		661	639	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939626	76939626	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	126	788	0	ENST00000373344.5:c.1122A>T	p.Leu374Phe	p.L374F	ENST00000373344	NM_000489.3	374	ttA/ttT	9/35	0.317506932105442	1	FACETS	0.498	0.451	0.546	0.498	0.451	0.546	INDETERMINATE	1	TRUE	0	0.574742269927218	1		788	628	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1064795203	NA	P-0020069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	127	852	0	ENST00000269305.4:c.532C>G	p.His178Asp	p.H178D	ENST00000269305	NM_001126112.2	178	Cac/Gac	5/11	0.460611670730187	1	FACETS	0.837	0.763	0.915	0.837	0.763	0.915	CLONAL	1	TRUE	0	0.460611670730187	1		852	507	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023676	27023676	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs867647567	NA	P-0020069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	121	523	0	ENST00000324856.7:c.782C>A	p.Ser261Ter	p.S261*	ENST00000324856	NM_006015.4	261	tCg/tAg	1/20	0.460611670730187	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.460611670730187	1		523	359	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7167908	7168064	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGCACAAACGTAGCAAGCACAGAGCCAGCCAGCCCTCGCCTCCTCAGCGTCTCTCTAACTCTTCTACTTACGCCTCTTTGTAGAACAGCATGAACCCCAAGAGGTCTCGGAAGTCGGGGGGCCAGTACGGCTCCCATCTCAGCAAGATCTTGTCAAA	AGCACAAACGTAGCAAGCACAGAGCCAGCCAGCCCTCGCCTCCTCAGCGTCTCTCTAACTCTTCTACTTACGCCTCTTTGTAGAACAGCATGAACCCCAAGAGGTCTCGGAAGTCGGGGGGCCAGTACGGCTCCCATCTCAGCAAGATCTTGTCAAA	-	novel	NA	P-0020069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	40	235	0	ENST00000302850.5:c.1525_1610+71del		p.X509_splice	ENST00000302850	NM_000208.2	509		7/22	NA	2	FACETS	1	0.909	1			1	INDETERMINATE	1	TRUE	NA	0.460611670730187	2		235	156	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753196	128753215	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	TGTGCGTAAGGAAAAGTAAG	TGTGCGTAAGGAAAAGTAAG	-	novel	NA	P-0020069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	147	363	0	ENST00000377970.2:c.1357_*11del		p.*453*	ENST00000377970	NM_002467.4	453		3/3	0.460611670730187	8	FACETS	1	0.944	1			1	CLONAL	2	TRUE	NA	0.460611670730187	8		363	730	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164860	36164872	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCGGGGAACTG	GCGCGGGGAACTG	-	novel	NA	P-0020070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	195	1226	0	ENST00000300305.3:c.1003_1015del	p.Gln335CysfsTer255	p.Q335Cfs*255	ENST00000300305		335	CAGTTCCCCGCGCtg/tg	8/8	0.161088282070207	2	FACETS	1	0.988	1	0.682	0.631	0.737	CLONAL	1	TRUE	0	0.243172998228334	2		1226	1175	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578490	7578490	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	276	1091	1	ENST00000269305.4:c.440T>A	p.Val147Asp	p.V147D	ENST00000269305	NM_001126112.2	147	gTt/gAt	5/11	0.219659441794922	2	FACETS	0.806	0.755	0.859	0.806	0.755	0.859	CLONAL	2	TRUE	0	0.243172998228334	2		1092	1408	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591846	48591846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	75	683	0	ENST00000342988.3:c.1009G>A	p.Glu337Lys	p.E337K	ENST00000342988	NM_005359.5	337	Gag/Aag	9/12	0.243172998228334	1	FACETS	0.739	0.647	0.839	0.739	0.647	0.839	SUBCLONAL	1	TRUE	0	0.243172998228334	1		683	733	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164898	36164899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGGGTGCCGCTGCAGGG	novel	NA	P-0020070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	129	841	0	ENST00000300305.3:c.968-8_976dup	p.Asp326AlafsTer8	p.D326Afs*8	ENST00000300305		326	gac/gCCCTGCAGCGGCACCCGac	8/8	0.161088282070207	2	FACETS	1	0.956	1	0.548	0.496	0.603	CLONAL	1	TRUE	0	0.243172998228334	2		841	968	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259490	89259490	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	98	657	0	ENST00000336596.2:c.634T>A	p.Phe212Ile	p.F212I	ENST00000336596	NM_005233.5	212	Ttt/Att	3/17	1	2	FACETS	0.989	0.882	1	0.989	0.882	1	CLONAL	1	TRUE	1	0.243172998228334	2		657	815	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44919396	44919396	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	145	221	0	ENST00000377967.4:c.1324C>T	p.Gln442Ter	p.Q442*	ENST00000377967	NM_021140.2	442	Cag/Tag	13/29	0.243240501957235	2	FACETS	1	0.976	1			1	CLONAL	3	TRUE	NA	0.243172998228334	2		221	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	450	727	2	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.479487628824228	5	FACETS	0.952	0.922	0.98			1	CLONAL	5	TRUE	NA	0.529514238861547	5		729	641	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0020073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	443	647	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.649379359002391	3	FACETS	0.965	0.936	0.993	0.965	0.936	0.993	CLONAL	3	TRUE	0	0.672544843294752	3		647	608	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578247	7578247	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	589	902	0	ENST00000269305.4:c.602del	p.Leu201CysfsTer46	p.L201Cfs*46	ENST00000269305	NM_001126112.2	201	tTg/tg	6/11	0.672544843294752	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	0	0.672544843294752	3		902	778	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971122	21971123	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	306	721	0	ENST00000304494.5:c.235dup	p.Thr79AsnfsTer41	p.T79Nfs*41	ENST00000304494	NM_000077.4	79	acc/aAcc	2/3	0.672544843294752	2	FACETS	0.976	0.937	1	0.976	0.937	1	CLONAL	2	TRUE	0	0.672544843294752	2		721	466	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15943806	15943806	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	273	519	0	ENST00000268712.3:c.6682G>C	p.Ala2228Pro	p.A2228P	ENST00000268712	NM_006311.3	2228	Gct/Cct	43/46	0.672544843294752	3	FACETS	1	0.992	1	0.807	0.77	0.843	CLONAL	2	TRUE	0	0.672544843294752	3		519	448	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758852	41758852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756510536	NA	P-0020073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	100	773	0	ENST00000301178.4:c.1906C>T	p.Arg636Trp	p.R636W	ENST00000301178	NM_021913.4	636	Cgg/Tgg	16/20	0.425284411557689	4	FACETS	0.694	0.62	0.772	0.231	0.206	0.258	SUBCLONAL	1	TRUE	1	0.672544843294752	4		773	717	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0020074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	173	352	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.895	0.826	0.965	0.895	0.826	0.965	CLONAL	1	TRUE	1	0.572983376818845	2		352	675	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6439807	6439807	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	95	588	0	ENST00000356142.4:c.333T>A	p.Asn111Lys	p.N111K	ENST00000356142	NM_018890.3	111	aaT/aaA	5/7	1	2	FACETS	0.352	0.312	0.394	0.352	0.312	0.394	SUBCLONAL	1	TRUE	1	0.572983376818845	2		588	943	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0020075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	121	786	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.954	0.862	1	0.954	0.862	1	CLONAL	1	TRUE	1	0.352958803712135	2		786	719	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0020075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	138	453	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.142200305127368	3	FACETS	1	0.979	1	0.622	0.567	0.68	INDETERMINATE	1	TRUE	1	0.352958803712135	3		453	739	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0020075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	175	622	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.352958803712135	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.352958803712135	1		623	708	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519896	NA	P-0020075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	111	512	0	ENST00000281708.4:c.1514G>T	p.Arg505Leu	p.R505L	ENST00000281708	NM_033632.3	505	cGc/cTc	10/12	0.143839249081061	3	FACETS	1	0.975	1	0.63	0.568	0.696	INDETERMINATE	1	TRUE	1	0.352958803712135	3		512	587	SUCCESS
APC	324	MSKCC	GRCh37	5	112175749	112175753	+	frameshift_variant	Frame_Shift_Del	DEL	TACTT	TACTT	-	novel	NA	P-0020075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	164	420	0	ENST00000257430.4:c.4460_4464del	p.Thr1487IlefsTer25	p.T1487Ifs*25	ENST00000257430	NM_000038.5	1486	gaTACTTta/gata	16/16	0.310729814872111	3	FACETS	1	0.979	1	0.767	0.71	0.825	CLONAL	2	TRUE	0	0.352958803712135	3		420	475	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212450	5212450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196839847	NA	P-0020075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	65	879	0	ENST00000357368.4:c.4667C>T	p.Pro1556Leu	p.P1556L	ENST00000357368	NM_002850.3	1556	cCg/cTg	31/38	1	2	FACETS	0.54	0.468	0.619	0.54	0.468	0.619	SUBCLONAL	1	TRUE	1	0.352958803712135	2		879	682	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720678	89720678	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1564568216	NA	P-0020075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	67	311	0	ENST00000371953.3:c.829A>G	p.Thr277Ala	p.T277A	ENST00000371953	NM_000314.4	277	Aca/Gca	8/9	0.352958803712135	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.352958803712135	1		311	293	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94200987	94200987	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs371077728	NA	P-0020075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	119	546	0	ENST00000323929.3:c.1090C>T	p.Arg364Ter	p.R364*	ENST00000323929	NM_005591.3	364	Cga/Tga	10/20	0.143839249081061	3	FACETS	1	0.984	1	0.717	0.65	0.788	INDETERMINATE	1	TRUE	1	0.352958803712135	3		546	553	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0020076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	63	549	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.219450074558818	3	FACETS	1	0.949	1	0.603	0.521	0.691	CLONAL	1	TRUE	1	0.2	3		549	575	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636057	28636057	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	78	816	0	ENST00000241453.7:c.315G>C	p.Trp105Cys	p.W105C	ENST00000241453	NM_004119.2	105	tgG/tgC	3/24	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.2	2		816	630	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519988	NA	P-0020076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	81	741	1	ENST00000269305.4:c.808T>A	p.Phe270Ile	p.F270I	ENST00000269305	NM_001126112.2	270	Ttt/Att	8/11	1	2	FACETS	0.797	0.704	0.896	1	0.979	1	SUBCLONAL	2	TRUE	1	0.2	2		742	508	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	99	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.313201375537455	2	FACETS	0.862	0.777	0.951	0.862	0.777	0.951	CLONAL	2	TRUE	0	0.318131926270824	2		555	361	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974809	21974809	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	23	118	0	ENST00000304494.5:c.18del	p.Ser7AlafsTer19	p.S7Afs*19	ENST00000304494	NM_000077.4	6	ggG/gg	1/3	0.295264432838148	2	FACETS	0.794	0.634	0.971	0.794	0.634	0.971	CLONAL	2	TRUE	0	0.318131926270824	2		118	91	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578181	7578181	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	178	855	0	ENST00000269305.4:c.668del	p.Pro223LeufsTer24	p.P223Lfs*24	ENST00000269305	NM_001126112.2	223	cCt/ct	6/11	0.313201375537455	2	FACETS	0.966	0.896	1	0.966	0.896	1	CLONAL	2	TRUE	0	0.318131926270824	2		855	579	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430258	181430258	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	52	494	0	ENST00000325404.1:c.110G>A	p.Ser37Asn	p.S37N	ENST00000325404	NM_003106.3	37	aGc/aAc	1/1	0.318131926270824	3	FACETS	0.959	0.819	1	0.48	0.409	0.556	CLONAL	1	TRUE	1	0.318131926270824	3		494	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912656	NA	P-0020078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	249	624	0	ENST00000269305.4:c.734G>C	p.Gly245Ala	p.G245A	ENST00000269305	NM_001126112.2	245	gGc/gCc	7/11	0.320217426047398	0	FACETS	0.689	0.652	0.726			1	SUBCLONAL	3	FALSE	0	0.325525607868584	0		624	499	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589698	69589698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	61	85	1	ENST00000168712.1:c.155C>T	p.Ala52Val	p.A52V	ENST00000168712	NM_002007.2	52	gCg/gTg	1/3	1	2	FACETS	0.899	0.798	1	1	0.985	1	CLONAL	3	FALSE	1	0.325525607868584	2		86	139	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624274	89624274	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs587782187	NA	P-0020078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	221	437	0	ENST00000371953.3:c.48T>G	p.Tyr16Ter	p.Y16*	ENST00000371953	NM_000314.4	16	taT/taG	1/9	0.320217426047398	0	FACETS	0.773	0.732	0.814			1	SUBCLONAL	3	FALSE	0	0.325525607868584	0		437	395	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114131	115114132	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0020078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	199	520	0	ENST00000257566.3:c.1085_1086insCC	p.Ser363HisfsTer270	p.S363Hfs*270	ENST00000257566	NM_016569.3	362	aca/acCCa	6/8	0.274121939501251	3	FACETS	0.883	0.82	0.948	0.883	0.82	0.948	CLONAL	2	FALSE	1	0.325525607868584	3		520	805	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872018	35872018	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs779399614	NA	P-0020078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	93	535	0	ENST00000216797.5:c.595G>C	p.Val199Leu	p.V199L	ENST00000216797	NM_020529.2	199	Gtg/Ctg	4/6	0.275291554255562	1	FACETS	0.706	0.628	0.789	0.706	0.628	0.789	SUBCLONAL	1	FALSE	0	0.325525607868584	1		535	678	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	212	122	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.92	2		122	460	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0020079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	457	733	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	1	2	FACETS	0.993	0.953	1	0.993	0.953	1	CLONAL	1	TRUE	1	0.92	2		733	1000	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176715853	176715853	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	390	672	0	ENST00000439151.2:c.6185G>A	p.Cys2062Tyr	p.C2062Y	ENST00000439151	NM_022455.4	2062	tGt/tAt	21/23	1	2	FACETS	0.981	0.938	1	0.981	0.938	1	CLONAL	1	TRUE	1	0.92	2		672	864	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169912	32169912	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	515	802	0	ENST00000375023.3:c.3696G>C	p.Gln1232His	p.Q1232H	ENST00000375023	NM_004557.3	1232	caG/caC	21/30	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.92	2		802	1044	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209457	98209457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753535745	NA	P-0020080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	231	554	0	ENST00000331920.6:c.4081G>A	p.Val1361Met	p.V1361M	ENST00000331920	NM_000264.3	1361	Gtg/Atg	23/24	0.362464570136082	3	FACETS	0.943	0.89	0.997	0.943	0.89	0.997	INDETERMINATE	2	TRUE	1	0.666260220099864	3		554	490	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	152	424	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.814	0.747	0.885	0.814	0.747	0.885	CLONAL	1	TRUE	1	0.561309705143032	2		424	665	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390873	139390873	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	244	884	2	ENST00000277541.6:c.7318C>T	p.Gln2440Ter	p.Q2440*	ENST00000277541	NM_017617.3	2440	Cag/Tag	34/34	NA	2	FACETS	1	0.967	1			1	INDETERMINATE	1	TRUE	NA	0.561309705143032	2		886	828	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243708856	243708856	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	214	742	0	ENST00000263826.5:c.1207A>G	p.Ser403Gly	p.S403G	ENST00000263826	NM_005465.4	403	Agt/Ggt	11/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.561309705143032	2		742	699	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733227	40733227	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	64	720	0	ENST00000373198.4:c.3579A>T	p.Gln1193His	p.Q1193H	ENST00000373198	NM_133170.3	1193	caA/caT	26/32	1	2	FACETS	0.34	0.294	0.39	0.34	0.294	0.39	SUBCLONAL	1	TRUE	1	0.561309705143032	2		720	670	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265861	41266231	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAA	GAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAA	-	novel	NA	P-0020081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	27	13	0	ENST00000349496.5:c.14-154_230del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.559795109481886	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.561309705143032	2		13	39	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904892	101904893	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0020081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	105	497	0	ENST00000374994.4:c.881_882del	p.Arg294IlefsTer38	p.R294Ifs*38	ENST00000374994	NM_004612.2	294	AGa/a	5/9	0.561309705143032	1	FACETS	0.773	0.7	0.849	0.773	0.7	0.849	SUBCLONAL	1	TRUE	0	0.561309705143032	1		497	348	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857127	9857127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs976259560	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	60	416	0	ENST00000330684.3:c.4274C>T	p.Ser1425Leu	p.S1425L	ENST00000330684	NM_001134407.1	1425	tCg/tTg	13/13	0.621107567665349	3	FACETS	0.698	0.604	0.798	0.349	0.302	0.399	SUBCLONAL	1	TRUE	1	0.621107567665349	3		416	363	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873660	35873660	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs201559094	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	196	530	1	ENST00000303115.3:c.616C>T	p.Arg206Ter	p.R206*	ENST00000303115	NM_002185.3	206	Cga/Tga	5/8	0.524194679264954	4	FACETS	0.855	0.797	0.916	0.855	0.797	0.916	CLONAL	2	TRUE	2	0.621107567665349	4		531	598	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264489	16264490	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	154	779	0	ENST00000375759.3:c.10692_10693delinsTT	p.Arg3565Ter	p.R3565*	ENST00000375759	NM_015001.2	3564	gcCCga/gcTTga	13/15	0.552259175816525	3	FACETS	0.785	0.719	0.854	0.392	0.359	0.427	SUBCLONAL	1	TRUE	1	0.621107567665349	3		779	828	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805194	43805194	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	225	864	0	ENST00000372470.3:c.644C>A	p.Thr215Lys	p.T215K	ENST00000372470	NM_005373.2	215	aCa/aAa	4/12	0.552259175816525	3	FACETS	1	0.957	1	0.518	0.482	0.554	CLONAL	1	TRUE	1	0.621107567665349	3		864	917	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458221	120458221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	334	781	0	ENST00000256646.2:c.7124C>T	p.Pro2375Leu	p.P2375L	ENST00000256646	NM_024408.3	2375	cCt/cTt	34/34	0.524194679264954	4	FACETS	0.938	0.89	0.988	0.938	0.89	0.988	CLONAL	2	TRUE	2	0.621107567665349	4		781	929	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717705	89717705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064794675	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	171	601	0	ENST00000371953.3:c.730C>T	p.Pro244Ser	p.P244S	ENST00000371953	NM_000314.4	244	Cct/Tct	7/9	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.621107567665349	2		601	519	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123245041	123245041	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	140	620	1	ENST00000358487.5:c.2063C>T	p.Ser688Phe	p.S688F	ENST00000358487	NM_000141.4	688	tCc/tTc	16/18	1	2	FACETS	0.905	0.83	0.983	0.905	0.83	0.983	CLONAL	1	TRUE	1	0.621107567665349	2		621	498	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247618	123247618	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1466101220	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	137	580	1	ENST00000358487.5:c.1873C>T	p.Arg625Ter	p.R625*	ENST00000358487	NM_000141.4	625	Cga/Tga	14/18	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.621107567665349	2		581	425	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	111	467	0	ENST00000256196.4:c.68del	p.Gly23AlafsTer18	p.G23Afs*18	ENST00000256196		23	gGc/gc	1/6	1	2	FACETS	0.789	0.714	0.868	0.789	0.714	0.868	SUBCLONAL	1	TRUE	1	0.621107567665349	2		467	453	SUCCESS
EED	8726	MSKCC	GRCh37	11	85977242	85977242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	33	480	0	ENST00000263360.6:c.844C>T	p.Pro282Ser	p.P282S	ENST00000263360	NM_003797.3	282	Cca/Tca	8/12	0.577950578093238	1	FACETS	0.314	0.257	0.378	0.314	0.257	0.378	SUBCLONAL	1	TRUE	0	0.621107567665349	1		480	233	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143500	108143500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751714261	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	40	651	0	ENST00000278616.4:c.3205C>T	p.Pro1069Ser	p.P1069S	ENST00000278616	NM_000051.3	1069	Cct/Tct	22/63	0.577950578093238	1	FACETS	0.248	0.206	0.294	0.248	0.206	0.294	SUBCLONAL	1	TRUE	0	0.621107567665349	1		651	358	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125525198	125525198	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	126	554	0	ENST00000428830.2:c.1414T>G	p.Trp472Gly	p.W472G	ENST00000428830	NM_001114121.2	472	Tgg/Ggg	13/14	0.577950578093238	1	FACETS	0.758	0.694	0.824	0.758	0.694	0.824	SUBCLONAL	1	TRUE	0	0.621107567665349	1		554	369	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380309	25380309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1407509439	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	261	640	0	ENST00000311936.3:c.149C>T	p.Thr50Ile	p.T50I	ENST00000311936	NM_004985.3	50	aCc/aTc	3/5	0.196482240733674	6	FACETS	0.931	0.877	0.985			1	INDETERMINATE	3	TRUE	NA	0.621107567665349	6		640	675	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428010	49428010	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	548	753	0	ENST00000301067.7:c.10580T>G	p.Val3527Gly	p.V3527G	ENST00000301067	NM_003482.3	3527	gTg/gGg	38/54	0.621107567665349	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	0	0.621107567665349	3		753	770	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112244	115112244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	258	270	2	ENST00000257566.3:c.1496C>T	p.Pro499Leu	p.P499L	ENST00000257566	NM_016569.3	499	cCt/cTt	7/8	0.621107567665349	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.621107567665349	3		272	336	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28599037	28599037	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	129	705	0	ENST00000241453.7:c.2251C>T	p.Gln751Ter	p.Q751*	ENST00000241453	NM_004119.2	751	Caa/Taa	18/24	1	2	FACETS	0.853	0.778	0.931	0.853	0.778	0.931	CLONAL	1	TRUE	1	0.621107567665349	2		705	487	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28883029	28883029	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	141	666	0	ENST00000282397.4:c.3671G>A	p.Arg1224Lys	p.R1224K	ENST00000282397	NM_002019.4	1224	aGa/aAa	28/30	1	2	FACETS	0.889	0.814	0.965	0.889	0.814	0.965	CLONAL	1	TRUE	1	0.621107567665349	2		666	511	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001354	29001354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	110	506	0	ENST00000282397.4:c.1378C>T	p.Pro460Ser	p.P460S	ENST00000282397	NM_002019.4	460	Cct/Tct	10/30	1	2	FACETS	0.935	0.847	1	0.935	0.847	1	CLONAL	1	TRUE	1	0.621107567665349	2		506	379	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004206	29004206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	103	520	0	ENST00000282397.4:c.1087C>T	p.Pro363Ser	p.P363S	ENST00000282397	NM_002019.4	363	Ccc/Tcc	8/30	1	2	FACETS	0.88	0.794	0.969	0.88	0.794	0.969	CLONAL	1	TRUE	1	0.621107567665349	2		520	377	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606081	81606081	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746685925	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	160	783	0	ENST00000298171.2:c.751G>A	p.Glu251Lys	p.E251K	ENST00000298171	NM_000369.2	251	Gaa/Aaa	9/10	0.600099901897824	3	FACETS	0.82	0.753	0.891	0.41	0.376	0.446	CLONAL	1	TRUE	1	0.621107567665349	3		783	823	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727471	66727471	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	180	620	0	ENST00000307102.5:c.187C>A	p.Leu63Met	p.L63M	ENST00000307102	NM_002755.3	63	Ctg/Atg	2/11	0.600099901897824	3	FACETS	0.973	0.899	1	0.486	0.449	0.525	CLONAL	1	TRUE	1	0.621107567665349	3		620	781	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630480	90630481	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	318	729	0	ENST00000330062.3:c.830_831del	p.Asp277ValfsTer5	p.D277Vfs*5	ENST00000330062	NM_002168.2	277	gAC/g	7/11	0.600099901897824	3	FACETS	0.875	0.83	0.92	0.875	0.83	0.92	CLONAL	2	TRUE	1	0.621107567665349	3		729	767	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304363	91304363	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	175	684	0	ENST00000355112.3:c.1760T>C	p.Ile587Thr	p.I587T	ENST00000355112	NM_000057.2	587	aTc/aCc	7/22	0.600099901897824	3	FACETS	0.92	0.848	0.994	0.46	0.424	0.497	CLONAL	1	TRUE	1	0.621107567665349	3		684	803	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923318	9923318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867335598	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	261	650	0	ENST00000330684.3:c.1969G>A	p.Glu657Lys	p.E657K	ENST00000330684	NM_001134407.1	657	Gaa/Aaa	9/13	0.621107567665349	3	FACETS	0.874	0.825	0.924	0.874	0.825	0.924	CLONAL	2	TRUE	1	0.621107567665349	3		650	630	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578540	7578563	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGGGCAGGGGAGTACTGTAGGAA	GAGGGCAGGGGAGTACTGTAGGAA	-	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	755	1095	1	ENST00000269305.4:c.376-9_390del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	0.607394581780466	4	FACETS	1	0.995	1	0.825	0.803	0.847	CLONAL	3	TRUE	0	0.621107567665349	4		1096	1194	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971403	15971403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1364517763	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	710	743	0	ENST00000268712.3:c.4546G>A	p.Glu1516Lys	p.E1516K	ENST00000268712	NM_006311.3	1516	Gaa/Aaa	32/46	0.607394581780466	4	FACETS	0.953	0.931	0.975	0.953	0.931	0.975	CLONAL	4	TRUE	0	0.621107567665349	4		743	972	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557909	29557909	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs866069972	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	42	121	1	ENST00000356175.3:c.3163C>T	p.Gln1055Ter	p.Q1055*	ENST00000356175	NM_000267.3	1055	Caa/Taa	24/57	0.605253359937778	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	0	0.621107567665349	2		122	63	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244375	5244376	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	426	878	1	ENST00000357368.4:c.1106_1107delinsTT	p.Ser369Phe	p.S369F	ENST00000357368	NM_002850.3	369	tCC/tTT	11/38	0.524194679264954	4	FACETS	0.929	0.886	0.972	0.929	0.886	0.972	CLONAL	2	TRUE	2	0.621107567665349	4		879	1197	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166335	7166335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	362	894	0	ENST00000302850.5:c.1691C>T	p.Pro564Leu	p.P564L	ENST00000302850	NM_000208.2	564	cCc/cTc	8/22	0.524194679264954	4	FACETS	0.89	0.845	0.935	0.89	0.845	0.935	CLONAL	2	TRUE	2	0.621107567665349	4		894	1062	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10273392	10273392	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	428	702	2	ENST00000340748.4:c.911C>T	p.Pro304Leu	p.P304L	ENST00000340748		304	cCt/cTt	12/40	0.524194679264954	4	FACETS	0.956	0.913	1	0.956	0.913	1	CLONAL	2	TRUE	2	0.621107567665349	4		704	1168	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276815	15276815	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161550693	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	378	890	0	ENST00000263388.2:c.5450C>T	p.Ser1817Leu	p.S1817L	ENST00000263388	NM_000435.2	1817	tCa/tTa	30/33	0.524194679264954	4	FACETS	0.977	0.93	1	0.977	0.93	1	CLONAL	2	TRUE	2	0.621107567665349	4		890	1010	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292436	15292436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	469	842	3	ENST00000263388.2:c.2743G>A	p.Gly915Ser	p.G915S	ENST00000263388	NM_000435.2	915	Ggc/Agc	17/33	0.524194679264954	4	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	2	0.621107567665349	4		845	1223	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30311630	30311630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	173	501	0	ENST00000262643.3:c.484C>T	p.His162Tyr	p.H162Y	ENST00000262643	NM_001238.2	162	Cac/Tac	7/12	0.600099901897824	3	FACETS	1	0.974	1	0.561	0.518	0.605	CLONAL	1	TRUE	1	0.621107567665349	3		501	651	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606962	47606962	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	132	650	0	ENST00000263735.4:c.712G>A	p.Glu238Lys	p.E238K	ENST00000263735	NM_002354.2	238	Gaa/Aaa	7/9	0.597908632008883	4	FACETS	0.893	0.811	0.978	0.298	0.27	0.326	CLONAL	1	TRUE	1	0.621107567665349	4		650	772	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370816	225370816	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	276	633	0	ENST00000264414.4:c.1063T>C	p.Phe355Leu	p.F355L	ENST00000264414	NM_003590.4	355	Ttc/Ctc	8/16	0.600099901897824	3	FACETS	0.947	0.897	0.997	0.947	0.897	0.997	CLONAL	2	TRUE	1	0.621107567665349	3		633	615	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40709539	40709539	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159851	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	312	804	0	ENST00000373198.4:c.4363G>A	p.Glu1455Lys	p.E1455K	ENST00000373198	NM_133170.3	1455	Gaa/Aaa	32/32	0.524194679264954	4	FACETS	0.92	0.871	0.97	0.92	0.871	0.97	CLONAL	2	TRUE	2	0.621107567665349	4		804	885	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710534	40710534	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	281	726	0	ENST00000373198.4:c.4317G>A	p.Met1439Ile	p.M1439I	ENST00000373198	NM_133170.3	1439	atG/atA	31/32	0.524194679264954	4	FACETS	0.846	0.797	0.896	0.846	0.797	0.896	CLONAL	2	TRUE	2	0.621107567665349	4		726	867	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713349	40713349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758242008	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	350	849	0	ENST00000373198.4:c.4166G>A	p.Arg1389Lys	p.R1389K	ENST00000373198	NM_133170.3	1389	aGg/aAg	30/32	0.524194679264954	4	FACETS	0.954	0.906	1	0.954	0.906	1	CLONAL	2	TRUE	2	0.621107567665349	4		849	958	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076955	41076955	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs724159838	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	236	645	1	ENST00000373198.4:c.1465C>T	p.Pro489Ser	p.P489S	ENST00000373198	NM_133170.3	489	Cct/Tct	9/32	0.524194679264954	4	FACETS	0.837	0.784	0.891	0.837	0.784	0.891	CLONAL	2	TRUE	2	0.621107567665349	4		646	736	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420093	41420093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	164	341	0	ENST00000373198.4:c.228G>A	p.Met76Ile	p.M76I	ENST00000373198	NM_133170.3	76	atG/atA	3/32	0.524194679264954	4	FACETS	0.923	0.855	0.992	0.923	0.855	0.992	CLONAL	2	TRUE	2	0.621107567665349	4		341	464	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264449	46264449	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	217	441	0	ENST00000371998.3:c.1496C>T	p.Pro499Leu	p.P499L	ENST00000371998		499	cCt/cTt	11/23	0.524194679264954	4	FACETS	0.878	0.821	0.936	0.878	0.821	0.936	CLONAL	2	TRUE	2	0.621107567665349	4		441	645	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39762919	39762919	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	149	684	0	ENST00000288319.7:c.917C>T	p.Pro306Leu	p.P306L	ENST00000288319	NM_182918.3	306	cCa/cTa	9/10	1	2	FACETS	0.943	0.867	1	0.943	0.867	1	CLONAL	1	TRUE	1	0.621107567665349	2		684	509	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536181	41536181	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	676	762	0	ENST00000263253.7:c.1798T>A	p.Leu600Ile	p.L600I	ENST00000263253	NM_001429.3	600	Tta/Ata	9/31	0.621107567665349	5	FACETS	0.917	0.89	0.944	0.917	0.89	0.944	CLONAL	4	TRUE	1	0.621107567665349	5		762	1146	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259301	89259301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	337	495	2	ENST00000336596.2:c.445G>A	p.Asp149Asn	p.D149N	ENST00000336596	NM_005233.5	149	Gat/Aat	3/17	0.621107567665349	5	FACETS	1	0.961	1			1	CLONAL	3	TRUE	NA	0.621107567665349	5		497	693	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119595289	119595289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	145	469	0	ENST00000316626.5:c.880C>T	p.Pro294Ser	p.P294S	ENST00000316626		294	Cct/Tct	8/12	0.524194679264954	4	FACETS	0.85	0.783	0.92	0.85	0.783	0.92	CLONAL	2	TRUE	2	0.621107567665349	4		469	445	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526145	189526145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	347	833	2	ENST00000264731.3:c.409G>A	p.Asp137Asn	p.D137N	ENST00000264731	NM_003722.4	137	Gac/Aac	4/14	0.555599859089742	5	FACETS	0.889	0.841	0.937	0.593	0.561	0.625	CLONAL	2	TRUE	2	0.621107567665349	5		835	1214	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189585621	189585621	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	247	543	0	ENST00000264731.3:c.883-1G>A		p.X295_splice	ENST00000264731	NM_003722.4	295			0.555599859089742	5	FACETS	1	0.961	1	0.687	0.645	0.73	CLONAL	2	TRUE	2	0.621107567665349	5		543	745	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510187	187510187	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	122	650	1	ENST00000441802.2:c.13326C>A	p.Phe4442Leu	p.F4442L	ENST00000441802	NM_005245.3	4442	ttC/ttA	27/27	0.59200724526473	2	FACETS	0.852	0.775	0.932	0.426	0.387	0.466	CLONAL	1	TRUE	0	0.621107567665349	2		651	461	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	189	488	3				ENST00000310581	NM_198253.2	-/1132			0.524194679264954	4	FACETS	0.94	0.875	1	0.94	0.875	1	CLONAL	2	TRUE	2	0.621107567665349	4		491	525	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874636	35874636	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	224	459	0	ENST00000303115.3:c.792G>A	p.Trp264Ter	p.W264*	ENST00000303115	NM_002185.3	264	tgG/tgA	6/8	0.524194679264954	4	FACETS	0.986	0.925	1	0.986	0.925	1	CLONAL	2	TRUE	2	0.621107567665349	4		459	593	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459714	149459714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	357	870	1	ENST00000286301.3:c.493C>T	p.His165Tyr	p.H165Y	ENST00000286301	NM_005211.3	165	Cac/Tac	4/22	NA	2	FACETS	0.961	0.922	0.999			1	INDETERMINATE	2	TRUE	NA	0.621107567665349	2		871	598	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515237	149515237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	394	815	1	ENST00000261799.4:c.245C>T	p.Ser82Phe	p.S82F	ENST00000261799	NM_002609.3	82	tCc/tTc	3/23	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	2	TRUE	NA	0.621107567665349	2		816	628	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858353	27858353	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138060838	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	159	643	0	ENST00000359303.2:c.218G>A	p.Arg73Gln	p.R73Q	ENST00000359303	NM_003535.2	73	cGa/cAa	1/1	0.524194679264954	4	FACETS	0.988	0.906	1	0.494	0.453	0.537	CLONAL	1	TRUE	2	0.621107567665349	4		643	840	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287475	33287475	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	323	651	1	ENST00000374542.5:c.1622C>T	p.Ser541Phe	p.S541F	ENST00000374542	NM_001141970.1	541	tCc/tTc	6/8	0.524194679264954	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.621107567665349	4		652	773	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709028	117709028	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	331	736	0	ENST00000368508.3:c.1929G>A	p.Met643Ile	p.M643I	ENST00000368508	NM_002944.2	643	atG/atA	13/43	0.605253359937778	2	FACETS	0.948	0.908	0.988	0.948	0.908	0.988	CLONAL	2	TRUE	0	0.621107567665349	2		736	562	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718190	117718190	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	286	693	0	ENST00000368508.3:c.667G>A	p.Gly223Arg	p.G223R	ENST00000368508	NM_002944.2	223	Gga/Aga	7/43	0.605253359937778	2	FACETS	0.944	0.901	0.986	0.944	0.901	0.986	CLONAL	2	TRUE	0	0.621107567665349	2		693	488	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481408	140481408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867748453	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	236	552	0	ENST00000288602.6:c.1400C>T	p.Ser467Leu	p.S467L	ENST00000288602	NM_004333.4	467	tCa/tTa	11/18	0.621107567665349	7	FACETS	1	0.958	1	0.414	0.386	0.442	CLONAL	2	TRUE	2	0.621107567665349	7		552	938	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878458	151878458	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	350	786	0	ENST00000262189.6:c.6487C>T	p.Pro2163Ser	p.P2163S	ENST00000262189	NM_170606.2	2163	Cct/Tct	36/59	0.621107567665349	7	FACETS	1	0.975	1	0.42	0.397	0.444	CLONAL	2	TRUE	2	0.621107567665349	7		786	1370	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028124	69028124	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	543	990	0	ENST00000288368.4:c.3283G>A	p.Glu1095Lys	p.E1095K	ENST00000288368	NM_024870.2	1095	Gaa/Aaa	26/40	0.59777201493797	3	FACETS	0.947	0.918	0.974	0.947	0.918	0.974	CLONAL	3	TRUE	0	0.621107567665349	3		990	807	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436635	8436635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	125	815	2	ENST00000356435.5:c.4043G>A	p.Arg1348Lys	p.R1348K	ENST00000356435		1348	aGa/aAa	24/35	0.59777201493797	3	FACETS	0.957	0.87	1	0.319	0.29	0.35	CLONAL	1	TRUE	0	0.621107567665349	3		817	551	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499707	8499707	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	117	711	0	ENST00000356435.5:c.2262G>A	p.Met754Ile	p.M754I	ENST00000356435		754	atG/atA	14/35	0.59777201493797	3	FACETS	0.84	0.759	0.924	0.28	0.253	0.308	CLONAL	1	TRUE	0	0.621107567665349	3		711	588	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185596	27185596	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	372	818	1	ENST00000380036.4:c.1296G>A	p.Met432Ile	p.M432I	ENST00000380036	NM_000459.3	432	atG/atA	9/23	0.59777201493797	3	FACETS	0.899	0.857	0.941	0.599	0.571	0.628	CLONAL	2	TRUE	0	0.621107567665349	3		819	873	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801081	135801081	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1463772907	NA	P-0020082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	236	611	2	ENST00000298552.3:c.256C>T	p.Arg86Cys	p.R86C	ENST00000298552	NM_001162426.1	86	Cgt/Tgt	5/23	0.524194679264954	4	FACETS	0.799	0.748	0.851	0.799	0.748	0.851	SUBCLONAL	2	TRUE	2	0.621107567665349	4		613	771	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7978975	7978975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769562383	NA	P-0020083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	178	606	0	ENST00000319144.4:c.1592C>T	p.Pro531Leu	p.P531L	ENST00000319144	NM_001139.2	531	cCg/cTg	12/15	0.445886445027438	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.445886445027438	1		606	573	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248579	8248579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253559924	NA	P-0020083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	177	763	1	ENST00000335790.3:c.308G>A	p.Arg103Gln	p.R103Q	ENST00000335790	NM_002315.2	103	cGg/cAg	3/4	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.445886445027438	2		764	785	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs28934577	NA	P-0020084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	868	666	0	ENST00000269305.4:c.770T>G	p.Leu257Arg	p.L257R	ENST00000269305	NM_001126112.2	257	cTg/cGg	7/11	0.939592905076897	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.939592905076897	2		666	909	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560231	29560231	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	164	224	0	ENST00000356175.3:c.3708G>A	p.Trp1236Ter	p.W1236*	ENST00000356175	NM_000267.3	1236	tgG/tgA	27/57	0.939592905076897	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.939592905076897	1		224	182	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223350	2223350	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	572	818	0	ENST00000398665.3:c.3461C>G	p.Pro1154Arg	p.P1154R	ENST00000398665	NM_032482.2	1154	cCt/cGt	25/28	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.939592905076897	2		818	1149	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291527	10291528	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0020084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	343	620	3	ENST00000340748.4:c.151_152delinsAT	p.Glu51Ile	p.E51I	ENST00000340748		51	GAa/ATa	3/40	1	2	FACETS	0.906	0.862	0.95	0.906	0.862	0.95	CLONAL	1	TRUE	1	0.939592905076897	2		623	806	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517503	176517503	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	524	795	1	ENST00000292408.4:c.204G>T	p.Lys68Asn	p.K68N	ENST00000292408	NM_213647.1	68	aaG/aaT	3/18	0.939592905076897	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.939592905076897	1		796	571	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	64	424	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.715	0.619	0.821	0.715	0.619	0.821	SUBCLONAL	1	TRUE	1	0.251644095127876	2		424	711	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575199	48575199	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0020085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	48	299	0	ENST00000342988.3:c.393T>G	p.Tyr131Ter	p.Y131*	ENST00000342988	NM_005359.5	131	taT/taG	3/12	0.220300031330275	1	FACETS	0.828	0.701	0.966	0.828	0.701	0.966	CLONAL	1	TRUE	0	0.251644095127876	1		299	403	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21968236	21968239	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GGAT	GGAT	-	novel	NA	P-0020085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	55	482	0	ENST00000304494.5:c.460_463del	p.Ile154ProfsTer38	p.I154Pfs*38	ENST00000304494	NM_000077.4	154	ATCCcc/cc	3/3	0.251644095127876	1	FACETS	0.64	0.547	0.742	0.64	0.547	0.742	SUBCLONAL	1	TRUE	0	0.251644095127876	1		482	597	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	114	122	0				ENST00000310581	NM_198253.2	-/1132			0.460548225105099	4	FACETS	0.763	0.691	0.838	0.763	0.691	0.838	SUBCLONAL	2	TRUE	2	0.460548225105099	4		122	474	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088787	27088788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	253	508	0	ENST00000324856.7:c.2402dup	p.Gln802SerfsTer15	p.Q802Sfs*15	ENST00000324856	NM_006015.4	799	cag/caGg	7/20	0.460548225105099	3	FACETS	0.839	0.793	0.885	1	0.991	1	CLONAL	3	TRUE	1	0.460548225105099	3		508	537	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652198	36652199	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	220	537	0	ENST00000244741.5:c.322dup	p.Glu108GlyfsTer21	p.E108Gfs*21	ENST00000244741	NM_000389.4	107	gag/gaGg	2/3	0.428771331378321	3	FACETS	0.948	0.888	1	0.948	0.888	1	CLONAL	2	TRUE	1	0.460548225105099	3		537	620	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481620	56481620	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	112	519	0	ENST00000267101.3:c.655T>C	p.Phe219Leu	p.F219L	ENST00000267101	NM_001982.3	219	Ttt/Ctt	6/28	0.428771331378321	3	FACETS	0.862	0.776	0.953	0.431	0.388	0.477	CLONAL	1	TRUE	1	0.460548225105099	3		519	694	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106882	27106882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	93	439	0	ENST00000324856.7:c.6493G>A	p.Glu2165Lys	p.E2165K	ENST00000324856	NM_006015.4	2165	Gag/Aag	20/20	0.460548225105099	3	FACETS	1	0.963	1	0.587	0.525	0.653	CLONAL	1	TRUE	1	0.460548225105099	3		439	423	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938228	36938228	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	130	639	0	ENST00000361632.4:c.733C>G	p.Gln245Glu	p.Q245E	ENST00000361632		245	Cag/Gag	6/16	0.460548225105099	3	FACETS	0.966	0.877	1	0.483	0.438	0.53	CLONAL	1	TRUE	1	0.460548225105099	3		639	719	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165510	118165510	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	41	204	0	ENST00000369448.3:c.20G>C	p.Cys7Ser	p.C7S	ENST00000369448	NM_017709.3	7	tGt/tCt	2/2	NA	2	FACETS	0.927	0.782	1			1	INDETERMINATE	1	TRUE	NA	0.460548225105099	2		204	192	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205208	46205208	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	71	332	0	ENST00000334344.6:c.292G>C	p.Glu98Gln	p.E98Q	ENST00000334344	NM_152641.2	98	Gaa/Caa	4/21	0.428771331378321	3	FACETS	0.925	0.811	1	0.463	0.405	0.524	CLONAL	1	TRUE	1	0.460548225105099	3		332	410	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906448	32906475	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGCAAAGACCACATTGGAAAGTCAAT	GCTGCAAAGACCACATTGGAAAGTCAAT	-	novel	NA	P-0020086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	79	494	0	ENST00000380152.3:c.835_862del	p.Cys279GlnfsTer4	p.C279Qfs*4	ENST00000380152		278	aGCTGCAAAGACCACATTGGAAAGTCAATg/ag	10/27	0.460548225105099	1	FACETS	0.92	0.818	1	0.92	0.818	1	CLONAL	1	TRUE	0	0.460548225105099	1		494	287	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988523	41988523	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	169	668	2	ENST00000219905.7:c.1315G>C	p.Asp439His	p.D439H	ENST00000219905	NM_001164273.1	439	Gac/Cac	3/24	0.460548225105099	2	FACETS	1	0.972	1	0.556	0.513	0.601	CLONAL	1	TRUE	0	0.460548225105099	2		670	660	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225341	2225341	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753585181	NA	P-0020086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	127	602	0	ENST00000326181.6:c.1426C>T	p.Arg476Trp	p.R476W	ENST00000326181	NM_032271.2	476	Cgg/Tgg	16/21	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.460548225105099	2		602	548	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650883	37650885	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0020086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	303	681	0	ENST00000447079.4:c.2359_2361del	p.Val787del	p.V787del	ENST00000447079	NM_015083.1	785	agTGTt/agt	5/14	0.428771331378321	3	FACETS	0.946	0.894	0.998	0.946	0.894	0.998	CLONAL	2	TRUE	1	0.460548225105099	3		681	856	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533854	63533854	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	109	398	0	ENST00000307078.5:c.1300G>A	p.Asp434Asn	p.D434N	ENST00000307078	NM_004655.3	434	Gac/Aac	6/11	0.371149779326123	4	FACETS	1	0.958	1	0.56	0.504	0.62	CLONAL	1	TRUE	2	0.460548225105099	4		398	617	SUCCESS
CALR	811	MSKCC	GRCh37	19	13049555	13049577	+	protein_altering_variant	In_Frame_Del	DEL	TCTACTTCAAGGAGCAGTTTCTG	TCTACTTCAAGGAGCAGTTTCTG	GC	novel	NA	P-0020086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	34	569	2	ENST00000316448.5:c.62_84delinsGC	p.Val21_Leu28delinsGly	p.V21_L28delinsG	ENST00000316448	NM_004343.3	21	gTCTACTTCAAGGAGCAGTTTCTG/gGC	1/9	0.460548225105099	3	FACETS	0.287	0.233	0.347	0.143	0.116	0.174	SUBCLONAL	1	TRUE	1	0.460548225105099	3		571	634	SUCCESS
APC	324	MSKCC	GRCh37	5	112173221	112173268	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AATTTTGTGATCTCTTGATTTTATTTCAGGCAAATCCTAAGAGAGAAC	AATTTTGTGATCTCTTGATTTTATTTCAGGCAAATCCTAAGAGAGAAC	-	novel	NA	P-0020086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	23	121	0	ENST00000257430.4:c.1959-27_1979del		p.X653_splice	ENST00000257430	NM_000038.5	653		16/16	0.460548225105099	2	FACETS	0.793	0.627	0.979	0.396	0.313	0.49	CLONAL	1	TRUE	0	0.460548225105099	2		121	126	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631232	176631232	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	114	472	0	ENST00000439151.2:c.1175T>A	p.Phe392Tyr	p.F392Y	ENST00000439151	NM_022455.4	392	tTc/tAc	4/23	NA	2	FACETS	1	0.925	1			1	INDETERMINATE	1	TRUE	NA	0.460548225105099	2		472	483	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652031	36652031	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	154	699	0	ENST00000244741.5:c.153C>G	p.Phe51Leu	p.F51L	ENST00000244741	NM_000389.4	51	ttC/ttG	2/3	0.428771331378321	3	FACETS	1	0.929	1	0.508	0.465	0.553	CLONAL	1	TRUE	1	0.460548225105099	3		699	810	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120217	94120217	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0020086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	55	201	0	ENST00000369303.4:c.832+2T>G		p.X278_splice	ENST00000369303	NM_004440.3	278			0.271871374092259	5	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.460548225105099	5		201	302	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336385	80336385	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs372746608	NA	P-0020086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	67	432	0	ENST00000286548.4:c.934A>G	p.Met312Val	p.M312V	ENST00000286548	NM_002072.3	312	Atg/Gtg	7/7	0.390706473315654	3	FACETS	0.651	0.566	0.742			1	SUBCLONAL	1	TRUE	NA	0.460548225105099	3		432	550	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336417	80336417	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	51	333	0	ENST00000286548.4:c.902A>C	p.Asp301Ala	p.D301A	ENST00000286548	NM_002072.3	301	gAt/gCt	7/7	0.390706473315654	3	FACETS	0.634	0.539	0.737			1	SUBCLONAL	1	TRUE	NA	0.460548225105099	3		333	430	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0020087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	195	554	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	TRUE	1	0.349520409059711	2		554	967	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	97	122	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.349520409059711	2		122	452	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665042	29665042	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0020087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	120	428	0	ENST00000356175.3:c.6642-1G>T		p.X2214_splice	ENST00000356175	NM_000267.3	2214			1	2	FACETS	0.918	0.83	1	0.918	0.83	1	CLONAL	1	TRUE	1	0.349520409059711	2		428	748	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470018	25470018	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	91	435	0	ENST00000264709.3:c.1024G>T	p.Glu342Ter	p.E342*	ENST00000264709	NM_175629.2	342	Gag/Tag	9/23	1	2	FACETS	0.769	0.683	0.861	0.769	0.683	0.861	SUBCLONAL	1	TRUE	1	0.349520409059711	2		435	677	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399545	139399545	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	154	551	0	ENST00000277541.6:c.4598A>T	p.Asp1533Val	p.D1533V	ENST00000277541	NM_017617.3	1533	gAc/gTc	26/34	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.349520409059711	2		551	836	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857322	68857322	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0020090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	66	488	0	ENST00000261769.5:c.1957A>T	p.Lys653Ter	p.K653*	ENST00000261769	NM_004360.3	653	Aag/Tag	13/16	0.246667882096845	1	FACETS	0.761	0.662	0.869	0.761	0.662	0.869	SUBCLONAL	1	TRUE	0	0.285346895711184	1		488	521	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971420	15971420	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	86	598	0	ENST00000268712.3:c.4529del	p.Asn1510ThrfsTer12	p.N1510Tfs*12	ENST00000268712	NM_006311.3	1510	aAc/ac	32/46	0.217975714213295	1	FACETS	0.73	0.646	0.82	0.73	0.646	0.82	SUBCLONAL	1	TRUE	0	0.285346895711184	1		598	708	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115701	8115704	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GATT	GATT	-	novel	NA	P-0020091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	94	337	0	ENST00000346208.3:c.1048-1_1050del		p.X350_splice	ENST00000346208		350		6/6	1	2	FACETS	0.998	0.892	1	0.998	0.892	1	CLONAL	1	TRUE	1	0.395833177759135	2		337	476	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171657	36171657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	90	364	0	ENST00000300305.3:c.908C>A	p.Ser303Ter	p.S303*	ENST00000300305		303	tCa/tAa	7/8	1	2	FACETS	0.776	0.69	0.868	0.776	0.69	0.868	SUBCLONAL	1	TRUE	1	0.395833177759135	2		364	586	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	157	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.425055817802607	3	FACETS	1	0.985	1	0.655	0.602	0.71	CLONAL	1	FALSE	1	0.47366947784584	3		555	626	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555526097	NA	P-0020103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	108	992	0	ENST00000269305.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000269305	NM_001126112.2	167	Cag/Tag	5/11	0.47366947784584	1	FACETS	0.941	0.852	1	0.941	0.852	1	CLONAL	1	FALSE	0	0.47366947784584	1		992	370	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1268645	1268645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1322978833	NA	P-0020103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	115	1049	1	ENST00000310581.5:c.2572C>T	p.Arg858Trp	p.R858W	ENST00000310581	NM_198253.2	858	Cgg/Tgg	9/16	0.395568790096475	1	FACETS	0.717	0.649	0.788	0.717	0.649	0.788	SUBCLONAL	1	FALSE	0	0.47366947784584	1		1050	517	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211656	46211656	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	101	471	0	ENST00000334344.6:c.625del	p.Val209CysfsTer6	p.V209Cfs*6	ENST00000334344	NM_152641.2	208	Ggg/gg	5/21	0.425055817802607	3	FACETS	0.94	0.843	1	0.47	0.421	0.522	CLONAL	1	FALSE	1	0.47366947784584	3		471	561	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46215255	46215271	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TAGAGACTTCGTTAAGG	TAGAGACTTCGTTAAGG	-	novel	NA	P-0020103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	123	636	0	ENST00000334344.6:c.692_705+3del		p.X231_splice	ENST00000334344	NM_152641.2	231		6/21	0.425055817802607	3	FACETS	1	0.971	1	0.587	0.533	0.644	CLONAL	1	FALSE	1	0.47366947784584	3		636	547	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0020104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	42	146	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.922	0.777	1	0.922	0.777	1	CLONAL	1	TRUE	1	0.419947274774396	2		146	217	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0020104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	30	465	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.752	0.611	0.909	0.752	0.611	0.909	CLONAL	1	TRUE	1	0.419947274774396	2		465	190	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144113	11144113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	73	792	0	ENST00000358026.2:c.3694G>A	p.Gly1232Ser	p.G1232S	ENST00000358026	NM_001128849.1	1232	Ggc/Agc	26/36	1	2	FACETS	0.612	0.536	0.694	0.612	0.536	0.694	SUBCLONAL	1	TRUE	1	0.419947274774396	2		792	568	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682989	241682989	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199912971	NA	P-0020104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	136	486	0	ENST00000366560.3:c.34C>T	p.Arg12Cys	p.R12C	ENST00000366560	NM_000143.3	12	Cgt/Tgt	1/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.419947274774396	2		486	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0020107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	884	644	1	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		645	1232	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913514	NA	P-0020108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	607	713	0	ENST00000288135.5:c.2466T>G	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaG	17/21	0.726336088065107	8	FACETS	0.947	0.916	0.978			1	CLONAL	5	TRUE	NA	0.726336088065107	8		713	1122	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032401	10032401	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs78631453	NA	P-0020108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	24	360	0	ENST00000330684.3:c.422C>A	p.Thr141Lys	p.T141K	ENST00000330684	NM_001134407.1	141	aCg/aAg	3/13	0.614288814619715	1	FACETS	0.345	0.274	0.424	0.345	0.274	0.424	SUBCLONAL	1	TRUE	0	0.726336088065107	1		360	122	SUCCESS
NF2	4771	MSKCC	GRCh37	22	29999997	30000006	+	frameshift_variant	Frame_Shift_Del	DEL	GCCATCGCTT	GCCATCGCTT	-	novel	NA	P-0020108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	14	343	0	ENST00000338641.4:c.10_19del	p.Ala4ProfsTer3	p.A4Pfs*3	ENST00000338641	NM_000268.3	4	GCCATCGCTTcc/cc	1/16	0.737076800137203	1	FACETS	0.356	0.263	0.463	0.356	0.263	0.463	SUBCLONAL	1	TRUE	0	0.726336088065107	1		343	69	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913514	NA	P-0020108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	802	713	0	ENST00000288135.5:c.2466T>G	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaG	17/21	0.497057794784647	4	FACETS	0.888	0.866	0.91			1	INDETERMINATE	3	TRUE	NA	0.950830955667355	4		713	1235	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032401	10032401	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs78631453	NA	P-0020108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	258	360	0	ENST00000330684.3:c.422C>A	p.Thr141Lys	p.T141K	ENST00000330684	NM_001134407.1	141	aCg/aAg	3/13	1	2	FACETS	0.944	0.892	0.996	0.944	0.892	0.996	CLONAL	1	TRUE	1	0.950830955667355	2		360	575	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035031	42035031	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	462	847	0	ENST00000219905.7:c.4873G>A	p.Glu1625Lys	p.E1625K	ENST00000219905	NM_001164273.1	1625	Gaa/Aaa	15/24	0.950830955667355	1	FACETS	0.807	0.783	0.83	0.807	0.783	0.83	CLONAL	1	TRUE	0	0.950830955667355	1		847	632	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0020109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	103	591	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.510421630415917	3	FACETS	0.802	0.73	0.875	0.802	0.73	0.875	CLONAL	2	TRUE	1	0.659516905023451	3		591	259	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098973	178098973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	67	462	0	ENST00000397062.3:c.72G>C	p.Trp24Cys	p.W24C	ENST00000397062	NM_006164.4	24	tgG/tgC	2/5	0.644501110797544	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.659516905023451	3		462	122	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420427	49420430	+	frameshift_variant	Frame_Shift_Del	DEL	GCAT	GCAT	-	novel	NA	P-0020109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	148	887	0	ENST00000301067.7:c.15319_15322del	p.Met5107ValfsTer39	p.M5107Vfs*39	ENST00000301067	NM_003482.3	5107	ATGCgt/gt	48/54	0.659516905023451	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	1	0.659516905023451	3		887	292	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89335056	89335056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	33	529	0	ENST00000301030.4:c.7822C>T	p.Arg2608Trp	p.R2608W	ENST00000301030	NM_001256183.1	2608	Cgg/Tgg	13/13	0.652220467081619	2	FACETS	0.695	0.575	0.826	0.347	0.287	0.413	SUBCLONAL	1	TRUE	0	0.659516905023451	2		529	144	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579715	7579726	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGAAGTCTGAA	AGGAAGTCTGAA	-	novel	NA	P-0020109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	51	1010	0	ENST00000269305.4:c.75-5_81del		p.X25_splice	ENST00000269305	NM_001126112.2	25		3/11	0.510421630415917	3	FACETS	0.97	0.835	1	0.485	0.417	0.557	CLONAL	1	TRUE	1	0.659516905023451	3		1010	212	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253852	153253852	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	39	668	0	ENST00000281708.4:c.881C>A	p.Ser294Ter	p.S294*	ENST00000281708	NM_033632.3	294	tCa/tAa	6/12	0.610606163152277	2	FACETS	0.883	0.773	0.988	0.883	0.773	0.988	CLONAL	2	TRUE	0	0.659516905023451	2		668	67	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020350	69020350	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	22	703	0	ENST00000288368.4:c.2722C>A	p.Arg908Ser	p.R908S	ENST00000288368	NM_024870.2	908	Cgt/Agt	24/40	0.659516905023451	3	FACETS	0.837	0.66	1	0.418	0.33	0.517	CLONAL	1	TRUE	1	0.659516905023451	3		703	106	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664873	138664902	+	inframe_deletion	In_Frame_Del	DEL	GCCGCAGCTGCTGCAGCCGCTGCGGCTGCC	GCCGCAGCTGCTGCAGCCGCTGCGGCTGCC	-	rs764243782	NA	P-0020111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	37	149	0	ENST00000330315.3:c.663_692del	p.Ala225_Ala234del	p.A225_A234del	ENST00000330315	NM_023067.3	221	gcGGCAGCCGCAGCGGCTGCAGCAGCTGCGGCt/gct	1/1	1	2	FACETS	0.737	0.616	0.87	0.737	0.616	0.87	SUBCLONAL	1	TRUE	1	0.58	2		149	173	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906958	32906958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358423	NA	P-0020112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	87	530	0	ENST00000380152.3:c.1343G>A	p.Arg448His	p.R448H	ENST00000380152		448	cGt/cAt	10/27	0.326704770964582	3	FACETS	0.749	0.663	0.841	0.375	0.331	0.421	SUBCLONAL	1	TRUE	1	0.4089271798145	3		530	684	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579321	7579322	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs587780067	NA	P-0020112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	501	679	2	ENST00000269305.4:c.365_366del	p.Val122AspfsTer26	p.V122Dfs*26	ENST00000269305	NM_001126112.2	122	gTG/g	4/11	0.4089271798145	3	FACETS	0.931	0.895	0.967	0.931	0.895	0.967	CLONAL	3	TRUE	0	0.4089271798145	3		681	1057	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712647	43712647	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1305746795	NA	P-0020112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1268	135	927	2	ENST00000382044.4:c.4537C>T	p.Arg1513Ter	p.R1513*	ENST00000382044	NM_001141980.1	1513	Cga/Tga	21/28	0.4089271798145	3	FACETS	0.567	0.513	0.624	0.189	0.171	0.208	SUBCLONAL	1	TRUE	0	0.4089271798145	3		929	1403	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543635	148543635	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	111	642	0	ENST00000320356.2:c.173A>G	p.Gln58Arg	p.Q58R	ENST00000320356	NM_004456.4	58	cAa/cGa	3/20	0.4089271798145	6	FACETS	0.842	0.755	0.935	0.281	0.251	0.312	CLONAL	1	TRUE	3	0.4089271798145	6		642	1172	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566522	41566522	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs200897987	NA	P-0020113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	198	622	0	ENST00000263253.7:c.4399T>A	p.Tyr1467Asn	p.Y1467N	ENST00000263253	NM_001429.3	1467	Tac/Aac	27/31	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.621667989843393	2		622	561	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692979	89692979	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs398123325	NA	P-0020113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	128	675	0	ENST00000371953.3:c.463T>A	p.Tyr155Asn	p.Y155N	ENST00000371953	NM_000314.4	155	Tat/Aat	5/9	0.621667989843393	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.621667989843393	1		675	244	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881717	111881717	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0020113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	60	612	0	ENST00000393256.3:c.394+1G>T		p.X132_splice	ENST00000393256	NM_006538.4	132			1	2	FACETS	0.321	0.276	0.37	0.321	0.276	0.37	SUBCLONAL	1	TRUE	1	0.621667989843393	2		612	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0020114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	265	532	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.292149664070261	2	FACETS	0.975	0.92	1	0.975	0.92	1	CLONAL	2	TRUE	0	0.411384927762171	2		533	661	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0020114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	116	667	0	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.411384927762171	2		667	464	SUCCESS
APC	324	MSKCC	GRCh37	5	112175358	112175358	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1554085480	NA	P-0020114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	65	396	0	ENST00000257430.4:c.4067C>G	p.Ser1356Ter	p.S1356*	ENST00000257430	NM_000038.5	1356	tCa/tGa	16/16	0.352801108138185	2	FACETS	1	0.965	1	0.65	0.571	0.734	CLONAL	1	TRUE	0	0.411384927762171	2		396	243	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526071	189526071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	106	657	3	ENST00000264731.3:c.335C>T	p.Thr112Met	p.T112M	ENST00000264731	NM_003722.4	112	aCg/aTg	4/14	0.411384927762171	3	FACETS	0.788	0.707	0.875	0.394	0.353	0.438	SUBCLONAL	1	TRUE	1	0.411384927762171	3		660	788	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445566	49445566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	181	1103	1	ENST00000301067.7:c.1900C>T	p.Pro634Ser	p.P634S	ENST00000301067	NM_003482.3	634	Cct/Tct	10/54	0.169525715919376	5	FACETS	1	0.982	1	0.407	0.374	0.441	INDETERMINATE	1	TRUE	2	0.411384927762171	5		1104	1166	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727439	66727439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	79	581	0	ENST00000307102.5:c.155C>T	p.Ala52Val	p.A52V	ENST00000307102	NM_002755.3	52	gCc/gTc	2/11	1	2	FACETS	0.686	0.604	0.773	0.686	0.604	0.773	SUBCLONAL	1	TRUE	1	0.411384927762171	2		581	560	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778141	3778141	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs867563115	NA	P-0020114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	140	1121	2	ENST00000262367.5:c.6907C>A	p.Gln2303Lys	p.Q2303K	ENST00000262367	NM_004380.2	2303	Cag/Aag	31/31	0.373008504733908	3	FACETS	0.883	0.804	0.967	0.442	0.402	0.484	CLONAL	1	TRUE	1	0.411384927762171	3		1123	929	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0020115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	564	591	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.808406929239476	2	FACETS	0.982	0.96	1	0.982	0.96	1	CLONAL	2	FALSE	0	0.834806278944034	2		591	688	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725207	49725207	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373890576	NA	P-0020116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	22	222	0	ENST00000449682.2:c.218G>A	p.Arg73His	p.R73H	ENST00000449682	NM_020998.3	73	cGc/cAc	2/18	1	2	FACETS	1	0.833	1	1	0.833	1	CLONAL	1	TRUE	1	0.283830967050471	2		222	144	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0020117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	1293	352	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.601268584654453	6	FACETS	0.982	0.963	1			1	CLONAL	5	TRUE	NA	0.601268584654453	6		352	1929	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026606	48026606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1358771617	NA	P-0020117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	125	767	0	ENST00000234420.5:c.1484G>A	p.Arg495Gln	p.R495Q	ENST00000234420	NM_000179.2	495	cGa/cAa	4/10	1	2	FACETS	0.488	0.441	0.537	0.488	0.441	0.537	SUBCLONAL	1	TRUE	1	0.601268584654453	2		767	852	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0020119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	160	760	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.377023658135282	3	FACETS	0.921	0.843	1	0.461	0.421	0.502	CLONAL	1	TRUE	1	0.377023658135282	3		760	1095	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577093	7577093	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882008	NA	P-0020119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	34	820	0	ENST00000269305.4:c.845G>C	p.Arg282Pro	p.R282P	ENST00000269305	NM_001126112.2	282	cGg/cCg	8/11	1	2	FACETS	0.172	0.139	0.208	0.172	0.139	0.208	SUBCLONAL	1	TRUE	1	0.377023658135282	2		820	1051	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916831	48916831	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	17	669	1	ENST00000267163.4:c.361C>T	p.Gln121Ter	p.Q121*	ENST00000267163	NM_000321.2	121	Cag/Tag	3/27	1	2	FACETS	0.355	0.265	0.462	0.355	0.265	0.462	SUBCLONAL	1	TRUE	1	0.377023658135282	2		670	254	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164860	36164872	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCGGGGAACTG	GCGCGGGGAACTG	-	novel	NA	P-0020120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	893	1226	0	ENST00000300305.3:c.1003_1015del	p.Gln335CysfsTer255	p.Q335Cfs*255	ENST00000300305		335	CAGTTCCCCGCGCtg/tg	8/8	0.821034383957486	3	FACETS	0.926	0.909	0.942	0.926	0.909	0.942	CLONAL	3	TRUE	0	0.822725348664177	3		1226	1103	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0020120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	921	817	3	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.822725348664177	3	FACETS	1	0.987	1			1	CLONAL	3	TRUE	NA	0.822725348664177	3		820	1051	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913315	NA	P-0020120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	651	881	0	ENST00000326873.7:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000326873	NM_000455.4	194	Gac/Tac	4/10	0.819243252435559	3	FACETS	0.993	0.975	1	0.993	0.975	1	CLONAL	3	TRUE	0	0.822725348664177	3		881	750	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953894	55953894	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	194	895	1	ENST00000263923.4:c.3542C>A	p.Ser1181Ter	p.S1181*	ENST00000263923	NM_002253.2	1181	tCa/tAa	27/30	1	2	FACETS	0.991	0.926	1	0.991	0.926	1	CLONAL	1	TRUE	1	0.822725348664177	2		896	476	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919214	48919214	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0020120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	178	381	0	ENST00000267163.4:c.381-2A>G		p.X127_splice	ENST00000267163	NM_000321.2	127			0.799988189150398	2	FACETS	0.962	0.921	0.999	0.962	0.921	0.999	CLONAL	2	TRUE	0	0.822725348664177	2		381	225	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588172	69588172	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs550329316	NA	P-0020120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	555	1105	1	ENST00000168712.1:c.526G>T	p.Gly176Cys	p.G176C	ENST00000168712	NM_002007.2	176	Ggc/Tgc	3/3	0.815650759749904	3	FACETS	1	0.985	1			1	CLONAL	2	TRUE	NA	0.822725348664177	3		1106	925	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844417	156844417	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	300	1324	0	ENST00000524377.1:c.1250G>T	p.Gly417Val	p.G417V	ENST00000524377	NM_002529.3	417	gGg/gTg	10/17	1	2	FACETS	0.995	0.943	1	0.995	0.943	1	CLONAL	1	TRUE	1	0.822725348664177	2		1324	733	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727117	243727117	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs774991430	NA	P-0020120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	203	924	0	ENST00000263826.5:c.853A>G	p.Ile285Val	p.I285V	ENST00000263826	NM_005465.4	285	Ata/Gta	9/13	1	2	FACETS	0.987	0.924	1	0.987	0.924	1	CLONAL	1	TRUE	1	0.822725348664177	2		924	500	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14317361	14317361	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	47	945	0	ENST00000256196.4:c.149C>G	p.Ser50Cys	p.S50C	ENST00000256196		50	tCt/tGt	2/6	NA	2	FACETS	0.126	0.105	0.148			1	INDETERMINATE	1	TRUE	NA	0.822725348664177	2		945	910	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922173	100922173	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	164	869	1	ENST00000325455.5:c.2339C>A	p.Pro780His	p.P780H	ENST00000325455	NM_001202474.3	780	cCt/cAt	5/8	0.822725348664177	6	FACETS	0.862	0.789	0.938	0.172	0.157	0.188	CLONAL	1	TRUE	1	0.822725348664177	6		870	1224	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	493280	493280	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	218	1023	0	ENST00000399788.2:c.283G>C	p.Ala95Pro	p.A95P	ENST00000399788	NM_001042603.1	95	Gca/Cca	3/28	0.577269851375418	4	FACETS	0.904	0.841	0.97	0.452	0.42	0.485	CLONAL	1	TRUE	2	0.822725348664177	4		1023	1068	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420793	49420793	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765693458	NA	P-0020120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	482	913	1	ENST00000301067.7:c.14956C>T	p.Arg4986Cys	p.R4986C	ENST00000301067	NM_003482.3	4986	Cgc/Tgc	48/54	0.577269851375418	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.822725348664177	4		914	1020	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490607	56490607	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	191	893	2	ENST00000267101.3:c.2251C>T	p.Gln751Ter	p.Q751*	ENST00000267101	NM_001982.3	751	Cag/Tag	19/28	0.577269851375418	4	FACETS	0.951	0.88	1	0.475	0.44	0.513	CLONAL	1	TRUE	2	0.822725348664177	4		895	890	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060990	38060990	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1367737391	NA	P-0020120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	112	591	0	ENST00000250448.2:c.999G>T	p.Gln333His	p.Q333H	ENST00000250448	NM_004496.3	333	caG/caT	2/2	0.780695252213966	3	FACETS	0.913	0.827	1	0.456	0.413	0.501	CLONAL	1	TRUE	1	0.822725348664177	3		591	421	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748681	43748681	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	311	1318	1	ENST00000382044.4:c.2125C>T	p.Gln709Ter	p.Q709*	ENST00000382044	NM_001141980.1	709	Caa/Taa	12/28	0.822725348664177	2	FACETS	0.957	0.907	1	0.478	0.453	0.504	CLONAL	1	TRUE	0	0.822725348664177	2		1319	790	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108236	8108236	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	584	1167	1	ENST00000585124.1:c.988A>T	p.Asn330Tyr	p.N330Y	ENST00000585124	NM_004217.3	330	Aac/Tac	9/9	0.822725348664177	3	FACETS	0.785	0.756	0.813			1	SUBCLONAL	2	TRUE	NA	0.822725348664177	3		1168	1277	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383634	42383634	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	216	868	0	ENST00000221972.3:c.409G>T	p.Gly137Trp	p.G137W	ENST00000221972	NM_021601.3	137	Ggg/Tgg	3/5	0.265578867471711	3	FACETS	1	0.964	1	0.349	0.326	0.374	INDETERMINATE	1	TRUE	0	0.822725348664177	3		868	707	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46252698	46252698	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	191	806	0	ENST00000371998.3:c.127A>G	p.Lys43Glu	p.K43E	ENST00000371998		43	Aaa/Gaa	4/23	0.780695252213966	3	FACETS	1	0.944	1	0.51	0.473	0.547	CLONAL	1	TRUE	1	0.822725348664177	3		806	643	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875643	35875643	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	318	949	3	ENST00000303115.3:c.830C>A	p.Pro277His	p.P277H	ENST00000303115	NM_002185.3	277	cCc/cAc	7/8	0.520206625431715	4	FACETS	0.859	0.815	0.904	0.859	0.815	0.904	CLONAL	2	TRUE	2	0.822725348664177	4		952	820	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909223	41909223	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	566	1153	0	ENST00000372991.4:c.165C>A	p.His55Gln	p.H55Q	ENST00000372991	NM_001760.3	55	caC/caA	1/5	0.708531153596234	4	FACETS	0.978	0.942	1	0.978	0.942	1	CLONAL	2	TRUE	2	0.822725348664177	4		1153	1282	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909242	41909242	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	540	1114	0	ENST00000372991.4:c.146A>G	p.Gln49Arg	p.Q49R	ENST00000372991	NM_001760.3	49	cAg/cGg	1/5	0.708531153596234	4	FACETS	0.964	0.927	1	0.964	0.927	1	CLONAL	2	TRUE	2	0.822725348664177	4		1114	1241	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099969	157099969	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	79	515	2	ENST00000346085.5:c.906C>A	p.Ser302Arg	p.S302R	ENST00000346085	NM_020732.3	302	agC/agA	1/20	0.708531153596234	4	FACETS	0.485	0.426	0.548	0.242	0.213	0.274	SUBCLONAL	1	TRUE	2	0.822725348664177	4		517	722	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983932	2983932	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	567	1336	2	ENST00000396946.4:c.598G>T	p.Asp200Tyr	p.D200Y	ENST00000396946	NM_032415.4	200	Gac/Tac	5/25	0.780695252213966	3	FACETS	0.947	0.915	0.979	0.947	0.915	0.979	CLONAL	2	TRUE	1	0.822725348664177	3		1338	1027	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412727	139412727	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	150	1022	0	ENST00000277541.6:c.1117A>C	p.Asn373His	p.N373H	ENST00000277541	NM_017617.3	373	Aac/Cac	7/34	0.822725348664177	2	FACETS	0.561	0.514	0.61	0.28	0.257	0.305	SUBCLONAL	1	TRUE	0	0.822725348664177	2		1022	650	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410442	63410442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	149	560	0	ENST00000330258.3:c.2725del	p.Ser909ProfsTer67	p.S909Pfs*67	ENST00000330258	NM_152424.3	909	Tcc/cc	2/2	0.822725348664177	2	FACETS	0.846	0.781	0.913			1	CLONAL	1	TRUE	NA	0.822725348664177	2		560	428	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	312	122	0				ENST00000310581	NM_198253.2	-/1132			0.746056688738066	3	FACETS	0.988	0.943	1	0.988	0.943	1	CLONAL	2	TRUE	1	0.746056688738066	3		122	581	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0020122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	35	499	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.538693768964723	4	FACETS	0.464	0.381	0.557	0.155	0.127	0.186	SUBCLONAL	1	TRUE	1	0.746056688738066	4		499	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577102	7577102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793881	NA	P-0020122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	550	1022	2	ENST00000269305.4:c.836G>A	p.Gly279Glu	p.G279E	ENST00000269305	NM_001126112.2	279	gGg/gAg	8/11	0.742932593838103	2	FACETS	0.995	0.969	1	0.995	0.969	1	CLONAL	2	TRUE	0	0.746056688738066	2		1024	741	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231551	5231551	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	171	729	1	ENST00000357368.4:c.1925C>T	p.Pro642Leu	p.P642L	ENST00000357368	NM_002850.3	642	cCg/cTg	14/38	0.746056688738066	3	FACETS	0.897	0.827	0.969	0.448	0.413	0.485	CLONAL	1	TRUE	1	0.746056688738066	3		730	702	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313222	30313222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	225	934	1	ENST00000262643.3:c.916C>T	p.His306Tyr	p.H306Y	ENST00000262643	NM_001238.2	306	Cat/Tat	10/12	0.746056688738066	3	FACETS	1	0.944	1	0.506	0.472	0.541	CLONAL	1	TRUE	1	0.746056688738066	3		935	818	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412967	49412967	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1663	241	1146	0	ENST00000418115.1:c.56C>G	p.Thr19Arg	p.T19R	ENST00000418115	NM_001664.2	19	aCa/aGa	2/5	0.746056688738066	6	FACETS	0.846	0.786	0.907	0.211	0.196	0.227	CLONAL	1	TRUE	2	0.746056688738066	6		1146	1904	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332348	70332348	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368770710	NA	P-0020122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	189	827	0	ENST00000373644.4:c.253G>A	p.Asp85Asn	p.D85N	ENST00000373644	NM_030625.2	85	Gat/Aat	2/12	1	2	FACETS	0.993	0.926	1	0.993	0.926	1	CLONAL	1	TRUE	1	0.746056688738066	2		827	510	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367296	50367296	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1432663785	NA	P-0020122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	156	783	0	ENST00000331340.3:c.103G>A	p.Glu35Lys	p.E35K	ENST00000331340	NM_006060.4	35	Gag/Aag	3/8	0.528092928502615	4	FACETS	1	0.958	1	0.356	0.326	0.386	CLONAL	1	TRUE	1	0.746056688738066	4		783	684	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181426	185181426	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1311413742	NA	P-0020122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	244	920	1	ENST00000265026.3:c.1367G>A	p.Arg456Gln	p.R456Q	ENST00000265026	NM_004721.4	456	cGa/cAa	8/14	0.538693768964723	4	FACETS	1	0.983	1	0.383	0.358	0.409	CLONAL	1	TRUE	1	0.746056688738066	4		921	993	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733044	74733044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	173	821	1	ENST00000359995.5:c.199G>A	p.Asp67Asn	p.D67N	ENST00000359995	NM_001195427.1	67	Gac/Aac	1/3	0.715268563008712	4	FACETS	0.82	0.755	0.889	0.41	0.377	0.445	CLONAL	1	TRUE	2	0.746056688738066	4		822	987	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11273581	11273581	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	162	801	2	ENST00000361445.4:c.3160C>A	p.Leu1054Ile	p.L1054I	ENST00000361445	NM_004958.3	1054	Ctt/Att	21/58	0.658248950121163	4	FACETS	0.811	0.744	0.881	0.405	0.372	0.441	CLONAL	1	TRUE	2	0.746056688738066	4		803	935	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259580	16259580	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	193	913	0	ENST00000375759.3:c.6845C>G	p.Ser2282Cys	p.S2282C	ENST00000375759	NM_015001.2	2282	tCt/tGt	11/15	0.658248950121163	4	FACETS	0.907	0.839	0.978	0.454	0.419	0.489	CLONAL	1	TRUE	2	0.746056688738066	4		913	996	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405106	70405106	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	239	1099	1	ENST00000373644.4:c.2620C>T	p.Gln874Ter	p.Q874*	ENST00000373644	NM_030625.2	874	Caa/Taa	4/12	1	2	FACETS	0.965	0.906	1	0.965	0.906	1	CLONAL	1	TRUE	1	0.746056688738066	2		1100	664	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173652	108173652	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs879254274	NA	P-0020122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	94	924	0	ENST00000278616.4:c.5392C>G	p.Leu1798Val	p.L1798V	ENST00000278616	NM_000051.3	1798	Cta/Gta	36/63	0.746056688738066	3	FACETS	0.878	0.787	0.974	0.439	0.393	0.487	CLONAL	1	TRUE	1	0.746056688738066	3		924	394	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11803068	11803068	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	60	667	0	ENST00000396373.4:c.7G>C	p.Glu3Gln	p.E3Q	ENST00000396373	NM_001987.4	3	Gag/Cag	1/8	1	2	FACETS	0.337	0.291	0.388	0.337	0.291	0.388	SUBCLONAL	1	TRUE	1	0.746056688738066	2		667	477	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726698	88726698	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375475747	NA	P-0020122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	208	810	2	ENST00000360948.2:c.346C>T	p.Arg116Trp	p.R116W	ENST00000360948	NM_001012338.2	116	Cgg/Tgg	4/19	0.746056688738066	3	FACETS	1	0.984	1	0.586	0.547	0.627	CLONAL	1	TRUE	1	0.746056688738066	3		812	653	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250104	39250104	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	205	1027	0	ENST00000402219.2:c.1465C>T	p.Arg489Cys	p.R489C	ENST00000402219	NM_005633.3	489	Cgt/Tgt	10/23	0.658248950121163	4	FACETS	0.913	0.846	0.982	0.456	0.423	0.491	CLONAL	1	TRUE	2	0.746056688738066	4		1027	1051	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29115441	29115441	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1569149953	NA	P-0020122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	183	803	0	ENST00000328354.6:c.625C>T	p.Gln209Ter	p.Q209*	ENST00000328354	NM_007194.3	209	Cag/Tag	5/15	0.742932593838103	2	FACETS	1	0.962	1	0.523	0.487	0.559	CLONAL	1	TRUE	0	0.746056688738066	2		803	469	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588158	67588158	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	157	835	0	ENST00000274335.5:c.988G>C	p.Asp330His	p.D330H	ENST00000274335		330	Gat/Cat	7/15	0.742932593838103	2	FACETS	0.909	0.84	0.98	0.455	0.42	0.49	CLONAL	1	TRUE	0	0.746056688738066	2		835	463	SUCCESS
APC	324	MSKCC	GRCh37	5	112103077	112103077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	124	519	0	ENST00000257430.4:c.412G>A	p.Glu138Lys	p.E138K	ENST00000257430	NM_000038.5	138	Gag/Aag	4/16	0.742932593838103	2	FACETS	0.983	0.901	1	0.492	0.45	0.534	CLONAL	1	TRUE	0	0.746056688738066	2		519	338	SUCCESS
APC	324	MSKCC	GRCh37	5	112157607	112157607	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	181	852	0	ENST00000257430.4:c.1327G>C	p.Glu443Gln	p.E443Q	ENST00000257430	NM_000038.5	443	Gaa/Caa	11/16	0.742932593838103	2	FACETS	0.951	0.885	1	0.476	0.442	0.51	CLONAL	1	TRUE	0	0.746056688738066	2		852	510	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287839	33287839	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	279	1132	0	ENST00000374542.5:c.1414G>A	p.Glu472Lys	p.E472K	ENST00000374542	NM_001141970.1	472	Gag/Aag	5/8	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.746056688738066	2		1132	721	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553715	106553715	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	238	848	1	ENST00000369096.4:c.1680G>T	p.Lys560Asn	p.K560N	ENST00000369096	NM_001198.3	560	aaG/aaT	5/7	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.746056688738066	2		849	610	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554851	106554851	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	197	773	0	ENST00000369096.4:c.1968G>C	p.Glu656Asp	p.E656D	ENST00000369096	NM_001198.3	656	gaG/gaC	7/7	1	2	FACETS	0.976	0.911	1	0.976	0.911	1	CLONAL	1	TRUE	1	0.746056688738066	2		773	541	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367269	50367269	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	143	708	1	ENST00000331340.3:c.76G>T	p.Glu26Ter	p.E26*	ENST00000331340	NM_006060.4	26	Gag/Tag	3/8	0.528092928502615	4	FACETS	1	0.942	1	0.346	0.316	0.377	CLONAL	1	TRUE	1	0.746056688738066	4		709	645	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802521	139802521	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0020122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	197	866	4	ENST00000247668.2:c.367-1G>T		p.X123_splice	ENST00000247668	NM_021138.3	123			0.746056688738066	3	FACETS	0.963	0.894	1	0.481	0.447	0.517	CLONAL	1	TRUE	1	0.746056688738066	3		870	753	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882019	NA	P-0020123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	501	939	36	ENST00000269305.4:c.455dup	p.Pro153AlafsTer28	p.P153Afs*28	ENST00000269305	NM_001126112.2	152	ccg/ccCg	5/11	0.947467758094858	1	FACETS	0.911	0.89	0.931	0.911	0.89	0.931	CLONAL	1	TRUE	0	0.947467758094858	1		975	611	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033916	49033916	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs878853949	NA	P-0020123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	364	832	0	ENST00000267163.4:c.2053C>T	p.Gln685Ter	p.Q685*	ENST00000267163	NM_000321.2	685	Cag/Tag	20/27	0.947467758094858	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.947467758094858	1		832	394	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99460060	99460060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs544049409	NA	P-0020123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	248	687	2	ENST00000268035.6:c.2156G>A	p.Arg719His	p.R719H	ENST00000268035	NM_000875.3	719	cGc/cAc	10/21	0.947467758094858	1	FACETS	0.619	0.588	0.65	0.619	0.588	0.65	SUBCLONAL	1	TRUE	0	0.947467758094858	1		689	445	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652397	48652397	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	402	971	0	ENST00000376670.3:c.1073del	p.Pro358GlnfsTer74	p.P358Qfs*74	ENST00000376670	NM_002049.3	356	ggC/gg	6/6	1	2	FACETS	0.962	0.92	1	0.962	0.92	1	CLONAL	1	TRUE	1	0.947467758094858	2		971	882	SUCCESS
APC	324	MSKCC	GRCh37	5	112137018	112137018	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	397	817	0	ENST00000257430.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000257430	NM_000038.5	258	Gag/Tag	8/16	0.947467758094858	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.947467758094858	1		817	437	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434959	49434959	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555192751	NA	P-0020123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	402	758	0	ENST00000301067.7:c.6594del	p.Tyr2199IlefsTer65	p.Y2199Ifs*65	ENST00000301067	NM_003482.3	2198	ccC/cc	31/54	1	2	FACETS	0.975	0.933	1	0.975	0.933	1	CLONAL	1	TRUE	1	0.947467758094858	2		758	870	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457704	149457704	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1454473722	NA	P-0020123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	544	843	0	ENST00000286301.3:c.700G>T	p.Asp234Tyr	p.D234Y	ENST00000286301	NM_005211.3	234	Gat/Tat	5/22	0.947467758094858	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.947467758094858	1		843	582	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652159	36652160	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0020123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	396	788	1	ENST00000244741.5:c.281_282delinsTT	p.Arg94Leu	p.R94L	ENST00000244741	NM_000389.4	94	cGG/cTT	2/3	1	2	FACETS	0.966	0.924	1	0.966	0.924	1	CLONAL	1	TRUE	1	0.947467758094858	2		789	865	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534459	140534459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	347	612	0	ENST00000288602.6:c.454C>T	p.Pro152Ser	p.P152S	ENST00000288602	NM_004333.4	152	Cca/Tca	3/18	1	2	FACETS	0.946	0.902	0.991	0.946	0.902	0.991	CLONAL	1	TRUE	1	0.947467758094858	2		612	774	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002813	69002813	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0020123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	62	364	0	ENST00000288368.4:c.2114-1G>A		p.X705_splice	ENST00000288368	NM_024870.2	705			1	2	FACETS	0.358	0.31	0.409	0.358	0.31	0.409	SUBCLONAL	1	TRUE	1	0.947467758094858	2		364	366	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437121	110437121	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	28	133	0	ENST00000375856.3:c.1280A>G	p.His427Arg	p.H427R	ENST00000375856	NM_003749.2	427	cAc/cGc	1/2	1	2	FACETS	0.893	0.731	1	0.893	0.731	1	CLONAL	1	TRUE	1	0.633355525511216	2		133	99	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578464	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	673	1033	0	ENST00000269305.4:c.466C>G	p.Arg156Gly	p.R156G	ENST00000269305	NM_001126112.2	156	Cgc/Ggc	5/11	0.654001453920318	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	0	0.654001453920318	3		1033	905	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562273	95562273	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	111	668	0	ENST00000393063.1:c.4984C>G	p.Leu1662Val	p.L1662V	ENST00000393063	NM_030621.3	1662	Ctt/Gtt	24/28	0.654001453920318	3	FACETS	0.597	0.536	0.66	0.298	0.268	0.33	SUBCLONAL	1	TRUE	1	0.654001453920318	3		668	755	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912204	97912204	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1057517125	NA	P-0020126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	209	766	0	ENST00000289081.3:c.686+1G>T		p.X229_splice	ENST00000289081	NM_000136.2	229			0.377603714834599	4	FACETS	1	0.967	1	0.535	0.496	0.575	INDETERMINATE	1	TRUE	2	0.654001453920318	4		766	988	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650371	48650371	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	266	977	0	ENST00000376670.3:c.341A>G	p.Glu114Gly	p.E114G	ENST00000376670	NM_002049.3	114	gAg/gGg	3/6	0.654001453920318	4	FACETS	0.905	0.847	0.966			1	CLONAL	1	TRUE	NA	0.654001453920318	4		977	1486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0020127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	500	532	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.660082037957375	1	FACETS	0.926	0.898	0.954	0.926	0.898	0.954	CLONAL	1	TRUE	0	0.849483882215905	1		533	731	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	367	122	0				ENST00000310581	NM_198253.2	-/1132			0.849483882215905	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.849483882215905	1		122	440	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0020127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	569	647	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.551019742576917	2	FACETS	0.794	0.771	0.816	0.794	0.771	0.816	SUBCLONAL	2	TRUE	0	0.849483882215905	2		647	844	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453179	140453179	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913340	NA	P-0020127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	382	666	0	ENST00000288602.6:c.1756G>A	p.Glu586Lys	p.E586K	ENST00000288602	NM_004333.4	586	Gaa/Aaa	15/18	0.849483882215905	3	FACETS	0.938	0.9	0.976	0.938	0.9	0.976	CLONAL	2	TRUE	1	0.849483882215905	3		666	683	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480549	120480549	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	111	780	0	ENST00000256646.2:c.3268C>T	p.Pro1090Ser	p.P1090S	ENST00000256646	NM_024408.3	1090	Cca/Tca	20/34	0.551019742576917	2	FACETS	0.311	0.28	0.345	0.156	0.14	0.173	SUBCLONAL	1	TRUE	0	0.849483882215905	2		780	839	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858388	89858388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	421	954	2	ENST00000389301.3:c.1172C>T	p.Ser391Phe	p.S391F	ENST00000389301	NM_000135.2	391	tCc/tTc	13/43	0.283841028956994	1	FACETS	0.561	0.536	0.586	0.561	0.536	0.586	INDETERMINATE	1	TRUE	0	0.849483882215905	1		956	1017	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843574	156843574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	128	963	0	ENST00000524377.1:c.1000G>A	p.Glu334Lys	p.E334K	ENST00000524377	NM_002529.3	334	Gag/Aag	8/17	0.604830340363061	2	FACETS	0.317	0.286	0.349	0.158	0.143	0.175	SUBCLONAL	1	TRUE	0	0.849483882215905	2		963	952	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176145049	176145049	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	83	759	0	ENST00000367669.3:c.562T>A	p.Leu188Met	p.L188M	ENST00000367669	NM_022457.5	188	Ttg/Atg	3/20	0.649103136676407	1	FACETS	0.209	0.184	0.235	0.209	0.184	0.235	SUBCLONAL	1	TRUE	0	0.849483882215905	1		759	539	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813380	102813380	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	429	770	0	ENST00000307046.8:c.309G>T	p.Arg103Ser	p.R103S	ENST00000307046	NM_001111285.1	103	agG/agT	3/4	0.649103136676407	1	FACETS	0.895	0.865	0.925	0.895	0.865	0.925	CLONAL	1	TRUE	0	0.849483882215905	1		770	649	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49280956	49280956	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0020127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	140	714	0	ENST00000282018.3:c.3G>A	p.Met1?	p.M1?	ENST00000282018	NM_020377.2	1	atG/atA	1/1	0.337308696292709	2	FACETS	0.516	0.471	0.563	0.258	0.235	0.282	INDETERMINATE	1	TRUE	0	0.849483882215905	2		714	639	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348214	348214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	425	945	1	ENST00000262320.3:c.1292C>T	p.Pro431Leu	p.P431L	ENST00000262320	NM_003502.3	431	cCc/cTc	6/11	0.283841028956994	1	FACETS	0.565	0.54	0.591	0.565	0.54	0.591	INDETERMINATE	1	TRUE	0	0.849483882215905	1		946	1018	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781392	3781392	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	350	852	1	ENST00000262367.5:c.4973G>T	p.Cys1658Phe	p.C1658F	ENST00000262367	NM_004380.2	1658	tGt/tTt	30/31	0.283841028956994	1	FACETS	0.533	0.506	0.559	0.533	0.506	0.559	INDETERMINATE	1	TRUE	0	0.849483882215905	1		853	890	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934567	9934567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	288	857	1	ENST00000330684.3:c.1588G>A	p.Glu530Lys	p.E530K	ENST00000330684	NM_001134407.1	530	Gaa/Aaa	7/13	0.283841028956994	1	FACETS	0.52	0.491	0.549	0.52	0.491	0.549	INDETERMINATE	1	TRUE	0	0.849483882215905	1		858	750	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031545	11031545	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	612	1027	1	ENST00000327064.4:c.1460C>T	p.Ser487Phe	p.S487F	ENST00000327064	NM_199141.1	487	tCc/tTc	13/16	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.849483882215905	2		1028	1196	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650313	12650313	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	506	844	2	ENST00000251849.4:c.533C>T	p.Thr178Ile	p.T178I	ENST00000251849	NM_002880.3	178	aCc/aTc	5/17	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.849483882215905	2		846	968	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169191	32169191	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	605	900	0	ENST00000375023.3:c.3842G>A	p.Gly1281Glu	p.G1281E	ENST00000375023	NM_004557.3	1281	gGa/gAa	22/30	0.191736714598084	3	FACETS	0.866	0.836	0.895	0.577	0.557	0.597	INDETERMINATE	2	TRUE	0	0.849483882215905	3		900	1172	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678985	117678985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	194	762	0	ENST00000368508.3:c.3836C>T	p.Ser1279Phe	p.S1279F	ENST00000368508	NM_002944.2	1279	tCt/tTt	24/43	0.849483882215905	1	FACETS	0.915	0.87	0.959	0.915	0.87	0.959	CLONAL	1	TRUE	0	0.849483882215905	1		762	287	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959090	2959090	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	370	894	0	ENST00000396946.4:c.2426A>C	p.Gln809Pro	p.Q809P	ENST00000396946	NM_032415.4	809	cAg/cCg	18/25	0.301609666156174	5	FACETS	1	0.993	1	0.26	0.246	0.274	INDETERMINATE	1	TRUE	0	0.849483882215905	5		894	1525	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372292	55372292	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774273287	NA	P-0020127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	109	764	1	ENST00000297316.4:c.982C>T	p.Pro328Ser	p.P328S	ENST00000297316	NM_022454.3	328	Ccg/Tcg	2/2	0.849483882215905	3	FACETS	0.287	0.257	0.32	0.144	0.128	0.16	SUBCLONAL	1	TRUE	1	0.849483882215905	3		765	1272	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321405	1321405	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	294	527	0	ENST00000400841.2:c.350T>G	p.Leu117Arg	p.L117R	ENST00000400841		117	cTg/cGg	4/6	1	1	FACETS	0.549	0.52	0.579	0.549	0.52	0.579	SUBCLONAL	1	TRUE	0	0.849483882215905	1		527	725	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215897	36215898	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	A	novel	NA	P-0020127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	381	952	0	ENST00000222270.7:c.3437_3438delinsA	p.Leu1146Ter	p.L1146*	ENST00000222270	NM_014727.1	1146	tTG/tA	10/37	1	2	FACETS	0.853	0.811	0.895	0.853	0.811	0.895	CLONAL	1	TRUE	1	0.849483882215905	2		952	1052	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218473	1218474	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	400	1119	0	ENST00000326873.7:c.350dup	p.Leu117PhefsTer46	p.L117Ffs*46	ENST00000326873	NM_000455.4	116	-/T	2/10	0.855330136856155	1	FACETS	0.988	0.957	1	0.988	0.957	1	CLONAL	1	TRUE	0	0.855330136856155	1		1119	542	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944394	40944394	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	318	998	1	ENST00000373198.4:c.2108T>A	p.Ile703Asn	p.I703N	ENST00000373198	NM_133170.3	703	aTc/aAc	12/32	1	2	FACETS	0.959	0.911	1	0.959	0.911	1	CLONAL	1	TRUE	1	0.855330136856155	2		999	775	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060863	38060863	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	156	885	0	ENST00000250448.2:c.1126del	p.Ala376HisfsTer13	p.A376Hfs*13	ENST00000250448	NM_004496.3	376	Gca/ca	2/2	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.350510898140025	2		885	822	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579530	7579530	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	179	1167	0	ENST00000269305.4:c.157del	p.Trp53GlyfsTer70	p.W53Gfs*70	ENST00000269305	NM_001126112.2	53	Tgg/gg	4/11	0.350510898140025	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.350510898140025	1		1167	787	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557630	95557630	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	352	981	0	ENST00000393063.1:c.5437G>C	p.Glu1813Gln	p.E1813Q	ENST00000393063	NM_030621.3	1813	Gag/Cag	26/28	1	2	FACETS	0.946	0.9	0.993	0.946	0.9	0.993	CLONAL	1	TRUE	1	0.861195949367554	2		981	864	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003799	45003799	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	330	783	0	ENST00000558401.1:c.55G>T	p.Glu19Ter	p.E19*	ENST00000558401	NM_004048.2	19	Gag/Tag	1/4	0.861195949367554	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.861195949367554	1		783	426	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165678	47165678	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	301	888	1	ENST00000409792.3:c.448C>T	p.His150Tyr	p.H150Y	ENST00000409792	NM_014159.6	150	Cat/Tat	3/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.861195949367554	2		889	687	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039625	47039626	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTGCAGATC	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	175	865	0	ENST00000377604.3:c.1084_1092dup	p.Ile362_Gln364dup	p.I362_Q364dup	ENST00000377604	NM_001204468.1	362	-/CTGCAGATC	11/24	1	2	FACETS	0.645	0.597	0.695	0.645	0.597	0.695	SUBCLONAL	1	TRUE	1	0.861195949367554	2		865	630	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528553	89528553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	195	520	0	ENST00000336596.2:c.2853G>A	p.Met951Ile	p.M951I	ENST00000336596	NM_005233.5	951	atG/atA	17/17	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.861195949367554	2		520	446	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897336	78897336	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs757484259	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	285	1003	0	ENST00000306801.3:c.2671G>T	p.Asp891Tyr	p.D891Y	ENST00000306801	NM_020761.2	891	Gat/Tat	23/34	1	2	FACETS	0.966	0.915	1	0.966	0.915	1	CLONAL	1	TRUE	1	0.861195949367554	2		1003	685	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028539	42028539	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	413	1001	0	ENST00000219905.7:c.4077C>G	p.Ile1359Met	p.I1359M	ENST00000219905	NM_001164273.1	1359	atC/atG	13/24	0.861195949367554	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.861195949367554	1		1001	524	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288502	15288502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	141	316	0	ENST00000263388.2:c.4237G>A	p.Asp1413Asn	p.D1413N	ENST00000263388	NM_000435.2	1413	Gac/Aac	24/33	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.861195949367554	2		316	307	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645687	12645687	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397516828	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	206	548	0	ENST00000251849.4:c.782C>T	p.Pro261Leu	p.P261L	ENST00000251849	NM_002880.3	261	cCt/cTt	7/17	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.861195949367554	2		548	472	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600470	10600470	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	323	946	2	ENST00000171111.5:c.1385G>T	p.Gly462Val	p.G462V	ENST00000171111	NM_203500.1	462	gGg/gTg	4/6	0.861195949367554	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.861195949367554	1		948	420	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562606	95562606	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	218	652	0	ENST00000393063.1:c.4651G>C	p.Glu1551Gln	p.E1551Q	ENST00000393063	NM_030621.3	1551	Gag/Cag	24/28	1	2	FACETS	0.983	0.923	1	0.983	0.923	1	CLONAL	1	TRUE	1	0.861195949367554	2		652	515	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028481	42028481	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	292	797	0	ENST00000219905.7:c.4019C>G	p.Ser1340Ter	p.S1340*	ENST00000219905	NM_001164273.1	1340	tCa/tGa	13/24	0.861195949367554	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.861195949367554	1		797	386	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911971	32911971	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	293	898	0	ENST00000380152.3:c.3479G>C	p.Arg1160Thr	p.R1160T	ENST00000380152		1160	aGa/aCa	11/27	1	2	FACETS	0.989	0.937	1	0.989	0.937	1	CLONAL	1	TRUE	1	0.861195949367554	2		898	688	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256441	16256441	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	321	976	0	ENST00000375759.3:c.3706G>C	p.Asp1236His	p.D1236H	ENST00000375759	NM_015001.2	1236	Gat/Cat	11/15	1	2	FACETS	0.966	0.917	1	0.966	0.917	1	CLONAL	1	TRUE	1	0.861195949367554	2		976	772	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256988	16256988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs938826668	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	392	1017	1	ENST00000375759.3:c.4253G>A	p.Arg1418Gln	p.R1418Q	ENST00000375759	NM_015001.2	1418	cGa/cAa	11/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.861195949367554	2		1018	871	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023006	27023006	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	29	88	0	ENST00000324856.7:c.112G>C	p.Glu38Gln	p.E38Q	ENST00000324856	NM_006015.4	38	Gag/Cag	1/20	1	2	FACETS	0.91	0.758	1	0.91	0.758	1	CLONAL	1	TRUE	1	0.861195949367554	2		88	74	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023610	27023610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471878830	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	274	618	0	ENST00000324856.7:c.716C>T	p.Pro239Leu	p.P239L	ENST00000324856	NM_006015.4	239	cCg/cTg	1/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.861195949367554	2		618	561	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439599	51439599	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	209	740	0	ENST00000262662.1:c.164G>C	p.Arg55Thr	p.R55T	ENST00000262662		55	aGa/aCa	4/4	1	2	FACETS	0.897	0.84	0.955	0.897	0.84	0.955	CLONAL	1	TRUE	1	0.861195949367554	2		740	541	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120457999	120457999	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	313	873	0	ENST00000256646.2:c.7346G>A	p.Gly2449Glu	p.G2449E	ENST00000256646	NM_024408.3	2449	gGa/gAa	34/34	1	2	FACETS	0.96	0.911	1	0.96	0.911	1	CLONAL	1	TRUE	1	0.861195949367554	2		873	757	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450591	70450591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	363	919	0	ENST00000373644.4:c.5431G>A	p.Glu1811Lys	p.E1811K	ENST00000373644	NM_030625.2	1811	Gaa/Aaa	12/12	0.861195949367554	1	FACETS	0.994	0.962	1	0.994	0.962	1	CLONAL	1	TRUE	0	0.861195949367554	1		919	483	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160368	108160368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	225	686	0	ENST00000278616.4:c.4276G>A	p.Ala1426Thr	p.A1426T	ENST00000278616	NM_000051.3	1426	Gca/Aca	29/63	1	2	FACETS	0.899	0.844	0.956	0.899	0.844	0.956	CLONAL	1	TRUE	1	0.861195949367554	2		686	581	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307593	118307593	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	291	866	0	ENST00000534358.1:c.366C>G	p.Ile122Met	p.I122M	ENST00000534358	NM_005933.3	122	atC/atG	1/36	1	2	FACETS	0.939	0.888	0.989	0.939	0.888	0.989	CLONAL	1	TRUE	1	0.861195949367554	2		866	720	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426469	49426469	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs188017299	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	416	1158	0	ENST00000301067.7:c.12019C>T	p.Gln4007Ter	p.Q4007*	ENST00000301067	NM_003482.3	4007	Caa/Taa	39/54	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.861195949367554	2		1158	940	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924315	112924315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1355732645	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	350	1020	0	ENST00000351677.2:c.1261C>T	p.Arg421Trp	p.R421W	ENST00000351677	NM_002834.3	421	Cgg/Tgg	11/16	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.861195949367554	2		1020	802	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120535159	120535159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	243	826	0	ENST00000229340.5:c.496G>A	p.Glu166Lys	p.E166K	ENST00000229340	NM_006861.6	166	Gag/Aag	6/6	1	2	FACETS	0.915	0.861	0.969	0.915	0.861	0.969	CLONAL	1	TRUE	1	0.861195949367554	2		826	617	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608067	28608067	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	343	1080	0	ENST00000241453.7:c.1899C>G	p.Ser633Arg	p.S633R	ENST00000241453	NM_004119.2	633	agC/agG	15/24	1	2	FACETS	0.947	0.901	0.994	0.947	0.901	0.994	CLONAL	1	TRUE	1	0.861195949367554	2		1080	841	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28931812	28931812	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	246	706	2	ENST00000282397.4:c.2127A>T	p.Leu709Phe	p.L709F	ENST00000282397	NM_002019.4	709	ttA/ttT	15/30	1	2	FACETS	0.907	0.854	0.961	0.907	0.854	0.961	CLONAL	1	TRUE	1	0.861195949367554	2		708	630	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911387	32911387	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	244	891	0	ENST00000380152.3:c.2895G>A	p.Met965Ile	p.M965I	ENST00000380152		965	atG/atA	11/27	1	2	FACETS	0.932	0.878	0.987	0.932	0.878	0.987	CLONAL	1	TRUE	1	0.861195949367554	2		891	608	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039134	49039134	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	174	460	0	ENST00000267163.4:c.2212A>G	p.Thr738Ala	p.T738A	ENST00000267163	NM_000321.2	738	Aca/Gca	22/27	1	2	FACETS	0.962	0.896	1	0.962	0.896	1	CLONAL	1	TRUE	1	0.861195949367554	2		460	420	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436695	110436695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	369	1033	2	ENST00000375856.3:c.1706G>A	p.Arg569Gln	p.R569Q	ENST00000375856	NM_003749.2	569	cGa/cAa	1/2	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.861195949367554	2		1035	795	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609582	81609582	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	286	815	0	ENST00000298171.2:c.1180G>A	p.Glu394Lys	p.E394K	ENST00000298171	NM_000369.2	394	Gaa/Aaa	10/10	1	2	FACETS	0.921	0.871	0.972	0.921	0.871	0.972	CLONAL	1	TRUE	1	0.861195949367554	2		815	721	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610140	81610140	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	261	661	0	ENST00000298171.2:c.1738C>G	p.Leu580Val	p.L580V	ENST00000298171	NM_000369.2	580	Ctg/Gtg	10/10	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.861195949367554	2		661	597	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95563014	95563014	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	206	692	0	ENST00000393063.1:c.4243G>A	p.Glu1415Lys	p.E1415K	ENST00000393063	NM_030621.3	1415	Gag/Aag	24/28	1	2	FACETS	0.925	0.866	0.985	0.925	0.866	0.985	CLONAL	1	TRUE	1	0.861195949367554	2		692	517	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572056	95572056	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	394	1108	0	ENST00000393063.1:c.3052G>A	p.Glu1018Lys	p.E1018K	ENST00000393063	NM_030621.3	1018	Gag/Aag	20/28	1	2	FACETS	0.99	0.945	1	0.99	0.945	1	CLONAL	1	TRUE	1	0.861195949367554	2		1108	924	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350663	89350663	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	458	1511	0	ENST00000301030.4:c.2287G>C	p.Glu763Gln	p.E763Q	ENST00000301030	NM_001256183.1	763	Gag/Cag	9/13	1	2	FACETS	0.916	0.877	0.956	0.916	0.877	0.956	CLONAL	1	TRUE	1	0.861195949367554	2		1511	1161	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684037	29684037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	288	1073	3	ENST00000356175.3:c.7735G>A	p.Glu2579Lys	p.E2579K	ENST00000356175	NM_000267.3	2579	Gaa/Aaa	52/57	1	2	FACETS	0.882	0.834	0.931	0.882	0.834	0.931	CLONAL	1	TRUE	1	0.861195949367554	2		1076	758	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428030	33428030	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	350	1023	0	ENST00000345365.6:c.929A>T	p.Asp310Val	p.D310V	ENST00000345365	NM_002878.3	310	gAc/gTc	10/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.861195949367554	2		1023	808	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618746	37618746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	295	836	0	ENST00000447079.4:c.422G>A	p.Gly141Glu	p.G141E	ENST00000447079	NM_015083.1	141	gGa/gAa	1/14	1	2	FACETS	0.986	0.934	1	0.986	0.934	1	CLONAL	1	TRUE	1	0.861195949367554	2		836	695	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372095	45372095	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	362	1105	0	ENST00000262160.6:c.1074G>C	p.Gln358His	p.Q358H	ENST00000262160	NM_005901.5	358	caG/caC	9/11	0.861195949367554	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.861195949367554	1		1105	471	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45377654	45377654	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	200	669	0	ENST00000262160.6:c.775C>G	p.His259Asp	p.H259D	ENST00000262160	NM_005901.5	259	Cat/Gat	7/11	0.861195949367554	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.861195949367554	1		669	263	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390357	56390357	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	204	832	0	ENST00000348428.3:c.1096G>A	p.Val366Met	p.V366M	ENST00000348428	NM_006785.3	366	Gtg/Atg	10/17	0.861195949367554	1	FACETS	0.921	0.878	0.962	0.921	0.878	0.962	CLONAL	1	TRUE	0	0.861195949367554	1		832	293	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218492	1218492	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	348	868	1	ENST00000326873.7:c.367del	p.Gln123ArgfsTer6	p.Q123Rfs*6	ENST00000326873	NM_000455.4	123	Cag/ag	2/10	0.861195949367554	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.861195949367554	1		869	458	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2180744	2180749	+	inframe_deletion	In_Frame_Del	DEL	CGAGAC	CGAGAC	-	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	350	1078	0	ENST00000398665.3:c.115_120del	p.Glu39_Thr40del	p.E39_T40del	ENST00000398665	NM_032482.2	38	atCGAGACc/atc	2/28	0.861195949367554	1	FACETS	0.939	0.906	0.971	0.939	0.906	0.971	CLONAL	1	TRUE	0	0.861195949367554	1		1078	493	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107030	11107030	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	207	673	1	ENST00000358026.2:c.1735G>T	p.Glu579Ter	p.E579*	ENST00000358026	NM_001128849.1	579	Gag/Tag	10/36	0.861195949367554	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.861195949367554	1		674	272	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170438	11170438	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	314	976	0	ENST00000358026.2:c.4741G>C	p.Asp1581His	p.D1581H	ENST00000358026	NM_001128849.1	1581	Gac/Cac	34/36	0.861195949367554	1	FACETS	0.998	0.964	1	0.998	0.964	1	CLONAL	1	TRUE	0	0.861195949367554	1		976	416	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170531	11170531	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	310	993	0	ENST00000358026.2:c.4834G>C	p.Glu1612Gln	p.E1612Q	ENST00000358026	NM_001128849.1	1612	Gag/Cag	34/36	0.861195949367554	1	FACETS	0.974	0.939	1	0.974	0.939	1	CLONAL	1	TRUE	0	0.861195949367554	1		993	421	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288582	15288582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1312905150	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	23	32	0	ENST00000263388.2:c.4157G>A	p.Arg1386Gln	p.R1386Q	ENST00000263388	NM_000435.2	1386	cGg/cAg	24/33	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.861195949367554	2		32	39	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791217	42791217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	368	1048	0	ENST00000575354.2:c.277G>A	p.Asp93Asn	p.D93N	ENST00000575354	NM_015125.3	93	Gac/Aac	3/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.861195949367554	2		1048	798	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793231	42793231	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	342	952	0	ENST00000575354.2:c.1123G>T	p.Glu375Ter	p.E375*	ENST00000575354	NM_015125.3	375	Gaa/Taa	7/20	1	2	FACETS	0.912	0.866	0.958	0.912	0.866	0.958	CLONAL	1	TRUE	1	0.861195949367554	2		952	871	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096291	178096291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	323	864	1	ENST00000397062.3:c.1040C>T	p.Ser347Leu	p.S347L	ENST00000397062	NM_006164.4	347	tCa/tTa	5/5	1	2	FACETS	0.973	0.924	1	0.973	0.924	1	CLONAL	1	TRUE	1	0.861195949367554	2		865	771	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190708774	190708774	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	327	1040	0	ENST00000441310.2:c.667G>C	p.Glu223Gln	p.E223Q	ENST00000441310	NM_000534.4	223	Gaa/Caa	6/13	1	2	FACETS	0.982	0.934	1	0.982	0.934	1	CLONAL	1	TRUE	1	0.861195949367554	2		1040	773	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266792	198266792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	366	651	0	ENST00000335508.6:c.2140G>A	p.Glu714Lys	p.E714K	ENST00000335508	NM_012433.2	714	Gaa/Aaa	15/25	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.861195949367554	2		651	792	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37056016	37056016	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	262	845	0	ENST00000231790.2:c.771C>G	p.Ile257Met	p.I257M	ENST00000231790	NM_000249.3	257	atC/atG	9/19	1	2	FACETS	0.908	0.856	0.961	0.908	0.856	0.961	CLONAL	1	TRUE	1	0.861195949367554	2		845	670	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162312	47162312	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs115542291	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	244	695	0	ENST00000409792.3:c.3814C>T	p.Gln1272Ter	p.Q1272*	ENST00000409792	NM_014159.6	1272	Cag/Tag	3/21	1	2	FACETS	0.957	0.902	1	0.957	0.902	1	CLONAL	1	TRUE	1	0.861195949367554	2		695	592	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165587	47165587	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1559750451	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	272	919	1	ENST00000409792.3:c.539C>T	p.Ser180Leu	p.S180L	ENST00000409792	NM_014159.6	180	tCa/tTa	3/21	1	2	FACETS	0.981	0.927	1	0.981	0.927	1	CLONAL	1	TRUE	1	0.861195949367554	2		920	644	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620479	52620479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	420	963	3	ENST00000394830.3:c.3274G>A	p.Glu1092Lys	p.E1092K	ENST00000394830	NM_018313.4	1092	Gag/Aag	21/30	1	2	FACETS	0.998	0.955	1	0.998	0.955	1	CLONAL	1	TRUE	1	0.861195949367554	2		966	977	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668829	52668829	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	203	601	1	ENST00000394830.3:c.1090G>A	p.Ala364Thr	p.A364T	ENST00000394830	NM_018313.4	364	Gca/Aca	12/30	1	2	FACETS	0.88	0.822	0.938	0.88	0.822	0.938	CLONAL	1	TRUE	1	0.861195949367554	2		602	536	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217479	142217479	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	319	937	0	ENST00000350721.4:c.5518G>C	p.Glu1840Gln	p.E1840Q	ENST00000350721	NM_001184.3	1840	Gaa/Caa	32/47	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.861195949367554	2		937	738	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081560	143081560	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	305	968	0	ENST00000262992.4:c.1514G>C	p.Arg505Thr	p.R505T	ENST00000262992	NM_001101669.1	505	aGa/aCa	15/24	1	2	FACETS	0.927	0.878	0.976	0.927	0.878	0.976	CLONAL	1	TRUE	1	0.861195949367554	2		968	764	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584674	187584674	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	341	1083	1	ENST00000441802.2:c.3359C>T	p.Ser1120Leu	p.S1120L	ENST00000441802	NM_005245.3	1120	tCa/tTa	3/27	1	2	FACETS	0.918	0.872	0.964	0.918	0.872	0.964	CLONAL	1	TRUE	1	0.861195949367554	2		1084	863	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730104	41730104	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	239	728	0	ENST00000242208.4:c.425A>T	p.Lys142Met	p.K142M	ENST00000242208	NM_002192.2	142	aAg/aTg	3/3	1	2	FACETS	0.998	0.941	1	0.998	0.941	1	CLONAL	1	TRUE	1	0.861195949367554	2		728	556	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851972	128851972	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	325	1052	1	ENST00000249373.3:c.2044G>T	p.Val682Leu	p.V682L	ENST00000249373	NM_005631.4	682	Gtg/Ttg	12/12	1	2	FACETS	0.991	0.941	1	0.991	0.941	1	CLONAL	1	TRUE	1	0.861195949367554	2		1053	762	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151892994	151892994	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	206	647	0	ENST00000262189.6:c.4376C>G	p.Ser1459Ter	p.S1459*	ENST00000262189	NM_170606.2	1459	tCa/tGa	28/59	1	2	FACETS	0.896	0.838	0.954	0.896	0.838	0.954	CLONAL	1	TRUE	1	0.861195949367554	2		647	534	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207636	29207636	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	245	842	0	ENST00000240100.2:c.160C>G	p.Leu54Val	p.L54V	ENST00000240100	NM_001394.6	54	Ctg/Gtg	1/4	1	2	FACETS	0.9	0.847	0.954	0.9	0.847	0.954	CLONAL	1	TRUE	1	0.861195949367554	2		842	632	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741860	145741860	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs749049274	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	363	1078	0	ENST00000428558.2:c.643G>C	p.Glu215Gln	p.E215Q	ENST00000428558	NM_004260.3	215	Gag/Cag	5/22	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.861195949367554	2		1078	831	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815559	139815559	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	413	1145	0	ENST00000247668.2:c.1030G>C	p.Glu344Gln	p.E344Q	ENST00000247668	NM_021138.3	344	Gag/Cag	9/11	0.861195949367554	2	FACETS	1	0.971	1	0.51	0.487	0.532	CLONAL	1	TRUE	0	0.861195949367554	2		1145	941	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184073	123184073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	271	919	0	ENST00000218089.9:c.931G>A	p.Glu311Lys	p.E311K	ENST00000218089	NM_001042749.1	311	Gag/Aag	11/35	1	2	FACETS	0.954	0.901	1	0.954	0.901	1	CLONAL	1	TRUE	1	0.861195949367554	2		919	660	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0020134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	13	786	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.661	0.471	0.894	0.661	0.471	0.894	SUBCLONAL	1	TRUE	1	0.14	2		786	281	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604673	48604673	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060500738	NA	P-0020134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	34	720	0	ENST00000342988.3:c.1495T>C	p.Cys499Arg	p.C499R	ENST00000342988	NM_005359.5	499	Tgc/Cgc	12/12	1	2	FACETS	0.979	0.805	1	1	0.962	1	CLONAL	2	TRUE	1	0.14	2		720	248	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578428	+	frameshift_variant	Frame_Shift_Del	DEL	CAACCTCCGTCATGTG	CAACCTCCGTCATGTG	-	novel	NA	P-0020134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	131	852	25	ENST00000269305.4:c.502_517del	p.His168Ter	p.H168*	ENST00000269305	NM_001126112.2	168	CACATGACGGAGGTTGtg/tg	5/11	0.295602661629113	1	FACETS	1	0.942	1	1	0.993	1	CLONAL	4	TRUE	0	0.14	1		877	420	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0020135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	72	399	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	0.347650915951913	1	FACETS	0.847	0.744	0.958	0.847	0.744	0.958	CLONAL	1	TRUE	0	0.347650915951913	1		399	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0020135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	136	843	2	ENST00000269305.4:c.673-2A>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.347650915951913	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.347650915951913	1		845	631	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0020139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	550	644	1	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.589825513297225	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.911025406809754	1		645	640	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188188	32188188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370312303	NA	P-0020139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	307	759	0	ENST00000375023.3:c.1153C>T	p.Arg385Cys	p.R385C	ENST00000375023	NM_004557.3	385	Cgc/Tgc	6/30	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.911025406809754	2		759	654	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526347	31526347	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1452	545	1358	0	ENST00000344624.3:c.693C>G	p.His231Gln	p.H231Q	ENST00000344624		231	caC/caG	2/33	0.584114283742772	4	FACETS	1	0.992	1	0.382	0.365	0.399	CLONAL	1	TRUE	1	0.911025406809754	4		1358	1997	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578281	7578281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	364	1046	1	ENST00000269305.4:c.568C>T	p.Pro190Ser	p.P190S	ENST00000269305	NM_001126112.2	190	Cct/Tct	6/11	0.838475712891212	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.839447446785726	1		1047	503	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	59	891	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.773	0.665	0.891	0.773	0.665	0.891	SUBCLONAL	1	TRUE	1	0.24	2		891	636	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	86	685	5	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.24	2		690	677	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	64	778	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	1	2	FACETS	0.898	0.778	1	0.898	0.778	1	CLONAL	1	TRUE	1	0.24	2		778	594	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	83	751	2	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.24	2		753	646	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	29	453	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.685	0.55	0.838	0.685	0.55	0.838	SUBCLONAL	1	TRUE	1	0.24	2		453	353	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109924	115109924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754142951	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	36	890	2	ENST00000257566.3:c.1954G>A	p.Gly652Ser	p.G652S	ENST00000257566	NM_016569.3	652	Ggc/Agc	8/8	1	2	FACETS	0.462	0.379	0.556	0.462	0.379	0.556	SUBCLONAL	1	TRUE	1	0.24	2		892	649	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	56	844	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	1	2	FACETS	0.69	0.591	0.8	0.69	0.591	0.8	SUBCLONAL	1	TRUE	1	0.24	2		844	676	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	71	837	2	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.989	0.864	1	0.989	0.864	1	CLONAL	1	TRUE	1	0.24	2		839	598	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497245	149497245	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	94	1044	3	ENST00000261799.4:c.3073del	p.Leu1025CysfsTer20	p.L1025Cfs*20	ENST00000261799	NM_002609.3	1025	Ctg/tg	22/23	1	2	FACETS	0.947	0.842	1	0.947	0.842	1	CLONAL	1	TRUE	1	0.24	2		1047	827	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247367	153247367	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	41	574	1	ENST00000281708.4:c.1435C>T	p.Arg479Ter	p.R479*	ENST00000281708	NM_033632.3	479	Cga/Tga	10/12	1	2	FACETS	0.702	0.584	0.832	0.702	0.584	0.832	SUBCLONAL	1	TRUE	1	0.24	2		575	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	33	872	0	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	1	2	FACETS	0.325	0.263	0.395	0.325	0.263	0.395	SUBCLONAL	1	TRUE	1	0.24	2		872	847	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843374	128843374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772755154	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	110	937	4	ENST00000249373.3:c.481C>T	p.Arg161Trp	p.R161W	ENST00000249373	NM_005631.4	161	Cgg/Tgg	2/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.24	2		941	730	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007731	62007731	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1443194987	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	25	510	0	ENST00000392795.3:c.136C>T	p.Arg46Trp	p.R46W	ENST00000392795	NM_001039933.1	46	Cgg/Tgg	3/6	1	2	FACETS	0.483	0.38	0.602	0.483	0.38	0.602	SUBCLONAL	1	TRUE	1	0.24	2		510	431	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821890	72821890	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	78	506	0	ENST00000268489.5:c.10285del	p.Arg3429ValfsTer56	p.R3429Vfs*56	ENST00000268489	NM_006885.3	3429	Cgt/gt	10/10	1	2	FACETS	0.998	0.878	1	0.998	0.878	1	CLONAL	1	TRUE	1	0.24	2		506	651	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001374	150001374	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	56	1107	2	ENST00000253339.5:c.2230C>T	p.Arg744Ter	p.R744*	ENST00000253339		744	Cga/Tga	4/7	1	2	FACETS	0.814	0.698	0.942	0.814	0.698	0.942	CLONAL	1	TRUE	1	0.24	2		1109	573	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243960	5243960	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1260947679	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	57	771	1	ENST00000357368.4:c.1522G>A	p.Gly508Ser	p.G508S	ENST00000357368	NM_002850.3	508	Ggc/Agc	11/38	1	2	FACETS	0.714	0.612	0.826	0.714	0.612	0.826	SUBCLONAL	1	TRUE	1	0.24	2		772	665	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	30	855	8	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	1	2	FACETS	0.512	0.412	0.626	0.512	0.412	0.626	SUBCLONAL	1	TRUE	1	0.24	2		863	488	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	77	518	0	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	1	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.24	1		518	384	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713345	30713345	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748195637	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	34	732	0	ENST00000295754.5:c.670C>T	p.Arg224Cys	p.R224C	ENST00000295754	NM_003242.5	224	Cgc/Tgc	4/7	1	2	FACETS	0.468	0.382	0.566	0.468	0.382	0.566	SUBCLONAL	1	TRUE	1	0.24	2		732	605	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485403	57485403	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1394557997	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	46	627	0	ENST00000371085.3:c.985G>A	p.Gly329Arg	p.G329R	ENST00000371085	NM_000516.4	329	Gga/Aga	12/13	1	2	FACETS	0.753	0.634	0.884	0.753	0.634	0.884	SUBCLONAL	1	TRUE	1	0.24	2		627	509	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288969	212288969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148791072	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	58	1012	2	ENST00000342788.4:c.2777C>T	p.Thr926Met	p.T926M	ENST00000342788	NM_005235.2	926	aCg/aTg	23/28	1	2	FACETS	0.917	0.789	1	0.917	0.789	1	CLONAL	1	TRUE	1	0.24	2		1014	527	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119909	70119910	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	77	765	2	ENST00000245479.2:c.916dup	p.Val306GlyfsTer272	p.V306Gfs*272	ENST00000245479	NM_000346.3	304	ccg/ccGg	3/3	1	2	FACETS	0.925	0.811	1	0.925	0.811	1	CLONAL	1	TRUE	1	0.24	2		767	694	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612344	1612344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1320707074	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	104	1071	2	ENST00000344749.5:c.1675G>A	p.Val559Met	p.V559M	ENST00000344749	NM_001136139.2	559	Gtg/Atg	18/19	1	2	FACETS	0.919	0.822	1	0.919	0.822	1	CLONAL	1	TRUE	1	0.24	2		1073	943	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780289	9780289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201282174	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	45	685	5	ENST00000377346.4:c.1459G>A	p.Ala487Thr	p.A487T	ENST00000377346	NM_005026.3	487	Gcc/Acc	11/24	1	2	FACETS	0.692	0.581	0.815	0.692	0.581	0.815	SUBCLONAL	1	TRUE	1	0.24	2		690	542	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279530	1279530	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	101	1134	1	ENST00000310581.5:c.2006G>A	p.Arg669Gln	p.R669Q	ENST00000310581	NM_198253.2	669	cGg/cAg	5/16	1	2	FACETS	0.971	0.867	1	0.971	0.867	1	CLONAL	1	TRUE	1	0.24	2		1135	867	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	105	1075	2	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.24	2		1077	825	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224124	36224124	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	43	903	0	ENST00000222270.7:c.6678del	p.Thr2227ArgfsTer34	p.T2227Rfs*34	ENST00000222270	NM_014727.1	2225	tCc/tc	28/37	1	2	FACETS	0.531	0.443	0.629	0.531	0.443	0.629	SUBCLONAL	1	TRUE	1	0.24	2		903	675	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862845	9862845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764289741	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	91	968	1	ENST00000330684.3:c.2458G>A	p.Val820Ile	p.V820I	ENST00000330684	NM_001134407.1	820	Gta/Ata	12/13	1	2	FACETS	0.94	0.834	1	0.94	0.834	1	CLONAL	1	TRUE	1	0.24	2		969	807	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097688	27097688	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	98	1022	0	ENST00000324856.7:c.3281del	p.Lys1094SerfsTer67	p.K1094Sfs*67	ENST00000324856	NM_006015.4	1093	Aaa/aa	12/20	1	2	FACETS	0.921	0.82	1	0.921	0.82	1	CLONAL	1	TRUE	1	0.24	2		1022	887	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798454	45798454	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	122	1004	0	ENST00000450313.1:c.557T>A	p.Leu186Gln	p.L186Q	ENST00000450313	NM_012222.2	186	cTg/cAg	7/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.24	2		1004	903	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298104	123298104	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	50	806	0	ENST00000358487.5:c.748+2T>G		p.X250_splice	ENST00000358487	NM_000141.4	250			1	2	FACETS	0.545	0.461	0.637	0.545	0.461	0.637	SUBCLONAL	1	TRUE	1	0.24	2		806	765	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198960	67198960	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	56	780	0	ENST00000312629.5:c.431T>C	p.Leu144Pro	p.L144P	ENST00000312629	NM_003952.2	144	cTc/cCc	5/15	1	2	FACETS	0.7	0.599	0.81	0.7	0.599	0.81	SUBCLONAL	1	TRUE	1	0.24	2		780	667	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999337	100999337	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	96	1094	1	ENST00000325455.5:c.465del	p.Ala156ProfsTer10	p.A156Pfs*10	ENST00000325455	NM_001202474.3	155	ccC/cc	1/8	1	2	FACETS	0.942	0.839	1	0.942	0.839	1	CLONAL	1	TRUE	1	0.24	2		1095	849	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394723	394723	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	54	977	0	ENST00000399788.2:c.4972T>G	p.Cys1658Gly	p.C1658G	ENST00000399788	NM_001042603.1	1658	Tgt/Ggt	28/28	0.3	2	FACETS	0.578	0.493	0.673			1	SUBCLONAL	1	TRUE	NA	0.24	2		977	778	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432497	49432497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775911186	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	74	783	0	ENST00000301067.7:c.8642G>A	p.Arg2881Gln	p.R2881Q	ENST00000301067	NM_003482.3	2881	cGg/cAg	34/54	1	2	FACETS	0.802	0.701	0.911	0.802	0.701	0.911	CLONAL	1	TRUE	1	0.24	2		783	769	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112404	115112404	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	76	750	0	ENST00000257566.3:c.1336A>G	p.Thr446Ala	p.T446A	ENST00000257566	NM_016569.3	446	Act/Gct	7/8	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.24	2		750	621	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563152	21563152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774128777	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	85	963	1	ENST00000382592.4:c.767C>T	p.Pro256Leu	p.P256L	ENST00000382592	NM_014572.2	256	cCg/cTg	4/8	1	2	FACETS	0.956	0.845	1	0.956	0.845	1	CLONAL	1	TRUE	1	0.24	2		964	741	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560418	95560418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	98	861	2	ENST00000393063.1:c.5171C>T	p.Pro1724Leu	p.P1724L	ENST00000393063	NM_030621.3	1724	cCg/cTg	25/28	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.24	2		863	806	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293027	91293027	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	35	963	0	ENST00000355112.3:c.531del	p.Phe177LeufsTer2	p.F177Lfs*2	ENST00000355112	NM_000057.2	177	Ttt/tt	3/22	1	2	FACETS	0.425	0.347	0.513	0.425	0.347	0.513	SUBCLONAL	1	TRUE	1	0.24	2		963	686	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662322	67662322	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs112271126	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	80	802	0	ENST00000264010.4:c.1568A>G	p.Tyr523Cys	p.Y523C	ENST00000264010	NM_006565.3	523	tAc/tGc	9/12	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.24	2		802	627	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872075	37872075	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	51	1033	0	ENST00000269571.5:c.1396G>C	p.Ala466Pro	p.A466P	ENST00000269571		466	Gcc/Ccc	12/27	1	2	FACETS	0.477	0.404	0.558	0.477	0.404	0.558	SUBCLONAL	1	TRUE	1	0.24	2		1033	891	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245584	41245584	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	59	1109	0	ENST00000357654.3:c.1964A>G	p.Tyr655Cys	p.Y655C	ENST00000357654	NM_007294.3	655	tAc/tGc	10/23	1	2	FACETS	0.561	0.481	0.649	0.561	0.481	0.649	SUBCLONAL	1	TRUE	1	0.24	2		1109	876	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761361	59761361	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	92	861	2	ENST00000259008.2:c.3046del	p.Ile1016TyrfsTer43	p.I1016Yfs*43	ENST00000259008	NM_032043.2	1016	Ata/ta	20/20	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.24	2		863	723	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097039	11097039	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	93	1044	0	ENST00000358026.2:c.530T>C	p.Leu177Pro	p.L177P	ENST00000358026	NM_001128849.1	177	cTg/cCg	4/36	1	2	FACETS	0.956	0.849	1	0.956	0.849	1	CLONAL	1	TRUE	1	0.24	2		1044	811	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272054	15272054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	104	854	0	ENST00000263388.2:c.6385G>A	p.Ala2129Thr	p.A2129T	ENST00000263388	NM_000435.2	2129	Gct/Act	33/33	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.24	2		854	707	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278019	18278019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762411607	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	46	847	1	ENST00000222254.8:c.1639C>T	p.Arg547Trp	p.R547W	ENST00000222254	NM_005027.3	547	Cgg/Tgg	13/16	1	2	FACETS	0.482	0.404	0.568	0.482	0.404	0.568	SUBCLONAL	1	TRUE	1	0.24	2		848	796	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471099	25471099	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	102	1008	0	ENST00000264709.3:c.662T>G	p.Ile221Ser	p.I221S	ENST00000264709	NM_175629.2	221	aTt/aGt	7/23	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.24	2		1008	830	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248446	212248446	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	26	615	0	ENST00000342788.4:c.3821T>C	p.Ile1274Thr	p.I1274T	ENST00000342788	NM_005235.2	1274	aTc/aCc	28/28	1	2	FACETS	0.43	0.34	0.534	0.43	0.34	0.534	SUBCLONAL	1	TRUE	1	0.24	2		615	504	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660553	227660553	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373195857	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	48	756	1	ENST00000305123.5:c.2902G>A	p.Ala968Thr	p.A968T	ENST00000305123	NM_005544.2	968	Gca/Aca	1/2	1	2	FACETS	0.653	0.551	0.765	0.653	0.551	0.765	SUBCLONAL	1	TRUE	1	0.24	2		757	613	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023284	31023284	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	35	926	0	ENST00000375687.4:c.2769G>T	p.Glu923Asp	p.E923D	ENST00000375687	NM_015338.5	923	gaG/gaT	13/13	1	2	FACETS	0.428	0.35	0.517	0.428	0.35	0.517	SUBCLONAL	1	TRUE	1	0.24	2		926	681	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375142	31375142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537913125	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	91	1030	2	ENST00000328111.2:c.539C>T	p.Thr180Met	p.T180M	ENST00000328111	NM_006892.3	180	aCg/aTg	6/23	1	2	FACETS	0.925	0.82	1	0.925	0.82	1	CLONAL	1	TRUE	1	0.24	2		1032	820	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551047	41551047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1195853173	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	86	953	3	ENST00000263253.7:c.3191C>T	p.Ala1064Val	p.A1064V	ENST00000263253	NM_001429.3	1064	gCa/gTa	17/31	1	2	FACETS	0.826	0.729	0.929	0.826	0.729	0.929	CLONAL	1	TRUE	1	0.24	2		956	868	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035155	37035155	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs267607709	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	48	534	0	ENST00000231790.2:c.116+1G>T		p.X39_splice	ENST00000231790	NM_000249.3	39			1	2	FACETS	0.837	0.708	0.979	0.837	0.708	0.979	CLONAL	1	TRUE	1	0.24	2		534	478	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067140	37067140	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1437454428	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	36	521	1	ENST00000231790.2:c.1051G>T	p.Gly351Ter	p.G351*	ENST00000231790	NM_000249.3	351	Gga/Tga	12/19	1	2	FACETS	0.775	0.638	0.929	0.775	0.638	0.929	CLONAL	1	TRUE	1	0.24	2		522	387	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911480	134911480	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	69	942	0	ENST00000398015.3:c.1945G>A	p.Ala649Thr	p.A649T	ENST00000398015	NM_004441.4	649	Gcc/Acc	11/16	1	2	FACETS	0.734	0.639	0.838	0.734	0.639	0.838	SUBCLONAL	1	TRUE	1	0.24	2		942	783	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750489	41750490	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	40	777	2	ENST00000226382.2:c.138_139delinsTT	p.Ile47Leu	p.I47L	ENST00000226382	NM_003924.3	46	ccGAta/ccTTta	1/3	1	2	FACETS	0.548	0.455	0.653	0.548	0.455	0.653	SUBCLONAL	1	TRUE	1	0.24	2		779	608	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197299	106197299	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	54	586	0	ENST00000380013.4:c.5632C>A	p.Arg1878Ser	p.R1878S	ENST00000380013	NM_001127208.2	1878	Cgt/Agt	11/11	1	2	FACETS	0.966	0.826	1	0.966	0.826	1	CLONAL	1	TRUE	1	0.24	2		586	466	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540992	187540992	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	60	678	0	ENST00000441802.2:c.6748T>C	p.Tyr2250His	p.Y2250H	ENST00000441802	NM_005245.3	2250	Tat/Cat	10/27	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.24	2		678	430	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639097	176639097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771467409	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	66	920	0	ENST00000439151.2:c.3697C>T	p.Arg1233Trp	p.R1233W	ENST00000439151	NM_022455.4	1233	Cgg/Tgg	5/23	1	2	FACETS	0.678	0.587	0.777	0.678	0.587	0.777	SUBCLONAL	1	TRUE	1	0.24	2		920	811	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056458	26056458	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	23	486	0	ENST00000343677.2:c.199G>C	p.Ala67Pro	p.A67P	ENST00000343677	NM_005319.3	67	Gct/Cct	1/1	1	2	FACETS	0.47	0.366	0.591	0.47	0.366	0.591	SUBCLONAL	1	TRUE	1	0.24	2		486	408	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845973	151845973	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	96	858	3	ENST00000262189.6:c.13039C>T	p.Pro4347Ser	p.P4347S	ENST00000262189	NM_170606.2	4347	Ccg/Tcg	52/59	1	2	FACETS	0.986	0.878	1	0.986	0.878	1	CLONAL	1	TRUE	1	0.24	2		861	811	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849897	151849897	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	45	655	0	ENST00000262189.6:c.12419A>C	p.Gln4140Pro	p.Q4140P	ENST00000262189	NM_170606.2	4140	cAg/cCg	49/59	1	2	FACETS	0.551	0.462	0.65	0.551	0.462	0.65	SUBCLONAL	1	TRUE	1	0.24	2		655	680	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500893	8500893	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	56	969	0	ENST00000356435.5:c.1989G>C	p.Leu663Phe	p.L663F	ENST00000356435		663	ttG/ttC	13/35	1	2	FACETS	0.603	0.515	0.699	0.603	0.515	0.699	SUBCLONAL	1	TRUE	1	0.24	2		969	774	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209367	98209367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45535032	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	76	767	2	ENST00000331920.6:c.4171C>T	p.Arg1391Trp	p.R1391W	ENST00000331920	NM_000264.3	1391	Cgg/Tgg	23/24	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.24	2		769	567	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937723	44937723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	62	450	0	ENST00000377967.4:c.2911C>T	p.Arg971Cys	p.R971C	ENST00000377967	NM_021140.2	971	Cgt/Tgt	19/29	1	1	FACETS	0.771	0.671	0.877	1	0.973	1	SUBCLONAL	2	TRUE	0	0.24	1		450	295	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422464	47422464	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	41	468	0	ENST00000377045.4:c.96+2T>C		p.X32_splice	ENST00000377045	NM_001654.4	32			1	1	FACETS	0.716	0.597	0.848	0.716	0.597	0.848	SUBCLONAL	1	TRUE	0	0.24	1		468	420	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53253924	53253924	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	66	352	1	ENST00000375401.3:c.148G>A	p.Ala50Thr	p.A50T	ENST00000375401	NM_004187.3	50	Gcg/Acg	1/26	1	1	FACETS	0.776	0.679	0.879	1	0.975	1	SUBCLONAL	2	TRUE	0	0.24	1		353	312	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098953	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	76	551	0	ENST00000397062.3:c.92G>C	p.Gly31Ala	p.G31A	ENST00000397062	NM_006164.4	31	gGa/gCa	2/5	1	2	FACETS	0.945	0.829	1	0.945	0.829	1	CLONAL	1	TRUE	1	0.26954619792137	2		551	597	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163295915	163295915	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	109	1141	1	ENST00000271452.3:c.74G>T	p.Gly25Val	p.G25V	ENST00000271452	NM_145697.2	25	gGa/gTa	2/14	0.26954619792137	3	FACETS	0.771	0.69	0.857	0.385	0.345	0.429	SUBCLONAL	1	TRUE	1	0.26954619792137	3		1142	1191	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827316	72827316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371948268	NA	P-0020147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	119	1020	1	ENST00000268489.5:c.9265G>A	p.Glu3089Lys	p.E3089K	ENST00000268489	NM_006885.3	3089	Gag/Aag	9/10	1	2	FACETS	0.907	0.818	1	0.907	0.818	1	CLONAL	1	TRUE	1	0.26954619792137	2		1021	973	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111404	56111405	+	missense_variant	Missense_Mutation	DNP	GC	GC	AT	novel	NA	P-0020147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	137	545	0	ENST00000399503.3:c.4_5delinsAT	p.Ala2Met	p.A2M	ENST00000399503	NM_005921.1	2	GCg/ATg	1/20	0.26954619792137	3	FACETS	0.942	0.86	1	0.942	0.86	1	CLONAL	2	TRUE	1	0.26954619792137	3		545	612	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043438	180043438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373876329	NA	P-0020147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	137	1143	2	ENST00000261937.6:c.3148G>A	p.Val1050Met	p.V1050M	ENST00000261937	NM_182925.4	1050	Gtg/Atg	23/30	0.171585615739596	3	FACETS	1	0.93	1			1	CLONAL	1	TRUE	NA	0.26954619792137	3		1145	1121	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396248	139396248	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	384	1138	0	ENST00000277541.6:c.5590del	p.Gln1864ArgfsTer23	p.Q1864Rfs*23	ENST00000277541	NM_017617.3	1864	Cag/ag	30/34	0.253515783770022	3	FACETS	0.952	0.905	0.999	0.952	0.905	0.999	CLONAL	3	TRUE	0	0.26954619792137	3		1138	1132	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0020148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	465	1157	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.594567847485026	2	FACETS	0.817	0.785	0.849	0.817	0.785	0.849	CLONAL	2	TRUE	0	0.612658415452403	2		1157	929	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0020148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	85	673	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.560731579020352	2	FACETS	0.442	0.391	0.497	0.221	0.195	0.249	SUBCLONAL	1	TRUE	0	0.612658415452403	2		673	628	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412610	63412610	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	146	552	1	ENST00000330258.3:c.557G>T	p.Gly186Val	p.G186V	ENST00000330258	NM_152424.3	186	gGg/gTg	2/2	1	1	FACETS	0.801	0.738	0.864	0.801	0.738	0.864	CLONAL	1	TRUE	0	0.612658415452403	1		553	413	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118365075	118365075	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs886041896	NA	P-0020148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	137	1199	1	ENST00000534358.1:c.5251A>T	p.Lys1751Ter	p.K1751*	ENST00000534358	NM_005933.3	1751	Aaa/Taa	17/36	1	2	FACETS	0.877	0.802	0.954	0.877	0.802	0.954	CLONAL	1	TRUE	1	0.612658415452403	2		1200	510	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092851	27092855	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TCTGC	TCTGC	GCT	novel	NA	P-0020148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	55	1170	3	ENST00000324856.7:c.2872_2876delinsGCT	p.Ser958AlafsTer48	p.S958Afs*48	ENST00000324856	NM_006015.4	958	TCTGCa/GCTa	9/20	0.398958056583087	3	FACETS	0.39	0.333	0.452	0.13	0.111	0.151	SUBCLONAL	1	TRUE	0	0.612658415452403	3		1173	601	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918520	94918520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	24	1138	0	ENST00000536441.1:c.662C>T	p.Ser221Phe	p.S221F	ENST00000536441	NM_144665.3	221	tCc/tTc	5/10	1	2	FACETS	0.166	0.129	0.208	0.166	0.129	0.208	SUBCLONAL	1	TRUE	1	0.612658415452403	2		1138	472	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437546	110437546	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	287	1261	0	ENST00000375856.3:c.855G>T	p.Glu285Asp	p.E285D	ENST00000375856	NM_003749.2	285	gaG/gaT	1/2	1	2	FACETS	0.928	0.873	0.983	0.928	0.873	0.983	CLONAL	1	TRUE	1	0.612658415452403	2		1261	1010	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430799	181430799	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1368	268	1362	0	ENST00000325404.1:c.651G>C	p.Met217Ile	p.M217I	ENST00000325404	NM_003106.3	217	atG/atC	1/1	0.19211293091243	6	FACETS	1	0.986	1	0.397	0.371	0.424	INDETERMINATE	1	TRUE	3	0.612658415452403	6		1362	1636	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455611	189455628	+	inframe_deletion	In_Frame_Del	DEL	TTCCTCAGTCCAGAGGTT	TTCCTCAGTCCAGAGGTT	-	novel	NA	P-0020148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	95	1175	0	ENST00000264731.3:c.149_166del	p.Leu50_Phe55del	p.L50_F55del	ENST00000264731	NM_003722.4	49	TTCCTCAGTCCAGAGGTT/-	2/14	0.19211293091243	6	FACETS	0.887	0.789	0.991	0.296	0.263	0.331	INDETERMINATE	1	TRUE	3	0.612658415452403	6		1175	778	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68999996	68999996	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	159	1172	2	ENST00000288368.4:c.2065T>C	p.Phe689Leu	p.F689L	ENST00000288368	NM_024870.2	689	Ttc/Ctc	19/40	1	2	FACETS	0.839	0.772	0.908	0.839	0.772	0.908	CLONAL	1	TRUE	1	0.612658415452403	2		1174	619	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449746	8449746	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	113	1084	1	ENST00000356435.5:c.3967C>A	p.Arg1323Ser	p.R1323S	ENST00000356435		1323	Cgc/Agc	23/35	0.560731579020352	2	FACETS	0.642	0.579	0.707	0.321	0.289	0.354	SUBCLONAL	1	TRUE	0	0.612658415452403	2		1085	575	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031791	11031791	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	65	1142	0	ENST00000327064.4:c.1603C>G	p.Leu535Val	p.L535V	ENST00000327064	NM_199141.1	535	Ctg/Gtg	14/16	1	2	FACETS	0.801	0.692	0.92	0.801	0.692	0.92	CLONAL	1	TRUE	1	0.15	2		1142	1082	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436661	52436661	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	108	1132	1	ENST00000460680.1:c.2013C>A	p.Tyr671Ter	p.Y671*	ENST00000460680	NM_004656.3	671	taC/taA	16/17	1	2	FACETS	0.787	0.705	0.874	1	0.984	1	SUBCLONAL	2	TRUE	1	0.15	2		1133	915	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231707	66231707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1211795184	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	51	737	1	ENST00000273854.3:c.1993G>A	p.Glu665Lys	p.E665K	ENST00000273854	NM_004439.5	665	Gaa/Aaa	11/18	0.154340119625568	1	FACETS	0.875	0.744	1	0.875	0.744	1	CLONAL	1	TRUE	0	0.18	1		738	589	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390539	139390539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774680812	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	54	964	1	ENST00000277541.6:c.7652C>T	p.Pro2551Leu	p.P2551L	ENST00000277541	NM_017617.3	2551	cCg/cTg	34/34	1	2	FACETS	0.68	0.579	0.792	0.68	0.579	0.792	SUBCLONAL	1	TRUE	1	0.18	2		965	882	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520724	176520724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	55	831	0	ENST00000292408.4:c.1467G>A	p.Met489Ile	p.M489I	ENST00000292408	NM_213647.1	489	atG/atA	11/18	1	2	FACETS	0.745	0.636	0.865	0.745	0.636	0.865	SUBCLONAL	1	TRUE	1	0.18	2		831	820	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574004	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	79	970	3	ENST00000269305.4:c.1023_1024delinsTT	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	341	ttCCga/ttTTga	10/11	1	2	FACETS	0.922	0.809	1	0.922	0.809	1	CLONAL	1	TRUE	1	0.18	2		973	952	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521384	8521384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777779009	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	34	837	0	ENST00000356435.5:c.854G>A	p.Gly285Glu	p.G285E	ENST00000356435		285	gGa/gAa	9/35	1	2	FACETS	0.583	0.475	0.705	0.583	0.475	0.705	SUBCLONAL	1	TRUE	1	0.18	2		837	648	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961408	41961408	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	63	678	0	ENST00000219905.7:c.316C>T	p.Pro106Ser	p.P106S	ENST00000219905	NM_001164273.1	106	Cct/Tct	2/24	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.18	2		678	606	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366928	40366928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	51	729	0	ENST00000397332.2:c.269C>T	p.Pro90Leu	p.P90L	ENST00000397332	NM_001033082.2	90	cCc/cTc	2/3	1	2	FACETS	0.913	0.775	1	0.913	0.775	1	CLONAL	1	TRUE	1	0.18	2		729	621	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045954	26045954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	48	594	1	ENST00000540144.1:c.316G>A	p.Glu106Lys	p.E106K	ENST00000540144	NM_003531.2	106	Gaa/Aaa	1/1	1	2	FACETS	0.758	0.639	0.889	0.758	0.639	0.889	SUBCLONAL	1	TRUE	1	0.18	2		595	704	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857097	9857097	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	23	502	0	ENST00000330684.3:c.4304A>G	p.Lys1435Arg	p.K1435R	ENST00000330684	NM_001134407.1	1435	aAg/aGg	13/13	1	2	FACETS	0.799	0.623	1	0.799	0.623	1	CLONAL	1	TRUE	1	0.18	2		502	320	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81962179	81962179	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	73	881	1	ENST00000359376.3:c.2531C>T	p.Pro844Leu	p.P844L	ENST00000359376	NM_002661.3	844	cCc/cTc	24/33	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.18	2		882	734	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431588	49431588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1305161243	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	42	838	1	ENST00000301067.7:c.9551C>T	p.Ser3184Phe	p.S3184F	ENST00000301067	NM_003482.3	3184	tCc/tTc	34/54	0.199649759768245	3	FACETS	0.639	0.532	0.759	0.32	0.266	0.38	SUBCLONAL	1	TRUE	1	0.18	3		839	796	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609087	43609087	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	49	1003	0	ENST00000355710.3:c.1843G>A	p.Glu615Lys	p.E615K	ENST00000355710	NM_020975.4	615	Gag/Aag	10/20	1	2	FACETS	0.746	0.63	0.874	0.746	0.63	0.874	SUBCLONAL	1	TRUE	1	0.18	2		1003	730	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169212	119169212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1433717520	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	44	650	0	ENST00000264033.4:c.2396C>T	p.Ser799Phe	p.S799F	ENST00000264033	NM_005188.3	799	tCc/tTc	15/16	1	2	FACETS	0.701	0.587	0.829	0.701	0.587	0.829	SUBCLONAL	1	TRUE	1	0.18	2		650	697	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780275	9780275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	62	722	0	ENST00000377346.4:c.1445C>T	p.Pro482Leu	p.P482L	ENST00000377346	NM_005026.3	482	cCc/cTc	11/24	1	2	FACETS	0.948	0.817	1	0.948	0.817	1	CLONAL	1	TRUE	1	0.18	2		722	727	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257170	16257170	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	74	879	0	ENST00000375759.3:c.4435G>A	p.Asp1479Asn	p.D1479N	ENST00000375759	NM_015001.2	1479	Gat/Aat	11/15	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.18	2		879	757	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101406	27101406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	73	605	0	ENST00000324856.7:c.4688C>T	p.Pro1563Leu	p.P1563L	ENST00000324856	NM_006015.4	1563	cCc/cTc	18/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.18	2		605	666	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932082	36932082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	48	710	0	ENST00000361632.4:c.2387C>T	p.Pro796Leu	p.P796L	ENST00000361632		796	cCc/cTc	16/16	1	2	FACETS	0.848	0.716	0.994	0.848	0.716	0.994	CLONAL	1	TRUE	1	0.18	2		710	629	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125499337	125499337	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	65	728	0	ENST00000428830.2:c.406C>T	p.Leu136Phe	p.L136F	ENST00000428830	NM_001114121.2	136	Ctt/Ttt	5/14	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.18	2		728	697	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230543	46230543	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	55	569	0	ENST00000334344.6:c.792G>A	p.Trp264Ter	p.W264*	ENST00000334344	NM_152641.2	264	tgG/tgA	8/21	0.199649759768245	3	FACETS	1	0.945	1	0.614	0.526	0.712	CLONAL	1	TRUE	1	0.18	3		569	542	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233249	46233249	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs865903558	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	62	573	1	ENST00000334344.6:c.1468C>T	p.Gln490Ter	p.Q490*	ENST00000334344	NM_152641.2	490	Caa/Taa	11/21	0.199649759768245	3	FACETS	1	0.958	1	0.648	0.56	0.744	CLONAL	1	TRUE	1	0.18	3		574	579	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285873	46285873	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753168445	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	98	768	0	ENST00000334344.6:c.5141C>T	p.Ser1714Phe	p.S1714F	ENST00000334344	NM_152641.2	1714	tCt/tTt	18/21	0.199649759768245	3	FACETS	0.78	0.695	0.87	0.78	0.695	0.87	SUBCLONAL	2	TRUE	1	0.18	3		768	761	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416133	49416133	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1422752351	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	37	472	2	ENST00000301067.7:c.16342C>T	p.Arg5448Ter	p.R5448*	ENST00000301067	NM_003482.3	5448	Cga/Tga	52/54	0.199649759768245	3	FACETS	0.81	0.667	0.971	0.405	0.333	0.486	CLONAL	1	TRUE	1	0.18	3		474	553	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425785	49425785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	54	729	0	ENST00000301067.7:c.12703C>T	p.Gln4235Ter	p.Q4235*	ENST00000301067	NM_003482.3	4235	Cag/Tag	39/54	0.199649759768245	3	FACETS	1	0.91	1	0.546	0.466	0.634	CLONAL	1	TRUE	1	0.18	3		729	599	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427180	49427180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	109	942	2	ENST00000301067.7:c.11308G>A	p.Gly3770Ser	p.G3770S	ENST00000301067	NM_003482.3	3770	Ggt/Agt	39/54	0.199649759768245	3	FACETS	0.763	0.685	0.846	0.763	0.685	0.846	SUBCLONAL	2	TRUE	1	0.18	3		944	865	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233178	69233178	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	38	530	0	ENST00000462284.1:c.1043C>T	p.Ser348Phe	p.S348F	ENST00000462284	NM_002392.5	348	tCt/tTt	11/11	0.199649759768245	3	FACETS	0.863	0.713	1	0.432	0.356	0.516	CLONAL	1	TRUE	1	0.18	3		530	533	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134219	41134219	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	49	544	0	ENST00000379561.5:c.1409C>T	p.Ser470Phe	p.S470F	ENST00000379561	NM_002015.3	470	tCt/tTt	2/3	1	2	FACETS	0.952	0.806	1	0.952	0.806	1	CLONAL	1	TRUE	1	0.18	2		544	572	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606103	81606103	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	63	887	1	ENST00000298171.2:c.773G>A	p.Trp258Ter	p.W258*	ENST00000298171	NM_000369.2	258	tGg/tAg	9/10	1	2	FACETS	0.894	0.772	1	0.894	0.772	1	CLONAL	1	TRUE	1	0.18	2		888	783	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034879	42034879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	48	731	0	ENST00000219905.7:c.4721C>T	p.Pro1574Leu	p.P1574L	ENST00000219905	NM_001164273.1	1574	cCa/cTa	15/24	1	2	FACETS	0.707	0.596	0.83	0.707	0.596	0.83	SUBCLONAL	1	TRUE	1	0.18	2		731	754	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748906	43748906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	67	1053	0	ENST00000382044.4:c.1900C>T	p.Pro634Ser	p.P634S	ENST00000382044	NM_001141980.1	634	Ccg/Tcg	12/28	1	2	FACETS	0.749	0.649	0.858	0.749	0.649	0.858	SUBCLONAL	1	TRUE	1	0.18	2		1053	994	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678335	88678335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	36	739	0	ENST00000360948.2:c.1201C>T	p.Pro401Ser	p.P401S	ENST00000360948	NM_001012338.2	401	Cca/Tca	9/19	1	2	FACETS	0.678	0.556	0.815	0.678	0.556	0.815	SUBCLONAL	1	TRUE	1	0.18	2		739	590	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99482452	99482452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	46	690	0	ENST00000268035.6:c.3320C>T	p.Pro1107Leu	p.P1107L	ENST00000268035	NM_000875.3	1107	cCa/cTa	18/21	1	2	FACETS	0.757	0.636	0.891	0.757	0.636	0.891	SUBCLONAL	1	TRUE	1	0.18	2		690	675	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779599	3779599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	82	1115	1	ENST00000262367.5:c.5449C>T	p.Pro1817Ser	p.P1817S	ENST00000262367	NM_004380.2	1817	Ccg/Tcg	31/31	1	2	FACETS	0.918	0.807	1	0.918	0.807	1	CLONAL	1	TRUE	1	0.18	2		1116	993	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858332	9858332	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	34	450	0	ENST00000330684.3:c.3069G>T	p.Gln1023His	p.Q1023H	ENST00000330684	NM_001134407.1	1023	caG/caT	13/13	1	2	FACETS	0.954	0.78	1	0.954	0.78	1	CLONAL	1	TRUE	1	0.18	2		450	396	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020564	14020564	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	65	814	0	ENST00000311895.7:c.535G>A	p.Glu179Lys	p.E179K	ENST00000311895	NM_005236.2	179	Gaa/Aaa	3/11	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.18	2		814	666	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868680	56868680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	48	744	0	ENST00000308159.5:c.1772G>A	p.Gly591Glu	p.G591E	ENST00000308159	NM_014669.4	591	gGa/gAa	16/22	1	2	FACETS	0.658	0.554	0.772	0.658	0.554	0.772	SUBCLONAL	1	TRUE	1	0.18	2		744	811	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350753	89350753	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886041791	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	70	995	4	ENST00000301030.4:c.2197C>T	p.Arg733Ter	p.R733*	ENST00000301030	NM_001256183.1	733	Cga/Tga	9/13	1	2	FACETS	0.927	0.807	1	0.927	0.807	1	CLONAL	1	TRUE	1	0.18	2		999	839	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89825076	89825076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	83	844	0	ENST00000389301.3:c.2890C>T	p.Leu964Phe	p.L964F	ENST00000389301	NM_000135.2	964	Ctc/Ttc	30/43	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.18	2		844	837	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577540	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	rs1555525498	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	50	877	1	ENST00000269305.4:c.741_742delinsTT	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	247	aaCCgg/aaTTgg	7/11	1	2	FACETS	0.696	0.589	0.815	0.696	0.589	0.815	SUBCLONAL	1	TRUE	1	0.18	2		878	798	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621185	1621185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1159477032	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	46	804	2	ENST00000344749.5:c.961C>T	p.Arg321Ter	p.R321*	ENST00000344749	NM_001136139.2	321	Cga/Tga	12/19	1	2	FACETS	0.746	0.627	0.878	0.746	0.627	0.878	SUBCLONAL	1	TRUE	1	0.18	2		806	685	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210686	2210686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773830034	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	86	959	1	ENST00000398665.3:c.1183C>T	p.Arg395Cys	p.R395C	ENST00000398665	NM_032482.2	395	Cgc/Tgc	14/28	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.18	2		960	864	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224189	36224190	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	56	714	2	ENST00000222270.7:c.6739_6740delinsAA	p.Gly2247Lys	p.G2247K	ENST00000222270	NM_014727.1	2247	GGa/AAa	28/37	1	2	FACETS	0.9	0.77	1	0.9	0.77	1	CLONAL	1	TRUE	1	0.18	2		716	691	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743976	41743976	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	63	1031	0	ENST00000301178.4:c.911C>T	p.Pro304Leu	p.P304L	ENST00000301178	NM_021913.4	304	cCt/cTt	7/20	1	2	FACETS	0.722	0.623	0.831	0.722	0.623	0.831	SUBCLONAL	1	TRUE	1	0.18	2		1031	969	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918786	50918786	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	73	1018	1	ENST00000440232.2:c.2656G>A	p.Glu886Lys	p.E886K	ENST00000440232	NM_002691.3	886	Gag/Aag	21/27	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.18	2		1019	780	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994308	25994308	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	51	475	1	ENST00000435504.4:c.504+1G>A		p.X168_splice	ENST00000435504		168			1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.18	2		476	529	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576775	212576775	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	25	644	0	ENST00000342788.4:c.1124G>A	p.Gly375Glu	p.G375E	ENST00000342788	NM_005235.2	375	gGg/gAg	9/28	1	2	FACETS	0.568	0.447	0.708	0.568	0.447	0.708	SUBCLONAL	1	TRUE	1	0.18	2		644	489	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022454	31022455	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TA	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	14	303	0	ENST00000375687.4:c.1939_1940delinsTA	p.Pro647Ter	p.P647*	ENST00000375687	NM_015338.5	647	CCg/TAg	13/13	1	2	FACETS	0.594	0.429	0.794	0.594	0.429	0.794	SUBCLONAL	1	TRUE	1	0.18	2		303	262	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275253	41275254	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	33	534	2	ENST00000349496.5:c.1419_1420delinsTT	p.Arg474Ter	p.R474*	ENST00000349496	NM_001904.3	473	agCCga/agTTga	9/15	1	2	FACETS	0.646	0.525	0.782	0.646	0.525	0.782	SUBCLONAL	1	TRUE	1	0.18	2		536	568	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164489	47164489	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	57	615	0	ENST00000409792.3:c.1637C>T	p.Ser546Phe	p.S546F	ENST00000409792	NM_014159.6	546	tCt/tTt	3/21	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.18	2		615	571	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014293	70014293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	41	899	0	ENST00000394351.3:c.1154C>T	p.Pro385Leu	p.P385L	ENST00000394351	NM_000248.3	385	cCc/cTc	9/9	1	2	FACETS	0.616	0.512	0.733	0.616	0.512	0.733	SUBCLONAL	1	TRUE	1	0.18	2		899	739	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582175	189582176	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	79	789	2	ENST00000264731.3:c.734_735delinsTT	p.Pro245Leu	p.P245L	ENST00000264731	NM_003722.4	245	cCC/cTT	5/14	1	2	FACETS	0.924	0.811	1	0.924	0.811	1	CLONAL	1	TRUE	1	0.18	2		791	950	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976857	55976857	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs151317075	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	51	841	0	ENST00000263923.4:c.1055C>G	p.Ala352Gly	p.A352G	ENST00000263923	NM_002253.2	352	gCg/gGg	8/30	0.154340119625568	1	FACETS	0.622	0.527	0.727	0.622	0.527	0.727	SUBCLONAL	1	TRUE	0	0.18	1		841	829	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961043	79961043	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	71	823	0	ENST00000265081.6:c.440C>T	p.Pro147Leu	p.P147L	ENST00000265081	NM_002439.4	147	cCt/cTt	3/24	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.18	2		823	738	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80024709	80024709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	80	872	2	ENST00000265081.6:c.1493C>T	p.Pro498Leu	p.P498L	ENST00000265081	NM_002439.4	498	cCt/cTt	10/24	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.18	2		874	781	SUCCESS
APC	324	MSKCC	GRCh37	5	112173365	112173365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561574669	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	40	592	1	ENST00000257430.4:c.2074C>T	p.Pro692Ser	p.P692S	ENST00000257430	NM_000038.5	692	Cct/Tct	16/16	1	2	FACETS	0.877	0.728	1	0.877	0.728	1	CLONAL	1	TRUE	1	0.18	2		593	507	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672410	30672410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	41	749	0	ENST00000376406.3:c.4550G>A	p.Gly1517Glu	p.G1517E	ENST00000376406	NM_014641.2	1517	gGa/gAa	10/15	1	2	FACETS	0.648	0.538	0.771	0.648	0.538	0.771	SUBCLONAL	1	TRUE	1	0.18	2		749	703	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940079	31940079	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	44	857	1	ENST00000375333.2:c.221G>A	p.Gly74Glu	p.G74E	ENST00000375333	NM_032454.1	74	gGa/gAa	2/8	1	2	FACETS	0.703	0.589	0.831	0.703	0.589	0.831	SUBCLONAL	1	TRUE	1	0.18	2		858	695	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93953241	93953241	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267601169	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	48	814	1	ENST00000369303.4:c.2900G>A	p.Gly967Glu	p.G967E	ENST00000369303	NM_004440.3	967	gGg/gAg	17/17	1	2	FACETS	0.874	0.738	1	0.874	0.738	1	CLONAL	1	TRUE	1	0.18	2		815	610	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967867	93967867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	45	855	1	ENST00000369303.4:c.2060G>A	p.Gly687Glu	p.G687E	ENST00000369303	NM_004440.3	687	gGg/gAg	11/17	1	2	FACETS	0.644	0.539	0.759	0.644	0.539	0.759	SUBCLONAL	1	TRUE	1	0.18	2		856	777	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112035550	112035550	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1417100825	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	52	511	0	ENST00000368678.4:c.344C>T	p.Ser115Leu	p.S115L	ENST00000368678		115	tCg/tTg	4/13	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.18	2		511	473	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708091	117708091	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	47	774	0	ENST00000368508.3:c.2086C>T	p.Pro696Ser	p.P696S	ENST00000368508	NM_002944.2	696	Cca/Tca	14/43	0.3	1	FACETS	0.843	0.71	0.989	0.843	0.71	0.989	CLONAL	1	TRUE	0	0.18	1		774	564	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710701	117710701	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	26	560	1	ENST00000368508.3:c.1571C>T	p.Ser524Phe	p.S524F	ENST00000368508	NM_002944.2	524	tCt/tTt	12/43	0.3	1	FACETS	0.578	0.457	0.717	0.578	0.457	0.717	SUBCLONAL	1	TRUE	0	0.18	1		561	455	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419979	152419979	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	52	841	0	ENST00000206249.3:c.1666G>A	p.Gly556Arg	p.G556R	ENST00000206249	NM_000125.3	556	Gga/Aga	8/8	1	2	FACETS	0.699	0.594	0.816	0.699	0.594	0.816	SUBCLONAL	1	TRUE	1	0.18	2		841	826	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954927	2954927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	54	884	0	ENST00000396946.4:c.2783G>A	p.Gly928Glu	p.G928E	ENST00000396946	NM_032415.4	928	gGg/gAg	21/25	1	2	FACETS	0.805	0.686	0.936	0.805	0.686	0.936	CLONAL	1	TRUE	1	0.18	2		884	745	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979529	2979529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	54	736	0	ENST00000396946.4:c.718G>A	p.Glu240Lys	p.E240K	ENST00000396946	NM_032415.4	240	Gag/Aag	6/25	1	2	FACETS	0.922	0.786	1	0.922	0.786	1	CLONAL	1	TRUE	1	0.18	2		736	651	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508962	106508962	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	44	676	0	ENST00000359195.3:c.956G>A	p.Arg319Lys	p.R319K	ENST00000359195	NM_002649.2	319	aGg/aAg	2/11	1	2	FACETS	0.767	0.642	0.906	0.767	0.642	0.906	CLONAL	1	TRUE	1	0.18	2		676	637	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339822	116339822	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	60	707	1	ENST00000397752.3:c.684T>A	p.Phe228Leu	p.F228L	ENST00000397752	NM_000245.2	228	ttT/ttA	2/21	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.18	2		708	666	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380073	116380073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	77	866	0	ENST00000397752.3:c.1462C>T	p.Pro488Ser	p.P488S	ENST00000397752	NM_000245.2	488	Cca/Tca	4/21	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.18	2		866	701	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878051	151878052	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	33	545	1	ENST00000262189.6:c.6893_6894delinsTT	p.Pro2298Leu	p.P2298L	ENST00000262189	NM_170606.2	2298	cCC/cTT	36/59	1	2	FACETS	0.777	0.632	0.94	0.777	0.632	0.94	CLONAL	1	TRUE	1	0.18	2		546	472	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539044	23539044	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754870999	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	40	726	0	ENST00000380871.4:c.395C>T	p.Ser132Phe	p.S132F	ENST00000380871	NM_006167.3	132	tCc/tTc	2/2	1	2	FACETS	0.684	0.567	0.815	0.684	0.567	0.815	SUBCLONAL	1	TRUE	1	0.18	2		726	650	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981825	70981825	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	41	1039	1	ENST00000276594.2:c.271G>A	p.Asp91Asn	p.D91N	ENST00000276594	NM_024504.3	91	Gat/Aat	2/8	1	2	FACETS	0.609	0.506	0.725	0.609	0.506	0.725	SUBCLONAL	1	TRUE	1	0.18	2		1040	748	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209681	98209681	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	52	835	0	ENST00000331920.6:c.3857C>T	p.Pro1286Leu	p.P1286L	ENST00000331920	NM_000264.3	1286	cCc/cTc	23/24	1	2	FACETS	0.717	0.609	0.836	0.717	0.609	0.836	SUBCLONAL	1	TRUE	1	0.18	2		835	806	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400999	139400999	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	37	757	0	ENST00000277541.6:c.3994T>C	p.Phe1332Leu	p.F1332L	ENST00000277541	NM_017617.3	1332	Ttc/Ctc	24/34	1	2	FACETS	0.561	0.461	0.673	0.561	0.461	0.673	SUBCLONAL	1	TRUE	1	0.18	2		757	733	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650524	48650524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	62	447	0	ENST00000376670.3:c.494G>A	p.Gly165Asp	p.G165D	ENST00000376670	NM_002049.3	165	gGc/gAc	3/6	1	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.18	1		447	435	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411537	63411537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772837332	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	41	476	1	ENST00000330258.3:c.1630C>T	p.Pro544Ser	p.P544S	ENST00000330258	NM_152424.3	544	Ccc/Tcc	2/2	1	1	FACETS	0.951	0.793	1	0.951	0.793	1	CLONAL	1	TRUE	0	0.18	1		477	436	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224520	123224520	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	76	493	0	ENST00000218089.9:c.3373A>G	p.Ile1125Val	p.I1125V	ENST00000218089	NM_001042749.1	1125	Att/Gtt	31/35	1	1	FACETS	0.861	0.759	0.971	1	0.98	1	CLONAL	2	TRUE	0	0.18	1		493	446	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0020153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	10	265	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.183500699382357	3	FACETS	0.54	0.367	0.757	0.27	0.183	0.379	SUBCLONAL	1	TRUE	1	0.273124483195673	3		265	154	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579419	7579420	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs587783062	NA	P-0020153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	16	1040	0	ENST00000269305.4:c.267dup	p.Ser90LeufsTer59	p.S90Lfs*59	ENST00000269305	NM_001126112.2	89	-/C	4/11	1	2	FACETS	0.566	0.419	0.74	0.566	0.419	0.74	SUBCLONAL	1	TRUE	1	0.273124483195673	2		1040	207	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421519	32421519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	23	895	2	ENST00000332351.3:c.1073C>T	p.Thr358Met	p.T358M	ENST00000332351	NM_024426.4	358	aCg/aTg	6/10	0.184718845867322	3	FACETS	0.636	0.496	0.797	0.318	0.248	0.399	SUBCLONAL	1	TRUE	1	0.273124483195673	3		897	301	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0020154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	143	554	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.93	0.853	1	0.93	0.853	1	CLONAL	1	TRUE	1	0.591403392777261	2		554	520	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0020154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	206	146	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.591403392777261	2		146	558	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0020155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	153	465	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.902	0.832	0.974	0.902	0.832	0.974	CLONAL	1	TRUE	1	0.715661892278728	2		465	474	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938407	76938407	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	359	910	0	ENST00000373344.5:c.2341C>T	p.Arg781Ter	p.R781*	ENST00000373344	NM_000489.3	781	Cga/Tga	9/35	0.715661892278728	1	FACETS	0.934	0.893	0.974	0.934	0.893	0.974	CLONAL	1	TRUE	0	0.715661892278728	1		910	690	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576867	7576868	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	653	900	0	ENST00000269305.4:c.978_979insG	p.Tyr327ValfsTer10	p.Y327Vfs*10	ENST00000269305	NM_001126112.2	326	-/G	9/11	0.715661892278728	2	FACETS	0.98	0.955	1	0.98	0.955	1	CLONAL	2	TRUE	0	0.715661892278728	2		900	931	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702521	52702521	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	276	699	0	ENST00000394830.3:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000394830	NM_018313.4	126	tAt/tGt	4/30	1	2	FACETS	0.916	0.863	0.97	0.916	0.863	0.97	CLONAL	1	TRUE	1	0.715661892278728	2		699	842	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860613	45860614	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCAG	novel	NA	P-0020157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	142	921	0	ENST00000391945.4:c.1390_1393dup	p.Asp465AlafsTer37	p.D465Afs*37	ENST00000391945	NM_000400.3	465	gac/gCTGGac	15/23	0.210653011454902	3	FACETS	0.855	0.788	0.923	0.57	0.525	0.616	INDETERMINATE	2	TRUE	0	0.55551909776614	3		921	382	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663651	117663651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	59	596	0	ENST00000368508.3:c.4581G>A	p.Met1527Ile	p.M1527I	ENST00000368508	NM_002944.2	1527	atG/atA	28/43	0.414563913382477	1	FACETS	0.99	0.872	1	0.99	0.872	1	CLONAL	1	TRUE	0	0.55551909776614	1		596	155	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524992	8524992	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	75	466	0	ENST00000356435.5:c.612A>C	p.Lys204Asn	p.K204N	ENST00000356435		204	aaA/aaC	7/35	0.183343825434731	0	FACETS	0.448	0.397	0.501			1	INDETERMINATE	1	TRUE	0	0.55551909776614	0		466	268	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0020158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	155	817	3	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.264411872438986	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.264411872438986	1		820	834	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880997	37880998	+	protein_altering_variant	In_Frame_Ins	INS	-	-	TGT	rs397516979	NA	P-0020158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	112	808	0	ENST00000269571.5:c.2326_2327insTGT	p.Gly776delinsValCys	p.G776delinsVC	ENST00000269571		776	ggt/gTGTgt	20/27	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.264411872438986	2		808	843	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249155	10249155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765098980	NA	P-0020158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	68	789	0	ENST00000340748.4:c.4027G>A	p.Val1343Met	p.V1343M	ENST00000340748		1343	Gtg/Atg	34/40	1	2	FACETS	0.598	0.519	0.684	0.598	0.519	0.684	SUBCLONAL	1	TRUE	1	0.264411872438986	2		789	860	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980846	40980846	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	129	691	0	ENST00000373198.4:c.1640A>G	p.Asn547Ser	p.N547S	ENST00000373198	NM_133170.3	547	aAt/aGt	10/32	0.264411872438986	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.264411872438986	1		691	650	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1955162	1955162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	114	752	1	ENST00000382891.5:c.2249C>T	p.Thr750Ile	p.T750I	ENST00000382891	NM_133335.3	750	aCt/aTt	12/22	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.264411872438986	2		753	862	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190317	32190317	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	71	519	0	ENST00000375023.3:c.422del	p.Pro141HisfsTer111	p.P141Hfs*111	ENST00000375023	NM_004557.3	141	cCa/ca	3/30	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.264411872438986	2		519	535	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066693	94066693	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	97	655	0	ENST00000369303.4:c.1066G>T	p.Asp356Tyr	p.D356Y	ENST00000369303	NM_004440.3	356	Gac/Tac	5/17	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.264411872438986	2		655	671	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	12	424	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.333	0.235	0.454	0.333	0.235	0.454	SUBCLONAL	1	TRUE	1	0.431074175490221	2		424	167	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220594	1220595	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0020160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	80	831	0	ENST00000326873.7:c.614_615del	p.Ala205GlyfsTer60	p.A205Gfs*60	ENST00000326873	NM_000455.4	204	ttCGcg/ttcg	5/10	NA	2	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.431074175490221	2		831	303	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39237746	39237746	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs397517158	NA	P-0020160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	17	621	0	ENST00000402219.2:c.2489A>G	p.Asn830Ser	p.N830S	ENST00000402219	NM_005633.3	830	aAc/aGc	15/23	1	2	FACETS	0.95	0.724	1	0.95	0.724	1	CLONAL	1	TRUE	1	0.431074175490221	2		621	83	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181472	38181472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs963509901	NA	P-0020160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	31	799	1	ENST00000396334.3:c.485C>T	p.Thr162Ile	p.T162I	ENST00000396334	NM_002468.4	162	aCa/aTa	2/5	0.375992155478355	1	FACETS	0.688	0.563	0.826	0.688	0.563	0.826	SUBCLONAL	1	TRUE	0	0.431074175490221	1		800	164	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247385	153247385	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0020160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	12	477	0	ENST00000281708.4:c.1419-2A>G		p.X473_splice	ENST00000281708	NM_033632.3	473			0.375992155478355	1	FACETS	0.575	0.41	0.769	0.575	0.41	0.769	SUBCLONAL	1	TRUE	0	0.431074175490221	1		477	76	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593606	55593614	+	inframe_deletion	In_Frame_Del	DEL	AAGGTTGTT	AAGGTTGTT	-	rs121913511	NA	P-0020162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	209	636	0	ENST00000288135.5:c.1672_1680del	p.Lys558_Val560del	p.K558_V560del	ENST00000288135	NM_000222.2	558	AAGGTTGTT/-	11/21	1	2	FACETS	0.758	0.705	0.812	0.758	0.705	0.812	SUBCLONAL	1	TRUE	1	0.712815937990919	2		636	774	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599321	55599321	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913507	NA	P-0020163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	279	692	1	ENST00000288135.5:c.2447A>T	p.Asp816Val	p.D816V	ENST00000288135	NM_000222.2	816	gAc/gTc	17/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.745799458387801	2		693	707	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0020165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	409	604	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.457060515953014	2	FACETS	0.91	0.87	0.951	0.91	0.87	0.951	CLONAL	2	TRUE	0	0.471109350570588	2		606	954	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112222	115112223	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	208	426	0	ENST00000257566.3:c.1517dup	p.Leu507ProfsTer185	p.L507Pfs*185	ENST00000257566	NM_016569.3	506	ggc/ggGc	7/8	0.462348697061933	3	FACETS	0.926	0.865	0.988			1	CLONAL	2	TRUE	NA	0.471109350570588	3		426	589	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196523	106196523	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	TTACCG	novel	NA	P-0020165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	244	539	0	ENST00000380013.4:c.4856delinsTTACCG	p.Pro1619LeufsTer6	p.P1619Lfs*6	ENST00000380013	NM_001127208.2	1619	cCt/cTTACCGt	11/11	0.182115016563721	5	FACETS	0.839	0.788	0.892			1	INDETERMINATE	3	TRUE	NA	0.471109350570588	5		539	702	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226826	2226826	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1259363492	NA	P-0020167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	57	400	4	ENST00000398665.3:c.4306G>A	p.Gly1436Arg	p.G1436R	ENST00000398665	NM_032482.2	1436	Gga/Aga	27/28	1	2	FACETS	0.291	0.249	0.337	0.291	0.249	0.337	SUBCLONAL	1	TRUE	1	0.599317820453744	2		404	654	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427051	49427064	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGCTGCAACACA	GCTGCTGCAACACA	-	novel	NA	P-0020167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	196	449	0	ENST00000301067.7:c.11424_11437del	p.Val3809AlafsTer198	p.V3809Afs*198	ENST00000301067	NM_003482.3	3808	gcTGTGTTGCAGCAGCag/gcag	39/54	1	2	FACETS	0.878	0.815	0.943	0.878	0.815	0.943	CLONAL	1	TRUE	1	0.599317820453744	2		449	745	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440064	49440065	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	316	672	0	ENST00000301067.7:c.4561dup	p.Ile1521AsnfsTer7	p.I1521Nfs*7	ENST00000301067	NM_003482.3	1521	atc/aAtc	16/54	1	2	FACETS	0.897	0.846	0.949	0.897	0.846	0.949	CLONAL	1	TRUE	1	0.599317820453744	2		672	1176	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597379	52597380	+	stop_gained,frameshift_variant,splice_region_variant	Nonsense_Mutation	INS	-	-	CTCA	novel	NA	P-0020167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	303	625	0	ENST00000394830.3:c.3927_3930dup	p.Ser1311Ter	p.S1311*	ENST00000394830	NM_018313.4	1310	-/TGAG		0.599317820453744	1	FACETS	0.929	0.88	0.979	0.929	0.88	0.979	CLONAL	1	TRUE	0	0.599317820453744	1		625	762	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902676	1902676	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779422565	NA	P-0020167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	354	732	5	ENST00000382891.5:c.295C>T	p.Arg99Cys	p.R99C	ENST00000382891	NM_133335.3	99	Cgt/Tgt	2/22	1	2	FACETS	0.965	0.914	1	0.965	0.914	1	CLONAL	1	TRUE	1	0.599317820453744	2		737	1224	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574022	+	frameshift_variant	Frame_Shift_Del	DEL	CGAAGCGCTCA	CGAAGCGCTCA	-	novel	NA	P-0020168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	104	795	0	ENST00000269305.4:c.1005_1015del	p.Glu336AspfsTer7	p.E336Dfs*7	ENST00000269305	NM_001126112.2	335	cgTGAGCGCTTCGag/cgag	10/11	0.241718870864633	1	FACETS	0.861	0.77	0.957	0.861	0.77	0.957	CLONAL	1	TRUE	0	0.241718870864633	1		795	879	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132522	11132522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778175819	NA	P-0020169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	68	890	0	ENST00000358026.2:c.2738C>T	p.Pro913Leu	p.P913L	ENST00000358026	NM_001128849.1	913	cCg/cTg	19/36	1	2	FACETS	0.898	0.784	1	0.898	0.784	1	CLONAL	1	TRUE	1	0.338756215607738	2		890	447	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214619	5214619	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376549612	NA	P-0020169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	58	890	3	ENST00000357368.4:c.4447C>T	p.Arg1483Trp	p.R1483W	ENST00000357368	NM_002850.3	1483	Cgg/Tgg	29/38	1	2	FACETS	0.823	0.709	0.946	0.823	0.709	0.946	CLONAL	1	TRUE	1	0.338756215607738	2		893	416	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371942	55371942	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	69	664	0	ENST00000297316.4:c.632C>T	p.Ala211Val	p.A211V	ENST00000297316	NM_022454.3	211	gCg/gTg	2/2	0.188516517061598	4	FACETS	1	0.964	1	0.649	0.568	0.737	INDETERMINATE	1	TRUE	2	0.338756215607738	4		664	420	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143278	108143278	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0020169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	34	564	1	ENST00000278616.4:c.3097A>T	p.Lys1033Ter	p.K1033*	ENST00000278616	NM_000051.3	1033	Aaa/Taa	21/63	0.338756215607738	3	FACETS	0.705	0.577	0.848	0.352	0.288	0.424	SUBCLONAL	1	TRUE	1	0.338756215607738	3		565	333	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959029	28959031	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs1173235571	NA	P-0020169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	18	448	0	ENST00000282397.4:c.2107_2109del	p.Gln703del	p.Q703del	ENST00000282397	NM_002019.4	703	CAA/-	14/30	0.204203961231013	3	FACETS	0.462	0.348	0.597	0.154	0.116	0.199	SUBCLONAL	1	TRUE	0	0.338756215607738	3		448	269	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474003	29474003	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs771511785	NA	P-0020169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	32	787	2	ENST00000389048.3:c.2172G>T	p.Gln724His	p.Q724H	ENST00000389048	NM_004304.4	724	caG/caT	12/29	0.204203961231013	3	FACETS	0.554	0.449	0.671	0.185	0.149	0.224	SUBCLONAL	1	TRUE	0	0.338756215607738	3		789	399	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972082	55972082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772912254	NA	P-0020169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	18	587	2	ENST00000263923.4:c.1562C>T	p.Ala521Val	p.A521V	ENST00000263923	NM_002253.2	521	gCg/gTg	12/30	0.296929468752729	3	FACETS	0.354	0.266	0.458	0.177	0.133	0.229	SUBCLONAL	1	TRUE	1	0.338756215607738	3		589	351	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0020170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	531	549	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.414277354799192	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.414277354799192	2		549	1107	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602799	10602799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	523	1061	0	ENST00000171111.5:c.779G>T	p.Arg260Leu	p.R260L	ENST00000171111	NM_203500.1	260	cGa/cTa	3/6	0.403932150403464	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.414277354799192	2		1061	1241	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171462	123171462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	328	401	0	ENST00000218089.9:c.374C>T	p.Ser125Leu	p.S125L	ENST00000218089	NM_001042749.1	125	tCa/tTa	6/35	0.387407269632936	2	FACETS	1	0.959	1			1	CLONAL	3	TRUE	NA	0.414277354799192	2		401	528	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026697	6026697	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554297342	NA	P-0020170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1380	338	1063	3	ENST00000265849.7:c.1699C>T	p.Gln567Ter	p.Q567*	ENST00000265849	NM_000535.5	567	Cag/Tag	11/15	0.414277354799192	5	FACETS	0.77	0.726	0.815	0.513	0.484	0.544	SUBCLONAL	2	TRUE	2	0.414277354799192	5		1066	1718	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035154	30035154	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	520	854	1	ENST00000338641.4:c.316G>T	p.Glu106Ter	p.E106*	ENST00000338641	NM_000268.3	106	Gaa/Taa	3/16	0.34738698863466	3	FACETS	0.981	0.945	1	0.981	0.945	1	CLONAL	3	TRUE	0	0.414277354799192	3		855	1030	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126100	2126100	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	126	963	0	ENST00000219476.3:c.2671C>G	p.His891Asp	p.H891D	ENST00000219476	NM_000548.3	891	Cac/Gac	24/42	0.394906785374242	3	FACETS	0.587	0.53	0.648	0.293	0.265	0.324	SUBCLONAL	1	TRUE	1	0.414277354799192	3		963	1251	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959190	2959190	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1174	106	1000	0	ENST00000396946.4:c.2326T>G	p.Phe776Val	p.F776V	ENST00000396946	NM_032415.4	776	Ttc/Gtc	18/25	0.414277354799192	3	FACETS	0.483	0.431	0.538			1	SUBCLONAL	1	TRUE	NA	0.414277354799192	3		1000	1280	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891308	101891308	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	387	1037	1	ENST00000374994.4:c.269C>A	p.Ser90Ter	p.S90*	ENST00000374994	NM_004612.2	90	tCa/tAa	2/9	0.414277354799192	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.414277354799192	2		1038	907	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044487	47044506	+	frameshift_variant	Frame_Shift_Del	DEL	CTCAACAAACAAAAAGAAAA	CTCAACAAACAAAAAGAAAA	-	novel	NA	P-0020170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	227	478	0	ENST00000377604.3:c.1986_2005del	p.Asn663GlnfsTer3	p.N663Qfs*3	ENST00000377604	NM_001204468.1	662	CTCAACAAACAAAAAGAAAAc/c	18/24	0.414277354799192	2	FACETS	1	0.964	1			1	CLONAL	2	TRUE	NA	0.414277354799192	2		478	530	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244997	46244997	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs868082376	NA	P-0020171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	387	674	0	ENST00000334344.6:c.3091C>T	p.Gln1031Ter	p.Q1031*	ENST00000334344	NM_152641.2	1031	Cag/Tag	15/21	0.396330809555769	3	FACETS	0.937	0.895	0.978	0.937	0.895	0.978	CLONAL	3	TRUE	0	0.39905920305998	3		674	828	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089778	27089778	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0020171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	127	543	1	ENST00000324856.7:c.2732+2T>A		p.X911_splice	ENST00000324856	NM_006015.4	911			0.39905920305998	3	FACETS	1	0.949	1	0.534	0.484	0.586	CLONAL	1	TRUE	1	0.39905920305998	3		544	715	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282450	115282450	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	120	649	0	ENST00000438362.2:c.200C>A	p.Ser67Ter	p.S67*	ENST00000438362	NM_001242891.1	67	tCa/tAa	3/20	0.39905920305998	3	FACETS	0.809	0.73	0.892	0.404	0.365	0.446	CLONAL	1	TRUE	1	0.39905920305998	3		649	892	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601870	43601870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1184	120	666	0	ENST00000355710.3:c.914C>T	p.Pro305Leu	p.P305L	ENST00000355710	NM_020975.4	305	cCt/cTt	5/20	0.39905920305998	6	FACETS	0.829	0.746	0.917	0.207	0.186	0.23	CLONAL	1	TRUE	2	0.39905920305998	6		666	1304	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156109	119156109	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	110	686	0	ENST00000264033.4:c.1777del	p.Arg593GlyfsTer22	p.R593Gfs*22	ENST00000264033	NM_005188.3	592	Ccc/cc	11/16	0.39905920305998	4	FACETS	0.773	0.693	0.858	0.258	0.231	0.286	SUBCLONAL	1	TRUE	1	0.39905920305998	4		686	998	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477192	67477192	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	96	465	0	ENST00000327367.4:c.999G>C	p.Lys333Asn	p.K333N	ENST00000327367	NM_005902.3	333	aaG/aaC	7/9	0.398086525706994	2	FACETS	0.881	0.787	0.981	0.441	0.393	0.491	CLONAL	1	TRUE	0	0.39905920305998	2		465	546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577599	7577608	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CAGAGCCAAC	CAGAGCCAAC	-	novel	NA	P-0020171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	230	651	0	ENST00000269305.4:c.673_682del	p.Val225ThrfsTer19	p.V225Tfs*19	ENST00000269305	NM_001126112.2	225	GTTGGCTCTGac/ac	7/11	0.398086525706994	2	FACETS	0.835	0.782	0.889	0.835	0.782	0.889	CLONAL	2	TRUE	0	0.39905920305998	2		651	690	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556484	29556484	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1131691122	NA	P-0020171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	229	349	0	ENST00000356175.3:c.2850+1G>T		p.X950_splice	ENST00000356175	NM_000267.3	950			0.396330809555769	3	FACETS	1	0.944	1	1	0.944	1	CLONAL	3	TRUE	0	0.39905920305998	3		349	459	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268381	46268381	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	232	588	0	ENST00000371998.3:c.2768C>T	p.Pro923Leu	p.P923L	ENST00000371998		923	cCa/cTa	15/23	0.398086525706994	2	FACETS	0.926	0.869	0.984	0.926	0.869	0.984	CLONAL	2	TRUE	0	0.39905920305998	2		588	628	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527226	187527226	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	101	526	0	ENST00000441802.2:c.10348C>G	p.Gln3450Glu	p.Q3450E	ENST00000441802	NM_005245.3	3450	Cag/Gag	17/27	0.39905920305998	3	FACETS	0.962	0.861	1	0.481	0.43	0.535	CLONAL	1	TRUE	1	0.39905920305998	3		526	631	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499772	8499772	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs773166856	NA	P-0020171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	104	611	0	ENST00000356435.5:c.2197C>G	p.Arg733Gly	p.R733G	ENST00000356435		733	Cgc/Ggc	14/35	0.39905920305998	1	FACETS	0.831	0.747	0.919	0.831	0.747	0.919	CLONAL	1	TRUE	0	0.39905920305998	1		611	502	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0020172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	104	453	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.770417847103386	3	FACETS	0.898	0.825	0.971	0.898	0.825	0.971	CLONAL	2	TRUE	1	0.78209666388297	3		453	206	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913315	NA	P-0020172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	215	881	0	ENST00000326873.7:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000326873	NM_000455.4	194	Gac/Tac	4/10	0.775792986786239	2	FACETS	0.989	0.949	1	0.989	0.949	1	CLONAL	2	TRUE	0	0.78209666388297	2		881	278	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346338	73346338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	80	704	0	ENST00000377767.4:c.1462G>A	p.Asp488Asn	p.D488N	ENST00000377767	NM_014953.3	488	Gat/Aat	10/21	0.70910148095559	4	FACETS	0.949	0.855	1	0.949	0.855	1	CLONAL	2	TRUE	2	0.78209666388297	4		704	192	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770588	40770588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1389160956	NA	P-0020172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	133	722	1	ENST00000373198.4:c.2794C>T	p.Arg932Cys	p.R932C	ENST00000373198	NM_133170.3	932	Cgc/Tgc	19/32	0.70910148095559	4	FACETS	0.938	0.865	1	0.938	0.865	1	CLONAL	2	TRUE	2	0.78209666388297	4		723	323	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366871	40366871	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs753802769	NA	P-0020172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	120	913	0	ENST00000397332.2:c.326C>G	p.Ser109Trp	p.S109W	ENST00000397332	NM_001033082.2	109	tCg/tGg	2/3	0.78209666388297	3	FACETS	1	0.94	1	0.521	0.474	0.569	CLONAL	1	TRUE	1	0.78209666388297	3		913	410	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944257	206944257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	170	539	0	ENST00000423557.1:c.373C>T	p.Arg125Cys	p.R125C	ENST00000423557	NM_000572.2	125	Cgc/Tgc	3/5	0.78209666388297	6	FACETS	1	0.964	1	0.533	0.493	0.573	CLONAL	2	TRUE	2	0.78209666388297	6		539	523	SUCCESS
FH	2271	MSKCC	GRCh37	1	241669468	241669468	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	34	447	0	ENST00000366560.3:c.739G>A	p.Glu247Lys	p.E247K	ENST00000366560	NM_000143.3	247	Gaa/Aaa	6/10	0.78209666388297	6	FACETS	0.823	0.675	0.987	0.206	0.168	0.247	CLONAL	1	TRUE	2	0.78209666388297	6		447	271	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445224	49445224	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	105	998	0	ENST00000301067.7:c.2242G>C	p.Glu748Gln	p.E748Q	ENST00000301067	NM_003482.3	748	Gag/Cag	10/54	0.770417847103386	3	FACETS	0.941	0.85	1	0.47	0.425	0.518	CLONAL	1	TRUE	1	0.78209666388297	3		998	397	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911151	32911151	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658391	NA	P-0020172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	41	851	1	ENST00000380152.3:c.2659G>A	p.Glu887Lys	p.E887K	ENST00000380152		887	Gag/Aag	11/27	0.78209666388297	3	FACETS	1	0.865	1	0.51	0.433	0.592	CLONAL	1	TRUE	1	0.78209666388297	3		852	143	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934806	9934806	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	139	841	0	ENST00000330684.3:c.1484G>A	p.Gly495Glu	p.G495E	ENST00000330684	NM_001134407.1	495	gGa/gAa	6/13	0.311541444189577	6	FACETS	1	0.977	1	0.841	0.782	0.9	INDETERMINATE	3	TRUE	2	0.78209666388297	6		841	271	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577527	7577534	+	frameshift_variant	Frame_Shift_Del	DEL	GGATGGGC	GGATGGGC	-	novel	NA	P-0020172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	190	871	0	ENST00000269305.4:c.747_754del	p.Arg249SerfsTer12	p.R249Sfs*12	ENST00000269305	NM_001126112.2	249	agGCCCATCCtc/agtc	7/11	0.731953082130468	2	FACETS	0.934	0.891	0.975	0.934	0.891	0.975	CLONAL	2	TRUE	0	0.78209666388297	2		871	260	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044551	12044551	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	163	850	0	ENST00000353533.5:c.1174C>A	p.Pro392Thr	p.P392T	ENST00000353533	NM_003010.3	392	Ccc/Acc	11/11	0.731953082130468	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.78209666388297	2		850	203	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556262	29556262	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	192	778	0	ENST00000356175.3:c.2629A>T	p.Met877Leu	p.M877L	ENST00000356175	NM_000267.3	877	Atg/Ttg	21/57	0.70910148095559	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	2	0.78209666388297	4		778	427	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560068	29560068	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	117	571	0	ENST00000356175.3:c.3545T>G	p.Val1182Gly	p.V1182G	ENST00000356175	NM_000267.3	1182	gTt/gGt	27/57	0.70910148095559	4	FACETS	0.945	0.867	1	0.945	0.867	1	CLONAL	2	TRUE	2	0.78209666388297	4		571	282	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243610	41243610	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	146	936	0	ENST00000357654.3:c.3938A>T	p.Gln1313Leu	p.Q1313L	ENST00000357654	NM_007294.3	1313	cAg/cTg	10/23	0.70910148095559	4	FACETS	0.906	0.838	0.976	0.906	0.838	0.976	CLONAL	2	TRUE	2	0.78209666388297	4		936	367	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663165	227663166	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	169	764	0	ENST00000305123.5:c.289dup	p.Ala97GlyfsTer22	p.A97Gfs*22	ENST00000305123	NM_005544.2	97	gcg/gGcg	1/2	0.70910148095559	4	FACETS	0.869	0.807	0.932	0.869	0.807	0.932	CLONAL	2	TRUE	2	0.78209666388297	4		764	443	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873601	35873601	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	44	428	0	ENST00000303115.3:c.557C>A	p.Thr186Lys	p.T186K	ENST00000303115	NM_002185.3	186	aCa/aAa	5/8	0.78209666388297	6	FACETS	0.869	0.732	1	0.174	0.146	0.204	CLONAL	1	TRUE	1	0.78209666388297	6		428	332	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045853	26045853	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	310	789	0	ENST00000540144.1:c.215T>A	p.Val72Glu	p.V72E	ENST00000540144	NM_003531.2	72	gTg/gAg	1/1	0.78209666388297	5	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	2	0.78209666388297	5		789	558	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672870	30672870	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777960614	NA	P-0020172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	209	987	0	ENST00000376406.3:c.4090G>A	p.Glu1364Lys	p.E1364K	ENST00000376406	NM_014641.2	1364	Gaa/Aaa	10/15	0.78209666388297	5	FACETS	0.86	0.802	0.92	0.574	0.535	0.613	CLONAL	2	TRUE	2	0.78209666388297	5		987	675	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687355	117687355	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	140	611	0	ENST00000368508.3:c.2696A>G	p.Asn899Ser	p.N899S	ENST00000368508	NM_002944.2	899	aAt/aGt	18/43	0.748427048903982	2	FACETS	0.932	0.882	0.98	0.932	0.882	0.98	CLONAL	2	TRUE	0	0.78209666388297	2		611	192	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350112	81350113	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	115	728	0	ENST00000222390.5:c.1219dup	p.Arg407LysfsTer28	p.R407Kfs*28	ENST00000222390	NM_000601.4	407	aga/aAga	10/18	0.750842901734647	2	FACETS	0.886	0.83	0.939	0.886	0.83	0.939	CLONAL	2	TRUE	0	0.78209666388297	2		728	166	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859588	151859588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780489514	NA	P-0020172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	147	622	0	ENST00000262189.6:c.11074G>A	p.Ala3692Thr	p.A3692T	ENST00000262189	NM_170606.2	3692	Gca/Aca	43/59	0.750842901734647	2	FACETS	0.984	0.936	1	0.984	0.936	1	CLONAL	2	TRUE	0	0.78209666388297	2		622	191	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342696	70342696	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	87	798	0	ENST00000374080.3:c.1457G>C	p.Gly486Ala	p.G486A	ENST00000374080		486	gGa/gCa	10/45	0.628802195733829	4	FACETS	0.889	0.791	0.993	0.444	0.395	0.497	CLONAL	1	TRUE	2	0.78209666388297	4		798	446	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0020175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	127	532	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.218761959273532	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.218761959273532	1		533	833	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs483352695	NA	P-0020175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	39	944	0	ENST00000269305.4:c.736A>C	p.Met246Leu	p.M246L	ENST00000269305	NM_001126112.2	246	Atg/Ctg	7/11	0.218761959273532	1	FACETS	0.317	0.262	0.38	0.317	0.262	0.38	SUBCLONAL	1	TRUE	0	0.218761959273532	1		944	1001	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106782	27106782	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	115	889	0	ENST00000324856.7:c.6393del	p.Asn2131LysfsTer4	p.N2131Kfs*4	ENST00000324856	NM_006015.4	2131	aaT/aa	20/20	1	2	FACETS	0.997	0.896	1	0.997	0.896	1	CLONAL	1	TRUE	1	0.218761959273532	2		889	1055	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480501	120480501	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	89	592	0	ENST00000256646.2:c.3316G>A	p.Asp1106Asn	p.D1106N	ENST00000256646	NM_024408.3	1106	Gac/Aac	20/34	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.218761959273532	2		592	704	SUCCESS
APC	324	MSKCC	GRCh37	5	112176740	112176740	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	70	524	0	ENST00000257430.4:c.5449A>C	p.Lys1817Gln	p.K1817Q	ENST00000257430	NM_000038.5	1817	Aaa/Caa	16/16	1	2	FACETS	0.977	0.852	1	0.977	0.852	1	CLONAL	1	TRUE	1	0.218761959273532	2		524	655	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	106	122	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.718953268475312	2		122	292	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717735	89717739	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGT	AAAGT	-	rs606231169	NA	P-0020176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	516	675	0	ENST00000371953.3:c.761_765del	p.Lys254ArgfsTer42	p.K254Rfs*42	ENST00000371953	NM_000314.4	254	AAAGTa/a	7/9	0.718953268475312	2	FACETS	0.991	0.963	1	0.991	0.963	1	CLONAL	2	TRUE	0	0.718953268475312	2		675	724	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631946	90631946	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs749063791	NA	P-0020176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	251	899	0	ENST00000330062.3:c.407A>G	p.Asn136Ser	p.N136S	ENST00000330062	NM_002168.2	136	aAt/aGt	4/11	1	2	FACETS	0.929	0.872	0.986	0.929	0.872	0.986	CLONAL	1	TRUE	1	0.718953268475312	2		899	752	SUCCESS
APC	324	MSKCC	GRCh37	5	112174851	112174851	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730881246	NA	P-0020176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	195	572	0	ENST00000257430.4:c.3560T>C	p.Ile1187Thr	p.I1187T	ENST00000257430	NM_000038.5	1187	aTt/aCt	16/16	1	2	FACETS	0.932	0.868	0.997	0.932	0.868	0.997	CLONAL	1	TRUE	1	0.718953268475312	2		572	582	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0020177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	455	549	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.45382647212755	5	FACETS	0.964	0.922	1	0.964	0.922	1	CLONAL	3	TRUE	2	0.45382647212755	5		549	1165	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519988	NA	P-0020177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	283	667	0	ENST00000269305.4:c.808T>G	p.Phe270Val	p.F270V	ENST00000269305	NM_001126112.2	270	Ttt/Gtt	8/11	0.349980366393638	2	FACETS	0.812	0.767	0.858	0.812	0.767	0.858	CLONAL	2	TRUE	0	0.45382647212755	2		667	768	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970865	79970865	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	54	707	0	ENST00000265081.6:c.1091C>G	p.Ser364Cys	p.S364C	ENST00000265081	NM_002439.4	364	tCt/tGt	7/24	0.192981024788821	3	FACETS	0.333	0.283	0.388	0.111	0.094	0.13	INDETERMINATE	1	TRUE	0	0.45382647212755	3		707	877	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155725	56155726	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0020178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	105	600	0	ENST00000399503.3:c.819_820del	p.Arg273SerfsTer27	p.R273Sfs*27	ENST00000399503	NM_005921.1	273	AGa/a	3/20	1	2	FACETS	0.907	0.813	1	0.907	0.813	1	CLONAL	1	TRUE	1	0.319961663940263	2		600	724	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180584	56180584	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	145	691	0	ENST00000399503.3:c.3913A>G	p.Asn1305Asp	p.N1305D	ENST00000399503	NM_005921.1	1305	Aac/Gac	16/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.319961663940263	2		691	831	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047151	77047151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	160	756	0	ENST00000356341.3:c.1393C>T	p.Leu465Phe	p.L465F	ENST00000356341	NM_002576.4	465	Ctc/Ttc	13/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.723324500887338	2		756	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	190	622	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.723324500887338	2		623	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	272	912	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.723324500887338	2		912	679	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521711	89521711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	106	781	1	ENST00000336596.2:c.2788G>A	p.Glu930Lys	p.E930K	ENST00000336596	NM_005233.5	930	Gaa/Aaa	16/17	NA	2	FACETS	0.891	0.808	0.977			1	INDETERMINATE	1	TRUE	NA	0.723324500887338	2		782	329	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330546	65330546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	176	801	0	ENST00000342505.4:c.1100C>T	p.Ser367Phe	p.S367F	ENST00000342505	NM_002227.2	367	tCt/tTt	8/25	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.723324500887338	2		801	461	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202301	133202301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	137	878	0	ENST00000320574.5:c.6587C>T	p.Ser2196Phe	p.S2196F	ENST00000320574	NM_006231.2	2196	tCc/tTc	47/49	1	2	FACETS	0.999	0.92	1	0.999	0.92	1	CLONAL	1	TRUE	1	0.723324500887338	2		878	379	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101468	27101468	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	358	788	1	ENST00000324856.7:c.4750C>T	p.Gln1584Ter	p.Q1584*	ENST00000324856	NM_006015.4	1584	Cag/Tag	18/20	0.616646684775339	3	FACETS	0.928	0.898	0.958	0.928	0.898	0.958	CLONAL	3	TRUE	0	0.723324500887338	3		789	484	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636820	8636820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369741244	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	73	720	3	ENST00000356435.5:c.89C>T	p.Pro30Leu	p.P30L	ENST00000356435		30	cCc/cTc	2/35	0.253110695048254	1	FACETS	0.355	0.312	0.4	0.355	0.312	0.4	INDETERMINATE	1	TRUE	0	0.723324500887338	1		723	363	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4102441	4102441	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1291541587	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	113	802	0	ENST00000262948.5:c.461C>T	p.Ser154Phe	p.S154F	ENST00000262948	NM_030662.3	154	tCc/tTc	4/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.723324500887338	2		802	291	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983953	2983953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	111	1010	0	ENST00000396946.4:c.577G>A	p.Glu193Lys	p.E193K	ENST00000396946	NM_032415.4	193	Gag/Aag	5/25	0.723324500887338	1	FACETS	0.597	0.543	0.653	0.597	0.543	0.653	SUBCLONAL	1	TRUE	0	0.723324500887338	1		1010	328	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295705	212295705	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	101	753	0	ENST00000342788.4:c.2608G>A	p.Gly870Arg	p.G870R	ENST00000342788	NM_005235.2	870	Gga/Aga	21/28	1	2	FACETS	0.96	0.87	1	0.96	0.87	1	CLONAL	1	TRUE	1	0.723324500887338	2		753	291	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576148	88576148	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	111	927	0	ENST00000360948.2:c.1525C>T	p.Pro509Ser	p.P509S	ENST00000360948	NM_001012338.2	509	Cct/Tct	13/19	0.723324500887338	1	FACETS	0.765	0.701	0.831	0.765	0.701	0.831	SUBCLONAL	1	TRUE	0	0.723324500887338	1		927	256	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46275850	46275850	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1206893490	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	109	872	1	ENST00000371998.3:c.3286C>T	p.Gln1096Ter	p.Q1096*	ENST00000371998		1096	Caa/Taa	18/23	1	2	FACETS	0.721	0.652	0.793	0.721	0.652	0.793	SUBCLONAL	1	TRUE	1	0.723324500887338	2		873	418	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270180	66270180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763063348	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	83	480	0	ENST00000273854.3:c.1702G>A	p.Asp568Asn	p.D568N	ENST00000273854	NM_004439.5	568	Gat/Aat	8/18	0.186697033980074	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.723324500887338	0		480	244	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651315	45651315	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	124	746	1	ENST00000407780.3:c.710G>A	p.Gly237Glu	p.G237E	ENST00000407780	NM_001283052.1	237	gGa/gAa	5/7	0.186697033980074	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.723324500887338	0		747	388	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520241	176520241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	17	932	0	ENST00000292408.4:c.1160C>T	p.Ala387Val	p.A387V	ENST00000292408	NM_213647.1	387	gCc/gTc	9/18	0.723324500887338	1	FACETS	0.196	0.147	0.254	0.196	0.147	0.254	SUBCLONAL	1	TRUE	0	0.723324500887338	1		932	153	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891642	28891642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	85	822	0	ENST00000282397.4:c.3379C>T	p.Pro1127Ser	p.P1127S	ENST00000282397	NM_002019.4	1127	Cct/Tct	25/30	0.352940878916368	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.723324500887338	0		822	193	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993833	72993833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374747520	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	48	580	0	ENST00000268489.5:c.212C>T	p.Pro71Leu	p.P71L	ENST00000268489	NM_006885.3	71	cCc/cTc	2/10	1	2	FACETS	0.915	0.791	1	0.915	0.791	1	CLONAL	1	TRUE	1	0.723324500887338	2		580	145	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66520180	66520180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568696484	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	128	706	4	ENST00000358598.2:c.464C>T	p.Ser155Leu	p.S155L	ENST00000358598	NM_212471.2	155	tCg/tTg	5/11	0.227116041453938	3	FACETS	1	0.946	1	0.525	0.479	0.573	INDETERMINATE	1	TRUE	1	0.723324500887338	3		710	459	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238322	98238323	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	256	559	0	ENST00000331920.6:c.1721_1722delinsTT	p.Ser574Phe	p.S574F	ENST00000331920	NM_000264.3	574	tCC/tTT	12/24	0.249559200150796	3	FACETS	0.974	0.938	1			1	INDETERMINATE	3	TRUE	NA	0.723324500887338	3		559	330	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609942	43609942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767407	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	73	1026	0	ENST00000355710.3:c.1894G>A	p.Glu632Lys	p.E632K	ENST00000355710	NM_020975.4	632	Gag/Aag	11/20	0.521982969372446	1	FACETS	0.486	0.43	0.545	0.486	0.43	0.545	SUBCLONAL	1	TRUE	0	0.723324500887338	1		1026	265	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850663	63850663	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	227	615	0	ENST00000279873.7:c.1441C>T	p.Gln481Ter	p.Q481*	ENST00000279873	NM_032199.2	481	Cag/Tag	10/10	0.491061770276308	4	FACETS	1	0.992	1			1	CLONAL	1	TRUE	NA	0.723324500887338	4		615	741	SUCCESS
CBL	867	MSKCC	GRCh37	11	119077177	119077177	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1222060551	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	147	742	1	ENST00000264033.4:c.50C>A	p.Ser17Tyr	p.S17Y	ENST00000264033	NM_005188.3	17	tCc/tAc	1/16	1	2	FACETS	0.972	0.897	1	0.972	0.897	1	CLONAL	1	TRUE	1	0.723324500887338	2		743	418	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434130	49434130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	169	727	0	ENST00000301067.7:c.7423C>T	p.Pro2475Ser	p.P2475S	ENST00000301067	NM_003482.3	2475	Cct/Tct	31/54	0.464102009934508	4	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	2	0.723324500887338	4		727	400	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856608	111856608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	67	321	0	ENST00000341259.2:c.659G>A	p.Gly220Glu	p.G220E	ENST00000341259	NM_005475.2	220	gGg/gAg	2/8	1	2	FACETS	0.96	0.85	1	0.96	0.85	1	CLONAL	1	TRUE	1	0.723324500887338	2		321	193	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030468	49030468	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	138	736	0	ENST00000267163.4:c.1943C>T	p.Ser648Leu	p.S648L	ENST00000267163	NM_000321.2	648	tCa/tTa	19/27	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.723324500887338	2		736	362	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352674	68352674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199981178	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	250	641	0	ENST00000487270.1:c.541C>T	p.Arg181Trp	p.R181W	ENST00000487270	NM_133509.3	181	Cgg/Tgg	6/11	0.253110695048254	1	FACETS	0.994	0.944	1	0.994	0.944	1	INDETERMINATE	1	TRUE	0	0.723324500887338	1		641	444	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028729	42028729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	112	779	0	ENST00000219905.7:c.4267C>T	p.Pro1423Ser	p.P1423S	ENST00000219905	NM_001164273.1	1423	Cct/Tct	13/24	1	2	FACETS	0.922	0.839	1	0.922	0.839	1	CLONAL	1	TRUE	1	0.723324500887338	2		779	336	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73995358	73995358	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	74	426	0	ENST00000318443.5:c.664G>T	p.Val222Leu	p.V222L	ENST00000318443	NM_001024736.1	222	Gtg/Ttg	4/10	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.723324500887338	2		426	196	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122360	2122360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	132	708	0	ENST00000219476.3:c.2216C>T	p.Ser739Phe	p.S739F	ENST00000219476	NM_000548.3	739	tCc/tTc	20/42	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.723324500887338	2		708	309	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813746	50813746	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	110	945	1	ENST00000398568.2:c.1300C>T	p.Pro434Ser	p.P434S	ENST00000398568	NM_001042412.1	434	Cca/Tca	8/18	1	2	FACETS	0.869	0.789	0.952	0.869	0.789	0.952	CLONAL	1	TRUE	1	0.723324500887338	2		946	350	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829653	72829653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	109	891	2	ENST00000268489.5:c.6928G>A	p.Gly2310Arg	p.G2310R	ENST00000268489	NM_006885.3	2310	Gga/Aga	9/10	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.723324500887338	2		893	301	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832610	72832610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777084031	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	54	360	0	ENST00000268489.5:c.3971C>T	p.Thr1324Ile	p.T1324I	ENST00000268489	NM_006885.3	1324	aCc/aTc	9/10	1	2	FACETS	0.982	0.858	1	0.982	0.858	1	CLONAL	1	TRUE	1	0.723324500887338	2		360	152	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347244	89347245	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	97	719	2	ENST00000301030.4:c.5705_5706delinsTT	p.Ser1902Phe	p.S1902F	ENST00000301030	NM_001256183.1	1902	tCC/tTT	9/13	1	2	FACETS	0.909	0.821	1	0.909	0.821	1	CLONAL	1	TRUE	1	0.723324500887338	2		721	295	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577541	7577541	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	188	871	0	ENST00000269305.4:c.740A>C	p.Asn247Thr	p.N247T	ENST00000269305	NM_001126112.2	247	aAc/aCc	7/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.723324500887338	2		871	511	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260151	10260151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	157	763	0	ENST00000340748.4:c.2516C>T	p.Pro839Leu	p.P839L	ENST00000340748		839	cCc/cTc	25/40	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.723324500887338	2		763	428	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228800	36228800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393734909	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	211	905	0	ENST00000222270.7:c.7699C>T	p.Arg2567Cys	p.R2567C	ENST00000222270	NM_014727.1	2567	Cgt/Tgt	35/37	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.723324500887338	2		905	563	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917021	50917021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	165	728	0	ENST00000440232.2:c.2273C>T	p.Ser758Phe	p.S758F	ENST00000440232	NM_002691.3	758	tCc/tTc	19/27	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.723324500887338	2		728	384	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919774	50919774	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	119	718	0	ENST00000440232.2:c.2942C>T	p.Ala981Val	p.A981V	ENST00000440232	NM_002691.3	981	gCt/gTt	23/27	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.723324500887338	2		718	278	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021550	31021550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs755464186	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	171	751	0	ENST00000375687.4:c.1549C>T	p.Gln517Ter	p.Q517*	ENST00000375687	NM_015338.5	517	Cag/Tag	12/13	1	2	FACETS	0.877	0.812	0.944	0.877	0.812	0.944	CLONAL	1	TRUE	1	0.723324500887338	2		751	539	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545097	41545097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760686401	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	173	885	1	ENST00000263253.7:c.2297C>T	p.Pro766Leu	p.P766L	ENST00000263253	NM_001429.3	766	cCt/cTt	13/31	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.723324500887338	2		886	478	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468364	89468364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	55	329	0	ENST00000336596.2:c.1898G>A	p.Gly633Glu	p.G633E	ENST00000336596	NM_005233.5	633	gGa/gAa	11/17	NA	2	FACETS	0.845	0.736	0.96			1	INDETERMINATE	1	TRUE	NA	0.723324500887338	2		329	180	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521619	89521619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	94	613	1	ENST00000336596.2:c.2696C>T	p.Ser899Leu	p.S899L	ENST00000336596	NM_005233.5	899	tCa/tTa	16/17	NA	2	FACETS	0.932	0.841	1			1	INDETERMINATE	1	TRUE	NA	0.723324500887338	2		614	279	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851769	134851769	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	100	805	1	ENST00000398015.3:c.1175C>T	p.Ser392Phe	p.S392F	ENST00000398015	NM_004441.4	392	tCc/tTc	5/16	NA	2	FACETS	1	0.944	1			1	INDETERMINATE	1	TRUE	NA	0.723324500887338	2		806	262	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911655	134911655	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	54	503	0	ENST00000398015.3:c.2120C>T	p.Ser707Phe	p.S707F	ENST00000398015	NM_004441.4	707	tCt/tTt	11/16	NA	2	FACETS	0.982	0.858	1			1	INDETERMINATE	1	TRUE	NA	0.723324500887338	2		503	152	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665252	138665252	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	107	966	0	ENST00000330315.3:c.313A>T	p.Asn105Tyr	p.N105Y	ENST00000330315	NM_023067.3	105	Aac/Tac	1/1	NA	2	FACETS	0.996	0.906	1			1	INDETERMINATE	1	TRUE	NA	0.723324500887338	2		966	297	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938933	178938933	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	102	548	0	ENST00000263967.3:c.2175T>A	p.Asp725Glu	p.D725E	ENST00000263967	NM_006218.2	725	gaT/gaA	14/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.723324500887338	2		548	264	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751230	57751230	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	141	563	1	ENST00000274289.3:c.1637A>T	p.Tyr546Phe	p.Y546F	ENST00000274289	NM_006622.3	546	tAt/tTt	12/14	1	2	FACETS	0.913	0.84	0.989	0.913	0.84	0.989	CLONAL	1	TRUE	1	0.723324500887338	2		564	427	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501595	149501595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	81	479	0	ENST00000261799.4:c.2192C>T	p.Ser731Phe	p.S731F	ENST00000261799	NM_002609.3	731	tCc/tTc	16/23	0.158140380699127	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.723324500887338	0		479	225	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562495	176562495	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	36	971	0	ENST00000439151.2:c.391T>C	p.Ser131Pro	p.S131P	ENST00000439151	NM_022455.4	131	Tct/Cct	2/23	0.723324500887338	1	FACETS	0.21	0.173	0.251	0.21	0.173	0.251	SUBCLONAL	1	TRUE	0	0.723324500887338	1		971	303	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200308	138200308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	118	556	1	ENST00000237289.4:c.1726C>T	p.Pro576Ser	p.P576S	ENST00000237289	NM_001270507.1	576	Ccg/Tcg	7/9	0.227116041453938	3	FACETS	1	0.977	1	0.609	0.555	0.664	INDETERMINATE	1	TRUE	1	0.723324500887338	3		557	365	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984094	2984094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	75	543	1	ENST00000396946.4:c.436G>A	p.Asp146Asn	p.D146N	ENST00000396946	NM_032415.4	146	Gac/Aac	5/25	0.723324500887338	1	FACETS	0.693	0.62	0.768	0.693	0.62	0.768	SUBCLONAL	1	TRUE	0	0.723324500887338	1		544	191	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080342	5080342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	64	583	2	ENST00000381652.3:c.2245G>A	p.Gly749Arg	p.G749R	ENST00000381652	NM_004972.3	749	Gga/Aga	17/25	0.253110695048254	1	FACETS	0.338	0.294	0.385	0.338	0.294	0.385	INDETERMINATE	1	TRUE	0	0.723324500887338	1		585	334	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518284	8518284	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	38	431	0	ENST00000356435.5:c.1107A>C	p.Glu369Asp	p.E369D	ENST00000356435		369	gaA/gaC	10/35	0.253110695048254	1	FACETS	0.344	0.287	0.406	0.344	0.287	0.406	INDETERMINATE	1	TRUE	0	0.723324500887338	1		431	195	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221991	98221992	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	255	625	2	ENST00000331920.6:c.2777_2778delinsAA	p.Trp926Ter	p.W926*	ENST00000331920	NM_000264.3	926	tGG/tAA	17/24	0.249559200150796	3	FACETS	0.97	0.934	1			1	INDETERMINATE	3	TRUE	NA	0.723324500887338	3		627	330	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164455	36164455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	106	380	0	ENST00000300305.3:c.1420G>A	p.Glu474Lys	p.E474K	ENST00000300305		474	Gag/Aag	8/8	0.186697033980074	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.723324500887338	0		380	270	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720983	176720983	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	23	646	0	ENST00000439151.2:c.6614A>C	p.His2205Pro	p.H2205P	ENST00000439151	NM_022455.4	2205	cAt/cCt	23/23	NA	2	FACETS	0.249	0.195	0.312			1	INDETERMINATE	1	TRUE	NA	0.723324500887338	2		646	255	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047151	77047151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	303	756	0	ENST00000356341.3:c.1393C>T	p.Leu465Phe	p.L465F	ENST00000356341	NM_002576.4	465	Ctc/Ttc	13/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.568000339427117	2		756	1048	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	393	622	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.568000339427117	2		623	1368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	452	912	0	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	0.568000339427117	2		912	1423	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521711	89521711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	272	781	1	ENST00000336596.2:c.2788G>A	p.Glu930Lys	p.E930K	ENST00000336596	NM_005233.5	930	Gaa/Aaa	16/17	1	2	FACETS	0.964	0.905	1	0.964	0.905	1	CLONAL	1	TRUE	1	0.568000339427117	2		782	994	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330546	65330546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	698	801	0	ENST00000342505.4:c.1100C>T	p.Ser367Phe	p.S367F	ENST00000342505	NM_002227.2	367	tCt/tTt	8/25	0.439712241355497	3	FACETS	1	0.996	1	0.781	0.756	0.806	CLONAL	2	TRUE	0	0.568000339427117	3		801	1347	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202301	133202301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	347	878	0	ENST00000320574.5:c.6587C>T	p.Ser2196Phe	p.S2196F	ENST00000320574	NM_006231.2	2196	tCc/tTc	47/49	1	2	FACETS	0.964	0.912	1	0.964	0.912	1	CLONAL	1	TRUE	1	0.568000339427117	2		878	1268	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101468	27101468	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	1167	788	1	ENST00000324856.7:c.4750C>T	p.Gln1584Ter	p.Q1584*	ENST00000324856	NM_006015.4	1584	Cag/Tag	18/20	0.568000339427117	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.568000339427117	3		789	1666	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636820	8636820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369741244	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	300	720	3	ENST00000356435.5:c.89C>T	p.Pro30Leu	p.P30L	ENST00000356435		30	cCc/cTc	2/35	0.559727237948782	3	FACETS	1	0.956	1	0.51	0.479	0.541	CLONAL	1	TRUE	1	0.568000339427117	3		723	1331	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4102441	4102441	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1291541587	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	347	802	0	ENST00000262948.5:c.461C>T	p.Ser154Phe	p.S154F	ENST00000262948	NM_030662.3	154	tCc/tTc	4/11	1	2	FACETS	0.974	0.922	1	0.974	0.922	1	CLONAL	1	TRUE	1	0.568000339427117	2		802	1254	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295705	212295705	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	180	753	0	ENST00000342788.4:c.2608G>A	p.Gly870Arg	p.G870R	ENST00000342788	NM_005235.2	870	Gga/Aga	21/28	1	2	FACETS	0.832	0.769	0.897	0.832	0.769	0.897	CLONAL	1	TRUE	1	0.568000339427117	2		753	762	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576148	88576148	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	395	927	0	ENST00000360948.2:c.1525C>T	p.Pro509Ser	p.P509S	ENST00000360948	NM_001012338.2	509	Cct/Tct	13/19	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.568000339427117	2		927	1179	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46275850	46275850	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1206893490	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	286	872	1	ENST00000371998.3:c.3286C>T	p.Gln1096Ter	p.Q1096*	ENST00000371998		1096	Caa/Taa	18/23	1	2	FACETS	0.866	0.814	0.919	0.866	0.814	0.919	CLONAL	1	TRUE	1	0.568000339427117	2		873	1163	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270180	66270180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763063348	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	201	480	0	ENST00000273854.3:c.1702G>A	p.Asp568Asn	p.D568N	ENST00000273854	NM_004439.5	568	Gat/Aat	8/18	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.568000339427117	2		480	688	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651315	45651315	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	343	746	1	ENST00000407780.3:c.710G>A	p.Gly237Glu	p.G237E	ENST00000407780	NM_001283052.1	237	gGa/gAa	5/7	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.568000339427117	2		747	1130	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520241	176520241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	342	932	0	ENST00000292408.4:c.1160C>T	p.Ala387Val	p.A387V	ENST00000292408	NM_213647.1	387	gCc/gTc	9/18	1	2	FACETS	0.993	0.939	1	0.993	0.939	1	CLONAL	1	TRUE	1	0.568000339427117	2		932	1213	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891642	28891642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	309	822	0	ENST00000282397.4:c.3379C>T	p.Pro1127Ser	p.P1127S	ENST00000282397	NM_002019.4	1127	Cct/Tct	25/30	1	2	FACETS	0.949	0.895	1	0.949	0.895	1	CLONAL	1	TRUE	1	0.568000339427117	2		822	1146	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993833	72993833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374747520	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	229	580	0	ENST00000268489.5:c.212C>T	p.Pro71Leu	p.P71L	ENST00000268489	NM_006885.3	71	cCc/cTc	2/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.568000339427117	2		580	759	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66520180	66520180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568696484	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	243	706	4	ENST00000358598.2:c.464C>T	p.Ser155Leu	p.S155L	ENST00000358598	NM_212471.2	155	tCg/tTg	5/11	1	2	FACETS	0.928	0.868	0.989	0.928	0.868	0.989	CLONAL	1	TRUE	1	0.568000339427117	2		710	922	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238322	98238323	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	202	559	0	ENST00000331920.6:c.1721_1722delinsTT	p.Ser574Phe	p.S574F	ENST00000331920	NM_000264.3	574	tCC/tTT	12/24	0.568000339427117	1	FACETS	0.976	0.912	1	0.976	0.912	1	CLONAL	1	TRUE	0	0.568000339427117	1		559	522	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609942	43609942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767407	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	393	1026	0	ENST00000355710.3:c.1894G>A	p.Glu632Lys	p.E632K	ENST00000355710	NM_020975.4	632	Gag/Aag	11/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.568000339427117	2		1026	1348	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850663	63850663	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	224	615	0	ENST00000279873.7:c.1441C>T	p.Gln481Ter	p.Q481*	ENST00000279873	NM_032199.2	481	Cag/Tag	10/10	1	2	FACETS	0.96	0.896	1	0.96	0.896	1	CLONAL	1	TRUE	1	0.568000339427117	2		615	822	SUCCESS
CBL	867	MSKCC	GRCh37	11	119077177	119077177	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1222060551	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	341	742	1	ENST00000264033.4:c.50C>A	p.Ser17Tyr	p.S17Y	ENST00000264033	NM_005188.3	17	tCc/tAc	1/16	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.568000339427117	2		743	1082	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434130	49434130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	359	727	0	ENST00000301067.7:c.7423C>T	p.Pro2475Ser	p.P2475S	ENST00000301067	NM_003482.3	2475	Cct/Tct	31/54	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.568000339427117	2		727	1108	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856608	111856608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	218	321	0	ENST00000341259.2:c.659G>A	p.Gly220Glu	p.G220E	ENST00000341259	NM_005475.2	220	gGg/gAg	2/8	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.568000339427117	2		321	582	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030468	49030468	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	189	736	0	ENST00000267163.4:c.1943C>T	p.Ser648Leu	p.S648L	ENST00000267163	NM_000321.2	648	tCa/tTa	19/27	1	2	FACETS	0.893	0.828	0.961	0.893	0.828	0.961	CLONAL	1	TRUE	1	0.568000339427117	2		736	745	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352674	68352674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199981178	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	144	641	0	ENST00000487270.1:c.541C>T	p.Arg181Trp	p.R181W	ENST00000487270	NM_133509.3	181	Cgg/Tgg	6/11	1	2	FACETS	0.747	0.683	0.814	0.747	0.683	0.814	SUBCLONAL	1	TRUE	1	0.568000339427117	2		641	679	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028729	42028729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	272	779	0	ENST00000219905.7:c.4267C>T	p.Pro1423Ser	p.P1423S	ENST00000219905	NM_001164273.1	1423	Cct/Tct	13/24	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.568000339427117	2		779	956	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73995358	73995358	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	203	426	0	ENST00000318443.5:c.664G>T	p.Val222Leu	p.V222L	ENST00000318443	NM_001024736.1	222	Gtg/Ttg	4/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.568000339427117	2		426	670	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122360	2122360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	317	708	0	ENST00000219476.3:c.2216C>T	p.Ser739Phe	p.S739F	ENST00000219476	NM_000548.3	739	tCc/tTc	20/42	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.568000339427117	2		708	1075	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813746	50813746	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	399	945	1	ENST00000398568.2:c.1300C>T	p.Pro434Ser	p.P434S	ENST00000398568	NM_001042412.1	434	Cca/Tca	8/18	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.568000339427117	2		946	1286	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829653	72829653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	377	891	2	ENST00000268489.5:c.6928G>A	p.Gly2310Arg	p.G2310R	ENST00000268489	NM_006885.3	2310	Gga/Aga	9/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.568000339427117	2		893	1201	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832610	72832610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777084031	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	118	360	0	ENST00000268489.5:c.3971C>T	p.Thr1324Ile	p.T1324I	ENST00000268489	NM_006885.3	1324	aCc/aTc	9/10	1	2	FACETS	0.913	0.829	1	0.913	0.829	1	CLONAL	1	TRUE	1	0.568000339427117	2		360	455	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347244	89347245	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	269	719	2	ENST00000301030.4:c.5705_5706delinsTT	p.Ser1902Phe	p.S1902F	ENST00000301030	NM_001256183.1	1902	tCC/tTT	9/13	1	2	FACETS	0.965	0.906	1	0.965	0.906	1	CLONAL	1	TRUE	1	0.568000339427117	2		721	982	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577541	7577541	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	394	871	0	ENST00000269305.4:c.740A>C	p.Asn247Thr	p.N247T	ENST00000269305	NM_001126112.2	247	aAc/aCc	7/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.568000339427117	2		871	1383	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260151	10260151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	336	763	0	ENST00000340748.4:c.2516C>T	p.Pro839Leu	p.P839L	ENST00000340748		839	cCc/cTc	25/40	1	2	FACETS	0.938	0.887	0.991	0.938	0.887	0.991	CLONAL	1	TRUE	1	0.568000339427117	2		763	1261	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228800	36228800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393734909	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	422	905	0	ENST00000222270.7:c.7699C>T	p.Arg2567Cys	p.R2567C	ENST00000222270	NM_014727.1	2567	Cgt/Tgt	35/37	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.568000339427117	2		905	1432	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917021	50917021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	263	728	0	ENST00000440232.2:c.2273C>T	p.Ser758Phe	p.S758F	ENST00000440232	NM_002691.3	758	tCc/tTc	19/27	1	2	FACETS	0.922	0.865	0.981	0.922	0.865	0.981	CLONAL	1	TRUE	1	0.568000339427117	2		728	1004	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919774	50919774	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	302	718	0	ENST00000440232.2:c.2942C>T	p.Ala981Val	p.A981V	ENST00000440232	NM_002691.3	981	gCt/gTt	23/27	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.568000339427117	2		718	1025	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021550	31021550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs755464186	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	301	751	0	ENST00000375687.4:c.1549C>T	p.Gln517Ter	p.Q517*	ENST00000375687	NM_015338.5	517	Cag/Tag	12/13	1	2	FACETS	0.961	0.905	1	0.961	0.905	1	CLONAL	1	TRUE	1	0.568000339427117	2		751	1103	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545097	41545097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760686401	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	380	885	1	ENST00000263253.7:c.2297C>T	p.Pro766Leu	p.P766L	ENST00000263253	NM_001429.3	766	cCt/cTt	13/31	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.568000339427117	2		886	1254	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468364	89468364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	104	329	0	ENST00000336596.2:c.1898G>A	p.Gly633Glu	p.G633E	ENST00000336596	NM_005233.5	633	gGa/gAa	11/17	1	2	FACETS	0.964	0.87	1	0.964	0.87	1	CLONAL	1	TRUE	1	0.568000339427117	2		329	380	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521619	89521619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	229	613	1	ENST00000336596.2:c.2696C>T	p.Ser899Leu	p.S899L	ENST00000336596	NM_005233.5	899	tCa/tTa	16/17	1	2	FACETS	0.974	0.91	1	0.974	0.91	1	CLONAL	1	TRUE	1	0.568000339427117	2		614	828	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851769	134851769	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	341	805	1	ENST00000398015.3:c.1175C>T	p.Ser392Phe	p.S392F	ENST00000398015	NM_004441.4	392	tCc/tTc	5/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.568000339427117	2		806	1101	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911655	134911655	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	221	503	0	ENST00000398015.3:c.2120C>T	p.Ser707Phe	p.S707F	ENST00000398015	NM_004441.4	707	tCt/tTt	11/16	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.568000339427117	2		503	711	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665252	138665252	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	426	966	0	ENST00000330315.3:c.313A>T	p.Asn105Tyr	p.N105Y	ENST00000330315	NM_023067.3	105	Aac/Tac	1/1	1	2	FACETS	0.964	0.917	1	0.964	0.917	1	CLONAL	1	TRUE	1	0.568000339427117	2		966	1556	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938933	178938933	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	221	548	0	ENST00000263967.3:c.2175T>A	p.Asp725Glu	p.D725E	ENST00000263967	NM_006218.2	725	gaT/gaA	14/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.568000339427117	2		548	748	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751230	57751230	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	225	563	1	ENST00000274289.3:c.1637A>T	p.Tyr546Phe	p.Y546F	ENST00000274289	NM_006622.3	546	tAt/tTt	12/14	1	2	FACETS	0.994	0.928	1	0.994	0.928	1	CLONAL	1	TRUE	1	0.568000339427117	2		564	797	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501595	149501595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	197	479	0	ENST00000261799.4:c.2192C>T	p.Ser731Phe	p.S731F	ENST00000261799	NM_002609.3	731	tCc/tTc	16/23	1	2	FACETS	0.988	0.918	1	0.988	0.918	1	CLONAL	1	TRUE	1	0.568000339427117	2		479	702	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562495	176562495	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	386	971	0	ENST00000439151.2:c.391T>C	p.Ser131Pro	p.S131P	ENST00000439151	NM_022455.4	131	Tct/Cct	2/23	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.568000339427117	2		971	1347	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200308	138200308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	264	556	1	ENST00000237289.4:c.1726C>T	p.Pro576Ser	p.P576S	ENST00000237289	NM_001270507.1	576	Ccg/Tcg	7/9	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.568000339427117	2		557	858	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984094	2984094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	230	543	1	ENST00000396946.4:c.436G>A	p.Asp146Asn	p.D146N	ENST00000396946	NM_032415.4	146	Gac/Aac	5/25	1	2	FACETS	0.915	0.854	0.978	0.915	0.854	0.978	CLONAL	1	TRUE	1	0.568000339427117	2		544	885	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080342	5080342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	118	583	2	ENST00000381652.3:c.2245G>A	p.Gly749Arg	p.G749R	ENST00000381652	NM_004972.3	749	Gga/Aga	17/25	0.559727237948782	3	FACETS	0.77	0.695	0.848	0.385	0.347	0.424	SUBCLONAL	1	TRUE	1	0.568000339427117	3		585	693	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518284	8518284	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	185	431	0	ENST00000356435.5:c.1107A>C	p.Glu369Asp	p.E369D	ENST00000356435		369	gaA/gaC	10/35	0.559727237948782	3	FACETS	1	0.956	1	0.524	0.485	0.565	CLONAL	1	TRUE	1	0.568000339427117	3		431	798	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221991	98221992	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	289	625	2	ENST00000331920.6:c.2777_2778delinsAA	p.Trp926Ter	p.W926*	ENST00000331920	NM_000264.3	926	tGG/tAA	17/24	0.568000339427117	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.568000339427117	1		627	724	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164455	36164455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	146	380	0	ENST00000300305.3:c.1420G>A	p.Glu474Lys	p.E474K	ENST00000300305		474	Gag/Aag	8/8	1	2	FACETS	0.948	0.87	1	0.948	0.87	1	CLONAL	1	TRUE	1	0.568000339427117	2		380	542	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059314	42059314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	226	529	1	ENST00000219905.7:c.9034C>T	p.Pro3012Ser	p.P3012S	ENST00000219905	NM_001164273.1	3012	Cct/Tct	24/24	1	2	FACETS	0.948	0.885	1	0.948	0.885	1	CLONAL	1	TRUE	1	0.568000339427117	2		530	839	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	122	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.855	0.773	0.942	0.855	0.773	0.942	CLONAL	1	TRUE	1	0.366755549830148	2		555	778	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520008	NA	P-0020182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	164	1014	0	ENST00000269305.4:c.613T>C	p.Tyr205His	p.Y205H	ENST00000269305	NM_001126112.2	205	Tat/Cat	6/11	0.366755549830148	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.366755549830148	1		1014	651	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575137	48575137	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	142	520	0	ENST00000342988.3:c.331C>G	p.His111Asp	p.H111D	ENST00000342988	NM_005359.5	111	Cat/Gat	3/12	0.366755549830148	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.366755549830148	1		520	579	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0020182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	58	853	0	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	1	2	FACETS	0.452	0.387	0.522	0.452	0.387	0.522	SUBCLONAL	1	TRUE	1	0.366755549830148	2		853	700	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170346	32170346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	165	1050	0	ENST00000375023.3:c.3262G>A	p.Ala1088Thr	p.A1088T	ENST00000375023	NM_004557.3	1088	Gcc/Acc	21/30	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.366755549830148	2		1050	839	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914728	39914729	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0020182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	160	850	0	ENST00000378444.4:c.4633_4634del	p.Ile1545CysfsTer10	p.I1545Cfs*10	ENST00000378444	NM_001123385.1	1545	ATt/t	12/15	0.366755549830148	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.366755549830148	1		850	650	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	565	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.319646614033422	5	FACETS	0.985	0.947	1			1	CLONAL	4	TRUE	NA	0.319646614033422	5		555	1328	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971026	21971026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	187	731	0	ENST00000304494.5:c.332G>T	p.Gly111Val	p.G111V	ENST00000304494	NM_000077.4	111	gGc/gTc	2/3	0.319646614033422	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.319646614033422	2		731	502	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068919	30068919	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	55	1038	0	ENST00000331968.5:c.2010C>G	p.Ile670Met	p.I670M	ENST00000331968	NM_002742.2	670	atC/atG	14/18	0.233741338609416	2	FACETS	0.413	0.352	0.479	0.206	0.176	0.24	SUBCLONAL	1	TRUE	0	0.319646614033422	2		1038	834	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986630	36986631	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTGC	novel	NA	P-0020184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	31	274	0	ENST00000354822.5:c.1055_1058dup	p.Ser353ArgfsTer87	p.S353Rfs*87	ENST00000354822	NM_001079668.2	353	agc/agGCAGc	3/3	0.319646614033422	1	FACETS	0.926	0.757	1	0.926	0.757	1	CLONAL	1	TRUE	0	0.319646614033422	1		274	176	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349904	89349904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141871215	NA	P-0020184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	292	1193	0	ENST00000301030.4:c.3046G>A	p.Asp1016Asn	p.D1016N	ENST00000301030	NM_001256183.1	1016	Gat/Aat	9/13	0.233072316039691	4	FACETS	0.998	0.938	1	0.998	0.938	1	CLONAL	2	TRUE	2	0.319646614033422	4		1193	1208	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579363	+	inframe_deletion	In_Frame_Del	DEL	AGACGGAAA	AGACGGAAA	-	novel	NA	P-0020184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	201	961	0	ENST00000269305.4:c.324_332del	p.Phe109_Leu111del	p.F109_L111del	ENST00000269305	NM_001126112.2	108	ggTTTCCGTCTg/ggg	4/11	0.319646614033422	2	FACETS	0.99	0.923	1	0.99	0.923	1	CLONAL	2	TRUE	0	0.319646614033422	2		961	635	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554635	63554635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748495558	NA	P-0020184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	94	776	0	ENST00000307078.5:c.104C>T	p.Pro35Leu	p.P35L	ENST00000307078	NM_004655.3	35	cCg/cTg	2/11	0.319646614033422	3	FACETS	0.932	0.829	1	0.466	0.414	0.521	CLONAL	1	TRUE	1	0.319646614033422	3		776	732	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120810	115120810	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	23	619	0	ENST00000257566.3:c.196del	p.Asp66IlefsTer22	p.D66Ifs*22	ENST00000257566	NM_016569.3	66	Gat/at	1/8	1	2	FACETS	0.418	0.325	0.526	0.418	0.325	0.526	SUBCLONAL	1	TRUE	1	0.25	2		619	440	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0020187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	43	1334	0	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	1	2	FACETS	0.328	0.273	0.39	0.328	0.273	0.39	SUBCLONAL	1	TRUE	1	0.25	2		1334	1048	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984085	2984085	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	27	606	1	ENST00000396946.4:c.445C>T	p.Arg149Cys	p.R149C	ENST00000396946	NM_032415.4	149	Cgc/Tgc	5/25	0.312034056449531	0	FACETS	0.451	0.359	0.557			1	SUBCLONAL	1	TRUE	0	0.25	0		607	359	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604673	48604673	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060500738	NA	P-0020189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	216	720	0	ENST00000342988.3:c.1495T>C	p.Cys499Arg	p.C499R	ENST00000342988	NM_005359.5	499	Tgc/Cgc	12/12	0.60742398877609	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.60742398877609	2		720	329	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0020189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	244	674	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.473654300972406	4	FACETS	0.936	0.879	0.993	0.936	0.879	0.993	CLONAL	2	TRUE	2	0.60742398877609	4		674	690	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152055	11152055	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs878854224	NA	P-0020189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	337	825	2	ENST00000358026.2:c.4339C>T	p.Arg1447Ter	p.R1447*	ENST00000358026	NM_001128849.1	1447	Cga/Tga	31/36	0.60742398877609	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.60742398877609	2		827	494	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244853	46244853	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	410	1189	0	ENST00000334344.6:c.2947C>T	p.Gln983Ter	p.Q983*	ENST00000334344	NM_152641.2	983	Caa/Taa	15/21	0.473654300972406	4	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	2	0.60742398877609	4		1189	1080	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46603791	46603791	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	150	1073	0	ENST00000263734.3:c.1148C>T	p.Ser383Phe	p.S383F	ENST00000263734	NM_001430.4	383	tCt/tTt	9/16	0.60742398877609	3	FACETS	0.982	0.9	1	0.491	0.45	0.534	CLONAL	1	TRUE	1	0.60742398877609	3		1073	656	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358955	81358955	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs549654942	NA	P-0020189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	250	963	3	ENST00000222390.5:c.1006G>A	p.Glu336Lys	p.E336K	ENST00000222390	NM_000601.4	336	Gag/Aag	8/18	0.473654300972406	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	2	0.60742398877609	4		966	650	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945675	151945677	+	frameshift_variant	Frame_Shift_Del	DEL	AAT	AAT	C	novel	NA	P-0020190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	46	1226	0	ENST00000262189.6:c.1842_1844delinsG	p.Leu615GlyfsTer6	p.L615Gfs*6	ENST00000262189	NM_170606.2	614	gaATTg/gaGg	14/59	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		1226	701	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0020192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	225	773	1	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.376851425584118	6	FACETS	1	0.961	1	0.777	0.727	0.828	CLONAL	3	TRUE	2	0.376851425584118	6		774	674	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0020192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	24	930	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	1	2	FACETS	0.376	0.294	0.469	0.376	0.294	0.469	SUBCLONAL	1	TRUE	1	0.376851425584118	2		930	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579575	7579575	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	25	834	0	ENST00000269305.4:c.112C>T	p.Gln38Ter	p.Q38*	ENST00000269305	NM_001126112.2	38	Caa/Taa	4/11	1	2	FACETS	0.351	0.276	0.437	0.351	0.276	0.437	SUBCLONAL	1	TRUE	1	0.376851425584118	2		834	378	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334738	81334738	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	89	867	1	ENST00000222390.5:c.1978G>T	p.Gly660Trp	p.G660W	ENST00000222390	NM_000601.4	660	Ggg/Tgg	17/18	0.346901673315395	3	FACETS	1	0.959	1	0.581	0.517	0.649	CLONAL	1	TRUE	1	0.376851425584118	3		868	483	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719140	190719140	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0020192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	19	541	0	ENST00000441310.2:c.1142C>G	p.Ser381Ter	p.S381*	ENST00000441310	NM_000534.4	381	tCa/tGa	9/13	0.341971080008999	3	FACETS	0.39	0.296	0.501	0.195	0.148	0.251	SUBCLONAL	1	TRUE	1	0.376851425584118	3		541	307	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579581	7579581	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	24	786	0	ENST00000269305.4:c.106C>G	p.Pro36Ala	p.P36A	ENST00000269305	NM_001126112.2	36	Ccg/Gcg	4/11	1	2	FACETS	0.362	0.283	0.452	0.362	0.283	0.452	SUBCLONAL	1	TRUE	1	0.376851425584118	2		786	352	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246277	41246277	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	29	921	1	ENST00000357654.3:c.1271del	p.Gly424ValfsTer6	p.G424Vfs*6	ENST00000357654	NM_007294.3	424	gGt/gt	10/23	NA	2	FACETS	0.363	0.291	0.445			1	INDETERMINATE	1	TRUE	NA	0.376851425584118	2		922	424	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944516	40944516	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	42	744	0	ENST00000373198.4:c.1986C>A	p.His662Gln	p.H662Q	ENST00000373198	NM_133170.3	662	caC/caA	12/32	0.376851425584118	3	FACETS	0.534	0.446	0.632	0.267	0.223	0.316	SUBCLONAL	1	TRUE	1	0.376851425584118	3		744	496	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93953249	93953249	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	21	825	1	ENST00000369303.4:c.2892G>T	p.Met964Ile	p.M964I	ENST00000369303	NM_004440.3	964	atG/atT	17/17	0.220615307599333	3	FACETS	0.336	0.258	0.427	0.168	0.129	0.214	INDETERMINATE	1	TRUE	1	0.376851425584118	3		826	394	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157952	27157952	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	77	808	0	ENST00000380036.4:c.176G>C	p.Arg59Thr	p.R59T	ENST00000380036	NM_000459.3	59	aGg/aCg	2/23	0.269524060014052	5	FACETS	1	0.914	1	0.35	0.307	0.396	CLONAL	1	TRUE	2	0.376851425584118	5		808	609	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045858	47045883	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCCTCCCTCACACAGGCCCAAACACG	GCCTCCCTCACACAGGCCCAAACACG	A	novel	NA	P-0020192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	36	597	0	ENST00000377604.3:c.2668-15_2678delinsA		p.X890_splice	ENST00000377604	NM_001204468.1	890		24/24	1	2	FACETS	0.614	0.507	0.734	0.614	0.507	0.734	SUBCLONAL	1	TRUE	1	0.376851425584118	2		597	311	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	304	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.467162751984335	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.467162751984335	3		555	750	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	351	932	0	ENST00000269305.4:c.470T>G	p.Val157Gly	p.V157G	ENST00000269305	NM_001126112.2	157	gTc/gGc	5/11	NA	2	FACETS	0.994	0.948	1			1	INDETERMINATE	2	TRUE	NA	0.467162751984335	2		932	756	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399158	139399158	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774808496	NA	P-0020213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	154	856	0	ENST00000277541.6:c.4985G>A	p.Arg1662Gln	p.R1662Q	ENST00000277541	NM_017617.3	1662	cGg/cAg	26/34	0.449109835344251	3	FACETS	0.985	0.902	1	0.492	0.451	0.536	CLONAL	1	TRUE	1	0.467162751984335	3		856	826	SUCCESS
EED	8726	MSKCC	GRCh37	11	85979511	85979511	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	270	535	2	ENST00000263360.6:c.874C>T	p.Gln292Ter	p.Q292*	ENST00000263360	NM_003797.3	292	Cag/Tag	9/12	0.291797131871008	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.291797131871008	2		537	833	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923060	44923060	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	243	709	0	ENST00000377967.4:c.1921C>T	p.Gln641Ter	p.Q641*	ENST00000377967	NM_021140.2	641	Cag/Tag	16/29	0.291797131871008	2	FACETS	0.942	0.882	1	0.942	0.882	1	CLONAL	2	TRUE	0	0.291797131871008	2		709	884	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710981	114710981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	171	469	0	ENST00000543371.1:c.205C>T	p.Pro69Ser	p.P69S	ENST00000543371	NM_001198531.1	69	Ccg/Tcg	2/14	0.291797131871008	3	FACETS	0.973	0.898	1	0.973	0.898	1	CLONAL	2	TRUE	1	0.291797131871008	3		469	690	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281494	15281494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	130	768	1	ENST00000263388.2:c.4879C>T	p.Arg1627Trp	p.R1627W	ENST00000263388	NM_000435.2	1627	Cgg/Tgg	26/33	0.291797131871008	3	FACETS	0.932	0.843	1	0.466	0.421	0.513	CLONAL	1	TRUE	1	0.291797131871008	3		769	1096	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0020215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	45	408	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.868	0.73	1	0.868	0.73	1	CLONAL	1	TRUE	1	0.234665308178221	2		408	442	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653784	89653785	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0020215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	33	457	0	ENST00000371953.3:c.82_83insCT	p.Ile28ThrfsTer27	p.I28Tfs*27	ENST00000371953	NM_000314.4	28	att/aCTtt	2/9	1	2	FACETS	0.605	0.492	0.732	0.605	0.492	0.732	SUBCLONAL	1	TRUE	1	0.234665308178221	2		457	465	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905489	11905489	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs781022272	NA	P-0020215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	54	378	0	ENST00000396373.4:c.139T>G	p.Ser47Ala	p.S47A	ENST00000396373	NM_001987.4	47	Tcg/Gcg	2/8	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.234665308178221	2		378	397	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0020218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	750	511	1	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.856762688482013	3	FACETS	0.993	0.977	1	0.993	0.977	1	CLONAL	3	TRUE	0	0.852141594593329	3		512	843	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867546	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGC	GGCGGCGGC	-	rs11466445	NA	P-0020218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	15	43	0	ENST00000374994.4:c.70_78del	p.Ala24_Ala26del	p.A24_A26del	ENST00000374994	NM_004612.2	17	ctGGCGGCGGCg/ctg	1/9	1	2	FACETS	0.733	0.558	0.926	0.733	0.558	0.926	CLONAL	1	TRUE	1	0.852141594593329	2		43	48	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394946	394946	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	263	537	0	ENST00000380956.4:c.342C>A	p.Ser114Arg	p.S114R	ENST00000380956	NM_001195286.1	114	agC/agA	3/9	NA	2	FACETS	1	0.961	1			1	INDETERMINATE	1	TRUE	NA	0.852141594593329	2		537	605	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853790	59853790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878855144	NA	P-0020218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	279	609	2	ENST00000259008.2:c.2069G>A	p.Gly690Glu	p.G690E	ENST00000259008	NM_032043.2	690	gGa/gAa	14/20	1	2	FACETS	0.972	0.919	1	0.972	0.919	1	CLONAL	1	TRUE	1	0.852141594593329	2		611	674	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54956557	54956557	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	50	679	1	ENST00000312783.6:c.637G>T	p.Ala213Ser	p.A213S	ENST00000312783	NM_198436.1	213	Gca/Tca	7/10	NA	2	FACETS	0.154	0.13	0.18			1	INDETERMINATE	1	TRUE	NA	0.852141594593329	2		680	764	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439713	140439713	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	278	508	0	ENST00000288602.6:c.2026C>G	p.Pro676Ala	p.P676A	ENST00000288602	NM_004333.4	676	Cca/Gca	17/18	0.856762688482013	3	FACETS	1	0.969	1	0.348	0.327	0.369	CLONAL	1	TRUE	0	0.852141594593329	3		508	892	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	210	122	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.866	0.81	0.924	0.866	0.81	0.924	CLONAL	1	TRUE	1	0.831669816654367	2		122	583	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0020219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	123	375	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.831669816654367	2		375	283	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167772	56167772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	109	593	0	ENST00000399503.3:c.1337G>A	p.Cys446Tyr	p.C446Y	ENST00000399503	NM_005921.1	446	tGc/tAc	7/20	1	2	FACETS	0.463	0.417	0.512	0.463	0.417	0.512	SUBCLONAL	1	TRUE	1	0.831669816654367	2		593	566	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706937	117706937	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	457	777	0	ENST00000368508.3:c.2213A>G	p.Glu738Gly	p.E738G	ENST00000368508	NM_002944.2	738	gAg/gGg	15/43	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.831669816654367	2		777	984	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859764	151859764	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748311863	NA	P-0020219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	115	490	0	ENST00000262189.6:c.10898C>T	p.Pro3633Leu	p.P3633L	ENST00000262189	NM_170606.2	3633	cCg/cTg	43/59	0.831669816654367	3	FACETS	0.537	0.484	0.593	0.269	0.242	0.297	SUBCLONAL	1	TRUE	1	0.831669816654367	3		490	729	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061141	38061141	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	76	254	0	ENST00000250448.2:c.848G>A	p.Gly283Glu	p.G283E	ENST00000250448	NM_004496.3	283	gGg/gAg	2/2	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.562499878043726	2		254	258	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061154	38061154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	91	292	0	ENST00000250448.2:c.835G>A	p.Gly279Arg	p.G279R	ENST00000250448	NM_004496.3	279	Ggg/Agg	2/2	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.562499878043726	2		292	310	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38064160	38064160	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	249	656	1	ENST00000250448.2:c.18G>T	p.Lys6Asn	p.K6N	ENST00000250448	NM_004496.3	6	aaG/aaT	1/2	1	2	FACETS	0.993	0.93	1	0.993	0.93	1	CLONAL	1	TRUE	1	0.562499878043726	2		657	892	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857509	68857516	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGAATT	GAGGAATT	-	novel	NA	P-0020220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	202	631	0	ENST00000261769.5:c.2144_2151del	p.Gly715AlafsTer30	p.G715Afs*30	ENST00000261769	NM_004360.3	715	gGAGGAATT/g	13/16	0.562499878043726	1	FACETS	0.879	0.821	0.94	0.879	0.821	0.94	CLONAL	1	TRUE	0	0.562499878043726	1		631	587	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026323	48026323	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	158	499	0	ENST00000234420.5:c.1201G>A	p.Asp401Asn	p.D401N	ENST00000234420	NM_000179.2	401	Gat/Aat	4/10	1	2	FACETS	0.918	0.845	0.994	0.918	0.845	0.994	CLONAL	1	TRUE	1	0.562499878043726	2		499	612	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730828	40730835	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCGGTC	CAGCGGTC	-	novel	NA	P-0020220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	54	879	0	ENST00000373198.4:c.3700_3707del	p.Asp1234ProfsTer22	p.D1234Pfs*22	ENST00000373198	NM_133170.3	1234	GACCGCTGc/c	27/32	1	2	FACETS	0.185	0.157	0.216	0.185	0.157	0.216	SUBCLONAL	1	TRUE	1	0.562499878043726	2		879	1036	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	363	971	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	0.239570818705056	5	FACETS	1	0.988	1	0.753	0.714	0.793	INDETERMINATE	2	TRUE	2	0.44530057977108	5		971	1203	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0020223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	366	828	3	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	0.438083884745991	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.44530057977108	2		831	806	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533676	63533676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367697282	NA	P-0020223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1278	81	648	0	ENST00000307078.5:c.1478C>T	p.Ser493Leu	p.S493L	ENST00000307078	NM_004655.3	493	tCg/tTg	6/11	0.44530057977108	8	FACETS	0.625	0.549	0.708			1	SUBCLONAL	1	TRUE	NA	0.44530057977108	8		648	1359	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942670	48942671	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs587778829	NA	P-0020223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	34	488	0	ENST00000267163.4:c.1060_1061del	p.Gln354GlufsTer7	p.Q354Efs*7	ENST00000267163	NM_000321.2	353	ACa/a	11/27	0.239570818705056	5	FACETS	0.451	0.367	0.545	0.15	0.122	0.182	INDETERMINATE	1	TRUE	2	0.44530057977108	5		488	565	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16041455	16041488	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGCAAACCATGTCTTACCTTCCTCTCCAAGTATG	TGCAAACCATGTCTTACCTTCCTCTCCAAGTATG	-	novel	NA	P-0020223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	89	445	0	ENST00000268712.3:c.1391_1407+17del		p.X464_splice	ENST00000268712	NM_006311.3	464		13/46	0.438083884745991	2	FACETS	1	0.977	1	0.678	0.608	0.75	CLONAL	1	TRUE	0	0.44530057977108	2		445	295	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38506052	38506052	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	47	703	2	ENST00000254066.5:c.344G>T	p.Ser115Ile	p.S115I	ENST00000254066	NM_000964.3	115	aGc/aTc	4/9	0.259417368329431	5	FACETS	0.375	0.315	0.442			1	INDETERMINATE	1	TRUE	NA	0.44530057977108	5		705	939	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607161	189607161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	111	977	1	ENST00000264731.3:c.1540G>A	p.Gly514Arg	p.G514R	ENST00000264731	NM_003722.4	514	Gga/Aga	12/14	0.419245720108667	4	FACETS	0.638	0.572	0.708	0.319	0.286	0.354	SUBCLONAL	1	TRUE	2	0.44530057977108	4		978	1130	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748273	41748273	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	403	915	0	ENST00000226382.2:c.496G>A	p.Ala166Thr	p.A166T	ENST00000226382	NM_003924.3	166	Gcg/Acg	3/3	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.44530057977108	2		915	838	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031684	69031684	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	68	719	1	ENST00000288368.4:c.3439A>T	p.Ser1147Cys	p.S1147C	ENST00000288368	NM_024870.2	1147	Agt/Tgt	28/40	0.259417368329431	5	FACETS	0.682	0.592	0.779			1	INDETERMINATE	1	TRUE	NA	0.44530057977108	5		720	747	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641388	18641389	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1229278001	NA	P-0020225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	49	323	0	ENST00000266497.5:c.2393dup	p.Asn798LysfsTer5	p.N798Kfs*5	ENST00000266497		796	cta/ctAa	17/31	0.608786606119723	2	FACETS	0.797	0.684	0.918	0.398	0.342	0.459	CLONAL	1	FALSE	0	0.608786606119723	2		323	202	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102192	27102193	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	138	574	0	ENST00000324856.7:c.5119dup	p.Ser1707LysfsTer20	p.S1707Kfs*20	ENST00000324856	NM_006015.4	1706	-/A	19/20	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	1	0.608786606119723	2		574	446	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265643	152265644	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0020225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	82	449	0	ENST00000206249.3:c.1096+1_1096+2dup		p.G366fs	ENST00000206249	NM_000125.3	366	ggc/gGTgc		0.608786606119723	2	FACETS	0.837	0.745	0.933	0.418	0.372	0.467	CLONAL	1	FALSE	0	0.608786606119723	2		449	322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579416	7579416	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	224	920	0	ENST00000269305.4:c.271del	p.Trp91GlyfsTer32	p.W91Gfs*32	ENST00000269305	NM_001126112.2	91	Tgg/gg	4/11	0.204646674547394	2	FACETS	0.818	0.761	0.876	0.818	0.761	0.876	CLONAL	2	TRUE	0	0.257431341397629	2		920	1064	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	231	640	2	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.828	0.777	0.881	1	0.994	1	CLONAL	2	TRUE	1	0.440503745499381	2		642	633	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	244	709	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.43314045795708	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.440503745499381	2		709	544	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	171	440	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.98	0.903	1	0.98	0.903	1	CLONAL	1	TRUE	1	0.440503745499381	2		440	792	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	86	417	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.43314045795708	2	FACETS	0.941	0.837	1	0.47	0.418	0.526	CLONAL	1	TRUE	0	0.440503745499381	2		417	415	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	171	474	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.937	0.862	1	0.937	0.862	1	CLONAL	1	TRUE	1	0.440503745499381	2		477	829	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749415085	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	51	545	0	ENST00000263967.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000263967	NM_006218.2	38	Cgt/Tgt	2/21	1	2	FACETS	0.579	0.493	0.672	0.579	0.493	0.672	SUBCLONAL	1	TRUE	1	0.440503745499381	2		545	400	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772901	135772902	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	96	928	0	ENST00000298552.3:c.2721dup	p.Arg908ThrfsTer42	p.R908Tfs*42	ENST00000298552	NM_001162426.1	907	-/A	21/23	1	2	FACETS	0.436	0.387	0.488	0.436	0.387	0.488	SUBCLONAL	1	TRUE	1	0.440503745499381	2		928	1000	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	195	972	8	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.891	0.824	0.96	0.891	0.824	0.96	CLONAL	1	TRUE	1	0.440503745499381	2		980	994	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937410	178937410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	16	198	0	ENST00000263967.3:c.1798G>A	p.Glu600Lys	p.E600K	ENST00000263967	NM_006218.2	600	Gaa/Aaa	12/21	1	2	FACETS	0.526	0.392	0.684	0.526	0.392	0.684	SUBCLONAL	1	TRUE	1	0.440503745499381	2		198	138	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993237	72993237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567606533	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	85	1163	1	ENST00000268489.5:c.808G>A	p.Asp270Asn	p.D270N	ENST00000268489	NM_006885.3	270	Gat/Aat	2/10	1	2	FACETS	0.312	0.275	0.353	0.312	0.275	0.353	SUBCLONAL	1	TRUE	1	0.440503745499381	2		1164	1235	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	161	677	1	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	0.931	0.855	1	0.931	0.855	1	CLONAL	1	TRUE	1	0.440503745499381	2		678	785	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	180	403	4	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.43314045795708	2	FACETS	1	0.978	1	0.576	0.533	0.621	CLONAL	1	TRUE	0	0.440503745499381	2		407	709	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	191	772	4	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.440503745499381	2		776	842	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916726	178916726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772110575	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	30	555	0	ENST00000263967.3:c.113G>A	p.Arg38His	p.R38H	ENST00000263967	NM_006218.2	38	cGt/cAt	2/21	1	2	FACETS	0.333	0.268	0.407	0.333	0.268	0.407	SUBCLONAL	1	TRUE	1	0.440503745499381	2		555	409	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714462	40714462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167887381	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	105	677	1	ENST00000373198.4:c.3935C>T	p.Ser1312Phe	p.S1312F	ENST00000373198	NM_133170.3	1312	tCc/tTc	29/32	1	2	FACETS	0.642	0.576	0.713	0.642	0.576	0.713	SUBCLONAL	1	TRUE	1	0.440503745499381	2		678	742	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787845	135787845	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1564490210	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	90	541	0	ENST00000298552.3:c.738-1G>A		p.X246_splice	ENST00000298552	NM_001162426.1	246			1	2	FACETS	0.89	0.794	0.993	0.89	0.794	0.993	CLONAL	1	TRUE	1	0.440503745499381	2		541	459	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858195	9858195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777249842	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	44	762	0	ENST00000330684.3:c.3206C>T	p.Thr1069Met	p.T1069M	ENST00000330684	NM_001134407.1	1069	aCg/aTg	13/13	1	2	FACETS	0.26	0.217	0.308	0.26	0.217	0.308	SUBCLONAL	1	TRUE	1	0.440503745499381	2		762	768	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214866	36214866	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568372429	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	88	1197	9	ENST00000222270.7:c.3296del	p.Gly1099AlafsTer83	p.G1099Afs*83	ENST00000222270	NM_014727.1	1098	Ggg/gg	8/37	1	2	FACETS	0.335	0.295	0.377	0.335	0.295	0.377	SUBCLONAL	1	TRUE	1	0.440503745499381	2		1206	1194	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335134	65335134	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	45	689	1	ENST00000342505.4:c.507C>A	p.Cys169Ter	p.C169*	ENST00000342505	NM_002227.2	169	tgC/tgA	6/25	1	2	FACETS	0.287	0.24	0.339	0.287	0.24	0.339	SUBCLONAL	1	TRUE	1	0.440503745499381	2		690	712	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429280	78429280	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	44	816	0	ENST00000370768.2:c.1162del	p.Thr388LeufsTer3	p.T388Lfs*3	ENST00000370768	NM_003902.3	388	Act/ct	13/20	1	2	FACETS	0.263	0.219	0.311	0.263	0.219	0.311	SUBCLONAL	1	TRUE	1	0.440503745499381	2		816	760	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464911	120464911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115013051	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	43	673	1	ENST00000256646.2:c.5161G>A	p.Ala1721Thr	p.A1721T	ENST00000256646	NM_024408.3	1721	Gca/Aca	28/34	1	2	FACETS	0.254	0.211	0.301	0.254	0.211	0.301	SUBCLONAL	1	TRUE	1	0.440503745499381	2		674	770	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	248	1055	0	ENST00000227507.2:c.859C>A	p.Pro287Thr	p.P287T	ENST00000227507	NM_053056.2	287	Ccc/Acc	5/5	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.440503745499381	2		1055	1064	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94908662	94908662	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	115	869	0	ENST00000536441.1:c.1392del	p.Val465PhefsTer7	p.V465Ffs*7	ENST00000536441	NM_144665.3	464	aaA/aa	9/10	1	2	FACETS	0.665	0.599	0.735	0.665	0.599	0.735	SUBCLONAL	1	TRUE	1	0.440503745499381	2		869	785	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343475	118343475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	43	596	0	ENST00000534358.1:c.1601C>T	p.Ser534Leu	p.S534L	ENST00000534358	NM_005933.3	534	tCg/tTg	3/36	1	2	FACETS	0.339	0.283	0.401	0.339	0.283	0.401	SUBCLONAL	1	TRUE	1	0.440503745499381	2		596	576	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343508	118343508	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	42	604	0	ENST00000534358.1:c.1634A>G	p.Lys545Arg	p.K545R	ENST00000534358	NM_005933.3	545	aAa/aGa	3/36	1	2	FACETS	0.316	0.263	0.375	0.316	0.263	0.375	SUBCLONAL	1	TRUE	1	0.440503745499381	2		604	603	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415639	49415639	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	74	516	0	ENST00000301067.7:c.16538A>G	p.Gln5513Arg	p.Q5513R	ENST00000301067	NM_003482.3	5513	cAg/cGg	54/54	1	2	FACETS	0.642	0.563	0.727	0.642	0.563	0.727	SUBCLONAL	1	TRUE	1	0.440503745499381	2		516	523	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117348	115117348	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	147	637	2	ENST00000257566.3:c.826A>G	p.Thr276Ala	p.T276A	ENST00000257566	NM_016569.3	276	Act/Gct	4/8	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.440503745499381	2		639	596	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562925	21562925	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	68	922	0	ENST00000382592.4:c.994G>T	p.Gly332Cys	p.G332C	ENST00000382592	NM_014572.2	332	Ggc/Tgc	4/8	1	2	FACETS	0.325	0.282	0.372	0.325	0.282	0.372	SUBCLONAL	1	TRUE	1	0.440503745499381	2		922	950	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619905	21619905	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	174	814	0	ENST00000382592.4:c.261del	p.Phe87LeufsTer13	p.F87Lfs*13	ENST00000382592	NM_014572.2	87	ttT/tt	2/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.440503745499381	2		814	731	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477067	67477067	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	152	628	0	ENST00000327367.4:c.874A>G	p.Arg292Gly	p.R292G	ENST00000327367	NM_005902.3	292	Aga/Gga	7/9	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.440503745499381	2		628	621	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658595	3658595	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	282	1093	0	ENST00000294008.3:c.371G>T	p.Arg124Met	p.R124M	ENST00000294008	NM_032444.2	124	aGg/aTg	2/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.440503745499381	2		1093	1210	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778275	3778275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	49	781	2	ENST00000262367.5:c.6773G>A	p.Gly2258Asp	p.G2258D	ENST00000262367	NM_004380.2	2258	gGc/gAc	31/31	1	2	FACETS	0.321	0.271	0.376	0.321	0.271	0.376	SUBCLONAL	1	TRUE	1	0.440503745499381	2		783	693	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56852589	56852589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	108	876	0	ENST00000308159.5:c.503G>A	p.Ser168Asn	p.S168N	ENST00000308159	NM_014669.4	168	aGt/aAt	6/22	1	2	FACETS	0.583	0.523	0.647	0.583	0.523	0.647	SUBCLONAL	1	TRUE	1	0.440503745499381	2		876	841	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350533	89350533	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	99	1028	0	ENST00000301030.4:c.2417del	p.Lys806ArgfsTer57	p.K806Rfs*57	ENST00000301030	NM_001256183.1	806	aAg/ag	9/13	1	2	FACETS	0.426	0.379	0.476	0.426	0.379	0.476	SUBCLONAL	1	TRUE	1	0.440503745499381	2		1028	1056	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119769	70119769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	48	907	0	ENST00000245479.2:c.774del	p.Leu259CysfsTer20	p.L259Cfs*20	ENST00000245479	NM_000346.3	257	cgC/cg	3/3	1	2	FACETS	0.261	0.22	0.307	0.261	0.22	0.307	SUBCLONAL	1	TRUE	1	0.440503745499381	2		907	834	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724543	724543	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	45	282	1	ENST00000314574.4:c.1513A>T	p.Met505Leu	p.M505L	ENST00000314574	NM_005433.3	505	Atg/Ttg	12/12	1	2	FACETS	0.831	0.704	0.968	0.831	0.704	0.968	CLONAL	1	TRUE	1	0.440503745499381	2		283	246	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223134	5223134	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	72	1113	1	ENST00000357368.4:c.2669A>G	p.Tyr890Cys	p.Y890C	ENST00000357368	NM_002850.3	890	tAc/tGc	18/38	1	2	FACETS	0.295	0.257	0.337	0.295	0.257	0.337	SUBCLONAL	1	TRUE	1	0.440503745499381	2		1114	1108	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052918	180052918	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	256	1153	0	ENST00000261937.6:c.1372T>A	p.Trp458Arg	p.W458R	ENST00000261937	NM_182925.4	458	Tgg/Agg	10/30	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.440503745499381	2		1153	1119	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566035	141566035	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	72	729	0	ENST00000220592.5:c.1229G>T	p.Gly410Val	p.G410V	ENST00000220592	NM_012154.3	410	gGg/gTg	10/19	1	2	FACETS	0.401	0.349	0.456	0.401	0.349	0.456	SUBCLONAL	1	TRUE	1	0.440503745499381	2		729	816	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141567244	141567244	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	187	975	1	ENST00000220592.5:c.970del	p.His324ThrfsTer33	p.H324Tfs*33	ENST00000220592	NM_012154.3	324	Cac/ac	8/19	1	2	FACETS	0.76	0.701	0.822	0.76	0.701	0.822	SUBCLONAL	1	TRUE	1	0.440503745499381	2		976	1117	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785984	135785984	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	76	814	1	ENST00000298552.3:c.1237del	p.Gln413ArgfsTer27	p.Q413Rfs*27	ENST00000298552	NM_001162426.1	413	Cag/ag	12/23	1	2	FACETS	0.405	0.354	0.46	0.405	0.354	0.46	SUBCLONAL	1	TRUE	1	0.440503745499381	2		815	852	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937492	76937492	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	76	861	1	ENST00000373344.5:c.3256G>T	p.Ala1086Ser	p.A1086S	ENST00000373344	NM_000489.3	1086	Gca/Tca	9/35	1	2	FACETS	0.575	0.505	0.651	0.575	0.505	0.651	SUBCLONAL	1	TRUE	1	0.440503745499381	2		862	600	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	366	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.988	0.942	1	1	0.997	1	CLONAL	2	TRUE	1	0.441121467991061	2		555	840	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0020228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	193	465	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.966	1	1	0.994	1	CLONAL	2	TRUE	1	0.441121467991061	2		465	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876659675	NA	P-0020228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	914	1016	0	ENST00000269305.4:c.764T>G	p.Ile255Ser	p.I255S	ENST00000269305	NM_001126112.2	255	aTc/aGc	7/11	0.441121467991061	2	FACETS	1	0.995	1	1	0.999	1	CLONAL	4	TRUE	0	0.441121467991061	2		1016	1018	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40368034	40368034	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	183	832	0	ENST00000293328.3:c.1471C>A	p.Pro491Thr	p.P491T	ENST00000293328	NM_012448.3	491	Cct/Act	12/19	1	2	FACETS	0.856	0.79	0.925	0.856	0.79	0.925	CLONAL	1	TRUE	1	0.441121467991061	2		832	969	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937915	76937915	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0020228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	395	876	1	ENST00000373344.5:c.2833A>T	p.Lys945Ter	p.K945*	ENST00000373344	NM_000489.3	945	Aag/Tag	9/35	0.441121467991061	1	FACETS	1	0.987	1	1	0.997	1	CLONAL	2	TRUE	0	0.441121467991061	1		877	661	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	207	837	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.741383747288264	2		837	546	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609950	43609950	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs77709286	NA	P-0020230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	797	1194	0	ENST00000355710.3:c.1902C>G	p.Cys634Trp	p.C634W	ENST00000355710	NM_020975.4	634	tgC/tgG	11/20	0.741383747288264	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.741383747288264	2		1194	1010	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0020231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	78	281	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	0.272474112499885	3	FACETS	1	0.95	1	0.571	0.504	0.642	CLONAL	1	TRUE	1	0.39095216050957	3		281	418	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245332	46245333	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0020231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	181	737	0	ENST00000334344.6:c.3428_3429del	p.Val1143AlafsTer16	p.V1143Afs*16	ENST00000334344	NM_152641.2	1142	acTGtg/actg	15/21	0.324078624077543	5	FACETS	0.833	0.769	0.899	0.555	0.512	0.6	CLONAL	2	TRUE	2	0.39095216050957	5		737	882	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990368	81990368	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	154	923	0	ENST00000359376.3:c.3639G>T	p.Gln1213His	p.Q1213H	ENST00000359376	NM_002661.3	1213	caG/caT	32/33	0.272474112499885	3	FACETS	1	0.976	1	0.586	0.536	0.637	CLONAL	1	TRUE	1	0.39095216050957	3		923	804	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876545	59876545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748105919	NA	P-0020231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	131	805	6	ENST00000259008.2:c.1256G>A	p.Arg419Gln	p.R419Q	ENST00000259008	NM_032043.2	419	cGg/cAg	9/20	0.206239439209888	5	FACETS	0.835	0.759	0.913	0.556	0.506	0.609	INDETERMINATE	2	TRUE	2	0.39095216050957	5		811	637	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207068	1207070	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0020231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	278	1084	0	ENST00000326873.7:c.156_158del	p.Asp53del	p.D53del	ENST00000326873	NM_000455.4	52	ggGGAc/ggc	1/10	0.161612903639493	3	FACETS	0.828	0.778	0.879			1	INDETERMINATE	2	TRUE	NA	0.39095216050957	3		1084	1027	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271648	15271648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	86	1488	0	ENST00000263388.2:c.6791C>T	p.Ser2264Leu	p.S2264L	ENST00000263388	NM_000435.2	2264	tCa/tTa	33/33	0.327351413112197	2	FACETS	0.349	0.307	0.393	0.174	0.153	0.197	SUBCLONAL	1	TRUE	0	0.39095216050957	2		1488	1262	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250268	39250268	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	275	1390	0	ENST00000402219.2:c.1301G>T	p.Gly434Val	p.G434V	ENST00000402219	NM_005633.3	434	gGa/gTa	10/23	0.206239439209888	5	FACETS	1	0.956	1	0.681	0.64	0.724	INDETERMINATE	2	TRUE	2	0.39095216050957	5		1390	1092	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11554273	NA	P-0020231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	14	645	0	ENST00000371085.3:c.601C>G	p.Arg201Gly	p.R201G	ENST00000371085	NM_000516.4	201	Cgt/Ggt	8/13	0.355154368230189	3	FACETS	0.122	0.088	0.165	0.061	0.044	0.083	SUBCLONAL	1	TRUE	1	0.39095216050957	3		645	700	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521428	8521428	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	202	929	0	ENST00000356435.5:c.810G>T	p.Met270Ile	p.M270I	ENST00000356435		270	atG/atT	9/35	0.349721080638905	2	FACETS	1	0.991	1	0.734	0.683	0.786	CLONAL	1	TRUE	0	0.39095216050957	2		929	704	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0020232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	125	604	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.22896651318978	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.22896651318978	1		606	714	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0020232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	35	931	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.611	0.501	0.736	0.611	0.501	0.736	SUBCLONAL	1	TRUE	1	0.22896651318978	2		931	500	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591925	48591925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660556	NA	P-0020232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	28	728	1	ENST00000342988.3:c.1088G>A	p.Cys363Tyr	p.C363Y	ENST00000342988	NM_005359.5	363	tGt/tAt	9/12	0.22896651318978	1	FACETS	0.63	0.503	0.773	0.63	0.503	0.773	SUBCLONAL	1	TRUE	0	0.22896651318978	1		729	344	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423505	88423505	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754383313	NA	P-0020232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	78	868	1	ENST00000360948.2:c.2330C>T	p.Thr777Met	p.T777M	ENST00000360948	NM_001012338.2	777	aCg/aTg	18/19	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.22896651318978	2		869	592	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711945	89711945	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	68	774	0	ENST00000371953.3:c.563A>G	p.Tyr188Cys	p.Y188C	ENST00000371953	NM_000314.4	188	tAt/tGt	6/9	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.22896651318978	2		774	470	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911605	114911606	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAGAAAGCGCGGCCATC	novel	NA	P-0020232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	83	828	0	ENST00000543371.1:c.1126_1142dup	p.Asn381LysfsTer116	p.N381Kfs*116	ENST00000543371	NM_001198531.1	375	aaa/aAAGAAAGCGCGGCCATCaa	10/14	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.22896651318978	2		828	616	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867058	45867058	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	78	741	2	ENST00000391945.4:c.1061C>T	p.Pro354Leu	p.P354L	ENST00000391945	NM_000400.3	354	cCg/cTg	11/23	1	2	FACETS	0.993	0.873	1	0.993	0.873	1	CLONAL	1	TRUE	1	0.22896651318978	2		743	686	SUCCESS
APC	324	MSKCC	GRCh37	5	112173325	112173325	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	23	483	0	ENST00000257430.4:c.2034del	p.Ser678ArgfsTer40	p.S678Rfs*40	ENST00000257430	NM_000038.5	678	agT/ag	16/16	1	2	FACETS	0.844	0.66	1	0.844	0.66	1	CLONAL	1	TRUE	1	0.22896651318978	2		483	238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574024	7574024	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375444154	NA	P-0020233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	146	1106	3	ENST00000269305.4:c.1003C>T	p.Arg335Cys	p.R335C	ENST00000269305	NM_001126112.2	335	Cgt/Tgt	10/11	1	2	FACETS	0.618	0.563	0.676	0.618	0.563	0.676	SUBCLONAL	1	TRUE	1	0.462592232645694	2		1109	1021	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226566899	226566900	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0020233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	191	957	0	ENST00000366794.5:c.1688_1689del	p.Val563GlufsTer35	p.V563Efs*35	ENST00000366794	NM_001618.3	563	gTT/g	12/23	0.326693273279803	1	FACETS	0.822	0.762	0.885	0.822	0.762	0.885	CLONAL	1	TRUE	0	0.462592232645694	1		957	772	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0020234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	67	786	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.29	2		786	449	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0020234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	93	723	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.223354401305932	2	FACETS	0.893	0.801	0.99	0.893	0.801	0.99	CLONAL	2	TRUE	0	0.29	2		723	359	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0020234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	105	453	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.283880704703128	3	FACETS	0.893	0.805	0.986	0.893	0.805	0.986	CLONAL	2	TRUE	1	0.29	3		453	464	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419986	41419986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372989163	NA	P-0020234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	78	778	2	ENST00000373198.4:c.335G>A	p.Arg112His	p.R112H	ENST00000373198	NM_133170.3	112	cGt/cAt	3/32	0.283880704703128	3	FACETS	1	0.915	1	0.525	0.461	0.593	CLONAL	1	TRUE	1	0.29	3		780	587	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118924	70118926	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0020234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	53	1294	0	ENST00000245479.2:c.499_501del	p.Lys167del	p.K167del	ENST00000245479	NM_000346.3	166	AAG/-	2/3	1	2	FACETS	0.584	0.497	0.679	0.584	0.497	0.679	SUBCLONAL	1	TRUE	1	0.29	2		1294	626	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266063	41266577	+	splice_donor_variant,splice_acceptor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	GGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTT	GGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTT	-	novel	NA	P-0020234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	49	550	0	ENST00000349496.5:c.65_379del		p.X22_splice	ENST00000349496	NM_001904.3	22	gcGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTg/gcg	3-4/15	1	2	FACETS	0.952	0.809	1	0.952	0.809	1	CLONAL	1	TRUE	1	0.29	2		550	355	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980304	55980304	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587778429	NA	P-0020234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	66	877	2	ENST00000263923.4:c.787C>A	p.Pro263Thr	p.P263T	ENST00000263923	NM_002253.2	263	Cct/Act	6/30	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.29	2		879	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1555525585	NA	P-0020235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	520	712	1	ENST00000269305.4:c.673-2A>G		p.X225_splice	ENST00000269305	NM_001126112.2	225			NA	2	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.949500212559182	2		713	543	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8113519	8113519	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs745736983	NA	P-0020235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	732	1071	0	ENST00000585124.1:c.24C>A	p.Tyr8Ter	p.Y8*	ENST00000585124	NM_004217.3	8	taC/taA	2/9	0.155874351107059	6	FACETS	0.956	0.93	0.982			1	INDETERMINATE	4	TRUE	NA	0.949500212559182	6		1071	1169	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0020236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	394	549	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.898576047062774	5	FACETS	1	0.991	1			1	CLONAL	3	TRUE	NA	0.898576047062774	5		549	625	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0020236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	207	759	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.898576047062774	5	FACETS	1	0.976	1			1	CLONAL	1	TRUE	NA	0.898576047062774	5		759	971	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932865	36932865	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	97	1180	1	ENST00000361632.4:c.2006G>T	p.Ser669Ile	p.S669I	ENST00000361632		669	aGc/aTc	15/16	0.898576047062774	3	FACETS	0.462	0.412	0.515	0.231	0.206	0.258	SUBCLONAL	1	TRUE	1	0.898576047062774	3		1181	678	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001231	150001231	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	246	930	1	ENST00000253339.5:c.2373G>C	p.Met791Ile	p.M791I	ENST00000253339		791	atG/atC	4/7	0.898576047062774	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.898576047062774	2		931	269	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0020236-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	114	549	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.155067594902928	5	FACETS	1	0.921	1	0.685	0.616	0.758	CLONAL	2	TRUE	2	0.155067594902928	5		549	882	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001231	150001231	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020236-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	97	930	1	ENST00000253339.5:c.2373G>C	p.Met791Ile	p.M791I	ENST00000253339		791	atG/atC	4/7	0.155067594902928	2	FACETS	0.881	0.786	0.982	0.881	0.786	0.982	CLONAL	2	TRUE	0	0.155067594902928	2		931	710	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0020237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	79	604	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.795	0.697	0.9	0.795	0.697	0.9	SUBCLONAL	1	TRUE	1	0.20842463359877	2		606	954	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123837	46123837	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0020238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	33	447	0	ENST00000334344.6:c.103A>T	p.Lys35Ter	p.K35*	ENST00000334344	NM_152641.2	35	Aaa/Taa	2/21	1	2	FACETS	0.786	0.641	0.949	0.786	0.641	0.949	CLONAL	1	TRUE	1	0.22826311016829	2		447	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0020238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	52	773	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.469	0.397	0.547	0.469	0.397	0.547	SUBCLONAL	1	TRUE	1	0.22826311016829	2		774	972	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481806	56481806	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	142	941	0	ENST00000267101.3:c.734C>T	p.Ala245Val	p.A245V	ENST00000267101	NM_001982.3	245	gCc/gTc	7/28	1	2	FACETS	0.977	0.893	1	1	0.991	1	CLONAL	2	TRUE	1	0.22826311016829	2		941	637	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443599	52443601	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0020238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	166	864	0	ENST00000460680.1:c.91_93del	p.Glu31del	p.E31del	ENST00000460680	NM_004656.3	31	GAG/-	3/17	0.219434147479356	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.22826311016829	2		864	694	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	216	122	0				ENST00000310581	NM_198253.2	-/1132			0.169492912857519	5	FACETS	1	0.984	1	0.781	0.729	0.834	INDETERMINATE	2	TRUE	2	0.43740943713202	5		122	698	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0020240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	492	1054	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.296286529042473	3	FACETS	0.901	0.866	0.936	0.901	0.866	0.936	CLONAL	3	TRUE	0	0.43740943713202	3		1055	1014	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182858	123182858	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	222	395	0	ENST00000218089.9:c.823C>T	p.Gln275Ter	p.Q275*	ENST00000218089	NM_001042749.1	275	Cag/Tag	10/35	0.409190177500405	2	FACETS	0.942	0.884	0.999	0.942	0.884	0.999	CLONAL	2	TRUE	0	0.43740943713202	2		395	539	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107180	27107180	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0020240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	343	600	0	ENST00000324856.7:c.6791C>G	p.Ser2264Ter	p.S2264*	ENST00000324856	NM_006015.4	2264	tCa/tGa	20/20	0.210262316557103	5	FACETS	1	0.99	1	0.787	0.745	0.829	INDETERMINATE	2	TRUE	2	0.43740943713202	5		600	1100	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242872	142242872	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0020240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	332	629	0	ENST00000350721.4:c.4115C>G	p.Ser1372Ter	p.S1372*	ENST00000350721	NM_001184.3	1372	tCa/tGa	22/47	0.286349458870634	5	FACETS	1	0.977	1	0.708	0.669	0.747	CLONAL	2	TRUE	2	0.43740943713202	5		629	1184	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332658	65332658	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	196	430	1	ENST00000342505.4:c.881C>A	p.Ser294Ter	p.S294*	ENST00000342505	NM_002227.2	294	tCa/tAa	7/25	0.210262316557103	5	FACETS	0.87	0.806	0.936	0.58	0.537	0.624	INDETERMINATE	2	TRUE	2	0.43740943713202	5		431	853	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136069	64136069	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	133	655	0	ENST00000334205.4:c.1330C>A	p.Arg444Ser	p.R444S	ENST00000334205	NM_003942.2	444	Cgc/Agc	11/17	0.407586517631014	2	FACETS	0.71	0.644	0.778	0.355	0.322	0.389	SUBCLONAL	1	TRUE	0	0.43740943713202	2		655	857	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123880929	123880929	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	79	429	0	ENST00000330479.4:c.547G>A	p.Asp183Asn	p.D183N	ENST00000330479	NM_020382.3	183	Gat/Aat	5/9	0.346367881326699	3	FACETS	0.661	0.581	0.747	0.33	0.29	0.374	SUBCLONAL	1	TRUE	1	0.43740943713202	3		429	666	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216566	7216566	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	282	512	0	ENST00000380728.2:c.769del	p.Glu257AsnfsTer88	p.E257Nfs*88	ENST00000380728		257	Gaa/aa	9/11	0.296286529042473	3	FACETS	1	0.99	1	0.798	0.756	0.841	CLONAL	2	TRUE	0	0.43740943713202	3		512	656	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532583	63532596	+	frameshift_variant	Frame_Shift_Del	DEL	TGCCCCCCCACAGA	TGCCCCCCCACAGA	-	novel	NA	P-0020240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	148	735	2	ENST00000307078.5:c.1983_1996del	p.His661GlnfsTer41	p.H661Qfs*41	ENST00000307078	NM_004655.3	661	caTCTGTGGGGGGGCAac/caac	8/11	0.318195458805139	5	FACETS	0.832	0.758	0.91	0.277	0.252	0.304	CLONAL	1	TRUE	2	0.43740943713202	5		737	1347	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053343	37053343	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63751480	NA	P-0020240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	212	499	0	ENST00000231790.2:c.578C>T	p.Ser193Leu	p.S193L	ENST00000231790	NM_000249.3	193	tCa/tTa	7/19	0.346367881326699	3	FACETS	1	0.991	1	0.736	0.685	0.788	CLONAL	1	TRUE	1	0.43740943713202	3		499	803	SUCCESS
ATR	545	MSKCC	GRCh37	3	142222289	142222289	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	254	392	0	ENST00000350721.4:c.5203C>G	p.His1735Asp	p.H1735D	ENST00000350721	NM_001184.3	1735	Cat/Gat	30/47	0.286349458870634	5	FACETS	1	0.987	1	0.793	0.745	0.843	CLONAL	2	TRUE	2	0.43740943713202	5		392	808	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281398	142281415	+	inframe_deletion	In_Frame_Del	DEL	TTCTACAAGGTGTTTTAA	TTCTACAAGGTGTTTTAA	-	novel	NA	P-0020240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1280	161	667	0	ENST00000350721.4:c.829_846del	p.Leu277_Glu282del	p.L277_E282del	ENST00000350721	NM_001184.3	277	TTAAAACACCTTGTAGAA/-	4/47	0.286349458870634	5	FACETS	0.846	0.773	0.922	0.282	0.257	0.308	CLONAL	1	TRUE	2	0.43740943713202	5		667	1441	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945173	44945227	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTTTGTTGTTCCTGAAGGTTACTGGGGTGTTCTGAATGACTTCTGTGAAAAGTA	GGTTTGTTGTTCCTGAAGGTTACTGGGGTGTTCTGAATGACTTCTGTGAAAAGTA	-	novel	NA	P-0020240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	130	691	0	ENST00000377967.4:c.3502_3548+8del		p.X1168_splice	ENST00000377967	NM_021140.2	1168		24/29	0.409190177500405	2	FACETS	0.894	0.813	0.979	0.447	0.406	0.49	CLONAL	1	TRUE	0	0.43740943713202	2		691	665	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179385	56179386	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	73	359	0	ENST00000399503.3:c.3702dup	p.Gln1235ThrfsTer4	p.Q1235Tfs*4	ENST00000399503	NM_005921.1	1233	gca/gcAa	15/20	1	2	FACETS	0.996	0.88	1	0.996	0.88	1	CLONAL	1	TRUE	1	0.501958373809218	2		359	292	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179459	56179460	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0020241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	103	503	0	ENST00000399503.3:c.3773dup	p.Tyr1258Ter	p.Y1258*	ENST00000399503	NM_005921.1	1258	tat/tAat	15/20	1	2	FACETS	0.886	0.797	0.98	0.886	0.797	0.98	CLONAL	1	TRUE	1	0.501958373809218	2		503	463	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	336	122	0				ENST00000310581	NM_198253.2	-/1132			0.10472437993654	5	FACETS	1	0.991	1	0.786	0.749	0.824	INDETERMINATE	2	TRUE	2	0.923348381460699	5		122	736	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0020243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	1028	804	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.923348381460699	2		805	1113	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557630	95557630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	533	718	0	ENST00000393063.1:c.5437G>A	p.Glu1813Lys	p.E1813K	ENST00000393063	NM_030621.3	1813	Gag/Aag	26/28	0.258800347037254	4	FACETS	0.917	0.881	0.952	0.917	0.881	0.952	INDETERMINATE	2	TRUE	2	0.923348381460699	4		718	1211	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49413009	49413009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519953	NA	P-0020243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	657	832	0	ENST00000418115.1:c.14G>A	p.Arg5Gln	p.R5Q	ENST00000418115	NM_001664.2	5	cGg/cAg	2/5	0.258800347037254	4	FACETS	0.988	0.955	1	0.988	0.955	1	INDETERMINATE	2	TRUE	2	0.923348381460699	4		832	1385	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434181	49434181	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	803	1116	0	ENST00000301067.7:c.7372C>T	p.Gln2458Ter	p.Q2458*	ENST00000301067	NM_003482.3	2458	Cag/Tag	31/54	0.303917514806478	2	FACETS	1	0.998	1	0.665	0.647	0.682	INDETERMINATE	1	TRUE	0	0.923348381460699	2		1116	1308	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240208	41240208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755011775	NA	P-0020243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	21	153	1	ENST00000379561.5:c.142G>A	p.Ala48Thr	p.A48T	ENST00000379561	NM_002015.3	48	Gcg/Acg	1/3	0.258800347037254	4	FACETS	0.305	0.235	0.386	0.152	0.117	0.193	INDETERMINATE	1	TRUE	2	0.923348381460699	4		154	287	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881523	48881523	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	309	415	0	ENST00000267163.4:c.245C>A	p.Ser82Ter	p.S82*	ENST00000267163	NM_000321.2	82	tCa/tAa	2/27	0.258800347037254	4	FACETS	0.893	0.847	0.939	0.893	0.847	0.939	INDETERMINATE	2	TRUE	2	0.923348381460699	4		415	721	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934220	48934220	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	363	718	0	ENST00000267163.4:c.678del	p.Phe226LeufsTer38	p.F226Lfs*38	ENST00000267163	NM_000321.2	225	taT/ta	7/27	0.258800347037254	4	FACETS	0.974	0.93	1	0.974	0.93	1	INDETERMINATE	2	TRUE	2	0.923348381460699	4		718	776	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128594	30128594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	392	532	2	ENST00000263025.4:c.788C>T	p.Ser263Phe	p.S263F	ENST00000263025	NM_002746.2	263	tCc/tTc	6/9	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.923348381460699	2		534	806	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856099	68856099	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	592	833	0	ENST00000261769.5:c.1908del	p.Asn637ThrfsTer16	p.N637Tfs*16	ENST00000261769	NM_004360.3	636	gCc/gc	12/16	0.923348381460699	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.923348381460699	1		833	667	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774737	73774737	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	251	269	1	ENST00000254810.4:c.350G>A	p.Arg117Lys	p.R117K	ENST00000254810	NM_005324.3	117	aGa/aAa	4/4	0.296770050449202	2	FACETS	1	0.994	1	0.676	0.645	0.707	INDETERMINATE	1	TRUE	0	0.923348381460699	2		270	402	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942086	17942086	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs780525165	NA	P-0020243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	297	1001	0	ENST00000458235.1:c.2929G>C	p.Asp977His	p.D977H	ENST00000458235	NM_000215.3	977	Gac/Cac	21/24	0.10472437993654	5	FACETS	1	0.978	1	0.361	0.339	0.384	INDETERMINATE	1	TRUE	2	0.923348381460699	5		1001	1416	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483985	212483985	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	178	594	0	ENST00000342788.4:c.2218G>A	p.Glu740Lys	p.E740K	ENST00000342788	NM_005235.2	740	Gaa/Aaa	19/28	1	2	FACETS	0.847	0.789	0.907	0.847	0.789	0.907	CLONAL	1	TRUE	1	0.923348381460699	2		594	455	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623143	52623143	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	326	802	0	ENST00000394830.3:c.2908G>C	p.Glu970Gln	p.E970Q	ENST00000394830	NM_018313.4	970	Gag/Cag	19/30	0.258800347037254	4	FACETS	0.928	0.875	0.983	0.464	0.437	0.492	INDETERMINATE	1	TRUE	2	0.923348381460699	4		802	1463	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916699	178916699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	261	499	1	ENST00000263967.3:c.86G>A	p.Gly29Glu	p.G29E	ENST00000263967	NM_006218.2	29	gGa/gAa	2/21	0.258800347037254	4	FACETS	0.933	0.882	0.984	0.933	0.882	0.984	INDETERMINATE	2	TRUE	2	0.923348381460699	4		500	583	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524621	187524621	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	298	824	1	ENST00000441802.2:c.11059G>A	p.Glu3687Lys	p.E3687K	ENST00000441802	NM_005245.3	3687	Gaa/Aaa	19/27	0.21478057406967	4	FACETS	0.942	0.886	1	0.471	0.443	0.5	INDETERMINATE	1	TRUE	2	0.923348381460699	4		825	1318	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540784	187540784	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0020243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	290	458	0	ENST00000441802.2:c.6956C>G	p.Ser2319Ter	p.S2319*	ENST00000441802	NM_005245.3	2319	tCa/tGa	10/27	0.21478057406967	4	FACETS	0.938	0.89	0.987	0.938	0.89	0.987	INDETERMINATE	2	TRUE	2	0.923348381460699	4		458	644	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959337	38959337	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	215	708	1	ENST00000357387.3:c.2138C>T	p.Ala713Val	p.A713V	ENST00000357387	NM_152756.3	713	gCt/gTt	22/38	0.10472437993654	5	FACETS	0.985	0.923	1	0.656	0.615	0.699	INDETERMINATE	2	TRUE	2	0.923348381460699	5		709	564	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679702	30679702	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	269	903	1	ENST00000376406.3:c.2017G>A	p.Glu673Lys	p.E673K	ENST00000376406	NM_014641.2	673	Gag/Aag	5/15	0.303917514806478	2	FACETS	0.65	0.611	0.69	0.325	0.305	0.345	INDETERMINATE	1	TRUE	0	0.923348381460699	2		904	897	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287851	33287851	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	330	980	0	ENST00000374542.5:c.1402G>A	p.Glu468Lys	p.E468K	ENST00000374542	NM_001141970.1	468	Gaa/Aaa	5/8	0.303917514806478	2	FACETS	0.622	0.588	0.657	0.311	0.294	0.329	INDETERMINATE	1	TRUE	0	0.923348381460699	2		980	1149	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206744	27206744	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	230	701	1	ENST00000380036.4:c.2529C>G	p.Ile843Met	p.I843M	ENST00000380036	NM_000459.3	843	atC/atG	15/23	0.21478057406967	4	FACETS	0.901	0.839	0.964	0.45	0.419	0.482	INDETERMINATE	1	TRUE	2	0.923348381460699	4		702	1064	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0020244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	51	655	1	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.13	2		656	769	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952141	178952142	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0020244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	16	292	0	ENST00000263967.3:c.3196_3197delinsTT	p.Ala1066Leu	p.A1066L	ENST00000263967	NM_006218.2	1066	GCa/TTa	21/21	1	2	FACETS	0.504	0.371	0.665	0.504	0.371	0.665	SUBCLONAL	1	TRUE	1	0.13	2		292	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577129	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519986	NA	P-0020247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	691	825	0	ENST00000269305.4:c.809T>G	p.Phe270Cys	p.F270C	ENST00000269305	NM_001126112.2	270	tTt/tGt	8/11	1	2	FACETS	0.963	0.933	0.992	1	0.998	1	CLONAL	2	TRUE	1	0.571451466260796	2		825	1256	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582302	119582302	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	210	500	1	ENST00000316626.5:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000316626		367	Cga/Tga	10/12	0.571451466260796	3	FACETS	1	0.964	1	0.529	0.492	0.568	CLONAL	1	TRUE	1	0.571451466260796	3		501	893	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877430	40877430	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	290	761	3	ENST00000373198.4:c.2266C>A	p.Pro756Thr	p.P756T	ENST00000373198	NM_133170.3	756	Cca/Aca	15/32	1	2	FACETS	0.924	0.87	0.98	0.924	0.87	0.98	CLONAL	1	TRUE	1	0.571451466260796	2		764	1098	SUCCESS
ATR	545	MSKCC	GRCh37	3	142218479	142218479	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0020247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	187	592	0	ENST00000350721.4:c.5370T>A	p.Tyr1790Ter	p.Y1790*	ENST00000350721	NM_001184.3	1790	taT/taA	31/47	0.571451466260796	3	FACETS	0.83	0.766	0.896	0.415	0.383	0.448	CLONAL	1	TRUE	1	0.571451466260796	3		592	1014	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317113	87317113	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1233368130	NA	P-0020247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	218	641	0	ENST00000277120.3:c.252A>T	p.Glu84Asp	p.E84D	ENST00000277120		84	gaA/gaT	3/19	1	2	FACETS	0.935	0.872	1	0.935	0.872	1	CLONAL	1	TRUE	1	0.571451466260796	2		641	816	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411686	63411686	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1335	177	955	0	ENST00000330258.3:c.1481G>C	p.Cys494Ser	p.C494S	ENST00000330258	NM_152424.3	494	tGt/tCt	2/2	1	2	FACETS	0.41	0.376	0.445	0.41	0.376	0.445	SUBCLONAL	1	TRUE	1	0.571451466260796	2		955	1512	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76876000	76876000	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	120	409	0	ENST00000373344.5:c.5135G>T	p.Gly1712Val	p.G1712V	ENST00000373344	NM_000489.3	1712	gGc/gTc	20/35	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.571451466260796	2		409	415	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0020248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	1447	496	0				ENST00000310581	NM_198253.2	-/1132			0.558387263176112	6	FACETS	0.992	0.976	1			1	CLONAL	5	TRUE	NA	0.773224771699043	6		496	1922	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619823	21619823	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0020248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	62	357	0	ENST00000382592.4:c.342+1G>C		p.X114_splice	ENST00000382592	NM_014572.2	114			0.773224771699043	1	FACETS	0.279	0.242	0.318	0.279	0.242	0.318	SUBCLONAL	1	TRUE	0	0.773224771699043	1		357	353	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188206	10188206	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	429	709	0	ENST00000256474.2:c.349T>G	p.Trp117Gly	p.W117G	ENST00000256474	NM_000551.3	117	Tgg/Ggg	2/3	0.773224771699043	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.773224771699043	1		709	677	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509421	149509421	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	366	878	0	ENST00000261799.4:c.1478G>T	p.Ser493Ile	p.S493I	ENST00000261799	NM_002609.3	493	aGc/aTc	10/23	0.773224771699043	1	FACETS	0.575	0.546	0.604	0.575	0.546	0.604	SUBCLONAL	1	TRUE	0	0.773224771699043	1		878	1010	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227886	123227890	+	frameshift_variant	Frame_Shift_Del	DEL	AATGG	AATGG	-	novel	NA	P-0020248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	167	200	0	ENST00000218089.9:c.3599_3603del	p.Met1200ArgfsTer2	p.M1200Rfs*2	ENST00000218089	NM_001042749.1	1199	ctAATGGaa/ctaa	33/35	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.773224771699043	1		200	220	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0020249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	297	591	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.286404635617221	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.286404635617221	2		591	956	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342518	118342518	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	19	290	0	ENST00000534358.1:c.644C>T	p.Ser215Phe	p.S215F	ENST00000534358	NM_005933.3	215	tCt/tTt	3/36	0.286404635617221	2	FACETS	0.453	0.344	0.581	0.226	0.172	0.291	SUBCLONAL	1	TRUE	0	0.286404635617221	2		290	293	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81971387	81971387	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	64	551	0	ENST00000359376.3:c.3077C>A	p.Ala1026Glu	p.A1026E	ENST00000359376	NM_002661.3	1026	gCa/gAa	28/33	0.28326992250001	3	FACETS	0.587	0.507	0.675	0.294	0.253	0.338	SUBCLONAL	1	TRUE	1	0.286404635617221	3		551	870	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881046	37881046	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23137	1959	888	0	ENST00000269571.5:c.2375C>T	p.Ser792Phe	p.S792F	ENST00000269571		792	tCc/tTc	20/27	0.286404635617221	39	FACETS	1	0.997	1			1	CLONAL	3	TRUE	NA	0.286404635617221	39		888	25096	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190670429	190670430	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TAGA	novel	NA	P-0020249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	90	629	0	ENST00000441310.2:c.369_372dup	p.Gly125ArgfsTer27	p.G125Rfs*27	ENST00000441310	NM_000534.4	123	tta/tTAGAta	4/13	0.286404635617221	3	FACETS	1	0.932	1	0.535	0.474	0.599	CLONAL	1	TRUE	1	0.286404635617221	3		629	672	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259608	89259608	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	48	426	0	ENST00000336596.2:c.752T>C	p.Leu251Pro	p.L251P	ENST00000336596	NM_005233.5	251	cTt/cCt	3/17	0.18833279615844	3	FACETS	0.887	0.751	1	0.444	0.375	0.518	CLONAL	1	TRUE	1	0.286404635617221	3		426	432	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739592	41739592	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	43	504	0	ENST00000242208.4:c.381del	p.Glu128SerfsTer32	p.E128Sfs*32	ENST00000242208	NM_002192.2	127	gcC/gc	2/3	0.286404635617221	5	FACETS	0.566	0.472	0.671	0.189	0.157	0.224	SUBCLONAL	1	TRUE	2	0.286404635617221	5		504	758	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381559	81381559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777026877	NA	P-0020249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	103	382	1	ENST00000222390.5:c.502C>T	p.Arg168Trp	p.R168W	ENST00000222390	NM_000601.4	168	Cgg/Tgg	5/18	0.198774053955616	4	FACETS	0.946	0.851	1	0.946	0.851	1	CLONAL	2	TRUE	2	0.286404635617221	4		383	489	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939553	68939553	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	109	438	0	ENST00000288368.4:c.538T>G	p.Leu180Val	p.L180V	ENST00000288368	NM_024870.2	180	Ttg/Gtg	5/40	0.286404635617221	4	FACETS	0.876	0.789	0.967	0.584	0.526	0.645	CLONAL	2	TRUE	1	0.286404635617221	4		438	559	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741394	145741394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377494266	NA	P-0020249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1398	181	1094	0	ENST00000428558.2:c.1109G>A	p.Arg370His	p.R370H	ENST00000428558	NM_004260.3	370	cGt/cAt	5/22	0.286404635617221	4	FACETS	1	0.942	1	0.343	0.315	0.373	CLONAL	1	TRUE	1	0.286404635617221	4		1094	1579	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340393	8340393	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	62	597	0	ENST00000356435.5:c.5203C>A	p.His1735Asn	p.H1735N	ENST00000356435		1735	Cac/Aac	31/35	0.175430144423429	0	FACETS	0.466	0.402	0.536			1	SUBCLONAL	1	TRUE	0	0.286404635617221	0		597	663	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636771	8636771	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	44	679	0	ENST00000356435.5:c.138A>T	p.Gln46His	p.Q46H	ENST00000356435		46	caA/caT	2/35	0.175430144423429	0	FACETS	0.318	0.266	0.376			1	SUBCLONAL	1	TRUE	0	0.286404635617221	0		679	689	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0020250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	205	146	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.768	0.716	0.822	0.768	0.716	0.822	SUBCLONAL	1	TRUE	1	0.80713562344269	2		146	661	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0020250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	127	465	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.889	0.815	0.965	0.889	0.815	0.965	CLONAL	1	TRUE	1	0.80713562344269	2		465	354	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791328	42791328	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	65	862	1	ENST00000575354.2:c.388G>T	p.Glu130Ter	p.E130*	ENST00000575354	NM_015125.3	130	Gag/Tag	3/20	0.80713562344269	1	FACETS	0.188	0.163	0.215	0.188	0.163	0.215	SUBCLONAL	1	TRUE	0	0.80713562344269	1		863	511	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791740	42791740	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	56	805	0	ENST00000575354.2:c.626T>A	p.Ile209Asn	p.I209N	ENST00000575354	NM_015125.3	209	aTc/aAc	5/20	0.80713562344269	1	FACETS	0.143	0.122	0.166	0.143	0.122	0.166	SUBCLONAL	1	TRUE	0	0.80713562344269	1		805	578	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793462	42793462	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	200	854	3	ENST00000575354.2:c.1264C>T	p.Arg422Ter	p.R422*	ENST00000575354	NM_015125.3	422	Cga/Tga	8/20	0.80713562344269	1	FACETS	0.557	0.52	0.594	0.557	0.52	0.594	SUBCLONAL	1	TRUE	0	0.80713562344269	1		857	531	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139411834	139411834	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	79	995	0	ENST00000277541.6:c.1445A>G	p.Tyr482Cys	p.Y482C	ENST00000277541	NM_017617.3	482	tAc/tGc	9/34	1	2	FACETS	0.195	0.171	0.222	0.195	0.171	0.222	SUBCLONAL	1	TRUE	1	0.80713562344269	2		995	1002	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0020251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	290	453	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.918	0.865	0.973	0.918	0.865	0.973	CLONAL	1	TRUE	1	0.615084637791392	2		453	1027	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0020251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	384	839	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.604687352000159	1	FACETS	0.963	0.919	1	0.963	0.919	1	CLONAL	1	TRUE	0	0.615084637791392	1		841	898	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0020251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	248	592	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	0.615084637791392	2		592	787	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584709	48584709	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0020251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	204	529	0	ENST00000342988.3:c.788-1G>C		p.X263_splice	ENST00000342988	NM_005359.5	263			0.615084637791392	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.615084637791392	1		529	456	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947190	178947190	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	119	353	0	ENST00000263967.3:c.2626A>C	p.Thr876Pro	p.T876P	ENST00000263967	NM_006218.2	876	Aca/Cca	18/21	1	2	FACETS	0.873	0.794	0.956	0.873	0.794	0.956	CLONAL	1	TRUE	1	0.615084637791392	2		353	443	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3634851	3634853	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	rs760517738	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	163	826	0	ENST00000294008.3:c.4656_4658del	p.Lys1552del	p.K1552del	ENST00000294008	NM_032444.2	1552	aaGAAc/aac	13/15	1	2	FACETS	0.903	0.829	0.979	0.903	0.829	0.979	CLONAL	1	TRUE	1	0.441038511396091	2		826	819	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	132	752	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.921	0.838	1	0.921	0.838	1	CLONAL	1	TRUE	1	0.441038511396091	2		755	650	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	206	965	6	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	1	2	FACETS	0.97	0.9	1	0.97	0.9	1	CLONAL	1	TRUE	1	0.441038511396091	2		971	963	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614463	38614463	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	159	764	2	ENST00000299084.4:c.234del	p.Asp79ThrfsTer42	p.D79Tfs*42	ENST00000299084	NM_152594.2	77	Aaa/aa	3/7	1	2	FACETS	0.955	0.877	1	0.955	0.877	1	CLONAL	1	TRUE	1	0.441038511396091	2		766	755	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	253	403	4	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	0.996	1	CLONAL	2	TRUE	1	0.441038511396091	2		407	534	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	181	993	0	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	1	2	FACETS	0.92	0.849	0.994	0.92	0.849	0.994	CLONAL	1	TRUE	1	0.441038511396091	2		993	892	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	93	406	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.935	0.836	1	0.935	0.836	1	CLONAL	1	TRUE	1	0.441038511396091	2		406	451	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779211	3779211	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783507	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	37	440	4	ENST00000262367.5:c.5837del	p.Pro1946HisfsTer30	p.P1946Hfs*30	ENST00000262367	NM_004380.2	1946	cCa/ca	31/31	1	2	FACETS	0.666	0.552	0.791	0.666	0.552	0.791	SUBCLONAL	1	TRUE	1	0.441038511396091	2		444	252	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	142	641	2	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.441038511396091	2		643	621	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779218	3779218	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	43	419	0	ENST00000262367.5:c.5830G>C	p.Ala1944Pro	p.A1944P	ENST00000262367	NM_004380.2	1944	Gcc/Ccc	31/31	1	2	FACETS	0.793	0.669	0.928	0.793	0.669	0.928	CLONAL	1	TRUE	1	0.441038511396091	2		419	246	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	173	734	0	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.441038511396091	2		734	627	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778972	9778972	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1214315014	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	112	567	0	ENST00000377346.4:c.1241C>T	p.Ala414Val	p.A414V	ENST00000377346	NM_005026.3	414	gCg/gTg	9/24	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.441038511396091	2		567	497	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899079	40899079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs951719751	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	149	839	1	ENST00000373198.4:c.2191G>A	p.Ala731Thr	p.A731T	ENST00000373198	NM_133170.3	731	Gcc/Acc	14/32	1	2	FACETS	0.949	0.869	1	0.949	0.869	1	CLONAL	1	TRUE	1	0.441038511396091	2		840	712	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	81	400	2	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	1	2	FACETS	0.977	0.866	1	0.977	0.866	1	CLONAL	1	TRUE	1	0.441038511396091	2		402	376	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491273	2491273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771419721	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	179	867	7	ENST00000355716.4:c.316C>T	p.Arg106Cys	p.R106C	ENST00000355716	NM_003820.2	106	Cgc/Tgc	4/8	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.441038511396091	2		874	755	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244454	46244454	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs751704736	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	144	725	0	ENST00000334344.6:c.2552del	p.Pro851HisfsTer4	p.P851Hfs*4	ENST00000334344	NM_152641.2	850	Ccc/cc	15/21	1	2	FACETS	0.94	0.859	1	0.94	0.859	1	CLONAL	1	TRUE	1	0.441038511396091	2		725	695	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287315	46287315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1565642121	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	192	802	0	ENST00000334344.6:c.5260C>T	p.Arg1754Ter	p.R1754*	ENST00000334344	NM_152641.2	1754	Cga/Tga	19/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.441038511396091	2		802	791	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835781	68835781	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060501215	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	167	755	2	ENST00000261769.5:c.377del	p.Pro126ArgfsTer89	p.P126Rfs*89	ENST00000261769	NM_004360.3	124	cgC/cg	3/16	1	2	FACETS	0.966	0.889	1	0.966	0.889	1	CLONAL	1	TRUE	1	0.441038511396091	2		757	784	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	94	525	5	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.847	0.757	0.943	0.847	0.757	0.943	CLONAL	1	TRUE	1	0.441038511396091	2		530	503	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533732	63533733	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGG	rs570443161	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	70	584	0	ENST00000307078.5:c.1419_1421dup	p.His474dup	p.H474dup	ENST00000307078	NM_004655.3	474	cat/caCCAt	6/11	1	2	FACETS	0.769	0.673	0.871	0.769	0.673	0.871	SUBCLONAL	1	TRUE	1	0.441038511396091	2		584	413	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951085	17951085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	182	935	0	ENST00000458235.1:c.1208G>A	p.Arg403His	p.R403H	ENST00000458235	NM_000215.3	403	cGc/cAc	9/24	1	2	FACETS	0.941	0.869	1	0.941	0.869	1	CLONAL	1	TRUE	1	0.441038511396091	2		935	877	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570063	212570063	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746784831	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	193	702	1	ENST00000342788.4:c.1178G>A	p.Arg393Gln	p.R393Q	ENST00000342788	NM_005235.2	393	cGg/cAg	10/28	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.441038511396091	2		703	831	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	172	862	7	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.441038511396091	2		869	695	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11193166	11193166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755987187	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	157	764	3	ENST00000361445.4:c.5335G>A	p.Ala1779Thr	p.A1779T	ENST00000361445	NM_004958.3	1779	Gcc/Acc	38/58	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.441038511396091	2		767	685	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157385	106157385	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	88	455	0	ENST00000380013.4:c.2290del	p.Gln764LysfsTer49	p.Q764Kfs*49	ENST00000380013	NM_001127208.2	762	caC/ca	3/11	1	2	FACETS	0.873	0.777	0.975	0.873	0.777	0.975	CLONAL	1	TRUE	1	0.441038511396091	2		455	457	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	214	910	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.818	0.759	0.879	0.818	0.759	0.879	CLONAL	1	TRUE	1	0.441038511396091	2		915	1186	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	157	791	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	0.815	0.746	0.886	0.815	0.746	0.886	CLONAL	1	TRUE	1	0.441038511396091	2		791	874	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647133	23647133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571063157	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	241	1098	3	ENST00000261584.4:c.734C>T	p.Ala245Val	p.A245V	ENST00000261584	NM_024675.3	245	gCg/gTg	4/13	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.441038511396091	2		1101	1059	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990386	69990386	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	67	439	0	ENST00000394351.3:c.346-1G>A		p.X116_splice	ENST00000394351	NM_000248.3	116			1	2	FACETS	0.715	0.623	0.813	0.715	0.623	0.813	SUBCLONAL	1	TRUE	1	0.441038511396091	2		439	425	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374702	118374702	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587783680	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	104	629	0	ENST00000534358.1:c.8095C>T	p.Arg2699Ter	p.R2699*	ENST00000534358	NM_005933.3	2699	Cga/Tga	27/36	1	2	FACETS	0.897	0.806	0.992	0.897	0.806	0.992	CLONAL	1	TRUE	1	0.441038511396091	2		629	526	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073431	8073432	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	196	790	0	ENST00000377482.5:c.1227dup	p.Phe410IlefsTer3	p.F410Ifs*3	ENST00000377482	NM_018948.3	409	-/A	4/4	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.441038511396091	2		790	774	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298590	11298590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs913197212	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	161	778	1	ENST00000361445.4:c.1871G>A	p.Arg624His	p.R624H	ENST00000361445	NM_004958.3	624	cGc/cAc	12/58	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.441038511396091	2		779	683	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258893	16258893	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs74842071	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	193	1014	0	ENST00000375759.3:c.6158A>C	p.Asn2053Thr	p.N2053T	ENST00000375759	NM_015001.2	2053	aAc/aCc	11/15	1	2	FACETS	0.964	0.892	1	0.964	0.892	1	CLONAL	1	TRUE	1	0.441038511396091	2		1014	908	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099401	27099401	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	139	762	1	ENST00000324856.7:c.3638C>A	p.Pro1213His	p.P1213H	ENST00000324856	NM_006015.4	1213	cCc/cAc	14/20	1	2	FACETS	0.814	0.742	0.89	0.814	0.742	0.89	CLONAL	1	TRUE	1	0.441038511396091	2		763	774	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106507	27106507	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	190	904	0	ENST00000324856.7:c.6121del	p.Val2041Ter	p.V2041*	ENST00000324856	NM_006015.4	2040	Ggg/gg	20/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.441038511396091	2		904	805	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807387	36807387	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	180	912	0	ENST00000373129.3:c.1277C>T	p.Ala426Val	p.A426V	ENST00000373129	NM_032017.1	426	gCc/gTc	12/12	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.441038511396091	2		912	764	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103164	119103164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730880429	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	158	622	1	ENST00000264033.4:c.202C>T	p.Arg68Trp	p.R68W	ENST00000264033	NM_005188.3	68	Cgg/Tgg	2/16	1	2	FACETS	0.998	0.917	1	0.998	0.917	1	CLONAL	1	TRUE	1	0.441038511396091	2		623	718	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420109	49420109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123728	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	113	695	1	ENST00000301067.7:c.15640C>T	p.Arg5214Cys	p.R5214C	ENST00000301067	NM_003482.3	5214	Cgc/Tgc	48/54	1	2	FACETS	0.902	0.814	0.994	0.902	0.814	0.994	CLONAL	1	TRUE	1	0.441038511396091	2		696	568	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420204	49420204	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	180	855	4	ENST00000301067.7:c.15545del	p.Gly5182AlafsTer61	p.G5182Afs*61	ENST00000301067	NM_003482.3	5182	gGc/gc	48/54	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.441038511396091	2		859	782	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428410	49428411	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1284500089	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	139	959	0	ENST00000301067.7:c.10394dup	p.Pro3466ThrfsTer2	p.P3466Tfs*2	ENST00000301067	NM_003482.3	3465	gga/ggGa	36/54	1	2	FACETS	0.755	0.687	0.826	0.755	0.687	0.826	SUBCLONAL	1	TRUE	1	0.441038511396091	2		959	835	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440431	49440431	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1240601136	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	200	916	3	ENST00000301067.7:c.4379del	p.Pro1460HisfsTer46	p.P1460Hfs*46	ENST00000301067	NM_003482.3	1460	cCa/ca	15/54	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.441038511396091	2		919	858	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906853	32906853	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	181	843	0	ENST00000380152.3:c.1238T>C	p.Leu413Pro	p.L413P	ENST00000380152		413	cTa/cCa	10/27	1	2	FACETS	0.984	0.909	1	0.984	0.909	1	CLONAL	1	TRUE	1	0.441038511396091	2		843	834	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396618	30396618	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	38	316	0	ENST00000331968.5:c.101G>C	p.Gly34Ala	p.G34A	ENST00000331968	NM_002742.2	34	gGg/gCg	1/18	1	2	FACETS	0.733	0.611	0.868	0.733	0.611	0.868	SUBCLONAL	1	TRUE	1	0.441038511396091	2		316	235	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590886	95590886	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	127	563	0	ENST00000393063.1:c.1023del	p.His341GlnfsTer12	p.H341Qfs*12	ENST00000393063	NM_030621.3	341	caC/ca	9/28	1	2	FACETS	0.973	0.884	1	0.973	0.884	1	CLONAL	1	TRUE	1	0.441038511396091	2		563	592	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054402	42054403	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	142	547	0	ENST00000219905.7:c.7592dup	p.Lys2532GlufsTer6	p.K2532Efs*6	ENST00000219905	NM_001164273.1	2529	aga/agAa	22/24	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.441038511396091	2		547	622	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500302	99500302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	160	898	1	ENST00000268035.6:c.3735G>A	p.Met1245Ile	p.M1245I	ENST00000268035	NM_000875.3	1245	atG/atA	21/21	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.441038511396091	2		899	699	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396539	396539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	207	1073	2	ENST00000262320.3:c.487G>A	p.Ala163Thr	p.A163T	ENST00000262320	NM_003502.3	163	Gcc/Acc	2/11	1	2	FACETS	0.964	0.895	1	0.964	0.895	1	CLONAL	1	TRUE	1	0.441038511396091	2		1075	974	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134310	2134310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751203255	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	136	985	1	ENST00000219476.3:c.4087G>A	p.Val1363Ile	p.V1363I	ENST00000219476	NM_000548.3	1363	Gtc/Atc	34/42	1	2	FACETS	0.838	0.763	0.917	0.838	0.763	0.917	CLONAL	1	TRUE	1	0.441038511396091	2		986	736	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652290	3652290	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	129	780	1	ENST00000294008.3:c.779del	p.Pro260LeufsTer11	p.P260Lfs*11	ENST00000294008	NM_032444.2	260	cCt/ct	4/15	1	2	FACETS	0.91	0.827	0.997	0.91	0.827	0.997	CLONAL	1	TRUE	1	0.441038511396091	2		781	643	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842456	68842456	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	185	796	0	ENST00000261769.5:c.517A>T	p.Lys173Ter	p.K173*	ENST00000261769	NM_004360.3	173	Aaa/Taa	4/16	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.441038511396091	2		796	811	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81971441	81971441	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	145	778	0	ENST00000359376.3:c.3131G>T	p.Arg1044Met	p.R1044M	ENST00000359376	NM_002661.3	1044	aGg/aTg	28/33	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.441038511396091	2		778	605	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440750	56440750	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	137	703	1	ENST00000407977.2:c.468del	p.Leu157Ter	p.L157*	ENST00000407977		156	ggG/gg	5/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.441038511396091	2		704	583	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511562	66511562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1224297486	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	89	476	0	ENST00000358598.2:c.22G>A	p.Ala8Thr	p.A8T	ENST00000358598	NM_212471.2	8	Gcc/Acc	2/11	1	2	FACETS	0.956	0.853	1	0.956	0.853	1	CLONAL	1	TRUE	1	0.441038511396091	2		476	422	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281310	15281310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	185	933	1	ENST00000263388.2:c.4946C>T	p.Ala1649Val	p.A1649V	ENST00000263388	NM_000435.2	1649	gCg/gTg	27/33	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.441038511396091	2		934	746	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953878	17953878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776089693	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	175	1001	0	ENST00000458235.1:c.524G>A	p.Arg175Gln	p.R175Q	ENST00000458235	NM_000215.3	175	cGa/cAa	5/24	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.441038511396091	2		1001	763	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218451	36218451	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs34078597	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	111	799	2	ENST00000222270.7:c.4235del	p.Gly1412AlafsTer10	p.G1412Afs*10	ENST00000222270	NM_014727.1	1410	caG/ca	16/37	1	2	FACETS	0.934	0.843	1	0.934	0.843	1	CLONAL	1	TRUE	1	0.441038511396091	2		801	539	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222872	36222872	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200461439	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	195	1149	0	ENST00000222270.7:c.5501G>A	p.Arg1834His	p.R1834H	ENST00000222270	NM_014727.1	1834	cGc/cAc	27/37	1	2	FACETS	0.974	0.902	1	0.974	0.902	1	CLONAL	1	TRUE	1	0.441038511396091	2		1149	908	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634702	158634702	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201452185	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	123	547	1	ENST00000263640.3:c.484G>A	p.Val162Met	p.V162M	ENST00000263640	NM_001105.4	162	Gtg/Atg	5/11	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.441038511396091	2		548	550	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36028589	36028589	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	151	916	0	ENST00000358208.4:c.931C>A	p.Leu311Met	p.L311M	ENST00000358208		311	Ctg/Atg	8/12	1	2	FACETS	0.991	0.908	1	0.991	0.908	1	CLONAL	1	TRUE	1	0.441038511396091	2		916	691	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42842590	42842590	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs771443342	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	141	923	1	ENST00000398585.3:c.1267del	p.Ala423ProfsTer12	p.A423Pfs*12	ENST00000398585	NM_001135099.1	423	Gcc/cc	11/14	1	2	FACETS	0.861	0.785	0.94	0.861	0.785	0.94	CLONAL	1	TRUE	1	0.441038511396091	2		924	743	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522550	187522550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	197	707	0	ENST00000441802.2:c.11513G>A	p.Ser3838Asn	p.S3838N	ENST00000441802	NM_005245.3	3838	aGc/aAc	21/27	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.441038511396091	2		707	808	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540374	187540374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370340394	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	96	642	1	ENST00000441802.2:c.7366G>A	p.Ala2456Thr	p.A2456T	ENST00000441802	NM_005245.3	2456	Gcc/Acc	10/27	1	2	FACETS	0.815	0.729	0.907	0.815	0.729	0.907	CLONAL	1	TRUE	1	0.441038511396091	2		643	534	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541507	187541507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758885671	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	122	559	0	ENST00000441802.2:c.6233C>T	p.Ala2078Val	p.A2078V	ENST00000441802	NM_005245.3	2078	gCg/gTg	10/27	1	2	FACETS	0.939	0.852	1	0.939	0.852	1	CLONAL	1	TRUE	1	0.441038511396091	2		559	589	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753348	57753348	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	168	705	0	ENST00000274289.3:c.776G>A	p.Cys259Tyr	p.C259Y	ENST00000274289	NM_006622.3	259	tGt/tAt	6/14	1	2	FACETS	0.975	0.898	1	0.975	0.898	1	CLONAL	1	TRUE	1	0.441038511396091	2		705	781	SUCCESS
APC	324	MSKCC	GRCh37	5	112173306	112173307	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	101	389	0	ENST00000257430.4:c.2016_2017del	p.His672GlnfsTer7	p.H672Qfs*7	ENST00000257430	NM_000038.5	672	cAT/c	16/16	1	2	FACETS	0.97	0.872	1	0.97	0.872	1	CLONAL	1	TRUE	1	0.441038511396091	2		389	472	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797290	32797290	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	192	919	1	ENST00000374899.4:c.1819C>A	p.Leu607Met	p.L607M	ENST00000374899	NM_018833.2	607	Ctg/Atg	11/12	1	2	FACETS	0.951	0.88	1	0.951	0.88	1	CLONAL	1	TRUE	1	0.441038511396091	2		920	916	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109321801	109321802	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	230	1010	0	ENST00000436639.2:c.621dup	p.Lys208GlnfsTer20	p.K208Qfs*20	ENST00000436639	NM_014454.2	207	-/C	4/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.441038511396091	2		1010	995	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137522041	137522041	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	115	530	0	ENST00000367739.4:c.838del	p.Ser280AlafsTer2	p.S280Afs*2	ENST00000367739	NM_000416.2	280	Agc/gc	6/7	1	2	FACETS	0.824	0.744	0.908	0.824	0.744	0.908	CLONAL	1	TRUE	1	0.441038511396091	2		530	633	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505447	157505447	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	132	708	1	ENST00000346085.5:c.3428A>G	p.Lys1143Arg	p.K1143R	ENST00000346085	NM_020732.3	1143	aAg/aGg	13/20	1	2	FACETS	0.978	0.891	1	0.978	0.891	1	CLONAL	1	TRUE	1	0.441038511396091	2		709	612	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403177	116403178	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	165	797	0	ENST00000397752.3:c.2443dup	p.Leu815ProfsTer18	p.L815Pfs*18	ENST00000397752	NM_000245.2	813	ctc/ctCc	11/21	1	2	FACETS	0.927	0.852	1	0.927	0.852	1	CLONAL	1	TRUE	1	0.441038511396091	2		797	807	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148544339	148544339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771352080	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	233	940	1	ENST00000320356.2:c.52C>T	p.Arg18Cys	p.R18C	ENST00000320356	NM_004456.4	18	Cgt/Tgt	2/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.441038511396091	2		941	973	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133981	38133981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	185	947	0	ENST00000317025.8:c.3905del	p.Asn1302MetfsTer4	p.N1302Mfs*4	ENST00000317025	NM_023034.1	1302	aAt/at	23/24	1	2	FACETS	0.817	0.754	0.883	0.817	0.754	0.883	CLONAL	1	TRUE	1	0.441038511396091	2		947	1027	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500868	8500869	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	154	789	0	ENST00000356435.5:c.2013dup	p.Tyr672IlefsTer11	p.Y672Ifs*11	ENST00000356435		671	-/A	13/35	1	2	FACETS	0.894	0.819	0.972	0.894	0.819	0.972	CLONAL	1	TRUE	1	0.441038511396091	2		789	781	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044965	47044965	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	193	1171	0	ENST00000377604.3:c.2291G>A	p.Cys764Tyr	p.C764Y	ENST00000377604	NM_001204468.1	764	tGc/tAc	20/24	0.441038511396091	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.441038511396091	1		1171	663	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0020259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	409	549	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.200158586173364	7	FACETS	0.986	0.942	1			1	CLONAL	6	TRUE	NA	0.200158586173364	7		549	1036	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0020259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	13	281	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.317	0.225	0.43	0.317	0.225	0.43	SUBCLONAL	1	TRUE	1	0.200158586173364	2		281	410	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056575	26056575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs75040909	NA	P-0020259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	23	379	0	ENST00000343677.2:c.82G>A	p.Ala28Thr	p.A28T	ENST00000343677	NM_005319.3	28	Gct/Act	1/1	1	2	FACETS	0.97	0.759	1	0.97	0.759	1	CLONAL	1	TRUE	1	0.200158586173364	2		379	237	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434974	110434974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	71	825	0	ENST00000375856.3:c.3427G>A	p.Gly1143Ser	p.G1143S	ENST00000375856	NM_003749.2	1143	Ggc/Agc	1/2	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.200158586173364	2		825	548	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041205	47041205	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	99	1437	0	ENST00000377604.3:c.1634del	p.Pro545LeufsTer159	p.P545Lfs*159	ENST00000377604	NM_001204468.1	545	Cct/ct	15/24	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.200158586173364	2		1437	941	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0020261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	119	763	2	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.429837673722301	2		765	520	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0020261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	26	571	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.276	0.218	0.342	0.276	0.218	0.342	SUBCLONAL	1	TRUE	1	0.429837673722301	2		571	439	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0020261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	41	542	1	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	0.443	0.369	0.525	0.443	0.369	0.525	SUBCLONAL	1	TRUE	1	0.429837673722301	2		543	431	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653842	89653842	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057518425	NA	P-0020261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	50	717	0	ENST00000371953.3:c.140G>A	p.Arg47Lys	p.R47K	ENST00000371953	NM_000314.4	47	aGg/aAg	2/9	1	2	FACETS	0.398	0.337	0.465	0.398	0.337	0.465	SUBCLONAL	1	TRUE	1	0.429837673722301	2		717	585	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30310017	30310017	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	60	676	1	ENST00000307677.4:c.5C>A	p.Ser2Tyr	p.S2Y	ENST00000307677	NM_138578.1	2	tCt/tAt	2/3	1	2	FACETS	0.447	0.384	0.515	0.447	0.384	0.515	SUBCLONAL	1	TRUE	1	0.429837673722301	2		677	625	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585521	29585521	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1555618572	NA	P-0020262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	20	153	0	ENST00000356175.3:c.4269+1G>A		p.X1423_splice	ENST00000356175	NM_000267.3	1423			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		153	112	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	535	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.398728693127439	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	1	0.398728693127439	4		555	1166	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106481	27106482	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	356	814	13	ENST00000324856.7:c.6093dup	p.Glu2032Ter	p.E2032*	ENST00000324856	NM_006015.4	2031	tat/taTt	20/20	0.356809853659866	2	FACETS	0.958	0.911	1	0.958	0.911	1	CLONAL	2	TRUE	0	0.398728693127439	2		827	932	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421027	49421027	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	230	632	4	ENST00000301067.7:c.14722G>A	p.Ala4908Thr	p.A4908T	ENST00000301067	NM_003482.3	4908	Gcc/Acc	48/54	0.398728693127439	3	FACETS	0.903	0.845	0.963			1	CLONAL	2	TRUE	NA	0.398728693127439	3		636	766	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	60	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.352736530211632	5	FACETS	0.856	0.743	0.976	0.57	0.495	0.651	CLONAL	2	FALSE	2	0.352736530211632	5		555	304	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732996	30732996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893809	NA	P-0020264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	36	635	0	ENST00000295754.5:c.1609C>T	p.Arg537Cys	p.R537C	ENST00000295754	NM_003242.5	537	Cgc/Tgc	7/7	0.341219223331288	1	FACETS	0.692	0.572	0.824	0.692	0.572	0.824	SUBCLONAL	1	FALSE	0	0.352736530211632	1		635	243	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs985033810	NA	P-0020264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	66	1056	1	ENST00000269305.4:c.731G>T	p.Gly244Val	p.G244V	ENST00000269305	NM_001126112.2	244	gGc/gTc	7/11	0.296861199864255	3	FACETS	0.853	0.742	0.974	0.427	0.371	0.487	CLONAL	1	FALSE	1	0.352736530211632	3		1057	516	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056425	26056427	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	rs774779034	NA	P-0020265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	39	476	0	ENST00000343677.2:c.230_232del	p.Asn77del	p.N77del	ENST00000343677	NM_005319.3	77	aACAgc/agc	1/1	0.240758028170491	3	FACETS	0.51	0.423	0.607	0.255	0.211	0.304	INDETERMINATE	1	TRUE	1	0.421703222218164	3		476	439	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651642	48651642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	238	1044	0	ENST00000376670.3:c.808C>T	p.Arg270Trp	p.R270W	ENST00000376670	NM_002049.3	270	Cgg/Tgg	5/6	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.421703222218164	2		1044	850	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099955	27099970	+	frameshift_variant	Frame_Shift_Del	DEL	CTATCCCTATGGAGGT	CTATCCCTATGGAGGT	-	novel	NA	P-0020265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	168	899	0	ENST00000324856.7:c.3835_3850del	p.Tyr1279LeufsTer5	p.Y1279Lfs*5	ENST00000324856	NM_006015.4	1278	caCTATCCCTATGGAGGT/ca	15/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.421703222218164	2		899	705	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266703	18266703	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	165	876	0	ENST00000222254.8:c.14A>T	p.Glu5Val	p.E5V	ENST00000222254	NM_005027.3	5	gAg/gTg	2/16	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.421703222218164	2		876	770	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118817	61118818	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	TT	novel	NA	P-0020265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	52	302	1	ENST00000295025.8:c.11-1_11delinsTT		p.X4_splice	ENST00000295025	NM_002908.2	4		2/11	0.421703222218164	3	FACETS	1	0.963	1	0.698	0.601	0.8	CLONAL	1	TRUE	1	0.421703222218164	3		303	214	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292678	62292678	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1589	193	874	0	ENST00000360203.5:c.130A>G	p.Thr44Ala	p.T44A	ENST00000360203	NM_001283009.1	44	Acg/Gcg	3/35	0.421703222218164	10	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.421703222218164	10		874	1782	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380973	116380973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	142	924	1	ENST00000397752.3:c.1595C>T	p.Ala532Val	p.A532V	ENST00000397752	NM_000245.2	532	gCc/gTc	5/21	0.260829011462481	3	FACETS	1	0.951	1	0.531	0.484	0.58	CLONAL	1	TRUE	1	0.421703222218164	3		925	768	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0020266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	18	146	0				ENST00000310581	NM_198253.2	-/1132			0.222097849218114	1	FACETS	0.419	0.317	0.539	0.419	0.317	0.539	INDETERMINATE	1	TRUE	0	0.371687110652422	1		146	188	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0020266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	40	631	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.478	0.397	0.568	0.478	0.397	0.568	SUBCLONAL	1	TRUE	1	0.371687110652422	2		631	450	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0020266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	51	602	1	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.661	0.563	0.768	0.661	0.563	0.768	SUBCLONAL	1	TRUE	1	0.371687110652422	2		603	415	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063320	67063320	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	17	353	0	ENST00000412916.2:c.10G>T	p.Val4Phe	p.V4F	ENST00000412916		4	Gtc/Ttc	1/6	0.222097849218114	1	FACETS	0.405	0.303	0.524	0.405	0.303	0.524	INDETERMINATE	1	TRUE	0	0.371687110652422	1		353	184	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447410	12447410	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	43	789	0	ENST00000287820.6:c.649G>C	p.Glu217Gln	p.E217Q	ENST00000287820	NM_015869.4	217	Gag/Cag	5/7	1	2	FACETS	0.412	0.344	0.487	0.412	0.344	0.487	SUBCLONAL	1	TRUE	1	0.371687110652422	2		789	562	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115971	8115972	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	165	522	1	ENST00000346208.3:c.1318dup	p.Thr440AsnfsTer67	p.T440Nfs*67	ENST00000346208		439	-/A	6/6	0.498773822212863	4	FACETS	0.816	0.755	0.879	0.816	0.755	0.879	CLONAL	2	TRUE	2	0.642090184192538	4		523	517	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273879	10273880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	152	1202	0	ENST00000330684.3:c.389dup	p.Ala131ArgfsTer7	p.A131Rfs*7	ENST00000330684	NM_001134407.1	130	ggc/ggGc	2/13	0.642090184192538	3	FACETS	0.641	0.585	0.699	0.32	0.292	0.35	SUBCLONAL	1	TRUE	1	0.642090184192538	3		1202	976	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48586265	48586265	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	127	946	0	ENST00000342988.3:c.934C>A	p.Pro312Thr	p.P312T	ENST00000342988	NM_005359.5	312	Cct/Act	8/12	0.597977558465465	4	FACETS	0.754	0.683	0.83	0.377	0.341	0.415	SUBCLONAL	1	TRUE	2	0.642090184192538	4		946	861	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478917	56478917	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	87	1005	0	ENST00000267101.3:c.373A>C	p.Thr125Pro	p.T125P	ENST00000267101	NM_001982.3	125	Acc/Ccc	3/28	1	2	FACETS	0.794	0.702	0.894	0.794	0.702	0.894	SUBCLONAL	1	TRUE	1	0.226547699514471	2		1005	967	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984835	11984835	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	99	722	0	ENST00000353533.5:c.382del	p.Met128TrpfsTer24	p.M128Wfs*24	ENST00000353533	NM_003010.3	127	atA/at	3/11	0.368581780573927	1	FACETS	0.436	0.392	0.483	0.436	0.392	0.483	INDETERMINATE	1	TRUE	0	0.689827931127115	1		722	431	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029404	16029408	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTT	TTCTT	-	novel	NA	P-0020269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	92	1112	0	ENST00000268712.3:c.1622_1626del	p.Lys541ArgfsTer20	p.K541Rfs*20	ENST00000268712	NM_006311.3	541	aAAGAA/a	15/46	0.368581780573927	1	FACETS	0.247	0.219	0.276	0.247	0.219	0.276	INDETERMINATE	1	TRUE	0	0.689827931127115	1		1112	708	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	260	122	0				ENST00000310581	NM_198253.2	-/1132			0.433485027980083	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	1	0.433485027980083	4		122	493	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433784	49433784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760007799	NA	P-0020270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	387	1354	2	ENST00000301067.7:c.7769C>T	p.Ser2590Leu	p.S2590L	ENST00000301067	NM_003482.3	2590	tCg/tTg	31/54	0.433485027980083	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.433485027980083	1		1356	1122	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731213	162731213	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	188	502	1	ENST00000367921.3:c.1068G>A	p.Trp356Ter	p.W356*	ENST00000367921	NM_006182.2	356	tgG/tgA	9/18	0.201537812125051	3	FACETS	1	0.97	1	0.715	0.667	0.764	INDETERMINATE	2	TRUE	0	0.433485027980083	3		503	492	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94169044	94169044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	68	587	0	ENST00000323929.3:c.1948G>A	p.Asp650Asn	p.D650N	ENST00000323929	NM_005591.3	650	Gat/Aat	18/20	0.201112807292105	2	FACETS	0.552	0.481	0.63	0.276	0.24	0.315	INDETERMINATE	1	TRUE	0	0.433485027980083	2		587	568	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047496	49047496	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	233	643	0	ENST00000267163.4:c.2491del	p.Ile831SerfsTer2	p.I831Sfs*2	ENST00000267163	NM_000321.2	830	agA/ag	24/27	0.433485027980083	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	0	0.433485027980083	2		643	537	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817823	3817823	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	631	1165	2	ENST00000262367.5:c.3148G>T	p.Glu1050Ter	p.E1050*	ENST00000262367	NM_004380.2	1050	Gaa/Taa	16/31	0.380220195058473	3	FACETS	0.913	0.882	0.944	0.913	0.882	0.944	CLONAL	3	TRUE	0	0.433485027980083	3		1167	1293	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291458	10291458	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	208	1138	0	ENST00000340748.4:c.221C>G	p.Ser74Cys	p.S74C	ENST00000340748		74	tCc/tGc	3/40	0.296292575810019	1	FACETS	0.78	0.724	0.838	0.78	0.724	0.838	SUBCLONAL	1	TRUE	0	0.433485027980083	1		1138	964	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117746817	117746817	+	start_lost	Translation_Start_Site	SNP	C	C	T	rs767435564	NA	P-0020270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	51	570	0	ENST00000368508.3:c.3G>A	p.Met1?	p.M1?	ENST00000368508	NM_002944.2	1	atG/atA	1/43	0.340033270260351	3	FACETS	0.432	0.366	0.504	0.216	0.183	0.252	SUBCLONAL	1	TRUE	1	0.433485027980083	3		570	663	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500770	8500771	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	ATCAACAC	novel	NA	P-0020270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	48	534	0	ENST00000356435.5:c.2104_2111dup	p.Ile704MetfsTer3	p.I704Mfs*3	ENST00000356435		704	att/atGTGTTGATt	13/35	0.28480685337356	3	FACETS	0.445	0.375	0.521	0.222	0.187	0.261	SUBCLONAL	1	TRUE	1	0.433485027980083	3		534	606	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0020272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	80	631	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.278878309699394	2		631	466	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0020272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	16	425	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.188645575023882	3	FACETS	0.183	0.134	0.242	0.092	0.067	0.121	SUBCLONAL	1	TRUE	1	0.278878309699394	3		425	714	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038242	30038242	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	77	928	0	ENST00000338641.4:c.415G>A	p.Val139Met	p.V139M	ENST00000338641	NM_000268.3	139	Gtg/Atg	4/16	1	2	FACETS	0.781	0.685	0.884	0.781	0.685	0.884	SUBCLONAL	1	TRUE	1	0.278878309699394	2		928	707	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160758	56160762	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TCAGG	TCAGG	-	novel	NA	P-0020272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	41	592	0	ENST00000399503.3:c.1033_1035+2del		p.X345_splice	ENST00000399503	NM_005921.1	345		4/20	1	2	FACETS	0.641	0.534	0.759	0.641	0.534	0.759	SUBCLONAL	1	TRUE	1	0.278878309699394	2		592	459	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177505	56177514	+	frameshift_variant	Frame_Shift_Del	DEL	GGTTACTACA	GGTTACTACA	-	novel	NA	P-0020272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	67	671	0	ENST00000399503.3:c.2479_2488del	p.Val827TyrfsTer9	p.V827Yfs*9	ENST00000399503	NM_005921.1	826	atGGTTACTACA/at	14/20	1	2	FACETS	0.863	0.75	0.984	0.863	0.75	0.984	CLONAL	1	TRUE	1	0.278878309699394	2		671	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0020273-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	68	1054	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.552	0.479	0.631	0.552	0.479	0.631	SUBCLONAL	1	TRUE	1	0.316826076082276	2		1055	778	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984460	7984460	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020273-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	36	860	0	ENST00000319144.4:c.398G>C	p.Arg133Thr	p.R133T	ENST00000319144	NM_001139.2	133	aGa/aCa	3/15	1	2	FACETS	0.377	0.309	0.454	0.377	0.309	0.454	SUBCLONAL	1	TRUE	1	0.316826076082276	2		860	602	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158113	47158113	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020273-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	31	818	0	ENST00000409792.3:c.4586G>T	p.Cys1529Phe	p.C1529F	ENST00000409792	NM_014159.6	1529	tGt/tTt	4/21	1	2	FACETS	0.391	0.315	0.476	0.391	0.315	0.476	SUBCLONAL	1	TRUE	1	0.316826076082276	2		818	501	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0020287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	30	465	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.646	0.526	0.779	0.646	0.526	0.779	SUBCLONAL	1	TRUE	1	0.546362598676297	2		465	170	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	67	122	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.94	0.826	1	0.94	0.826	1	CLONAL	1	TRUE	1	0.546362598676297	2		122	261	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519938	NA	P-0020287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	71	564	0	ENST00000263967.3:c.1034A>T	p.Asn345Ile	p.N345I	ENST00000263967	NM_006218.2	345	aAt/aTt	5/21	1	2	FACETS	0.932	0.822	1	0.932	0.822	1	CLONAL	1	TRUE	1	0.546362598676297	2		564	279	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430635	78430635	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	47	675	1	ENST00000370768.2:c.655del	p.Met219TrpfsTer3	p.M219Wfs*3	ENST00000370768	NM_003902.3	219	Atg/tg	9/20	0.538799824855114	1	FACETS	0.553	0.472	0.641	0.553	0.472	0.641	SUBCLONAL	1	TRUE	0	0.546362598676297	1		676	226	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791817	42791817	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	64	837	0	ENST00000575354.2:c.703G>C	p.Gly235Arg	p.G235R	ENST00000575354	NM_015125.3	235	Ggc/Cgc	5/20	0.546362598676297	1	FACETS	0.535	0.467	0.609	0.535	0.467	0.609	SUBCLONAL	1	TRUE	0	0.546362598676297	1		837	318	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447609	187447609	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	42	696	0	ENST00000232014.4:c.584A>G	p.Tyr195Cys	p.Y195C	ENST00000232014	NM_001130845.1	195	tAt/tGt	5/10	1	2	FACETS	0.351	0.293	0.415	0.351	0.293	0.415	SUBCLONAL	1	TRUE	1	0.546362598676297	2		696	438	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803153	1803153	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1222728854	NA	P-0020287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	41	842	1	ENST00000260795.2:c.505G>A	p.Ala169Thr	p.A169T	ENST00000260795		169	Gcc/Acc	4/17	1	2	FACETS	0.272	0.226	0.324	0.272	0.226	0.324	SUBCLONAL	1	TRUE	1	0.546362598676297	2		843	551	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0020288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	116	352	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.984	0.894	1	1	0.989	1	CLONAL	2	FALSE	1	0.286789610510798	2		352	411	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602662	55602662	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0020288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	80	420	0	ENST00000288135.5:c.2485-2A>T		p.X829_splice	ENST00000288135	NM_000222.2	829			0.286789610510798	1	FACETS	0.905	0.807	1	1	0.984	1	CLONAL	2	FALSE	0	0.286789610510798	1		420	264	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099977	157099977	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	96	310	1	ENST00000346085.5:c.914G>A	p.Gly305Asp	p.G305D	ENST00000346085	NM_020732.3	305	gGc/gAc	1/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.3	2		311	511	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244179	153244179	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	122	758	1	ENST00000281708.4:c.1978C>G	p.Leu660Val	p.L660V	ENST00000281708	NM_033632.3	660	Cta/Gta	12/12	1	2	FACETS	0.737	0.664	0.813	0.737	0.664	0.813	SUBCLONAL	1	TRUE	1	0.3	2		759	1104	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	475	424	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.645117506526858	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.645117506526858	3		424	885	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0020291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	193	779	4	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.912	0.848	0.978	0.912	0.848	0.978	CLONAL	1	TRUE	1	0.645117506526858	2		783	656	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821553	72821554	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	135	418	0	ENST00000268489.5:c.10621dup	p.Glu3541GlyfsTer30	p.E3541Gfs*30	ENST00000268489	NM_006885.3	3541	gag/gGag	10/10	1	2	FACETS	0.967	0.886	1	0.967	0.886	1	CLONAL	1	TRUE	1	0.645117506526858	2		418	433	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268760	41268760	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	45	442	0	ENST00000349496.5:c.998A>T	p.Tyr333Phe	p.Y333F	ENST00000349496	NM_001904.3	333	tAc/tTc	7/15	1	2	FACETS	0.25	0.21	0.295	0.25	0.21	0.295	SUBCLONAL	1	TRUE	1	0.645117506526858	2		442	557	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219465	5219465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1452566818	NA	P-0020291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	186	753	0	ENST00000357368.4:c.3779G>A	p.Ser1260Asn	p.S1260N	ENST00000357368	NM_002850.3	1260	aGt/aAt	23/38	1	2	FACETS	0.898	0.833	0.965	0.898	0.833	0.965	CLONAL	1	TRUE	1	0.645117506526858	2		753	642	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200067	128200067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	92	1070	0	ENST00000341105.2:c.1238G>A	p.Cys413Tyr	p.C413Y	ENST00000341105	NM_032638.4	413	tGc/tAc	6/6	1	2	FACETS	0.317	0.281	0.355	0.317	0.281	0.355	SUBCLONAL	1	TRUE	1	0.645117506526858	2		1070	901	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696461	47696461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	129	550	0	ENST00000347630.2:c.362G>A	p.Arg121Gln	p.R121Q	ENST00000347630	NM_001007230.1	121	cGg/cAg	6/11	0.31253716707672	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.31253716707672	1		550	522	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0020293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	215	839	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA	2	FACETS	0.828	0.771	0.886			1	INDETERMINATE	2	TRUE	NA	0.31253716707672	2		841	831	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928072	178928101	+	inframe_deletion	In_Frame_Del	DEL	TGGATTAGAAGATTTGCTGAACCCTATTGG	TGGATTAGAAGATTTGCTGAACCCTATTGG	-	novel	NA	P-0020293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	80	855	0	ENST00000263967.3:c.1352_1381del	p.Gly451_Gly460del	p.G451_G460del	ENST00000263967	NM_006218.2	450	caTGGATTAGAAGATTTGCTGAACCCTATTGGt/cat	8/21	1	2	FACETS	0.724	0.637	0.818	0.724	0.637	0.818	SUBCLONAL	1	TRUE	1	0.31253716707672	2		855	707	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992811	72992811	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0020293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	111	678	0	ENST00000268489.5:c.1234A>T	p.Lys412Ter	p.K412*	ENST00000268489	NM_006885.3	412	Aag/Tag	2/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.31253716707672	2		678	635	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209103910	209103910	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	79	603	0	ENST00000345146.2:c.1039G>C	p.Asp347His	p.D347H	ENST00000345146	NM_005896.2	347	Gat/Cat	9/10	1	2	FACETS	0.781	0.687	0.882	0.781	0.687	0.882	SUBCLONAL	1	TRUE	1	0.31253716707672	2		603	647	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737356	145737356	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	82	876	0	ENST00000428558.2:c.3331G>C	p.Glu1111Gln	p.E1111Q	ENST00000428558	NM_004260.3	1111	Gag/Cag	20/22	0.31253716707672	3	FACETS	0.637	0.561	0.72	0.319	0.28	0.36	SUBCLONAL	1	TRUE	1	0.31253716707672	3		876	952	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105512	27105512	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0020294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	176	517	0	ENST00000324856.7:c.5125-2A>C		p.X1709_splice	ENST00000324856	NM_006015.4	1709			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		517	564	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059183	27059183	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	151	521	0	ENST00000324856.7:c.1820C>A	p.Ser607Ter	p.S607*	ENST00000324856	NM_006015.4	607	tCa/tAa	4/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.52	2		521	544	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	230	684	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	0.52	2		684	837	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761219	59761219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs575998972	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	76	893	1	ENST00000259008.2:c.3188C>T	p.Ser1063Leu	p.S1063L	ENST00000259008	NM_032043.2	1063	tCg/tTg	20/20	1	2	FACETS	0.378	0.331	0.429	0.378	0.331	0.429	SUBCLONAL	1	TRUE	1	0.52	2		894	773	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260151	149260151	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1307297959	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	201	558	1	ENST00000360632.3:c.742C>T	p.Arg248Ter	p.R248*	ENST00000360632	NM_015472.4	248	Cga/Tga	4/7	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.52	2		559	650	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	190	453	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.52	2		453	677	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	227	852	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.52	2		852	801	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	111	590	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	1	2	FACETS	0.918	0.83	1	0.918	0.83	1	CLONAL	1	TRUE	1	0.52	2		590	465	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453486	138453486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451809865	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	87	579	0	ENST00000289153.2:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000289153	NM_006219.2	321	cGa/cAa	5/22	1	2	FACETS	0.672	0.597	0.752	0.672	0.597	0.752	SUBCLONAL	1	TRUE	1	0.52	2		579	498	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573894	18573894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759658584	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	78	650	0	ENST00000266497.5:c.2212C>T	p.Arg738Cys	p.R738C	ENST00000266497		738	Cgt/Tgt	15/31	1	2	FACETS	0.542	0.476	0.611	0.542	0.476	0.611	SUBCLONAL	1	TRUE	1	0.52	2		650	554	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	189	653	1	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.52	2		654	688	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692790	89692790	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554898067	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	140	531	0	ENST00000371953.3:c.274G>T	p.Asp92Tyr	p.D92Y	ENST00000371953	NM_000314.4	92	Gac/Tac	5/9	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.52	2		531	430	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514563	41514563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	57	561	0	ENST00000373198.4:c.98C>T	p.Ser33Phe	p.S33F	ENST00000373198	NM_133170.3	33	tCc/tTc	2/32	1	2	FACETS	0.387	0.332	0.448	0.387	0.332	0.448	SUBCLONAL	1	TRUE	1	0.52	2		561	566	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	148	468	0	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.52	2		468	473	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650710	67650710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243010179	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	275	751	1	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	0.983	1	CLONAL	1	TRUE	1	0.52	2		752	948	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	128	558	2	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.943	0.859	1	0.943	0.859	1	CLONAL	1	TRUE	1	0.52	2		560	522	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131412	202131412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339962485	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	135	658	3	ENST00000358485.4:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000358485	NM_001080125.1	127	cGa/cAa	2/9	1	2	FACETS	0.876	0.799	0.956	0.876	0.799	0.956	CLONAL	1	TRUE	1	0.52	2		661	593	SUCCESS
APC	324	MSKCC	GRCh37	5	112173495	112173495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147655929	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	89	506	1	ENST00000257430.4:c.2204C>T	p.Ala735Val	p.A735V	ENST00000257430	NM_000038.5	735	gCg/gTg	16/16	1	2	FACETS	0.981	0.877	1	0.981	0.877	1	CLONAL	1	TRUE	1	0.52	2		507	349	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698180	47698180	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63751411	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	79	490	0	ENST00000233146.2:c.1738G>T	p.Glu580Ter	p.E580*	ENST00000233146	NM_000251.2	580	Gaa/Taa	11/16	1	2	FACETS	0.634	0.56	0.714	0.634	0.56	0.714	SUBCLONAL	1	TRUE	1	0.52	2		490	479	SUCCESS
APC	324	MSKCC	GRCh37	5	112177203	112177203	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs754691867	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	123	433	0	ENST00000257430.4:c.5912C>A	p.Ser1971Tyr	p.S1971Y	ENST00000257430	NM_000038.5	1971	tCt/tAt	16/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.52	2		433	372	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519560	137519560	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	93	532	0	ENST00000367739.4:c.1078G>T	p.Glu360Ter	p.E360*	ENST00000367739	NM_000416.2	360	Gaa/Taa	7/7	1	2	FACETS	0.621	0.553	0.693	0.621	0.553	0.693	SUBCLONAL	1	TRUE	1	0.52	2		532	576	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651293	45651293	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	117	816	0	ENST00000407780.3:c.732G>T	p.Glu244Asp	p.E244D	ENST00000407780	NM_001283052.1	244	gaG/gaT	5/7	1	2	FACETS	0.523	0.471	0.578	0.523	0.471	0.578	SUBCLONAL	1	TRUE	1	0.52	2		816	860	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027317	48027317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749746725	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	131	460	3	ENST00000234420.5:c.2195G>A	p.Arg732Gln	p.R732Q	ENST00000234420	NM_000179.2	732	cGa/cAa	4/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.52	2		463	446	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546725	9546725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210292896	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	116	335	0	ENST00000353224.5:c.1297C>T	p.Arg433Trp	p.R433W	ENST00000353224	NM_177990.2	433	Cgg/Tgg	5/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.52	2		335	374	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332415	70332415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1419371452	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	123	710	2	ENST00000373644.4:c.320G>A	p.Arg107Gln	p.R107Q	ENST00000373644	NM_030625.2	107	cGa/cAa	2/12	1	2	FACETS	0.577	0.521	0.635	0.577	0.521	0.635	SUBCLONAL	1	TRUE	1	0.52	2		712	820	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045784	47045784	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	113	764	0	ENST00000377604.3:c.2665G>A	p.Glu889Lys	p.E889K	ENST00000377604	NM_001204468.1	889	Gag/Aag	23/24	1	2	FACETS	0.546	0.491	0.604	0.546	0.491	0.604	SUBCLONAL	1	TRUE	1	0.52	2		764	796	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052626	42052626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	64	665	5	ENST00000219905.7:c.7297C>T	p.Arg2433Trp	p.R2433W	ENST00000219905	NM_001164273.1	2433	Cgg/Tgg	20/24	1	2	FACETS	0.323	0.279	0.371	0.323	0.279	0.371	SUBCLONAL	1	TRUE	1	0.52	2		670	762	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285871	87285871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408094711	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	185	641	0	ENST00000277120.3:c.208G>A	p.Glu70Lys	p.E70K	ENST00000277120		70	Gaa/Aaa	2/19	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.52	2		641	653	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162107	22162107	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	46	584	2	ENST00000215832.6:c.148C>T	p.Arg50Ter	p.R50*	ENST00000215832	NM_002745.4	50	Cga/Tga	2/9	1	2	FACETS	0.331	0.279	0.39	0.331	0.279	0.39	SUBCLONAL	1	TRUE	1	0.52	2		586	534	SUCCESS
REL	5966	MSKCC	GRCh37	2	61128173	61128173	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	62	495	1	ENST00000295025.8:c.349G>T	p.Glu117Ter	p.E117*	ENST00000295025	NM_002908.2	117	Gaa/Taa	4/11	1	2	FACETS	0.452	0.391	0.519	0.452	0.391	0.519	SUBCLONAL	1	TRUE	1	0.52	2		496	527	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788637	3788637	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	164	601	0	ENST00000262367.5:c.4317C>A	p.Phe1439Leu	p.F1439L	ENST00000262367	NM_004380.2	1439	ttC/ttA	26/31	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.52	2		601	588	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144623	55144623	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	49	564	0	ENST00000257290.5:c.2097G>T	p.Glu699Asp	p.E699D	ENST00000257290	NM_006206.4	699	gaG/gaT	15/23	1	2	FACETS	0.366	0.31	0.428	0.366	0.31	0.428	SUBCLONAL	1	TRUE	1	0.52	2		564	515	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518428	204518428	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	88	542	0	ENST00000367182.3:c.1091G>T	p.Arg364Ile	p.R364I	ENST00000367182	NM_001278516.1	364	aGa/aTa	11/11	1	2	FACETS	0.639	0.567	0.715	0.639	0.567	0.715	SUBCLONAL	1	TRUE	1	0.52	2		542	530	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939260	71939260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	259	803	2	ENST00000298229.2:c.209G>A	p.Arg70His	p.R70H	ENST00000298229	NM_001567.3	70	cGc/cAc	2/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.52	2		805	876	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004277	29004277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370686484	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	59	523	1	ENST00000282397.4:c.1016G>A	p.Arg339Gln	p.R339Q	ENST00000282397	NM_002019.4	339	cGa/cAa	8/30	1	2	FACETS	0.39	0.335	0.449	0.39	0.335	0.449	SUBCLONAL	1	TRUE	1	0.52	2		524	582	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720871	89720871	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	139	430	0	ENST00000371953.3:c.1022T>G	p.Phe341Cys	p.F341C	ENST00000371953	NM_000314.4	341	tTt/tGt	8/9	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.52	2		430	430	SUCCESS
ATM	472	MSKCC	GRCh37	11	108159816	108159816	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	16	169	0	ENST00000278616.4:c.4222C>A	p.Leu1408Ile	p.L1408I	ENST00000278616	NM_000051.3	1408	Ctt/Att	28/63	1	2	FACETS	0.463	0.345	0.601	0.463	0.345	0.601	SUBCLONAL	1	TRUE	1	0.52	2		169	133	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639116	3639116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs112694849	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	115	772	0	ENST00000294008.3:c.4523C>T	p.Ser1508Leu	p.S1508L	ENST00000294008	NM_032444.2	1508	tCg/tTg	12/15	1	2	FACETS	0.501	0.451	0.555	0.501	0.451	0.555	SUBCLONAL	1	TRUE	1	0.52	2		772	882	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699372	47699372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	156	635	1	ENST00000347630.2:c.136G>A	p.Glu46Lys	p.E46K	ENST00000347630	NM_001007230.1	46	Gag/Aag	4/11	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.52	2		636	593	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117524	4117524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371852537	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	77	253	2	ENST00000262948.5:c.196G>A	p.Glu66Lys	p.E66K	ENST00000262948	NM_030662.3	66	Gaa/Aaa	2/11	1	2	FACETS	0.968	0.858	1	0.968	0.858	1	CLONAL	1	TRUE	1	0.52	2		255	306	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212851	94212851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368403414	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	33	588	1	ENST00000323929.3:c.391G>A	p.Asp131Asn	p.D131N	ENST00000323929	NM_005591.3	131	Gat/Aat	5/20	1	2	FACETS	0.269	0.219	0.326	0.269	0.219	0.326	SUBCLONAL	1	TRUE	1	0.52	2		589	471	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527318	137527318	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	285	831	0	ENST00000367739.4:c.328G>T	p.Glu110Ter	p.E110*	ENST00000367739	NM_000416.2	110	Gaa/Taa	3/7	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.52	2		831	760	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795032	45795032	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs768671057	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	121	756	0	ENST00000450313.1:c.1596C>A	p.Phe532Leu	p.F532L	ENST00000450313	NM_012222.2	532	ttC/ttA	16/16	1	2	FACETS	0.537	0.485	0.593	0.537	0.485	0.593	SUBCLONAL	1	TRUE	1	0.52	2		756	866	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46597552	46597552	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	77	627	0	ENST00000262741.5:c.73G>T	p.Glu25Ter	p.E25*	ENST00000262741	NM_003629.3	25	Gaa/Taa	1/10	1	2	FACETS	0.455	0.399	0.515	0.455	0.399	0.515	SUBCLONAL	1	TRUE	1	0.52	2		627	651	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115284279	115284279	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	132	519	0	ENST00000438362.2:c.7A>C	p.Asn3His	p.N3H	ENST00000438362	NM_001242891.1	3	Aac/Cac	2/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.52	2		519	479	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70411606	70411606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303423182	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	48	549	0	ENST00000373644.4:c.4280G>A	p.Arg1427Gln	p.R1427Q	ENST00000373644	NM_030625.2	1427	cGa/cAa	5/12	1	2	FACETS	0.341	0.288	0.399	0.341	0.288	0.399	SUBCLONAL	1	TRUE	1	0.52	2		549	542	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724138	112724138	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	53	542	0	ENST00000369452.4:c.22G>T	p.Glu8Ter	p.E8*	ENST00000369452	NM_007373.3	8	Gaa/Taa	2/9	1	2	FACETS	0.336	0.286	0.391	0.336	0.286	0.391	SUBCLONAL	1	TRUE	1	0.52	2		542	607	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741669	17741669	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1432646693	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	104	522	4	ENST00000250003.3:c.340G>A	p.Ala114Thr	p.A114T	ENST00000250003	NM_002478.4	114	Gcc/Acc	1/3	1	2	FACETS	0.614	0.551	0.682	0.614	0.551	0.682	SUBCLONAL	1	TRUE	1	0.52	2		526	651	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462775	69462775	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	103	652	0	ENST00000227507.2:c.588T>G	p.Ile196Met	p.I196M	ENST00000227507	NM_053056.2	196	atT/atG	4/5	1	2	FACETS	0.609	0.545	0.676	0.609	0.545	0.676	SUBCLONAL	1	TRUE	1	0.52	2		652	651	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342428	118342428	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782442429	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	73	458	2	ENST00000534358.1:c.554G>A	p.Arg185Gln	p.R185Q	ENST00000534358	NM_005933.3	185	cGa/cAa	3/36	1	2	FACETS	0.741	0.652	0.836	0.741	0.652	0.836	SUBCLONAL	1	TRUE	1	0.52	2		460	379	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475146	475146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	108	788	1	ENST00000399788.2:c.491G>A	p.Arg164Lys	p.R164K	ENST00000399788	NM_001042603.1	164	aGa/aAa	4/28	1	2	FACETS	0.681	0.612	0.753	0.681	0.612	0.753	SUBCLONAL	1	TRUE	1	0.52	2		789	610	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499680	18499680	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	54	761	2	ENST00000266497.5:c.1535G>T	p.Arg512Ile	p.R512I	ENST00000266497		512	aGa/aTa	10/31	1	2	FACETS	0.3	0.256	0.349	0.3	0.256	0.349	SUBCLONAL	1	TRUE	1	0.52	2		763	692	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800921	18800921	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	66	633	0	ENST00000266497.5:c.4297G>T	p.Asp1433Tyr	p.D1433Y	ENST00000266497		1433	Gat/Tat	31/31	1	2	FACETS	0.486	0.422	0.555	0.486	0.422	0.555	SUBCLONAL	1	TRUE	1	0.52	2		633	522	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246200	46246200	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	44	598	0	ENST00000334344.6:c.4294C>T	p.Gln1432Ter	p.Q1432*	ENST00000334344	NM_152641.2	1432	Cag/Tag	15/21	1	2	FACETS	0.303	0.254	0.358	0.303	0.254	0.358	SUBCLONAL	1	TRUE	1	0.52	2		598	558	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864545	57864545	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	57	788	1	ENST00000228682.2:c.2022G>T	p.Gln674His	p.Q674H	ENST00000228682	NM_005269.2	674	caG/caT	12/12	1	2	FACETS	0.292	0.25	0.339	0.292	0.25	0.339	SUBCLONAL	1	TRUE	1	0.52	2		789	750	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012395	29012395	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766436940	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	106	743	0	ENST00000282397.4:c.476G>A	p.Arg159Gln	p.R159Q	ENST00000282397	NM_002019.4	159	cGg/cAg	4/30	1	2	FACETS	0.589	0.528	0.653	0.589	0.528	0.653	SUBCLONAL	1	TRUE	1	0.52	2		743	692	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912495	32912495	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs747070579	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	73	591	0	ENST00000380152.3:c.4003G>T	p.Glu1335Ter	p.E1335*	ENST00000380152		1335	Gaa/Taa	11/27	1	2	FACETS	0.547	0.479	0.62	0.547	0.479	0.62	SUBCLONAL	1	TRUE	1	0.52	2		591	513	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32932000	32932000	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	60	504	0	ENST00000380152.3:c.7739A>C	p.Gln2580Pro	p.Q2580P	ENST00000380152		2580	cAg/cCg	16/27	1	2	FACETS	0.538	0.465	0.617	0.538	0.465	0.617	SUBCLONAL	1	TRUE	1	0.52	2		504	429	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281852	49281852	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	133	803	0	ENST00000282018.3:c.899T>G	p.Phe300Cys	p.F300C	ENST00000282018	NM_020377.2	300	tTc/tGc	1/1	1	2	FACETS	0.7	0.636	0.766	0.7	0.636	0.766	SUBCLONAL	1	TRUE	1	0.52	2		803	731	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506179	103506179	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	156	440	0	ENST00000355739.4:c.337T>C	p.Phe113Leu	p.F113L	ENST00000355739	NM_000123.3	113	Ttt/Ctt	3/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.52	2		440	523	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436784	110436784	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	193	721	0	ENST00000375856.3:c.1617C>A	p.Phe539Leu	p.F539L	ENST00000375856	NM_003749.2	539	ttC/ttA	1/2	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.52	2		721	700	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562660	95562660	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	101	593	1	ENST00000393063.1:c.4597G>T	p.Glu1533Ter	p.E1533*	ENST00000393063	NM_030621.3	1533	Gaa/Taa	24/28	1	2	FACETS	0.64	0.573	0.711	0.64	0.573	0.711	SUBCLONAL	1	TRUE	1	0.52	2		594	607	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43739654	43739654	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	81	370	0	ENST00000382044.4:c.2746G>A	p.Glu916Lys	p.E916K	ENST00000382044	NM_001141980.1	916	Gaa/Aaa	13/28	1	2	FACETS	0.947	0.842	1	0.947	0.842	1	CLONAL	1	TRUE	1	0.52	2		370	329	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098638	2098638	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	61	568	2	ENST00000219476.3:c.22G>T	p.Asp8Tyr	p.D8Y	ENST00000219476	NM_000548.3	8	Gat/Tat	2/42	1	2	FACETS	0.334	0.287	0.384	0.334	0.287	0.384	SUBCLONAL	1	TRUE	1	0.52	2		570	703	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696611	47696611	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	171	626	0	ENST00000347630.2:c.337G>T	p.Glu113Ter	p.E113*	ENST00000347630	NM_001007230.1	113	Gaa/Taa	5/11	1	2	FACETS	0.992	0.916	1	0.992	0.916	1	CLONAL	1	TRUE	1	0.52	2		626	663	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740561	58740561	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	106	670	0	ENST00000305921.3:c.1466C>A	p.Ser489Tyr	p.S489Y	ENST00000305921	NM_003620.3	489	tCt/tAt	6/6	1	2	FACETS	0.611	0.548	0.678	0.611	0.548	0.678	SUBCLONAL	1	TRUE	1	0.52	2		670	667	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143028	7143028	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	70	713	0	ENST00000302850.5:c.2341C>A	p.Pro781Thr	p.P781T	ENST00000302850	NM_000208.2	781	Ccc/Acc	12/22	1	2	FACETS	0.34	0.296	0.388	0.34	0.296	0.388	SUBCLONAL	1	TRUE	1	0.52	2		713	792	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216131	36216131	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	66	599	0	ENST00000222270.7:c.3539A>G	p.Asp1180Gly	p.D1180G	ENST00000222270	NM_014727.1	1180	gAt/gGt	11/37	1	2	FACETS	0.39	0.338	0.446	0.39	0.338	0.446	SUBCLONAL	1	TRUE	1	0.52	2		599	651	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288191	21288191	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	58	741	0	ENST00000354336.3:c.436A>C	p.Lys146Gln	p.K146Q	ENST00000354336	NM_005207.3	146	Aag/Cag	2/3	1	2	FACETS	0.311	0.266	0.359	0.311	0.266	0.359	SUBCLONAL	1	TRUE	1	0.52	2		741	718	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095873	29095873	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1555915433	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	72	788	1	ENST00000328354.6:c.961G>T	p.Glu321Ter	p.E321*	ENST00000328354	NM_007194.3	321	Gaa/Taa	9/15	1	2	FACETS	0.303	0.264	0.346	0.303	0.264	0.346	SUBCLONAL	1	TRUE	1	0.52	2		789	913	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121024	29121024	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	72	891	2	ENST00000328354.6:c.533G>T	p.Gly178Val	p.G178V	ENST00000328354	NM_007194.3	178	gGa/gTa	4/15	1	2	FACETS	0.318	0.277	0.362	0.318	0.277	0.362	SUBCLONAL	1	TRUE	1	0.52	2		893	872	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984925	55984925	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	206	602	0	ENST00000263923.4:c.204T>G	p.Ser68Arg	p.S68R	ENST00000263923	NM_002253.2	68	agT/agG	3/30	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.52	2		602	748	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271269	153271269	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	36	371	1	ENST00000281708.4:c.509G>T	p.Arg170Ile	p.R170I	ENST00000281708	NM_033632.3	170	aGa/aTa	3/12	1	2	FACETS	0.382	0.315	0.458	0.382	0.315	0.458	SUBCLONAL	1	TRUE	1	0.52	2		372	362	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629163	187629163	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	166	644	0	ENST00000441802.2:c.1819G>T	p.Glu607Ter	p.E607*	ENST00000441802	NM_005245.3	607	Gaa/Taa	2/27	1	2	FACETS	0.985	0.908	1	0.985	0.908	1	CLONAL	1	TRUE	1	0.52	2		644	648	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526994	31526994	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs373494822	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	57	664	1	ENST00000344624.3:c.46C>T	p.Arg16Ter	p.R16*	ENST00000344624		16	Cga/Tga	2/33	1	2	FACETS	0.294	0.251	0.34	0.294	0.251	0.34	SUBCLONAL	1	TRUE	1	0.52	2		665	746	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961137	79961137	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs569679162	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	112	739	1	ENST00000265081.6:c.534G>T	p.Lys178Asn	p.K178N	ENST00000265081	NM_002439.4	178	aaG/aaT	3/24	1	2	FACETS	0.571	0.513	0.631	0.571	0.513	0.631	SUBCLONAL	1	TRUE	1	0.52	2		740	755	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638318	176638318	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	124	799	0	ENST00000439151.2:c.2918A>C	p.Gln973Pro	p.Q973P	ENST00000439151	NM_022455.4	973	cAg/cCg	5/23	1	2	FACETS	0.576	0.521	0.634	0.576	0.521	0.634	SUBCLONAL	1	TRUE	1	0.52	2		799	828	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117639407	117639407	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	127	626	0	ENST00000368508.3:c.5949G>T	p.Lys1983Asn	p.K1983N	ENST00000368508	NM_002944.2	1983	aaG/aaT	37/43	1	2	FACETS	0.999	0.91	1	0.999	0.91	1	CLONAL	1	TRUE	1	0.52	2		626	489	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100358	157100358	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1297021537	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	105	302	0	ENST00000346085.5:c.1295G>A	p.Ser432Asn	p.S432N	ENST00000346085	NM_020732.3	432	aGc/aAc	1/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.52	2		302	365	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946111	13946111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	158	637	0	ENST00000405192.2:c.985C>A	p.His329Asn	p.H329N	ENST00000405192	NM_001163147.1	329	Cat/Aat	10/12	1	2	FACETS	0.974	0.896	1	0.974	0.896	1	CLONAL	1	TRUE	1	0.52	2		637	624	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975514	13975514	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	84	341	0	ENST00000405192.2:c.373G>T	p.Asp125Tyr	p.D125Y	ENST00000405192	NM_001163147.1	125	Gat/Tat	7/12	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.52	2		341	304	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972993	68972993	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	44	560	0	ENST00000288368.4:c.1318G>T	p.Glu440Ter	p.E440*	ENST00000288368	NM_024870.2	440	Gaa/Taa	11/40	1	2	FACETS	0.31	0.259	0.366	0.31	0.259	0.366	SUBCLONAL	1	TRUE	1	0.52	2		560	546	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485254	8485254	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	151	659	0	ENST00000356435.5:c.3126G>T	p.Glu1042Asp	p.E1042D	ENST00000356435		1042	gaG/gaT	18/35	1	2	FACETS	0.947	0.87	1	0.947	0.87	1	CLONAL	1	TRUE	1	0.52	2		659	613	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485948	8485948	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	61	523	0	ENST00000356435.5:c.2869C>A	p.Leu957Ile	p.L957I	ENST00000356435		957	Ctt/Att	17/35	1	2	FACETS	0.527	0.456	0.604	0.527	0.456	0.604	SUBCLONAL	1	TRUE	1	0.52	2		523	445	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606528	93606528	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	76	825	1	ENST00000375746.1:c.348G>T	p.Lys116Asn	p.K116N	ENST00000375746	NM_001174167.1	116	aaG/aaT	2/14	1	2	FACETS	0.362	0.317	0.411	0.362	0.317	0.411	SUBCLONAL	1	TRUE	1	0.52	2		826	807	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782149	135782149	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	45	742	1	ENST00000298552.3:c.1407A>C	p.Glu469Asp	p.E469D	ENST00000298552	NM_001162426.1	469	gaA/gaC	14/23	1	2	FACETS	0.228	0.191	0.269	0.228	0.191	0.269	SUBCLONAL	1	TRUE	1	0.52	2		743	759	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796753	135796753	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755859330	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	46	468	0	ENST00000298552.3:c.734G>A	p.Arg245Gln	p.R245Q	ENST00000298552	NM_001162426.1	245	cGa/cAa	8/23	1	2	FACETS	0.392	0.33	0.46	0.392	0.33	0.46	SUBCLONAL	1	TRUE	1	0.52	2		468	451	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032587	47032587	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	141	756	0	ENST00000377604.3:c.493A>C	p.Lys165Gln	p.K165Q	ENST00000377604	NM_001204468.1	165	Aaa/Caa	5/24	1	2	FACETS	0.695	0.634	0.76	0.695	0.634	0.76	SUBCLONAL	1	TRUE	1	0.52	2		756	780	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412107	63412107	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	93	1094	0	ENST00000330258.3:c.1060G>T	p.Asp354Tyr	p.D354Y	ENST00000330258	NM_152424.3	354	Gat/Tat	2/2	1	2	FACETS	0.352	0.312	0.395	0.352	0.312	0.395	SUBCLONAL	1	TRUE	1	0.52	2		1094	1016	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70350029	70350029	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	147	612	0	ENST00000374080.3:c.4012A>C	p.Asn1338His	p.N1338H	ENST00000374080		1338	Aac/Cac	28/45	1	2	FACETS	0.965	0.885	1	0.965	0.885	1	CLONAL	1	TRUE	1	0.52	2		612	586	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352727	70352727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1488661030	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	255	682	1	ENST00000374080.3:c.4448C>T	p.Ser1483Leu	p.S1483L	ENST00000374080		1483	tCg/tTg	32/45	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.52	2		683	738	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907720	76907720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	197	815	1	ENST00000373344.5:c.4441C>T	p.Arg1481Trp	p.R1481W	ENST00000373344	NM_000489.3	1481	Cgg/Tgg	15/35	1	2	FACETS	0.945	0.877	1	0.945	0.877	1	CLONAL	1	TRUE	1	0.52	2		816	802	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937356	76937356	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	76	713	1	ENST00000373344.5:c.3392G>T	p.Arg1131Ile	p.R1131I	ENST00000373344	NM_000489.3	1131	aGa/aTa	9/35	1	2	FACETS	0.498	0.437	0.563	0.498	0.437	0.563	SUBCLONAL	1	TRUE	1	0.52	2		714	587	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0020300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	346	453	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	0.543792396986964	2		453	1235	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0020300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	146	406	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	0.776	0.921	0.847	0.776	0.921	CLONAL	1	TRUE	1	0.543792396986964	2		406	634	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411366	63411366	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	259	418	1	ENST00000330258.3:c.1801C>T	p.Arg601Ter	p.R601*	ENST00000330258	NM_152424.3	601	Cga/Tga	2/2	1	1	FACETS	0.774	0.737	0.811	1	0.995	1	SUBCLONAL	2	TRUE	0	0.543792396986964	1		419	448	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120351	70120351	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0020300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	399	1032	0	ENST00000245479.2:c.1353C>G	p.Tyr451Ter	p.Y451*	ENST00000245479	NM_000346.3	451	taC/taG	3/3	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.543792396986964	2		1032	1396	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815757	32815757	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	256	763	0	ENST00000354258.4:c.1859del	p.Gly620AspfsTer44	p.G620Dfs*44	ENST00000354258	NM_000593.5	620	gGa/ga	8/11	0.541361422879906	1	FACETS	0.897	0.844	0.952	0.897	0.844	0.952	CLONAL	1	TRUE	0	0.543792396986964	1		763	764	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482606	56482606	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	342	823	0	ENST00000267101.3:c.1063A>G	p.Thr355Ala	p.T355A	ENST00000267101	NM_001982.3	355	Acc/Gcc	9/28	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.543792396986964	2		823	1129	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572962	7572962	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	281	718	2	ENST00000269305.4:c.1147del	p.Leu383SerfsTer39	p.L383Sfs*39	ENST00000269305	NM_001126112.2	383	Ctc/tc	11/11	0.543792396986964	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.543792396986964	1		720	715	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383691	42383691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782150073	NA	P-0020300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	260	794	2	ENST00000221972.3:c.466G>A	p.Ala156Thr	p.A156T	ENST00000221972	NM_021601.3	156	Gcg/Acg	3/5	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.543792396986964	2		796	942	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-0020300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	226	573	0	ENST00000335508.6:c.3756+2_3757del		p.X1252_splice	ENST00000335508	NM_012433.2	1252		25/25	NA	2	FACETS	0.796	0.741	0.853			1	INDETERMINATE	1	TRUE	NA	0.543792396986964	2		573	1044	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-0020300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	240	393	0	ENST00000335508.6:c.3134+2_3135del		p.X1045_splice	ENST00000335508	NM_012433.2	1045		22/25	NA	2	FACETS	1	0.94	1			1	INDETERMINATE	1	TRUE	NA	0.543792396986964	2		393	878	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198264890	198264974	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTATAATAAAACAAATAATGTTAAAATGTTACTATTTACATTAAACTATTTGGGGAAGAAGTAAGAATTTGATGCAAAAGTTTA	CCTATAATAAAACAAATAATGTTAAAATGTTACTATTTACATTAAACTATTTGGGGAAGAAGTAAGAATTTGATGCAAAAGTTTA	-	novel	NA	P-0020300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	222	661	0	ENST00000335508.6:c.2901+2_2902del		p.X967_splice	ENST00000335508	NM_012433.2	967		20/25	NA	2	FACETS	0.699	0.65	0.75			1	INDETERMINATE	1	TRUE	NA	0.543792396986964	2		661	1168	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265158	198265437	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTAAAAAATAAATTTAAAAAAAAGACATATTCATTTGGTTTATGACTGCACAGTTGAAATACACTAAGAGTCAACCTTTTCTAACCACCCAAACATCTGTTGCTGTTTTTTTACATCAAATCTTAAAACTTGAGGTAGAATAATATCGTTTGGTAACCCCCTGAGCATTTTAAAAATTACTTCAAATTCAATTGCATTCTAGAAAAATTTGCTTGACAACTAATATGCTTTTCTACAAATATTAAAGTTAGTAGCAATGTGCCATAATAGTTTTCATTA	CCTAAAAAATAAATTTAAAAAAAAGACATATTCATTTGGTTTATGACTGCACAGTTGAAATACACTAAGAGTCAACCTTTTCTAACCACCCAAACATCTGTTGCTGTTTTTTTACATCAAATCTTAAAACTTGAGGTAGAATAATATCGTTTGGTAACCCCCTGAGCATTTTAAAAATTACTTCAAATTCAATTGCATTCTAGAAAAATTTGCTTGACAACTAATATGCTTTTCTACAAATATTAAAGTTAGTAGCAATGTGCCATAATAGTTTTCATTA	-	novel	NA	P-0020300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	273	405	0	ENST00000335508.6:c.2718+2_2719del		p.X906_splice	ENST00000335508	NM_012433.2	906		19/25	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.543792396986964	2		405	896	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266248	198266463	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACCTAAAAGGTTAAGAAATAGTAATAATAAATCAACTGACCTGAAATGAAGAGAATACTCATTGCTGATTACGTGATTTTAAAAAATAAAATTTAAAAACAAATCAAACAGTATTCGTGTAACATACAGTTTTTTTTGTTGATTTTTAAAAACACTTTAAAATTCTGTTAGAACCATGAAACATATCCAGTTTACATTAACAAATCTGGAATAATT	ACCTAAAAGGTTAAGAAATAGTAATAATAAATCAACTGACCTGAAATGAAGAGAATACTCATTGCTGATTACGTGATTTTAAAAAATAAAATTTAAAAACAAATCAAACAGTATTCGTGTAACATACAGTTTTTTTTGTTGATTTTTAAAAACACTTTAAAATTCTGTTAGAACCATGAAACATATCCAGTTTACATTAACAAATCTGGAATAATT	-	novel	NA	P-0020300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	280	457	0	ENST00000335508.6:c.2370+3_2372del		p.X790_splice	ENST00000335508	NM_012433.2	790		17/25	NA	2	FACETS	0.998	0.938	1			1	INDETERMINATE	1	TRUE	NA	0.543792396986964	2		457	1032	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266612	198266707	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTATTTTTAAATAAAAAATATATGTACTTTAGTAATTTAGATTTATGTCGCCTTAACTTTAATGAAGATAAATCAAAAGGTAATTGGTGGATTTA	CCTATTTTTAAATAAAAAATATATGTACTTTAGTAATTTAGATTTATGTCGCCTTAACTTTAATGAAGATAAATCAAAAGGTAATTGGTGGATTTA	-	novel	NA	P-0020300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	287	572	0	ENST00000335508.6:c.2223+2_2224del		p.X741_splice	ENST00000335508	NM_012433.2	741		16/25	NA	2	FACETS	0.984	0.925	1			1	INDETERMINATE	1	TRUE	NA	0.543792396986964	2		572	1073	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266824	198266825	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0020300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	124	677	0	ENST00000335508.6:c.2107_2108del	p.Thr703HisfsTer11	p.T703Hfs*11	ENST00000335508	NM_012433.2	703	ACc/c	15/25	NA	2	FACETS	0.403	0.363	0.445			1	INDETERMINATE	1	TRUE	NA	0.543792396986964	2		677	1132	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245409	153245411	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0020300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	301	753	0	ENST00000281708.4:c.1780_1782del	p.Leu594del	p.L594del	ENST00000281708	NM_033632.3	594	CTT/-	11/12	0.543792396986964	1	FACETS	0.943	0.891	0.995	0.943	0.891	0.995	CLONAL	1	TRUE	0	0.543792396986964	1		753	855	SUCCESS
APC	324	MSKCC	GRCh37	5	112175294	112175295	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCAGACTG	novel	NA	P-0020300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	132	382	0	ENST00000257430.4:c.4004_4011dup	p.Gln1338AlafsTer80	p.Q1338Afs*80	ENST00000257430	NM_000038.5	1335	agc/aGCAGACTGgc	16/16	1	2	FACETS	0.886	0.808	0.967	0.886	0.808	0.967	CLONAL	1	TRUE	1	0.543792396986964	2		382	548	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879522	151879522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	223	548	0	ENST00000262189.6:c.5423G>A	p.Ser1808Asn	p.S1808N	ENST00000262189	NM_170606.2	1808	aGt/aAt	36/59	1	2	FACETS	0.997	0.93	1	0.997	0.93	1	CLONAL	1	TRUE	1	0.543792396986964	2		548	823	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0020301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	403	794	1	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.635622835241858	2		795	1203	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217380	123217380	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	352	755	0	ENST00000218089.9:c.3034C>T	p.Arg1012Ter	p.R1012*	ENST00000218089	NM_001042749.1	1012	Cga/Tga	29/35	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.635622835241858	2		755	1107	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927979	178927984	+	inframe_deletion	In_Frame_Del	DEL	CTGTCC	CTGTCC	-	novel	NA	P-0020301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	207	416	0	ENST00000263967.3:c.1257_1262del	p.His419_Pro421delinsGln	p.H419_P421delinsQ	ENST00000263967	NM_006218.2	419	caCTGTCCa/caa	8/21	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.635622835241858	2		416	636	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998891	11998891	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0020301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	184	459	0	ENST00000353533.5:c.394-1G>C		p.X132_splice	ENST00000353533	NM_003010.3	132			1	2	FACETS	0.902	0.836	0.969	0.902	0.836	0.969	CLONAL	1	TRUE	1	0.635622835241858	2		459	642	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574348	41574348	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	357	781	0	ENST00000263253.7:c.6633C>A	p.Phe2211Leu	p.F2211L	ENST00000263253	NM_001429.3	2211	ttC/ttA	31/31	1	2	FACETS	0.994	0.943	1	0.994	0.943	1	CLONAL	1	TRUE	1	0.635622835241858	2		781	1130	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398565	116398565	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	354	805	0	ENST00000397752.3:c.2155G>C	p.Glu719Gln	p.E719Q	ENST00000397752	NM_000245.2	719	Gag/Cag	9/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.635622835241858	2		805	1091	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845551	151845551	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	386	764	2	ENST00000262189.6:c.13461C>A	p.Cys4487Ter	p.C4487*	ENST00000262189	NM_170606.2	4487	tgC/tgA	52/59	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.635622835241858	2		766	1112	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0020302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	280	1054	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.328507958402049	2	FACETS	1	0.994	1	0.738	0.697	0.78	CLONAL	1	TRUE	0	0.499799664676133	2		1055	759	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0020302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	168	466	2	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.185631156895246	4	FACETS	1	0.988	1	0.72	0.664	0.779	INDETERMINATE	1	TRUE	2	0.499799664676133	4		468	700	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783886	50783886	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	259	813	0	ENST00000398568.2:c.277A>G	p.Asn93Asp	p.N93D	ENST00000398568	NM_001042412.1	93	Aat/Gat	3/18	0.150348327029297	4	FACETS	0.791	0.741	0.841	0.791	0.741	0.841	INDETERMINATE	2	TRUE	2	0.499799664676133	4		813	983	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468517	89468517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372257039	NA	P-0020302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	105	416	0	ENST00000336596.2:c.2051G>A	p.Arg684Gln	p.R684Q	ENST00000336596	NM_005233.5	684	cGa/cAa	11/17	0.185631156895246	4	FACETS	1	0.972	1	0.615	0.553	0.681	INDETERMINATE	1	TRUE	2	0.499799664676133	4		416	512	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841241	15841241	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770119952	NA	P-0020302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	79	325	0	ENST00000307771.7:c.1325G>A	p.Arg442Gln	p.R442Q	ENST00000307771	NM_005089.3	442	cGg/cAg	11/11	NA	2	FACETS	0.689	0.608	0.775			1	INDETERMINATE	1	TRUE	NA	0.499799664676133	2		325	459	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	200	122	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.956	0.892	1	0.956	0.892	1	CLONAL	1	TRUE	1	0.731580438120699	2		122	572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0020304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	352	834	0	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	0.731580438120699	1	FACETS	0.964	0.923	1	0.964	0.923	1	CLONAL	1	TRUE	0	0.731580438120699	1		834	633	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305399	65305399	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	400	801	0	ENST00000342505.4:c.2729T>C	p.Leu910Pro	p.L910P	ENST00000342505	NM_002227.2	910	cTg/cCg	20/25	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.731580438120699	2		801	1077	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861844	57861844	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	361	756	2	ENST00000228682.2:c.1145A>G	p.His382Arg	p.H382R	ENST00000228682	NM_005269.2	382	cAt/cGt	10/12	1	2	FACETS	0.969	0.92	1	0.969	0.92	1	CLONAL	1	TRUE	1	0.731580438120699	2		758	1019	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774189	66774189	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	572	1294	0	ENST00000307102.5:c.665C>G	p.Ser222Cys	p.S222C	ENST00000307102	NM_002755.3	222	tCc/tGc	6/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.731580438120699	2		1294	1553	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218460	1218461	+	missense_variant	Missense_Mutation	DNP	AG	AG	CC	novel	NA	P-0020304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	399	902	2	ENST00000326873.7:c.335_336delinsCC	p.Gln112Pro	p.Q112P	ENST00000326873	NM_000455.4	112	cAG/cCC	2/10	NA	2	FACETS	0.987	0.94	1			1	INDETERMINATE	1	TRUE	NA	0.731580438120699	2		904	1105	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170011253	170011253	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	390	976	0	ENST00000295797.4:c.1374C>A	p.Ser458Arg	p.S458R	ENST00000295797	NM_002740.5	458	agC/agA	14/18	1	2	FACETS	0.931	0.886	0.977	0.931	0.886	0.977	CLONAL	1	TRUE	1	0.731580438120699	2		976	1145	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709014	117709014	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	142	809	4	ENST00000368508.3:c.1943C>A	p.Ser648Tyr	p.S648Y	ENST00000368508	NM_002944.2	648	tCt/tAt	13/43	0.731580438120699	1	FACETS	0.398	0.363	0.433	0.398	0.363	0.433	SUBCLONAL	1	TRUE	0	0.731580438120699	1		813	619	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801045	135801045	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0020304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	315	672	1	ENST00000298552.3:c.292A>T	p.Arg98Ter	p.R98*	ENST00000298552	NM_001162426.1	98	Aga/Tga	5/23	0.731580438120699	1	FACETS	0.945	0.902	0.988	0.945	0.902	0.988	CLONAL	1	TRUE	0	0.731580438120699	1		673	578	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs121913468	NA	P-0020305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	7682	588	0	ENST00000269571.5:c.2305G>C	p.Asp769His	p.D769H	ENST00000269571		769	Gac/Cac	19/27	0.594883390447728	17	FACETS	0.986	0.983	0.989			1	CLONAL	18	TRUE	NA	0.594883390447728	17		588	7945	SUCCESS
APC	324	MSKCC	GRCh37	5	112177853	112177853	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	168	442	0	ENST00000257430.4:c.6562A>G	p.Ile2188Val	p.I2188V	ENST00000257430	NM_000038.5	2188	Atc/Gtc	16/16	1	2	FACETS	0.994	0.919	1	0.994	0.919	1	CLONAL	1	TRUE	1	0.594883390447728	2		442	568	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335011	81335011	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs765890500	NA	P-0020305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	249	628	0	ENST00000222390.5:c.1816A>G	p.Ile606Val	p.I606V	ENST00000222390	NM_000601.4	606	Att/Gtt	16/18	0.594883390447728	3	FACETS	1	0.979	1	0.554	0.518	0.59	CLONAL	1	TRUE	1	0.594883390447728	3		628	981	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945418	71945418	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	513	738	0	ENST00000298229.2:c.2306T>C	p.Phe769Ser	p.F769S	ENST00000298229	NM_001567.3	769	tTc/tCc	20/28	0.594883390447728	3	FACETS	0.897	0.861	0.934	0.598	0.574	0.623	CLONAL	2	TRUE	0	0.594883390447728	3		738	1247	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195956	102195956	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs764452461	NA	P-0020305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	159	407	0	ENST00000263464.3:c.716T>C	p.Leu239Pro	p.L239P	ENST00000263464	NM_001165.4	239	cTt/cCt	2/9	0.594883390447728	3	FACETS	0.965	0.886	1	0.322	0.295	0.349	CLONAL	1	TRUE	0	0.594883390447728	3		407	719	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349229	11349229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	76	146	0	ENST00000332029.2:c.107C>T	p.Pro36Leu	p.P36L	ENST00000332029	NM_003745.1	36	cCc/cTc	2/2	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.594883390447728	2		146	212	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578381	7578424	+	frameshift_variant	Frame_Shift_Del	DEL	TGAGCAGCGCTCATGGTGGGGGCAGCGCCTCACAACCTCCGTCA	TGAGCAGCGCTCATGGTGGGGGCAGCGCCTCACAACCTCCGTCA	-	novel	NA	P-0020305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	439	584	0	ENST00000269305.4:c.506_549del	p.Met169ArgfsTer2	p.M169Rfs*2	ENST00000269305	NM_001126112.2	169	aTGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCA/a	5/11	0.594883390447728	2	FACETS	0.97	0.934	1	0.97	0.934	1	CLONAL	2	TRUE	0	0.594883390447728	2		584	761	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687556	37687556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	244	349	0	ENST00000447079.4:c.4460G>A	p.Gly1487Glu	p.G1487E	ENST00000447079	NM_015083.1	1487	gGa/gAa	14/14	0.396137872969621	5	FACETS	1	0.979	1			1	CLONAL	2	TRUE	NA	0.594883390447728	5		349	710	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42759139	42759139	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	155	395	0	ENST00000222329.4:c.13G>A	p.Ala5Thr	p.A5T	ENST00000222329	NM_006494.2	5	Gcg/Acg	1/4	0.594883390447728	3	FACETS	1	0.931	1	0.508	0.466	0.551	CLONAL	1	TRUE	1	0.594883390447728	3		395	666	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607741	46607769	+	frameshift_variant	Frame_Shift_Del	DEL	CCATTACATTTTGGGCCCACAAAGTGGGC	CCATTACATTTTGGGCCCACAAAGTGGGC	-	novel	NA	P-0020305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	240	801	0	ENST00000263734.3:c.1931_1959del	p.Pro644ArgfsTer62	p.P644Rfs*62	ENST00000263734	NM_001430.4	644	CCATTACATTTTGGGCCCACAAAGTGGGCc/c	12/16	1	2	FACETS	0.886	0.828	0.945	0.886	0.828	0.945	CLONAL	1	TRUE	1	0.594883390447728	2		801	911	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641499	47641499	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	245	612	0	ENST00000233146.2:c.884A>T	p.Asp295Val	p.D295V	ENST00000233146	NM_000251.2	295	gAc/gTc	5/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.594883390447728	2		612	775	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872688	136872688	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs755484217	NA	P-0020305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	156	521	0	ENST00000241393.3:c.810C>G	p.Ile270Met	p.I270M	ENST00000241393	NM_003467.2	270	atC/atG	2/2	0.594883390447728	3	FACETS	0.825	0.756	0.897	0.412	0.378	0.449	CLONAL	1	TRUE	1	0.594883390447728	3		521	825	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610607	52610608	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0020305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	264	730	0	ENST00000394830.3:c.3565_3566del	p.Glu1189SerfsTer5	p.E1189Sfs*5	ENST00000394830	NM_018313.4	1189	GAa/a	23/30	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.594883390447728	2		730	879	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426045	138426045	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	516	628	1	ENST00000289153.2:c.1486C>A	p.Pro496Thr	p.P496T	ENST00000289153	NM_006219.2	496	Cca/Aca	9/22	0.563331544562956	4	FACETS	0.954	0.914	0.994	0.954	0.914	0.994	CLONAL	2	TRUE	2	0.594883390447728	4		629	1450	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841162	15841162	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	192	252	0	ENST00000307771.7:c.1246G>T	p.Glu416Ter	p.E416*	ENST00000307771	NM_005089.3	416	Gag/Tag	11/11	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.594883390447728	1		252	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0020306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	123	532	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.300375527901754	1	FACETS	0.911	0.824	1	0.911	0.824	1	CLONAL	1	TRUE	0	0.28	1		533	829	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029218	14029218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41557814	NA	P-0020306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	109	455	0	ENST00000311895.7:c.1429C>T	p.Arg477Trp	p.R477W	ENST00000311895	NM_005236.2	477	Cgg/Tgg	8/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.28	2		455	613	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573651	48573651	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	87	715	0	ENST00000342988.3:c.235G>T	p.Asp79Tyr	p.D79Y	ENST00000342988	NM_005359.5	79	Gat/Tat	2/12	0.300375527901754	1	FACETS	0.869	0.77	0.974	0.869	0.77	0.974	CLONAL	1	TRUE	0	0.28	1		715	615	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266093	41266258	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATT	CCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATT	-	novel	NA	P-0020306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	82	487	0	ENST00000349496.5:c.90_241+14del		p.X30_splice	ENST00000349496	NM_001904.3	30		3/15	0.236591104007366	2	FACETS	0.959	0.846	1	0.479	0.423	0.54	CLONAL	1	TRUE	0	0.28	2		487	611	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	127	122	0				ENST00000310581	NM_198253.2	-/1132			0.584601108700513	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.584601108700513	1		122	295	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0020308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	302	839	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.584601108700513	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.584601108700513	1		841	686	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947579	48947579	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs587778845	NA	P-0020308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	270	891	2	ENST00000267163.4:c.1166T>A	p.Leu389Ter	p.L389*	ENST00000267163	NM_000321.2	389	tTa/tAa	12/27	0.584601108700513	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.584601108700513	1		893	633	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0020308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	175	530	5	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	0.584601108700513	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.584601108700513	1		535	390	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653802	89653802	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	175	749	0	ENST00000371953.3:c.100G>C	p.Ala34Pro	p.A34P	ENST00000371953	NM_000314.4	34	Gct/Cct	2/9	0.584601108700513	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.584601108700513	1		749	395	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959029	2959029	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	209	708	2	ENST00000396946.4:c.2487G>A	p.Met829Ile	p.M829I	ENST00000396946	NM_032415.4	829	atG/atA	18/25	0.584601108700513	3	FACETS	0.971	0.901	1	0.485	0.45	0.521	CLONAL	1	TRUE	1	0.584601108700513	3		710	952	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0020309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	782	649	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.856182325833433	1	FACETS	0.979	0.96	0.997	0.979	0.96	0.997	CLONAL	1	TRUE	0	0.902281150610035	1		649	972	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0020309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	21	182	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.902281150610035	1	FACETS	0.35	0.277	0.429	0.35	0.277	0.429	SUBCLONAL	1	TRUE	0	0.902281150610035	1		182	73	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251907	153251907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	136	776	1	ENST00000281708.4:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000281708	NM_033632.3	367	Cga/Tga	7/12	0.861934168168674	1	FACETS	0.742	0.694	0.789	0.742	0.694	0.789	SUBCLONAL	1	TRUE	0	0.902281150610035	1		777	223	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730882	40730882	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	2089	754	2	ENST00000373198.4:c.3653T>C	p.Leu1218Pro	p.L1218P	ENST00000373198	NM_133170.3	1218	cTg/cCg	27/32	0.902281150610035	4	FACETS	0.981	0.967	0.996			1	CLONAL	3	TRUE	NA	0.902281150610035	4		756	2992	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425799	49425805	+	frameshift_variant	Frame_Shift_Del	DEL	TGCCGCT	TGCCGCT	-	novel	NA	P-0020309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	1201	621	0	ENST00000301067.7:c.12683_12689del	p.Gln4228ArgfsTer48	p.Q4228Rfs*48	ENST00000301067	NM_003482.3	4228	cAGCGGCAg/cg	39/54	0.876541112382697	2	FACETS	0.99	0.978	1	0.99	0.978	1	CLONAL	2	TRUE	0	0.902281150610035	2		621	1345	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194868	30194868	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	261	618	0	ENST00000331968.5:c.277G>C	p.Gly93Arg	p.G93R	ENST00000331968	NM_002742.2	93	Ggt/Cgt	2/18	1	2	FACETS	0.908	0.857	0.96	0.908	0.857	0.96	CLONAL	1	TRUE	1	0.902281150610035	2		618	637	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40500534	40500534	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0020309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	643	652	0	ENST00000264657.5:c.1A>G	p.Met1?	p.M1?	ENST00000264657	NM_139276.2	1	Atg/Gtg	2/24	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.902281150610035	2		652	1389	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41201203	41201203	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs397509268	NA	P-0020309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	484	778	2	ENST00000357654.3:c.5341G>T	p.Glu1781Ter	p.E1781*	ENST00000357654	NM_007294.3	1781	Gaa/Taa	21/23	1	2	FACETS	0.868	0.831	0.905	0.868	0.831	0.905	CLONAL	1	TRUE	1	0.902281150610035	2		780	1236	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942169	17942169	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	619	677	0	ENST00000458235.1:c.2846A>G	p.Asp949Gly	p.D949G	ENST00000458235	NM_000215.3	949	gAc/gGc	21/24	1	2	FACETS	0.85	0.818	0.882	0.85	0.818	0.882	CLONAL	1	TRUE	1	0.902281150610035	2		677	1614	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0020310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	168	825	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.436095783340109	7	FACETS	0.789	0.724	0.856	0.315	0.289	0.343	SUBCLONAL	2	FALSE	2	0.436095783340109	7		825	1021	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37665979	37665979	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	139	673	1	ENST00000447079.4:c.2631T>A	p.Asp877Glu	p.D877E	ENST00000447079	NM_015083.1	877	gaT/gaA	7/14	0.00959745884570884	4	FACETS	0.925	0.847	1	0.925	0.847	1	INDETERMINATE	2	FALSE	2	0.436095783340109	4		674	495	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555687605	NA	P-0020311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	13	536	0	ENST00000342988.3:c.1610A>G	p.Asp537Gly	p.D537G	ENST00000342988	NM_005359.5	537	gAc/gGc	12/12	1	2	FACETS	0.395	0.28	0.537	0.395	0.28	0.537	SUBCLONAL	1	TRUE	1	0.11	2		536	598	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0020311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	31	793	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	1	2	FACETS	0.673	0.542	0.822	0.673	0.542	0.822	SUBCLONAL	1	TRUE	1	0.11	2		793	838	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556852	29556852	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0020311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	26	516	0	ENST00000356175.3:c.2851-1G>A		p.X951_splice	ENST00000356175	NM_000267.3	951			1	2	FACETS	0.999	0.79	1	0.999	0.79	1	CLONAL	1	TRUE	1	0.11	2		516	473	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	130	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.788	0.718	0.861	1	0.987	1	SUBCLONAL	2	TRUE	1	0.307751118900883	2		555	536	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	81	640	2	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	0.307751118900883	2		642	434	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682399	52682400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	128	779	0	ENST00000394830.3:c.773dup	p.Asn258LysfsTer6	p.N258Kfs*6	ENST00000394830	NM_018313.4	258	aat/aaAt	8/30	1	2	FACETS	0.845	0.771	0.923	1	0.988	1	CLONAL	2	TRUE	1	0.307751118900883	2		779	492	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	138	403	4	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.876	0.802	0.953	1	0.99	1	CLONAL	2	TRUE	1	0.307751118900883	2		407	512	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2488162	2488162	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	184	1063	0	ENST00000355716.4:c.59T>C	p.Val20Ala	p.V20A	ENST00000355716	NM_003820.2	20	gTc/gCc	1/8	1	2	FACETS	0.771	0.714	0.831	1	0.991	1	SUBCLONAL	2	TRUE	1	0.307751118900883	2		1063	775	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16203173	16203173	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	111	667	0	ENST00000375759.3:c.881G>T	p.Ser294Ile	p.S294I	ENST00000375759	NM_015001.2	294	aGc/aTc	3/15	1	2	FACETS	0.809	0.732	0.889	1	0.986	1	CLONAL	2	TRUE	1	0.307751118900883	2		667	446	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261887	16261887	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	200	877	1	ENST00000375759.3:c.9152C>T	p.Ser3051Phe	p.S3051F	ENST00000375759	NM_015001.2	3051	tCc/tTc	11/15	1	2	FACETS	0.997	0.928	1	1	0.994	1	CLONAL	2	TRUE	1	0.307751118900883	2		878	652	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17355222	17355222	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	40	766	0	ENST00000375499.3:c.296G>T	p.Gly99Val	p.G99V	ENST00000375499	NM_003000.2	99	gGc/gTc	4/8	1	2	FACETS	0.568	0.472	0.674	0.568	0.472	0.674	SUBCLONAL	1	TRUE	1	0.307751118900883	2		766	458	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088726	27088726	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	256	1086	0	ENST00000324856.7:c.2335G>T	p.Gly779Ter	p.G779*	ENST00000324856	NM_006015.4	779	Gga/Tga	7/20	1	2	FACETS	0.903	0.847	0.961	1	0.994	1	CLONAL	2	TRUE	1	0.307751118900883	2		1086	921	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097621	27097622	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	175	821	0	ENST00000324856.7:c.3216dup	p.Trp1073MetfsTer32	p.W1073Mfs*32	ENST00000324856	NM_006015.4	1070	-/A	12/20	1	2	FACETS	0.969	0.897	1	1	0.993	1	CLONAL	2	TRUE	1	0.307751118900883	2		821	587	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102190	27102190	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	120	713	1	ENST00000324856.7:c.5116C>A	p.Leu1706Ile	p.L1706I	ENST00000324856	NM_006015.4	1706	Ctc/Atc	19/20	1	2	FACETS	0.92	0.837	1	1	0.989	1	CLONAL	2	TRUE	1	0.307751118900883	2		714	424	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599935	28599935	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	197	1104	0	ENST00000253063.3:c.817C>A	p.Leu273Met	p.L273M	ENST00000253063	NM_031459.4	273	Ctg/Atg	6/10	1	2	FACETS	0.904	0.84	0.97	1	0.993	1	CLONAL	2	TRUE	1	0.307751118900883	2		1104	708	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	227	1121	3	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	0.948	0.886	1	1	0.994	1	CLONAL	2	TRUE	1	0.307751118900883	2		1124	778	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325247	39325247	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	239	900	0	ENST00000373001.3:c.72G>T	p.Lys24Asn	p.K24N	ENST00000373001	NM_022157.3	24	aaG/aaT	1/7	1	2	FACETS	1	0.956	1	1	0.995	1	CLONAL	2	TRUE	1	0.307751118900883	2		900	758	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313253	65313253	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	172	983	1	ENST00000342505.4:c.1861C>A	p.Leu621Ile	p.L621I	ENST00000342505	NM_002227.2	621	Ctc/Atc	13/25	1	2	FACETS	0.875	0.808	0.943	1	0.992	1	CLONAL	2	TRUE	1	0.307751118900883	2		984	639	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330610	65330611	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	116	791	0	ENST00000342505.4:c.1035dup	p.Leu346ThrfsTer4	p.L346Tfs*4	ENST00000342505	NM_002227.2	345	-/A	8/25	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.307751118900883	2		791	586	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458436	120458436	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs771237928	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	160	877	1	ENST00000256646.2:c.6909del	p.Ile2304LeufsTer2	p.I2304Lfs*2	ENST00000256646	NM_024408.3	2303	ccC/cc	34/34	1	2	FACETS	0.979	0.904	1	1	0.992	1	CLONAL	2	TRUE	1	0.307751118900883	2		878	531	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163315467	163315467	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	65	684	0	ENST00000271452.3:c.808-1G>A		p.X270_splice	ENST00000271452	NM_145697.2	270			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.307751118900883	2		684	348	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111005	193111006	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	56	405	0	ENST00000367435.3:c.544dup	p.Ile182AsnfsTer11	p.I182Nfs*11	ENST00000367435	NM_024529.4	180	gaa/gAaa	7/17	1	2	FACETS	0.905	0.787	1	1	0.977	1	CLONAL	2	TRUE	1	0.307751118900883	2		405	201	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63817039	63817039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1269760932	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	69	408	0	ENST00000279873.7:c.1010C>T	p.Thr337Met	p.T337M	ENST00000279873	NM_032199.2	337	aCg/aTg	6/10	1	2	FACETS	0.843	0.742	0.949	1	0.979	1	CLONAL	2	TRUE	1	0.307751118900883	2		408	266	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104389853	104389854	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	217	1015	2	ENST00000369902.3:c.1400dup	p.Lys468GlufsTer9	p.K468Efs*9	ENST00000369902	NM_016169.3	466	gaa/gAaa	12/12	1	2	FACETS	0.825	0.768	0.883	1	0.993	1	CLONAL	2	TRUE	1	0.307751118900883	2		1017	855	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129476	64129476	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	204	1080	0	ENST00000334205.4:c.906+2T>C		p.X302_splice	ENST00000334205	NM_003942.2	302			1	2	FACETS	0.81	0.753	0.87	1	0.992	1	CLONAL	2	TRUE	1	0.307751118900883	2		1080	818	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948586	71948586	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	225	1082	3	ENST00000298229.2:c.3302del	p.Pro1101GlnfsTer30	p.P1101Qfs*30	ENST00000298229	NM_001567.3	1100	Ccc/cc	26/28	1	2	FACETS	0.934	0.872	0.997	1	0.994	1	CLONAL	2	TRUE	1	0.307751118900883	2		1085	783	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94923006	94923007	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	160	1119	0	ENST00000536441.1:c.461dup	p.Asn154LysfsTer3	p.N154Kfs*3	ENST00000536441	NM_144665.3	154	aat/aaAt	4/10	1	2	FACETS	0.864	0.795	0.934	1	0.991	1	CLONAL	2	TRUE	1	0.307751118900883	2		1119	602	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924713	94924713	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	159	1226	0	ENST00000536441.1:c.197A>G	p.Tyr66Cys	p.Y66C	ENST00000536441	NM_144665.3	66	tAc/tGc	3/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.307751118900883	2		1226	700	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102056786	102056786	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	110	717	2	ENST00000282441.5:c.726G>T	p.Gln242His	p.Q242H	ENST00000282441	NM_001130145.2	242	caG/caT	4/9	1	2	FACETS	0.865	0.783	0.951	1	0.987	1	CLONAL	2	TRUE	1	0.307751118900883	2		719	413	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143537	108143537	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs368111672	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	119	868	0	ENST00000278616.4:c.3242A>G	p.Asn1081Ser	p.N1081S	ENST00000278616	NM_000051.3	1081	aAt/aGt	22/63	1	2	FACETS	0.964	0.878	1	1	0.989	1	CLONAL	2	TRUE	1	0.307751118900883	2		868	401	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025543	1025543	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	266	1139	1	ENST00000358495.3:c.832C>T	p.Arg278Ter	p.R278*	ENST00000358495	NM_134424.2	278	Cga/Tga	9/12	1	2	FACETS	0.877	0.824	0.933	1	0.994	1	CLONAL	2	TRUE	1	0.307751118900883	2		1140	985	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1036407	1036407	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	211	888	0	ENST00000358495.3:c.371T>C	p.Val124Ala	p.V124A	ENST00000358495	NM_134424.2	124	gTt/gCt	6/12	1	2	FACETS	0.962	0.897	1	1	0.994	1	CLONAL	2	TRUE	1	0.307751118900883	2		888	713	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1036430	1036430	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	155	690	1	ENST00000358495.3:c.349-1G>T		p.X117_splice	ENST00000358495	NM_134424.2	117			1	2	FACETS	0.986	0.909	1	1	0.992	1	CLONAL	2	TRUE	1	0.307751118900883	2		691	511	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491389	18491390	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	81	657	0	ENST00000266497.5:c.1309dup	p.Ile437AsnfsTer19	p.I437Nfs*19	ENST00000266497		434	-/A	8/31	1	2	FACETS	0.774	0.688	0.865	1	0.98	1	SUBCLONAL	2	TRUE	1	0.307751118900883	2		657	340	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420412	49420412	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	39	1018	0	ENST00000301067.7:c.15337T>C	p.Tyr5113His	p.Y5113H	ENST00000301067	NM_003482.3	5113	Tac/Cac	48/54	1	2	FACETS	0.331	0.273	0.396	0.331	0.273	0.396	SUBCLONAL	1	TRUE	1	0.307751118900883	2		1018	765	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420906	49420906	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	206	954	2	ENST00000301067.7:c.14843C>A	p.Ser4948Ter	p.S4948*	ENST00000301067	NM_003482.3	4948	tCa/tAa	48/54	1	2	FACETS	0.876	0.815	0.939	1	0.993	1	CLONAL	2	TRUE	1	0.307751118900883	2		956	764	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425644	49425644	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057517992	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	168	1093	1	ENST00000301067.7:c.12844C>T	p.Arg4282Ter	p.R4282*	ENST00000301067	NM_003482.3	4282	Cga/Tga	39/54	1	2	FACETS	0.928	0.858	1	1	0.992	1	CLONAL	2	TRUE	1	0.307751118900883	2		1094	588	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427926	49427926	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	242	1123	0	ENST00000301067.7:c.10664A>G	p.Glu3555Gly	p.E3555G	ENST00000301067	NM_003482.3	3555	gAg/gGg	38/54	1	2	FACETS	0.902	0.844	0.961	1	0.994	1	CLONAL	2	TRUE	1	0.307751118900883	2		1123	872	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444808	49444809	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	256	1265	0	ENST00000301067.7:c.2657dup	p.Gly887TrpfsTer16	p.G887Wfs*16	ENST00000301067	NM_003482.3	886	cct/ccCt	10/54	1	2	FACETS	0.954	0.895	1	1	0.995	1	CLONAL	2	TRUE	1	0.307751118900883	2		1265	872	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444987	49444987	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	169	820	2	ENST00000301067.7:c.2479del	p.Gln827AsnfsTer103	p.Q827Nfs*103	ENST00000301067	NM_003482.3	827	Caa/aa	10/54	1	2	FACETS	0.844	0.778	0.911	1	0.991	1	CLONAL	2	TRUE	1	0.307751118900883	2		822	651	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	234	558	3	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.773	0.721	0.826	1	0.992	1	SUBCLONAL	2	TRUE	1	0.307751118900883	2		561	984	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143047	58143047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372604524	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	279	1078	1	ENST00000257904.6:c.737G>A	p.Arg246His	p.R246H	ENST00000257904	NM_000075.3	246	cGt/cAt	7/8	1	2	FACETS	0.952	0.896	1	1	0.995	1	CLONAL	2	TRUE	1	0.307751118900883	2		1079	952	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69203017	69203017	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	183	932	0	ENST00000462284.1:c.44C>A	p.Pro15His	p.P15H	ENST00000462284	NM_002392.5	15	cCt/cAt	2/11	1	2	FACETS	0.918	0.851	0.987	1	0.993	1	CLONAL	2	TRUE	1	0.307751118900883	2		932	648	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218379	69218379	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	114	968	1	ENST00000462284.1:c.471T>G	p.His157Gln	p.H157Q	ENST00000462284	NM_002392.5	157	caT/caG	7/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.307751118900883	2		969	495	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233089	69233090	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs746910913	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	64	666	0	ENST00000462284.1:c.961dup	p.Leu321ProfsTer13	p.L321Pfs*13	ENST00000462284	NM_002392.5	318	-/C	11/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.307751118900883	2		666	342	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885484	111885484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs925290350	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	243	914	4	ENST00000341259.2:c.1261C>T	p.Arg421Trp	p.R421W	ENST00000341259	NM_005475.2	421	Cgg/Tgg	7/8	1	2	FACETS	0.996	0.933	1	1	0.995	1	CLONAL	2	TRUE	1	0.307751118900883	2		918	793	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112630	115112648	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGACATAAATCTACCACA	GGGACATAAATCTACCACA	-	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	219	1169	0	ENST00000257566.3:c.1100-8_1110del		p.X367_splice	ENST00000257566	NM_016569.3	367		7/8	1	2	FACETS	0.78	0.727	0.836	1	0.992	1	SUBCLONAL	2	TRUE	1	0.307751118900883	2		1169	912	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	242	1086	8	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.985	0.923	1	1	0.995	1	CLONAL	2	TRUE	1	0.307751118900883	2		1094	798	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434356	121434356	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	179	972	3	ENST00000257555.6:c.1124del	p.Gly375AlafsTer9	p.G375Afs*9	ENST00000257555		374	Ggg/gg	6/10	1	2	FACETS	0.944	0.875	1	1	0.993	1	CLONAL	2	TRUE	1	0.307751118900883	2		975	616	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257766	133257766	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	245	1084	0	ENST00000320574.5:c.162G>T	p.Lys54Asn	p.K54N	ENST00000320574	NM_006231.2	54	aaG/aaT	2/49	1	2	FACETS	0.869	0.813	0.926	1	0.994	1	CLONAL	2	TRUE	1	0.307751118900883	2		1084	916	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913669	32913669	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359491	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	63	667	2	ENST00000380152.3:c.5180del	p.Asn1727MetfsTer14	p.N1727Mfs*14	ENST00000380152		1726	gAa/ga	11/27	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.307751118900883	2		669	299	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954022	32954023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs397507419	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	128	710	8	ENST00000380152.3:c.9097dup	p.Thr3033AsnfsTer11	p.T3033Nfs*11	ENST00000380152		3030	aca/acAa	23/27	1	2	FACETS	0.898	0.82	0.98	1	0.989	1	CLONAL	2	TRUE	1	0.307751118900883	2		718	463	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32968829	32968829	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	30	476	0	ENST00000380152.3:c.9260T>C	p.Leu3087Pro	p.L3087P	ENST00000380152		3087	cTt/cCt	25/27	1	2	FACETS	0.833	0.675	1	0.833	0.675	1	CLONAL	1	TRUE	1	0.307751118900883	2		476	234	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039143	49039143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs529366765	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	57	463	1	ENST00000267163.4:c.2221C>T	p.Arg741Cys	p.R741C	ENST00000267163	NM_000321.2	741	Cgt/Tgt	22/27	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.307751118900883	2		464	261	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068939	30068939	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	159	1142	1	ENST00000331968.5:c.1990G>T	p.Gly664Ter	p.G664*	ENST00000331968	NM_002742.2	664	Gga/Tga	14/18	0.307751118900883	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.307751118900883	1		1143	619	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81574745	81574746	+	missense_variant	Missense_Mutation	DNP	CA	CA	TG	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	85	708	2	ENST00000298171.2:c.641_642inv	p.Thr214Met	p.T214M	ENST00000298171	NM_000369.2	214	aCA/aTG	8/10	0.307751118900883	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.307751118900883	1		710	338	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574752	95574752	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	38	735	0	ENST00000393063.1:c.2345C>A	p.Pro782His	p.P782H	ENST00000393063	NM_030621.3	782	cCt/cAt	16/28	0.307751118900883	1	FACETS	0.513	0.425	0.612	0.513	0.425	0.612	SUBCLONAL	1	TRUE	0	0.307751118900883	1		735	407	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38631946	38631946	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	47	956	0	ENST00000299084.4:c.432A>C	p.Glu144Asp	p.E144D	ENST00000299084	NM_152594.2	144	gaA/gaC	5/7	0.307751118900883	1	FACETS	0.529	0.446	0.619	0.529	0.446	0.619	SUBCLONAL	1	TRUE	0	0.307751118900883	1		956	489	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749288	43749289	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	148	1129	0	ENST00000382044.4:c.1517dup	p.Glu507Ter	p.E507*	ENST00000382044	NM_001141980.1	506	cct/ccCt	12/28	0.307751118900883	1	FACETS	0.812	0.747	0.88	1	0.99	1	CLONAL	2	TRUE	0	0.307751118900883	1		1129	501	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576147	88576147	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	204	1125	1	ENST00000360948.2:c.1526C>T	p.Pro509Leu	p.P509L	ENST00000360948	NM_001012338.2	509	cCt/cTt	13/19	0.307751118900883	1	FACETS	0.789	0.734	0.845	1	0.992	1	SUBCLONAL	2	TRUE	0	0.307751118900883	1		1126	711	SUCCESS
BLM	641	MSKCC	GRCh37	15	91298042	91298042	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	36	551	0	ENST00000355112.3:c.961A>G	p.Thr321Ala	p.T321A	ENST00000355112	NM_000057.2	321	Acg/Gcg	5/22	0.307751118900883	1	FACETS	0.639	0.527	0.763	0.639	0.527	0.763	SUBCLONAL	1	TRUE	0	0.307751118900883	1		551	310	SUCCESS
BLM	641	MSKCC	GRCh37	15	91337455	91337455	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	134	787	0	ENST00000355112.3:c.3078G>T	p.Met1026Ile	p.M1026I	ENST00000355112	NM_000057.2	1026	atG/atT	16/22	0.307751118900883	1	FACETS	0.877	0.804	0.952	1	0.99	1	CLONAL	2	TRUE	0	0.307751118900883	1		787	420	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354634	91354634	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	83	520	0	ENST00000355112.3:c.4074G>T	p.Lys1358Asn	p.K1358N	ENST00000355112	NM_000057.2	1358	aaG/aaT	21/22	0.307751118900883	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.307751118900883	1		520	407	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347092	347092	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	148	1272	0	ENST00000262320.3:c.1919A>G	p.Glu640Gly	p.E640G	ENST00000262320	NM_003502.3	640	gAa/gGa	7/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.307751118900883	2		1272	892	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2093651	2093651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	261	1290	0	ENST00000219066.1:c.626C>T	p.Ala209Val	p.A209V	ENST00000219066	NM_002528.5	209	gCc/gTc	4/6	1	2	FACETS	0.969	0.91	1	1	0.995	1	CLONAL	2	TRUE	1	0.307751118900883	2		1290	875	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226559	2226559	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	199	1166	0	ENST00000326181.6:c.1999-2A>C		p.X667_splice	ENST00000326181	NM_032271.2	667			1	2	FACETS	0.862	0.801	0.925	1	0.993	1	CLONAL	2	TRUE	1	0.307751118900883	2		1166	750	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647973	3647973	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	293	1269	0	ENST00000294008.3:c.1191del	p.Lys397AsnfsTer55	p.K397Nfs*55	ENST00000294008	NM_032444.2	397	aaA/aa	6/15	1	2	FACETS	0.981	0.924	1	1	0.995	1	CLONAL	2	TRUE	1	0.307751118900883	2		1269	971	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819257	3819257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767573846	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	251	1024	1	ENST00000262367.5:c.2978C>T	p.Pro993Leu	p.P993L	ENST00000262367	NM_004380.2	993	cCt/cTt	15/31	1	2	FACETS	0.955	0.896	1	1	0.995	1	CLONAL	2	TRUE	1	0.307751118900883	2		1025	854	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650711	67650711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567610917	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	221	975	2	ENST00000264010.4:c.1016G>A	p.Arg339Gln	p.R339Q	ENST00000264010	NM_006565.3	339	cGg/cAg	5/12	1	2	FACETS	0.835	0.778	0.893	1	0.993	1	CLONAL	2	TRUE	1	0.307751118900883	2		977	860	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821381	72821382	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	79	667	0	ENST00000268489.5:c.10793dup	p.Pro3599SerfsTer67	p.P3599Sfs*67	ENST00000268489	NM_006885.3	3598	cct/ccCt	10/10	1	2	FACETS	0.96	0.846	1	0.96	0.846	1	CLONAL	1	TRUE	1	0.307751118900883	2		667	535	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822537	72822537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780937804	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	183	832	3	ENST00000268489.5:c.9638C>T	p.Pro3213Leu	p.P3213L	ENST00000268489	NM_006885.3	3213	cCg/cTg	10/10	1	2	FACETS	1	0.96	1	1	0.993	1	CLONAL	2	TRUE	1	0.307751118900883	2		835	567	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831182	72831182	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	141	778	0	ENST00000268489.5:c.5399del	p.Phe1800SerfsTer14	p.F1800Sfs*14	ENST00000268489	NM_006885.3	1800	tTc/tc	9/10	1	2	FACETS	0.863	0.79	0.938	1	0.99	1	CLONAL	2	TRUE	1	0.307751118900883	2		778	531	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923820	72923820	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	156	948	1	ENST00000268489.5:c.3258C>A	p.Cys1086Ter	p.C1086*	ENST00000268489	NM_006885.3	1086	tgC/tgA	4/10	1	2	FACETS	0.751	0.69	0.815	1	0.988	1	SUBCLONAL	2	TRUE	1	0.307751118900883	2		949	675	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81939065	81939065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867345397	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	159	915	1	ENST00000359376.3:c.1420G>A	p.Glu474Lys	p.E474K	ENST00000359376	NM_002661.3	474	Gaa/Aaa	15/33	1	2	FACETS	0.879	0.809	0.95	1	0.991	1	CLONAL	2	TRUE	1	0.307751118900883	2		916	588	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347224	89347224	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	142	840	5	ENST00000301030.4:c.5726del	p.Pro1909ArgfsTer54	p.P1909Rfs*54	ENST00000301030	NM_001256183.1	1909	cCg/cg	9/13	1	2	FACETS	0.907	0.831	0.984	1	0.99	1	CLONAL	2	TRUE	1	0.307751118900883	2		845	509	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348562	89348562	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	287	1313	1	ENST00000301030.4:c.4388A>T	p.Glu1463Val	p.E1463V	ENST00000301030	NM_001256183.1	1463	gAg/gTg	9/13	1	2	FACETS	0.95	0.894	1	1	0.995	1	CLONAL	2	TRUE	1	0.307751118900883	2		1314	982	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357043	89357043	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	169	861	0	ENST00000301030.4:c.591G>T	p.Lys197Asn	p.K197N	ENST00000301030	NM_001256183.1	197	aaG/aaT	6/13	1	2	FACETS	0.937	0.866	1	1	0.992	1	CLONAL	2	TRUE	1	0.307751118900883	2		861	586	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857935	89857935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11646374	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	192	951	1	ENST00000389301.3:c.1235C>T	p.Ala412Val	p.A412V	ENST00000389301	NM_000135.2	412	gCg/gTg	14/43	1	2	FACETS	0.825	0.765	0.887	1	0.992	1	CLONAL	2	TRUE	1	0.307751118900883	2		952	756	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16021222	16021222	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	28	628	0	ENST00000268712.3:c.2035T>G	p.Leu679Val	p.L679V	ENST00000268712	NM_006311.3	679	Tta/Gta	18/46	1	2	FACETS	0.414	0.33	0.509	0.414	0.33	0.509	SUBCLONAL	1	TRUE	1	0.307751118900883	2		628	440	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	207	790	4	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	1	2	FACETS	0.899	0.842	0.956	1	0.995	1	CLONAL	3	TRUE	1	0.307751118900883	2		794	499	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552143	29552144	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1555613558	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	44	417	1	ENST00000356175.3:c.1882dup	p.Tyr628LeufsTer6	p.Y628Lfs*6	ENST00000356175	NM_000267.3	626	ctt/cTtt	17/57	1	2	FACETS	0.812	0.691	0.942	1	0.966	1	CLONAL	2	TRUE	1	0.307751118900883	2		418	176	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	209	1050	2	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.307751118900883	2		1052	913	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667819	37667819	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	105	783	2	ENST00000447079.4:c.2704C>T	p.Arg902Ter	p.R902*	ENST00000447079	NM_015083.1	902	Cga/Tga	8/14	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.307751118900883	2		785	469	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38504662	38504662	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	258	1185	0	ENST00000254066.5:c.273T>A	p.Cys91Ter	p.C91*	ENST00000254066	NM_000964.3	91	tgT/tgA	3/9	1	2	FACETS	0.946	0.888	1	1	0.995	1	CLONAL	2	TRUE	1	0.307751118900883	2		1185	886	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354384	40354384	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	305	1662	2	ENST00000293328.3:c.2211G>T	p.Gln737His	p.Q737H	ENST00000293328	NM_012448.3	737	caG/caT	18/19	1	2	FACETS	0.862	0.812	0.913	1	0.995	1	CLONAL	2	TRUE	1	0.307751118900883	2		1664	1150	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370236	40370236	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs761761205	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	166	1252	19	ENST00000293328.3:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000293328	NM_012448.3	368	Cag/ag	9/19	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.307751118900883	2		1271	783	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245506	41245506	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1452826319	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	50	1301	0	ENST00000357654.3:c.2042G>A	p.Ser681Asn	p.S681N	ENST00000357654	NM_007294.3	681	aGt/aAt	10/23	1	2	FACETS	0.421	0.356	0.493	0.421	0.356	0.493	SUBCLONAL	1	TRUE	1	0.307751118900883	2		1301	771	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696430	47696430	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519970	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	134	968	1	ENST00000347630.2:c.393G>T	p.Trp131Cys	p.W131C	ENST00000347630	NM_001007230.1	131	tgG/tgT	6/11	1	2	FACETS	0.799	0.729	0.871	1	0.988	1	SUBCLONAL	2	TRUE	1	0.307751118900883	2		969	545	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435290	56435290	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	144	902	0	ENST00000407977.2:c.1847C>A	p.Pro616His	p.P616H	ENST00000407977		616	cCc/cAc	9/10	1	2	FACETS	0.79	0.724	0.86	1	0.989	1	SUBCLONAL	2	TRUE	1	0.307751118900883	2		902	592	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436161	56436161	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	171	918	0	ENST00000407977.2:c.976C>A	p.Leu326Met	p.L326M	ENST00000407977		326	Ctg/Atg	9/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.307751118900883	2		918	749	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740726	58740727	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1194694298	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	141	771	0	ENST00000305921.3:c.1636dup	p.Leu546ProfsTer6	p.L546Pfs*6	ENST00000305921	NM_003620.3	544	ggc/ggCc	6/6	1	2	FACETS	0.805	0.737	0.876	1	0.989	1	CLONAL	2	TRUE	1	0.307751118900883	2		771	569	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120113	70120113	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	14	170	0	ENST00000245479.2:c.1115C>T	p.Ala372Val	p.A372V	ENST00000245479	NM_000346.3	372	gCa/gTa	3/3	1	2	FACETS	0.835	0.61	1	0.835	0.61	1	CLONAL	1	TRUE	1	0.307751118900883	2		170	109	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191069	2191069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746714270	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	153	854	1	ENST00000398665.3:c.323G>A	p.Arg108His	p.R108H	ENST00000398665	NM_032482.2	108	cGc/cAc	5/28	1	2	FACETS	0.818	0.751	0.887	1	0.99	1	CLONAL	2	TRUE	1	0.307751118900883	2		855	608	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231345	5231345	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765642813	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	207	971	1	ENST00000357368.4:c.2131G>A	p.Val711Met	p.V711M	ENST00000357368	NM_002850.3	711	Gtg/Atg	14/38	1	2	FACETS	0.918	0.854	0.983	1	0.993	1	CLONAL	2	TRUE	1	0.307751118900883	2		972	733	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	41	235	1	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.307751118900883	2		236	191	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10274028	10274028	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	40	1027	0	ENST00000340748.4:c.852G>T	p.Lys284Asn	p.K284N	ENST00000340748		284	aaG/aaT	11/40	1	2	FACETS	0.419	0.347	0.5	0.419	0.347	0.5	SUBCLONAL	1	TRUE	1	0.307751118900883	2		1027	620	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030338	11030340	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	166	887	0	ENST00000327064.4:c.1091_1093del	p.Glu364del	p.E364del	ENST00000327064	NM_199141.1	363	aAAGaa/aaa	9/16	1	2	FACETS	0.858	0.791	0.926	1	0.991	1	CLONAL	2	TRUE	1	0.307751118900883	2		887	629	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051574	13051574	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	132	788	1	ENST00000316448.5:c.833G>T	p.Arg278Leu	p.R278L	ENST00000316448	NM_004343.3	278	cGg/cTg	7/9	1	2	FACETS	0.763	0.696	0.833	1	0.987	1	SUBCLONAL	2	TRUE	1	0.307751118900883	2		789	562	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626900	14626900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760777348	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	66	997	1	ENST00000254322.2:c.875G>A	p.Gly292Asp	p.G292D	ENST00000254322	NM_006145.1	292	gGc/gAc	3/3	1	2	FACETS	0.456	0.394	0.523	0.456	0.394	0.523	SUBCLONAL	1	TRUE	1	0.307751118900883	2		998	941	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272336	15272337	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs771517374	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	234	1275	5	ENST00000263388.2:c.6102dup	p.Gly2035ArgfsTer60	p.G2035Rfs*60	ENST00000263388	NM_000435.2	2034	-/C	33/33	1	2	FACETS	0.801	0.748	0.856	1	0.993	1	CLONAL	2	TRUE	1	0.307751118900883	2		1280	949	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302676	15302676	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	214	1129	0	ENST00000263388.2:c.682T>G	p.Phe228Val	p.F228V	ENST00000263388	NM_000435.2	228	Ttt/Gtt	5/33	1	2	FACETS	0.921	0.859	0.985	1	0.994	1	CLONAL	2	TRUE	1	0.307751118900883	2		1129	755	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302978	15302978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs544773641	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	245	1346	4	ENST00000263388.2:c.472G>A	p.Asp158Asn	p.D158N	ENST00000263388	NM_000435.2	158	Gac/Aac	4/33	1	2	FACETS	0.873	0.817	0.93	1	0.994	1	CLONAL	2	TRUE	1	0.307751118900883	2		1350	912	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350589	15350589	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1423798513	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	287	1291	0	ENST00000263377.2:c.3326T>C	p.Val1109Ala	p.V1109A	ENST00000263377	NM_058243.2	1109	gTg/gCg	16/20	1	2	FACETS	0.967	0.911	1	1	0.995	1	CLONAL	2	TRUE	1	0.307751118900883	2		1291	964	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266700	18266700	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	265	1096	0	ENST00000222254.8:c.11C>A	p.Pro4His	p.P4H	ENST00000222254	NM_005027.3	4	cCt/cAt	2/16	1	2	FACETS	0.92	0.864	0.977	1	0.995	1	CLONAL	2	TRUE	1	0.307751118900883	2		1096	936	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974979	18974979	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	177	1018	2	ENST00000262803.5:c.2776G>A	p.Gly926Arg	p.G926R	ENST00000262803	NM_002911.3	926	Gga/Aga	20/24	1	2	FACETS	0.758	0.7	0.818	1	0.99	1	SUBCLONAL	2	TRUE	1	0.307751118900883	2		1020	759	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256768	19256769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	77	811	0	ENST00000162023.5:c.943_944dup	p.Val316GlnfsTer?	p.V316Qfs*?	ENST00000162023		315	cca/ccCCa	13/13	1	2	FACETS	0.852	0.749	0.963	0.852	0.749	0.963	CLONAL	1	TRUE	1	0.307751118900883	2		811	587	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212669	36212669	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	257	1122	0	ENST00000222270.7:c.2420A>G	p.Asp807Gly	p.D807G	ENST00000222270	NM_014727.1	807	gAt/gGt	3/37	1	2	FACETS	0.915	0.858	0.973	1	0.994	1	CLONAL	2	TRUE	1	0.307751118900883	2		1122	913	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216712	36216712	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780411851	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	174	735	0	ENST00000222270.7:c.3878G>A	p.Arg1293His	p.R1293H	ENST00000222270	NM_014727.1	1293	cGc/cAc	13/37	1	2	FACETS	0.987	0.914	1	1	0.993	1	CLONAL	2	TRUE	1	0.307751118900883	2		735	573	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753099	42753099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	185	991	1	ENST00000222329.4:c.1165C>T	p.Arg389Trp	p.R389W	ENST00000222329	NM_006494.2	389	Cgg/Tgg	4/4	1	2	FACETS	0.829	0.768	0.893	1	0.992	1	CLONAL	2	TRUE	1	0.307751118900883	2		992	725	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791278	42791279	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	197	1056	1	ENST00000575354.2:c.341dup	p.Leu114PhefsTer8	p.L114Ffs*8	ENST00000575354	NM_015125.3	113	cct/ccTt	3/20	1	2	FACETS	0.878	0.816	0.942	1	0.993	1	CLONAL	2	TRUE	1	0.307751118900883	2		1057	729	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793406	42793406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757404366	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	149	790	0	ENST00000575354.2:c.1208C>T	p.Ala403Val	p.A403V	ENST00000575354	NM_015125.3	403	gCc/gTc	8/20	1	2	FACETS	0.903	0.83	0.979	1	0.991	1	CLONAL	2	TRUE	1	0.307751118900883	2		790	536	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856353	45856353	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	216	1110	1	ENST00000391945.4:c.1819G>T	p.Gly607Ter	p.G607*	ENST00000391945	NM_000400.3	607	Gga/Tga	19/23	1	2	FACETS	0.867	0.807	0.927	1	0.993	1	CLONAL	2	TRUE	1	0.307751118900883	2		1111	810	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905061	50905061	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs754917939	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	208	946	2	ENST00000440232.2:c.343C>G	p.Pro115Ala	p.P115A	ENST00000440232	NM_002691.3	115	Ccc/Gcc	4/27	1	2	FACETS	1	0.975	1	1	0.994	1	CLONAL	2	TRUE	1	0.307751118900883	2		948	620	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906816	50906816	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426325954	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	251	1105	3	ENST00000440232.2:c.1204G>A	p.Asp402Asn	p.D402N	ENST00000440232	NM_002691.3	402	Gac/Aac	10/27	1	2	FACETS	0.954	0.895	1	1	0.995	1	CLONAL	2	TRUE	1	0.307751118900883	2		1108	855	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703495	47703502	+	splice_region_variant,intron_variant	Splice_Region	DEL	TTGTTTTG	TTGTTTTG	-	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	66	655	0	ENST00000233146.2:c.2006-10_2006-3del		p.X669_splice	ENST00000233146	NM_000251.2	669			1	2	FACETS	0.755	0.662	0.854	1	0.974	1	SUBCLONAL	2	TRUE	1	0.307751118900883	2		655	284	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703520	47703520	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs63750234	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	132	880	0	ENST00000233146.2:c.2020G>C	p.Gly674Arg	p.G674R	ENST00000233146	NM_000251.2	674	Ggt/Cgt	13/16	1	2	FACETS	1	0.939	1	1	0.991	1	CLONAL	2	TRUE	1	0.307751118900883	2		880	416	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156071	99156071	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	222	971	0	ENST00000074304.5:c.751G>A	p.Glu251Lys	p.E251K	ENST00000074304	NM_001134224.1	251	Gag/Aag	10/26	1	2	FACETS	0.88	0.821	0.94	1	0.993	1	CLONAL	2	TRUE	1	0.307751118900883	2		971	820	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99181137	99181137	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	219	1047	0	ENST00000074304.5:c.2078T>C	p.Leu693Pro	p.L693P	ENST00000074304	NM_001134224.1	693	cTg/cCg	20/26	1	2	FACETS	0.874	0.815	0.935	1	0.993	1	CLONAL	2	TRUE	1	0.307751118900883	2		1047	814	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182521	99182521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373911327	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	249	923	0	ENST00000074304.5:c.2324C>T	p.Pro775Leu	p.P775L	ENST00000074304	NM_001134224.1	775	cCg/cTg	22/26	1	2	FACETS	0.951	0.891	1	1	0.995	1	CLONAL	2	TRUE	1	0.307751118900883	2		923	851	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038148	128038149	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	188	857	0	ENST00000285398.2:c.1401dup	p.Ala468CysfsTer8	p.A468Cfs*8	ENST00000285398	NM_000122.1	467	-/T	9/15	1	2	FACETS	0.857	0.794	0.921	1	0.992	1	CLONAL	2	TRUE	1	0.307751118900883	2		857	713	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872924	136872924	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	26	506	0	ENST00000241393.3:c.574A>G	p.Asn192Asp	p.N192D	ENST00000241393	NM_003467.2	192	Aat/Gat	2/2	1	2	FACETS	0.448	0.355	0.555	0.448	0.355	0.555	SUBCLONAL	1	TRUE	1	0.307751118900883	2		506	377	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098885	178098886	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	160	900	2	ENST00000397062.3:c.159dup	p.Leu54ThrfsTer2	p.L54Tfs*2	ENST00000397062	NM_006164.4	53	-/A	2/5	1	2	FACETS	0.837	0.771	0.906	1	0.99	1	CLONAL	2	TRUE	1	0.307751118900883	2		902	621	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198264891	198264891	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	84	672	1	ENST00000335508.6:c.2902-1G>T		p.X968_splice	ENST00000335508	NM_012433.2	968			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.307751118900883	2		673	386	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131514	202131514	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	87	621	3	ENST00000358485.4:c.482G>T	p.Arg161Met	p.R161M	ENST00000358485	NM_001080125.1	161	aGg/aTg	2/9	1	2	FACETS	0.762	0.68	0.849	1	0.98	1	SUBCLONAL	2	TRUE	1	0.307751118900883	2		624	371	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568865	212568866	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	101	973	0	ENST00000342788.4:c.1252dup	p.Ser418PhefsTer2	p.S418Ffs*2	ENST00000342788	NM_005235.2	418	tct/tTct	11/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.307751118900883	2		973	469	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652870	212652870	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	63	621	1	ENST00000342788.4:c.436G>T	p.Gly146Ter	p.G146*	ENST00000342788	NM_005235.2	146	Gga/Tga	4/28	1	2	FACETS	0.875	0.766	0.989	1	0.978	1	CLONAL	2	TRUE	1	0.307751118900883	2		622	234	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660754	227660754	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs755878633	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	142	1033	0	ENST00000305123.5:c.2701T>G	p.Phe901Val	p.F901V	ENST00000305123	NM_005544.2	901	Ttt/Gtt	1/2	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.307751118900883	2		1033	708	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023982	31023983	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1569336425	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	94	921	0	ENST00000375687.4:c.3473dup	p.Asn1158LysfsTer6	p.N1158Kfs*6	ENST00000375687	NM_015338.5	1156	gga/ggAa	13/13	0.307751118900883	1	FACETS	0.693	0.616	0.775	0.693	0.616	0.775	SUBCLONAL	1	TRUE	0	0.307751118900883	1		921	746	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36028611	36028611	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	191	1106	0	ENST00000358208.4:c.953A>C	p.Lys318Thr	p.K318T	ENST00000358208		318	aAg/aCg	8/12	0.307751118900883	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.307751118900883	1		1106	789	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40828029	40828029	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	101	562	2	ENST00000373198.4:c.2400-1G>T		p.X800_splice	ENST00000373198	NM_133170.3	800			0.307751118900883	1	FACETS	0.873	0.79	0.96	1	0.987	1	CLONAL	2	TRUE	0	0.307751118900883	1		564	318	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655259	45655259	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	81	1153	0	ENST00000407780.3:c.593A>G	p.Asp198Gly	p.D198G	ENST00000407780	NM_001283052.1	198	gAc/gGc	4/7	1	2	FACETS	0.603	0.53	0.681	0.603	0.53	0.681	SUBCLONAL	1	TRUE	1	0.307751118900883	2		1153	873	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627411	37627411	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	214	1161	0	ENST00000249071.6:c.308A>G	p.His103Arg	p.H103R	ENST00000249071	NM_002872.4	103	cAc/cGc	5/7	0.307751118900883	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.307751118900883	1		1161	902	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49413006	49413006	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	215	1071	0	ENST00000418115.1:c.17A>C	p.Lys6Thr	p.K6T	ENST00000418115	NM_001664.2	6	aAg/aCg	2/5	1	2	FACETS	0.906	0.845	0.969	1	0.993	1	CLONAL	2	TRUE	1	0.307751118900883	2		1071	771	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610689	52610689	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	96	756	0	ENST00000394830.3:c.3484G>T	p.Gly1162Ter	p.G1162*	ENST00000394830	NM_018313.4	1162	Gga/Tga	23/30	1	2	FACETS	0.806	0.724	0.892	1	0.984	1	CLONAL	2	TRUE	1	0.307751118900883	2		756	387	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643788	52643788	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	166	941	1	ENST00000394830.3:c.2108C>A	p.Pro703His	p.P703H	ENST00000394830	NM_018313.4	703	cCc/cAc	17/30	1	2	FACETS	1	0.933	1	1	0.993	1	CLONAL	2	TRUE	1	0.307751118900883	2		942	534	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014209	70014209	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1297217487	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	202	987	0	ENST00000394351.3:c.1070G>T	p.Gly357Val	p.G357V	ENST00000394351	NM_000248.3	357	gGg/gTg	9/9	1	2	FACETS	0.852	0.792	0.914	1	0.993	1	CLONAL	2	TRUE	1	0.307751118900883	2		987	770	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021757	71021757	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	132	770	0	ENST00000318789.4:c.1601G>T	p.Trp534Leu	p.W534L	ENST00000318789	NM_032682.5	534	tGg/tTg	18/21	1	2	FACETS	0.884	0.808	0.964	1	0.989	1	CLONAL	2	TRUE	1	0.307751118900883	2		770	485	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027086	71027087	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs797044652	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	146	737	0	ENST00000318789.4:c.1240dup	p.Leu414ProfsTer47	p.L414Pfs*47	ENST00000318789	NM_032682.5	414	ctg/cCtg	15/21	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.307751118900883	2		737	665	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204841	128204842	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs768767517	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	210	1294	3	ENST00000341105.2:c.599dup	p.Ser201Ter	p.S201*	ENST00000341105	NM_032638.4	200	ggt/ggGt	3/6	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.307751118900883	2		1297	917	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433329	138433329	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	104	756	0	ENST00000289153.2:c.1283T>C	p.Ile428Thr	p.I428T	ENST00000289153	NM_006219.2	428	aTc/aCc	7/22	1	2	FACETS	0.814	0.734	0.898	1	0.985	1	CLONAL	2	TRUE	1	0.307751118900883	2		756	415	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664711	138664711	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs797044531	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	119	487	0	ENST00000330315.3:c.854del	p.Pro285ArgfsTer71	p.P285Rfs*71	ENST00000330315	NM_023067.3	285	cCg/cg	1/1	1	2	FACETS	0.891	0.81	0.975	1	0.988	1	CLONAL	2	TRUE	1	0.307751118900883	2		487	434	SUCCESS
ATR	545	MSKCC	GRCh37	3	142255002	142255002	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	58	656	0	ENST00000350721.4:c.3767C>A	p.Pro1256His	p.P1256H	ENST00000350721	NM_001184.3	1256	cCt/cAt	20/47	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.307751118900883	2		656	300	SUCCESS
ATR	545	MSKCC	GRCh37	3	142255005	142255005	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	92	643	0	ENST00000350721.4:c.3764del	p.Leu1255TyrfsTer7	p.L1255Yfs*7	ENST00000350721	NM_001184.3	1255	tTa/ta	20/47	1	2	FACETS	0.99	0.89	1	1	0.987	1	CLONAL	2	TRUE	1	0.307751118900883	2		643	302	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269045	142269045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	142	851	0	ENST00000350721.4:c.2905G>A	p.Glu969Lys	p.E969K	ENST00000350721	NM_001184.3	969	Gaa/Aaa	14/47	1	2	FACETS	0.791	0.724	0.861	1	0.988	1	SUBCLONAL	2	TRUE	1	0.307751118900883	2		851	583	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269063	142269063	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	136	844	0	ENST00000350721.4:c.2887G>A	p.Asp963Asn	p.D963N	ENST00000350721	NM_001184.3	963	Gat/Aat	14/47	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.307751118900883	2		844	594	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526302	189526302	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866938979	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	204	643	0	ENST00000264731.3:c.566C>T	p.Ser189Leu	p.S189L	ENST00000264731	NM_003722.4	189	tCg/tTg	4/14	1	2	FACETS	1	0.956	1	1	0.994	1	CLONAL	2	TRUE	1	0.307751118900883	2		643	642	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803438	1803438	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	290	1120	3	ENST00000260795.2:c.707G>T	p.Ser236Ile	p.S236I	ENST00000260795		236	aGc/aTc	5/17	1	2	FACETS	1	0.944	1	1	0.995	1	CLONAL	2	TRUE	1	0.307751118900883	2		1123	941	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	202	959	6	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	1	2	FACETS	0.879	0.817	0.942	1	0.993	1	CLONAL	2	TRUE	1	0.307751118900883	2		965	747	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242778	66242778	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	106	493	0	ENST00000273854.3:c.1794C>A	p.Cys598Ter	p.C598*	ENST00000273854	NM_004439.5	598	tgC/tgA	9/18	1	2	FACETS	0.807	0.728	0.889	1	0.985	1	CLONAL	2	TRUE	1	0.307751118900883	2		493	427	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467573	66467573	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	109	662	0	ENST00000273854.3:c.696del	p.Lys232AsnfsTer36	p.K232Nfs*36	ENST00000273854	NM_004439.5	232	aaA/aa	3/18	1	2	FACETS	0.91	0.825	1	1	0.988	1	CLONAL	2	TRUE	1	0.307751118900883	2		662	389	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164056	106164056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	58	564	0	ENST00000380013.4:c.3566G>A	p.Ser1189Asn	p.S1189N	ENST00000380013	NM_001127208.2	1189	aGt/aAt	5/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.307751118900883	2		564	257	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509829	187509829	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs752119953	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	82	468	0	ENST00000441802.2:c.13684A>G	p.Ser4562Gly	p.S4562G	ENST00000441802	NM_005245.3	4562	Agt/Ggt	27/27	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.307751118900883	2		468	417	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530344	187530344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775447002	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	79	588	0	ENST00000441802.2:c.10199G>A	p.Arg3400Gln	p.R3400Q	ENST00000441802	NM_005245.3	3400	cGa/cAa	16/27	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.307751118900883	2		588	357	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534473	187534473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	87	608	1	ENST00000441802.2:c.9253del	p.Asp3086IlefsTer30	p.D3086Ifs*30	ENST00000441802	NM_005245.3	3085	Ctt/tt	13/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.307751118900883	2		609	377	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539029	187539029	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	71	863	0	ENST00000441802.2:c.8711T>C	p.Val2904Ala	p.V2904A	ENST00000441802	NM_005245.3	2904	gTg/gCg	10/27	1	2	FACETS	0.674	0.587	0.767	0.674	0.587	0.767	SUBCLONAL	1	TRUE	1	0.307751118900883	2		863	685	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251513	251513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750327309	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	112	377	2	ENST00000264932.6:c.1724C>T	p.Ala575Val	p.A575V	ENST00000264932	NM_004168.2	575	gCg/gTg	13/15	1	2	FACETS	1	0.929	1	1	0.989	1	CLONAL	2	TRUE	1	0.307751118900883	2		379	355	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264660	1264660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772974254	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	276	1223	4	ENST00000310581.5:c.2702G>A	p.Arg901Gln	p.R901Q	ENST00000310581	NM_198253.2	901	cGg/cAg	11/16	1	2	FACETS	1	0.966	1	1	0.995	1	CLONAL	2	TRUE	1	0.307751118900883	2		1227	866	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293661	1293661	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	209	1204	6	ENST00000310581.5:c.1340G>A	p.Arg447His	p.R447H	ENST00000310581	NM_198253.2	447	cGc/cAc	2/16	1	2	FACETS	0.88	0.819	0.942	1	0.993	1	CLONAL	2	TRUE	1	0.307751118900883	2		1210	772	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39021187	39021187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	62	914	0	ENST00000357387.3:c.149G>A	p.Gly50Glu	p.G50E	ENST00000357387	NM_152756.3	50	gGa/gAa	3/38	1	2	FACETS	0.992	0.861	1	0.992	0.861	1	CLONAL	1	TRUE	1	0.307751118900883	2		914	406	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589175	67589175	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	78	616	0	ENST00000274335.5:c.1163G>A	p.Gly388Glu	p.G388E	ENST00000274335		388	gGg/gAg	9/15	1	2	FACETS	1	0.9	1	1	0.985	1	CLONAL	2	TRUE	1	0.307751118900883	2		616	251	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80074646	80074647	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	112	758	0	ENST00000265081.6:c.2430dup	p.Leu811SerfsTer6	p.L811Sfs*6	ENST00000265081	NM_002439.4	809	gat/gaTt	17/24	1	2	FACETS	0.786	0.711	0.864	1	0.985	1	SUBCLONAL	2	TRUE	1	0.307751118900883	2		758	463	SUCCESS
APC	324	MSKCC	GRCh37	5	112170714	112170714	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	104	961	3	ENST00000257430.4:c.1810G>T	p.Ala604Ser	p.A604S	ENST00000257430	NM_000038.5	604	Gct/Tct	15/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.307751118900883	2		964	510	SUCCESS
APC	324	MSKCC	GRCh37	5	112173396	112173396	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	62	568	0	ENST00000257430.4:c.2105G>T	p.Gly702Val	p.G702V	ENST00000257430	NM_000038.5	702	gGg/gTg	16/16	1	2	FACETS	0.772	0.674	0.876	1	0.974	1	SUBCLONAL	2	TRUE	1	0.307751118900883	2		568	261	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176719048	176719048	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	129	565	0	ENST00000439151.2:c.6352G>T	p.Glu2118Ter	p.E2118*	ENST00000439151	NM_022455.4	2118	Gaa/Taa	22/23	1	2	FACETS	0.825	0.752	0.901	1	0.988	1	CLONAL	2	TRUE	1	0.307751118900883	2		565	508	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721128	176721128	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	93	610	0	ENST00000439151.2:c.6759A>C	p.Lys2253Asn	p.K2253N	ENST00000439151	NM_022455.4	2253	aaA/aaC	23/23	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.307751118900883	2		610	436	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056464	26056465	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	87	459	0	ENST00000343677.2:c.192dup	p.Ala65SerfsTer8	p.A65Sfs*8	ENST00000343677	NM_005319.3	64	-/A	1/1	1	2	FACETS	0.783	0.699	0.872	1	0.981	1	SUBCLONAL	2	TRUE	1	0.307751118900883	2		459	361	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188297	32188297	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs753855314	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	283	1213	6	ENST00000375023.3:c.1044del	p.Gly349AlafsTer49	p.G349Afs*49	ENST00000375023	NM_004557.3	348	ggC/gg	6/30	1	2	FACETS	1	0.946	1	1	0.995	1	CLONAL	2	TRUE	1	0.307751118900883	2		1219	915	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793794	89793794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	52	858	1	ENST00000336032.3:c.863C>T	p.Pro288Leu	p.P288L	ENST00000336032	NM_006813.2	288	cCt/cTt	2/2	1	2	FACETS	0.673	0.573	0.782	0.673	0.573	0.782	SUBCLONAL	1	TRUE	1	0.307751118900883	2		859	502	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724425	117724425	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	156	884	0	ENST00000368508.3:c.454T>C	p.Ser152Pro	p.S152P	ENST00000368508	NM_002944.2	152	Tcc/Ccc	6/43	1	2	FACETS	0.88	0.81	0.953	1	0.991	1	CLONAL	2	TRUE	1	0.307751118900883	2		884	576	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525643	137525643	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	28	647	0	ENST00000367739.4:c.374-2A>G		p.X125_splice	ENST00000367739	NM_000416.2	125			1	2	FACETS	0.657	0.527	0.805	0.657	0.527	0.805	SUBCLONAL	1	TRUE	1	0.307751118900883	2		647	277	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001400	150001401	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	133	995	0	ENST00000253339.5:c.2203dup	p.Thr735AsnfsTer17	p.T735Nfs*17	ENST00000253339		735	act/aAct	4/7	1	2	FACETS	0.889	0.813	0.968	1	0.99	1	CLONAL	2	TRUE	1	0.307751118900883	2		995	486	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016297	150016297	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	134	1019	0	ENST00000253339.5:c.409T>A	p.Phe137Ile	p.F137I	ENST00000253339		137	Ttc/Atc	2/7	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.307751118900883	2		1019	601	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163848	152163848	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	166	847	0	ENST00000206249.3:c.569A>T	p.Asp190Val	p.D190V	ENST00000206249	NM_000125.3	190	gAc/gTc	2/8	1	2	FACETS	0.93	0.859	1	1	0.992	1	CLONAL	2	TRUE	1	0.307751118900883	2		847	580	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946298	2946298	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	309	1173	0	ENST00000396946.4:c.3439A>G	p.Ile1147Val	p.I1147V	ENST00000396946	NM_032415.4	1147	Atc/Gtc	25/25	1	2	FACETS	0.953	0.899	1	1	0.996	1	CLONAL	2	TRUE	1	0.307751118900883	2		1173	1054	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355206	81355206	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	54	398	0	ENST00000222390.5:c.1168G>T	p.Asp390Tyr	p.D390Y	ENST00000222390	NM_000601.4	390	Gat/Tat	9/18	1	2	FACETS	0.753	0.65	0.863	1	0.969	1	SUBCLONAL	2	TRUE	1	0.307751118900883	2		398	233	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439728	140439728	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	85	759	0	ENST00000288602.6:c.2011C>T	p.Arg671Ter	p.R671*	ENST00000288602	NM_004333.4	671	Cga/Tga	17/18	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.307751118900883	2		759	400	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900066	151900066	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	137	853	2	ENST00000262189.6:c.4045C>T	p.Arg1349Ter	p.R1349*	ENST00000262189	NM_170606.2	1349	Cga/Tga	26/59	1	2	FACETS	0.859	0.786	0.935	1	0.989	1	CLONAL	2	TRUE	1	0.307751118900883	2		855	518	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902311	151902311	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	46	346	0	ENST00000262189.6:c.3842-1G>T		p.X1281_splice	ENST00000262189	NM_170606.2	1281			1	2	FACETS	1	0.909	1	1	0.976	1	CLONAL	2	TRUE	1	0.307751118900883	2		346	139	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370782	55370782	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	160	940	2	ENST00000297316.4:c.87del	p.Cys30AlafsTer7	p.C30Afs*7	ENST00000297316	NM_022454.3	28	ggC/gg	1/2	0.300564154263042	4	FACETS	0.764	0.7	0.83	0.509	0.467	0.554	SUBCLONAL	2	TRUE	1	0.307751118900883	4		942	890	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992721	68992721	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs764112302	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	89	817	8	ENST00000288368.4:c.1693del	p.Ser565ArgfsTer10	p.S565Rfs*10	ENST00000288368	NM_024870.2	562	cgT/cg	16/40	0.300564154263042	4	FACETS	1	0.949	1	0.374	0.332	0.419	CLONAL	1	TRUE	1	0.307751118900883	4		825	674	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741585	145741585	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	510	1339	1	ENST00000428558.2:c.918G>T	p.Gln306His	p.Q306H	ENST00000428558	NM_004260.3	306	caG/caT	5/22	0.300564154263042	4	FACETS	0.956	0.918	0.993	1	0.995	1	CLONAL	4	TRUE	1	0.307751118900883	4		1340	1134	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742056	145742056	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	443	1111	1	ENST00000428558.2:c.447del	p.Ser150ProfsTer30	p.S150Pfs*30	ENST00000428558	NM_004260.3	149	ccC/cc	5/22	0.300564154263042	4	FACETS	0.919	0.88	0.959	1	0.994	1	CLONAL	4	TRUE	1	0.307751118900883	4		1112	1024	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341713	8341713	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	153	953	0	ENST00000356435.5:c.4927G>T	p.Gly1643Ter	p.G1643*	ENST00000356435		1643	Gga/Tga	29/35	1	2	FACETS	0.919	0.846	0.995	1	0.991	1	CLONAL	2	TRUE	1	0.307751118900883	2		953	541	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484302	8484302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	188	922	0	ENST00000356435.5:c.3230C>A	p.Pro1077His	p.P1077H	ENST00000356435		1077	cCt/cAt	19/35	1	2	FACETS	0.867	0.803	0.932	1	0.992	1	CLONAL	2	TRUE	1	0.307751118900883	2		922	705	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570292	87570292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1463968979	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	112	866	0	ENST00000277120.3:c.2032G>A	p.Ala678Thr	p.A678T	ENST00000277120		678	Gcg/Acg	17/19	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.307751118900883	2		866	603	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209616	98209617	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761353734	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	118	796	0	ENST00000331920.6:c.3921dup	p.Arg1308GlnfsTer17	p.R1308Qfs*17	ENST00000331920	NM_000264.3	1307	-/C	23/24	1	2	FACETS	0.761	0.69	0.835	1	0.985	1	SUBCLONAL	2	TRUE	1	0.307751118900883	2		796	504	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231105	98231105	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	169	874	2	ENST00000331920.6:c.2178del	p.Cys727ValfsTer19	p.C727Vfs*19	ENST00000331920	NM_000264.3	726	ccC/cc	14/24	1	2	FACETS	0.836	0.771	0.903	1	0.991	1	CLONAL	2	TRUE	1	0.307751118900883	2		876	657	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249725	110249725	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	263	1192	0	ENST00000374672.4:c.950C>T	p.Pro317Leu	p.P317L	ENST00000374672	NM_004235.4	317	cCg/cTg	3/5	1	2	FACETS	0.986	0.926	1	1	0.995	1	CLONAL	2	TRUE	1	0.307751118900883	2		1192	867	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393615	139393615	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	263	1214	0	ENST00000277541.6:c.6031C>A	p.Leu2011Met	p.L2011M	ENST00000277541	NM_017617.3	2011	Ctg/Atg	32/34	1	2	FACETS	0.96	0.902	1	1	0.995	1	CLONAL	2	TRUE	1	0.307751118900883	2		1214	890	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139794895	139794895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758348510	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	163	715	1	ENST00000247668.2:c.289C>T	p.Arg97Cys	p.R97C	ENST00000247668	NM_021138.3	97	Cgc/Tgc	4/11	1	2	FACETS	0.99	0.915	1	1	0.992	1	CLONAL	2	TRUE	1	0.307751118900883	2		716	535	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20150320	20150320	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	44	466	0	ENST00000379607.5:c.317A>G	p.Tyr106Cys	p.Y106C	ENST00000379607	NM_001412.3	106	tAc/tGc	5/7	1	1	FACETS	0.834	0.704	0.977	0.834	0.704	0.977	CLONAL	1	TRUE	0	0.307751118900883	1		466	290	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913566	39913566	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	179	435	0	ENST00000378444.4:c.4762G>T	p.Gly1588Cys	p.G1588C	ENST00000378444	NM_001123385.1	1588	Ggt/Tgt	13/15	1	1	FACETS	1	0.943	1	1	0.995	1	CLONAL	3	TRUE	0	0.307751118900883	1		435	327	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44921935	44921935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	134	494	1	ENST00000377967.4:c.1469C>T	p.Ala490Val	p.A490V	ENST00000377967	NM_021140.2	490	gCa/gTa	15/29	1	1	FACETS	0.937	0.87	1	1	0.993	1	CLONAL	3	TRUE	0	0.307751118900883	1		495	262	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045958	47045958	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	280	629	0	ENST00000377604.3:c.2753T>C	p.Leu918Pro	p.L918P	ENST00000377604	NM_001204468.1	918	cTg/cCg	24/24	1	1	FACETS	1	0.989	1	1	0.997	1	CLONAL	3	TRUE	0	0.307751118900883	1		629	458	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650778	48650778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104894809	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	239	616	0	ENST00000376670.3:c.647G>A	p.Arg216Gln	p.R216Q	ENST00000376670	NM_002049.3	216	cGg/cAg	4/6	1	1	FACETS	1	0.974	1	1	0.996	1	CLONAL	3	TRUE	0	0.307751118900883	1		616	421	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100037	157100037	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1399325046	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	17	255	0	ENST00000346085.5:c.974G>C	p.Gly325Ala	p.G325A	ENST00000346085	NM_020732.3	325	gGa/gCa	1/20	1	2	FACETS	0.722	0.543	0.932	0.722	0.543	0.932	CLONAL	1	TRUE	1	0.307751118900883	2		255	153	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100031	157100031	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1387109269	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	19	280	0	ENST00000346085.5:c.968G>C	p.Gly323Ala	p.G323A	ENST00000346085	NM_020732.3	323	gGa/gCa	1/20	1	2	FACETS	0.714	0.545	0.91	0.714	0.545	0.91	CLONAL	1	TRUE	1	0.307751118900883	2		280	173	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279831	46279836	+	inframe_deletion	In_Frame_Del	DEL	CAGCAA	CAGCAA	-	rs764026511	NA	P-0020312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	64	637	1	ENST00000371998.3:c.3762_3767del	p.Gln1275_Gln1276del	p.Q1275_Q1276del	ENST00000371998		1253	CAGCAA/-	20/23	0.307751118900883	1	FACETS	0.668	0.579	0.764	0.668	0.579	0.764	SUBCLONAL	1	TRUE	0	0.307751118900883	1		638	527	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264586	1264586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs547377569	NA	P-0020313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	372	773	2	ENST00000310581.5:c.2776G>A	p.Gly926Ser	p.G926S	ENST00000310581	NM_198253.2	926	Ggc/Agc	11/16	0.488113564926432	3	FACETS	0.884	0.841	0.929	0.884	0.841	0.929	CLONAL	2	TRUE	1	0.488113564926432	3		775	1072	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243507	41243510	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	rs431825404	NA	P-0020313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	416	922	0	ENST00000357654.3:c.4038_4041del	p.Arg1347GlufsTer18	p.R1347Efs*18	ENST00000357654	NM_007294.3	1346	gaAAGA/ga	10/23	0.466165851609325	2	FACETS	0.901	0.862	0.94	0.901	0.862	0.94	CLONAL	2	TRUE	0	0.488113564926432	2		922	946	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662353	117662353	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	187	706	0	ENST00000368508.3:c.5024A>C	p.Asn1675Thr	p.N1675T	ENST00000368508	NM_002944.2	1675	aAt/aCt	30/43	0.488113564926432	4	FACETS	0.996	0.919	1	0.332	0.306	0.359	CLONAL	1	TRUE	1	0.488113564926432	4		706	1145	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001454	150001454	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	680	946	0	ENST00000253339.5:c.2150G>T	p.Gly717Val	p.G717V	ENST00000253339		717	gGt/gTt	4/7	0.488113564926432	3	FACETS	0.984	0.955	1			1	CLONAL	3	TRUE	NA	0.488113564926432	3		946	1174	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120580	2120580	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs45438400	NA	P-0020316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	113	994	0	ENST00000219476.3:c.1839+1G>A		p.X613_splice	ENST00000219476	NM_000548.3	613			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.292931822401348	2		994	614	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121865	2121866	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs397515050	NA	P-0020316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	96	927	1	ENST00000219476.3:c.2031dup	p.Ala678ArgfsTer25	p.A678Rfs*25	ENST00000219476	NM_000548.3	676	ggc/ggCc	19/42	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.292931822401348	2		928	526	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0020317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	40	352	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.788	0.654	0.938	0.788	0.654	0.938	CLONAL	1	TRUE	1	0.17	2		352	597	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178511	56178511	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	35	437	0	ENST00000399503.3:c.3484G>T	p.Glu1162Ter	p.E1162*	ENST00000399503	NM_005921.1	1162	Gaa/Taa	14/20	1	2	FACETS	1	0.829	1	1	0.829	1	CLONAL	1	TRUE	1	0.17	2		437	407	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177812	56177813	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0020317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	27	538	0	ENST00000399503.3:c.2789_2790del	p.Arg930ThrfsTer10	p.R930Tfs*10	ENST00000399503	NM_005921.1	929	GAg/g	14/20	1	2	FACETS	0.683	0.543	0.844	0.683	0.543	0.844	SUBCLONAL	1	TRUE	1	0.17	2		538	465	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845504	151845504	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	58	865	1	ENST00000262189.6:c.13508G>T	p.Cys4503Phe	p.C4503F	ENST00000262189	NM_170606.2	4503	tGc/tTc	52/59	1	2	FACETS	0.815	0.699	0.943	0.815	0.699	0.943	CLONAL	1	TRUE	1	0.17	2		866	837	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938464	44938464	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	77	821	2	ENST00000377967.4:c.3012G>T	p.Leu1004Phe	p.L1004F	ENST00000377967	NM_021140.2	1004	ttG/ttT	20/29	1	2	FACETS	0.981	0.86	1	0.981	0.86	1	CLONAL	1	TRUE	1	0.17	2		823	923	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750639	128750639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775522201	NA	P-0020318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	52	680	1	ENST00000377970.2:c.176C>T	p.Ala59Val	p.A59V	ENST00000377970	NM_002467.4	59	gCg/gTg	2/3	1	2	FACETS	0.971	0.825	1	0.971	0.825	1	CLONAL	1	TRUE	1	0.14	2		681	765	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331643	8331643	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	52	747	0	ENST00000356435.5:c.5473G>C	p.Gly1825Arg	p.G1825R	ENST00000356435		1825	Ggc/Cgc	33/35	1	2	FACETS	0.95	0.807	1	0.95	0.807	1	CLONAL	1	TRUE	1	0.14	2		747	782	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220873	36220873	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	18	272	0	ENST00000222270.7:c.4923C>A	p.Cys1641Ter	p.C1641*	ENST00000222270	NM_014727.1	1641	tgC/tgA	23/37	1	2	FACETS	0.872	0.656	1	0.872	0.656	1	CLONAL	1	TRUE	1	0.14	2		272	295	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0020320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	73	465	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.935	0.837	1	1	0.988	1	CLONAL	4	TRUE	1	0.227079382140611	2		465	172	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0020320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	474	532	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.227079382140611	6	FACETS	0.993	0.971	1			1	CLONAL	11	TRUE	NA	0.227079382140611	6		533	556	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570292	87570292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1463968979	NA	P-0020320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	214	866	0	ENST00000277120.3:c.2032G>A	p.Ala678Thr	p.A678T	ENST00000277120		678	Gcg/Acg	17/19	0.218994684921549	3	FACETS	1	0.973	1	1	0.995	1	CLONAL	4	TRUE	1	0.227079382140611	3		866	493	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849205	76849209	+	frameshift_variant	Frame_Shift_Del	DEL	AAGAG	AAGAG	-	novel	NA	P-0020320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	16	428	0	ENST00000373344.5:c.6067_6071del	p.Leu2023Ter	p.L2023*	ENST00000373344	NM_000489.3	2023	CTCTTt/t	26/35	0.209216895939089	2	FACETS	0.81	0.609	1			1	CLONAL	2	TRUE	NA	0.227079382140611	2		428	87	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855014	76855017	+	frameshift_variant	Frame_Shift_Del	DEL	CTAT	CTAT	-	novel	NA	P-0020320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	44	474	0	ENST00000373344.5:c.5819_5822del	p.Asp1940ValfsTer14	p.D1940Vfs*14	ENST00000373344	NM_000489.3	1940	gATAGt/gt	25/35	0.209216895939089	2	FACETS	0.971	0.834	1			1	CLONAL	3	TRUE	NA	0.227079382140611	2		474	133	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	65	122	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.785	0.692	0.882	1	0.977	1	SUBCLONAL	2	FALSE	1	0.405886336849804	2		122	204	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381559	81381559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777026877	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	10	382	1	ENST00000222390.5:c.502C>T	p.Arg168Trp	p.R168W	ENST00000222390	NM_000601.4	168	Cgg/Tgg	5/18	0.303000781603676	4	FACETS	0.352	0.238	0.494	0.176	0.119	0.247	SUBCLONAL	1	FALSE	2	0.405886336849804	4		383	197	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266845	18266845	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	67	812	0	ENST00000222254.8:c.156G>C	p.Gln52His	p.Q52H	ENST00000222254	NM_005027.3	52	caG/caC	2/16	0.161881771211393	2	FACETS	0.501	0.435	0.573	0.25	0.217	0.287	INDETERMINATE	1	FALSE	0	0.405886336849804	2		812	659	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69229702	69229702	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	39	505	0	ENST00000462284.1:c.778C>G	p.Leu260Val	p.L260V	ENST00000462284	NM_002392.5	260	Ctc/Gtc	9/11	0.405886336849804	3	FACETS	0.739	0.614	0.876	0.369	0.307	0.438	SUBCLONAL	1	FALSE	1	0.405886336849804	3		505	313	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1268701	1268701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748503447	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	37	855	1	ENST00000310581.5:c.2516C>T	p.Thr839Met	p.T839M	ENST00000310581	NM_198253.2	839	aCg/aTg	9/16	1	2	FACETS	0.402	0.332	0.482	0.402	0.332	0.482	SUBCLONAL	1	FALSE	1	0.405886336849804	2		856	453	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985525	2985525	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	56	744	0	ENST00000396946.4:c.286G>C	p.Glu96Gln	p.E96Q	ENST00000396946	NM_032415.4	96	Gaa/Caa	4/25	0.303000781603676	4	FACETS	1	0.951	1	0.62	0.534	0.712	CLONAL	1	FALSE	2	0.405886336849804	4		744	313	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841276	15841276	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756515856	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	14	341	2	ENST00000307771.7:c.1360C>T	p.Arg454Trp	p.R454W	ENST00000307771	NM_005089.3	454	Cgg/Tgg	11/11	1	1	FACETS	0.241	0.174	0.322	0.241	0.174	0.322	SUBCLONAL	1	FALSE	0	0.405886336849804	1		343	228	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885731	23885731	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	87	793	2	ENST00000374561.5:c.187C>T	p.Gln63Ter	p.Q63*	ENST00000374561	NM_002167.4	63	Cag/Tag	1/3	0.405455048516132	3	FACETS	0.781	0.692	0.877	0.391	0.346	0.439	SUBCLONAL	1	FALSE	1	0.405886336849804	3		795	660	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797180	45797180	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	74	852	3	ENST00000450313.1:c.1235C>A	p.Ser412Ter	p.S412*	ENST00000450313	NM_012222.2	412	tCa/tAa	13/16	0.218258785963303	3	FACETS	1	0.894	1	0.339	0.298	0.383	INDETERMINATE	1	FALSE	0	0.405886336849804	3		855	431	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552856	226552856	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	37	556	0	ENST00000366794.5:c.2506-1G>C		p.X836_splice	ENST00000366794	NM_001618.3	836			1	2	FACETS	0.912	0.759	1	0.912	0.759	1	CLONAL	1	FALSE	1	0.405886336849804	2		556	200	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63810739	63810739	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201704836	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	57	614	0	ENST00000279873.7:c.826G>A	p.Asp276Asn	p.D276N	ENST00000279873	NM_032199.2	276	Gat/Aat	5/10	0.405886336849804	6	FACETS	1	0.864	1			1	CLONAL	1	FALSE	NA	0.405886336849804	6		614	506	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63810754	63810754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	44	593	0	ENST00000279873.7:c.841G>A	p.Ala281Thr	p.A281T	ENST00000279873	NM_032199.2	281	Gcc/Acc	5/10	0.405886336849804	6	FACETS	0.77	0.646	0.908			1	CLONAL	1	FALSE	NA	0.405886336849804	6		593	510	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	401975	401975	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	39	536	0	ENST00000399788.2:c.4816G>C	p.Glu1606Gln	p.E1606Q	ENST00000399788	NM_001042603.1	1606	Gag/Cag	27/28	NA	2	FACETS	0.54	0.448	0.641			1	INDETERMINATE	1	FALSE	NA	0.405886336849804	2		536	356	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438048	438048	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372588426	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	34	598	0	ENST00000399788.2:c.1921C>T	p.Leu641Phe	p.L641F	ENST00000399788	NM_001042603.1	641	Ctc/Ttc	14/28	NA	2	FACETS	0.549	0.45	0.66			1	INDETERMINATE	1	FALSE	NA	0.405886336849804	2		598	305	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992172	11992172	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	75	645	0	ENST00000396373.4:c.262G>C	p.Glu88Gln	p.E88Q	ENST00000396373	NM_001987.4	88	Gaa/Caa	3/8	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.405886336849804	NA		645	437	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144796	58144796	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1165503595	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	45	657	0	ENST00000257904.6:c.432G>C	p.Glu144Asp	p.E144D	ENST00000257904	NM_000075.3	144	gaG/gaC	4/8	0.405886336849804	3	FACETS	0.444	0.372	0.523	0.222	0.186	0.262	SUBCLONAL	1	FALSE	1	0.405886336849804	3		657	601	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145470	58145470	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	34	532	0	ENST00000257904.6:c.31G>T	p.Glu11Ter	p.E11*	ENST00000257904	NM_000075.3	11	Gaa/Taa	2/8	0.405886336849804	3	FACETS	0.425	0.347	0.513	0.213	0.173	0.257	SUBCLONAL	1	FALSE	1	0.405886336849804	3		532	474	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906744	32906744	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876658625	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	32	740	0	ENST00000380152.3:c.1129G>C	p.Glu377Gln	p.E377Q	ENST00000380152		377	Gag/Cag	10/27	1	2	FACETS	0.555	0.452	0.671	0.555	0.452	0.671	SUBCLONAL	1	FALSE	1	0.405886336849804	2		740	284	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907300	32907300	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	27	631	0	ENST00000380152.3:c.1685G>C	p.Ser562Thr	p.S562T	ENST00000380152		562	aGc/aCc	10/27	1	2	FACETS	0.569	0.454	0.698	0.569	0.454	0.698	SUBCLONAL	1	FALSE	1	0.405886336849804	2		631	234	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925165	81925165	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs746915998	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	44	689	0	ENST00000359376.3:c.956C>G	p.Ser319Cys	p.S319C	ENST00000359376	NM_002661.3	319	tCt/tGt	11/33	0.405455048516132	3	FACETS	0.701	0.589	0.824	0.351	0.294	0.412	SUBCLONAL	1	FALSE	1	0.405886336849804	3		689	372	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217458	7217458	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	65	641	2	ENST00000380728.2:c.338C>A	p.Ser113Ter	p.S113*	ENST00000380728		113	tCa/tAa	5/11	0.302646107415235	1	FACETS	0.64	0.557	0.729	0.64	0.557	0.729	SUBCLONAL	1	FALSE	0	0.405886336849804	1		643	399	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687129	37687129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	22	649	1	ENST00000447079.4:c.4033G>A	p.Glu1345Lys	p.E1345K	ENST00000447079	NM_015083.1	1345	Gaa/Aaa	14/14	0.405886336849804	61	FACETS	1	0.793	1			1	CLONAL	4	FALSE	NA	0.405886336849804	61		650	343	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221069	5221069	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	36	745	0	ENST00000357368.4:c.3397G>C	p.Asp1133His	p.D1133H	ENST00000357368	NM_002850.3	1133	Gat/Cat	20/38	0.161881771211393	2	FACETS	0.514	0.423	0.615	0.257	0.211	0.308	INDETERMINATE	1	FALSE	0	0.405886336849804	2		745	345	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942190	17942190	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	31	617	2	ENST00000458235.1:c.2825C>A	p.Ser942Tyr	p.S942Y	ENST00000458235	NM_000215.3	942	tCc/tAc	21/24	0.161881771211393	2	FACETS	0.466	0.377	0.566	0.233	0.188	0.283	INDETERMINATE	1	FALSE	0	0.405886336849804	2		619	328	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791367	42791367	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	102	866	0	ENST00000575354.2:c.427G>C	p.Glu143Gln	p.E143Q	ENST00000575354	NM_015125.3	143	Gag/Cag	3/20	0.161881771211393	2	FACETS	1	0.92	1	0.514	0.461	0.569	INDETERMINATE	1	FALSE	0	0.405886336849804	2		866	489	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794690	42794690	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	67	773	1	ENST00000575354.2:c.1770C>A	p.Phe590Leu	p.F590L	ENST00000575354	NM_015125.3	590	ttC/ttA	10/20	0.161881771211393	2	FACETS	0.605	0.526	0.69	0.302	0.263	0.345	INDETERMINATE	1	FALSE	0	0.405886336849804	2		774	546	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609216	46609216	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs773061058	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	166	658	0	ENST00000263734.3:c.2275A>G	p.Asn759Asp	p.N759D	ENST00000263734	NM_001430.4	759	Aat/Gat	14/16	0.364289397019156	2	FACETS	0.993	0.923	1	0.993	0.923	1	CLONAL	2	FALSE	0	0.405886336849804	2		658	412	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657035	45657035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	23	607	0	ENST00000407780.3:c.121G>A	p.Glu41Lys	p.E41K	ENST00000407780	NM_001283052.1	41	Gaa/Aaa	3/7	1	2	FACETS	0.283	0.22	0.356	0.283	0.22	0.356	SUBCLONAL	1	FALSE	1	0.405886336849804	2		607	400	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428497	72428497	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	20	661	0	ENST00000477973.2:c.507G>C	p.Lys169Asn	p.K169N	ENST00000477973	NM_012234.5	169	aaG/aaC	2/4	0.161881771211393	2	FACETS	0.425	0.325	0.54	0.212	0.162	0.27	INDETERMINATE	1	FALSE	0	0.405886336849804	2		661	232	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589169	67589169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766524768	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	30	383	0	ENST00000274335.5:c.1157G>A	p.Arg386Gln	p.R386Q	ENST00000274335		386	cGa/cAa	9/15	1	2	FACETS	0.803	0.653	0.97	0.803	0.653	0.97	CLONAL	1	FALSE	1	0.405886336849804	2		383	184	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80109449	80109449	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	27	626	0	ENST00000265081.6:c.2702G>A	p.Gly901Glu	p.G901E	ENST00000265081	NM_002439.4	901	gGa/gAa	20/24	1	2	FACETS	0.652	0.522	0.798	0.652	0.522	0.798	SUBCLONAL	1	FALSE	1	0.405886336849804	2		626	204	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056296	180056296	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	60	866	0	ENST00000261937.6:c.948C>G	p.Ile316Met	p.I316M	ENST00000261937	NM_182925.4	316	atC/atG	7/30	1	2	FACETS	0.921	0.799	1	0.921	0.799	1	CLONAL	1	FALSE	1	0.405886336849804	2		866	321	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099925	157099925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1409610710	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	51	737	1	ENST00000346085.5:c.862G>A	p.Glu288Lys	p.E288K	ENST00000346085	NM_020732.3	288	Gaa/Aaa	1/20	1	2	FACETS	0.398	0.337	0.464	0.398	0.337	0.464	SUBCLONAL	1	FALSE	1	0.405886336849804	2		738	632	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151855967	151855967	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140246095	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	27	594	0	ENST00000262189.6:c.11651C>T	p.Thr3884Met	p.T3884M	ENST00000262189	NM_170606.2	3884	aCg/aTg	44/59	0.303000781603676	4	FACETS	0.552	0.439	0.68	0.276	0.219	0.34	SUBCLONAL	1	FALSE	2	0.405886336849804	4		594	339	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891528	151891528	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	32	491	0	ENST00000262189.6:c.4504G>A	p.Asp1502Asn	p.D1502N	ENST00000262189	NM_170606.2	1502	Gat/Aat	29/59	0.303000781603676	4	FACETS	0.905	0.738	1	0.452	0.369	0.545	CLONAL	1	FALSE	2	0.405886336849804	4		491	245	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346080	152346080	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1215678098	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	33	668	0	ENST00000359321.1:c.490G>C	p.Glu164Gln	p.E164Q	ENST00000359321	NM_005431.1	164	Gaa/Caa	3/3	0.303000781603676	4	FACETS	0.847	0.693	1	0.423	0.346	0.51	CLONAL	1	FALSE	2	0.405886336849804	4		668	270	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968159	68968159	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	20	697	0	ENST00000288368.4:c.1188C>G	p.Ile396Met	p.I396M	ENST00000288368	NM_024870.2	396	atC/atG	10/40	0.405886336849804	3	FACETS	0.368	0.281	0.47	0.184	0.14	0.235	SUBCLONAL	1	FALSE	1	0.405886336849804	3		697	322	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741730	145741730	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	103	839	0	ENST00000428558.2:c.773G>C	p.Gly258Ala	p.G258A	ENST00000428558	NM_004260.3	258	gGa/gCa	5/22	0.405886336849804	3	FACETS	0.978	0.877	1	0.489	0.438	0.543	CLONAL	1	FALSE	1	0.405886336849804	3		839	624	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342605	87342605	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	99	610	0	ENST00000277120.3:c.890C>G	p.Ser297Ter	p.S297*	ENST00000277120		297	tCa/tGa	9/19	0.405886336849804	2	FACETS	0.942	0.855	1	0.942	0.855	1	CLONAL	2	FALSE	0	0.405886336849804	2		610	259	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76931791	76931791	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	17	322	0	ENST00000373344.5:c.3739G>C	p.Asp1247His	p.D1247H	ENST00000373344	NM_000489.3	1247	Gat/Cat	10/35	1	1	FACETS	0.42	0.315	0.543	0.42	0.315	0.543	SUBCLONAL	1	FALSE	0	0.405886336849804	1		322	159	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938292	76938292	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0020321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	14	343	0	ENST00000373344.5:c.2456C>G	p.Ser819Ter	p.S819*	ENST00000373344	NM_000489.3	819	tCa/tGa	9/35	1	1	FACETS	0.591	0.433	0.776	0.591	0.433	0.776	SUBCLONAL	1	FALSE	0	0.405886336849804	1		343	93	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344107	118344107	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs727503777	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	401	513	1	ENST00000534358.1:c.2233C>T	p.Arg745Ter	p.R745*	ENST00000534358	NM_005933.3	745	Cga/Tga	3/36	1	2	FACETS	0.995	0.952	1	0.995	0.952	1	CLONAL	1	TRUE	1	0.936988270341775	2		514	860	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	384	654	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	1	2	FACETS	0.855	0.815	0.895	0.855	0.815	0.895	CLONAL	1	TRUE	1	0.936988270341775	2		654	959	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	686	922	1	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.936988270341775	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.936988270341775	1		923	776	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486101	8486101	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	409	610	1	ENST00000356435.5:c.2716G>A	p.Glu906Lys	p.E906K	ENST00000356435		906	Gag/Aag	17/35	1	2	FACETS	0.914	0.874	0.955	0.914	0.874	0.955	CLONAL	1	TRUE	1	0.936988270341775	2		611	955	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881512	48881512	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	268	464	0	ENST00000267163.4:c.234G>A	p.Trp78Ter	p.W78*	ENST00000267163	NM_000321.2	78	tgG/tgA	2/27	1	2	FACETS	0.895	0.846	0.945	0.895	0.846	0.945	CLONAL	1	TRUE	1	0.936988270341775	2		464	639	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814253	76814253	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	334	643	0	ENST00000373344.5:c.6391C>T	p.Arg2131Ter	p.R2131*	ENST00000373344	NM_000489.3	2131	Cga/Tga	29/35	0.936988270341775	1	FACETS	0.967	0.941	0.99	0.967	0.941	0.99	CLONAL	1	TRUE	0	0.936988270341775	1		643	392	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972008	55972008	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	473	550	0	ENST00000263923.4:c.1636C>T	p.His546Tyr	p.H546Y	ENST00000263923	NM_002253.2	546	Cac/Tac	12/30	0.483685869338544	4	FACETS	1	0.995	1	0.431	0.411	0.451	INDETERMINATE	1	TRUE	1	0.936988270341775	4		550	1514	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508059	106508059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142380460	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	236	291	0	ENST00000359195.3:c.53G>A	p.Arg18Gln	p.R18Q	ENST00000359195	NM_002649.2	18	cGa/cAa	2/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.936988270341775	2		291	485	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549116	21549116	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	508	609	1	ENST00000382592.4:c.3160C>T	p.Arg1054Ter	p.R1054*	ENST00000382592	NM_014572.2	1054	Cga/Tga	8/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.936988270341775	2		610	1037	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503099	125503099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140276570	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	342	493	0	ENST00000428830.2:c.466C>T	p.Arg156Trp	p.R156W	ENST00000428830	NM_001114121.2	156	Cgg/Tgg	6/14	1	2	FACETS	0.967	0.921	1	0.967	0.921	1	CLONAL	1	TRUE	1	0.936988270341775	2		493	755	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460582	149460582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	512	706	0	ENST00000286301.3:c.55G>A	p.Gly19Arg	p.G19R	ENST00000286301	NM_005211.3	19	Gga/Aga	3/22	1	2	FACETS	0.841	0.807	0.876	0.841	0.807	0.876	CLONAL	1	TRUE	1	0.936988270341775	2		706	1299	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138856	64138857	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	754	777	0	ENST00000334205.4:c.2223_2224delinsTT	p.Arg742Cys	p.R742C	ENST00000334205	NM_003942.2	741	tcCCgc/tcTTgc	17/17	1	2	FACETS	0.984	0.953	1	0.984	0.953	1	CLONAL	1	TRUE	1	0.936988270341775	2		777	1635	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347819	347819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746435850	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	921	953	3	ENST00000262320.3:c.1687G>A	p.Ala563Thr	p.A563T	ENST00000262320	NM_003502.3	563	Gcc/Acc	6/11	0.936988270341775	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.936988270341775	1		956	1015	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166772	32166772	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753820483	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	781	833	0	ENST00000375023.3:c.4466G>A	p.Arg1489Gln	p.R1489Q	ENST00000375023	NM_004557.3	1489	cGa/cAa	24/30	0.936988270341775	1	FACETS	0.905	0.887	0.922	0.905	0.887	0.922	CLONAL	1	TRUE	0	0.936988270341775	1		833	979	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	140	946	0	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	0.936988270341775	1	FACETS	0.143	0.13	0.158	0.143	0.13	0.158	SUBCLONAL	1	TRUE	0	0.936988270341775	1		946	1108	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745609	162745609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	550	681	0	ENST00000367921.3:c.2024C>T	p.Ser675Phe	p.S675F	ENST00000367921	NM_006182.2	675	tCc/tTc	15/18	1	2	FACETS	0.921	0.886	0.956	0.921	0.886	0.956	CLONAL	1	TRUE	1	0.936988270341775	2		681	1275	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050791	5050791	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	433	711	1	ENST00000381652.3:c.574G>T	p.Glu192Ter	p.E192*	ENST00000381652	NM_004972.3	192	Gaa/Taa	6/25	1	2	FACETS	0.976	0.935	1	0.976	0.935	1	CLONAL	1	TRUE	1	0.936988270341775	2		712	947	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780953	9780953	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1215767354	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	576	694	0	ENST00000377346.4:c.1675G>A	p.Glu559Lys	p.E559K	ENST00000377346	NM_005026.3	559	Gag/Aag	13/24	1	2	FACETS	0.993	0.957	1	0.993	0.957	1	CLONAL	1	TRUE	1	0.936988270341775	2		694	1238	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156848969	156848969	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	675	821	1	ENST00000524377.1:c.1861C>T	p.Pro621Ser	p.P621S	ENST00000524377	NM_002529.3	621	Ccc/Tcc	15/17	1	2	FACETS	0.911	0.879	0.943	0.911	0.879	0.943	CLONAL	1	TRUE	1	0.936988270341775	2		822	1582	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949095	71949098	+	frameshift_variant	Frame_Shift_Del	DEL	CTGC	CTGC	TGT	novel	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	590	685	3	ENST00000298229.2:c.3562_3565delinsTGT	p.Leu1188CysfsTer14	p.L1188Cfs*14	ENST00000298229	NM_001567.3	1188	CTGCag/TGTag	27/28	1	2	FACETS	0.978	0.942	1	0.978	0.942	1	CLONAL	1	TRUE	1	0.936988270341775	2		688	1288	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949098	71949098	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	590	684	3	ENST00000298229.2:c.3565C>T	p.Gln1189Ter	p.Q1189*	ENST00000298229	NM_001567.3	1189	Cag/Tag	27/28	1	2	FACETS	0.996	0.96	1	0.996	0.96	1	CLONAL	1	TRUE	1	0.936988270341775	2		687	1265	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949368	71949368	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144762578	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	784	725	0	ENST00000298229.2:c.3748C>T	p.Leu1250Phe	p.L1250F	ENST00000298229	NM_001567.3	1250	Ctt/Ttt	28/28	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.936988270341775	2		725	1627	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206910	102206910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776938400	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	298	525	0	ENST00000263464.3:c.1538C>T	p.Ser513Phe	p.S513F	ENST00000263464	NM_001165.4	513	tCt/tTt	7/9	1	2	FACETS	0.919	0.872	0.967	0.919	0.872	0.967	CLONAL	1	TRUE	1	0.936988270341775	2		525	692	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446117	49446117	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	880	880	0	ENST00000301067.7:c.1349C>T	p.Ser450Phe	p.S450F	ENST00000301067	NM_003482.3	450	tCc/tTc	10/54	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.936988270341775	2		880	1843	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954195	48954196	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	190	449	0	ENST00000267163.4:c.1398dup	p.Arg467ThrfsTer8	p.R467Tfs*8	ENST00000267163	NM_000321.2	466	gaa/gAaa	15/27	1	2	FACETS	0.735	0.684	0.787	0.735	0.684	0.787	SUBCLONAL	1	TRUE	1	0.936988270341775	2		449	552	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675049	40675049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764271025	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	634	742	0	ENST00000249776.8:c.13G>A	p.Glu5Lys	p.E5K	ENST00000249776	NM_033286.3	5	Gaa/Aaa	1/9	1	2	FACETS	0.964	0.93	0.998	0.964	0.93	0.998	CLONAL	1	TRUE	1	0.936988270341775	2		742	1404	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646944	23646944	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	480	823	0	ENST00000261584.4:c.923C>T	p.Ala308Val	p.A308V	ENST00000261584	NM_024675.3	308	gCt/gTt	4/13	0.936988270341775	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.936988270341775	1		823	539	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351694	89351694	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373149812	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	867	849	1	ENST00000301030.4:c.1256C>T	p.Thr419Ile	p.T419I	ENST00000301030	NM_001256183.1	419	aCc/aTc	9/13	0.936988270341775	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.936988270341775	1		850	959	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78923245	78923245	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1745	850	705	0	ENST00000306801.3:c.3268G>A	p.Asp1090Asn	p.D1090N	ENST00000306801	NM_020761.2	1090	Gat/Aat	28/34	0.936988270341775	5	FACETS	0.841	0.813	0.869	0.561	0.542	0.58	CLONAL	2	TRUE	2	0.936988270341775	5		705	2595	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56413008	56413029	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTGCAAAAATTAAAGGTTACT	ACTGCAAAAATTAAAGGTTACT	-	novel	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	228	605	0	ENST00000348428.3:c.2024_2037+8del		p.X675_splice	ENST00000348428	NM_006785.3	675		16/17	0.933246093690753	2	FACETS	0.759	0.712	0.808	0.38	0.356	0.404	SUBCLONAL	1	TRUE	0	0.936988270341775	2		605	641	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602341	10602342	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1888	716	904	3	ENST00000171111.5:c.1236_1237delinsTT	p.Arg413Cys	p.R413C	ENST00000171111	NM_203500.1	412	ccCCgt/ccTTgt	3/6	0.705009834706884	3	FACETS	0.862	0.829	0.895			1	CLONAL	1	TRUE	NA	0.936988270341775	3		907	2604	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290093	15290093	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	631	788	0	ENST00000263388.2:c.3461G>A	p.Gly1154Glu	p.G1154E	ENST00000263388	NM_000435.2	1154	gGg/gAg	22/33	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.936988270341775	2		788	1259	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366215	15366215	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	723	911	3	ENST00000263377.2:c.1940C>T	p.Ser647Phe	p.S647F	ENST00000263377	NM_058243.2	647	tCc/tTc	10/20	1	2	FACETS	0.986	0.954	1	0.986	0.954	1	CLONAL	1	TRUE	1	0.936988270341775	2		914	1565	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765639	41765639	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	1263	913	0	ENST00000301178.4:c.2515G>A	p.Gly839Arg	p.G839R	ENST00000301178	NM_021913.4	839	Gga/Aga	20/20	0.806574928631285	3	FACETS	0.957	0.936	0.977	0.957	0.936	0.977	CLONAL	2	TRUE	1	0.936988270341775	3		913	2069	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906336	50906336	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	641	798	0	ENST00000440232.2:c.997C>T	p.Pro333Ser	p.P333S	ENST00000440232	NM_002691.3	333	Cct/Tct	9/27	0.936988270341775	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.936988270341775	1		798	724	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39216446	39216446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	287	537	0	ENST00000402219.2:c.3356C>T	p.Thr1119Ile	p.T1119I	ENST00000402219	NM_005633.3	1119	aCc/aTc	21/23	1	2	FACETS	0.809	0.765	0.854	0.809	0.765	0.854	CLONAL	1	TRUE	1	0.936988270341775	2		537	757	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248401	212248401	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1365124530	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	331	398	0	ENST00000342788.4:c.3866C>T	p.Ser1289Phe	p.S1289F	ENST00000342788	NM_005235.2	1289	tCc/tTc	28/28	1	2	FACETS	0.99	0.942	1	0.99	0.942	1	CLONAL	1	TRUE	1	0.936988270341775	2		398	714	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546734	9546734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	317	387	0	ENST00000353224.5:c.1288G>A	p.Glu430Lys	p.E430K	ENST00000353224	NM_177990.2	430	Gaa/Aaa	5/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.936988270341775	2		387	629	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458651	12458651	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	320	497	0	ENST00000287820.6:c.1268G>A	p.Gly423Glu	p.G423E	ENST00000287820	NM_015869.4	423	gGa/gAa	6/7	1	2	FACETS	0.993	0.945	1	0.993	0.945	1	CLONAL	1	TRUE	1	0.936988270341775	2		497	688	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890216	72890216	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1313298181	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	512	686	0	ENST00000325599.8:c.466G>A	p.Gly156Arg	p.G156R	ENST00000325599	NM_018130.2	156	Gga/Aga	4/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.936988270341775	2		686	1060	SUCCESS
ATR	545	MSKCC	GRCh37	3	142255018	142255018	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	230	419	0	ENST00000350721.4:c.3751G>A	p.Glu1251Lys	p.E1251K	ENST00000350721	NM_001184.3	1251	Gaa/Aaa	20/47	1	2	FACETS	0.921	0.867	0.976	0.921	0.867	0.976	CLONAL	1	TRUE	1	0.936988270341775	2		419	533	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066599	94066599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	506	651	0	ENST00000369303.4:c.1160G>A	p.Gly387Glu	p.G387E	ENST00000369303	NM_004440.3	387	gGa/gAa	5/17	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.936988270341775	2		651	1051	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547190	106547190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	239	335	0	ENST00000369096.4:c.427G>A	p.Glu143Lys	p.E143K	ENST00000369096	NM_001198.3	143	Gag/Aag	4/7	0.936988270341775	1	FACETS	0.986	0.957	1	0.986	0.957	1	CLONAL	1	TRUE	0	0.936988270341775	1		335	275	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265613	152265613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	453	528	0	ENST00000206249.3:c.1066C>T	p.His356Tyr	p.H356Y	ENST00000206249	NM_000125.3	356	Cac/Tac	4/8	0.936988270341775	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.936988270341775	1		528	501	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954904	2954904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	776	759	0	ENST00000396946.4:c.2806G>A	p.Asp936Asn	p.D936N	ENST00000396946	NM_032415.4	936	Gac/Aac	21/25	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.936988270341775	2		759	1645	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945108	151945108	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1328148849	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	76	583	0	ENST00000262189.6:c.2411T>C	p.Leu804Pro	p.L804P	ENST00000262189	NM_170606.2	804	cTt/cCt	14/59	0.936988270341775	1	FACETS	0.117	0.102	0.133	0.117	0.102	0.133	SUBCLONAL	1	TRUE	0	0.936988270341775	1		583	737	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370862	55370862	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs893686270	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	665	760	2	ENST00000297316.4:c.164C>T	p.Pro55Leu	p.P55L	ENST00000297316	NM_022454.3	55	cCg/cTg	1/2	0.936988270341775	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.936988270341775	1		762	742	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005901	69005901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	451	724	0	ENST00000288368.4:c.2312C>T	p.Ser771Phe	p.S771F	ENST00000288368	NM_024870.2	771	tCt/tTt	21/40	0.936988270341775	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.936988270341775	1		724	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0020323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	425	581	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.295842609836704	5	FACETS	1	0.992	1			1	INDETERMINATE	4	TRUE	NA	0.638738609449516	5		581	606	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434682	110434682	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	162	1076	0	ENST00000375856.3:c.3719G>C	p.Arg1240Pro	p.R1240P	ENST00000375856	NM_003749.2	1240	cGc/cCc	1/2	0.637054344345915	1	FACETS	0.816	0.757	0.876	0.816	0.757	0.876	CLONAL	1	TRUE	0	0.638738609449516	1		1076	423	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618547	37618547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	104	819	0	ENST00000447079.4:c.223G>A	p.Asp75Asn	p.D75N	ENST00000447079	NM_015083.1	75	Gat/Aat	1/14	0.610289601357155	2	FACETS	0.646	0.581	0.715	0.323	0.29	0.358	SUBCLONAL	1	TRUE	0	0.638738609449516	2		819	504	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440919	56440919	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	656	958	0	ENST00000407977.2:c.418G>C	p.Asp140His	p.D140H	ENST00000407977		140	Gac/Cac	4/10	0.638738609449516	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	0	0.638738609449516	3		958	888	SUCCESS
YES1	7525	MSKCC	GRCh37	18	742923	742923	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0020323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	48	624	0	ENST00000314574.4:c.1055C>G	p.Ser352Ter	p.S352*	ENST00000314574	NM_005433.3	352	tCa/tGa	8/12	0.493484816225074	4	FACETS	1	0.871	1	0.511	0.436	0.592	CLONAL	1	TRUE	2	0.638738609449516	4		624	241	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436369	52436369	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	184	960	1	ENST00000460680.1:c.2125C>A	p.Leu709Ile	p.L709I	ENST00000460680	NM_004656.3	709	Ctc/Atc	17/17	0.627386158394981	2	FACETS	0.981	0.911	1	0.491	0.455	0.527	CLONAL	1	TRUE	0	0.638738609449516	2		961	587	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557629	95557629	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	95	783	0	ENST00000393063.1:c.5438A>G	p.Glu1813Gly	p.E1813G	ENST00000393063	NM_030621.3	1813	gAg/gGg	26/28	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		783	839	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582890	95582890	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	113	564	1	ENST00000393063.1:c.1652del	p.Gly551GlufsTer11	p.G551Efs*11	ENST00000393063	NM_030621.3	551	gGa/ga	11/28	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		565	611	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372010	55372010	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	92	672	0	ENST00000297316.4:c.700C>G	p.Pro234Ala	p.P234A	ENST00000297316	NM_022454.3	234	Ccg/Gcg	2/2	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		672	669	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579357	7579363	+	frameshift_variant	Frame_Shift_Del	DEL	ACGGAAA	ACGGAAA	TTT	novel	NA	P-0020327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	236	769	5	ENST00000269305.4:c.324_330delinsAAA	p.Phe109AsnfsTer13	p.F109Nfs*13	ENST00000269305	NM_001126112.2	108	ggTTTCCGT/ggAAA	4/11	0.220860160535582	3	FACETS	0.852	0.797	0.907	0.852	0.797	0.907	CLONAL	3	TRUE	0	0.271032038277531	3		774	774	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555775	21555776	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	86	837	0	ENST00000382592.4:c.2494dup	p.Arg832LysfsTer13	p.R832Kfs*13	ENST00000382592	NM_014572.2	832	aga/aAga	6/8	0.245707333870386	1	FACETS	0.725	0.64	0.816	0.725	0.64	0.816	SUBCLONAL	1	TRUE	0	0.245707333870386	1		837	847	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125859	47125859	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	59	335	0	ENST00000409792.3:c.5411T>C	p.Leu1804Ser	p.L1804S	ENST00000409792	NM_014159.6	1804	tTg/tCg	12/21	0.245707333870386	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.245707333870386	1		335	391	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436823	52436824	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	90	929	0	ENST00000460680.1:c.1954dup	p.Glu652GlyfsTer12	p.E652Gfs*12	ENST00000460680	NM_004656.3	652	gag/gGag	15/17	0.245707333870386	1	FACETS	0.713	0.632	0.801	0.713	0.632	0.801	SUBCLONAL	1	TRUE	0	0.245707333870386	1		929	901	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	271	424	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.550665452759065	4	FACETS	0.944	0.896	0.992	0.944	0.896	0.992	CLONAL	3	TRUE	1	0.550665452759065	4		424	539	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0020329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	400	644	1	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.526028137554446	3	FACETS	0.973	0.937	1	0.973	0.937	1	CLONAL	3	TRUE	0	0.550665452759065	3		645	635	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998256	100998256	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	140	349	0	ENST00000325455.5:c.1546G>A	p.Gly516Ser	p.G516S	ENST00000325455	NM_001202474.3	516	Ggc/Agc	1/8	0.550665452759065	3	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	1	0.550665452759065	3		349	321	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	179	554	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	0.386521705553161	2		554	662	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	286	752	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.386521705553161	2		755	992	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427721	72427721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1382885623	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	222	604	0	ENST00000477973.2:c.769G>A	p.Val257Ile	p.V257I	ENST00000477973	NM_012234.5	257	Gtc/Atc	4/4	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.386521705553161	2		604	843	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375194	31375194	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	124	826	2	ENST00000328111.2:c.596del	p.Gly199AlafsTer27	p.G199Afs*27	ENST00000328111	NM_006892.3	197	caG/ca	6/23	1	2	FACETS	0.541	0.488	0.597	0.541	0.488	0.597	SUBCLONAL	1	TRUE	1	0.386521705553161	2		828	1186	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821890	72821890	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	88	506	0	ENST00000268489.5:c.10285del	p.Arg3429ValfsTer56	p.R3429Vfs*56	ENST00000268489	NM_006885.3	3429	Cgt/gt	10/10	1	2	FACETS	0.676	0.599	0.758	0.676	0.599	0.758	SUBCLONAL	1	TRUE	1	0.386521705553161	2		506	674	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	219	673	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.386521705553161	2		673	859	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	335	734	0	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	0.876	0.83	0.923	1	0.996	1	CLONAL	2	TRUE	1	0.386521705553161	2		734	989	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	323	910	5	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	0.386521705553161	2		915	1171	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	174	558	3	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.721	0.662	0.782	0.721	0.662	0.782	SUBCLONAL	1	TRUE	1	0.386521705553161	2		561	1249	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954022	32954023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs397507419	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	158	710	8	ENST00000380152.3:c.9097dup	p.Thr3033AsnfsTer11	p.T3033Nfs*11	ENST00000380152		3030	aca/acAa	23/27	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.386521705553161	2		718	723	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	83	272	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.784	0.7	0.87	1	0.981	1	SUBCLONAL	2	TRUE	1	0.386521705553161	2		272	274	SUCCESS
APC	324	MSKCC	GRCh37	5	112177787	112177787	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764527706	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	105	486	0	ENST00000257430.4:c.6496C>T	p.Arg2166Ter	p.R2166*	ENST00000257430	NM_000038.5	2166	Cga/Tga	16/16	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.386521705553161	2		486	523	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332337	70332337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761821309	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	250	696	2	ENST00000373644.4:c.242G>A	p.Arg81His	p.R81H	ENST00000373644	NM_030625.2	81	cGc/cAc	2/12	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.386521705553161	2		698	952	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023559	27023560	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	88	787	1	ENST00000324856.7:c.671dup	p.Pro225AlafsTer175	p.P225Afs*175	ENST00000324856	NM_006015.4	222	tac/taCc	1/20	1	2	FACETS	0.45	0.397	0.506	0.45	0.397	0.506	SUBCLONAL	1	TRUE	1	0.386521705553161	2		788	1012	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023327	27023327	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	66	367	0	ENST00000324856.7:c.437del	p.Pro146GlnfsTer86	p.P146Qfs*86	ENST00000324856	NM_006015.4	145	Ccc/cc	1/20	1	2	FACETS	0.691	0.601	0.789	0.691	0.601	0.789	SUBCLONAL	1	TRUE	1	0.386521705553161	2		367	494	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572252	41572254	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	89	709	0	ENST00000263253.7:c.4785_4787del	p.Phe1596del	p.F1596del	ENST00000263253	NM_001429.3	1594	gTCTtc/gtc	30/31	1	2	FACETS	0.469	0.415	0.528	0.469	0.415	0.528	SUBCLONAL	1	TRUE	1	0.386521705553161	2		709	981	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	103	623	1	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	1	2	FACETS	0.61	0.545	0.679	0.61	0.545	0.679	SUBCLONAL	1	TRUE	1	0.386521705553161	2		624	874	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	82	364	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.553	0.487	0.624	0.553	0.487	0.624	SUBCLONAL	1	TRUE	1	0.386521705553161	2		364	767	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894230	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	149	712	0	ENST00000451590.1:c.35G>A	p.Gly12Asp	p.G12D	ENST00000451590	NM_001130442.1	12	gGc/gAc	2/5	1	2	FACETS	0.929	0.849	1	0.929	0.849	1	CLONAL	1	TRUE	1	0.386521705553161	2		712	830	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913322	28913322	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765475765	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	116	910	3	ENST00000282397.4:c.2471G>A	p.Arg824Gln	p.R824Q	ENST00000282397	NM_002019.4	824	cGg/cAg	17/30	1	2	FACETS	0.503	0.452	0.557	0.503	0.452	0.557	SUBCLONAL	1	TRUE	1	0.386521705553161	2		913	1194	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	179	283	9	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	0.875	0.82	0.929	1	0.994	1	CLONAL	3	TRUE	1	0.386521705553161	2		292	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	129	769	0	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	1	2	FACETS	0.63	0.57	0.694	0.63	0.57	0.694	SUBCLONAL	1	TRUE	1	0.386521705553161	2		769	1059	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890149	76890150	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	187	832	0	ENST00000373344.5:c.4744dup	p.Thr1582AsnfsTer19	p.T1582Nfs*19	ENST00000373344	NM_000489.3	1582	aca/aAca	17/35	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.386521705553161	2		832	951	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281250	15281250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184522923	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	328	925	4	ENST00000263388.2:c.5006G>A	p.Arg1669His	p.R1669H	ENST00000263388	NM_000435.2	1669	cGc/cAc	27/33	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.386521705553161	2		929	1213	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347983	347983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760961378	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	185	851	4	ENST00000262320.3:c.1523del	p.Gly508ValfsTer197	p.G508Vfs*197	ENST00000262320	NM_003502.3	508	gGt/gt	6/11	1	2	FACETS	0.884	0.815	0.956	0.884	0.815	0.956	CLONAL	1	TRUE	1	0.386521705553161	2		855	1083	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923087	39923087	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	155	792	1	ENST00000378444.4:c.3621del	p.Lys1207AsnfsTer31	p.K1207Nfs*31	ENST00000378444	NM_001123385.1	1207	aaA/aa	8/15	1	2	FACETS	0.718	0.656	0.783	0.718	0.656	0.783	SUBCLONAL	1	TRUE	1	0.386521705553161	2		793	1117	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782620	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1218	221	980	0	ENST00000269305.4:c.427G>A	p.Val143Met	p.V143M	ENST00000269305	NM_001126112.2	143	Gtg/Atg	5/11	1	2	FACETS	0.795	0.737	0.854	0.795	0.737	0.854	SUBCLONAL	1	TRUE	1	0.386521705553161	2		980	1439	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501260	140501260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730880413	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	190	764	0	ENST00000288602.6:c.812G>A	p.Arg271His	p.R271H	ENST00000288602	NM_004333.4	271	cGt/cAt	6/18	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.386521705553161	2		764	723	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961011	15961011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142717545	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	199	576	0	ENST00000268712.3:c.6209C>T	p.Ser2070Leu	p.S2070L	ENST00000268712	NM_006311.3	2070	tCg/tTg	40/46	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.386521705553161	2		576	888	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527648	157527648	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	130	799	3	ENST00000346085.5:c.5373A>G	p.Ile1791Met	p.I1791M	ENST00000346085	NM_020732.3	1791	atA/atG	20/20	1	2	FACETS	0.641	0.58	0.705	0.641	0.58	0.705	SUBCLONAL	1	TRUE	1	0.386521705553161	2		802	1049	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101117	27101117	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	196	879	1	ENST00000324856.7:c.4403del	p.Pro1468LeufsTer13	p.P1468Lfs*13	ENST00000324856	NM_006015.4	1467	Ccc/cc	18/20	1	2	FACETS	0.834	0.771	0.9	0.834	0.771	0.9	CLONAL	1	TRUE	1	0.386521705553161	2		880	1216	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966872	25966873	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	240	645	1	ENST00000435504.4:c.2333dup	p.Val779SerfsTer25	p.V779Sfs*25	ENST00000435504		778	cca/ccCa	13/13	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.386521705553161	2		646	934	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500845	8500845	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1476255325	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	209	749	1	ENST00000356435.5:c.2037del	p.Lys679AsnfsTer9	p.K679Nfs*9	ENST00000356435		679	aaA/aa	13/35	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.386521705553161	2		750	964	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021211	31021211	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs373145711	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	283	774	1	ENST00000375687.4:c.1210C>T	p.Arg404Ter	p.R404*	ENST00000375687	NM_015338.5	404	Cga/Tga	12/13	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.386521705553161	2		775	1060	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940112	49940112	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760002850	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	260	766	3	ENST00000296474.3:c.931del	p.Ala311ProfsTer27	p.A311Pfs*27	ENST00000296474	NM_002447.2	311	Gcc/cc	1/20	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.386521705553161	2		769	1014	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012207	16012207	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	254	679	0	ENST00000268712.3:c.2075A>T	p.Glu692Val	p.E692V	ENST00000268712	NM_006311.3	692	gAa/gTa	19/46	1	2	FACETS	0.754	0.707	0.802	1	0.993	1	SUBCLONAL	2	TRUE	1	0.386521705553161	2		679	872	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748583	40748583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444440253	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	82	624	3	ENST00000373198.4:c.2933C>T	p.Ala978Val	p.A978V	ENST00000373198	NM_133170.3	978	gCg/gTg	21/32	1	2	FACETS	0.532	0.468	0.6	0.532	0.468	0.6	SUBCLONAL	1	TRUE	1	0.386521705553161	2		627	798	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546835	9546835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	169	594	1	ENST00000353224.5:c.1187C>T	p.Ser396Phe	p.S396F	ENST00000353224	NM_177990.2	396	tCc/tTc	5/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.386521705553161	2		595	714	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1918681	1918681	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1033486520	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	193	773	1	ENST00000382891.5:c.844G>A	p.Val282Ile	p.V282I	ENST00000382891	NM_133335.3	282	Gta/Ata	4/22	1	2	FACETS	0.885	0.818	0.956	0.885	0.818	0.956	CLONAL	1	TRUE	1	0.386521705553161	2		774	1128	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432420	49432420	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	182	823	0	ENST00000301067.7:c.8719del	p.Tyr2907ThrfsTer3	p.Y2907Tfs*3	ENST00000301067	NM_003482.3	2907	Tac/ac	34/54	1	2	FACETS	0.828	0.762	0.896	0.828	0.762	0.896	CLONAL	1	TRUE	1	0.386521705553161	2		823	1138	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390435	56390435	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757096789	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	227	625	2	ENST00000348428.3:c.1174C>T	p.Arg392Cys	p.R392C	ENST00000348428	NM_006785.3	392	Cgt/Tgt	10/17	1	2	FACETS	0.759	0.709	0.81	1	0.992	1	SUBCLONAL	2	TRUE	1	0.386521705553161	2		627	774	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778839	9778839	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	135	897	0	ENST00000377346.4:c.1108del	p.Val370CysfsTer28	p.V370Cfs*28	ENST00000377346	NM_005026.3	370	Gtg/tg	9/24	1	2	FACETS	0.58	0.525	0.637	0.58	0.525	0.637	SUBCLONAL	1	TRUE	1	0.386521705553161	2		897	1205	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023010	27023010	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	32	86	0	ENST00000324856.7:c.116C>A	p.Ala39Glu	p.A39E	ENST00000324856	NM_006015.4	39	gCg/gAg	1/20	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.386521705553161	2		86	142	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598294	28598294	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	350	979	0	ENST00000253063.3:c.266A>G	p.Tyr89Cys	p.Y89C	ENST00000253063	NM_031459.4	89	tAc/tGc	3/10	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.386521705553161	2		979	1244	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280601	115280601	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	292	851	0	ENST00000438362.2:c.430G>T	p.Glu144Ter	p.E144*	ENST00000438362	NM_001242891.1	144	Gaa/Taa	4/20	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.386521705553161	2		851	1021	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111138	193111138	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1330160847	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	94	596	0	ENST00000367435.3:c.671T>C	p.Ile224Thr	p.I224T	ENST00000367435	NM_024529.4	224	aTt/aCt	7/17	1	2	FACETS	0.904	0.807	1	0.904	0.807	1	CLONAL	1	TRUE	1	0.386521705553161	2		596	538	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675272	241675272	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	61	719	0	ENST00000366560.3:c.550del	p.Ser184AlafsTer18	p.S184Afs*18	ENST00000366560	NM_000143.3	184	Agc/gc	4/10	1	2	FACETS	0.434	0.374	0.5	0.434	0.374	0.5	SUBCLONAL	1	TRUE	1	0.386521705553161	2		719	727	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246021902	246021902	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	340	900	0	ENST00000388985.4:c.972C>A	p.Asn324Lys	p.N324K	ENST00000388985		324	aaC/aaA	10/12	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.386521705553161	2		900	1251	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720853	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GATACTT	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	106	457	0	ENST00000371953.3:c.1004_1010dup	p.Phe337LeufsTer8	p.F337Lfs*8	ENST00000371953	NM_000314.4	335	cga/cGATACTTga	8/9	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.386521705553161	2		457	415	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104268945	104268945	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	180	793	0	ENST00000369902.3:c.202T>A	p.Leu68Met	p.L68M	ENST00000369902	NM_016169.3	68	Ttg/Atg	2/12	1	2	FACETS	0.813	0.748	0.88	0.813	0.748	0.88	CLONAL	1	TRUE	1	0.386521705553161	2		793	1146	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274711	123274711	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	190	835	0	ENST00000358487.5:c.1207A>T	p.Thr403Ser	p.T403S	ENST00000358487	NM_000141.4	403	Acg/Tcg	9/18	1	2	FACETS	0.832	0.768	0.899	0.832	0.768	0.899	CLONAL	1	TRUE	1	0.386521705553161	2		835	1182	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274833	123274833	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs757846343	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	198	592	0	ENST00000358487.5:c.1085C>T	p.Ala362Val	p.A362V	ENST00000358487	NM_000141.4	362	gCg/gTg	9/18	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.386521705553161	2		592	743	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457949	69457949	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	233	777	0	ENST00000227507.2:c.349A>G	p.Ile117Val	p.I117V	ENST00000227507	NM_053056.2	117	Atc/Gtc	2/5	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.386521705553161	2		777	863	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374039	118374039	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	228	613	1	ENST00000534358.1:c.7432G>T	p.Gly2478Cys	p.G2478C	ENST00000534358	NM_005933.3	2478	Ggc/Tgc	27/36	1	2	FACETS	0.83	0.776	0.884	1	0.993	1	CLONAL	2	TRUE	1	0.386521705553161	2		614	711	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298717	46298717	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	182	580	0	ENST00000334344.6:c.5364A>T	p.Arg1788Ser	p.R1788S	ENST00000334344	NM_152641.2	1788	agA/agT	21/21	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.386521705553161	2		580	637	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431797	49431798	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	95	742	0	ENST00000301067.7:c.9341_9342del	p.Val3114AlafsTer3	p.V3114Afs*3	ENST00000301067	NM_003482.3	3114	gTG/g	34/54	1	2	FACETS	0.537	0.477	0.601	0.537	0.477	0.601	SUBCLONAL	1	TRUE	1	0.386521705553161	2		742	916	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434562	49434562	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	160	844	4	ENST00000301067.7:c.6991del	p.Leu2331Ter	p.L2331*	ENST00000301067	NM_003482.3	2331	Ctg/tg	31/54	1	2	FACETS	0.801	0.733	0.871	0.801	0.733	0.871	CLONAL	1	TRUE	1	0.386521705553161	2		848	1034	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434839	49434839	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1191	170	968	0	ENST00000301067.7:c.6714del	p.Ser2239ProfsTer25	p.S2239Pfs*25	ENST00000301067	NM_003482.3	2238	ccC/cc	31/54	1	2	FACETS	0.646	0.593	0.703	0.646	0.593	0.703	SUBCLONAL	1	TRUE	1	0.386521705553161	2		968	1361	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495104	56495104	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	105	854	0	ENST00000267101.3:c.3461A>C	p.Glu1154Ala	p.E1154A	ENST00000267101	NM_001982.3	1154	gAg/gCg	27/28	1	2	FACETS	0.46	0.41	0.512	0.46	0.41	0.512	SUBCLONAL	1	TRUE	1	0.386521705553161	2		854	1182	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856113	111856122	+	frameshift_variant	Frame_Shift_Del	DEL	ACGCGCCGCT	ACGCGCCGCT	-	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	97	686	0	ENST00000341259.2:c.164_173del	p.His55ArgfsTer139	p.H55Rfs*139	ENST00000341259	NM_005475.2	55	cACGCGCCGCTg/cg	2/8	1	2	FACETS	0.528	0.47	0.591	0.528	0.47	0.591	SUBCLONAL	1	TRUE	1	0.386521705553161	2		686	950	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434524	121434524	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	200	830	0	ENST00000257555.6:c.1288G>T	p.Gly430Cys	p.G430C	ENST00000257555		430	Ggt/Tgt	6/10	1	2	FACETS	0.873	0.807	0.941	0.873	0.807	0.941	CLONAL	1	TRUE	1	0.386521705553161	2		830	1186	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215778	133215778	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	334	831	0	ENST00000320574.5:c.5485T>C	p.Ser1829Pro	p.S1829P	ENST00000320574	NM_006231.2	1829	Tcc/Ccc	40/49	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.386521705553161	2		831	1215	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219459	133219459	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1174	100	943	0	ENST00000320574.5:c.4675A>G	p.Thr1559Ala	p.T1559A	ENST00000320574	NM_006231.2	1559	Act/Gct	36/49	1	2	FACETS	0.406	0.361	0.454	0.406	0.361	0.454	SUBCLONAL	1	TRUE	1	0.386521705553161	2		943	1274	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253132	133253132	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	209	714	0	ENST00000320574.5:c.909G>T	p.Gln303His	p.Q303H	ENST00000320574	NM_006231.2	303	caG/caT	9/49	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.386521705553161	2		714	831	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623783	28623783	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	134	810	0	ENST00000241453.7:c.871G>T	p.Ala291Ser	p.A291S	ENST00000241453	NM_004119.2	291	Gca/Tca	7/24	1	2	FACETS	0.741	0.672	0.813	0.741	0.672	0.813	SUBCLONAL	1	TRUE	1	0.386521705553161	2		810	936	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893605	28893605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867241812	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	107	645	0	ENST00000282397.4:c.3241G>A	p.Asp1081Asn	p.D1081N	ENST00000282397	NM_002019.4	1081	Gac/Aac	24/30	1	2	FACETS	0.562	0.503	0.624	0.562	0.503	0.624	SUBCLONAL	1	TRUE	1	0.386521705553161	2		645	986	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524568	103524568	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	213	422	4	ENST00000355739.4:c.2705del	p.Asn902IlefsTer4	p.N902Ifs*4	ENST00000355739	NM_000123.3	900	cAa/ca	13/15	1	2	FACETS	0.835	0.786	0.884	1	0.995	1	CLONAL	3	TRUE	1	0.386521705553161	2		426	440	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022973	33022973	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	100	544	2	ENST00000300177.4:c.82G>T	p.Gly28Trp	p.G28W	ENST00000300177	NM_001191322.1	28	Ggg/Tgg	2/2	1	2	FACETS	0.707	0.631	0.787	0.707	0.631	0.787	SUBCLONAL	1	TRUE	1	0.386521705553161	2		546	732	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022989	33022990	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	74	566	0	ENST00000300177.4:c.104dup	p.Pro36AlafsTer8	p.P36Afs*8	ENST00000300177	NM_001191322.1	33	atc/atCc	2/2	1	2	FACETS	0.514	0.449	0.584	0.514	0.449	0.584	SUBCLONAL	1	TRUE	1	0.386521705553161	2		566	745	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38631981	38631981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1255149646	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	150	966	5	ENST00000299084.4:c.471del	p.Gln158SerfsTer16	p.Q158Sfs*16	ENST00000299084	NM_152594.2	156	cTt/ct	5/7	1	2	FACETS	0.82	0.749	0.894	0.82	0.749	0.894	CLONAL	1	TRUE	1	0.386521705553161	2		971	947	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991104	41991104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	223	683	1	ENST00000219905.7:c.2057C>T	p.Ser686Phe	p.S686F	ENST00000219905	NM_001164273.1	686	tCt/tTt	4/24	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.386521705553161	2		684	804	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041419	42041419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1344025543	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	254	807	1	ENST00000219905.7:c.5614G>A	p.Gly1872Arg	p.G1872R	ENST00000219905	NM_001164273.1	1872	Ggg/Agg	17/24	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.386521705553161	2		808	1116	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007690	45007690	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1435502075	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	128	636	0	ENST00000558401.1:c.137A>G	p.Tyr46Cys	p.Y46C	ENST00000558401	NM_004048.2	46	tAt/tGt	2/4	1	2	FACETS	0.836	0.758	0.918	0.836	0.758	0.918	CLONAL	1	TRUE	1	0.386521705553161	2		636	792	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678547	88678547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	144	523	2	ENST00000360948.2:c.989del	p.Pro330HisfsTer84	p.P330Hfs*84	ENST00000360948	NM_001012338.2	330	cCa/ca	9/19	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.386521705553161	2		525	553	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99452077	99452077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1441621301	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	63	601	0	ENST00000268035.6:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000268035	NM_000875.3	471	Cgc/Tgc	6/21	1	2	FACETS	0.471	0.407	0.541	0.471	0.407	0.541	SUBCLONAL	1	TRUE	1	0.386521705553161	2		601	692	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131634	2131634	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	145	870	0	ENST00000219476.3:c.3649A>G	p.Ser1217Gly	p.S1217G	ENST00000219476	NM_000548.3	1217	Agc/Ggc	31/42	1	2	FACETS	0.676	0.615	0.74	0.676	0.615	0.74	SUBCLONAL	1	TRUE	1	0.386521705553161	2		870	1110	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2215907	2215907	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746647663	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	77	799	0	ENST00000326181.6:c.109G>A	p.Ala37Thr	p.A37T	ENST00000326181	NM_032271.2	37	Gcc/Acc	3/21	1	2	FACETS	0.337	0.294	0.382	0.337	0.294	0.382	SUBCLONAL	1	TRUE	1	0.386521705553161	2		799	1184	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778713	3778713	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	181	855	0	ENST00000262367.5:c.6335A>G	p.Gln2112Arg	p.Q2112R	ENST00000262367	NM_004380.2	2112	cAg/cGg	31/31	1	2	FACETS	0.798	0.735	0.865	0.798	0.735	0.865	SUBCLONAL	1	TRUE	1	0.386521705553161	2		855	1173	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781802	3781802	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	108	743	0	ENST00000262367.5:c.4865A>T	p.Tyr1622Phe	p.Y1622F	ENST00000262367	NM_004380.2	1622	tAt/tTt	29/31	1	2	FACETS	0.57	0.51	0.633	0.57	0.51	0.633	SUBCLONAL	1	TRUE	1	0.386521705553161	2		743	981	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788558	3788558	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	67	556	0	ENST00000262367.5:c.4394+2T>G		p.X1465_splice	ENST00000262367	NM_004380.2	1465			1	2	FACETS	0.495	0.429	0.565	0.495	0.429	0.565	SUBCLONAL	1	TRUE	1	0.386521705553161	2		556	701	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808944	3808944	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	193	863	0	ENST00000262367.5:c.3280C>T	p.Leu1094Phe	p.L1094F	ENST00000262367	NM_004380.2	1094	Ctc/Ttc	17/31	1	2	FACETS	0.895	0.827	0.966	0.895	0.827	0.966	CLONAL	1	TRUE	1	0.386521705553161	2		863	1116	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641509	23641510	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	208	971	0	ENST00000261584.4:c.1965dup	p.Pro656SerfsTer7	p.P656Sfs*7	ENST00000261584	NM_024675.3	655	-/T	5/13	1	2	FACETS	0.951	0.881	1	0.951	0.881	1	CLONAL	1	TRUE	1	0.386521705553161	2		971	1132	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645887	67645887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	172	870	1	ENST00000264010.4:c.815G>A	p.Ser272Asn	p.S272N	ENST00000264010	NM_006565.3	272	aGt/aAt	4/12	1	2	FACETS	0.8	0.735	0.868	0.8	0.735	0.868	SUBCLONAL	1	TRUE	1	0.386521705553161	2		871	1113	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993930	72993930	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs764894848	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	144	889	0	ENST00000268489.5:c.115A>G	p.Met39Val	p.M39V	ENST00000268489	NM_006885.3	39	Atg/Gtg	2/10	1	2	FACETS	0.687	0.625	0.752	0.687	0.625	0.752	SUBCLONAL	1	TRUE	1	0.386521705553161	2		889	1085	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	284	906	0	ENST00000269305.4:c.818del	p.Arg273LeufsTer72	p.R273Lfs*72	ENST00000269305	NM_001126112.2	273	cGt/ct	8/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.386521705553161	2		906	1206	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30293209	30293209	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	209	664	0	ENST00000322652.5:c.503del	p.Asn168MetfsTer22	p.N168Mfs*22	ENST00000322652	NM_015355.2	167	Aaa/aa	5/16	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.386521705553161	2		664	799	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435926	56435926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759290047	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	210	577	0	ENST00000407977.2:c.1211G>A	p.Arg404His	p.R404H	ENST00000407977		404	cGc/cAc	9/10	1	2	FACETS	0.787	0.734	0.842	1	0.992	1	SUBCLONAL	2	TRUE	1	0.386521705553161	2		577	690	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492791	56492792	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	313	873	0	ENST00000407977.2:c.147_148del	p.Arg49SerfsTer25	p.R49Sfs*25	ENST00000407977		49	agAGtg/agtg	2/10	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.386521705553161	2		873	1103	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59934572	59934572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769573395	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	190	511	0	ENST00000259008.2:c.226G>A	p.Val76Ile	p.V76I	ENST00000259008	NM_032043.2	76	Gta/Ata	4/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.386521705553161	2		511	678	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603011	48603011	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	88	450	0	ENST00000342988.3:c.1312T>C	p.Phe438Leu	p.F438L	ENST00000342988	NM_005359.5	438	Ttt/Ctt	11/12	1	2	FACETS	0.67	0.593	0.751	0.67	0.593	0.751	SUBCLONAL	1	TRUE	1	0.386521705553161	2		450	680	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11015752	11015752	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	217	528	3	ENST00000327064.4:c.346G>A	p.Asp116Asn	p.D116N	ENST00000327064	NM_199141.1	116	Gat/Aat	2/16	1	2	FACETS	0.753	0.702	0.804	1	0.992	1	SUBCLONAL	2	TRUE	1	0.386521705553161	2		531	746	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031523	11031523	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	146	1022	0	ENST00000327064.4:c.1438A>G	p.Thr480Ala	p.T480A	ENST00000327064	NM_199141.1	480	Acg/Gcg	13/16	1	2	FACETS	0.588	0.535	0.644	0.588	0.535	0.644	SUBCLONAL	1	TRUE	1	0.386521705553161	2		1022	1284	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132435	11132435	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	114	872	0	ENST00000358026.2:c.2651A>T	p.His884Leu	p.H884L	ENST00000358026	NM_001128849.1	884	cAc/cTc	19/36	1	2	FACETS	0.525	0.471	0.582	0.525	0.471	0.582	SUBCLONAL	1	TRUE	1	0.386521705553161	2		872	1124	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281520	15281520	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	120	853	0	ENST00000263388.2:c.4853A>C	p.Glu1618Ala	p.E1618A	ENST00000263388	NM_000435.2	1618	gAg/gCg	26/33	1	2	FACETS	0.573	0.516	0.633	0.573	0.516	0.633	SUBCLONAL	1	TRUE	1	0.386521705553161	2		853	1084	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17389766	17389766	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568337338	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	169	969	1	ENST00000359435.4:c.899C>T	p.Ala300Val	p.A300V	ENST00000359435	NM_001033549.1	300	gCc/gTc	9/9	1	2	FACETS	0.678	0.622	0.737	0.678	0.622	0.737	SUBCLONAL	1	TRUE	1	0.386521705553161	2		970	1290	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271341	18271341	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs749206374	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	331	792	0	ENST00000222254.8:c.383T>C	p.Leu128Pro	p.L128P	ENST00000222254	NM_005027.3	128	cTg/cCg	3/16	1	2	FACETS	0.761	0.719	0.803	1	0.995	1	SUBCLONAL	2	TRUE	1	0.386521705553161	2		792	1126	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212612	36212612	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	179	989	0	ENST00000222270.7:c.2363T>C	p.Val788Ala	p.V788A	ENST00000222270	NM_014727.1	788	gTa/gCa	3/37	1	2	FACETS	0.706	0.649	0.766	0.706	0.649	0.766	SUBCLONAL	1	TRUE	1	0.386521705553161	2		989	1312	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725151	47725151	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1404097158	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	365	915	2	ENST00000449228.1:c.593C>T	p.Pro198Leu	p.P198L	ENST00000449228	NM_001127240.2	198	cCg/cTg	4/4	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.386521705553161	2		917	1323	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905999	50905999	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1337231648	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	237	744	0	ENST00000440232.2:c.970+1G>A		p.X324_splice	ENST00000440232	NM_002691.3	324			1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.386521705553161	2		744	1017	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918151	50918151	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771734704	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	327	863	2	ENST00000440232.2:c.2468G>A	p.Arg823His	p.R823H	ENST00000440232	NM_002691.3	823	cGc/cAc	20/27	1	2	FACETS	0.808	0.764	0.853	1	0.995	1	CLONAL	2	TRUE	1	0.386521705553161	2		865	1047	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467428	25467428	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763336898	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	283	772	2	ENST00000264709.3:c.1648G>A	p.Gly550Arg	p.G550R	ENST00000264709	NM_175629.2	550	Gga/Aga	14/23	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.386521705553161	2		774	1034	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630430	47630430	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793541	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	314	799	0	ENST00000233146.2:c.100G>A	p.Val34Met	p.V34M	ENST00000233146	NM_000251.2	34	Gtg/Atg	1/16	1	2	FACETS	0.844	0.798	0.891	1	0.995	1	CLONAL	2	TRUE	1	0.386521705553161	2		799	963	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023271	31023271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs549809573	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	326	822	0	ENST00000375687.4:c.2756T>C	p.Ile919Thr	p.I919T	ENST00000375687	NM_015338.5	919	aTa/aCa	13/13	1	2	FACETS	0.78	0.737	0.823	1	0.995	1	SUBCLONAL	2	TRUE	1	0.386521705553161	2		822	1082	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565533	41565533	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	142	756	1	ENST00000263253.7:c.4199G>T	p.Ser1400Ile	p.S1400I	ENST00000263253	NM_001429.3	1400	aGt/aTt	26/31	1	2	FACETS	0.782	0.713	0.856	0.782	0.713	0.856	SUBCLONAL	1	TRUE	1	0.386521705553161	2		757	939	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927952	49927952	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	159	873	0	ENST00000296474.3:c.3776T>C	p.Leu1259Pro	p.L1259P	ENST00000296474	NM_002447.2	1259	cTg/cCg	18/20	1	2	FACETS	0.719	0.657	0.783	0.719	0.657	0.783	SUBCLONAL	1	TRUE	1	0.386521705553161	2		873	1145	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934053	49934053	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	132	801	1	ENST00000296474.3:c.2359A>T	p.Thr787Ser	p.T787S	ENST00000296474	NM_002447.2	787	Acc/Tcc	9/20	1	2	FACETS	0.58	0.525	0.638	0.58	0.525	0.638	SUBCLONAL	1	TRUE	1	0.386521705553161	2		802	1178	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668777	52668777	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	115	724	0	ENST00000394830.3:c.1142A>C	p.Asp381Ala	p.D381A	ENST00000394830	NM_018313.4	381	gAt/gCt	12/30	1	2	FACETS	0.644	0.579	0.713	0.644	0.579	0.713	SUBCLONAL	1	TRUE	1	0.386521705553161	2		724	924	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670324	134670324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775406650	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	118	620	0	ENST00000398015.3:c.235C>T	p.Arg79Trp	p.R79W	ENST00000398015	NM_004441.4	79	Cgg/Tgg	3/16	1	2	FACETS	0.78	0.704	0.86	0.78	0.704	0.86	SUBCLONAL	1	TRUE	1	0.386521705553161	2		620	783	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1952803	1952803	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144714547	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	193	606	3	ENST00000382891.5:c.1886C>T	p.Ser629Leu	p.S629L	ENST00000382891	NM_133335.3	629	tCg/tTg	10/22	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.386521705553161	2		609	779	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217148	66217148	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	215	817	0	ENST00000273854.3:c.2467del	p.Arg823GlyfsTer28	p.R823Gfs*28	ENST00000273854	NM_004439.5	823	Cgg/gg	14/18	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.386521705553161	2		817	858	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958816	38958816	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	107	627	0	ENST00000357387.3:c.2296A>T	p.Ile766Phe	p.I766F	ENST00000357387	NM_152756.3	766	Att/Ttt	23/38	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.386521705553161	2		627	539	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963040	38963040	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	62	651	0	ENST00000357387.3:c.1504A>G	p.Ile502Val	p.I502V	ENST00000357387	NM_152756.3	502	Att/Gtt	17/38	1	2	FACETS	0.52	0.449	0.597	0.52	0.449	0.597	SUBCLONAL	1	TRUE	1	0.386521705553161	2		651	617	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189395	56189395	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	124	867	0	ENST00000399503.3:c.4427A>G	p.His1476Arg	p.H1476R	ENST00000399503	NM_005921.1	1476	cAt/cGt	20/20	1	2	FACETS	0.572	0.516	0.632	0.572	0.516	0.632	SUBCLONAL	1	TRUE	1	0.386521705553161	2		867	1121	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79960995	79960995	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	129	727	0	ENST00000265081.6:c.392C>A	p.Ser131Ter	p.S131*	ENST00000265081	NM_002439.4	131	tCa/tAa	3/24	1	2	FACETS	0.822	0.745	0.903	0.822	0.745	0.903	CLONAL	1	TRUE	1	0.386521705553161	2		727	812	SUCCESS
APC	324	MSKCC	GRCh37	5	112164671	112164671	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	49	412	0	ENST00000257430.4:c.1743+2T>C		p.X581_splice	ENST00000257430	NM_000038.5	581			1	2	FACETS	0.45	0.38	0.526	0.45	0.38	0.526	SUBCLONAL	1	TRUE	1	0.386521705553161	2		412	564	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176719097	176719097	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	95	437	0	ENST00000439151.2:c.6401A>G	p.Lys2134Arg	p.K2134R	ENST00000439151	NM_022455.4	2134	aAg/aGg	22/23	1	2	FACETS	0.733	0.653	0.818	0.733	0.653	0.818	SUBCLONAL	1	TRUE	1	0.386521705553161	2		437	671	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401624	401624	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	101	639	0	ENST00000380956.4:c.946G>C	p.Val316Leu	p.V316L	ENST00000380956	NM_001195286.1	316	Gtc/Ctc	7/9	NA	2	FACETS	0.655	0.585	0.729			1	INDETERMINATE	1	TRUE	NA	0.386521705553161	2		639	798	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910782	29910782	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199474463	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	132	798	0	ENST00000376809.5:c.322T>C	p.Tyr108His	p.Y108H	ENST00000376809	NM_002116.7	108	Tac/Cac	2/8	1	2	FACETS	0.708	0.642	0.777	0.708	0.642	0.777	SUBCLONAL	1	TRUE	1	0.386521705553161	2		798	965	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816544	32816544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376553490	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	371	966	4	ENST00000354258.4:c.1631G>A	p.Arg544His	p.R544H	ENST00000354258	NM_000593.5	544	cGc/cAc	7/11	1	2	FACETS	0.778	0.738	0.818	1	0.995	1	SUBCLONAL	2	TRUE	1	0.386521705553161	2		970	1234	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035163	6035163	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs878854059	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	160	576	0	ENST00000265849.7:c.903+2T>C		p.X301_splice	ENST00000265849	NM_000535.5	301			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.386521705553161	2		576	721	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221773	55221773	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	134	769	1	ENST00000275493.2:c.817A>G	p.Thr273Ala	p.T273A	ENST00000275493	NM_005228.3	273	Acc/Gcc	7/28	1	2	FACETS	0.636	0.576	0.698	0.636	0.576	0.698	SUBCLONAL	1	TRUE	1	0.386521705553161	2		770	1091	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55270246	55270246	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	331	807	0	ENST00000275493.2:c.3199C>T	p.Gln1067Ter	p.Q1067*	ENST00000275493	NM_005228.3	1067	Cag/Tag	27/28	1	2	FACETS	0.754	0.713	0.797	1	0.995	1	SUBCLONAL	2	TRUE	1	0.386521705553161	2		807	1135	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848622	151848622	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376118166	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	68	626	0	ENST00000262189.6:c.12571G>A	p.Ala4191Thr	p.A4191T	ENST00000262189	NM_170606.2	4191	Gca/Aca	50/59	1	2	FACETS	0.543	0.472	0.62	0.543	0.472	0.62	SUBCLONAL	1	TRUE	1	0.386521705553161	2		626	648	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900017	151900017	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	63	742	0	ENST00000262189.6:c.4092+2T>C		p.X1364_splice	ENST00000262189	NM_170606.2	1364			1	2	FACETS	0.55	0.475	0.63	0.55	0.475	0.63	SUBCLONAL	1	TRUE	1	0.386521705553161	2		742	593	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864700	68864700	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	263	595	0	ENST00000288368.4:c.71G>A	p.Arg24His	p.R24H	ENST00000288368	NM_024870.2	24	cGc/cAc	1/40	1	2	FACETS	0.866	0.814	0.918	1	0.994	1	CLONAL	2	TRUE	1	0.386521705553161	2		595	786	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141583011	141583011	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs750394835	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1225	299	873	1	ENST00000220592.5:c.236T>C	p.Val79Ala	p.V79A	ENST00000220592	NM_012154.3	79	gTc/gCc	3/19	0.126223573697607	4	FACETS	1	0.993	1	0.704	0.661	0.748	INDETERMINATE	1	TRUE	2	0.386521705553161	4		874	1524	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249447	110249447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	194	951	0	ENST00000374672.4:c.1126C>T	p.Pro376Ser	p.P376S	ENST00000374672	NM_004235.4	376	Cca/Tca	4/5	1	2	FACETS	0.789	0.728	0.852	0.789	0.728	0.852	SUBCLONAL	1	TRUE	1	0.386521705553161	2		951	1273	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396353	139396353	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765486614	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	128	821	3	ENST00000277541.6:c.5485G>A	p.Val1829Met	p.V1829M	ENST00000277541	NM_017617.3	1829	Gtg/Atg	30/34	1	2	FACETS	0.662	0.599	0.729	0.662	0.599	0.729	SUBCLONAL	1	TRUE	1	0.386521705553161	2		824	1000	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399519	139399519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1339004050	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	142	760	2	ENST00000277541.6:c.4624G>A	p.Asp1542Asn	p.D1542N	ENST00000277541	NM_017617.3	1542	Gac/Aac	26/34	1	2	FACETS	0.685	0.623	0.751	0.685	0.623	0.751	SUBCLONAL	1	TRUE	1	0.386521705553161	2		762	1072	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407952	139407952	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	202	923	3	ENST00000277541.6:c.2245A>T	p.Asn749Tyr	p.N749Y	ENST00000277541	NM_017617.3	749	Aac/Tac	14/34	1	2	FACETS	0.88	0.814	0.948	0.88	0.814	0.948	CLONAL	1	TRUE	1	0.386521705553161	2		926	1188	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802604	139802604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780585355	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	325	852	2	ENST00000247668.2:c.449G>A	p.Arg150His	p.R150H	ENST00000247668	NM_021138.3	150	cGc/cAc	5/11	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.386521705553161	2		854	1160	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916525	39916525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	155	925	2	ENST00000378444.4:c.4478G>A	p.Arg1493Gln	p.R1493Q	ENST00000378444	NM_001123385.1	1493	cGg/cAg	11/15	1	2	FACETS	0.656	0.599	0.716	0.656	0.599	0.716	SUBCLONAL	1	TRUE	1	0.386521705553161	2		927	1223	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933523	39933523	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	191	860	0	ENST00000378444.4:c.1076A>G	p.Lys359Arg	p.K359R	ENST00000378444	NM_001123385.1	359	aAg/aGg	4/15	1	2	FACETS	0.861	0.795	0.93	0.861	0.795	0.93	CLONAL	1	TRUE	1	0.386521705553161	2		860	1148	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934231	39934231	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	136	903	0	ENST00000378444.4:c.368A>G	p.Gln123Arg	p.Q123R	ENST00000378444	NM_001123385.1	123	cAg/cGg	4/15	1	2	FACETS	0.553	0.501	0.608	0.553	0.501	0.608	SUBCLONAL	1	TRUE	1	0.386521705553161	2		903	1273	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030482	47030482	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1459036800	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	116	864	0	ENST00000377604.3:c.257A>G	p.His86Arg	p.H86R	ENST00000377604	NM_001204468.1	86	cAc/cGc	4/24	1	2	FACETS	0.584	0.526	0.647	0.584	0.526	0.647	SUBCLONAL	1	TRUE	1	0.386521705553161	2		864	1027	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215268	123215268	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	85	731	0	ENST00000218089.9:c.2814T>A	p.Phe938Leu	p.F938L	ENST00000218089	NM_001042749.1	938	ttT/ttA	28/35	1	2	FACETS	0.546	0.482	0.614	0.546	0.482	0.614	SUBCLONAL	1	TRUE	1	0.386521705553161	2		731	806	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	79	453	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.785	0.691	0.885	0.785	0.691	0.885	SUBCLONAL	1	TRUE	1	0.35	2		453	575	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800902	120800903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs748469666	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	101	828	3	ENST00000257552.2:c.345dup	p.Leu116AlafsTer15	p.L116Afs*15	ENST00000257552	NM_002442.3	115	-/G	6/15	1	2	FACETS	0.934	0.836	1	0.934	0.836	1	CLONAL	1	TRUE	1	0.35	2		831	618	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686901	37686901	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	66	588	0	ENST00000447079.4:c.3810del	p.Gly1271AspfsTer23	p.G1271Dfs*23	ENST00000447079	NM_015083.1	1269	Ccc/cc	14/14	1	2	FACETS	0.987	0.861	1	0.987	0.861	1	CLONAL	1	TRUE	1	0.35	2		588	382	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	88	752	3	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	0.35	2		755	472	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	63	622	4	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.781	0.677	0.893	0.781	0.677	0.893	SUBCLONAL	1	TRUE	1	0.35	2		626	461	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	82	697	3	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.35	2		700	424	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	116	685	5	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.841	0.765	0.92	1	0.988	1	CLONAL	2	TRUE	1	0.35	2		690	394	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	219	910	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.94	0.878	1	1	0.994	1	CLONAL	2	TRUE	1	0.35	2		915	666	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	98	558	3	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.932	0.833	1	0.932	0.833	1	CLONAL	1	TRUE	1	0.35	2		561	601	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992721	68992721	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs764112302	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	85	817	8	ENST00000288368.4:c.1693del	p.Ser565ArgfsTer10	p.S565Rfs*10	ENST00000288368	NM_024870.2	562	cgT/cg	16/40	1	2	FACETS	0.769	0.68	0.863	0.769	0.68	0.863	SUBCLONAL	1	TRUE	1	0.35	2		825	632	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	58	272	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.35	2		272	252	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	82	726	1	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	0.831	0.734	0.934	0.831	0.734	0.934	CLONAL	1	TRUE	1	0.35	2		727	564	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	80	617	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	0.983	0.869	1	0.983	0.869	1	CLONAL	1	TRUE	1	0.35	2		617	465	SUCCESS
APC	324	MSKCC	GRCh37	5	112175675	112175676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	44	458	0	ENST00000257430.4:c.4393_4394dup	p.Ser1465ArgfsTer9	p.S1465Rfs*9	ENST00000257430	NM_000038.5	1462	aag/aAGag	16/16	1	2	FACETS	0.769	0.647	0.902	0.769	0.647	0.902	CLONAL	1	TRUE	1	0.35	2		458	327	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	84	400	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.35	2		400	415	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103755	47103756	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	91	720	1	ENST00000409792.3:c.6190_6191del	p.Asp2064ProfsTer8	p.D2064Pfs*8	ENST00000409792	NM_014159.6	2064	GAc/c	14/21	1	2	FACETS	0.908	0.807	1	0.908	0.807	1	CLONAL	1	TRUE	1	0.35	2		721	573	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909629	76909629	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs919106518	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	81	841	2	ENST00000373344.5:c.4276C>T	p.Arg1426Ter	p.R1426*	ENST00000373344	NM_000489.3	1426	Cga/Tga	14/35	1	2	FACETS	0.658	0.58	0.743	0.658	0.58	0.743	SUBCLONAL	1	TRUE	1	0.35	2		843	703	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346884	73346884	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	20	493	3	ENST00000377767.4:c.1333del	p.Ser445HisfsTer20	p.S445Hfs*20	ENST00000377767	NM_014953.3	445	Tca/ca	9/21	0.326142623665591	3	FACETS	0.344	0.263	0.44	0.172	0.131	0.22	SUBCLONAL	1	TRUE	1	0.35	3		496	390	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	50	485	0	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	0.809	0.689	0.94	0.809	0.689	0.94	CLONAL	1	TRUE	1	0.35	2		485	353	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231290	98231290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767947110	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	90	804	1	ENST00000331920.6:c.1993C>T	p.Arg665Cys	p.R665C	ENST00000331920	NM_000264.3	665	Cgc/Tgc	14/24	1	2	FACETS	0.901	0.801	1	0.901	0.801	1	CLONAL	1	TRUE	1	0.35	2		805	571	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945129	32945129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80359104	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	122	511	1	ENST00000380152.3:c.8524C>T	p.Arg2842Cys	p.R2842C	ENST00000380152		2842	Cgc/Tgc	20/27	0.326142623665591	3	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	1	0.35	3		512	404	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724626	162724626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879065950	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	81	575	1	ENST00000367921.3:c.398G>A	p.Arg133Gln	p.R133Q	ENST00000367921	NM_006182.2	133	cGg/cAg	5/18	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.35	2		576	424	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522601	176522601	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	34	777	1	ENST00000292408.4:c.1703del	p.Pro568GlnfsTer53	p.P568Qfs*53	ENST00000292408	NM_213647.1	566	cgC/cg	13/18	1	2	FACETS	0.459	0.375	0.554	0.459	0.375	0.554	SUBCLONAL	1	TRUE	1	0.35	2		778	423	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	95	821	5	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.35	2		826	500	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	28	759	4	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	0.405	0.323	0.498	0.405	0.323	0.498	SUBCLONAL	1	TRUE	1	0.35	2		763	395	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	26	606	3	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.431	0.341	0.533	0.431	0.341	0.533	SUBCLONAL	1	TRUE	1	0.35	2		609	345	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422384	47422384	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	24	547	2	ENST00000377045.4:c.23del	p.Pro8LeufsTer26	p.P8Lfs*26	ENST00000377045	NM_001654.4	6	ggC/gg	2/16	1	2	FACETS	0.421	0.33	0.525	0.421	0.33	0.525	SUBCLONAL	1	TRUE	1	0.35	2		549	326	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245587	41245587	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357522	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	120	889	3	ENST00000357654.3:c.1961del	p.Lys654SerfsTer47	p.K654Sfs*47	ENST00000357654	NM_007294.3	654	aAg/ag	10/23	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.35	2		892	564	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900984	114900984	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778855667	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	73	748	1	ENST00000543371.1:c.598del	p.Leu200SerfsTer25	p.L200Sfs*25	ENST00000543371	NM_001198531.1	198	caC/ca	6/14	1	2	FACETS	0.752	0.658	0.852	0.752	0.658	0.852	SUBCLONAL	1	TRUE	1	0.35	2		749	555	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934243	49934243	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1407832113	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	69	747	2	ENST00000296474.3:c.2264del	p.Gly755ValfsTer19	p.G755Vfs*19	ENST00000296474	NM_002447.2	755	gGt/gt	8/20	1	2	FACETS	0.937	0.819	1	0.937	0.819	1	CLONAL	1	TRUE	1	0.35	2		749	421	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233090	69233090	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746910913	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	52	541	1	ENST00000462284.1:c.961del	p.Leu321PhefsTer52	p.L321Ffs*52	ENST00000462284	NM_002392.5	319	Ccc/cc	11/11	1	2	FACETS	0.776	0.663	0.899	0.776	0.663	0.899	SUBCLONAL	1	TRUE	1	0.35	2		542	383	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499363	89499363	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1317589623	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	65	562	2	ENST00000336596.2:c.2538del	p.Met847TrpfsTer10	p.M847Wfs*10	ENST00000336596	NM_005233.5	845	Ccc/cc	15/17	1	2	FACETS	0.967	0.843	1	0.967	0.843	1	CLONAL	1	TRUE	1	0.35	2		564	384	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427568	72427568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs912857100	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	59	352	1	ENST00000477973.2:c.922G>A	p.Asp308Asn	p.D308N	ENST00000477973	NM_012234.5	308	Gac/Aac	4/4	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.35	2		353	262	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151290	202151290	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	107	723	0	ENST00000358485.4:c.1596del	p.Lys532AsnfsTer73	p.K532Nfs*73	ENST00000358485	NM_001080125.1	530	agA/ag	9/9	1	2	FACETS	0.958	0.861	1	0.958	0.861	1	CLONAL	1	TRUE	1	0.35	2		723	638	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450582	70450582	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150708897	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	59	643	1	ENST00000373644.4:c.5422G>A	p.Val1808Met	p.V1808M	ENST00000373644	NM_030625.2	1808	Gtg/Atg	12/12	1	2	FACETS	0.705	0.608	0.811	0.705	0.608	0.811	SUBCLONAL	1	TRUE	1	0.35	2		644	478	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681463	30681463	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	80	643	2	ENST00000376406.3:c.549del	p.Lys183AsnfsTer9	p.K183Nfs*9	ENST00000376406	NM_014641.2	183	aaA/aa	4/15	1	2	FACETS	0.874	0.771	0.984	0.874	0.771	0.984	CLONAL	1	TRUE	1	0.35	2		645	523	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144708	58144708	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs780052789	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	67	594	1	ENST00000257904.6:c.520G>A	p.Val174Met	p.V174M	ENST00000257904	NM_000075.3	174	Gtg/Atg	4/8	1	2	FACETS	0.934	0.815	1	0.934	0.815	1	CLONAL	1	TRUE	1	0.35	2		595	410	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508133	106508133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1346474355	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	27	300	0	ENST00000359195.3:c.127G>A	p.Val43Met	p.V43M	ENST00000359195	NM_002649.2	43	Gtg/Atg	2/11	1	2	FACETS	0.689	0.551	0.844	0.689	0.551	0.844	SUBCLONAL	1	TRUE	1	0.35	2		300	224	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403254	213403254	+	frameshift_variant,start_lost,start_retained_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	40	644	1	ENST00000342788.4:c.1del	p.Met1?	p.M1?	ENST00000342788	NM_005235.2	1	Atg/tg	1/28	1	2	FACETS	0.515	0.428	0.612	0.515	0.428	0.612	SUBCLONAL	1	TRUE	1	0.35	2		645	444	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41562635	41562635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	121	706	0	ENST00000263253.7:c.3839C>T	p.Ala1280Val	p.A1280V	ENST00000263253	NM_001429.3	1280	gCa/gTa	23/31	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.35	2		706	637	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682810	190682810	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	66	625	3	ENST00000441310.2:c.492del	p.Lys164AsnfsTer6	p.K164Nfs*6	ENST00000441310	NM_000534.4	162	gcA/gc	5/13	1	2	FACETS	0.818	0.712	0.932	0.818	0.712	0.932	CLONAL	1	TRUE	1	0.35	2		628	461	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164745	36164745	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	38	778	0	ENST00000300305.3:c.1130A>G	p.Tyr377Cys	p.Y377C	ENST00000300305		377	tAc/tGc	8/8	1	2	FACETS	0.38	0.314	0.455	0.38	0.314	0.455	SUBCLONAL	1	TRUE	1	0.35	2		778	571	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998128	169998128	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs753143066	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	137	813	7	ENST00000295797.4:c.826del	p.Thr276GlnfsTer7	p.T276Qfs*7	ENST00000295797	NM_002740.5	273	ttA/tt	9/18	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.35	2		820	734	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863054	56863054	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1266824391	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	86	802	0	ENST00000519728.1:c.327del	p.Glu110LysfsTer15	p.E110Kfs*15	ENST00000519728	NM_002350.3	107	acA/ac	5/13	1	2	FACETS	0.925	0.821	1	0.925	0.821	1	CLONAL	1	TRUE	1	0.35	2		802	531	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391932	139391932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373806373	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	91	846	2	ENST00000277541.6:c.6259C>T	p.Arg2087Trp	p.R2087W	ENST00000277541	NM_017617.3	2087	Cgg/Tgg	34/34	1	2	FACETS	0.906	0.806	1	0.906	0.806	1	CLONAL	1	TRUE	1	0.35	2		848	574	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942857	15942857	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	67	661	2	ENST00000268712.3:c.6845A>G	p.His2282Arg	p.H2282R	ENST00000268712	NM_006311.3	2282	cAt/cGt	44/46	1	2	FACETS	0.841	0.733	0.958	0.841	0.733	0.958	CLONAL	1	TRUE	1	0.35	2		663	455	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776086	9776086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1250682190	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	46	685	2	ENST00000377346.4:c.550C>T	p.Arg184Trp	p.R184W	ENST00000377346	NM_005026.3	184	Cgg/Tgg	5/24	1	2	FACETS	0.597	0.504	0.701	0.597	0.504	0.701	SUBCLONAL	1	TRUE	1	0.35	2		687	440	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294235	11294235	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs951016084	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	88	708	3	ENST00000361445.4:c.2296C>T	p.Arg766Ter	p.R766*	ENST00000361445	NM_004958.3	766	Cga/Tga	14/58	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.35	2		711	471	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11297916	11297916	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	26	601	0	ENST00000361445.4:c.2192G>A	p.Arg731His	p.R731H	ENST00000361445	NM_004958.3	731	cGc/cAc	13/58	1	2	FACETS	0.316	0.25	0.393	0.316	0.25	0.393	SUBCLONAL	1	TRUE	1	0.35	2		601	470	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300569	11300569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1363405074	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	91	772	1	ENST00000361445.4:c.1577G>A	p.Arg526His	p.R526H	ENST00000361445	NM_004958.3	526	cGt/cAt	11/58	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.35	2		773	497	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317100	11317100	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747458067	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	81	760	1	ENST00000361445.4:c.394C>T	p.Arg132Cys	p.R132C	ENST00000361445	NM_004958.3	132	Cgt/Tgt	4/58	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.35	2		761	463	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102110	27102110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	83	792	2	ENST00000324856.7:c.5036G>A	p.Gly1679Asp	p.G1679D	ENST00000324856	NM_006015.4	1679	gGt/gAt	19/20	1	2	FACETS	0.988	0.875	1	0.988	0.875	1	CLONAL	1	TRUE	1	0.35	2		794	480	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163315514	163315514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	80	752	0	ENST00000271452.3:c.854G>A	p.Cys285Tyr	p.C285Y	ENST00000271452	NM_145697.2	285	tGc/tAc	11/14	1	2	FACETS	0.856	0.755	0.964	0.856	0.755	0.964	CLONAL	1	TRUE	1	0.35	2		752	534	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958497	175958497	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	69	577	2	ENST00000367669.3:c.1847+1G>A		p.X616_splice	ENST00000367669	NM_022457.5	616			1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.35	2		579	379	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253362	226253362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	61	442	0	ENST00000366813.1:c.134G>A	p.Gly45Asp	p.G45D	ENST00000366813		45	gGt/gAt	2/3	1	2	FACETS	0.78	0.674	0.894	0.78	0.674	0.894	SUBCLONAL	1	TRUE	1	0.35	2		442	447	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601845	43601845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	64	618	3	ENST00000355710.3:c.889C>T	p.Arg297Cys	p.R297C	ENST00000355710	NM_020975.4	297	Cgt/Tgt	5/20	1	2	FACETS	0.858	0.746	0.98	0.858	0.746	0.98	CLONAL	1	TRUE	1	0.35	2		621	426	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533503	533503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1389157073	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	118	842	4	ENST00000451590.1:c.400G>A	p.Ala134Thr	p.A134T	ENST00000451590	NM_001130442.1	134	Gcc/Acc	4/5	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.35	2		846	570	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380391	14380391	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	49	366	0	ENST00000256196.4:c.26G>A	p.Gly9Asp	p.G9D	ENST00000256196		9	gGc/gAc	1/6	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.35	2		366	275	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941274	71941274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754842505	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	73	799	2	ENST00000298229.2:c.1049G>A	p.Arg350Gln	p.R350Q	ENST00000298229	NM_001567.3	350	cGg/cAg	9/28	1	2	FACETS	0.882	0.774	0.998	0.882	0.774	0.998	CLONAL	1	TRUE	1	0.35	2		801	473	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200990	108200990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755418571	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	68	651	2	ENST00000278616.4:c.7357C>T	p.Arg2453Cys	p.R2453C	ENST00000278616	NM_000051.3	2453	Cgt/Tgt	50/63	1	2	FACETS	0.875	0.764	0.995	0.875	0.764	0.995	CLONAL	1	TRUE	1	0.35	2		653	444	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148465	119148465	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	34	535	0	ENST00000264033.4:c.1008-2A>T		p.X336_splice	ENST00000264033	NM_005188.3	336			1	2	FACETS	0.482	0.394	0.581	0.482	0.394	0.581	SUBCLONAL	1	TRUE	1	0.35	2		535	403	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125499325	125499325	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	101	739	1	ENST00000428830.2:c.394A>T	p.Lys132Ter	p.K132*	ENST00000428830	NM_001114121.2	132	Aaa/Taa	5/14	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.35	2		740	564	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514476	125514477	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	53	604	0	ENST00000428830.2:c.1173dup	p.Cys392MetfsTer7	p.C392Mfs*7	ENST00000428830	NM_001114121.2	391	caa/cAaa	11/14	1	2	FACETS	0.681	0.581	0.789	0.681	0.581	0.789	SUBCLONAL	1	TRUE	1	0.35	2		604	445	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856268	111856268	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	12	112	0	ENST00000341259.2:c.320del	p.Gly107AlafsTer90	p.G107Afs*90	ENST00000341259	NM_005475.2	107	Ggc/gc	2/8	1	2	FACETS	0.826	0.589	1	0.826	0.589	1	CLONAL	1	TRUE	1	0.35	2		112	83	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432208	121432208	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs137853240	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	57	580	2	ENST00000257555.6:c.955G>A	p.Gly319Ser	p.G319S	ENST00000257555		319	Ggt/Agt	4/10	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.35	2		582	309	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123889488	123889488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	27	207	0	ENST00000330479.4:c.715G>A	p.Gly239Ser	p.G239S	ENST00000330479	NM_020382.3	239	Ggt/Agt	7/9	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.35	2		207	130	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226262	133226262	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	81	777	0	ENST00000320574.5:c.3795+1G>C		p.X1265_splice	ENST00000320574	NM_006231.2	1265			1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.35	2		777	461	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592704	28592704	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	76	738	1	ENST00000241453.7:c.2441C>T	p.Ala814Val	p.A814V	ENST00000241453	NM_004119.2	814	gCc/gTc	20/24	0.326142623665591	3	FACETS	0.778	0.682	0.881	0.389	0.341	0.441	SUBCLONAL	1	TRUE	1	0.35	3		739	656	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911178	32911178	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	162	688	0	ENST00000380152.3:c.2686A>G	p.Asn896Asp	p.N896D	ENST00000380152		896	Aat/Gat	11/27	0.326142623665591	3	FACETS	0.939	0.866	1	0.939	0.866	1	CLONAL	2	TRUE	1	0.35	3		688	579	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972625	32972626	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1328254546	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	55	580	0	ENST00000380152.3:c.9981dup	p.Phe3328IlefsTer3	p.F3328Ifs*3	ENST00000380152		3325	-/A	27/27	0.326142623665591	3	FACETS	0.73	0.625	0.844	0.365	0.312	0.422	SUBCLONAL	1	TRUE	1	0.35	3		580	506	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30102152	30102152	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs775376594	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	86	646	8	ENST00000331968.5:c.1315C>T	p.Arg439Trp	p.R439W	ENST00000331968	NM_002742.2	439	Cgg/Tgg	9/18	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.35	2		654	484	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023085	33023085	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	40	464	1	ENST00000300177.4:c.194G>A	p.Gly65Asp	p.G65D	ENST00000300177	NM_001191322.1	65	gGc/gAc	2/2	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.35	2		465	184	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714237	43714237	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	75	862	2	ENST00000382044.4:c.3916del	p.Asp1306IlefsTer61	p.D1306Ifs*61	ENST00000382044	NM_001141980.1	1306	Gat/at	19/28	1	2	FACETS	0.775	0.68	0.877	0.775	0.68	0.877	SUBCLONAL	1	TRUE	1	0.35	2		864	553	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724684	43724684	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	74	777	0	ENST00000382044.4:c.3383A>T	p.Asp1128Val	p.D1128V	ENST00000382044	NM_001141980.1	1128	gAt/gTt	17/28	1	2	FACETS	0.955	0.839	1	0.955	0.839	1	CLONAL	1	TRUE	1	0.35	2		777	443	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66779571	66779571	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773890369	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	89	626	2	ENST00000307102.5:c.901G>A	p.Gly301Arg	p.G301R	ENST00000307102	NM_002755.3	301	Gga/Aga	8/11	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.35	2		628	471	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778228	3778228	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1306100144	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	44	732	0	ENST00000262367.5:c.6820A>G	p.Met2274Val	p.M2274V	ENST00000262367	NM_004380.2	2274	Atg/Gtg	31/31	1	2	FACETS	0.742	0.624	0.871	0.742	0.624	0.871	SUBCLONAL	1	TRUE	1	0.35	2		732	339	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778549	3778549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	79	841	1	ENST00000262367.5:c.6499del	p.Gln2167ArgfsTer5	p.Q2167Rfs*5	ENST00000262367	NM_004380.2	2167	Cag/ag	31/31	1	2	FACETS	0.954	0.842	1	0.954	0.842	1	CLONAL	1	TRUE	1	0.35	2		842	473	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832823	3832823	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	44	724	0	ENST00000262367.5:c.1435A>G	p.Ser479Gly	p.S479G	ENST00000262367	NM_004380.2	479	Agc/Ggc	6/31	1	2	FACETS	0.535	0.449	0.63	0.535	0.449	0.63	SUBCLONAL	1	TRUE	1	0.35	2		724	470	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647310	23647310	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	109	827	1	ENST00000261584.4:c.557del	p.Asn186IlefsTer7	p.N186Ifs*7	ENST00000261584	NM_024675.3	186	aAt/at	4/13	1	2	FACETS	0.961	0.865	1	0.961	0.865	1	CLONAL	1	TRUE	1	0.35	2		828	648	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346437	89346437	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555525603	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	82	775	0	ENST00000301030.4:c.6513del	p.Val2173SerfsTer2	p.V2173Sfs*2	ENST00000301030	NM_001256183.1	2171	ccC/cc	9/13	1	2	FACETS	0.993	0.879	1	0.993	0.879	1	CLONAL	1	TRUE	1	0.35	2		775	472	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347194	89347194	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773848887	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	51	604	3	ENST00000301030.4:c.5756C>T	p.Ala1919Val	p.A1919V	ENST00000301030	NM_001256183.1	1919	gCg/gTg	9/13	1	2	FACETS	0.86	0.734	0.996	0.86	0.734	0.996	CLONAL	1	TRUE	1	0.35	2		607	339	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89839684	89839684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537923341	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	66	596	1	ENST00000389301.3:c.2009G>A	p.Arg670His	p.R670H	ENST00000389301	NM_000135.2	670	cGt/cAt	22/43	1	2	FACETS	0.965	0.841	1	0.965	0.841	1	CLONAL	1	TRUE	1	0.35	2		597	391	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664386	29664386	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	30	418	0	ENST00000356175.3:c.6365A>C	p.Glu2122Ala	p.E2122A	ENST00000356175	NM_000267.3	2122	gAa/gCa	42/57	1	2	FACETS	0.434	0.349	0.53	0.434	0.349	0.53	SUBCLONAL	1	TRUE	1	0.35	2		418	395	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533883	63533884	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	73	653	0	ENST00000307078.5:c.1270_1271del	p.Ser424ProfsTer37	p.S424Pfs*37	ENST00000307078	NM_004655.3	424	TCc/c	6/11	1	2	FACETS	0.942	0.827	1	0.942	0.827	1	CLONAL	1	TRUE	1	0.35	2		653	443	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985628	60985628	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	21	211	0	ENST00000333681.4:c.272C>A	p.Pro91His	p.P91H	ENST00000333681		91	cCt/cAt	2/3	1	2	FACETS	0.774	0.601	0.972	0.774	0.601	0.972	CLONAL	1	TRUE	1	0.35	2		211	155	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615719	1615719	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs375552133	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	65	965	0	ENST00000344749.5:c.1552A>G	p.Lys518Glu	p.K518E	ENST00000344749	NM_001136139.2	518	Aag/Gag	17/19	1	2	FACETS	0.774	0.672	0.883	0.774	0.672	0.883	SUBCLONAL	1	TRUE	1	0.35	2		965	480	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222478	2222478	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1372238674	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	87	695	0	ENST00000398665.3:c.3310T>A	p.Ser1104Thr	p.S1104T	ENST00000398665	NM_032482.2	1104	Tcc/Acc	24/28	1	2	FACETS	0.994	0.883	1	0.994	0.883	1	CLONAL	1	TRUE	1	0.35	2		695	500	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115009	3115009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	136	1073	0	ENST00000078429.4:c.544G>A	p.Val182Ile	p.V182I	ENST00000078429	NM_002067.2	182	Gtc/Atc	4/7	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.35	2		1073	712	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110566	4110566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397517413	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	83	788	1	ENST00000262948.5:c.391G>A	p.Val131Met	p.V131M	ENST00000262948	NM_030662.3	131	Gtg/Atg	3/11	1	2	FACETS	0.845	0.747	0.95	0.845	0.747	0.95	CLONAL	1	TRUE	1	0.35	2		789	561	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244325	5244325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	96	898	0	ENST00000357368.4:c.1157G>A	p.Arg386His	p.R386H	ENST00000357368	NM_002850.3	386	cGt/cAt	11/38	1	2	FACETS	0.863	0.769	0.961	0.863	0.769	0.961	CLONAL	1	TRUE	1	0.35	2		898	636	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246485	10246485	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	81	776	1	ENST00000340748.4:c.4652G>T	p.Arg1551Leu	p.R1551L	ENST00000340748		1551	cGg/cTg	38/40	1	2	FACETS	0.924	0.816	1	0.924	0.816	1	CLONAL	1	TRUE	1	0.35	2		777	501	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279666	18279666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	68	659	0	ENST00000222254.8:c.1939C>T	p.Arg647Cys	p.R647C	ENST00000222254	NM_005027.3	647	Cgc/Tgc	15/16	1	2	FACETS	0.891	0.778	1	0.891	0.778	1	CLONAL	1	TRUE	1	0.35	2		659	436	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224111	36224111	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	61	673	2	ENST00000222270.7:c.6666del	p.Thr2223ProfsTer38	p.T2223Pfs*38	ENST00000222270	NM_014727.1	2221	Ccc/cc	28/37	1	2	FACETS	0.805	0.696	0.922	0.805	0.696	0.922	CLONAL	1	TRUE	1	0.35	2		675	433	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795043	42795043	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	29	888	3	ENST00000575354.2:c.2123G>T	p.Arg708Met	p.R708M	ENST00000575354	NM_015125.3	708	aGg/aTg	10/20	1	2	FACETS	0.31	0.248	0.381	0.31	0.248	0.381	SUBCLONAL	1	TRUE	1	0.35	2		891	534	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905962	50905962	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371612922	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	89	851	0	ENST00000440232.2:c.934G>A	p.Val312Met	p.V312M	ENST00000440232	NM_002691.3	312	Gtg/Atg	8/27	1	2	FACETS	0.988	0.878	1	0.988	0.878	1	CLONAL	1	TRUE	1	0.35	2		851	515	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241108	39241108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	63	716	1	ENST00000402219.2:c.1963C>T	p.Pro655Ser	p.P655S	ENST00000402219	NM_005633.3	655	Cca/Tca	12/23	1	2	FACETS	0.633	0.547	0.725	0.633	0.547	0.725	SUBCLONAL	1	TRUE	1	0.35	2		717	569	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419833	41419833	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	57	504	0	ENST00000373198.4:c.486+2T>C		p.X162_splice	ENST00000373198	NM_133170.3	162			1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.35	2		504	288	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319711	62319711	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	71	753	0	ENST00000360203.5:c.1694T>C	p.Val565Ala	p.V565A	ENST00000360203	NM_001283009.1	565	gTc/gCc	20/35	1	2	FACETS	0.803	0.703	0.912	0.803	0.703	0.912	CLONAL	1	TRUE	1	0.35	2		753	505	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655350	45655350	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	129	963	0	ENST00000407780.3:c.502A>G	p.Asn168Asp	p.N168D	ENST00000407780	NM_001283052.1	168	Aac/Gac	4/7	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.35	2		963	671	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038267	30038267	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	91	593	0	ENST00000338641.4:c.440A>G	p.Gln147Arg	p.Q147R	ENST00000338641	NM_000268.3	147	cAg/cGg	4/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.35	2		593	421	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527551	41527551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs533244094	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	80	665	1	ENST00000263253.7:c.1442C>T	p.Pro481Leu	p.P481L	ENST00000263253	NM_001429.3	481	cCg/cTg	6/31	1	2	FACETS	0.914	0.807	1	0.914	0.807	1	CLONAL	1	TRUE	1	0.35	2		666	500	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37038201	37038201	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs267607718	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	38	324	0	ENST00000231790.2:c.207+1G>T		p.X69_splice	ENST00000231790	NM_000249.3	69			1	2	FACETS	0.883	0.735	1	0.883	0.735	1	CLONAL	1	TRUE	1	0.35	2		324	246	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070382	37070382	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs63749916	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	42	514	0	ENST00000231790.2:c.1520del	p.Leu507Ter	p.L507*	ENST00000231790	NM_000249.3	506	gTt/gt	13/19	1	2	FACETS	0.628	0.526	0.742	0.628	0.526	0.742	SUBCLONAL	1	TRUE	1	0.35	2		514	382	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070413	37070413	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	40	430	0	ENST00000231790.2:c.1550del	p.Gly517AspfsTer18	p.G517Dfs*18	ENST00000231790	NM_000249.3	516	caG/ca	13/19	1	2	FACETS	0.752	0.627	0.889	0.752	0.627	0.889	SUBCLONAL	1	TRUE	1	0.35	2		430	304	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397785	49397785	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	99	819	0	ENST00000418115.1:c.439A>G	p.Met147Val	p.M147V	ENST00000418115	NM_001664.2	147	Atg/Gtg	5/5	1	2	FACETS	0.853	0.762	0.95	0.853	0.762	0.95	CLONAL	1	TRUE	1	0.35	2		819	663	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595860	52595860	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	98	743	0	ENST00000394830.3:c.4055A>G	p.Tyr1352Cys	p.Y1352C	ENST00000394830	NM_018313.4	1352	tAc/tGc	26/30	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.35	2		743	557	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541907	187541907	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	49	757	1	ENST00000441802.2:c.5833A>G	p.Arg1945Gly	p.R1945G	ENST00000441802	NM_005245.3	1945	Aga/Gga	10/27	1	2	FACETS	0.454	0.384	0.531	0.454	0.384	0.531	SUBCLONAL	1	TRUE	1	0.35	2		758	617	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557989	187557989	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1490273216	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	47	559	0	ENST00000441802.2:c.3722A>G	p.Asn1241Ser	p.N1241S	ENST00000441802	NM_005245.3	1241	aAc/aGc	5/27	1	2	FACETS	0.629	0.531	0.736	0.629	0.531	0.736	SUBCLONAL	1	TRUE	1	0.35	2		559	427	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155687	56155687	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768948038	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	73	519	1	ENST00000399503.3:c.779G>A	p.Arg260His	p.R260H	ENST00000399503	NM_005921.1	260	cGc/cAc	3/20	1	2	FACETS	0.95	0.834	1	0.95	0.834	1	CLONAL	1	TRUE	1	0.35	2		520	439	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590975	67590975	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	21	214	0	ENST00000274335.5:c.1569-1G>T		p.X523_splice	ENST00000274335		523			1	2	FACETS	0.732	0.568	0.92	0.732	0.568	0.92	CLONAL	1	TRUE	1	0.35	2		214	164	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80057448	80057448	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764683130	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	73	657	0	ENST00000265081.6:c.1847G>A	p.Arg616His	p.R616H	ENST00000265081	NM_002439.4	616	cGt/cAt	13/24	1	2	FACETS	0.913	0.801	1	0.913	0.801	1	CLONAL	1	TRUE	1	0.35	2		657	457	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924462	131924462	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	40	625	0	ENST00000265335.6:c.1135G>T	p.Glu379Ter	p.E379*	ENST00000265335		379	Gaa/Taa	8/25	1	2	FACETS	0.446	0.37	0.53	0.446	0.37	0.53	SUBCLONAL	1	TRUE	1	0.35	2		625	513	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977893	131977893	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1561661762	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	42	560	0	ENST00000265335.6:c.3776A>G	p.Gln1259Arg	p.Q1259R	ENST00000265335		1259	cAg/cGg	25/25	1	2	FACETS	0.593	0.495	0.7	0.593	0.495	0.7	SUBCLONAL	1	TRUE	1	0.35	2		560	405	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149452996	149452996	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	37	661	0	ENST00000286301.3:c.950A>G	p.Glu317Gly	p.E317G	ENST00000286301	NM_005211.3	317	gAg/gGg	7/22	1	2	FACETS	0.609	0.503	0.727	0.609	0.503	0.727	SUBCLONAL	1	TRUE	1	0.35	2		661	347	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056977	180056977	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	60	942	0	ENST00000261937.6:c.642C>A	p.Asp214Glu	p.D214E	ENST00000261937	NM_182925.4	214	gaC/gaA	5/30	1	2	FACETS	0.694	0.599	0.797	0.694	0.599	0.797	SUBCLONAL	1	TRUE	1	0.35	2		942	494	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394872	394872	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	40	621	0	ENST00000380956.4:c.268C>A	p.Pro90Thr	p.P90T	ENST00000380956	NM_001195286.1	90	Cct/Act	3/9	1	2	FACETS	0.505	0.419	0.6	0.505	0.419	0.6	SUBCLONAL	1	TRUE	1	0.35	2		621	453	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910540	29910540	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	24	696	0	ENST00000376809.5:c.80A>G	p.His27Arg	p.H27R	ENST00000376809	NM_002116.7	27	cAc/cGc	2/8	1	2	FACETS	0.336	0.263	0.421	0.336	0.263	0.421	SUBCLONAL	1	TRUE	1	0.35	2		696	408	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912306	29912308	+	frameshift_variant	Frame_Shift_Del	DEL	GTG	GTG	TT	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	68	757	1	ENST00000376809.5:c.925_927delinsTT	p.Val309LeufsTer13	p.V309Lfs*13	ENST00000376809	NM_002116.7	309	GTG/TT	5/8	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.35	2		758	379	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813523	32813523	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	80	565	0	ENST00000354258.4:c.2260C>A	p.Arg754Ser	p.R754S	ENST00000354258	NM_000593.5	754	Cgc/Agc	11/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.35	2		565	343	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200101	138200101	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs769339129	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	36	539	0	ENST00000237289.4:c.1519A>G	p.Ser507Gly	p.S507G	ENST00000237289	NM_001270507.1	507	Agc/Ggc	7/9	1	2	FACETS	0.452	0.371	0.543	0.452	0.371	0.543	SUBCLONAL	1	TRUE	1	0.35	2		539	455	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522287	157522287	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	61	895	0	ENST00000346085.5:c.4559A>G	p.Gln1520Arg	p.Q1520R	ENST00000346085	NM_020732.3	1520	cAg/cGg	18/20	1	2	FACETS	0.567	0.489	0.652	0.567	0.489	0.652	SUBCLONAL	1	TRUE	1	0.35	2		895	615	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508352	106508352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs890365557	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	41	453	0	ENST00000359195.3:c.346G>A	p.Val116Met	p.V116M	ENST00000359195	NM_002649.2	116	Gtg/Atg	2/11	1	2	FACETS	0.813	0.681	0.959	0.813	0.681	0.959	CLONAL	1	TRUE	1	0.35	2		453	288	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	55	769	1	ENST00000262189.6:c.8390A>G	p.Lys2797Arg	p.K2797R	ENST00000262189	NM_170606.2	2797	aAg/aGg	38/59	1	2	FACETS	0.476	0.407	0.552	0.476	0.407	0.552	SUBCLONAL	1	TRUE	1	0.35	2		770	660	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209583	98209583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375998275	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	58	666	1	ENST00000331920.6:c.3955C>T	p.Arg1319Cys	p.R1319C	ENST00000331920	NM_000264.3	1319	Cgc/Tgc	23/24	1	2	FACETS	0.893	0.771	1	0.893	0.771	1	CLONAL	1	TRUE	1	0.35	2		667	371	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759592	133759592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	83	785	1	ENST00000318560.5:c.1915C>T	p.Arg639Ter	p.R639*	ENST00000318560	NM_005157.4	639	Cga/Tga	11/11	1	2	FACETS	0.99	0.877	1	0.99	0.877	1	CLONAL	1	TRUE	1	0.35	2		786	479	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760343	133760344	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	43	684	0	ENST00000318560.5:c.2670dup	p.Lys891GlufsTer49	p.K891Efs*49	ENST00000318560	NM_005157.4	889	aag/aaGg	11/11	1	2	FACETS	0.683	0.573	0.804	0.683	0.573	0.804	SUBCLONAL	1	TRUE	1	0.35	2		684	360	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391778	139391778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756571156	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	68	689	1	ENST00000277541.6:c.6413C>T	p.Pro2138Leu	p.P2138L	ENST00000277541	NM_017617.3	2138	cCg/cTg	34/34	1	2	FACETS	0.86	0.75	0.977	0.86	0.75	0.977	CLONAL	1	TRUE	1	0.35	2		690	452	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401242	139401242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	118	800	0	ENST00000277541.6:c.3827G>A	p.Cys1276Tyr	p.C1276Y	ENST00000277541	NM_017617.3	1276	tGc/tAc	23/34	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.35	2		800	599	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411584	63411584	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	27	868	0	ENST00000330258.3:c.1583T>C	p.Leu528Pro	p.L528P	ENST00000330258	NM_152424.3	528	cTc/cCc	2/2	1	2	FACETS	0.292	0.231	0.361	0.292	0.231	0.361	SUBCLONAL	1	TRUE	1	0.35	2		868	529	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339954	70339954	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	78	683	0	ENST00000374080.3:c.487A>G	p.Thr163Ala	p.T163A	ENST00000374080		163	Acc/Gcc	4/45	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.35	2		683	432	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341551	70341551	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	116	860	0	ENST00000374080.3:c.986C>A	p.Pro329His	p.P329H	ENST00000374080		329	cCc/cAc	7/45	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.35	2		860	564	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361086	70361091	+	inframe_deletion	In_Frame_Del	DEL	CAGCAA	CAGCAA	-	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	26	392	0	ENST00000374080.3:c.6285_6290del	p.Gln2114_Gln2115del	p.Q2114_Q2115del	ENST00000374080		2092	CAGCAA/-	43/45	1	2	FACETS	0.54	0.429	0.667	0.54	0.429	0.667	SUBCLONAL	1	TRUE	1	0.35	2		392	275	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361174	70361174	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1213251626	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	84	723	0	ENST00000374080.3:c.6362A>G	p.Gln2121Arg	p.Q2121R	ENST00000374080		2121	cAg/cGg	43/45	1	2	FACETS	0.998	0.885	1	0.998	0.885	1	CLONAL	1	TRUE	1	0.35	2		723	481	SUCCESS
BTK	695	MSKCC	GRCh37	X	100629549	100629549	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	81	865	0	ENST00000308731.7:c.215del	p.Asn72IlefsTer49	p.N72Ifs*49	ENST00000308731	NM_000061.2	72	aAt/at	3/19	1	2	FACETS	0.706	0.622	0.796	0.706	0.622	0.796	SUBCLONAL	1	TRUE	1	0.35	2		865	656	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860039	152860041	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0020331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	48	612	0	ENST00000406277.2:c.387_389del	p.Leu130del	p.L130del	ENST00000406277	NM_152274.4	129	gtTCTg/gtg	5/7	1		FACETS		0.627	0.862				SUBCLONAL	1	TRUE	1	0.35	2		612	371	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097691	27097691	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0020333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	229	575	0	ENST00000324856.7:c.3280A>T	p.Lys1094Ter	p.K1094*	ENST00000324856	NM_006015.4	1094	Aag/Tag	12/20	0.681585560831239	1	FACETS	0.867	0.816	0.918	0.867	0.816	0.918	CLONAL	1	TRUE	0	0.681585560831239	1		575	511	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438158	438158	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	227	439	0	ENST00000399788.2:c.1811G>C	p.Arg604Pro	p.R604P	ENST00000399788	NM_001042603.1	604	cGc/cCc	14/28	NA	2	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.681585560831239	2		439	646	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042647	42042648	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	194	497	0	ENST00000219905.7:c.6843dup	p.Gln2282ThrfsTer14	p.Q2282Tfs*14	ENST00000219905	NM_001164273.1	2281	ata/atAa	17/24	0.681585560831239	1	FACETS	0.887	0.832	0.943	0.887	0.832	0.943	CLONAL	1	TRUE	0	0.681585560831239	1		497	423	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14015940	14015940	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371487368	NA	P-0020333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	151	376	0	ENST00000311895.7:c.260G>A	p.Arg87His	p.R87H	ENST00000311895	NM_005236.2	87	cGt/cAt	2/11	0.11249766343779	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.681585560831239	0		376	551	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752759	42752759	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	240	609	1	ENST00000222329.4:c.1505G>T	p.Gly502Val	p.G502V	ENST00000222329	NM_006494.2	502	gGg/gTg	4/4	NA	2	FACETS	0.878	0.822	0.935			1	INDETERMINATE	1	TRUE	NA	0.681585560831239	2		610	802	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876353	35876353	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	217	488	0	ENST00000303115.3:c.1145T>A	p.Leu382His	p.L382H	ENST00000303115	NM_002185.3	382	cTc/cAc	8/8	1	2	FACETS	0.95	0.888	1	0.95	0.888	1	CLONAL	1	TRUE	1	0.681585560831239	2		488	670	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271309	26271309	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	243	511	0	ENST00000305910.3:c.304G>C	p.Val102Leu	p.V102L	ENST00000305910	NM_003534.2	102	Gtg/Ctg	1/1	0.240387318193775	4	FACETS	1	0.993	1	0.739	0.693	0.787	INDETERMINATE	1	TRUE	2	0.681585560831239	4		511	811	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	175	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.269853220772573	1	FACETS	0.82	0.757	0.885	0.82	0.757	0.885	INDETERMINATE	1	TRUE	0	0.450516354465418	1		555	734	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0020334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	162	528	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.450516354465418	1	FACETS	0.966	0.891	1	0.966	0.891	1	CLONAL	1	TRUE	0	0.450516354465418	1		530	577	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0020334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	136	312	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	0.219021653702703	5	FACETS	0.903	0.825	0.985	0.602	0.55	0.657	INDETERMINATE	2	TRUE	2	0.450516354465418	5		312	560	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423511	88423511	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0020334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	99	709	0	ENST00000360948.2:c.2324C>G	p.Ser775Ter	p.S775*	ENST00000360948	NM_001012338.2	775	tCa/tGa	18/19	0.269853220772573	1	FACETS	0.463	0.413	0.516	0.463	0.413	0.516	INDETERMINATE	1	TRUE	0	0.450516354465418	1		709	735	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0020335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	149	668	1	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.42154676072685	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.42154676072685	1		669	529	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584497	48584497	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	77	460	2	ENST00000342988.3:c.670C>T	p.Gln224Ter	p.Q224*	ENST00000342988	NM_005359.5	224	Cag/Tag	6/12	0.42154676072685	1	FACETS	0.948	0.841	1	0.948	0.841	1	CLONAL	1	TRUE	0	0.42154676072685	1		462	304	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0020336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	412	715	0	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	0.674738358585191	3	FACETS	0.913	0.875	0.952			1	CLONAL	2	TRUE	NA	0.722702916575963	3		715	850	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524489	44524489	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	80	402	0	ENST00000291552.4:c.68A>G	p.Lys23Arg	p.K23R	ENST00000291552	NM_006758.2	23	aAa/aGa	2/8	0.361515064307756	1	FACETS	0.38	0.337	0.426	0.38	0.337	0.426	INDETERMINATE	1	TRUE	0	0.722702916575963	1		402	372	SUCCESS
ALK	238	MSKCC	GRCh37	2	29419724	29419724	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs748787875	NA	P-0020336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	214	482	0	ENST00000389048.3:c.4076A>G	p.Tyr1359Cys	p.Y1359C	ENST00000389048	NM_004304.4	1359	tAc/tGc	28/29	1	2	FACETS	0.976	0.913	1	0.976	0.913	1	CLONAL	1	TRUE	1	0.722702916575963	2		482	607	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589557	67589562	+	inframe_deletion	In_Frame_Del	DEL	TAATAT	TAATAT	-	novel	NA	P-0020336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	131	393	0	ENST00000274335.5:c.1321_1326del	p.Asn441_Ile442del	p.N441_I442del	ENST00000274335		440	gaTAATATt/gat	10/15	0.532064174720523	1	FACETS	0.689	0.634	0.745	0.689	0.634	0.745	SUBCLONAL	1	TRUE	0	0.722702916575963	1		393	336	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349036	70349036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1336321422	NA	P-0020336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	200	751	0	ENST00000374080.3:c.3548C>T	p.Pro1183Leu	p.P1183L	ENST00000374080		1183	cCg/cTg	25/45	1	2	FACETS	0.744	0.691	0.798	0.744	0.691	0.798	SUBCLONAL	1	TRUE	1	0.722702916575963	2		751	744	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0020337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	125	408	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.835	0.759	0.914	0.835	0.759	0.914	CLONAL	1	TRUE	1	0.556698917186202	2		408	538	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942685	48942685	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913301	NA	P-0020337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	126	563	1	ENST00000267163.4:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000267163	NM_000321.2	358	Cga/Tga	11/27	0.556698917186202	1	FACETS	0.646	0.588	0.706	0.646	0.588	0.706	SUBCLONAL	1	TRUE	0	0.556698917186202	1		564	506	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012660	36012660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	15	261	0	ENST00000358208.4:c.104C>T	p.Ser35Leu	p.S35L	ENST00000358208		35	tCg/tTg	2/12	1	2	FACETS	0.183	0.133	0.242	0.183	0.133	0.242	SUBCLONAL	1	TRUE	1	0.556698917186202	2		261	295	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996161	73996161	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1223303121	NA	P-0020337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	266	882	5	ENST00000318443.5:c.895G>A	p.Glu299Lys	p.E299K	ENST00000318443	NM_001024736.1	299	Gaa/Aaa	5/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.556698917186202	2		887	856	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976544	18976544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	222	933	0	ENST00000262803.5:c.3194C>T	p.Ser1065Phe	p.S1065F	ENST00000262803	NM_002911.3	1065	tCc/tTc	22/24	1	2	FACETS	0.951	0.887	1	0.951	0.887	1	CLONAL	1	TRUE	1	0.556698917186202	2		933	839	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0020338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	59	591	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.738	0.633	0.854	0.738	0.633	0.854	SUBCLONAL	1	TRUE	1	0.16443443783476	2		591	972	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0020338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	62	724	4	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.16443443783476	2		728	669	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882049	36882050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs780753361	NA	P-0020338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	54	1074	0	ENST00000358127.4:c.963dup	p.Ala322ArgfsTer19	p.A322Rfs*19	ENST00000358127	NM_001280556.1	321	-/C	8/10	1	2	FACETS	0.634	0.539	0.738	0.634	0.539	0.738	SUBCLONAL	1	TRUE	1	0.16443443783476	2		1074	1036	SUCCESS
APC	324	MSKCC	GRCh37	5	112175530	112175530	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	26	499	0	ENST00000257430.4:c.4240del	p.Val1414Ter	p.V1414*	ENST00000257430	NM_000038.5	1413	atG/at	16/16	0.151850694912861	1	FACETS	0.607	0.48	0.754	0.607	0.48	0.754	SUBCLONAL	1	TRUE	0	0.16443443783476	1		499	478	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874217	155874217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748272466	NA	P-0020338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	107	935	1	ENST00000368323.3:c.314G>A	p.Arg105His	p.R105H	ENST00000368323	NM_006912.5	105	cGt/cAt	5/6	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.16443443783476	2		936	1017	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	207	424	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	1	0.943	1			1	INDETERMINATE	1	TRUE	NA	0.485180639194388	2		424	840	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0020339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	272	860	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.485180639194388	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.485180639194388	1		861	773	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911141	32911141	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	32	424	0	ENST00000380152.3:c.2649C>A	p.Phe883Leu	p.F883L	ENST00000380152		883	ttC/ttA	11/27	1	2	FACETS	0.211	0.17	0.257	0.211	0.17	0.257	SUBCLONAL	1	TRUE	1	0.485180639194388	2		424	625	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591889	48591889	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	192	573	0	ENST00000342988.3:c.1052A>G	p.Asp351Gly	p.D351G	ENST00000342988	NM_005359.5	351	gAt/gGt	9/12	0.485180639194388	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.485180639194388	1		573	567	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197126	106197126	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	20	416	0	ENST00000380013.4:c.5459G>A	p.Ser1820Asn	p.S1820N	ENST00000380013	NM_001127208.2	1820	aGt/aAt	11/11	0.485180639194388	1	FACETS	0.158	0.121	0.203	0.158	0.121	0.203	SUBCLONAL	1	TRUE	0	0.485180639194388	1		416	394	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974800	21974801	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0020339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	82	265	0	ENST00000304494.5:c.25_26dup	p.Met9IlefsTer18	p.M9Ifs*18	ENST00000304494	NM_000077.4	9	atg/atATg	1/3	0.485180639194388	1	FACETS	0.97	0.867	1	0.97	0.867	1	CLONAL	1	TRUE	0	0.485180639194388	1		265	264	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0020340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	330	926	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.259303247793744	5	FACETS	0.97	0.923	1	0.97	0.923	1	CLONAL	5	TRUE	0	0.259303247793744	5		926	729	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729180	66729180	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs397516793	NA	P-0020340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	60	1103	0	ENST00000307102.5:c.388T>C	p.Tyr130His	p.Y130H	ENST00000307102	NM_002755.3	130	Tat/Cat	3/11	0.259303247793744	3	FACETS	0.758	0.652	0.873	0.379	0.326	0.437	SUBCLONAL	1	TRUE	1	0.259303247793744	3		1103	690	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0020340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	163	1038	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.259303247793744	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.259303247793744	2		1038	585	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512242	120512242	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	115	912	0	ENST00000256646.2:c.1000G>T	p.Asp334Tyr	p.D334Y	ENST00000256646	NM_024408.3	334	Gac/Tac	6/34	0.219915535635518	3	FACETS	0.868	0.785	0.956	0.868	0.785	0.956	CLONAL	2	TRUE	1	0.259303247793744	3		912	577	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551447	150551447	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	141	1216	0	ENST00000369026.2:c.560G>T	p.Arg187Leu	p.R187L	ENST00000369026	NM_021960.4	187	cGg/cTg	1/3	0.259303247793744	4	FACETS	1	0.915	1	1	0.915	1	CLONAL	2	TRUE	2	0.259303247793744	4		1216	683	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851408	156851408	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762112317	NA	P-0020340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	125	1053	1	ENST00000524377.1:c.2365C>A	p.Pro789Thr	p.P789T	ENST00000524377	NM_002529.3	789	Cct/Act	17/17	0.259303247793744	3	FACETS	0.797	0.723	0.876	0.797	0.723	0.876	SUBCLONAL	2	TRUE	1	0.259303247793744	3		1054	683	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194741	30194741	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0020340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	72	722	1	ENST00000331968.5:c.403+1del		p.X135_splice	ENST00000331968	NM_002742.2	135			0.196531572116788	4	FACETS	1	0.972	1	0.717	0.628	0.812	CLONAL	1	TRUE	2	0.259303247793744	4		723	488	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883113	37883113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780434636	NA	P-0020340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	115	1215	1	ENST00000269571.5:c.3016C>T	p.Arg1006Cys	p.R1006C	ENST00000269571		1006	Cgc/Tgc	25/27	0.219915535635518	3	FACETS	1	0.981	1	0.698	0.629	0.77	CLONAL	1	TRUE	1	0.259303247793744	3		1216	718	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554358	63554359	+	inframe_insertion	In_Frame_Ins	INS	-	-	TAC	novel	NA	P-0020340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	41	1021	0	ENST00000307078.5:c.380_381insGTA	p.Thr127_Leu128insTyr	p.T127_L128insY	ENST00000307078	NM_004655.3	127	act/acGTAt	2/11	0.259303247793744	4	FACETS	0.562	0.467	0.669	0.187	0.155	0.223	SUBCLONAL	1	TRUE	1	0.259303247793744	4		1021	708	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727982	78727982	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	42	537	1	ENST00000306801.3:c.827G>T	p.Arg276Leu	p.R276L	ENST00000306801	NM_020761.2	276	cGc/cTc	6/34	0.259303247793744	4	FACETS	0.936	0.782	1	0.312	0.26	0.369	CLONAL	1	TRUE	1	0.259303247793744	4		538	436	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728880	39728880	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	71	471	1	ENST00000361337.2:c.1160G>T	p.Ser387Ile	p.S387I	ENST00000361337	NM_003286.2	387	aGc/aTc	12/21	0.219915535635518	3	FACETS	1	0.895	1	1	0.895	1	CLONAL	2	TRUE	1	0.259303247793744	3		472	304	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877410	40877410	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	88	909	0	ENST00000373198.4:c.2286C>A	p.Asn762Lys	p.N762K	ENST00000373198	NM_133170.3	762	aaC/aaA	15/32	0.222641442636836	2	FACETS	1	0.976	1	0.697	0.62	0.779	CLONAL	1	TRUE	0	0.259303247793744	2		909	487	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72842185	72842185	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0020340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	41	438	0	ENST00000325599.8:c.1063A>T	p.Lys355Ter	p.K355*	ENST00000325599	NM_018130.2	355	Aaa/Taa	10/11	0.219915535635518	3	FACETS	1	0.948	1	0.682	0.571	0.803	CLONAL	1	TRUE	1	0.259303247793744	3		438	262	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202803	128202803	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	37	1018	0	ENST00000341105.2:c.917G>T	p.Trp306Leu	p.W306L	ENST00000341105	NM_032638.4	306	tGg/tTg	4/6	0.219915535635518	3	FACETS	0.541	0.445	0.649	0.27	0.222	0.325	SUBCLONAL	1	TRUE	1	0.259303247793744	3		1018	596	SUCCESS
APC	324	MSKCC	GRCh37	5	112175382	112175382	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	23	440	2	ENST00000257430.4:c.4091G>T	p.Ser1364Ile	p.S1364I	ENST00000257430	NM_000038.5	1364	aGt/aTt	16/16	1	2	FACETS	0.669	0.523	0.838	0.669	0.523	0.838	SUBCLONAL	1	TRUE	1	0.259303247793744	2		442	265	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335630	81335630	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	68	719	0	ENST00000222390.5:c.1730C>A	p.Ser577Ter	p.S577*	ENST00000222390	NM_000601.4	577	tCa/tAa	15/18	0.219915535635518	3	FACETS	1	0.973	1	0.739	0.646	0.839	CLONAL	1	TRUE	1	0.259303247793744	3		719	401	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882039	36882039	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	52	1034	1	ENST00000358127.4:c.974G>A	p.Gly325Asp	p.G325D	ENST00000358127	NM_001280556.1	325	gGc/gAc	8/10	1	2	FACETS	0.695	0.591	0.809	0.695	0.591	0.809	SUBCLONAL	1	TRUE	1	0.259303247793744	2		1035	577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578259	7578259	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	217	923	0	ENST00000269305.4:c.590T>G	p.Val197Gly	p.V197G	ENST00000269305	NM_001126112.2	197	gTg/gGg	6/11	0.293628379898286	2	FACETS	1	0.991	1	0.734	0.684	0.786	CLONAL	1	TRUE	0	0.337358835603003	2		923	876	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0020344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	29	375	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	1	2	FACETS	0.323	0.259	0.396	0.323	0.259	0.396	SUBCLONAL	1	TRUE	1	0.511198641864156	2		375	351	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855991	68855992	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATTCTTCTGTGAGAGGA	novel	NA	P-0020344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	126	875	0	ENST00000261769.5:c.1802_1818dup	p.Pro607SerfsTer12	p.P607Sfs*12	ENST00000261769	NM_004360.3	600	ata/atATTCTTCTGTGAGAGGAa	12/16	0.511198641864156	1	FACETS	0.572	0.519	0.627	0.572	0.519	0.627	SUBCLONAL	1	TRUE	0	0.511198641864156	1		875	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0020345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	244	1054	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.287507274357833	2	FACETS	0.971	0.909	1	0.971	0.909	1	CLONAL	2	TRUE	0	0.287507274357833	2		1055	874	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86648999	86648999	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs975191415	NA	P-0020345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	85	564	0	ENST00000274376.6:c.1279C>T	p.Arg427Ter	p.R427*	ENST00000274376	NM_002890.2	427	Cga/Tga	9/25	0.21597454824727	4	FACETS	0.961	0.855	1	0.961	0.855	1	CLONAL	2	TRUE	2	0.287507274357833	4		564	396	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438541	52438541	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	202	920	0	ENST00000460680.1:c.1178del	p.Gln393ArgfsTer37	p.Q393Rfs*37	ENST00000460680	NM_004656.3	393	cAg/cg	12/17	0.287507274357833	2	FACETS	0.864	0.803	0.928	0.864	0.803	0.928	CLONAL	2	TRUE	0	0.287507274357833	2		920	813	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797244	135797248	+	frameshift_variant	Frame_Shift_Del	DEL	TACTG	TACTG	-	novel	NA	P-0020345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	51	418	0	ENST00000298552.3:c.621_625del	p.Ser208GlufsTer8	p.S208Efs*8	ENST00000298552	NM_001162426.1	207	taCAGTAtg/tatg	7/23	0.287507274357833	2	FACETS	1	0.964	1	0.724	0.621	0.834	CLONAL	1	TRUE	0	0.287507274357833	2		418	245	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	131	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.238509190905806	1	FACETS	0.864	0.787	0.944	1	0.989	1	CLONAL	2	TRUE	0	0.238509190905806	1		555	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0020347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	119	809	7	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.191493455159653	0	FACETS	0.745	0.676	0.817			1	SUBCLONAL	2	TRUE	0	0.238509190905806	0		816	510	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247411	71247411	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756099573	NA	P-0020347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	140	694	1	ENST00000318789.4:c.122C>T	p.Thr41Met	p.T41M	ENST00000318789	NM_032682.5	41	aCg/aTg	6/21	0.189393768937895	2	FACETS	0.849	0.779	0.921	1	0.983	1	CLONAL	3	TRUE	0	0.238509190905806	2		695	461	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220505	1220505	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs886039554	NA	P-0020347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	100	783	0	ENST00000326873.7:c.597+1G>T		p.X199_splice	ENST00000326873	NM_000455.4	199			0.191493455159653	0	FACETS	0.66	0.592	0.731			1	SUBCLONAL	2	TRUE	0	0.238509190905806	0		783	484	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692790	89692790	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554898067	NA	P-0020348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	93	531	0	ENST00000371953.3:c.274G>T	p.Asp92Tyr	p.D92Y	ENST00000371953	NM_000314.4	92	Gac/Tac	5/9	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.37944949870348	2		531	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578523	7578523	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1567554216	NA	P-0020348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	320	1192	0	ENST00000269305.4:c.407A>C	p.Gln136Pro	p.Q136P	ENST00000269305	NM_001126112.2	136	cAa/cCa	5/11	0.37944949870348	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.37944949870348	1		1192	1262	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0020348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	32	404	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	0.421	0.341	0.51	0.421	0.341	0.51	SUBCLONAL	1	TRUE	1	0.37944949870348	2		404	401	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945628	71945643	+	frameshift_variant	Frame_Shift_Del	DEL	AAGTGCAGTGGTCTTC	AAGTGCAGTGGTCTTC	-	novel	NA	P-0020348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	128	854	0	ENST00000298229.2:c.2385_2400del	p.Lys795AsnfsTer45	p.K795Nfs*45	ENST00000298229	NM_001567.3	795	aAAGTGCAGTGGTCTTCa/aa	21/28	0.329377851142736	1	FACETS	0.683	0.619	0.751	0.683	0.619	0.751	SUBCLONAL	1	TRUE	0	0.37944949870348	1		854	800	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871640	35871640	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs957688002	NA	P-0020348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	62	575	0	ENST00000216797.5:c.866A>G	p.Tyr289Cys	p.Y289C	ENST00000216797	NM_020529.2	289	tAt/tGt	5/6	1	2	FACETS	0.56	0.483	0.642	0.56	0.483	0.642	SUBCLONAL	1	TRUE	1	0.37944949870348	2		575	584	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554509	63554509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778517452	NA	P-0020348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	49	768	1	ENST00000307078.5:c.230G>A	p.Arg77Gln	p.R77Q	ENST00000307078	NM_004655.3	77	cGg/cAg	2/11	1	2	FACETS	0.347	0.293	0.406	0.347	0.293	0.406	SUBCLONAL	1	TRUE	1	0.37944949870348	2		769	745	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228622	36228622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	116	1081	3	ENST00000222270.7:c.7636G>A	p.Glu2546Lys	p.E2546K	ENST00000222270	NM_014727.1	2546	Gag/Aag	34/37	0.262762500112362	1	FACETS	0.426	0.382	0.472	0.426	0.382	0.472	SUBCLONAL	1	TRUE	0	0.37944949870348	1		1084	1164	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228310	228310	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1235961098	NA	P-0020348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	71	296	0	ENST00000264932.6:c.632A>G	p.Tyr211Cys	p.Y211C	ENST00000264932	NM_004168.2	211	tAt/tGt	6/15	1	2	FACETS	0.9	0.789	1	0.9	0.789	1	CLONAL	1	TRUE	1	0.37944949870348	2		296	416	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0020349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	171	146	0				ENST00000310581	NM_198253.2	-/1132			0.195130401473669	0	FACETS	0.91	0.862	0.957			1	CLONAL	4	TRUE	0	0.27	0		146	254	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426181	49426181	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	189	806	1	ENST00000301067.7:c.12307C>T	p.Gln4103Ter	p.Q4103*	ENST00000301067	NM_003482.3	4103	Cag/Tag	39/54	0.261135647564471	5	FACETS	0.997	0.93	1	1	0.989	1	CLONAL	4	TRUE	2	0.27	5		807	493	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	221	122	0				ENST00000310581	NM_198253.2	-/1132			0.365459696068057	3	FACETS	0.977	0.916	1	0.977	0.916	1	CLONAL	2	TRUE	1	0.477472370288764	3		122	587	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652129	36652129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34916193	NA	P-0020351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	48	589	0	ENST00000244741.5:c.251G>A	p.Arg84Gln	p.R84Q	ENST00000244741	NM_000389.4	84	cGa/cAa	2/3	0.182263271396425	5	FACETS	0.389	0.327	0.457	0.13	0.109	0.153	INDETERMINATE	1	TRUE	2	0.477472370288764	5		589	888	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101054	27101054	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	255	670	0	ENST00000324856.7:c.4336C>T	p.Arg1446Ter	p.R1446*	ENST00000324856	NM_006015.4	1446	Cga/Tga	18/20	0.182263271396425	5	FACETS	0.821	0.768	0.875	0.547	0.512	0.584	INDETERMINATE	2	TRUE	2	0.477472370288764	5		670	1117	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972596	32972596	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	124	386	0	ENST00000380152.3:c.9946G>C	p.Glu3316Gln	p.E3316Q	ENST00000380152		3316	Gaa/Caa	27/27	0.403002074767321	3	FACETS	1	0.986	1	0.738	0.673	0.805	CLONAL	1	TRUE	1	0.477472370288764	3		386	436	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	209	592	1	ENST00000335508.6:c.2704G>A	p.Glu902Lys	p.E902K	ENST00000335508	NM_012433.2	902	Gaa/Aaa	18/25	0.477472370288764	3	FACETS	0.958	0.896	1	0.958	0.896	1	CLONAL	2	TRUE	1	0.477472370288764	3		593	566	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796754	135796754	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203434	NA	P-0020351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	105	357	0	ENST00000298552.3:c.733C>T	p.Arg245Ter	p.R245*	ENST00000298552	NM_001162426.1	245	Cga/Tga	8/23	0.399460847007615	2	FACETS	0.766	0.697	0.838	0.766	0.697	0.838	SUBCLONAL	2	TRUE	0	0.477472370288764	2		357	287	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15976770	15976770	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	84	785	0	ENST00000268712.3:c.3784G>T	p.Glu1262Ter	p.E1262*	ENST00000268712	NM_006311.3	1262	Gag/Tag	28/46	1	2	FACETS	0.623	0.551	0.699	0.623	0.551	0.699	SUBCLONAL	1	TRUE	1	0.477472370288764	2		785	565	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95584000	95584000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777894117	NA	P-0020351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	74	524	0	ENST00000393063.1:c.1468C>T	p.Arg490Cys	p.R490C	ENST00000393063	NM_030621.3	490	Cgc/Tgc	10/28	0.357794798228339	2	FACETS	0.829	0.73	0.934	0.414	0.365	0.467	CLONAL	1	TRUE	0	0.477472370288764	2		524	374	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652242	36652242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753529000	NA	P-0020351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	135	642	1	ENST00000244741.5:c.364C>T	p.Arg122Cys	p.R122C	ENST00000244741	NM_000389.4	122	Cgc/Tgc	2/3	0.182263271396425	5	FACETS	1	0.958	1	0.364	0.331	0.4	INDETERMINATE	1	TRUE	2	0.477472370288764	5		643	888	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117319	115117319	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	142	397	0	ENST00000257566.3:c.855G>C	p.Gln285His	p.Q285H	ENST00000257566	NM_016569.3	285	caG/caC	4/8	0.182263271396425	5	FACETS	0.963	0.883	1	0.642	0.588	0.698	INDETERMINATE	2	TRUE	2	0.477472370288764	5		397	530	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143332	108143332	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs774935453	NA	P-0020351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	105	430	0	ENST00000278616.4:c.3151G>C	p.Glu1051Gln	p.E1051Q	ENST00000278616	NM_000051.3	1051	Gag/Cag	21/63	0.377493878175242	3	FACETS	1	0.976	1	0.425	0.383	0.469	CLONAL	1	TRUE	0	0.477472370288764	3		430	427	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727494	66727494	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	58	452	0	ENST00000307102.5:c.210G>C	p.Lys70Asn	p.K70N	ENST00000307102	NM_002755.3	70	aaG/aaC	2/11	0.182263271396425	5	FACETS	0.582	0.499	0.673	0.194	0.166	0.225	INDETERMINATE	1	TRUE	2	0.477472370288764	5		452	716	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40379580	40379580	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	124	777	0	ENST00000293328.3:c.252G>C	p.Lys84Asn	p.K84N	ENST00000293328	NM_012448.3	84	aaG/aaC	3/19	0.477472370288764	3	FACETS	0.605	0.546	0.668	0.303	0.273	0.334	SUBCLONAL	1	TRUE	1	0.477472370288764	3		777	1063	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46251035	46251035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	44	481	0	ENST00000371998.3:c.44C>T	p.Ser15Leu	p.S15L	ENST00000371998		15	tCa/tTa	3/23	0.477472370288764	3	FACETS	0.305	0.255	0.361	0.152	0.127	0.181	SUBCLONAL	1	TRUE	1	0.477472370288764	3		481	749	SUCCESS
ATR	545	MSKCC	GRCh37	3	142177823	142177823	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	95	360	0	ENST00000350721.4:c.7480G>C	p.Asp2494His	p.D2494H	ENST00000350721	NM_001184.3	2494	Gat/Cat	44/47	0.477472370288764	4	FACETS	1	0.955	1	0.377	0.336	0.42	CLONAL	1	TRUE	1	0.477472370288764	4		360	520	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114749	108114749	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79075295	NA	P-0020353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	231	829	0	ENST00000278616.4:c.566G>C	p.Arg189Thr	p.R189T	ENST00000278616	NM_000051.3	189	aGa/aCa	6/63	1	2	FACETS	0.963	0.9	1	0.963	0.9	1	CLONAL	1	TRUE	1	0.555883757577965	2		829	863	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428238	47428238	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	230	1011	0	ENST00000377045.4:c.1198C>A	p.Arg400Ser	p.R400S	ENST00000377045	NM_001654.4	400	Cgc/Agc	11/16	1	2	FACETS	0.966	0.902	1	0.966	0.902	1	CLONAL	1	TRUE	1	0.555883757577965	2		1011	857	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578505	7578506	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0020354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	340	1294	0	ENST00000269305.4:c.424_425del	p.Pro142CysfsTer6	p.P142Cfs*6	ENST00000269305	NM_001126112.2	142	CCt/t	5/11	0.337112790380834	2	FACETS	0.784	0.743	0.826	0.784	0.743	0.826	SUBCLONAL	2	TRUE	0	0.413623509007881	2		1294	1048	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294228	11294228	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	42	875	0	ENST00000361445.4:c.2303T>C	p.Ile768Thr	p.I768T	ENST00000361445	NM_004958.3	768	aTc/aCc	14/58	1	2	FACETS	0.424	0.353	0.504	0.424	0.353	0.504	SUBCLONAL	1	FALSE	1	0.261930244457426	2		875	756	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843461	156843471	+	frameshift_variant	Frame_Shift_Del	DEL	TGCACCACTGG	TGCACCACTGG	-	novel	NA	P-0020355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	74	782	0	ENST00000524377.1:c.891_901del	p.His298ProfsTer23	p.H298Pfs*23	ENST00000524377	NM_002529.3	296	aTGCACCACTGG/a	8/17	0.0210802419717759	4	FACETS	1	0.898	1	0.515	0.451	0.585	INDETERMINATE	1	FALSE	2	0.261930244457426	4		782	692	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576960	7577127	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AATCTGAGGCATAACTGCACCCTTGGTCTCCTCCACCGCTTCTTGTCCTGCTTGCTTACCTCGCTTAGTGCTCCCTGGGGGCAGCTCGTGGTGAGGCTCCCCTTTCTTGCGGAGATTCTCTTCCTCTGTGCGCCGGTCTCTCCCAGGACAGGCACAAACACGCACCTC	AATCTGAGGCATAACTGCACCCTTGGTCTCCTCCACCGCTTCTTGTCCTGCTTGCTTACCTCGCTTAGTGCTCCCTGGGGGCAGCTCGTGGTGAGGCTCCCCTTTCTTGCGGAGATTCTCTTCCTCTGTGCGCCGGTCTCTCCCAGGACAGGCACAAACACGCACCTC	-	novel	NA	P-0020355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	55	743	0	ENST00000269305.4:c.811_920-34del		p.X271_splice	ENST00000269305	NM_001126112.2	271		8/11	1	2	FACETS	0.935	0.802	1	0.935	0.802	1	CLONAL	1	FALSE	1	0.261930244457426	2		743	449	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939856	49939856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781591594	NA	P-0020355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	47	964	3	ENST00000296474.3:c.1187G>A	p.Arg396Gln	p.R396Q	ENST00000296474	NM_002447.2	396	cGa/cAa	1/20	0.203651741552657	2	FACETS	0.45	0.379	0.53	0.225	0.189	0.265	SUBCLONAL	1	FALSE	0	0.261930244457426	2		967	797	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374959	149374960	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	162	1127	0	ENST00000360632.3:c.134dup	p.Lys46GlufsTer9	p.K46Efs*9	ENST00000360632	NM_015472.4	45	aag/aaAg	2/7	0.231623281045721	3	FACETS	1	0.966	1	0.554	0.507	0.603	CLONAL	1	FALSE	1	0.261930244457426	3		1127	1263	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530954	187530954	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0020355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	32	581	0	ENST00000441802.2:c.10068+1G>A		p.X3356_splice	ENST00000441802	NM_005245.3	3356			1	2	FACETS	0.564	0.458	0.685	0.564	0.458	0.685	SUBCLONAL	1	FALSE	1	0.261930244457426	2		581	433	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294709	1294709	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	38	784	0	ENST00000310581.5:c.292G>C	p.Ala98Pro	p.A98P	ENST00000310581	NM_198253.2	98	Gcc/Ccc	2/16	0.261930244457426	3	FACETS	0.433	0.357	0.519	0.217	0.178	0.26	SUBCLONAL	1	FALSE	1	0.261930244457426	3		784	757	SUCCESS
APC	324	MSKCC	GRCh37	5	112173513	112173513	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	15	488	0	ENST00000257430.4:c.2222A>C	p.Asn741Thr	p.N741T	ENST00000257430	NM_000038.5	741	aAt/aCt	16/16	1	2	FACETS	0.382	0.279	0.506	0.382	0.279	0.506	SUBCLONAL	1	FALSE	1	0.261930244457426	2		488	300	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671444	30671444	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	58	940	0	ENST00000376406.3:c.5516T>C	p.Ile1839Thr	p.I1839T	ENST00000376406	NM_014641.2	1839	aTc/aCc	10/15	0.261930244457426	3	FACETS	0.612	0.524	0.707	0.306	0.262	0.354	SUBCLONAL	1	FALSE	1	0.261930244457426	3		940	819	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171953	32171953	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1403160197	NA	P-0020355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	80	631	2	ENST00000375023.3:c.3079G>A	p.Ala1027Thr	p.A1027T	ENST00000375023	NM_004557.3	1027	Gcc/Acc	19/30	0.261930244457426	3	FACETS	1	0.965	1	0.627	0.553	0.706	CLONAL	1	FALSE	1	0.261930244457426	3		633	551	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390845	139390845	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	101	1101	2	ENST00000277541.6:c.7346G>T	p.Ser2449Ile	p.S2449I	ENST00000277541	NM_017617.3	2449	aGc/aTc	34/34	0.261930244457426	1	FACETS	0.866	0.774	0.964	0.866	0.774	0.964	CLONAL	1	FALSE	0	0.261930244457426	1		1103	774	SUCCESS
AR	367	MSKCC	GRCh37	X	66766539	66766540	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0020355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	40	551	0	ENST00000374690.3:c.1552_1553del	p.Thr518LeufsTer12	p.T518Lfs*12	ENST00000374690	NM_000044.3	517	ccCAct/ccct	1/8	1	1	FACETS	0.63	0.524	0.748	0.63	0.524	0.748	SUBCLONAL	1	FALSE	0	0.261930244457426	1		551	421	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348200	70348216	+	frameshift_variant	Frame_Shift_Del	DEL	GAGTGCAGAATGGCTAG	GAGTGCAGAATGGCTAG	-	novel	NA	P-0020355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	35	470	0	ENST00000374080.3:c.3270_3286del	p.Glu1091Ter	p.E1091*	ENST00000374080		1088	ctGAGTGCAGAATGGCTAGga/ctga	23/45	1	1	FACETS	0.568	0.465	0.683	0.568	0.465	0.683	SUBCLONAL	1	FALSE	0	0.261930244457426	1		470	409	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357190	70357190	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	27	385	0	ENST00000374080.3:c.5705A>G	p.Gln1902Arg	p.Q1902R	ENST00000374080		1902	cAa/cGa	39/45	1	1	FACETS	0.491	0.39	0.606	0.491	0.39	0.606	SUBCLONAL	1	FALSE	0	0.261930244457426	1		385	365	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250869	153250874	+	frameshift_variant	Frame_Shift_Del	DEL	ACCACT	ACCACT	C	novel	NA	P-0020355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	32	655	0	ENST00000281708.4:c.1186_1191delinsG	p.Ser396ValfsTer2	p.S396Vfs*2	ENST00000281708	NM_033632.3	396	AGTGGT/G	8/12	1	2	FACETS	0.52	0.421	0.631	0.52	0.421	0.631	SUBCLONAL	1	FALSE	1	0.261930244457426	2		655	470	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0020356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	98	786	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	2	FALSE	NA	0.149900895616208	2		786	551	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs121913468	NA	P-0020356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	280	588	0	ENST00000269571.5:c.2305G>C	p.Asp769His	p.D769H	ENST00000269571		769	Gac/Cac	19/27	0.149900895616208	15	FACETS	1	0.948	1			1	CLONAL	10	FALSE	NA	0.149900895616208	15		588	735	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209274	133209274	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs181570274	NA	P-0020356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	41	873	2	ENST00000320574.5:c.6112G>A	p.Glu2038Lys	p.E2038K	ENST00000320574	NM_006231.2	2038	Gag/Aag	44/49	0.149900895616208	7	FACETS	1	0.914	1	0.233	0.193	0.277	CLONAL	1	FALSE	2	0.149900895616208	7		875	645	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	93	604	0	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	0.149900895616208	6	FACETS	0.855	0.761	0.954	0.641	0.571	0.716	CLONAL	3	FALSE	2	0.149900895616208	6		604	629	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351578	89351578	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	103	953	1	ENST00000301030.4:c.1372C>T	p.Arg458Ter	p.R458*	ENST00000301030	NM_001256183.1	458	Cga/Tga	9/13	0.149900895616208	6	FACETS	1	0.937	1	0.427	0.382	0.476	CLONAL	2	FALSE	1	0.149900895616208	6		954	836	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11273609	11273609	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	37	458	0	ENST00000361445.4:c.3132G>C	p.Met1044Ile	p.M1044I	ENST00000361445	NM_004958.3	1044	atG/atC	21/58	NA	3	FACETS	0.861	0.713	1			1	INDETERMINATE	2	FALSE	NA	0.149900895616208	3		458	308	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695839	117695839	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	132	803	0	ENST00000369458.3:c.598G>A	p.Glu200Lys	p.E200K	ENST00000369458	NM_024626.3	200	Gag/Aag	4/6	0.149900895616208	3	FACETS	0.917	0.837	1	1	0.99	1	CLONAL	4	FALSE	1	0.149900895616208	3		803	516	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518721	204518721	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	59	438	0	ENST00000367182.3:c.1384C>G	p.His462Asp	p.H462D	ENST00000367182	NM_001278516.1	462	Cac/Gac	11/11	0.149900895616208	8	FACETS	0.889	0.767	1			1	CLONAL	3	FALSE	NA	0.149900895616208	8		438	428	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663847	241663847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	79	323	0	ENST00000366560.3:c.1280C>T	p.Ser427Leu	p.S427L	ENST00000366560	NM_000143.3	427	tCa/tTa	9/10	NA	3	FACETS	1	0.946	1			1	INDETERMINATE	4	FALSE	NA	0.149900895616208	3		323	257	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376403	118376403	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	86	727	0	ENST00000534358.1:c.9796C>A	p.Pro3266Thr	p.P3266T	ENST00000534358	NM_005933.3	3266	Cct/Act	27/36	0.149900895616208	6	FACETS	0.893	0.791	1	0.893	0.791	1	CLONAL	3	FALSE	3	0.149900895616208	6		727	557	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438042	49438042	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778457	NA	P-0020356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	251	869	0	ENST00000301067.7:c.5129C>T	p.Thr1710Met	p.T1710M	ENST00000301067	NM_003482.3	1710	aCg/aTg	21/54	0.149900895616208	13	FACETS	0.937	0.877	0.997	0.819	0.768	0.873	CLONAL	7	FALSE	5	0.149900895616208	13		869	932	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865014	57865014	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148731765	NA	P-0020356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	235	907	1	ENST00000228682.2:c.2491C>T	p.Pro831Ser	p.P831S	ENST00000228682	NM_005269.2	831	Ccc/Tcc	12/12	0.149900895616208	13	FACETS	0.933	0.872	0.995	0.816	0.763	0.871	CLONAL	7	FALSE	5	0.149900895616208	13		908	876	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623847	28623847	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	65	739	0	ENST00000241453.7:c.807G>C	p.Trp269Cys	p.W269C	ENST00000241453	NM_004119.2	269	tgG/tgC	7/24	0.149900895616208	0	FACETS	0.917	0.798	1			1	CLONAL	2	FALSE	0	0.149900895616208	0		739	402	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060942	38060942	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763720398	NA	P-0020356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	84	626	0	ENST00000250448.2:c.1047G>T	p.Leu349Phe	p.L349F	ENST00000250448	NM_004496.3	349	ttG/ttT	2/2	0.149900895616208	5	FACETS	0.935	0.832	1	1	0.968	1	CLONAL	4	FALSE	2	0.149900895616208	5		626	367	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961922	41961922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	36	426	0	ENST00000219905.7:c.830C>T	p.Ser277Phe	p.S277F	ENST00000219905	NM_001164273.1	277	tCt/tTt	2/24	0.149900895616208	6	FACETS	0.87	0.716	1	0.435	0.358	0.521	CLONAL	2	FALSE	2	0.149900895616208	6		426	359	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234460	41234460	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555584070	NA	P-0020356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	74	769	0	ENST00000357654.3:c.4318G>C	p.Glu1440Gln	p.E1440Q	ENST00000357654	NM_007294.3	1440	Gag/Cag	12/23	0.149900895616208	6	FACETS	1	0.891	1	0.509	0.446	0.578	CLONAL	2	FALSE	2	0.149900895616208	6		769	630	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2206781	2206783	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0020356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	155	710	0	ENST00000398665.3:c.843_845del	p.Ser281del	p.S281del	ENST00000398665	NM_032482.2	281	AGT/-	10/28	0.149900895616208	3	FACETS	1	0.939	1	1	0.989	1	CLONAL	3	FALSE	1	0.149900895616208	3		710	721	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965703	18965703	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	131	855	0	ENST00000262803.5:c.1281G>C	p.Leu427Phe	p.L427F	ENST00000262803	NM_002911.3	427	ttG/ttC	10/24	0.149900895616208	6	FACETS	0.9	0.817	0.988	0.675	0.613	0.741	CLONAL	3	FALSE	2	0.149900895616208	6		855	841	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394123	31394123	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	77	535	0	ENST00000328111.2:c.2410G>C	p.Glu804Gln	p.E804Q	ENST00000328111	NM_006892.3	804	Gag/Cag	22/23	0.149900895616208	3	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	FALSE	1	0.149900895616208	3		535	486	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52663035	52663035	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	83	342	0	ENST00000394830.3:c.1318C>T	p.Gln440Ter	p.Q440*	ENST00000394830	NM_018313.4	440	Caa/Taa	13/30	0.149900895616208	5	FACETS	1	0.955	1	1	0.955	1	CLONAL	3	FALSE	2	0.149900895616208	5		342	392	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391183	89391183	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	48	641	0	ENST00000336596.2:c.1249G>C	p.Glu417Gln	p.E417Q	ENST00000336596	NM_005233.5	417	Gag/Cag	5/17	0.149900895616208	5	FACETS	1	0.959	1	0.489	0.413	0.572	CLONAL	1	FALSE	2	0.149900895616208	5		641	535	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140785	55140785	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	60	570	0	ENST00000257290.5:c.1646G>C	p.Trp549Ser	p.W549S	ENST00000257290	NM_006206.4	549	tGg/tCg	11/23	0.149900895616208	3	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	FALSE	1	0.149900895616208	3		570	385	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629220	187629220	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	109	775	1	ENST00000441802.2:c.1762A>G	p.Ile588Val	p.I588V	ENST00000441802	NM_005245.3	588	Ata/Gta	2/27	0.149900895616208	3	FACETS	0.866	0.779	0.957	1	0.977	1	CLONAL	3	FALSE	1	0.149900895616208	3		776	602	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31431733	31431733	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	61	698	0	ENST00000344624.3:c.3095G>C	p.Arg1032Thr	p.R1032T	ENST00000344624		1032	aGa/aCa	23/33	0.149900895616208	0	FACETS	1	0.95	1			1	CLONAL	1	FALSE	0	0.149900895616208	0		698	565	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048146	180048146	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	146	946	0	ENST00000261937.6:c.2127C>G	p.Ile709Met	p.I709M	ENST00000261937	NM_182925.4	709	atC/atG	14/30	0.149900895616208	0	FACETS	1	0.927	1			1	CLONAL	3	FALSE	0	0.149900895616208	0		946	546	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982060	93982060	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	95	641	1	ENST00000369303.4:c.1405C>A	p.Pro469Thr	p.P469T	ENST00000369303	NM_004440.3	469	Ccc/Acc	6/17	0.149900895616208	3	FACETS	0.996	0.891	1	1	0.981	1	CLONAL	3	FALSE	1	0.149900895616208	3		642	456	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023085	150023085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771059780	NA	P-0020356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	70	753	0	ENST00000253339.5:c.178G>A	p.Glu60Lys	p.E60K	ENST00000253339		60	Gaa/Aaa	1/7	0.149900895616208	6	FACETS	0.862	0.751	0.982	0.431	0.375	0.491	CLONAL	2	FALSE	2	0.149900895616208	6		753	704	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104673	69104673	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	90	692	0	ENST00000288368.4:c.4517C>G	p.Ser1506Cys	p.S1506C	ENST00000288368	NM_024870.2	1506	tCt/tGt	37/40	0.149900895616208	0	FACETS	1	0.914	1			1	CLONAL	2	FALSE	0	0.149900895616208	0		692	495	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650073	93650073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	89	721	2	ENST00000375746.1:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000375746	NM_001174167.1	542	Gaa/Aaa	12/14	0.149900895616208	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	FALSE	1	0.149900895616208	3		723	548	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692929	89692929	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1554898159	NA	P-0020357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	80	783	0	ENST00000371953.3:c.413A>G	p.Tyr138Cys	p.Y138C	ENST00000371953	NM_000314.4	138	tAt/tGt	5/9	0.263470438958771	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.263470438958771	2		783	277	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125088	46125088	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs772882172	NA	P-0020357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	35	333	0	ENST00000334344.6:c.275A>G	p.Tyr92Cys	p.Y92C	ENST00000334344	NM_152641.2	92	tAt/tGt	3/21	0.160828795072669	5	FACETS	0.95	0.787	1	0.634	0.524	0.754	CLONAL	2	TRUE	2	0.263470438958771	5		333	195	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028443	42028443	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	45	547	0	ENST00000219905.7:c.3981G>T	p.Arg1327Ser	p.R1327S	ENST00000219905	NM_001164273.1	1327	agG/agT	13/24	0.0975270375536279	4	FACETS	0.765	0.647	0.894	0.765	0.647	0.894	INDETERMINATE	2	TRUE	2	0.263470438958771	4		547	282	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191560	10191560	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	140	678	0	ENST00000256474.2:c.553del	p.Tyr185ThrfsTer17	p.Y185Tfs*17	ENST00000256474	NM_000551.3	185	Tac/ac	3/3	0.263470438958771	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	2	TRUE	0	0.263470438958771	2		678	530	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163607	47163607	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	31	538	0	ENST00000409792.3:c.2519del	p.Asn840IlefsTer2	p.N840Ifs*2	ENST00000409792	NM_014159.6	840	aAt/at	3/21	0.263470438958771	2	FACETS	1	0.929	1	0.657	0.537	0.79	CLONAL	1	TRUE	0	0.263470438958771	2		538	179	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436409	52436412	+	frameshift_variant	Frame_Shift_Del	DEL	GTTC	GTTC	-	novel	NA	P-0020357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	145	845	0	ENST00000460680.1:c.2082_2085del	p.Asn695SerfsTer40	p.N695Sfs*40	ENST00000460680	NM_004656.3	694	caGAAC/ca	17/17	0.263470438958771	2	FACETS	0.874	0.8	0.95	0.874	0.8	0.95	CLONAL	2	TRUE	0	0.263470438958771	2		845	630	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198031	185198031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767214456	NA	P-0020357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	38	504	0	ENST00000265026.3:c.2513G>A	p.Cys838Tyr	p.C838Y	ENST00000265026	NM_004721.4	838	tGt/tAt	13/14	0.26227203218695	3	FACETS	1	0.84	1	0.507	0.42	0.603	CLONAL	1	TRUE	1	0.263470438958771	3		504	322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0020358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	767	922	1	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.311608129776581	3	FACETS	0.852	0.827	0.876			1	INDETERMINATE	3	TRUE	NA	0.564631266954802	3		923	1363	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	216	122	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.962	1			1	INDETERMINATE	1	TRUE	NA	0.784571539029919	2		122	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0020359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	352	591	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.784571539029919	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.784571539029919	1		591	514	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69202261	69202261	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1390633476	NA	P-0020359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	245	636	0	ENST00000462284.1:c.4G>T	p.Val2Leu	p.V2L	ENST00000462284	NM_002392.5	2	Gtg/Ttg	1/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.784571539029919	2		636	591	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15809122	15809142	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GACTGAGAGACTCAGGTGATG	GACTGAGAGACTCAGGTGATG	-	novel	NA	P-0020359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	89	338	0	ENST00000307771.7:c.111_121+10del		p.X37_splice	ENST00000307771	NM_005089.3	37		2/11	1	1	FACETS	0.762	0.694	0.83	0.762	0.694	0.83	SUBCLONAL	1	TRUE	0	0.784571539029919	1		338	181	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0020360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	451	1120	2	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.438956967595237	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	TRUE	0	0.462536998016711	3		1122	788	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	105	964	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.440951083559834	3	FACETS	0.903	0.811	1	0.452	0.405	0.501	CLONAL	1	TRUE	1	0.462536998016711	3		964	619	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160760	56160761	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	109	544	0	ENST00000399503.3:c.1035+1dup		p.Q345fs	ENST00000399503	NM_005921.1	345	cag/caGg	4/20	0.450840650325522	2	FACETS	0.836	0.762	0.911	0.836	0.762	0.911	CLONAL	2	TRUE	0	0.462536998016711	2		544	282	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0020361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	167	521	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.5	2		521	512	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183817	10183817	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690959	NA	P-0020362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	219	887	0	ENST00000256474.2:c.286C>T	p.Gln96Ter	p.Q96*	ENST00000256474	NM_000551.3	96	Cag/Tag	1/3	0.3	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.33	2		887	647	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127800	47127800	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	92	536	0	ENST00000409792.3:c.5282C>G	p.Thr1761Arg	p.T1761R	ENST00000409792	NM_014159.6	1761	aCa/aGa	11/21	0.3	1	FACETS	0.964	0.86	1	0.964	0.86	1	CLONAL	1	TRUE	0	0.33	1		536	483	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439853	52439861	+	frameshift_variant	Frame_Shift_Del	DEL	ACTTGGACT	ACTTGGACT	G	novel	NA	P-0020362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	98	814	0	ENST00000460680.1:c.851_859delinsC	p.Glu284AlafsTer20	p.E284Afs*20	ENST00000460680	NM_004656.3	284	gAGTCCAAGTca/gCca	10/17	0.3	1	FACETS	0.912	0.816	1	0.912	0.816	1	CLONAL	1	TRUE	0	0.33	1		814	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578412	7578412	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519747	NA	P-0020364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	506	870	0	ENST00000269305.4:c.518T>G	p.Val173Gly	p.V173G	ENST00000269305	NM_001126112.2	173	gTg/gGg	5/11	0.298390908770044	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	4	TRUE	0	0.33	4		870	949	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920691	96920691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752938517	NA	P-0020364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	71	644	0	ENST00000258439.3:c.289G>A	p.Ala97Thr	p.A97T	ENST00000258439	NM_001193304.2	97	Gcc/Acc	3/4	0.298390908770044	5	FACETS	1	0.882	1	0.337	0.294	0.384	CLONAL	1	TRUE	2	0.33	5		644	636	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0020365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	392	501	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.518751457607641	2	FACETS	0.819	0.785	0.853	0.819	0.785	0.853	CLONAL	2	TRUE	0	0.633991732054784	2		501	755	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0020365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	104	623	2	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.682	0.614	0.754	0.682	0.614	0.754	SUBCLONAL	1	TRUE	1	0.633991732054784	2		625	481	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130180	2130180	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45451497	NA	P-0020365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	209	884	1	ENST00000219476.3:c.3412C>T	p.Arg1138Ter	p.R1138*	ENST00000219476	NM_000548.3	1138	Cga/Tga	30/42	0.333338294483978	4	FACETS	0.857	0.794	0.923	0.429	0.397	0.462	INDETERMINATE	1	TRUE	2	0.633991732054784	4		885	1257	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920401	114920401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1422891742	NA	P-0020365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	300	785	1	ENST00000543371.1:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000543371	NM_001198531.1	448	Cgg/Tgg	13/14	0.511556002672011	3	FACETS	0.761	0.72	0.803	0.761	0.72	0.803	SUBCLONAL	2	TRUE	1	0.633991732054784	3		786	819	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441800	49441802	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0020365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	175	854	0	ENST00000301067.7:c.4182_4184del	p.Leu1395del	p.L1395del	ENST00000301067	NM_003482.3	1394	ctCCTt/ctt	14/54	0.511556002672011	3	FACETS	0.861	0.794	0.932	0.431	0.397	0.466	CLONAL	1	TRUE	1	0.633991732054784	3		854	844	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913482	32913482	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	249	771	0	ENST00000380152.3:c.4990A>T	p.Ile1664Phe	p.I1664F	ENST00000380152		1664	Att/Ttt	11/27	0.633991732054784	5	FACETS	1	0.992	1	0.492	0.46	0.525	CLONAL	1	TRUE	2	0.633991732054784	5		771	1038	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103510585	103510624	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	GAAATGTAAATTTCATGGTGCTGTGATTTTATCTTTACAG	GAAATGTAAATTTCATGGTGCTGTGATTTTATCTTTACAG	-	novel	NA	P-0020365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	41	272	0	ENST00000355739.4:c.529-37_531del		p.X177_splice	ENST00000355739	NM_000123.3	177			0.633991732054784	5	FACETS	0.855	0.716	1	0.285	0.238	0.337	CLONAL	1	TRUE	2	0.633991732054784	5		272	295	SUCCESS
APC	324	MSKCC	GRCh37	5	112175417	112175417	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	77	435	0	ENST00000257430.4:c.4126del	p.Tyr1376MetfsTer39	p.Y1376Mfs*39	ENST00000257430	NM_000038.5	1376	Tat/at	16/16	1	2	FACETS	0.721	0.638	0.809	0.721	0.638	0.809	SUBCLONAL	1	TRUE	1	0.633991732054784	2		435	337	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907680	76907680	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	155	910	0	ENST00000373344.5:c.4481A>C	p.Gln1494Pro	p.Q1494P	ENST00000373344	NM_000489.3	1494	cAa/cCa	15/35	0.483929551983313	2	FACETS	0.686	0.629	0.745	0.343	0.314	0.373	SUBCLONAL	1	TRUE	0	0.633991732054784	2		910	713	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	47	424	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.19545247688782	0	FACETS	0.873	0.738	1			1	CLONAL	1	TRUE	0	0.19545247688782	0		424	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577497	7577497	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0020377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	120	766	0	ENST00000269305.4:c.782+2T>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.19545247688782	2		766	819	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519938	NA	P-0020383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	212	564	0	ENST00000263967.3:c.1034A>T	p.Asn345Ile	p.N345I	ENST00000263967	NM_006218.2	345	aAt/aTt	5/21	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.726604819068439	2		564	449	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0020383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	197	722	2	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.877	0.817	0.939	0.877	0.817	0.939	CLONAL	1	TRUE	1	0.726604819068439	2		724	618	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913250	NA	P-0020383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	234	706	0	ENST00000369535.4:c.34G>T	p.Gly12Cys	p.G12C	ENST00000369535	NM_002524.4	12	Ggt/Tgt	2/7	0.726604819068439	1	FACETS	0.993	0.942	1	0.993	0.942	1	CLONAL	1	TRUE	0	0.726604819068439	1		706	413	SUCCESS
APC	324	MSKCC	GRCh37	5	112173835	112173838	+	frameshift_variant	Frame_Shift_Del	DEL	AGAT	AGAT	-	rs398123118	NA	P-0020383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	127	480	0	ENST00000257430.4:c.2547_2550del	p.Asp849GlufsTer11	p.D849Efs*11	ENST00000257430	NM_000038.5	848	aaAGAT/aa	16/16	0.726604819068439	1	FACETS	0.827	0.764	0.891	0.827	0.764	0.891	CLONAL	1	TRUE	0	0.726604819068439	1		480	269	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711272	114711273	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	240	785	0	ENST00000543371.1:c.291dup	p.Pro98AlafsTer47	p.P98Afs*47	ENST00000543371	NM_001198531.1	96	aag/aaGg	3/14	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.726604819068439	2		785	637	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120783407	120783407	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	252	921	0	ENST00000257552.2:c.1076A>G	p.Asn359Ser	p.N359S	ENST00000257552	NM_002442.3	359	aAt/aGt	14/15	1	2	FACETS	0.866	0.813	0.92	0.866	0.813	0.92	CLONAL	1	TRUE	1	0.726604819068439	2		921	801	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0020384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	105	532	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.238230755064834	1	FACETS	0.968	0.867	1	0.968	0.867	1	CLONAL	1	TRUE	0	0.238230755064834	1		533	802	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0020384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	87	453	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.238230755064834	1	FACETS	0.985	0.873	1	0.985	0.873	1	CLONAL	1	TRUE	0	0.238230755064834	1		453	653	SUCCESS
AXL	558	MSKCC	GRCh37	19	41737136	41737136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761251235	NA	P-0020384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	139	1279	1	ENST00000301178.4:c.716C>T	p.Thr239Met	p.T239M	ENST00000301178	NM_021913.4	239	aCg/aTg	6/20	0.236686332866368	2	FACETS	1	0.91	1	0.501	0.455	0.55	CLONAL	1	TRUE	0	0.238230755064834	2		1280	1165	SUCCESS
APC	324	MSKCC	GRCh37	5	112137036	112137036	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	57	698	0	ENST00000257430.4:c.790C>T	p.Gln264Ter	p.Q264*	ENST00000257430	NM_000038.5	264	Caa/Taa	8/16	1	2	FACETS	0.794	0.681	0.917	0.794	0.681	0.917	CLONAL	1	TRUE	1	0.238230755064834	2		698	603	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331723	8331723	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367558329	NA	P-0020384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	95	575	1	ENST00000356435.5:c.5393G>A	p.Arg1798Gln	p.R1798Q	ENST00000356435		1798	cGa/cAa	33/35	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.238230755064834	2		576	593	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112253	115112253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024919027	NA	P-0020384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	96	454	0	ENST00000257566.3:c.1487G>A	p.Gly496Asp	p.G496D	ENST00000257566	NM_016569.3	496	gGc/gAc	7/8	1	2	FACETS	0.868	0.778	0.964	1	0.985	1	CLONAL	2	TRUE	1	0.238230755064834	2		454	464	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924295	112924295	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1193000800	NA	P-0020384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	70	1069	2	ENST00000351677.2:c.1241C>T	p.Thr414Met	p.T414M	ENST00000351677	NM_002834.3	414	aCg/aTg	11/16	1	2	FACETS	0.571	0.496	0.652	0.571	0.496	0.652	SUBCLONAL	1	TRUE	1	0.238230755064834	2		1071	1029	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981538	201981538	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	158	1338	1	ENST00000359651.3:c.452A>G	p.Gln151Arg	p.Q151R	ENST00000359651		151	cAg/cGg	3/8	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.238230755064834	2		1339	1262	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112248	115112248	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	95	509	1	ENST00000257566.3:c.1492del	p.Leu498CysfsTer134	p.L498Cfs*134	ENST00000257566	NM_016569.3	498	Ctg/tg	7/8	1	2	FACETS	0.773	0.69	0.86	1	0.982	1	SUBCLONAL	2	TRUE	1	0.238230755064834	2		510	516	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410598	63410598	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1394000391	NA	P-0020384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	110	1152	0	ENST00000330258.3:c.2569C>T	p.Arg857Ter	p.R857*	ENST00000330258	NM_152424.3	857	Cga/Tga	2/2	1	2	FACETS	0.887	0.795	0.985	0.887	0.795	0.985	CLONAL	1	TRUE	1	0.238230755064834	2		1152	1041	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0020385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	41	707	7	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	0.349503034796031	3	FACETS	1	0.946	1	0.434	0.366	0.506	CLONAL	1	TRUE	0	0.465265431667086	3		714	167	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358677	67358677	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	82	678	8	ENST00000327367.4:c.185C>G	p.Thr62Ser	p.T62S	ENST00000327367	NM_005902.3	62	aCc/aGc	1/9	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.465265431667086	2		686	276	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121933	2121933	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	118	1076	5	ENST00000219476.3:c.2095C>A	p.Gln699Lys	p.Q699K	ENST00000219476	NM_000548.3	699	Cag/Aag	19/42	0.368226634239725	5	FACETS	1	0.98	1	0.446	0.403	0.491	CLONAL	1	TRUE	2	0.465265431667086	5		1081	644	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577523	7577524	+	missense_variant	Missense_Mutation	DNP	GT	GT	TC	novel	NA	P-0020385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	205	1009	17	ENST00000269305.4:c.757_758delinsGA	p.Thr253Asp	p.T253D	ENST00000269305	NM_001126112.2	253	ACc/GAc	7/11	0.349503034796031	3	FACETS	0.892	0.84	0.944	0.892	0.84	0.944	CLONAL	3	TRUE	0	0.465265431667086	3		1026	406	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650879	37650880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	55	868	16	ENST00000447079.4:c.2353dup	p.Ser785LysfsTer4	p.S785Kfs*4	ENST00000447079	NM_015083.1	784	cga/cgAa	5/14	0.349503034796031	3	FACETS	0.857	0.747	0.972	0.571	0.498	0.648	CLONAL	2	TRUE	0	0.465265431667086	3		884	170	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40461482	40461484	+	inframe_deletion	In_Frame_Del	DEL	CTA	CTA	-	novel	NA	P-0020385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	85	1163	6	ENST00000345506.4:c.2202_2204del	p.Tyr735del	p.Y735del	ENST00000345506	NM_003152.3	734	ccCTAt/cct	19/20	0.349503034796031	3	FACETS	1	0.936	1	0.359	0.319	0.402	CLONAL	1	TRUE	0	0.465265431667086	3		1169	418	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564270	86564270	+	start_lost	Translation_Start_Site	SNP	T	T	G	novel	NA	P-0020385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	27	327	4	ENST00000274376.6:c.2T>G	p.Met1?	p.M1?	ENST00000274376	NM_002890.2	1	aTg/aGg	1/25	0.349503034796031	3	FACETS	0.688	0.551	0.842	0.229	0.183	0.281	SUBCLONAL	1	TRUE	0	0.465265431667086	3		331	208	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158404	26158404	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	87	1259	3	ENST00000289316.2:c.7G>C	p.Glu3Gln	p.E3Q	ENST00000289316	NM_138720.2	3	Gaa/Caa	1/2	0.465265431667086	10	FACETS	0.993	0.881	1	0.331	0.293	0.371	CLONAL	2	TRUE	4	0.465265431667086	10		1262	539	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798432	42798432	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1403097993	NA	P-0020386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	207	1104	0	ENST00000575354.2:c.4303G>C	p.Asp1435His	p.D1435H	ENST00000575354	NM_015125.3	1435	Gac/Cac	18/20	0.545527050456333	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.545527050456333	1		1104	529	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593584	55593598	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	ACCCATGTATGAAGT	ACCCATGTATGAAGT	-	rs587776804	NA	P-0020389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	344	434	0	ENST00000288135.5:c.1652_1666del	p.Pro551_Val555del	p.P551_V555del	ENST00000288135	NM_000222.2	550	aaACCCATGTATGAAGTa/aaa	11/21	0.854921040154624	2	FACETS	0.991	0.965	1	0.991	0.965	1	CLONAL	2	TRUE	0	0.854921040154624	2		434	406	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719129	52719129	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	173	788	0	ENST00000322088.6:c.906del	p.Ser303ProfsTer19	p.S303Pfs*19	ENST00000322088	NM_014225.5	302	gCc/gc	7/15	1	2	FACETS	0.959	0.883	1	0.959	0.883	1	CLONAL	1	TRUE	1	0.433328546603442	2		788	833	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	324	122	0				ENST00000310581	NM_198253.2	-/1132			0.520462238562987	4	FACETS	0.904	0.855	0.953	0.904	0.855	0.953	CLONAL	2	TRUE	2	0.569409761998612	4		122	988	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0020394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	387	645	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	0.520462238562987	4	FACETS	0.905	0.86	0.95	0.905	0.86	0.95	CLONAL	2	TRUE	2	0.569409761998612	4		645	1179	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874101	155874101	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0020394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	176	534	0	ENST00000368323.3:c.429+1G>T		p.X143_splice	ENST00000368323	NM_006912.5	143			0.520462238562987	4	FACETS	0.964	0.888	1	0.482	0.444	0.522	CLONAL	1	TRUE	2	0.569409761998612	4		534	1006	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851258	156851258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1178809694	NA	P-0020394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	229	695	0	ENST00000524377.1:c.2215T>C	p.Cys739Arg	p.C739R	ENST00000524377	NM_002529.3	739	Tgc/Cgc	17/17	0.520462238562987	4	FACETS	0.987	0.918	1	0.493	0.459	0.529	CLONAL	1	TRUE	2	0.569409761998612	4		695	1279	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416440	49416441	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0020394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	410	657	0	ENST00000301067.7:c.16270_16271del	p.Ile5424ArgfsTer34	p.I5424Rfs*34	ENST00000301067	NM_003482.3	5424	ATc/c	51/54	0.569409761998612	3	FACETS	0.92	0.879	0.962	0.92	0.879	0.962	CLONAL	2	TRUE	1	0.569409761998612	3		657	1005	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578502	7578511	+	frameshift_variant	Frame_Shift_Del	DEL	ACAGGGCAGG	ACAGGGCAGG	-	novel	NA	P-0020394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	659	1039	0	ENST00000269305.4:c.419_428del	p.Thr140SerfsTer27	p.T140Sfs*27	ENST00000269305	NM_001126112.2	140	aCCTGCCCTGTg/ag	5/11	0.539600494652211	2	FACETS	0.956	0.926	0.986	0.956	0.926	0.986	CLONAL	2	TRUE	0	0.569409761998612	2		1039	1211	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	223	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.171335428930991	2	FACETS	0.989	0.923	1	0.989	0.923	1	CLONAL	2	FALSE	0	0.279522715901555	2		555	807	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0020395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	226	1191	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.279522715901555	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	0	0.279522715901555	1		1191	1119	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839952	27839952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777522650	NA	P-0020395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	68	1006	0	ENST00000328488.2:c.142G>A	p.Ala48Thr	p.A48T	ENST00000328488	NM_003533.2	48	Gcc/Acc	1/1	0.232386381999091	1	FACETS	0.517	0.449	0.591	0.517	0.449	0.591	SUBCLONAL	1	FALSE	0	0.279522715901555	1		1006	810	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21627858	21627858	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	143	1255	0	ENST00000421138.2:c.1272C>G	p.Phe424Leu	p.F424L	ENST00000421138		424	ttC/ttG	12/16	0.171335428930991	2	FACETS	0.953	0.867	1	0.476	0.433	0.522	CLONAL	1	FALSE	0	0.279522715901555	2		1255	1074	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715625	30715625	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	64	466	0	ENST00000295754.5:c.1283A>T	p.Glu428Val	p.E428V	ENST00000295754	NM_003242.5	428	gAa/gTa	5/7	0.279522715901555	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	0	0.279522715901555	1		466	322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0020396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	716	649	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.960912912912846	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.961953623569502	2		649	739	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972434	81972434	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1490608295	NA	P-0020396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	564	449	1	ENST00000359376.3:c.3227T>A	p.Leu1076His	p.L1076H	ENST00000359376	NM_002661.3	1076	cTt/cAt	29/33	0.960912912912846	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.961953623569502	2		450	584	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624493	93624493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1276980680	NA	P-0020396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	62	340	0	ENST00000375746.1:c.584G>A	p.Arg195Gln	p.R195Q	ENST00000375746	NM_001174167.1	195	cGa/cAa	4/14	0.960912912912846	2	FACETS	0.316	0.274	0.362	0.158	0.137	0.181	SUBCLONAL	1	TRUE	0	0.961953623569502	2		340	408	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0020398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	290	786	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	0.595081283204559	2		786	939	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215787	98215787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376844749	NA	P-0020398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	271	750	0	ENST00000331920.6:c.3422C>T	p.Ala1141Val	p.A1141V	ENST00000331920	NM_000264.3	1141	gCg/gTg	20/24	1	2	FACETS	0.988	0.929	1	0.988	0.929	1	CLONAL	1	TRUE	1	0.595081283204559	2		750	922	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087548	27087548	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	300	781	5	ENST00000324856.7:c.2122C>T	p.Gln708Ter	p.Q708*	ENST00000324856	NM_006015.4	708	Cag/Tag	5/20	1	2	FACETS	0.912	0.86	0.967	0.912	0.86	0.967	CLONAL	1	TRUE	1	0.595081283204559	2		786	1105	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023849	27023869	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCCCCAGGACGGGGGCGCC	GGGCCCCAGGACGGGGGCGCC	CGCG	novel	NA	P-0020398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	201	458	3	ENST00000324856.7:c.955_975delinsCGCG	p.Gly319ArgfsTer75	p.G319Rfs*75	ENST00000324856	NM_006015.4	319	GGGCCCCAGGACGGGGGCGCC/CGCG	1/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.595081283204559	2		461	634	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495786	56495786	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs751707747	NA	P-0020398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	196	506	1	ENST00000267101.3:c.3976C>G	p.Pro1326Ala	p.P1326A	ENST00000267101	NM_001982.3	1326	Cct/Gct	28/28	1	2	FACETS	0.926	0.861	0.994	0.926	0.861	0.994	CLONAL	1	TRUE	1	0.595081283204559	2		507	711	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093435	30093435	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	271	683	0	ENST00000331968.5:c.1828G>A	p.Ala610Thr	p.A610T	ENST00000331968	NM_002742.2	610	Gct/Act	13/18	1	2	FACETS	0.983	0.924	1	0.983	0.924	1	CLONAL	1	TRUE	1	0.595081283204559	2		683	927	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184179	56184179	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	318	384	0	ENST00000399503.3:c.4384T>G	p.Phe1462Val	p.F1462V	ENST00000399503	NM_005921.1	1462	Ttt/Gtt	19/20	0.590994221313864	2	FACETS	0.981	0.938	1	0.981	0.938	1	CLONAL	2	TRUE	0	0.595081283204559	2		384	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0020400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	291	860	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.28753403150512	2	FACETS	0.868	0.818	0.92	0.868	0.818	0.92	CLONAL	2	TRUE	0	0.341625475120929	2		861	981	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348452	89348475	+	inframe_deletion	In_Frame_Del	DEL	GCTCGTCCCTGTGATGCCGCAGGA	GCTCGTCCCTGTGATGCCGCAGGA	-	rs534329317	NA	P-0020400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	271	883	0	ENST00000301030.4:c.4475_4498del	p.Leu1492_Glu1499del	p.L1492_E1499del	ENST00000301030	NM_001256183.1	1492	cTCCTGCGGCATCACAGGGACGAGCag/cag	9/13	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.341625475120929	2		883	1176	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882362	89882362	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	252	890	0	ENST00000389301.3:c.112G>C	p.Glu38Gln	p.E38Q	ENST00000389301	NM_000135.2	38	Gaa/Caa	2/43	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.341625475120929	2		890	1097	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990669	7990669	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	103	943	0	ENST00000319144.4:c.92G>C	p.Gly31Ala	p.G31A	ENST00000319144	NM_001139.2	31	gGa/gCa	1/15	0.28753403150512	2	FACETS	0.512	0.457	0.571	0.256	0.228	0.286	SUBCLONAL	1	TRUE	0	0.341625475120929	2		943	1177	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857236	78857236	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs746088030	NA	P-0020400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	290	885	0	ENST00000306801.3:c.1602G>C	p.Met534Ile	p.M534I	ENST00000306801	NM_020761.2	534	atG/atC	15/34	0.341625475120929	3	FACETS	1	0.993	1	0.47	0.441	0.5	CLONAL	1	TRUE	0	0.341625475120929	3		885	1410	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471122	25471122	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0020400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	115	694	0	ENST00000264709.3:c.640-1G>A		p.X214_splice	ENST00000264709	NM_175629.2	214			0.171029520003547	4	FACETS	0.885	0.795	0.979	0.442	0.397	0.49	INDETERMINATE	1	TRUE	2	0.341625475120929	4		694	1021	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573735	41573735	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	152	933	0	ENST00000263253.7:c.6020A>T	p.Gln2007Leu	p.Q2007L	ENST00000263253	NM_001429.3	2007	cAg/cTg	31/31	0.304956038815135	3	FACETS	0.854	0.779	0.933	0.427	0.389	0.467	CLONAL	1	TRUE	1	0.341625475120929	3		933	1220	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226810	142226810	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	73	606	0	ENST00000350721.4:c.4994A>G	p.Lys1665Arg	p.K1665R	ENST00000350721	NM_001184.3	1665	aAg/aGg	28/47	0.339103828550459	5	FACETS	0.627	0.547	0.714	0.157	0.136	0.179	SUBCLONAL	1	TRUE	1	0.341625475120929	5		606	1031	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679661	30679661	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1310	140	819	1	ENST00000376406.3:c.2058C>A	p.Asp686Glu	p.D686E	ENST00000376406	NM_014641.2	686	gaC/gaA	5/15	0.341625475120929	4	FACETS	0.758	0.688	0.833			1	SUBCLONAL	1	TRUE	NA	0.341625475120929	4		820	1450	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002885	69002886	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0020400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	84	522	0	ENST00000288368.4:c.2186_2187del	p.Lys729ArgfsTer30	p.K729Rfs*30	ENST00000288368	NM_024870.2	729	AAa/a	20/40	0.28186700552798	3	FACETS	0.749	0.661	0.843	0.25	0.22	0.281	SUBCLONAL	1	TRUE	0	0.341625475120929	3		522	769	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577061	7577064	+	frameshift_variant	Frame_Shift_Del	DEL	CTTT	CTTT	-	novel	NA	P-0020401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	588	845	72	ENST00000269305.4:c.874_877del	p.Lys292GlyfsTer52	p.K292Gfs*52	ENST00000269305	NM_001126112.2	292	AAAGgg/gg	8/11	0.45697435930968	3	FACETS	0.966	0.933	0.998	0.966	0.933	0.998	CLONAL	3	TRUE	0	0.461819348971302	3		917	1082	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854945	76854945	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	249	588	0	ENST00000373344.5:c.5891G>T	p.Gly1964Val	p.G1964V	ENST00000373344	NM_000489.3	1964	gGa/gTa	25/35	1	1	FACETS	0.94	0.893	0.987	1	0.995	1	CLONAL	2	TRUE	0	0.461819348971302	1		588	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0020402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	16	532	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.364993085698951	1	FACETS	0.107	0.079	0.142	0.107	0.079	0.142	SUBCLONAL	1	TRUE	0	0.364993085698951	1		533	667	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0020402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	146	352	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.228215574509758	3	FACETS	0.906	0.832	0.983	0.906	0.832	0.983	CLONAL	2	TRUE	1	0.364993085698951	3		352	522	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0020402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	307	1191	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.364993085698951	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.364993085698951	1		1191	1160	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0020403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	260	499	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.955	0.901	1	0.955	0.901	1	CLONAL	1	TRUE	1	0.850865928095017	2		499	640	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720833	89720836	+	frameshift_variant	Frame_Shift_Del	DEL	AAAT	AAAT	-	rs587782304	NA	P-0020403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	264	498	0	ENST00000371953.3:c.987_990del	p.Asn329LysfsTer14	p.N329Kfs*14	ENST00000371953	NM_000314.4	328	gcAAAT/gc	8/9	0.175494365605035	3	FACETS	1	0.993	1	0.713	0.674	0.753	INDETERMINATE	1	TRUE	1	0.850865928095017	3		498	620	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0020403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	212	310	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.850865928095017	2		310	471	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624227	89624234	+	frameshift_variant,start_lost	Frame_Shift_Del	DEL	ATGACAGC	ATGACAGC	CTGA	novel	NA	P-0020403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	106	209	1	ENST00000371953.3:c.1_8delinsCTGA	p.Met1_?3	p.M1_?3	ENST00000371953	NM_000314.4	1	ATGACAGCc/CTGAc	1/9	0.175494365605035	3	FACETS	1	0.983	1	0.68	0.621	0.741	INDETERMINATE	1	TRUE	1	0.850865928095017	3		210	261	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433689	49433689	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	554	1030	2	ENST00000301067.7:c.7864del	p.Asp2622ThrfsTer69	p.D2622Tfs*69	ENST00000301067	NM_003482.3	2622	Gac/ac	31/54	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.850865928095017	2		1032	1207	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828953	72828954	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CAAATGA	novel	NA	P-0020403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	334	751	2	ENST00000268489.5:c.7621_7627dup	p.Glu2543ValfsTer3	p.E2543Vfs*3	ENST00000268489	NM_006885.3	2543	gag/gTCATTTGag	9/10	1	2	FACETS	0.961	0.913	1	0.961	0.913	1	CLONAL	1	TRUE	1	0.850865928095017	2		753	817	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581189	48581189	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	266	592	0	ENST00000342988.3:c.493G>C	p.Asp165His	p.D165H	ENST00000342988	NM_005359.5	165	Gac/Cac	5/12	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.850865928095017	2		592	556	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465600	8465600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1427192894	NA	P-0020403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	337	725	5	ENST00000356435.5:c.3580G>A	p.Ala1194Thr	p.A1194T	ENST00000356435		1194	Gct/Act	21/35	1	2	FACETS	0.989	0.94	1	0.989	0.94	1	CLONAL	1	TRUE	1	0.850865928095017	2		730	801	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519938	NA	P-0020404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	58	564	0	ENST00000263967.3:c.1034A>T	p.Asn345Ile	p.N345I	ENST00000263967	NM_006218.2	345	aAt/aTt	5/21	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.17	2		564	627	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412034	116412058	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTCCAGAAGGTATATTTCAGTTTA	TTTCCAGAAGGTATATTTCAGTTTA	-	novel	NA	P-0020404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	109	1179	0	ENST00000397752.3:c.3021_3028+17del		p.X1007_splice	ENST00000397752	NM_000245.2	1007		14/21	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.17	2		1179	1270	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0020406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	62	300	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.303050673999422	1	FACETS	0.434	0.379	0.493	0.434	0.379	0.493	INDETERMINATE	1	FALSE	0	0.732346318130574	1		300	247	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913355	NA	P-0020406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	79	470	0	ENST00000288602.6:c.1406G>T	p.Gly469Val	p.G469V	ENST00000288602	NM_004333.4	469	gGa/gTa	11/18	1	2	FACETS	0.881	0.786	0.979	0.881	0.786	0.979	CLONAL	1	FALSE	1	0.732346318130574	2		470	245	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913237	NA	P-0020406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	1711	497	0	ENST00000369535.4:c.35G>T	p.Gly12Val	p.G12V	ENST00000369535	NM_002524.4	12	gGt/gTt	2/7	0.718927596288169	5	FACETS	0.959	0.947	0.97			1	CLONAL	5	FALSE	NA	0.732346318130574	5		497	2046	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459021	120459022	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	1037	731	4	ENST00000256646.2:c.6323_6324delinsTT	p.Ala2108Val	p.A2108V	ENST00000256646	NM_024408.3	2108	gCC/gTT	34/34	0.718927596288169	5	FACETS	1	0.996	1			1	CLONAL	4	FALSE	NA	0.732346318130574	5		735	1404	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741733	17741733	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	451	755	2	ENST00000250003.3:c.404G>T	p.Cys135Phe	p.C135F	ENST00000250003	NM_002478.4	135	tGc/tTc	1/3	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	1	0.732346318130574	2		757	1091	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609622	81609622	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs367815744	NA	P-0020406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	241	625	2	ENST00000298171.2:c.1220C>A	p.Pro407Gln	p.P407Q	ENST00000298171	NM_000369.2	407	cCg/cAg	10/10	1	2	FACETS	0.961	0.902	1	0.961	0.902	1	CLONAL	1	FALSE	1	0.732346318130574	2		627	685	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90634877	90634877	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0020406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	311	551	1	ENST00000330062.3:c.116-1G>A		p.X39_splice	ENST00000330062	NM_002168.2	39			0.389010851579957	1	FACETS	0.743	0.705	0.781	0.743	0.705	0.781	INDETERMINATE	1	FALSE	0	0.732346318130574	1		552	725	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924238	11924238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	75	71	0	ENST00000353533.5:c.35C>T	p.Ser12Phe	p.S12F	ENST00000353533	NM_003010.3	12	tCc/tTc	1/11	0.732346318130574	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	0	0.732346318130574	1		71	100	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144161	11144161	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	472	758	0	ENST00000358026.2:c.3742C>T	p.Gln1248Ter	p.Q1248*	ENST00000358026	NM_001128849.1	1248	Cag/Tag	26/36	0.732346318130574	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	FALSE	0	0.732346318130574	1		758	690	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659994	227659995	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	A	novel	NA	P-0020406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	229	646	1	ENST00000305123.5:c.3460_3461delinsT	p.Gly1154TrpfsTer27	p.G1154Wfs*27	ENST00000305123	NM_005544.2	1154	GGg/Tg	1/2	0.303050673999422	1	FACETS	0.476	0.444	0.508	0.476	0.444	0.508	INDETERMINATE	1	FALSE	0	0.732346318130574	1		647	833	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	58	424	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	0.17	2		424	606	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032604	12032604	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	40	680	0	ENST00000353533.5:c.1040G>A	p.Cys347Tyr	p.C347Y	ENST00000353533	NM_003010.3	347	tGc/tAc	9/11	1	2	FACETS	0.657	0.545	0.783	0.657	0.545	0.783	SUBCLONAL	1	TRUE	1	0.17	2		680	716	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591928	48591928	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	45	564	0	ENST00000342988.3:c.1091T>C	p.Leu364Ser	p.L364S	ENST00000342988	NM_005359.5	364	tTg/tCg	9/12	1	2	FACETS	0.957	0.804	1	0.957	0.804	1	CLONAL	1	TRUE	1	0.17	2		564	553	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807872	1807872	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1244	87	1035	0	ENST00000260795.2:c.1931A>G	p.Asn644Ser	p.N644S	ENST00000260795		644	aAc/aGc	13/17	1	2	FACETS	0.769	0.678	0.867	0.769	0.678	0.867	SUBCLONAL	1	TRUE	1	0.17	2		1035	1331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0020408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	110	930	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.243124412970447	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.3198769591626	1		930	539	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762445	41762445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1159339376	NA	P-0020408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	85	844	1	ENST00000301178.4:c.2125G>A	p.Ala709Thr	p.A709T	ENST00000301178	NM_021913.4	709	Gcc/Acc	18/20	1	2	FACETS	0.837	0.74	0.94	0.837	0.74	0.94	CLONAL	1	TRUE	1	0.3198769591626	2		845	635	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443631	29443631	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519784	NA	P-0020408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	118	1071	0	ENST00000389048.3:c.3586C>A	p.Leu1196Met	p.L1196M	ENST00000389048	NM_004304.4	1196	Ctg/Atg	23/29	0.3198769591626	3	FACETS	0.976	0.88	1			1	CLONAL	1	TRUE	NA	0.3198769591626	3		1071	877	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443610	29443610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759845895	NA	P-0020408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	115	1010	2	ENST00000389048.3:c.3607G>A	p.Asp1203Asn	p.D1203N	ENST00000389048	NM_004304.4	1203	Gac/Aac	23/29	0.3198769591626	3	FACETS	0.993	0.894	1			1	CLONAL	1	TRUE	NA	0.3198769591626	3		1012	840	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211473	98211473	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	61	751	0	ENST00000331920.6:c.3682C>A	p.Gln1228Lys	p.Q1228K	ENST00000331920	NM_000264.3	1228	Cag/Aag	22/24	1	2	FACETS	0.758	0.655	0.87	0.758	0.655	0.87	SUBCLONAL	1	TRUE	1	0.3198769591626	2		751	503	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0020409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	19	466	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.293	0.221	0.378	0.293	0.221	0.378	SUBCLONAL	1	TRUE	1	0.18	2		467	721	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727455	66727455	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs869025608	NA	P-0020409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	24	592	0	ENST00000307102.5:c.171G>T	p.Lys57Asn	p.K57N	ENST00000307102	NM_002755.3	57	aaG/aaT	2/11	1	2	FACETS	0.388	0.302	0.487	0.388	0.302	0.487	SUBCLONAL	1	TRUE	1	0.18	2		592	688	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127164	22127164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057519911	NA	P-0020409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	25	685	2	ENST00000215832.6:c.964G>A	p.Glu322Lys	p.E322K	ENST00000215832	NM_002745.4	322	Gag/Aag	7/9	1	2	FACETS	0.393	0.308	0.491	0.393	0.308	0.491	SUBCLONAL	1	TRUE	1	0.18	2		687	707	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732969	30732969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893810	NA	P-0020409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	49	536	3	ENST00000295754.5:c.1582C>T	p.Arg528Cys	p.R528C	ENST00000295754	NM_003242.5	528	Cgt/Tgt	7/7	1	2	FACETS	0.972	0.823	1	0.972	0.823	1	CLONAL	1	TRUE	1	0.18	2		539	560	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923604	39923604	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	33	490	0	ENST00000378444.4:c.3487C>T	p.Arg1163Ter	p.R1163*	ENST00000378444	NM_001123385.1	1163	Cga/Tga	7/15	1	1	FACETS	0.591	0.48	0.716	0.591	0.48	0.716	SUBCLONAL	1	TRUE	0	0.18	1		490	565	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	315	424	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.675610784750758	3	FACETS	0.917	0.875	0.959	0.917	0.875	0.959	CLONAL	2	TRUE	1	0.841223544446235	3		424	580	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	145	505	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	0.827220241171586	3	FACETS	0.951	0.873	1	0.475	0.436	0.516	CLONAL	1	TRUE	1	0.841223544446235	3		505	515	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699528	117699528	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	108	325	1	ENST00000369458.3:c.113C>T	p.Thr38Ile	p.T38I	ENST00000369458	NM_024626.3	38	aCa/aTa	3/6	1	2	FACETS	0.853	0.776	0.932	0.853	0.776	0.932	CLONAL	1	TRUE	1	0.841223544446235	2		326	301	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786728	3786750	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGTATTTTTTGATCAGGTGGG	TGGGTATTTTTTGATCAGGTGGG	-	novel	NA	P-0020412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	78	682	0	ENST00000262367.5:c.4461_4483del	p.His1487GlnfsTer24	p.H1487Qfs*24	ENST00000262367	NM_004380.2	1487	caCCCACCTGATCAAAAAATACCCAag/caag	27/31	0.827220241171586	3	FACETS	0.267	0.234	0.303	0.134	0.117	0.152	SUBCLONAL	1	TRUE	1	0.841223544446235	3		682	986	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672749	30672750	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0020412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	211	770	0	ENST00000376406.3:c.4210_4211del	p.Pro1404Ter	p.P1404*	ENST00000376406	NM_014641.2	1404	CCt/t	10/15	1	2	FACETS	0.679	0.632	0.726	0.679	0.632	0.726	SUBCLONAL	1	TRUE	1	0.841223544446235	2		770	739	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	98	424	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.864	0.774	0.96	0.864	0.774	0.96	CLONAL	1	TRUE	1	0.438703136561537	2		424	517	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0020414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	93	499	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	0.438703136561537	2		499	369	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604770	48604770	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs377767378	NA	P-0020414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	83	477	0	ENST00000342988.3:c.1594del	p.Ala532ProfsTer5	p.A532Pfs*5	ENST00000342988	NM_005359.5	531	cGg/cg	12/12	0.438703136561537	1	FACETS	0.892	0.795	0.995	0.892	0.795	0.995	CLONAL	1	TRUE	0	0.438703136561537	1		477	331	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228164	36228164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	141	827	2	ENST00000222270.7:c.7550G>A	p.Arg2517Gln	p.R2517Q	ENST00000222270	NM_014727.1	2517	cGg/cAg	33/37	1	2	FACETS	0.945	0.863	1	0.945	0.863	1	CLONAL	1	TRUE	1	0.438703136561537	2		829	680	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480306	89480306	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	49	247	0	ENST00000336596.2:c.2143G>A	p.Asp715Asn	p.D715N	ENST00000336596	NM_005233.5	715	Gat/Aat	13/17	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.438703136561537	2		247	195	SUCCESS
APC	324	MSKCC	GRCh37	5	112163677	112163677	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0020418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	56	403	1	ENST00000257430.4:c.1600A>T	p.Lys534Ter	p.K534*	ENST00000257430	NM_000038.5	534	Aaa/Taa	13/16	1	2	FACETS	0.757	0.654	0.869	0.757	0.654	0.869	SUBCLONAL	1	TRUE	1	0.508241725045681	2		404	291	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0020418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	41	259	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	1	2	FACETS	0.996	0.843	1	0.996	0.843	1	CLONAL	1	TRUE	1	0.508241725045681	2		259	162	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236173	108236173	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555152009	NA	P-0020418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	245	732	0	ENST00000278616.4:c.9109C>T	p.Gln3037Ter	p.Q3037*	ENST00000278616	NM_000051.3	3037	Cag/Tag	63/63	0.508241725045681	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.508241725045681	2		732	478	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387093	31387093	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	158	784	0	ENST00000328111.2:c.1718G>T	p.Arg573Leu	p.R573L	ENST00000328111	NM_006892.3	573	cGg/cTg	16/23	0.349439371680676	6	FACETS	1	0.975	1	0.292	0.266	0.318	CLONAL	1	TRUE	2	0.508241725045681	6		784	1075	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508783	31508783	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	322	781	1	ENST00000344624.3:c.1532A>G	p.Lys511Arg	p.K511R	ENST00000344624		511	aAa/aGa	7/33	0.491534898458483	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.508241725045681	3		782	773	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589012	67589116	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATACTCTTACACTAAGGTAAGCCAGGGAATATAGCTGAAATTAGGGTTTTGGGCTGATATTAAAACATATTTCCTTATTCCAAAATGTTAATACCTTTATTTTTA	ATACTCTTACACTAAGGTAAGCCAGGGAATATAGCTGAAATTAGGGTTTTGGGCTGATATTAAAACATATTTCCTTATTCCAAAATGTTAATACCTTTATTTTTA	-	novel	NA	P-0020418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	55	331	2	ENST00000274335.5:c.1103_1119-15del		p.X368_splice	ENST00000274335		368		8/15	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.508241725045681	2		333	212	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589171	67589171	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	20	375	0	ENST00000274335.5:c.1159G>C	p.Asp387His	p.D387H	ENST00000274335		387	Gat/Cat	9/15	1	2	FACETS	0.341	0.261	0.433	0.341	0.261	0.433	SUBCLONAL	1	TRUE	1	0.508241725045681	2		375	231	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0020419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	74	927	1	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	1	2	FACETS	0.995	0.869	1	0.995	0.869	1	CLONAL	1	TRUE	1	0.14	2		928	1062	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245065	46245067	+	frameshift_variant	Frame_Shift_Del	DEL	CTC	CTC	GT	novel	NA	P-0020419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	60	638	0	ENST00000334344.6:c.3159_3161delinsGT	p.Ser1054LeufsTer6	p.S1054Lfs*6	ENST00000334344	NM_152641.2	1053	gcCTCt/gcGTt	15/21	1	2	FACETS	0.998	0.858	1	0.998	0.858	1	CLONAL	1	TRUE	1	0.14	2		638	859	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023282	31023282	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	47	706	0	ENST00000375687.4:c.2767G>T	p.Glu923Ter	p.E923*	ENST00000375687	NM_015338.5	923	Gag/Tag	13/13	1	2	FACETS	0.783	0.659	0.922	0.783	0.659	0.922	CLONAL	1	TRUE	1	0.14	2		706	857	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55229241	55229241	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	44	657	0	ENST00000275493.2:c.1548G>T	p.Trp516Cys	p.W516C	ENST00000275493	NM_005228.3	516	tgG/tgT	13/28	1	2	FACETS	0.873	0.73	1	0.873	0.73	1	CLONAL	1	TRUE	1	0.14	2		657	720	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0020424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	369	532	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.590918356732533	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.612379590865546	1		533	746	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307529	118307529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	269	1095	1	ENST00000534358.1:c.302C>T	p.Ser101Leu	p.S101L	ENST00000534358	NM_005933.3	101	tCa/tTa	1/36	1	2	FACETS	0.778	0.73	0.828	0.778	0.73	0.828	SUBCLONAL	1	TRUE	1	0.612379590865546	2		1096	1129	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916645	48916762	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGAAAAAATCAGTTATAATACAGTTTTAACATAGTATCCAGTGTGTGAATTATTTAATGAAATATTTGATCTTTATTTTTTGTTCCCAGGGAGGTTATATTCAAAAGAAAAAGGAAC	AAGAAAAAATCAGTTATAATACAGTTTTAACATAGTATCCAGTGTGTGAATTATTTAATGAAATATTTGATCTTTATTTTTTGTTCCCAGGGAGGTTATATTCAAAAGAAAAAGGAAC	-	novel	NA	P-0020424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	133	89	1	ENST00000267163.4:c.265-90_292del		p.X89_splice	ENST00000267163	NM_000321.2	89		3/27	0.612379590865546	1	FACETS	0.842	0.796	0.884	1	0.992	1	CLONAL	2	TRUE	0	0.612379590865546	1		90	179	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223646	36223646	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs755914378	NA	P-0020424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	461	1112	4	ENST00000222270.7:c.6196G>T	p.Asp2066Tyr	p.D2066Y	ENST00000222270	NM_014727.1	2066	Gac/Tac	28/37	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.612379590865546	2		1116	1275	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76953104	76953977	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTCTGAAGAGCTAGTTCCCTAGATGTGAGACATAAATATAAAAGTGAATAAAATTCTCGAAACGGCATCCCTACAATTAGCTATTTCCCTATAGCAACTTCAATACAGTGATATAATGAGATGCTATTTATGTGCCTAGAATATTTTTCTAAAAGGAACTTCAAAAACTAATTCTCTACCACATAAGGAACACAGATGCAAAAAAATAAAAATTAAAACTAATTCTCATTTACTGCCAGGTTTCCTTGGCTGAAGATTAAATTTCTCGTTTTTTACATGGTTGCTGTGGCATGCTGCGGGGAATACACTGCTGCAAAATGATCATGGCCCCAGTCAACAAAGACAAAACAAAGATGCAGAAGTAATCAGATCTCAAGAGAAGTAGGGAGTTTCAAGGATCTAAATATGTTTCATTCTTCTCTAAGCTAACATATGGCATGAAGTAACTTCTACAACTTGCTTTGAGATACTAAACTTACCCTCATTTTGCCAGTATAATCAATATATTTTACTGGATTCAGTTTTTTTTTACAGTAGGTCAAAAAATTCCCAAAACCACAGTTGTGGACCTGTGTATCAGGCAAAGGACCTTGTTATGAGTTGCTATAATAATGCTTAGCAGACTCTAGATACCAAGTTTTGAGAGATTTCACAACCATGGAGTTCATGCCCTTAACATCCACCTCAAACACCTTTGGGGCAATATAAAGACAGTTTAATATCTATCTGTTGGAAGTCTTCAGTTGTCTGACTTTAGGTAAACCACTGAAGTGAACCACAACAATAACAGAAACAATGAACACCTGTTCTCAAACTGGAAAACAACGAAACTGAAGTATAATGACAACTGGGTATCAGTAGCCTTCGACACA	TTTTCTGAAGAGCTAGTTCCCTAGATGTGAGACATAAATATAAAAGTGAATAAAATTCTCGAAACGGCATCCCTACAATTAGCTATTTCCCTATAGCAACTTCAATACAGTGATATAATGAGATGCTATTTATGTGCCTAGAATATTTTTCTAAAAGGAACTTCAAAAACTAATTCTCTACCACATAAGGAACACAGATGCAAAAAAATAAAAATTAAAACTAATTCTCATTTACTGCCAGGTTTCCTTGGCTGAAGATTAAATTTCTCGTTTTTTACATGGTTGCTGTGGCATGCTGCGGGGAATACACTGCTGCAAAATGATCATGGCCCCAGTCAACAAAGACAAAACAAAGATGCAGAAGTAATCAGATCTCAAGAGAAGTAGGGAGTTTCAAGGATCTAAATATGTTTCATTCTTCTCTAAGCTAACATATGGCATGAAGTAACTTCTACAACTTGCTTTGAGATACTAAACTTACCCTCATTTTGCCAGTATAATCAATATATTTTACTGGATTCAGTTTTTTTTTACAGTAGGTCAAAAAATTCCCAAAACCACAGTTGTGGACCTGTGTATCAGGCAAAGGACCTTGTTATGAGTTGCTATAATAATGCTTAGCAGACTCTAGATACCAAGTTTTGAGAGATTTCACAACCATGGAGTTCATGCCCTTAACATCCACCTCAAACACCTTTGGGGCAATATAAAGACAGTTTAATATCTATCTGTTGGAAGTCTTCAGTTGTCTGACTTTAGGTAAACCACTGAAGTGAACCACAACAATAACAGAAACAATGAACACCTGTTCTCAAACTGGAAAACAACGAAACTGAAGTATAATGACAACTGGGTATCAGTAGCCTTCGACACA	-	novel	NA	P-0020424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	95	390	0	ENST00000373344.5:c.189+85_209del		p.X63_splice	ENST00000373344	NM_000489.3	63		4/35	1	1	FACETS	0.448	0.401	0.499	0.448	0.401	0.499	SUBCLONAL	1	TRUE	0	0.612379590865546	1		390	480	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085971	16085971	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	35	749	0	ENST00000281043.3:c.1147C>T	p.Arg383Cys	p.R383C	ENST00000281043	NM_005378.4	383	Cgc/Tgc	3/3	1	2	FACETS	0.113	0.092	0.136	0.113	0.092	0.136	SUBCLONAL	1	TRUE	1	0.90909711771628	2		749	684	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683923	117683923	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	54	984	1	ENST00000368508.3:c.3224A>T	p.Glu1075Val	p.E1075V	ENST00000368508	NM_002944.2	1075	gAa/gTa	21/43	NA	2	FACETS	0.175	0.149	0.204			1	INDETERMINATE	1	TRUE	NA	0.90909711771628	2		985	678	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190708750	190708750	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	90	703	0	ENST00000441310.2:c.643G>C	p.Gly215Arg	p.G215R	ENST00000441310	NM_000534.4	215	Ggg/Cgg	6/13	1	2	FACETS	0.874	0.776	0.978	0.874	0.776	0.978	CLONAL	1	FALSE	1	0.307061436133135	2		703	671	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139506	47139507	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	118	730	0	ENST00000409792.3:c.5080dup	p.Arg1694LysfsTer18	p.R1694Kfs*18	ENST00000409792	NM_014159.6	1694	aga/aAga	9/21	0.281580680866405	1	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	FALSE	0	0.307061436133135	1		730	650	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436835	52436835	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	81	756	0	ENST00000460680.1:c.1943del	p.Ala648GlyfsTer7	p.A648Gfs*7	ENST00000460680	NM_004656.3	648	gCg/gg	15/17	0.281580680866405	1	FACETS	0.654	0.576	0.737	0.654	0.576	0.737	SUBCLONAL	1	FALSE	0	0.307061436133135	1		756	683	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	43	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.614	0.513	0.725	0.614	0.513	0.725	SUBCLONAL	1	TRUE	1	0.27526756020044	2		555	509	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	26	352	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.412	0.326	0.512	0.412	0.326	0.512	SUBCLONAL	1	TRUE	1	0.27526756020044	2		352	458	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	56	474	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.619	0.53	0.717	0.619	0.53	0.717	SUBCLONAL	1	TRUE	1	0.27526756020044	2		477	657	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087503	27087503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	79	694	2	ENST00000324856.7:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000324856	NM_006015.4	693	Cga/Tga	5/20	1	2	FACETS	0.662	0.581	0.749	0.662	0.581	0.749	SUBCLONAL	1	TRUE	1	0.27526756020044	2		696	867	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053022	180053023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750808726	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	32	661	0	ENST00000261937.6:c.1267dup	p.Gln423ProfsTer4	p.Q423Pfs*4	ENST00000261937	NM_182925.4	423	cag/cCag	10/30	1	2	FACETS	0.389	0.315	0.474	0.389	0.315	0.474	SUBCLONAL	1	TRUE	1	0.27526756020044	2		661	597	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097084	11097084	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	57	709	0	ENST00000358026.2:c.579del	p.Gln194SerfsTer109	p.Q194Sfs*109	ENST00000358026	NM_001128849.1	192	aGg/ag	4/36	1	2	FACETS	0.531	0.454	0.615	0.531	0.454	0.615	SUBCLONAL	1	TRUE	1	0.27526756020044	2		709	780	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619289	37619289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	39	424	0	ENST00000447079.4:c.965G>A	p.Arg322Gln	p.R322Q	ENST00000447079	NM_015083.1	322	cGa/cAa	1/14	1	2	FACETS	0.611	0.506	0.727	0.611	0.506	0.727	SUBCLONAL	1	TRUE	1	0.27526756020044	2		424	464	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121873	2121873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746315218	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	64	698	1	ENST00000219476.3:c.2035G>A	p.Val679Met	p.V679M	ENST00000219476	NM_000548.3	679	Gtg/Atg	19/42	1	2	FACETS	0.605	0.523	0.694	0.605	0.523	0.694	SUBCLONAL	1	TRUE	1	0.27526756020044	2		699	769	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497347	149497347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140261309	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	40	514	2	ENST00000261799.4:c.2971C>T	p.Arg991Cys	p.R991C	ENST00000261799	NM_002609.3	991	Cgc/Tgc	22/23	1	2	FACETS	0.464	0.384	0.552	0.464	0.384	0.552	SUBCLONAL	1	TRUE	1	0.27526756020044	2		516	627	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372389	55372389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1274955948	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	70	841	4	ENST00000297316.4:c.1079G>A	p.Arg360His	p.R360H	ENST00000297316	NM_022454.3	360	cGc/cAc	2/2	0.201702940195986	3	FACETS	0.613	0.533	0.7	0.306	0.266	0.35	SUBCLONAL	1	TRUE	1	0.27526756020044	3		845	944	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007901	45007901	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	32	326	0	ENST00000558401.1:c.346+2T>C		p.X116_splice	ENST00000558401	NM_004048.2	116			1	2	FACETS	0.555	0.45	0.673	0.555	0.45	0.673	SUBCLONAL	1	TRUE	1	0.27526756020044	2		326	419	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615698	1615698	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	46	741	1	ENST00000344749.5:c.1573del	p.Arg525GlyfsTer18	p.R525Gfs*18	ENST00000344749	NM_001136139.2	525	Cgg/gg	17/19	1	2	FACETS	0.458	0.385	0.54	0.458	0.385	0.54	SUBCLONAL	1	TRUE	1	0.27526756020044	2		742	729	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176329	24176329	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1568963596	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	40	648	6	ENST00000263121.7:c.1120C>T	p.Arg374Trp	p.R374W	ENST00000263121	NM_003073.3	374	Cgg/Tgg	9/9	1	2	FACETS	0.368	0.305	0.44	0.368	0.305	0.44	SUBCLONAL	1	TRUE	1	0.27526756020044	2		654	789	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274207	10274207	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749314552	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	21	304	0	ENST00000330684.3:c.62C>T	p.Pro21Leu	p.P21L	ENST00000330684	NM_001134407.1	21	cCg/cTg	2/13	1	2	FACETS	0.405	0.311	0.514	0.405	0.311	0.514	SUBCLONAL	1	TRUE	1	0.27526756020044	2		304	377	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163374	108163374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754181173	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	26	522	1	ENST00000278616.4:c.4465C>T	p.Arg1489Cys	p.R1489C	ENST00000278616	NM_000051.3	1489	Cgt/Tgt	30/63	1	2	FACETS	0.477	0.377	0.591	0.477	0.377	0.591	SUBCLONAL	1	TRUE	1	0.27526756020044	2		523	396	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	80	520	3	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	1	2	FACETS	0.649	0.57	0.735	0.649	0.57	0.735	SUBCLONAL	1	TRUE	1	0.27526756020044	2		523	895	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240613	133240613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201115064	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	41	479	0	ENST00000320574.5:c.2683G>A	p.Ala895Thr	p.A895T	ENST00000320574	NM_006231.2	895	Gcc/Acc	23/49	1	2	FACETS	0.54	0.449	0.641	0.54	0.449	0.641	SUBCLONAL	1	TRUE	1	0.27526756020044	2		479	552	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825539	50825539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762650238	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	33	523	0	ENST00000398568.2:c.2170G>A	p.Val724Ile	p.V724I	ENST00000398568	NM_001042412.1	724	Gtt/Att	14/18	1	2	FACETS	0.559	0.455	0.676	0.559	0.455	0.676	SUBCLONAL	1	TRUE	1	0.27526756020044	2		523	429	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248737	212248737	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	44	321	0	ENST00000342788.4:c.3530del	p.Asn1177MetfsTer27	p.N1177Mfs*27	ENST00000342788	NM_005235.2	1177	aAt/at	28/28	1	2	FACETS	0.895	0.753	1	0.895	0.753	1	CLONAL	1	TRUE	1	0.27526756020044	2		321	357	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280036	18280036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	40	366	2	ENST00000222254.8:c.2119G>A	p.Ala707Thr	p.A707T	ENST00000222254	NM_005027.3	707	Gcg/Acg	16/16	1	2	FACETS	0.545	0.452	0.649	0.545	0.452	0.649	SUBCLONAL	1	TRUE	1	0.27526756020044	2		368	533	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776616	9776616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762485999	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	63	606	1	ENST00000377346.4:c.719C>T	p.Thr240Met	p.T240M	ENST00000377346	NM_005026.3	240	aCg/aTg	6/24	1	2	FACETS	0.571	0.492	0.656	0.571	0.492	0.656	SUBCLONAL	1	TRUE	1	0.27526756020044	2		607	802	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087378	27087378	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs756561081	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	49	605	0	ENST00000324856.7:c.1952T>C	p.Met651Thr	p.M651T	ENST00000324856	NM_006015.4	651	aTg/aCg	5/20	1	2	FACETS	0.598	0.506	0.7	0.598	0.506	0.7	SUBCLONAL	1	TRUE	1	0.27526756020044	2		605	595	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088712	27088712	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754046530	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	74	742	1	ENST00000324856.7:c.2321G>A	p.Arg774His	p.R774H	ENST00000324856	NM_006015.4	774	cGt/cAt	7/20	1	2	FACETS	0.543	0.474	0.618	0.543	0.474	0.618	SUBCLONAL	1	TRUE	1	0.27526756020044	2		743	990	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981273	201981273	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1298110845	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	119	670	1	ENST00000359651.3:c.352G>A	p.Gly118Arg	p.G118R	ENST00000359651		118	Ggg/Agg	2/8	0.27526756020044	3	FACETS	1	0.973	1	0.607	0.548	0.67	CLONAL	1	TRUE	1	0.27526756020044	3		671	810	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246027125	246027125	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1558435001	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	70	721	1	ENST00000388985.4:c.877del	p.Ile293LeufsTer4	p.I293Lfs*4	ENST00000388985		293	Att/tt	9/12	0.27526756020044	3	FACETS	0.592	0.514	0.676	0.296	0.257	0.338	SUBCLONAL	1	TRUE	1	0.27526756020044	3		722	978	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246368	46246368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776372381	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	27	307	0	ENST00000334344.6:c.4462G>A	p.Asp1488Asn	p.D1488N	ENST00000334344	NM_152641.2	1488	Gac/Aac	15/21	1	2	FACETS	0.477	0.379	0.589	0.477	0.379	0.589	SUBCLONAL	1	TRUE	1	0.27526756020044	2		307	411	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991671	72991671	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	46	425	0	ENST00000268489.5:c.2374G>C	p.Ala792Pro	p.A792P	ENST00000268489	NM_006885.3	792	Gcc/Ccc	2/10	1	2	FACETS	0.668	0.563	0.785	0.668	0.563	0.785	SUBCLONAL	1	TRUE	1	0.27526756020044	2		425	500	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971393	15971393	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	48	570	0	ENST00000268712.3:c.4556C>A	p.Ser1519Ter	p.S1519*	ENST00000268712	NM_006311.3	1519	tCg/tAg	32/46	1	2	FACETS	0.471	0.397	0.552	0.471	0.397	0.552	SUBCLONAL	1	TRUE	1	0.27526756020044	2		570	741	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794637	42794637	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	52	655	0	ENST00000575354.2:c.1721del	p.Pro574HisfsTer154	p.P574Hfs*154	ENST00000575354	NM_015125.3	573	Ccc/cc	10/20	1	2	FACETS	0.586	0.498	0.682	0.586	0.498	0.682	SUBCLONAL	1	TRUE	1	0.27526756020044	2		655	645	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069435	30069435	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs992662337	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	60	513	0	ENST00000338641.4:c.1300G>A	p.Glu434Lys	p.E434K	ENST00000338641	NM_000268.3	434	Gag/Aag	12/16	1	2	FACETS	0.741	0.639	0.853	0.741	0.639	0.853	SUBCLONAL	1	TRUE	1	0.27526756020044	2		513	588	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933996	49933996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528906916	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	72	670	0	ENST00000296474.3:c.2416G>A	p.Gly806Arg	p.G806R	ENST00000296474	NM_002447.2	806	Ggg/Agg	9/20	1	2	FACETS	0.673	0.587	0.766	0.673	0.587	0.766	SUBCLONAL	1	TRUE	1	0.27526756020044	2		670	777	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911609	134911609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	51	496	0	ENST00000398015.3:c.2074C>T	p.Pro692Ser	p.P692S	ENST00000398015	NM_004441.4	692	Cct/Tct	11/16	1	2	FACETS	0.577	0.49	0.673	0.577	0.49	0.673	SUBCLONAL	1	TRUE	1	0.27526756020044	2		496	642	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444528	187444528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1438511659	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	52	536	1	ENST00000232014.4:c.1699G>A	p.Val567Ile	p.V567I	ENST00000232014	NM_001130845.1	567	Gtc/Atc	7/10	1	2	FACETS	0.574	0.488	0.669	0.574	0.488	0.669	SUBCLONAL	1	TRUE	1	0.27526756020044	2		537	658	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868967	117868969	+	inframe_deletion	In_Frame_Del	DEL	ATC	ATC	-	novel	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	44	458	0	ENST00000297338.2:c.730_732del	p.Asp244del	p.D244del	ENST00000297338	NM_006265.2	244	GAT/-	7/14	0.201702940195986	3	FACETS	0.611	0.512	0.722	0.306	0.256	0.361	SUBCLONAL	1	TRUE	1	0.27526756020044	3		458	595	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738058	145738058	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	123	790	1	ENST00000428558.2:c.2852G>T	p.Gly951Val	p.G951V	ENST00000428558	NM_004260.3	951	gGg/gTg	17/22	0.201702940195986	3	FACETS	1	0.972	1	0.598	0.54	0.659	CLONAL	1	TRUE	1	0.27526756020044	3		791	850	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250403	110250404	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	72	611	1	ENST00000374672.4:c.271_272insA	p.Leu91HisfsTer166	p.L91Hfs*166	ENST00000374672	NM_004235.4	91	cta/cAta	3/5	1	2	FACETS	0.807	0.705	0.917	0.807	0.705	0.917	CLONAL	1	TRUE	1	0.27526756020044	2		612	648	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451077	70451077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	68	684	1	ENST00000373644.4:c.5917G>A	p.Glu1973Lys	p.E1973K	ENST00000373644	NM_030625.2	1973	Gaa/Aaa	12/12	0.179980213423105	5	FACETS	0.852	0.741	0.972	0.284	0.247	0.324	INDETERMINATE	1	TRUE	2	0.427310779811304	5		685	613	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784894	9784894	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	86	810	0	ENST00000377346.4:c.2897T>A	p.Ile966Asn	p.I966N	ENST00000377346	NM_005026.3	966	aTc/aAc	23/24	0.387764461353067	2	FACETS	0.634	0.561	0.712	0.317	0.28	0.356	SUBCLONAL	1	TRUE	0	0.427310779811304	2		810	635	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420329	88420329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	34	475	1	ENST00000360948.2:c.2357G>A	p.Gly786Asp	p.G786D	ENST00000360948	NM_001012338.2	786	gGt/gAt	19/19	0.179980213423105	5	FACETS	0.497	0.406	0.601	0.166	0.135	0.201	INDETERMINATE	1	TRUE	2	0.427310779811304	5		476	525	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579442	7579442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	276	802	0	ENST00000269305.4:c.245del	p.Pro82ArgfsTer41	p.P82Rfs*41	ENST00000269305	NM_001126112.2	82	cCg/cg	4/11	0.427310779811304	2	FACETS	0.958	0.906	1	0.958	0.906	1	CLONAL	2	TRUE	0	0.427310779811304	2		802	674	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776671	9776672	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0020432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	27	784	0	ENST00000377346.4:c.774_775del	p.Gln258HisfsTer30	p.Q258Hfs*30	ENST00000377346	NM_005026.3	258	caGTtc/catc	6/24	0.387764461353067	2	FACETS	0.242	0.192	0.3	0.121	0.096	0.15	SUBCLONAL	1	TRUE	0	0.427310779811304	2		784	522	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0020436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	1369	807	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.768208159873096	4	FACETS	0.994	0.984	1			1	CLONAL	4	TRUE	NA	0.834749911870986	4		807	1513	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939037	76939037	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0020436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	264	875	0	ENST00000373344.5:c.1711A>T	p.Arg571Ter	p.R571*	ENST00000373344	NM_000489.3	571	Aga/Tga	9/35	0.694327372568827	4	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	2	0.834749911870986	4		875	567	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204495487	204495487	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0020438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	252	493	1	ENST00000367182.3:c.79-1G>T		p.X27_splice	ENST00000367182	NM_001278516.1	27			0.268080433509195	5	FACETS	0.903	0.846	0.962	0.677	0.634	0.722	CLONAL	3	TRUE	1	0.268080433509195	5		494	973	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637979	39637979	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	449	765	1	ENST00000262039.4:c.2396G>T	p.Arg799Leu	p.R799L	ENST00000262039	NM_002647.2	799	cGt/cTt	22/25	0.268080433509195	0	FACETS	0.873	0.843	0.902			1	CLONAL	4	TRUE	0	0.268080433509195	0		766	702	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219357	1219357	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730881970	NA	P-0020438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	466	1005	0	ENST00000326873.7:c.409C>T	p.Gln137Ter	p.Q137*	ENST00000326873	NM_000455.4	137	Cag/Tag	3/10	0.268080433509195	0	FACETS	0.795	0.772	0.818			1	SUBCLONAL	5	TRUE	0	0.268080433509195	0		1005	640	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098806	178098806	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1553487947	NA	P-0020438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	736	862	2	ENST00000397062.3:c.239C>A	p.Thr80Lys	p.T80K	ENST00000397062	NM_006164.4	80	aCa/aAa	2/5	0.0949238015946801	3	FACETS	0.943	0.912	0.974	1	0.998	1	INDETERMINATE	4	TRUE	1	0.268080433509195	3		864	1651	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800541	32800541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243600800	NA	P-0020438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	481	979	2	ENST00000374899.4:c.1006G>A	p.Val336Ile	p.V336I	ENST00000374899	NM_018833.2	336	Gtt/Att	6/12	0.210915301556724	4	FACETS	1	0.989	1	1	0.997	1	CLONAL	3	TRUE	2	0.268080433509195	4		981	1378	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020336	123020337	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0020438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	206	645	2	ENST00000355640.3:c.824_825delinsTT	p.Trp275Phe	p.W275F	ENST00000355640		275	tGG/tTT	2/7	0.268080433509195	1	FACETS	0.849	0.789	0.91	1	0.993	1	CLONAL	2	TRUE	0	0.268080433509195	1		647	784	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0020551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	228	786	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.969	0.908	1	0.969	0.908	1	CLONAL	1	TRUE	1	0.686758824879671	2		786	685	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106058	8106058	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	208	555	1	ENST00000346208.3:c.878T>A	p.Met293Lys	p.M293K	ENST00000346208		293	aTg/aAg	4/6	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.686758824879671	2		556	554	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0020551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	104	616	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.535	0.48	0.593	0.535	0.48	0.593	SUBCLONAL	1	TRUE	1	0.686758824879671	2		616	566	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0020551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	138	495	2	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.260889526870701	2	FACETS	0.776	0.71	0.844	0.388	0.355	0.422	INDETERMINATE	1	TRUE	0	0.686758824879671	2		497	518	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119789	70119789	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	68	742	0	ENST00000245479.2:c.791G>C	p.Arg264Thr	p.R264T	ENST00000245479	NM_000346.3	264	aGa/aCa	3/3	1	2	FACETS	0.4	0.348	0.456	0.4	0.348	0.456	SUBCLONAL	1	TRUE	1	0.686758824879671	2		742	495	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280031	66280031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867811974	NA	P-0020551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	105	245	0	ENST00000273854.3:c.1658G>A	p.Arg553Gln	p.R553Q	ENST00000273854	NM_004439.5	553	cGa/cAa	7/18	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.686758824879671	2		245	287	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114205	115114205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1456819388	NA	P-0020551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	149	633	0	ENST00000257566.3:c.1012G>A	p.Glu338Lys	p.E338K	ENST00000257566	NM_016569.3	338	Gag/Aag	6/8	1	2	FACETS	0.761	0.699	0.826	0.761	0.699	0.826	SUBCLONAL	1	TRUE	1	0.686758824879671	2		633	570	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958295	11958295	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	125	398	0	ENST00000353533.5:c.205C>T	p.Gln69Ter	p.Q69*	ENST00000353533	NM_003010.3	69	Caa/Taa	2/11	0.686758824879671	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.686758824879671	1		398	237	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587782272	NA	P-0020551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	40	749	0	ENST00000269305.4:c.994-1G>C		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.686758824879671	1	FACETS	0.226	0.188	0.268	0.226	0.188	0.268	SUBCLONAL	1	TRUE	0	0.686758824879671	1		749	338	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549403	5549403	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	39	701	0	ENST00000397747.3:c.430C>A	p.Gln144Lys	p.Q144K	ENST00000397747	NM_025239.3	144	Cag/Aag	4/7	1	2	FACETS	0.164	0.135	0.196	0.164	0.135	0.196	SUBCLONAL	1	TRUE	1	0.686758824879671	2		701	693	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740603	58740603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	98	557	0	ENST00000305921.3:c.1508C>T	p.Ser503Leu	p.S503L	ENST00000305921	NM_003620.3	503	tCa/tTa	6/6	1	2	FACETS	0.491	0.439	0.547	0.491	0.439	0.547	SUBCLONAL	1	TRUE	1	0.686758824879671	2		557	581	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255058	16255058	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1414658127	NA	P-0020551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	256	325	0	ENST00000375759.3:c.2323G>A	p.Glu775Lys	p.E775K	ENST00000375759	NM_015001.2	775	Gag/Aag	11/15	0.102575294108428	3	FACETS	0.849	0.812	0.886			1	INDETERMINATE	3	TRUE	NA	0.686758824879671	3		325	393	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255592	16255592	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	284	466	1	ENST00000375759.3:c.2857G>T	p.Glu953Ter	p.E953*	ENST00000375759	NM_015001.2	953	Gag/Tag	11/15	0.102575294108428	3	FACETS	0.89	0.854	0.925			1	INDETERMINATE	3	TRUE	NA	0.686758824879671	3		467	416	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023501	27023501	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	31	634	0	ENST00000324856.7:c.607C>A	p.His203Asn	p.H203N	ENST00000324856	NM_006015.4	203	Cac/Aac	1/20	NA	2	FACETS	0.226	0.183	0.276			1	INDETERMINATE	1	TRUE	NA	0.686758824879671	2		634	399	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797114	45797114	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780084	NA	P-0020551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	111	769	1	ENST00000450313.1:c.1301C>T	p.Thr434Met	p.T434M	ENST00000450313	NM_012222.2	434	aCg/aTg	13/16	0.510678205290167	3	FACETS	0.588	0.529	0.651	0.294	0.264	0.326	SUBCLONAL	1	TRUE	1	0.686758824879671	3		770	738	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100667	8100667	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	83	680	0	ENST00000346208.3:c.641C>G	p.Ser214Trp	p.S214W	ENST00000346208		214	tCg/tGg	3/6	1	2	FACETS	0.449	0.397	0.505	0.449	0.397	0.505	SUBCLONAL	1	TRUE	1	0.686758824879671	2		680	538	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475242	475242	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	198	647	0	ENST00000399788.2:c.395del	p.Met132ArgfsTer27	p.M132Rfs*27	ENST00000399788	NM_001042603.1	132	aTg/ag	4/28	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.686758824879671	2		647	548	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061239	38061240	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	144	692	1	ENST00000250448.2:c.749_750delinsTT	p.Ser250Phe	p.S250F	ENST00000250448	NM_004496.3	250	tCC/tTT	2/2	1	2	FACETS	0.892	0.82	0.967	0.892	0.82	0.967	CLONAL	1	TRUE	1	0.686758824879671	2		693	470	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019496	42019496	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567040247	NA	P-0020551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	112	599	0	ENST00000219905.7:c.3549G>A	p.Met1183Ile	p.M1183I	ENST00000219905	NM_001164273.1	1183	atG/atA	10/24	1	2	FACETS	0.539	0.486	0.595	0.539	0.486	0.595	SUBCLONAL	1	TRUE	1	0.686758824879671	2		599	605	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81902885	81902885	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	109	496	0	ENST00000359376.3:c.546C>A	p.Phe182Leu	p.F182L	ENST00000359376	NM_002661.3	182	ttC/ttA	6/33	0.686758824879671	1	FACETS	0.608	0.552	0.666	0.608	0.552	0.666	SUBCLONAL	1	TRUE	0	0.686758824879671	1		496	343	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341349	89341349	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	22	633	0	ENST00000301030.4:c.7586C>A	p.Ser2529Tyr	p.S2529Y	ENST00000301030	NM_001256183.1	2529	tCc/tAc	11/13	0.686758824879671	1	FACETS	0.169	0.131	0.213	0.169	0.131	0.213	SUBCLONAL	1	TRUE	0	0.686758824879671	1		633	249	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664426	29664426	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs768464936	NA	P-0020551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	38	456	0	ENST00000356175.3:c.6405C>G	p.Phe2135Leu	p.F2135L	ENST00000356175	NM_000267.3	2135	ttC/ttG	42/57	1	2	FACETS	0.196	0.162	0.235	0.196	0.162	0.235	SUBCLONAL	1	TRUE	1	0.686758824879671	2		456	564	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56809902	56809902	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	124	570	0	ENST00000337432.4:c.1023C>G	p.Ile341Met	p.I341M	ENST00000337432	NM_058216.2	341	atC/atG	8/9	1	2	FACETS	0.611	0.554	0.67	0.611	0.554	0.67	SUBCLONAL	1	TRUE	1	0.686758824879671	2		570	591	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702397	47702397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	42	248	0	ENST00000233146.2:c.1993C>T	p.His665Tyr	p.H665Y	ENST00000233146	NM_000251.2	665	Cac/Tac	12/16	1	2	FACETS	0.388	0.325	0.458	0.388	0.325	0.458	SUBCLONAL	1	TRUE	1	0.686758824879671	2		248	315	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265002	198265002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	54	338	1	ENST00000335508.6:c.2875G>A	p.Ala959Thr	p.A959T	ENST00000335508	NM_012433.2	959	Gct/Act	19/25	1	2	FACETS	0.377	0.323	0.436	0.377	0.323	0.436	SUBCLONAL	1	TRUE	1	0.686758824879671	2		339	417	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662301	227662301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1289819083	NA	P-0020551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	41	600	0	ENST00000305123.5:c.1154C>T	p.Ser385Leu	p.S385L	ENST00000305123	NM_005544.2	385	tCg/tTg	1/2	1	2	FACETS	0.282	0.235	0.335	0.282	0.235	0.335	SUBCLONAL	1	TRUE	1	0.686758824879671	2		600	423	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845478	151845478	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	81	610	0	ENST00000262189.6:c.13534C>T	p.His4512Tyr	p.H4512Y	ENST00000262189	NM_170606.2	4512	Cat/Tat	52/59	1	2	FACETS	0.386	0.34	0.435	0.386	0.34	0.435	SUBCLONAL	1	TRUE	1	0.686758824879671	2		610	611	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345800	152345800	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730882047	NA	P-0020551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	101	456	0	ENST00000359321.1:c.770C>T	p.Ser257Leu	p.S257L	ENST00000359321	NM_005431.1	257	tCa/tTa	3/3	1	2	FACETS	0.614	0.551	0.68	0.614	0.551	0.68	SUBCLONAL	1	TRUE	1	0.686758824879671	2		456	479	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932609	39932609	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	85	951	0	ENST00000378444.4:c.1990G>T	p.Glu664Ter	p.E664*	ENST00000378444	NM_001123385.1	664	Gag/Tag	4/15	NA	2	FACETS	0.402	0.355	0.452			1	INDETERMINATE	1	TRUE	NA	0.686758824879671	2		951	616	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0020573-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	222	528	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.377233687257705	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.377233687257705	1		530	869	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475550	12475550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479145908	NA	P-0020573-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	179	568	0	ENST00000287820.6:c.1424C>T	p.Thr475Met	p.T475M	ENST00000287820	NM_015869.4	475	aCg/aTg	7/7	NA	2	FACETS	1	0.929	1			1	INDETERMINATE	1	TRUE	NA	0.377233687257705	2		568	941	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0020845-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	253	531	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	0.515277489495068	2		531	834	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245449	153245449	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020845-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	435	649	0	ENST00000281708.4:c.1742A>C	p.Gln581Pro	p.Q581P	ENST00000281708	NM_033632.3	581	cAg/cCg	11/12	0.495709431774168	2	FACETS	0.937	0.898	0.976	0.937	0.898	0.976	CLONAL	2	TRUE	0	0.515277489495068	2		649	901	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411678	63411678	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020845-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	336	442	0	ENST00000330258.3:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000330258	NM_152424.3	497	Cga/Tga	2/2	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.515277489495068	1		442	664	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482607	56482607	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020845-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	406	747	1	ENST00000267101.3:c.1064C>A	p.Thr355Asn	p.T355N	ENST00000267101	NM_001982.3	355	aCc/aAc	9/28	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.515277489495068	2		748	1276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578493	7578502	+	frameshift_variant	Frame_Shift_Del	DEL	CACAGCTGCA	CACAGCTGCA	-	novel	NA	P-0020845-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	829	1148	0	ENST00000269305.4:c.428_437del	p.Val143GlyfsTer24	p.V143Gfs*24	ENST00000269305	NM_001126112.2	143	gTGCAGCTGTGg/gg	5/11	0.515277489495068	2	FACETS	0.997	0.968	1	0.997	0.968	1	CLONAL	2	TRUE	0	0.515277489495068	2		1148	1613	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374941	45374944	+	frameshift_variant	Frame_Shift_Del	DEL	CCAT	CCAT	-	novel	NA	P-0020845-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	485	581	0	ENST00000262160.6:c.899_902del	p.Asp300AlafsTer13	p.D300Afs*13	ENST00000262160	NM_005901.5	300	gATGGc/gc	8/11	0.495709431774168	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.515277489495068	2		581	923	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276618	15276618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021466-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	40	506	0	ENST00000263388.2:c.5647G>A	p.Asp1883Asn	p.D1883N	ENST00000263388	NM_000435.2	1883	Gat/Aat	30/33	0.0805082471708771	0	FACETS	0.804	0.667	0.958			1	INDETERMINATE	1	TRUE	0	0.14	0		506	611	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034920	42034920	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs368677841	NA	P-0021466-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	34	478	0	ENST00000219905.7:c.4762C>T	p.Gln1588Ter	p.Q1588*	ENST00000219905	NM_001164273.1	1588	Cag/Tag	15/24	1	2	FACETS	0.714	0.582	0.864	0.714	0.582	0.864	SUBCLONAL	1	TRUE	1	0.14	2		478	680	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115809	8115809	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021466-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	56	515	0	ENST00000346208.3:c.1158del	p.Lys387ArgfsTer17	p.K387Rfs*17	ENST00000346208		385	ttC/tt	6/6	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.14	2		515	690	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578199	7578199	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021466-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	24	589	0	ENST00000269305.4:c.650T>C	p.Val217Ala	p.V217A	ENST00000269305	NM_001126112.2	217	gTg/gCg	6/11	1	2	FACETS	0.548	0.428	0.687	0.548	0.428	0.687	SUBCLONAL	1	TRUE	1	0.14	2		589	626	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104356996	104356996	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs564728455	NA	P-0021466-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	27	450	0	ENST00000369902.3:c.856G>A	p.Glu286Lys	p.E286K	ENST00000369902	NM_016169.3	286	Gag/Aag	7/12	0.0805082471708771	0	FACETS	0.627	0.498	0.776			1	INDETERMINATE	1	TRUE	0	0.14	0		450	529	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540353	187540353	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021466-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	34	492	0	ENST00000441802.2:c.7387C>G	p.Leu2463Val	p.L2463V	ENST00000441802	NM_005245.3	2463	Ctt/Gtt	10/27	1	2	FACETS	0.715	0.583	0.865	0.715	0.583	0.865	SUBCLONAL	1	TRUE	1	0.14	2		492	679	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80150026	80150026	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021466-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	46	563	0	ENST00000265081.6:c.2891G>C	p.Arg964Thr	p.R964T	ENST00000265081	NM_002439.4	964	aGa/aCa	21/24	0.193353982916844	3	FACETS	0.82	0.688	0.966	0.41	0.344	0.483	CLONAL	1	TRUE	1	0.14	3		563	858	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088788	27088788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	221	520	0	ENST00000324856.7:c.2402del	p.Gly801ValfsTer32	p.G801Vfs*32	ENST00000324856	NM_006015.4	799	caG/ca	7/20	0.0644195176712183	4	FACETS	0.865	0.808	0.923	0.865	0.808	0.923	INDETERMINATE	2	TRUE	2	0.566099156281516	4		520	707	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041974	14041974	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	190	386	0	ENST00000311895.7:c.2521T>G	p.Ser841Ala	p.S841A	ENST00000311895	NM_005236.2	841	Tca/Gca	11/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.566099156281516	2		386	606	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693002	89693003	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022843-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	62	297	0	ENST00000371953.3:c.491dup	p.Val166SerfsTer14	p.V166Sfs*14	ENST00000371953	NM_000314.4	162	-/A	5/9	0.443010191898407	1	FACETS	0.539	0.467	0.617	0.539	0.467	0.617	SUBCLONAL	1	TRUE	0	0.443010191898407	1		297	404	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50815159	50815160	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0022843-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	59	328	0	ENST00000398568.2:c.1513_1514del	p.Asp505Ter	p.D505*	ENST00000398568	NM_001042412.1	504	gaAGat/gaat	9/18	NA	2	FACETS	0.395	0.339	0.456			1	INDETERMINATE	1	TRUE	NA	0.443010191898407	2		328	674	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621935	1621935	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022843-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	106	512	0	ENST00000344749.5:c.857G>T	p.Gly286Val	p.G286V	ENST00000344749	NM_001136139.2	286	gGg/gTg	11/19	1	2	FACETS	0.814	0.731	0.901	0.814	0.731	0.901	CLONAL	1	TRUE	1	0.443010191898407	2		512	588	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2208957	2208958	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022843-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	43	389	0	ENST00000398665.3:c.992dup	p.Asn331LysfsTer28	p.N331Kfs*28	ENST00000398665	NM_032482.2	329	-/A	12/28	1	2	FACETS	0.298	0.249	0.353	0.298	0.249	0.353	SUBCLONAL	1	TRUE	1	0.443010191898407	2		389	651	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222473	2222473	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022843-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	72	406	0	ENST00000398665.3:c.3305G>T	p.Gly1102Val	p.G1102V	ENST00000398665	NM_032482.2	1102	gGc/gTc	24/28	1	2	FACETS	0.645	0.565	0.731	0.645	0.565	0.731	SUBCLONAL	1	TRUE	1	0.443010191898407	2		406	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0024101-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	391	773	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.860879507777317	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.860879507777317	1		774	498	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0024101-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	123	182	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.860879507777317	1	FACETS	0.638	0.589	0.688	0.638	0.589	0.688	SUBCLONAL	1	TRUE	0	0.860879507777317	1		182	255	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0025328-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	159	406	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	0.518105818129893	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.518105818129893	1		406	388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0025328-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	498	796	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.518105818129893	2		796	840	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910476	32910476	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025328-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	139	474	0	ENST00000380152.3:c.1984T>A	p.Ser662Thr	p.S662T	ENST00000380152		662	Tct/Act	11/27	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.518105818129893	2		474	480	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40740954	40740954	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs778976738	NA	P-0025328-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	128	665	0	ENST00000392038.2:c.1364G>T	p.Arg455Leu	p.R455L	ENST00000392038	NM_001626.4	455	cGc/cTc	13/14	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.518105818129893	2		665	481	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480502	89480502	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025328-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	88	249	0	ENST00000336596.2:c.2339C>G	p.Thr780Arg	p.T780R	ENST00000336596	NM_005233.5	780	aCa/aGa	13/17	0.518105818129893	1	FACETS	0.905	0.813	1	0.905	0.813	1	CLONAL	1	TRUE	0	0.518105818129893	1		249	278	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249011	55249011	+	protein_altering_variant	In_Frame_Ins	INS	A	A	GCGGCAC	novel	NA	P-0025328-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	239	491	0	ENST00000275493.2:c.2309delinsGCGGCAC	p.Asp770delinsGlyGlyThr	p.D770delinsGGT	ENST00000275493	NM_005228.3	770	gAc/gGCGGCACc	20/28	0.518105818129893	4	FACETS	1	0.981	1			1	CLONAL	2	TRUE	NA	0.518105818129893	4		491	632	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574005	7574005	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	422	578	0	ENST00000269305.4:c.1022del	p.Phe341SerfsTer4	p.F341Sfs*4	ENST00000269305	NM_001126112.2	341	tTc/tc	10/11	0.600158655743526	2	FACETS	0.941	0.907	0.975	0.941	0.907	0.975	CLONAL	2	TRUE	0	0.649682103850189	2		578	690	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108239	8108239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	118	659	2	ENST00000585124.1:c.985G>A	p.Ala329Thr	p.A329T	ENST00000585124	NM_004217.3	329	Gcc/Acc	9/9	0.600158655743526	2	FACETS	0.561	0.507	0.617	0.28	0.253	0.309	SUBCLONAL	1	TRUE	0	0.649682103850189	2		661	648	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528428	29528428	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0025466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	83	342	0	ENST00000356175.3:c.1186-1G>A		p.X396_splice	ENST00000356175	NM_000267.3	396			0.649682103850189	2	FACETS	0.51	0.451	0.573	0.255	0.225	0.287	SUBCLONAL	1	TRUE	0	0.649682103850189	2		342	501	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976166	18976166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1010786745	NA	P-0025466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	145	648	2	ENST00000262803.5:c.2926G>A	p.Val976Met	p.V976M	ENST00000262803	NM_002911.3	976	Gtg/Atg	21/24	0.649682103850189	3	FACETS	0.533	0.485	0.583	0.266	0.242	0.292	SUBCLONAL	1	TRUE	1	0.649682103850189	3		650	1110	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763976	76763976	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	265	605	0	ENST00000373344.5:c.7332G>T	p.Leu2444Phe	p.L2444F	ENST00000373344	NM_000489.3	2444	ttG/ttT	35/35	0.649682103850189	2	FACETS	0.949	0.892	1	0.474	0.446	0.504	CLONAL	1	TRUE	0	0.649682103850189	2		605	860	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0025554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	63	606	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.841	0.728	0.964	0.841	0.728	0.964	CLONAL	1	TRUE	1	0.26	2		606	576	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0025554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	98	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.836	0.75	0.926	1	0.984	1	CLONAL	2	TRUE	1	0.26	2		555	451	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0025554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	33	288	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.926	0.758	1	0.926	0.758	1	CLONAL	1	TRUE	1	0.26	2		288	274	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211899	36211899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	36	546	2	ENST00000222270.7:c.1656del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	550	gaC/ga	3/37	1	2	FACETS	0.631	0.518	0.757	0.631	0.518	0.757	SUBCLONAL	1	TRUE	1	0.26	2		548	439	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0025554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	36	558	3	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.527	0.433	0.634	0.527	0.433	0.634	SUBCLONAL	1	TRUE	1	0.26	2		561	525	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0025554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	60	520	3	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	1	2	FACETS	0.944	0.814	1	0.944	0.814	1	CLONAL	1	TRUE	1	0.26	2		523	489	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0025554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	22	288	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.469	0.363	0.592	0.469	0.363	0.592	SUBCLONAL	1	TRUE	1	0.26	2		288	361	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056320	27056320	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	64	373	0	ENST00000324856.7:c.1316del	p.Gln439ArgfsTer180	p.Q439Rfs*180	ENST00000324856	NM_006015.4	439	cAg/cg	2/20	1	2	FACETS	0.804	0.702	0.913	1	0.975	1	CLONAL	2	TRUE	1	0.26	2		373	306	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	55	365	5	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	0.26	2		370	331	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685289	89685289	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554897267	NA	P-0025554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	25	293	0	ENST00000371953.3:c.188del	p.Asn63ThrfsTer36	p.N63Tfs*36	ENST00000371953	NM_000314.4	62	Aaa/aa	3/9	1	2	FACETS	0.62	0.489	0.771	0.62	0.489	0.771	SUBCLONAL	1	TRUE	1	0.26	2		293	310	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0025554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	34	487	2	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.536	0.437	0.647	0.536	0.437	0.647	SUBCLONAL	1	TRUE	1	0.26	2		489	488	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198870	67198871	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs746624387	NA	P-0025554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	31	377	0	ENST00000312629.5:c.348_349del	p.Arg117GlyfsTer2	p.R117Gfs*2	ENST00000312629	NM_003952.2	114	gCA/g	5/15	1	2	FACETS	0.526	0.425	0.641	0.526	0.425	0.641	SUBCLONAL	1	TRUE	1	0.26	2		377	453	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206729	102206729	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	50	395	0	ENST00000263464.3:c.1357G>A	p.Ala453Thr	p.A453T	ENST00000263464	NM_001165.4	453	Gca/Aca	7/9	1	2	FACETS	0.996	0.848	1	0.996	0.848	1	CLONAL	1	TRUE	1	0.26	2		395	386	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427743	49427743	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	54	466	0	ENST00000301067.7:c.10745G>A	p.Arg3582Gln	p.R3582Q	ENST00000301067	NM_003482.3	3582	cGg/cAg	39/54	1	2	FACETS	0.948	0.812	1	0.948	0.812	1	CLONAL	1	TRUE	1	0.26	2		466	438	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256123	133256123	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1565979764	NA	P-0025554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	56	485	1	ENST00000320574.5:c.538C>T	p.Gln180Ter	p.Q180*	ENST00000320574	NM_006231.2	180	Cag/Tag	6/49	1	2	FACETS	0.772	0.661	0.893	0.772	0.661	0.893	SUBCLONAL	1	TRUE	1	0.26	2		486	558	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865818	56865818	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	39	297	0	ENST00000308159.5:c.1150G>T	p.Asp384Tyr	p.D384Y	ENST00000308159	NM_014669.4	384	Gat/Tat	11/22	1	2	FACETS	0.877	0.729	1	0.877	0.729	1	CLONAL	1	TRUE	1	0.26	2		297	342	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532475	63532475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1244431726	NA	P-0025554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	117	479	0	ENST00000307078.5:c.2104C>T	p.Arg702Cys	p.R702C	ENST00000307078	NM_004655.3	702	Cgc/Tgc	8/11	1	2	FACETS	0.947	0.859	1	1	0.989	1	CLONAL	2	TRUE	1	0.26	2		479	475	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122771	7122771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202160383	NA	P-0025554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	35	388	0	ENST00000302850.5:c.3383G>A	p.Arg1128His	p.R1128H	ENST00000302850	NM_000208.2	1128	cGc/cAc	19/22	1	2	FACETS	0.72	0.591	0.864	0.72	0.591	0.864	SUBCLONAL	1	TRUE	1	0.26	2		388	374	SUCCESS
AXL	558	MSKCC	GRCh37	19	41749573	41749573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144824336	NA	P-0025554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	51	431	0	ENST00000301178.4:c.1498G>A	p.Val500Met	p.V500M	ENST00000301178	NM_021913.4	500	Gtg/Atg	12/20	1	2	FACETS	0.781	0.665	0.91	0.781	0.665	0.91	CLONAL	1	TRUE	1	0.26	2		431	502	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172022	99172023	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0025554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	84	424	0	ENST00000074304.5:c.1591_1592del	p.Trp531AlafsTer29	p.W531Afs*29	ENST00000074304	NM_001134224.1	530	GTg/g	17/26	1	2	FACETS	0.788	0.7	0.881	1	0.98	1	SUBCLONAL	2	TRUE	1	0.26	2		424	410	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602719	55602719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752695117	NA	P-0025554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	28	425	1	ENST00000288135.5:c.2540C>T	p.Thr847Met	p.T847M	ENST00000288135	NM_000222.2	847	aCg/aTg	18/21	1	2	FACETS	0.562	0.449	0.691	0.562	0.449	0.691	SUBCLONAL	1	TRUE	1	0.26	2		426	383	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508787	31508787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370207689	NA	P-0025554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	79	499	0	ENST00000344624.3:c.1528C>T	p.Arg510Cys	p.R510C	ENST00000344624		510	Cgc/Tgc	7/33	1	2	FACETS	0.963	0.847	1	0.963	0.847	1	CLONAL	1	TRUE	1	0.26	2		499	631	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875632	35875632	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	42	409	0	ENST00000303115.3:c.819G>A	p.Trp273Ter	p.W273*	ENST00000303115	NM_002185.3	273	tgG/tgA	7/8	1	2	FACETS	0.771	0.644	0.911	0.771	0.644	0.911	CLONAL	1	TRUE	1	0.26	2		409	419	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523068	176523068	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1387211815	NA	P-0025554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	22	415	0	ENST00000292408.4:c.1832G>A	p.Arg611Gln	p.R611Q	ENST00000292408	NM_213647.1	611	cGg/cAg	14/18	1	2	FACETS	0.424	0.328	0.536	0.424	0.328	0.536	SUBCLONAL	1	TRUE	1	0.26	2		415	399	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903705	41903706	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGAGTGCTGGTCTGGCTGGGCCC	novel	NA	P-0025554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	44	485	0	ENST00000372991.4:c.829_851dup	p.Thr285GlyfsTer27	p.T285Gfs*27	ENST00000372991	NM_001760.3	284	cct/ccGGGCCCAGCCAGACCAGCACTCCt	5/5	1	2	FACETS	0.677	0.568	0.798	0.677	0.568	0.798	SUBCLONAL	1	TRUE	1	0.26	2		485	500	SUCCESS
AR	367	MSKCC	GRCh37	X	66905873	66905873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	45	379	0	ENST00000374690.3:c.1790C>T	p.Ala597Val	p.A597V	ENST00000374690	NM_000044.3	597	gCc/gTc	3/8	1	2	FACETS	0.888	0.748	1	0.888	0.748	1	CLONAL	1	TRUE	1	0.26	2		379	390	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0025601-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	699	674	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.78906446658089	7	FACETS	1	0.975	1	0.805	0.78	0.83	CLONAL	4	TRUE	2	0.78906446658089	7		674	1308	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025601-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	487	537	0	ENST00000269305.4:c.517G>C	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ctg	5/11	0.78906446658089	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.78906446658089	2		537	589	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910387	29910392	+	inframe_deletion	In_Frame_Del	DEL	GACCCA	GACCCA	-	novel	NA	P-0025601-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1480	237	771	0	ENST00000376809.5:c.61_66del	p.Gln21_Thr22del	p.Q21_T22del	ENST00000376809	NM_002116.7	19	ctGACCCAg/ctg	1/8	0.78906446658089	4	FACETS	0.626	0.582	0.672	0.209	0.194	0.224	SUBCLONAL	1	TRUE	1	0.78906446658089	4		771	1717	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778894	3778894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1421133831	NA	P-0025601-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	93	372	3	ENST00000262367.5:c.6154C>T	p.Arg2052Trp	p.R2052W	ENST00000262367	NM_004380.2	2052	Cgg/Tgg	31/31	0.622369456451956	6	FACETS	0.619	0.55	0.694	0.206	0.183	0.232	SUBCLONAL	1	TRUE	3	0.78906446658089	6		375	981	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0025729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	114	499	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	0.54	2		499	422	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133238247	133238247	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0025729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	109	458	1	ENST00000320574.5:c.2730C>G	p.Tyr910Ter	p.Y910*	ENST00000320574	NM_006231.2	910	taC/taG	24/49	1	2	FACETS	0.891	0.805	0.981	0.891	0.805	0.981	CLONAL	1	TRUE	1	0.54	2		459	453	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179387	56179387	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0025729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	88	319	0	ENST00000399503.3:c.3700A>T	p.Lys1234Ter	p.K1234*	ENST00000399503	NM_005921.1	1234	Aaa/Taa	15/20	0.525624378691723	1	FACETS	0.905	0.813	0.999	0.905	0.813	0.999	CLONAL	1	TRUE	0	0.54	1		319	263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578507	7578507	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519977	NA	P-0025730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	218	1016	0	ENST00000269305.4:c.423C>G	p.Cys141Trp	p.C141W	ENST00000269305	NM_001126112.2	141	tgC/tgG	5/11	0.344863384215853	3	FACETS	0.816	0.76	0.874	0.816	0.76	0.874	CLONAL	2	TRUE	1	0.344863384215853	3		1016	908	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934178	39934179	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	104	389	0	ENST00000378444.4:c.420dup	p.Pro141ThrfsTer45	p.P141Tfs*45	ENST00000378444	NM_001123385.1	140	-/A	4/15	0.27118733213643	2	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.344863384215853	2		389	413	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0025733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	313	603	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.430474110842066	1	FACETS	0.883	0.843	0.922	0.883	0.843	0.922	INDETERMINATE	1	TRUE	0	0.782260946544902	1		603	552	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	64	122	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.831	0.732	0.933	0.831	0.732	0.933	CLONAL	1	TRUE	1	0.782260946544902	2		122	197	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0025733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	190	310	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.782260946544902	2		310	471	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259262	89259262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770780950	NA	P-0025733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	185	401	1	ENST00000336596.2:c.406C>T	p.Arg136Ter	p.R136*	ENST00000336596	NM_005233.5	136	Cga/Tga	3/17	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.782260946544902	2		402	444	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857944	9857944	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267604687	NA	P-0025733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	272	513	0	ENST00000330684.3:c.3457G>A	p.Asp1153Asn	p.D1153N	ENST00000330684	NM_001134407.1	1153	Gat/Aat	13/13	0.285445613978699	3	FACETS	0.771	0.73	0.814	0.771	0.73	0.814	INDETERMINATE	2	TRUE	1	0.782260946544902	3		513	627	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517948	176517948	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	171	493	0	ENST00000292408.4:c.446G>A	p.Trp149Ter	p.W149*	ENST00000292408	NM_213647.1	149	tGg/tAg	5/18	1	2	FACETS	0.957	0.889	1	0.957	0.889	1	CLONAL	1	TRUE	1	0.782260946544902	2		493	457	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466994	18466994	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773615749	NA	P-0025733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	218	368	0	ENST00000266497.5:c.1133G>A	p.Arg378Gln	p.R378Q	ENST00000266497		378	cGa/cAa	5/31	0.131519902676268	5	FACETS	0.838	0.788	0.888	0.838	0.788	0.888	INDETERMINATE	3	TRUE	2	0.782260946544902	5		368	482	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157053	106157053	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778729965	NA	P-0025733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	247	454	0	ENST00000380013.4:c.1954C>T	p.Gln652Ter	p.Q652*	ENST00000380013	NM_001127208.2	652	Cag/Tag	3/11	0.323063514735761	1	FACETS	0.712	0.672	0.752	0.712	0.672	0.752	INDETERMINATE	1	TRUE	0	0.782260946544902	1		454	540	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966792	18966792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	210	579	0	ENST00000262803.5:c.1603C>T	p.His535Tyr	p.H535Y	ENST00000262803	NM_002911.3	535	Cac/Tac	12/24	0.25212366473127	2	FACETS	0.678	0.631	0.726	0.339	0.315	0.363	INDETERMINATE	1	TRUE	0	0.782260946544902	2		579	792	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912292	29912292	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1487650695	NA	P-0025733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	273	1111	0	ENST00000376809.5:c.911C>T	p.Pro304Leu	p.P304L	ENST00000376809	NM_002116.7	304	cCc/cTc	5/8	0.285445613978699	3	FACETS	0.819	0.768	0.871	0.409	0.384	0.436	INDETERMINATE	1	TRUE	1	0.782260946544902	3		1111	1186	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647535	117647535	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	202	537	0	ENST00000368508.3:c.5409G>A	p.Trp1803Ter	p.W1803*	ENST00000368508	NM_002944.2	1803	tgG/tgA	33/43	0.285445613978699	3	FACETS	1	0.984	1	0.59	0.55	0.631	INDETERMINATE	1	TRUE	1	0.782260946544902	3		537	609	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0025734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	155	528	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.215972349731822	2	FACETS	0.986	0.904	1	0.986	0.904	1	CLONAL	2	TRUE	0	0.216040762520388	2		530	728	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913535	NA	P-0025734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	181	446	0	ENST00000311936.3:c.37G>C	p.Gly13Arg	p.G13R	ENST00000311936	NM_004985.3	13	Ggc/Cgc	2/5	0.216040762520388	3	FACETS	0.981	0.909	1	0.981	0.909	1	CLONAL	3	TRUE	0	0.216040762520388	3		446	631	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220275	55220275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751295137	NA	P-0025734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	86	506	1	ENST00000275493.2:c.665G>A	p.Arg222His	p.R222H	ENST00000275493	NM_005228.3	222	cGc/cAc	6/28	0.195330517402029	3	FACETS	1	0.904	1	0.513	0.453	0.578	CLONAL	1	TRUE	1	0.216040762520388	3		507	859	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112434	115112434	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs906508818	NA	P-0025734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	49	328	1	ENST00000257566.3:c.1306C>T	p.Arg436Cys	p.R436C	ENST00000257566	NM_016569.3	436	Cgc/Tgc	7/8	0.195330517402029	3	FACETS	0.921	0.779	1	0.46	0.389	0.538	CLONAL	1	TRUE	1	0.216040762520388	3		329	546	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0025735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	172	453	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.552806722244447	2		453	518	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0025735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	162	440	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.955	0.88	1	0.955	0.88	1	CLONAL	1	TRUE	1	0.552806722244447	2		440	614	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	189	622	4	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.941	0.872	1	0.941	0.872	1	CLONAL	1	TRUE	1	0.552806722244447	2		626	727	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	232	653	1	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.552806722244447	2		654	823	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0025735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	209	474	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	0.552806722244447	2		477	650	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0025735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	178	403	4	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	0.552806722244447	2		407	587	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0025735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	52	182	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.697	0.598	0.803	0.697	0.598	0.803	SUBCLONAL	1	TRUE	1	0.552806722244447	2		182	270	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	149	323	0	ENST00000397062.3:c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	NM_006164.4	34	Cga/Gga	2/5	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.552806722244447	2		323	468	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851848	134851848	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	145	615	0	ENST00000398015.3:c.1259del	p.Pro420HisfsTer28	p.P420Hfs*28	ENST00000398015	NM_004441.4	418	ttC/tt	5/16	0.552806722244447	3	FACETS	0.771	0.703	0.841	0.385	0.351	0.421	SUBCLONAL	1	TRUE	1	0.552806722244447	3		615	869	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163554	32163554	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	114	398	0	ENST00000375023.3:c.5672del	p.Gly1891AlafsTer13	p.G1891Afs*13	ENST00000375023	NM_004557.3	1891	gGc/gc	30/30	1	2	FACETS	0.931	0.844	1	0.931	0.844	1	CLONAL	1	TRUE	1	0.552806722244447	2		398	443	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220506	1220506	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0025735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	138	438	0	ENST00000326873.7:c.597+2T>C		p.X199_splice	ENST00000326873	NM_000455.4	199			1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.552806722244447	2		438	489	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100312	27100312	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	203	571	0	ENST00000324856.7:c.4024C>T	p.Gln1342Ter	p.Q1342*	ENST00000324856	NM_006015.4	1342	Cag/Tag	17/20	1	2	FACETS	0.942	0.875	1	0.942	0.875	1	CLONAL	1	TRUE	1	0.552806722244447	2		571	780	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998685	100998685	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	158	522	0	ENST00000325455.5:c.1117G>A	p.Ala373Thr	p.A373T	ENST00000325455	NM_001202474.3	373	Gcg/Acg	1/8	1	2	FACETS	0.979	0.901	1	0.979	0.901	1	CLONAL	1	TRUE	1	0.552806722244447	2		522	584	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430905	78430906	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1405120226	NA	P-0025735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	131	377	0	ENST00000370768.2:c.483dup	p.Arg162ThrfsTer8	p.R162Tfs*8	ENST00000370768	NM_003902.3	161	-/A	8/20	1	2	FACETS	0.823	0.75	0.899	0.823	0.75	0.899	CLONAL	1	TRUE	1	0.552806722244447	2		377	576	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653797	89653797	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	148	452	0	ENST00000371953.3:c.96del	p.Ile33LeufsTer21	p.I33Lfs*21	ENST00000371953	NM_000314.4	32	aTt/at	2/9	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.552806722244447	2		452	508	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375303	118375303	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	143	303	0	ENST00000534358.1:c.8696T>A	p.Val2899Glu	p.V2899E	ENST00000534358	NM_005933.3	2899	gTa/gAa	27/36	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.552806722244447	2		303	466	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427572	49427572	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs745634784	NA	P-0025735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	143	442	0	ENST00000301067.7:c.10916A>G	p.His3639Arg	p.H3639R	ENST00000301067	NM_003482.3	3639	cAt/cGt	39/54	1	2	FACETS	0.984	0.902	1	0.984	0.902	1	CLONAL	1	TRUE	1	0.552806722244447	2		442	526	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112301	115112301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1284348347	NA	P-0025735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	13	26	0	ENST00000257566.3:c.1439C>T	p.Ala480Val	p.A480V	ENST00000257566	NM_016569.3	480	gCg/gTg	7/8	1	2	FACETS	0.784	0.574	1	0.784	0.574	1	CLONAL	1	TRUE	1	0.552806722244447	2		26	60	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975760	26975760	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	158	338	0	ENST00000381527.3:c.1268A>G	p.Gln423Arg	p.Q423R	ENST00000381527	NM_001260.1	423	cAg/cGg	12/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.552806722244447	2		338	485	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609957	81609957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756016910	NA	P-0025735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	102	229	0	ENST00000298171.2:c.1555C>T	p.Arg519Cys	p.R519C	ENST00000298171	NM_000369.2	519	Cgc/Tgc	10/10	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.552806722244447	2		229	350	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858807	9858807	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0025735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	45	131	0	ENST00000330684.3:c.2596-2A>T		p.X866_splice	ENST00000330684	NM_001134407.1	866			1	2	FACETS	0.848	0.722	0.983	0.848	0.722	0.983	CLONAL	1	TRUE	1	0.552806722244447	2		131	192	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348742	11348742	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	147	448	0	ENST00000332029.2:c.594del	p.Val199SerfsTer6	p.V199Sfs*6	ENST00000332029	NM_003745.1	198	ccC/cc	2/2	1	2	FACETS	0.858	0.786	0.932	0.858	0.786	0.932	CLONAL	1	TRUE	1	0.552806722244447	2		448	620	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993398	72993398	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200201291	NA	P-0025735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	200	566	1	ENST00000268489.5:c.647C>T	p.Pro216Leu	p.P216L	ENST00000268489	NM_006885.3	216	cCg/cTg	2/10	1	2	FACETS	0.952	0.885	1	0.952	0.885	1	CLONAL	1	TRUE	1	0.552806722244447	2		567	760	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953977	17953977	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs964736085	NA	P-0025735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	176	489	1	ENST00000458235.1:c.425G>A	p.Arg142His	p.R142H	ENST00000458235	NM_000215.3	142	cGc/cAc	5/24	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.552806722244447	2		490	618	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278070	18278070	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs886041602	NA	P-0025735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	242	628	0	ENST00000222254.8:c.1690A>G	p.Lys564Glu	p.K564E	ENST00000222254	NM_005027.3	564	Aag/Gag	13/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.552806722244447	2		628	795	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753327	42753327	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	276	664	0	ENST00000222329.4:c.937T>C	p.Tyr313His	p.Y313H	ENST00000222329	NM_006494.2	313	Tac/Cac	4/4	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.552806722244447	2		664	861	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589632	67589636	+	frameshift_variant	Frame_Shift_Del	DEL	ATTAT	ATTAT	-	novel	NA	P-0025735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	123	390	0	ENST00000274335.5:c.1397_1401del	p.Leu466Ter	p.L466*	ENST00000274335		465	agATTATat/agat	10/15	1	2	FACETS	0.947	0.862	1	0.947	0.862	1	CLONAL	1	TRUE	1	0.552806722244447	2		390	470	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951871	2951871	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	220	589	1	ENST00000396946.4:c.3079C>T	p.Arg1027Ter	p.R1027*	ENST00000396946	NM_032415.4	1027	Cga/Tga	23/25	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.552806722244447	2		590	727	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006791	47006791	+	5_prime_UTR_variant	5'UTR	SNP	C	C	T	novel	NA	P-0025735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	185	539	1	ENST00000377604.3:c.-90C>T		p.*30*	ENST00000377604	NM_001204468.1	-/852		2/24	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.552806722244447	2		540	663	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0025741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	159	655	0	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	0.344602244289215	1	FACETS	0.869	0.797	0.944	0.869	0.797	0.944	CLONAL	1	TRUE	0	0.344602244289215	1		655	879	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	protein_altering_variant	In_Frame_Ins	INS	-	-	GTT	rs1554350347	NA	P-0025741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	492	441	0	ENST00000275493.2:c.2308_2309insGTT	p.Asp770delinsGlyTyr	p.D770delinsGY	ENST00000275493	NM_005228.3	770	gac/gGTTac	20/28	0.344602244289215	6	FACETS	0.928	0.888	0.967	0.928	0.888	0.967	CLONAL	4	TRUE	2	0.344602244289215	6		441	1300	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842606	68842606	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	127	629	0	ENST00000261769.5:c.542A>G	p.Asn181Ser	p.N181S	ENST00000261769	NM_004360.3	181	aAc/aGc	5/16	0.310663047809634	3	FACETS	0.983	0.89	1	0.492	0.445	0.541	CLONAL	1	TRUE	1	0.344602244289215	3		629	879	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719415	190719415	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	42	370	3	ENST00000441310.2:c.1417G>T	p.Asp473Tyr	p.D473Y	ENST00000441310	NM_000534.4	473	Gac/Tac	9/13	0.310651372746353	2	FACETS	0.927	0.779	1	0.463	0.389	0.545	CLONAL	1	TRUE	0	0.344602244289215	2		373	263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0025741-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	142	655	0	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	0.223979339277613	1	FACETS	0.869	0.791	0.951	0.869	0.791	0.951	CLONAL	1	TRUE	0	0.283518334762083	1		655	989	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	protein_altering_variant	In_Frame_Ins	INS	-	-	GTT	rs1554350347	NA	P-0025741-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	423	441	0	ENST00000275493.2:c.2308_2309insGTT	p.Asp770delinsGlyTyr	p.D770delinsGY	ENST00000275493	NM_005228.3	770	gac/gGTTac	20/28	0.283518334762083	6	FACETS	0.954	0.91	0.999	0.954	0.91	0.999	CLONAL	4	TRUE	2	0.283518334762083	6		441	1225	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842606	68842606	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025741-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	152	629	0	ENST00000261769.5:c.542A>G	p.Asn181Ser	p.N181S	ENST00000261769	NM_004360.3	181	aAc/aGc	5/16	0.271177978873768	3	FACETS	1	0.948	1	0.527	0.481	0.575	CLONAL	1	TRUE	1	0.283518334762083	3		629	1162	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719415	190719415	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025741-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	67	370	3	ENST00000441310.2:c.1417G>T	p.Asp473Tyr	p.D473Y	ENST00000441310	NM_000534.4	473	Gac/Tac	9/13	0.280351473417806	2	FACETS	0.745	0.648	0.851	0.373	0.324	0.426	SUBCLONAL	1	TRUE	0	0.283518334762083	2		373	634	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911162	29911162	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025741-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	70	364	0	ENST00000376809.5:c.461T>A	p.Leu154Gln	p.L154Q	ENST00000376809	NM_002116.7	154	cTg/cAg	3/8	0.260725335630926	4	FACETS	0.873	0.76	0.995	0.436	0.38	0.498	CLONAL	1	TRUE	2	0.283518334762083	4		364	726	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0025808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	32	499	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.576002753615209	2		499	88	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	59	671	0	ENST00000206249.3:c.1610A>G	p.Tyr537Cys	p.Y537C	ENST00000206249	NM_000125.3	537	tAt/tGt	8/8	1	2	FACETS	0.75	0.651	0.856	0.75	0.651	0.856	SUBCLONAL	1	TRUE	1	0.576002753615209	2		671	273	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463583	25463583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772368909	NA	P-0025808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	84	674	0	ENST00000264709.3:c.2099C>T	p.Pro700Leu	p.P700L	ENST00000264709	NM_175629.2	700	cCa/cTa	18/23	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.576002753615209	2		674	255	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603029	48603059	+	frameshift_variant	Frame_Shift_Del	DEL	CATCGACAGATGCAGCAGCAGGCGGCTACTG	CATCGACAGATGCAGCAGCAGGCGGCTACTG	-	novel	NA	P-0025808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	35	377	0	ENST00000342988.3:c.1332_1362del	p.Arg445LysfsTer21	p.R445Kfs*21	ENST00000342988	NM_005359.5	444	CATCGACAGATGCAGCAGCAGGCGGCTACTGca/ca	11/12	0.567771695320519	1	FACETS	0.901	0.762	1	0.901	0.762	1	CLONAL	1	TRUE	0	0.576002753615209	1		377	96	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900050	151900050	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	37	633	0	ENST00000262189.6:c.4061del	p.Lys1354SerfsTer20	p.K1354Sfs*20	ENST00000262189	NM_170606.2	1354	aAg/ag	26/59	1	2	FACETS	0.931	0.782	1	0.931	0.782	1	CLONAL	1	TRUE	1	0.576002753615209	2		633	138	SUCCESS
AR	367	MSKCC	GRCh37	X	66765487	66765487	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1327744655	NA	P-0025808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	44	761	0	ENST00000374690.3:c.499C>A	p.Leu167Met	p.L167M	ENST00000374690	NM_000044.3	167	Ctg/Atg	1/8	0.440887653590377	3	FACETS	0.506	0.425	0.595	0.253	0.212	0.298	SUBCLONAL	1	TRUE	1	0.576002753615209	3		761	389	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249013	55249014	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACCCCC	novel	NA	P-0025812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	332	489	1	ENST00000275493.2:c.2314_2319dup	p.Pro772_His773dup	p.P772_H773dup	ENST00000275493	NM_005228.3	772	aac/aACCCCCac	20/28	0.492207843151242	5	FACETS	0.889	0.844	0.935	0.889	0.844	0.935	CLONAL	3	TRUE	2	0.492207843151242	5		490	879	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0025812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	73	281	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.862	0.76	0.971	0.862	0.76	0.971	CLONAL	1	TRUE	1	0.492207843151242	2		281	344	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0025812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	87	312	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	1	2	FACETS	0.93	0.829	1	0.93	0.829	1	CLONAL	1	TRUE	1	0.492207843151242	2		312	380	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0025812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	113	601	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.806	0.727	0.888	0.806	0.727	0.888	CLONAL	1	TRUE	1	0.492207843151242	2		601	570	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0025812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	107	340	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	1	2	FACETS	0.923	0.832	1	0.923	0.832	1	CLONAL	1	TRUE	1	0.492207843151242	2		340	471	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121909229	NA	P-0025812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	298	460	1	ENST00000371953.3:c.389G>C	p.Arg130Pro	p.R130P	ENST00000371953	NM_000314.4	130	cGa/cCa	5/9	0.492207843151242	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.492207843151242	3		461	684	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711906	89711906	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	165	475	0	ENST00000371953.3:c.524T>A	p.Val175Glu	p.V175E	ENST00000371953	NM_000314.4	175	gTg/gAg	6/9	0.492207843151242	3	FACETS	1	0.965	1	0.545	0.501	0.59	CLONAL	1	TRUE	1	0.492207843151242	3		475	767	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485984	40485984	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	156	581	0	ENST00000264657.5:c.881A>T	p.Lys294Ile	p.K294I	ENST00000264657	NM_139276.2	294	aAa/aTa	9/24	1	2	FACETS	0.96	0.882	1	0.96	0.882	1	CLONAL	1	TRUE	1	0.492207843151242	2		581	660	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0025832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	447	531	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.598717013651537	3	FACETS	0.934	0.894	0.974	0.934	0.894	0.974	CLONAL	2	TRUE	1	0.598717013651537	3		531	1039	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776783	NA	P-0025832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	170	318	0	ENST00000267163.4:c.1215+1G>A		p.X405_splice	ENST00000267163	NM_000321.2	405			0.598717013651537	4	FACETS	0.947	0.87	1	0.316	0.29	0.342	CLONAL	1	TRUE	1	0.598717013651537	4		318	959	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0025832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	82	265	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.75	0.666	0.839	0.75	0.666	0.839	SUBCLONAL	1	TRUE	1	0.598717013651537	2		265	365	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552891	106552891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771056895	NA	P-0025832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	296	694	2	ENST00000369096.4:c.856C>T	p.Arg286Cys	p.R286C	ENST00000369096	NM_001198.3	286	Cgt/Tgt	5/7	1	2	FACETS	0.915	0.862	0.969	0.915	0.862	0.969	CLONAL	1	TRUE	1	0.598717013651537	2		696	1081	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106607	27106607	+	frameshift_variant	Frame_Shift_Ins	INS	T	T	CCAACTGCCCC	novel	NA	P-0025832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	132	417	0	ENST00000324856.7:c.6218delinsCCAACTGCCCC	p.Leu2073ProfsTer29	p.L2073Pfs*29	ENST00000324856	NM_006015.4	2073	cTa/cCCAACTGCCCCa	20/20	0.570599997093082	1	FACETS	0.663	0.606	0.722	0.663	0.606	0.722	SUBCLONAL	1	TRUE	0	0.598717013651537	1		417	466	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141986	108141986	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660628	NA	P-0025832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	190	389	1	ENST00000278616.4:c.2930G>A	p.Cys977Tyr	p.C977Y	ENST00000278616	NM_000051.3	977	tGt/tAt	20/63	1	2	FACETS	0.905	0.84	0.973	0.905	0.84	0.973	CLONAL	1	TRUE	1	0.598717013651537	2		390	701	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117858	70117858	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	146	322	1	ENST00000245479.2:c.326T>C	p.Met109Thr	p.M109T	ENST00000245479	NM_000346.3	109	aTg/aCg	1/3	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.598717013651537	2		323	482	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119717	70119717	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	280	495	0	ENST00000245479.2:c.723del	p.Thr243ProfsTer10	p.T243Pfs*10	ENST00000245479	NM_000346.3	240	aCc/ac	3/3	1	2	FACETS	0.993	0.935	1	0.993	0.935	1	CLONAL	1	TRUE	1	0.598717013651537	2		495	942	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604665	48604665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660045	NA	P-0025832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	165	310	1	ENST00000342988.3:c.1487G>A	p.Arg496His	p.R496H	ENST00000342988	NM_005359.5	496	cGt/cAt	12/12	0.598717013651537	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.598717013651537	1		311	371	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11027413	11027413	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	278	507	4	ENST00000327064.4:c.980G>A	p.Arg327Gln	p.R327Q	ENST00000327064	NM_199141.1	327	cGa/cAa	8/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.598717013651537	2		511	846	SUCCESS
APC	324	MSKCC	GRCh37	5	112173393	112173394	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs587783030	NA	P-0025832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	156	313	2	ENST00000257430.4:c.2107dup	p.Ala703GlyfsTer3	p.A703Gfs*3	ENST00000257430	NM_000038.5	701	atg/atGg	16/16	1	2	FACETS	0.922	0.849	0.998	0.922	0.849	0.998	CLONAL	1	TRUE	1	0.598717013651537	2		315	565	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962849	2962849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs562372731	NA	P-0025832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	249	511	1	ENST00000396946.4:c.2059G>A	p.Ala687Thr	p.A687T	ENST00000396946	NM_032415.4	687	Gcg/Acg	16/25	0.598717013651537	3	FACETS	1	0.97	1	0.531	0.497	0.567	CLONAL	1	TRUE	1	0.598717013651537	3		512	1017	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0025833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	80	655	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	1	2	FACETS	0.819	0.721	0.924	0.819	0.721	0.924	CLONAL	1	TRUE	1	0.281161408984224	2		655	695	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266513	198266513	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	44	462	0	ENST00000335508.6:c.2323C>G	p.Arg775Gly	p.R775G	ENST00000335508	NM_012433.2	775	Cga/Gga	16/25	0.259075256772514	2	FACETS	0.696	0.584	0.819	0.348	0.292	0.41	SUBCLONAL	1	TRUE	0	0.281161408984224	2		462	450	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18972906	18972906	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	132	741	0	ENST00000262803.5:c.2545G>T	p.Gly849Cys	p.G849C	ENST00000262803	NM_002911.3	849	Ggc/Tgc	18/24	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.281161408984224	2		741	793	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40738999	40738999	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	150	492	0	ENST00000373198.4:c.3285A>C	p.Glu1095Asp	p.E1095D	ENST00000373198	NM_133170.3	1095	gaA/gaC	24/32	0.258637286267076	4	FACETS	0.876	0.802	0.953	0.876	0.802	0.953	CLONAL	2	TRUE	2	0.318428482906376	4		492	709	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986497	36986497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471733047	NA	P-0025834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	236	552	0	ENST00000354822.5:c.1192G>A	p.Gly398Ser	p.G398S	ENST00000354822	NM_001079668.2	398	Ggt/Agt	3/3	0.318428482906376	6	FACETS	1	0.979	1	0.56	0.522	0.599	CLONAL	2	TRUE	2	0.318428482906376	6		552	1083	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179460	56179468	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	ATCAGGCTC	ATCAGGCTC	-	novel	NA	P-0025834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	117	372	0	ENST00000399503.3:c.3774_3782del	p.Tyr1258_Gln1261delinsTer	p.Y1258_Q1261delins*	ENST00000399503	NM_005921.1	1258	tATCAGGCTCaa/taa	15/20	0.258637286267076	4	FACETS	1	0.982	1	0.711	0.642	0.784	CLONAL	1	TRUE	2	0.318428482906376	4		372	681	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0025835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	30	146	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.852	0.694	1	1	0.952	1	CLONAL	2	TRUE	1	0.201195336409886	2		146	175	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441261	52441261	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	82	590	0	ENST00000460680.1:c.509T>G	p.Phe170Cys	p.F170C	ENST00000460680	NM_004656.3	170	tTt/tGt	7/17	0.201195336409886	1	FACETS	0.773	0.684	0.868	1	0.979	1	SUBCLONAL	2	TRUE	0	0.201195336409886	1		590	474	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52685809	52685809	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0025835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	102	537	0	ENST00000394830.3:c.663T>A	p.Tyr221Ter	p.Y221*	ENST00000394830	NM_018313.4	221	taT/taA	7/30	0.201195336409886	1	FACETS	0.806	0.722	0.893	1	0.984	1	CLONAL	2	TRUE	0	0.201195336409886	1		537	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0025836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	423	748	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.503658750095557	2	FACETS	0.99	0.95	1	0.99	0.95	1	CLONAL	2	TRUE	0	0.523835362279942	2		749	816	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974744	21974775	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTCCTCTACCCGACCCCGGGCCGCGGCCGT	ACCTCCTCTACCCGACCCCGGGCCGCGGCCGT	-	novel	NA	P-0025836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	95	214	0	ENST00000304494.5:c.52_83del	p.Thr18AlafsTer15	p.T18Afs*15	ENST00000304494	NM_000077.4	18	ACGGCCGCGGCCCGGGGTCGGGTAGAGGAGGTg/g	1/3	0.52240067779468	2	FACETS	0.93	0.849	1	0.93	0.849	1	CLONAL	2	TRUE	0	0.523835362279942	2		214	195	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0025838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	417	731	1	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.902596529434822	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.911640636088633	1		732	472	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892194	9892194	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555488115	NA	P-0025838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	238	580	0	ENST00000330684.3:c.2296C>T	p.Gln766Ter	p.Q766*	ENST00000330684	NM_001134407.1	766	Cag/Tag	11/13	1	2	FACETS	0.987	0.931	1	0.987	0.931	1	CLONAL	1	TRUE	1	0.911640636088633	2		580	529	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044521	128044521	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0025838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	30	443	0	ENST00000285398.2:c.1100C>G	p.Ser367Ter	p.S367*	ENST00000285398	NM_000122.1	367	tCa/tGa	8/15	1	2	FACETS	0.118	0.094	0.144	0.118	0.094	0.144	SUBCLONAL	1	TRUE	1	0.911640636088633	2		443	560	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805728	32805728	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1037701053	NA	P-0025838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	260	521	0	ENST00000374899.4:c.283G>T	p.Ala95Ser	p.A95S	ENST00000374899	NM_018833.2	95	Gct/Tct	2/12	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.911640636088633	2		521	564	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932878	36932878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	68	583	1	ENST00000361632.4:c.1993C>T	p.Pro665Ser	p.P665S	ENST00000361632		665	Cca/Tca	15/16	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		584	376	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	191	424	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.200602600266122	5	FACETS	0.869	0.808	0.93	0.869	0.808	0.93	INDETERMINATE	3	TRUE	2	0.411605573892349	5		424	576	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974678	21974678	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs587778189	NA	P-0025840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	101	350	0	ENST00000304494.5:c.149A>C	p.Gln50Pro	p.Q50P	ENST00000304494	NM_000077.4	50	cAg/cCg	1/3	0.411605573892349	2	FACETS	0.955	0.868	1	0.955	0.868	1	CLONAL	2	TRUE	0	0.411605573892349	2		350	257	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923059	39923059	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	141	517	0	ENST00000378444.4:c.3649C>T	p.Arg1217Ter	p.R1217*	ENST00000378444	NM_001123385.1	1217	Cga/Tga	8/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.411605573892349	2		517	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0025840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	235	475	1	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.411605573892349	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.411605573892349	2		476	467	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002760	37002761	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0025840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	72	331	1	ENST00000358127.4:c.488_489delinsTT	p.Ser163Phe	p.S163F	ENST00000358127	NM_001280556.1	163	tCC/tTT	5/10	0.411605573892349	5	FACETS	1	0.959	1			1	CLONAL	1	TRUE	NA	0.411605573892349	5		332	461	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0025841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	162	540	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.327841557227445	1	FACETS	0.785	0.72	0.854	0.785	0.72	0.854	SUBCLONAL	1	TRUE	0	0.327841557227445	1		540	1052	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0025841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	190	589	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.327841557227445	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.327841557227445	1		589	890	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678456	88678456	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	159	575	0	ENST00000360948.2:c.1080G>T	p.Glu360Asp	p.E360D	ENST00000360948	NM_001012338.2	360	gaG/gaT	9/19	0.270699609412096	3	FACETS	0.983	0.899	1			1	CLONAL	1	TRUE	NA	0.327841557227445	3		575	1149	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849315	89849315	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	165	534	0	ENST00000389301.3:c.1578A>T	p.Glu526Asp	p.E526D	ENST00000389301	NM_000135.2	526	gaA/gaT	17/43	1	2	FACETS	0.948	0.869	1	0.948	0.869	1	CLONAL	1	TRUE	1	0.327841557227445	2		534	1062	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	923	424	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.873143836632149	8	FACETS	0.981	0.96	1	0.841	0.823	0.859	CLONAL	6	TRUE	1	0.873143836632149	8		424	1300	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105554	27105554	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	135	517	0	ENST00000324856.7:c.5165del	p.Arg1722HisfsTer3	p.R1722Hfs*3	ENST00000324856	NM_006015.4	1722	cGa/ca	20/20	1	2	FACETS	0.76	0.697	0.824	0.76	0.697	0.824	SUBCLONAL	1	TRUE	1	0.873143836632149	2		517	407	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205315	46205315	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	137	454	0	ENST00000334344.6:c.399C>A	p.Tyr133Ter	p.Y133*	ENST00000334344	NM_152641.2	133	taC/taA	4/21	0.858620590607301	3	FACETS	0.933	0.855	1	0.467	0.427	0.508	CLONAL	1	TRUE	1	0.873143836632149	3		454	483	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47596699	47596699	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	67	348	0	ENST00000263735.4:c.55A>G	p.Thr19Ala	p.T19A	ENST00000263735	NM_002354.2	19	Act/Gct	1/9	0.858282692785888	4	FACETS	0.636	0.554	0.724	0.212	0.184	0.242	SUBCLONAL	1	TRUE	1	0.873143836632149	4		348	452	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480557	123480557	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	164	328	0	ENST00000371139.4:c.66del	p.Thr23LeufsTer9	p.T23Lfs*9	ENST00000371139	NM_001114937.2	22	gCc/gc	1/4	0.841516153952239	2	FACETS	0.826	0.765	0.887			1	CLONAL	1	TRUE	NA	0.873143836632149	2		328	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0025861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	665	807	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.62165544309076	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.62165544309076	2		807	1068	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999677	100999677	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	676	897	1	ENST00000325455.5:c.125C>A	p.Ser42Ter	p.S42*	ENST00000325455	NM_001202474.3	42	tCg/tAg	1/8	0.619254310252888	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.62165544309076	3		898	1412	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860101	57860101	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	701	854	6	ENST00000228682.2:c.841C>A	p.Pro281Thr	p.P281T	ENST00000228682	NM_005269.2	281	Ccc/Acc	8/12	0.62165544309076	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.62165544309076	4		860	1768	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954220	48954220	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1555286575	NA	P-0025861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	216	385	0	ENST00000267163.4:c.1421G>T	p.Ser474Ile	p.S474I	ENST00000267163	NM_000321.2	474	aGc/aTc	15/27	0.62165544309076	2	FACETS	0.905	0.856	0.953	0.905	0.856	0.953	CLONAL	2	TRUE	0	0.62165544309076	2		385	384	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019509	42020283	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTGCCTCAGCCAGAAGTTTTATCTCCTACTGTGAAGGGCAAACTGCTCACTGGAATTAAATCTCCACGGTCATATACTCCCAAACCCAATCCTGTGGTAAGTCTGGAATTTAATCTTTTATTACAAGTTACCAAAGTCATGTGTAAAGATGGTGTGTTTCAAGCAGATTTTTGGTTGATATTTTGTGAATCATTTTGCTTTCAGTAATATGTTTATAAGATATCTTCCTTTCTGGTTTAATCAGTTTAGTGCTGGCACTTTAAAAATGTCTTAAAAGTAGAAATGAGTAGTAGTAATTTTAAAAAATAACCATCTTCAAGAAGATCATAGAAACATAGGCTTTTTTACATGGCTTGGAAAAAGTTTTTTAAAGATACTACTCCTGTATTGTAGAATATTAGTAATCAATATAAGCAGTATATATTATTAGTAGAAAAACATTAGGAAAAAGCTTTTAAAAGCTTTTAAAAGCAAATTTAAAAATGCATAATAATATCAGTAAAGTTTAAGATTTAAAGTAACAGTTGATATAATATGACTGAAGACTGGTAGGTAAAAGTAGGAAGTTATTCATTGTGTTAATGGCTTAAGCAAGTCTTATTATCAAATCCATGTGTCCTCCTAGTCCATTAGATTGAAGAAAAATCCTATACTACGATGCTACTGAATATGTTCTTTGTAGCAGAGCTATTATAGTATAAAACTGTTTCTGGTCTGTGATGAAATAAGCAAGGGTGGGCCGGGCGCGGTGGCTCACGCTTGTAATCCCAGCACT	TTGCCTCAGCCAGAAGTTTTATCTCCTACTGTGAAGGGCAAACTGCTCACTGGAATTAAATCTCCACGGTCATATACTCCCAAACCCAATCCTGTGGTAAGTCTGGAATTTAATCTTTTATTACAAGTTACCAAAGTCATGTGTAAAGATGGTGTGTTTCAAGCAGATTTTTGGTTGATATTTTGTGAATCATTTTGCTTTCAGTAATATGTTTATAAGATATCTTCCTTTCTGGTTTAATCAGTTTAGTGCTGGCACTTTAAAAATGTCTTAAAAGTAGAAATGAGTAGTAGTAATTTTAAAAAATAACCATCTTCAAGAAGATCATAGAAACATAGGCTTTTTTACATGGCTTGGAAAAAGTTTTTTAAAGATACTACTCCTGTATTGTAGAATATTAGTAATCAATATAAGCAGTATATATTATTAGTAGAAAAACATTAGGAAAAAGCTTTTAAAAGCTTTTAAAAGCAAATTTAAAAATGCATAATAATATCAGTAAAGTTTAAGATTTAAAGTAACAGTTGATATAATATGACTGAAGACTGGTAGGTAAAAGTAGGAAGTTATTCATTGTGTTAATGGCTTAAGCAAGTCTTATTATCAAATCCATGTGTCCTCCTAGTCCATTAGATTGAAGAAAAATCCTATACTACGATGCTACTGAATATGTTCTTTGTAGCAGAGCTATTATAGTATAAAACTGTTTCTGGTCTGTGATGAAATAAGCAAGGGTGGGCCGGGCGCGGTGGCTCACGCTTGTAATCCCAGCACT	-	novel	NA	P-0025861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	103	763	0	ENST00000219905.7:c.3565_3657+682del		p.X1189_splice	ENST00000219905	NM_001164273.1	1189		10/24	0.62165544309076	3	FACETS	0.421	0.376	0.47	0.211	0.188	0.235	SUBCLONAL	1	TRUE	1	0.62165544309076	3		763	1031	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019561	42019562	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AATTA	novel	NA	P-0025861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	471	724	0	ENST00000219905.7:c.3618_3622dup	p.Ser1208LeufsTer14	p.S1208Lfs*14	ENST00000219905	NM_001164273.1	1205	gga/ggAATTAa	10/24	0.62165544309076	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.62165544309076	3		724	946	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89874749	89874749	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs758528624	NA	P-0025861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	262	696	3	ENST00000389301.3:c.549G>T	p.Trp183Cys	p.W183C	ENST00000389301	NM_000135.2	183	tgG/tgT	6/43	0.619254310252888	3	FACETS	0.874	0.818	0.932	0.437	0.409	0.466	CLONAL	1	TRUE	1	0.62165544309076	3		699	1264	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492884	56492884	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	276	346	2	ENST00000407977.2:c.55G>C	p.Ala19Pro	p.A19P	ENST00000407977		19	Gct/Cct	2/10	0.62165544309076	3	FACETS	0.96	0.91	1	0.96	0.91	1	CLONAL	2	TRUE	1	0.62165544309076	3		348	606	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610265	10610265	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	772	841	1	ENST00000171111.5:c.445G>T	p.Glu149Ter	p.E149*	ENST00000171111	NM_203500.1	149	Gag/Tag	2/6	0.62165544309076	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.62165544309076	2		842	1188	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145614	11145614	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	643	738	3	ENST00000358026.2:c.3976G>T	p.Glu1326Ter	p.E1326*	ENST00000358026	NM_001128849.1	1326	Gag/Tag	29/36	0.62165544309076	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.62165544309076	2		741	998	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379730	17379730	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	712	918	6	ENST00000359435.4:c.115G>T	p.Val39Leu	p.V39L	ENST00000359435	NM_001033549.1	39	Gta/Tta	2/9	0.62165544309076	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.62165544309076	2		924	1069	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47079212	47079212	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	295	614	0	ENST00000409792.3:c.7294G>T	p.Glu2432Ter	p.E2432*	ENST00000409792	NM_014159.6	2432	Gag/Tag	18/21	0.62165544309076	3	FACETS	1	0.968	1	0.521	0.49	0.553	CLONAL	1	TRUE	1	0.62165544309076	3		614	1193	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026978	71026978	+	splice_donor_variant	Splice_Site	SNP	C	C	G	rs1559619762	NA	P-0025861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	398	530	0	ENST00000318789.4:c.1348+1G>C		p.X450_splice	ENST00000318789	NM_032682.5	450			0.62165544309076	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.62165544309076	3		530	824	SUCCESS
ATR	545	MSKCC	GRCh37	3	142238564	142238564	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	274	392	0	ENST00000350721.4:c.4329G>C	p.Trp1443Cys	p.W1443C	ENST00000350721	NM_001184.3	1443	tgG/tgC	24/47	0.329772505230188	5	FACETS	0.834	0.788	0.88	0.834	0.788	0.88	INDETERMINATE	3	TRUE	2	0.62165544309076	5		392	681	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902812	1902812	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	550	714	4	ENST00000382891.5:c.431G>T	p.Cys144Phe	p.C144F	ENST00000382891	NM_133335.3	144	tGt/tTt	2/22	0.619254310252888	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.62165544309076	3		718	1115	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133763	55133763	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	463	614	0	ENST00000257290.5:c.976G>C	p.Ala326Pro	p.A326P	ENST00000257290	NM_006206.4	326	Gct/Cct	7/23	0.619254310252888	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.62165544309076	3		614	944	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032217	26032217	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	256	293	1	ENST00000244661.2:c.72G>T	p.Lys24Asn	p.K24N	ENST00000244661	NM_003537.3	24	aaG/aaT	1/1	0.384712481707281	5	FACETS	0.905	0.855	0.956	0.905	0.855	0.956	CLONAL	3	TRUE	2	0.62165544309076	5		294	586	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166717	32166717	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	498	860	2	ENST00000375023.3:c.4521C>A	p.Asp1507Glu	p.D1507E	ENST00000375023	NM_004557.3	1507	gaC/gaA	24/30	0.384712481707281	5	FACETS	0.968	0.925	1	0.645	0.617	0.674	CLONAL	2	TRUE	2	0.62165544309076	5		862	1600	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150436	157150436	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554256703	NA	P-0025861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	276	682	0	ENST00000346085.5:c.1618C>T	p.Gln540Ter	p.Q540*	ENST00000346085	NM_020732.3	540	Cag/Tag	2/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.62165544309076	2		682	830	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231161	98231161	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	501	620	0	ENST00000331920.6:c.2122A>C	p.Thr708Pro	p.T708P	ENST00000331920	NM_000264.3	708	Aca/Cca	14/24	0.619254310252888	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.62165544309076	3		620	1021	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930302	39930302	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	648	338	2	ENST00000378444.4:c.3162G>T	p.Leu1054Phe	p.L1054F	ENST00000378444	NM_001123385.1	1054	ttG/ttT	6/15	0.579631441324521	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.62165544309076	2		340	840	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0025863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	133	146	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.656735663386535	2		146	339	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720671	89720671	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587782607	NA	P-0025863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	84	233	0	ENST00000371953.3:c.822G>A	p.Trp274Ter	p.W274*	ENST00000371953	NM_000314.4	274	tgG/tgA	8/9	0.656735663386535	1	FACETS	0.939	0.85	1	0.939	0.85	1	CLONAL	1	TRUE	0	0.656735663386535	1		233	183	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367264	50367264	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	181	333	0	ENST00000331340.3:c.71C>T	p.Pro24Leu	p.P24L	ENST00000331340	NM_006060.4	24	cCa/cTa	3/8	0.656735663386535	3	FACETS	0.998	0.923	1	0.499	0.461	0.538	CLONAL	1	TRUE	1	0.656735663386535	3		333	734	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0025865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	270	396	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.615760584067771	2	FACETS	0.947	0.902	0.991	0.947	0.902	0.991	CLONAL	2	TRUE	0	0.615760584067771	2		396	463	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43738686	43738686	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	515	617	2	ENST00000382044.4:c.2939C>G	p.Ser980Cys	p.S980C	ENST00000382044	NM_001141980.1	980	tCt/tGt	14/28	0.615760584067771	4	FACETS	0.978	0.937	1	0.978	0.937	1	CLONAL	2	TRUE	2	0.615760584067771	4		619	1382	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057520005	NA	P-0025866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	193	730	0	ENST00000269305.4:c.820G>T	p.Val274Phe	p.V274F	ENST00000269305	NM_001126112.2	274	Gtt/Ttt	8/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.22	2		730	1315	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130266	11130266	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0025866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	442	483	1	ENST00000358026.2:c.2506-1G>T		p.X836_splice	ENST00000358026	NM_001128849.1	836			0.280764936172522	4	FACETS	1	0.99	1			1	CLONAL	4	TRUE	NA	0.22	4		484	1106	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598204	28598204	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1304	96	763	0	ENST00000253063.3:c.176A>C	p.Glu59Ala	p.E59A	ENST00000253063	NM_031459.4	59	gAg/gCg	3/10	1	2	FACETS	0.623	0.553	0.699	0.623	0.553	0.699	SUBCLONAL	1	TRUE	1	0.22	2		763	1400	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256439	115256439	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	55	490	1	ENST00000369535.4:c.272C>A	p.Ala91Glu	p.A91E	ENST00000369535	NM_002524.4	91	gCg/gAg	3/7	1	2	FACETS	0.671	0.573	0.779	0.671	0.573	0.779	SUBCLONAL	1	TRUE	1	0.22	2		491	745	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176176047	176176047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752538197	NA	P-0025866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	72	686	1	ENST00000367669.3:c.68C>T	p.Ser23Leu	p.S23L	ENST00000367669	NM_022457.5	23	tCg/tTg	1/20	0.251437445803373	3	FACETS	0.624	0.543	0.712	0.312	0.271	0.356	SUBCLONAL	1	TRUE	1	0.22	3		687	1164	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610042	81610042	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	44	379	0	ENST00000298171.2:c.1640T>A	p.Val547Asp	p.V547D	ENST00000298171	NM_000369.2	547	gTt/gAt	10/10	1	2	FACETS	0.644	0.539	0.761	0.644	0.539	0.761	SUBCLONAL	1	TRUE	1	0.22	2		379	621	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121934	2121934	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	165	796	0	ENST00000219476.3:c.2096A>C	p.Gln699Pro	p.Q699P	ENST00000219476	NM_000548.3	699	cAg/cCg	19/42	NA	2	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.22	2		796	1261	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321581	30321581	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0025866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	55	322	0	ENST00000322652.5:c.1438-2A>T		p.X480_splice	ENST00000322652	NM_015355.2	480			1	2	FACETS	0.803	0.686	0.93	0.803	0.686	0.93	CLONAL	1	TRUE	1	0.22	2		322	623	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39613853	39613855	+	inframe_deletion	In_Frame_Del	DEL	ATC	ATC	-	novel	NA	P-0025866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	59	570	1	ENST00000262039.4:c.1771_1773del	p.Ile591del	p.I591del	ENST00000262039	NM_002647.2	591	ATC/-	16/25	1	2	FACETS	0.555	0.476	0.642	0.555	0.476	0.642	SUBCLONAL	1	TRUE	1	0.22	2		571	966	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375029	45375029	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	38	434	1	ENST00000262160.6:c.814G>T	p.Ala272Ser	p.A272S	ENST00000262160	NM_005901.5	272	Gca/Tca	8/11	1	2	FACETS	0.513	0.423	0.615	0.513	0.423	0.615	SUBCLONAL	1	TRUE	1	0.22	2		435	673	SUCCESS
REL	5966	MSKCC	GRCh37	2	61128201	61128201	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	45	384	1	ENST00000295025.8:c.377G>T	p.Gly126Val	p.G126V	ENST00000295025	NM_002908.2	126	gGa/gTa	4/11	0.132098193336992	4	FACETS	0.567	0.475	0.67	0.284	0.237	0.335	SUBCLONAL	1	TRUE	2	0.22	4		385	880	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37045897	37045897	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	58	541	0	ENST00000231790.2:c.312G>T	p.Leu104Phe	p.L104F	ENST00000231790	NM_000249.3	104	ttG/ttT	4/19	1	2	FACETS	0.599	0.513	0.693	0.599	0.513	0.693	SUBCLONAL	1	TRUE	1	0.22	2		541	880	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259463	89259464	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0025866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	95	594	1	ENST00000336596.2:c.607_608delinsAA	p.Pro203Lys	p.P203K	ENST00000336596	NM_005233.5	203	CCa/AAa	3/17	1	2	FACETS	0.985	0.876	1	0.985	0.876	1	CLONAL	1	TRUE	1	0.22	2		595	877	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968320	134968320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	223	617	1	ENST00000398015.3:c.2833C>A	p.Gln945Lys	p.Q945K	ENST00000398015	NM_004441.4	945	Cag/Aag	15/16	0.3	3	FACETS	0.934	0.869	1	0.934	0.869	1	CLONAL	2	TRUE	1	0.22	3		618	1204	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665151	138665151	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	195	583	0	ENST00000330315.3:c.414C>A	p.Phe138Leu	p.F138L	ENST00000330315	NM_023067.3	138	ttC/ttA	1/1	0.3	3	FACETS	0.832	0.768	0.898	0.832	0.768	0.898	CLONAL	2	TRUE	1	0.22	3		583	1183	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750485	41750485	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	78	675	1	ENST00000226382.2:c.143G>T	p.Arg48Met	p.R48M	ENST00000226382	NM_003924.3	48	aGg/aTg	1/3	1	2	FACETS	0.679	0.594	0.77	0.679	0.594	0.77	SUBCLONAL	1	TRUE	1	0.22	2		676	1045	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595594	55595594	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	56	381	0	ENST00000288135.5:c.2084A>T	p.Glu695Val	p.E695V	ENST00000288135	NM_000222.2	695	gAa/gTa	14/21	1	2	FACETS	0.749	0.64	0.867	0.749	0.64	0.867	SUBCLONAL	1	TRUE	1	0.22	2		381	680	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797297	32797298	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0025866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	73	677	0	ENST00000374899.4:c.1811dup	p.Ser605LysfsTer28	p.S605Kfs*28	ENST00000374899	NM_018833.2	604	gga/ggGa	11/12	1	2	FACETS	0.569	0.496	0.649	0.569	0.496	0.649	SUBCLONAL	1	TRUE	1	0.22	2		677	1166	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068078	94068078	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	47	453	0	ENST00000369303.4:c.884G>C	p.Arg295Pro	p.R295P	ENST00000369303	NM_004440.3	295	cGt/cCt	4/17	1	2	FACETS	0.529	0.445	0.623	0.529	0.445	0.623	SUBCLONAL	1	TRUE	1	0.22	2		453	807	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715782	117715782	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	42	411	0	ENST00000368508.3:c.976A>G	p.Thr326Ala	p.T326A	ENST00000368508	NM_002944.2	326	Aca/Gca	9/43	1	2	FACETS	0.486	0.405	0.578	0.486	0.405	0.578	SUBCLONAL	1	TRUE	1	0.22	2		411	785	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715902	117715902	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0025866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	57	369	0	ENST00000368508.3:c.857-1G>C		p.X286_splice	ENST00000368508	NM_002944.2	286			1	2	FACETS	0.764	0.655	0.884	0.764	0.655	0.884	SUBCLONAL	1	TRUE	1	0.22	2		369	678	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508079	106508079	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	40	192	0	ENST00000359195.3:c.73C>A	p.Pro25Thr	p.P25T	ENST00000359195	NM_002649.2	25	Ccg/Acg	2/11	NA	2	FACETS	0.874	0.727	1			1	INDETERMINATE	1	TRUE	NA	0.22	2		192	416	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197397	27197397	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	71	809	0	ENST00000380036.4:c.1709C>A	p.Ser570Ter	p.S570*	ENST00000380036	NM_000459.3	570	tCg/tAg	12/23	1	2	FACETS	0.548	0.477	0.626	0.548	0.477	0.626	SUBCLONAL	1	TRUE	1	0.22	2		809	1177	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411873	63411873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1303	193	1021	1	ENST00000330258.3:c.1294G>A	p.Gly432Ser	p.G432S	ENST00000330258	NM_152424.3	432	Ggc/Agc	2/2	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.22	2		1022	1496	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763974	76763974	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057520923	NA	P-0025866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	72	612	0	ENST00000373344.5:c.7334T>A	p.Ile2445Asn	p.I2445N	ENST00000373344	NM_000489.3	2445	aTc/aAc	35/35	1	2	FACETS	0.635	0.553	0.724	0.635	0.553	0.724	SUBCLONAL	1	TRUE	1	0.22	2		612	1031	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615100	100615100	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782264410	NA	P-0025866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	137	629	2	ENST00000308731.7:c.815C>T	p.Ala272Val	p.A272V	ENST00000308731	NM_000061.2	272	gCa/gTa	9/19	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.22	2		631	1141	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020177	123020177	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1228	70	762	0	ENST00000355640.3:c.665G>T	p.Arg222Leu	p.R222L	ENST00000355640		222	cGa/cTa	2/7	1	2	FACETS	0.49	0.426	0.561	0.49	0.426	0.561	SUBCLONAL	1	TRUE	1	0.22	2		762	1298	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181342	123181342	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	63	407	0	ENST00000218089.9:c.806A>G	p.Gln269Arg	p.Q269R	ENST00000218089	NM_001042749.1	269	cAa/cGa	9/35	1	2	FACETS	0.877	0.758	1	0.877	0.758	1	CLONAL	1	TRUE	1	0.22	2		407	653	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858089	152858089	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	69	725	0	ENST00000406277.2:c.526T>A	p.Tyr176Asn	p.Y176N	ENST00000406277	NM_152274.4	176	Tac/Aac	6/7	1	2	FACETS	0.547	0.474	0.626	0.547	0.474	0.626	SUBCLONAL	1	TRUE	1	0.22	2		725	1147	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0025867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	174	218	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.32333163744952	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.4586594077225	4		218	505	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572520	64572520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	347	438	0	ENST00000312049.6:c.1336C>T	p.Arg446Cys	p.R446C	ENST00000312049	NM_130799.2	446	Cgt/Tgt	9/10	1	2	FACETS	1	0.981	1	1	0.997	1	CLONAL	2	TRUE	1	0.4586594077225	2		438	718	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	133	424	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.228644381040652	4	FACETS	1	0.985	1	0.73	0.664	0.8	CLONAL	1	TRUE	2	0.332523240126117	4		424	730	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	84	301	0	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	0.229981738777483	3	FACETS	1	0.974	1	0.676	0.6	0.756	CLONAL	1	TRUE	1	0.332523240126117	3		301	436	SUCCESS
AR	367	MSKCC	GRCh37	X	66766357	66766392	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	-	rs746853821	NA	P-0025869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	75	38	0	ENST00000374690.3:c.1385_1420del	p.Gly462_Gly473del	p.G462_G473del	ENST00000374690	NM_000044.3	457	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC/-	1/8	0.332523240126117	2	FACETS	0.89	0.8	0.981			1	CLONAL	3	TRUE	NA	0.332523240126117	2		38	169	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574035	7574035	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs867389695	NA	P-0025869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	208	590	0	ENST00000269305.4:c.994-2A>G		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.247853769293642	2	FACETS	1	0.991	1	0.746	0.694	0.801	CLONAL	1	TRUE	0	0.332523240126117	2		590	838	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983140	201983141	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0025869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	104	654	0	ENST00000359651.3:c.990_991dup	p.Arg331ProfsTer4	p.R331Pfs*4	ENST00000359651		330	agc/agCCc	7/8	0.229981738777483	3	FACETS	0.741	0.663	0.825	0.371	0.331	0.413	SUBCLONAL	1	TRUE	1	0.332523240126117	3		654	984	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989544	212989544	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	61	367	0	ENST00000342788.4:c.167G>T	p.Cys56Phe	p.C56F	ENST00000342788	NM_005235.2	56	tGt/tTt	2/28	0.247853769293642	2	FACETS	0.7	0.605	0.804	0.35	0.302	0.402	SUBCLONAL	1	TRUE	0	0.332523240126117	2		367	524	SUCCESS
APC	324	MSKCC	GRCh37	5	112137078	112137078	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1554076217	NA	P-0025869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	62	449	0	ENST00000257430.4:c.832C>T	p.Gln278Ter	p.Q278*	ENST00000257430	NM_000038.5	278	Cag/Tag	8/16	0.229981738777483	3	FACETS	0.725	0.626	0.832	0.362	0.313	0.416	SUBCLONAL	1	TRUE	1	0.332523240126117	3		449	600	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0025870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	137	532	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.755	0.686	0.828	1	0.986	1	SUBCLONAL	2	TRUE	1	0.193782380545509	2		533	936	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	44	122	0				ENST00000310581	NM_198253.2	-/1132			0.193782380545509	3	FACETS	0.752	0.633	0.883	0.752	0.633	0.883	SUBCLONAL	2	TRUE	1	0.193782380545509	3		122	331	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953741	48953742	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0025870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	32	308	0	ENST00000267163.4:c.1346dup	p.Val450SerfsTer13	p.V450Sfs*13	ENST00000267163	NM_000321.2	448	-/G	14/27	1	2	FACETS	0.701	0.569	0.851	0.701	0.569	0.851	SUBCLONAL	1	TRUE	1	0.193782380545509	2		308	471	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717631	89717631	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1554825172	NA	P-0025870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	107	388	0	ENST00000371953.3:c.656A>C	p.Gln219Pro	p.Q219P	ENST00000371953	NM_000314.4	219	cAg/cCg	7/9	0.193782380545509	3	FACETS	0.993	0.893	1	0.993	0.893	1	CLONAL	2	TRUE	1	0.193782380545509	3		388	610	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653271	29653271	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0025870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	48	223	0	ENST00000356175.3:c.5205+1G>T		p.X1735_splice	ENST00000356175	NM_000267.3	1735			1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.193782380545509	2		223	388	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070841	30070841	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	154	507	0	ENST00000338641.4:c.1357C>A	p.Gln453Lys	p.Q453K	ENST00000338641	NM_000268.3	453	Cag/Aag	13/16	0.193782380545509	3	FACETS	0.974	0.891	1	0.974	0.891	1	CLONAL	2	TRUE	1	0.193782380545509	3		507	895	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190383	32190383	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	165	698	0	ENST00000375023.3:c.356A>G	p.Glu119Gly	p.E119G	ENST00000375023	NM_004557.3	119	gAa/gGa	3/30	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.193782380545509	2		698	1219	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913351	NA	P-0025872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	77	461	0	ENST00000288602.6:c.1397G>C	p.Gly466Ala	p.G466A	ENST00000288602	NM_004333.4	466	gGa/gCa	11/18	1	2	FACETS	0.766	0.674	0.865	0.766	0.674	0.865	SUBCLONAL	1	TRUE	1	0.376525532571487	2		461	534	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353821	40353821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1177305205	NA	P-0025872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	108	547	1	ENST00000293328.3:c.2299C>T	p.Arg767Trp	p.R767W	ENST00000293328	NM_012448.3	767	Cgg/Tgg	19/19	1	2	FACETS	0.746	0.669	0.827	0.746	0.669	0.827	SUBCLONAL	1	TRUE	1	0.376525532571487	2		548	769	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056210	26056210	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	33	389	0	ENST00000343677.2:c.447G>C	p.Lys149Asn	p.K149N	ENST00000343677	NM_005319.3	149	aaG/aaC	1/1	1	2	FACETS	0.295	0.239	0.358	0.295	0.239	0.358	SUBCLONAL	1	TRUE	1	0.376525532571487	2		389	594	SUCCESS
ATR	545	MSKCC	GRCh37	3	142184073	142184073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	76	350	0	ENST00000350721.4:c.6907C>T	p.Leu2303Phe	p.L2303F	ENST00000350721	NM_001184.3	2303	Ctt/Ttt	41/47	1	2	FACETS	0.885	0.779	0.998	0.885	0.779	0.998	CLONAL	1	TRUE	1	0.376525532571487	2		350	456	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220428	1220428	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	131	717	0	ENST00000326873.7:c.521A>C	p.His174Pro	p.H174P	ENST00000326873	NM_000455.4	174	cAc/cCc	4/10	0.376525532571487	1	FACETS	0.825	0.75	0.903	0.825	0.75	0.903	CLONAL	1	TRUE	0	0.376525532571487	1		717	685	SUCCESS
FH	2271	MSKCC	GRCh37	1	241665755	241665755	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	63	510	0	ENST00000366560.3:c.1224C>G	p.Phe408Leu	p.F408L	ENST00000366560	NM_000143.3	408	ttC/ttG	8/10	0.363416277609982	3	FACETS	0.621	0.537	0.713	0.311	0.268	0.357	SUBCLONAL	1	TRUE	1	0.376525532571487	3		510	640	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942174	71942174	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	182	726	0	ENST00000298229.2:c.1438G>C	p.Glu480Gln	p.E480Q	ENST00000298229	NM_001567.3	480	Gag/Cag	12/28	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.376525532571487	2		726	966	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118716	115118716	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	134	602	0	ENST00000257566.3:c.625C>T	p.Leu209Phe	p.L209F	ENST00000257566	NM_016569.3	209	Ctc/Ttc	2/8	1	2	FACETS	0.93	0.846	1	0.93	0.846	1	CLONAL	1	TRUE	1	0.376525532571487	2		602	765	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572934	7572934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	126	522	0	ENST00000269305.4:c.1175C>T	p.Ser392Leu	p.S392L	ENST00000269305	NM_001126112.2	392	tCa/tTa	11/11	1	2	FACETS	0.928	0.842	1	0.928	0.842	1	CLONAL	1	TRUE	1	0.376525532571487	2		522	721	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602934	10602934	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	141	714	0	ENST00000171111.5:c.644C>G	p.Ala215Gly	p.A215G	ENST00000171111	NM_203500.1	215	gCc/gGc	3/6	0.376525532571487	1	FACETS	0.853	0.778	0.931	0.853	0.778	0.931	CLONAL	1	TRUE	0	0.376525532571487	1		714	713	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662146	227662149	+	missense_variant	Missense_Mutation	ONP	CGCA	CGCA	GCAT	novel	NA	P-0025872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	141	671	2	ENST00000305123.5:c.1306_1309delinsATGC	p.Cys436_Asp437delinsMetHis	p.C436_D437delinsMH	ENST00000305123	NM_005544.2	436	TGCGat/ATGCat	1/2	1	2	FACETS	0.971	0.886	1	0.971	0.886	1	CLONAL	1	TRUE	1	0.376525532571487	2		673	771	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481448	140481448	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	96	592	0	ENST00000288602.6:c.1360G>C	p.Asp454His	p.D454H	ENST00000288602	NM_004333.4	454	Gat/Cat	11/18	1	2	FACETS	0.748	0.667	0.834	0.748	0.667	0.834	SUBCLONAL	1	TRUE	1	0.376525532571487	2		592	682	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974763	21974763	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	47	152	0	ENST00000304494.5:c.64del	p.Arg22GlyfsTer4	p.R22Gfs*4	ENST00000304494	NM_000077.4	22	Cgg/gg	1/3	0.373692324591851	1	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	0	0.373692324591851	1		152	195	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0025874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	216	655	0	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	0.299504563466648	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.312226307100566	2		655	588	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205531	38205531	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	171	785	2	ENST00000317025.8:c.159del	p.Leu53PhefsTer91	p.L53Ffs*91	ENST00000317025	NM_023034.1	53	ttG/tt	2/24	0.312226307100566	3	FACETS	0.999	0.923	1	0.999	0.923	1	CLONAL	2	TRUE	1	0.312226307100566	3		787	634	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	20	424	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.771	1	1	0.771	1	CLONAL	1	TRUE	1	0.17	2		424	234	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579362	7579362	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057523496	NA	P-0025875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	52	671	0	ENST00000269305.4:c.325T>G	p.Phe109Val	p.F109V	ENST00000269305	NM_001126112.2	109	Ttc/Gtc	4/11	1	2	FACETS	0.985	0.838	1	0.985	0.838	1	CLONAL	1	TRUE	1	0.17	2		671	621	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241726	55241726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767505234	NA	P-0025888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	36	540	0	ENST00000275493.2:c.2174C>T	p.Thr725Met	p.T725M	ENST00000275493	NM_005228.3	725	aCg/aTg	18/28	1	2	FACETS	0.506	0.416	0.608	0.506	0.416	0.608	SUBCLONAL	1	TRUE	1	0.290888791432168	2		540	489	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729604	41729604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	33	470	0	ENST00000242208.4:c.925C>T	p.Arg309Trp	p.R309W	ENST00000242208	NM_002192.2	309	Cgg/Tgg	3/3	1	2	FACETS	0.531	0.433	0.643	0.531	0.433	0.643	SUBCLONAL	1	TRUE	1	0.290888791432168	2		470	427	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165896	118165896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	27	380	0	ENST00000369448.3:c.406G>A	p.Glu136Lys	p.E136K	ENST00000369448	NM_017709.3	136	Gag/Aag	2/2	0.115472541038517	3	FACETS	0.469	0.373	0.58	0.235	0.186	0.29	INDETERMINATE	1	TRUE	1	0.290888791432168	3		380	453	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16046928	16046928	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	28	401	0	ENST00000268712.3:c.1165G>C	p.Glu389Gln	p.E389Q	ENST00000268712	NM_006311.3	389	Gag/Cag	11/46	1	2	FACETS	0.449	0.358	0.552	0.449	0.358	0.552	SUBCLONAL	1	TRUE	1	0.290888791432168	2		401	429	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40469211	40469211	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	41	416	0	ENST00000264657.5:c.2133C>G	p.Ile711Met	p.I711M	ENST00000264657	NM_139276.2	711	atC/atG	22/24	1	2	FACETS	0.5	0.416	0.594	0.5	0.416	0.594	SUBCLONAL	1	TRUE	1	0.290888791432168	2		416	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0025889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	253	860	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.269261649183451	1	FACETS	0.754	0.705	0.804	1	0.993	1	SUBCLONAL	2	TRUE	0	0.269261649183451	1		861	1079	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0025891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	171	146	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.62395549306102	2		146	544	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992223	11992223	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	179	341	0	ENST00000396373.4:c.313C>G	p.Arg105Gly	p.R105G	ENST00000396373	NM_001987.4	105	Cga/Gga	3/8	0.62395549306102	4	FACETS	0.787	0.729	0.846	0.525	0.486	0.564	SUBCLONAL	2	TRUE	1	0.62395549306102	4		341	592	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030426	49030426	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0025891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	244	519	0	ENST00000267163.4:c.1901C>G	p.Ser634Ter	p.S634*	ENST00000267163	NM_000321.2	634	tCa/tGa	19/27	1	2	FACETS	0.912	0.854	0.971	0.912	0.854	0.971	CLONAL	1	TRUE	1	0.62395549306102	2		519	858	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039374	49039374	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853293	NA	P-0025891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	357	723	1	ENST00000267163.4:c.2359C>T	p.Arg787Ter	p.R787*	ENST00000267163	NM_000321.2	787	Cga/Tga	23/27	1	2	FACETS	0.985	0.934	1	0.985	0.934	1	CLONAL	1	TRUE	1	0.62395549306102	2		724	1162	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436080	110436080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	356	783	2	ENST00000375856.3:c.2321C>T	p.Ala774Val	p.A774V	ENST00000375856	NM_003749.2	774	gCg/gTg	1/2	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.62395549306102	2		785	1129	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50811745	50811745	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0025891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	194	518	0	ENST00000398568.2:c.1022C>G	p.Ser341Ter	p.S341*	ENST00000398568	NM_001042412.1	341	tCa/tGa	7/18	0.62395549306102	1	FACETS	0.884	0.826	0.943	0.884	0.826	0.943	CLONAL	1	TRUE	0	0.62395549306102	1		518	484	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41558779	41558779	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	271	578	0	ENST00000263253.7:c.3724G>A	p.Glu1242Lys	p.E1242K	ENST00000263253	NM_001429.3	1242	Gaa/Aaa	21/31	1	2	FACETS	0.9	0.846	0.956	0.9	0.846	0.956	CLONAL	1	TRUE	1	0.62395549306102	2		578	965	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963016	38963016	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	150	329	0	ENST00000357387.3:c.1528C>A	p.Gln510Lys	p.Q510K	ENST00000357387	NM_152756.3	510	Cag/Aag	17/38	1	2	FACETS	0.987	0.909	1	0.987	0.909	1	CLONAL	1	TRUE	1	0.62395549306102	2		329	487	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910797	29910797	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs41559912	NA	P-0025891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	674	625	0	ENST00000376809.5:c.337G>T	p.Glu113Ter	p.E113*	ENST00000376809	NM_002116.7	113	Gag/Tag	2/8	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	2	TRUE	NA	0.62395549306102	2		625	966	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151927370	151927370	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	34	76	0	ENST00000262189.6:c.2806G>A	p.Glu936Lys	p.E936K	ENST00000262189	NM_170606.2	936	Gaa/Aaa	17/59	1	2	FACETS	0.762	0.633	0.902	0.762	0.633	0.902	CLONAL	1	TRUE	1	0.62395549306102	2		76	143	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023253	27023271	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCCGGCGGCGGCGGTGG	CGCCCGGCGGCGGCGGTGG	-	novel	NA	P-0025892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	68	204	0	ENST00000324856.7:c.361_379del	p.Pro121AlafsTer105	p.P121Afs*105	ENST00000324856	NM_006015.4	120	cCGCCCGGCGGCGGCGGTGGc/cc	1/20	0.393029737779833	1	FACETS	0.804	0.715	0.894	1	0.98	1	CLONAL	2	TRUE	0	0.393029737779833	1		204	173	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953785	48953785	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	30	209	0	ENST00000267163.4:c.1388C>T	p.Ser463Leu	p.S463L	ENST00000267163	NM_000321.2	463	tCa/tTa	14/27	1	2	FACETS	0.541	0.437	0.658	0.541	0.437	0.658	SUBCLONAL	1	TRUE	1	0.393029737779833	2		209	282	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678757	52678757	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	132	549	0	ENST00000394830.3:c.862G>T	p.Glu288Ter	p.E288*	ENST00000394830	NM_018313.4	288	Gaa/Taa	9/30	0.177809509771594	2	FACETS	1	0.975	1	0.598	0.545	0.653	INDETERMINATE	1	TRUE	0	0.393029737779833	2		549	562	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911636	134911636	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	105	444	0	ENST00000398015.3:c.2101G>T	p.Glu701Ter	p.E701*	ENST00000398015	NM_004441.4	701	Gag/Tag	11/16	0.393029737779833	3	FACETS	1	0.976	1	0.641	0.576	0.708	CLONAL	1	TRUE	1	0.393029737779833	3		444	499	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467878	66467878	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	45	382	0	ENST00000273854.3:c.391A>G	p.Lys131Glu	p.K131E	ENST00000273854	NM_004439.5	131	Aaa/Gaa	3/18	1	2	FACETS	0.658	0.555	0.771	0.658	0.555	0.771	SUBCLONAL	1	TRUE	1	0.393029737779833	2		382	348	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11554273	NA	P-0025893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	42	535	0	ENST00000371085.3:c.601C>A	p.Arg201Ser	p.R201S	ENST00000371085	NM_000516.4	201	Cgt/Agt	8/13	1	2	FACETS	0.481	0.401	0.571	0.481	0.401	0.571	SUBCLONAL	1	TRUE	1	0.306120450610366	2		535	570	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430786	181430786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	43	1278	1	ENST00000325404.1:c.638C>T	p.Ser213Leu	p.S213L	ENST00000325404	NM_003106.3	213	tCg/tTg	1/1	1	2	FACETS	0.365	0.305	0.433	0.365	0.305	0.433	SUBCLONAL	1	TRUE	1	0.306120450610366	2		1279	769	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872913	35872913	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1170189396	NA	P-0025893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	39	587	0	ENST00000216797.5:c.319C>T	p.Gln107Ter	p.Q107*	ENST00000216797	NM_020529.2	107	Cag/Tag	2/6	1	2	FACETS	0.411	0.34	0.491	0.411	0.34	0.491	SUBCLONAL	1	TRUE	1	0.306120450610366	2		587	620	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461061	120461061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	241	542	1	ENST00000256646.2:c.5897G>A	p.Cys1966Tyr	p.C1966Y	ENST00000256646	NM_024408.3	1966	tGc/tAc	32/34	0.161610825831646	3	FACETS	0.882	0.828	0.936	1	0.994	1	CLONAL	4	TRUE	1	0.229429313390025	3		543	664	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0025897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	157	287	0	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	0.920629899776076	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.920629899776076	1		287	172	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578491	7578491	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1567553924	NA	P-0025897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	986	1468	0	ENST00000269305.4:c.439del	p.Val147LeufsTer23	p.V147Lfs*23	ENST00000269305	NM_001126112.2	147	Gtt/tt	5/11	0.920629899776076	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.920629899776076	1		1468	1155	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937934	36937934	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	792	1412	0	ENST00000361632.4:c.902C>A	p.Thr301Lys	p.T301K	ENST00000361632		301	aCg/aAg	7/16	1	2	FACETS	0.995	0.963	1	0.995	0.963	1	CLONAL	1	TRUE	1	0.920629899776076	2		1412	1730	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391938	139391938	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	949	1529	0	ENST00000277541.6:c.6253G>T	p.Ala2085Ser	p.A2085S	ENST00000277541	NM_017617.3	2085	Gcc/Tcc	34/34	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.920629899776076	2		1529	2038	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933701	39933701	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	447	638	0	ENST00000378444.4:c.898G>C	p.Asp300His	p.D300H	ENST00000378444	NM_001123385.1	300	Gat/Cat	4/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.920629899776076	2		638	915	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920178	76920202	+	frameshift_variant	Frame_Shift_Del	DEL	TTCCCTTCTTCTGGCTCATCATCTG	TTCCCTTCTTCTGGCTCATCATCTG	-	novel	NA	P-0025897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	312	573	0	ENST00000373344.5:c.3875_3899del	p.Ser1292Ter	p.S1292*	ENST00000373344	NM_000489.3	1292	tCAGATGATGAGCCAGAAGAAGGGAAa/ta	11/35	1	2	FACETS	0.847	0.803	0.892	0.847	0.803	0.892	CLONAL	1	TRUE	1	0.920629899776076	2		573	800	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	94	122	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.870921731205393	2		122	198	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0025899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	474	656	2	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.870921731205393	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.870921731205393	2		658	540	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176476	123176479	+	frameshift_variant	Frame_Shift_Del	DEL	TGAC	TGAC	-	novel	NA	P-0025899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	241	555	0	ENST00000218089.9:c.446_449del	p.Thr149LysfsTer33	p.T149Kfs*33	ENST00000218089	NM_001042749.1	148	aTGACt/at	7/35	1	2	FACETS	0.953	0.897	1	0.953	0.897	1	CLONAL	1	TRUE	1	0.870921731205393	2		555	581	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250670	26250670	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	43	545	0	ENST00000446824.2:c.164A>G	p.Tyr55Cys	p.Y55C	ENST00000446824	NM_021018.2	55	tAt/tGt	1/1	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.18	2		545	455	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349261	70349261	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	37	372	0	ENST00000374080.3:c.3673A>C	p.Lys1225Gln	p.K1225Q	ENST00000374080		1225	Aag/Cag	26/45	1	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.18	1		372	317	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0025902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	110	146	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.358319632752486	2		146	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0025902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	218	773	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.358319632752486	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.358319632752486	1		774	683	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254962	16254962	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	116	456	0	ENST00000375759.3:c.2227C>G	p.Gln743Glu	p.Q743E	ENST00000375759	NM_015001.2	743	Cag/Gag	11/15	0.137873956794158	3	FACETS	1	0.977	1	0.635	0.574	0.7	INDETERMINATE	1	TRUE	1	0.358319632752486	3		456	601	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410452	139410453	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs864622059	NA	P-0025902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	179	836	0	ENST00000277541.6:c.1649dup	p.Tyr550Ter	p.Y550*	ENST00000277541	NM_017617.3	550	tac/taAc	10/34	0.358319632752486	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.358319632752486	1		836	597	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879904	44879904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs912069418	NA	P-0025902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	123	698	0	ENST00000377967.4:c.493C>T	p.Arg165Ter	p.R165*	ENST00000377967	NM_021140.2	165	Cga/Tga	6/29	NA	2	FACETS	0.929	0.841	1			1	INDETERMINATE	1	TRUE	NA	0.358319632752486	2		698	739	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31015952	31015952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781684559	NA	P-0025902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	77	457	1	ENST00000375687.4:c.274C>T	p.Arg92Cys	p.R92C	ENST00000375687	NM_015338.5	92	Cgc/Tgc	5/13	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.358319632752486	2		458	427	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254711	16254711	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0025902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	228	683	0	ENST00000375759.3:c.1976C>G	p.Ser659Ter	p.S659*	ENST00000375759	NM_015001.2	659	tCa/tGa	11/15	0.137873956794158	3	FACETS	0.754	0.703	0.807	0.754	0.703	0.807	INDETERMINATE	2	TRUE	1	0.358319632752486	3		683	995	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255220	16255220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1482043812	NA	P-0025902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	188	583	0	ENST00000375759.3:c.2485C>T	p.His829Tyr	p.H829Y	ENST00000375759	NM_015001.2	829	Cac/Tac	11/15	0.137873956794158	3	FACETS	0.771	0.714	0.831	0.771	0.714	0.831	INDETERMINATE	2	TRUE	1	0.358319632752486	3		583	802	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255868	16255868	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	180	567	0	ENST00000375759.3:c.3133C>A	p.Leu1045Ile	p.L1045I	ENST00000375759	NM_015001.2	1045	Ctt/Att	11/15	0.137873956794158	3	FACETS	0.828	0.766	0.893	0.828	0.766	0.893	INDETERMINATE	2	TRUE	1	0.358319632752486	3		567	715	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257128	16257128	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	187	716	1	ENST00000375759.3:c.4393C>A	p.Leu1465Ile	p.L1465I	ENST00000375759	NM_015001.2	1465	Ctt/Att	11/15	0.137873956794158	3	FACETS	1	0.989	1	0.721	0.667	0.778	INDETERMINATE	1	TRUE	1	0.358319632752486	3		717	853	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257581	16257581	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	160	679	0	ENST00000375759.3:c.4846C>T	p.His1616Tyr	p.H1616Y	ENST00000375759	NM_015001.2	1616	Cat/Tat	11/15	0.137873956794158	3	FACETS	1	0.987	1	0.692	0.635	0.751	INDETERMINATE	1	TRUE	1	0.358319632752486	3		679	761	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831471	89831471	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1286812517	NA	P-0025902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	121	642	1	ENST00000389301.3:c.2605C>T	p.Gln869Ter	p.Q869*	ENST00000389301	NM_000135.2	869	Cag/Tag	28/43	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.358319632752486	2		643	602	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259652	89259653	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0025902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	100	350	0	ENST00000336596.2:c.798_799del	p.Gly267PhefsTer17	p.G267Ffs*17	ENST00000336596	NM_005233.5	266	AGa/a	3/17	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.358319632752486	2		350	391	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6045555	6045557	+	missense_variant	Missense_Mutation	TNP	TCT	TCT	AAA	novel	NA	P-0025902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	36	374	1	ENST00000265849.7:c.129_131delinsTTT	p.Glu44Leu	p.E44L	ENST00000265849	NM_000535.5	43	gtAGAa/gtTTTa	2/15	1	2	FACETS	0.369	0.302	0.443	0.369	0.302	0.443	SUBCLONAL	1	TRUE	1	0.358319632752486	2		375	545	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557673	21557673	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs762544451	NA	P-0025904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	95	474	0	ENST00000382592.4:c.2172C>A	p.Asp724Glu	p.D724E	ENST00000382592	NM_014572.2	724	gaC/gaA	5/8	1	2	FACETS	0.849	0.76	0.944	0.849	0.76	0.944	CLONAL	1	FALSE	1	0.464056817735709	2		474	482	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805052	43805052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs6088	NA	P-0025904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	56	429	0	ENST00000372470.3:c.502G>A	p.Glu168Lys	p.E168K	ENST00000372470	NM_005373.2	168	Gaa/Aaa	4/12	1	2	FACETS	0.59	0.507	0.68	0.59	0.507	0.68	SUBCLONAL	1	FALSE	1	0.464056817735709	2		429	409	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974962	15974962	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	18	286	0	ENST00000268712.3:c.3913A>T	p.Thr1305Ser	p.T1305S	ENST00000268712	NM_006311.3	1305	Act/Tct	30/46	1	2	FACETS	0.219	0.164	0.283	0.219	0.164	0.283	SUBCLONAL	1	FALSE	1	0.464056817735709	2		286	355	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210770	2210770	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	22	413	0	ENST00000398665.3:c.1267G>T	p.Glu423Ter	p.E423*	ENST00000398665	NM_032482.2	423	Gag/Tag	14/28	1	2	FACETS	0.238	0.184	0.301	0.238	0.184	0.301	SUBCLONAL	1	FALSE	1	0.464056817735709	2		413	398	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	59	122	0				ENST00000310581	NM_198253.2	-/1132			0.114986308549524	5	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.403521654280187	5		122	314	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0025905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	72	273	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	0.403521654280187	3	FACETS	1	0.964	1	0.631	0.555	0.711	CLONAL	1	TRUE	1	0.403521654280187	3		273	340	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253821	30253821	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	85	470	0	ENST00000307677.4:c.633C>A	p.Asn211Lys	p.N211K	ENST00000307677	NM_138578.1	211	aaC/aaA	3/3	1	2	FACETS	0.766	0.678	0.859	0.766	0.678	0.859	SUBCLONAL	1	TRUE	1	0.403521654280187	2		470	550	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098815	178098815	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	209	856	0	ENST00000397062.3:c.230A>G	p.Asp77Gly	p.D77G	ENST00000397062	NM_006164.4	77	gAt/gGt	2/5	0.188910080481708	2	FACETS	1	0.99	1	0.675	0.631	0.719	INDETERMINATE	1	TRUE	0	0.536856746525014	2		856	577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578266	7578266	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs942158624	NA	P-0025910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	104	818	0	ENST00000269305.4:c.583A>T	p.Ile195Phe	p.I195F	ENST00000269305	NM_001126112.2	195	Atc/Ttc	6/11	0.188910080481708	2	FACETS	0.627	0.562	0.695	0.313	0.281	0.348	INDETERMINATE	1	TRUE	0	0.536856746525014	2		818	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs483352695	NA	P-0025910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	264	816	0	ENST00000269305.4:c.736A>T	p.Met246Leu	p.M246L	ENST00000269305	NM_001126112.2	246	Atg/Ttg	7/11	0.188910080481708	2	FACETS	1	0.991	1	0.642	0.604	0.68	INDETERMINATE	1	TRUE	0	0.536856746525014	2		816	766	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885570	111885570	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	146	861	0	ENST00000341259.2:c.1347G>C	p.Glu449Asp	p.E449D	ENST00000341259	NM_005475.2	449	gaG/gaC	7/8	0.188910080481708	2	FACETS	0.628	0.573	0.686	0.314	0.286	0.343	INDETERMINATE	1	TRUE	0	0.536856746525014	2		861	866	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916743	48916743	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	128	583	0	ENST00000267163.4:c.273del	p.Tyr91Ter	p.Y91*	ENST00000267163	NM_000321.2	91	taT/ta	3/27	0.536856746525014	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.536856746525014	1		583	298	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521716	89521716	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	21	621	0	ENST00000336596.2:c.2793C>G	p.Ile931Met	p.I931M	ENST00000336596	NM_005233.5	931	atC/atG	16/17	0.536856746525014	1	FACETS	0.141	0.108	0.179	0.141	0.108	0.179	SUBCLONAL	1	TRUE	0	0.536856746525014	1		621	407	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178477	56178477	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	30	412	0	ENST00000399503.3:c.3450del	p.Lys1150AsnfsTer22	p.K1150Nfs*22	ENST00000399503	NM_005921.1	1150	aaG/aa	14/20	0.536856746525014	1	FACETS	0.391	0.317	0.474	0.391	0.317	0.474	SUBCLONAL	1	TRUE	0	0.536856746525014	1		412	209	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268760	41268760	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	73	442	0	ENST00000349496.5:c.998A>T	p.Tyr333Phe	p.Y333F	ENST00000349496	NM_001904.3	333	tAc/tTc	7/15	0.792229678825377	3	FACETS	0.321	0.28	0.365	0.16	0.14	0.183	SUBCLONAL	1	TRUE	1	0.792229678825377	3		442	802	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266792	198266792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	109	651	0	ENST00000335508.6:c.2140G>A	p.Glu714Lys	p.E714K	ENST00000335508	NM_012433.2	714	Gaa/Aaa	15/25	1	2	FACETS	0.679	0.609	0.753	0.679	0.609	0.753	SUBCLONAL	1	TRUE	1	0.367352818443062	2		651	874	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0025927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	95	674	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.275666406573223	3	FACETS	0.794	0.707	0.887	0.397	0.353	0.444	SUBCLONAL	1	TRUE	1	0.367352818443062	3		674	771	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0025927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	98	759	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.275666406573223	3	FACETS	0.764	0.681	0.852	0.382	0.34	0.426	SUBCLONAL	1	TRUE	1	0.367352818443062	3		759	827	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0025927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	53	310	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.641	0.548	0.743	0.641	0.548	0.743	SUBCLONAL	1	TRUE	1	0.367352818443062	2		310	450	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821817	59821817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780235	NA	P-0025927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	119	576	2	ENST00000259008.2:c.2233G>A	p.Ala745Thr	p.A745T	ENST00000259008	NM_032043.2	745	Gca/Aca	15/20	0.285739118939962	3	FACETS	0.754	0.679	0.833	0.377	0.339	0.417	SUBCLONAL	1	TRUE	1	0.367352818443062	3		578	1017	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346025	73346025	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	138	371	0	ENST00000377767.4:c.1513C>T	p.His505Tyr	p.H505Y	ENST00000377767	NM_014953.3	505	Cat/Tat	11/21	0.154010970185812	4	FACETS	1	0.964	1	0.371	0.337	0.406	INDETERMINATE	1	TRUE	1	0.440984893007448	4		371	811	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248572	10248572	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	199	654	0	ENST00000340748.4:c.4181C>G	p.Ser1394Cys	p.S1394C	ENST00000340748		1394	tCc/tGc	35/40	1	2	FACETS	0.68	0.628	0.734	0.68	0.628	0.734	SUBCLONAL	1	TRUE	1	0.440984893007448	2		654	1327	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161850	47161850	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0025928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	208	373	0	ENST00000409792.3:c.4276A>T	p.Lys1426Ter	p.K1426*	ENST00000409792	NM_014159.6	1426	Aaa/Taa	3/21	0.440984893007448	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.440984893007448	1		373	626	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577560	7577560	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	480	702	0	ENST00000269305.4:c.721T>A	p.Ser241Thr	p.S241T	ENST00000269305	NM_001126112.2	241	Tcc/Acc	7/11	0.905949795701808	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.905949795701808	1		702	554	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169988328	169988328	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	300	400	1	ENST00000295797.4:c.570T>G	p.Cys190Trp	p.C190W	ENST00000295797	NM_002740.5	190	tgT/tgG	6/18	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.905949795701808	2		401	640	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0025930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	109	770	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.214977175942724	5	FACETS	1	0.923	1	0.345	0.309	0.383	CLONAL	1	TRUE	2	0.323544480160412	5		770	967	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0025930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	218	552	0	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	0.323544480160412	3	FACETS	1	0.991	1	0.714	0.664	0.767	CLONAL	1	TRUE	1	0.323544480160412	3		552	1096	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251560	251560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1042170	NA	P-0025930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	58	1116	0	ENST00000264932.6:c.1771G>A	p.Ala591Thr	p.A591T	ENST00000264932	NM_004168.2	591	Gcg/Acg	13/15	0.323544480160412	3	FACETS	0.383	0.327	0.444	0.191	0.163	0.222	SUBCLONAL	1	TRUE	1	0.323544480160412	3		1116	1088	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0025931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	22	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.364	0.281	0.462	0.364	0.281	0.462	SUBCLONAL	1	TRUE	1	0.18	2		555	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0025931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	37	687	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	0.541	0.444	0.65	0.541	0.444	0.65	SUBCLONAL	1	TRUE	1	0.18	2		687	760	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044595	47044595	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	47	810	0	ENST00000377604.3:c.2092G>T	p.Glu698Ter	p.E698*	ENST00000377604	NM_001204468.1	698	Gag/Tag	18/24	1	2	FACETS	0.665	0.56	0.782	0.665	0.56	0.782	SUBCLONAL	1	TRUE	1	0.18	2		810	785	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	54	370	0	ENST00000304494.5:c.262G>A	p.Glu88Lys	p.E88K	ENST00000304494	NM_000077.4	88	Gag/Aag	2/3	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.18	2		370	488	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683597	29683599	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	ATG	ATG	TT	novel	NA	P-0025931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	50	386	1	ENST00000356175.3:c.7672_7674delinsTT	p.Met2558LeufsTer45	p.M2558Lfs*45	ENST00000356175	NM_000267.3	2558	ATG/TT	51/57	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.18	2		387	496	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739113	40739113	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	24	418	1	ENST00000373198.4:c.3171G>T	p.Glu1057Asp	p.E1057D	ENST00000373198	NM_133170.3	1057	gaG/gaT	24/32	1	2	FACETS	0.622	0.486	0.778	0.622	0.486	0.778	SUBCLONAL	1	TRUE	1	0.18	2		419	429	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980802	40980802	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	42	496	0	ENST00000373198.4:c.1684T>A	p.Tyr562Asn	p.Y562N	ENST00000373198	NM_133170.3	562	Tat/Aat	10/32	1	2	FACETS	0.832	0.694	0.985	0.832	0.694	0.985	CLONAL	1	TRUE	1	0.18	2		496	561	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170015170	170015170	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	43	660	0	ENST00000295797.4:c.1576G>A	p.Asp526Asn	p.D526N	ENST00000295797	NM_002740.5	526	Gat/Aat	16/18	1	2	FACETS	0.61	0.509	0.723	0.61	0.509	0.723	SUBCLONAL	1	TRUE	1	0.18	2		660	783	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748270	41748270	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	39	741	0	ENST00000226382.2:c.499G>T	p.Ala167Ser	p.A167S	ENST00000226382	NM_003924.3	167	Gcc/Tcc	3/3	1	2	FACETS	0.686	0.567	0.819	0.686	0.567	0.819	SUBCLONAL	1	TRUE	1	0.18	2		741	632	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361226	66361226	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	27	314	0	ENST00000273854.3:c.946A>C	p.Ile316Leu	p.I316L	ENST00000273854	NM_004439.5	316	Atc/Ctc	4/18	1	2	FACETS	0.668	0.531	0.826	0.668	0.531	0.826	SUBCLONAL	1	TRUE	1	0.18	2		314	449	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485854	8485855	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0025931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	28	354	0	ENST00000356435.5:c.2962_2963insG	p.Thr988SerfsTer19	p.T988Sfs*19	ENST00000356435		988	acc/aGcc	17/35	1	2	FACETS	0.876	0.701	1	0.876	0.701	1	CLONAL	1	TRUE	1	0.18	2		354	355	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411648	63411648	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	37	757	0	ENST00000330258.3:c.1519G>C	p.Glu507Gln	p.E507Q	ENST00000330258	NM_152424.3	507	Gag/Cag	2/2	1	2	FACETS	0.573	0.471	0.687	0.573	0.471	0.687	SUBCLONAL	1	TRUE	1	0.18	2		757	718	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691025	NA	P-0025932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	471	579	0	ENST00000269305.4:c.785G>T	p.Gly262Val	p.G262V	ENST00000269305	NM_001126112.2	262	gGt/gTt	8/11	0.578487574284495	5	FACETS	0.971	0.946	0.995	0.971	0.946	0.995	CLONAL	5	TRUE	0	0.637922196440712	5		579	595	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15838385	15838385	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775221448	NA	P-0025932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	198	471	0	ENST00000307771.7:c.883C>T	p.Arg295Ter	p.R295*	ENST00000307771	NM_005089.3	295	Cga/Tga	10/11	0.637922196440712	3	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.637922196440712	3		471	579	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622048	43622048	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	104	324	0	ENST00000355710.3:c.3065C>A	p.Thr1022Asn	p.T1022N	ENST00000355710	NM_020975.4	1022	aCt/aAt	19/20	0.593872292440539	3	FACETS	1	0.982	1	0.462	0.419	0.507	CLONAL	1	TRUE	0	0.637922196440712	3		324	310	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760715	133760715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1285701996	NA	P-0025932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	40	848	0	ENST00000318560.5:c.3038G>A	p.Arg1013Gln	p.R1013Q	ENST00000318560	NM_005157.4	1013	cGg/cAg	11/11	0.181584987964279	3	FACETS	0.304	0.252	0.362	0.101	0.084	0.121	INDETERMINATE	1	TRUE	0	0.637922196440712	3		848	544	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909691	76909691	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0025932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	147	329	1	ENST00000373344.5:c.4215-1G>C		p.X1405_splice	ENST00000373344	NM_000489.3	1405			0.607446094179554	2	FACETS	0.88	0.822	0.936	0.88	0.822	0.936	CLONAL	2	TRUE	0	0.637922196440712	2		330	262	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594221	55594221	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913512	NA	P-0025934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	935	475	0	ENST00000288135.5:c.1924A>G	p.Lys642Glu	p.K642E	ENST00000288135	NM_000222.2	642	Aaa/Gaa	13/21	0.248174312154495	5	FACETS	0.892	0.871	0.913	0.714	0.697	0.73	INDETERMINATE	4	TRUE	0	0.801293754670375	5		475	1440	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564479	55564479	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	337	487	0	ENST00000288135.5:c.367T>A	p.Ser123Thr	p.S123T	ENST00000288135	NM_000222.2	123	Tcc/Acc	3/21	0.248174312154495	5	FACETS	1	0.992	1	0.258	0.243	0.273	INDETERMINATE	1	TRUE	0	0.801293754670375	5		487	1435	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0025935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	436	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.346838551197473	5	FACETS	1	0.987	1			1	CLONAL	3	TRUE	NA	0.346838551197473	5		555	1179	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0025935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	60	499	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.346838551197473	5	FACETS	0.442	0.379	0.511	0.111	0.094	0.128	SUBCLONAL	1	TRUE	1	0.346838551197473	5		499	1189	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0025935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	287	341	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	0.346838551197473	3	FACETS	1	0.976	1	1	0.995	1	CLONAL	4	TRUE	0	0.346838551197473	3		341	471	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433722	49433722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572359740	NA	P-0025935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1237	632	1111	4	ENST00000301067.7:c.7831C>T	p.Arg2611Cys	p.R2611C	ENST00000301067	NM_003482.3	2611	Cgc/Tgc	31/54	0.346838551197473	7	FACETS	0.91	0.875	0.946	0.91	0.875	0.946	CLONAL	4	TRUE	3	0.346838551197473	7		1115	1869	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736555	85736555	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	98	278	0	ENST00000370580.1:c.92A>G	p.Lys31Arg	p.K31R	ENST00000370580	NM_003921.4	31	aAa/aGa	2/3	0.346838551197473	3	FACETS	1	0.973	1	0.423	0.379	0.471	CLONAL	1	TRUE	0	0.346838551197473	3		278	522	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711026	114711026	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	44	347	1	ENST00000543371.1:c.250G>A	p.Glu84Lys	p.E84K	ENST00000543371	NM_001198531.1	84	Gaa/Aaa	2/14	0.346838551197473	5	FACETS	0.543	0.454	0.641	0.181	0.151	0.214	SUBCLONAL	1	TRUE	2	0.346838551197473	5		348	711	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871108	12871109	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0025935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	67	294	0	ENST00000228872.4:c.337dup	p.Arg113ProfsTer12	p.R113Pfs*12	ENST00000228872	NM_004064.3	112	agc/agCc	1/3	0.346838551197473	7	FACETS	1	0.951	1	0.3	0.26	0.343	CLONAL	1	TRUE	3	0.346838551197473	7		294	601	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888106	81888106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746298243	NA	P-0025935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	172	619	0	ENST00000359376.3:c.251G>A	p.Arg84Gln	p.R84Q	ENST00000359376	NM_002661.3	84	cGa/cAa	3/33	0.346838551197473	5	FACETS	0.799	0.735	0.865	0.532	0.49	0.577	SUBCLONAL	2	TRUE	2	0.346838551197473	5		619	944	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523329	9523329	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	317	492	0	ENST00000353224.5:c.1908G>T	p.Met636Ile	p.M636I	ENST00000353224	NM_177990.2	636	atG/atT	9/10	0.346838551197473	5	FACETS	1	0.977	1			1	CLONAL	3	TRUE	NA	0.346838551197473	5		492	877	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032752	30032752	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	144	392	0	ENST00000338641.4:c.127G>T	p.Gly43Trp	p.G43W	ENST00000338641	NM_000268.3	43	Ggg/Tgg	2/16	0.346838551197473	5	FACETS	0.898	0.821	0.979	0.599	0.547	0.653	CLONAL	2	TRUE	2	0.346838551197473	5		392	703	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965602	93965602	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	297	642	0	ENST00000369303.4:c.2326G>T	p.Asp776Tyr	p.D776Y	ENST00000369303	NM_004440.3	776	Gat/Tat	13/17	0.168463740218772	5	FACETS	0.982	0.927	1	0.982	0.927	1	INDETERMINATE	3	TRUE	2	0.346838551197473	5		642	884	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0025936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	185	531	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.582	0.538	0.629	0.582	0.538	0.629	SUBCLONAL	1	TRUE	1	0.664508124609065	2		531	956	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	472220	472220	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	126	444	1	ENST00000399788.2:c.581C>A	p.Pro194His	p.P194H	ENST00000399788	NM_001042603.1	194	cCt/cAt	5/28	1	2	FACETS	0.557	0.505	0.611	0.557	0.505	0.611	SUBCLONAL	1	TRUE	1	0.664508124609065	2		445	681	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865474	57865474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	183	803	0	ENST00000228682.2:c.2951G>A	p.Arg984Lys	p.R984K	ENST00000228682	NM_005269.2	984	aGg/aAg	12/12	1	2	FACETS	0.57	0.526	0.616	0.57	0.526	0.616	SUBCLONAL	1	TRUE	1	0.664508124609065	2		803	966	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601265	28601265	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	151	524	0	ENST00000241453.7:c.2167T>G	p.Phe723Val	p.F723V	ENST00000241453	NM_004119.2	723	Ttc/Gtc	17/24	1	2	FACETS	0.473	0.432	0.517	0.473	0.432	0.517	SUBCLONAL	1	TRUE	1	0.664508124609065	2		524	960	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514574	103514574	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	79	309	0	ENST00000355739.4:c.1075G>C	p.Glu359Gln	p.E359Q	ENST00000355739	NM_000123.3	359	Gag/Cag	8/15	1	2	FACETS	0.496	0.438	0.559	0.496	0.438	0.559	SUBCLONAL	1	TRUE	1	0.664508124609065	2		309	479	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95573946	95573946	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0025936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	97	299	0	ENST00000393063.1:c.2803A>T	p.Arg935Ter	p.R935*	ENST00000393063	NM_030621.3	935	Aga/Tga	18/28	1	2	FACETS	0.552	0.493	0.614	0.552	0.493	0.614	SUBCLONAL	1	TRUE	1	0.664508124609065	2		299	529	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675100	40675100	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	191	896	0	ENST00000249776.8:c.64T>G	p.Cys22Gly	p.C22G	ENST00000249776	NM_033286.3	22	Tgc/Ggc	1/9	1	2	FACETS	0.419	0.386	0.454	0.419	0.386	0.454	SUBCLONAL	1	TRUE	1	0.664508124609065	2		896	1371	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72863696	72863696	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	194	694	0	ENST00000268489.5:c.3511A>G	p.Lys1171Glu	p.K1171E	ENST00000268489	NM_006885.3	1171	Aag/Gag	5/10	0.368098230755363	3	FACETS	0.622	0.574	0.672	0.311	0.287	0.336	INDETERMINATE	1	TRUE	1	0.664508124609065	3		694	1250	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332923	152332923	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0025936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	106	323	0	ENST00000206249.3:c.1229T>A	p.Leu410Ter	p.L410*	ENST00000206249	NM_000125.3	410	tTg/tAg	5/8	0.391201209571301	1	FACETS	0.489	0.441	0.539	0.489	0.441	0.539	INDETERMINATE	1	TRUE	0	0.664508124609065	1		323	436	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352797	70352797	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	205	774	0	ENST00000374080.3:c.4518G>T	p.Gln1506His	p.Q1506H	ENST00000374080		1506	caG/caT	32/45	1	2	FACETS	0.57	0.528	0.614	0.57	0.528	0.614	SUBCLONAL	1	TRUE	1	0.664508124609065	2		774	1082	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0025936-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	45	531	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.16	2		531	547	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0025936-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	25	471	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	1	2	FACETS	0.339	0.266	0.425	0.339	0.266	0.425	SUBCLONAL	1	TRUE	1	0.16	2		471	921	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667464	241667464	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs768483509	NA	P-0025936-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	28	269	0	ENST00000366560.3:c.986A>G	p.Asn329Ser	p.N329S	ENST00000366560	NM_000143.3	329	aAc/aGc	7/10	1	2	FACETS	0.676	0.539	0.832	0.676	0.539	0.832	SUBCLONAL	1	TRUE	1	0.16	2		269	518	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195293	102195293	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025936-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	31	353	0	ENST00000263464.3:c.53A>T	p.Asn18Ile	p.N18I	ENST00000263464	NM_001165.4	18	aAc/aTc	2/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.16	NA		353	612	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47088107	47088107	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025936-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	38	328	0	ENST00000409792.3:c.6968del	p.Tyr2323LeufsTer30	p.Y2323Lfs*30	ENST00000409792	NM_014159.6	2323	tAt/tt	16/21	1	2	FACETS	0.739	0.609	0.884	0.739	0.609	0.884	SUBCLONAL	1	TRUE	1	0.16	2		328	643	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	136	122	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.895	0.823	0.969	0.895	0.823	0.969	CLONAL	1	TRUE	1	0.812425951845765	2		122	374	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273864	10273864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	279	905	0	ENST00000330684.3:c.405G>A	p.Met135Ile	p.M135I	ENST00000330684	NM_001134407.1	135	atG/atA	2/13	1	2	FACETS	0.662	0.622	0.703	0.662	0.622	0.703	SUBCLONAL	1	TRUE	1	0.812425951845765	2		905	1037	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57567467	57567467	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	190	406	0	ENST00000316660.6:c.58G>T	p.Glu20Ter	p.E20*	ENST00000316660	NM_021127.2	20	Gag/Tag	1/2	1	2	FACETS	0.941	0.878	1	0.941	0.878	1	CLONAL	1	TRUE	1	0.812425951845765	2		406	497	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045656	26045656	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	109	206	0	ENST00000540144.1:c.18A>C	p.Gln6His	p.Q6H	ENST00000540144	NM_003531.2	6	caA/caC	1/1	1	2	FACETS	0.958	0.874	1	0.958	0.874	1	CLONAL	1	TRUE	1	0.812425951845765	2		206	280	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0025975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	581	499	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.935698189695654	3	FACETS	1	0.987	1	0.686	0.665	0.706	CLONAL	2	TRUE	0	0.935698189695654	3		499	886	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0025975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	242	549	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.528054803827119	1	FACETS	0.328	0.307	0.349	0.328	0.307	0.349	INDETERMINATE	1	TRUE	0	0.935698189695654	1		549	840	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578517	7578517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750600586	NA	P-0025975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	1347	832	0	ENST00000269305.4:c.413C>T	p.Ala138Val	p.A138V	ENST00000269305	NM_001126112.2	138	gCc/gTc	5/11	0.935698189695654	2	FACETS	1	0.999	1	1	0.999	1	CLONAL	2	TRUE	0	0.935698189695654	2		832	1378	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947514	48947568	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACATTTTCCTATTTTTATCCCCTCTAGGACTGTTATGAACACTATCCAACAATTA	ACATTTTCCTATTTTTATCCCCTCTAGGACTGTTATGAACACTATCCAACAATTA	-	novel	NA	P-0025975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	235	338	0	ENST00000267163.4:c.1128-26_1156del		p.X376_splice	ENST00000267163	NM_000321.2	376		12/27	0.935698189695654	2	FACETS	0.973	0.949	0.995	0.973	0.949	0.995	CLONAL	2	TRUE	0	0.935698189695654	2		338	258	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007327	143007327	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	149	424	0	ENST00000262992.4:c.2457G>C	p.Lys819Asn	p.K819N	ENST00000262992	NM_001101669.1	819	aaG/aaC	22/24	0.494080228066399	2	FACETS	0.517	0.474	0.562	0.259	0.237	0.281	INDETERMINATE	1	TRUE	0	0.935698189695654	2		424	616	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426725	47426725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773318953	NA	P-0025975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	189	716	0	ENST00000377045.4:c.970G>A	p.Val324Met	p.V324M	ENST00000377045	NM_001654.4	324	Gtg/Atg	10/16	0.233255645807998	3	FACETS	0.5	0.461	0.541	0.167	0.153	0.181	INDETERMINATE	1	TRUE	0	0.935698189695654	3		716	1186	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	113	424	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.817	0.735	0.903	1	0.985	1	CLONAL	2	TRUE	1	0.187758360752248	2		424	737	SUCCESS
CBL	867	MSKCC	GRCh37	11	119146825	119146825	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	63	449	0	ENST00000264033.4:c.988G>T	p.Asp330Tyr	p.D330Y	ENST00000264033	NM_005188.3	330	Gat/Tat	6/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.187758360752248	2		449	538	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207203	1207204	+	splice_donor_variant	Splice_Site	DEL	GT	GT	-	novel	NA	P-0025976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	95	688	0	ENST00000326873.7:c.290+1_290+2del		p.X97_splice	ENST00000326873	NM_000455.4	97			0.187758360752248	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.187758360752248	1		688	758	SUCCESS
APC	324	MSKCC	GRCh37	5	112151270	112151270	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	48	361	0	ENST00000257430.4:c.913del	p.Thr305GlnfsTer31	p.T305Qfs*31	ENST00000257430	NM_000038.5	305	Aca/ca	9/16	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.187758360752248	2		361	416	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0025977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	188	603	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.83	2		603	453	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	183	122	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.83	2		122	440	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196860	108196860	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	133	420	1	ENST00000278616.4:c.6883G>T	p.Glu2295Ter	p.E2295*	ENST00000278616	NM_000051.3	2295	Gaa/Taa	47/63	1	2	FACETS	0.932	0.857	1	0.932	0.857	1	CLONAL	1	TRUE	1	0.83	2		421	344	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117874129	117874129	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	105	539	0	ENST00000297338.2:c.325A>G	p.Thr109Ala	p.T109A	ENST00000297338	NM_006265.2	109	Act/Gct	4/14	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.83	2		539	252	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148726	20148727	+	splice_acceptor_variant	Splice_Site	DEL	CT	CT	-	novel	NA	P-0025977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	69	248	0	ENST00000379607.5:c.338-2_338-1del		p.X113_splice	ENST00000379607	NM_001412.3	113			1	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.83	1		248	87	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0025979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	170	218	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.348110078664828	4	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	2	0.389261658846035	4		218	593	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971673	18971674	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0025979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	620	619	2	ENST00000262803.5:c.2340dup	p.Leu781AlafsTer75	p.L781Afs*75	ENST00000262803	NM_002911.3	780	ttg/ttGg	17/24	0.389261658846035	5	FACETS	0.987	0.953	1			1	CLONAL	4	TRUE	NA	0.389261658846035	5		621	1278	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800445	32800445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs905027019	NA	P-0025979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	188	766	1	ENST00000374899.4:c.1102C>T	p.Arg368Trp	p.R368W	ENST00000374899	NM_018833.2	368	Cgg/Tgg	6/12	0.389261658846035	3	FACETS	0.987	0.911	1	0.494	0.455	0.534	CLONAL	1	TRUE	1	0.389261658846035	3		767	1169	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0025980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	134	575	0	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	0.148744387554104	2	FACETS	1	0.973	1	0.595	0.54	0.654	CLONAL	1	FALSE	0	0.211745546892484	2		575	1063	SUCCESS
AR	367	MSKCC	GRCh37	X	66765173	66765173	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs746341152	NA	P-0025980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	12	163	1	ENST00000374690.3:c.185A>T	p.Gln62Leu	p.Q62L	ENST00000374690	NM_000044.3	62	cAg/cTg	1/8	1	2	FACETS	0.511	0.359	0.698	0.511	0.359	0.698	SUBCLONAL	1	FALSE	1	0.211745546892484	2		164	222	SUCCESS
AR	367	MSKCC	GRCh37	X	66863125	66863125	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139524801	NA	P-0025980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	55	534	1	ENST00000374690.3:c.1644G>T	p.Leu548Phe	p.L548F	ENST00000374690	NM_000044.3	548	ttG/ttT	2/8	1	2	FACETS	0.517	0.441	0.602	0.517	0.441	0.602	SUBCLONAL	1	FALSE	1	0.211745546892484	2		535	1004	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801794	3801794	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	64	547	1	ENST00000262367.5:c.3712G>T	p.Glu1238Ter	p.E1238*	ENST00000262367	NM_004380.2	1238	Gag/Tag	20/31	1	2	FACETS	0.661	0.57	0.759	0.661	0.57	0.759	SUBCLONAL	1	FALSE	1	0.211745546892484	2		548	915	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858470	9858470	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	56	515	0	ENST00000330684.3:c.2931C>A	p.Asn977Lys	p.N977K	ENST00000330684	NM_001134407.1	977	aaC/aaA	13/13	1	2	FACETS	0.747	0.639	0.866	0.747	0.639	0.866	SUBCLONAL	1	FALSE	1	0.211745546892484	2		515	708	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0025981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	144	528	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.191481145919099	2	FACETS	0.893	0.817	0.972	0.893	0.817	0.972	CLONAL	2	TRUE	0	0.255631803444553	2		530	631	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953162	38953162	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs200255149	NA	P-0025981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	40	299	0	ENST00000357387.3:c.2822A>G	p.Asn941Ser	p.N941S	ENST00000357387	NM_152756.3	941	aAt/aGt	29/38	0.255631803444553	3	FACETS	1	0.84	1	0.504	0.42	0.598	CLONAL	1	TRUE	1	0.255631803444553	3		299	350	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974678	21974678	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs587778189	NA	P-0025981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	48	350	0	ENST00000304494.5:c.149A>C	p.Gln50Pro	p.Q50P	ENST00000304494	NM_000077.4	50	cAg/cCg	1/3	0.255631803444553	1	FACETS	0.763	0.646	0.892	0.763	0.646	0.892	SUBCLONAL	1	TRUE	0	0.255631803444553	1		350	429	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0025982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	179	425	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.252683611433488	4	FACETS	0.902	0.835	0.971	0.902	0.835	0.971	CLONAL	3	TRUE	1	0.252683611433488	4		425	656	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574030	7574030	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	162	519	1	ENST00000269305.4:c.997del	p.Arg333ValfsTer12	p.R333Vfs*12	ENST00000269305	NM_001126112.2	333	Cgt/gt	10/11	0.230838718804444	2	FACETS	0.974	0.897	1	0.974	0.897	1	CLONAL	2	TRUE	0	0.252683611433488	2		520	658	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591108	67591119	+	inframe_deletion	In_Frame_Del	DEL	ACCAGACCTTAT	ACCAGACCTTAT	-	novel	NA	P-0025982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	58	363	0	ENST00000274335.5:c.1701_1712del	p.Lys567_Ile571delinsAsn	p.K567_I571delinsN	ENST00000274335		567	aaACCAGACCTTATc/aac	12/15	0.252683611433488	3	FACETS	0.947	0.814	1	0.474	0.407	0.546	CLONAL	1	TRUE	1	0.252683611433488	3		363	546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0025983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	482	804	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.655730939152772	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.655730939152772	1		805	893	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0025983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	175	406	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.655730939152772	1	FACETS	0.829	0.772	0.886	0.829	0.772	0.886	CLONAL	1	TRUE	0	0.655730939152772	1		406	433	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219336	1219336	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	461	776	4	ENST00000326873.7:c.388G>T	p.Glu130Ter	p.E130*	ENST00000326873	NM_000455.4	130	Gag/Tag	3/10	0.655730939152772	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.655730939152772	1		780	880	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117932	70117932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	124	423	1	ENST00000245479.2:c.400G>A	p.Glu134Lys	p.E134K	ENST00000245479	NM_000346.3	134	Gag/Aag	1/3	0.348500881533702	1	FACETS	0.38	0.344	0.418	0.38	0.344	0.418	INDETERMINATE	1	TRUE	0	0.655730939152772	1		424	669	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610306	10610306	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	504	936	1	ENST00000171111.5:c.404G>T	p.Arg135Leu	p.R135L	ENST00000171111	NM_203500.1	135	cGc/cTc	2/6	0.655730939152772	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.655730939152772	1		937	933	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790959	89790959	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	129	515	0	ENST00000336032.3:c.346C>G	p.Gln116Glu	p.Q116E	ENST00000336032	NM_006813.2	116	Cag/Gag	1/2	0.340079098215384	1	FACETS	0.416	0.378	0.456	0.416	0.378	0.456	INDETERMINATE	1	TRUE	0	0.655730939152772	1		515	635	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012397	152012397	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	112	446	1	ENST00000262189.6:c.416G>T	p.Cys139Phe	p.C139F	ENST00000262189	NM_170606.2	139	tGt/tTt	4/59	0.348500881533702	1	FACETS	0.473	0.428	0.521	0.473	0.428	0.521	INDETERMINATE	1	TRUE	0	0.655730939152772	1		447	485	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0025984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	119	748	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	1	2	FACETS	0.791	0.713	0.874	0.791	0.713	0.874	SUBCLONAL	1	TRUE	1	0.31	2		748	970	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210075	55210075	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	107	720	0	ENST00000275493.2:c.185T>G	p.Leu62Arg	p.L62R	ENST00000275493	NM_005228.3	62	cTt/cGt	2/28	1	2	FACETS	0.701	0.627	0.779	0.701	0.627	0.779	SUBCLONAL	1	TRUE	1	0.31	2		720	985	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420202	88420202	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	45	660	1	ENST00000360948.2:c.2484del	p.Lys829ArgfsTer18	p.K829Rfs*18	ENST00000360948	NM_001012338.2	828	ggG/gg	19/19	1	2	FACETS	0.369	0.309	0.436	0.369	0.309	0.436	SUBCLONAL	1	TRUE	1	0.31	2		661	787	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578530	7578530	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs267605077	NA	P-0025984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	167	1138	2	ENST00000269305.4:c.400T>A	p.Phe134Ile	p.F134I	ENST00000269305	NM_001126112.2	134	Ttt/Att	5/11	0.236991514073515	1	FACETS	0.731	0.67	0.795	0.731	0.67	0.795	SUBCLONAL	1	TRUE	0	0.31	1		1140	1246	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561532	9561532	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	92	592	0	ENST00000353224.5:c.250G>T	p.Gly84Cys	p.G84C	ENST00000353224	NM_177990.2	84	Ggc/Tgc	4/10	0.241976605922148	1	FACETS	0.637	0.566	0.714	0.637	0.566	0.714	SUBCLONAL	1	TRUE	0	0.31	1		592	787	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813385	102813385	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	141	559	0	ENST00000307046.8:c.304C>G	p.Leu102Val	p.L102V	ENST00000307046	NM_001111285.1	102	Cta/Gta	3/4	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.31	2		559	823	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63545660	63545661	+	missense_variant	Missense_Mutation	DNP	TG	TG	AT	novel	NA	P-0025984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	92	591	0	ENST00000307078.5:c.933_934delinsAT	p.Met312Leu	p.M312L	ENST00000307078	NM_004655.3	311	tcCAtg/tcATtg	3/11	0.201726652581466	3	FACETS	0.813	0.722	0.911	0.407	0.361	0.456	CLONAL	1	TRUE	1	0.31	3		591	843	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267538	198267538	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	44	466	0	ENST00000335508.6:c.1819G>T	p.Ala607Ser	p.A607S	ENST00000335508	NM_012433.2	607	Gct/Tct	14/25	1	2	FACETS	0.435	0.364	0.514	0.435	0.364	0.514	SUBCLONAL	1	TRUE	1	0.31	2		466	653	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212615426	212615426	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	105	682	0	ENST00000342788.4:c.560G>T	p.Gly187Val	p.G187V	ENST00000342788	NM_005235.2	187	gGa/gTa	5/28	1	2	FACETS	0.751	0.672	0.835	0.751	0.672	0.835	SUBCLONAL	1	TRUE	1	0.31	2		682	902	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138375069	138375069	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	131	814	1	ENST00000289153.2:c.2990G>T	p.Gly997Val	p.G997V	ENST00000289153	NM_006219.2	997	gGg/gTg	21/22	1	2	FACETS	0.812	0.735	0.893	0.812	0.735	0.893	CLONAL	1	TRUE	1	0.31	2		815	1041	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143191848	143191848	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	101	573	0	ENST00000262992.4:c.583G>T	p.Asp195Tyr	p.D195Y	ENST00000262992	NM_001101669.1	195	Gac/Tac	8/24	1	2	FACETS	0.812	0.726	0.905	0.812	0.726	0.905	CLONAL	1	TRUE	1	0.31	2		573	802	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79952317	79952317	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	113	772	0	ENST00000265081.6:c.325G>T	p.Gly109Ter	p.G109*	ENST00000265081	NM_002439.4	109	Gga/Tga	2/24	1	2	FACETS	0.665	0.597	0.738	0.665	0.597	0.738	SUBCLONAL	1	TRUE	1	0.31	2		772	1096	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564302	86564302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	97	416	0	ENST00000274376.6:c.34G>T	p.Gly12Cys	p.G12C	ENST00000274376	NM_002890.2	12	Ggc/Tgc	1/25	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.31	2		416	557	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004482	150004482	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	127	721	0	ENST00000253339.5:c.1743A>C	p.Lys581Asn	p.K581N	ENST00000253339		581	aaA/aaC	3/7	1	2	FACETS	0.759	0.686	0.836	0.759	0.686	0.836	SUBCLONAL	1	TRUE	1	0.31	2		721	1080	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039309	47039309	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	180	1025	0	ENST00000377604.3:c.932G>T	p.Ser311Ile	p.S311I	ENST00000377604	NM_001204468.1	311	aGc/aTc	10/24	1	2	FACETS	0.894	0.822	0.969	0.894	0.822	0.969	CLONAL	1	TRUE	1	0.31	2		1025	1299	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345512	70345512	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0025984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	101	718	1	ENST00000374080.3:c.2372-1G>T		p.X791_splice	ENST00000374080		791			1	2	FACETS	0.679	0.606	0.758	0.679	0.606	0.758	SUBCLONAL	1	TRUE	1	0.31	2		719	959	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0025986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	299	453	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.435683827394012	5	FACETS	0.884	0.839	0.928	0.884	0.839	0.928	CLONAL	4	TRUE	1	0.435683827394012	5		453	642	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0025986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	189	399	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	0.432592314001012	3	FACETS	0.847	0.793	0.901	0.847	0.793	0.901	CLONAL	3	TRUE	0	0.435683827394012	3		399	416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0025986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	378	668	1	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.432592314001012	3	FACETS	0.981	0.94	1	0.981	0.94	1	CLONAL	3	TRUE	0	0.435683827394012	3		669	718	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0025986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	107	677	1	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	0.420866462645587	3	FACETS	0.769	0.69	0.853	0.384	0.345	0.427	SUBCLONAL	1	TRUE	1	0.435683827394012	3		678	778	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032541	12032541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267604739	NA	P-0025986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	261	428	0	ENST00000353533.5:c.977C>T	p.Pro326Leu	p.P326L	ENST00000353533	NM_003010.3	326	cCg/cTg	9/11	0.432592314001012	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	0	0.435683827394012	3		428	465	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497272	149497272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201061735	NA	P-0025986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	409	677	0	ENST00000261799.4:c.3046G>A	p.Glu1016Lys	p.E1016K	ENST00000261799	NM_002609.3	1016	Gag/Aag	22/23	0.432592314001012	3	FACETS	0.994	0.954	1	0.994	0.954	1	CLONAL	3	TRUE	0	0.435683827394012	3		677	767	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128432131	128432132	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	101	588	0	ENST00000265960.3:c.314dup	p.Asn105LysfsTer10	p.N105Kfs*10	ENST00000265960	NM_001006617.1	105	aat/aaAt	3/12	1	2	FACETS	0.897	0.805	0.994	0.897	0.805	0.994	CLONAL	1	TRUE	1	0.435683827394012	2		588	517	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309018	137309018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771883272	NA	P-0025988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	448	840	2	ENST00000481739.1:c.625C>T	p.Arg209Trp	p.R209W	ENST00000481739	NM_002957.4	209	Cgg/Tgg	5/10	0.578343818382212	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.580061390247297	3		842	944	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639441	3639441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376112909	NA	P-0025988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	233	787	1	ENST00000294008.3:c.4198G>A	p.Asp1400Asn	p.D1400N	ENST00000294008	NM_032444.2	1400	Gat/Aat	12/15	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.580061390247297	2		788	686	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618876	37618877	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0025988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	245	752	0	ENST00000447079.4:c.552_553del	p.Arg185GlufsTer14	p.R185Efs*14	ENST00000447079	NM_015083.1	184	acCAgg/acgg	1/14	1	2	FACETS	0.945	0.885	1	0.945	0.885	1	CLONAL	1	TRUE	1	0.580061390247297	2		752	894	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37672049	37672049	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	191	625	0	ENST00000447079.4:c.2834T>C	p.Leu945Pro	p.L945P	ENST00000447079	NM_015083.1	945	cTa/cCa	9/14	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.580061390247297	2		625	642	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447439	187447439	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747597566	NA	P-0025988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	283	697	2	ENST00000232014.4:c.754A>G	p.Asn252Asp	p.N252D	ENST00000232014	NM_001130845.1	252	Aat/Gat	5/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.580061390247297	2		699	865	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599341	55599341	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519761	NA	P-0025989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	639	540	0	ENST00000288135.5:c.2467T>G	p.Tyr823Asp	p.Y823D	ENST00000288135	NM_000222.2	823	Tat/Gat	17/21	0.770358959553833	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.774217848785259	2		540	824	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600421	43600421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	285	446	0	ENST00000355710.3:c.647G>A	p.Cys216Tyr	p.C216Y	ENST00000355710	NM_020975.4	216	tGc/tAc	4/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.774217848785259	2		446	726	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578237	7578237	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	397	734	0	ENST00000269305.4:c.612G>C	p.Glu204Asp	p.E204D	ENST00000269305	NM_001126112.2	204	gaG/gaC	6/11	1	2	FACETS	0.973	0.927	1	0.973	0.927	1	CLONAL	1	TRUE	1	0.774217848785259	2		734	1054	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593594	55593647	+	inframe_deletion	In_Frame_Del	DEL	GAAGTACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATA	GAAGTACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATA	-	novel	NA	P-0025989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	463	423	0	ENST00000288135.5:c.1662_1715del	p.Glu554_Ile571del	p.E554_I571del	ENST00000288135	NM_000222.2	554	GAAGTACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATA/-	11/21	0.770358959553833	2	FACETS	0.929	0.901	0.956	0.929	0.901	0.956	CLONAL	2	TRUE	0	0.774217848785259	2		423	644	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577148	7577148	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1060501194	NA	P-0025993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	451	538	0	ENST00000269305.4:c.790del	p.Leu264TyrfsTer81	p.L264Yfs*81	ENST00000269305	NM_001126112.2	264	Cta/ta	8/11	0.851307356213549	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.857121311916657	2		538	514	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004741	150004741	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	109	427	0	ENST00000253339.5:c.1484A>C	p.Gln495Pro	p.Q495P	ENST00000253339		495	cAa/cCa	3/7	0.224731758807509	3	FACETS	1	0.981	1	0.653	0.596	0.712	INDETERMINATE	1	TRUE	1	0.857121311916657	3		427	278	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123018	5123050	+	inframe_deletion	In_Frame_Del	DEL	CACTGACAGAGAGCAAGTTTTCTGTGGCCTCAG	CACTGACAGAGAGCAAGTTTTCTGTGGCCTCAG	-	novel	NA	P-0025993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	59	335	0	ENST00000381652.3:c.3074_3106del	p.Ser1025_Asp1036delinsTyr	p.S1025_D1036delinsY	ENST00000381652	NM_004972.3	1025	tCACTGACAGAGAGCAAGTTTTCTGTGGCCTCAGat/tat	23/25	0.851680490974476	4	FACETS	0.638	0.55	0.732	0.159	0.137	0.183	SUBCLONAL	1	TRUE	0	0.857121311916657	4		335	401	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0025994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	417	704	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.527004661099525	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.527004661099525	1		704	1113	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9786991	9786991	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	285	593	2	ENST00000377346.4:c.3022G>A	p.Glu1008Lys	p.E1008K	ENST00000377346	NM_005026.3	1008	Gag/Aag	24/24	1	2	FACETS	0.963	0.905	1	0.963	0.905	1	CLONAL	1	TRUE	1	0.527004661099525	2		595	1123	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254193	133254193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146592584	NA	P-0025994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	307	558	1	ENST00000320574.5:c.691C>T	p.Arg231Cys	p.R231C	ENST00000320574	NM_006231.2	231	Cgc/Tgc	7/49	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.527004661099525	2		559	1067	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417858	138417858	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	323	611	0	ENST00000289153.2:c.1661A>G	p.Glu554Gly	p.E554G	ENST00000289153	NM_006219.2	554	gAa/gGa	11/22	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.527004661099525	2		611	1225	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683404	182683404	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	258	483	0	ENST00000292782.4:c.141T>A	p.Asn47Lys	p.N47K	ENST00000292782	NM_020640.2	47	aaT/aaA	2/7	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.527004661099525	2		483	953	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230818	66230818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs910705978	NA	P-0025994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	184	421	2	ENST00000273854.3:c.2153G>A	p.Arg718His	p.R718H	ENST00000273854	NM_004439.5	718	cGc/cAc	12/18	1	2	FACETS	0.934	0.864	1	0.934	0.864	1	CLONAL	1	TRUE	1	0.527004661099525	2		423	748	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0025995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	544	647	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.717201042017539	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.717201042017539	2		647	716	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256556	115256556	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	485	604	0	ENST00000369535.4:c.155T>G	p.Leu52Trp	p.L52W	ENST00000369535	NM_002524.4	52	tTg/tGg	3/7	0.717201042017539	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.717201042017539	2		604	642	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0025996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	439	592	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.452323187729686	2	FACETS	0.974	0.933	1	0.974	0.933	1	CLONAL	2	TRUE	0	0.452323187729686	2		592	996	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177450	56177450	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	128	401	0	ENST00000399503.3:c.2425del	p.His809ThrfsTer13	p.H809Tfs*13	ENST00000399503	NM_005921.1	808	tCc/tc	14/20	1	2	FACETS	0.864	0.785	0.947	0.864	0.785	0.947	CLONAL	1	TRUE	1	0.452323187729686	2		401	655	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879794	37879794	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	247	419	0	ENST00000269571.5:c.2089G>T	p.Val697Leu	p.V697L	ENST00000269571		697	Gtg/Ttg	18/27	0.452323187729686	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.452323187729686	2		419	503	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171704	36171704	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121912499	NA	P-0025996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	134	459	0	ENST00000300305.3:c.861C>A	p.Tyr287Ter	p.Y287*	ENST00000300305		287	taC/taA	7/8	1	2	FACETS	0.878	0.799	0.96	0.878	0.799	0.96	CLONAL	1	TRUE	1	0.452323187729686	2		459	675	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177555	56177555	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	136	361	0	ENST00000399503.3:c.2530del	p.Ser844ProfsTer13	p.S844Pfs*13	ENST00000399503	NM_005921.1	843	gTt/gt	14/20	1	2	FACETS	0.852	0.776	0.931	0.852	0.776	0.931	CLONAL	1	TRUE	1	0.452323187729686	2		361	706	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0025997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	433	333	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.890373579791236	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.890373579791236	2		333	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578471	7578471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	376	721	0	ENST00000269305.4:c.459del	p.Gly154AlafsTer16	p.G154Afs*16	ENST00000269305	NM_001126112.2	153	ccC/cc	5/11	0.890373579791236	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.890373579791236	1		721	412	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947540	48947540	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0025997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	273	471	0	ENST00000267163.4:c.1128-1G>C		p.X376_splice	ENST00000267163	NM_000321.2	376			0.890373579791236	1	FACETS	0.983	0.95	1	0.983	0.95	1	CLONAL	1	TRUE	0	0.890373579791236	1		471	346	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210774	2210774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772047684	NA	P-0025997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	283	602	1	ENST00000398665.3:c.1271G>A	p.Arg424Gln	p.R424Q	ENST00000398665	NM_032482.2	424	cGg/cAg	14/28	0.150412247236161	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.890373579791236	0		603	607	SUCCESS
CBL	867	MSKCC	GRCh37	11	119146795	119146795	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	262	474	0	ENST00000264033.4:c.958C>T	p.His320Tyr	p.H320Y	ENST00000264033	NM_005188.3	320	Cac/Tac	6/16	0.890373579791236	1	FACETS	0.992	0.958	1	0.992	0.958	1	CLONAL	1	TRUE	0	0.890373579791236	1		474	329	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123892075	123892075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	193	347	0	ENST00000330479.4:c.884G>A	p.Arg295Lys	p.R295K	ENST00000330479	NM_020382.3	295	aGa/aAa	8/9	0.115591905924675	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.890373579791236	0		347	370	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873302	136873302	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	230	374	0	ENST00000241393.3:c.196C>G	p.Gln66Glu	p.Q66E	ENST00000241393	NM_003467.2	66	Cag/Gag	2/2	0.890373579791236	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.890373579791236	1		374	286	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568555	41568555	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	279	602	0	ENST00000263253.7:c.4505C>G	p.Pro1502Arg	p.P1502R	ENST00000263253	NM_001429.3	1502	cCt/cGt	28/31	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.890373579791236	2		602	607	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220564	98220564	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	174	327	0	ENST00000331920.6:c.2899G>A	p.Glu967Lys	p.E967K	ENST00000331920	NM_000264.3	967	Gag/Aag	18/24	1	2	FACETS	0.928	0.865	0.993	0.928	0.865	0.993	CLONAL	1	TRUE	1	0.890373579791236	2		327	421	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	53	122	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.925	0.79	1	0.925	0.79	1	CLONAL	1	TRUE	1	0.255333917717045	2		122	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0026003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	167	591	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.255333917717045	3	FACETS	1	0.987	1	0.701	0.643	0.761	CLONAL	1	TRUE	1	0.255333917717045	3		591	1052	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	39	353	0	ENST00000335508.6:c.2704G>C	p.Glu902Gln	p.E902Q	ENST00000335508	NM_012433.2	902	Gaa/Caa	18/25	1	2	FACETS	0.668	0.554	0.796	0.668	0.554	0.796	SUBCLONAL	1	TRUE	1	0.255333917717045	2		353	457	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165969	47165969	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1461772708	NA	P-0026003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	40	329	0	ENST00000409792.3:c.157C>T	p.Arg53Ter	p.R53*	ENST00000409792	NM_014159.6	53	Cga/Tga	3/21	0.255333917717045	3	FACETS	0.608	0.504	0.724	0.304	0.252	0.362	SUBCLONAL	1	TRUE	1	0.255333917717045	3		329	581	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121151	11121151	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	59	577	0	ENST00000358026.2:c.2218G>T	p.Glu740Ter	p.E740*	ENST00000358026	NM_001128849.1	740	Gag/Tag	15/36	1	2	FACETS	0.445	0.381	0.515	0.445	0.381	0.515	SUBCLONAL	1	TRUE	1	0.255333917717045	2		577	1039	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115955	8115956	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0026003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	32	273	0	ENST00000346208.3:c.1304_1305dup	p.Ser436ProfsTer40	p.S436Pfs*40	ENST00000346208		434	cac/caCCc	6/6	1	2	FACETS	0.614	0.499	0.745	0.614	0.499	0.745	SUBCLONAL	1	TRUE	1	0.255333917717045	2		273	408	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561201	9561201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	60	342	0	ENST00000353224.5:c.581G>A	p.Arg194Lys	p.R194K	ENST00000353224	NM_177990.2	194	aGa/aAa	4/10	1	2	FACETS	0.585	0.502	0.674	0.585	0.502	0.674	SUBCLONAL	1	TRUE	1	0.255333917717045	2		342	804	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805422	46805422	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	175	606	0	ENST00000290295.7:c.534G>C	p.Trp178Cys	p.W178C	ENST00000290295	NM_006361.5	178	tgG/tgC	1/2	0.255333917717045	3	FACETS	0.884	0.815	0.957	0.884	0.815	0.957	CLONAL	2	TRUE	1	0.255333917717045	3		606	874	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182167	99182167	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	53	498	0	ENST00000074304.5:c.2232C>G	p.Phe744Leu	p.F744L	ENST00000074304	NM_001134224.1	744	ttC/ttG	21/26	1	2	FACETS	0.466	0.396	0.543	0.466	0.396	0.543	SUBCLONAL	1	TRUE	1	0.255333917717045	2		498	891	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266137	198266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	29	343	0	ENST00000335508.6:c.2483G>A	p.Arg828Lys	p.R828K	ENST00000335508	NM_012433.2	828	aGa/aAa	17/25	1	2	FACETS	0.517	0.415	0.634	0.517	0.415	0.634	SUBCLONAL	1	TRUE	1	0.255333917717045	2		343	439	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309890	30309890	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs770213331	NA	P-0026003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	48	386	0	ENST00000307677.4:c.132G>C	p.Glu44Asp	p.E44D	ENST00000307677	NM_138578.1	44	gaG/gaC	2/3	1	2	FACETS	0.56	0.473	0.657	0.56	0.473	0.657	SUBCLONAL	1	TRUE	1	0.255333917717045	2		386	671	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52649382	52649382	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	80	491	0	ENST00000394830.3:c.1909C>T	p.Pro637Ser	p.P637S	ENST00000394830	NM_018313.4	637	Ccc/Tcc	16/30	0.255333917717045	3	FACETS	0.956	0.841	1	0.478	0.42	0.54	CLONAL	1	TRUE	1	0.255333917717045	3		491	739	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188943	32188943	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	188	589	0	ENST00000375023.3:c.611C>A	p.Pro204His	p.P204H	ENST00000375023	NM_004557.3	204	cCc/cAc	4/30	0.255333917717045	3	FACETS	0.86	0.795	0.928	0.86	0.795	0.928	CLONAL	2	TRUE	1	0.255333917717045	3		589	965	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44733223	44733225	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	TAC	TAC	AGTAA	novel	NA	P-0026003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	72	258	0	ENST00000377967.4:c.215_217delinsAGTAA	p.Leu72GlnfsTer2	p.L72Qfs*2	ENST00000377967	NM_021140.2	72	cTACtg/cAGTAAtg	2/29	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.255333917717045	2		258	489	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971153	21971153	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913383	NA	P-0026004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	224	526	1	ENST00000304494.5:c.205G>T	p.Glu69Ter	p.E69*	ENST00000304494	NM_000077.4	69	Gag/Tag	2/3	0.332577305583405	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.332577305583405	2		527	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	522	712	0	ENST00000269305.4:c.641del	p.His214LeufsTer33	p.H214Lfs*33	ENST00000269305	NM_001126112.2	214	cAt/ct	6/11	0.259654581224199	4	FACETS	1	0.992	1			1	CLONAL	3	TRUE	NA	0.332577305583405	4		712	1244	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210541	5210541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1440460687	NA	P-0026004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	82	653	1	ENST00000357368.4:c.5426C>T	p.Pro1809Leu	p.P1809L	ENST00000357368	NM_002850.3	1809	cCg/cTg	35/38	1	2	FACETS	0.588	0.517	0.663	0.588	0.517	0.663	SUBCLONAL	1	TRUE	1	0.332577305583405	2		654	839	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837911	156837911	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	373	895	1	ENST00000524377.1:c.444C>A	p.Asn148Lys	p.N148K	ENST00000524377	NM_002529.3	148	aaC/aaA	5/17	0.332577305583405	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.332577305583405	3		896	1230	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14303211	14303212	+	missense_variant	Missense_Mutation	DNP	TC	TC	CA	novel	NA	P-0026004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	153	687	1	ENST00000256196.4:c.463_464delinsTG	p.Glu155Trp	p.E155W	ENST00000256196		155	GAg/TGg	5/6	0.332577305583405	3	FACETS	0.946	0.864	1	0.473	0.432	0.517	CLONAL	1	TRUE	1	0.332577305583405	3		688	1134	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123898	46123898	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	87	411	0	ENST00000334344.6:c.164del	p.Thr55IlefsTer3	p.T55Ifs*3	ENST00000334344	NM_152641.2	55	aCt/at	2/21	0.259654581224199	4	FACETS	1	0.941	1			1	CLONAL	1	TRUE	NA	0.332577305583405	4		411	635	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554596	63554596	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	46	488	0	ENST00000307078.5:c.143C>A	p.Pro48His	p.P48H	ENST00000307078	NM_004655.3	48	cCc/cAc	2/11	0.332577305583405	4	FACETS	0.401	0.336	0.473	0.1	0.084	0.119	SUBCLONAL	1	TRUE	0	0.332577305583405	4		488	919	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374348	31374348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	226	670	0	ENST00000328111.2:c.347G>A	p.Arg116Lys	p.R116K	ENST00000328111	NM_006892.3	116	aGg/aAg	5/23	0.332577305583405	3	FACETS	0.776	0.723	0.831	0.776	0.723	0.831	SUBCLONAL	2	TRUE	1	0.332577305583405	3		670	1021	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467956	50467957	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACGGA	novel	NA	P-0026004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	137	543	0	ENST00000331340.3:c.1192_1196dup	p.Asp399GlufsTer18	p.D399Efs*18	ENST00000331340	NM_006060.4	397	-/ACGGA	8/8	0.177721223862549	5	FACETS	1	0.986	1	0.495	0.45	0.542	INDETERMINATE	1	TRUE	2	0.332577305583405	5		543	831	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453125	140453138	+	protein_altering_variant	In_Frame_Del	DEL	ATCGAGATTTCACT	ATCGAGATTTCACT	CATCA	novel	NA	P-0026004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	87	533	2	ENST00000288602.6:c.1797_1810delinsTGATG	p.Val600_Trp604delinsAspGly	p.V600_W604delinsDG	ENST00000288602	NM_004333.4	599	acAGTGAAATCTCGATgg/acTGATGgg	15/18	1	2	FACETS	0.738	0.653	0.829	0.738	0.653	0.829	SUBCLONAL	1	TRUE	1	0.332577305583405	2		535	709	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572092	64572093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs767319284	NA	P-0026006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	335	581	3	ENST00000312049.6:c.1546dup	p.Arg516ProfsTer15	p.R516Pfs*15	ENST00000312049	NM_130799.2	516	cgg/cCgg	10/10	0.748732216685218	1	FACETS	0.743	0.707	0.779	0.743	0.707	0.779	SUBCLONAL	1	TRUE	0	0.748732216685218	1		584	754	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600022	10600023	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0026006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	494	741	2	ENST00000171111.5:c.1553_1554del	p.Cys518TyrfsTer8	p.C518Yfs*8	ENST00000171111	NM_203500.1	518	tGT/t	5/6	0.748732216685218	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.748732216685218	1		743	808	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	67	122	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.542	0.471	0.62	0.542	0.471	0.62	SUBCLONAL	1	TRUE	1	0.344573252219988	2		122	717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0026007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	228	604	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.344573252219988	2		604	1081	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205268	46205268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	113	521	0	ENST00000334344.6:c.353del	p.Pro118GlnfsTer97	p.P118Qfs*97	ENST00000334344	NM_152641.2	118	Cca/ca	4/21	1	2	FACETS	0.671	0.602	0.743	0.671	0.602	0.743	SUBCLONAL	1	TRUE	1	0.344573252219988	2		521	978	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240288	41240288	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	51	390	0	ENST00000379561.5:c.62G>T	p.Arg21Leu	p.R21L	ENST00000379561	NM_002015.3	21	cGc/cTc	1/3	1	2	FACETS	0.367	0.311	0.429	0.367	0.311	0.429	SUBCLONAL	1	TRUE	1	0.344573252219988	2		390	806	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214148	36214148	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1268	525	764	0	ENST00000222270.7:c.2974G>T	p.Gly992Cys	p.G992C	ENST00000222270	NM_014727.1	992	Ggc/Tgc	6/37	0.26318194730695	4	FACETS	1	0.992	1	0.762	0.729	0.795	CLONAL	2	TRUE	1	0.344573252219988	4		764	1793	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905968	50905968	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	68	692	0	ENST00000440232.2:c.940A>T	p.Ser314Cys	p.S314C	ENST00000440232	NM_002691.3	314	Agc/Tgc	8/27	NA	2	FACETS	0.358	0.311	0.411			1	INDETERMINATE	1	TRUE	NA	0.344573252219988	2		692	1101	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715770	61715770	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	42	368	0	ENST00000401558.2:c.2159T>C	p.Val720Ala	p.V720A	ENST00000401558	NM_003400.3	720	gTa/gCa	18/25	1	2	FACETS	0.334	0.278	0.397	0.334	0.278	0.397	SUBCLONAL	1	TRUE	1	0.344573252219988	2		368	730	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	193	122	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.999	0.927	1	0.999	0.927	1	CLONAL	1	TRUE	1	0.542183692029926	2		122	713	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561263	9561263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769939031	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	168	367	0	ENST00000353224.5:c.519G>A	p.Met173Ile	p.M173I	ENST00000353224	NM_177990.2	173	atG/atA	4/10	1	2	FACETS	0.882	0.812	0.953	0.882	0.812	0.953	CLONAL	1	TRUE	1	0.542183692029926	2		367	703	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554008	63554008	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199798353	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	217	394	0	ENST00000307078.5:c.731C>T	p.Ser244Leu	p.S244L	ENST00000307078	NM_004655.3	244	tCg/tTg	2/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.542183692029926	2		394	779	SUCCESS
MET	4233	MSKCC	GRCh37	7	116409831	116409831	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778115147	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	142	332	0	ENST00000397752.3:c.2716G>A	p.Glu906Lys	p.E906K	ENST00000397752	NM_000245.2	906	Gag/Aag	12/21	1	2	FACETS	0.949	0.869	1	0.949	0.869	1	CLONAL	1	TRUE	1	0.542183692029926	2		332	552	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566827	212566827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202247795	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	141	290	0	ENST00000342788.4:c.1354G>A	p.Glu452Lys	p.E452K	ENST00000342788	NM_005235.2	452	Gaa/Aaa	12/28	1	2	FACETS	0.996	0.913	1	0.996	0.913	1	CLONAL	1	TRUE	1	0.542183692029926	2		290	522	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556367	29556367	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	246	421	2	ENST00000356175.3:c.2734C>T	p.Gln912Ter	p.Q912*	ENST00000356175	NM_000267.3	912	Caa/Taa	21/57	0.524732078165257	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.542183692029926	1		423	651	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945795	17945795	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	294	608	0	ENST00000458235.1:c.2065C>T	p.Pro689Ser	p.P689S	ENST00000458235	NM_000215.3	689	Ccc/Tcc	16/24	0.540793101099851	2	FACETS	1	0.956	1	0.509	0.479	0.539	CLONAL	1	TRUE	0	0.542183692029926	2		608	1066	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367278	50367278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	180	390	0	ENST00000331340.3:c.85G>A	p.Glu29Lys	p.E29K	ENST00000331340	NM_006060.4	29	Gag/Aag	3/8	1	2	FACETS	0.929	0.859	1	0.929	0.859	1	CLONAL	1	TRUE	1	0.542183692029926	2		390	715	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944527	40944527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371433526	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	207	547	3	ENST00000373198.4:c.1975G>A	p.Asp659Asn	p.D659N	ENST00000373198	NM_133170.3	659	Gat/Aat	12/32	1	2	FACETS	0.913	0.849	0.98	0.913	0.849	0.98	CLONAL	1	TRUE	1	0.542183692029926	2		550	836	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044542	47044542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782739450	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	71	671	0	ENST00000377604.3:c.2039G>A	p.Arg680Gln	p.R680Q	ENST00000377604	NM_001204468.1	680	cGa/cAa	18/24	0.402426378213835	1	FACETS	0.204	0.178	0.233	0.204	0.178	0.233	SUBCLONAL	1	TRUE	0	0.542183692029926	1		671	934	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586422	189586422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866267914	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	155	447	0	ENST00000264731.3:c.1046G>A	p.Gly349Glu	p.G349E	ENST00000264731	NM_003722.4	349	gGa/gAa	8/14	1	2	FACETS	0.786	0.721	0.854	0.786	0.721	0.854	SUBCLONAL	1	TRUE	1	0.542183692029926	2		447	727	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873748	35873748	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs766555082	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	140	331	0	ENST00000303115.3:c.704C>T	p.Ser235Leu	p.S235L	ENST00000303115	NM_002185.3	235	tCa/tTa	5/8	1	2	FACETS	0.995	0.911	1	0.995	0.911	1	CLONAL	1	TRUE	1	0.542183692029926	2		331	519	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372152	55372152	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	247	463	0	ENST00000297316.4:c.842C>T	p.Pro281Leu	p.P281L	ENST00000297316	NM_022454.3	281	cCc/cTc	2/2	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.542183692029926	2		463	896	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995569	68995569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775560862	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	262	599	1	ENST00000288368.4:c.1973C>T	p.Ser658Leu	p.S658L	ENST00000288368	NM_024870.2	658	tCg/tTg	18/40	1	2	FACETS	0.94	0.881	1	0.94	0.881	1	CLONAL	1	TRUE	1	0.542183692029926	2		600	1028	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852443	42852443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139092674	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	263	541	0	ENST00000398585.3:c.643G>A	p.Glu215Lys	p.E215K	ENST00000398585	NM_001135099.1	215	Gag/Aag	6/14	0.542183692029926	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.542183692029926	1		541	691	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813089	76813089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057517707	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	243	576	0	ENST00000373344.5:c.6532C>T	p.Arg2178Trp	p.R2178W	ENST00000373344	NM_000489.3	2178	Cgg/Tgg	30/35	0.402426378213835	1	FACETS	0.888	0.833	0.944	0.888	0.833	0.944	CLONAL	1	TRUE	0	0.542183692029926	1		576	736	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359404	118359404	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	212	439	0	ENST00000534358.1:c.4408C>T	p.Gln1470Ter	p.Q1470*	ENST00000534358	NM_005933.3	1470	Cag/Tag	11/36	1	2	FACETS	0.997	0.929	1	0.997	0.929	1	CLONAL	1	TRUE	1	0.542183692029926	2		439	784	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716070	243716070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	204	531	1	ENST00000263826.5:c.1124C>T	p.Ser375Leu	p.S375L	ENST00000263826	NM_005465.4	375	tCa/tTa	10/13	0.153470774687297	5	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.542183692029926	5		532	1069	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166436	118166436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764287568	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	150	321	0	ENST00000369448.3:c.946G>A	p.Glu316Lys	p.E316K	ENST00000369448	NM_017709.3	316	Gag/Aag	2/2	1	2	FACETS	0.947	0.87	1	0.947	0.87	1	CLONAL	1	TRUE	1	0.542183692029926	2		321	584	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970945	70970945	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1242917883	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	295	703	2	ENST00000276594.2:c.1316G>A	p.Arg439Gln	p.R439Q	ENST00000276594	NM_024504.3	439	cGa/cAa	6/8	1	2	FACETS	0.977	0.92	1	0.977	0.92	1	CLONAL	1	TRUE	1	0.542183692029926	2		705	1114	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056226	27056226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	295	556	0	ENST00000324856.7:c.1222C>T	p.Pro408Ser	p.P408S	ENST00000324856	NM_006015.4	408	Ccg/Tcg	2/20	0.542183692029926	3	FACETS	1	0.956	1	0.511	0.48	0.543	CLONAL	1	TRUE	1	0.542183692029926	3		556	1354	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100857	27100857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	236	436	0	ENST00000324856.7:c.4139C>T	p.Pro1380Leu	p.P1380L	ENST00000324856	NM_006015.4	1380	cCt/cTt	18/20	0.542183692029926	3	FACETS	0.952	0.888	1	0.476	0.444	0.51	CLONAL	1	TRUE	1	0.542183692029926	3		436	1162	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363400	40363400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	280	636	0	ENST00000397332.2:c.829G>A	p.Glu277Lys	p.E277K	ENST00000397332	NM_001033082.2	277	Gaa/Aaa	3/3	0.542183692029926	3	FACETS	1	0.969	1	0.526	0.493	0.56	CLONAL	1	TRUE	1	0.542183692029926	3		636	1248	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814658	43814658	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	210	418	0	ENST00000372470.3:c.1453A>C	p.Thr485Pro	p.T485P	ENST00000372470	NM_005373.2	485	Acc/Ccc	9/12	0.542183692029926	3	FACETS	0.983	0.912	1	0.491	0.456	0.528	CLONAL	1	TRUE	1	0.542183692029926	3		418	1002	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797121	45797122	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1210	340	705	0	ENST00000450313.1:c.1293_1294delinsTT	p.Pro432Ser	p.P432S	ENST00000450313	NM_012222.2	431	ctCCca/ctTTca	13/16	0.542183692029926	3	FACETS	1	0.964	1	0.514	0.485	0.544	CLONAL	1	TRUE	1	0.542183692029926	3		705	1550	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506378	120506379	+	missense_variant	Missense_Mutation	DNP	AG	AG	CA	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	261	558	1	ENST00000256646.2:c.1733_1734delinsTG	p.Pro578Leu	p.P578L	ENST00000256646	NM_024408.3	578	cCT/cTG	11/34	1	2	FACETS	0.975	0.915	1	0.975	0.915	1	CLONAL	1	TRUE	1	0.542183692029926	2		559	987	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015432	176015432	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	115	410	0	ENST00000367669.3:c.1306T>G	p.Phe436Val	p.F436V	ENST00000367669	NM_022457.5	436	Ttt/Gtt	12/20	1	2	FACETS	0.746	0.674	0.821	0.746	0.674	0.821	SUBCLONAL	1	TRUE	1	0.542183692029926	2		410	569	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119441	193119441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	181	431	0	ENST00000367435.3:c.836C>T	p.Thr279Ile	p.T279I	ENST00000367435	NM_024529.4	279	aCt/aTt	9/17	1	2	FACETS	0.927	0.858	0.999	0.927	0.858	0.999	CLONAL	1	TRUE	1	0.542183692029926	2		431	720	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604641	43604641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	247	551	0	ENST00000355710.3:c.1226C>T	p.Ser409Phe	p.S409F	ENST00000355710	NM_020975.4	409	tCc/tTc	6/20	1	2	FACETS	0.978	0.915	1	0.978	0.915	1	CLONAL	1	TRUE	1	0.542183692029926	2		551	932	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114724348	114724348	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	231	513	0	ENST00000543371.1:c.415G>T	p.Ala139Ser	p.A139S	ENST00000543371	NM_001198531.1	139	Gcg/Tcg	4/14	1	2	FACETS	0.911	0.851	0.974	0.911	0.851	0.974	CLONAL	1	TRUE	1	0.542183692029926	2		513	935	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239535	123239535	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs763622845	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	399	832	1	ENST00000358487.5:c.2302G>A	p.Glu768Lys	p.E768K	ENST00000358487	NM_000141.4	768	Gaa/Aaa	18/18	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.542183692029926	2		833	1366	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316076	14316076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782490571	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	159	289	0	ENST00000256196.4:c.349C>T	p.Arg117Cys	p.R117C	ENST00000256196		117	Cgt/Tgt	4/6	1	2	FACETS	0.991	0.912	1	0.991	0.912	1	CLONAL	1	TRUE	1	0.542183692029926	2		289	592	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911911	94911911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	265	631	0	ENST00000536441.1:c.1019G>A	p.Arg340Lys	p.R340K	ENST00000536441	NM_144665.3	340	aGa/aAa	7/10	1	2	FACETS	0.873	0.818	0.929	0.873	0.818	0.929	CLONAL	1	TRUE	1	0.542183692029926	2		631	1120	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163465	108163466	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	258	534	0	ENST00000278616.4:c.4556_4557del	p.Val1519AspfsTer11	p.V1519Dfs*11	ENST00000278616	NM_000051.3	1519	gTT/g	30/63	1	2	FACETS	0.89	0.834	0.948	0.89	0.834	0.948	CLONAL	1	TRUE	1	0.542183692029926	2		534	1069	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369169	118369169	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	213	442	1	ENST00000534358.1:c.5887C>T	p.Arg1963Ter	p.R1963*	ENST00000534358	NM_005933.3	1963	Cga/Tga	22/36	1	2	FACETS	0.933	0.869	1	0.933	0.869	1	CLONAL	1	TRUE	1	0.542183692029926	2		443	842	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374532	118374532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	151	344	0	ENST00000534358.1:c.7925C>T	p.Ser2642Phe	p.S2642F	ENST00000534358	NM_005933.3	2642	tCc/tTc	27/36	1	2	FACETS	0.979	0.899	1	0.979	0.899	1	CLONAL	1	TRUE	1	0.542183692029926	2		344	569	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1039291	1039291	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	260	607	0	ENST00000358495.3:c.206A>G	p.His69Arg	p.H69R	ENST00000358495	NM_134424.2	69	cAt/cGt	4/12	1	2	FACETS	0.886	0.83	0.944	0.886	0.83	0.944	CLONAL	1	TRUE	1	0.542183692029926	2		607	1082	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287504	46287505	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	201	402	1	ENST00000334344.6:c.5363_5363+1delinsAA		p.X1788_splice	ENST00000334344	NM_152641.2	1788		20/21	0.537466044968741	1	FACETS	0.958	0.895	1	0.958	0.895	1	CLONAL	1	TRUE	0	0.542183692029926	1		403	564	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926851	112926852	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	315	713	2	ENST00000351677.2:c.1471_1472delinsTT	p.Pro491Phe	p.P491F	ENST00000351677	NM_002834.3	491	CCc/TTc	13/16	0.542183692029926	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.542183692029926	1		715	806	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26911748	26911748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	135	398	0	ENST00000381527.3:c.173G>A	p.Gly58Glu	p.G58E	ENST00000381527	NM_001260.1	58	gGg/gAg	2/13	1	2	FACETS	0.635	0.578	0.696	0.635	0.578	0.696	SUBCLONAL	1	TRUE	1	0.542183692029926	2		398	784	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953773	48953773	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	93	260	0	ENST00000267163.4:c.1376C>T	p.Ser459Phe	p.S459F	ENST00000267163	NM_000321.2	459	tCc/tTc	14/27	1	2	FACETS	0.789	0.705	0.877	0.789	0.705	0.877	SUBCLONAL	1	TRUE	1	0.542183692029926	2		260	435	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436407	110436407	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	170	615	0	ENST00000375856.3:c.1994G>C	p.Ser665Thr	p.S665T	ENST00000375856	NM_003749.2	665	aGt/aCt	1/2	1	2	FACETS	0.698	0.642	0.756	0.698	0.642	0.756	SUBCLONAL	1	TRUE	1	0.542183692029926	2		615	899	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42057125	42057125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	165	568	0	ENST00000219905.7:c.7786C>T	p.Leu2596Phe	p.L2596F	ENST00000219905	NM_001164273.1	2596	Ctt/Ttt	23/24	1	2	FACETS	0.596	0.547	0.648	0.596	0.547	0.648	SUBCLONAL	1	TRUE	1	0.542183692029926	2		568	1021	SUCCESS
BLM	641	MSKCC	GRCh37	15	91333954	91333954	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	250	548	0	ENST00000355112.3:c.2899C>T	p.Pro967Ser	p.P967S	ENST00000355112	NM_000057.2	967	Cct/Tct	15/22	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.542183692029926	2		548	905	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100431	2100431	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1430159201	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	285	509	1	ENST00000219476.3:c.169C>T	p.Arg57Cys	p.R57C	ENST00000219476	NM_000548.3	57	Cgc/Tgc	3/42	0.542183692029926	1	FACETS	0.925	0.873	0.979	0.925	0.873	0.979	CLONAL	1	TRUE	0	0.542183692029926	1		510	828	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822283	72822284	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	294	691	1	ENST00000268489.5:c.9891_9892delinsAA	p.Asp3298Asn	p.D3298N	ENST00000268489	NM_006885.3	3297	tcGGac/tcAAac	10/10	0.542183692029926	1	FACETS	0.891	0.841	0.942	0.891	0.841	0.942	CLONAL	1	TRUE	0	0.542183692029926	1		692	887	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579478	7579480	+	frameshift_variant	Frame_Shift_Del	DEL	GCA	GCA	AC	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	284	661	2	ENST00000269305.4:c.207_209delinsGT	p.Ala70PhefsTer53	p.A70Ffs*53	ENST00000269305	NM_001126112.2	69	gcTGCt/gcGTt	4/11	0.524732078165257	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.542183692029926	1		663	753	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867528	78867528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759154872	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	277	561	0	ENST00000306801.3:c.2264C>T	p.Ser755Phe	p.S755F	ENST00000306801	NM_020761.2	755	tCc/tTc	20/34	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.542183692029926	2		561	946	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56402487	56402487	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	175	349	0	ENST00000348428.3:c.1529T>G	p.Ile510Ser	p.I510S	ENST00000348428	NM_006785.3	510	aTc/aGc	13/17	0.402426378213835	1	FACETS	0.834	0.773	0.897	0.834	0.773	0.897	CLONAL	1	TRUE	0	0.542183692029926	1		349	564	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1206946	1206946	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	242	563	0	ENST00000326873.7:c.34T>C	p.Phe12Leu	p.F12L	ENST00000326873	NM_000455.4	12	Ttc/Ctc	1/10	0.540793101099851	2	FACETS	0.916	0.856	0.977	0.458	0.428	0.489	CLONAL	1	TRUE	0	0.542183692029926	2		563	975	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094885	11094885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	527	670	0	ENST00000358026.2:c.58C>T	p.Pro20Ser	p.P20S	ENST00000358026	NM_001128849.1	20	Cct/Tct	2/36	0.540793101099851	2	FACETS	0.926	0.892	0.96	0.926	0.892	0.96	CLONAL	2	TRUE	0	0.542183692029926	2		670	1050	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375438	15375438	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	302	594	0	ENST00000263377.2:c.989C>T	p.Pro330Leu	p.P330L	ENST00000263377	NM_058243.2	330	cCt/cTt	6/20	0.540793101099851	2	FACETS	1	0.974	1	0.528	0.498	0.559	CLONAL	1	TRUE	0	0.542183692029926	2		594	1055	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210921	36210922	+	missense_variant	Missense_Mutation	DNP	AG	AG	TA	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	282	749	2	ENST00000222270.7:c.672_673delinsTA	p.Gly225Arg	p.G225R	ENST00000222270	NM_014727.1	224	ccAGga/ccTAga	3/37	1	2	FACETS	0.879	0.825	0.934	0.879	0.825	0.934	CLONAL	1	TRUE	1	0.542183692029926	2		751	1184	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744044	41744044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	288	632	1	ENST00000301178.4:c.979G>A	p.Glu327Lys	p.E327K	ENST00000301178	NM_021913.4	327	Gag/Aag	7/20	1	2	FACETS	0.991	0.932	1	0.991	0.932	1	CLONAL	1	TRUE	1	0.542183692029926	2		633	1072	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758775	41758775	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374737642	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	295	668	0	ENST00000301178.4:c.1829G>A	p.Arg610Gln	p.R610Q	ENST00000301178	NM_021913.4	610	cGa/cAa	16/20	1	2	FACETS	0.959	0.902	1	0.959	0.902	1	CLONAL	1	TRUE	1	0.542183692029926	2		668	1135	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793469	42793469	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764440532	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	269	653	1	ENST00000575354.2:c.1271C>T	p.Ser424Phe	p.S424F	ENST00000575354	NM_015125.3	424	tCt/tTt	8/20	1	2	FACETS	0.943	0.885	1	0.943	0.885	1	CLONAL	1	TRUE	1	0.542183692029926	2		654	1052	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902140	50902140	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs922648487	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	219	563	1	ENST00000440232.2:c.32C>T	p.Pro11Leu	p.P11L	ENST00000440232	NM_002691.3	11	cCc/cTc	2/27	1	2	FACETS	0.942	0.877	1	0.942	0.877	1	CLONAL	1	TRUE	1	0.542183692029926	2		564	858	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718777	190718777	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	211	290	0	ENST00000441310.2:c.935C>T	p.Pro312Leu	p.P312L	ENST00000441310	NM_000534.4	312	cCa/cTa	8/13	0.21428449126718	3	FACETS	1	0.992	1	0.743	0.693	0.794	INDETERMINATE	1	TRUE	1	0.542183692029926	3		290	666	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248768	212248768	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866912060	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	114	249	0	ENST00000342788.4:c.3499G>A	p.Glu1167Lys	p.E1167K	ENST00000342788	NM_005235.2	1167	Gag/Aag	28/28	1	2	FACETS	0.983	0.891	1	0.983	0.891	1	CLONAL	1	TRUE	1	0.542183692029926	2		249	428	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440012	220440012	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1233392744	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	406	798	0	ENST00000243786.2:c.865C>T	p.His289Tyr	p.H289Y	ENST00000243786	NM_002191.3	289	Cac/Tac	2/2	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.542183692029926	2		798	1431	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713398	40713398	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	255	584	0	ENST00000373198.4:c.4117C>T	p.Leu1373Phe	p.L1373F	ENST00000373198	NM_133170.3	1373	Ctc/Ttc	30/32	1	2	FACETS	0.94	0.88	1	0.94	0.88	1	CLONAL	1	TRUE	1	0.542183692029926	2		584	1001	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62305312	62305312	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772044888	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	327	760	1	ENST00000360203.5:c.785C>T	p.Ser262Leu	p.S262L	ENST00000360203	NM_001283009.1	262	tCg/tTg	10/35	1	2	FACETS	0.956	0.902	1	0.956	0.902	1	CLONAL	1	TRUE	1	0.542183692029926	2		761	1262	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458329	12458329	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1364613522	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	240	591	0	ENST00000287820.6:c.946C>T	p.Arg316Cys	p.R316C	ENST00000287820	NM_015869.4	316	Cgc/Tgc	6/7	1	2	FACETS	0.855	0.798	0.913	0.855	0.798	0.913	CLONAL	1	TRUE	1	0.542183692029926	2		591	1036	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162889	47162890	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	166	399	1	ENST00000409792.3:c.3236_3237delinsTT	p.Pro1079Leu	p.P1079L	ENST00000409792	NM_014159.6	1079	cCC/cTT	3/21	1	2	FACETS	0.887	0.818	0.96	0.887	0.818	0.96	CLONAL	1	TRUE	1	0.542183692029926	2		400	690	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932976	49932976	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	259	632	1	ENST00000296474.3:c.2968C>T	p.Pro990Ser	p.P990S	ENST00000296474	NM_002447.2	990	Cct/Tct	13/20	1	2	FACETS	0.927	0.868	0.987	0.927	0.868	0.987	CLONAL	1	TRUE	1	0.542183692029926	2		633	1031	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936329	49936329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	236	542	1	ENST00000296474.3:c.1519G>A	p.Asp507Asn	p.D507N	ENST00000296474	NM_002447.2	507	Gac/Aac	3/20	1	2	FACETS	0.925	0.864	0.988	0.925	0.864	0.988	CLONAL	1	TRUE	1	0.542183692029926	2		543	941	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119595288	119595288	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	126	339	0	ENST00000316626.5:c.881C>T	p.Pro294Leu	p.P294L	ENST00000316626		294	cCt/cTt	8/12	1	2	FACETS	0.906	0.825	0.991	0.906	0.825	0.991	CLONAL	1	TRUE	1	0.542183692029926	2		339	513	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961822	55961822	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	247	423	0	ENST00000263923.4:c.2739G>A	p.Met913Ile	p.M913I	ENST00000263923	NM_002253.2	913	atG/atA	20/30	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.542183692029926	2		423	770	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264619	1264619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	311	646	0	ENST00000310581.5:c.2743G>A	p.Gly915Ser	p.G915S	ENST00000310581	NM_198253.2	915	Ggt/Agt	11/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.542183692029926	2		646	1126	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526597	31526597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749384962	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	247	448	1	ENST00000344624.3:c.443C>T	p.Pro148Leu	p.P148L	ENST00000344624		148	cCt/cTt	2/33	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.542183692029926	2		449	811	SUCCESS
APC	324	MSKCC	GRCh37	5	112176362	112176362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	141	278	0	ENST00000257430.4:c.5071C>T	p.Pro1691Ser	p.P1691S	ENST00000257430	NM_000038.5	1691	Cct/Tct	16/16	1	2	FACETS	0.974	0.892	1	0.974	0.892	1	CLONAL	1	TRUE	1	0.542183692029926	2		278	534	SUCCESS
APC	324	MSKCC	GRCh37	5	112176861	112176861	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	161	314	0	ENST00000257430.4:c.5570C>T	p.Ser1857Leu	p.S1857L	ENST00000257430	NM_000038.5	1857	tCa/tTa	16/16	1	2	FACETS	0.915	0.842	0.991	0.915	0.842	0.991	CLONAL	1	TRUE	1	0.542183692029926	2		314	649	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057250	180057250	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	285	671	0	ENST00000261937.6:c.488C>T	p.Pro163Leu	p.P163L	ENST00000261937	NM_182925.4	163	cCc/cTc	4/30	1	2	FACETS	0.946	0.89	1	0.946	0.89	1	CLONAL	1	TRUE	1	0.542183692029926	2		671	1111	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710821	117710821	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	211	377	0	ENST00000368508.3:c.1451G>A	p.Gly484Asp	p.G484D	ENST00000368508	NM_002944.2	484	gGc/gAc	12/43	0.542183692029926	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.542183692029926	1		377	554	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730086	41730086	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	204	450	0	ENST00000242208.4:c.443C>T	p.Ser148Leu	p.S148L	ENST00000242208	NM_002192.2	148	tCa/tTa	3/3	1	2	FACETS	0.966	0.898	1	0.966	0.898	1	CLONAL	1	TRUE	1	0.542183692029926	2		450	779	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481412	140481412	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913353	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	176	451	0	ENST00000288602.6:c.1396G>C	p.Gly466Arg	p.G466R	ENST00000288602	NM_004333.4	466	Gga/Cga	11/18	1	2	FACETS	0.937	0.866	1	0.937	0.866	1	CLONAL	1	TRUE	1	0.542183692029926	2		451	693	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031669	69031669	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	190	349	0	ENST00000288368.4:c.3424G>A	p.Asp1142Asn	p.D1142N	ENST00000288368	NM_024870.2	1142	Gat/Aat	28/40	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.542183692029926	2		349	672	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054612	5054612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	133	344	0	ENST00000381652.3:c.664C>T	p.His222Tyr	p.H222Y	ENST00000381652	NM_004972.3	222	Cat/Tat	7/25	0.542183692029926	1	FACETS	0.87	0.798	0.945	0.87	0.798	0.945	CLONAL	1	TRUE	0	0.542183692029926	1		344	411	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449764	8449764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	257	497	0	ENST00000356435.5:c.3949G>A	p.Asp1317Asn	p.D1317N	ENST00000356435		1317	Gac/Aac	23/35	0.542183692029926	1	FACETS	0.984	0.927	1	0.984	0.927	1	CLONAL	1	TRUE	0	0.542183692029926	1		497	702	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87366934	87366934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	323	647	0	ENST00000277120.3:c.1330G>A	p.Gly444Arg	p.G444R	ENST00000277120		444	Gga/Aga	12/19	0.542183692029926	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.542183692029926	1		647	843	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430809	47430809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	78	633	0	ENST00000377045.4:c.1774G>A	p.Asp592Asn	p.D592N	ENST00000377045	NM_001654.4	592	Gat/Aat	16/16	0.402426378213835	1	FACETS	0.221	0.194	0.251	0.221	0.194	0.251	SUBCLONAL	1	TRUE	0	0.542183692029926	1		633	948	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410077	63410077	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	94	625	0	ENST00000330258.3:c.3090G>A	p.Met1030Ile	p.M1030I	ENST00000330258	NM_152424.3	1030	atG/atA	2/2	0.402426378213835	1	FACETS	0.309	0.274	0.346	0.309	0.274	0.346	SUBCLONAL	1	TRUE	0	0.542183692029926	1		625	818	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938788	76938788	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1557140492	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	60	574	0	ENST00000373344.5:c.1960C>G	p.Arg654Gly	p.R654G	ENST00000373344	NM_000489.3	654	Cga/Gga	9/35	0.402426378213835	1	FACETS	0.214	0.183	0.247	0.214	0.183	0.247	SUBCLONAL	1	TRUE	0	0.542183692029926	1		574	755	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195705	123195705	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	68	599	0	ENST00000218089.9:c.1619G>A	p.Gly540Glu	p.G540E	ENST00000218089	NM_001042749.1	540	gGa/gAa	17/35	0.402426378213835	1	FACETS	0.223	0.193	0.255	0.223	0.193	0.255	SUBCLONAL	1	TRUE	0	0.542183692029926	1		599	820	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552891	106552891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771056895	NA	P-0026009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	125	694	2	ENST00000369096.4:c.856C>T	p.Arg286Cys	p.R286C	ENST00000369096	NM_001198.3	286	Cgt/Tgt	5/7	1	2	FACETS	0.921	0.832	1	0.921	0.832	1	CLONAL	1	TRUE	1	0.23	2		696	1180	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303621	65303621	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	43	516	0	ENST00000342505.4:c.3134T>G	p.Val1045Gly	p.V1045G	ENST00000342505	NM_002227.2	1045	gTg/gGg	22/25	1	2	FACETS	0.526	0.439	0.623	0.526	0.439	0.623	SUBCLONAL	1	TRUE	1	0.23	2		516	711	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40709551	40709551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568484928	NA	P-0026010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	57	537	0	ENST00000373198.4:c.4351G>A	p.Glu1451Lys	p.E1451K	ENST00000373198	NM_133170.3	1451	Gag/Aag	32/32	0.305111807736142	1	FACETS	0.389	0.333	0.45	0.389	0.333	0.45	SUBCLONAL	1	TRUE	0	0.330198295669399	1		537	741	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983136	201983136	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	44	612	0	ENST00000359651.3:c.985C>G	p.Leu329Val	p.L329V	ENST00000359651		329	Ctg/Gtg	7/8	0.312496513909824	1	FACETS	0.34	0.284	0.402	0.34	0.284	0.402	SUBCLONAL	1	TRUE	0	0.330198295669399	1		612	655	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636352	21636352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	65	665	0	ENST00000421138.2:c.658G>A	p.Glu220Lys	p.E220K	ENST00000421138		220	Gaa/Aaa	7/16	0.123256305029491	3	FACETS	0.436	0.376	0.5	0.218	0.188	0.25	INDETERMINATE	1	TRUE	1	0.330198295669399	3		665	1053	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099298	4099298	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	104	716	0	ENST00000262948.5:c.820G>C	p.Glu274Gln	p.E274Q	ENST00000262948	NM_030662.3	274	Gag/Cag	7/11	0.241294904122474	0	FACETS	0.55	0.492	0.611			1	SUBCLONAL	1	TRUE	0	0.330198295669399	0		716	767	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927382	49927382	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	112	674	0	ENST00000296474.3:c.3922C>A	p.Gln1308Lys	p.Q1308K	ENST00000296474	NM_002447.2	1308	Cag/Aag	19/20	1	2	FACETS	0.758	0.681	0.84	0.758	0.681	0.84	SUBCLONAL	1	TRUE	1	0.330198295669399	2		674	895	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448529	89448529	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	40	460	0	ENST00000336596.2:c.1493G>A	p.Ser498Asn	p.S498N	ENST00000336596	NM_005233.5	498	aGc/aAc	7/17	1	2	FACETS	0.309	0.256	0.369	0.309	0.256	0.369	SUBCLONAL	1	TRUE	1	0.330198295669399	2		460	783	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	260	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.390054243049837	3	FACETS	0.978	0.92	1	0.978	0.92	1	CLONAL	2	TRUE	1	0.411919012435569	3		555	778	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0026011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	412	773	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.411919012435569	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.411919012435569	2		774	883	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0026011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	107	554	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.905	0.814	1	0.905	0.814	1	CLONAL	1	TRUE	1	0.411919012435569	2		554	574	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0026011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	267	533	0	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	0.411919012435569	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.411919012435569	2		533	604	SUCCESS
APC	324	MSKCC	GRCh37	5	112175600	112175600	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	156	365	0	ENST00000257430.4:c.4312del	p.Thr1438HisfsTer35	p.T1438Hfs*35	ENST00000257430	NM_000038.5	1437	Aaa/aa	16/16	0.320475018419602	2	FACETS	0.836	0.773	0.901	0.836	0.773	0.901	CLONAL	2	TRUE	0	0.411919012435569	2		365	453	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843748	151843748	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778512	NA	P-0026011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	127	456	0	ENST00000262189.6:c.13967C>T	p.Ala4656Val	p.A4656V	ENST00000262189	NM_170606.2	4656	gCg/gTg	53/59	1	2	FACETS	0.937	0.851	1	0.937	0.851	1	CLONAL	1	TRUE	1	0.411919012435569	2		456	658	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260375	16260375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1475471010	NA	P-0026011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	241	504	0	ENST00000375759.3:c.7640C>T	p.Thr2547Ile	p.T2547I	ENST00000375759	NM_015001.2	2547	aCa/aTa	11/15	0.411919012435569	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.411919012435569	2		504	532	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114799801	114799801	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	171	480	0	ENST00000543371.1:c.468G>A	p.Trp156Ter	p.W156*	ENST00000543371	NM_001198531.1	156	tgG/tgA	5/14	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.411919012435569	2		480	725	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857958	9857958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140536516	NA	P-0026011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	277	618	2	ENST00000330684.3:c.3443C>T	p.Pro1148Leu	p.P1148L	ENST00000330684	NM_001134407.1	1148	cCg/cTg	13/13	0.390054243049837	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.411919012435569	3		620	726	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967216	93967216	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	89	516	0	ENST00000369303.4:c.2136G>T	p.Glu712Asp	p.E712D	ENST00000369303	NM_004440.3	712	gaG/gaT	12/17	0.40232191526782	3	FACETS	0.832	0.739	0.932	0.416	0.369	0.466	CLONAL	1	TRUE	1	0.411919012435569	3		516	626	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0026012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	41	786	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.708	0.588	0.841	0.708	0.588	0.841	SUBCLONAL	1	TRUE	1	0.19	2		786	610	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0026012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	42	408	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.785	0.655	0.93	0.785	0.655	0.93	CLONAL	1	TRUE	1	0.19	2		408	563	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849663	68849663	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587780113	NA	P-0026012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	80	447	0	ENST00000261769.5:c.1565+1G>T		p.X522_splice	ENST00000261769	NM_004360.3	522			0.304769823804043	1	FACETS	0.765	0.675	0.861	1	0.978	1	SUBCLONAL	2	TRUE	0	0.19	1		447	498	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0026013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	76	400	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.650046954919934	3	FACETS	0.729	0.642	0.822	0.365	0.321	0.411	SUBCLONAL	1	TRUE	1	0.650046954919934	3		400	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579415	7579415	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	502	583	1	ENST00000269305.4:c.272G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tGg/tAg	4/11	0.650046954919934	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.650046954919934	2		584	752	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175481	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0026013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	226	264	0	ENST00000257430.4:c.4192_4193del	p.Arg1399PhefsTer9	p.R1399Ffs*9	ENST00000257430	NM_000038.5	1397	GAg/g	16/16	0.650046954919934	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.650046954919934	3		264	450	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821541	72821541	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs758277523	NA	P-0026013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	201	324	0	ENST00000268489.5:c.10634G>C	p.Ser3545Thr	p.S3545T	ENST00000268489	NM_006885.3	3545	aGt/aCt	10/10	0.650046954919934	3	FACETS	1	0.985	1	0.608	0.566	0.651	CLONAL	1	TRUE	1	0.650046954919934	3		324	674	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395654	45395667	+	frameshift_variant	Frame_Shift_Del	DEL	TACTTCATCCTTTT	TACTTCATCCTTTT	-	novel	NA	P-0026013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	220	392	1	ENST00000262160.6:c.467_480del	p.Lys156MetfsTer11	p.K156Mfs*11	ENST00000262160	NM_005901.5	156	aAAAAGGATGAAGTA/a	4/11	0.650046954919934	2	FACETS	0.9	0.853	0.946	0.9	0.853	0.946	CLONAL	2	TRUE	0	0.650046954919934	2		393	376	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266939	18266980	+	inframe_deletion	In_Frame_Del	DEL	GCCCGGCCCGGCCCTCGCCCACGGGGCCCCCGCCCACTGCCC	GCCCGGCCCGGCCCTCGCCCACGGGGCCCCCGCCCACTGCCC	-	novel	NA	P-0026013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	225	242	0	ENST00000222254.8:c.253_294del	p.Gly87_Pro100del	p.G87_P100del	ENST00000222254	NM_005027.3	84	GCCCGGCCCGGCCCTCGCCCACGGGGCCCCCGCCCACTGCCC/-	2/16	0.60042884153548	4	FACETS	0.845	0.791	0.9	0.845	0.791	0.9	CLONAL	2	TRUE	2	0.650046954919934	4		242	676	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0026015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	131	146	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.974	0.89	1	0.974	0.89	1	CLONAL	1	TRUE	1	0.57000081743819	2		146	472	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0026015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	472	603	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.222074898544512	6	FACETS	0.886	0.851	0.921			1	INDETERMINATE	4	TRUE	NA	0.57000081743819	6		603	1000	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406427	70406427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	196	544	0	ENST00000373644.4:c.3941C>T	p.Ala1314Val	p.A1314V	ENST00000373644	NM_030625.2	1314	gCa/gTa	4/12	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.57000081743819	2		544	677	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964515	93964515	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0026015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	121	329	0	ENST00000369303.4:c.2383-1G>A		p.X795_splice	ENST00000369303	NM_004440.3	795			1	2	FACETS	0.913	0.83	0.999	0.913	0.83	0.999	CLONAL	1	TRUE	1	0.57000081743819	2		329	465	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182889	123182889	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	174	201	0	ENST00000218089.9:c.854T>G	p.Met285Arg	p.M285R	ENST00000218089	NM_001042749.1	285	aTg/aGg	10/35	1	1	FACETS	0.753	0.709	0.795	1	0.992	1	SUBCLONAL	2	TRUE	0	0.57000081743819	1		201	290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0026016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	415	581	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.34725292046223	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.361714970349042	3		581	848	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81973572	81973572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1017069056	NA	P-0026016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	156	617	0	ENST00000359376.3:c.3389C>T	p.Ala1130Val	p.A1130V	ENST00000359376	NM_002661.3	1130	gCa/gTa	30/33	0.361714970349042	3	FACETS	1	0.96	1	0.541	0.495	0.589	CLONAL	1	TRUE	1	0.361714970349042	3		617	941	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183797	10183797	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs5030807	NA	P-0026017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	248	623	0	ENST00000256474.2:c.266T>A	p.Leu89His	p.L89H	ENST00000256474	NM_000551.3	89	cTc/cAc	1/3	0.64518593458197	1	FACETS	0.904	0.853	0.956	0.904	0.853	0.956	CLONAL	1	TRUE	0	0.64518593458197	1		623	576	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983127	201983127	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	286	587	0	ENST00000359651.3:c.976T>C	p.Tyr326His	p.Y326H	ENST00000359651		326	Tac/Cac	7/8	1	2	FACETS	0.983	0.926	1	0.983	0.926	1	CLONAL	1	TRUE	1	0.64518593458197	2		587	902	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55704644	55704644	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	316	569	0	ENST00000284073.2:c.707G>A	p.Ser236Asn	p.S236N	ENST00000284073	NM_138962.2	236	aGc/aAc	10/14	1	2	FACETS	0.968	0.915	1	0.968	0.915	1	CLONAL	1	TRUE	1	0.64518593458197	2		569	1012	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436408	52436408	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	204	462	0	ENST00000460680.1:c.2086del	p.Ile696SerfsTer40	p.I696Sfs*40	ENST00000460680	NM_004656.3	696	Atc/tc	17/17	0.64518593458197	1	FACETS	0.967	0.908	1	0.967	0.908	1	CLONAL	1	TRUE	0	0.64518593458197	1		462	443	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	153	553	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.983	0.902	1	0.983	0.902	1	CLONAL	1	TRUE	1	0.439565818783014	2		555	708	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0026018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	236	604	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.439565818783014	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.439565818783014	1		606	737	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0026018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	110	364	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.955	0.862	1	0.955	0.862	1	CLONAL	1	TRUE	1	0.439565818783014	2		364	524	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119050	70119050	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	167	441	0	ENST00000245479.2:c.622C>T	p.Gln208Ter	p.Q208*	ENST00000245479	NM_000346.3	208	Cag/Tag	2/3	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.439565818783014	2		441	669	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21623946	21623946	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	22	145	1	ENST00000421138.2:c.1754C>T	p.Ala585Val	p.A585V	ENST00000421138		585	gCt/gTt	15/16	1	2	FACETS	0.654	0.512	0.816	0.654	0.512	0.816	SUBCLONAL	1	TRUE	1	0.439565818783014	2		146	153	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774126	66774131	+	inframe_deletion	In_Frame_Del	DEL	GTGGGG	GTGGGG	-	novel	NA	P-0026018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	255	878	1	ENST00000307102.5:c.602_607del	p.Arg201_Glu203delinsGln	p.R201_E203delinsQ	ENST00000307102	NM_002755.3	201	cGTGGGGag/cag	6/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.439565818783014	2		879	1098	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0026019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	74	622	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.723	0.632	0.821	0.723	0.632	0.821	SUBCLONAL	1	TRUE	1	0.25	2		623	819	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742959	17742959	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	69	527	0	ENST00000250003.3:c.867C>A	p.Ser289Arg	p.S289R	ENST00000250003	NM_002478.4	289	agC/agA	3/3	1	2	FACETS	0.98	0.855	1	0.98	0.855	1	CLONAL	1	TRUE	1	0.25	2		527	563	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861939	57861939	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	58	516	1	ENST00000228682.2:c.1240C>A	p.Pro414Thr	p.P414T	ENST00000228682	NM_005269.2	414	Ccc/Acc	10/12	0.247033627441247	3	FACETS	0.614	0.526	0.71	0.307	0.263	0.355	SUBCLONAL	1	TRUE	1	0.25	3		517	850	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28897069	28897069	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	40	398	0	ENST00000282397.4:c.2811C>A	p.His937Gln	p.H937Q	ENST00000282397	NM_002019.4	937	caC/caA	21/30	1	2	FACETS	0.63	0.523	0.749	0.63	0.523	0.749	SUBCLONAL	1	TRUE	1	0.25	2		398	508	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959028	28959028	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	45	355	0	ENST00000282397.4:c.2110G>T	p.Glu704Ter	p.E704*	ENST00000282397	NM_002019.4	704	Gag/Tag	14/30	1	2	FACETS	0.675	0.567	0.795	0.675	0.567	0.795	SUBCLONAL	1	TRUE	1	0.25	2		355	533	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632376	215632376	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	62	284	0	ENST00000260947.4:c.1398T>G	p.His466Gln	p.H466Q	ENST00000260947	NM_000465.2	466	caT/caG	6/11	1	2	FACETS	0.943	0.815	1	0.943	0.815	1	CLONAL	1	TRUE	1	0.25	2		284	526	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0026019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	523	707	0	ENST00000397752.3:c.3028+1G>C		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.3	5	FACETS	0.909	0.871	0.948			1	CLONAL	4	TRUE	NA	0.25	5		707	1582	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0026020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	113	554	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.958	0.867	1	0.958	0.867	1	CLONAL	1	TRUE	1	0.478459218153975	2		554	493	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604785	48604785	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	106	425	0	ENST00000342988.3:c.1607T>C	p.Leu536Pro	p.L536P	ENST00000342988	NM_005359.5	536	cTa/cCa	12/12	0.468100574668865	1	FACETS	0.824	0.744	0.907	0.824	0.744	0.907	CLONAL	1	TRUE	0	0.478459218153975	1		425	409	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683357	88683357	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201040	NA	P-0026020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	192	686	0	ENST00000372037.3:c.1480C>T	p.Arg494Ter	p.R494*	ENST00000372037	NM_004329.2	494	Cga/Tga	13/13	1	2	FACETS	0.95	0.88	1	0.95	0.88	1	CLONAL	1	TRUE	1	0.478459218153975	2		686	845	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022914	27022945	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCCGCCGCCAGCAGCCTGGGCAACCCGCCG	CCGCCGCCGCCAGCAGCCTGGGCAACCCGCCG	-	novel	NA	P-0026020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	20	95	0	ENST00000324856.7:c.31_62del	p.Ser11LeufsTer89	p.S11Lfs*89	ENST00000324856	NM_006015.4	7	cCCGCCGCCGCCAGCAGCCTGGGCAACCCGCCG/c	1/20	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.478459218153975	2		95	67	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659620	88659620	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	139	521	1	ENST00000372037.3:c.403C>T	p.Gln135Ter	p.Q135*	ENST00000372037	NM_004329.2	135	Caa/Taa	6/13	1	2	FACETS	0.988	0.903	1	0.988	0.903	1	CLONAL	1	TRUE	1	0.478459218153975	2		522	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0026020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	164	665	0	ENST00000269305.4:c.215_216insG	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	ccc/ccGc	4/11	0.468100574668865	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.478459218153975	1		665	486	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853788	59853788	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782356	NA	P-0026020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	250	511	0	ENST00000259008.2:c.2071A>G	p.Ile691Val	p.I691V	ENST00000259008	NM_032043.2	691	Att/Gtt	14/20	0.478459218153975	2	FACETS	0.855	0.806	0.905	0.855	0.806	0.905	CLONAL	2	TRUE	0	0.478459218153975	2		511	611	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864434	162864434	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0026020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	136	582	1	ENST00000366898.1:c.79A>T	p.Lys27Ter	p.K27*	ENST00000366898	NM_004562.2	27	Aag/Tag	2/12	1	2	FACETS	0.913	0.832	0.996	0.913	0.832	0.996	CLONAL	1	TRUE	1	0.478459218153975	2		583	623	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829040	128829042	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	rs570242755	NA	P-0026026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	12	65	1	ENST00000249373.3:c.67_69del	p.Leu23del	p.L23del	ENST00000249373	NM_005631.4	16	ggGCTg/ggg	1/12	0.371407384592164	1	FACETS	0.203	0.144	0.275	0.203	0.144	0.275	INDETERMINATE	1	TRUE	0	0.706984192818614	1		66	108	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115849	8115850	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	123	628	0	ENST00000346208.3:c.1196dup	p.His399GlnfsTer108	p.H399Qfs*108	ENST00000346208		399	cac/cAac	6/6	0.443881981533704	1	FACETS	0.31	0.281	0.342	0.31	0.281	0.342	SUBCLONAL	1	TRUE	0	0.706984192818614	1		628	725	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540336	187540336	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	202	523	0	ENST00000441802.2:c.7404del	p.Asp2469MetfsTer12	p.D2469Mfs*12	ENST00000441802	NM_005245.3	2468	tcT/tc	10/27	1	2	FACETS	0.965	0.901	1	0.965	0.901	1	CLONAL	1	TRUE	1	0.706984192818614	2		523	592	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	140	122	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.752	0.695	0.811			1	INDETERMINATE	2	FALSE	NA	0.539403371137313	2		122	345	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0026028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	839	560	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.539403371137313	7	FACETS	0.988	0.964	1			1	CLONAL	6	FALSE	NA	0.539403371137313	7		560	1233	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858517	9858517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765370528	NA	P-0026028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	154	473	0	ENST00000330684.3:c.2884G>A	p.Glu962Lys	p.E962K	ENST00000330684	NM_001134407.1	962	Gaa/Aaa	13/13	0.401578618266086	4	FACETS	0.839	0.772	0.907	0.839	0.772	0.907	CLONAL	2	FALSE	2	0.539403371137313	4		473	524	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086157	16086157	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	117	550	0	ENST00000281043.3:c.1333G>A	p.Glu445Lys	p.E445K	ENST00000281043	NM_005378.4	445	Gaa/Aaa	3/3	0.539403371137313	3	FACETS	0.943	0.853	1	0.472	0.426	0.519	CLONAL	1	FALSE	1	0.539403371137313	3		550	584	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056291	180056291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199942873	NA	P-0026028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	268	738	0	ENST00000261937.6:c.953G>A	p.Arg318Gln	p.R318Q	ENST00000261937	NM_182925.4	318	cGa/cAa	7/30	0.339837783700774	4	FACETS	0.905	0.851	0.96	0.905	0.851	0.96	CLONAL	2	FALSE	2	0.539403371137313	4		738	845	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873008	134873008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201012406	NA	P-0026028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	99	521	0	ENST00000398015.3:c.1312C>T	p.Pro438Ser	p.P438S	ENST00000398015	NM_004441.4	438	Ccc/Tcc	6/16	0.194260411647084	5	FACETS	1	0.922	1	0.346	0.309	0.385	INDETERMINATE	1	FALSE	2	0.539403371137313	5		521	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578473	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGGGTGCCGGG	CGCGGGTGCCGGG	-	novel	NA	P-0026028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	383	739	0	ENST00000269305.4:c.457_469del	p.Pro153SerfsTer13	p.P153Sfs*13	ENST00000269305	NM_001126112.2	153	CCCGGCACCCGCGtc/tc	5/11	0.539403371137313	2	FACETS	0.989	0.948	1	0.989	0.948	1	CLONAL	2	FALSE	0	0.539403371137313	2		739	718	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429758	78429758	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	121	305	0	ENST00000370768.2:c.1030C>T	p.Arg344Ter	p.R344*	ENST00000370768	NM_003902.3	344	Cga/Tga	12/20	0.539403371137313	3	FACETS	0.975	0.896	1	0.975	0.896	1	CLONAL	2	FALSE	1	0.539403371137313	3		305	292	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405491	70405491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	213	532	1	ENST00000373644.4:c.3005C>T	p.Ser1002Leu	p.S1002L	ENST00000373644	NM_030625.2	1002	tCa/tTa	4/12	0.401578618266086	4	FACETS	0.867	0.809	0.927	0.867	0.809	0.927	CLONAL	2	FALSE	2	0.539403371137313	4		533	701	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485939	8485939	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1381492310	NA	P-0026028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	148	405	0	ENST00000356435.5:c.2878G>A	p.Asp960Asn	p.D960N	ENST00000356435		960	Gat/Aat	17/35	0.521831830038841	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	FALSE	0	0.539403371137313	2		405	254	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805683	43805683	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	163	513	0	ENST00000372470.3:c.739C>T	p.Gln247Ter	p.Q247*	ENST00000372470	NM_005373.2	247	Cag/Tag	5/12	0.539403371137313	3	FACETS	1	0.985	1	0.646	0.596	0.698	CLONAL	1	FALSE	1	0.539403371137313	3		513	594	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22413289	22413289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	47	99	0	ENST00000344548.3:c.416C>T	p.Pro139Leu	p.P139L	ENST00000344548	NM_001039802.1	139	cCa/cTa	6/7	0.539403371137313	3	FACETS	0.997	0.868	1	0.997	0.868	1	CLONAL	2	FALSE	1	0.539403371137313	3		99	111	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122668	108122668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	163	582	0	ENST00000278616.4:c.1712C>T	p.Ser571Phe	p.S571F	ENST00000278616	NM_000051.3	571	tCt/tTt	11/63	0.339837783700774	4	FACETS	0.957	0.886	1	0.957	0.886	1	CLONAL	2	FALSE	2	0.539403371137313	4		582	486	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385315	4385315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	188	372	0	ENST00000261254.3:c.340G>A	p.Glu114Lys	p.E114K	ENST00000261254	NM_001759.3	114	Gag/Aag	2/5	NA	2	FACETS	0.982	0.923	1			1	INDETERMINATE	2	FALSE	NA	0.539403371137313	2		372	355	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118845	115118845	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	86	412	0	ENST00000257566.3:c.496C>T	p.His166Tyr	p.H166Y	ENST00000257566	NM_016569.3	166	Cac/Tac	2/8	0.539403371137313	2	FACETS	0.881	0.785	0.981	0.44	0.392	0.491	CLONAL	1	FALSE	0	0.539403371137313	2		412	362	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435842	110435843	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0026028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	150	481	0	ENST00000375856.3:c.2558_2559delinsTT	p.Ala853Val	p.A853V	ENST00000375856	NM_003749.2	853	gCC/gTT	1/2	0.194260411647084	5	FACETS	1	0.969	1	0.732	0.675	0.791	INDETERMINATE	2	FALSE	2	0.539403371137313	5		481	458	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005440	42005440	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	320	680	0	ENST00000219905.7:c.3176C>T	p.Ser1059Phe	p.S1059F	ENST00000219905	NM_001164273.1	1059	tCc/tTc	9/24	0.194260411647084	5	FACETS	1	0.992	1	0.82	0.776	0.863	INDETERMINATE	2	FALSE	2	0.539403371137313	5		680	873	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748645	43748645	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs149567425	NA	P-0026028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	248	788	0	ENST00000382044.4:c.2161A>G	p.Met721Val	p.M721V	ENST00000382044	NM_001141980.1	721	Atg/Gtg	12/28	0.194260411647084	5	FACETS	0.971	0.91	1	0.647	0.606	0.689	INDETERMINATE	2	FALSE	2	0.539403371137313	5		788	857	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88428931	88428931	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	103	535	0	ENST00000360948.2:c.2169G>A	p.Trp723Ter	p.W723*	ENST00000360948	NM_001012338.2	723	tgG/tgA	17/19	0.194260411647084	5	FACETS	0.957	0.864	1	0.638	0.576	0.702	INDETERMINATE	2	FALSE	2	0.539403371137313	5		535	361	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953235	81953235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199516791	NA	P-0026028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	32	327	0	ENST00000359376.3:c.2201C>T	p.Pro734Leu	p.P734L	ENST00000359376	NM_002661.3	734	cCc/cTc	20/33	0.401578618266086	4	FACETS	0.422	0.342	0.512	0.211	0.171	0.256	SUBCLONAL	1	FALSE	2	0.539403371137313	4		327	433	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350409	89350409	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	98	756	0	ENST00000301030.4:c.2541T>G	p.Asp847Glu	p.D847E	ENST00000301030	NM_001256183.1	847	gaT/gaG	9/13	0.319625783008802	6	FACETS	0.623	0.554	0.697			1	INDETERMINATE	1	FALSE	NA	0.539403371137313	6		756	1213	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15280923	15280923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	270	680	0	ENST00000263388.2:c.5173G>A	p.Glu1725Lys	p.E1725K	ENST00000263388	NM_000435.2	1725	Gag/Aag	28/33	0.401578618266086	4	FACETS	0.918	0.864	0.974	0.918	0.864	0.974	CLONAL	2	FALSE	2	0.539403371137313	4		680	839	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096471	178096471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	127	360	0	ENST00000397062.3:c.860C>T	p.Ser287Phe	p.S287F	ENST00000397062	NM_006164.4	287	tCt/tTt	5/5	0.20701089071996	5	FACETS	1	0.978	1	0.798	0.731	0.866	INDETERMINATE	2	FALSE	2	0.539403371137313	5		360	356	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505643	186505644	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0026028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	110	397	1	ENST00000323963.5:c.1051_1052delinsTT	p.Pro351Phe	p.P351F	ENST00000323963		351	CCt/TTt	10/11	0.194260411647084	5	FACETS	1	0.957	1	0.728	0.661	0.796	INDETERMINATE	2	FALSE	2	0.539403371137313	5		398	338	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637953	176637955	+	frameshift_variant	Frame_Shift_Del	DEL	CAT	CAT	TA	novel	NA	P-0026028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	205	718	0	ENST00000439151.2:c.2553_2555delinsTA	p.Ile852LysfsTer6	p.I852Kfs*6	ENST00000439151	NM_022455.4	851	gaCATa/gaTAa	5/23	0.339837783700774	4	FACETS	0.845	0.787	0.905	0.845	0.787	0.905	CLONAL	2	FALSE	2	0.539403371137313	4		718	692	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020815	26020816	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0026028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	77	255	2	ENST00000357647.3:c.98_99delinsTT	p.Thr33Ile	p.T33I	ENST00000357647	NM_003529.2	33	aCC/aTT	1/1	0.144822105067812	5	FACETS	0.906	0.804	1	0.604	0.536	0.675	INDETERMINATE	2	FALSE	2	0.539403371137313	5		257	285	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962956	2962956	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	136	699	0	ENST00000396946.4:c.1952C>T	p.Pro651Leu	p.P651L	ENST00000396946	NM_032415.4	651	cCt/cTt	16/25	0.453711857760369	4	FACETS	0.886	0.806	0.971	0.443	0.403	0.486	CLONAL	1	FALSE	2	0.539403371137313	4		699	876	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518415	8518415	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	42	217	0	ENST00000356435.5:c.976C>T	p.Pro326Ser	p.P326S	ENST00000356435		326	Cca/Tca	10/35	0.521831830038841	2	FACETS	0.992	0.843	1	0.496	0.421	0.576	CLONAL	1	FALSE	0	0.539403371137313	2		217	157	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0026029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	364	424	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.170956304038852	7	FACETS	1	0.959	1			1	CLONAL	7	TRUE	NA	0.170956304038852	7		424	862	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045157	47045157	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	63	372	0	ENST00000377604.3:c.2398G>T	p.Glu800Ter	p.E800*	ENST00000377604	NM_001204468.1	800	Gag/Tag	21/24	1	1	FACETS	1	0.894	1	1	0.98	1	CLONAL	2	TRUE	0	0.170956304038852	1		372	327	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106528	27106528	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	47	712	1	ENST00000324856.7:c.6139G>T	p.Glu2047Ter	p.E2047*	ENST00000324856	NM_006015.4	2047	Gag/Tag	20/20	1	2	FACETS	0.654	0.55	0.769	0.654	0.55	0.769	SUBCLONAL	1	TRUE	1	0.170956304038852	2		713	841	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745539	162745539	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	65	491	1	ENST00000367921.3:c.1954A>G	p.Met652Val	p.M652V	ENST00000367921	NM_006182.2	652	Atg/Gtg	15/18	0.159274126732908	3	FACETS	1	0.969	1	0.718	0.623	0.821	CLONAL	1	TRUE	1	0.170956304038852	3		492	575	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199901	108199901	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	25	270	0	ENST00000278616.4:c.7243G>C	p.Ala2415Pro	p.A2415P	ENST00000278616	NM_000051.3	2415	Gct/Cct	49/63	1	2	FACETS	0.715	0.563	0.89	0.715	0.563	0.89	SUBCLONAL	1	TRUE	1	0.170956304038852	2		270	409	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344074	118344074	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	51	321	0	ENST00000534358.1:c.2200A>G	p.Arg734Gly	p.R734G	ENST00000534358	NM_005933.3	734	Aga/Gga	3/36	1	2	FACETS	0.767	0.654	0.89	1	0.965	1	SUBCLONAL	2	TRUE	1	0.170956304038852	2		321	389	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416706	121416706	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	55	651	0	ENST00000257555.6:c.135C>A	p.Asp45Glu	p.D45E	ENST00000257555		45	gaC/gaA	1/10	1	2	FACETS	0.942	0.805	1	0.942	0.805	1	CLONAL	1	TRUE	1	0.170956304038852	2		651	683	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562891	21562891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752716919	NA	P-0026029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	65	686	0	ENST00000382592.4:c.1028C>T	p.Pro343Leu	p.P343L	ENST00000382592	NM_014572.2	343	cCc/cTc	4/8	1	2	FACETS	0.967	0.837	1	0.967	0.837	1	CLONAL	1	TRUE	1	0.170956304038852	2		686	786	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066913	30066913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	39	490	2	ENST00000331968.5:c.2218C>T	p.Arg740Trp	p.R740W	ENST00000331968	NM_002742.2	740	Cgg/Tgg	16/18	0.170956304038852	3	FACETS	0.639	0.528	0.764	0.32	0.264	0.382	SUBCLONAL	1	TRUE	1	0.170956304038852	3		492	775	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89869669	89869669	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	58	563	0	ENST00000389301.3:c.790C>A	p.Gln264Lys	p.Q264K	ENST00000389301	NM_000135.2	264	Cag/Aag	8/43	1	2	FACETS	0.923	0.792	1	0.923	0.792	1	CLONAL	1	TRUE	1	0.170956304038852	2		563	735	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278074	18278074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1131691683	NA	P-0026029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	83	673	0	ENST00000222254.8:c.1694C>G	p.Pro565Arg	p.P565R	ENST00000222254	NM_005027.3	565	cCg/cGg	13/16	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.170956304038852	2		673	888	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867028	45867028	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	51	472	1	ENST00000391945.4:c.1091G>T	p.Arg364Leu	p.R364L	ENST00000391945	NM_000400.3	364	cGc/cTc	11/23	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.170956304038852	2		473	586	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024236	31024236	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	54	472	0	ENST00000375687.4:c.3721G>T	p.Glu1241Ter	p.E1241*	ENST00000375687	NM_015338.5	1241	Gaa/Taa	13/13	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.170956304038852	2		472	565	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64288920	64288920	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	52	509	0	ENST00000370651.3:c.316G>T	p.Ala106Ser	p.A106S	ENST00000370651	NM_003463.4	106	Gca/Tca	4/6	0.170956304038852	2	FACETS	0.908	0.772	1	0.454	0.386	0.529	CLONAL	1	TRUE	0	0.170956304038852	2		509	670	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521935	157521935	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	38	497	0	ENST00000346085.5:c.4207A>G	p.Met1403Val	p.M1403V	ENST00000346085	NM_020732.3	1403	Atg/Gtg	18/20	1	2	FACETS	0.808	0.667	0.966	0.808	0.667	0.966	CLONAL	1	TRUE	1	0.170956304038852	2		497	550	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522200	157522201	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0026029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	64	471	0	ENST00000346085.5:c.4472_4473insT	p.Gly1492ArgfsTer18	p.G1492Rfs*18	ENST00000346085	NM_020732.3	1491	cca/ccTa	18/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.170956304038852	2		471	586	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0026042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	136	529	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		529	598	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090890	5090890	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs777259241	NA	P-0026042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	14	231	0	ENST00000381652.3:c.3038C>G	p.Pro1013Arg	p.P1013R	ENST00000381652	NM_004972.3	1013	cCt/cGt	22/25	0.395197083764026	3	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	3		231	228	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244997	46244997	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs868082376	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	461	674	0	ENST00000334344.6:c.3091C>T	p.Gln1031Ter	p.Q1031*	ENST00000334344	NM_152641.2	1031	Cag/Tag	15/21	0.427846893842216	3	FACETS	0.895	0.859	0.93	0.895	0.859	0.93	CLONAL	3	TRUE	0	0.446079898920174	3		674	942	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430441	181430441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	470	922	2	ENST00000325404.1:c.293G>A	p.Arg98Gln	p.R98Q	ENST00000325404	NM_003106.3	98	cGa/cAa	1/1	0.446079898920174	3	FACETS	0.923	0.882	0.965	0.615	0.588	0.643	CLONAL	2	TRUE	0	0.446079898920174	3		924	1396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	559	779	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.427846893842216	3	FACETS	0.978	0.944	1	0.978	0.944	1	CLONAL	3	TRUE	0	0.446079898920174	3		779	1045	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18439825	18439825	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	132	579	0	ENST00000266497.5:c.723C>A	p.Ser241Arg	p.S241R	ENST00000266497		241	agC/agA	2/31	0.446079898920174	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.446079898920174	1		579	452	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112292	115112292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1282046318	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	46	175	0	ENST00000257566.3:c.1448C>T	p.Thr483Met	p.T483M	ENST00000257566	NM_016569.3	483	aCg/aTg	7/8	0.427846893842216	3	FACETS	0.993	0.843	1	0.331	0.281	0.386	CLONAL	1	TRUE	0	0.446079898920174	3		175	254	SUCCESS
MET	4233	MSKCC	GRCh37	7	116417463	116417463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913244	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	260	395	0	ENST00000397752.3:c.3280C>T	p.His1094Tyr	p.H1094Y	ENST00000397752	NM_000245.2	1094	Cat/Tat	16/21	0.441093026492411	5	FACETS	0.947	0.892	1	0.568	0.535	0.601	CLONAL	3	TRUE	0	0.446079898920174	5		395	685	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390964	89390964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	83	499	0	ENST00000336596.2:c.1030G>A	p.Asp344Asn	p.D344N	ENST00000336596	NM_005233.5	344	Gac/Aac	5/17	0.446079898920174	2	FACETS	0.575	0.508	0.647	0.288	0.254	0.324	SUBCLONAL	1	TRUE	0	0.446079898920174	2		499	647	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463578	25463578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770938712	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	98	692	2	ENST00000264709.3:c.2104G>A	p.Asp702Asn	p.D702N	ENST00000264709	NM_175629.2	702	Gat/Aat	18/23	0.446079898920174	3	FACETS	0.578	0.514	0.645	0.289	0.257	0.323	SUBCLONAL	1	TRUE	1	0.446079898920174	3		694	930	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075157	16075157	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	75	391	0	ENST00000268712.3:c.395C>G	p.Pro132Arg	p.P132R	ENST00000268712	NM_006311.3	132	cCg/cGg	4/46	0.427846893842216	3	FACETS	0.681	0.597	0.771	0.227	0.199	0.257	SUBCLONAL	1	TRUE	0	0.446079898920174	3		391	604	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663871	241663871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1131691244	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	101	571	0	ENST00000366560.3:c.1256C>T	p.Ser419Leu	p.S419L	ENST00000366560	NM_000143.3	419	tCa/tTa	9/10	0.356405768360705	3	FACETS	0.751	0.672	0.836	0.376	0.336	0.418	SUBCLONAL	1	TRUE	1	0.446079898920174	3		571	737	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873005	134873005	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	454	580	0	ENST00000398015.3:c.1309G>T	p.Val437Phe	p.V437F	ENST00000398015	NM_004441.4	437	Gtt/Ttt	6/16	0.446079898920174	3	FACETS	0.968	0.931	1	0.968	0.931	1	CLONAL	3	TRUE	0	0.446079898920174	3		580	857	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259757	16259757	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	206	616	0	ENST00000375759.3:c.7022A>T	p.Lys2341Met	p.K2341M	ENST00000375759	NM_015001.2	2341	aAg/aTg	11/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.446079898920174	2		616	865	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462852	120462852	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	59	232	0	ENST00000256646.2:c.5479G>C	p.Asp1827His	p.D1827H	ENST00000256646	NM_024408.3	1827	Gat/Cat	30/34	1	2	FACETS	0.856	0.742	0.979	0.856	0.742	0.979	CLONAL	1	TRUE	1	0.446079898920174	2		232	309	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843669	156843669	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	286	1070	0	ENST00000524377.1:c.1095C>A	p.Asn365Lys	p.N365K	ENST00000524377	NM_002529.3	365	aaC/aaA	8/17	0.356405768360705	3	FACETS	1	0.975	1	0.536	0.503	0.57	CLONAL	1	TRUE	1	0.446079898920174	3		1070	1463	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246493815	246493815	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	80	508	0	ENST00000388985.4:c.361G>C	p.Glu121Gln	p.E121Q	ENST00000388985		121	Gag/Cag	4/12	0.356405768360705	3	FACETS	0.641	0.564	0.724	0.321	0.282	0.362	SUBCLONAL	1	TRUE	1	0.446079898920174	3		508	684	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405082	70405082	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	43	738	0	ENST00000373644.4:c.2596G>C	p.Glu866Gln	p.E866Q	ENST00000373644	NM_030625.2	866	Gaa/Caa	4/12	0.135623467983523	0	FACETS	0.163	0.136	0.193			1	INDETERMINATE	1	TRUE	0	0.446079898920174	0		738	656	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69458693	69458693	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	206	673	1	ENST00000227507.2:c.508G>A	p.Glu170Lys	p.E170K	ENST00000227507	NM_053056.2	170	Gag/Aag	3/5	0.446079898920174	3	FACETS	1	0.975	1	0.556	0.516	0.598	CLONAL	1	TRUE	1	0.446079898920174	3		674	1015	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121627	108121627	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	201	589	0	ENST00000278616.4:c.1435G>C	p.Asp479His	p.D479H	ENST00000278616	NM_000051.3	479	Gat/Cat	10/63	0.446079898920174	3	FACETS	1	0.983	1	0.599	0.555	0.644	CLONAL	1	TRUE	1	0.446079898920174	3		589	920	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112919996	112919996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	174	1107	1	ENST00000351677.2:c.1211C>T	p.Ser404Leu	p.S404L	ENST00000351677	NM_002834.3	404	tCa/tTa	10/16	0.427846893842216	3	FACETS	0.741	0.68	0.804	0.247	0.226	0.268	SUBCLONAL	1	TRUE	0	0.446079898920174	3		1108	1288	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281550	49281550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	111	784	2	ENST00000282018.3:c.597G>T	p.Gln199His	p.Q199H	ENST00000282018	NM_020377.2	199	caG/caT	1/1	1	2	FACETS	0.51	0.457	0.566	0.51	0.457	0.566	SUBCLONAL	1	TRUE	1	0.446079898920174	2		786	976	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987024	36987024	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	414	644	1	ENST00000354822.5:c.665A>T	p.Glu222Val	p.E222V	ENST00000354822	NM_001079668.2	222	gAg/gTg	3/3	0.421509797894128	4	FACETS	0.866	0.827	0.906	0.866	0.827	0.906	CLONAL	3	TRUE	1	0.446079898920174	4		645	1033	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991354	41991354	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	61	571	0	ENST00000219905.7:c.2185G>C	p.Glu729Gln	p.E729Q	ENST00000219905	NM_001164273.1	729	Gaa/Caa	5/24	0.176607585563336	1	FACETS	0.337	0.29	0.388	0.337	0.29	0.388	INDETERMINATE	1	TRUE	0	0.446079898920174	1		571	631	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042295	42042295	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	206	681	1	ENST00000219905.7:c.6490G>T	p.Gly2164Ter	p.G2164*	ENST00000219905	NM_001164273.1	2164	Gga/Tga	17/24	0.176607585563336	1	FACETS	0.965	0.898	1	0.965	0.898	1	INDETERMINATE	1	TRUE	0	0.446079898920174	1		682	744	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680771	88680771	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	123	731	0	ENST00000360948.2:c.486C>G	p.Phe162Leu	p.F162L	ENST00000360948	NM_001012338.2	162	ttC/ttG	6/19	0.176607585563336	1	FACETS	0.563	0.509	0.62	0.563	0.509	0.62	INDETERMINATE	1	TRUE	0	0.446079898920174	1		731	761	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783894	50783894	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	104	880	1	ENST00000398568.2:c.285G>T	p.Lys95Asn	p.K95N	ENST00000398568	NM_001042412.1	95	aaG/aaT	3/18	0.176607585563336	1	FACETS	0.417	0.373	0.464	0.417	0.373	0.464	INDETERMINATE	1	TRUE	0	0.446079898920174	1		881	869	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627691	37627691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	624	866	1	ENST00000447079.4:c.1606C>T	p.Pro536Ser	p.P536S	ENST00000447079	NM_015083.1	536	Cca/Tca	2/14	0.446079898920174	4	FACETS	0.892	0.859	0.925	0.892	0.859	0.925	CLONAL	3	TRUE	1	0.446079898920174	4		867	1512	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870589	40870589	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs933828283	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1285	121	789	0	ENST00000428826.2:c.814C>G	p.Gln272Glu	p.Q272E	ENST00000428826		272	Cag/Gag	9/21	0.446079898920174	4	FACETS	0.558	0.502	0.617	0.186	0.167	0.206	SUBCLONAL	1	TRUE	1	0.446079898920174	4		789	1406	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554272	63554272	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060502159	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	134	669	1	ENST00000307078.5:c.467A>G	p.Tyr156Cys	p.Y156C	ENST00000307078	NM_004655.3	156	tAc/tGc	2/11	0.446079898920174	4	FACETS	0.705	0.638	0.775	0.235	0.212	0.259	SUBCLONAL	1	TRUE	1	0.446079898920174	4		670	1233	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212159	5212159	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	163	979	0	ENST00000357368.4:c.4872G>C	p.Met1624Ile	p.M1624I	ENST00000357368	NM_002850.3	1624	atG/atC	32/38	0.446079898920174	1	FACETS	0.563	0.516	0.612	0.563	0.516	0.612	SUBCLONAL	1	TRUE	0	0.446079898920174	1		979	1009	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276694	15276711	+	inframe_deletion	In_Frame_Del	DEL	CCGCTTGGCTGCATCAGC	CCGCTTGGCTGCATCAGC	-	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	655	854	1	ENST00000263388.2:c.5554_5571del	p.Ala1852_Arg1857del	p.A1852_R1857del	ENST00000263388	NM_000435.2	1852	GCTGATGCAGCCAAGCGG/-	30/33	0.446079898920174	4	FACETS	0.912	0.879	0.944	0.684	0.659	0.708	CLONAL	3	TRUE	0	0.446079898920174	4		855	1553	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272088	18272088	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	27	76	0	ENST00000222254.8:c.599-1G>A		p.X200_splice	ENST00000222254	NM_005027.3	200			0.258888295024064	1	FACETS	1	0.897	1	1	0.897	1	INDETERMINATE	1	TRUE	0	0.446079898920174	1		76	82	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313196	30313196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	454	709	0	ENST00000262643.3:c.890G>A	p.Gly297Asp	p.G297D	ENST00000262643	NM_001238.2	297	gGt/gAt	10/12	0.411774682664991	3	FACETS	0.898	0.862	0.934	0.898	0.862	0.934	CLONAL	3	TRUE	0	0.446079898920174	3		709	924	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606986	47606986	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	86	608	0	ENST00000263735.4:c.736C>G	p.Gln246Glu	p.Q246E	ENST00000263735	NM_002354.2	246	Caa/Gaa	7/9	0.446079898920174	3	FACETS	0.629	0.556	0.707	0.314	0.278	0.354	SUBCLONAL	1	TRUE	1	0.446079898920174	3		608	750	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919823	96919823	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	94	494	1	ENST00000258439.3:c.440C>T	p.Ser147Phe	p.S147F	ENST00000258439	NM_001193304.2	147	tCt/tTt	4/4	0.227671819590545	2	FACETS	0.6	0.534	0.671	0.3	0.267	0.336	INDETERMINATE	1	TRUE	0	0.446079898920174	2		495	702	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378288	225378288	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	150	428	0	ENST00000264414.4:c.607G>T	p.Glu203Ter	p.E203*	ENST00000264414	NM_003590.4	203	Gaa/Taa	5/16	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.446079898920174	2		428	513	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225449679	225449679	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	67	423	0	ENST00000264414.4:c.48G>T	p.Met16Ile	p.M16I	ENST00000264414	NM_003590.4	16	atG/atT	1/16	1	2	FACETS	0.694	0.605	0.789	0.694	0.605	0.789	SUBCLONAL	1	TRUE	1	0.446079898920174	2		423	433	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023144	31023144	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	143	787	0	ENST00000375687.4:c.2629G>A	p.Glu877Lys	p.E877K	ENST00000375687	NM_015338.5	877	Gaa/Aaa	13/13	0.23249848342833	4	FACETS	0.9	0.82	0.985	0.45	0.41	0.493	INDETERMINATE	1	TRUE	2	0.446079898920174	4		787	1030	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730876	40730876	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	152	750	0	ENST00000373198.4:c.3659G>T	p.Arg1220Leu	p.R1220L	ENST00000373198	NM_133170.3	1220	cGg/cTg	27/32	0.23249848342833	4	FACETS	0.984	0.899	1	0.492	0.449	0.537	INDETERMINATE	1	TRUE	2	0.446079898920174	4		750	1002	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790171	40790171	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs760735173	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	170	434	1	ENST00000373198.4:c.2560C>A	p.Arg854Ser	p.R854S	ENST00000373198	NM_133170.3	854	Cgc/Agc	18/32	0.23249848342833	4	FACETS	0.81	0.748	0.875	0.81	0.748	0.875	INDETERMINATE	2	TRUE	2	0.446079898920174	4		435	680	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40828007	40828007	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	31	343	0	ENST00000373198.4:c.2421G>T	p.Lys807Asn	p.K807N	ENST00000373198	NM_133170.3	807	aaG/aaT	17/32	0.23249848342833	4	FACETS	0.348	0.28	0.424	0.174	0.14	0.212	INDETERMINATE	1	TRUE	2	0.446079898920174	4		343	578	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62316925	62316925	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	280	630	0	ENST00000360203.5:c.1241G>T	p.Gly414Val	p.G414V	ENST00000360203	NM_001283009.1	414	gGg/gTg	15/35	0.23249848342833	4	FACETS	0.941	0.885	0.998	0.941	0.885	0.998	INDETERMINATE	2	TRUE	2	0.446079898920174	4		630	965	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39762958	39762958	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	76	595	0	ENST00000288319.7:c.878A>T	p.Tyr293Phe	p.Y293F	ENST00000288319	NM_182918.3	293	tAt/tTt	9/10	1	2	FACETS	0.599	0.526	0.677	0.599	0.526	0.677	SUBCLONAL	1	TRUE	1	0.446079898920174	2		595	569	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021740	71021740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	165	486	0	ENST00000318789.4:c.1618G>A	p.Glu540Lys	p.E540K	ENST00000318789	NM_032682.5	540	Gaa/Aaa	18/21	0.446079898920174	2	FACETS	1	0.987	1	0.679	0.627	0.732	CLONAL	1	TRUE	0	0.446079898920174	2		486	545	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946227	55946228	+	missense_variant	Missense_Mutation	DNP	CG	CG	TT	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	69	372	3	ENST00000263923.4:c.3951_3952delinsAA	p.Val1318Met	p.V1318M	ENST00000263923	NM_002253.2	1317	acCGtg/acAAtg	30/30	0.446079898920174	4	FACETS	0.687	0.598	0.783	0.229	0.199	0.261	SUBCLONAL	1	TRUE	1	0.446079898920174	4		375	651	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31421402	31421402	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	322	579	0	ENST00000344624.3:c.3502G>T	p.Asp1168Tyr	p.D1168Y	ENST00000344624		1168	Gat/Tat	27/33	0.446079898920174	5	FACETS	1	0.985	1	0.74	0.7	0.782	CLONAL	2	TRUE	2	0.446079898920174	5		579	1085	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519478	176519478	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1288	366	1086	1	ENST00000292408.4:c.884G>T	p.Gly295Val	p.G295V	ENST00000292408	NM_213647.1	295	gGa/gTa	7/18	0.446079898920174	3	FACETS	1	0.991	1	0.607	0.574	0.641	CLONAL	1	TRUE	1	0.446079898920174	3		1087	1654	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523718	176523718	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	255	775	0	ENST00000292408.4:c.2129G>T	p.Arg710Leu	p.R710L	ENST00000292408	NM_213647.1	710	cGa/cTa	16/18	0.446079898920174	3	FACETS	1	0.984	1	0.578	0.541	0.617	CLONAL	1	TRUE	1	0.446079898920174	3		775	1209	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048756	180048756	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1297327643	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	502	878	0	ENST00000261937.6:c.1806C>A	p.His602Gln	p.H602Q	ENST00000261937	NM_182925.4	602	caC/caA	13/30	0.446079898920174	3	FACETS	0.953	0.912	0.994	0.953	0.912	0.994	CLONAL	2	TRUE	1	0.446079898920174	3		878	1444	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031889	26031889	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	40	270	0	ENST00000244661.2:c.400G>T	p.Glu134Ter	p.E134*	ENST00000244661	NM_003537.3	134	Gaa/Taa	1/1	0.157228242085743	2	FACETS	0.502	0.418	0.595	0.251	0.209	0.298	INDETERMINATE	1	TRUE	0	0.446079898920174	2		270	357	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032015	26032015	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs779220917	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	63	417	0	ENST00000244661.2:c.274G>T	p.Ala92Ser	p.A92S	ENST00000244661	NM_003537.3	92	Gcg/Tcg	1/1	0.157228242085743	2	FACETS	0.536	0.464	0.614	0.268	0.232	0.307	INDETERMINATE	1	TRUE	0	0.446079898920174	2		417	527	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324214	31324214	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs281864614	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	97	652	0	ENST00000412585.2:c.349C>G	p.His117Asp	p.H117D	ENST00000412585	NM_005514.6	117	Cac/Gac	3/8	0.157228242085743	2	FACETS	0.585	0.521	0.652	0.292	0.26	0.326	INDETERMINATE	1	TRUE	0	0.446079898920174	2		652	744	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068121	94068121	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	102	330	0	ENST00000369303.4:c.841C>G	p.Arg281Gly	p.R281G	ENST00000369303	NM_004440.3	281	Cgt/Ggt	4/17	0.446079898920174	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.446079898920174	1		330	319	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622234	162622234	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	147	516	0	ENST00000366898.1:c.463C>G	p.Gln155Glu	p.Q155E	ENST00000366898	NM_004562.2	155	Caa/Gaa	4/12	0.446079898920174	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.446079898920174	1		516	472	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55272995	55272995	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	224	711	0	ENST00000275493.2:c.3318G>T	p.Gln1106His	p.Q1106H	ENST00000275493	NM_005228.3	1106	caG/caT	28/28	0.279131268647233	3	FACETS	1	0.99	1	0.666	0.621	0.713	CLONAL	1	TRUE	1	0.446079898920174	3		711	922	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92404147	92404147	+	splice_acceptor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	161	354	0	ENST00000265734.4:c.234-2del		p.X78_splice	ENST00000265734	NM_001259.6	78			0.41944134347133	5	FACETS	0.819	0.752	0.887	0.409	0.376	0.444	CLONAL	2	TRUE	1	0.446079898920174	5		354	736	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340196	116340196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	50	327	0	ENST00000397752.3:c.1058C>T	p.Ser353Phe	p.S353F	ENST00000397752	NM_000245.2	353	tCt/tTt	2/21	0.441093026492411	5	FACETS	0.531	0.449	0.621	0.106	0.089	0.125	SUBCLONAL	1	TRUE	0	0.446079898920174	5		327	705	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141549478	141549478	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	64	437	0	ENST00000220592.5:c.2110T>G	p.Phe704Val	p.F704V	ENST00000220592	NM_012154.3	704	Ttc/Gtc	16/19	0.446079898920174	3	FACETS	0.562	0.486	0.644	0.281	0.243	0.322	SUBCLONAL	1	TRUE	1	0.446079898920174	3		437	625	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949138	44949138	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	99	600	0	ENST00000377967.4:c.3699G>T	p.Trp1233Cys	p.W1233C	ENST00000377967	NM_021140.2	1233	tgG/tgT	25/29	1	2	FACETS	0.622	0.555	0.693	0.622	0.555	0.693	SUBCLONAL	1	TRUE	1	0.446079898920174	2		600	714	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412464	63412464	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	170	965	0	ENST00000330258.3:c.703C>A	p.Pro235Thr	p.P235T	ENST00000330258	NM_152424.3	235	Cct/Act	2/2	1	2	FACETS	0.705	0.647	0.765	0.705	0.647	0.765	SUBCLONAL	1	TRUE	1	0.446079898920174	2		965	1081	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413055	63413055	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	295	1015	0	ENST00000330258.3:c.112G>T	p.Glu38Ter	p.E38*	ENST00000330258	NM_152424.3	38	Gaa/Taa	2/2	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.446079898920174	2		1015	1071	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938572	76938572	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	113	589	0	ENST00000373344.5:c.2176G>T	p.Asp726Tyr	p.D726Y	ENST00000373344	NM_000489.3	726	Gat/Tat	9/35	1	2	FACETS	0.678	0.61	0.75	0.678	0.61	0.75	SUBCLONAL	1	TRUE	1	0.446079898920174	2		589	747	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615634	100615634	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	151	707	0	ENST00000308731.7:c.698T>A	p.Leu233Gln	p.L233Q	ENST00000308731	NM_000061.2	233	cTa/cAa	8/19	1	2	FACETS	0.805	0.736	0.877	0.805	0.736	0.877	CLONAL	1	TRUE	1	0.446079898920174	2		707	841	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123025112	123025112	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	TT	novel	NA	P-0026043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	82	805	0	ENST00000355640.3:c.1002delinsTT	p.Lys334AsnfsTer16	p.K334Nfs*16	ENST00000355640		334	aaG/aaTT	4/7	1	2	FACETS	0.498	0.439	0.562	0.498	0.439	0.562	SUBCLONAL	1	TRUE	1	0.446079898920174	2		805	738	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0121426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1768	127	965	6	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	1	2	FACETS	0.469	0.423	0.518	0.469	0.423	0.518	SUBCLONAL	1	NA	1	0.285835067554403	2		971	1895	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248123	59248123	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs370122841	NA	P-0121426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	23	116	0	ENST00000371222.2:c.620C>A	p.Pro207Gln	p.P207Q	ENST00000371222	NM_002228.3	207	cCg/cAg	1/1	1	2	FACETS	0.592	0.462	0.741	0.592	0.462	0.741	SUBCLONAL	1	NA	1	0.285835067554403	2		116	272	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202586	67202587	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0121426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1596	111	805	8	ENST00000312629.5:c.1401dup	p.Ser468LeufsTer54	p.S468Lfs*54	ENST00000312629	NM_003952.2	465	-/C	15/15	1	2	FACETS	0.455	0.407	0.506	0.455	0.407	0.506	SUBCLONAL	1	NA	1	0.285835067554403	2		813	1707	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882019	NA	P-0026047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	472	939	36	ENST00000269305.4:c.455dup	p.Pro153AlafsTer28	p.P153Afs*28	ENST00000269305	NM_001126112.2	152	ccg/ccCg	5/11	0.69362860221977	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.69362860221977	1		975	866	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932365	36932365	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	715	673	80	ENST00000361632.4:c.2104G>A	p.Asp702Asn	p.D702N	ENST00000361632		702	Gat/Aat	16/16	0.602210219797083	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.69362860221977	3		753	1294	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426885	49426885	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	227	450	12	ENST00000301067.7:c.11603G>T	p.Gly3868Val	p.G3868V	ENST00000301067	NM_003482.3	3868	gGg/gTg	39/54	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.69362860221977	2		462	570	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937023	48937024	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	602	513	47	ENST00000267163.4:c.795dup	p.Gln266ThrfsTer5	p.Q266Tfs*5	ENST00000267163	NM_000321.2	264	gca/gcAa	8/27	0.69362860221977	2	FACETS	0.983	0.956	1	0.983	0.956	1	CLONAL	2	TRUE	0	0.69362860221977	2		560	883	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918759	50918759	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	398	823	29	ENST00000440232.2:c.2629G>T	p.Asp877Tyr	p.D877Y	ENST00000440232	NM_002691.3	877	Gat/Tat	21/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.69362860221977	2		852	1092	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919855	96919855	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs121908826	NA	P-0026047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	145	340	21	ENST00000258439.3:c.410-2A>G		p.X137_splice	ENST00000258439	NM_001193304.2	137			1	2	FACETS	0.919	0.845	0.995	0.919	0.845	0.995	CLONAL	1	TRUE	1	0.69362860221977	2		361	455	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73108204	73108204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	50	63	3	ENST00000356692.5:c.304C>T	p.Gln102Ter	p.Q102*	ENST00000356692		102	Cag/Tag	4/9	0.69362860221977	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.69362860221977	1		66	81	SUCCESS
ATR	545	MSKCC	GRCh37	3	142222296	142222296	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0026047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	219	413	18	ENST00000350721.4:c.5197-1G>C		p.X1733_splice	ENST00000350721	NM_001184.3	1733			0.602210219797083	3	FACETS	0.959	0.893	1	0.479	0.446	0.514	CLONAL	1	TRUE	1	0.69362860221977	3		431	887	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139849	55139849	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0026047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	221	406	27	ENST00000257290.5:c.1510A>T	p.Lys504Ter	p.K504*	ENST00000257290	NM_006206.4	504	Aag/Tag	10/23	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.69362860221977	2		433	612	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829791	76829791	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	100	377	0	ENST00000373344.5:c.6250T>G	p.Tyr2084Asp	p.Y2084D	ENST00000373344	NM_000489.3	2084	Tac/Gac	28/35	1	1	FACETS	0.344	0.308	0.382	0.344	0.308	0.382	SUBCLONAL	1	TRUE	0	0.69362860221977	1		377	547	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594201	55594203	+	missense_variant	Missense_Mutation	TNP	AAG	AAG	GAT	novel	NA	P-0026047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	250	370	14	ENST00000288135.5:c.1904_1906delinsGAT	p.Glu635_Ala636delinsGlySer	p.E635_A636delinsGS	ENST00000288135	NM_000222.2	635	gAAGcc/gGATcc	13/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.69362860221977	2		384	644	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772964	135772964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763169786	NA	P-0026047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	196	412	25	ENST00000298552.3:c.2659G>A	p.Glu887Lys	p.E887K	ENST00000298552	NM_001162426.1	887	Gag/Aag	21/23	0.609341255319082	3	FACETS	0.981	0.91	1	0.49	0.455	0.527	CLONAL	1	TRUE	1	0.69362860221977	3		437	776	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0026050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	1435	748	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.28867229609225	12	FACETS	0.96	0.941	0.979			1	CLONAL	11	TRUE	NA	0.28867229609225	12		748	2300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579585	7579585	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	187	677	0	ENST00000269305.4:c.102del	p.Leu35CysfsTer9	p.L35Cfs*9	ENST00000269305	NM_001126112.2	34	ccC/cc	4/11	0.195399913495992	3	FACETS	0.824	0.761	0.888	0.549	0.507	0.592	CLONAL	2	TRUE	0	0.28867229609225	3		677	900	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265138	5265138	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	241	1043	0	ENST00000357368.4:c.449G>T	p.Arg150Leu	p.R150L	ENST00000357368	NM_002850.3	150	cGg/cTg	5/38	0.28867229609225	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.28867229609225	1		1043	986	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040903	42040903	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	157	661	1	ENST00000219905.7:c.5281C>T	p.Arg1761Ter	p.R1761*	ENST00000219905	NM_001164273.1	1761	Cga/Tga	16/24	0.28867229609225	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.28867229609225	1		662	819	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577137	7577137	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	82	858	0	ENST00000269305.4:c.801del	p.Asn268ThrfsTer77	p.N268Tfs*77	ENST00000269305	NM_001126112.2	267	cgG/cg	8/11	0.195399913495992	3	FACETS	0.61	0.537	0.69	0.203	0.179	0.23	SUBCLONAL	1	TRUE	0	0.28867229609225	3		858	1065	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914526	32914526	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	123	823	0	ENST00000380152.3:c.6034T>C	p.Ser2012Pro	p.S2012P	ENST00000380152		2012	Tcc/Ccc	11/27	0.141087388569376	0	FACETS	0.595	0.537	0.656			1	INDETERMINATE	1	TRUE	0	0.28867229609225	0		823	1019	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781345	3781345	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	146	1101	0	ENST00000262367.5:c.5020A>G	p.Lys1674Glu	p.K1674E	ENST00000262367	NM_004380.2	1674	Aag/Gag	30/31	1	2	FACETS	0.775	0.705	0.848	0.775	0.705	0.848	SUBCLONAL	1	TRUE	1	0.28867229609225	2		1101	1306	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391196	89391196	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs144998277	NA	P-0026050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	53	489	0	ENST00000336596.2:c.1262C>A	p.Pro421Gln	p.P421Q	ENST00000336596	NM_005233.5	421	cCa/cAa	5/17	1	2	FACETS	0.636	0.542	0.739	0.636	0.542	0.739	SUBCLONAL	1	TRUE	1	0.28867229609225	2		489	577	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512360	149512361	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0026050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	56	739	2	ENST00000261799.4:c.1079_1080delinsAA	p.Ser360Ter	p.S360*	ENST00000261799	NM_002609.3	360	tCC/tAA	7/23	0.28867229609225	1	FACETS	0.38	0.324	0.441	0.38	0.324	0.441	SUBCLONAL	1	TRUE	0	0.28867229609225	1		741	874	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878233	151878233	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs762198582	NA	P-0026050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	217	684	0	ENST00000262189.6:c.6712A>G	p.Met2238Val	p.M2238V	ENST00000262189	NM_170606.2	2238	Atg/Gtg	36/59	0.232177903210833	4	FACETS	0.841	0.781	0.903	0.841	0.781	0.903	CLONAL	2	TRUE	2	0.28867229609225	4		684	1152	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782177	NA	P-0026052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	96	1087	1	ENST00000269305.4:c.644G>A	p.Ser215Asn	p.S215N	ENST00000269305	NM_001126112.2	215	aGt/aAt	6/11	0.3	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.2	1		1088	691	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245891	5245891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1045893958	NA	P-0026052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	88	1444	1	ENST00000357368.4:c.884G>A	p.Arg295Gln	p.R295Q	ENST00000357368	NM_002850.3	295	cGg/cAg	10/38	0.3	1	FACETS	0.971	0.859	1	0.971	0.859	1	CLONAL	1	TRUE	0	0.2	1		1445	816	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1022599	1022599	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs772665164	NA	P-0026052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	43	821	0	ENST00000358495.3:c.1215del	p.Lys406ArgfsTer5	p.K406Rfs*5	ENST00000358495	NM_134424.2	405	agG/ag	12/12	NA	2	FACETS	0.714	0.597	0.845			1	INDETERMINATE	1	TRUE	NA	0.2	2		821	602	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584725	48584725	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	41	630	1	ENST00000342988.3:c.803G>A	p.Trp268Ter	p.W268*	ENST00000342988	NM_005359.5	268	tGg/tAg	7/12	0.3	1	FACETS	0.872	0.727	1	0.872	0.727	1	CLONAL	1	TRUE	0	0.2	1		631	423	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69011988	69011988	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	86	1084	0	ENST00000288368.4:c.2625A>C	p.Glu875Asp	p.E875D	ENST00000288368	NM_024870.2	875	gaA/gaC	23/40	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.2	2		1084	854	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0026054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	230	424	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.665154373064114	2		424	595	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121856	2121856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745897413	NA	P-0026054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	599	681	4	ENST00000219476.3:c.2018C>T	p.Ala673Val	p.A673V	ENST00000219476	NM_000548.3	673	gCg/gTg	19/42	0.665154373064114	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.665154373064114	1		685	930	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577128	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAAGCTGTT	novel	NA	P-0026054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	379	785	0	ENST00000269305.4:c.802_810dup	p.Asn268_Phe270dup	p.N268_F270dup	ENST00000269305	NM_001126112.2	268	-/AACAGCTTT	8/11	0.665154373064114	1	FACETS	0.88	0.84	0.921	0.88	0.84	0.921	CLONAL	1	TRUE	0	0.665154373064114	1		785	864	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143333	30143333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343353214	NA	P-0026054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	370	906	0	ENST00000389048.3:c.193C>T	p.Arg65Cys	p.R65C	ENST00000389048	NM_004304.4	65	Cgt/Tgt	1/29	1	2	FACETS	0.948	0.9	0.997	0.948	0.9	0.997	CLONAL	1	TRUE	1	0.665154373064114	2		906	1173	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0026054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	180	473	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	0.185240550985649	3	FACETS	1	0.977	1	0.566	0.524	0.609	INDETERMINATE	1	TRUE	1	0.665154373064114	3		473	637	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0026054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	232	288	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.185240550985649	3	FACETS	1	0.992	1	0.699	0.655	0.743	INDETERMINATE	1	TRUE	1	0.665154373064114	3		288	665	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907098	101907098	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554701911	NA	P-0026054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	245	473	2	ENST00000374994.4:c.1058G>T	p.Gly353Val	p.G353V	ENST00000374994	NM_004612.2	353	gGa/gTa	6/9	0.36873263176183	2	FACETS	1	0.993	1	0.686	0.648	0.725	INDETERMINATE	1	TRUE	0	0.665154373064114	2		475	537	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412095	63412095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852217	NA	P-0026054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	551	920	0	ENST00000330258.3:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000330258	NM_152424.3	358	Cga/Tga	2/2	0.450346937540612	2	FACETS	1	0.997	1	0.742	0.715	0.769	CLONAL	1	TRUE	0	0.665154373064114	2		920	1117	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540074	187540074	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs921535768	NA	P-0000034-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	78	788	0	ENST00000441802.2:c.7666C>T	p.Arg2556Ter	p.R2556*	ENST00000441802	NM_005245.3	2556	Cga/Tga	10/27	0.309413607679074	3	FACETS	0.79	0.694	0.894			1	SUBCLONAL	1	TRUE	NA	0.309413607679074	3		788	737	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023307	27023307	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0000034-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	27	70	0	ENST00000324856.7:c.413C>G	p.Ser138Ter	p.S138*	ENST00000324856	NM_006015.4	138	tCa/tGa	1/20	0.216437455506463	5	FACETS	0.799	0.642	0.973	0.532	0.428	0.649	CLONAL	2	TRUE	2	0.309413607679074	5		70	160	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427550	72427550	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000034-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	102	393	0	ENST00000477973.2:c.940G>C	p.Asp314His	p.D314H	ENST00000477973	NM_012234.5	314	Gat/Cat	4/4	0.216437455506463	5	FACETS	1	0.952	1	0.733	0.659	0.81	CLONAL	2	TRUE	2	0.309413607679074	5		393	439	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518800	176518800	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000034-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	24	405	0	ENST00000292408.4:c.718G>C	p.Asp240His	p.D240H	ENST00000292408	NM_213647.1	240	Gat/Cat	6/18	0.309413607679074	1	FACETS	0.874	0.693	1	0.874	0.693	1	CLONAL	1	TRUE	0	0.309413607679074	1		405	150	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292745	91292745	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000034-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	59	598	0	ENST00000355112.3:c.247C>T	p.Gln83Ter	p.Q83*	ENST00000355112	NM_000057.2	83	Cag/Tag	3/22	0.21783653633498	3	FACETS	0.565	0.485	0.652	0.282	0.242	0.326	SUBCLONAL	1	TRUE	1	0.309413607679074	3		598	780	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292809	91292809	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367543030	NA	P-0000034-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	51	613	0	ENST00000355112.3:c.311C>T	p.Ser104Leu	p.S104L	ENST00000355112	NM_000057.2	104	tCa/tTa	3/22	0.21783653633498	3	FACETS	0.558	0.473	0.651	0.279	0.236	0.326	SUBCLONAL	1	TRUE	1	0.309413607679074	3		613	682	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292815	91292815	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000034-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	51	618	0	ENST00000355112.3:c.317C>A	p.Ser106Ter	p.S106*	ENST00000355112	NM_000057.2	106	tCa/tAa	3/22	0.21783653633498	3	FACETS	0.55	0.467	0.642	0.275	0.233	0.321	SUBCLONAL	1	TRUE	1	0.309413607679074	3		618	692	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292904	91292904	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000034-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	44	584	0	ENST00000355112.3:c.406C>G	p.Leu136Val	p.L136V	ENST00000355112	NM_000057.2	136	Ctc/Gtc	3/22	0.21783653633498	3	FACETS	0.45	0.377	0.533	0.225	0.188	0.267	SUBCLONAL	1	TRUE	1	0.309413607679074	3		584	729	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292951	91292951	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000034-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	42	618	0	ENST00000355112.3:c.453C>G	p.Ile151Met	p.I151M	ENST00000355112	NM_000057.2	151	atC/atG	3/22	0.21783653633498	3	FACETS	0.417	0.347	0.496	0.209	0.173	0.248	SUBCLONAL	1	TRUE	1	0.309413607679074	3		618	751	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293024	91293024	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000034-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	45	670	0	ENST00000355112.3:c.526C>G	p.His176Asp	p.H176D	ENST00000355112	NM_000057.2	176	Cac/Gac	3/22	0.21783653633498	3	FACETS	0.397	0.332	0.468	0.198	0.166	0.234	SUBCLONAL	1	TRUE	1	0.309413607679074	3		670	847	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796756	42796756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781265178	NA	P-0000034-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	76	439	0	ENST00000575354.2:c.3214G>A	p.Val1072Met	p.V1072M	ENST00000575354	NM_015125.3	1072	Gtg/Atg	14/20	0.21783653633498	3	FACETS	0.968	0.858	1	0.968	0.858	1	CLONAL	2	TRUE	1	0.309413607679074	3		439	293	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969425	44969425	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000034-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	284	408	0	ENST00000377967.4:c.4108del	p.Glu1370LysfsTer6	p.E1370Kfs*6	ENST00000377967	NM_021140.2	1369	ttG/tt	28/29	0.309413607679074	2	FACETS	0.878	0.835	0.919			1	CLONAL	4	TRUE	NA	0.309413607679074	2		408	523	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0000061-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	155	215	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	1	2	FACETS	1	0.956	1	1	0.992	1	CLONAL	2	FALSE	1	0.157921779914777	2		215	917	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539969	187539969	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000061-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	173	241	0	ENST00000441802.2:c.7771G>C	p.Asp2591His	p.D2591H	ENST00000441802	NM_005245.3	2591	Gac/Cac	10/27	0.123807611126151	4	FACETS	0.902	0.83	0.976	1	0.987	1	CLONAL	3	FALSE	2	0.157921779914777	4		241	938	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144146	11144146	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000061-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	81	220	0	ENST00000358026.2:c.3727C>G	p.Arg1243Gly	p.R1243G	ENST00000358026	NM_001128849.1	1243	Cgg/Ggg	26/36	0.157921779914777	0	FACETS	1	0.897	1			1	CLONAL	3	FALSE	0	0.157921779914777	0		220	286	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521219	187521219	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs781096830	NA	P-0000106-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	82	715	0	ENST00000441802.2:c.11936C>G	p.Ser3979Cys	p.S3979C	ENST00000441802	NM_005245.3	3979	tCc/tGc	22/27	0.291417931848819	1	FACETS	0.344	0.303	0.389	0.344	0.303	0.389	SUBCLONAL	1	TRUE	0	0.477609017578801	1		715	759	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212482	133212482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000106-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	61	410	0	ENST00000320574.5:c.5807G>A	p.Gly1936Glu	p.G1936E	ENST00000320574	NM_006231.2	1936	gGa/gAa	42/49	0.477609017578801	1	FACETS	0.456	0.395	0.523	0.456	0.395	0.523	SUBCLONAL	1	TRUE	0	0.477609017578801	1		410	426	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17129492	17129492	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000106-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	24	379	0	ENST00000285071.4:c.394G>A	p.Glu132Lys	p.E132K	ENST00000285071	NM_144997.5	132	Gag/Aag	5/14	0.477609017578801	1	FACETS	0.228	0.178	0.285	0.228	0.178	0.285	SUBCLONAL	1	TRUE	0	0.477609017578801	1		379	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1060501197	NA	P-0000106-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	97	350	0	ENST00000269305.4:c.716del	p.Asn239ThrfsTer8	p.N239Tfs*8	ENST00000269305	NM_001126112.2	239	aAc/ac	7/11	0.477609017578801	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.477609017578801	1		350	266	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0000122-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	399	347	1	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	0.944463214590099	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.944463214590099	1		348	431	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354254	70354258	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGT	GGAGT	-	novel	NA	P-0000122-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	157	481	0	ENST00000374080.3:c.4667_4671del	p.Glu1556GlyfsTer20	p.E1556Gfs*20	ENST00000374080		1555	acGGAGTgg/acgg	34/45	NA	2	FACETS	0.323	0.296	0.353			1	INDETERMINATE	1	TRUE	NA	0.944463214590099	2		481	1028	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567336	226567336	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000132-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	565	335	1	ENST00000366794.5:c.1550A>G	p.Asn517Ser	p.N517S	ENST00000366794	NM_001618.3	517	aAc/aGc	11/23	0.877613750259179	4	FACETS	0.989	0.961	1	0.989	0.961	1	CLONAL	3	TRUE	1	0.877613750259179	4		336	815	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143020	47143020	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000132-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	374	317	0	ENST00000409792.3:c.4943T>G	p.Val1648Gly	p.V1648G	ENST00000409792	NM_014159.6	1648	gTt/gGt	8/21	0.843822827593056	2	FACETS	0.945	0.92	0.968	0.945	0.92	0.968	CLONAL	2	TRUE	0	0.877613750259179	2		317	451	SUCCESS
ATR	545	MSKCC	GRCh37	3	142253975	142253975	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000132-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	355	234	1	ENST00000350721.4:c.3892G>T	p.Asp1298Tyr	p.D1298Y	ENST00000350721	NM_001184.3	1298	Gat/Tat	21/47	0.877613750259179	6	FACETS	0.949	0.9	1	0.475	0.45	0.5	CLONAL	2	TRUE	2	0.877613750259179	6		235	1174	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949794	151949794	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000132-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	243	208	0	ENST00000262189.6:c.1306A>G	p.Arg436Gly	p.R436G	ENST00000262189	NM_170606.2	436	Aga/Gga	10/59	0.839111421146782	4	FACETS	0.833	0.784	0.883			1	CLONAL	2	TRUE	NA	0.877613750259179	4		208	624	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578523	7578523	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1567554216	NA	P-0000132-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	619	313	8	ENST00000269305.4:c.407A>C	p.Gln136Pro	p.Q136P	ENST00000269305	NM_001126112.2	136	cAa/cCa	5/11	0.822242472725285	4	FACETS	0.946	0.93	0.961	0.946	0.93	0.961	CLONAL	4	TRUE	0	0.877613750259179	4		321	700	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145650	11145650	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555785383	NA	P-0000132-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	160	369	0	ENST00000358026.2:c.4012A>G	p.Met1338Val	p.M1338V	ENST00000358026	NM_001128849.1	1338	Atg/Gtg	29/36	0.672477730837246	4	FACETS	0.814	0.747	0.884	0.407	0.373	0.442	CLONAL	1	TRUE	2	0.877613750259179	4		369	841	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484750	57484750	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs777939817	NA	P-0000132-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	331	299	0	ENST00000371085.3:c.730A>G	p.Ile244Val	p.I244V	ENST00000371085	NM_000516.4	244	Atc/Gtc	10/13	0.746219996019398	4	FACETS	0.956	0.909	1			1	CLONAL	2	TRUE	NA	0.877613750259179	4		299	741	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033871	49033871	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000132-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	718	378	0	ENST00000267163.4:c.2008del	p.Leu670CysfsTer7	p.L670Cfs*7	ENST00000267163	NM_000321.2	670	Ctg/tg	20/27	0.877613750259179	4	FACETS	0.941	0.926	0.956	0.941	0.926	0.956	CLONAL	4	TRUE	0	0.877613750259179	4		378	816	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0000142-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	273	340	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.276970892628148	4	FACETS		NA	1			1	NA	NA	FALSE	2	NA	4		340	1404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0000142-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	53	800	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		800	671	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657066	47657066	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000142-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	31	209	0	ENST00000233146.2:c.1262T>G	p.Leu421Arg	p.L421R	ENST00000233146	NM_000251.2	421	cTg/cGg	7/16	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		209	481	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279525	1279525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060503011	NA	P-0000142-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	34	354	0	ENST00000310581.5:c.2011C>T	p.Arg671Trp	p.R671W	ENST00000310581	NM_198253.2	671	Cgg/Tgg	5/16	0.3	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		354	227	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000152-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	129	284	1	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.558327698734534	1	FACETS	0.908	0.832	0.985	0.908	0.832	0.985	CLONAL	1	TRUE	0	0.558327698734534	1		285	367	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984848	11984848	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0000152-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	182	212	0	ENST00000353533.5:c.393+1G>A		p.X131_splice	ENST00000353533	NM_003010.3	131			0.559065518790615	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.558327698734534	2		212	317	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882049	36882049	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs34810717	NA	P-0000152-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	184	403	0	ENST00000358127.4:c.964G>A	p.Ala322Thr	p.A322T	ENST00000358127	NM_001280556.1	322	Gct/Act	8/10	1	2	FACETS	0.951	0.881	1	0.951	0.881	1	CLONAL	1	TRUE	1	0.558327698734534	2		403	693	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865491	57865491	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1184432538	NA	P-0000152-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	468	570	1	ENST00000228682.2:c.2968C>T	p.Arg990Ter	p.R990*	ENST00000228682	NM_005269.2	990	Cga/Tga	12/12	0.559065518790615	3	FACETS	0.918	0.879	0.957	0.918	0.879	0.957	CLONAL	2	TRUE	1	0.558327698734534	3		571	1168	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120512	70120512	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000152-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	105	294	0	ENST00000245479.2:c.1514A>T	p.Gln505Leu	p.Q505L	ENST00000245479	NM_000346.3	505	cAg/cTg	3/3	0.559065518790615	3	FACETS	0.767	0.689	0.851	0.384	0.344	0.426	SUBCLONAL	1	TRUE	1	0.558327698734534	3		294	627	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145635	11145635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000152-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	148	295	2	ENST00000358026.2:c.3997C>T	p.Arg1333Trp	p.R1333W	ENST00000358026	NM_001128849.1	1333	Cgg/Tgg	29/36	0.559065518790615	3	FACETS	1	0.942	1	0.345	0.316	0.376	CLONAL	1	TRUE	0	0.558327698734534	3		297	655	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0000155-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	102	675	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.257286031392136	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	0	0.417181932466435	2		675	236	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921566	178921566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793349	NA	P-0000155-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	81	269	0	ENST00000263967.3:c.1048G>A	p.Asp350Asn	p.D350N	ENST00000263967	NM_006218.2	350	Gac/Aac	5/21	0.257286031392136	2	FACETS	0.912	0.819	1	0.912	0.819	1	CLONAL	2	TRUE	0	0.417181932466435	2		269	213	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161217	56161217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000155-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	91	390	0	ENST00000399503.3:c.1086G>A	p.Met362Ile	p.M362I	ENST00000399503	NM_005921.1	362	atG/atA	5/20	0.214567796941776	4	FACETS	1	0.978	1	0.474	0.423	0.528	INDETERMINATE	1	TRUE	1	0.417181932466435	4		390	435	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344177	118344177	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000155-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	90	288	0	ENST00000534358.1:c.2303C>T	p.Ser768Leu	p.S768L	ENST00000534358	NM_005933.3	768	tCa/tTa	3/36	0.417181932466435	1	FACETS	0.933	0.85	1	1	0.987	1	CLONAL	2	TRUE	0	0.417181932466435	1		288	183	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160634	56160634	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0000155-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	174	305	0	ENST00000399503.3:c.910del	p.Thr304GlnfsTer8	p.T304Qfs*8	ENST00000399503	NM_005921.1	303	gAa/ga	4/20	0.214567796941776	4	FACETS	0.963	0.898	1	0.963	0.898	1	INDETERMINATE	3	TRUE	1	0.417181932466435	4		305	409	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849488	68849489	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0000155-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	153	488	0	ENST00000261769.5:c.1397_1398del	p.Leu466HisfsTer16	p.L466Hfs*16	ENST00000261769	NM_004360.3	464	gTC/g	10/16	0.417181932466435	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.417181932466435	2		488	296	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0000185-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	2123	340	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.574980210507487	4	FACETS	1	0.997	1			1	CLONAL	3	TRUE	NA	0.81318543340687	4		340	2995	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0000185-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	484	285	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.81318543340687	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.81318543340687	1		285	645	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331973	81331973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000191-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1173	470	520	0	ENST00000222390.5:c.2111G>A	p.Gly704Asp	p.G704D	ENST00000222390	NM_000601.4	704	gGt/gAt	18/18	1	2	FACETS	0.855	0.815	0.895	0.855	0.815	0.895	CLONAL	1	TRUE	1	0.669525931614707	2		520	1643	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404947	404947	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000191-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1798	284	620	0	ENST00000399788.2:c.4247C>G	p.Pro1416Arg	p.P1416R	ENST00000399788	NM_001042603.1	1416	cCa/cGa	26/28	0.213947455148429	3	FACETS	0.544	0.509	0.58	0.272	0.254	0.29	INDETERMINATE	1	TRUE	1	0.669525931614707	3		620	2082	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811750	102811750	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000191-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1653	92	593	0	ENST00000307046.8:c.434A>G	p.Lys145Arg	p.K145R	ENST00000307046	NM_001111285.1	145	aAg/aGg	4/4	1	2	FACETS	0.157	0.139	0.178	0.157	0.139	0.178	SUBCLONAL	1	TRUE	1	0.669525931614707	2		593	1745	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0000191-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	612	323	0	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.669525931614707	2		323	861	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0000192-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	126	340	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.938	0.849	1	0.938	0.849	1	CLONAL	1	TRUE	1	0.316491007565852	2		340	849	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871119	12871119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000192-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	38	341	0	ENST00000228872.4:c.346G>A	p.Ala116Thr	p.A116T	ENST00000228872	NM_004064.3	116	Gcg/Acg	1/3	1	2	FACETS	0.469	0.387	0.561	0.469	0.387	0.561	SUBCLONAL	1	TRUE	1	0.316491007565852	2		341	512	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575153	64575153	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0000203-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	317	243	0	ENST00000312049.6:c.655-1G>T		p.X219_splice	ENST00000312049	NM_130799.2	219			0.927447104706646	1	FACETS	0.921	0.892	0.948	0.921	0.892	0.948	CLONAL	1	TRUE	0	0.927447104706646	1		243	398	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0000203-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	596	379	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	1	2	FACETS	0.992	0.956	1	0.992	0.956	1	CLONAL	1	TRUE	1	0.927447104706646	2		379	1296	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913499	NA	P-0000223-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	551	399	0	ENST00000345146.2:c.394C>A	p.Arg132Ser	p.R132S	ENST00000345146	NM_005896.2	132	Cgt/Agt	4/10	1	2	FACETS	1	0.982	1	1	0.998	1	CLONAL	5	FALSE	1	0.168246259741698	2		399	1267	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629296	187629296	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000223-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	177	479	0	ENST00000441802.2:c.1686G>T	p.Leu562Phe	p.L562F	ENST00000441802	NM_005245.3	562	ttG/ttT	2/27	0.168246259741698	1	FACETS	0.809	0.744	0.877	1	0.99	1	CLONAL	2	FALSE	0	0.168246259741698	1		479	1191	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0000223-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	1461	479	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.168246259741698	6	FACETS	0.976	0.967	0.985			1	CLONAL	15	FALSE	NA	0.168246259741698	6		479	1585	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950106	44950106	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000223-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	344	375	0	ENST00000377967.4:c.3875T>G	p.Ile1292Ser	p.I1292S	ENST00000377967	NM_021140.2	1292	aTt/aGt	26/29	0.168246259741698	0	FACETS	0.988	0.935	1			1	CLONAL	3	FALSE	0	0.168246259741698	0		375	1148	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872163	76872187	+	frameshift_variant	Frame_Shift_Del	DEL	AGGCAAGAATTTTGTTAATGCTGTA	AGGCAAGAATTTTGTTAATGCTGTA	-	novel	NA	P-0000223-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	221	475	0	ENST00000373344.5:c.5460_5484del	p.Thr1821GlnfsTer7	p.T1821Qfs*7	ENST00000373344	NM_000489.3	1820	taTACAGCATTAACAAAATTCTTGCCT/ta	22/35	0.168246259741698	0	FACETS	0.817	0.761	0.874			1	CLONAL	3	FALSE	0	0.168246259741698	0		475	892	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0000233-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	20	611	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		611	924	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176710908	176710908	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000236-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	148	407	0	ENST00000439151.2:c.6130G>T	p.Ala2044Ser	p.A2044S	ENST00000439151	NM_022455.4	2044	Gca/Tca	20/23	1	2	FACETS	0.982	0.899	1	0.982	0.899	1	CLONAL	1	TRUE	1	0.431675151981314	2		407	698	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2952978	2952978	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000236-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	103	275	0	ENST00000396946.4:c.2962C>A	p.Leu988Met	p.L988M	ENST00000396946	NM_032415.4	988	Ctg/Atg	22/25	0.431675151981314	1	FACETS	0.995	0.898	1	0.995	0.898	1	CLONAL	1	TRUE	0	0.431675151981314	1		275	376	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259476	55259476	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000236-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	80	270	0	ENST00000275493.2:c.2534T>A	p.Val845Glu	p.V845E	ENST00000275493	NM_005228.3	845	gTg/gAg	21/28	1	2	FACETS	0.731	0.645	0.823	0.731	0.645	0.823	SUBCLONAL	1	TRUE	1	0.431675151981314	2		270	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1064795203	NA	P-0000236-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	80	272	0	ENST00000269305.4:c.532C>G	p.His178Asp	p.H178D	ENST00000269305	NM_001126112.2	178	Cac/Gac	5/11	0.431675151981314	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.431675151981314	1		272	273	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533676	63533676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367697282	NA	P-0000247-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	164	242	0	ENST00000307078.5:c.1478C>T	p.Ser493Leu	p.S493L	ENST00000307078	NM_004655.3	493	tCg/tTg	6/11	0.640054092709591	5	FACETS	1	0.956	1			1	CLONAL	1	FALSE	NA	0.769022624998141	5		242	865	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0000247-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	94	187	0	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	0.769022624998141	4	FACETS	0.753	0.672	0.84	0.377	0.336	0.42	SUBCLONAL	1	FALSE	2	0.769022624998141	4		187	574	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11227508	11227508	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000247-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	193	289	0	ENST00000361445.4:c.4320T>G	p.Phe1440Leu	p.F1440L	ENST00000361445	NM_004958.3	1440	ttT/ttG	29/58	0.595091488804647	3	FACETS	0.996	0.924	1			1	CLONAL	1	FALSE	NA	0.769022624998141	3		289	698	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726982	46726982	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs762075828	NA	P-0000247-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	212	296	0	ENST00000371975.4:c.816C>G	p.Ile272Met	p.I272M	ENST00000371975	NM_003579.3	272	atC/atG	8/18	0.711926180802991	3	FACETS	0.94	0.875	1	0.47	0.437	0.504	CLONAL	1	FALSE	1	0.769022624998141	3		296	812	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464902	120464902	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000247-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	93	166	0	ENST00000256646.2:c.5170C>T	p.His1724Tyr	p.H1724Y	ENST00000256646	NM_024408.3	1724	Cac/Tac	28/34	0.711926180802991	3	FACETS	0.831	0.744	0.923	0.415	0.372	0.462	CLONAL	1	FALSE	1	0.769022624998141	3		166	403	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612900	228612900	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000247-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	189	359	0	ENST00000366696.1:c.127C>T	p.Arg43Trp	p.R43W	ENST00000366696	NM_003493.2	43	Cgg/Tgg	1/1	0.640054092709591	5	FACETS	0.864	0.797	0.934			1	CLONAL	1	FALSE	NA	0.769022624998141	5		359	1225	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288964	212288964	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000247-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	114	275	0	ENST00000342788.4:c.2782G>C	p.Glu928Gln	p.E928Q	ENST00000342788	NM_005235.2	928	Gaa/Caa	23/28	0.645482364160531	3	FACETS	0.834	0.755	0.917	0.417	0.377	0.459	CLONAL	1	FALSE	1	0.769022624998141	3		275	492	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72866395	72866395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000247-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	99	208	0	ENST00000325599.8:c.868G>A	p.Glu290Lys	p.E290K	ENST00000325599	NM_018130.2	290	Gaa/Aaa	7/11	0.645482364160531	3	FACETS	0.898	0.808	0.992	0.449	0.404	0.496	CLONAL	1	FALSE	1	0.769022624998141	3		208	397	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913274	NA	P-0000247-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	13	143	0	ENST00000263967.3:c.1634A>C	p.Glu545Ala	p.E545A	ENST00000263967	NM_006218.2	545	gAg/gCg	10/21	0.769022624998141	4	FACETS	0.308	0.22	0.416	0.154	0.11	0.208	SUBCLONAL	1	FALSE	2	0.769022624998141	4		143	194	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180049816	180049816	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000247-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	71	253	0	ENST00000261937.6:c.1572G>C	p.Gln524His	p.Q524H	ENST00000261937	NM_182925.4	524	caG/caC	12/30	0.450671374436097	5	FACETS	0.489	0.425	0.557	0.122	0.106	0.14	INDETERMINATE	1	FALSE	1	0.769022624998141	5		253	814	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163720	32163720	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000247-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	114	159	0	ENST00000375023.3:c.5506G>T	p.Glu1836Ter	p.E1836*	ENST00000375023	NM_004557.3	1836	Gag/Tag	30/30	0.711926180802991	3	FACETS	1	0.917	1	0.506	0.459	0.554	CLONAL	1	FALSE	1	0.769022624998141	3		159	406	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43746215	43746215	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000247-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	206	295	0	ENST00000523873.1:c.334C>T	p.His112Tyr	p.H112Y	ENST00000523873		112	Cac/Tac	4/8	0.711926180802991	3	FACETS	1	0.961	1	0.523	0.487	0.56	CLONAL	1	FALSE	1	0.769022624998141	3		295	709	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005260	150005260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1029205428	NA	P-0000247-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	128	225	0	ENST00000253339.5:c.965C>T	p.Ser322Phe	p.S322F	ENST00000253339		322	tCt/tTt	3/7	1	2	FACETS	0.812	0.743	0.884	0.812	0.743	0.884	CLONAL	1	FALSE	1	0.769022624998141	2		225	410	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388097	81388097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs189052337	NA	P-0000247-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	111	210	0	ENST00000222390.5:c.278G>C	p.Arg93Thr	p.R93T	ENST00000222390	NM_000601.4	93	aGa/aCa	3/18	0.645482364160531	3	FACETS	0.852	0.77	0.938	0.426	0.385	0.469	CLONAL	1	FALSE	1	0.769022624998141	3		210	469	SUCCESS
MET	4233	MSKCC	GRCh37	7	116422057	116422057	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000247-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	109	230	0	ENST00000397752.3:c.3538G>T	p.Asp1180Tyr	p.D1180Y	ENST00000397752	NM_000245.2	1180	Gat/Tat	18/21	0.645482364160531	3	FACETS	0.77	0.694	0.849	0.385	0.347	0.425	SUBCLONAL	1	FALSE	1	0.769022624998141	3		230	510	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050797	5050797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1383887415	NA	P-0000247-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	101	196	1	ENST00000381652.3:c.580G>A	p.Asp194Asn	p.D194N	ENST00000381652	NM_004972.3	194	Gat/Aat	6/25	0.694610591623126	2	FACETS	0.887	0.804	0.973	0.444	0.402	0.487	CLONAL	1	FALSE	0	0.769022624998141	2		197	296	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120663	115120663	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000247-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	159	287	0	ENST00000257566.3:c.343C>T	p.Gln115Ter	p.Q115*	ENST00000257566	NM_016569.3	115	Cag/Tag	1/8	0.567967789310415	4	FACETS	0.832	0.763	0.905	0.416	0.381	0.453	CLONAL	1	FALSE	2	0.769022624998141	4		287	879	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	364565	364565	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000247-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3079	186	296	0	ENST00000262320.3:c.997C>G	p.Leu333Val	p.L333V	ENST00000262320	NM_003502.3	333	Ctg/Gtg	3/11	0.769022624998141	14	FACETS	0.832	0.763	0.904			1	CLONAL	1	FALSE	NA	0.769022624998141	14		296	3265	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223461	2223461	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000247-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	127	188	0	ENST00000398665.3:c.3572C>G	p.Ser1191Cys	p.S1191C	ENST00000398665	NM_032482.2	1191	tCt/tGt	25/28	NA	2	FACETS	0.944	0.865	1			1	INDETERMINATE	1	FALSE	NA	0.769022624998141	2		188	350	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308098	30308098	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1240513553	NA	P-0000247-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	167	236	0	ENST00000262643.3:c.235G>A	p.Asp79Asn	p.D79N	ENST00000262643	NM_001238.2	79	Gac/Aac	5/12	0.336330204883031	5	FACETS	1	0.984	1	0.423	0.389	0.458	INDETERMINATE	1	FALSE	2	0.769022624998141	5		236	737	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0000252-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	157	800	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.563474999711173	1	FACETS	0.96	0.889	1	0.96	0.889	1	CLONAL	1	TRUE	0	0.563474999711173	1		800	417	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541675	187541675	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000252-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	134	267	1	ENST00000441802.2:c.6065G>T	p.Arg2022Ile	p.R2022I	ENST00000441802	NM_005245.3	2022	aGa/aTa	10/27	0.563474999711173	3	FACETS	1	0.941	1	0.52	0.474	0.568	CLONAL	1	TRUE	1	0.563474999711173	3		268	586	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30293194	30293194	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000252-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	145	321	0	ENST00000322652.5:c.484A>C	p.Thr162Pro	p.T162P	ENST00000322652	NM_015355.2	162	Act/Cct	5/16	0.563474999711173	1	FACETS	0.973	0.898	1	0.973	0.898	1	CLONAL	1	TRUE	0	0.563474999711173	1		321	380	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183764	10183764	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs5030804	NA	P-0000272-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	24	259	0	ENST00000256474.2:c.233A>G	p.Asn78Ser	p.N78S	ENST00000256474	NM_000551.3	78	aAt/aGt	1/3	1	2	FACETS	0.982	0.77	1	0.982	0.77	1	CLONAL	1	TRUE	1	0.15	2		259	326	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37083818	37083818	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0000272-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	58	446	0	ENST00000231790.2:c.1727T>A	p.Leu576Ter	p.L576*	ENST00000231790	NM_000249.3	576	tTa/tAa	15/19	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.15	2		446	615	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962294	2962294	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1003847451	NA	P-0000272-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	55	439	0	ENST00000396946.4:c.2243C>T	p.Thr748Met	p.T748M	ENST00000396946	NM_032415.4	748	aCg/aTg	17/25	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.15	2		439	517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579572	7579572	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000272-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	20	309	0	ENST00000269305.4:c.115G>T	p.Ala39Ser	p.A39S	ENST00000269305	NM_001126112.2	39	Gca/Tca	4/11	1	2	FACETS	0.721	0.55	0.921	0.721	0.55	0.921	CLONAL	1	TRUE	1	0.15	2		309	370	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442556	52442557	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0000272-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	26	223	0	ENST00000460680.1:c.188_189del	p.Ser63TyrfsTer5	p.S63Yfs*5	ENST00000460680	NM_004656.3	63	tCT/t	4/17	1	2	FACETS	0.985	0.78	1	0.985	0.78	1	CLONAL	1	TRUE	1	0.15	2		223	352	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584583	52584583	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000272-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	26	414	0	ENST00000394830.3:c.4430del	p.Pro1477LeufsTer12	p.P1477Lfs*12	ENST00000394830	NM_018313.4	1477	cCt/ct	29/30	1	2	FACETS	0.806	0.638	1	0.806	0.638	1	CLONAL	1	TRUE	1	0.15	2		414	430	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310879	123310879	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1164513666	NA	P-0000272-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	33	435	0	ENST00000358487.5:c.549del	p.Asn184ThrfsTer9	p.N184Tfs*9	ENST00000358487	NM_000141.4	183	ggG/gg	5/18	1	2	FACETS	0.835	0.679	1	0.835	0.679	1	CLONAL	1	TRUE	1	0.15	2		435	527	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0000282-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	152	711	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	1	0.971	1	1	0.992	1	CLONAL	2	TRUE	1	0.151130448190105	2		711	883	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412030	116412044	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TACTTTTCCAGAAGG	TACTTTTCCAGAAGG	-	novel	NA	P-0000289-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	58	158	0	ENST00000397752.3:c.3017_3028+3del		p.X1006_splice	ENST00000397752	NM_000245.2	1006		14/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		158	239	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0000292-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	96	675	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.364014962792627	4	FACETS	0.779	0.698	0.863	0.779	0.698	0.863	SUBCLONAL	2	TRUE	2	0.41821123072091	4		675	418	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471040	25471040	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761452501	NA	P-0000292-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	116	478	0	ENST00000264709.3:c.721G>A	p.Glu241Lys	p.E241K	ENST00000264709	NM_175629.2	241	Gag/Aag	7/23	0.191911410060086	5	FACETS	0.772	0.697	0.849	0.514	0.465	0.566	INDETERMINATE	2	TRUE	2	0.41821123072091	5		478	585	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544679	65544679	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000292-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	186	456	0	ENST00000358664.4:c.247C>T	p.Gln83Ter	p.Q83*	ENST00000358664	NM_002382.4	83	Caa/Taa	4/5	0.41821123072091	4	FACETS	0.945	0.883	1	0.945	0.883	1	CLONAL	3	TRUE	1	0.41821123072091	4		456	445	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847276	68847276	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000292-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	106	356	0	ENST00000261769.5:c.1198G>A	p.Asp400Asn	p.D400N	ENST00000261769	NM_004360.3	400	Gat/Aat	9/16	0.228919396402359	1	FACETS	1	0.98	1	1	0.98	1	INDETERMINATE	1	TRUE	0	0.41821123072091	1		356	303	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0000299-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	121	611	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.30797180769725	1	FACETS	0.911	0.823	1	0.911	0.823	1	CLONAL	1	TRUE	0	0.30797180769725	1		611	730	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17371265	17371265	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs200131173	NA	P-0000299-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	114	225	0	ENST00000375499.3:c.191A>C	p.Asp64Ala	p.D64A	ENST00000375499	NM_003000.2	64	gAc/gCc	2/8	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.30797180769725	2		225	713	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154815	2154815	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000299-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	125	410	1	ENST00000434045.2:c.406C>A	p.Leu136Met	p.L136M	ENST00000434045	NM_001127598.1	136	Ctg/Atg	4/5	1	2	FACETS	0.836	0.756	0.921	0.836	0.756	0.921	CLONAL	1	TRUE	1	0.30797180769725	2		411	971	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896463	28896463	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000299-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	55	233	0	ENST00000282397.4:c.2987T>C	p.Met996Thr	p.M996T	ENST00000282397	NM_002019.4	996	aTg/aCg	22/30	0.150930232981857	1	FACETS	0.455	0.389	0.528	0.455	0.389	0.528	INDETERMINATE	1	TRUE	0	0.30797180769725	1		233	664	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654718	29654718	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs370858405	NA	P-0000299-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	93	218	0	ENST00000356175.3:c.5407A>G	p.Ile1803Val	p.I1803V	ENST00000356175	NM_000267.3	1803	Atc/Gtc	37/57	1	2	FACETS	0.844	0.75	0.943	0.844	0.75	0.943	CLONAL	1	TRUE	1	0.30797180769725	2		218	716	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63553924	63553924	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000299-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	118	293	0	ENST00000307078.5:c.815G>T	p.Arg272Met	p.R272M	ENST00000307078	NM_004655.3	272	aGg/aTg	2/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.30797180769725	2		293	701	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220427	1220427	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000299-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	112	380	0	ENST00000326873.7:c.520C>G	p.His174Asp	p.H174D	ENST00000326873	NM_000455.4	174	Cac/Gac	4/10	0.30797180769725	1	FACETS	0.972	0.876	1	0.972	0.876	1	CLONAL	1	TRUE	0	0.30797180769725	1		380	633	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226579931	226579931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765535441	NA	P-0000314-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	354	648	1	ENST00000366794.5:c.371C>T	p.Thr124Met	p.T124M	ENST00000366794	NM_001618.3	124	aCg/aTg	3/23	1	2	FACETS	0.948	0.899	0.999	0.948	0.899	0.999	CLONAL	1	TRUE	1	0.634451172338204	2		649	1177	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646150	215646150	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730881411	NA	P-0000314-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	374	411	0	ENST00000260947.4:c.448C>T	p.Arg150Ter	p.R150*	ENST00000260947	NM_000465.2	150	Cga/Tga	4/11	0.344477437254585	3	FACETS	0.938	0.895	0.981	0.938	0.895	0.981	INDETERMINATE	2	TRUE	1	0.634451172338204	3		411	828	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143044479	143044479	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000314-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	153	546	0	ENST00000262992.4:c.1983G>C	p.Leu661Phe	p.L661F	ENST00000262992	NM_001101669.1	661	ttG/ttC	18/24	1	2	FACETS	0.467	0.426	0.509	0.467	0.426	0.509	SUBCLONAL	1	TRUE	1	0.634451172338204	2		546	1033	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554840	187554840	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000314-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	107	441	0	ENST00000441802.2:c.4321C>T	p.Gln1441Ter	p.Q1441*	ENST00000441802	NM_005245.3	1441	Cag/Tag	7/27	1	2	FACETS	0.505	0.453	0.56	0.505	0.453	0.56	SUBCLONAL	1	TRUE	1	0.634451172338204	2		441	668	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056153	26056153	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs534420299	NA	P-0000314-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	155	391	0	ENST00000343677.2:c.504G>C	p.Lys168Asn	p.K168N	ENST00000343677	NM_005319.3	168	aaG/aaC	1/1	0.401456729879873	4	FACETS	0.803	0.735	0.875			1	CLONAL	1	TRUE	NA	0.634451172338204	4		391	994	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923603	39923603	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1048287551	NA	P-0000314-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	59	248	0	ENST00000378444.4:c.3488G>A	p.Arg1163Gln	p.R1163Q	ENST00000378444	NM_001123385.1	1163	cGa/cAa	7/15	1	1	FACETS	0.206	0.177	0.238	0.206	0.177	0.238	SUBCLONAL	1	TRUE	0	0.634451172338204	1		248	616	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922058	39922058	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000314-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	636	409	0	ENST00000378444.4:c.4114del	p.Glu1372SerfsTer8	p.E1372Sfs*8	ENST00000378444	NM_001123385.1	1372	Gag/ag	9/15	1	1	FACETS	0.766	0.747	0.786	1	0.998	1	SUBCLONAL	2	TRUE	0	0.634451172338204	1		409	893	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0000317-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	100	206	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.585935518995967	2	FACETS	0.855	0.803	0.904	1	0.987	1	CLONAL	3	FALSE	0	0.585935518995967	2		207	133	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994790	73994790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs562558740	NA	P-0000317-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	52	347	0	ENST00000318443.5:c.274C>T	p.Arg92Cys	p.R92C	ENST00000318443	NM_001024736.1	92	Cgc/Tgc	3/10	0.585935518995967	3	FACETS	1	0.947	1	0.604	0.522	0.691	CLONAL	1	FALSE	1	0.585935518995967	3		347	190	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42788872	42788872	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1161639394	NA	P-0000317-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	92	383	2	ENST00000575354.2:c.16A>G	p.Arg6Gly	p.R6G	ENST00000575354	NM_015125.3	6	Agg/Ggg	1/20	0.207856533530099	5	FACETS	0.952	0.855	1	0.634	0.57	0.701	INDETERMINATE	2	FALSE	2	0.585935518995967	5		385	310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0000321-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	538	715	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.686944664983146	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.686944664983146	3		715	663	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339328	70339339	+	splice_donor_variant,intron_variant	Splice_Site	DEL	GTGAGACAACTC	GTGAGACAACTC	-	novel	NA	P-0000321-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	150	236	0	ENST00000374080.3:c.204+1_204+12del		p.X68_splice	ENST00000374080		68			0.525675751219282	3	FACETS	0.824	0.764	0.885	0.824	0.764	0.885	CLONAL	2	TRUE	1	0.686944664983146	3		236	356	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0000321-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	147	140	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	0.650434149690772	4	FACETS	0.965	0.892	1	0.965	0.892	1	CLONAL	2	TRUE	2	0.686944664983146	4		140	374	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54956542	54956542	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000321-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	70	364	0	ENST00000312783.6:c.652G>T	p.Val218Phe	p.V218F	ENST00000312783	NM_198436.1	218	Gtt/Ttt	7/10	0.686944664983146	4	FACETS	0.439	0.382	0.501	0.22	0.191	0.251	SUBCLONAL	1	TRUE	2	0.686944664983146	4		364	783	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591092	67591093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0000321-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	138	141	0	ENST00000274335.5:c.1686dup	p.Met563TyrfsTer5	p.M563Yfs*5	ENST00000274335		562	cgt/cgTt	12/15	0.650434149690772	4	FACETS	0.926	0.853	1	0.926	0.853	1	CLONAL	2	TRUE	2	0.686944664983146	4		141	366	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845814	151845831	+	inframe_deletion	In_Frame_Del	DEL	GATAGTCTTTGGGCACAG	GATAGTCTTTGGGCACAG	-	novel	NA	P-0000321-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	33	337	0	ENST00000262189.6:c.13181_13198del	p.Pro4394_Tyr4399del	p.P4394_Y4399del	ENST00000262189	NM_170606.2	4394	cCTGTGCCCAAAGACTATCgg/cgg	52/59	0.650434149690772	4	FACETS	0.287	0.233	0.349	0.144	0.116	0.175	SUBCLONAL	1	TRUE	2	0.686944664983146	4		337	564	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0000327-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	320	378	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.456654938464858	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.567751473018436	4		378	798	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094461	27094461	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000327-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	132	256	0	ENST00000324856.7:c.3169T>C	p.Ser1057Pro	p.S1057P	ENST00000324856	NM_006015.4	1057	Tct/Cct	11/20	0.567751473018436	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.567751473018436	1		256	245	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226796	2226796	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1358779949	NA	P-0000327-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	25	347	0	ENST00000398665.3:c.4276C>T	p.Leu1426Phe	p.L1426F	ENST00000398665	NM_032482.2	1426	Ctc/Ttc	27/28	0.336825225045964	1	FACETS	0.327	0.259	0.403	0.327	0.259	0.403	INDETERMINATE	1	TRUE	0	0.567751473018436	1		347	193	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226564961	226564961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1352340038	NA	P-0000337-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	100	416	0	ENST00000366794.5:c.1789G>A	p.Gly597Ser	p.G597S	ENST00000366794	NM_001618.3	597	Ggt/Agt	13/23	0.181970771271718	6	FACETS	0.75	0.669	0.837	0.5	0.446	0.558	SUBCLONAL	2	TRUE	3	0.181970771271718	6		416	999	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371908	55371908	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs750714789	NA	P-0000337-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	19	268	0	ENST00000297316.4:c.598G>T	p.Gly200Cys	p.G200C	ENST00000297316	NM_022454.3	200	Ggc/Tgc	2/2	0.181970771271718	3	FACETS	1	0.78	1	0.513	0.39	0.656	CLONAL	1	TRUE	1	0.181970771271718	3		268	222	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115854	8115855	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0000337-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1195	116	1289	0	ENST00000346208.3:c.1201dup	p.Ser401PhefsTer106	p.S401Ffs*106	ENST00000346208		400	-/T	6/6	0.181970771271718	8	FACETS	0.752	0.675	0.833			1	SUBCLONAL	2	TRUE	NA	0.181970771271718	8		1289	1311	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0000347-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	769	385	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.39438754697244	16	FACETS	0.956	0.929	0.984			1	CLONAL	11	TRUE	NA	0.39438754697244	16		385	1394	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0000347-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	1189	362	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.39438754697244	16	FACETS	0.962	0.942	0.981			1	CLONAL	13	TRUE	NA	0.39438754697244	16		362	1814	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953788	48953788	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0000347-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	212	495	0	ENST00000267163.4:c.1389+2T>C		p.X463_splice	ENST00000267163	NM_000321.2	463			0.327060734431966	2	FACETS	0.848	0.792	0.905	0.848	0.792	0.905	CLONAL	2	TRUE	0	0.39438754697244	2		495	634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000347-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	192	799	0	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	0.25649307065975	3	FACETS	0.799	0.742	0.859	0.799	0.742	0.859	SUBCLONAL	2	TRUE	1	0.39438754697244	3		799	729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578464	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000347-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	74	450	0	ENST00000269305.4:c.466C>G	p.Arg156Gly	p.R156G	ENST00000269305	NM_001126112.2	156	Cgc/Ggc	5/11	0.25649307065975	3	FACETS	0.921	0.808	1	0.46	0.404	0.521	CLONAL	1	TRUE	1	0.39438754697244	3		450	488	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627290	12627290	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000353-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1222	146	472	0	ENST00000251849.4:c.1426C>G	p.Leu476Val	p.L476V	ENST00000251849	NM_002880.3	476	Ctc/Gtc	14/17	0.281870378180136	3	FACETS	0.802	0.73	0.879			1	CLONAL	1	TRUE	NA	0.306838104484024	3		472	1368	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138382789	138382789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000353-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	72	331	0	ENST00000289153.2:c.2755G>A	p.Asp919Asn	p.D919N	ENST00000289153	NM_006219.2	919	Gac/Aac	19/22	1	2	FACETS	0.426	0.371	0.486	0.426	0.371	0.486	SUBCLONAL	1	TRUE	1	0.306838104484024	2		331	1101	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0000353-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	135	262	0	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	NA	2	FACETS	0.95	0.87	1			1	INDETERMINATE	2	TRUE	NA	0.306838104484024	2		262	463	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457390	67457390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782977	NA	P-0000373-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	95	373	0	ENST00000327367.4:c.364G>A	p.Val122Met	p.V122M	ENST00000327367	NM_005902.3	122	Gtg/Atg	2/9	0.194794432653418	5	FACETS	0.994	0.887	1	0.331	0.295	0.37	INDETERMINATE	1	TRUE	2	0.662445298551853	5		373	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0000383-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	120	316	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.705646148880516	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.705646148880516	1		317	199	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641142	23641142	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000383-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	273	370	0	ENST00000261584.4:c.2333G>A	p.Ser778Asn	p.S778N	ENST00000261584	NM_024675.3	778	aGt/aAt	5/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.705646148880516	2		370	730	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0000383-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	180	622	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	0.167414654179178	4	FACETS	0.912	0.849	0.976	0.912	0.849	0.976	INDETERMINATE	2	TRUE	2	0.705646148880516	4		622	477	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0000408-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	255	316	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.278582582479596	1	FACETS	1	0.949	1	1	0.949	1	INDETERMINATE	1	TRUE	0	0.701726657145805	1		317	472	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609311	81609311	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs780949533	NA	P-0000408-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	137	409	0	ENST00000298171.2:c.909G>C	p.Glu303Asp	p.E303D	ENST00000298171	NM_000369.2	303	gaG/gaC	10/10	NA	2	FACETS	0.767	0.702	0.835			1	INDETERMINATE	1	TRUE	NA	0.701726657145805	2		409	509	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774136	56774136	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000408-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	182	535	0	ENST00000337432.4:c.487A>C	p.Ser163Arg	p.S163R	ENST00000337432	NM_058216.2	163	Agt/Cgt	3/9	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.701726657145805	2		535	508	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47724981	47724981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754077264	NA	P-0000408-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	73	771	0	ENST00000449228.1:c.763G>A	p.Gly255Arg	p.G255R	ENST00000449228	NM_001127240.2	255	Ggg/Agg	4/4	1	2	FACETS	0.191	0.166	0.218	0.191	0.166	0.218	SUBCLONAL	1	TRUE	1	0.701726657145805	2		771	1087	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419920	41419920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000408-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	259	671	0	ENST00000373198.4:c.401C>T	p.Pro134Leu	p.P134L	ENST00000373198	NM_133170.3	134	cCt/cTt	3/32	0.489892260525796	3	FACETS	0.849	0.794	0.905			1	CLONAL	1	TRUE	NA	0.701726657145805	3		671	1175	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691953	30691954	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0000408-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	143	215	0	ENST00000295754.5:c.454+2dup		p.X152_splice	ENST00000295754	NM_003242.5	152			0.570869610088874	2	FACETS	0.79	0.737	0.842	0.79	0.737	0.842	SUBCLONAL	2	TRUE	0	0.701726657145805	2		215	258	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653834	89653834	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000408-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	86	397	0	ENST00000371953.3:c.132del	p.Val45TyrfsTer9	p.V45Yfs*9	ENST00000371953	NM_000314.4	44	ggC/gg	2/9	0.701726657145805	1	FACETS	0.74	0.668	0.814	0.74	0.668	0.814	SUBCLONAL	1	TRUE	0	0.701726657145805	1		397	215	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0000418-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	168	265	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.53411214811084	5	FACETS	0.948	0.9	0.995			1	CLONAL	5	TRUE	NA	0.53411214811084	5		267	239	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421790	49421790	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0000418-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	180	535	5	ENST00000301067.7:c.14515+2T>C		p.X4839_splice	ENST00000301067	NM_003482.3	4839			0.424834056800813	4	FACETS	1	0.951	1			1	CLONAL	2	TRUE	NA	0.53411214811084	4		540	503	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725042	89725042	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1085308041	NA	P-0000428-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	226	358	2	ENST00000371953.3:c.1027-2A>G		p.X343_splice	ENST00000371953	NM_000314.4	343			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		360	861	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624301	89624306	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	GACCTG	GACCTG	-	novel	NA	P-0000428-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	77	130	0	ENST00000371953.3:c.75_79+1del		p.X25_splice	ENST00000371953	NM_000314.4	25		1/9	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		130	406	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202977	16202977	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000454-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	51	238	1	ENST00000375759.3:c.685C>T	p.Arg229Ter	p.R229*	ENST00000375759	NM_015001.2	229	Cga/Tga	3/15	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		239	870	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607188	189607188	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000454-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	71	276	0	ENST00000264731.3:c.1567C>T	p.Gln523Ter	p.Q523*	ENST00000264731	NM_003722.4	523	Cag/Tag	12/14	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		276	1193	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057520000	NA	P-0000464-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	152	392	0	ENST00000269305.4:c.452C>A	p.Pro151His	p.P151H	ENST00000269305	NM_001126112.2	151	cCc/cAc	5/11	1	2	FACETS	0.988	0.908	1	1	0.992	1	CLONAL	2	TRUE	1	0.26196539756755	2		392	587	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247774	59247774	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000464-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1736	134	809	0	ENST00000371222.2:c.969del	p.Met323IlefsTer2	p.M323Ifs*2	ENST00000371222	NM_002228.3	323	atG/at	1/1	0.26196539756755	3	FACETS	0.619	0.559	0.682			1	SUBCLONAL	1	TRUE	NA	0.26196539756755	3		809	1870	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156740	20156740	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000477-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	417	466	0	ENST00000379607.5:c.17G>A	p.Gly6Asp	p.G6D	ENST00000379607	NM_001412.3	6	gGt/gAt	2/7	0.443948209210211	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.443948209210211	1		466	1041	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089562	27089562	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000480-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1480	250	514	0	ENST00000324856.7:c.2518C>T	p.Gln840Ter	p.Q840*	ENST00000324856	NM_006015.4	840	Caa/Taa	8/20	1	2	FACETS	0.703	0.655	0.753	0.703	0.655	0.753	SUBCLONAL	1	TRUE	1	0.411071647671071	2		514	1730	SUCCESS
AR	367	MSKCC	GRCh37	X	66943571	66943571	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000480-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1300	70	229	0	ENST00000374690.3:c.2651A>C	p.Lys884Thr	p.K884T	ENST00000374690	NM_000044.3	884	aAg/aCg	8/8	1	1	FACETS	0.197	0.171	0.226	0.197	0.171	0.226	SUBCLONAL	1	TRUE	0	0.411071647671071	1		229	1370	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094445	27094446	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0000480-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	128	114	0	ENST00000324856.7:c.3154dup	p.Tyr1052LeufsTer53	p.Y1052Lfs*53	ENST00000324856	NM_006015.4	1051	-/T	11/20	1	2	FACETS	0.602	0.544	0.662	0.602	0.544	0.662	SUBCLONAL	1	TRUE	1	0.411071647671071	2		114	1035	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941830	44941831	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000480-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	427	159	0	ENST00000377967.4:c.3160dup	p.Arg1054LysfsTer5	p.R1054Kfs*5	ENST00000377967	NM_021140.2	1052	gaa/gAaa	21/29	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.411071647671071	1		159	1450	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117746743	117746743	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000484-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	65	362	0	ENST00000368508.3:c.77A>G	p.Gln26Arg	p.Q26R	ENST00000368508	NM_002944.2	26	cAg/cGg	1/43	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	NA	NA		362	870	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945155	44945155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000484-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	59	333	0	ENST00000377967.4:c.3479G>T	p.Gly1160Val	p.G1160V	ENST00000377967	NM_021140.2	1160	gGc/gTc	24/29	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		333	471	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402732	139402732	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000497-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	169	173	0	ENST00000277541.6:c.3277T>C	p.Tyr1093His	p.Y1093H	ENST00000277541	NM_017617.3	1093	Tac/Cac	20/34	0.71300831084792	3	FACETS	1	0.975	1	0.561	0.519	0.605	CLONAL	1	TRUE	1	0.71300831084792	3		173	573	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741694	17741694	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000497-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	1255	434	0	ENST00000250003.3:c.365T>G	p.Leu122Arg	p.L122R	ENST00000250003	NM_002478.4	122	cTg/cGg	1/3	0.427017380767597	4	FACETS		NA	1			1	INDETERMINATE	5	TRUE	2	0.71300831084792	4		434	1284	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210801	133210801	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000497-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	414	517	0	ENST00000320574.5:c.5975G>C	p.Cys1992Ser	p.C1992S	ENST00000320574	NM_006231.2	1992	tGc/tCc	43/49	0.71300831084792	3	FACETS	1	0.992	1	0.593	0.564	0.622	CLONAL	1	TRUE	1	0.71300831084792	3		517	1328	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732724	204732724	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000509-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	138	771	1	ENST00000302823.3:c.59G>A	p.Trp20Ter	p.W20*	ENST00000302823	NM_005214.4	20	tGg/tAg	1/4	1	2	FACETS	0.824	0.748	0.903	0.824	0.748	0.903	CLONAL	1	FALSE	1	0.319482420419622	2		772	1049	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859653	151859653	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000509-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	111	454	0	ENST00000262189.6:c.11009A>C	p.Asn3670Thr	p.N3670T	ENST00000262189	NM_170606.2	3670	aAt/aCt	43/59	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.319482420419622	2		454	650	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732724	204732724	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000509-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	533	771	1	ENST00000302823.3:c.59G>A	p.Trp20Ter	p.W20*	ENST00000302823	NM_005214.4	20	tGg/tAg	1/4	1	2	FACETS	0.908	0.87	0.946	0.908	0.87	0.946	CLONAL	1	TRUE	1	0.785058925638685	2		772	1496	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859653	151859653	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000509-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	410	454	0	ENST00000262189.6:c.11009A>C	p.Asn3670Thr	p.N3670T	ENST00000262189	NM_170606.2	3670	aAt/aCt	43/59	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.785058925638685	2		454	961	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265862	16265869	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCCTTG	CCTCCTTG	-	novel	NA	P-0000509-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	78	720	0	ENST00000375759.3:c.10937_10944del	p.Leu3646GlnfsTer20	p.L3646Qfs*20	ENST00000375759	NM_015001.2	3645	gaCCTCCTTGcc/gacc	15/15	0.387245082572516	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.785058925638685	0		720	1021	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0000515-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	68	299	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.792	0.695	0.894	1	0.976	1	SUBCLONAL	2	TRUE	1	0.286310643796621	2		299	300	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0000515-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	68	612	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.287219001832017	0	FACETS	0.7	0.617	0.788			1	SUBCLONAL	2	TRUE	0	0.286310643796621	0		612	242	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0000515-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	33	469	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.86	0.704	1	0.86	0.704	1	CLONAL	1	TRUE	1	0.286310643796621	2		469	268	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692892	89692892	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554898129	NA	P-0000515-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	39	165	1	ENST00000371953.3:c.376G>T	p.Ala126Ser	p.A126S	ENST00000371953	NM_000314.4	126	Gct/Tct	5/9	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.286310643796621	2		166	237	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57567429	57567429	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000515-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	53	480	1	ENST00000316660.6:c.20G>T	p.Arg7Leu	p.R7L	ENST00000316660	NM_021127.2	7	cGc/cTc	1/2	0.160072777040441	3	FACETS	0.799	0.687	0.919	0.799	0.687	0.919	INDETERMINATE	2	TRUE	1	0.286310643796621	3		481	265	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023217	27023227	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCTAGGCCC	GCCCTAGGCCC	-	novel	NA	P-0000515-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	16	168	0	ENST00000324856.7:c.328_338del	p.Arg110GlufsTer3	p.R110Efs*3	ENST00000324856	NM_006015.4	108	gGCCCTAGGCCC/g	1/20	0.173884765493822	4	FACETS	0.666	0.493	0.871			1	SUBCLONAL	1	TRUE	NA	0.286310643796621	4		168	216	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097621	27097622	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000515-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	60	406	0	ENST00000324856.7:c.3216dup	p.Trp1073MetfsTer32	p.W1073Mfs*32	ENST00000324856	NM_006015.4	1070	-/A	12/20	0.173884765493822	4	FACETS	0.835	0.724	0.953			1	CLONAL	2	TRUE	NA	0.286310643796621	4		406	323	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711928	89711928	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554900593	NA	P-0000515-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	54	317	0	ENST00000371953.3:c.548del	p.Lys183ArgfsTer16	p.K183Rfs*16	ENST00000371953	NM_000314.4	182	ttA/tt	6/9	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.286310643796621	2		317	295	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0000525-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	9	265	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.275024226091678	1	FACETS	0.29	0.192	0.416	0.29	0.192	0.416	SUBCLONAL	1	TRUE	0	0.281880393475847	1		267	189	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0000525-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	60	206	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.219404053366906	3	FACETS	0.829	0.72	0.945	0.829	0.72	0.945	CLONAL	2	TRUE	1	0.281880393475847	3		207	293	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0000525-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	12	285	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.275024226091678	1	FACETS	0.264	0.185	0.362	0.264	0.185	0.362	SUBCLONAL	1	TRUE	0	0.281880393475847	1		285	277	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259206	36259206	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000525-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	102	356	0	ENST00000300305.3:c.285del	p.Asn96ThrfsTer26	p.N96Tfs*26	ENST00000300305		95	ccC/cc	3/8	1	2	FACETS	0.797	0.717	0.881	1	0.984	1	SUBCLONAL	2	TRUE	1	0.281880393475847	2		356	454	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0000525-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	92	206	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.322078702099537	3	FACETS	1	0.951	1	0.561	0.499	0.626	CLONAL	1	TRUE	1	0.345986827281608	3		207	556	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259206	36259206	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000525-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	77	356	0	ENST00000300305.3:c.285del	p.Asn96ThrfsTer26	p.N96Tfs*26	ENST00000300305		95	ccC/cc	3/8	0.220177809412225	5	FACETS	0.788	0.691	0.893	0.263	0.23	0.298	SUBCLONAL	1	TRUE	2	0.345986827281608	5		356	858	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0000525-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	93	486	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	1	2	FACETS	0.641	0.569	0.717	0.641	0.569	0.717	SUBCLONAL	1	TRUE	1	0.345986827281608	2		486	839	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97933379	97933379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000525-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	72	392	0	ENST00000289081.3:c.503G>A	p.Gly168Glu	p.G168E	ENST00000289081	NM_000136.2	168	gGa/gAa	6/15	1	2	FACETS	0.523	0.456	0.595	0.523	0.456	0.595	SUBCLONAL	1	TRUE	1	0.345986827281608	2		392	796	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263850	133263850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000525-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	31	145	0	ENST00000320574.5:c.52G>A	p.Glu18Lys	p.E18K	ENST00000320574	NM_006231.2	18	Gag/Aag	1/49	NA	2	FACETS	0.674	0.547	0.816			1	INDETERMINATE	1	TRUE	NA	0.345986827281608	2		145	266	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220502	1220502	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs121913317	NA	P-0000525-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	72	475	0	ENST00000326873.7:c.595G>A	p.Glu199Lys	p.E199K	ENST00000326873	NM_000455.4	199	Gag/Aag	4/10	NA	2	FACETS	0.593	0.517	0.674			1	INDETERMINATE	1	TRUE	NA	0.345986827281608	2		475	702	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545822	41545822	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000525-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	122	599	0	ENST00000263253.7:c.2437C>T	p.Gln813Ter	p.Q813*	ENST00000263253	NM_001429.3	813	Cag/Tag	14/31	1	2	FACETS	0.598	0.539	0.661	0.598	0.539	0.661	SUBCLONAL	1	TRUE	1	0.345986827281608	2		599	1179	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs17849781	NA	P-0000532-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	86	861	0	ENST00000269305.4:c.832C>A	p.Pro278Thr	p.P278T	ENST00000269305	NM_001126112.2	278	Cct/Act	8/11	0.367172785877224	1	FACETS	0.904	0.804	1	0.904	0.804	1	CLONAL	1	TRUE	0	0.367172785877224	1		861	423	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0000535-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	194	310	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.463622206525237	2		310	775	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054935	176054935	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000535-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	129	529	0	ENST00000367669.3:c.1118C>G	p.Ser373Cys	p.S373C	ENST00000367669	NM_022457.5	373	tCt/tGt	10/20	1	2	FACETS	0.53	0.48	0.584	0.53	0.48	0.584	SUBCLONAL	1	TRUE	1	0.463622206525237	2		529	1049	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584651	187584651	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000535-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	205	615	0	ENST00000441802.2:c.3382G>C	p.Glu1128Gln	p.E1128Q	ENST00000441802	NM_005245.3	1128	Gag/Cag	3/27	0.218172745041925	2	FACETS	0.745	0.69	0.802	0.373	0.345	0.401	INDETERMINATE	1	TRUE	0	0.463622206525237	2		615	1187	SUCCESS
APC	324	MSKCC	GRCh37	5	112174059	112174059	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519194	NA	P-0000535-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	67	287	0	ENST00000257430.4:c.2768G>C	p.Arg923Thr	p.R923T	ENST00000257430	NM_000038.5	923	aGa/aCa	16/16	1	2	FACETS	0.486	0.422	0.555	0.486	0.422	0.555	SUBCLONAL	1	TRUE	1	0.463622206525237	2		287	595	SUCCESS
APC	324	MSKCC	GRCh37	5	112174426	112174426	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000535-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	51	180	0	ENST00000257430.4:c.3135G>C	p.Gln1045His	p.Q1045H	ENST00000257430	NM_000038.5	1045	caG/caC	16/16	1	2	FACETS	0.541	0.46	0.628	0.541	0.46	0.628	SUBCLONAL	1	TRUE	1	0.463622206525237	2		180	407	SUCCESS
APC	324	MSKCC	GRCh37	5	112174432	112174432	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000535-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	51	186	0	ENST00000257430.4:c.3141A>C	p.Glu1047Asp	p.E1047D	ENST00000257430	NM_000038.5	1047	gaA/gaC	16/16	1	2	FACETS	0.558	0.476	0.649	0.558	0.476	0.649	SUBCLONAL	1	TRUE	1	0.463622206525237	2		186	394	SUCCESS
APC	324	MSKCC	GRCh37	5	112178449	112178449	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000535-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	169	399	0	ENST00000257430.4:c.7158G>C	p.Lys2386Asn	p.K2386N	ENST00000257430	NM_000038.5	2386	aaG/aaC	16/16	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.463622206525237	2		399	728	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522696	176522696	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000535-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	146	521	0	ENST00000292408.4:c.1793G>C	p.Arg598Pro	p.R598P	ENST00000292408	NM_213647.1	598	cGa/cCa	13/18	0.22313916038875	1	FACETS	0.697	0.638	0.759	0.697	0.638	0.759	INDETERMINATE	1	TRUE	0	0.463622206525237	1		521	694	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960169	151960169	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0000535-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	250	329	0	ENST00000262189.6:c.1231A>T	p.Lys411Ter	p.K411*	ENST00000262189	NM_170606.2	411	Aaa/Taa	9/59	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.463622206525237	2		329	843	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285905	38285905	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000535-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	88	490	0	ENST00000425967.3:c.506C>T	p.Ser169Leu	p.S169L	ENST00000425967	NM_001174067.1	169	tCa/tTa	5/19	1	2	FACETS	0.458	0.405	0.515	0.458	0.405	0.515	SUBCLONAL	1	TRUE	1	0.463622206525237	2		490	829	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5055729	5055729	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000535-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	35	265	0	ENST00000381652.3:c.997C>T	p.Gln333Ter	p.Q333*	ENST00000381652	NM_004972.3	333	Caa/Taa	8/25	0.409251074943444	1	FACETS	0.224	0.183	0.271	0.224	0.183	0.271	SUBCLONAL	1	TRUE	0	0.463622206525237	1		265	517	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs79184941	NA	P-0000535-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	13	166	0	ENST00000358487.5:c.755C>T	p.Ser252Leu	p.S252L	ENST00000358487	NM_000141.4	252	tCg/tTg	7/18	0.463622206525237	1	FACETS	0.235	0.168	0.317	0.235	0.168	0.317	SUBCLONAL	1	TRUE	0	0.463622206525237	1		166	183	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244997	46244997	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs868082376	NA	P-0000535-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	267	427	0	ENST00000334344.6:c.3091C>T	p.Gln1031Ter	p.Q1031*	ENST00000334344	NM_152641.2	1031	Cag/Tag	15/21	0.433268098383312	2	FACETS	0.8	0.754	0.846	0.8	0.754	0.846	SUBCLONAL	2	TRUE	0	0.463622206525237	2		427	720	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438647	49438647	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000535-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	203	355	0	ENST00000301067.7:c.4843C>T	p.Arg1615Ter	p.R1615*	ENST00000301067	NM_003482.3	1615	Cga/Tga	19/54	0.433268098383312	2	FACETS	0.876	0.82	0.932	0.876	0.82	0.932	CLONAL	2	TRUE	0	0.463622206525237	2		355	500	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99454587	99454587	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000535-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	103	474	0	ENST00000268035.6:c.1506G>C	p.Lys502Asn	p.K502N	ENST00000268035	NM_000875.3	502	aaG/aaC	7/21	0.343563137050688	1	FACETS	0.49	0.439	0.545	0.49	0.439	0.545	SUBCLONAL	1	TRUE	0	0.463622206525237	1		474	696	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106696	2106696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000535-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	185	651	0	ENST00000219476.3:c.700G>A	p.Glu234Lys	p.E234K	ENST00000219476	NM_000548.3	234	Gag/Aag	8/42	1	2	FACETS	0.85	0.785	0.918	0.85	0.785	0.918	CLONAL	1	TRUE	1	0.463622206525237	2		651	939	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973686	15973686	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000535-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	213	371	0	ENST00000268712.3:c.4306G>T	p.Glu1436Ter	p.E1436*	ENST00000268712	NM_006311.3	1436	Gag/Tag	31/46	0.463622206525237	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.463622206525237	1		371	611	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217046	2217046	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs750665206	NA	P-0000535-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	65	369	0	ENST00000398665.3:c.2501C>G	p.Ser834Cys	p.S834C	ENST00000398665	NM_032482.2	834	tCc/tGc	21/28	NA	2	FACETS	0.412	0.356	0.472			1	INDETERMINATE	1	TRUE	NA	0.463622206525237	2		369	681	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943694	17943694	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201241352	NA	P-0000535-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	163	362	0	ENST00000458235.1:c.2395C>T	p.Arg799Cys	p.R799C	ENST00000458235	NM_000215.3	799	Cgt/Tgt	18/24	0.222251312851674	3	FACETS	1	0.986	1	0.67	0.617	0.725	INDETERMINATE	1	TRUE	1	0.463622206525237	3		362	646	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303481	30303481	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000535-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	10	27	0	ENST00000262643.3:c.19G>T	p.Glu7Ter	p.E7*	ENST00000262643	NM_001238.2	7	Gag/Tag	2/12	0.222251312851674	3	FACETS	0.805	0.555	1	0.403	0.277	0.554	INDETERMINATE	1	TRUE	1	0.463622206525237	3		27	66	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57470707	57470707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000535-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	69	196	0	ENST00000371085.3:c.180G>A	p.Met60Ile	p.M60I	ENST00000371085	NM_000516.4	60	atG/atA	2/13	1	2	FACETS	0.675	0.59	0.766	0.675	0.59	0.766	SUBCLONAL	1	TRUE	1	0.463622206525237	2		196	441	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851369	151851369	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000535-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	176	348	0	ENST00000262189.6:c.12122del	p.Pro4041LeufsTer42	p.P4041Lfs*42	ENST00000262189	NM_170606.2	4041	cCt/ct	47/59	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.463622206525237	2		348	722	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	TT	rs730881673	NA	P-0000535-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	205	545	0	ENST00000304494.5:c.131_132insAA	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAAc	1/3	0.463622206525237	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.463622206525237	1		545	619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0000542-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	132	302	0	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	0.56736658753187	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.56736658753187	1		302	249	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249855	110249855	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1277813128	NA	P-0000542-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	26	145	0	ENST00000374672.4:c.820T>G	p.Cys274Gly	p.C274G	ENST00000374672	NM_004235.4	274	Tgc/Ggc	3/5	0.56736658753187	1	FACETS	0.429	0.343	0.525	0.429	0.343	0.525	SUBCLONAL	1	TRUE	0	0.56736658753187	1		145	153	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725047	89725047	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1554826022	NA	P-0000542-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	288	521	0	ENST00000371953.3:c.1030A>T	p.Lys344Ter	p.K344*	ENST00000371953	NM_000314.4	344	Aag/Tag	9/9	0.56736658753187	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.56736658753187	1		521	655	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910866	32910866	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1484798037	NA	P-0000542-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	36	302	2	ENST00000380152.3:c.2374T>C	p.Tyr792His	p.Y792H	ENST00000380152		792	Tac/Cac	11/27	0.56736658753187	1	FACETS	0.219	0.18	0.263	0.219	0.18	0.263	SUBCLONAL	1	TRUE	0	0.56736658753187	1		304	415	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105258970	105258970	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000542-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	66	551	0	ENST00000349310.3:c.11T>G	p.Val4Gly	p.V4G	ENST00000349310	NM_001014432.1	4	gTg/gGg	3/15	0.56736658753187	1	FACETS	0.492	0.429	0.558	0.492	0.429	0.558	SUBCLONAL	1	TRUE	0	0.56736658753187	1		551	339	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657063	215657063	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0000542-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	246	452	0	ENST00000260947.4:c.322del	p.Cys108ValfsTer16	p.C108Vfs*16	ENST00000260947	NM_000465.2	108	Tgt/gt	3/11	0.56736658753187	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.56736658753187	1		452	609	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000558-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	96	716	0	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	0.866	0.77	0.968	0.866	0.77	0.968	CLONAL	1	FALSE	1	0.232421385675837	2		716	954	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000558-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	33	819	1	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	0.178270229932996	0	FACETS	0.454	0.369	0.55			1	SUBCLONAL	1	FALSE	0	0.232421385675837	0		820	480	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0000558-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	48	204	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.192097835966203	2	FACETS	1	0.955	1	0.677	0.576	0.788	CLONAL	1	FALSE	0	0.232421385675837	2		204	305	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812465	43812465	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs373621350	NA	P-0000558-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	23	404	1	ENST00000372470.3:c.1168C>T	p.Arg390Cys	p.R390C	ENST00000372470	NM_005373.2	390	Cgc/Tgc	8/12	1	2	FACETS	0.722	0.564	0.905	0.722	0.564	0.905	CLONAL	1	FALSE	1	0.232421385675837	2		405	274	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427625	72427625	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000558-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	51	422	0	ENST00000477973.2:c.865A>G	p.Ser289Gly	p.S289G	ENST00000477973	NM_012234.5	289	Agc/Ggc	4/4	1	2	FACETS	0.95	0.808	1	0.95	0.808	1	CLONAL	1	FALSE	1	0.232421385675837	2		422	462	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593601	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000558-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	36	707	0	ENST00000288135.5:c.1667A>T	p.Gln556Leu	p.Q556L	ENST00000288135	NM_000222.2	556	cAg/cTg	11/21	1	2	FACETS	0.46	0.377	0.554	0.46	0.377	0.554	SUBCLONAL	1	FALSE	1	0.232421385675837	2		707	673	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224542	224542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000558-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	42	293	0	ENST00000264932.6:c.218G>A	p.Gly73Asp	p.G73D	ENST00000264932	NM_004168.2	73	gGc/gAc	3/15	0.200519226505414	0	FACETS	0.991	0.832	1			1	CLONAL	1	FALSE	0	0.232421385675837	0		293	280	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155669	56155669	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000558-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	51	286	0	ENST00000399503.3:c.761G>A	p.Gly254Asp	p.G254D	ENST00000399503	NM_005921.1	254	gGc/gAc	3/20	0.204484681218118	4	FACETS	1	0.946	1	0.627	0.534	0.729	CLONAL	1	FALSE	2	0.232421385675837	4		286	431	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591145	67591145	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000558-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	50	272	0	ENST00000274335.5:c.1738T>A	p.Tyr580Asn	p.Y580N	ENST00000274335		580	Tac/Aac	12/15	0.204484681218118	4	FACETS	1	0.947	1	0.636	0.54	0.74	CLONAL	1	FALSE	2	0.232421385675837	4		272	417	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288800	33288800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200273259	NA	P-0000558-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	22	214	0	ENST00000374542.5:c.752G>A	p.Arg251His	p.R251H	ENST00000374542	NM_001141970.1	251	cGt/cAt	3/8	0.153740082330555	4	FACETS	1	0.798	1	0.514	0.4	0.646	CLONAL	1	FALSE	2	0.232421385675837	4		214	227	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0000558-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	26	236	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.192097835966203	2	FACETS	0.909	0.732	1	0.909	0.732	1	CLONAL	2	FALSE	0	0.232421385675837	2		236	123	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495646	56495646	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000558-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	20	387	0	ENST00000267101.3:c.3836T>C	p.Met1279Thr	p.M1279T	ENST00000267101	NM_001982.3	1279	aTg/aCg	28/28	1	2	FACETS	0.657	0.503	0.836	0.657	0.503	0.836	SUBCLONAL	1	FALSE	1	0.232421385675837	2		387	262	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202239	133202239	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000558-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	35	432	1	ENST00000320574.5:c.6649C>T	p.Gln2217Ter	p.Q2217*	ENST00000320574	NM_006231.2	2217	Cag/Tag	47/49	1	2	FACETS	0.944	0.776	1	0.944	0.776	1	CLONAL	1	FALSE	1	0.232421385675837	2		433	319	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479811	67479811	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500766	NA	P-0000558-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	36	523	0	ENST00000327367.4:c.1118G>A	p.Arg373His	p.R373H	ENST00000327367	NM_005902.3	373	cGc/cAc	8/9	0.232421385675837	1	FACETS	0.507	0.416	0.609	0.507	0.416	0.609	SUBCLONAL	1	FALSE	0	0.232421385675837	1		523	540	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136805	2136805	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000558-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	41	548	0	ENST00000219476.3:c.4922T>C	p.Leu1641Pro	p.L1641P	ENST00000219476	NM_000548.3	1641	cTg/cCg	38/42	0.144799822991734	0	FACETS	0.674	0.562	0.798			1	SUBCLONAL	1	FALSE	0	0.232421385675837	0		548	402	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835797	68835797	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587781919	NA	P-0000558-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	35	548	0	ENST00000261769.5:c.387+1G>A		p.X129_splice	ENST00000261769	NM_004360.3	129			0.144799822991734	0	FACETS	0.701	0.576	0.84			1	SUBCLONAL	1	FALSE	0	0.232421385675837	0		548	330	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216560	2216560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777525091	NA	P-0000558-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	24	498	0	ENST00000398665.3:c.2204C>T	p.Thr735Met	p.T735M	ENST00000398665	NM_032482.2	735	aCg/aTg	20/28	0.178270229932996	0	FACETS	0.686	0.54	0.853			1	SUBCLONAL	1	FALSE	0	0.232421385675837	0		498	231	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135064	11135064	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000558-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	32	303	0	ENST00000358026.2:c.3031A>G	p.Met1011Val	p.M1011V	ENST00000358026	NM_001128849.1	1011	Atg/Gtg	21/36	0.178270229932996	0	FACETS	0.961	0.785	1			1	CLONAL	1	FALSE	0	0.232421385675837	0		303	220	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089706	27089706	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000558-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	18	359	1	ENST00000324856.7:c.2666del	p.Gly889AlafsTer2	p.G889Afs*2	ENST00000324856	NM_006015.4	888	Ggg/gg	8/20	1	2	FACETS	0.688	0.519	0.887	0.688	0.519	0.887	SUBCLONAL	1	FALSE	1	0.232421385675837	2		360	225	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0000558-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	33	335	0	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.871	0.711	1	0.871	0.711	1	CLONAL	1	FALSE	1	0.232421385675837	2		335	326	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339111	65339111	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000558-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	64	538	4	ENST00000342505.4:c.425del	p.Lys142ArgfsTer26	p.K142Rfs*26	ENST00000342505	NM_002227.2	142	aAg/ag	5/25	1	2	FACETS	0.627	0.542	0.721	0.627	0.542	0.721	SUBCLONAL	1	FALSE	1	0.232421385675837	2		542	878	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100171	157100172	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0000558-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	11	7	0	ENST00000346085.5:c.1114dup	p.Arg372ProfsTer163	p.R372Pfs*163	ENST00000346085	NM_020732.3	370	tcc/tCcc	1/20	0.153740082330555	4	FACETS	1	0.735	1	1	0.735	1	CLONAL	2	FALSE	2	0.232421385675837	4		7	56	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372193	55372194	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0000558-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	22	100	0	ENST00000297316.4:c.885_886del	p.Tyr296LeufsTer68	p.Y296Lfs*68	ENST00000297316	NM_022454.3	295	GTg/g	2/2	0.157498370917155	3	FACETS	1	0.88	1	0.604	0.471	0.755	CLONAL	1	FALSE	1	0.232421385675837	3		100	175	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121791	2121792	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs137854144	NA	P-0000558-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	17	456	0	ENST00000219476.3:c.1959_1960del	p.Gly654LeufsTer2	p.G654Lfs*2	ENST00000219476	NM_000548.3	651	ccAGag/ccag	19/42	0.144799822991734	0	FACETS	0.54	0.404	0.7			1	SUBCLONAL	1	FALSE	0	0.232421385675837	0		456	208	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220615	2220615	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	rs774508592	NA	P-0000558-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	29	674	0	ENST00000326181.6:c.237del	p.Ile80SerfsTer48	p.I80Sfs*48	ENST00000326181	NM_032271.2	78	Ccc/cc	5/21	0.144799822991734	0	FACETS	0.643	0.517	0.785			1	SUBCLONAL	1	FALSE	0	0.232421385675837	0		674	298	SUCCESS
AR	367	MSKCC	GRCh37	X	66765667	66765667	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000558-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	73	1113	1	ENST00000374690.3:c.683del	p.Gly228AlafsTer30	p.G228Afs*30	ENST00000374690	NM_000044.3	227	Ggg/gg	1/8	0.178270229932996	0	FACETS	0.629	0.549	0.715			1	SUBCLONAL	1	FALSE	0	0.232421385675837	0		1114	767	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0000561-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	93	386	3	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.224979368529178	2		389	718	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0000561-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	49	675	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	FALSE	1	0.224979368529178	2		675	342	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000561-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	22	319	1	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	0.224979368529178	1	FACETS	0.954	0.744	1	0.954	0.744	1	CLONAL	1	FALSE	0	0.224979368529178	1		320	182	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828102	243828102	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000561-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	84	299	0	ENST00000263826.5:c.256A>T	p.Thr86Ser	p.T86S	ENST00000263826	NM_005465.4	86	Aca/Tca	3/13	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.224979368529178	2		299	624	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99181109	99181109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757028003	NA	P-0000561-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	21	193	0	ENST00000074304.5:c.2050G>A	p.Ala684Thr	p.A684T	ENST00000074304	NM_001134224.1	684	Gcc/Acc	20/26	1	2	FACETS	1	0.845	1	1	0.845	1	CLONAL	1	FALSE	1	0.224979368529178	2		193	167	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568896	212568896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000561-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	40	249	0	ENST00000342788.4:c.1222C>T	p.Pro408Ser	p.P408S	ENST00000342788	NM_005235.2	408	Cca/Tca	11/28	0.224979368529178	1	FACETS	0.77	0.64	0.913	0.77	0.64	0.913	CLONAL	1	FALSE	0	0.224979368529178	1		249	410	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370767	225370767	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000561-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	42	265	0	ENST00000264414.4:c.1112C>T	p.Ala371Val	p.A371V	ENST00000264414	NM_003590.4	371	gCg/gTg	8/16	NA	3	FACETS	0.791	0.66	0.937			1	INDETERMINATE	1	FALSE	NA	0.224979368529178	3		265	525	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228402	228402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764534044	NA	P-0000561-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	47	297	1	ENST00000264932.6:c.724G>A	p.Gly242Arg	p.G242R	ENST00000264932	NM_004168.2	242	Ggg/Agg	6/15	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	1	0.224979368529178	2		298	321	SUCCESS
APC	324	MSKCC	GRCh37	5	112173572	112173572	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000561-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	44	237	0	ENST00000257430.4:c.2281G>T	p.Glu761Ter	p.E761*	ENST00000257430	NM_000038.5	761	Gaa/Taa	16/16	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.224979368529178	2		237	305	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517592	176517592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767045353	NA	P-0000561-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	31	406	1	ENST00000292408.4:c.293G>A	p.Arg98His	p.R98H	ENST00000292408	NM_213647.1	98	cGc/cAc	3/18	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	FALSE	1	0.224979368529178	2		407	194	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601863	43601863	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000561-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	24	270	0	ENST00000355710.3:c.907G>A	p.Val303Met	p.V303M	ENST00000355710	NM_020975.4	303	Gtg/Atg	5/20	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	FALSE	1	0.224979368529178	2		270	181	SUCCESS
ATM	472	MSKCC	GRCh37	11	108168020	108168020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752459491	NA	P-0000561-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	68	181	0	ENST00000278616.4:c.4916C>T	p.Pro1639Leu	p.P1639L	ENST00000278616	NM_000051.3	1639	cCg/cTg	33/63	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.224979368529178	2		181	448	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2115530	2115530	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372681603	NA	P-0000561-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	34	415	0	ENST00000219476.3:c.1610G>A	p.Arg537His	p.R537H	ENST00000219476	NM_000548.3	537	cGc/cAc	16/42	0.224979368529178	1	FACETS	0.794	0.65	0.955	0.794	0.65	0.955	CLONAL	1	FALSE	0	0.224979368529178	1		415	338	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779452	3779452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000561-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	21	332	1	ENST00000262367.5:c.5596C>T	p.Arg1866Cys	p.R1866C	ENST00000262367	NM_004380.2	1866	Cgc/Tgc	31/31	0.224979368529178	1	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	FALSE	0	0.224979368529178	1		333	135	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858883	89858883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747141831	NA	P-0000561-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	13	165	0	ENST00000389301.3:c.1079G>A	p.Arg360His	p.R360H	ENST00000389301	NM_000135.2	360	cGc/cAc	12/43	0.224979368529178	1	FACETS	0.548	0.392	0.739	0.548	0.392	0.739	SUBCLONAL	1	FALSE	0	0.224979368529178	1		165	187	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724596	724596	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777211673	NA	P-0000561-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	29	294	0	ENST00000314574.4:c.1460G>A	p.Arg487Gln	p.R487Q	ENST00000314574	NM_005433.3	487	cGa/cAa	12/12	1	2	FACETS	0.824	0.662	1	0.824	0.662	1	CLONAL	1	FALSE	1	0.224979368529178	2		294	313	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222379	2222379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201872028	NA	P-0000561-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	13	152	0	ENST00000398665.3:c.3211G>A	p.Ala1071Thr	p.A1071T	ENST00000398665	NM_032482.2	1071	Gcc/Acc	24/28	0.224979368529178	1	FACETS	1	0.784	1	1	0.784	1	CLONAL	1	FALSE	0	0.224979368529178	1		152	93	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101925	11101925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000561-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	15	197	0	ENST00000358026.2:c.1345G>A	p.Glu449Lys	p.E449K	ENST00000358026	NM_001128849.1	449	Gag/Aag	8/36	0.224979368529178	1	FACETS	1	0.759	1	1	0.759	1	CLONAL	1	FALSE	0	0.224979368529178	1		197	115	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922271	39922271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000561-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	16	340	0	ENST00000378444.4:c.3901G>A	p.Ala1301Thr	p.A1301T	ENST00000378444	NM_001123385.1	1301	Gca/Aca	9/15	NA	2	FACETS	0.556	0.411	0.729			1	INDETERMINATE	1	FALSE	NA	0.224979368529178	2		340	256	SUCCESS
APC	324	MSKCC	GRCh37	5	112175675	112175676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0000561-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	39	298	0	ENST00000257430.4:c.4393_4394dup	p.Ser1465ArgfsTer9	p.S1465Rfs*9	ENST00000257430	NM_000038.5	1462	aag/aAGag	16/16	1	2	FACETS	0.937	0.778	1	0.937	0.778	1	CLONAL	1	FALSE	1	0.224979368529178	2		298	370	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37672019	37672019	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000561-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	81	469	0	ENST00000447079.4:c.2808del	p.Gln937LysfsTer9	p.Q937Kfs*9	ENST00000447079	NM_015083.1	935	aTt/at	9/14	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	FALSE	1	0.224979368529178	2		469	699	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256769	19256769	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000561-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	15	156	0	ENST00000162023.5:c.944del	p.Pro315GlnfsTer?	p.P315Qfs*?	ENST00000162023		315	cCa/ca	13/13	0.224979368529178	2	FACETS	0.973	0.717	1	0.487	0.358	0.638	CLONAL	1	FALSE	0	0.224979368529178	2		156	137	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743932	41743933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs778012871	NA	P-0000561-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	33	516	0	ENST00000301178.4:c.874dup	p.His292ProfsTer47	p.H292Pfs*47	ENST00000301178	NM_021913.4	289	-/C	7/20	0.224979368529178	1	FACETS	0.811	0.662	0.978	0.811	0.662	0.978	CLONAL	1	FALSE	0	0.224979368529178	1		516	321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0000575-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1321	119	715	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.323	0.29	0.358	0.323	0.29	0.358	SUBCLONAL	1	TRUE	1	0.511938702963554	2		715	1440	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0000575-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	142	252	1	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.855	0.781	0.931	0.855	0.781	0.931	CLONAL	1	TRUE	1	0.511938702963554	2		253	649	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217792	2217792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760010356	NA	P-0000575-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	112	501	0	ENST00000398665.3:c.2566G>A	p.Gly856Ser	p.G856S	ENST00000398665	NM_032482.2	856	Ggc/Agc	22/28	1	2	FACETS	0.417	0.374	0.462	0.417	0.374	0.462	SUBCLONAL	1	TRUE	1	0.511938702963554	2		501	1050	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0000575-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	228	532	1	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	0.184762984032329	3	FACETS	1	0.984	1	0.393	0.367	0.421	INDETERMINATE	1	TRUE	0	0.511938702963554	3		533	948	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916939	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAGAAA	novel	NA	P-0000575-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	98	323	0	ENST00000263967.3:c.327_332dup	p.Glu110_Lys111dup	p.E110_K111dup	ENST00000263967	NM_006218.2	110	gaa/gAAGAAAaa	2/21	0.511938702963554	3	FACETS	0.461	0.411	0.516	0.231	0.205	0.258	SUBCLONAL	1	TRUE	1	0.511938702963554	3		323	1042	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593378	67593383	+	inframe_deletion	In_Frame_Del	DEL	CTCCCT	CTCCCT	-	novel	NA	P-0000575-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	101	452	0	ENST00000274335.5:c.2125_2130del	p.Ser709_Leu710del	p.S709_L710del	ENST00000274335		708	gaCTCCCTc/gac	15/15	1	2	FACETS	0.373	0.332	0.416	0.373	0.332	0.416	SUBCLONAL	1	TRUE	1	0.511938702963554	2		452	1058	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0000578-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	98	435	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		435	955	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000591-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	59	396	0	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		396	721	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913250	NA	P-0000591-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	43	411	0	ENST00000369535.4:c.34G>A	p.Gly12Ser	p.G12S	ENST00000369535	NM_002524.4	12	Ggt/Agt	2/7	0.133929018714647	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		411	1011	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412904	49412904	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000591-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	35	578	0	ENST00000418115.1:c.119A>T	p.Glu40Val	p.E40V	ENST00000418115	NM_001664.2	40	gAg/gTg	2/5	0.133929018714647	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		578	1172	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918694	44918694	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000591-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	45	250	0	ENST00000377967.4:c.1177C>T	p.Arg393Ter	p.R393*	ENST00000377967	NM_021140.2	393	Cga/Tga	12/29	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		250	508	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412972	49412973	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0000591-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	57	476	0	ENST00000418115.1:c.50_51del	p.Gly17GlufsTer23	p.G17Efs*23	ENST00000418115	NM_001664.2	17	gGA/g	2/5	0.133929018714647	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		476	990	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115956	8115956	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000595-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	69	192	0	ENST00000346208.3:c.1305del	p.Ser436ProfsTer39	p.S436Pfs*39	ENST00000346208		434	caC/ca	6/6	NA	2	FACETS	0.666	0.585	0.752			1	INDETERMINATE	1	TRUE	NA	0.668657971640647	2		192	310	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0000616-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	641	417	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.616611655718926	6	FACETS	0.957	0.922	0.992			1	CLONAL	3	TRUE	NA	0.616611655718926	6		417	1618	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268766	41268766	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000616-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	599	480	0	ENST00000349496.5:c.1004A>T	p.Lys335Ile	p.K335I	ENST00000349496	NM_001904.3	335	aAa/aTa	7/15	0.616611655718926	3	FACETS	0.994	0.959	1	0.994	0.959	1	CLONAL	2	TRUE	1	0.616611655718926	3		480	1278	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528031	157528031	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000616-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	84	154	0	ENST00000346085.5:c.5756T>A	p.Leu1919Gln	p.L1919Q	ENST00000346085	NM_020732.3	1919	cTg/cAg	20/20	0.616611655718926	3	FACETS	0.941	0.836	1	0.47	0.418	0.525	CLONAL	1	TRUE	1	0.616611655718926	3		154	379	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245419	41245419	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000616-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	308	481	0	ENST00000357654.3:c.2129C>T	p.Thr710Ile	p.T710I	ENST00000357654	NM_007294.3	710	aCt/aTt	10/23	0.616611655718926	2	FACETS	0.994	0.939	1	0.497	0.469	0.526	CLONAL	1	TRUE	0	0.616611655718926	2		481	1005	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216376	2216376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs573741033	NA	P-0000616-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	101	286	0	ENST00000398665.3:c.2020C>T	p.Arg674Cys	p.R674C	ENST00000398665	NM_032482.2	674	Cgt/Tgt	20/28	0.616611655718926	2	FACETS	0.972	0.878	1	0.486	0.439	0.535	CLONAL	1	TRUE	0	0.616611655718926	2		286	337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578244	7578261	+	inframe_deletion	In_Frame_Del	DEL	CGCAAATTTCCTTCCACT	CGCAAATTTCCTTCCACT	-	novel	NA	P-0000616-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	255	517	0	ENST00000269305.4:c.588_605del	p.Gly199_Glu204del	p.G199_E204del	ENST00000269305	NM_001126112.2	196	cgAGTGGAAGGAAATTTGCGt/cgt	6/11	0.616611655718926	2	FACETS	1	0.993	1	0.719	0.679	0.759	CLONAL	1	TRUE	0	0.616611655718926	2		517	575	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435160	56435161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755128667	NA	P-0000616-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	188	218	1	ENST00000407977.2:c.1976dup	p.Pro660SerfsTer87	p.P660Sfs*87	ENST00000407977		659	ggt/ggGt	9/10	0.616611655718926	2	FACETS	0.869	0.817	0.92	0.869	0.817	0.92	CLONAL	2	TRUE	0	0.616611655718926	2		219	351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578445	7578445	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000639-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	140	304	0	ENST00000269305.4:c.485T>A	p.Ile162Asn	p.I162N	ENST00000269305	NM_001126112.2	162	aTc/aAc	5/11	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.782451299059367	2		304	350	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230797	53230806	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCTGCCGC	CAGCTGCCGC	-	novel	NA	P-0000639-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	188	371	0	ENST00000375401.3:c.1987_1996del	p.Ala663CysfsTer98	p.A663Cfs*98	ENST00000375401	NM_004187.3	663	GCGGCAGCTGtg/tg	14/26	1	1	FACETS	0.985	0.933	1	0.985	0.933	1	CLONAL	1	TRUE	0	0.782451299059367	1		371	297	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206647803	206647803	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs372072572	NA	P-0000642-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	90	269	2	ENST00000367120.3:c.217G>T	p.Val73Leu	p.V73L	ENST00000367120	NM_014002.3	73	Gtg/Ttg	4/22	0.278476460979085	5	FACETS	1	0.912	1	0.344	0.305	0.386	CLONAL	1	TRUE	2	0.412032663414109	5		271	685	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878186	48878186	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0000642-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	14	53	0	ENST00000267163.4:c.137+1G>C		p.X46_splice	ENST00000267163	NM_000321.2	46			0.385357943040814	2	FACETS	0.819	0.602	1	0.409	0.301	0.536	CLONAL	1	TRUE	0	0.412032663414109	2		53	83	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933093	39933093	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000642-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	51	351	0	ENST00000378444.4:c.1506C>G	p.Ile502Met	p.I502M	ENST00000378444	NM_001123385.1	502	atC/atG	4/15	1	1	FACETS	0.281	0.238	0.328	0.281	0.238	0.328	SUBCLONAL	1	TRUE	0	0.412032663414109	1		351	700	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933115	39933115	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000642-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	48	334	0	ENST00000378444.4:c.1484C>G	p.Ala495Gly	p.A495G	ENST00000378444	NM_001123385.1	495	gCt/gGt	4/15	1	1	FACETS	0.27	0.228	0.317	0.27	0.228	0.317	SUBCLONAL	1	TRUE	0	0.412032663414109	1		334	685	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249017	55249018	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCA	rs1554350381	NA	P-0000642-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	1006	400	0	ENST00000275493.2:c.2317_2319dup	p.His773dup	p.H773dup	ENST00000275493	NM_005228.3	773	ccc/ccCCAc	20/28	0.412032663414109	9	FACETS	0.973	0.949	0.997	0.852	0.831	0.873	CLONAL	7	TRUE	1	0.412032663414109	9		400	1750	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0000642-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	238	344	0	ENST00000269305.4:c.403del	p.Cys135AlafsTer35	p.C135Afs*35	ENST00000269305	NM_001126112.2	135	Tgc/gc	5/11	NA	2	FACETS	0.907	0.852	0.962			1	INDETERMINATE	2	TRUE	NA	0.412032663414109	2		344	637	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223345	53223348	+	frameshift_variant	Frame_Shift_Del	DEL	CTCT	CTCT	-	novel	NA	P-0000642-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	86	304	0	ENST00000375401.3:c.4011_4014del	p.Glu1338AlafsTer19	p.E1338Afs*19	ENST00000375401	NM_004187.3	1337	agAGAG/ag	23/26	1	1	FACETS	0.609	0.54	0.683	0.609	0.54	0.683	SUBCLONAL	1	TRUE	0	0.412032663414109	1		304	544	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482438	56482438	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000656-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	79	366	0	ENST00000267101.3:c.986A>C	p.Lys329Thr	p.K329T	ENST00000267101	NM_001982.3	329	aAa/aCa	8/28	1	2	FACETS	0.882	0.779	0.992	0.882	0.779	0.992	CLONAL	1	TRUE	1	0.387661463805246	2		366	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0000656-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	95	331	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.387661463805246	1	FACETS	0.76	0.679	0.846	0.76	0.679	0.846	SUBCLONAL	1	TRUE	0	0.387661463805246	1		331	520	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574907	41574907	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540813452	NA	P-0000656-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	129	570	0	ENST00000263253.7:c.7192G>A	p.Asp2398Asn	p.D2398N	ENST00000263253	NM_001429.3	2398	Gat/Aat	31/31	NA	2	FACETS	0.812	0.736	0.891			1	INDETERMINATE	1	TRUE	NA	0.387661463805246	2		570	820	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852628	63852628	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000659-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	548	529	0	ENST00000279873.7:c.3406A>G	p.Asn1136Asp	p.N1136D	ENST00000279873	NM_032199.2	1136	Aat/Gat	10/10	0.463487787647314	4	FACETS	0.992	0.951	1	0.992	0.951	1	CLONAL	2	TRUE	2	0.502242273331611	4		529	1652	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727455	66727455	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs869025608	NA	P-0000659-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	431	413	1	ENST00000307102.5:c.171G>T	p.Lys57Asn	p.K57N	ENST00000307102	NM_002755.3	57	aaG/aaT	2/11	0.502242273331611	4	FACETS	0.953	0.913	0.992	0.953	0.913	0.992	CLONAL	3	TRUE	1	0.502242273331611	4		414	902	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665722	29665722	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000659-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	311	658	0	ENST00000356175.3:c.6757G>A	p.Ala2253Thr	p.A2253T	ENST00000356175	NM_000267.3	2253	Gca/Aca	45/57	0.502242273331611	3	FACETS	0.838	0.793	0.885	0.838	0.793	0.885	CLONAL	2	TRUE	1	0.502242273331611	3		658	924	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941836	44941838	+	frameshift_variant	Frame_Shift_Del	DEL	AGA	AGA	GC	novel	NA	P-0000659-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	545	477	0	ENST00000377967.4:c.3160_3162delinsGC	p.Arg1054AlafsTer29	p.R1054Afs*29	ENST00000377967	NM_021140.2	1054	AGA/GC	21/29	0.419482194798699	2	FACETS	1	0.986	1			1	CLONAL	2	TRUE	NA	0.502242273331611	2		477	1043	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096227	71096227	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000669-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	159	118	0	ENST00000318789.4:c.530A>T	p.Gln177Leu	p.Q177L	ENST00000318789	NM_032682.5	177	cAg/cTg	10/21	0.459717851310652	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.534369932510709	3		118	360	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670958	30670958	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs766714687	NA	P-0000669-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	36	240	0	ENST00000376406.3:c.5788C>A	p.Arg1930Ser	p.R1930S	ENST00000376406	NM_014641.2	1930	Cgc/Agc	12/15	0.532671314704526	2	FACETS	0.221	0.181	0.266	0.111	0.09	0.133	SUBCLONAL	1	TRUE	0	0.534369932510709	2		240	609	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579347	7579352	+	frameshift_variant	Frame_Shift_Del	DEL	AGAAGC	AGAAGC	CA	novel	NA	P-0000669-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	126	196	0	ENST00000269305.4:c.335_340delinsTG	p.Gly112ValfsTer10	p.G112Vfs*10	ENST00000269305	NM_001126112.2	112	gGCTTCTtg/gTGtg	4/11	0.529192150834916	2	FACETS	0.781	0.718	0.844	0.781	0.718	0.844	SUBCLONAL	2	TRUE	0	0.534369932510709	2		196	302	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911334	32911335	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0000672-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	94	225	0	ENST00000380152.3:c.2845dup	p.Tyr949LeufsTer10	p.Y949Lfs*10	ENST00000380152		948	gtt/gTtt	11/27	1	2	FACETS	0.838	0.749	0.933	1	0.984	1	CLONAL	2	FALSE	1	0.222476914162311	2		225	504	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0000682-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	151	340	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	1	0.967	1			1	INDETERMINATE	1	TRUE	NA	0.283937880527718	2		340	950	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0000682-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	44	296	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.283937880527718	2		296	259	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0000682-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	115	183	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	0.0777588067480341	4	FACETS	1	0.983	1	0.729	0.658	0.805	INDETERMINATE	1	TRUE	2	0.283937880527718	4		183	713	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0000682-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	99	285	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.283937880527718	2		285	576	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313289	65313289	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000682-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	159	482	0	ENST00000342505.4:c.1825G>T	p.Glu609Ter	p.E609*	ENST00000342505	NM_002227.2	609	Gaa/Taa	13/25	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.283937880527718	2		482	763	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551981	150551981	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000682-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	142	412	0	ENST00000369026.2:c.26T>C	p.Val9Ala	p.V9A	ENST00000369026	NM_021960.4	9	gTa/gCa	1/3	0.283937880527718	5	FACETS	1	0.967	1	0.284	0.258	0.312	CLONAL	1	TRUE	1	0.283937880527718	5		412	1255	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202719	128202719	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000682-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	76	267	0	ENST00000341105.2:c.1001A>C	p.Lys334Thr	p.K334T	ENST00000341105	NM_032638.4	334	aAg/aCg	4/6	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.283937880527718	2		267	390	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023246	1023246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs184776294	NA	P-0000682-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	63	203	0	ENST00000358495.3:c.1009G>A	p.Asp337Asn	p.D337N	ENST00000358495	NM_134424.2	337	Gat/Aat	11/12	NA	2	FACETS	0.765	0.667	0.869			1	INDETERMINATE	2	TRUE	NA	0.283937880527718	2		203	290	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911691	32911691	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000682-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	72	212	0	ENST00000380152.3:c.3199A>T	p.Thr1067Ser	p.T1067S	ENST00000380152		1067	Act/Tct	11/27	0.251460684151921	4	FACETS	1	0.961	1	0.419	0.367	0.475	CLONAL	1	TRUE	1	0.283937880527718	4		212	518	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006893	47006893	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0000682-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	88	152	0	ENST00000377604.3:c.13A>T	p.Arg5Ter	p.R5*	ENST00000377604	NM_001204468.1	5	Aga/Tga	2/24	1	1	FACETS	1	0.964	1	1	0.988	1	CLONAL	2	TRUE	0	0.283937880527718	1		152	231	SUCCESS
APC	324	MSKCC	GRCh37	5	112173847	112173848	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0000682-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	55	233	0	ENST00000257430.4:c.2563_2564dup	p.Arg856AsnfsTer6	p.R856Nfs*6	ENST00000257430	NM_000038.5	852	-/GA	16/16	0.0777588067480341	4	FACETS	0.955	0.817	1	0.477	0.408	0.553	INDETERMINATE	1	TRUE	2	0.283937880527718	4		233	521	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112292	115112293	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0000682-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	31	50	0	ENST00000257566.3:c.1447dup	p.Thr483AsnfsTer209	p.T483Nfs*209	ENST00000257566	NM_016569.3	483	acg/aAcg	7/8	0.283937880527718	2	FACETS	1	0.852	1	1	0.955	1	CLONAL	3	TRUE	0	0.283937880527718	2		50	72	SUCCESS
APC	324	MSKCC	GRCh37	5	112163677	112163677	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0000699-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	213	337	0	ENST00000257430.4:c.1600A>T	p.Lys534Ter	p.K534*	ENST00000257430	NM_000038.5	534	Aaa/Taa	13/16	0.300773472477182	2	FACETS	0.906	0.844	0.969	0.906	0.844	0.969	CLONAL	2	FALSE	0	0.300773472477182	2		337	782	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491645	56491645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000699-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	186	238	0	ENST00000267101.3:c.2537G>T	p.Ser846Ile	p.S846I	ENST00000267101	NM_001982.3	846	aGt/aTt	21/28	0.176433651559852	5	FACETS	0.941	0.873	1	0.941	0.873	1	INDETERMINATE	3	FALSE	2	0.300773472477182	5		238	636	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557629	95557629	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000699-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	231	332	0	ENST00000393063.1:c.5438A>G	p.Glu1813Gly	p.E1813G	ENST00000393063	NM_030621.3	1813	gAg/gGg	26/28	0.286025002000125	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	FALSE	2	0.300773472477182	4		332	868	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226290	2226290	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746101642	NA	P-0000699-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	137	396	0	ENST00000398665.3:c.3770C>T	p.Ala1257Val	p.A1257V	ENST00000398665	NM_032482.2	1257	gCg/gTg	27/28	0.211696345269654	3	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	FALSE	1	0.300773472477182	3		396	501	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117883	70117903	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGCGCAGGAAGCTCGC	GGCGGCGCGCAGGAAGCTCGC	-	novel	NA	P-0000699-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	65	180	0	ENST00000245479.2:c.353_373del	p.Ala118_Ala124del	p.A118_A124del	ENST00000245479	NM_000346.3	117	caGGCGGCGCGCAGGAAGCTCGCg/cag	1/3	0.176433651559852	5	FACETS	1	0.881	1	0.672	0.587	0.763	INDETERMINATE	2	FALSE	2	0.300773472477182	5		180	311	SUCCESS
MET	4233	MSKCC	GRCh37	7	116417485	116417485	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000710-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	174	382	0	ENST00000397752.3:c.3302A>T	p.Asp1101Val	p.D1101V	ENST00000397752	NM_000245.2	1101	gAt/gTt	16/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		382	548	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271190	38271190	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs775166971	NA	P-0000710-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	113	193	0	ENST00000425967.3:c.2518C>T	p.Arg840Ter	p.R840*	ENST00000425967	NM_001174067.1	840	Cga/Tga	19/19	0.244757719713798	4	FACETS		NA	1			1	NA	NA	FALSE	2	NA	4		193	292	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803166	1803166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1441656357	NA	P-0000730-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	77	417	0	ENST00000260795.2:c.518G>A	p.Arg173His	p.R173H	ENST00000260795		173	cGc/cAc	4/17	1	2	FACETS	0.968	0.849	1	0.968	0.849	1	CLONAL	1	TRUE	1	0.22218634372604	2		417	716	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653808	89653808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000730-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	53	332	0	ENST00000371953.3:c.106G>A	p.Gly36Arg	p.G36R	ENST00000371953	NM_000314.4	36	Gga/Aga	2/9	1	2	FACETS	0.778	0.663	0.905	0.778	0.663	0.905	CLONAL	1	TRUE	1	0.22218634372604	2		332	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0000730-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	219	235	0	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	0.22218634372604	5	FACETS	1	0.973	1			1	CLONAL	5	TRUE	NA	0.22218634372604	5		235	495	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0000737-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	85	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.122514060901162	4	FACETS	0.847	0.754	0.944	0.847	0.754	0.944	INDETERMINATE	2	TRUE	2	0.375212144053933	4		371	368	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0000737-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	68	183	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	NA	2	FACETS	0.959	0.851	1			1	INDETERMINATE	2	TRUE	NA	0.375212144053933	2		183	189	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0000737-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	72	84	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	0.360417558536356	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.375212144053933	2		84	173	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714388	40714388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760880188	NA	P-0000737-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	59	142	0	ENST00000373198.4:c.4009C>T	p.Arg1337Cys	p.R1337C	ENST00000373198	NM_133170.3	1337	Cgc/Tgc	29/32	0.375212144053933	7	FACETS	0.891	0.771	1	0.446	0.385	0.51	CLONAL	2	TRUE	3	0.375212144053933	7		142	342	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0000743-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	115	197	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.949	0.86	1	0.949	0.86	1	CLONAL	1	TRUE	1	0.51	2		197	475	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0000743-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	109	250	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.459449442619832	1	FACETS	0.821	0.743	0.901	0.821	0.743	0.901	CLONAL	1	TRUE	0	0.51	1		250	388	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098534	108098534	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659324	NA	P-0000743-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	17	157	0	ENST00000278616.4:c.104G>A	p.Arg35Gln	p.R35Q	ENST00000278616	NM_000051.3	35	cGa/cAa	3/63	0.51377231574616	1	FACETS	0.151	0.112	0.197	0.151	0.112	0.197	SUBCLONAL	1	TRUE	0	0.51	1		157	329	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0000756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	147	611	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.230087215648592	5	FACETS	0.98	0.904	1			1	INDETERMINATE	3	TRUE	NA	0.398579395260295	5		611	401	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0000756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	44	269	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	NA	2	FACETS	1	0.957	1			1	INDETERMINATE	1	TRUE	NA	0.398579395260295	2		269	159	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162686	47162686	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	115	622	0	ENST00000409792.3:c.3440A>T	p.Gln1147Leu	p.Q1147L	ENST00000409792	NM_014159.6	1147	cAg/cTg	3/21	0.383764881043072	2	FACETS	0.949	0.867	1	0.949	0.867	1	CLONAL	2	TRUE	0	0.398579395260295	2		622	304	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057230	180057230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780661773	NA	P-0000756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	42	186	0	ENST00000261937.6:c.508C>T	p.Arg170Cys	p.R170C	ENST00000261937	NM_182925.4	170	Cgc/Tgc	4/30	0.350803956518516	2	FACETS	0.976	0.839	1	0.976	0.839	1	CLONAL	2	TRUE	0	0.398579395260295	2		186	108	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056113	26056113	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	117	278	0	ENST00000343677.2:c.544C>G	p.Pro182Ala	p.P182A	ENST00000343677	NM_005319.3	182	Ccc/Gcc	1/1	0.398579395260295	5	FACETS	0.928	0.847	1			1	CLONAL	3	TRUE	NA	0.398579395260295	5		278	337	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499739	8499739	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	81	394	0	ENST00000356435.5:c.2230A>C	p.Ile744Leu	p.I744L	ENST00000356435		744	Ata/Cta	14/35	0.383764881043072	2	FACETS	0.758	0.677	0.843	0.758	0.677	0.843	SUBCLONAL	2	TRUE	0	0.398579395260295	2		394	268	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482282	87482282	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	106	470	0	ENST00000277120.3:c.1569G>T	p.Lys523Asn	p.K523N	ENST00000277120		523	aaG/aaT	14/19	0.383764881043072	2	FACETS	0.886	0.806	0.97	0.886	0.806	0.97	CLONAL	2	TRUE	0	0.398579395260295	2		470	300	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0000763-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	40	296	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.788586848931408	3	FACETS	0.888	0.75	1	0.296	0.25	0.345	CLONAL	1	TRUE	0	0.827450011682164	3		296	154	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0000763-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	396	435	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.788586848931408	3	FACETS	0.976	0.953	0.998	0.976	0.953	0.998	CLONAL	3	TRUE	0	0.827450011682164	3		435	462	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0000763-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	337	339	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.808446510551949	4	FACETS	0.904	0.867	0.94	0.904	0.867	0.94	CLONAL	3	TRUE	1	0.827450011682164	4		339	549	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691776	30691776	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1182342277	NA	P-0000763-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	82	333	0	ENST00000295754.5:c.278A>G	p.Glu93Gly	p.E93G	ENST00000295754	NM_003242.5	93	gAg/gGg	3/7	0.820143338553659	2	FACETS	0.383	0.338	0.43	0.191	0.169	0.215	SUBCLONAL	1	TRUE	0	0.827450011682164	2		333	518	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133805	55133805	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376626935	NA	P-0000763-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	388	454	0	ENST00000257290.5:c.1018C>T	p.Arg340Trp	p.R340W	ENST00000257290	NM_006206.4	340	Cgg/Tgg	7/23	0.802712755296312	2	FACETS	0.983	0.956	1	0.983	0.956	1	CLONAL	2	TRUE	0	0.827450011682164	2		454	477	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043665	6043665	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000763-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	65	415	0	ENST00000265849.7:c.188T>C	p.Val63Ala	p.V63A	ENST00000265849	NM_000535.5	63	gTg/gCg	3/15	0.371861277368469	6	FACETS	0.889	0.773	1	0.296	0.257	0.339	INDETERMINATE	1	TRUE	3	0.827450011682164	6		415	469	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140454008	140454008	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397516894	NA	P-0000763-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	118	268	1	ENST00000288602.6:c.1720C>T	p.His574Tyr	p.H574Y	ENST00000288602	NM_004333.4	574	Cac/Tac	14/18	0.75151738001537	3	FACETS	1	0.95	1	0.532	0.484	0.581	CLONAL	1	TRUE	1	0.827450011682164	3		269	379	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332414	70332414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs771320434	NA	P-0000763-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	505	434	0	ENST00000373644.4:c.319C>T	p.Arg107Ter	p.R107*	ENST00000373644	NM_030625.2	107	Cga/Tga	2/12	0.430972635993202	5	FACETS	0.884	0.856	0.911			1	INDETERMINATE	4	TRUE	NA	0.827450011682164	5		434	774	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266074	41266097	+	inframe_deletion	In_Frame_Del	DEL	ACTGGCAGCAACAGTCTTACCTGG	ACTGGCAGCAACAGTCTTACCTGG	-	rs121913417	NA	P-0000763-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	180	330	0	ENST00000349496.5:c.74_97del	p.Trp25_Asp32del	p.W25_D32del	ENST00000349496	NM_001904.3	24	cACTGGCAGCAACAGTCTTACCTGGac/cac	3/15	0.820143338553659	2	FACETS	1	0.987	1	0.608	0.57	0.646	CLONAL	1	TRUE	0	0.827450011682164	2		330	358	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028690	12028690	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0000778-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	141	306	0	ENST00000353533.5:c.891+2T>A		p.X297_splice	ENST00000353533	NM_003010.3	297			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		306	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs760043106	NA	P-0000824-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	50	498	0	ENST00000269305.4:c.584T>A	p.Ile195Asn	p.I195N	ENST00000269305	NM_001126112.2	195	aTc/aAc	6/11	0.176898905293807	3	FACETS	1	0.903	1	1	0.903	1	CLONAL	2	TRUE	1	0.218928964596787	3		498	237	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125702	47125709	+	frameshift_variant	Frame_Shift_Del	DEL	GTTGAGTG	GTTGAGTG	-	novel	NA	P-0000824-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	82	422	0	ENST00000409792.3:c.5561_5568del	p.Pro1854HisfsTer3	p.P1854Hfs*3	ENST00000409792	NM_014159.6	1854	cCACTCAAC/c	12/21	0.218928964596787	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.218928964596787	1		422	473	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436417	52436417	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000824-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	18	261	0	ENST00000460680.1:c.2077del	p.Glu693SerfsTer43	p.E693Sfs*43	ENST00000460680	NM_004656.3	693	Gag/ag	17/17	0.218928964596787	1	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	0	0.218928964596787	1		261	99	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941684	48941684	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000828-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	73	462	0	ENST00000267163.4:c.994G>C	p.Asp332His	p.D332H	ENST00000267163	NM_000321.2	332	Gat/Cat	10/27	NA	2	FACETS	0.547	0.48	0.619			1	INDETERMINATE	1	TRUE	NA	0.585545931403758	2		462	456	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553661	29553661	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000828-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	39	341	0	ENST00000356175.3:c.2210C>T	p.Thr737Ile	p.T737I	ENST00000356175	NM_000267.3	737	aCa/aTa	18/57	1	2	FACETS	0.215	0.177	0.256	0.215	0.177	0.256	SUBCLONAL	1	TRUE	1	0.585545931403758	2		341	621	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394805	45394805	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000828-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	47	347	1	ENST00000262160.6:c.544C>T	p.Arg182Ter	p.R182*	ENST00000262160	NM_005901.5	182	Cga/Tga	5/11	0.585545931403758	1	FACETS	0.353	0.299	0.411	0.353	0.299	0.411	SUBCLONAL	1	TRUE	0	0.585545931403758	1		348	322	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0000838-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	52	96	0	ENST00000397752.3:c.3028+1G>A		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.204529167368624	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		96	325	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687605	29687605	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000838-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	39	238	0	ENST00000356175.3:c.8200del	p.Leu2734SerfsTer2	p.L2734Sfs*2	ENST00000356175	NM_000267.3	2733	tCc/tc	56/57	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		238	685	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061208	38061208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000847-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	133	366	0	ENST00000250448.2:c.781C>T	p.Arg261Cys	p.R261C	ENST00000250448	NM_004496.3	261	Cgc/Tgc	2/2	0.184576282150945	5	FACETS	0.776	0.705	0.851	0.518	0.47	0.568	SUBCLONAL	2	FALSE	2	0.3	5		366	828	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578505	7578506	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0000847-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	243	702	1	ENST00000269305.4:c.424_425del	p.Pro142CysfsTer6	p.P142Cfs*6	ENST00000269305	NM_001126112.2	142	CCt/t	5/11	0.200201473053014	2	FACETS	0.762	0.712	0.814	0.762	0.712	0.814	SUBCLONAL	2	FALSE	0	0.3	2		703	1063	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0000854-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	145	183	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.45978154518329	2		183	483	SUCCESS
APC	324	MSKCC	GRCh37	5	112174096	112174096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs137854575	NA	P-0000854-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	97	124	0	ENST00000257430.4:c.2805C>A	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	taC/taA	16/16	1	2	FACETS	0.872	0.781	0.968	0.872	0.781	0.968	CLONAL	1	TRUE	1	0.45978154518329	2		124	484	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089710	27089710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000854-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	74	114	0	ENST00000324856.7:c.2666G>A	p.Gly889Asp	p.G889D	ENST00000324856	NM_006015.4	889	gGc/gAc	8/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.45978154518329	2		114	272	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412922	49412922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000854-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	99	241	0	ENST00000418115.1:c.101A>T	p.Tyr34Phe	p.Y34F	ENST00000418115	NM_001664.2	34	tAt/tTt	2/5	0.290766494094216	1	FACETS	0.682	0.612	0.757	0.682	0.612	0.757	SUBCLONAL	1	TRUE	0	0.45978154518329	1		241	486	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438191	49438191	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780507577	NA	P-0000854-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	114	274	0	ENST00000301067.7:c.5078G>A	p.Arg1693Gln	p.R1693Q	ENST00000301067	NM_003482.3	1693	cGg/cAg	20/54	0.45978154518329	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.45978154518329	1		274	313	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492608	56492608	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000854-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	108	110	0	ENST00000267101.3:c.2758G>C	p.Val920Leu	p.V920L	ENST00000267101	NM_001982.3	920	Gta/Cta	23/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.45978154518329	2		110	346	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858408	9858408	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000854-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	69	118	0	ENST00000330684.3:c.2993T>G	p.Val998Gly	p.V998G	ENST00000330684	NM_001134407.1	998	gTg/gGg	13/13	0.453243739006546	1	FACETS	0.533	0.465	0.605	0.533	0.465	0.605	SUBCLONAL	1	TRUE	0	0.45978154518329	1		118	434	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120173	70120173	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000854-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	50	110	0	ENST00000245479.2:c.1177del	p.Gln393SerfsTer10	p.Q393Sfs*10	ENST00000245479	NM_000346.3	392	tCc/tc	3/3	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.45978154518329	2		110	200	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0000860-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	11	265	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.268	0.184	0.374	0.268	0.184	0.374	SUBCLONAL	1	FALSE	1	0.211817835960624	2		267	387	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000860-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	28	58	0	ENST00000257430.4:c.3919dup	p.Ile1307AsnfsTer8	p.I1307Nfs*8	ENST00000257430	NM_000038.5	1306	gaa/gAaa	16/16	1	2	FACETS	0.811	0.655	0.984	1	0.946	1	CLONAL	2	FALSE	1	0.211817835960624	2		58	163	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579355	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519997	NA	P-0000860-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	43	137	1	ENST00000269305.4:c.332T>C	p.Leu111Pro	p.L111P	ENST00000269305	NM_001126112.2	111	cTg/cCg	4/11	1	2	FACETS	0.802	0.671	0.948	0.802	0.671	0.948	CLONAL	1	FALSE	1	0.211817835960624	2		138	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0000870-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	27	129	0	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.250924318887601	3	FACETS	0.999	0.802	1	0.5	0.401	0.61	CLONAL	1	TRUE	1	0.357931764427971	3		129	178	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106036	8106036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000870-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	18	126	0	ENST00000346208.3:c.856G>A	p.Ala286Thr	p.A286T	ENST00000346208		286	Gcc/Acc	4/6	1	2	FACETS	0.348	0.262	0.45	0.348	0.262	0.45	SUBCLONAL	1	TRUE	1	0.357931764427971	2		126	289	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374780	118374780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000870-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	36	132	0	ENST00000534358.1:c.8173G>A	p.Asp2725Asn	p.D2725N	ENST00000534358	NM_005933.3	2725	Gat/Aat	27/36	0.357931764427971	3	FACETS	0.611	0.503	0.732	0.306	0.251	0.366	SUBCLONAL	1	TRUE	1	0.357931764427971	3		132	388	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099065	157099065	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0000871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	128	235	1	ENST00000346085.5:c.2T>C	p.Met1?	p.M1?	ENST00000346085	NM_020732.3	1	aTg/aCg	1/20	1	2	FACETS	0.838	0.766	0.911	0.838	0.766	0.911	CLONAL	1	TRUE	1	0.769907643417025	2		236	397	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257817	16257817	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	263	465	0	ENST00000375759.3:c.5083del	p.Glu1695AsnfsTer6	p.E1695Nfs*6	ENST00000375759	NM_015001.2	1694	gtG/gt	11/15	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.769907643417025	2		465	678	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0000887-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	144	206	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.296666261418325	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.35	3		207	429	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209283	98209283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139942632	NA	P-0000887-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	65	610	0	ENST00000331920.6:c.4255C>T	p.Arg1419Trp	p.R1419W	ENST00000331920	NM_000264.3	1419	Cgg/Tgg	23/24	1	2	FACETS	0.537	0.465	0.615	0.537	0.465	0.615	SUBCLONAL	1	TRUE	1	0.35	2		610	692	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562135	21562135	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1307289826	NA	P-0000887-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	118	1004	2	ENST00000382592.4:c.1784A>G	p.Lys595Arg	p.K595R	ENST00000382592	NM_014572.2	595	aAg/aGg	4/8	0.3	0	FACETS	0.589	0.532	0.65			1	SUBCLONAL	1	TRUE	0	0.35	0		1006	744	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691022	NA	P-0000887-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	75	600	0	ENST00000269305.4:c.1024del	p.Arg342GlufsTer3	p.R342Efs*3	ENST00000269305	NM_001126112.2	342	Cga/ga	10/11	0.3	0	FACETS	0.571	0.501	0.645			1	SUBCLONAL	1	TRUE	0	0.35	0		600	488	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645511	67645519	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGAAAGGTA	AGAAAGGTA	G	novel	NA	P-0000887-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	17	55	0	ENST00000264010.4:c.776_781+3delinsG		p.X259_splice	ENST00000264010	NM_006565.3	259		3/12	0.352779959581392	1	FACETS	0.735	0.556	0.942	0.735	0.556	0.942	CLONAL	1	TRUE	0	0.35	1		55	109	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0000902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	272	503	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.3	1	FACETS	0.886	0.835	0.936	1	0.995	1	CLONAL	2	TRUE	0	0.35	1		503	724	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105761	27105761	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0000902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	120	267	0	ENST00000324856.7:c.5372C>G	p.Ser1791Ter	p.S1791*	ENST00000324856	NM_006015.4	1791	tCa/tGa	20/20	0.146924913167712	3	FACETS	0.917	0.841	0.993	1	0.985	1	INDETERMINATE	3	TRUE	1	0.35	3		267	293	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741694	17741694	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000905-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	193	434	0	ENST00000250003.3:c.365T>G	p.Leu122Arg	p.L122R	ENST00000250003	NM_002478.4	122	cTg/cGg	1/3	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	2	TRUE	NA	0.680007766826512	2		434	267	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624249	89624252	+	frameshift_variant	Frame_Shift_Del	DEL	TCGT	TCGT	-	novel	NA	P-0000905-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	40	88	0	ENST00000371953.3:c.24_27del	p.Val9AlafsTer14	p.V9Afs*14	ENST00000371953	NM_000314.4	8	aTCGTt/at	1/9	0.680007766826512	1	FACETS	0.882	0.762	1	0.882	0.762	1	CLONAL	1	TRUE	0	0.680007766826512	1		88	88	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0000913-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	2665	385	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.453085959649978	24	FACETS	0.978	0.968	0.988			1	CLONAL	22	TRUE	NA	0.453085959649978	24		385	3271	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0000913-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3616	201	362	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.453085959649978	24	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.453085959649978	24		362	3817	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0000913-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	253	563	1	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	0.220725524909305	3	FACETS	1	0.955	1	0.677	0.638	0.718	INDETERMINATE	2	TRUE	0	0.453085959649978	3		564	674	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99162464	99162464	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000913-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	98	387	0	ENST00000074304.5:c.982G>C	p.Asp328His	p.D328H	ENST00000074304	NM_001134224.1	328	Gat/Cat	12/26	0.392740335325306	4	FACETS	0.75	0.668	0.837	0.375	0.334	0.419	SUBCLONAL	1	TRUE	2	0.453085959649978	4		387	838	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944329	206944329	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000913-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	86	530	0	ENST00000423557.1:c.301C>T	p.Gln101Ter	p.Q101*	ENST00000423557	NM_000572.2	101	Caa/Taa	3/5	0.453085959649978	4	FACETS	0.586	0.517	0.66	0.293	0.258	0.33	SUBCLONAL	1	TRUE	2	0.453085959649978	4		530	942	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803111	1803111	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1361311749	NA	P-0000913-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	42	398	2	ENST00000260795.2:c.463C>T	p.Arg155Trp	p.R155W	ENST00000260795		155	Cgg/Tgg	4/17	1	2	FACETS	0.487	0.407	0.575	0.487	0.407	0.575	SUBCLONAL	1	TRUE	1	0.453085959649978	2		400	381	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914722	39914722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000913-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	143	672	0	ENST00000378444.4:c.4640G>A	p.Arg1547Gln	p.R1547Q	ENST00000378444	NM_001123385.1	1547	cGa/cAa	12/15	0.0889026894367735	1	FACETS	0.52	0.474	0.569	0.52	0.474	0.569	INDETERMINATE	1	TRUE	0	0.453085959649978	1		672	938	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0000921-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	92	675	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.392573102379278	4	FACETS	0.874	0.793	0.956			1	CLONAL	3	FALSE	NA	0.491573183468234	4		675	213	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013691	12013691	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0000921-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	151	276	0	ENST00000353533.5:c.634-1G>C		p.X212_splice	ENST00000353533	NM_003010.3	212			0.491573183468234	2	FACETS	0.927	0.875	0.976	1	0.991	1	CLONAL	3	FALSE	0	0.491573183468234	2		276	221	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47601095	47601095	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000925-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	112	147	0	ENST00000263735.4:c.333C>G	p.Asn111Lys	p.N111K	ENST00000263735	NM_002354.2	111	aaC/aaG	3/9	1	2	FACETS	0.586	0.529	0.646	0.586	0.529	0.646	SUBCLONAL	1	TRUE	1	0.70348544123911	2		147	543	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71064736	71064736	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000925-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	302	241	0	ENST00000318789.4:c.938G>C	p.Cys313Ser	p.C313S	ENST00000318789	NM_032682.5	313	tGt/tCt	12/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.70348544123911	2		241	812	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646341	23646341	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000925-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	169	434	0	ENST00000261584.4:c.1526G>C	p.Gly509Ala	p.G509A	ENST00000261584	NM_024675.3	509	gGt/gCt	4/13	0.426842899765947	1	FACETS	0.367	0.337	0.398	0.367	0.337	0.398	SUBCLONAL	1	TRUE	0	0.70348544123911	1		434	849	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0000925-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	197	341	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.70348544123911	1	FACETS	0.987	0.93	1	0.987	0.93	1	CLONAL	1	TRUE	0	0.70348544123911	1		341	368	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942034	44942036	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	AGT	AGT	-	novel	NA	P-0000925-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	262	345	0	ENST00000377967.4:c.3284+1_3284+3del		p.X1095_splice	ENST00000377967	NM_021140.2	1095		22/29	0.70348544123911	1	FACETS	0.841	0.796	0.887	0.841	0.796	0.887	CLONAL	1	TRUE	0	0.70348544123911	1		345	574	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0000939-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	77	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.391409709434467	2		215	392	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911534	101911534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111426349	NA	P-0000939-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	163	415	0	ENST00000374994.4:c.1459C>T	p.Arg487Trp	p.R487W	ENST00000374994	NM_004612.2	487	Cgg/Tgg	9/9	0.391409709434467	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.391409709434467	1		415	567	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0000939-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	131	371	2	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.258641495454778	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.391409709434467	1		373	537	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239878	98239879	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0000939-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	156	434	0	ENST00000331920.6:c.1453dup	p.Leu485ProfsTer12	p.L485Pfs*12	ENST00000331920	NM_000264.3	485	ctg/cCtg	10/24	0.391409709434467	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.391409709434467	1		434	632	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846031	128846031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1307431013	NA	P-0000939-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	63	587	4	ENST00000249373.3:c.961G>A	p.Val321Met	p.V321M	ENST00000249373	NM_005631.4	321	Gtg/Atg	5/12	0.110827310543738	4	FACETS	0.425	0.366	0.489	0.212	0.183	0.245	INDETERMINATE	1	TRUE	2	0.391409709434467	4		591	1054	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821125	72821125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747085182	NA	P-0000939-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	87	760	1	ENST00000268489.5:c.11050G>A	p.Asp3684Asn	p.D3684N	ENST00000268489	NM_006885.3	3684	Gac/Aac	10/10	0.268276181166879	0	FACETS	0.385	0.341	0.433			1	SUBCLONAL	1	TRUE	0	0.391409709434467	0		761	702	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0000952-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	414	395	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	0.730358297099393	2		395	1060	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0000952-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	1542	206	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.730358297099393	6	FACETS	1	0.998	1			1	CLONAL	6	TRUE	NA	0.730358297099393	6		207	1685	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087503	27087503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000952-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	438	519	0	ENST00000324856.7:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000324856	NM_006015.4	693	Cga/Tga	5/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.730358297099393	2		519	1086	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0000952-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	427	530	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.730358297099393	2		530	1105	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554954	187554955	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0000952-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	440	539	1	ENST00000441802.2:c.4206_4207insA	p.Asp1403ArgfsTer16	p.D1403Rfs*16	ENST00000441802	NM_005245.3	1402	-/A	7/27	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.730358297099393	2		540	1147	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117769	70117807	+	inframe_deletion	In_Frame_Del	DEL	GGTGCTCAAAGGCTACGACTGGACGCTGGTGCCCATGCC	GGTGCTCAAAGGCTACGACTGGACGCTGGTGCCCATGCC	-	novel	NA	P-0000952-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1269	73	567	0	ENST00000245479.2:c.242_280del	p.Leu81_Val93del	p.L81_V93del	ENST00000245479	NM_000346.3	79	caGGTGCTCAAAGGCTACGACTGGACGCTGGTGCCCATGCCg/cag	1/3	0.730358297099393	3	FACETS	0.203	0.177	0.232	0.102	0.088	0.116	SUBCLONAL	1	TRUE	1	0.730358297099393	3		567	1342	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0000958-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	110	417	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.781	0.703	0.863	0.781	0.703	0.863	SUBCLONAL	1	FALSE	1	0.437464117081875	2		417	644	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555526097	NA	P-0000958-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	86	383	0	ENST00000269305.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000269305	NM_001126112.2	167	Cag/Tag	5/11	0.437464117081875	1	FACETS	0.645	0.573	0.722	0.645	0.573	0.722	SUBCLONAL	1	FALSE	0	0.437464117081875	1		383	476	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0000978-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	9	375	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		375	388	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0000984-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	393	675	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.45786872122802	5	FACETS	1	0.97	1	1	0.97	1	CLONAL	4	TRUE	1	0.45786872122802	5		675	715	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099406	157099426	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAGCAA	CAGCAGCAGCAGCAGCAGCAA	-	rs762617219	NA	P-0000984-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	42	151	0	ENST00000346085.5:c.363_383del	p.Gln125_Gln131del	p.Q125_Q131del	ENST00000346085	NM_020732.3	115	CAGCAGCAGCAGCAGCAGCAA/-	1/20	1	2	FACETS	0.692	0.582	0.813	0.692	0.582	0.813	SUBCLONAL	1	TRUE	1	0.45786872122802	2		151	265	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138642	55138642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143344944	NA	P-0000984-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	128	287	0	ENST00000257290.5:c.1319C>T	p.Thr440Met	p.T440M	ENST00000257290	NM_006206.4	440	aCg/aTg	9/23	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.45786872122802	2		287	411	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645934	67645934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000984-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	148	267	0	ENST00000264010.4:c.862C>T	p.His288Tyr	p.H288Y	ENST00000264010	NM_006565.3	288	Cac/Tac	4/12	0.372295719309241	0	FACETS	0.6	0.559	0.641			1	SUBCLONAL	2	TRUE	0	0.45786872122802	0		267	292	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0000994-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	155	552	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.346193140223118	2	FACETS	0.899	0.832	0.968	0.899	0.832	0.968	CLONAL	2	TRUE	0	0.409366045930663	2		552	421	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0000994-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	134	344	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.40857002896719	1	FACETS	0.962	0.879	1	0.962	0.879	1	CLONAL	1	TRUE	0	0.409366045930663	1		344	541	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604756	48604756	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000994-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	147	304	0	ENST00000342988.3:c.1578A>C	p.Glu526Asp	p.E526D	ENST00000342988	NM_005359.5	526	gaA/gaC	12/12	0.409366045930663	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.409366045930663	1		304	534	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412884	49412884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001039-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	248	648	0	ENST00000418115.1:c.139G>A	p.Glu47Lys	p.E47K	ENST00000418115	NM_001664.2	47	Gag/Aag	2/5	0.168865964269558	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		648	739	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044943	47044943	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001039-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	122	189	0	ENST00000377604.3:c.2269C>T	p.Gln757Ter	p.Q757*	ENST00000377604	NM_001204468.1	757	Cag/Tag	20/24	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	0	NA	2		189	172	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449566	187449572	+	frameshift_variant	Frame_Shift_Del	DEL	ACAGCCA	ACAGCCA	-	novel	NA	P-0001039-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	156	265	0	ENST00000232014.4:c.308_314del	p.Met103ArgfsTer45	p.M103Rfs*45	ENST00000232014	NM_001130845.1	103	aTGGCTGTg/ag	4/10	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		265	495	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001059-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	101	387	0				ENST00000310581	NM_198253.2	-/1132			0.368689758055501	6	FACETS	1	0.942	1	1	0.942	1	CLONAL	5	TRUE	1	0.368689758055501	6		387	185	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0001059-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	81	92	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.368689758055501	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.368689758055501	2		92	201	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001059-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	170	339	0	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	1	2	FACETS	1	0.977	1	1	0.994	1	CLONAL	2	TRUE	1	0.368689758055501	2		339	412	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524966	187524966	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001059-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	132	470	0	ENST00000441802.2:c.10714C>T	p.Gln3572Ter	p.Q3572*	ENST00000441802	NM_005245.3	3572	Cag/Tag	19/27	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.368689758055501	2		470	677	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524930	187524949	+	frameshift_variant	Frame_Shift_Del	DEL	GGTCGAGACTGTAGGTTAGA	GGTCGAGACTGTAGGTTAGA	-	novel	NA	P-0001059-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	82	523	0	ENST00000441802.2:c.10731_10750del	p.Leu3578SerfsTer74	p.L3578Sfs*74	ENST00000441802	NM_005245.3	3577	acTCTAACCTACAGTCTCGACCct/acct	19/27	1	2	FACETS	0.594	0.523	0.67	0.594	0.523	0.67	SUBCLONAL	1	TRUE	1	0.368689758055501	2		523	749	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397683	139397684	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGCGCTCCCAGGA	novel	NA	P-0001059-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	29	354	0	ENST00000277541.6:c.5105_5117dup	p.Ala1707ProfsTer22	p.A1707Pfs*22	ENST00000277541	NM_017617.3	1706	ctc/ctTCCTGGGAGCGCTc	27/34	0.368689758055501	1	FACETS	0.467	0.375	0.569	0.467	0.375	0.569	SUBCLONAL	1	TRUE	0	0.368689758055501	1		354	275	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136856	55136856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001098-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	50	567	0	ENST00000257290.5:c.1178C>T	p.Thr393Ile	p.T393I	ENST00000257290	NM_006206.4	393	aCt/aTt	8/23	1	2	FACETS	0.682	0.578	0.797	0.682	0.578	0.797	SUBCLONAL	1	FALSE	1	0.230098621183662	2		567	637	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372701	81372701	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001098-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	38	498	0	ENST00000222390.5:c.833C>A	p.Thr278Asn	p.T278N	ENST00000222390	NM_000601.4	278	aCc/aAc	7/18	0.230098621183662	5	FACETS	0.591	0.487	0.708	0.197	0.162	0.236	SUBCLONAL	1	FALSE	2	0.230098621183662	5		498	752	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115916	8115916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771315353	NA	P-0001098-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	58	269	0	ENST00000346208.3:c.1262C>T	p.Pro421Leu	p.P421L	ENST00000346208		421	cCg/cTg	6/6	0.230098621183662	3	FACETS	0.808	0.698	0.926			1	CLONAL	2	FALSE	NA	0.230098621183662	3		269	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578181	7578181	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138983188	NA	P-0001098-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	86	599	0	ENST00000269305.4:c.668C>T	p.Pro223Leu	p.P223L	ENST00000269305	NM_001126112.2	223	cCt/cTt	6/11	0.221023672904576	3	FACETS	0.863	0.766	0.966	0.863	0.766	0.966	CLONAL	2	FALSE	1	0.230098621183662	3		599	483	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368208	45368208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001098-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	97	367	2	ENST00000262160.6:c.1394G>A	p.Ser465Asn	p.S465N	ENST00000262160	NM_005901.5	465	aGc/aAc	11/11	0.221023672904576	3	FACETS	0.874	0.781	0.971	0.874	0.781	0.971	CLONAL	2	FALSE	1	0.230098621183662	3		369	538	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793517	42793517	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001098-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	30	273	0	ENST00000575354.2:c.1319G>T	p.Arg440Leu	p.R440L	ENST00000575354	NM_015125.3	440	cGc/cTc	8/20	0.230098621183662	3	FACETS	0.746	0.601	0.91	0.373	0.3	0.455	CLONAL	1	FALSE	1	0.230098621183662	3		273	390	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138091	2138091	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001113-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	236	354	0	ENST00000219476.3:c.5111C>G	p.Ser1704Cys	p.S1704C	ENST00000219476	NM_000548.3	1704	tCt/tGt	40/42	0.195688555586712	1	FACETS	0.664	0.625	0.704	0.664	0.625	0.704	INDETERMINATE	1	TRUE	0	0.760568447711296	1		354	579	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0001114-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	12	83	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.532	0.373	0.73	0.532	0.373	0.73	SUBCLONAL	1	TRUE	1	0.13	2		83	347	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396271	139396271	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001114-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	30	420	0	ENST00000277541.6:c.5567C>G	p.Ser1856Cys	p.S1856C	ENST00000277541	NM_017617.3	1856	tCt/tGt	30/34	1	2	FACETS	0.797	0.641	0.976	0.797	0.641	0.976	CLONAL	1	TRUE	1	0.13	2		420	579	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0001123-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	569	607	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.487613662847559	7	FACETS	0.938	0.902	0.974	0.938	0.902	0.974	CLONAL	4	TRUE	3	0.487613662847559	7		607	1381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0001123-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	448	479	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.436466008107288	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.487613662847559	4		479	1274	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0001123-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	101	212	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	0.436466008107288	4	FACETS	0.999	0.894	1	0.499	0.447	0.555	CLONAL	1	TRUE	2	0.487613662847559	4		212	617	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339203	116339203	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001123-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	232	403	0	ENST00000397752.3:c.65G>A	p.Ser22Asn	p.S22N	ENST00000397752	NM_000245.2	22	aGc/aAc	2/21	0.487613662847559	3	FACETS	1	0.987	1	0.406	0.378	0.434	CLONAL	1	TRUE	0	0.487613662847559	3		403	972	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587782272	NA	P-0001136-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	150	466	0	ENST00000269305.4:c.994-1G>C		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.325831512513448	1	FACETS	0.978	0.895	1	0.978	0.895	1	CLONAL	1	TRUE	0	0.329321959178008	1		466	778	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272925	11272925	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001136-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	96	301	0	ENST00000361445.4:c.3326A>G	p.Asp1109Gly	p.D1109G	ENST00000361445	NM_004958.3	1109	gAc/gGc	22/58	0.329321959178008	3	FACETS	0.768	0.683	0.859			1	SUBCLONAL	1	TRUE	NA	0.329321959178008	3		301	884	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662667	117662667	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001136-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	152	449	0	ENST00000368508.3:c.4798C>A	p.Leu1600Met	p.L1600M	ENST00000368508	NM_002944.2	1600	Ctg/Atg	29/43	1	2	FACETS	0.863	0.788	0.941	0.863	0.788	0.941	CLONAL	1	TRUE	1	0.329321959178008	2		449	1070	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110251261	110251261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1183818686	NA	P-0001136-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	125	397	0	ENST00000374672.4:c.76G>A	p.Gly26Ser	p.G26S	ENST00000374672	NM_004235.4	26	Ggc/Agc	2/5	1	2	FACETS	0.898	0.813	0.989	0.898	0.813	0.989	CLONAL	1	TRUE	1	0.329321959178008	2		397	845	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796518	42796537	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTGGAACAGTCACCTCGT	GGCTGGAACAGTCACCTCGT	C	novel	NA	P-0001136-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	46	412	0	ENST00000575354.2:c.3075_3094delinsC	p.Gln1025HisfsTer8	p.Q1025Hfs*8	ENST00000575354	NM_015125.3	1025	caGGCTGGAACAGTCACCTCGTac/caCac	13/20	0.325831512513448	1	FACETS	0.355	0.298	0.418	0.355	0.298	0.418	SUBCLONAL	1	TRUE	0	0.329321959178008	1		412	658	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135777009	135777011	+	stop_gained	Nonsense_Mutation	TNP	GTG	GTG	CTA	novel	NA	P-0001136-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	128	435	0	ENST00000298552.3:c.2467_2469delinsTAG	p.His823Ter	p.H823*	ENST00000298552	NM_001162426.1	823	CAC/TAG	19/23	0.329321959178008	1	FACETS	0.827	0.75	0.908	0.827	0.75	0.908	CLONAL	1	TRUE	0	0.329321959178008	1		435	785	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0001156-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	27	265	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.274058843848763	1	FACETS	0.983	0.79	1	0.983	0.79	1	CLONAL	1	TRUE	0	0.274058843848763	1		267	173	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0001156-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	93	675	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.131864449193024	4	FACETS	0.831	0.742	0.927	0.831	0.742	0.927	INDETERMINATE	2	TRUE	2	0.274058843848763	4		675	520	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355574	15355574	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0001156-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	28	381	0	ENST00000263377.2:c.2159-1G>A		p.X720_splice	ENST00000263377	NM_058243.2	720			1	2	FACETS	0.566	0.452	0.695	0.566	0.452	0.695	SUBCLONAL	1	TRUE	1	0.274058843848763	2		381	361	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0001179-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	197	566	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	0.270843854182071	3	FACETS	0.843	0.789	0.897	1	0.989	1	CLONAL	3	FALSE	1	0.412313091484405	3		566	456	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205766	108205766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001179-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	107	549	0	ENST00000278616.4:c.8081G>A	p.Gly2694Glu	p.G2694E	ENST00000278616	NM_000051.3	2694	gGa/gAa	55/63	0.412313091484405	1	FACETS	0.998	0.902	1	0.998	0.902	1	CLONAL	1	FALSE	0	0.412313091484405	1		549	413	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939075	76939075	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001179-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	129	767	0	ENST00000373344.5:c.1673del	p.Ser558IlefsTer4	p.S558Ifs*4	ENST00000373344	NM_000489.3	558	aGt/at	9/35	0.29817064763688	0	FACETS	0.76	0.693	0.829			1	SUBCLONAL	1	FALSE	0	0.412313091484405	0		767	484	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0001189-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	5832	311	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.880453618384542	20	FACETS	1	0.998	1			1	CLONAL	19	TRUE	NA	0.880453618384542	20		311	6203	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455301	29455301	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001189-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	341	348	0	ENST00000389048.3:c.2501T>C	p.Val834Ala	p.V834A	ENST00000389048	NM_004304.4	834	gTg/gCg	15/29	0.880453618384542	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.880453618384542	2		348	375	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718731	190718731	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs146040262	NA	P-0001189-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	615	471	0	ENST00000441310.2:c.889C>G	p.Leu297Val	p.L297V	ENST00000441310	NM_000534.4	297	Ctg/Gtg	8/13	0.843123707462166	2	FACETS	0.93	0.91	0.949	0.93	0.91	0.949	CLONAL	2	TRUE	0	0.880453618384542	2		471	751	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662745	227662745	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001189-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	467	323	0	ENST00000305123.5:c.710G>T	p.Trp237Leu	p.W237L	ENST00000305123	NM_005544.2	237	tGg/tTg	1/2	0.843123707462166	2	FACETS	0.984	0.963	1	0.984	0.963	1	CLONAL	2	TRUE	0	0.880453618384542	2		323	539	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794105	242794105	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs773454593	NA	P-0001189-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	183	388	0	ENST00000334409.5:c.623C>A	p.Pro208His	p.P208H	ENST00000334409	NM_005018.2	208	cCc/cAc	4/5	0.843123707462166	2	FACETS	1	0.989	1	0.622	0.585	0.659	CLONAL	1	TRUE	0	0.880453618384542	2		388	334	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643372	52643372	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001189-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	504	618	0	ENST00000394830.3:c.2524G>T	p.Glu842Ter	p.E842*	ENST00000394830	NM_018313.4	842	Gag/Tag	17/30	0.808067080102774	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.880453618384542	1		618	593	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386551	81386551	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001189-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	390	356	0	ENST00000222390.5:c.436G>T	p.Gly146Cys	p.G146C	ENST00000222390	NM_000601.4	146	Ggc/Tgc	4/18	0.131984144444814	4	FACETS	0.903	0.862	0.945	0.903	0.862	0.945	INDETERMINATE	2	TRUE	2	0.880453618384542	4		356	922	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446141	70446141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339691951	NA	P-0001189-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	204	293	1	ENST00000373644.4:c.5081G>A	p.Arg1694His	p.R1694H	ENST00000373644	NM_030625.2	1694	cGc/cAc	11/12	NA	2	FACETS	0.729	0.679	0.779			1	INDETERMINATE	1	TRUE	NA	0.880453618384542	2		294	636	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870898	12870898	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200422211	NA	P-0001189-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	426	268	0	ENST00000228872.4:c.125C>T	p.Thr42Ile	p.T42I	ENST00000228872	NM_004064.3	42	aCc/aTc	1/3	0.517574948364395	6	FACETS	0.874	0.836	0.913	0.874	0.836	0.913	INDETERMINATE	3	TRUE	3	0.880453618384542	6		268	1019	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495661	56495661	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001189-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	144	285	0	ENST00000267101.3:c.3851C>T	p.Ala1284Val	p.A1284V	ENST00000267101	NM_001982.3	1284	gCa/gTa	28/28	0.634831231506108	6	FACETS	1	0.965	1	0.277	0.253	0.303	CLONAL	1	TRUE	2	0.880453618384542	6		285	814	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858613	9858613	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001189-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	242	639	0	ENST00000330684.3:c.2788C>A	p.Leu930Ile	p.L930I	ENST00000330684	NM_001134407.1	930	Ctc/Atc	13/13	NA	2	FACETS	0.798	0.749	0.847			1	INDETERMINATE	1	TRUE	NA	0.880453618384542	2		639	689	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757274881	NA	P-0001189-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	436	323	1	ENST00000269305.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	144	Cag/Tag	5/11	0.875810307513585	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.880453618384542	2		324	474	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141515	11141515	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001189-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	326	407	1	ENST00000358026.2:c.3492C>A	p.Asn1164Lys	p.N1164K	ENST00000358026	NM_001128849.1	1164	aaC/aaA	25/36	0.880453618384542	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.880453618384542	1		408	363	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353917	15353917	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001189-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	81	106	0	ENST00000263377.2:c.2963A>T	p.Gln988Leu	p.Q988L	ENST00000263377	NM_058243.2	988	cAg/cTg	14/20	0.880453618384542	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.880453618384542	1		106	91	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757404	40757404	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001189-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	170	414	0	ENST00000373198.4:c.2894A>G	p.Asn965Ser	p.N965S	ENST00000373198	NM_133170.3	965	aAc/aGc	20/32	NA	2	FACETS	0.636	0.588	0.686			1	INDETERMINATE	1	TRUE	NA	0.880453618384542	2		414	607	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750521	41750522	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0001189-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	307	380	0	ENST00000226382.2:c.106dup	p.Cys36LeufsTer10	p.C36Lfs*10	ENST00000226382	NM_003924.3	36	tgc/tTgc	1/3	0.439016506488745	5	FACETS	0.896	0.853	0.939			1	INDETERMINATE	3	TRUE	NA	0.880453618384542	5		380	602	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714439	40714441	+	missense_variant	Missense_Mutation	TNP	CCT	CCT	TCC	novel	NA	P-0001189-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	106	269	0	ENST00000373198.4:c.3956_3958delinsGGA	p.Gln1319_Val1320delinsArgMet	p.Q1319_V1320delinsRM	ENST00000373198	NM_133170.3	1319	cAGGtg/cGGAtg	29/32	NA	2	FACETS	0.644	0.582	0.708			1	INDETERMINATE	1	TRUE	NA	0.880453618384542	2		269	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519975	NA	P-0001196-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	123	363	0	ENST00000269305.4:c.403T>C	p.Cys135Arg	p.C135R	ENST00000269305	NM_001126112.2	135	Tgc/Cgc	5/11	0.381295728423098	1	FACETS	0.826	0.749	0.907	0.826	0.749	0.907	CLONAL	1	TRUE	0	0.381295728423098	1		363	632	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948775	55948775	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001196-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	184	450	0	ENST00000263923.4:c.3690G>C	p.Lys1230Asn	p.K1230N	ENST00000263923	NM_002253.2	1230	aaG/aaC	28/30	0.381295728423098	1	FACETS	0.972	0.898	1	0.972	0.898	1	CLONAL	1	TRUE	0	0.381295728423098	1		450	804	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524597	103524597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765051569	NA	P-0001196-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	85	539	0	ENST00000355739.4:c.2728C>T	p.His910Tyr	p.H910Y	ENST00000355739	NM_000123.3	910	Cat/Tat	13/15	NA	2	FACETS	0.577	0.509	0.649			1	INDETERMINATE	1	TRUE	NA	0.381295728423098	2		539	773	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842351	68842351	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001196-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	54	687	0	ENST00000261769.5:c.412G>C	p.Glu138Gln	p.E138Q	ENST00000261769	NM_004360.3	138	Gaa/Caa	4/16	0.381295728423098	1	FACETS	0.243	0.206	0.283	0.243	0.206	0.283	SUBCLONAL	1	TRUE	0	0.381295728423098	1		687	945	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0001199-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	193	611	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.51769365114317	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.51769365114317	1		611	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782177	NA	P-0001199-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	125	699	0	ENST00000269305.4:c.644G>T	p.Ser215Ile	p.S215I	ENST00000269305	NM_001126112.2	215	aGt/aTt	6/11	0.51769365114317	1	FACETS	0.934	0.854	1	0.934	0.854	1	CLONAL	1	TRUE	0	0.51769365114317	1		699	383	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138409963	138409963	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001199-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	65	348	0	ENST00000289153.2:c.1915C>G	p.Leu639Val	p.L639V	ENST00000289153	NM_006219.2	639	Ctt/Gtt	13/22	0.51769365114317	1	FACETS	0.496	0.432	0.565	0.496	0.432	0.565	SUBCLONAL	1	TRUE	0	0.51769365114317	1		348	375	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540239	187540239	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001199-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	59	618	0	ENST00000441802.2:c.7501C>G	p.Leu2501Val	p.L2501V	ENST00000441802	NM_005245.3	2501	Cta/Gta	10/27	0.306366507201401	2	FACETS	0.433	0.372	0.498	0.216	0.186	0.249	INDETERMINATE	1	TRUE	0	0.51769365114317	2		618	527	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944651	38944651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001199-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	49	378	0	ENST00000357387.3:c.4810G>A	p.Asp1604Asn	p.D1604N	ENST00000357387	NM_152756.3	1604	Gat/Aat	36/38	0.51769365114317	4	FACETS	0.495	0.419	0.579	0.165	0.139	0.193	SUBCLONAL	1	TRUE	1	0.51769365114317	4		378	580	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171636	32171636	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001199-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	38	475	0	ENST00000375023.3:c.3142G>A	p.Asp1048Asn	p.D1048N	ENST00000375023	NM_004557.3	1048	Gac/Aac	20/30	0.51769365114317	3	FACETS	0.446	0.369	0.533	0.223	0.184	0.267	SUBCLONAL	1	TRUE	1	0.51769365114317	3		475	414	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344797	118344797	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001199-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	71	627	0	ENST00000534358.1:c.2923G>C	p.Asp975His	p.D975H	ENST00000534358	NM_005933.3	975	Gac/Cac	3/36	1	2	FACETS	0.532	0.465	0.604	0.532	0.465	0.604	SUBCLONAL	1	TRUE	1	0.51769365114317	2		627	516	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024740	14024740	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001199-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	84	404	0	ENST00000311895.7:c.966G>C	p.Gln322His	p.Q322H	ENST00000311895	NM_005236.2	322	caG/caC	5/11	0.318841701300457	4	FACETS	0.836	0.74	0.939	0.418	0.37	0.47	CLONAL	1	TRUE	2	0.51769365114317	4		404	589	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646591	23646591	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001199-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	50	355	0	ENST00000261584.4:c.1276G>C	p.Glu426Gln	p.E426Q	ENST00000261584	NM_024675.3	426	Gag/Cag	4/13	0.318841701300457	4	FACETS	0.496	0.42	0.579	0.248	0.21	0.29	SUBCLONAL	1	TRUE	2	0.51769365114317	4		355	591	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952321	17952321	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001199-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	48	464	0	ENST00000458235.1:c.1019C>G	p.Ser340Trp	p.S340W	ENST00000458235	NM_000215.3	340	tCg/tGg	8/24	0.51769365114317	3	FACETS	0.437	0.369	0.512	0.219	0.184	0.256	SUBCLONAL	1	TRUE	1	0.51769365114317	3		464	534	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735547	40735547	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001199-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	66	340	0	ENST00000373198.4:c.3326G>T	p.Arg1109Leu	p.R1109L	ENST00000373198	NM_133170.3	1109	cGg/cTg	25/32	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.51769365114317	2		340	252	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855256	76855256	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs942968288	NA	P-0001199-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	60	943	0	ENST00000373344.5:c.5731A>G	p.Ile1911Val	p.I1911V	ENST00000373344	NM_000489.3	1911	Ata/Gta	24/35	0.51769365114317	0	FACETS	0.311	0.269	0.356			1	SUBCLONAL	1	TRUE	0	0.51769365114317	0		943	360	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217317	123217317	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001199-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	77	782	0	ENST00000218089.9:c.2971A>G	p.Ser991Gly	p.S991G	ENST00000218089	NM_001042749.1	991	Agc/Ggc	29/35	0.473928035088535	1	FACETS	0.396	0.348	0.447	0.396	0.348	0.447	SUBCLONAL	1	TRUE	0	0.51769365114317	1		782	557	SUCCESS
APC	324	MSKCC	GRCh37	5	112174742	112174742	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001200-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	70	345	0	ENST00000257430.4:c.3451G>T	p.Glu1151Ter	p.E1151*	ENST00000257430	NM_000038.5	1151	Gaa/Taa	16/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.218394511245763	2		345	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0001200-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	82	749	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.218394511245763	2		749	589	SUCCESS
APC	324	MSKCC	GRCh37	5	112175536	112175536	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001200-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	42	457	0	ENST00000257430.4:c.4245del	p.Ser1415ArgfsTer4	p.S1415Rfs*4	ENST00000257430	NM_000038.5	1415	agT/ag	16/16	1	2	FACETS	0.507	0.422	0.602	0.507	0.422	0.602	SUBCLONAL	1	TRUE	1	0.218394511245763	2		457	759	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158551	26158551	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001204-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	144	243	0	ENST00000289316.2:c.154G>C	p.Asp52His	p.D52H	ENST00000289316	NM_138720.2	52	Gac/Cac	1/2	0.279000730713903	5	FACETS	0.944	0.865	1	0.629	0.576	0.684	CLONAL	2	TRUE	2	0.436957267720545	5		243	578	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001204-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	185	437	0	ENST00000347630.2:c.399C>A	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttA	6/11	0.323239487185649	4	FACETS	0.919	0.852	0.988	0.919	0.852	0.988	CLONAL	2	TRUE	2	0.436957267720545	4		437	662	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527594	29527594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001204-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	66	339	0	ENST00000356175.3:c.1043C>T	p.Ser348Phe	p.S348F	ENST00000356175	NM_000267.3	348	tCc/tTc	9/57	0.323239487185649	4	FACETS	1	0.917	1	0.535	0.466	0.608	CLONAL	1	TRUE	2	0.436957267720545	4		339	406	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0001217-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	269	711	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.516177512511451	4	FACETS	0.866	0.814	0.92	0.866	0.814	0.92	CLONAL	2	TRUE	2	0.516177512511451	4		711	912	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333135	70333135	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001217-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	242	553	0	ENST00000373644.4:c.1040A>G	p.Glu347Gly	p.E347G	ENST00000373644	NM_030625.2	347	gAg/gGg	2/12	0.108634804624801	3	FACETS	0.861	0.809	0.914			1	INDETERMINATE	2	TRUE	NA	0.516177512511451	3		553	685	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988249	36988249	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001217-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	18	176	0	ENST00000354822.5:c.404G>T	p.Arg135Met	p.R135M	ENST00000354822	NM_001079668.2	135	aGg/aTg	2/3	0.396951738680551	4	FACETS	0.433	0.327	0.559	0.217	0.163	0.28	SUBCLONAL	1	TRUE	2	0.516177512511451	4		176	244	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201059	NA	P-0001217-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	275	519	0	ENST00000269305.4:c.856G>T	p.Glu286Ter	p.E286*	ENST00000269305	NM_001126112.2	286	Gaa/Taa	8/11	0.516177512511451	4	FACETS	0.972	0.916	1	0.972	0.916	1	CLONAL	2	TRUE	2	0.516177512511451	4		519	831	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530055	212530055	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001230-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	159	272	0	ENST00000342788.4:c.1864A>T	p.Thr622Ser	p.T622S	ENST00000342788	NM_005235.2	622	Acc/Tcc	15/28	1	2	FACETS	0.857	0.789	0.927	1	0.993	1	CLONAL	3	FALSE	1	0.20417361210642	2		272	606	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37048544	37048544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001230-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	136	331	0	ENST00000231790.2:c.443C>T	p.Thr148Ile	p.T148I	ENST00000231790	NM_000249.3	148	aCc/aTc	5/19	0.173831912763535	3	FACETS	0.85	0.776	0.927	1	0.981	1	CLONAL	3	FALSE	1	0.20417361210642	3		331	576	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696689	47696689	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519972	NA	P-0001230-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	193	529	0	ENST00000347630.2:c.259T>A	p.Tyr87Asn	p.Y87N	ENST00000347630	NM_001007230.1	87	Tac/Aac	5/11	1	2	FACETS	0.854	0.792	0.918	1	0.994	1	CLONAL	3	FALSE	1	0.20417361210642	2		529	738	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519886	NA	P-0001244-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	236	241	0	ENST00000349496.5:c.97T>C	p.Ser33Pro	p.S33P	ENST00000349496	NM_001904.3	33	Tct/Cct	3/15	0.652138367372981	4	FACETS	1	0.992	1	0.71	0.664	0.757	CLONAL	1	FALSE	2	0.652138367372981	4		241	842	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0001253-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	129	378	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.941824228261017	3	FACETS	0.946	0.865	1	0.473	0.432	0.515	CLONAL	1	FALSE	1	0.941824228261017	3		378	426	SUCCESS
AR	367	MSKCC	GRCh37	X	66766350	66766351	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGT	rs746958859	NA	P-0001253-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	48	75	0	ENST00000374690.3:c.1368_1370dup	p.Gly473dup	p.G473dup	ENST00000374690	NM_000044.3	473	-/GGT	1/8	0.583045262267186	4	FACETS	1	0.968	1	0.75	0.65	0.854	CLONAL	1	FALSE	2	0.941824228261017	4		75	132	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0001253-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	83	208	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	1	2	FACETS	0.847	0.763	0.934	0.847	0.763	0.934	CLONAL	1	FALSE	1	0.941824228261017	2		208	208	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577544	7577544	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587780074	NA	P-0001253-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	96	225	0	ENST00000269305.4:c.737T>C	p.Met246Thr	p.M246T	ENST00000269305	NM_001126112.2	246	aTg/aCg	7/11	1	2	FACETS	0.902	0.82	0.985	0.902	0.82	0.985	CLONAL	1	FALSE	1	0.941824228261017	2		225	226	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152093	55152093	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121908585	NA	P-0001254-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	397	660	0	ENST00000257290.5:c.2525A>T	p.Asp842Val	p.D842V	ENST00000257290	NM_006206.4	842	gAc/gTc	18/23	0.643112152295447	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.643112152295447	2		660	562	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672980	30672980	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001260-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	145	463	0	ENST00000376406.3:c.3980C>G	p.Pro1327Arg	p.P1327R	ENST00000376406	NM_014641.2	1327	cCc/cGc	10/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.217595157356917	2		463	926	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0001260-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	70	288	0	ENST00000269305.4:c.97-1G>T		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.217595157356917	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	0	0.217595157356917	1		288	500	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591933	48591933	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001260-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	73	400	0	ENST00000342988.3:c.1096C>A	p.Gln366Lys	p.Q366K	ENST00000342988	NM_005359.5	366	Caa/Aaa	9/12	0.217595157356917	1	FACETS	0.703	0.614	0.8	0.703	0.614	0.8	SUBCLONAL	1	FALSE	0	0.217595157356917	1		400	850	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404893	70404893	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765094207	NA	P-0001263-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	215	307	0	ENST00000373644.4:c.2407G>A	p.Ala803Thr	p.A803T	ENST00000373644	NM_030625.2	803	Gct/Act	4/12	0.27290144077196	5	FACETS	1	0.98	1	0.744	0.695	0.794	INDETERMINATE	2	TRUE	2	0.547146082288284	5		307	641	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14028135	14028135	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001263-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	62	197	0	ENST00000311895.7:c.1189G>A	p.Glu397Lys	p.E397K	ENST00000311895	NM_005236.2	397	Gag/Aag	7/11	0.547146082288284	6	FACETS	0.82	0.708	0.941			1	CLONAL	1	TRUE	NA	0.547146082288284	6		197	579	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66518960	66518960	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001263-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	255	313	0	ENST00000358598.2:c.241G>A	p.Glu81Lys	p.E81K	ENST00000358598	NM_212471.2	81	Gag/Aag	3/11	0.547146082288284	6	FACETS	0.924	0.865	0.985			1	CLONAL	2	TRUE	NA	0.547146082288284	6		313	1056	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0001283-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	126	219	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	0.911262952694518	2		219	268	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866987936	NA	P-0001283-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	157	236	0	ENST00000281708.4:c.1436G>C	p.Arg479Pro	p.R479P	ENST00000281708	NM_033632.3	479	cGa/cCa	10/12	1	2	FACETS	0.957	0.89	1	0.957	0.89	1	CLONAL	1	TRUE	1	0.911262952694518	2		236	360	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610650	52610650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001283-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	26	551	0	ENST00000394830.3:c.3523G>A	p.Glu1175Lys	p.E1175K	ENST00000394830	NM_018313.4	1175	Gaa/Aaa	23/30	0.911262952694518	1	FACETS	0.085	0.067	0.106	0.085	0.067	0.106	SUBCLONAL	1	TRUE	0	0.911262952694518	1		551	366	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590669	189590669	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001283-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	249	369	0	ENST00000264731.3:c.1234G>C	p.Glu412Gln	p.E412Q	ENST00000264731	NM_003722.4	412	Gaa/Caa	10/14	0.911262952694518	5	FACETS	0.816	0.765	0.867	0.544	0.51	0.578	CLONAL	2	TRUE	2	0.911262952694518	5		369	793	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245543	153245543	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001283-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	206	237	0	ENST00000281708.4:c.1648G>C	p.Asp550His	p.D550H	ENST00000281708	NM_033632.3	550	Gat/Cat	11/12	1	2	FACETS	0.936	0.878	0.995	0.936	0.878	0.995	CLONAL	1	TRUE	1	0.911262952694518	2		237	483	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856077	151856077	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001283-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	268	591	0	ENST00000262189.6:c.11541G>C	p.Lys3847Asn	p.K3847N	ENST00000262189	NM_170606.2	3847	aaG/aaC	44/59	0.911262952694518	1	FACETS	0.985	0.954	1	0.985	0.954	1	CLONAL	1	TRUE	0	0.911262952694518	1		591	325	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970900	21970900	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0001283-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	225	308	0	ENST00000304494.5:c.457+1G>T		p.X153_splice	ENST00000304494	NM_000077.4	153			0.911262952694518	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.911262952694518	1		308	256	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781386	135781386	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203549	NA	P-0001283-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	249	298	2	ENST00000298552.3:c.1579C>T	p.Gln527Ter	p.Q527*	ENST00000298552	NM_001162426.1	527	Cag/Tag	15/23	0.911262952694518	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.911262952694518	1		300	275	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097634	8097634	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001283-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	98	200	0	ENST00000346208.3:c.16G>C	p.Asp6His	p.D6H	ENST00000346208		6	Gac/Cac	2/6	1	2	FACETS	0.996	0.908	1	0.996	0.908	1	CLONAL	1	TRUE	1	0.911262952694518	2		200	216	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100646	8100646	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1778076	NA	P-0001283-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	248	575	0	ENST00000346208.3:c.620C>A	p.Ala207Asp	p.A207D	ENST00000346208		207	gCc/gAc	3/6	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.911262952694518	2		575	544	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404780	404780	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001283-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	255	428	0	ENST00000399788.2:c.4414A>T	p.Thr1472Ser	p.T1472S	ENST00000399788	NM_001042603.1	1472	Aca/Tca	26/28	NA	2	FACETS	0.963	0.91	1			1	INDETERMINATE	1	TRUE	NA	0.911262952694518	2		428	581	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519999	NA	P-0001283-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	189	212	0	ENST00000269305.4:c.716A>G	p.Asn239Ser	p.N239S	ENST00000269305	NM_001126112.2	239	aAc/aGc	7/11	0.911262952694518	1	FACETS	0.999	0.962	1	0.999	0.962	1	CLONAL	1	TRUE	0	0.911262952694518	1		212	226	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257845	19257845	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001283-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	240	422	0	ENST00000162023.5:c.541G>T	p.Gly181Cys	p.G181C	ENST00000162023		181	Ggc/Tgc	9/13	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.911262952694518	2		422	520	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028806	47028806	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001283-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	221	566	2	ENST00000377604.3:c.110G>T	p.Arg37Leu	p.R37L	ENST00000377604	NM_001204468.1	37	cGg/cTg	3/24	NA	2	FACETS	0.852	0.8	0.906			1	INDETERMINATE	1	TRUE	NA	0.911262952694518	2		568	569	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028885	47028885	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001283-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	124	288	0	ENST00000377604.3:c.189G>T	p.Glu63Asp	p.E63D	ENST00000377604	NM_001204468.1	63	gaG/gaT	3/24	NA	2	FACETS	0.822	0.754	0.892			1	INDETERMINATE	1	TRUE	NA	0.911262952694518	2		288	331	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794906	242794906	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001283-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	220	310	1	ENST00000334409.5:c.303del	p.Asn102ThrfsTer7	p.N102Tfs*7	ENST00000334409	NM_005018.2	101	ccC/cc	2/5	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.911262952694518	2		311	464	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513213	106513213	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001283-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	331	217	0	ENST00000359195.3:c.2118del	p.Arg707AspfsTer9	p.R707Dfs*9	ENST00000359195	NM_002649.2	706	tCc/tc	4/11	0.287170802446931	1	FACETS	1	0.994	1	1	0.994	1	INDETERMINATE	1	TRUE	0	0.911262952694518	1		217	372	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0001296-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	175	607	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.549278389002104	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.549278389002104	3		607	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0001296-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	39	248	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	0.379838723640426	0	FACETS	0.383	0.322	0.449			1	SUBCLONAL	1	TRUE	0	0.549278389002104	0		248	167	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45391499	45391499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001296-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	43	342	0	ENST00000262160.6:c.661C>T	p.Pro221Ser	p.P221S	ENST00000262160	NM_005901.5	221	Cca/Tca	6/11	0.20551626383521	2	FACETS	0.497	0.418	0.584	0.249	0.209	0.292	INDETERMINATE	1	TRUE	0	0.549278389002104	2		342	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0001301-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	402	276	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.735162712205574	2	FACETS	0.886	0.855	0.917	0.886	0.855	0.917	CLONAL	2	TRUE	0	0.735162712205574	2		276	617	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812298	212812298	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001301-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	131	287	0	ENST00000342788.4:c.278A>T	p.Gln93Leu	p.Q93L	ENST00000342788	NM_005235.2	93	cAg/cTg	3/28	0.735162712205574	3	FACETS	0.673	0.612	0.738	0.337	0.306	0.369	SUBCLONAL	1	TRUE	1	0.735162712205574	3		287	724	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849663	68849663	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587780113	NA	P-0001301-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	467	221	0	ENST00000261769.5:c.1565+1G>A		p.X522_splice	ENST00000261769	NM_004360.3	522			0.665484267187798	5	FACETS	0.981	0.943	1	0.981	0.943	1	CLONAL	3	TRUE	2	0.735162712205574	5		221	908	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0001304-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	53	340	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.51	0.433	0.594	0.51	0.433	0.594	SUBCLONAL	1	FALSE	1	0.218664355541565	2		340	951	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671004	30671005	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0001304-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	24	295	1	ENST00000376406.3:c.5741dup	p.Ser1915LysfsTer15	p.S1915Kfs*15	ENST00000376406	NM_014641.2	1914	gga/ggGa	12/15	NA	2	FACETS	0.459	0.359	0.575			1	INDETERMINATE	1	FALSE	NA	0.218664355541565	2		296	478	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595596	55595596	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001319-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	17	323	0	ENST00000288135.5:c.2086G>T	p.Asp696Tyr	p.D696Y	ENST00000288135	NM_000222.2	696	Gat/Tat	14/21	1	2	FACETS	0.428	0.319	0.559	0.428	0.319	0.559	SUBCLONAL	1	TRUE	1	0.235491327706227	2		323	337	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591300	67591330	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AATGAAAACACTGAAGAGTAAGTAGTTACTA	AATGAAAACACTGAAGAGTAAGTAGTTACTA	-	novel	NA	P-0001319-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	39	207	0	ENST00000274335.5:c.1800_1814+16del		p.X600_splice	ENST00000274335		600		13/15	0.190776934415692	1	FACETS	1	0.845	1	1	0.845	1	CLONAL	1	TRUE	0	0.235491327706227	1		207	288	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217858	7217858	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001319-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	151	897	0	ENST00000380728.2:c.153del	p.Lys52ArgfsTer11	p.K52Rfs*11	ENST00000380728		51	agG/ag	3/11	0.235491327706227	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.235491327706227	1		897	969	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	110	154	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.799904835950601	2		154	244	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	284	360	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.155461948238638	3	FACETS	0.788	0.747	0.829	0.788	0.747	0.829	INDETERMINATE	2	TRUE	1	0.799904835950601	3		360	631	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	197	285	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.799904835950601	2		285	450	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389135	31389135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1165118132	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	269	370	1	ENST00000328111.2:c.2048G>A	p.Arg683His	p.R683H	ENST00000328111	NM_006892.3	683	cGc/cAc	19/23	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.799904835950601	2		371	574	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	371	778	1	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	NA	2	FACETS	1	0.958	1			1	INDETERMINATE	1	TRUE	NA	0.799904835950601	2		779	922	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9770626	9770626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761349863	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	670	439	1	ENST00000377346.4:c.113G>A	p.Arg38His	p.R38H	ENST00000377346	NM_005026.3	38	cGc/cAc	3/24	0.772992325043707	3	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.799904835950601	3		440	1023	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784113	9784113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771951762	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	431	277	0	ENST00000377346.4:c.2681G>A	p.Arg894Gln	p.R894Q	ENST00000377346	NM_005026.3	894	cGg/cAg	21/24	0.772992325043707	3	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.799904835950601	3		277	680	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17349180	17349180	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138996609	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	248	301	0	ENST00000375499.3:c.688C>T	p.Arg230Cys	p.R230C	ENST00000375499	NM_003000.2	230	Cgc/Tgc	7/8	0.504019628873567	4	FACETS	1	0.993	1	0.499	0.468	0.53	CLONAL	1	TRUE	1	0.799904835950601	4		301	746	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125722	47125722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376063996	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	332	456	0	ENST00000409792.3:c.5548C>T	p.Arg1850Cys	p.R1850C	ENST00000409792	NM_014159.6	1850	Cgt/Tgt	12/21	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.799904835950601	2		456	678	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525017	187525017	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	216	310	0	ENST00000441802.2:c.10663T>C	p.Ser3555Pro	p.S3555P	ENST00000441802	NM_005245.3	3555	Tct/Cct	19/27	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.799904835950601	2		310	452	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517609	176517609	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs755455944	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	287	495	2	ENST00000292408.4:c.310C>T	p.Arg104Ter	p.R104*	ENST00000292408	NM_213647.1	104	Cga/Tga	3/18	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.799904835950601	2		497	631	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707759	176707759	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	293	419	0	ENST00000439151.2:c.5816G>A	p.Arg1939His	p.R1939H	ENST00000439151	NM_022455.4	1939	cGc/cAc	18/23	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.799904835950601	2		419	659	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469811	157469811	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145635490	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	398	500	0	ENST00000346085.5:c.2605G>A	p.Gly869Ser	p.G869S	ENST00000346085	NM_020732.3	869	Ggc/Agc	9/20	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.799904835950601	2		500	781	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104268939	104268939	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	501	440	2	ENST00000369902.3:c.196G>T	p.Asp66Tyr	p.D66Y	ENST00000369902	NM_016169.3	66	Gac/Tac	2/12	0.799904835950601	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.799904835950601	3		442	814	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129428	64129428	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61736650	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	228	319	0	ENST00000334205.4:c.860C>T	p.Ala287Val	p.A287V	ENST00000334205	NM_003942.2	287	gCg/gTg	8/17	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.799904835950601	2		319	481	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390716	118390716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555052977	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	276	396	1	ENST00000534358.1:c.11366G>A	p.Arg3789His	p.R3789H	ENST00000534358	NM_005933.3	3789	cGt/cAt	33/36	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.799904835950601	2		397	560	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944812	31944812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866971809	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	293	522	1	ENST00000340398.3:c.289G>A	p.Glu97Lys	p.E97K	ENST00000340398	NM_001013699.2	97	Gaa/Aaa	1/1	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.799904835950601	2		523	606	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244144	133244144	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	290	390	0	ENST00000320574.5:c.2264T>C	p.Val755Ala	p.V755A	ENST00000320574	NM_006231.2	755	gTg/gCg	20/49	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.799904835950601	2		390	560	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003176	42003176	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1015277089	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	493	780	1	ENST00000219905.7:c.2713G>A	p.Ala905Thr	p.A905T	ENST00000219905	NM_001164273.1	905	Gca/Aca	8/24	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.799904835950601	2		781	1045	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900776	3900776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766844540	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	159	219	0	ENST00000262367.5:c.320C>T	p.Pro107Leu	p.P107L	ENST00000262367	NM_004380.2	107	cCg/cTg	2/31	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.799904835950601	2		219	348	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857895	9857895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761399460	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	226	339	0	ENST00000330684.3:c.3506G>A	p.Arg1169Gln	p.R1169Q	ENST00000330684	NM_001134407.1	1169	cGg/cAg	13/13	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.799904835950601	2		339	449	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993336	72993336	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	44	773	0	ENST00000268489.5:c.709C>T	p.Arg237Ter	p.R237*	ENST00000268489	NM_006885.3	237	Cga/Tga	2/10	NA	2	FACETS	0.129	0.108	0.153			1	INDETERMINATE	1	TRUE	NA	0.799904835950601	2		773	851	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351053	89351053	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	448	700	0	ENST00000301030.4:c.1897A>G	p.Lys633Glu	p.K633E	ENST00000301030	NM_001256183.1	633	Aaa/Gaa	9/13	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.799904835950601	2		700	928	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	161	198	0	ENST00000269305.4:c.673-2A>C		p.X225_splice	ENST00000269305	NM_001126112.2	225			1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.799904835950601	2		198	331	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37871997	37871997	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756345214	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	224	439	0	ENST00000269571.5:c.1318G>A	p.Ala440Thr	p.A440T	ENST00000269571		440	Gcc/Acc	12/27	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.799904835950601	2		439	508	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40376853	40376853	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1177773526	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	397	606	1	ENST00000293328.3:c.319C>T	p.Arg107Cys	p.R107C	ENST00000293328	NM_012448.3	107	Cgc/Tgc	4/19	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.799904835950601	2		607	818	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226443	2226443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773019943	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	258	361	0	ENST00000398665.3:c.3923C>T	p.Pro1308Leu	p.P1308L	ENST00000398665	NM_032482.2	1308	cCg/cTg	27/28	0.799904835950601	3	FACETS	1	0.982	1	0.557	0.524	0.592	CLONAL	1	TRUE	1	0.799904835950601	3		361	810	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412110	63412110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852216	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	411	400	0	ENST00000330258.3:c.1057C>T	p.Arg353Ter	p.R353*	ENST00000330258	NM_152424.3	353	Cga/Tga	2/2	1	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.799904835950601	1		400	420	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061169	38061169	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1489466891	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	124	148	0	ENST00000250448.2:c.820del	p.Ala274ProfsTer47	p.A274Pfs*47	ENST00000250448	NM_004496.3	274	Gcc/cc	2/2	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.799904835950601	2		148	234	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944382	131944382	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs748536322	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	205	259	3	ENST00000265335.6:c.2801del	p.Asn934IlefsTer6	p.N934Ifs*6	ENST00000265335		932	Aaa/aa	17/25	0.155461948238638	3	FACETS	0.836	0.786	0.887	0.836	0.786	0.887	INDETERMINATE	2	TRUE	1	0.799904835950601	3		262	429	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910372	29910372	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs41548119	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	132	515	1	ENST00000376809.5:c.46del	p.Ala16ProfsTer4	p.A16Pfs*4	ENST00000376809	NM_002116.7	14	tcG/tc	1/8	1	2	FACETS	0.494	0.449	0.541	0.494	0.449	0.541	SUBCLONAL	1	TRUE	1	0.799904835950601	2		516	668	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263661	16263663	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-	rs768147844	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	330	243	0	ENST00000375759.3:c.10036_10038del	p.Pro3346del	p.P3346del	ENST00000375759	NM_015001.2	3344	CCT/-	12/15	0.504019628873567	4	FACETS	0.948	0.91	0.986	0.948	0.91	0.986	CLONAL	3	TRUE	1	0.799904835950601	4		243	522	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822585	72822586	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs764626362	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	245	530	0	ENST00000268489.5:c.9589dup	p.Gln3197ProfsTer42	p.Q3197Pfs*42	ENST00000268489	NM_006885.3	3197	cag/cCag	10/10	NA	2	FACETS	0.937	0.881	0.993			1	INDETERMINATE	1	TRUE	NA	0.799904835950601	2		530	654	SUCCESS
APC	324	MSKCC	GRCh37	5	112173831	112173831	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	259	290	0	ENST00000257430.4:c.2544del	p.Asp849IlefsTer12	p.D849Ifs*12	ENST00000257430	NM_000038.5	847	gAa/ga	16/16	0.155461948238638	3	FACETS	0.808	0.764	0.852	0.808	0.764	0.852	INDETERMINATE	2	TRUE	1	0.799904835950601	3		290	561	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913837	32913837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359507	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	479	691	2	ENST00000380152.3:c.5351del	p.Asn1784ThrfsTer7	p.N1784Tfs*7	ENST00000380152		1782	cAa/ca	11/27	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.799904835950601	2		693	1060	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916766	48916766	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	231	251	0	ENST00000267163.4:c.299del	p.Gly100GlufsTer11	p.G100Efs*11	ENST00000267163	NM_000321.2	99	tGg/tg	3/27	0.799904835950601	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.799904835950601	1		251	245	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579359	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587780066	NA	P-0001331-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	17	371	0	ENST00000269305.4:c.328del	p.Arg110ValfsTer13	p.R110Vfs*13	ENST00000269305	NM_001126112.2	110	Cgt/gt	4/11	0.185362718284483	4	FACETS	0.888	0.67	1			1	INDETERMINATE	1	FALSE	NA	0.451962790553674	4		371	123	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038659	14038659	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs2020955	NA	P-0001331-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	11	274	0	ENST00000311895.7:c.1984T>C	p.Ser662Pro	p.S662P	ENST00000311895	NM_005236.2	662	Tct/Cct	10/11	1	2	FACETS	0.409	0.284	0.562	0.409	0.284	0.562	SUBCLONAL	1	FALSE	1	0.451962790553674	2		274	119	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524525	187524525	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35670235	NA	P-0001331-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	12	539	0	ENST00000441802.2:c.11155G>A	p.Val3719Met	p.V3719M	ENST00000441802	NM_005245.3	3719	Gtg/Atg	19/27	0.379896689786809	0	FACETS	0.297	0.211	0.4			1	SUBCLONAL	1	FALSE	0	0.451962790553674	0		539	98	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233204	46233204	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139689510	NA	P-0001331-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	12	566	0	ENST00000334344.6:c.1423C>T	p.His475Tyr	p.H475Y	ENST00000334344	NM_152641.2	475	Cat/Tat	11/21	NA	2	FACETS	0.374	0.264	0.508			1	INDETERMINATE	1	FALSE	NA	0.451962790553674	2		566	142	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579366	7579366	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs770776262	NA	P-0001331-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	27	372	0	ENST00000269305.4:c.321C>A	p.Tyr107Ter	p.Y107*	ENST00000269305	NM_001126112.2	107	taC/taA	4/11	0.185362718284483	4	FACETS	1	0.93	1			1	INDETERMINATE	1	FALSE	NA	0.451962790553674	4		372	125	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0001351-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	21	83	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.726	0.558	0.923	0.726	0.558	0.923	CLONAL	1	TRUE	1	0.14	2		83	413	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0001351-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	20	191	1	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.727	0.555	0.929	0.727	0.555	0.929	CLONAL	1	TRUE	1	0.14	2		192	393	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752375	57752375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777774366	NA	P-0001351-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	54	334	1	ENST00000274289.3:c.1198C>T	p.His400Tyr	p.H400Y	ENST00000274289	NM_006622.3	400	Cat/Tat	9/14	1	2	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	TRUE	1	0.14	2		335	768	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873831	151873831	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs754466956	NA	P-0001351-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	57	502	0	ENST00000262189.6:c.8707C>G	p.Gln2903Glu	p.Q2903E	ENST00000262189	NM_170606.2	2903	Caa/Gaa	38/59	1	2	FACETS	0.739	0.632	0.857	0.739	0.632	0.857	SUBCLONAL	1	TRUE	1	0.14	2		502	1102	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874176	151874176	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001351-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	42	284	0	ENST00000262189.6:c.8362C>T	p.Gln2788Ter	p.Q2788*	ENST00000262189	NM_170606.2	2788	Cag/Tag	38/59	1	2	FACETS	0.851	0.709	1	0.851	0.709	1	CLONAL	1	TRUE	1	0.14	2		284	705	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431659	431659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001351-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	42	352	0	ENST00000399788.2:c.2350C>T	p.Leu784Phe	p.L784F	ENST00000399788	NM_001042603.1	784	Ctc/Ttc	17/28	0.0772716621747946	3	FACETS	0.768	0.639	0.912	0.384	0.319	0.456	INDETERMINATE	1	TRUE	1	0.14	3		352	836	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115436	115115436	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001351-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	91	451	0	ENST00000257566.3:c.890A>G	p.Asn297Ser	p.N297S	ENST00000257566	NM_016569.3	297	aAc/aGc	5/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.14	2		451	878	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856040	68856041	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0001351-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	109	513	0	ENST00000261769.5:c.1849dup	p.Ala617GlyfsTer46	p.A617Gfs*46	ENST00000261769	NM_004360.3	616	-/G	12/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.14	2		513	1227	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907822	76907822	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001364-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	50	295	0	ENST00000373344.5:c.4339G>T	p.Glu1447Ter	p.E1447*	ENST00000373344	NM_000489.3	1447	Gag/Tag	15/35	0.151929993155144	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		295	941	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0001370-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	150	423	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.49725155667269	2	FACETS	0.941	0.881	0.999	0.941	0.881	0.999	CLONAL	2	FALSE	0	0.615733922831915	2		423	259	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984021	2984021	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001370-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	119	507	1	ENST00000396946.4:c.509G>T	p.Arg170Leu	p.R170L	ENST00000396946	NM_032415.4	170	cGc/cTc	5/25	0.615733922831915	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	0	0.615733922831915	1		508	214	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250061	110250061	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001370-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	78	272	0	ENST00000374672.4:c.614G>C	p.Arg205Pro	p.R205P	ENST00000374672	NM_004235.4	205	cGg/cCg	3/5	0.479024816389309	2	FACETS	0.85	0.771	0.929	0.85	0.771	0.929	CLONAL	2	FALSE	0	0.615733922831915	2		272	149	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307529	118307529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001370-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	49	316	0	ENST00000534358.1:c.302C>T	p.Ser101Leu	p.S101L	ENST00000534358	NM_005933.3	101	tCa/tTa	1/36	0.249858868937328	4	FACETS	0.956	0.816	1	0.478	0.408	0.554	INDETERMINATE	1	FALSE	2	0.615733922831915	4		316	269	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39593437	39593437	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001370-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	51	180	0	ENST00000262039.4:c.1202A>G	p.Gln401Arg	p.Q401R	ENST00000262039	NM_002647.2	401	cAg/cGg	11/25	0.222377050801534	4	FACETS	1	0.936	1	0.388	0.333	0.447	INDETERMINATE	1	FALSE	1	0.615733922831915	4		180	230	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113836	11113836	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0001370-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	106	206	0	ENST00000358026.2:c.1943+1G>T		p.X648_splice	ENST00000358026	NM_001128849.1	648			0.594638122547229	2	FACETS	0.967	0.896	1	0.967	0.896	1	CLONAL	2	FALSE	0	0.615733922831915	2		206	178	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100950	41100950	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001370-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	62	222	2	ENST00000373198.4:c.1406G>T	p.Gly469Val	p.G469V	ENST00000373198	NM_133170.3	469	gGc/gTc	8/32	0.577957937796236	3	FACETS	1	0.971	1	0.704	0.62	0.792	CLONAL	1	FALSE	1	0.615733922831915	3		224	187	SUCCESS
AR	367	MSKCC	GRCh37	X	66931503	66931503	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001370-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	43	193	0	ENST00000374690.3:c.2145C>G	p.His715Gln	p.H715Q	ENST00000374690	NM_000044.3	715	caC/caG	4/8	0.615733922831915	0	FACETS	0.559	0.485	0.635			1	SUBCLONAL	1	FALSE	NA	0.615733922831915	0		193	96	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720709	89720709	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs863224909	NA	P-0001384-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	28	43	0	ENST00000371953.3:c.860C>G	p.Ser287Ter	p.S287*	ENST00000371953	NM_000314.4	287	tCa/tGa	8/9	0.318644365232523	2	FACETS	0.955	0.784	1	0.955	0.784	1	CLONAL	2	TRUE	0	0.318644365232523	2		43	92	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0001384-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	172	384	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	0.318644365232523	1	FACETS	0.911	0.845	0.979	1	0.992	1	CLONAL	2	TRUE	0	0.318644365232523	1		384	498	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463184	25463184	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs758845779	NA	P-0001384-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	129	278	0	ENST00000264709.3:c.2309C>A	p.Ser770Ter	p.S770*	ENST00000264709	NM_175629.2	770	tCg/tAg	19/23	0.318644365232523	2	FACETS	0.948	0.867	1	0.948	0.867	1	CLONAL	2	TRUE	0	0.318644365232523	2		278	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0001384-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	45	184	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	0.318644365232523	2	FACETS	1	0.94	1	0.617	0.523	0.718	CLONAL	1	TRUE	0	0.318644365232523	2		184	229	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056189	27056189	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0001415-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	103	278	0	ENST00000324856.7:c.1185T>A	p.Tyr395Ter	p.Y395*	ENST00000324856	NM_006015.4	395	taT/taA	2/20	0.514902002629501	1	FACETS	0.669	0.605	0.735	0.669	0.605	0.735	SUBCLONAL	1	TRUE	0	0.637596300767162	1		278	329	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142909	30142909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1337143722	NA	P-0001415-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	25	353	0	ENST00000389048.3:c.617C>T	p.Ala206Val	p.A206V	ENST00000389048	NM_004304.4	206	gCg/gTg	1/29	0.447567035934193	1	FACETS	0.222	0.175	0.275	0.222	0.175	0.275	SUBCLONAL	1	TRUE	0	0.637596300767162	1		353	241	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111512	8111513	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0001415-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	298	451	0	ENST00000346208.3:c.999dup	p.Gly334TrpfsTer18	p.G334Wfs*18	ENST00000346208		333	aat/aaTt	5/6	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.637596300767162	2		451	734	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443695	29443695	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs863225281	NA	P-0121574-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	189	265	0	ENST00000389048.3:c.3522C>G	p.Phe1174Leu	p.F1174L	ENST00000389048	NM_004304.4	1174	ttC/ttG	23/29	0.302499095967224	4	FACETS	1	0.96	1			1	CLONAL	2	NA	NA	0.302499095967224	4		265	771	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930247	39930247	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0121574-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	141	531	1	ENST00000378444.4:c.3217G>T	p.Glu1073Ter	p.E1073*	ENST00000378444	NM_001123385.1	1073	Gaa/Taa	6/15	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	NA	1	0.302499095967224	2		532	883	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220354	98220354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001435-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	102	131	0	ENST00000331920.6:c.3109G>A	p.Ala1037Thr	p.A1037T	ENST00000331920	NM_000264.3	1037	Gcc/Acc	18/24	0.512729491793043	2	FACETS	1	0.961	1	0.563	0.509	0.62	CLONAL	1	TRUE	0	0.512819157984054	2		131	353	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0001442-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	101	362	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.280642003644591	3	FACETS	1	0.922	1	0.52	0.464	0.58	CLONAL	1	TRUE	1	0.26	3		362	844	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0001442-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	86	607	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.280642003644591	3	FACETS	0.801	0.707	0.902	0.401	0.353	0.451	CLONAL	1	TRUE	1	0.26	3		607	933	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0001442-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	91	410	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.926	0.822	1	0.926	0.822	1	CLONAL	1	TRUE	1	0.26	2		410	756	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0001442-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	103	559	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	0.942	0.842	1	0.942	0.842	1	CLONAL	1	TRUE	1	0.26	2		559	841	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242511	55242511	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913418	NA	P-0001442-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	76	374	0	ENST00000275493.2:c.2281G>T	p.Asp761Tyr	p.D761Y	ENST00000275493	NM_005228.3	761	Gat/Tat	19/28	0.280642003644591	3	FACETS	0.946	0.83	1	0.473	0.415	0.536	CLONAL	1	TRUE	1	0.26	3		374	698	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28934577	NA	P-0001445-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	236	185	0	ENST00000269305.4:c.770T>C	p.Leu257Pro	p.L257P	ENST00000269305	NM_001126112.2	257	cTg/cCg	7/11	0.498929142533713	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	0	0.564833513928359	3		185	345	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955423	48955424	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0001445-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	96	266	0	ENST00000267163.4:c.1540_1541del	p.Phe514ProfsTer8	p.F514Pfs*8	ENST00000267163	NM_000321.2	513	tcTTtc/tctc	17/27	0.564833513928359	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.564833513928359	1		266	234	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060853	38060859	+	frameshift_variant	Frame_Shift_Del	DEL	AAGCCGT	AAGCCGT	-	novel	NA	P-0001445-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	607	431	0	ENST00000250448.2:c.1130_1136del	p.His377ArgfsTer10	p.H377Rfs*10	ENST00000250448	NM_004496.3	377	cACGGCTTg/cg	2/2	0.564833513928359	6	FACETS	1	0.992	1	1	0.992	1	CLONAL	4	TRUE	2	0.564833513928359	6		431	1070	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751237	57751237	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001449-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	260	274	0	ENST00000274289.3:c.1630G>C	p.Val544Leu	p.V544L	ENST00000274289	NM_006622.3	544	Gtt/Ctt	12/14	0.775072143788704	1	FACETS	0.985	0.94	1	0.985	0.94	1	CLONAL	1	TRUE	0	0.775072143788704	1		274	417	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	443454	443454	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001449-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	313	285	0	ENST00000399788.2:c.1443C>A	p.Cys481Ter	p.C481*	ENST00000399788	NM_001042603.1	481	tgC/tgA	11/28	0.775245028496826	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.775072143788704	1		285	492	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953632	32953633	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359732	NA	P-0001449-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	356	482	0	ENST00000380152.3:c.8940dup	p.Glu2981ArgfsTer37	p.E2981Rfs*37	ENST00000380152		2978	tca/tcAa	22/27	0.775245028496826	1	FACETS	0.897	0.86	0.934	0.897	0.86	0.934	CLONAL	1	TRUE	0	0.775072143788704	1		482	627	SUCCESS
APC	324	MSKCC	GRCh37	5	112175687	112175687	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001449-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	323	280	0	ENST00000257430.4:c.4396G>T	p.Gly1466Ter	p.G1466*	ENST00000257430	NM_000038.5	1466	Gga/Tga	16/16	0.775072143788704	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.775072143788704	1		280	496	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143352406	143352406	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001458-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	40	412	0	ENST00000262992.4:c.7del	p.Ile3LeufsTer57	p.I3Lfs*57	ENST00000262992	NM_001101669.1	3	Att/tt	2/24	0.188570571494811	3	FACETS	0.852	0.707	1	0.426	0.353	0.507	CLONAL	1	FALSE	1	0.188570571494811	3		412	545	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6414399	6414399	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001465-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	49	57	0	ENST00000356142.4:c.33C>A	p.Asp11Glu	p.D11E	ENST00000356142	NM_018890.3	11	gaC/gaA	1/7	NA	2	FACETS	1	0.899	1			1	INDETERMINATE	1	TRUE	NA	0.530950471279766	2		57	175	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0001475-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	88	675	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	0.678305295717986	2		675	208	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457134	5457134	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001475-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	96	241	16	ENST00000381577.3:c.108G>A	p.Met36Ile	p.M36I	ENST00000381577	NM_014143.3	36	atG/atA	3/7	0.394755225109017	1	FACETS	0.979	0.896	1	0.979	0.896	1	INDETERMINATE	1	TRUE	0	0.678305295717986	1		257	191	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759553	133759553	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767173632	NA	P-0001475-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	96	567	0	ENST00000318560.5:c.1876G>A	p.Gly626Ser	p.G626S	ENST00000318560	NM_005157.4	626	Ggc/Agc	11/11	0.261988775048042	3	FACETS	0.467	0.416	0.522	0.156	0.138	0.174	INDETERMINATE	1	TRUE	0	0.678305295717986	3		567	811	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387080	31387080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1007955291	NA	P-0001475-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	102	403	0	ENST00000328111.2:c.1705G>A	p.Ala569Thr	p.A569T	ENST00000328111	NM_006892.3	569	Gca/Aca	16/23	0.117866428049409	6	FACETS	0.786	0.702	0.875			1	INDETERMINATE	1	TRUE	NA	0.678305295717986	6		403	902	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112637	115112637	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001475-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	67	267	0	ENST00000257566.3:c.1103del	p.Leu368TyrfsTer264	p.L368Yfs*264	ENST00000257566	NM_016569.3	368	tTa/ta	7/8	0.678305295717986	1	FACETS	0.616	0.544	0.691	0.616	0.544	0.691	SUBCLONAL	1	TRUE	0	0.678305295717986	1		267	212	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0001481-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	38	296	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.241380847328197	3	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	1	0.243997984380071	3		296	144	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847379	68847380	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0001481-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	154	385	0	ENST00000261769.5:c.1302dup	p.Ile435HisfsTer11	p.I435Hfs*11	ENST00000261769	NM_004360.3	434	ggc/ggCc	9/16	0.232373443421146	3	FACETS	0.896	0.825	0.969	0.896	0.825	0.969	CLONAL	3	TRUE	0	0.243997984380071	3		385	527	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0001488-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	99	83	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.603427421855435	2	FACETS	1	0.964	1	0.563	0.511	0.616	CLONAL	1	TRUE	0	0.679115931985837	2		83	259	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581157	48581157	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1555685624	NA	P-0001488-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	96	191	0	ENST00000342988.3:c.461C>G	p.Ser154Ter	p.S154*	ENST00000342988	NM_005359.5	154	tCa/tGa	5/12	NA	2	FACETS	0.607	0.543	0.674			1	INDETERMINATE	1	TRUE	NA	0.679115931985837	2		191	466	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117630048	117630048	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001488-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	196	452	0	ENST00000368508.3:c.6478C>T	p.Gln2160Ter	p.Q2160*	ENST00000368508	NM_002944.2	2160	Cag/Tag	41/43	0.679115931985837	1	FACETS	0.568	0.528	0.609	0.568	0.528	0.609	SUBCLONAL	1	TRUE	0	0.679115931985837	1		452	671	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024029	27024029	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001488-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	20	13	0	ENST00000324856.7:c.1135C>T	p.Gln379Ter	p.Q379*	ENST00000324856	NM_006015.4	379	Cag/Tag	1/20	0.389513616230216	1	FACETS	0.48	0.376	0.596	0.48	0.376	0.596	INDETERMINATE	1	TRUE	0	0.679115931985837	1		13	81	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050348	176050348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760439427	NA	P-0001488-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	136	416	0	ENST00000367669.3:c.1217G>A	p.Arg406Gln	p.R406Q	ENST00000367669	NM_022457.5	406	cGa/cAa	11/20	1	2	FACETS	0.49	0.446	0.537	0.49	0.446	0.537	SUBCLONAL	1	TRUE	1	0.679115931985837	2		416	817	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107287	193107287	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001488-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	68	198	0	ENST00000367435.3:c.496C>G	p.Gln166Glu	p.Q166E	ENST00000367435	NM_024529.4	166	Cag/Gag	6/17	1	2	FACETS	0.419	0.365	0.477	0.419	0.365	0.477	SUBCLONAL	1	TRUE	1	0.679115931985837	2		198	478	SUCCESS
ATR	545	MSKCC	GRCh37	3	142243011	142243011	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001488-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	100	299	1	ENST00000350721.4:c.3976G>T	p.Glu1326Ter	p.E1326*	ENST00000350721	NM_001184.3	1326	Gaa/Taa	22/47	0.475793703214086	1	FACETS	0.364	0.326	0.404	0.364	0.326	0.404	SUBCLONAL	1	TRUE	0	0.679115931985837	1		300	534	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637210	176637210	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784076	NA	P-0001488-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	136	331	0	ENST00000439151.2:c.1810C>T	p.Arg604Ter	p.R604*	ENST00000439151	NM_022455.4	604	Cga/Tga	5/23	0.183101015041762	1	FACETS	0.349	0.318	0.383	0.349	0.318	0.383	INDETERMINATE	1	TRUE	0	0.679115931985837	1		331	757	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004451	150004451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001488-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	154	466	0	ENST00000253339.5:c.1774G>A	p.Glu592Lys	p.E592K	ENST00000253339		592	Gag/Aag	3/7	0.679115931985837	1	FACETS	0.509	0.467	0.551	0.509	0.467	0.551	SUBCLONAL	1	TRUE	0	0.679115931985837	1		466	589	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467866	50467866	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001488-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	98	252	0	ENST00000331340.3:c.1101C>G	p.Asp367Glu	p.D367E	ENST00000331340	NM_006060.4	367	gaC/gaG	8/8	0.182249377994491	2	FACETS	0.506	0.453	0.563	0.253	0.226	0.282	INDETERMINATE	1	TRUE	0	0.679115931985837	2		252	570	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467997	50467997	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001488-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	140	305	0	ENST00000331340.3:c.1232T>A	p.Leu411His	p.L411H	ENST00000331340	NM_006060.4	411	cTc/cAc	8/8	0.182249377994491	2	FACETS	0.668	0.61	0.728	0.334	0.305	0.364	INDETERMINATE	1	TRUE	0	0.679115931985837	2		305	617	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891654	151891654	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0001488-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	95	199	0	ENST00000262189.6:c.4379-1G>C		p.X1460_splice	ENST00000262189	NM_170606.2	1460			0.408390859856187	3	FACETS	0.645	0.575	0.719	0.323	0.287	0.36	SUBCLONAL	1	TRUE	1	0.679115931985837	3		199	581	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750855	128750855	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001488-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1465	172	550	0	ENST00000377970.2:c.392T>A	p.Ile131Asn	p.I131N	ENST00000377970	NM_002467.4	131	aTc/aAc	2/3	0.632476496216729	5	FACETS	0.625	0.572	0.68			1	SUBCLONAL	1	TRUE	NA	0.679115931985837	5		550	1637	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738506	145738506	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001488-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	131	257	0	ENST00000428558.2:c.2479G>C	p.Glu827Gln	p.E827Q	ENST00000428558	NM_004260.3	827	Gag/Cag	16/22	0.632476496216729	5	FACETS	0.755	0.684	0.83			1	SUBCLONAL	1	TRUE	NA	0.679115931985837	5		257	1031	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907127	101907127	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001488-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	112	320	0	ENST00000374994.4:c.1087G>A	p.Asp363Asn	p.D363N	ENST00000374994	NM_004612.2	363	Gat/Aat	6/9	0.321783553907244	1	FACETS	0.335	0.302	0.37	0.335	0.302	0.37	INDETERMINATE	1	TRUE	0	0.679115931985837	1		320	650	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589571	69589571	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001488-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	26	77	0	ENST00000168712.1:c.282C>A	p.Phe94Leu	p.F94L	ENST00000168712	NM_002007.2	94	ttC/ttA	1/3	0.371460978134823	3	FACETS	0.405	0.322	0.5	0.203	0.161	0.25	INDETERMINATE	1	TRUE	1	0.679115931985837	3		77	253	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447898	49447898	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001488-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	58	133	0	ENST00000301067.7:c.536G>T	p.Gly179Val	p.G179V	ENST00000301067	NM_003482.3	179	gGt/gTt	5/54	0.420746237405031	1	FACETS	0.33	0.285	0.379	0.33	0.285	0.379	SUBCLONAL	1	TRUE	0	0.679115931985837	1		133	342	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130232	2130232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500948	NA	P-0001488-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	201	595	0	ENST00000219476.3:c.3464C>T	p.Ser1155Phe	p.S1155F	ENST00000219476	NM_000548.3	1155	tCt/tTt	30/42	0.183101015041762	1	FACETS	0.365	0.338	0.394	0.365	0.338	0.394	INDETERMINATE	1	TRUE	0	0.679115931985837	1		595	1070	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020487	14020487	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913050	NA	P-0001488-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	166	488	0	ENST00000311895.7:c.458G>C	p.Arg153Pro	p.R153P	ENST00000311895	NM_005236.2	153	cGc/cCc	3/11	0.183101015041762	1	FACETS	0.306	0.28	0.333	0.306	0.28	0.333	INDETERMINATE	1	TRUE	0	0.679115931985837	1		488	1055	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16005000	16005000	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001488-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	143	393	0	ENST00000268712.3:c.2254G>C	p.Glu752Gln	p.E752Q	ENST00000268712	NM_006311.3	752	Gag/Cag	20/46	NA	2	FACETS	0.441	0.401	0.483			1	INDETERMINATE	1	TRUE	NA	0.679115931985837	2		393	955	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368202	45368202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001488-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	131	303	0	ENST00000262160.6:c.1400C>T	p.Ser467Leu	p.S467L	ENST00000262160	NM_005901.5	467	tCa/tTa	11/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.679115931985837	NA		303	358	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553210	41553210	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001488-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	137	394	0	ENST00000263253.7:c.3299C>A	p.Ser1100Tyr	p.S1100Y	ENST00000263253	NM_001429.3	1100	tCt/tAt	18/31	NA	2	FACETS	0.457	0.415	0.501			1	INDETERMINATE	1	TRUE	NA	0.679115931985837	2		394	883	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933035	39933035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001488-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	196	599	0	ENST00000378444.4:c.1564G>A	p.Gly522Ser	p.G522S	ENST00000378444	NM_001123385.1	522	Ggc/Agc	4/15	0.679115931985837	1	FACETS	0.391	0.362	0.421	0.391	0.362	0.421	SUBCLONAL	1	TRUE	0	0.679115931985837	1		599	975	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223419	53223419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370060257	NA	P-0001488-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	153	473	0	ENST00000375401.3:c.3940C>T	p.Arg1314Trp	p.R1314W	ENST00000375401	NM_004187.3	1314	Cgg/Tgg	23/26	0.468560152083341	1	FACETS	0.304	0.278	0.332	0.304	0.278	0.332	SUBCLONAL	1	TRUE	0	0.679115931985837	1		473	979	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0001491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	69	83	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.154997031944154	1	FACETS	0.661	0.586	0.739	0.661	0.586	0.739	INDETERMINATE	1	TRUE	0	0.68357854357572	1		83	201	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0001491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	234	506	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	0.193874272012176	4	FACETS	0.827	0.775	0.88	0.827	0.775	0.88	INDETERMINATE	2	TRUE	2	0.68357854357572	4		506	697	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522551	176522551	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	389	465	0	ENST00000292408.4:c.1648G>C	p.Val550Leu	p.V550L	ENST00000292408	NM_213647.1	550	Gtg/Ctg	13/18	0.68357854357572	4	FACETS	1	0.987	1	0.726	0.693	0.759	CLONAL	2	TRUE	1	0.68357854357572	4		465	880	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700310	117700310	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1274193277	NA	P-0001491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	101	387	0	ENST00000368508.3:c.2509A>G	p.Thr837Ala	p.T837A	ENST00000368508	NM_002944.2	837	Act/Gct	17/43	0.147359773527123	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.68357854357572	0		387	269	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849317	89849317	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1274321707	NA	P-0001491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	169	508	0	ENST00000389301.3:c.1576G>C	p.Glu526Gln	p.E526Q	ENST00000389301	NM_000135.2	526	Gaa/Caa	17/43	0.68357854357572	1	FACETS	0.98	0.918	1	0.98	0.918	1	CLONAL	1	TRUE	0	0.68357854357572	1		508	332	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220400	1220400	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	186	513	0	ENST00000326873.7:c.493G>C	p.Glu165Gln	p.E165Q	ENST00000326873	NM_000455.4	165	Gag/Cag	4/10	0.154997031944154	1	FACETS	0.719	0.67	0.769	0.719	0.67	0.769	INDETERMINATE	1	TRUE	0	0.68357854357572	1		513	498	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30090761	30090761	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	194	681	0	ENST00000338641.4:c.1758G>T	p.Lys586Asn	p.K586N	ENST00000338641	NM_000268.3	586	aaG/aaT	16/16	NA	2	FACETS	1	0.934	1			1	INDETERMINATE	1	TRUE	NA	0.68357854357572	2		681	566	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179131	123179131	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	138	578	0	ENST00000218089.9:c.580G>A	p.Glu194Lys	p.E194K	ENST00000218089	NM_001042749.1	194	Gag/Aag	8/35	0.305322137464385	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.68357854357572	0		578	356	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179139	123179139	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	137	596	0	ENST00000218089.9:c.588G>A	p.Met196Ile	p.M196I	ENST00000218089	NM_001042749.1	196	atG/atA	8/35	0.305322137464385	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.68357854357572	0		596	357	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0001495-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	114	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	0.526	0.473	0.582			1	INDETERMINATE	1	TRUE	NA	0.543778146727613	2		371	797	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0001495-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	692	552	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.543778146727613	2		552	1163	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268156	153268156	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001495-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	275	444	2	ENST00000281708.4:c.652C>T	p.Gln218Ter	p.Q218*	ENST00000281708	NM_033632.3	218	Caa/Taa	4/12	0.543778146727613	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.543778146727613	1		446	637	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373919	118373919	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001495-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	532	469	0	ENST00000534358.1:c.7312G>A	p.Glu2438Lys	p.E2438K	ENST00000534358	NM_005933.3	2438	Gaa/Aaa	27/36	0.536591777678297	3	FACETS	0.994	0.955	1	0.994	0.955	1	CLONAL	2	TRUE	1	0.543778146727613	3		469	1252	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9787087	9787087	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001495-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	248	352	0	ENST00000377346.4:c.3120del	p.Asp1041ThrfsTer28	p.D1041Tfs*28	ENST00000377346	NM_005026.3	1040	Aaa/aa	24/24	1	2	FACETS	0.748	0.699	0.8	0.748	0.699	0.8	SUBCLONAL	1	TRUE	1	0.543778146727613	2		352	1219	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373928	118373928	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001495-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	550	464	0	ENST00000534358.1:c.7323del	p.Glu2442LysfsTer14	p.E2442Kfs*14	ENST00000534358	NM_005933.3	2441	Aaa/aa	27/36	0.536591777678297	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.543778146727613	3		464	1285	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185770	32185770	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0001495-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	136	356	0	ENST00000375023.3:c.1624+2T>A		p.X542_splice	ENST00000375023	NM_004557.3	542			1	2	FACETS	0.511	0.464	0.561	0.511	0.464	0.561	SUBCLONAL	1	TRUE	1	0.543778146727613	2		356	978	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0001503-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	43	675	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.291079615033949	4	FACETS	0.902	0.757	1	0.451	0.378	0.531	CLONAL	1	TRUE	2	0.36	4		675	360	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217162	66217162	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001503-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	55	362	0	ENST00000273854.3:c.2453A>G	p.Asp818Gly	p.D818G	ENST00000273854	NM_004439.5	818	gAc/gGc	14/18	0.176855170870793	5	FACETS	0.875	0.748	1	0.292	0.249	0.338	INDETERMINATE	1	TRUE	2	0.36	5		362	538	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944946	31944946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001503-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	29	141	0	ENST00000340398.3:c.155G>A	p.Arg52His	p.R52H	ENST00000340398	NM_001013699.2	52	cGt/cAt	1/1	0.230681523639782	3	FACETS	1	0.862	1	0.54	0.438	0.654	CLONAL	1	TRUE	1	0.36	3		141	176	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115111972	115111973	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGAGGCC	novel	NA	P-0001503-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	13	154	0	ENST00000257566.3:c.1761_1767dup	p.Gln590GlyfsTer104	p.Q590Gfs*104	ENST00000257566	NM_016569.3	589	-/GGCCTCT	7/8	0.230681523639782	3	FACETS	0.604	0.433	0.81	0.302	0.216	0.405	SUBCLONAL	1	TRUE	1	0.36	3		154	141	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120708	115120709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0001503-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	73	570	0	ENST00000257566.3:c.296_297dup	p.Glu100TrpfsTer40	p.E100Wfs*40	ENST00000257566	NM_016569.3	99	-/TG	1/8	0.230681523639782	3	FACETS	1	0.956	1	0.598	0.526	0.676	CLONAL	1	TRUE	1	0.36	3		570	400	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063718	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0001503-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	14	221	0	ENST00000412916.2:c.165+2dup		p.X55_splice	ENST00000412916		55			0.3	1	FACETS	0.459	0.334	0.608	0.459	0.334	0.608	SUBCLONAL	1	TRUE	0	0.36	1		221	139	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847257	68847273	+	frameshift_variant	Frame_Shift_Del	DEL	CACCACACTGAAAGTGA	CACCACACTGAAAGTGA	-	novel	NA	P-0001503-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	25	313	0	ENST00000261769.5:c.1180_1196del	p.Thr394Ter	p.T394*	ENST00000261769	NM_004360.3	393	atCACCACACTGAAAGTGAct/atct	9/16	0.3	1	FACETS	0.513	0.406	0.635	0.513	0.406	0.635	SUBCLONAL	1	TRUE	0	0.36	1		313	222	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164686	36164686	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001503-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	44	432	0	ENST00000300305.3:c.1189del	p.Gln397LysfsTer197	p.Q397Kfs*197	ENST00000300305		397	Caa/aa	8/8	0.230681523639782	5	FACETS	1	0.922	1	0.387	0.326	0.455	CLONAL	1	TRUE	2	0.36	5		432	324	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0001506-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	150	280	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.204775919042852	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.218934853974214	2		280	591	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0001506-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1914	46	594	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	0.218934853974214	3	FACETS	0.238	0.199	0.281			1	SUBCLONAL	1	TRUE	NA	0.218934853974214	3		594	1960	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098950	178098950	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001506-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	459	436	0	ENST00000397062.3:c.95T>G	p.Val32Gly	p.V32G	ENST00000397062	NM_006164.4	32	gTa/gGa	2/5	0.218934853974214	3	FACETS	1	0.983	1			1	CLONAL	3	TRUE	NA	0.218934853974214	3		436	1466	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266440	55266440	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001506-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2151	157	428	0	ENST00000275493.2:c.2732G>C	p.Gly911Ala	p.G911A	ENST00000275493	NM_005228.3	911	gGa/gCa	23/28	0.218934853974214	13	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.218934853974214	13		428	2308	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266543	55266543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001506-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1638	128	330	0	ENST00000275493.2:c.2835G>A	p.Met945Ile	p.M945I	ENST00000275493	NM_005228.3	945	atG/atA	23/28	0.218934853974214	13	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.218934853974214	13		330	1766	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104358	2104358	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001506-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	246	410	0	ENST00000219476.3:c.398A>G	p.Asn133Ser	p.N133S	ENST00000219476	NM_000548.3	133	aAc/aGc	5/42	0.19321287510946	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.218934853974214	2		410	1054	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465580	8465581	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	T	novel	NA	P-0001506-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	77	490	0	ENST00000356435.5:c.3599_3600delinsA	p.Pro1200GlnfsTer31	p.P1200Qfs*31	ENST00000356435		1200	cCC/cA	21/35	0.19321287510946	2	FACETS	0.687	0.601	0.78	0.343	0.3	0.39	SUBCLONAL	1	TRUE	0	0.218934853974214	2		490	1024	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs878854073	NA	P-0001513-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	79	220	0	ENST00000269305.4:c.673-1G>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		220	253	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0001516-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	260	206	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.248493184874913	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.248493184874913	3		207	945	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517201	NA	P-0001516-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	59	207	0	ENST00000263967.3:c.1637A>C	p.Gln546Pro	p.Q546P	ENST00000263967	NM_006218.2	546	cAg/cCg	10/21	0.180376179537663	2	FACETS	0.754	0.653	0.862	0.754	0.653	0.862	SUBCLONAL	2	TRUE	0	0.248493184874913	2		207	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs483352695	NA	P-0001516-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	53	358	0	ENST00000269305.4:c.736A>C	p.Met246Leu	p.M246L	ENST00000269305	NM_001126112.2	246	Atg/Ctg	7/11	0.185219894469038	1	FACETS	0.679	0.579	0.789	0.679	0.579	0.789	SUBCLONAL	1	TRUE	0	0.248493184874913	1		358	550	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164881	36164881	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001516-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	26	284	0	ENST00000300305.3:c.994G>C	p.Asp332His	p.D332H	ENST00000300305		332	Gac/Cac	8/8	0.248493184874913	3	FACETS	0.458	0.361	0.569	0.229	0.18	0.285	SUBCLONAL	1	TRUE	1	0.248493184874913	3		284	514	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644880	67644881	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGGT	novel	NA	P-0001516-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	107	462	0	ENST00000264010.4:c.146_149dup	p.Val51GlyfsTer27	p.V51Gfs*27	ENST00000264010	NM_006565.3	49	gag/gAGGTag	3/12	0.20892713885572	2	FACETS	1	0.965	1	0.587	0.526	0.651	CLONAL	1	TRUE	0	0.248493184874913	2		462	734	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574693	64574693	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1114167472	NA	P-0001526-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	120	346	0	ENST00000312049.6:c.784-2A>G		p.X262_splice	ENST00000312049	NM_130799.2	262			0.762474899437207	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.762555958832921	1		346	187	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457820	69457822	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0001526-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	82	308	0	ENST00000227507.2:c.227_229del	p.Glu76del	p.E76del	ENST00000227507	NM_053056.2	74	GAG/-	2/5	0.762474899437207	1	FACETS	0.579	0.519	0.64	0.579	0.519	0.64	SUBCLONAL	1	TRUE	0	0.762555958832921	1		308	230	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0001536-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	51	341	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.157842207886679	3	FACETS	0.964	0.818	1			1	CLONAL	1	TRUE	NA	0.19	3		341	610	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188317	32188317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144492578	NA	P-0001539-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	60	743	0	ENST00000375023.3:c.1024G>A	p.Val342Met	p.V342M	ENST00000375023	NM_004557.3	342	Gtg/Atg	6/30	1	2	FACETS	0.778	0.671	0.894	0.778	0.671	0.894	SUBCLONAL	1	TRUE	1	0.320040003177224	2		743	482	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133710842	133710842	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001539-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	68	415	0	ENST00000318560.5:c.9G>C	p.Glu3Asp	p.E3D	ENST00000318560	NM_005157.4	3	gaG/gaC	1/11	0.243054097482809	3	FACETS	1	0.956	1	0.406	0.354	0.461	CLONAL	1	TRUE	0	0.320040003177224	3		415	405	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104359246	104359246	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1420089970	NA	P-0001539-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	67	664	0	ENST00000369902.3:c.967G>A	p.Val323Ile	p.V323I	ENST00000369902	NM_016169.3	323	Gtc/Atc	8/12	0.242713654709361	2	FACETS	0.818	0.712	0.932	0.409	0.356	0.466	CLONAL	1	TRUE	0	0.320040003177224	2		664	512	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs869320707	NA	P-0001546-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	134	293	1	ENST00000397752.3:c.3028+1G>T		p.X1010_splice	ENST00000397752	NM_000245.2	1010			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		294	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0001549-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	561	711	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.87697275148374	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.87697275148374	2		711	604	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599339	55599341	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	novel	NA	P-0001562-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	86	525	0	ENST00000288135.5:c.2467_2469del	p.Tyr823del	p.Y823del	ENST00000288135	NM_000222.2	822	aATTat/aat	17/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.279122680649968	2		525	461	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001566-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	64	284	1	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		285	1008	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134449	2134449	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768684515	NA	P-0001569-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	146	528	0	ENST00000219476.3:c.4226G>A	p.Arg1409Gln	p.R1409Q	ENST00000219476	NM_000548.3	1409	cGg/cAg	34/42	1	2	FACETS	0.993	0.911	1	0.993	0.911	1	CLONAL	1	TRUE	1	0.532538287661268	2		528	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0001569-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	140	499	0	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	0.532538287661268	1	FACETS	0.941	0.865	1	0.941	0.865	1	CLONAL	1	TRUE	0	0.532538287661268	1		499	410	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032553	12032553	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001569-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	85	265	0	ENST00000353533.5:c.989A>C	p.Asn330Thr	p.N330T	ENST00000353533	NM_003010.3	330	aAt/aCt	9/11	1	2	FACETS	0.956	0.853	1	0.956	0.853	1	CLONAL	1	TRUE	1	0.532538287661268	2		265	334	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354278	70354278	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001569-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	72	582	0	ENST00000374080.3:c.4689G>T	p.Glu1563Asp	p.E1563D	ENST00000374080		1563	gaG/gaT	34/45	0.144287360105892	0	FACETS	0.252	0.22	0.286			1	INDETERMINATE	1	TRUE	0	0.532538287661268	0		582	502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577572	7577574	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0001572-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	399	450	0	ENST00000269305.4:c.707_709del	p.Tyr236_Met237delinsLeu	p.Y236_M237delinsL	ENST00000269305	NM_001126112.2	236	tACAtg/ttg	7/11	0.71960054603694	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.740470482508868	2		450	522	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482437	56482437	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001589-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	714	352	0	ENST00000267101.3:c.985A>G	p.Lys329Glu	p.K329E	ENST00000267101	NM_001982.3	329	Aaa/Gaa	8/28	0.551556695381612	8	FACETS	0.992	0.961	1			1	CLONAL	5	TRUE	NA	0.551556695381612	8		352	1386	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879794	37879794	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001589-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	158	224	0	ENST00000269571.5:c.2089G>C	p.Val697Leu	p.V697L	ENST00000269571		697	Gtg/Ctg	18/27	0.316444585616272	6	FACETS	1	0.986	1	0.457	0.419	0.498	INDETERMINATE	1	TRUE	3	0.551556695381612	6		224	878	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482437	56482437	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001600-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	167	352	0	ENST00000267101.3:c.985A>G	p.Lys329Glu	p.K329E	ENST00000267101	NM_001982.3	329	Aaa/Gaa	8/28	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.22	2		352	1188	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678727	52678727	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001600-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1688	118	559	0	ENST00000394830.3:c.892C>T	p.Arg298Ter	p.R298*	ENST00000394830	NM_018313.4	298	Cga/Tga	9/30	1	2	FACETS	0.594	0.533	0.659	0.594	0.533	0.659	SUBCLONAL	1	TRUE	1	0.22	2		559	1806	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486241	8486241	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001600-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1467	107	507	0	ENST00000356435.5:c.2576A>C	p.Lys859Thr	p.K859T	ENST00000356435		859	aAa/aCa	17/35	1	2	FACETS	0.618	0.552	0.689	0.618	0.552	0.689	SUBCLONAL	1	TRUE	1	0.22	2		507	1574	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425677	49425678	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0001600-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	143	469	0	ENST00000301067.7:c.12810dup	p.Thr4271AspfsTer63	p.T4271Dfs*63	ENST00000301067	NM_003482.3	4270	-/G	39/54	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.22	2		469	1041	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0001610-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	20	296	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.242094909872043	4	FACETS	0.708	0.539	0.907	0.354	0.269	0.454	CLONAL	1	TRUE	2	0.11	4		296	570	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482437	56482437	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001610-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	31	352	0	ENST00000267101.3:c.985A>G	p.Lys329Glu	p.K329E	ENST00000267101	NM_001982.3	329	Aaa/Gaa	8/28	0.242094909872043	4	FACETS	1	0.909	1	0.615	0.496	0.749	CLONAL	1	TRUE	2	0.11	4		352	509	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266713	142266713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001610-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	52	451	0	ENST00000350721.4:c.3211G>A	p.Asp1071Asn	p.D1071N	ENST00000350721	NM_001184.3	1071	Gat/Aat	16/47	0.242094909872043	4	FACETS	1	0.857	1	0.506	0.429	0.591	CLONAL	1	TRUE	2	0.11	4		451	1038	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0001610-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	14	385	0	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	1	2	FACETS	0.86	0.621	1	0.86	0.621	1	CLONAL	1	TRUE	1	0.11	2		385	296	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533361	29533361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001610-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	56	365	0	ENST00000356175.3:c.1364G>A	p.Gly455Glu	p.G455E	ENST00000356175	NM_000267.3	455	gGa/gAa	12/57	0.325594395896828	3	FACETS	1	0.882	1			1	CLONAL	1	TRUE	NA	0.11	3		365	1035	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938459	44938459	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001610-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	52	294	0	ENST00000377967.4:c.3007C>T	p.Gln1003Ter	p.Q1003*	ENST00000377967	NM_021140.2	1003	Cag/Tag	20/29	0.325594395896828	2	FACETS	1	0.936	1	0.598	0.508	0.698	CLONAL	1	TRUE	0	0.11	2		294	790	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649640	206649640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782100237	NA	P-0001643-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	78	166	0	ENST00000367120.3:c.475G>A	p.Gly159Ser	p.G159S	ENST00000367120	NM_014002.3	159	Ggc/Agc	6/22	0.357989350692016	6	FACETS	0.753	0.664	0.848	0.376	0.332	0.424	SUBCLONAL	2	FALSE	2	0.416460651885704	6		166	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579569	7579575	+	frameshift_variant	Frame_Shift_Del	DEL	TTGCTTG	TTGCTTG	-	novel	NA	P-0001643-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	116	242	1	ENST00000269305.4:c.112_118del	p.Gln38TrpfsTer4	p.Q38Wfs*4	ENST00000269305	NM_001126112.2	38	CAAGCAAtg/tg	4/11	0.29779890540393	3	FACETS	1	0.97	1	0.758	0.694	0.824	CLONAL	2	FALSE	0	0.416460651885704	3		243	296	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0001647-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	362	568	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.387457467093089	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.397746162135038	3		568	977	SUCCESS
APC	324	MSKCC	GRCh37	5	112175513	112175513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001647-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	241	411	0	ENST00000257430.4:c.4222G>T	p.Glu1408Ter	p.E1408*	ENST00000257430	NM_000038.5	1408	Gaa/Taa	16/16	0.387457467093089	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.397746162135038	3		411	686	SUCCESS
APC	324	MSKCC	GRCh37	5	112174379	112174379	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs587779786	NA	P-0001647-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	80	360	0	ENST00000257430.4:c.3088A>T	p.Lys1030Ter	p.K1030*	ENST00000257430	NM_000038.5	1030	Aaa/Taa	16/16	0.387457467093089	3	FACETS	0.907	0.8	1	0.453	0.4	0.511	CLONAL	1	TRUE	1	0.397746162135038	3		360	532	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980832	40980832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465279954	NA	P-0001647-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	486	515	1	ENST00000373198.4:c.1654C>T	p.Leu552Phe	p.L552F	ENST00000373198	NM_133170.3	552	Ctc/Ttc	10/32	0.397746162135038	5	FACETS	0.964	0.923	1	0.964	0.923	1	CLONAL	3	TRUE	2	0.397746162135038	5		516	1349	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0001653-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	352	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.632460716439572	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.64985612480267	2		371	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577095	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519984	NA	P-0001653-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	119	512	0	ENST00000269305.4:c.843C>G	p.Asp281Glu	p.D281E	ENST00000269305	NM_001126112.2	281	gaC/gaG	8/11	0.64985612480267	2	FACETS	0.969	0.904	1	0.969	0.904	1	CLONAL	2	TRUE	0	0.64985612480267	2		512	189	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245426	46245426	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	311	392	2	ENST00000334344.6:c.3520A>C	p.Ile1174Leu	p.I1174L	ENST00000334344	NM_152641.2	1174	Ata/Cta	15/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.88928806956584	2		394	679	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434108	49434108	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	131	252	0	ENST00000301067.7:c.7445G>A	p.Gly2482Glu	p.G2482E	ENST00000301067	NM_003482.3	2482	gGg/gAg	31/54	1	2	FACETS	0.953	0.879	1	0.953	0.879	1	CLONAL	1	FALSE	1	0.88928806956584	2		252	309	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007611	45007621	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TATTCCTCAGG	TATTCCTCAGG	-	novel	NA	P-0001686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	81	224	0	ENST00000558401.1:c.68-8_70del		p.X23_splice	ENST00000558401	NM_004048.2	23		2/4	0.860891986175933	1	FACETS	0.575	0.519	0.631	0.575	0.519	0.631	SUBCLONAL	1	FALSE	0	0.88928806956584	1		224	176	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587399	29587400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0001686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	242	367	0	ENST00000356175.3:c.4381dup	p.Ile1461AsnfsTer4	p.I1461Nfs*4	ENST00000356175	NM_000267.3	1460	-/A	33/57	1	2	FACETS	0.974	0.918	1	0.974	0.918	1	CLONAL	1	FALSE	1	0.88928806956584	2		367	559	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664534	29664535	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0001686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	210	403	0	ENST00000356175.3:c.6522_6523dup	p.Thr2175ArgfsTer5	p.T2175Rfs*5	ENST00000356175	NM_000267.3	2171	-/GA	42/57	1	2	FACETS	0.764	0.714	0.816	0.764	0.714	0.816	SUBCLONAL	1	FALSE	1	0.88928806956584	2		403	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0001696-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	320	405	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.688848438165445	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.688848438165445	1		406	557	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149447787	149447787	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001696-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	140	197	0	ENST00000286301.3:c.1617G>C	p.Lys539Asn	p.K539N	ENST00000286301	NM_005211.3	539	aaG/aaC	11/22	0.688848438165445	1	FACETS	0.808	0.746	0.869	0.808	0.746	0.869	CLONAL	1	TRUE	0	0.688848438165445	1		197	330	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484278	8484278	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001696-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	299	424	0	ENST00000356435.5:c.3254T>G	p.Leu1085Arg	p.L1085R	ENST00000356435		1085	cTg/cGg	19/35	0.662663702294617	4	FACETS	0.987	0.928	1	0.329	0.309	0.35	CLONAL	1	TRUE	1	0.688848438165445	4		424	1485	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256646	16256669	+	inframe_deletion	In_Frame_Del	DEL	AAGAGTCTTTAAAATTTAATCCTT	AAGAGTCTTTAAAATTTAATCCTT	-	novel	NA	P-0001696-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	161	332	0	ENST00000375759.3:c.3912_3935del	p.Glu1304_Tyr1312delinsAsp	p.E1304_Y1312delinsD	ENST00000375759	NM_015001.2	1304	gAAGAGTCTTTAAAATTTAATCCTTat/gat	11/15	0.688848438165445	1	FACETS	0.721	0.668	0.775	0.721	0.668	0.775	SUBCLONAL	1	TRUE	0	0.688848438165445	1		332	425	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434404	121434407	+	missense_variant	Missense_Mutation	ONP	GAGC	GAGC	AAGA	novel	NA	P-0001696-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	285	410	0	ENST00000257555.6:c.1168_1171delinsAAGA	p.Glu390_Gln391delinsLysLys	p.E390_Q391delinsKK	ENST00000257555		390	GAGCag/AAGAag	6/10	0.688848438165445	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.688848438165445	1		410	535	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0001701-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	74	435	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.81280080871756	2		435	156	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587782272	NA	P-0001701-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	75	466	0	ENST00000269305.4:c.994-1G>C		p.X332_splice	ENST00000269305	NM_001126112.2	332			NA	2	FACETS	0.998	0.894	1			1	INDETERMINATE	1	TRUE	NA	0.81280080871756	2		466	185	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609911	117609911	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001701-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	107	560	0	ENST00000368508.3:c.6788T>C	p.Leu2263Ser	p.L2263S	ENST00000368508	NM_002944.2	2263	tTa/tCa	43/43	0.812697026192961	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.81280080871756	1		560	150	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0001708-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	223	627	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.783634934037225	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.783634934037225	1		627	331	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693796	47693796	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs267607964	NA	P-0001708-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	146	403	0	ENST00000233146.2:c.1511-1G>T		p.X504_splice	ENST00000233146	NM_000251.2	504			0.783634934037225	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.783634934037225	1		403	209	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615601	43615601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001708-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	181	482	0	ENST00000355710.3:c.2680G>A	p.Gly894Ser	p.G894S	ENST00000355710	NM_020975.4	894	Ggc/Agc	15/20	0.237999569364415	3	FACETS	0.769	0.718	0.82	0.769	0.718	0.82	INDETERMINATE	2	TRUE	1	0.783634934037225	3		482	418	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100441	102100441	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001708-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	32	568	0	ENST00000282441.5:c.1285A>C	p.Ile429Leu	p.I429L	ENST00000282441	NM_001130145.2	429	Atc/Ctc	9/9	0.783634934037225	1	FACETS	0.133	0.107	0.161	0.133	0.107	0.161	SUBCLONAL	1	TRUE	0	0.783634934037225	1		568	374	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142000	108142000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779830	NA	P-0001708-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	131	457	0	ENST00000278616.4:c.2944C>T	p.Arg982Cys	p.R982C	ENST00000278616	NM_000051.3	982	Cgt/Tgt	20/63	0.783634934037225	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.783634934037225	1		457	192	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434352	49434352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748969699	NA	P-0001708-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	197	461	0	ENST00000301067.7:c.7201C>T	p.Arg2401Cys	p.R2401C	ENST00000301067	NM_003482.3	2401	Cgc/Tgc	31/54	0.237999569364415	3	FACETS	0.812	0.761	0.863	0.812	0.761	0.863	INDETERMINATE	2	TRUE	1	0.783634934037225	3		461	431	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437167	49437167	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs975418578	NA	P-0001708-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	266	574	0	ENST00000301067.7:c.5512G>A	p.Glu1838Lys	p.E1838K	ENST00000301067	NM_003482.3	1838	Gag/Aag	24/54	0.237999569364415	3	FACETS	0.803	0.76	0.847	0.803	0.76	0.847	INDETERMINATE	2	TRUE	1	0.783634934037225	3		574	588	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588590	28588590	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs145998293	NA	P-0001708-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	26	507	0	ENST00000241453.7:c.2858C>T	p.Ala953Val	p.A953V	ENST00000241453	NM_004119.2	953	gCg/gTg	23/24	0.783634934037225	1	FACETS	0.133	0.105	0.165	0.133	0.105	0.165	SUBCLONAL	1	TRUE	0	0.783634934037225	1		507	303	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857424	9857424	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001708-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	219	553	0	ENST00000330684.3:c.3977G>T	p.Gly1326Val	p.G1326V	ENST00000330684	NM_001134407.1	1326	gGc/gTc	13/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.783634934037225	2		553	496	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533378	29533378	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs878853865	NA	P-0001708-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	151	342	0	ENST00000356175.3:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000356175	NM_000267.3	461	Cga/Tga	12/57	0.783634934037225	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.783634934037225	1		342	228	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652960	29652960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763413441	NA	P-0001708-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	38	589	0	ENST00000356175.3:c.4895G>A	p.Arg1632His	p.R1632H	ENST00000356175	NM_000267.3	1632	cGc/cAc	36/57	0.783634934037225	1	FACETS	0.145	0.12	0.173	0.145	0.12	0.173	SUBCLONAL	1	TRUE	0	0.783634934037225	1		589	407	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951088	17951088	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767428670	NA	P-0001708-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	254	484	2	ENST00000458235.1:c.1205G>A	p.Arg402His	p.R402H	ENST00000458235	NM_000215.3	402	cGc/cAc	9/24	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.783634934037225	2		486	623	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293739	1293739	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001708-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	43	413	3	ENST00000310581.5:c.1262del	p.Pro421GlnfsTer88	p.P421Qfs*88	ENST00000310581	NM_198253.2	421	cCa/ca	2/16	NA	2	FACETS	0.327	0.274	0.384			1	INDETERMINATE	1	TRUE	NA	0.783634934037225	2		416	336	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001728-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	241	387	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.795279252076968	2		387	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0001728-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	488	627	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.924	0.885	0.964	0.924	0.885	0.964	CLONAL	1	TRUE	1	0.795279252076968	2		627	1328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0001728-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	544	615	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	0.992	1	CLONAL	1	TRUE	1	0.795279252076968	2		615	1233	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976884	55976884	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1480331564	NA	P-0001728-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1478	242	511	3	ENST00000263923.4:c.1028C>A	p.Thr343Lys	p.T343K	ENST00000263923	NM_002253.2	343	aCg/aAg	8/30	0.795279252076968	5	FACETS	0.776	0.722	0.832			1	SUBCLONAL	1	TRUE	NA	0.795279252076968	5		514	1720	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720877	89720877	+	splice_donor_variant	Splice_Site	SNP	T	T	G	rs1114167624	NA	P-0001728-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	124	229	0	ENST00000371953.3:c.1026+2T>G		p.X342_splice	ENST00000371953	NM_000314.4	342			0.795279252076968	1	FACETS	0.954	0.891	1	0.954	0.891	1	CLONAL	1	TRUE	0	0.795279252076968	1		229	197	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915297	32915297	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001728-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	516	903	0	ENST00000380152.3:c.6805A>G	p.Ile2269Val	p.I2269V	ENST00000380152		2269	Att/Gtt	11/27	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.795279252076968	2		903	1293	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0001734-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	21	296	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.519	0.399	0.66	0.519	0.399	0.66	SUBCLONAL	1	TRUE	1	0.19	2		296	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0001734-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	40	715	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.624	0.517	0.743	0.624	0.517	0.743	SUBCLONAL	1	TRUE	1	0.19	2		715	675	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0001734-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	163	417	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	0.992	1	CLONAL	2	TRUE	1	0.19	2		417	846	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0001734-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	150	671	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.955	1	1	0.992	1	CLONAL	2	TRUE	1	0.19	2		671	740	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0001734-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	63	424	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.19	2		424	554	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245976	5245976	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001734-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	24	684	0	ENST00000357368.4:c.799G>A	p.Val267Met	p.V267M	ENST00000357368	NM_002850.3	267	Gtg/Atg	10/38	0.265926642826278	0	FACETS	0.51	0.399	0.638			1	SUBCLONAL	1	TRUE	0	0.19	0		684	401	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291846	15291846	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747234439	NA	P-0001734-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	64	529	0	ENST00000263388.2:c.2920G>A	p.Gly974Arg	p.G974R	ENST00000263388	NM_000435.2	974	Ggg/Agg	18/33	0.3	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.19	1		529	411	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375045	31375045	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745506485	NA	P-0001734-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	87	489	0	ENST00000328111.2:c.442C>T	p.Arg148Trp	p.R148W	ENST00000328111	NM_006892.3	148	Cgg/Tgg	6/23	0.110836872488662	0	FACETS	0.734	0.652	0.822			1	INDETERMINATE	2	TRUE	0	0.19	0		489	505	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0001741-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	446	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.749620839679915	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.749620839679915	1		371	639	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101286	27101286	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1238182894	NA	P-0001741-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	229	304	0	ENST00000324856.7:c.4568A>G	p.Tyr1523Cys	p.Y1523C	ENST00000324856	NM_006015.4	1523	tAt/tGt	18/20	0.442350244154432	1	FACETS	0.755	0.711	0.799	0.755	0.711	0.799	INDETERMINATE	1	TRUE	0	0.749620839679915	1		304	506	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690261	47690261	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001741-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	134	243	0	ENST00000233146.2:c.1478A>C	p.Gln493Pro	p.Q493P	ENST00000233146	NM_000251.2	493	cAg/cCg	9/16	0.520257058270754	1	FACETS	0.408	0.372	0.445	0.408	0.372	0.445	SUBCLONAL	1	TRUE	0	0.749620839679915	1		243	548	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202810	128202810	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001741-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	203	295	0	ENST00000341105.2:c.910C>A	p.Pro304Thr	p.P304T	ENST00000341105	NM_032638.4	304	Cct/Act	4/6	1	2	FACETS	0.976	0.912	1	0.976	0.912	1	CLONAL	1	TRUE	1	0.749620839679915	2		295	555	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390546	139390546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200893930	NA	P-0001741-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	115	316	0	ENST00000277541.6:c.7645C>T	p.Arg2549Cys	p.R2549C	ENST00000277541	NM_017617.3	2549	Cgc/Tgc	34/34	0.442350244154432	1	FACETS	0.304	0.274	0.335	0.304	0.274	0.335	INDETERMINATE	1	TRUE	0	0.749620839679915	1		316	632	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121438927	121438927	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001741-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	139	319	0	ENST00000257555.6:c.1828C>G	p.Leu610Val	p.L610V	ENST00000257555		610	Ctg/Gtg	10/10	0.36693573860588	2	FACETS	0.528	0.482	0.577	0.264	0.241	0.289	INDETERMINATE	1	TRUE	0	0.749620839679915	2		319	702	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191129	2191129	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001741-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	457	311	0	ENST00000398665.3:c.383A>T	p.Tyr128Phe	p.Y128F	ENST00000398665	NM_032482.2	128	tAc/tTc	5/28	0.706183840538475	2	FACETS	0.985	0.956	1	0.985	0.956	1	CLONAL	2	TRUE	0	0.749620839679915	2		311	619	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602314	10602314	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001741-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	391	298	0	ENST00000171111.5:c.1264G>T	p.Asp422Tyr	p.D422Y	ENST00000171111	NM_203500.1	422	Gat/Tat	3/6	0.706183840538475	2	FACETS	0.992	0.961	1	0.992	0.961	1	CLONAL	2	TRUE	0	0.749620839679915	2		298	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579585	7579585	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001741-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	188	268	0	ENST00000269305.4:c.102del	p.Leu35CysfsTer9	p.L35Cfs*9	ENST00000269305	NM_001126112.2	34	ccC/cc	4/11	0.72308000157143	1	FACETS	0.98	0.925	1	0.98	0.925	1	CLONAL	1	TRUE	0	0.749620839679915	1		268	320	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096913	11096914	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0001741-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	378	370	0	ENST00000358026.2:c.404_405del	p.Pro135ArgfsTer23	p.P135Rfs*23	ENST00000358026	NM_001128849.1	135	cCA/c	4/36	0.706183840538475	2	FACETS	0.871	0.839	0.902	0.871	0.839	0.902	CLONAL	2	TRUE	0	0.749620839679915	2		370	579	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807822	3807823	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0001741-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	87	277	0	ENST00000262367.5:c.3596_3597delinsTT	p.Cys1199Phe	p.C1199F	ENST00000262367	NM_004380.2	1199	tGC/tTT	18/31	0.36693573860588	2	FACETS	0.386	0.342	0.433	0.193	0.171	0.217	INDETERMINATE	1	TRUE	0	0.749620839679915	2		277	602	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	43	616	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.208571748558024	1	FACETS	0.919	0.778	1	1	0.969	1	CLONAL	2	FALSE	0	0.208571748558024	1		617	201	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259674	11259674	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	54	531	2	ENST00000361445.4:c.4031C>T	p.Ala1344Val	p.A1344V	ENST00000361445	NM_004958.3	1344	gCc/gTc	27/58	0.181882068737726	2	FACETS	0.766	0.658	0.883	0.766	0.658	0.883	SUBCLONAL	2	FALSE	0	0.208571748558024	2		533	338	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807550	36807550	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	30	390	0	ENST00000373129.3:c.1114C>T	p.Gln372Ter	p.Q372*	ENST00000373129	NM_032017.1	372	Cag/Tag	12/12	0.208571748558024	3	FACETS	0.974	0.794	1	0.974	0.794	1	CLONAL	2	FALSE	1	0.208571748558024	3		390	163	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363468	40363468	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755352384	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	73	568	0	ENST00000397332.2:c.761C>T	p.Ser254Phe	p.S254F	ENST00000397332	NM_001033082.2	254	tCc/tTc	3/3	0.208571748558024	3	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	FALSE	1	0.208571748558024	3		568	350	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46725644	46725645	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	47	597	0	ENST00000371975.4:c.280_281delinsAA	p.Gly94Asn	p.G94N	ENST00000371975	NM_003579.3	94	GGc/AAc	5/18	0.208571748558024	3	FACETS	0.821	0.697	0.957	0.821	0.697	0.957	CLONAL	2	FALSE	1	0.208571748558024	3		597	303	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330546	65330546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	94	678	0	ENST00000342505.4:c.1100C>T	p.Ser367Phe	p.S367F	ENST00000342505	NM_002227.2	367	tCt/tTt	8/25	0.208571748558024	3	FACETS	1	0.911	1	1	0.911	1	CLONAL	2	FALSE	1	0.208571748558024	3		678	487	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468217	120468217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	61	417	0	ENST00000256646.2:c.4222G>A	p.Gly1408Ser	p.G1408S	ENST00000256646	NM_024408.3	1408	Ggt/Agt	25/34	0.208571748558024	3	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	FALSE	1	0.208571748558024	3		417	284	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193121534	193121534	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	95	559	0	ENST00000367435.3:c.932C>T	p.Thr311Ile	p.T311I	ENST00000367435	NM_024529.4	311	aCt/aTt	10/17	0.208571748558024	3	FACETS	0.945	0.844	1	0.945	0.844	1	CLONAL	2	FALSE	1	0.208571748558024	3		559	532	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226573347	226573348	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	49	377	0	ENST00000366794.5:c.868_869delinsAA	p.Gly290Asn	p.G290N	ENST00000366794	NM_001618.3	290	GGt/AAt	7/23	0.208571748558024	3	FACETS	1	0.874	1	1	0.874	1	CLONAL	2	FALSE	1	0.208571748558024	3		377	253	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719467	190719467	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	85	444	0	ENST00000441310.2:c.1469C>T	p.Ser490Phe	p.S490F	ENST00000441310	NM_000534.4	490	tCt/tTt	9/13	0.208571748558024	6	FACETS	1	0.962	1	0.799	0.709	0.895	CLONAL	2	FALSE	3	0.208571748558024	6		444	482	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274527	198274527	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	69	623	1	ENST00000335508.6:c.871A>T	p.Asn291Tyr	p.N291Y	ENST00000335508	NM_012433.2	291	Aac/Tac	7/25	1	2	FACETS	0.899	0.787	1	1	0.98	1	CLONAL	2	FALSE	1	0.208571748558024	2		624	368	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248746	212248746	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762661533	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	61	456	0	ENST00000342788.4:c.3521G>A	p.Arg1174Gln	p.R1174Q	ENST00000342788	NM_005235.2	1174	cGg/cAg	28/28	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.208571748558024	2		456	451	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589874	212589874	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	84	442	0	ENST00000342788.4:c.668G>A	p.Gly223Glu	p.G223E	ENST00000342788	NM_005235.2	223	gGa/gAa	6/28	1	2	FACETS	0.766	0.678	0.859	1	0.979	1	SUBCLONAL	2	FALSE	1	0.208571748558024	2		442	526	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162068	47162068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	34	520	0	ENST00000409792.3:c.4058C>T	p.Ser1353Phe	p.S1353F	ENST00000409792	NM_014159.6	1353	tCc/tTc	3/21	1	2	FACETS	0.776	0.634	0.936	0.776	0.634	0.936	CLONAL	1	FALSE	1	0.208571748558024	2		520	420	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588800	52588800	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	54	446	0	ENST00000394830.3:c.4228G>A	p.Gly1410Arg	p.G1410R	ENST00000394830	NM_018313.4	1410	Ggg/Agg	27/30	1	2	FACETS	0.887	0.763	1	1	0.974	1	CLONAL	2	FALSE	1	0.208571748558024	2		446	292	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979555	55979555	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	35	690	0	ENST00000263923.4:c.892A>G	p.Thr298Ala	p.T298A	ENST00000263923	NM_002253.2	298	Acc/Gcc	7/30	0.208571748558024	1	FACETS	0.683	0.56	0.822	0.683	0.56	0.822	SUBCLONAL	1	FALSE	0	0.208571748558024	1		690	440	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231707	66231707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1211795184	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	49	572	0	ENST00000273854.3:c.1993G>A	p.Glu665Lys	p.E665K	ENST00000273854	NM_004439.5	665	Gaa/Aaa	11/18	0.208571748558024	3	FACETS	0.99	0.839	1	0.495	0.419	0.579	CLONAL	1	FALSE	1	0.208571748558024	3		572	524	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521088	187521088	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	52	436	0	ENST00000441802.2:c.12067C>T	p.Gln4023Ter	p.Q4023*	ENST00000441802	NM_005245.3	4023	Cag/Tag	22/27	0.183948329385452	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	0	0.208571748558024	1		436	328	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630072	187630072	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	36	562	0	ENST00000441802.2:c.910A>T	p.Arg304Ter	p.R304*	ENST00000441802	NM_005245.3	304	Aga/Tga	2/27	0.183948329385452	1	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	FALSE	0	0.208571748558024	1		562	292	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38991102	38991102	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	143	553	0	ENST00000357387.3:c.532C>T	p.Gln178Ter	p.Q178*	ENST00000357387	NM_152756.3	178	Caa/Taa	7/38	0.208571748558024	5	FACETS	1	0.961	1	0.812	0.744	0.883	CLONAL	3	FALSE	1	0.208571748558024	5		553	554	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39074461	39074461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1263565009	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	17	273	0	ENST00000357387.3:c.19G>A	p.Gly7Ser	p.G7S	ENST00000357387	NM_152756.3	7	Ggc/Agc	1/38	0.208571748558024	5	FACETS	1	0.851	1	0.302	0.226	0.391	CLONAL	1	FALSE	1	0.208571748558024	5		273	177	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86658431	86658431	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	126	559	1	ENST00000274376.6:c.1396A>T	p.Lys466Ter	p.K466*	ENST00000274376	NM_002890.2	466	Aaa/Taa	10/25	0.208571748558024	5	FACETS	0.924	0.84	1	0.693	0.63	0.759	CLONAL	3	FALSE	1	0.208571748558024	5		560	572	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647407	117647407	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	87	590	0	ENST00000368508.3:c.5537A>T	p.Glu1846Val	p.E1846V	ENST00000368508	NM_002944.2	1846	gAg/gTg	33/43	1	2	FACETS	0.913	0.812	1	1	0.984	1	CLONAL	2	FALSE	1	0.208571748558024	2		590	457	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005449	150005449	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	32	534	1	ENST00000253339.5:c.776G>A	p.Arg259Lys	p.R259K	ENST00000253339		259	aGa/aAa	3/7	NA	2	FACETS	1	0.886	1			1	INDETERMINATE	1	FALSE	NA	0.208571748558024	2		535	273	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335007	81335007	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1384023893	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	111	573	0	ENST00000222390.5:c.1820C>T	p.Pro607Leu	p.P607L	ENST00000222390	NM_000601.4	607	cCt/cTt	16/18	0.208571748558024	4	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	FALSE	2	0.208571748558024	4		573	594	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522619	106522619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	69	598	0	ENST00000359195.3:c.2596C>T	p.Pro866Ser	p.P866S	ENST00000359195	NM_002649.2	866	Cca/Tca	7/11	0.208571748558024	4	FACETS	0.966	0.845	1	0.966	0.845	1	CLONAL	2	FALSE	2	0.208571748558024	4		598	414	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874632	151874632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	60	524	0	ENST00000262189.6:c.7906G>A	p.Gly2636Ser	p.G2636S	ENST00000262189	NM_170606.2	2636	Ggt/Agt	38/59	NA	2	FACETS	1	0.967	1			1	INDETERMINATE	1	FALSE	NA	0.208571748558024	2		524	404	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132732	152132733	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	29	286	0	ENST00000262189.6:c.139_140delinsTT	p.Pro47Phe	p.P47F	ENST00000262189	NM_170606.2	47	CCt/TTt	1/59	NA	2	FACETS	0.853	0.692	1			1	INDETERMINATE	2	FALSE	NA	0.208571748558024	2		286	163	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486101	8486101	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	102	675	0	ENST00000356435.5:c.2716G>A	p.Glu906Lys	p.E906K	ENST00000356435		906	Gag/Aag	17/35	0.208571748558024	3	FACETS	0.923	0.832	1	0.923	0.832	1	CLONAL	3	FALSE	0	0.208571748558024	3		675	390	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970901	21970901	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs45476696	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	96	505	0	ENST00000304494.5:c.457G>A	p.Asp153Asn	p.D153N	ENST00000304494	NM_000077.4	153	Gac/Aac	2/3	0.208571748558024	3	FACETS	0.895	0.808	0.984	1	0.97	1	CLONAL	4	FALSE	0	0.208571748558024	3		505	284	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401834	139401834	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	41	614	0	ENST00000277541.6:c.3566C>T	p.Ser1189Phe	p.S1189F	ENST00000277541	NM_017617.3	1189	tCc/tTc	22/34	0.208571748558024	5	FACETS	1	0.881	1	1	0.962	1	CLONAL	3	FALSE	3	0.208571748558024	5		614	164	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418261	139418261	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	48	520	0	ENST00000277541.6:c.311A>T	p.Asn104Ile	p.N104I	ENST00000277541	NM_017617.3	104	aAt/aTt	3/34	NA	2	FACETS	0.852	0.732	0.981			1	INDETERMINATE	3	FALSE	NA	0.208571748558024	2		520	180	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851953	63851953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	56	383	0	ENST00000279873.7:c.2731C>T	p.Pro911Ser	p.P911S	ENST00000279873	NM_032199.2	911	Ccc/Tcc	10/10	0.208571748558024	8	FACETS	0.921	0.794	1			1	CLONAL	3	FALSE	NA	0.208571748558024	8		383	316	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332628	70332628	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457729740	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	23	513	0	ENST00000373644.4:c.533C>T	p.Pro178Leu	p.P178L	ENST00000373644	NM_030625.2	178	cCc/cTc	2/12	0.153953511264641	0	FACETS	0.701	0.548	0.877			1	SUBCLONAL	1	FALSE	0	0.208571748558024	0		513	249	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405899	70405899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	31	693	0	ENST00000373644.4:c.3413C>T	p.Ser1138Leu	p.S1138L	ENST00000373644	NM_030625.2	1138	tCa/tTa	4/12	0.153953511264641	0	FACETS	0.617	0.5	0.751			1	SUBCLONAL	1	FALSE	0	0.208571748558024	0		693	381	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104352456	104352456	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	41	594	0	ENST00000369902.3:c.572C>G	p.Pro191Arg	p.P191R	ENST00000369902	NM_016169.3	191	cCc/cGc	4/12	0.208571748558024	3	FACETS	0.841	0.706	0.99	0.841	0.706	0.99	CLONAL	2	FALSE	1	0.208571748558024	3		594	258	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279500	123279500	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	50	584	0	ENST00000358487.5:c.932T>C	p.Val311Ala	p.V311A	ENST00000358487	NM_000141.4	311	gTt/gCt	7/18	0.208571748558024	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	0	0.208571748558024	1		584	311	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	532643	532643	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	14	459	0	ENST00000451590.1:c.563T>C	p.Leu188Pro	p.L188P	ENST00000451590	NM_001130442.1	188	cTc/cCc	5/5	0.181882068737726	2	FACETS	1	0.789	1	0.55	0.401	0.727	CLONAL	1	FALSE	0	0.208571748558024	2		459	122	SUCCESS
ATM	472	MSKCC	GRCh37	11	108168019	108168019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	75	477	1	ENST00000278616.4:c.4915C>T	p.Pro1639Ser	p.P1639S	ENST00000278616	NM_000051.3	1639	Ccg/Tcg	33/63	NA	2	FACETS	0.852	0.75	0.961			1	INDETERMINATE	2	FALSE	NA	0.208571748558024	2		478	422	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202276	108202276	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	59	405	0	ENST00000278616.4:c.7621C>A	p.Leu2541Ile	p.L2541I	ENST00000278616	NM_000051.3	2541	Ctc/Atc	51/63	NA	2	FACETS	0.777	0.672	0.891			1	INDETERMINATE	2	FALSE	NA	0.208571748558024	2		405	364	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374837	118374837	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	50	461	0	ENST00000534358.1:c.8230C>T	p.Pro2744Ser	p.P2744S	ENST00000534358	NM_005933.3	2744	Cca/Tca	27/36	0.208571748558024	1	FACETS	0.751	0.641	0.869	1	0.965	1	SUBCLONAL	2	FALSE	0	0.208571748558024	1		461	286	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475134	475135	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	51	597	0	ENST00000399788.2:c.502_503delinsTT	p.Pro168Leu	p.P168L	ENST00000399788	NM_001042603.1	168	CCa/TTa	4/28	0.163066720699981	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	0	0.208571748558024	1		597	346	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1022604	1022604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	65	653	0	ENST00000358495.3:c.1210C>T	p.His404Tyr	p.H404Y	ENST00000358495	NM_134424.2	404	Cat/Tat	12/12	0.163066720699981	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	0	0.208571748558024	1		653	396	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435047	18435047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	71	594	0	ENST00000266497.5:c.32C>T	p.Pro11Leu	p.P11L	ENST00000266497		11	cCt/cTt	1/31	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.208571748558024	2		594	515	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435256	18435256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	98	615	0	ENST00000266497.5:c.241G>A	p.Ala81Thr	p.A81T	ENST00000266497		81	Gca/Aca	1/31	1	2	FACETS	0.905	0.811	1	1	0.986	1	CLONAL	2	FALSE	1	0.208571748558024	2		615	519	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18576974	18576974	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	58	499	0	ENST00000266497.5:c.2381+1G>A		p.X794_splice	ENST00000266497		794			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.208571748558024	2		499	447	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243379	46243379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	70	537	0	ENST00000334344.6:c.1732C>T	p.His578Tyr	p.H578Y	ENST00000334344	NM_152641.2	578	Cat/Tat	14/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.208571748558024	2		537	493	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420694	49420694	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	49	422	0	ENST00000301067.7:c.15055G>A	p.Ala5019Thr	p.A5019T	ENST00000301067	NM_003482.3	5019	Gcc/Acc	48/54	1	2	FACETS	1	0.859	1	1	0.975	1	CLONAL	2	FALSE	1	0.208571748558024	2		422	234	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440570	49440570	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1275834731	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	42	411	0	ENST00000301067.7:c.4240A>G	p.Thr1414Ala	p.T1414A	ENST00000301067	NM_003482.3	1414	Acc/Gcc	15/54	1	2	FACETS	0.963	0.813	1	1	0.97	1	CLONAL	2	FALSE	1	0.208571748558024	2		411	209	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448410	49448410	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771228283	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	40	556	0	ENST00000301067.7:c.301G>A	p.Gly101Arg	p.G101R	ENST00000301067	NM_003482.3	101	Ggg/Agg	3/54	1	2	FACETS	0.813	0.681	0.957	1	0.961	1	CLONAL	2	FALSE	1	0.208571748558024	2		556	236	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219305	133219305	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201950040	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	56	463	0	ENST00000320574.5:c.4739G>A	p.Arg1580Gln	p.R1580Q	ENST00000320574	NM_006231.2	1580	cGg/cAg	37/49	NA	2	FACETS	1	0.882	1			1	INDETERMINATE	3	FALSE	NA	0.208571748558024	2		463	177	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245002	133245002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200621883	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	77	593	0	ENST00000320574.5:c.2113C>T	p.Arg705Trp	p.R705W	ENST00000320574	NM_006231.2	705	Cgg/Tgg	19/49	NA	2	FACETS	0.988	0.88	1			1	INDETERMINATE	3	FALSE	NA	0.208571748558024	2		593	249	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28963960	28963960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773035381	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	59	687	0	ENST00000282397.4:c.1942C>T	p.Leu648Phe	p.L648F	ENST00000282397	NM_002019.4	648	Ctc/Ttc	13/30	0.208571748558024	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	0	0.208571748558024	1		687	410	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514425	103514425	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	85	448	0	ENST00000355739.4:c.926C>T	p.Pro309Leu	p.P309L	ENST00000355739	NM_000123.3	309	cCt/cTt	8/15	0.208571748558024	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	FALSE	1	0.208571748558024	3		448	404	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515078	103515078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	36	351	0	ENST00000355739.4:c.1579C>T	p.Pro527Ser	p.P527S	ENST00000355739	NM_000123.3	527	Cca/Tca	8/15	0.208571748558024	3	FACETS	1	0.898	1	0.567	0.467	0.679	CLONAL	1	FALSE	1	0.208571748558024	3		351	336	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434778	110434779	+	missense_variant	Missense_Mutation	DNP	TG	TG	CT	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	25	444	0	ENST00000375856.3:c.3622_3623delinsAG	p.Gln1208Arg	p.Q1208R	ENST00000375856	NM_003749.2	1208	CAg/AGg	1/2	0.208571748558024	3	FACETS	0.788	0.627	0.97	0.788	0.627	0.97	CLONAL	2	FALSE	1	0.208571748558024	3		444	168	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857784	9857784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145861983	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	53	657	0	ENST00000330684.3:c.3617G>A	p.Arg1206Gln	p.R1206Q	ENST00000330684	NM_001134407.1	1206	cGa/cAa	13/13	1	2	FACETS	0.892	0.766	1	1	0.974	1	CLONAL	2	FALSE	1	0.208571748558024	2		657	285	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032306	10032306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	41	363	0	ENST00000330684.3:c.517G>A	p.Val173Met	p.V173M	ENST00000330684	NM_001134407.1	173	Gtg/Atg	3/13	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.208571748558024	2		363	268	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014047	14014047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326609617	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	81	574	0	ENST00000311895.7:c.25C>T	p.Arg9Trp	p.R9W	ENST00000311895	NM_005236.2	9	Cgg/Tgg	1/11	1	2	FACETS	1	0.954	1	1	0.986	1	CLONAL	2	FALSE	1	0.208571748558024	2		574	339	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857469	68857469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149127230	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	58	475	0	ENST00000261769.5:c.2104G>A	p.Glu702Lys	p.E702K	ENST00000261769	NM_004360.3	702	Gaa/Aaa	13/16	0.117404844921815	0	FACETS	0.683	0.591	0.783			1	INDETERMINATE	2	FALSE	0	0.208571748558024	0		475	322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	19	567	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.208571748558024	1	FACETS	0.745	0.567	0.953	0.745	0.567	0.953	CLONAL	1	FALSE	0	0.208571748558024	1		567	219	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687583	29687583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	68	685	1	ENST00000356175.3:c.8176G>A	p.Asp2726Asn	p.D2726N	ENST00000356175	NM_000267.3	2726	Gat/Aat	56/57	0.208571748558024	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	0	0.208571748558024	1		686	405	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512437	38512438	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	17	459	0	ENST00000254066.5:c.1348_1349delinsTT	p.Pro450Phe	p.P450F	ENST00000254066	NM_000964.3	450	CCc/TTc	9/9	0.208571748558024	1	FACETS	1	0.842	1	1	0.842	1	CLONAL	1	FALSE	0	0.208571748558024	1		459	125	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243605	41243605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	35	694	0	ENST00000357654.3:c.3943C>T	p.Pro1315Ser	p.P1315S	ENST00000357654	NM_007294.3	1315	Cct/Tct	10/23	0.208571748558024	1	FACETS	0.728	0.597	0.875	0.728	0.597	0.875	SUBCLONAL	1	FALSE	0	0.208571748558024	1		694	413	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533703	63533704	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	15	439	0	ENST00000307078.5:c.1450_1451delinsAA	p.Gly484Asn	p.G484N	ENST00000307078	NM_004655.3	484	GGt/AAt	6/11	0.208571748558024	1	FACETS	1	0.78	1	1	0.78	1	CLONAL	1	FALSE	0	0.208571748558024	1		439	121	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097021	11097021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1378355850	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	10	636	0	ENST00000358026.2:c.512C>T	p.Pro171Leu	p.P171L	ENST00000358026	NM_001128849.1	171	cCa/cTa	4/36	0.208571748558024	0	FACETS	0.506	0.343	0.709			1	SUBCLONAL	1	FALSE	0	0.208571748558024	0		636	150	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271748	15271748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	26	439	0	ENST00000263388.2:c.6691C>T	p.Pro2231Ser	p.P2231S	ENST00000263388	NM_000435.2	2231	Cca/Tca	33/33	0.208571748558024	0	FACETS	0.747	0.601	0.91			1	CLONAL	2	FALSE	0	0.208571748558024	0		439	132	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797822	42797822	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	28	416	0	ENST00000575354.2:c.3874C>T	p.Pro1292Ser	p.P1292S	ENST00000575354	NM_015125.3	1292	Cct/Tct	16/20	0.183948329385452	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	FALSE	0	0.208571748558024	1		416	182	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31390252	31390253	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	53	575	0	ENST00000328111.2:c.2207_2208delinsAA	p.Trp736Ter	p.W736*	ENST00000328111	NM_006892.3	736	tGG/tAA	20/23	0.208571748558024	3	FACETS	0.897	0.769	1	0.897	0.769	1	CLONAL	2	FALSE	1	0.208571748558024	3		575	313	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714447	40714447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs911474865	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	43	436	0	ENST00000373198.4:c.3950C>T	p.Pro1317Leu	p.P1317L	ENST00000373198	NM_133170.3	1317	cCc/cTc	29/32	0.208571748558024	3	FACETS	0.922	0.777	1	0.922	0.777	1	CLONAL	2	FALSE	1	0.208571748558024	3		436	247	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932294	39932294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	78	376	0	ENST00000378444.4:c.2305G>A	p.Glu769Lys	p.E769K	ENST00000378444	NM_001123385.1	769	Gaa/Aaa	4/15	0.208571748558024	2	FACETS	1	0.948	1			1	CLONAL	4	FALSE	NA	0.208571748558024	2		376	173	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243888	53243888	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	98	353	0	ENST00000375401.3:c.1105C>T	p.Pro369Ser	p.P369S	ENST00000375401	NM_004187.3	369	Cca/Tca	8/26	0.208571748558024	2	FACETS	0.974	0.892	1			1	CLONAL	5	FALSE	NA	0.208571748558024	2		353	193	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0001750-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	3508	611	3	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.78304076096543	19	FACETS	1	0.999	1			1	CLONAL	18	TRUE	NA	0.78304076096543	19		614	3720	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs863224683	NA	P-0001750-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	546	428	0	ENST00000269305.4:c.388C>G	p.Leu130Val	p.L130V	ENST00000269305	NM_001126112.2	130	Ctc/Gtc	5/11	NA	2	FACETS	0.941	0.916	0.965			1	INDETERMINATE	2	TRUE	NA	0.78304076096543	2		428	741	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728864	190728864	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001750-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	94	376	0	ENST00000441310.2:c.2252G>A	p.Arg751Lys	p.R751K	ENST00000441310	NM_000534.4	751	aGa/aAa	10/13	0.648185542952716	2	FACETS	0.472	0.421	0.525	0.236	0.21	0.263	SUBCLONAL	1	TRUE	0	0.78304076096543	2		376	509	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396740	139396740	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001750-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	61	371	0	ENST00000277541.6:c.5368G>T	p.Asp1790Tyr	p.D1790Y	ENST00000277541	NM_017617.3	1790	Gac/Tac	28/34	0.709436149110472	2	FACETS	0.29	0.25	0.333	0.145	0.125	0.167	SUBCLONAL	1	TRUE	0	0.78304076096543	2		371	538	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857569	9857569	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001750-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	175	590	0	ENST00000330684.3:c.3832C>A	p.Gln1278Lys	p.Q1278K	ENST00000330684	NM_001134407.1	1278	Caa/Aaa	13/13	0.668098280867858	3	FACETS	0.558	0.513	0.605			1	SUBCLONAL	1	TRUE	NA	0.78304076096543	3		590	1114	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207197	1207199	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0001750-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	116	369	1	ENST00000326873.7:c.289_290+1del		p.VKdel	ENST00000326873	NM_000455.4	95	gtGAAg/gtg	1/10	NA	2	FACETS	0.436	0.394	0.481			1	INDETERMINATE	1	TRUE	NA	0.78304076096543	2		370	679	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0001767-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1179	364	410	0	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	0.692777894867031	3	FACETS	0.917	0.868	0.968	0.458	0.434	0.484	CLONAL	1	TRUE	1	0.692777894867031	3		410	1543	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0001767-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	860	466	2	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.682634578670565	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.692777894867031	2		468	1238	SUCCESS
APC	324	MSKCC	GRCh37	5	112155042	112155042	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs863225310	NA	P-0001767-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	204	320	0	ENST00000257430.4:c.1312+1G>A		p.X438_splice	ENST00000257430	NM_000038.5	438			1	2	FACETS	0.956	0.892	1	0.956	0.892	1	CLONAL	1	TRUE	1	0.692777894867031	2		320	616	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288967	212288967	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs537458255	NA	P-0001767-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	515	480	0	ENST00000342788.4:c.2779C>T	p.Arg927Ter	p.R927*	ENST00000342788	NM_005235.2	927	Cga/Tga	23/28	0.692777894867031	3	FACETS	0.999	0.962	1	0.999	0.962	1	CLONAL	2	TRUE	1	0.692777894867031	3		480	1002	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001767-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	235	379	0	ENST00000257430.4:c.4199C>A	p.Ser1400Ter	p.S1400*	ENST00000257430	NM_000038.5	1400	tCg/tAg	16/16	1	2	FACETS	0.889	0.833	0.947	0.889	0.833	0.947	CLONAL	1	TRUE	1	0.692777894867031	2		379	763	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163405	108163405	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001767-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	309	473	0	ENST00000278616.4:c.4496G>T	p.Ser1499Ile	p.S1499I	ENST00000278616	NM_000051.3	1499	aGt/aTt	30/63	1	2	FACETS	0.98	0.927	1	0.98	0.927	1	CLONAL	1	TRUE	1	0.692777894867031	2		473	910	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937769	76937770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0001767-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1508	270	576	1	ENST00000373344.5:c.2978dup	p.Lys994GlufsTer6	p.K994Efs*6	ENST00000373344	NM_000489.3	993	aag/aaAg	9/35	0.643492708025344	4	FACETS	0.742	0.694	0.792	0.247	0.231	0.264	SUBCLONAL	1	TRUE	1	0.692777894867031	4		577	1778	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577126	7577126	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001776-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	55	459	0	ENST00000269305.4:c.812A>T	p.Glu271Val	p.E271V	ENST00000269305	NM_001126112.2	271	gAg/gTg	8/11	0.351691210124249	1	FACETS	0.431	0.368	0.5	0.431	0.368	0.5	SUBCLONAL	1	TRUE	0	0.351691210124249	1		459	598	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0001777-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	177	506	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	0.943	0.868	1	0.943	0.868	1	CLONAL	1	TRUE	1	0.353158376142352	2		506	1063	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0001777-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	119	433	1	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	0.353158376142352	1	FACETS	0.858	0.776	0.944	0.858	0.776	0.944	CLONAL	1	TRUE	0	0.353158376142352	1		434	647	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0001784-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	200	265	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.684487405391518	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.717124539553041	2		267	273	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0001784-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	323	675	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.695806026597034	4	FACETS	0.999	0.949	1	0.999	0.949	1	CLONAL	2	TRUE	2	0.717124539553041	4		675	774	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522597	176522597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200766146	NA	P-0001784-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	115	393	2	ENST00000292408.4:c.1694G>A	p.Arg565Gln	p.R565Q	ENST00000292408	NM_213647.1	565	cGg/cAg	13/18	0.699978481755918	4	FACETS	1	0.909	1			1	CLONAL	1	TRUE	NA	0.717124539553041	4		395	548	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555603	21555603	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0001784-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	133	386	0	ENST00000382592.4:c.2665+2T>A		p.X889_splice	ENST00000382592	NM_014572.2	889			0.710770754394515	3	FACETS	1	0.947	1			1	CLONAL	1	TRUE	NA	0.717124539553041	3		386	480	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221320	1221320	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587776656	NA	P-0001787-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	55	407	0	ENST00000326873.7:c.843del	p.Leu282SerfsTer5	p.L282Sfs*5	ENST00000326873	NM_000455.4	281	ccG/cc	6/10	0.232345035933387	2	FACETS	0.882	0.763	1	0.882	0.763	1	CLONAL	2	TRUE	0	0.27	2		407	231	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001787-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	69	327	0	ENST00000269305.4:c.859G>T	p.Glu287Ter	p.E287*	ENST00000269305	NM_001126112.2	287	Gag/Tag	8/11	0.230339315951295	2	FACETS	0.961	0.846	1	0.961	0.846	1	CLONAL	2	TRUE	0	0.27	2		327	266	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661316	227661316	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001787-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	46	482	0	ENST00000305123.5:c.2139C>A	p.His713Gln	p.H713Q	ENST00000305123	NM_005544.2	713	caC/caA	1/2	0.296773663157354	3	FACETS	0.796	0.676	0.925	0.796	0.676	0.925	CLONAL	2	TRUE	1	0.27	3		482	243	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050389	37050389	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1559524603	NA	P-0001787-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	64	464	0	ENST00000231790.2:c.538G>T	p.Val180Phe	p.V180F	ENST00000231790	NM_000249.3	180	Gtt/Ttt	6/19	0.229494662782576	2	FACETS	0.971	0.852	1	0.971	0.852	1	CLONAL	2	TRUE	0	0.27	2		464	244	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153670	55153670	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001787-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	28	554	0	ENST00000257290.5:c.2636G>A	p.Trp879Ter	p.W879*	ENST00000257290	NM_006206.4	879	tGg/tAg	19/23	1	2	FACETS	0.774	0.621	0.947	0.774	0.621	0.947	CLONAL	1	TRUE	1	0.27	2		554	268	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170834713	170834713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001787-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	43	473	0	ENST00000296930.5:c.781C>T	p.Leu261Phe	p.L261F	ENST00000296930	NM_002520.6	261	Ctt/Ttt	10/11	0.230339315951295	2	FACETS	1	0.947	1	0.655	0.553	0.767	CLONAL	1	TRUE	0	0.27	2		473	243	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426075	49426075	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001787-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	21	358	0	ENST00000301067.7:c.12413C>A	p.Ser4138Tyr	p.S4138Y	ENST00000301067	NM_003482.3	4138	tCt/tAt	39/54	0.296773663157354	5	FACETS	0.786	0.606	0.996			1	CLONAL	1	TRUE	NA	0.27	5		358	278	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736915	736915	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001787-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	69	591	0	ENST00000314574.4:c.1184G>T	p.Arg395Leu	p.R395L	ENST00000314574	NM_005433.3	395	cGa/cTa	10/12	0.225368282771107	3	FACETS	1	0.88	1	0.667	0.586	0.752	CLONAL	2	TRUE	0	0.27	3		591	290	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867709	45867709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200895828	NA	P-0001787-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	80	495	1	ENST00000391945.4:c.691G>A	p.Val231Met	p.V231M	ENST00000391945	NM_000400.3	231	Gtg/Atg	8/23	0.235565150037528	4	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	2	0.27	4		496	313	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624868	9624868	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001787-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	62	502	0	ENST00000353224.5:c.109C>A	p.Gln37Lys	p.Q37K	ENST00000353224	NM_177990.2	37	Cag/Aag	3/10	0.296773663157354	3	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	1	0.27	3		502	240	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922100	39922100	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001787-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	18	647	0	ENST00000378444.4:c.4072T>A	p.Ser1358Thr	p.S1358T	ENST00000378444	NM_001123385.1	1358	Tcc/Acc	9/15	1	2	FACETS	0.474	0.357	0.613	0.474	0.357	0.613	SUBCLONAL	1	TRUE	1	0.27	2		647	281	SUCCESS
AR	367	MSKCC	GRCh37	X	66937445	66937445	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001787-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	27	535	0	ENST00000374690.3:c.2299C>A	p.Pro767Thr	p.P767T	ENST00000374690	NM_000044.3	767	Cct/Act	5/8	1	2	FACETS	0.93	0.745	1	0.93	0.745	1	CLONAL	1	TRUE	1	0.27	2		535	215	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844801	156844801	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0001790-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	746	646	0	ENST00000524377.1:c.1354+1G>C		p.X452_splice	ENST00000524377	NM_002529.3	452			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.955025193500713	2		646	1561	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911588	134911588	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001790-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	498	645	0	ENST00000398015.3:c.2053G>T	p.Gly685Cys	p.G685C	ENST00000398015	NM_004441.4	685	Ggt/Tgt	11/16	0.434854597928943	1	FACETS	0.402	0.385	0.42	0.402	0.385	0.42	INDETERMINATE	1	TRUE	0	0.955025193500713	1		645	1355	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140716	55140716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs904415979	NA	P-0001790-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	1051	800	0	ENST00000257290.5:c.1577C>T	p.Thr526Met	p.T526M	ENST00000257290	NM_006206.4	526	aCg/aTg	11/23	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.955025193500713	2		800	2065	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153709	55153709	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0001790-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	476	684	0	ENST00000257290.5:c.2674+1G>A		p.X892_splice	ENST00000257290	NM_006206.4	892			1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.955025193500713	2		684	913	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964423	55964423	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001790-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	921	769	0	ENST00000263923.4:c.2390T>A	p.Leu797Gln	p.L797Q	ENST00000263923	NM_002253.2	797	cTg/cAg	17/30	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.955025193500713	2		769	1748	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280109	66280109	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001790-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	796	663	1	ENST00000273854.3:c.1580C>T	p.Ala527Val	p.A527V	ENST00000273854	NM_004439.5	527	gCa/gTa	7/18	1	2	FACETS	0.989	0.958	1	0.989	0.958	1	CLONAL	1	TRUE	1	0.955025193500713	2		664	1686	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045899	143045899	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs143791426	NA	P-0001790-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	637	492	1	ENST00000262992.4:c.1735C>A	p.Gln579Lys	p.Q579K	ENST00000262992	NM_001101669.1	579	Cag/Aag	17/24	1	2	FACETS	0.965	0.931	0.998	0.965	0.931	0.998	CLONAL	1	TRUE	1	0.955025193500713	2		493	1383	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541475	187541475	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001790-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1340	1134	974	0	ENST00000441802.2:c.6265G>T	p.Val2089Phe	p.V2089F	ENST00000441802	NM_005245.3	2089	Gtt/Ttt	10/27	1	2	FACETS	0.96	0.935	0.985	0.96	0.935	0.985	CLONAL	1	TRUE	1	0.955025193500713	2		974	2474	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294328	1294328	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1060502999	NA	P-0001790-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	409	371	0	ENST00000310581.5:c.673G>C	p.Gly225Arg	p.G225R	ENST00000310581	NM_198253.2	225	Ggg/Cgg	2/16	1	2	FACETS	0.994	0.951	1	0.994	0.951	1	CLONAL	1	TRUE	1	0.955025193500713	2		371	862	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117707013	117707013	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001790-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	606	538	0	ENST00000368508.3:c.2137T>A	p.Tyr713Asn	p.Y713N	ENST00000368508	NM_002944.2	713	Tat/Aat	15/43	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.955025193500713	2		538	1250	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381556	81381556	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001790-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	910	614	0	ENST00000222390.5:c.505G>T	p.Gly169Cys	p.G169C	ENST00000222390	NM_000601.4	169	Ggt/Tgt	5/18	1	2	FACETS	0.998	0.97	1	0.998	0.97	1	CLONAL	1	TRUE	1	0.955025193500713	2		614	1909	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140508753	140508753	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0001790-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	915	602	0	ENST00000288602.6:c.547A>T	p.Lys183Ter	p.K183*	ENST00000288602	NM_004333.4	183	Aaa/Taa	4/18	1	2	FACETS	0.959	0.931	0.987	0.959	0.931	0.987	CLONAL	1	TRUE	1	0.955025193500713	2		602	1999	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878130	151878130	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1458072384	NA	P-0001790-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	644	633	1	ENST00000262189.6:c.6815G>A	p.Cys2272Tyr	p.C2272Y	ENST00000262189	NM_170606.2	2272	tGt/tAt	36/59	1	2	FACETS	0.993	0.959	1	0.993	0.959	1	CLONAL	1	TRUE	1	0.955025193500713	2		634	1358	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375964	8375964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144763077	NA	P-0001790-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	811	708	0	ENST00000356435.5:c.4633G>A	p.Asp1545Asn	p.D1545N	ENST00000356435		1545	Gat/Aat	28/35	0.955025193500713	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.955025193500713	1		708	862	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881496	48881496	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001790-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	851	679	0	ENST00000267163.4:c.218G>T	p.Arg73Ile	p.R73I	ENST00000267163	NM_000321.2	73	aGa/aTa	2/27	0.955025193500713	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.955025193500713	1		679	894	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955573	48955573	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001790-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	565	497	0	ENST00000267163.4:c.1689G>C	p.Trp563Cys	p.W563C	ENST00000267163	NM_000321.2	563	tgG/tgC	17/27	0.955025193500713	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.955025193500713	1		497	587	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858588	9858588	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001790-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	1036	823	1	ENST00000330684.3:c.2813A>T	p.Lys938Met	p.K938M	ENST00000330684	NM_001134407.1	938	aAg/aTg	13/13	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.955025193500713	2		824	2077	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578541	7578541	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001790-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	594	593	0	ENST00000269305.4:c.389T>G	p.Leu130Arg	p.L130R	ENST00000269305	NM_001126112.2	130	cTc/cGc	5/11	0.955025193500713	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.955025193500713	1		593	615	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281518	15281518	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1368023123	NA	P-0001790-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	612	609	3	ENST00000263388.2:c.4855C>T	p.Arg1619Cys	p.R1619C	ENST00000263388	NM_000435.2	1619	Cgc/Tgc	26/33	0.955025193500713	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.955025193500713	1		612	646	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933471	39933471	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001790-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	869	779	0	ENST00000378444.4:c.1128C>A	p.Tyr376Ter	p.Y376*	ENST00000378444	NM_001123385.1	376	taC/taA	4/15	1	2	FACETS	0.944	0.916	0.972	0.944	0.916	0.972	CLONAL	1	TRUE	1	0.955025193500713	2		779	1928	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038720	47038720	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001790-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	567	550	0	ENST00000377604.3:c.727G>T	p.Ala243Ser	p.A243S	ENST00000377604	NM_001204468.1	243	Gca/Tca	9/24	1	2	FACETS	0.897	0.863	0.931	0.897	0.863	0.931	CLONAL	1	TRUE	1	0.955025193500713	2		550	1324	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019784	123019784	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001790-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	554	710	2	ENST00000355640.3:c.272G>T	p.Arg91Ile	p.R91I	ENST00000355640		91	aGa/aTa	2/7	1	2	FACETS	0.884	0.85	0.919	0.884	0.85	0.919	CLONAL	1	TRUE	1	0.955025193500713	2		712	1312	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200217	123200217	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001790-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	933	735	0	ENST00000218089.9:c.2196C>A	p.His732Gln	p.H732Q	ENST00000218089	NM_001042749.1	732	caC/caA	23/35	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.955025193500713	2		735	1950	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0001797-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	26	83	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.656	0.527	0.798	0.656	0.527	0.798	SUBCLONAL	1	TRUE	1	0.624440170632022	2		83	127	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254929	16254929	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs751475729	NA	P-0001797-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	82	433	4	ENST00000375759.3:c.2194C>T	p.Arg732Ter	p.R732*	ENST00000375759	NM_015001.2	732	Cga/Tga	11/15	0.624440170632022	1	FACETS	0.852	0.766	0.94	0.852	0.766	0.94	CLONAL	1	TRUE	0	0.624440170632022	1		437	212	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382152	152382154	+	inframe_deletion	In_Frame_Del	DEL	TGG	TGG	-	novel	NA	P-0001797-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	75	507	0	ENST00000206249.3:c.1265_1267del	p.Val422del	p.V422del	ENST00000206249	NM_000125.3	421	aTGGtg/atg	6/8	1	2	FACETS	0.834	0.739	0.934	0.834	0.739	0.934	CLONAL	1	TRUE	1	0.624440170632022	2		507	288	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115952	8115953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0001797-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	145	382	0	ENST00000346208.3:c.1299_1300dup	p.His434ProfsTer42	p.H434Pfs*42	ENST00000346208		433	cac/caCCc	6/6	0.29607876620662	4	FACETS	0.813	0.748	0.88	0.813	0.748	0.88	INDETERMINATE	2	TRUE	2	0.624440170632022	4		382	464	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531782	46531782	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001803-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	105	625	0	ENST00000262741.5:c.565C>G	p.Gln189Glu	p.Q189E	ENST00000262741	NM_003629.3	189	Cag/Gag	5/10	0.284491505973179	5	FACETS	0.812	0.727	0.902			1	INDETERMINATE	1	TRUE	NA	0.634084498264495	5		625	796	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437623	52437623	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0001803-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	199	393	0	ENST00000460680.1:c.1538C>G	p.Ser513Ter	p.S513*	ENST00000460680	NM_004656.3	513	tCa/tGa	13/17	0.634084498264495	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.634084498264495	1		393	349	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294454	1294454	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001803-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	46	184	0	ENST00000310581.5:c.547C>G	p.Gln183Glu	p.Q183E	ENST00000310581	NM_198253.2	183	Cag/Gag	2/16	0.634084498264495	1	FACETS	0.768	0.663	0.878	0.768	0.663	0.878	SUBCLONAL	1	TRUE	0	0.634084498264495	1		184	129	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24135756	24135791	+	inframe_deletion	In_Frame_Del	DEL	CACGACTCTAGCCACCAGTGTGACCCTGTTAAAAGC	CACGACTCTAGCCACCAGTGTGACCCTGTTAAAAGC	-	novel	NA	P-0001803-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	32	385	0	ENST00000263121.7:c.244_279del	p.Thr82_Ala93del	p.T82_A93del	ENST00000263121	NM_003073.3	81	taCACGACTCTAGCCACCAGTGTGACCCTGTTAAAAGCc/tac	3/9	1	2	FACETS	0.301	0.245	0.365	0.301	0.245	0.365	SUBCLONAL	1	TRUE	1	0.634084498264495	2		385	335	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397695	116397695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001825-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	53	456	4	ENST00000397752.3:c.1969C>T	p.Pro657Ser	p.P657S	ENST00000397752	NM_000245.2	657	Cct/Tct	8/21	1	2	FACETS	0.634	0.541	0.736	0.634	0.541	0.736	SUBCLONAL	1	TRUE	1	0.334835493415388	2		460	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	rs786202799	NA	P-0001825-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	105	258	0	ENST00000269305.4:c.376-2A>T		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.273676880621929	2	FACETS	0.928	0.84	1	0.928	0.84	1	CLONAL	2	TRUE	0	0.334835493415388	2		258	338	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39746854	39746854	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001825-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	15	165	0	ENST00000361337.2:c.1868A>G	p.Asn623Ser	p.N623S	ENST00000361337	NM_003286.2	623	aAt/aGt	18/21	1	2	FACETS	0.404	0.295	0.533	0.404	0.295	0.533	SUBCLONAL	1	TRUE	1	0.334835493415388	2		165	222	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129753	108129753	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1565399936	NA	P-0001829-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	309	531	0	ENST00000278616.4:c.2417T>G	p.Leu806Trp	p.L806W	ENST00000278616	NM_000051.3	806	tTg/tGg	16/63	1	2	FACETS	0.929	0.876	0.982	0.929	0.876	0.982	CLONAL	1	TRUE	1	0.633841318943433	2		531	1050	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237609	16237610	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GATG	novel	NA	P-0001829-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	206	364	0	ENST00000375759.3:c.1058_1061dup	p.Leu355TrpfsTer5	p.L355Wfs*5	ENST00000375759	NM_015001.2	352	-/GATG	5/15	0.613456528018146	1	FACETS	0.833	0.779	0.887	0.833	0.779	0.887	CLONAL	1	TRUE	0	0.633841318943433	1		364	533	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332200	70332200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001829-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1308	577	939	0	ENST00000373644.4:c.105C>A	p.Asn35Lys	p.N35K	ENST00000373644	NM_030625.2	35	aaC/aaA	2/12	1	2	FACETS	0.966	0.926	1	0.966	0.926	1	CLONAL	1	TRUE	1	0.633841318943433	2		939	1885	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954022	32954023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs397507419	NA	P-0001829-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	242	495	12	ENST00000380152.3:c.9097dup	p.Thr3033AsnfsTer11	p.T3033Nfs*11	ENST00000380152		3030	aca/acAa	23/27	1	2	FACETS	0.819	0.766	0.874	0.819	0.766	0.874	CLONAL	1	TRUE	1	0.633841318943433	2		507	932	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372758	81372758	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001832-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	196	540	0	ENST00000222390.5:c.776A>G	p.Tyr259Cys	p.Y259C	ENST00000222390	NM_000601.4	259	tAt/tGt	7/18	0.21978866385471	3	FACETS	0.934	0.865	1	0.622	0.577	0.67	CLONAL	2	TRUE	0	0.276204800935476	3		540	865	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0001832-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	897	649	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.276204800935476	11	FACETS	1	0.99	1			1	CLONAL	9	TRUE	NA	0.276204800935476	11		649	1565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578414	7578414	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001832-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	177	657	0	ENST00000269305.4:c.516del	p.Val173Ter	p.V173*	ENST00000269305	NM_001126112.2	172	gtT/gt	5/11	0.276204800935476	3	FACETS	0.933	0.861	1	0.933	0.861	1	CLONAL	2	TRUE	1	0.276204800935476	3		657	782	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097199	11097200	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCCCT	rs372601826	NA	P-0001832-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	57	635	0	ENST00000358026.2:c.708_713dup	p.Gly243_Pro244dup	p.G243_P244dup	ENST00000358026	NM_001128849.1	243	-/GGCCCT	4/36	0.222674686116997	1	FACETS	0.548	0.47	0.634	0.548	0.47	0.634	SUBCLONAL	1	TRUE	0	0.276204800935476	1		635	649	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574027	7574027	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882028	NA	P-0001832-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	135	660	0	ENST00000269305.4:c.1000G>T	p.Gly334Trp	p.G334W	ENST00000269305	NM_001126112.2	334	Ggg/Tgg	10/11	0.276204800935476	3	FACETS	1	0.978	1	0.626	0.569	0.687	CLONAL	1	TRUE	1	0.276204800935476	3		660	888	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0001848-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	183	193	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.654217726583282	5	FACETS	0.933	0.873	0.993	0.933	0.873	0.993	CLONAL	3	FALSE	2	0.654217726583282	5		193	396	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121913370	NA	P-0001848-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	153	203	0	ENST00000288602.6:c.1742A>G	p.Asn581Ser	p.N581S	ENST00000288602	NM_004333.4	581	aAt/aGt	15/18	0.654217726583282	3	FACETS	0.992	0.924	1	0.992	0.924	1	CLONAL	2	FALSE	1	0.654217726583282	3		203	313	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100375	27100375	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001848-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	313	311	0	ENST00000324856.7:c.4087C>T	p.Gln1363Ter	p.Q1363*	ENST00000324856	NM_006015.4	1363	Caa/Taa	17/20	0.654217726583282	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	FALSE	0	0.654217726583282	3		311	405	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754846	57754846	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001848-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	127	364	0	ENST00000274289.3:c.344A>T	p.His115Leu	p.H115L	ENST00000274289	NM_006622.3	115	cAc/cTc	2/14	0.654217726583282	4	FACETS	1	0.924	1	0.51	0.463	0.559	CLONAL	1	FALSE	2	0.654217726583282	4		364	630	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119032	70119032	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001848-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	56	240	1	ENST00000245479.2:c.604G>A	p.Ala202Thr	p.A202T	ENST00000245479	NM_000346.3	202	Gcc/Acc	2/3	0.654217726583282	5	FACETS	0.532	0.455	0.616	0.177	0.151	0.206	SUBCLONAL	1	FALSE	2	0.654217726583282	5		241	638	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911143	40911143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370795038	NA	P-0001848-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	244	360	0	ENST00000373198.4:c.2162G>A	p.Arg721His	p.R721H	ENST00000373198	NM_133170.3	721	cGt/cAt	13/32	0.654217726583282	4	FACETS	0.966	0.908	1	0.966	0.908	1	CLONAL	2	FALSE	2	0.654217726583282	4		360	639	SUCCESS
AR	367	MSKCC	GRCh37	X	66905902	66905902	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001848-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	146	423	0	ENST00000374690.3:c.1819T>C	p.Phe607Leu	p.F607L	ENST00000374690	NM_000044.3	607	Ttc/Ctc	3/8	0.567002198742944	5	FACETS	1	0.972	1	0.384	0.35	0.419	CLONAL	1	FALSE	2	0.654217726583282	5		423	768	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713603	52713603	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001858-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	150	507	0	ENST00000394830.3:c.125del	p.Pro42GlnfsTer3	p.P42Qfs*3	ENST00000394830	NM_018313.4	42	cCa/ca	2/30	0.529589460617643	2	FACETS	0.892	0.835	0.948	0.892	0.835	0.948	CLONAL	2	TRUE	0	0.636957489209672	2		507	264	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0001871-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	39	219	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.124119125546388	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		219	238	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425503	49425503	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555187758	NA	P-0001871-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	48	490	0	ENST00000301067.7:c.12985C>T	p.Gln4329Ter	p.Q4329*	ENST00000301067	NM_003482.3	4329	Cag/Tag	39/54	0.124119125546388	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		490	471	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121241	29121241	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001871-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	40	569	0	ENST00000328354.6:c.434G>T	p.Arg145Leu	p.R145L	ENST00000328354	NM_007194.3	145	cGg/cTg	3/15	0.124119125546388	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		569	571	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918514	44918514	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001871-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	62	608	0	ENST00000377967.4:c.997C>T	p.Gln333Ter	p.Q333*	ENST00000377967	NM_021140.2	333	Cag/Tag	12/29	0.169667483328227	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		608	629	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184118	123184122	+	frameshift_variant	Frame_Shift_Del	DEL	GACAG	GACAG	A	novel	NA	P-0001871-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	46	547	0	ENST00000218089.9:c.976_980delinsA	p.Asp326IlefsTer3	p.D326Ifs*3	ENST00000218089	NM_001042749.1	326	GACAGt/At	11/35	0.169667483328227	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		547	589	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	132	287	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.31989787820967	4	FACETS	0.759	0.692	0.829			1	SUBCLONAL	2	TRUE	NA	0.451451221612488	4		287	559	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0001878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	248	472	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	0.21901527059467	3	FACETS	1	0.992	1	0.703	0.658	0.749	INDETERMINATE	1	TRUE	1	0.451451221612488	3		472	958	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665752	29665755	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1555535032	NA	P-0001878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	247	432	0	ENST00000356175.3:c.6789_6792del	p.Tyr2264ThrfsTer5	p.Y2264Tfs*5	ENST00000356175	NM_000267.3	2263	ACTTac/ac	45/57	0.21901527059467	3	FACETS	1	0.991	1	0.69	0.645	0.736	INDETERMINATE	1	TRUE	1	0.451451221612488	3		432	972	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0001878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	39	134	1	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	1	2	FACETS	0.793	0.663	0.934	0.793	0.663	0.934	CLONAL	1	TRUE	1	0.451451221612488	2		135	218	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216596	108216596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778080	NA	P-0001878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	254	417	0	ENST00000278616.4:c.8545C>T	p.Arg2849Ter	p.R2849*	ENST00000278616	NM_000051.3	2849	Cga/Tga	58/63	0.21901527059467	3	FACETS	1	0.992	1	0.699	0.655	0.745	INDETERMINATE	1	TRUE	1	0.451451221612488	3		417	986	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489534	56489534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775164134	NA	P-0001878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	206	450	0	ENST00000267101.3:c.1999C>T	p.Arg667Cys	p.R667C	ENST00000267101	NM_001982.3	667	Cgt/Tgt	17/28	0.21901527059467	3	FACETS	1	0.989	1	0.669	0.622	0.718	INDETERMINATE	1	TRUE	1	0.451451221612488	3		450	836	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818415	43818415	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	51	440	0	ENST00000372470.3:c.1880T>C	p.Leu627Pro	p.L627P	ENST00000372470	NM_005373.2	627	cTa/cCa	12/12	0.451451221612488	1	FACETS	0.291	0.247	0.34	0.291	0.247	0.34	SUBCLONAL	1	TRUE	0	0.451451221612488	1		440	601	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303788	65303788	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0001878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	220	360	0	ENST00000342505.4:c.2968-1G>T		p.X990_splice	ENST00000342505	NM_002227.2	990			0.293986523459433	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.451451221612488	1		360	655	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033780	48033780	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs267608094	NA	P-0001878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	38	371	0	ENST00000234420.5:c.3991C>T	p.Arg1331Ter	p.R1331*	ENST00000234420	NM_000179.2	1331	Cga/Tga	9/10	0.119748020680067	4	FACETS	0.329	0.271	0.395	0.165	0.135	0.198	INDETERMINATE	1	TRUE	2	0.451451221612488	4		371	742	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61724120	61724120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781425578	NA	P-0001878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	209	399	0	ENST00000401558.2:c.782G>A	p.Arg261Gln	p.R261Q	ENST00000401558	NM_003400.3	261	cGa/cAa	10/25	0.119748020680067	4	FACETS	0.81	0.753	0.868	0.81	0.753	0.868	INDETERMINATE	2	TRUE	2	0.451451221612488	4		399	830	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356269	66356269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200754741	NA	P-0001878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	272	465	0	ENST00000273854.3:c.1228G>A	p.Gly410Ser	p.G410S	ENST00000273854	NM_004439.5	410	Ggt/Agt	5/18	0.179977414820518	4	FACETS	0.848	0.796	0.901	0.848	0.796	0.901	INDETERMINATE	2	TRUE	2	0.451451221612488	4		465	1031	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535427	66535427	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1472517358	NA	P-0001878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	115	172	0	ENST00000273854.3:c.34C>T	p.Arg12Trp	p.R12W	ENST00000273854	NM_004439.5	12	Cgg/Tgg	1/18	0.179977414820518	4	FACETS	0.856	0.783	0.93	1	0.981	1	INDETERMINATE	3	TRUE	2	0.451451221612488	4		172	288	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167763	56167763	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	217	492	2	ENST00000399503.3:c.1328G>A	p.Cys443Tyr	p.C443Y	ENST00000399503	NM_005921.1	443	tGt/tAt	7/20	0.201682189628735	4	FACETS	1	0.991	1	0.711	0.661	0.763	INDETERMINATE	1	TRUE	2	0.451451221612488	4		494	981	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150022976	150022976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373625760	NA	P-0001878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	270	518	2	ENST00000253339.5:c.287G>A	p.Arg96Gln	p.R96Q	ENST00000253339		96	cGg/cAg	1/7	0.179977414820518	4	FACETS	0.815	0.765	0.867	0.815	0.765	0.867	INDETERMINATE	2	TRUE	2	0.451451221612488	4		520	1065	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959019	2959019	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	102	318	0	ENST00000396946.4:c.2497C>T	p.Pro833Ser	p.P833S	ENST00000396946	NM_032415.4	833	Ccc/Tcc	18/25	1	2	FACETS	0.895	0.804	0.991	0.895	0.804	0.991	CLONAL	1	TRUE	1	0.451451221612488	2		318	505	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476880	140476880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	159	371	0	ENST00000288602.6:c.1526G>A	p.Arg509Gln	p.R509Q	ENST00000288602	NM_004333.4	509	cGa/cAa	13/18	0.119748020680067	4	FACETS	1	0.987	1	0.712	0.654	0.772	INDETERMINATE	1	TRUE	2	0.451451221612488	4		371	718	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347829	347829	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	141	527	0	ENST00000262320.3:c.1677G>T	p.Gln559His	p.Q559H	ENST00000262320	NM_003502.3	559	caG/caT	6/11	1	2	FACETS	0.979	0.895	1	0.979	0.895	1	CLONAL	1	TRUE	1	0.451451221612488	2		527	638	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777897	3777897	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	170	497	0	ENST00000262367.5:c.7151A>G	p.His2384Arg	p.H2384R	ENST00000262367	NM_004380.2	2384	cAc/cGc	31/31	1	2	FACETS	0.972	0.895	1	0.972	0.895	1	CLONAL	1	TRUE	1	0.451451221612488	2		497	775	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983656	7983656	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	119	397	0	ENST00000319144.4:c.651G>T	p.Met217Ile	p.M217I	ENST00000319144	NM_001139.2	217	atG/atT	6/15	0.21901527059467	3	FACETS	1	0.957	1	0.55	0.498	0.605	INDETERMINATE	1	TRUE	1	0.451451221612488	3		397	587	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610622	10610622	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537634437	NA	P-0001878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	150	367	1	ENST00000171111.5:c.88G>A	p.Ala30Thr	p.A30T	ENST00000171111	NM_203500.1	30	Gcg/Acg	2/6	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.451451221612488	2		368	558	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292438	15292438	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs908559600	NA	P-0001878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	123	446	0	ENST00000263388.2:c.2741C>T	p.Pro914Leu	p.P914L	ENST00000263388	NM_000435.2	914	cCa/cTa	17/33	1	2	FACETS	0.865	0.784	0.95	0.865	0.784	0.95	CLONAL	1	TRUE	1	0.451451221612488	2		446	630	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092945	29092945	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	190	492	0	ENST00000328354.6:c.1039G>T	p.Asp347Tyr	p.D347Y	ENST00000328354	NM_007194.3	347	Gac/Tac	10/15	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.451451221612488	2		492	808	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092948	29092948	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs201206424	NA	P-0001878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	237	491	0	ENST00000328354.6:c.1036C>A	p.Arg346Ser	p.R346S	ENST00000328354	NM_007194.3	346	Cgt/Agt	10/15	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.451451221612488	2		491	794	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637699	52637700	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0001878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	487	432	0	ENST00000394830.3:c.2616dup	p.Ile873TyrfsTer2	p.I873Yfs*2	ENST00000394830	NM_018313.4	872	-/T	18/30	0.451451221612488	3	FACETS	0.865	0.831	0.899	0.865	0.831	0.899	CLONAL	3	TRUE	0	0.451451221612488	3		432	1019	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673750	176673750	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	189	462	0	ENST00000439151.2:c.4455del	p.Val1486Ter	p.V1486*	ENST00000439151	NM_022455.4	1484	Aaa/aa	10/23	1	2	FACETS	0.934	0.864	1	0.934	0.864	1	CLONAL	1	TRUE	1	0.451451221612488	2		462	896	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332273	70332273	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	252	588	0	ENST00000373644.4:c.184del	p.Thr62GlnfsTer13	p.T62Qfs*13	ENST00000373644	NM_030625.2	60	Aaa/aa	2/12	0.21901527059467	3	FACETS	1	0.992	1	0.695	0.65	0.74	INDETERMINATE	1	TRUE	1	0.451451221612488	3		588	985	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447086	49447087	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0001878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	222	387	0	ENST00000301067.7:c.857_858del	p.Ser286Ter	p.S286*	ENST00000301067	NM_003482.3	286	tCT/t	7/54	0.31989787820967	4	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.451451221612488	4		387	1002	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556463	29556463	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1567849208	NA	P-0001878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	150	215	0	ENST00000356175.3:c.2835del	p.Phe945LeufsTer9	p.F945Lfs*9	ENST00000356175	NM_000267.3	944	Ttt/tt	21/57	0.21901527059467	3	FACETS	1	0.987	1	0.702	0.645	0.762	INDETERMINATE	1	TRUE	1	0.451451221612488	3		215	580	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155373	106155373	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001879-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	36	660	0	ENST00000380013.4:c.274G>C	p.Gly92Arg	p.G92R	ENST00000380013	NM_001127208.2	92	Gga/Cga	3/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.744034676016245	2		660	77	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0001881-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	138	620	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	0.742606795702605	2		620	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0001881-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	297	552	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.742606795702605	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.742606795702605	3		552	339	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457209	25457209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs750515748	NA	P-0001881-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	81	582	0	ENST00000264709.3:c.2678G>A	p.Trp893Ter	p.W893*	ENST00000264709	NM_175629.2	893	tGg/tAg	23/23	0.164809597563277	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.742606795702605	0		582	178	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0001891-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	41	193	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.676089141730874	4	FACETS	0.656	0.548	0.774	0.219	0.182	0.258	SUBCLONAL	1	TRUE	1	0.676089141730874	4		193	310	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520776	176520776	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001891-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	214	196	0	ENST00000292408.4:c.1519G>T	p.Asp507Tyr	p.D507Y	ENST00000292408	NM_213647.1	507	Gac/Tac	11/18	0.676089141730874	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	3	TRUE	0	0.676089141730874	3		196	280	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140778	37140778	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001891-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	266	226	1	ENST00000373509.5:c.614G>T	p.Arg205Leu	p.R205L	ENST00000373509	NM_002648.3	205	cGa/cTa	5/6	0.339487863398708	4	FACETS	1	0.98	1	0.783	0.748	0.818	INDETERMINATE	3	TRUE	0	0.676089141730874	4		227	421	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739097	145739097	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs386833849	NA	P-0001891-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	114	128	0	ENST00000428558.2:c.2059-1G>A		p.X687_splice	ENST00000428558	NM_004260.3	687			0.676089141730874	5	FACETS	0.864	0.785	0.946	0.576	0.523	0.631	CLONAL	2	TRUE	2	0.676089141730874	5		128	393	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341727	8341727	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs369304072	NA	P-0001891-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	435	337	0	ENST00000356435.5:c.4913G>T	p.Gly1638Val	p.G1638V	ENST00000356435		1638	gGa/gTa	29/35	0.676089141730874	4	FACETS	0.979	0.944	1	0.979	0.944	1	CLONAL	3	TRUE	1	0.676089141730874	4		337	734	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518121	103518121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001891-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	135	179	0	ENST00000355739.4:c.2059G>A	p.Gly687Arg	p.G687R	ENST00000355739	NM_000123.3	687	Gga/Aga	9/15	0.282181269968081	3	FACETS	0.924	0.856	0.994	0.616	0.57	0.663	INDETERMINATE	2	TRUE	0	0.676089141730874	3		179	289	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577084	7577084	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121912667	NA	P-0001891-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	207	258	0	ENST00000269305.4:c.854A>T	p.Glu285Val	p.E285V	ENST00000269305	NM_001126112.2	285	gAg/gTg	8/11	0.672452339125065	2	FACETS	0.931	0.883	0.977	0.931	0.883	0.977	CLONAL	2	TRUE	0	0.676089141730874	2		258	329	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101079	41101079	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001891-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	243	257	0	ENST00000373198.4:c.1277A>G	p.Tyr426Cys	p.Y426C	ENST00000373198	NM_133170.3	426	tAc/tGc	8/32	0.469751417978242	4	FACETS	0.961	0.913	1	0.961	0.913	1	CLONAL	3	TRUE	1	0.676089141730874	4		257	418	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222996	1223003	+	frameshift_variant	Frame_Shift_Del	DEL	GAAACATC	GAAACATC	-	novel	NA	P-0001891-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	135	125	0	ENST00000326873.7:c.933_940del	p.Lys311AsnfsTer4	p.K311Nfs*4	ENST00000326873	NM_000455.4	311	aaGAAACATCct/aact	8/10	0.676089141730874	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.676089141730874	2		125	190	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0001906-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	554	800	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.615497949569007	3	FACETS	0.978	0.951	1	0.978	0.951	1	CLONAL	3	TRUE	0	0.634394341993337	3		800	784	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0001929-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	231	314	0	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.731961263642093	2		314	479	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0001929-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	229	620	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.731961263642093	2		620	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0001929-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	249	333	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.731961263642093	2		333	501	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0001949-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	347	374	0	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	0.543119939943794	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.570955510624981	2		374	567	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138452225	138452225	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001949-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	133	434	0	ENST00000289153.2:c.1028T>G	p.Leu343Arg	p.L343R	ENST00000289153	NM_006219.2	343	cTt/cGt	6/22	0.440655932207492	3	FACETS	0.634	0.575	0.696	0.317	0.287	0.348	SUBCLONAL	1	TRUE	1	0.570955510624981	3		434	945	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628545	187628545	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001949-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	120	412	0	ENST00000441802.2:c.2437G>C	p.Val813Leu	p.V813L	ENST00000441802	NM_005245.3	813	Gtc/Ctc	2/27	0.570955510624981	1	FACETS	0.601	0.545	0.659	0.601	0.545	0.659	SUBCLONAL	1	TRUE	0	0.570955510624981	1		412	500	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117737472	117737472	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001949-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	73	338	0	ENST00000368508.3:c.177A>T	p.Gln59His	p.Q59H	ENST00000368508	NM_002944.2	59	caA/caT	3/43	0.570955510624981	3	FACETS	0.352	0.307	0.401	0.176	0.153	0.201	SUBCLONAL	1	TRUE	1	0.570955510624981	3		338	933	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206845	162206845	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001949-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	176	336	0	ENST00000366898.1:c.830T>G	p.Phe277Cys	p.F277C	ENST00000366898	NM_004562.2	277	tTt/tGt	7/12	0.570955510624981	3	FACETS	0.894	0.824	0.967	0.447	0.412	0.484	CLONAL	1	TRUE	1	0.570955510624981	3		336	886	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538846	23538846	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746822077	NA	P-0001949-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	111	318	1	ENST00000380871.4:c.593C>T	p.Pro198Leu	p.P198L	ENST00000380871	NM_006167.3	198	cCg/cTg	2/2	0.49899490541475	1	FACETS	0.829	0.754	0.907	0.829	0.754	0.907	CLONAL	1	TRUE	0	0.570955510624981	1		319	335	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750936	128750936	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001949-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	120	329	0	ENST00000377970.2:c.473A>C	p.Lys158Thr	p.K158T	ENST00000377970	NM_002467.4	158	aAg/aCg	2/3	0.176891981663216	6	FACETS	0.791	0.717	0.869			1	INDETERMINATE	2	TRUE	NA	0.570955510624981	6		329	569	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484264	8484264	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001949-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	105	415	0	ENST00000356435.5:c.3268A>T	p.Asn1090Tyr	p.N1090Y	ENST00000356435		1090	Aac/Tac	19/35	0.362562806973651	4	FACETS	0.582	0.52	0.648	0.145	0.13	0.162	SUBCLONAL	1	TRUE	0	0.570955510624981	4		415	993	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500448	99500448	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001949-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	93	348	0	ENST00000268035.6:c.3881A>T	p.Asp1294Val	p.D1294V	ENST00000268035	NM_000875.3	1294	gAc/gTc	21/21	0.570955510624981	2	FACETS	0.699	0.624	0.778	0.35	0.312	0.389	SUBCLONAL	1	TRUE	0	0.570955510624981	2		348	466	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266069	41266101	+	inframe_deletion	In_Frame_Del	DEL	TAGTCACTGGCAGCAACAGTCTTACCTGGACTC	TAGTCACTGGCAGCAACAGTCTTACCTGGACTC	-	novel	NA	P-0001949-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	424	389	0	ENST00000349496.5:c.67_99del	p.Ser23_Ser33del	p.S23_S33del	ENST00000349496	NM_001904.3	22	gtTAGTCACTGGCAGCAACAGTCTTACCTGGACTCt/gtt	3/15	0.531756651043744	3	FACETS	0.842	0.809	0.874	0.842	0.809	0.874	CLONAL	3	TRUE	0	0.570955510624981	3		389	756	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391039	139391047	+	inframe_deletion	In_Frame_Del	DEL	CTGCTGGGT	CTGCTGGGT	-	novel	NA	P-0001949-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	61	292	0	ENST00000277541.6:c.7144_7152del	p.Thr2382_Gln2384del	p.T2382_Q2384del	ENST00000277541	NM_017617.3	2382	ACCCAGCAG/-	34/34	0.440655932207492	3	FACETS	0.569	0.491	0.653	0.284	0.245	0.327	SUBCLONAL	1	TRUE	1	0.570955510624981	3		292	483	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0001972-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	201	378	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.316226265384968	6	FACETS	0.845	0.788	0.903	0.845	0.788	0.903	INDETERMINATE	3	FALSE	3	0.555130667387763	6		378	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0001972-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	267	312	0	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	0.555130667387763	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	3	FALSE	0	0.555130667387763	3		312	408	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673769	30673769	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774126007	NA	P-0001972-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	70	328	0	ENST00000376406.3:c.3191C>T	p.Pro1064Leu	p.P1064L	ENST00000376406	NM_014641.2	1064	cCg/cTg	10/15	0.538146701129558	4	FACETS	0.794	0.694	0.902	0.265	0.231	0.301	CLONAL	1	FALSE	1	0.555130667387763	4		328	494	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425853	49425853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772665565	NA	P-0001972-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	81	312	1	ENST00000301067.7:c.12635G>A	p.Arg4212Gln	p.R4212Q	ENST00000301067	NM_003482.3	4212	cGg/cAg	39/54	0.24349751253146	3	FACETS	0.934	0.828	1			1	INDETERMINATE	1	FALSE	NA	0.555130667387763	3		313	399	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103520577	103520577	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001972-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	208	419	0	ENST00000355739.4:c.2648G>T	p.Gly883Val	p.G883V	ENST00000355739	NM_000123.3	883	gGg/gTg	12/15	0.555130667387763	4	FACETS	1	0.947	1			1	CLONAL	2	FALSE	NA	0.555130667387763	4		419	574	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312768	91312768	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001972-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	98	440	0	ENST00000355112.3:c.2507G>T	p.Arg836Met	p.R836M	ENST00000355112	NM_000057.2	836	aGg/aTg	12/22	0.555130667387763	5	FACETS	0.947	0.846	1	0.316	0.282	0.352	CLONAL	1	FALSE	2	0.555130667387763	5		440	683	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098588	11098588	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001972-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	201	202	0	ENST00000358026.2:c.1106A>T	p.Glu369Val	p.E369V	ENST00000358026	NM_001128849.1	369	gAg/gTg	6/36	0.555130667387763	5	FACETS	0.883	0.826	0.941			1	CLONAL	3	FALSE	NA	0.555130667387763	5		202	501	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39744979	39744979	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001972-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	221	414	0	ENST00000361337.2:c.1769G>A	p.Arg590His	p.R590H	ENST00000361337	NM_003286.2	590	cGt/cAt	17/21	0.442937573787614	6	FACETS	0.909	0.852	0.968	0.909	0.852	0.968	CLONAL	3	FALSE	3	0.555130667387763	6		414	616	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249013	55249014	+	protein_altering_variant	In_Frame_Ins	INS	-	-	GCACCC	novel	NA	P-0001972-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	3617	314	7	ENST00000275493.2:c.2311_2312insGCACCC	p.Asn771delinsSerThrHis	p.N771delinsSTH	ENST00000275493	NM_005228.3	771	aac/aGCACCCac	20/28	0.555130667387763	42	FACETS	1	0.995	1			1	CLONAL	41	FALSE	NA	0.555130667387763	42		321	3843	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0001982-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	294	317	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.879862719618251	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.879862719618251	1		317	363	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143011	47143011	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001982-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	384	354	0	ENST00000409792.3:c.4952T>G	p.Phe1651Cys	p.F1651C	ENST00000409792	NM_014159.6	1651	tTt/tGt	8/21	0.879862719618251	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.879862719618251	1		354	484	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368317	45368317	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1420438415	NA	P-0001982-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	256	270	1	ENST00000262160.6:c.1285C>T	p.Gln429Ter	p.Q429*	ENST00000262160	NM_005901.5	429	Cag/Tag	11/11	NA	2	FACETS	0.845	0.795	0.895			1	INDETERMINATE	1	TRUE	NA	0.879862719618251	2		271	689	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366276	15366276	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752762666	NA	P-0001982-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	228	350	0	ENST00000263377.2:c.1879G>A	p.Gly627Ser	p.G627S	ENST00000263377	NM_058243.2	627	Ggc/Agc	10/20	1	2	FACETS	0.87	0.816	0.924	0.87	0.816	0.924	CLONAL	1	TRUE	1	0.879862719618251	2		350	596	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933146	39933146	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001982-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	324	379	0	ENST00000378444.4:c.1453G>T	p.Glu485Ter	p.E485*	ENST00000378444	NM_001123385.1	485	Gaa/Taa	4/15	0.17552568518457	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.879862719618251	0		379	674	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15374289	15374289	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001995-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	342	528	0	ENST00000263377.2:c.1283A>G	p.Asn428Ser	p.N428S	ENST00000263377	NM_058243.2	428	aAc/aGc	7/20	1	2	FACETS	0.987	0.94	1	0.987	0.94	1	CLONAL	1	TRUE	1	0.902106556903004	2		528	768	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76931795	76931795	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0001995-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	205	508	0	ENST00000373344.5:c.3737-2A>G		p.X1246_splice	ENST00000373344	NM_000489.3	1246			0.902106556903004	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.902106556903004	1		508	242	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287424	46287424	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001995-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	191	437	0	ENST00000334344.6:c.5285del	p.Gly1762AspfsTer3	p.G1762Dfs*3	ENST00000334344	NM_152641.2	1761	gaG/ga	20/21	1	2	FACETS	0.98	0.918	1	0.98	0.918	1	CLONAL	1	TRUE	1	0.902106556903004	2		437	432	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021127	31021127	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002003-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	71	371	1	ENST00000375687.4:c.1126G>T	p.Gly376Cys	p.G376C	ENST00000375687	NM_015338.5	376	Ggc/Tgc	12/13	0.566467732628884	3	FACETS	0.991	0.872	1	0.495	0.436	0.558	CLONAL	1	TRUE	1	0.596273395924149	3		372	312	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66524020	66524030	+	frameshift_variant	Frame_Shift_Del	DEL	CTTAGTAAAGT	CTTAGTAAAGT	-	novel	NA	P-0002003-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	146	343	0	ENST00000358598.2:c.750_760del	p.Ser251TyrfsTer15	p.S251Yfs*15	ENST00000358598	NM_212471.2	250	CTTAGTAAAGTc/c	8/11	0.596273395924149	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.596273395924149	2		343	234	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0002010-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	236	675	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.9	0.846	0.955	0.9	0.846	0.955	CLONAL	1	TRUE	1	0.879853282875431	2		675	596	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404791	70404791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002010-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	748	327	0	ENST00000373644.4:c.2305G>A	p.Glu769Lys	p.E769K	ENST00000373644	NM_030625.2	769	Gaa/Aaa	4/12	0.819419602317018	4	FACETS	0.967	0.943	0.991	0.967	0.943	0.991	CLONAL	3	TRUE	1	0.879853282875431	4		327	1102	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223541	53223541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002010-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	134	182	0	ENST00000375401.3:c.3818C>T	p.Pro1273Leu	p.P1273L	ENST00000375401	NM_004187.3	1273	cCc/cTc	23/26	0.139195945673844	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.879853282875431	0		182	284	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088788	27088788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002010-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	438	313	0	ENST00000324856.7:c.2402del	p.Gly801ValfsTer32	p.G801Vfs*32	ENST00000324856	NM_006015.4	799	caG/ca	7/20	NA	2	FACETS	0.93	0.907	0.953			1	INDETERMINATE	2	TRUE	NA	0.879853282875431	2		313	535	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481471	40481471	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002010-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	575	688	0	ENST00000264657.5:c.1238T>G	p.Leu413Arg	p.L413R	ENST00000264657	NM_139276.2	413	cTg/cGg	14/24	NA	2	FACETS	0.972	0.935	1			1	INDETERMINATE	1	TRUE	NA	0.879853282875431	2		688	1345	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483982	212483982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002046-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	54	462	0	ENST00000342788.4:c.2221G>A	p.Gly741Arg	p.G741R	ENST00000342788	NM_005235.2	741	Gga/Aga	19/28	1	2	FACETS	0.68	0.582	0.788	0.68	0.582	0.788	SUBCLONAL	1	TRUE	1	0.345031090492826	2		462	460	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644679	134644679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773064927	NA	P-0002046-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	41	429	0	ENST00000398015.3:c.80C>T	p.Thr27Met	p.T27M	ENST00000398015	NM_004441.4	27	aCg/aTg	2/16	0.216350697374031	3	FACETS	0.478	0.397	0.568			1	SUBCLONAL	1	TRUE	NA	0.345031090492826	3		429	583	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	218	386	3	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	FALSE	NA	0.456901620948618	2		389	718	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394805	45394805	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	204	347	1	ENST00000262160.6:c.544C>T	p.Arg182Ter	p.R182*	ENST00000262160	NM_005901.5	182	Cga/Tga	5/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.456901620948618	2		348	639	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	154	305	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.456901620948618	2		305	515	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106078	27106078	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	114	254	0	ENST00000324856.7:c.5693del	p.Pro1898HisfsTer25	p.P1898Hfs*25	ENST00000324856	NM_006015.4	1897	Ccc/cc	20/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.456901620948618	2		254	381	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101099	27101099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	137	417	0	ENST00000324856.7:c.4381C>T	p.Arg1461Ter	p.R1461*	ENST00000324856	NM_006015.4	1461	Cga/Tga	18/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.456901620948618	2		417	465	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	161	425	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.456901620948618	2		425	612	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491273	2491273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771419721	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	123	276	0	ENST00000355716.4:c.316C>T	p.Arg106Cys	p.R106C	ENST00000355716	NM_003820.2	106	Cgc/Tgc	4/8	NA	2	FACETS	0.783	0.716	0.85			1	INDETERMINATE	2	FALSE	NA	0.456901620948618	2		276	344	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11273611	11273611	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	73	223	0	ENST00000361445.4:c.3130A>G	p.Met1044Val	p.M1044V	ENST00000361445	NM_004958.3	1044	Atg/Gtg	21/58	NA	2	FACETS	1	0.942	1			1	INDETERMINATE	1	FALSE	NA	0.456901620948618	2		223	288	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65316543	65316543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs961932195	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	129	293	1	ENST00000342505.4:c.1699G>A	p.Val567Ile	p.V567I	ENST00000342505	NM_002227.2	567	Gtc/Atc	12/25	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.456901620948618	2		294	440	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719178	61719178	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	133	363	0	ENST00000401558.2:c.1879C>T	p.Pro627Ser	p.P627S	ENST00000401558	NM_003400.3	627	Cct/Tct	16/25	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.456901620948618	2		363	515	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149795	202149795	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	57	400	0	ENST00000358485.4:c.1236A>C	p.Lys412Asn	p.K412N	ENST00000358485	NM_001080125.1	412	aaA/aaC	8/9	1	2	FACETS	0.561	0.482	0.646	0.561	0.482	0.646	SUBCLONAL	1	FALSE	1	0.456901620948618	2		400	445	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209103931	209103931	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	78	357	0	ENST00000345146.2:c.1018T>G	p.Leu340Val	p.L340V	ENST00000345146	NM_005896.2	340	Tta/Gta	9/10	1	2	FACETS	0.68	0.599	0.767	0.68	0.599	0.767	SUBCLONAL	1	FALSE	1	0.456901620948618	2		357	502	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278118	41278118	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	37	387	0	ENST00000349496.5:c.1994A>G	p.Asp665Gly	p.D665G	ENST00000349496	NM_001904.3	665	gAc/gGc	13/15	1	2	FACETS	0.288	0.237	0.346	0.288	0.237	0.346	SUBCLONAL	1	FALSE	1	0.456901620948618	2		387	562	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928347	69928347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	158	269	0	ENST00000352241.4:c.167G>A	p.Arg56His	p.R56H	ENST00000352241	NM_198159.2	56	cGc/cAc	2/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.456901620948618	2		269	515	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182681721	182681721	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	170	383	0	ENST00000292782.4:c.337A>C	p.Thr113Pro	p.T113P	ENST00000292782	NM_020640.2	113	Aca/Cca	3/7	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.456901620948618	2		383	627	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750572	41750572	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	100	379	2	ENST00000226382.2:c.56C>A	p.Ala19Asp	p.A19D	ENST00000226382	NM_003924.3	19	gCt/gAt	1/3	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.456901620948618	2		381	340	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111711	56111711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	23	22	0	ENST00000399503.3:c.311G>A	p.Gly104Asp	p.G104D	ENST00000399503	NM_005921.1	104	gGc/gAc	1/20	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	FALSE	1	0.456901620948618	2		22	78	SUCCESS
APC	324	MSKCC	GRCh37	5	112154998	112154998	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	160	383	0	ENST00000257430.4:c.1269G>A	p.Trp423Ter	p.W423*	ENST00000257430	NM_000038.5	423	tgG/tgA	10/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.456901620948618	2		383	588	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509457	149509457	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758072563	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	100	400	0	ENST00000261799.4:c.1442C>T	p.Thr481Met	p.T481M	ENST00000261799	NM_002609.3	481	aCg/aTg	10/23	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.456901620948618	2		400	381	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707573	176707573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554204064	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	27	341	0	ENST00000439151.2:c.5630G>A	p.Arg1877His	p.R1877H	ENST00000439151	NM_022455.4	1877	cGt/cAt	18/23	1	2	FACETS	0.248	0.197	0.307	0.248	0.197	0.307	SUBCLONAL	1	FALSE	1	0.456901620948618	2		341	476	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402537	20402537	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	52	140	1	ENST00000346618.3:c.74T>C	p.Val25Ala	p.V25A	ENST00000346618	NM_001949.4	25	gTc/gCc	1/7	NA	2	FACETS	1	0.867	1			1	INDETERMINATE	1	FALSE	NA	0.456901620948618	2		141	226	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005337	150005337	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	103	451	1	ENST00000253339.5:c.888G>A	p.Trp296Ter	p.W296*	ENST00000253339		296	tgG/tgA	3/7	1	2	FACETS	0.991	0.892	1	0.991	0.892	1	CLONAL	1	FALSE	1	0.456901620948618	2		452	455	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419955	152419955	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182943916	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	99	308	0	ENST00000206249.3:c.1642C>T	p.Arg548Cys	p.R548C	ENST00000206249	NM_000125.3	548	Cgc/Tgc	8/8	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.456901620948618	2		308	391	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469823	157469823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542660265	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	107	379	2	ENST00000346085.5:c.2617G>A	p.Gly873Ser	p.G873S	ENST00000346085	NM_020732.3	873	Ggt/Agt	9/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.456901620948618	2		381	409	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396316	139396316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1290643339	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	115	362	0	ENST00000277541.6:c.5522G>A	p.Arg1841Gln	p.R1841Q	ENST00000277541	NM_017617.3	1841	cGg/cAg	30/34	1	2	FACETS	0.782	0.713	0.852	1	0.987	1	SUBCLONAL	2	FALSE	1	0.456901620948618	2		362	322	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601972	43601972	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774829203	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	99	375	1	ENST00000355710.3:c.1016C>T	p.Ser339Leu	p.S339L	ENST00000355710	NM_020975.4	339	tCg/tTg	5/20	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	1	FALSE	NA	0.456901620948618	2		376	312	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625281	69625281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35983315	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	50	385	1	ENST00000334134.2:c.512G>A	p.Arg171His	p.R171H	ENST00000334134	NM_005247.2	171	cGc/cAc	3/3	0.288416080195312	0	FACETS	0.457	0.391	0.529			1	SUBCLONAL	1	FALSE	0	0.456901620948618	0		386	260	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392082	118392082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200134640	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	139	363	0	ENST00000534358.1:c.11593G>A	p.Val3865Ile	p.V3865I	ENST00000534358	NM_005933.3	3865	Gtc/Atc	35/36	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.456901620948618	2		363	417	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218912	133218912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1011938171	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	121	370	0	ENST00000320574.5:c.5024G>A	p.Arg1675His	p.R1675H	ENST00000320574	NM_006231.2	1675	cGc/cAc	38/49	1	2	FACETS	0.8	0.732	0.87	1	0.988	1	SUBCLONAL	2	FALSE	1	0.456901620948618	2		370	331	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254004	133254004	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1331349861	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	142	345	0	ENST00000320574.5:c.746G>A	p.Arg249Gln	p.R249Q	ENST00000320574	NM_006231.2	249	cGa/cAa	8/49	1	2	FACETS	0.754	0.694	0.816	1	0.988	1	SUBCLONAL	2	FALSE	1	0.456901620948618	2		345	412	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514619	103514619	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759875052	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	104	226	0	ENST00000355739.4:c.1120G>A	p.Ala374Thr	p.A374T	ENST00000355739	NM_000123.3	374	Gca/Aca	8/15	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	FALSE	1	0.456901620948618	2		226	447	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554314	81554314	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	143	442	0	ENST00000298171.2:c.334A>G	p.Arg112Gly	p.R112G	ENST00000298171	NM_000369.2	112	Agg/Ggg	4/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.456901620948618	2		442	533	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89825003	89825003	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	130	399	1	ENST00000389301.3:c.2963T>C	p.Leu988Pro	p.L988P	ENST00000389301	NM_000135.2	988	cTg/cCg	30/43	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	1	FALSE	NA	0.456901620948618	2		400	488	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989529	7989529	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1231568614	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	55	154	0	ENST00000319144.4:c.157T>C	p.Tyr53His	p.Y53H	ENST00000319144	NM_001139.2	53	Tac/Cac	2/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.456901620948618	2		154	190	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435372	56435372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	112	251	0	ENST00000407977.2:c.1765C>T	p.Pro589Ser	p.P589S	ENST00000407977		589	Cca/Tca	9/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.456901620948618	2		251	346	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440912	56440912	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	136	408	0	ENST00000407977.2:c.425C>T	p.Thr142Ile	p.T142I	ENST00000407977		142	aCt/aTt	4/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.456901620948618	2		408	485	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118988	70118988	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	93	353	1	ENST00000245479.2:c.560C>T	p.Ala187Val	p.A187V	ENST00000245479	NM_000346.3	187	gCg/gTg	2/3	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	FALSE	1	0.456901620948618	2		354	383	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78935205	78935205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138318172	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	83	315	0	ENST00000306801.3:c.3617C>T	p.Thr1206Met	p.T1206M	ENST00000306801	NM_020761.2	1206	aCg/aTg	31/34	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.456901620948618	2		315	273	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395776	45395776	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	158	244	0	ENST00000262160.6:c.358C>T	p.Arg120Ter	p.R120*	ENST00000262160	NM_005901.5	120	Cga/Tga	4/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.456901620948618	2		244	527	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216358	2216358	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370276763	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	83	301	0	ENST00000398665.3:c.2002G>A	p.Ala668Thr	p.A668T	ENST00000398665	NM_032482.2	668	Gcc/Acc	20/28	0.178451345066751	0	FACETS	0.854	0.767	0.944			1	INDETERMINATE	1	FALSE	0	0.456901620948618	0		301	231	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262079	10262079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762172122	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	120	399	2	ENST00000340748.4:c.2212G>A	p.Val738Ile	p.V738I	ENST00000340748		738	Gtc/Atc	23/40	0.178451345066751	0	FACETS	0.825	0.753	0.898			1	INDETERMINATE	1	FALSE	0	0.456901620948618	0		401	346	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290214	15290214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373181668	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	131	324	0	ENST00000263388.2:c.3421G>A	p.Val1141Met	p.V1141M	ENST00000263388	NM_000435.2	1141	Gtg/Atg	21/33	1	2	FACETS	0.817	0.751	0.885	1	0.989	1	CLONAL	2	FALSE	1	0.456901620948618	2		324	351	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309510	30309510	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	57	385	3	ENST00000307677.4:c.512C>T	p.Ala171Val	p.A171V	ENST00000307677	NM_138578.1	171	gCc/gTc	2/3	1	2	FACETS	0.435	0.373	0.502	0.435	0.373	0.502	SUBCLONAL	1	FALSE	1	0.456901620948618	2		388	574	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573302	41573302	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1297677732	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	126	395	0	ENST00000263253.7:c.5587C>T	p.Pro1863Ser	p.P1863S	ENST00000263253	NM_001429.3	1863	Cca/Tca	31/31	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.456901620948618	2		395	394	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156742	20156742	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	151	355	0	ENST00000379607.5:c.17-2A>G		p.X6_splice	ENST00000379607	NM_001412.3	6			NA	2	FACETS	1	0.978	1			1	INDETERMINATE	1	FALSE	NA	0.456901620948618	2		355	558	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930411	39930411	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs751015767	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	82	218	0	ENST00000378444.4:c.3053G>A	p.Arg1018His	p.R1018H	ENST00000378444	NM_001123385.1	1018	cGt/cAt	6/15	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	1	FALSE	NA	0.456901620948618	2		218	268	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651631	48651631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	118	467	0	ENST00000376670.3:c.797C>T	p.Thr266Met	p.T266M	ENST00000376670	NM_002049.3	266	aCg/aTg	5/6	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	FALSE	NA	0.456901620948618	2		467	363	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032153	48032154	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	127	393	1	ENST00000234420.5:c.3545_3546dup	p.Ile1183GlufsTer2	p.I1183Efs*2	ENST00000234420	NM_000179.2	1181	-/AG	6/10	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	1	0.456901620948618	2		394	533	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39644789	39644789	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	101	302	0	ENST00000262039.4:c.2522del	p.Lys841ArgfsTer8	p.K841Rfs*8	ENST00000262039	NM_002647.2	840	Aaa/aa	23/25	1	2	FACETS	0.773	0.693	0.858	0.773	0.693	0.858	SUBCLONAL	1	FALSE	1	0.456901620948618	2		302	572	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0002056-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	468	675	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.164819534154119	5	FACETS	1	0.988	1			1	INDETERMINATE	3	TRUE	NA	0.610165496596344	5		675	920	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680487	30680487	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002056-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	140	336	0	ENST00000376406.3:c.1232C>T	p.Ser411Leu	p.S411L	ENST00000376406	NM_014641.2	411	tCa/tTa	5/15	NA	2	FACETS	0.582	0.53	0.636			1	INDETERMINATE	1	TRUE	NA	0.610165496596344	2		336	789	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937175	39937175	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0002056-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	140	320	0	ENST00000378444.4:c.8C>G	p.Ser3Ter	p.S3*	ENST00000378444	NM_001123385.1	3	tCa/tGa	2/15	0.610165496596344	3	FACETS	0.684	0.622	0.748			1	SUBCLONAL	1	TRUE	NA	0.610165496596344	3		320	876	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0002069-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	425	611	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.256133745645655	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.270023253159825	3		611	1105	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2969624	2969624	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0002069-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	239	381	0	ENST00000396946.4:c.1653+2T>A		p.X551_splice	ENST00000396946	NM_032415.4	551			0.220219971835376	4	FACETS	0.918	0.86	0.978	0.918	0.86	0.978	CLONAL	3	TRUE	1	0.270023253159825	4		381	816	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14028655	14028655	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002069-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	374	604	0	ENST00000405192.2:c.23A>C	p.Gln8Pro	p.Q8P	ENST00000405192	NM_001163147.1	8	cAa/cCa	2/12	0.220219971835376	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	3	TRUE	1	0.270023253159825	4		604	1146	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174885	11174885	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002079-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	145	382	0	ENST00000361445.4:c.7149G>C	p.Leu2383Phe	p.L2383F	ENST00000361445	NM_004958.3	2383	ttG/ttC	52/58	1	2	FACETS	0.866	0.79	0.946	0.866	0.79	0.946	CLONAL	1	TRUE	1	0.354743142081869	2		382	944	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259291	16259291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002079-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	79	118	1	ENST00000375759.3:c.6556G>A	p.Ala2186Thr	p.A2186T	ENST00000375759	NM_015001.2	2186	Gcc/Acc	11/15	1	2	FACETS	0.994	0.878	1	0.994	0.878	1	CLONAL	1	TRUE	1	0.354743142081869	2		119	448	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101324	27101324	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs999125494	NA	P-0002079-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	189	284	0	ENST00000324856.7:c.4606G>C	p.Asp1536His	p.D1536H	ENST00000324856	NM_006015.4	1536	Gat/Cat	18/20	1	2	FACETS	0.927	0.856	1	0.927	0.856	1	CLONAL	1	TRUE	1	0.354743142081869	2		284	1149	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512166	120512166	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002079-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	176	259	0	ENST00000256646.2:c.1076C>T	p.Ser359Phe	p.S359F	ENST00000256646	NM_024408.3	359	tCc/tTc	6/34	1	2	FACETS	0.886	0.815	0.96	0.886	0.815	0.96	CLONAL	1	TRUE	1	0.354743142081869	2		259	1120	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914629	32914629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002079-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	147	295	0	ENST00000380152.3:c.6137C>T	p.Ser2046Leu	p.S2046L	ENST00000380152		2046	tCa/tTa	11/27	0.325915091269661	2	FACETS	1	0.974	1	0.58	0.531	0.632	CLONAL	1	TRUE	0	0.354743142081869	2		295	714	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630494	90630494	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002079-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	123	274	0	ENST00000330062.3:c.817C>G	p.His273Asp	p.H273D	ENST00000330062	NM_002168.2	273	Cac/Gac	7/11	1	2	FACETS	0.795	0.719	0.876	0.795	0.719	0.876	SUBCLONAL	1	TRUE	1	0.354743142081869	2		274	872	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874399	151874401	+	stop_gained	Nonsense_Mutation	TNP	ATC	ATC	TTA	novel	NA	P-0002079-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	607	341	1	ENST00000262189.6:c.8137_8139delinsTAA	p.Asp2713Ter	p.D2713*	ENST00000262189	NM_170606.2	2713	GAT/TAA	38/59	0.354743142081869	7	FACETS	0.925	0.889	0.962			1	CLONAL	4	TRUE	NA	0.354743142081869	7		342	1745	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057520005	NA	P-0002100-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	476	533	0	ENST00000269305.4:c.820G>T	p.Val274Phe	p.V274F	ENST00000269305	NM_001126112.2	274	Gtt/Ttt	8/11	0.342886711098482	4	FACETS	1	0.982	1			1	CLONAL	4	TRUE	NA	0.476416732597115	4		533	722	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20483019	20483019	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766868785	NA	P-0002107-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	71	290	7	ENST00000346618.3:c.752G>A	p.Gly251Asp	p.G251D	ENST00000346618	NM_001949.4	251	gGc/gAc	4/7	0.3	2	FACETS	0.908	0.795	1			1	CLONAL	1	TRUE	NA	0.34	2		297	460	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431615	6431615	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002107-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	45	196	5	ENST00000356142.4:c.168G>A	p.Trp56Ter	p.W56*	ENST00000356142	NM_018890.3	56	tgG/tgA	3/7	1	2	FACETS	0.82	0.692	0.959	0.82	0.692	0.959	CLONAL	1	TRUE	1	0.34	2		201	323	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557752	21557752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002107-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	95	460	15	ENST00000382592.4:c.2093C>T	p.Thr698Ile	p.T698I	ENST00000382592	NM_014572.2	698	aCc/aTc	5/8	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.34	2		475	546	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478612	99478612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002107-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	83	422	13	ENST00000268035.6:c.3254G>A	p.Gly1085Asp	p.G1085D	ENST00000268035	NM_000875.3	1085	gGc/gAc	17/21	1	2	FACETS	0.83	0.734	0.934	0.83	0.734	0.934	CLONAL	1	TRUE	1	0.34	2		435	588	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779044	3779044	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1194053924	NA	P-0002107-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	41	139	4	ENST00000262367.5:c.6004G>A	p.Val2002Met	p.V2002M	ENST00000262367	NM_004380.2	2002	Gtg/Atg	31/31	1	2	FACETS	0.887	0.743	1	0.887	0.743	1	CLONAL	1	TRUE	1	0.34	2		143	272	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231366	5231366	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002107-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	62	264	7	ENST00000357368.4:c.2110C>T	p.Pro704Ser	p.P704S	ENST00000357368	NM_002850.3	704	Cca/Tca	14/38	1	2	FACETS	0.89	0.771	1	0.89	0.771	1	CLONAL	1	TRUE	1	0.34	2		271	410	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41489033	41489033	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1264361255	NA	P-0002107-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	121	343	10	ENST00000263253.7:c.25G>A	p.Gly9Arg	p.G9R	ENST00000263253	NM_001429.3	9	Ggg/Agg	1/31	0.3	2	FACETS	1	0.951	1			1	CLONAL	1	TRUE	NA	0.34	2		353	660	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159750	20159750	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002127-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	349	151	0	ENST00000379607.5:c.9G>C	p.Lys3Asn	p.K3N	ENST00000379607	NM_001412.3	3	aaG/aaC	1/7	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.678842623387873	1		151	502	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266821	198266829	+	inframe_deletion	In_Frame_Del	DEL	ATGGTCCGA	ATGGTCCGA	-	novel	NA	P-0002127-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	367	402	0	ENST00000335508.6:c.2103_2111del	p.Arg702_Ile704del	p.R702_I704del	ENST00000335508	NM_012433.2	701	gtTCGGACCATc/gtc	15/25	1	2	FACETS	0.87	0.825	0.916	0.87	0.825	0.916	CLONAL	1	TRUE	1	0.678842623387873	2		402	1243	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0002133-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	90	675	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	NA	2	FACETS	1	0.904	1			1	INDETERMINATE	1	TRUE	NA	0.486378657179014	2		675	366	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101468	27101468	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002133-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	64	476	0	ENST00000324856.7:c.4750C>T	p.Gln1584Ter	p.Q1584*	ENST00000324856	NM_006015.4	1584	Cag/Tag	18/20	0.486378657179014	1	FACETS	0.823	0.722	0.93	0.823	0.722	0.93	CLONAL	1	TRUE	0	0.486378657179014	1		476	242	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867305	68867306	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0002133-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	103	463	0	ENST00000261769.5:c.2553dup	p.Glu852ArgfsTer9	p.E852Rfs*9	ENST00000261769	NM_004360.3	851	tca/tcAa	16/16	0.486378657179014	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.486378657179014	1		463	289	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645693	12645693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397516827	NA	P-0002140-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	95	259	0	ENST00000251849.4:c.776C>T	p.Ser259Phe	p.S259F	ENST00000251849	NM_002880.3	259	tCc/tTc	7/17	0.195649440845546	4	FACETS	0.763	0.682	0.85	0.763	0.682	0.85	SUBCLONAL	2	FALSE	2	0.312225990888019	4		259	523	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0002140-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	115	358	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.290613755411931	4	FACETS	1	0.983	1			1	CLONAL	1	FALSE	NA	0.312225990888019	4		358	657	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935633	13935633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756650303	NA	P-0002140-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	44	316	0	ENST00000405192.2:c.1223G>A	p.Arg408His	p.R408H	ENST00000405192	NM_001163147.1	408	cGt/cAt	12/12	1	2	FACETS	0.673	0.565	0.792	0.673	0.565	0.792	SUBCLONAL	1	FALSE	1	0.312225990888019	2		316	419	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453987	140453987	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002140-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	88	324	0	ENST00000288602.6:c.1741A>T	p.Asn581Tyr	p.N581Y	ENST00000288602	NM_004333.4	581	Aat/Tat	14/18	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.312225990888019	2		324	472	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727483	66727483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504317	NA	P-0002140-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	85	302	0	ENST00000307102.5:c.199G>A	p.Asp67Asn	p.D67N	ENST00000307102	NM_002755.3	67	Gac/Aac	2/11	0.238060461050754	4	FACETS	0.787	0.698	0.881			1	SUBCLONAL	2	FALSE	NA	0.312225990888019	4		302	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876659675	NA	P-0002140-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	90	247	0	ENST00000269305.4:c.764T>G	p.Ile255Ser	p.I255S	ENST00000269305	NM_001126112.2	255	aTc/aGc	7/11	0.269875988420293	2	FACETS	1	0.976	1	0.678	0.605	0.755	CLONAL	1	FALSE	0	0.312225990888019	2		247	425	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240810	53240810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002140-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	61	377	0	ENST00000375401.3:c.1270G>A	p.Glu424Lys	p.E424K	ENST00000375401	NM_004187.3	424	Gag/Aag	10/26	0.312225990888019	0	FACETS	0.686	0.594	0.785			1	SUBCLONAL	1	FALSE	0	0.312225990888019	0		377	392	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0002150-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	25	417	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		417	1030	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0002160-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	167	418	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.225528383982593	2	FACETS	0.848	0.781	0.918	0.848	0.781	0.918	CLONAL	2	TRUE	0	0.27	2		418	729	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412964	49412964	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002160-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	185	567	0	ENST00000418115.1:c.59G>T	p.Cys20Phe	p.C20F	ENST00000418115	NM_001664.2	20	tGc/tTc	2/5	0.213310542204782	2	FACETS	1	0.989	1	0.716	0.661	0.773	CLONAL	1	TRUE	0	0.27	2		567	957	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584524	189584524	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002160-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	97	428	0	ENST00000264731.3:c.820C>G	p.Gln274Glu	p.Q274E	ENST00000264731	NM_003722.4	274	Cag/Gag	6/14	0.267770581685588	4	FACETS	1	0.946	1	0.551	0.491	0.615	CLONAL	1	TRUE	2	0.27	4		428	828	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518162	187518162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002160-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	131	453	0	ENST00000441802.2:c.12532G>A	p.Gly4178Arg	p.G4178R	ENST00000441802	NM_005245.3	4178	Ggg/Agg	25/27	0.297051106907124	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.27	1		453	580	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163695	32163695	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002160-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	49	180	0	ENST00000375023.3:c.5531G>C	p.Arg1844Pro	p.R1844P	ENST00000375023	NM_004557.3	1844	cGg/cCg	30/30	0.297051106907124	4	FACETS	1	0.869	1			1	CLONAL	1	TRUE	NA	0.27	4		180	449	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366500	118366500	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1350646662	NA	P-0002160-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	162	408	0	ENST00000534358.1:c.5449A>G	p.Thr1817Ala	p.T1817A	ENST00000534358	NM_005933.3	1817	Act/Gct	19/36	0.225528383982593	2	FACETS	0.777	0.714	0.843	0.777	0.714	0.843	SUBCLONAL	2	TRUE	0	0.27	2		408	772	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878151	48878151	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778869	NA	P-0002160-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	23	47	0	ENST00000267163.4:c.103C>T	p.Gln35Ter	p.Q35*	ENST00000267163	NM_000321.2	35	Cag/Tag	1/27	0.185287306591842	3	FACETS	1	0.906	1	0.436	0.343	0.54	CLONAL	1	TRUE	0	0.27	3		47	148	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	360007	360007	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002160-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	79	443	0	ENST00000262320.3:c.1082A>T	p.Gln361Leu	p.Q361L	ENST00000262320	NM_003502.3	361	cAg/cTg	4/11	0.241857654538465	2	FACETS	0.948	0.835	1	0.474	0.417	0.535	CLONAL	1	TRUE	0	0.27	2		443	617	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118581	11118581	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002160-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	80	220	1	ENST00000358026.2:c.2005G>T	p.Glu669Ter	p.E669*	ENST00000358026	NM_001128849.1	669	Gag/Tag	14/36	0.297051106907124	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.27	1		221	359	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123742	11123742	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002160-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	117	363	0	ENST00000358026.2:c.2392G>T	p.Glu798Ter	p.E798*	ENST00000358026	NM_001128849.1	798	Gag/Tag	16/36	0.297051106907124	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.27	1		363	587	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220237	55220238	+	splice_acceptor_variant	Splice_Site	DNP	AG	AG	CC	novel	NA	P-0002160-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	99	423	0	ENST00000275493.2:c.629-2_629-1delinsCC		p.X210_splice	ENST00000275493	NM_005228.3	210			0.204714064345352	3	FACETS	1	0.968	1	0.608	0.543	0.678	CLONAL	1	TRUE	1	0.27	3		423	684	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44919298	44919300	+	missense_variant	Missense_Mutation	TNP	TAC	TAC	CAA	novel	NA	P-0002160-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	41	135	0	ENST00000377967.4:c.1226_1228delinsCAA	p.Leu409_Gln410delinsProLys	p.L409_Q410delinsPK	ENST00000377967	NM_021140.2	409	cTACag/cCAAag	13/29	1	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.27	1		135	211	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41011079	41011079	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	323	607	0	ENST00000267868.3:c.512T>C	p.Leu171Pro	p.L171P	ENST00000267868	NM_002875.4	171	cTg/cCg	6/10	0.669118151888494	3	FACETS	0.915	0.871	0.96	0.915	0.871	0.96	CLONAL	2	TRUE	1	0.669118151888494	3		607	704	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519068	66519068	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0002177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	104	320	0	ENST00000358598.2:c.348+1G>T		p.X116_splice	ENST00000358598	NM_212471.2	116			0.669118151888494	5	FACETS	1	0.9	1	0.334	0.3	0.371	CLONAL	1	TRUE	2	0.669118151888494	5		320	621	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631246	117631250	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TACAT	TACAT	-	novel	NA	P-0002177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	124	458	0	ENST00000368508.3:c.6428_6432del	p.Asp2143ValfsTer25	p.D2143Vfs*25	ENST00000368508	NM_002944.2	2143	gATGTA/g	40/43	0.669118151888494	2	FACETS	1	0.934	1	0.512	0.468	0.557	CLONAL	1	TRUE	0	0.669118151888494	2		458	362	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431439	49431439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	239	791	4	ENST00000301067.7:c.9700G>A	p.Asp3234Asn	p.D3234N	ENST00000301067	NM_003482.3	3234	Gac/Aac	34/54	0.535798213264506	4	FACETS	1	0.989	1	0.42	0.392	0.449	CLONAL	1	TRUE	1	0.669118151888494	4		795	946	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028766	42028766	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	153	585	0	ENST00000219905.7:c.4304A>G	p.Asp1435Gly	p.D1435G	ENST00000219905	NM_001164273.1	1435	gAt/gGt	13/24	0.669118151888494	3	FACETS	0.932	0.855	1	0.466	0.427	0.506	CLONAL	1	TRUE	1	0.669118151888494	3		585	655	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437882	52437882	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	159	838	0	ENST00000460680.1:c.1279G>C	p.Gly427Arg	p.G427R	ENST00000460680	NM_004656.3	427	Ggg/Cgg	13/17	0.669118151888494	3	FACETS	0.76	0.697	0.826	0.38	0.348	0.413	SUBCLONAL	1	TRUE	1	0.669118151888494	3		838	834	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973802	15973802	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002183-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	149	347	0	ENST00000268712.3:c.4190C>G	p.Ser1397Cys	p.S1397C	ENST00000268712	NM_006311.3	1397	tCt/tGt	31/46	0.337516570051689	2	FACETS	1	0.969	1	0.558	0.512	0.606	CLONAL	1	TRUE	0	0.466031593160767	2		347	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578280	+	frameshift_variant	Frame_Shift_Del	DEL	AGATGCTGAGGAG	AGATGCTGAGGAG	-	novel	NA	P-0002183-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	280	385	0	ENST00000269305.4:c.569_581del	p.Pro190LeufsTer53	p.P190Lfs*53	ENST00000269305	NM_001126112.2	190	cCTCCTCAGCATCTt/ct	6/11	0.337516570051689	2	FACETS	0.977	0.926	1	0.977	0.926	1	CLONAL	2	TRUE	0	0.466031593160767	2		385	615	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003747	45003747	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs1057519877	NA	P-0002193-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	196	417	1	ENST00000558401.1:c.3G>A	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	atG/atA	1/4	0.12980693985076	1	FACETS	0.681	0.629	0.735	0.681	0.629	0.735	INDETERMINATE	1	TRUE	0	0.39	1		418	1188	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0002208-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	267	265	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.522696587486887	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.545184342961859	2		267	486	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197766	66197766	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002208-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	162	496	1	ENST00000273854.3:c.2933A>G	p.Lys978Arg	p.K978R	ENST00000273854	NM_004439.5	978	aAg/aGg	17/18	0.545184342961859	1	FACETS	0.628	0.578	0.681	0.628	0.578	0.681	SUBCLONAL	1	TRUE	0	0.545184342961859	1		497	688	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002211-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	191	380	0	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	0.309144993020445	3	FACETS	0.794	0.735	0.856	0.794	0.735	0.856	SUBCLONAL	2	TRUE	1	0.309144993020445	3		380	898	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106916	27106917	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0002211-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	92	351	0	ENST00000324856.7:c.6527_6528del	p.Gln2176ArgfsTer48	p.Q2176Rfs*48	ENST00000324856	NM_006015.4	2176	cAG/c	20/20	0.231720851032444	4	FACETS	0.962	0.854	1	0.481	0.427	0.539	CLONAL	1	TRUE	2	0.309144993020445	4		351	810	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0002218-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2311	506	385	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.380838088734245	8	FACETS	1	0.962	1			1	CLONAL	2	TRUE	NA	0.380838088734245	8		385	2817	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0002218-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2463	91	362	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.380838088734245	8	FACETS	0.401	0.354	0.452			1	SUBCLONAL	1	TRUE	NA	0.380838088734245	8		362	2554	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121912651	NA	P-0002218-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	456	326	0	ENST00000269305.4:c.742C>G	p.Arg248Gly	p.R248G	ENST00000269305	NM_001126112.2	248	Cgg/Ggg	7/11	0.37898950614917	2	FACETS	0.981	0.938	1	0.981	0.938	1	CLONAL	2	TRUE	0	0.380838088734245	2		326	1220	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867546	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGC	GGCGGCGGC	-	rs11466445	NA	P-0002218-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	10	6	0	ENST00000374994.4:c.70_78del	p.Ala24_Ala26del	p.A24_A26del	ENST00000374994	NM_004612.2	17	ctGGCGGCGGCg/ctg	1/9	0.223270516474361	1	FACETS	0.709	0.49	0.971	0.709	0.49	0.971	INDETERMINATE	1	TRUE	0	0.380838088734245	1		6	60	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941696	48941696	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002218-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	203	314	2	ENST00000267163.4:c.1010del	p.Leu337TrpfsTer12	p.L337Wfs*12	ENST00000267163	NM_000321.2	336	Ttt/tt	10/27	0.380838088734245	1	FACETS	0.961	0.892	1	0.961	0.892	1	CLONAL	1	TRUE	0	0.380838088734245	1		316	898	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873202	71873202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002218-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1996	145	630	0	ENST00000357731.5:c.992C>T	p.Ser331Phe	p.S331F	ENST00000357731	NM_173808.2	331	tCc/tTc	7/7	0.37898950614917	2	FACETS	0.356	0.323	0.391	0.178	0.161	0.196	SUBCLONAL	1	TRUE	0	0.380838088734245	2		630	2141	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652168	36652168	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002218-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	70	229	0	ENST00000244741.5:c.290C>T	p.Thr97Ile	p.T97I	ENST00000244741	NM_000389.4	97	aCc/aTc	2/3	1	2	FACETS	0.433	0.377	0.494	0.433	0.377	0.494	SUBCLONAL	1	TRUE	1	0.380838088734245	2		229	849	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121438948	121438948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146855738	NA	P-0002225-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1181	171	736	0	ENST00000257555.6:c.1849G>A	p.Val617Ile	p.V617I	ENST00000257555		617	Gtc/Atc	10/10	1	2	FACETS	0.783	0.719	0.851	0.783	0.719	0.851	SUBCLONAL	1	TRUE	1	0.322875149116782	2		736	1352	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349127	11349127	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002225-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	84	144	0	ENST00000332029.2:c.209C>T	p.Ala70Val	p.A70V	ENST00000332029	NM_003745.1	70	gCc/gTc	2/2	0.332067103604205	3	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.322875149116782	3		144	414	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843395	128843395	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146797066	NA	P-0002225-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	115	389	0	ENST00000249373.3:c.502C>T	p.Arg168Cys	p.R168C	ENST00000249373	NM_005631.4	168	Cgc/Tgc	2/12	0.332067103604205	3	FACETS	0.965	0.869	1	0.483	0.434	0.534	CLONAL	1	TRUE	1	0.322875149116782	3		389	857	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147543	47147543	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002254-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	181	645	0	ENST00000409792.3:c.4783G>T	p.Glu1595Ter	p.E1595*	ENST00000409792	NM_014159.6	1595	Gag/Tag	6/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.389709962880677	2		645	799	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361115	66361115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002254-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	176	715	0	ENST00000273854.3:c.1057G>A	p.Ala353Thr	p.A353T	ENST00000273854	NM_004439.5	353	Gca/Aca	4/18	1	2	FACETS	0.99	0.913	1	0.99	0.913	1	CLONAL	1	TRUE	1	0.389709962880677	2		715	912	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771171	161771171	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853056	NA	P-0002254-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	118	681	0	ENST00000366898.1:c.1358G>A	p.Trp453Ter	p.W453*	ENST00000366898	NM_004562.2	453	tGg/tAg	12/12	1	2	FACETS	0.929	0.84	1	0.929	0.84	1	CLONAL	1	TRUE	1	0.389709962880677	2		681	652	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0002274-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	137	395	0	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	0.488944348485926	3	FACETS	0.903	0.843	0.963	0.903	0.843	0.963	CLONAL	3	TRUE	0	0.533920850059746	3		395	240	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913355	NA	P-0002274-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	15	410	0	ENST00000288602.6:c.1406G>T	p.Gly469Val	p.G469V	ENST00000288602	NM_004333.4	469	gGa/gTa	11/18	0.533920850059746	3	FACETS	0.574	0.424	0.751	0.287	0.212	0.376	SUBCLONAL	1	TRUE	1	0.533920850059746	3		410	124	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057781	27057781	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002274-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	93	672	0	ENST00000324856.7:c.1489C>T	p.Gln497Ter	p.Q497*	ENST00000324856	NM_006015.4	497	Caa/Taa	3/20	0.383411051405651	3	FACETS	1	0.966	1	0.751	0.684	0.818	CLONAL	2	TRUE	0	0.533920850059746	3		672	196	SUCCESS
ATR	545	MSKCC	GRCh37	3	142286929	142286929	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002274-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	31	445	0	ENST00000350721.4:c.127C>T	p.Arg43Trp	p.R43W	ENST00000350721	NM_001184.3	43	Cgg/Tgg	2/47	0.48590976212486	2	FACETS	0.528	0.43	0.637	0.264	0.215	0.319	SUBCLONAL	1	TRUE	0	0.533920850059746	2		445	220	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430427	181430427	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002274-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	32	594	0	ENST00000325404.1:c.279G>T	p.Glu93Asp	p.E93D	ENST00000325404	NM_003106.3	93	gaG/gaT	1/1	0.48590976212486	2	FACETS	0.624	0.511	0.749	0.312	0.255	0.375	SUBCLONAL	1	TRUE	0	0.533920850059746	2		594	192	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518038	187518038	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002274-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	55	510	0	ENST00000441802.2:c.12656A>C	p.Lys4219Thr	p.K4219T	ENST00000441802	NM_005245.3	4219	aAg/aCg	25/27	0.533920850059746	3	FACETS	1	0.864	1	0.5	0.432	0.573	CLONAL	1	TRUE	1	0.533920850059746	3		510	261	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629345	187629345	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1373737710	NA	P-0002274-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	51	498	0	ENST00000441802.2:c.1637C>T	p.Pro546Leu	p.P546L	ENST00000441802	NM_005245.3	546	cCg/cTg	2/27	0.533920850059746	3	FACETS	0.964	0.827	1	0.482	0.413	0.556	CLONAL	1	TRUE	1	0.533920850059746	3		498	251	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760384	133760384	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002274-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	115	440	0	ENST00000318560.5:c.2707C>G	p.Pro903Ala	p.P903A	ENST00000318560	NM_005157.4	903	Cca/Gca	11/11	0.36863745416705	3	FACETS	0.919	0.853	0.984	0.919	0.853	0.984	CLONAL	3	TRUE	0	0.533920850059746	3		440	198	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002284-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	594	327	0	ENST00000269305.4:c.859G>T	p.Glu287Ter	p.E287*	ENST00000269305	NM_001126112.2	287	Gag/Tag	8/11	0.488544842443824	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	4	TRUE	0	0.534626473583404	4		327	845	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199469669	NA	P-0002284-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	391	402	2	ENST00000374080.3:c.130G>T	p.Gly44Cys	p.G44C	ENST00000374080		44	Ggt/Tgt	2/45	NA	2	FACETS	0.91	0.87	0.949			1	INDETERMINATE	2	TRUE	NA	0.534626473583404	2		404	804	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0002290-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	307	576	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.409930666997578	3	FACETS	0.852	0.809	0.896	0.852	0.809	0.896	CLONAL	3	TRUE	0	0.407898164043669	3		576	709	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222704	69222704	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002290-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	47	505	0	ENST00000462284.1:c.677C>A	p.Ser226Ter	p.S226*	ENST00000462284	NM_002392.5	226	tCg/tAg	8/11	0.407898164043669	4	FACETS	0.609	0.513	0.714	0.304	0.256	0.357	SUBCLONAL	1	TRUE	2	0.407898164043669	4		505	533	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	343	620	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.550344284086373	3	FACETS	0.881	0.839	0.923			1	CLONAL	2	TRUE	NA	0.687231195544166	3		620	761	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233052	55233052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201498575	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	110	317	2	ENST00000275493.2:c.1802G>A	p.Gly601Glu	p.G601E	ENST00000275493	NM_005228.3	601	gGa/gAa	15/28	0.204651245506855	3	FACETS	0.96	0.868	1	0.32	0.289	0.352	INDETERMINATE	1	TRUE	0	0.687231195544166	3		319	448	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	71	469	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	NA	2	FACETS	0.384	0.335	0.436			1	INDETERMINATE	1	TRUE	NA	0.687231195544166	2		469	538	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074151	8074151	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748264404	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1244	76	863	0	ENST00000377482.5:c.508G>A	p.Glu170Lys	p.E170K	ENST00000377482	NM_018948.3	170	Gag/Aag	4/4	0.236147765781193	3	FACETS	0.225	0.196	0.256			1	INDETERMINATE	1	TRUE	NA	0.687231195544166	3		863	1320	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781572	9781572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1287221059	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	118	351	0	ENST00000377346.4:c.1882G>A	p.Glu628Lys	p.E628K	ENST00000377346	NM_005026.3	628	Gag/Aag	15/24	0.318780323493478	1	FACETS	0.716	0.655	0.778	0.716	0.655	0.778	INDETERMINATE	1	TRUE	0	0.687231195544166	1		351	315	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300494	11300494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	142	468	0	ENST00000361445.4:c.1652C>T	p.Pro551Leu	p.P551L	ENST00000361445	NM_004958.3	551	cCc/cTc	11/58	0.318780323493478	1	FACETS	0.654	0.601	0.707	0.654	0.601	0.707	INDETERMINATE	1	TRUE	0	0.687231195544166	1		468	415	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242707	16242707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	106	674	2	ENST00000375759.3:c.1328G>A	p.Gly443Asp	p.G443D	ENST00000375759	NM_015001.2	443	gGc/gAc	6/15	0.692995481861713	3	FACETS	0.371	0.331	0.413			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	3		676	1118	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258308	16258308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	163	403	0	ENST00000375759.3:c.5573C>T	p.Pro1858Leu	p.P1858L	ENST00000375759	NM_015001.2	1858	cCt/cTt	11/15	0.692995481861713	3	FACETS	0.914	0.842	0.99			1	CLONAL	1	TRUE	NA	0.687231195544166	3		403	697	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262153	16262153	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	26	77	0	ENST00000375759.3:c.9418C>T	p.Pro3140Ser	p.P3140S	ENST00000375759	NM_015001.2	3140	Ccg/Tcg	11/15	0.692995481861713	3	FACETS	0.997	0.807	1			1	CLONAL	1	TRUE	NA	0.687231195544166	3		77	102	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932077	36932077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769614883	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	54	622	1	ENST00000361632.4:c.2392G>A	p.Gly798Arg	p.G798R	ENST00000361632		798	Ggg/Agg	16/16	0.17736393676166	1	FACETS	0.19	0.162	0.22	0.19	0.162	0.22	INDETERMINATE	1	TRUE	0	0.687231195544166	1		623	544	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932146	36932146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	153	622	0	ENST00000361632.4:c.2323C>T	p.Pro775Ser	p.P775S	ENST00000361632		775	Ccc/Tcc	16/16	0.17736393676166	1	FACETS	0.568	0.522	0.614	0.568	0.522	0.614	INDETERMINATE	1	TRUE	0	0.687231195544166	1		622	515	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366904	40366904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	35	374	0	ENST00000397332.2:c.293G>A	p.Cys98Tyr	p.C98Y	ENST00000397332	NM_001033082.2	98	tGc/tAc	2/3	0.17736393676166	1	FACETS	0.218	0.179	0.262	0.218	0.179	0.262	INDETERMINATE	1	TRUE	0	0.687231195544166	1		374	306	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511644	46511644	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	63	446	0	ENST00000262741.5:c.1133G>A	p.Gly378Asp	p.G378D	ENST00000262741	NM_003629.3	378	gGt/gAt	9/10	NA	2	FACETS	0.296	0.256	0.34			1	INDETERMINATE	1	TRUE	NA	0.687231195544166	2		446	619	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301190	65301190	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	39	366	0	ENST00000342505.4:c.3259-1G>A		p.X1087_splice	ENST00000342505	NM_002227.2	1087			NA	2	FACETS	0.251	0.207	0.299			1	INDETERMINATE	1	TRUE	NA	0.687231195544166	2		366	453	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303670	65303670	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	147	590	0	ENST00000342505.4:c.3085G>A	p.Glu1029Lys	p.E1029K	ENST00000342505	NM_002227.2	1029	Gaa/Aaa	22/25	NA	2	FACETS	0.791	0.726	0.858			1	INDETERMINATE	1	TRUE	NA	0.687231195544166	2		590	541	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332803	65332803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	32	507	2	ENST00000342505.4:c.736G>A	p.Asp246Asn	p.D246N	ENST00000342505	NM_002227.2	246	Gat/Aat	7/25	NA	2	FACETS	0.165	0.133	0.201			1	INDETERMINATE	1	TRUE	NA	0.687231195544166	2		509	565	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414456	78414456	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	39	389	2	ENST00000370768.2:c.1930C>T	p.Gln644Ter	p.Q644*	ENST00000370768	NM_003902.3	644	Caa/Taa	20/20	NA	2	FACETS	0.183	0.151	0.219			1	INDETERMINATE	1	TRUE	NA	0.687231195544166	2		391	620	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429995	78429995	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	62	361	1	ENST00000370768.2:c.884G>A	p.Gly295Glu	p.G295E	ENST00000370768	NM_003902.3	295	gGa/gAa	11/20	NA	2	FACETS	0.279	0.241	0.321			1	INDETERMINATE	1	TRUE	NA	0.687231195544166	2		362	646	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458381	120458381	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781030729	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	25	195	0	ENST00000256646.2:c.6964C>T	p.Pro2322Ser	p.P2322S	ENST00000256646	NM_024408.3	2322	Ccc/Tcc	34/34	0.662175203007836	5	FACETS	0.382	0.3	0.475	0.127	0.1	0.159	SUBCLONAL	1	TRUE	2	0.687231195544166	5		195	387	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458897	120458897	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	69	429	0	ENST00000256646.2:c.6448C>T	p.Pro2150Ser	p.P2150S	ENST00000256646	NM_024408.3	2150	Cct/Tct	34/34	0.662175203007836	5	FACETS	0.399	0.346	0.456	0.133	0.115	0.152	SUBCLONAL	1	TRUE	2	0.687231195544166	5		429	1023	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480515	120480515	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553195968	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	72	465	0	ENST00000256646.2:c.3302C>T	p.Pro1101Leu	p.P1101L	ENST00000256646	NM_024408.3	1101	cCc/cTc	20/34	0.662175203007836	5	FACETS	0.389	0.338	0.443	0.13	0.112	0.148	SUBCLONAL	1	TRUE	2	0.687231195544166	5		465	1095	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120496175	120496175	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1678	222	692	0	ENST00000256646.2:c.2356G>A	p.Gly786Ser	p.G786S	ENST00000256646	NM_024408.3	786	Ggc/Agc	14/34	0.662175203007836	5	FACETS	0.691	0.64	0.743	0.23	0.213	0.248	SUBCLONAL	1	TRUE	2	0.687231195544166	5		692	1900	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658383	206658383	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	67	296	0	ENST00000367120.3:c.1477G>A	p.Ala493Thr	p.A493T	ENST00000367120	NM_014002.3	493	Gca/Aca	14/22	0.662175203007836	5	FACETS	0.628	0.545	0.717	0.209	0.181	0.239	SUBCLONAL	1	TRUE	2	0.687231195544166	5		296	631	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226553663	226553663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	60	359	1	ENST00000366794.5:c.2497G>A	p.Val833Ile	p.V833I	ENST00000366794	NM_001618.3	833	Gtc/Atc	18/23	0.495935630927764	4	FACETS	0.5	0.431	0.576			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	4		360	589	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226553705	226553705	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	44	435	0	ENST00000366794.5:c.2455A>G	p.Lys819Glu	p.K819E	ENST00000366794	NM_001618.3	819	Aag/Gag	18/23	0.495935630927764	4	FACETS	0.334	0.279	0.395			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	4		435	647	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226595516	226595516	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142025196	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	25	264	0	ENST00000366794.5:c.115G>A	p.Val39Met	p.V39M	ENST00000366794	NM_001618.3	39	Gtg/Atg	1/23	0.495935630927764	4	FACETS	0.279	0.219	0.348			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	4		264	440	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082962	16082962	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1421384102	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	15	101	0	ENST00000281043.3:c.776C>T	p.Thr259Ile	p.T259I	ENST00000281043	NM_005378.4	259	aCc/aTc	2/3	0.236147765781193	3	FACETS	0.319	0.234	0.42			1	INDETERMINATE	1	TRUE	NA	0.687231195544166	3		101	184	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469513	25469513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	36	381	0	ENST00000264709.3:c.1255C>T	p.Pro419Ser	p.P419S	ENST00000264709	NM_175629.2	419	Cct/Tct	10/23	0.692995481861713	3	FACETS	0.267	0.219	0.321			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	3		381	527	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026045	48026045	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553412354	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	62	408	0	ENST00000234420.5:c.923G>A	p.Gly308Asp	p.G308D	ENST00000234420	NM_000179.2	308	gGc/gAc	4/10	0.379504209707308	5	FACETS	0.451	0.389	0.519	0.15	0.129	0.173	INDETERMINATE	1	TRUE	2	0.687231195544166	5		408	812	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032048	48032048	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	83	473	0	ENST00000234420.5:c.3439-1G>A		p.X1147_splice	ENST00000234420	NM_000179.2	1147			0.379504209707308	5	FACETS	0.464	0.408	0.524	0.155	0.136	0.175	INDETERMINATE	1	TRUE	2	0.687231195544166	5		473	1058	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050386	128050386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1438551749	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	67	340	0	ENST00000285398.2:c.271C>T	p.Pro91Ser	p.P91S	ENST00000285398	NM_000122.1	91	Cca/Tca	3/15	0.519766403004828	4	FACETS	0.417	0.361	0.477	0.208	0.18	0.239	SUBCLONAL	1	TRUE	2	0.687231195544166	4		340	789	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519922	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1394	281	690	0	ENST00000397062.3:c.235G>A	p.Glu79Lys	p.E79K	ENST00000397062	NM_006164.4	79	Gag/Aag	2/5	0.519766403004828	4	FACETS	0.824	0.771	0.878	0.412	0.385	0.439	CLONAL	1	TRUE	2	0.687231195544166	4		690	1675	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209103933	209103933	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	49	445	0	ENST00000345146.2:c.1016G>A	p.Gly339Glu	p.G339E	ENST00000345146	NM_005896.2	339	gGg/gAg	9/10	0.550344284086373	3	FACETS	0.247	0.209	0.29			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	3		445	775	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645750	215645750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	51	437	0	ENST00000260947.4:c.848C>T	p.Ala283Val	p.A283V	ENST00000260947	NM_000465.2	283	gCt/gTt	4/11	0.631266676992801	2	FACETS	0.233	0.198	0.273	0.117	0.099	0.137	SUBCLONAL	1	TRUE	0	0.687231195544166	2		437	636	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090054	37090054	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750610	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	206	570	0	ENST00000231790.2:c.1943C>T	p.Pro648Leu	p.P648L	ENST00000231790	NM_000249.3	648	cCc/cTc	17/19	0.692995481861713	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.687231195544166	1		570	374	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277885	41277885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1168206875	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	61	502	2	ENST00000349496.5:c.1849G>A	p.Val617Ile	p.V617I	ENST00000349496	NM_001904.3	617	Gtc/Atc	12/15	NA	2	FACETS	0.315	0.272	0.363			1	INDETERMINATE	1	TRUE	NA	0.687231195544166	2		504	563	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664991	138664991	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	12	59	0	ENST00000330315.3:c.574C>T	p.Pro192Ser	p.P192S	ENST00000330315	NM_023067.3	192	Ccc/Tcc	1/1	NA	2	FACETS	0.492	0.352	0.657			1	INDETERMINATE	1	TRUE	NA	0.687231195544166	2		59	71	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430717	181430717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1297025198	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	104	203	0	ENST00000325404.1:c.569G>A	p.Gly190Asp	p.G190D	ENST00000325404	NM_003106.3	190	gGc/gAc	1/1	0.692995481861713	3	FACETS	0.888	0.799	0.981	0.444	0.399	0.491	CLONAL	1	TRUE	1	0.687231195544166	3		203	458	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503690	186503690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	206	735	1	ENST00000323963.5:c.367G>A	p.Ala123Thr	p.A123T	ENST00000323963		123	Gca/Aca	5/11	0.692995481861713	3	FACETS	0.716	0.663	0.771	0.358	0.331	0.386	SUBCLONAL	1	TRUE	1	0.687231195544166	3		736	1125	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561690	55561690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1307431391	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	62	288	0	ENST00000288135.5:c.80C>T	p.Pro27Leu	p.P27L	ENST00000288135	NM_000222.2	27	cCa/cTa	2/21	0.687231195544166	7	FACETS	0.644	0.556	0.741			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	7		288	761	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55569990	55569990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1472	166	551	0	ENST00000288135.5:c.857G>A	p.Gly286Glu	p.G286E	ENST00000288135	NM_000222.2	286	gGa/gAa	5/21	0.677196063483317	5	FACETS	0.599	0.548	0.653			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	5		551	1638	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594063	55594063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	92	366	0	ENST00000288135.5:c.1849G>A	p.Ala617Thr	p.A617T	ENST00000288135	NM_000222.2	617	Gcc/Acc	12/21	0.677196063483317	5	FACETS	0.484	0.428	0.543			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	5		366	1124	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535405	66535405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	29	170	0	ENST00000273854.3:c.56G>A	p.Gly19Asp	p.G19D	ENST00000273854	NM_004439.5	19	gGc/gAc	1/18	0.692995481861713	2	FACETS	0.389	0.314	0.473	0.194	0.157	0.237	SUBCLONAL	1	TRUE	0	0.687231195544166	2		170	217	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99809048	99809048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	236	546	0	ENST00000280892.6:c.337C>T	p.Leu113Phe	p.L113F	ENST00000280892	NM_001130678.1	113	Ctt/Ttt	4/7	0.692995481861713	2	FACETS	0.973	0.912	1	0.486	0.456	0.518	CLONAL	1	TRUE	0	0.687231195544166	2		546	706	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164791	106164791	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750669382	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	51	268	0	ENST00000380013.4:c.3659C>T	p.Thr1220Ile	p.T1220I	ENST00000380013	NM_001127208.2	1220	aCc/aTc	6/11	0.692995481861713	2	FACETS	0.419	0.358	0.486	0.21	0.179	0.243	SUBCLONAL	1	TRUE	0	0.687231195544166	2		268	354	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180877	106180877	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	145	488	0	ENST00000380013.4:c.3905G>T	p.Arg1302Ile	p.R1302I	ENST00000380013	NM_001127208.2	1302	aGa/aTa	7/11	0.692995481861713	2	FACETS	0.644	0.589	0.701	0.322	0.294	0.351	SUBCLONAL	1	TRUE	0	0.687231195544166	2		488	655	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541939	187541939	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1373349051	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	26	479	0	ENST00000441802.2:c.5801G>A	p.Gly1934Asp	p.G1934D	ENST00000441802	NM_005245.3	1934	gGt/gAt	10/27	0.692995481861713	2	FACETS	0.156	0.123	0.194	0.078	0.061	0.097	SUBCLONAL	1	TRUE	0	0.687231195544166	2		479	484	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294567	1294567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	16	93	0	ENST00000310581.5:c.434G>A	p.Gly145Asp	p.G145D	ENST00000310581	NM_198253.2	145	gGc/gAc	2/16	0.692995481861713	1	FACETS	0.322	0.241	0.415	0.322	0.241	0.415	SUBCLONAL	1	TRUE	0	0.687231195544166	1		93	95	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873633	35873633	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	132	430	0	ENST00000303115.3:c.589C>T	p.Pro197Ser	p.P197S	ENST00000303115	NM_002185.3	197	Ccg/Tcg	5/8	0.692995481861713	2	FACETS	0.835	0.764	0.909	0.418	0.382	0.455	CLONAL	1	TRUE	0	0.687231195544166	2		430	460	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963132	38963132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167728976	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	131	396	1	ENST00000357387.3:c.1412C>T	p.Ala471Val	p.A471V	ENST00000357387	NM_152756.3	471	gCa/gTa	17/38	0.236147765781193	3	FACETS	0.854	0.777	0.934			1	INDETERMINATE	1	TRUE	NA	0.687231195544166	3		397	600	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167820	56167820	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	93	395	0	ENST00000399503.3:c.1385G>A	p.Gly462Asp	p.G462D	ENST00000399503	NM_005921.1	462	gGc/gAc	7/20	0.692995481861713	4	FACETS	0.411	0.364	0.461	0.205	0.182	0.231	SUBCLONAL	1	TRUE	2	0.687231195544166	4		395	1112	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184141	56184141	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1365	115	485	0	ENST00000399503.3:c.4346G>A	p.Trp1449Ter	p.W1449*	ENST00000399503	NM_005921.1	1449	tGg/tAg	19/20	0.692995481861713	4	FACETS	0.382	0.342	0.424	0.191	0.171	0.212	SUBCLONAL	1	TRUE	2	0.687231195544166	4		485	1480	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755707	57755707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746929950	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	94	261	0	ENST00000274289.3:c.80G>A	p.Gly27Glu	p.G27E	ENST00000274289	NM_006622.3	27	gGa/gAa	1/14	0.692995481861713	4	FACETS	0.777	0.693	0.867	0.389	0.346	0.434	SUBCLONAL	1	TRUE	2	0.687231195544166	4		261	594	SUCCESS
APC	324	MSKCC	GRCh37	5	112178700	112178700	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	61	520	0	ENST00000257430.4:c.7409G>A	p.Arg2470Lys	p.R2470K	ENST00000257430	NM_000038.5	2470	aGa/aAa	16/16	0.692995481861713	2	FACETS	0.318	0.274	0.366	0.159	0.137	0.183	SUBCLONAL	1	TRUE	0	0.687231195544166	2		520	558	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694650	176694650	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	74	557	0	ENST00000439151.2:c.5234G>A	p.Cys1745Tyr	p.C1745Y	ENST00000439151	NM_022455.4	1745	tGc/tAc	15/23	0.692995481861713	1	FACETS	0.347	0.305	0.392	0.347	0.305	0.392	SUBCLONAL	1	TRUE	0	0.687231195544166	1		557	407	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681897	30681897	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755140078	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	22	262	0	ENST00000376406.3:c.200C>T	p.Pro67Leu	p.P67L	ENST00000376406	NM_014641.2	67	cCc/cTc	3/15	1	2	FACETS	0.205	0.158	0.258	0.205	0.158	0.258	SUBCLONAL	1	TRUE	1	0.687231195544166	2		262	313	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289116	33289116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	40	304	0	ENST00000374542.5:c.436G>A	p.Ala146Thr	p.A146T	ENST00000374542	NM_001141970.1	146	Gcc/Acc	3/8	0.692995481861713	3	FACETS	0.389	0.323	0.462	0.195	0.161	0.231	SUBCLONAL	1	TRUE	1	0.687231195544166	3		304	402	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793673	89793673	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	82	576	0	ENST00000336032.3:c.742C>T	p.Gln248Ter	p.Q248*	ENST00000336032	NM_006813.2	248	Cag/Tag	2/2	0.692995481861713	3	FACETS	0.287	0.252	0.325	0.144	0.126	0.163	SUBCLONAL	1	TRUE	1	0.687231195544166	3		576	1117	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100258	157100258	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	16	66	0	ENST00000346085.5:c.1195G>A	p.Ala399Thr	p.A399T	ENST00000346085	NM_020732.3	399	Gcg/Acg	1/20	0.37978172760471	1	FACETS	0.456	0.346	0.58	0.456	0.346	0.58	INDETERMINATE	1	TRUE	0	0.687231195544166	1		66	67	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222526	157222526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	42	461	1	ENST00000346085.5:c.1793G>A	p.Gly598Glu	p.G598E	ENST00000346085	NM_020732.3	598	gGa/gAa	4/20	0.37978172760471	1	FACETS	0.174	0.145	0.206	0.174	0.145	0.206	INDETERMINATE	1	TRUE	0	0.687231195544166	1		462	462	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502163	157502163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	49	247	0	ENST00000346085.5:c.3196G>A	p.Glu1066Lys	p.E1066K	ENST00000346085	NM_020732.3	1066	Gag/Aag	12/20	0.37978172760471	1	FACETS	0.331	0.282	0.384	0.331	0.282	0.384	INDETERMINATE	1	TRUE	0	0.687231195544166	1		247	283	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528201	157528201	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	36	300	1	ENST00000346085.5:c.5926G>A	p.Gly1976Arg	p.G1976R	ENST00000346085	NM_020732.3	1976	Ggg/Agg	20/20	0.37978172760471	1	FACETS	0.257	0.212	0.306	0.257	0.212	0.306	INDETERMINATE	1	TRUE	0	0.687231195544166	1		301	268	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969966	161969966	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	23	351	1	ENST00000366898.1:c.1003C>T	p.Pro335Ser	p.P335S	ENST00000366898	NM_004562.2	335	Cct/Tct	9/12	0.37978172760471	1	FACETS	0.142	0.111	0.179	0.142	0.111	0.179	INDETERMINATE	1	TRUE	0	0.687231195544166	1		352	309	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206834	162206834	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	49	398	0	ENST00000366898.1:c.841C>T	p.Pro281Ser	p.P281S	ENST00000366898	NM_004562.2	281	Cct/Tct	7/12	0.37978172760471	1	FACETS	0.228	0.193	0.266	0.228	0.193	0.266	INDETERMINATE	1	TRUE	0	0.687231195544166	1		398	410	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951805	2951805	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	23	462	1	ENST00000396946.4:c.3144+1G>A		p.X1048_splice	ENST00000396946	NM_032415.4	1048			0.639100234678085	1	FACETS	0.171	0.133	0.214	0.171	0.133	0.214	SUBCLONAL	1	TRUE	0	0.687231195544166	1		463	257	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55238907	55238907	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	48	432	0	ENST00000275493.2:c.1919+1G>A		p.X640_splice	ENST00000275493	NM_005228.3	640			0.204651245506855	3	FACETS	0.31	0.262	0.364	0.103	0.087	0.122	INDETERMINATE	1	TRUE	0	0.687231195544166	3		432	605	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346575	81346575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1306	71	535	1	ENST00000222390.5:c.1378C>T	p.Pro460Ser	p.P460S	ENST00000222390	NM_000601.4	460	Cct/Tct	11/18	0.367053762628839	6	FACETS	0.356	0.309	0.407	0.119	0.103	0.136	INDETERMINATE	1	TRUE	3	0.687231195544166	6		536	1377	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346589	81346589	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1274	80	561	0	ENST00000222390.5:c.1364G>A	p.Gly455Glu	p.G455E	ENST00000222390	NM_000601.4	455	gGa/gAa	11/18	0.367053762628839	6	FACETS	0.408	0.358	0.463	0.136	0.119	0.155	INDETERMINATE	1	TRUE	3	0.687231195544166	6		561	1354	SUCCESS
MET	4233	MSKCC	GRCh37	7	116414994	116414994	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5389	1062	512	0	ENST00000397752.3:c.3088G>T	p.Asp1030Tyr	p.D1030Y	ENST00000397752	NM_000245.2	1030	Gac/Tac	15/21	0.687231195544166	22	FACETS	0.943	0.912	0.975			1	CLONAL	4	TRUE	NA	0.687231195544166	22		512	6451	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879226	151879226	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	84	457	1	ENST00000262189.6:c.5719C>T	p.Pro1907Ser	p.P1907S	ENST00000262189	NM_170606.2	1907	Cca/Tca	36/59	0.685621440877242	5	FACETS	0.412	0.362	0.466			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	5		458	1205	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945037	151945037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	17	166	0	ENST00000262189.6:c.2482C>T	p.Pro828Ser	p.P828S	ENST00000262189	NM_170606.2	828	Cca/Tca	14/59	0.550344284086373	3	FACETS	0.327	0.245	0.425			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	3		166	203	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	42	434	0	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	0.692995481861713	3	FACETS	0.27	0.224	0.32	0.135	0.112	0.16	SUBCLONAL	1	TRUE	1	0.687231195544166	3		434	609	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868983	117868983	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	167	637	0	ENST00000297338.2:c.716G>A	p.Gly239Asp	p.G239D	ENST00000297338	NM_006265.2	239	gGc/gAc	7/14	0.550344284086373	3	FACETS	0.574	0.526	0.624			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	3		637	1138	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484118	8484118	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	37	388	1	ENST00000356435.5:c.3413+1G>A		p.X1138_splice	ENST00000356435		1138			NA	2	FACETS	0.218	0.179	0.261			1	INDETERMINATE	1	TRUE	NA	0.687231195544166	2		389	495	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486262	8486262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	148	386	0	ENST00000356435.5:c.2555C>T	p.Pro852Leu	p.P852L	ENST00000356435		852	cCt/cTt	17/35	NA	2	FACETS	0.861	0.792	0.933			1	INDETERMINATE	1	TRUE	NA	0.687231195544166	2		386	500	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97888862	97888862	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	122	514	0	ENST00000289081.3:c.845C>T	p.Pro282Leu	p.P282L	ENST00000289081	NM_000136.2	282	cCt/cTt	9/15	0.692995481861713	4	FACETS	0.565	0.509	0.623			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	4		514	1061	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760264	133760264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064159	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	32	229	0	ENST00000318560.5:c.2587G>A	p.Gly863Arg	p.G863R	ENST00000318560	NM_005157.4	863	Ggg/Agg	11/11	NA	2	FACETS	0.457	0.373	0.549			1	INDETERMINATE	1	TRUE	NA	0.687231195544166	2		229	204	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787668	135787668	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs118203470	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	82	539	1	ENST00000298552.3:c.913+1G>A		p.X305_splice	ENST00000298552	NM_001162426.1	305			NA	2	FACETS	0.37	0.326	0.417			1	INDETERMINATE	1	TRUE	NA	0.687231195544166	2		540	645	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390572	139390572	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	117	547	0	ENST00000277541.6:c.7619C>T	p.Pro2540Leu	p.P2540L	ENST00000277541	NM_017617.3	2540	cCc/cTc	34/34	NA	2	FACETS	0.776	0.704	0.85			1	INDETERMINATE	1	TRUE	NA	0.687231195544166	2		547	439	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623713	43623713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	52	333	0	ENST00000355710.3:c.3341G>A	p.Ser1114Asn	p.S1114N	ENST00000355710	NM_020975.4	1114	aGt/aAt	20/20	0.495935630927764	4	FACETS	0.392	0.333	0.456			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	4		333	652	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274699	123274699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	117	487	0	ENST00000358487.5:c.1219C>T	p.Pro407Ser	p.P407S	ENST00000358487	NM_000141.4	407	Cca/Tca	9/18	0.674948078753537	1	FACETS	0.523	0.475	0.573	0.523	0.475	0.573	SUBCLONAL	1	TRUE	0	0.687231195544166	1		487	427	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115514	108115514	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	36	312	0	ENST00000278616.4:c.663-1G>A		p.X221_splice	ENST00000278616	NM_000051.3	221			0.692995481861713	2	FACETS	0.224	0.184	0.27	0.112	0.092	0.135	SUBCLONAL	1	TRUE	0	0.687231195544166	2		312	467	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121696	108121696	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	95	609	0	ENST00000278616.4:c.1504G>T	p.Ala502Ser	p.A502S	ENST00000278616	NM_000051.3	502	Gct/Tct	10/63	0.692995481861713	2	FACETS	0.364	0.324	0.407	0.182	0.162	0.204	SUBCLONAL	1	TRUE	0	0.687231195544166	2		609	760	SUCCESS
ATM	472	MSKCC	GRCh37	11	108137929	108137929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs552010421	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	47	478	0	ENST00000278616.4:c.2498G>A	p.Gly833Glu	p.G833E	ENST00000278616	NM_000051.3	833	gGa/gAa	17/63	0.692995481861713	2	FACETS	0.215	0.181	0.253	0.108	0.09	0.127	SUBCLONAL	1	TRUE	0	0.687231195544166	2		478	635	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198459	108198459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	60	404	1	ENST00000278616.4:c.7063G>A	p.Val2355Ile	p.V2355I	ENST00000278616	NM_000051.3	2355	Gtc/Atc	48/63	0.692995481861713	2	FACETS	0.372	0.321	0.428	0.186	0.16	0.214	SUBCLONAL	1	TRUE	0	0.687231195544166	2		405	469	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344593	118344593	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064797056	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	110	785	0	ENST00000534358.1:c.2719C>T	p.Pro907Ser	p.P907S	ENST00000534358	NM_005933.3	907	Cct/Tct	3/36	0.692995481861713	2	FACETS	0.397	0.356	0.44	0.198	0.178	0.22	SUBCLONAL	1	TRUE	0	0.687231195544166	2		785	807	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118345019	118345019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	44	216	0	ENST00000534358.1:c.3145C>T	p.Pro1049Ser	p.P1049S	ENST00000534358	NM_005933.3	1049	Ccc/Tcc	3/36	0.692995481861713	2	FACETS	0.425	0.358	0.499	0.213	0.179	0.25	SUBCLONAL	1	TRUE	0	0.687231195544166	2		216	301	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376602	118376602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	59	374	0	ENST00000534358.1:c.9995G>A	p.Gly3332Glu	p.G3332E	ENST00000534358	NM_005933.3	3332	gGg/gAg	27/36	0.692995481861713	2	FACETS	0.363	0.313	0.418	0.182	0.156	0.209	SUBCLONAL	1	TRUE	0	0.687231195544166	2		374	473	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142527	119142527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	209	460	0	ENST00000264033.4:c.526G>A	p.Gly176Arg	p.G176R	ENST00000264033	NM_005188.3	176	Gga/Aga	3/16	0.692995481861713	2	FACETS	0.88	0.821	0.941	0.44	0.41	0.471	CLONAL	1	TRUE	0	0.687231195544166	2		460	691	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	465646	465646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2920	165	589	0	ENST00000399788.2:c.730G>A	p.Ala244Thr	p.A244T	ENST00000399788	NM_001042603.1	244	Gct/Act	6/28	0.687231195544166	10	FACETS	0.584	0.532	0.638			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	10		589	3085	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498224	498224	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	74	191	0	ENST00000399788.2:c.34G>A	p.Glu12Lys	p.E12K	ENST00000399788	NM_001042603.1	12	Gag/Aag	1/28	0.687231195544166	10	FACETS	0.816	0.712	0.928			1	CLONAL	1	TRUE	NA	0.687231195544166	10		191	990	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18762514	18762514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	162	575	0	ENST00000266497.5:c.4010C>T	p.Ser1337Phe	p.S1337F	ENST00000266497		1337	tCc/tTc	29/31	0.236147765781193	3	FACETS	0.683	0.627	0.743			1	INDETERMINATE	1	TRUE	NA	0.687231195544166	3		575	927	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245214	46245214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565623485	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	50	259	0	ENST00000334344.6:c.3308G>A	p.Ser1103Asn	p.S1103N	ENST00000334344	NM_152641.2	1103	aGt/aAt	15/21	0.687231195544166	6	FACETS	0.364	0.308	0.427			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	6		259	948	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425446	49425446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1328256473	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	47	535	0	ENST00000301067.7:c.13042G>A	p.Gly4348Arg	p.G4348R	ENST00000301067	NM_003482.3	4348	Ggg/Agg	39/54	0.692995481861713	4	FACETS	0.275	0.231	0.323	0.092	0.077	0.108	SUBCLONAL	1	TRUE	1	0.687231195544166	4		535	840	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425931	49425931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371517968	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	70	582	0	ENST00000301067.7:c.12557C>T	p.Pro4186Leu	p.P4186L	ENST00000301067	NM_003482.3	4186	cCt/cTt	39/54	0.692995481861713	4	FACETS	0.394	0.342	0.45	0.131	0.114	0.15	SUBCLONAL	1	TRUE	1	0.687231195544166	4		582	873	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428608	49428608	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752712305	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	175	542	0	ENST00000301067.7:c.10342C>T	p.Pro3448Ser	p.P3448S	ENST00000301067	NM_003482.3	3448	Cct/Tct	35/54	0.692995481861713	4	FACETS	1	0.959	1	0.354	0.326	0.383	CLONAL	1	TRUE	1	0.687231195544166	4		542	809	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432249	49432249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	64	481	0	ENST00000301067.7:c.8890G>A	p.Val2964Ile	p.V2964I	ENST00000301067	NM_003482.3	2964	Gtc/Atc	34/54	0.692995481861713	4	FACETS	0.381	0.329	0.438	0.127	0.109	0.146	SUBCLONAL	1	TRUE	1	0.687231195544166	4		481	824	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489468	56489468	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	42	387	0	ENST00000267101.3:c.1933G>A	p.Ala645Thr	p.A645T	ENST00000267101	NM_001982.3	645	Gct/Act	17/28	0.692995481861713	4	FACETS	0.281	0.233	0.333	0.094	0.077	0.111	SUBCLONAL	1	TRUE	1	0.687231195544166	4		387	735	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813465	102813465	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	76	200	0	ENST00000307046.8:c.224A>T	p.Lys75Met	p.K75M	ENST00000307046	NM_001111285.1	75	aAg/aTg	3/4	0.692995481861713	3	FACETS	1	0.968	1	0.627	0.558	0.699	CLONAL	1	TRUE	1	0.687231195544166	3		200	237	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888198	112888198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121918453	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	163	612	1	ENST00000351677.2:c.214G>A	p.Ala72Thr	p.A72T	ENST00000351677	NM_002834.3	72	Gcc/Acc	3/16	NA	2	FACETS	0.586	0.538	0.635			1	INDETERMINATE	1	TRUE	NA	0.687231195544166	2		613	810	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926851	112926851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507539	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	69	621	1	ENST00000351677.2:c.1471C>T	p.Pro491Ser	p.P491S	ENST00000351677	NM_002834.3	491	Ccc/Tcc	13/16	NA	2	FACETS	0.255	0.222	0.292			1	INDETERMINATE	1	TRUE	NA	0.687231195544166	2		622	786	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896971	28896971	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	42	446	0	ENST00000282397.4:c.2909G>A	p.Gly970Asp	p.G970D	ENST00000282397	NM_002019.4	970	gGc/gAc	21/30	0.692995481861713	3	FACETS	0.202	0.168	0.241	0.067	0.056	0.081	SUBCLONAL	1	TRUE	0	0.687231195544166	3		446	812	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959025	28959025	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	80	572	1	ENST00000282397.4:c.2113C>T	p.Pro705Ser	p.P705S	ENST00000282397	NM_002019.4	705	Cct/Tct	14/30	0.692995481861713	3	FACETS	0.281	0.247	0.319	0.094	0.082	0.107	SUBCLONAL	1	TRUE	0	0.687231195544166	3		573	1112	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964212	28964212	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	96	354	0	ENST00000282397.4:c.1690G>A	p.Glu564Lys	p.E564K	ENST00000282397	NM_002019.4	564	Gaa/Aaa	13/30	0.692995481861713	3	FACETS	0.474	0.422	0.53	0.158	0.14	0.177	SUBCLONAL	1	TRUE	0	0.687231195544166	3		354	792	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912144	32912144	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4210	254	930	2	ENST00000380152.3:c.3652G>A	p.Gly1218Ser	p.G1218S	ENST00000380152		1218	Ggc/Agc	11/27	0.687231195544166	9	FACETS	0.564	0.524	0.606			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	9		932	4464	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914998	32914998	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555284726	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4562	388	996	3	ENST00000380152.3:c.6506C>T	p.Thr2169Ile	p.T2169I	ENST00000380152		2169	aCc/aTc	11/27	0.687231195544166	9	FACETS	0.777	0.733	0.823			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	9		999	4950	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133743	41133743	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1359	188	832	0	ENST00000379561.5:c.1885G>A	p.Asp629Asn	p.D629N	ENST00000379561	NM_002015.3	629	Gat/Aat	2/3	0.692995481861713	4	FACETS	0.597	0.549	0.646			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	4		832	1547	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337603	73337603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	101	485	0	ENST00000377767.4:c.2113G>A	p.Ala705Thr	p.A705T	ENST00000377767	NM_014953.3	705	Gca/Aca	16/21	0.674948078753537	1	FACETS	0.421	0.378	0.466	0.421	0.378	0.466	SUBCLONAL	1	TRUE	0	0.687231195544166	1		485	458	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986886	36986886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	42	128	0	ENST00000354822.5:c.803G>A	p.Gly268Asp	p.G268D	ENST00000354822	NM_001079668.2	268	gGc/gAc	3/3	0.692995481861713	4	FACETS	0.977	0.825	1	0.244	0.206	0.286	CLONAL	1	TRUE	0	0.687231195544166	4		128	211	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061132	38061132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	37	62	0	ENST00000250448.2:c.857G>A	p.Gly286Asp	p.G286D	ENST00000250448	NM_004496.3	286	gGc/gAc	2/2	0.692995481861713	4	FACETS	0.811	0.686	0.943	0.406	0.343	0.472	CLONAL	2	TRUE	0	0.687231195544166	4		62	112	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40991018	40991018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1339	77	626	0	ENST00000267868.3:c.62G>A	p.Gly21Asp	p.G21D	ENST00000267868	NM_002875.4	21	gGc/gAc	2/10	0.584806888739601	4	FACETS	0.267	0.233	0.304			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	4		626	1416	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41020923	41020923	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	140	592	0	ENST00000267868.3:c.545G>A	p.Gly182Asp	p.G182D	ENST00000267868	NM_002875.4	182	gGc/gAc	7/10	0.584806888739601	4	FACETS	0.606	0.55	0.664			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	4		592	1135	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988944	41988944	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1702	111	876	0	ENST00000219905.7:c.1736G>A	p.Gly579Glu	p.G579E	ENST00000219905	NM_001164273.1	579	gGa/gAa	3/24	0.584806888739601	4	FACETS	0.301	0.269	0.335			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	4		876	1813	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040852	42040852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1422	111	580	2	ENST00000219905.7:c.5230C>T	p.Pro1744Ser	p.P1744S	ENST00000219905	NM_001164273.1	1744	Cca/Tca	16/24	0.584806888739601	4	FACETS	0.356	0.318	0.396			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	4		582	1533	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046683	42046683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1616	123	820	0	ENST00000219905.7:c.7057G>A	p.Glu2353Lys	p.E2353K	ENST00000219905	NM_001164273.1	2353	Gag/Aag	18/24	0.584806888739601	4	FACETS	0.347	0.312	0.384			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	4		820	1739	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42057227	42057227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1504	84	807	0	ENST00000219905.7:c.7888C>T	p.Pro2630Ser	p.P2630S	ENST00000219905	NM_001164273.1	2630	Cct/Tct	23/24	0.584806888739601	4	FACETS	0.26	0.228	0.294			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	4		807	1588	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358689	67358689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	76	282	0	ENST00000327367.4:c.197C>T	p.Thr66Ile	p.T66I	ENST00000327367	NM_005902.3	66	aCc/aTc	1/9	0.692995481861713	4	FACETS	0.668	0.586	0.755	0.334	0.293	0.378	SUBCLONAL	1	TRUE	2	0.687231195544166	4		282	559	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996146	73996146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	56	415	0	ENST00000318443.5:c.880G>A	p.Val294Met	p.V294M	ENST00000318443	NM_001024736.1	294	Gtg/Atg	5/10	0.692995481861713	4	FACETS	0.301	0.257	0.349	0.15	0.128	0.175	SUBCLONAL	1	TRUE	2	0.687231195544166	4		415	914	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500487	99500487	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1314178071	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	43	335	0	ENST00000268035.6:c.3920C>T	p.Pro1307Leu	p.P1307L	ENST00000268035	NM_000875.3	1307	cCc/cTc	21/21	0.550344284086373	3	FACETS	0.397	0.332	0.468			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	3		335	424	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396173	396173	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370974968	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	23	321	0	ENST00000262320.3:c.853C>T	p.Arg285Trp	p.R285W	ENST00000262320	NM_003502.3	285	Cgg/Tgg	2/11	NA	2	FACETS	0.265	0.206	0.331			1	INDETERMINATE	1	TRUE	NA	0.687231195544166	2		321	253	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778540	3778540	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753468490	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	134	547	1	ENST00000262367.5:c.6508G>A	p.Ala2170Thr	p.A2170T	ENST00000262367	NM_004380.2	2170	Gcc/Acc	31/31	0.236147765781193	3	FACETS	0.958	0.874	1			1	INDETERMINATE	1	TRUE	NA	0.687231195544166	3		548	547	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820680	3820680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	62	306	0	ENST00000262367.5:c.2771C>T	p.Ala924Val	p.A924V	ENST00000262367	NM_004380.2	924	gCc/gTc	14/31	0.236147765781193	3	FACETS	0.65	0.564	0.742			1	INDETERMINATE	1	TRUE	NA	0.687231195544166	3		306	373	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923335	9923335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	76	460	0	ENST00000330684.3:c.1952C>T	p.Ala651Val	p.A651V	ENST00000330684	NM_001134407.1	651	gCc/gTc	9/13	NA	2	FACETS	0.438	0.385	0.495			1	INDETERMINATE	1	TRUE	NA	0.687231195544166	2		460	505	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853262	68853262	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659525	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	117	492	0	ENST00000261769.5:c.1645G>A	p.Asp549Asn	p.D549N	ENST00000261769	NM_004360.3	549	Gac/Aac	11/16	0.692995481861713	3	FACETS	0.741	0.67	0.816	0.371	0.335	0.408	SUBCLONAL	1	TRUE	1	0.687231195544166	3		492	617	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993900	72993900	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	79	533	0	ENST00000268489.5:c.145C>T	p.Pro49Ser	p.P49S	ENST00000268489	NM_006885.3	49	Ccc/Tcc	2/10	0.692995481861713	3	FACETS	0.462	0.406	0.522	0.231	0.203	0.261	SUBCLONAL	1	TRUE	1	0.687231195544166	3		533	669	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946303	81946303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	36	631	1	ENST00000359376.3:c.2036C>T	p.Ser679Phe	p.S679F	ENST00000359376	NM_002661.3	679	tCc/tTc	19/33	NA	2	FACETS	0.182	0.149	0.219			1	INDETERMINATE	1	TRUE	NA	0.687231195544166	2		632	576	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81973635	81973635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	118	680	0	ENST00000359376.3:c.3452C>T	p.Ala1151Val	p.A1151V	ENST00000359376	NM_002661.3	1151	gCc/gTc	30/33	NA	2	FACETS	0.439	0.396	0.485			1	INDETERMINATE	1	TRUE	NA	0.687231195544166	2		680	782	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346214	89346214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1031398540	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	38	325	0	ENST00000301030.4:c.6736C>T	p.Pro2246Ser	p.P2246S	ENST00000301030	NM_001256183.1	2246	Cca/Tca	9/13	0.692995481861713	3	FACETS	0.399	0.331	0.476			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	3		325	372	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573937	7573937	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	139	386	0	ENST00000269305.4:c.1090G>A	p.Ala364Thr	p.A364T	ENST00000269305	NM_001126112.2	364	Gct/Act	10/11	0.692995481861713	4	FACETS	0.947	0.863	1			1	CLONAL	1	TRUE	NA	0.687231195544166	4		386	721	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578518	7578518	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934875	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	738	373	1	ENST00000269305.4:c.412G>C	p.Ala138Pro	p.A138P	ENST00000269305	NM_001126112.2	138	Gcc/Ccc	5/11	0.692995481861713	4	FACETS		NA	1			1	NA	5	TRUE	NA	0.687231195544166	4		374	785	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16040725	16040725	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1195304107	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	117	452	0	ENST00000268712.3:c.1409G>A	p.Ser470Asn	p.S470N	ENST00000268712	NM_006311.3	470	aGt/aAt	14/46	0.606230984496104	4	FACETS	0.49	0.441	0.543	0.245	0.22	0.272	SUBCLONAL	1	TRUE	2	0.687231195544166	4		452	1172	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557342	29557342	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567849826	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1807	96	559	1	ENST00000356175.3:c.3055G>A	p.Val1019Ile	p.V1019I	ENST00000356175	NM_000267.3	1019	Gtt/Att	23/57	0.687231195544166	6	FACETS	0.349	0.309	0.391			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	6		560	1903	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653058	29653058	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1416	129	445	1	ENST00000356175.3:c.4993G>A	p.Val1665Ile	p.V1665I	ENST00000356175	NM_000267.3	1665	Gtc/Atc	36/57	0.687231195544166	6	FACETS	0.577	0.521	0.636			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	6		446	1545	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264356	30264356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	45	142	0	ENST00000322652.5:c.91G>A	p.Val31Met	p.V31M	ENST00000322652	NM_015355.2	31	Gtg/Atg	1/16	0.687231195544166	6	FACETS	1	0.952	1			1	CLONAL	1	TRUE	NA	0.687231195544166	6		142	231	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510710	38510710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	31	299	0	ENST00000254066.5:c.964G>A	p.Asp322Asn	p.D322N	ENST00000254066	NM_000964.3	322	Gat/Aat	7/9	0.584806888739601	4	FACETS	0.275	0.222	0.336			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	4		299	553	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40457662	40457662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	161	595	0	ENST00000345506.4:c.1415G>A	p.Gly472Asp	p.G472D	ENST00000345506	NM_003152.3	472	gGc/gAc	13/20	0.584806888739601	4	FACETS	0.832	0.763	0.905			1	CLONAL	1	TRUE	NA	0.687231195544166	4		595	950	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40461454	40461454	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	112	750	1	ENST00000345506.4:c.2174C>T	p.Pro725Leu	p.P725L	ENST00000345506	NM_003152.3	725	cCc/cTc	19/20	0.584806888739601	4	FACETS	0.459	0.411	0.509			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	4		751	1199	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40500524	40500524	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	74	594	0	ENST00000264657.5:c.11G>A	p.Trp4Ter	p.W4*	ENST00000264657	NM_139276.2	4	tGg/tAg	2/24	0.584806888739601	4	FACETS	0.342	0.298	0.389			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	4		594	1064	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244135	41244135	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879251628	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1582	98	638	0	ENST00000357654.3:c.3413G>A	p.Gly1138Glu	p.G1138E	ENST00000357654	NM_007294.3	1138	gGa/gAa	10/23	0.677196063483317	5	FACETS	0.345	0.306	0.386			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	5		638	1680	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696611	47696611	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	155	634	0	ENST00000347630.2:c.337G>A	p.Glu113Lys	p.E113K	ENST00000347630	NM_001007230.1	113	Gaa/Aaa	5/11	0.584806888739601	4	FACETS	0.608	0.555	0.664			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	4		634	1251	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435825	56435825	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	56	191	0	ENST00000407977.2:c.1312G>A	p.Ala438Thr	p.A438T	ENST00000407977		438	Gcc/Acc	9/10	0.584806888739601	4	FACETS	0.694	0.597	0.8			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	4		191	396	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440892	56440892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1200828033	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	46	477	0	ENST00000407977.2:c.445G>A	p.Glu149Lys	p.E149K	ENST00000407977		149	Gag/Aag	4/10	0.584806888739601	4	FACETS	0.285	0.239	0.336			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	4		477	793	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59861673	59861673	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138784299	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1281	168	666	0	ENST00000259008.2:c.1586G>A	p.Gly529Glu	p.G529E	ENST00000259008	NM_032043.2	529	gGa/gAa	11/20	0.584806888739601	4	FACETS	0.569	0.521	0.62			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	4		666	1449	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400772	56400772	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1816	248	887	0	ENST00000348428.3:c.1366C>T	p.Leu456Phe	p.L456F	ENST00000348428	NM_006785.3	456	Ctt/Ttt	11/17	0.367053762628839	6	FACETS	0.83	0.773	0.89	0.277	0.257	0.297	INDETERMINATE	1	TRUE	3	0.687231195544166	6		887	2064	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216461	2216461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	30	270	0	ENST00000398665.3:c.2105C>T	p.Pro702Leu	p.P702L	ENST00000398665	NM_032482.2	702	cCt/cTt	20/28	0.495935630927764	4	FACETS	0.327	0.263	0.399			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	4		270	451	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096964	11096964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777272957	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	43	473	0	ENST00000358026.2:c.455C>T	p.Ala152Val	p.A152V	ENST00000358026	NM_001128849.1	152	gCc/gTc	4/36	0.379504209707308	5	FACETS	0.388	0.324	0.459	0.129	0.108	0.153	INDETERMINATE	1	TRUE	2	0.687231195544166	5		473	655	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289725	15289725	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	41	396	0	ENST00000263388.2:c.3746C>T	p.Pro1249Leu	p.P1249L	ENST00000263388	NM_000435.2	1249	cCc/cTc	23/33	0.379504209707308	5	FACETS	0.496	0.412	0.588	0.165	0.137	0.196	INDETERMINATE	1	TRUE	2	0.687231195544166	5		396	489	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295195	15295195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	47	470	1	ENST00000263388.2:c.2477G>A	p.Cys826Tyr	p.C826Y	ENST00000263388	NM_000435.2	826	tGc/tAc	16/33	0.379504209707308	5	FACETS	0.477	0.402	0.56	0.159	0.134	0.187	INDETERMINATE	1	TRUE	2	0.687231195544166	5		471	582	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302555	15302555	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	39	356	0	ENST00000263388.2:c.802+1G>A		p.X268_splice	ENST00000263388	NM_000435.2	268			0.379504209707308	5	FACETS	0.454	0.376	0.541	0.151	0.125	0.181	INDETERMINATE	1	TRUE	2	0.687231195544166	5		356	508	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313493	30313493	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	109	425	0	ENST00000262643.3:c.1093G>A	p.Asp365Asn	p.D365N	ENST00000262643	NM_001238.2	365	Gac/Aac	11/12	0.692995481861713	4	FACETS	0.593	0.532	0.659			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	4		425	902	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796762	42796762	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	41	329	0	ENST00000575354.2:c.3220C>T	p.Pro1074Ser	p.P1074S	ENST00000575354	NM_015125.3	1074	Cct/Tct	14/20	0.420392842739275	5	FACETS	0.461	0.383	0.547			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	5		329	526	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906465	50906465	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773891726	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	27	401	1	ENST00000440232.2:c.1126G>A	p.Asp376Asn	p.D376N	ENST00000440232	NM_002691.3	376	Gac/Aac	9/27	0.236147765781193	3	FACETS	0.236	0.187	0.292			1	INDETERMINATE	1	TRUE	NA	0.687231195544166	3		402	447	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561045	9561045	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	43	290	0	ENST00000353224.5:c.737C>T	p.Ser246Phe	p.S246F	ENST00000353224	NM_177990.2	246	tCc/tTc	4/10	0.420392842739275	5	FACETS	0.392	0.327	0.464			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	5		290	648	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264932	46264932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1228109191	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1547	97	993	1	ENST00000371998.3:c.1802G>A	p.Ser601Asn	p.S601N	ENST00000371998		601	aGc/aAc	12/23	0.416608001202504	3	FACETS	0.231	0.204	0.259	0.115	0.102	0.13	SUBCLONAL	1	TRUE	1	0.687231195544166	3		994	1644	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573434	41573434	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1034013330	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	57	360	0	ENST00000263253.7:c.5719C>T	p.Pro1907Ser	p.P1907S	ENST00000263253	NM_001429.3	1907	Cct/Tct	31/31	0.382994269000773	3	FACETS	0.496	0.427	0.572	0.165	0.142	0.191	INDETERMINATE	1	TRUE	0	0.687231195544166	3		360	449	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15821867	15821867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	122	884	2	ENST00000307771.7:c.260G>A	p.Arg87Lys	p.R87K	ENST00000307771	NM_005089.3	87	aGa/aAa	4/11	NA	2	FACETS	0.339	0.306	0.375			1	INDETERMINATE	1	TRUE	NA	0.687231195544166	2		886	1046	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040783	47040783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	60	387	0	ENST00000377604.3:c.1418G>A	p.Gly473Glu	p.G473E	ENST00000377604	NM_001204468.1	473	gGg/gAg	13/24	0.550344284086373	3	FACETS	0.444	0.383	0.511			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	3		387	528	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428433	47428433	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	189	758	2	ENST00000377045.4:c.1300+1G>A		p.X434_splice	ENST00000377045	NM_001654.4	434			0.550344284086373	3	FACETS	0.81	0.749	0.874			1	CLONAL	1	TRUE	NA	0.687231195544166	3		760	912	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228008	53228008	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	146	681	1	ENST00000375401.3:c.2306C>T	p.Ser769Phe	p.S769F	ENST00000375401	NM_004187.3	769	tCc/tTc	16/26	0.550344284086373	3	FACETS	0.68	0.62	0.742			1	SUBCLONAL	1	TRUE	NA	0.687231195544166	3		682	840	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410283	63410283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777905301	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	45	574	0	ENST00000330258.3:c.2884G>A	p.Ala962Thr	p.A962T	ENST00000330258	NM_152424.3	962	Gct/Act	2/2	NA	2	FACETS	0.241	0.202	0.284			1	INDETERMINATE	1	TRUE	NA	0.687231195544166	2		574	544	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939994	76939994	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	705	677	0	ENST00000373344.5:c.754G>C	p.Glu252Gln	p.E252Q	ENST00000373344	NM_000489.3	252	Gag/Cag	9/35	NA	2	FACETS		NA	1			1	INDETERMINATE	3	TRUE	NA	0.687231195544166	2		677	777	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912079	76912079	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	978	864	0	ENST00000373344.5:c.4185del	p.Glu1395AspfsTer95	p.E1395Dfs*95	ENST00000373344	NM_000489.3	1395	gaA/ga	13/35	NA	2	FACETS		NA	1			1	INDETERMINATE	3	TRUE	NA	0.687231195544166	2		864	1136	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554257	29554275	+	frameshift_variant	Frame_Shift_Del	DEL	GAGTGATGGCACTGCTGAG	GAGTGATGGCACTGCTGAG	-	novel	NA	P-0002294-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	1134	411	0	ENST00000356175.3:c.2274_2292del	p.Arg758SerfsTer27	p.R758Sfs*27	ENST00000356175	NM_000267.3	758	aGAGTGATGGCACTGCTGAGg/ag	19/57	0.687231195544166	6	FACETS		NA	1			1	NA	7	TRUE	NA	0.687231195544166	6		411	1176	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0002312-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	41	675	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.371492859504622	3	FACETS	0.8	0.669	0.945	0.4	0.334	0.473	CLONAL	1	TRUE	1	0.371492859504622	3		675	327	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937001	48937001	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002312-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	159	765	0	ENST00000267163.4:c.769C>T	p.Gln257Ter	p.Q257*	ENST00000267163	NM_000321.2	257	Cag/Tag	8/27	0.371492859504622	3	FACETS	0.881	0.818	0.945	0.881	0.818	0.945	CLONAL	3	TRUE	0	0.371492859504622	3		765	384	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087961	27087961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002322-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	80	407	0	ENST00000324856.7:c.2248C>T	p.Arg750Ter	p.R750*	ENST00000324856	NM_006015.4	750	Cga/Tga	6/20	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.306903601803531	2		407	470	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922973	44922973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002322-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	125	532	0	ENST00000377967.4:c.1834C>T	p.Arg612Ter	p.R612*	ENST00000377967	NM_021140.2	612	Cga/Tga	16/29	0.306903601803531	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.306903601803531	1		532	665	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591929	48591967	+	inframe_deletion	In_Frame_Del	DEL	GGGTCAACTCTCCAATGTCCACAGGACAGAAGCCATTGA	GGGTCAACTCTCCAATGTCCACAGGACAGAAGCCATTGA	-	novel	NA	P-0002322-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	51	386	0	ENST00000342988.3:c.1093_1131del	p.Gly365_Glu377del	p.G365_E377del	ENST00000342988	NM_005359.5	364	ttGGGTCAACTCTCCAATGTCCACAGGACAGAAGCCATTGAg/ttg	9/12	1	2	FACETS	0.701	0.596	0.816	0.701	0.596	0.816	SUBCLONAL	1	TRUE	1	0.306903601803531	2		386	474	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0002329-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	101	339	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.27	2		339	516	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055985	180055985	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002329-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	37	379	2	ENST00000261937.6:c.1000A>G	p.Ser334Gly	p.S334G	ENST00000261937	NM_182925.4	334	Agc/Ggc	8/30	0.3	1	FACETS	0.514	0.424	0.616	0.514	0.424	0.616	SUBCLONAL	1	TRUE	0	0.27	1		381	461	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28929495	NA	P-0002329-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	123	328	0	ENST00000275493.2:c.2155G>T	p.Gly719Cys	p.G719C	ENST00000275493	NM_005228.3	719	Ggc/Tgc	18/28	1	2	FACETS	0.752	0.682	0.825	1	0.985	1	SUBCLONAL	2	TRUE	1	0.27	2		328	606	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456647	32456647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002329-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	15	131	0	ENST00000332351.3:c.245C>T	p.Ala82Val	p.A82V	ENST00000332351	NM_024426.4	82	gCc/gTc	1/10	1	2	FACETS	0.708	0.52	0.93	0.708	0.52	0.93	CLONAL	1	TRUE	1	0.27	2		131	157	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534325	63534325	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765865516	NA	P-0002329-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	34	412	0	ENST00000307078.5:c.1196G>A	p.Arg399Gln	p.R399Q	ENST00000307078	NM_004655.3	399	cGa/cAa	5/11	1	2	FACETS	0.415	0.338	0.502	0.415	0.338	0.502	SUBCLONAL	1	TRUE	1	0.27	2		412	607	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0002335-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	303	620	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.982	0.93	1	0.982	0.93	1	CLONAL	1	TRUE	1	0.813414314309224	2		620	759	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs17849781	NA	P-0002335-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	353	861	0	ENST00000269305.4:c.832C>A	p.Pro278Thr	p.P278T	ENST00000269305	NM_001126112.2	278	Cct/Act	8/11	1	2	FACETS	0.954	0.907	1	0.954	0.907	1	CLONAL	1	TRUE	1	0.813414314309224	2		861	910	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156720	20156720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002335-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	449	409	0	ENST00000379607.5:c.37C>T	p.Arg13Cys	p.R13C	ENST00000379607	NM_001412.3	13	Cgc/Tgc	2/7	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.813414314309224	1		409	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578193	7578193	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002335-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	414	828	0	ENST00000269305.4:c.656C>G	p.Pro219Arg	p.P219R	ENST00000269305	NM_001126112.2	219	cCc/cGc	6/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.813414314309224	2		828	981	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094291	27094292	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002335-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	80	517	0	ENST00000324856.7:c.3001dup	p.Ser1001PhefsTer6	p.S1001Ffs*6	ENST00000324856	NM_006015.4	1000	tct/tcTt	11/20	1	2	FACETS	0.311	0.273	0.351	0.311	0.273	0.351	SUBCLONAL	1	TRUE	1	0.813414314309224	2		517	633	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938138	76938138	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002335-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	388	448	0	ENST00000373344.5:c.2610del	p.Ser871HisfsTer34	p.S871Hfs*34	ENST00000373344	NM_000489.3	870	acC/ac	9/35	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.813414314309224	1		448	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0002341-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	184	800	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.418091337854674	2		800	643	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781324	3781326	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs587783502	NA	P-0002341-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	187	748	0	ENST00000262367.5:c.5039_5041del	p.Ser1680del	p.S1680del	ENST00000262367	NM_004380.2	1680	tCCTtg/ttg	30/31	0.418091337854674	3	FACETS	1	0.99	1	0.728	0.674	0.783	CLONAL	1	TRUE	1	0.418091337854674	3		748	743	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298465	11298465	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002341-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	48	633	0	ENST00000361445.4:c.1996G>C	p.Asp666His	p.D666H	ENST00000361445	NM_004958.3	666	Gat/Cat	12/58	0.325743470151414	4	FACETS	0.374	0.315	0.44			1	SUBCLONAL	1	TRUE	NA	0.418091337854674	4		633	870	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726987	46726987	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002341-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	88	1000	0	ENST00000371975.4:c.821C>G	p.Ser274Cys	p.S274C	ENST00000371975	NM_003579.3	274	tCc/tGc	8/18	0.418091337854674	5	FACETS	0.581	0.513	0.654	0.145	0.128	0.164	SUBCLONAL	1	TRUE	1	0.418091337854674	5		1000	1179	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127693	47127693	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002341-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	106	612	0	ENST00000409792.3:c.5389C>T	p.Gln1797Ter	p.Q1797*	ENST00000409792	NM_014159.6	1797	Cag/Tag	11/21	1	2	FACETS	0.841	0.756	0.931	0.841	0.756	0.931	CLONAL	1	TRUE	1	0.418091337854674	2		612	603	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540689	187540689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs544202909	NA	P-0002341-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	82	757	0	ENST00000441802.2:c.7051G>A	p.Glu2351Lys	p.E2351K	ENST00000441802	NM_005245.3	2351	Gag/Aag	10/27	0.35366016418342	3	FACETS	0.561	0.494	0.634	0.281	0.247	0.317	SUBCLONAL	1	TRUE	1	0.418091337854674	3		757	845	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508733	148508733	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0002341-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	438	845	0	ENST00000320356.2:c.1931C>G	p.Ser644Ter	p.S644*	ENST00000320356	NM_004456.4	644	tCa/tGa	16/20	0.418091337854674	2	FACETS	1	0.985	1	1	0.997	1	CLONAL	3	TRUE	0	0.418091337854674	2		845	674	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917721	151917721	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0002341-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	35	181	0	ENST00000262189.6:c.3599C>G	p.Ser1200Ter	p.S1200*	ENST00000262189	NM_170606.2	1200	tCa/tGa	23/59	0.418091337854674	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	2	TRUE	0	0.418091337854674	2		181	83	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533469	533469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002341-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	117	551	0	ENST00000451590.1:c.434C>T	p.Ser145Leu	p.S145L	ENST00000451590	NM_001130442.1	145	tCg/tTg	4/5	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.418091337854674	2		551	456	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420789	49420789	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002341-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	69	640	1	ENST00000301067.7:c.14960G>A	p.Trp4987Ter	p.W4987*	ENST00000301067	NM_003482.3	4987	tGg/tAg	48/54	1	2	FACETS	0.595	0.518	0.677	0.595	0.518	0.677	SUBCLONAL	1	TRUE	1	0.418091337854674	2		641	555	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427647	49427647	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0002341-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	50	480	0	ENST00000301067.7:c.10841C>G	p.Ser3614Ter	p.S3614*	ENST00000301067	NM_003482.3	3614	tCa/tGa	39/54	1	2	FACETS	0.613	0.522	0.713	0.613	0.522	0.713	SUBCLONAL	1	TRUE	1	0.418091337854674	2		480	390	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900276	32900276	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs377639990	NA	P-0002341-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	62	671	0	ENST00000380152.3:c.464G>C	p.Arg155Thr	p.R155T	ENST00000380152		155	aGa/aCa	5/27	0.418091337854674	2	FACETS	0.447	0.386	0.514	0.224	0.193	0.257	SUBCLONAL	1	TRUE	0	0.418091337854674	2		671	663	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914890	32914890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002341-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	96	679	0	ENST00000380152.3:c.6398C>T	p.Ser2133Leu	p.S2133L	ENST00000380152		2133	tCa/tTa	11/27	0.418091337854674	2	FACETS	0.744	0.664	0.829	0.372	0.332	0.415	SUBCLONAL	1	TRUE	0	0.418091337854674	2		679	617	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645968	67645968	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002341-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	80	715	0	ENST00000264010.4:c.896G>A	p.Cys299Tyr	p.C299Y	ENST00000264010	NM_006565.3	299	tGt/tAt	4/12	0.262860790001183	3	FACETS	0.711	0.626	0.802	0.237	0.208	0.268	SUBCLONAL	1	TRUE	0	0.418091337854674	3		715	651	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0002345-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	1191	358	2	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.860419600168294	3	FACETS	1	0.998	1	1	0.998	1	CLONAL	3	TRUE	0	0.860419600168294	3		360	1278	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731079	162731079	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002345-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2254	552	657	1	ENST00000367921.3:c.934G>T	p.Glu312Ter	p.E312*	ENST00000367921	NM_006182.2	312	Gag/Tag	9/18	0.860419600168294	5	FACETS	1	0.981	1	0.349	0.333	0.366	CLONAL	1	TRUE	2	0.860419600168294	5		658	2806	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754809	29754809	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002345-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	361	431	0	ENST00000389048.3:c.1126C>G	p.Leu376Val	p.L376V	ENST00000389048	NM_004304.4	376	Ctc/Gtc	4/29	0.860419600168294	3	FACETS	1	0.974	1	0.521	0.494	0.549	CLONAL	1	TRUE	1	0.860419600168294	3		431	1151	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37055939	37055939	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002345-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	734	570	2	ENST00000231790.2:c.694G>T	p.Gly232Ter	p.G232*	ENST00000231790	NM_000249.3	232	Gga/Tga	9/19	0.145813820176453	3	FACETS	0.914	0.887	0.941	0.609	0.591	0.627	INDETERMINATE	2	TRUE	0	0.860419600168294	3		572	1335	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259148	89259148	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002345-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	500	424	0	ENST00000336596.2:c.292G>T	p.Glu98Ter	p.E98*	ENST00000336596	NM_005233.5	98	Gag/Tag	3/17	0.145813820176453	3	FACETS	0.909	0.877	0.942	0.606	0.584	0.628	INDETERMINATE	2	TRUE	0	0.860419600168294	3		424	914	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920506	134920506	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs967317783	NA	P-0002345-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	446	496	0	ENST00000398015.3:c.2321C>T	p.Ser774Leu	p.S774L	ENST00000398015	NM_004441.4	774	tCa/tTa	12/16	0.145813820176453	3	FACETS	1	0.993	1	0.397	0.379	0.415	INDETERMINATE	1	TRUE	0	0.860419600168294	3		496	1245	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947067	178947067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002345-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1432	635	468	0	ENST00000263967.3:c.2503C>T	p.Pro835Ser	p.P835S	ENST00000263967	NM_006218.2	835	Cct/Tct	18/21	0.715121409192485	6	FACETS	0.971	0.933	1	0.486	0.466	0.505	CLONAL	2	TRUE	2	0.860419600168294	6		468	2067	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155255	185155255	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002345-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1401	385	438	0	ENST00000265026.3:c.496G>C	p.Glu166Gln	p.E166Q	ENST00000265026	NM_004721.4	166	Gag/Cag	3/14	0.715121409192485	6	FACETS	1	0.994	1	0.341	0.322	0.36	CLONAL	1	TRUE	2	0.860419600168294	6		438	1786	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711891	89711891	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660507	NA	P-0002345-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	883	464	0	ENST00000371953.3:c.509G>T	p.Ser170Ile	p.S170I	ENST00000371953	NM_000314.4	170	aGt/aTt	6/9	0.860419600168294	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.860419600168294	2		464	971	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871138	12871138	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002345-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	300	219	0	ENST00000228872.4:c.365C>A	p.Pro122Gln	p.P122Q	ENST00000228872	NM_004064.3	122	cCg/cAg	1/3	0.407935916306537	4	FACETS	0.921	0.874	0.97			1	INDETERMINATE	2	TRUE	NA	0.860419600168294	4		219	704	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871186	12871186	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002345-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	198	152	0	ENST00000228872.4:c.413C>A	p.Ser138Ter	p.S138*	ENST00000228872	NM_004064.3	138	tCg/tAg	1/3	0.407935916306537	4	FACETS	0.797	0.744	0.851			1	INDETERMINATE	2	TRUE	NA	0.860419600168294	4		152	537	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919331	48919331	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1131690874	NA	P-0002345-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	623	303	0	ENST00000267163.4:c.496G>T	p.Glu166Ter	p.E166*	ENST00000267163	NM_000321.2	166	Gaa/Taa	4/27	0.860419600168294	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.860419600168294	3		303	680	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003281-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	344	284	1	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.801194468438651	1	FACETS	0.95	0.912	0.986	0.95	0.912	0.986	CLONAL	1	TRUE	0	0.801194468438651	1		285	542	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11194409	11194409	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs752198342	NA	P-0003281-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	259	446	0	ENST00000361445.4:c.5245C>T	p.Arg1749Ter	p.R1749*	ENST00000361445	NM_004958.3	1749	Cga/Tga	37/58	1	2	FACETS	0.945	0.891	1	0.945	0.891	1	CLONAL	1	TRUE	1	0.801194468438651	2		446	684	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106421	27106421	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003281-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	308	521	0	ENST00000324856.7:c.6032T>G	p.Leu2011Arg	p.L2011R	ENST00000324856	NM_006015.4	2011	cTg/cGg	20/20	1	2	FACETS	0.934	0.884	0.985	0.934	0.884	0.985	CLONAL	1	TRUE	1	0.801194468438651	2		521	823	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288975	33288975	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004307-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	313	348	0	ENST00000374542.5:c.577C>T	p.Gln193Ter	p.Q193*	ENST00000374542	NM_001141970.1	193	Cag/Tag	3/8	0.834784723266171	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.834784723266171	1		348	426	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575021	64575035	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CACCTGCTGCAGCTG	CACCTGCTGCAGCTG	-	novel	NA	P-0004307-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	282	310	0	ENST00000312049.6:c.772_783+3del		p.X258_splice	ENST00000312049	NM_130799.2	258		4/10	0.834784723266171	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.834784723266171	1		310	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0007358-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	223	265	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.598674416043815	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.598674416043815	1		267	490	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665029	182665029	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007358-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1420	131	579	0	ENST00000292782.4:c.697G>T	p.Glu233Ter	p.E233*	ENST00000292782	NM_020640.2	233	Gaa/Taa	6/7	1	2	FACETS	0.282	0.255	0.311	0.282	0.255	0.311	SUBCLONAL	1	TRUE	1	0.598674416043815	2		579	1551	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446734	49446734	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779668384	NA	P-0007358-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	244	314	0	ENST00000301067.7:c.1076G>A	p.Arg359His	p.R359H	ENST00000301067	NM_003482.3	359	cGc/cAc	8/54	1	2	FACETS	0.946	0.886	1	0.946	0.886	1	CLONAL	1	TRUE	1	0.598674416043815	2		314	862	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481442	40481442	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1290480970	NA	P-0007358-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	518	653	1	ENST00000264657.5:c.1267C>T	p.Arg423Ter	p.R423*	ENST00000264657	NM_139276.2	423	Cga/Tga	14/24	0.598674416043815	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.598674416043815	1		654	1121	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653453	206653464	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCATGTGAGTAA	TCATGTGAGTAA	-	novel	NA	P-0007358-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	58	172	0	ENST00000367120.3:c.1340+2_1340+13del		p.X447_splice	ENST00000367120	NM_014002.3	447		12/22	0.324321407286672	1	FACETS	0.342	0.295	0.393	0.342	0.295	0.393	INDETERMINATE	1	TRUE	0	0.598674416043815	1		172	397	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272421	11272421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777142056	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	94	182	0	ENST00000361445.4:c.3509G>A	p.Arg1170His	p.R1170H	ENST00000361445	NM_004958.3	1170	cGc/cAc	23/58	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.4185054081564	2		182	409	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245516	16245517	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	59	217	0	ENST00000375759.3:c.1495dup	p.Glu499GlyfsTer6	p.E499Gfs*6	ENST00000375759	NM_015001.2	497	-/G	7/15	1	2	FACETS	0.665	0.574	0.764	0.665	0.574	0.764	SUBCLONAL	1	TRUE	1	0.4185054081564	2		217	424	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16248844	16248844	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	72	156	0	ENST00000375759.3:c.1850G>A	p.Arg617Lys	p.R617K	ENST00000375759	NM_015001.2	617	aGa/aAa	10/15	1	2	FACETS	0.951	0.836	1	0.951	0.836	1	CLONAL	1	TRUE	1	0.4185054081564	2		156	362	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264466	16264466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	93	155	2	ENST00000375759.3:c.10669G>A	p.Ala3557Thr	p.A3557T	ENST00000375759	NM_015001.2	3557	Gca/Aca	13/15	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.4185054081564	2		157	397	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846331	156846331	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	78	120	0	ENST00000524377.1:c.1772A>T	p.Tyr591Phe	p.Y591F	ENST00000524377	NM_002529.3	591	tAt/tTt	14/17	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.4185054081564	2		120	314	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746063	162746063	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	66	178	0	ENST00000367921.3:c.2186T>G	p.Phe729Cys	p.F729C	ENST00000367921	NM_006182.2	729	tTt/tGt	16/18	1	2	FACETS	0.904	0.789	1	0.904	0.789	1	CLONAL	1	TRUE	1	0.4185054081564	2		178	349	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099338	193099338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	72	176	0	ENST00000367435.3:c.272G>A	p.Arg91Gln	p.R91Q	ENST00000367435	NM_024529.4	91	cGa/cAa	3/17	1	2	FACETS	0.915	0.804	1	0.915	0.804	1	CLONAL	1	TRUE	1	0.4185054081564	2		176	376	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243801041	243801041	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	69	189	0	ENST00000263826.5:c.433A>G	p.Met145Val	p.M145V	ENST00000263826	NM_005465.4	145	Atg/Gtg	5/13	1	2	FACETS	0.926	0.812	1	0.926	0.812	1	CLONAL	1	TRUE	1	0.4185054081564	2		189	356	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518493	69518493	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	31	45	0	ENST00000294312.3:c.152G>C	p.Gly51Ala	p.G51A	ENST00000294312	NM_005117.2	51	gGc/gCc	1/3	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.4185054081564	2		45	120	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942232	71942232	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs775939148	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	52	121	0	ENST00000298229.2:c.1496C>T	p.Pro499Leu	p.P499L	ENST00000298229	NM_001567.3	499	cCg/cTg	12/28	1	2	FACETS	0.938	0.805	1	0.938	0.805	1	CLONAL	1	TRUE	1	0.4185054081564	2		121	265	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943705	71943705	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	101	198	0	ENST00000298229.2:c.1748T>G	p.Leu583Arg	p.L583R	ENST00000298229	NM_001567.3	583	cTc/cGc	15/28	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.4185054081564	2		198	466	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719951	18719951	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1333356873	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	77	261	0	ENST00000266497.5:c.3848A>G	p.Tyr1283Cys	p.Y1283C	ENST00000266497		1283	tAc/tGc	27/31	1	2	FACETS	0.842	0.742	0.948	0.842	0.742	0.948	CLONAL	1	TRUE	1	0.4185054081564	2		261	437	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644545	21644545	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	75	244	0	ENST00000421138.2:c.122T>C	p.Val41Ala	p.V41A	ENST00000421138		41	gTc/gCc	4/16	1	2	FACETS	0.826	0.727	0.932	0.826	0.727	0.932	CLONAL	1	TRUE	1	0.4185054081564	2		244	434	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421097	49421097	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	57	75	0	ENST00000301067.7:c.14652del	p.Ala4885ProfsTer110	p.A4885Pfs*110	ENST00000301067	NM_003482.3	4884	ccC/cc	48/54	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.4185054081564	2		75	228	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	97	287	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.4185054081564	2		287	344	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436396	49436396	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	78	162	0	ENST00000301067.7:c.5815A>G	p.Ser1939Gly	p.S1939G	ENST00000301067	NM_003482.3	1939	Agc/Ggc	27/54	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.4185054081564	2		162	363	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441773	49441773	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	70	143	0	ENST00000301067.7:c.4211A>G	p.Tyr1404Cys	p.Y1404C	ENST00000301067	NM_003482.3	1404	tAt/tGt	14/54	1	2	FACETS	0.978	0.859	1	0.978	0.859	1	CLONAL	1	TRUE	1	0.4185054081564	2		143	342	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563349	21563349	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	85	187	0	ENST00000382592.4:c.570del	p.Tyr191ThrfsTer49	p.Y191Tfs*49	ENST00000382592	NM_014572.2	190	ccC/cc	4/8	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.4185054081564	2		187	406	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906501	32906501	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1347459118	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	75	174	0	ENST00000380152.3:c.886T>C	p.Tyr296His	p.Y296H	ENST00000380152		296	Tat/Cat	10/27	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.4185054081564	2		174	355	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	98	205	1	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.4185054081564	2		206	439	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988426	36988426	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1341967476	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	42	41	0	ENST00000354822.5:c.227C>T	p.Ala76Val	p.A76V	ENST00000354822	NM_001079668.2	76	gCg/gTg	2/3	1	2	FACETS	0.836	0.716	0.962	1	0.968	1	CLONAL	2	TRUE	1	0.4185054081564	2		41	120	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103385	2103385	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45517099	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	87	140	0	ENST00000219476.3:c.268C>T	p.Gln90Ter	p.Q90*	ENST00000219476	NM_000548.3	90	Cag/Tag	4/42	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.4185054081564	2		140	379	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639636	3639636	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367562934	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	51	166	0	ENST00000294008.3:c.4003G>A	p.Gly1335Ser	p.G1335S	ENST00000294008	NM_032444.2	1335	Ggc/Agc	12/15	1	2	FACETS	0.548	0.466	0.637	0.548	0.466	0.637	SUBCLONAL	1	TRUE	1	0.4185054081564	2		166	445	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656513	3656513	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	117	249	0	ENST00000294008.3:c.722T>A	p.Val241Asp	p.V241D	ENST00000294008	NM_032444.2	241	gTc/gAc	3/15	1	2	FACETS	0.988	0.894	1	0.988	0.894	1	CLONAL	1	TRUE	1	0.4185054081564	2		249	566	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778277	3778277	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	25	144	0	ENST00000262367.5:c.6771G>T	p.Gln2257His	p.Q2257H	ENST00000262367	NM_004380.2	2257	caG/caT	31/31	1	2	FACETS	0.404	0.318	0.501	0.404	0.318	0.501	SUBCLONAL	1	TRUE	1	0.4185054081564	2		144	296	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830806	72830807	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	74	174	0	ENST00000268489.5:c.5774dup	p.Gly1926TrpfsTer3	p.G1926Wfs*3	ENST00000268489	NM_006885.3	1925	ggt/ggGt	9/10	1	2	FACETS	0.895	0.788	1	0.895	0.788	1	CLONAL	1	TRUE	1	0.4185054081564	2		174	395	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944250	81944250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147396004	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	74	159	0	ENST00000359376.3:c.1859C>T	p.Thr620Met	p.T620M	ENST00000359376	NM_002661.3	620	aCg/aTg	18/33	1	2	FACETS	0.958	0.844	1	0.958	0.844	1	CLONAL	1	TRUE	1	0.4185054081564	2		159	369	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348566	89348568	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs753054998	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	99	233	1	ENST00000301030.4:c.4382_4384del	p.Lys1461del	p.K1461del	ENST00000301030	NM_001256183.1	1461	aAGAga/aga	9/13	1	2	FACETS	0.768	0.687	0.854	0.768	0.687	0.854	SUBCLONAL	1	TRUE	1	0.4185054081564	2		234	616	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439919	56439919	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	98	195	0	ENST00000407977.2:c.673del	p.Arg225AlafsTer194	p.R225Afs*194	ENST00000407977		225	Cgc/gc	6/10	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.4185054081564	2		195	447	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448325	56448325	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	90	182	0	ENST00000407977.2:c.322A>G	p.Lys108Glu	p.K108E	ENST00000407977		108	Aag/Gag	3/10	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.4185054081564	2		182	390	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732986	74732986	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	38	47	0	ENST00000359995.5:c.257G>T	p.Arg86Leu	p.R86L	ENST00000359995	NM_001195427.1	86	cGg/cTg	1/3	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.4185054081564	2		47	156	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4090613	4090613	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	63	110	0	ENST00000262948.5:c.1186A>G	p.Thr396Ala	p.T396A	ENST00000262948	NM_030662.3	396	Acg/Gcg	11/11	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.4185054081564	2		110	277	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602918	10602918	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	81	156	0	ENST00000171111.5:c.660C>A	p.Phe220Leu	p.F220L	ENST00000171111	NM_203500.1	220	ttC/ttA	3/6	1	2	FACETS	0.926	0.82	1	0.926	0.82	1	CLONAL	1	TRUE	1	0.4185054081564	2		156	418	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030586	11030586	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	83	183	0	ENST00000327064.4:c.1140T>A	p.His380Gln	p.H380Q	ENST00000327064	NM_199141.1	380	caT/caA	10/16	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.4185054081564	2		183	391	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030613	11030613	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	71	158	0	ENST00000327064.4:c.1167C>A	p.Phe389Leu	p.F389L	ENST00000327064	NM_199141.1	389	ttC/ttA	10/16	1	2	FACETS	0.94	0.825	1	0.94	0.825	1	CLONAL	1	TRUE	1	0.4185054081564	2		158	361	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096048	11096048	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	82	147	2	ENST00000358026.2:c.326del	p.Pro109ArgfsTer194	p.P109Rfs*194	ENST00000358026	NM_001128849.1	108	Ccc/cc	3/36	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.4185054081564	2		149	332	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097083	11097084	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	71	128	0	ENST00000358026.2:c.579dup	p.Gln194AlafsTer93	p.Q194Afs*93	ENST00000358026	NM_001128849.1	192	agg/aGgg	4/36	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.4185054081564	2		128	329	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285059	15285059	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs367543285	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	43	115	0	ENST00000263388.2:c.4556T>C	p.Leu1519Pro	p.L1519P	ENST00000263388	NM_000435.2	1519	cTg/cCg	25/33	1	2	FACETS	0.734	0.618	0.861	0.734	0.618	0.861	SUBCLONAL	1	TRUE	1	0.4185054081564	2		115	280	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354260	15354260	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	76	140	0	ENST00000263377.2:c.2620A>G	p.Ser874Gly	p.S874G	ENST00000263377	NM_058243.2	874	Agc/Ggc	14/20	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.4185054081564	2		140	331	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216153	36216153	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	88	137	0	ENST00000222270.7:c.3566del	p.Gly1189AlafsTer2	p.G1189Afs*2	ENST00000222270	NM_014727.1	1187	atG/at	11/37	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.4185054081564	2		137	391	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741201	40741201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	33	155	0	ENST00000392038.2:c.1232G>A	p.Ser411Asn	p.S411N	ENST00000392038	NM_001626.4	411	aGc/aAc	12/14	1	2	FACETS	0.533	0.435	0.642	0.533	0.435	0.642	SUBCLONAL	1	TRUE	1	0.4185054081564	2		155	296	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752768	42752768	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	61	120	0	ENST00000222329.4:c.1496del	p.Gly499AlafsTer32	p.G499Afs*32	ENST00000222329	NM_006494.2	499	gGc/gc	4/4	1	2	FACETS	0.826	0.716	0.944	0.826	0.716	0.944	CLONAL	1	TRUE	1	0.4185054081564	2		120	353	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791190	42791190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1225908345	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	57	124	0	ENST00000575354.2:c.250C>T	p.Arg84Trp	p.R84W	ENST00000575354	NM_015125.3	84	Cgg/Tgg	3/20	1	2	FACETS	0.865	0.747	0.992	0.865	0.747	0.992	CLONAL	1	TRUE	1	0.4185054081564	2		124	315	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50916729	50916729	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	74	136	0	ENST00000440232.2:c.2201T>C	p.Leu734Pro	p.L734P	ENST00000440232	NM_002691.3	734	cTg/cCg	18/27	1	2	FACETS	0.943	0.831	1	0.943	0.831	1	CLONAL	1	TRUE	1	0.4185054081564	2		136	375	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919036	50919036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746950229	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	96	108	1	ENST00000440232.2:c.2773G>A	p.Val925Met	p.V925M	ENST00000440232	NM_002691.3	925	Gtg/Atg	22/27	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.4185054081564	2		109	387	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139625	202139626	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	70	173	0	ENST00000358485.4:c.790dup	p.Val264GlyfsTer13	p.V264Gfs*13	ENST00000358485	NM_001080125.1	262	-/G	6/9	1	2	FACETS	0.894	0.784	1	0.894	0.784	1	CLONAL	1	TRUE	1	0.4185054081564	2		173	374	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022470	31022470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	10	64	0	ENST00000375687.4:c.1955G>A	p.Gly652Asp	p.G652D	ENST00000375687	NM_015338.5	652	gGc/gAc	13/13	1	2	FACETS	0.319	0.216	0.446	0.319	0.216	0.446	SUBCLONAL	1	TRUE	1	0.4185054081564	2		64	150	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279885	46279887	+	inframe_deletion	In_Frame_Del	DEL	CAG	CAG	-	rs772979098	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	30	149	0	ENST00000371998.3:c.3816_3818del	p.Gln1276del	p.Q1276del	ENST00000371998		1271	CAG/-	20/23	1	2	FACETS	0.427	0.344	0.52	0.427	0.344	0.52	SUBCLONAL	1	TRUE	1	0.4185054081564	2		149	336	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574890	41574890	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	113	230	0	ENST00000263253.7:c.7175A>G	p.Asp2392Gly	p.D2392G	ENST00000263253	NM_001429.3	2392	gAc/gGc	31/31	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.4185054081564	2		230	518	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723623	49723623	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	12	40	0	ENST00000449682.2:c.1019A>G	p.Asp340Gly	p.D340G	ENST00000449682	NM_020998.3	340	gAc/gGc	9/18	0.4185054081564	2	FACETS	0.652	0.464	0.876	0.326	0.232	0.438	SUBCLONAL	1	TRUE	0	0.4185054081564	2		40	88	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588830	52588830	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	52	140	0	ENST00000394830.3:c.4198A>G	p.Met1400Val	p.M1400V	ENST00000394830	NM_018313.4	1400	Atg/Gtg	27/30	0.4185054081564	2	FACETS	0.863	0.74	0.996	0.431	0.37	0.498	CLONAL	1	TRUE	0	0.4185054081564	2		140	288	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480481	89480481	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	41	182	0	ENST00000336596.2:c.2318A>G	p.Asp773Gly	p.D773G	ENST00000336596	NM_005233.5	773	gAt/gGt	13/17	1	2	FACETS	0.671	0.562	0.791	0.671	0.562	0.791	SUBCLONAL	1	TRUE	1	0.4185054081564	2		182	292	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281404	142281404	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	97	232	0	ENST00000350721.4:c.840del	p.Val281Ter	p.V281*	ENST00000350721	NM_001184.3	280	ctT/ct	4/47	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.4185054081564	2		232	420	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504339	186504339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1560085211	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	31	122	0	ENST00000323963.5:c.681del	p.Lys227AsnfsTer3	p.K227Nfs*3	ENST00000323963		226	Aaa/aa	7/11	1	2	FACETS	0.581	0.472	0.703	0.581	0.472	0.703	SUBCLONAL	1	TRUE	1	0.4185054081564	2		122	255	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808898	1808898	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1416045205	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	61	110	0	ENST00000260795.2:c.2334del	p.Ser779AlafsTer41	p.S779Afs*41	ENST00000260795		777	aCc/ac	17/17	1	2	FACETS	0.956	0.831	1	0.956	0.831	1	CLONAL	1	TRUE	1	0.4185054081564	2		110	305	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808915	1808915	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	74	111	0	ENST00000260795.2:c.2347T>G	p.Ser783Ala	p.S783A	ENST00000260795		783	Tca/Gca	17/17	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.4185054081564	2		111	321	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1955175	1955175	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	101	212	0	ENST00000382891.5:c.2262C>A	p.Ser754Arg	p.S754R	ENST00000382891	NM_133335.3	754	agC/agA	12/22	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.4185054081564	2		212	409	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604695	55604695	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	80	166	0	ENST00000288135.5:c.2903A>G	p.Gln968Arg	p.Q968R	ENST00000288135	NM_000222.2	968	cAg/cGg	21/21	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.4185054081564	2		166	373	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156238	106156238	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	70	136	0	ENST00000380013.4:c.1139A>G	p.Tyr380Cys	p.Y380C	ENST00000380013	NM_001127208.2	380	tAc/tGc	3/11	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.4185054081564	2		136	306	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517795	187517795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs539528886	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	60	95	0	ENST00000441802.2:c.12899C>T	p.Ala4300Val	p.A4300V	ENST00000441802	NM_005245.3	4300	gCg/gTg	25/27	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.4185054081564	2		95	247	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521225	187521225	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	89	161	0	ENST00000441802.2:c.11930T>C	p.Met3977Thr	p.M3977T	ENST00000441802	NM_005245.3	3977	aTg/aCg	22/27	1	2	FACETS	0.982	0.876	1	0.982	0.876	1	CLONAL	1	TRUE	1	0.4185054081564	2		161	433	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31472274	31472274	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	124	265	0	ENST00000344624.3:c.2137C>A	p.Leu713Met	p.L713M	ENST00000344624		713	Ctg/Atg	14/33	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.4185054081564	2		265	504	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873603	35873603	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs776330345	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	49	133	0	ENST00000303115.3:c.559A>G	p.Lys187Glu	p.K187E	ENST00000303115	NM_002185.3	187	Aag/Gag	5/8	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.4185054081564	2		133	219	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	194	628	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.852	0.794	0.911	1	0.993	1	CLONAL	2	TRUE	1	0.4185054081564	2		633	544	SUCCESS
APC	324	MSKCC	GRCh37	5	112178774	112178774	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	31	168	0	ENST00000257430.4:c.7483A>G	p.Thr2495Ala	p.T2495A	ENST00000257430	NM_000038.5	2495	Aca/Gca	16/16	1	2	FACETS	0.375	0.303	0.456	0.375	0.303	0.456	SUBCLONAL	1	TRUE	1	0.4185054081564	2		168	395	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394942	394942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs944381620	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	84	182	0	ENST00000380956.4:c.338G>A	p.Arg113Gln	p.R113Q	ENST00000380956	NM_001195286.1	113	cGg/cAg	3/9	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.4185054081564	2		182	348	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031928	26031928	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	55	143	0	ENST00000244661.2:c.361A>G	p.Met121Val	p.M121V	ENST00000244661	NM_003537.3	121	Atg/Gtg	1/1	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.4185054081564	2		143	258	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	37	75	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	0.838	0.697	0.992	0.838	0.697	0.992	CLONAL	1	TRUE	1	0.4185054081564	2		75	211	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324735	31324735	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	15	36	0	ENST00000412585.2:c.74-1G>T		p.X25_splice	ENST00000412585	NM_005514.6	25			1	2	FACETS	0.779	0.579	1	0.779	0.579	1	CLONAL	1	TRUE	1	0.4185054081564	2		36	92	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31947216	31947216	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs534553211	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	95	147	0	ENST00000375333.2:c.701C>T	p.Pro234Leu	p.P234L	ENST00000375333	NM_032454.1	234	cCg/cTg	5/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.4185054081564	2		147	370	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129329	152129329	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	44	71	0	ENST00000206249.3:c.287del	p.Gly96ValfsTer13	p.G96Vfs*13	ENST00000206249	NM_000125.3	94	ctG/ct	1/8	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.4185054081564	2		71	193	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469764	157469764	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	92	209	0	ENST00000346085.5:c.2558A>G	p.Tyr853Cys	p.Y853C	ENST00000346085	NM_020732.3	853	tAc/tGc	9/20	1	2	FACETS	0.933	0.833	1	0.933	0.833	1	CLONAL	1	TRUE	1	0.4185054081564	2		209	471	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467635	50467635	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	41	97	0	ENST00000331340.3:c.870C>G	p.Asp290Glu	p.D290E	ENST00000331340	NM_006060.4	290	gaC/gaG	8/8	1	2	FACETS	0.757	0.634	0.89	0.757	0.634	0.89	SUBCLONAL	1	TRUE	1	0.4185054081564	2		97	259	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878556	151878556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	87	176	0	ENST00000262189.6:c.6389C>T	p.Pro2130Leu	p.P2130L	ENST00000262189	NM_170606.2	2130	cCa/cTa	36/59	1	2	FACETS	0.988	0.879	1	0.988	0.879	1	CLONAL	1	TRUE	1	0.4185054081564	2		176	421	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151882679	151882679	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	59	165	0	ENST00000262189.6:c.5046G>T	p.Trp1682Cys	p.W1682C	ENST00000262189	NM_170606.2	1682	tgG/tgT	34/59	1	2	FACETS	0.94	0.815	1	0.94	0.815	1	CLONAL	1	TRUE	1	0.4185054081564	2		165	300	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945664	151945664	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1482538393	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	107	288	0	ENST00000262189.6:c.1855A>G	p.Ile619Val	p.I619V	ENST00000262189	NM_170606.2	619	Att/Gtt	14/59	1	2	FACETS	0.963	0.867	1	0.963	0.867	1	CLONAL	1	TRUE	1	0.4185054081564	2		288	531	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021665	69021665	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs912103539	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	75	167	0	ENST00000288368.4:c.2953A>G	p.Met985Val	p.M985V	ENST00000288368	NM_024870.2	985	Atg/Gtg	25/40	1	2	FACETS	0.926	0.816	1	0.926	0.816	1	CLONAL	1	TRUE	1	0.4185054081564	2		167	387	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993674	90993674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1438838735	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	71	184	0	ENST00000265433.3:c.249G>A	p.Met83Ile	p.M83I	ENST00000265433	NM_002485.4	83	atG/atA	3/16	1	2	FACETS	0.884	0.775	0.999	0.884	0.775	0.999	CLONAL	1	TRUE	1	0.4185054081564	2		184	384	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206633	27206633	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	62	127	1	ENST00000380036.4:c.2418G>T	p.Lys806Asn	p.K806N	ENST00000380036	NM_000459.3	806	aaG/aaT	15/23	1	2	FACETS	0.728	0.631	0.832	0.728	0.631	0.832	SUBCLONAL	1	TRUE	1	0.4185054081564	2		128	407	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87338509	87338509	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1437483265	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	67	169	0	ENST00000277120.3:c.605C>A	p.Ala202Asp	p.A202D	ENST00000277120		202	gCc/gAc	7/19	1	2	FACETS	0.904	0.791	1	0.904	0.791	1	CLONAL	1	TRUE	1	0.4185054081564	2		169	354	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220567	98220567	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253559528	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	57	137	0	ENST00000331920.6:c.2896G>A	p.Ala966Thr	p.A966T	ENST00000331920	NM_000264.3	966	Gca/Aca	18/24	1	2	FACETS	0.976	0.845	1	0.976	0.845	1	CLONAL	1	TRUE	1	0.4185054081564	2		137	279	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401035	139401035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1268504383	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	114	148	0	ENST00000277541.6:c.3958G>A	p.Gly1320Ser	p.G1320S	ENST00000277541	NM_017617.3	1320	Ggc/Agc	24/34	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.4185054081564	2		148	422	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15833883	15833883	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1321533826	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	14	34	0	ENST00000307771.7:c.641G>A	p.Cys214Tyr	p.C214Y	ENST00000307771	NM_005089.3	214	tGc/tAc	8/11	1	1	FACETS	1	0.787	1	1	0.787	1	CLONAL	1	TRUE	0	0.4185054081564	1		34	50	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933233	39933233	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	47	127	0	ENST00000378444.4:c.1366G>A	p.Asp456Asn	p.D456N	ENST00000378444	NM_001123385.1	456	Gac/Aac	4/15	1	1	FACETS	0.719	0.612	0.835	0.719	0.612	0.835	SUBCLONAL	1	TRUE	0	0.4185054081564	1		127	247	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239687	53239687	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	82	100	0	ENST00000375401.3:c.1655T>C	p.Leu552Pro	p.L552P	ENST00000375401	NM_004187.3	552	cTg/cCg	12/26	1	1	FACETS	0.861	0.778	0.944	1	0.985	1	CLONAL	2	TRUE	0	0.4185054081564	1		100	180	SUCCESS
AR	367	MSKCC	GRCh37	X	66766562	66766562	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	26	65	0	ENST00000374690.3:c.1574G>C	p.Gly525Ala	p.G525A	ENST00000374690	NM_000044.3	525	gGc/gCc	1/8	1	1	FACETS	0.739	0.593	0.9	0.739	0.593	0.9	SUBCLONAL	1	TRUE	0	0.4185054081564	1		65	133	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357657	70357657	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	89	107	0	ENST00000374080.3:c.5908A>T	p.Ser1970Cys	p.S1970C	ENST00000374080		1970	Agc/Tgc	41/45	1	1	FACETS	0.793	0.718	0.87	1	0.984	1	SUBCLONAL	2	TRUE	0	0.4185054081564	1		107	212	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324886	31324887	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760037174	NA	P-0008504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	32	36	0	ENST00000412585.2:c.49_50insG	p.Leu17ArgfsTer82	p.L17Rfs*82	ENST00000412585	NM_005514.6	17	ctg/cGtg	1/8	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.4185054081564	2		36	109	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	144	387	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.565794553418201	2		387	432	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0009003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	373	735	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	0.565794553418201	2		735	1243	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468357	89468357	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs867931903	NA	P-0009003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	77	177	0	ENST00000336596.2:c.1891G>A	p.Glu631Lys	p.E631K	ENST00000336596	NM_005233.5	631	Gaa/Aaa	11/17	1	2	FACETS	0.775	0.686	0.87	0.775	0.686	0.87	SUBCLONAL	1	TRUE	1	0.565794553418201	2		177	351	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468526	89468526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	150	321	0	ENST00000336596.2:c.2060G>A	p.Gly687Glu	p.G687E	ENST00000336596	NM_005233.5	687	gGa/gAa	11/17	1	2	FACETS	0.943	0.867	1	0.943	0.867	1	CLONAL	1	TRUE	1	0.565794553418201	2		321	562	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156355	106156355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780355921	NA	P-0009003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	144	332	0	ENST00000380013.4:c.1256C>T	p.Pro419Leu	p.P419L	ENST00000380013	NM_001127208.2	419	cCt/cTt	3/11	1	2	FACETS	0.869	0.796	0.945	0.869	0.796	0.945	CLONAL	1	TRUE	1	0.565794553418201	2		332	586	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873648	35873648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867618621	NA	P-0009003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	180	404	0	ENST00000303115.3:c.604G>A	p.Glu202Lys	p.E202K	ENST00000303115	NM_002185.3	202	Gag/Aag	5/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.565794553418201	2		404	605	SUCCESS
APC	324	MSKCC	GRCh37	5	112175124	112175124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	104	252	0	ENST00000257430.4:c.3833C>T	p.Ser1278Leu	p.S1278L	ENST00000257430	NM_000038.5	1278	tCa/tTa	16/16	1	2	FACETS	0.857	0.772	0.945	0.857	0.772	0.945	CLONAL	1	TRUE	1	0.565794553418201	2		252	429	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439267	149439267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762329575	NA	P-0009003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	221	561	0	ENST00000286301.3:c.2128C>T	p.Arg710Cys	p.R710C	ENST00000286301	NM_005211.3	710	Cgc/Tgc	15/22	1	2	FACETS	0.908	0.847	0.972	0.908	0.847	0.972	CLONAL	1	TRUE	1	0.565794553418201	2		561	860	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117650567	117650567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	321	615	0	ENST00000368508.3:c.5291G>A	p.Gly1764Glu	p.G1764E	ENST00000368508	NM_002944.2	1764	gGg/gAg	32/43	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.565794553418201	2		615	1108	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005419	29005419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55687105	NA	P-0009003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	200	398	0	ENST00000282397.4:c.842G>A	p.Arg281Gln	p.R281Q	ENST00000282397	NM_002019.4	281	cGa/cAa	7/30	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.565794553418201	2		398	701	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098601	11098601	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0009003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	284	672	0	ENST00000358026.2:c.1118+1G>T		p.X373_splice	ENST00000358026	NM_001128849.1	373			0.565794553418201	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.565794553418201	1		672	699	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770630	40770630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	162	407	0	ENST00000373198.4:c.2752G>A	p.Gly918Arg	p.G918R	ENST00000373198	NM_133170.3	918	Ggg/Agg	19/32	1	2	FACETS	0.953	0.878	1	0.953	0.878	1	CLONAL	1	TRUE	1	0.565794553418201	2		407	601	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553007	106553008	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0009003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	259	663	0	ENST00000369096.4:c.973dup	p.Thr325AsnfsTer99	p.T325Nfs*99	ENST00000369096	NM_001198.3	324	-/A	5/7	1	2	FACETS	0.944	0.885	1	0.944	0.885	1	CLONAL	1	TRUE	1	0.565794553418201	2		663	970	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412366	139412367	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGCATGCT	novel	NA	P-0009003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	158	537	0	ENST00000277541.6:c.1271_1278dup	p.Gly427SerfsTer207	p.G427Sfs*207	ENST00000277541	NM_017617.3	426	-/AGCATGCG	8/34	0.565794553418201	2	FACETS	0.672	0.616	0.73	0.336	0.308	0.365	SUBCLONAL	1	TRUE	0	0.565794553418201	2		537	831	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242753	98242756	+	frameshift_variant	Frame_Shift_Del	DEL	ACCA	ACCA	-	novel	NA	P-0009003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	503	626	0	ENST00000331920.6:c.861_864del	p.Gly288MetfsTer35	p.G288Mfs*35	ENST00000331920	NM_000264.3	287	gtTGGT/gt	6/24	0.565794553418201	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.565794553418201	2		626	878	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445208	49445208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	297	817	0	ENST00000301067.7:c.2258C>T	p.Ser753Phe	p.S753F	ENST00000301067	NM_003482.3	753	tCc/tTc	10/54	1	2	FACETS	0.878	0.826	0.931	0.878	0.826	0.931	CLONAL	1	TRUE	1	0.565794553418201	2		817	1196	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219373	1219374	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGTGC	novel	NA	P-0009003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	67	679	0	ENST00000326873.7:c.428_432dup	p.Glu145CysfsTer18	p.E145Cfs*18	ENST00000326873	NM_000455.4	142	agc/agCGTGCc	3/10	0.565794553418201	1	FACETS	0.227	0.197	0.26	0.227	0.197	0.26	SUBCLONAL	1	TRUE	0	0.565794553418201	1		679	748	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850323	128850323	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	220	686	0	ENST00000249373.3:c.1586G>T	p.Gly529Val	p.G529V	ENST00000249373	NM_005631.4	529	gGc/gTc	9/12	1	2	FACETS	0.73	0.679	0.783	0.73	0.679	0.783	SUBCLONAL	1	TRUE	1	0.565794553418201	2		686	1065	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879358	151879358	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	206	413	0	ENST00000262189.6:c.5587C>T	p.Pro1863Ser	p.P1863S	ENST00000262189	NM_170606.2	1863	Ccc/Tcc	36/59	1	2	FACETS	0.963	0.896	1	0.963	0.896	1	CLONAL	1	TRUE	1	0.565794553418201	2		413	756	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372163	45372163	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010301-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	172	430	0	ENST00000262160.6:c.1006G>T	p.Val336Leu	p.V336L	ENST00000262160	NM_005901.5	336	Gtg/Ttg	9/11	0.553021465887524	4	FACETS	0.993	0.924	1	0.993	0.924	1	CLONAL	2	TRUE	2	0.69623219631791	4		430	422	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426492	49426492	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010301-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	47	787	0	ENST00000301067.7:c.11996C>G	p.Pro3999Arg	p.P3999R	ENST00000301067	NM_003482.3	3999	cCt/cGt	39/54	0.669516466245948	2	FACETS	0.204	0.171	0.24	0.102	0.085	0.12	SUBCLONAL	1	TRUE	0	0.69623219631791	2		787	662	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112217	115112217	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766332681	NA	P-0010301-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	32	249	2	ENST00000257566.3:c.1523C>T	p.Ala508Val	p.A508V	ENST00000257566	NM_016569.3	508	gCg/gTg	7/8	NA	2	FACETS	0.331	0.269	0.4			1	INDETERMINATE	1	TRUE	NA	0.69623219631791	2		251	278	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670492	134670492	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010301-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	26	528	0	ENST00000398015.3:c.403C>A	p.Leu135Ile	p.L135I	ENST00000398015	NM_004441.4	135	Ctc/Atc	3/16	0.69623219631791	2	FACETS	0.167	0.131	0.207	0.083	0.065	0.104	SUBCLONAL	1	TRUE	0	0.69623219631791	2		528	448	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	78	387	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.998	0.892	1	0.998	0.892	1	CLONAL	1	FALSE	1	0.69158147161341	2		387	226	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380254	25380254	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	284	464	0	ENST00000311936.3:c.204G>C	p.Arg68Ser	p.R68S	ENST00000311936	NM_004985.3	68	agG/agC	3/5	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.69158147161341	2		464	796	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309887	65309887	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1304838920	NA	P-0010654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	190	328	0	ENST00000342505.4:c.2263C>T	p.Arg755Ter	p.R755*	ENST00000342505	NM_002227.2	755	Cga/Tga	17/25	0.69158147161341	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	0	0.69158147161341	1		328	341	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931847	39931848	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTAA	novel	NA	P-0010654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	170	185	0	ENST00000378444.4:c.2751_2752insTTAC	p.Gln918LeufsTer29	p.Q918Lfs*29	ENST00000378444	NM_001123385.1	917	-/TTAC	4/15	1	1	FACETS	0.946	0.885	1	0.946	0.885	1	CLONAL	1	FALSE	0	0.69158147161341	1		185	340	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40460234	40460234	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	260	604	0	ENST00000345506.4:c.1945C>T	p.Arg649Trp	p.R649W	ENST00000345506	NM_003152.3	649	Cgg/Tgg	17/20	0.646819889704524	2	FACETS	1	0.986	1	0.575	0.542	0.609	CLONAL	1	TRUE	0	0.646819889704524	2		604	699	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170054	32170054	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	340	823	0	ENST00000375023.3:c.3554G>T	p.Gly1185Val	p.G1185V	ENST00000375023	NM_004557.3	1185	gGg/gTg	21/30	0.646819889704524	3	FACETS	1	0.984	1	0.55	0.52	0.581	CLONAL	1	TRUE	1	0.646819889704524	3		823	1265	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061192	38061192	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	565	431	0	ENST00000250448.2:c.797T>G	p.Phe266Cys	p.F266C	ENST00000250448	NM_004496.3	266	tTc/tGc	2/2	0.646819889704524	6	FACETS	0.919	0.887	0.951			1	CLONAL	4	TRUE	NA	0.646819889704524	6		431	1090	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577115	7577115	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	595	673	1	ENST00000269305.4:c.823T>G	p.Cys275Gly	p.C275G	ENST00000269305	NM_001126112.2	275	Tgt/Ggt	8/11	0.646819889704524	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.646819889704524	2		674	820	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76812945	76812947	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs1557059596	NA	P-0010823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	216	292	3	ENST00000373344.5:c.6674_6676del	p.Lys2225del	p.K2225del	ENST00000373344	NM_000489.3	2225	aAGAgg/agg	30/35	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.646819889704524	1		295	355	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106002	8106002	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	217	428	0	ENST00000346208.3:c.822G>T	p.Trp274Cys	p.W274C	ENST00000346208		274	tgG/tgT	4/6	0.521242132906215	3	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.646819889704524	3		428	729	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682445	52682445	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs775203392	NA	P-0010823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	181	423	0	ENST00000394830.3:c.728A>G	p.Lys243Arg	p.K243R	ENST00000394830	NM_018313.4	243	aAa/aGa	8/30	0.646819889704524	3	FACETS	0.957	0.884	1	0.478	0.442	0.516	CLONAL	1	TRUE	1	0.646819889704524	3		423	774	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539789	187539789	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	188	434	0	ENST00000441802.2:c.7951C>A	p.Leu2651Met	p.L2651M	ENST00000441802	NM_005245.3	2651	Ctg/Atg	10/27	0.646819889704524	4	FACETS	0.992	0.917	1	0.331	0.305	0.357	CLONAL	1	TRUE	1	0.646819889704524	4		434	965	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964366	70964366	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3413	373	432	0	ENST00000276594.2:c.1662C>G	p.Ile554Met	p.I554M	ENST00000276594	NM_024504.3	554	atC/atG	8/8	0.646819889704524	18	FACETS	0.94	0.886	0.996			1	CLONAL	2	TRUE	NA	0.646819889704524	18		432	3786	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098816	178098816	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	441	669	0	ENST00000397062.3:c.229G>T	p.Asp77Tyr	p.D77Y	ENST00000397062	NM_006164.4	77	Gat/Tat	2/5	0.406143302272512	4	FACETS	0.932	0.893	0.971	0.932	0.893	0.971	CLONAL	3	FALSE	1	0.484699619407029	4		669	966	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264416	46264416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	161	467	0	ENST00000371998.3:c.1463G>A	p.Gly488Glu	p.G488E	ENST00000371998		488	gGg/gAg	11/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.484699619407029	2		467	573	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961751	55961751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	145	520	0	ENST00000263923.4:c.2810C>T	p.Pro937Leu	p.P937L	ENST00000263923	NM_002253.2	937	cCc/cTc	20/30	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.484699619407029	2		520	486	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214368	55214368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761795138	NA	P-0011205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	205	639	2	ENST00000275493.2:c.494G>A	p.Arg165Gln	p.R165Q	ENST00000275493	NM_005228.3	165	cGg/cAg	4/28	0.20381067196312	4	FACETS	0.929	0.866	0.994	0.929	0.866	0.994	INDETERMINATE	2	FALSE	2	0.484699619407029	4		641	676	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0012419-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	241	563	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.455971572831224	2	FACETS	0.964	0.909	1	0.964	0.909	1	CLONAL	2	TRUE	0	0.455971572831224	2		563	548	SUCCESS
APC	324	MSKCC	GRCh37	5	112155042	112155042	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs863225310	NA	P-0012419-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	190	320	0	ENST00000257430.4:c.1312+1G>A		p.X438_splice	ENST00000257430	NM_000038.5	438			0.455971572831224	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	0	0.455971572831224	2		320	411	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012419-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	10	297	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	0.455971572831224	2	FACETS	0.199	0.135	0.281	0.1	0.067	0.141	SUBCLONAL	1	TRUE	0	0.455971572831224	2		297	220	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432674	29432674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770027238	NA	P-0012419-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	106	536	1	ENST00000389048.3:c.3814G>A	p.Gly1272Arg	p.G1272R	ENST00000389048	NM_004304.4	1272	Ggg/Agg	25/29	0.455971572831224	3	FACETS	0.969	0.871	1	0.485	0.435	0.537	CLONAL	1	TRUE	1	0.455971572831224	3		537	589	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917631	94917634	+	frameshift_variant	Frame_Shift_Del	DEL	CTTT	CTTT	-	novel	NA	P-0012419-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	113	617	0	ENST00000536441.1:c.887_890del	p.Glu296ValfsTer22	p.E296Vfs*22	ENST00000536441	NM_144665.3	296	gAAAGt/gt	6/10	0.455971572831224	3	FACETS	0.919	0.829	1	0.46	0.414	0.508	CLONAL	1	TRUE	1	0.455971572831224	3		617	662	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591130	67591135	+	inframe_deletion	In_Frame_Del	DEL	AAGACG	AAGACG	-	novel	NA	P-0012419-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	22	306	0	ENST00000274335.5:c.1724_1729del	p.Lys575_Thr576del	p.K575_T576del	ENST00000274335		575	AAGACG/-	12/15	0.455971572831224	2	FACETS	0.435	0.338	0.546	0.217	0.169	0.273	SUBCLONAL	1	TRUE	0	0.455971572831224	2		306	222	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020792	112020792	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012419-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	113	445	1	ENST00000368678.4:c.779C>A	p.Ala260Asp	p.A260D	ENST00000368678		260	gCt/gAt	8/13	0.455971572831224	2	FACETS	0.957	0.865	1	0.478	0.432	0.527	CLONAL	1	TRUE	0	0.455971572831224	2		446	518	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894228	NA	P-0012656-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	67	278	0	ENST00000451590.1:c.37G>C	p.Gly13Arg	p.G13R	ENST00000451590	NM_001130442.1	13	Ggt/Cgt	2/5	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.18	2		278	635	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913338	NA	P-0012656-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	55	402	0	ENST00000288602.6:c.1781A>C	p.Asp594Ala	p.D594A	ENST00000288602	NM_004333.4	594	gAt/gCt	15/18	1	2	FACETS	0.821	0.701	0.953	0.821	0.701	0.953	CLONAL	1	TRUE	1	0.18	2		402	744	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928077	178928097	+	inframe_deletion	In_Frame_Del	DEL	TAGAAGATTTGCTGAACCCTA	TAGAAGATTTGCTGAACCCTA	-	novel	NA	P-0012656-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	44	482	0	ENST00000263967.3:c.1356_1376del	p.Leu452_Ile459delinsPhe	p.L452_I459delinsF	ENST00000263967	NM_006218.2	452	tTAGAAGATTTGCTGAACCCTAtt/ttt	8/21	1	2	FACETS	0.557	0.465	0.659	0.557	0.465	0.659	SUBCLONAL	1	TRUE	1	0.18	2		482	878	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0013121-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	311	627	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.601660386922231	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.601660386922231	1		627	665	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0013121-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	604	603	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.601660386922231	3	FACETS	0.961	0.926	0.996	0.961	0.926	0.996	CLONAL	2	TRUE	1	0.601660386922231	3		603	1359	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403244	213403244	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs748663394	NA	P-0013121-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	153	345	0	ENST00000342788.4:c.11C>A	p.Ala4Glu	p.A4E	ENST00000342788	NM_005235.2	4	gCg/gAg	1/28	0.601660386922231	3	FACETS	0.848	0.777	0.923	0.424	0.388	0.462	CLONAL	1	TRUE	1	0.601660386922231	3		345	780	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372070	55372070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013121-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	158	226	1	ENST00000297316.4:c.760G>A	p.Ala254Thr	p.A254T	ENST00000297316	NM_022454.3	254	Gcg/Acg	2/2	0.601660386922231	3	FACETS	1	0.974	1	0.567	0.522	0.614	CLONAL	1	TRUE	1	0.601660386922231	3		227	602	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882073	36882073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1372104492	NA	P-0013121-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	242	435	0	ENST00000358127.4:c.940G>A	p.Gly314Arg	p.G314R	ENST00000358127	NM_001280556.1	314	Ggg/Agg	8/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.601660386922231	2		435	779	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346901	89346901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1455558820	NA	P-0013121-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	93	161	0	ENST00000301030.4:c.6049G>A	p.Ala2017Thr	p.A2017T	ENST00000301030	NM_001256183.1	2017	Gcc/Acc	9/13	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.601660386922231	2		161	309	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256445	46256445	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013121-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	285	476	0	ENST00000371998.3:c.673C>T	p.Gln225Ter	p.Q225*	ENST00000371998		225	Cag/Tag	7/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.601660386922231	2		476	902	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944367	76944367	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013121-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	323	642	0	ENST00000373344.5:c.538C>G	p.His180Asp	p.H180D	ENST00000373344	NM_000489.3	180	Cat/Gat	7/35	0.601660386922231	1	FACETS	0.972	0.924	1	0.972	0.924	1	CLONAL	1	TRUE	0	0.601660386922231	1		642	772	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988316	36988316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013121-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	159	279	0	ENST00000354822.5:c.337G>A	p.Val113Met	p.V113M	ENST00000354822	NM_001079668.2	113	Gtg/Atg	2/3	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.601660386922231	2		279	482	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581309	48581309	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013121-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	333	523	1	ENST00000342988.3:c.613G>T	p.Glu205Ter	p.E205*	ENST00000342988	NM_005359.5	205	Gag/Tag	5/12	0.601660386922231	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.601660386922231	1		524	708	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0013618-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1184	37	362	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	1	2	FACETS	0.266	0.218	0.32	0.266	0.218	0.32	SUBCLONAL	1	TRUE	1	0.228165850640146	2		362	1221	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0013618-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	120	607	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.832	0.749	0.92	0.832	0.749	0.92	CLONAL	1	TRUE	1	0.228165850640146	2		607	1265	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578499	7578529	+	frameshift_variant	Frame_Shift_Del	DEL	TGCACAGGGCAGGTCTTGGCCAGTTGGCAAA	TGCACAGGGCAGGTCTTGGCCAGTTGGCAAA	-	novel	NA	P-0013618-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1453	186	813	1	ENST00000269305.4:c.401_431del	p.Phe134CysfsTer26	p.F134Cfs*26	ENST00000269305	NM_001126112.2	134	tTTTGCCAACTGGCCAAGACCTGCCCTGTGCAg/tg	5/11	NA	2	FACETS	0.995	0.915	1			1	INDETERMINATE	1	TRUE	NA	0.228165850640146	2		814	1639	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0014842-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	259	193	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.667027206745261	2	FACETS	0.994	0.951	1	0.994	0.951	1	CLONAL	2	TRUE	0	0.673617455600351	2		193	387	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578349	212578349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1484791833	NA	P-0014842-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	239	275	1	ENST00000342788.4:c.908C>T	p.Ser303Phe	p.S303F	ENST00000342788	NM_005235.2	303	tCt/tTt	8/28	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.673617455600351	2		276	544	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202314	133202314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014842-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	240	451	0	ENST00000320574.5:c.6574del	p.Ala2192ArgfsTer10	p.A2192Rfs*10	ENST00000320574	NM_006231.2	2192	Gcg/cg	47/49	1	2	FACETS	0.992	0.931	1	0.992	0.931	1	CLONAL	1	TRUE	1	0.673617455600351	2		451	718	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835732	68835733	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0014842-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	255	464	1	ENST00000261769.5:c.326dup	p.Phe110ValfsTer58	p.F110Vfs*58	ENST00000261769	NM_004360.3	108	aga/agAa	3/16	0.673617455600351	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.673617455600351	1		465	480	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206838	36206838	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014842-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	371	291	0	ENST00000300305.3:c.674del	p.Leu225ProfsTer12	p.L225Pfs*12	ENST00000300305		225	cTc/cc	6/8	0.673617455600351	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.673617455600351	3		291	686	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989048	41989048	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0014842-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	200	484	0	ENST00000219905.7:c.1840A>T	p.Arg614Ter	p.R614*	ENST00000219905	NM_001164273.1	614	Aga/Tga	3/24	1	2	FACETS	0.946	0.881	1	0.946	0.881	1	CLONAL	1	TRUE	1	0.673617455600351	2		484	628	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015310-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	145	387	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.55	2		387	413	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351208	89351208	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015310-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	88	619	0	ENST00000301030.4:c.1742C>G	p.Ser581Cys	p.S581C	ENST00000301030	NM_001256183.1	581	tCt/tGt	9/13	1	2	FACETS	0.321	0.283	0.361	0.321	0.283	0.361	SUBCLONAL	1	TRUE	1	0.55	2		619	997	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245515	41245515	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555590634	NA	P-0015310-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1387	131	901	0	ENST00000357654.3:c.2033C>T	p.Ala678Val	p.A678V	ENST00000357654	NM_007294.3	678	gCc/gTc	10/23	1	2	FACETS	0.314	0.283	0.346	0.314	0.283	0.346	SUBCLONAL	1	TRUE	1	0.55	2		901	1518	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037193	71037193	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015310-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	75	474	0	ENST00000318789.4:c.1098G>C	p.Met366Ile	p.M366I	ENST00000318789	NM_032682.5	366	atG/atC	14/21	1	2	FACETS	0.31	0.271	0.353	0.31	0.271	0.353	SUBCLONAL	1	TRUE	1	0.55	2		474	879	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922023	39922023	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0015310-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	199	634	0	ENST00000378444.4:c.4149C>G	p.Tyr1383Ter	p.Y1383*	ENST00000378444	NM_001123385.1	1383	taC/taG	9/15	1	2	FACETS	0.717	0.664	0.772	0.717	0.664	0.772	SUBCLONAL	1	TRUE	1	0.55	2		634	1009	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115971	8115972	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016468-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	60	223	0	ENST00000346208.3:c.1318dup	p.Thr440AsnfsTer67	p.T440Nfs*67	ENST00000346208		439	-/A	6/6	1	2	FACETS	0.901	0.78	1	0.901	0.78	1	CLONAL	1	TRUE	1	0.343983939571693	2		223	387	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78704367	78704367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780768526	NA	P-0016468-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	181	268	0	ENST00000306801.3:c.515C>T	p.Thr172Met	p.T172M	ENST00000306801	NM_020761.2	172	aCg/aTg	5/34	0.343983939571693	6	FACETS	0.888	0.822	0.956	0.533	0.493	0.574	CLONAL	3	TRUE	1	0.343983939571693	6		268	667	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0017002-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	15	506	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.3	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		506	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0017002-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	80	302	0	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		302	622	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199469672	NA	P-0017002-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	29	500	2	ENST00000374080.3:c.131G>T	p.Gly44Val	p.G44V	ENST00000374080		44	gGt/gTt	2/45	0.25006285131116	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		502	635	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519975	NA	P-0017605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	459	363	0	ENST00000269305.4:c.403T>C	p.Cys135Arg	p.C135R	ENST00000269305	NM_001126112.2	135	Tgc/Cgc	5/11	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	2	TRUE	NA	0.545746808575428	2		363	833	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911387	32911387	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	287	528	0	ENST00000380152.3:c.2895G>T	p.Met965Ile	p.M965I	ENST00000380152		965	atG/atT	11/27	0.537142091338551	2	FACETS	0.871	0.826	0.915	0.871	0.826	0.915	CLONAL	2	TRUE	0	0.545746808575428	2		528	604	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061284	38061285	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGGAGCGT	novel	NA	P-0017605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	173	687	0	ENST00000250448.2:c.696_704dup	p.Arg233_Pro235dup	p.R233_P235dup	ENST00000250448	NM_004496.3	233	ccg/ccACGCTCCCCg	2/2	0.537142091338551	2	FACETS	0.687	0.632	0.744	0.343	0.316	0.372	SUBCLONAL	1	TRUE	0	0.545746808575428	2		687	923	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780068	NA	P-0019556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	268	624	1	ENST00000269305.4:c.472C>T	p.Arg158Cys	p.R158C	ENST00000269305	NM_001126112.2	158	Cgc/Tgc	5/11	0.533309740089392	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.533309740089392	1		625	662	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540654	NA	P-0019556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	229	641	0	ENST00000269305.4:c.329G>A	p.Arg110His	p.R110H	ENST00000269305	NM_001126112.2	110	cGt/cAt	4/11	0.533309740089392	1	FACETS	0.953	0.893	1	0.953	0.893	1	CLONAL	1	TRUE	0	0.533309740089392	1		641	661	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464537	25464537	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752434188	NA	P-0019556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	251	609	1	ENST00000264709.3:c.1976G>A	p.Arg659His	p.R659H	ENST00000264709	NM_175629.2	659	cGc/cAc	17/23	0.533309740089392	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.533309740089392	1		610	587	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426650	121426650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139016696	NA	P-0019556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	117	420	0	ENST00000257555.6:c.341G>A	p.Arg114His	p.R114H	ENST00000257555		114	cGt/cAt	2/10	0.533309740089392	1	FACETS	0.649	0.588	0.712	0.649	0.588	0.712	SUBCLONAL	1	TRUE	0	0.533309740089392	1		420	496	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692940	89692940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746152219	NA	P-0019556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	241	583	1	ENST00000371953.3:c.424C>T	p.Arg142Trp	p.R142W	ENST00000371953	NM_000314.4	142	Cgg/Tgg	5/9	0.533309740089392	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.533309740089392	1		584	603	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300837	137300837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	206	562	1	ENST00000481739.1:c.482G>A	p.Arg161Gln	p.R161Q	ENST00000481739	NM_002957.4	161	cGg/cAg	4/10	1	2	FACETS	0.929	0.863	0.996	0.929	0.863	0.996	CLONAL	1	TRUE	1	0.533309740089392	2		563	832	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059133	47059133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	200	424	0	ENST00000409792.3:c.7528C>T	p.Arg2510Cys	p.R2510C	ENST00000409792	NM_014159.6	2510	Cgc/Tgc	20/21	0.533309740089392	1	FACETS	0.953	0.889	1	0.953	0.889	1	CLONAL	1	TRUE	0	0.533309740089392	1		424	577	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395161	139395161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771407924	NA	P-0019556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	228	617	0	ENST00000277541.6:c.5777G>A	p.Arg1926His	p.R1926H	ENST00000277541	NM_017617.3	1926	cGc/cAc	31/34	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.533309740089392	2		617	783	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804367	43804367	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1443655691	NA	P-0019556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	186	378	0	ENST00000372470.3:c.367C>T	p.Arg123Ter	p.R123*	ENST00000372470	NM_005373.2	123	Cga/Tga	3/12	0.533309740089392	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.533309740089392	1		378	454	SUCCESS
EED	8726	MSKCC	GRCh37	11	85966300	85966300	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745786094	NA	P-0019556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	181	328	0	ENST00000263360.6:c.397C>T	p.Arg133Trp	p.R133W	ENST00000263360	NM_003797.3	133	Cgg/Tgg	4/12	0.533309740089392	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.533309740089392	1		328	417	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243365	46243365	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs76994389	NA	P-0019556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	101	229	0	ENST00000334344.6:c.1718C>T	p.Thr573Met	p.T573M	ENST00000334344	NM_152641.2	573	aCg/aTg	14/21	0.533309740089392	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.533309740089392	1		229	257	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966765	18966765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	47	590	0	ENST00000262803.5:c.1576G>A	p.Ala526Thr	p.A526T	ENST00000262803	NM_002911.3	526	Gcc/Acc	12/24	0.533309740089392	1	FACETS	0.179	0.15	0.211	0.179	0.15	0.211	SUBCLONAL	1	TRUE	0	0.533309740089392	1		590	722	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702410	47702410	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs267607986	NA	P-0019556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	105	201	0	ENST00000233146.2:c.2005+1G>A		p.X669_splice	ENST00000233146	NM_000251.2	669			0.533309740089392	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.533309740089392	1		201	231	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651506	52651508	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	novel	NA	P-0019556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	228	640	0	ENST00000394830.3:c.1588_1590del	p.Val530del	p.V530del	ENST00000394830	NM_018313.4	530	GTT/-	15/30	0.533309740089392	1	FACETS	0.911	0.853	0.971	0.911	0.853	0.971	CLONAL	1	TRUE	0	0.533309740089392	1		640	688	SUCCESS
ATR	545	MSKCC	GRCh37	3	142168389	142168389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199948706	NA	P-0019556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	210	524	1	ENST00000350721.4:c.7817G>A	p.Arg2606Gln	p.R2606Q	ENST00000350721	NM_001184.3	2606	cGa/cAa	47/47	0.533309740089392	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.533309740089392	1		525	570	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201815	66201815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764665078	NA	P-0019556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	156	411	1	ENST00000273854.3:c.2687G>A	p.Arg896His	p.R896H	ENST00000273854	NM_004439.5	896	cGt/cAt	16/18	1	2	FACETS	0.886	0.814	0.961	0.886	0.814	0.961	CLONAL	1	TRUE	1	0.533309740089392	2		412	660	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396913	139396913	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768040014	NA	P-0019556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	130	298	0	ENST00000277541.6:c.5195C>T	p.Ala1732Val	p.A1732V	ENST00000277541	NM_017617.3	1732	gCg/gTg	28/34	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.533309740089392	2		298	431	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227777	53227777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556839568	NA	P-0019556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	248	542	0	ENST00000375401.3:c.2411G>A	p.Arg804Gln	p.R804Q	ENST00000375401	NM_004187.3	804	cGg/cAg	17/26	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.533309740089392	2		542	857	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712005	89712005	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	80	203	0	ENST00000371953.3:c.623G>T	p.Gly208Val	p.G208V	ENST00000371953	NM_000314.4	208	gGc/gTc	6/9	0.533309740089392	1	FACETS	0.677	0.601	0.757	0.677	0.601	0.757	SUBCLONAL	1	TRUE	0	0.533309740089392	1		203	325	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196818	108196818	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1291249685	NA	P-0019556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	40	317	0	ENST00000278616.4:c.6841T>C	p.Tyr2281His	p.Y2281H	ENST00000278616	NM_000051.3	2281	Tac/Cac	47/63	0.533309740089392	1	FACETS	0.239	0.198	0.284	0.239	0.198	0.284	SUBCLONAL	1	TRUE	0	0.533309740089392	1		317	460	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126498	2126498	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781587135	NA	P-0019556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	122	496	1	ENST00000219476.3:c.2749C>T	p.Arg917Trp	p.R917W	ENST00000219476	NM_000548.3	917	Cgg/Tgg	25/42	0.533309740089392	1	FACETS	0.689	0.626	0.754	0.689	0.626	0.754	SUBCLONAL	1	TRUE	0	0.533309740089392	1		497	487	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211883	36211883	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202218975	NA	P-0019556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	55	676	0	ENST00000222270.7:c.1634G>A	p.Arg545Gln	p.R545Q	ENST00000222270	NM_014727.1	545	cGa/cAa	3/37	0.533309740089392	1	FACETS	0.198	0.168	0.23	0.198	0.168	0.23	SUBCLONAL	1	TRUE	0	0.533309740089392	1		676	765	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385105	31385105	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs777301633	NA	P-0019556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	22	392	0	ENST00000328111.2:c.1490G>A	p.Arg497Gln	p.R497Q	ENST00000328111	NM_006892.3	497	cGg/cAg	14/23	0.533309740089392	1	FACETS	0.142	0.109	0.18	0.142	0.109	0.18	SUBCLONAL	1	TRUE	0	0.533309740089392	1		392	427	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44515595	44515595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	129	675	1	ENST00000291552.4:c.301G>A	p.Val101Ile	p.V101I	ENST00000291552	NM_006758.2	101	Gtc/Atc	5/8	0.533309740089392	1	FACETS	0.503	0.456	0.551	0.503	0.456	0.551	SUBCLONAL	1	TRUE	0	0.533309740089392	1		676	706	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540539	187540539	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767321821	NA	P-0019556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	62	346	0	ENST00000441802.2:c.7201G>A	p.Glu2401Lys	p.E2401K	ENST00000441802	NM_005245.3	2401	Gag/Aag	10/27	1	2	FACETS	0.417	0.36	0.478	0.417	0.36	0.478	SUBCLONAL	1	TRUE	1	0.533309740089392	2		346	558	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0020938-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	194	675	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.261441577179679	5	FACETS	0.921	0.858	0.985	0.921	0.858	0.985	CLONAL	4	TRUE	1	0.261441577179679	5		675	561	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs879253911	NA	P-0020938-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	85	602	1	ENST00000269305.4:c.538G>T	p.Glu180Ter	p.E180*	ENST00000269305	NM_001126112.2	180	Gag/Tag	5/11	0.261441577179679	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.261441577179679	1		603	494	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293481	1293481	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021170-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2338	456	750	0	ENST00000310581.5:c.1520A>G	p.Glu507Gly	p.E507G	ENST00000310581	NM_198253.2	507	gAg/gGg	2/16	0.876278063051271	5	FACETS	0.862	0.819	0.907			1	CLONAL	1	TRUE	NA	0.876278063051271	5		750	2794	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849107	156849107	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021170-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1278	522	818	0	ENST00000524377.1:c.1999G>T	p.Gly667Cys	p.G667C	ENST00000524377	NM_002529.3	667	Ggt/Tgt	15/17	0.865289226647104	3	FACETS	0.952	0.91	0.994	0.476	0.455	0.497	CLONAL	1	TRUE	1	0.876278063051271	3		818	1800	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0021405-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	128	507	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	0.231345943785214	3	FACETS	0.946	0.86	1	0.946	0.86	1	CLONAL	2	TRUE	1	0.26	3		507	588	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431855	49431855	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021405-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	136	553	2	ENST00000301067.7:c.9284G>A	p.Gly3095Asp	p.G3095D	ENST00000301067	NM_003482.3	3095	gGc/gAc	34/54	0.231345943785214	3	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	1	0.26	3		555	582	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535316	66535316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021405-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	82	477	0	ENST00000273854.3:c.145G>A	p.Ala49Thr	p.A49T	ENST00000273854	NM_004439.5	49	Gca/Aca	1/18	0.102216408947234	0	FACETS	0.699	0.621	0.78			1	INDETERMINATE	2	TRUE	0	0.26	0		477	334	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64288369	64288369	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1420598115	NA	P-0021405-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	102	475	0	ENST00000370651.3:c.133A>G	p.Ile45Val	p.I45V	ENST00000370651	NM_003463.4	45	Ata/Gta	3/6	0.231345943785214	3	FACETS	0.912	0.82	1	0.912	0.82	1	CLONAL	2	TRUE	1	0.26	3		475	486	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	92	387	0				ENST00000310581	NM_198253.2	-/1132			0.438308877857772	0	FACETS	0.489	0.436	0.545			1	SUBCLONAL	1	FALSE	0	0.438308877857772	0		387	482	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106940	27106940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1179332640	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	120	424	0	ENST00000324856.7:c.6551C>T	p.Ala2184Val	p.A2184V	ENST00000324856	NM_006015.4	2184	gCc/gTc	20/20	0.438308877857772	0	FACETS	0.587	0.532	0.644			1	SUBCLONAL	1	FALSE	0	0.438308877857772	0		424	524	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937970	36937970	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	176	675	0	ENST00000361632.4:c.866C>T	p.Ala289Val	p.A289V	ENST00000361632		289	gCc/gTc	7/16	0.438308877857772	0	FACETS	0.583	0.538	0.63			1	SUBCLONAL	1	FALSE	0	0.438308877857772	0		675	774	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226566857	226566857	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	121	580	0	ENST00000366794.5:c.1731C>A	p.Asp577Glu	p.D577E	ENST00000366794	NM_001618.3	577	gaC/gaA	12/23	0.438308877857772	0	FACETS	0.465	0.421	0.512			1	SUBCLONAL	1	FALSE	0	0.438308877857772	0		580	667	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720717	89720717	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	31	76	0	ENST00000371953.3:c.868G>A	p.Val290Ile	p.V290I	ENST00000371953	NM_000314.4	290	Gta/Ata	8/9	1	2	FACETS	0.969	0.795	1	0.969	0.795	1	CLONAL	1	FALSE	1	0.438308877857772	2		76	146	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194164	94194164	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	176	566	0	ENST00000323929.3:c.1264T>A	p.Ser422Thr	p.S422T	ENST00000323929	NM_005591.3	422	Tca/Aca	12/20	0.438308877857772	0	FACETS	0.524	0.483	0.567			1	SUBCLONAL	1	FALSE	0	0.438308877857772	0		566	861	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205756	108205756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531980488	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	114	477	2	ENST00000278616.4:c.8071C>T	p.Arg2691Cys	p.R2691C	ENST00000278616	NM_000051.3	2691	Cgc/Tgc	55/63	0.438308877857772	0	FACETS	0.46	0.415	0.508			1	SUBCLONAL	1	FALSE	0	0.438308877857772	0		479	635	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230691	46230691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424958105	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	91	519	0	ENST00000334344.6:c.940C>T	p.Arg314Cys	p.R314C	ENST00000334344	NM_152641.2	314	Cgt/Tgt	8/21	1	2	FACETS	0.703	0.625	0.785	0.703	0.625	0.785	SUBCLONAL	1	FALSE	1	0.438308877857772	2		519	591	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813307	102813307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764732420	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	139	526	4	ENST00000307046.8:c.382G>A	p.Asp128Asn	p.D128N	ENST00000307046	NM_001111285.1	128	Gac/Aac	3/4	1	2	FACETS	0.951	0.868	1	0.951	0.868	1	CLONAL	1	FALSE	1	0.438308877857772	2		530	667	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112383	115112383	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	106	457	1	ENST00000257566.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000257566	NM_016569.3	453	Gag/Aag	7/8	1	2	FACETS	0.876	0.788	0.969	0.876	0.788	0.969	CLONAL	1	FALSE	1	0.438308877857772	2		458	552	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610608	81610608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	123	382	0	ENST00000298171.2:c.2206G>A	p.Glu736Lys	p.E736K	ENST00000298171	NM_000369.2	736	Gaa/Aaa	10/10	0.438308877857772	0	FACETS	0.621	0.564	0.68			1	SUBCLONAL	1	FALSE	0	0.438308877857772	0		382	508	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923459	9923459	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	151	502	0	ENST00000330684.3:c.1828G>A	p.Gly610Ser	p.G610S	ENST00000330684	NM_001134407.1	610	Ggc/Agc	9/13	0.438308877857772	0	FACETS	0.568	0.521	0.618			1	SUBCLONAL	1	FALSE	0	0.438308877857772	0		502	681	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992171	72992171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	160	560	0	ENST00000268489.5:c.1874C>T	p.Ser625Phe	p.S625F	ENST00000268489	NM_006885.3	625	tCc/tTc	2/10	0.438308877857772	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	0	0.438308877857772	1		560	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	162	711	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.438308877857772	1	FACETS	0.841	0.774	0.911	0.841	0.774	0.911	CLONAL	1	FALSE	0	0.438308877857772	1		711	686	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528489	29528489	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764079291	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	154	537	0	ENST00000356175.3:c.1246C>T	p.Arg416Ter	p.R416*	ENST00000356175	NM_000267.3	416	Cga/Tga	11/57	0.438308877857772	0	FACETS	0.542	0.497	0.589			1	SUBCLONAL	1	FALSE	0	0.438308877857772	0		537	728	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556985	29557036	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGGTCAGGTAAGCATTCTACTGAAATGTAGCAGAAACATTTTAAGAGATAA	CTGGTCAGGTAAGCATTCTACTGAAATGTAGCAGAAACATTTTAAGAGATAA	-	novel	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	14	99	0	ENST00000356175.3:c.2983_2990+44del		p.X995_splice	ENST00000356175	NM_000267.3	995		22/57	0.438308877857772	0	FACETS	0.285	0.207	0.377			1	SUBCLONAL	1	FALSE	0	0.438308877857772	0		99	126	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78811795	78811795	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	141	464	0	ENST00000306801.3:c.1210C>T	p.Arg404Trp	p.R404W	ENST00000306801	NM_020761.2	404	Cgg/Tgg	10/34	0.438308877857772	0	FACETS	0.575	0.526	0.627			1	SUBCLONAL	1	FALSE	0	0.438308877857772	0		464	628	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619810	1619810	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1302173832	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	157	700	2	ENST00000344749.5:c.1136C>T	p.Ser379Leu	p.S379L	ENST00000344749	NM_001136139.2	379	tCg/tTg	14/19	0.438308877857772	0	FACETS	0.508	0.466	0.552			1	SUBCLONAL	1	FALSE	0	0.438308877857772	0		702	792	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226908	2226908	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	112	388	0	ENST00000398665.3:c.4388C>T	p.Ser1463Phe	p.S1463F	ENST00000398665	NM_032482.2	1463	tCc/tTc	27/28	0.438308877857772	0	FACETS	0.546	0.493	0.601			1	SUBCLONAL	1	FALSE	0	0.438308877857772	0		388	526	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276875	15276875	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	159	626	2	ENST00000263388.2:c.5390C>T	p.Ser1797Phe	p.S1797F	ENST00000263388	NM_000435.2	1797	tCc/tTc	30/33	0.438308877857772	0	FACETS	0.535	0.491	0.581			1	SUBCLONAL	1	FALSE	0	0.438308877857772	0		628	762	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291056	15291056	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	186	674	0	ENST00000263388.2:c.3154G>A	p.Glu1052Lys	p.E1052K	ENST00000263388	NM_000435.2	1052	Gag/Aag	20/33	0.438308877857772	0	FACETS	0.542	0.501	0.585			1	SUBCLONAL	1	FALSE	0	0.438308877857772	0		674	879	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313039	30313039	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	92	526	0	ENST00000262643.3:c.840+2T>G		p.X280_splice	ENST00000262643	NM_001238.2	280			0.438308877857772	0	FACETS	0.439	0.391	0.49			1	SUBCLONAL	1	FALSE	0	0.438308877857772	0		526	537	SUCCESS
ALK	238	MSKCC	GRCh37	2	29419721	29419721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1215186876	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	123	454	0	ENST00000389048.3:c.4079G>A	p.Arg1360Gln	p.R1360Q	ENST00000389048	NM_004304.4	1360	cGg/cAg	28/29	0.438308877857772	0	FACETS	0.541	0.49	0.593			1	SUBCLONAL	1	FALSE	0	0.438308877857772	0		454	583	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609599	46609599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	179	749	0	ENST00000263734.3:c.2323C>T	p.His775Tyr	p.H775Y	ENST00000263734	NM_001430.4	775	Cat/Tat	15/16	0.438308877857772	0	FACETS	0.514	0.474	0.556			1	SUBCLONAL	1	FALSE	0	0.438308877857772	0		749	892	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158637091	158637091	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	150	560	1	ENST00000263640.3:c.89C>T	p.Pro30Leu	p.P30L	ENST00000263640	NM_001105.4	30	cCc/cTc	4/11	1	2	FACETS	0.874	0.8	0.952	0.874	0.8	0.952	CLONAL	1	FALSE	1	0.438308877857772	2		561	783	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31381354	31381354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766544393	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	167	484	0	ENST00000328111.2:c.1079C>T	p.Ser360Leu	p.S360L	ENST00000328111	NM_006892.3	360	tCg/tTg	10/23	0.438308877857772	0	FACETS	0.521	0.479	0.564			1	SUBCLONAL	1	FALSE	0	0.438308877857772	0		484	822	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447519	12447519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	176	513	1	ENST00000287820.6:c.758C>T	p.Ser253Phe	p.S253F	ENST00000287820	NM_015869.4	253	tCc/tTc	5/7	0.438308877857772	0	FACETS	0.603	0.557	0.651			1	SUBCLONAL	1	FALSE	0	0.438308877857772	0		514	748	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144868	47144868	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	153	648	0	ENST00000409792.3:c.4885C>T	p.His1629Tyr	p.H1629Y	ENST00000409792	NM_014159.6	1629	Cac/Tac	7/21	0.438308877857772	0	FACETS	0.513	0.469	0.558			1	SUBCLONAL	1	FALSE	0	0.438308877857772	0		648	765	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934214	49934214	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	171	715	2	ENST00000296474.3:c.2293C>T	p.Gln765Ter	p.Q765*	ENST00000296474	NM_002447.2	765	Cag/Tag	8/20	0.438308877857772	0	FACETS	0.588	0.542	0.636			1	SUBCLONAL	1	FALSE	0	0.438308877857772	0		717	745	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584500	189584500	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	90	387	1	ENST00000264731.3:c.796C>T	p.Arg266Ter	p.R266*	ENST00000264731	NM_003722.4	266	Cga/Tga	6/14	0.438308877857772	0	FACETS	0.441	0.392	0.493			1	SUBCLONAL	1	FALSE	0	0.438308877857772	0		388	523	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153703	55153703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	120	531	0	ENST00000257290.5:c.2669C>T	p.Ser890Phe	p.S890F	ENST00000257290	NM_006206.4	890	tCc/tTc	19/23	0.418098046412167	3	FACETS	0.774	0.698	0.853	0.387	0.349	0.427	SUBCLONAL	1	FALSE	1	0.438308877857772	3		531	863	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149465980	149465980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	175	654	0	ENST00000286301.3:c.11G>A	p.Gly4Glu	p.G4E	ENST00000286301	NM_005211.3	4	gGa/gAa	2/22	0.438308877857772	1	FACETS	0.977	0.904	1	0.977	0.904	1	CLONAL	1	FALSE	0	0.438308877857772	1		654	638	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057251	180057251	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	166	648	0	ENST00000261937.6:c.487C>T	p.Pro163Ser	p.P163S	ENST00000261937	NM_182925.4	163	Ccc/Tcc	4/30	0.438308877857772	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	FALSE	0	0.438308877857772	1		648	590	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271294	26271295	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	119	537	1	ENST00000305910.3:c.318_319delinsAA	p.Asp107Asn	p.D107N	ENST00000305910	NM_003534.2	106	gaGGat/gaAAat	1/1	1	2	FACETS	0.796	0.72	0.877	0.796	0.72	0.877	SUBCLONAL	1	FALSE	1	0.438308877857772	2		538	682	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93973602	93973602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	96	489	0	ENST00000369303.4:c.1774G>A	p.Gly592Ser	p.G592S	ENST00000369303	NM_004440.3	592	Ggc/Agc	9/17	0.438308877857772	0	FACETS	0.392	0.349	0.437			1	SUBCLONAL	1	FALSE	0	0.438308877857772	0		489	628	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555353	106555353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	89	415	0	ENST00000369096.4:c.2470G>A	p.Asp824Asn	p.D824N	ENST00000369096	NM_001198.3	824	Gat/Aat	7/7	0.438308877857772	0	FACETS	0.443	0.394	0.495			1	SUBCLONAL	1	FALSE	0	0.438308877857772	0		415	515	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265323	152265323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866869178	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	89	358	0	ENST00000206249.3:c.776G>A	p.Arg259Gln	p.R259Q	ENST00000206249	NM_000125.3	259	cGa/cAa	4/8	0.438308877857772	0	FACETS	0.501	0.446	0.56			1	SUBCLONAL	1	FALSE	0	0.438308877857772	0		358	455	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521965	157521965	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	92	549	0	ENST00000346085.5:c.4237G>A	p.Gly1413Ser	p.G1413S	ENST00000346085	NM_020732.3	1413	Ggc/Agc	18/20	0.438308877857772	0	FACETS	0.429	0.382	0.48			1	SUBCLONAL	1	FALSE	0	0.438308877857772	0		549	549	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249088	55249088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754426793	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	139	597	2	ENST00000275493.2:c.2386G>A	p.Gly796Ser	p.G796S	ENST00000275493	NM_005228.3	796	Ggc/Agc	20/28	0.438308877857772	0	FACETS	0.519	0.473	0.566			1	SUBCLONAL	1	FALSE	0	0.438308877857772	0		599	687	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509849	106509849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426277818	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	154	592	2	ENST00000359195.3:c.1843G>A	p.Glu615Lys	p.E615K	ENST00000359195	NM_002649.2	615	Gaa/Aaa	2/11	1	2	FACETS	0.878	0.805	0.955	0.878	0.805	0.955	CLONAL	1	FALSE	1	0.438308877857772	2		594	800	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69000044	69000044	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	126	559	0	ENST00000288368.4:c.2113G>A	p.Gly705Arg	p.G705R	ENST00000288368	NM_024870.2	705	Gga/Aga	19/40	0.438308877857772	0	FACETS	0.488	0.442	0.535			1	SUBCLONAL	1	FALSE	0	0.438308877857772	0		559	662	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058515	69058515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	126	628	0	ENST00000288368.4:c.4159C>T	p.His1387Tyr	p.H1387Y	ENST00000288368	NM_024870.2	1387	Cat/Tat	34/40	0.438308877857772	0	FACETS	0.441	0.4	0.485			1	SUBCLONAL	1	FALSE	0	0.438308877857772	0		628	732	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980602	70980602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	135	490	1	ENST00000276594.2:c.775G>A	p.Val259Met	p.V259M	ENST00000276594	NM_024504.3	259	Gtg/Atg	4/8	0.438308877857772	0	FACETS	0.575	0.524	0.628			1	SUBCLONAL	1	FALSE	0	0.438308877857772	0		491	602	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492876	8492876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	127	512	0	ENST00000356435.5:c.2453C>T	p.Ser818Phe	p.S818F	ENST00000356435		818	tCc/tTc	16/35	0.438308877857772	0	FACETS	0.614	0.559	0.672			1	SUBCLONAL	1	FALSE	0	0.438308877857772	0		512	530	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209493	98209493	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	156	596	1	ENST00000331920.6:c.4045C>T	p.Pro1349Ser	p.P1349S	ENST00000331920	NM_000264.3	1349	Cct/Tct	23/24	0.438308877857772	0	FACETS	0.813	0.75	0.877			1	CLONAL	1	FALSE	0	0.438308877857772	0		597	492	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980865	40980865	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs746154941	NA	P-0022827-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	144	517	0	ENST00000373198.4:c.1621A>G	p.Lys541Glu	p.K541E	ENST00000373198	NM_133170.3	541	Aaa/Gaa	10/32	0.438308877857772	0	FACETS	0.554	0.507	0.604			1	SUBCLONAL	1	FALSE	0	0.438308877857772	0		517	666	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0023805-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	194	314	0	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	0.660919894456082	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.660919894456082	1		314	367	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240274	41240274	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024620-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	131	255	1	ENST00000379561.5:c.76C>T	p.Pro26Ser	p.P26S	ENST00000379561	NM_002015.3	26	Ccg/Tcg	1/3	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.755709483884476	2		256	327	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348798	118348798	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs868985556	NA	P-0024911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	418	549	0	ENST00000534358.1:c.3451C>T	p.Arg1151Ter	p.R1151*	ENST00000534358	NM_005933.3	1151	Cga/Tga	5/36	0.566800157160125	3	FACETS	0.92	0.886	0.953	0.92	0.886	0.953	CLONAL	3	TRUE	0	0.566800157160125	3		549	686	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617710	39617710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	92	645	0	ENST00000262039.4:c.1894C>T	p.Pro632Ser	p.P632S	ENST00000262039	NM_002647.2	632	Cca/Tca	17/25	0.566800157160125	4	FACETS	0.591	0.524	0.662	0.148	0.131	0.166	SUBCLONAL	1	TRUE	0	0.566800157160125	4		645	861	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300172	15300173	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0024911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1212	165	898	1	ENST00000263388.2:c.1103_1104del	p.Thr368LysfsTer21	p.T368Kfs*21	ENST00000263388	NM_000435.2	368	aCA/a	7/33	0.537948972585814	5	FACETS	0.782	0.716	0.852	0.261	0.238	0.284	SUBCLONAL	1	TRUE	2	0.566800157160125	5		899	1377	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	26	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.189456274028794	3	FACETS	0.862	0.708	1	1	0.927	1	INDETERMINATE	3	TRUE	1	0.335643538278815	3		371	70	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0025067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	11	285	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.124901539861334	4	FACETS	0.858	0.61	1	0.858	0.61	1	INDETERMINATE	2	TRUE	2	0.335643538278815	4		285	51	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913233	NA	P-0025077-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	323	777	0	ENST00000451590.1:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000451590	NM_001130442.1	61	cAg/cTg	3/5	NA	2	FACETS	1	0.95	1			1	INDETERMINATE	1	TRUE	NA	0.668843337272756	2		777	962	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831354	72831354	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025077-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	190	328	0	ENST00000268489.5:c.5227C>T	p.Gln1743Ter	p.Q1743*	ENST00000268489	NM_006885.3	1743	Caa/Taa	9/10	0.30875558787582	1	FACETS	0.84	0.786	0.896	0.84	0.786	0.896	INDETERMINATE	1	TRUE	0	0.668843337272756	1		328	450	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	129	387	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.783	0.711	0.858	1	0.987	1	SUBCLONAL	2	TRUE	1	0.23990762366513	2		387	687	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005419	29005419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55687105	NA	P-0025373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	55	398	0	ENST00000282397.4:c.842G>A	p.Arg281Gln	p.R281Q	ENST00000282397	NM_002019.4	281	cGa/cAa	7/30	1	2	FACETS	0.626	0.534	0.726	0.626	0.534	0.726	SUBCLONAL	1	TRUE	1	0.23990762366513	2		398	733	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0025373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	133	601	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.232771420561054	2	FACETS	0.957	0.868	1	0.479	0.434	0.527	CLONAL	1	TRUE	0	0.23990762366513	2		602	1158	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412204	139412204	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1448146225	NA	P-0025373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	156	508	1	ENST00000277541.6:c.1441G>A	p.Gly481Ser	p.G481S	ENST00000277541	NM_017617.3	481	Ggc/Agc	8/34	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.23990762366513	2		509	880	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038902	12038902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159945	NA	P-0025373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	102	450	0	ENST00000396373.4:c.1195C>T	p.Arg399Cys	p.R399C	ENST00000396373	NM_001987.4	399	Cgc/Tgc	7/8	1	2	FACETS	0.979	0.874	1	0.979	0.874	1	CLONAL	1	TRUE	1	0.23990762366513	2		450	869	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539951	187539951	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs777631605	NA	P-0025373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	82	406	0	ENST00000441802.2:c.7789C>T	p.Arg2597Ter	p.R2597*	ENST00000441802	NM_005245.3	2597	Cga/Tga	10/27	0.23990762366513	1	FACETS	0.93	0.82	1	0.93	0.82	1	CLONAL	1	TRUE	0	0.23990762366513	1		406	647	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0025373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	204	445	1	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	0.232771420561054	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	0	0.23990762366513	2		446	850	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263824	16263824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1035625124	NA	P-0025373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	63	428	0	ENST00000375759.3:c.10193G>A	p.Gly3398Glu	p.G3398E	ENST00000375759	NM_015001.2	3398	gGa/gAa	12/15	0.232771420561054	2	FACETS	0.591	0.51	0.679	0.295	0.255	0.34	SUBCLONAL	1	TRUE	0	0.23990762366513	2		428	889	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745964	162745964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	77	301	0	ENST00000367921.3:c.2087C>T	p.Ser696Phe	p.S696F	ENST00000367921	NM_006182.2	696	tCt/tTt	16/18	1	2	FACETS	0.928	0.814	1	0.928	0.814	1	CLONAL	1	TRUE	1	0.23990762366513	2		301	692	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66679759	66679759	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	101	338	0	ENST00000307102.5:c.74C>G	p.Ser25Cys	p.S25C	ENST00000307102	NM_002755.3	25	tCt/tGt	1/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.23990762366513	2		338	604	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650924	37650924	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	55	514	1	ENST00000447079.4:c.2396C>A	p.Ala799Glu	p.A799E	ENST00000447079	NM_015083.1	799	gCa/gAa	5/14	1	2	FACETS	0.455	0.388	0.529	0.455	0.388	0.529	SUBCLONAL	1	TRUE	1	0.23990762366513	2		515	1008	SUCCESS
APC	324	MSKCC	GRCh37	5	112176962	112176962	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	44	392	0	ENST00000257430.4:c.5671G>C	p.Glu1891Gln	p.E1891Q	ENST00000257430	NM_000038.5	1891	Gag/Cag	16/16	1	2	FACETS	0.466	0.39	0.551	0.466	0.39	0.551	SUBCLONAL	1	TRUE	1	0.23990762366513	2		392	787	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249346	110249346	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	224	632	0	ENST00000374672.4:c.1227G>C	p.Lys409Asn	p.K409N	ENST00000374672	NM_004235.4	409	aaG/aaC	4/5	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.23990762366513	2		632	1355	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391889	139391890	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0025373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	131	534	0	ENST00000277541.6:c.6301_6302del	p.Ala2101ThrfsTer166	p.A2101Tfs*166	ENST00000277541	NM_017617.3	2101	GCa/a	34/34	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.23990762366513	2		534	1066	SUCCESS
CBL	867	MSKCC	GRCh37	11	119077220	119077230	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCTTCCAGC	CGCCTTCCAGC	-	novel	NA	P-0025374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	148	257	0	ENST00000264033.4:c.96_106del	p.Phe33ProfsTer44	p.F33Pfs*44	ENST00000264033	NM_005188.3	31	gaCGCCTTCCAGCcg/gacg	1/16	1	2	FACETS	0.667	0.614	0.722	0.667	0.614	0.722	SUBCLONAL	1	TRUE	1	0.927763062663833	2		257	478	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855979	76855984	+	inframe_deletion	In_Frame_Del	DEL	TGGAAA	TGGAAA	-	novel	NA	P-0025374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	322	501	0	ENST00000373344.5:c.5616_5621del	p.Phe1873_Gln1874del	p.F1873_Q1874del	ENST00000373344	NM_000489.3	1872	ctTTTCCAa/cta	23/35	1	2	FACETS	0.913	0.868	0.96	0.913	0.868	0.96	CLONAL	1	TRUE	1	0.927763062663833	2		501	760	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101289	27101290	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	45	375	0	ENST00000324856.7:c.4572dup	p.Gly1525TrpfsTer7	p.G1525Wfs*7	ENST00000324856	NM_006015.4	1524	cat/caTt	18/20	0.288518429320942	1	FACETS	0.89	0.752	1	0.89	0.752	1	CLONAL	1	TRUE	0	0.288518429320942	1		375	300	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671697	67671697	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	91	436	0	ENST00000264010.4:c.2106G>C	p.Glu702Asp	p.E702D	ENST00000264010	NM_006565.3	702	gaG/gaC	12/12	0.182084973716795	2	FACETS	1	0.975	1	0.673	0.6	0.75	CLONAL	1	TRUE	0	0.288518429320942	2		436	469	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082566	16082566	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	38	187	0	ENST00000281043.3:c.380A>C	p.Glu127Ala	p.E127A	ENST00000281043	NM_005378.4	127	gAg/gCg	2/3	0.288518429320942	1	FACETS	0.895	0.744	1	0.895	0.744	1	CLONAL	1	TRUE	0	0.288518429320942	1		187	252	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188303	10188303	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	41	452	0	ENST00000256474.2:c.447del	p.Asn150IlefsTer9	p.N150Ifs*9	ENST00000256474	NM_000551.3	149	gCc/gc	2/3	1	2	FACETS	0.772	0.652	0.903	1	0.961	1	CLONAL	2	TRUE	1	0.288518429320942	2		452	184	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678720	52678720	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	42	479	0	ENST00000394830.3:c.899G>T	p.Arg300Met	p.R300M	ENST00000394830	NM_018313.4	300	aGg/aTg	9/30	1	2	FACETS	0.997	0.837	1	0.997	0.837	1	CLONAL	1	TRUE	1	0.288518429320942	2		479	292	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31464399	31464399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	48	669	1	ENST00000344624.3:c.2518G>A	p.Val840Met	p.V840M	ENST00000344624		840	Gtg/Atg	17/33	1	2	FACETS	0.836	0.708	0.976	0.836	0.708	0.976	CLONAL	1	TRUE	1	0.288518429320942	2		670	398	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1234	226	387	0				ENST00000310581	NM_198253.2	-/1132			0.316897781443125	3	FACETS	1	0.973	1	0.547	0.508	0.588	CLONAL	1	TRUE	1	0.329666664112064	3		387	1460	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0025377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	143	611	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.745	0.677	0.816	0.745	0.677	0.816	SUBCLONAL	1	TRUE	1	0.329666664112064	2		611	1165	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0025377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	257	405	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.329666664112064	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.329666664112064	1		406	1226	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097754	8097754	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	256	524	1	ENST00000346208.3:c.136G>T	p.Glu46Ter	p.E46*	ENST00000346208		46	Gag/Tag	2/6	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.329666664112064	2		525	1464	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70411648	70411648	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	163	535	2	ENST00000373644.4:c.4322G>T	p.Gly1441Val	p.G1441V	ENST00000373644	NM_030625.2	1441	gGg/gTg	5/12	1	2	FACETS	0.989	0.907	1	0.989	0.907	1	CLONAL	1	TRUE	1	0.329666664112064	2		537	1000	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375351	118375351	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	104	376	0	ENST00000534358.1:c.8744C>G	p.Ser2915Cys	p.S2915C	ENST00000534358	NM_005933.3	2915	tCt/tGt	27/36	1	2	FACETS	0.776	0.694	0.863	0.776	0.694	0.863	SUBCLONAL	1	TRUE	1	0.329666664112064	2		376	813	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26927985	26927985	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	121	461	0	ENST00000381527.3:c.424C>G	p.Leu142Val	p.L142V	ENST00000381527	NM_001260.1	142	Ctg/Gtg	4/13	1	2	FACETS	0.861	0.777	0.949	0.861	0.777	0.949	CLONAL	1	TRUE	1	0.329666664112064	2		461	853	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059422	42059422	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	183	424	0	ENST00000219905.7:c.9142C>G	p.Pro3048Ala	p.P3048A	ENST00000219905	NM_001164273.1	3048	Cct/Gct	24/24	1	2	FACETS	0.995	0.917	1	0.995	0.917	1	CLONAL	1	TRUE	1	0.329666664112064	2		424	1116	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946227	81946228	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0025377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	161	479	2	ENST00000359376.3:c.1960_1961delinsTT	p.Gly654Leu	p.G654L	ENST00000359376	NM_002661.3	654	GGa/TTa	19/33	1	2	FACETS	0.737	0.674	0.803	0.737	0.674	0.803	SUBCLONAL	1	TRUE	1	0.329666664112064	2		481	1326	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140707	55140707	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1358	210	552	1	ENST00000257290.5:c.1568C>A	p.Ser523Tyr	p.S523Y	ENST00000257290	NM_006206.4	523	tCt/tAt	11/23	1	2	FACETS	0.813	0.752	0.876	0.813	0.752	0.876	CLONAL	1	TRUE	1	0.329666664112064	2		553	1568	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55991444	55991444	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1326	223	584	0	ENST00000263923.4:c.17T>C	p.Leu6Pro	p.L6P	ENST00000263923	NM_002253.2	6	cTg/cCg	1/30	1	2	FACETS	0.873	0.81	0.939	0.873	0.81	0.939	CLONAL	1	TRUE	1	0.329666664112064	2		584	1549	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361258	66361258	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	121	330	0	ENST00000273854.3:c.914G>T	p.Cys305Phe	p.C305F	ENST00000273854	NM_004439.5	305	tGc/tTc	4/18	1	2	FACETS	0.92	0.831	1	0.92	0.831	1	CLONAL	1	TRUE	1	0.329666664112064	2		330	798	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439329	149439329	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	289	570	0	ENST00000286301.3:c.2066C>A	p.Pro689His	p.P689H	ENST00000286301	NM_005211.3	689	cCc/cAc	15/22	0.329666664112064	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.329666664112064	1		570	1265	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163807	32163807	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751250725	NA	P-0025377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	229	406	0	ENST00000375023.3:c.5419G>A	p.Ala1807Thr	p.A1807T	ENST00000375023	NM_004557.3	1807	Gct/Act	30/30	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.329666664112064	2		406	1257	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974412	93974412	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	124	441	0	ENST00000369303.4:c.1642G>T	p.Val548Phe	p.V548F	ENST00000369303	NM_004440.3	548	Gtc/Ttc	8/17	1	2	FACETS	0.939	0.85	1	0.939	0.85	1	CLONAL	1	TRUE	1	0.329666664112064	2		441	801	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932732	39932732	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1579	285	652	0	ENST00000378444.4:c.1867G>T	p.Glu623Ter	p.E623*	ENST00000378444	NM_001123385.1	623	Gaa/Taa	4/15	1	2	FACETS	0.928	0.869	0.989	0.928	0.869	0.989	CLONAL	1	TRUE	1	0.329666664112064	2		652	1864	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410327	63410327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1420	288	604	1	ENST00000330258.3:c.2840C>T	p.Ser947Phe	p.S947F	ENST00000330258	NM_152424.3	947	tCc/tTc	2/2	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.329666664112064	2		605	1708	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411993	63411993	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	233	569	1	ENST00000330258.3:c.1174G>T	p.Glu392Ter	p.E392*	ENST00000330258	NM_152424.3	392	Gag/Tag	2/2	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.329666664112064	2		570	1302	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	81	387	0				ENST00000310581	NM_198253.2	-/1132			0.565487002557442	3	FACETS	1	0.979	1	0.707	0.634	0.781	CLONAL	1	TRUE	1	0.731659866978573	3		387	214	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0025379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	96	285	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.528	0.472	0.587	0.528	0.472	0.587	SUBCLONAL	1	TRUE	1	0.731659866978573	2		285	497	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0025379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	121	608	0	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	0.370648448070091	1	FACETS	0.416	0.378	0.456	0.416	0.378	0.456	INDETERMINATE	1	TRUE	0	0.731659866978573	1		608	504	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844420	156844420	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0025379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	542	644	1	ENST00000524377.1:c.1251+2T>A		p.X417_splice	ENST00000524377	NM_002529.3	417			0.731659866978573	5	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	2	0.731659866978573	5		645	974	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123889489	123889489	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	60	168	0	ENST00000330479.4:c.716G>A	p.Gly239Asp	p.G239D	ENST00000330479	NM_020382.3	239	gGt/gAt	7/9	1	2	FACETS	0.943	0.829	1	0.943	0.829	1	CLONAL	1	TRUE	1	0.731659866978573	2		168	174	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134748	41134748	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	153	315	0	ENST00000379561.5:c.880A>G	p.Lys294Glu	p.K294E	ENST00000379561	NM_002015.3	294	Aaa/Gaa	2/3	0.731659866978573	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.731659866978573	1		315	229	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250790	99250790	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0025379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	64	335	0	ENST00000268035.6:c.95-1G>A		p.X32_splice	ENST00000268035	NM_000875.3	32			1	2	FACETS	0.454	0.395	0.518	0.454	0.395	0.518	SUBCLONAL	1	TRUE	1	0.731659866978573	2		335	385	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400131	41400131	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	203	555	0	ENST00000373198.4:c.628A>T	p.Thr210Ser	p.T210S	ENST00000373198	NM_133170.3	210	Aca/Tca	5/32	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.731659866978573	2		555	543	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612028	189612028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs900140738	NA	P-0025382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	452	414	1	ENST00000264731.3:c.1780C>T	p.Arg594Ter	p.R594*	ENST00000264731	NM_003722.4	594	Cga/Tga	14/14	0.384977178413899	3	FACETS	0.817	0.782	0.852	0.817	0.782	0.852	INDETERMINATE	2	TRUE	1	0.690478822817014	3		415	1078	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849053	156849053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369353892	NA	P-0025382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	212	530	1	ENST00000524377.1:c.1945C>T	p.Arg649Trp	p.R649W	ENST00000524377	NM_002529.3	649	Cgg/Tgg	15/17	NA	2	FACETS	0.526	0.488	0.566			1	INDETERMINATE	1	TRUE	NA	0.690478822817014	2		531	1167	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857547	57857547	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	402	406	0	ENST00000228682.2:c.73C>A	p.Gln25Lys	p.Q25K	ENST00000228682	NM_005269.2	25	Cag/Aag	2/12	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.690478822817014	2		406	995	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252384	133252384	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	262	408	0	ENST00000320574.5:c.1043T>G	p.Phe348Cys	p.F348C	ENST00000320574	NM_006231.2	348	tTt/tGt	11/49	1	2	FACETS	0.923	0.868	0.98	0.923	0.868	0.98	CLONAL	1	TRUE	1	0.690478822817014	2		408	822	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862845	9862845	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	364	537	0	ENST00000330684.3:c.2458G>T	p.Val820Leu	p.V820L	ENST00000330684	NM_001134407.1	820	Gta/Tta	12/13	0.364484085971244	1	FACETS	0.788	0.751	0.826	0.788	0.751	0.826	INDETERMINATE	1	TRUE	0	0.690478822817014	1		537	876	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0025382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	534	470	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.630708677398989	2	FACETS	0.915	0.886	0.944	0.915	0.886	0.944	CLONAL	2	TRUE	0	0.690478822817014	2		470	845	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207168	1207168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520039	NA	P-0025382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	473	532	0	ENST00000326873.7:c.256C>T	p.Arg86Ter	p.R86*	ENST00000326873	NM_000455.4	86	Cga/Tga	1/10	0.690478822817014	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.690478822817014	1		532	857	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600470	10600470	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	468	494	0	ENST00000171111.5:c.1385G>A	p.Gly462Glu	p.G462E	ENST00000171111	NM_203500.1	462	gGg/gAg	4/6	0.690478822817014	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.690478822817014	1		494	828	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775433	39775433	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	313	359	0	ENST00000288319.7:c.587G>T	p.Arg196Ile	p.R196I	ENST00000288319	NM_182918.3	196	aGa/aTa	4/10	0.690478822817014	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.690478822817014	1		359	555	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52676020	52676021	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	433	582	0	ENST00000394830.3:c.1036dup	p.Thr346AsnfsTer11	p.T346Nfs*11	ENST00000394830	NM_018313.4	346	aca/aAca	11/30	0.690478822817014	1	FACETS	0.986	0.947	1	0.986	0.947	1	CLONAL	1	TRUE	0	0.690478822817014	1		582	833	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250530	26250530	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	361	502	0	ENST00000446824.2:c.304G>C	p.Val102Leu	p.V102L	ENST00000446824	NM_021018.2	102	Gtg/Ctg	1/1	0.690478822817014	1	FACETS	0.975	0.933	1	0.975	0.933	1	CLONAL	1	TRUE	0	0.690478822817014	1		502	702	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509032	106509032	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	277	468	0	ENST00000359195.3:c.1026C>A	p.His342Gln	p.H342Q	ENST00000359195	NM_002649.2	342	caC/caA	2/11	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.690478822817014	2		468	796	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121913370	NA	P-0025382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	372	203	0	ENST00000288602.6:c.1742A>G	p.Asn581Ser	p.N581S	ENST00000288602	NM_004333.4	581	aAt/aGt	15/18	0.384977178413899	3	FACETS	0.811	0.773	0.849	0.811	0.773	0.849	INDETERMINATE	2	TRUE	1	0.690478822817014	3		203	894	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317512	1317513	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0025382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	434	584	1	ENST00000400841.2:c.552_553delinsTT	p.Trp184_Val185delinsCysPhe	p.W184_V185delinsCF	ENST00000400841		184	tgGGtc/tgTTtc	5/6	1	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.690478822817014	1		585	813	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051667	30051667	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0025383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	40	324	0	ENST00000338641.4:c.599+2T>A		p.X200_splice	ENST00000338641	NM_000268.3	200			0.4069212543659	1	FACETS	0.546	0.456	0.645	0.546	0.456	0.645	SUBCLONAL	1	TRUE	0	0.4069212543659	1		324	287	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410076	139410076	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	105	640	0	ENST00000277541.6:c.1762A>T	p.Thr588Ser	p.T588S	ENST00000277541	NM_017617.3	588	Acc/Tcc	11/34	1	2	FACETS	0.728	0.652	0.808	0.728	0.652	0.808	SUBCLONAL	1	TRUE	1	0.4069212543659	2		640	709	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0025385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	74	340	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	0.240269376650993	2		340	439	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0025385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	64	675	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.873	0.762	0.992	1	0.978	1	CLONAL	2	TRUE	1	0.240269376650993	2		675	305	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0025385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	90	612	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.769	0.685	0.858	1	0.981	1	SUBCLONAL	2	TRUE	1	0.240269376650993	2		612	487	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105570	27105571	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	141	511	0	ENST00000324856.7:c.5184dup	p.Gly1729TrpfsTer7	p.G1729Wfs*7	ENST00000324856	NM_006015.4	1727	-/T	20/20	0.240269376650993	2	FACETS	0.858	0.788	0.93	1	0.983	1	CLONAL	3	TRUE	0	0.240269376650993	2		511	456	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	56	391	0	ENST00000371953.3:c.388del	p.Arg130GlufsTer4	p.R130Efs*4	ENST00000371953	NM_000314.4	130	Cga/ga	5/9	1	2	FACETS	0.835	0.722	0.957	1	0.973	1	CLONAL	2	TRUE	1	0.240269376650993	2		391	279	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725059	89725059	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	23	212	0	ENST00000371953.3:c.1042A>C	p.Thr348Pro	p.T348P	ENST00000371953	NM_000314.4	348	Aca/Cca	9/9	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.240269376650993	2		212	155	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0025405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	83	519	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.22	2		519	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579553	7579606	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGCATCAAATCATCCATTGCTTGGGACGGCAAGGGGGACTGTAGATGGGTGAAA	AGCATCAAATCATCCATTGCTTGGGACGGCAAGGGGGACTGTAGATGGGTGAAA	-	novel	NA	P-0025405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	69	559	0	ENST00000269305.4:c.97-16_134del		p.X33_splice	ENST00000269305	NM_001126112.2	33		4/11	1	2	FACETS	0.912	0.794	1	0.912	0.794	1	CLONAL	1	TRUE	1	0.22	2		559	688	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618743	37618743	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs905721300	NA	P-0025405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1423	75	535	2	ENST00000447079.4:c.419C>T	p.Ser140Leu	p.S140L	ENST00000447079	NM_015083.1	140	tCg/tTg	1/14	0.3	9	FACETS	0.806	0.703	0.917			1	CLONAL	1	TRUE	NA	0.22	9		537	1498	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757438	40757438	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	98	581	0	ENST00000373198.4:c.2860G>C	p.Asp954His	p.D954H	ENST00000373198	NM_133170.3	954	Gat/Cat	20/32	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.22	2		581	873	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778244	27778244	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	108	437	0	ENST00000369163.2:c.393C>G	p.Ile131Met	p.I131M	ENST00000369163	NM_003536.2	131	atC/atG	1/1	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.22	2		437	669	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912148	127912148	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	36	388	0	ENST00000373547.4:c.722A>G	p.His241Arg	p.H241R	ENST00000373547	NM_002721.4	241	cAc/cGc	7/7	1	2	FACETS	0.653	0.536	0.784	0.653	0.536	0.784	SUBCLONAL	1	TRUE	1	0.22	2		388	501	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs985033810	NA	P-0025439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	323	618	0	ENST00000269305.4:c.731G>C	p.Gly244Ala	p.G244A	ENST00000269305	NM_001126112.2	244	gGc/gCc	7/11	0.792290084067926	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.792290084067926	1		618	474	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249012	55249013	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGT	novel	NA	P-0025439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	197	555	0	ENST00000275493.2:c.2310_2311insGGT	p.Asp770_Asn771insGly	p.D770_N771insG	ENST00000275493	NM_005228.3	770	-/GGT	20/28	0.792290084067926	3	FACETS	0.777	0.72	0.837	0.389	0.36	0.419	SUBCLONAL	1	TRUE	1	0.792290084067926	3		555	893	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913541	32913541	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs773973434	NA	P-0025439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	330	537	0	ENST00000380152.3:c.5049G>C	p.Gln1683His	p.Q1683H	ENST00000380152		1683	caG/caC	11/27	0.792290084067926	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.792290084067926	1		537	460	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492931	8492931	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201412075	NA	P-0025439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	47	500	1	ENST00000356435.5:c.2398G>A	p.Val800Ile	p.V800I	ENST00000356435		800	Gtc/Atc	16/35	0.792290084067926	1	FACETS	0.164	0.138	0.192	0.164	0.138	0.192	SUBCLONAL	1	TRUE	0	0.792290084067926	1		501	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0025444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	115	711	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.207079311773195	2	FACETS	0.777	0.703	0.854	0.777	0.703	0.854	SUBCLONAL	2	TRUE	0	0.292584339089103	2		711	506	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683357	88683357	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201040	NA	P-0025444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	86	690	0	ENST00000372037.3:c.1480C>T	p.Arg494Ter	p.R494*	ENST00000372037	NM_004329.2	494	Cga/Tga	13/13	1	2	FACETS	0.909	0.804	1	0.909	0.804	1	CLONAL	1	TRUE	1	0.292584339089103	2		690	647	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518108	69518108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	115	516	0	ENST00000294312.3:c.257C>T	p.Ala86Val	p.A86V	ENST00000294312	NM_005117.2	86	gCt/gTt	2/3	1	2	FACETS	0.895	0.812	0.982	1	0.988	1	CLONAL	2	TRUE	1	0.292584339089103	2		516	439	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435897	56435897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	67	363	0	ENST00000407977.2:c.1240C>T	p.Gln414Ter	p.Q414*	ENST00000407977		414	Caa/Taa	9/10	0.207079311773195	2	FACETS	0.95	0.837	1	0.95	0.837	1	CLONAL	2	TRUE	0	0.292584339089103	2		363	241	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437612	56437612	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	71	337	0	ENST00000407977.2:c.850G>T	p.Glu284Ter	p.E284*	ENST00000407977		284	Gag/Tag	8/10	0.207079311773195	2	FACETS	0.867	0.764	0.974	0.867	0.764	0.974	CLONAL	2	TRUE	0	0.292584339089103	2		337	280	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961393	54961393	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	43	288	0	ENST00000312783.6:c.239A>G	p.Gln80Arg	p.Q80R	ENST00000312783	NM_198436.1	80	cAg/cGg	4/10	0.313355412218254	3	FACETS	0.889	0.746	1	0.445	0.373	0.524	CLONAL	1	TRUE	1	0.292584339089103	3		288	379	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268138	153268138	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1406877044	NA	P-0025444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	52	351	0	ENST00000281708.4:c.670C>T	p.Arg224Ter	p.R224*	ENST00000281708	NM_033632.3	224	Cga/Tga	4/12	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.292584339089103	2		351	348	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0025451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	325	385	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.647121685577041	3	FACETS	0.777	0.737	0.818	0.777	0.737	0.818	SUBCLONAL	2	TRUE	1	0.647121685577041	3		385	855	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0025451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	414	519	2	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	0.601629680831275	2	FACETS	0.866	0.832	0.899	0.866	0.832	0.899	CLONAL	2	TRUE	0	0.647121685577041	2		521	739	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258893	16258893	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs74842071	NA	P-0025451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	77	740	0	ENST00000375759.3:c.6158A>C	p.Asn2053Thr	p.N2053T	ENST00000375759	NM_015001.2	2053	aAc/aCc	11/15	0.647121685577041	3	FACETS	0.275	0.24	0.312	0.137	0.12	0.156	SUBCLONAL	1	TRUE	1	0.647121685577041	3		740	1147	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	76	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.718	0.629	0.814	0.718	0.629	0.814	SUBCLONAL	1	TRUE	1	0.261101325991715	2		371	811	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519988	NA	P-0025452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	78	497	0	ENST00000269305.4:c.808T>C	p.Phe270Leu	p.F270L	ENST00000269305	NM_001126112.2	270	Ttt/Ctt	8/11	0.261101325991715	1	FACETS	0.717	0.629	0.811	0.717	0.629	0.811	SUBCLONAL	1	TRUE	0	0.261101325991715	1		497	725	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918491	44918491	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0025452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	30	143	0	ENST00000377967.4:c.975-1G>A		p.X325_splice	ENST00000377967	NM_021140.2	325			1	1	FACETS	0.989	0.803	1	0.989	0.803	1	CLONAL	1	TRUE	0	0.261101325991715	1		143	202	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0025454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	288	552	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.707307592744234	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	0	0.707307592744234	1		552	524	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260064	19260064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774866350	NA	P-0025454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	376	684	0	ENST00000162023.5:c.229G>A	p.Glu77Lys	p.E77K	ENST00000162023		77	Gag/Aag	7/13	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.707307592744234	2		684	1055	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252084	226252084	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	78	132	0	ENST00000366813.1:c.32C>T	p.Ser11Leu	p.S11L	ENST00000366813		11	tCg/tTg	1/3	0.707307592744234	3	FACETS	0.919	0.814	1	0.459	0.407	0.515	CLONAL	1	FALSE	1	0.707307592744234	3		132	325	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248830	133248830	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	151	528	0	ENST00000320574.5:c.1765C>G	p.Pro589Ala	p.P589A	ENST00000320574	NM_006231.2	589	Cct/Gct	16/49	1	2	FACETS	0.503	0.46	0.548	0.503	0.46	0.548	SUBCLONAL	1	FALSE	1	0.707307592744234	2		528	849	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911905	32911905	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	290	468	0	ENST00000380152.3:c.3413del	p.Gln1138ArgfsTer12	p.Q1138Rfs*12	ENST00000380152		1138	cAg/cg	11/27	0.688570531821553	2	FACETS	0.869	0.831	0.906	0.869	0.831	0.906	CLONAL	2	FALSE	0	0.707307592744234	2		468	472	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90645529	90645529	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	14	72	0	ENST00000330062.3:c.94C>G	p.Gln32Glu	p.Q32E	ENST00000330062	NM_002168.2	32	Caa/Gaa	1/11	0.309620470434205	3	FACETS	0.331	0.24	0.44	0.165	0.12	0.22	INDETERMINATE	1	FALSE	1	0.707307592744234	3		72	162	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129665	2129665	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	114	617	0	ENST00000219476.3:c.3392T>G	p.Met1131Arg	p.M1131R	ENST00000219476	NM_000548.3	1131	aTg/aGg	29/42	1	2	FACETS	0.351	0.315	0.389	0.351	0.315	0.389	SUBCLONAL	1	FALSE	1	0.707307592744234	2		617	918	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207665	2207665	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	261	529	0	ENST00000398665.3:c.949A>G	p.Ile317Val	p.I317V	ENST00000398665	NM_032482.2	317	Atc/Gtc	11/28	0.707307592744234	1	FACETS	0.923	0.875	0.97	0.923	0.875	0.97	CLONAL	1	FALSE	0	0.707307592744234	1		529	517	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159126	143159150	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGAAATCTATATAATTTACATAC	TGGGAAATCTATATAATTTACATAC	-	novel	NA	P-0025454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	105	366	0	ENST00000262992.4:c.703_727del	p.Val235HisfsTer26	p.V235Hfs*26	ENST00000262992	NM_001101669.1	235	GTATGTAAATTATATAGATTTCCCAca/ca	10/24	0.707307592744234	1	FACETS	0.774	0.706	0.842	0.774	0.706	0.842	SUBCLONAL	1	FALSE	0	0.707307592744234	1		366	248	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465532	8465532	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	187	571	0	ENST00000356435.5:c.3648C>A	p.Asn1216Lys	p.N1216K	ENST00000356435		1216	aaC/aaA	21/35	1	2	FACETS	0.834	0.774	0.896	0.834	0.774	0.896	CLONAL	1	FALSE	1	0.707307592744234	2		571	634	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934519	9934519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	87	361	0	ENST00000330684.3:c.1636C>T	p.Pro546Ser	p.P546S	ENST00000330684	NM_001134407.1	546	Cct/Tct	7/13	1	2	FACETS	0.596	0.529	0.668	0.596	0.529	0.668	SUBCLONAL	1	TRUE	1	0.514809993609708	2		361	567	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857361	68857361	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	163	506	0	ENST00000261769.5:c.1996A>T	p.Asn666Tyr	p.N666Y	ENST00000261769	NM_004360.3	666	Aat/Tat	13/16	1	2	FACETS	0.977	0.9	1	0.977	0.9	1	CLONAL	1	TRUE	1	0.514809993609708	2		506	648	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437567	56437567	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	101	491	0	ENST00000407977.2:c.895del	p.Val299TrpfsTer120	p.V299Wfs*120	ENST00000407977		299	Gtg/tg	8/10	0.44463534044097	1	FACETS	0.389	0.347	0.433	0.389	0.347	0.433	SUBCLONAL	1	TRUE	0	0.514809993609708	1		491	750	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248157	110248157	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	163	437	0	ENST00000374672.4:c.1315C>G	p.Arg439Gly	p.R439G	ENST00000374672	NM_004235.4	439	Cgc/Ggc	5/5	1	2	FACETS	0.952	0.877	1	0.952	0.877	1	CLONAL	1	TRUE	1	0.514809993609708	2		437	665	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99162496	99162496	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	86	334	0	ENST00000074304.5:c.1014G>C	p.Leu338Phe	p.L338F	ENST00000074304	NM_001134224.1	338	ttG/ttC	12/26	0.614364276548736	3	FACETS	0.942	0.839	1	0.471	0.419	0.526	CLONAL	1	TRUE	1	0.636630883824117	3		334	378	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0025458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	77	675	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.226414136529306	3	FACETS	1	0.975	1	0.71	0.629	0.796	INDETERMINATE	1	TRUE	1	0.401906451246432	3		675	324	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	108	496	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.346652212793501	1	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	0	0.401906451246432	1		496	429	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560401	95560401	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	170	417	0	ENST00000393063.1:c.5188G>A	p.Gly1730Arg	p.G1730R	ENST00000393063	NM_030621.3	1730	Ggg/Agg	25/28	0.185609407221297	3	FACETS	0.823	0.761	0.888	0.823	0.761	0.888	INDETERMINATE	2	TRUE	1	0.401906451246432	3		417	617	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0025460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	71	627	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.157788084831005	2		627	632	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0025460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	132	562	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	1	0.956	1	1	0.993	1	CLONAL	3	TRUE	1	0.157788084831005	2		562	519	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610322	81610322	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	60	261	0	ENST00000298171.2:c.1920C>G	p.Ile640Met	p.I640M	ENST00000298171	NM_000369.2	640	atC/atG	10/10	1	2	FACETS	0.833	0.719	0.958	0.833	0.719	0.958	CLONAL	1	TRUE	1	0.26863192453145	2		261	536	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	279	387	0				ENST00000310581	NM_198253.2	-/1132			0.154124596604228	2	FACETS	0.764	0.725	0.803	0.764	0.725	0.803	INDETERMINATE	2	TRUE	0	0.638671058319058	2		387	572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0025462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	52	639	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.638671058319058	1	FACETS	0.172	0.145	0.2	0.172	0.145	0.2	SUBCLONAL	1	TRUE	0	0.638671058319058	1		639	646	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	362	752	2	ENST00000269305.4:c.166G>T	p.Glu56Ter	p.E56*	ENST00000269305	NM_001126112.2	56	Gaa/Taa	4/11	0.638671058319058	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.638671058319058	1		754	704	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123353331	123353331	+	start_lost	Translation_Start_Site	SNP	T	T	C	rs774885289	NA	P-0025462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	148	697	1	ENST00000358487.5:c.1A>G	p.Met1?	p.M1?	ENST00000358487	NM_000141.4	1	Atg/Gtg	2/18	0.338096688546706	1	FACETS	0.379	0.346	0.413	0.379	0.346	0.413	INDETERMINATE	1	TRUE	0	0.638671058319058	1		698	833	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577329	64577329	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	374	581	1	ENST00000312049.6:c.253A>G	p.Ile85Val	p.I85V	ENST00000312049	NM_130799.2	85	Atc/Gtc	2/10	0.638671058319058	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.638671058319058	1		582	635	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647148	2647148	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	214	436	1	ENST00000342085.4:c.1426C>G	p.Leu476Val	p.L476V	ENST00000342085	NM_002613.4	476	Ctg/Gtg	13/14	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.638671058319058	2		437	666	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538173	187538173	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	42	590	1	ENST00000441802.2:c.9061C>T	p.Pro3021Ser	p.P3021S	ENST00000441802	NM_005245.3	3021	Cca/Tca	11/27	0.638671058319058	1	FACETS	0.165	0.137	0.195	0.165	0.137	0.195	SUBCLONAL	1	TRUE	0	0.638671058319058	1		591	544	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526667	106526667	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	185	502	0	ENST00000359195.3:c.2960T>G	p.Leu987Arg	p.L987R	ENST00000359195	NM_002649.2	987	cTa/cGa	10/11	1	2	FACETS	0.927	0.86	0.996	0.927	0.86	0.996	CLONAL	1	TRUE	1	0.638671058319058	2		502	625	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94963988	94963988	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	61	444	0	ENST00000536441.1:c.37A>G	p.Asn13Asp	p.N13D	ENST00000536441	NM_144665.3	13	Aac/Gac	1/10	0.638671058319058	1	FACETS	0.323	0.279	0.37	0.323	0.279	0.37	SUBCLONAL	1	TRUE	0	0.638671058319058	1		444	403	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94963988	94964002	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCGGCGGCCGACG	TGGCGGCGGCCGACG	C	novel	NA	P-0025462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	158	444	0	ENST00000536441.1:c.23_37delinsG	p.Pro8ArgfsTer16	p.P8Rfs*16	ENST00000536441	NM_144665.3	8	cCGTCGGCCGCCGCCAac/cGac	1/10	0.638671058319058	1	FACETS	0.836	0.775	0.898	0.836	0.775	0.898	CLONAL	1	TRUE	0	0.638671058319058	1		444	403	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348214	348214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	52	708	0	ENST00000262320.3:c.1292C>T	p.Pro431Leu	p.P431L	ENST00000262320	NM_003502.3	431	cCc/cTc	6/11	1	2	FACETS	0.983	0.834	1	0.983	0.834	1	CLONAL	1	TRUE	1	0.12	2		708	882	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589519	69589519	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs779390973	NA	P-0025465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	17	165	0	ENST00000168712.1:c.334C>G	p.Arg112Gly	p.R112G	ENST00000168712	NM_002007.2	112	Cgc/Ggc	1/3	1	2	FACETS	1	0.832	1	1	0.832	1	CLONAL	1	TRUE	1	0.12	2		165	245	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952117	178952117	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	44	335	0	ENST00000263967.3:c.3172A>C	p.Ile1058Leu	p.I1058L	ENST00000263967	NM_006218.2	1058	Atc/Ctc	21/21	1	2	FACETS	0.821	0.69	0.965	1	0.964	1	CLONAL	2	TRUE	1	0.14	2		335	383	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14021910	14021910	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	51	511	0	ENST00000311895.7:c.610T>G	p.Leu204Val	p.L204V	ENST00000311895	NM_005236.2	204	Tta/Gta	4/11	1	2	FACETS	0.971	0.824	1	0.971	0.824	1	CLONAL	1	TRUE	1	0.14	2		511	750	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66518915	66518915	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	29	361	0	ENST00000358598.2:c.196C>G	p.Gln66Glu	p.Q66E	ENST00000358598	NM_212471.2	66	Cag/Gag	3/11	1	2	FACETS	0.955	0.766	1	0.955	0.766	1	CLONAL	1	TRUE	1	0.14	2		361	434	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46611718	46611719	+	stop_gained	Nonsense_Mutation	DNP	TG	TG	AT	novel	NA	P-0025467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	38	640	0	ENST00000263734.3:c.2532_2533delinsAT	p.Cys844_Glu845delinsTer	p.C844_E845delins*	ENST00000263734	NM_001430.4	844	tgTGag/tgATag	16/16	1	2	FACETS	0.765	0.63	0.916	0.765	0.63	0.916	CLONAL	1	TRUE	1	0.14	2		640	710	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455091	50455091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1422790468	NA	P-0025468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	110	371	0	ENST00000331340.3:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000331340	NM_006060.4	213	cGa/cAa	6/8	0.267337579431274	6	FACETS	0.857	0.774	0.945	0.643	0.58	0.709	CLONAL	3	TRUE	2	0.267337579431274	6		371	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	200	339	0	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.267337579431274	2	FACETS	0.889	0.83	0.949	1	0.99	1	CLONAL	3	TRUE	0	0.267337579431274	2		339	561	SUCCESS
APC	324	MSKCC	GRCh37	5	112175756	112175756	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	42	349	0	ENST00000257430.4:c.4466del	p.Leu1489TyrfsTer18	p.L1489Yfs*18	ENST00000257430	NM_000038.5	1489	Tta/ta	16/16	0.267337579431274	1	FACETS	0.917	0.769	1	0.917	0.769	1	CLONAL	1	TRUE	0	0.267337579431274	1		349	297	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0025470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	152	340	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.411970277469171	2	FACETS	0.858	0.793	0.925	0.858	0.793	0.925	CLONAL	2	TRUE	0	0.417735598985238	2		340	424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0025470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	162	569	1	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	0.356872530031525	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.417735598985238	2		570	381	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0025470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	84	430	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.417735598985238	3	FACETS	1	0.979	1	0.734	0.654	0.818	CLONAL	1	TRUE	1	0.417735598985238	3		430	331	SUCCESS
APC	324	MSKCC	GRCh37	5	112175153	112175153	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	36	264	1	ENST00000257430.4:c.3862G>T	p.Gly1288Ter	p.G1288*	ENST00000257430	NM_000038.5	1288	Gga/Tga	16/16	0.417735598985238	3	FACETS	0.769	0.635	0.917	0.384	0.317	0.459	CLONAL	1	TRUE	1	0.417735598985238	3		265	271	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117730805	117730805	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	182	480	0	ENST00000368508.3:c.229C>T	p.Arg77Trp	p.R77W	ENST00000368508	NM_002944.2	77	Cgg/Tgg	4/43	0.417735598985238	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.417735598985238	4		480	559	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214133	36214134	+	missense_variant	Missense_Mutation	DNP	AA	AA	GG	novel	NA	P-0025470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	67	744	1	ENST00000222270.7:c.2959_2960delinsGG	p.Lys987Gly	p.K987G	ENST00000222270	NM_014727.1	987	AAg/GGg	6/37	0.417735598985238	3	FACETS	0.688	0.598	0.784	0.344	0.299	0.392	SUBCLONAL	1	TRUE	1	0.417735598985238	3		745	564	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572351	41572351	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	311	622	1	ENST00000263253.7:c.4880G>A	p.Arg1627Gln	p.R1627Q	ENST00000263253	NM_001429.3	1627	cGg/cAg	30/31	0.417735598985238	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	0	0.417735598985238	3		623	575	SUCCESS
APC	324	MSKCC	GRCh37	5	112175350	112175350	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	56	260	0	ENST00000257430.4:c.4059A>T	p.Glu1353Asp	p.E1353D	ENST00000257430	NM_000038.5	1353	gaA/gaT	16/16	0.417735598985238	3	FACETS	1	0.945	1	0.596	0.515	0.683	CLONAL	1	TRUE	1	0.417735598985238	3		260	272	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974336	93974336	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	121	526	0	ENST00000369303.4:c.1718T>C	p.Val573Ala	p.V573A	ENST00000369303	NM_004440.3	573	gTc/gCc	8/17	0.417735598985238	4	FACETS	0.909	0.826	0.994	0.909	0.826	0.994	CLONAL	2	TRUE	2	0.417735598985238	4		526	452	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843413	128843413	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	49	378	0	ENST00000249373.3:c.520T>G	p.Phe174Val	p.F174V	ENST00000249373	NM_005631.4	174	Ttc/Gtc	2/12	1	2	FACETS	0.841	0.717	0.975	0.841	0.717	0.975	CLONAL	1	TRUE	1	0.417735598985238	2		378	279	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551318	141551318	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	105	768	0	ENST00000220592.5:c.1979A>T	p.Lys660Met	p.K660M	ENST00000220592	NM_012154.3	660	aAg/aTg	15/19	0.417735598985238	4	FACETS	0.935	0.838	1	0.312	0.279	0.347	CLONAL	1	TRUE	1	0.417735598985238	4		768	762	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148663	20148663	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	170	618	0	ENST00000379607.5:c.400A>G	p.Ile134Val	p.I134V	ENST00000379607	NM_001412.3	134	Att/Gtt	6/7	0.403968190038857	3	FACETS	0.986	0.914	1	0.986	0.914	1	CLONAL	2	TRUE	1	0.417735598985238	3		618	499	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914651	39914651	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	187	552	0	ENST00000378444.4:c.4711del	p.His1571ThrfsTer9	p.H1571Tfs*9	ENST00000378444	NM_001123385.1	1571	Cac/ac	12/15	0.403968190038857	3	FACETS	0.925	0.86	0.992	0.925	0.86	0.992	CLONAL	2	TRUE	1	0.417735598985238	3		552	585	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0025472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	102	611	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.146228434606671	3	FACETS	1	0.96	1	0.577	0.516	0.641	INDETERMINATE	1	TRUE	1	0.28	3		611	720	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0025472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	107	83	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.146228434606671	3	FACETS	1	0.98	1	0.696	0.625	0.77	INDETERMINATE	1	TRUE	1	0.28	3		83	626	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0025472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	32	248	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	1	2	FACETS	0.956	0.781	1	0.956	0.781	1	CLONAL	1	TRUE	1	0.28	2		248	239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0025472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	124	285	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.176616115509759	2	FACETS	0.842	0.765	0.922	0.842	0.765	0.922	CLONAL	2	TRUE	0	0.28	2		285	526	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0025472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	66	284	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.941	0.818	1	0.941	0.818	1	CLONAL	1	TRUE	1	0.28	2		284	501	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224163	98224163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138154222	NA	P-0025472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	44	223	0	ENST00000331920.6:c.2678G>A	p.Arg893His	p.R893H	ENST00000331920	NM_000264.3	893	cGc/cAc	16/24	1	2	FACETS	0.988	0.833	1	0.988	0.833	1	CLONAL	1	TRUE	1	0.28	2		223	318	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920450	114920450	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	86	345	0	ENST00000543371.1:c.1391G>A	p.Arg464Lys	p.R464K	ENST00000543371	NM_001198531.1	464	aGg/aAg	13/14	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.28	2		345	534	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679258	88679258	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	55	534	0	ENST00000360948.2:c.779G>T	p.Trp260Leu	p.W260L	ENST00000360948	NM_001012338.2	260	tGg/tTg	8/19	1	2	FACETS	0.707	0.604	0.818	0.707	0.604	0.818	SUBCLONAL	1	TRUE	1	0.28	2		534	556	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339245	70339245	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	205	212	0	ENST00000374080.3:c.122T>A	p.Val41Glu	p.V41E	ENST00000374080		41	gTa/gAa	2/45	0.236358713461554	2	FACETS	1	0.981	1			1	CLONAL	3	TRUE	NA	0.28	2		212	441	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	309	487	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	0.199365142767011	4	FACETS	0.912	0.86	0.964			1	CLONAL	3	TRUE	NA	0.27	4		487	1063	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870976	12870976	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs971444878	NA	P-0025476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	344	224	0	ENST00000228872.4:c.203A>G	p.Lys68Arg	p.K68R	ENST00000228872	NM_004064.3	68	aAa/aGa	1/3	0.29608061613127	7	FACETS	0.963	0.921	1	1	0.995	1	CLONAL	7	TRUE	2	0.27	7		224	633	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129346	152129355	+	frameshift_variant	Frame_Shift_Del	DEL	TCAACAGCGT	TCAACAGCGT	GC	novel	NA	P-0025476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	105	273	2	ENST00000206249.3:c.299_308delinsGC	p.Leu100ArgfsTer54	p.L100Rfs*54	ENST00000206249	NM_000125.3	100	cTCAACAGCGTg/cGCg	1/8	1	2	FACETS	0.807	0.726	0.891	1	0.985	1	CLONAL	2	TRUE	1	0.27	2		275	482	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860558	151860558	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	434	385	0	ENST00000262189.6:c.10104del	p.Thr3369GlnfsTer15	p.T3369Qfs*15	ENST00000262189	NM_170606.2	3368	ggG/gg	43/59	0.29608061613127	5	FACETS	0.945	0.908	0.981	1	0.996	1	CLONAL	6	TRUE	1	0.27	5		385	797	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151947965	151947965	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	369	555	0	ENST00000262189.6:c.1708G>T	p.Glu570Ter	p.E570*	ENST00000262189	NM_170606.2	570	Gag/Tag	12/59	0.29608061613127	5	FACETS	1	0.979	1	0.793	0.753	0.835	CLONAL	3	TRUE	1	0.27	5		555	1210	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	97	387	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.974	1			1	INDETERMINATE	1	FALSE	NA	0.782403770170627	2		387	208	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888210	112888210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121918464	NA	P-0025480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	34	586	1	ENST00000351677.2:c.226G>A	p.Glu76Lys	p.E76K	ENST00000351677	NM_002834.3	76	Gag/Aag	3/16	0.155829652734023	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.782403770170627	0		587	533	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776783	NA	P-0025480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	193	426	0	ENST00000267163.4:c.1215+1G>A		p.X405_splice	ENST00000267163	NM_000321.2	405			0.6950173948378	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	0	0.782403770170627	1		426	299	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653809	89653809	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554893792	NA	P-0025480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	227	506	0	ENST00000371953.3:c.107G>A	p.Gly36Glu	p.G36E	ENST00000371953	NM_000314.4	36	gGa/gAa	2/9	0.782403770170627	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	0	0.782403770170627	1		506	347	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591094	67591102	+	inframe_deletion	In_Frame_Del	DEL	ATGAACAGC	ATGAACAGC	-	novel	NA	P-0025480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	80	331	0	ENST00000274335.5:c.1689_1697del	p.Met563_Ser565del	p.M563_S565del	ENST00000274335		563	ATGAACAGC/-	12/15	1	2	FACETS	0.493	0.436	0.553	0.493	0.436	0.553	SUBCLONAL	1	FALSE	1	0.782403770170627	2		331	415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579861	7579861	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs876658627	NA	P-0025481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	640	484	0	ENST00000269305.4:c.52del	p.Thr18HisfsTer26	p.T18Hfs*26	ENST00000269305	NM_001126112.2	18	Aca/ca	2/11	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.780674836538791	2		484	801	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974744	21974775	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTCCTCTACCCGACCCCGGGCCGCGGCCGT	ACCTCCTCTACCCGACCCCGGGCCGCGGCCGT	-	novel	NA	P-0025481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	53	147	0	ENST00000304494.5:c.52_83del	p.Thr18AlafsTer15	p.T18Afs*15	ENST00000304494	NM_000077.4	18	ACGGCCGCGGCCCGGGGTCGGGTAGAGGAGGTg/g	1/3	0.361742555591753	2	FACETS	0.535	0.46	0.615	0.267	0.23	0.308	INDETERMINATE	1	TRUE	0	0.780674836538791	2		147	254	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173667	108173667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	74	501	0	ENST00000278616.4:c.5407G>A	p.Asp1803Asn	p.D1803N	ENST00000278616	NM_000051.3	1803	Gac/Aac	36/63	0.75372402491415	2	FACETS	0.614	0.542	0.689	0.307	0.271	0.345	SUBCLONAL	1	TRUE	0	0.780674836538791	2		501	309	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932965	39932965	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149621463	NA	P-0025481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	144	472	0	ENST00000378444.4:c.1634C>T	p.Pro545Leu	p.P545L	ENST00000378444	NM_001123385.1	545	cCg/cTg	4/15	NA	2	FACETS	0.475	0.434	0.519			1	INDETERMINATE	1	TRUE	NA	0.780674836538791	2		472	776	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129157	152129157	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	151	490	0	ENST00000206249.3:c.110G>A	p.Arg37Gln	p.R37Q	ENST00000206249	NM_000125.3	37	cGg/cAg	1/8	1	2	FACETS	0.5	0.457	0.544	0.5	0.457	0.544	SUBCLONAL	1	TRUE	1	0.780674836538791	2		490	774	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069620	69069620	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	145	536	0	ENST00000288368.4:c.4295A>G	p.Gln1432Arg	p.Q1432R	ENST00000288368	NM_024870.2	1432	cAg/cGg	35/40	NA	2	FACETS	0.893	0.823	0.965			1	INDETERMINATE	1	TRUE	NA	0.780674836538791	2		536	416	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933779	39933779	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs781778869	NA	P-0025481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	120	440	0	ENST00000378444.4:c.820C>G	p.Pro274Ala	p.P274A	ENST00000378444	NM_001123385.1	274	Cca/Gca	4/15	NA	2	FACETS	0.421	0.38	0.464			1	INDETERMINATE	1	TRUE	NA	0.780674836538791	2		440	730	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111506	8111507	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCCAATGGGGACCCTGTCTGCAATGCCTGTGGGCTCTAC	novel	NA	P-0025483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	69	583	0	ENST00000346208.3:c.994_1033dup	p.Tyr345CysfsTer20	p.Y345Cfs*20	ENST00000346208		331	aat/aaTGCCAATGGGGACCCTGTCTGCAATGCCTGTGGGCTCTACt	5/6	0.458022617795631	3	FACETS	0.435	0.378	0.497	0.218	0.189	0.249	SUBCLONAL	1	FALSE	1	0.47294372023267	3		583	829	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578384	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	GAG	GAG	-	novel	NA	P-0025483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	201	426	1	ENST00000269305.4:c.546_548del	p.Cys182_Ser183delinsTer	p.C182_S183delins*	ENST00000269305	NM_001126112.2	182	tgCTCa/tga	5/11	0.391268390621242	2	FACETS	0.85	0.795	0.905	0.85	0.795	0.905	CLONAL	2	FALSE	0	0.47294372023267	2		427	500	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691919	30691919	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	42	432	1	ENST00000295754.5:c.421G>A	p.Asp141Asn	p.D141N	ENST00000295754	NM_003242.5	141	Gat/Aat	3/7	0.155390291471698	4	FACETS	0.406	0.338	0.481	0.203	0.169	0.241	INDETERMINATE	1	FALSE	2	0.47294372023267	4		433	645	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125697	47125697	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750379129	NA	P-0025483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	148	378	0	ENST00000409792.3:c.5573C>T	p.Pro1858Leu	p.P1858L	ENST00000409792	NM_014159.6	1858	cCt/cTt	12/21	0.155390291471698	4	FACETS	0.831	0.762	0.901	0.831	0.762	0.901	INDETERMINATE	2	FALSE	2	0.47294372023267	4		378	555	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618534	37618534	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	46	396	0	ENST00000447079.4:c.210G>C	p.Leu70Phe	p.L70F	ENST00000447079	NM_015083.1	70	ttG/ttC	1/14	0.47294372023267	6	FACETS	0.64	0.539	0.753			1	SUBCLONAL	1	FALSE	NA	0.47294372023267	6		396	591	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591825	48591825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767342	NA	P-0025484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	56	458	0	ENST00000342988.3:c.988G>A	p.Glu330Lys	p.E330K	ENST00000342988	NM_005359.5	330	Gaa/Aaa	9/12	0.558398854549548	1	FACETS	0.936	0.822	1	0.936	0.822	1	CLONAL	1	TRUE	0	0.584316787348336	1		458	145	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291041	10291041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765353997	NA	P-0025484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	100	413	0	ENST00000340748.4:c.430G>A	p.Asp144Asn	p.D144N	ENST00000340748		144	Gat/Aat	4/40	0.544126030155605	3	FACETS	0.849	0.761	0.942	0.424	0.38	0.471	CLONAL	1	TRUE	1	0.584316787348336	3		413	521	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508733	106508733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1207051578	NA	P-0025484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	148	487	0	ENST00000359195.3:c.727G>A	p.Ala243Thr	p.A243T	ENST00000359195	NM_002649.2	243	Gcc/Acc	2/11	1	2	FACETS	0.887	0.814	0.963	0.887	0.814	0.963	CLONAL	1	TRUE	1	0.584316787348336	2		487	571	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216439	7216439	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs772570395	NA	P-0025484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	34	531	0	ENST00000380728.2:c.809C>G	p.Ser270Cys	p.S270C	ENST00000380728		270	tCt/tGt	10/11	NA	2	FACETS	0.176	0.143	0.213			1	INDETERMINATE	1	TRUE	NA	0.584316787348336	2		531	661	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280663	115280663	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760552812	NA	P-0025484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	113	628	0	ENST00000438362.2:c.368G>A	p.Arg123Gln	p.R123Q	ENST00000438362	NM_001242891.1	123	cGa/cAa	4/20	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.584316787348336	2		628	363	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309863	104309863	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	131	279	0	ENST00000369902.3:c.454G>A	p.Glu152Lys	p.E152K	ENST00000369902	NM_016169.3	152	Gag/Aag	3/12	0.580968898892812	2	FACETS	0.904	0.84	0.968	0.904	0.84	0.968	CLONAL	2	TRUE	0	0.584316787348336	2		279	248	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557161	187557183	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATGAGGGGGAATGCTTACCAGTG	ATGAGGGGGAATGCTTACCAGTG	-	novel	NA	P-0025484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	66	287	0	ENST00000441802.2:c.4179_4183+18del		p.X1393_splice	ENST00000441802	NM_005245.3	1393		6/27	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.584316787348336	2		287	194	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0025487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	47	340	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.833	0.701	0.98	0.833	0.701	0.98	CLONAL	1	TRUE	1	0.15	2		340	752	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0025487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	50	206	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.15	2		207	650	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0025487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	46	612	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.781	0.656	0.92	0.781	0.656	0.92	CLONAL	1	TRUE	1	0.15	2		612	785	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098803	178098803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	104	796	1	ENST00000397062.3:c.242G>A	p.Gly81Asp	p.G81D	ENST00000397062	NM_006164.4	81	gGt/gAt	2/5	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.15	2		797	1037	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589599	67589601	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	novel	NA	P-0025487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	35	395	0	ENST00000274335.5:c.1362_1364del	p.Gln455del	p.Q455del	ENST00000274335		454	acTCAg/acg	10/15	1	2	FACETS	0.886	0.725	1	0.886	0.725	1	CLONAL	1	TRUE	1	0.15	2		395	527	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092710	27092710	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0025487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	25	369	0	ENST00000324856.7:c.2733-2A>G		p.X911_splice	ENST00000324856	NM_006015.4	911			1	2	FACETS	0.742	0.584	0.925	0.742	0.584	0.925	CLONAL	1	TRUE	1	0.15	2		369	449	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106289	27106290	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0025487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	57	688	0	ENST00000324856.7:c.5901dup	p.Cys1968ValfsTer31	p.C1968Vfs*31	ENST00000324856	NM_006015.4	1967	ctg/ctGg	20/20	1	2	FACETS	0.849	0.727	0.984	0.849	0.727	0.984	CLONAL	1	TRUE	1	0.15	2		688	895	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660532	67660532	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	47	608	0	ENST00000264010.4:c.1432G>T	p.Glu478Ter	p.E478*	ENST00000264010	NM_006565.3	478	Gag/Tag	8/12	1	2	FACETS	0.689	0.579	0.81	0.689	0.579	0.81	SUBCLONAL	1	TRUE	1	0.15	2		608	910	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0025491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	51	491	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.81153812284637	2		491	108	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0025491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	106	620	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	0.81153812284637	2		620	245	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49430837	49431424	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGCCTCAGTGCCCATTTAGGGATAACAATAATCACCCTGAGTAACTTGGCTATGTTACCAGCTGAGGTTACCTGTATCTGGGAAGAAGCTGTTTGCCAGCTGCTGCTGCATTGCCAATTGCTGCGGCTTCATGCACATGGAAGGTGGCATGGTGCCCATGGGCTTCTGTGATAGCACTGGCTGTGAGCTCTGCTGGGGTACCAAGCCTGCCTGCCCTCCATGCTGCCCACTTAGCATATGCCCTTGATTGGACACCATAGCCATGGATGGAGCCAGGCGTTGCTGGAGGGCATGAGCTGGTGGCTGGGTGGGCATCAGTGGCTGGGGCAAACCTGGCTGTCGGGCACCTGCAAGACCCAGGGAAAGCTGCTGTTGGGACCCAGCCAAACTGGGAGAAGAGCCCTCATGTGGCAAAGACATGGCCTGGGCAGGGCCTGGTGCAGACAGTAGGGAATGCTGCTGCTGCTGTTGCTGCTGCTGCTGGGCAGGCTGCAACTGTGCTGAAAGCTGCTGCTTCTTCTGCAGCTCCTTCTTCTCATGCTCCAACAGGTCCTCAATGAGCAGGGGTAACTCGCTGGCTACCAGTGA	AGCCTCAGTGCCCATTTAGGGATAACAATAATCACCCTGAGTAACTTGGCTATGTTACCAGCTGAGGTTACCTGTATCTGGGAAGAAGCTGTTTGCCAGCTGCTGCTGCATTGCCAATTGCTGCGGCTTCATGCACATGGAAGGTGGCATGGTGCCCATGGGCTTCTGTGATAGCACTGGCTGTGAGCTCTGCTGGGGTACCAAGCCTGCCTGCCCTCCATGCTGCCCACTTAGCATATGCCCTTGATTGGACACCATAGCCATGGATGGAGCCAGGCGTTGCTGGAGGGCATGAGCTGGTGGCTGGGTGGGCATCAGTGGCTGGGGCAAACCTGGCTGTCGGGCACCTGCAAGACCCAGGGAAAGCTGCTGTTGGGACCCAGCCAAACTGGGAGAAGAGCCCTCATGTGGCAAAGACATGGCCTGGGCAGGGCCTGGTGCAGACAGTAGGGAATGCTGCTGCTGCTGTTGCTGCTGCTGCTGGGCAGGCTGCAACTGTGCTGAAAGCTGCTGCTTCTTCTGCAGCTCCTTCTTCTCATGCTCCAACAGGTCCTCAATGAGCAGGGGTAACTCGCTGGCTACCAGTGA	-	novel	NA	P-0025492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	26	96	2	ENST00000301067.7:c.9715_10231+71del		p.X3239_splice	ENST00000301067	NM_003482.3	3239		34/54	0.540127649398764	1	FACETS	0.399	0.319	0.489	0.399	0.319	0.489	SUBCLONAL	1	TRUE	0	0.563431556311769	1		98	166	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518055	103518075	+	inframe_deletion	In_Frame_Del	DEL	GAACTTCAAGCAGAATTCCCT	GAACTTCAAGCAGAATTCCCT	-	novel	NA	P-0025492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	142	307	0	ENST00000355739.4:c.1996_2016del	p.Leu666_Glu672del	p.L666_E672del	ENST00000355739	NM_000123.3	665	GAACTTCAAGCAGAATTCCCT/-	9/15	0.563431556311769	1	FACETS	0.883	0.813	0.955	0.883	0.813	0.955	CLONAL	1	TRUE	0	0.563431556311769	1		307	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577115	7577115	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	353	641	0	ENST00000269305.4:c.823del	p.Cys275ValfsTer70	p.C275Vfs*70	ENST00000269305	NM_001126112.2	275	Tgt/gt	8/11	0.563431556311769	1	FACETS	0.935	0.888	0.982	0.935	0.888	0.982	CLONAL	1	TRUE	0	0.563431556311769	1		641	963	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143370	30143370	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	138	399	0	ENST00000389048.3:c.156G>T	p.Lys52Asn	p.K52N	ENST00000389048	NM_004304.4	52	aaG/aaT	1/29	NA	2	FACETS	0.637	0.58	0.697			1	INDETERMINATE	1	TRUE	NA	0.563431556311769	2		399	769	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876231	35876251	+	inframe_deletion	In_Frame_Del	DEL	AGGGGATGTGCAGAGCCCCAA	AGGGGATGTGCAGAGCCCCAA	-	novel	NA	P-0025492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	75	505	0	ENST00000303115.3:c.1023_1043del	p.Gly342_Asn348del	p.G342_N348del	ENST00000303115	NM_002185.3	341	ggAGGGGATGTGCAGAGCCCCAAc/ggc	8/8	1	2	FACETS	0.307	0.268	0.349	0.307	0.268	0.349	SUBCLONAL	1	TRUE	1	0.563431556311769	2		505	867	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0025494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	280	651	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.509286120079291	2	FACETS	0.963	0.914	1	0.963	0.914	1	CLONAL	2	TRUE	0	0.509286120079291	2		651	571	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0025501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	330	715	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.283398370862358	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	3	TRUE	0	0.358866784747405	2		715	553	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0025501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	75	620	0	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	0.358866784747405	2		620	295	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246525	105246526	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0025501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	33	617	0	ENST00000349310.3:c.74_75del	p.Arg25LeufsTer7	p.R25Lfs*7	ENST00000349310	NM_001014432.1	25	cGC/c	4/15	1	2	FACETS	0.363	0.295	0.44	0.363	0.295	0.44	SUBCLONAL	1	TRUE	1	0.358866784747405	2		617	507	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47600604	47600604	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	27	395	0	ENST00000263735.4:c.79T>C	p.Cys27Arg	p.C27R	ENST00000263735	NM_002354.2	27	Tgt/Cgt	2/9	1	2	FACETS	0.339	0.269	0.419	0.339	0.269	0.419	SUBCLONAL	1	TRUE	1	0.358866784747405	2		395	444	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-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	83	345	0	ENST00000265433.3:c.38-365_40del		p.X13_splice	ENST00000265433	NM_002485.4	13		2/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.358866784747405	2		345	387	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907690	76907697	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTCAGT	TTCTCAGT	-	novel	NA	P-0025501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	90	300	0	ENST00000373344.5:c.4464_4471del	p.Lys1488AsnfsTer8	p.K1488Nfs*8	ENST00000373344	NM_000489.3	1488	aaACTGAGAAca/aaca	15/35	1	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.358866784747405	1		300	325	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395570	116395570	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1013431413	NA	P-0025503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	44	472	1	ENST00000397752.3:c.1862+1G>A		p.X621_splice	ENST00000397752	NM_000245.2	621			1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		473	844	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871094	12871094	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	57	298	0	ENST00000228872.4:c.322del	p.Asp108MetfsTer11	p.D108Mfs*11	ENST00000228872	NM_004064.3	107	caG/ca	1/3	0.146579504533803	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		298	586	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62320877	62320877	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs865802900	NA	P-0025503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	99	873	0	ENST00000360203.5:c.1901C>T	p.Ser634Leu	p.S634L	ENST00000360203	NM_001283009.1	634	tCa/tTa	23/35	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		873	1120	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117375	115117381	+	frameshift_variant	Frame_Shift_Del	DEL	TACTATA	TACTATA	-	novel	NA	P-0025503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	97	495	0	ENST00000257566.3:c.793_799del	p.Tyr265HisfsTer15	p.Y265Hfs*15	ENST00000257566	NM_016569.3	265	TATAGTAca/ca	4/8	0.107075119945072	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		495	921	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0025504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	407	569	1	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	0.503584262051313	3	FACETS	0.98	0.943	1	0.98	0.943	1	CLONAL	3	TRUE	0	0.503584262051313	3		570	688	SUCCESS
AR	367	MSKCC	GRCh37	X	66765659	66765659	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	145	442	0	ENST00000374690.3:c.671A>G	p.Asn224Ser	p.N224S	ENST00000374690	NM_000044.3	224	aAt/aGt	1/8	1	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.503584262051313	1		442	354	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491677	56491677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1219696574	NA	P-0025504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	93	412	0	ENST00000267101.3:c.2569G>C	p.Asp857His	p.D857H	ENST00000267101	NM_001982.3	857	Gac/Cac	21/28	0.34437676224142	5	FACETS	1	0.892	1	0.334	0.297	0.373	CLONAL	1	TRUE	2	0.503584262051313	5		412	647	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281934	39281934	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	77	381	0	ENST00000402219.2:c.541G>C	p.Glu181Gln	p.E181Q	ENST00000402219	NM_005633.3	181	Gaa/Caa	5/23	0.282161057698024	5	FACETS	1	0.957	1	0.396	0.349	0.446	INDETERMINATE	1	TRUE	2	0.503584262051313	5		381	452	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0025505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	385	339	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.856433065126054	2		339	845	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106423	27106423	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	310	455	0	ENST00000324856.7:c.6034G>T	p.Gly2012Cys	p.G2012C	ENST00000324856	NM_006015.4	2012	Ggc/Tgc	20/20	0.856433065126054	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.856433065126054	1		455	400	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575428	64575444	+	frameshift_variant	Frame_Shift_Del	DEL	TGACCTCAGCTGTCTGC	TGACCTCAGCTGTCTGC	-	novel	NA	P-0025505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	387	618	0	ENST00000312049.6:c.573_589del	p.Glu191AspfsTer21	p.E191Dfs*21	ENST00000312049	NM_130799.2	191	gaGCAGACAGCTGAGGTCAcc/gacc	3/10	0.856433065126054	1	FACETS	0.986	0.955	1	0.986	0.955	1	CLONAL	1	TRUE	0	0.856433065126054	1		618	524	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390732	139390732	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	121	531	0	ENST00000277541.6:c.7459C>T	p.Gln2487Ter	p.Q2487*	ENST00000277541	NM_017617.3	2487	Cag/Tag	34/34	0.16066737101567	3	FACETS	0.848	0.767	0.932	1	0.978	1	CLONAL	3	TRUE	1	0.16066737101567	3		531	640	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0025510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	122	83	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.187898197134658	2	FACETS	1	0.978	1	0.635	0.575	0.698	CLONAL	1	FALSE	0	0.3	2		83	640	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0025510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	51	200	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	0.24838633931456	3	FACETS	0.798	0.685	0.92	0.798	0.685	0.92	CLONAL	2	FALSE	1	0.3	3		200	245	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578493	7578493	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1206165503	NA	P-0025510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	174	842	0	ENST00000269305.4:c.437G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tGg/tAg	5/11	0.187898197134658	2	FACETS	1	0.984	1	0.629	0.579	0.681	CLONAL	1	FALSE	0	0.3	2		842	922	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258992	153258992	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	71	401	0	ENST00000281708.4:c.823del	p.Gln275SerfsTer67	p.Q275Sfs*67	ENST00000281708	NM_033632.3	275	Cag/ag	5/12	0.187898197134658	2	FACETS	1	0.916	1	0.529	0.463	0.6	CLONAL	1	FALSE	0	0.3	2		401	447	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128036890	128036890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	95	649	2	ENST00000285398.2:c.1589G>A	p.Arg530Gln	p.R530Q	ENST00000285398	NM_000122.1	530	cGa/cAa	10/15	0.3	3	FACETS	0.763	0.678	0.854	0.381	0.339	0.427	SUBCLONAL	1	FALSE	1	0.3	3		651	955	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67197011	67197011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773737464	NA	P-0025510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	58	401	0	ENST00000312629.5:c.254G>A	p.Arg85Gln	p.R85Q	ENST00000312629	NM_003952.2	85	cGa/cAa	4/15	1	2	FACETS	0.664	0.571	0.767	0.664	0.571	0.767	SUBCLONAL	1	FALSE	1	0.3	2		401	582	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945583	71945583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	60	634	0	ENST00000298229.2:c.2339G>A	p.Ser780Asn	p.S780N	ENST00000298229	NM_001567.3	780	aGc/aAc	21/28	1	2	FACETS	0.563	0.485	0.649	0.563	0.485	0.649	SUBCLONAL	1	FALSE	1	0.3	2		634	710	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134626	2134632	+	frameshift_variant	Frame_Shift_Del	DEL	CATCACG	CATCACG	-	novel	NA	P-0025510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	65	708	0	ENST00000219476.3:c.4405_4411del	p.Ser1469GlyfsTer5	p.S1469Gfs*5	ENST00000219476	NM_000548.3	1468	cCATCACGc/cc	34/42	NA	2	FACETS	0.523	0.452	0.6			1	INDETERMINATE	1	FALSE	NA	0.3	2		708	829	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794947	242794947	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	113	792	0	ENST00000334409.5:c.262C>T	p.Gln88Ter	p.Q88*	ENST00000334409	NM_005018.2	88	Cag/Tag	2/5	NA	2	FACETS	0.808	0.726	0.895			1	INDETERMINATE	1	FALSE	NA	0.3	2		792	932	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258996	153258996	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	73	393	0	ENST00000281708.4:c.819A>T	p.Glu273Asp	p.E273D	ENST00000281708	NM_033632.3	273	gaA/gaT	5/12	0.187898197134658	2	FACETS	1	0.939	1	0.557	0.489	0.63	CLONAL	1	FALSE	0	0.3	2		393	437	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687031	176687031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1164947711	NA	P-0025510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	127	498	0	ENST00000439151.2:c.5008G>A	p.Ala1670Thr	p.A1670T	ENST00000439151	NM_022455.4	1670	Gcc/Acc	14/23	0.208976914924473	2	FACETS	1	0.982	1	0.67	0.608	0.734	CLONAL	1	FALSE	0	0.3	2		498	632	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0025512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	547	193	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.825857585197883	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.827380050018026	2		193	623	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0025512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	629	435	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.825857585197883	2	FACETS	0.999	0.978	1	0.999	0.978	1	CLONAL	2	TRUE	0	0.827380050018026	2		435	761	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39542551	39542551	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	225	501	0	ENST00000262039.4:c.355G>A	p.Ala119Thr	p.A119T	ENST00000262039	NM_002647.2	119	Gca/Aca	3/25	0.827380050018026	1	FACETS	0.966	0.922	1	0.966	0.922	1	CLONAL	1	TRUE	0	0.827380050018026	1		501	330	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665109	182665109	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	484	468	0	ENST00000292782.4:c.617G>A	p.Arg206Gln	p.R206Q	ENST00000292782	NM_020640.2	206	cGa/cAa	6/7	0.822954887418148	5	FACETS	0.864	0.826	0.903	0.346	0.33	0.362	CLONAL	2	TRUE	0	0.827380050018026	5		468	1517	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450300	50450300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	380	554	3	ENST00000331340.3:c.484C>T	p.Arg162Trp	p.R162W	ENST00000331340	NM_006060.4	162	Cgg/Tgg	5/8	0.882451073993763	3	FACETS	0.969	0.92	1	0.484	0.46	0.51	CLONAL	1	TRUE	1	0.882451073993763	3		557	1281	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655425	67655426	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0025527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	180	740	0	ENST00000264010.4:c.1292_1293del	p.Thr431ArgfsTer12	p.T431Rfs*12	ENST00000264010	NM_006565.3	430	CAc/c	7/12	1	2	FACETS	0.373	0.343	0.404	0.373	0.343	0.404	SUBCLONAL	1	TRUE	1	0.882451073993763	2		740	1094	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72861900	72861901	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCTTCTT	novel	NA	P-0025527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	438	649	2	ENST00000325599.8:c.975_981dup	p.Val328LysfsTer30	p.V328Kfs*30	ENST00000325599	NM_018130.2	327	-/AAGAAGG	9/11	1	2	FACETS	0.866	0.828	0.905	0.866	0.828	0.905	CLONAL	1	TRUE	1	0.882451073993763	2		651	1146	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0025528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	363	675	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.37499277321953	3	FACETS	0.979	0.934	1	0.979	0.934	1	CLONAL	3	TRUE	0	0.37499277321953	3		675	783	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936096	178936096	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	348	638	0	ENST00000263967.3:c.1638G>C	p.Gln546His	p.Q546H	ENST00000263967	NM_006218.2	546	caG/caC	10/21	0.37499277321953	3	FACETS	0.971	0.92	1	0.647	0.613	0.682	CLONAL	2	TRUE	0	0.37499277321953	3		638	1135	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061208	38061208	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	120	451	0	ENST00000250448.2:c.781C>A	p.Arg261Ser	p.R261S	ENST00000250448	NM_004496.3	261	Cgc/Agc	2/2	1	2	FACETS	0.988	0.894	1	0.988	0.894	1	CLONAL	1	TRUE	1	0.37499277321953	2		451	648	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49280981	49280981	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs201474852	NA	P-0025528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	192	655	0	ENST00000282018.3:c.28C>A	p.Pro10Thr	p.P10T	ENST00000282018	NM_020377.2	10	Cca/Aca	1/1	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.37499277321953	2		655	963	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267383	198267383	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	145	610	3	ENST00000335508.6:c.1974G>T	p.Trp658Cys	p.W658C	ENST00000335508	NM_012433.2	658	tgG/tgT	14/25	0.37499277321953	3	FACETS	0.813	0.741	0.89			1	CLONAL	1	TRUE	NA	0.37499277321953	3		613	1129	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6038902	6038902	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs863224681	NA	P-0025528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	131	472	0	ENST00000265849.7:c.542A>T	p.Tyr181Phe	p.Y181F	ENST00000265849	NM_000535.5	181	tAt/tTt	6/15	1	2	FACETS	0.888	0.806	0.974	0.888	0.806	0.974	CLONAL	1	TRUE	1	0.37499277321953	2		472	787	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204864	NA	P-0025529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	19	402	1	ENST00000371953.3:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000371953	NM_000314.4	171	Cag/Tag	6/9	1	2	FACETS	0.744	0.564	0.956	0.744	0.564	0.956	CLONAL	1	TRUE	1	0.14	2		403	365	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482606	56482606	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	41	453	0	ENST00000267101.3:c.1063A>C	p.Thr355Pro	p.T355P	ENST00000267101	NM_001982.3	355	Acc/Ccc	9/28	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.14	2		453	511	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	67	387	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.816	0.718	0.92	0.816	0.718	0.92	CLONAL	1	TRUE	1	0.638761734290656	2		387	257	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0025530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	225	503	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.927	0.866	0.989	0.927	0.866	0.989	CLONAL	1	TRUE	1	0.638761734290656	2		503	760	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954211	48954242	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAAATTTTAGGTAAATTTTTTACTTTTAGTAA	AAAATTTTAGGTAAATTTTTTACTTTTAGTAA	-	novel	NA	P-0025530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	75	428	0	ENST00000267163.4:c.1420_1421+30del		p.X474_splice	ENST00000267163	NM_000321.2	474		15/27	0.638761734290656	2	FACETS	0.51	0.449	0.577	0.255	0.224	0.289	SUBCLONAL	1	TRUE	0	0.638761734290656	2		428	460	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261727	16261727	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	203	546	0	ENST00000375759.3:c.8992G>A	p.Val2998Ile	p.V2998I	ENST00000375759	NM_015001.2	2998	Gtc/Atc	11/15	1	2	FACETS	0.913	0.85	0.978	0.913	0.85	0.978	CLONAL	1	TRUE	1	0.638761734290656	2		546	696	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325161	123325161	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	229	505	0	ENST00000358487.5:c.167A>T	p.Glu56Val	p.E56V	ENST00000358487	NM_000141.4	56	gAg/gTg	3/18	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.638761734290656	2		505	678	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235929	133235930	+	missense_variant	Missense_Mutation	DNP	CA	CA	AC	novel	NA	P-0025530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	181	525	2	ENST00000320574.5:c.3226_3227delinsGT	p.Cys1076Val	p.C1076V	ENST00000320574	NM_006231.2	1076	TGc/GTc	26/49	1	2	FACETS	0.904	0.838	0.972	0.904	0.838	0.972	CLONAL	1	TRUE	1	0.638761734290656	2		527	627	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574406	95574407	+	missense_variant	Missense_Mutation	DNP	GT	GT	AG	novel	NA	P-0025530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	79	293	1	ENST00000393063.1:c.2460_2461delinsCT	p.Arg821Cys	p.R821C	ENST00000393063	NM_030621.3	820	acACgc/acCTgc	17/28	0.624726453885034	1	FACETS	0.809	0.726	0.895	0.809	0.726	0.895	CLONAL	1	TRUE	0	0.638761734290656	1		294	208	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245756	41245756	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	192	685	0	ENST00000357654.3:c.1792T>A	p.Leu598Ile	p.L598I	ENST00000357654	NM_007294.3	598	Tta/Ata	10/23	1	2	FACETS	0.808	0.749	0.869	0.808	0.749	0.869	CLONAL	1	TRUE	1	0.638761734290656	2		685	744	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221210	1221210	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0025530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	203	646	0	ENST00000326873.7:c.735-2A>T		p.X245_splice	ENST00000326873	NM_000455.4	245			0.624726453885034	1	FACETS	0.798	0.746	0.851	0.798	0.746	0.851	SUBCLONAL	1	TRUE	0	0.638761734290656	1		646	542	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716009	52716009	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	444	541	0	ENST00000322088.6:c.574T>C	p.Phe192Leu	p.F192L	ENST00000322088	NM_014225.5	192	Ttt/Ctt	5/15	0.578033665385525	3	FACETS	0.977	0.937	1	0.977	0.937	1	CLONAL	2	TRUE	1	0.638761734290656	3		541	939	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727072	40727072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	157	501	0	ENST00000373198.4:c.3892G>A	p.Asp1298Asn	p.D1298N	ENST00000373198	NM_133170.3	1298	Gac/Aac	28/32	1	2	FACETS	0.822	0.756	0.89	0.822	0.756	0.89	CLONAL	1	TRUE	1	0.638761734290656	2		501	598	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036017	180036017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	249	641	0	ENST00000261937.6:c.3844G>A	p.Glu1282Lys	p.E1282K	ENST00000261937	NM_182925.4	1282	Gag/Aag	29/30	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.638761734290656	2		641	762	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187533	32187533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	255	571	1	ENST00000375023.3:c.1346G>A	p.Gly449Asp	p.G449D	ENST00000375023	NM_004557.3	449	gGc/gAc	8/30	0.568429003339058	4	FACETS	1	0.983	1	0.382	0.357	0.407	CLONAL	1	TRUE	1	0.638761734290656	4		572	1143	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146928	38146928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	184	752	0	ENST00000317025.8:c.3214C>T	p.Pro1072Ser	p.P1072S	ENST00000317025	NM_023034.1	1072	Ccc/Tcc	18/24	1	2	FACETS	0.814	0.753	0.876	0.814	0.753	0.876	CLONAL	1	TRUE	1	0.638761734290656	2		752	708	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123199774	123199775	+	missense_variant	Missense_Mutation	DNP	AA	AA	GG	novel	NA	P-0025530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	91	535	0	ENST00000218089.9:c.2074_2075delinsGG	p.Lys692Gly	p.K692G	ENST00000218089	NM_001042749.1	692	AAg/GGg	21/35	1	2	FACETS	0.77	0.689	0.855	0.77	0.689	0.855	SUBCLONAL	1	TRUE	1	0.638761734290656	2		535	370	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092831	27092833	+	frameshift_variant	Frame_Shift_Del	DEL	GTG	GTG	T	novel	NA	P-0025530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	236	626	0	ENST00000324856.7:c.2852_2854delinsT	p.Gly951ValfsTer55	p.G951Vfs*55	ENST00000324856	NM_006015.4	951	gGTGga/gTga	9/20	1	2	FACETS	0.977	0.916	1	0.977	0.916	1	CLONAL	1	TRUE	1	0.638761734290656	2		626	756	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0025531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	202	607	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.292978354072304	3	FACETS	0.87	0.807	0.934	0.87	0.807	0.934	CLONAL	2	TRUE	1	0.313452869030533	3		607	857	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242470	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs397517097	NA	P-0025531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	198	364	2	ENST00000275493.2:c.2240T>C	p.Leu747Ser	p.L747S	ENST00000275493	NM_005228.3	747	tTa/tCa	19/28	0.292978354072304	3	FACETS	0.966	0.898	1	0.966	0.898	1	CLONAL	2	TRUE	1	0.313452869030533	3		366	756	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745624	162745624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765562219	NA	P-0025531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	108	350	3	ENST00000367921.3:c.2039G>A	p.Arg680His	p.R680H	ENST00000367921	NM_006182.2	680	cGc/cAc	15/18	1	2	FACETS	0.957	0.86	1	0.957	0.86	1	CLONAL	1	TRUE	1	0.313452869030533	2		353	720	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491274	2491274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368302066	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	24	400	0	ENST00000355716.4:c.317G>A	p.Arg106His	p.R106H	ENST00000355716	NM_003820.2	106	cGc/cAc	4/8	0.3	1	FACETS	0.733	0.574	0.916	0.733	0.574	0.916	CLONAL	1	TRUE	0	0.15	1		400	404	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	15	454	0	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	0.371	0.27	0.494	0.371	0.27	0.494	SUBCLONAL	1	TRUE	1	0.15	2		454	539	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	26	458	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	1	2	FACETS	0.631	0.499	0.785	0.631	0.499	0.785	SUBCLONAL	1	TRUE	1	0.15	2		458	549	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123260369	123260369	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770309121	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	45	514	0	ENST00000358487.5:c.1532C>T	p.Ala511Val	p.A511V	ENST00000358487	NM_000141.4	511	gCg/gTg	11/18	1	2	FACETS	0.917	0.77	1	0.917	0.77	1	CLONAL	1	TRUE	1	0.15	2		514	654	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741486	17741486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	19	321	0	ENST00000250003.3:c.157G>A	p.Val53Met	p.V53M	ENST00000250003	NM_002478.4	53	Gtg/Atg	1/3	1	2	FACETS	0.777	0.589	0.998	0.777	0.589	0.998	CLONAL	1	TRUE	1	0.15	2		321	326	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691191	18691191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774205366	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	25	392	2	ENST00000266497.5:c.3302G>A	p.Arg1101His	p.R1101H	ENST00000266497		1101	cGt/cAt	23/31	1	2	FACETS	0.729	0.574	0.909	0.729	0.574	0.909	CLONAL	1	TRUE	1	0.15	2		394	457	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444349	49444349	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	27	476	0	ENST00000301067.7:c.3022C>A	p.Pro1008Thr	p.P1008T	ENST00000301067	NM_003482.3	1008	Cca/Aca	11/54	0.129931694592121	3	FACETS	0.763	0.606	0.944	0.382	0.303	0.472	CLONAL	1	TRUE	1	0.15	3		476	507	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444960	49444960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	20	290	1	ENST00000301067.7:c.2506del	p.Gln836SerfsTer94	p.Q836Sfs*94	ENST00000301067	NM_003482.3	836	Cag/ag	10/54	0.129931694592121	3	FACETS	0.808	0.617	1	0.404	0.308	0.516	CLONAL	1	TRUE	1	0.15	3		291	355	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	38	472	2	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	0.129931694592121	3	FACETS	1	0.869	1	0.532	0.439	0.636	CLONAL	1	TRUE	1	0.15	3		474	512	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	37	458	3	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	0.129931694592121	3	FACETS	0.893	0.735	1	0.446	0.367	0.535	CLONAL	1	TRUE	1	0.15	3		461	594	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712845	43712845	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	31	532	0	ENST00000382044.4:c.4339del	p.Arg1447GlufsTer36	p.R1447Efs*36	ENST00000382044	NM_001141980.1	1447	Cga/ga	21/28	1	2	FACETS	0.699	0.564	0.853	0.699	0.564	0.853	SUBCLONAL	1	TRUE	1	0.15	2		532	591	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112983	2112983	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45517169	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	22	311	1	ENST00000219476.3:c.1372C>T	p.Arg458Ter	p.R458*	ENST00000219476	NM_000548.3	458	Cga/Tga	14/42	0.0910163125608416	0	FACETS	0.826	0.64	1			1	CLONAL	1	TRUE	0	0.15	0		312	302	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136784	2136784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201694466	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	47	530	0	ENST00000219476.3:c.4901G>A	p.Arg1634His	p.R1634H	ENST00000219476	NM_000548.3	1634	cGc/cAc	38/42	0.0910163125608416	0	FACETS	0.979	0.826	1			1	CLONAL	1	TRUE	0	0.15	0		530	544	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647400	3647400	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763869769	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	21	404	0	ENST00000294008.3:c.1663G>A	p.Val555Met	p.V555M	ENST00000294008	NM_032444.2	555	Gtg/Atg	7/15	0.0910163125608416	0	FACETS	0.692	0.532	0.878			1	SUBCLONAL	1	TRUE	0	0.15	0		404	344	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820602	3820602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749011678	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	28	434	1	ENST00000262367.5:c.2849C>T	p.Thr950Met	p.T950M	ENST00000262367	NM_004380.2	950	aCg/aTg	14/31	0.0910163125608416	0	FACETS	0.62	0.494	0.764			1	SUBCLONAL	1	TRUE	0	0.15	0		435	512	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357108	89357108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs900210533	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	27	486	0	ENST00000301030.4:c.526G>A	p.Ala176Thr	p.A176T	ENST00000301030	NM_001256183.1	176	Gcc/Acc	6/13	0.0910163125608416	0	FACETS	0.611	0.485	0.755			1	SUBCLONAL	1	TRUE	0	0.15	0		486	501	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474338	40474338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	30	418	0	ENST00000264657.5:c.2063G>A	p.Arg688Gln	p.R688Q	ENST00000264657	NM_139276.2	688	cGg/cAg	21/24	1	2	FACETS	0.679	0.546	0.831	0.679	0.546	0.831	SUBCLONAL	1	TRUE	1	0.15	2		418	589	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	38	154	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.15	2		154	423	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440757	56440757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774211426	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	19	333	0	ENST00000407977.2:c.461C>T	p.Pro154Leu	p.P154L	ENST00000407977		154	cCg/cTg	5/10	1	2	FACETS	0.734	0.557	0.944	0.734	0.557	0.944	CLONAL	1	TRUE	1	0.15	2		333	345	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	44	408	0	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.15	2		408	533	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168962	11168962	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	23	357	0	ENST00000358026.2:c.4552A>G	p.Ile1518Val	p.I1518V	ENST00000358026	NM_001128849.1	1518	Atc/Gtc	32/36	0.0910163125608416	0	FACETS	0.753	0.587	0.946			1	CLONAL	1	TRUE	0	0.15	0		357	346	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216507	36216507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749257014	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	29	507	1	ENST00000222270.7:c.3770G>A	p.Arg1257His	p.R1257H	ENST00000222270	NM_014727.1	1257	cGc/cAc	12/37	0.0910163125608416	0	FACETS	0.583	0.466	0.716			1	SUBCLONAL	1	TRUE	0	0.15	0		508	564	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753629	42753629	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777136618	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	36	361	0	ENST00000222329.4:c.635C>T	p.Pro212Leu	p.P212L	ENST00000222329	NM_006494.2	212	cCg/cTg	4/4	0.3	3	FACETS	0.901	0.739	1			1	CLONAL	1	TRUE	NA	0.15	3		361	573	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799098	42799098	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	34	425	0	ENST00000575354.2:c.4586del	p.Pro1529LeufsTer91	p.P1529Lfs*91	ENST00000575354	NM_015125.3	1528	Ccc/cc	20/20	0.3	3	FACETS	0.983	0.802	1			1	CLONAL	1	TRUE	NA	0.15	3		425	496	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918799	50918799	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146344351	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	23	423	0	ENST00000440232.2:c.2669C>T	p.Ala890Val	p.A890V	ENST00000440232	NM_002691.3	890	gCg/gTg	21/27	0.129931694592121	0	FACETS	0.652	0.507	0.819			1	SUBCLONAL	1	TRUE	0	0.15	0		423	400	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919914	50919914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs550922227	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	23	342	0	ENST00000440232.2:c.3001G>A	p.Gly1001Ser	p.G1001S	ENST00000440232	NM_002691.3	1001	Ggc/Agc	24/27	0.129931694592121	0	FACETS	0.778	0.607	0.976			1	CLONAL	1	TRUE	0	0.15	0		342	335	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497907	25497907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	21	361	1	ENST00000264709.3:c.542G>A	p.Arg181His	p.R181H	ENST00000264709	NM_175629.2	181	cGt/cAt	6/23	1	2	FACETS	0.685	0.526	0.87	0.685	0.526	0.87	SUBCLONAL	1	TRUE	1	0.15	2		362	409	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	53	455	6	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	0.15	2		461	553	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439668	220439668	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs192760521	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	20	409	0	ENST00000243786.2:c.521C>A	p.Pro174His	p.P174H	ENST00000243786	NM_002191.3	174	cCt/cAt	2/2	1	2	FACETS	0.713	0.544	0.911	0.713	0.544	0.911	CLONAL	1	TRUE	1	0.15	2		409	374	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662461	227662461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1172214075	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	26	335	0	ENST00000305123.5:c.994G>A	p.Gly332Ser	p.G332S	ENST00000305123	NM_005544.2	332	Ggc/Agc	1/2	1	2	FACETS	0.947	0.75	1	0.947	0.75	1	CLONAL	1	TRUE	1	0.15	2		335	366	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023474	31023474	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376074119	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	27	371	0	ENST00000375687.4:c.2959G>A	p.Gly987Arg	p.G987R	ENST00000375687	NM_015338.5	987	Gga/Aga	13/13	1	2	FACETS	0.989	0.787	1	0.989	0.787	1	CLONAL	1	TRUE	1	0.15	2		371	364	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012698	36012698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	15	39	0	ENST00000358208.4:c.142C>T	p.Arg48Cys	p.R48C	ENST00000358208		48	Cgc/Tgc	2/12	1	2	FACETS	1	0.803	1	1	0.926	1	CLONAL	2	TRUE	1	0.15	2		39	91	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292757	62292757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61736616	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	31	417	0	ENST00000360203.5:c.209G>A	p.Arg70His	p.R70H	ENST00000360203	NM_001283009.1	70	cGc/cAc	3/35	1	2	FACETS	0.944	0.763	1	0.944	0.763	1	CLONAL	1	TRUE	1	0.15	2		417	438	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321791	62321791	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	17	282	0	ENST00000360203.5:c.2410T>C	p.Ser804Pro	p.S804P	ENST00000360203	NM_001283009.1	804	Tca/Cca	26/35	1	2	FACETS	0.81	0.604	1	0.81	0.604	1	CLONAL	1	TRUE	1	0.15	2		282	280	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655225	45655225	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	40	382	0	ENST00000407780.3:c.627del	p.Ser210AlafsTer2	p.S210Afs*2	ENST00000407780	NM_001283052.1	209	ccC/cc	4/7	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.15	2		382	482	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934985	49934985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768318968	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	29	440	1	ENST00000296474.3:c.2014G>A	p.Gly672Ser	p.G672S	ENST00000296474	NM_002447.2	672	Ggc/Agc	6/20	1	2	FACETS	0.841	0.674	1	0.841	0.674	1	CLONAL	1	TRUE	1	0.15	2		441	460	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940582	49940582	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	25	323	1	ENST00000296474.3:c.461C>T	p.Ala154Val	p.A154V	ENST00000296474	NM_002447.2	154	gCc/gTc	1/20	1	2	FACETS	1	0.801	1	1	0.801	1	CLONAL	1	TRUE	1	0.15	2		324	328	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	17	326	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.516	0.384	0.674	0.516	0.384	0.674	SUBCLONAL	1	TRUE	1	0.15	2		326	439	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541247	187541247	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	24	394	0	ENST00000441802.2:c.6493del	p.Ser2165GlnfsTer11	p.S2165Qfs*11	ENST00000441802	NM_005245.3	2165	Tca/ca	10/27	1	2	FACETS	0.669	0.524	0.838	0.669	0.524	0.838	SUBCLONAL	1	TRUE	1	0.15	2		394	478	SUCCESS
APC	324	MSKCC	GRCh37	5	112111327	112111327	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	12	181	0	ENST00000257430.4:c.424T>C	p.Ser142Pro	p.S142P	ENST00000257430	NM_000038.5	142	Tca/Cca	5/16	1	2	FACETS	0.678	0.476	0.927	0.678	0.476	0.927	SUBCLONAL	1	TRUE	1	0.15	2		181	236	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100302	157100302	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1417035592	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	13	153	0	ENST00000346085.5:c.1243del	p.Ala415ProfsTer15	p.A415Pfs*15	ENST00000346085	NM_020732.3	413	tcG/tc	1/20	0.129931694592121	3	FACETS	1	0.735	1	0.515	0.368	0.693	CLONAL	1	TRUE	1	0.15	3		153	181	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162867	38162867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779630054	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	35	468	0	ENST00000317025.8:c.2339G>A	p.Arg780His	p.R780H	ENST00000317025	NM_023034.1	780	cGc/cAc	13/24	1	2	FACETS	0.686	0.561	0.828	0.686	0.561	0.828	SUBCLONAL	1	TRUE	1	0.15	2		468	680	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27203069	27203069	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	39	529	0	ENST00000380036.4:c.2161A>C	p.Ser721Arg	p.S721R	ENST00000380036	NM_000459.3	721	Agc/Cgc	13/23	1	2	FACETS	0.776	0.642	0.927	0.776	0.642	0.927	CLONAL	1	TRUE	1	0.15	2		529	670	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209357	98209357	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748812637	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	21	360	0	ENST00000331920.6:c.4181G>A	p.Arg1394Gln	p.R1394Q	ENST00000331920	NM_000264.3	1394	cGa/cAa	23/24	1	2	FACETS	0.909	0.7	1	0.909	0.7	1	CLONAL	1	TRUE	1	0.15	2		360	308	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128268684	128268684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779168610	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	27	459	0	ENST00000265960.3:c.971G>A	p.Arg324His	p.R324H	ENST00000265960	NM_001006617.1	324	cGc/cAc	8/12	1	2	FACETS	0.678	0.538	0.839	0.678	0.538	0.839	SUBCLONAL	1	TRUE	1	0.15	2		459	531	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933613	39933613	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	23	363	0	ENST00000378444.4:c.986C>T	p.Thr329Ile	p.T329I	ENST00000378444	NM_001123385.1	329	aCa/aTa	4/15	0.0910163125608416	0	FACETS	0.697	0.543	0.876			1	SUBCLONAL	1	TRUE	0	0.15	0		363	374	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934031	39934031	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	36	451	1	ENST00000378444.4:c.568C>T	p.Pro190Ser	p.P190S	ENST00000378444	NM_001123385.1	190	Ccc/Tcc	4/15	0.0910163125608416	0	FACETS	0.879	0.723	1			1	CLONAL	1	TRUE	0	0.15	0		452	464	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0025534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	122	285	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.901	0.814	0.993	0.901	0.814	0.993	CLONAL	1	TRUE	1	0.32	2		285	846	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0025534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	126	496	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	1	2	FACETS	0.814	0.736	0.896	0.814	0.736	0.896	CLONAL	1	TRUE	1	0.32	2		496	968	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581272	48581273	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0025534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	327	525	0	ENST00000342988.3:c.579_580del	p.Glu193AspfsTer12	p.E193Dfs*12	ENST00000342988	NM_005359.5	192	acAGag/acag	5/12	0.250764014999592	2	FACETS	0.998	0.944	1	0.998	0.944	1	CLONAL	2	TRUE	0	0.32	2		525	1024	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438298	110438298	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	52	159	0	ENST00000375856.3:c.103G>A	p.Gly35Ser	p.G35S	ENST00000375856	NM_003749.2	35	Ggc/Agc	1/2	1	2	FACETS	0.7	0.597	0.813	0.7	0.597	0.813	SUBCLONAL	1	TRUE	1	0.32	2		159	464	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0025537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	531	735	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.647607415941131	2		735	1452	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0025537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	421	374	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.647607415941131	3	FACETS	0.976	0.935	1	0.976	0.935	1	CLONAL	2	TRUE	1	0.647607415941131	3		374	882	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193507	99193507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1471383993	NA	P-0025537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	454	645	1	ENST00000074304.5:c.2702G>A	p.Arg901His	p.R901H	ENST00000074304	NM_001134224.1	901	cGt/cAt	25/26	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.647607415941131	2		646	1375	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931589	NA	P-0025537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	228	425	0	ENST00000349496.5:c.101G>A	p.Gly34Glu	p.G34E	ENST00000349496	NM_001904.3	34	gGa/gAa	3/15	1	2	FACETS	0.929	0.869	0.991	0.929	0.869	0.991	CLONAL	1	TRUE	1	0.647607415941131	2		425	758	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370985	55370985	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	427	597	1	ENST00000297316.4:c.287C>G	p.Ala96Gly	p.A96G	ENST00000297316	NM_022454.3	96	gCc/gGc	1/2	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.647607415941131	2		598	1209	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916726	178916726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772110575	NA	P-0025537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	151	427	0	ENST00000263967.3:c.113G>A	p.Arg38His	p.R38H	ENST00000263967	NM_006218.2	38	cGt/cAt	2/21	1	2	FACETS	0.992	0.915	1	0.992	0.915	1	CLONAL	1	TRUE	1	0.647607415941131	2		427	470	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420825	49420825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757011865	NA	P-0025537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1182	355	574	0	ENST00000301067.7:c.14924G>A	p.Arg4975His	p.R4975H	ENST00000301067	NM_003482.3	4975	cGt/cAt	48/54	0.647607415941131	3	FACETS	0.944	0.893	0.997	0.472	0.446	0.499	CLONAL	1	TRUE	1	0.647607415941131	3		574	1537	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105690	27105693	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	novel	NA	P-0025537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	190	375	0	ENST00000324856.7:c.5301_5304del	p.Glu1767AspfsTer2	p.E1767Dfs*2	ENST00000324856	NM_006015.4	1767	gaACTT/ga	20/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.647607415941131	2		375	514	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690842	89690842	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1554897879	NA	P-0025537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	98	412	0	ENST00000371953.3:c.249C>A	p.Cys83Ter	p.C83*	ENST00000371953	NM_000314.4	83	tgC/tgA	4/9	0.647607415941131	3	FACETS	0.741	0.663	0.823	0.37	0.331	0.412	SUBCLONAL	1	TRUE	1	0.647607415941131	3		412	541	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149905	99149906	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCACCCCT	novel	NA	P-0025537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	337	617	0	ENST00000074304.5:c.220_227dup	p.Gln77ProfsTer25	p.Q77Pfs*25	ENST00000074304	NM_001134224.1	73	acc/aCCACCCCTcc	5/26	1	2	FACETS	0.875	0.828	0.924	0.875	0.828	0.924	CLONAL	1	TRUE	1	0.647607415941131	2		617	1189	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687148	176687155	+	frameshift_variant	Frame_Shift_Del	DEL	TGGTGCTT	TGGTGCTT	-	novel	NA	P-0025537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	221	537	0	ENST00000439151.2:c.5127_5134del	p.Trp1709CysfsTer12	p.W1709Cfs*12	ENST00000439151	NM_022455.4	1709	TGGTGCTTt/t	14/23	1	2	FACETS	0.873	0.815	0.933	0.873	0.815	0.933	CLONAL	1	TRUE	1	0.647607415941131	2		537	782	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720852	176720852	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	248	562	0	ENST00000439151.2:c.6483G>A	p.Trp2161Ter	p.W2161*	ENST00000439151	NM_022455.4	2161	tgG/tgA	23/23	1	2	FACETS	0.957	0.898	1	0.957	0.898	1	CLONAL	1	TRUE	1	0.647607415941131	2		562	800	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433861	78433861	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754339243	NA	P-0025542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	238	473	1	ENST00000370768.2:c.238C>T	p.Pro80Ser	p.P80S	ENST00000370768	NM_003902.3	80	Cct/Tct	3/20	1	2	FACETS	0.94	0.881	0.999	1	0.994	1	CLONAL	2	TRUE	1	0.356255108592656	2		474	711	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	65	387	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.907	0.796	1			1	INDETERMINATE	1	TRUE	NA	0.582348354045016	2		387	246	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0025543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	148	702	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.582348354045016	2		702	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0025543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	148	741	1	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	1	2	FACETS	0.835	0.765	0.907	0.835	0.765	0.907	CLONAL	1	TRUE	1	0.582348354045016	2		742	609	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271892	15271892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	106	676	1	ENST00000263388.2:c.6547C>T	p.Pro2183Ser	p.P2183S	ENST00000263388	NM_000435.2	2183	Ccc/Tcc	33/33	0.246485385325296	1	FACETS	0.555	0.5	0.612	0.555	0.5	0.612	INDETERMINATE	1	TRUE	0	0.582348354045016	1		677	465	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690802	89690802	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1114167621	NA	P-0025543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	176	433	0	ENST00000371953.3:c.210-1G>A		p.X70_splice	ENST00000371953	NM_000314.4	70			0.582348354045016	1	FACETS	0.963	0.896	1	0.963	0.896	1	CLONAL	1	TRUE	0	0.582348354045016	1		433	445	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039220	49039220	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	179	629	0	ENST00000267163.4:c.2300del	p.Asn767IlefsTer43	p.N767Ifs*43	ENST00000267163	NM_000321.2	766	acA/ac	22/27	1	2	FACETS	0.947	0.877	1	0.947	0.877	1	CLONAL	1	TRUE	1	0.582348354045016	2		629	649	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0025546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	187	611	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.936	0.865	1	1	0.992	1	CLONAL	2	TRUE	1	0.222899827822356	2		611	896	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0025546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	152	466	2	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.167106918627686	2	FACETS	1	0.986	1	0.716	0.655	0.781	CLONAL	1	TRUE	0	0.222899827822356	2		468	952	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941668	48941669	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0025546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	65	378	0	ENST00000267163.4:c.983dup	p.Asn328LysfsTer2	p.N328Kfs*2	ENST00000267163	NM_000321.2	326	-/A	10/27	0.222899827822356	1	FACETS	0.912	0.791	1	0.912	0.791	1	CLONAL	1	TRUE	0	0.222899827822356	1		378	568	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444666	78444666	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	55	381	0	ENST00000370768.2:c.23del	p.Pro8LeufsTer46	p.P8Lfs*46	ENST00000370768	NM_003902.3	8	cCt/ct	1/20	1	2	FACETS	0.783	0.669	0.908	0.783	0.669	0.908	CLONAL	1	TRUE	1	0.222899827822356	2		381	630	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720717	89720717	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	15	111	0	ENST00000371953.3:c.868del	p.Val290Ter	p.V290*	ENST00000371953	NM_000314.4	290	Gta/ta	8/9	0.222899827822356	1	FACETS	0.762	0.56	1	0.762	0.56	1	CLONAL	1	TRUE	0	0.222899827822356	1		111	157	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426578	49426592	+	inframe_deletion	In_Frame_Del	DEL	CTGCTGCTGTTGAAA	CTGCTGCTGTTGAAA	-	rs1195849154	NA	P-0025546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	109	564	0	ENST00000301067.7:c.11896_11910del	p.Phe3966_Gln3970del	p.F3966_Q3970del	ENST00000301067	NM_003482.3	3966	TTTCAACAGCAGCAG/-	39/54	1	2	FACETS	0.847	0.758	0.941	0.847	0.758	0.941	CLONAL	1	TRUE	1	0.222899827822356	2		564	1155	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865120	57865120	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	122	757	1	ENST00000228682.2:c.2597C>A	p.Thr866Asn	p.T866N	ENST00000228682	NM_005269.2	866	aCc/aAc	12/12	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.222899827822356	2		758	1039	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631604	119631604	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	55	420	0	ENST00000316626.5:c.662A>T	p.Tyr221Phe	p.Y221F	ENST00000316626		221	tAc/tTc	6/12	1	2	FACETS	0.769	0.657	0.891	0.769	0.657	0.891	SUBCLONAL	1	TRUE	1	0.222899827822356	2		420	642	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176940	56176940	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	48	436	0	ENST00000399503.3:c.2210T>A	p.Val737Asp	p.V737D	ENST00000399503	NM_005921.1	737	gTc/gAc	13/20	1	2	FACETS	0.669	0.564	0.784	0.669	0.564	0.784	SUBCLONAL	1	TRUE	1	0.222899827822356	2		436	644	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465563	8465563	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	105	643	0	ENST00000356435.5:c.3617G>T	p.Gly1206Val	p.G1206V	ENST00000356435		1206	gGg/gTg	21/35	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.222899827822356	2		643	889	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197720	123197720	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	54	460	0	ENST00000218089.9:c.1844A>G	p.Gln615Arg	p.Q615R	ENST00000218089	NM_001042749.1	615	cAg/cGg	20/35	1	2	FACETS	0.798	0.681	0.926	0.798	0.681	0.926	CLONAL	1	TRUE	1	0.222899827822356	2		460	607	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0025548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	208	631	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.915	0.851	0.98	1	0.993	1	CLONAL	2	TRUE	1	0.29	2		631	784	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591901	48591901	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	79	456	0	ENST00000342988.3:c.1064A>G	p.Asp355Gly	p.D355G	ENST00000342988	NM_005359.5	355	gAc/gGc	9/12	0.296843811268385	1	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	0	0.29	1		456	464	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512490	149512490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1443597666	NA	P-0025548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	45	390	0	ENST00000261799.4:c.950G>A	p.Arg317Gln	p.R317Q	ENST00000261799	NM_002609.3	317	cGg/cAg	7/23	1	2	FACETS	0.792	0.667	0.929	0.792	0.667	0.929	CLONAL	1	TRUE	1	0.29	2		390	392	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830519	72830521	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0025548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	77	517	0	ENST00000268489.5:c.6060_6062del	p.Gln2021del	p.Q2021del	ENST00000268489	NM_006885.3	2020	aaACAg/aag	9/10	1	2	FACETS	0.903	0.794	1	0.903	0.794	1	CLONAL	1	TRUE	1	0.29	2		517	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577546	7577557	+	inframe_deletion	In_Frame_Del	DEL	GCCGCCCATGCA	GCCGCCCATGCA	-	novel	NA	P-0025548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	83	549	0	ENST00000269305.4:c.724_735del	p.Cys242_Gly245del	p.C242_G245del	ENST00000269305	NM_001126112.2	242	TGCATGGGCGGC/-	7/11	0.296843811268385	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.29	1		549	466	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436002	56436002	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1366537134	NA	P-0025548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	41	317	0	ENST00000407977.2:c.1135C>T	p.Gln379Ter	p.Q379*	ENST00000407977		379	Cag/Tag	9/10	0.296843811268385	1	FACETS	0.831	0.695	0.98	0.831	0.695	0.98	CLONAL	1	TRUE	0	0.29	1		317	291	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048637	180048637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1448080273	NA	P-0025548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	67	476	0	ENST00000261937.6:c.1925G>A	p.Arg642His	p.R642H	ENST00000261937	NM_182925.4	642	cGc/cAc	13/30	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.29	2		476	447	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933416	39933416	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0025548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	79	280	0	ENST00000378444.4:c.1183A>T	p.Lys395Ter	p.K395*	ENST00000378444	NM_001123385.1	395	Aag/Tag	4/15	1	1	FACETS	0.761	0.676	0.851	1	0.979	1	SUBCLONAL	2	TRUE	0	0.29	1		280	306	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453149	140453149	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913361	NA	P-0025549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	182	428	0	ENST00000288602.6:c.1786G>C	p.Gly596Arg	p.G596R	ENST00000288602	NM_004333.4	596	Ggt/Cgt	15/18	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.554472005148989	2		428	597	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730008	41730008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537531066	NA	P-0025549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	194	476	1	ENST00000242208.4:c.521G>A	p.Arg174His	p.R174H	ENST00000242208	NM_002192.2	174	cGc/cAc	3/3	1	2	FACETS	0.991	0.92	1	0.991	0.92	1	CLONAL	1	TRUE	1	0.554472005148989	2		477	706	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220506	1220506	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0025549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	143	385	1	ENST00000326873.7:c.597+2T>A		p.X199_splice	ENST00000326873	NM_000455.4	199			0.554472005148989	1	FACETS	0.997	0.92	1	0.997	0.92	1	CLONAL	1	TRUE	0	0.554472005148989	1		386	374	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967828	18967828	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	202	567	0	ENST00000262803.5:c.1967A>G	p.Gln656Arg	p.Q656R	ENST00000262803	NM_002911.3	656	cAg/cGg	14/24	0.554472005148989	1	FACETS	0.979	0.915	1	0.979	0.915	1	CLONAL	1	TRUE	0	0.554472005148989	1		567	538	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792521	33792521	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	78	156	0	ENST00000498907.2:c.800G>T	p.Gly267Val	p.G267V	ENST00000498907	NM_004364.3	267	gGc/gTc	1/1	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.554472005148989	2		156	251	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467441	25467441	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	178	483	0	ENST00000264709.3:c.1635G>T	p.Glu545Asp	p.E545D	ENST00000264709	NM_175629.2	545	gaG/gaT	14/23	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.554472005148989	2		483	618	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31431743	31431743	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	178	417	0	ENST00000344624.3:c.3085G>A	p.Asp1029Asn	p.D1029N	ENST00000344624		1029	Gac/Aac	23/33	0.554472005148989	4	FACETS	0.924	0.851	1	0.308	0.283	0.334	CLONAL	1	TRUE	1	0.554472005148989	4		417	1080	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386596	81386596	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	201	458	1	ENST00000222390.5:c.391G>T	p.Gly131Cys	p.G131C	ENST00000222390	NM_000601.4	131	Ggt/Tgt	4/18	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.554472005148989	2		459	659	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528625	8528625	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	128	399	0	ENST00000356435.5:c.507C>A	p.Ser169Arg	p.S169R	ENST00000356435		169	agC/agA	4/35	0.554472005148989	1	FACETS	0.816	0.746	0.888	0.816	0.746	0.888	CLONAL	1	TRUE	0	0.554472005148989	1		399	409	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044473	47044473	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	146	225	1	ENST00000377604.3:c.1970G>A	p.Arg657His	p.R657H	ENST00000377604	NM_001204468.1	657	cGc/cAc	18/24	1	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.554472005148989	1		226	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0025550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	365	715	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.782274754716269	4	FACETS	0.982	0.936	1	0.982	0.936	1	CLONAL	2	TRUE	2	0.793591340428018	4		715	840	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725043	89725043	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0025550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	83	260	0	ENST00000371953.3:c.1027-1G>T		p.X343_splice	ENST00000371953	NM_000314.4	343			0.78761877737109	2	FACETS	0.886	0.822	0.947	0.886	0.822	0.947	CLONAL	2	TRUE	0	0.793591340428018	2		260	118	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645309	67645309	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	114	444	0	ENST00000264010.4:c.574C>G	p.Gln192Glu	p.Q192E	ENST00000264010	NM_006565.3	192	Caa/Gaa	3/12	NA	2	FACETS	1	0.944	1			1	INDETERMINATE	1	TRUE	NA	0.793591340428018	2		444	276	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15960859	15960859	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	129	308	0	ENST00000268712.3:c.6361C>G	p.Pro2121Ala	p.P2121A	ENST00000268712	NM_006311.3	2121	Cca/Gca	40/46	0.782274754716269	4	FACETS	0.926	0.852	1	0.926	0.852	1	CLONAL	2	TRUE	2	0.793591340428018	4		308	315	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71050178	71050178	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	86	497	0	ENST00000318789.4:c.1007G>C	p.Arg336Thr	p.R336T	ENST00000318789	NM_032682.5	336	aGa/aCa	13/21	0.383834135784264	4	FACETS	1	0.973	1	0.641	0.574	0.712	INDETERMINATE	1	TRUE	2	0.793591340428018	4		497	303	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	326	387	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.8558852451131	2		387	733	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0025555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	384	219	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	0.8558852451131	2		219	872	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233009	55233009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	340	518	0	ENST00000275493.2:c.1759G>A	p.Asp587Asn	p.D587N	ENST00000275493	NM_005228.3	587	Gac/Aac	15/28	1	2	FACETS	0.97	0.922	1	0.97	0.922	1	CLONAL	1	TRUE	1	0.8558852451131	2		518	819	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188177	11188177	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	334	488	1	ENST00000361445.4:c.5917A>T	p.Ile1973Phe	p.I1973F	ENST00000361445	NM_004958.3	1973	Atc/Ttc	43/58	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.8558852451131	2		489	763	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259511	16259511	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	75	462	0	ENST00000375759.3:c.6776C>G	p.Ser2259Cys	p.S2259C	ENST00000375759	NM_015001.2	2259	tCt/tGt	11/15	1	2	FACETS	0.21	0.183	0.238	0.21	0.183	0.238	SUBCLONAL	1	TRUE	1	0.8558852451131	2		462	836	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118656	11118656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	162	654	0	ENST00000358026.2:c.2080G>A	p.Asp694Asn	p.D694N	ENST00000358026	NM_001128849.1	694	Gac/Aac	14/36	1	2	FACETS	0.296	0.27	0.322	0.296	0.27	0.322	SUBCLONAL	1	TRUE	1	0.8558852451131	2		654	1280	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629119	14629119	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs761547055	NA	P-0025555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	80	427	1	ENST00000254322.2:c.43G>T	p.Ala15Ser	p.A15S	ENST00000254322	NM_006145.1	15	Gcg/Tcg	1/3	1	2	FACETS	0.255	0.224	0.288	0.255	0.224	0.288	SUBCLONAL	1	TRUE	1	0.8558852451131	2		428	733	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252861	36252862	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0025555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	313	420	0	ENST00000300305.3:c.500dup	p.Ser167ArgfsTer46	p.S167Rfs*46	ENST00000300305		167	agt/agGt	4/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.8558852451131	2		420	680	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878871	151878871	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0025555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	411	627	0	ENST00000262189.6:c.6074C>G	p.Ser2025Ter	p.S2025*	ENST00000262189	NM_170606.2	2025	tCa/tGa	36/59	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.8558852451131	2		627	948	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	410	627	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.298920804280494	3	FACETS	0.961	0.919	1	0.961	0.919	1	CLONAL	3	TRUE	0	0.360475035376581	3		627	931	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258893	16258893	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs74842071	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	283	740	0	ENST00000375759.3:c.6158A>C	p.Asn2053Thr	p.N2053T	ENST00000375759	NM_015001.2	2053	aAc/aCc	11/15	0.0954144313535467	5	FACETS	1	0.971	1	0.704	0.661	0.747	INDETERMINATE	2	TRUE	2	0.360475035376581	5		740	1146	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487554	38487554	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	51	654	1	ENST00000254066.5:c.89del	p.Pro30LeufsTer12	p.P30Lfs*12	ENST00000254066	NM_000964.3	28	ttC/tt	2/9	1	2	FACETS	0.286	0.242	0.335	0.286	0.242	0.335	SUBCLONAL	1	TRUE	1	0.360475035376581	2		655	989	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	77	546	2	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.637	0.559	0.72	0.637	0.559	0.72	SUBCLONAL	1	TRUE	1	0.360475035376581	2		548	671	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	145	488	2	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	0.0954144313535467	5	FACETS	0.825	0.754	0.9	0.55	0.502	0.6	INDETERMINATE	2	TRUE	2	0.360475035376581	5		490	751	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	111	462	7	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.794	0.713	0.879	0.794	0.713	0.879	SUBCLONAL	1	TRUE	1	0.360475035376581	2		469	776	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	163	660	19	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	0.360475035376581	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.360475035376581	1		679	506	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	85	171	1	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.360475035376581	2		172	379	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46725738	46725738	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147941516	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	50	541	0	ENST00000371975.4:c.374C>T	p.Pro125Leu	p.P125L	ENST00000371975	NM_003579.3	125	cCg/cTg	5/18	1	2	FACETS	0.35	0.296	0.41	0.35	0.296	0.41	SUBCLONAL	1	TRUE	1	0.360475035376581	2		541	793	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389135	31389135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1165118132	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	43	370	1	ENST00000328111.2:c.2048G>A	p.Arg683His	p.R683H	ENST00000328111	NM_006892.3	683	cGc/cAc	19/23	0.360475035376581	1	FACETS	0.279	0.232	0.33	0.279	0.232	0.33	SUBCLONAL	1	TRUE	0	0.360475035376581	1		371	702	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851104	63851104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148232588	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	60	562	0	ENST00000279873.7:c.1882G>A	p.Val628Met	p.V628M	ENST00000279873	NM_032199.2	628	Gtg/Atg	10/10	1	2	FACETS	0.379	0.325	0.437	0.379	0.325	0.437	SUBCLONAL	1	TRUE	1	0.360475035376581	2		562	879	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	152	843	5	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	0.841	0.768	0.917	0.841	0.768	0.917	CLONAL	1	TRUE	1	0.360475035376581	2		848	1003	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500488	149500488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1060499540	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	44	658	0	ENST00000261799.4:c.2549A>T	p.Asp850Val	p.D850V	ENST00000261799	NM_002609.3	850	gAc/gTc	18/23	1	2	FACETS	0.282	0.236	0.334	0.282	0.236	0.334	SUBCLONAL	1	TRUE	1	0.360475035376581	2		658	865	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874637	35874637	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	169	474	1	ENST00000303115.3:c.799del	p.Arg267GlyfsTer28	p.R267Gfs*28	ENST00000303115	NM_002185.3	265	Aaa/aa	6/8	0.117392203910802	3	FACETS	1	0.987	1	0.68	0.626	0.736	INDETERMINATE	1	TRUE	1	0.360475035376581	3		475	814	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852118	63852118	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	120	599	2	ENST00000279873.7:c.2901del	p.Lys967AsnfsTer15	p.K967Nfs*15	ENST00000279873	NM_032199.2	966	Aaa/aa	10/10	1	2	FACETS	0.743	0.67	0.82	0.743	0.67	0.82	SUBCLONAL	1	TRUE	1	0.360475035376581	2		601	896	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	40	778	1	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	0.326	0.27	0.389	0.326	0.27	0.389	SUBCLONAL	1	TRUE	1	0.360475035376581	2		779	680	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136949	64136949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749917386	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	148	521	0	ENST00000334205.4:c.1460G>A	p.Arg487Gln	p.R487Q	ENST00000334205	NM_003942.2	487	cGg/cAg	13/17	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.360475035376581	2		521	605	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319406	11319406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149221273	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	178	633	0	ENST00000361445.4:c.61G>A	p.Val21Ile	p.V21I	ENST00000361445	NM_004958.3	21	Gtc/Atc	2/58	NA	2	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.360475035376581	2		633	875	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310208	91310208	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs747341586	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	74	633	3	ENST00000355112.3:c.2268del	p.Asp757ThrfsTer4	p.D757Tfs*4	ENST00000355112	NM_000057.2	754	tcA/tc	10/22	0.360475035376581	2	FACETS	0.428	0.374	0.487	0.214	0.187	0.244	SUBCLONAL	1	TRUE	0	0.360475035376581	2		636	959	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375459	40375459	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	64	742	0	ENST00000293328.3:c.491del	p.Lys164SerfsTer17	p.K164Sfs*17	ENST00000293328	NM_012448.3	164	aAg/ag	5/19	1	2	FACETS	0.335	0.289	0.385	0.335	0.289	0.385	SUBCLONAL	1	TRUE	1	0.360475035376581	2		742	1060	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499363	89499363	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1317589623	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	140	501	1	ENST00000336596.2:c.2538del	p.Met847TrpfsTer10	p.M847Wfs*10	ENST00000336596	NM_005233.5	845	Ccc/cc	15/17	0.145225604868456	3	FACETS	1	0.984	1	0.672	0.613	0.734	INDETERMINATE	1	TRUE	1	0.360475035376581	3		502	682	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430566	80430566	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	112	457	0	ENST00000286548.4:c.442C>T	p.Arg148Ter	p.R148*	ENST00000286548	NM_002072.3	148	Cga/Tga	3/7	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.360475035376581	2		457	569	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427428	427428	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373590748	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	161	752	0	ENST00000399788.2:c.2741C>T	p.Pro914Leu	p.P914L	ENST00000399788	NM_001042603.1	914	cCg/cTg	19/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.360475035376581	2		752	734	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	170	686	3	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	0.145225604868456	3	FACETS	0.905	0.83	0.983	0.453	0.415	0.492	INDETERMINATE	1	TRUE	1	0.360475035376581	3		689	1230	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	213	742	1	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.360475035376581	2		743	1035	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800902	120800903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs748469666	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	72	652	4	ENST00000257552.2:c.345dup	p.Leu116AlafsTer15	p.L116Afs*15	ENST00000257552	NM_002442.3	115	-/G	6/15	0.360475035376581	1	FACETS	0.479	0.418	0.545	0.479	0.418	0.545	SUBCLONAL	1	TRUE	0	0.360475035376581	1		656	683	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379674	17379674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766735279	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	83	509	0	ENST00000359435.4:c.59C>T	p.Ser20Leu	p.S20L	ENST00000359435	NM_001033549.1	20	tCg/tTg	2/9	1	2	FACETS	0.702	0.62	0.79	0.702	0.62	0.79	SUBCLONAL	1	TRUE	1	0.360475035376581	2		509	656	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463308	25463308	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200018028	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	141	527	1	ENST00000264709.3:c.2185C>T	p.Arg729Trp	p.R729W	ENST00000264709	NM_175629.2	729	Cgg/Tgg	19/23	0.360475035376581	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.360475035376581	1		528	504	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967290	25967290	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	97	472	0	ENST00000435504.4:c.1916G>T	p.Arg639Met	p.R639M	ENST00000435504		639	aGg/aTg	13/13	0.360475035376581	1	FACETS	0.874	0.782	0.971	0.874	0.782	0.971	CLONAL	1	TRUE	0	0.360475035376581	1		472	505	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11193219	11193219	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	193	666	0	ENST00000361445.4:c.5282T>A	p.Leu1761Gln	p.L1761Q	ENST00000361445	NM_004958.3	1761	cTa/cAa	38/58	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.360475035376581	2		666	815	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546784	9546784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1252319558	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	50	382	0	ENST00000353224.5:c.1238C>T	p.Pro413Leu	p.P413L	ENST00000353224	NM_177990.2	413	cCg/cTg	5/10	0.360475035376581	1	FACETS	0.655	0.558	0.761	0.655	0.558	0.761	SUBCLONAL	1	TRUE	0	0.360475035376581	1		382	347	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300039	137300040	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755912201	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	133	742	7	ENST00000481739.1:c.331dup	p.Leu111ProfsTer70	p.L111Pfs*70	ENST00000481739	NM_002957.4	108	-/C	3/10	1	2	FACETS	0.898	0.815	0.984	0.898	0.815	0.984	CLONAL	1	TRUE	1	0.360475035376581	2		749	822	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302611	15302611	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	41	749	2	ENST00000263388.2:c.747del	p.Thr250HisfsTer122	p.T250Hfs*122	ENST00000263388	NM_000435.2	249	ggG/gg	5/33	1	2	FACETS	0.299	0.248	0.355	0.299	0.248	0.355	SUBCLONAL	1	TRUE	1	0.360475035376581	2		751	762	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830309	72830309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773210288	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	85	438	0	ENST00000268489.5:c.6272C>T	p.Pro2091Leu	p.P2091L	ENST00000268489	NM_006885.3	2091	cCg/cTg	9/10	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.360475035376581	2		438	426	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144518	11144518	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765989895	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	107	600	1	ENST00000358026.2:c.3850G>A	p.Asp1284Asn	p.D1284N	ENST00000358026	NM_001128849.1	1284	Gac/Aac	27/36	1	2	FACETS	0.87	0.782	0.964	0.87	0.782	0.964	CLONAL	1	TRUE	1	0.360475035376581	2		601	682	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123593	108123593	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1057517300	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	98	605	0	ENST00000278616.4:c.1856del	p.Asn619ThrfsTer6	p.N619Tfs*6	ENST00000278616	NM_000051.3	618	Aaa/aa	12/63	1	2	FACETS	0.711	0.634	0.793	0.711	0.634	0.793	SUBCLONAL	1	TRUE	1	0.360475035376581	2		605	765	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782079	9782079	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	141	723	0	ENST00000377346.4:c.2102T>G	p.Leu701Arg	p.L701R	ENST00000377346	NM_005026.3	701	cTg/cGg	17/24	NA	2	FACETS	1	0.934	1			1	INDETERMINATE	1	TRUE	NA	0.360475035376581	2		723	760	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552825	226552825	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs186612310	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	39	567	0	ENST00000366794.5:c.2536C>A	p.Gln846Lys	p.Q846K	ENST00000366794	NM_001618.3	846	Cag/Aag	19/23	1	2	FACETS	0.292	0.241	0.349	0.292	0.241	0.349	SUBCLONAL	1	TRUE	1	0.360475035376581	2		567	742	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344655	118344656	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	73	572	0	ENST00000534358.1:c.2787dup	p.Ala930SerfsTer11	p.A930Sfs*11	ENST00000534358	NM_005933.3	927	-/A	3/36	1	2	FACETS	0.664	0.581	0.753	0.664	0.581	0.753	SUBCLONAL	1	TRUE	1	0.360475035376581	2		572	610	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378621	25378621	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	75	699	0	ENST00000311936.3:c.377A>T	p.Asp126Val	p.D126V	ENST00000311936	NM_004985.3	126	gAc/gTc	4/5	0.145225604868456	3	FACETS	0.492	0.43	0.56	0.246	0.215	0.28	INDETERMINATE	1	TRUE	1	0.360475035376581	3		699	998	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380179	25380179	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	72	522	0	ENST00000311936.3:c.279T>G	p.Ile93Met	p.I93M	ENST00000311936	NM_004985.3	93	atT/atG	3/5	0.145225604868456	3	FACETS	0.653	0.57	0.743	0.327	0.285	0.372	INDETERMINATE	1	TRUE	1	0.360475035376581	3		522	722	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211575	46211575	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	60	443	0	ENST00000334344.6:c.541A>G	p.Thr181Ala	p.T181A	ENST00000334344	NM_152641.2	181	Act/Gct	5/21	0.145225604868456	3	FACETS	0.591	0.508	0.681	0.295	0.254	0.341	INDETERMINATE	1	TRUE	1	0.360475035376581	3		443	665	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433332	49433332	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	55	670	0	ENST00000301067.7:c.8115A>C	p.Glu2705Asp	p.E2705D	ENST00000301067	NM_003482.3	2705	gaA/gaC	32/54	0.145225604868456	3	FACETS	0.491	0.419	0.57	0.246	0.209	0.285	INDETERMINATE	1	TRUE	1	0.360475035376581	3		670	733	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444186	49444186	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	51	792	0	ENST00000301067.7:c.3185T>G	p.Val1062Gly	p.V1062G	ENST00000301067	NM_003482.3	1062	gTg/gGg	11/54	0.145225604868456	3	FACETS	0.363	0.308	0.425	0.182	0.154	0.213	INDETERMINATE	1	TRUE	1	0.360475035376581	3		792	919	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249317	133249317	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	63	840	0	ENST00000320574.5:c.1582A>T	p.Thr528Ser	p.T528S	ENST00000320574	NM_006231.2	528	Acg/Tcg	15/49	0.360475035376581	1	FACETS	0.329	0.283	0.378	0.329	0.283	0.378	SUBCLONAL	1	TRUE	0	0.360475035376581	1		840	872	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911410	32911410	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507296	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	127	580	0	ENST00000380152.3:c.2918C>T	p.Ser973Leu	p.S973L	ENST00000380152		973	tCg/tTg	11/27	0.284640108935557	2	FACETS	1	0.952	1	0.538	0.488	0.59	CLONAL	1	TRUE	0	0.360475035376581	2		580	655	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878058	48878058	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1226865525	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	67	242	0	ENST00000267163.4:c.13del	p.Thr5ProfsTer60	p.T5Pfs*60	ENST00000267163	NM_000321.2	4	Aaa/aa	1/27	0.284640108935557	2	FACETS	1	0.94	1	0.563	0.493	0.638	CLONAL	1	TRUE	0	0.360475035376581	2		242	330	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95595945	95595945	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	158	619	0	ENST00000393063.1:c.598C>A	p.Pro200Thr	p.P200T	ENST00000393063	NM_030621.3	200	Cct/Act	7/28	0.145225604868456	3	FACETS	1	0.977	1	0.591	0.541	0.642	INDETERMINATE	1	TRUE	1	0.360475035376581	3		619	876	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40998411	40998411	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	56	673	1	ENST00000267868.3:c.262A>G	p.Thr88Ala	p.T88A	ENST00000267868	NM_002875.4	88	Act/Gct	4/10	0.360475035376581	1	FACETS	0.328	0.28	0.381	0.328	0.28	0.381	SUBCLONAL	1	TRUE	0	0.360475035376581	1		674	776	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473705	67473705	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	39	620	0	ENST00000327367.4:c.785A>C	p.Asp262Ala	p.D262A	ENST00000327367	NM_005902.3	262	gAc/gCc	6/9	0.360475035376581	2	FACETS	0.285	0.235	0.341	0.143	0.117	0.171	SUBCLONAL	1	TRUE	0	0.360475035376581	2		620	759	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106717	2106717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200943828	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	88	692	0	ENST00000219476.3:c.721G>A	p.Val241Ile	p.V241I	ENST00000219476	NM_000548.3	241	Gtt/Att	8/42	1	2	FACETS	0.509	0.45	0.573	0.509	0.45	0.573	SUBCLONAL	1	TRUE	1	0.360475035376581	2		692	959	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827616	72827617	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	40	651	0	ENST00000268489.5:c.8964_8965del	p.Arg2988SerfsTer32	p.R2988Sfs*32	ENST00000268489	NM_006885.3	2988	agAGtc/agtc	9/10	1	2	FACETS	0.285	0.235	0.34	0.285	0.235	0.34	SUBCLONAL	1	TRUE	1	0.360475035376581	2		651	780	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622365	1622365	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1186454682	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	40	747	0	ENST00000344749.5:c.599A>G	p.Tyr200Cys	p.Y200C	ENST00000344749	NM_001136139.2	200	tAc/tGc	9/19	1	2	FACETS	0.313	0.259	0.374	0.313	0.259	0.374	SUBCLONAL	1	TRUE	1	0.360475035376581	2		747	708	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1627417	1627417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201841190	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	119	633	1	ENST00000344749.5:c.307G>A	p.Gly103Ser	p.G103S	ENST00000344749	NM_001136139.2	103	Ggt/Agt	6/19	1	2	FACETS	0.946	0.855	1	0.946	0.855	1	CLONAL	1	TRUE	1	0.360475035376581	2		634	698	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2225401	2225401	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	175	639	0	ENST00000398665.3:c.3611T>G	p.Ile1204Ser	p.I1204S	ENST00000398665	NM_032482.2	1204	aTt/aGt	26/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.360475035376581	2		639	807	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132572	11132572	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	49	678	0	ENST00000358026.2:c.2788C>A	p.Pro930Thr	p.P930T	ENST00000358026	NM_001128849.1	930	Ccc/Acc	19/36	1	2	FACETS	0.346	0.292	0.406	0.346	0.292	0.406	SUBCLONAL	1	TRUE	1	0.360475035376581	2		678	786	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635695	47635695	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs267607924	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	145	499	0	ENST00000233146.2:c.366+1G>T		p.X122_splice	ENST00000233146	NM_000251.2	122			0.360475035376581	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.360475035376581	1		499	599	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193545	99193545	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	143	617	0	ENST00000074304.5:c.2740C>A	p.Leu914Met	p.L914M	ENST00000074304	NM_001134224.1	914	Ctg/Atg	25/26	0.360475035376581	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.360475035376581	1		617	533	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794883	242794883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1371267560	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	160	745	0	ENST00000334409.5:c.326G>A	p.Ser109Asn	p.S109N	ENST00000334409	NM_005018.2	109	aGc/aAc	2/5	0.274948975717491	2	FACETS	1	0.976	1	0.583	0.536	0.633	CLONAL	1	TRUE	0	0.360475035376581	2		745	761	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524448	44524448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	41	440	0	ENST00000291552.4:c.109C>T	p.His37Tyr	p.H37Y	ENST00000291552	NM_006758.2	37	Cac/Tac	2/8	0.0954144313535467	5	FACETS	0.455	0.377	0.541	0.152	0.125	0.181	INDETERMINATE	1	TRUE	2	0.360475035376581	5		440	771	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125487	47125487	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	49	569	0	ENST00000409792.3:c.5783T>C	p.Leu1928Pro	p.L1928P	ENST00000409792	NM_014159.6	1928	cTa/cCa	12/21	0.145225604868456	3	FACETS	0.497	0.42	0.581	0.248	0.21	0.291	INDETERMINATE	1	TRUE	1	0.360475035376581	3		569	646	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453583	138453583	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1382110566	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	45	524	0	ENST00000289153.2:c.865A>G	p.Ile289Val	p.I289V	ENST00000289153	NM_006219.2	289	Atc/Gtc	5/22	0.360475035376581	1	FACETS	0.264	0.221	0.312	0.264	0.221	0.312	SUBCLONAL	1	TRUE	0	0.360475035376581	1		524	776	SUCCESS
ATR	545	MSKCC	GRCh37	3	142211980	142211980	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs34576460	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	149	522	2	ENST00000350721.4:c.6072del	p.Lys2024AsnfsTer5	p.K2024Nfs*5	ENST00000350721	NM_001184.3	2024	aaA/aa	35/47	0.145225604868456	3	FACETS	1	0.985	1	0.673	0.616	0.732	INDETERMINATE	1	TRUE	1	0.360475035376581	3		524	725	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803735	1803735	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	44	697	0	ENST00000260795.2:c.913T>C	p.Tyr305His	p.Y305H	ENST00000260795		305	Tac/Cac	6/17	0.360475035376581	1	FACETS	0.328	0.274	0.387	0.328	0.274	0.387	SUBCLONAL	1	TRUE	0	0.360475035376581	1		697	611	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180638	56180638	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs767994462	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	127	625	0	ENST00000399503.3:c.3967A>G	p.Ile1323Val	p.I1323V	ENST00000399503	NM_005921.1	1323	Att/Gtt	16/20	0.117392203910802	3	FACETS	1	0.959	1	0.551	0.5	0.606	INDETERMINATE	1	TRUE	1	0.360475035376581	3		625	754	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111995801	111995801	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	151	572	0	ENST00000368678.4:c.1297G>A	p.Glu433Lys	p.E433K	ENST00000368678		433	Gag/Aag	12/13	0.145225604868456	3	FACETS	1	0.986	1	0.706	0.647	0.768	INDETERMINATE	1	TRUE	1	0.360475035376581	3		572	700	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199610	138199610	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	88	477	0	ENST00000237289.4:c.1028A>C	p.Asp343Ala	p.D343A	ENST00000237289	NM_001270507.1	343	gAt/gCt	7/9	0.145225604868456	3	FACETS	0.731	0.647	0.821	0.366	0.323	0.411	INDETERMINATE	1	TRUE	1	0.360475035376581	3		477	788	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405899	157405899	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	135	534	1	ENST00000346085.5:c.2141A>G	p.Asn714Ser	p.N714S	ENST00000346085	NM_020732.3	714	aAc/aGc	6/20	0.145225604868456	3	FACETS	1	0.965	1	0.562	0.511	0.616	INDETERMINATE	1	TRUE	1	0.360475035376581	3		535	786	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5081835	5081835	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	52	423	0	ENST00000381652.3:c.2545T>G	p.Leu849Val	p.L849V	ENST00000381652	NM_004972.3	849	Ttg/Gtg	19/25	0.360475035376581	4	FACETS	0.484	0.411	0.565	0.161	0.137	0.189	SUBCLONAL	1	TRUE	1	0.360475035376581	4		423	811	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923031	39923031	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	33	357	0	ENST00000378444.4:c.3677A>C	p.Asp1226Ala	p.D1226A	ENST00000378444	NM_001123385.1	1226	gAt/gCt	8/15	0.305960371598321	2	FACETS	0.393	0.319	0.476			1	SUBCLONAL	1	TRUE	NA	0.360475035376581	2		357	466	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247106	53247106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	330	300	1	ENST00000375401.3:c.394C>T	p.Arg132Cys	p.R132C	ENST00000375401	NM_004187.3	132	Cgt/Tgt	4/26	0.360475035376581	2	FACETS	1	0.99	1			1	CLONAL	3	TRUE	NA	0.360475035376581	2		301	549	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938777	76938778	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0025557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	248	406	0	ENST00000373344.5:c.1970dup	p.Arg658ThrfsTer14	p.R658Tfs*14	ENST00000373344	NM_000489.3	657	cca/ccCa	9/35	0.305960371598321	2	FACETS	1	0.978	1			1	CLONAL	2	TRUE	NA	0.360475035376581	2		406	639	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0025558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	73	733	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.849	0.741	0.967	0.849	0.741	0.967	CLONAL	1	TRUE	1	0.17	2		733	1011	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119069	70119069	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	90	512	0	ENST00000245479.2:c.642del	p.Ser215ProfsTer4	p.S215Pfs*4	ENST00000245479	NM_000346.3	214	tCc/tc	2/3	1	2	FACETS	0.913	0.811	1	1	0.984	1	CLONAL	2	TRUE	1	0.17	2		512	580	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420314	88420314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767941638	NA	P-0025558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	31	531	2	ENST00000360948.2:c.2372G>A	p.Arg791Gln	p.R791Q	ENST00000360948	NM_001012338.2	791	cGg/cAg	19/19	1	2	FACETS	0.597	0.481	0.728	0.597	0.481	0.728	SUBCLONAL	1	TRUE	1	0.17	2		533	611	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713759	30713759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	37	561	0	ENST00000295754.5:c.1084C>T	p.His362Tyr	p.H362Y	ENST00000295754	NM_003242.5	362	Cac/Tac	4/7	1	2	FACETS	0.601	0.494	0.722	0.601	0.494	0.722	SUBCLONAL	1	TRUE	1	0.17	2		561	724	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983019	201983019	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149307595	NA	P-0025558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	83	770	2	ENST00000359651.3:c.868G>A	p.Glu290Lys	p.E290K	ENST00000359651		290	Gag/Aag	7/8	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.17	2		772	910	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446386	29446386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371521416	NA	P-0025558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	77	798	2	ENST00000389048.3:c.3181C>T	p.Arg1061Trp	p.R1061W	ENST00000389048	NM_004304.4	1061	Cgg/Tgg	20/29	1	2	FACETS	0.984	0.862	1	0.984	0.862	1	CLONAL	1	TRUE	1	0.17	2		800	921	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274859	41274859	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	48	666	0	ENST00000349496.5:c.1109T>G	p.Leu370Arg	p.L370R	ENST00000349496	NM_001904.3	370	cTg/cGg	8/15	1	2	FACETS	0.713	0.601	0.837	0.713	0.601	0.837	SUBCLONAL	1	TRUE	1	0.17	2		666	792	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0025564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	171	362	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.896003518919788	3	FACETS	0.872	0.818	0.925	0.872	0.818	0.925	CLONAL	2	TRUE	1	0.896003518919788	3		362	317	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913476	NA	P-0025564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	280	601	0	ENST00000358487.5:c.1647T>G	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaG	12/18	0.896003518919788	2	FACETS	1	0.989	1	0.573	0.545	0.602	CLONAL	1	TRUE	0	0.896003518919788	2		601	545	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692887	89692887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660535	NA	P-0025564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	242	364	0	ENST00000371953.3:c.371G>A	p.Cys124Tyr	p.C124Y	ENST00000371953	NM_000314.4	124	tGt/tAt	5/9	0.896003518919788	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.896003518919788	2		364	260	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178641	108178641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775036118	NA	P-0025564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	121	370	2	ENST00000278616.4:c.5692C>T	p.Arg1898Ter	p.R1898*	ENST00000278616	NM_000051.3	1898	Cga/Tga	38/63	0.896003518919788	1	FACETS	0.987	0.938	1	0.987	0.938	1	CLONAL	1	TRUE	0	0.896003518919788	1		372	151	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920786	100920786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752995251	NA	P-0025564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	114	489	0	ENST00000325455.5:c.2362C>T	p.Arg788Trp	p.R788W	ENST00000325455	NM_001202474.3	788	Cgg/Tgg	6/8	0.896003518919788	1	FACETS	0.982	0.931	1	0.982	0.931	1	CLONAL	1	TRUE	0	0.896003518919788	1		489	143	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435941	49435941	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	401	705	0	ENST00000301067.7:c.6040C>T	p.Gln2014Ter	p.Q2014*	ENST00000301067	NM_003482.3	2014	Cag/Tag	28/54	0.163732764953628	3	FACETS	0.759	0.726	0.792	0.759	0.726	0.792	INDETERMINATE	2	TRUE	1	0.896003518919788	3		705	854	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579882	7579882	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201382018	NA	P-0025564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	370	642	0	ENST00000269305.4:c.31G>A	p.Glu11Lys	p.E11K	ENST00000269305	NM_001126112.2	11	Gag/Aag	2/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.896003518919788	2		642	815	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211882	36211882	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519279	NA	P-0025564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	399	828	1	ENST00000222270.7:c.1633C>T	p.Arg545Ter	p.R545*	ENST00000222270	NM_014727.1	545	Cga/Tga	3/37	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.896003518919788	2		829	868	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022290	31022290	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	246	454	0	ENST00000375687.4:c.1775del	p.Gln592ArgfsTer111	p.Q592Rfs*111	ENST00000375687	NM_015338.5	592	cAg/cg	13/13	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.896003518919788	2		454	547	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182004	38182004	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775840670	NA	P-0025564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	299	513	1	ENST00000396334.3:c.628G>A	p.Asp210Asn	p.D210N	ENST00000396334	NM_002468.4	210	Gat/Aat	3/5	1	2	FACETS	0.898	0.851	0.946	0.898	0.851	0.946	CLONAL	1	TRUE	1	0.896003518919788	2		514	743	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225422	26225422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201329172	NA	P-0025564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	177	226	0	ENST00000360408.1:c.40G>A	p.Gly14Ser	p.G14S	ENST00000360408	NM_003532.2	14	Ggt/Agt	1/1	0.564128494046193	4	FACETS	1	0.99	1	0.483	0.448	0.519	CLONAL	1	TRUE	1	0.896003518919788	4		226	517	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786477	135786477	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	117	553	0	ENST00000298552.3:c.1053G>T	p.Met351Ile	p.M351I	ENST00000298552	NM_001162426.1	351	atG/atT	11/23	0.896003518919788	1	FACETS	0.57	0.524	0.616	0.57	0.524	0.616	SUBCLONAL	1	TRUE	0	0.896003518919788	1		553	253	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786476	135786477	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0025564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	117	553	0	ENST00000298552.3:c.1053_1054insTA	p.Val352Ter	p.V352*	ENST00000298552	NM_001162426.1	351	-/TA	11/23	0.896003518919788	1	FACETS	0.57	0.524	0.616	0.57	0.524	0.616	SUBCLONAL	1	TRUE	0	0.896003518919788	1		553	253	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242442	55242443	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTAAAATTCCCGTCGCTA	novel	NA	P-0025566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	183	555	0	ENST00000275493.2:c.2214_2231dup	p.Ile740_Lys745dup	p.I740_K745dup	ENST00000275493	NM_005228.3	740	gtt/gTTAAAATTCCCGTCGCTAtt	19/28	0.322245164047957	2	FACETS	1	0.986	1	0.64	0.592	0.69	CLONAL	1	TRUE	0	0.396942659392832	2		555	720	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649957	88649957	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1554888137	NA	P-0025566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	222	637	0	ENST00000372037.3:c.206A>G	p.Asp69Gly	p.D69G	ENST00000372037	NM_004329.2	69	gAt/gGt	4/13	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.396942659392832	2		637	789	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0025568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	69	611	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.775	0.673	0.886	0.775	0.673	0.886	SUBCLONAL	1	TRUE	1	0.195002002309066	2		611	913	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023696	27023696	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	60	310	0	ENST00000324856.7:c.802C>T	p.Gln268Ter	p.Q268*	ENST00000324856	NM_006015.4	268	Cag/Tag	1/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.195002002309066	2		310	500	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025510	1025510	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	63	405	0	ENST00000358495.3:c.865G>A	p.Ala289Thr	p.A289T	ENST00000358495	NM_134424.2	289	Gca/Aca	9/12	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.195002002309066	2		405	582	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961363	41961363	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	95	461	0	ENST00000219905.7:c.271C>T	p.Arg91Ter	p.R91*	ENST00000219905	NM_001164273.1	91	Cga/Tga	2/24	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.195002002309066	2		461	713	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731107	162731107	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	148	540	0	ENST00000367921.3:c.962C>A	p.Pro321His	p.P321H	ENST00000367921	NM_006182.2	321	cCc/cAc	9/18	0.195002002309066	3	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	1	0.195002002309066	3		540	801	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226032	133226032	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs770036124	NA	P-0025568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	57	485	0	ENST00000320574.5:c.3865C>A	p.Arg1289Ser	p.R1289S	ENST00000320574	NM_006231.2	1289	Cgc/Agc	31/49	1	2	FACETS	0.931	0.798	1	0.931	0.798	1	CLONAL	1	TRUE	1	0.195002002309066	2		485	628	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987179	36987193	+	inframe_deletion	In_Frame_Del	DEL	CATGCCGCTCATGTT	CATGCCGCTCATGTT	-	novel	NA	P-0025568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	39	408	0	ENST00000354822.5:c.496_510del	p.Asn166_Met170del	p.N166_M170del	ENST00000354822	NM_001079668.2	166	AACATGAGCGGCATG/-	3/3	0.195002002309066	3	FACETS	0.753	0.623	0.898	0.376	0.311	0.449	SUBCLONAL	1	TRUE	1	0.195002002309066	3		408	583	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43700188	43700188	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	88	456	0	ENST00000382044.4:c.5699del	p.Gly1900ValfsTer6	p.G1900Vfs*6	ENST00000382044	NM_001141980.1	1900	gGt/gt	27/28	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.195002002309066	2		456	692	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713554	30713555	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	110	418	0	ENST00000295754.5:c.881dup	p.Ser295LeufsTer8	p.S295Lfs*8	ENST00000295754	NM_003242.5	293	-/T	4/7	0.195002002309066	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	2	TRUE	0	0.195002002309066	2		418	564	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541970	187541970	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs189271562	NA	P-0025568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	84	495	1	ENST00000441802.2:c.5770G>A	p.Gly1924Arg	p.G1924R	ENST00000441802	NM_005245.3	1924	Ggg/Agg	10/27	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.195002002309066	2		496	675	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039321	47039321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	88	533	0	ENST00000377604.3:c.944C>T	p.Ser315Phe	p.S315F	ENST00000377604	NM_001204468.1	315	tCc/tTc	10/24	0.195002002309066	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.195002002309066	1		533	653	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0025569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	281	611	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.269022063917534	2	FACETS	1	0.953	1	1	0.994	1	CLONAL	3	TRUE	0	0.17	2		611	1084	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0025569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	42	285	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	0.3	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.17	1		285	370	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220382	1220382	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	58	380	0	ENST00000326873.7:c.475C>T	p.Gln159Ter	p.Q159*	ENST00000326873	NM_000455.4	159	Cag/Tag	4/10	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.17	2		380	587	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455230	29455230	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	64	531	0	ENST00000389048.3:c.2572C>A	p.Pro858Thr	p.P858T	ENST00000389048	NM_004304.4	858	Cca/Aca	15/29	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.17	2		531	698	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499327	89499327	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	57	416	0	ENST00000336596.2:c.2497G>T	p.Val833Leu	p.V833L	ENST00000336596	NM_005233.5	833	Gta/Tta	15/17	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.17	2		416	615	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124447	94124447	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	68	649	0	ENST00000369303.4:c.136G>T	p.Glu46Ter	p.E46*	ENST00000369303	NM_004440.3	46	Gag/Tag	2/17	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.17	2		649	737	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39935750	39935750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	64	563	0	ENST00000378444.4:c.122C>A	p.Ala41Asp	p.A41D	ENST00000378444	NM_001123385.1	41	gCc/gAc	3/15	1	2	FACETS	0.874	0.756	1	0.874	0.756	1	CLONAL	1	TRUE	1	0.17	2		563	861	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0025570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	49	340	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.811	0.686	0.95	0.811	0.686	0.95	CLONAL	1	TRUE	1	0.18191532465512	2		340	664	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0025570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	51	667	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.144462073736902	1	FACETS	0.901	0.765	1	0.901	0.765	1	CLONAL	1	TRUE	0	0.18191532465512	1		667	566	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971176	21971177	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0025570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	37	462	0	ENST00000304494.5:c.181dup	p.Glu61GlyfsTer59	p.E61Gfs*59	ENST00000304494	NM_000077.4	61	gag/gGag	2/3	0.18191532465512	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.18191532465512	1		462	314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0025571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	235	276	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.421616369811804	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.421616369811804	2		276	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0025573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	163	316	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.651923183507213	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.651923183507213	1		317	319	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378663	25378663	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	151	422	0	ENST00000311936.3:c.335T>C	p.Val112Ala	p.V112A	ENST00000311936	NM_004985.3	112	gTc/gCc	4/5	1	2	FACETS	0.963	0.887	1	0.963	0.887	1	CLONAL	1	TRUE	1	0.651923183507213	2		422	481	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431269	49431270	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0025573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	123	344	0	ENST00000301067.7:c.9869dup	p.Ala3292CysfsTer9	p.A3292Cfs*9	ENST00000301067	NM_003482.3	3290	ggc/ggGc	34/54	0.625681889620189	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.651923183507213	1		344	231	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900792	3900792	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	264	308	0	ENST00000262367.5:c.304C>T	p.Gln102Ter	p.Q102*	ENST00000262367	NM_004380.2	102	Cag/Tag	2/31	0.651923183507213	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.651923183507213	2		308	392	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242884	142242884	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs868817417	NA	P-0025573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	146	507	2	ENST00000350721.4:c.4103G>T	p.Arg1368Leu	p.R1368L	ENST00000350721	NM_001184.3	1368	cGa/cTa	22/47	0.651923183507213	3	FACETS	0.789	0.721	0.86	0.394	0.36	0.43	SUBCLONAL	1	TRUE	1	0.651923183507213	3		509	753	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56854511	56854511	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	159	497	0	ENST00000519728.1:c.93T>G	p.Ile31Met	p.I31M	ENST00000519728	NM_002350.3	31	atT/atG	2/13	1	2	FACETS	0.933	0.861	1	0.933	0.861	1	CLONAL	1	TRUE	1	0.651923183507213	2		497	523	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0025574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	79	83	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.919	0.809	1	0.919	0.809	1	CLONAL	1	TRUE	1	0.264895015245557	2		83	649	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117330	115117330	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	102	500	0	ENST00000257566.3:c.844A>G	p.Thr282Ala	p.T282A	ENST00000257566	NM_016569.3	282	Act/Gct	4/8	0.264895015245557	1	FACETS	0.954	0.854	1	0.954	0.854	1	CLONAL	1	TRUE	0	0.264895015245557	1		500	700	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346281	70346281	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	123	610	0	ENST00000374080.3:c.2632G>T	p.Asp878Tyr	p.D878Y	ENST00000374080		878	Gac/Tac	19/45	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.264895015245557	2		610	849	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0025575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	69	607	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	FALSE	1	0.345298099211024	2		607	385	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259442	55259442	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397517127	NA	P-0025575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	63	328	0	ENST00000275493.2:c.2500G>C	p.Val834Leu	p.V834L	ENST00000275493	NM_005228.3	834	Gtg/Ctg	21/28	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	1	0.345298099211024	2		328	330	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754654	42754654	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	51	436	0	ENST00000222329.4:c.86T>A	p.Leu29Gln	p.L29Q	ENST00000222329	NM_006494.2	29	cTg/cAg	2/4	0.131267182115801	4	FACETS	1	0.907	1	1	0.907	1	CLONAL	2	FALSE	2	0.205377981823928	4		436	277	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55086998	55087018	+	inframe_deletion	In_Frame_Del	DEL	GCGCTCCTGGCGCTGCTGGCT	GCGCTCCTGGCGCTGCTGGCT	-	novel	NA	P-0025576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	23	347	0	ENST00000275493.2:c.34_54del	p.Leu12_Leu18del	p.L12_L18del	ENST00000275493	NM_005228.3	10	GCGCTCCTGGCGCTGCTGGCT/-	1/28	1	2	FACETS	0.582	0.453	0.731	0.582	0.453	0.731	SUBCLONAL	1	FALSE	1	0.205377981823928	2		347	385	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650858	48650858	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782632688	NA	P-0025578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	38	385	1	ENST00000376670.3:c.727C>T	p.Arg243Trp	p.R243W	ENST00000376670	NM_002049.3	243	Cgg/Tgg	4/6	0.309015843390149	4	FACETS	0.813	0.673	0.969			1	CLONAL	1	TRUE	NA	0.309015843390149	4		386	396	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612811	228612811	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	53	662	0	ENST00000366696.1:c.216G>T	p.Met72Ile	p.M72I	ENST00000366696	NM_003493.2	72	atG/atT	1/1	0.281154939409754	5	FACETS	1	0.92	1	0.373	0.318	0.432	CLONAL	1	TRUE	2	0.309015843390149	5		662	449	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186589	108186589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	109	499	1	ENST00000278616.4:c.6046G>A	p.Asp2016Asn	p.D2016N	ENST00000278616	NM_000051.3	2016	Gat/Aat	41/63	0.230350838830273	4	FACETS	0.907	0.818	1	0.605	0.545	0.667	CLONAL	2	TRUE	1	0.309015843390149	4		500	509	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438064	49438064	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	95	638	0	ENST00000301067.7:c.5107C>T	p.Gln1703Ter	p.Q1703*	ENST00000301067	NM_003482.3	1703	Cag/Tag	21/54	0.309015843390149	5	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.309015843390149	5		638	625	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0025579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	287	265	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.648727535227177	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.648727535227177	1		267	513	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046313	128046313	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	67	428	0	ENST00000285398.2:c.950G>C	p.Arg317Thr	p.R317T	ENST00000285398	NM_000122.1	317	aGa/aCa	7/15	1	2	FACETS	0.699	0.605	0.8	0.699	0.605	0.8	SUBCLONAL	1	TRUE	1	0.214102010867149	2		428	896	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776216	135776217	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs118203709	NA	P-0025588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	126	388	0	ENST00000298552.3:c.2510dup	p.Asn837LysfsTer3	p.N837Kfs*3	ENST00000298552	NM_001162426.1	837	aac/aaAc	20/23	0.214102010867148	2	FACETS	0.884	0.802	0.97	0.884	0.802	0.97	CLONAL	2	TRUE	0	0.214102010867149	2		388	666	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123875190	123875190	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	24	408	0	ENST00000330479.4:c.146C>G	p.Thr49Ser	p.T49S	ENST00000330479	NM_020382.3	49	aCc/aGc	3/9	0.332123013746336	2	FACETS	0.308	0.24	0.385	0.154	0.12	0.193	SUBCLONAL	1	TRUE	0	0.364621469803643	2		408	428	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591950	48591958	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CAGGACAGA	CAGGACAGA	TTGAGAG	novel	NA	P-0025589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	70	372	0	ENST00000342988.3:c.1113_1121delinsTTGAGAG	p.Arg372Ter	p.R372*	ENST00000342988	NM_005359.5	371	caCAGGACAGAa/caTTGAGAGa	9/12	0.364621469803643	1	FACETS	0.842	0.738	0.952	0.842	0.738	0.952	CLONAL	1	TRUE	0	0.364621469803643	1		372	373	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175867	24175867	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	64	471	0	ENST00000263121.7:c.1096del	p.Arg366AlafsTer10	p.R366Afs*10	ENST00000263121	NM_003073.3	365	atC/at	8/9	NA	2	FACETS	0.856	0.744	0.977			1	INDETERMINATE	1	TRUE	NA	0.364621469803643	2		471	410	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589782	55589782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1560414398	NA	P-0025589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	70	388	0	ENST00000288135.5:c.1264G>A	p.Val422Met	p.V422M	ENST00000288135	NM_000222.2	422	Gtg/Atg	8/21	0.249380490998485	1	FACETS	0.739	0.647	0.837	0.739	0.647	0.837	SUBCLONAL	1	TRUE	0	0.364621469803643	1		388	425	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772946	135772965	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTGTTTTTTTCTAGCTCT	TTCTGTTTTTTTCTAGCTCT	-	novel	NA	P-0025589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	35	383	0	ENST00000298552.3:c.2658_2677del	p.Glu887ProfsTer10	p.E887Pfs*10	ENST00000298552	NM_001162426.1	886	aaAGAGCTAGAAAAAAACAGAAgc/aagc	21/23	0.215585133318706	1	FACETS	0.451	0.37	0.541	0.451	0.37	0.541	INDETERMINATE	1	TRUE	0	0.364621469803643	1		383	348	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261814	16261814	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	187	485	2	ENST00000375759.3:c.9079C>T	p.Arg3027Ter	p.R3027*	ENST00000375759	NM_015001.2	3027	Cga/Tga	11/15	0.823442168429641	4	FACETS	1	0.99	1	0.705	0.655	0.756	CLONAL	1	TRUE	2	0.827977703609945	4		487	586	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462996	120462996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754237679	NA	P-0025590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	130	461	0	ENST00000256646.2:c.5335G>A	p.Glu1779Lys	p.E1779K	ENST00000256646	NM_024408.3	1779	Gaa/Aaa	30/34	0.834443465417685	4	FACETS	0.963	0.877	1	0.321	0.292	0.351	CLONAL	1	TRUE	1	0.827977703609945	4		461	596	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310863	123310872	+	frameshift_variant	Frame_Shift_Del	DEL	TGGTTGGCAT	TGGTTGGCAT	-	novel	NA	P-0025590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42554	4593	437	1	ENST00000358487.5:c.556_565del	p.Met186CysfsTer4	p.M186Cfs*4	ENST00000358487	NM_000141.4	186	ATGCCAACCAtg/tg	5/18	0.827977703609945	34	FACETS	1	0.998	1			1	CLONAL	3	TRUE	NA	0.827977703609945	34		438	47147	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	396	393	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	0.834443465417685	4	FACETS	0.952	0.918	0.986			1	CLONAL	3	TRUE	NA	0.827977703609945	4		393	612	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176718999	176718999	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	123	309	0	ENST00000439151.2:c.6303G>C	p.Lys2101Asn	p.K2101N	ENST00000439151	NM_022455.4	2101	aaG/aaC	22/23	0.834443465417685	2	FACETS	1	0.971	1	0.556	0.513	0.6	CLONAL	1	TRUE	0	0.827977703609945	2		309	267	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117746771	117746771	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	187	466	0	ENST00000368508.3:c.49C>G	p.Leu17Val	p.L17V	ENST00000368508	NM_002944.2	17	Ctt/Gtt	1/43	0.834443465417685	4	FACETS	1	0.957	1	0.349	0.323	0.376	CLONAL	1	TRUE	1	0.827977703609945	4		466	788	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508323	106508323	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	85	260	0	ENST00000359195.3:c.317G>A	p.Trp106Ter	p.W106*	ENST00000359195	NM_002649.2	106	tGg/tAg	2/11	0.834443465417685	3	FACETS	1	0.927	1	0.522	0.467	0.579	CLONAL	1	TRUE	1	0.827977703609945	3		260	278	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882021	36882021	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs982302460	NA	P-0025590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	163	567	2	ENST00000358127.4:c.992C>T	p.Thr331Met	p.T331M	ENST00000358127	NM_001280556.1	331	aCg/aTg	8/10	1	2	FACETS	0.8	0.74	0.862	0.8	0.74	0.862	SUBCLONAL	1	TRUE	1	0.827977703609945	2		569	492	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0025591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	385	611	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.267747923533974	5	FACETS	1	0.989	1	0.756	0.719	0.794	INDETERMINATE	2	TRUE	2	0.55106725938681	5		611	1125	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0025591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	301	296	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.267747923533974	5	FACETS	1	0.991	1	0.81	0.766	0.855	INDETERMINATE	2	TRUE	2	0.55106725938681	5		296	821	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1555525367	NA	P-0025591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	299	437	0	ENST00000269305.4:c.783-1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.55106725938681	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.55106725938681	2		437	516	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325107	39325107	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	439	346	0	ENST00000373001.3:c.212G>C	p.Arg71Pro	p.R71P	ENST00000373001	NM_022157.3	71	cGc/cCc	1/7	0.541861818762507	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	4	TRUE	0	0.55106725938681	4		346	584	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265584	41266314	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAAATCTTTAGTTACTGAATTGGGGCTCTGCTTCGTTGCCATTAAGCCAGTCTGGCTGAGATCCCCCTGCTTTCCTCTCTCCCTGCTTACTTGTCAGGCTACCTTTTGCTCCATTTTCTGCTCACTCCTCCTAATGGCTTGGTGAAATAGCAAACAAGCCACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTA	TAAATCTTTAGTTACTGAATTGGGGCTCTGCTTCGTTGCCATTAAGCCAGTCTGGCTGAGATCCCCCTGCTTTCCTCTCTCCCTGCTTACTTGTCAGGCTACCTTTTGCTCCATTTTCTGCTCACTCCTCCTAATGGCTTGGTGAAATAGCAAACAAGCCACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTA	-	novel	NA	P-0025591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	486	482	0	ENST00000349496.5:c.13+15_241+73del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.541861818762507	4	FACETS	1	0.992	1	0.825	0.796	0.854	CLONAL	3	TRUE	0	0.55106725938681	4		482	829	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86682717	86682718	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0025591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	145	322	0	ENST00000274376.6:c.2925+1dup		p.-974fs	ENST00000274376	NM_002890.2	974	-/G	23/25	0.220011044680275	5	FACETS	0.767	0.702	0.834	0.511	0.468	0.556	INDETERMINATE	2	TRUE	2	0.55106725938681	5		322	627	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0025592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	34	417	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.283757917046891	3	FACETS	1	0.904	1	0.584	0.479	0.703	CLONAL	1	TRUE	1	0.2	3		417	320	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043378	180043378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774554521	NA	P-0025592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	63	610	0	ENST00000261937.6:c.3208C>T	p.Arg1070Cys	p.R1070C	ENST00000261937	NM_182925.4	1070	Cgc/Tgc	23/30	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.2	2		610	596	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56376664	56376664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	63	629	1	ENST00000348428.3:c.704C>T	p.Ser235Phe	p.S235F	ENST00000348428	NM_006785.3	235	tCc/tTc	5/17	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.2	2		630	510	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506381	120506381	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	81	613	0	ENST00000256646.2:c.1731T>A	p.Asp577Glu	p.D577E	ENST00000256646	NM_024408.3	577	gaT/gaA	11/34	0.283757917046891	3	FACETS	1	0.969	1	0.661	0.582	0.745	CLONAL	1	TRUE	1	0.2	3		613	674	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639148	3639149	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0025592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	67	733	0	ENST00000294008.3:c.4490_4491delinsTT	p.Ser1497Phe	p.S1497F	ENST00000294008	NM_032444.2	1497	tCC/tTT	12/15	1	2	FACETS	0.868	0.753	0.993	0.868	0.753	0.993	CLONAL	1	TRUE	1	0.2	2		733	772	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004816	16004816	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	65	614	2	ENST00000268712.3:c.2438C>T	p.Pro813Leu	p.P813L	ENST00000268712	NM_006311.3	813	cCc/cTc	20/46	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.2	2		616	645	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17949092	17949092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	80	712	0	ENST00000458235.1:c.1549C>T	p.Pro517Ser	p.P517S	ENST00000458235	NM_000215.3	517	Cct/Tct	11/24	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.2	2		712	637	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662720	117662740	+	inframe_deletion	In_Frame_Del	DEL	TGAGATTCTCTCCAAGATATA	TGAGATTCTCTCCAAGATATA	-	novel	NA	P-0025592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	33	495	0	ENST00000368508.3:c.4725_4745del	p.Ile1576_His1582del	p.I1576_H1582del	ENST00000368508	NM_002944.2	1575	atTATATCTTGGAGAGAATCTCAc/atc	29/43	0.285569869025514	1	FACETS	0.758	0.617	0.916	0.758	0.617	0.916	CLONAL	1	TRUE	0	0.2	1		495	392	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92462538	92462538	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	62	574	0	ENST00000265734.4:c.100A>C	p.Lys34Gln	p.K34Q	ENST00000265734	NM_001259.6	34	Aag/Cag	2/8	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.2	2		574	586	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453112	140453112	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	31	516	2	ENST00000288602.6:c.1823A>G	p.His608Arg	p.H608R	ENST00000288602	NM_004333.4	608	cAt/cGt	15/18	0.283757917046891	3	FACETS	1	0.884	1	0.565	0.458	0.685	CLONAL	1	TRUE	1	0.2	3		518	302	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0025593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	458	206	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.336665925488456	3	FACETS	1	0.977	1	1	0.996	1	CLONAL	3	TRUE	1	0.336665925488456	3		207	1030	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332836	65332836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	108	399	0	ENST00000342505.4:c.703C>T	p.Leu235Phe	p.L235F	ENST00000342505	NM_002227.2	235	Ctc/Ttc	7/25	0.336665925488456	3	FACETS	0.998	0.896	1	0.499	0.448	0.553	CLONAL	1	TRUE	1	0.336665925488456	3		399	751	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846036	68846036	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0025593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	286	522	0	ENST00000261769.5:c.1009-2A>C		p.X337_splice	ENST00000261769	NM_004360.3	337			NA	2	FACETS	0.961	0.906	1			1	INDETERMINATE	2	TRUE	NA	0.336665925488456	2		522	884	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550567	29550571	+	frameshift_variant	Frame_Shift_Del	DEL	ATTTC	ATTTC	-	novel	NA	P-0025593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	185	330	0	ENST00000356175.3:c.1827_1831del	p.Lys609AsnfsTer3	p.K609Nfs*3	ENST00000356175	NM_000267.3	609	aaATTTCtt/aatt	16/57	0.275418807895408	2	FACETS	0.992	0.922	1	0.992	0.922	1	CLONAL	2	TRUE	0	0.336665925488456	2		330	554	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855781	45855781	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	232	531	0	ENST00000391945.4:c.2029A>G	p.Met677Val	p.M677V	ENST00000391945	NM_000400.3	677	Atg/Gtg	21/23	0.256459029036499	4	FACETS	0.896	0.836	0.958	0.896	0.836	0.958	CLONAL	2	TRUE	2	0.336665925488456	4		531	1028	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751487	57751487	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	126	507	0	ENST00000274289.3:c.1504C>T	p.Gln502Ter	p.Q502*	ENST00000274289	NM_006622.3	502	Cag/Tag	11/14	0.336665925488456	3	FACETS	1	0.909	1	0.502	0.454	0.553	CLONAL	1	TRUE	1	0.336665925488456	3		507	871	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0025594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	220	491	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.828331181538068	2		491	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0025594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	453	302	0	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.828331181538068	2		302	1032	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0025594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	476	654	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.828331181538068	2		654	1121	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685286	89685286	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	164	365	0	ENST00000371953.3:c.181C>A	p.His61Asn	p.H61N	ENST00000371953	NM_000314.4	61	Cat/Aat	3/9	0.828331181538068	1	FACETS	0.837	0.787	0.887	0.837	0.787	0.887	CLONAL	1	TRUE	0	0.828331181538068	1		365	277	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947560	48947560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690846	NA	P-0025594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	327	677	0	ENST00000267163.4:c.1147C>T	p.Gln383Ter	p.Q383*	ENST00000267163	NM_000321.2	383	Caa/Taa	12/27	0.828331181538068	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.828331181538068	1		677	460	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056221	27056221	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324226146	NA	P-0025594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	722	594	0	ENST00000324856.7:c.1217G>A	p.Gly406Glu	p.G406E	ENST00000324856	NM_006015.4	406	gGa/gAa	2/20	0.802652511920489	3	FACETS	0.982	0.954	1	0.982	0.954	1	CLONAL	2	TRUE	1	0.828331181538068	3		594	1255	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856230	111856230	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	142	128	1	ENST00000341259.2:c.281G>A	p.Arg94His	p.R94H	ENST00000341259	NM_005475.2	94	cGt/cAt	2/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.828331181538068	2		129	289	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387663	17387663	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	427	784	0	ENST00000359435.4:c.731A>G	p.Asp244Gly	p.D244G	ENST00000359435	NM_001033549.1	244	gAc/gGc	8/9	0.809233847879542	3	FACETS	0.986	0.939	1	0.493	0.469	0.518	CLONAL	1	TRUE	1	0.828331181538068	3		784	1478	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577070	7577070	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	298	641	0	ENST00000269305.4:c.868del	p.Arg290AlafsTer55	p.R290Afs*55	ENST00000269305	NM_001126112.2	290	Cgc/gc	8/11	0.241876772620419	2	FACETS	0.995	0.936	1	0.995	0.936	1	CLONAL	2	TRUE	0	0.241876772620419	2		641	1238	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244878	46244878	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	125	647	0	ENST00000334344.6:c.2972C>G	p.Ser991Cys	p.S991C	ENST00000334344	NM_152641.2	991	tCc/tGc	15/21	0.241876772620419	3	FACETS	0.94	0.849	1	0.47	0.424	0.519	CLONAL	1	TRUE	1	0.241876772620419	3		647	1232	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579533	7579533	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	276	609	0	ENST00000269305.4:c.154C>T	p.Gln52Ter	p.Q52*	ENST00000269305	NM_001126112.2	52	Caa/Taa	4/11	0.357087199162175	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.377470888231925	2		609	726	SUCCESS
APC	324	MSKCC	GRCh37	5	112175476	112175476	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	142	352	0	ENST00000257430.4:c.4188del	p.Phe1396LeufsTer19	p.F1396Lfs*19	ENST00000257430	NM_000038.5	1395	agT/ag	16/16	0.377470888231925	2	FACETS	0.995	0.918	1	0.995	0.918	1	CLONAL	2	TRUE	0	0.377470888231925	2		352	378	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288985	212288985	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	39	605	0	ENST00000342788.4:c.2761T>G	p.Tyr921Asp	p.Y921D	ENST00000342788	NM_005235.2	921	Tat/Gat	23/28	0.225447627946451	4	FACETS	0.558	0.462	0.665	0.279	0.231	0.333	INDETERMINATE	1	TRUE	2	0.377470888231925	4		605	510	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858567	27858567	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	45	224	0	ENST00000359303.2:c.4G>C	p.Ala2Pro	p.A2P	ENST00000359303	NM_003535.2	2	Gcc/Ccc	1/1	0.285562564743123	4	FACETS	0.864	0.728	1	0.432	0.364	0.507	CLONAL	1	TRUE	2	0.377470888231925	4		224	380	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951928	2951928	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	107	443	0	ENST00000396946.4:c.3022A>G	p.Ile1008Val	p.I1008V	ENST00000396946	NM_032415.4	1008	Atc/Gtc	23/25	0.377470888231925	5	FACETS	1	0.954	1	0.371	0.332	0.412	CLONAL	1	TRUE	2	0.377470888231925	5		443	798	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069643	69069643	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0025596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	228	611	0	ENST00000288368.4:c.4318A>T	p.Lys1440Ter	p.K1440*	ENST00000288368	NM_024870.2	1440	Aag/Tag	35/40	0.370424939667777	4	FACETS	1	0.945	1	1	0.945	1	CLONAL	3	TRUE	1	0.377470888231925	4		611	552	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575550	64575550	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs794728648	NA	P-0025597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	146	453	0	ENST00000312049.6:c.467G>T	p.Gly156Val	p.G156V	ENST00000312049	NM_130799.2	156	gGt/gTt	3/10	0.196407369243523	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.200597220883913	2		453	672	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212729	27212729	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	106	702	0	ENST00000380036.4:c.2711A>G	p.Tyr904Cys	p.Y904C	ENST00000380036	NM_000459.3	904	tAc/tGc	17/23	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.200597220883913	2		702	977	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs377622327	NA	P-0025597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	142	460	0	ENST00000324856.7:c.3972C>A	p.Tyr1324Ter	p.Y1324*	ENST00000324856	NM_006015.4	1324	taC/taA	16/20	0.196407369243523	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.200597220883913	2		460	621	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169511	27169511	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	132	643	0	ENST00000380036.4:c.512C>G	p.Pro171Arg	p.P171R	ENST00000380036	NM_000459.3	171	cCt/cGt	4/23	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.200597220883913	2		643	1066	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0025598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	433	611	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.41566483337034	3	FACETS	0.948	0.904	0.993	0.948	0.904	0.993	CLONAL	2	TRUE	1	0.41566483337034	3		611	1327	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220691	1220691	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs878853247	NA	P-0025598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	143	457	0	ENST00000326873.7:c.709G>C	p.Asp237His	p.D237H	ENST00000326873	NM_000455.4	237	Gac/Cac	5/10	0.41566483337034	1	FACETS	0.809	0.739	0.881	0.809	0.739	0.881	CLONAL	1	TRUE	0	0.41566483337034	1		457	674	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600005	10600005	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	248	565	0	ENST00000171111.5:c.1571del	p.Gly524AlafsTer8	p.G524Afs*8	ENST00000171111	NM_203500.1	524	gGc/gc	5/6	0.41566483337034	1	FACETS	0.997	0.933	1	0.997	0.933	1	CLONAL	1	TRUE	0	0.41566483337034	1		565	948	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870833	12870833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	158	135	0	ENST00000228872.4:c.61del	p.Ala21ArgfsTer21	p.A21Rfs*21	ENST00000228872	NM_004064.3	20	caG/ca	1/3	0.41566483337034	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.41566483337034	3		135	428	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774057	56774057	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	196	461	0	ENST00000337432.4:c.408G>T	p.Met136Ile	p.M136I	ENST00000337432	NM_058216.2	136	atG/atT	3/9	0.176270613626842	3	FACETS	1	0.982	1	0.593	0.549	0.638	INDETERMINATE	1	TRUE	1	0.41566483337034	3		461	961	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132621	11132621	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	244	478	0	ENST00000358026.2:c.2837C>A	p.Pro946His	p.P946H	ENST00000358026	NM_001128849.1	946	cCc/cAc	19/36	0.41566483337034	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.41566483337034	1		478	847	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388653	31388653	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	230	432	0	ENST00000328111.2:c.1918G>T	p.Gly640Cys	p.G640C	ENST00000328111	NM_006892.3	640	Ggc/Tgc	18/23	0.176270613626842	3	FACETS	1	0.991	1	0.7	0.653	0.748	INDETERMINATE	1	TRUE	1	0.41566483337034	3		432	955	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121337	29121337	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs770343235	NA	P-0025598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	262	599	0	ENST00000328354.6:c.338A>G	p.Tyr113Cys	p.Y113C	ENST00000328354	NM_007194.3	113	tAc/tGc	3/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.41566483337034	2		599	1140	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499486	89499486	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs373736475	NA	P-0025598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	153	331	0	ENST00000336596.2:c.2656G>T	p.Gly886Cys	p.G886C	ENST00000336596	NM_005233.5	886	Ggc/Tgc	15/17	1	2	FACETS	0.959	0.878	1	0.959	0.878	1	CLONAL	1	TRUE	1	0.41566483337034	2		331	768	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294553	1294554	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0025598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	74	258	0	ENST00000310581.5:c.447_448delinsTT	p.Val150Phe	p.V150F	ENST00000310581	NM_198253.2	149	ctGGtt/ctTTtt	2/16	1	2	FACETS	0.709	0.622	0.803	0.709	0.622	0.803	SUBCLONAL	1	TRUE	1	0.41566483337034	2		258	502	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31405810	31405810	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	110	380	0	ENST00000344624.3:c.3968G>T	p.Gly1323Val	p.G1323V	ENST00000344624		1323	gGa/gTa	32/33	1	2	FACETS	0.731	0.657	0.809	0.731	0.657	0.809	SUBCLONAL	1	TRUE	1	0.41566483337034	2		380	724	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196135	138196135	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	139	364	0	ENST00000237289.4:c.449A>C	p.Gln150Pro	p.Q150P	ENST00000237289	NM_001270507.1	150	cAg/cCg	3/9	1	2	FACETS	0.961	0.877	1	0.961	0.877	1	CLONAL	1	TRUE	1	0.41566483337034	2		364	696	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341818	8341818	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	228	630	0	ENST00000356435.5:c.4822G>T	p.Ala1608Ser	p.A1608S	ENST00000356435		1608	Gca/Tca	29/35	0.41566483337034	1	FACETS	0.957	0.893	1	0.957	0.893	1	CLONAL	1	TRUE	0	0.41566483337034	1		630	908	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028757	47028757	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	222	501	1	ENST00000377604.3:c.61C>A	p.Arg21Ser	p.R21S	ENST00000377604	NM_001204468.1	21	Cgc/Agc	3/24	1	2	FACETS	0.963	0.896	1	0.963	0.896	1	CLONAL	1	TRUE	1	0.41566483337034	2		502	1109	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651700	48651700	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	177	392	0	ENST00000376670.3:c.866A>T	p.His289Leu	p.H289L	ENST00000376670	NM_002049.3	289	cAc/cTc	5/6	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.41566483337034	2		392	826	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	712	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.410071302353581	5	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	2	0.410071302353581	5		371	1617	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578196	7578196	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	431	665	0	ENST00000269305.4:c.653T>A	p.Val218Glu	p.V218E	ENST00000269305	NM_001126112.2	218	gTg/gAg	6/11	0.350371498183007	3	FACETS	1	0.994	1	0.823	0.787	0.859	CLONAL	2	TRUE	0	0.410071302353581	3		665	1026	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356412	66356412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763166233	NA	P-0025599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	83	472	0	ENST00000273854.3:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000273854	NM_004439.5	362	cGg/cAg	5/18	1	2	FACETS	0.711	0.629	0.8	0.711	0.629	0.8	SUBCLONAL	1	TRUE	1	0.410071302353581	2		472	569	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849798	151849798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774784010	NA	P-0025599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	33	274	0	ENST00000262189.6:c.12518C>T	p.Thr4173Ile	p.T4173I	ENST00000262189	NM_170606.2	4173	aCa/aTa	49/59	0.358341818020122	4	FACETS	0.374	0.303	0.454	0.125	0.101	0.152	SUBCLONAL	1	TRUE	1	0.410071302353581	4		274	607	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0025601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	522	437	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.560840858863234	7	FACETS	0.906	0.87	0.942	0.725	0.696	0.754	CLONAL	4	FALSE	2	0.560840858863234	7		437	1234	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	478	563	0	ENST00000269305.4:c.517G>C	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ctg	5/11	0.560139551786322	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	FALSE	0	0.560840858863234	2		563	741	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910387	29910392	+	inframe_deletion	In_Frame_Del	DEL	GACCCA	GACCCA	-	novel	NA	P-0025601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1359	164	678	0	ENST00000376809.5:c.61_66del	p.Gln21_Thr22del	p.Q21_T22del	ENST00000376809	NM_002116.7	19	ctGACCCAg/ctg	1/8	0.523261647714535	4	FACETS	0.599	0.548	0.653	0.2	0.182	0.218	SUBCLONAL	1	FALSE	1	0.560840858863234	4		678	1523	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362221	40362221	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	87	498	0	ENST00000293328.3:c.1874G>A	p.Gly625Asp	p.G625D	ENST00000293328	NM_012448.3	625	gGc/gAc	15/19	1	2	FACETS	0.931	0.824	1	0.931	0.824	1	CLONAL	1	TRUE	1	0.251531769164427	2		498	743	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593609	55593659	+	inframe_deletion	In_Frame_Del	DEL	GTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAA	GTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAA	-	novel	NA	P-0025602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	68	538	0	ENST00000288135.5:c.1675_1725del	p.Val559_Gln575del	p.V559_Q575del	ENST00000288135	NM_000222.2	559	GTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAA/-	11/21	1	2	FACETS	0.882	0.767	1	0.882	0.767	1	CLONAL	1	TRUE	1	0.251531769164427	2		538	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0025603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	746	800	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.443249791544002	3	FACETS	0.974	0.947	1			1	CLONAL	3	TRUE	NA	0.524674380224323	3		800	1228	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417943	32417943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554416372	NA	P-0025603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1376	188	618	0	ENST00000332351.3:c.1109G>A	p.Arg370His	p.R370H	ENST00000332351	NM_024426.4	370	cGt/cAt	7/10	0.524674380224323	5	FACETS	0.819	0.754	0.887			1	CLONAL	1	TRUE	NA	0.524674380224323	5		618	1564	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	39	387	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.816	0.683	0.962	0.816	0.683	0.962	CLONAL	1	TRUE	1	0.448742849815545	2		387	213	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405951	49405951	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	137	519	1	ENST00000418115.1:c.187C>A	p.Gln63Lys	p.Q63K	ENST00000418115	NM_001664.2	63	Cag/Aag	3/5	1	2	FACETS	0.836	0.762	0.915	0.836	0.762	0.915	CLONAL	1	TRUE	1	0.448742849815545	2		520	730	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169512	11169512	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	142	472	0	ENST00000358026.2:c.4678G>T	p.Asp1560Tyr	p.D1560Y	ENST00000358026	NM_001128849.1	1560	Gac/Tac	33/36	1	2	FACETS	0.971	0.887	1	0.971	0.887	1	CLONAL	1	TRUE	1	0.448742849815545	2		472	652	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797314	135797314	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	47	316	0	ENST00000298552.3:c.555del	p.Tyr185Ter	p.Y185*	ENST00000298552	NM_001162426.1	185	taC/ta	7/23	0.443414093578673	1	FACETS	0.445	0.377	0.52	0.445	0.377	0.52	SUBCLONAL	1	TRUE	0	0.448742849815545	1		316	365	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797313	135797313	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	24	315	0	ENST00000298552.3:c.556G>C	p.Ala186Pro	p.A186P	ENST00000298552	NM_001162426.1	186	Gca/Cca	7/23	0.443414093578673	1	FACETS	0.226	0.177	0.283	0.226	0.177	0.283	SUBCLONAL	1	TRUE	0	0.448742849815545	1		315	367	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0025608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	227	491	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.999	0.935	1	0.999	0.935	1	CLONAL	1	TRUE	1	0.665667639974209	2		491	683	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0025608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	884	417	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.543167265840203	4	FACETS	0.9	0.876	0.925			1	CLONAL	3	TRUE	NA	0.665667639974209	4		417	1638	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367257	50367257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1245618829	NA	P-0025608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	245	525	1	ENST00000331340.3:c.64G>A	p.Asp22Asn	p.D22N	ENST00000331340	NM_006060.4	22	Gat/Aat	3/8	1	2	FACETS	0.907	0.85	0.965	0.907	0.85	0.965	CLONAL	1	TRUE	1	0.665667639974209	2		526	812	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643419	38643419	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	431	693	0	ENST00000299084.4:c.889G>A	p.Gly297Arg	p.G297R	ENST00000299084	NM_152594.2	297	Ggg/Agg	7/7	0.665667639974209	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.665667639974209	1		693	862	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127389	17127390	+	missense_variant	Missense_Mutation	DNP	GG	GG	AC	novel	NA	P-0025608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	381	797	3	ENST00000285071.4:c.464_465delinsGT	p.Thr155Ser	p.T155S	ENST00000285071	NM_144997.5	155	aCC/aGT	6/14	0.665667639974209	1	FACETS	0.955	0.913	0.997	0.955	0.913	0.997	CLONAL	1	TRUE	0	0.665667639974209	1		800	800	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273042	18273042	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs546337739	NA	P-0025608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	233	787	2	ENST00000222254.8:c.932C>T	p.Pro311Leu	p.P311L	ENST00000222254	NM_005027.3	311	cCg/cTg	8/16	0.522979572440017	1	FACETS	0.454	0.423	0.486	0.454	0.423	0.486	SUBCLONAL	1	TRUE	0	0.665667639974209	1		789	1029	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517884	8517884	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	491	433	0	ENST00000356435.5:c.1507C>G	p.Leu503Val	p.L503V	ENST00000356435		503	Ctt/Gtt	10/35	NA	2	FACETS	0.974	0.943	1			1	INDETERMINATE	2	TRUE	NA	0.665667639974209	2		433	757	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0025612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	174	814	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.628390964526331	3	FACETS	0.937	0.89	0.982	0.937	0.89	0.982	CLONAL	3	TRUE	0	0.668419395462569	3		814	247	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16052797	16052801	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAT	AAAAT	-	novel	NA	P-0025612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	139	727	0	ENST00000268712.3:c.873_877del	p.Leu291PhefsTer2	p.L291Ffs*2	ENST00000268712	NM_006311.3	291	ttATTTTtt/tttt	9/46	0.628390964526331	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	0	0.668419395462569	3		727	178	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0025612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	12	781	0	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	0.668419395462569	3	FACETS	0.224	0.157	0.306	0.112	0.078	0.153	SUBCLONAL	1	TRUE	1	0.668419395462569	3		781	214	SUCCESS
AR	367	MSKCC	GRCh37	X	66765163	66765163	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	12	314	0	ENST00000374690.3:c.175C>T	p.Gln59Ter	p.Q59*	ENST00000374690	NM_000044.3	59	Cag/Tag	1/8	0.668419395462569	3	FACETS	0.577	0.411	0.774	0.289	0.205	0.387	SUBCLONAL	1	TRUE	1	0.668419395462569	3		314	83	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871059	12871059	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0025612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	103	411	0	ENST00000228872.4:c.286A>T	p.Lys96Ter	p.K96*	ENST00000228872	NM_004064.3	96	Aaa/Taa	1/3	0.652515950416043	5	FACETS	1	0.981	1	0.474	0.427	0.524	CLONAL	1	TRUE	2	0.668419395462569	5		411	434	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38545402	38545402	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	32	778	0	ENST00000299084.4:c.16G>C	p.Ala6Pro	p.A6P	ENST00000299084	NM_152594.2	6	Gcg/Ccg	1/7	0.612836082194378	3	FACETS	0.315	0.256	0.383	0.158	0.128	0.192	SUBCLONAL	1	TRUE	1	0.668419395462569	3		778	405	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155599	56155599	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	205	587	0	ENST00000399503.3:c.691G>T	p.Glu231Ter	p.E231*	ENST00000399503	NM_005921.1	231	Gag/Tag	3/20	0.652515950416043	5	FACETS	0.963	0.927	0.998	1	0.995	1	CLONAL	5	TRUE	2	0.668419395462569	5		587	255	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	57	387	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.290486621058126	NA		387	99	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0025613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	150	909	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	0.182166892574074	3	FACETS	1	0.964	1			1	CLONAL	4	FALSE	NA	0.290486621058126	3		909	282	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099846	27099847	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	74	621	0	ENST00000324856.7:c.3726dup	p.Asp1243Ter	p.D1243*	ENST00000324856	NM_006015.4	1242	agt/agTt	15/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.290486621058126	2		621	371	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981874	201981875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0025613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	206	1019	0	ENST00000359651.3:c.586dup	p.Val196GlyfsTer21	p.V196Gfs*21	ENST00000359651		195	-/G	4/8	1	2	FACETS	0.967	0.906	1	1	0.995	1	CLONAL	3	FALSE	1	0.290486621058126	2		1019	489	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219955	36219955	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	161	744	0	ENST00000222270.7:c.4757A>G	p.Lys1586Arg	p.K1586R	ENST00000222270	NM_014727.1	1586	aAa/aGa	21/37	1	2	FACETS	0.908	0.842	0.974	1	0.994	1	CLONAL	3	FALSE	1	0.290486621058126	2		744	407	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163446	47163446	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	53	532	0	ENST00000409792.3:c.2680A>G	p.Ser894Gly	p.S894G	ENST00000409792	NM_014159.6	894	Agt/Ggt	3/21	0.127342891480063	3	FACETS	1	0.959	1	0.681	0.584	0.785	INDETERMINATE	1	FALSE	1	0.290486621058126	3		532	307	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651910	36651911	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0025613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	324	700	0	ENST00000244741.5:c.35dup	p.Cys13MetfsTer23	p.C13Mfs*23	ENST00000244741	NM_000389.4	11	aac/aaCc	2/3	0.212242382171046	3	FACETS	1	0.969	1	1	0.997	1	CLONAL	6	FALSE	1	0.290486621058126	3		700	425	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0025630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	149	620	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.839	0.775	0.904	0.839	0.775	0.904	CLONAL	1	TRUE	1	0.908524770468874	2		620	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0025630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	570	814	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.859699138006565	2	FACETS	0.92	0.901	0.938	0.92	0.901	0.938	CLONAL	2	TRUE	0	0.908524770468874	2		814	682	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144120	11144120	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	297	750	0	ENST00000358026.2:c.3701T>G	p.Phe1234Cys	p.F1234C	ENST00000358026	NM_001128849.1	1234	tTc/tGc	26/36	1	2	FACETS	0.821	0.777	0.867	0.821	0.777	0.867	CLONAL	1	TRUE	1	0.908524770468874	2		750	796	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940481	76940482	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0025630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	376	519	0	ENST00000373344.5:c.611dup	p.Tyr204Ter	p.Y204*	ENST00000373344	NM_000489.3	204	tac/taAc	8/35	1	2	FACETS	0.901	0.858	0.943	0.901	0.858	0.943	CLONAL	1	TRUE	1	0.908524770468874	2		519	919	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506467	148506467	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519833	NA	P-0025631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	102	302	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		302	293	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0025632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	16	427	2	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.441	0.325	0.579	0.441	0.325	0.579	SUBCLONAL	1	TRUE	1	0.2296446569054	2		429	316	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0025632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	35	647	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.688	0.564	0.828	0.688	0.564	0.828	SUBCLONAL	1	TRUE	1	0.2296446569054	2		647	443	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188164	11188164	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587777893	NA	P-0025632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	31	414	0	ENST00000361445.4:c.5930C>A	p.Thr1977Lys	p.T1977K	ENST00000361445	NM_004958.3	1977	aCa/aAa	43/58	1	2	FACETS	0.581	0.469	0.707	0.581	0.469	0.707	SUBCLONAL	1	TRUE	1	0.2296446569054	2		414	465	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101434	27101434	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0025632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	25	408	0	ENST00000324856.7:c.4716C>G	p.Tyr1572Ter	p.Y1572*	ENST00000324856	NM_006015.4	1572	taC/taG	18/20	1	2	FACETS	0.505	0.397	0.629	0.505	0.397	0.629	SUBCLONAL	1	TRUE	1	0.2296446569054	2		408	431	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	37	387	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.916	0.756	1	0.916	0.756	1	CLONAL	1	TRUE	1	0.19	2		387	425	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519710	176519710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150737523	NA	P-0025634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	86	681	1	ENST00000292408.4:c.982G>A	p.Ala328Thr	p.A328T	ENST00000292408	NM_213647.1	328	Gca/Aca	8/18	1	2	FACETS	0.932	0.823	1	0.932	0.823	1	CLONAL	1	TRUE	1	0.19	2		682	971	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578440	7578440	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs879254249	NA	P-0025634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	74	749	0	ENST00000269305.4:c.490A>G	p.Lys164Glu	p.K164E	ENST00000269305	NM_001126112.2	164	Aag/Gag	5/11	1	2	FACETS	0.655	0.571	0.746	0.655	0.571	0.746	SUBCLONAL	1	TRUE	1	0.19	2		749	1189	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0025634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	40	314	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.19	2		314	383	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779194	3779194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	47	400	0	ENST00000262367.5:c.5854C>T	p.Pro1952Ser	p.P1952S	ENST00000262367	NM_004380.2	1952	Cct/Tct	31/31	1	2	FACETS	0.773	0.651	0.908	0.773	0.651	0.908	CLONAL	1	TRUE	1	0.19	2		400	640	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560150	29560150	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1401669485	NA	P-0025634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	48	354	0	ENST00000356175.3:c.3628del	p.Glu1210AsnfsTer5	p.E1210Nfs*5	ENST00000356175	NM_000267.3	1209	gtG/gt	27/57	1	2	FACETS	0.861	0.727	1	0.861	0.727	1	CLONAL	1	TRUE	1	0.19	2		354	587	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023190	31023191	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	483	542	0	ENST00000375687.4:c.2676dup	p.Asn893Ter	p.N893*	ENST00000375687	NM_015338.5	892	tct/tcTt	13/13	1	2	FACETS	0.964	0.925	1	0.964	0.925	1	CLONAL	1	TRUE	1	0.92	2		542	1089	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227914	55227914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	275	386	0	ENST00000275493.2:c.1381G>A	p.Val461Met	p.V461M	ENST00000275493	NM_005228.3	461	Gtg/Atg	12/28	1	2	FACETS	0.84	0.793	0.887	0.84	0.793	0.887	CLONAL	1	TRUE	1	0.92	2		386	712	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0025636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	181	83	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.87	0.802	0.941	0.87	0.802	0.941	CLONAL	1	TRUE	1	0.406295561281925	2		83	1024	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106058	8106058	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	199	537	0	ENST00000346208.3:c.878T>A	p.Met293Lys	p.M293K	ENST00000346208		293	aTg/aAg	4/6	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.406295561281925	2		537	907	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855984	68855984	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121964877	NA	P-0025636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	233	535	1	ENST00000261769.5:c.1792C>T	p.Arg598Ter	p.R598*	ENST00000261769	NM_004360.3	598	Cga/Tga	12/16	0.406295561281925	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.406295561281925	1		536	896	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089676	27089676	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	231	536	1	ENST00000324856.7:c.2632C>T	p.Gln878Ter	p.Q878*	ENST00000324856	NM_006015.4	878	Cag/Tag	8/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.406295561281925	2		537	1005	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602620	10602620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	235	412	0	ENST00000171111.5:c.958C>T	p.Arg320Trp	p.R320W	ENST00000171111	NM_203500.1	320	Cgg/Tgg	3/6	0.572567142082511	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.572567142082511	1		412	576	SUCCESS
APC	324	MSKCC	GRCh37	5	112173600	112173600	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1060503310	NA	P-0025637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	171	229	0	ENST00000257430.4:c.2309C>G	p.Ser770Ter	p.S770*	ENST00000257430	NM_000038.5	770	tCa/tGa	16/16	0.572567142082511	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.572567142082511	1		229	396	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226046	133226046	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	272	432	0	ENST00000320574.5:c.3851G>T	p.Arg1284Leu	p.R1284L	ENST00000320574	NM_006231.2	1284	cGg/cTg	31/49	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.572567142082511	2		432	894	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81562982	81562982	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0025637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	209	346	0	ENST00000298171.2:c.546-1G>A		p.X182_splice	ENST00000298171	NM_000369.2	182			1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.572567142082511	2		346	706	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220612	1220612	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201213	NA	P-0025637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	185	374	2	ENST00000326873.7:c.630C>A	p.Cys210Ter	p.C210*	ENST00000326873	NM_000455.4	210	tgC/tgA	5/10	0.572567142082511	1	FACETS	0.959	0.894	1	0.959	0.894	1	CLONAL	1	TRUE	0	0.572567142082511	1		376	481	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149982926	149982926	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	245	399	1	ENST00000253339.5:c.3332C>A	p.Ser1111Ter	p.S1111*	ENST00000253339		1111	tCg/tAg	7/7	0.572567142082511	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.572567142082511	1		400	584	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099805	157099805	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	166	205	1	ENST00000346085.5:c.742G>T	p.Ala248Ser	p.A248S	ENST00000346085	NM_020732.3	248	Gct/Tct	1/20	0.572567142082511	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.572567142082511	1		206	370	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039904	47039904	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	251	235	0	ENST00000377604.3:c.1247A>G	p.Gln416Arg	p.Q416R	ENST00000377604	NM_001204468.1	416	cAg/cGg	12/24	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.572567142082511	1		235	428	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0025638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	59	83	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.255792691195182	5	FACETS	0.798	0.689	0.916	0.532	0.459	0.611	CLONAL	2	TRUE	2	0.255792691195182	5		83	400	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578496	7578496	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782197	NA	P-0025638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	195	463	0	ENST00000269305.4:c.434T>C	p.Leu145Pro	p.L145P	ENST00000269305	NM_001126112.2	145	cTg/cCg	5/11	0.218396311125832	3	FACETS	1	0.983	1	0.79	0.733	0.848	CLONAL	2	TRUE	0	0.255792691195182	3		463	726	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610154	10610154	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	116	482	0	ENST00000171111.5:c.556G>T	p.Gly186Cys	p.G186C	ENST00000171111	NM_203500.1	186	Ggc/Tgc	2/6	0.255792691195182	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.255792691195182	1		482	551	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59770854	59770854	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	54	329	0	ENST00000259008.2:c.2512G>C	p.Asp838His	p.D838H	ENST00000259008	NM_032043.2	838	Gat/Cat	18/20	0.0541544482486649	4	FACETS	1	0.966	1	0.749	0.642	0.864	INDETERMINATE	1	TRUE	2	0.255792691195182	4		329	354	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58725410	58725410	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1216368028	NA	P-0025638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	101	438	0	ENST00000305921.3:c.984G>A	p.Met328Ile	p.M328I	ENST00000305921	NM_003620.3	328	atG/atA	4/6	0.0541544482486649	4	FACETS	0.932	0.836	1	0.932	0.836	1	INDETERMINATE	2	TRUE	2	0.255792691195182	4		438	532	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717609	89717609	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs876661024	NA	P-0025638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	51	262	0	ENST00000371953.3:c.635-1G>C		p.X212_splice	ENST00000371953	NM_000314.4	212			0.255792691195182	1	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	0	0.255792691195182	1		262	332	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383185	42383185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782563209	NA	P-0025638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	89	516	2	ENST00000221972.3:c.205G>A	p.Val69Ile	p.V69I	ENST00000221972	NM_021601.3	69	Gtc/Atc	2/5	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.255792691195182	2		518	612	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974258	18974258	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	58	335	0	ENST00000262803.5:c.2612T>A	p.Ile871Asn	p.I871N	ENST00000262803	NM_002911.3	871	aTc/aAc	19/24	0.255792691195182	1	FACETS	0.944	0.813	1	0.944	0.813	1	CLONAL	1	TRUE	0	0.255792691195182	1		335	419	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308378	30308378	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	75	460	0	ENST00000262643.3:c.392A>G	p.Gln131Arg	p.Q131R	ENST00000262643	NM_001238.2	131	cAg/cGg	6/12	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.255792691195182	2		460	563	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578259	212578259	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0025638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	58	351	0	ENST00000342788.4:c.997+1G>T		p.X333_splice	ENST00000342788	NM_005235.2	333			0.0541544482486649	4	FACETS	0.84	0.726	0.963	0.84	0.726	0.963	INDETERMINATE	2	TRUE	2	0.255792691195182	4		351	339	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019156	31019156	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	81	367	0	ENST00000375687.4:c.751G>A	p.Asp251Asn	p.D251N	ENST00000375687	NM_015338.5	251	Gat/Aat	9/13	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.255792691195182	2		367	534	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285908	38285908	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	62	371	0	ENST00000425967.3:c.503C>G	p.Ser168Cys	p.S168C	ENST00000425967	NM_001174067.1	168	tCt/tGt	5/19	0.171530065243694	5	FACETS	1	0.968	1	0.478	0.413	0.547	CLONAL	1	TRUE	2	0.255792691195182	5		371	468	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391869	139391869	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	62	392	0	ENST00000277541.6:c.6322G>T	p.Asp2108Tyr	p.D2108Y	ENST00000277541	NM_017617.3	2108	Gac/Tac	34/34	0.255792691195182	1	FACETS	0.888	0.769	1	0.888	0.769	1	CLONAL	1	TRUE	0	0.255792691195182	1		392	476	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508977	106508977	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	79	243	0	ENST00000359195.3:c.971C>A	p.Pro324Gln	p.P324Q	ENST00000359195	NM_002649.2	324	cCa/cAa	2/11	0.255792691195182	5	FACETS	0.931	0.822	1	0.372	0.328	0.419	CLONAL	2	TRUE	0	0.255792691195182	5		243	459	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557320	29557326	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAACG	AAAAACG	-	novel	NA	P-0121508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	53	336	0	ENST00000356175.3:c.3036_3042del	p.Lys1012AsnfsTer5	p.K1012Nfs*5	ENST00000356175	NM_000267.3	1011	atAAAAACG/at	23/57	0.212133172628586	1	FACETS	0.738	0.631	0.854	0.738	0.631	0.854	SUBCLONAL	1	NA	0	0.3	1		336	407	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0025640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	222	435	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.462338380844398	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.477022300209091	1		435	519	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244139	46244139	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	30	395	1	ENST00000334344.6:c.2233C>T	p.Gln745Ter	p.Q745*	ENST00000334344	NM_152641.2	745	Cag/Tag	15/21	1	2	FACETS	0.323	0.26	0.395	0.323	0.26	0.395	SUBCLONAL	1	TRUE	1	0.477022300209091	2		396	389	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396541	30396541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746045993	NA	P-0025640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	17	471	0	ENST00000331968.5:c.178G>A	p.Glu60Lys	p.E60K	ENST00000331968	NM_002742.2	60	Gag/Aag	1/18	1	2	FACETS	0.246	0.183	0.32	0.246	0.183	0.32	SUBCLONAL	1	TRUE	1	0.477022300209091	2		471	290	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857727	9857727	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0025640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	31	404	0	ENST00000330684.3:c.3674C>G	p.Ser1225Ter	p.S1225*	ENST00000330684	NM_001134407.1	1225	tCa/tGa	13/13	1	2	FACETS	0.372	0.301	0.453	0.372	0.301	0.453	SUBCLONAL	1	TRUE	1	0.477022300209091	2		404	349	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40462677	40462677	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	26	435	0	ENST00000345506.4:c.2375C>A	p.Ser792Tyr	p.S792Y	ENST00000345506	NM_003152.3	792	tCc/tAc	20/20	0.477022300209091	1	FACETS	0.226	0.178	0.28	0.226	0.178	0.28	SUBCLONAL	1	TRUE	0	0.477022300209091	1		435	368	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906777	50906777	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	50	729	0	ENST00000440232.2:c.1165G>T	p.Asp389Tyr	p.D389Y	ENST00000440232	NM_002691.3	389	Gac/Tac	10/27	0.477022300209091	3	FACETS	0.401	0.339	0.468	0.2	0.169	0.234	SUBCLONAL	1	TRUE	1	0.477022300209091	3		729	648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0025641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	500	405	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.410489357699916	3	FACETS	0.975	0.938	1	0.975	0.938	1	CLONAL	3	TRUE	0	0.410489357699916	3		406	1004	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0025641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	169	234	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.410489357699916	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.410489357699916	2		234	388	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149290773	149290774	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	112	398	0	ENST00000360632.3:c.445dup	p.Ile149AsnfsTer8	p.I149Nfs*8	ENST00000360632	NM_015472.4	149	atc/aAtc	3/7	0.410489357699916	3	FACETS	0.93	0.837	1	0.465	0.418	0.514	CLONAL	1	TRUE	1	0.410489357699916	3		398	707	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285537	38285537	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	79	539	0	ENST00000425967.3:c.616A>C	p.Lys206Gln	p.K206Q	ENST00000425967	NM_001174067.1	206	Aag/Cag	6/19	0.389809855840801	2	FACETS	0.473	0.415	0.535	0.236	0.207	0.268	SUBCLONAL	1	TRUE	0	0.410489357699916	2		539	814	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750768	128750768	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs750561207	NA	P-0025641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1383	236	439	0	ENST00000377970.2:c.305A>G	p.Asp102Gly	p.D102G	ENST00000377970	NM_002467.4	102	gAc/gGc	2/3	0.410489357699916	8	FACETS	0.792	0.737	0.85	0.264	0.245	0.284	SUBCLONAL	2	TRUE	2	0.410489357699916	8		439	1619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0025642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	30	278	7	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	1	2	FACETS	0.889	0.716	1	1	0.951	1	CLONAL	2	TRUE	1	0.08	2		285	422	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	287	760	1	ENST00000397752.3:c.3028G>C	p.Asp1010His	p.D1010H	ENST00000397752	NM_000245.2	1010	Gat/Cat	14/21	0.261546898128002	3	FACETS	0.975	0.917	1	1	0.996	1	CLONAL	7	TRUE	0	0.08	3		761	1093	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033934	49033934	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	32	515	1	ENST00000267163.4:c.2071G>T	p.Glu691Ter	p.E691*	ENST00000267163	NM_000321.2	691	Gag/Tag	20/27	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.08	2		516	608	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944863	131944863	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	35	332	0	ENST00000265335.6:c.2884G>C	p.Glu962Gln	p.E962Q	ENST00000265335		962	Gag/Cag	18/25	0.192807888129106	3	FACETS	0.942	0.772	1	0.942	0.772	1	CLONAL	2	TRUE	1	0.08	3		332	483	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62293900	62293900	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	48	823	0	ENST00000360203.5:c.397C>T	p.Pro133Ser	p.P133S	ENST00000360203	NM_001283009.1	133	Cct/Tct	5/35	1	2	FACETS	1	0.872	1	1	0.973	1	CLONAL	2	TRUE	1	0.08	2		823	579	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045464	47045464	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	31	506	0	ENST00000377604.3:c.2431C>T	p.Gln811Ter	p.Q811*	ENST00000377604	NM_001204468.1	811	Caa/Taa	22/24	1	2	FACETS	0.863	0.697	1	1	0.951	1	CLONAL	2	TRUE	1	0.08	2		506	449	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0025644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	115	206	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.272835961640485	2	FACETS	1	0.972	1	0.59	0.535	0.646	INDETERMINATE	1	TRUE	0	0.475776978786246	2		207	410	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0025644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	61	299	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.716	0.621	0.819	0.716	0.621	0.819	SUBCLONAL	1	TRUE	1	0.475776978786246	2		299	358	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186681	11186681	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1024737469	NA	P-0025644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	63	513	0	ENST00000361445.4:c.6524T>C	p.Met2175Thr	p.M2175T	ENST00000361445	NM_004958.3	2175	aTg/aCg	46/58	1	2	FACETS	0.596	0.517	0.682	0.596	0.517	0.682	SUBCLONAL	1	TRUE	1	0.475776978786246	2		513	444	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120920	115120921	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGAA	novel	NA	P-0025644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	43	460	0	ENST00000257566.3:c.82_85dup	p.Ala29ValfsTer83	p.A29Vfs*83	ENST00000257566	NM_016569.3	29	gcc/gTTCGcc	1/8	1	2	FACETS	0.498	0.418	0.586	0.498	0.418	0.586	SUBCLONAL	1	TRUE	1	0.475776978786246	2		460	363	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0025647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	25	466	2	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	0.345	0.27	0.432	0.345	0.27	0.432	SUBCLONAL	1	TRUE	1	0.16	2		468	906	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827958	40827958	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs200990749	NA	P-0025647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	43	515	0	ENST00000373198.4:c.2470G>T	p.Asp824Tyr	p.D824Y	ENST00000373198	NM_133170.3	824	Gac/Tac	17/32	1	2	FACETS	0.799	0.667	0.945	0.799	0.667	0.945	CLONAL	1	TRUE	1	0.16	2		515	673	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140165	50140165	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	63	581	0	ENST00000246792.3:c.260A>T	p.Gln87Leu	p.Q87L	ENST00000246792	NM_006270.3	87	cAg/cTg	3/6	1	2	FACETS	0.908	0.784	1	0.908	0.784	1	CLONAL	1	TRUE	1	0.16	2		581	867	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0025647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	54	573	1	ENST00000269305.4:c.994-1G>T		p.X332_splice	ENST00000269305	NM_001126112.2	332			1	2	FACETS	0.839	0.714	0.975	0.839	0.714	0.975	CLONAL	1	TRUE	1	0.16	2		574	805	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953115	81953115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1336595726	NA	P-0025647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	27	280	0	ENST00000359376.3:c.2081G>A	p.Arg694His	p.R694H	ENST00000359376	NM_002661.3	694	cGc/cAc	20/33	1	2	FACETS	0.693	0.55	0.857	0.693	0.55	0.857	SUBCLONAL	1	TRUE	1	0.16	2		280	487	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650671	18650671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	26	432	0	ENST00000266497.5:c.2882G>T	p.Gly961Val	p.G961V	ENST00000266497		961	gGa/gTa	20/31	1	2	FACETS	0.641	0.506	0.796	0.641	0.506	0.796	SUBCLONAL	1	TRUE	1	0.16	2		432	507	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716199	243716199	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	43	638	0	ENST00000263826.5:c.995T>C	p.Leu332Pro	p.L332P	ENST00000263826	NM_005465.4	332	cTa/cCa	10/13	1	2	FACETS	0.627	0.523	0.744	0.627	0.523	0.744	SUBCLONAL	1	TRUE	1	0.16	2		638	857	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112575	115112575	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	67	694	0	ENST00000257566.3:c.1165G>T	p.Ala389Ser	p.A389S	ENST00000257566	NM_016569.3	389	Gcc/Tcc	7/8	1	2	FACETS	0.985	0.854	1	0.985	0.854	1	CLONAL	1	TRUE	1	0.16	2		694	850	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953262	81953262	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	28	294	1	ENST00000359376.3:c.2228A>T	p.Tyr743Phe	p.Y743F	ENST00000359376	NM_002661.3	743	tAc/tTc	20/33	1	2	FACETS	0.875	0.699	1	0.875	0.699	1	CLONAL	1	TRUE	1	0.16	2		295	400	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716302	52716302	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	66	578	0	ENST00000322088.6:c.746G>C	p.Arg249Pro	p.R249P	ENST00000322088	NM_014225.5	249	cGc/cCc	6/15	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.16	2		578	775	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714388	40714388	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	44	586	0	ENST00000373198.4:c.4009C>A	p.Arg1337Ser	p.R1337S	ENST00000373198	NM_133170.3	1337	Cgc/Agc	29/32	1	2	FACETS	0.836	0.7	0.987	0.836	0.7	0.987	CLONAL	1	TRUE	1	0.16	2		586	658	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62294205	62294205	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	43	659	0	ENST00000360203.5:c.502del	p.Ala168GlnfsTer11	p.A168Qfs*11	ENST00000360203	NM_001283009.1	167	gtG/gt	6/35	1	2	FACETS	0.662	0.552	0.785	0.662	0.552	0.785	SUBCLONAL	1	TRUE	1	0.16	2		659	812	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133836	55133836	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	34	415	0	ENST00000257290.5:c.1049T>A	p.Leu350Gln	p.L350Q	ENST00000257290	NM_006206.4	350	cTg/cAg	7/23	1	2	FACETS	0.737	0.601	0.89	0.737	0.601	0.89	SUBCLONAL	1	TRUE	1	0.16	2		415	577	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86681116	86681116	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0025647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	30	311	0	ENST00000274376.6:c.2759-2A>G		p.X920_splice	ENST00000274376	NM_002890.2	920			1	2	FACETS	0.839	0.675	1	0.839	0.675	1	CLONAL	1	TRUE	1	0.16	2		311	447	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522603	106522603	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	40	552	0	ENST00000359195.3:c.2580G>T	p.Leu860Phe	p.L860F	ENST00000359195	NM_002649.2	860	ttG/ttT	7/11	1	2	FACETS	0.756	0.627	0.901	0.756	0.627	0.901	CLONAL	1	TRUE	1	0.16	2		552	661	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974760	21974760	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691186	NA	P-0025647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	30	228	0	ENST00000304494.5:c.67G>T	p.Gly23Cys	p.G23C	ENST00000304494	NM_000077.4	23	Ggt/Tgt	1/3	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.16	2		228	279	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27218804	27218804	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	40	577	0	ENST00000380036.4:c.3092T>C	p.Ile1031Thr	p.I1031T	ENST00000380036	NM_000459.3	1031	aTt/aCt	20/23	1	2	FACETS	0.698	0.579	0.832	0.698	0.579	0.832	SUBCLONAL	1	TRUE	1	0.16	2		577	716	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390997	139390997	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	58	803	1	ENST00000277541.6:c.7194G>T	p.Gln2398His	p.Q2398H	ENST00000277541	NM_017617.3	2398	caG/caT	34/34	1	2	FACETS	0.705	0.604	0.817	0.705	0.604	0.817	SUBCLONAL	1	TRUE	1	0.16	2		804	1028	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	119	647	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.737	0.665	0.812	0.737	0.665	0.812	SUBCLONAL	1	TRUE	1	0.41	2		647	788	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782183	9782183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs547875116	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	91	478	1	ENST00000377346.4:c.2206G>A	p.Asp736Asn	p.D736N	ENST00000377346	NM_005026.3	736	Gac/Aac	17/24	1	2	FACETS	0.855	0.762	0.954	0.855	0.762	0.954	CLONAL	1	TRUE	1	0.41	2		479	519	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783342	9783342	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	126	510	0	ENST00000377346.4:c.2586G>T	p.Lys862Asn	p.K862N	ENST00000377346	NM_005026.3	862	aaG/aaT	20/24	1	2	FACETS	0.959	0.87	1	0.959	0.87	1	CLONAL	1	TRUE	1	0.41	2		510	641	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188578	11188578	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	137	493	0	ENST00000361445.4:c.5843C>T	p.Thr1948Met	p.T1948M	ENST00000361445	NM_004958.3	1948	aCg/aTg	42/58	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.41	2		493	651	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11273622	11273622	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	69	316	0	ENST00000361445.4:c.3119A>C	p.Glu1040Ala	p.E1040A	ENST00000361445	NM_004958.3	1040	gAa/gCa	21/58	1	2	FACETS	0.831	0.727	0.942	0.831	0.727	0.942	CLONAL	1	TRUE	1	0.41	2		316	405	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094441	27094441	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	104	575	0	ENST00000324856.7:c.3149A>G	p.Asp1050Gly	p.D1050G	ENST00000324856	NM_006015.4	1050	gAc/gGc	11/20	1	2	FACETS	0.787	0.705	0.873	0.787	0.705	0.873	SUBCLONAL	1	TRUE	1	0.41	2		575	645	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	131	530	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.937	0.852	1	0.937	0.852	1	CLONAL	1	TRUE	1	0.41	2		530	682	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491163	120491163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	116	524	1	ENST00000256646.2:c.2626G>A	p.Glu876Lys	p.E876K	ENST00000256646	NM_024408.3	876	Gag/Aag	17/34	1	2	FACETS	0.981	0.887	1	0.981	0.887	1	CLONAL	1	TRUE	1	0.41	2		525	577	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550886	150550886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370931690	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	133	518	1	ENST00000369026.2:c.770G>A	p.Gly257Asp	p.G257D	ENST00000369026	NM_021960.4	257	gGc/gAc	2/3	1	2	FACETS	0.889	0.808	0.973	0.889	0.808	0.973	CLONAL	1	TRUE	1	0.41	2		519	730	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745466	162745466	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	90	477	0	ENST00000367921.3:c.1881G>T	p.Lys627Asn	p.K627N	ENST00000367921	NM_006182.2	627	aaG/aaT	15/18	1	2	FACETS	0.913	0.813	1	0.913	0.813	1	CLONAL	1	TRUE	1	0.41	2		477	481	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945656	206945656	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767158016	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	115	531	0	ENST00000423557.1:c.125G>A	p.Arg42Gln	p.R42Q	ENST00000423557	NM_000572.2	42	cGa/cAa	1/5	1	2	FACETS	0.831	0.75	0.917	0.831	0.75	0.917	CLONAL	1	TRUE	1	0.41	2		531	675	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809234	243809234	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	81	638	0	ENST00000263826.5:c.390G>T	p.Glu130Asp	p.E130D	ENST00000263826	NM_005465.4	130	gaG/gaT	4/13	1	2	FACETS	0.671	0.592	0.756	0.671	0.592	0.756	SUBCLONAL	1	TRUE	1	0.41	2		638	589	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405334	70405334	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	131	684	1	ENST00000373644.4:c.2848C>T	p.Pro950Ser	p.P950S	ENST00000373644	NM_030625.2	950	Cca/Tca	4/12	1	2	FACETS	0.858	0.779	0.94	0.858	0.779	0.94	CLONAL	1	TRUE	1	0.41	2		685	745	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406078	70406078	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	116	623	0	ENST00000373644.4:c.3592T>G	p.Phe1198Val	p.F1198V	ENST00000373644	NM_030625.2	1198	Ttt/Gtt	4/12	1	2	FACETS	0.773	0.697	0.853	0.773	0.697	0.853	SUBCLONAL	1	TRUE	1	0.41	2		623	732	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624245	89624245	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554890335	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	70	192	1	ENST00000371953.3:c.19G>T	p.Glu7Ter	p.E7*	ENST00000371953	NM_000314.4	7	Gag/Tag	1/9	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.41	2		193	260	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720744	89720744	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167674	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	11	193	0	ENST00000371953.3:c.895G>T	p.Glu299Ter	p.E299*	ENST00000371953	NM_000314.4	299	Gaa/Taa	8/9	1	2	FACETS	0.301	0.208	0.417	0.301	0.208	0.417	SUBCLONAL	1	TRUE	1	0.41	2		193	178	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197297	94197297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1235074095	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	28	527	1	ENST00000323929.3:c.1207G>A	p.Glu403Lys	p.E403K	ENST00000323929	NM_005591.3	403	Gaa/Aaa	11/20	1	2	FACETS	0.251	0.2	0.31	0.251	0.2	0.31	SUBCLONAL	1	TRUE	1	0.41	2		528	544	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922251	100922251	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	112	504	1	ENST00000325455.5:c.2261C>A	p.Ser754Tyr	p.S754Y	ENST00000325455	NM_001202474.3	754	tCt/tAt	5/8	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.41	2		505	546	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102033294	102033294	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376161041	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	165	646	0	ENST00000282441.5:c.680C>T	p.Ser227Leu	p.S227L	ENST00000282441	NM_001130145.2	227	tCg/tTg	3/9	1	2	FACETS	0.994	0.914	1	0.994	0.914	1	CLONAL	1	TRUE	1	0.41	2		646	810	SUCCESS
ATM	472	MSKCC	GRCh37	11	108099946	108099946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	84	330	0	ENST00000278616.4:c.227G>T	p.Arg76Ile	p.R76I	ENST00000278616	NM_000051.3	76	aGa/aTa	4/63	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.41	2		330	400	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196825	108196825	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	98	469	0	ENST00000278616.4:c.6848C>A	p.Ser2283Ter	p.S2283*	ENST00000278616	NM_000051.3	2283	tCa/tAa	47/63	1	2	FACETS	0.871	0.779	0.968	0.871	0.779	0.968	CLONAL	1	TRUE	1	0.41	2		469	549	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216568	108216568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs767845728	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	84	561	0	ENST00000278616.4:c.8517C>A	p.Phe2839Leu	p.F2839L	ENST00000278616	NM_000051.3	2839	ttC/ttA	58/63	1	2	FACETS	0.723	0.639	0.812	0.723	0.639	0.812	SUBCLONAL	1	TRUE	1	0.41	2		561	567	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371854	118371854	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	106	500	0	ENST00000534358.1:c.6311C>A	p.Ser2104Tyr	p.S2104Y	ENST00000534358	NM_005933.3	2104	tCt/tAt	25/36	1	2	FACETS	0.902	0.811	0.998	0.902	0.811	0.998	CLONAL	1	TRUE	1	0.41	2		500	573	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392038	118392038	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	140	612	0	ENST00000534358.1:c.11549G>T	p.Arg3850Ile	p.R3850I	ENST00000534358	NM_005933.3	3850	aGa/aTa	35/36	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.41	2		612	673	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656292	18656292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867409592	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	118	583	0	ENST00000266497.5:c.2971G>A	p.Glu991Lys	p.E991K	ENST00000266497		991	Gaa/Aaa	21/31	1	2	FACETS	0.866	0.782	0.953	0.866	0.782	0.953	CLONAL	1	TRUE	1	0.41	2		583	665	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380289	25380289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	101	687	0	ENST00000311936.3:c.169G>A	p.Asp57Asn	p.D57N	ENST00000311936	NM_004985.3	57	Gac/Aac	3/5	1	2	FACETS	0.743	0.665	0.826	0.743	0.665	0.826	SUBCLONAL	1	TRUE	1	0.41	2		687	663	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	169	380	0	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	1	2	FACETS	0.899	0.827	0.975	0.899	0.827	0.975	CLONAL	1	TRUE	1	0.41	2		380	917	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487277	56487277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035001455	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	126	534	0	ENST00000267101.3:c.1423C>T	p.Arg475Trp	p.R475W	ENST00000267101	NM_001982.3	475	Cgg/Tgg	12/28	1	2	FACETS	0.844	0.765	0.927	0.844	0.765	0.927	CLONAL	1	TRUE	1	0.41	2		534	728	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864398	57864398	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	107	631	0	ENST00000228682.2:c.1875G>T	p.Glu625Asp	p.E625D	ENST00000228682	NM_005269.2	625	gaG/gaT	12/12	1	2	FACETS	0.857	0.77	0.948	0.857	0.77	0.948	CLONAL	1	TRUE	1	0.41	2		631	609	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865732	57865732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	156	662	0	ENST00000228682.2:c.3209G>A	p.Ser1070Asn	p.S1070N	ENST00000228682	NM_005269.2	1070	aGc/aAc	12/12	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.41	2		662	738	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244944	133244944	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs61734163	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	155	753	0	ENST00000320574.5:c.2171C>T	p.Ala724Val	p.A724V	ENST00000320574	NM_006231.2	724	gCg/gTg	19/49	1	2	FACETS	0.849	0.777	0.924	0.849	0.777	0.924	CLONAL	1	TRUE	1	0.41	2		753	891	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	128	506	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	0.824	0.747	0.904	0.824	0.747	0.904	CLONAL	1	TRUE	1	0.41	2		506	758	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601268	28601268	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs761555525	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	143	625	0	ENST00000241453.7:c.2164A>G	p.Asn722Asp	p.N722D	ENST00000241453	NM_004119.2	722	Aat/Gat	17/24	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.41	2		625	689	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28883013	28883013	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	129	644	0	ENST00000282397.4:c.3687A>C	p.Glu1229Asp	p.E1229D	ENST00000282397	NM_002019.4	1229	gaA/gaC	28/30	1	2	FACETS	0.852	0.773	0.934	0.852	0.773	0.934	CLONAL	1	TRUE	1	0.41	2		644	739	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28931789	28931789	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	102	445	0	ENST00000282397.4:c.2150T>G	p.Phe717Cys	p.F717C	ENST00000282397	NM_002019.4	717	tTt/tGt	15/30	1	2	FACETS	0.821	0.736	0.911	0.821	0.736	0.911	CLONAL	1	TRUE	1	0.41	2		445	606	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912321	32912321	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	110	521	0	ENST00000380152.3:c.3829A>C	p.Asn1277His	p.N1277H	ENST00000380152		1277	Aat/Cat	11/27	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.41	2		521	495	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912414	32912414	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs80358638	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	84	455	0	ENST00000380152.3:c.3922G>T	p.Glu1308Ter	p.E1308*	ENST00000380152		1308	Gaa/Taa	11/27	1	2	FACETS	0.879	0.78	0.985	0.879	0.78	0.985	CLONAL	1	TRUE	1	0.41	2		455	466	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914175	32914175	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146351301	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	87	654	0	ENST00000380152.3:c.5683G>A	p.Glu1895Lys	p.E1895K	ENST00000380152		1895	Gag/Aag	11/27	1	2	FACETS	0.795	0.705	0.89	0.795	0.705	0.89	SUBCLONAL	1	TRUE	1	0.41	2		654	534	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915129	32915129	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	118	582	0	ENST00000380152.3:c.6637T>G	p.Ser2213Ala	p.S2213A	ENST00000380152		2213	Tct/Gct	11/27	1	2	FACETS	0.934	0.845	1	0.934	0.845	1	CLONAL	1	TRUE	1	0.41	2		582	616	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134988	41134988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	48	222	1	ENST00000379561.5:c.640C>T	p.Arg214Cys	p.R214C	ENST00000379561	NM_002015.3	214	Cgt/Tgt	2/3	1	2	FACETS	0.673	0.571	0.784	0.673	0.571	0.784	SUBCLONAL	1	TRUE	1	0.41	2		223	348	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030340	49030340	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1472724809	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	85	340	0	ENST00000267163.4:c.1815G>A	p.Met605Ile	p.M605I	ENST00000267163	NM_000321.2	605	atG/atA	19/27	1	2	FACETS	0.955	0.849	1	0.955	0.849	1	CLONAL	1	TRUE	1	0.41	2		340	434	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347916	73347916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139907646	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	80	380	0	ENST00000377767.4:c.1145G>A	p.Arg382Gln	p.R382Q	ENST00000377767	NM_014953.3	382	cGa/cAa	8/21	1	2	FACETS	0.914	0.808	1	0.914	0.808	1	CLONAL	1	TRUE	1	0.41	2		380	427	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504585	103504585	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747957305	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	127	509	1	ENST00000355739.4:c.206G>A	p.Arg69Gln	p.R69Q	ENST00000355739	NM_000123.3	69	cGa/cAa	2/15	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.41	2		510	609	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103520557	103520557	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	74	398	0	ENST00000355739.4:c.2628A>C	p.Glu876Asp	p.E876D	ENST00000355739	NM_000123.3	876	gaA/gaC	12/15	1	2	FACETS	0.832	0.731	0.939	0.832	0.731	0.939	CLONAL	1	TRUE	1	0.41	2		398	434	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609899	81609899	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	68	314	0	ENST00000298171.2:c.1497C>A	p.Phe499Leu	p.F499L	ENST00000298171	NM_000369.2	499	ttC/ttA	10/10	1	2	FACETS	0.712	0.621	0.81	0.712	0.621	0.81	SUBCLONAL	1	TRUE	1	0.41	2		314	466	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639407	3639407	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	100	641	1	ENST00000294008.3:c.4232G>T	p.Arg1411Ile	p.R1411I	ENST00000294008	NM_032444.2	1411	aGa/aTa	12/15	1	2	FACETS	0.718	0.642	0.799	0.718	0.642	0.799	SUBCLONAL	1	TRUE	1	0.41	2		642	679	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658919	3658919	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	133	633	1	ENST00000294008.3:c.47C>A	p.Ser16Ter	p.S16*	ENST00000294008	NM_032444.2	16	tCa/tAa	2/15	1	2	FACETS	0.853	0.775	0.934	0.853	0.775	0.934	CLONAL	1	TRUE	1	0.41	2		634	761	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788637	3788637	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	38	527	1	ENST00000262367.5:c.4317C>A	p.Phe1439Leu	p.F1439L	ENST00000262367	NM_004380.2	1439	ttC/ttA	26/31	1	2	FACETS	0.265	0.218	0.318	0.265	0.218	0.318	SUBCLONAL	1	TRUE	1	0.41	2		528	699	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862106	68862106	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs864622198	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	141	506	1	ENST00000261769.5:c.2194C>T	p.Arg732Trp	p.R732W	ENST00000261769	NM_004360.3	732	Cgg/Tgg	14/16	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.41	2		507	658	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990354	81990354	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	128	569	0	ENST00000359376.3:c.3625G>T	p.Glu1209Ter	p.E1209*	ENST00000359376	NM_002661.3	1209	Gaa/Taa	32/33	1	2	FACETS	0.884	0.803	0.97	0.884	0.803	0.97	CLONAL	1	TRUE	1	0.41	2		569	706	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350734	89350734	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146294483	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	134	984	1	ENST00000301030.4:c.2216C>T	p.Ser739Leu	p.S739L	ENST00000301030	NM_001256183.1	739	tCg/tTg	9/13	1	2	FACETS	0.548	0.497	0.603	0.548	0.497	0.603	SUBCLONAL	1	TRUE	1	0.41	2		985	1192	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350854	89350854	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	202	923	0	ENST00000301030.4:c.2096A>C	p.Lys699Thr	p.K699T	ENST00000301030	NM_001256183.1	699	aAa/aCa	9/13	1	2	FACETS	0.807	0.747	0.87	0.807	0.747	0.87	CLONAL	1	TRUE	1	0.41	2		923	1221	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350856	89350856	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	216	919	1	ENST00000301030.4:c.2094G>T	p.Glu698Asp	p.E698D	ENST00000301030	NM_001256183.1	698	gaG/gaT	9/13	1	2	FACETS	0.88	0.816	0.945	0.88	0.816	0.945	CLONAL	1	TRUE	1	0.41	2		920	1198	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980361	7980361	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	139	622	1	ENST00000319144.4:c.1222G>A	p.Ala408Thr	p.A408T	ENST00000319144	NM_001139.2	408	Gcc/Acc	9/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.41	2		623	619	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012103	16012103	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	96	500	0	ENST00000268712.3:c.2179G>A	p.Glu727Lys	p.E727K	ENST00000268712	NM_006311.3	727	Gaa/Aaa	19/46	1	2	FACETS	0.856	0.765	0.953	0.856	0.765	0.953	CLONAL	1	TRUE	1	0.41	2		500	547	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049801	16049801	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	108	537	0	ENST00000268712.3:c.971G>T	p.Arg324Ile	p.R324I	ENST00000268712	NM_006311.3	324	aGa/aTa	10/46	1	2	FACETS	0.852	0.767	0.943	0.852	0.767	0.943	CLONAL	1	TRUE	1	0.41	2		537	618	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40460234	40460234	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	126	604	0	ENST00000345506.4:c.1945C>T	p.Arg649Trp	p.R649W	ENST00000345506	NM_003152.3	649	Cgg/Tgg	17/20	1	2	FACETS	0.822	0.745	0.903	0.822	0.745	0.903	CLONAL	1	TRUE	1	0.41	2		604	748	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234548	41234548	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	106	585	0	ENST00000357654.3:c.4230A>C	p.Glu1410Asp	p.E1410D	ENST00000357654	NM_007294.3	1410	gaA/gaC	12/23	1	2	FACETS	0.774	0.695	0.858	0.774	0.695	0.858	SUBCLONAL	1	TRUE	1	0.41	2		585	668	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56801452	56801452	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367846829	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	114	553	1	ENST00000337432.4:c.956G>A	p.Arg319Gln	p.R319Q	ENST00000337432	NM_058216.2	319	cGa/cAa	7/9	1	2	FACETS	0.952	0.86	1	0.952	0.86	1	CLONAL	1	TRUE	1	0.41	2		554	584	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734155	58734155	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	130	739	0	ENST00000305921.3:c.1213G>T	p.Glu405Ter	p.E405*	ENST00000305921	NM_003620.3	405	Gaa/Taa	5/6	1	2	FACETS	0.855	0.776	0.937	0.855	0.776	0.937	CLONAL	1	TRUE	1	0.41	2		739	742	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39575956	39575956	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	87	393	0	ENST00000262039.4:c.889A>C	p.Asn297His	p.N297H	ENST00000262039	NM_002647.2	297	Aat/Cat	8/25	1	2	FACETS	0.971	0.864	1	0.971	0.864	1	CLONAL	1	TRUE	1	0.41	2		393	437	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56415044	56415044	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs772139375	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	96	468	1	ENST00000348428.3:c.2445C>A	p.Phe815Leu	p.F815L	ENST00000348428	NM_006785.3	815	ttC/ttA	17/17	1	2	FACETS	0.774	0.691	0.862	0.774	0.691	0.862	SUBCLONAL	1	TRUE	1	0.41	2		469	605	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125473	7125473	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913144	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	173	669	0	ENST00000302850.5:c.3079C>T	p.Arg1027Ter	p.R1027*	ENST00000302850	NM_000208.2	1027	Cga/Tga	17/22	1	2	FACETS	0.952	0.877	1	0.952	0.877	1	CLONAL	1	TRUE	1	0.41	2		669	886	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7152773	7152773	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	152	719	0	ENST00000302850.5:c.2195T>G	p.Phe732Cys	p.F732C	ENST00000302850	NM_000208.2	732	tTt/tGt	10/22	1	2	FACETS	0.827	0.756	0.901	0.827	0.756	0.901	CLONAL	1	TRUE	1	0.41	2		719	897	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10259612	10259612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	147	629	4	ENST00000340748.4:c.2620G>A	p.Ala874Thr	p.A874T	ENST00000340748		874	Gcg/Acg	26/40	1	2	FACETS	0.891	0.814	0.971	0.891	0.814	0.971	CLONAL	1	TRUE	1	0.41	2		633	805	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10279024	10279024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1419372864	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	165	646	1	ENST00000340748.4:c.737G>A	p.Arg246Gln	p.R246Q	ENST00000340748		246	cGa/cAa	9/40	1	2	FACETS	0.889	0.817	0.965	0.889	0.817	0.965	CLONAL	1	TRUE	1	0.41	2		647	905	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955132	17955132	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	122	670	0	ENST00000458235.1:c.95C>A	p.Ala32Asp	p.A32D	ENST00000458235	NM_000215.3	32	gCt/gAt	2/24	1	2	FACETS	0.838	0.758	0.922	0.838	0.758	0.922	CLONAL	1	TRUE	1	0.41	2		670	710	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277005	18277005	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	112	549	0	ENST00000222254.8:c.1452C>A	p.Phe484Leu	p.F484L	ENST00000222254	NM_005027.3	484	ttC/ttA	12/16	1	2	FACETS	0.962	0.868	1	0.962	0.868	1	CLONAL	1	TRUE	1	0.41	2		549	568	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257194	19257194	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	87	574	0	ENST00000162023.5:c.770-1G>T		p.X257_splice	ENST00000162023		257			1	2	FACETS	0.737	0.653	0.826	0.737	0.653	0.826	SUBCLONAL	1	TRUE	1	0.41	2		574	576	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228800	36228800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393734909	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	150	731	0	ENST00000222270.7:c.7699C>T	p.Arg2567Cys	p.R2567C	ENST00000222270	NM_014727.1	2567	Cgt/Tgt	35/37	1	2	FACETS	0.792	0.723	0.864	0.792	0.723	0.864	SUBCLONAL	1	TRUE	1	0.41	2		731	924	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726557	41726557	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	124	564	0	ENST00000301178.4:c.102A>C	p.Glu34Asp	p.E34D	ENST00000301178	NM_021913.4	34	gaA/gaC	2/20	1	2	FACETS	0.974	0.884	1	0.974	0.884	1	CLONAL	1	TRUE	1	0.41	2		564	621	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99185041	99185041	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536365553	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	125	418	0	ENST00000074304.5:c.2443G>A	p.Asp815Asn	p.D815N	ENST00000074304	NM_001134224.1	815	Gat/Aat	23/26	1	2	FACETS	0.966	0.877	1	0.966	0.877	1	CLONAL	1	TRUE	1	0.41	2		418	631	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128036895	128036895	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	176	660	1	ENST00000285398.2:c.1584G>T	p.Lys528Asn	p.K528N	ENST00000285398	NM_000122.1	528	aaG/aaT	10/15	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.41	2		661	843	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630626	158630626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912678	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	80	350	0	ENST00000263640.3:c.617G>A	p.Arg206His	p.R206H	ENST00000263640	NM_001105.4	206	cGc/cAc	6/11	1	2	FACETS	0.912	0.806	1	0.912	0.806	1	CLONAL	1	TRUE	1	0.41	2		350	428	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095920	178095920	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	118	469	0	ENST00000397062.3:c.1411G>T	p.Glu471Ter	p.E471*	ENST00000397062	NM_006164.4	471	Gaa/Taa	5/5	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.41	2		469	558	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131412	202131412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339962485	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	121	550	0	ENST00000358485.4:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000358485	NM_001080125.1	127	cGa/cAa	2/9	1	2	FACETS	0.963	0.872	1	0.963	0.872	1	CLONAL	1	TRUE	1	0.41	2		550	613	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136279	202136279	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	148	703	0	ENST00000358485.4:c.523G>T	p.Glu175Ter	p.E175*	ENST00000358485	NM_001080125.1	175	Gaa/Taa	3/9	1	2	FACETS	0.877	0.802	0.956	0.877	0.802	0.956	CLONAL	1	TRUE	1	0.41	2		703	823	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342999	225342999	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	201	765	0	ENST00000264414.4:c.2093A>G	p.Asp698Gly	p.D698G	ENST00000264414	NM_003590.4	698	gAc/gGc	15/16	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.41	2		765	926	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394052	31394052	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	122	474	0	ENST00000328111.2:c.2339C>T	p.Ser780Leu	p.S780L	ENST00000328111	NM_006892.3	780	tCg/tTg	22/23	1	2	FACETS	0.913	0.827	1	0.913	0.827	1	CLONAL	1	TRUE	1	0.41	2		474	652	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741497	39741497	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	117	413	1	ENST00000361337.2:c.1384C>T	p.Arg462Ter	p.R462*	ENST00000361337	NM_003286.2	462	Cga/Tga	14/21	1	2	FACETS	0.964	0.872	1	0.964	0.872	1	CLONAL	1	TRUE	1	0.41	2		414	592	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62294236	62294236	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs184051277	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	156	594	1	ENST00000360203.5:c.532G>A	p.Val178Ile	p.V178I	ENST00000360203	NM_001283009.1	178	Gta/Ata	6/35	1	2	FACETS	0.96	0.88	1	0.96	0.88	1	CLONAL	1	TRUE	1	0.41	2		595	793	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755477	39755477	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	121	435	0	ENST00000288319.7:c.1288T>G	p.Phe430Val	p.F430V	ENST00000288319	NM_182918.3	430	Ttt/Gtt	10/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.41	2		435	560	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22143009	22143009	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	126	546	0	ENST00000215832.6:c.698A>C	p.Tyr233Ser	p.Y233S	ENST00000215832	NM_002745.4	233	tAt/tCt	5/9	1	2	FACETS	0.928	0.842	1	0.928	0.842	1	CLONAL	1	TRUE	1	0.41	2		546	662	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545781	41545781	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	138	608	0	ENST00000263253.7:c.2396C>A	p.Ser799Tyr	p.S799Y	ENST00000263253	NM_001429.3	799	tCt/tAt	14/31	1	2	FACETS	0.999	0.911	1	0.999	0.911	1	CLONAL	1	TRUE	1	0.41	2		608	674	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547910	41547910	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1342949087	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	139	554	1	ENST00000263253.7:c.2891C>A	p.Ser964Tyr	p.S964Y	ENST00000263253	NM_001429.3	964	tCt/tAt	15/31	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.41	2		555	661	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12653459	12653459	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs896491732	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	118	455	0	ENST00000251849.4:c.310G>A	p.Glu104Lys	p.E104K	ENST00000251849	NM_002880.3	104	Gaa/Aaa	3/17	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.41	2		455	552	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47108593	47108593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	122	577	1	ENST00000409792.3:c.6076C>T	p.Pro2026Ser	p.P2026S	ENST00000409792	NM_014159.6	2026	Cca/Tca	13/21	1	2	FACETS	0.879	0.796	0.966	0.879	0.796	0.966	CLONAL	1	TRUE	1	0.41	2		578	677	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73096457	73096458	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	48	275	0	ENST00000356692.5:c.240dup	p.Asp81Ter	p.D81*	ENST00000356692		79	-/T	3/9	1	2	FACETS	0.89	0.759	1	0.89	0.759	1	CLONAL	1	TRUE	1	0.41	2		275	263	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259409	89259409	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	113	587	0	ENST00000336596.2:c.553G>T	p.Asp185Tyr	p.D185Y	ENST00000336596	NM_005233.5	185	Gat/Tat	3/17	1	2	FACETS	0.875	0.789	0.966	0.875	0.789	0.966	CLONAL	1	TRUE	1	0.41	2		587	630	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119721018	119721018	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	174	627	0	ENST00000316626.5:c.157G>T	p.Glu53Ter	p.E53*	ENST00000316626		53	Gaa/Taa	2/12	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.41	2		627	801	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922301	178922301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	103	524	0	ENST00000263967.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000263967	NM_006218.2	357	cGa/cAa	6/21	1	2	FACETS	0.957	0.86	1	0.957	0.86	1	CLONAL	1	TRUE	1	0.41	2		524	525	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612028	189612028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs900140738	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	116	414	1	ENST00000264731.3:c.1780C>T	p.Arg594Ter	p.R594*	ENST00000264731	NM_003722.4	594	Cga/Tga	14/14	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.41	2		415	547	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749491	41749491	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	141	468	0	ENST00000226382.2:c.304C>A	p.Arg102Ser	p.R102S	ENST00000226382	NM_003924.3	102	Cgc/Agc	2/3	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.41	2		468	656	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151648	55151648	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	183	605	0	ENST00000257290.5:c.2434A>G	p.Lys812Glu	p.K812E	ENST00000257290	NM_006206.4	812	Aaa/Gaa	17/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.41	2		605	807	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565858	55565858	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	136	585	0	ENST00000288135.5:c.682G>T	p.Glu228Ter	p.E228*	ENST00000288135	NM_000222.2	228	Gaa/Taa	4/21	1	2	FACETS	0.845	0.769	0.925	0.845	0.769	0.925	CLONAL	1	TRUE	1	0.41	2		585	785	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55569934	55569934	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	81	441	0	ENST00000288135.5:c.801C>A	p.Phe267Leu	p.F267L	ENST00000288135	NM_000222.2	267	ttC/ttA	5/21	1	2	FACETS	0.968	0.858	1	0.968	0.858	1	CLONAL	1	TRUE	1	0.41	2		441	408	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980349	55980349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	104	584	1	ENST00000263923.4:c.742G>A	p.Ala248Thr	p.A248T	ENST00000263923	NM_002253.2	248	Gca/Aca	6/30	1	2	FACETS	0.807	0.723	0.894	0.807	0.723	0.894	CLONAL	1	TRUE	1	0.41	2		585	629	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197841	66197841	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs776432090	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	63	321	0	ENST00000273854.3:c.2858C>A	p.Ser953Tyr	p.S953Y	ENST00000273854	NM_004439.5	953	tCt/tAt	17/18	1	2	FACETS	0.813	0.706	0.928	0.813	0.706	0.928	CLONAL	1	TRUE	1	0.41	2		321	378	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213872	66213872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772452750	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	128	593	0	ENST00000273854.3:c.2558G>A	p.Arg853Gln	p.R853Q	ENST00000273854	NM_004439.5	853	cGa/cAa	15/18	1	2	FACETS	0.95	0.863	1	0.95	0.863	1	CLONAL	1	TRUE	1	0.41	2		593	657	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280068	66280068	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	73	368	0	ENST00000273854.3:c.1621C>T	p.Arg541Ter	p.R541*	ENST00000273854	NM_004439.5	541	Cga/Tga	7/18	1	2	FACETS	0.731	0.641	0.828	0.731	0.641	0.828	SUBCLONAL	1	TRUE	1	0.41	2		368	487	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383932	84383932	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	139	645	1	ENST00000321945.7:c.920C>A	p.Ser307Tyr	p.S307Y	ENST00000321945	NM_139076.2	307	tCt/tAt	9/9	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.41	2		646	656	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193889	106193889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1395976555	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	109	348	0	ENST00000380013.4:c.4351C>T	p.Arg1451Trp	p.R1451W	ENST00000380013	NM_001127208.2	1451	Cgg/Tgg	10/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.41	2		348	477	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159099	143159099	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1332432216	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	160	602	0	ENST00000262992.4:c.754C>T	p.Arg252Ter	p.R252*	ENST00000262992	NM_001101669.1	252	Cga/Tga	10/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.41	2		602	605	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522574	187522574	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	90	430	0	ENST00000441802.2:c.11489C>A	p.Ser3830Ter	p.S3830*	ENST00000441802	NM_005245.3	3830	tCa/tAa	21/27	1	2	FACETS	0.907	0.808	1	0.907	0.808	1	CLONAL	1	TRUE	1	0.41	2		430	484	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539630	187539630	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	80	489	0	ENST00000441802.2:c.8110T>G	p.Ser2704Ala	p.S2704A	ENST00000441802	NM_005245.3	2704	Tca/Gca	10/27	1	2	FACETS	0.883	0.781	0.992	0.883	0.781	0.992	CLONAL	1	TRUE	1	0.41	2		489	442	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540418	187540418	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	101	453	0	ENST00000441802.2:c.7322A>G	p.Asp2441Gly	p.D2441G	ENST00000441802	NM_005245.3	2441	gAc/gGc	10/27	1	2	FACETS	0.911	0.817	1	0.911	0.817	1	CLONAL	1	TRUE	1	0.41	2		453	541	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540974	187540974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752611276	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	113	368	2	ENST00000441802.2:c.6766G>A	p.Ala2256Thr	p.A2256T	ENST00000441802	NM_005245.3	2256	Gca/Aca	10/27	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.41	2		370	440	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629775	187629776	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	152	757	0	ENST00000441802.2:c.1206dup	p.Lys403Ter	p.K403*	ENST00000441802	NM_005245.3	402	-/T	2/27	1	2	FACETS	0.856	0.783	0.933	0.856	0.783	0.933	CLONAL	1	TRUE	1	0.41	2		757	866	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282603	1282603	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	151	663	2	ENST00000310581.5:c.1710G>T	p.Lys570Asn	p.K570N	ENST00000310581	NM_198253.2	570	aaG/aaT	3/16	1	2	FACETS	0.86	0.787	0.938	0.86	0.787	0.938	CLONAL	1	TRUE	1	0.41	2		665	856	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282650	1282650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1413965241	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	144	686	1	ENST00000310581.5:c.1663G>A	p.Glu555Lys	p.E555K	ENST00000310581	NM_198253.2	555	Gag/Aag	3/16	1	2	FACETS	0.787	0.718	0.86	0.787	0.718	0.86	SUBCLONAL	1	TRUE	1	0.41	2		687	892	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31435876	31435876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	28	445	0	ENST00000344624.3:c.3038C>T	p.Ala1013Val	p.A1013V	ENST00000344624		1013	gCa/gTa	22/33	1	2	FACETS	0.285	0.227	0.351	0.285	0.227	0.351	SUBCLONAL	1	TRUE	1	0.41	2		445	479	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515591	31515591	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	94	440	0	ENST00000344624.3:c.1028C>A	p.Ser343Tyr	p.S343Y	ENST00000344624		343	tCt/tAt	4/33	1	2	FACETS	0.88	0.786	0.98	0.88	0.786	0.98	CLONAL	1	TRUE	1	0.41	2		440	521	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35860991	35860991	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	82	412	0	ENST00000303115.3:c.120C>A	p.Phe40Leu	p.F40L	ENST00000303115	NM_002185.3	40	ttC/ttA	2/8	1	2	FACETS	0.815	0.721	0.915	0.815	0.721	0.915	CLONAL	1	TRUE	1	0.41	2		412	491	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944612	38944612	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs777123686	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	118	610	1	ENST00000357387.3:c.4849C>A	p.Leu1617Ile	p.L1617I	ENST00000357387	NM_152756.3	1617	Cta/Ata	36/38	1	2	FACETS	0.914	0.826	1	0.914	0.826	1	CLONAL	1	TRUE	1	0.41	2		611	630	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183255	56183255	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	132	563	1	ENST00000399503.3:c.4165T>A	p.Phe1389Ile	p.F1389I	ENST00000399503	NM_005921.1	1389	Ttt/Att	18/20	1	2	FACETS	0.985	0.896	1	0.985	0.896	1	CLONAL	1	TRUE	1	0.41	2		564	654	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	115	451	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.41	2		451	513	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649005	86649005	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	81	462	1	ENST00000274376.6:c.1285G>T	p.Glu429Ter	p.E429*	ENST00000274376	NM_002890.2	429	Gaa/Taa	9/25	1	2	FACETS	0.751	0.663	0.845	0.751	0.663	0.845	SUBCLONAL	1	TRUE	1	0.41	2		463	526	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86658429	86658429	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs181630831	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	66	360	0	ENST00000274376.6:c.1394G>A	p.Arg465His	p.R465H	ENST00000274376	NM_002890.2	465	cGt/cAt	10/25	1	2	FACETS	0.922	0.806	1	0.922	0.806	1	CLONAL	1	TRUE	1	0.41	2		360	349	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86667972	86667972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377099473	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	70	427	1	ENST00000274376.6:c.1736G>A	p.Arg579Gln	p.R579Q	ENST00000274376	NM_002890.2	579	cGg/cAg	13/25	1	2	FACETS	0.757	0.662	0.859	0.757	0.662	0.859	SUBCLONAL	1	TRUE	1	0.41	2		428	451	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86682712	86682712	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	37	306	0	ENST00000274376.6:c.2917G>T	p.Glu973Ter	p.E973*	ENST00000274376	NM_002890.2	973	Gaa/Taa	23/25	1	2	FACETS	0.532	0.44	0.635	0.532	0.44	0.635	SUBCLONAL	1	TRUE	1	0.41	2		306	339	SUCCESS
APC	324	MSKCC	GRCh37	5	112151262	112151262	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764841552	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	118	485	0	ENST00000257430.4:c.905G>A	p.Arg302Gln	p.R302Q	ENST00000257430	NM_000038.5	302	cGa/cAa	9/16	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.41	2		485	541	SUCCESS
APC	324	MSKCC	GRCh37	5	112178000	112178000	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768922431	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	101	452	0	ENST00000257430.4:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000257430	NM_000038.5	2237	Cga/Tga	16/16	1	2	FACETS	0.938	0.842	1	0.938	0.842	1	CLONAL	1	TRUE	1	0.41	2		452	525	SUCCESS
APC	324	MSKCC	GRCh37	5	112178211	112178211	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	89	369	2	ENST00000257430.4:c.6920C>A	p.Ser2307Ter	p.S2307*	ENST00000257430	NM_000038.5	2307	tCg/tAg	16/16	1	2	FACETS	0.969	0.863	1	0.969	0.863	1	CLONAL	1	TRUE	1	0.41	2		371	448	SUCCESS
APC	324	MSKCC	GRCh37	5	112179582	112179582	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	74	396	1	ENST00000257430.4:c.8291C>A	p.Ser2764Tyr	p.S2764Y	ENST00000257430	NM_000038.5	2764	tCt/tAt	16/16	1	2	FACETS	0.725	0.636	0.82	0.725	0.636	0.82	SUBCLONAL	1	TRUE	1	0.41	2		397	498	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665452	176665452	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1562245010	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	106	452	0	ENST00000439151.2:c.4136C>T	p.Pro1379Leu	p.P1379L	ENST00000439151	NM_022455.4	1379	cCg/cTg	7/23	1	2	FACETS	0.935	0.841	1	0.935	0.841	1	CLONAL	1	TRUE	1	0.41	2		452	553	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176715908	176715908	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	53	610	1	ENST00000439151.2:c.6240C>A	p.Phe2080Leu	p.F2080L	ENST00000439151	NM_022455.4	2080	ttC/ttA	21/23	1	2	FACETS	0.342	0.291	0.399	0.342	0.291	0.399	SUBCLONAL	1	TRUE	1	0.41	2		611	755	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170084	32170084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	42	717	1	ENST00000375023.3:c.3524C>T	p.Ala1175Val	p.A1175V	ENST00000375023	NM_004557.3	1175	gCc/gTc	21/30	1	2	FACETS	0.268	0.223	0.318	0.268	0.223	0.318	SUBCLONAL	1	TRUE	1	0.41	2		718	765	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185028	32185028	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140082058	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	147	584	0	ENST00000375023.3:c.1640G>A	p.Arg547Gln	p.R547Q	ENST00000375023	NM_004557.3	547	cGa/cAa	10/30	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.41	2		584	711	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748479	43748479	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45533131	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	134	329	1	ENST00000523873.1:c.433C>T	p.Arg145Ter	p.R145*	ENST00000523873		145	Cga/Tga	6/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.41	2		330	465	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109312010	109312010	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	41	690	1	ENST00000436639.2:c.1262C>A	p.Ser421Tyr	p.S421Y	ENST00000436639	NM_014454.2	421	tCt/tAt	8/10	1	2	FACETS	0.294	0.244	0.35	0.294	0.244	0.35	SUBCLONAL	1	TRUE	1	0.41	2		691	680	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020771	112020771	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374907658	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	137	442	0	ENST00000368678.4:c.800C>T	p.Ser267Leu	p.S267L	ENST00000368678		267	tCg/tTg	8/13	1	2	FACETS	0.904	0.824	0.989	0.904	0.824	0.989	CLONAL	1	TRUE	1	0.41	2		442	739	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117639408	117639408	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	107	601	0	ENST00000368508.3:c.5948A>C	p.Lys1983Thr	p.K1983T	ENST00000368508	NM_002944.2	1983	aAg/aCg	37/43	1	2	FACETS	0.838	0.753	0.927	0.838	0.753	0.927	CLONAL	1	TRUE	1	0.41	2		601	623	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662700	117662700	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	100	543	1	ENST00000368508.3:c.4765G>T	p.Glu1589Ter	p.E1589*	ENST00000368508	NM_002944.2	1589	Gaa/Taa	29/43	1	2	FACETS	0.895	0.802	0.993	0.895	0.802	0.993	CLONAL	1	TRUE	1	0.41	2		544	545	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700267	117700267	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	119	612	0	ENST00000368508.3:c.2552A>C	p.Asp851Ala	p.D851A	ENST00000368508	NM_002944.2	851	gAc/gCc	17/43	1	2	FACETS	0.963	0.871	1	0.963	0.871	1	CLONAL	1	TRUE	1	0.41	2		612	603	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715865	117715865	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	123	531	0	ENST00000368508.3:c.893A>C	p.Lys298Thr	p.K298T	ENST00000368508	NM_002944.2	298	aAa/aCa	9/43	1	2	FACETS	0.995	0.903	1	0.995	0.903	1	CLONAL	1	TRUE	1	0.41	2		531	603	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374327	81374327	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	40	346	0	ENST00000222390.5:c.735C>A	p.Phe245Leu	p.F245L	ENST00000222390	NM_000601.4	245	ttC/ttA	6/18	1	2	FACETS	0.437	0.363	0.519	0.437	0.363	0.519	SUBCLONAL	1	TRUE	1	0.41	2		346	447	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509723	106509723	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	112	504	0	ENST00000359195.3:c.1717G>T	p.Glu573Ter	p.E573*	ENST00000359195	NM_002649.2	573	Gaa/Taa	2/11	1	2	FACETS	0.992	0.895	1	0.992	0.895	1	CLONAL	1	TRUE	1	0.41	2		504	551	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864383	151864383	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	136	556	1	ENST00000262189.6:c.9598G>T	p.Glu3200Ter	p.E3200*	ENST00000262189	NM_170606.2	3200	Gaa/Taa	42/59	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.41	2		557	630	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205107	38205107	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	152	698	0	ENST00000317025.8:c.583G>T	p.Glu195Ter	p.E195*	ENST00000317025	NM_023034.1	195	Gaa/Taa	2/24	1	2	FACETS	0.906	0.83	0.987	0.906	0.83	0.987	CLONAL	1	TRUE	1	0.41	2		698	818	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980488	70980488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267601982	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	181	764	3	ENST00000276594.2:c.889G>A	p.Gly297Arg	p.G297R	ENST00000276594	NM_024504.3	297	Gga/Aga	4/8	1	2	FACETS	0.947	0.874	1	0.947	0.874	1	CLONAL	1	TRUE	1	0.41	2		767	932	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566057	141566057	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	167	682	1	ENST00000220592.5:c.1207G>T	p.Asp403Tyr	p.D403Y	ENST00000220592	NM_012154.3	403	Gat/Tat	10/19	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.41	2		683	772	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054631	5054631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760174050	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	95	394	0	ENST00000381652.3:c.683G>A	p.Arg228Gln	p.R228Q	ENST00000381652	NM_004972.3	228	cGa/cAa	7/25	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.41	2		394	421	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054768	5054768	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	67	472	1	ENST00000381652.3:c.820G>T	p.Glu274Ter	p.E274*	ENST00000381652	NM_004972.3	274	Gaa/Taa	7/25	1	2	FACETS	0.698	0.608	0.795	0.698	0.608	0.795	SUBCLONAL	1	TRUE	1	0.41	2		473	468	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5066740	5066740	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777015472	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	98	536	1	ENST00000381652.3:c.1277G>A	p.Arg426Gln	p.R426Q	ENST00000381652	NM_004972.3	426	cGa/cAa	10/25	1	2	FACETS	0.907	0.812	1	0.907	0.812	1	CLONAL	1	TRUE	1	0.41	2		537	527	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090886	5090886	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	42	217	0	ENST00000381652.3:c.3034G>T	p.Glu1012Ter	p.E1012*	ENST00000381652	NM_004972.3	1012	Gaa/Taa	22/25	1	2	FACETS	0.887	0.747	1	0.887	0.747	1	CLONAL	1	TRUE	1	0.41	2		217	231	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87322770	87322770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781137734	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	119	583	0	ENST00000277120.3:c.371G>A	p.Arg124Gln	p.R124Q	ENST00000277120		124	cGa/cAa	5/19	1	2	FACETS	0.86	0.777	0.947	0.86	0.777	0.947	CLONAL	1	TRUE	1	0.41	2		583	675	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891367	101891367	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	84	561	0	ENST00000374994.4:c.328G>T	p.Glu110Ter	p.E110*	ENST00000374994	NM_004612.2	110	Gaa/Taa	2/9	1	2	FACETS	0.691	0.611	0.776	0.691	0.611	0.776	SUBCLONAL	1	TRUE	1	0.41	2		561	593	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916526	39916526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265777184	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	178	741	7	ENST00000378444.4:c.4477C>T	p.Arg1493Trp	p.R1493W	ENST00000378444	NM_001123385.1	1493	Cgg/Tgg	11/15	1	2	FACETS	0.936	0.862	1	0.936	0.862	1	CLONAL	1	TRUE	1	0.41	2		748	928	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931741	39931741	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	130	682	0	ENST00000378444.4:c.2858A>C	p.Lys953Thr	p.K953T	ENST00000378444	NM_001123385.1	953	aAa/aCa	4/15	1	2	FACETS	0.819	0.744	0.899	0.819	0.744	0.899	CLONAL	1	TRUE	1	0.41	2		682	774	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430353	47430353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773486607	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	128	719	3	ENST00000377045.4:c.1628G>A	p.Arg543Gln	p.R543Q	ENST00000377045	NM_001654.4	543	cGg/cAg	15/16	1	2	FACETS	0.796	0.722	0.875	0.796	0.722	0.875	SUBCLONAL	1	TRUE	1	0.41	2		722	784	SUCCESS
AR	367	MSKCC	GRCh37	X	66765883	66765883	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1213709903	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	125	787	0	ENST00000374690.3:c.895G>A	p.Ala299Thr	p.A299T	ENST00000374690	NM_000044.3	299	Gca/Aca	1/8	1	2	FACETS	0.721	0.652	0.793	0.721	0.652	0.793	SUBCLONAL	1	TRUE	1	0.41	2		787	846	SUCCESS
AR	367	MSKCC	GRCh37	X	66766507	66766507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746446953	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	126	600	0	ENST00000374690.3:c.1519G>A	p.Gly507Ser	p.G507S	ENST00000374690	NM_000044.3	507	Ggc/Agc	1/8	1	2	FACETS	0.903	0.819	0.991	0.903	0.819	0.991	CLONAL	1	TRUE	1	0.41	2		600	681	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888736	76888736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	116	669	2	ENST00000373344.5:c.5093G>A	p.Arg1698Gln	p.R1698Q	ENST00000373344	NM_000489.3	1698	cGg/cAg	19/35	1	2	FACETS	0.821	0.741	0.906	0.821	0.741	0.906	CLONAL	1	TRUE	1	0.41	2		671	689	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891508	76891508	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1557107880	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	120	663	0	ENST00000373344.5:c.4597A>G	p.Ile1533Val	p.I1533V	ENST00000373344	NM_000489.3	1533	Ata/Gta	16/35	1	2	FACETS	0.83	0.751	0.914	0.83	0.751	0.914	CLONAL	1	TRUE	1	0.41	2		663	705	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937587	76937587	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	73	515	0	ENST00000373344.5:c.3161C>A	p.Ser1054Tyr	p.S1054Y	ENST00000373344	NM_000489.3	1054	tCt/tAt	9/35	1	2	FACETS	0.705	0.618	0.799	0.705	0.618	0.799	SUBCLONAL	1	TRUE	1	0.41	2		515	505	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939051	76939051	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	115	636	1	ENST00000373344.5:c.1697C>A	p.Ser566Tyr	p.S566Y	ENST00000373344	NM_000489.3	566	tCt/tAt	9/35	1	2	FACETS	0.824	0.743	0.909	0.824	0.743	0.909	CLONAL	1	TRUE	1	0.41	2		637	681	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76949379	76949379	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	117	667	2	ENST00000373344.5:c.418G>T	p.Asp140Tyr	p.D140Y	ENST00000373344	NM_000489.3	140	Gat/Tat	6/35	1	2	FACETS	0.844	0.762	0.93	0.844	0.762	0.93	CLONAL	1	TRUE	1	0.41	2		669	676	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020155	123020155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778612322	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	211	719	0	ENST00000355640.3:c.643C>T	p.Arg215Cys	p.R215C	ENST00000355640		215	Cgt/Tgt	2/7	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.41	2		719	875	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123234427	123234427	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1304348952	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	96	609	0	ENST00000218089.9:c.3787C>A	p.Leu1263Ile	p.L1263I	ENST00000218089	NM_001042749.1	1263	Ctt/Att	35/35	1	2	FACETS	0.736	0.657	0.821	0.736	0.657	0.821	SUBCLONAL	1	TRUE	1	0.41	2		609	636	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861587	152861587	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	199	712	0	ENST00000406277.2:c.165G>T	p.Lys55Asn	p.K55N	ENST00000406277	NM_152274.4	55	aaG/aaT	4/7	1		FACETS		0.98	1				CLONAL	1	TRUE	1	0.41	2		712	844	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047507	49047507	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1131690906	NA	P-0025650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	335	495	0	ENST00000267163.4:c.2501C>A	p.Ser834Ter	p.S834*	ENST00000267163	NM_000321.2	834	tCa/tAa	24/27	0.811393232840087	1	FACETS	0.96	0.923	0.997	0.96	0.923	0.997	CLONAL	1	TRUE	0	0.811393232840087	1		495	511	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560468	65560468	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	413	543	0	ENST00000358664.4:c.129del	p.His44ThrfsTer21	p.H44Tfs*21	ENST00000358664	NM_002382.4	43	ttT/tt	3/5	NA	2	FACETS	0.943	0.9	0.987			1	INDETERMINATE	1	TRUE	NA	0.811393232840087	2		543	1079	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341195	8341195	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755582635	NA	P-0025650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	341	539	1	ENST00000356435.5:c.5021G>A	p.Arg1674His	p.R1674H	ENST00000356435		1674	cGc/cAc	30/35	1	2	FACETS	0.972	0.923	1	0.972	0.923	1	CLONAL	1	TRUE	1	0.811393232840087	2		540	865	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100784	8100784	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	105	595	0	ENST00000346208.3:c.758C>A	p.Pro253His	p.P253H	ENST00000346208		253	cCc/cAc	3/6	0.193931855068294	2	FACETS	1	0.896	1	0.501	0.448	0.557	CLONAL	1	TRUE	0	0.220490504891206	2		595	951	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118836	115118836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1430142395	NA	P-0025651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	50	480	1	ENST00000257566.3:c.505C>T	p.Arg169Trp	p.R169W	ENST00000257566	NM_016569.3	169	Cgg/Tgg	2/8	0.212933193210493	1	FACETS	0.498	0.421	0.583	0.498	0.421	0.583	SUBCLONAL	1	TRUE	0	0.220490504891206	1		481	810	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579374	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1060501195	NA	P-0025651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	116	639	0	ENST00000269305.4:c.313G>C	p.Gly105Arg	p.G105R	ENST00000269305	NM_001126112.2	105	Ggc/Cgc	4/11	0.212933193210493	1	FACETS	0.877	0.788	0.97	0.877	0.788	0.97	CLONAL	1	TRUE	0	0.220490504891206	1		639	1068	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1952899	1952899	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs758747210	NA	P-0025651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	118	501	0	ENST00000382891.5:c.1982G>T	p.Gly661Val	p.G661V	ENST00000382891	NM_133335.3	661	gGa/gTa	10/22	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.220490504891206	2		501	1046	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38148195	38148195	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	79	409	0	ENST00000317025.8:c.2916A>T	p.Arg972Ser	p.R972S	ENST00000317025	NM_023034.1	972	agA/agT	17/24	0.212933193210493	1	FACETS	0.908	0.799	1	0.908	0.799	1	CLONAL	1	TRUE	0	0.220490504891206	1		409	702	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995601	68995601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	142	583	0	ENST00000288368.4:c.2005C>T	p.Leu669Phe	p.L669F	ENST00000288368	NM_024870.2	669	Ctt/Ttt	18/40	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.220490504891206	2		583	1022	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970966	21970967	+	missense_variant	Missense_Mutation	DNP	CG	CG	AT	novel	NA	P-0025651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	128	466	2	ENST00000304494.5:c.391_392delinsAT	p.Arg131Ile	p.R131I	ENST00000304494	NM_000077.4	131	CGc/ATc	2/3	0.212933193210493	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.220490504891206	1		468	848	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971026	21971026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	107	316	0	ENST00000304494.5:c.332G>T	p.Gly111Val	p.G111V	ENST00000304494	NM_000077.4	111	gGc/gTc	2/3	0.212933193210493				0.983	1				CLONAL	1	TRUE	0	0.220490504891206	1		316	581	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0025652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	146	607	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.235325154873532	4	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	2	0.235325154873532	4		607	735	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0025652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	79	569	1	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	0.235325154873532	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.235325154873532	1		570	520	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165701	185165701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	56	471	1	ENST00000265026.3:c.976C>T	p.Arg326Trp	p.R326W	ENST00000265026	NM_004721.4	326	Cgg/Tgg	5/14	1	2	FACETS	0.908	0.779	1	0.908	0.779	1	CLONAL	1	TRUE	1	0.235325154873532	2		472	524	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256326	16256326	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	108	645	0	ENST00000375759.3:c.3591A>T	p.Lys1197Asn	p.K1197N	ENST00000375759	NM_015001.2	1197	aaA/aaT	11/15	0.20144514518014	3	FACETS	0.775	0.696	0.858	0.775	0.696	0.858	SUBCLONAL	2	TRUE	1	0.235325154873532	3		645	662	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125462	47125462	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	30	484	0	ENST00000409792.3:c.5808C>A	p.Cys1936Ter	p.C1936*	ENST00000409792	NM_014159.6	1936	tgC/tgA	12/21	1	2	FACETS	0.538	0.433	0.658	0.538	0.433	0.658	SUBCLONAL	1	TRUE	1	0.235325154873532	2		484	474	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14028634	14028634	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	127	564	0	ENST00000405192.2:c.44A>G	p.Asn15Ser	p.N15S	ENST00000405192	NM_001163147.1	15	aAt/aGt	2/12	0.235325154873532	4	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	2	0.235325154873532	4		564	619	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593603	55593603	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913235	NA	P-0025653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	233	440	0	ENST00000288135.5:c.1669T>C	p.Trp557Arg	p.W557R	ENST00000288135	NM_000222.2	557	Tgg/Cgg	11/21	1	2	FACETS	0.982	0.924	1	0.982	0.924	1	CLONAL	1	TRUE	1	0.834140242740763	2		440	569	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	60	387	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.496654594349609	2		387	197	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0025654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	240	296	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.496654594349609	3	FACETS	0.995	0.937	1	0.995	0.937	1	CLONAL	2	TRUE	1	0.496654594349609	3		296	606	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102196062	102196062	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	37	302	0	ENST00000263464.3:c.822G>T	p.Glu274Asp	p.E274D	ENST00000263464	NM_001165.4	274	gaG/gaT	2/9	0.425776882404174	1	FACETS	0.399	0.329	0.476	0.399	0.329	0.476	SUBCLONAL	1	TRUE	0	0.425776882404174	1		302	343	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646921	23646921	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	65	687	0	ENST00000261584.4:c.946C>A	p.Pro316Thr	p.P316T	ENST00000261584	NM_024675.3	316	Ccc/Acc	4/13	NA	2	FACETS	0.526	0.456	0.601			1	INDETERMINATE	1	TRUE	NA	0.425776882404174	2		687	581	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832563	72832563	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	21	430	0	ENST00000268489.5:c.4018C>A	p.Gln1340Lys	p.Q1340K	ENST00000268489	NM_006885.3	1340	Caa/Aaa	9/10	1	2	FACETS	0.3	0.231	0.381	0.3	0.231	0.381	SUBCLONAL	1	TRUE	1	0.425776882404174	2		430	329	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182662958	182662958	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	40	467	0	ENST00000292782.4:c.704C>A	p.Ala235Glu	p.A235E	ENST00000292782	NM_020640.2	235	gCa/gAa	7/7	0.409873081323174	3	FACETS	0.577	0.48	0.685	0.288	0.24	0.343	SUBCLONAL	1	TRUE	1	0.425776882404174	3		467	395	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339940	70339940	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	23	273	0	ENST00000374080.3:c.473G>T	p.Trp158Leu	p.W158L	ENST00000374080		158	tGg/tTg	4/45	1	1	FACETS	0.253	0.197	0.318	0.253	0.197	0.318	SUBCLONAL	1	TRUE	0	0.425776882404174	1		273	336	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074279	8074279	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	43	533	0	ENST00000377482.5:c.380C>A	p.Thr127Asn	p.T127N	ENST00000377482	NM_018948.3	127	aCc/aAc	4/4	1	2	FACETS	0.434	0.363	0.513	0.434	0.363	0.513	SUBCLONAL	1	TRUE	1	0.425776882404174	2		533	465	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562792	21562792	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	26	460	0	ENST00000382592.4:c.1127C>A	p.Ala376Asp	p.A376D	ENST00000382592	NM_014572.2	376	gCc/gAc	4/8	1	2	FACETS	0.304	0.24	0.377	0.304	0.24	0.377	SUBCLONAL	1	TRUE	1	0.425776882404174	2		460	402	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418607	49418607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs980258889	NA	P-0025656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	120	580	0	ENST00000301067.7:c.15907C>T	p.Arg5303Cys	p.R5303C	ENST00000301067	NM_003482.3	5303	Cgc/Tgc	49/54	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.425776882404174	2		580	541	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433129	49433129	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	27	689	0	ENST00000301067.7:c.8242C>A	p.Leu2748Ile	p.L2748I	ENST00000301067	NM_003482.3	2748	Ctt/Att	33/54	1	2	FACETS	0.249	0.197	0.308	0.249	0.197	0.308	SUBCLONAL	1	TRUE	1	0.425776882404174	2		689	510	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590990	95590990	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	11	243	0	ENST00000393063.1:c.919C>A	p.Arg307Ser	p.R307S	ENST00000393063	NM_030621.3	307	Cgt/Agt	9/28	0.381428173895185	2	FACETS	0.266	0.184	0.369	0.133	0.092	0.185	SUBCLONAL	1	TRUE	0	0.425776882404174	2		243	194	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2097742	2097742	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	36	668	0	ENST00000219066.1:c.107C>A	p.Pro36His	p.P36H	ENST00000219066	NM_002528.5	36	cCc/cAc	1/6	NA	2	FACETS	0.347	0.285	0.417			1	INDETERMINATE	1	TRUE	NA	0.425776882404174	2		668	487	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826550	50826560	+	frameshift_variant	Frame_Shift_Del	DEL	GACTTTAAACT	GACTTTAAACT	TCG	novel	NA	P-0025656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	91	510	1	ENST00000398568.2:c.2275_2285delinsTCG	p.Asp759SerfsTer3	p.D759Sfs*3	ENST00000398568	NM_001042412.1	759	GACTTTAAACTa/TCGa	15/18	0.425776882404174	1	FACETS	0.937	0.839	1	0.937	0.839	1	CLONAL	1	TRUE	0	0.425776882404174	1		511	359	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016664	12016664	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	21	416	0	ENST00000353533.5:c.800G>T	p.Arg267Met	p.R267M	ENST00000353533	NM_003010.3	267	aGg/aTg	7/11	1	2	FACETS	0.261	0.2	0.332	0.261	0.2	0.332	SUBCLONAL	1	TRUE	1	0.425776882404174	2		416	378	SUCCESS
CALR	811	MSKCC	GRCh37	19	13049531	13049531	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	33	739	1	ENST00000316448.5:c.38G>T	p.Gly13Val	p.G13V	ENST00000316448	NM_004343.3	13	gGc/gTc	1/9	1	2	FACETS	0.24	0.195	0.291	0.24	0.195	0.291	SUBCLONAL	1	TRUE	1	0.425776882404174	2		740	646	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661096	227661096	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	35	626	0	ENST00000305123.5:c.2359C>A	p.Gln787Lys	p.Q787K	ENST00000305123	NM_005544.2	787	Cag/Aag	1/2	0.409873081323174	3	FACETS	0.321	0.262	0.387	0.16	0.131	0.194	SUBCLONAL	1	TRUE	1	0.425776882404174	3		626	622	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268368	46268368	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	23	428	0	ENST00000371998.3:c.2755G>T	p.Asp919Tyr	p.D919Y	ENST00000371998		919	Gac/Tac	15/23	0.425776882404174	1	FACETS	0.203	0.158	0.256	0.203	0.158	0.256	SUBCLONAL	1	TRUE	0	0.425776882404174	1		428	419	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665530	138665530	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	21	439	0	ENST00000330315.3:c.35C>A	p.Ala12Glu	p.A12E	ENST00000330315	NM_023067.3	12	gCg/gAg	1/1	0.409873081323174	3	FACETS	0.309	0.237	0.393	0.155	0.118	0.197	SUBCLONAL	1	TRUE	1	0.425776882404174	3		439	387	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247190	153247190	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	82	352	1	ENST00000281708.4:c.1612C>T	p.Gln538Ter	p.Q538*	ENST00000281708	NM_033632.3	538	Cag/Tag	10/12	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.425776882404174	2		353	378	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324627	31324635	+	inframe_deletion	In_Frame_Del	DEL	CGAACCTCA	CGAACCTCA	-	novel	NA	P-0025656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	85	368	0	ENST00000412585.2:c.173_181del	p.Val58_Phe60del	p.V58_F60del	ENST00000412585	NM_005514.6	58	gTGAGGTTCGac/gac	2/8	0.314130830569814	3	FACETS	0.791	0.707	0.879	0.528	0.471	0.586	SUBCLONAL	2	TRUE	0	0.425776882404174	3		368	306	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044544	47044544	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	18	373	0	ENST00000377604.3:c.2041G>T	p.Asp681Tyr	p.D681Y	ENST00000377604	NM_001204468.1	681	Gat/Tat	18/24	1	1	FACETS	0.189	0.142	0.245	0.189	0.142	0.245	SUBCLONAL	1	TRUE	0	0.425776882404174	1		373	352	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0025659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	48	375	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	1	0.15	2		375	636	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198307	185198307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374643532	NA	P-0025659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	47	434	0	ENST00000265026.3:c.2789G>A	p.Arg930His	p.R930H	ENST00000265026	NM_004721.4	930	cGt/cAt	13/14	1	2	FACETS	0.954	0.803	1	0.954	0.803	1	CLONAL	1	TRUE	1	0.15	2		434	657	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2107112	2107112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45517130	NA	P-0025659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	48	549	0	ENST00000219476.3:c.781C>T	p.Arg261Trp	p.R261W	ENST00000219476	NM_000548.3	261	Cgg/Tgg	9/42	1	2	FACETS	0.9	0.759	1	0.9	0.759	1	CLONAL	1	TRUE	1	0.15	2		549	711	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845649	68845649	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	75	652	0	ENST00000261769.5:c.895G>A	p.Ala299Thr	p.A299T	ENST00000261769	NM_004360.3	299	Gcc/Acc	7/16	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.15	2		652	899	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	125	284	1	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.935	0.848	1	0.935	0.848	1	CLONAL	1	TRUE	1	0.41	2		285	652	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	67	314	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.936	0.819	1	0.936	0.819	1	CLONAL	1	TRUE	1	0.41	2		314	349	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	142	506	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	0.92	0.839	1	0.92	0.839	1	CLONAL	1	TRUE	1	0.41	2		506	753	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134988	41134988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	20	222	1	ENST00000379561.5:c.640C>T	p.Arg214Cys	p.R214C	ENST00000379561	NM_002015.3	214	Cgt/Tgt	2/3	1	2	FACETS	0.323	0.247	0.412	0.323	0.247	0.412	SUBCLONAL	1	TRUE	1	0.41	2		223	302	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	15	375	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.157	0.114	0.21	0.157	0.114	0.21	SUBCLONAL	1	TRUE	1	0.41	2		375	465	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540074	187540074	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs921535768	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	67	788	0	ENST00000441802.2:c.7666C>T	p.Arg2556Ter	p.R2556*	ENST00000441802	NM_005245.3	2556	Cga/Tga	10/27	1	2	FACETS	0.667	0.581	0.76	0.667	0.581	0.76	SUBCLONAL	1	TRUE	1	0.41	2		788	490	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	54	176	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.41	2		176	255	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518099	8518099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764400127	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	16	337	0	ENST00000356435.5:c.1292C>T	p.Ser431Leu	p.S431L	ENST00000356435		431	tCg/tTg	10/35	1	2	FACETS	0.154	0.113	0.204	0.154	0.113	0.204	SUBCLONAL	1	TRUE	1	0.41	2		337	506	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778972	9778972	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1214315014	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	59	294	0	ENST00000377346.4:c.1241C>T	p.Ala414Val	p.A414V	ENST00000377346	NM_005026.3	414	gCg/gTg	9/24	1	2	FACETS	0.672	0.58	0.772	0.672	0.58	0.772	SUBCLONAL	1	TRUE	1	0.41	2		294	428	SUCCESS
APC	324	MSKCC	GRCh37	5	112157650	112157650	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1060503333	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	99	451	0	ENST00000257430.4:c.1370C>A	p.Ser457Ter	p.S457*	ENST00000257430	NM_000038.5	457	tCa/tAa	11/16	1	2	FACETS	0.988	0.886	1	0.988	0.886	1	CLONAL	1	TRUE	1	0.41	2		451	489	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	493276	493276	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	40	497	0	ENST00000399788.2:c.287A>C	p.Lys96Thr	p.K96T	ENST00000399788	NM_001042603.1	96	aAa/aCa	3/28	1	2	FACETS	0.278	0.23	0.332	0.278	0.23	0.332	SUBCLONAL	1	TRUE	1	0.41	2		497	702	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692791	89692791	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1114167623	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	49	328	0	ENST00000371953.3:c.275A>G	p.Asp92Gly	p.D92G	ENST00000371953	NM_000314.4	92	gAc/gGc	5/9	1	2	FACETS	0.675	0.574	0.786	0.675	0.574	0.786	SUBCLONAL	1	TRUE	1	0.41	2		328	354	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881438	48881438	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	42	203	1	ENST00000267163.4:c.160G>T	p.Glu54Ter	p.E54*	ENST00000267163	NM_000321.2	54	Gaa/Taa	2/27	1	2	FACETS	0.833	0.701	0.977	0.833	0.701	0.977	CLONAL	1	TRUE	1	0.41	2		204	246	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729636	41729636	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	98	317	0	ENST00000242208.4:c.893G>A	p.Arg298Gln	p.R298Q	ENST00000242208	NM_002192.2	298	cGg/cAg	3/3	1	2	FACETS	0.921	0.825	1	0.921	0.825	1	CLONAL	1	TRUE	1	0.41	2		317	519	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518437	204518437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201947927	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	97	345	0	ENST00000367182.3:c.1100C>T	p.Ser367Leu	p.S367L	ENST00000367182	NM_001278516.1	367	tCg/tTg	11/11	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.41	2		345	458	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181765	56181765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1287268127	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	8	280	1	ENST00000399503.3:c.3989C>T	p.Ser1330Leu	p.S1330L	ENST00000399503	NM_005921.1	1330	tCg/tTg	17/20	1	2	FACETS	0.118	0.075	0.173	0.118	0.075	0.173	SUBCLONAL	1	TRUE	1	0.41	2		281	332	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752839	57752839	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	95	377	0	ENST00000274289.3:c.1089C>A	p.Phe363Leu	p.F363L	ENST00000274289	NM_006622.3	363	ttC/ttA	8/14	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.41	2		377	448	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115600	108115600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772821016	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	64	482	0	ENST00000278616.4:c.748C>T	p.Arg250Ter	p.R250*	ENST00000278616	NM_000051.3	250	Cga/Tga	7/63	1	2	FACETS	0.627	0.544	0.717	0.627	0.544	0.717	SUBCLONAL	1	TRUE	1	0.41	2		482	498	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720803	89720804	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs786204892	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	25	256	0	ENST00000371953.3:c.955dup	p.Thr319AsnfsTer6	p.T319Nfs*6	ENST00000371953	NM_000314.4	318	-/A	8/9	1	2	FACETS	0.552	0.437	0.682	0.552	0.437	0.682	SUBCLONAL	1	TRUE	1	0.41	2		256	221	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711911	89711911	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	132	497	0	ENST00000371953.3:c.529T>G	p.Tyr177Asp	p.Y177D	ENST00000371953	NM_000314.4	177	Tat/Gat	6/9	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.41	2		497	542	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519938	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	46	316	0	ENST00000263967.3:c.1034A>C	p.Asn345Thr	p.N345T	ENST00000263967	NM_006218.2	345	aAt/aCt	5/21	1	2	FACETS	0.793	0.672	0.925	0.793	0.672	0.925	CLONAL	1	TRUE	1	0.41	2		316	283	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033753	48033753	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1553333707	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	44	311	0	ENST00000234420.5:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000234420	NM_000179.2	1322	Gaa/Taa	9/10	1	2	FACETS	0.767	0.647	0.897	0.767	0.647	0.897	SUBCLONAL	1	TRUE	1	0.41	2		311	280	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737579	145737579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199658221	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	118	424	3	ENST00000428558.2:c.3184C>T	p.Arg1062Trp	p.R1062W	ENST00000428558	NM_004260.3	1062	Cgg/Tgg	19/22	1	2	FACETS	0.837	0.756	0.922	0.837	0.756	0.922	CLONAL	1	TRUE	1	0.41	2		427	688	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215315	123215315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	95	481	0	ENST00000218089.9:c.2861G>A	p.Arg954His	p.R954H	ENST00000218089	NM_001042749.1	954	cGt/cAt	28/35	1	2	FACETS	0.659	0.587	0.736	0.659	0.587	0.736	SUBCLONAL	1	TRUE	1	0.41	2		481	703	SUCCESS
APC	324	MSKCC	GRCh37	5	112177368	112177368	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	68	287	0	ENST00000257430.4:c.6077C>A	p.Ser2026Tyr	p.S2026Y	ENST00000257430	NM_000038.5	2026	tCt/tAt	16/16	1	2	FACETS	0.981	0.86	1	0.981	0.86	1	CLONAL	1	TRUE	1	0.41	2		287	338	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050414	176050414	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148950158	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	16	261	0	ENST00000367669.3:c.1151G>A	p.Arg384Gln	p.R384Q	ENST00000367669	NM_022457.5	384	cGa/cAa	11/20	1	2	FACETS	0.274	0.202	0.36	0.274	0.202	0.36	SUBCLONAL	1	TRUE	1	0.41	2		261	285	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453531	138453531	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372119491	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	89	425	0	ENST00000289153.2:c.917G>A	p.Arg306Gln	p.R306Q	ENST00000289153	NM_006219.2	306	cGa/cAa	5/22	1	2	FACETS	0.908	0.809	1	0.908	0.809	1	CLONAL	1	TRUE	1	0.41	2		425	478	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525883	148525883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778968366	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	102	473	3	ENST00000320356.2:c.574G>A	p.Asp192Asn	p.D192N	ENST00000320356	NM_004456.4	192	Gat/Aat	6/20	1	2	FACETS	0.92	0.825	1	0.92	0.825	1	CLONAL	1	TRUE	1	0.41	2		476	541	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81902892	81902892	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	106	421	0	ENST00000359376.3:c.553G>T	p.Asp185Tyr	p.D185Y	ENST00000359376	NM_002661.3	185	Gat/Tat	6/33	1	2	FACETS	0.844	0.758	0.934	0.844	0.758	0.934	CLONAL	1	TRUE	1	0.41	2		421	613	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936083	178936083	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519927	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	101	441	0	ENST00000263967.3:c.1625A>G	p.Glu542Gly	p.E542G	ENST00000263967	NM_006218.2	542	gAa/gGa	10/21	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.41	2		441	462	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102056857	102056857	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	90	383	0	ENST00000282441.5:c.797G>A	p.Arg266His	p.R266H	ENST00000282441	NM_001130145.2	266	cGt/cAt	4/9	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.41	2		383	439	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504048	123504048	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	65	369	0	ENST00000371139.4:c.224G>T	p.Arg75Ile	p.R75I	ENST00000371139	NM_001114937.2	75	aGa/aTa	3/4	1	2	FACETS	0.893	0.779	1	0.893	0.779	1	CLONAL	1	TRUE	1	0.41	2		369	355	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165729	108165729	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs762083530	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	75	391	0	ENST00000278616.4:c.4852C>T	p.Arg1618Ter	p.R1618*	ENST00000278616	NM_000051.3	1618	Cga/Tga	32/63	1	2	FACETS	0.806	0.709	0.91	0.806	0.709	0.91	CLONAL	1	TRUE	1	0.41	2		391	454	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013719	170013719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388201066	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	144	525	0	ENST00000295797.4:c.1438C>T	p.Arg480Cys	p.R480C	ENST00000295797	NM_002740.5	480	Cgc/Tgc	15/18	1	2	FACETS	0.944	0.862	1	0.944	0.862	1	CLONAL	1	TRUE	1	0.41	2		525	744	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56409144	56409144	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	18	391	0	ENST00000348428.3:c.1651C>T	p.Arg551Ter	p.R551*	ENST00000348428	NM_006785.3	551	Cga/Tga	14/17	1	2	FACETS	0.268	0.201	0.347	0.268	0.201	0.347	SUBCLONAL	1	TRUE	1	0.41	2		391	328	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803500	32803500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550712305	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	221	540	0	ENST00000374899.4:c.659G>A	p.Arg220Gln	p.R220Q	ENST00000374899	NM_018833.2	220	cGa/cAa	4/12	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.41	2		540	1050	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439638	51439638	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750990884	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	36	349	0	ENST00000262662.1:c.203G>A	p.Arg68Gln	p.R68Q	ENST00000262662		68	cGa/cAa	4/4	1	2	FACETS	0.32	0.263	0.385	0.32	0.263	0.385	SUBCLONAL	1	TRUE	1	0.41	2		349	548	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430824	78430824	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	127	500	0	ENST00000370768.2:c.565G>T	p.Glu189Ter	p.E189*	ENST00000370768	NM_003902.3	189	Gaa/Taa	8/20	1	2	FACETS	0.91	0.826	0.998	0.91	0.826	0.998	CLONAL	1	TRUE	1	0.41	2		500	681	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166161	118166161	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	93	282	0	ENST00000369448.3:c.671A>C	p.Asp224Ala	p.D224A	ENST00000369448	NM_017709.3	224	gAc/gCc	2/2	1	2	FACETS	0.982	0.877	1	0.982	0.877	1	CLONAL	1	TRUE	1	0.41	2		282	462	SUCCESS
FH	2271	MSKCC	GRCh37	1	241672031	241672031	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs863223996	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	86	485	1	ENST00000366560.3:c.610C>A	p.His204Asn	p.H204N	ENST00000366560	NM_000143.3	204	Cat/Aat	5/10	1	2	FACETS	0.992	0.882	1	0.992	0.882	1	CLONAL	1	TRUE	1	0.41	2		486	423	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851828	63851828	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs201944744	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	99	378	0	ENST00000279873.7:c.2606C>A	p.Ser869Tyr	p.S869Y	ENST00000279873	NM_032199.2	869	tCt/tAt	10/10	1	2	FACETS	0.668	0.596	0.744	0.668	0.596	0.744	SUBCLONAL	1	TRUE	1	0.41	2		378	723	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852049	63852049	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	117	405	0	ENST00000279873.7:c.2827T>G	p.Leu943Val	p.L943V	ENST00000279873	NM_032199.2	943	Tta/Gta	10/10	1	2	FACETS	0.888	0.802	0.978	0.888	0.802	0.978	CLONAL	1	TRUE	1	0.41	2		405	643	SUCCESS
ATM	472	MSKCC	GRCh37	11	108137941	108137941	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	73	392	0	ENST00000278616.4:c.2510C>A	p.Ser837Ter	p.S837*	ENST00000278616	NM_000051.3	837	tCa/tAa	17/63	1	2	FACETS	0.761	0.667	0.861	0.761	0.667	0.861	SUBCLONAL	1	TRUE	1	0.41	2		392	468	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186745	108186745	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659555	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	79	366	0	ENST00000278616.4:c.6103A>G	p.Thr2035Ala	p.T2035A	ENST00000278616	NM_000051.3	2035	Aca/Gca	42/63	1	2	FACETS	0.922	0.815	1	0.922	0.815	1	CLONAL	1	TRUE	1	0.41	2		366	418	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864173	57864173	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	92	387	0	ENST00000228682.2:c.1650C>A	p.Ser550Arg	p.S550R	ENST00000228682	NM_005269.2	550	agC/agA	12/12	1	2	FACETS	0.722	0.642	0.806	0.722	0.642	0.806	SUBCLONAL	1	TRUE	1	0.41	2		387	622	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117434	115117434	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	36	370	0	ENST00000257566.3:c.740A>G	p.Lys247Arg	p.K247R	ENST00000257566	NM_016569.3	247	aAa/aGa	4/8	1	2	FACETS	0.402	0.33	0.482	0.402	0.33	0.482	SUBCLONAL	1	TRUE	1	0.41	2		370	437	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32918727	32918727	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	56	283	0	ENST00000380152.3:c.6874G>T	p.Glu2292Ter	p.E2292*	ENST00000380152		2292	Gaa/Taa	12/27	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.41	2		283	261	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346959	73346959	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	21	314	0	ENST00000377767.4:c.1258T>G	p.Leu420Val	p.L420V	ENST00000377767	NM_014953.3	420	Tta/Gta	9/21	1	2	FACETS	0.278	0.214	0.354	0.278	0.214	0.354	SUBCLONAL	1	TRUE	1	0.41	2		314	368	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194832	30194832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1434470951	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	111	516	1	ENST00000331968.5:c.313C>T	p.Arg105Cys	p.R105C	ENST00000331968	NM_002742.2	105	Cgc/Tgc	2/18	1	2	FACETS	0.8	0.72	0.884	0.8	0.72	0.884	SUBCLONAL	1	TRUE	1	0.41	2		517	677	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060728	38060728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	167	610	0	ENST00000250448.2:c.1261G>A	p.Glu421Lys	p.E421K	ENST00000250448	NM_004496.3	421	Gaa/Aaa	2/2	1	2	FACETS	0.864	0.794	0.937	0.864	0.794	0.937	CLONAL	1	TRUE	1	0.41	2		610	943	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614469	38614469	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	113	495	0	ENST00000299084.4:c.235G>T	p.Asp79Tyr	p.D79Y	ENST00000299084	NM_152594.2	79	Gac/Tac	3/7	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.41	2		495	493	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961919	41961919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1566953349	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	22	320	0	ENST00000219905.7:c.827G>A	p.Ser276Asn	p.S276N	ENST00000219905	NM_001164273.1	276	aGc/aAc	2/24	1	2	FACETS	0.266	0.205	0.336	0.266	0.205	0.336	SUBCLONAL	1	TRUE	1	0.41	2		320	404	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782937	66782937	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	82	292	0	ENST00000307102.5:c.1166A>G	p.His389Arg	p.H389R	ENST00000307102	NM_002755.3	389	cAt/cGt	11/11	1	2	FACETS	0.797	0.705	0.895	0.797	0.705	0.895	SUBCLONAL	1	TRUE	1	0.41	2		292	502	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351238	89351238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1266962947	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	134	489	0	ENST00000301030.4:c.1712C>T	p.Thr571Met	p.T571M	ENST00000301030	NM_001256183.1	571	aCg/aTg	9/13	1	2	FACETS	0.742	0.674	0.814	0.742	0.674	0.814	SUBCLONAL	1	TRUE	1	0.41	2		489	881	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351419	89351419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	101	357	1	ENST00000301030.4:c.1531G>A	p.Asp511Asn	p.D511N	ENST00000301030	NM_001256183.1	511	Gac/Aac	9/13	1	2	FACETS	0.858	0.769	0.953	0.858	0.769	0.953	CLONAL	1	TRUE	1	0.41	2		358	574	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866671	37866671	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	145	584	0	ENST00000269571.5:c.838G>T	p.Glu280Ter	p.E280*	ENST00000269571		280	Gag/Tag	7/27	1	2	FACETS	0.728	0.664	0.796	0.728	0.664	0.796	SUBCLONAL	1	TRUE	1	0.41	2		584	971	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5260822	5260822	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	93	388	0	ENST00000357368.4:c.589A>C	p.Ile197Leu	p.I197L	ENST00000357368	NM_002850.3	197	Att/Ctt	7/38	1	2	FACETS	0.678	0.603	0.758	0.678	0.603	0.758	SUBCLONAL	1	TRUE	1	0.41	2		388	669	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254565	10254565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	50	462	0	ENST00000340748.4:c.2945G>A	p.Gly982Asp	p.G982D	ENST00000340748		982	gGc/gAc	28/40	1	2	FACETS	0.327	0.276	0.382	0.327	0.276	0.382	SUBCLONAL	1	TRUE	1	0.41	2		462	747	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295255	15295255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752312396	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	152	559	1	ENST00000263388.2:c.2417G>A	p.Arg806Gln	p.R806Q	ENST00000263388	NM_000435.2	806	cGa/cAa	16/33	1	2	FACETS	0.791	0.723	0.863	0.791	0.723	0.863	SUBCLONAL	1	TRUE	1	0.41	2		560	937	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349196	15349196	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	90	425	0	ENST00000263377.2:c.4081C>A	p.Leu1361Ile	p.L1361I	ENST00000263377	NM_058243.2	1361	Ctt/Att	20/20	1	2	FACETS	0.689	0.612	0.771	0.689	0.612	0.771	SUBCLONAL	1	TRUE	1	0.41	2		425	637	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068360	26068360	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	88	464	0	ENST00000435504.4:c.130A>C	p.Lys44Gln	p.K44Q	ENST00000435504		44	Aaa/Caa	2/13	1	2	FACETS	0.892	0.794	0.997	0.892	0.794	0.997	CLONAL	1	TRUE	1	0.41	2		464	481	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39237759	39237759	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	106	420	0	ENST00000402219.2:c.2476C>T	p.Arg826Ter	p.R826*	ENST00000402219	NM_005633.3	826	Cga/Tga	15/23	1	2	FACETS	0.942	0.847	1	0.942	0.847	1	CLONAL	1	TRUE	1	0.41	2		420	549	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278359	39278359	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	133	626	0	ENST00000402219.2:c.790G>A	p.Glu264Lys	p.E264K	ENST00000402219	NM_005633.3	264	Gaa/Aaa	6/23	1	2	FACETS	0.947	0.862	1	0.947	0.862	1	CLONAL	1	TRUE	1	0.41	2		626	685	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096314	178096314	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	119	409	1	ENST00000397062.3:c.1017C>A	p.Phe339Leu	p.F339L	ENST00000397062	NM_006164.4	339	ttC/ttA	5/5	1	2	FACETS	0.89	0.805	0.98	0.89	0.805	0.98	CLONAL	1	TRUE	1	0.41	2		410	652	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198260829	198260829	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	109	511	0	ENST00000335508.6:c.3490G>T	p.Asp1164Tyr	p.D1164Y	ENST00000335508	NM_012433.2	1164	Gac/Tac	23/25	1	2	FACETS	0.972	0.876	1	0.972	0.876	1	CLONAL	1	TRUE	1	0.41	2		511	547	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524496	44524496	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	72	257	1	ENST00000291552.4:c.61T>C	p.Tyr21His	p.Y21H	ENST00000291552	NM_006758.2	21	Tat/Cat	2/8	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.41	2		258	303	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89176370	89176370	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	46	416	0	ENST00000336596.2:c.100G>T	p.Asp34Tyr	p.D34Y	ENST00000336596	NM_005233.5	34	Gat/Tat	2/17	1	2	FACETS	0.62	0.524	0.725	0.62	0.524	0.725	SUBCLONAL	1	TRUE	1	0.41	2		416	362	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480399	89480399	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	153	235	0	ENST00000336596.2:c.2236G>T	p.Asp746Tyr	p.D746Y	ENST00000336596	NM_005233.5	746	Gac/Tac	13/17	1	2	FACETS	0.882	0.815	0.95	1	0.991	1	CLONAL	2	TRUE	1	0.41	2		235	423	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119585471	119585471	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	63	323	0	ENST00000316626.5:c.914C>A	p.Ser305Ter	p.S305*	ENST00000316626		305	tCg/tAg	9/12	1	2	FACETS	0.899	0.782	1	0.899	0.782	1	CLONAL	1	TRUE	1	0.41	2		323	342	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127349	55127349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	133	462	0	ENST00000257290.5:c.137C>A	p.Ser46Tyr	p.S46Y	ENST00000257290	NM_006206.4	46	tCt/tAt	3/23	1	2	FACETS	0.854	0.776	0.935	0.854	0.776	0.935	CLONAL	1	TRUE	1	0.41	2		462	760	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535355	66535355	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	39	337	1	ENST00000273854.3:c.106C>T	p.Arg36Ter	p.R36*	ENST00000273854	NM_004439.5	36	Cga/Tga	1/18	1	2	FACETS	0.287	0.237	0.343	0.287	0.237	0.343	SUBCLONAL	1	TRUE	1	0.41	2		338	662	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383743	84383743	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	141	540	1	ENST00000321945.7:c.1109C>T	p.Ser370Phe	p.S370F	ENST00000321945	NM_139076.2	370	tCt/tTt	9/9	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.41	2		541	646	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629272	187629272	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	111	497	1	ENST00000441802.2:c.1710G>T	p.Glu570Asp	p.E570D	ENST00000441802	NM_005245.3	570	gaG/gaT	2/27	1	2	FACETS	0.692	0.622	0.767	0.692	0.622	0.767	SUBCLONAL	1	TRUE	1	0.41	2		498	782	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970800	79970800	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	52	235	0	ENST00000265081.6:c.1028-2A>C		p.X343_splice	ENST00000265081	NM_002439.4	343			1	2	FACETS	0.995	0.855	1	0.995	0.855	1	CLONAL	1	TRUE	1	0.41	2		235	255	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43742126	43742126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1193943585	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	183	584	0	ENST00000523873.1:c.115G>A	p.Glu39Lys	p.E39K	ENST00000523873		39	Gaa/Aaa	2/8	1	2	FACETS	0.886	0.818	0.958	0.886	0.818	0.958	CLONAL	1	TRUE	1	0.41	2		584	1007	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109314029	109314029	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	80	463	1	ENST00000436639.2:c.1194C>A	p.Phe398Leu	p.F398L	ENST00000436639	NM_014454.2	398	ttC/ttA	7/10	1	2	FACETS	0.823	0.727	0.926	0.823	0.727	0.926	CLONAL	1	TRUE	1	0.41	2		464	474	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622286	117622286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	104	499	0	ENST00000368508.3:c.6584C>T	p.Thr2195Ile	p.T2195I	ENST00000368508	NM_002944.2	2195	aCc/aTc	42/43	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.41	2		499	431	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963878	2963878	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	37	490	0	ENST00000396946.4:c.1929C>A	p.Phe643Leu	p.F643L	ENST00000396946	NM_032415.4	643	ttC/ttA	15/25	1	2	FACETS	0.247	0.203	0.297	0.247	0.203	0.297	SUBCLONAL	1	TRUE	1	0.41	2		490	730	SUCCESS
MET	4233	MSKCC	GRCh37	7	116422147	116422147	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	89	417	0	ENST00000397752.3:c.3628T>G	p.Cys1210Gly	p.C1210G	ENST00000397752	NM_000245.2	1210	Tgt/Ggt	18/21	1	2	FACETS	0.936	0.833	1	0.936	0.833	1	CLONAL	1	TRUE	1	0.41	2		417	464	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846335	128846335	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	106	426	0	ENST00000249373.3:c.1171T>G	p.Phe391Val	p.F391V	ENST00000249373	NM_005631.4	391	Ttt/Gtt	6/12	1	2	FACETS	0.749	0.672	0.831	0.749	0.672	0.831	SUBCLONAL	1	TRUE	1	0.41	2		426	690	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525974	148525974	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	73	369	0	ENST00000320356.2:c.485-2A>C		p.X162_splice	ENST00000320356	NM_004456.4	162			1	2	FACETS	0.877	0.771	0.991	0.877	0.771	0.991	CLONAL	1	TRUE	1	0.41	2		369	406	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5055781	5055781	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	83	362	0	ENST00000381652.3:c.1049A>C	p.Lys350Thr	p.K350T	ENST00000381652	NM_004972.3	350	aAa/aCa	8/25	1	2	FACETS	0.995	0.883	1	0.995	0.883	1	CLONAL	1	TRUE	1	0.41	2		362	407	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635191	87635191	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367769334	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	126	412	0	ENST00000277120.3:c.2243C>T	p.Thr748Met	p.T748M	ENST00000277120		748	aCg/aTg	18/19	1	2	FACETS	0.877	0.795	0.963	0.877	0.795	0.963	CLONAL	1	TRUE	1	0.41	2		412	701	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929330	44929330	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	143	560	0	ENST00000377967.4:c.2430G>T	p.Lys810Asn	p.K810N	ENST00000377967	NM_021140.2	810	aaG/aaT	17/29	1	2	FACETS	0.812	0.74	0.887	0.812	0.74	0.887	CLONAL	1	TRUE	1	0.41	2		560	859	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937437	76937437	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	91	568	0	ENST00000373344.5:c.3311G>T	p.Arg1104Ile	p.R1104I	ENST00000373344	NM_000489.3	1104	aGa/aTa	9/35	1	2	FACETS	0.893	0.796	0.996	0.893	0.796	0.996	CLONAL	1	TRUE	1	0.41	2		568	497	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0025663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	57	215	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.256739696510306	3	FACETS	0.969	0.834	1			1	CLONAL	1	TRUE	NA	0.339853906943685	3		215	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912657	NA	P-0025663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	72	473	0	ENST00000269305.4:c.814G>C	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ctg	8/11	0.31756834841691	1	FACETS	0.785	0.688	0.889	0.785	0.688	0.889	SUBCLONAL	1	TRUE	0	0.339853906943685	1		473	448	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157256628	157256628	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	86	264	0	ENST00000346085.5:c.1955G>C	p.Arg652Thr	p.R652T	ENST00000346085	NM_020732.3	652	aGa/aCa	5/20	1	2	FACETS	0.445	0.394	0.499	0.445	0.394	0.499	SUBCLONAL	1	TRUE	1	0.736161777266387	2		264	525	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413556	32413556	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	282	342	0	ENST00000332351.3:c.1394A>G	p.His465Arg	p.H465R	ENST00000332351	NM_024426.4	465	cAc/cGc	9/10	0.361822790823287	1	FACETS	0.812	0.771	0.854	0.812	0.771	0.854	INDETERMINATE	1	TRUE	0	0.736161777266387	1		342	596	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446072	49446073	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0025664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	298	645	3	ENST00000301067.7:c.1392_1393dup	p.Ser465TyrfsTer466	p.S465Yfs*466	ENST00000301067	NM_003482.3	465	tca/tATca	10/54	1	2	FACETS	0.872	0.823	0.922	0.872	0.823	0.922	CLONAL	1	TRUE	1	0.736161777266387	2		648	928	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221984	1221984	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	209	391	0	ENST00000326873.7:c.899T>A	p.Ile300Asn	p.I300N	ENST00000326873	NM_000455.4	300	aTc/aAc	7/10	0.736161777266387	1	FACETS	0.98	0.927	1	0.98	0.927	1	CLONAL	1	TRUE	0	0.736161777266387	1		391	366	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602669	10602669	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	145	487	1	ENST00000171111.5:c.909G>C	p.Lys303Asn	p.K303N	ENST00000171111	NM_203500.1	303	aaG/aaC	3/6	1	2	FACETS	0.568	0.519	0.619	0.568	0.519	0.619	SUBCLONAL	1	TRUE	1	0.736161777266387	2		488	694	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714491	40714491	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	141	238	1	ENST00000373198.4:c.3906C>G	p.Phe1302Leu	p.F1302L	ENST00000373198	NM_133170.3	1302	ttC/ttG	29/32	0.639482796170656	3	FACETS	0.905	0.828	0.985	0.453	0.414	0.493	CLONAL	1	TRUE	1	0.736161777266387	3		239	579	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447775	187447775	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779270221	NA	P-0025664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	96	285	0	ENST00000232014.4:c.418C>T	p.Arg140Cys	p.R140C	ENST00000232014	NM_001130845.1	140	Cgt/Tgt	5/10	0.736161777266387	3	FACETS	0.505	0.45	0.564	0.253	0.225	0.282	SUBCLONAL	1	TRUE	1	0.736161777266387	3		285	706	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244148	153244148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	123	381	1	ENST00000281708.4:c.2009G>A	p.Gly670Glu	p.G670E	ENST00000281708	NM_033632.3	670	gGa/gAa	12/12	0.736161777266387	1	FACETS	0.488	0.444	0.533	0.488	0.444	0.533	SUBCLONAL	1	TRUE	0	0.736161777266387	1		382	433	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	113	387	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.701798055933886	2		387	301	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	271	435	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.917	0.863	0.972	0.917	0.863	0.972	CLONAL	1	TRUE	1	0.701798055933886	2		435	842	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295825	212295825	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	182	386	0	ENST00000342788.4:c.2488G>A	p.Gly830Arg	p.G830R	ENST00000342788	NM_005235.2	830	Gga/Aga	21/28	1	2	FACETS	0.9	0.836	0.967	0.9	0.836	0.967	CLONAL	1	TRUE	1	0.701798055933886	2		386	576	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59878691	59878691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	261	474	1	ENST00000259008.2:c.1063G>A	p.Ala355Thr	p.A355T	ENST00000259008	NM_032043.2	355	Gcc/Acc	8/20	1	2	FACETS	0.972	0.915	1	0.972	0.915	1	CLONAL	1	TRUE	1	0.701798055933886	2		475	765	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233052	55233052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201498575	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	86	317	2	ENST00000275493.2:c.1802G>A	p.Gly601Glu	p.G601E	ENST00000275493	NM_005228.3	601	gGa/gAa	15/28	0.666866355320062	3	FACETS	0.383	0.338	0.432	0.192	0.169	0.216	SUBCLONAL	1	TRUE	1	0.701798055933886	3		319	864	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074397	8074397	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	160	256	0	ENST00000377482.5:c.262C>T	p.Gln88Ter	p.Q88*	ENST00000377482	NM_018948.3	88	Caa/Taa	4/4	1	2	FACETS	0.894	0.826	0.964	0.894	0.826	0.964	CLONAL	1	TRUE	1	0.701798055933886	2		256	510	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591086	67591086	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	139	265	0	ENST00000274335.5:c.1679A>G	p.Asp560Gly	p.D560G	ENST00000274335		560	gAc/gGc	12/15	1	2	FACETS	0.976	0.897	1	0.976	0.897	1	CLONAL	1	TRUE	1	0.701798055933886	2		265	406	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	86	189	3	ENST00000256196.4:c.68G>A	p.Gly23Asp	p.G23D	ENST00000256196		23	gGc/gAc	1/6	1	2	FACETS	0.732	0.653	0.814	0.732	0.653	0.814	SUBCLONAL	1	TRUE	1	0.701798055933886	2		192	335	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984290	7984290	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	192	349	0	ENST00000319144.4:c.439C>T	p.Arg147Ter	p.R147*	ENST00000319144	NM_001139.2	147	Cga/Tga	4/15	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.701798055933886	2		349	544	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2492117	2492117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs944782838	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	81	568	0	ENST00000355716.4:c.515C>T	p.Pro172Leu	p.P172L	ENST00000355716	NM_003820.2	172	cCc/cTc	5/8	1	2	FACETS	0.277	0.244	0.314	0.277	0.244	0.314	SUBCLONAL	1	TRUE	1	0.701798055933886	2		568	832	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047163	77047163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	93	461	0	ENST00000356341.3:c.1381G>A	p.Glu461Lys	p.E461K	ENST00000356341	NM_002576.4	461	Gag/Aag	13/15	1	2	FACETS	0.341	0.303	0.382	0.341	0.303	0.382	SUBCLONAL	1	TRUE	1	0.701798055933886	2		461	777	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99192888	99192888	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	19	240	0	ENST00000268035.6:c.78G>A	p.Trp26Ter	p.W26*	ENST00000268035	NM_000875.3	26	tgG/tgA	1/21	1	2	FACETS	0.159	0.12	0.204	0.159	0.12	0.204	SUBCLONAL	1	TRUE	1	0.701798055933886	2		240	341	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098720	47098720	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	240	448	0	ENST00000409792.3:c.6554G>A	p.Gly2185Glu	p.G2185E	ENST00000409792	NM_014159.6	2185	gGa/gAa	15/21	1	2	FACETS	0.933	0.875	0.992	0.933	0.875	0.992	CLONAL	1	TRUE	1	0.701798055933886	2		448	733	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727078	40727078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs896375033	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	47	385	0	ENST00000373198.4:c.3886G>A	p.Glu1296Lys	p.E1296K	ENST00000373198	NM_133170.3	1296	Gag/Aag	28/32	1	2	FACETS	0.213	0.179	0.251	0.213	0.179	0.251	SUBCLONAL	1	TRUE	1	0.701798055933886	2		385	628	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053501	37053501	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	233	317	0	ENST00000231790.2:c.589-1G>A		p.X197_splice	ENST00000231790	NM_000249.3	197			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.701798055933886	2		317	637	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166098	118166098	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	62	300	1	ENST00000369448.3:c.608C>G	p.Ser203Cys	p.S203C	ENST00000369448	NM_017709.3	203	tCt/tGt	2/2	1	2	FACETS	0.354	0.306	0.406	0.354	0.306	0.406	SUBCLONAL	1	TRUE	1	0.701798055933886	2		301	499	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462096	120462096	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	58	488	1	ENST00000256646.2:c.5620G>A	p.Asp1874Asn	p.D1874N	ENST00000256646	NM_024408.3	1874	Gac/Aac	31/34	1	2	FACETS	0.23	0.197	0.266	0.23	0.197	0.266	SUBCLONAL	1	TRUE	1	0.701798055933886	2		489	719	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809326	243809326	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	199	395	3	ENST00000263826.5:c.298G>A	p.Glu100Lys	p.E100K	ENST00000263826	NM_005465.4	100	Gaa/Aaa	4/13	1	2	FACETS	0.879	0.819	0.942	0.879	0.819	0.942	CLONAL	1	TRUE	1	0.701798055933886	2		398	645	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161387	2161387	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1264097668	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	37	399	0	ENST00000434045.2:c.140C>T	p.Thr47Ile	p.T47I	ENST00000434045	NM_001127598.1	47	aCc/aTc	2/5	1	2	FACETS	0.173	0.142	0.208	0.173	0.142	0.208	SUBCLONAL	1	TRUE	1	0.701798055933886	2		399	610	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205564	61205564	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	58	462	0	ENST00000301761.2:c.349G>A	p.Asp117Asn	p.D117N	ENST00000301761	NM_017841.2	117	Gat/Aat	3/4	1	2	FACETS	0.219	0.187	0.253	0.219	0.187	0.253	SUBCLONAL	1	TRUE	1	0.701798055933886	2		462	755	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998394	100998394	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs907410956	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	47	94	0	ENST00000325455.5:c.1408C>T	p.Pro470Ser	p.P470S	ENST00000325455	NM_001202474.3	470	Ccc/Tcc	1/8	1	2	FACETS	0.937	0.808	1	0.937	0.808	1	CLONAL	1	TRUE	1	0.701798055933886	2		94	143	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206804	102206804	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	155	435	0	ENST00000263464.3:c.1432G>A	p.Glu478Lys	p.E478K	ENST00000263464	NM_001165.4	478	Gaa/Aaa	7/9	1	2	FACETS	0.547	0.501	0.595	0.547	0.501	0.595	SUBCLONAL	1	TRUE	1	0.701798055933886	2		435	807	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112884189	112884189	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397507501	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	107	544	0	ENST00000351677.2:c.124A>G	p.Thr42Ala	p.T42A	ENST00000351677	NM_002834.3	42	Aca/Gca	2/16	1	2	FACETS	0.357	0.32	0.397	0.357	0.32	0.397	SUBCLONAL	1	TRUE	1	0.701798055933886	2		544	853	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28901642	28901642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	64	402	1	ENST00000282397.4:c.2753C>T	p.Ser918Phe	p.S918F	ENST00000282397	NM_002019.4	918	tCc/tTc	20/30	1	2	FACETS	0.242	0.209	0.278	0.242	0.209	0.278	SUBCLONAL	1	TRUE	1	0.701798055933886	2		403	755	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504530	103504530	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	205	320	0	ENST00000355739.4:c.151G>A	p.Glu51Lys	p.E51K	ENST00000355739	NM_000123.3	51	Gaa/Aaa	2/15	1	2	FACETS	0.995	0.929	1	0.995	0.929	1	CLONAL	1	TRUE	1	0.701798055933886	2		320	587	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712907	43712907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	252	430	0	ENST00000382044.4:c.4277G>A	p.Gly1426Asp	p.G1426D	ENST00000382044	NM_001141980.1	1426	gGc/gAc	21/28	1	2	FACETS	0.989	0.93	1	0.989	0.93	1	CLONAL	1	TRUE	1	0.701798055933886	2		430	726	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649444	23649444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	28	266	0	ENST00000261584.4:c.55G>A	p.Glu19Lys	p.E19K	ENST00000261584	NM_024675.3	19	Gag/Aag	2/13	1	2	FACETS	0.167	0.133	0.205	0.167	0.133	0.205	SUBCLONAL	1	TRUE	1	0.701798055933886	2		266	479	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813809	50813809	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	305	615	2	ENST00000398568.2:c.1363C>T	p.Pro455Ser	p.P455S	ENST00000398568	NM_001042412.1	455	Cca/Tca	8/18	1	2	FACETS	0.891	0.842	0.942	0.891	0.842	0.942	CLONAL	1	TRUE	1	0.701798055933886	2		617	975	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831453	72831453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	50	358	0	ENST00000268489.5:c.5128G>A	p.Ala1710Thr	p.A1710T	ENST00000268489	NM_006885.3	1710	Gcc/Acc	9/10	1	2	FACETS	0.228	0.193	0.266	0.228	0.193	0.266	SUBCLONAL	1	TRUE	1	0.701798055933886	2		358	626	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347834	89347834	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763092437	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	196	337	0	ENST00000301030.4:c.5116C>T	p.Pro1706Ser	p.P1706S	ENST00000301030	NM_001256183.1	1706	Cct/Tct	9/13	1	2	FACETS	0.982	0.915	1	0.982	0.915	1	CLONAL	1	TRUE	1	0.701798055933886	2		337	569	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805569	89805569	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	45	422	1	ENST00000389301.3:c.4139C>T	p.Ala1380Val	p.A1380V	ENST00000389301	NM_000135.2	1380	gCt/gTt	41/43	1	2	FACETS	0.187	0.156	0.221	0.187	0.156	0.221	SUBCLONAL	1	TRUE	1	0.701798055933886	2		423	686	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559119	29559119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	28	167	0	ENST00000356175.3:c.3226G>A	p.Val1076Ile	p.V1076I	ENST00000356175	NM_000267.3	1076	Gta/Ata	25/57	1	2	FACETS	0.249	0.199	0.305	0.249	0.199	0.305	SUBCLONAL	1	TRUE	1	0.701798055933886	2		167	321	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560232	29560232	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1420779915	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	109	186	0	ENST00000356175.3:c.3708+1G>A		p.X1236_splice	ENST00000356175	NM_000267.3	1236			1	2	FACETS	0.938	0.853	1	0.938	0.853	1	CLONAL	1	TRUE	1	0.701798055933886	2		186	331	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864725	37864725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	61	404	0	ENST00000269571.5:c.377C>T	p.Thr126Ile	p.T126I	ENST00000269571		126	aCc/aTc	3/27	1	2	FACETS	0.241	0.207	0.278	0.241	0.207	0.278	SUBCLONAL	1	TRUE	1	0.701798055933886	2		404	722	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40880950	40880950	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	223	405	0	ENST00000428826.2:c.10C>T	p.Pro4Ser	p.P4S	ENST00000428826		4	Cca/Tca	3/21	1	2	FACETS	0.884	0.826	0.943	0.884	0.826	0.943	CLONAL	1	TRUE	1	0.701798055933886	2		405	719	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234420	41234420	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs80358027	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	55	401	0	ENST00000357654.3:c.4357+1G>A		p.X1453_splice	ENST00000357654	NM_007294.3	1453			1	2	FACETS	0.22	0.187	0.255	0.22	0.187	0.255	SUBCLONAL	1	TRUE	1	0.701798055933886	2		401	714	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438223	56438223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	70	431	0	ENST00000407977.2:c.770G>A	p.Gly257Asp	p.G257D	ENST00000407977		257	gGt/gAt	7/10	1	2	FACETS	0.276	0.24	0.315	0.276	0.24	0.315	SUBCLONAL	1	TRUE	1	0.701798055933886	2		431	722	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772291	56772291	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1555593458	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	44	204	0	ENST00000337432.4:c.146-1G>A		p.X49_splice	ENST00000337432	NM_058216.2	49			1	2	FACETS	0.302	0.253	0.356	0.302	0.253	0.356	SUBCLONAL	1	TRUE	1	0.701798055933886	2		204	415	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78882680	78882680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	260	444	1	ENST00000306801.3:c.2471C>T	p.Pro824Leu	p.P824L	ENST00000306801	NM_020761.2	824	cCa/cTa	21/34	1	2	FACETS	0.949	0.892	1	0.949	0.892	1	CLONAL	1	TRUE	1	0.701798055933886	2		445	781	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611813	1611813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367895437	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	301	511	4	ENST00000344749.5:c.1849C>T	p.Arg617Trp	p.R617W	ENST00000344749	NM_001136139.2	617	Cgg/Tgg	19/19	0.666866355320062	3	FACETS	0.985	0.928	1	0.493	0.464	0.522	CLONAL	1	TRUE	1	0.701798055933886	3		515	1176	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117443	4117443	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	298	478	0	ENST00000262948.5:c.277C>T	p.Pro93Ser	p.P93S	ENST00000262948	NM_030662.3	93	Ccc/Tcc	2/11	0.666866355320062	3	FACETS	1	0.947	1	0.503	0.474	0.534	CLONAL	1	TRUE	1	0.701798055933886	3		478	1140	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7119584	7119584	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765638025	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	82	380	0	ENST00000302850.5:c.3670G>A	p.Val1224Met	p.V1224M	ENST00000302850	NM_000208.2	1224	Gtg/Atg	21/22	0.666866355320062	3	FACETS	0.356	0.313	0.402	0.178	0.156	0.201	SUBCLONAL	1	TRUE	1	0.701798055933886	3		380	888	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10277339	10277339	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	300	535	0	ENST00000340748.4:c.778G>A	p.Glu260Lys	p.E260K	ENST00000340748		260	Gag/Aag	10/40	0.666866355320062	3	FACETS	1	0.967	1	0.519	0.489	0.55	CLONAL	1	TRUE	1	0.701798055933886	3		535	1112	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145656	11145656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	248	476	0	ENST00000358026.2:c.4018G>A	p.Glu1340Lys	p.E1340K	ENST00000358026	NM_001128849.1	1340	Gag/Aag	29/36	0.666866355320062	3	FACETS	0.898	0.84	0.958	0.449	0.42	0.479	CLONAL	1	TRUE	1	0.701798055933886	3		476	1063	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350604	15350604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	58	508	0	ENST00000263377.2:c.3311C>T	p.Pro1104Leu	p.P1104L	ENST00000263377	NM_058243.2	1104	cCc/cTc	16/20	0.666866355320062	3	FACETS	0.205	0.175	0.238	0.103	0.087	0.119	SUBCLONAL	1	TRUE	1	0.701798055933886	3		508	1088	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223182	36223182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	71	616	0	ENST00000222270.7:c.5732G>A	p.Arg1911Lys	p.R1911K	ENST00000222270	NM_014727.1	1911	aGa/aAa	28/37	1	2	FACETS	0.199	0.173	0.227	0.199	0.173	0.227	SUBCLONAL	1	TRUE	1	0.701798055933886	2		616	1018	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223259	36223259	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758813577	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	348	615	0	ENST00000222270.7:c.5809C>T	p.Pro1937Ser	p.P1937S	ENST00000222270	NM_014727.1	1937	Cct/Tct	28/37	1	2	FACETS	0.994	0.943	1	0.994	0.943	1	CLONAL	1	TRUE	1	0.701798055933886	2		615	998	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793240	42793240	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	236	460	1	ENST00000575354.2:c.1132C>T	p.Gln378Ter	p.Q378*	ENST00000575354	NM_015125.3	378	Cag/Tag	7/20	1	2	FACETS	0.84	0.786	0.895	0.84	0.786	0.895	CLONAL	1	TRUE	1	0.701798055933886	2		461	801	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795791	42795791	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1266819634	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	156	468	1	ENST00000575354.2:c.2780C>T	p.Ala927Val	p.A927V	ENST00000575354	NM_015125.3	927	gCc/gTc	11/20	1	2	FACETS	0.614	0.563	0.667	0.614	0.563	0.667	SUBCLONAL	1	TRUE	1	0.701798055933886	2		469	724	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905608	50905608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	76	490	1	ENST00000440232.2:c.736G>A	p.Ala246Thr	p.A246T	ENST00000440232	NM_002691.3	246	Gcc/Acc	6/27	1	2	FACETS	0.29	0.254	0.329	0.29	0.254	0.329	SUBCLONAL	1	TRUE	1	0.701798055933886	2		491	746	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25459843	25459843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	76	518	0	ENST00000264709.3:c.2440G>A	p.Glu814Lys	p.E814K	ENST00000264709	NM_175629.2	814	Gag/Aag	21/23	1	2	FACETS	0.28	0.245	0.318	0.28	0.245	0.318	SUBCLONAL	1	TRUE	1	0.701798055933886	2		518	774	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009099	27009099	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	53	90	1	ENST00000335756.4:c.35C>T	p.Ala12Val	p.A12V	ENST00000335756	NM_001809.3	12	gCc/gTc	1/5	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.701798055933886	2		91	143	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451765	29451765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	236	519	1	ENST00000389048.3:c.2800G>A	p.Gly934Ser	p.G934S	ENST00000389048	NM_004304.4	934	Ggc/Agc	16/29	1	2	FACETS	0.903	0.846	0.961	0.903	0.846	0.961	CLONAL	1	TRUE	1	0.701798055933886	2		520	745	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213432	39213432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770107427	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	211	424	0	ENST00000402219.2:c.3535C>T	p.Pro1179Ser	p.P1179S	ENST00000402219	NM_005633.3	1179	Ccc/Tcc	23/23	1	2	FACETS	0.97	0.906	1	0.97	0.906	1	CLONAL	1	TRUE	1	0.701798055933886	2		424	620	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705493	47705493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750368	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	187	314	0	ENST00000233146.2:c.2293G>A	p.Ala765Thr	p.A765T	ENST00000233146	NM_000251.2	765	Gct/Act	14/16	1	2	FACETS	0.821	0.762	0.882	0.821	0.762	0.882	CLONAL	1	TRUE	1	0.701798055933886	2		314	649	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027040	48027040	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	178	319	0	ENST00000234420.5:c.1918G>A	p.Glu640Lys	p.E640K	ENST00000234420	NM_000179.2	640	Gaa/Aaa	4/10	1	2	FACETS	0.961	0.892	1	0.961	0.892	1	CLONAL	1	TRUE	1	0.701798055933886	2		319	528	SUCCESS
REL	5966	MSKCC	GRCh37	2	61121605	61121605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	64	499	1	ENST00000295025.8:c.227C>T	p.Pro76Leu	p.P76L	ENST00000295025	NM_002908.2	76	cCt/cTt	3/11	1	2	FACETS	0.257	0.222	0.295	0.257	0.222	0.295	SUBCLONAL	1	TRUE	1	0.701798055933886	2		500	710	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645424	215645424	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	255	482	0	ENST00000260947.4:c.1174C>T	p.Pro392Ser	p.P392S	ENST00000260947	NM_000465.2	392	Cca/Tca	4/11	1	2	FACETS	0.87	0.817	0.925	0.87	0.817	0.925	CLONAL	1	TRUE	1	0.701798055933886	2		482	835	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023747	31023747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	264	410	1	ENST00000375687.4:c.3232G>A	p.Asp1078Asn	p.D1078N	ENST00000375687	NM_015338.5	1078	Gat/Aat	13/13	1	2	FACETS	0.925	0.87	0.982	0.925	0.87	0.982	CLONAL	1	TRUE	1	0.701798055933886	2		411	813	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408939	41408939	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	146	271	0	ENST00000373198.4:c.487G>A	p.Val163Met	p.V163M	ENST00000373198	NM_133170.3	163	Gtg/Atg	4/32	1	2	FACETS	0.916	0.843	0.992	0.916	0.843	0.992	CLONAL	1	TRUE	1	0.701798055933886	2		271	454	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41818307	41818307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1338054687	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	14	20	0	ENST00000373198.4:c.67G>A	p.Ala23Thr	p.A23T	ENST00000373198	NM_133170.3	23	Gcc/Acc	1/32	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.701798055933886	2		20	31	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326738	62326738	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	117	592	1	ENST00000360203.5:c.3557G>A	p.Arg1186Lys	p.R1186K	ENST00000360203	NM_001283009.1	1186	aGa/aAa	34/35	1	2	FACETS	0.325	0.292	0.36	0.325	0.292	0.36	SUBCLONAL	1	TRUE	1	0.701798055933886	2		593	1025	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090030	37090030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267607875	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	303	479	0	ENST00000231790.2:c.1919C>T	p.Pro640Leu	p.P640L	ENST00000231790	NM_000249.3	640	cCc/cTc	17/19	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.701798055933886	2		479	781	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163439	47163439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	28	315	0	ENST00000409792.3:c.2687C>T	p.Thr896Ile	p.T896I	ENST00000409792	NM_014159.6	896	aCt/aTt	3/21	1	2	FACETS	0.167	0.133	0.206	0.167	0.133	0.206	SUBCLONAL	1	TRUE	1	0.701798055933886	2		315	477	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119642257	119642257	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576401632	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	290	488	0	ENST00000316626.5:c.440G>A	p.Ser147Asn	p.S147N	ENST00000316626		147	aGt/aAt	4/12	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.701798055933886	2		488	794	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665344	138665344	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	65	508	0	ENST00000330315.3:c.221G>A	p.Arg74Lys	p.R74K	ENST00000330315	NM_023067.3	74	aGg/aAg	1/1	1	2	FACETS	0.214	0.185	0.246	0.214	0.185	0.246	SUBCLONAL	1	TRUE	1	0.701798055933886	2		508	864	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170009646	170009646	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	198	360	0	ENST00000295797.4:c.1208G>A	p.Gly403Glu	p.G403E	ENST00000295797	NM_002740.5	403	gGa/gAa	13/18	1	2	FACETS	0.915	0.852	0.979	0.915	0.852	0.979	CLONAL	1	TRUE	1	0.701798055933886	2		360	617	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455588	189455588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1042354976	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	83	491	1	ENST00000264731.3:c.122C>T	p.Ser41Phe	p.S41F	ENST00000264731	NM_003722.4	41	tCc/tTc	2/14	1	2	FACETS	0.267	0.235	0.301	0.267	0.235	0.301	SUBCLONAL	1	TRUE	1	0.701798055933886	2		492	887	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193815	106193815	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	163	313	0	ENST00000380013.4:c.4277T>A	p.Val1426Glu	p.V1426E	ENST00000380013	NM_001127208.2	1426	gTg/gAg	10/11	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.701798055933886	2		313	456	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584505	187584505	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	203	360	0	ENST00000441802.2:c.3528C>A	p.Tyr1176Ter	p.Y1176*	ENST00000441802	NM_005245.3	1176	taC/taA	3/27	1	2	FACETS	0.92	0.857	0.983	0.92	0.857	0.983	CLONAL	1	TRUE	1	0.701798055933886	2		360	629	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628041	187628041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	63	451	0	ENST00000441802.2:c.2941G>A	p.Gly981Arg	p.G981R	ENST00000441802	NM_005245.3	981	Gga/Aga	2/27	1	2	FACETS	0.237	0.204	0.272	0.237	0.204	0.272	SUBCLONAL	1	TRUE	1	0.701798055933886	2		451	758	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628418	187628418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	90	556	1	ENST00000441802.2:c.2564G>A	p.Gly855Glu	p.G855E	ENST00000441802	NM_005245.3	855	gGa/gAa	2/27	1	2	FACETS	0.251	0.222	0.283	0.251	0.222	0.283	SUBCLONAL	1	TRUE	1	0.701798055933886	2		557	1021	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178580	56178580	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	24	256	0	ENST00000399503.3:c.3553G>A	p.Glu1185Lys	p.E1185K	ENST00000399503	NM_005921.1	1185	Gaa/Aaa	14/20	1	2	FACETS	0.166	0.129	0.208	0.166	0.129	0.208	SUBCLONAL	1	TRUE	1	0.701798055933886	2		256	413	SUCCESS
APC	324	MSKCC	GRCh37	5	112178109	112178109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781364	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	129	282	0	ENST00000257430.4:c.6818G>A	p.Gly2273Glu	p.G2273E	ENST00000257430	NM_000038.5	2273	gGa/gAa	16/16	1	2	FACETS	0.834	0.762	0.908	0.834	0.762	0.908	CLONAL	1	TRUE	1	0.701798055933886	2		282	441	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131930706	131930706	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	202	373	1	ENST00000265335.6:c.1939G>A	p.Glu647Lys	p.E647K	ENST00000265335		647	Gag/Aag	12/25	1	2	FACETS	0.939	0.876	1	0.939	0.876	1	CLONAL	1	TRUE	1	0.701798055933886	2		374	613	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149511562	149511562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	193	417	1	ENST00000261799.4:c.1223C>T	p.Ser408Phe	p.S408F	ENST00000261799	NM_002609.3	408	tCc/tTc	8/23	1	2	FACETS	0.811	0.753	0.871	0.811	0.753	0.871	CLONAL	1	TRUE	1	0.701798055933886	2		418	678	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639046	176639046	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	252	421	0	ENST00000439151.2:c.3646G>A	p.Glu1216Lys	p.E1216K	ENST00000439151	NM_022455.4	1216	Gaa/Aaa	5/23	1	2	FACETS	0.941	0.884	0.999	0.941	0.884	0.999	CLONAL	1	TRUE	1	0.701798055933886	2		421	763	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679752	30679752	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1309321043	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	238	446	1	ENST00000376406.3:c.1967G>A	p.Gly656Glu	p.G656E	ENST00000376406	NM_014641.2	656	gGg/gAg	5/15	1	2	FACETS	0.891	0.835	0.949	0.891	0.835	0.949	CLONAL	1	TRUE	1	0.701798055933886	2		447	761	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004415	150004415	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	73	406	0	ENST00000253339.5:c.1810G>A	p.Asp604Asn	p.D604N	ENST00000253339		604	Gat/Aat	3/7	1	2	FACETS	0.282	0.246	0.321	0.282	0.246	0.321	SUBCLONAL	1	TRUE	1	0.701798055933886	2		406	738	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099565	157099565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	22	65	1	ENST00000346085.5:c.502G>A	p.Gly168Ser	p.G168S	ENST00000346085	NM_020732.3	168	Ggc/Agc	1/20	1	2	FACETS	0.674	0.534	0.829	0.674	0.534	0.829	SUBCLONAL	1	TRUE	1	0.701798055933886	2		66	93	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008946	152008946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	49	490	0	ENST00000262189.6:c.676G>A	p.Asp226Asn	p.D226N	ENST00000262189	NM_170606.2	226	Gat/Aat	5/59	NA	2	FACETS	0.176	0.148	0.207			1	INDETERMINATE	1	TRUE	NA	0.701798055933886	2		490	793	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028086	69028086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774652439	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	279	575	2	ENST00000288368.4:c.3245G>A	p.Ser1082Asn	p.S1082N	ENST00000288368	NM_024870.2	1082	aGc/aAc	26/40	1	2	FACETS	0.926	0.872	0.98	0.926	0.872	0.98	CLONAL	1	TRUE	1	0.701798055933886	2		577	859	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5463112	5463112	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	28	209	0	ENST00000381577.3:c.673G>A	p.Val225Ile	p.V225I	ENST00000381577	NM_014143.3	225	Gtc/Atc	4/7	1	2	FACETS	0.222	0.177	0.273	0.222	0.177	0.273	SUBCLONAL	1	TRUE	1	0.701798055933886	2		209	360	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218598	98218598	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	222	448	0	ENST00000331920.6:c.3266C>T	p.Ser1089Phe	p.S1089F	ENST00000331920	NM_000264.3	1089	tCt/tTt	19/24	1	2	FACETS	0.937	0.877	0.999	0.937	0.877	0.999	CLONAL	1	TRUE	1	0.701798055933886	2		448	675	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239903	98239903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	70	369	1	ENST00000331920.6:c.1429G>A	p.Val477Ile	p.V477I	ENST00000331920	NM_000264.3	477	Gtt/Att	10/24	1	2	FACETS	0.336	0.293	0.382	0.336	0.293	0.382	SUBCLONAL	1	TRUE	1	0.701798055933886	2		370	594	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1327796	1327796	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759760274	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	241	453	0	ENST00000400841.2:c.85G>A	p.Gly29Arg	p.G29R	ENST00000400841		29	Gga/Aga	2/6	1	2	FACETS	0.951	0.893	1	0.951	0.893	1	CLONAL	1	TRUE	1	0.701798055933886	2		453	722	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932226	39932226	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	72	716	0	ENST00000378444.4:c.2373G>A	p.Trp791Ter	p.W791*	ENST00000378444	NM_001123385.1	791	tgG/tgA	4/15	1	2	FACETS	0.19	0.165	0.217	0.19	0.165	0.217	SUBCLONAL	1	TRUE	1	0.701798055933886	2		716	1080	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932785	39932785	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	287	610	0	ENST00000378444.4:c.1814C>T	p.Pro605Leu	p.P605L	ENST00000378444	NM_001123385.1	605	cCt/cTt	4/15	1	2	FACETS	0.906	0.854	0.959	0.906	0.854	0.959	CLONAL	1	TRUE	1	0.701798055933886	2		610	903	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226196	53226196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	247	414	0	ENST00000375401.3:c.2653G>A	p.Ala885Thr	p.A885T	ENST00000375401	NM_004187.3	885	Gct/Act	19/26	1	2	FACETS	0.98	0.921	1	0.98	0.921	1	CLONAL	1	TRUE	1	0.701798055933886	2		414	718	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410397	63410397	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	268	542	0	ENST00000330258.3:c.2770del	p.Gln924SerfsTer52	p.Q924Sfs*52	ENST00000330258	NM_152424.3	924	Cag/ag	2/2	1	2	FACETS	0.892	0.839	0.946	0.892	0.839	0.946	CLONAL	1	TRUE	1	0.701798055933886	2		542	856	SUCCESS
AR	367	MSKCC	GRCh37	X	66765671	66765671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	95	609	2	ENST00000374690.3:c.683G>A	p.Gly228Asp	p.G228D	ENST00000374690	NM_000044.3	228	gGc/gAc	1/8	1	2	FACETS	0.283	0.251	0.317	0.283	0.251	0.317	SUBCLONAL	1	TRUE	1	0.701798055933886	2		611	957	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626662	100626662	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	61	386	0	ENST00000308731.7:c.268G>A	p.Glu90Lys	p.E90K	ENST00000308731	NM_000061.2	90	Gag/Aag	4/19	1	2	FACETS	0.256	0.22	0.295	0.256	0.22	0.295	SUBCLONAL	1	TRUE	1	0.701798055933886	2		386	680	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0025667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	126	491	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.649145391904069	2		491	292	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913286	NA	P-0025667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	176	612	0	ENST00000263967.3:c.1636C>G	p.Gln546Glu	p.Q546E	ENST00000263967	NM_006218.2	546	Cag/Gag	10/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.649145391904069	2		612	508	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151862	108151863	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs768356403	NA	P-0025667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	124	474	0	ENST00000278616.4:c.3546_3547del	p.Asn1183TrpfsTer16	p.N1183Wfs*16	ENST00000278616	NM_000051.3	1181	aaAGag/aaag	24/63	1	2	FACETS	0.809	0.737	0.885	0.809	0.737	0.885	CLONAL	1	TRUE	1	0.649145391904069	2		474	472	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676179	29676180	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0025667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	110	377	1	ENST00000356175.3:c.7169_7170del	p.Arg2390AsnfsTer10	p.R2390Nfs*10	ENST00000356175	NM_000267.3	2390	AGa/a	48/57	0.594538134094545	1	FACETS	0.763	0.695	0.832	0.763	0.695	0.832	SUBCLONAL	1	TRUE	0	0.649145391904069	1		378	300	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184736	32184736	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	145	499	2	ENST00000375023.3:c.1847C>T	p.Pro616Leu	p.P616L	ENST00000375023	NM_004557.3	616	cCc/cTc	11/30	0.0923268513002076	3	FACETS	1	0.986	1	0.668	0.615	0.723	INDETERMINATE	1	TRUE	1	0.649145391904069	3		501	443	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602493	10602493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	24	372	0	ENST00000171111.5:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000171111	NM_203500.1	362	cGg/cAg	3/6	0.421796892612181	2	FACETS	0.293	0.229	0.366	0.146	0.114	0.183	SUBCLONAL	1	TRUE	0	0.421796892612181	2		372	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0025668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	219	565	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.421796892612181	2	FACETS	0.926	0.868	0.984	0.926	0.868	0.984	CLONAL	2	TRUE	0	0.421796892612181	2		565	561	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222983	1222983	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs398123406	NA	P-0025668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	162	380	0	ENST00000326873.7:c.921-1G>C		p.X307_splice	ENST00000326873	NM_000455.4	307			0.421796892612181	2	FACETS	0.925	0.859	0.993	0.925	0.859	0.993	CLONAL	2	TRUE	0	0.421796892612181	2		380	415	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65311224	65311224	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	73	358	0	ENST00000342505.4:c.2087A>G	p.Lys696Arg	p.K696R	ENST00000342505	NM_002227.2	696	aAa/aGa	15/25	0.42283126968405	3	FACETS	0.838	0.735	0.949	0.419	0.367	0.475	CLONAL	1	TRUE	1	0.421796892612181	3		358	500	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608300	43608300	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0025668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	108	610	0	ENST00000355710.3:c.1649-1G>C		p.X550_splice	ENST00000355710	NM_020975.4	550			0.277858845798462	3	FACETS	1	0.924	1	0.516	0.464	0.571	CLONAL	1	TRUE	1	0.421796892612181	3		610	601	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456271	32456271	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	154	517	0	ENST00000332351.3:c.621G>T	p.Glu207Asp	p.E207D	ENST00000332351	NM_024426.4	207	gaG/gaT	1/10	0.395511431601898	4	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	2	0.421796892612181	4		517	511	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427026	49427026	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	141	398	0	ENST00000301067.7:c.11462A>T	p.Gln3821Leu	p.Q3821L	ENST00000301067	NM_003482.3	3821	cAg/cTg	39/54	0.395511431601898	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.421796892612181	4		398	431	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427395	49427395	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs931451601	NA	P-0025668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	205	575	2	ENST00000301067.7:c.11093G>A	p.Gly3698Asp	p.G3698D	ENST00000301067	NM_003482.3	3698	gGc/gAc	39/54	0.395511431601898	4	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	2	0.421796892612181	4		577	681	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906702	32906702	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1060502440	NA	P-0025668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	119	428	0	ENST00000380152.3:c.1087A>G	p.Thr363Ala	p.T363A	ENST00000380152		363	Act/Gct	10/27	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.421796892612181	2		428	508	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500637	99500637	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	115	320	0	ENST00000268035.6:c.4070G>T	p.Arg1357Leu	p.R1357L	ENST00000268035	NM_000875.3	1357	cGg/cTg	21/21	0.421007365477413	3	FACETS	0.782	0.71	0.857	0.782	0.71	0.857	SUBCLONAL	2	TRUE	1	0.421796892612181	3		320	422	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212257	5212257	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	163	415	0	ENST00000357368.4:c.4774G>T	p.Gly1592Cys	p.G1592C	ENST00000357368	NM_002850.3	1592	Ggt/Tgt	32/38	0.421796892612181	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	0	0.421796892612181	2		415	384	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606972	47606972	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	188	404	0	ENST00000263735.4:c.722A>G	p.Asp241Gly	p.D241G	ENST00000263735	NM_002354.2	241	gAt/gGt	7/9	0.421007365477413	3	FACETS	0.98	0.912	1	0.98	0.912	1	CLONAL	2	TRUE	1	0.421796892612181	3		404	551	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873005	134873005	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	177	536	1	ENST00000398015.3:c.1309G>T	p.Val437Phe	p.V437F	ENST00000398015	NM_004441.4	437	Gtt/Ttt	6/16	0.42283126968405	4	FACETS	0.955	0.884	1	0.955	0.884	1	CLONAL	2	TRUE	2	0.421796892612181	4		537	625	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197772	66197772	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	132	476	0	ENST00000273854.3:c.2927C>A	p.Ala976Glu	p.A976E	ENST00000273854	NM_004439.5	976	gCa/gAa	17/18	0.390357779746789	2	FACETS	0.79	0.725	0.858	0.79	0.725	0.858	SUBCLONAL	2	TRUE	0	0.421796892612181	2		476	396	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953613	38953613	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	148	356	0	ENST00000357387.3:c.2740T>G	p.Leu914Val	p.L914V	ENST00000357387	NM_152756.3	914	Ttg/Gtg	28/38	0.409910226893883	5	FACETS	1	0.977	1	0.781	0.718	0.846	CLONAL	2	TRUE	2	0.421796892612181	5		356	489	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569238	67569238	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	143	418	0	ENST00000274335.5:c.355G>C	p.Ala119Pro	p.A119P	ENST00000274335		119	Gca/Cca	2/15	0.421796892612181	5	FACETS	0.881	0.806	0.96			1	CLONAL	2	TRUE	NA	0.421796892612181	5		418	628	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449496	149449496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	165	513	0	ENST00000286301.3:c.1450G>A	p.Glu484Lys	p.E484K	ENST00000286301	NM_005211.3	484	Gag/Aag	10/22	0.390357779746789	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.421796892612181	2		513	366	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265377	152265377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	101	359	1	ENST00000206249.3:c.830G>A	p.Arg277Lys	p.R277K	ENST00000206249	NM_000125.3	277	aGg/aAg	4/8	0.218425890460645	4	FACETS	0.866	0.78	0.956	0.866	0.78	0.956	INDETERMINATE	2	TRUE	2	0.421796892612181	4		360	393	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622219	162622219	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	93	411	1	ENST00000366898.1:c.478G>T	p.Gly160Ter	p.G160*	ENST00000366898	NM_004562.2	160	Gga/Tga	4/12	0.218425890460645	4	FACETS	1	0.978	1	0.698	0.624	0.777	INDETERMINATE	1	TRUE	2	0.421796892612181	4		412	449	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388100	81388100	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	149	402	0	ENST00000222390.5:c.275C>A	p.Ala92Glu	p.A92E	ENST00000222390	NM_000601.4	92	gCa/gAa	3/18	0.42283126968405	3	FACETS	0.924	0.851	0.999	0.924	0.851	0.999	CLONAL	2	TRUE	1	0.421796892612181	3		402	463	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509716	106509716	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	97	432	1	ENST00000359195.3:c.1710G>T	p.Glu570Asp	p.E570D	ENST00000359195	NM_002649.2	570	gaG/gaT	2/11	0.42283126968405	3	FACETS	1	0.913	1	0.512	0.458	0.569	CLONAL	1	TRUE	1	0.421796892612181	3		433	544	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376642	8376642	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	177	471	1	ENST00000356435.5:c.4471G>T	p.Ala1491Ser	p.A1491S	ENST00000356435		1491	Gcc/Tcc	27/35	0.392987038821726	2	FACETS	0.906	0.843	0.97	0.906	0.843	0.97	CLONAL	2	TRUE	0	0.421796892612181	2		472	463	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391700	139391700	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs535160267	NA	P-0025668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	292	582	0	ENST00000277541.6:c.6491A>G	p.Lys2164Arg	p.K2164R	ENST00000277541	NM_017617.3	2164	aAa/aGa	34/34	0.42283126968405	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	TRUE	0	0.421796892612181	3		582	540	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	64	472	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	1	0.959	1	1	0.983	1	CLONAL	2	TRUE	1	0.197799875831504	2		472	260	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	67	319	1	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	1	0.934	1	1	0.983	1	CLONAL	2	TRUE	1	0.197799875831504	2		320	307	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	77	324	0	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.964	1	1	0.986	1	CLONAL	2	TRUE	1	0.197799875831504	2		324	318	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671655	67671655	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1400980130	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	73	415	1	ENST00000264010.4:c.2070del	p.Glu691SerfsTer30	p.E691Sfs*30	ENST00000264010	NM_006565.3	688	gtA/gt	12/12	1	2	FACETS	1	0.95	1	1	0.985	1	CLONAL	2	TRUE	1	0.197799875831504	2		416	322	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50481162	50481162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	78	352	0	ENST00000394963.4:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000394963	NM_003076.4	183	cGa/cAa	5/13	1	2	FACETS	1	0.964	1	1	0.986	1	CLONAL	2	TRUE	1	0.197799875831504	2		352	322	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450138	32450138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777166391	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	66	465	1	ENST00000332351.3:c.674C>T	p.Thr225Met	p.T225M	ENST00000332351	NM_024426.4	225	aCg/aTg	2/10	1	2	FACETS	0.885	0.772	1	1	0.978	1	CLONAL	2	TRUE	1	0.197799875831504	2		466	377	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	12	46	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	1	2	FACETS	1	0.759	1	1	0.927	1	CLONAL	3	TRUE	1	0.197799875831504	2		46	39	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270530	98270530	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs751977093	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	23	193	0	ENST00000331920.6:c.114del	p.Leu39CysfsTer41	p.L39Cfs*41	ENST00000331920	NM_000264.3	38	ggG/gg	1/24	1	2	FACETS	1	0.887	1	1	0.954	1	CLONAL	2	TRUE	1	0.197799875831504	2		193	98	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972419	81972419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778251162	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	86	351	0	ENST00000359376.3:c.3212G>A	p.Arg1071His	p.R1071H	ENST00000359376	NM_002661.3	1071	cGc/cAc	29/33	1	2	FACETS	0.897	0.802	0.998	1	0.988	1	CLONAL	3	TRUE	1	0.197799875831504	2		351	323	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618715	37618716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	42	364	0	ENST00000447079.4:c.397dup	p.Ser133LysfsTer24	p.S133Kfs*24	ENST00000447079	NM_015083.1	131	gaa/gAaa	1/14	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.197799875831504	2		364	405	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44910953	44910953	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	69	350	0	ENST00000377967.4:c.655-1G>A		p.X219_splice	ENST00000377967	NM_021140.2	219			0.197799875831504	1	FACETS	1	0.96	1	1	0.985	1	CLONAL	2	TRUE	0	0.197799875831504	1		350	258	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845624	63845627	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	novel	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	64	217	0	ENST00000279873.7:c.1366_1369del	p.Glu456MetfsTer22	p.E456Mfs*22	ENST00000279873	NM_032199.2	455	AAAGaa/aa	9/10	1	2	FACETS	1	0.938	1	1	0.982	1	CLONAL	2	TRUE	1	0.197799875831504	2		217	288	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907420	32907421	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359306	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	15	312	2	ENST00000380152.3:c.1813dup	p.Ile605AsnfsTer11	p.I605Nfs*11	ENST00000380152		602	gga/ggAa	10/27	1	2	FACETS	0.523	0.382	0.693	0.523	0.382	0.693	SUBCLONAL	1	TRUE	1	0.197799875831504	2		314	290	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436548	110436548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	30	529	1	ENST00000375856.3:c.1853C>T	p.Ala618Val	p.A618V	ENST00000375856	NM_003749.2	618	gCg/gTg	1/2	1	2	FACETS	0.869	0.701	1	0.869	0.701	1	CLONAL	1	TRUE	1	0.197799875831504	2		530	349	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760598	133760598	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	23	648	0	ENST00000318560.5:c.2925del	p.Ile976SerfsTer93	p.I976Sfs*93	ENST00000318560	NM_005157.4	974	aCc/ac	11/11	1	2	FACETS	0.538	0.419	0.677	0.538	0.419	0.677	SUBCLONAL	1	TRUE	1	0.197799875831504	2		648	432	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686962	37686962	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	91	383	4	ENST00000447079.4:c.3871del	p.Gln1291ArgfsTer3	p.Q1291Rfs*3	ENST00000447079	NM_015083.1	1289	gCc/gc	14/14	1	2	FACETS	0.843	0.754	0.935	1	0.988	1	CLONAL	3	TRUE	1	0.197799875831504	2		387	364	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226566960	226566960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371066735	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	58	292	0	ENST00000366794.5:c.1628C>T	p.Ala543Val	p.A543V	ENST00000366794	NM_001618.3	543	gCg/gTg	12/23	1	2	FACETS	1	0.916	1	1	0.98	1	CLONAL	2	TRUE	1	0.197799875831504	2		292	272	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363529	40363529	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	111	460	0	ENST00000397332.2:c.700C>A	p.His234Asn	p.H234N	ENST00000397332	NM_001033082.2	234	Cac/Aac	3/3	1	2	FACETS	0.964	0.874	1	1	0.991	1	CLONAL	3	TRUE	1	0.197799875831504	2		460	388	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241956	72241956	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	25	287	0	ENST00000357731.5:c.434C>A	p.Ser145Ter	p.S145*	ENST00000357731	NM_173808.2	145	tCa/tAa	3/7	1	2	FACETS	0.878	0.693	1	0.878	0.693	1	CLONAL	1	TRUE	1	0.197799875831504	2		287	288	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226553695	226553695	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs767454108	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	65	380	0	ENST00000366794.5:c.2465A>G	p.His822Arg	p.H822R	ENST00000366794	NM_001618.3	822	cAt/cGt	18/23	1	2	FACETS	1	0.883	1	1	0.981	1	CLONAL	2	TRUE	1	0.197799875831504	2		380	325	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246498697	246498697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143920876	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	32	466	2	ENST00000388985.4:c.308G>A	p.Arg103Gln	p.R103Q	ENST00000388985		103	cGa/cAa	3/12	1	2	FACETS	0.634	0.514	0.771	0.634	0.514	0.771	SUBCLONAL	1	TRUE	1	0.197799875831504	2		468	510	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514173	69514173	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370768233	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	30	462	0	ENST00000294312.3:c.508C>T	p.Pro170Ser	p.P170S	ENST00000294312	NM_005117.2	170	Ccc/Tcc	3/3	1	2	FACETS	0.798	0.643	0.974	0.798	0.643	0.974	CLONAL	1	TRUE	1	0.197799875831504	2		462	380	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103264	119103264	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	36	436	0	ENST00000264033.4:c.302G>T	p.Arg101Ile	p.R101I	ENST00000264033	NM_005188.3	101	aGa/aTa	2/16	1	2	FACETS	0.818	0.672	0.981	0.818	0.672	0.981	CLONAL	1	TRUE	1	0.197799875831504	2		436	445	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235887	133235887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1030360914	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	33	325	2	ENST00000320574.5:c.3269C>T	p.Thr1090Met	p.T1090M	ENST00000320574	NM_006231.2	1090	aCg/aTg	26/49	1	2	FACETS	0.883	0.726	1	1	0.958	1	CLONAL	2	TRUE	1	0.197799875831504	2		327	189	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514649	103514649	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	15	298	0	ENST00000355739.4:c.1150T>C	p.Ser384Pro	p.S384P	ENST00000355739	NM_000123.3	384	Tca/Cca	8/15	1	2	FACETS	0.516	0.377	0.684	0.516	0.377	0.684	SUBCLONAL	1	TRUE	1	0.197799875831504	2		298	294	SUCCESS
BLM	641	MSKCC	GRCh37	15	91295074	91295074	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	53	405	0	ENST00000355112.3:c.857T>A	p.Val286Asp	p.V286D	ENST00000355112	NM_000057.2	286	gTt/gAt	4/22	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.197799875831504	2		405	382	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40879742	40879742	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	60	509	0	ENST00000428826.2:c.157A>C	p.Thr53Pro	p.T53P	ENST00000428826		53	Acc/Ccc	4/21	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.197799875831504	2		509	461	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15374231	15374231	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	31	243	0	ENST00000263377.2:c.1341G>T	p.Gln447His	p.Q447H	ENST00000263377	NM_058243.2	447	caG/caT	7/20	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.197799875831504	2		243	244	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945895	17945895	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	102	562	0	ENST00000458235.1:c.2044G>T	p.Glu682Ter	p.E682*	ENST00000458235	NM_000215.3	682	Gag/Tag	15/24	1	2	FACETS	0.864	0.778	0.953	1	0.99	1	CLONAL	3	TRUE	1	0.197799875831504	2		562	398	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18964120	18964121	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	27	434	0	ENST00000262803.5:c.1117_1118insA	p.Leu373HisfsTer13	p.L373Hfs*13	ENST00000262803	NM_002911.3	373	ctg/cAtg	8/24	1	2	FACETS	0.696	0.554	0.86	0.696	0.554	0.86	SUBCLONAL	1	TRUE	1	0.197799875831504	2		434	392	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753644	42753644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759092904	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	19	501	0	ENST00000222329.4:c.620G>A	p.Arg207Gln	p.R207Q	ENST00000222329	NM_006494.2	207	cGa/cAa	4/4	1	2	FACETS	0.557	0.422	0.716	0.557	0.422	0.716	SUBCLONAL	1	TRUE	1	0.197799875831504	2		501	345	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209101805	209101806	+	frameshift_variant,stop_lost	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	74	420	0	ENST00000345146.2:c.1242_1243del	p.Ter415SerfsTer6	p.*415Sfs*6	ENST00000345146	NM_005896.2	414	ctTTaa/ctaa	10/10	1	2	FACETS	1	0.917	1	1	0.984	1	CLONAL	2	TRUE	1	0.197799875831504	2		420	356	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39690130	39690130	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	54	276	1	ENST00000361337.2:c.155G>T	p.Ser52Ile	p.S52I	ENST00000361337	NM_003286.2	52	aGt/aTt	3/21	1	2	FACETS	1	0.879	1	1	0.977	1	CLONAL	2	TRUE	1	0.197799875831504	2		277	267	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37045916	37045916	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587779005	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	168	475	0	ENST00000231790.2:c.331G>C	p.Ala111Pro	p.A111P	ENST00000231790	NM_000249.3	111	Gct/Cct	4/19	0.197856391863809	2	FACETS	1	0.937	1	1	0.994	1	CLONAL	5	TRUE	0	0.197799875831504	2		475	339	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259539	89259539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	47	346	0	ENST00000336596.2:c.683G>T	p.Gly228Val	p.G228V	ENST00000336596	NM_005233.5	228	gGg/gTg	3/17	1	2	FACETS	0.808	0.686	0.941	1	0.966	1	CLONAL	2	TRUE	1	0.197799875831504	2		346	294	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55570053	55570053	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	41	318	0	ENST00000288135.5:c.920T>A	p.Val307Glu	p.V307E	ENST00000288135	NM_000222.2	307	gTa/gAa	5/21	1	2	FACETS	0.909	0.764	1	1	0.967	1	CLONAL	2	TRUE	1	0.197799875831504	2		318	228	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224596	224596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	36	400	0	ENST00000264932.6:c.272C>T	p.Thr91Ile	p.T91I	ENST00000264932	NM_004168.2	91	aCc/aTc	3/15	0.197799875831504	1	FACETS	0.985	0.812	1	0.985	0.812	1	CLONAL	1	TRUE	0	0.197799875831504	1		400	333	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293512	1293512	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	24	599	1	ENST00000310581.5:c.1489C>A	p.Leu497Met	p.L497M	ENST00000310581	NM_198253.2	497	Ctg/Atg	2/16	0.197799875831504	1	FACETS	0.543	0.425	0.679	0.543	0.425	0.679	SUBCLONAL	1	TRUE	0	0.197799875831504	1		600	403	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169022	32169022	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	105	612	0	ENST00000375023.3:c.4011C>G	p.Asp1337Glu	p.D1337E	ENST00000375023	NM_004557.3	1337	gaC/gaG	22/30	1	2	FACETS	0.889	0.803	0.979	1	0.99	1	CLONAL	3	TRUE	1	0.197799875831504	2		612	398	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852045	128852045	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	99	538	0	ENST00000249373.3:c.2117A>G	p.Gln706Arg	p.Q706R	ENST00000249373	NM_005631.4	706	cAg/cGg	12/12	1	2	FACETS	1	0.973	1	1	0.989	1	CLONAL	2	TRUE	1	0.197799875831504	2		538	401	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845757	151845757	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	105	486	0	ENST00000262189.6:c.13255C>G	p.Leu4419Val	p.L4419V	ENST00000262189	NM_170606.2	4419	Cta/Gta	52/59	1	2	FACETS	1	0.972	1	1	0.99	1	CLONAL	2	TRUE	1	0.197799875831504	2		486	435	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841040	15841040	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	107	470	0	ENST00000307771.7:c.1124G>A	p.Ser375Asn	p.S375N	ENST00000307771	NM_005089.3	375	aGc/aAc	11/11	0.197799875831504	1	FACETS	1	0.935	1	1	0.989	1	CLONAL	2	TRUE	0	0.197799875831504	1		470	465	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223710	53223710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	58	605	0	ENST00000375401.3:c.3649C>T	p.Pro1217Ser	p.P1217S	ENST00000375401	NM_004187.3	1217	Cct/Tct	23/26	0.197799875831504	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.197799875831504	1		605	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0025670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	209	302	0	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	0.279230991257245	2	FACETS	0.88	0.82	0.943	0.88	0.82	0.943	CLONAL	2	FALSE	0	0.310787265572321	2		302	764	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017802	31017802	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780662350	NA	P-0025670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	91	585	0	ENST00000375687.4:c.664G>A	p.Glu222Lys	p.E222K	ENST00000375687	NM_015338.5	222	Gag/Aag	8/13	0.241691325383889	4	FACETS	0.886	0.786	0.994	0.295	0.262	0.332	CLONAL	1	FALSE	1	0.310787265572321	4		585	866	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873843	151873843	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	109	453	1	ENST00000262189.6:c.8695C>T	p.Gln2899Ter	p.Q2899*	ENST00000262189	NM_170606.2	2899	Caa/Taa	38/59	0.279230991257245	2	FACETS	1	0.982	1	0.722	0.651	0.795	CLONAL	1	FALSE	0	0.310787265572321	2		454	486	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272095	15272095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	67	472	0	ENST00000263388.2:c.6344C>T	p.Pro2115Leu	p.P2115L	ENST00000263388	NM_000435.2	2115	cCt/cTt	33/33	0.280083007800363	3	FACETS	0.853	0.742	0.973	0.427	0.371	0.487	CLONAL	1	FALSE	1	0.310787265572321	3		472	584	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183836	10183836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1379270197	NA	P-0025670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	164	458	0	ENST00000256474.2:c.305C>T	p.Pro102Leu	p.P102L	ENST00000256474	NM_000551.3	102	cCg/cTg	1/3	0.279230991257245	2	FACETS	0.921	0.85	0.994	0.921	0.85	0.994	CLONAL	2	FALSE	0	0.310787265572321	2		458	573	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80646064	80646064	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	29	163	0	ENST00000286548.4:c.88C>T	p.Arg30Cys	p.R30C	ENST00000286548	NM_002072.3	30	Cgc/Tgc	1/7	0.299739302837962	4	FACETS	0.934	0.752	1	0.233	0.188	0.285	CLONAL	1	FALSE	0	0.310787265572321	4		163	262	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0025674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	24	435	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.464	0.363	0.58	0.464	0.363	0.58	SUBCLONAL	1	TRUE	1	0.253679596749709	2		435	408	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242474	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGA	GAATTAAGA	-	rs121913436	NA	P-0025674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	134	598	0	ENST00000275493.2:c.2239_2247del	p.Leu747_Glu749del	p.L747_E749del	ENST00000275493	NM_005228.3	746	GAATTAAGA/-	19/28	0.253679596749709	5	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	3	0.253679596749709	5		598	599	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175843	176175843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	109	151	0	ENST00000367669.3:c.272G>A	p.Cys91Tyr	p.C91Y	ENST00000367669	NM_022457.5	91	tGc/tAc	1/20	0.253679596749709	7	FACETS	1	0.957	1	1	0.982	1	CLONAL	7	TRUE	1	0.253679596749709	7		151	191	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196131	108196143	+	frameshift_variant	Frame_Shift_Del	DEL	ATCATGGCTCTAC	ATCATGGCTCTAC	-	novel	NA	P-0025674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	81	606	0	ENST00000278616.4:c.6667_6679del	p.Ile2223AlafsTer8	p.I2223Afs*8	ENST00000278616	NM_000051.3	2223	ATCATGGCTCTACgc/gc	46/63	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.253679596749709	2		606	440	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029494	14029494	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	42	443	0	ENST00000311895.7:c.1705G>T	p.Val569Leu	p.V569L	ENST00000311895	NM_005236.2	569	Gta/Tta	8/11	0.253679596749709	3	FACETS	0.906	0.757	1	0.453	0.378	0.535	CLONAL	1	TRUE	1	0.253679596749709	3		443	412	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47079255	47079255	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	68	554	0	ENST00000409792.3:c.7251G>A	p.Trp2417Ter	p.W2417*	ENST00000409792	NM_014159.6	2417	tgG/tgA	18/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.253679596749709	2		554	373	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47205375	47205375	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	17	330	0	ENST00000409792.3:c.40G>T	p.Asp14Tyr	p.D14Y	ENST00000409792	NM_014159.6	14	Gat/Tat	1/21	1	2	FACETS	0.568	0.424	0.738	0.568	0.424	0.738	SUBCLONAL	1	TRUE	1	0.253679596749709	2		330	236	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196170	138196170	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs587778710	NA	P-0025676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	82	219	0	ENST00000237289.4:c.484C>T	p.Arg162Trp	p.R162W	ENST00000237289	NM_001270507.1	162	Cgg/Tgg	3/9	0.859175481560502	3	FACETS	0.726	0.644	0.812	0.363	0.322	0.406	SUBCLONAL	1	TRUE	1	0.859175481560502	3		219	376	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122563	108122563	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs1565385010	NA	P-0025676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	302	272	0	ENST00000278616.4:c.1608-1G>C		p.X536_splice	ENST00000278616	NM_000051.3	536			0.825395443193557	2	FACETS	0.976	0.948	1	0.976	0.948	1	CLONAL	2	TRUE	0	0.859175481560502	2		272	360	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896549	78896549	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774124294	NA	P-0025676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	177	426	0	ENST00000306801.3:c.2546G>A	p.Arg849His	p.R849H	ENST00000306801	NM_020761.2	849	cGc/cAc	22/34	0.782677441925342	4	FACETS	0.971	0.896	1	0.485	0.448	0.524	CLONAL	1	TRUE	2	0.859175481560502	4		426	789	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0025678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	68	542	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.205260137087233	2		542	529	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610695	52610695	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	38	319	1	ENST00000394830.3:c.3478C>T	p.Arg1160Ter	p.R1160*	ENST00000394830	NM_018313.4	1160	Cga/Tga	23/30	0.204246066709274	1	FACETS	0.903	0.748	1	0.903	0.748	1	CLONAL	1	FALSE	0	0.205260137087233	1		320	368	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039206	49039206	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	50	562	0	ENST00000267163.4:c.2284del	p.Gln762ArgfsTer3	p.Q762Rfs*3	ENST00000267163	NM_000321.2	762	Cag/ag	22/27	1	2	FACETS	0.892	0.757	1	0.892	0.757	1	CLONAL	1	FALSE	1	0.205260137087233	2		562	546	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801058	1801058	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	78	686	1	ENST00000260795.2:c.187C>T	p.Pro63Ser	p.P63S	ENST00000260795		63	Ccg/Tcg	2/17	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	FALSE	1	0.205260137087233	2		687	693	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023172	27023186	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCCGGCGCGGAGC	GGCCCGGCGCGGAGC	CCCG	novel	NA	P-0025678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	23	74	0	ENST00000324856.7:c.278_292delinsCCCG	p.Gly93AlafsTer14	p.G93Afs*14	ENST00000324856	NM_006015.4	93	gGGCCCGGCGCGGAGCcg/gCCCGcg	1/20	0.204246066709274	1	FACETS	1	0.849	1	1	0.952	1	CLONAL	2	FALSE	0	0.205260137087233	1		74	93	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288600	33288600	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs779014832	NA	P-0025679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	120	346	0	ENST00000374542.5:c.952C>T	p.Arg318Ter	p.R318*	ENST00000374542	NM_001141970.1	318	Cga/Tga	3/8	0.387174678834217	1	FACETS	0.941	0.854	1	0.941	0.854	1	CLONAL	1	TRUE	0	0.387174678834217	1		346	531	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577204	64577204	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1114167492	NA	P-0025679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	216	557	1	ENST00000312049.6:c.378del	p.Trp126Ter	p.W126*	ENST00000312049	NM_130799.2	126	tgG/tg	2/10	0.387174678834217	1	FACETS	0.976	0.908	1	0.976	0.908	1	CLONAL	1	TRUE	0	0.387174678834217	1		558	922	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439634	51439634	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	144	384	0	ENST00000262662.1:c.199G>C	p.Asp67His	p.D67H	ENST00000262662		67	Gac/Cac	4/4	0.387174678834217	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.387174678834217	1		384	519	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124308	2124317	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGCTGCCT	GGCGCTGCCT	-	novel	NA	P-0025679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	212	639	0	ENST00000219476.3:c.2464_2473del	p.Ala822PhefsTer4	p.A822Ffs*4	ENST00000219476	NM_000548.3	821	aaGGCGCTGCCT/aa	22/42	0.387174678834217	1	FACETS	0.949	0.882	1	0.949	0.882	1	CLONAL	1	TRUE	0	0.387174678834217	1		639	931	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0025679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	9	410	0	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	0.581678954264763	4	FACETS	0.14	0.092	0.201	0.07	0.046	0.101	SUBCLONAL	1	TRUE	2	0.666347070188086	4		410	322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781371	NA	P-0025679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	8	492	2	ENST00000269305.4:c.328C>T	p.Arg110Cys	p.R110C	ENST00000269305	NM_001126112.2	110	Cgt/Tgt	4/11	0.43263362459168	5	FACETS	0.199	0.128	0.292	0.066	0.042	0.098	SUBCLONAL	1	TRUE	2	0.666347070188086	5		494	241	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288600	33288600	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs779014832	NA	P-0025679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	94	346	0	ENST00000374542.5:c.952C>T	p.Arg318Ter	p.R318*	ENST00000374542	NM_001141970.1	318	Cga/Tga	3/8	0.666347070188086	6	FACETS	0.976	0.877	1	0.488	0.438	0.54	CLONAL	2	TRUE	2	0.666347070188086	6		346	337	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577204	64577204	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1114167492	NA	P-0025679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	99	557	1	ENST00000312049.6:c.378del	p.Trp126Ter	p.W126*	ENST00000312049	NM_130799.2	126	tgG/tg	2/10	0.353261417873308	3	FACETS	1	0.98	1	0.454	0.41	0.499	INDETERMINATE	1	TRUE	0	0.666347070188086	3		558	291	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124337	2124337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774380711	NA	P-0025679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	10	442	2	ENST00000219476.3:c.2492C>T	p.Thr831Met	p.T831M	ENST00000219476	NM_000548.3	831	aCg/aTg	22/42	0.539726595126594	2	FACETS	0.152	0.102	0.213	0.076	0.051	0.107	SUBCLONAL	1	TRUE	0	0.666347070188086	2		444	198	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135321	2135321	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	50	347	0	ENST00000219476.3:c.4660C>T	p.Gln1554Ter	p.Q1554*	ENST00000219476	NM_000548.3	1554	Cag/Tag	36/42	0.539726595126594	2	FACETS	0.692	0.594	0.796	0.346	0.297	0.398	SUBCLONAL	1	TRUE	0	0.666347070188086	2		347	217	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351280	89351280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs539367470	NA	P-0025679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	10	494	2	ENST00000301030.4:c.1670C>T	p.Pro557Leu	p.P557L	ENST00000301030	NM_001256183.1	557	cCg/cTg	9/13	0.539726595126594	2	FACETS	0.178	0.12	0.25	0.089	0.06	0.125	SUBCLONAL	1	TRUE	0	0.666347070188086	2		496	169	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821176	72821176	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	37	697	0	ENST00000268489.5:c.10999G>A	p.Asp3667Asn	p.D3667N	ENST00000268489	NM_006885.3	3667	Gat/Aat	10/10	1	2	FACETS	0.907	0.746	1	0.907	0.746	1	CLONAL	1	TRUE	1	0.14	2		697	583	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0025681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	198	647	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.746849193943488	4	FACETS	0.986	0.914	1	0.329	0.304	0.354	CLONAL	1	TRUE	1	0.746849193943488	4		647	939	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953950	17953950	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs55778349	NA	P-0025681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	178	604	0	ENST00000458235.1:c.452C>G	p.Pro151Arg	p.P151R	ENST00000458235	NM_000215.3	151	cCc/cGc	5/24	0.746849193943488	3	FACETS	0.961	0.889	1	0.481	0.444	0.518	CLONAL	1	TRUE	1	0.746849193943488	3		604	681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0025681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	357	511	0	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	0.746849193943488	2	FACETS	0.996	0.963	1	0.996	0.963	1	CLONAL	2	TRUE	0	0.746849193943488	2		511	480	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294277	1294277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	104	440	0	ENST00000310581.5:c.724G>A	p.Ala242Thr	p.A242T	ENST00000310581	NM_198253.2	242	Gct/Act	2/16	NA	2	FACETS	0.78	0.705	0.858			1	INDETERMINATE	1	TRUE	NA	0.746849193943488	2		440	357	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380346	14380346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	322	315	1	ENST00000256196.4:c.71G>A	p.Gly24Asp	p.G24D	ENST00000256196		24	gGc/gAc	1/6	0.746849193943488	3	FACETS	1	0.975	1	1	0.997	1	CLONAL	3	TRUE	1	0.746849193943488	3		316	393	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134872996	134872996	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	138	435	0	ENST00000398015.3:c.1300C>A	p.Pro434Thr	p.P434T	ENST00000398015	NM_004441.4	434	Ccc/Acc	6/16	0.746849193943488	4	FACETS	1	0.959	1	0.361	0.329	0.394	CLONAL	1	TRUE	1	0.746849193943488	4		435	596	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0025682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	28	503	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.955	0.798	1	1	0.972	1	CLONAL	6	FALSE	1	0.152686843643419	2		503	64	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55269020	55269020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182857647	NA	P-0025682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	11	391	0	ENST00000275493.2:c.3086C>T	p.Thr1029Met	p.T1029M	ENST00000275493	NM_005228.3	1029	aCg/aTg	25/28	1	2	FACETS	0.906	0.628	1	0.906	0.628	1	CLONAL	1	FALSE	1	0.152686843643419	2		391	159	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0025683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	362	715	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.57787909616807	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.57787909616807	2		715	602	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0025683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	42	248	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.533811595730099	3	FACETS	0.738	0.62	0.866	0.369	0.31	0.433	SUBCLONAL	1	TRUE	1	0.57787909616807	3		248	254	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631101	69631101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150581924	NA	P-0025683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	128	476	1	ENST00000334134.2:c.311G>A	p.Arg104Gln	p.R104Q	ENST00000334134	NM_005247.2	104	cGa/cAa	2/3	0.537055507173669	4	FACETS	0.987	0.896	1	0.329	0.298	0.361	CLONAL	1	TRUE	1	0.57787909616807	4		477	708	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200305	67200305	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1007508504	NA	P-0025683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	118	433	0	ENST00000312629.5:c.613C>T	p.Gln205Ter	p.Q205*	ENST00000312629	NM_003952.2	205	Cag/Tag	7/15	0.537055507173669	4	FACETS	0.906	0.818	0.999	0.302	0.272	0.333	CLONAL	1	TRUE	1	0.57787909616807	4		433	711	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61711103	61711103	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	70	455	0	ENST00000401558.2:c.2646C>G	p.Phe882Leu	p.F882L	ENST00000401558	NM_003400.3	882	ttC/ttG	21/25	0.57787909616807	3	FACETS	0.842	0.738	0.952	0.421	0.369	0.476	CLONAL	1	TRUE	1	0.57787909616807	3		455	371	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189585706	189585706	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	92	448	0	ENST00000264731.3:c.967A>C	p.Ile323Leu	p.I323L	ENST00000264731	NM_003722.4	323	Atc/Ctc	7/14	0.57787909616807	3	FACETS	0.937	0.837	1	0.468	0.418	0.521	CLONAL	1	TRUE	1	0.57787909616807	3		448	438	SUCCESS
APC	324	MSKCC	GRCh37	5	112173780	112173780	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	112	328	0	ENST00000257430.4:c.2489del	p.Val830GlyfsTer12	p.V830Gfs*12	ENST00000257430	NM_000038.5	830	gTg/gg	16/16	0.533811595730099	3	FACETS	0.976	0.895	1	0.976	0.895	1	CLONAL	2	TRUE	1	0.57787909616807	3		328	256	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858443	27858443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750959072	NA	P-0025683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	146	343	0	ENST00000359303.2:c.128G>A	p.Arg43Lys	p.R43K	ENST00000359303	NM_003535.2	43	aGg/aAg	1/1	0.554903588764816	5	FACETS	0.93	0.855	1	0.465	0.427	0.504	CLONAL	2	TRUE	1	0.57787909616807	5		343	507	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508508	106508508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	99	171	0	ENST00000359195.3:c.502G>A	p.Val168Met	p.V168M	ENST00000359195	NM_002649.2	168	Gtg/Atg	2/11	0.539799605965623	4	FACETS	0.979	0.887	1	0.979	0.887	1	CLONAL	2	TRUE	2	0.57787909616807	4		171	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0025684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	457	522	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.523114163673926	3	FACETS	0.878	0.852	0.904	1	0.996	1	CLONAL	4	FALSE	0	0.518421662691385	3		522	632	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588751	29588751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760703505	NA	P-0025684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	41	362	1	ENST00000356175.3:c.4537C>T	p.Arg1513Ter	p.R1513*	ENST00000356175	NM_000267.3	1513	Cga/Tga	34/57	0.386000212088033	4	FACETS	0.536	0.447	0.635			1	SUBCLONAL	1	FALSE	NA	0.518421662691385	4		363	448	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023154	1023154	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs766789173	NA	P-0025684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	77	560	0	ENST00000358495.3:c.1101G>C	p.Gln367His	p.Q367H	ENST00000358495	NM_134424.2	367	caG/caC	11/12	0.386000212088033	4	FACETS	0.677	0.594	0.766			1	SUBCLONAL	1	FALSE	NA	0.518421662691385	4		560	666	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433005	49433005	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1208681909	NA	P-0025684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	34	497	2	ENST00000301067.7:c.8366G>A	p.Arg2789Gln	p.R2789Q	ENST00000301067	NM_003482.3	2789	cGg/cAg	33/54	0.286314508845793	5	FACETS	0.345	0.281	0.418	0.115	0.093	0.14	INDETERMINATE	1	FALSE	2	0.518421662691385	5		499	675	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698153	47698154	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0025684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	69	533	3	ENST00000233146.2:c.1711_1712delinsAT	p.Glu571Ile	p.E571I	ENST00000233146	NM_000251.2	571	GAa/ATa	11/16	0.523114163673926	3	FACETS	0.478	0.416	0.546	0.239	0.208	0.273	SUBCLONAL	1	FALSE	1	0.518421662691385	3		536	701	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39726902	39726902	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0025684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	39	372	0	ENST00000361337.2:c.900T>A	p.Cys300Ter	p.C300*	ENST00000361337	NM_003286.2	300	tgT/tgA	11/21	0.518421662691385	6	FACETS	0.43	0.356	0.514			1	SUBCLONAL	1	FALSE	NA	0.518421662691385	6		372	712	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670337	30670337	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	97	462	0	ENST00000376406.3:c.6095C>G	p.Ser2032Cys	p.S2032C	ENST00000376406	NM_014641.2	2032	tCc/tGc	14/15	0.518421662691385	8	FACETS	0.912	0.812	1			1	CLONAL	1	FALSE	NA	0.518421662691385	8		462	1048	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673400	30673400	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	358	615	1	ENST00000376406.3:c.3560C>G	p.Thr1187Ser	p.T1187S	ENST00000376406	NM_014641.2	1187	aCt/aGt	10/15	0.518421662691385	8	FACETS	1	0.955	1			1	CLONAL	3	FALSE	NA	0.518421662691385	8		616	1167	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429397	47429397	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	27	561	0	ENST00000377045.4:c.1525T>C	p.Tyr509His	p.Y509H	ENST00000377045	NM_001654.4	509	Tac/Cac	14/16	0.523114163673926	2	FACETS	0.31	0.247	0.382	0.155	0.123	0.191	SUBCLONAL	1	FALSE	0	0.518421662691385	2		561	336	SUCCESS
APC	324	MSKCC	GRCh37	5	112175772	112175772	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	154	340	0	ENST00000257430.4:c.4483del	p.Ser1495ValfsTer12	p.S1495Vfs*12	ENST00000257430	NM_000038.5	1494	gAa/ga	16/16	0.64527460038144	1	FACETS	0.998	0.932	1	0.998	0.932	1	CLONAL	1	TRUE	0	0.691681852915261	1		340	292	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863224683	NA	P-0025685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	438	795	1	ENST00000269305.4:c.388C>T	p.Leu130Phe	p.L130F	ENST00000269305	NM_001126112.2	130	Ctc/Ttc	5/11	0.691681852915261	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.691681852915261	1		796	770	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971193	21971193	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	221	372	0	ENST00000304494.5:c.165del	p.Ser56AlafsTer90	p.S56Afs*90	ENST00000304494	NM_000077.4	55	ggC/gg	2/3	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.691681852915261	2		372	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0025686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	300	616	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.478559252224328	5	FACETS	1	0.987	1	0.756	0.715	0.797	CLONAL	2	TRUE	2	0.622597915580137	5		616	822	SUCCESS
APC	324	MSKCC	GRCh37	5	112163696	112163697	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1131691555	NA	P-0025686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	137	348	0	ENST00000257430.4:c.1620dup	p.Gln541ThrfsTer19	p.Q541Tfs*19	ENST00000257430	NM_000038.5	540	tta/ttAa	13/16	0.622597915580137	3	FACETS	0.995	0.922	1	0.995	0.922	1	CLONAL	2	TRUE	1	0.622597915580137	3		348	290	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306559	163306559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781627921	NA	P-0025686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	112	488	2	ENST00000271452.3:c.356G>A	p.Arg119Gln	p.R119Q	ENST00000271452	NM_145697.2	119	cGg/cAg	6/14	0.478559252224328	5	FACETS	1	0.96	1	0.376	0.339	0.415	CLONAL	1	TRUE	2	0.622597915580137	5		490	617	SUCCESS
APC	324	MSKCC	GRCh37	5	112162945	112162946	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0025686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	69	323	0	ENST00000257430.4:c.1548+2dup		p.X516_splice	ENST00000257430	NM_000038.5	516			0.622597915580137	3	FACETS	1	0.949	1	0.572	0.504	0.644	CLONAL	1	TRUE	1	0.622597915580137	3		323	254	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945112	151945112	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	16	394	2	ENST00000262189.6:c.2407G>T	p.Ala803Ser	p.A803S	ENST00000262189	NM_170606.2	803	Gct/Tct	14/59	0.622597915580137	3	FACETS	0.342	0.253	0.447	0.171	0.126	0.224	SUBCLONAL	1	TRUE	1	0.622597915580137	3		396	197	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0025691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	102	607	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.128887241852181	5	FACETS	1	0.938	1	1	0.938	1	CLONAL	4	TRUE	1	0.128887241852181	5		607	446	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0025691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	82	339	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.128887241852181	5	FACETS	1	0.908	1	1	0.908	1	CLONAL	4	TRUE	1	0.128887241852181	5		339	370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578217	7578217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	33	461	0	ENST00000269305.4:c.632C>T	p.Thr211Ile	p.T211I	ENST00000269305	NM_001126112.2	211	aCt/aTt	6/11	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.128887241852181	2		461	393	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933561	36933561	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs373888342	NA	P-0025691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	33	413	0	ENST00000361632.4:c.1726G>A	p.Ala576Thr	p.A576T	ENST00000361632		576	Gcc/Acc	13/16	0.128887241852181	5	FACETS	1	0.918	1	0.313	0.254	0.379	CLONAL	1	TRUE	1	0.128887241852181	5		413	488	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16248837	16248837	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767352538	NA	P-0025691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	29	412	0	ENST00000375759.3:c.1843G>A	p.Glu615Lys	p.E615K	ENST00000375759	NM_015001.2	615	Gaa/Aaa	10/15	1	2	FACETS	0.98	0.786	1	0.98	0.786	1	CLONAL	1	TRUE	1	0.128887241852181	2		412	459	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012845	176012845	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0025691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	55	352	0	ENST00000367669.3:c.1530+1del		p.X510_splice	ENST00000367669	NM_022457.5	510			1	2	FACETS	1	0.888	1	1	0.977	1	CLONAL	2	TRUE	1	0.128887241852181	2		352	410	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201739	66201739	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	24	410	0	ENST00000273854.3:c.2763C>A	p.Ser921Arg	p.S921R	ENST00000273854	NM_004439.5	921	agC/agA	16/18	1	2	FACETS	0.962	0.754	1	0.962	0.754	1	CLONAL	1	TRUE	1	0.128887241852181	2		410	387	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293461	1293461	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	166	430	0	ENST00000310581.5:c.1540G>T	p.Val514Leu	p.V514L	ENST00000310581	NM_198253.2	514	Gtg/Ttg	2/16	0.128887241852181	9	FACETS	1	0.965	1	1	0.965	1	CLONAL	6	TRUE	3	0.128887241852181	9		430	579	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671655	30671655	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	46	425	0	ENST00000376406.3:c.5305G>A	p.Ala1769Thr	p.A1769T	ENST00000376406	NM_014641.2	1769	Gcc/Acc	10/15	0.0967318498895575	4	FACETS	0.903	0.762	1	0.903	0.762	1	CLONAL	2	TRUE	2	0.128887241852181	4		425	446	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0025692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	171	616	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.461626281294801	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.461626281294801	1		617	539	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0025692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	15	133	0	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	1	FACETS	0.685	0.512	0.882	0.685	0.512	0.882	SUBCLONAL	1	TRUE	0	0.461626281294801	1		133	73	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517201	NA	P-0025692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	109	207	0	ENST00000263967.3:c.1637A>C	p.Gln546Pro	p.Q546P	ENST00000263967	NM_006218.2	546	cAg/cCg	10/21	0.461626281294801	5	FACETS	0.932	0.836	1	0.311	0.278	0.345	CLONAL	1	TRUE	2	0.461626281294801	5		207	858	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023068	1023068	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs572909764	NA	P-0025692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	163	461	0	ENST00000358495.3:c.1187G>A	p.Arg396His	p.R396H	ENST00000358495	NM_134424.2	396	cGc/cAc	11/12	0.461626281294801	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.461626281294801	1		461	439	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435300	110435302	+	inframe_deletion	In_Frame_Del	DEL	GGT	GGT	-	rs765493638	NA	P-0025692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	14	123	2	ENST00000375856.3:c.3099_3101del	p.Pro1036del	p.P1036del	ENST00000375856	NM_003749.2	1033	ccACCg/ccg	1/2	0.455658355644826	2	FACETS	0.578	0.422	0.761	0.289	0.211	0.381	SUBCLONAL	1	TRUE	0	0.461626281294801	2		125	105	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233090	69233090	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746910913	NA	P-0025692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	75	324	0	ENST00000462284.1:c.961del	p.Leu321PhefsTer52	p.L321Ffs*52	ENST00000462284	NM_002392.5	319	Ccc/cc	11/11	1	2	FACETS	0.774	0.681	0.873	0.774	0.681	0.873	SUBCLONAL	1	TRUE	1	0.461626281294801	2		324	420	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255142	16255145	+	frameshift_variant	Frame_Shift_Del	DEL	GAGA	GAGA	-	novel	NA	P-0025692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	79	370	0	ENST00000375759.3:c.2415_2418del	p.Glu805AspfsTer3	p.E805Dfs*3	ENST00000375759	NM_015001.2	803	GAGAga/ga	11/15	1	2	FACETS	0.86	0.761	0.965	0.86	0.761	0.965	CLONAL	1	TRUE	1	0.461626281294801	2		370	398	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368387	225368388	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	110	474	0	ENST00000264414.4:c.1358dup	p.Asn453LysfsTer5	p.N453Kfs*5	ENST00000264414	NM_003590.4	453	aac/aaAc	9/16	1	2	FACETS	0.797	0.718	0.88	0.797	0.718	0.88	SUBCLONAL	1	TRUE	1	0.461626281294801	2		474	598	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874092	151874092	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	165	597	0	ENST00000262189.6:c.8446T>A	p.Ser2816Thr	p.S2816T	ENST00000262189	NM_170606.2	2816	Tcc/Acc	38/59	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.461626281294801	2		597	658	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77054906	77054906	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	131	544	0	ENST00000356341.3:c.956T>C	p.Met319Thr	p.M319T	ENST00000356341	NM_002576.4	319	aTg/aCg	10/15	1	2	FACETS	0.989	0.901	1	0.989	0.901	1	CLONAL	1	TRUE	1	0.461626281294801	2		544	574	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920723	100920723	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	90	536	0	ENST00000325455.5:c.2425G>C	p.Val809Leu	p.V809L	ENST00000325455	NM_001202474.3	809	Gtc/Ctc	6/8	1	2	FACETS	0.781	0.696	0.872	0.781	0.696	0.872	SUBCLONAL	1	TRUE	1	0.461626281294801	2		536	499	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379748	17379748	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202199976	NA	P-0025692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	136	947	0	ENST00000359435.4:c.133G>A	p.Val45Met	p.V45M	ENST00000359435	NM_001033549.1	45	Gtg/Atg	2/9	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.461626281294801	2		947	579	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570054	212570054	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	123	474	0	ENST00000342788.4:c.1187G>C	p.Arg396Thr	p.R396T	ENST00000342788	NM_005235.2	396	aGa/aCa	10/28	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.461626281294801	2		474	528	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37083818	37083818	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	101	444	1	ENST00000231790.2:c.1727T>C	p.Leu576Ser	p.L576S	ENST00000231790	NM_000249.3	576	tTa/tCa	15/19	0.461626281294801	1	FACETS	0.898	0.809	0.99	0.898	0.809	0.99	CLONAL	1	TRUE	0	0.461626281294801	1		445	375	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161387	55161388	+	missense_variant	Missense_Mutation	DNP	TG	TG	AT	novel	NA	P-0025692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	202	503	1	ENST00000257290.5:c.3218_3219delinsAT	p.Met1073Asn	p.M1073N	ENST00000257290	NM_006206.4	1073	aTG/aAT	23/23	0.461626281294801	3	FACETS	0.844	0.787	0.903	0.844	0.787	0.903	CLONAL	2	TRUE	1	0.461626281294801	3		504	638	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393186	393186	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	103	335	0	ENST00000380956.4:c.34T>G	p.Phe12Val	p.F12V	ENST00000380956	NM_001195286.1	12	Ttc/Gtc	2/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.461626281294801	NA		335	259	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008931	152008931	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	133	536	0	ENST00000262189.6:c.691G>C	p.Val231Leu	p.V231L	ENST00000262189	NM_170606.2	231	Gtt/Ctt	5/59	1	2	FACETS	0.98	0.893	1	0.98	0.893	1	CLONAL	1	TRUE	1	0.461626281294801	2		536	588	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141570600	141570600	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	66	395	1	ENST00000220592.5:c.528del	p.Val177TrpfsTer37	p.V177Wfs*37	ENST00000220592	NM_012154.3	176	ccC/cc	5/19	1	2	FACETS	0.805	0.703	0.915	0.805	0.703	0.915	CLONAL	1	TRUE	1	0.461626281294801	2		396	355	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971050	21971059	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGCCCCGG	CGCGCCCCGG	AGCCCCCGC	novel	NA	P-0025692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	111	302	2	ENST00000304494.5:c.299_308delinsGCGGGGGCT	p.Ala100GlyfsTer46	p.A100Gfs*46	ENST00000304494	NM_000077.4	100	gCCGGGGCGCGg/gGCGGGGGCTg	2/3	0.461626281294801	1	FACETS	0.752	0.689	0.815	1	0.987	1	SUBCLONAL	2	TRUE	0	0.461626281294801	1		304	246	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405179	139405179	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	116	775	0	ENST00000277541.6:c.2666del	p.Gly889AlafsTer290	p.G889Afs*290	ENST00000277541	NM_017617.3	889	gGc/gc	17/34	1	2	FACETS	0.894	0.809	0.984	0.894	0.809	0.984	CLONAL	1	TRUE	1	0.461626281294801	2		775	562	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	226	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.295503549908457	3	FACETS	0.954	0.89	1	0.954	0.89	1	CLONAL	2	TRUE	1	0.295503549908457	3		371	920	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0025694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	89	430	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.295503549908457	2		430	508	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	175	464	0	ENST00000342988.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000342988	NM_005359.5	356	cCt/cTt	9/12	0.295503549908457	2	FACETS	0.999	0.925	1	0.999	0.925	1	CLONAL	2	TRUE	0	0.295503549908457	2		464	593	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920401	114920401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1422891742	NA	P-0025694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	160	528	2	ENST00000543371.1:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000543371	NM_001198531.1	448	Cgg/Tgg	13/14	0.276459235093541	2	FACETS	0.893	0.823	0.967	0.893	0.823	0.967	CLONAL	2	TRUE	0	0.295503549908457	2		530	606	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266678	41266680	+	inframe_deletion	In_Frame_Del	DEL	CTG	CTG	-	novel	NA	P-0025694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	75	423	0	ENST00000349496.5:c.477_479del	p.Leu160del	p.L160del	ENST00000349496	NM_001904.3	159	CTG/-	4/15	0.295503549908457	3	FACETS	0.829	0.726	0.94	0.414	0.363	0.47	CLONAL	1	TRUE	1	0.295503549908457	3		423	703	SUCCESS
APC	324	MSKCC	GRCh37	5	112175155	112175161	+	frameshift_variant	Frame_Shift_Del	DEL	ATGTAAT	ATGTAAT	-	novel	NA	P-0025694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	45	213	0	ENST00000257430.4:c.3864_3870del	p.Cys1289ArgfsTer14	p.C1289Rfs*14	ENST00000257430	NM_000038.5	1288	ggATGTAAT/gg	16/16	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.295503549908457	2		213	299	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	114	340	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.772	0.698	0.849	0.772	0.698	0.849	SUBCLONAL	1	TRUE	1	0.562726115320755	2		340	525	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	9	83	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.098	0.064	0.141	0.098	0.064	0.141	SUBCLONAL	1	TRUE	1	0.562726115320755	2		83	327	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	337	628	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.921	0.88	0.963	1	0.996	1	CLONAL	2	TRUE	1	0.562726115320755	2		633	650	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	183	154	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.562726115320755	2		154	618	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383185	42383185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782563209	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	169	516	2	ENST00000221972.3:c.205G>A	p.Val69Ile	p.V69I	ENST00000221972	NM_021601.3	69	Gtc/Atc	2/5	1	2	FACETS	0.898	0.828	0.97	0.898	0.828	0.97	CLONAL	1	TRUE	1	0.562726115320755	2		518	669	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	249	389	2	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.962	0.913	1	1	0.995	1	CLONAL	2	TRUE	1	0.562726115320755	2		391	460	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	100	171	1	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	0.949	1	CLONAL	1	TRUE	1	0.562726115320755	2		172	329	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913559	32913559	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359479	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	113	347	0	ENST00000380152.3:c.5073del	p.Lys1691AsnfsTer15	p.K1691Nfs*15	ENST00000380152		1689	gcA/gc	11/27	1	2	FACETS	0.911	0.825	1	0.911	0.825	1	CLONAL	1	TRUE	1	0.562726115320755	2		347	441	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	87	671	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.849	0.758	0.946	0.849	0.758	0.946	CLONAL	1	TRUE	1	0.562726115320755	2		671	364	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	90	373	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.526083744675659	1	FACETS	0.877	0.79	0.967	0.877	0.79	0.967	CLONAL	1	TRUE	0	0.562726115320755	1		373	262	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808659	1808659	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs56266857	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	242	692	0	ENST00000260795.2:c.2272G>A	p.Asp758Asn	p.D758N	ENST00000260795		758	Gac/Aac	16/17	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.562726115320755	2		692	792	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	163	574	5	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.863	0.795	0.934	0.863	0.795	0.934	CLONAL	1	TRUE	1	0.562726115320755	2		579	671	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795103	242795104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs768249210	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	172	682	0	ENST00000334409.5:c.105dup	p.Thr36HisfsTer70	p.T36Hfs*70	ENST00000334409	NM_005018.2	35	-/C	2/5	1	2	FACETS	0.833	0.768	0.9	0.833	0.768	0.9	CLONAL	1	TRUE	1	0.562726115320755	2		682	734	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	17	562	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	0.178	0.132	0.233	0.178	0.132	0.233	SUBCLONAL	1	TRUE	1	0.562726115320755	2		562	339	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288710	15288710	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	14	33	0	ENST00000263388.2:c.4029del	p.Cys1344ValfsTer76	p.C1344Vfs*76	ENST00000263388	NM_000435.2	1343	ccC/cc	24/33	1	2	FACETS	0.905	0.674	1	0.905	0.674	1	CLONAL	1	TRUE	1	0.562726115320755	2		33	55	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	120	322	2	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.562726115320755	2		324	426	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687471	37687472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs760014508	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	66	262	0	ENST00000447079.4:c.4382dup	p.Thr1463AsnfsTer50	p.T1463Nfs*50	ENST00000447079	NM_015083.1	1459	tgg/tGgg	14/14	1	2	FACETS	0.801	0.701	0.906	0.801	0.701	0.906	CLONAL	1	TRUE	1	0.562726115320755	2		262	293	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306996	65306997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	94	329	4	ENST00000342505.4:c.2580dup	p.Pro861ThrfsTer4	p.P861Tfs*4	ENST00000342505	NM_002227.2	860	-/A	19/25	1	2	FACETS	0.758	0.678	0.842	0.758	0.678	0.842	SUBCLONAL	1	TRUE	1	0.562726115320755	2		333	441	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517552	176517552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs569265847	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	230	675	4	ENST00000292408.4:c.253C>T	p.Arg85Cys	p.R85C	ENST00000292408	NM_213647.1	85	Cgc/Tgc	3/18	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.562726115320755	2		679	739	SUCCESS
APC	324	MSKCC	GRCh37	5	112174484	112174484	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	96	251	2	ENST00000257430.4:c.3193C>T	p.Gln1065Ter	p.Q1065*	ENST00000257430	NM_000038.5	1065	Caa/Taa	16/16	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.562726115320755	2		253	338	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098423	11098423	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs549254467	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	98	326	0	ENST00000358026.2:c.941C>T	p.Ala314Val	p.A314V	ENST00000358026	NM_001128849.1	314	gCg/gTg	6/36	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.562726115320755	2		326	327	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337684	73337684	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771690280	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	71	273	2	ENST00000377767.4:c.2032del	p.Ile678PhefsTer59	p.I678Ffs*59	ENST00000377767	NM_014953.3	678	Att/tt	16/21	1	2	FACETS	0.85	0.749	0.956	0.85	0.749	0.956	CLONAL	1	TRUE	1	0.562726115320755	2		275	297	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661395	227661396	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGC	rs138975702	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	68	410	0	ENST00000305123.5:c.2057_2059dup	p.Ser686dup	p.S686dup	ENST00000305123	NM_005544.2	686	aac/aGCAac	1/2	1	2	FACETS	0.534	0.465	0.607	0.534	0.465	0.607	SUBCLONAL	1	TRUE	1	0.562726115320755	2		410	453	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190326	32190326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781213120	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	137	484	0	ENST00000375023.3:c.413C>T	p.Ser138Leu	p.S138L	ENST00000375023	NM_004557.3	138	tCg/tTg	3/30	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.562726115320755	2		484	461	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	128	318	0	ENST00000264010.4:c.609_610dup	p.Thr204LysfsTer19	p.T204Kfs*19	ENST00000264010	NM_006565.3	201	-/AA	3/12	1	2	FACETS	0.98	0.895	1	0.98	0.895	1	CLONAL	1	TRUE	1	0.562726115320755	2		318	464	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686900	37686901	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs772711685	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	136	425	0	ENST00000447079.4:c.3810dup	p.Gly1271ArgfsTer13	p.G1271Rfs*13	ENST00000447079	NM_015083.1	1268	-/C	14/14	1	2	FACETS	0.959	0.877	1	0.959	0.877	1	CLONAL	1	TRUE	1	0.562726115320755	2		425	504	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656840	45656840	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	164	483	2	ENST00000407780.3:c.316del	p.Gln106ArgfsTer11	p.Q106Rfs*11	ENST00000407780	NM_001283052.1	106	Cag/ag	3/7	1	2	FACETS	0.875	0.806	0.947	0.875	0.806	0.947	CLONAL	1	TRUE	1	0.562726115320755	2		485	666	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682831	190682831	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	152	393	0	ENST00000441310.2:c.512del	p.Lys171ArgfsTer7	p.K171Rfs*7	ENST00000441310	NM_000534.4	169	atA/at	5/13	1	2	FACETS	0.993	0.913	1	0.993	0.913	1	CLONAL	1	TRUE	1	0.562726115320755	2		393	544	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138112	64138112	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	186	472	0	ENST00000334205.4:c.2035G>A	p.Ala679Thr	p.A679T	ENST00000334205	NM_003942.2	679	Gcg/Acg	16/17	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.562726115320755	2		472	589	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120269	94120269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	88	257	0	ENST00000369303.4:c.782G>A	p.Gly261Glu	p.G261E	ENST00000369303	NM_004440.3	261	gGa/gAa	3/17	1	2	FACETS	0.83	0.74	0.924	0.83	0.74	0.924	CLONAL	1	TRUE	1	0.562726115320755	2		257	377	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462032	120462032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201996575	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	169	474	0	ENST00000256646.2:c.5684G>A	p.Arg1895His	p.R1895H	ENST00000256646	NM_024408.3	1895	cGt/cAt	31/34	1	2	FACETS	0.986	0.911	1	0.986	0.911	1	CLONAL	1	TRUE	1	0.562726115320755	2		474	609	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104269023	104269023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	174	550	1	ENST00000369902.3:c.280G>A	p.Gly94Ser	p.G94S	ENST00000369902	NM_016169.3	94	Ggc/Agc	2/12	1	2	FACETS	0.98	0.906	1	0.98	0.906	1	CLONAL	1	TRUE	1	0.562726115320755	2		551	631	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048772	180048772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758587669	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	207	652	0	ENST00000261937.6:c.1790C>T	p.Thr597Met	p.T597M	ENST00000261937	NM_182925.4	597	aCg/aTg	13/30	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.562726115320755	2		652	713	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216189	36216189	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	165	535	1	ENST00000222270.7:c.3602del	p.Pro1201ArgfsTer154	p.P1201Rfs*154	ENST00000222270	NM_014727.1	1199	ggC/gg	11/37	1	2	FACETS	0.982	0.906	1	0.982	0.906	1	CLONAL	1	TRUE	1	0.562726115320755	2		536	597	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645975	215645975	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs587780033	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	121	454	2	ENST00000260947.4:c.623del	p.Lys208ArgfsTer4	p.K208Rfs*4	ENST00000260947	NM_000465.2	208	aAg/ag	4/11	1	2	FACETS	0.829	0.752	0.908	0.829	0.752	0.908	CLONAL	1	TRUE	1	0.562726115320755	2		456	519	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119769	70119769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	172	514	0	ENST00000245479.2:c.774del	p.Leu259CysfsTer20	p.L259Cfs*20	ENST00000245479	NM_000346.3	257	cgC/cg	3/3	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.562726115320755	2		514	585	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257644	16257644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746087066	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	176	489	0	ENST00000375759.3:c.4909G>A	p.Val1637Ile	p.V1637I	ENST00000375759	NM_015001.2	1637	Gtt/Att	11/15	1	2	FACETS	0.959	0.887	1	0.959	0.887	1	CLONAL	1	TRUE	1	0.562726115320755	2		489	652	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612347	1612347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200962332	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	243	687	7	ENST00000344749.5:c.1672C>T	p.Arg558Cys	p.R558C	ENST00000344749	NM_001136139.2	558	Cgc/Tgc	18/19	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.562726115320755	2		694	837	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560403	95560403	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	170	452	1	ENST00000393063.1:c.5186C>T	p.Pro1729Leu	p.P1729L	ENST00000393063	NM_030621.3	1729	cCg/cTg	25/28	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.562726115320755	2		453	575	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518446	69518446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs987211751	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	53	151	0	ENST00000294312.3:c.199G>A	p.Val67Ile	p.V67I	ENST00000294312	NM_005117.2	67	Gtc/Atc	1/3	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.562726115320755	2		151	158	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416497	49416497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs566674356	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	183	470	0	ENST00000301067.7:c.16214G>A	p.Arg5405His	p.R5405H	ENST00000301067	NM_003482.3	5405	cGt/cAt	51/54	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.562726115320755	2		470	634	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425556	49425556	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	200	765	0	ENST00000301067.7:c.12932C>A	p.Pro4311Gln	p.P4311Q	ENST00000301067	NM_003482.3	4311	cCa/cAa	39/54	1	2	FACETS	0.935	0.869	1	0.935	0.869	1	CLONAL	1	TRUE	1	0.562726115320755	2		765	760	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434958	49434959	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1555192751	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	102	427	0	ENST00000301067.7:c.6594dup	p.Tyr2199LeufsTer3	p.Y2199Lfs*3	ENST00000301067	NM_003482.3	2198	-/C	31/54	1	2	FACETS	0.78	0.701	0.862	0.78	0.701	0.862	SUBCLONAL	1	TRUE	1	0.562726115320755	2		427	465	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432117	121432118	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	rs587776825	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	93	564	0	ENST00000257555.6:c.871_872dup	p.Gly292GlnfsTer51	p.G292Qfs*51	ENST00000257555		288	-/CC	4/10	1	2	FACETS	0.483	0.429	0.54	0.483	0.429	0.54	SUBCLONAL	1	TRUE	1	0.562726115320755	2		564	685	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32968855	32968855	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80359199	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	106	295	0	ENST00000380152.3:c.9286G>A	p.Glu3096Lys	p.E3096K	ENST00000380152		3096	Gaa/Aaa	25/27	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.562726115320755	2		295	374	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435907	110435907	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	135	513	0	ENST00000375856.3:c.2494C>T	p.Arg832Cys	p.R832C	ENST00000375856	NM_003749.2	832	Cgc/Tgc	1/2	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.562726115320755	2		513	462	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3645613	3645613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200807331	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	212	550	2	ENST00000294008.3:c.2006G>A	p.Arg669His	p.R669H	ENST00000294008	NM_032444.2	669	cGc/cAc	9/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.562726115320755	2		552	711	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845496	72845496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1042149925	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	147	449	0	ENST00000268489.5:c.3844G>A	p.Val1282Met	p.V1282M	ENST00000268489	NM_006885.3	1282	Gtg/Atg	7/10	1	2	FACETS	0.957	0.878	1	0.957	0.878	1	CLONAL	1	TRUE	1	0.562726115320755	2		449	546	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351959	89351959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1323276539	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	256	791	0	ENST00000301030.4:c.991G>A	p.Ala331Thr	p.A331T	ENST00000301030	NM_001256183.1	331	Gcc/Acc	9/13	1	2	FACETS	0.997	0.935	1	0.997	0.935	1	CLONAL	1	TRUE	1	0.562726115320755	2		791	913	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533369	29533369	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	81	177	0	ENST00000356175.3:c.1372C>A	p.Pro458Thr	p.P458T	ENST00000356175	NM_000267.3	458	Cca/Aca	12/57	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.562726115320755	2		177	288	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664546	29664546	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	143	477	0	ENST00000356175.3:c.6528del	p.Phe2176LeufsTer3	p.F2176Lfs*3	ENST00000356175	NM_000267.3	2175	acT/ac	42/57	1	2	FACETS	0.893	0.818	0.971	0.893	0.818	0.971	CLONAL	1	TRUE	1	0.562726115320755	2		477	569	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246294	41246294	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	192	560	0	ENST00000357654.3:c.1254G>T	p.Glu418Asp	p.E418D	ENST00000357654	NM_007294.3	418	gaG/gaT	10/23	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.562726115320755	2		560	667	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207591	2207591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	160	504	0	ENST00000398665.3:c.875G>A	p.Arg292His	p.R292H	ENST00000398665	NM_032482.2	292	cGc/cAc	11/28	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.562726115320755	2		504	561	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014293	70014293	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	178	560	0	ENST00000394351.3:c.1154C>A	p.Pro385His	p.P385H	ENST00000394351	NM_000248.3	385	cCc/cAc	9/9	1	2	FACETS	0.902	0.834	0.973	0.902	0.834	0.973	CLONAL	1	TRUE	1	0.562726115320755	2		560	701	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032275	26032275	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	58	215	0	ENST00000244661.2:c.14A>G	p.Lys5Arg	p.K5R	ENST00000244661	NM_003537.3	5	aAa/aGa	1/1	1	2	FACETS	0.742	0.643	0.847	0.742	0.643	0.847	SUBCLONAL	1	TRUE	1	0.562726115320755	2		215	278	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948517	31948517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751305169	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	57	155	2	ENST00000375333.2:c.1000G>A	p.Val334Met	p.V334M	ENST00000375333	NM_032454.1	334	Gtg/Atg	7/8	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.562726115320755	2		157	148	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956658	93956658	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	81	340	0	ENST00000369303.4:c.2578G>A	p.Asp860Asn	p.D860N	ENST00000369303	NM_004440.3	860	Gac/Aac	15/17	1	2	FACETS	0.647	0.572	0.726	0.647	0.572	0.726	SUBCLONAL	1	TRUE	1	0.562726115320755	2		340	445	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202350	138202351	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775280214	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	120	455	0	ENST00000237289.4:c.2274dup	p.Lys759GlnfsTer10	p.K759Qfs*10	ENST00000237289	NM_001270507.1	756	gac/gaCc	9/9	1	2	FACETS	0.707	0.64	0.777	0.707	0.64	0.777	SUBCLONAL	1	TRUE	1	0.562726115320755	2		455	603	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026721	6026721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751153838	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	164	510	0	ENST00000265849.7:c.1675G>A	p.Gly559Arg	p.G559R	ENST00000265849	NM_000535.5	559	Gga/Aga	11/15	1	2	FACETS	0.919	0.847	0.994	0.919	0.847	0.994	CLONAL	1	TRUE	1	0.562726115320755	2		510	634	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845523	151845524	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	155	523	0	ENST00000262189.6:c.13488dup	p.Lys4497Ter	p.K4497*	ENST00000262189	NM_170606.2	4496	-/T	52/59	1	2	FACETS	0.831	0.763	0.901	0.831	0.763	0.901	CLONAL	1	TRUE	1	0.562726115320755	2		523	663	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874679	151874679	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	144	406	0	ENST00000262189.6:c.7859C>A	p.Pro2620His	p.P2620H	ENST00000262189	NM_170606.2	2620	cCt/cAt	38/59	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.562726115320755	2		406	461	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268849	98268849	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554708787	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	88	289	0	ENST00000331920.6:c.234G>A	p.Trp78Ter	p.W78*	ENST00000331920	NM_000264.3	78	tgG/tgA	2/24	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.562726115320755	2		289	307	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900238	101900238	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs201021249	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	117	384	0	ENST00000374994.4:c.672G>A	p.Trp224Ter	p.W224*	ENST00000374994	NM_004612.2	224	tgG/tgA	4/9	1	2	FACETS	0.941	0.854	1	0.941	0.854	1	CLONAL	1	TRUE	1	0.562726115320755	2		384	442	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904896	101904897	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	93	329	0	ENST00000374994.4:c.887_888del	p.Thr296SerfsTer36	p.T296Sfs*36	ENST00000374994	NM_004612.2	295	tAC/t	5/9	1	2	FACETS	0.7	0.625	0.779	0.7	0.625	0.779	SUBCLONAL	1	TRUE	1	0.562726115320755	2		329	472	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341208	70341208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	127	231	0	ENST00000374080.3:c.767C>T	p.Thr256Ile	p.T256I	ENST00000374080		256	aCc/aTc	6/45	1	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.562726115320755	1		231	274	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219832	133219832	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	117	377	0	ENST00000320574.5:c.4529C>T	p.Ala1510Val	p.A1510V	ENST00000320574	NM_006231.2	1510	gCa/gTa	35/49	1	2	FACETS	0.771	0.698	0.848	0.771	0.698	0.848	SUBCLONAL	1	TRUE	1	0.562726115320755	2		377	539	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099173	157099173	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	23	195	0	ENST00000346085.5:c.110C>A	p.Ser37Tyr	p.S37Y	ENST00000346085	NM_020732.3	37	tCc/tAc	1/20	0.304447418450745	1	FACETS	0.258	0.202	0.322	0.258	0.202	0.322	INDETERMINATE	1	TRUE	0	0.591991036224349	1		195	212	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858600	57858600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756282060	NA	P-0025696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	51	425	0	ENST00000228682.2:c.338G>A	p.Arg113Gln	p.R113Q	ENST00000228682	NM_005269.2	113	cGa/cAa	4/12	0.591991036224349	3	FACETS	0.326	0.277	0.381	0.163	0.138	0.191	SUBCLONAL	1	TRUE	1	0.591991036224349	3		425	684	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390361	56390361	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	175	320	0	ENST00000348428.3:c.1100A>G	p.Tyr367Cys	p.Y367C	ENST00000348428	NM_006785.3	367	tAc/tGc	10/17	0.563010072293863	2	FACETS	1	0.99	1	0.701	0.653	0.749	CLONAL	1	TRUE	0	0.591991036224349	2		320	422	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348984	70348984	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	159	411	0	ENST00000374080.3:c.3496G>T	p.Glu1166Ter	p.E1166*	ENST00000374080		1166	Gag/Tag	25/45	0.443390415185558	3	FACETS	0.893	0.819	0.969	0.446	0.409	0.485	CLONAL	1	TRUE	1	0.591991036224349	3		411	780	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0025698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	60	285	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.217841490217938	2		285	526	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891251	101891251	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	44	390	0	ENST00000374994.4:c.212G>T	p.Cys71Phe	p.C71F	ENST00000374994	NM_004612.2	71	tGt/tTt	2/9	0.217841490217938	1	FACETS	0.658	0.551	0.776	0.658	0.551	0.776	SUBCLONAL	1	TRUE	0	0.217841490217938	1		390	547	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244000	46244010	+	frameshift_variant	Frame_Shift_Del	DEL	TCCAGTGACTG	TCCAGTGACTG	-	novel	NA	P-0025698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	59	415	1	ENST00000334344.6:c.2096_2106del	p.Pro699HisfsTer4	p.P699Hfs*4	ENST00000334344	NM_152641.2	698	gcTCCAGTGACTGtc/gctc	15/21	1	2	FACETS	0.753	0.647	0.869	0.753	0.647	0.869	SUBCLONAL	1	TRUE	1	0.217841490217938	2		416	719	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0025699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	124	278	7	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.252934131165038	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.23	1		285	723	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0025699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	155	437	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.206489322901975	4	FACETS	0.859	0.786	0.936	0.859	0.786	0.936	CLONAL	2	TRUE	2	0.23	4		437	965	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870257	155870257	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	114	494	0	ENST00000368323.3:c.582G>T	p.Glu194Asp	p.E194D	ENST00000368323	NM_006912.5	194	gaG/gaT	6/6	0.25062179053318	4	FACETS	1	0.965	1	0.583	0.524	0.646	CLONAL	1	TRUE	2	0.23	4		494	1045	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176153806	176153806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1366705437	NA	P-0025699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	35	417	0	ENST00000367669.3:c.430G>A	p.Glu144Lys	p.E144K	ENST00000367669	NM_022457.5	144	Gaa/Aaa	2/20	0.113353897610943	3	FACETS	0.855	0.701	1	0.285	0.233	0.343	INDETERMINATE	1	TRUE	0	0.23	3		417	397	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690810	89690810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	29	326	0	ENST00000371953.3:c.217G>A	p.Glu73Lys	p.E73K	ENST00000371953	NM_000314.4	73	Gaa/Aaa	4/9	1	2	FACETS	0.858	0.69	1	0.858	0.69	1	CLONAL	1	TRUE	1	0.23	2		326	294	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602532	10602532	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1237235830	NA	P-0025699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	74	406	0	ENST00000171111.5:c.1046A>G	p.Asp349Gly	p.D349G	ENST00000171111	NM_203500.1	349	gAc/gGc	3/6	1	2	FACETS	0.871	0.762	0.989	0.871	0.762	0.989	CLONAL	1	TRUE	1	0.23	2		406	739	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531867	41531867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	190	490	0	ENST00000263253.7:c.1579C>T	p.Leu527Phe	p.L527F	ENST00000263253	NM_001429.3	527	Ctt/Ttt	7/31	0.260381791140397	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.23	2		490	698	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207162	1207162	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs137853076	NA	P-0025700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	202	564	0	ENST00000326873.7:c.250A>T	p.Lys84Ter	p.K84*	ENST00000326873	NM_000455.4	84	Aag/Tag	1/10	0.683785898879163	1	FACETS	0.941	0.885	0.998	0.941	0.885	0.998	CLONAL	1	TRUE	0	0.683785898879163	1		564	413	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782144	NA	P-0025700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	204	551	0	ENST00000269305.4:c.473G>C	p.Arg158Pro	p.R158P	ENST00000269305	NM_001126112.2	158	cGc/cCc	5/11	0.636999031404674	1	FACETS	0.972	0.915	1	0.972	0.915	1	CLONAL	1	TRUE	0	0.683785898879163	1		551	404	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123789	11123789	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1555774786	NA	P-0025700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	162	374	0	ENST00000358026.2:c.2438+1G>A		p.X813_splice	ENST00000358026	NM_001128849.1	813			0.683785898879163	1	FACETS	0.917	0.855	0.979	0.917	0.855	0.979	CLONAL	1	TRUE	0	0.683785898879163	1		374	340	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984365	201984366	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0025700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	307	463	0	ENST00000359651.3:c.1033dup	p.Val345GlyfsTer126	p.V345Gfs*126	ENST00000359651		344	cgg/cGgg	8/8	0.662025842591642	2	FACETS	0.873	0.836	0.911	0.873	0.836	0.911	CLONAL	2	TRUE	0	0.683785898879163	2		463	514	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602293	10602293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1320679251	NA	P-0025700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	184	502	0	ENST00000171111.5:c.1285G>A	p.Gly429Ser	p.G429S	ENST00000171111	NM_203500.1	429	Ggc/Agc	3/6	0.683785898879163	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.683785898879163	1		502	342	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	88	412	4	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.838	0.745	0.937	1	0.987	1	CLONAL	3	TRUE	1	0.14	2		416	500	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	98	458	3	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	0.298804386426705	3	FACETS	0.993	0.889	1	1	0.981	1	CLONAL	3	TRUE	1	0.14	3		461	503	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	83	374	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.3	3	FACETS	0.909	0.806	1			1	CLONAL	3	TRUE	NA	0.14	3		374	465	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	90	374	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.3	3	FACETS	0.986	0.879	1			1	CLONAL	3	TRUE	NA	0.14	3		374	465	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850705	63850705	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs201178069	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	64	275	0	ENST00000279873.7:c.1489del	p.Ile497Ter	p.I497*	ENST00000279873	NM_032199.2	495	Aaa/aa	10/10	0.3	4	FACETS	0.949	0.826	1			1	CLONAL	3	TRUE	NA	0.14	4		275	366	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519886	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	74	241	0	ENST00000349496.5:c.97T>C	p.Ser33Pro	p.S33P	ENST00000349496	NM_001904.3	33	Tct/Cct	3/15	0.240853342852802	3	FACETS	1	0.896	1			1	CLONAL	3	TRUE	NA	0.14	3		241	370	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916648	178916648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	69	311	0	ENST00000263967.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000263967	NM_006218.2	12	gGc/gAc	2/21	1	2	FACETS	0.91	0.797	1	1	0.985	1	CLONAL	3	TRUE	1	0.14	2		311	361	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395910	395910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755460615	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	53	328	0	ENST00000380956.4:c.467C>T	p.Thr156Met	p.T156M	ENST00000380956	NM_001195286.1	156	aCg/aTg	4/9	NA	2	FACETS	0.861	0.74	0.993			1	INDETERMINATE	3	TRUE	NA	0.14	2		328	293	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	70	389	2	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.109518616427479	0	FACETS	0.995	0.876	1			1	CLONAL	3	TRUE	0	0.14	0		391	288	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648328	206648328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782549877	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	75	389	1	ENST00000367120.3:c.349C>T	p.Arg117Cys	p.R117C	ENST00000367120	NM_014002.3	117	Cgc/Tgc	5/22	0.3	5	FACETS	0.851	0.747	0.962	0.638	0.56	0.721	CLONAL	3	TRUE	1	0.14	5		390	508	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984813	55984813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200544155	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	102	399	0	ENST00000263923.4:c.316C>T	p.Arg106Trp	p.R106W	ENST00000263923	NM_002253.2	106	Cgg/Tgg	3/30	0.3	1	FACETS	1	0.91	1	1	0.99	1	CLONAL	3	TRUE	0	0.14	1		399	446	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202585	67202585	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374915842	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	86	396	0	ENST00000312629.5:c.1394G>A	p.Arg465His	p.R465H	ENST00000312629	NM_003952.2	465	cGt/cAt	15/15	1	2	FACETS	0.886	0.787	0.991	1	0.988	1	CLONAL	3	TRUE	1	0.14	2		396	462	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199945	138199945	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	48	226	0	ENST00000237289.4:c.1368del	p.Pro457LeufsTer20	p.P457Lfs*20	ENST00000237289	NM_001270507.1	455	Ggg/gg	7/9	0.116011896489052	4	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	2	0.14	4		226	322	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832025	72832025	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	65	365	0	ENST00000268489.5:c.4556C>G	p.Ser1519Ter	p.S1519*	ENST00000268489	NM_006885.3	1519	tCa/tGa	9/10	0.109518616427479	0	FACETS	0.795	0.693	0.903			1	CLONAL	3	TRUE	0	0.14	0		365	335	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981721	101981721	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555075353	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	39	108	0	ENST00000282441.5:c.147del	p.Ala50ProfsTer24	p.A50Pfs*24	ENST00000282441	NM_001130145.2	48	Ccc/cc	1/9	1	2	FACETS	0.986	0.839	1	1	0.979	1	CLONAL	5	TRUE	1	0.14	2		108	113	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	82	527	0	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.856	0.758	0.961	1	0.987	1	CLONAL	3	TRUE	1	0.14	2		527	456	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	72	439	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.982	0.864	1	1	0.986	1	CLONAL	3	TRUE	1	0.14	2		440	349	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852216	128852216	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167098287	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	105	510	1	ENST00000249373.3:c.2288G>A	p.Arg763Gln	p.R763Q	ENST00000249373	NM_005631.4	763	cGa/cAa	12/12	0.181666198390378	1	FACETS	1	0.958	1	1	0.991	1	CLONAL	3	TRUE	0	0.14	1		511	418	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459795	149459795	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755093010	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	78	374	1	ENST00000286301.3:c.412G>A	p.Val138Ile	p.V138I	ENST00000286301	NM_005211.3	138	Gtc/Atc	4/22	1	2	FACETS	1	0.93	1	1	0.988	1	CLONAL	3	TRUE	1	0.14	2		375	347	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376290	118376290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782434873	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	87	382	0	ENST00000534358.1:c.9683G>A	p.Arg3228His	p.R3228H	ENST00000534358	NM_005933.3	3228	cGt/cAt	27/36	1	2	FACETS	1	0.901	1	1	0.989	1	CLONAL	3	TRUE	1	0.14	2		382	409	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133898	41133898	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	29	215	0	ENST00000379561.5:c.1730del	p.Gly577AlafsTer5	p.G577Afs*5	ENST00000379561	NM_002015.3	577	gGc/gc	2/3	0.3	3	FACETS	0.89	0.718	1			1	CLONAL	2	TRUE	NA	0.14	3		215	249	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593346	67593346	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	82	253	0	ENST00000274335.5:c.2092T>A	p.Tyr698Asn	p.Y698N	ENST00000274335		698	Tac/Aac	15/15	0.116011896489052	4	FACETS	0.888	0.788	0.993	1	0.983	1	CLONAL	4	TRUE	2	0.14	4		253	376	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023326	27023327	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	21	35	0	ENST00000324856.7:c.437dup	p.Ala147SerfsTer253	p.A147Sfs*253	ENST00000324856	NM_006015.4	144	-/C	1/20	1	2	FACETS	0.949	0.75	1	1	0.959	1	CLONAL	4	TRUE	1	0.14	2		35	79	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275418	115275418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	94	319	0	ENST00000438362.2:c.995G>A	p.Arg332His	p.R332H	ENST00000438362	NM_001242891.1	332	cGc/cAc	10/20	1	2	FACETS	1	0.956	1	1	0.99	1	CLONAL	3	TRUE	1	0.14	2		319	398	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874257	155874257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	92	419	0	ENST00000368323.3:c.274G>A	p.Ala92Thr	p.A92T	ENST00000368323	NM_006912.5	92	Gca/Aca	5/6	0.3	7	FACETS	0.839	0.746	0.939			1	CLONAL	3	TRUE	NA	0.14	7		419	705	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851963	63851963	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779966636	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	76	336	0	ENST00000279873.7:c.2741C>T	p.Pro914Leu	p.P914L	ENST00000279873	NM_032199.2	914	cCg/cTg	10/10	0.3	4	FACETS	0.851	0.748	0.96			1	CLONAL	3	TRUE	NA	0.14	4		336	485	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530117	63530118	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	37	433	0	ENST00000307078.5:c.2317dup	p.Glu773GlyfsTer20	p.E773Gfs*20	ENST00000307078	NM_004655.3	773	gaa/gGaa	10/11	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.14	2		433	482	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231545	5231545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758460182	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	59	288	1	ENST00000357368.4:c.1931C>T	p.Pro644Leu	p.P644L	ENST00000357368	NM_002850.3	644	cCg/cTg	14/38	0.262995239053462	0	FACETS	0.867	0.757	0.983			1	CLONAL	4	TRUE	0	0.14	0		289	209	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184642	7184642	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749094324	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	31	140	2	ENST00000302850.5:c.659C>T	p.Pro220Leu	p.P220L	ENST00000302850	NM_000208.2	220	cCg/cTg	3/22	0.252879984531364	1	FACETS	0.909	0.746	1	1	0.968	1	CLONAL	3	TRUE	0	0.14	1		142	151	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270571	10270571	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	71	411	1	ENST00000340748.4:c.1069G>A	p.Gly357Arg	p.G357R	ENST00000340748		357	Ggg/Agg	15/40	1	2	FACETS	0.934	0.82	1	1	0.986	1	CLONAL	3	TRUE	1	0.14	2		412	362	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291170	10291170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369196079	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	110	449	1	ENST00000340748.4:c.301C>T	p.Arg101Trp	p.R101W	ENST00000340748		101	Cgg/Tgg	4/40	1	2	FACETS	1	0.924	1	1	0.991	1	CLONAL	3	TRUE	1	0.14	2		450	510	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193506	99193506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	51	376	0	ENST00000074304.5:c.2701C>T	p.Arg901Cys	p.R901C	ENST00000074304	NM_001134224.1	901	Cgt/Tgt	25/26	1	2	FACETS	1	0.902	1	1	0.976	1	CLONAL	2	TRUE	1	0.14	2		376	339	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44515645	44515645	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	34	473	0	ENST00000291552.4:c.251A>G	p.Glu84Gly	p.E84G	ENST00000291552	NM_006758.2	84	gAg/gGg	5/8	0.139649120309061	0	FACETS	0.878	0.716	1			1	CLONAL	1	TRUE	0	0.14	0		473	476	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196281	106196282	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAG	rs1163323186	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	41	167	0	ENST00000380013.4:c.4624_4626dup	p.Gln1542dup	p.Q1542dup	ENST00000380013	NM_001127208.2	1542	-/CAG	11/11	1	2	FACETS	1	0.931	1	1	0.973	1	CLONAL	2	TRUE	1	0.14	2		167	241	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247184	153247185	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	82	249	0	ENST00000281708.4:c.1617dup	p.His540AlafsTer3	p.H540Afs*3	ENST00000281708	NM_033632.3	539	-/G	10/12	1	2	FACETS	1	0.895	1	1	0.988	1	CLONAL	3	TRUE	1	0.14	2		249	387	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592115	67592115	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	64	220	0	ENST00000274335.5:c.1931G>T	p.Gly644Val	p.G644V	ENST00000274335		644	gGc/gTc	14/15	0.116011896489052	4	FACETS	1	0.917	1	1	0.975	1	CLONAL	3	TRUE	2	0.14	4		220	325	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638209	176638209	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780991637	NA	P-0025701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	113	503	0	ENST00000439151.2:c.2809C>T	p.Arg937Trp	p.R937W	ENST00000439151	NM_022455.4	937	Cgg/Tgg	5/23	1	2	FACETS	1	0.941	1	1	0.991	1	CLONAL	3	TRUE	1	0.14	2		503	510	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0025702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	238	360	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.80774646056049	2	FACETS	0.824	0.788	0.858	0.824	0.788	0.858	CLONAL	2	TRUE	0	0.847458652599244	2		360	341	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0025702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	284	323	0	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.847458652599244	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.847458652599244	1		323	360	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913351	NA	P-0025702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	191	440	1	ENST00000288602.6:c.1397G>A	p.Gly466Glu	p.G466E	ENST00000288602	NM_004333.4	466	gGa/gAa	11/18	NA	2	FACETS	0.846	0.788	0.904			1	INDETERMINATE	1	TRUE	NA	0.847458652599244	2		441	533	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0025702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	293	449	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.424156043408995	1	FACETS	0.752	0.717	0.787	0.752	0.717	0.787	INDETERMINATE	1	TRUE	0	0.847458652599244	1		449	530	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909655	76909655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557118749	NA	P-0025702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	145	287	0	ENST00000373344.5:c.4250G>A	p.Arg1417Gln	p.R1417Q	ENST00000373344	NM_000489.3	1417	cGg/cAg	14/35	1	1	FACETS	0.599	0.555	0.644	0.599	0.555	0.644	SUBCLONAL	1	TRUE	0	0.847458652599244	1		287	329	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604797	48604797	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	254	406	0	ENST00000342988.3:c.1619T>G	p.Leu540Arg	p.L540R	ENST00000342988	NM_005359.5	540	cTt/cGt	12/12	0.847458652599244	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.847458652599244	1		406	338	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412002	63412002	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	232	323	1	ENST00000330258.3:c.1165G>T	p.Glu389Ter	p.E389*	ENST00000330258	NM_152424.3	389	Gaa/Taa	2/2	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.847458652599244	1		324	263	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	40	387	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.1887061697333	2		387	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	133	496	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	1	2	FACETS	0.766	0.695	0.841	1	0.986	1	SUBCLONAL	2	TRUE	1	0.1887061697333	2		496	920	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058033	27058033	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	44	371	0	ENST00000324856.7:c.1741C>T	p.Gln581Ter	p.Q581*	ENST00000324856	NM_006015.4	581	Cag/Tag	3/20	1	2	FACETS	0.634	0.53	0.749	0.634	0.53	0.749	SUBCLONAL	1	TRUE	1	0.1887061697333	2		371	736	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032069	26032069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	71	317	0	ENST00000244661.2:c.220G>A	p.Glu74Lys	p.E74K	ENST00000244661	NM_003537.3	74	Gaa/Aaa	1/1	0.180496887367616	3	FACETS	1	0.963	1	0.648	0.566	0.738	CLONAL	1	TRUE	1	0.1887061697333	3		317	635	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489544	56489544	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761002408	NA	P-0025703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	200	433	0	ENST00000267101.3:c.2009G>A	p.Arg670Gln	p.R670Q	ENST00000267101	NM_001982.3	670	cGg/cAg	17/28	0.180496887367616	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.1887061697333	3		433	1006	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983120	201983121	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0025703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	111	448	1	ENST00000359651.3:c.970dup	p.Met324AsnfsTer147	p.M324Nfs*147	ENST00000359651		323	-/A	7/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.1887061697333	2		449	818	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444684	49444684	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	115	642	1	ENST00000301067.7:c.2782C>T	p.Gln928Ter	p.Q928*	ENST00000301067	NM_003482.3	928	Cag/Tag	10/54	0.180496887367616	3	FACETS	1	0.952	1	0.55	0.494	0.61	CLONAL	1	TRUE	1	0.1887061697333	3		643	1213	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444695	49444695	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	119	665	0	ENST00000301067.7:c.2771C>G	p.Ser924Cys	p.S924C	ENST00000301067	NM_003482.3	924	tCc/tGc	10/54	0.180496887367616	3	FACETS	1	0.957	1	0.557	0.501	0.616	CLONAL	1	TRUE	1	0.1887061697333	3		665	1239	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444956	49444956	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs749344235	NA	P-0025703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	84	383	0	ENST00000301067.7:c.2510C>G	p.Ser837Cys	p.S837C	ENST00000301067	NM_003482.3	837	tCt/tGt	10/54	0.180496887367616	3	FACETS	1	0.958	1	0.596	0.526	0.672	CLONAL	1	TRUE	1	0.1887061697333	3		383	817	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347854	73347854	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	32	300	0	ENST00000377767.4:c.1207G>C	p.Asp403His	p.D403H	ENST00000377767	NM_014953.3	403	Gat/Cat	8/21	1	2	FACETS	0.556	0.45	0.676	0.556	0.45	0.676	SUBCLONAL	1	TRUE	1	0.1887061697333	2		300	610	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347898	73347898	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	42	354	0	ENST00000377767.4:c.1163G>C	p.Arg388Thr	p.R388T	ENST00000377767	NM_014953.3	388	aGa/aCa	8/21	1	2	FACETS	0.657	0.547	0.779	0.657	0.547	0.779	SUBCLONAL	1	TRUE	1	0.1887061697333	2		354	678	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347927	73347927	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	37	275	0	ENST00000377767.4:c.1134G>C	p.Lys378Asn	p.K378N	ENST00000377767	NM_014953.3	378	aaG/aaC	8/21	1	2	FACETS	0.73	0.601	0.875	0.73	0.601	0.875	SUBCLONAL	1	TRUE	1	0.1887061697333	2		275	537	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396863	396863	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	77	500	0	ENST00000262320.3:c.163G>C	p.Glu55Gln	p.E55Q	ENST00000262320	NM_003502.3	55	Gag/Cag	2/11	NA	2	FACETS	0.926	0.812	1			1	INDETERMINATE	1	TRUE	NA	0.1887061697333	2		500	881	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296095	15296095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	79	513	3	ENST00000263388.2:c.2269C>T	p.His757Tyr	p.H757Y	ENST00000263388	NM_000435.2	757	Cac/Tac	14/33	1	2	FACETS	0.796	0.698	0.902	0.796	0.698	0.902	CLONAL	1	TRUE	1	0.1887061697333	2		516	1052	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631253	117631253	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	47	377	0	ENST00000368508.3:c.6425C>T	p.Ser2142Phe	p.S2142F	ENST00000368508	NM_002944.2	2142	tCt/tTt	40/43	0.146905038822659	1	FACETS	0.654	0.55	0.768	0.654	0.55	0.768	SUBCLONAL	1	TRUE	0	0.1887061697333	1		377	690	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528052	157528052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747819482	NA	P-0025703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	36	326	1	ENST00000346085.5:c.5777G>A	p.Arg1926Gln	p.R1926Q	ENST00000346085	NM_020732.3	1926	cGa/cAa	20/20	1	2	FACETS	0.575	0.472	0.692	0.575	0.472	0.692	SUBCLONAL	1	TRUE	1	0.1887061697333	2		327	663	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528852	157528852	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	43	410	0	ENST00000346085.5:c.6577G>C	p.Asp2193His	p.D2193H	ENST00000346085	NM_020732.3	2193	Gac/Cac	20/20	1	2	FACETS	0.613	0.512	0.727	0.613	0.512	0.727	SUBCLONAL	1	TRUE	1	0.1887061697333	2		410	743	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978720	70978720	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	96	440	0	ENST00000276594.2:c.933G>C	p.Leu311Phe	p.L311F	ENST00000276594	NM_024504.3	311	ttG/ttC	5/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.1887061697333	2		440	869	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922973	44922973	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	113	214	0	ENST00000377967.4:c.1834del	p.Arg612GlufsTer13	p.R612Efs*13	ENST00000377967	NM_021140.2	612	Cga/ga	16/29	1	1	FACETS	1	0.948	1	1	0.989	1	CLONAL	2	TRUE	0	0.1887061697333	1		214	505	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346398	73346400	+	stop_gained	Nonsense_Mutation	TNP	CTC	CTC	ATT	novel	NA	P-0025703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	59	338	0	ENST00000377767.4:c.1400_1402delinsAAT	p.Arg467_Glu468delinsGlnTer	p.R467_E468delinsQ*	ENST00000377767	NM_014953.3	467	cGAGaa/cAATaa	10/21	1	2	FACETS	0.868	0.746	1	0.868	0.746	1	CLONAL	1	TRUE	1	0.1887061697333	2		338	720	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871182	12871182	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1328655695	NA	P-0025704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	310	236	0	ENST00000228872.4:c.410del	p.Pro137ArgfsTer8	p.P137Rfs*8	ENST00000228872	NM_004064.3	137	Ccg/cg	1/3	0.814364213360448	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	4	TRUE	0	0.814364213360448	4		236	342	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660832	227660832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs767551071	NA	P-0025704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	95	497	0	ENST00000305123.5:c.2623C>G	p.Arg875Gly	p.R875G	ENST00000305123	NM_005544.2	875	Cga/Gga	1/2	0.775689899279403	2	FACETS	0.824	0.744	0.907	0.412	0.372	0.454	CLONAL	1	TRUE	0	0.814364213360448	2		497	283	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40674826	40675230	+	coding_sequence_variant,5_prime_UTR_variant	In_Frame_Del	DEL	CCCTAACAATCCCAAACTAAATAAAGAGGATTGTGACATGGACCCTAAATGTCGCCACGTTTGCGTCTCCATCCCGGAATATGACGCTGGTAGCTCATTAGCTCCATTCAAGCCTACAAATTGCATCACCCTCCTCCTCTGCCCAGACCTGGGGGCTCCAACACCTTTCGCTAGGTCTGGCTCTGGCCTCTGAGCGAACCTTCCGTACAGTATGGCGGCTCCCGAAGCCCCGCCCCTGGACAGAGTTTTCCGTACAACATGGCTGTCTACAGAGTGCGATTCCCACCCACTTCCGCCTAGCTACCGGAAGTTTCTATTTGAAACCCAGGCGGCCGACTTAGCCGGTGGCACGACAGTTGCTGCAGGGAATCTTTTAAACGAGAGCGAGAAGGACTGCGGGCAGGA	CCCTAACAATCCCAAACTAAATAAAGAGGATTGTGACATGGACCCTAAATGTCGCCACGTTTGCGTCTCCATCCCGGAATATGACGCTGGTAGCTCATTAGCTCCATTCAAGCCTACAAATTGCATCACCCTCCTCCTCTGCCCAGACCTGGGGGCTCCAACACCTTTCGCTAGGTCTGGCTCTGGCCTCTGAGCGAACCTTCCGTACAGTATGGCGGCTCCCGAAGCCCCGCCCCTGGACAGAGTTTTCCGTACAACATGGCTGTCTACAGAGTGCGATTCCCACCCACTTCCGCCTAGCTACCGGAAGTTTCTATTTGAAACCCAGGCGGCCGACTTAGCCGGTGGCACGACAGTTGCTGCAGGGAATCTTTTAAACGAGAGCGAGAAGGACTGCGGGCAGGA	-	novel	NA	P-0025704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	11	14	0				ENST00000249776	NM_033286.3	?-65/316		1/9	0.662526810921076	3	FACETS	1	0.758	1	0.528	0.381	0.692	CLONAL	1	TRUE	1	0.814364213360448	3		14	36	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682863	190682863	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	64	596	0	ENST00000441310.2:c.539G>A	p.Gly180Asp	p.G180D	ENST00000441310	NM_000534.4	180	gGt/gAt	5/13	0.485884625208701	4	FACETS	0.779	0.678	0.887			1	INDETERMINATE	1	TRUE	NA	0.814364213360448	4		596	366	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873075	134873075	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	154	670	0	ENST00000398015.3:c.1379C>A	p.Pro460His	p.P460H	ENST00000398015	NM_004441.4	460	cCc/cAc	6/16	0.814364213360448	3	FACETS	1	0.94	1	0.512	0.471	0.554	CLONAL	1	TRUE	1	0.814364213360448	3		670	520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0025708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	168	715	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.227178627210395	2		715	1065	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006449	12006450	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0025708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	148	556	0	ENST00000396373.4:c.419_420del	p.Ile140ThrfsTer13	p.I140Tfs*13	ENST00000396373	NM_001987.4	139	tcTAta/tcta	4/8	0.158988539695752	3	FACETS	1	0.957	1	0.542	0.494	0.594	CLONAL	1	TRUE	1	0.227178627210395	3		556	1338	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992720	68992721	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs764112302	NA	P-0025708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	316	544	11	ENST00000288368.4:c.1693dup	p.Ser565PhefsTer3	p.S565Ffs*3	ENST00000288368	NM_024870.2	562	cgt/cgTt	16/40	0.227178627210395	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.227178627210395	3		555	1418	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448532	49448532	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1421460851	NA	P-0025708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	79	347	0	ENST00000301067.7:c.179G>T	p.Gly60Val	p.G60V	ENST00000301067	NM_003482.3	60	gGg/gTg	3/54	1	2	FACETS	0.982	0.864	1	0.982	0.864	1	CLONAL	1	TRUE	1	0.227178627210395	2		347	708	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304429	91304429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	41	354	0	ENST00000355112.3:c.1826C>T	p.Pro609Leu	p.P609L	ENST00000355112	NM_000057.2	609	cCa/cTa	7/22	1	2	FACETS	0.488	0.406	0.581	0.488	0.406	0.581	SUBCLONAL	1	TRUE	1	0.227178627210395	2		354	739	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118902	70118903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGC	novel	NA	P-0025708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	114	458	0	ENST00000245479.2:c.476_479dup	p.Leu161AlafsTer92	p.L161Afs*92	ENST00000245479	NM_000346.3	158	-/GAGC	2/3	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.227178627210395	2		458	957	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266041	41266373	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTA	CCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTA	-	novel	NA	P-0025708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	29	231	0	ENST00000349496.5:c.42_242-68del		p.X14_splice	ENST00000349496	NM_001904.3	14		3/15	1	2	FACETS	0.542	0.434	0.665	0.542	0.434	0.665	SUBCLONAL	1	TRUE	1	0.227178627210395	2		231	471	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178943755	178943755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200671228	NA	P-0025708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	78	322	0	ENST00000263967.3:c.2422C>T	p.Arg808Trp	p.R808W	ENST00000263967	NM_006218.2	808	Cgg/Tgg	17/21	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.227178627210395	2		322	616	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001284	150001284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	56	496	0	ENST00000253339.5:c.2320G>A	p.Asp774Asn	p.D774N	ENST00000253339		774	Gat/Aat	4/7	1	2	FACETS	0.513	0.438	0.596	0.513	0.438	0.596	SUBCLONAL	1	TRUE	1	0.227178627210395	2		496	961	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533552	533552	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	16	782	0	ENST00000451590.1:c.351G>C	p.Lys117Asn	p.K117N	ENST00000451590	NM_001130442.1	117	aaG/aaC	4/5	0.172911002171617	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		782	290	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945148	44945148	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	130	285	0	ENST00000377967.4:c.3472A>T	p.Asn1158Tyr	p.N1158Y	ENST00000377967	NM_021140.2	1158	Aat/Tat	24/29	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	0	NA	2		285	256	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0025710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	112	317	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		317	1141	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515241	106515241	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143259740	NA	P-0025710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	36	315	0	ENST00000359195.3:c.2384C>T	p.Ala795Val	p.A795V	ENST00000359195	NM_002649.2	795	gCg/gTg	5/11	0.11058834345526	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		315	706	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520006	NA	P-0025711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	525	747	0	ENST00000269305.4:c.821T>G	p.Val274Gly	p.V274G	ENST00000269305	NM_001126112.2	274	gTt/gGt	8/11	0.508072745693047	2	FACETS	0.974	0.939	1	0.974	0.939	1	CLONAL	2	TRUE	0	0.541241895409402	2		747	996	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0025711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	285	721	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	0.366379828217238	3	FACETS	1	0.991	1	0.802	0.763	0.842	CLONAL	2	TRUE	0	0.541241895409402	3		721	556	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385177	41385177	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201332786	NA	P-0025711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	451	669	1	ENST00000373198.4:c.784G>A	p.Val262Ile	p.V262I	ENST00000373198	NM_133170.3	262	Gtc/Atc	6/32	0.493744870856923	4	FACETS	0.971	0.928	1	0.971	0.928	1	CLONAL	2	TRUE	2	0.541241895409402	4		670	1322	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717727	89717727	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554825226	NA	P-0025711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	505	490	0	ENST00000371953.3:c.752G>T	p.Gly251Val	p.G251V	ENST00000371953	NM_000314.4	251	gGt/gTt	7/9	0.530983519348316	4	FACETS	0.957	0.928	0.986	0.957	0.928	0.986	CLONAL	4	TRUE	0	0.541241895409402	4		490	751	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0025713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	44	675	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.728	0.61	0.86	0.728	0.61	0.86	SUBCLONAL	1	TRUE	1	0.19	2		675	636	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0025713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	67	385	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	0.643	0.849	0.742	0.643	0.849	SUBCLONAL	1	TRUE	1	0.19	2		385	951	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233079	69233180	+	inframe_deletion	In_Frame_Del	DEL	ATGAAATGAATCCCCCCCTTCCATCACATTGCAACAGATGTTGGGCCCTTCGTGAGAATTGGCTTCCTGAAGATAAAGGGAAAGATAAAGGGGAAATCTCTG	ATGAAATGAATCCCCCCCTTCCATCACATTGCAACAGATGTTGGGCCCTTCGTGAGAATTGGCTTCCTGAAGATAAAGGGAAAGATAAAGGGGAAATCTCTG	-	novel	NA	P-0025713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	66	448	0	ENST00000462284.1:c.945_1046del	p.Asn315_Glu349delinsLys	p.N315_E349delinsK	ENST00000462284	NM_002392.5	315	aATGAAATGAATCCCCCCCTTCCATCACATTGCAACAGATGTTGGGCCCTTCGTGAGAATTGGCTTCCTGAAGATAAAGGGAAAGATAAAGGGGAAATCTCTGag/aag	11/11	0.3	3	FACETS	1	0.971	1	0.733	0.637	0.836	CLONAL	1	TRUE	1	0.19	3		448	519	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057519990	NA	P-0025714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	348	569	0	ENST00000269305.4:c.796G>T	p.Gly266Ter	p.G266*	ENST00000269305	NM_001126112.2	266	Gga/Tga	8/11	NA	2	FACETS	0.917	0.878	0.955			1	INDETERMINATE	2	TRUE	NA	0.611418345125902	2		569	621	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221320	1221320	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587776656	NA	P-0025714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	309	407	0	ENST00000326873.7:c.843del	p.Leu282SerfsTer5	p.L282Sfs*5	ENST00000326873	NM_000455.4	281	ccG/cc	6/10	NA	2	FACETS	0.952	0.91	0.993			1	INDETERMINATE	2	TRUE	NA	0.611418345125902	2		407	531	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713427	40713427	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752787425	NA	P-0025714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	326	599	0	ENST00000373198.4:c.4088G>A	p.Arg1363Gln	p.R1363Q	ENST00000373198	NM_133170.3	1363	cGg/cAg	30/32	0.540325068438928	3	FACETS	0.914	0.868	0.959	0.914	0.868	0.959	CLONAL	2	TRUE	1	0.611418345125902	3		599	762	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77051698	77051698	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	295	407	0	ENST00000356341.3:c.1109G>T	p.Cys370Phe	p.C370F	ENST00000356341	NM_002576.4	370	tGc/tTc	11/15	0.587528038212471	2	FACETS	0.93	0.887	0.972	0.93	0.887	0.972	CLONAL	2	TRUE	0	0.611418345125902	2		407	519	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615551	43615551	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	171	456	0	ENST00000355710.3:c.2630C>G	p.Ala877Gly	p.A877G	ENST00000355710	NM_020975.4	877	gCc/gGc	15/20	0.336184683841489	3	FACETS	1	0.926	1			1	INDETERMINATE	1	TRUE	NA	0.611418345125902	3		456	727	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572260	64572260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200035619	NA	P-0025714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	190	341	1	ENST00000312049.6:c.1379G>A	p.Arg460Gln	p.R460Q	ENST00000312049	NM_130799.2	460	cGa/cAa	10/10	0.587528038212471	2	FACETS	0.965	0.911	1	0.965	0.911	1	CLONAL	2	TRUE	0	0.611418345125902	2		342	322	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42842598	42842598	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	212	568	1	ENST00000398585.3:c.1259G>T	p.Gly420Val	p.G420V	ENST00000398585	NM_001135099.1	420	gGg/gTg	11/14	0.533944971926032	4	FACETS	1	0.98	1	0.381	0.354	0.41	CLONAL	1	TRUE	1	0.611418345125902	4		569	977	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5077461	5077461	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	200	447	0	ENST00000381652.3:c.1873G>T	p.Val625Phe	p.V625F	ENST00000381652	NM_004972.3	625	Gtt/Ttt	15/25	0.608164584781649	2	FACETS	0.914	0.862	0.964	0.914	0.862	0.964	CLONAL	2	TRUE	0	0.611418345125902	2		447	358	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56363603	56363603	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0025714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	101	262	0	ENST00000348428.3:c.382A>T	p.Lys128Ter	p.K128*	ENST00000348428	NM_006785.3	128	Aag/Tag	3/17	0.540325068438928	3	FACETS	0.773	0.701	0.847	0.773	0.701	0.847	SUBCLONAL	2	TRUE	1	0.611418345125902	3		262	279	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914271	32914271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	51	532	1	ENST00000380152.3:c.5779G>A	p.Glu1927Lys	p.E1927K	ENST00000380152		1927	Gaa/Aaa	11/27	0.206621562127656	3	FACETS	0.413	0.351	0.482	0.138	0.117	0.161	INDETERMINATE	1	TRUE	0	0.611418345125902	3		533	527	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0025716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	110	503	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.984	0.884	1	0.984	0.884	1	CLONAL	1	TRUE	1	0.257529867270749	2		503	868	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0025716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	161	358	2	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.257529867270749	1	FACETS	0.918	0.84	0.999	0.918	0.84	0.999	CLONAL	1	TRUE	0	0.257529867270749	1		360	1187	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968259	2968259	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	204	716	2	ENST00000396946.4:c.1727G>A	p.Arg576His	p.R576H	ENST00000396946	NM_032415.4	576	cGc/cAc	13/25	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.257529867270749	2		718	1253	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20152120	20152120	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	87	678	0	ENST00000379607.5:c.210G>T	p.Trp70Cys	p.W70C	ENST00000379607	NM_001412.3	70	tgG/tgT	4/7	0.257529867270749	1	FACETS	0.794	0.703	0.892	0.794	0.703	0.892	SUBCLONAL	1	TRUE	0	0.257529867270749	1		678	741	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505026	149505026	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	53	442	0	ENST00000261799.4:c.1789C>T	p.Arg597Trp	p.R597W	ENST00000261799	NM_002609.3	597	Cgg/Tgg	12/23	1	2	FACETS	0.655	0.558	0.762	0.655	0.558	0.762	SUBCLONAL	1	TRUE	1	0.257529867270749	2		442	628	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366149	15366149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35824241	NA	P-0025716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	65	625	0	ENST00000263377.2:c.2006G>A	p.Arg669His	p.R669H	ENST00000263377	NM_058243.2	669	cGc/cAc	10/20	1	2	FACETS	0.445	0.384	0.511	0.445	0.384	0.511	SUBCLONAL	1	TRUE	1	0.257529867270749	2		625	1135	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483016	29483016	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	57	588	0	ENST00000356175.3:c.76G>T	p.Gly26Ter	p.G26*	ENST00000356175	NM_000267.3	26	Gga/Tga	2/57	0.257529867270749	1	FACETS	0.758	0.651	0.874	0.758	0.651	0.874	SUBCLONAL	1	TRUE	0	0.257529867270749	1		588	509	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209302	133209302	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	129	792	0	ENST00000320574.5:c.6084G>T	p.Arg2028Ser	p.R2028S	ENST00000320574	NM_006231.2	2028	agG/agT	44/49	1	2	FACETS	0.885	0.801	0.974	0.885	0.801	0.974	CLONAL	1	TRUE	1	0.257529867270749	2		792	1132	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740683	58740683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	237	738	0	ENST00000305921.3:c.1588C>T	p.Pro530Ser	p.P530S	ENST00000305921	NM_003620.3	530	Cct/Tct	6/6	0.23520509854037	3	FACETS	0.856	0.797	0.916	0.856	0.797	0.916	CLONAL	2	TRUE	1	0.257529867270749	3		738	1214	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456461	89456461	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	105	507	0	ENST00000336596.2:c.1637C>A	p.Ala546Asp	p.A546D	ENST00000336596	NM_005233.5	546	gCc/gAc	8/17	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.257529867270749	2		507	686	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729438	41729438	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	131	588	0	ENST00000242208.4:c.1091C>A	p.Ser364Tyr	p.S364Y	ENST00000242208	NM_002192.2	364	tCc/tAc	3/3	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.257529867270749	2		588	904	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998186	100998186	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	63	431	0	ENST00000325455.5:c.1616C>A	p.Pro539Gln	p.P539Q	ENST00000325455	NM_001202474.3	539	cCg/cAg	1/8	1	2	FACETS	0.831	0.719	0.952	0.831	0.719	0.952	CLONAL	1	TRUE	1	0.257529867270749	2		431	589	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100563	102100563	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	104	652	0	ENST00000282441.5:c.1407G>T	p.Glu469Asp	p.E469D	ENST00000282441	NM_001130145.2	469	gaG/gaT	9/9	1	2	FACETS	0.88	0.787	0.979	0.88	0.787	0.979	CLONAL	1	TRUE	1	0.257529867270749	2		652	918	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482591	56482591	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1479967163	NA	P-0025716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	119	803	0	ENST00000267101.3:c.1048G>A	p.Gly350Arg	p.G350R	ENST00000267101	NM_001982.3	350	Gga/Aga	9/28	1	2	FACETS	0.842	0.758	0.931	0.842	0.758	0.931	CLONAL	1	TRUE	1	0.257529867270749	2		803	1098	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120782	115120782	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	56	525	0	ENST00000257566.3:c.224G>T	p.Gly75Val	p.G75V	ENST00000257566	NM_016569.3	75	gGc/gTc	1/8	1	2	FACETS	0.664	0.568	0.769	0.664	0.568	0.769	SUBCLONAL	1	TRUE	1	0.257529867270749	2		525	655	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518630	103518630	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	93	368	0	ENST00000355739.4:c.2218G>C	p.Glu740Gln	p.E740Q	ENST00000355739	NM_000123.3	740	Gag/Cag	10/15	0.257529867270749	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.257529867270749	1		368	548	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347734	347734	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	66	630	0	ENST00000262320.3:c.1772G>T	p.Gly591Val	p.G591V	ENST00000262320	NM_003502.3	591	gGc/gTc	6/11	0.257529867270749	1	FACETS	0.481	0.416	0.551	0.481	0.416	0.551	SUBCLONAL	1	TRUE	0	0.257529867270749	1		630	929	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512334	38512334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	113	589	0	ENST00000254066.5:c.1245G>T	p.Glu415Asp	p.E415D	ENST00000254066	NM_000964.3	415	gaG/gaT	9/9	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.257529867270749	2		589	867	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665410	182665410	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	59	481	0	ENST00000292782.4:c.531G>T	p.Met177Ile	p.M177I	ENST00000292782	NM_020640.2	177	atG/atT	5/7	0.23520509854037	3	FACETS	0.836	0.719	0.963	0.418	0.359	0.482	CLONAL	1	TRUE	1	0.257529867270749	3		481	619	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622278	162622278	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	82	457	2	ENST00000366898.1:c.419G>T	p.Arg140Ile	p.R140I	ENST00000366898	NM_004562.2	140	aGa/aTa	4/12	0.257529867270749	1	FACETS	0.967	0.854	1	0.967	0.854	1	CLONAL	1	TRUE	0	0.257529867270749	1		459	574	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346600	81346600	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	78	487	2	ENST00000222390.5:c.1353G>T	p.Trp451Cys	p.W451C	ENST00000222390	NM_000601.4	451	tgG/tgT	11/18	1	2	FACETS	0.988	0.869	1	0.988	0.869	1	CLONAL	1	TRUE	1	0.257529867270749	2		489	613	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242251	98242251	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	99	577	0	ENST00000331920.6:c.1067G>C	p.Ser356Thr	p.S356T	ENST00000331920	NM_000264.3	356	aGc/aCc	7/24	1	2	FACETS	0.907	0.809	1	0.907	0.809	1	CLONAL	1	TRUE	1	0.257529867270749	2		577	848	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0025717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	54	620	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.973	0.834	1	0.973	0.834	1	CLONAL	1	FALSE	1	0.3	2		620	370	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324917	31324917	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs776780353	NA	P-0025719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	290	585	0	ENST00000412585.2:c.19C>T	p.Arg7Ter	p.R7*	ENST00000412585	NM_005514.6	7	Cga/Tga	1/8	0.447849000803714	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.447849000803714	2		585	550	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857917	9857917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	137	584	0	ENST00000330684.3:c.3484G>A	p.Asp1162Asn	p.D1162N	ENST00000330684	NM_001134407.1	1162	Gac/Aac	13/13	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.447849000803714	2		584	573	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775653	9775653	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	42	556	2	ENST00000377346.4:c.196G>T	p.Glu66Ter	p.E66*	ENST00000377346	NM_005026.3	66	Gag/Tag	4/24	1	2	FACETS	0.359	0.3	0.426	0.359	0.3	0.426	SUBCLONAL	1	TRUE	1	0.447849000803714	2		558	522	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63699973	63699973	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs759668203	NA	P-0025719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	24	282	0	ENST00000279873.7:c.308T>C	p.Ile103Thr	p.I103T	ENST00000279873	NM_032199.2	103	aTt/aCt	3/10	1	2	FACETS	0.29	0.227	0.363	0.29	0.227	0.363	SUBCLONAL	1	TRUE	1	0.447849000803714	2		282	369	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229626	5229626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	17	53	0	ENST00000357368.4:c.2225G>A	p.Arg742His	p.R742H	ENST00000357368	NM_002850.3	742	cGc/cAc	15/38	1	2	FACETS	0.808	0.63	0.997	1	0.923	1	CLONAL	2	TRUE	1	0.447849000803714	2		53	47	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959903	38959903	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	29	368	0	ENST00000357387.3:c.2029G>C	p.Glu677Gln	p.E677Q	ENST00000357387	NM_152756.3	677	Gaa/Caa	21/38	0.447849000803714	3	FACETS	0.286	0.229	0.352	0.143	0.114	0.176	SUBCLONAL	1	TRUE	1	0.447849000803714	3		368	554	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032213	26032214	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0025719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	34	260	0	ENST00000244661.2:c.75dup	p.Ala26CysfsTer73	p.A26Cfs*73	ENST00000244661	NM_003537.3	25	-/T	1/1	0.447849000803714	2	FACETS	0.638	0.524	0.764	0.319	0.262	0.382	SUBCLONAL	1	TRUE	0	0.447849000803714	2		260	238	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340270	116340270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749738523	NA	P-0025719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	37	370	1	ENST00000397752.3:c.1132G>A	p.Val378Ile	p.V378I	ENST00000397752	NM_000245.2	378	Gtc/Atc	2/21	1	2	FACETS	0.339	0.279	0.406	0.339	0.279	0.406	SUBCLONAL	1	TRUE	1	0.447849000803714	2		371	488	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0025720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	241	206	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.733024735898297	2		207	657	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432067	121432067	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555212014	NA	P-0025720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	333	536	0	ENST00000257555.6:c.814C>T	p.Arg272Cys	p.R272C	ENST00000257555		272	Cgc/Tgc	4/10	1	2	FACETS	0.977	0.926	1	0.977	0.926	1	CLONAL	1	TRUE	1	0.733024735898297	2		536	930	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157797	106157797	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs751193037	NA	P-0025720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	183	324	0	ENST00000380013.4:c.2702del	p.Asn901IlefsTer20	p.N901Ifs*20	ENST00000380013	NM_001127208.2	900	Aaa/aa	3/11	1	2	FACETS	0.958	0.891	1	0.958	0.891	1	CLONAL	1	TRUE	1	0.733024735898297	2		324	521	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057326	180057326	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	352	505	0	ENST00000261937.6:c.412C>T	p.Pro138Ser	p.P138S	ENST00000261937	NM_182925.4	138	Cca/Tca	4/30	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.733024735898297	2		505	909	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46602879	46602879	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	77	539	2	ENST00000263734.3:c.937C>A	p.His313Asn	p.H313N	ENST00000263734	NM_001430.4	313	Cat/Aat	8/16	1	2	FACETS	0.214	0.187	0.244	0.214	0.187	0.244	SUBCLONAL	1	TRUE	1	0.733024735898297	2		541	980	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639513	3639513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1379159016	NA	P-0025720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	66	564	1	ENST00000294008.3:c.4126C>T	p.His1376Tyr	p.H1376Y	ENST00000294008	NM_032444.2	1376	Cac/Tac	12/15	1	2	FACETS	0.192	0.165	0.22	0.192	0.165	0.22	SUBCLONAL	1	TRUE	1	0.733024735898297	2		565	940	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223076	1223077	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCGTACTTGGAGGACCTGCACGGC	novel	NA	P-0025720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	237	542	0	ENST00000326873.7:c.1016_1040dup	p.Asp348ValfsTer20	p.D348Vfs*20	ENST00000326873	NM_000455.4	338	gtg/gtGCCGTACTTGGAGGACCTGCACGGCg	8/10	0.733024735898297	1	FACETS	0.616	0.578	0.655	0.616	0.578	0.655	SUBCLONAL	1	TRUE	0	0.733024735898297	1		542	665	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0025721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	322	611	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.240115726331735	4	FACETS	0.909	0.861	0.958	1	0.991	1	CLONAL	4	TRUE	1	0.240115726331735	4		611	915	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743881	40743881	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	166	709	0	ENST00000373198.4:c.3114G>T	p.Glu1038Asp	p.E1038D	ENST00000373198	NM_133170.3	1038	gaG/gaT	23/32	NA	2	FACETS	0.933	0.859	1			1	INDETERMINATE	2	TRUE	NA	0.240115726331735	2		709	741	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs587781702	NA	P-0025721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	180	667	3	ENST00000269305.4:c.920-1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			NA	2	FACETS	1	0.944	1			1	INDETERMINATE	2	TRUE	NA	0.240115726331735	2		670	731	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191101	2191101	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	273	728	1	ENST00000398665.3:c.355G>T	p.Val119Leu	p.V119L	ENST00000398665	NM_032482.2	119	Gtg/Ttg	5/28	0.224191683475377	3	FACETS	1	0.979	1			1	CLONAL	3	TRUE	NA	0.240115726331735	3		729	788	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037162	71037162	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs886058865	NA	P-0025721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	150	462	0	ENST00000318789.4:c.1129A>G	p.Lys377Glu	p.K377E	ENST00000318789	NM_032682.5	377	Aaa/Gaa	14/21	0.240115726331735	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.240115726331735	4		462	689	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636003	28636004	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0025721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	84	657	1	ENST00000241453.7:c.368_368+1delinsTT		p.X123_splice	ENST00000241453	NM_004119.2	123		3/24	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.240115726331735	2		658	694	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003794	45003794	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	60	496	0	ENST00000558401.1:c.50G>T	p.Gly17Val	p.G17V	ENST00000558401	NM_004048.2	17	gGc/gTc	1/4	0.240115726331735	3	FACETS	0.985	0.849	1	0.493	0.424	0.567	CLONAL	1	TRUE	1	0.240115726331735	3		496	568	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561324	9561324	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	58	435	1	ENST00000353224.5:c.458G>T	p.Gly153Val	p.G153V	ENST00000353224	NM_177990.2	153	gGa/gTa	4/10	0.240115726331735	3	FACETS	0.845	0.726	0.976	0.423	0.363	0.488	CLONAL	1	TRUE	1	0.240115726331735	3		436	640	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0025722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	135	340	0	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	FALSE	1	0.313552894845508	2		340	647	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409152	4409152	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	60	615	0	ENST00000261254.3:c.847G>T	p.Asp283Tyr	p.D283Y	ENST00000261254	NM_001759.3	283	Gac/Tac	5/5	1	2	FACETS	0.575	0.494	0.662	0.575	0.494	0.662	SUBCLONAL	1	FALSE	1	0.313552894845508	2		615	666	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045172	47045172	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	91	796	0	ENST00000377604.3:c.2413G>T	p.Glu805Ter	p.E805*	ENST00000377604	NM_001204468.1	805	Gag/Tag	21/24	1	2	FACETS	0.908	0.807	1	0.908	0.807	1	CLONAL	1	FALSE	1	0.313552894845508	2		796	639	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456470	89456470	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	55	535	2	ENST00000336596.2:c.1646C>A	p.Ala549Glu	p.A549E	ENST00000336596	NM_005233.5	549	gCg/gAg	8/17	1	2	FACETS	0.696	0.596	0.805	0.696	0.596	0.805	SUBCLONAL	1	FALSE	1	0.313552894845508	2		537	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0025753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	187	265	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.748802056610335	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.758328255819382	2		267	245	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731235	162731235	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	96	242	0	ENST00000367921.3:c.1090T>A	p.Phe364Ile	p.F364I	ENST00000367921	NM_006182.2	364	Ttc/Atc	9/18	0.758328255819382	3	FACETS	1	0.977	1	0.64	0.578	0.703	CLONAL	1	TRUE	1	0.758328255819382	3		242	273	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475342	40475344	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0025753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	297	402	0	ENST00000264657.5:c.1682_1684del	p.Phe561del	p.F561del	ENST00000264657	NM_139276.2	561	tTCTgg/tgg	19/24	0.758328255819382	3	FACETS	0.963	0.932	0.992	0.963	0.932	0.992	CLONAL	3	TRUE	0	0.758328255819382	3		402	374	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401552	401552	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	109	397	0	ENST00000380956.4:c.874T>C	p.Phe292Leu	p.F292L	ENST00000380956	NM_001195286.1	292	Ttc/Ctc	7/9	0.739910337245805	4	FACETS	1	0.949	1	0.539	0.486	0.594	CLONAL	1	TRUE	2	0.758328255819382	4		397	469	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70355092	70355092	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	267	451	0	ENST00000374080.3:c.5014T>G	p.Phe1672Val	p.F1672V	ENST00000374080		1672	Ttc/Gtc	36/45	0.753847234677844	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.758328255819382	2		451	330	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0025757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	63	340	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	0.213673069186887	2		340	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0025757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	115	276	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.213673069186887	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.213673069186887	1		276	717	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11019828	11019828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	91	449	1	ENST00000327064.4:c.503G>A	p.Arg168Gln	p.R168Q	ENST00000327064	NM_199141.1	168	cGg/cAg	4/16	0.213673069186887	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.213673069186887	1		450	610	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56171055	56171055	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0121525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	26	311	0	ENST00000399503.3:c.1883C>A	p.Ser628Ter	p.S628*	ENST00000399503	NM_005921.1	628	tCa/tAa	10/20	1	2	FACETS	0.15	0.119	0.187	0.15	0.119	0.187	SUBCLONAL	1	NA	1	0.784179557975012	2		311	441	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878721	151878721	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0121525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	28	377	0	ENST00000262189.6:c.6224C>G	p.Pro2075Arg	p.P2075R	ENST00000262189	NM_170606.2	2075	cCt/cGt	36/59	1	2	FACETS	0.146	0.116	0.181	0.146	0.116	0.181	SUBCLONAL	1	NA	1	0.784179557975012	2		377	488	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038796	47038796	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs782470345	NA	P-0121525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	25	192	0	ENST00000377604.3:c.803G>T	p.Gly268Val	p.G268V	ENST00000377604	NM_001204468.1	268	gGc/gTc	9/24	0.728970766979374	2	FACETS	0.169	0.132	0.21			1	SUBCLONAL	1	NA	NA	0.784179557975012	2		192	378	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0025759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	150	197	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.157563229391648	4	FACETS	1	0.985	1	0.681	0.622	0.743	INDETERMINATE	1	TRUE	2	0.32408990246361	4		197	900	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934575	NA	P-0025759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	199	633	0	ENST00000269305.4:c.733G>C	p.Gly245Arg	p.G245R	ENST00000269305	NM_001126112.2	245	Ggc/Cgc	7/11	0.146234386490159	1	FACETS	1	0.983	1	1	0.983	1	INDETERMINATE	1	TRUE	0	0.32408990246361	1		633	858	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696431	47696431	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519969	NA	P-0025760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	88	590	0	ENST00000347630.2:c.392G>C	p.Trp131Ser	p.W131S	ENST00000347630	NM_001007230.1	131	tGg/tCg	6/11	0.20458285751818	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.20458285751818	1		590	592	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024102	31024102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766307575	NA	P-0025760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	66	569	0	ENST00000375687.4:c.3587C>T	p.Ala1196Val	p.A1196V	ENST00000375687	NM_015338.5	1196	gCt/gTt	13/13	0.20458285751818	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.20458285751818	1		569	468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0025761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	454	587	1	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.898797927542755	2	FACETS	0.996	0.979	1	0.996	0.979	1	CLONAL	2	TRUE	0	0.918942410577635	2		588	496	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	39	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.746	0.62	0.885	0.746	0.62	0.885	SUBCLONAL	1	FALSE	1	0.298878504538515	2		371	350	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544642	65544642	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs878854499	NA	P-0025762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	40	486	0	ENST00000358664.4:c.284T>C	p.Leu95Pro	p.L95P	ENST00000358664	NM_002382.4	95	cTg/cCg	4/5	1	2	FACETS	0.553	0.459	0.657	0.553	0.459	0.657	SUBCLONAL	1	FALSE	1	0.298878504538515	2		486	484	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165806	118165806	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	96	486	0	ENST00000369448.3:c.316C>T	p.Gln106Ter	p.Q106*	ENST00000369448	NM_017709.3	106	Cag/Tag	2/2	NA	2	FACETS	0.864	0.771	0.962			1	INDETERMINATE	1	TRUE	NA	0.386589438482755	2		486	575	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831980	72831980	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	148	547	0	ENST00000268489.5:c.4601C>G	p.Thr1534Ser	p.T1534S	ENST00000268489	NM_006885.3	1534	aCt/aGt	9/10	0.361693652668362	5	FACETS	0.953	0.868	1	0.191	0.173	0.209	CLONAL	1	TRUE	0	0.386589438482755	5		547	1269	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845890	72845890	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	263	540	1	ENST00000268489.5:c.3577T>A	p.Ser1193Thr	p.S1193T	ENST00000268489	NM_006885.3	1193	Tcc/Acc	6/10	0.361693652668362	5	FACETS	0.887	0.83	0.945	0.355	0.332	0.378	CLONAL	2	TRUE	0	0.386589438482755	5		541	1212	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0025763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	404	592	1	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.385870849845559	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.386589438482755	2		593	911	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579437	7579437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781307	NA	P-0025763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	146	577	1	ENST00000269305.4:c.250G>A	p.Ala84Thr	p.A84T	ENST00000269305	NM_001126112.2	84	Gcc/Acc	4/11	0.385870849845559	2	FACETS	1	0.926	1	0.507	0.463	0.553	CLONAL	1	TRUE	0	0.386589438482755	2		578	745	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042450	16042450	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	139	554	0	ENST00000268712.3:c.1224T>A	p.Phe408Leu	p.F408L	ENST00000268712	NM_006311.3	408	ttT/ttA	12/46	0.385870849845559	2	FACETS	0.969	0.883	1	0.485	0.441	0.53	CLONAL	1	TRUE	0	0.386589438482755	2		554	742	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918795	50918795	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777468034	NA	P-0025763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1326	151	565	1	ENST00000440232.2:c.2665C>T	p.Arg889Cys	p.R889C	ENST00000440232	NM_002691.3	889	Cgc/Tgc	21/27	0.386589438482755	6	FACETS	0.938	0.854	1	0.313	0.284	0.342	CLONAL	1	TRUE	3	0.386589438482755	6		566	1477	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936030	49936030	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	157	586	0	ENST00000296474.3:c.1640G>C	p.Trp547Ser	p.W547S	ENST00000296474	NM_002447.2	547	tGg/tCg	4/20	0.385870849845559	2	FACETS	0.92	0.843	1	0.46	0.421	0.5	CLONAL	1	TRUE	0	0.386589438482755	2		586	883	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936367	49936367	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	162	588	1	ENST00000296474.3:c.1481G>T	p.Ser494Ile	p.S494I	ENST00000296474	NM_002447.2	494	aGt/aTt	3/20	0.385870849845559	2	FACETS	1	0.95	1	0.523	0.48	0.568	CLONAL	1	TRUE	0	0.386589438482755	2		589	801	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940933	49940933	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1391612870	NA	P-0025763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	166	532	0	ENST00000296474.3:c.110C>G	p.Ser37Cys	p.S37C	ENST00000296474	NM_002447.2	37	tCt/tGt	1/20	0.385870849845559	2	FACETS	1	0.967	1	0.548	0.504	0.594	CLONAL	1	TRUE	0	0.386589438482755	2		532	784	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981132	55981132	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	132	551	0	ENST00000263923.4:c.567C>A	p.Ser189Arg	p.S189R	ENST00000263923	NM_002253.2	189	agC/agA	5/30	0.335734093992112	4	FACETS	0.878	0.795	0.965	0.293	0.265	0.322	CLONAL	1	TRUE	1	0.386589438482755	4		551	1079	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449513	31449513	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	92	313	0	ENST00000344624.3:c.2696A>C	p.His899Pro	p.H899P	ENST00000344624		899	cAt/cCt	19/33	0.385870849845559	3	FACETS	1	0.943	1	0.363	0.324	0.406	CLONAL	1	TRUE	0	0.386589438482755	3		313	521	SUCCESS
APC	324	MSKCC	GRCh37	5	112137040	112137040	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs755437577	NA	P-0025763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	142	574	0	ENST00000257430.4:c.794G>C	p.Gly265Ala	p.G265A	ENST00000257430	NM_000038.5	265	gGa/gCa	8/16	0.386589438482755	5	FACETS	0.961	0.874	1			1	CLONAL	1	TRUE	NA	0.386589438482755	5		574	1208	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	159	284	1	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.385870849845559	2	FACETS	1	0.952	1	0.527	0.483	0.572	CLONAL	1	TRUE	0	0.386589438482755	2		285	781	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874689	151874689	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	209	438	0	ENST00000262189.6:c.7849A>G	p.Asn2617Asp	p.N2617D	ENST00000262189	NM_170606.2	2617	Aat/Gat	38/59	0.385870849845559	2	FACETS	0.882	0.824	0.941	0.882	0.824	0.941	CLONAL	2	TRUE	0	0.386589438482755	2		438	613	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980483	70980483	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1484	158	636	1	ENST00000276594.2:c.894C>A	p.Asp298Glu	p.D298E	ENST00000276594	NM_024504.3	298	gaC/gaA	4/8	0.386589438482755	6	FACETS	0.883	0.806	0.964			1	CLONAL	1	TRUE	NA	0.386589438482755	6		637	1642	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551357	141551357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1552	150	629	1	ENST00000220592.5:c.1940G>A	p.Arg647His	p.R647H	ENST00000220592	NM_012154.3	647	cGc/cAc	15/19	0.386589438482755	6	FACETS	0.808	0.736	0.885			1	CLONAL	1	TRUE	NA	0.386589438482755	6		630	1702	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891228	101891228	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	125	440	0	ENST00000374994.4:c.189C>G	p.Asp63Glu	p.D63E	ENST00000374994	NM_004612.2	63	gaC/gaG	2/9	0.385870849845559	2	FACETS	1	0.919	1	0.507	0.46	0.556	CLONAL	1	TRUE	0	0.386589438482755	2		440	638	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	102	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.150639945755194	3	FACETS	1	0.957	1	0.754	0.675	0.837	CLONAL	2	TRUE	0	0.150639945755194	3		371	644	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	26	387	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.87	0.688	1	0.87	0.688	1	CLONAL	1	TRUE	1	0.150639945755194	2		387	397	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849069	156849069	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	83	514	0	ENST00000524377.1:c.1961G>T	p.Arg654Leu	p.R654L	ENST00000524377	NM_002529.3	654	cGc/cTc	15/17	0.150639945755194	3	FACETS	1	0.975	1	0.723	0.638	0.816	CLONAL	1	TRUE	1	0.150639945755194	3		514	819	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	57	558	0	ENST00000269305.4:c.848G>T	p.Arg283Leu	p.R283L	ENST00000269305	NM_001126112.2	283	cGc/cTc	8/11	1	2	FACETS	0.944	0.808	1	0.944	0.808	1	CLONAL	1	TRUE	1	0.150639945755194	2		558	802	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260318	149260318	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	38	551	0	ENST00000360632.3:c.575A>G	p.Asn192Ser	p.N192S	ENST00000360632	NM_015472.4	192	aAt/aGt	4/7	1	2	FACETS	0.673	0.554	0.806	0.673	0.554	0.806	SUBCLONAL	1	TRUE	1	0.150639945755194	2		551	750	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006854	47006950	+	splice_donor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	AGCAGCCCCCGAAGGCCCTATCAGGACATGGAGTATGAAAGACGGTGAGTTATCTGTTCTCAGCTTCCCAGACAGCCTAGGCTTGCGTCTATGTGAG	AGCAGCCCCCGAAGGCCCTATCAGGACATGGAGTATGAAAGACGGTGAGTTATCTGTTCTCAGCTTCCCAGACAGCCTAGGCTTGCGTCTATGTGAG	-	novel	NA	P-0025766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	30	257	0	ENST00000377604.3:c.-26_17+54del		p.X9_splice	ENST00000377604	NM_001204468.1	9		2/24	1	1	FACETS	0.831	0.669	1	0.831	0.669	1	CLONAL	1	TRUE	0	0.150639945755194	1		257	443	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	36	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.814	0.669	0.976	0.814	0.669	0.976	CLONAL	1	TRUE	1	0.203339616865895	2		371	435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0025768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	101	423	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.203339616865895	2		423	924	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281635	198281635	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	113	330	1	ENST00000335508.6:c.496C>T	p.Arg166Ter	p.R166*	ENST00000335508	NM_012433.2	166	Cga/Tga	6/25	0.600257957682125	3	FACETS	0.965	0.873	1	0.483	0.436	0.531	CLONAL	1	TRUE	1	0.600257957682125	3		331	507	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730068	41730068	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	278	424	1	ENST00000242208.4:c.461A>T	p.Glu154Val	p.E154V	ENST00000242208	NM_002192.2	154	gAa/gTa	3/3	0.296151356606432	5	FACETS	1	0.984	1	0.742	0.699	0.785	INDETERMINATE	2	TRUE	2	0.600257957682125	5		425	791	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68984736	68984736	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	36	345	0	ENST00000288368.4:c.1500A>T	p.Lys500Asn	p.K500N	ENST00000288368	NM_024870.2	500	aaA/aaT	14/40	0.296799654722591	5	FACETS	0.416	0.341	0.5	0.139	0.113	0.167	INDETERMINATE	1	TRUE	2	0.600257957682125	5		345	548	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0025771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	20	611	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.109	0.083	0.14	0.109	0.083	0.14	SUBCLONAL	1	TRUE	1	0.411643366296707	2		611	891	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0025771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	114	285	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.411643366296707	2		285	523	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	80	387	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.488286043897441	2		387	276	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0025773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	104	611	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.878	0.79	0.971	0.878	0.79	0.971	CLONAL	1	TRUE	1	0.488286043897441	2		611	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0025773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	172	265	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.488286043897441	2		267	640	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0025773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	107	372	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	0.488286043897441	2		372	394	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720709	89720709	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs863224909	NA	P-0025773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	66	43	0	ENST00000371953.3:c.860C>G	p.Ser287Ter	p.S287*	ENST00000371953	NM_000314.4	287	tCa/tGa	8/9	0.488286043897441	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.488286043897441	2		43	118	SUCCESS
APC	324	MSKCC	GRCh37	5	112175772	112175772	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	84	340	0	ENST00000257430.4:c.4483del	p.Ser1495ValfsTer12	p.S1495Vfs*12	ENST00000257430	NM_000038.5	1494	gAa/ga	16/16	1	2	FACETS	0.896	0.797	1	0.896	0.797	1	CLONAL	1	TRUE	1	0.488286043897441	2		340	384	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951086	17951086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1257606008	NA	P-0025773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	226	588	0	ENST00000458235.1:c.1207C>T	p.Arg403Cys	p.R403C	ENST00000458235	NM_000215.3	403	Cgc/Tgc	9/24	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.488286043897441	2		588	911	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81979857	81979857	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764693069	NA	P-0025773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	42	376	0	ENST00000359376.3:c.3559C>T	p.Arg1187Trp	p.R1187W	ENST00000359376	NM_002661.3	1187	Cgg/Tgg	31/33	1	2	FACETS	0.287	0.239	0.341	0.287	0.239	0.341	SUBCLONAL	1	TRUE	1	0.488286043897441	2		376	599	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663358	227663358	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762833254	NA	P-0025773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	106	336	0	ENST00000305123.5:c.97C>T	p.Arg33Cys	p.R33C	ENST00000305123	NM_005544.2	33	Cgc/Tgc	1/2	1	2	FACETS	0.967	0.872	1	0.967	0.872	1	CLONAL	1	TRUE	1	0.488286043897441	2		336	449	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844172	68844172	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1555515445	NA	P-0025775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	160	520	0	ENST00000261769.5:c.760G>T	p.Asp254Tyr	p.D254Y	ENST00000261769	NM_004360.3	254	Gat/Tat	6/16	0.463105662029149	1	FACETS	0.863	0.795	0.934	0.863	0.795	0.934	CLONAL	1	TRUE	0	0.463105662029149	1		520	615	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111434	8111434	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0025775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	128	322	0	ENST00000346208.3:c.922-2A>G		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.905	0.822	0.991	0.905	0.822	0.991	CLONAL	1	TRUE	1	0.463105662029149	2		322	611	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657480	29657480	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1135402880	NA	P-0025775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	107	403	0	ENST00000356175.3:c.5717del	p.Leu1906TrpfsTer15	p.L1906Wfs*15	ENST00000356175	NM_000267.3	1905	Ttt/tt	38/57	0.463105662029149	1	FACETS	0.85	0.767	0.935	0.85	0.767	0.935	CLONAL	1	TRUE	0	0.463105662029149	1		403	418	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426444	47426444	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1439786171	NA	P-0025775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	185	449	0	ENST00000377045.4:c.787G>A	p.Val263Met	p.V263M	ENST00000377045	NM_001654.4	263	Gtg/Atg	9/16	1	2	FACETS	0.977	0.903	1	0.977	0.903	1	CLONAL	1	TRUE	1	0.463105662029149	2		449	818	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0025777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	199	340	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	0.949	0.883	1			1	INDETERMINATE	1	TRUE	NA	0.667028269950584	2		340	629	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602714	10602714	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	336	544	0	ENST00000171111.5:c.864C>A	p.Cys288Ter	p.C288*	ENST00000171111	NM_203500.1	288	tgC/tgA	3/6	0.667028269950584	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.667028269950584	1		544	654	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220644	1220645	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	T	novel	NA	P-0025777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	266	456	0	ENST00000326873.7:c.662_663delinsT	p.Pro221LeufsTer66	p.P221Lfs*66	ENST00000326873	NM_000455.4	221	cCG/cT	5/10	0.667028269950584	1	FACETS	0.99	0.939	1	0.99	0.939	1	CLONAL	1	TRUE	0	0.667028269950584	1		456	537	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098944	178098944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	156	377	0	ENST00000397062.3:c.101G>A	p.Arg34Gln	p.R34Q	ENST00000397062	NM_006164.4	34	cGa/cAa	2/5	1	2	FACETS	0.976	0.903	1	0.976	0.903	1	CLONAL	1	TRUE	1	0.718097954711277	2		377	445	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715660	30715660	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	189	394	0	ENST00000295754.5:c.1318G>T	p.Glu440Ter	p.E440*	ENST00000295754	NM_003242.5	440	Gag/Tag	5/7	0.701849202956545	1	FACETS	0.972	0.915	1	0.972	0.915	1	CLONAL	1	TRUE	0	0.718097954711277	1		394	347	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056220	27056220	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	229	592	0	ENST00000324856.7:c.1216G>T	p.Gly406Ter	p.G406*	ENST00000324856	NM_006015.4	406	Gga/Tga	2/20	0.701849202956545	1	FACETS	0.944	0.893	0.995	0.944	0.893	0.995	CLONAL	1	TRUE	0	0.718097954711277	1		592	433	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003804	45003805	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0025778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	152	450	0	ENST00000558401.1:c.61_62del	p.Ile21ProfsTer35	p.I21Pfs*35	ENST00000558401	NM_004048.2	20	gcTAtc/gctc	1/4	0.701849202956545	1	FACETS	0.994	0.93	1	0.994	0.93	1	CLONAL	1	TRUE	0	0.718097954711277	1		450	273	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098561	11098561	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	190	604	1	ENST00000358026.2:c.1079G>T	p.Gly360Val	p.G360V	ENST00000358026	NM_001128849.1	360	gGc/gTc	6/36	0.465971354866678	1	FACETS	0.829	0.777	0.882	0.829	0.777	0.882	CLONAL	1	TRUE	0	0.718097954711277	1		605	409	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524183	187524183	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	231	417	2	ENST00000441802.2:c.11356A>T	p.Arg3786Trp	p.R3786W	ENST00000441802	NM_005245.3	3786	Agg/Tgg	20/27	0.701849202956545	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.718097954711277	1		419	395	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739355	145739355	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs772696526	NA	P-0025778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	234	675	0	ENST00000428558.2:c.2015C>G	p.Thr672Ser	p.T672S	ENST00000428558	NM_004260.3	672	aCc/aGc	12/22	0.393741176829481	1	FACETS	0.742	0.698	0.786	0.742	0.698	0.786	INDETERMINATE	1	TRUE	0	0.718097954711277	1		675	563	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0025779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	393	340	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.356114020077046	4	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.356114020077046	4		340	1220	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0025779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	70	395	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.512	0.445	0.584	0.512	0.445	0.584	SUBCLONAL	1	TRUE	1	0.356114020077046	2		395	768	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577505	7577506	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTTC	novel	NA	P-0025779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	189	435	0	ENST00000269305.4:c.772_775dup	p.Asp259GlyfsTer6	p.D259Gfs*6	ENST00000269305	NM_001126112.2	259	gac/gGAAGac	7/11	0.265218866666807	2	FACETS	1	0.989	1	0.708	0.656	0.761	CLONAL	1	TRUE	0	0.356114020077046	2		435	750	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578540	7578541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGGGC	novel	NA	P-0025780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	116	643	0	ENST00000269305.4:c.385_389dup	p.Asn131ProfsTer41	p.N131Pfs*41	ENST00000269305	NM_001126112.2	130	ctc/ctGCCCTc	5/11	0.330349601200453	1	FACETS	0.782	0.709	0.859	0.782	0.709	0.859	SUBCLONAL	1	TRUE	0	0.474199780387734	1		643	477	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214720	36214720	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772989623	NA	P-0025780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	37	356	0	ENST00000222270.7:c.3146C>T	p.Ala1049Val	p.A1049V	ENST00000222270	NM_014727.1	1049	gCg/gTg	8/37	1	2	FACETS	0.576	0.477	0.685	0.576	0.477	0.685	SUBCLONAL	1	TRUE	1	0.474199780387734	2		356	271	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0025781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	297	386	3	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.42518537951034	3	FACETS	0.917	0.868	0.965	0.917	0.868	0.965	CLONAL	2	TRUE	1	0.578634925672581	3		389	722	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0025781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	270	523	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.55094176707032	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.578634925672581	1		523	650	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662872	227662872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	210	515	2	ENST00000305123.5:c.583G>A	p.Val195Met	p.V195M	ENST00000305123	NM_005544.2	195	Gtg/Atg	1/2	0.42518537951034	3	FACETS	1	0.941	1	0.507	0.471	0.544	CLONAL	1	TRUE	1	0.578634925672581	3		517	923	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155280	185155300	+	inframe_deletion	In_Frame_Del	DEL	TGGGTAGTGGAGCCCAAGGAG	TGGGTAGTGGAGCCCAAGGAG	-	novel	NA	P-0025781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	215	484	0	ENST00000265026.3:c.521_541del	p.Leu174_Ala181delinsPro	p.L174_A181delinsP	ENST00000265026	NM_004721.4	174	cTGGGTAGTGGAGCCCAAGGAGcg/ccg	3/14	1	2	FACETS	0.915	0.853	0.98	0.915	0.853	0.98	CLONAL	1	TRUE	1	0.578634925672581	2		484	812	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878643	151878643	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	199	425	0	ENST00000262189.6:c.6302del	p.Pro2101HisfsTer5	p.P2101Hfs*5	ENST00000262189	NM_170606.2	2101	cCa/ca	36/59	0.55094176707032	1	FACETS	0.862	0.804	0.921	0.862	0.804	0.921	CLONAL	1	TRUE	0	0.578634925672581	1		425	567	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69000026	69000026	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	260	547	0	ENST00000288368.4:c.2095G>T	p.Val699Leu	p.V699L	ENST00000288368	NM_024870.2	699	Gtg/Ttg	19/40	1	2	FACETS	0.986	0.926	1	0.986	0.926	1	CLONAL	1	TRUE	1	0.578634925672581	2		547	911	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0025781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	212	193	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.578634925672581	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.578634925672581	1		193	441	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931765	39931765	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	171	555	0	ENST00000378444.4:c.2834A>G	p.Asp945Gly	p.D945G	ENST00000378444	NM_001123385.1	945	gAt/gGt	4/15	0.22032910775154	1	FACETS	0.539	0.497	0.583	0.539	0.497	0.583	INDETERMINATE	1	TRUE	0	0.578634925672581	1		555	779	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0025783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	86	423	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.16724753688083	4	FACETS	1	0.943	1	0.556	0.491	0.626	CLONAL	1	TRUE	2	0.224397521701965	4		423	844	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0025784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	294	83	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.480146462260425	4	FACETS	0.915	0.865	0.966			1	CLONAL	2	TRUE	NA	0.691348444510096	4		83	786	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573996	7573996	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121912662	NA	P-0025784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	381	747	0	ENST00000269305.4:c.1031T>C	p.Leu344Pro	p.L344P	ENST00000269305	NM_001126112.2	344	cTg/cCg	10/11	0.528291832749932	2	FACETS	1	0.994	1	0.641	0.612	0.67	CLONAL	1	TRUE	0	0.691348444510096	2		747	860	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170847	56170872	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTTTGATACAGGTGTTTGGAATGGA	TGTTTGATACAGGTGTTTGGAATGGA	-	novel	NA	P-0025784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	122	310	0	ENST00000399503.3:c.1687-12_1700del		p.X563_splice	ENST00000399503	NM_005921.1	563		10/20	0.570455701169521	3	FACETS	1	0.985	1	0.696	0.637	0.757	CLONAL	1	TRUE	1	0.691348444510096	3		310	341	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181870	56181870	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	102	436	0	ENST00000399503.3:c.4094T>A	p.Ile1365Asn	p.I1365N	ENST00000399503	NM_005921.1	1365	aTc/aAc	17/20	0.570455701169521	3	FACETS	0.666	0.597	0.739	0.333	0.298	0.37	SUBCLONAL	1	TRUE	1	0.691348444510096	3		436	596	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590479	67590479	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	106	373	0	ENST00000274335.5:c.1541G>T	p.Arg514Leu	p.R514L	ENST00000274335		514	cGt/cTt	11/15	0.570455701169521	3	FACETS	0.786	0.707	0.869	0.393	0.353	0.435	SUBCLONAL	1	TRUE	1	0.691348444510096	3		373	525	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317081	87317081	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201490630	NA	P-0025784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	68	510	0	ENST00000277120.3:c.220G>A	p.Ala74Thr	p.A74T	ENST00000277120		74	Gca/Aca	3/19	0.216060563454677	2	FACETS	0.291	0.252	0.332	0.145	0.126	0.166	INDETERMINATE	1	TRUE	0	0.691348444510096	2		510	677	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136381	2136381	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs45517375	NA	P-0025785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	482	615	0	ENST00000219476.3:c.4849+1G>A		p.X1617_splice	ENST00000219476	NM_000548.3	1617			1	2	FACETS	0.975	0.935	1	0.975	0.935	1	CLONAL	1	TRUE	1	0.837036864086557	2		615	1181	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138294	2138294	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs45517412	NA	P-0025785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	646	760	1	ENST00000219476.3:c.5227C>G	p.Arg1743Gly	p.R1743G	ENST00000219476	NM_000548.3	1743	Cgg/Ggg	41/42	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.837036864086557	2		761	1525	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123722	11123722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1263140481	NA	P-0025786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	46	784	1	ENST00000358026.2:c.2372C>T	p.Ala791Val	p.A791V	ENST00000358026	NM_001128849.1	791	gCg/gTg	16/36	0.690032505224498	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.690032505224498	1		785	72	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180292	38180292	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	37	665	0	ENST00000396334.3:c.140C>G	p.Ser47Cys	p.S47C	ENST00000396334	NM_002468.4	47	tCt/tGt	1/5	0.690032505224498	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.690032505224498	1		665	57	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958193	2958193	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	24	659	0	ENST00000396946.4:c.2539C>G	p.Gln847Glu	p.Q847E	ENST00000396946	NM_032415.4	847	Cag/Gag	19/25	1	2	FACETS	0.87	0.702	1	0.87	0.702	1	CLONAL	1	TRUE	1	0.690032505224498	2		659	80	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139408986	139408986	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	37	845	0	ENST00000277541.6:c.2183G>A	p.Gly728Glu	p.G728E	ENST00000277541	NM_017617.3	728	gGg/gAg	13/34	0.234722668779472	1	FACETS	0.798	0.682	0.917	0.798	0.682	0.917	INDETERMINATE	1	TRUE	0	0.690032505224498	1		845	88	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163671	47163680	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTCATAAC	TCTTCATAAC	-	novel	NA	P-0025787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	66	399	0	ENST00000409792.3:c.2446_2455del	p.Val816PhefsTer7	p.V816Ffs*7	ENST00000409792	NM_014159.6	816	GTTATGAAGAtt/tt	3/21	0.483179290782363	1	FACETS	0.73	0.639	0.825	0.73	0.639	0.825	SUBCLONAL	1	TRUE	0	0.483179290782363	1		399	284	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651307	52651307	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	50	481	0	ENST00000394830.3:c.1789G>T	p.Ala597Ser	p.A597S	ENST00000394830	NM_018313.4	597	Gcc/Tcc	15/30	0.483179290782363	1	FACETS	0.304	0.257	0.354	0.304	0.257	0.354	SUBCLONAL	1	TRUE	0	0.483179290782363	1		481	517	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0025788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	152	206	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.888	0.822	0.955	0.888	0.822	0.955	CLONAL	1	TRUE	1	0.886641243795327	2		207	386	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063717	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0025788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	115	144	1	ENST00000412916.2:c.165+1G>T		p.X55_splice	ENST00000412916		55			0.886641243795327	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.886641243795327	1		145	144	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144152	11144152	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	232	493	0	ENST00000358026.2:c.3733G>A	p.Ala1245Thr	p.A1245T	ENST00000358026	NM_001128849.1	1245	Gcc/Acc	26/36	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.886641243795327	2		493	510	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0025791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	61	675	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.891	0.769	1	0.891	0.769	1	CLONAL	1	TRUE	1	0.25135897661003	2		675	545	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481526	20481526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	67	365	0	ENST00000346618.3:c.595G>A	p.Asp199Asn	p.D199N	ENST00000346618	NM_001949.4	199	Gat/Aat	3/7	0.25135897661003	4	FACETS	0.988	0.858	1	0.247	0.214	0.283	CLONAL	1	TRUE	0	0.25135897661003	4		365	675	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	328	804	0	ENST00000269305.4:c.376T>C	p.Tyr126His	p.Y126H	ENST00000269305	NM_001126112.2	126	Tac/Cac	5/11	0.25135897661003	3	FACETS	0.952	0.901	1	0.952	0.901	1	CLONAL	3	TRUE	0	0.25135897661003	3		804	1029	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612157	189612157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	83	572	1	ENST00000264731.3:c.1909C>T	p.Arg637Cys	p.R637C	ENST00000264731	NM_003722.4	637	Cgt/Tgt	14/14	1	2	FACETS	0.939	0.829	1	0.939	0.829	1	CLONAL	1	TRUE	1	0.25135897661003	2		573	703	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256239	16256239	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	140	642	0	ENST00000375759.3:c.3504T>G	p.Ser1168Arg	p.S1168R	ENST00000375759	NM_015001.2	1168	agT/agG	11/15	0.25135897661003	3	FACETS	1	0.984	1	0.69	0.628	0.755	CLONAL	1	TRUE	1	0.25135897661003	3		642	909	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433872	49433872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747213352	NA	P-0025791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	114	808	0	ENST00000301067.7:c.7681G>A	p.Gly2561Arg	p.G2561R	ENST00000301067	NM_003482.3	2561	Ggg/Agg	31/54	0.25135897661003	3	FACETS	1	0.927	1	0.519	0.466	0.575	CLONAL	1	TRUE	1	0.25135897661003	3		808	984	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0025792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	145	627	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.440024041871164	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.440024041871164	1		627	495	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0025792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	187	296	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.440024041871164	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.440024041871164	3		296	468	SUCCESS
APC	324	MSKCC	GRCh37	5	112175746	112175746	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	198	306	0	ENST00000257430.4:c.4455del	p.Asp1486IlefsTer21	p.D1486Ifs*21	ENST00000257430	NM_000038.5	1485	gcT/gc	16/16	0.440024041871164	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.440024041871164	2		306	439	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813599	50813599	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	113	417	0	ENST00000398568.2:c.1153C>G	p.Leu385Val	p.L385V	ENST00000398568	NM_001042412.1	385	Ctt/Gtt	8/18	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.440024041871164	2		417	490	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794787	42794787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747706524	NA	P-0025792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	106	454	0	ENST00000575354.2:c.1867G>A	p.Gly623Arg	p.G623R	ENST00000575354	NM_015125.3	623	Gga/Aga	10/20	1	2	FACETS	0.989	0.891	1	0.989	0.891	1	CLONAL	1	TRUE	1	0.440024041871164	2		454	487	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936073	178936074	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTCTCT	novel	NA	P-0025792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	111	352	0	ENST00000263967.3:c.1618_1623dup	p.Leu540_Ser541dup	p.L540_S541dup	ENST00000263967	NM_006218.2	540	cct/cCTCTCTct	10/21	0.440024041871164	3	FACETS	0.775	0.703	0.851	0.775	0.703	0.851	SUBCLONAL	2	TRUE	1	0.440024041871164	3		352	397	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347223	70347223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	259	263	0	ENST00000374080.3:c.2887G>A	p.Asp963Asn	p.D963N	ENST00000374080		963	Gat/Aat	21/45	0.41813961146843	2	FACETS	0.913	0.87	0.955			1	CLONAL	3	TRUE	NA	0.440024041871164	2		263	430	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41562652	41562653	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0025793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	255	328	1	ENST00000263253.7:c.3858_3859dup	p.Lys1287IlefsTer17	p.K1287Ifs*17	ENST00000263253	NM_001429.3	1286	aat/aATat	23/31	1	2	FACETS	0.992	0.934	1	0.992	0.934	1	CLONAL	1	TRUE	1	0.749729349420847	2		329	686	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	130	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.88	0.808	0.954	0.88	0.808	0.954	CLONAL	1	TRUE	1	0.818256276953322	2		371	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0025803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	323	715	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.805619480411723	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.818256276953322	1		715	434	SUCCESS
APC	324	MSKCC	GRCh37	5	112175358	112175358	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1554085480	NA	P-0025803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	196	290	0	ENST00000257430.4:c.4067C>G	p.Ser1356Ter	p.S1356*	ENST00000257430	NM_000038.5	1356	tCa/tGa	16/16	0.818256276953322	2	FACETS	0.994	0.956	1	0.994	0.956	1	CLONAL	2	TRUE	0	0.818256276953322	2		290	241	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981551	201981552	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0025803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	273	863	0	ENST00000359651.3:c.465_466insTA	p.Pro156TyrfsTer99	p.P156Yfs*99	ENST00000359651		155	-/TA	3/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.818256276953322	2		863	648	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998706	100998706	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	182	841	1	ENST00000325455.5:c.1096G>T	p.Asp366Tyr	p.D366Y	ENST00000325455	NM_001202474.3	366	Gac/Tac	1/8	0.805619480411723	1	FACETS	0.769	0.722	0.815	0.769	0.722	0.815	SUBCLONAL	1	TRUE	0	0.818256276953322	1		842	342	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240268	5240268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750655279	NA	P-0025803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	299	855	0	ENST00000357368.4:c.1646G>A	p.Arg549Gln	p.R549Q	ENST00000357368	NM_002850.3	549	cGg/cAg	12/38	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.818256276953322	2		855	673	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055990	180055990	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	235	763	0	ENST00000261937.6:c.995T>C	p.Phe332Ser	p.F332S	ENST00000261937	NM_182925.4	332	tTc/tCc	8/30	0.818256276953322	2	FACETS	1	0.96	1	0.513	0.483	0.544	CLONAL	1	TRUE	0	0.818256276953322	2		763	560	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509025	106509025	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	203	527	0	ENST00000359195.3:c.1019C>T	p.Thr340Ile	p.T340I	ENST00000359195	NM_002649.2	340	aCc/aTc	2/11	1	2	FACETS	0.965	0.903	1	0.965	0.903	1	CLONAL	1	TRUE	1	0.818256276953322	2		527	514	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552130	29552131	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0121546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	242	205	0	ENST00000356175.3:c.1864dup	p.Cys622LeufsTer12	p.C622Lfs*12	ENST00000356175	NM_000267.3	621	-/T	17/57	0.781442249551703	2	FACETS	0.999	0.962	1	0.999	0.962	1	CLONAL	2	NA	0	0.781442249551703	2		205	310	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684339	29684339	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876658205	NA	P-0121546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	33	406	0	ENST00000356175.3:c.7859A>T	p.Glu2620Val	p.E2620V	ENST00000356175	NM_000267.3	2620	gAa/gTa	53/57	0.781442249551703	2	FACETS	0.136	0.11	0.165	0.068	0.055	0.083	SUBCLONAL	1	NA	0	0.781442249551703	2		406	622	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682375	37682375	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0121546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	244	420	0	ENST00000447079.4:c.3566T>C	p.Leu1189Pro	p.L1189P	ENST00000447079	NM_015083.1	1189	cTg/cCg	13/14	0.781442249551703	3	FACETS	0.998	0.935	1	0.499	0.467	0.532	CLONAL	1	NA	1	0.781442249551703	3		420	870	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747902	41747903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0121546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	186	404	0	ENST00000226382.2:c.866dup	p.Pro290SerfsTer70	p.P290Sfs*70	ENST00000226382	NM_003924.3	289	ggt/ggGt	3/3	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	NA	1	0.781442249551703	2		404	466	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187560875	187560875	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0121546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	168	347	1	ENST00000441802.2:c.3642+1G>A		p.X1214_splice	ENST00000441802	NM_005245.3	1214			1	2	FACETS	0.913	0.847	0.981	0.913	0.847	0.981	CLONAL	1	NA	1	0.781442249551703	2		348	471	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057947	27057947	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	64	376	0	ENST00000324856.7:c.1655C>G	p.Ser552Ter	p.S552*	ENST00000324856	NM_006015.4	552	tCa/tGa	3/20	0.242699106049095	1	FACETS	0.261	0.227	0.298	0.261	0.227	0.298	INDETERMINATE	1	TRUE	0	0.795143458503687	1		376	371	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011144	12011144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	237	324	0	ENST00000353533.5:c.551C>T	p.Ser184Leu	p.S184L	ENST00000353533	NM_003010.3	184	tCg/tTg	5/11	0.795143458503687	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.795143458503687	1		324	334	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057835	27057835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	57	509	2	ENST00000324856.7:c.1543C>T	p.Gln515Ter	p.Q515*	ENST00000324856	NM_006015.4	515	Cag/Tag	3/20	0.242699106049095	1	FACETS	0.201	0.173	0.232	0.201	0.173	0.232	INDETERMINATE	1	TRUE	0	0.795143458503687	1		511	429	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719140	190719140	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	36	250	0	ENST00000441310.2:c.1142C>G	p.Ser381Ter	p.S381*	ENST00000441310	NM_000534.4	381	tCa/tGa	9/13	0.155032079028957	2	FACETS	0.255	0.21	0.306	0.128	0.105	0.153	INDETERMINATE	1	TRUE	0	0.795143458503687	2		250	355	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980872	40980872	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	37	322	0	ENST00000373198.4:c.1614G>C	p.Gln538His	p.Q538H	ENST00000373198	NM_133170.3	538	caG/caC	10/32	0.541154678536212	1	FACETS	0.219	0.181	0.261	0.219	0.181	0.261	SUBCLONAL	1	TRUE	0	0.795143458503687	1		322	256	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881363	111881363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	49	360	1	ENST00000393256.3:c.41G>A	p.Arg14Gln	p.R14Q	ENST00000393256	NM_006538.4	14	cGa/cAa	2/4	0.422750522180444	1	FACETS	0.187	0.158	0.218	0.187	0.158	0.218	INDETERMINATE	1	TRUE	0	0.795143458503687	1		361	398	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29120995	29120995	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	51	476	0	ENST00000328354.6:c.562G>A	p.Glu188Lys	p.E188K	ENST00000328354	NM_007194.3	188	Gaa/Aaa	4/15	0.278767524121149	4	FACETS	0.371	0.315	0.433	0.185	0.157	0.217	INDETERMINATE	1	TRUE	2	0.795143458503687	4		476	621	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287404	33287404	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	44	362	0	ENST00000374542.5:c.1693C>T	p.Gln565Ter	p.Q565*	ENST00000374542	NM_001141970.1	565	Cag/Tag	6/8	1	2	FACETS	0.259	0.217	0.305	0.259	0.217	0.305	SUBCLONAL	1	TRUE	1	0.795143458503687	2		362	427	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024332	31024332	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778060	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	66	374	1	ENST00000375687.4:c.3817C>T	p.Arg1273Cys	p.R1273C	ENST00000375687	NM_015338.5	1273	Cgt/Tgt	13/13	0.795143458503687	1	FACETS	0.385	0.337	0.435	0.385	0.337	0.435	SUBCLONAL	1	TRUE	0	0.795143458503687	1		375	260	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	184	356	0	ENST00000269305.4:c.559+1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.795143458503687	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.795143458503687	1		356	259	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243911	41243911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	37	400	0	ENST00000357654.3:c.3637G>A	p.Glu1213Lys	p.E1213K	ENST00000357654	NM_007294.3	1213	Gaa/Aaa	10/23	0.795143458503687	1	FACETS	0.18	0.148	0.215	0.18	0.148	0.215	SUBCLONAL	1	TRUE	0	0.795143458503687	1		400	312	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665346	138665346	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	47	524	0	ENST00000330315.3:c.219G>C	p.Lys73Asn	p.K73N	ENST00000330315	NM_023067.3	73	aaG/aaC	1/1	0.39312296442242	3	FACETS	0.362	0.306	0.425	0.181	0.153	0.213	INDETERMINATE	1	TRUE	1	0.795143458503687	3		524	456	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780869	9780869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	43	453	0	ENST00000377346.4:c.1591G>A	p.Val531Met	p.V531M	ENST00000377346	NM_005026.3	531	Gtg/Atg	13/24	1	2	FACETS	0.322	0.27	0.379	0.322	0.27	0.379	SUBCLONAL	1	TRUE	1	0.795143458503687	2		453	336	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782306	9782306	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	32	361	0	ENST00000377346.4:c.2239G>C	p.Glu747Gln	p.E747Q	ENST00000377346	NM_005026.3	747	Gag/Cag	18/24	1	2	FACETS	0.275	0.223	0.332	0.275	0.223	0.332	SUBCLONAL	1	TRUE	1	0.795143458503687	2		361	293	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784475	9784475	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	22	320	0	ENST00000377346.4:c.2860G>C	p.Glu954Gln	p.E954Q	ENST00000377346	NM_005026.3	954	Gaa/Caa	22/24	1	2	FACETS	0.21	0.163	0.265	0.21	0.163	0.265	SUBCLONAL	1	TRUE	1	0.795143458503687	2		320	263	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300369	11300369	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	47	346	0	ENST00000361445.4:c.1777G>C	p.Glu593Gln	p.E593Q	ENST00000361445	NM_004958.3	593	Gaa/Caa	11/58	1	2	FACETS	0.36	0.305	0.421	0.36	0.305	0.421	SUBCLONAL	1	TRUE	1	0.795143458503687	2		346	328	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325136	123325136	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	45	441	0	ENST00000358487.5:c.192G>C	p.Leu64Phe	p.L64F	ENST00000358487	NM_000141.4	64	ttG/ttC	3/18	0.759022323587001	2	FACETS	0.308	0.26	0.362	0.154	0.13	0.181	SUBCLONAL	1	TRUE	0	0.795143458503687	2		441	367	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195253	102195253	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	41	232	0	ENST00000263464.3:c.13G>C	p.Glu5Gln	p.E5Q	ENST00000263464	NM_001165.4	5	Gaa/Caa	2/9	0.391191302773179	3	FACETS	0.414	0.346	0.49	0.207	0.173	0.245	INDETERMINATE	1	TRUE	1	0.795143458503687	3		232	348	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858524	57858524	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	66	467	0	ENST00000228682.2:c.262C>G	p.Leu88Val	p.L88V	ENST00000228682	NM_005269.2	88	Ctg/Gtg	4/12	1	2	FACETS	0.372	0.324	0.424	0.372	0.324	0.424	SUBCLONAL	1	TRUE	1	0.795143458503687	2		467	446	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858629	57858629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	46	302	0	ENST00000228682.2:c.367C>T	p.His123Tyr	p.H123Y	ENST00000228682	NM_005269.2	123	Cat/Tat	4/12	1	2	FACETS	0.303	0.255	0.355	0.303	0.255	0.355	SUBCLONAL	1	TRUE	1	0.795143458503687	2		302	382	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060728	38060728	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	42	602	0	ENST00000250448.2:c.1261G>C	p.Glu421Gln	p.E421Q	ENST00000250448	NM_004496.3	421	Gaa/Caa	2/2	0.39312296442242	3	FACETS	0.284	0.237	0.336	0.142	0.118	0.168	INDETERMINATE	1	TRUE	1	0.795143458503687	3		602	520	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749170	43749170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	82	523	1	ENST00000382044.4:c.1636G>A	p.Glu546Lys	p.E546K	ENST00000382044	NM_001141980.1	546	Gaa/Aaa	12/28	1	2	FACETS	0.394	0.348	0.443	0.394	0.348	0.443	SUBCLONAL	1	TRUE	1	0.795143458503687	2		524	524	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729222	66729222	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	116	369	0	ENST00000307102.5:c.430G>C	p.Glu144Gln	p.E144Q	ENST00000307102	NM_002755.3	144	Gag/Cag	3/11	1	2	FACETS	0.813	0.74	0.887	0.813	0.74	0.887	CLONAL	1	TRUE	1	0.795143458503687	2		369	359	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136368	2136368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	153	360	2	ENST00000219476.3:c.4837G>A	p.Asp1613Asn	p.D1613N	ENST00000219476	NM_000548.3	1613	Gac/Aac	37/42	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.795143458503687	2		362	351	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029392	14029392	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	52	245	0	ENST00000311895.7:c.1603G>A	p.Asp535Asn	p.D535N	ENST00000311895	NM_005236.2	535	Gat/Aat	8/11	1	2	FACETS	0.371	0.317	0.429	0.371	0.317	0.429	SUBCLONAL	1	TRUE	1	0.795143458503687	2		245	353	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862207	68862207	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	216	411	0	ENST00000261769.5:c.2295G>C	p.Gln765His	p.Q765H	ENST00000261769	NM_004360.3	765	caG/caC	14/16	0.795143458503687	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.795143458503687	1		411	300	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349612	89349612	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	389	611	1	ENST00000301030.4:c.3338G>A	p.Trp1113Ter	p.W1113*	ENST00000301030	NM_001256183.1	1113	tGg/tAg	9/13	0.759022323587001	2	FACETS	0.971	0.942	0.998	0.971	0.942	0.998	CLONAL	2	TRUE	0	0.795143458503687	2		612	504	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223183	41223183	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	61	393	0	ENST00000357654.3:c.4748G>C	p.Arg1583Thr	p.R1583T	ENST00000357654	NM_007294.3	1583	aGa/aCa	15/23	0.795143458503687	1	FACETS	0.273	0.236	0.312	0.273	0.236	0.312	SUBCLONAL	1	TRUE	0	0.795143458503687	1		393	339	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244274	41244274	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876658360	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	71	577	0	ENST00000357654.3:c.3274G>A	p.Glu1092Lys	p.E1092K	ENST00000357654	NM_007294.3	1092	Gag/Aag	10/23	0.795143458503687	1	FACETS	0.301	0.264	0.34	0.301	0.264	0.34	SUBCLONAL	1	TRUE	0	0.795143458503687	1		577	358	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41276089	41276089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	74	408	0	ENST00000357654.3:c.25G>A	p.Glu9Lys	p.E9K	ENST00000357654	NM_007294.3	9	Gaa/Aaa	2/23	0.795143458503687	1	FACETS	0.276	0.243	0.312	0.276	0.243	0.312	SUBCLONAL	1	TRUE	0	0.795143458503687	1		408	406	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63545744	63545744	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	39	392	1	ENST00000307078.5:c.850C>T	p.His284Tyr	p.H284Y	ENST00000307078	NM_004655.3	284	Cac/Tac	3/11	0.795143458503687	1	FACETS	0.234	0.195	0.276	0.234	0.195	0.276	SUBCLONAL	1	TRUE	0	0.795143458503687	1		393	253	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223466	2223466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	35	274	1	ENST00000398665.3:c.3577G>A	p.Asp1193Asn	p.D1193N	ENST00000398665	NM_032482.2	1193	Gac/Aac	25/28	0.39312296442242	3	FACETS	0.383	0.315	0.46	0.192	0.157	0.23	INDETERMINATE	1	TRUE	1	0.795143458503687	3		275	321	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231618	5231618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	11	76	0	ENST00000357368.4:c.1858G>A	p.Ala620Thr	p.A620T	ENST00000357368	NM_002850.3	620	Gcc/Acc	14/38	0.39312296442242	3	FACETS	0.365	0.254	0.5	0.182	0.127	0.25	INDETERMINATE	1	TRUE	1	0.795143458503687	3		76	106	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054400	13054400	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs889138519	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	68	507	1	ENST00000316448.5:c.1010C>T	p.Ala337Val	p.A337V	ENST00000316448	NM_004343.3	337	gCa/gTa	8/9	0.155032079028957	2	FACETS	0.296	0.257	0.338	0.148	0.128	0.169	INDETERMINATE	1	TRUE	0	0.795143458503687	2		508	578	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353760	15353760	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs772226713	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	55	504	0	ENST00000263377.2:c.3120C>G	p.Ile1040Met	p.I1040M	ENST00000263377	NM_058243.2	1040	atC/atG	14/20	0.155032079028957	2	FACETS	0.266	0.227	0.308	0.133	0.113	0.154	INDETERMINATE	1	TRUE	0	0.795143458503687	2		504	521	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220908	36220908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	98	199	0	ENST00000222270.7:c.4958G>A	p.Cys1653Tyr	p.C1653Y	ENST00000222270	NM_014727.1	1653	tGc/tAc	23/37	0.155032079028957	2	FACETS	1	0.977	1	0.607	0.555	0.66	INDETERMINATE	1	TRUE	0	0.795143458503687	2		199	203	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139048	50139048	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754342165	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	76	513	1	ENST00000246792.3:c.515C>T	p.Ser172Leu	p.S172L	ENST00000246792	NM_006270.3	172	tCg/tTg	5/6	0.155032079028957	2	FACETS	0.35	0.307	0.396	0.175	0.153	0.198	INDETERMINATE	1	TRUE	0	0.795143458503687	2		514	546	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703608	47703608	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs267607999	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	46	396	0	ENST00000233146.2:c.2108C>G	p.Ser703Cys	p.S703C	ENST00000233146	NM_000251.2	703	tCc/tGc	13/16	0.155032079028957	2	FACETS	0.234	0.197	0.275	0.117	0.098	0.138	INDETERMINATE	1	TRUE	0	0.795143458503687	2		396	494	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661158	227661158	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	35	477	0	ENST00000305123.5:c.2297C>G	p.Ser766Ter	p.S766*	ENST00000305123	NM_005544.2	766	tCa/tGa	1/2	0.155032079028957	2	FACETS	0.233	0.191	0.28	0.116	0.095	0.14	INDETERMINATE	1	TRUE	0	0.795143458503687	2		477	378	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62290843	62290843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	131	273	0	ENST00000360203.5:c.88G>A	p.Glu30Lys	p.E30K	ENST00000360203	NM_001283009.1	30	Gaa/Aaa	2/35	NA	2	FACETS	1	0.954	1			1	INDETERMINATE	1	TRUE	NA	0.795143458503687	2		273	314	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44515634	44515634	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	54	472	0	ENST00000291552.4:c.262G>C	p.Glu88Gln	p.E88Q	ENST00000291552	NM_006758.2	88	Gaa/Caa	5/8	0.391191302773179	3	FACETS	0.323	0.276	0.376	0.162	0.138	0.188	INDETERMINATE	1	TRUE	1	0.795143458503687	3		472	587	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683383	182683383	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs887598113	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	55	396	0	ENST00000292782.4:c.162G>C	p.Glu54Asp	p.E54D	ENST00000292782	NM_020640.2	54	gaG/gaC	2/7	0.39312296442242	3	FACETS	0.413	0.354	0.478	0.207	0.177	0.239	INDETERMINATE	1	TRUE	1	0.795143458503687	3		396	468	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131893142	131893142	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs754823399	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	39	216	0	ENST00000265335.6:c.126G>C	p.Lys42Asn	p.K42N	ENST00000265335		42	aaG/aaC	1/25	0.737725323338181	2	FACETS	0.446	0.373	0.526	0.223	0.186	0.263	SUBCLONAL	1	TRUE	0	0.795143458503687	2		216	220	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696616	176696616	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	46	158	0	ENST00000439151.2:c.5317G>A	p.Glu1773Lys	p.E1773K	ENST00000439151	NM_022455.4	1773	Gag/Aag	16/23	0.238597580436026	5	FACETS	0.89	0.754	1	0.297	0.251	0.346	INDETERMINATE	1	TRUE	2	0.795143458503687	5		158	285	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696731	176696731	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587784149	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	108	359	0	ENST00000439151.2:c.5432G>A	p.Arg1811Gln	p.R1811Q	ENST00000439151	NM_022455.4	1811	cGa/cAa	16/23	0.238597580436026	5	FACETS	1	0.957	1	0.372	0.335	0.411	INDETERMINATE	1	TRUE	2	0.795143458503687	5		359	534	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350074	81350074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	46	303	0	ENST00000222390.5:c.1258G>A	p.Glu420Lys	p.E420K	ENST00000222390	NM_000601.4	420	Gaa/Aaa	10/18	0.278767524121149	4	FACETS	0.399	0.336	0.469	0.2	0.168	0.235	INDETERMINATE	1	TRUE	2	0.795143458503687	4		303	520	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509042	106509042	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs904952642	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	41	338	0	ENST00000359195.3:c.1036C>A	p.His346Asn	p.H346N	ENST00000359195	NM_002649.2	346	Cac/Aac	2/11	0.278767524121149	4	FACETS	0.52	0.434	0.615	0.26	0.217	0.308	INDETERMINATE	1	TRUE	2	0.795143458503687	4		338	356	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528593	8528593	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	49	255	0	ENST00000356435.5:c.539C>T	p.Ser180Leu	p.S180L	ENST00000356435		180	tCa/tTa	4/35	0.391191302773179	3	FACETS	0.411	0.349	0.48	0.206	0.174	0.24	INDETERMINATE	1	TRUE	1	0.795143458503687	3		255	419	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	391	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.358947741545407	7	FACETS	0.91	0.869	0.952			1	CLONAL	5	TRUE	NA	0.358947741545407	7		371	908	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0025806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	141	183	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	0.358947741545407	2	FACETS	0.877	0.805	0.95	0.877	0.805	0.95	CLONAL	2	TRUE	0	0.358947741545407	2		183	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576899	7576900	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0025806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	388	611	0	ENST00000269305.4:c.945_946dup	p.Pro316LeufsTer30	p.P316Lfs*30	ENST00000269305	NM_001126112.2	316	ccc/cTCcc	9/11	0.358947741545407	3	FACETS	0.947	0.904	0.99	0.947	0.904	0.99	CLONAL	3	TRUE	0	0.358947741545407	3		611	898	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416615	121416615	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	203	551	0	ENST00000257555.6:c.46del	p.Leu16CysfsTer6	p.L16Cfs*6	ENST00000257555		15	gCc/gc	1/10	0.335051562005117	3	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	1	0.358947741545407	3		551	651	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480496	123480496	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	136	409	0	ENST00000371139.4:c.4G>C	p.Asp2His	p.D2H	ENST00000371139	NM_001114937.2	2	Gac/Cac	1/4	0.318918040087232	4	FACETS	0.892	0.815	0.973	0.892	0.815	0.973	CLONAL	2	TRUE	2	0.358947741545407	4		409	577	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432533	49432533	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	135	558	0	ENST00000301067.7:c.8606C>G	p.Pro2869Arg	p.P2869R	ENST00000301067	NM_003482.3	2869	cCt/cGt	34/54	1	2	FACETS	0.897	0.817	0.981	0.897	0.817	0.981	CLONAL	1	TRUE	1	0.427464323385614	2		558	704	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437896	52437896	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	144	626	0	ENST00000460680.1:c.1265del	p.Gly422GlufsTer8	p.G422Efs*8	ENST00000460680	NM_004656.3	422	gGa/ga	13/17	0.427464323385614	1	FACETS	0.769	0.703	0.838	0.769	0.703	0.838	SUBCLONAL	1	TRUE	0	0.427464323385614	1		626	689	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253800	153253800	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	138	411	0	ENST00000281708.4:c.933G>A	p.Trp311Ter	p.W311*	ENST00000281708	NM_033632.3	311	tgG/tgA	6/12	0.427464323385614	1	FACETS	0.965	0.883	1	0.965	0.883	1	CLONAL	1	TRUE	0	0.427464323385614	1		411	526	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776348	76776348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	163	564	0	ENST00000373344.5:c.7118C>T	p.Ala2373Val	p.A2373V	ENST00000373344	NM_000489.3	2373	gCa/gTa	34/35	1	2	FACETS	0.944	0.867	1	0.944	0.867	1	CLONAL	1	TRUE	1	0.427464323385614	2		564	808	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	97	452	0	ENST00000304494.5:c.247C>A	p.His83Asn	p.H83N	ENST00000304494	NM_000077.4	83	Cac/Aac	2/3	0.625368539850299	1	FACETS	0.711	0.642	0.782	0.711	0.642	0.782	SUBCLONAL	1	TRUE	0	0.625368539850299	1		452	300	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889163	76889163	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs782819703	NA	P-0025809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	153	477	0	ENST00000373344.5:c.4847A>G	p.Lys1616Arg	p.K1616R	ENST00000373344	NM_000489.3	1616	aAa/aGa	18/35	0.596346216452649	1	FACETS	0.878	0.813	0.944	0.878	0.813	0.944	CLONAL	1	TRUE	0	0.625368539850299	1		477	383	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957537	175957540	+	frameshift_variant	Frame_Shift_Del	DEL	CTGT	CTGT	-	novel	NA	P-0025811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	36	408	0	ENST00000367669.3:c.1856_1859del	p.Asp619ValfsTer3	p.D619Vfs*3	ENST00000367669	NM_022457.5	619	gACAGt/gt	17/20	0.571866188590107	3	FACETS	0.276	0.226	0.332	0.138	0.113	0.166	SUBCLONAL	1	TRUE	1	0.571866188590107	3		408	586	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102056841	102056841	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	175	501	0	ENST00000282441.5:c.781C>T	p.Pro261Ser	p.P261S	ENST00000282441	NM_001130145.2	261	Cca/Tca	4/9	0.571866188590107	3	FACETS	0.994	0.917	1	0.331	0.305	0.358	CLONAL	1	TRUE	0	0.571866188590107	3		501	792	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579430	7579430	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	495	647	1	ENST00000269305.4:c.257del	p.Ala86AspfsTer37	p.A86Dfs*37	ENST00000269305	NM_001126112.2	86	gCa/ga	4/11	0.448863018930848	3	FACETS	1	0.982	1			1	CLONAL	3	TRUE	NA	0.571866188590107	3		648	728	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289720	15289720	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369213011	NA	P-0025811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1386	185	708	0	ENST00000263388.2:c.3751G>A	p.Glu1251Lys	p.E1251K	ENST00000263388	NM_000435.2	1251	Gag/Aag	23/33	0.571866188590107	7	FACETS	1	0.921	1	0.2	0.184	0.217	CLONAL	1	TRUE	2	0.571866188590107	7		708	1571	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690802	89690802	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs1114167621	NA	P-0025823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	193	298	0	ENST00000371953.3:c.210-1G>C		p.X70_splice	ENST00000371953	NM_000314.4	70			0.803927845056312	1	FACETS	0.923	0.874	0.971	0.923	0.874	0.971	CLONAL	1	TRUE	0	0.803927845056312	1		298	311	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911713	32911713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	315	531	0	ENST00000380152.3:c.3221G>A	p.Ser1074Asn	p.S1074N	ENST00000380152		1074	aGt/aAt	11/27	0.552936333017782	1	FACETS	0.468	0.442	0.494	0.468	0.442	0.494	SUBCLONAL	1	TRUE	0	0.803927845056312	1		531	1002	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0025824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1273	210	965	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.199381624949072	2	FACETS	0.867	0.803	0.934	0.434	0.401	0.467	CLONAL	1	TRUE	0	0.326639850206733	2		965	1483	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876449	35876449	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	77	637	0	ENST00000303115.3:c.1241C>A	p.Thr414Lys	p.T414K	ENST00000303115	NM_002185.3	414	aCg/aAg	8/8	1	2	FACETS	0.436	0.381	0.495	0.436	0.381	0.495	SUBCLONAL	1	TRUE	1	0.326639850206733	2		637	1082	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937465	32937465	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	96	692	1	ENST00000380152.3:c.8126G>T	p.Ser2709Ile	p.S2709I	ENST00000380152		2709	aGt/aTt	18/27	1	2	FACETS	0.506	0.449	0.567	0.506	0.449	0.567	SUBCLONAL	1	TRUE	1	0.326639850206733	2		693	1162	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632303	215632303	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	128	554	1	ENST00000260947.4:c.1471G>T	p.Gly491Trp	p.G491W	ENST00000260947	NM_000465.2	491	Ggg/Tgg	6/11	0.289793864187243	3	FACETS	0.847	0.766	0.932	0.423	0.383	0.466	CLONAL	1	TRUE	1	0.326639850206733	3		555	1077	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707797	176707797	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	49	431	0	ENST00000439151.2:c.5854C>G	p.Arg1952Gly	p.R1952G	ENST00000439151	NM_022455.4	1952	Cgg/Ggg	18/23	1	2	FACETS	0.409	0.346	0.48	0.409	0.346	0.48	SUBCLONAL	1	TRUE	1	0.326639850206733	2		431	733	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647387	117647387	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	152	754	0	ENST00000368508.3:c.5557G>T	p.Asp1853Tyr	p.D1853Y	ENST00000368508	NM_002944.2	1853	Gat/Tat	33/43	1	2	FACETS	0.739	0.674	0.808	0.739	0.674	0.808	SUBCLONAL	1	TRUE	1	0.326639850206733	2		754	1259	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528723	8528723	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	44	408	0	ENST00000356435.5:c.409G>T	p.Val137Phe	p.V137F	ENST00000356435		137	Gtt/Ttt	4/35	1	2	FACETS	0.431	0.361	0.509	0.431	0.361	0.509	SUBCLONAL	1	TRUE	1	0.326639850206733	2		408	625	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938857	76938857	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	58	626	0	ENST00000373344.5:c.1891C>T	p.Gln631Ter	p.Q631*	ENST00000373344	NM_000489.3	631	Cag/Tag	9/35	1	2	FACETS	0.327	0.28	0.379	0.327	0.28	0.379	SUBCLONAL	1	TRUE	1	0.326639850206733	2		626	1085	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344075	118344076	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0025826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	145	362	0	ENST00000534358.1:c.2206dup	p.Arg736LysfsTer7	p.R736Kfs*7	ENST00000534358	NM_005933.3	734	aga/agAa	3/36	0.512299919940806	4	FACETS	0.868	0.798	0.939	0.868	0.798	0.939	CLONAL	2	TRUE	2	0.582626109104225	4		362	454	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122373	17122373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375352888	NA	P-0025826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	82	528	0	ENST00000285071.4:c.1022G>A	p.Arg341Gln	p.R341Q	ENST00000285071	NM_144997.5	341	cGg/cAg	9/14	0.508846459816722	2	FACETS	0.869	0.773	0.969	0.434	0.386	0.485	CLONAL	1	TRUE	0	0.582626109104225	2		528	324	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100271	8100272	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0025826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	97	562	0	ENST00000346208.3:c.245_246del	p.Ser82ThrfsTer220	p.S82Tfs*220	ENST00000346208		82	aGC/a	3/6	0.512299919940806	4	FACETS	0.862	0.77	0.96	0.431	0.385	0.48	CLONAL	1	TRUE	2	0.582626109104225	4		562	611	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983972	2983972	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	73	693	1	ENST00000396946.4:c.558G>T	p.Glu186Asp	p.E186D	ENST00000396946	NM_032415.4	186	gaG/gaT	5/25	0.501284910371201	5	FACETS	0.54	0.471	0.615	0.18	0.157	0.205	SUBCLONAL	1	TRUE	2	0.582626109104225	5		694	869	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0025829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	112	506	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	NA	2	FACETS	1	0.954	1			1	INDETERMINATE	1	FALSE	NA	0.506175542709454	2		506	408	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0025829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	254	616	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.216469300696364	3	FACETS	0.846	0.796	0.898	0.564	0.53	0.599	INDETERMINATE	2	FALSE	0	0.506175542709454	3		617	743	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380282	25380282	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	195	652	0	ENST00000311936.3:c.176C>G	p.Ala59Gly	p.A59G	ENST00000311936	NM_004985.3	59	gCa/gGa	3/5	0.506512247016662	4	FACETS	0.795	0.738	0.854	0.53	0.492	0.569	SUBCLONAL	2	FALSE	1	0.506175542709454	4		652	730	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937422	178937422	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	81	475	0	ENST00000263967.3:c.1810T>C	p.Cys604Arg	p.C604R	ENST00000263967	NM_006218.2	604	Tgt/Cgt	12/21	0.173455905251903	6	FACETS	1	0.975	1	0.472	0.417	0.53	INDETERMINATE	1	FALSE	3	0.506175542709454	6		475	455	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557303	29557303	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	35	564	0	ENST00000356175.3:c.3016G>C	p.Val1006Leu	p.V1006L	ENST00000356175	NM_000267.3	1006	Gtc/Ctc	23/57	1	2	FACETS	0.254	0.207	0.306	0.254	0.207	0.306	SUBCLONAL	1	FALSE	1	0.506175542709454	2		564	545	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629085	187629085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	42	816	0	ENST00000441802.2:c.1897G>A	p.Gly633Ser	p.G633S	ENST00000441802	NM_005245.3	633	Ggc/Agc	2/27	0.211116303050764	3	FACETS	0.418	0.348	0.494	0.209	0.174	0.247	INDETERMINATE	1	FALSE	1	0.506175542709454	3		816	498	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222695	53222695	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	39	1492	0	ENST00000375401.3:c.4241A>T	p.Asp1414Val	p.D1414V	ENST00000375401	NM_004187.3	1414	gAt/gTt	25/26	0.405080210747793	1	FACETS	0.223	0.184	0.266	0.223	0.184	0.266	SUBCLONAL	1	FALSE	0	0.506175542709454	1		1492	517	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155365	47155365	+	splice_donor_variant	Splice_Site	SNP	C	C	G	rs1485723437	NA	P-0025830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	313	400	0	ENST00000409792.3:c.4715+1G>C		p.X1572_splice	ENST00000409792	NM_014159.6	1572			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		400	328	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0025876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	215	422	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	0.786233145640407	3	FACETS	0.943	0.891	0.995	0.943	0.891	0.995	CLONAL	2	TRUE	1	0.81120117312985	3		422	395	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913355	NA	P-0025876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	189	396	0	ENST00000288602.6:c.1406G>A	p.Gly469Glu	p.G469E	ENST00000288602	NM_004333.4	469	gGa/gAa	11/18	0.770277680577622	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	2	0.81120117312985	4		396	413	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604787	48604787	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519741	NA	P-0025876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	156	380	0	ENST00000342988.3:c.1609G>T	p.Asp537Tyr	p.D537Y	ENST00000342988	NM_005359.5	537	Gac/Tac	12/12	0.81120117312985	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.81120117312985	1		380	222	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912748	100912748	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	151	493	0	ENST00000325455.5:c.2574G>C	p.Leu858Phe	p.L858F	ENST00000325455	NM_001202474.3	858	ttG/ttC	7/8	0.81120117312985	3	FACETS	0.989	0.91	1	0.495	0.455	0.536	CLONAL	1	TRUE	1	0.81120117312985	3		493	529	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467177	25467177	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	188	364	0	ENST00000264709.3:c.1698G>T	p.Leu566Phe	p.L566F	ENST00000264709	NM_175629.2	566	ttG/ttT	15/23	0.786233145640407	3	FACETS	0.94	0.872	1	0.47	0.436	0.506	CLONAL	1	TRUE	1	0.81120117312985	3		364	693	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0025877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	184	811	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.287899371356512	3	FACETS	1	0.982	1	0.755	0.707	0.803	INDETERMINATE	2	FALSE	0	0.526015237004663	3		811	390	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037144	71037144	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0025877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	80	394	2	ENST00000318789.4:c.1146+1G>A		p.X382_splice	ENST00000318789	NM_032682.5	382			0.304422038071647	3	FACETS	1	0.956	1	0.579	0.514	0.647	INDETERMINATE	1	FALSE	1	0.526015237004663	3		396	332	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670324	134670324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775406650	NA	P-0025877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	96	498	1	ENST00000398015.3:c.235C>T	p.Arg79Trp	p.R79W	ENST00000398015	NM_004441.4	79	Cgg/Tgg	3/16	0.304422038071647	3	FACETS	0.792	0.715	0.872	0.792	0.715	0.872	INDETERMINATE	2	FALSE	1	0.526015237004663	3		499	291	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158614	26158614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	51	368	0	ENST00000289316.2:c.217C>T	p.Arg73Cys	p.R73C	ENST00000289316	NM_138720.2	73	Cgc/Tgc	1/2	0.526015237004663	6	FACETS	1	0.947	1			1	CLONAL	1	FALSE	NA	0.526015237004663	6		368	319	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0025878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	251	491	0				ENST00000310581	NM_198253.2	-/1132			0.703220747698436	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	1	0.703220747698436	3		491	480	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0025878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	709	503	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.703220747698436	5	FACETS	1	0.988	1	1	0.988	1	CLONAL	4	TRUE	1	0.703220747698436	5		503	1013	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857436	9857437	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	123	436	0	ENST00000330684.3:c.3964_3965delinsAA	p.Gly1322Lys	p.G1322K	ENST00000330684	NM_001134407.1	1322	GGa/AAa	13/13	0.703220747698436	3	FACETS	0.805	0.731	0.884	0.403	0.365	0.442	CLONAL	1	TRUE	1	0.703220747698436	3		436	587	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191165	2191165	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	241	871	0	ENST00000398665.3:c.419C>T	p.Ser140Phe	p.S140F	ENST00000398665	NM_032482.2	140	tCc/tTc	5/28	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.703220747698436	2		871	658	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0025879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	162	675	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.195558245749527	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	1	0.22	3		675	765	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849517	68849517	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	232	567	0	ENST00000261769.5:c.1420del	p.Thr474ProfsTer7	p.T474Pfs*7	ENST00000261769	NM_004360.3	474	Acc/cc	10/16	0.3	1	FACETS	0.942	0.884	1	1	0.995	1	CLONAL	3	TRUE	0	0.22	1		567	664	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0025879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	62	435	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.849	0.732	0.976	0.849	0.732	0.976	CLONAL	1	TRUE	1	0.19	2		435	769	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041758	14041758	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373135011	NA	P-0025879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	41	436	0	ENST00000311895.7:c.2305C>T	p.Leu769Phe	p.L769F	ENST00000311895	NM_005236.2	769	Ctc/Ttc	11/11	1	2	FACETS	0.692	0.575	0.822	0.692	0.575	0.822	SUBCLONAL	1	TRUE	1	0.19	2		436	624	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223152	5223152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745426688	NA	P-0025879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	51	721	0	ENST00000357368.4:c.2651C>T	p.Pro884Leu	p.P884L	ENST00000357368	NM_002850.3	884	cCg/cTg	18/38	0.257355336369566	0	FACETS	0.654	0.555	0.763			1	SUBCLONAL	1	TRUE	0	0.19	0		721	665	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0025880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	82	83	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.228174193588365	1	FACETS	0.989	0.875	1	0.989	0.875	1	CLONAL	1	TRUE	0	0.308383016595033	1		83	455	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0025880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	54	472	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.228174193588365	1	FACETS	0.884	0.759	1	0.884	0.759	1	CLONAL	1	TRUE	0	0.308383016595033	1		472	335	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121433	108121435	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0025880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	13	239	0	ENST00000278616.4:c.1241_1243del	p.Gln414_Ile415delinsLeu	p.Q414_I415delinsL	ENST00000278616	NM_000051.3	414	cAGAtt/ctt	10/63	0.308383016595033	1	FACETS	0.407	0.291	0.548	0.407	0.291	0.548	SUBCLONAL	1	TRUE	0	0.308383016595033	1		239	175	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982382	25982382	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	35	353	0	ENST00000435504.4:c.908T>A	p.Leu303Gln	p.L303Q	ENST00000435504		303	cTg/cAg	9/13	0.308383016595033	1	FACETS	0.706	0.581	0.844	0.706	0.581	0.844	SUBCLONAL	1	TRUE	0	0.308383016595033	1		353	272	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012413	152012413	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs755920056	NA	P-0025880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	32	301	0	ENST00000262189.6:c.400T>A	p.Cys134Ser	p.C134S	ENST00000262189	NM_170606.2	134	Tgc/Agc	4/59	1	2	FACETS	0.701	0.571	0.847	0.701	0.571	0.847	SUBCLONAL	1	TRUE	1	0.308383016595033	2		301	296	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0025881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	463	675	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.681250273046756	6	FACETS	0.965	0.929	1			1	CLONAL	4	FALSE	NA	0.681250273046756	6		675	832	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0025881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	386	627	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.646170219619625	2	FACETS	0.964	0.929	0.998	0.964	0.929	0.998	CLONAL	2	FALSE	0	0.681250273046756	2		627	588	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555267	106555267	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3889	272	625	1	ENST00000369096.4:c.2384C>A	p.Ser795Ter	p.S795*	ENST00000369096	NM_001198.3	795	tCa/tAa	7/7	0.681250273046756	28	FACETS	0.946	0.881	1			1	CLONAL	2	FALSE	NA	0.681250273046756	28		626	4161	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586470	189586470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147148566	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	128	431	0	ENST00000264731.3:c.1094C>T	p.Ser365Leu	p.S365L	ENST00000264731	NM_003722.4	365	tCg/tTg	8/14	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.3	2		431	783	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156088	119156088	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs187952822	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	46	509	0	ENST00000264033.4:c.1753C>T	p.Arg585Cys	p.R585C	ENST00000264033	NM_005188.3	585	Cgc/Tgc	11/16	0.3	2	FACETS	0.423	0.355	0.498			1	SUBCLONAL	1	TRUE	NA	0.3	2		509	725	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	134	297	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	1	0.925	1	1	0.991	1	CLONAL	2	TRUE	1	0.3	2		297	442	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	118	507	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.3	2		507	691	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	74	391	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.889	0.779	1	0.889	0.779	1	CLONAL	1	TRUE	1	0.3	2		392	555	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	51	412	4	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.574	0.488	0.67	0.574	0.488	0.67	SUBCLONAL	1	TRUE	1	0.3	2		416	592	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207153	1207155	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs587782056	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	69	617	0	ENST00000326873.7:c.250_252del	p.Lys84del	p.K84del	ENST00000326873	NM_000455.4	81	AAG/-	1/10	0.0834238171339065	0	FACETS	0.405	0.351	0.462			1	INDETERMINATE	1	TRUE	0	0.3	0		617	796	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527568	29527569	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555610903	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	34	523	0	ENST00000356175.3:c.1019_1020del	p.Ser340CysfsTer12	p.S340Cfs*12	ENST00000356175	NM_000267.3	339	aaCTct/aact	9/57	1	2	FACETS	0.372	0.303	0.45	0.372	0.303	0.45	SUBCLONAL	1	TRUE	1	0.3	2		523	609	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65323452	65323452	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765489448	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	28	351	1	ENST00000342505.4:c.1345G>A	p.Ala449Thr	p.A449T	ENST00000342505	NM_002227.2	449	Gcc/Acc	10/25	1	2	FACETS	0.348	0.277	0.429	0.348	0.277	0.429	SUBCLONAL	1	TRUE	1	0.3	2		352	536	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	95	504	2	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	0.0834238171339065	0	FACETS	0.779	0.695	0.868			1	INDETERMINATE	1	TRUE	0	0.3	0		506	569	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703538	47703538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63749932	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	196	485	0	ENST00000233146.2:c.2038C>T	p.Arg680Ter	p.R680*	ENST00000233146	NM_000251.2	680	Cga/Tga	13/16	0.294987005782566	2	FACETS	0.931	0.865	0.999	0.931	0.865	0.999	CLONAL	2	TRUE	0	0.3	2		485	702	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61711074	61711074	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs755621083	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	95	383	0	ENST00000401558.2:c.2675C>T	p.Thr892Met	p.T892M	ENST00000401558	NM_003400.3	892	aCg/aTg	21/25	0.294987005782566	2	FACETS	1	0.953	1	0.561	0.501	0.626	CLONAL	1	TRUE	0	0.3	2		383	564	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662384	67662384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112926498	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	49	536	2	ENST00000264010.4:c.1630C>T	p.Arg544Cys	p.R544C	ENST00000264010	NM_006565.3	544	Cgc/Tgc	9/12	1	2	FACETS	0.4	0.337	0.469	0.4	0.337	0.469	SUBCLONAL	1	TRUE	1	0.3	2		538	817	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101117	27101117	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	60	555	0	ENST00000324856.7:c.4403del	p.Pro1468LeufsTer13	p.P1468Lfs*13	ENST00000324856	NM_006015.4	1467	Ccc/cc	18/20	1	2	FACETS	0.557	0.479	0.642	0.557	0.479	0.642	SUBCLONAL	1	TRUE	1	0.3	2		555	718	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29497003	29497003	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397514641	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	57	268	1	ENST00000356175.3:c.574C>T	p.Arg192Ter	p.R192*	ENST00000356175	NM_000267.3	192	Cga/Tga	5/57	1	2	FACETS	0.784	0.673	0.904	0.784	0.673	0.904	CLONAL	1	TRUE	1	0.3	2		269	485	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380350	14380350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	63	254	0	ENST00000256196.4:c.67G>A	p.Gly23Ser	p.G23S	ENST00000256196		23	Ggc/Agc	1/6	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.3	2		254	389	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096133	2096133	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs763525759	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	47	435	0	ENST00000219066.1:c.374del	p.Pro125GlnfsTer12	p.P125Qfs*12	ENST00000219066	NM_002528.5	125	cCa/ca	2/6	1	2	FACETS	0.628	0.53	0.736	0.628	0.53	0.736	SUBCLONAL	1	TRUE	1	0.3	2		435	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579705	7579705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201753350	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	72	549	0	ENST00000269305.4:c.91G>A	p.Val31Ile	p.V31I	ENST00000269305	NM_001126112.2	31	Gtt/Att	3/11	1	2	FACETS	0.649	0.566	0.738	0.649	0.566	0.738	SUBCLONAL	1	TRUE	1	0.3	2		549	740	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	50	599	3	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	0.0834238171339065	0	FACETS	0.326	0.276	0.381			1	INDETERMINATE	1	TRUE	0	0.3	0		602	716	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610306	10610306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	99	610	1	ENST00000171111.5:c.404G>A	p.Arg135His	p.R135H	ENST00000171111	NM_203500.1	135	cGc/cAc	2/6	0.0834238171339065	0	FACETS	0.711	0.635	0.791			1	INDETERMINATE	1	TRUE	0	0.3	0		611	650	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118365112	118365112	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs781944403	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	53	415	0	ENST00000534358.1:c.5288G>A	p.Arg1763Gln	p.R1763Q	ENST00000534358	NM_005933.3	1763	cGg/cAg	17/36	0.3	2	FACETS	0.564	0.48	0.655			1	SUBCLONAL	1	TRUE	NA	0.3	2		415	627	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101165	27101165	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1466575457	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	97	537	0	ENST00000324856.7:c.4447G>A	p.Gly1483Ser	p.G1483S	ENST00000324856	NM_006015.4	1483	Ggc/Agc	18/20	1	2	FACETS	0.944	0.842	1	0.944	0.842	1	CLONAL	1	TRUE	1	0.3	2		537	685	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998997	100998997	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	30	362	0	ENST00000325455.5:c.805C>A	p.Pro269Thr	p.P269T	ENST00000325455	NM_001202474.3	269	Ccc/Acc	1/8	1	2	FACETS	0.526	0.424	0.642	0.526	0.424	0.642	SUBCLONAL	1	TRUE	1	0.3	2		362	380	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246471	46246471	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	33	297	0	ENST00000334344.6:c.4565C>T	p.Thr1522Ile	p.T1522I	ENST00000334344	NM_152641.2	1522	aCt/aTt	15/21	1	2	FACETS	0.466	0.379	0.564	0.466	0.379	0.564	SUBCLONAL	1	TRUE	1	0.3	2		297	472	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434945	49434945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770692765	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	53	416	0	ENST00000301067.7:c.6608C>T	p.Thr2203Met	p.T2203M	ENST00000301067	NM_003482.3	2203	aCg/aTg	31/54	1	2	FACETS	0.839	0.717	0.972	0.839	0.717	0.972	CLONAL	1	TRUE	1	0.3	2		416	421	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912973	32912973	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	137	549	0	ENST00000380152.3:c.4481G>A	p.Ser1494Asn	p.S1494N	ENST00000380152		1494	aGt/aAt	11/27	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.3	2		549	902	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701142	43701144	+	inframe_deletion	In_Frame_Del	DEL	ATA	ATA	-	novel	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	99	446	0	ENST00000382044.4:c.5551_5553del	p.Tyr1851del	p.Y1851del	ENST00000382044	NM_001141980.1	1851	TAT/-	26/28	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.3	2		446	651	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293158	91293158	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	41	403	0	ENST00000355112.3:c.660G>T	p.Leu220Phe	p.L220F	ENST00000355112	NM_000057.2	220	ttG/ttT	3/22	1	2	FACETS	0.42	0.349	0.499	0.42	0.349	0.499	SUBCLONAL	1	TRUE	1	0.3	2		403	651	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456394	99456394	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	99	440	0	ENST00000268035.6:c.1711C>A	p.Leu571Met	p.L571M	ENST00000268035	NM_000875.3	571	Ctg/Atg	8/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.3	2		440	582	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216736	7216737	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCTGT	rs748493582	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	25	358	0	ENST00000380728.2:c.681_686dup	p.Gln228_Pro229dup	p.Q228_P229dup	ENST00000380728		228	ccc/ccACAGCCc	8/11	1	2	FACETS	0.336	0.264	0.419	0.336	0.264	0.419	SUBCLONAL	1	TRUE	1	0.3	2		358	496	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15938174	15938174	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779636265	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	35	458	0	ENST00000268712.3:c.7040C>T	p.Thr2347Met	p.T2347M	ENST00000268712	NM_006311.3	2347	aCg/aTg	45/46	1	2	FACETS	0.4	0.327	0.483	0.4	0.327	0.483	SUBCLONAL	1	TRUE	1	0.3	2		458	583	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600335	10600335	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1339695646	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	52	476	2	ENST00000171111.5:c.1520G>A	p.Arg507Gln	p.R507Q	ENST00000171111	NM_203500.1	507	cGa/cAa	4/6	0.0834238171339065	0	FACETS	0.434	0.369	0.505			1	INDETERMINATE	1	TRUE	0	0.3	0		478	559	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602684	10602684	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	64	563	0	ENST00000171111.5:c.894G>T	p.Lys298Asn	p.K298N	ENST00000171111	NM_203500.1	298	aaG/aaT	3/6	0.0834238171339065	0	FACETS	0.461	0.399	0.528			1	INDETERMINATE	1	TRUE	0	0.3	0		563	648	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213971	36213971	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	47	553	0	ENST00000222270.7:c.2801del	p.Gly934GlufsTer52	p.G934Efs*52	ENST00000222270	NM_014727.1	933	Ggg/gg	6/37	0.0834238171339065	0	FACETS	0.341	0.287	0.4			1	INDETERMINATE	1	TRUE	0	0.3	0		553	644	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921124	50921124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1307047144	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	83	514	1	ENST00000440232.2:c.3244C>T	p.Arg1082Cys	p.R1082C	ENST00000440232	NM_002691.3	1082	Cgc/Tgc	27/27	0.0834238171339065	0	FACETS	0.68	0.601	0.764			1	INDETERMINATE	1	TRUE	0	0.3	0		515	570	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143421	30143421	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	54	322	0	ENST00000389048.3:c.105del	p.Pro36ArgfsTer45	p.P36Rfs*45	ENST00000389048	NM_004304.4	35	ggG/gg	1/29	0.294987005782566	2	FACETS	1	0.869	1	0.507	0.435	0.585	CLONAL	1	TRUE	0	0.3	2		322	355	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015218	128015218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372094432	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	49	413	2	ENST00000285398.2:c.2303C>T	p.Ala768Val	p.A768V	ENST00000285398	NM_000122.1	768	gCg/gTg	15/15	1	2	FACETS	0.497	0.42	0.582	0.497	0.42	0.582	SUBCLONAL	1	TRUE	1	0.3	2		415	657	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451363	187451363	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs573866973	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	56	367	0	ENST00000232014.4:c.119G>A	p.Arg40His	p.R40H	ENST00000232014	NM_001130845.1	40	cGt/cAt	3/10	1	2	FACETS	0.694	0.595	0.802	0.694	0.595	0.802	SUBCLONAL	1	TRUE	1	0.3	2		367	538	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819803	170819803	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	41	553	2	ENST00000296930.5:c.442G>T	p.Gly148Cys	p.G148C	ENST00000296930	NM_002520.6	148	Ggt/Tgt	5/11	1	2	FACETS	0.379	0.314	0.45	0.379	0.314	0.45	SUBCLONAL	1	TRUE	1	0.3	2		555	722	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549387	5549387	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	58	505	0	ENST00000397747.3:c.414G>T	p.Glu138Asp	p.E138D	ENST00000397747	NM_025239.3	138	gaG/gaT	4/7	1	2	FACETS	0.523	0.448	0.604	0.523	0.448	0.604	SUBCLONAL	1	TRUE	1	0.3	2		505	740	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341872	8341872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	38	521	0	ENST00000356435.5:c.4768G>A	p.Ala1590Thr	p.A1590T	ENST00000356435		1590	Gcc/Acc	29/35	1	2	FACETS	0.383	0.316	0.459	0.383	0.316	0.459	SUBCLONAL	1	TRUE	1	0.3	2		521	661	SUCCESS
AR	367	MSKCC	GRCh37	X	66765233	66765233	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	38	269	0	ENST00000374690.3:c.245C>G	p.Thr82Ser	p.T82S	ENST00000374690	NM_000044.3	82	aCt/aGt	1/8	1	2	FACETS	0.967	0.804	1	0.967	0.804	1	CLONAL	1	TRUE	1	0.3	2		269	262	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196792	123196792	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	47	477	2	ENST00000218089.9:c.1679G>T	p.Arg560Met	p.R560M	ENST00000218089	NM_001042749.1	560	aGg/aTg	18/35	1	2	FACETS	0.468	0.394	0.55	0.468	0.394	0.55	SUBCLONAL	1	TRUE	1	0.3	2		479	670	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28934577	NA	P-0025886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	48	185	0	ENST00000269305.4:c.770T>C	p.Leu257Pro	p.L257P	ENST00000269305	NM_001126112.2	257	cTg/cCg	7/11	0.268145293685323	1	FACETS	0.957	0.813	1	0.957	0.813	1	CLONAL	1	TRUE	0	0.268145293685323	1		185	324	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307276	65307277	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0025886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	33	321	0	ENST00000342505.4:c.2411_2412del	p.Arg804IlefsTer3	p.R804Ifs*3	ENST00000342505	NM_002227.2	804	aGA/a	18/25	1	2	FACETS	0.786	0.642	0.948	0.786	0.642	0.948	CLONAL	1	TRUE	1	0.268145293685323	2		321	313	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457630	67457630	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377026877	NA	P-0025886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	62	483	1	ENST00000327367.4:c.440C>T	p.Pro147Leu	p.P147L	ENST00000327367	NM_005902.3	147	cCg/cTg	3/9	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.268145293685323	2		484	433	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844112	68844112	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	91	422	1	ENST00000261769.5:c.700G>T	p.Ala234Ser	p.A234S	ENST00000261769	NM_004360.3	234	Gct/Tct	6/16	0.194695703083871	3	FACETS	0.785	0.7	0.876	0.785	0.7	0.876	SUBCLONAL	2	TRUE	1	0.268145293685323	3		423	490	SUCCESS
APC	324	MSKCC	GRCh37	5	112175422	112175435	+	frameshift_variant	Frame_Shift_Del	DEL	TCAGGAGACCCCAC	TCAGGAGACCCCAC	-	novel	NA	P-0025886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	24	225	0	ENST00000257430.4:c.4134_4147del	p.Gln1378HisfsTer3	p.Q1378Hfs*3	ENST00000257430	NM_000038.5	1377	gtTCAGGAGACCCCACtc/gttc	16/16	1	2	FACETS	0.699	0.55	0.871	0.699	0.55	0.871	SUBCLONAL	1	TRUE	1	0.268145293685323	2		225	256	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	402	371	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	0.850500370362834	2		371	938	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0025887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	354	306	5	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	NA	2	FACETS	0.952	0.925	0.978			1	INDETERMINATE	2	TRUE	NA	0.850500370362834	2		311	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0025887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	539	631	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.772079895759739	1	FACETS	0.994	0.967	1	0.994	0.967	1	CLONAL	1	TRUE	0	0.850500370362834	1		631	733	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692871	89692871	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139767111	NA	P-0025887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	280	285	0	ENST00000371953.3:c.355G>T	p.Val119Phe	p.V119F	ENST00000371953	NM_000314.4	119	Gtt/Ttt	5/9	0.849163985211864	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.850500370362834	1		285	351	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	84	371	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	0.29	2		371	547	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0025913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	210	92	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.297751658841791	2	FACETS	0.936	0.877	0.995	1	0.991	1	CLONAL	3	TRUE	0	0.29	2		92	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0025913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	102	689	0	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	0.297751658841791	1	FACETS	0.969	0.868	1	0.969	0.868	1	CLONAL	1	TRUE	0	0.29	1		689	621	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0025914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	213	465	1	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.444444711297095	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.456026168087057	2		466	455	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456804	32456804	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	107	469	0	ENST00000332351.3:c.88C>A	p.Gln30Lys	p.Q30K	ENST00000332351	NM_024426.4	30	Cag/Aag	1/10	0.452861612085841	3	FACETS	0.924	0.839	1	0.924	0.839	1	CLONAL	2	TRUE	1	0.456026168087057	3		469	312	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615153	43615153	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	93	537	0	ENST00000355710.3:c.2568del	p.Trp856CysfsTer13	p.W856Cfs*13	ENST00000355710	NM_020975.4	856	tGg/tg	14/20	0.456026168087057	4	FACETS	0.9	0.801	1			1	CLONAL	1	TRUE	NA	0.456026168087057	4		537	660	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104356906	104356906	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	171	421	0	ENST00000369902.3:c.766G>T	p.Asp256Tyr	p.D256Y	ENST00000369902	NM_016169.3	256	Gac/Tac	7/12	0.456026168087057	2	FACETS	0.872	0.811	0.934	0.872	0.811	0.934	CLONAL	2	TRUE	0	0.456026168087057	2		421	430	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425098	49425098	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	212	605	1	ENST00000301067.7:c.13390C>T	p.Gln4464Ter	p.Q4464*	ENST00000301067	NM_003482.3	4464	Cag/Tag	39/54	0.385336224029735	3	FACETS	0.968	0.905	1			1	CLONAL	2	TRUE	NA	0.456026168087057	3		606	590	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440398	49440398	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	100	610	1	ENST00000301067.7:c.4412G>A	p.Cys1471Tyr	p.C1471Y	ENST00000301067	NM_003482.3	1471	tGc/tAc	15/54	0.385336224029735	3	FACETS	0.816	0.73	0.908			1	CLONAL	1	TRUE	NA	0.456026168087057	3		611	660	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481361	56481361	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs368392747	NA	P-0025914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	306	630	0	ENST00000267101.3:c.548G>T	p.Cys183Phe	p.C183F	ENST00000267101	NM_001982.3	183	tGt/tTt	5/28	0.456026168087057	4	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.456026168087057	4		630	787	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435151	110435151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	57	441	0	ENST00000375856.3:c.3250C>T	p.Pro1084Ser	p.P1084S	ENST00000375856	NM_003749.2	1084	Ccg/Tcg	1/2	0.445214240054668	1	FACETS	0.91	0.792	1	0.91	0.792	1	CLONAL	1	TRUE	0	0.456026168087057	1		441	212	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375211	31375211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147945634	NA	P-0025914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	117	676	1	ENST00000328111.2:c.608C>T	p.Pro203Leu	p.P203L	ENST00000328111	NM_006892.3	203	cCg/cTg	6/23	0.104454499714763	1	FACETS	0.822	0.745	0.902	0.822	0.745	0.902	INDETERMINATE	1	TRUE	0	0.456026168087057	1		677	482	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187560902	187560902	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs765424396	NA	P-0025914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	181	498	0	ENST00000441802.2:c.3616G>T	p.Glu1206Ter	p.E1206*	ENST00000441802	NM_005245.3	1206	Gaa/Taa	4/27	0.444444711297095	2	FACETS	0.919	0.857	0.981	0.919	0.857	0.981	CLONAL	2	TRUE	0	0.456026168087057	2		498	432	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56171132	56171132	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	99	263	0	ENST00000399503.3:c.1960G>T	p.Ala654Ser	p.A654S	ENST00000399503	NM_005921.1	654	Gct/Tct	10/20	0.444444711297095	2	FACETS	0.944	0.86	1	0.944	0.86	1	CLONAL	2	TRUE	0	0.456026168087057	2		263	230	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185798	32185798	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	164	526	0	ENST00000375023.3:c.1598A>G	p.Asn533Ser	p.N533S	ENST00000375023	NM_004557.3	533	aAc/aGc	9/30	0.444444711297095	2	FACETS	0.939	0.874	1	0.939	0.874	1	CLONAL	2	TRUE	0	0.456026168087057	2		526	383	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527537	157527537	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	225	498	0	ENST00000346085.5:c.5262G>T	p.Lys1754Asn	p.K1754N	ENST00000346085	NM_020732.3	1754	aaG/aaT	20/20	0.357277050989665	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	2	0.456026168087057	4		498	657	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405685	139405685	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	197	710	0	ENST00000277541.6:c.2506del	p.Ser836AlafsTer40	p.S836Afs*40	ENST00000277541	NM_017617.3	836	Agc/gc	16/34	0.444444711297095	2	FACETS	0.933	0.874	0.993	0.933	0.874	0.993	CLONAL	2	TRUE	0	0.456026168087057	2		710	463	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039821	47039821	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	274	602	0	ENST00000377604.3:c.1164C>G	p.Asp388Glu	p.D388E	ENST00000377604	NM_001204468.1	388	gaC/gaG	12/24	0.456026168087057	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.456026168087057	4		602	747	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814178	76814178	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	194	390	0	ENST00000373344.5:c.6466C>A	p.Gln2156Lys	p.Q2156K	ENST00000373344	NM_000489.3	2156	Caa/Aaa	29/35	0.456026168087057	4	FACETS	0.974	0.906	1	0.974	0.906	1	CLONAL	2	TRUE	2	0.456026168087057	4		390	636	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0025915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	169	611	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.902	0.829	0.977	0.902	0.829	0.977	CLONAL	1	TRUE	1	0.418842904611571	2		611	895	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286209	66286209	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	156	438	0	ENST00000273854.3:c.1477G>T	p.Asp493Tyr	p.D493Y	ENST00000273854	NM_004439.5	493	Gat/Tat	6/18	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.418842904611571	2		438	732	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732957	30732957	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504421	NA	P-0025915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	30	249	0	ENST00000295754.5:c.1570G>A	p.Asp524Asn	p.D524N	ENST00000295754	NM_003242.5	524	Gac/Aac	7/7	0.418842904611571	1	FACETS	0.294	0.237	0.359	0.294	0.237	0.359	SUBCLONAL	1	TRUE	0	0.418842904611571	1		249	385	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106423	108106423	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	98	209	0	ENST00000278616.4:c.358C>T	p.Leu120Phe	p.L120F	ENST00000278616	NM_000051.3	120	Ctc/Ttc	5/63	1	2	FACETS	0.923	0.827	1	0.923	0.827	1	CLONAL	1	TRUE	1	0.418842904611571	2		209	507	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	184	461	0	ENST00000326873.7:c.580G>C	p.Asp194His	p.D194H	ENST00000326873	NM_000455.4	194	Gac/Cac	4/10	0.418842904611571	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.418842904611571	1		461	666	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715616	30715616	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	66	257	0	ENST00000295754.5:c.1274T>G	p.Met425Arg	p.M425R	ENST00000295754	NM_003242.5	425	aTg/aGg	5/7	0.418842904611571	1	FACETS	0.681	0.594	0.774	0.681	0.594	0.774	SUBCLONAL	1	TRUE	0	0.418842904611571	1		257	366	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168468	56168468	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	102	171	0	ENST00000399503.3:c.1424G>T	p.Trp475Leu	p.W475L	ENST00000399503	NM_005921.1	475	tGg/tTg	8/20	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.418842904611571	2		171	449	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965410	68965410	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	273	635	0	ENST00000288368.4:c.1022G>T	p.Cys341Phe	p.C341F	ENST00000288368	NM_024870.2	341	tGt/tTt	9/40	1	2	FACETS	0.974	0.913	1	0.974	0.913	1	CLONAL	1	TRUE	1	0.418842904611571	2		635	1338	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309025	137309025	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	210	480	0	ENST00000481739.1:c.632G>T	p.Arg211Leu	p.R211L	ENST00000481739	NM_002957.4	211	cGt/cTt	5/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.418842904611571	2		480	934	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241678	55241678	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517085	NA	P-0025916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	330	583	0	ENST00000275493.2:c.2126A>C	p.Glu709Ala	p.E709A	ENST00000275493	NM_005228.3	709	gAa/gCa	18/28	0.250738682001804	3	FACETS	0.833	0.788	0.879	0.833	0.788	0.879	INDETERMINATE	2	TRUE	1	0.454696111097421	3		583	1069	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913444	NA	P-0025916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	300	613	0	ENST00000275493.2:c.2582T>G	p.Leu861Arg	p.L861R	ENST00000275493	NM_005228.3	861	cTg/cGg	21/28	0.250738682001804	3	FACETS	0.779	0.735	0.825	0.779	0.735	0.825	INDETERMINATE	2	TRUE	1	0.454696111097421	3		613	1039	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604787	48604787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	138	365	1	ENST00000342988.3:c.1609G>A	p.Asp537Asn	p.D537N	ENST00000342988	NM_005359.5	537	Gac/Aac	12/12	0.454696111097421	1	FACETS	0.887	0.811	0.965	0.887	0.811	0.965	CLONAL	1	TRUE	0	0.454696111097421	1		366	529	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702546	52702546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	183	539	0	ENST00000394830.3:c.352C>T	p.Leu118Phe	p.L118F	ENST00000394830	NM_018313.4	118	Ctt/Ttt	4/30	0.453083271167753	1	FACETS	0.983	0.911	1	0.983	0.911	1	CLONAL	1	TRUE	0	0.454696111097421	1		539	633	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	60	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.763	0.656	0.879	0.763	0.656	0.879	SUBCLONAL	1	TRUE	1	0.23	2		371	684	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0025920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	50	576	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.913	0.776	1	0.913	0.776	1	CLONAL	1	TRUE	1	0.23	2		576	476	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9770571	9770571	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143116020	NA	P-0025920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	50	621	1	ENST00000377346.4:c.58G>A	p.Val20Ile	p.V20I	ENST00000377346	NM_005026.3	20	Gtt/Att	3/24	1	2	FACETS	0.843	0.715	0.983	0.843	0.715	0.983	CLONAL	1	TRUE	1	0.23	2		622	516	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0025920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	24	393	4	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	0.502	0.393	0.628	0.502	0.393	0.628	SUBCLONAL	1	TRUE	1	0.23	2		397	416	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434510	121434510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1401743626	NA	P-0025920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	94	639	0	ENST00000257555.6:c.1274C>T	p.Thr425Met	p.T425M	ENST00000257555		425	aCg/aTg	6/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.23	2		639	577	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	85	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.204916121699127	1	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	0	0.204916121699127	1		371	733	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121578	108121641	+	frameshift_variant	Frame_Shift_Del	DEL	TGCATTGTGTCAAGACAAGAGGTCAAACCTAGAAAGCTCACAAAAGTCAGATTTATTAAAACTC	TGCATTGTGTCAAGACAAGAGGTCAAACCTAGAAAGCTCACAAAAGTCAGATTTATTAAAACTC	CGCAT	novel	NA	P-0025922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	73	591	2	ENST00000278616.4:c.1386_1449delinsCGCAT	p.Cys465GlufsTer2	p.C465Efs*2	ENST00000278616	NM_000051.3	462	gtTGCATTGTGTCAAGACAAGAGGTCAAACCTAGAAAGCTCACAAAAGTCAGATTTATTAAAACTC/gtCGCAT	10/63	1	2	FACETS	0.853	0.745	0.971	0.853	0.745	0.971	CLONAL	1	TRUE	1	0.204916121699127	2		593	835	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937044	178937044	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	51	445	0	ENST00000263967.3:c.1725T>G	p.Asn575Lys	p.N575K	ENST00000263967	NM_006218.2	575	aaT/aaG	11/21	1	2	FACETS	0.851	0.723	0.992	0.851	0.723	0.992	CLONAL	1	TRUE	1	0.204916121699127	2		445	585	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592031	67592031	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	58	293	0	ENST00000274335.5:c.1847T>C	p.Leu616Ser	p.L616S	ENST00000274335		616	tTg/tCg	14/15	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.204916121699127	2		293	471	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	218	387	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.808323641335051	2		387	536	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216546	108216546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529296539	NA	P-0025923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	122	470	0	ENST00000278616.4:c.8495G>A	p.Arg2832His	p.R2832H	ENST00000278616	NM_000051.3	2832	cGt/cAt	58/63	1	2	FACETS	0.977	0.896	1	0.977	0.896	1	CLONAL	1	TRUE	1	0.808323641335051	2		470	309	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0025923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	297	650	0	ENST00000307078.5:c.1993_1994dup	p.Asn666AlafsTer24	p.N666Afs*24	ENST00000307078	NM_004655.3	665	ggc/ggGGc	8/11	NA	2	FACETS	0.755	0.712	0.799			1	INDETERMINATE	1	TRUE	NA	0.808323641335051	2		650	973	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944836	31944836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148314204	NA	P-0025923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	274	680	0	ENST00000340398.3:c.265G>A	p.Val89Ile	p.V89I	ENST00000340398	NM_001013699.2	89	Gtc/Atc	1/1	1	2	FACETS	0.868	0.818	0.919	0.868	0.818	0.919	CLONAL	1	TRUE	1	0.808323641335051	2		680	781	SUCCESS
APC	324	MSKCC	GRCh37	5	112173451	112173452	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGAA	novel	NA	P-0025923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	130	346	0	ENST00000257430.4:c.2162_2165dup	p.Ser722ArgfsTer13	p.S722Rfs*13	ENST00000257430	NM_000038.5	720	-/GGAA	16/16	0.808323641335051	1	FACETS	0.863	0.805	0.921	0.863	0.805	0.921	CLONAL	1	TRUE	0	0.808323641335051	1		346	222	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115920	8115921	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CACCCGCCATCCAGCCTGT	novel	NA	P-0025924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	86	507	0	ENST00000346208.3:c.1268_1286dup	p.Phe430ProfsTer83	p.F430Pfs*83	ENST00000346208		422	-/CACCCGCCATCCAGCCTGT	6/6	0.35471235693895	1	FACETS	0.241	0.213	0.272	0.241	0.213	0.272	INDETERMINATE	1	TRUE	0	0.634638379695739	1		507	767	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128028995	128028995	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	190	686	0	ENST00000285398.2:c.1862A>T	p.Asn621Ile	p.N621I	ENST00000285398	NM_000122.1	621	aAt/aTt	12/15	0.35471235693895	1	FACETS	0.405	0.374	0.437	0.405	0.374	0.437	INDETERMINATE	1	TRUE	0	0.634638379695739	1		686	1010	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513263	106513263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	229	444	0	ENST00000359195.3:c.2167G>A	p.Gly723Ser	p.G723S	ENST00000359195	NM_002649.2	723	Ggc/Agc	4/11	0.256001445913706	1	FACETS	0.685	0.641	0.73	0.685	0.641	0.73	INDETERMINATE	1	TRUE	0	0.634638379695739	1		444	719	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877140	151877140	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	307	552	0	ENST00000262189.6:c.7221del	p.Ser2408HisfsTer44	p.S2408Hfs*44	ENST00000262189	NM_170606.2	2407	ggG/gg	37/59	0.256001445913706	1	FACETS	0.709	0.67	0.749	0.709	0.67	0.749	INDETERMINATE	1	TRUE	0	0.634638379695739	1		552	931	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0025925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	167	627	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.412938251336052	2		627	716	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0025925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	106	248	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.412938251336052	2	FACETS	0.879	0.8	0.961	0.879	0.8	0.961	CLONAL	2	TRUE	0	0.412938251336052	2		248	292	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920422	114920422	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	156	583	2	ENST00000543371.1:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000543371	NM_001198531.1	455	Cga/Tga	13/14	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.412938251336052	2		585	721	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799185	45799187	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0025925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	123	591	2	ENST00000450313.1:c.246_248del	p.Ser83del	p.S83del	ENST00000450313	NM_012222.2	82	tcCTCa/tca	3/16	1	2	FACETS	0.956	0.867	1	0.956	0.867	1	CLONAL	1	TRUE	1	0.412938251336052	2		593	623	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896539	78896539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	142	760	2	ENST00000306801.3:c.2536C>T	p.Arg846Trp	p.R846W	ENST00000306801	NM_020761.2	846	Cgg/Tgg	22/34	1	2	FACETS	0.894	0.816	0.976	0.894	0.816	0.976	CLONAL	1	TRUE	1	0.412938251336052	2		762	769	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715629	30715629	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	72	368	0	ENST00000295754.5:c.1288del	p.Leu430Ter	p.L430*	ENST00000295754	NM_003242.5	429	gtC/gt	5/7	0.412938251336052	1	FACETS	0.898	0.792	1	0.898	0.792	1	CLONAL	1	TRUE	0	0.412938251336052	1		368	308	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921524	178921525	+	inframe_insertion	In_Frame_Ins	INS	-	-	TAAAAATTCTTTGTGCAACCTACG	novel	NA	P-0025925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	29	594	0	ENST00000263967.3:c.1008_1031dup	p.Lys337_Val344dup	p.K337_V344dup	ENST00000263967	NM_006218.2	337	ata/aTAAAAATTCTTTGTGCAACCTACGta	5/21	1	2	FACETS	0.349	0.279	0.427	0.349	0.279	0.427	SUBCLONAL	1	TRUE	1	0.412938251336052	2		594	403	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268083	153268083	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	84	260	0	ENST00000281708.4:c.725A>C	p.Gln242Pro	p.Q242P	ENST00000281708	NM_033632.3	242	cAg/cCg	4/12	1	2	FACETS	0.942	0.836	1	0.942	0.836	1	CLONAL	1	TRUE	1	0.412938251336052	2		260	432	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0025942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	299	340	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.587447683045061	3	FACETS	0.835	0.792	0.879	0.835	0.792	0.879	CLONAL	2	TRUE	1	0.665241961580332	3		340	717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0025942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	105	616	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.537	0.482	0.595	0.537	0.482	0.595	SUBCLONAL	1	TRUE	1	0.665241961580332	2		617	588	SUCCESS
APC	324	MSKCC	GRCh37	5	112174091	112174094	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1131691143	NA	P-0025942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	154	324	0	ENST00000257430.4:c.2802_2805del	p.Tyr935IlefsTer19	p.Y935Ifs*19	ENST00000257430	NM_000038.5	934	ACTTac/ac	16/16	1	2	FACETS	0.975	0.899	1	0.975	0.899	1	CLONAL	1	TRUE	1	0.665241961580332	2		324	475	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439717	51439719	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0025942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	68	331	0	ENST00000262662.1:c.284_286del	p.Asp95del	p.D95del	ENST00000262662		94	gcTGAt/gct	4/4	1	2	FACETS	0.454	0.396	0.517	0.454	0.396	0.517	SUBCLONAL	1	TRUE	1	0.665241961580332	2		331	450	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175516	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAGTGAAC	CAGAGTGAAC	-	novel	NA	P-0025942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	147	320	1	ENST00000257430.4:c.4218_4227del	p.Gln1406HisfsTer6	p.Q1406Hfs*6	ENST00000257430	NM_000038.5	1406	CAGAGTGAACca/ca	16/16	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.665241961580332	2		321	422	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859693	151859693	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146298908	NA	P-0025942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	53	294	0	ENST00000262189.6:c.10969G>A	p.Asp3657Asn	p.D3657N	ENST00000262189	NM_170606.2	3657	Gac/Aac	43/59	0.64748081964793	3	FACETS	0.417	0.356	0.484	0.209	0.178	0.242	SUBCLONAL	1	TRUE	1	0.665241961580332	3		294	509	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372202	55372202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764648837	NA	P-0025942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	59	192	1	ENST00000297316.4:c.892G>A	p.Gly298Ser	p.G298S	ENST00000297316	NM_022454.3	298	Ggc/Agc	2/2	1	2	FACETS	0.597	0.518	0.682	0.597	0.518	0.682	SUBCLONAL	1	TRUE	1	0.665241961580332	2		193	297	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0002349-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	216	396	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	0.217568085211905	2	FACETS	1	0.989	1	0.677	0.629	0.726	CLONAL	1	TRUE	0	0.331493994520152	2		396	963	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211539	98211539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772537644	NA	P-0002349-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	54	142	1	ENST00000331920.6:c.3616C>T	p.Arg1206Cys	p.R1206C	ENST00000331920	NM_000264.3	1206	Cgc/Tgc	22/24	1	2	FACETS	0.382	0.325	0.445	0.382	0.325	0.445	SUBCLONAL	1	TRUE	1	0.331493994520152	2		143	853	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427363	427363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002349-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	47	122	0	ENST00000399788.2:c.2806C>T	p.His936Tyr	p.H936Y	ENST00000399788	NM_001042603.1	936	Cat/Tat	19/28	NA	2	FACETS	0.531	0.448	0.623			1	INDETERMINATE	1	TRUE	NA	0.331493994520152	2		122	534	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975630	26975630	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002349-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	20	146	0	ENST00000381527.3:c.1138A>C	p.Asn380His	p.N380H	ENST00000381527	NM_001260.1	380	Aac/Cac	12/13	1	2	FACETS	0.314	0.24	0.402	0.314	0.24	0.402	SUBCLONAL	1	TRUE	1	0.331493994520152	2		146	384	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965144	15965144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139463526	NA	P-0002349-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	40	46	0	ENST00000268712.3:c.5452G>A	p.Ala1818Thr	p.A1818T	ENST00000268712	NM_006311.3	1818	Gcg/Acg	37/46	0.190666989250669	3	FACETS	0.811	0.676	0.96	0.405	0.338	0.48	INDETERMINATE	1	TRUE	1	0.331493994520152	3		46	347	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523252	9523252	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002349-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	135	137	0	ENST00000353224.5:c.1985G>C	p.Arg662Thr	p.R662T	ENST00000353224	NM_177990.2	662	aGa/aCa	9/10	0.190666989250669	3	FACETS	1	0.98	1	0.642	0.584	0.702	INDETERMINATE	1	TRUE	1	0.331493994520152	3		137	740	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921579	39921579	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002349-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	251	74	0	ENST00000378444.4:c.4241A>G	p.Gln1414Arg	p.Q1414R	ENST00000378444	NM_001123385.1	1414	cAg/cGg	10/15	0.278252114827411	2	FACETS	1	0.983	1			1	CLONAL	2	TRUE	NA	0.331493994520152	2		74	681	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067817	30067817	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002349-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	156	102	1	ENST00000338641.4:c.1003del	p.Glu335SerfsTer11	p.E335Sfs*11	ENST00000338641	NM_000268.3	334	atG/at	11/16	0.217568085211905	2	FACETS	1	0.978	1	0.596	0.547	0.648	CLONAL	1	TRUE	0	0.331493994520152	2		103	789	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0002386-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	87	300	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.546407957178531	3	FACETS	0.725	0.643	0.813	0.363	0.321	0.407	SUBCLONAL	1	TRUE	1	0.546407957178531	3		300	559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0002386-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	384	290	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.546407957178531	3	FACETS	0.991	0.954	1	0.991	0.954	1	CLONAL	3	TRUE	0	0.546407957178531	3		290	602	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0002386-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	192	378	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	NA	2	FACETS	0.947	0.878	1			1	INDETERMINATE	1	TRUE	NA	0.546407957178531	2		378	742	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727453	66727453	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397516790	NA	P-0002386-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	31	554	0	ENST00000307102.5:c.169A>G	p.Lys57Glu	p.K57E	ENST00000307102	NM_002755.3	57	Aag/Gag	2/11	1	2	FACETS	0.138	0.111	0.17	0.138	0.111	0.17	SUBCLONAL	1	TRUE	1	0.546407957178531	2		554	820	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939600	76939601	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002386-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1303	683	465	0	ENST00000373344.5:c.1147dup	p.Ile383AsnfsTer11	p.I383Nfs*11	ENST00000373344	NM_000489.3	383	atc/aAtc	9/35	0.149188239996866	6	FACETS	0.878	0.846	0.911			1	INDETERMINATE	3	TRUE	NA	0.546407957178531	6		465	1986	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246438	53246438	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002386-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2099	278	439	0	ENST00000375401.3:c.544G>T	p.Asp182Tyr	p.D182Y	ENST00000375401	NM_004187.3	182	Gat/Tat	5/26	0.546407957178531	5	FACETS	0.779	0.728	0.832			1	SUBCLONAL	1	TRUE	NA	0.546407957178531	5		439	2377	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971059	21971103	+	inframe_deletion	In_Frame_Del	DEL	GCCCGGTGCAGCACCACCAGCGTGTCCAGGAAGCCCTCCCGGGCA	GCCCGGTGCAGCACCACCAGCGTGTCCAGGAAGCCCTCCCGGGCA	-	novel	NA	P-0002386-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	67	192	0	ENST00000304494.5:c.255_299del	p.Ala86_Ala100del	p.A86_A100del	ENST00000304494	NM_000077.4	85	gcTGCCCGGGAGGGCTTCCTGGACACGCTGGTGGTGCTGCACCGGGCc/gcc	2/3	0.451493217945236	1	FACETS	0.702	0.617	0.791	0.702	0.617	0.791	SUBCLONAL	1	TRUE	0	0.546407957178531	1		192	254	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774188	56774188	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002386-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	288	422	0	ENST00000337432.4:c.540del	p.Gln181SerfsTer3	p.Q181Sfs*3	ENST00000337432	NM_058216.2	180	cTt/ct	3/9	0.546407957178531	3	FACETS	1	0.966	1	0.52	0.488	0.553	CLONAL	1	TRUE	1	0.546407957178531	3		422	1290	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272518	11272521	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	novel	NA	P-0002386-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	142	284	0	ENST00000361445.4:c.3409_3412del	p.Glu1137LeufsTer5	p.E1137Lfs*5	ENST00000361445	NM_004958.3	1137	GAGAct/ct	23/58	0.247468388459033	3	FACETS	0.988	0.902	1			1	INDETERMINATE	1	TRUE	NA	0.546407957178531	3		284	670	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0002388-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	262	205	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.216249437430831	4	FACETS	0.898	0.845	0.951	1	0.992	1	CLONAL	3	TRUE	2	0.359381100164695	4		205	736	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402145	402145	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002388-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	278	922	0	ENST00000399788.2:c.4646A>G	p.Asn1549Ser	p.N1549S	ENST00000399788	NM_001042603.1	1549	aAt/aGt	27/28	0.269351021904489	3	FACETS	0.926	0.871	0.983			1	CLONAL	2	TRUE	NA	0.359381100164695	3		922	985	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118704	115118706	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0002388-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	274	559	0	ENST00000257566.3:c.635_637del	p.Asn212del	p.N212del	ENST00000257566	NM_016569.3	212	aACAtt/att	2/8	0.359381100164695	1	FACETS	0.956	0.904	1	1	0.995	1	CLONAL	2	TRUE	0	0.359381100164695	1		559	654	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603006	48603007	+	splice_acceptor_variant	Splice_Site	INS	-	-	GGTCTTT	novel	NA	P-0002388-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	19	288	0	ENST00000342988.3:c.1309_1315dup		p.X437_splice	ENST00000342988	NM_005359.5	437			0.359381100164695	1	FACETS	0.235	0.178	0.303	0.235	0.178	0.303	SUBCLONAL	1	TRUE	0	0.359381100164695	1		288	369	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251554	251554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906780	NA	P-0002395-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	77	302	1	ENST00000264932.6:c.1765C>T	p.Arg589Trp	p.R589W	ENST00000264932	NM_004168.2	589	Cgg/Tgg	13/15	1	2	FACETS	0.898	0.801	0.999	1	0.987	1	CLONAL	3	TRUE	1	0.241144116594996	2		303	237	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750401	133750401	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002395-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	50	514	0	ENST00000318560.5:c.1232T>C	p.Leu411Pro	p.L411P	ENST00000318560	NM_005157.4	411	cTg/cCg	7/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.241144116594996	2		514	314	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880222	151880222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002398-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	27	195	0	ENST00000262189.6:c.5102G>A	p.Arg1701Lys	p.R1701K	ENST00000262189	NM_170606.2	1701	aGa/aAa	35/59	NA	2	FACETS	0.156	0.124	0.194			1	INDETERMINATE	1	TRUE	NA	0.669794859321619	2		195	516	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002643	37002643	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0002398-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	95	147	0	ENST00000358127.4:c.604+2T>A		p.X202_splice	ENST00000358127	NM_001280556.1	202			1	2	FACETS	0.737	0.661	0.816	0.737	0.661	0.816	SUBCLONAL	1	TRUE	1	0.669794859321619	2		147	385	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533656	41533656	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002398-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	222	249	0	ENST00000263253.7:c.1623-1G>A		p.X541_splice	ENST00000263253	NM_001429.3	541			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.669794859321619	2		249	643	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0002416-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	188	283	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.229367278841591	2	FACETS	0.868	0.804	0.934	0.868	0.804	0.934	CLONAL	2	TRUE	0	0.29	2		283	747	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598114	55598114	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002416-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	96	455	0	ENST00000288135.5:c.2311A>T	p.Ser771Cys	p.S771C	ENST00000288135	NM_000222.2	771	Agc/Tgc	16/21	1	2	FACETS	0.823	0.733	0.92	0.823	0.733	0.92	CLONAL	1	TRUE	1	0.29	2		455	804	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485806	8485806	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs755101026	NA	P-0002416-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	65	390	0	ENST00000356435.5:c.3011C>A	p.Pro1004Gln	p.P1004Q	ENST00000356435		1004	cCa/cAa	17/35	1	2	FACETS	0.809	0.702	0.925	0.809	0.702	0.925	CLONAL	1	TRUE	1	0.29	2		390	554	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486025	8486025	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002416-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	60	470	0	ENST00000356435.5:c.2792C>G	p.Thr931Ser	p.T931S	ENST00000356435		931	aCt/aGt	17/35	1	2	FACETS	0.712	0.614	0.82	0.712	0.614	0.82	SUBCLONAL	1	TRUE	1	0.29	2		470	581	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590969	95590969	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002416-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	49	321	0	ENST00000393063.1:c.940G>T	p.Gly314Ter	p.G314*	ENST00000393063	NM_030621.3	314	Gga/Tga	9/28	1	2	FACETS	0.661	0.56	0.773	0.661	0.56	0.773	SUBCLONAL	1	TRUE	1	0.29	2		321	511	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678619	88678619	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002416-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	26	184	1	ENST00000360948.2:c.917G>T	p.Arg306Leu	p.R306L	ENST00000360948	NM_001012338.2	306	cGt/cTt	9/19	0.180566003697618	2	FACETS	0.854	0.68	1	0.427	0.34	0.525	CLONAL	1	TRUE	0	0.29	2		185	210	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219409	1219409	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002416-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	50	244	0	ENST00000326873.7:c.461A>T	p.His154Leu	p.H154L	ENST00000326873	NM_000455.4	154	cAc/cTc	3/10	0.180566003697618	2	FACETS	1	0.957	1	0.673	0.576	0.778	CLONAL	1	TRUE	0	0.29	2		244	256	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867682	45867682	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002416-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	42	359	0	ENST00000391945.4:c.718G>C	p.Asp240His	p.D240H	ENST00000391945	NM_000400.3	240	Gac/Cac	8/23	1	2	FACETS	0.86	0.72	1	0.86	0.72	1	CLONAL	1	TRUE	1	0.29	2		359	337	SUCCESS
ALK	238	MSKCC	GRCh37	2	29541212	29541212	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002416-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	43	378	0	ENST00000389048.3:c.1605del	p.Ser536ValfsTer25	p.S536Vfs*25	ENST00000389048	NM_004304.4	535	acC/ac	8/29	1	2	FACETS	0.646	0.541	0.763	0.646	0.541	0.763	SUBCLONAL	1	TRUE	1	0.29	2		378	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0002422-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	478	513	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.662398342758827	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.665347126188936	2		515	659	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097617	11097617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371045201	NA	P-0002422-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	79	388	0	ENST00000358026.2:c.797C>T	p.Ser266Leu	p.S266L	ENST00000358026	NM_001128849.1	266	tCg/tTg	5/36	0.612880177023331	4	FACETS	0.39	0.342	0.442	0.195	0.171	0.221	SUBCLONAL	1	TRUE	2	0.665347126188936	4		388	1013	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0002426-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	334	440	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.317660271147704	4	FACETS	0.945	0.896	0.996	0.709	0.672	0.747	CLONAL	3	TRUE	0	0.317660271147704	4		440	977	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817469	39817469	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002426-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	74	286	0	ENST00000288319.7:c.94G>C	p.Glu32Gln	p.E32Q	ENST00000288319	NM_182918.3	32	Gag/Cag	2/10	0.317660271147704	3	FACETS	0.514	0.449	0.585	0.257	0.224	0.293	SUBCLONAL	1	TRUE	1	0.317660271147704	3		286	1050	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0002426-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	86	307	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	0.218257895051571	3	FACETS	0.576	0.508	0.649	0.192	0.169	0.217	SUBCLONAL	1	TRUE	0	0.317660271147704	3		307	1090	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0002426-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	174	290	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.19152172189947	2	FACETS	0.774	0.714	0.835	0.774	0.714	0.835	SUBCLONAL	2	TRUE	0	0.317660271147704	2		290	708	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593667	55593669	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	rs1060502543	NA	P-0002426-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	42	218	0	ENST00000288135.5:c.1735_1737del	p.Asp579del	p.D579del	ENST00000288135	NM_000222.2	578	tATGat/tat	11/21	0.19152172189947	2	FACETS	0.307	0.256	0.366	0.154	0.128	0.183	SUBCLONAL	1	TRUE	0	0.317660271147704	2		218	860	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426355	49426355	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002436-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	274	362	1	ENST00000301067.7:c.12133C>T	p.Gln4045Ter	p.Q4045*	ENST00000301067	NM_003482.3	4045	Cag/Tag	39/54	0.335622399281316	3	FACETS	0.769	0.727	0.812	0.769	0.727	0.812	INDETERMINATE	2	TRUE	1	0.718345806885351	3		363	674	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437193	52437204	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCACCATCCC	CCTCACCATCCC	A	novel	NA	P-0002462-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	29	337	0	ENST00000460680.1:c.1840_1851delinsT	p.Gly614SerfsTer25	p.G614Sfs*25	ENST00000460680	NM_004656.3	614	GGGATGGTGAGG/T	14/17	1	2	FACETS	0.92	0.738	1	0.92	0.738	1	CLONAL	1	TRUE	1	0.16	2		337	394	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	155	381	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.766	0.702	0.832	1	0.989	1	SUBCLONAL	2	TRUE	1	0.267050083280701	2		382	758	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	173	463	1	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.267050083280701	2		464	952	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	138	457	6	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	0.190038095022662	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.267050083280701	1		463	803	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	131	585	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	0.267050083280701	2		585	810	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	38	283	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.942	0.782	1	0.942	0.782	1	CLONAL	1	TRUE	1	0.267050083280701	2		283	302	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412375	139412375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1341448592	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	57	235	0	ENST00000277541.6:c.1270G>A	p.Glu424Lys	p.E424K	ENST00000277541	NM_017617.3	424	Gag/Aag	8/34	1	2	FACETS	0.765	0.662	0.876	1	0.97	1	SUBCLONAL	2	TRUE	1	0.267050083280701	2		235	279	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474110	29474110	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	81	348	0	ENST00000389048.3:c.2065G>T	p.Gly689Trp	p.G689W	ENST00000389048	NM_004304.4	689	Ggg/Tgg	12/29	1	2	FACETS	0.751	0.665	0.842	1	0.978	1	SUBCLONAL	2	TRUE	1	0.267050083280701	2		348	404	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165831	118165831	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	82	359	0	ENST00000369448.3:c.341G>A	p.Cys114Tyr	p.C114Y	ENST00000369448	NM_017709.3	114	tGt/tAt	2/2	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.267050083280701	2		359	574	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724560	162724560	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	129	411	1	ENST00000367921.3:c.332G>A	p.Gly111Asp	p.G111D	ENST00000367921	NM_006182.2	111	gGc/gAc	5/18	1	2	FACETS	0.773	0.703	0.846	1	0.987	1	SUBCLONAL	2	TRUE	1	0.267050083280701	2		412	625	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104571	193104571	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	155	441	0	ENST00000367435.3:c.358C>T	p.Arg120Ter	p.R120*	ENST00000367435	NM_024529.4	120	Cga/Tga	4/17	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.267050083280701	2		441	869	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293184	212293184	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	145	288	0	ENST00000342788.4:c.2668G>T	p.Glu890Ter	p.E890*	ENST00000342788	NM_005235.2	890	Gag/Tag	22/28	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.267050083280701	2		288	767	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662389	227662389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773817315	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	22	220	0	ENST00000305123.5:c.1066G>A	p.Ala356Thr	p.A356T	ENST00000305123	NM_005544.2	356	Gcc/Acc	1/2	1	2	FACETS	0.462	0.357	0.583	0.462	0.357	0.583	SUBCLONAL	1	TRUE	1	0.267050083280701	2		220	357	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435645	149435645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780804532	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	95	401	0	ENST00000286301.3:c.2498C>T	p.Thr833Met	p.T833M	ENST00000286301	NM_005211.3	833	aCg/aTg	19/22	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.267050083280701	2		401	590	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449504	149449504	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs374872712	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	98	455	0	ENST00000286301.3:c.1442A>G	p.Gln481Arg	p.Q481R	ENST00000286301	NM_005211.3	481	cAa/cGa	10/22	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.267050083280701	2		455	598	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515229	149515229	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1414956735	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	95	481	0	ENST00000261799.4:c.253C>T	p.Leu85Phe	p.L85F	ENST00000261799	NM_002609.3	85	Ctc/Ttc	3/23	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.267050083280701	2		481	600	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158662	26158662	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	10	17	0	ENST00000289316.2:c.265A>G	p.Thr89Ala	p.T89A	ENST00000289316	NM_138720.2	89	Acc/Gcc	1/2	0.216973498419777	4	FACETS	1	0.795	1	1	0.795	1	CLONAL	2	TRUE	2	0.267050083280701	4		17	40	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015133	37015133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223489007	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	103	443	0	ENST00000358127.4:c.271G>A	p.Ala91Thr	p.A91T	ENST00000358127	NM_001280556.1	91	Gcc/Acc	3/10	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.267050083280701	2		443	676	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80646042	80646042	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	61	222	0	ENST00000286548.4:c.110G>A	p.Arg37His	p.R37H	ENST00000286548	NM_002072.3	37	cGc/cAc	1/7	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.267050083280701	2		222	319	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413964	139413964	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	94	445	0	ENST00000277541.6:c.796T>G	p.Cys266Gly	p.C266G	ENST00000277541	NM_017617.3	266	Tgc/Ggc	5/34	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.267050083280701	2		445	573	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247618	123247618	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1466101220	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	109	393	1	ENST00000358487.5:c.1873C>T	p.Arg625Ter	p.R625*	ENST00000358487	NM_000141.4	625	Cga/Tga	14/18	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.267050083280701	2		394	625	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202788	133202788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201165149	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	32	445	0	ENST00000320574.5:c.6446G>A	p.Arg2149His	p.R2149H	ENST00000320574	NM_006231.2	2149	cGc/cAc	46/49	0.139792968580777	5	FACETS	0.557	0.451	0.677	0.139	0.112	0.17	INDETERMINATE	1	TRUE	1	0.267050083280701	5		445	603	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337696	73337696	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	129	405	0	ENST00000377767.4:c.2020G>T	p.Val674Phe	p.V674F	ENST00000377767	NM_014953.3	674	Gtt/Ttt	16/21	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.267050083280701	2		405	910	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15960949	15960949	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199804512	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	106	373	0	ENST00000268712.3:c.6271A>G	p.Thr2091Ala	p.T2091A	ENST00000268712	NM_006311.3	2091	Aca/Gca	40/46	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.267050083280701	2		373	685	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78704462	78704462	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	33	314	0	ENST00000306801.3:c.610A>G	p.Lys204Glu	p.K204E	ENST00000306801	NM_020761.2	204	Aag/Gag	5/34	1	2	FACETS	0.445	0.361	0.539	0.445	0.361	0.539	SUBCLONAL	1	TRUE	1	0.267050083280701	2		314	556	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375038	45375038	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	97	220	0	ENST00000262160.6:c.805T>C	p.Ser269Pro	p.S269P	ENST00000262160	NM_005901.5	269	Tca/Cca	8/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.267050083280701	2		220	536	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226989	2226989	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	81	257	0	ENST00000398665.3:c.4469G>A	p.Gly1490Asp	p.G1490D	ENST00000398665	NM_032482.2	1490	gGc/gAc	27/28	0.163144476539792	0	FACETS	0.686	0.61	0.766			1	SUBCLONAL	2	TRUE	0	0.267050083280701	0		257	324	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5216740	5216740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	90	440	0	ENST00000357368.4:c.4087C>T	p.His1363Tyr	p.H1363Y	ENST00000357368	NM_002850.3	1363	Cac/Tac	26/38	0.163144476539792	0	FACETS	0.967	0.861	1			1	CLONAL	1	TRUE	0	0.267050083280701	0		440	511	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145644	11145644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555785374	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	90	353	0	ENST00000358026.2:c.4006C>T	p.Arg1336Cys	p.R1336C	ENST00000358026	NM_001128849.1	1336	Cgc/Tgc	29/36	0.190038095022662	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.267050083280701	1		353	397	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276202	15276202	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	111	469	0	ENST00000263388.2:c.5792A>T	p.Asp1931Val	p.D1931V	ENST00000263388	NM_000435.2	1931	gAt/gTt	31/33	0.190038095022662	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.267050083280701	1		469	613	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302456	15302456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749561286	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	92	393	2	ENST00000263388.2:c.815C>T	p.Thr272Met	p.T272M	ENST00000263388	NM_000435.2	272	aCg/aTg	6/33	0.190038095022662	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.267050083280701	1		395	434	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478776	57478776	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	92	368	0	ENST00000371085.3:c.362A>G	p.Asn121Ser	p.N121S	ENST00000371085	NM_000516.4	121	aAc/aGc	5/13	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.267050083280701	2		368	604	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655447	45655447	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	42	171	0	ENST00000407780.3:c.407-2A>G		p.X136_splice	ENST00000407780	NM_001283052.1	136			1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.267050083280701	2		171	234	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176118141	176118142	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	160	360	0	ENST00000367669.3:c.830_831dup	p.Gln278SerfsTer10	p.Q278Sfs*10	ENST00000367669	NM_022457.5	277	-/AG		1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.267050083280701	2		360	860	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403253	213403254	+	frameshift_variant,start_lost,start_retained_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	105	414	0	ENST00000342788.4:c.1dup	p.Met1?	p.M1?	ENST00000342788	NM_005235.2	1	atg/aAtg	1/28	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.267050083280701	2		414	624	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795103	242795104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs768249210	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	40	295	0	ENST00000334409.5:c.105dup	p.Thr36HisfsTer70	p.T36Hfs*70	ENST00000334409	NM_005018.2	35	-/C	2/5	1	2	FACETS	0.868	0.724	1	0.868	0.724	1	CLONAL	1	TRUE	1	0.267050083280701	2		295	345	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636729	8636729	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	90	268	0	ENST00000356435.5:c.180del	p.Gly61GlufsTer11	p.G61Efs*11	ENST00000356435		60	aaA/aa	2/35	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.267050083280701	2		268	575	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244454	46244454	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs751704736	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	337	482	0	ENST00000334344.6:c.2552del	p.Pro851HisfsTer4	p.P851Hfs*4	ENST00000334344	NM_152641.2	850	Ccc/cc	15/21	0.199959701660146	4	FACETS	0.962	0.911	1	0.962	0.911	1	CLONAL	3	TRUE	1	0.267050083280701	4		482	1108	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420204	49420204	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	106	366	0	ENST00000301067.7:c.15545del	p.Gly5182AlafsTer61	p.G5182Afs*61	ENST00000301067	NM_003482.3	5182	gGc/gc	48/54	0.199959701660146	4	FACETS	0.773	0.694	0.856	0.515	0.462	0.571	SUBCLONAL	2	TRUE	1	0.267050083280701	4		366	651	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67459125	67459125	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	137	481	2	ENST00000327367.4:c.545del	p.Pro182LeufsTer4	p.P182Lfs*4	ENST00000327367	NM_005902.3	181	Ccc/cc	4/9	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.267050083280701	2		483	816	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832688	3832688	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	114	303	0	ENST00000262367.5:c.1570del	p.Leu524TrpfsTer6	p.L524Wfs*6	ENST00000262367	NM_004380.2	524	Ctg/tg	6/31	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.267050083280701	2		303	570	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349090	11349090	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	45	186	0	ENST00000332029.2:c.246del	p.Leu84Ter	p.L84*	ENST00000332029	NM_003745.1	82	ggG/gg	2/2	NA	2	FACETS	1	0.893	1			1	INDETERMINATE	1	TRUE	NA	0.267050083280701	2		186	314	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223376	2223376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	108	507	1	ENST00000398665.3:c.3492del	p.Val1165CysfsTer8	p.V1165Cfs*8	ENST00000398665	NM_032482.2	1163	Ccc/cc	25/28	0.163144476539792	0	FACETS	1	0.927	1			1	CLONAL	1	TRUE	0	0.267050083280701	0		508	572	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938173	76938174	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	76	515	0	ENST00000373344.5:c.2574dup	p.Gly859ArgfsTer4	p.G859Rfs*4	ENST00000373344	NM_000489.3	858	-/A	9/35	0.267050083280701	1	FACETS	0.537	0.47	0.61	0.537	0.47	0.61	SUBCLONAL	1	TRUE	0	0.267050083280701	1		515	918	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874163	155874163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs977405637	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	61	501	0	ENST00000368323.3:c.368G>A	p.Arg123His	p.R123H	ENST00000368323	NM_006912.5	123	cGt/cAt	5/6	1	2	FACETS	0.589	0.507	0.678	0.589	0.507	0.678	SUBCLONAL	1	TRUE	1	0.267050083280701	2		501	776	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911116	29911116	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs199474504	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	153	328	0	ENST00000376809.5:c.415C>T	p.Gln139Ter	p.Q139*	ENST00000376809	NM_002116.7	139	Cag/Tag	3/8	0.216973498419777	4	FACETS	0.878	0.808	0.951	1	0.985	1	CLONAL	3	TRUE	2	0.267050083280701	4		328	551	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485954	8485954	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs764368859	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	51	479	0	ENST00000356435.5:c.2863A>G	p.Thr955Ala	p.T955A	ENST00000356435		955	Acc/Gcc	17/35	1	2	FACETS	0.518	0.439	0.605	0.518	0.439	0.605	SUBCLONAL	1	TRUE	1	0.267050083280701	2		479	737	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240232	41240232	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	13	136	0	ENST00000379561.5:c.118T>G	p.Ser40Ala	p.S40A	ENST00000379561	NM_002015.3	40	Tcc/Gcc	1/3	1	2	FACETS	0.553	0.395	0.744	0.553	0.395	0.744	SUBCLONAL	1	TRUE	1	0.267050083280701	2		136	176	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352575	89352575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1301722354	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	144	465	0	ENST00000301030.4:c.764G>A	p.Arg255Gln	p.R255Q	ENST00000301030	NM_001256183.1	255	cGg/cAg	8/13	0.220027464887668	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.267050083280701	1		465	696	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16040642	16040642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	71	493	1	ENST00000268712.3:c.1492C>T	p.Arg498Cys	p.R498C	ENST00000268712	NM_006311.3	498	Cgc/Tgc	14/46	1	2	FACETS	0.54	0.47	0.616	0.54	0.47	0.616	SUBCLONAL	1	TRUE	1	0.267050083280701	2		494	985	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281743	46281743	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	193	566	0	ENST00000371998.3:c.4190G>A	p.Gly1397Asp	p.G1397D	ENST00000371998		1397	gGc/gAc	22/23	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.267050083280701	2		566	984	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568502	41568502	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	40	282	1	ENST00000263253.7:c.4453-1G>T		p.X1485_splice	ENST00000263253	NM_001429.3	1485			0.190038095022662	1	FACETS	0.467	0.387	0.556	0.467	0.387	0.556	SUBCLONAL	1	TRUE	0	0.267050083280701	1		283	556	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865276	57865276	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	289	617	1	ENST00000228682.2:c.2757del	p.Ala920ProfsTer26	p.A920Pfs*26	ENST00000228682	NM_005269.2	918	gCc/gc	12/12	0.199959701660146	4	FACETS	0.939	0.885	0.995	0.939	0.885	0.995	CLONAL	3	TRUE	1	0.267050083280701	4		618	973	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931788	39931788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	66	577	0	ENST00000378444.4:c.2811del	p.Thr938ProfsTer18	p.T938Pfs*18	ENST00000378444	NM_001123385.1	937	ccC/cc	4/15	NA	2	FACETS	0.734	0.637	0.84			1	INDETERMINATE	1	TRUE	NA	0.267050083280701	2		577	673	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255883	16255883	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	32	290	0	ENST00000375759.3:c.3154del	p.Ile1052SerfsTer40	p.I1052Sfs*40	ENST00000375759	NM_015001.2	1050	Aaa/aa	11/15	1	2	FACETS	0.486	0.394	0.591	0.486	0.394	0.591	SUBCLONAL	1	TRUE	1	0.267050083280701	2		290	493	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890149	76890150	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002463-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	92	549	0	ENST00000373344.5:c.4744dup	p.Thr1582AsnfsTer19	p.T1582Nfs*19	ENST00000373344	NM_000489.3	1582	aca/aAca	17/35	0.267050083280701	1	FACETS	0.584	0.517	0.655	0.584	0.517	0.655	SUBCLONAL	1	TRUE	0	0.267050083280701	1		549	1023	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0002482-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	76	440	2	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	0.144866620338609	3	FACETS	1	0.966	1	0.654	0.573	0.74	CLONAL	1	TRUE	1	0.19	3		442	670	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068362	26068362	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002482-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	71	393	0	ENST00000435504.4:c.128T>C	p.Leu43Pro	p.L43P	ENST00000435504		43	cTa/cCa	2/13	0.3	2	FACETS	1	0.903	1			1	CLONAL	1	TRUE	NA	0.19	2		393	717	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518393	8518393	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002482-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	32	168	0	ENST00000356435.5:c.998A>G	p.Glu333Gly	p.E333G	ENST00000356435		333	gAg/gGg	10/35	1	2	FACETS	0.74	0.6	0.899	0.74	0.6	0.899	SUBCLONAL	1	TRUE	1	0.19	2		168	455	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900171	101900171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564161322	NA	P-0002482-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	55	285	0	ENST00000374994.4:c.605C>T	p.Ala202Val	p.A202V	ENST00000374994	NM_004612.2	202	gCg/gTg	4/9	1	2	FACETS	0.954	0.815	1	0.954	0.815	1	CLONAL	1	TRUE	1	0.19	2		285	607	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441836	49441836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064794026	NA	P-0002482-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	47	323	0	ENST00000301067.7:c.4148G>A	p.Cys1383Tyr	p.C1383Y	ENST00000301067	NM_003482.3	1383	tGt/tAt	14/54	0.144866620338609	3	FACETS	1	0.857	1	0.508	0.428	0.596	CLONAL	1	TRUE	1	0.19	3		323	533	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28929495	NA	P-0002489-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	344	473	0	ENST00000275493.2:c.2155G>A	p.Gly719Ser	p.G719S	ENST00000275493	NM_005228.3	719	Ggc/Agc	18/28	0.398943312356694	8	FACETS	1	0.983	1	1	0.983	1	CLONAL	6	TRUE	2	0.398943312356694	8		473	600	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241677	55241677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504256	NA	P-0002489-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	360	481	0	ENST00000275493.2:c.2125G>A	p.Glu709Lys	p.E709K	ENST00000275493	NM_005228.3	709	Gaa/Aaa	18/28	0.398943312356694	8	FACETS	1	0.983	1	1	0.983	1	CLONAL	6	TRUE	2	0.398943312356694	8		481	632	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485273	8485273	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002489-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	58	542	0	ENST00000356435.5:c.3107T>C	p.Leu1036Pro	p.L1036P	ENST00000356435		1036	cTg/cCg	18/35	1	2	FACETS	0.761	0.657	0.874	0.761	0.657	0.874	SUBCLONAL	1	TRUE	1	0.398943312356694	2		542	382	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206578	108206578	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002489-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	119	378	0	ENST00000278616.4:c.8158G>T	p.Asp2720Tyr	p.D2720Y	ENST00000278616	NM_000051.3	2720	Gat/Tat	56/63	0.369738583756586	2	FACETS	0.755	0.688	0.825	0.755	0.688	0.825	SUBCLONAL	2	TRUE	0	0.398943312356694	2		378	395	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251260	99251260	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002489-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	39	446	0	ENST00000268035.6:c.564G>C	p.Glu188Asp	p.E188D	ENST00000268035	NM_000875.3	188	gaG/gaC	2/21	0.177842508233569	1	FACETS	0.591	0.492	0.699	0.591	0.492	0.699	INDETERMINATE	1	TRUE	0	0.398943312356694	1		446	265	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251278	99251278	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002489-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	39	446	0	ENST00000268035.6:c.582G>C	p.Lys194Asn	p.K194N	ENST00000268035	NM_000875.3	194	aaG/aaC	2/21	0.177842508233569	1	FACETS	0.591	0.492	0.699	0.591	0.492	0.699	INDETERMINATE	1	TRUE	0	0.398943312356694	1		446	265	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938185	76938185	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002489-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	155	578	0	ENST00000373344.5:c.2563C>G	p.His855Asp	p.H855D	ENST00000373344	NM_000489.3	855	Cac/Gac	9/35	0.239385053211071	2	FACETS	0.82	0.756	0.885	0.82	0.756	0.885	CLONAL	2	TRUE	0	0.398943312356694	2		578	474	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289196	33289196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771284147	NA	P-0002533-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	180	384	0	ENST00000374542.5:c.356G>A	p.Arg119Gln	p.R119Q	ENST00000374542	NM_001141970.1	119	cGg/cAg	3/8	0.916497553584208	4	FACETS	0.905	0.835	0.977	0.302	0.278	0.326	CLONAL	1	TRUE	1	0.916497553584208	4		384	832	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518112	8518112	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs533774328	NA	P-0002533-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	443	500	0	ENST00000356435.5:c.1279C>T	p.Arg427Ter	p.R427*	ENST00000356435		427	Cga/Tga	10/35	0.916497553584208	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.916497553584208	3		500	660	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061207	38061207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002537-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	252	219	0	ENST00000250448.2:c.782G>A	p.Arg261His	p.R261H	ENST00000250448	NM_004496.3	261	cGc/cAc	2/2	0.537394682842894	3	FACETS	0.894	0.846	0.943	1	0.995	1	CLONAL	4	TRUE	1	0.31	3		219	525	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676232	37676232	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0002537-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	295	457	1	ENST00000447079.4:c.2987T>G	p.Leu996Ter	p.L996*	ENST00000447079	NM_015083.1	996	tTa/tGa	11/14	0.537394682842894	1	FACETS	0.923	0.878	0.968	1	0.997	1	CLONAL	3	TRUE	0	0.31	1		458	581	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115744	8115744	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002543-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	384	555	2	ENST00000346208.3:c.1090A>G	p.Arg364Gly	p.R364G	ENST00000346208		364	Aga/Gga	6/6	0.150406874204641	3	FACETS	0.89	0.847	0.933	0.89	0.847	0.933	INDETERMINATE	2	TRUE	1	0.531278587157034	3		557	1028	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41001238	41001238	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002543-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	191	541	0	ENST00000267868.3:c.359G>C	p.Gly120Ala	p.G120A	ENST00000267868	NM_002875.4	120	gGa/gCa	5/10	0.125384826002093	4	FACETS	0.753	0.698	0.81	0.753	0.698	0.81	INDETERMINATE	2	TRUE	2	0.531278587157034	4		541	731	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011144	12011144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002543-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	196	415	0	ENST00000353533.5:c.551C>T	p.Ser184Leu	p.S184L	ENST00000353533	NM_003010.3	184	tCg/tTg	5/11	0.523436714957717	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.531278587157034	1		415	467	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063718	+	splice_donor_variant	Splice_Site	INS	-	-	TT	novel	NA	P-0002543-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	203	162	0	ENST00000412916.2:c.165+2_165+3insTT		p.X55_splice	ENST00000412916		55			NA	2	FACETS	1	0.987	1			1	INDETERMINATE	2	TRUE	NA	0.531278587157034	2		162	334	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618832	37618900	+	inframe_deletion	In_Frame_Del	DEL	AGCAGCAAGGAATCCAGGTCATCCAAGCTCCACAAGGAGAAGACCAGGAAAGAACGGGAGCTGAAGTCT	AGCAGCAAGGAATCCAGGTCATCCAAGCTCCACAAGGAGAAGACCAGGAAAGAACGGGAGCTGAAGTCT	-	novel	NA	P-0002543-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	55	398	0	ENST00000447079.4:c.508_576del	p.Ser170_Ser192del	p.S170_S192del	ENST00000447079	NM_015083.1	170	AGCAGCAAGGAATCCAGGTCATCCAAGCTCCACAAGGAGAAGACCAGGAAAGAACGGGAGCTGAAGTCT/-	1/14	NA	2	FACETS	0.353	0.301	0.409			1	INDETERMINATE	1	TRUE	NA	0.531278587157034	2		398	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0002593-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	299	467	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.733993152489368	1	FACETS	0.969	0.925	1	0.969	0.925	1	CLONAL	1	TRUE	0	0.733993152489368	1		467	532	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138389	37138389	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002593-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	209	260	0	ENST00000373509.5:c.38G>C	p.Arg13Pro	p.R13P	ENST00000373509	NM_002648.3	13	cGc/cCc	1/6	1	2	FACETS	0.897	0.837	0.958	0.897	0.837	0.958	CLONAL	1	TRUE	1	0.733993152489368	2		260	635	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687422	117687422	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002593-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	337	428	0	ENST00000368508.3:c.2629G>T	p.Ala877Ser	p.A877S	ENST00000368508	NM_002944.2	877	Gcc/Tcc	18/43	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.733993152489368	2		428	881	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771828	135771828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779599439	NA	P-0002593-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	703	469	0	ENST00000298552.3:c.3289C>T	p.Arg1097Cys	p.R1097C	ENST00000298552	NM_001162426.1	1097	Cgt/Tgt	23/23	0.691083987843388	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.733993152489368	2		469	955	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913131	44913131	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002593-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	386	612	2	ENST00000377967.4:c.806C>T	p.Ala269Val	p.A269V	ENST00000377967	NM_021140.2	269	gCt/gTt	10/29	NA	2	FACETS	0.932	0.886	0.978			1	INDETERMINATE	1	TRUE	NA	0.733993152489368	2		614	1129	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589619	67589630	+	inframe_deletion	In_Frame_Del	DEL	GAGAATATGATA	GAGAATATGATA	-	novel	NA	P-0002593-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	344	394	0	ENST00000274335.5:c.1384_1395del	p.Glu462_Arg465del	p.E462_R465del	ENST00000274335		461	cGAGAATATGATAga/cga	10/15	1	2	FACETS	0.888	0.842	0.936	0.888	0.842	0.936	CLONAL	1	TRUE	1	0.733993152489368	2		394	1055	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338640	70338653	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCCTGAAGCGGC	GCCCCTGAAGCGGC	CGAACAT	novel	NA	P-0002593-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	124	420	0	ENST00000374080.3:c.36_49delinsCGAACAT	p.Pro13GlufsTer22	p.P13Efs*22	ENST00000374080		12	cgGCCCCTGAAGCGGCcg/cgCGAACATcg	1/45	0.310426190760335	1	FACETS	0.285	0.257	0.314	0.285	0.257	0.314	INDETERMINATE	1	TRUE	0	0.733993152489368	1		420	751	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923215	26923215	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs769996123	NA	P-0002596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	34	424	0	ENST00000381527.3:c.211C>T	p.Arg71Ter	p.R71*	ENST00000381527	NM_001260.1	71	Cga/Tga	3/13	NA	2	FACETS	0.683	0.56	0.822			1	INDETERMINATE	1	TRUE	NA	0.31187798954489	2		424	319	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73351626	73351626	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	69	471	0	ENST00000377767.4:c.586G>C	p.Glu196Gln	p.E196Q	ENST00000377767	NM_014953.3	196	Gaa/Caa	4/21	0.235644401441324	3	FACETS	1	0.96	1	0.624	0.545	0.708	CLONAL	1	TRUE	1	0.31187798954489	3		471	410	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289061	33289064	+	frameshift_variant	Frame_Shift_Del	DEL	AGGT	AGGT	-	novel	NA	P-0002597-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	103	190	0	ENST00000374542.5:c.488_491del	p.His163ProfsTer65	p.H163Pfs*65	ENST00000374542	NM_001141970.1	163	cACCTc/cc	3/8	0.289346454415344	4	FACETS	0.987	0.894	1			1	CLONAL	2	TRUE	NA	0.46633356919833	4		190	328	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147516	47147516	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002597-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	40	312	0	ENST00000409792.3:c.4810T>G	p.Tyr1604Asp	p.Y1604D	ENST00000409792	NM_014159.6	1604	Tac/Gac	6/21	0.339285152428867	1	FACETS	0.743	0.626	0.87	0.743	0.626	0.87	SUBCLONAL	1	TRUE	0	0.46633356919833	1		312	177	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272497	15272497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771678721	NA	P-0002597-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	30	194	0	ENST00000263388.2:c.5942G>A	p.Arg1981His	p.R1981H	ENST00000263388	NM_000435.2	1981	cGc/cAc	33/33	0.139770784661467	4	FACETS	1	0.937	1	0.694	0.568	0.831	INDETERMINATE	1	TRUE	2	0.46633356919833	4		194	136	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038257	30038258	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0002608-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	65	333	1	ENST00000338641.4:c.431dup	p.Tyr144Ter	p.Y144*	ENST00000338641	NM_000268.3	144	tac/tAac	4/16	0.20739096242767	1	FACETS	0.534	0.464	0.609	0.534	0.464	0.609	INDETERMINATE	1	TRUE	0	0.42	1		334	458	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495742	72495748	+	frameshift_variant	Frame_Shift_Del	DEL	GTCTGCG	GTCTGCG	-	novel	NA	P-0002608-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	50	284	0	ENST00000477973.2:c.322_328del	p.Ala109LysfsTer25	p.A109Kfs*25	ENST00000477973	NM_012234.5	108	gcCGCAGAC/gc	1/4	1	2	FACETS	0.459	0.389	0.535	0.459	0.389	0.535	SUBCLONAL	1	TRUE	1	0.42	2		284	519	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0002614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	38	300	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.359590010582687	4	FACETS	0.732	0.607	0.872	0.366	0.303	0.436	SUBCLONAL	1	TRUE	2	0.428495234717918	4		300	346	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0002614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	164	232	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	1	2	FACETS	0.845	0.783	0.908	1	0.991	1	CLONAL	2	TRUE	1	0.428495234717918	2		232	453	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781419	135781419	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	114	214	0	ENST00000298552.3:c.1546C>T	p.Gln516Ter	p.Q516*	ENST00000298552	NM_001162426.1	516	Cag/Tag	15/23	0.368169905373739	2	FACETS	0.821	0.749	0.895	0.821	0.749	0.895	CLONAL	2	TRUE	0	0.428495234717918	2		214	324	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241678	55241678	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517085	NA	P-0002614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	190	268	0	ENST00000275493.2:c.2126A>C	p.Glu709Ala	p.E709A	ENST00000275493	NM_005228.3	709	gAa/gCa	18/28	1	2	FACETS	0.845	0.787	0.903	1	0.993	1	CLONAL	2	TRUE	1	0.428495234717918	2		268	525	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896419	28896419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	47	333	0	ENST00000282397.4:c.3031G>A	p.Glu1011Lys	p.E1011K	ENST00000282397	NM_002019.4	1011	Gag/Aag	22/30	0.24882107898743	0	FACETS	0.349	0.295	0.408			1	INDETERMINATE	1	TRUE	0	0.428495234717918	0		333	359	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743924	40743924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199514226	NA	P-0002614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	56	257	0	ENST00000373198.4:c.3071C>T	p.Thr1024Met	p.T1024M	ENST00000373198	NM_133170.3	1024	aCg/aTg	23/32	0.436154663701437	1	FACETS	0.658	0.568	0.756	0.658	0.568	0.756	SUBCLONAL	1	TRUE	0	0.428495234717918	1		257	312	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652097	36652098	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0002614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	216	212	0	ENST00000244741.5:c.222dup	p.Lys75GlnfsTer14	p.K75Qfs*14	ENST00000244741	NM_000389.4	73	-/C	2/3	0.428495234717918	5	FACETS	1	0.987	1			1	CLONAL	2	TRUE	NA	0.428495234717918	5		212	676	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852180	128852180	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002624-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	52	608	0	ENST00000249373.3:c.2252G>T	p.Ser751Ile	p.S751I	ENST00000249373	NM_005631.4	751	aGt/aTt	12/12	0.682196741052855	5	FACETS	0.76	0.648	0.881	0.253	0.216	0.294	SUBCLONAL	1	TRUE	2	0.682196741052855	5		608	406	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0002634-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	101	510	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.227375340722256	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.22	3		510	413	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599321	55599321	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002634-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	14	250	0	ENST00000288135.5:c.2447A>C	p.Asp816Ala	p.D816A	ENST00000288135	NM_000222.2	816	gAc/gCc	17/21	0.227375340722256	0	FACETS	0.383	0.277	0.512			1	SUBCLONAL	1	TRUE	0	0.22	0		250	259	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101402	27101402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002637-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	378	219	0	ENST00000324856.7:c.4689del	p.Met1564Ter	p.M1564*	ENST00000324856	NM_006015.4	1562	Ccc/cc	18/20	0.747375693250033	3	FACETS	0.903	0.864	0.942	0.903	0.864	0.942	CLONAL	2	TRUE	1	0.756005311242309	3		219	763	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0002637-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	606	264	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.756005311242309	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.756005311242309	2		264	725	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176132110	176132110	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002637-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	352	318	0	ENST00000367669.3:c.657G>T	p.Trp219Cys	p.W219C	ENST00000367669	NM_022457.5	219	tgG/tgT	5/20	0.747375693250033	3	FACETS	1	0.976	1	0.526	0.498	0.555	CLONAL	1	TRUE	1	0.756005311242309	3		318	1219	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285806	198285806	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002637-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	338	333	0	ENST00000335508.6:c.247G>T	p.Gly83Ter	p.G83*	ENST00000335508	NM_012433.2	83	Gga/Tga	3/25	0.756005311242309	3	FACETS	1	0.966	1	0.514	0.486	0.543	CLONAL	1	TRUE	1	0.756005311242309	3		333	1198	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426646	212426646	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002637-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	276	387	0	ENST00000342788.4:c.2469G>T	p.Trp823Cys	p.W823C	ENST00000342788	NM_005235.2	823	tgG/tgT	20/28	0.756005311242309	3	FACETS	0.99	0.931	1	0.495	0.465	0.526	CLONAL	1	TRUE	1	0.756005311242309	3		387	1016	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589871	212589871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1451769238	NA	P-0002637-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	288	353	0	ENST00000342788.4:c.671C>T	p.Pro224Leu	p.P224L	ENST00000342788	NM_005235.2	224	cCt/cTt	6/28	0.756005311242309	3	FACETS	1	0.952	1	0.507	0.477	0.537	CLONAL	1	TRUE	1	0.756005311242309	3		353	1036	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242765	66242765	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002637-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	492	298	0	ENST00000273854.3:c.1807T>C	p.Cys603Arg	p.C603R	ENST00000273854	NM_004439.5	603	Tgt/Cgt	9/18	0.756005311242309	3	FACETS	0.985	0.949	1	0.985	0.949	1	CLONAL	2	TRUE	1	0.756005311242309	3		298	910	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094800	143094800	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002637-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	522	329	1	ENST00000262992.4:c.1344G>T	p.Lys448Asn	p.K448N	ENST00000262992	NM_001101669.1	448	aaG/aaT	14/24	0.538895872068893	4	FACETS	0.941	0.904	0.979	0.941	0.904	0.979	CLONAL	2	TRUE	2	0.756005311242309	4		330	1288	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845452	128845452	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002637-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	535	298	0	ENST00000249373.3:c.749C>A	p.Ala250Asp	p.A250D	ENST00000249373	NM_005631.4	250	gCc/gAc	4/12	0.752850693868267	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.756005311242309	4		298	1170	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492920	8492920	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0002637-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	536	329	1	ENST00000356435.5:c.2409C>G	p.Tyr803Ter	p.Y803*	ENST00000356435		803	taC/taG	16/35	0.756005311242309	2	FACETS	0.999	0.973	1	0.999	0.973	1	CLONAL	2	TRUE	0	0.756005311242309	2		330	710	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840576	36840576	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002637-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	479	320	0	ENST00000358127.4:c.1157C>A	p.Thr386Asn	p.T386N	ENST00000358127	NM_001280556.1	386	aCt/aAt	10/10	0.756005311242309	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.756005311242309	2		320	607	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402781	139402781	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002637-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	227	258	0	ENST00000277541.6:c.3228G>T	p.Gln1076His	p.Q1076H	ENST00000277541	NM_017617.3	1076	caG/caT	20/34	0.732446525052915	3	FACETS	1	0.959	1	0.518	0.484	0.553	CLONAL	1	TRUE	1	0.756005311242309	3		258	799	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333563	70333563	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002637-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	290	399	0	ENST00000373644.4:c.1468C>A	p.Pro490Thr	p.P490T	ENST00000373644	NM_030625.2	490	Cca/Aca	2/12	0.233175298024144	2	FACETS	0.995	0.941	1	0.498	0.47	0.525	INDETERMINATE	1	TRUE	0	0.756005311242309	2		399	771	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524709	103524709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002637-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	792	376	0	ENST00000355739.4:c.2840C>T	p.Ser947Phe	p.S947F	ENST00000355739	NM_000123.3	947	tCc/tTc	13/15	0.756005311242309	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.756005311242309	2		376	985	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602584	10602584	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002637-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	558	316	0	ENST00000171111.5:c.994G>A	p.Gly332Ser	p.G332S	ENST00000171111	NM_203500.1	332	Ggc/Agc	3/6	0.756005311242309	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.756005311242309	2		316	698	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101119	41101119	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002637-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	380	245	0	ENST00000373198.4:c.1237G>T	p.Ala413Ser	p.A413S	ENST00000373198	NM_133170.3	413	Gcg/Tcg	8/32	0.572557774976066	4	FACETS	0.944	0.9	0.989	0.944	0.9	0.989	CLONAL	2	TRUE	2	0.756005311242309	4		245	935	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955453	48955453	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002637-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	847	388	0	ENST00000267163.4:c.1572del	p.Ala525ProfsTer7	p.A525Pfs*7	ENST00000267163	NM_000321.2	523	ttA/tt	17/27	0.756005311242309	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.756005311242309	2		388	1095	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0002648-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	157	378	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.99	0.911	1	0.99	0.911	1	CLONAL	1	TRUE	1	0.522549058084333	2		378	607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691003	NA	P-0002648-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	190	467	0	ENST00000269305.4:c.96+1G>T		p.X32_splice	ENST00000269305	NM_001126112.2	32			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.522549058084333	2		467	649	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577146	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0002648-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	225	545	1	ENST00000269305.4:c.792_794del	p.Leu265del	p.L265del	ENST00000269305	NM_001126112.2	264	ctACTg/ctg	8/11	1	2	FACETS	0.943	0.879	1	0.943	0.879	1	CLONAL	1	TRUE	1	0.522549058084333	2		546	913	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0002650-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	50	375	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		375	724	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987033	36987033	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002650-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	19	163	0	ENST00000354822.5:c.656del	p.Pro219ArgfsTer9	p.P219Rfs*9	ENST00000354822	NM_001079668.2	219	cCg/cg	3/3	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		163	282	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0002657-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	160	284	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.19887298289379	3	FACETS	0.981	0.915	1	0.654	0.61	0.699	INDETERMINATE	2	TRUE	0	0.648409041423712	3		284	333	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922321	178922321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002657-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	44	295	0	ENST00000263967.3:c.1090G>A	p.Gly364Arg	p.G364R	ENST00000263967	NM_006218.2	364	Gga/Aga	6/21	0.19887298289379	3	FACETS	0.337	0.282	0.398	0.112	0.094	0.133	INDETERMINATE	1	TRUE	0	0.648409041423712	3		295	533	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857446	68857446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002657-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	285	302	0	ENST00000261769.5:c.2081del	p.Val694AlafsTer28	p.V694Afs*28	ENST00000261769	NM_004360.3	694	gTc/gc	13/16	NA	2	FACETS	1	0.967	1			1	INDETERMINATE	2	TRUE	NA	0.648409041423712	2		302	435	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0002667-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	260	585	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.733667392545257	2		585	644	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002667-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	207	376	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.987	0.922	1	0.987	0.922	1	CLONAL	1	TRUE	1	0.733667392545257	2		376	572	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119634913	119634913	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002667-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	272	330	0	ENST00000316626.5:c.586T>G	p.Leu196Val	p.L196V	ENST00000316626		196	Tta/Gta	5/12	1	2	FACETS	0.969	0.914	1	0.969	0.914	1	CLONAL	1	TRUE	1	0.733667392545257	2		330	765	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916933	178916933	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002667-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	192	294	0	ENST00000263967.3:c.320A>T	p.Asn107Ile	p.N107I	ENST00000263967	NM_006218.2	107	aAc/aTc	2/21	1	2	FACETS	0.928	0.864	0.993	0.928	0.864	0.993	CLONAL	1	TRUE	1	0.733667392545257	2		294	564	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060784	38060784	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002667-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	340	540	0	ENST00000250448.2:c.1205T>A	p.Ile402Asn	p.I402N	ENST00000250448	NM_004496.3	402	aTc/aAc	2/2	1	2	FACETS	0.984	0.934	1	0.984	0.934	1	CLONAL	1	TRUE	1	0.733667392545257	2		540	942	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061261	38061264	+	missense_variant	Missense_Mutation	ONP	TAGG	TAGG	GAGC	novel	NA	P-0002667-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	226	382	0	ENST00000250448.2:c.725_728delinsGCTC	p.Ser242_Tyr243delinsCysSer	p.S242_Y243delinsCS	ENST00000250448	NM_004496.3	242	tCCTAc/tGCTCc	2/2	1	2	FACETS	0.889	0.832	0.947	0.889	0.832	0.947	CLONAL	1	TRUE	1	0.733667392545257	2		382	693	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591865	48591865	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0002667-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	273	419	0	ENST00000342988.3:c.1028C>G	p.Ser343Ter	p.S343*	ENST00000342988	NM_005359.5	343	tCa/tGa	9/12	0.733667392545257	1	FACETS	0.97	0.923	1	0.97	0.923	1	CLONAL	1	TRUE	0	0.733667392545257	1		419	486	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602806	10602806	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002677-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	57	299	0	ENST00000171111.5:c.772G>T	p.Glu258Ter	p.E258*	ENST00000171111	NM_203500.1	258	Gaa/Taa	3/6	0.733179845367365	1	FACETS	0.92	0.822	1	0.92	0.822	1	CLONAL	1	TRUE	0	0.733179845367365	1		299	107	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983122	149983122	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0002677-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	51	333	0	ENST00000253339.5:c.3136A>T	p.Lys1046Ter	p.K1046*	ENST00000253339		1046	Aaa/Taa	7/7	0.72368269416967	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.733179845367365	1		333	82	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518189	8518189	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002677-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	52	315	0	ENST00000356435.5:c.1202G>T	p.Arg401Leu	p.R401L	ENST00000356435		401	cGg/cTg	10/35	0.733179845367365	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.733179845367365	1		315	83	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123734	11123734	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002677-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	55	320	0	ENST00000358026.2:c.2384A>G	p.Tyr795Cys	p.Y795C	ENST00000358026	NM_001128849.1	795	tAc/tGc	16/36	0.733179845367365	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.733179845367365	1		320	90	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207065	1207065	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002677-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	52	303	0	ENST00000326873.7:c.157del	p.Asp53ThrfsTer11	p.D53Tfs*11	ENST00000326873	NM_000455.4	51	atG/at	1/10	0.733179845367365	1	FACETS	0.872	0.772	0.973	0.872	0.772	0.973	CLONAL	1	TRUE	0	0.733179845367365	1		303	103	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129380	30129380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002694-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	44	588	0	ENST00000263025.4:c.648G>A	p.Met216Ile	p.M216I	ENST00000263025	NM_002746.2	216	atG/atA	4/9	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		588	829	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032583	12032583	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	184	484	0	ENST00000353533.5:c.1019T>C	p.Phe340Ser	p.F340S	ENST00000353533	NM_003010.3	340	tTc/tCc	9/11	0.590419704607271	1	FACETS	0.974	0.909	1	0.974	0.909	1	CLONAL	1	TRUE	0	0.590419704607271	1		484	451	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0002718-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	101	338	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.237111961445181	3	FACETS	0.931	0.831	1	0.466	0.415	0.52	CLONAL	1	TRUE	1	0.237111961445181	3		339	1023	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409068	4409068	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002718-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	59	554	0	ENST00000261254.3:c.763C>T	p.Leu255Phe	p.L255F	ENST00000261254	NM_001759.3	255	Ctc/Ttc	5/5	0.169768368158042	4	FACETS	0.729	0.625	0.842			1	SUBCLONAL	1	TRUE	NA	0.237111961445181	4		554	845	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584787	48584787	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002718-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	150	610	0	ENST00000342988.3:c.865C>T	p.Gln289Ter	p.Q289*	ENST00000342988	NM_005359.5	289	Cag/Tag	7/12	0.217767216894439	2	FACETS	0.876	0.802	0.953	0.876	0.802	0.953	CLONAL	2	TRUE	0	0.237111961445181	2		610	722	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220715	1220715	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002718-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	63	487	0	ENST00000326873.7:c.733C>A	p.Leu245Ile	p.L245I	ENST00000326873	NM_000455.4	245	Ctc/Atc	5/10	0.237111961445181	3	FACETS	0.75	0.648	0.862	0.25	0.216	0.288	SUBCLONAL	1	TRUE	0	0.237111961445181	3		487	792	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868129	45868130	+	missense_variant	Missense_Mutation	DNP	CT	CT	AC	novel	NA	P-0002718-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	63	576	0	ENST00000391945.4:c.560_561delinsGT	p.Gln187Arg	p.Q187R	ENST00000391945	NM_000400.3	187	cAG/cGT	7/23	1	2	FACETS	0.709	0.612	0.814	0.709	0.612	0.814	SUBCLONAL	1	TRUE	1	0.237111961445181	2		576	750	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0002738-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	158	352	0	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	0.81958876612844	2	FACETS	0.958	0.915	0.997	0.958	0.915	0.997	CLONAL	2	TRUE	0	0.833287655372318	2		352	198	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0002738-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	134	324	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.833287655372318	6	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	TRUE	3	0.833287655372318	6		324	262	SUCCESS
APC	324	MSKCC	GRCh37	5	112176425	112176425	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002738-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	86	302	0	ENST00000257430.4:c.5134G>C	p.Glu1712Gln	p.E1712Q	ENST00000257430	NM_000038.5	1712	Gaa/Caa	16/16	0.829766545669824	3	FACETS	0.968	0.866	1	0.484	0.433	0.538	CLONAL	1	TRUE	1	0.833287655372318	3		302	302	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717661	89717661	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0002738-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	79	334	0	ENST00000371953.3:c.686C>G	p.Ser229Ter	p.S229*	ENST00000371953	NM_000314.4	229	tCa/tGa	7/9	0.649668590921885	1	FACETS	0.996	0.923	1	0.996	0.923	1	CLONAL	1	TRUE	0	0.833287655372318	1		334	111	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154887	2154887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1212009594	NA	P-0002738-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	46	256	0	ENST00000434045.2:c.334G>A	p.Ala112Thr	p.A112T	ENST00000434045	NM_001127598.1	112	Gca/Aca	4/5	0.171859133091117	2	FACETS	0.772	0.664	0.885	0.386	0.332	0.443	INDETERMINATE	1	TRUE	0	0.833287655372318	2		256	143	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684320	29684320	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002738-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	201	382	0	ENST00000356175.3:c.7840G>C	p.Asp2614His	p.D2614H	ENST00000356175	NM_000267.3	2614	Gat/Cat	53/57	0.833287655372318	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.833287655372318	4		382	402	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435112	18435125	+	frameshift_variant	Frame_Shift_Del	DEL	TCTAGCCAAGTCAG	TCTAGCCAAGTCAG	-	novel	NA	P-0002738-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	82	402	0	ENST00000266497.5:c.100_113del	p.Ser34GlyfsTer3	p.S34Gfs*3	ENST00000266497		33	TCTAGCCAAGTCAGt/t	1/31	0.833287655372318	3	FACETS	0.948	0.846	1	0.474	0.423	0.528	CLONAL	1	TRUE	1	0.833287655372318	3		402	294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0002755-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	544	210	0	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	0.720705037473953	2	FACETS	0.904	0.876	0.931	0.904	0.876	0.931	CLONAL	2	TRUE	0	0.720705037473953	2		210	835	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945140	44945141	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0002755-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	251	418	0	ENST00000377967.4:c.3464_3465insG	p.Asn1156Ter	p.N1156*	ENST00000377967	NM_021140.2	1155	gtt/gtGt	24/29	0.14487944657621	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.720705037473953	0		418	653	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0002761-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	108	69	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.555694344873087	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.555694344873087	1		69	268	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998985	11998985	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002761-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	97	113	0	ENST00000353533.5:c.487C>T	p.Gln163Ter	p.Q163*	ENST00000353533	NM_003010.3	163	Cag/Tag	4/11	0.555694344873087	1	FACETS	0.57	0.511	0.633	0.57	0.511	0.633	SUBCLONAL	1	TRUE	0	0.555694344873087	1		113	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579319	7579319	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002761-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	173	66	0	ENST00000269305.4:c.368del	p.Thr123IlefsTer47	p.T123Ifs*47	ENST00000269305	NM_001126112.2	123	aCt/at	4/11	0.555694344873087	1	FACETS	0.98	0.911	1	0.98	0.911	1	CLONAL	1	TRUE	0	0.555694344873087	1		66	459	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0002768-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	126	352	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	1	2	FACETS	0.553	0.502	0.606	0.553	0.502	0.606	SUBCLONAL	1	TRUE	1	0.782742713725301	2		352	582	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374244	138374244	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002768-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	133	367	0	ENST00000289153.2:c.3200A>T	p.Asp1067Val	p.D1067V	ENST00000289153	NM_006219.2	1067	gAc/gTc	22/22	1	2	FACETS	0.54	0.492	0.591	0.54	0.492	0.591	SUBCLONAL	1	TRUE	1	0.782742713725301	2		367	629	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0002768-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	125	339	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	1	2	FACETS	0.63	0.573	0.689	0.63	0.573	0.689	SUBCLONAL	1	TRUE	1	0.782742713725301	2		339	507	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231127	46231131	+	frameshift_variant	Frame_Shift_Del	DEL	CAAAA	CAAAA	-	novel	NA	P-0002768-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	156	373	0	ENST00000334344.6:c.1048_1052del	p.Lys350TyrfsTer17	p.K350Yfs*17	ENST00000334344	NM_152641.2	349	ttCAAAAct/ttct	9/21	1	2	FACETS	0.572	0.525	0.621	0.572	0.525	0.621	SUBCLONAL	1	TRUE	1	0.782742713725301	2		373	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576870	7576870	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs876659384	NA	P-0002771-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	643	399	0	ENST00000269305.4:c.976G>T	p.Glu326Ter	p.E326*	ENST00000269305	NM_001126112.2	326	Gaa/Taa	9/11	0.556482060721072	4	FACETS	0.905	0.886	0.924			1	CLONAL	5	TRUE	NA	0.549804334127241	4		399	801	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627182	37627182	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0002771-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	275	365	0	ENST00000447079.4:c.1097C>G	p.Ser366Ter	p.S366*	ENST00000447079	NM_015083.1	366	tCa/tGa	2/14	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	2	TRUE	NA	0.549804334127241	2		365	469	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945121	44945121	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002771-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	160	400	0	ENST00000377967.4:c.3445A>C	p.Asn1149His	p.N1149H	ENST00000377967	NM_021140.2	1149	Aat/Cat	24/29	0.178849686259669	6	FACETS	1	0.944	1			1	INDETERMINATE	2	TRUE	NA	0.549804334127241	6		400	593	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226186	53226186	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002771-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	51	441	1	ENST00000375401.3:c.2663G>C	p.Arg888Pro	p.R888P	ENST00000375401	NM_004187.3	888	cGt/cCt	19/26	0.556482060721072	1	FACETS	0.513	0.44	0.593	0.513	0.44	0.593	SUBCLONAL	1	TRUE	0	0.549804334127241	1		442	262	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0002781-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	176	240	0	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	0.856520202865849	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.920050928200991	1		240	199	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859999	151860032	+	frameshift_variant	Frame_Shift_Del	DEL	GTGTAAAAGAAGGCCTCACTGGGGACTGCTGGAA	GTGTAAAAGAAGGCCTCACTGGGGACTGCTGGAA	-	novel	NA	P-0002781-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	436	240	0	ENST00000262189.6:c.10630_10663del	p.Phe3544LeufsTer9	p.F3544Lfs*9	ENST00000262189	NM_170606.2	3544	TTCCAGCAGTCCCCAGTGAGGCCTTCTTTTACACct/ct	43/59	0.916463712404574	3	FACETS	0.971	0.954	0.986	0.971	0.954	0.986	CLONAL	3	TRUE	0	0.920050928200991	3		240	475	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0002788-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	421	510	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.652669869266733	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.652669869266733	3		510	844	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0002788-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	247	324	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.652669869266733	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.652669869266733	3		324	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0002788-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	438	575	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.652669869266733	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.652669869266733	2		576	617	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0002788-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	203	278	3	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.941	0.877	1	0.941	0.877	1	CLONAL	1	TRUE	1	0.652669869266733	2		281	661	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0002788-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	188	420	2	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.616278307526988	1	FACETS	0.963	0.902	1	0.963	0.902	1	CLONAL	1	TRUE	0	0.652669869266733	1		422	403	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0002788-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	161	467	1	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	0.652669869266733	3	FACETS	1	0.965	1	0.542	0.499	0.586	CLONAL	1	TRUE	1	0.652669869266733	3		468	604	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0002788-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	414	406	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.652669869266733	2	FACETS	0.997	0.962	1	0.997	0.962	1	CLONAL	2	TRUE	0	0.652669869266733	2		406	636	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0002788-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	150	285	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.946	0.871	1	0.946	0.871	1	CLONAL	1	TRUE	1	0.652669869266733	2		285	486	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244136	153244136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002788-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	525	483	0	ENST00000281708.4:c.2021G>A	p.Arg674Gln	p.R674Q	ENST00000281708	NM_033632.3	674	cGg/cAg	12/12	0.652669869266733	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.652669869266733	2		483	779	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042184	6042184	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002788-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	178	365	0	ENST00000265849.7:c.437A>G	p.Lys146Arg	p.K146R	ENST00000265849	NM_000535.5	146	aAa/aGa	5/15	1	2	FACETS	0.954	0.884	1	0.954	0.884	1	CLONAL	1	TRUE	1	0.652669869266733	2		365	572	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94201032	94201032	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs570102851	NA	P-0002788-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	285	418	0	ENST00000323929.3:c.1045C>T	p.Arg349Trp	p.R349W	ENST00000323929	NM_005591.3	349	Cgg/Tgg	10/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.652669869266733	2		418	762	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434452	121434452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002788-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	141	425	0	ENST00000257555.6:c.1216G>A	p.Ala406Thr	p.A406T	ENST00000257555		406	Gcc/Acc	6/10	0.194941183167013	3	FACETS	0.904	0.826	0.985	0.301	0.275	0.329	INDETERMINATE	1	TRUE	0	0.652669869266733	3		425	634	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135046	11135046	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002788-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	191	258	0	ENST00000358026.2:c.3013C>T	p.Arg1005Ter	p.R1005*	ENST00000358026	NM_001128849.1	1005	Cga/Tga	21/36	0.652669869266733	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.652669869266733	1		258	309	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750762	128750764	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	rs1274246760	NA	P-0002788-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	356	376	0	ENST00000377970.2:c.301_303del	p.Asn101del	p.N101del	ENST00000377970	NM_002467.4	100	gACAac/gac	2/3	0.652669869266733	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.652669869266733	3		376	722	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0002791-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	145	595	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	0.432627494223421	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.432627494223421	1		595	505	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162134	47162134	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002791-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	317	264	0	ENST00000409792.3:c.3992T>C	p.Leu1331Pro	p.L1331P	ENST00000409792	NM_014159.6	1331	cTa/cCa	3/21	0.11476123106666	6	FACETS	1	0.99	1			1	INDETERMINATE	3	TRUE	NA	0.432627494223421	6		264	785	SUCCESS
APC	324	MSKCC	GRCh37	5	112175360	112175360	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002791-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	228	255	0	ENST00000257430.4:c.4069G>T	p.Gly1357Ter	p.G1357*	ENST00000257430	NM_000038.5	1357	Gga/Tga	16/16	0.432627494223421	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.432627494223421	2		255	501	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0002798-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	238	316	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	0.966	0.907	1	0.966	0.907	1	CLONAL	1	TRUE	1	0.748012745706722	2		316	659	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437677	52437678	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002798-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	469	252	0	ENST00000460680.1:c.1483dup	p.Thr495AsnfsTer4	p.T495Nfs*4	ENST00000460680	NM_004656.3	495	acg/aAcg	13/17	0.748012745706722	2	FACETS	0.956	0.927	0.984	0.956	0.927	0.984	CLONAL	2	TRUE	0	0.748012745706722	2		252	656	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0002802-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	142	759	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.28878268970994	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.324620276546985	2		759	384	SUCCESS
AR	367	MSKCC	GRCh37	X	66937416	66937416	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs141425171	NA	P-0002802-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	132	703	0	ENST00000374690.3:c.2270A>G	p.Asn757Ser	p.N757S	ENST00000374690	NM_000044.3	757	aAt/aGt	5/8	0.324620276546985	1	FACETS	0.807	0.739	0.877	1	0.989	1	CLONAL	2	TRUE	0	0.324620276546985	1		703	422	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510572	38510572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786205678	NA	P-0002812-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	62	330	0	ENST00000254066.5:c.826C>T	p.Arg276Trp	p.R276W	ENST00000254066	NM_000964.3	276	Cgg/Tgg	7/9	0.268386993615184	6	FACETS	1	0.957	1	0.427	0.369	0.49	CLONAL	1	TRUE	3	0.268386993615184	6		330	554	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202816	133202816	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs5745066	NA	P-0002812-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	59	326	0	ENST00000320574.5:c.6418G>A	p.Glu2140Lys	p.E2140K	ENST00000320574	NM_006231.2	2140	Gag/Aag	46/49	0.268386993615184	5	FACETS	0.886	0.766	1	0.591	0.511	0.677	CLONAL	2	TRUE	2	0.268386993615184	5		326	348	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938279	76938280	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0002812-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	60	485	0	ENST00000373344.5:c.2468_2469del	p.Lys823ArgfsTer7	p.K823Rfs*7	ENST00000373344	NM_000489.3	823	aAA/a	9/35	0.268386993615184	1	FACETS	1	0.929	1	1	0.985	1	CLONAL	3	TRUE	0	0.268386993615184	1		485	122	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0002812-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	143	366	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.268386993615184	3	FACETS	0.959	0.896	1	1	0.991	1	CLONAL	5	TRUE	0	0.268386993615184	3		366	252	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812522	43812522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002812-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	57	336	0	ENST00000372470.3:c.1225G>A	p.Glu409Lys	p.E409K	ENST00000372470	NM_005373.2	409	Gag/Aag	8/12	0.268386993615184	5	FACETS	0.934	0.806	1			1	CLONAL	2	TRUE	NA	0.268386993615184	5		336	319	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713244	30713244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780542125	NA	P-0002812-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	60	218	0	ENST00000295754.5:c.569G>A	p.Arg190His	p.R190H	ENST00000295754	NM_003242.5	190	cGc/cAc	4/7	0.268386993615184	5	FACETS	0.93	0.806	1	0.62	0.537	0.709	CLONAL	2	TRUE	2	0.268386993615184	5		218	337	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638456	176638456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750354456	NA	P-0002812-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	97	349	0	ENST00000439151.2:c.3056G>A	p.Arg1019His	p.R1019H	ENST00000439151	NM_022455.4	1019	cGc/cAc	5/23	0.268386993615184	2	FACETS	0.946	0.866	1	1	0.989	1	CLONAL	4	TRUE	0	0.268386993615184	2		349	191	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042235	6042235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752284380	NA	P-0002812-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	29	278	0	ENST00000265849.7:c.386C>T	p.Ala129Val	p.A129V	ENST00000265849	NM_000535.5	129	gCg/gTg	5/15	0.268256985265542	3	FACETS	1	0.846	1	0.352	0.284	0.429	CLONAL	1	TRUE	0	0.268386993615184	3		278	232	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467654	50467654	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002812-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	110	280	0	ENST00000331340.3:c.889G>A	p.Ala297Thr	p.A297T	ENST00000331340	NM_006060.4	297	Gcc/Acc	8/8	0.268386993615184	7	FACETS	0.965	0.876	1	0.965	0.876	1	CLONAL	4	TRUE	3	0.268386993615184	7		280	355	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521538	8521538	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002812-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	30	261	0	ENST00000356435.5:c.700G>C	p.Val234Leu	p.V234L	ENST00000356435		234	Gtc/Ctc	9/35	0.247575060926851	4	FACETS	1	0.854	1	0.7	0.573	0.839	CLONAL	2	TRUE	1	0.268386993615184	4		261	135	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154388	2154388	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002812-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	71	345	0	ENST00000434045.2:c.540G>C	p.Gln180His	p.Q180H	ENST00000434045	NM_001127598.1	180	caG/caC	5/5	0.0170943323449375	3	FACETS	0.985	0.876	1			1	INDETERMINATE	3	TRUE	NA	0.268386993615184	3		345	203	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343697	118343697	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002812-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	35	300	0	ENST00000534358.1:c.1823G>A	p.Arg608Gln	p.R608Q	ENST00000534358	NM_005933.3	608	cGa/cAa	3/36	0.268386993615184	1	FACETS	0.99	0.831	1	1	0.967	1	CLONAL	2	TRUE	0	0.268386993615184	1		300	114	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245103	46245103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1004162984	NA	P-0002812-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	95	327	0	ENST00000334344.6:c.3197C>T	p.Pro1066Leu	p.P1066L	ENST00000334344	NM_152641.2	1066	cCg/cTg	15/21	0.268386993615184	7	FACETS	0.96	0.865	1	0.96	0.865	1	CLONAL	4	TRUE	3	0.268386993615184	7		327	308	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877366	28877366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1392528455	NA	P-0002812-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	39	293	0	ENST00000282397.4:c.3955G>A	p.Ala1319Thr	p.A1319T	ENST00000282397	NM_002019.4	1319	Gcg/Acg	30/30	0.268386993615184	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.268386993615184	1		293	200	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273539	5273539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002812-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	140	369	0	ENST00000357368.4:c.293C>T	p.Thr98Ile	p.T98I	ENST00000357368	NM_002850.3	98	aCa/aTa	4/38	0.268386993615184	4	FACETS	1	0.946	1	1	0.946	1	CLONAL	4	TRUE	0	0.268386993615184	4		369	322	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69788830	69788831	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0002812-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	29	237	0	ENST00000352241.4:c.84_85del	p.Gln30ThrfsTer36	p.Q30Tfs*36	ENST00000352241	NM_198159.2	28	AAa/a	1/10	0.268386993615184	5	FACETS	0.924	0.75	1	0.616	0.5	0.745	CLONAL	2	TRUE	2	0.268386993615184	5		237	164	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910661	32910662	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs276174819	NA	P-0002812-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	23	273	0	ENST00000380152.3:c.2175dup	p.Val726SerfsTer25	p.V726Sfs*25	ENST00000380152		723	-/A	11/27	0.268386993615184	3	FACETS	0.759	0.6	0.938	0.759	0.6	0.938	CLONAL	2	TRUE	1	0.268386993615184	3		273	128	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878061	48878062	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1131690852	NA	P-0002812-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	35	126	0	ENST00000267163.4:c.19dup	p.Arg7ProfsTer24	p.R7Pfs*24	ENST00000267163	NM_000321.2	5	acc/aCcc	1/27	0.268386993615184	3	FACETS	1	0.873	1	1	0.873	1	CLONAL	2	TRUE	1	0.268386993615184	3		126	140	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44911001	44911004	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	novel	NA	P-0002812-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	84	471	0	ENST00000377967.4:c.703_706del	p.Glu235IlefsTer6	p.E235Ifs*6	ENST00000377967	NM_021140.2	234	acAGAG/ac	9/29	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	3	TRUE	NA	0.268386993615184	2		471	182	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577528	7577528	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs878854074	NA	P-0002819-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	144	409	0	ENST00000269305.4:c.753C>G	p.Ile251Met	p.I251M	ENST00000269305	NM_001126112.2	251	atC/atG	7/11	0.627642377101894	1	FACETS	0.615	0.564	0.667	0.615	0.564	0.667	SUBCLONAL	1	TRUE	0	0.627642377101894	1		409	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577121	+	frameshift_variant	Frame_Shift_Del	DEL	CACG	CACG	-	novel	NA	P-0002819-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	253	692	0	ENST00000269305.4:c.817_820del	p.Arg273PhefsTer71	p.R273Ffs*71	ENST00000269305	NM_001126112.2	273	CGTGtt/tt	8/11	0.627642377101894	1	FACETS	0.726	0.682	0.771	0.726	0.682	0.771	SUBCLONAL	1	TRUE	0	0.627642377101894	1		692	762	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578277	7578281	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGG	GGAGG	-	novel	NA	P-0002819-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	42	485	0	ENST00000269305.4:c.568_572del	p.Pro190SerfsTer17	p.P190Sfs*17	ENST00000269305	NM_001126112.2	190	CCTCCt/t	6/11	0.627642377101894	1	FACETS	0.15	0.124	0.178	0.15	0.124	0.178	SUBCLONAL	1	TRUE	0	0.627642377101894	1		485	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579874	7579875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1555527002	NA	P-0002819-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	37	557	0	ENST00000269305.4:c.38dup	p.Leu14SerfsTer15	p.L14Sfs*15	ENST00000269305	NM_001126112.2	13	cct/ccCt	2/11	0.627642377101894	1	FACETS	0.118	0.097	0.142	0.118	0.097	0.142	SUBCLONAL	1	TRUE	0	0.627642377101894	1		557	685	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780071	NA	P-0002823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	387	673	1	ENST00000269305.4:c.580C>T	p.Leu194Phe	p.L194F	ENST00000269305	NM_001126112.2	194	Ctt/Ttt	6/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.555366765605209	2		674	1343	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	679	249	0	ENST00000397752.3:c.3028G>A	p.Asp1010Asn	p.D1010N	ENST00000397752	NM_000245.2	1010	Gat/Aat	14/21	0.542002304429316	2	FACETS	0.948	0.918	0.978	0.948	0.918	0.978	CLONAL	2	TRUE	0	0.555366765605209	2		249	1290	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033964	49033964	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	122	675	1	ENST00000267163.4:c.2101G>T	p.Asp701Tyr	p.D701Y	ENST00000267163	NM_000321.2	701	Gac/Tac	20/27	0.555662376510704	1	FACETS	0.551	0.5	0.605	0.551	0.5	0.605	SUBCLONAL	1	TRUE	0	0.555366765605209	1		676	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577543	7577543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1019340046	NA	P-0002823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	428	678	0	ENST00000269305.4:c.738G>A	p.Met246Ile	p.M246I	ENST00000269305	NM_001126112.2	246	atG/atA	7/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.555366765605209	2		678	1499	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771344	68771344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555509646	NA	P-0002823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	175	320	1	ENST00000261769.5:c.26C>T	p.Ser9Leu	p.S9L	ENST00000261769	NM_004360.3	9	tCg/tTg	1/16	0.287996332562015	1	FACETS	0.477	0.439	0.517	0.477	0.439	0.517	INDETERMINATE	1	TRUE	0	0.555366765605209	1		321	954	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943349	17943349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759015510	NA	P-0002823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	434	729	0	ENST00000458235.1:c.2659C>T	p.Arg887Cys	p.R887C	ENST00000458235	NM_000215.3	887	Cgt/Tgt	19/24	0.180279274452015	3	FACETS	1	0.994	1	0.434	0.413	0.456	INDETERMINATE	1	TRUE	0	0.555366765605209	3		729	1532	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608277	100608277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1462	194	963	1	ENST00000308731.7:c.1813G>A	p.Glu605Lys	p.E605K	ENST00000308731	NM_000061.2	605	Gag/Aag	18/19	1	2	FACETS	0.422	0.389	0.457	0.422	0.389	0.457	SUBCLONAL	1	TRUE	1	0.555366765605209	2		964	1656	SUCCESS
EED	8726	MSKCC	GRCh37	11	85961469	85961469	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	117	348	0	ENST00000263360.6:c.246C>G	p.Phe82Leu	p.F82L	ENST00000263360	NM_003797.3	82	ttC/ttG	2/12	1	2	FACETS	0.798	0.723	0.877	0.798	0.723	0.877	SUBCLONAL	1	TRUE	1	0.555366765605209	2		348	528	SUCCESS
ATM	472	MSKCC	GRCh37	11	108168072	108168072	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	84	623	0	ENST00000278616.4:c.4968G>C	p.Lys1656Asn	p.K1656N	ENST00000278616	NM_000051.3	1656	aaG/aaC	33/63	1	2	FACETS	0.41	0.362	0.462	0.41	0.362	0.462	SUBCLONAL	1	TRUE	1	0.555366765605209	2		623	737	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428690	49428690	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1458	197	632	2	ENST00000301067.7:c.10260del	p.Ile3421LeufsTer12	p.I3421Lfs*12	ENST00000301067	NM_003482.3	3420	atC/at	35/54	0.222064274110584	4	FACETS	0.667	0.615	0.721	0.333	0.307	0.361	INDETERMINATE	1	TRUE	2	0.555366765605209	4		634	1655	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41020956	41020956	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1171	213	972	1	ENST00000267868.3:c.578G>A	p.Arg193Gln	p.R193Q	ENST00000267868	NM_002875.4	193	cGa/cAa	7/10	0.301958796907647	1	FACETS	0.4	0.371	0.431	0.4	0.371	0.431	INDETERMINATE	1	TRUE	0	0.555366765605209	1		973	1384	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042523	42042523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	142	664	2	ENST00000219905.7:c.6718G>A	p.Glu2240Lys	p.E2240K	ENST00000219905	NM_001164273.1	2240	Gaa/Aaa	17/24	0.301958796907647	1	FACETS	0.436	0.397	0.476	0.436	0.397	0.476	INDETERMINATE	1	TRUE	0	0.555366765605209	1		666	848	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029041	14029046	+	inframe_deletion	In_Frame_Del	DEL	TCCCAG	TCCCAG	-	novel	NA	P-0002823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	145	363	0	ENST00000311895.7:c.1252_1257del	p.Ser418_Gln419del	p.S418_Q419del	ENST00000311895	NM_005236.2	418	TCCCAG/-	8/11	0.287996332562015	1	FACETS	0.731	0.671	0.793	0.731	0.671	0.793	INDETERMINATE	1	TRUE	0	0.555366765605209	1		363	516	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830129	72830129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	183	683	0	ENST00000268489.5:c.6452G>A	p.Arg2151Lys	p.R2151K	ENST00000268489	NM_006885.3	2151	aGg/aAg	9/10	0.287996332562015	1	FACETS	0.414	0.381	0.448	0.414	0.381	0.448	INDETERMINATE	1	TRUE	0	0.555366765605209	1		683	1151	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753139	42753139	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1356484827	NA	P-0002823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1231	396	471	0	ENST00000222329.4:c.1125C>G	p.Phe375Leu	p.F375L	ENST00000222329	NM_006494.2	375	ttC/ttG	4/4	0.180279274452015	3	FACETS	1	0.987	1	0.373	0.354	0.393	INDETERMINATE	1	TRUE	0	0.555366765605209	3		471	1627	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794805	42794805	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	332	467	1	ENST00000575354.2:c.1885C>A	p.Gln629Lys	p.Q629K	ENST00000575354	NM_015125.3	629	Cag/Aag	10/20	0.180279274452015	3	FACETS	1	0.984	1	0.371	0.35	0.392	INDETERMINATE	1	TRUE	0	0.555366765605209	3		468	1374	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167853	56167853	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0002823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	124	564	0	ENST00000399503.3:c.1418C>G	p.Ser473Ter	p.S473*	ENST00000399503	NM_005921.1	473	tCa/tGa	7/20	0.301958796907647	1	FACETS	0.368	0.332	0.405	0.368	0.332	0.405	INDETERMINATE	1	TRUE	0	0.555366765605209	1		564	877	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672738	86672738	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0002823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	78	465	0	ENST00000274376.6:c.2225C>G	p.Ser742Ter	p.S742*	ENST00000274376	NM_002890.2	742	tCa/tGa	17/25	0.301958796907647	1	FACETS	0.384	0.338	0.434	0.384	0.338	0.434	INDETERMINATE	1	TRUE	0	0.555366765605209	1		465	528	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858188	27858188	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	776	534	0	ENST00000359303.2:c.383C>T	p.Ala128Val	p.A128V	ENST00000359303	NM_003535.2	128	gCg/gTg	1/1	0.555662376510704	4	FACETS	0.925	0.896	0.953			1	CLONAL	3	TRUE	NA	0.555366765605209	4		534	1567	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6414378	6414378	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	112	199	0	ENST00000356142.4:c.12C>G	p.Ile4Met	p.I4M	ENST00000356142	NM_018890.3	4	atC/atG	1/7	0.53048942339267	3	FACETS	0.604	0.543	0.669	0.201	0.181	0.223	SUBCLONAL	1	TRUE	0	0.555366765605209	3		199	853	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485256	8485256	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159854	NA	P-0002823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	124	680	0	ENST00000356435.5:c.3124G>A	p.Glu1042Lys	p.E1042K	ENST00000356435		1042	Gag/Aag	18/35	0.519111160950655	3	FACETS	0.475	0.429	0.525	0.238	0.214	0.263	SUBCLONAL	1	TRUE	1	0.555366765605209	3		680	1200	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0002829-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	125	585	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.269284983289302	4	FACETS	1	0.925	1	0.342	0.309	0.377	CLONAL	1	TRUE	1	0.332344627058416	4		585	976	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0002829-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	105	646	4	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.322742755642642	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.332344627058416	1		650	472	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339650	116339650	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002829-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	78	324	0	ENST00000397752.3:c.512A>G	p.Gln171Arg	p.Q171R	ENST00000397752	NM_000245.2	171	cAg/cGg	2/21	0.322742755642642	1	FACETS	0.872	0.769	0.981	0.872	0.769	0.981	CLONAL	1	TRUE	0	0.332344627058416	1		324	449	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087347	27087355	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GATCTATCT	GATCTATCT	TC	novel	NA	P-0002829-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	81	445	0	ENST00000324856.7:c.1921_1929delinsTC	p.Asp641SerfsTer4	p.D641Sfs*4	ENST00000324856	NM_006015.4	641	GATCTATCT/TC	5/20	1	2	FACETS	0.954	0.843	1	0.954	0.843	1	CLONAL	1	TRUE	1	0.332344627058416	2		445	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0002839-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	170	646	4	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.294504210499225	6	FACETS	1	0.987	1	0.342	0.314	0.37	INDETERMINATE	1	TRUE	2	0.698110908132803	6		650	854	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572117	64572117	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002839-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	218	238	0	ENST00000312049.6:c.1522C>T	p.Gln508Ter	p.Q508*	ENST00000312049	NM_130799.2	508	Cag/Tag	10/10	0.698110908132803	2	FACETS	0.979	0.934	1	0.979	0.934	1	CLONAL	2	TRUE	0	0.698110908132803	2		238	319	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920263	76920263	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002839-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	393	424	0	ENST00000373344.5:c.3814G>C	p.Ala1272Pro	p.A1272P	ENST00000373344	NM_000489.3	1272	Gcc/Ccc	11/35	0.698110908132803	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.698110908132803	2		424	544	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0002846-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	49	381	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		382	997	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61725999	61725999	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0002849-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	72	474	0	ENST00000401558.2:c.639+1G>C		p.X213_splice	ENST00000401558	NM_003400.3	213			0.300603796051719	3	FACETS	0.968	0.847	1	0.484	0.423	0.549	CLONAL	1	TRUE	1	0.34	3		474	512	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725099	89725099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002849-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	24	142	0	ENST00000371953.3:c.1082G>A	p.Ser361Asn	p.S361N	ENST00000371953	NM_000314.4	361	aGt/aAt	9/9	0.143400157789566	1	FACETS	0.837	0.664	1	0.837	0.664	1	INDETERMINATE	1	TRUE	0	0.34	1		142	140	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312689	91312689	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs765143263	NA	P-0002849-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	60	460	0	ENST00000355112.3:c.2428G>C	p.Asp810His	p.D810H	ENST00000355112	NM_000057.2	810	Gat/Cat	12/22	0.13604914287811	4	FACETS	0.904	0.78	1	0.452	0.39	0.52	INDETERMINATE	1	TRUE	2	0.34	4		460	523	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0002852-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	176	510	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	0.993	1	CLONAL	2	TRUE	1	0.200707980549437	2		510	788	SUCCESS
APC	324	MSKCC	GRCh37	5	112175417	112175418	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	rs1554085533	NA	P-0002852-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	59	336	0	ENST00000257430.4:c.4127_4128del	p.Tyr1376CysfsTer9	p.Y1376Cfs*9	ENST00000257430	NM_000038.5	1376	TAt/t	16/16	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.200707980549437	2		336	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0002852-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	72	441	0	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	0.200707980549437	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.200707980549437	1		441	578	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0002852-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	81	354	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.200707980549437	2		355	681	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247367	153247367	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002852-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	9	288	1	ENST00000281708.4:c.1435C>T	p.Arg479Ter	p.R479*	ENST00000281708	NM_033632.3	479	Cga/Tga	10/12	0.164920904772674	1	FACETS	0.194	0.128	0.28	0.194	0.128	0.28	SUBCLONAL	1	TRUE	0	0.200707980549437	1		289	415	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002852-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	80	441	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	0.164920904772674	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.200707980549437	1		441	609	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732969	30732969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893810	NA	P-0002852-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	63	338	2	ENST00000295754.5:c.1582C>T	p.Arg528Cys	p.R528C	ENST00000295754	NM_003242.5	528	Cgt/Tgt	7/7	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.200707980549437	2		340	624	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7174662	7174662	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1246004221	NA	P-0002852-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	60	502	0	ENST00000302850.5:c.1055C>T	p.Thr352Met	p.T352M	ENST00000302850	NM_000208.2	352	aCg/aTg	4/22	1	2	FACETS	0.949	0.817	1	0.949	0.817	1	CLONAL	1	TRUE	1	0.200707980549437	2		502	630	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891541	76891541	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002852-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	76	450	0	ENST00000373344.5:c.4564G>T	p.Glu1522Ter	p.E1522*	ENST00000373344	NM_000489.3	1522	Gaa/Taa	16/35	0.200707980549437	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.200707980549437	1		450	580	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0002872-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	335	407	0	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.2643184777416	5	FACETS	0.96	0.917	1	0.96	0.917	1	CLONAL	5	TRUE	0	0.318048481039327	5		407	648	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059260	27059260	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002872-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	140	390	0	ENST00000324856.7:c.1897C>T	p.Gln633Ter	p.Q633*	ENST00000324856	NM_006015.4	633	Cag/Tag	4/20	0.318048481039327	3	FACETS	0.97	0.888	1	0.97	0.888	1	CLONAL	2	TRUE	1	0.318048481039327	3		390	526	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628184	187628184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61733570	NA	P-0002872-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	81	356	0	ENST00000441802.2:c.2798G>A	p.Arg933His	p.R933H	ENST00000441802	NM_005245.3	933	cGt/cAt	2/27	0.121810111991009	1	FACETS	0.727	0.641	0.819	0.727	0.641	0.819	INDETERMINATE	1	TRUE	0	0.318048481039327	1		356	589	SUCCESS
APC	324	MSKCC	GRCh37	5	112175084	112175084	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002872-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	112	223	0	ENST00000257430.4:c.3793G>T	p.Glu1265Ter	p.E1265*	ENST00000257430	NM_000038.5	1265	Gaa/Taa	16/16	0.318048481039327	2	FACETS	0.973	0.884	1	0.973	0.884	1	CLONAL	2	TRUE	0	0.318048481039327	2		223	362	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152009008	152009008	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1343528180	NA	P-0002872-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	62	289	0	ENST00000262189.6:c.614T>C	p.Ile205Thr	p.I205T	ENST00000262189	NM_170606.2	205	aTa/aCa	5/59	0.318048481039327	3	FACETS	1	0.92	1	0.543	0.471	0.621	CLONAL	1	TRUE	1	0.318048481039327	3		289	416	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602797	10602797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002872-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	233	361	2	ENST00000171111.5:c.781C>T	p.Arg261Trp	p.R261W	ENST00000171111	NM_203500.1	261	Cgg/Tgg	3/6	0.318048481039327	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.318048481039327	2		363	679	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944349	76944349	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002872-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	66	474	0	ENST00000373344.5:c.556A>G	p.Ile186Val	p.I186V	ENST00000373344	NM_000489.3	186	Att/Gtt	7/35	0.193571523480465	2	FACETS	0.639	0.555	0.731	0.32	0.277	0.366	SUBCLONAL	1	TRUE	0	0.318048481039327	2		474	649	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0002879-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	72	500	0	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	0.200808852050305	1	FACETS	0.98	0.856	1	0.98	0.856	1	CLONAL	1	TRUE	0	0.200808852050305	1		500	658	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105709	27105709	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002879-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	42	220	0	ENST00000324856.7:c.5320G>C	p.Glu1774Gln	p.E1774Q	ENST00000324856	NM_006015.4	1774	Gaa/Caa	20/20	1	2	FACETS	0.686	0.572	0.813	0.686	0.572	0.813	SUBCLONAL	1	TRUE	1	0.200808852050305	2		220	610	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366972	40366972	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002879-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	55	239	0	ENST00000397332.2:c.225G>T	p.Trp75Cys	p.W75C	ENST00000397332	NM_001033082.2	75	tgG/tgT	2/3	1	2	FACETS	0.849	0.726	0.985	0.849	0.726	0.985	CLONAL	1	TRUE	1	0.200808852050305	2		239	645	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155278	106155278	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002879-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	76	294	0	ENST00000380013.4:c.179A>T	p.Tyr60Phe	p.Y60F	ENST00000380013	NM_001127208.2	60	tAt/tTt	3/11	0.200808852050305	1	FACETS	0.92	0.806	1	0.92	0.806	1	CLONAL	1	TRUE	0	0.200808852050305	1		294	740	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265457	152265457	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002879-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	79	213	0	ENST00000206249.3:c.910A>C	p.Asn304His	p.N304H	ENST00000206249	NM_000125.3	304	Aac/Cac	4/8	0.165404080003668	3	FACETS	1	0.91	1	0.522	0.458	0.591	CLONAL	1	TRUE	1	0.200808852050305	3		213	829	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333096	70333096	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0002879-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	73	404	0	ENST00000373644.4:c.1001C>G	p.Ser334Ter	p.S334*	ENST00000373644	NM_030625.2	334	tCa/tGa	2/12	1	2	FACETS	0.748	0.652	0.852	0.748	0.652	0.852	SUBCLONAL	1	TRUE	1	0.200808852050305	2		404	972	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030368	49030368	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0002879-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	128	248	0	ENST00000267163.4:c.1843A>T	p.Lys615Ter	p.K615*	ENST00000267163	NM_000321.2	615	Aaa/Taa	19/27	0.200808852050305	2	FACETS	0.976	0.887	1	0.976	0.887	1	CLONAL	2	TRUE	0	0.200808852050305	2		248	653	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39550367	39550367	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002879-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	54	307	0	ENST00000262039.4:c.478C>G	p.Pro160Ala	p.P160A	ENST00000262039	NM_002647.2	160	Cct/Gct	4/25	1	2	FACETS	0.745	0.635	0.866	0.745	0.635	0.866	SUBCLONAL	1	TRUE	1	0.200808852050305	2		307	722	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877381	40877381	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002879-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	75	206	0	ENST00000373198.4:c.2315G>A	p.Gly772Asp	p.G772D	ENST00000373198	NM_133170.3	772	gGc/gAc	15/32	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.200808852050305	2		206	722	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356443	70356443	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002879-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	65	326	0	ENST00000374080.3:c.5338G>T	p.Glu1780Ter	p.E1780*	ENST00000374080		1780	Gag/Tag	37/45	0.200808852050305	1	FACETS	0.572	0.494	0.657	0.572	0.494	0.657	SUBCLONAL	1	TRUE	0	0.200808852050305	1		326	1018	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0002900-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	36	585	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.51	0.419	0.612	0.51	0.419	0.612	SUBCLONAL	1	TRUE	1	0.29	2		585	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0002900-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	13	226	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	1	2	FACETS	0.16	0.113	0.217	0.16	0.113	0.217	SUBCLONAL	1	TRUE	1	0.29	2		226	562	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0002900-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	105	222	0	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.29	2		222	492	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0002917-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	70	338	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.360903862031657	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.360903862031657	1		339	264	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149324	61149324	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002917-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	28	604	2	ENST00000295025.8:c.1514G>A	p.Ser505Asn	p.S505N	ENST00000295025	NM_002908.2	505	aGc/aAc	11/11	0.273079482020232	3	FACETS	0.779	0.626	0.952	0.39	0.313	0.476	CLONAL	1	TRUE	1	0.360903862031657	3		606	235	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254540	1254540	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1429555334	NA	P-0002917-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	20	704	0	ENST00000310581.5:c.3238C>T	p.Leu1080Phe	p.L1080F	ENST00000310581	NM_198253.2	1080	Ctc/Ttc	15/16	0.360903862031657	1	FACETS	0.704	0.545	0.886	0.704	0.545	0.886	SUBCLONAL	1	TRUE	0	0.360903862031657	1		704	129	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459632	149459632	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs751557861	NA	P-0002917-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	23	741	0	ENST00000286301.3:c.575G>T	p.Arg192Leu	p.R192L	ENST00000286301	NM_005211.3	192	cGg/cTg	4/22	1	2	FACETS	0.654	0.513	0.815	0.654	0.513	0.815	SUBCLONAL	1	TRUE	1	0.360903862031657	2		741	195	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842316	151842316	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002917-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	42	698	0	ENST00000262189.6:c.14096T>C	p.Leu4699Pro	p.L4699P	ENST00000262189	NM_170606.2	4699	cTt/cCt	54/59	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.360903862031657	2		698	228	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207198	1207198	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0002917-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	47	431	0	ENST00000326873.7:c.286A>T	p.Lys96Ter	p.K96*	ENST00000326873	NM_000455.4	96	Aag/Tag	1/10	0.356885332016733	1	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	0	0.360903862031657	1		431	205	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0002920-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	467	360	0	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	0.406593179183129	3	FACETS	0.953	0.919	0.988			1	CLONAL	3	TRUE	NA	0.492000673605546	3		360	827	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007733	62007733	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002920-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	135	141	0	ENST00000392795.3:c.134C>A	p.Ser45Ter	p.S45*	ENST00000392795	NM_001039933.1	45	tCg/tAg	3/6	0.490965774893569	3	FACETS	0.977	0.9	1	0.977	0.9	1	CLONAL	2	TRUE	1	0.492000673605546	3		141	350	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432005	49432022	+	inframe_deletion	In_Frame_Del	DEL	TCTCCATTGAGCAGGTCA	TCTCCATTGAGCAGGTCA	-	novel	NA	P-0002920-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	239	470	0	ENST00000301067.7:c.9117_9134del	p.Asp3040_Asp3045del	p.D3040_D3045del	ENST00000301067	NM_003482.3	3039	gaTGACCTGCTCAATGGAGAc/gac	34/54	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.492000673605546	2		470	966	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188240	10188240	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002976-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	116	382	0	ENST00000256474.2:c.383T>A	p.Leu128His	p.L128H	ENST00000256474	NM_000551.3	128	cTt/cAt	2/3	0.320344729476282	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.443629593243162	1		382	285	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307186	65307187	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002976-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	102	378	0	ENST00000342505.4:c.2501dup	p.Arg835GlufsTer12	p.R835Efs*12	ENST00000342505	NM_002227.2	834	cag/caAg	18/25	0.379351915533145	4	FACETS	0.822	0.74	0.907	0.822	0.74	0.907	CLONAL	2	TRUE	2	0.443629593243162	4		378	404	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750684	128750684	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002978-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	369	954	0	ENST00000377970.2:c.221C>A	p.Pro74Gln	p.P74Q	ENST00000377970	NM_002467.4	74	cCg/cAg	2/3	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.548788639629464	2		954	1319	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878081	48878112	+	frameshift_variant	Frame_Shift_Del	DEL	CACCGCCGCCGCTGCCGCCGCGGAACCCCCGG	CACCGCCGCCGCTGCCGCCGCGGAACCCCCGG	-	novel	NA	P-0002978-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	180	309	0	ENST00000267163.4:c.45_76del	p.Ala17ProfsTer3	p.A17Pfs*3	ENST00000267163	NM_000321.2	11	gcCACCGCCGCCGCTGCCGCCGCGGAACCCCCGGca/gcca	1/27	0.544836364275256	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.548788639629464	1		309	459	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476265	88476265	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002978-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	355	787	0	ENST00000360948.2:c.1867G>A	p.Gly623Arg	p.G623R	ENST00000360948	NM_001012338.2	623	Gga/Aga	15/19	0.530651522854984	2	FACETS	1	0.963	1	0.51	0.483	0.538	CLONAL	1	TRUE	0	0.548788639629464	2		787	1268	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578192	7578193	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	A	novel	NA	P-0002979-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	77	438	0	ENST00000269305.4:c.656_657delinsT	p.Pro219LeufsTer28	p.P219Lfs*28	ENST00000269305	NM_001126112.2	219	cCC/cT	6/11	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.16	2		438	913	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2113016	2113020	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTC	CTGTC	-	novel	NA	P-0002979-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	131	432	0	ENST00000219476.3:c.1407_1411del	p.Ser470CysfsTer10	p.S470Cfs*10	ENST00000219476	NM_000548.3	469	CTGTCc/c	14/42	0.3	2	FACETS	1	0.951	1			1	CLONAL	2	TRUE	NA	0.16	2		432	763	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0002990-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	333	451	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.853473843590633	2		451	776	SUCCESS
AR	367	MSKCC	GRCh37	X	66943552	66943552	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137852578	NA	P-0002990-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	434	416	0	ENST00000374690.3:c.2632A>G	p.Thr878Ala	p.T878A	ENST00000374690	NM_000044.3	878	Act/Gct	8/8	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.853473843590633	1		416	544	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421807	49421808	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0002990-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	639	912	0	ENST00000301067.7:c.14499_14500del	p.Glu4834SerfsTer2	p.E4834Sfs*2	ENST00000301067	NM_003482.3	4833	ggGGaa/ggaa	46/54	1	2	FACETS	0.953	0.918	0.987	0.953	0.918	0.987	CLONAL	1	TRUE	1	0.853473843590633	2		912	1572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578410	7578410	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003007-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	222	259	2	ENST00000269305.4:c.520A>T	p.Arg174Trp	p.R174W	ENST00000269305	NM_001126112.2	174	Agg/Tgg	5/11	0.300453835320091	1	FACETS	1	0.981	1	1	0.981	1	INDETERMINATE	1	TRUE	0	0.765006460542829	1		261	339	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0003007-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	147	243	0	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	0.754362226563563	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.765006460542829	1		243	235	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743864	41743864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753706427	NA	P-0003007-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	136	455	1	ENST00000301178.4:c.799G>A	p.Asp267Asn	p.D267N	ENST00000301178	NM_021913.4	267	Gat/Aat	7/20	0.724155006007308	2	FACETS	0.745	0.682	0.811	0.373	0.341	0.406	SUBCLONAL	1	TRUE	0	0.765006460542829	2		456	477	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175916331	175916331	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003007-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	230	451	0	ENST00000367669.3:c.2178G>T	p.Lys726Asn	p.K726N	ENST00000367669	NM_022457.5	726	aaG/aaT	19/20	0.765006460542829	3	FACETS	0.891	0.831	0.952	0.445	0.415	0.476	CLONAL	1	TRUE	1	0.765006460542829	3		451	933	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968185	55968185	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003007-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	109	481	1	ENST00000263923.4:c.2145G>C	p.Leu715Phe	p.L715F	ENST00000263923	NM_002253.2	715	ttG/ttC	15/30	0.703952564648627	2	FACETS	0.491	0.442	0.543	0.246	0.221	0.272	SUBCLONAL	1	TRUE	0	0.765006460542829	2		482	580	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541076	187541076	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003007-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	273	322	0	ENST00000441802.2:c.6664G>T	p.Asp2222Tyr	p.D2222Y	ENST00000441802	NM_005245.3	2222	Gac/Tac	10/27	0.703952564648627	2	FACETS	0.944	0.907	0.979	0.944	0.907	0.979	CLONAL	2	TRUE	0	0.765006460542829	2		322	378	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433917	149433917	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1187766051	NA	P-0003007-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	478	516	2	ENST00000286301.3:c.2731C>T	p.Gln911Ter	p.Q911*	ENST00000286301	NM_005211.3	911	Cag/Tag	21/22	0.728363909697724	2	FACETS	0.976	0.949	1	0.976	0.949	1	CLONAL	2	TRUE	0	0.765006460542829	2		518	640	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696763	176696763	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003007-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	412	343	2	ENST00000439151.2:c.5464A>T	p.Ser1822Cys	p.S1822C	ENST00000439151	NM_022455.4	1822	Agc/Tgc	16/23	0.728363909697724	2	FACETS	0.985	0.955	1	0.985	0.955	1	CLONAL	2	TRUE	0	0.765006460542829	2		345	547	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864377	151864377	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003007-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	128	482	0	ENST00000262189.6:c.9604A>C	p.Ile3202Leu	p.I3202L	ENST00000262189	NM_170606.2	3202	Att/Ctt	42/59	0.259379380079213	5	FACETS	0.794	0.719	0.873	0.265	0.239	0.291	INDETERMINATE	1	TRUE	2	0.765006460542829	5		482	905	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372232	55372232	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003007-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	95	119	0	ENST00000297316.4:c.922G>C	p.Gly308Arg	p.G308R	ENST00000297316	NM_022454.3	308	Ggg/Cgg	2/2	0.542604065317583	4	FACETS	0.978	0.889	1	0.978	0.889	1	CLONAL	2	TRUE	2	0.765006460542829	4		119	224	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492943	8492943	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003007-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	97	342	0	ENST00000356435.5:c.2386T>C	p.Tyr796His	p.Y796H	ENST00000356435		796	Tac/Cac	16/35	0.754362226563563	1	FACETS	0.492	0.444	0.543	0.492	0.444	0.543	SUBCLONAL	1	TRUE	0	0.765006460542829	1		342	318	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391794	139391794	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003007-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	143	315	1	ENST00000277541.6:c.6397C>G	p.Pro2133Ala	p.P2133A	ENST00000277541	NM_017617.3	2133	Ccc/Gcc	34/34	0.484186958413573	3	FACETS	1	0.955	1	0.53	0.486	0.575	CLONAL	1	TRUE	1	0.765006460542829	3		316	488	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680718	88680718	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003007-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	143	495	0	ENST00000360948.2:c.539C>G	p.Ala180Gly	p.A180G	ENST00000360948	NM_001012338.2	180	gCc/gGc	6/19	0.527900342403348	3	FACETS	0.819	0.749	0.892	0.41	0.374	0.446	CLONAL	1	TRUE	1	0.765006460542829	3		495	631	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820986	3820986	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003007-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	151	147	0	ENST00000262367.5:c.2465G>C	p.Gly822Ala	p.G822A	ENST00000262367	NM_004380.2	822	gGa/gCa	14/31	0.527900342403348	3	FACETS	0.895	0.833	0.956	0.895	0.833	0.956	CLONAL	2	TRUE	1	0.765006460542829	3		147	305	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274114	10274114	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003007-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	193	447	0	ENST00000330684.3:c.155G>T	p.Arg52Leu	p.R52L	ENST00000330684	NM_001134407.1	52	cGa/cTa	2/13	0.527900342403348	3	FACETS	1	0.98	1	0.57	0.53	0.611	CLONAL	1	TRUE	1	0.765006460542829	3		447	612	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827990	40827990	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003007-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	257	310	1	ENST00000373198.4:c.2438C>A	p.Ala813Asp	p.A813D	ENST00000373198	NM_133170.3	813	gCc/gAc	17/32	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.765006460542829	2		311	528	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14026263	14026265	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0003007-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	254	351	1	ENST00000405192.2:c.179_181del	p.Glu60del	p.E60del	ENST00000405192	NM_001163147.1	60	gAAGct/gct	4/12	0.765006460542829	6	FACETS	0.789	0.738	0.841	0.394	0.369	0.421	SUBCLONAL	2	TRUE	2	0.765006460542829	6		352	1065	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872038	37872038	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003007-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	300	479	0	ENST00000269571.5:c.1362del	p.Leu455CysfsTer4	p.L455Cfs*4	ENST00000269571		453	ctG/ct	12/27	0.381535832472195	3	FACETS	0.81	0.769	0.852	0.81	0.769	0.852	INDETERMINATE	2	TRUE	1	0.765006460542829	3		479	669	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0003017-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	220	338	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.244802829290993	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.248428785268283	2		339	863	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730365	133730365	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003017-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	92	461	0	ENST00000318560.5:c.431G>A	p.Gly144Glu	p.G144E	ENST00000318560	NM_005157.4	144	gGg/gAg	3/11	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.248428785268283	2		461	723	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101986	11101986	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003017-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	55	346	0	ENST00000358026.2:c.1406G>T	p.Arg469Leu	p.R469L	ENST00000358026	NM_001128849.1	469	cGg/cTg	8/36	1	2	FACETS	0.837	0.716	0.969	0.837	0.716	0.969	CLONAL	1	TRUE	1	0.248428785268283	2		346	529	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954648	17954648	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003017-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	77	443	1	ENST00000458235.1:c.246C>A	p.Phe82Leu	p.F82L	ENST00000458235	NM_000215.3	82	ttC/ttA	3/24	1	2	FACETS	0.842	0.739	0.954	0.842	0.739	0.954	CLONAL	1	TRUE	1	0.248428785268283	2		444	736	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247168	153247168	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1560758208	NA	P-0003027-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	43	410	0	ENST00000281708.4:c.1634A>G	p.Tyr545Cys	p.Y545C	ENST00000281708	NM_033632.3	545	tAt/tGt	10/12	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		410	414	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0003030-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	135	573	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.198740877847596	3	FACETS	1	0.982	1	0.658	0.601	0.719	INDETERMINATE	1	TRUE	1	0.4222781706387	3		573	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0003030-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	254	369	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.241393814469195	4	FACETS	1	0.974	1			1	INDETERMINATE	3	TRUE	NA	0.4222781706387	4		369	543	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271315	1271315	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003030-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	227	257	1	ENST00000310581.5:c.2387C>A	p.Ser796Tyr	p.S796Y	ENST00000310581	NM_198253.2	796	tCc/tAc	8/16	0.414550024651542	3	FACETS	0.889	0.838	0.941	0.889	0.838	0.941	CLONAL	3	TRUE	0	0.4222781706387	3		258	488	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246473	46246473	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003030-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	30	310	0	ENST00000334344.6:c.4567G>A	p.Asp1523Asn	p.D1523N	ENST00000334344	NM_152641.2	1523	Gat/Aat	15/21	0.197121385847156	1	FACETS	0.198	0.159	0.243	0.198	0.159	0.243	INDETERMINATE	1	TRUE	0	0.4222781706387	1		310	565	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954039	32954039	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs202155613	NA	P-0003030-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	42	406	0	ENST00000380152.3:c.9106C>G	p.Gln3036Glu	p.Q3036E	ENST00000380152		3036	Caa/Gaa	23/27	0.4222781706387	3	FACETS	0.287	0.239	0.341	0.096	0.079	0.114	SUBCLONAL	1	TRUE	0	0.4222781706387	3		406	839	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144114	11144114	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003030-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	250	321	0	ENST00000358026.2:c.3695G>T	p.Gly1232Val	p.G1232V	ENST00000358026	NM_001128849.1	1232	gGc/gTc	26/36	0.384038211742144	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.4222781706387	2		321	576	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518506	204518506	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1393081884	NA	P-0003033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	176	201	0	ENST00000367182.3:c.1169A>G	p.Asn390Ser	p.N390S	ENST00000367182	NM_001278516.1	390	aAc/aGc	11/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.687379439333166	2		201	485	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402475	139402475	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	318	310	0	ENST00000277541.6:c.3442G>T	p.Glu1148Ter	p.E1148*	ENST00000277541	NM_017617.3	1148	Gag/Tag	21/34	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.687379439333166	2		310	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579381	7579381	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	199	191	0	ENST00000269305.4:c.306del	p.Tyr103ThrfsTer20	p.Y103Tfs*20	ENST00000269305	NM_001126112.2	102	acC/ac	4/11	0.687379439333166	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.687379439333166	1		191	294	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349730	15349730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750347317	NA	P-0003040-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	118	128	0	ENST00000263377.2:c.3844C>T	p.Arg1282Cys	p.R1282C	ENST00000263377	NM_058243.2	1282	Cgc/Tgc	19/20	0.592294260550087	4	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	2	0.592294260550087	4		128	304	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630172	187630172	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1372551319	NA	P-0003040-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	108	258	0	ENST00000441802.2:c.810C>A	p.Asp270Glu	p.D270E	ENST00000441802	NM_005245.3	270	gaC/gaA	2/27	0.522892179973765	4	FACETS	0.973	0.875	1			1	CLONAL	1	TRUE	NA	0.592294260550087	4		258	597	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475078	40475078	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003040-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	463	548	0	ENST00000264657.5:c.1832G>T	p.Ser611Ile	p.S611I	ENST00000264657	NM_139276.2	611	aGt/aTt	20/24	0.592294260550087	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	2	0.592294260550087	4		548	1119	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608039	28608039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762198688	NA	P-0003050-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	30	593	1	ENST00000241453.7:c.1927G>A	p.Val643Ile	p.V643I	ENST00000241453	NM_004119.2	643	Gtc/Atc	15/24	0.782502178585273	1	FACETS	0.144	0.116	0.175	0.144	0.116	0.175	SUBCLONAL	1	TRUE	0	0.782502178585273	1		594	325	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519980	NA	P-0003050-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	304	297	0	ENST00000269305.4:c.528C>G	p.Cys176Trp	p.C176W	ENST00000269305	NM_001126112.2	176	tgC/tgG	5/11	0.782502178585273	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.782502178585273	2		297	350	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003054-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	29	324	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.575708053514667	4	FACETS	0.331	0.265	0.406	0.166	0.132	0.203	SUBCLONAL	1	TRUE	2	0.594391982128741	4		324	470	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0003054-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	288	205	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.594391982128741	14	FACETS	1	0.982	1			1	CLONAL	7	TRUE	NA	0.594391982128741	14		205	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0003054-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	464	640	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.594391982128741	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.594391982128741	2		640	771	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685287	89685287	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs398123316	NA	P-0003054-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1518	164	166	0	ENST00000371953.3:c.182A>G	p.His61Arg	p.H61R	ENST00000371953	NM_000314.4	61	cAt/cGt	3/9	0.594391982128741	14	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.594391982128741	14		166	1682	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098380	11098380	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003054-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	298	556	0	ENST00000358026.2:c.898C>T	p.Gln300Ter	p.Q300*	ENST00000358026	NM_001128849.1	300	Cag/Tag	6/36	0.594391982128741	2	FACETS	1	0.986	1	0.567	0.535	0.599	CLONAL	1	TRUE	0	0.594391982128741	2		556	885	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226558219	226558219	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0003054-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	151	379	0	ENST00000366794.5:c.2071-1G>C		p.X691_splice	ENST00000366794	NM_001618.3	691			0.594391982128741	6	FACETS	0.862	0.786	0.942	0.216	0.196	0.236	CLONAL	1	TRUE	2	0.594391982128741	6		379	1290	SUCCESS
APC	324	MSKCC	GRCh37	5	112178121	112178121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003054-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	224	433	0	ENST00000257430.4:c.6830C>T	p.Ser2277Phe	p.S2277F	ENST00000257430	NM_000038.5	2277	tCt/tTt	16/16	0.370226514903131	4	FACETS	1	0.988	1	0.641	0.597	0.686	CLONAL	1	TRUE	2	0.594391982128741	4		433	937	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117632205	117632205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003054-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	226	410	1	ENST00000368508.3:c.6211G>A	p.Glu2071Lys	p.E2071K	ENST00000368508	NM_002944.2	2071	Gaa/Aaa	39/43	0.594391982128741	3	FACETS	1	0.954	1	0.343	0.32	0.368	CLONAL	1	TRUE	0	0.594391982128741	3		411	958	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14017054	14017054	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003054-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	91	249	0	ENST00000405192.2:c.233G>A	p.Ser78Asn	p.S78N	ENST00000405192	NM_001163147.1	78	aGt/aAt	5/12	0.594391982128741	6	FACETS	0.685	0.606	0.768	0.171	0.151	0.192	SUBCLONAL	1	TRUE	2	0.594391982128741	6		249	979	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69456106	69456106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003054-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	212	499	1	ENST00000227507.2:c.25G>A	p.Glu9Lys	p.E9K	ENST00000227507	NM_053056.2	9	Gaa/Aaa	1/5	0.488422829748312	4	FACETS	0.942	0.874	1			1	CLONAL	1	TRUE	NA	0.594391982128741	4		500	1207	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444286	49444286	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003054-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1755	330	808	1	ENST00000301067.7:c.3085C>T	p.Gln1029Ter	p.Q1029*	ENST00000301067	NM_003482.3	1029	Cag/Tag	11/54	0.582801597331087	5	FACETS	1	0.948	1	0.336	0.316	0.357	CLONAL	1	TRUE	2	0.594391982128741	5		809	2085	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871602	35871602	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs116801398	NA	P-0003054-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	252	531	0	ENST00000216797.5:c.904G>A	p.Glu302Lys	p.E302K	ENST00000216797	NM_020529.2	302	Gag/Aag	5/6	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.594391982128741	2		531	791	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061115	38061115	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1016447126	NA	P-0003054-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	44	54	0	ENST00000250448.2:c.874G>A	p.Glu292Lys	p.E292K	ENST00000250448	NM_004496.3	292	Gag/Aag	2/2	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.594391982128741	2		54	111	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256730	19256730	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003054-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	72	405	0	ENST00000162023.5:c.983G>T	p.Gly328Val	p.G328V	ENST00000162023		328	gGg/gTg	13/13	0.515005788160462	3	FACETS	0.392	0.342	0.447			1	SUBCLONAL	1	TRUE	NA	0.594391982128741	3		405	801	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380276	+	missense_variant	Missense_Mutation	DNP	TT	TT	AA	novel	NA	P-0003054-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	400	453	1	ENST00000311936.3:c.182_183inv	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAA/cTT	3/5	0.488422829748312	4	FACETS	0.979	0.933	1			1	CLONAL	2	TRUE	NA	0.594391982128741	4		454	1096	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0003067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	740	510	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.489469214939124	5	FACETS	1	0.98	1	1	0.98	1	CLONAL	4	TRUE	1	0.494802609710539	5		510	1289	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187847	11187847	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003073-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	116	221	1	ENST00000361445.4:c.6050T>G	p.Ile2017Ser	p.I2017S	ENST00000361445	NM_004958.3	2017	aTc/aGc	44/58	0.434729506739103	1	FACETS	0.972	0.884	1	0.972	0.884	1	CLONAL	1	TRUE	0	0.46488683815872	1		222	394	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945624	206945624	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003073-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	162	315	0	ENST00000423557.1:c.157A>G	p.Thr53Ala	p.T53A	ENST00000423557	NM_000572.2	53	Act/Gct	1/5	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.46488683815872	2		315	684	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28611321	28611321	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0003073-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	103	380	5	ENST00000241453.7:c.1309+1G>T		p.X437_splice	ENST00000241453	NM_004119.2	437			0.46488683815872	1	FACETS	0.865	0.781	0.954	0.865	0.781	0.954	CLONAL	1	TRUE	0	0.46488683815872	1		385	393	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031854	10031854	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003073-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	42	284	0	ENST00000330684.3:c.969G>T	p.Gln323His	p.Q323H	ENST00000330684	NM_001134407.1	323	caG/caT	3/13	1	2	FACETS	0.289	0.24	0.343	0.289	0.24	0.343	SUBCLONAL	1	TRUE	1	0.46488683815872	2		284	626	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29701075	29701075	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003073-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	89	264	1	ENST00000356175.3:c.8359T>A	p.Cys2787Ser	p.C2787S	ENST00000356175	NM_000267.3	2787	Tgt/Agt	57/57	1	2	FACETS	0.992	0.886	1	0.992	0.886	1	CLONAL	1	TRUE	1	0.46488683815872	2		265	386	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069429	30069429	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003073-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	160	238	0	ENST00000338641.4:c.1294G>T	p.Glu432Ter	p.E432*	ENST00000338641	NM_000268.3	432	Gaa/Taa	12/16	0.375395660151331	1	FACETS	0.993	0.917	1	0.993	0.917	1	CLONAL	1	TRUE	0	0.46488683815872	1		238	532	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540161	187540161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373112377	NA	P-0003108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	467	324	2	ENST00000441802.2:c.7579G>A	p.Val2527Ile	p.V2527I	ENST00000441802	NM_005245.3	2527	Gtt/Att	10/27	0.666021893723716	5	FACETS	0.996	0.952	1	0.498	0.476	0.52	CLONAL	2	TRUE	1	0.729819891784348	5		326	1346	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321371	65321371	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	113	189	0	ENST00000342505.4:c.1469G>C	p.Gly490Ala	p.G490A	ENST00000342505	NM_002227.2	490	gGt/gCt	11/25	0.729819891784348	3	FACETS	0.821	0.742	0.903	0.41	0.371	0.452	CLONAL	1	TRUE	1	0.729819891784348	3		189	515	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604265	189604265	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	378	335	0	ENST00000264731.3:c.1432G>C	p.Val478Leu	p.V478L	ENST00000264731	NM_003722.4	478	Gtg/Ctg	11/14	0.729819891784348	4	FACETS	0.932	0.888	0.977	0.932	0.888	0.977	CLONAL	2	TRUE	2	0.729819891784348	4		335	961	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876553	35876553	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	172	164	0	ENST00000303115.3:c.1345T>A	p.Tyr449Asn	p.Y449N	ENST00000303115	NM_002185.3	449	Tat/Aat	8/8	0.729819891784348	6	FACETS	0.919	0.849	0.991	0.459	0.424	0.496	CLONAL	2	TRUE	2	0.729819891784348	6		164	631	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220275	55220275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751295137	NA	P-0003108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	240	261	3	ENST00000275493.2:c.665G>A	p.Arg222His	p.R222H	ENST00000275493	NM_005228.3	222	cGc/cAc	6/28	0.117890093272033	1	FACETS	1	0.99	1	1	0.99	1	INDETERMINATE	1	TRUE	0	0.729819891784348	1		264	365	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742885	17742885	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1408588266	NA	P-0003108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	156	170	0	ENST00000250003.3:c.793G>T	p.Ala265Ser	p.A265S	ENST00000250003	NM_002478.4	265	Gcg/Tcg	3/3	0.568015855331758	6	FACETS	0.878	0.814	0.944			1	CLONAL	3	TRUE	NA	0.729819891784348	6		170	399	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563318	21563318	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	138	251	0	ENST00000382592.4:c.601C>T	p.Pro201Ser	p.P201S	ENST00000382592	NM_014572.2	201	Ccc/Tcc	4/8	0.6922804511719	2	FACETS	0.95	0.874	1	0.475	0.437	0.515	CLONAL	1	TRUE	0	0.729819891784348	2		251	398	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0003154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	129	510	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.261062160703374	4	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	2	0.16	4		510	835	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0003154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	26	347	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	1	2	FACETS	0.846	0.67	1	0.846	0.67	1	CLONAL	1	TRUE	1	0.16	2		347	384	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481393	140481393	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	33	332	0	ENST00000288602.6:c.1415A>C	p.Tyr472Ser	p.Y472S	ENST00000288602	NM_004333.4	472	tAc/tCc	11/18	1	2	FACETS	0.649	0.527	0.787	0.649	0.527	0.787	SUBCLONAL	1	TRUE	1	0.16	2		332	636	SUCCESS
APC	324	MSKCC	GRCh37	5	112175351	112175352	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0003154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	66	243	0	ENST00000257430.4:c.4062_4063del	p.Ser1355PhefsTer19	p.S1355Ffs*19	ENST00000257430	NM_000038.5	1354	TTt/t	16/16	1	2	FACETS	0.893	0.777	1	1	0.978	1	CLONAL	2	TRUE	1	0.16	2		243	462	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784040	9784040	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	51	405	0	ENST00000377346.4:c.2608C>T	p.Arg870Ter	p.R870*	ENST00000377346	NM_005026.3	870	Cga/Tga	21/24	0.453635449929951	1	FACETS	0.431	0.372	0.493	0.431	0.372	0.493	INDETERMINATE	1	TRUE	0	0.785440866815212	1		405	183	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0003184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	14	212	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	1	2	FACETS	0.805	0.584	1	0.805	0.584	1	CLONAL	1	TRUE	1	0.19	2		212	183	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0003184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	27	440	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.223746871756285	3	FACETS	1	0.888	1	0.589	0.47	0.724	CLONAL	1	TRUE	1	0.19	3		441	264	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0003190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	37	416	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	FALSE	1	0.223477279798584	2		416	283	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721579	176721579	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	60	267	0	ENST00000439151.2:c.7210G>C	p.Asp2404His	p.D2404H	ENST00000439151	NM_022455.4	2404	Gac/Cac	23/23	1	2	FACETS	0.756	0.651	0.872	0.756	0.651	0.872	SUBCLONAL	1	FALSE	1	0.223477279798584	2		267	710	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425121	49425121	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555187461	NA	P-0003190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	78	382	0	ENST00000301067.7:c.13367C>G	p.Ser4456Ter	p.S4456*	ENST00000301067	NM_003482.3	4456	tCa/tGa	39/54	1	2	FACETS	0.971	0.853	1	0.971	0.853	1	CLONAL	1	FALSE	1	0.223477279798584	2		382	719	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822211	72822211	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	79	575	0	ENST00000268489.5:c.9964C>T	p.Gln3322Ter	p.Q3322*	ENST00000268489	NM_006885.3	3322	Cag/Tag	10/10	1	2	FACETS	0.739	0.648	0.837	0.739	0.648	0.837	SUBCLONAL	1	FALSE	1	0.223477279798584	2		575	957	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938460	44938460	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	91	257	0	ENST00000377967.4:c.3008A>C	p.Gln1003Pro	p.Q1003P	ENST00000377967	NM_021140.2	1003	cAg/cCg	20/29	1	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	0	0.223477279798584	1		257	505	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0003190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	14	135	0				ENST00000310581	NM_198253.2	-/1132			0.168828753847994	3	FACETS	0.725	0.525	0.966	0.363	0.262	0.483	CLONAL	1	FALSE	1	0.223477279798584	3		135	192	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0003197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	122	316	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	1	0.947	1	1	0.993	1	CLONAL	5	TRUE	1	0.19	2		316	249	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159754	20159754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	318	102	0	ENST00000379607.5:c.5C>T	p.Pro2Leu	p.P2L	ENST00000379607	NM_001412.3	2	cCc/cTc	1/7	1	1	FACETS	1	0.985	1	1	0.997	1	CLONAL	9	TRUE	0	0.19	1		102	336	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0003202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	31	283	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		283	981	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913396	NA	P-0003212-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	283	366	0	ENST00000349496.5:c.95A>T	p.Asp32Val	p.D32V	ENST00000349496	NM_001904.3	32	gAc/gTc	3/15	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.762720766735958	2		366	637	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573302	55573302	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs147540142	NA	P-0003212-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	225	278	0	ENST00000288135.5:c.964A>G	p.Thr322Ala	p.T322A	ENST00000288135	NM_000222.2	322	Aca/Gca	6/21	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.762720766735958	2		278	575	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0003219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	18	379	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.3	1	FACETS	0.352	0.264	0.456	0.352	0.264	0.456	SUBCLONAL	1	TRUE	0	0.22	1		379	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0003219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	25	168	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	1	0.22	2		168	211	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690318	117690318	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	57	272	0	ENST00000369458.3:c.811G>T	p.Ala271Ser	p.A271S	ENST00000369458	NM_024626.3	271	Gca/Tca	5/6	0.17341384012113	3	FACETS	0.788	0.675	0.912	0.394	0.337	0.456	CLONAL	1	TRUE	1	0.22	3		272	730	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	45	138	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.931	0.799	1	0.931	0.799	1	CLONAL	1	TRUE	1	0.695780128950011	2		138	139	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	229	787	1	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.695780128950011	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.695780128950011	1		788	377	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945129	32945129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80359104	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	142	433	0	ENST00000380152.3:c.8524C>T	p.Arg2842Cys	p.R2842C	ENST00000380152		2842	Cgc/Tgc	20/27	1	2	FACETS	0.802	0.735	0.871	0.802	0.735	0.871	CLONAL	1	TRUE	1	0.695780128950011	2		433	509	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027168	49027168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913305	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	205	502	0	ENST00000267163.4:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	579	Cga/Tga	18/27	1	2	FACETS	0.96	0.896	1	0.96	0.896	1	CLONAL	1	TRUE	1	0.695780128950011	2		502	614	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937075	36937075	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	335	692	0	ENST00000361632.4:c.1244G>A	p.Gly415Glu	p.G415E	ENST00000361632		415	gGg/gAg	9/16	0.695780128950011	3	FACETS	1	0.989	1	0.587	0.555	0.619	CLONAL	1	TRUE	1	0.695780128950011	3		692	1106	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082772	16082772	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	18	48	0	ENST00000281043.3:c.586C>T	p.Pro196Ser	p.P196S	ENST00000281043	NM_005378.4	196	Ccc/Tcc	2/3	1	2	FACETS	0.976	0.765	1	0.976	0.765	1	CLONAL	1	TRUE	1	0.695780128950011	2		48	53	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597496	52597496	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776550567	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	162	375	0	ENST00000394830.3:c.3814C>T	p.Pro1272Ser	p.P1272S	ENST00000394830	NM_018313.4	1272	Cct/Tct	25/30	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.695780128950011	2		375	419	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564552	55564552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	178	463	0	ENST00000288135.5:c.440C>T	p.Ser147Phe	p.S147F	ENST00000288135	NM_000222.2	147	tCc/tTc	3/21	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.695780128950011	2		463	502	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516966	187516966	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	162	442	0	ENST00000441802.2:c.13015C>T	p.Leu4339Phe	p.L4339F	ENST00000441802	NM_005245.3	4339	Ctt/Ttt	26/27	1	2	FACETS	0.974	0.901	1	0.974	0.901	1	CLONAL	1	TRUE	1	0.695780128950011	2		442	478	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944842	131944842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	124	319	0	ENST00000265335.6:c.2863C>T	p.His955Tyr	p.H955Y	ENST00000265335		955	Cat/Tat	18/25	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.695780128950011	2		319	331	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515250	149515250	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	179	487	0	ENST00000261799.4:c.232G>A	p.Asp78Asn	p.D78N	ENST00000261799	NM_002609.3	78	Gat/Aat	3/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.695780128950011	2		487	478	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287871	33287871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237131098	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	184	602	0	ENST00000374542.5:c.1382C>T	p.Ser461Phe	p.S461F	ENST00000374542	NM_001141970.1	461	tCt/tTt	5/8	1	2	FACETS	0.963	0.896	1	0.963	0.896	1	CLONAL	1	TRUE	1	0.695780128950011	2		602	549	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553024	106553024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	169	468	0	ENST00000369096.4:c.989C>T	p.Pro330Leu	p.P330L	ENST00000369096	NM_001198.3	330	cCa/cTa	5/7	0.66024012558268	3	FACETS	1	0.961	1	0.531	0.491	0.574	CLONAL	1	TRUE	1	0.695780128950011	3		468	616	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509561	106509561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	174	475	0	ENST00000359195.3:c.1555C>T	p.Leu519Phe	p.L519F	ENST00000359195	NM_002649.2	519	Ctt/Ttt	2/11	1	2	FACETS	0.896	0.83	0.964	0.896	0.83	0.964	CLONAL	1	TRUE	1	0.695780128950011	2		475	558	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836762	151836762	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	134	482	0	ENST00000262189.6:c.14458C>T	p.Gln4820Ter	p.Q4820*	ENST00000262189	NM_170606.2	4820	Cag/Tag	56/59	1	2	FACETS	0.797	0.729	0.868	0.797	0.729	0.868	SUBCLONAL	1	TRUE	1	0.695780128950011	2		482	483	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151947956	151947956	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	179	465	0	ENST00000262189.6:c.1717C>T	p.Pro573Ser	p.P573S	ENST00000262189	NM_170606.2	573	Cct/Tct	12/59	1	2	FACETS	0.936	0.868	1	0.936	0.868	1	CLONAL	1	TRUE	1	0.695780128950011	2		465	550	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741232	145741232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	217	633	0	ENST00000428558.2:c.1174G>A	p.Gly392Ser	p.G392S	ENST00000428558	NM_004260.3	392	Ggt/Agt	6/22	1	2	FACETS	0.927	0.866	0.989	0.927	0.866	0.989	CLONAL	1	TRUE	1	0.695780128950011	2		633	673	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971062	21971062	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754806883	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	125	220	0	ENST00000304494.5:c.296G>A	p.Arg99Gln	p.R99Q	ENST00000304494	NM_000077.4	99	cGg/cAg	2/3	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.695780128950011	2		220	299	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779042	135779042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	128	308	0	ENST00000298552.3:c.2204C>T	p.Ala735Val	p.A735V	ENST00000298552	NM_001162426.1	735	gCc/gTc	17/23	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.695780128950011	2		308	339	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409746	139409746	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	139	328	0	ENST00000277541.6:c.2010C>A	p.Tyr670Ter	p.Y670*	ENST00000277541	NM_017617.3	670	taC/taA	12/34	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.695780128950011	2		328	382	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412230	139412230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	167	492	0	ENST00000277541.6:c.1415G>A	p.Gly472Glu	p.G472E	ENST00000277541	NM_017617.3	472	gGg/gAg	8/34	1	2	FACETS	0.936	0.866	1	0.936	0.866	1	CLONAL	1	TRUE	1	0.695780128950011	2		492	513	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285562	46285562	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	92	287	0	ENST00000334344.6:c.4923-1G>A		p.X1641_splice	ENST00000334344	NM_152641.2	1641			1	2	FACETS	0.938	0.845	1	0.938	0.845	1	CLONAL	1	TRUE	1	0.695780128950011	2		287	282	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26974677	26974677	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	162	419	0	ENST00000381527.3:c.1021C>T	p.Pro341Ser	p.P341S	ENST00000381527	NM_001260.1	341	Cct/Tct	10/13	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.695780128950011	2		419	380	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895712	28895712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377450424	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	117	399	0	ENST00000282397.4:c.3062G>A	p.Arg1021Gln	p.R1021Q	ENST00000282397	NM_002019.4	1021	cGg/cAg	23/30	1	2	FACETS	0.921	0.84	1	0.921	0.84	1	CLONAL	1	TRUE	1	0.695780128950011	2		399	365	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910831	32910831	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	352	830	1	ENST00000380152.3:c.2339C>T	p.Ser780Leu	p.S780L	ENST00000380152		780	tCa/tTa	11/27	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.695780128950011	2		831	983	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562606	95562606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	160	417	0	ENST00000393063.1:c.4651G>A	p.Glu1551Lys	p.E1551K	ENST00000393063	NM_030621.3	1551	Gag/Aag	24/28	1	2	FACETS	0.937	0.866	1	0.937	0.866	1	CLONAL	1	TRUE	1	0.695780128950011	2		417	491	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845641	68845641	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	277	555	0	ENST00000261769.5:c.887A>T	p.Tyr296Phe	p.Y296F	ENST00000261769	NM_004360.3	296	tAc/tTc	7/16	0.695780128950011	2	FACETS	1	0.983	1	0.551	0.521	0.583	CLONAL	1	TRUE	0	0.695780128950011	2		555	722	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349226	89349226	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1193737081	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	889	1026	0	ENST00000301030.4:c.3724G>A	p.Ala1242Thr	p.A1242T	ENST00000301030	NM_001256183.1	1242	Gct/Act	9/13	0.695780128950011	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.695780128950011	2		1026	1197	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805489	46805489	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1427616006	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	337	839	0	ENST00000290295.7:c.467G>A	p.Gly156Glu	p.G156E	ENST00000290295	NM_006361.5	156	gGa/gAa	1/2	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.695780128950011	2		839	776	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2220150	2220150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	464	570	0	ENST00000398665.3:c.2735C>T	p.Ser912Phe	p.S912F	ENST00000398665	NM_032482.2	912	tCc/tTc	23/28	0.695780128950011	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.695780128950011	3		570	855	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383236	42383236	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs565069569	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	255	709	0	ENST00000221972.3:c.256G>A	p.Asp86Asn	p.D86N	ENST00000221972	NM_021601.3	86	Gac/Aac	2/5	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.695780128950011	2		709	683	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909460	50909460	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	254	641	0	ENST00000440232.2:c.1264G>A	p.Gly422Ser	p.G422S	ENST00000440232	NM_002691.3	422	Ggc/Agc	11/27	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.695780128950011	2		641	716	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827988	40827988	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	110	313	0	ENST00000373198.4:c.2440C>T	p.Gln814Ter	p.Q814*	ENST00000373198	NM_133170.3	814	Cag/Tag	17/32	1	2	FACETS	0.958	0.871	1	0.958	0.871	1	CLONAL	1	TRUE	1	0.695780128950011	2		313	330	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321372	1321372	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1319865856	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	172	433	0	ENST00000400841.2:c.383C>T	p.Ser128Leu	p.S128L	ENST00000400841		128	tCg/tTg	4/6	1	1	FACETS	0.645	0.598	0.693	0.645	0.598	0.693	SUBCLONAL	1	TRUE	0	0.695780128950011	1		433	500	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881512	48881513	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	126	294	0	ENST00000267163.4:c.234_235delinsAA	p.Trp78_Glu79delinsTer	p.W78_E79delins*	ENST00000267163	NM_000321.2	78	tgGGag/tgAAag	2/27	1	2	FACETS	0.956	0.874	1	0.956	0.874	1	CLONAL	1	TRUE	1	0.695780128950011	2		294	379	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527815	103527816	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	236	461	0	ENST00000355739.4:c.3123_3124delinsAA	p.Met1041_Glu1042delinsIleLys	p.M1041_E1042delinsIK	ENST00000355739	NM_000123.3	1041	atGGag/atAAag	15/15	0.66024012558268	3	FACETS	0.878	0.827	0.928	0.878	0.827	0.928	CLONAL	2	TRUE	1	0.695780128950011	3		461	521	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584581	189584582	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	135	443	0	ENST00000264731.3:c.877_878delinsTT	p.Pro293Phe	p.P293F	ENST00000264731	NM_003722.4	293	CCc/TTc	6/14	1	2	FACETS	0.847	0.776	0.921	0.847	0.776	0.921	CLONAL	1	TRUE	1	0.695780128950011	2		443	458	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127447	55127448	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0003235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	170	460	2	ENST00000257290.5:c.235_236delinsAA	p.Gly79Asn	p.G79N	ENST00000257290	NM_006206.4	79	GGc/AAc	3/23	1	2	FACETS	0.919	0.851	0.988	0.919	0.851	0.988	CLONAL	1	TRUE	1	0.695780128950011	2		462	532	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0003245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	27	338	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.215411384061948	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		339	507	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0003255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	279	381	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.176804264338697	6	FACETS	0.895	0.846	0.944			1	INDETERMINATE	4	TRUE	NA	0.410073916604486	6		382	692	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0003255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	50	331	0				ENST00000310581	NM_198253.2	-/1132			0.410073916604486	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.410073916604486	1		331	179	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0003255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	130	371	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	0.410073916604486	2		371	581	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976476	25976476	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	138	509	0	ENST00000435504.4:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000435504		357	Cga/Tga	11/13	NA	2	FACETS	0.922	0.84	1			1	INDETERMINATE	1	TRUE	NA	0.410073916604486	2		509	730	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871172	35871172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893894	NA	P-0003255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	81	254	0	ENST00000303115.3:c.394C>T	p.Pro132Ser	p.P132S	ENST00000303115	NM_002185.3	132	Cct/Tct	4/8	0.410073916604486	1	FACETS	0.892	0.792	0.998	0.892	0.792	0.998	CLONAL	1	TRUE	0	0.410073916604486	1		254	352	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969137	93969137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	155	617	0	ENST00000369303.4:c.1859C>T	p.Ala620Val	p.A620V	ENST00000369303	NM_004440.3	620	gCt/gTt	10/17	NA	2	FACETS	0.877	0.803	0.954			1	INDETERMINATE	1	TRUE	NA	0.410073916604486	2		617	862	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553189	106553189	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	85	300	0	ENST00000369096.4:c.1154G>A	p.Gly385Asp	p.G385D	ENST00000369096	NM_001198.3	385	gGt/gAt	5/7	0.103353186216918	3	FACETS	1	0.901	1			1	INDETERMINATE	1	TRUE	NA	0.410073916604486	3		300	491	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949069	151949069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776295921	NA	P-0003255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	137	427	0	ENST00000262189.6:c.1576C>T	p.Arg526Cys	p.R526C	ENST00000262189	NM_170606.2	526	Cgt/Tgt	11/59	0.138894101060114	5	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.410073916604486	5		427	863	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858267	9858267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	80	321	0	ENST00000330684.3:c.3134C>T	p.Ser1045Phe	p.S1045F	ENST00000330684	NM_001134407.1	1045	tCc/tTc	13/13	0.205163527141329	1	FACETS	0.673	0.594	0.756	0.673	0.594	0.756	INDETERMINATE	1	TRUE	0	0.410073916604486	1		321	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0003255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	78	259	0	ENST00000269305.4:c.782+1G>C		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.410073916604486	1	FACETS	0.976	0.866	1	0.976	0.866	1	CLONAL	1	TRUE	0	0.410073916604486	1		259	310	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692715	89692769	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	AATTAAAAATTCAAGAGTTTTTTTTTCTTATTCTGAGGTTATCTTTTTACCACAG	AATTAAAAATTCAAGAGTTTTTTTTTCTTATTCTGAGGTTATCTTTTTACCACAG	-	novel	NA	P-0003255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	68	117	0	ENST00000371953.3:c.254-55_254-1del		p.X85_splice	ENST00000371953	NM_000314.4	85			0.410073916604486	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.410073916604486	1		117	222	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199958	138199958	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	154	180	0	ENST00000237289.4:c.1376C>T	p.Ser459Leu	p.S459L	ENST00000237289	NM_001270507.1	459	tCg/tTg	7/9	0.364407116454577	43	FACETS		NA	1			1	NA	NA	TRUE	NA	NA	43		180	542	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286761	212286761	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	90	239	0	ENST00000342788.4:c.2935C>T	p.Arg979Ter	p.R979*	ENST00000342788	NM_005235.2	979	Cga/Tga	24/28	0.146746611027877	4	FACETS	0.725	0.644	0.812	0.363	0.322	0.406	INDETERMINATE	1	TRUE	2	0.592918504680174	4		239	667	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528575	89528575	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1336569315	NA	P-0003278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	95	229	0	ENST00000336596.2:c.2875G>T	p.Val959Phe	p.V959F	ENST00000336596	NM_005233.5	959	Gtt/Ttt	17/17	0.191001778352121	2	FACETS	0.573	0.512	0.639	0.287	0.256	0.32	INDETERMINATE	1	TRUE	0	0.592918504680174	2		229	559	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201845	66201845	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0003278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	153	189	0	ENST00000273854.3:c.2659-2A>T		p.X887_splice	ENST00000273854	NM_004439.5	887			0.189490739012739	2	FACETS	1	0.988	1	0.679	0.629	0.73	INDETERMINATE	1	TRUE	0	0.592918504680174	2		189	380	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190582	32190582	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	70	189	0	ENST00000375023.3:c.157T>A	p.Cys53Ser	p.C53S	ENST00000375023	NM_004557.3	53	Tgt/Agt	3/30	NA	2	FACETS	0.919	0.811	1			1	INDETERMINATE	1	TRUE	NA	0.592918504680174	2		189	257	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	53	95	0	ENST00000304494.5:c.247C>A	p.His83Asn	p.H83N	ENST00000304494	NM_000077.4	83	Cac/Aac	2/3	0.189490739012739	2	FACETS	0.641	0.551	0.738	0.32	0.275	0.369	INDETERMINATE	1	TRUE	0	0.592918504680174	2		95	279	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774104	66774104	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	102	246	0	ENST00000307102.5:c.580T>G	p.Ser194Ala	p.S194A	ENST00000307102	NM_002755.3	194	Tcc/Gcc	6/11	0.189490739012739	2	FACETS	0.706	0.635	0.782	0.353	0.317	0.391	INDETERMINATE	1	TRUE	0	0.592918504680174	2		246	487	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646611	23646611	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866387173	NA	P-0003278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	143	253	0	ENST00000261584.4:c.1256G>T	p.Cys419Phe	p.C419F	ENST00000261584	NM_024675.3	419	tGc/tTc	4/13	0.116433444428135	4	FACETS	0.787	0.723	0.854	0.787	0.723	0.854	INDETERMINATE	2	TRUE	2	0.592918504680174	4		253	488	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760667	59760667	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	236	347	0	ENST00000259008.2:c.3740G>C	p.Gly1247Ala	p.G1247A	ENST00000259008	NM_032043.2	1247	gGt/gCt	20/20	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.592918504680174	2		347	785	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7120721	7120721	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	217	426	0	ENST00000302850.5:c.3569A>G	p.Tyr1190Cys	p.Y1190C	ENST00000302850	NM_000208.2	1190	tAc/tGc	20/22	0.125532288304676	0	FACETS	0.435	0.406	0.465			1	INDETERMINATE	1	TRUE	0	0.592918504680174	0		426	685	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735560	40735560	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	71	217	0	ENST00000373198.4:c.3313G>T	p.Ala1105Ser	p.A1105S	ENST00000373198	NM_133170.3	1105	Gct/Tct	25/32	0.133734660266532	5	FACETS	1	0.95	1			1	INDETERMINATE	1	TRUE	NA	0.592918504680174	5		217	388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576899	7576900	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	146	295	0	ENST00000269305.4:c.946_947insT	p.Pro316LeufsTer21	p.P316Lfs*21	ENST00000269305	NM_001126112.2	316	ccc/cTcc	9/11	0.592918504680174	1	FACETS	0.976	0.903	1	0.976	0.903	1	CLONAL	1	TRUE	0	0.592918504680174	1		295	355	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453138	140453139	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTA	rs727502902	NA	P-0003278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	612	281	0	ENST00000288602.6:c.1794_1796dup	p.Thr599dup	p.T599dup	ENST00000288602	NM_004333.4	599	aca/acTACa	15/18	0.592918504680174	4	FACETS	0.962	0.93	0.993	0.962	0.93	0.993	CLONAL	3	TRUE	1	0.592918504680174	4		281	1140	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231416	46231416	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	128	307	0	ENST00000334344.6:c.1256del	p.Leu419ProfsTer21	p.L419Pfs*21	ENST00000334344	NM_152641.2	419	cTc/cc	10/21	0.189490739012739	2	FACETS	0.65	0.59	0.713	0.325	0.295	0.357	INDETERMINATE	1	TRUE	0	0.592918504680174	2		307	664	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971112	+	missense_variant	Missense_Mutation	DNP	GC	GC	TG	novel	NA	P-0003278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	53	95	0	ENST00000304494.5:c.246_247delinsCA	p.His83Asn	p.H83N	ENST00000304494	NM_000077.4	82	gtGCac/gtCAac	2/3	0.189490739012739				0.551	0.738				INDETERMINATE	1	TRUE	0	0.592918504680174	2		95	279	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248621	10248621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	104	222	2	ENST00000340748.4:c.4132C>T	p.Arg1378Trp	p.R1378W	ENST00000340748		1378	Cgg/Tgg	35/40	1	2	FACETS	0.387	0.347	0.43	0.387	0.347	0.43	SUBCLONAL	1	TRUE	1	0.746886622206671	2		224	719	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11194409	11194409	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs752198342	NA	P-0003281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	268	215	0	ENST00000361445.4:c.5245C>T	p.Arg1749Ter	p.R1749*	ENST00000361445	NM_004958.3	1749	Cga/Tga	37/58	1	2	FACETS	0.986	0.929	1	0.986	0.929	1	CLONAL	1	TRUE	1	0.746886622206671	2		215	728	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106421	27106421	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	207	211	0	ENST00000324856.7:c.6032T>G	p.Leu2011Arg	p.L2011R	ENST00000324856	NM_006015.4	2011	cTg/cGg	20/20	1	2	FACETS	0.954	0.892	1	0.954	0.892	1	CLONAL	1	TRUE	1	0.746886622206671	2		211	581	SUCCESS
AR	367	MSKCC	GRCh37	X	66766322	66766322	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	150	84	0	ENST00000374690.3:c.1334A>C	p.Gln445Pro	p.Q445P	ENST00000374690	NM_000044.3	445	cAg/cCg	1/8	0.459504962232303	3	FACETS	0.857	0.796	0.917	0.857	0.796	0.917	CLONAL	2	TRUE	1	0.746886622206671	3		84	322	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161243	56161243	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1430249397	NA	P-0003285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	81	339	0	ENST00000399503.3:c.1112C>T	p.Ser371Leu	p.S371L	ENST00000399503	NM_005921.1	371	tCa/tTa	5/20	1	2	FACETS	0.663	0.584	0.748	0.663	0.584	0.748	SUBCLONAL	1	TRUE	1	0.364464785596956	2		339	670	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983911	2983911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237589286	NA	P-0003285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	131	442	0	ENST00000396946.4:c.619C>T	p.Arg207Cys	p.R207C	ENST00000396946	NM_032415.4	207	Cgc/Tgc	5/25	0.364464785596956	3	FACETS	0.764	0.692	0.841	0.382	0.346	0.421	SUBCLONAL	1	TRUE	1	0.364464785596956	3		442	1112	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904913	101904913	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	166	286	0	ENST00000374994.4:c.902del	p.Gly301GlufsTer2	p.G301Efs*2	ENST00000374994	NM_004612.2	301	Gga/ga	5/9	0.331677247808114	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.364464785596956	1		286	673	SUCCESS
APC	324	MSKCC	GRCh37	5	112174094	112174095	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs863225332	NA	P-0003285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	140	339	0	ENST00000257430.4:c.2804dup	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	tac/tAac	16/16	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.364464785596956	2		339	748	SUCCESS
APC	324	MSKCC	GRCh37	5	112175764	112175765	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	107	244	0	ENST00000257430.4:c.4473_4474insA	p.Ala1492SerfsTer22	p.A1492Sfs*22	ENST00000257430	NM_000038.5	1491	-/A	16/16	1	2	FACETS	0.992	0.892	1	0.992	0.892	1	CLONAL	1	TRUE	1	0.364464785596956	2		244	592	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003291-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	20	192	0				ENST00000310581	NM_198253.2	-/1132			0.148995952292621	4	FACETS	1	0.902	1	0.68	0.525	0.856	INDETERMINATE	1	TRUE	2	0.284065354974976	4		192	133	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0003291-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	32	549	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.729	0.593	0.882	0.729	0.593	0.882	SUBCLONAL	1	TRUE	1	0.284065354974976	2		549	309	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs121913292	NA	P-0003291-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	38	143	0	ENST00000371953.3:c.389del	p.Arg130GlnfsTer4	p.R130Qfs*4	ENST00000371953	NM_000314.4	130	cGa/ca	5/9	0.284065354974976	1	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	0	0.284065354974976	1		143	219	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127749	64127749	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003291-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	25	140	0	ENST00000334205.4:c.242A>C	p.His81Pro	p.H81P	ENST00000334205	NM_003942.2	81	cAc/cCc	3/17	1	2	FACETS	0.68	0.537	0.842	0.68	0.537	0.842	SUBCLONAL	1	TRUE	1	0.284065354974976	2		140	259	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578217	7578217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003291-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	33	352	0	ENST00000269305.4:c.632C>T	p.Thr211Ile	p.T211I	ENST00000269305	NM_001126112.2	211	aCt/aTt	6/11	0.190613629012645	2	FACETS	0.542	0.441	0.655	0.271	0.22	0.328	SUBCLONAL	1	TRUE	0	0.284065354974976	2		352	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577552	7577607	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CATGCAGGAACTGTTACACATGTAGTTGTAGTGGATGGTGGTACAGTCAGAGCCAA	CATGCAGGAACTGTTACACATGTAGTTGTAGTGGATGGTGGTACAGTCAGAGCCAA	-	novel	NA	P-0003291-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	21	178	0	ENST00000269305.4:c.674_729del	p.Val225GlyfsTer20	p.V225Gfs*20	ENST00000269305	NM_001126112.2	225	gTTGGCTCTGACTGTACCACCATCCACTACAACTACATGTGTAACAGTTCCTGCATG/g	7/11	0.190613629012645	2	FACETS	0.466	0.359	0.592	0.233	0.179	0.296	SUBCLONAL	1	TRUE	0	0.284065354974976	2		178	317	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	57	324	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.926	0.801	1	0.926	0.801	1	CLONAL	1	TRUE	1	0.424607730083173	2		324	290	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0003298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	238	278	3	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.417677175880575	3	FACETS	0.842	0.788	0.897	0.842	0.788	0.897	CLONAL	2	TRUE	1	0.424607730083173	3		281	807	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0003298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	295	679	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.417677175880575	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.424607730083173	3		679	782	SUCCESS
APC	324	MSKCC	GRCh37	5	112175060	112175060	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	85	199	0	ENST00000257430.4:c.3769G>T	p.Glu1257Ter	p.E1257*	ENST00000257430	NM_000038.5	1257	Gaa/Taa	16/16	0.417677175880575	3	FACETS	0.735	0.65	0.827	0.368	0.325	0.414	SUBCLONAL	1	TRUE	1	0.424607730083173	3		199	660	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871036	12871036	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	27	185	0	ENST00000228872.4:c.263A>G	p.Tyr88Cys	p.Y88C	ENST00000228872	NM_004064.3	88	tAc/tGc	1/3	0.261111311832282	5	FACETS	0.402	0.319	0.497			1	SUBCLONAL	1	TRUE	NA	0.424607730083173	5		185	518	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412110	63412110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852216	NA	P-0003298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	422	598	0	ENST00000330258.3:c.1057C>T	p.Arg353Ter	p.R353*	ENST00000330258	NM_152424.3	353	Cga/Tga	2/2	0.153777977372124	3	FACETS	0.976	0.931	1	0.651	0.62	0.682	INDETERMINATE	2	TRUE	0	0.424607730083173	3		598	1234	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120181	70120182	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CG	novel	NA	P-0003298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	145	198	0	ENST00000245479.2:c.1185_1186dup	p.His396ArgfsTer8	p.H396Rfs*8	ENST00000245479	NM_000346.3	395	acg/aCGcg	3/3	0.425191731579467	2	FACETS	0.787	0.724	0.851	0.787	0.724	0.851	SUBCLONAL	2	TRUE	0	0.424607730083173	2		198	434	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0003313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	156	375	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.275434080308463	6	FACETS	0.823	0.753	0.897	0.549	0.502	0.598	CLONAL	2	TRUE	3	0.275434080308463	6		375	1067	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042342	42042342	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	141	666	2	ENST00000219905.7:c.6537G>T	p.Lys2179Asn	p.K2179N	ENST00000219905	NM_001164273.1	2179	aaG/aaT	17/24	0.267679097288764	2	FACETS	1	0.932	1	0.514	0.468	0.563	CLONAL	1	TRUE	0	0.275434080308463	2		668	995	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241677	55241677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504256	NA	P-0003316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	209	481	0	ENST00000275493.2:c.2125G>A	p.Glu709Lys	p.E709K	ENST00000275493	NM_005228.3	709	Gaa/Aaa	18/28	0.459878196348795	3	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	1	0.459568217719409	3		481	556	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0003316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	149	573	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.459878196348795	3	FACETS	0.831	0.765	0.899	0.831	0.765	0.899	CLONAL	2	TRUE	1	0.459568217719409	3		573	480	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158408	26158408	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	60	359	2	ENST00000289316.2:c.11C>A	p.Pro4His	p.P4H	ENST00000289316	NM_138720.2	4	cCt/cAt	1/2	0.136475712384233	3	FACETS	0.669	0.577	0.768	0.223	0.192	0.256	INDETERMINATE	1	TRUE	0	0.459568217719409	3		361	480	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165786	108165786	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs753870656	NA	P-0003316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	64	370	0	ENST00000278616.4:c.4909G>T	p.Asp1637Tyr	p.D1637Y	ENST00000278616	NM_000051.3	1637	Gat/Tat	32/63	0.429560434945955	1	FACETS	0.694	0.606	0.789	0.694	0.606	0.789	SUBCLONAL	1	TRUE	0	0.459568217719409	1		370	309	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921394	39921394	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	42	366	0	ENST00000378444.4:c.4426G>T	p.Glu1476Ter	p.E1476*	ENST00000378444	NM_001123385.1	1476	Gag/Tag	10/15	0.459878196348795	1	FACETS	0.476	0.399	0.56	0.476	0.399	0.56	SUBCLONAL	1	TRUE	0	0.459568217719409	1		366	296	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626759	14626759	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775128939	NA	P-0003326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	44	340	0	ENST00000254322.2:c.1016C>T	p.Pro339Leu	p.P339L	ENST00000254322	NM_006145.1	339	cCa/cTa	3/3	0.160879493798825	3	FACETS	0.643	0.539	0.758	0.214	0.179	0.253	INDETERMINATE	1	TRUE	0	0.31	3		340	510	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0003332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	153	283	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.495087288088535	1	FACETS	0.936	0.866	1	0.936	0.866	1	CLONAL	1	TRUE	0	0.581281202341495	1		283	399	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0003332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	132	759	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.509567863136213	1	FACETS	0.885	0.813	0.959	0.885	0.813	0.959	CLONAL	1	TRUE	0	0.581281202341495	1		759	364	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099918	27099918	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	76	670	0	ENST00000324856.7:c.3797C>G	p.Pro1266Arg	p.P1266R	ENST00000324856	NM_006015.4	1266	cCt/cGt	15/20	1	2	FACETS	0.685	0.604	0.77	0.685	0.604	0.77	SUBCLONAL	1	TRUE	1	0.581281202341495	2		670	382	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416509	29416509	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	143	796	0	ENST00000389048.3:c.4444C>A	p.Gln1482Lys	p.Q1482K	ENST00000389048	NM_004304.4	1482	Cag/Aag	29/29	1	2	FACETS	0.841	0.77	0.915	0.841	0.77	0.915	CLONAL	1	TRUE	1	0.581281202341495	2		796	585	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231679	66231679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	97	772	0	ENST00000273854.3:c.2021G>A	p.Cys674Tyr	p.C674Y	ENST00000273854	NM_004439.5	674	tGt/tAt	11/18	1	2	FACETS	0.914	0.822	1	0.914	0.822	1	CLONAL	1	TRUE	1	0.581281202341495	2		772	365	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220400	1220400	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1359582062	NA	P-0003332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	116	816	0	ENST00000326873.7:c.493G>T	p.Glu165Ter	p.E165*	ENST00000326873	NM_000455.4	165	Gag/Tag	4/10	0.509567863136213	1	FACETS	0.833	0.759	0.908	0.833	0.759	0.908	CLONAL	1	TRUE	0	0.581281202341495	1		816	340	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572952	41572952	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	155	840	0	ENST00000263253.7:c.5237G>C	p.Cys1746Ser	p.C1746S	ENST00000263253	NM_001429.3	1746	tGc/tCc	31/31	0.491827683640471	1	FACETS	0.87	0.804	0.937	0.87	0.804	0.937	CLONAL	1	TRUE	0	0.581281202341495	1		840	435	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574138	41574138	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	112	581	0	ENST00000263253.7:c.6423G>C	p.Gln2141His	p.Q2141H	ENST00000263253	NM_001429.3	2141	caG/caC	31/31	0.491827683640471	1	FACETS	0.89	0.812	0.971	0.89	0.812	0.971	CLONAL	1	TRUE	0	0.581281202341495	1		581	307	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2206776	2206797	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TAAACAGTAGAAACTTGAGTGG	TAAACAGTAGAAACTTGAGTGG	-	novel	NA	P-0003332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	115	863	0	ENST00000398665.3:c.839_856+4del		p.X280_splice	ENST00000398665	NM_032482.2	280		10/28	0.509567863136213	1	FACETS	0.705	0.641	0.772	0.705	0.641	0.772	SUBCLONAL	1	TRUE	0	0.581281202341495	1		863	398	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46240623	46240637	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	GTATTTTTTTCTTTA	GTATTTTTTTCTTTA	-	novel	NA	P-0003332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	47	325	0	ENST00000334344.6:c.1499-15_1499-1del		p.X500_splice	ENST00000334344	NM_152641.2	500			0.495087288088535	1	FACETS	0.721	0.62	0.829	0.721	0.62	0.829	SUBCLONAL	1	TRUE	0	0.581281202341495	1		325	159	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	75	192	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.785820948814091	2		192	157	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0003352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	254	396	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.785820948814091	2		396	626	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0003352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	490	636	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	1	0.985	1	1	0.998	1	CLONAL	2	TRUE	1	0.785820948814091	2		636	615	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297716	15297716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568359179	NA	P-0003352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	386	386	0	ENST00000263388.2:c.1924G>A	p.Asp642Asn	p.D642N	ENST00000263388	NM_000435.2	642	Gac/Aac	12/33	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.785820948814091	2		386	880	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868416	45868416	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1434217756	NA	P-0003352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	215	267	0	ENST00000391945.4:c.361G>A	p.Val121Met	p.V121M	ENST00000391945	NM_000400.3	121	Gtg/Atg	6/23	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.785820948814091	2		267	538	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870250	44870250	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0003352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	347	228	0	ENST00000377967.4:c.429T>A	p.Tyr143Ter	p.Y143*	ENST00000377967	NM_021140.2	143	taT/taA	5/29	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.785820948814091	1		228	440	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0003359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	182	180	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	0.991	0.926	1	0.991	0.926	1	CLONAL	1	TRUE	1	0.87008324215174	2		180	422	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913492	NA	P-0003359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	106	141	0	ENST00000286548.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000286548	NM_002072.3	209	cAa/cTa	5/7	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.87008324215174	2		141	233	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484250	120484250	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	265	355	0	ENST00000256646.2:c.2880T>G	p.Asn960Lys	p.N960K	ENST00000256646	NM_024408.3	960	aaT/aaG	18/34	1	2	FACETS	0.883	0.833	0.934	0.883	0.833	0.934	CLONAL	1	TRUE	1	0.87008324215174	2		355	690	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259166	89259166	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	92	330	0	ENST00000336596.2:c.310C>T	p.Arg104Ter	p.R104*	ENST00000336596	NM_005233.5	104	Cga/Tga	3/17	1	2	FACETS	0.449	0.399	0.502	0.449	0.399	0.502	SUBCLONAL	1	TRUE	1	0.638855168301517	2		330	641	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0003389-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	23	549	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.294195933367108	6	FACETS	1	0.852	1	1	0.852	1	CLONAL	3	TRUE	3	0.294195933367108	6		549	77	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652129	36652129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34916193	NA	P-0003389-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	26	204	0	ENST00000244741.5:c.251G>A	p.Arg84Gln	p.R84Q	ENST00000244741	NM_000389.4	84	cGa/cAa	2/3	0.294195933367108	13	FACETS	0.964	0.787	1			1	CLONAL	6	TRUE	NA	0.294195933367108	13		204	80	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574222	95574222	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003389-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	14	194	1	ENST00000393063.1:c.2645A>G	p.Asn882Ser	p.N882S	ENST00000393063	NM_030621.3	882	aAt/aGt	17/28	0.24755838354361	4	FACETS	1	0.814	1	0.747	0.556	0.961	CLONAL	2	TRUE	1	0.294195933367108	4		195	55	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937816	76937820	+	frameshift_variant	Frame_Shift_Del	DEL	AAGTT	AAGTT	-	novel	NA	P-0003389-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	24	412	0	ENST00000373344.5:c.2928_2932del	p.Glu976AspfsTer2	p.E976Dfs*2	ENST00000373344	NM_000489.3	976	gaAACTTct/gact	9/35	0.284113409126087	0	FACETS	0.8	0.648	0.962			1	CLONAL	2	TRUE	0	0.294195933367108	0		412	72	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913499	NA	P-0003392-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	50	267	0	ENST00000345146.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000345146	NM_005896.2	132	Cgt/Ggt	4/10	0.157977713253755	2	FACETS	0.985	0.86	1	1	0.97	1	INDETERMINATE	3	TRUE	0	0.27284540018719	2		267	124	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003392-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	95	185	0	ENST00000269305.4:c.772G>C	p.Glu258Gln	p.E258Q	ENST00000269305	NM_001126112.2	258	Gaa/Caa	7/11	0.27284540018719	11	FACETS	0.994	0.936	1			1	CLONAL	13	TRUE	NA	0.27284540018719	11		185	120	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907649	76907650	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0003392-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	71	481	0	ENST00000373344.5:c.4511_4512del	p.Arg1504GlnfsTer5	p.R1504Qfs*5	ENST00000373344	NM_000489.3	1504	cGA/c	15/35	0.27284540018719	1	FACETS	0.979	0.879	1	1	0.987	1	CLONAL	3	TRUE	0	0.27284540018719	1		481	153	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0003395-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	119	290	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.176518270870588	1	FACETS	0.828	0.766	0.889	1	0.99	1	INDETERMINATE	2	TRUE	0	0.489234030047852	1		290	222	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508394	106508394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1462095883	NA	P-0003395-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	35	125	0	ENST00000359195.3:c.388C>T	p.Arg130Trp	p.R130W	ENST00000359195	NM_002649.2	130	Cgg/Tgg	2/11	0.296685462703172	6	FACETS	1	0.941	1	0.34	0.281	0.405	CLONAL	1	TRUE	2	0.489234030047852	6		125	208	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0003400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	35	585	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.398	0.325	0.48	0.398	0.325	0.48	SUBCLONAL	1	TRUE	1	0.272994766323851	2		585	644	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729496	41729496	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	227	612	0	ENST00000242208.4:c.1033T>A	p.Tyr345Asn	p.Y345N	ENST00000242208	NM_002192.2	345	Tat/Aat	3/3	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.272994766323851	2		612	1122	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343055	118343055	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	84	165	0	ENST00000534358.1:c.1181T>G	p.Leu394Arg	p.L394R	ENST00000534358	NM_005933.3	394	cTg/cGg	3/36	1	2	FACETS	0.827	0.736	0.924	1	0.982	1	CLONAL	2	TRUE	1	0.272994766323851	2		165	372	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068294	16068315	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TGTTTCTTTTTCAGTTTAAGGA	TGTTTCTTTTTCAGTTTAAGGA	-	novel	NA	P-0003400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	28	124	0	ENST00000268712.3:c.596_617del	p.Ile199AsnfsTer79	p.I199Nfs*79	ENST00000268712	NM_006311.3	199	aTCCTTAAACTGAAAAAGAAACAa/aa	5/46	1	2	FACETS	0.866	0.695	1	0.866	0.695	1	CLONAL	1	TRUE	1	0.272994766323851	2		124	237	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760542	133760543	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	86	477	0	ENST00000318560.5:c.2870dup	p.Pro958AlafsTer88	p.P958Afs*88	ENST00000318560	NM_005157.4	955	-/A	11/11	1	2	FACETS	0.755	0.667	0.85	0.755	0.667	0.85	SUBCLONAL	1	TRUE	1	0.272994766323851	2		477	834	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0003407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	34	356	0	ENST00000269305.4:c.376-1G>T		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.3	1	FACETS	0.887	0.726	1	0.887	0.726	1	CLONAL	1	TRUE	0	0.2	1		356	345	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488225	56488225	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	82	536	0	ENST00000267101.3:c.1744G>T	p.Gly582Trp	p.G582W	ENST00000267101	NM_001982.3	582	Ggg/Tgg	15/28	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.2	2		536	733	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195701	123195701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777363856	NA	P-0003407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	47	934	0	ENST00000218089.9:c.1615G>A	p.Val539Met	p.V539M	ENST00000218089	NM_001042749.1	539	Gtg/Atg	17/35	0.179097674117388	1	FACETS	0.672	0.567	0.79	0.672	0.567	0.79	SUBCLONAL	1	TRUE	0	0.2	1		934	629	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217302	11217302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	78	366	0	ENST00000361445.4:c.4376C>A	p.Ala1459Asp	p.A1459D	ENST00000361445	NM_004958.3	1459	gCc/gAc	30/58	1	2	FACETS	0.754	0.663	0.853	0.754	0.663	0.853	SUBCLONAL	1	TRUE	1	0.29	2		366	713	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220265	55220265	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	84	434	0	ENST00000275493.2:c.655T>G	p.Cys219Gly	p.C219G	ENST00000275493	NM_005228.3	219	Tgc/Ggc	6/28	0.3	3	FACETS	0.813	0.717	0.916			1	CLONAL	1	TRUE	NA	0.29	3		434	816	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712515	52712515	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	83	366	0	ENST00000394830.3:c.236+1G>A		p.X79_splice	ENST00000394830	NM_018313.4	79			0.3	1	FACETS	0.859	0.759	0.965	0.859	0.759	0.965	CLONAL	1	TRUE	0	0.29	1		366	570	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851366	151851366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	60	262	0	ENST00000262189.6:c.12125G>A	p.Ser4042Asn	p.S4042N	ENST00000262189	NM_170606.2	4042	aGc/aAc	47/59	1	2	FACETS	0.902	0.778	1	0.902	0.778	1	CLONAL	1	TRUE	1	0.29	2		262	459	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406705	70406705	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	48	262	0	ENST00000373644.4:c.4219A>C	p.Thr1407Pro	p.T1407P	ENST00000373644	NM_030625.2	1407	Aca/Cca	4/12	1	2	FACETS	0.606	0.512	0.71	0.606	0.512	0.71	SUBCLONAL	1	TRUE	1	0.29	2		262	546	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435578	18435578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747513676	NA	P-0003417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	64	230	0	ENST00000266497.5:c.563C>T	p.Pro188Leu	p.P188L	ENST00000266497		188	cCg/cTg	1/31	1	2	FACETS	0.99	0.859	1	0.99	0.859	1	CLONAL	1	TRUE	1	0.29	2		230	446	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103244	119103244	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	60	246	0	ENST00000264033.4:c.282del	p.Leu95SerfsTer28	p.L95Sfs*28	ENST00000264033	NM_005188.3	94	caT/ca	2/16	1	2	FACETS	0.905	0.782	1	0.905	0.782	1	CLONAL	1	TRUE	1	0.29	2		246	457	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188317	10188317	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	55	254	1	ENST00000256474.2:c.461del	p.Pro154GlnfsTer5	p.P154Qfs*5	ENST00000256474	NM_000551.3	154	Cca/ca	2/3	0.3	1	FACETS	0.801	0.687	0.924	0.801	0.687	0.924	CLONAL	1	TRUE	0	0.29	1		255	405	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156610	106156613	+	frameshift_variant	Frame_Shift_Del	DEL	AAAC	AAAC	-	novel	NA	P-0003417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	56	368	0	ENST00000380013.4:c.1513_1516del	p.Thr505AspfsTer27	p.T505Dfs*27	ENST00000380013	NM_001127208.2	504	aAAACa/aa	3/11	1	2	FACETS	0.62	0.531	0.718	0.62	0.531	0.718	SUBCLONAL	1	TRUE	1	0.29	2		368	623	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240792	53240797	+	inframe_deletion	In_Frame_Del	DEL	TTACCA	TTACCA	-	novel	NA	P-0003417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	87	278	0	ENST00000375401.3:c.1283_1288del	p.Leu428_Asn430delinsHis	p.L428_N430delinsH	ENST00000375401	NM_004187.3	428	cTGGTAAat/cat	10/26	1	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.29	1		278	419	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	283	650	0	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	0.3890523169649	1	FACETS	1	0.992	1	1	0.992	1	INDETERMINATE	1	TRUE	0	0.674768389107988	1		650	471	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729980	30729980	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	53	340	0	ENST00000295754.5:c.1501C>A	p.Pro501Thr	p.P501T	ENST00000295754	NM_003242.5	501	Ccc/Acc	6/7	0.372292683379072	1	FACETS	0.35	0.301	0.404	0.35	0.301	0.404	INDETERMINATE	1	TRUE	0	0.674768389107988	1		340	297	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710818	117710818	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	185	644	0	ENST00000368508.3:c.1454C>A	p.Ser485Tyr	p.S485Y	ENST00000368508	NM_002944.2	485	tCt/tAt	12/43	0.372292683379072	1	FACETS	0.79	0.737	0.844	0.79	0.737	0.844	INDETERMINATE	1	TRUE	0	0.674768389107988	1		644	460	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467637	50467637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1262982300	NA	P-0003423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	43	396	0	ENST00000331340.3:c.872C>T	p.Thr291Met	p.T291M	ENST00000331340	NM_006060.4	291	aCg/aTg	8/8	1	2	FACETS	0.393	0.33	0.463	0.393	0.33	0.463	SUBCLONAL	1	TRUE	1	0.674768389107988	2		396	324	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9927968	9927968	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	49	641	0	ENST00000330684.3:c.1771G>T	p.Gly591Trp	p.G591W	ENST00000330684	NM_001134407.1	591	Ggg/Tgg	8/13	1	2	FACETS	0.284	0.24	0.332	0.284	0.24	0.332	SUBCLONAL	1	TRUE	1	0.674768389107988	2		641	511	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750529	128750531	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0003423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	158	720	0	ENST00000377970.2:c.68_70del	p.Thr23del	p.T23del	ENST00000377970	NM_002467.4	22	ttCACc/ttc	2/3	1	2	FACETS	0.922	0.851	0.995	0.922	0.851	0.995	CLONAL	1	TRUE	1	0.674768389107988	2		720	508	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	84	324	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.7706272183314	2		324	214	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	180	192	0				ENST00000310581	NM_198253.2	-/1132			0.7706272183314	3	FACETS	0.987	0.928	1	0.987	0.928	1	CLONAL	2	TRUE	1	0.7706272183314	3		192	328	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	148	607	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.7706272183314	2		607	384	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921606	39921606	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	389	235	0	ENST00000378444.4:c.4214C>T	p.Ser1405Leu	p.S1405L	ENST00000378444	NM_001123385.1	1405	tCg/tTg	10/15	0.178762980260411	2	FACETS	1	0.972	1			1	INDETERMINATE	2	TRUE	NA	0.7706272183314	2		235	504	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78820291	78820291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	281	364	0	ENST00000306801.3:c.1231G>A	p.Glu411Lys	p.E411K	ENST00000306801	NM_020761.2	411	Gag/Aag	11/34	0.7706272183314	3	FACETS	0.952	0.895	1	0.476	0.447	0.506	CLONAL	1	TRUE	1	0.7706272183314	3		364	1061	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440379	52440379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	415	255	0	ENST00000460680.1:c.673G>A	p.Asp225Asn	p.D225N	ENST00000460680	NM_004656.3	225	Gac/Aac	9/17	0.7706272183314	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.7706272183314	3		255	721	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6048638	6048638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	272	333	0	ENST00000265849.7:c.13G>A	p.Glu5Lys	p.E5K	ENST00000265849	NM_000535.5	5	Gag/Aag	1/15	NA	2	FACETS	0.963	0.908	1			1	INDETERMINATE	1	TRUE	NA	0.7706272183314	2		333	733	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814530	43814530	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	262	321	0	ENST00000372470.3:c.1325T>G	p.Leu442Arg	p.L442R	ENST00000372470	NM_005373.2	442	cTc/cGc	9/12	1	2	FACETS	0.998	0.941	1	0.998	0.941	1	CLONAL	1	TRUE	1	0.7706272183314	2		321	681	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256542	115256542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465850103	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	234	392	0	ENST00000369535.4:c.169G>A	p.Asp57Asn	p.D57N	ENST00000369535	NM_002524.4	57	Gat/Aat	3/7	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.7706272183314	2		392	574	SUCCESS
FH	2271	MSKCC	GRCh37	1	241683007	241683007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	202	260	0	ENST00000366560.3:c.16C>T	p.Arg6Trp	p.R6W	ENST00000366560	NM_000143.3	6	Cgg/Tgg	1/10	1	2	FACETS	0.918	0.857	0.98	0.918	0.857	0.98	CLONAL	1	TRUE	1	0.7706272183314	2		260	571	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505454	25505454	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	319	384	0	ENST00000264709.3:c.304G>A	p.Glu102Lys	p.E102K	ENST00000264709	NM_175629.2	102	Gag/Aag	4/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.7706272183314	2		384	779	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143521	30143521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1459946897	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	58	73	0	ENST00000389048.3:c.5G>A	p.Gly2Glu	p.G2E	ENST00000389048	NM_004304.4	2	gGa/gAa	1/29	1	2	FACETS	0.984	0.866	1	0.984	0.866	1	CLONAL	1	TRUE	1	0.7706272183314	2		73	153	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097188	178097188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	178	407	0	ENST00000397062.3:c.526G>A	p.Asp176Asn	p.D176N	ENST00000397062	NM_006164.4	176	Gat/Aat	4/5	1	2	FACETS	0.945	0.878	1	0.945	0.878	1	CLONAL	1	TRUE	1	0.7706272183314	2		407	489	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650326	12650326	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	206	481	0	ENST00000251849.4:c.520G>A	p.Glu174Lys	p.E174K	ENST00000251849	NM_002880.3	174	Gag/Aag	5/17	0.7706272183314	3	FACETS	1	0.968	1	0.532	0.495	0.57	CLONAL	1	TRUE	1	0.7706272183314	3		481	696	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277969	41277969	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	182	443	0	ENST00000349496.5:c.1933C>T	p.His645Tyr	p.H645Y	ENST00000349496	NM_001904.3	645	Cac/Tac	12/15	0.7706272183314	3	FACETS	1	0.935	1	0.505	0.468	0.543	CLONAL	1	TRUE	1	0.7706272183314	3		443	648	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939929	49939929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	1023	695	0	ENST00000296474.3:c.1114G>A	p.Asp372Asn	p.D372N	ENST00000296474	NM_002447.2	372	Gac/Aac	1/20	0.7706272183314	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.7706272183314	3		695	1816	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441976	52441976	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	294	289	0	ENST00000460680.1:c.373G>A	p.Glu125Lys	p.E125K	ENST00000460680	NM_004656.3	125	Gag/Aag	5/17	0.7706272183314	3	FACETS	1	0.967	1	0.519	0.489	0.55	CLONAL	1	TRUE	1	0.7706272183314	3		289	1018	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713693	52713693	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	152	364	0	ENST00000394830.3:c.35C>T	p.Ser12Phe	p.S12F	ENST00000394830	NM_018313.4	12	tCc/tTc	2/30	0.7706272183314	3	FACETS	0.908	0.834	0.985	0.454	0.417	0.493	CLONAL	1	TRUE	1	0.7706272183314	3		364	602	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186793	142186793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	174	348	0	ENST00000350721.4:c.6670G>A	p.Glu2224Lys	p.E2224K	ENST00000350721	NM_001184.3	2224	Gaa/Aaa	39/47	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.7706272183314	2		348	437	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155502	106155502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	163	324	0	ENST00000380013.4:c.403G>A	p.Glu135Lys	p.E135K	ENST00000380013	NM_001127208.2	135	Gaa/Aaa	3/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.7706272183314	2		324	399	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157213	106157213	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	191	345	0	ENST00000380013.4:c.2114A>C	p.Gln705Pro	p.Q705P	ENST00000380013	NM_001127208.2	705	cAa/cCa	3/11	1	2	FACETS	0.946	0.882	1	0.946	0.882	1	CLONAL	1	TRUE	1	0.7706272183314	2		345	524	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250916	153250916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	163	381	0	ENST00000281708.4:c.1144C>T	p.His382Tyr	p.H382Y	ENST00000281708	NM_033632.3	382	Cat/Tat	8/12	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.7706272183314	2		381	420	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184094	56184094	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	212	433	0	ENST00000399503.3:c.4299G>A	p.Trp1433Ter	p.W1433*	ENST00000399503	NM_005921.1	1433	tgG/tgA	19/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.7706272183314	2		433	529	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819963	170819963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1449984649	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	147	284	0	ENST00000296930.5:c.505G>A	p.Glu169Lys	p.E169K	ENST00000296930	NM_002520.6	169	Gaa/Aaa	6/11	1	2	FACETS	0.898	0.828	0.969	0.898	0.828	0.969	CLONAL	1	TRUE	1	0.7706272183314	2		284	425	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058707	180058707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs918215332	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	224	365	0	ENST00000261937.6:c.130G>A	p.Gly44Ser	p.G44S	ENST00000261937	NM_182925.4	44	Ggt/Agt	2/30	NA	2	FACETS	1	0.939	1			1	INDETERMINATE	1	TRUE	NA	0.7706272183314	2		365	581	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271321	26271321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	609	897	1	ENST00000305910.3:c.292G>A	p.Glu98Lys	p.E98K	ENST00000305910	NM_003534.2	98	Gag/Aag	1/1	1	2	FACETS	0.97	0.933	1	0.97	0.933	1	CLONAL	1	TRUE	1	0.7706272183314	2		898	1629	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066561	94066561	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	91	632	0	ENST00000369303.4:c.1198G>C	p.Val400Leu	p.V400L	ENST00000369303	NM_004440.3	400	Gtc/Ctc	5/17	1	2	FACETS	0.313	0.278	0.351	0.313	0.278	0.351	SUBCLONAL	1	TRUE	1	0.7706272183314	2		632	754	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015881	112015881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	256	583	0	ENST00000368678.4:c.1060G>A	p.Gly354Arg	p.G354R	ENST00000368678		354	Gga/Aga	10/13	1	2	FACETS	0.976	0.919	1	0.976	0.919	1	CLONAL	1	TRUE	1	0.7706272183314	2		583	681	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502230	157502230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	264	323	0	ENST00000346085.5:c.3263C>T	p.Ser1088Leu	p.S1088L	ENST00000346085	NM_020732.3	1088	tCa/tTa	12/20	1	2	FACETS	0.972	0.916	1	0.972	0.916	1	CLONAL	1	TRUE	1	0.7706272183314	2		323	705	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380960	116380960	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	286	470	0	ENST00000397752.3:c.1582C>T	p.Gln528Ter	p.Q528*	ENST00000397752	NM_000245.2	528	Caa/Taa	5/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.7706272183314	2		470	726	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341255	8341255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	93	245	0	ENST00000356435.5:c.4961C>T	p.Ser1654Leu	p.S1654L	ENST00000356435		1654	tCa/tTa	30/35	NA	2	FACETS	0.962	0.869	1			1	INDETERMINATE	1	TRUE	NA	0.7706272183314	2		245	251	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97869410	97869410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	373	435	0	ENST00000289081.3:c.1471C>T	p.Leu491Phe	p.L491F	ENST00000289081	NM_000136.2	491	Ctc/Ttc	14/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.7706272183314	2		435	933	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209514	98209514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781539921	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	216	281	0	ENST00000331920.6:c.4024C>T	p.Arg1342Cys	p.R1342C	ENST00000331920	NM_000264.3	1342	Cgc/Tgc	23/24	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.7706272183314	2		281	556	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797220	135797220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	194	406	0	ENST00000298552.3:c.649G>A	p.Glu217Lys	p.E217K	ENST00000298552	NM_001162426.1	217	Gaa/Aaa	7/23	1	2	FACETS	0.965	0.9	1	0.965	0.9	1	CLONAL	1	TRUE	1	0.7706272183314	2		406	522	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457985	69457985	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771952150	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	322	453	0	ENST00000227507.2:c.385G>A	p.Asp129Asn	p.D129N	ENST00000227507	NM_053056.2	129	Gac/Aac	2/5	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.7706272183314	2		453	825	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448392	49448392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	371	528	0	ENST00000301067.7:c.319G>A	p.Glu107Lys	p.E107K	ENST00000301067	NM_003482.3	107	Gag/Aag	3/54	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.7706272183314	2		528	952	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118919	115118919	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	165	278	0	ENST00000257566.3:c.422C>T	p.Ser141Phe	p.S141F	ENST00000257566	NM_016569.3	141	tCt/tTt	2/8	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.7706272183314	2		278	412	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202825	133202825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879783561	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	327	371	0	ENST00000320574.5:c.6409G>A	p.Glu2137Lys	p.E2137K	ENST00000320574	NM_006231.2	2137	Gag/Aag	46/49	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.7706272183314	2		371	835	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911589	32911589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	249	610	0	ENST00000380152.3:c.3097G>A	p.Asp1033Asn	p.D1033N	ENST00000380152		1033	Gat/Aat	11/27	1	2	FACETS	0.925	0.869	0.981	0.925	0.869	0.981	CLONAL	1	TRUE	1	0.7706272183314	2		610	699	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041321	42041321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	203	595	0	ENST00000219905.7:c.5516G>A	p.Gly1839Glu	p.G1839E	ENST00000219905	NM_001164273.1	1839	gGa/gAa	17/24	1	2	FACETS	0.901	0.841	0.962	0.901	0.841	0.962	CLONAL	1	TRUE	1	0.7706272183314	2		595	585	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293136	91293136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	127	293	0	ENST00000355112.3:c.638C>T	p.Ser213Phe	p.S213F	ENST00000355112	NM_000057.2	213	tCt/tTt	3/22	NA	2	FACETS	0.934	0.856	1			1	INDETERMINATE	1	TRUE	NA	0.7706272183314	2		293	353	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467776	99467776	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	196	384	0	ENST00000268035.6:c.2645G>A	p.Arg882Lys	p.R882K	ENST00000268035	NM_000875.3	882	aGa/aAa	13/21	NA	2	FACETS	0.997	0.932	1			1	INDETERMINATE	1	TRUE	NA	0.7706272183314	2		384	510	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779715	3779715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1220965943	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	226	282	0	ENST00000262367.5:c.5333C>T	p.Ser1778Leu	p.S1778L	ENST00000262367	NM_004380.2	1778	tCg/tTg	31/31	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.7706272183314	2		282	521	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81902826	81902826	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	171	584	1	ENST00000359376.3:c.487C>A	p.Leu163Ile	p.L163I	ENST00000359376	NM_002661.3	163	Ctc/Atc	6/33	1	2	FACETS	0.884	0.82	0.95	0.884	0.82	0.95	CLONAL	1	TRUE	1	0.7706272183314	2		585	502	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349276	89349276	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	481	912	1	ENST00000301030.4:c.3674C>T	p.Ser1225Leu	p.S1225L	ENST00000301030	NM_001256183.1	1225	tCa/tTa	9/13	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.7706272183314	2		913	1241	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351466	89351466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1243371355	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	438	635	0	ENST00000301030.4:c.1484C>T	p.Ser495Phe	p.S495F	ENST00000301030	NM_001256183.1	495	tCt/tTt	9/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.7706272183314	2		635	1092	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983280	15983280	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	172	409	0	ENST00000268712.3:c.3499C>T	p.Gln1167Ter	p.Q1167*	ENST00000268712	NM_006311.3	1167	Cag/Tag	26/46	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.7706272183314	2		409	408	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29701042	29701042	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567634460	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	124	291	0	ENST00000356175.3:c.8326G>A	p.Glu2776Lys	p.E2776K	ENST00000356175	NM_000267.3	2776	Gag/Aag	57/57	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.7706272183314	2		291	292	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533164	63533164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760939811	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	341	420	0	ENST00000307078.5:c.1730C>T	p.Thr577Ile	p.T577I	ENST00000307078	NM_004655.3	577	aCc/aTc	7/11	0.7706272183314	3	FACETS	1	0.968	1	0.516	0.488	0.545	CLONAL	1	TRUE	1	0.7706272183314	3		420	1187	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56402494	56402494	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs552555480	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	250	511	0	ENST00000348428.3:c.1536G>A	p.Met512Ile	p.M512I	ENST00000348428	NM_006785.3	512	atG/atA	13/17	1	2	FACETS	0.974	0.917	1	0.974	0.917	1	CLONAL	1	TRUE	1	0.7706272183314	2		511	666	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414830	56414830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	263	606	0	ENST00000348428.3:c.2231C>T	p.Ser744Leu	p.S744L	ENST00000348428	NM_006785.3	744	tCa/tTa	17/17	1	2	FACETS	0.957	0.902	1	0.957	0.902	1	CLONAL	1	TRUE	1	0.7706272183314	2		606	713	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7152923	7152923	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	202	337	0	ENST00000302850.5:c.2045C>T	p.Ser682Leu	p.S682L	ENST00000302850	NM_000208.2	682	tCg/tTg	10/22	1	2	FACETS	0.984	0.919	1	0.984	0.919	1	CLONAL	1	TRUE	1	0.7706272183314	2		337	533	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129655	11129655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	349	303	0	ENST00000358026.2:c.2461G>A	p.Glu821Lys	p.E821K	ENST00000358026	NM_001128849.1	821	Gag/Aag	17/36	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.7706272183314	2		303	815	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257113	19257113	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	110	134	0	ENST00000162023.5:c.850G>A	p.Asp284Asn	p.D284N	ENST00000162023		284	Gat/Aat	12/13	1	2	FACETS	0.974	0.889	1	0.974	0.889	1	CLONAL	1	TRUE	1	0.7706272183314	2		134	293	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795752	42795752	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	742	460	0	ENST00000575354.2:c.2741C>A	p.Ser914Ter	p.S914*	ENST00000575354	NM_015125.3	914	tCa/tAa	11/20	0.7706272183314	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.7706272183314	2		460	963	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860557	45860557	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	626	480	0	ENST00000391945.4:c.1450A>G	p.Thr484Ala	p.T484A	ENST00000391945	NM_000400.3	484	Acg/Gcg	15/23	0.7706272183314	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.7706272183314	2		480	808	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918207	50918207	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	311	555	0	ENST00000440232.2:c.2524A>T	p.Asn842Tyr	p.N842Y	ENST00000440232	NM_002691.3	842	Aac/Tac	20/27	0.7706272183314	2	FACETS	0.814	0.769	0.86	0.407	0.384	0.43	CLONAL	1	TRUE	0	0.7706272183314	2		555	992	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022824	31022824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	229	408	0	ENST00000375687.4:c.2309C>T	p.Ser770Leu	p.S770L	ENST00000375687	NM_015338.5	770	tCa/tTa	13/13	1	2	FACETS	0.942	0.883	1	0.942	0.883	1	CLONAL	1	TRUE	1	0.7706272183314	2		408	631	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325482	1325482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766121638	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	147	225	0	ENST00000400841.2:c.193G>A	p.Asp65Asn	p.D65N	ENST00000400841		65	Gat/Aat	3/6	0.178762980260411	2	FACETS	1	0.954	1			1	INDETERMINATE	1	TRUE	NA	0.7706272183314	2		225	366	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045783	47045783	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs377461139	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	302	249	0	ENST00000377604.3:c.2664C>G	p.Ile888Met	p.I888M	ENST00000377604	NM_001204468.1	888	atC/atG	23/24	0.178762980260411	2	FACETS	0.935	0.901	0.969			1	INDETERMINATE	2	TRUE	NA	0.7706272183314	2		249	419	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652075	36652100	+	frameshift_variant	Frame_Shift_Del	DEL	AGCGTGTGCGGGGCCTTGGCCTGCCC	AGCGTGTGCGGGGCCTTGGCCTGCCC	-	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	290	414	0	ENST00000244741.5:c.198_223del	p.Arg67AlafsTer13	p.R67Afs*13	ENST00000244741	NM_000389.4	66	gAGCGTGTGCGGGGCCTTGGCCTGCCC/g	2/3	1	2	FACETS	0.911	0.86	0.963	0.911	0.86	0.963	CLONAL	1	TRUE	1	0.7706272183314	2		414	826	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760387	133760400	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGCCTCTGCAGG	GCAGCCTCTGCAGG	-	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	226	379	0	ENST00000318560.5:c.2711_2724del	p.Ala904GlufsTer31	p.A904Efs*31	ENST00000318560	NM_005157.4	904	GCAGCCTCTGCAGGg/g	11/11	1	2	FACETS	0.823	0.77	0.877	0.823	0.77	0.877	CLONAL	1	TRUE	1	0.7706272183314	2		379	713	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511534	66511534	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	93	165	2	ENST00000358598.2:c.-6-1G>A		p.X2_splice	ENST00000358598	NM_212471.2	2			0.7706272183314	3	FACETS	1	0.909	1	0.507	0.455	0.561	CLONAL	1	TRUE	1	0.7706272183314	3		167	330	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379281	225379328	+	splice_donor_variant,intron_variant	Splice_Site	DEL	ATATAATCACTAAAACCAAAACCACAAGAGTAAAGAGAGAAATTTTAC	ATATAATCACTAAAACCAAAACCACAAGAGTAAAGAGAGAAATTTTAC	-	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	166	201	0	ENST00000264414.4:c.539+1_539+48del		p.X180_splice	ENST00000264414	NM_003590.4	180			1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.7706272183314	2		201	328	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760412	133760418	+	protein_altering_variant	In_Frame_Del	DEL	GAAAGCC	GAAAGCC	CTTT	novel	NA	P-0003433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	226	356	0	ENST00000318560.5:c.2735_2741delinsCTTT	p.Gly912_Pro914delinsAlaPhe	p.G912_P914delinsAF	ENST00000318560	NM_005157.4	912	gGAAAGCCc/gCTTTc	11/11	1	2	FACETS	0.872	0.816	0.928	0.872	0.816	0.928	CLONAL	1	TRUE	1	0.7706272183314	2		356	673	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0003453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	340	348	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	0.295956371785923	5	FACETS	0.948	0.897	1			1	CLONAL	3	TRUE	NA	0.28	5		348	1212	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692896	89692896	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs398123322	NA	P-0003453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	119	188	0	ENST00000371953.3:c.380G>T	p.Gly127Val	p.G127V	ENST00000371953	NM_000314.4	127	gGa/gTa	5/9	0.295956371785923	3	FACETS	0.823	0.745	0.904	0.548	0.496	0.603	CLONAL	2	TRUE	0	0.28	3		188	589	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	415	436	0	ENST00000397062.3:c.246A>T	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaT	2/5	1	2	FACETS	0.864	0.824	0.904	1	0.997	1	CLONAL	3	TRUE	1	0.28	2		436	1144	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11194488	11194488	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	340	426	0	ENST00000361445.4:c.5166G>T	p.Gln1722His	p.Q1722H	ENST00000361445	NM_004958.3	1722	caG/caT	37/58	NA	2	FACETS	0.867	0.822	0.912			1	INDETERMINATE	3	TRUE	NA	0.28	2		426	934	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363189	40363189	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	292	374	1	ENST00000397332.2:c.1040C>G	p.Ala347Gly	p.A347G	ENST00000397332	NM_001033082.2	347	gCc/gGc	3/3	1	2	FACETS	1	0.98	1	1	0.996	1	CLONAL	2	TRUE	1	0.28	2		375	960	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61717911	61717911	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	333	371	0	ENST00000401558.2:c.1888G>A	p.Val630Ile	p.V630I	ENST00000401558	NM_003400.3	630	Gtt/Att	17/25	1	2	FACETS	0.846	0.802	0.891	1	0.997	1	CLONAL	3	TRUE	1	0.28	2		371	937	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86658411	86658411	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	195	309	0	ENST00000274376.6:c.1376T>C	p.Ile459Thr	p.I459T	ENST00000274376	NM_002890.2	459	aTc/aCc	10/25	1	2	FACETS	0.894	0.829	0.961	1	0.993	1	CLONAL	2	TRUE	1	0.28	2		309	779	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520327	176520327	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs762709356	NA	P-0003453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	336	401	0	ENST00000292408.4:c.1246C>T	p.Arg416Ter	p.R416*	ENST00000292408	NM_213647.1	416	Cga/Tga	9/18	1	2	FACETS	0.874	0.829	0.92	1	0.997	1	CLONAL	3	TRUE	1	0.28	2		401	915	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692919	89692919	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782360	NA	P-0003453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	353	244	0	ENST00000371953.3:c.403A>G	p.Ile135Val	p.I135V	ENST00000371953	NM_000314.4	135	Ata/Gta	5/9	0.295956371785923	3	FACETS	1	0.974	1	1	0.995	1	CLONAL	4	TRUE	0	0.28	3		244	699	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481600	56481600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1176464861	NA	P-0003453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	383	450	0	ENST00000267101.3:c.635C>T	p.Pro212Leu	p.P212L	ENST00000267101	NM_001982.3	212	cCt/cTt	6/28	1	2	FACETS	0.858	0.816	0.9	1	0.997	1	CLONAL	3	TRUE	1	0.28	2		450	1063	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805604	46805604	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1369403058	NA	P-0003453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	467	629	0	ENST00000290295.7:c.352G>A	p.Glu118Lys	p.E118K	ENST00000290295	NM_006361.5	118	Gaa/Aaa	1/2	1	2	FACETS	0.905	0.866	0.944	1	0.997	1	CLONAL	3	TRUE	1	0.28	2		629	1229	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420003	41420003	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	293	392	0	ENST00000373198.4:c.318T>A	p.His106Gln	p.H106Q	ENST00000373198	NM_133170.3	106	caT/caA	3/32	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.28	2		392	871	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29115390	29115390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	426	408	0	ENST00000328354.6:c.676C>T	p.Leu226Phe	p.L226F	ENST00000328354	NM_007194.3	226	Ctt/Ttt	5/15	NA	2	FACETS	0.841	0.802	0.88			1	INDETERMINATE	3	TRUE	NA	0.28	2		408	1206	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0003466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	29	510	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.285875564695854	3	FACETS	0.269	0.215	0.332			1	SUBCLONAL	1	FALSE	NA	0.317360526925983	3		510	786	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0003466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	22	292	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.317360526925983	4	FACETS	0.211	0.162	0.268	0.105	0.081	0.134	SUBCLONAL	1	FALSE	2	0.317360526925983	4		292	867	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577035	7577036	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0003466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	256	253	0	ENST00000269305.4:c.902dup	p.Gly302ArgfsTer4	p.G302Rfs*4	ENST00000269305	NM_001126112.2	301	cca/ccCa	8/11	0.317360526925983	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	3	FALSE	0	0.317360526925983	2		253	484	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039133	49039133	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0003466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	191	152	0	ENST00000267163.4:c.2212-1G>C		p.X738_splice	ENST00000267163	NM_000321.2	738			0.317360526925983	4	FACETS	1	0.949	1	1	0.992	1	CLONAL	3	FALSE	2	0.317360526925983	4		152	518	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021437	42021437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	154	560	0	ENST00000219905.7:c.3733G>A	p.Glu1245Lys	p.E1245K	ENST00000219905	NM_001164273.1	1245	Gag/Aag	11/24	0.317360526925983	4	FACETS	1	0.959	1	0.271	0.247	0.296	CLONAL	1	FALSE	0	0.317360526925983	4		560	1181	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677801	58677801	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	33	264	0	ENST00000305921.3:c.26T>C	p.Val9Ala	p.V9A	ENST00000305921	NM_003620.3	9	gTg/gCg	1/6	0.317360526925983	4	FACETS	0.468	0.38	0.567	0.234	0.19	0.284	SUBCLONAL	1	FALSE	2	0.317360526925983	4		264	586	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271918	15271918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1337328035	NA	P-0003466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	11	98	0	ENST00000263388.2:c.6521G>A	p.Arg2174Gln	p.R2174Q	ENST00000263388	NM_000435.2	2174	cGg/cAg	33/33	1	2	FACETS	0.398	0.275	0.55	0.398	0.275	0.55	SUBCLONAL	1	FALSE	1	0.317360526925983	2		98	174	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210293	123210293	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	421	375	0	ENST00000218089.9:c.2645C>G	p.Ala882Gly	p.A882G	ENST00000218089	NM_001042749.1	882	gCt/gGt	26/35	0.317360526925983	1	FACETS	1	0.98	1	1	0.998	1	CLONAL	3	FALSE	0	0.317360526925983	1		375	724	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0003466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	155	337	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	0.317360526925983	0	FACETS	0.842	0.78	0.905			1	CLONAL	2	FALSE	0	0.317360526925983	0		337	396	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946302	2946302	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	268	358	0	ENST00000396946.4:c.3435G>T	p.Lys1145Asn	p.K1145N	ENST00000396946	NM_032415.4	1145	aaG/aaT	25/25	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.894378143807728	2		358	578	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864715	57864715	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	404	456	0	ENST00000228682.2:c.2192G>C	p.Gly731Ala	p.G731A	ENST00000228682	NM_005269.2	731	gGa/gCa	12/12	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.894378143807728	2		456	860	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631836	90631836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	144	293	0	ENST00000330062.3:c.517C>T	p.His173Tyr	p.H173Y	ENST00000330062	NM_002168.2	173	Cac/Tac	4/11	0.587000419575438	5	FACETS	0.834	0.76	0.911			1	CLONAL	1	TRUE	NA	0.894378143807728	5		293	904	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872079	76872079	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0003476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	419	451	0	ENST00000373344.5:c.5566+2T>C		p.X1856_splice	ENST00000373344	NM_000489.3	1856			0.894378143807728	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.894378143807728	1		451	472	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0003483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	107	283	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.252209862966361	1	FACETS	0.924	0.831	1	0.924	0.831	1	CLONAL	1	TRUE	0	0.32	1		283	608	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0003483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	91	792	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.248313612813916	1	FACETS	0.791	0.703	0.884	0.791	0.703	0.884	SUBCLONAL	1	TRUE	0	0.32	1		792	604	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11297917	11297917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1331182647	NA	P-0003483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	26	389	1	ENST00000361445.4:c.2191C>T	p.Arg731Cys	p.R731C	ENST00000361445	NM_004958.3	731	Cgc/Tgc	13/58	0.252209862966361	1	FACETS	0.293	0.231	0.364	0.293	0.231	0.364	SUBCLONAL	1	TRUE	0	0.32	1		390	466	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951964	178951964	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	86	427	0	ENST00000263967.3:c.3019G>C	p.Gly1007Arg	p.G1007R	ENST00000263967	NM_006218.2	1007	Ggc/Cgc	21/21	1	2	FACETS	0.78	0.69	0.876	0.78	0.69	0.876	SUBCLONAL	1	TRUE	1	0.32	2		427	689	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437605	56437605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329721997	NA	P-0003483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	49	513	0	ENST00000407977.2:c.857G>A	p.Arg286Gln	p.R286Q	ENST00000407977		286	cGg/cAg	8/10	0.248313612813916	1	FACETS	0.684	0.581	0.797	0.684	0.581	0.797	SUBCLONAL	1	TRUE	0	0.32	1		513	376	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0003493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	552	205	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.77415670955278	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	1	0.77415670955278	3		205	848	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0003493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	142	365	0	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	1	2	FACETS	0.572	0.523	0.624	0.572	0.523	0.624	SUBCLONAL	1	TRUE	1	0.77415670955278	2		365	641	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378348	225378348	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs369362585	NA	P-0003493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	145	255	0	ENST00000264414.4:c.547A>G	p.Ile183Val	p.I183V	ENST00000264414	NM_003590.4	183	Ata/Gta	5/16	1	2	FACETS	0.941	0.868	1	0.941	0.868	1	CLONAL	1	TRUE	1	0.77415670955278	2		255	398	SUCCESS
ATR	545	MSKCC	GRCh37	3	142224052	142224052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	508	339	0	ENST00000350721.4:c.5125C>T	p.His1709Tyr	p.H1709Y	ENST00000350721	NM_001184.3	1709	Cat/Tat	29/47	0.77415670955278	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.77415670955278	3		339	883	SUCCESS
ATR	545	MSKCC	GRCh37	3	142232464	142232464	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	190	253	0	ENST00000350721.4:c.4520C>A	p.Ala1507Asp	p.A1507D	ENST00000350721	NM_001184.3	1507	gCc/gAc	26/47	0.77415670955278	3	FACETS	1	0.955	1	0.519	0.482	0.557	CLONAL	1	TRUE	1	0.77415670955278	3		253	656	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118902	115118928	+	inframe_deletion	In_Frame_Del	DEL	CTTTTTTATCCAGCCCAGAACATCTCA	CTTTTTTATCCAGCCCAGAACATCTCA	-	novel	NA	P-0003493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	111	255	0	ENST00000257566.3:c.413_439del	p.Val138_Lys146del	p.V138_K146del	ENST00000257566	NM_016569.3	138	gTGAGATGTTCTGGGCTGGATAAAAAAGcc/gcc	2/8	1	2	FACETS	0.676	0.612	0.743	0.676	0.612	0.743	SUBCLONAL	1	TRUE	1	0.77415670955278	2		255	424	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061206	38061217	+	inframe_deletion	In_Frame_Del	DEL	GCGCAAGTAGCA	GCGCAAGTAGCA	-	novel	NA	P-0003493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	124	212	0	ENST00000250448.2:c.772_783del	p.Cys258_Arg261del	p.C258_R261del	ENST00000250448	NM_004496.3	258	TGCTACTTGCGC/-	2/2	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.77415670955278	2		212	311	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	183	192	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.788	0.744	0.831			1	INDETERMINATE	2	TRUE	NA	0.776672866541281	2		192	299	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793368	242793368	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	447	293	0	ENST00000334409.5:c.709C>G	p.Pro237Ala	p.P237A	ENST00000334409	NM_005018.2	237	Ccc/Gcc	5/5	0.776672866541281	2	FACETS	1	0.995	1	0.639	0.614	0.665	CLONAL	1	TRUE	0	0.776672866541281	2		293	900	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30664751	30664751	+	intron_variant	Intron	SNP	A	A	T	novel	NA	P-0003504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	119	248	0	ENST00000295754.5:c.94+16282A>T		p.*32*	ENST00000295754	NM_003242.5	52/592			NA	2	FACETS	0.426	0.385	0.47			1	INDETERMINATE	1	TRUE	NA	0.776672866541281	2		248	719	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268798	41268798	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	358	320	0	ENST00000349496.5:c.1036G>T	p.Val346Leu	p.V346L	ENST00000349496	NM_001904.3	346	Gtg/Ttg	7/15	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.776672866541281	2		320	812	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56474143	56474143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs34379766	NA	P-0003504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	1171	294	2	ENST00000267101.3:c.59C>T	p.Ser20Phe	p.S20F	ENST00000267101	NM_001982.3	20	tCc/tTc	1/28	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.776672866541281	NA		296	1756	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	1405	410	1	ENST00000267101.3:c.273G>A	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atA	3/28	0.776672866541281	4	FACETS	1	0.995	1			1	CLONAL	3	TRUE	NA	0.776672866541281	4		411	2071	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2111975	2111975	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1555501123	NA	P-0003504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	341	281	0	ENST00000219476.3:c.1223T>G	p.Phe408Cys	p.F408C	ENST00000219476	NM_000548.3	408	tTt/tGt	12/42	0.591734758735393	3	FACETS	1	0.982	1	0.54	0.511	0.57	CLONAL	1	TRUE	1	0.776672866541281	3		281	1128	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217447	7217447	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	678	442	0	ENST00000380728.2:c.349C>T	p.Gln117Ter	p.Q117*	ENST00000380728		117	Cag/Tag	5/11	0.776672866541281	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.776672866541281	1		442	942	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868216	37868216	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3133	452	290	0	ENST00000269571.5:c.937C>G	p.Leu313Val	p.L313V	ENST00000269571		313	Ctc/Gtc	8/27	0.776672866541281	9	FACETS	1	0.992	1			1	CLONAL	1	TRUE	NA	0.776672866541281	9		290	3585	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5258064	5258064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759053243	NA	P-0003504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	577	286	0	ENST00000357368.4:c.670G>A	p.Val224Met	p.V224M	ENST00000357368	NM_002850.3	224	Gtg/Atg	8/38	0.313571854848374	3	FACETS	0.913	0.881	0.945	0.913	0.881	0.945	INDETERMINATE	2	TRUE	1	0.776672866541281	3		286	1130	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548243	41548243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775368605	NA	P-0003504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	351	341	0	ENST00000263253.7:c.3031G>A	p.Glu1011Lys	p.E1011K	ENST00000263253	NM_001429.3	1011	Gaa/Aaa	16/31	0.24759022690072	2	FACETS	1	0.995	1	0.667	0.637	0.696	INDETERMINATE	1	TRUE	0	0.776672866541281	2		341	678	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	624	237	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	0.377433110709374	2	FACETS	1	0.996	1			1	INDETERMINATE	2	TRUE	NA	0.776672866541281	2		237	748	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040630	47040630	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	140	148	0	ENST00000377604.3:c.1265A>G	p.Glu422Gly	p.E422G	ENST00000377604	NM_001204468.1	422	gAg/gGg	13/24	0.377433110709374	2	FACETS	0.574	0.524	0.626			1	INDETERMINATE	1	TRUE	NA	0.776672866541281	2		148	628	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0003514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	280	510	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.211299065179196	3	FACETS	0.781	0.736	0.826	0.781	0.736	0.826	INDETERMINATE	2	TRUE	1	0.572098326180899	3		510	806	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440943	56440943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786205215	NA	P-0003514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	389	225	1	ENST00000407977.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000407977		132	Cga/Tga	4/10	0.551225756931606	3	FACETS	0.934	0.899	0.969	0.934	0.899	0.969	CLONAL	3	TRUE	0	0.572098326180899	3		226	624	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158452	26158452	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs749866903	NA	P-0003514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	226	215	0	ENST00000289316.2:c.55G>T	p.Val19Leu	p.V19L	ENST00000289316	NM_138720.2	19	Gtg/Ttg	1/2	0.182871647908103	4	FACETS	0.87	0.814	0.927	0.87	0.814	0.927	INDETERMINATE	2	TRUE	2	0.572098326180899	4		215	714	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514436	125514436	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	63	246	0	ENST00000428830.2:c.1131G>A	p.Met377Ile	p.M377I	ENST00000428830	NM_001114121.2	377	atG/atA	11/14	NA	2	FACETS	0.275	0.237	0.317			1	INDETERMINATE	1	TRUE	NA	0.572098326180899	2		246	800	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577144	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs879253942	NA	P-0003514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	316	299	1	ENST00000269305.4:c.794T>C	p.Leu265Pro	p.L265P	ENST00000269305	NM_001126112.2	265	cTg/cCg	8/11	0.401055746552509	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.572098326180899	1		300	635	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554354	63554354	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	536	298	0	ENST00000307078.5:c.385C>T	p.Arg129Ter	p.R129*	ENST00000307078	NM_004655.3	129	Cga/Tga	2/11	0.551225756931606	3	FACETS	0.937	0.907	0.967	0.937	0.907	0.967	CLONAL	3	TRUE	0	0.572098326180899	3		298	857	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	54	283	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.113126101511493	0	FACETS	0.32	0.276	0.368			1	INDETERMINATE	1	TRUE	0	0.56	0		283	265	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057788	27057788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748935625	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	66	505	0	ENST00000324856.7:c.1496C>T	p.Ser499Leu	p.S499L	ENST00000324856	NM_006015.4	499	tCg/tTg	3/20	1	2	FACETS	0.286	0.248	0.328	0.286	0.248	0.328	SUBCLONAL	1	TRUE	1	0.56	2		505	823	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932136	36932136	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759549054	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	171	504	1	ENST00000361632.4:c.2333C>T	p.Ala778Val	p.A778V	ENST00000361632		778	gCg/gTg	16/16	1	2	FACETS	0.98	0.906	1	0.98	0.906	1	CLONAL	1	TRUE	1	0.56	2		505	623	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248444	212248444	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397514263	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	145	336	0	ENST00000342788.4:c.3823C>T	p.Arg1275Trp	p.R1275W	ENST00000342788	NM_005235.2	1275	Cgg/Tgg	28/28	1	2	FACETS	0.848	0.776	0.922	0.848	0.776	0.922	CLONAL	1	TRUE	1	0.56	2		336	611	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164921	47164921	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182736967	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	94	316	0	ENST00000409792.3:c.1205G>A	p.Arg402Gln	p.R402Q	ENST00000409792	NM_014159.6	402	cGg/cAg	3/21	1	2	FACETS	0.872	0.782	0.967	0.872	0.782	0.967	CLONAL	1	TRUE	1	0.56	2		316	385	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447754	187447754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754091486	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	96	201	0	ENST00000232014.4:c.439C>T	p.Arg147Trp	p.R147W	ENST00000232014	NM_001130845.1	147	Cgg/Tgg	5/10	1	2	FACETS	0.741	0.663	0.822	0.741	0.663	0.822	SUBCLONAL	1	TRUE	1	0.56	2		201	463	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	82	225	0	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.56	2		225	242	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806108	1806108	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs767787097	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	171	343	0	ENST00000260795.2:c.1127T>C	p.Ile376Thr	p.I376T	ENST00000260795		376	aTc/aCc	8/17	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.56	2		343	509	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155851	106155851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1332525138	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	46	341	0	ENST00000380013.4:c.752C>T	p.Ala251Val	p.A251V	ENST00000380013	NM_001127208.2	251	gCc/gTc	3/11	1	2	FACETS	0.321	0.27	0.377	0.321	0.27	0.377	SUBCLONAL	1	TRUE	1	0.56	2		341	512	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665274	176665274	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121908070	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	114	290	0	ENST00000439151.2:c.3958C>T	p.Arg1320Ter	p.R1320*	ENST00000439151	NM_022455.4	1320	Cga/Tga	7/23	1	2	FACETS	0.77	0.696	0.847	0.77	0.696	0.847	SUBCLONAL	1	TRUE	1	0.56	2		290	529	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100323	157100323	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	136	200	0	ENST00000346085.5:c.1260T>A	p.Asn420Lys	p.N420K	ENST00000346085	NM_020732.3	420	aaT/aaA	1/20	0.113896831846978	3	FACETS	1	0.986	1	0.708	0.649	0.769	INDETERMINATE	1	TRUE	1	0.56	3		200	439	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509421	106509421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751167601	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	107	381	1	ENST00000359195.3:c.1415G>A	p.Arg472His	p.R472H	ENST00000359195	NM_002649.2	472	cGt/cAt	2/11	1	2	FACETS	0.564	0.506	0.625	0.564	0.506	0.625	SUBCLONAL	1	TRUE	1	0.56	2		382	678	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	62	153	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.56	2		153	199	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779129	135779129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	71	342	0	ENST00000298552.3:c.2117G>A	p.Arg706His	p.R706H	ENST00000298552	NM_001162426.1	706	cGt/cAt	17/23	1	2	FACETS	0.375	0.327	0.427	0.375	0.327	0.427	SUBCLONAL	1	TRUE	1	0.56	2		342	676	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63760023	63760023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	140	265	0	ENST00000279873.7:c.676C>T	p.Arg226Trp	p.R226W	ENST00000279873	NM_032199.2	226	Cgg/Tgg	4/10	0.3	3	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.56	3		265	535	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205807	108205807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782719	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	64	245	0	ENST00000278616.4:c.8122G>A	p.Asp2708Asn	p.D2708N	ENST00000278616	NM_000051.3	2708	Gat/Aat	55/63	1	2	FACETS	0.796	0.696	0.903	0.796	0.696	0.903	CLONAL	1	TRUE	1	0.56	2		245	287	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236087	108236087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781894	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	132	364	1	ENST00000278616.4:c.9023G>A	p.Arg3008His	p.R3008H	ENST00000278616	NM_000051.3	3008	cGt/cAt	63/63	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.56	2		365	471	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352585	118352585	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555039343	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	166	422	1	ENST00000534358.1:c.3790C>T	p.Arg1264Ter	p.R1264*	ENST00000534358	NM_005933.3	1264	Cga/Tga	7/36	1	2	FACETS	0.863	0.795	0.933	0.863	0.795	0.933	CLONAL	1	TRUE	1	0.56	2		423	687	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418670	49418670	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783698	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	186	315	0	ENST00000301067.7:c.15844C>T	p.Arg5282Ter	p.R5282*	ENST00000301067	NM_003482.3	5282	Cga/Tga	49/54	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.56	2		315	647	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254192	133254192	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500835	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	174	412	2	ENST00000320574.5:c.692G>A	p.Arg231His	p.R231H	ENST00000320574	NM_006231.2	231	cGc/cAc	7/49	1	2	FACETS	0.878	0.81	0.947	0.878	0.81	0.947	CLONAL	1	TRUE	1	0.56	2		414	708	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134823	41134823	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	218	594	0	ENST00000379561.5:c.805C>T	p.Arg269Ter	p.R269*	ENST00000379561	NM_002015.3	269	Cga/Tga	2/3	1	2	FACETS	0.934	0.87	0.999	0.934	0.87	0.999	CLONAL	1	TRUE	1	0.56	2		594	834	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647754	2647754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs901482387	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	115	243	0	ENST00000342085.4:c.1657G>A	p.Ala553Thr	p.A553T	ENST00000342085	NM_002613.4	553	Gcc/Acc	14/14	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.56	2		243	397	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15967400	15967400	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567787429	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	195	335	1	ENST00000268712.3:c.5203G>A	p.Asp1735Asn	p.D1735N	ENST00000268712	NM_006311.3	1735	Gac/Aac	35/46	1	2	FACETS	0.935	0.868	1	0.935	0.868	1	CLONAL	1	TRUE	1	0.56	2		336	745	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974781	15974781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1454297938	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	99	456	0	ENST00000268712.3:c.4094G>A	p.Arg1365Gln	p.R1365Q	ENST00000268712	NM_006311.3	1365	cGg/cAg	30/46	1	2	FACETS	0.854	0.768	0.945	0.854	0.768	0.945	CLONAL	1	TRUE	1	0.56	2		456	414	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554008	63554008	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199798353	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	174	382	2	ENST00000307078.5:c.731C>T	p.Ser244Leu	p.S244L	ENST00000307078	NM_004655.3	244	tCg/tTg	2/11	1	2	FACETS	0.87	0.803	0.94	0.87	0.803	0.94	CLONAL	1	TRUE	1	0.56	2		384	714	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211167	2211167	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759039532	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	195	302	0	ENST00000398665.3:c.1421C>T	p.Pro474Leu	p.P474L	ENST00000398665	NM_032482.2	474	cCg/cTg	15/28	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.56	2		302	567	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143985	11143985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	166	239	0	ENST00000358026.2:c.3566G>A	p.Arg1189Gln	p.R1189Q	ENST00000358026	NM_001128849.1	1189	cGa/cAa	26/36	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.56	2		239	561	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743883	41743883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374699228	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	182	391	0	ENST00000301178.4:c.818C>T	p.Ala273Val	p.A273V	ENST00000301178	NM_021913.4	273	gCg/gTg	7/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.56	2		391	622	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921170	50921170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375328523	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	130	459	0	ENST00000440232.2:c.3290G>A	p.Arg1097Gln	p.R1097Q	ENST00000440232	NM_002691.3	1097	cGg/cAg	27/27	1	2	FACETS	0.66	0.6	0.724	0.66	0.6	0.724	SUBCLONAL	1	TRUE	1	0.56	2		459	703	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770588	40770588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1389160956	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	111	274	1	ENST00000373198.4:c.2794C>T	p.Arg932Cys	p.R932C	ENST00000373198	NM_133170.3	932	Cgc/Tgc	19/32	1	2	FACETS	0.843	0.762	0.928	0.843	0.762	0.928	CLONAL	1	TRUE	1	0.56	2		275	470	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424204	47424204	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199527940	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	42	173	0	ENST00000377045.4:c.209C>T	p.Thr70Met	p.T70M	ENST00000377045	NM_001654.4	70	aCg/aTg	4/16	1	1	FACETS	0.28	0.234	0.331	0.28	0.234	0.331	SUBCLONAL	1	TRUE	0	0.56	1		173	386	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940012	76940012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs122445105	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	132	226	0	ENST00000373344.5:c.736C>T	p.Arg246Cys	p.R246C	ENST00000373344	NM_000489.3	246	Cgc/Tgc	9/35	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.56	1		226	253	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	145	404	3	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.955	0.876	1	0.955	0.876	1	CLONAL	1	TRUE	1	0.56	2		407	542	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	151	490	1	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.56	2		491	517	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	98	333	1	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.829	0.745	0.918	0.829	0.745	0.918	CLONAL	1	TRUE	1	0.56	2		334	422	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	112	309	2	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.885	0.801	0.973	0.885	0.801	0.973	CLONAL	1	TRUE	1	0.56	2		311	452	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	160	384	0	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.854	0.786	0.925	0.854	0.786	0.925	CLONAL	1	TRUE	1	0.56	2		384	669	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	55	263	4	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	0.897	0.777	1	0.897	0.777	1	CLONAL	1	TRUE	1	0.56	2		267	219	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781157	135781157	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	48	618	1	ENST00000298552.3:c.1808del	p.Pro603ArgfsTer26	p.P603Rfs*26	ENST00000298552	NM_001162426.1	603	cCg/cg	15/23	1	2	FACETS	0.219	0.184	0.258	0.219	0.184	0.258	SUBCLONAL	1	TRUE	1	0.56	2		619	782	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49423190	49423196	+	frameshift_variant	Frame_Shift_Del	DEL	TCCTCAG	TCCTCAG	-	novel	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	141	303	0	ENST00000301067.7:c.14063_14069del	p.Thr4688MetfsTer107	p.T4688Mfs*107	ENST00000301067	NM_003482.3	4688	aCTGAGGAt/at	43/54	1	2	FACETS	0.904	0.828	0.983	0.904	0.828	0.983	CLONAL	1	TRUE	1	0.56	2		303	557	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772951	135772951	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs118203724	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	27	318	3	ENST00000298552.3:c.2672del	p.Asn891ThrfsTer40	p.N891Tfs*40	ENST00000298552	NM_001162426.1	891	aAc/ac	21/23	1	2	FACETS	0.22	0.175	0.272	0.22	0.175	0.272	SUBCLONAL	1	TRUE	1	0.56	2		321	438	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0003524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	183	710	5	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.56	2		715	621	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0003540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	83	510	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.169258227747733	3	FACETS	0.894	0.79	1	0.894	0.79	1	CLONAL	2	FALSE	1	0.176079270359502	3		510	574	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0003540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	81	792	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.154002051926216	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	2	FALSE	0	0.176079270359502	2		792	443	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713864	30713864	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs863223845	NA	P-0003540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	30	266	0	ENST00000295754.5:c.1189G>T	p.Asp397Tyr	p.D397Y	ENST00000295754	NM_003242.5	397	Gac/Tac	4/7	0.0657758900298608	3	FACETS	1	0.846	1			1	INDETERMINATE	1	FALSE	NA	0.176079270359502	3		266	351	SUCCESS
EED	8726	MSKCC	GRCh37	11	85956357	85956357	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	28	188	1	ENST00000263360.6:c.86G>A	p.Ser29Asn	p.S29N	ENST00000263360	NM_003797.3	29	aGc/aAc	1/12	0.176079270359502	3	FACETS	1	0.853	1	0.541	0.433	0.663	CLONAL	1	FALSE	1	0.176079270359502	3		189	320	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0003547-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	112	646	4	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.449556246347026	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.449556246347026	1		650	324	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220574	1220607	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCACAGGCACTGCACCCGTTCGCGGCGGACGACA	CCACAGGCACTGCACCCGTTCGCGGCGGACGACA	-	novel	NA	P-0003547-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	76	334	0	ENST00000326873.7:c.598-4_627del		p.X200_splice	ENST00000326873	NM_000455.4	200		5/10	NA	2	FACETS	0.894	0.789	1			1	INDETERMINATE	1	TRUE	NA	0.449556246347026	2		334	378	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573507	48573518	+	frameshift_variant	Frame_Shift_Del	DEL	GAGAGTGAAACA	GAGAGTGAAACA	TT	novel	NA	P-0003547-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	86	323	0	ENST00000342988.3:c.91_102delinsTT	p.Glu31PhefsTer11	p.E31Ffs*11	ENST00000342988	NM_005359.5	31	GAGAGTGAAACA/TT	2/12	0.416914431689137	1	FACETS	0.705	0.627	0.787	0.705	0.627	0.787	SUBCLONAL	1	TRUE	0	0.449556246347026	1		323	421	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	42	300	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.715743211801683	3	FACETS	0.176	0.146	0.209	0.059	0.048	0.07	SUBCLONAL	1	TRUE	0	0.715743211801683	3		300	908	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	60	324	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.715743211801683	3	FACETS	0.287	0.247	0.332	0.096	0.082	0.111	SUBCLONAL	1	TRUE	0	0.715743211801683	3		324	792	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0003551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	3050	573	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.715743211801683	13	FACETS	1	0.998	1			1	CLONAL	11	TRUE	NA	0.715743211801683	13		573	3661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0003551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	622	1100	1	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.584367825839175	2	FACETS	0.825	0.8	0.851	0.825	0.8	0.851	CLONAL	2	TRUE	0	0.715743211801683	2		1101	1053	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254863	16254863	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	134	743	0	ENST00000375759.3:c.2128G>C	p.Glu710Gln	p.E710Q	ENST00000375759	NM_015001.2	710	Gag/Cag	11/15	0.653035022578632	3	FACETS	0.636	0.578	0.696	0.318	0.289	0.348	SUBCLONAL	1	TRUE	1	0.715743211801683	3		743	800	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858570	57858570	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	163	977	0	ENST00000228682.2:c.308C>G	p.Pro103Arg	p.P103R	ENST00000228682	NM_005269.2	103	cCc/cGc	4/12	0.583369884493619	2	FACETS	0.493	0.452	0.536	0.246	0.226	0.268	SUBCLONAL	1	TRUE	0	0.715743211801683	2		977	924	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56875697	56875697	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	522	805	0	ENST00000308159.5:c.2301T>G	p.Ser767Arg	p.S767R	ENST00000308159	NM_014669.4	767	agT/agG	21/22	0.540690785597265	3	FACETS	1	0.996	1	0.799	0.774	0.825	CLONAL	2	TRUE	0	0.715743211801683	3		805	826	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578486	7578486	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	640	1115	1	ENST00000269305.4:c.444T>A	p.Asp148Glu	p.D148E	ENST00000269305	NM_001126112.2	148	gaT/gaA	5/11	0.584367825839175	2	FACETS	0.824	0.799	0.849	0.824	0.799	0.849	CLONAL	2	TRUE	0	0.715743211801683	2		1116	1085	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752425	55752425	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756674568	NA	P-0003551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	103	1084	1	ENST00000284073.2:c.883G>A	p.Val295Met	p.V295M	ENST00000284073	NM_138962.2	295	Gtg/Atg	12/14	0.547844167428176	3	FACETS	0.34	0.303	0.379	0.113	0.101	0.127	SUBCLONAL	1	TRUE	0	0.715743211801683	3		1085	1150	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986782	36986782	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	29	236	0	ENST00000354822.5:c.907G>T	p.Gly303Cys	p.G303C	ENST00000354822	NM_001079668.2	303	Ggt/Tgt	3/3	0.266358716147616	5	FACETS	0.455	0.365	0.558	0.091	0.073	0.112	INDETERMINATE	1	TRUE	0	0.715743211801683	5		236	369	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760922	59760922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	82	908	1	ENST00000259008.2:c.3485C>T	p.Ser1162Leu	p.S1162L	ENST00000259008	NM_032043.2	1162	tCa/tTa	20/20	0.547844167428176	3	FACETS	0.315	0.277	0.356	0.105	0.092	0.119	SUBCLONAL	1	TRUE	0	0.715743211801683	3		909	988	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131178	55131178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854832	NA	P-0003551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	47	762	2	ENST00000257290.5:c.721G>A	p.Glu241Lys	p.E241K	ENST00000257290	NM_006206.4	241	Gag/Aag	5/23	0.568016072373654	2	FACETS	0.179	0.151	0.211	0.09	0.075	0.106	SUBCLONAL	1	TRUE	0	0.715743211801683	2		764	732	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412776	63412776	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	63	809	0	ENST00000330258.3:c.391C>G	p.Gln131Glu	p.Q131E	ENST00000330258	NM_152424.3	131	Cag/Gag	2/2	0.520409797199561	3	FACETS	0.301	0.259	0.346	0.1	0.086	0.116	SUBCLONAL	1	TRUE	0	0.715743211801683	3		809	795	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0003557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	337	585	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.69395796437862	6	FACETS	0.917	0.877	0.958	0.917	0.877	0.958	CLONAL	4	TRUE	2	0.69395796437862	6		585	632	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582168	189582168	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121908835	NA	P-0003557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	189	495	0	ENST00000264731.3:c.727C>T	p.Arg243Trp	p.R243W	ENST00000264731	NM_003722.4	243	Cgg/Tgg	5/14	0.69395796437862	6	FACETS	1	0.949	1	0.514	0.477	0.552	CLONAL	2	TRUE	2	0.69395796437862	6		495	633	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914305	32914305	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	376	849	2	ENST00000380152.3:c.5813G>T	p.Gly1938Val	p.G1938V	ENST00000380152		1938	gGa/gTa	11/27	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	2	TRUE	NA	0.69395796437862	2		851	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1064795203	NA	P-0003564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	86	254	0	ENST00000269305.4:c.532C>G	p.His178Asp	p.H178D	ENST00000269305	NM_001126112.2	178	Cac/Gac	5/11	0.338336225213627	1	FACETS	0.775	0.698	0.856	0.775	0.698	0.856	INDETERMINATE	1	TRUE	0	0.635715826765228	1		254	238	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599332	55599332	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519710	NA	P-0003564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	149	383	0	ENST00000288135.5:c.2458G>T	p.Asp820Tyr	p.D820Y	ENST00000288135	NM_000222.2	820	Gat/Tat	17/21	0.338336225213627	1	FACETS	0.888	0.823	0.955	0.888	0.823	0.955	INDETERMINATE	1	TRUE	0	0.635715826765228	1		383	360	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	35	192	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	FALSE	1	0.553286328922559	2		192	105	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637689	52637689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	144	427	0	ENST00000394830.3:c.2627G>A	p.Arg876His	p.R876H	ENST00000394830	NM_018313.4	876	cGt/cAt	18/30	1	2	FACETS	0.893	0.818	0.971	0.893	0.818	0.971	CLONAL	1	FALSE	1	0.553286328922559	2		427	583	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720677	89720677	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	15	63	0	ENST00000371953.3:c.828T>G	p.Asn276Lys	p.N276K	ENST00000371953	NM_000314.4	276	aaT/aaG	8/9	0.553286328922559	1	FACETS	0.484	0.361	0.627	0.484	0.361	0.627	SUBCLONAL	1	FALSE	0	0.553286328922559	1		63	81	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546134	29546134	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	78	258	0	ENST00000356175.3:c.1639G>T	p.Glu547Ter	p.E547*	ENST00000356175	NM_000267.3	547	Gag/Tag	14/57	1	2	FACETS	0.972	0.864	1	0.972	0.864	1	CLONAL	1	FALSE	1	0.553286328922559	2		258	290	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0003577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	95	381	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.25629541753376	3	FACETS	1	0.975	1	0.661	0.59	0.737	CLONAL	1	TRUE	1	0.281644323048063	3		382	582	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606101	47606101	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	71	266	0	ENST00000263735.4:c.565A>G	p.Asn189Asp	p.N189D	ENST00000263735	NM_002354.2	189	Aat/Gat	6/9	1	2	FACETS	0.875	0.765	0.995	0.875	0.765	0.995	CLONAL	1	TRUE	1	0.281644323048063	2		266	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579861	7579861	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs876658627	NA	P-0003577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	91	340	0	ENST00000269305.4:c.52del	p.Thr18HisfsTer26	p.T18Hfs*26	ENST00000269305	NM_001126112.2	18	Aca/ca	2/11	0.196195729111079	2	FACETS	1	0.978	1	0.71	0.633	0.791	CLONAL	1	TRUE	0	0.281644323048063	2		340	455	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0003580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	60	302	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.3	2	FACETS	0.759	0.653	0.876			1	SUBCLONAL	1	TRUE	NA	0.2	2		302	790	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46240659	46240659	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	235	190	0	ENST00000334344.6:c.1519C>T	p.Gln507Ter	p.Q507*	ENST00000334344	NM_152641.2	507	Cag/Tag	12/21	0.3	5	FACETS	0.922	0.865	0.979			1	CLONAL	5	TRUE	NA	0.2	5		190	663	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256532	115256532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267606920	NA	P-0003580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	78	379	0	ENST00000369535.4:c.179G>A	p.Gly60Glu	p.G60E	ENST00000369535	NM_002524.4	60	gGa/gAa	3/7	1	2	FACETS	0.986	0.865	1	0.986	0.865	1	CLONAL	1	TRUE	1	0.2	2		379	791	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435269	49435269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374216845	NA	P-0003580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	149	194	0	ENST00000301067.7:c.6284G>A	p.Arg2095His	p.R2095H	ENST00000301067	NM_003482.3	2095	cGt/cAt	31/54	0.3	5	FACETS	0.94	0.865	1			1	CLONAL	4	TRUE	NA	0.2	5		194	515	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40467798	40467798	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	81	483	0	ENST00000264657.5:c.2278G>T	p.Glu760Ter	p.E760*	ENST00000264657	NM_139276.2	760	Gag/Tag	24/24	1	2	FACETS	0.793	0.696	0.896	0.793	0.696	0.896	SUBCLONAL	1	TRUE	1	0.2	2		483	1022	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604656	48604656	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	38	281	0	ENST00000342988.3:c.1478A>G	p.Asp493Gly	p.D493G	ENST00000342988	NM_005359.5	493	gAt/gGt	12/12	1	2	FACETS	0.729	0.602	0.872	0.729	0.602	0.872	SUBCLONAL	1	TRUE	1	0.2	2		281	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577557	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGG	novel	NA	P-0003580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	56	291	0	ENST00000269305.4:c.722_724dup	p.Ser241dup	p.S241dup	ENST00000269305	NM_001126112.2	241	tgc/tCCTgc	7/11	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.2	2		291	550	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	35	192	0				ENST00000310581	NM_198253.2	-/1132			0.253219093984153	4	FACETS	1	0.915	1	1	0.915	1	INDETERMINATE	2	TRUE	2	0.647409393313131	4		192	80	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0003587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	72	172	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			1	2	FACETS	0.997	0.885	1	0.997	0.885	1	CLONAL	1	TRUE	1	0.647409393313131	2		172	223	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265073	198265073	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	98	299	0	ENST00000335508.6:c.2804C>A	p.Thr935Lys	p.T935K	ENST00000335508	NM_012433.2	935	aCa/aAa	19/25	1	2	FACETS	0.863	0.777	0.952	0.863	0.777	0.952	CLONAL	1	TRUE	1	0.647409393313131	2		299	351	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984726	11984726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	19	122	0	ENST00000353533.5:c.272C>T	p.Pro91Leu	p.P91L	ENST00000353533	NM_003010.3	91	cCt/cTt	3/11	1	2	FACETS	0.337	0.257	0.43	0.337	0.257	0.43	SUBCLONAL	1	TRUE	1	0.647409393313131	2		122	174	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508601	38508601	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	111	486	0	ENST00000254066.5:c.649C>G	p.Arg217Gly	p.R217G	ENST00000254066	NM_000964.3	217	Cgt/Ggt	6/9	1	2	FACETS	0.9	0.816	0.987	0.9	0.816	0.987	CLONAL	1	TRUE	1	0.647409393313131	2		486	381	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033948	49033949	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0003587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	94	282	0	ENST00000267163.4:c.2089_2090del	p.Asp697GlnfsTer23	p.D697Qfs*23	ENST00000267163	NM_000321.2	695	atGAga/atga	20/27	0.105247568402907	4	FACETS	1	0.979	1	0.693	0.623	0.767	INDETERMINATE	1	TRUE	2	0.647409393313131	4		282	345	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339258	70339278	+	inframe_deletion	In_Frame_Del	DEL	CAATAACCAGCCTGCTGTCTC	CAATAACCAGCCTGCTGTCTC	-	novel	NA	P-0003587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	159	474	0	ENST00000374080.3:c.135_155del	p.Asn46_Ser52del	p.N46_S52del	ENST00000374080		45	ttCAATAACCAGCCTGCTGTCTCt/ttt	2/45	0.647409393313131	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.647409393313131	1		474	317	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0003597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	53	646	4	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.3496086625916	1	FACETS	1	0.886	1	1	0.979	1	CLONAL	2	TRUE	0	0.3496086625916	1		650	124	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442530	52442530	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	90	316	0	ENST00000460680.1:c.215T>C	p.Ile72Thr	p.I72T	ENST00000460680	NM_004656.3	72	aTt/aCt	4/17	1	2	FACETS	0.964	0.868	1	1	0.986	1	CLONAL	2	TRUE	1	0.3496086625916	2		316	267	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857679	9857679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886042648	NA	P-0003597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	56	429	0	ENST00000330684.3:c.3722G>A	p.Arg1241Gln	p.R1241Q	ENST00000330684	NM_001134407.1	1241	cGg/cAg	13/13	0.3496086625916	3	FACETS	0.853	0.749	0.961	1	0.963	1	CLONAL	3	TRUE	1	0.3496086625916	3		429	147	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540230	23540235	+	inframe_deletion	In_Frame_Del	DEL	GGCTCC	GGCTCC	-	rs753037741	NA	P-0003597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	58	87	0	ENST00000380871.4:c.168_173del	p.Pro62_Glu63del	p.P62_E63del	ENST00000380871	NM_006167.3	56	ccGGAGCCa/cca	1/2	0.3496086625916	1	FACETS	0.938	0.826	1	1	0.98	1	CLONAL	2	TRUE	0	0.3496086625916	1		87	146	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217233	66217233	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1400014333	NA	P-0003615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	28	341	0	ENST00000273854.3:c.2382G>C	p.Met794Ile	p.M794I	ENST00000273854	NM_004439.5	794	atG/atC	14/18	0.318109597763236	2	FACETS	0.401	0.32	0.494	0.201	0.16	0.247	SUBCLONAL	1	TRUE	0	0.318109597763236	2		341	439	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402577	139402577	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751398945	NA	P-0003615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	24	304	0	ENST00000277541.6:c.3340C>T	p.Arg1114Cys	p.R1114C	ENST00000277541	NM_017617.3	1114	Cgc/Tgc	21/34	0.318109597763236	2	FACETS	0.555	0.436	0.691	0.277	0.218	0.346	SUBCLONAL	1	TRUE	0	0.318109597763236	2		304	272	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42790944	42790944	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367972487	NA	P-0003615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	22	459	1	ENST00000575354.2:c.89G>A	p.Arg30His	p.R30H	ENST00000575354	NM_015125.3	30	cGc/cAc	2/20	0.176592492124337	3	FACETS	0.382	0.295	0.483	0.191	0.147	0.242	INDETERMINATE	1	TRUE	1	0.318109597763236	3		460	420	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593667	55593669	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	rs1060502543	NA	P-0003621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	24	218	0	ENST00000288135.5:c.1735_1737del	p.Asp579del	p.D579del	ENST00000288135	NM_000222.2	578	tATGat/tat	11/21	1	2	FACETS	0.103	0.08	0.129	0.103	0.08	0.129	SUBCLONAL	1	TRUE	1	1	2		218	467	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858931	243858931	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	50	321	0	ENST00000263826.5:c.134T>G	p.Val45Gly	p.V45G	ENST00000263826	NM_005465.4	45	gTg/gGg	2/13	0.3	3	FACETS	0.229	0.194	0.268			1	INDETERMINATE	1	TRUE	NA	1	3		321	655	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0003621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	44	239	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.205139534501307	4	FACETS	0.32	0.268	0.378	0.16	0.134	0.189	INDETERMINATE	1	TRUE	2	1	4		239	550	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0003635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	320	392	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.728976356871257	5	FACETS	0.981	0.928	1			1	CLONAL	2	TRUE	NA	0.728976356871257	5		392	937	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0003635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	210	343	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	0.574137316628303	4	FACETS	1	0.99	1	0.346	0.323	0.371	CLONAL	1	TRUE	0	0.728976356871257	4		343	719	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574002	7574002	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs375338359	NA	P-0003635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	434	829	0	ENST00000269305.4:c.1025G>C	p.Arg342Pro	p.R342P	ENST00000269305	NM_001126112.2	342	cGa/cCa	10/11	0.644393089076031	2	FACETS	0.903	0.873	0.933	0.903	0.873	0.933	CLONAL	2	TRUE	0	0.728976356871257	2		829	659	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096370	178096370	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	115	334	0	ENST00000397062.3:c.961G>A	p.Asp321Asn	p.D321N	ENST00000397062	NM_006164.4	321	Gat/Aat	5/5	0.626599014105696	3	FACETS	0.653	0.589	0.721	0.218	0.196	0.241	SUBCLONAL	1	TRUE	0	0.728976356871257	3		334	659	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681058	30681058	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	75	249	0	ENST00000376406.3:c.661G>A	p.Asp221Asn	p.D221N	ENST00000376406	NM_014641.2	221	Gat/Aat	5/15	0.295393508583352	6	FACETS	0.878	0.77	0.994	0.22	0.192	0.249	INDETERMINATE	1	TRUE	2	0.728976356871257	6		249	576	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776783	NA	P-0003635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	117	147	0	ENST00000267163.4:c.1215+1G>A		p.X405_splice	ENST00000267163	NM_000321.2	405			0.690439172474009	1	FACETS	0.788	0.724	0.852	0.788	0.724	0.852	SUBCLONAL	1	TRUE	0	0.728976356871257	1		147	259	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923805	39923805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	151	564	1	ENST00000378444.4:c.3286G>A	p.Glu1096Lys	p.E1096K	ENST00000378444	NM_001123385.1	1096	Gag/Aag	7/15	0.633545062162538	4	FACETS	0.593	0.541	0.648	0.297	0.27	0.324	SUBCLONAL	1	TRUE	2	0.728976356871257	4		565	1207	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003635-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	311	300	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.678358854858971	3	FACETS	0.86	0.829	0.89	0.86	0.829	0.89	CLONAL	3	TRUE	0	0.784569048473541	3		300	428	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0003635-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	54	352	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.784569048473541	3	FACETS	0.158	0.134	0.184	0.079	0.067	0.092	SUBCLONAL	1	TRUE	1	0.784569048473541	3		352	1214	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0003635-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	487	392	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.784569048473541	3	FACETS	0.848	0.815	0.881	0.848	0.815	0.881	CLONAL	2	TRUE	1	0.784569048473541	3		392	1019	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574002	7574002	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs375338359	NA	P-0003635-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	1016	829	0	ENST00000269305.4:c.1025G>C	p.Arg342Pro	p.R342P	ENST00000269305	NM_001126112.2	342	cGa/cCa	10/11	0.678358854858971	3	FACETS	0.922	0.905	0.938	0.922	0.905	0.938	CLONAL	3	TRUE	0	0.784569048473541	3		829	1304	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776783	NA	P-0003635-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	249	147	0	ENST00000267163.4:c.1215+1G>A		p.X405_splice	ENST00000267163	NM_000321.2	405			0.682015749182543	2	FACETS	0.899	0.862	0.935	0.899	0.862	0.935	CLONAL	2	TRUE	0	0.784569048473541	2		147	353	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468297	50468297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343071492	NA	P-0003635-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	42	337	0	ENST00000331340.3:c.1532G>A	p.Arg511Gln	p.R511Q	ENST00000331340	NM_006060.4	511	cGa/cAa	8/8	0.784569048473541	3	FACETS	0.255	0.212	0.302	0.127	0.106	0.151	SUBCLONAL	1	TRUE	1	0.784569048473541	3		337	585	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	58	300	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.292987225807594	5	FACETS	1	0.952	1	0.797	0.697	0.902	CLONAL	2	TRUE	2	0.431853429274208	5		300	185	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0003638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	97	513	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.324653473317773	2	FACETS	0.956	0.869	1	0.956	0.869	1	CLONAL	2	TRUE	0	0.431853429274208	2		515	235	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164792	47164792	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs935586454	NA	P-0003638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	33	139	0	ENST00000409792.3:c.1334G>A	p.Arg445His	p.R445H	ENST00000409792	NM_014159.6	445	cGc/cAc	3/21	0.431853429274208	1	FACETS	0.749	0.618	0.892	0.749	0.618	0.892	SUBCLONAL	1	TRUE	0	0.431853429274208	1		139	160	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424062	49424062	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs886041779	NA	P-0003638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	79	353	0	ENST00000301067.7:c.13999+1G>A		p.X4667_splice	ENST00000301067	NM_003482.3	4667			0.266874119944148	5	FACETS	1	0.958	1	0.77	0.686	0.857	CLONAL	2	TRUE	2	0.431853429274208	5		353	261	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422032	81422032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1263008401	NA	P-0003638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	29	119	0	ENST00000298171.2:c.8C>T	p.Pro3Leu	p.P3L	ENST00000298171	NM_000369.2	3	cCg/cTg	1/10	0.431853429274208	4	FACETS	1	0.877	1	0.556	0.45	0.673	CLONAL	1	TRUE	2	0.431853429274208	4		119	173	SUCCESS
AR	367	MSKCC	GRCh37	X	66766567	66766567	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	47	361	0	ENST00000374690.3:c.1579T>C	p.Trp527Arg	p.W527R	ENST00000374690	NM_000044.3	527	Tgg/Cgg	1/8	0.295642867953881	0	FACETS	0.824	0.71	0.945			1	CLONAL	1	TRUE	0	0.431853429274208	0		361	150	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47061249	47061249	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0003645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	28	571	0	ENST00000409792.3:c.7431+1G>C		p.X2477_splice	ENST00000409792	NM_014159.6	2477			0.548908481898273	1	FACETS	0.733	0.6	0.877	0.733	0.6	0.877	SUBCLONAL	1	TRUE	0	0.548908481898273	1		571	101	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459198	99459198	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	63	547	0	ENST00000268035.6:c.1834T>C	p.Ser612Pro	p.S612P	ENST00000268035	NM_000875.3	612	Tcc/Ccc	9/21	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.548908481898273	2		547	185	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191562	10191563	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0003645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	50	442	0	ENST00000256474.2:c.556dup	p.Glu186GlyfsTer70	p.E186Gfs*70	ENST00000256474	NM_000551.3	185	-/G	3/3	0.548908481898273	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.548908481898273	1		442	118	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595804	52595805	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0003645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	39	496	0	ENST00000394830.3:c.4110_4111del	p.Ala1371GlnfsTer6	p.A1371Qfs*6	ENST00000394830	NM_018313.4	1370	acAGcc/accc	26/30	0.548908481898273	1	FACETS	0.881	0.749	1	0.881	0.749	1	CLONAL	1	TRUE	0	0.548908481898273	1		496	117	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240024	53240034	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CACTGGTAGCA	CACTGGTAGCA	-	novel	NA	P-0003645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	16	286	0	ENST00000375401.3:c.1407_1417del	p.Tyr469Ter	p.Y469*	ENST00000375401	NM_004187.3	469	taTGCTACCAGTGgt/tagt	11/26	0.346129833838637	0	FACETS	0.506	0.388	0.635			1	SUBCLONAL	1	TRUE	NA	0.548908481898273	0		286	52	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713754	30713754	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	41	155	0	ENST00000295754.5:c.1079A>C	p.His360Pro	p.H360P	ENST00000295754	NM_003242.5	360	cAc/cCc	4/7	NA	2	FACETS	0.489	0.409	0.577			1	INDETERMINATE	1	TRUE	NA	0.53416375178823	2		155	314	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0003661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	179	454	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.293966591428815	4	FACETS	1	0.983	1	0.799	0.741	0.858	CLONAL	2	TRUE	1	0.366547029741225	4		454	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0003661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	234	495	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.276384433416763	2	FACETS	0.936	0.878	0.996	0.936	0.878	0.996	CLONAL	2	TRUE	0	0.366547029741225	2		496	682	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644740	67644740	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	170	321	0	ENST00000264010.4:c.5A>T	p.Glu2Val	p.E2V	ENST00000264010	NM_006565.3	2	gAa/gTa	3/12	0.2825245808164	4	FACETS	0.797	0.734	0.863	0.797	0.734	0.863	SUBCLONAL	2	TRUE	2	0.366547029741225	4		321	795	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873809	35873832	+	inframe_deletion	In_Frame_Del	DEL	CTCCATGGCCCACTCCTGGGGGCG	CTCCATGGCCCACTCCTGGGGGCG	-	novel	NA	P-0003661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	43	258	0	ENST00000216797.5:c.19_42del	p.Arg7_Glu14del	p.R7_E14del	ENST00000216797	NM_020529.2	7	CGCCCCCAGGAGTGGGCCATGGAG/-	1/6	0.293966591428815	4	FACETS	0.579	0.484	0.684	0.193	0.161	0.228	SUBCLONAL	1	TRUE	1	0.366547029741225	4		258	554	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713546	30713546	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003668-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	219	183	0	ENST00000295754.5:c.871A>G	p.Lys291Glu	p.K291E	ENST00000295754	NM_003242.5	291	Aag/Gag	4/7	1	2	FACETS	0.969	0.91	1	0.969	0.91	1	CLONAL	1	TRUE	1	0.830532470968993	2		183	544	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48922000	48922000	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1566187856	NA	P-0003668-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	181	196	0	ENST00000267163.4:c.539+1G>A		p.X180_splice	ENST00000267163	NM_000321.2	180			0.830532470968993	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.830532470968993	1		196	242	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99482526	99482526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747578999	NA	P-0003668-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	46	216	0	ENST00000268035.6:c.3394G>A	p.Val1132Ile	p.V1132I	ENST00000268035	NM_000875.3	1132	Gtc/Atc	18/21	1	2	FACETS	0.125	0.105	0.148	0.125	0.105	0.148	SUBCLONAL	1	TRUE	1	0.830532470968993	2		216	886	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855262	76855262	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003668-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	946	164	0	ENST00000373344.5:c.5725G>T	p.Glu1909Ter	p.E1909*	ENST00000373344	NM_000489.3	1909	Gaa/Taa	24/35	0.729963189741096	3	FACETS	1	0.998	1			1	CLONAL	3	TRUE	NA	0.830532470968993	3		164	1027	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577093	7577094	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0003668-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	797	244	0	ENST00000269305.4:c.844_845del	p.Arg282AlafsTer23	p.R282Afs*23	ENST00000269305	NM_001126112.2	282	CGg/g	8/11	0.830532470968993	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.830532470968993	2		244	949	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	19	324	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.3	0.228	0.385	0.3	0.228	0.385	SUBCLONAL	1	TRUE	1	0.51	2		324	248	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518437	204518437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201947927	NA	P-0003671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	38	366	0	ENST00000367182.3:c.1100C>T	p.Ser367Leu	p.S367L	ENST00000367182	NM_001278516.1	367	tCg/tTg	11/11	0.15573698650422	3	FACETS	0.398	0.329	0.475	0.199	0.164	0.238	INDETERMINATE	1	TRUE	1	0.51	3		366	470	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52685760	52685760	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	88	417	0	ENST00000394830.3:c.712C>T	p.Gln238Ter	p.Q238*	ENST00000394830	NM_018313.4	238	Cag/Tag	7/30	0.3	0	FACETS	0.542	0.485	0.601			1	INDETERMINATE	1	TRUE	0	0.51	0		417	312	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097656	8097656	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1399335578	NA	P-0003671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	37	206	0	ENST00000346208.3:c.38A>G	p.His13Arg	p.H13R	ENST00000346208		13	cAc/cGc	2/6	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.51	2		206	121	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188251	10188252	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	136	359	0	ENST00000256474.2:c.397dup	p.Thr133AsnfsTer2	p.T133Nfs*2	ENST00000256474	NM_000551.3	132	caa/cAaa	2/3	0.3	1	FACETS	1	0.974	1	1	0.974	1	INDETERMINATE	1	TRUE	0	0.51	1		359	350	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098964	47098964	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0003671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	90	202	0	ENST00000409792.3:c.6310del	p.Ser2104LeufsTer43	p.S2104Lfs*43	ENST00000409792	NM_014159.6	2104	Tct/ct	15/21	0.3	1	FACETS	1	0.907	1	1	0.907	1	INDETERMINATE	1	TRUE	0	0.51	1		202	261	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155358	106155358	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0003671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	28	329	0	ENST00000380013.4:c.260del	p.Lys87SerfsTer8	p.K87Sfs*8	ENST00000380013	NM_001127208.2	87	Aag/ag	3/11	0.3	1	FACETS	0.222	0.177	0.273	0.222	0.177	0.273	INDETERMINATE	1	TRUE	0	0.51	1		329	368	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637700	52637700	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0003671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	35	342	0	ENST00000394830.3:c.2616del	p.Phe872LeufsTer43	p.F872Lfs*43	ENST00000394830	NM_018313.4	872	ttT/tt	18/30	0.3	0	FACETS	0.234	0.192	0.281			1	INDETERMINATE	1	TRUE	0	0.51	0		342	287	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0003674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	105	198	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.338068731739065	2	FACETS	0.9	0.816	0.987	0.9	0.816	0.987	CLONAL	2	TRUE	0	0.362252981009002	2		198	322	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610099	43610099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760088950	NA	P-0003674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	81	304	0	ENST00000355710.3:c.2051C>T	p.Pro684Leu	p.P684L	ENST00000355710	NM_020975.4	684	cCg/cTg	11/20	1	2	FACETS	0.966	0.854	1	0.966	0.854	1	CLONAL	1	TRUE	1	0.362252981009002	2		304	463	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746086	162746086	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	173	340	0	ENST00000367921.3:c.2209A>T	p.Ser737Cys	p.S737C	ENST00000367921	NM_006182.2	737	Agt/Tgt	16/18	0.209484924148079	5	FACETS	0.935	0.862	1	0.624	0.575	0.674	INDETERMINATE	2	TRUE	2	0.362252981009002	5		340	788	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974730	21974730	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	157	218	0	ENST00000304494.5:c.97G>T	p.Glu33Ter	p.E33*	ENST00000304494	NM_000077.4	33	Gag/Tag	1/3	0.362252981009002	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.362252981009002	2		218	365	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106720	27106720	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770028290	NA	P-0003674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	100	295	0	ENST00000324856.7:c.6331G>A	p.Val2111Ile	p.V2111I	ENST00000324856	NM_006015.4	2111	Gtc/Atc	20/20	0.362252981009002	3	FACETS	1	0.957	1	0.565	0.506	0.628	CLONAL	1	TRUE	1	0.362252981009002	3		295	577	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65316538	65316538	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	89	263	2	ENST00000342505.4:c.1704C>A	p.Tyr568Ter	p.Y568*	ENST00000342505	NM_002227.2	568	taC/taA	12/25	0.362252981009002	3	FACETS	1	0.911	1	0.515	0.457	0.576	CLONAL	1	TRUE	1	0.362252981009002	3		265	564	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566773	212566773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	98	362	0	ENST00000342788.4:c.1408C>T	p.His470Tyr	p.H470Y	ENST00000342788	NM_005235.2	470	Cat/Tat	12/28	0.122078490666093	5	FACETS	1	0.962	1	0.293	0.261	0.327	INDETERMINATE	1	TRUE	1	0.362252981009002	5		362	712	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670683	134670683	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs778514646	NA	P-0003674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	105	347	0	ENST00000398015.3:c.594C>A	p.Ser198Arg	p.S198R	ENST00000398015	NM_004441.4	198	agC/agA	3/16	0.219744743948013	1	FACETS	0.857	0.77	0.948	0.857	0.77	0.948	CLONAL	1	TRUE	0	0.362252981009002	1		347	554	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542182	187542182	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	216	337	0	ENST00000441802.2:c.5558G>A	p.Gly1853Glu	p.G1853E	ENST00000441802	NM_005245.3	1853	gGa/gAa	10/27	0.362252981009002	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.362252981009002	2		337	575	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876109	35876109	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	85	327	0	ENST00000303115.3:c.901G>T	p.Glu301Ter	p.E301*	ENST00000303115	NM_002185.3	301	Gaa/Taa	8/8	0.362252981009002	3	FACETS	0.853	0.754	0.958	0.426	0.377	0.479	CLONAL	1	TRUE	1	0.362252981009002	3		327	650	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187912	32187912	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	59	225	0	ENST00000375023.3:c.1309C>A	p.Leu437Met	p.L437M	ENST00000375023	NM_004557.3	437	Ctg/Atg	7/30	0.362252981009002	6	FACETS	0.902	0.775	1	0.18	0.155	0.208	CLONAL	1	TRUE	1	0.362252981009002	6		225	623	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188394	32188394	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	268	233	0	ENST00000375023.3:c.947A>T	p.Asp316Val	p.D316V	ENST00000375023	NM_004557.3	316	gAt/gTt	6/30	0.362252981009002	6	FACETS	1	0.983	1	0.875	0.829	0.922	CLONAL	4	TRUE	1	0.362252981009002	6		233	583	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729862	41729862	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	215	450	0	ENST00000242208.4:c.667G>T	p.Val223Phe	p.V223F	ENST00000242208	NM_002192.2	223	Gtc/Ttc	3/3	0.350897616853901	4	FACETS	0.992	0.924	1	0.992	0.924	1	CLONAL	2	TRUE	2	0.362252981009002	4		450	815	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739890	41739890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs972161023	NA	P-0003674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	192	398	0	ENST00000242208.4:c.83G>A	p.Gly28Glu	p.G28E	ENST00000242208	NM_002192.2	28	gGg/gAg	2/3	0.350897616853901	4	FACETS	0.989	0.918	1	0.989	0.918	1	CLONAL	2	TRUE	2	0.362252981009002	4		398	730	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334805	81334805	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	217	370	0	ENST00000222390.5:c.1911G>T	p.Met637Ile	p.M637I	ENST00000222390	NM_000601.4	637	atG/atT	17/18	0.350897616853901	4	FACETS	0.933	0.868	0.999	0.933	0.868	0.999	CLONAL	2	TRUE	2	0.362252981009002	4		370	875	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485815	8485815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	188	296	0	ENST00000356435.5:c.3002G>A	p.Gly1001Glu	p.G1001E	ENST00000356435		1001	gGg/gAg	17/35	0.362252981009002	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	0	0.362252981009002	2		296	514	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117353	115117353	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	176	343	0	ENST00000257566.3:c.821C>A	p.Pro274His	p.P274H	ENST00000257566	NM_016569.3	274	cCc/cAc	4/8	NA	2	FACETS	0.868	0.804	0.933			1	INDETERMINATE	2	TRUE	NA	0.362252981009002	2		343	560	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514386	103514386	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	120	186	0	ENST00000355739.4:c.887A>C	p.Gln296Pro	p.Q296P	ENST00000355739	NM_000123.3	296	cAa/cCa	8/15	0.362252981009002	2	FACETS	0.769	0.699	0.841	0.769	0.699	0.841	SUBCLONAL	2	TRUE	0	0.362252981009002	2		186	431	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679697	88679697	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	146	267	0	ENST00000360948.2:c.765+1G>A		p.X255_splice	ENST00000360948	NM_001012338.2	255			0.350897616853901	4	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	2	0.362252981009002	4		267	536	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680683	88680683	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	153	302	0	ENST00000360948.2:c.574G>T	p.Ala192Ser	p.A192S	ENST00000360948	NM_001012338.2	192	Gct/Tct	6/19	0.350897616853901	4	FACETS	0.946	0.869	1	0.946	0.869	1	CLONAL	2	TRUE	2	0.362252981009002	4		302	608	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	359995	359995	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	225	326	1	ENST00000262320.3:c.1094G>T	p.Arg365Leu	p.R365L	ENST00000262320	NM_003502.3	365	cGg/cTg	4/11	0.338068731739065	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.362252981009002	2		327	568	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843492	3843492	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	192	278	0	ENST00000262367.5:c.1111G>C	p.Glu371Gln	p.E371Q	ENST00000262367	NM_004380.2	371	Gag/Cag	4/31	0.338068731739065	2	FACETS	0.938	0.874	1	0.938	0.874	1	CLONAL	2	TRUE	0	0.362252981009002	2		278	565	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857631	9857631	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	147	264	1	ENST00000330684.3:c.3770C>T	p.Thr1257Ile	p.T1257I	ENST00000330684	NM_001134407.1	1257	aCa/aTa	13/13	0.338068731739065	2	FACETS	0.794	0.73	0.861	0.794	0.73	0.861	SUBCLONAL	2	TRUE	0	0.362252981009002	2		265	511	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221994	1221994	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	121	507	0	ENST00000326873.7:c.909C>G	p.Ile303Met	p.I303M	ENST00000326873	NM_000455.4	303	atC/atG	7/10	0.362252981009002	2	FACETS	0.925	0.845	1	0.925	0.845	1	CLONAL	2	TRUE	0	0.362252981009002	2		507	361	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792654	33792654	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	47	29	0	ENST00000498907.2:c.667G>C	p.Gly223Arg	p.G223R	ENST00000498907	NM_004364.3	223	Ggt/Cgt	1/1	0.362252981009002	6	FACETS	0.983	0.866	1			1	CLONAL	5	TRUE	NA	0.362252981009002	6		29	91	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794599	42794599	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs893757075	NA	P-0003674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	148	264	0	ENST00000575354.2:c.1679A>G	p.Gln560Arg	p.Q560R	ENST00000575354	NM_015125.3	560	cAg/cGg	10/20	0.316204678997607	4	FACETS	0.92	0.844	0.999			1	CLONAL	2	TRUE	NA	0.362252981009002	4		264	605	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101039	41101039	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	137	251	0	ENST00000373198.4:c.1317G>T	p.Glu439Asp	p.E439D	ENST00000373198	NM_133170.3	439	gaG/gaT	8/32	NA	2	FACETS	0.871	0.8	0.945			1	INDETERMINATE	2	TRUE	NA	0.362252981009002	2		251	434	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101416	27101417	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0003674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	113	271	0	ENST00000324856.7:c.4703dup	p.Pro1569SerfsTer3	p.P1569Sfs*3	ENST00000324856	NM_006015.4	1566	-/C	18/20	0.362252981009002	3	FACETS	0.853	0.773	0.936	0.853	0.773	0.936	CLONAL	2	TRUE	1	0.362252981009002	3		271	432	SUCCESS
INSRR	3645	MSKCC	GRCh37	1	156811535	156811536	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0003674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	14	14	0	ENST00000368195.3:c.3448_3449delinsAT	p.Gly1150Met	p.G1150M	ENST00000368195	NM_014215.2	1150	GGg/ATg	20/22	0.314346320742809	5	FACETS	1	0.827	1	0.765	0.571	0.981	CLONAL	2	TRUE	2	0.362252981009002	5		14	52	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279971	18279971	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	44	337	0	ENST00000222254.8:c.2054T>G	p.Leu685Arg	p.L685R	ENST00000222254	NM_005027.3	685	cTg/cGg	16/16	1	2	FACETS	0.951	0.797	1	0.951	0.797	1	CLONAL	1	TRUE	1	0.18	2		337	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578229	7578237	+	inframe_deletion	In_Frame_Del	DEL	TCCAAATAC	TCCAAATAC	-	novel	NA	P-0003678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	49	419	0	ENST00000269305.4:c.612_620del	p.Glu204_Leu206del	p.E204_L206del	ENST00000269305	NM_001126112.2	204	gaGTATTTGGAt/gat	6/11	1	2	FACETS	0.739	0.624	0.865	0.739	0.624	0.865	SUBCLONAL	1	TRUE	1	0.18	2		419	737	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	42	192	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.987	0.842	1	0.987	0.842	1	CLONAL	1	TRUE	1	0.64	2		192	133	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0003691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	202	422	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.142933687119702	3	FACETS	1	0.991	1	0.713	0.666	0.762	INDETERMINATE	1	TRUE	1	0.64	3		422	584	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191507	10191507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs5030821	NA	P-0003691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	11	329	1	ENST00000256474.2:c.500G>A	p.Arg167Gln	p.R167Q	ENST00000256474	NM_000551.3	167	cGg/cAg	3/3	0.142933687119702	3	FACETS	0.084	0.058	0.118	0.042	0.029	0.059	INDETERMINATE	1	TRUE	1	0.64	3		330	538	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175873	24175873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	138	322	0	ENST00000263121.7:c.1101C>A	p.Asp367Glu	p.D367E	ENST00000263121	NM_003073.3	367	gaC/gaA	8/9	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.64	2		322	424	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0003709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	147	283	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.370199007046829	2		283	762	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915013	131915013	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	86	282	0	ENST00000265335.6:c.370G>T	p.Gly124Cys	p.G124C	ENST00000265335		124	Ggt/Tgt	4/25	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.370199007046829	2		282	464	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945131	151945131	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	18	78	0	ENST00000262189.6:c.2388G>T	p.Met796Ile	p.M796I	ENST00000262189	NM_170606.2	796	atG/atT	14/59	1	2	FACETS	0.909	0.694	1	0.909	0.694	1	CLONAL	1	TRUE	1	0.370199007046829	2		78	107	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986988	36986988	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	79	363	0	ENST00000354822.5:c.701A>T	p.Gln234Leu	p.Q234L	ENST00000354822	NM_001079668.2	234	cAg/cTg	3/3	1	2	FACETS	0.745	0.656	0.84	0.745	0.656	0.84	SUBCLONAL	1	TRUE	1	0.370199007046829	2		363	573	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987055	36987055	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	85	291	0	ENST00000354822.5:c.634C>T	p.Gln212Ter	p.Q212*	ENST00000354822	NM_001079668.2	212	Caa/Taa	3/3	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.370199007046829	2		291	443	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038526	47038526	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	43	209	0	ENST00000377604.3:c.688C>T	p.Arg230Ter	p.R230*	ENST00000377604	NM_001204468.1	230	Cga/Tga	8/24	1	1	FACETS	0.412	0.344	0.486	0.412	0.344	0.486	SUBCLONAL	1	TRUE	0	0.370199007046829	1		209	460	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272169	15272170	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0003709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	31	109	0	ENST00000263388.2:c.6269dup	p.Leu2092ProfsTer3	p.L2092Pfs*3	ENST00000263388	NM_000435.2	2090	ggc/ggGc	33/33	1	2	FACETS	0.915	0.748	1	0.915	0.748	1	CLONAL	1	TRUE	1	0.370199007046829	2		109	183	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9787016	9787016	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	193	343	0	ENST00000377346.4:c.3047G>C	p.Arg1016Pro	p.R1016P	ENST00000377346	NM_005026.3	1016	cGa/cCa	24/24	1	2	FACETS	0.925	0.861	0.99	0.925	0.861	0.99	CLONAL	1	TRUE	1	0.724600679175025	2		343	576	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695881	117695881	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	177	319	0	ENST00000369458.3:c.556G>C	p.Asp186His	p.D186H	ENST00000369458	NM_024626.3	186	Gac/Cac	4/6	1	2	FACETS	0.917	0.851	0.984	0.917	0.851	0.984	CLONAL	1	TRUE	1	0.724600679175025	2		319	533	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117712771	117712771	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	242	446	0	ENST00000369458.3:c.55C>G	p.Leu19Val	p.L19V	ENST00000369458	NM_024626.3	19	Ctg/Gtg	2/6	1	2	FACETS	0.984	0.924	1	0.984	0.924	1	CLONAL	1	TRUE	1	0.724600679175025	2		446	679	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182032	38182032	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	178	274	0	ENST00000396334.3:c.656C>G	p.Ser219Cys	p.S219C	ENST00000396334	NM_002468.4	219	tCt/tGt	3/5	1	2	FACETS	0.958	0.89	1	0.958	0.89	1	CLONAL	1	TRUE	1	0.724600679175025	2		274	513	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610570	52610570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	243	404	1	ENST00000394830.3:c.3603G>A	p.Met1201Ile	p.M1201I	ENST00000394830	NM_018313.4	1201	atG/atA	23/30	1	2	FACETS	0.96	0.901	1	0.96	0.901	1	CLONAL	1	TRUE	1	0.724600679175025	2		405	699	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462359	89462359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	192	316	0	ENST00000336596.2:c.1831G>A	p.Glu611Lys	p.E611K	ENST00000336596	NM_005233.5	611	Gag/Aag	10/17	1	2	FACETS	0.903	0.84	0.967	0.903	0.84	0.967	CLONAL	1	TRUE	1	0.724600679175025	2		316	587	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670645	134670645	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	252	438	0	ENST00000398015.3:c.556C>G	p.Leu186Val	p.L186V	ENST00000398015	NM_004441.4	186	Ctt/Gtt	3/16	1	2	FACETS	0.965	0.907	1	0.965	0.907	1	CLONAL	1	TRUE	1	0.724600679175025	2		438	721	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272702	142272702	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	302	551	0	ENST00000350721.4:c.2497G>C	p.Glu833Gln	p.E833Q	ENST00000350721	NM_001184.3	833	Gaa/Caa	11/47	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.724600679175025	2		551	784	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947199	178947199	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	154	247	0	ENST00000263967.3:c.2635C>T	p.Gln879Ter	p.Q879*	ENST00000263967	NM_006218.2	879	Cag/Tag	18/21	1	2	FACETS	0.871	0.803	0.941	0.871	0.803	0.941	CLONAL	1	TRUE	1	0.724600679175025	2		247	488	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430873	181430873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	262	524	0	ENST00000325404.1:c.725C>T	p.Ser242Leu	p.S242L	ENST00000325404	NM_003106.3	242	tCg/tTg	1/1	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.724600679175025	2		524	690	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191541	185191541	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	84	163	0	ENST00000265026.3:c.2422C>G	p.Leu808Val	p.L808V	ENST00000265026	NM_004721.4	808	Ctg/Gtg	11/14	1	2	FACETS	0.678	0.604	0.756	0.678	0.604	0.756	SUBCLONAL	1	TRUE	1	0.724600679175025	2		163	342	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249465	153249465	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	263	317	0	ENST00000281708.4:c.1313C>A	p.Ser438Tyr	p.S438Y	ENST00000281708	NM_033632.3	438	tCt/tAt	9/12	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.724600679175025	2		317	650	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973818	131973818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	189	278	1	ENST00000265335.6:c.3521C>T	p.Ser1174Leu	p.S1174L	ENST00000265335		1174	tCa/tTa	23/25	1	2	FACETS	0.895	0.832	0.959	0.895	0.832	0.959	CLONAL	1	TRUE	1	0.724600679175025	2		279	583	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041149	180041149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	210	292	0	ENST00000261937.6:c.3250G>A	p.Glu1084Lys	p.E1084K	ENST00000261937	NM_182925.4	1084	Gaa/Aaa	24/30	1	2	FACETS	0.989	0.925	1	0.989	0.925	1	CLONAL	1	TRUE	1	0.724600679175025	2		292	586	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158610	26158610	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	89	155	0	ENST00000289316.2:c.213C>G	p.Phe71Leu	p.F71L	ENST00000289316	NM_138720.2	71	ttC/ttG	1/2	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.724600679175025	2		155	228	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288711	33288711	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	136	269	0	ENST00000374542.5:c.841G>C	p.Asp281His	p.D281H	ENST00000374542	NM_001141970.1	281	Gat/Cat	3/8	1	2	FACETS	0.963	0.885	1	0.963	0.885	1	CLONAL	1	TRUE	1	0.724600679175025	2		269	390	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647553	117647553	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	349	590	0	ENST00000368508.3:c.5391G>C	p.Gln1797His	p.Q1797H	ENST00000368508	NM_002944.2	1797	caG/caC	33/43	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.724600679175025	2		590	936	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512009	148512009	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	183	259	0	ENST00000320356.2:c.1669G>C	p.Glu557Gln	p.E557Q	ENST00000320356	NM_004456.4	557	Gag/Cag	14/20	1	2	FACETS	0.934	0.868	1	0.934	0.868	1	CLONAL	1	TRUE	1	0.724600679175025	2		259	541	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008892	152008892	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	212	377	0	ENST00000262189.6:c.730G>C	p.Asp244His	p.D244H	ENST00000262189	NM_170606.2	244	Gat/Cat	5/59	1	2	FACETS	0.97	0.907	1	0.97	0.907	1	CLONAL	1	TRUE	1	0.724600679175025	2		377	603	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341929	8341929	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	207	340	0	ENST00000356435.5:c.4711G>C	p.Glu1571Gln	p.E1571Q	ENST00000356435		1571	Gaa/Caa	29/35	NA	2	FACETS	1	0.95	1			1	INDETERMINATE	1	TRUE	NA	0.724600679175025	2		340	561	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339223	87339223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	191	345	0	ENST00000277120.3:c.805G>A	p.Glu269Lys	p.E269K	ENST00000277120		269	Gaa/Aaa	8/19	1	2	FACETS	0.9	0.837	0.964	0.9	0.837	0.964	CLONAL	1	TRUE	1	0.724600679175025	2		345	586	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229601	98229601	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	191	342	0	ENST00000331920.6:c.2357G>C	p.Arg786Thr	p.R786T	ENST00000331920	NM_000264.3	786	aGa/aCa	15/24	1	2	FACETS	0.922	0.858	0.987	0.922	0.858	0.987	CLONAL	1	TRUE	1	0.724600679175025	2		342	572	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405251	70405251	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	164	276	0	ENST00000373644.4:c.2765G>C	p.Arg922Thr	p.R922T	ENST00000373644	NM_030625.2	922	aGa/aCa	4/12	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.724600679175025	2		276	452	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88678997	88678997	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	66	90	0	ENST00000372037.3:c.937G>T	p.Glu313Ter	p.E313*	ENST00000372037	NM_004329.2	313	Gaa/Taa	10/13	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.724600679175025	2		90	154	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491408	18491408	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	223	328	0	ENST00000266497.5:c.1321C>G	p.Leu441Val	p.L441V	ENST00000266497		441	Cta/Gta	8/31	NA	2	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.724600679175025	2		328	587	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499579	18499579	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	211	414	1	ENST00000266497.5:c.1434G>C	p.Leu478Phe	p.L478F	ENST00000266497		478	ttG/ttC	10/31	NA	2	FACETS	0.902	0.842	0.963			1	INDETERMINATE	1	TRUE	NA	0.724600679175025	2		415	646	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287292	46287292	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	168	308	0	ENST00000334344.6:c.5237G>C	p.Arg1746Thr	p.R1746T	ENST00000334344	NM_152641.2	1746	aGa/aCa	19/21	1	2	FACETS	0.849	0.786	0.915	0.849	0.786	0.915	CLONAL	1	TRUE	1	0.724600679175025	2		308	546	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425315	49425315	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	259	390	0	ENST00000301067.7:c.13173G>C	p.Gln4391His	p.Q4391H	ENST00000301067	NM_003482.3	4391	caG/caC	39/54	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.724600679175025	2		390	699	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445170	49445170	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	85	156	0	ENST00000301067.7:c.2296G>T	p.Glu766Ter	p.E766*	ENST00000301067	NM_003482.3	766	Gag/Tag	10/54	1	2	FACETS	0.866	0.775	0.959	0.866	0.775	0.959	CLONAL	1	TRUE	1	0.724600679175025	2		156	271	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133236047	133236047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs948001596	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	42	332	0	ENST00000320574.5:c.3109C>T	p.Arg1037Cys	p.R1037C	ENST00000320574	NM_006231.2	1037	Cgt/Tgt	26/49	1	2	FACETS	0.221	0.184	0.262	0.221	0.184	0.262	SUBCLONAL	1	TRUE	1	0.724600679175025	2		332	524	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254277	133254277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778186722	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	259	371	0	ENST00000320574.5:c.607G>A	p.Asp203Asn	p.D203N	ENST00000320574	NM_006231.2	203	Gat/Aat	7/49	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.724600679175025	2		371	628	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964063	28964063	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	220	440	1	ENST00000282397.4:c.1839G>T	p.Lys613Asn	p.K613N	ENST00000282397	NM_002019.4	613	aaG/aaT	13/30	1	2	FACETS	0.926	0.866	0.987	0.926	0.866	0.987	CLONAL	1	TRUE	1	0.724600679175025	2		441	656	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32931966	32931966	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555286424	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	245	436	0	ENST00000380152.3:c.7705G>A	p.Gly2569Ser	p.G2569S	ENST00000380152		2569	Ggt/Agt	16/27	1	2	FACETS	0.944	0.887	1	0.944	0.887	1	CLONAL	1	TRUE	1	0.724600679175025	2		436	716	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437548	110437548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	170	283	0	ENST00000375856.3:c.853G>A	p.Glu285Lys	p.E285K	ENST00000375856	NM_003749.2	285	Gag/Aag	1/2	0.724982878465704	3	FACETS	0.996	0.919	1	0.498	0.459	0.538	CLONAL	1	TRUE	1	0.724600679175025	3		283	642	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239245	105239245	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	106	282	0	ENST00000349310.3:c.1142C>G	p.Ser381Ter	p.S381*	ENST00000349310	NM_001014432.1	381	tCa/tGa	12/15	1	2	FACETS	0.649	0.585	0.716	0.649	0.585	0.716	SUBCLONAL	1	TRUE	1	0.724600679175025	2		282	451	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130267	2130267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768292319	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	232	467	0	ENST00000219476.3:c.3499G>A	p.Glu1167Lys	p.E1167K	ENST00000219476	NM_000548.3	1167	Gag/Aag	30/42	1	2	FACETS	0.861	0.806	0.917	0.861	0.806	0.917	CLONAL	1	TRUE	1	0.724600679175025	2		467	744	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007556	62007556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	502	439	0	ENST00000392795.3:c.311C>T	p.Ser104Phe	p.S104F	ENST00000392795	NM_001039933.1	104	tCt/tTt	3/6	0.724982878465704	2	FACETS	0.969	0.94	0.997	0.969	0.94	0.997	CLONAL	2	TRUE	0	0.724600679175025	2		439	715	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637900	39637900	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	201	353	0	ENST00000262039.4:c.2317C>G	p.Leu773Val	p.L773V	ENST00000262039	NM_002647.2	773	Ctt/Gtt	22/25	1	2	FACETS	0.917	0.855	0.98	0.917	0.855	0.98	CLONAL	1	TRUE	1	0.724600679175025	2		353	605	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274225	5274225	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	242	411	0	ENST00000357368.4:c.222C>A	p.Asn74Lys	p.N74K	ENST00000357368	NM_002850.3	74	aaC/aaA	3/38	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.724600679175025	2		411	662	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7119467	7119467	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	257	498	2	ENST00000302850.5:c.3787G>C	p.Glu1263Gln	p.E1263Q	ENST00000302850	NM_000208.2	1263	Gag/Cag	21/22	1	2	FACETS	0.94	0.884	0.997	0.94	0.884	0.997	CLONAL	1	TRUE	1	0.724600679175025	2		500	755	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7126655	7126655	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	113	234	0	ENST00000302850.5:c.2953G>C	p.Asp985His	p.D985H	ENST00000302850	NM_000208.2	985	Gat/Cat	16/22	1	2	FACETS	0.681	0.616	0.748	0.681	0.616	0.748	SUBCLONAL	1	TRUE	1	0.724600679175025	2		234	458	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546988	9546988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	49	148	0	ENST00000353224.5:c.1034C>T	p.Ser345Leu	p.S345L	ENST00000353224	NM_177990.2	345	tCa/tTa	5/10	NA	2	FACETS	0.591	0.505	0.682			1	INDETERMINATE	1	TRUE	NA	0.724600679175025	2		148	229	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022238	31022238	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs747847938	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1423	221	404	0	ENST00000375687.4:c.1723C>T	p.Gln575Ter	p.Q575*	ENST00000375687	NM_015338.5	575	Caa/Taa	13/13	0.724600679175025	6	FACETS	0.909	0.843	0.978	0.182	0.168	0.196	CLONAL	1	TRUE	1	0.724600679175025	6		404	1644	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741485	39741485	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	189	286	0	ENST00000361337.2:c.1372C>G	p.Arg458Gly	p.R458G	ENST00000361337	NM_003286.2	458	Cgg/Ggg	14/21	NA	2	FACETS	0.962	0.896	1			1	INDETERMINATE	1	TRUE	NA	0.724600679175025	2		286	542	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259331	36259331	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	136	193	0	ENST00000300305.3:c.160G>A	p.Glu54Lys	p.E54K	ENST00000300305		54	Gag/Aag	3/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.724600679175025	2		193	337	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755594	39755594	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	28	306	0	ENST00000288319.7:c.1171G>C	p.Asp391His	p.D391H	ENST00000288319	NM_182918.3	391	Gac/Cac	10/10	1	2	FACETS	0.165	0.131	0.204	0.165	0.131	0.204	SUBCLONAL	1	TRUE	1	0.724600679175025	2		306	468	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29099515	29099515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	281	450	0	ENST00000328354.6:c.886G>A	p.Asp296Asn	p.D296N	ENST00000328354	NM_007194.3	296	Gat/Aat	8/15	1	2	FACETS	0.962	0.908	1	0.962	0.908	1	CLONAL	1	TRUE	1	0.724600679175025	2		450	806	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513400	41513400	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	299	435	0	ENST00000263253.7:c.304C>T	p.Gln102Ter	p.Q102*	ENST00000263253	NM_001429.3	102	Caa/Taa	2/31	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.724600679175025	2		435	784	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680258	30680259	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0003719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	247	491	0	ENST00000376406.3:c.1460dup	p.Asp488GlyfsTer9	p.D488Gfs*9	ENST00000376406	NM_014641.2	487	aag/aaAg	5/15	1	2	FACETS	0.903	0.848	0.96	0.903	0.848	0.96	CLONAL	1	TRUE	1	0.724600679175025	2		491	755	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0003736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	23	312	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.7	0.545	0.878	0.7	0.545	0.878	SUBCLONAL	1	TRUE	1	0.19	2		312	346	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16001745	16001745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1198223775	NA	P-0003736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	46	583	0	ENST00000268712.3:c.2756C>T	p.Pro919Leu	p.P919L	ENST00000268712	NM_006311.3	919	cCg/cTg	21/46	1	2	FACETS	0.842	0.708	0.99	0.842	0.708	0.99	CLONAL	1	TRUE	1	0.19	2		583	575	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121070	29121070	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	51	586	0	ENST00000328354.6:c.487C>G	p.His163Asp	p.H163D	ENST00000328354	NM_007194.3	163	Cac/Gac	4/15	1	2	FACETS	0.838	0.711	0.977	0.838	0.711	0.977	CLONAL	1	TRUE	1	0.19	2		586	641	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713564	30713564	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs772678321	NA	P-0003739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	32	312	0	ENST00000295754.5:c.889A>G	p.Ile297Val	p.I297V	ENST00000295754	NM_003242.5	297	Atc/Gtc	4/7	1	2	FACETS	0.78	0.633	0.946	0.78	0.633	0.946	CLONAL	1	TRUE	1	0.2	2		312	410	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554366	106554366	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	33	405	0	ENST00000369096.4:c.1894G>A	p.Glu632Lys	p.E632K	ENST00000369096	NM_001198.3	632	Gaa/Aaa	6/7	0.226733849069496	1	FACETS	0.677	0.551	0.818	0.677	0.551	0.818	SUBCLONAL	1	TRUE	0	0.2	1		405	439	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714472	117714472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768400134	NA	P-0003739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	23	339	0	ENST00000368508.3:c.1177G>A	p.Asp393Asn	p.D393N	ENST00000368508	NM_002944.2	393	Gat/Aat	11/43	0.226733849069496	1	FACETS	0.655	0.511	0.822	0.655	0.511	0.822	SUBCLONAL	1	TRUE	0	0.2	1		339	316	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444390	50444390	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	36	243	0	ENST00000331340.3:c.320T>C	p.Val107Ala	p.V107A	ENST00000331340	NM_006060.4	107	gTt/gCt	4/8	0.167744486130847	3	FACETS	1	0.873	1	0.538	0.443	0.644	CLONAL	1	TRUE	1	0.2	3		243	368	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233114	55233114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	38	324	0	ENST00000275493.2:c.1864C>T	p.Pro622Ser	p.P622S	ENST00000275493	NM_005228.3	622	Cca/Tca	15/28	0.167744486130847	3	FACETS	1	0.892	1	0.554	0.459	0.661	CLONAL	1	TRUE	1	0.2	3		324	377	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499732	8499732	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	27	466	0	ENST00000356435.5:c.2237G>A	p.Gly746Glu	p.G746E	ENST00000356435		746	gGa/gAa	14/35	1	2	FACETS	0.538	0.427	0.665	0.538	0.427	0.665	SUBCLONAL	1	TRUE	1	0.2	2		466	502	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287235	46287235	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	45	354	0	ENST00000334344.6:c.5180C>T	p.Pro1727Leu	p.P1727L	ENST00000334344	NM_152641.2	1727	cCt/cTt	19/21	1	2	FACETS	0.947	0.797	1	0.947	0.797	1	CLONAL	1	TRUE	1	0.2	2		354	475	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423552	88423552	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	57	503	0	ENST00000360948.2:c.2283G>A	p.Trp761Ter	p.W761*	ENST00000360948	NM_001012338.2	761	tgG/tgA	18/19	1	2	FACETS	0.981	0.842	1	0.981	0.842	1	CLONAL	1	TRUE	1	0.2	2		503	581	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126532	2126533	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0003739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	29	504	0	ENST00000219476.3:c.2783_2784delinsTT	p.Pro928Leu	p.P928L	ENST00000219476	NM_000548.3	928	cCC/cTT	25/42	1	2	FACETS	0.63	0.505	0.773	0.63	0.505	0.773	SUBCLONAL	1	TRUE	1	0.2	2		504	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0003739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	39	289	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.2	2		289	343	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578505	7578505	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779196500	NA	P-0003739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	43	343	0	ENST00000269305.4:c.425C>T	p.Pro142Leu	p.P142L	ENST00000269305	NM_001126112.2	142	cCt/cTt	5/11	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.2	2		343	404	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799162	42799162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775743872	NA	P-0003739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	20	237	0	ENST00000575354.2:c.4646C>T	p.Pro1549Leu	p.P1549L	ENST00000575354	NM_015125.3	1549	cCc/cTc	20/20	1	2	FACETS	0.699	0.535	0.891	0.699	0.535	0.891	SUBCLONAL	1	TRUE	1	0.2	2		237	286	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321329	1321330	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0003739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	31	389	0	ENST00000400841.2:c.425_426delinsTT	p.Ser142Phe	p.S142F	ENST00000400841		142	tCC/tTT	4/6	1	1	FACETS	0.591	0.477	0.72	0.591	0.477	0.72	SUBCLONAL	1	TRUE	0	0.2	1		389	472	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412213	63412214	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0003739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	47	332	0	ENST00000330258.3:c.953_954delinsTT	p.Ser318Phe	p.S318F	ENST00000330258	NM_152424.3	318	tCC/tTT	2/2	1	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.2	1		332	326	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937594	76937594	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0003739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	34	271	0	ENST00000373344.5:c.3154A>T	p.Lys1052Ter	p.K1052*	ENST00000373344	NM_000489.3	1052	Aaa/Taa	9/35	1	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.2	1		271	217	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0003742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	271	381	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.705944726866287	4	FACETS	0.936	0.883	0.989	0.936	0.883	0.989	CLONAL	2	TRUE	2	0.71282246349541	4		382	696	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	204	271	0	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.71282246349541	2	FACETS	0.892	0.846	0.936	0.892	0.846	0.936	CLONAL	2	TRUE	0	0.71282246349541	2		271	321	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266107	41266107	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	339	313	2	ENST00000349496.5:c.104T>G	p.Ile35Ser	p.I35S	ENST00000349496	NM_001904.3	35	aTc/aGc	3/15	0.71282246349541	2	FACETS	0.973	0.937	1	0.973	0.937	1	CLONAL	2	TRUE	0	0.71282246349541	2		315	489	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258647	16258647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	183	237	0	ENST00000375759.3:c.5912C>T	p.Pro1971Leu	p.P1971L	ENST00000375759	NM_015001.2	1971	cCt/cTt	11/15	0.627959311399527	4	FACETS	0.934	0.87	0.998	0.934	0.87	0.998	CLONAL	2	TRUE	2	0.71282246349541	4		237	471	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344760	65344760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768706312	NA	P-0003742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	290	303	0	ENST00000342505.4:c.277C>T	p.Arg93Cys	p.R93C	ENST00000342505	NM_002227.2	93	Cgc/Tgc	4/25	0.627959311399527	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.71282246349541	4		303	630	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0003742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	67	155	0				ENST00000310581	NM_198253.2	-/1132			0.298387976891228	4	FACETS	0.894	0.808	0.979			1	INDETERMINATE	3	TRUE	NA	0.71282246349541	4		155	120	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0003755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	91	322	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.344750431735571	2		322	416	SUCCESS
APC	324	MSKCC	GRCh37	5	112175225	112175225	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	53	251	0	ENST00000257430.4:c.3935del	p.Gly1312GlufsTer9	p.G1312Efs*9	ENST00000257430	NM_000038.5	1312	Gga/ga	16/16	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.344750431735571	2		251	281	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577095	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519984	NA	P-0003762-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	223	308	0	ENST00000269305.4:c.843C>A	p.Asp281Glu	p.D281E	ENST00000269305	NM_001126112.2	281	gaC/gaA	8/11	0.243051208602008	3	FACETS	0.931	0.87	0.993	0.931	0.87	0.993	CLONAL	3	TRUE	0	0.243051208602008	3		308	737	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652411	206652411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781909564	NA	P-0003762-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	247	275	0	ENST00000367120.3:c.1118C>T	p.Thr373Met	p.T373M	ENST00000367120	NM_014002.3	373	aCg/aTg	10/22	0.243051208602008	7	FACETS	0.967	0.906	1	0.773	0.725	0.823	CLONAL	4	TRUE	2	0.243051208602008	7		275	845	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0003779-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	52	205	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	1	0.872	1	1	0.977	1	CLONAL	2	TRUE	1	0.219984713735468	2		205	233	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811734	102811734	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003779-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	240	414	0	ENST00000307046.8:c.450A>C	p.Lys150Asn	p.K150N	ENST00000307046	NM_001111285.1	150	aaA/aaC	4/4	0.219984713735468	5	FACETS	0.969	0.912	1	1	0.989	1	CLONAL	5	TRUE	1	0.219984713735468	5		414	599	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111543	8111545	+	inframe_deletion	In_Frame_Del	DEL	CTA	CTA	-	novel	NA	P-0003779-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	57	259	0	ENST00000346208.3:c.1033_1035del	p.Tyr345del	p.Y345del	ENST00000346208		343	ctCTAc/ctc	5/6	0.0750915958199754	4	FACETS	0.911	0.786	1			1	INDETERMINATE	2	TRUE	NA	0.219984713735468	4		259	347	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	26	324	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.86	0.681	1	0.86	0.681	1	CLONAL	1	TRUE	1	0.18	2		324	336	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0003785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	72	220	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.18	2		220	763	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582380	119582380	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs753950587	NA	P-0003785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	52	164	0	ENST00000316626.5:c.1021C>T	p.Arg341Ter	p.R341*	ENST00000316626		341	Cga/Tga	10/12	1	2	FACETS	0.89	0.757	1	0.89	0.757	1	CLONAL	1	TRUE	1	0.18	2		164	649	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466578	120466578	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs893877808	NA	P-0003785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	66	296	0	ENST00000256646.2:c.4541A>G	p.Lys1514Arg	p.K1514R	ENST00000256646	NM_024408.3	1514	aAa/aGa	26/34	1	2	FACETS	0.919	0.796	1	0.919	0.796	1	CLONAL	1	TRUE	1	0.18	2		296	798	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217294	66217294	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	50	170	0	ENST00000273854.3:c.2321T>A	p.Val774Glu	p.V774E	ENST00000273854	NM_004439.5	774	gTg/gAg	14/18	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.18	2		170	497	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524456	187524456	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	48	209	0	ENST00000441802.2:c.11224G>C	p.Asp3742His	p.D3742H	ENST00000441802	NM_005245.3	3742	Gac/Cac	19/27	1	2	FACETS	0.694	0.585	0.814	0.694	0.585	0.814	SUBCLONAL	1	TRUE	1	0.18	2		209	769	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789600	3789600	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	70	272	0	ENST00000262367.5:c.4259A>C	p.Asp1420Ala	p.D1420A	ENST00000262367	NM_004380.2	1420	gAt/gCt	25/31	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.18	2		272	775	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932412	39932412	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	323	366	1	ENST00000378444.4:c.2187G>T	p.Leu729Phe	p.L729F	ENST00000378444	NM_001123385.1	729	ttG/ttT	4/15	0.221563955595155	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.18	3		367	1160	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424454	47424454	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	351	385	0	ENST00000377045.4:c.374G>C	p.Cys125Ser	p.C125S	ENST00000377045	NM_001654.4	125	tGc/tCc	5/16	0.221563955595155	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.18	3		385	1275	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541485	29541485	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs746149047	NA	P-0003785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	32	85	0	ENST00000356175.3:c.1413del	p.Val472Ter	p.V472*	ENST00000356175	NM_000267.3	470	gAa/ga	13/57	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.18	2		85	247	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0003795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	63	405	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.597	0.517	0.684	0.597	0.517	0.684	SUBCLONAL	1	TRUE	1	0.383621738400886	2		405	550	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577095	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519984	NA	P-0003795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	164	404	0	ENST00000269305.4:c.843C>G	p.Asp281Glu	p.D281E	ENST00000269305	NM_001126112.2	281	gaC/gaG	8/11	0.383621738400886	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.383621738400886	1		404	568	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256327	16256327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	80	290	0	ENST00000375759.3:c.3592G>A	p.Asp1198Asn	p.D1198N	ENST00000375759	NM_015001.2	1198	Gat/Aat	11/15	0.285694035541767	1	FACETS	0.741	0.655	0.833	0.741	0.655	0.833	SUBCLONAL	1	TRUE	0	0.383621738400886	1		290	455	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398153	4398153	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	56	179	0	ENST00000261254.3:c.717C>A	p.Asp239Glu	p.D239E	ENST00000261254	NM_001759.3	239	gaC/gaA	4/5	1	2	FACETS	0.948	0.818	1	0.948	0.818	1	CLONAL	1	TRUE	1	0.383621738400886	2		179	308	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578494	7578494	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs786203064	NA	P-0003799-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	376	448	0	ENST00000269305.4:c.436T>G	p.Trp146Gly	p.W146G	ENST00000269305	NM_001126112.2	146	Tgg/Ggg	5/11	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.821086780204748	2		448	436	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0003807-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	36	440	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.996	0.818	1	0.996	0.818	1	CLONAL	1	TRUE	1	0.13	2		441	556	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0003807-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	18	251	2	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.581	0.436	0.753	0.581	0.436	0.753	SUBCLONAL	1	TRUE	1	0.13	2		253	477	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907164	101907164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003807-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	29	221	0	ENST00000374994.4:c.1124C>T	p.Thr375Ile	p.T375I	ENST00000374994	NM_004612.2	375	aCa/aTa	6/9	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.13	2		221	411	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	18	300	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.768	1	1	0.768	1	CLONAL	1	TRUE	1	0.16	2		300	221	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894228	NA	P-0003817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	75	327	0	ENST00000451590.1:c.37G>C	p.Gly13Arg	p.G13R	ENST00000451590	NM_001130442.1	13	Ggt/Cgt	2/5	1	2	FACETS	0.836	0.733	0.946	1	0.979	1	CLONAL	2	TRUE	1	0.16	2		327	561	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163720	32163720	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253487294	NA	P-0003817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	38	166	0	ENST00000375023.3:c.5506G>A	p.Glu1836Lys	p.E1836K	ENST00000375023	NM_004557.3	1836	Gag/Aag	30/30	0.151196121412853	3	FACETS	1	0.948	1	0.718	0.595	0.856	CLONAL	1	TRUE	1	0.16	3		166	357	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266713	198266713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776846119	NA	P-0003817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	42	320	0	ENST00000335508.6:c.2219G>A	p.Gly740Glu	p.G740E	ENST00000335508	NM_012433.2	740	gGa/gAa	15/25	1	2	FACETS	0.804	0.67	0.954	0.804	0.67	0.954	CLONAL	1	TRUE	1	0.16	2		320	653	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485442	57485442	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	33	265	0	ENST00000371085.3:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000371085	NM_000516.4	342	Cga/Tga	12/13	1	2	FACETS	0.657	0.533	0.797	0.657	0.533	0.797	SUBCLONAL	1	TRUE	1	0.16	2		265	628	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969327	44969327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	44	172	0	ENST00000377967.4:c.4009G>A	p.Glu1337Lys	p.E1337K	ENST00000377967	NM_021140.2	1337	Gag/Aag	28/29	1	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.16	1		172	407	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197842	123197842	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	60	242	0	ENST00000218089.9:c.1966C>T	p.Gln656Ter	p.Q656*	ENST00000218089	NM_001042749.1	656	Caa/Taa	20/35	1	1	FACETS	0.76	0.656	0.872	1	0.97	1	SUBCLONAL	2	TRUE	0	0.16	1		242	454	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	151	192	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.96	0.891	1	0.96	0.891	1	CLONAL	1	TRUE	1	0.901012722067286	2		192	349	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	16	607	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.069	0.05	0.091	0.069	0.05	0.091	SUBCLONAL	1	TRUE	1	0.901012722067286	2		607	515	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783289	9783289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	27	756	1	ENST00000377346.4:c.2533G>A	p.Ala845Thr	p.A845T	ENST00000377346	NM_005026.3	845	Gca/Aca	20/24	0.901012722067286	1	FACETS	0.075	0.059	0.093	0.075	0.059	0.093	SUBCLONAL	1	TRUE	0	0.901012722067286	1		757	438	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202927	16202927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	49	526	1	ENST00000375759.3:c.635C>T	p.Pro212Leu	p.P212L	ENST00000375759	NM_015001.2	212	cCc/cTc	3/15	NA	2	FACETS	0.219	0.185	0.256			1	INDETERMINATE	1	TRUE	NA	0.901012722067286	2		527	496	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259070	16259070	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1200850750	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	43	510	0	ENST00000375759.3:c.6335G>A	p.Arg2112Lys	p.R2112K	ENST00000375759	NM_015001.2	2112	aGg/aAg	11/15	NA	2	FACETS	0.184	0.153	0.218			1	INDETERMINATE	1	TRUE	NA	0.901012722067286	2		510	519	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885824	23885824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759191680	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	190	511	0	ENST00000374561.5:c.94C>T	p.Pro32Ser	p.P32S	ENST00000374561	NM_002167.4	32	Ccg/Tcg	1/3	0.82932139938498	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.901012722067286	1		511	217	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101637	27101637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771093077	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	186	1011	2	ENST00000324856.7:c.4919C>T	p.Thr1640Ile	p.T1640I	ENST00000324856	NM_006015.4	1640	aCc/aTc	18/20	1	2	FACETS	0.454	0.419	0.49	0.454	0.419	0.49	SUBCLONAL	1	TRUE	1	0.901012722067286	2		1013	909	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45805920	45805920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659091	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	28	658	0	ENST00000450313.1:c.7C>T	p.Pro3Ser	p.P3S	ENST00000450313	NM_012222.2	3	Ccg/Tcg	1/16	1	2	FACETS	0.116	0.092	0.143	0.116	0.092	0.143	SUBCLONAL	1	TRUE	1	0.901012722067286	2		658	536	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46715765	46715765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	171	638	0	ENST00000371975.4:c.184C>T	p.Pro62Ser	p.P62S	ENST00000371975	NM_003579.3	62	Cca/Tca	3/18	1	2	FACETS	0.601	0.555	0.648	0.601	0.555	0.648	SUBCLONAL	1	TRUE	1	0.901012722067286	2		638	632	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247787	59247787	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	194	936	1	ENST00000371222.2:c.956G>A	p.Gly319Glu	p.G319E	ENST00000371222	NM_002228.3	319	gGg/gAg	1/1	1	2	FACETS	0.492	0.456	0.53	0.492	0.456	0.53	SUBCLONAL	1	TRUE	1	0.901012722067286	2		937	875	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65323415	65323415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388402406	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	262	679	1	ENST00000342505.4:c.1382G>A	p.Gly461Glu	p.G461E	ENST00000342505	NM_002227.2	461	gGg/gAg	10/25	1	2	FACETS	0.763	0.718	0.809	0.763	0.718	0.809	SUBCLONAL	1	TRUE	1	0.901012722067286	2		680	762	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273218	115273218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	29	630	1	ENST00000438362.2:c.1240C>T	p.Arg414Cys	p.R414C	ENST00000438362	NM_001242891.1	414	Cgt/Tgt	11/20	1	2	FACETS	0.131	0.104	0.161	0.131	0.104	0.161	SUBCLONAL	1	TRUE	1	0.901012722067286	2		631	493	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462237	120462237	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	67	388	0	ENST00000256646.2:c.5480-1G>A		p.X1827_splice	ENST00000256646	NM_024408.3	1827			1	2	FACETS	0.449	0.393	0.509	0.449	0.393	0.509	SUBCLONAL	1	TRUE	1	0.901012722067286	2		388	331	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480495	120480495	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	22	376	1	ENST00000256646.2:c.3322G>A	p.Ala1108Thr	p.A1108T	ENST00000256646	NM_024408.3	1108	Gca/Aca	20/34	1	2	FACETS	0.118	0.091	0.149	0.118	0.091	0.149	SUBCLONAL	1	TRUE	1	0.901012722067286	2		377	415	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958541	175958541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	53	638	1	ENST00000367669.3:c.1804G>A	p.Val602Ile	p.V602I	ENST00000367669	NM_022457.5	602	Gtc/Atc	16/20	1	2	FACETS	0.235	0.2	0.273	0.235	0.2	0.273	SUBCLONAL	1	TRUE	1	0.901012722067286	2		639	500	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176105662	176105662	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	156	642	0	ENST00000367669.3:c.853G>A	p.Glu285Lys	p.E285K	ENST00000367669	NM_022457.5	285	Gag/Aag	7/20	1	2	FACETS	0.66	0.608	0.713	0.66	0.608	0.713	SUBCLONAL	1	TRUE	1	0.901012722067286	2		642	525	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175991	176175991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	76	380	2	ENST00000367669.3:c.124G>A	p.Val42Ile	p.V42I	ENST00000367669	NM_022457.5	42	Gtt/Att	1/20	1	2	FACETS	0.59	0.523	0.66	0.59	0.523	0.66	SUBCLONAL	1	TRUE	1	0.901012722067286	2		382	286	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204513745	204513745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	16	307	0	ENST00000367182.3:c.755G>A	p.Gly252Glu	p.G252E	ENST00000367182	NM_001278516.1	252	gGa/gAa	9/11	1	2	FACETS	0.125	0.092	0.165	0.125	0.092	0.165	SUBCLONAL	1	TRUE	1	0.901012722067286	2		307	283	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653808	89653808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	15	530	0	ENST00000371953.3:c.106G>A	p.Gly36Arg	p.G36R	ENST00000371953	NM_000314.4	36	Gga/Aga	2/9	0.901012722067286	1	FACETS	0.098	0.071	0.129	0.098	0.071	0.129	SUBCLONAL	1	TRUE	0	0.901012722067286	1		530	187	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	192	565	2	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	0.901012722067286	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.901012722067286	1		567	230	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200233	67200233	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	209	787	1	ENST00000312629.5:c.541G>A	p.Ala181Thr	p.A181T	ENST00000312629	NM_003952.2	181	Gcc/Acc	7/15	1	2	FACETS	0.691	0.645	0.739	0.691	0.645	0.739	SUBCLONAL	1	TRUE	1	0.901012722067286	2		788	671	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949102	71949102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	130	607	0	ENST00000298229.2:c.3569G>A	p.Gly1190Asp	p.G1190D	ENST00000298229	NM_001567.3	1190	gGc/gAc	27/28	1	2	FACETS	0.54	0.492	0.59	0.54	0.492	0.59	SUBCLONAL	1	TRUE	1	0.901012722067286	2		607	534	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180435	94180435	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	38	682	0	ENST00000323929.3:c.1733G>A	p.Gly578Asp	p.G578D	ENST00000323929	NM_005591.3	578	gGt/gAt	15/20	1	2	FACETS	0.125	0.103	0.15	0.125	0.103	0.15	SUBCLONAL	1	TRUE	1	0.901012722067286	2		682	675	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94200993	94200993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	70	504	0	ENST00000323929.3:c.1084C>T	p.Leu362Phe	p.L362F	ENST00000323929	NM_005591.3	362	Ctt/Ttt	10/20	1	2	FACETS	0.477	0.419	0.538	0.477	0.419	0.538	SUBCLONAL	1	TRUE	1	0.901012722067286	2		504	326	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94211946	94211946	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1263915515	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	29	715	0	ENST00000323929.3:c.499G>A	p.Val167Ile	p.V167I	ENST00000323929	NM_005591.3	167	Gtt/Att	6/20	1	2	FACETS	0.132	0.106	0.163	0.132	0.106	0.163	SUBCLONAL	1	TRUE	1	0.901012722067286	2		715	486	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999680	100999680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs577094242	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	109	1060	1	ENST00000325455.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000325455	NM_001202474.3	41	aCc/aTc	1/8	1	2	FACETS	0.301	0.27	0.334	0.301	0.27	0.334	SUBCLONAL	1	TRUE	1	0.901012722067286	2		1061	804	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158442	108158442	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	66	463	0	ENST00000278616.4:c.4109G>A	p.Gly1370Glu	p.G1370E	ENST00000278616	NM_000051.3	1370	gGg/gAg	27/63	1	2	FACETS	0.369	0.321	0.42	0.369	0.321	0.42	SUBCLONAL	1	TRUE	1	0.901012722067286	2		463	397	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206638	108206638	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs866402530	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	71	557	0	ENST00000278616.4:c.8218C>T	p.Gln2740Ter	p.Q2740*	ENST00000278616	NM_000051.3	2740	Cag/Tag	56/63	1	2	FACETS	0.353	0.308	0.4	0.353	0.308	0.4	SUBCLONAL	1	TRUE	1	0.901012722067286	2		557	447	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385331	4385331	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	24	426	0	ENST00000261254.3:c.356C>T	p.Thr119Ile	p.T119I	ENST00000261254	NM_001759.3	119	aCc/aTc	2/5	1	2	FACETS	0.124	0.096	0.155	0.124	0.096	0.155	SUBCLONAL	1	TRUE	1	0.901012722067286	2		426	431	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992112	11992112	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	59	417	0	ENST00000396373.4:c.202C>T	p.Gln68Ter	p.Q68*	ENST00000396373	NM_001987.4	68	Cag/Tag	3/8	1	2	FACETS	0.313	0.27	0.36	0.313	0.27	0.36	SUBCLONAL	1	TRUE	1	0.901012722067286	2		417	418	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534794	18534794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1179216411	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	71	508	1	ENST00000266497.5:c.1852C>T	p.Pro618Ser	p.P618S	ENST00000266497		618	Cca/Tca	12/31	1	2	FACETS	0.36	0.315	0.408	0.36	0.315	0.408	SUBCLONAL	1	TRUE	1	0.901012722067286	2		509	438	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46215208	46215208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	80	346	0	ENST00000334344.6:c.643G>A	p.Gly215Arg	p.G215R	ENST00000334344	NM_152641.2	215	Gga/Aga	6/21	1	2	FACETS	0.678	0.605	0.754	0.678	0.605	0.754	SUBCLONAL	1	TRUE	1	0.901012722067286	2		346	262	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231172	46231172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	23	458	0	ENST00000334344.6:c.1092G>A	p.Met364Ile	p.M364I	ENST00000334344	NM_152641.2	364	atG/atA	9/21	1	2	FACETS	0.127	0.098	0.16	0.127	0.098	0.16	SUBCLONAL	1	TRUE	1	0.901012722067286	2		458	402	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418360	49418360	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	25	455	1	ENST00000301067.7:c.16052+1G>A		p.X5351_splice	ENST00000301067	NM_003482.3	5351			1	2	FACETS	0.118	0.092	0.147	0.118	0.092	0.147	SUBCLONAL	1	TRUE	1	0.901012722067286	2		456	472	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438263	49438263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	95	682	0	ENST00000301067.7:c.5006C>T	p.Pro1669Leu	p.P1669L	ENST00000301067	NM_003482.3	1669	cCc/cTc	20/54	1	2	FACETS	0.28	0.249	0.313	0.28	0.249	0.313	SUBCLONAL	1	TRUE	1	0.901012722067286	2		682	754	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438703	49438703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	101	807	0	ENST00000301067.7:c.4787G>A	p.Gly1596Asp	p.G1596D	ENST00000301067	NM_003482.3	1596	gGc/gAc	19/54	1	2	FACETS	0.261	0.233	0.291	0.261	0.233	0.291	SUBCLONAL	1	TRUE	1	0.901012722067286	2		807	858	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145418	58145418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	77	517	0	ENST00000257904.6:c.83G>A	p.Ser28Asn	p.S28N	ENST00000257904	NM_000075.3	28	aGt/aAt	2/8	1	2	FACETS	0.332	0.292	0.375	0.332	0.292	0.375	SUBCLONAL	1	TRUE	1	0.901012722067286	2		517	515	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888189	112888189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507511	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	15	793	0	ENST00000351677.2:c.205G>A	p.Glu69Lys	p.E69K	ENST00000351677	NM_002834.3	69	Gag/Aag	3/16	1	2	FACETS	0.062	0.045	0.083	0.062	0.045	0.083	SUBCLONAL	1	TRUE	1	0.901012722067286	2		793	534	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888199	112888199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918454	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	28	748	0	ENST00000351677.2:c.215C>T	p.Ala72Val	p.A72V	ENST00000351677	NM_002834.3	72	gCc/gTc	3/16	1	2	FACETS	0.12	0.095	0.148	0.12	0.095	0.148	SUBCLONAL	1	TRUE	1	0.901012722067286	2		748	518	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120857	115120857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	17	409	0	ENST00000257566.3:c.149G>A	p.Gly50Asp	p.G50D	ENST00000257566	NM_016569.3	50	gGc/gAc	1/8	1	2	FACETS	0.113	0.084	0.148	0.113	0.084	0.148	SUBCLONAL	1	TRUE	1	0.901012722067286	2		409	333	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133234456	133234456	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	26	591	0	ENST00000320574.5:c.3376G>A	p.Ala1126Thr	p.A1126T	ENST00000320574	NM_006231.2	1126	Gca/Aca	27/49	1	2	FACETS	0.118	0.092	0.146	0.118	0.092	0.146	SUBCLONAL	1	TRUE	1	0.901012722067286	2		591	491	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964235	28964235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1489420353	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	17	258	0	ENST00000282397.4:c.1667C>T	p.Pro556Leu	p.P556L	ENST00000282397	NM_002019.4	556	cCa/cTa	13/30	1	2	FACETS	0.159	0.119	0.207	0.159	0.119	0.207	SUBCLONAL	1	TRUE	1	0.901012722067286	2		258	237	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004212	29004212	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	21	382	0	ENST00000282397.4:c.1081G>A	p.Ala361Thr	p.A361T	ENST00000282397	NM_002019.4	361	Gca/Aca	8/30	1	2	FACETS	0.117	0.09	0.149	0.117	0.09	0.149	SUBCLONAL	1	TRUE	1	0.901012722067286	2		382	398	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911229	32911229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	28	616	0	ENST00000380152.3:c.2737G>A	p.Asp913Asn	p.D913N	ENST00000380152		913	Gac/Aac	11/27	1	2	FACETS	0.12	0.095	0.148	0.12	0.095	0.148	SUBCLONAL	1	TRUE	1	0.901012722067286	2		616	520	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133754	41133754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	27	444	0	ENST00000379561.5:c.1874G>A	p.Gly625Glu	p.G625E	ENST00000379561	NM_002015.3	625	gGa/gAa	2/3	1	2	FACETS	0.15	0.119	0.186	0.15	0.119	0.186	SUBCLONAL	1	TRUE	1	0.901012722067286	2		444	399	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437052	110437052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	61	223	0	ENST00000375856.3:c.1349C>T	p.Ser450Phe	p.S450F	ENST00000375856	NM_003749.2	450	tCc/tTc	1/2	1	2	FACETS	0.831	0.733	0.932	0.831	0.733	0.932	CLONAL	1	TRUE	1	0.901012722067286	2		223	163	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438108	110438108	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	103	778	1	ENST00000375856.3:c.293G>A	p.Cys98Tyr	p.C98Y	ENST00000375856	NM_003749.2	98	tGc/tAc	1/2	1	2	FACETS	0.356	0.318	0.395	0.356	0.318	0.395	SUBCLONAL	1	TRUE	1	0.901012722067286	2		779	643	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046562	30046562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753135852	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	174	647	1	ENST00000331968.5:c.2621G>A	p.Gly874Asp	p.G874D	ENST00000331968	NM_002742.2	874	gGc/gAc	18/18	1	2	FACETS	0.619	0.572	0.667	0.619	0.572	0.667	SUBCLONAL	1	TRUE	1	0.901012722067286	2		648	624	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729175	66729175	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908596	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	96	791	1	ENST00000307102.5:c.383G>A	p.Gly128Asp	p.G128D	ENST00000307102	NM_002755.3	128	gGc/gAc	3/11	1	2	FACETS	0.294	0.262	0.329	0.294	0.262	0.329	SUBCLONAL	1	TRUE	1	0.901012722067286	2		792	724	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99452053	99452053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	28	429	1	ENST00000268035.6:c.1387G>A	p.Glu463Lys	p.E463K	ENST00000268035	NM_000875.3	463	Gag/Aag	6/21	1	2	FACETS	0.144	0.114	0.177	0.144	0.114	0.177	SUBCLONAL	1	TRUE	1	0.901012722067286	2		430	433	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347095	347095	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	45	1011	0	ENST00000262320.3:c.1916G>A	p.Gly639Glu	p.G639E	ENST00000262320	NM_003502.3	639	gGg/gAg	7/11	1	2	FACETS	0.116	0.097	0.138	0.116	0.097	0.138	SUBCLONAL	1	TRUE	1	0.901012722067286	2		1011	860	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396248	396248	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	149	795	0	ENST00000262320.3:c.778G>A	p.Asp260Asn	p.D260N	ENST00000262320	NM_003502.3	260	Gac/Aac	2/11	1	2	FACETS	0.492	0.451	0.535	0.492	0.451	0.535	SUBCLONAL	1	TRUE	1	0.901012722067286	2		795	672	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130169	2130169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766223343	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	220	792	0	ENST00000219476.3:c.3401G>A	p.Gly1134Asp	p.G1134D	ENST00000219476	NM_000548.3	1134	gGc/gAc	30/42	1	2	FACETS	0.802	0.751	0.854	0.802	0.751	0.854	CLONAL	1	TRUE	1	0.901012722067286	2		792	609	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632669	3632669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	183	894	0	ENST00000294008.3:c.5179G>A	p.Ala1727Thr	p.A1727T	ENST00000294008	NM_032444.2	1727	Gca/Aca	15/15	1	2	FACETS	0.522	0.483	0.563	0.522	0.483	0.563	SUBCLONAL	1	TRUE	1	0.901012722067286	2		894	778	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633207	3633207	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868774001	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	115	1253	2	ENST00000294008.3:c.5044C>T	p.Pro1682Ser	p.P1682S	ENST00000294008	NM_032444.2	1682	Ccc/Tcc	14/15	1	2	FACETS	0.302	0.271	0.334	0.302	0.271	0.334	SUBCLONAL	1	TRUE	1	0.901012722067286	2		1255	846	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3645638	3645638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	44	834	0	ENST00000294008.3:c.1981G>A	p.Asp661Asn	p.D661N	ENST00000294008	NM_032444.2	661	Gac/Aac	9/15	1	2	FACETS	0.123	0.102	0.146	0.123	0.102	0.146	SUBCLONAL	1	TRUE	1	0.901012722067286	2		834	796	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779004	3779004	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	114	577	1	ENST00000262367.5:c.6044G>A	p.Ser2015Asn	p.S2015N	ENST00000262367	NM_004380.2	2015	aGc/aAc	31/31	1	2	FACETS	0.542	0.491	0.595	0.542	0.491	0.595	SUBCLONAL	1	TRUE	1	0.901012722067286	2		578	467	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781922	3781922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	29	507	0	ENST00000262367.5:c.4745G>A	p.Ser1582Asn	p.S1582N	ENST00000262367	NM_004380.2	1582	aGc/aAc	29/31	1	2	FACETS	0.128	0.102	0.158	0.128	0.102	0.158	SUBCLONAL	1	TRUE	1	0.901012722067286	2		507	502	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645976	67645976	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	68	630	0	ENST00000264010.4:c.904G>A	p.Ala302Thr	p.A302T	ENST00000264010	NM_006565.3	302	Gca/Aca	4/12	1	2	FACETS	0.228	0.198	0.26	0.228	0.198	0.26	SUBCLONAL	1	TRUE	1	0.901012722067286	2		630	663	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853245	68853245	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148400889	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	37	493	1	ENST00000261769.5:c.1628C>T	p.Ser543Phe	p.S543F	ENST00000261769	NM_004360.3	543	tCc/tTc	11/16	1	2	FACETS	0.143	0.117	0.172	0.143	0.117	0.172	SUBCLONAL	1	TRUE	1	0.901012722067286	2		494	575	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347913	89347913	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	232	731	4	ENST00000301030.4:c.5037G>A	p.Trp1679Ter	p.W1679*	ENST00000301030	NM_001256183.1	1679	tgG/tgA	9/13	1	2	FACETS	0.779	0.731	0.829	0.779	0.731	0.829	SUBCLONAL	1	TRUE	1	0.901012722067286	2		735	661	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351440	89351440	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	31	644	0	ENST00000301030.4:c.1510G>A	p.Gly504Arg	p.G504R	ENST00000301030	NM_001256183.1	504	Ggg/Agg	9/13	1	2	FACETS	0.115	0.092	0.141	0.115	0.092	0.141	SUBCLONAL	1	TRUE	1	0.901012722067286	2		644	599	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762846821	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	32	864	1	ENST00000269305.4:c.461G>A	p.Gly154Asp	p.G154D	ENST00000269305	NM_001126112.2	154	gGc/gAc	5/11	1	2	FACETS	0.082	0.065	0.1	0.082	0.065	0.1	SUBCLONAL	1	TRUE	1	0.901012722067286	2		865	871	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501195	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	22	821	1	ENST00000269305.4:c.313G>A	p.Gly105Ser	p.G105S	ENST00000269305	NM_001126112.2	105	Ggc/Agc	4/11	1	2	FACETS	0.067	0.051	0.085	0.067	0.051	0.085	SUBCLONAL	1	TRUE	1	0.901012722067286	2		822	731	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032480	12032480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	23	362	0	ENST00000353533.5:c.916C>T	p.Pro306Ser	p.P306S	ENST00000353533	NM_003010.3	306	Cct/Tct	9/11	1	2	FACETS	0.171	0.133	0.215	0.171	0.133	0.215	SUBCLONAL	1	TRUE	1	0.901012722067286	2		362	298	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122515	17122515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	37	745	0	ENST00000285071.4:c.880G>A	p.Glu294Lys	p.E294K	ENST00000285071	NM_144997.5	294	Gag/Aag	9/14	1	2	FACETS	0.126	0.103	0.152	0.126	0.103	0.152	SUBCLONAL	1	TRUE	1	0.901012722067286	2		745	652	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40865380	40865380	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	325	810	0	ENST00000428826.2:c.1051C>A	p.His351Asn	p.H351N	ENST00000428826		351	Cac/Aac	11/21	1	2	FACETS	0.995	0.946	1	0.995	0.946	1	CLONAL	1	TRUE	1	0.901012722067286	2		810	725	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734137	58734137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1387369120	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	114	752	0	ENST00000305921.3:c.1195C>T	p.Pro399Ser	p.P399S	ENST00000305921	NM_003620.3	399	Cct/Tct	5/6	1	2	FACETS	0.388	0.349	0.428	0.388	0.349	0.428	SUBCLONAL	1	TRUE	1	0.901012722067286	2		752	653	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885925	59885925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	64	669	1	ENST00000259008.2:c.821C>T	p.Thr274Ile	p.T274I	ENST00000259008	NM_032043.2	274	aCt/aTt	7/20	1	2	FACETS	0.274	0.237	0.314	0.274	0.237	0.314	SUBCLONAL	1	TRUE	1	0.901012722067286	2		670	518	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857225	78857225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	232	788	0	ENST00000306801.3:c.1591C>T	p.His531Tyr	p.H531Y	ENST00000306801	NM_020761.2	531	Cac/Tac	15/34	1	2	FACETS	0.662	0.619	0.706	0.662	0.619	0.706	SUBCLONAL	1	TRUE	1	0.901012722067286	2		788	778	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394748	45394748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	53	600	1	ENST00000262160.6:c.601C>T	p.Pro201Ser	p.P201S	ENST00000262160	NM_005901.5	201	Cca/Tca	5/11	1	2	FACETS	0.252	0.215	0.293	0.252	0.215	0.293	SUBCLONAL	1	TRUE	1	0.901012722067286	2		601	466	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985710	60985710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	48	178	0	ENST00000333681.4:c.190G>A	p.Asp64Asn	p.D64N	ENST00000333681		64	Gac/Aac	2/3	1	2	FACETS	0.756	0.653	0.863	0.756	0.653	0.863	SUBCLONAL	1	TRUE	1	0.901012722067286	2		178	141	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254541	10254541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	115	697	0	ENST00000340748.4:c.2969C>T	p.Pro990Leu	p.P990L	ENST00000340748		990	cCc/cTc	28/40	0.749738040358694	3	FACETS	0.431	0.388	0.477	0.216	0.194	0.239	SUBCLONAL	1	TRUE	1	0.901012722067286	3		697	859	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602509	10602509	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	197	657	0	ENST00000171111.5:c.1069G>A	p.Asp357Asn	p.D357N	ENST00000171111	NM_203500.1	357	Gac/Aac	3/6	0.749738040358694	3	FACETS	0.789	0.732	0.848	0.394	0.366	0.424	SUBCLONAL	1	TRUE	1	0.901012722067286	3		657	804	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11114047	11114047	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	147	650	0	ENST00000358026.2:c.1975G>A	p.Glu659Lys	p.E659K	ENST00000358026	NM_001128849.1	659	Gaa/Aaa	13/36	0.749738040358694	3	FACETS	0.646	0.59	0.703	0.323	0.295	0.352	SUBCLONAL	1	TRUE	1	0.901012722067286	3		650	733	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134216	11134216	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	174	627	0	ENST00000358026.2:c.2882C>T	p.Thr961Ile	p.T961I	ENST00000358026	NM_001128849.1	961	aCc/aTc	20/36	0.749738040358694	3	FACETS	0.775	0.715	0.837	0.387	0.357	0.419	SUBCLONAL	1	TRUE	1	0.901012722067286	3		627	723	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170783	11170783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	199	731	1	ENST00000358026.2:c.4927G>A	p.Gly1643Ser	p.G1643S	ENST00000358026	NM_001128849.1	1643	Ggc/Agc	35/36	0.749738040358694	3	FACETS	0.677	0.627	0.729	0.339	0.313	0.365	SUBCLONAL	1	TRUE	1	0.901012722067286	3		732	946	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290899	15290899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145524535	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	266	1001	1	ENST00000263388.2:c.3311G>A	p.Gly1104Glu	p.G1104E	ENST00000263388	NM_000435.2	1104	gGg/gAg	20/33	0.749738040358694	3	FACETS	0.779	0.73	0.829	0.389	0.365	0.415	SUBCLONAL	1	TRUE	1	0.901012722067286	3		1002	1100	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354287	15354287	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1291730650	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	158	961	1	ENST00000263377.2:c.2593G>A	p.Ala865Thr	p.A865T	ENST00000263377	NM_058243.2	865	Gca/Aca	14/20	0.749738040358694	3	FACETS	0.386	0.352	0.421	0.193	0.176	0.211	SUBCLONAL	1	TRUE	1	0.901012722067286	3		962	1319	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953857	17953857	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471740073	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	94	855	2	ENST00000458235.1:c.545G>A	p.Gly182Glu	p.G182E	ENST00000458235	NM_000215.3	182	gGa/gAa	5/24	0.749738040358694	3	FACETS	0.267	0.236	0.3	0.133	0.118	0.15	SUBCLONAL	1	TRUE	1	0.901012722067286	3		857	1134	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18943164	18943164	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	44	195	3	ENST00000262803.5:c.146G>A	p.Gly49Asp	p.G49D	ENST00000262803	NM_002911.3	49	gGc/gAc	1/24	0.749738040358694	3	FACETS	0.583	0.493	0.681	0.291	0.246	0.341	SUBCLONAL	1	TRUE	1	0.901012722067286	3		198	243	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968289	18968289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	200	855	1	ENST00000262803.5:c.2129C>T	p.Ala710Val	p.A710V	ENST00000262803	NM_002911.3	710	gCc/gTc	15/24	0.749738040358694	3	FACETS	0.664	0.615	0.714	0.332	0.307	0.357	SUBCLONAL	1	TRUE	1	0.901012722067286	3		856	970	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976184	18976184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770076869	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	177	886	2	ENST00000262803.5:c.2944C>T	p.Pro982Ser	p.P982S	ENST00000262803	NM_002911.3	982	Ccc/Tcc	21/24	0.749738040358694	3	FACETS	0.552	0.508	0.598	0.276	0.254	0.299	SUBCLONAL	1	TRUE	1	0.901012722067286	3		888	1033	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209194	36209194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	14	187	0	ENST00000222270.7:c.274G>A	p.Gly92Ser	p.G92S	ENST00000222270	NM_014727.1	92	Ggc/Agc	1/37	0.749738040358694	3	FACETS	0.268	0.194	0.357	0.134	0.097	0.179	SUBCLONAL	1	TRUE	1	0.901012722067286	3		187	168	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139105	50139105	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	96	508	1	ENST00000246792.3:c.458C>T	p.Pro153Leu	p.P153L	ENST00000246792	NM_006270.3	153	cCc/cTc	5/6	0.749738040358694	3	FACETS	0.462	0.412	0.515	0.231	0.206	0.258	SUBCLONAL	1	TRUE	1	0.901012722067286	3		509	669	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912467	50912467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	236	760	1	ENST00000440232.2:c.1981G>A	p.Glu661Lys	p.E661K	ENST00000440232	NM_002691.3	661	Gag/Aag	16/27	0.749738040358694	3	FACETS	0.808	0.755	0.863	0.404	0.377	0.432	CLONAL	1	TRUE	1	0.901012722067286	3		761	940	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457177	25457177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1558650888	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	252	594	0	ENST00000264709.3:c.2710C>T	p.Pro904Ser	p.P904S	ENST00000264709	NM_175629.2	904	Ccg/Tcg	23/23	1	2	FACETS	0.825	0.776	0.874	0.825	0.776	0.874	CLONAL	1	TRUE	1	0.901012722067286	2		594	678	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965592	25965592	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	190	745	2	ENST00000435504.4:c.3614C>T	p.Ala1205Val	p.A1205V	ENST00000435504		1205	gCt/gTt	13/13	1	2	FACETS	0.626	0.581	0.672	0.626	0.581	0.672	SUBCLONAL	1	TRUE	1	0.901012722067286	2		747	674	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022264	26022264	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	169	667	0	ENST00000435504.4:c.393G>A	p.Trp131Ter	p.W131*	ENST00000435504		131	tgG/tgA	5/13	1	2	FACETS	0.687	0.636	0.74	0.687	0.636	0.74	SUBCLONAL	1	TRUE	1	0.901012722067286	2		667	546	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022268	26022268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	166	686	0	ENST00000435504.4:c.389G>A	p.Arg130Lys	p.R130K	ENST00000435504		130	aGg/aAg	5/13	1	2	FACETS	0.651	0.601	0.702	0.651	0.601	0.702	SUBCLONAL	1	TRUE	1	0.901012722067286	2		686	566	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39239490	39239490	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	100	400	0	ENST00000402219.2:c.2168-1G>A		p.X723_splice	ENST00000402219	NM_005633.3	723			1	2	FACETS	0.627	0.565	0.691	0.627	0.565	0.691	SUBCLONAL	1	TRUE	1	0.901012722067286	2		400	354	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630461	47630461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779085	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	38	703	0	ENST00000233146.2:c.131C>T	p.Thr44Met	p.T44M	ENST00000233146	NM_000251.2	44	aCg/aTg	1/16	1	2	FACETS	0.134	0.11	0.16	0.134	0.11	0.16	SUBCLONAL	1	TRUE	1	0.901012722067286	2		703	631	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026303	48026303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	108	454	0	ENST00000234420.5:c.1181C>T	p.Ser394Phe	p.S394F	ENST00000234420	NM_000179.2	394	tCt/tTt	4/10	1	2	FACETS	0.655	0.593	0.719	0.655	0.593	0.719	SUBCLONAL	1	TRUE	1	0.901012722067286	2		454	366	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028028	48028028	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs63749919	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	25	321	0	ENST00000234420.5:c.2906A>G	p.Tyr969Cys	p.Y969C	ENST00000234420	NM_000179.2	969	tAt/tGt	4/10	1	2	FACETS	0.194	0.153	0.241	0.194	0.153	0.241	SUBCLONAL	1	TRUE	1	0.901012722067286	2		321	286	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033352	48033352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750949	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	98	524	0	ENST00000234420.5:c.3656C>T	p.Thr1219Ile	p.T1219I	ENST00000234420	NM_000179.2	1219	aCt/aTt	8/10	1	2	FACETS	0.586	0.527	0.648	0.586	0.527	0.648	SUBCLONAL	1	TRUE	1	0.901012722067286	2		524	371	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033735	48033735	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773675555	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	28	385	0	ENST00000234420.5:c.3946G>A	p.Gly1316Arg	p.G1316R	ENST00000234420	NM_000179.2	1316	Gga/Aga	9/10	1	2	FACETS	0.174	0.138	0.214	0.174	0.138	0.214	SUBCLONAL	1	TRUE	1	0.901012722067286	2		385	358	SUCCESS
REL	5966	MSKCC	GRCh37	2	61148955	61148955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	13	481	0	ENST00000295025.8:c.1145G>A	p.Ser382Asn	p.S382N	ENST00000295025	NM_002908.2	382	aGt/aAt	11/11	0.82932139938498	1	FACETS	0.075	0.053	0.102	0.075	0.053	0.102	SUBCLONAL	1	TRUE	0	0.901012722067286	1		481	211	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881689	111881689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756773831	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	207	646	1	ENST00000393256.3:c.367G>A	p.Ala123Thr	p.A123T	ENST00000393256	NM_006538.4	123	Gcc/Acc	2/4	1	2	FACETS	0.648	0.604	0.694	0.648	0.604	0.694	SUBCLONAL	1	TRUE	1	0.901012722067286	2		647	709	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190656560	190656560	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	86	244	0	ENST00000441310.2:c.25G>A	p.Val9Ile	p.V9I	ENST00000441310	NM_000534.4	9	Gtt/Att	2/13	1	2	FACETS	0.718	0.644	0.794	0.718	0.644	0.794	SUBCLONAL	1	TRUE	1	0.901012722067286	2		244	266	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30946618	30946618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	56	442	2	ENST00000375687.4:c.40G>A	p.Ala14Thr	p.A14T	ENST00000375687	NM_015338.5	14	Gcc/Acc	1/13	0.901012722067286	3	FACETS	0.287	0.245	0.332	0.143	0.122	0.166	SUBCLONAL	1	TRUE	1	0.901012722067286	3		444	629	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017713	31017713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778674124	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	88	516	1	ENST00000375687.4:c.575G>A	p.Gly192Asp	p.G192D	ENST00000375687	NM_015338.5	192	gGc/gAc	8/13	0.901012722067286	3	FACETS	0.399	0.353	0.448	0.2	0.176	0.224	SUBCLONAL	1	TRUE	1	0.901012722067286	3		517	710	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023676	31023676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	181	796	0	ENST00000375687.4:c.3161C>T	p.Thr1054Ile	p.T1054I	ENST00000375687	NM_015338.5	1054	aCa/aTa	13/13	0.901012722067286	3	FACETS	0.593	0.547	0.642	0.297	0.273	0.321	SUBCLONAL	1	TRUE	1	0.901012722067286	3		796	982	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023936	31023936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	120	683	0	ENST00000375687.4:c.3421G>A	p.Asp1141Asn	p.D1141N	ENST00000375687	NM_015338.5	1141	Gac/Aac	13/13	0.901012722067286	3	FACETS	0.437	0.394	0.482	0.219	0.197	0.241	SUBCLONAL	1	TRUE	1	0.901012722067286	3		683	884	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31379461	31379461	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	186	608	1	ENST00000328111.2:c.868G>A	p.Ala290Thr	p.A290T	ENST00000328111	NM_006892.3	290	Gcc/Acc	8/23	0.901012722067286	3	FACETS	0.699	0.646	0.754	0.349	0.323	0.377	SUBCLONAL	1	TRUE	1	0.901012722067286	3		609	857	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31381341	31381341	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	65	420	0	ENST00000328111.2:c.1067-1G>A		p.X356_splice	ENST00000328111	NM_006892.3	356			0.901012722067286	3	FACETS	0.317	0.274	0.363	0.159	0.137	0.182	SUBCLONAL	1	TRUE	1	0.901012722067286	3		420	660	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264686	46264686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	46	359	0	ENST00000371998.3:c.1556C>T	p.Ser519Phe	p.S519F	ENST00000371998		519	tCc/tTc	12/23	0.901012722067286	3	FACETS	0.245	0.206	0.288	0.122	0.103	0.144	SUBCLONAL	1	TRUE	1	0.901012722067286	3		359	605	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139451	47139453	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	226	660	0	ENST00000409792.3:c.5134_5136del	p.Lys1712del	p.K1712del	ENST00000409792	NM_014159.6	1712	AAG/-	9/21	1	2	FACETS	0.874	0.821	0.928	0.874	0.821	0.928	CLONAL	1	TRUE	1	0.901012722067286	2		660	574	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139504	47139504	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	84	729	0	ENST00000409792.3:c.5083G>A	p.Val1695Ile	p.V1695I	ENST00000409792	NM_014159.6	1695	Gtc/Atc	9/21	1	2	FACETS	0.285	0.252	0.321	0.285	0.252	0.321	SUBCLONAL	1	TRUE	1	0.901012722067286	2		729	654	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725182	49725182	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	64	352	0	ENST00000449682.2:c.242+1G>A		p.X81_splice	ENST00000449682	NM_020998.3	81			1	2	FACETS	0.417	0.363	0.474	0.417	0.363	0.474	SUBCLONAL	1	TRUE	1	0.901012722067286	2		352	341	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678742	52678742	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	120	681	0	ENST00000394830.3:c.877G>A	p.Ala293Thr	p.A293T	ENST00000394830	NM_018313.4	293	Gct/Act	9/30	1	2	FACETS	0.413	0.373	0.455	0.413	0.373	0.455	SUBCLONAL	1	TRUE	1	0.901012722067286	2		681	645	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374293	138374293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	129	738	0	ENST00000289153.2:c.3151G>A	p.Glu1051Lys	p.E1051K	ENST00000289153	NM_006219.2	1051	Gaa/Aaa	22/22	1	2	FACETS	0.455	0.413	0.498	0.455	0.413	0.498	SUBCLONAL	1	TRUE	1	0.901012722067286	2		738	630	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430389	181430389	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	44	788	0	ENST00000325404.1:c.241C>T	p.Leu81Phe	p.L81F	ENST00000325404	NM_003106.3	81	Ctt/Ttt	1/1	1	2	FACETS	0.142	0.118	0.168	0.142	0.118	0.168	SUBCLONAL	1	TRUE	1	0.901012722067286	2		788	689	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430810	181430810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	95	956	1	ENST00000325404.1:c.662C>T	p.Pro221Leu	p.P221L	ENST00000325404	NM_003106.3	221	cCc/cTc	1/1	1	2	FACETS	0.241	0.214	0.27	0.241	0.214	0.27	SUBCLONAL	1	TRUE	1	0.901012722067286	2		957	874	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161241	185161241	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	35	721	1	ENST00000265026.3:c.668G>A	p.Cys223Tyr	p.C223Y	ENST00000265026	NM_004721.4	223	tGt/tAt	4/14	1	2	FACETS	0.137	0.111	0.165	0.137	0.111	0.165	SUBCLONAL	1	TRUE	1	0.901012722067286	2		722	568	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161244	185161244	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780508755	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	184	731	0	ENST00000265026.3:c.671C>T	p.Thr224Ile	p.T224I	ENST00000265026	NM_004721.4	224	aCt/aTt	4/14	1	2	FACETS	0.71	0.66	0.762	0.71	0.66	0.762	SUBCLONAL	1	TRUE	1	0.901012722067286	2		731	575	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604314	189604314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs910252082	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	184	527	0	ENST00000264731.3:c.1481C>T	p.Thr494Ile	p.T494I	ENST00000264731	NM_003722.4	494	aCc/aTc	11/14	1	2	FACETS	0.784	0.729	0.84	0.784	0.729	0.84	SUBCLONAL	1	TRUE	1	0.901012722067286	2		527	521	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961812	55961812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	27	548	0	ENST00000263923.4:c.2749G>A	p.Glu917Lys	p.E917K	ENST00000263923	NM_002253.2	917	Gaa/Aaa	20/30	1	2	FACETS	0.149	0.118	0.185	0.149	0.118	0.185	SUBCLONAL	1	TRUE	1	0.901012722067286	2		548	401	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984893	55984893	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	86	634	0	ENST00000263923.4:c.236G>A	p.Cys79Tyr	p.C79Y	ENST00000263923	NM_002253.2	79	tGc/tAc	3/30	1	2	FACETS	0.335	0.297	0.376	0.335	0.297	0.376	SUBCLONAL	1	TRUE	1	0.901012722067286	2		634	569	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201683	66201683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766614671	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	33	604	0	ENST00000273854.3:c.2819G>A	p.Ser940Asn	p.S940N	ENST00000273854	NM_004439.5	940	aGt/aAt	16/18	1	2	FACETS	0.132	0.107	0.16	0.132	0.107	0.16	SUBCLONAL	1	TRUE	1	0.901012722067286	2		604	555	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156574	106156574	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	24	389	0	ENST00000380013.4:c.1475C>T	p.Thr492Ile	p.T492I	ENST00000380013	NM_001127208.2	492	aCt/aTt	3/11	1	2	FACETS	0.155	0.121	0.194	0.155	0.121	0.194	SUBCLONAL	1	TRUE	1	0.901012722067286	2		389	344	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250835	153250835	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	44	486	0	ENST00000281708.4:c.1225G>A	p.Val409Ile	p.V409I	ENST00000281708	NM_033632.3	409	Gtc/Atc	8/12	1	2	FACETS	0.239	0.2	0.281	0.239	0.2	0.281	SUBCLONAL	1	TRUE	1	0.901012722067286	2		486	409	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539078	187539078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	105	703	0	ENST00000441802.2:c.8662G>A	p.Val2888Ile	p.V2888I	ENST00000441802	NM_005245.3	2888	Gtt/Att	10/27	1	2	FACETS	0.394	0.354	0.437	0.394	0.354	0.437	SUBCLONAL	1	TRUE	1	0.901012722067286	2		703	591	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515244	31515244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	60	962	0	ENST00000344624.3:c.1141G>A	p.Asp381Asn	p.D381N	ENST00000344624		381	Gac/Aac	5/33	1	2	FACETS	0.153	0.131	0.176	0.153	0.131	0.176	SUBCLONAL	1	TRUE	1	0.901012722067286	2		962	873	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38942952	38942952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	106	316	1	ENST00000357387.3:c.5035G>A	p.Asp1679Asn	p.D1679N	ENST00000357387	NM_152756.3	1679	Gat/Aat	37/38	1	2	FACETS	0.742	0.674	0.813	0.742	0.674	0.813	SUBCLONAL	1	TRUE	1	0.901012722067286	2		317	317	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160598	56160598	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	24	309	0	ENST00000399503.3:c.872C>T	p.Pro291Leu	p.P291L	ENST00000399503	NM_005921.1	291	cCt/cTt	4/20	1	2	FACETS	0.136	0.106	0.17	0.136	0.106	0.17	SUBCLONAL	1	TRUE	1	0.901012722067286	2		309	393	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591247	67591247	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	28	431	0	ENST00000274335.5:c.1746-1G>A		p.X582_splice	ENST00000274335		582			1	2	FACETS	0.138	0.11	0.17	0.138	0.11	0.17	SUBCLONAL	1	TRUE	1	0.901012722067286	2		431	450	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80021334	80021334	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773779617	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	199	661	0	ENST00000265081.6:c.1403C>T	p.Ala468Val	p.A468V	ENST00000265081	NM_002439.4	468	gCt/gTt	9/24	1	2	FACETS	0.722	0.672	0.772	0.722	0.672	0.772	SUBCLONAL	1	TRUE	1	0.901012722067286	2		661	612	SUCCESS
APC	324	MSKCC	GRCh37	5	112090654	112090654	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	79	368	0	ENST00000257430.4:c.67C>T	p.Leu23Phe	p.L23F	ENST00000257430	NM_000038.5	23	Ctt/Ttt	2/16	1	2	FACETS	0.577	0.512	0.645	0.577	0.512	0.645	SUBCLONAL	1	TRUE	1	0.901012722067286	2		368	304	SUCCESS
APC	324	MSKCC	GRCh37	5	112177266	112177266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	95	362	0	ENST00000257430.4:c.5975C>T	p.Pro1992Leu	p.P1992L	ENST00000257430	NM_000038.5	1992	cCc/cTc	16/16	1	2	FACETS	0.602	0.541	0.666	0.602	0.541	0.666	SUBCLONAL	1	TRUE	1	0.901012722067286	2		362	350	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131926969	131926969	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	10	235	1	ENST00000265335.6:c.1506G>A	p.Met502Ile	p.M502I	ENST00000265335		502	atG/atA	10/25	1	2	FACETS	0.119	0.08	0.168	0.119	0.08	0.168	SUBCLONAL	1	TRUE	1	0.901012722067286	2		236	186	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687106	176687106	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	124	655	0	ENST00000439151.2:c.5083C>T	p.Pro1695Ser	p.P1695S	ENST00000439151	NM_022455.4	1695	Cct/Tct	14/23	1	2	FACETS	0.445	0.404	0.489	0.445	0.404	0.489	SUBCLONAL	1	TRUE	1	0.901012722067286	2		655	618	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039520	180039520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	78	910	1	ENST00000261937.6:c.3523G>A	p.Gly1175Ser	p.G1175S	ENST00000261937	NM_182925.4	1175	Ggc/Agc	26/30	1	2	FACETS	0.28	0.246	0.317	0.28	0.246	0.317	SUBCLONAL	1	TRUE	1	0.901012722067286	2		911	618	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20482994	20482994	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	20	306	0	ENST00000346618.3:c.727G>A	p.Gly243Ser	p.G243S	ENST00000346618	NM_001949.4	243	Ggc/Agc	4/7	1	2	FACETS	0.125	0.095	0.161	0.125	0.095	0.161	SUBCLONAL	1	TRUE	1	0.901012722067286	2		306	354	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163787	32163787	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	159	674	1	ENST00000375023.3:c.5439G>A	p.Trp1813Ter	p.W1813*	ENST00000375023	NM_004557.3	1813	tgG/tgA	30/30	1	2	FACETS	0.68	0.627	0.734	0.68	0.627	0.734	SUBCLONAL	1	TRUE	1	0.901012722067286	2		675	519	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94067973	94067973	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	66	349	0	ENST00000369303.4:c.988+1G>A		p.X330_splice	ENST00000369303	NM_004440.3	330			1	2	FACETS	0.487	0.426	0.551	0.487	0.426	0.551	SUBCLONAL	1	TRUE	1	0.901012722067286	2		349	301	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536274	106536274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1450374584	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	183	550	1	ENST00000369096.4:c.241G>A	p.Ala81Thr	p.A81T	ENST00000369096	NM_001198.3	81	Gca/Aca	2/7	1	2	FACETS	0.752	0.699	0.807	0.752	0.699	0.807	SUBCLONAL	1	TRUE	1	0.901012722067286	2		551	540	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679100	117679100	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	31	558	2	ENST00000368508.3:c.3721G>A	p.Ala1241Thr	p.A1241T	ENST00000368508	NM_002944.2	1241	Gca/Aca	24/43	NA	2	FACETS	0.148	0.119	0.181			1	INDETERMINATE	1	TRUE	NA	0.901012722067286	2		560	465	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469914	157469914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	28	686	0	ENST00000346085.5:c.2708G>A	p.Gly903Glu	p.G903E	ENST00000346085	NM_020732.3	903	gGg/gAg	9/20	1	2	FACETS	0.112	0.089	0.138	0.112	0.089	0.138	SUBCLONAL	1	TRUE	1	0.901012722067286	2		686	557	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969983	161969983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774445597	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	136	659	0	ENST00000366898.1:c.986G>A	p.Gly329Asp	p.G329D	ENST00000366898	NM_004562.2	329	gGc/gAc	9/12	1	2	FACETS	0.447	0.407	0.488	0.447	0.407	0.488	SUBCLONAL	1	TRUE	1	0.901012722067286	2		659	676	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	43	752	1	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.901012722067286	3	FACETS	0.111	0.092	0.133	0.056	0.046	0.067	SUBCLONAL	1	TRUE	1	0.901012722067286	3		753	1243	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55238891	55238891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	48	658	0	ENST00000275493.2:c.1904G>A	p.Gly635Asp	p.G635D	ENST00000275493	NM_005228.3	635	gGc/gAc	16/28	0.901012722067286	3	FACETS	0.163	0.136	0.191	0.081	0.068	0.096	SUBCLONAL	1	TRUE	1	0.901012722067286	3		658	951	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411972	116411972	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1193904916	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	81	821	1	ENST00000397752.3:c.2957C>T	p.Ala986Val	p.A986V	ENST00000397752	NM_000245.2	986	gCc/gTc	14/21	0.901012722067286	3	FACETS	0.259	0.227	0.294	0.13	0.113	0.147	SUBCLONAL	1	TRUE	1	0.901012722067286	3		822	1006	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829039	128829039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	12	98	1	ENST00000249373.3:c.47G>A	p.Gly16Glu	p.G16E	ENST00000249373	NM_005631.4	16	gGg/gAg	1/12	0.901012722067286	3	FACETS	0.386	0.274	0.521	0.193	0.137	0.261	SUBCLONAL	1	TRUE	1	0.901012722067286	3		99	100	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913351	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	62	576	0	ENST00000288602.6:c.1397G>A	p.Gly466Glu	p.G466E	ENST00000288602	NM_004333.4	466	gGa/gAa	11/18	0.901012722067286	3	FACETS	0.345	0.298	0.397	0.173	0.149	0.199	SUBCLONAL	1	TRUE	1	0.901012722067286	3		576	578	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524255	148524255	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	57	436	0	ENST00000320356.2:c.728+1G>A		p.X243_splice	ENST00000320356	NM_004456.4	243			0.901012722067286	3	FACETS	0.375	0.322	0.433	0.188	0.161	0.217	SUBCLONAL	1	TRUE	1	0.901012722067286	3		436	489	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859768	151859768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778503	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	38	372	2	ENST00000262189.6:c.10894C>T	p.Pro3632Ser	p.P3632S	ENST00000262189	NM_170606.2	3632	Cca/Tca	43/59	0.901012722067286	3	FACETS	0.225	0.185	0.269	0.112	0.092	0.135	SUBCLONAL	1	TRUE	1	0.901012722067286	3		374	544	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879519	151879519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	80	482	1	ENST00000262189.6:c.5426C>T	p.Pro1809Leu	p.P1809L	ENST00000262189	NM_170606.2	1809	cCc/cTc	36/59	0.901012722067286	3	FACETS	0.413	0.364	0.467	0.207	0.182	0.234	SUBCLONAL	1	TRUE	1	0.901012722067286	3		483	623	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759467	133759467	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs557678853	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	43	670	0	ENST00000318560.5:c.1790C>T	p.Thr597Ile	p.T597I	ENST00000318560	NM_005157.4	597	aCc/aTc	11/11	1	2	FACETS	0.142	0.118	0.169	0.142	0.118	0.169	SUBCLONAL	1	TRUE	1	0.901012722067286	2		670	671	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801006	135801006	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748669519	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	104	470	0	ENST00000298552.3:c.331C>T	p.Pro111Ser	p.P111S	ENST00000298552	NM_001162426.1	111	Cct/Tct	5/23	1	2	FACETS	0.593	0.536	0.654	0.593	0.536	0.654	SUBCLONAL	1	TRUE	1	0.901012722067286	2		470	389	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223332	53223332	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	181	644	1	ENST00000375401.3:c.4027G>A	p.Asp1343Asn	p.D1343N	ENST00000375401	NM_004187.3	1343	Gat/Aat	23/26	1	2	FACETS	0.714	0.662	0.766	0.714	0.662	0.766	SUBCLONAL	1	TRUE	1	0.901012722067286	2		645	563	SUCCESS
AR	367	MSKCC	GRCh37	X	66766525	66766525	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1274441708	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	44	842	6	ENST00000374690.3:c.1537C>T	p.Pro513Ser	p.P513S	ENST00000374690	NM_000044.3	513	Ccc/Tcc	1/8	1	2	FACETS	0.123	0.102	0.146	0.123	0.102	0.146	SUBCLONAL	1	TRUE	1	0.901012722067286	2		848	795	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889197	76889197	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	20	442	0	ENST00000373344.5:c.4813G>A	p.Val1605Ile	p.V1605I	ENST00000373344	NM_000489.3	1605	Gta/Ata	18/35	1	2	FACETS	0.112	0.085	0.143	0.112	0.085	0.143	SUBCLONAL	1	TRUE	1	0.901012722067286	2		442	397	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0003833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	69	378	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.755	0.665	0.85	0.755	0.665	0.85	SUBCLONAL	1	TRUE	1	0.692424636861783	2		378	264	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	42	192	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.919	0.785	1	0.919	0.785	1	CLONAL	1	TRUE	1	0.692424636861783	2		192	132	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978823	13978824	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	112	320	0	ENST00000405192.2:c.283_284insT	p.Pro95LeufsTer16	p.P95Lfs*16	ENST00000405192	NM_001163147.1	95	cca/cTca	6/12	1	2	FACETS	0.983	0.895	1	0.983	0.895	1	CLONAL	1	TRUE	1	0.692424636861783	2		320	329	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795826	42795827	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCA	novel	NA	P-0003833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	158	309	0	ENST00000575354.2:c.2820_2823dup	p.Leu942AlafsTer210	p.L942Afs*210	ENST00000575354	NM_015125.3	939	ggc/gGCCAgc	11/20	0.692424636861783	1	FACETS	0.904	0.843	0.966	0.904	0.843	0.966	CLONAL	1	TRUE	0	0.692424636861783	1		309	330	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003866-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	54	300	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.122642870419503	4	FACETS	0.899	0.779	1	0.899	0.779	1	INDETERMINATE	2	FALSE	2	0.417494804997039	4		300	204	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0003876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	586	646	4	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.518570445423953	3	FACETS	0.983	0.953	1	0.983	0.953	1	CLONAL	3	TRUE	0	0.518325399917379	3		650	965	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517201	NA	P-0003876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	50	224	0	ENST00000263967.3:c.1637A>C	p.Gln546Pro	p.Q546P	ENST00000263967	NM_006218.2	546	cAg/cCg	10/21	0.117031503721567	6	FACETS	1	0.926	1			1	INDETERMINATE	1	TRUE	NA	0.518325399917379	6		224	343	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074392	8074392	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	601	681	0	ENST00000377482.5:c.267G>C	p.Lys89Asn	p.K89N	ENST00000377482	NM_018948.3	89	aaG/aaC	4/4	NA	2	FACETS	0.967	0.934	1			1	INDETERMINATE	2	TRUE	NA	0.518325399917379	2		681	1199	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054680	13054680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1409	237	576	0	ENST00000316448.5:c.1207G>A	p.Glu403Lys	p.E403K	ENST00000316448	NM_004343.3	403	Gaa/Aaa	9/9	0.513764168781083	4	FACETS	0.844	0.785	0.905	0.422	0.392	0.453	CLONAL	1	TRUE	2	0.518325399917379	4		576	1646	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0003886-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	139	285	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.499763626108469	1	FACETS	0.919	0.843	0.997	0.919	0.843	0.997	CLONAL	1	TRUE	0	0.499763626108469	1		285	454	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979551	55979551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375035755	NA	P-0003886-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	186	491	0	ENST00000263923.4:c.896G>A	p.Arg299Gln	p.R299Q	ENST00000263923	NM_002253.2	299	cGg/cAg	7/30	0.183610730580649	0	FACETS	0.497	0.46	0.535			1	INDETERMINATE	1	TRUE	0	0.499763626108469	0		491	749	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119050	70119050	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003886-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	249	250	0	ENST00000245479.2:c.622C>T	p.Gln208Ter	p.Q208*	ENST00000245479	NM_000346.3	208	Cag/Tag	2/3	0.499763626108469	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.499763626108469	2		250	493	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912580	NA	P-0003886-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	116	222	0	ENST00000342988.3:c.1157G>A	p.Gly386Asp	p.G386D	ENST00000342988	NM_005359.5	386	gGt/gAt	10/12	0.499763626108469	1	FACETS	0.891	0.81	0.974	0.891	0.81	0.974	CLONAL	1	TRUE	0	0.499763626108469	1		222	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579361	7579361	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0003886-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	182	312	0	ENST00000269305.4:c.326del	p.Phe109SerfsTer14	p.F109Sfs*14	ENST00000269305	NM_001126112.2	109	tTc/tc	4/11	0.433126313687724	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.499763626108469	1		312	503	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213912	66213912	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003886-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	148	300	0	ENST00000273854.3:c.2518del	p.Ile840PhefsTer11	p.I840Ffs*11	ENST00000273854	NM_004439.5	840	Att/tt	15/18	0.183610730580649	0	FACETS	0.539	0.494	0.585			1	INDETERMINATE	1	TRUE	0	0.499763626108469	0		300	550	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	153	331	0	ENST00000342988.3:c.1610A>T	p.Asp537Val	p.D537V	ENST00000342988	NM_005359.5	537	gAc/gTc	12/12	0.242973748039653	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.242973748039653	2		331	593	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0003892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	144	322	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.235344452287753	2	FACETS	0.917	0.839	0.999	0.917	0.839	0.999	CLONAL	2	TRUE	0	0.242973748039653	2		322	646	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922276	39922276	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	99	334	0	ENST00000378444.4:c.3896C>A	p.Thr1299Asn	p.T1299N	ENST00000378444	NM_001123385.1	1299	aCc/aAc	9/15	0.242973748039653	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.242973748039653	1		334	557	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0003901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	116	283	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.359052198530338	3	FACETS	0.897	0.814	0.982	0.897	0.814	0.982	CLONAL	2	TRUE	1	0.359052198530338	3		283	425	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0003901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	159	285	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.359052198530338	3	FACETS	0.987	0.911	1	0.987	0.911	1	CLONAL	2	TRUE	1	0.359052198530338	3		285	529	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0003901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	118	292	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.359052198530338	2	FACETS	0.805	0.733	0.881	0.805	0.733	0.881	CLONAL	2	TRUE	0	0.359052198530338	2		292	408	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0003901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	56	747	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.359052198530338	3	FACETS	0.897	0.771	1	0.449	0.385	0.517	CLONAL	1	TRUE	1	0.359052198530338	3		747	410	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411366	63411366	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	204	379	0	ENST00000330258.3:c.1801C>T	p.Arg601Ter	p.R601*	ENST00000330258	NM_152424.3	601	Cga/Tga	2/2	0.142443935668907	3	FACETS	1	0.946	1	0.678	0.632	0.725	INDETERMINATE	2	TRUE	0	0.359052198530338	3		379	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0003914-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	530	653	1	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	0.312900917833793	2	FACETS	0.964	0.924	1	0.964	0.924	1	CLONAL	2	TRUE	0	0.366229067524286	2		654	1502	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49413009	49413009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519953	NA	P-0003914-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	183	528	0	ENST00000418115.1:c.14G>A	p.Arg5Gln	p.R5Q	ENST00000418115	NM_001664.2	5	cGg/cAg	2/5	1	2	FACETS	0.81	0.746	0.877	0.81	0.746	0.877	CLONAL	1	TRUE	1	0.366229067524286	2		528	1234	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6031648	6031648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs116314131	NA	P-0003914-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	175	336	0	ENST00000265849.7:c.944G>A	p.Arg315Gln	p.R315Q	ENST00000265849	NM_000535.5	315	cGa/cAa	9/15	0.215616840626576	3	FACETS	1	0.985	1	0.645	0.594	0.697	INDETERMINATE	1	TRUE	1	0.366229067524286	3		336	877	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970969	21970969	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003914-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	218	416	0	ENST00000304494.5:c.389T>A	p.Leu130Gln	p.L130Q	ENST00000304494	NM_000077.4	130	cTg/cAg	2/3	0.302280879433704	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.366229067524286	1		416	931	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196272	108196272	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003914-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	105	358	0	ENST00000278616.4:c.6807+1G>A		p.X2269_splice	ENST00000278616	NM_000051.3	2269			1	2	FACETS	0.737	0.66	0.819	0.737	0.66	0.819	SUBCLONAL	1	TRUE	1	0.366229067524286	2		358	778	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070878	30070878	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003914-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	117	499	0	ENST00000338641.4:c.1394A>G	p.Glu465Gly	p.E465G	ENST00000338641	NM_000268.3	465	gAg/gGg	13/16	0.302280879433704	1	FACETS	0.572	0.515	0.632	0.572	0.515	0.632	SUBCLONAL	1	TRUE	0	0.366229067524286	1		499	913	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070882	30070883	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0003914-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	117	515	0	ENST00000338641.4:c.1398_1399del	p.Arg467SerfsTer27	p.R467Sfs*27	ENST00000338641	NM_000268.3	466	cgAAga/cgga	13/16	0.302280879433704	1	FACETS	0.564	0.507	0.623	0.564	0.507	0.623	SUBCLONAL	1	TRUE	0	0.366229067524286	1		515	926	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070877	30070883	+	frameshift_variant	Frame_Shift_Del	DEL	GAGCGAA	GAGCGAA	AGGCG	novel	NA	P-0003914-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	119	491	0	ENST00000338641.4:c.1393_1399delinsAGGCG	p.Glu465ArgfsTer29	p.E465Rfs*29	ENST00000338641	NM_000268.3	465	GAGCGAAga/AGGCGga	13/16	0.302280879433704	1	FACETS	0.578	0.521	0.639	0.578	0.521	0.639	SUBCLONAL	1	TRUE	0	0.366229067524286	1		491	918	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129655	11129655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	393	303	0	ENST00000358026.2:c.2461G>A	p.Glu821Lys	p.E821K	ENST00000358026	NM_001128849.1	821	Gag/Aag	17/36	0.335747657815997	1	FACETS	0.842	0.807	0.878	1	0.997	1	CLONAL	3	TRUE	0	0.335747657815997	1		303	771	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038526	47038526	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	389	209	0	ENST00000377604.3:c.688C>T	p.Arg230Ter	p.R230*	ENST00000377604	NM_001204468.1	230	Cga/Tga	8/24	1	1	FACETS	0.931	0.902	0.958	1	0.998	1	CLONAL	4	TRUE	0	0.335747657815997	1		209	518	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942137	17942137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	208	243	0	ENST00000458235.1:c.2878G>A	p.Glu960Lys	p.E960K	ENST00000458235	NM_000215.3	960	Gag/Aag	21/24	0.335747657815997	1	FACETS	1	0.983	1	1	0.995	1	CLONAL	2	TRUE	0	0.335747657815997	1		243	457	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0003920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	439	469	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.202719025854265	2	FACETS	0.964	0.925	1	1	0.996	1	CLONAL	3	TRUE	0	0.335747657815997	2		469	904	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0003920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	367	296	0	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	NA	2	FACETS	0.948	0.905	0.99			1	INDETERMINATE	3	TRUE	NA	0.335747657815997	2		296	769	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0003920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	42	556	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.202719025854265	2	FACETS	0.361	0.3	0.428	0.18	0.15	0.214	SUBCLONAL	1	TRUE	0	0.335747657815997	2		556	694	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	238	190	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	NA	2	FACETS	0.989	0.935	1			1	INDETERMINATE	3	TRUE	NA	0.335747657815997	2		190	478	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082254	16082254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	145	365	0	ENST00000281043.3:c.68C>T	p.Ser23Leu	p.S23L	ENST00000281043	NM_005378.4	23	tCg/tTg	2/3	0.335747657815997	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.335747657815997	1		365	707	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451860	29451860	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	289	374	0	ENST00000389048.3:c.2705G>A	p.Gly902Glu	p.G902E	ENST00000389048	NM_004304.4	902	gGa/gAa	16/29	0.335747657815997	1	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	0	0.335747657815997	1		374	611	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799775	72799775	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	250	281	0	ENST00000325599.8:c.1394C>T	p.Ser465Leu	p.S465L	ENST00000325599	NM_018130.2	465	tCa/tTa	11/11	1	2	FACETS	1	0.983	1	1	0.995	1	CLONAL	2	TRUE	1	0.335747657815997	2		281	666	SUCCESS
ATR	545	MSKCC	GRCh37	3	142238532	142238532	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	190	203	0	ENST00000350721.4:c.4361T>A	p.Leu1454Gln	p.L1454Q	ENST00000350721	NM_001184.3	1454	cTa/cAa	24/47	1	2	FACETS	1	0.967	1	1	0.994	1	CLONAL	2	TRUE	1	0.335747657815997	2		203	532	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244210	153244210	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	308	368	0	ENST00000281708.4:c.1947G>A	p.Trp649Ter	p.W649*	ENST00000281708	NM_033632.3	649	tgG/tgA	12/12	0.335747657815997	1	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	0	0.335747657815997	1		368	680	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628449	187628449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1346000368	NA	P-0003920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	264	285	0	ENST00000441802.2:c.2533G>A	p.Glu845Lys	p.E845K	ENST00000441802	NM_005245.3	845	Gaa/Aaa	2/27	0.335747657815997	1	FACETS	1	0.991	1	1	0.996	1	CLONAL	2	TRUE	0	0.335747657815997	1		285	539	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982728	90982728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	248	263	0	ENST00000265433.3:c.760G>A	p.Glu254Lys	p.E254K	ENST00000265433	NM_002485.4	254	Gaa/Aaa	7/16	0.236432222603638	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.335747657815997	3		263	693	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196860	108196860	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	212	202	0	ENST00000278616.4:c.6883G>T	p.Glu2295Ter	p.E2295*	ENST00000278616	NM_000051.3	2295	Gaa/Taa	47/63	0.335747657815997	1	FACETS	1	0.968	1	1	0.995	1	CLONAL	2	TRUE	0	0.335747657815997	1		202	501	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390416	118390416	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520053	NA	P-0003920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	40	304	1	ENST00000534358.1:c.11230C>T	p.Arg3744Ter	p.R3744*	ENST00000534358	NM_005933.3	3744	Cga/Tga	32/36	0.335747657815997	1	FACETS	0.289	0.239	0.345	0.289	0.239	0.345	SUBCLONAL	1	TRUE	0	0.335747657815997	1		305	686	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021428	42021428	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	356	563	0	ENST00000219905.7:c.3724C>T	p.Arg1242Ter	p.R1242*	ENST00000219905	NM_001164273.1	1242	Cga/Tga	11/24	0.335747657815997	1	FACETS	0.838	0.795	0.881	1	0.996	1	CLONAL	2	TRUE	0	0.335747657815997	1		563	1053	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434978	56434978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	136	244	0	ENST00000407977.2:c.2159C>T	p.Ser720Leu	p.S720L	ENST00000407977		720	tCa/tTa	9/10	0.326033865551167	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.335747657815997	1		244	593	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129632	11129632	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	148	298	0	ENST00000358026.2:c.2439-1G>A		p.X813_splice	ENST00000358026	NM_001128849.1	813			0.335747657815997	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.335747657815997	1		298	727	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792453	33792453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	357	432	0	ENST00000498907.2:c.868G>A	p.Glu290Lys	p.E290K	ENST00000498907	NM_004364.3	290	Gag/Aag	1/1	0.335747657815997	1	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	0	0.335747657815997	1		432	742	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872380	45872380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	169	263	0	ENST00000391945.4:c.131C>T	p.Ser44Leu	p.S44L	ENST00000391945	NM_000400.3	44	tCa/tTa	3/23	0.335747657815997	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.335747657815997	1		263	628	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969452	44969452	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	353	209	0	ENST00000377967.4:c.4134del	p.Tyr1378Ter	p.Y1378*	ENST00000377967	NM_021140.2	1378	taC/ta	28/29	1	1	FACETS	0.937	0.907	0.966	1	0.997	1	CLONAL	4	TRUE	0	0.335747657815997	1		209	467	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974820	21974843	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	GCTCCATGCTGCTCCCCGCCGCCC	GCTCCATGCTGCTCCCCGCCGCCC	-	novel	NA	P-0003920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	77	56	0	ENST00000304494.5:c.-17_7del		p.*6*	ENST00000304494	NM_000077.4	?-3/156		1/3	0.335747657815997	1	FACETS	1	0.932	1	1	0.986	1	CLONAL	2	TRUE	0	0.335747657815997	1		56	182	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115928	8115929	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0003920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	97	185	0	ENST00000346208.3:c.1275_1276dup	p.Ser426TyrfsTer50	p.S426Yfs*50	ENST00000346208		425	cca/ccATa	6/6	0.165398741721923	2	FACETS	0.816	0.734	0.901	0.816	0.734	0.901	INDETERMINATE	2	TRUE	0	0.335747657815997	2		185	354	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0003930-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	55	322	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.362205568383349	5	FACETS	0.383	0.326	0.445			1	SUBCLONAL	1	TRUE	NA	0.362205568383349	5		322	1225	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004202	29004202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137862999	NA	P-0003930-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1414	278	555	1	ENST00000282397.4:c.1091C>T	p.Ser364Leu	p.S364L	ENST00000282397	NM_002019.4	364	tCg/tTg	8/30	0.362205568383349	5	FACETS	1	0.992	1	0.35	0.327	0.374	CLONAL	1	TRUE	1	0.362205568383349	5		556	1692	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81534611	81534611	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003930-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1294	143	612	0	ENST00000298171.2:c.256G>A	p.Asp86Asn	p.D86N	ENST00000298171	NM_000369.2	86	Gat/Aat	3/10	0.362205568383349	4	FACETS	0.749	0.68	0.821	0.374	0.34	0.411	SUBCLONAL	1	TRUE	2	0.362205568383349	4		612	1437	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070628	67070628	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003930-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	354	533	1	ENST00000412916.2:c.252G>C	p.Glu84Asp	p.E84D	ENST00000412916		84	gaG/gaC	3/6	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.362205568383349	2		534	1454	SUCCESS
AR	367	MSKCC	GRCh37	X	66941780	66941780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003930-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	74	378	0	ENST00000374690.3:c.2424G>A	p.Met808Ile	p.M808I	ENST00000374690	NM_000044.3	808	atG/atA	6/8	0.250463964590361	2	FACETS	0.693	0.607	0.785			1	SUBCLONAL	1	TRUE	NA	0.362205568383349	2		378	590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578377	7578378	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0003930-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	100	406	0	ENST00000269305.4:c.552_553del	p.Asp184GlufsTer24	p.D184Efs*24	ENST00000269305	NM_001126112.2	184	gaTAgc/gagc	5/11	NA	2	FACETS	0.888	0.803	0.976			1	INDETERMINATE	2	TRUE	NA	0.362205568383349	2		406	311	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	66	376	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.796048166410195	2	FACETS	0.52	0.454	0.589	0.26	0.227	0.295	SUBCLONAL	1	TRUE	0	0.796048166410195	2		376	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0003950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	116	205	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.796048166410195	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.796048166410195	1		205	163	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115750	8115750	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs104894164	NA	P-0003950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	551	691	3	ENST00000346208.3:c.1096C>T	p.Arg366Ter	p.R366*	ENST00000346208		366	Cga/Tga	6/6	0.550721727037331	5	FACETS	0.84	0.808	0.871	0.84	0.808	0.871	CLONAL	3	TRUE	2	0.796048166410195	5		694	1206	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100663	67100663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	351	387	0	ENST00000412916.2:c.361G>A	p.Gly121Ser	p.G121S	ENST00000412916		121	Ggt/Agt	4/6	NA	2	FACETS	0.991	0.961	1			1	INDETERMINATE	2	TRUE	NA	0.796048166410195	2		387	445	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739066	40739066	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	56	228	0	ENST00000373198.4:c.3218G>A	p.Gly1073Asp	p.G1073D	ENST00000373198	NM_133170.3	1073	gGc/gAc	24/32	0.300099881895797	5	FACETS	0.77	0.662	0.887	0.154	0.132	0.178	INDETERMINATE	1	TRUE	0	0.796048166410195	5		228	401	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40761126	40761127	+	inframe_insertion	In_Frame_Ins	INS	-	-	TATGACAAAGGTGTTGGGTCGCGGCCTCTCGGTCTTCATCAGCTGGCA	novel	NA	P-0003950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	112	255	0	ENST00000392038.2:c.178_225dup	p.Cys60_Ile75dup	p.C60_I75dup	ENST00000392038	NM_001626.4	60	-/TGCCAGCTGATGAAGACCGAGAGGCCGCGACCCAACACCTTTGTCATA	4/14	0.390284632625077	3	FACETS	0.708	0.638	0.78	0.354	0.319	0.39	INDETERMINATE	1	TRUE	1	0.796048166410195	3		255	556	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0003967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	99	573	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.278010812208684	5	FACETS	1	0.928	1	0.694	0.623	0.767	CLONAL	2	TRUE	2	0.342016998504497	5		573	421	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333081	70333081	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	36	328	0	ENST00000373644.4:c.986T>A	p.Phe329Tyr	p.F329Y	ENST00000373644	NM_030625.2	329	tTc/tAc	2/12	NA	2	FACETS	0.388	0.319	0.467			1	INDETERMINATE	1	TRUE	NA	0.342016998504497	2		328	542	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920416	114920416	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	85	350	0	ENST00000543371.1:c.1357C>T	p.Leu453Phe	p.L453F	ENST00000543371	NM_001198531.1	453	Ctt/Ttt	13/14	0.312385904489874	1	FACETS	0.717	0.634	0.804	0.717	0.634	0.804	SUBCLONAL	1	TRUE	0	0.342016998504497	1		350	575	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039206	49039206	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	224	280	0	ENST00000267163.4:c.2284C>T	p.Gln762Ter	p.Q762*	ENST00000267163	NM_000321.2	762	Cag/Tag	22/27	0.342016998504497	3	FACETS	1	0.985	1	0.778	0.729	0.829	CLONAL	2	TRUE	0	0.342016998504497	3		280	657	SUCCESS
AR	367	MSKCC	GRCh37	X	66942741	66942741	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs9332969	NA	P-0003967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	85	520	0	ENST00000374690.3:c.2522G>T	p.Arg841Leu	p.R841L	ENST00000374690	NM_000044.3	841	cGt/cTt	7/8	0.342016998504497	1	FACETS	0.555	0.49	0.625	0.555	0.49	0.625	SUBCLONAL	1	TRUE	0	0.342016998504497	1		520	742	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936983	48936983	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690863	NA	P-0003973-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	288	405	0	ENST00000267163.4:c.751C>T	p.Arg251Ter	p.R251*	ENST00000267163	NM_000321.2	251	Cga/Tga	8/27	0.876370843766595	1	FACETS	0.957	0.922	0.99	0.957	0.922	0.99	CLONAL	1	TRUE	0	0.876370843766595	1		405	386	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718746	190718746	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003973-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	341	462	0	ENST00000441310.2:c.904C>T	p.Pro302Ser	p.P302S	ENST00000441310	NM_000534.4	302	Cct/Tct	8/13	0.174608418126524	3	FACETS	1	0.994	1	0.656	0.623	0.689	INDETERMINATE	1	TRUE	1	0.876370843766595	3		462	853	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728735	190728735	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003973-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	216	308	0	ENST00000441310.2:c.2123T>G	p.Ile708Arg	p.I708R	ENST00000441310	NM_000534.4	708	aTa/aGa	10/13	0.174608418126524	3	FACETS	1	0.993	1	0.748	0.703	0.793	INDETERMINATE	1	TRUE	1	0.876370843766595	3		308	474	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677851	117677851	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003973-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	240	420	0	ENST00000368508.3:c.4082G>A	p.Trp1361Ter	p.W1361*	ENST00000368508	NM_002944.2	1361	tGg/tAg	25/43	1	2	FACETS	0.99	0.934	1	0.99	0.934	1	CLONAL	1	TRUE	1	0.876370843766595	2		420	553	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830799	3830799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003973-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	185	376	0	ENST00000262367.5:c.1757C>T	p.Thr586Ile	p.T586I	ENST00000262367	NM_004380.2	586	aCc/aTc	8/31	0.876370843766595	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.876370843766595	1		376	236	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021130	31021130	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1386196069	NA	P-0003973-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	27	363	0	ENST00000375687.4:c.1129C>T	p.Gln377Ter	p.Q377*	ENST00000375687	NM_015338.5	377	Cag/Tag	12/13	1	2	FACETS	0.131	0.104	0.162	0.131	0.104	0.162	SUBCLONAL	1	TRUE	1	0.876370843766595	2		363	471	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303190	15303190	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs143385744	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	19	342	0	ENST00000263388.2:c.338G>A	p.Arg113Gln	p.R113Q	ENST00000263388	NM_000435.2	113	cGa/cAa	3/33	1	2	FACETS	0.716	0.542	0.92	0.716	0.542	0.92	CLONAL	1	TRUE	1	0.15	2		342	354	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202065	67202065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776495062	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	30	235	0	ENST00000312629.5:c.1168G>A	p.Val390Met	p.V390M	ENST00000312629	NM_003952.2	390	Gtg/Atg	14/15	0.0836944055658734	0	FACETS	0.717	0.577	0.877			1	INDETERMINATE	1	TRUE	0	0.15	0		235	474	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727451	66727451	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519729	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	10	191	0	ENST00000307102.5:c.167A>C	p.Gln56Pro	p.Q56P	ENST00000307102	NM_002755.3	56	cAg/cCg	2/11	0.3	3	FACETS	0.375	0.253	0.53			1	SUBCLONAL	1	TRUE	NA	0.15	3		191	382	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137785	64137785	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779751342	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	18	274	0	ENST00000334205.4:c.1886G>A	p.Arg629His	p.R629H	ENST00000334205	NM_003942.2	629	cGc/cAc	15/17	0.0836944055658734	0	FACETS	0.593	0.446	0.767			1	INDETERMINATE	1	TRUE	0	0.15	0		274	344	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	24	159	0	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	0.796	0.628	0.988	1	0.934	1	CLONAL	2	TRUE	1	0.15	2		159	201	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426123	138426123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217537873	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	24	185	0	ENST00000289153.2:c.1408G>A	p.Glu470Lys	p.E470K	ENST00000289153	NM_006219.2	470	Gaa/Aaa	9/22	1	2	FACETS	0.731	0.572	0.914	0.731	0.572	0.914	CLONAL	1	TRUE	1	0.15	2		185	438	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	22	199	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	0.126450618555662	3	FACETS	0.809	0.626	1	0.404	0.313	0.511	CLONAL	1	TRUE	1	0.15	3		199	390	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	35	497	0	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	1	2	FACETS	0.97	0.795	1	0.97	0.795	1	CLONAL	1	TRUE	1	0.15	2		497	481	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	19	170	0	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	0.3	3	FACETS	1	0.809	1			1	CLONAL	1	TRUE	NA	0.15	3		170	253	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791757	42791757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568504941	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	20	284	0	ENST00000575354.2:c.643C>T	p.Arg215Trp	p.R215W	ENST00000575354	NM_015125.3	215	Cgg/Tgg	5/20	1	2	FACETS	0.58	0.442	0.742	0.58	0.442	0.742	SUBCLONAL	1	TRUE	1	0.15	2		284	460	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564387	139564387	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146989870	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	27	206	0	ENST00000308874.7:c.335G>A	p.Arg112Gln	p.R112Q	ENST00000308874		112	cGg/cAg	6/10	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.15	2		206	290	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	18	133	0	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	1	0.15	2		133	203	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744385	41744385	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	27	349	0	ENST00000301178.4:c.1010del	p.Pro337LeufsTer29	p.P337Lfs*29	ENST00000301178	NM_021913.4	335	ggC/gg	8/20	1	2	FACETS	0.813	0.646	1	0.813	0.646	1	CLONAL	1	TRUE	1	0.15	2		349	443	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983228	149983228	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	24	222	0	ENST00000253339.5:c.3030del	p.Phe1010LeufsTer10	p.F1010Lfs*10	ENST00000253339		1010	ttT/tt	7/7	1	2	FACETS	0.703	0.55	0.881	0.703	0.55	0.881	SUBCLONAL	1	TRUE	1	0.15	2		222	455	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777120	9777120	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	29	467	0	ENST00000377346.4:c.884A>C	p.Gln295Pro	p.Q295P	ENST00000377346	NM_005026.3	295	cAg/cCg	7/24	1	2	FACETS	0.761	0.61	0.934	0.761	0.61	0.934	CLONAL	1	TRUE	1	0.15	2		467	508	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259486	16259486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759585687	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	17	156	0	ENST00000375759.3:c.6751G>A	p.Ala2251Thr	p.A2251T	ENST00000375759	NM_015001.2	2251	Gca/Aca	11/15	1	2	FACETS	0.862	0.644	1	0.862	0.644	1	CLONAL	1	TRUE	1	0.15	2		156	263	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106355	27106355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773909963	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	19	187	0	ENST00000324856.7:c.5966G>A	p.Arg1989Gln	p.R1989Q	ENST00000324856	NM_006015.4	1989	cGa/cAa	20/20	1	2	FACETS	0.698	0.529	0.897	0.698	0.529	0.897	SUBCLONAL	1	TRUE	1	0.15	2		187	363	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726490	46726490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149246216	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	15	196	0	ENST00000371975.4:c.569C>T	p.Thr190Met	p.T190M	ENST00000371975	NM_003579.3	190	aCg/aTg	7/18	1	2	FACETS	0.813	0.595	1	0.813	0.595	1	CLONAL	1	TRUE	1	0.15	2		196	246	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65323452	65323452	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765489448	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	24	153	0	ENST00000342505.4:c.1345G>A	p.Ala449Thr	p.A449T	ENST00000342505	NM_002227.2	449	Gcc/Acc	10/25	1	2	FACETS	1	0.79	1	1	0.79	1	CLONAL	1	TRUE	1	0.15	2		153	318	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651636	206651636	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	26	295	0	ENST00000367120.3:c.946C>A	p.Leu316Met	p.L316M	ENST00000367120	NM_014002.3	316	Ctg/Atg	9/22	1	2	FACETS	0.762	0.602	0.945	0.762	0.602	0.945	CLONAL	1	TRUE	1	0.15	2		295	455	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641507	47641507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750934	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	53	520	0	ENST00000233146.2:c.892C>T	p.Gln298Ter	p.Q298*	ENST00000233146	NM_000251.2	298	Cag/Tag	5/16	0.176244634936324	0	FACETS	0.777	0.661	0.905			1	CLONAL	1	TRUE	0	0.15	0		520	773	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662211	227662211	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	24	265	0	ENST00000305123.5:c.1244C>T	p.Ser415Leu	p.S415L	ENST00000305123	NM_005544.2	415	tCg/tTg	1/2	0.3	3	FACETS	0.935	0.733	1			1	CLONAL	1	TRUE	NA	0.15	3		265	368	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713292	30713292	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150022335	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	23	160	0	ENST00000295754.5:c.617C>T	p.Thr206Met	p.T206M	ENST00000295754	NM_003242.5	206	aCg/aTg	4/7	0.126450618555662	3	FACETS	0.874	0.681	1	0.437	0.34	0.549	CLONAL	1	TRUE	1	0.15	3		160	377	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183540	185183540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	22	191	0	ENST00000265026.3:c.1394C>T	p.Ala465Val	p.A465V	ENST00000265026	NM_004721.4	465	gCg/gTg	9/14	1	2	FACETS	0.752	0.582	0.95	0.752	0.582	0.95	CLONAL	1	TRUE	1	0.15	2		191	390	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527306	187527306	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1282821100	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	13	192	0	ENST00000441802.2:c.10268C>T	p.Thr3423Met	p.T3423M	ENST00000441802	NM_005245.3	3423	aCg/aTg	17/27	0.126450618555662	0	FACETS	0.599	0.427	0.809			1	SUBCLONAL	1	TRUE	0	0.15	0		192	246	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523313	176523313	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	19	213	0	ENST00000292408.4:c.1970C>T	p.Ala657Val	p.A657V	ENST00000292408	NM_213647.1	657	gCg/gTg	15/18	1	2	FACETS	0.931	0.708	1	0.931	0.708	1	CLONAL	1	TRUE	1	0.15	2		213	272	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829305	128829305	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	32	492	0	ENST00000249373.3:c.313A>G	p.Lys105Glu	p.K105E	ENST00000249373	NM_005631.4	105	Aag/Gag	1/12	1	2	FACETS	0.811	0.657	0.986	0.811	0.657	0.986	CLONAL	1	TRUE	1	0.15	2		492	526	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738073	145738073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773154902	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	51	282	0	ENST00000428558.2:c.2837G>A	p.Arg946His	p.R946H	ENST00000428558	NM_004260.3	946	cGt/cAt	17/22	1	2	FACETS	0.977	0.834	1	1	0.974	1	CLONAL	2	TRUE	1	0.15	2		282	348	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399156	139399156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769050541	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	19	224	0	ENST00000277541.6:c.4987C>T	p.Arg1663Trp	p.R1663W	ENST00000277541	NM_017617.3	1663	Cgg/Tgg	26/34	1	2	FACETS	1	0.767	1	1	0.767	1	CLONAL	1	TRUE	1	0.15	2		224	251	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310860	123310860	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147987917	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	37	354	2	ENST00000358487.5:c.568C>T	p.Arg190Trp	p.R190W	ENST00000358487	NM_000141.4	190	Cgg/Tgg	5/18	0.3	0	FACETS	0.949	0.782	1			1	CLONAL	1	TRUE	0	0.15	0		356	442	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424188	49424188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750738360	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	14	146	0	ENST00000301067.7:c.13874C>T	p.Ser4625Leu	p.S4625L	ENST00000301067	NM_003482.3	4625	tCg/tTg	42/54	1	2	FACETS	0.881	0.637	1	0.881	0.637	1	CLONAL	1	TRUE	1	0.15	2		146	212	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494996	56494996	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201958747	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	17	202	0	ENST00000267101.3:c.3353G>A	p.Arg1118Gln	p.R1118Q	ENST00000267101	NM_001982.3	1118	cGg/cAg	27/28	1	2	FACETS	0.689	0.513	0.898	0.689	0.513	0.898	SUBCLONAL	1	TRUE	1	0.15	2		202	329	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861781	57861781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373770232	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	54	616	0	ENST00000228682.2:c.1082C>T	p.Pro361Leu	p.P361L	ENST00000228682	NM_005269.2	361	cCg/cTg	10/12	1	2	FACETS	0.905	0.771	1	0.905	0.771	1	CLONAL	1	TRUE	1	0.15	2		616	796	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426812	121426812	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377110124	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	18	323	0	ENST00000257555.6:c.503G>A	p.Arg168His	p.R168H	ENST00000257555		168	cGc/cAc	2/10	0.126450618555662	0	FACETS	0.656	0.494	0.848			1	SUBCLONAL	1	TRUE	0	0.15	0		323	311	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250211	133250211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115047349	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	22	333	0	ENST00000320574.5:c.1309G>A	p.Val437Met	p.V437M	ENST00000320574	NM_006231.2	437	Gtg/Atg	13/49	0.126450618555662	0	FACETS	0.751	0.582	0.947			1	CLONAL	1	TRUE	0	0.15	0		333	332	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28611336	28611336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201905189	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	44	281	0	ENST00000241453.7:c.1295C>T	p.Thr432Met	p.T432M	ENST00000241453	NM_004119.2	432	aCg/aTg	10/24	1	2	FACETS	0.981	0.822	1	0.981	0.822	1	CLONAL	1	TRUE	1	0.15	2		281	598	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121873	2121873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746315218	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	17	225	0	ENST00000219476.3:c.2035G>A	p.Val679Met	p.V679M	ENST00000219476	NM_000548.3	679	Gtg/Atg	19/42	0.0836944055658734	0	FACETS	0.864	0.646	1			1	INDETERMINATE	1	TRUE	0	0.15	0		225	223	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371644	89371644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs949172972	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	29	432	0	ENST00000301030.4:c.196G>A	p.Ala66Thr	p.A66T	ENST00000301030	NM_001256183.1	66	Gcc/Acc	4/13	1	2	FACETS	0.783	0.627	0.96	0.783	0.627	0.96	CLONAL	1	TRUE	1	0.15	2		432	494	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805092	89805092	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748856769	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	24	240	0	ENST00000389301.3:c.4285G>A	p.Asp1429Asn	p.D1429N	ENST00000389301	NM_000135.2	1429	Gac/Aac	43/43	1	2	FACETS	0.952	0.747	1	0.952	0.747	1	CLONAL	1	TRUE	1	0.15	2		240	336	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858916	89858916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142620413	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	22	197	0	ENST00000389301.3:c.1046C>T	p.Ala349Val	p.A349V	ENST00000389301	NM_000135.2	349	gCg/gTg	12/43	1	2	FACETS	0.845	0.655	1	0.845	0.655	1	CLONAL	1	TRUE	1	0.15	2		197	347	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131277	17131277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778275358	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	40	383	2	ENST00000285071.4:c.175C>T	p.Arg59Cys	p.R59C	ENST00000285071	NM_144997.5	59	Cgt/Tgt	4/14	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.15	2		385	447	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131387	17131387	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768734584	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	21	266	0	ENST00000285071.4:c.65C>T	p.Thr22Met	p.T22M	ENST00000285071	NM_144997.5	22	aCg/aTg	4/14	1	2	FACETS	0.812	0.625	1	0.812	0.625	1	CLONAL	1	TRUE	1	0.15	2		266	345	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682455	37682455	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	23	222	0	ENST00000447079.4:c.3646C>T	p.Gln1216Ter	p.Q1216*	ENST00000447079	NM_015083.1	1216	Cag/Tag	13/14	1	2	FACETS	0.852	0.664	1	0.852	0.664	1	CLONAL	1	TRUE	1	0.15	2		222	360	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353821	40353821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1177305205	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	41	654	0	ENST00000293328.3:c.2299C>T	p.Arg767Trp	p.R767W	ENST00000293328	NM_012448.3	767	Cgg/Tgg	19/19	1	2	FACETS	0.752	0.625	0.894	0.752	0.625	0.894	SUBCLONAL	1	TRUE	1	0.15	2		654	727	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436097	56436097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	23	218	2	ENST00000407977.2:c.1040G>A	p.Gly347Asp	p.G347D	ENST00000407977		347	gGc/gAc	9/10	1	2	FACETS	0.884	0.689	1	0.884	0.689	1	CLONAL	1	TRUE	1	0.15	2		220	347	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612359	1612359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1341689226	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	49	646	1	ENST00000344749.5:c.1660C>T	p.Arg554Trp	p.R554W	ENST00000344749	NM_001136139.2	554	Cgg/Tgg	18/19	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.15	2		647	580	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244106	5244106	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	21	487	0	ENST00000357368.4:c.1376G>A	p.Gly459Asp	p.G459D	ENST00000357368	NM_002850.3	459	gGc/gAc	11/38	0.204061764651238	0	FACETS	0.607	0.467	0.771			1	SUBCLONAL	1	TRUE	0	0.15	0		487	392	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273534	5273534	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1397380294	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	33	385	0	ENST00000357368.4:c.298C>T	p.Arg100Trp	p.R100W	ENST00000357368	NM_002850.3	100	Cgg/Tgg	4/38	0.204061764651238	0	FACETS	0.949	0.774	1			1	CLONAL	1	TRUE	0	0.15	0		385	394	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600516	10600516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1384602464	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	24	258	0	ENST00000171111.5:c.1339C>T	p.Arg447Trp	p.R447W	ENST00000171111	NM_203500.1	447	Cgg/Tgg	4/6	1	2	FACETS	0.808	0.633	1	0.808	0.633	1	CLONAL	1	TRUE	1	0.15	2		258	396	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101911	11101911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1052250887	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	23	266	0	ENST00000358026.2:c.1331G>A	p.Arg444His	p.R444H	ENST00000358026	NM_001128849.1	444	cGc/cAc	8/36	1	2	FACETS	0.996	0.777	1	0.996	0.777	1	CLONAL	1	TRUE	1	0.15	2		266	308	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744408	41744408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374067962	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	28	392	0	ENST00000301178.4:c.1028C>T	p.Thr343Met	p.T343M	ENST00000301178	NM_021913.4	343	aCg/aTg	8/20	1	2	FACETS	0.765	0.61	0.942	0.765	0.61	0.942	CLONAL	1	TRUE	1	0.15	2		392	488	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714649	52714649	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776781710	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	19	256	0	ENST00000322088.6:c.407C>T	p.Ala136Val	p.A136V	ENST00000322088	NM_014225.5	136	gCg/gTg	4/15	0.3	1	FACETS	0.814	0.618	1	0.814	0.618	1	CLONAL	1	TRUE	0	0.15	1		256	288	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546608	9546608	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	30	315	0	ENST00000353224.5:c.1414G>T	p.Gly472Trp	p.G472W	ENST00000353224	NM_177990.2	472	Ggg/Tgg	5/10	1	2	FACETS	0.875	0.705	1	0.875	0.705	1	CLONAL	1	TRUE	1	0.15	2		315	457	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023408	31023408	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515401	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	23	139	1	ENST00000375687.4:c.2893C>T	p.Arg965Ter	p.R965*	ENST00000375687	NM_015338.5	965	Cga/Tga	13/13	1	2	FACETS	0.98	0.764	1	0.98	0.764	1	CLONAL	1	TRUE	1	0.15	2		140	313	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031696	36031696	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1305388441	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	23	373	1	ENST00000358208.4:c.1525C>T	p.Arg509Trp	p.R509W	ENST00000358208		509	Cgg/Tgg	12/12	1	2	FACETS	0.824	0.642	1	0.824	0.642	1	CLONAL	1	TRUE	1	0.15	2		374	372	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755732	39755732	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	14	156	0	ENST00000288319.7:c.1033G>A	p.Asp345Asn	p.D345N	ENST00000288319	NM_182918.3	345	Gac/Aac	10/10	0.0836944055658734	0	FACETS	0.712	0.515	0.949			1	INDETERMINATE	1	TRUE	0	0.15	0		156	223	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890150	76890150	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	39	278	0	ENST00000373344.5:c.4744del	p.Thr1582GlnfsTer24	p.T1582Qfs*24	ENST00000373344	NM_000489.3	1582	Aca/ca	17/35	1	1	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	0	0.15	1		278	442	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946828	17946828	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	32	284	0	ENST00000458235.1:c.1819del	p.Ala607ProfsTer2	p.A607Pfs*2	ENST00000458235	NM_000215.3	607	Gcc/cc	14/24	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.15	2		284	394	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440729	56440729	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	24	324	0	ENST00000407977.2:c.489del	p.Ile164SerfsTer9	p.I164Sfs*9	ENST00000407977		163	ttG/tt	5/10	1	2	FACETS	0.766	0.599	0.958	0.766	0.599	0.958	CLONAL	1	TRUE	1	0.15	2		324	418	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69456227	69456229	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	21	281	0	ENST00000227507.2:c.148_150del	p.Lys50del	p.K50del	ENST00000227507	NM_053056.2	49	cAGAag/cag	1/5	0.0836944055658734	0	FACETS	0.728	0.56	0.923			1	INDETERMINATE	1	TRUE	0	0.15	0		281	327	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348566	89348569	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	66	904	0	ENST00000301030.4:c.4381_4384del	p.Lys1461GlufsTer69	p.K1461Efs*69	ENST00000301030	NM_001256183.1	1461	AAGAga/ga	9/13	0.30977599026879	0	FACETS	0.911	0.789	1			1	CLONAL	1	TRUE	0	0.15	0		904	821	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900984	114900984	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778855667	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	49	802	0	ENST00000543371.1:c.598del	p.Leu200SerfsTer25	p.L200Sfs*25	ENST00000543371	NM_001198531.1	198	caC/ca	6/14	0.3	0	FACETS	0.801	0.677	0.938			1	CLONAL	1	TRUE	0	0.15	0		802	693	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461543	138461543	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	34	335	0	ENST00000289153.2:c.478del	p.Ile160SerfsTer13	p.I160Sfs*13	ENST00000289153	NM_006219.2	160	Atc/tc	3/22	1	2	FACETS	0.808	0.659	0.976	0.808	0.659	0.976	CLONAL	1	TRUE	1	0.15	2		335	561	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923670	72923670	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	34	581	0	ENST00000268489.5:c.3408del	p.Gln1137ArgfsTer50	p.Q1137Rfs*50	ENST00000268489	NM_006885.3	1136	ggG/gg	4/10	0.30977599026879	0	FACETS	0.718	0.585	0.867			1	SUBCLONAL	1	TRUE	0	0.15	0		581	537	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347748	347748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	26	292	0	ENST00000262320.3:c.1758del	p.Asn587ThrfsTer118	p.N587Tfs*118	ENST00000262320	NM_003502.3	586	ccC/cc	6/11	0.0836944055658734	0	FACETS	0.888	0.704	1			1	INDETERMINATE	1	TRUE	0	0.15	0		292	332	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120697	115120697	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	26	465	0	ENST00000257566.3:c.309del	p.Lys104ArgfsTer35	p.K104Rfs*35	ENST00000257566	NM_016569.3	103	ccC/cc	1/8	0.126450618555662	0	FACETS	0.636	0.503	0.79			1	SUBCLONAL	1	TRUE	0	0.15	0		465	463	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0004021-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	156	480	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	1	2	FACETS	0.784	0.721	0.85	0.784	0.721	0.85	SUBCLONAL	1	FALSE	1	0.643932125525642	2		480	618	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446270	187446270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767642014	NA	P-0004021-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	169	308	0	ENST00000232014.4:c.1418C>T	p.Pro473Leu	p.P473L	ENST00000232014	NM_001130845.1	473	cCg/cTg	6/10	1	2	FACETS	0.862	0.796	0.93	0.862	0.796	0.93	CLONAL	1	FALSE	1	0.643932125525642	2		308	609	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971370	13971370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748346103	NA	P-0004021-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	9	354	0	ENST00000405192.2:c.559C>T	p.Arg187Cys	p.R187C	ENST00000405192	NM_001163147.1	187	Cgc/Tgc	8/12	1	2	FACETS	0.068	0.044	0.098	0.068	0.044	0.098	SUBCLONAL	1	FALSE	1	0.643932125525642	2		354	412	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341141	8341141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1347452833	NA	P-0004021-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	130	487	2	ENST00000356435.5:c.5075G>A	p.Arg1692His	p.R1692H	ENST00000356435		1692	cGt/cAt	30/35	1	2	FACETS	0.905	0.828	0.986	0.905	0.828	0.986	CLONAL	1	FALSE	1	0.643932125525642	2		489	446	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028615	12028615	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004021-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	136	490	0	ENST00000353533.5:c.818A>G	p.Glu273Gly	p.E273G	ENST00000353533	NM_003010.3	273	gAa/gGa	8/11	0.643932125525642	1	FACETS	0.892	0.824	0.962	0.892	0.824	0.962	CLONAL	1	FALSE	0	0.643932125525642	1		490	321	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934080	39934080	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004021-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	158	519	0	ENST00000378444.4:c.519C>A	p.Ser173Arg	p.S173R	ENST00000378444	NM_001123385.1	173	agC/agA	4/15	0.259546864600334	0	FACETS	0.276	0.254	0.299			1	INDETERMINATE	1	FALSE	0	0.643932125525642	0		519	633	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004028-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	240	556	0	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	0.163791431719659	3	FACETS	1	0.989	1	0.623	0.584	0.664	INDETERMINATE	1	TRUE	1	0.61956342166352	3		556	814	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961367	15961367	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0004028-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	205	489	1	ENST00000268712.3:c.6022A>T	p.Arg2008Ter	p.R2008*	ENST00000268712	NM_006311.3	2008	Aga/Tga	39/46	0.61956342166352	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.61956342166352	1		490	439	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161663	56161664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTTGT	novel	NA	P-0004028-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	180	451	0	ENST00000399503.3:c.1162_1166dup	p.Gln390CysfsTer48	p.Q390Cfs*48	ENST00000399503	NM_005921.1	387	agt/agTTTGTt	6/20	0.477602058635201	4	FACETS	1	0.964	1	0.359	0.331	0.388	CLONAL	1	TRUE	1	0.61956342166352	4		451	874	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167803	56167804	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1402352674	NA	P-0004028-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	508	503	1	ENST00000399503.3:c.1369dup	p.Thr457AsnfsTer4	p.T457Nfs*4	ENST00000399503	NM_005921.1	456	-/A	7/20	0.477602058635201	4	FACETS	1	0.995	1	0.828	0.796	0.86	CLONAL	2	TRUE	1	0.61956342166352	4		504	1069	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952088	+	missense_variant	Missense_Mutation	ONP	ATCA	ATCA	GTCG	novel	NA	P-0004028-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	234	481	0	ENST00000263967.3:c.3140_3143delinsGTCG	p.His1047_His1048delinsArgArg	p.H1047_H1048delinsRR	ENST00000263967	NM_006218.2	1047	cATCAt/cGTCGt	21/21	0.61956342166352	3	FACETS	1	0.942	1	0.505	0.471	0.54	CLONAL	1	TRUE	1	0.61956342166352	3		481	980	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0004044-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	223	792	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.165341242214204	1	FACETS	1	0.979	1	1	0.995	1	CLONAL	3	TRUE	0	0.165341242214204	1		792	743	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156983	89156983	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004044-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	53	310	0	ENST00000336596.2:c.85G>A	p.Glu29Lys	p.E29K	ENST00000336596	NM_005233.5	29	Gaa/Aaa	1/17	NA	2	FACETS	0.83	0.707	0.967			1	INDETERMINATE	1	TRUE	NA	0.165341242214204	2		310	772	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230799	66230799	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004044-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	92	333	0	ENST00000273854.3:c.2172A>C	p.Glu724Asp	p.E724D	ENST00000273854	NM_004439.5	724	gaA/gaC	12/18	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.165341242214204	2		333	978	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333864	70333864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528233201	NA	P-0004044-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	42	326	0	ENST00000373644.4:c.1769G>A	p.Arg590Gln	p.R590Q	ENST00000373644	NM_030625.2	590	cGa/cAa	2/12	0.165341242214204	2	FACETS	0.745	0.62	0.884	0.372	0.31	0.442	SUBCLONAL	1	TRUE	0	0.165341242214204	2		326	682	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101203	41101203	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0004044-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	86	87	0	ENST00000373198.4:c.1154-1G>T		p.X385_splice	ENST00000373198	NM_133170.3	385			0.165341242214204	5	FACETS	0.937	0.848	1	1	0.985	1	CLONAL	7	TRUE	1	0.165341242214204	5		87	198	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	343	130	0	ENST00000269305.4:c.859G>T	p.Glu287Ter	p.E287*	ENST00000269305	NM_001126112.2	287	Gag/Tag	8/11	NA	2	FACETS	0.969	0.932	1			1	INDETERMINATE	2	TRUE	NA	0.661382466900751	2		130	535	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499374	89499374	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1267	99	110	0	ENST00000336596.2:c.2544C>G	p.Asp848Glu	p.D848E	ENST00000336596	NM_005233.5	848	gaC/gaG	15/17	0.661382466900751	8	FACETS	0.654	0.582	0.732			1	SUBCLONAL	1	TRUE	NA	0.661382466900751	8		110	1366	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233078	66233078	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	139	115	0	ENST00000273854.3:c.1921C>A	p.His641Asn	p.H641N	ENST00000273854	NM_004439.5	641	Cac/Aac	10/18	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.661382466900751	2		115	419	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356212	66356212	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	105	108	0	ENST00000273854.3:c.1285G>T	p.Val429Leu	p.V429L	ENST00000273854	NM_004439.5	429	Gtg/Ttg	5/18	1	2	FACETS	0.965	0.875	1	0.965	0.875	1	CLONAL	1	TRUE	1	0.661382466900751	2		108	329	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467548	66467548	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	150	133	0	ENST00000273854.3:c.721G>T	p.Ala241Ser	p.A241S	ENST00000273854	NM_004439.5	241	Gct/Tct	3/18	1	2	FACETS	0.995	0.917	1	0.995	0.917	1	CLONAL	1	TRUE	1	0.661382466900751	2		133	456	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729671	41729671	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	232	293	0	ENST00000242208.4:c.858G>C	p.Glu286Asp	p.E286D	ENST00000242208	NM_002192.2	286	gaG/gaC	3/3	1	2	FACETS	0.882	0.825	0.941	0.882	0.825	0.941	CLONAL	1	TRUE	1	0.661382466900751	2		293	795	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275842	38275842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367715495	NA	P-0004054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	90	81	1	ENST00000425967.3:c.1427G>A	p.Arg476Gln	p.R476Q	ENST00000425967	NM_001174067.1	476	cGg/cAg	11/19	0.661382466900751	5	FACETS	0.948	0.843	1			1	CLONAL	1	TRUE	NA	0.661382466900751	5		82	572	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5066676	5066676	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0004054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	198	124	0	ENST00000381652.3:c.1215-2A>G		p.X405_splice	ENST00000381652	NM_004972.3	405			0.661946822956577	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.661382466900751	1		124	368	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246440	41246440	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	169	163	0	ENST00000357654.3:c.1108G>A	p.Val370Ile	p.V370I	ENST00000357654	NM_007294.3	370	Gtt/Att	10/23	1	2	FACETS	0.911	0.843	0.981	0.911	0.843	0.981	CLONAL	1	TRUE	1	0.661382466900751	2		163	561	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220493	1220493	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	138	110	0	ENST00000326873.7:c.586G>C	p.Gly196Arg	p.G196R	ENST00000326873	NM_000455.4	196	Ggc/Cgc	4/10	0.658148526753027	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.661382466900751	1		110	254	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599910	10599910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	231	177	0	ENST00000171111.5:c.1666G>A	p.Ala556Thr	p.A556T	ENST00000171111	NM_203500.1	556	Gcc/Acc	5/6	0.658148526753027	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.661382466900751	1		177	460	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243529	46243529	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	233	91	0	ENST00000334344.6:c.1883del	p.Pro628LeufsTer19	p.P628Lfs*19	ENST00000334344	NM_152641.2	628	Cct/ct	14/21	0.658011082670698	2	FACETS	0.998	0.952	1	0.998	0.952	1	CLONAL	2	TRUE	0	0.661382466900751	2		91	353	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478605	57478606	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGG	novel	NA	P-0004054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	90	68	0	ENST00000371085.3:c.279_281dup	p.Gln93_Asp94insGlu	p.Q93_D94insE	ENST00000371085	NM_000516.4	93	cag/cAGGag	4/13	0.656989847566921	1	FACETS	0.902	0.819	0.986	0.902	0.819	0.986	CLONAL	1	TRUE	0	0.661382466900751	1		68	202	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691800	30691801	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCATGAC	novel	NA	P-0004054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	137	129	0	ENST00000295754.5:c.305_311dup	p.Lys105Ter	p.K105*	ENST00000295754	NM_003242.5	101	tgc/tgCCATGACc	3/7	0.650524289899275	1	FACETS	0.79	0.728	0.853	0.79	0.728	0.853	SUBCLONAL	1	TRUE	0	0.661382466900751	1		129	351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577140	7577144	+	frameshift_variant	Frame_Shift_Del	DEL	TCCCA	TCCCA	-	novel	NA	P-0004058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	86	273	0	ENST00000269305.4:c.794_798del	p.Leu265ProfsTer5	p.L265Pfs*5	ENST00000269305	NM_001126112.2	265	cTGGGA/c	8/11	0.216386304264021	3	FACETS	1	0.97	1			1	CLONAL	2	TRUE	NA	0.310834995832501	3		273	260	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0004074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	93	265	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.201943057046508	3	FACETS	0.884	0.786	0.988	0.442	0.393	0.494	INDETERMINATE	1	FALSE	1	0.346242970579772	3		265	713	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050327	176050327	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	77	221	0	ENST00000367669.3:c.1238A>G	p.Tyr413Cys	p.Y413C	ENST00000367669	NM_022457.5	413	tAt/tGt	11/20	0.242526277973168	4	FACETS	0.834	0.732	0.944	0.417	0.366	0.472	CLONAL	1	FALSE	2	0.346242970579772	4		221	718	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632356	215632356	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	64	224	2	ENST00000260947.4:c.1418A>T	p.His473Leu	p.H473L	ENST00000260947	NM_000465.2	473	cAc/cTc	6/11	1	2	FACETS	0.614	0.532	0.704	0.614	0.532	0.704	SUBCLONAL	1	FALSE	1	0.346242970579772	2		226	602	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518948	187518948	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0004074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	83	233	0	ENST00000441802.2:c.12258-2A>T		p.X4086_splice	ENST00000441802	NM_005245.3	4086			1	2	FACETS	0.85	0.751	0.955	0.85	0.751	0.955	CLONAL	1	FALSE	1	0.346242970579772	2		233	564	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294143	1294143	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	37	176	0	ENST00000310581.5:c.858G>T	p.Glu286Asp	p.E286D	ENST00000310581	NM_198253.2	286	gaG/gaT	2/16	NA	2	FACETS	0.742	0.614	0.883			1	INDETERMINATE	1	FALSE	NA	0.346242970579772	2		176	288	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876380	35876380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	67	156	0	ENST00000303115.3:c.1172G>A	p.Arg391Lys	p.R391K	ENST00000303115	NM_002185.3	391	aGg/aAg	8/8	0.210096015410229	4	FACETS	0.954	0.83	1	0.477	0.415	0.544	CLONAL	1	FALSE	2	0.346242970579772	4		156	546	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056352	180056352	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	36	262	0	ENST00000261937.6:c.892C>T	p.His298Tyr	p.H298Y	ENST00000261937	NM_182925.4	298	Cac/Tac	7/30	0.258231314428914	1	FACETS	0.376	0.309	0.452	0.376	0.309	0.452	SUBCLONAL	1	FALSE	0	0.346242970579772	1		262	457	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864811	57864811	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	112	326	0	ENST00000228682.2:c.2288C>A	p.Pro763His	p.P763H	ENST00000228682	NM_005269.2	763	cCc/cAc	12/12	1	2	FACETS	0.816	0.734	0.903	0.816	0.734	0.903	CLONAL	1	FALSE	1	0.346242970579772	2		326	793	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855966	68855966	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs35187787	NA	P-0004074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	65	310	1	ENST00000261769.5:c.1774G>T	p.Ala592Ser	p.A592S	ENST00000261769	NM_004360.3	592	Gcc/Tcc	12/16	0.194615247983719	0	FACETS	0.425	0.369	0.487			1	INDETERMINATE	1	FALSE	0	0.346242970579772	0		311	577	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804181	46804181	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	96	325	0	ENST00000290295.7:c.826G>T	p.Ala276Ser	p.A276S	ENST00000290295	NM_006361.5	276	Gcc/Tcc	2/2	NA	2	FACETS	0.741	0.66	0.828			1	INDETERMINATE	1	FALSE	NA	0.346242970579772	2		325	748	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220370	1220370	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	rs1131690931	NA	P-0004074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	57	172	0	ENST00000326873.7:c.465-2A>C		p.X155_splice	ENST00000326873	NM_000455.4	155			0.2356333142329	1	FACETS	0.765	0.659	0.879	0.765	0.659	0.879	SUBCLONAL	1	FALSE	0	0.346242970579772	1		172	356	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602298	10602298	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	39	189	0	ENST00000171111.5:c.1280C>A	p.Ala427Asp	p.A427D	ENST00000171111	NM_203500.1	427	gCc/gAc	3/6	0.346242970579772	1	FACETS	0.687	0.573	0.813	0.687	0.573	0.813	SUBCLONAL	1	FALSE	0	0.346242970579772	1		189	271	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52725351	52725351	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0004074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	42	149	0	ENST00000322088.6:c.1519-1G>T		p.X507_splice	ENST00000322088	NM_014225.5	507			0.182322285568008	1	FACETS	0.512	0.428	0.604	0.512	0.428	0.604	INDETERMINATE	1	FALSE	0	0.346242970579772	1		149	392	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230626	46230626	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	88	234	0	ENST00000334344.6:c.878del	p.Leu293Ter	p.L293*	ENST00000334344	NM_152641.2	292	aTt/at	8/21	0.201943057046508	3	FACETS	0.886	0.785	0.994	0.443	0.392	0.497	INDETERMINATE	1	FALSE	1	0.346242970579772	3		234	673	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161907	47161907	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	45	458	0	ENST00000409792.3:c.4219del	p.Arg1407GlyfsTer5	p.R1407Gfs*5	ENST00000409792	NM_014159.6	1407	Agg/gg	3/21	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.1	2		458	817	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs786202525	NA	P-0004097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	34	215	1	ENST00000269305.4:c.532del	p.His178ThrfsTer69	p.H178Tfs*69	ENST00000269305	NM_001126112.2	178	Cac/ac	5/11	1	2	FACETS	0.958	0.784	1	1	0.961	1	CLONAL	2	TRUE	1	0.1	2		216	355	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434005	49434005	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	26	258	0	ENST00000301067.7:c.7548del	p.Asn2517IlefsTer26	p.N2517Ifs*26	ENST00000301067	NM_003482.3	2516	ccC/cc	31/54	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.1	2		258	406	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231100	98231100	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs115556836	NA	P-0004097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	38	199	0	ENST00000331920.6:c.2183C>T	p.Thr728Met	p.T728M	ENST00000331920	NM_000264.3	728	aCg/aTg	14/24	1	2	FACETS	1	0.907	1	1	0.97	1	CLONAL	2	TRUE	1	0.1	2		199	331	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418395	49418395	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1565756115	NA	P-0004097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	34	231	0	ENST00000301067.7:c.16018C>T	p.Arg5340Ter	p.R5340*	ENST00000301067	NM_003482.3	5340	Cga/Tga	50/54	1	2	FACETS	0.751	0.613	0.905	1	0.946	1	CLONAL	2	TRUE	1	0.1	2		231	453	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434506	110434506	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1019316102	NA	P-0004097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	38	243	0	ENST00000375856.3:c.3895G>A	p.Val1299Ile	p.V1299I	ENST00000375856	NM_003749.2	1299	Gtc/Atc	1/2	1	2	FACETS	0.96	0.794	1	1	0.965	1	CLONAL	2	TRUE	1	0.1	2		243	396	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899272	78899272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368064754	NA	P-0004097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	18	215	0	ENST00000306801.3:c.2911G>A	p.Val971Ile	p.V971I	ENST00000306801	NM_020761.2	971	Gtc/Atc	24/34	1	2	FACETS	1	0.768	1	1	0.768	1	CLONAL	1	TRUE	1	0.1	2		215	352	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923087	39923087	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	56	331	0	ENST00000378444.4:c.3621del	p.Lys1207AsnfsTer31	p.K1207Nfs*31	ENST00000378444	NM_001123385.1	1207	aaA/aa	8/15	0.152102905750191	0	FACETS	0.962	0.825	1			1	CLONAL	2	TRUE	NA	0.1	0		331	524	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118365442	118365443	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0004097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	74	522	0	ENST00000534358.1:c.5326_5327del	p.Lys1776ValfsTer8	p.K1776Vfs*8	ENST00000534358	NM_005933.3	1775	AAa/a	18/36	1	2	FACETS	1	0.904	1	1	0.983	1	CLONAL	2	TRUE	1	0.1	2		522	712	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0004102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	175	378	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.383818170837717	3	FACETS	1	0.99	1	0.701	0.653	0.749	INDETERMINATE	1	TRUE	1	0.851409433392589	3		378	418	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	27	192	0				ENST00000310581	NM_198253.2	-/1132			0.77019059514916	1	FACETS	0.714	0.603	0.824	0.714	0.603	0.824	SUBCLONAL	1	TRUE	0	0.851409433392589	1		192	51	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133697	41133697	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	66	681	0	ENST00000379561.5:c.1931G>T	p.Ser644Ile	p.S644I	ENST00000379561	NM_002015.3	644	aGt/aTt	2/3	0.117217260895835	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.851409433392589	0		681	354	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798889	42798889	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0004102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	82	350	0	ENST00000575354.2:c.4459+2T>G		p.X1487_splice	ENST00000575354	NM_015125.3	1487			0.165212685989072	1	FACETS	0.567	0.511	0.624	0.567	0.511	0.624	INDETERMINATE	1	TRUE	0	0.851409433392589	1		350	195	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78435626	78435627	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	137	415	0	ENST00000370768.2:c.193dup	p.Arg65LysfsTer12	p.R65Kfs*12	ENST00000370768	NM_003902.3	65	aga/aAga	2/20	0.851409433392589	1	FACETS	0.55	0.507	0.593	0.55	0.507	0.593	SUBCLONAL	1	TRUE	0	0.851409433392589	1		415	336	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920154	76920154	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	45	560	0	ENST00000373344.5:c.3923A>G	p.Glu1308Gly	p.E1308G	ENST00000373344	NM_000489.3	1308	gAa/gGa	11/35	0.228003803517933	1	FACETS	0.741	0.624	0.871	0.741	0.624	0.871	SUBCLONAL	1	TRUE	0	0.253646548179538	1		560	418	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	51	192	0				ENST00000310581	NM_198253.2	-/1132			0.193347404444638	1	FACETS	0.635	0.553	0.719	0.635	0.553	0.719	INDETERMINATE	1	FALSE	0	0.746182067357796	1		192	135	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221710	55221710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10367	690	281	0	ENST00000275493.2:c.754C>T	p.Arg252Cys	p.R252C	ENST00000275493	NM_005228.3	252	Cgc/Tgc	7/28	0.746182067357796	31	FACETS	0.988	0.946	1			1	CLONAL	2	FALSE	NA	0.746182067357796	31		281	11057	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663336	227663336	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	82	143	0	ENST00000305123.5:c.119G>T	p.Gly40Val	p.G40V	ENST00000305123	NM_005544.2	40	gGc/gTc	1/2	1	2	FACETS	0.939	0.842	1	0.939	0.842	1	CLONAL	1	FALSE	1	0.746182067357796	2		143	234	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453095	140453095	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	225	254	0	ENST00000288602.6:c.1840T>C	p.Ser614Pro	p.S614P	ENST00000288602	NM_004333.4	614	Tct/Cct	15/18	0.746182067357796	3	FACETS	0.843	0.786	0.903	0.422	0.393	0.452	CLONAL	1	FALSE	1	0.746182067357796	3		254	982	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	21	192	0				ENST00000310581	NM_198253.2	-/1132			0.125390821234852	3	FACETS	1	0.905	1			1	INDETERMINATE	1	FALSE	NA	0.322286227565806	3		192	113	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0004125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	118	556	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.31679038257023	4	FACETS	0.996	0.904	1	0.996	0.904	1	CLONAL	2	FALSE	2	0.322286227565806	4		556	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0004125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	164	326	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.306285583019287	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	FALSE	0	0.322286227565806	2		326	459	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100925	27100925	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	95	240	0	ENST00000324856.7:c.4207C>T	p.Gln1403Ter	p.Q1403*	ENST00000324856	NM_006015.4	1403	Cag/Tag	18/20	0.162891150944166	4	FACETS	1	0.967	1	1	0.967	1	INDETERMINATE	2	FALSE	2	0.322286227565806	4		240	329	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911473	134911473	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs761326171	NA	P-0004125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	115	179	0	ENST00000398015.3:c.1938C>G	p.Ile646Met	p.I646M	ENST00000398015	NM_004441.4	646	atC/atG	11/16	0.322286227565806	5	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	FALSE	3	0.322286227565806	5		179	429	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681461	30681461	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	149	339	0	ENST00000376406.3:c.551C>T	p.Ser184Leu	p.S184L	ENST00000376406	NM_014641.2	184	tCa/tTa	4/15	0.31679038257023	4	FACETS	0.917	0.84	0.996	0.917	0.84	0.996	CLONAL	2	FALSE	2	0.322286227565806	4		339	667	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856500	111856500	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	33	170	0	ENST00000341259.2:c.551C>A	p.Pro184His	p.P184H	ENST00000341259	NM_005475.2	184	cCc/cAc	2/8	0.322286227565806	3	FACETS	0.701	0.572	0.846	0.351	0.286	0.423	SUBCLONAL	1	FALSE	1	0.322286227565806	3		170	339	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215366	41215366	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786203547	NA	P-0004125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	93	326	0	ENST00000357654.3:c.5177G>C	p.Arg1726Thr	p.R1726T	ENST00000357654	NM_007294.3	1726	aGa/aCa	18/23	0.322286227565806	3	FACETS	0.904	0.804	1	0.452	0.402	0.506	CLONAL	1	FALSE	1	0.322286227565806	3		326	741	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260586	10260586	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	90	397	0	ENST00000340748.4:c.2276T>C	p.Val759Ala	p.V759A	ENST00000340748		759	gTg/gCg	24/40	0.169488679371972	2	FACETS	0.968	0.861	1	0.484	0.43	0.541	INDETERMINATE	1	FALSE	0	0.322286227565806	2		397	577	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134287	11134287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415464964	NA	P-0004125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	97	176	1	ENST00000358026.2:c.2953G>A	p.Glu985Lys	p.E985K	ENST00000358026	NM_001128849.1	985	Gag/Aag	20/36	0.169488679371972	2	FACETS	0.959	0.865	1	0.959	0.865	1	INDETERMINATE	2	FALSE	0	0.322286227565806	2		177	314	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312684	30312684	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	159	326	0	ENST00000262643.3:c.665C>T	p.Ser222Leu	p.S222L	ENST00000262643	NM_001238.2	222	tCa/tTa	8/12	0.322286227565806	5	FACETS	0.898	0.824	0.975	0.449	0.412	0.488	CLONAL	2	FALSE	1	0.322286227565806	5		326	815	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54963225	54963225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381110341	NA	P-0004125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	198	316	0	ENST00000312783.6:c.29C>T	p.Ser10Leu	p.S10L	ENST00000312783	NM_198436.1	10	tCa/tTa	3/10	0.321934641570294	4	FACETS	1	0.965	1			1	CLONAL	2	FALSE	NA	0.322286227565806	4		316	765	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0004129-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	183	300	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.959	0.891	1	0.959	0.891	1	CLONAL	1	TRUE	1	0.71231893444518	2		300	536	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241679	55241681	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	rs397517086	NA	P-0004129-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	3222	473	0	ENST00000275493.2:c.2127_2129del	p.Glu709_Thr710delinsAsp	p.E709_T710delinsD	ENST00000275493	NM_005228.3	709	gaAACt/gat	18/28	0.71231893444518	10	FACETS	1	0.994	1			1	CLONAL	8	TRUE	NA	0.71231893444518	10		473	4315	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149436878	149436878	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004129-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	396	535	0	ENST00000286301.3:c.2291A>C	p.Gln764Pro	p.Q764P	ENST00000286301	NM_005211.3	764	cAg/cCg	17/22	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.71231893444518	2		535	1112	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46124999	46124999	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0004129-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	300	427	0	ENST00000334344.6:c.187-1G>T		p.X63_splice	ENST00000334344	NM_152641.2	63			1	2	FACETS	0.801	0.755	0.849	0.801	0.755	0.849	CLONAL	1	TRUE	1	0.71231893444518	2		427	1051	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035965	47035965	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004129-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	472	345	0	ENST00000377604.3:c.643G>T	p.Glu215Ter	p.E215*	ENST00000377604	NM_001204468.1	215	Gag/Tag	7/24	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.71231893444518	1		345	661	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412320	63412320	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004129-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	527	301	0	ENST00000330258.3:c.847G>T	p.Glu283Ter	p.E283*	ENST00000330258	NM_152424.3	283	Gag/Tag	2/2	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.71231893444518	1		301	756	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356506	70356506	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0004129-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	358	247	0	ENST00000374080.3:c.5400+1G>T		p.X1800_splice	ENST00000374080		1800			1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.71231893444518	1		247	486	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602797	10602797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004135-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	138	361	2	ENST00000171111.5:c.781C>T	p.Arg261Trp	p.R261W	ENST00000171111	NM_203500.1	261	Cgg/Tgg	3/6	0.440297214973678	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.440297214973678	1		363	488	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793700	89793700	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370470988	NA	P-0004135-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	137	343	0	ENST00000336032.3:c.769G>A	p.Glu257Lys	p.E257K	ENST00000336032	NM_006813.2	257	Gag/Aag	2/2	1	2	FACETS	0.844	0.769	0.923	0.844	0.769	0.923	CLONAL	1	TRUE	1	0.440297214973678	2		343	737	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2202733	2202733	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004135-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	38	471	0	ENST00000398665.3:c.742G>T	p.Glu248Ter	p.E248*	ENST00000398665	NM_032482.2	248	Gag/Tag	9/28	0.440297214973678	1	FACETS	0.229	0.189	0.275	0.229	0.189	0.275	SUBCLONAL	1	TRUE	0	0.440297214973678	1		471	587	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603120	48603121	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGTA	novel	NA	P-0004135-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	62	230	0	ENST00000342988.3:c.1422_1425dup	p.Gly476SerfsTer19	p.G476Sfs*19	ENST00000342988	NM_005359.5	474	tca/tcAGTAa	11/12	0.440297214973678	1	FACETS	0.755	0.657	0.858	0.755	0.657	0.858	SUBCLONAL	1	TRUE	0	0.440297214973678	1		230	291	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952091	178952091	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	63	283	0	ENST00000263967.3:c.3146G>C	p.Gly1049Ala	p.G1049A	ENST00000263967	NM_006218.2	1049	gGt/gCt	21/21	1	2	FACETS	0.78	0.676	0.891	0.78	0.676	0.891	SUBCLONAL	1	TRUE	1	0.36	2		283	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577529	7577529	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs730882027	NA	P-0004155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	61	195	0	ENST00000269305.4:c.752T>G	p.Ile251Ser	p.I251S	ENST00000269305	NM_001126112.2	251	aTc/aGc	7/11	0.3	3	FACETS	1	0.943	1			1	CLONAL	1	TRUE	NA	0.36	3		195	343	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229301	123229301	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0004161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	191	348	0	ENST00000218089.9:c.3783+2T>C		p.X1261_splice	ENST00000218089	NM_001042749.1	1261			0.3	2	FACETS	1	0.932	1			1	INDETERMINATE	1	TRUE	NA	0.64	2		348	596	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871145	12871146	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs786201011	NA	P-0004161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	71	140	0	ENST00000228872.4:c.374_375del	p.Ser125Ter	p.S125*	ENST00000228872	NM_004064.3	124	aaCTct/aact	1/3	1	2	FACETS	0.857	0.757	0.962	0.857	0.757	0.962	CLONAL	1	TRUE	1	0.64	2		140	259	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11210277	11210277	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs777916561	NA	P-0004168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	67	262	0	ENST00000361445.4:c.4476A>C	p.Gln1492His	p.Q1492H	ENST00000361445	NM_004958.3	1492	caA/caC	31/58	0.437710262243333	3	FACETS	0.722	0.629	0.823	0.361	0.314	0.412	SUBCLONAL	1	TRUE	1	0.48271787383959	3		262	477	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190717415	190717415	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	185	263	0	ENST00000441310.2:c.734C>T	p.Ala245Val	p.A245V	ENST00000441310	NM_000534.4	245	gCa/gTa	7/13	0.48271787383959	5	FACETS	0.754	0.697	0.814			1	SUBCLONAL	2	TRUE	NA	0.48271787383959	5		263	876	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155048	55155048	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	313	248	0	ENST00000257290.5:c.2757C>A	p.Asp919Glu	p.D919E	ENST00000257290	NM_006206.4	919	gaC/gaA	20/23	0.276533792428103	6	FACETS	0.988	0.94	1			1	INDETERMINATE	4	TRUE	NA	0.48271787383959	6		248	645	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992601	72992601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	120	310	0	ENST00000268489.5:c.1444G>A	p.Glu482Lys	p.E482K	ENST00000268489	NM_006885.3	482	Gaa/Aaa	2/10	0.387775755097152	4	FACETS	0.999	0.903	1	0.499	0.451	0.55	CLONAL	1	TRUE	2	0.48271787383959	4		310	738	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0004168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	206	217	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.478040068123843	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.48271787383959	2		217	377	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117435	115117436	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0004168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	143	196	0	ENST00000257566.3:c.738_739del	p.His246GlnfsTer13	p.H246Qfs*13	ENST00000257566	NM_016569.3	246	caCAaa/caaa	4/8	0.433620133208773	4	FACETS	0.898	0.825	0.974			1	CLONAL	2	TRUE	NA	0.48271787383959	4		196	489	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552762	18552762	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	28	306	0	ENST00000266497.5:c.2173C>G	p.Leu725Val	p.L725V	ENST00000266497		725	Ctt/Gtt	14/31	0.434042139622939	4	FACETS	0.723	0.58	0.884	0.241	0.193	0.295	SUBCLONAL	1	TRUE	1	0.434042139622939	4		306	256	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16062086	16062089	+	frameshift_variant	Frame_Shift_Del	DEL	ATAA	ATAA	-	novel	NA	P-0004178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	100	443	0	ENST00000268712.3:c.717_720del	p.Ile239MetfsTer45	p.I239Mfs*45	ENST00000268712	NM_006311.3	239	atTTAT/at	6/46	0.308938932702519	4	FACETS	1	0.928	1	0.524	0.468	0.582	CLONAL	1	TRUE	2	0.434042139622939	4		443	631	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0004195-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	151	454	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.938	0.857	1	0.938	0.857	1	CLONAL	1	TRUE	1	0.323118762751262	2		454	996	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413225	139413225	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004195-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1712	193	844	0	ENST00000277541.6:c.917G>C	p.Cys306Ser	p.C306S	ENST00000277541	NM_017617.3	306	tGc/tCc	6/34	0.323118762751262	3	FACETS	0.728	0.671	0.789	0.364	0.335	0.395	SUBCLONAL	1	TRUE	1	0.323118762751262	3		844	1905	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578410	7578410	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs864622115	NA	P-0004195-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	129	350	0	ENST00000269305.4:c.520A>G	p.Arg174Gly	p.R174G	ENST00000269305	NM_001126112.2	174	Agg/Ggg	5/11	0.323118762751262	1	FACETS	0.929	0.843	1	0.929	0.843	1	CLONAL	1	TRUE	0	0.323118762751262	1		350	721	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111502	8111503	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004195-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1252	238	543	0	ENST00000346208.3:c.990dup	p.Asn331GlufsTer21	p.N331Efs*21	ENST00000346208		330	agg/aGgg	5/6	1	2	FACETS	0.989	0.92	1	0.989	0.92	1	CLONAL	1	TRUE	1	0.323118762751262	2		543	1490	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs377767347	NA	P-0004195-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	123	486	0	ENST00000342988.3:c.1082G>T	p.Arg361Leu	p.R361L	ENST00000342988	NM_005359.5	361	cGc/cTc	9/12	0.323118762751262	1	FACETS	0.603	0.544	0.665	0.603	0.544	0.665	SUBCLONAL	1	TRUE	0	0.323118762751262	1		486	1059	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476814	140476814	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004195-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	104	394	0	ENST00000288602.6:c.1592G>C	p.Trp531Ser	p.W531S	ENST00000288602	NM_004333.4	531	tGg/tCg	13/18	1	2	FACETS	0.539	0.481	0.601	0.539	0.481	0.601	SUBCLONAL	1	TRUE	1	0.323118762751262	2		394	1195	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250996	10250997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004195-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	124	310	0	ENST00000340748.4:c.3483dup	p.Asp1162Ter	p.D1162*	ENST00000340748		1161	-/T	32/40	1	2	FACETS	0.962	0.87	1	0.962	0.87	1	CLONAL	1	TRUE	1	0.323118762751262	2		310	798	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317927	8317927	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004198-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	131	210	0	ENST00000356435.5:c.5686T>C	p.Ser1896Pro	p.S1896P	ENST00000356435		1896	Tcc/Ccc	35/35	0.78184084718952	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.78184084718952	1		210	194	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004206-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	194	510	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.226232642344685	3	FACETS	1	0.99	1	0.749	0.693	0.806	CLONAL	1	TRUE	1	0.322983221550417	3		510	932	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751502	57751502	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004206-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	158	237	0	ENST00000274289.3:c.1489C>G	p.Leu497Val	p.L497V	ENST00000274289	NM_006622.3	497	Ctg/Gtg	11/14	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.322983221550417	2		237	959	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573984	7573984	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004206-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	144	246	0	ENST00000269305.4:c.1043T>G	p.Leu348Trp	p.L348W	ENST00000269305	NM_001126112.2	348	tTg/tGg	10/11	0.319172968495526	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.322983221550417	1		246	612	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591877	48591885	+	inframe_deletion	In_Frame_Del	DEL	TTGTTACTG	TTGTTACTG	-	novel	NA	P-0004206-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	124	234	0	ENST00000342988.3:c.1043_1051del	p.Val348_Val350del	p.V348_V350del	ENST00000342988	NM_005359.5	347	aTTGTTACTGtt/att	9/12	0.309091950825347	1	FACETS	0.787	0.712	0.866	0.787	0.712	0.866	SUBCLONAL	1	TRUE	0	0.322983221550417	1		234	818	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250119	110250119	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	54	213	0	ENST00000374672.4:c.556A>T	p.Asn186Tyr	p.N186Y	ENST00000374672	NM_004235.4	186	Aac/Tac	3/5	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.435429976694757	2		213	225	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912807	50912807	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	90	551	1	ENST00000440232.2:c.2038C>A	p.Pro680Thr	p.P680T	ENST00000440232	NM_002691.3	680	Ccc/Acc	17/27	NA	2	FACETS	0.905	0.806	1			1	INDETERMINATE	1	TRUE	NA	0.435429976694757	2		552	457	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57473994	57473994	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0004216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	43	160	0	ENST00000371085.3:c.213-2A>T		p.X71_splice	ENST00000371085	NM_000516.4	71			0.435429976694757	9	FACETS	0.835	0.698	0.988			1	CLONAL	1	TRUE	NA	0.435429976694757	9		160	597	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805729	43805739	+	frameshift_variant	Frame_Shift_Del	DEL	GGATCTCCCTC	GGATCTCCCTC	-	novel	NA	P-0004216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	76	428	0	ENST00000372470.3:c.787_797del	p.Ile263TrpfsTer44	p.I263Wfs*44	ENST00000372470	NM_005373.2	262	gGGATCTCCCTC/g	5/12	NA	2	FACETS	0.951	0.84	1			1	INDETERMINATE	1	TRUE	NA	0.435429976694757	2		428	367	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	18	192	0				ENST00000310581	NM_198253.2	-/1132			0.134408156073932	1	FACETS	0.982	0.75	1	0.982	0.75	1	INDETERMINATE	1	TRUE	0	0.294832435266646	1		192	106	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0004226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	85	302	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.886	0.783	0.995	0.886	0.783	0.995	CLONAL	1	TRUE	1	0.294832435266646	2		302	651	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398262	25398262	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913538	NA	P-0004226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	87	476	0	ENST00000311936.3:c.57G>C	p.Leu19Phe	p.L19F	ENST00000311936	NM_004985.3	19	ttG/ttC	2/5	1	2	FACETS	0.857	0.758	0.961	0.857	0.758	0.961	CLONAL	1	TRUE	1	0.294832435266646	2		476	689	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158626	26158626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772836222	NA	P-0004226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	30	97	0	ENST00000289316.2:c.229G>A	p.Glu77Lys	p.E77K	ENST00000289316	NM_138720.2	77	Gag/Aag	1/2	0.148863398188875	4	FACETS	0.757	0.616	0.913	0.757	0.616	0.913	INDETERMINATE	2	TRUE	2	0.294832435266646	4		97	174	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645693	12645693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397516827	NA	P-0004226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	49	292	0	ENST00000251849.4:c.776C>T	p.Ser259Phe	p.S259F	ENST00000251849	NM_002880.3	259	tCc/tTc	7/17	0.201919881328533	3	FACETS	0.906	0.769	1	0.453	0.384	0.528	CLONAL	1	TRUE	1	0.294832435266646	3		292	421	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230772	46230772	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	46	311	0	ENST00000334344.6:c.1021G>C	p.Glu341Gln	p.E341Q	ENST00000334344	NM_152641.2	341	Gag/Cag	8/21	1	2	FACETS	0.748	0.631	0.877	0.748	0.631	0.877	SUBCLONAL	1	TRUE	1	0.294832435266646	2		311	417	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588849	69588849	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	60	506	0	ENST00000168712.1:c.387C>A	p.Phe129Leu	p.F129L	ENST00000168712	NM_002007.2	129	ttC/ttA	2/3	0.201919881328533	3	FACETS	1	0.883	1	0.512	0.442	0.588	CLONAL	1	TRUE	1	0.294832435266646	3		506	456	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0004236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	11	155	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.893	0.622	1	0.893	0.622	1	CLONAL	1	TRUE	1	0.230215410452331	2		155	107	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0004236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	21	405	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.837	0.647	1	0.837	0.647	1	CLONAL	1	TRUE	1	0.230215410452331	2		405	218	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0004236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	46	443	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.230215410452331	2		443	278	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107095	27107095	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763691986	NA	P-0004236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	31	247	0	ENST00000324856.7:c.6706C>T	p.Arg2236Cys	p.R2236C	ENST00000324856	NM_006015.4	2236	Cgc/Tgc	20/20	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.230215410452331	2		247	198	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259013	89259013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	10	210	0	ENST00000336596.2:c.157G>A	p.Glu53Lys	p.E53K	ENST00000336596	NM_005233.5	53	Gaa/Aaa	3/17	0.117466528545545	3	FACETS	0.788	0.536	1	0.394	0.268	0.55	INDETERMINATE	1	TRUE	1	0.230215410452331	3		210	123	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259169	89259169	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	33	325	0	ENST00000336596.2:c.313G>A	p.Asp105Asn	p.D105N	ENST00000336596	NM_005233.5	105	Gac/Aac	3/17	0.117466528545545	3	FACETS	1	0.922	1	0.627	0.513	0.754	INDETERMINATE	1	TRUE	1	0.230215410452331	3		325	255	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851717	134851717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150028142	NA	P-0004236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	30	345	0	ENST00000398015.3:c.1123G>A	p.Asp375Asn	p.D375N	ENST00000398015	NM_004441.4	375	Gac/Aac	5/16	0.117466528545545	3	FACETS	1	0.871	1	0.55	0.445	0.669	INDETERMINATE	1	TRUE	1	0.230215410452331	3		345	264	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374404	81374404	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1486090533	NA	P-0004236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	28	465	0	ENST00000222390.5:c.658C>T	p.Arg220Ter	p.R220*	ENST00000222390	NM_000601.4	220	Cga/Tga	6/18	0.117466528545545	3	FACETS	0.942	0.755	1	0.471	0.377	0.577	INDETERMINATE	1	TRUE	1	0.230215410452331	3		465	288	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523606	106523606	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0004236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	30	242	0	ENST00000359195.3:c.2758A>T	p.Lys920Ter	p.K920*	ENST00000359195	NM_002649.2	920	Aag/Tag	8/11	0.117466528545545	3	FACETS	1	0.927	1	0.667	0.541	0.807	INDETERMINATE	1	TRUE	1	0.230215410452331	3		242	218	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658254	18658254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	31	397	1	ENST00000266497.5:c.3059C>T	p.Ala1020Val	p.A1020V	ENST00000266497		1020	gCt/gTt	22/31	0.230215410452331	1	FACETS	0.973	0.791	1	0.973	0.791	1	CLONAL	1	TRUE	0	0.230215410452331	1		398	245	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459347	99459347	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	31	376	0	ENST00000268035.6:c.1983T>A	p.Asn661Lys	p.N661K	ENST00000268035	NM_000875.3	661	aaT/aaA	9/21	0.230215410452331	1	FACETS	0.657	0.531	0.798	0.657	0.531	0.798	SUBCLONAL	1	TRUE	0	0.230215410452331	1		376	363	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592263	29592263	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0004236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	47	402	0	ENST00000356175.3:c.4678A>T	p.Lys1560Ter	p.K1560*	ENST00000356175	NM_000267.3	1560	Aaa/Taa	35/57	0.230215410452331	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.230215410452331	1		402	300	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676249	37676249	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs772623113	NA	P-0004236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	48	621	0	ENST00000447079.4:c.3004A>G	p.Thr1002Ala	p.T1002A	ENST00000447079	NM_015083.1	1002	Aca/Gca	11/14	0.230215410452331	1	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	0	0.230215410452331	1		621	352	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099228	4099228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140111079	NA	P-0004236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	82	400	0	ENST00000262948.5:c.890G>A	p.Arg297Gln	p.R297Q	ENST00000262948	NM_030662.3	297	cGg/cAg	7/11	1	2	FACETS	1	0.892	1	1	0.985	1	CLONAL	2	TRUE	1	0.230215410452331	2		400	355	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938229	76938229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	57	638	0	ENST00000373344.5:c.2519G>A	p.Arg840Lys	p.R840K	ENST00000373344	NM_000489.3	840	aGa/aAa	9/35	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.230215410452331	2		638	414	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598064	52598064	+	splice_donor_variant	Splice_Site	DEL	A	A	-	novel	NA	P-0004236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	31	522	0	ENST00000394830.3:c.3800+2del		p.X1267_splice	ENST00000394830	NM_018313.4	1267			0.117466528545545	3	FACETS	0.809	0.655	0.984	0.405	0.327	0.492	INDETERMINATE	1	TRUE	1	0.230215410452331	3		522	371	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523669	176523670	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0004236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	29	539	0	ENST00000292408.4:c.2080_2081delinsTT	p.Pro694Leu	p.P694L	ENST00000292408	NM_213647.1	694	CCg/TTg	16/18	0.230215410452331	1	FACETS	0.729	0.586	0.89	0.729	0.586	0.89	SUBCLONAL	1	TRUE	0	0.230215410452331	1		539	306	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0004242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	93	290	0	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	0.912117542731914	2		290	189	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0004242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	164	378	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	0.912117542731914	2		378	343	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776783	NA	P-0004242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	151	147	0	ENST00000267163.4:c.1215+1G>A		p.X405_splice	ENST00000267163	NM_000321.2	405			0.912117542731914	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.912117542731914	1		147	173	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0004242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	178	362	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.912117542731914	2		363	341	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938029	76938029	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	205	293	0	ENST00000373344.5:c.2719C>T	p.Arg907Ter	p.R907*	ENST00000373344	NM_000489.3	907	Cga/Tga	9/35	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.912117542731914	2		293	394	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570058	212570058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1186772138	NA	P-0004242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	176	196	0	ENST00000342788.4:c.1183G>A	p.Val395Ile	p.V395I	ENST00000342788	NM_005235.2	395	Gtc/Atc	10/28	1	2	FACETS	0.946	0.882	1	0.946	0.882	1	CLONAL	1	TRUE	1	0.912117542731914	2		196	408	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157454219	157454219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	251	214	0	ENST00000346085.5:c.2429C>T	p.Thr810Ile	p.T810I	ENST00000346085	NM_020732.3	810	aCa/aTa	8/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.912117542731914	2		214	500	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120535068	120535068	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1012300179	NA	P-0004242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	211	342	0	ENST00000229340.5:c.587G>A	p.Arg196Gln	p.R196Q	ENST00000229340	NM_006861.6	196	cGa/cAa	6/6	1	2	FACETS	0.885	0.829	0.941	0.885	0.829	0.941	CLONAL	1	TRUE	1	0.912117542731914	2		342	523	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252869	36252869	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs993436723	NA	P-0004242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	176	211	0	ENST00000300305.3:c.493G>A	p.Gly165Ser	p.G165S	ENST00000300305		165	Ggt/Agt	4/8	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.912117542731914	2		211	385	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52661373	52661376	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0004242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	125	157	0	ENST00000394830.3:c.1454_1457del	p.Lys485SerfsTer14	p.K485Sfs*14	ENST00000394830	NM_018313.4	485	aAAGAg/ag	14/30	1	2	FACETS	0.878	0.807	0.951	0.878	0.807	0.951	CLONAL	1	TRUE	1	0.912117542731914	2		157	312	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0004256-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	44	405	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.187487559157375	4	FACETS	0.796	0.674	0.928	0.796	0.674	0.928	INDETERMINATE	2	TRUE	2	0.325716585244697	4		405	225	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416378	29416380	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs755556501	NA	P-0004256-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	39	773	0	ENST00000389048.3:c.4573_4575del	p.Lys1525del	p.K1525del	ENST00000389048	NM_004304.4	1525	AAG/-	29/29	0.187487559157375	4	FACETS	1	0.953	1	0.728	0.609	0.858	INDETERMINATE	1	TRUE	2	0.325716585244697	4		773	218	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918952	76918955	+	frameshift_variant	Frame_Shift_Del	DEL	CAGT	CAGT	-	novel	NA	P-0004256-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	86	561	0	ENST00000373344.5:c.4036_4039del	p.Thr1346Ter	p.T1346*	ENST00000373344	NM_000489.3	1346	ACTGtg/tg	12/35	1	1	FACETS	1	0.971	1	1	0.988	1	CLONAL	2	TRUE	0	0.325716585244697	1		561	186	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578504	7578505	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGG	novel	NA	P-0004256-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	61	611	0	ENST00000269305.4:c.423_425dup	p.Pro142dup	p.P142dup	ENST00000269305	NM_001126112.2	142	cct/ccCCCt	5/11	0.325716585244697	3	FACETS	0.949	0.839	1			1	CLONAL	3	TRUE	NA	0.325716585244697	3		611	153	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0004259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	135	378	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.57	2		378	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0004259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	160	575	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.57	2		576	499	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274901	142274901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369939610	NA	P-0004259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	54	312	0	ENST00000350721.4:c.2159G>A	p.Gly720Asp	p.G720D	ENST00000350721	NM_001184.3	720	gGc/gAc	10/47	1	2	FACETS	0.36	0.307	0.417	0.36	0.307	0.417	SUBCLONAL	1	TRUE	1	0.57	2		312	527	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890142	76890145	+	frameshift_variant	Frame_Shift_Del	DEL	TTTC	TTTC	-	novel	NA	P-0004259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	202	273	0	ENST00000373344.5:c.4749_4752del	p.Lys1583AsnfsTer22	p.K1583Nfs*22	ENST00000373344	NM_000489.3	1583	aaGAAA/aa	17/35	0.236653247198485	0	FACETS	0.849	0.802	0.896			1	INDETERMINATE	1	TRUE	NA	0.57	0		273	359	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747342068	NA	P-0004259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	76	228	0	ENST00000269305.4:c.394A>G	p.Lys132Glu	p.K132E	ENST00000269305	NM_001126112.2	132	Aag/Gag	5/11	1	2	FACETS	0.97	0.861	1	0.97	0.861	1	CLONAL	1	TRUE	1	0.57	2		228	275	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161306	55161306	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	42	220	0	ENST00000257290.5:c.3138del	p.Glu1047ArgfsTer26	p.E1047Rfs*26	ENST00000257290	NM_006206.4	1046	gAa/ga	23/23	1	2	FACETS	0.524	0.44	0.617	0.524	0.44	0.617	SUBCLONAL	1	TRUE	1	0.57	2		220	281	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0004275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	109	220	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.469615773470493	2		220	350	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032048	26032048	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs756087316	NA	P-0004275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1213	240	343	0	ENST00000244661.2:c.241A>G	p.Thr81Ala	p.T81A	ENST00000244661	NM_003537.3	81	Acc/Gcc	1/1	0.469615773470493	7	FACETS	0.765	0.712	0.819	0.255	0.237	0.273	SUBCLONAL	2	TRUE	1	0.469615773470493	7		343	1453	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951166	48951166	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1060503079	NA	P-0004275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	91	102	0	ENST00000267163.4:c.1328C>A	p.Ser443Ter	p.S443*	ENST00000267163	NM_000321.2	443	tCa/tAa	13/27	0.248819341608386	5	FACETS	1	0.908	1			1	INDETERMINATE	2	TRUE	NA	0.469615773470493	5		102	326	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556406	29556410	+	frameshift_variant	Frame_Shift_Del	DEL	TTGAG	TTGAG	-	novel	NA	P-0004275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	100	108	0	ENST00000356175.3:c.2774_2778del	p.Leu925SerfsTer9	p.L925Sfs*9	ENST00000356175	NM_000267.3	925	TTGAGt/t	21/57	0.469615773470493	0	FACETS	0.856	0.804	0.904			1	CLONAL	2	TRUE	0	0.469615773470493	0		108	132	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206587	108206587	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0004279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	200	361	1	ENST00000278616.4:c.8167A>T	p.Arg2723Ter	p.R2723*	ENST00000278616	NM_000051.3	2723	Aga/Tga	56/63	0.485715140795837	2	FACETS	1	0.992	1	0.71	0.667	0.754	CLONAL	1	TRUE	0	0.648697134528449	2		362	434	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743988	41743988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776310618	NA	P-0004279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	69	576	2	ENST00000301178.4:c.923G>A	p.Arg308His	p.R308H	ENST00000301178	NM_021913.4	308	cGc/cAc	7/20	0.231870565902086	3	FACETS	0.555	0.484	0.631			1	INDETERMINATE	1	TRUE	NA	0.648697134528449	3		578	508	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249002	55249003	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCGTGGA	rs397517109	NA	P-0004279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	259	401	0	ENST00000275493.2:c.2303_2311dup	p.Ser768_Asp770dup	p.S768_D770dup	ENST00000275493	NM_005228.3	768	gcc/gcCAGCGTGGAc	20/28	0.648697134528449	4	FACETS	1	0.989	1	0.789	0.747	0.832	CLONAL	2	TRUE	1	0.648697134528449	4		401	556	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0004285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	31	747	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.231075135570273	1	FACETS	0.577	0.466	0.702	0.577	0.466	0.702	SUBCLONAL	1	TRUE	0	0.233235445956264	1		747	407	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579533	7579533	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	39	280	0	ENST00000269305.4:c.154C>T	p.Gln52Ter	p.Q52*	ENST00000269305	NM_001126112.2	52	Caa/Taa	4/11	0.177998495205551	1	FACETS	0.985	0.82	1	0.985	0.82	1	CLONAL	1	TRUE	0	0.233235445956264	1		280	300	SUCCESS
ATR	545	MSKCC	GRCh37	3	142297500	142297500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	31	319	0	ENST00000350721.4:c.47G>A	p.Arg16Gln	p.R16Q	ENST00000350721	NM_001184.3	16	cGg/cAg	1/47	1	2	FACETS	0.663	0.536	0.806	0.663	0.536	0.806	SUBCLONAL	1	TRUE	1	0.233235445956264	2		319	401	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025826	1025826	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1054640166	NA	P-0004285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	25	315	0	ENST00000358495.3:c.704C>T	p.Ala235Val	p.A235V	ENST00000358495	NM_134424.2	235	gCg/gTg	8/12	0.177998495205551	1	FACETS	0.658	0.519	0.816	0.658	0.519	0.816	SUBCLONAL	1	TRUE	0	0.233235445956264	1		315	288	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244706	46244706	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	58	415	0	ENST00000334344.6:c.2800C>T	p.Gln934Ter	p.Q934*	ENST00000334344	NM_152641.2	934	Caa/Taa	15/21	1	2	FACETS	0.803	0.69	0.927	0.803	0.69	0.927	CLONAL	1	TRUE	1	0.233235445956264	2		415	619	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719580	61719580	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	29	537	0	ENST00000401558.2:c.1603G>T	p.Asp535Tyr	p.D535Y	ENST00000401558	NM_003400.3	535	Gat/Tat	15/25	0.17227491303071	4	FACETS	1	0.899	1	0.6	0.482	0.733	CLONAL	1	TRUE	2	0.17227491303071	4		537	329	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935629	49935629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	22	459	0	ENST00000296474.3:c.1735G>A	p.Gly579Arg	p.G579R	ENST00000296474	NM_002447.2	579	Gga/Aga	5/20	0.17227491303071	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.17227491303071	1		459	166	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822064	72822064	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	24	433	0	ENST00000268489.5:c.10111C>A	p.Leu3371Met	p.L3371M	ENST00000268489	NM_006885.3	3371	Ctg/Atg	10/10	0.17227491303071	0	FACETS	1	0.796	1			1	CLONAL	1	TRUE	0	0.17227491303071	0		433	228	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0004292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	55	326	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.858	0.742	0.983	1	0.981	1	CLONAL	3	TRUE	1	0.17227491303071	2		326	248	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47735825	47735825	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	26	505	0	ENST00000449228.1:c.35C>T	p.Pro12Leu	p.P12L	ENST00000449228	NM_001127240.2	12	cCa/cTa	1/4	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.17227491303071	2		505	264	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711912	89711913	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	33	468	0	ENST00000371953.3:c.532dup	p.Tyr178LeufsTer2	p.Y178Lfs*2	ENST00000371953	NM_000314.4	177	tat/taTt	6/9	0.17227491303071	2	FACETS	0.795	0.651	0.955	0.795	0.651	0.955	CLONAL	2	TRUE	0	0.17227491303071	2		468	241	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2969697	2969697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367917190	NA	P-0004299-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	326	588	0	ENST00000396946.4:c.1582G>A	p.Glu528Lys	p.E528K	ENST00000396946	NM_032415.4	528	Gag/Aag	12/25	0.587890249369859	3	FACETS	0.953	0.899	1	0.477	0.449	0.505	CLONAL	1	TRUE	1	0.631332072019975	3		588	1425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0004299-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	591	506	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.623455085941361	2	FACETS	0.94	0.91	0.969	0.94	0.91	0.969	CLONAL	2	TRUE	0	0.631332072019975	2		506	996	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509436	106509436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200175951	NA	P-0004299-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	202	565	2	ENST00000359195.3:c.1430G>A	p.Arg477His	p.R477H	ENST00000359195	NM_002649.2	477	cGt/cAt	2/11	0.631332072019975	1	FACETS	0.523	0.485	0.561	0.523	0.485	0.561	SUBCLONAL	1	TRUE	0	0.631332072019975	1		567	838	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851779	134851779	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs370911769	NA	P-0004299-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	77	580	0	ENST00000398015.3:c.1185C>A	p.Ser395Arg	p.S395R	ENST00000398015	NM_004441.4	395	agC/agA	5/16	0.631332072019975	3	FACETS	0.303	0.265	0.345	0.152	0.132	0.173	SUBCLONAL	1	TRUE	1	0.631332072019975	3		580	1058	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748282	41748282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs767837376	NA	P-0004299-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	111	591	1	ENST00000226382.2:c.487G>T	p.Ala163Ser	p.A163S	ENST00000226382	NM_003924.3	163	Gca/Tca	3/3	0.331874745081258	3	FACETS	0.403	0.361	0.447	0.201	0.18	0.224	INDETERMINATE	1	TRUE	1	0.631332072019975	3		592	1149	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045670	26045670	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004299-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1839	103	1064	0	ENST00000540144.1:c.32C>G	p.Ser11Cys	p.S11C	ENST00000540144	NM_003531.2	11	tCt/tGt	1/1	0.234453990573109	3	FACETS	0.221	0.196	0.247	0.074	0.065	0.083	INDETERMINATE	1	TRUE	0	0.631332072019975	3		1064	1942	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750901	128750901	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004299-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1633	102	576	0	ENST00000377970.2:c.438G>T	p.Gln146His	p.Q146H	ENST00000377970	NM_002467.4	146	caG/caT	2/3	0.521623589197211	4	FACETS	0.304	0.27	0.34			1	SUBCLONAL	1	TRUE	NA	0.631332072019975	4		576	1735	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118355613	118355613	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004299-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	68	535	0	ENST00000534358.1:c.4255G>A	p.Gly1419Ser	p.G1419S	ENST00000534358	NM_005933.3	1419	Ggc/Agc	10/36	0.627494806818412	1	FACETS	0.185	0.16	0.212	0.185	0.16	0.212	SUBCLONAL	1	TRUE	0	0.631332072019975	1		535	798	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253208	133253208	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764254754	NA	P-0004299-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	149	539	0	ENST00000320574.5:c.833C>T	p.Thr278Met	p.T278M	ENST00000320574	NM_006231.2	278	aCg/aTg	9/49	0.631332072019975	2	FACETS	0.478	0.436	0.522	0.239	0.218	0.261	SUBCLONAL	1	TRUE	0	0.631332072019975	2		539	987	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936751	32936751	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004299-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	99	396	0	ENST00000380152.3:c.7897G>C	p.Ala2633Pro	p.A2633P	ENST00000380152		2633	Gct/Cct	17/27	1	2	FACETS	0.356	0.317	0.397	0.356	0.317	0.397	SUBCLONAL	1	TRUE	1	0.631332072019975	2		396	881	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435864	110435864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004299-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	27	107	0	ENST00000375856.3:c.2537G>A	p.Gly846Glu	p.G846E	ENST00000375856	NM_003749.2	846	gGg/gAg	1/2	1	2	FACETS	0.407	0.326	0.499	0.407	0.326	0.499	SUBCLONAL	1	TRUE	1	0.631332072019975	2		107	210	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0004303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	27	392	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		392	1012	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288975	33288975	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	120	186	0	ENST00000374542.5:c.577C>T	p.Gln193Ter	p.Q193*	ENST00000374542	NM_001141970.1	193	Cag/Tag	3/8	0.510269883531234	4	FACETS	0.761	0.692	0.833	0.508	0.461	0.556	SUBCLONAL	2	TRUE	1	0.548387134488735	4		186	445	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575021	64575035	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CACCTGCTGCAGCTG	CACCTGCTGCAGCTG	-	novel	NA	P-0004307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	73	232	0	ENST00000312049.6:c.772_783+3del		p.X258_splice	ENST00000312049	NM_130799.2	258		4/10	0.479639705581093	4	FACETS	1	0.971	1			1	CLONAL	1	TRUE	NA	0.548387134488735	4		232	305	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0004323-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	48	290	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.374239338819797	1	FACETS	0.691	0.59	0.8	0.691	0.59	0.8	SUBCLONAL	1	TRUE	0	0.457857570501777	1		290	234	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0004323-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	148	247	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	NA	2	FACETS	0.837	0.774	0.902			1	INDETERMINATE	2	TRUE	NA	0.457857570501777	2		247	386	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257182	16257182	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1047995944	NA	P-0004323-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	117	385	0	ENST00000375759.3:c.4447G>A	p.Val1483Ile	p.V1483I	ENST00000375759	NM_015001.2	1483	Gtt/Att	11/15	1	2	FACETS	0.898	0.813	0.988	0.898	0.813	0.988	CLONAL	1	TRUE	1	0.457857570501777	2		385	569	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960136	134960136	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004323-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	71	281	0	ENST00000398015.3:c.2493A>C	p.Gln831His	p.Q831H	ENST00000398015	NM_004441.4	831	caA/caC	13/16	0.457857570501777	3	FACETS	0.749	0.655	0.85	0.374	0.327	0.425	SUBCLONAL	1	TRUE	1	0.457857570501777	3		281	509	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289089	33289089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004323-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	136	291	0	ENST00000374542.5:c.463C>T	p.Pro155Ser	p.P155S	ENST00000374542	NM_001141970.1	155	Ccc/Tcc	3/8	0.39980479884346	3	FACETS	0.802	0.735	0.872	0.802	0.735	0.872	CLONAL	2	TRUE	1	0.457857570501777	3		291	455	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610003	81610003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536364705	NA	P-0004323-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	75	237	0	ENST00000298171.2:c.1601G>A	p.Arg534His	p.R534H	ENST00000298171	NM_000369.2	534	cGc/cAc	10/10	0.39980479884346	3	FACETS	0.887	0.78	1	0.443	0.39	0.501	CLONAL	1	TRUE	1	0.457857570501777	3		237	454	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37665992	37665992	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004323-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	114	340	0	ENST00000447079.4:c.2644C>T	p.Arg882Trp	p.R882W	ENST00000447079	NM_015083.1	882	Cgg/Tgg	7/14	0.384910985470777	4	FACETS	0.914	0.823	1	0.305	0.274	0.337	CLONAL	1	TRUE	1	0.457857570501777	4		340	794	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11137009	11137009	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765857427	NA	P-0004323-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	161	384	1	ENST00000358026.2:c.3202G>A	p.Gly1068Ser	p.G1068S	ENST00000358026	NM_001128849.1	1068	Ggc/Agc	23/36	0.343739711573864	4	FACETS	0.884	0.815	0.955	0.884	0.815	0.955	CLONAL	2	TRUE	2	0.457857570501777	4		385	580	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0004340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	169	338	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.400732089448134	4	FACETS	0.866	0.802	0.932			1	CLONAL	2	TRUE	NA	0.574009013047972	4		339	535	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570120	95570120	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	70	333	0	ENST00000393063.1:c.3613T>G	p.Tyr1205Asp	p.Y1205D	ENST00000393063	NM_030621.3	1205	Tac/Gac	22/28	1	2	FACETS	0.81	0.713	0.913	0.81	0.713	0.913	CLONAL	1	TRUE	1	0.574009013047972	2		333	301	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0004356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	142	322	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.241863588601762	4	FACETS	0.75	0.684	0.82			1	SUBCLONAL	2	TRUE	NA	0.291864921720813	4		322	838	SUCCESS
ATM	472	MSKCC	GRCh37	11	108225582	108225583	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs786203030	NA	P-0004356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	281	324	0	ENST00000278616.4:c.8833_8834del	p.Leu2945ValfsTer10	p.L2945Vfs*10	ENST00000278616	NM_000051.3	2944	aCT/a	61/63	0.291864921720813	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	2	0.291864921720813	4		324	1018	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213869	66213869	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1787	195	523	0	ENST00000273854.3:c.2561A>G	p.Lys854Arg	p.K854R	ENST00000273854	NM_004439.5	854	aAg/aGg	15/18	0.291864921720813	9	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.291864921720813	9		523	1982	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576244	88576245	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTCCTCCTT	novel	NA	P-0004356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	67	185	0	ENST00000360948.2:c.1428_1429insAAGGAGGAC	p.Asp476_Ser477insLysGluAsp	p.D476_S477insKED	ENST00000360948	NM_001012338.2	476	-/AAGGAGGAC	13/19	0.150667120581396	3	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.291864921720813	3		185	382	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	29	510	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.624	0.499	0.766	0.624	0.499	0.766	SUBCLONAL	1	TRUE	1	0.16	2		510	581	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0004363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	64	759	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.3	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.16	1		759	634	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0004363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	18	331	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.755	1	1	0.755	1	CLONAL	1	TRUE	1	0.16	2		331	225	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0004363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	115	486	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	1	0.956	1	1	0.989	1	CLONAL	2	TRUE	1	0.16	2		486	650	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603023	48603023	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555687378	NA	P-0004363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	24	235	0	ENST00000342988.3:c.1324C>T	p.Gln442Ter	p.Q442*	ENST00000342988	NM_005359.5	442	Cag/Tag	11/12	0.147007584112539	1	FACETS	0.791	0.62	0.988	0.791	0.62	0.988	CLONAL	1	TRUE	0	0.16	1		235	349	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206941989	206941989	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs142726516	NA	P-0004363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	35	378	1	ENST00000423557.1:c.529C>T	p.Arg177Ter	p.R177*	ENST00000423557	NM_000572.2	177	Cga/Tga	5/5	1	2	FACETS	0.97	0.795	1	0.97	0.795	1	CLONAL	1	TRUE	1	0.16	2		379	451	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778162	27778162	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1185725802	NA	P-0004363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	67	1172	0	ENST00000369163.2:c.311T>C	p.Leu104Pro	p.L104P	ENST00000369163	NM_003536.2	104	cTc/cCc	1/1	1	2	FACETS	0.858	0.744	0.983	0.858	0.744	0.983	CLONAL	1	TRUE	1	0.16	2		1172	976	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302962	15302962	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761209241	NA	P-0004363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	24	310	1	ENST00000263388.2:c.488G>A	p.Arg163Gln	p.R163Q	ENST00000263388	NM_000435.2	163	cGg/cAg	4/33	1	2	FACETS	0.971	0.762	1	0.971	0.762	1	CLONAL	1	TRUE	1	0.16	2		311	309	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119071	70119071	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	18	282	0	ENST00000245479.2:c.643del	p.Ser215ProfsTer4	p.S215Pfs*4	ENST00000245479	NM_000346.3	215	Tcc/cc	2/3	1	2	FACETS	0.821	0.619	1	0.821	0.619	1	CLONAL	1	TRUE	1	0.16	2		282	274	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248179	110248184	+	inframe_deletion	In_Frame_Del	DEL	GTCCCA	GTCCCA	-	novel	NA	P-0004363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	44	305	0	ENST00000374672.4:c.1288_1293del	p.Trp430_Asp431del	p.W430_D431del	ENST00000374672	NM_004235.4	430	TGGGAC/-	5/5	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.16	2		305	419	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0004364-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	152	381	1	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	0.365859189189491	2		382	617	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276722	15276722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446718967	NA	P-0004364-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	101	666	0	ENST00000263388.2:c.5543G>A	p.Arg1848His	p.R1848H	ENST00000263388	NM_000435.2	1848	cGt/cAt	30/33	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.365859189189491	2		666	552	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	30	192	0				ENST00000310581	NM_198253.2	-/1132			0.160360784498075	3	FACETS	0.976	0.79	1	0.488	0.395	0.593	INDETERMINATE	1	TRUE	1	0.274115695202566	3		192	255	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0004366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	116	636	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.274115695202566	2		636	817	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778027	135778027	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203682	NA	P-0004366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	162	378	0	ENST00000298552.3:c.2356C>T	p.Arg786Ter	p.R786*	ENST00000298552	NM_001162426.1	786	Cga/Tga	18/23	0.274115695202566	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.274115695202566	1		378	766	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878137	48878137	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1482284498	NA	P-0004366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	18	101	0	ENST00000267163.4:c.89A>C	p.Glu30Ala	p.E30A	ENST00000267163	NM_000321.2	30	gAg/gCg	1/27	1	2	FACETS	0.517	0.39	0.667	0.517	0.39	0.667	SUBCLONAL	1	TRUE	1	0.274115695202566	2		101	254	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870231	44870231	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	107	548	0	ENST00000377967.4:c.410G>T	p.Gly137Val	p.G137V	ENST00000377967	NM_021140.2	137	gGt/gTt	5/29	0.215806737768886	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.274115695202566	1		548	651	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200024	123200024	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0004366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	51	233	0	ENST00000218089.9:c.2097-1G>A		p.X699_splice	ENST00000218089	NM_001042749.1	699			0.258776988984669	0	FACETS	0.989	0.848	1			1	CLONAL	1	TRUE	0	0.274115695202566	0		233	273	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648328	206648328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782549877	NA	P-0004373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	158	252	0	ENST00000367120.3:c.349C>T	p.Arg117Cys	p.R117C	ENST00000367120	NM_014002.3	117	Cgc/Tgc	5/22	0.477120841165501	3	FACETS	1	0.988	1	0.467	0.431	0.504	CLONAL	1	TRUE	0	0.605551296992897	3		252	485	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206943200	206943200	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	69	292	0	ENST00000423557.1:c.418G>C	p.Glu140Gln	p.E140Q	ENST00000423557	NM_000572.2	140	Gag/Cag	4/5	0.477120841165501	3	FACETS	0.453	0.394	0.516	0.151	0.131	0.172	SUBCLONAL	1	TRUE	0	0.605551296992897	3		292	656	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143984	11143984	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	274	321	0	ENST00000358026.2:c.3565C>G	p.Arg1189Gly	p.R1189G	ENST00000358026	NM_001128849.1	1189	Cga/Gga	26/36	1	2	FACETS	0.942	0.891	0.994	1	0.995	1	CLONAL	2	TRUE	1	0.441410201170649	2		321	659	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	83	510	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.236972218159093	4	FACETS	1	0.944	1	0.559	0.493	0.629	CLONAL	1	TRUE	2	0.29	4		510	661	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	48	263	4	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	0.3	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.29	1		267	217	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	233	710	5	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	1	2	FACETS	0.774	0.722	0.828	1	0.992	1	SUBCLONAL	2	TRUE	1	0.29	2		715	1038	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	103	577	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.29	2		578	539	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188865	32188865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138205668	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	52	511	0	ENST00000375023.3:c.689G>A	p.Arg230His	p.R230H	ENST00000375023	NM_004557.3	230	cGt/cAt	4/30	0.295621156405611	3	FACETS	0.876	0.746	1	0.438	0.373	0.509	CLONAL	1	TRUE	1	0.29	3		511	469	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646627	23646627	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs180177100	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	25	333	1	ENST00000261584.4:c.1240C>T	p.Arg414Ter	p.R414*	ENST00000261584	NM_024675.3	414	Cga/Tga	4/13	1	2	FACETS	0.592	0.468	0.735	0.592	0.468	0.735	SUBCLONAL	1	TRUE	1	0.29	2		334	291	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168695	32168695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143103753	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	104	593	0	ENST00000375023.3:c.4228C>T	p.Arg1410Cys	p.R1410C	ENST00000375023	NM_004557.3	1410	Cgc/Tgc	23/30	0.295621156405611	3	FACETS	0.985	0.881	1	0.492	0.44	0.548	CLONAL	1	TRUE	1	0.29	3		593	834	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	91	553	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.861	0.764	0.964	0.861	0.764	0.964	CLONAL	1	TRUE	1	0.29	2		553	729	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628248	187628248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200097846	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	46	415	0	ENST00000441802.2:c.2734G>A	p.Val912Ile	p.V912I	ENST00000441802	NM_005245.3	912	Gtt/Att	2/27	1	2	FACETS	0.896	0.757	1	0.896	0.757	1	CLONAL	1	TRUE	1	0.29	2		415	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	114	517	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.29	2		517	648	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037474	12037474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	16	421	1	ENST00000396373.4:c.1105C>T	p.Arg369Trp	p.R369W	ENST00000396373	NM_001987.4	369	Cgg/Tgg	6/8	0.236972218159093	4	FACETS	0.259	0.19	0.342	0.129	0.095	0.171	SUBCLONAL	1	TRUE	2	0.29	4		422	550	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473722	67473722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs794727798	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	114	577	0	ENST00000327367.4:c.802C>T	p.Arg268Cys	p.R268C	ENST00000327367	NM_005902.3	268	Cgc/Tgc	6/9	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.29	2		577	765	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	35	294	1	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.871	0.717	1	0.871	0.717	1	CLONAL	1	TRUE	1	0.29	2		295	277	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130334	11130334	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1480398200	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	91	644	2	ENST00000358026.2:c.2573C>T	p.Thr858Met	p.T858M	ENST00000358026	NM_001128849.1	858	aCg/aTg	18/36	0.3	1	FACETS	0.753	0.668	0.843	0.753	0.668	0.843	SUBCLONAL	1	TRUE	0	0.29	1		646	713	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	111	296	0	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	0.3	2	FACETS	0.907	0.821	0.996			1	CLONAL	2	TRUE	NA	0.29	2		296	422	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442575	52442575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	69	338	1	ENST00000460680.1:c.170G>A	p.Arg57Gln	p.R57Q	ENST00000460680	NM_004656.3	57	cGg/cAg	4/17	1	2	FACETS	0.688	0.598	0.784	0.688	0.598	0.784	SUBCLONAL	1	TRUE	1	0.29	2		339	692	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681725	78681725	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	88	574	1	ENST00000306801.3:c.433C>T	p.Arg145Ter	p.R145*	ENST00000306801	NM_020761.2	145	Cga/Tga	4/34	1	2	FACETS	0.812	0.719	0.912	0.812	0.719	0.912	CLONAL	1	TRUE	1	0.29	2		575	747	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497874	25497874	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	81	508	1	ENST00000264709.3:c.575C>T	p.Ala192Val	p.A192V	ENST00000264709	NM_175629.2	192	gCg/gTg	6/23	0.3	1	FACETS	0.663	0.584	0.749	0.663	0.584	0.749	SUBCLONAL	1	TRUE	0	0.29	1		509	720	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871286	35871286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145210284	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	31	306	0	ENST00000303115.3:c.508C>T	p.Arg170Cys	p.R170C	ENST00000303115	NM_002185.3	170	Cgc/Tgc	4/8	1	2	FACETS	0.597	0.483	0.726	0.597	0.483	0.726	SUBCLONAL	1	TRUE	1	0.29	2		306	358	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686961	37686961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367703051	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	114	543	2	ENST00000447079.4:c.3865G>A	p.Ala1289Thr	p.A1289T	ENST00000447079	NM_015083.1	1289	Gcc/Acc	14/14	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.29	2		545	771	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922694	44922694	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397514628	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	74	282	0	ENST00000377967.4:c.1555C>T	p.Arg519Ter	p.R519*	ENST00000377967	NM_021140.2	519	Cga/Tga	16/29	0.3	2	FACETS	1	0.971	1			1	CLONAL	1	TRUE	NA	0.29	2		282	376	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346901	89346901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1455558820	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	51	428	0	ENST00000301030.4:c.6049G>A	p.Ala2017Thr	p.A2017T	ENST00000301030	NM_001256183.1	2017	Gcc/Acc	9/13	1	2	FACETS	0.824	0.701	0.957	0.824	0.701	0.957	CLONAL	1	TRUE	1	0.29	2		428	427	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056251	27056251	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	74	493	0	ENST00000324856.7:c.1247G>A	p.Gly416Glu	p.G416E	ENST00000324856	NM_006015.4	416	gGg/gAg	2/20	1	2	FACETS	0.848	0.743	0.961	0.848	0.743	0.961	CLONAL	1	TRUE	1	0.29	2		493	602	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797375	45797375	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	91	617	0	ENST00000450313.1:c.1144G>A	p.Ala382Thr	p.A382T	ENST00000450313	NM_012222.2	382	Gcc/Acc	12/16	1	2	FACETS	0.891	0.792	0.998	0.891	0.792	0.998	CLONAL	1	TRUE	1	0.29	2		617	704	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176118188	176118188	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	34	343	0	ENST00000367669.3:c.785A>G	p.Gln262Arg	p.Q262R	ENST00000367669	NM_022457.5	262	cAg/cGg	6/20	1	2	FACETS	0.923	0.758	1	0.923	0.758	1	CLONAL	1	TRUE	1	0.29	2		343	254	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191473	10191473	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	60	405	0	ENST00000256474.2:c.466T>C	p.Tyr156His	p.Y156H	ENST00000256474	NM_000551.3	156	Tat/Cat	3/3	1	2	FACETS	0.846	0.73	0.972	0.846	0.73	0.972	CLONAL	1	TRUE	1	0.29	2		405	489	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49399972	49399972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	129	624	1	ENST00000418115.1:c.365G>A	p.Arg122Gln	p.R122Q	ENST00000418115	NM_001664.2	122	cGg/cAg	4/5	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.29	2		625	812	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696244	52696244	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	103	653	1	ENST00000394830.3:c.433C>A	p.Leu145Ile	p.L145I	ENST00000394830	NM_018313.4	145	Ctt/Att	5/30	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.29	2		654	678	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808331	1808331	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	12	691	1	ENST00000260795.2:c.2089G>A	p.Gly697Ser	p.G697S	ENST00000260795		697	Ggc/Agc	15/17	1	2	FACETS	0.147	0.102	0.202	0.147	0.102	0.202	SUBCLONAL	1	TRUE	1	0.29	2		692	563	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707731	176707731	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1468516072	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	45	603	1	ENST00000439151.2:c.5788C>T	p.Arg1930Cys	p.R1930C	ENST00000439151	NM_022455.4	1930	Cgc/Tgc	18/23	1	2	FACETS	0.441	0.369	0.52	0.441	0.369	0.52	SUBCLONAL	1	TRUE	1	0.29	2		604	704	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225474	26225474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1590	221	1134	3	ENST00000360408.1:c.92C>T	p.Pro31Leu	p.P31L	ENST00000360408	NM_003532.2	31	cCg/cTg	1/1	0.3	6	FACETS	1	0.988	1	0.332	0.308	0.358	CLONAL	1	TRUE	2	0.29	6		1137	1811	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394367	162394367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144032774	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	72	636	2	ENST00000366898.1:c.701G>A	p.Arg234Gln	p.R234Q	ENST00000366898	NM_004562.2	234	cGg/cAg	6/12	0.295621156405611	3	FACETS	0.815	0.711	0.926	0.407	0.355	0.463	CLONAL	1	TRUE	1	0.29	3		638	698	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273029	55273029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770749711	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	84	546	1	ENST00000275493.2:c.3352G>A	p.Ala1118Thr	p.A1118T	ENST00000275493	NM_005228.3	1118	Gcg/Acg	28/28	1	2	FACETS	0.829	0.732	0.933	0.829	0.732	0.933	CLONAL	1	TRUE	1	0.29	2		547	699	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74858939	74858939	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1371211651	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	46	493	2	ENST00000284811.8:c.265G>A	p.Glu89Lys	p.E89K	ENST00000284811		89	Gag/Aag	4/4	1	2	FACETS	0.555	0.466	0.652	0.555	0.466	0.652	SUBCLONAL	1	TRUE	1	0.29	2		495	572	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080608	5080608	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	57	584	0	ENST00000381652.3:c.2359T>C	p.Cys787Arg	p.C787R	ENST00000381652	NM_004972.3	787	Tgt/Cgt	18/25	1	2	FACETS	0.966	0.831	1	0.966	0.831	1	CLONAL	1	TRUE	1	0.29	2		584	407	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624492	93624492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	66	473	0	ENST00000375746.1:c.583C>T	p.Arg195Ter	p.R195*	ENST00000375746	NM_001174167.1	195	Cga/Tga	4/14	1	2	FACETS	0.822	0.714	0.938	0.822	0.714	0.938	CLONAL	1	TRUE	1	0.29	2		473	554	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209363	98209363	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	82	513	0	ENST00000331920.6:c.4175A>G	p.Asn1392Ser	p.N1392S	ENST00000331920	NM_000264.3	1392	aAc/aGc	23/24	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.29	2		513	504	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399781	139399781	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746025437	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	92	474	1	ENST00000277541.6:c.4567C>T	p.Arg1523Cys	p.R1523C	ENST00000277541	NM_017617.3	1523	Cgt/Tgt	25/34	1	2	FACETS	0.984	0.875	1	0.984	0.875	1	CLONAL	1	TRUE	1	0.29	2		475	645	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920694	100920694	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	71	804	2	ENST00000325455.5:c.2454C>A	p.Phe818Leu	p.F818L	ENST00000325455	NM_001202474.3	818	ttC/ttA	6/8	1	2	FACETS	0.947	0.828	1	0.947	0.828	1	CLONAL	1	TRUE	1	0.29	2		806	517	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362632	118362632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782721568	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	55	451	0	ENST00000534358.1:c.4993C>T	p.Arg1665Cys	p.R1665C	ENST00000534358	NM_005933.3	1665	Cgc/Tgc	15/36	1	2	FACETS	0.738	0.632	0.854	0.738	0.632	0.854	SUBCLONAL	1	TRUE	1	0.29	2		451	514	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377277	118377277	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs782404924	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	105	701	2	ENST00000534358.1:c.10670A>G	p.Lys3557Arg	p.K3557R	ENST00000534358	NM_005933.3	3557	aAg/aGg	27/36	1	2	FACETS	0.819	0.733	0.911	0.819	0.733	0.911	CLONAL	1	TRUE	1	0.29	2		703	884	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425430	49425430	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778418522	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	93	708	1	ENST00000301067.7:c.13058C>T	p.Pro4353Leu	p.P4353L	ENST00000301067	NM_003482.3	4353	cCg/cTg	39/54	0.236972218159093	4	FACETS	1	0.91	1	0.514	0.456	0.575	CLONAL	1	TRUE	2	0.29	4		709	805	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427983	49427983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866777837	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	86	505	1	ENST00000301067.7:c.10607G>A	p.Arg3536His	p.R3536H	ENST00000301067	NM_003482.3	3536	cGc/cAc	38/54	0.236972218159093	4	FACETS	0.996	0.881	1	0.498	0.44	0.56	CLONAL	1	TRUE	2	0.29	4		506	768	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69229766	69229766	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	14	272	0	ENST00000462284.1:c.840+2T>C		p.X280_splice	ENST00000462284	NM_002392.5	280			0.3	1	FACETS	0.472	0.342	0.628	0.472	0.342	0.628	SUBCLONAL	1	TRUE	0	0.29	1		272	175	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241276	105241276	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	31	510	0	ENST00000349310.3:c.632C>T	p.Thr211Ile	p.T211I	ENST00000349310	NM_001014432.1	211	aCa/aTa	8/15	1	2	FACETS	0.377	0.304	0.46	0.377	0.304	0.46	SUBCLONAL	1	TRUE	1	0.29	2		510	567	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512474	38512474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770732457	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	115	472	1	ENST00000254066.5:c.1385C>T	p.Pro462Leu	p.P462L	ENST00000254066	NM_000964.3	462	cCg/cTg	9/9	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.29	2		473	791	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805612	46805612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764401781	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	142	883	2	ENST00000290295.7:c.344C>T	p.Thr115Met	p.T115M	ENST00000290295	NM_006361.5	115	aCg/aTg	1/2	1	2	FACETS	0.99	0.901	1	0.99	0.901	1	CLONAL	1	TRUE	1	0.29	2		885	989	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222943	5222943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749987801	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	87	332	0	ENST00000357368.4:c.2860G>A	p.Val954Met	p.V954M	ENST00000357368	NM_002850.3	954	Gtg/Atg	18/38	0.3	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.29	1		332	389	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350509	15350509	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	58	308	1	ENST00000263377.2:c.3406C>T	p.His1136Tyr	p.H1136Y	ENST00000263377	NM_058243.2	1136	Cac/Tac	16/20	0.295621156405611	3	FACETS	0.907	0.78	1	0.453	0.39	0.523	CLONAL	1	TRUE	1	0.29	3		309	505	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350548	15350548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772431443	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	97	332	0	ENST00000263377.2:c.3367G>A	p.Glu1123Lys	p.E1123K	ENST00000263377	NM_058243.2	1123	Gag/Aag	16/20	0.295621156405611	3	FACETS	1	0.981	1	0.741	0.663	0.823	CLONAL	1	TRUE	1	0.29	3		332	517	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17947971	17947971	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199600889	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	43	582	0	ENST00000458235.1:c.1753G>A	p.Val585Met	p.V585M	ENST00000458235	NM_000215.3	585	Gtg/Atg	13/24	0.295621156405611	3	FACETS	0.406	0.339	0.482	0.203	0.169	0.241	SUBCLONAL	1	TRUE	1	0.29	3		582	836	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744030	41744030	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	100	627	0	ENST00000301178.4:c.965A>G	p.His322Arg	p.H322R	ENST00000301178	NM_021913.4	322	cAc/cGc	7/20	0.295621156405611	3	FACETS	0.992	0.886	1	0.496	0.443	0.553	CLONAL	1	TRUE	1	0.29	3		627	796	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918994	50918994	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854541	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	121	638	0	ENST00000440232.2:c.2731G>A	p.Asp911Asn	p.D911N	ENST00000440232	NM_002691.3	911	Gac/Aac	22/27	0.295621156405611	3	FACETS	1	0.952	1	0.544	0.49	0.6	CLONAL	1	TRUE	1	0.29	3		638	879	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253787	30253787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780264826	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	142	619	0	ENST00000307677.4:c.667G>A	p.Val223Met	p.V223M	ENST00000307677	NM_138578.1	223	Gtg/Atg	3/3	1	2	FACETS	0.914	0.832	1	0.914	0.832	1	CLONAL	1	TRUE	1	0.29	2		619	1071	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385239	41385239	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377294483	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	211	613	0	ENST00000373198.4:c.722G>A	p.Arg241His	p.R241H	ENST00000373198	NM_133170.3	241	cGt/cAt	6/32	1	2	FACETS	0.763	0.709	0.819	1	0.991	1	SUBCLONAL	2	TRUE	1	0.29	2		613	953	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942125	81942125	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	130	874	0	ENST00000359376.3:c.1667del	p.Gly556AlafsTer42	p.G556Afs*42	ENST00000359376	NM_002661.3	554	acG/ac	17/33	1	2	FACETS	0.768	0.694	0.845	0.768	0.694	0.845	SUBCLONAL	1	TRUE	1	0.29	2		874	1168	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155411	47155414	+	frameshift_variant	Frame_Shift_Del	DEL	GTGA	GTGA	-	novel	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	72	774	1	ENST00000409792.3:c.4667_4670del	p.Leu1556GlnfsTer8	p.L1556Qfs*8	ENST00000409792	NM_014159.6	1556	cTCACa/ca	5/21	1	2	FACETS	0.719	0.627	0.817	0.719	0.627	0.817	SUBCLONAL	1	TRUE	1	0.29	2		775	691	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911358	32911358	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507645	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	151	935	0	ENST00000380152.3:c.2870del	p.Asn957IlefsTer3	p.N957Ifs*3	ENST00000380152		956	Aaa/aa	11/27	0.25363752319747	2	FACETS	0.771	0.707	0.838	0.771	0.707	0.838	SUBCLONAL	2	TRUE	0	0.29	2		935	675	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178109	142178110	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	56	387	0	ENST00000350721.4:c.7308dup	p.His2437SerfsTer2	p.H2437Sfs*2	ENST00000350721	NM_001184.3	2436	-/T	43/47	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.29	2		387	355	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15378305	15378305	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004387-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	38	766	0	ENST00000263377.2:c.481del	p.Ile161Ter	p.I161*	ENST00000263377	NM_058243.2	161	Ata/ta	4/20	0.295621156405611	3	FACETS	0.439	0.361	0.525	0.219	0.18	0.263	SUBCLONAL	1	TRUE	1	0.29	3		766	684	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0004401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	178	396	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	0.600788246545947	1	FACETS	0.971	0.906	1	0.971	0.906	1	CLONAL	1	TRUE	0	0.613863142918602	1		396	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579585	7579585	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	184	226	0	ENST00000269305.4:c.102del	p.Leu35CysfsTer9	p.L35Cfs*9	ENST00000269305	NM_001126112.2	34	ccC/cc	4/11	0.613863142918602	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.613863142918602	2		226	298	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187093	11187093	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1386760919	NA	P-0004401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	142	312	0	ENST00000361445.4:c.6325C>T	p.Arg2109Ter	p.R2109*	ENST00000361445	NM_004958.3	2109	Cga/Tga	45/58	1	2	FACETS	0.966	0.887	1	0.966	0.887	1	CLONAL	1	TRUE	1	0.613863142918602	2		312	479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573991	7573991	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567542019	NA	P-0004414-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	38	569	0	ENST00000269305.4:c.1036G>T	p.Glu346Ter	p.E346*	ENST00000269305	NM_001126112.2	346	Gag/Tag	10/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		569	469	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795241	42795241	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs574832764	NA	P-0004414-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	60	360	0	ENST00000575354.2:c.2321C>T	p.Ala774Val	p.A774V	ENST00000575354	NM_015125.3	774	gCg/gTg	10/20	0.299866950810469	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		360	432	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs869320707	NA	P-0004421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	86	711	0	ENST00000397752.3:c.3028+1G>T		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.355899279956221	1	FACETS	0.947	0.845	1	0.947	0.845	1	CLONAL	1	TRUE	0	0.407312270004943	1		711	355	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891349	101891349	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	92	1006	2	ENST00000374994.4:c.310G>T	p.Asp104Tyr	p.D104Y	ENST00000374994	NM_004612.2	104	Gac/Tac	2/9	0.355899279956221	1	FACETS	0.711	0.634	0.793	0.711	0.634	0.793	SUBCLONAL	1	TRUE	0	0.407312270004943	1		1008	506	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148507499	148507499	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	78	962	0	ENST00000320356.2:c.1955C>G	p.Ser652Cys	p.S652C	ENST00000320356	NM_004456.4	652	tCt/tGt	17/20	0.355899279956221	1	FACETS	0.73	0.644	0.821	0.73	0.644	0.821	SUBCLONAL	1	TRUE	0	0.407312270004943	1		962	418	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349610	70349610	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	143	1595	0	ENST00000374080.3:c.3772A>T	p.Ser1258Cys	p.S1258C	ENST00000374080		1258	Agt/Tgt	27/45	0.263346739962755	1	FACETS	0.797	0.728	0.869	0.797	0.728	0.869	SUBCLONAL	1	TRUE	0	0.407312270004943	1		1595	702	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0004424-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	251	585	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.74039833127932	2		585	580	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0004424-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	11	324	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.087	0.059	0.121	0.087	0.059	0.121	SUBCLONAL	1	TRUE	1	0.74039833127932	2		324	343	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0004424-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	13	416	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	NA	2	FACETS	0.067	0.047	0.091			1	INDETERMINATE	1	TRUE	NA	0.74039833127932	2		416	528	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004424-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	125	192	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.74039833127932	2		192	277	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0004424-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	467	636	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.74039833127932	2		636	1061	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872953	136872953	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004424-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	704	1135	0	ENST00000241393.3:c.545A>G	p.Asp182Gly	p.D182G	ENST00000241393	NM_003467.2	182	gAc/gGc	2/2	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.74039833127932	2		1135	1612	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443556	49443556	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0004424-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	444	612	0	ENST00000301067.7:c.3815T>A	p.Leu1272Ter	p.L1272*	ENST00000301067	NM_003482.3	1272	tTg/tAg	11/54	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.74039833127932	2		612	1044	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44935941	44935941	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0004424-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	297	316	0	ENST00000377967.4:c.2703-1G>A		p.X901_splice	ENST00000377967	NM_021140.2	901			1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.74039833127932	1		316	344	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338668	70338668	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004424-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	72	415	0	ENST00000374080.3:c.64C>A	p.Pro22Thr	p.P22T	ENST00000374080		22	Ccc/Acc	1/45	1	1	FACETS	0.163	0.142	0.186	0.163	0.142	0.186	SUBCLONAL	1	TRUE	0	0.74039833127932	1		415	752	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347594	118347595	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004424-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	531	777	0	ENST00000534358.1:c.3232dup	p.Ala1078GlyfsTer11	p.A1078Gfs*11	ENST00000534358	NM_005933.3	1077	-/G	4/36	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.74039833127932	2		777	1248	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976426	25976426	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	337	683	0	ENST00000435504.4:c.1119C>G	p.Phe373Leu	p.F373L	ENST00000435504		373	ttC/ttG	11/13	0.535928392498496	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.535928392498496	1		683	798	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413071	139413071	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	146	485	0	ENST00000277541.6:c.1071C>G	p.Phe357Leu	p.F357L	ENST00000277541	NM_017617.3	357	ttC/ttG	6/34	0.535928392498496	3	FACETS	0.844	0.77	0.92	0.422	0.385	0.46	CLONAL	1	TRUE	1	0.535928392498496	3		485	819	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624263	89624263	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1554890348	NA	P-0004434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	75	147	0	ENST00000371953.3:c.37A>T	p.Lys13Ter	p.K13*	ENST00000371953	NM_000314.4	13	Aaa/Taa	1/9	1	2	FACETS	0.993	0.879	1	0.993	0.879	1	CLONAL	1	TRUE	1	0.535928392498496	2		147	282	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53254071	53254071	+	start_lost	Translation_Start_Site	SNP	T	T	A	novel	NA	P-0004434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	34	387	0	ENST00000375401.3:c.1A>T	p.Met1?	p.M1?	ENST00000375401	NM_004187.3	1	Atg/Ttg	1/26	1	2	FACETS	0.202	0.165	0.245	0.202	0.165	0.245	SUBCLONAL	1	TRUE	1	0.535928392498496	2		387	627	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844167	68844167	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	254	477	0	ENST00000261769.5:c.755del	p.Val252GlufsTer30	p.V252Efs*30	ENST00000261769	NM_004360.3	252	gTa/ga	6/16	0.423825072745033	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.535928392498496	1		477	621	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050914	49050918	+	frameshift_variant	Frame_Shift_Del	DEL	CAACC	CAACC	-	novel	NA	P-0004434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	27	296	0	ENST00000267163.4:c.2599_2603del	p.Asn867SerfsTer2	p.N867Sfs*2	ENST00000267163	NM_000321.2	866	agCAACCct/agct	25/27	0.522424669683724	1	FACETS	0.183	0.145	0.226	0.183	0.145	0.226	SUBCLONAL	1	TRUE	0	0.535928392498496	1		296	403	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0004444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	62	300	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.751	0.656	0.852	0.751	0.656	0.852	SUBCLONAL	1	TRUE	1	0.65	2		300	254	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0004444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	99	225	0	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	0.967	0.874	1	0.967	0.874	1	CLONAL	1	TRUE	1	0.65	2		225	315	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803571	1803571	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs4647924	NA	P-0004444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	111	253	0	ENST00000260795.2:c.749C>A	p.Pro250Gln	p.P250Q	ENST00000260795		250	cCg/cAg	6/17	1	2	FACETS	0.959	0.872	1	0.959	0.872	1	CLONAL	1	TRUE	1	0.65	2		253	356	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477854	140477854	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	181	482	0	ENST00000288602.6:c.1454T>G	p.Leu485Trp	p.L485W	ENST00000288602	NM_004333.4	485	tTg/tGg	12/18	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.65	2		482	512	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439917	52439918	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	139	279	0	ENST00000460680.1:c.794dup	p.Thr266AsnfsTer18	p.T266Nfs*18	ENST00000460680	NM_004656.3	265	gta/gtTa	10/17	0.3	0	FACETS	0.471	0.435	0.507			1	INDETERMINATE	1	TRUE	0	0.65	0		279	318	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0004447-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	177	397	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.335581714983822	4	FACETS	0.899	0.83	0.971	0.899	0.83	0.971	CLONAL	2	TRUE	2	0.34820331714478	4		397	762	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976830	55976830	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148390587	NA	P-0004447-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	142	494	0	ENST00000263923.4:c.1082A>G	p.Glu361Gly	p.E361G	ENST00000263923	NM_002253.2	361	gAa/gGa	8/30	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.34820331714478	2		494	727	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977959	131977959	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004447-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	109	420	0	ENST00000265335.6:c.3842A>T	p.Glu1281Val	p.E1281V	ENST00000265335		1281	gAa/gTa	25/25	0.308806555133634	3	FACETS	0.912	0.819	1	0.456	0.409	0.506	CLONAL	1	TRUE	1	0.34820331714478	3		420	806	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727442	66727442	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004447-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	91	360	0	ENST00000307102.5:c.158T>G	p.Phe53Cys	p.F53C	ENST00000307102	NM_002755.3	53	tTt/tGt	2/11	0.2705284796812	3	FACETS	1	0.921	1	0.522	0.464	0.583	CLONAL	1	TRUE	1	0.34820331714478	3		360	588	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207036	1207038	+	frameshift_variant	Frame_Shift_Del	DEL	CGG	CGG	TT	novel	NA	P-0004447-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	176	382	0	ENST00000326873.7:c.124_126delinsTT	p.Arg42LeufsTer9	p.R42Lfs*9	ENST00000326873	NM_000455.4	42	CGG/TT	1/10	0.34820331714478	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.34820331714478	2		382	488	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0004515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	190	378	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.739	0.685	0.794	0.739	0.685	0.794	SUBCLONAL	1	TRUE	1	0.75	2		378	686	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0004515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	491	646	4	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.885	0.857	0.912	1	0.997	1	CLONAL	2	TRUE	1	0.75	2		650	740	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448307	56448307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768842372	NA	P-0004515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	94	164	0	ENST00000407977.2:c.340C>T	p.Arg114Trp	p.R114W	ENST00000407977		114	Cgg/Tgg	3/10	1	2	FACETS	0.508	0.454	0.566	0.508	0.454	0.566	SUBCLONAL	1	TRUE	1	0.75	2		164	493	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939418	76939418	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	24	213	0	ENST00000373344.5:c.1330C>T	p.Arg444Ter	p.R444*	ENST00000373344	NM_000489.3	444	Cga/Tga	9/35	1	1	FACETS	0.101	0.079	0.127	0.101	0.079	0.127	SUBCLONAL	1	TRUE	0	0.75	1		213	396	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76919037	76919038	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	191	188	0	ENST00000373344.5:c.3953dup	p.Asn1318LysfsTer6	p.N1318Kfs*6	ENST00000373344	NM_000489.3	1318	aat/aaAt	12/35	1	1	FACETS	0.706	0.66	0.752	0.706	0.66	0.752	SUBCLONAL	1	TRUE	0	0.75	1		188	451	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0004526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	87	356	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	0.656	0.581	0.736	0.656	0.581	0.736	SUBCLONAL	1	FALSE	1	0.412521809451122	2		356	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0004526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	88	550	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			1	2	FACETS	0.792	0.703	0.886	0.792	0.703	0.886	SUBCLONAL	1	FALSE	1	0.412521809451122	2		550	539	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439706	51439706	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	139	370	0	ENST00000262662.1:c.271G>T	p.Glu91Ter	p.E91*	ENST00000262662		91	Gag/Tag	4/4	1	2	FACETS	0.784	0.72	0.849	1	0.989	1	SUBCLONAL	2	FALSE	1	0.412521809451122	2		370	430	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948376	71948376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746017563	NA	P-0004526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	121	824	0	ENST00000298229.2:c.3088C>T	p.Arg1030Trp	p.R1030W	ENST00000298229	NM_001567.3	1030	Cgg/Tgg	26/28	NA	2	FACETS	0.663	0.598	0.731			1	INDETERMINATE	1	FALSE	NA	0.412521809451122	2		824	885	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0004528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	25	379	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.296245287057719	0	FACETS	0.759	0.608	0.926			1	CLONAL	1	FALSE	0	0.358337759795774	0		379	118	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781324	3781326	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs587783502	NA	P-0004528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	25	399	0	ENST00000262367.5:c.5039_5041del	p.Ser1680del	p.S1680del	ENST00000262367	NM_004380.2	1680	tCCTtg/ttg	30/31	0.361134559564685	1	FACETS	0.716	0.57	0.88	0.716	0.57	0.88	SUBCLONAL	1	FALSE	0	0.358337759795774	1		399	160	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578397	7578397	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1555526004	NA	P-0004528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	76	261	0	ENST00000269305.4:c.533A>C	p.His178Pro	p.H178P	ENST00000269305	NM_001126112.2	178	cAc/cCc	5/11	0.302093504256261	4	FACETS	0.923	0.834	1	1	0.985	1	CLONAL	4	FALSE	2	0.358337759795774	4		261	156	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579559	7579559	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	21	286	0	ENST00000269305.4:c.128del	p.Leu43Ter	p.L43*	ENST00000269305	NM_001126112.2	43	tTg/tg	4/11	0.302093504256261	4	FACETS	0.931	0.722	1	0.466	0.361	0.586	CLONAL	1	FALSE	2	0.358337759795774	4		286	171	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099343	193099343	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	36	350	0	ENST00000367435.3:c.277G>T	p.Asp93Tyr	p.D93Y	ENST00000367435	NM_024529.4	93	Gat/Tat	3/17	0.302093504256261	4	FACETS	0.898	0.741	1	0.449	0.37	0.536	CLONAL	1	FALSE	2	0.358337759795774	4		350	304	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622419	28622419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776699712	NA	P-0004528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	21	306	0	ENST00000241453.7:c.1198G>A	p.Gly400Arg	p.G400R	ENST00000241453	NM_004119.2	400	Gga/Aga	9/24	0.361134559564685	1	FACETS	0.613	0.476	0.77	0.613	0.476	0.77	SUBCLONAL	1	FALSE	0	0.358337759795774	1		306	157	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022732	31022733	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	14	271	0	ENST00000375687.4:c.2218dup	p.Thr740AsnfsTer34	p.T740Nfs*34	ENST00000375687	NM_015338.5	739	-/A	13/13	0.256473063768241	5	FACETS	0.671	0.486	0.893	0.224	0.162	0.298	SUBCLONAL	1	FALSE	2	0.358337759795774	5		271	179	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0004538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	221	356	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	0.777	0.724	0.832	1	0.992	1	SUBCLONAL	2	TRUE	1	0.313950882290931	2		356	906	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0004545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	91	300	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	0.207007498619254	2		300	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0004545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	117	223	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	1	2	FACETS	0.896	0.809	0.986	1	0.988	1	CLONAL	2	TRUE	1	0.207007498619254	2		223	631	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171455	123171455	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	119	247	0	ENST00000218089.9:c.367C>T	p.Gln123Ter	p.Q123*	ENST00000218089	NM_001042749.1	123	Cag/Tag	6/35	0.097315656979162	0	FACETS	0.725	0.656	0.797			1	INDETERMINATE	2	TRUE	NA	0.207007498619254	0		247	629	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610710	52610710	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	128	319	0	ENST00000394830.3:c.3463G>T	p.Glu1155Ter	p.E1155*	ENST00000394830	NM_018313.4	1155	Gaa/Taa	23/30	0.176377404980459	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.207007498619254	1		319	892	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533548	533548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	109	340	0	ENST00000451590.1:c.355G>A	p.Asp119Asn	p.D119N	ENST00000451590	NM_001130442.1	119	Gac/Aac	4/5	0.207007498619254	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.207007498619254	1		340	792	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918831	50918831	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	100	416	0	ENST00000440232.2:c.2701G>A	p.Val901Met	p.V901M	ENST00000440232	NM_002691.3	901	Gtg/Atg	21/27	0.207007498619254	0	FACETS	0.877	0.782	0.977			1	CLONAL	1	TRUE	0	0.207007498619254	0		416	874	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918705	44918705	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0004545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	125	182	0	ENST00000377967.4:c.1188T>A	p.Tyr396Ter	p.Y396*	ENST00000377967	NM_021140.2	396	taT/taA	12/29	0.097315656979162	0	FACETS	0.745	0.676	0.817			1	INDETERMINATE	2	TRUE	NA	0.207007498619254	0		182	643	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171462	123171462	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0004545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	110	233	0	ENST00000218089.9:c.374C>G	p.Ser125Ter	p.S125*	ENST00000218089	NM_001042749.1	125	tCa/tGa	6/35	0.097315656979162	0	FACETS	0.712	0.641	0.786			1	INDETERMINATE	2	TRUE	NA	0.207007498619254	0		233	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0004551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	248	495	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.3	3	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	3		496	977	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847305	68847305	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	62	535	7	ENST00000261769.5:c.1227G>A	p.Trp409Ter	p.W409*	ENST00000261769	NM_004360.3	409	tgG/tgA	9/16	0.216401143999184	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		542	775	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49399980	49399982	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0004551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	96	642	1	ENST00000418115.1:c.355_357del	p.Lys119del	p.K119del	ENST00000418115	NM_001664.2	119	AAG/-	4/5	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		643	1062	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543787	212543787	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs746505492	NA	P-0004561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	55	307	1	ENST00000342788.4:c.1612C>A	p.Leu538Ile	p.L538I	ENST00000342788	NM_005235.2	538	Ctc/Atc	13/28	0.257137224201178	4	FACETS	0.645	0.551	0.749	0.323	0.275	0.375	SUBCLONAL	1	TRUE	2	0.298909185687384	4		308	741	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598099	52598099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	169	420	1	ENST00000394830.3:c.3767C>T	p.Ala1256Val	p.A1256V	ENST00000394830	NM_018313.4	1256	gCt/gTt	24/30	0.271246291772782	2	FACETS	0.859	0.793	0.928	0.859	0.793	0.928	CLONAL	2	TRUE	0	0.298909185687384	2		421	658	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692970	89692970	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	38	177	0	ENST00000371953.3:c.454C>G	p.Leu152Val	p.L152V	ENST00000371953	NM_000314.4	152	Cta/Gta	5/9	0.270386709509005	3	FACETS	0.961	0.798	1	0.481	0.399	0.571	CLONAL	1	TRUE	1	0.298909185687384	3		177	304	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907495	32907495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782055	NA	P-0004561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	59	294	0	ENST00000380152.3:c.1880C>T	p.Ala627Val	p.A627V	ENST00000380152		627	gCa/gTa	10/27	0.270386709509005	3	FACETS	0.734	0.631	0.846	0.367	0.315	0.423	SUBCLONAL	1	TRUE	1	0.298909185687384	3		294	618	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434976	110434976	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	85	219	0	ENST00000375856.3:c.3425G>A	p.Gly1142Glu	p.G1142E	ENST00000375856	NM_003749.2	1142	gGg/gAg	1/2	0.270386709509005	3	FACETS	0.767	0.682	0.858	0.767	0.682	0.858	SUBCLONAL	2	TRUE	1	0.298909185687384	3		219	426	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598105	52598106	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0004561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	161	428	1	ENST00000394830.3:c.3759_3760dup	p.Leu1254HisfsTer7	p.L1254Hfs*7	ENST00000394830	NM_018313.4	1254	ctc/cACtc	24/30	0.271246291772782	2	FACETS	0.815	0.75	0.882	0.815	0.75	0.882	CLONAL	2	TRUE	0	0.298909185687384	2		429	661	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183695	10183698	+	frameshift_variant	Frame_Shift_Del	DEL	AGGC	AGGC	-	novel	NA	P-0004561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	84	245	0	ENST00000256474.2:c.164_167del	p.Glu55AlafsTer11	p.E55Afs*11	ENST00000256474	NM_000551.3	55	gAGGCc/gc	1/3	0.271246291772782	2	FACETS	0.839	0.747	0.935	0.839	0.747	0.935	CLONAL	2	TRUE	0	0.298909185687384	2		245	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0004565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	131	506	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.594511789495523	2	FACETS	0.806	0.748	0.864	0.806	0.748	0.864	CLONAL	2	TRUE	0	0.64473588916135	2		506	252	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247204	153247204	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	23	542	1	ENST00000281708.4:c.1598G>T	p.Cys533Phe	p.C533F	ENST00000281708	NM_033632.3	533	tGt/tTt	10/12	0.593669321143232	1	FACETS	0.364	0.287	0.45	0.364	0.287	0.45	SUBCLONAL	1	TRUE	0	0.64473588916135	1		543	133	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340459	8340459	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1485033877	NA	P-0004565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	29	379	0	ENST00000356435.5:c.5137G>A	p.Ala1713Thr	p.A1713T	ENST00000356435		1713	Gcc/Acc	31/35	0.447021883826511	3	FACETS	0.589	0.476	0.715	0.294	0.238	0.358	SUBCLONAL	1	TRUE	1	0.64473588916135	3		379	202	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900942	114900942	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0004565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	117	623	2	ENST00000543371.1:c.553-1G>T		p.X185_splice	ENST00000543371	NM_001198531.1	185			0.64473588916135	1	FACETS	0.872	0.8	0.946	0.872	0.8	0.946	CLONAL	1	TRUE	0	0.64473588916135	1		625	282	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375540	15375540	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	131	316	0	ENST00000263377.2:c.887C>T	p.Thr296Ile	p.T296I	ENST00000263377	NM_058243.2	296	aCc/aTc	6/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.64473588916135	2		316	378	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881473	48881473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	27	439	0	ENST00000267163.4:c.195del	p.Ile66TyrfsTer11	p.I66Yfs*11	ENST00000267163	NM_000321.2	65	aaG/aa	2/27	0.508412711746677	1	FACETS	0.684	0.561	0.815	0.684	0.561	0.815	SUBCLONAL	1	TRUE	0	0.64473588916135	1		439	83	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196173	108196173	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0004568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	75	582	0	ENST00000278616.4:c.6709A>T	p.Lys2237Ter	p.K2237*	ENST00000278616	NM_000051.3	2237	Aag/Tag	46/63	1	2	FACETS	0.933	0.818	1	0.933	0.818	1	CLONAL	1	TRUE	1	0.25927065524799	2		582	620	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097747	27097748	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0004568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	100	538	0	ENST00000324856.7:c.3337_3338del	p.Pro1113SerfsTer9	p.P1113Sfs*9	ENST00000324856	NM_006015.4	1112	gaCCct/gact	12/20	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.25927065524799	2		538	739	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	27	192	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	TRUE	1	0.216719120496897	2		192	230	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508499	106508499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752602335	NA	P-0004584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	20	80	0	ENST00000359195.3:c.493G>A	p.Val165Ile	p.V165I	ENST00000359195	NM_002649.2	165	Gtc/Atc	2/11	1	2	FACETS	0.947	0.727	1	0.947	0.727	1	CLONAL	1	TRUE	1	0.216719120496897	2		80	195	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459050	120459050	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs201584590	NA	P-0004584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	84	361	0	ENST00000256646.2:c.6295A>G	p.Met2099Val	p.M2099V	ENST00000256646	NM_024408.3	2099	Atg/Gtg	34/34	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.216719120496897	2		361	676	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	464350	464350	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	54	451	0	ENST00000399788.2:c.844C>G	p.Arg282Gly	p.R282G	ENST00000399788	NM_001042603.1	282	Cgg/Ggg	7/28	NA	2	FACETS	0.497	0.423	0.579			1	INDETERMINATE	1	TRUE	NA	0.216719120496897	2		451	1002	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988634	41988634	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	53	571	0	ENST00000219905.7:c.1426G>A	p.Val476Ile	p.V476I	ENST00000219905	NM_001164273.1	476	Gtc/Atc	3/24	1	2	FACETS	0.477	0.405	0.556	0.477	0.405	0.556	SUBCLONAL	1	TRUE	1	0.216719120496897	2		571	1026	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548887	29548890	+	frameshift_variant	Frame_Shift_Del	DEL	AGTT	AGTT	-	novel	NA	P-0004584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	43	259	0	ENST00000356175.3:c.1663_1666del	p.Leu555IlefsTer12	p.L555Ifs*12	ENST00000356175	NM_000267.3	554	cAGTTa/ca	15/57	0.216719120496897	1	FACETS	0.586	0.489	0.693	0.586	0.489	0.693	SUBCLONAL	1	TRUE	0	0.216719120496897	1		259	604	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0004588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	141	283	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.156460592972115	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.12	3		283	1051	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0004588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	31	483	2	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	1	2	FACETS	0.994	0.802	1	0.994	0.802	1	CLONAL	1	TRUE	1	0.12	2		485	520	SUCCESS
REL	5966	MSKCC	GRCh37	2	61108985	61108985	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	32	290	0	ENST00000295025.8:c.10G>T	p.Gly4Cys	p.G4C	ENST00000295025	NM_002908.2	4	Ggt/Tgt	1/11	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.12	2		290	424	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420202	88420203	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0004588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	40	642	0	ENST00000360948.2:c.2483_2484delinsTT	p.Gly828Val	p.G828V	ENST00000360948	NM_001012338.2	828	gGG/gTT	19/19	1	2	FACETS	0.948	0.786	1	0.948	0.786	1	CLONAL	1	TRUE	1	0.12	2		642	703	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0004595-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	763	759	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.823218769453149	2		759	1714	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2105402	2105402	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs137854306	NA	P-0004595-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	526	754	1	ENST00000219476.3:c.482-1G>A		p.X161_splice	ENST00000219476	NM_000548.3	161			0.823218769453149	1	FACETS	0.987	0.958	1	0.987	0.958	1	CLONAL	1	TRUE	0	0.823218769453149	1		755	762	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786748	3786748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004595-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	737	1071	0	ENST00000262367.5:c.4463C>T	p.Pro1488Leu	p.P1488L	ENST00000262367	NM_004380.2	1488	cCa/cTa	27/31	0.823218769453149	1	FACETS	0.985	0.96	1	0.985	0.96	1	CLONAL	1	TRUE	0	0.823218769453149	1		1071	1070	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140500213	140500213	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757803696	NA	P-0004595-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	795	936	0	ENST00000288602.6:c.929C>T	p.Thr310Ile	p.T310I	ENST00000288602	NM_004333.4	310	aCt/aTt	7/18	0.823218769453149	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.823218769453149	1		936	1091	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573732	64573732	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004595-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	470	666	0	ENST00000312049.6:c.1021del	p.Trp341GlyfsTer27	p.W341Gfs*27	ENST00000312049	NM_130799.2	341	Tgg/gg	7/10	0.823218769453149	1	FACETS	0.974	0.943	1	0.974	0.943	1	CLONAL	1	TRUE	0	0.823218769453149	1		666	690	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562637	21562637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758639228	NA	P-0004595-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	213	232	0	ENST00000382592.4:c.1282G>A	p.Ala428Thr	p.A428T	ENST00000382592	NM_014572.2	428	Gcc/Acc	4/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.823218769453149	2		232	464	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954356	48954356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004595-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	304	459	0	ENST00000267163.4:c.1477G>A	p.Val493Ile	p.V493I	ENST00000267163	NM_000321.2	493	Gtt/Att	16/27	1	2	FACETS	0.823	0.778	0.869	0.823	0.778	0.869	CLONAL	1	TRUE	1	0.823218769453149	2		459	897	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73334666	73334666	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0004595-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	422	590	0	ENST00000377767.4:c.2793+1G>A		p.X931_splice	ENST00000377767	NM_014953.3	931			1	2	FACETS	0.903	0.861	0.944	0.903	0.861	0.944	CLONAL	1	TRUE	1	0.823218769453149	2		590	1136	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246685	41246685	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004595-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	564	705	0	ENST00000357654.3:c.863G>A	p.Ser288Asn	p.S288N	ENST00000357654	NM_007294.3	288	aGc/aAc	10/23	1	2	FACETS	0.966	0.929	1	0.966	0.929	1	CLONAL	1	TRUE	1	0.823218769453149	2		705	1418	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762961	40762961	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004595-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	392	536	0	ENST00000392038.2:c.47G>A	p.Gly16Asp	p.G16D	ENST00000392038	NM_001626.4	16	gGt/gAt	3/14	1	2	FACETS	0.969	0.924	1	0.969	0.924	1	CLONAL	1	TRUE	1	0.823218769453149	2		536	983	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972600	25972600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004595-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	593	728	0	ENST00000435504.4:c.1825G>A	p.Asp609Asn	p.D609N	ENST00000435504		609	Gac/Aac	12/13	0.823218769453149	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.823218769453149	1		728	838	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702388	47702388	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204321	NA	P-0004595-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	343	483	0	ENST00000233146.2:c.1984C>T	p.Gln662Ter	p.Q662*	ENST00000233146	NM_000251.2	662	Cag/Tag	12/16	0.823218769453149	1	FACETS	0.92	0.884	0.955	0.92	0.884	0.955	CLONAL	1	TRUE	0	0.823218769453149	1		483	533	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017141	31017141	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1190521844	NA	P-0004595-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	479	614	0	ENST00000375687.4:c.472G>A	p.Ala158Thr	p.A158T	ENST00000375687	NM_015338.5	158	Gcg/Acg	7/13	1	2	FACETS	0.994	0.952	1	0.994	0.952	1	CLONAL	1	TRUE	1	0.823218769453149	2		614	1171	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165534	47165544	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCAGGTGGA	GGGCAGGTGGA	-	novel	NA	P-0004595-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	695	957	0	ENST00000409792.3:c.582_592del	p.Pro195SerfsTer38	p.P195Sfs*38	ENST00000409792	NM_014159.6	194	ccTCCACCTGCCCaa/ccaa	3/21	0.823218769453149	1	FACETS	0.98	0.954	1	0.98	0.954	1	CLONAL	1	TRUE	0	0.823218769453149	1		957	1014	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289247	33289247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1455644209	NA	P-0004595-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	454	573	1	ENST00000374542.5:c.305C>T	p.Ser102Leu	p.S102L	ENST00000374542	NM_001141970.1	102	tCg/tTg	3/8	0.823218769453149	1	FACETS	0.989	0.958	1	0.989	0.958	1	CLONAL	1	TRUE	0	0.823218769453149	1		574	656	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100375	157100375	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004595-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	252	374	0	ENST00000346085.5:c.1312C>T	p.Pro438Ser	p.P438S	ENST00000346085	NM_020732.3	438	Ccc/Tcc	1/20	0.823218769453149	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.823218769453149	1		374	337	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391148	139391148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004595-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	351	491	1	ENST00000277541.6:c.7043G>A	p.Gly2348Asp	p.G2348D	ENST00000277541	NM_017617.3	2348	gGc/gAc	34/34	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.823218769453149	2		492	814	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397639	139397639	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	382	391	0	ENST00000277541.6:c.5162T>G	p.Val1721Gly	p.V1721G	ENST00000277541	NM_017617.3	1721	gTg/gGg	27/34	0.490745822947891	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.490745822947891	2		391	691	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219367	1219367	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555737790	NA	P-0004606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	425	414	0	ENST00000326873.7:c.419T>C	p.Leu140Pro	p.L140P	ENST00000326873	NM_000455.4	140	cTg/cCg	3/10	0.490745822947891	2	FACETS	0.984	0.943	1	0.984	0.943	1	CLONAL	2	TRUE	0	0.490745822947891	2		414	880	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123788	11123788	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1064795105	NA	P-0004606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	356	368	0	ENST00000358026.2:c.2438C>T	p.Ser813Leu	p.S813L	ENST00000358026	NM_001128849.1	813	tCa/tTa	16/36	0.490745822947891	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.490745822947891	2		368	698	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390758	139390776	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGTCACGGGTGGGACCA	GCGGTCACGGGTGGGACCA	-	novel	NA	P-0004606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	247	327	0	ENST00000277541.6:c.7415_7433del	p.Leu2472GlnfsTer5	p.L2472Qfs*5	ENST00000277541	NM_017617.3	2472	cTGGTCCCACCCGTGACCGCa/ca	34/34	0.490745822947891	2	FACETS	0.972	0.919	1	0.972	0.919	1	CLONAL	2	TRUE	0	0.490745822947891	2		327	518	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0004607-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	491	573	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.63208961601405	3	FACETS	0.98	0.942	1	0.98	0.942	1	CLONAL	2	TRUE	1	0.63208961601405	3		573	1043	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715721	30715721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893816	NA	P-0004607-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	296	514	1	ENST00000295754.5:c.1379G>A	p.Arg460His	p.R460H	ENST00000295754	NM_003242.5	460	cGc/cAc	5/7	0.631973885267819	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.63208961601405	1		515	586	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577569	7577569	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519981	NA	P-0004607-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	255	605	0	ENST00000269305.4:c.712T>C	p.Cys238Arg	p.C238R	ENST00000269305	NM_001126112.2	238	Tgt/Cgt	7/11	0.631973885267819	1	FACETS	0.934	0.882	0.986	0.934	0.882	0.986	CLONAL	1	TRUE	0	0.63208961601405	1		605	591	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218423	1218423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004607-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	279	624	0	ENST00000326873.7:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000326873	NM_000455.4	100	Caa/Taa	2/10	0.631973885267819	1	FACETS	0.991	0.94	1	0.991	0.94	1	CLONAL	1	TRUE	0	0.63208961601405	1		624	609	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204494673	204494673	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004607-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1538	268	504	1	ENST00000367182.3:c.27G>C	p.Gln9His	p.Q9H	ENST00000367182	NM_001278516.1	9	caG/caC	2/11	0.63208961601405	4	FACETS	0.766	0.716	0.819			1	SUBCLONAL	1	TRUE	NA	0.63208961601405	4		505	1806	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004609-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	49	192	0				ENST00000310581	NM_198253.2	-/1132			0.225538144147018	1	FACETS	1	0.892	1	1	0.978	1	CLONAL	2	FALSE	0	0.324992372451367	1		192	123	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0004609-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	140	305	0	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	0.296358614007659	1	FACETS	0.9	0.828	0.973	1	0.991	1	CLONAL	2	FALSE	0	0.324992372451367	1		305	401	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814541	43814541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561818288	NA	P-0004609-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	160	316	0	ENST00000372470.3:c.1336G>A	p.Gly446Arg	p.G446R	ENST00000372470	NM_005373.2	446	Gga/Aga	9/12	0.296358614007659	1	FACETS	1	0.972	1	1	0.993	1	CLONAL	2	FALSE	0	0.324992372451367	1		316	378	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690848	89690848	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1224040268	NA	P-0004609-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	143	178	0	ENST00000371953.3:c.253+2T>C		p.X85_splice	ENST00000371953	NM_000314.4	85			0.324992372451367	0	FACETS	0.711	0.67	0.749			1	SUBCLONAL	4	FALSE	0	0.324992372451367	0		178	209	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579329	7579329	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912658	NA	P-0004609-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	99	314	0	ENST00000269305.4:c.358A>G	p.Lys120Glu	p.K120E	ENST00000269305	NM_001126112.2	120	Aag/Gag	4/11	0.296358614007659	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	0	0.324992372451367	1		314	362	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0004616-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	332	362	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.44505818349237	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.460318185055875	2		363	718	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31381362	31381362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113400552	NA	P-0004616-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	41	232	2	ENST00000328111.2:c.1087C>T	p.Arg363Cys	p.R363C	ENST00000328111	NM_006892.3	363	Cgt/Tgt	10/23	0.460318185055875	4	FACETS	0.516	0.43	0.612	0.258	0.215	0.306	SUBCLONAL	1	TRUE	2	0.460318185055875	4		234	504	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390765	139390765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763785541	NA	P-0004616-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	119	241	0	ENST00000277541.6:c.7426G>A	p.Val2476Met	p.V2476M	ENST00000277541	NM_017617.3	2476	Gtg/Atg	34/34	0.460318185055875	3	FACETS	0.821	0.741	0.905	0.41	0.37	0.453	CLONAL	1	TRUE	1	0.460318185055875	3		241	775	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478926	56478926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004616-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	464	572	0	ENST00000267101.3:c.382A>G	p.Ser128Gly	p.S128G	ENST00000267101	NM_001982.3	128	Agc/Ggc	3/28	0.437172394046722	4	FACETS	0.91	0.868	0.953	0.91	0.868	0.953	CLONAL	2	TRUE	2	0.460318185055875	4		572	1617	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350090	89350090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745768322	NA	P-0004616-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	550	734	1	ENST00000301030.4:c.2860G>A	p.Ala954Thr	p.A954T	ENST00000301030	NM_001256183.1	954	Gcc/Acc	9/13	0.243746642840753	2	FACETS	0.751	0.72	0.782	0.751	0.72	0.782	INDETERMINATE	2	TRUE	0	0.460318185055875	2		735	1591	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40739856	40739856	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004616-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	82	227	0	ENST00000392038.2:c.1369G>A	p.Asp457Asn	p.D457N	ENST00000392038	NM_001626.4	457	Gac/Aac	14/14	0.437172394046722	4	FACETS	0.748	0.659	0.843	0.374	0.329	0.422	SUBCLONAL	1	TRUE	2	0.460318185055875	4		227	696	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31025023	31025023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004616-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	295	309	0	ENST00000375687.4:c.4508C>T	p.Ser1503Leu	p.S1503L	ENST00000375687	NM_015338.5	1503	tCg/tTg	13/13	0.460318185055875	4	FACETS	0.834	0.785	0.884	0.834	0.785	0.884	CLONAL	2	TRUE	2	0.460318185055875	4		309	1122	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307602	118307616	+	inframe_deletion	In_Frame_Del	DEL	CCTGCGCCGGTTCCG	CCTGCGCCGGTTCCG	-	novel	NA	P-0004616-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	149	221	0	ENST00000534358.1:c.375_389del	p.Asn125_Arg130delinsLys	p.N125_R130delinsK	ENST00000534358	NM_005933.3	125	aaCCTGCGCCGGTTCCGg/aag	1/36	0.460318185055875	3	FACETS	0.756	0.694	0.819	0.756	0.694	0.819	SUBCLONAL	2	TRUE	1	0.460318185055875	3		221	527	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968604	55968604	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004616-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	126	470	0	ENST00000263923.4:c.2059del	p.Ser687HisfsTer22	p.S687Hfs*22	ENST00000263923	NM_002253.2	687	Tca/ca	14/30	1	2	FACETS	0.925	0.84	1	0.925	0.84	1	CLONAL	1	TRUE	1	0.460318185055875	2		470	592	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0004619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	35	205	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.179034068251429	2	FACETS	1	0.95	1	0.743	0.616	0.881	CLONAL	1	TRUE	0	0.264796176899553	2		205	178	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0004619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	42	416	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.919	0.77	1	0.919	0.77	1	CLONAL	1	TRUE	1	0.264796176899553	2		416	345	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127164	22127164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057519911	NA	P-0004619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	48	620	0	ENST00000215832.6:c.964G>A	p.Glu322Lys	p.E322K	ENST00000215832	NM_002745.4	322	Gag/Aag	7/9	1	2	FACETS	0.543	0.458	0.637	0.543	0.458	0.637	SUBCLONAL	1	TRUE	1	0.264796176899553	2		620	668	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474685	138474685	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	59	830	0	ENST00000289153.2:c.308G>C	p.Arg103Thr	p.R103T	ENST00000289153	NM_006219.2	103	aGa/aCa	2/22	0.264796176899553	4	FACETS	0.59	0.506	0.682	0.197	0.168	0.228	SUBCLONAL	1	TRUE	1	0.264796176899553	4		830	955	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969912	161969912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1460011098	NA	P-0004619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	73	607	0	ENST00000366898.1:c.1057G>A	p.Glu353Lys	p.E353K	ENST00000366898	NM_004562.2	353	Gaa/Aaa	9/12	0.212443624491403	3	FACETS	1	0.949	1	0.581	0.509	0.659	CLONAL	1	TRUE	1	0.264796176899553	3		607	537	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248167	110248167	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	56	512	0	ENST00000374672.4:c.1305G>C	p.Trp435Cys	p.W435C	ENST00000374672	NM_004235.4	435	tgG/tgC	5/5	0.264796176899553	2	FACETS	0.763	0.654	0.883	0.382	0.327	0.442	SUBCLONAL	1	TRUE	0	0.264796176899553	2		512	554	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143566	108143566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	44	641	1	ENST00000278616.4:c.3271G>A	p.Glu1091Lys	p.E1091K	ENST00000278616	NM_000051.3	1091	Gag/Aag	22/63	0.248873912940996	1	FACETS	0.473	0.396	0.558	0.473	0.396	0.558	SUBCLONAL	1	TRUE	0	0.264796176899553	1		642	610	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884028	37884028	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	40	686	0	ENST00000269571.5:c.3499C>G	p.Leu1167Val	p.L1167V	ENST00000269571		1167	Ctg/Gtg	27/27	1	2	FACETS	0.521	0.432	0.62	0.521	0.432	0.62	SUBCLONAL	1	TRUE	1	0.264796176899553	2		686	580	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214591	5214591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770889503	NA	P-0004619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	33	684	0	ENST00000357368.4:c.4475G>A	p.Arg1492Gln	p.R1492Q	ENST00000357368	NM_002850.3	1492	cGg/cAg	29/38	1	2	FACETS	0.446	0.362	0.541	0.446	0.362	0.541	SUBCLONAL	1	TRUE	1	0.264796176899553	2		684	559	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872524	35872525	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	123	854	0	ENST00000216797.5:c.378dup	p.Ala127CysfsTer2	p.A127Cfs*2	ENST00000216797	NM_020529.2	126	-/T	3/6	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.264796176899553	2		854	851	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593603	55593603	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913235	NA	P-0004639-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	300	409	0	ENST00000288135.5:c.1669T>C	p.Trp557Arg	p.W557R	ENST00000288135	NM_000222.2	557	Tgg/Cgg	11/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.564937518087346	2		409	977	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599341	55599341	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519761	NA	P-0004639-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	213	487	0	ENST00000288135.5:c.2467T>G	p.Tyr823Asp	p.Y823D	ENST00000288135	NM_000222.2	823	Tat/Gat	17/21	1	2	FACETS	0.99	0.922	1	0.99	0.922	1	CLONAL	1	TRUE	1	0.564937518087346	2		487	762	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151583	55151583	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004639-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	331	369	0	ENST00000257290.5:c.2369T>G	p.Leu790Arg	p.L790R	ENST00000257290	NM_006206.4	790	cTt/cGt	17/23	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.564937518087346	2		369	1155	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41247863	41247863	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	440	403	0	ENST00000357654.3:c.670G>T	p.Ala224Ser	p.A224S	ENST00000357654	NM_007294.3	224	Gct/Tct	9/23	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.70054617057156	2		403	1143	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0004646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	430	300	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.387436065139386	10	FACETS	1	0.988	1			1	CLONAL	8	TRUE	NA	0.387436065139386	10		300	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0004646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	131	646	4	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.387436065139386	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.387436065139386	2		650	322	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56376768	56376768	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	83	618	0	ENST00000348428.3:c.808G>A	p.Glu270Lys	p.E270K	ENST00000348428	NM_006785.3	270	Gag/Aag	5/17	NA	2	FACETS	0.867	0.768	0.973			1	INDETERMINATE	1	TRUE	NA	0.387436065139386	2		618	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0004652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	61	513	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.761	0.655	0.875	0.761	0.655	0.875	SUBCLONAL	1	TRUE	1	0.236589717440801	2		515	678	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280804	41280804	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	54	418	0	ENST00000349496.5:c.2317C>T	p.Gln773Ter	p.Q773*	ENST00000349496	NM_001904.3	773	Cag/Tag	15/15	1	2	FACETS	0.732	0.624	0.849	0.732	0.624	0.849	SUBCLONAL	1	TRUE	1	0.236589717440801	2		418	624	SUCCESS
APC	324	MSKCC	GRCh37	5	112175466	112175466	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786204170	NA	P-0004652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	58	419	0	ENST00000257430.4:c.4175C>A	p.Ser1392Ter	p.S1392*	ENST00000257430	NM_000038.5	1392	tCa/tAa	16/16	1	2	FACETS	0.908	0.781	1	0.908	0.781	1	CLONAL	1	TRUE	1	0.236589717440801	2		419	540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577573	7577573	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	46	354	0	ENST00000269305.4:c.708C>A	p.Tyr236Ter	p.Y236*	ENST00000269305	NM_001126112.2	236	taC/taA	7/11	1	2	FACETS	0.773	0.651	0.908	0.773	0.651	0.908	CLONAL	1	TRUE	1	0.236589717440801	2		354	503	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191816	123191817	+	inframe_insertion	In_Frame_Ins	INS	-	-	TAG	novel	NA	P-0004652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	127	282	0	ENST00000218089.9:c.1406_1408dup	p.Leu469_Glu470insVal	p.L469_E470insV	ENST00000218089	NM_001042749.1	469	cta/cTAGta	15/35	0.114169635508595	2	FACETS	1	0.926	1			1	INDETERMINATE	2	TRUE	NA	0.236589717440801	2		282	527	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152198	11152200	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0004652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	81	443	0	ENST00000358026.2:c.4487_4489del	p.Lys1496del	p.K1496del	ENST00000358026	NM_001128849.1	1494	atGAAg/atg	31/36	0.236589717440801	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.236589717440801	1		443	409	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220649	1220649	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004659-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	88	496	0	ENST00000326873.7:c.667G>T	p.Glu223Ter	p.E223*	ENST00000326873	NM_000455.4	223	Gag/Tag	5/10	0.373324409665881	1	FACETS	0.935	0.834	1	0.935	0.834	1	CLONAL	1	TRUE	0	0.373324409665881	1		496	410	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261655	16261655	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004659-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	55	368	0	ENST00000375759.3:c.8920C>A	p.Gln2974Lys	p.Q2974K	ENST00000375759	NM_015001.2	2974	Cag/Aag	11/15	1	2	FACETS	0.769	0.66	0.887	0.769	0.66	0.887	SUBCLONAL	1	TRUE	1	0.373324409665881	2		368	383	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261698	16261698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004659-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	47	343	2	ENST00000375759.3:c.8963C>T	p.Pro2988Leu	p.P2988L	ENST00000375759	NM_015001.2	2988	cCt/cTt	11/15	1	2	FACETS	0.666	0.564	0.779	0.666	0.564	0.779	SUBCLONAL	1	TRUE	1	0.373324409665881	2		345	378	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286805	212286805	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004659-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	99	341	0	ENST00000342788.4:c.2891G>T	p.Arg964Ile	p.R964I	ENST00000342788	NM_005235.2	964	aGa/aTa	24/28	0.206600363720965	1	FACETS	0.934	0.838	1	0.934	0.838	1	INDETERMINATE	1	TRUE	0	0.373324409665881	1		341	462	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402500	20402500	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004659-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	32	226	0	ENST00000346618.3:c.37C>A	p.Leu13Met	p.L13M	ENST00000346618	NM_001949.4	13	Ctg/Atg	1/7	0.166708786398435	4	FACETS	0.823	0.67	0.994	0.412	0.335	0.497	INDETERMINATE	1	TRUE	2	0.373324409665881	4		226	286	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992270	72992270	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004659-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	87	771	0	ENST00000268489.5:c.1775A>C	p.Asp592Ala	p.D592A	ENST00000268489	NM_006885.3	592	gAc/gCc	2/10	0.211633633356342	0	FACETS	0.537	0.476	0.601			1	INDETERMINATE	1	TRUE	0	0.373324409665881	0		771	544	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770023	56770023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759759863	NA	P-0004659-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	58	362	0	ENST00000337432.4:c.19C>T	p.Arg7Cys	p.R7C	ENST00000337432	NM_058216.2	7	Cgc/Tgc	1/9	1	2	FACETS	0.824	0.711	0.946	0.824	0.711	0.946	CLONAL	1	TRUE	1	0.373324409665881	2		362	377	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602488	10602488	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1397945617	NA	P-0004659-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	75	285	0	ENST00000171111.5:c.1090G>T	p.Gly364Cys	p.G364C	ENST00000171111	NM_203500.1	364	Ggc/Tgc	3/6	0.338330087864487	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.373324409665881	1		285	248	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154394	2154395	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0004659-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	48	457	2	ENST00000434045.2:c.533_534delinsAT	p.Ser178Tyr	p.S178Y	ENST00000434045	NM_001127598.1	178	tCC/tAT	5/5	1	2	FACETS	0.86	0.731	1	0.86	0.731	1	CLONAL	1	TRUE	1	0.373324409665881	2		459	299	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	39	490	1	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.179	0.148	0.214	0.179	0.148	0.214	SUBCLONAL	1	TRUE	1	0.77764104380143	2		491	559	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300457	11300457	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	26	351	0	ENST00000361445.4:c.1689T>A	p.His563Gln	p.H563Q	ENST00000361445	NM_004958.3	563	caT/caA	11/58	0.68288625669028	1	FACETS	0.105	0.083	0.131	0.105	0.083	0.131	SUBCLONAL	1	TRUE	0	0.77764104380143	1		351	388	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021728	71021728	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1559602356	NA	P-0004665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	31	471	0	ENST00000318789.4:c.1630C>T	p.Arg544Ter	p.R544*	ENST00000318789	NM_032682.5	544	Cga/Tga	18/21	0.745012354980664	1	FACETS	0.086	0.069	0.106	0.086	0.069	0.106	SUBCLONAL	1	TRUE	0	0.77764104380143	1		471	565	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428200	72428200	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	44	315	0	ENST00000477973.2:c.692A>G	p.His231Arg	p.H231R	ENST00000477973	NM_012234.5	231	cAc/cGc	3/4	0.745012354980664	1	FACETS	0.151	0.126	0.178	0.151	0.126	0.178	SUBCLONAL	1	TRUE	0	0.77764104380143	1		315	458	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913517	NA	P-0004665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	36	369	0	ENST00000288135.5:c.1676T>G	p.Val559Gly	p.V559G	ENST00000288135	NM_000222.2	559	gTt/gGt	11/21	1	2	FACETS	0.121	0.098	0.146	0.121	0.098	0.146	SUBCLONAL	1	TRUE	1	0.77764104380143	2		369	768	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289049	33289049	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs757100759	NA	P-0004665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	48	232	0	ENST00000374542.5:c.503C>A	p.Pro168His	p.P168H	ENST00000374542	NM_001141970.1	168	cCc/cAc	3/8	0.77764104380143	3	FACETS	0.247	0.208	0.29	0.123	0.104	0.145	SUBCLONAL	1	TRUE	1	0.77764104380143	3		232	695	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055678	152055678	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	184	488	0	ENST00000262189.6:c.244G>T	p.Glu82Ter	p.E82*	ENST00000262189	NM_170606.2	82	Gaa/Taa	2/59	NA	2	FACETS	0.525	0.485	0.567			1	INDETERMINATE	1	TRUE	NA	0.77764104380143	2		488	901	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417827	32417827	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	52	348	0	ENST00000332351.3:c.1225C>T	p.Gln409Ter	p.Q409*	ENST00000332351	NM_024426.4	409	Cag/Tag	7/10	0.77764104380143	3	FACETS	0.198	0.167	0.231	0.099	0.083	0.116	SUBCLONAL	1	TRUE	1	0.77764104380143	3		348	940	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	461438	461438	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	90	453	0	ENST00000399788.2:c.1082A>C	p.Tyr361Ser	p.Y361S	ENST00000399788	NM_001042603.1	361	tAt/tCt	9/28	1	2	FACETS	0.227	0.201	0.256	0.227	0.201	0.256	SUBCLONAL	1	TRUE	1	0.77764104380143	2		453	1019	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937543	32937543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	273	339	0	ENST00000380152.3:c.8204C>T	p.Pro2735Leu	p.P2735L	ENST00000380152		2735	cCc/cTc	18/27	1	2	FACETS	0.999	0.943	1	0.999	0.943	1	CLONAL	1	TRUE	1	0.77764104380143	2		339	703	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347128	89347128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	40	548	0	ENST00000301030.4:c.5822C>T	p.Ala1941Val	p.A1941V	ENST00000301030	NM_001256183.1	1941	gCc/gTc	9/13	0.107714179244004	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.77764104380143	0		548	781	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0004669-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	92	302	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.35619111933359	4	FACETS	0.868	0.784	0.954	1	0.977	1	CLONAL	3	TRUE	2	0.38551987209127	4		302	254	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061904	38061904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004669-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	30	314	0	ENST00000250448.2:c.85G>A	p.Val29Ile	p.V29I	ENST00000250448	NM_004496.3	29	Gtc/Atc	2/2	0.38551987209127	2	FACETS	1	0.873	1	0.544	0.445	0.653	CLONAL	1	TRUE	0	0.38551987209127	2		314	143	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944326	81944326	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0004669-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	38	531	0	ENST00000359376.3:c.1934+1G>A		p.X645_splice	ENST00000359376	NM_002661.3	645			0.269792027598622	1	FACETS	0.692	0.576	0.819	0.692	0.576	0.819	SUBCLONAL	1	TRUE	0	0.38551987209127	1		531	230	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356288	70356288	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004669-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	21	490	0	ENST00000374080.3:c.5183C>A	p.Thr1728Lys	p.T1728K	ENST00000374080		1728	aCa/aAa	37/45	0.257220567203038	1	FACETS	0.421	0.325	0.531	0.421	0.325	0.531	SUBCLONAL	1	TRUE	0	0.38551987209127	1		490	209	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577512	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0004669-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	61	336	0	ENST00000269305.4:c.769_770del	p.Leu257GlyfsTer6	p.L257Gfs*6	ENST00000269305	NM_001126112.2	257	CTg/g	7/11	0.358411625263773	2	FACETS	0.915	0.805	1	0.915	0.805	1	CLONAL	2	TRUE	0	0.38551987209127	2		336	173	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067352	37067352	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	100	437	0	ENST00000231790.2:c.1263T>G	p.Ser421Arg	p.S421R	ENST00000231790	NM_000249.3	421	agT/agG	12/19	1	2	FACETS	0.756	0.676	0.842	0.756	0.676	0.842	SUBCLONAL	1	TRUE	1	0.366294559053246	2		437	722	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0004695-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	1176	440	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.372726644762519	13	FACETS	1	0.993	1			1	CLONAL	10	TRUE	NA	0.372726644762519	13		440	1865	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0004695-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2229	455	352	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.372726644762519	13	FACETS	0.925	0.878	0.972			1	CLONAL	3	TRUE	NA	0.372726644762519	13		352	2684	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0004695-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	176	578	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.279270733109566	2	FACETS	1	0.989	1	0.728	0.673	0.784	CLONAL	1	TRUE	0	0.372726644762519	2		579	649	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039610	180039610	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs202140363	NA	P-0004695-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	51	368	0	ENST00000261937.6:c.3433C>T	p.Arg1145Cys	p.R1145C	ENST00000261937	NM_182925.4	1145	Cgc/Tgc	26/30	0.372726644762519	3	FACETS	0.377	0.319	0.441			1	SUBCLONAL	1	TRUE	NA	0.372726644762519	3		368	861	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851381	156851381	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537948663	NA	P-0004695-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	98	444	0	ENST00000524377.1:c.2338C>T	p.Arg780Trp	p.R780W	ENST00000524377	NM_002529.3	780	Cgg/Tgg	17/17	0.372726644762519	4	FACETS	0.776	0.691	0.867	0.388	0.345	0.434	SUBCLONAL	1	TRUE	2	0.372726644762519	4		444	930	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372389	55372389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1274955948	NA	P-0004695-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	48	392	0	ENST00000297316.4:c.1079G>A	p.Arg360His	p.R360H	ENST00000297316	NM_022454.3	360	cGc/cAc	2/2	0.279270733109566	2	FACETS	0.342	0.288	0.401	0.171	0.144	0.201	SUBCLONAL	1	TRUE	0	0.372726644762519	2		392	754	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039435	49039435	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0004695-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	425	579	0	ENST00000267163.4:c.2420C>G	p.Ser807Ter	p.S807*	ENST00000267163	NM_000321.2	807	tCa/tGa	23/27	0.372726644762519	3	FACETS	0.875	0.836	0.914			1	CLONAL	3	TRUE	NA	0.372726644762519	3		579	1031	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0004699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	226	440	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.871	0.812	0.931	0.871	0.812	0.931	CLONAL	1	TRUE	1	0.582517212551985	2		441	891	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	401	657	1	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.582517212551985	2		658	1312	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207118	1207118	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	227	461	0	ENST00000326873.7:c.206C>A	p.Ser69Ter	p.S69*	ENST00000326873	NM_000455.4	69	tCg/tAg	1/10	0.582517212551985	1	FACETS	0.931	0.874	0.99	0.931	0.874	0.99	CLONAL	1	TRUE	0	0.582517212551985	1		461	593	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61711080	61711080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	227	478	0	ENST00000401558.2:c.2669C>T	p.Ala890Val	p.A890V	ENST00000401558	NM_003400.3	890	gCa/gTa	21/25	0.123684040159285	5	FACETS	0.821	0.766	0.878			1	INDETERMINATE	2	TRUE	NA	0.582517212551985	5		478	889	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876384	35876384	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs764922920	NA	P-0004699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	240	402	0	ENST00000303115.3:c.1176G>T	p.Glu392Asp	p.E392D	ENST00000303115	NM_002185.3	392	gaG/gaT	8/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.582517212551985	2		402	752	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287237	33287237	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	248	460	0	ENST00000374542.5:c.1860C>G	p.His620Gln	p.H620Q	ENST00000374542	NM_001141970.1	620	caC/caG	6/8	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.582517212551985	2		460	850	SUCCESS
ATM	472	MSKCC	GRCh37	11	108099967	108099967	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0004699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	206	358	0	ENST00000278616.4:c.248C>G	p.Ser83Ter	p.S83*	ENST00000278616	NM_000051.3	83	tCa/tGa	4/63	0.512685430756545	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.582517212551985	1		358	433	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007855	45007855	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	168	355	0	ENST00000558401.1:c.302G>C	p.Arg101Pro	p.R101P	ENST00000558401	NM_004048.2	101	cGt/cCt	2/4	0.582517212551985	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.582517212551985	1		355	395	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610247	10610247	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	310	579	0	ENST00000171111.5:c.463G>T	p.Val155Phe	p.V155F	ENST00000171111	NM_203500.1	155	Gtc/Ttc	2/6	0.552074866395017	1	FACETS	0.985	0.934	1	0.985	0.934	1	CLONAL	1	TRUE	0	0.582517212551985	1		579	766	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132400	11132400	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0004699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	290	554	0	ENST00000358026.2:c.2617-1G>A		p.X873_splice	ENST00000358026	NM_001128849.1	873			0.552074866395017	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.582517212551985	1		554	696	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299048	15299048	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs114207045	NA	P-0004699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	275	517	0	ENST00000263388.2:c.1490C>T	p.Ser497Leu	p.S497L	ENST00000263388	NM_000435.2	497	tCg/tTg	9/33	NA	2	FACETS	0.98	0.922	1			1	INDETERMINATE	1	TRUE	NA	0.582517212551985	2		517	963	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171705	36171705	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	127	410	0	ENST00000300305.3:c.860A>T	p.Tyr287Phe	p.Y287F	ENST00000300305		287	tAc/tTc	7/8	0.286168775902784	1	FACETS	0.415	0.376	0.456	0.415	0.376	0.456	INDETERMINATE	1	TRUE	0	0.582517212551985	1		410	745	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348978	70348978	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	325	264	0	ENST00000374080.3:c.3490G>C	p.Asp1164His	p.D1164H	ENST00000374080		1164	Gac/Cac	25/45	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.582517212551985	1		264	538	SUCCESS
APC	324	MSKCC	GRCh37	5	112164654	112164654	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	181	270	0	ENST00000257430.4:c.1730del	p.Leu577Ter	p.L577*	ENST00000257430	NM_000038.5	576	gcT/gc	14/16	0.582517212551985	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.582517212551985	1		270	410	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023339	31023340	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0004699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	163	360	0	ENST00000375687.4:c.2824_2825delinsTT	p.Gly942Leu	p.G942L	ENST00000375687	NM_015338.5	942	GGg/TTg	13/13	1	2	FACETS	0.789	0.726	0.855	0.789	0.726	0.855	SUBCLONAL	1	TRUE	1	0.582517212551985	2		360	709	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414922	78414922	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	255	285	2	ENST00000370768.2:c.1844G>A	p.Trp615Ter	p.W615*	ENST00000370768	NM_003902.3	615	tGg/tAg	19/20	1	2	FACETS	0.934	0.88	0.989	0.934	0.88	0.989	CLONAL	1	TRUE	1	0.823884448188184	2		287	663	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0004730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	166	392	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.3	4	FACETS	0.849	0.781	0.921	0.849	0.781	0.921	CLONAL	2	FALSE	2	0.3	4		392	847	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544678	65544680	+	inframe_deletion	In_Frame_Del	DEL	TGC	TGC	-	novel	NA	P-0004730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	219	319	0	ENST00000358664.4:c.246_248del	p.Gln83del	p.Q83del	ENST00000358664	NM_002382.4	82	caGCAa/caa	4/5	0.3	2	FACETS	0.921	0.859	0.984	0.921	0.859	0.984	CLONAL	2	FALSE	0	0.3	2		319	793	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0004733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	169	396	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.677780725827273	6	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	FALSE	3	0.677780725827273	6		396	363	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477854	140477854	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	307	482	0	ENST00000288602.6:c.1454T>G	p.Leu485Trp	p.L485W	ENST00000288602	NM_004333.4	485	tTg/tGg	12/18	0.677780725827273	6	FACETS	0.926	0.889	0.962	1	0.993	1	CLONAL	5	FALSE	2	0.677780725827273	6		482	461	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427206	49427206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	37	520	0	ENST00000301067.7:c.11282C>T	p.Pro3761Leu	p.P3761L	ENST00000301067	NM_003482.3	3761	cCt/cTt	39/54	0.425718117148188	3	FACETS	0.812	0.693	0.935			1	CLONAL	2	FALSE	NA	0.677780725827273	3		520	90	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772384	56772384	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	105	574	0	ENST00000337432.4:c.238G>C	p.Glu80Gln	p.E80Q	ENST00000337432	NM_058216.2	80	Gag/Cag	2/9	0.199956075463287	3	FACETS	0.96	0.881	1	0.96	0.881	1	INDETERMINATE	2	FALSE	1	0.677780725827273	3		574	216	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105667	11105667	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555762188	NA	P-0004733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	54	437	0	ENST00000358026.2:c.1583G>A	p.Arg528Gln	p.R528Q	ENST00000358026	NM_001128849.1	528	cGg/cAg	9/36	1	2	FACETS	0.759	0.674	0.844	1	0.975	1	SUBCLONAL	2	FALSE	1	0.677780725827273	2		437	105	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793157	42793157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	69	500	1	ENST00000575354.2:c.1049C>T	p.Ala350Val	p.A350V	ENST00000575354	NM_015125.3	350	gCc/gTc	7/20	0.515347936853929	3	FACETS	0.903	0.809	0.998			1	CLONAL	2	FALSE	NA	0.677780725827273	3		501	151	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339245	70339245	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	157	351	0	ENST00000374080.3:c.122T>G	p.Val41Gly	p.V41G	ENST00000374080		41	gTa/gGa	2/45	1	1	FACETS		NA	1	1	0.995	1	NA	2	FALSE	0	0.677780725827273	1		351	171	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845162	151845212	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	TCCACAATCCTGATGACAAACACTGGGCGCCCATCCTTCTCCTCAATGGAG	TCCACAATCCTGATGACAAACACTGGGCGCCCATCCTTCTCCTCAATGGAG	-	novel	NA	P-0004733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	102	522	0	ENST00000262189.6:c.13800_13850del	p.Cys4600_Glu4617delinsTer	p.C4600_E4617delins*	ENST00000262189	NM_170606.2	4600	tgCTCCATTGAGGAGAAGGATGGGCGCCCAGTGTTTGTCATCAGGATTGTGGAa/tga	52/59	0.691521397803989	5	FACETS	0.96	0.869	1	0.64	0.579	0.703	CLONAL	2	FALSE	2	0.677780725827273	5		522	316	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425091	49425113	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTTCTGCAAGAGCAGATGCCC	AGCTTCTGCAAGAGCAGATGCCC	-	novel	NA	P-0004733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	49	574	1	ENST00000301067.7:c.13375_13397del	p.Gly4459ThrfsTer20	p.G4459Tfs*20	ENST00000301067	NM_003482.3	4459	GGGCATCTGCTCTTGCAGAAGCTa/a	39/54	0.425718117148188	3	FACETS	1	0.966	1			1	CLONAL	1	FALSE	NA	0.677780725827273	3		575	136	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438287	49438288	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs797045667	NA	P-0004733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	64	372	0	ENST00000301067.7:c.4981dup	p.Glu1661GlyfsTer5	p.E1661Gfs*5	ENST00000301067	NM_003482.3	1661	gag/gGag	20/54	0.425718117148188	3	FACETS	0.943	0.843	1			1	CLONAL	2	FALSE	NA	0.677780725827273	3		372	134	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099113	27099113	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	68	455	0	ENST00000324856.7:c.3530del	p.Pro1177GlnfsTer3	p.P1177Qfs*3	ENST00000324856	NM_006015.4	1177	Cca/ca	13/20	0.617889716167152	4	FACETS	1	0.937	1			1	CLONAL	2	FALSE	NA	0.677780725827273	4		455	157	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778886	3778886	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	35	405	0	ENST00000262367.5:c.6162del	p.Ser2055AlafsTer20	p.S2055Afs*20	ENST00000262367	NM_004380.2	2054	ccC/cc	31/31	NA	2	FACETS	1	0.957	1			1	INDETERMINATE	1	FALSE	NA	0.677780725827273	2		405	73	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0004743-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	4428	339	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	0.659991229998728	33	FACETS	1	0.997	1			1	CLONAL	30	TRUE	NA	0.659991229998728	33		339	4992	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578517	7578517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750600586	NA	P-0004743-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	135	355	0	ENST00000269305.4:c.413C>T	p.Ala138Val	p.A138V	ENST00000269305	NM_001126112.2	138	gCc/gTc	5/11	0.659991229998728	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.659991229998728	1		355	252	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941628	48941628	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0004743-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	136	314	0	ENST00000267163.4:c.940-2A>G		p.X314_splice	ENST00000267163	NM_000321.2	314			0.659265983574541	1	FACETS	0.905	0.837	0.974	0.905	0.837	0.974	CLONAL	1	TRUE	0	0.659991229998728	1		314	305	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921551	178921551	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519939	NA	P-0004743-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	383	262	0	ENST00000263967.3:c.1033A>C	p.Asn345His	p.N345H	ENST00000263967	NM_006218.2	345	Aat/Cat	5/21	0.659991229998728	3	FACETS	0.995	0.964	1	0.995	0.964	1	CLONAL	3	TRUE	0	0.659991229998728	3		262	517	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	44	396	0	ENST00000347630.2:c.397T>C	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	Ttc/Ctc	6/11	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.237671944536308	2		396	337	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857794	57857794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1392573638	NA	P-0004756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	93	491	0	ENST00000228682.2:c.113C>T	p.Pro38Leu	p.P38L	ENST00000228682	NM_005269.2	38	cCg/cTg	3/12	1	2	FACETS	0.81	0.723	0.902	1	0.983	1	CLONAL	2	TRUE	1	0.237671944536308	2		491	483	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599341	55599341	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519761	NA	P-0004760-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	393	487	0	ENST00000288135.5:c.2467T>G	p.Tyr823Asp	p.Y823D	ENST00000288135	NM_000222.2	823	Tat/Gat	17/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.925166369811713	2		487	821	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593615	+	inframe_deletion	In_Frame_Del	DEL	AGTGGAAGGTTGTTG	AGTGGAAGGTTGTTG	-	novel	NA	P-0004760-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	410	682	0	ENST00000288135.5:c.1669_1683del	p.Trp557_Glu561del	p.W557_E561del	ENST00000288135	NM_000222.2	556	cAGTGGAAGGTTGTTGag/cag	11/21	1	2	FACETS	0.917	0.876	0.958	0.917	0.876	0.958	CLONAL	1	TRUE	1	0.925166369811713	2		682	967	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65349059	65349059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004776-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	286	260	15	ENST00000342505.4:c.106G>A	p.Val36Met	p.V36M	ENST00000342505	NM_002227.2	36	Gtg/Atg	3/25	1	2	FACETS	0.955	0.903	1	0.955	0.903	1	CLONAL	1	TRUE	1	0.816949828275493	2		275	733	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593589	55593597	+	inframe_deletion	In_Frame_Del	DEL	TGTATGAAG	TGTATGAAG	-	novel	NA	P-0004776-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	228	340	0	ENST00000288135.5:c.1656_1664del	p.Met552_Val555delinsIle	p.M552_V555delinsI	ENST00000288135	NM_000222.2	552	aTGTATGAAGta/ata	11/21	1	2	FACETS	0.783	0.733	0.834	0.783	0.733	0.834	SUBCLONAL	1	TRUE	1	0.816949828275493	2		340	713	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	113	510	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.472397222262034	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.472397222262034	1		510	360	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0004786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	397	338	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	NA	2	FACETS	0.933	0.891	0.975			1	INDETERMINATE	2	TRUE	NA	0.472397222262034	2		338	901	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0004786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	130	258	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	1	2	FACETS	0.855	0.777	0.936	0.855	0.777	0.936	CLONAL	1	TRUE	1	0.472397222262034	2		258	644	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156747	106156747	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs572712965	NA	P-0004786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	181	382	2	ENST00000380013.4:c.1648C>T	p.Arg550Ter	p.R550*	ENST00000380013	NM_001127208.2	550	Cga/Tga	3/11	1	2	FACETS	0.885	0.817	0.956	0.885	0.817	0.956	CLONAL	1	TRUE	1	0.472397222262034	2		384	866	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575117	48575117	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	45	376	0	ENST00000342988.3:c.311T>A	p.Leu104His	p.L104H	ENST00000342988	NM_005359.5	104	cTt/cAt	3/12	0.472397222262034	1	FACETS	0.281	0.236	0.332	0.281	0.236	0.332	SUBCLONAL	1	TRUE	0	0.472397222262034	1		376	517	SUCCESS
APC	324	MSKCC	GRCh37	5	112175182	112175198	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTGCTAATACCCTGC	TTCTGCTAATACCCTGC	G	novel	NA	P-0004786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	111	190	0	ENST00000257430.4:c.3891_3907delinsG	p.Asp1297GlufsTer3	p.D1297Efs*3	ENST00000257430	NM_000038.5	1297	gaTTCTGCTAATACCCTGCaa/gaGaa	16/16	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.472397222262034	2		190	459	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0004792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	125	381	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.977	0.885	1	0.977	0.885	1	CLONAL	1	TRUE	1	0.326267022960715	2		382	784	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394805	45394805	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	124	398	0	ENST00000262160.6:c.544C>T	p.Arg182Ter	p.R182*	ENST00000262160	NM_005901.5	182	Cga/Tga	5/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.326267022960715	2		398	565	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	116	497	1	ENST00000262160.6:c.1391C>A	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tAa	11/11	1	2	FACETS	0.905	0.815	0.999	0.905	0.815	0.999	CLONAL	1	TRUE	1	0.326267022960715	2		498	786	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431010	181431010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	145	430	1	ENST00000325404.1:c.862G>A	p.Ala288Thr	p.A288T	ENST00000325404	NM_003106.3	288	Gcc/Acc	1/1	1	2	FACETS	0.956	0.872	1	0.956	0.872	1	CLONAL	1	TRUE	1	0.326267022960715	2		431	930	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55569926	55569926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502570	NA	P-0004792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	110	461	1	ENST00000288135.5:c.793G>A	p.Gly265Ser	p.G265S	ENST00000288135	NM_000222.2	265	Ggt/Agt	5/21	0.264897785911283	1	FACETS	0.761	0.683	0.842	0.761	0.683	0.842	SUBCLONAL	1	TRUE	0	0.326267022960715	1		462	742	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446455	49446455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	141	365	0	ENST00000301067.7:c.1150G>A	p.Glu384Lys	p.E384K	ENST00000301067	NM_003482.3	384	Gag/Aag	9/54	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.326267022960715	2		365	824	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482870	67482870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	232	354	0	ENST00000327367.4:c.1274C>T	p.Ser425Phe	p.S425F	ENST00000327367	NM_005902.3	425	tCt/tTt	9/9	0.326267022960715	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.326267022960715	2		354	613	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844127	68844127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780537	NA	P-0004792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	197	608	1	ENST00000261769.5:c.715G>A	p.Gly239Arg	p.G239R	ENST00000261769	NM_004360.3	239	Ggg/Agg	6/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.326267022960715	2		609	993	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508445	29508445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555608643	NA	P-0004792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	152	494	0	ENST00000356175.3:c.592G>A	p.Ala198Thr	p.A198T	ENST00000356175	NM_000267.3	198	Gca/Aca	6/57	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.326267022960715	2		494	829	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790171	40790171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760735173	NA	P-0004792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	81	257	0	ENST00000373198.4:c.2560C>T	p.Arg854Cys	p.R854C	ENST00000373198	NM_133170.3	854	Cgc/Tgc	18/32	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.326267022960715	2		257	483	SUCCESS
AR	367	MSKCC	GRCh37	X	66863244	66863244	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	174	404	0	ENST00000374690.3:c.1763C>G	p.Ala588Gly	p.A588G	ENST00000374690	NM_000044.3	588	gCt/gGt	2/8	0.459030208915717	1	FACETS	0.991	0.921	1	0.991	0.921	1	CLONAL	1	TRUE	0	0.546451117966471	1		404	467	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874362	76874362	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	333	612	0	ENST00000373344.5:c.5360G>T	p.Gly1787Val	p.G1787V	ENST00000373344	NM_000489.3	1787	gGt/gTt	21/35	0.371418321535721	0	FACETS	0.783	0.746	0.82			1	SUBCLONAL	1	TRUE	0	0.546451117966471	0		612	706	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004807-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	10	192	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.591	0.405	0.817			1	INDETERMINATE	1	TRUE	NA	0.42310953782135	2		192	80	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690819	89690820	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0004807-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	96	159	0	ENST00000371953.3:c.227_228del	p.Tyr76Ter	p.Y76*	ENST00000371953	NM_000314.4	76	TAt/t	4/9	0.223753496593063	2	FACETS	1	0.977	1	0.656	0.59	0.725	INDETERMINATE	1	TRUE	0	0.42310953782135	2		159	346	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239881	41239881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004807-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	41	196	1	ENST00000379561.5:c.469C>T	p.Arg157Cys	p.R157C	ENST00000379561	NM_002015.3	157	Cgc/Tgc	1/3	NA	2	FACETS	1	0.961	1			1	INDETERMINATE	1	TRUE	NA	0.42310953782135	2		197	131	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676201	29676202	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0004807-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	159	300	0	ENST00000356175.3:c.7192_7193del	p.Leu2398GlyfsTer2	p.L2398Gfs*2	ENST00000356175	NM_000267.3	2397	aCT/a	48/57	NA	2	FACETS	0.872	0.807	0.938			1	INDETERMINATE	2	TRUE	NA	0.42310953782135	2		300	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0004830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	195	646	4	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.531528863682775	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	0	0.532979395463107	2		650	364	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681708	78681708	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767783333	NA	P-0004830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	201	303	2	ENST00000306801.3:c.416G>A	p.Arg139His	p.R139H	ENST00000306801	NM_020761.2	139	cGc/cAc	4/34	0.532979395463107	7	FACETS	1	0.985	1	0.485	0.451	0.521	CLONAL	2	TRUE	2	0.532979395463107	7		305	725	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218045	108218045	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782451	NA	P-0004830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	95	245	0	ENST00000278616.4:c.8624A>G	p.Asn2875Ser	p.N2875S	ENST00000278616	NM_000051.3	2875	aAt/aGt	59/63	0.532979395463107	2	FACETS	0.979	0.897	1	0.979	0.897	1	CLONAL	2	TRUE	0	0.532979395463107	2		245	182	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	288	192	0				ENST00000310581	NM_198253.2	-/1132			0.788761496199688	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.838330378490874	3		192	474	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0004837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4154	1011	417	3	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.838330378490874	22	FACETS	1	0.993	1			1	CLONAL	4	TRUE	NA	0.838330378490874	22		420	5165	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211079	55211079	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519888	NA	P-0004837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3532	1655	420	0	ENST00000275493.2:c.322A>G	p.Arg108Gly	p.R108G	ENST00000275493	NM_005228.3	108	Aga/Gga	3/28	0.838330378490874	22	FACETS	1	0.988	1			1	CLONAL	7	TRUE	NA	0.838330378490874	22		420	5187	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268870	55268888	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCTGCACCAGGGGGATGA	CTCTGCACCAGGGGGATGA	-	novel	NA	P-0004837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7073	486	301	0	ENST00000275493.2:c.2947-11_2954del		p.X983_splice	ENST00000275493	NM_005228.3	983		25/28	0.838330378490874	22	FACETS	1	0.995	1			1	CLONAL	1	TRUE	NA	0.838330378490874	22		301	7559	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0004847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	511	392	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.377552051152082	5	FACETS	0.934	0.897	0.971	0.934	0.897	0.971	CLONAL	4	TRUE	1	0.377552051152082	5		392	1135	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0004847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	492	318	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.377552051152082	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.377552051152082	3		318	895	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123769	11123769	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	71	350	0	ENST00000358026.2:c.2419C>T	p.Leu807Phe	p.L807F	ENST00000358026	NM_001128849.1	807	Ctc/Ttc	16/36	0.36387443709408	3	FACETS	0.598	0.521	0.681	0.199	0.173	0.227	SUBCLONAL	1	TRUE	0	0.377552051152082	3		350	748	SUCCESS
AR	367	MSKCC	GRCh37	X	66863126	66863128	+	missense_variant	Missense_Mutation	TNP	CCC	CCC	GCT	novel	NA	P-0004847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1292	85	534	0	ENST00000374690.3:c.1645_1647delinsGCT	p.Pro549Ala	p.P549A	ENST00000374690	NM_000044.3	549	CCC/GCT	2/8	0.230897671623107	5	FACETS	0.512	0.451	0.578	0.171	0.15	0.193	SUBCLONAL	1	TRUE	2	0.377552051152082	5		534	1377	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0004857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	130	300	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.251859402172943	4	FACETS	1	0.954	1	1	0.954	1	INDETERMINATE	2	TRUE	2	0.423950441390238	4		300	411	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0004857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	181	378	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.417321819879259	4	FACETS	0.855	0.791	0.921	0.855	0.791	0.921	CLONAL	2	TRUE	2	0.423950441390238	4		378	711	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	106	192	0				ENST00000310581	NM_198253.2	-/1132			0.200612833275225	5	FACETS	0.905	0.816	0.998	0.603	0.544	0.666	INDETERMINATE	2	TRUE	2	0.423950441390238	5		192	452	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167850	56167850	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	159	357	0	ENST00000399503.3:c.1415T>G	p.Met472Arg	p.M472R	ENST00000399503	NM_005921.1	472	aTg/aGg	7/20	0.200612833275225	5	FACETS	1	0.983	1	0.823	0.76	0.888	INDETERMINATE	2	TRUE	2	0.423950441390238	5		357	497	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587473	29587483	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTACATCGT	CTTTACATCGT	-	novel	NA	P-0004857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	458	441	0	ENST00000356175.3:c.4456_4466del	p.Leu1486ThrfsTer19	p.L1486Tfs*19	ENST00000356175	NM_000267.3	1485	gCTTTACATCGT/g	33/57	0.415553939863888	4	FACETS	0.959	0.924	0.994			1	CLONAL	4	TRUE	NA	0.423950441390238	4		441	802	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484148	120484148	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0004858-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	110	561	0	ENST00000256646.2:c.2981+1G>T		p.X994_splice	ENST00000256646	NM_024408.3	994			0.380713252985376	2	FACETS	0.996	0.898	1	0.498	0.449	0.55	CLONAL	1	TRUE	0	0.380713252985376	2		561	580	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14028655	14028655	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004858-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	113	684	1	ENST00000405192.2:c.23A>T	p.Gln8Leu	p.Q8L	ENST00000405192	NM_001163147.1	8	cAa/cTa	2/12	0.380713252985376	3	FACETS	0.922	0.83	1	0.461	0.415	0.51	CLONAL	1	TRUE	1	0.380713252985376	3		685	766	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868419	117868419	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004858-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	319	701	0	ENST00000297338.2:c.923C>T	p.Pro308Leu	p.P308L	ENST00000297338	NM_006265.2	308	cCt/cTt	8/14	0.251911189508921	5	FACETS	1	0.986	1	0.755	0.713	0.799	CLONAL	2	TRUE	2	0.380713252985376	5		701	1162	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100358	8100358	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004858-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	343	938	0	ENST00000346208.3:c.332C>A	p.Pro111His	p.P111H	ENST00000346208		111	cCc/cAc	3/6	0.300130167403547	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	2	0.380713252985376	4		938	1080	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220699	1220699	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004858-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	269	678	0	ENST00000326873.7:c.717G>T	p.Trp239Cys	p.W239C	ENST00000326873	NM_000455.4	239	tgG/tgT	5/10	0.380713252985376	2	FACETS	0.984	0.928	1	0.984	0.928	1	CLONAL	2	TRUE	0	0.380713252985376	2		678	718	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610321	10610321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004858-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	311	712	1	ENST00000171111.5:c.389C>T	p.Pro130Leu	p.P130L	ENST00000171111	NM_203500.1	130	cCc/cTc	2/6	0.380713252985376	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.380713252985376	2		713	719	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811726	102811726	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004858-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	211	919	1	ENST00000307046.8:c.458del	p.Pro153GlnfsTer49	p.P153Qfs*49	ENST00000307046	NM_001111285.1	153	cCa/ca	4/4	0.380713252985376	3	FACETS	1	0.973	1	0.551	0.511	0.593	CLONAL	1	TRUE	1	0.380713252985376	3		920	1197	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165746	108165751	+	inframe_deletion	In_Frame_Del	DEL	ACATAA	ACATAA	-	novel	NA	P-0004858-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	252	691	1	ENST00000278616.4:c.4870_4875del	p.His1624_Lys1625del	p.H1624_K1625del	ENST00000278616	NM_000051.3	1623	ctACATAAa/cta	32/63	0.380713252985376	3	FACETS	0.899	0.843	0.957	0.899	0.843	0.957	CLONAL	2	TRUE	1	0.380713252985376	3		692	876	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613657	100613657	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004858-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	169	680	0	ENST00000308731.7:c.922G>T	p.Asp308Tyr	p.D308Y	ENST00000308731	NM_000061.2	308	Gac/Tac	11/19	0.191136943995915	3	FACETS	1	0.927	1	0.337	0.309	0.366	INDETERMINATE	1	TRUE	0	0.380713252985376	3		680	1046	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0004860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	145	300	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.91	0.835	0.988	0.91	0.835	0.988	CLONAL	1	TRUE	1	0.605653977452093	2		300	526	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	218	510	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.605653977452093	1	FACETS	0.908	0.851	0.965	0.908	0.851	0.965	CLONAL	1	TRUE	0	0.605653977452093	1		510	553	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488694	212488694	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	239	362	0	ENST00000342788.4:c.2155A>C	p.Lys719Gln	p.K719Q	ENST00000342788	NM_005235.2	719	Aag/Cag	18/28	0.605653977452093	2	FACETS	1	0.944	1	0.504	0.472	0.537	CLONAL	1	TRUE	0	0.605653977452093	2		362	783	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187558023	187558023	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0004860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	173	228	0	ENST00000441802.2:c.3688A>T	p.Arg1230Ter	p.R1230*	ENST00000441802	NM_005245.3	1230	Aga/Tga	5/27	1	2	FACETS	0.975	0.902	1	0.975	0.902	1	CLONAL	1	TRUE	1	0.605653977452093	2		228	586	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174910	56174910	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	243	322	0	ENST00000399503.3:c.2069A>T	p.Lys690Ile	p.K690I	ENST00000399503	NM_005921.1	690	aAa/aTa	11/20	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.605653977452093	2		322	795	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056210	26056210	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	234	360	0	ENST00000343677.2:c.447G>C	p.Lys149Asn	p.K149N	ENST00000343677	NM_005319.3	149	aaG/aaC	1/1	1	2	FACETS	0.962	0.9	1	0.962	0.9	1	CLONAL	1	TRUE	1	0.605653977452093	2		360	803	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978792	13978792	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1197619453	NA	P-0004860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1231	158	409	0	ENST00000405192.2:c.315A>C	p.Gln105His	p.Q105H	ENST00000405192	NM_001163147.1	105	caA/caC	6/12	0.339176343846464	5	FACETS	0.717	0.655	0.782	0.239	0.218	0.261	INDETERMINATE	1	TRUE	2	0.605653977452093	5		409	1389	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37034015	37034015	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1430740493	NA	P-0004860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	240	329	1	ENST00000358127.4:c.14A>C	p.Lys5Thr	p.K5T	ENST00000358127	NM_001280556.1	5	aAa/aCa	1/10	0.605653977452093	3	FACETS	1	0.987	1	0.6	0.562	0.64	CLONAL	1	TRUE	1	0.605653977452093	3		330	860	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226031	133226031	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs781298285	NA	P-0004860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	192	363	0	ENST00000320574.5:c.3866G>T	p.Arg1289Leu	p.R1289L	ENST00000320574	NM_006231.2	1289	cGc/cTc	31/49	0.405272025130051	1	FACETS	0.814	0.759	0.871	0.814	0.759	0.871	CLONAL	1	TRUE	0	0.605653977452093	1		363	543	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1427441061	NA	P-0004860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	308	438	0	ENST00000269305.4:c.560-2A>G		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.605653977452093	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.605653977452093	1		438	679	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560844	9560844	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	290	388	0	ENST00000353224.5:c.938A>T	p.Tyr313Phe	p.Y313F	ENST00000353224	NM_177990.2	313	tAc/tTc	4/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.605653977452093	2		388	946	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410913	63410913	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	326	293	0	ENST00000330258.3:c.2254G>T	p.Glu752Ter	p.E752*	ENST00000330258	NM_152424.3	752	Gaa/Taa	2/2	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.605653977452093	1		293	537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0004867-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	268	394	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.36224741912632	3	FACETS	0.973	0.921	1	0.973	0.921	1	CLONAL	3	TRUE	0	0.376103251118819	3		394	580	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249960	110249960	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004867-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	116	213	0	ENST00000374672.4:c.715G>T	p.Gly239Cys	p.G239C	ENST00000374672	NM_004235.4	239	Ggc/Tgc	3/5	0.376103251118819	3	FACETS	1	0.97	1	0.763	0.697	0.831	CLONAL	2	TRUE	0	0.376103251118819	3		213	320	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691003	NA	P-0004873-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	102	467	0	ENST00000269305.4:c.96+1G>T		p.X32_splice	ENST00000269305	NM_001126112.2	32			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.226497645083616	2		467	647	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0004873-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	89	679	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.163881536410331	2	FACETS	1	0.965	1	0.61	0.541	0.684	CLONAL	1	TRUE	0	0.226497645083616	2		679	644	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142949972	142949972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004873-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	71	476	0	ENST00000262992.4:c.2738G>A	p.Arg913Lys	p.R913K	ENST00000262992	NM_001101669.1	913	aGa/aAa	24/24	0.172207359146917	1	FACETS	0.673	0.586	0.767	0.673	0.586	0.767	SUBCLONAL	1	TRUE	0	0.226497645083616	1		476	826	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294022	1294022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004873-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	74	658	0	ENST00000310581.5:c.979G>A	p.Glu327Lys	p.E327K	ENST00000310581	NM_198253.2	327	Gag/Aag	2/16	NA	2	FACETS	0.922	0.806	1			1	INDETERMINATE	1	TRUE	NA	0.226497645083616	2		658	709	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187456	32187456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004873-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	38	545	0	ENST00000375023.3:c.1423G>A	p.Asp475Asn	p.D475N	ENST00000375023	NM_004557.3	475	Gat/Aat	8/30	1	2	FACETS	0.48	0.396	0.575	0.48	0.396	0.575	SUBCLONAL	1	TRUE	1	0.226497645083616	2		545	699	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406731	70406731	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004873-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	85	326	0	ENST00000373644.4:c.4245A>T	p.Lys1415Asn	p.K1415N	ENST00000373644	NM_030625.2	1415	aaA/aaT	4/12	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.226497645083616	2		326	651	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512345	38512345	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004873-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	69	362	0	ENST00000254066.5:c.1256G>T	p.Gly419Val	p.G419V	ENST00000254066	NM_000964.3	419	gGc/gTc	9/9	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.226497645083616	2		362	487	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561034	9561034	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004873-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	29	400	1	ENST00000353224.5:c.748C>A	p.Leu250Met	p.L250M	ENST00000353224	NM_177990.2	250	Ctg/Atg	4/10	1	2	FACETS	0.485	0.388	0.595	0.485	0.388	0.595	SUBCLONAL	1	TRUE	1	0.226497645083616	2		401	528	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790177	40790177	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004873-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	46	182	0	ENST00000373198.4:c.2554G>T	p.Gly852Cys	p.G852C	ENST00000373198	NM_133170.3	852	Ggc/Tgc	18/32	0.226497645083616	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.226497645083616	1		182	242	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220469	1220469	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004873-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	73	531	0	ENST00000326873.7:c.563del	p.Gly188AlafsTer99	p.G188Afs*99	ENST00000326873	NM_000455.4	188	Ggc/gc	4/10	0.226497645083616	1	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	0	0.226497645083616	1		531	550	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865006	57865006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	99	690	0	ENST00000228682.2:c.2483G>A	p.Gly828Glu	p.G828E	ENST00000228682	NM_005269.2	828	gGa/gAa	12/12	0.284724094941907	4	FACETS	0.917	0.818	1	0.459	0.409	0.512	CLONAL	1	TRUE	2	0.314613814412832	4		690	902	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0004890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	283	283	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.631898246891609	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.631898246891609	3		283	553	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176132099	176132099	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	114	301	0	ENST00000367669.3:c.668A>C	p.Gln223Pro	p.Q223P	ENST00000367669	NM_022457.5	223	cAa/cCa	5/20	0.631898246891609	4	FACETS	0.891	0.803	0.983	0.297	0.267	0.328	CLONAL	1	TRUE	1	0.631898246891609	4		301	661	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722925	49722925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	41	252	0	ENST00000449682.2:c.1402C>T	p.Pro468Ser	p.P468S	ENST00000449682	NM_020998.3	468	Cca/Tca	12/18	NA	2	FACETS	0.837	0.709	0.974			1	INDETERMINATE	1	TRUE	NA	0.631898246891609	2		252	155	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480412	89480412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780417089	NA	P-0004890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	138	301	1	ENST00000336596.2:c.2249G>A	p.Arg750Gln	p.R750Q	ENST00000336596	NM_005233.5	750	cGg/cAg	13/17	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.631898246891609	2		302	409	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120339	94120339	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	380	388	1	ENST00000369303.4:c.712G>A	p.Ala238Thr	p.A238T	ENST00000369303	NM_004440.3	238	Gca/Aca	3/17	0.631898246891609	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.631898246891609	3		389	751	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955489	90955489	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	220	231	2	ENST00000265433.3:c.2176G>T	p.Glu726Ter	p.E726*	ENST00000265433	NM_002485.4	726	Gaa/Taa	14/16	0.605901126435067	2	FACETS	0.923	0.875	0.971	0.923	0.875	0.971	CLONAL	2	TRUE	0	0.631898246891609	2		233	377	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486269	8486269	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	93	262	0	ENST00000356435.5:c.2548T>C	p.Phe850Leu	p.F850L	ENST00000356435		850	Ttt/Ctt	17/35	0.631898246891609	3	FACETS	0.837	0.747	0.931	0.418	0.373	0.466	CLONAL	1	TRUE	1	0.631898246891609	3		262	463	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966598	36966598	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	245	423	0	ENST00000358127.4:c.728G>T	p.Arg243Met	p.R243M	ENST00000358127	NM_001280556.1	243	aGg/aTg	6/10	0.631898246891609	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.631898246891609	3		423	450	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877345	28877345	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	89	207	0	ENST00000282397.4:c.3976G>C	p.Asp1326His	p.D1326H	ENST00000282397	NM_002019.4	1326	Gac/Cac	30/30	0.166359243637635	1	FACETS	0.678	0.609	0.75	0.678	0.609	0.75	INDETERMINATE	1	TRUE	0	0.631898246891609	1		207	284	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437727	110437727	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	136	364	0	ENST00000375856.3:c.674C>A	p.Thr225Asn	p.T225N	ENST00000375856	NM_003749.2	225	aCc/aAc	1/2	0.125578043046742	4	FACETS	0.819	0.751	0.888	0.819	0.751	0.888	INDETERMINATE	2	TRUE	2	0.631898246891609	4		364	429	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3113332	3113332	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs751665166	NA	P-0004890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	234	510	0	ENST00000078429.4:c.326A>G	p.Asn109Ser	p.N109S	ENST00000078429	NM_002067.2	109	aAt/aGt	3/7	0.631898246891609	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.631898246891609	2		510	359	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207091	1207091	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	271	496	0	ENST00000326873.7:c.179del	p.Tyr60SerfsTer4	p.Y60Sfs*4	ENST00000326873	NM_000455.4	60	tAc/tc	1/10	0.631898246891609	2	FACETS	0.988	0.944	1	0.988	0.944	1	CLONAL	2	TRUE	0	0.631898246891609	2		496	434	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	183	467	1	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.420017441815935	2		468	756	SUCCESS
AR	367	MSKCC	GRCh37	X	66943552	66943552	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137852578	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	197	416	0	ENST00000374690.3:c.2632A>G	p.Thr878Ala	p.T878A	ENST00000374690	NM_000044.3	878	Act/Gct	8/8	1	1	FACETS	0.807	0.756	0.859	1	0.993	1	CLONAL	2	TRUE	0	0.420017441815935	1		416	459	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	106	747	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.420017441815935	1	FACETS	0.947	0.855	1	0.947	0.855	1	CLONAL	1	TRUE	0	0.420017441815935	1		747	421	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	95	592	6	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	0.393031619722361	1	FACETS	0.596	0.531	0.664	0.596	0.531	0.664	SUBCLONAL	1	TRUE	0	0.420017441815935	1		598	600	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	76	369	0	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.420017441815935	2		369	352	SUCCESS
AR	367	MSKCC	GRCh37	X	66943543	66943543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852581	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	186	400	0	ENST00000374690.3:c.2623C>T	p.His875Tyr	p.H875Y	ENST00000374690	NM_000044.3	875	Cat/Tat	8/8	1	1	FACETS	0.804	0.752	0.858	1	0.992	1	CLONAL	2	TRUE	0	0.420017441815935	1		400	435	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	100	263	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.420017441815935	2		263	475	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	133	570	5	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	1	2	FACETS	0.962	0.876	1	0.962	0.876	1	CLONAL	1	TRUE	1	0.420017441815935	2		575	658	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	119	546	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	0.897	0.811	0.986	0.897	0.811	0.986	CLONAL	1	TRUE	1	0.420017441815935	2		546	632	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664761	138664761	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs797044528	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	33	99	0	ENST00000330315.3:c.804del	p.Gly269AlafsTer2	p.G269Afs*2	ENST00000330315	NM_023067.3	268	ccC/cc	1/1	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.420017441815935	2		99	146	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269074	142269074	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	115	578	0	ENST00000350721.4:c.2876T>C	p.Val959Ala	p.V959A	ENST00000350721	NM_001184.3	959	gTg/gCg	14/47	1	2	FACETS	0.973	0.879	1	0.973	0.879	1	CLONAL	1	TRUE	1	0.420017441815935	2		578	563	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187560916	187560916	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	126	542	0	ENST00000441802.2:c.3602G>T	p.Arg1201Met	p.R1201M	ENST00000441802	NM_005245.3	1201	aGg/aTg	4/27	1	2	FACETS	0.916	0.831	1	0.916	0.831	1	CLONAL	1	TRUE	1	0.420017441815935	2		542	655	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652015	36652015	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1309823433	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	139	448	2	ENST00000244741.5:c.137G>A	p.Arg46His	p.R46H	ENST00000244741	NM_000389.4	46	cGt/cAt	2/3	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.420017441815935	2		450	597	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864309	117864309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301282588	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	132	680	1	ENST00000297338.2:c.1348C>T	p.Arg450Cys	p.R450C	ENST00000297338	NM_006265.2	450	Cgc/Tgc	11/14	1	2	FACETS	0.903	0.821	0.989	0.903	0.821	0.989	CLONAL	1	TRUE	1	0.420017441815935	2		681	696	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366990	118366990	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	143	633	1	ENST00000534358.1:c.5572C>T	p.Arg1858Ter	p.R1858*	ENST00000534358	NM_005933.3	1858	Cga/Tga	20/36	1	2	FACETS	0.955	0.872	1	0.955	0.872	1	CLONAL	1	TRUE	1	0.420017441815935	2		634	713	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117431	115117431	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	142	524	0	ENST00000257566.3:c.743A>G	p.Tyr248Cys	p.Y248C	ENST00000257566	NM_016569.3	248	tAc/tGc	4/8	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.420017441815935	2		524	665	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819655	81819655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	236	920	3	ENST00000359376.3:c.61G>A	p.Ala21Thr	p.A21T	ENST00000359376	NM_002661.3	21	Gcc/Acc	2/33	1	2	FACETS	0.875	0.815	0.937	0.875	0.815	0.937	CLONAL	1	TRUE	1	0.420017441815935	2		923	1284	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245891	5245891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1045893958	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	164	760	1	ENST00000357368.4:c.884G>A	p.Arg295Gln	p.R295Q	ENST00000357368	NM_002850.3	295	cGg/cAg	10/38	1	2	FACETS	0.91	0.836	0.987	0.91	0.836	0.987	CLONAL	1	TRUE	1	0.420017441815935	2		761	858	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118365074	118365075	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	106	501	0	ENST00000534358.1:c.5256dup	p.Ala1753SerfsTer32	p.A1753Sfs*32	ENST00000534358	NM_005933.3	1750	-/A	17/36	1	2	FACETS	0.784	0.704	0.868	0.784	0.704	0.868	SUBCLONAL	1	TRUE	1	0.420017441815935	2		501	644	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444437	50444437	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	74	278	0	ENST00000331340.3:c.369del	p.Ile124SerfsTer69	p.I124Sfs*69	ENST00000331340	NM_006060.4	123	Ggg/gg	4/8	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.420017441815935	2		278	335	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042482	37042482	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587778998	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	139	711	0	ENST00000231790.2:c.244A>G	p.Thr82Ala	p.T82A	ENST00000231790	NM_000249.3	82	Act/Gct	3/19	1	2	FACETS	0.862	0.785	0.942	0.862	0.785	0.942	CLONAL	1	TRUE	1	0.420017441815935	2		711	768	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161434	55161434	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	152	621	0	ENST00000257290.5:c.3265C>A	p.Leu1089Met	p.L1089M	ENST00000257290	NM_006206.4	1089	Ctg/Atg	23/23	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.420017441815935	2		621	724	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94224039	94224039	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	135	513	0	ENST00000323929.3:c.113T>C	p.Val38Ala	p.V38A	ENST00000323929	NM_005591.3	38	gTa/gCa	3/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.420017441815935	2		513	583	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582064	95582064	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	138	637	0	ENST00000393063.1:c.1847T>C	p.Leu616Ser	p.L616S	ENST00000393063	NM_030621.3	616	tTg/tCg	12/28	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.420017441815935	2		637	584	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260198	19260198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	146	609	1	ENST00000162023.5:c.95C>T	p.Ala32Val	p.A32V	ENST00000162023		32	gCc/gTc	7/13	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.420017441815935	2		610	695	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884218	37884218	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	126	481	1	ENST00000269571.5:c.3694del	p.Ala1232LeufsTer70	p.A1232Lfs*70	ENST00000269571		1230	cGg/cg	27/27	1	2	FACETS	0.913	0.829	1	0.913	0.829	1	CLONAL	1	TRUE	1	0.420017441815935	2		482	657	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181991	32181991	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1210569066	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	54	615	0	ENST00000375023.3:c.2063G>A	p.Cys688Tyr	p.C688Y	ENST00000375023	NM_004557.3	688	tGt/tAt	13/30	1	2	FACETS	0.32	0.272	0.372	0.32	0.272	0.372	SUBCLONAL	1	TRUE	1	0.420017441815935	2		615	804	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004812	150004812	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	123	386	0	ENST00000253339.5:c.1413T>A	p.Asn471Lys	p.N471K	ENST00000253339		471	aaT/aaA	3/7	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.420017441815935	2		386	546	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92404119	92404119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761377867	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	95	403	0	ENST00000265734.4:c.260G>A	p.Arg87Gln	p.R87Q	ENST00000265734	NM_001259.6	87	cGa/cAa	3/8	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.420017441815935	2		403	429	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190781	108190781	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	69	380	1	ENST00000278616.4:c.6448G>A	p.Ala2150Thr	p.A2150T	ENST00000278616	NM_000051.3	2150	Gcc/Acc	44/63	1	2	FACETS	0.762	0.666	0.865	0.762	0.666	0.865	SUBCLONAL	1	TRUE	1	0.420017441815935	2		381	431	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487655	56487655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	79	565	1	ENST00000267101.3:c.1588G>A	p.Val530Met	p.V530M	ENST00000267101	NM_001982.3	530	Gtg/Atg	13/28	1	2	FACETS	0.498	0.437	0.563	0.498	0.437	0.563	SUBCLONAL	1	TRUE	1	0.420017441815935	2		566	756	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112268	115112268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	38	124	0	ENST00000257566.3:c.1472C>T	p.Ala491Val	p.A491V	ENST00000257566	NM_016569.3	491	gCg/gTg	7/8	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.420017441815935	2		124	157	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256186	133256186	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs774952016	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	63	612	0	ENST00000320574.5:c.475A>G	p.Thr159Ala	p.T159A	ENST00000320574	NM_006231.2	159	Act/Gct	6/49	1	2	FACETS	0.436	0.376	0.501	0.436	0.376	0.501	SUBCLONAL	1	TRUE	1	0.420017441815935	2		612	688	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39595484	39595484	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs865812043	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	112	619	0	ENST00000262039.4:c.1370C>A	p.Pro457His	p.P457H	ENST00000262039	NM_002647.2	457	cCt/cAt	12/25	1	2	FACETS	0.883	0.796	0.974	0.883	0.796	0.974	CLONAL	1	TRUE	1	0.420017441815935	2		619	604	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223706	53223706	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782419957	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	96	404	0	ENST00000375401.3:c.3653G>A	p.Arg1218His	p.R1218H	ENST00000375401	NM_004187.3	1218	cGc/cAc	23/26	1	1	FACETS	0.812	0.727	0.901	0.812	0.727	0.901	CLONAL	1	TRUE	0	0.420017441815935	1		404	445	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961913	15961914	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	AC	AC	TA	novel	NA	P-0004910-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	71	297	0	ENST00000268712.3:c.5882-1_5882delinsTA		p.X1961_splice	ENST00000268712	NM_006311.3	1961		38/46	1	2	FACETS	0.856	0.751	0.968	0.856	0.751	0.968	CLONAL	1	TRUE	1	0.420017441815935	2		297	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0004911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	409	290	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.32661408237094	5	FACETS	1	0.978	1			1	CLONAL	5	TRUE	NA	0.411749407639045	5		290	631	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564364	86564365	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	131	472	2	ENST00000274376.6:c.97dup	p.Val33GlyfsTer79	p.V33Gfs*79	ENST00000274376	NM_002890.2	32	-/G	1/25	0.342749639977734	3	FACETS	0.971	0.89	1	0.648	0.593	0.703	CLONAL	2	TRUE	0	0.411749407639045	3		474	395	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0004918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	77	585	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.192877155121791	4	FACETS	0.974	0.871	1	1	0.979	1	INDETERMINATE	3	FALSE	2	0.337166470078148	4		585	209	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100304	8100304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	139	290	0	ENST00000346208.3:c.278C>T	p.Ser93Phe	p.S93F	ENST00000346208		93	tCc/tTc	3/6	1	2	FACETS	0.889	0.823	0.956	1	0.993	1	CLONAL	3	FALSE	1	0.337166470078148	2		290	309	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725275	49725279	+	frameshift_variant	Frame_Shift_Del	DEL	GTGCT	GTGCT	-	rs756341442	NA	P-0004918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	13	144	15	ENST00000449682.2:c.146_150del	p.Gln49ProfsTer18	p.Q49Pfs*18	ENST00000449682	NM_020998.3	49	cAGCAC/c	2/18	0.337166470078148	0	FACETS	0.799	0.583	1			1	CLONAL	1	FALSE	0	0.337166470078148	0		159	64	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17359566	17359566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	24	303	0	ENST00000375499.3:c.275C>T	p.Ser92Leu	p.S92L	ENST00000375499	NM_003000.2	92	tCa/tTa	3/8	1	2	FACETS	0.924	0.732	1	0.924	0.732	1	CLONAL	1	FALSE	1	0.337166470078148	2		303	154	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117443	115117444	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	AGTTCATATAT	novel	NA	P-0004918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	109	234	0	ENST00000257566.3:c.730_731insATATATGAACT	p.Ser244TyrfsTer3	p.S244Yfs*3	ENST00000257566	NM_016569.3	244	tcc/tATATATGAACTcc	4/8	0.129367188012781	4	FACETS	1	0.962	1	1	0.962	1	INDETERMINATE	2	FALSE	2	0.337166470078148	4		234	386	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579348	7579350	+	missense_variant	Missense_Mutation	TNP	GAA	GAA	AGG	novel	NA	P-0004918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	18	294	0	ENST00000269305.4:c.337_339delinsCCT	p.Phe113Pro	p.F113P	ENST00000269305	NM_001126112.2	113	TTC/CCT	4/11	0.309980821240232	1	FACETS	0.558	0.423	0.716	0.558	0.423	0.716	SUBCLONAL	1	FALSE	0	0.337166470078148	1		294	159	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0004928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	28	300	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.398817051676304	3	FACETS	0.396	0.317	0.486	0.198	0.158	0.243	SUBCLONAL	1	TRUE	1	0.614121950086883	3		300	301	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	241	510	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.226349495799685	2	FACETS	0.765	0.722	0.808	0.765	0.722	0.808	INDETERMINATE	2	TRUE	0	0.614121950086883	2		510	513	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0004928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	16	324	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.398817051676304	3	FACETS	0.251	0.185	0.33	0.126	0.092	0.165	SUBCLONAL	1	TRUE	1	0.614121950086883	3		324	271	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161807896	161807896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761213043	NA	P-0004928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	100	391	0	ENST00000366898.1:c.1097G>A	p.Arg366Gln	p.R366Q	ENST00000366898	NM_004562.2	366	cGg/cAg	10/12	NA	2	FACETS	0.738	0.663	0.817			1	INDETERMINATE	1	TRUE	NA	0.614121950086883	2		391	441	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925334	114925334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	528	587	3	ENST00000543371.1:c.1412G>A	p.Arg471His	p.R471H	ENST00000543371	NM_001198531.1	471	cGc/cAc	14/14	0.614121950086883	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.614121950086883	3		590	1074	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790422	3790422	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	261	390	1	ENST00000262367.5:c.4111G>T	p.Val1371Phe	p.V1371F	ENST00000262367	NM_004380.2	1371	Gtc/Ttc	24/31	0.325753855715066	3	FACETS	1	0.951	1			1	INDETERMINATE	2	TRUE	NA	0.614121950086883	3		391	553	SUCCESS
APC	324	MSKCC	GRCh37	5	112175481	112175481	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	271	289	0	ENST00000257430.4:c.4190del	p.Glu1397GlyfsTer18	p.E1397Gfs*18	ENST00000257430	NM_000038.5	1397	gAg/gg	16/16	0.614121950086883	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.614121950086883	2		289	416	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099888	27099889	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	107	348	0	ENST00000324856.7:c.3770dup	p.Asp1258Ter	p.D1258*	ENST00000324856	NM_006015.4	1256	atg/atGg	15/20	1	2	FACETS	0.679	0.612	0.75	0.679	0.612	0.75	SUBCLONAL	1	TRUE	1	0.614121950086883	2		348	513	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0004929-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	91	338	1	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	0.44118947695885	2		339	409	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453146	140453146	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913369	NA	P-0004929-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	70	443	0	ENST00000288602.6:c.1789C>G	p.Leu597Val	p.L597V	ENST00000288602	NM_004333.4	597	Cta/Gta	15/18	1	2	FACETS	0.77	0.674	0.873	0.77	0.674	0.873	SUBCLONAL	1	TRUE	1	0.44118947695885	2		443	412	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339931	70339931	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004929-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	137	850	2	ENST00000374080.3:c.464G>C	p.Arg155Pro	p.R155P	ENST00000374080		155	cGg/cCg	4/45	0.44118947695885	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.44118947695885	1		852	428	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578376	7578379	+	frameshift_variant	Frame_Shift_Del	DEL	CTAT	CTAT	-	novel	NA	P-0004929-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	58	314	0	ENST00000269305.4:c.551_554del	p.Asp184AlafsTer62	p.D184Afs*62	ENST00000269305	NM_001126112.2	184	gATAGc/gc	5/11	0.44118947695885	1	FACETS	0.868	0.755	0.989	0.868	0.755	0.989	CLONAL	1	TRUE	0	0.44118947695885	1		314	236	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435795	56435795	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004929-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	50	299	0	ENST00000407977.2:c.1342G>T	p.Glu448Ter	p.E448*	ENST00000407977		448	Gaa/Taa	9/10	0.44118947695885	1	FACETS	0.701	0.6	0.81	0.701	0.6	0.81	SUBCLONAL	1	TRUE	0	0.44118947695885	1		299	252	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56852621	56852645	+	frameshift_variant	Frame_Shift_Del	DEL	GATAACATCGAGATGGCCTATGCGC	GATAACATCGAGATGGCCTATGCGC	-	novel	NA	P-0004929-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	99	780	0	ENST00000308159.5:c.536_560del	p.Asp179GlyfsTer11	p.D179Gfs*11	ENST00000308159	NM_014669.4	179	GATAACATCGAGATGGCCTATGCGCgg/gg	6/22	0.410641994435417	1	FACETS	0.644	0.577	0.715	0.644	0.577	0.715	SUBCLONAL	1	TRUE	0	0.44118947695885	1		780	543	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	155	485	1	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	1	2	FACETS	0.763	0.702	0.825	0.763	0.702	0.825	SUBCLONAL	1	TRUE	1	0.739131745126432	2		486	550	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920358	134920358	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	188	524	1	ENST00000398015.3:c.2173C>A	p.Leu725Ile	p.L725I	ENST00000398015	NM_004441.4	725	Ctc/Atc	12/16	1	2	FACETS	0.851	0.79	0.912	0.851	0.79	0.912	CLONAL	1	TRUE	1	0.739131745126432	2		525	598	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376853	118376853	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	129	412	2	ENST00000534358.1:c.10246C>T	p.Gln3416Ter	p.Q3416*	ENST00000534358	NM_005933.3	3416	Cag/Tag	27/36	0.739131745126432	1	FACETS	0.738	0.681	0.797	0.738	0.681	0.797	SUBCLONAL	1	TRUE	0	0.739131745126432	1		414	298	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856122	68856122	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	150	429	0	ENST00000261769.5:c.1930del	p.Asp644ThrfsTer9	p.D644Tfs*9	ENST00000261769	NM_004360.3	644	Gac/ac	12/16	0.739131745126432	1	FACETS	0.859	0.8	0.917	0.859	0.8	0.917	CLONAL	1	TRUE	0	0.739131745126432	1		429	298	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066710	94066710	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004949-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	67	389	0	ENST00000369303.4:c.1049A>G	p.Glu350Gly	p.E350G	ENST00000369303	NM_004440.3	350	gAa/gGa	5/17	0.55416271346843	2	FACETS	0.24	0.208	0.276	0.12	0.104	0.138	SUBCLONAL	1	TRUE	0	0.55416271346843	2		389	1006	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15365022	15365022	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004949-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	153	257	0	ENST00000263377.2:c.2099C>A	p.Ser700Tyr	p.S700Y	ENST00000263377	NM_058243.2	700	tCc/tAc	11/20	0.488571839954894	3	FACETS	1	0.947	1	0.522	0.478	0.567	CLONAL	1	TRUE	1	0.55416271346843	3		257	676	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115955	8115956	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004949-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	129	123	0	ENST00000346208.3:c.1305dup	p.Ser436LeufsTer71	p.S436Lfs*71	ENST00000346208		434	cac/caCc	6/6	0.389634816424431	5	FACETS	0.759	0.69	0.829	0.506	0.46	0.553	SUBCLONAL	2	TRUE	2	0.55416271346843	5		123	562	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0004951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	16	324	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.848	1	1	0.934	1	CLONAL	2	FALSE	1	0.137669494697165	2		324	97	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0004951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	14	454	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.773	0.559	1	0.773	0.559	1	CLONAL	1	FALSE	1	0.137669494697165	2		454	263	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853184	68853185	+	stop_gained,frameshift_variant,splice_region_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0004951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	64	137	0	ENST00000261769.5:c.1568dup	p.Tyr523Ter	p.Y523*	ENST00000261769	NM_004360.3	523	tat/tAat	11/16	0.137669494697165	0	FACETS	1	0.912	1			1	CLONAL	3	FALSE	0	0.137669494697165	0		137	254	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	65	381	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.869	0.756	0.992	0.869	0.756	0.992	CLONAL	1	TRUE	1	0.324358428227633	2		382	461	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	186	283	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.791	0.733	0.851	1	0.991	1	SUBCLONAL	2	TRUE	1	0.324358428227633	2		283	725	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429978	78429978	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	71	318	1	ENST00000370768.2:c.901del	p.Ile301TyrfsTer22	p.I301Yfs*22	ENST00000370768	NM_003902.3	301	Ata/ta	11/20	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.324358428227633	2		319	393	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913559	32913559	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359479	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	102	817	1	ENST00000380152.3:c.5073del	p.Lys1691AsnfsTer15	p.K1691Nfs*15	ENST00000380152		1689	gcA/gc	11/27	1	2	FACETS	0.829	0.741	0.922	0.829	0.741	0.922	CLONAL	1	TRUE	1	0.324358428227633	2		818	759	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	150	176	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.317292901101353	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	3	TRUE	0	0.324358428227633	3		176	345	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	86	394	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.324358428227633	2		394	517	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649922	88649922	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786201038	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	103	334	1	ENST00000372037.3:c.176del	p.Leu59Ter	p.L59*	ENST00000372037	NM_004329.2	57	ccT/cc	4/13	0.317292901101353	3	FACETS	0.971	0.877	1	0.647	0.584	0.713	CLONAL	2	TRUE	0	0.324358428227633	3		335	380	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	161	479	9	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.977	0.895	1	0.977	0.895	1	CLONAL	1	TRUE	1	0.324358428227633	2		488	1016	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347983	347983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760961378	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	169	474	3	ENST00000262320.3:c.1523del	p.Gly508ValfsTer197	p.G508Vfs*197	ENST00000262320	NM_003502.3	508	gGt/gt	6/11	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.324358428227633	2		477	1036	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1247	240	668	11	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.317292901101353	3	FACETS	1	0.982	1	0.386	0.359	0.413	CLONAL	1	TRUE	0	0.324358428227633	3		679	1487	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533939	63533940	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs771001164	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	67	249	0	ENST00000307078.5:c.1214_1215del	p.Glu405GlyfsTer56	p.E405Gfs*56	ENST00000307078	NM_004655.3	405	gAG/g	6/11	1	2	FACETS	0.904	0.788	1	0.904	0.788	1	CLONAL	1	TRUE	1	0.324358428227633	2		249	457	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226589917	226589917	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	75	277	0	ENST00000366794.5:c.284C>T	p.Thr95Ile	p.T95I	ENST00000366794	NM_001618.3	95	aCa/aTa	2/23	1	2	FACETS	0.942	0.828	1	0.942	0.828	1	CLONAL	1	TRUE	1	0.324358428227633	2		277	491	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928424	69928424	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	103	405	0	ENST00000352241.4:c.244G>A	p.Ala82Thr	p.A82T	ENST00000352241	NM_198159.2	82	Gcg/Acg	2/10	1	2	FACETS	0.727	0.65	0.81	0.727	0.65	0.81	SUBCLONAL	1	TRUE	1	0.324358428227633	2		405	873	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518911	187518911	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	94	565	0	ENST00000441802.2:c.12293G>T	p.Cys4098Phe	p.C4098F	ENST00000441802	NM_005245.3	4098	tGt/tTt	24/27	1	2	FACETS	0.889	0.792	0.992	0.889	0.792	0.992	CLONAL	1	TRUE	1	0.324358428227633	2		565	652	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032090	26032090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1329616402	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1566	301	1012	2	ENST00000244661.2:c.199C>T	p.Pro67Ser	p.P67S	ENST00000244661	NM_003537.3	67	Ccg/Tcg	1/1	1	2	FACETS	0.994	0.933	1	0.994	0.933	1	CLONAL	1	TRUE	1	0.324358428227633	2		1014	1867	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220339	98220339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772406487	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	95	503	0	ENST00000331920.6:c.3124G>A	p.Val1042Met	p.V1042M	ENST00000331920	NM_000264.3	1042	Gtg/Atg	18/24	1	2	FACETS	0.61	0.542	0.683	0.61	0.542	0.683	SUBCLONAL	1	TRUE	1	0.324358428227633	2		503	960	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203770	94203770	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	67	391	0	ENST00000323929.3:c.884A>G	p.Asn295Ser	p.N295S	ENST00000323929	NM_005591.3	295	aAt/aGt	9/20	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.324358428227633	2		391	369	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359330	118359330	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	56	297	2	ENST00000534358.1:c.4334T>C	p.Phe1445Ser	p.F1445S	ENST00000534358	NM_005933.3	1445	tTt/tCt	11/36	1	2	FACETS	0.796	0.683	0.918	0.796	0.683	0.918	CLONAL	1	TRUE	1	0.324358428227633	2		299	434	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487640	56487640	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs543942622	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	112	496	3	ENST00000267101.3:c.1573C>T	p.Arg525Ter	p.R525*	ENST00000267101	NM_001982.3	525	Cga/Tga	13/28	1	2	FACETS	0.731	0.656	0.81	0.731	0.656	0.81	SUBCLONAL	1	TRUE	1	0.324358428227633	2		499	945	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495415	56495415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373454755	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	152	652	0	ENST00000267101.3:c.3605G>A	p.Arg1202Gln	p.R1202Q	ENST00000267101	NM_001982.3	1202	cGg/cAg	28/28	1	2	FACETS	0.97	0.887	1	0.97	0.887	1	CLONAL	1	TRUE	1	0.324358428227633	2		652	966	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052624	42052624	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	144	831	0	ENST00000219905.7:c.7295A>C	p.Glu2432Ala	p.E2432A	ENST00000219905	NM_001164273.1	2432	gAg/gCg	20/24	1	2	FACETS	0.948	0.864	1	0.948	0.864	1	CLONAL	1	TRUE	1	0.324358428227633	2		831	937	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354482	91354482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768010078	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	66	459	1	ENST00000355112.3:c.3922G>A	p.Gly1308Arg	p.G1308R	ENST00000355112	NM_000057.2	1308	Gga/Aga	21/22	1	2	FACETS	0.985	0.859	1	0.985	0.859	1	CLONAL	1	TRUE	1	0.324358428227633	2		460	413	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781302	3781302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781364836	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	190	589	0	ENST00000262367.5:c.5063C>T	p.Thr1688Met	p.T1688M	ENST00000262367	NM_004380.2	1688	aCg/aTg	30/31	1	2	FACETS	0.881	0.812	0.953	0.881	0.812	0.953	CLONAL	1	TRUE	1	0.324358428227633	2		589	1330	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108611	8108611	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	190	483	1	ENST00000585124.1:c.784C>T	p.Leu262Phe	p.L262F	ENST00000585124	NM_004217.3	262	Ctt/Ttt	8/9	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.324358428227633	2		484	1055	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492937	56492937	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	24	113	0	ENST00000407977.2:c.2T>C	p.Met1?	p.M1?	ENST00000407977		1	aTg/aCg	2/10	1	2	FACETS	0.711	0.561	0.883	0.711	0.561	0.883	SUBCLONAL	1	TRUE	1	0.324358428227633	2		113	208	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11102000	11102000	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	131	348	1	ENST00000358026.2:c.1419+1G>A		p.X473_splice	ENST00000358026	NM_001128849.1	473			1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.324358428227633	2		349	743	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145645	11145645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	191	480	0	ENST00000358026.2:c.4007G>A	p.Arg1336His	p.R1336H	ENST00000358026	NM_001128849.1	1336	cGc/cAc	29/36	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.324358428227633	2		480	1065	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866321	42866321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766047137	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	112	335	0	ENST00000398585.3:c.311C>T	p.Thr104Met	p.T104M	ENST00000398585	NM_001135099.1	104	aCg/aTg	3/14	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.324358428227633	2		335	656	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513598	41513598	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	105	567	1	ENST00000263253.7:c.502G>T	p.Gly168Trp	p.G168W	ENST00000263253	NM_001429.3	168	Ggg/Tgg	2/31	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.324358428227633	2		568	631	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041044	29041047	+	frameshift_variant	Frame_Shift_Del	DEL	AATA	AATA	-	novel	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	37	313	0	ENST00000282397.4:c.381_384del	p.Phe127LeufsTer9	p.F127Lfs*9	ENST00000282397	NM_002019.4	127	ttTATT/tt	3/30	1	2	FACETS	0.877	0.728	1	0.877	0.728	1	CLONAL	1	TRUE	1	0.324358428227633	2		313	260	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851848	134851848	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	132	477	0	ENST00000398015.3:c.1259del	p.Pro420HisfsTer28	p.P420Hfs*28	ENST00000398015	NM_004441.4	418	ttC/tt	5/16	1	2	FACETS	0.946	0.859	1	0.946	0.859	1	CLONAL	1	TRUE	1	0.324358428227633	2		477	860	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259454	11259454	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	39	433	0	ENST00000361445.4:c.4114del	p.Leu1372CysfsTer3	p.L1372Cfs*3	ENST00000361445	NM_004958.3	1372	Ctg/tg	28/58	1	2	FACETS	0.567	0.47	0.675	0.567	0.47	0.675	SUBCLONAL	1	TRUE	1	0.324358428227633	2		433	424	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268793	98268793	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1554708751	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	203	529	1	ENST00000331920.6:c.290del	p.Asn97ThrfsTer20	p.N97Tfs*20	ENST00000331920	NM_000264.3	97	aAc/ac	2/24	1	2	FACETS	0.993	0.919	1	0.993	0.919	1	CLONAL	1	TRUE	1	0.324358428227633	2		530	1260	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100405	157100406	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGT	novel	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	31	101	0	ENST00000346085.5:c.1344_1345insTCG	p.Pro448_Pro449insSer	p.P448_P449insS	ENST00000346085	NM_020732.3	448	ccg/cCGTcg	1/20	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.324358428227633	2		101	182	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831391	72831392	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGC	novel	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	103	557	0	ENST00000268489.5:c.5187_5189dup	p.Gln1741dup	p.Q1741dup	ENST00000268489	NM_006885.3	1741	caa/caGCAa	9/10	1	2	FACETS	0.708	0.633	0.788	0.708	0.633	0.788	SUBCLONAL	1	TRUE	1	0.324358428227633	2		557	897	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132494	11132494	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	177	500	0	ENST00000358026.2:c.2713del	p.Arg905AlafsTer5	p.R905Afs*5	ENST00000358026	NM_001128849.1	904	Ccc/cc	19/36	1	2	FACETS	0.983	0.905	1	0.983	0.905	1	CLONAL	1	TRUE	1	0.324358428227633	2		500	1110	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132896	64132896	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	199	621	3	ENST00000334205.4:c.1034del	p.Pro345LeufsTer30	p.P345Lfs*30	ENST00000334205	NM_003942.2	344	Ccc/cc	9/17	1	2	FACETS	0.914	0.844	0.986	0.914	0.844	0.986	CLONAL	1	TRUE	1	0.324358428227633	2		624	1343	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456497	32456497	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	23	54	0	ENST00000332351.3:c.395del	p.Pro132ArgfsTer26	p.P132Rfs*26	ENST00000332351	NM_024426.4	132	cCg/cg	1/10	1	2	FACETS	0.971	0.766	1	0.971	0.766	1	CLONAL	1	TRUE	1	0.324358428227633	2		54	146	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671478	30671478	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	166	552	0	ENST00000376406.3:c.5482del	p.Gln1828LysfsTer10	p.Q1828Kfs*10	ENST00000376406	NM_014641.2	1828	Caa/aa	10/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.324358428227633	2		552	935	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56857644	56857645	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1247	176	738	1	ENST00000308159.5:c.684dup	p.Gln229ThrfsTer35	p.Q229Tfs*35	ENST00000308159	NM_014669.4	227	gta/gtAa	8/22	1	2	FACETS	0.763	0.7	0.828	0.763	0.7	0.828	SUBCLONAL	1	TRUE	1	0.324358428227633	2		739	1423	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139625	202139626	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	228	509	0	ENST00000358485.4:c.790dup	p.Val264GlyfsTer13	p.V264Gfs*13	ENST00000358485	NM_001080125.1	262	-/G	6/9	0.324358428227633	2	FACETS	0.994	0.931	1	0.994	0.931	1	CLONAL	2	TRUE	0	0.324358428227633	2		509	707	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0004971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	101	331	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.989	0.888	1	0.989	0.888	1	CLONAL	1	TRUE	1	0.410264162111258	2		331	498	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0004971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13396	6469	752	1	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.410264162111258	37	FACETS	0.999	0.986	1			1	CLONAL	13	TRUE	NA	0.410264162111258	37		753	19865	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188977	32188977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760997487	NA	P-0004971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	214	690	2	ENST00000375023.3:c.577C>T	p.Arg193Cys	p.R193C	ENST00000375023	NM_004557.3	193	Cgt/Tgt	4/30	1	2	FACETS	0.928	0.862	0.997	0.928	0.862	0.997	CLONAL	1	TRUE	1	0.410264162111258	2		692	1124	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037972	49037972	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0004971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	174	472	1	ENST00000267163.4:c.2211+1G>A		p.X737_splice	ENST00000267163	NM_000321.2	737			0.410264162111258	1	FACETS	0.969	0.895	1	0.969	0.895	1	CLONAL	1	TRUE	0	0.410264162111258	1		473	696	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427498	427545	+	inframe_deletion	In_Frame_Del	DEL	ATTCAGGGAGTTCCACATAGAGACTAGAGCCCATATCTATCAACATCT	ATTCAGGGAGTTCCACATAGAGACTAGAGCCCATATCTATCAACATCT	-	novel	NA	P-0004971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	128	641	0	ENST00000399788.2:c.2624_2671del	p.Gln875_Glu890del	p.Q875_E890del	ENST00000399788	NM_001042603.1	875	cAGATGTTGATAGATATGGGCTCTAGTCTCTATGTGGAACTCCCTGAATta/cta	19/28	NA	2	FACETS	0.62	0.561	0.683			1	INDETERMINATE	1	TRUE	NA	0.410264162111258	2		641	1006	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0004988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	42	283	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.3	3	FACETS	0.774	0.646	0.915	0.387	0.323	0.458	CLONAL	1	TRUE	1	0.28	3		283	442	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0004988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	8	324	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.251195530821685	3	FACETS	0.232	0.148	0.34	0.116	0.074	0.17	SUBCLONAL	1	TRUE	1	0.28	3		324	281	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220371	1220371	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0004988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	50	395	0	ENST00000326873.7:c.465-1G>T		p.X155_splice	ENST00000326873	NM_000455.4	155			1	2	FACETS	0.653	0.554	0.762	0.653	0.554	0.762	SUBCLONAL	1	TRUE	1	0.28	2		395	547	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374438	81374438	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0004988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	26	373	0	ENST00000222390.5:c.626-2A>T		p.X209_splice	ENST00000222390	NM_000601.4	209			0.3	3	FACETS	0.568	0.449	0.703	0.284	0.224	0.352	SUBCLONAL	1	TRUE	1	0.28	3		373	373	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851646	134851646	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757558701	NA	P-0004988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	97	448	0	ENST00000398015.3:c.1052G>A	p.Arg351Gln	p.R351Q	ENST00000398015	NM_004441.4	351	cGg/cAg	5/16	0.251195530821685	3	FACETS	1	0.978	1	0.697	0.622	0.775	CLONAL	1	TRUE	1	0.28	3		448	567	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356240	66356240	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	32	350	0	ENST00000273854.3:c.1257C>G	p.Ser419Arg	p.S419R	ENST00000273854	NM_004439.5	419	agC/agG	5/18	1	2	FACETS	0.479	0.388	0.582	0.479	0.388	0.582	SUBCLONAL	1	TRUE	1	0.28	2		350	477	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877471	28877471	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	31	281	0	ENST00000282397.4:c.3850C>A	p.Leu1284Met	p.L1284M	ENST00000282397	NM_002019.4	1284	Ctg/Atg	30/30	NA	2	FACETS	0.583	0.471	0.709			1	INDETERMINATE	1	TRUE	NA	0.28	2		281	380	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226547	2226547	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1258754185	NA	P-0004988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	46	424	0	ENST00000398665.3:c.4027G>A	p.Glu1343Lys	p.E1343K	ENST00000398665	NM_032482.2	1343	Gag/Aag	27/28	1	2	FACETS	0.56	0.471	0.658	0.56	0.471	0.658	SUBCLONAL	1	TRUE	1	0.28	2		424	587	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039636	47039636	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	59	500	0	ENST00000377604.3:c.1088T>C	p.Leu363Pro	p.L363P	ENST00000377604	NM_001204468.1	363	cTg/cCg	11/24	1	2	FACETS	0.679	0.583	0.782	0.679	0.583	0.782	SUBCLONAL	1	TRUE	1	0.28	2		500	621	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508499	106508499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752602335	NA	P-0005002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	50	80	0	ENST00000359195.3:c.493G>A	p.Val165Ile	p.V165I	ENST00000359195	NM_002649.2	165	Gtc/Atc	2/11	0.348142039952852	1	FACETS	0.495	0.426	0.569	0.495	0.426	0.569	INDETERMINATE	1	TRUE	0	0.682092641380688	1		80	195	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560231	29560231	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	73	145	0	ENST00000356175.3:c.3708G>A	p.Trp1236Ter	p.W1236*	ENST00000356175	NM_000267.3	1236	tgG/tgA	27/57	0.167758103177268	3	FACETS	0.935	0.825	1	0.312	0.275	0.351	INDETERMINATE	1	TRUE	0	0.682092641380688	3		145	307	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435856	149435856	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	192	286	0	ENST00000286301.3:c.2368C>T	p.His790Tyr	p.H790Y	ENST00000286301	NM_005211.3	790	Cat/Tat	18/22	0.348142039952852	1	FACETS	0.793	0.741	0.845	0.793	0.741	0.845	INDETERMINATE	1	TRUE	0	0.682092641380688	1		286	468	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509334	106509334	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	94	285	0	ENST00000359195.3:c.1328G>C	p.Ser443Thr	p.S443T	ENST00000359195	NM_002649.2	443	aGc/aCc	2/11	0.348142039952852	1	FACETS	0.369	0.329	0.411	0.369	0.329	0.411	INDETERMINATE	1	TRUE	0	0.682092641380688	1		285	492	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575365	64575365	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs794728620	NA	P-0005002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	112	211	0	ENST00000312049.6:c.652C>T	p.Arg218Trp	p.R218W	ENST00000312049	NM_130799.2	218	Cgg/Tgg	3/10	0.348142039952852	1	FACETS	0.492	0.445	0.541	0.492	0.445	0.541	INDETERMINATE	1	TRUE	0	0.682092641380688	1		211	440	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2224275	2224275	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0005002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	363	340	0	ENST00000326181.6:c.1287C>G	p.Tyr429Ter	p.Y429*	ENST00000326181	NM_032271.2	429	taC/taG	14/21	0.648586181486403	2	FACETS	0.947	0.911	0.982	0.947	0.911	0.982	CLONAL	2	TRUE	0	0.682092641380688	2		340	562	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246741	41246741	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	250	298	0	ENST00000357654.3:c.807G>T	p.Leu269Phe	p.L269F	ENST00000357654	NM_007294.3	269	ttG/ttT	10/23	0.281822257495293	2	FACETS	1	0.993	1	0.708	0.669	0.746	INDETERMINATE	1	TRUE	0	0.682092641380688	2		298	518	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220394	1220394	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs730881972	NA	P-0005002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	214	291	0	ENST00000326873.7:c.487G>C	p.Gly163Arg	p.G163R	ENST00000326873	NM_000455.4	163	Ggc/Cgc	4/10	0.682092641380688	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.682092641380688	1		291	397	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610363	10610363	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	275	275	1	ENST00000171111.5:c.347G>C	p.Arg116Pro	p.R116P	ENST00000171111	NM_203500.1	116	cGg/cCg	2/6	0.682092641380688	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.682092641380688	1		276	437	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031269	36031269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752182272	NA	P-0005002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	112	216	0	ENST00000358208.4:c.1388G>A	p.Arg463Gln	p.R463Q	ENST00000358208		463	cGg/cAg	11/12	0.682092641380688	2	FACETS	0.568	0.512	0.627	0.284	0.256	0.314	SUBCLONAL	1	TRUE	0	0.682092641380688	2		216	578	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478835	57478835	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	96	175	0	ENST00000371085.3:c.421G>C	p.Asp141His	p.D141H	ENST00000371085	NM_000516.4	141	Gac/Cac	5/13	0.622614637584312	1	FACETS	0.528	0.475	0.584	0.528	0.475	0.584	SUBCLONAL	1	TRUE	0	0.682092641380688	1		175	351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579330	7579331	+	missense_variant	Missense_Mutation	DNP	GG	GG	AC	novel	NA	P-0005002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	234	227	0	ENST00000269305.4:c.356_357delinsGT	p.Ala119Gly	p.A119G	ENST00000269305	NM_001126112.2	119	gCC/gGT	4/11	0.682092641380688	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.682092641380688	1		227	394	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0005009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	10	585	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.191007472217404	4	FACETS	0.285	0.192	0.404	0.143	0.096	0.202	SUBCLONAL	1	TRUE	2	0.191007472217404	4		585	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579342	7579515	+	inframe_deletion	In_Frame_Del	DEL	ATGCAAGAAGCCCAGACGGAAACCGTAGCTGCCCTGGTAGGTTTTCTGGGAAGGGACAGAAGATGACAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTGCAGGGGCCACGGGGGGAGCAGCCTCTGGCATTCTGGGAGCTTCATCTGGACCTGG	ATGCAAGAAGCCCAGACGGAAACCGTAGCTGCCCTGGTAGGTTTTCTGGGAAGGGACAGAAGATGACAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTGCAGGGGCCACGGGGGGAGCAGCCTCTGGCATTCTGGGAGCTTCATCTGGACCTGG	-	novel	NA	P-0005009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	90	333	0	ENST00000269305.4:c.172_345del	p.Pro58_His115del	p.P58_H115del	ENST00000269305	NM_001126112.2	58	CCAGGTCCAGATGAAGCTCCCAGAATGCCAGAGGCTGCTCCCCCCGTGGCCCCTGCACCAGCAGCTCCTACACCGGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTGTCATCTTCTGTCCCTTCCCAGAAAACCTACCAGGGCAGCTACGGTTTCCGTCTGGGCTTCTTGCAT/-	4/11	0.191007472217404	3	FACETS	0.928	0.826	1	0.928	0.826	1	CLONAL	2	TRUE	1	0.191007472217404	3		333	556	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907621	76907621	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	64	333	0	ENST00000373344.5:c.4540C>T	p.Arg1514Ter	p.R1514*	ENST00000373344	NM_000489.3	1514	Cga/Tga	15/35	0.219243638848199	1	FACETS	0.68	0.589	0.779	0.68	0.589	0.779	SUBCLONAL	1	TRUE	0	0.28	1		333	578	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944259	81944259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	82	356	1	ENST00000359376.3:c.1868G>A	p.Arg623His	p.R623H	ENST00000359376	NM_002661.3	623	cGc/cAc	18/33	0.3	0	FACETS	0.909	0.805	1			1	CLONAL	1	TRUE	0	0.28	0		357	464	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863588	68863603	+	frameshift_variant	Frame_Shift_Del	DEL	TGGACGCTCGGCCTGA	TGGACGCTCGGCCTGA	-	novel	NA	P-0005015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	79	262	0	ENST00000261769.5:c.2327_2342del	p.Leu776GlnfsTer2	p.L776Qfs*2	ENST00000261769	NM_004360.3	776	cTGGACGCTCGGCCTGAa/ca	15/16	0.3	1	FACETS	0.984	0.868	1	0.984	0.868	1	CLONAL	1	TRUE	0	0.28	1		262	493	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0005025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	152	378	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	0.282045281526829	0	FACETS	0.965	0.896	1			1	CLONAL	2	TRUE	0	0.308513934753982	0		378	353	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247367	153247367	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	85	288	1	ENST00000281708.4:c.1435C>T	p.Arg479Ter	p.R479*	ENST00000281708	NM_033632.3	479	Cga/Tga	10/12	0.221683100746935	4	FACETS	1	0.897	1	1	0.897	1	CLONAL	2	TRUE	2	0.308513934753982	4		289	358	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582168	189582168	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121908835	NA	P-0005025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	151	495	0	ENST00000264731.3:c.727C>T	p.Arg243Trp	p.R243W	ENST00000264731	NM_003722.4	243	Cgg/Tgg	5/14	0.246043718735002	3	FACETS	1	0.944	1	0.523	0.477	0.571	CLONAL	1	TRUE	1	0.308513934753982	3		495	1081	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0005025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	330	578	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.285145629064732	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.308513934753982	2		579	1021	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549149	21549149	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1444091389	NA	P-0005025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1524	90	623	2	ENST00000382592.4:c.3127C>T	p.Arg1043Ter	p.R1043*	ENST00000382592	NM_014572.2	1043	Cga/Tga	8/8	0.308513934753982	4	FACETS	0.473	0.418	0.533	0.158	0.139	0.178	SUBCLONAL	1	TRUE	1	0.308513934753982	4		625	1614	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250856	153250858	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0005025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	132	544	0	ENST00000281708.4:c.1202_1204del	p.Asn401del	p.N401del	ENST00000281708	NM_033632.3	401	aACAct/act	8/12	0.221683100746935	4	FACETS	0.928	0.846	1	0.928	0.846	1	CLONAL	2	TRUE	2	0.308513934753982	4		544	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0005029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	595	575	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.763719507138155	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.775698889713986	2		576	759	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0005029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	434	440	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.775698889713986	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.775698889713986	2		441	552	SUCCESS
APC	324	MSKCC	GRCh37	5	112175240	112175240	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	416	553	1	ENST00000257430.4:c.3949G>T	p.Glu1317Ter	p.E1317*	ENST00000257430	NM_000038.5	1317	Gaa/Taa	16/16	0.775698889713986	2	FACETS	0.972	0.943	0.999	0.972	0.943	0.999	CLONAL	2	TRUE	0	0.775698889713986	2		554	552	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	128	192	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.3098617604722	2		192	761	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519985	NA	P-0005032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	221	492	0	ENST00000269305.4:c.857A>T	p.Glu286Val	p.E286V	ENST00000269305	NM_001126112.2	286	gAa/gTa	8/11	0.3098617604722	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.3098617604722	1		492	1112	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525044	157525044	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	159	613	1	ENST00000346085.5:c.4939C>A	p.Leu1647Ile	p.L1647I	ENST00000346085	NM_020732.3	1647	Ctt/Att	19/20	1	2	FACETS	0.938	0.859	1	0.938	0.859	1	CLONAL	1	TRUE	1	0.3098617604722	2		614	1094	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729700	162729700	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	190	561	0	ENST00000367921.3:c.786G>C	p.Glu262Asp	p.E262D	ENST00000367921	NM_006182.2	262	gaG/gaC	8/18	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.3098617604722	2		561	1101	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984928	55984928	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	101	470	0	ENST00000263923.4:c.201G>C	p.Gln67His	p.Q67H	ENST00000263923	NM_002253.2	67	caG/caC	3/30	1	2	FACETS	0.65	0.58	0.725	0.65	0.58	0.725	SUBCLONAL	1	TRUE	1	0.3098617604722	2		470	1003	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375572	118375572	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	32	453	1	ENST00000534358.1:c.8965G>C	p.Glu2989Gln	p.E2989Q	ENST00000534358	NM_005933.3	2989	Gaa/Caa	27/36	0.3098617604722	1	FACETS	0.279	0.225	0.339	0.279	0.225	0.339	SUBCLONAL	1	TRUE	0	0.3098617604722	1		454	626	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732832	44732832	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1236	142	431	0	ENST00000377967.4:c.35C>G	p.Ala12Gly	p.A12G	ENST00000377967	NM_021140.2	12	gCc/gGc	1/29	0.117698961792334	5	FACETS	0.974	0.885	1	0.244	0.221	0.267	INDETERMINATE	1	TRUE	1	0.3098617604722	5		431	1378	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061188	38061199	+	inframe_deletion	In_Frame_Del	DEL	CTTGAAGCGCTT	CTTGAAGCGCTT	-	novel	NA	P-0005032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	126	290	0	ENST00000250448.2:c.790_801del	p.Lys264_Lys267del	p.K264_K267del	ENST00000250448	NM_004496.3	264	AAGCGCTTCAAG/-	2/2	0.3098617604722	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.3098617604722	1		290	538	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928083	178928105	+	frameshift_variant	Frame_Shift_Del	DEL	ATTTGCTGAACCCTATTGGTGTT	ATTTGCTGAACCCTATTGGTGTT	-	novel	NA	P-0005032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	62	418	0	ENST00000263967.3:c.1362_1384del	p.Leu455TrpfsTer6	p.L455Wfs*6	ENST00000263967	NM_006218.2	454	gATTTGCTGAACCCTATTGGTGTT/g	8/21	1	2	FACETS	0.62	0.535	0.713	0.62	0.535	0.713	SUBCLONAL	1	TRUE	1	0.3098617604722	2		418	645	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928076	178928077	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	C	novel	NA	P-0005032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	67	425	0	ENST00000263967.3:c.1354_1355delinsC	p.Leu452GlnfsTer5	p.L452Qfs*5	ENST00000263967	NM_006218.2	452	TTa/Ca	8/21	1	2	FACETS	0.659	0.572	0.753	0.659	0.572	0.753	SUBCLONAL	1	TRUE	1	0.3098617604722	2		425	656	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0005048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	26	324	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.505	0.399	0.625	0.505	0.399	0.625	SUBCLONAL	1	TRUE	1	0.28	2		324	368	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0005048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	97	554	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.28	2		554	671	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671739	30671739	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	191	636	1	ENST00000376406.3:c.5221C>T	p.Pro1741Ser	p.P1741S	ENST00000376406	NM_014641.2	1741	Cct/Tct	10/15	1	2	FACETS	0.95	0.876	1	0.95	0.876	1	CLONAL	1	TRUE	1	0.28	2		637	1436	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005558	42005558	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	67	862	0	ENST00000219905.7:c.3297del	p.Gln1100ArgfsTer33	p.Q1100Rfs*33	ENST00000219905	NM_001164273.1	1098	caT/ca	9/24	1	2	FACETS	0.478	0.414	0.548	0.478	0.414	0.548	SUBCLONAL	1	TRUE	1	0.28	2		862	1001	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37083821	37083821	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs56185292	NA	P-0121571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	75	725	0	ENST00000231790.2:c.1730C>T	p.Ser577Leu	p.S577L	ENST00000231790	NM_000249.3	577	tCg/tTg	15/19	0.243251938935392	2	FACETS	0.443	0.389	0.501	0.222	0.194	0.251	INDETERMINATE	1	NA	0	0.672623078268204	2		725	503	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628272	187628272	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0121571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	58	520	0	ENST00000441802.2:c.2710G>T	p.Glu904Ter	p.E904*	ENST00000441802	NM_005245.3	904	Gag/Tag	2/27	0.672623078268204	3	FACETS	0.603	0.52	0.693	0.302	0.26	0.347	SUBCLONAL	1	NA	1	0.672623078268204	3		520	382	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131930633	131930633	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1060501948	NA	P-0121571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	89	635	1	ENST00000265335.6:c.1866G>T	p.Leu622Phe	p.L622F	ENST00000265335		622	ttG/ttT	12/25	0.222583890152505	2	FACETS	0.563	0.501	0.629	0.282	0.25	0.315	INDETERMINATE	1	NA	0	0.672623078268204	2		636	470	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874137	151874137	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0121571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	76	692	0	ENST00000262189.6:c.8401A>T	p.Asn2801Tyr	p.N2801Y	ENST00000262189	NM_170606.2	2801	Aac/Tac	38/59	0.672623078268204	3	FACETS	0.624	0.549	0.704	0.312	0.274	0.352	SUBCLONAL	1	NA	1	0.672623078268204	3		692	484	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038194	30038194	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0121571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	78	860	0	ENST00000338641.4:c.367A>T	p.Lys123Ter	p.K123*	ENST00000338641	NM_000268.3	123	Aag/Tag	4/16	1	2	FACETS	0.59	0.521	0.663	0.59	0.521	0.663	SUBCLONAL	1	NA	1	0.672623078268204	2		860	393	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0005085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	95	324	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.962	0.858	1	0.962	0.858	1	CLONAL	1	TRUE	1	0.335423997705034	2		324	589	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0005085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	306	575	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.304564016875116	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.335423997705034	1		576	1473	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0005085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1383	129	379	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.304564016875116	1	FACETS	0.423	0.382	0.467	0.423	0.382	0.467	SUBCLONAL	1	TRUE	0	0.335423997705034	1		379	1512	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293661	1293661	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	174	329	0	ENST00000310581.5:c.1340G>A	p.Arg447His	p.R447H	ENST00000310581	NM_198253.2	447	cGc/cAc	2/16	NA	2	FACETS	1	0.961	1			1	INDETERMINATE	1	TRUE	NA	0.335423997705034	2		329	968	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0005085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	176	237	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	0.98	0.902	1	0.98	0.902	1	CLONAL	1	TRUE	1	0.335423997705034	2		237	1071	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288843	15288843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	96	150	0	ENST00000263388.2:c.3896C>T	p.Pro1299Leu	p.P1299L	ENST00000263388	NM_000435.2	1299	cCg/cTg	24/33	0.261945814921021	2	FACETS	0.777	0.692	0.867	0.388	0.346	0.434	SUBCLONAL	1	TRUE	0	0.335423997705034	2		150	737	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366243	15366243	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1786	127	539	1	ENST00000263377.2:c.1912C>A	p.Gln638Lys	p.Q638K	ENST00000263377	NM_058243.2	638	Cag/Aag	10/20	0.261945814921021	2	FACETS	0.396	0.357	0.438	0.198	0.178	0.219	SUBCLONAL	1	TRUE	0	0.335423997705034	2		540	1913	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794968	42794968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	107	361	0	ENST00000575354.2:c.2048C>T	p.Pro683Leu	p.P683L	ENST00000575354	NM_015125.3	683	cCt/cTt	10/20	0.304564016875116	1	FACETS	0.501	0.449	0.558	0.501	0.449	0.558	SUBCLONAL	1	TRUE	0	0.335423997705034	1		361	1059	SUCCESS
APC	324	MSKCC	GRCh37	5	112173502	112173502	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	274	509	0	ENST00000257430.4:c.2211C>A	p.Tyr737Ter	p.Y737*	ENST00000257430	NM_000038.5	737	taC/taA	16/16	0.662812291310687	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.68894366628714	1		509	497	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162475154	162475154	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	402	702	0	ENST00000366898.1:c.587G>C	p.Cys196Ser	p.C196S	ENST00000366898	NM_004562.2	196	tGc/tCc	5/12	1	2	FACETS	0.978	0.931	1	0.978	0.931	1	CLONAL	1	TRUE	1	0.68894366628714	2		702	1193	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352567	89352599	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCCGTACCGCAGCAGCAGCTTCACCACCTACA	CTCCGTACCGCAGCAGCAGCTTCACCACCTACA	-	novel	NA	P-0005091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	76	553	0	ENST00000301030.4:c.745-5_772del		p.X249_splice	ENST00000301030	NM_001256183.1	249		8/13	1	2	FACETS	0.186	0.162	0.211	0.186	0.162	0.211	SUBCLONAL	1	TRUE	1	0.68894366628714	2		553	1188	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578467	7578468	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCGGGC	novel	NA	P-0005091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	609	515	2	ENST00000269305.4:c.456_462dup	p.Thr155AlafsTer28	p.T155Afs*28	ENST00000269305	NM_001126112.2	154	-/GCCCGGC	5/11	0.68894366628714	2	FACETS	0.841	0.814	0.867	0.841	0.814	0.867	CLONAL	2	TRUE	0	0.68894366628714	2		517	1051	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910664	32910666	+	missense_variant	Missense_Mutation	TNP	AAA	AAA	TAT	novel	NA	P-0005091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2955	421	905	3	ENST00000380152.3:c.2172_2174delinsTAT	p.Lys724_Lys725delinsAsnIle	p.K724_K725delinsNI	ENST00000380152		724	aaAAAa/aaTATa	11/27	0.68894366628714	6	FACETS	0.861	0.815	0.908	0.215	0.203	0.227	CLONAL	1	TRUE	2	0.68894366628714	6		908	3376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0005098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	121	595	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	0.374078215439804	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.374078215439804	1		595	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0005106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	296	792	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.73324531554079	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.725453274320297	1		792	382	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737028	162737028	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	36	596	2	ENST00000367921.3:c.1172T>C	p.Leu391Pro	p.L391P	ENST00000367921	NM_006182.2	391	cTt/cCt	11/18	0.615564399348528	3	FACETS	0.292	0.24	0.351	0.146	0.12	0.176	SUBCLONAL	1	TRUE	1	0.725453274320297	3		598	463	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664726	138664726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765807161	NA	P-0005106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	37	82	0	ENST00000330315.3:c.839C>T	p.Pro280Leu	p.P280L	ENST00000330315	NM_023067.3	280	cCg/cTg	1/1	0.307348121157875	3	FACETS	0.781	0.667	0.898	0.781	0.667	0.898	INDETERMINATE	2	TRUE	1	0.725453274320297	3		82	89	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622039	43622039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1371891301	NA	P-0005106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	159	602	0	ENST00000355710.3:c.3056C>T	p.Ala1019Val	p.A1019V	ENST00000355710	NM_020975.4	1019	gCg/gTg	19/20	0.42480630326514	3	FACETS	0.814	0.756	0.872	0.814	0.756	0.872	INDETERMINATE	2	TRUE	1	0.725453274320297	3		602	367	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734038	58734038	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	162	890	0	ENST00000305921.3:c.1096G>A	p.Asp366Asn	p.D366N	ENST00000305921	NM_003620.3	366	Gat/Aat	5/6	0.32509856231333	5	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.725453274320297	5		890	737	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575080	48575080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	236	609	0	ENST00000342988.3:c.274C>T	p.His92Tyr	p.H92Y	ENST00000342988	NM_005359.5	92	Cat/Tat	3/12	0.73324531554079	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.725453274320297	1		609	316	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376726	31376726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867559860	NA	P-0005106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	56	682	2	ENST00000328111.2:c.721G>A	p.Ala241Thr	p.A241T	ENST00000328111	NM_006892.3	241	Gcc/Acc	7/23	0.493058659161462	3	FACETS	0.417	0.357	0.482			1	SUBCLONAL	1	TRUE	NA	0.725453274320297	3		684	505	SUCCESS
AR	367	MSKCC	GRCh37	X	66766300	66766300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	16	220	0	ENST00000374690.3:c.1312C>T	p.Leu438Phe	p.L438F	ENST00000374690	NM_000044.3	438	Ctc/Ttc	1/8	0.151663891667994	2	FACETS	0.237	0.176	0.31			1	INDETERMINATE	1	TRUE	NA	0.725453274320297	2		220	186	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	52	192	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.847	0.736	0.963	0.847	0.736	0.963	CLONAL	1	TRUE	1	0.782246561291875	2		192	157	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711973	89711975	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	rs1064793244	NA	P-0005113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	106	516	0	ENST00000371953.3:c.595_597del	p.Met199del	p.M199del	ENST00000371953	NM_000314.4	197	aaGATg/aag	6/9	0.782246561291875	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.782246561291875	1		516	145	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152373145	152373145	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	190	871	1	ENST00000359321.1:c.20G>A	p.Arg7Lys	p.R7K	ENST00000359321	NM_005431.1	7	aGg/aAg	1/3	NA	2	FACETS	0.949	0.885	1			1	INDETERMINATE	1	TRUE	NA	0.782246561291875	2		872	512	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933268	100933268	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	193	1194	0	ENST00000325455.5:c.2122C>G	p.Pro708Ala	p.P708A	ENST00000325455	NM_001202474.3	708	Cct/Gct	4/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.782246561291875	2		1194	459	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019479	31019479	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	122	518	0	ENST00000375687.4:c.976G>T	p.Asp326Tyr	p.D326Y	ENST00000375687	NM_015338.5	326	Gat/Tat	10/13	0.782246561291875	3	FACETS	1	0.917	1	0.503	0.458	0.55	CLONAL	1	TRUE	1	0.782246561291875	3		518	431	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0005116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	58	494	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	1	2	FACETS	0.512	0.439	0.593	0.512	0.439	0.593	SUBCLONAL	1	TRUE	1	0.272542327086435	2		494	831	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005263	150005263	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	53	628	0	ENST00000253339.5:c.962G>C	p.Ser321Thr	p.S321T	ENST00000253339		321	aGt/aCt	3/7	1	2	FACETS	0.479	0.407	0.558	0.479	0.407	0.558	SUBCLONAL	1	TRUE	1	0.272542327086435	2		628	812	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0005117-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	216	290	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.435278938992527	3	FACETS	0.834	0.784	0.884	1	0.989	1	CLONAL	3	TRUE	1	0.435278938992527	3		290	483	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0005117-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	130	559	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.435278938992527	2		559	508	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98244236	98244237	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0005117-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	117	453	0	ENST00000331920.6:c.739_740dup	p.Leu248ThrfsTer3	p.L248Tfs*3	ENST00000331920	NM_000264.3	247	tac/taTAc	5/24	0.435278938992527	2	FACETS	0.996	0.914	1	0.996	0.914	1	CLONAL	2	TRUE	0	0.435278938992527	2		453	270	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217650	7217651	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005117-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	155	642	1	ENST00000380728.2:c.276dup	p.Val93SerfsTer4	p.V93Sfs*4	ENST00000380728		92	-/A	4/11	NA	2	FACETS	0.962	0.893	1			1	INDETERMINATE	2	TRUE	NA	0.435278938992527	2		643	370	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612170	189612170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793283	NA	P-0005117-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	100	556	0	ENST00000264731.3:c.1922C>T	p.Ala641Val	p.A641V	ENST00000264731	NM_003722.4	641	gCt/gTt	14/14	1	2	FACETS	0.936	0.84	1	0.936	0.84	1	CLONAL	1	TRUE	1	0.435278938992527	2		556	491	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226812	2226812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs911763223	NA	P-0005117-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	65	262	0	ENST00000398665.3:c.4292C>T	p.Ala1431Val	p.A1431V	ENST00000398665	NM_032482.2	1431	gCg/gTg	27/28	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.435278938992527	2		262	237	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0005126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	531	646	4	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.623549555465186	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.623549555465186	2		650	757	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913255	NA	P-0005126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	450	287	0	ENST00000369535.4:c.183A>T	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caT	3/7	0.623549555465186	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.623549555465186	3		287	920	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243778408	243778408	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	79	286	0	ENST00000263826.5:c.617C>A	p.Pro206His	p.P206H	ENST00000263826	NM_005465.4	206	cCc/cAc	6/13	0.395430841639613	4	FACETS	0.448	0.393	0.508			1	SUBCLONAL	1	TRUE	NA	0.623549555465186	4		286	918	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721118	176721118	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	152	185	0	ENST00000439151.2:c.6749T>G	p.Met2250Arg	p.M2250R	ENST00000439151	NM_022455.4	2250	aTg/aGg	23/23	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.623549555465186	2		185	459	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351379	89351379	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	306	590	0	ENST00000301030.4:c.1571C>G	p.Ser524Trp	p.S524W	ENST00000301030	NM_001256183.1	524	tCg/tGg	9/13	NA	2	FACETS	1	0.972	1			1	INDETERMINATE	1	TRUE	NA	0.623549555465186	2		590	939	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223146	5223146	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	197	281	0	ENST00000357368.4:c.2657C>A	p.Ser886Tyr	p.S886Y	ENST00000357368	NM_002850.3	886	tCc/tAc	18/38	0.623549555465186	3	FACETS	1	0.964	1	0.53	0.492	0.57	CLONAL	1	TRUE	1	0.623549555465186	3		281	782	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950308	17950319	+	inframe_deletion	In_Frame_Del	DEL	GGAAGTGAGGGT	GGAAGTGAGGGT	-	novel	NA	P-0005149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	512	224	0	ENST00000458235.1:c.1408_1419del	p.Thr470_Ser473del	p.T470_S473del	ENST00000458235	NM_000215.3	470	ACCCTCACTTCC/-	10/24	0.819826735937415	7	FACETS	0.941	0.906	0.976	0.941	0.906	0.976	CLONAL	4	TRUE	3	0.819826735937415	7		224	1012	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577554	7577555	+	missense_variant	Missense_Mutation	DNP	TG	TG	AC	novel	NA	P-0005149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	1700	337	0	ENST00000269305.4:c.726_727delinsGT	p.Cys242_Met243delinsTrpLeu	p.C242_M243delinsWL	ENST00000269305	NM_001126112.2	242	tgCAtg/tgGTtg	7/11	0.819826735937415	8	FACETS	1	0.998	1	1	0.998	1	CLONAL	8	TRUE	0	0.819826735937415	8		337	1764	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	57	192	0				ENST00000310581	NM_198253.2	-/1132			0.309271077342585	1	FACETS	0.697	0.607	0.791	0.697	0.607	0.791	INDETERMINATE	1	TRUE	0	0.584726479430311	1		192	198	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783205	9783205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	102	185	1	ENST00000377346.4:c.2449C>T	p.Pro817Ser	p.P817S	ENST00000377346	NM_005026.3	817	Ccc/Tcc	20/24	0.327513883177281	1	FACETS	0.365	0.326	0.405	0.365	0.326	0.405	INDETERMINATE	1	TRUE	0	0.584726479430311	1		186	677	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187129	11187129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	167	368	0	ENST00000361445.4:c.6289C>T	p.Leu2097Phe	p.L2097F	ENST00000361445	NM_004958.3	2097	Ctc/Ttc	45/58	0.327513883177281	1	FACETS	0.432	0.397	0.469	0.432	0.397	0.469	INDETERMINATE	1	TRUE	0	0.584726479430311	1		368	935	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255503	16255503	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	109	253	0	ENST00000375759.3:c.2768A>G	p.Glu923Gly	p.E923G	ENST00000375759	NM_015001.2	923	gAg/gGg	11/15	0.327513883177281	1	FACETS	0.376	0.338	0.417	0.376	0.338	0.417	INDETERMINATE	1	TRUE	0	0.584726479430311	1		253	701	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023220	27023220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	29	106	0	ENST00000324856.7:c.326C>A	p.Pro109His	p.P109H	ENST00000324856	NM_006015.4	109	cCt/cAt	1/20	1	2	FACETS	0.187	0.15	0.23	0.187	0.15	0.23	SUBCLONAL	1	TRUE	1	0.584726479430311	2		106	530	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430751	78430751	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	149	223	0	ENST00000370768.2:c.636+2T>C		p.X212_splice	ENST00000370768	NM_003902.3	212			1	2	FACETS	0.612	0.559	0.667	0.612	0.559	0.667	SUBCLONAL	1	TRUE	1	0.584726479430311	2		223	833	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176145100	176145100	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	120	299	0	ENST00000367669.3:c.511C>A	p.Pro171Thr	p.P171T	ENST00000367669	NM_022457.5	171	Ccc/Acc	3/20	0.309271077342585	1	FACETS	0.273	0.246	0.302	0.273	0.246	0.302	INDETERMINATE	1	TRUE	0	0.584726479430311	1		299	1064	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47709969	47709969	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	170	386	0	ENST00000233146.2:c.2686T>A	p.Phe896Ile	p.F896I	ENST00000233146	NM_000251.2	896	Ttt/Att	16/16	0.202131185010629	2	FACETS	0.54	0.496	0.586	0.27	0.248	0.293	INDETERMINATE	1	TRUE	0	0.584726479430311	2		386	1077	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248423	212248423	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771634130	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	136	257	0	ENST00000342788.4:c.3844C>T	p.Pro1282Ser	p.P1282S	ENST00000342788	NM_005235.2	1282	Cct/Tct	28/28	0.430432468032181	1	FACETS	0.474	0.431	0.518	0.474	0.431	0.518	SUBCLONAL	1	TRUE	0	0.584726479430311	1		257	695	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248460	212248460	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	292	283	0	ENST00000342788.4:c.3807A>T	p.Lys1269Asn	p.K1269N	ENST00000342788	NM_005235.2	1269	aaA/aaT	28/28	0.430432468032181	1	FACETS	0.947	0.896	0.999	0.947	0.896	0.999	CLONAL	1	TRUE	0	0.584726479430311	1		283	746	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293159	212293159	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	103	247	0	ENST00000342788.4:c.2693C>T	p.Thr898Ile	p.T898I	ENST00000342788	NM_005235.2	898	aCc/aTc	22/28	0.430432468032181	1	FACETS	0.329	0.294	0.366	0.329	0.294	0.366	SUBCLONAL	1	TRUE	0	0.584726479430311	1		247	757	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645898	215645898	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs905491643	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	226	415	0	ENST00000260947.4:c.700G>A	p.Glu234Lys	p.E234K	ENST00000260947	NM_000465.2	234	Gaa/Aaa	4/11	0.430432468032181	1	FACETS	0.525	0.489	0.563	0.525	0.489	0.563	SUBCLONAL	1	TRUE	0	0.584726479430311	1		415	1041	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183613	10183613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553619319	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	110	368	0	ENST00000256474.2:c.82G>A	p.Asp28Asn	p.D28N	ENST00000256474	NM_000551.3	28	Gac/Aac	1/3	NA	2	FACETS	0.327	0.293	0.364			1	INDETERMINATE	1	TRUE	NA	0.584726479430311	2		368	1149	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729980	30729980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	102	237	0	ENST00000295754.5:c.1501C>T	p.Pro501Ser	p.P501S	ENST00000295754	NM_003242.5	501	Ccc/Tcc	6/7	NA	2	FACETS	0.427	0.381	0.475			1	INDETERMINATE	1	TRUE	NA	0.584726479430311	2		237	818	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090475	37090475	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs550890395	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	232	222	0	ENST00000231790.2:c.2070C>A	p.Tyr690Ter	p.Y690*	ENST00000231790	NM_000249.3	690	taC/taA	18/19	0.584726479430311	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.584726479430311	1		222	506	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935641	49935641	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs191131637	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	121	238	0	ENST00000296474.3:c.1723C>T	p.His575Tyr	p.H575Y	ENST00000296474	NM_002447.2	575	Cac/Tac	5/20	0.584726479430311	1	FACETS	0.501	0.454	0.551	0.501	0.454	0.551	SUBCLONAL	1	TRUE	0	0.584726479430311	1		238	584	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702606	52702606	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	244	316	0	ENST00000394830.3:c.292C>T	p.Gln98Ter	p.Q98*	ENST00000394830	NM_018313.4	98	Caa/Taa	4/30	0.584726479430311	1	FACETS	0.924	0.869	0.98	0.924	0.869	0.98	CLONAL	1	TRUE	0	0.584726479430311	1		316	639	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021727	71021727	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	131	319	0	ENST00000318789.4:c.1631G>A	p.Arg544Gln	p.R544Q	ENST00000318789	NM_032682.5	544	cGa/cAa	18/21	NA	2	FACETS	0.439	0.398	0.483			1	INDETERMINATE	1	TRUE	NA	0.584726479430311	2		319	1020	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138400874	138400874	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	169	325	0	ENST00000289153.2:c.2439T>A	p.Asp813Glu	p.D813E	ENST00000289153	NM_006219.2	813	gaT/gaA	17/22	0.333585148876551	1	FACETS	0.443	0.407	0.48	0.443	0.407	0.48	INDETERMINATE	1	TRUE	0	0.584726479430311	1		325	924	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430901	181430901	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	182	340	0	ENST00000325404.1:c.753C>G	p.Ser251Arg	p.S251R	ENST00000325404	NM_003106.3	251	agC/agG	1/1	0.333585148876551	1	FACETS	0.407	0.375	0.441	0.407	0.375	0.441	INDETERMINATE	1	TRUE	0	0.584726479430311	1		340	1082	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984957	55984957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776989013	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	110	250	0	ENST00000263923.4:c.172G>A	p.Asp58Asn	p.D58N	ENST00000263923	NM_002253.2	58	Gac/Aac	3/30	0.327513883177281	1	FACETS	0.42	0.378	0.464	0.42	0.378	0.464	INDETERMINATE	1	TRUE	0	0.584726479430311	1		250	634	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155457	106155457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	138	325	0	ENST00000380013.4:c.358G>A	p.Gly120Arg	p.G120R	ENST00000380013	NM_001127208.2	120	Gga/Aga	3/11	0.327513883177281	1	FACETS	0.395	0.359	0.432	0.395	0.359	0.432	INDETERMINATE	1	TRUE	0	0.584726479430311	1		325	846	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156349	106156349	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	34	255	0	ENST00000380013.4:c.1250A>G	p.Gln417Arg	p.Q417R	ENST00000380013	NM_001127208.2	417	cAg/cGg	3/11	0.327513883177281	1	FACETS	0.17	0.138	0.206	0.17	0.138	0.206	INDETERMINATE	1	TRUE	0	0.584726479430311	1		255	484	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244298	153244298	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	66	133	0	ENST00000281708.4:c.1859C>T	p.Pro620Leu	p.P620L	ENST00000281708	NM_033632.3	620	cCc/cTc	12/12	0.327513883177281	1	FACETS	0.396	0.345	0.451	0.396	0.345	0.451	INDETERMINATE	1	TRUE	0	0.584726479430311	1		133	403	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524113	187524113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	138	326	0	ENST00000441802.2:c.11426C>T	p.Pro3809Leu	p.P3809L	ENST00000441802	NM_005245.3	3809	cCc/cTc	20/27	NA	2	FACETS	0.456	0.414	0.5			1	INDETERMINATE	1	TRUE	NA	0.584726479430311	2		326	1035	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530405	187530405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	371	335	0	ENST00000441802.2:c.10138G>A	p.Gly3380Arg	p.G3380R	ENST00000441802	NM_005245.3	3380	Gga/Aga	16/27	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.584726479430311	2		335	1095	SUCCESS
APC	324	MSKCC	GRCh37	5	112177901	112177901	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs752654519	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	81	254	0	ENST00000257430.4:c.6610C>T	p.Arg2204Ter	p.R2204*	ENST00000257430	NM_000038.5	2204	Cga/Tga	16/16	0.524580335408154	2	FACETS	0.448	0.395	0.505	0.224	0.197	0.253	SUBCLONAL	1	TRUE	0	0.584726479430311	2		254	618	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480137	20480137	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1207837753	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	121	247	0	ENST00000346618.3:c.454A>G	p.Thr152Ala	p.T152A	ENST00000346618	NM_001949.4	152	Acc/Gcc	2/7	1	2	FACETS	0.412	0.372	0.455	0.412	0.372	0.455	SUBCLONAL	1	TRUE	1	0.584726479430311	2		247	1004	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652051	36652051	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	143	319	0	ENST00000244741.5:c.173C>T	p.Pro58Leu	p.P58L	ENST00000244741	NM_000389.4	58	cCa/cTa	2/3	1	2	FACETS	0.408	0.371	0.447	0.408	0.371	0.447	SUBCLONAL	1	TRUE	1	0.584726479430311	2		319	1199	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748509	43748509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371177206	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1277	201	423	0	ENST00000523873.1:c.463C>T	p.Arg155Cys	p.R155C	ENST00000523873		155	Cgc/Tgc	6/8	1	2	FACETS	0.465	0.43	0.502	0.465	0.43	0.502	SUBCLONAL	1	TRUE	1	0.584726479430311	2		423	1478	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547193	106547193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	47	106	0	ENST00000369096.4:c.430C>T	p.Leu144Phe	p.L144F	ENST00000369096	NM_001198.3	144	Ctt/Ttt	4/7	0.390029124554369	1	FACETS	0.287	0.243	0.336	0.287	0.243	0.336	SUBCLONAL	1	TRUE	0	0.584726479430311	1		106	396	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017597	112017597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1359936085	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	188	383	0	ENST00000368678.4:c.916G>A	p.Glu306Lys	p.E306K	ENST00000368678		306	Gaa/Aaa	9/13	0.390029124554369	1	FACETS	0.394	0.363	0.426	0.394	0.363	0.426	SUBCLONAL	1	TRUE	0	0.584726479430311	1		383	1156	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946429	2946429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	336	315	0	ENST00000396946.4:c.3308G>A	p.Cys1103Tyr	p.C1103Y	ENST00000396946	NM_032415.4	1103	tGc/tAc	25/25	0.296234773675298	2	FACETS	0.961	0.909	1	0.48	0.454	0.507	INDETERMINATE	1	TRUE	0	0.584726479430311	2		315	1196	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467639	50467639	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	97	218	0	ENST00000331340.3:c.874C>T	p.Pro292Ser	p.P292S	ENST00000331340	NM_006060.4	292	Ccc/Tcc	8/8	0.296234773675298	2	FACETS	0.395	0.352	0.442	0.198	0.176	0.221	INDETERMINATE	1	TRUE	0	0.584726479430311	2		218	839	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467933	50467933	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	102	214	0	ENST00000331340.3:c.1168C>T	p.Pro390Ser	p.P390S	ENST00000331340	NM_006060.4	390	Ccg/Tcg	8/8	0.296234773675298	2	FACETS	0.416	0.371	0.463	0.208	0.185	0.232	INDETERMINATE	1	TRUE	0	0.584726479430311	2		214	839	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829248	128829248	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	151	293	0	ENST00000249373.3:c.256G>A	p.Gly86Arg	p.G86R	ENST00000249373	NM_005631.4	86	Ggg/Agg	1/12	0.296234773675298	2	FACETS	0.426	0.389	0.466	0.213	0.194	0.233	INDETERMINATE	1	TRUE	0	0.584726479430311	2		293	1211	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829293	128829293	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	175	336	0	ENST00000249373.3:c.301G>A	p.Glu101Lys	p.E101K	ENST00000249373	NM_005631.4	101	Gaa/Aaa	1/12	0.296234773675298	2	FACETS	0.435	0.399	0.473	0.218	0.199	0.237	INDETERMINATE	1	TRUE	0	0.584726479430311	2		336	1375	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	31	268	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.296234773675298	2	FACETS	0.134	0.107	0.164	0.067	0.053	0.082	INDETERMINATE	1	TRUE	0	0.584726479430311	2		268	793	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737790	145737790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	121	180	0	ENST00000428558.2:c.3040C>T	p.His1014Tyr	p.H1014Y	ENST00000428558	NM_004260.3	1014	Cac/Tac	18/22	0.333585148876551	1	FACETS	0.445	0.403	0.49	0.445	0.403	0.49	INDETERMINATE	1	TRUE	0	0.584726479430311	1		180	658	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341130	8341130	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	125	323	0	ENST00000356435.5:c.5086G>A	p.Gly1696Arg	p.G1696R	ENST00000356435		1696	Gga/Aga	30/35	0.584726479430311	1	FACETS	0.473	0.429	0.519	0.473	0.429	0.519	SUBCLONAL	1	TRUE	0	0.584726479430311	1		323	640	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341196	8341196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	105	308	0	ENST00000356435.5:c.5020C>T	p.Arg1674Cys	p.R1674C	ENST00000356435		1674	Cgc/Tgc	30/35	0.584726479430311	1	FACETS	0.425	0.381	0.471	0.425	0.381	0.471	SUBCLONAL	1	TRUE	0	0.584726479430311	1		308	598	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517994	8517994	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	166	359	1	ENST00000356435.5:c.1397G>A	p.Trp466Ter	p.W466*	ENST00000356435		466	tGg/tAg	10/35	0.584726479430311	1	FACETS	0.514	0.473	0.557	0.514	0.473	0.557	SUBCLONAL	1	TRUE	0	0.584726479430311	1		360	781	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971058	21971058	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660818	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	140	186	0	ENST00000579755.1:c.343C>T	p.Arg115Trp	p.R115W	ENST00000579755		115	Cgg/Tgg	2/3	0.584726479430311	1	FACETS	0.6	0.549	0.653	0.6	0.549	0.653	SUBCLONAL	1	TRUE	0	0.584726479430311	1		186	565	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417634	139417634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749786734	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	112	226	0	ENST00000277541.6:c.410C>T	p.Ser137Leu	p.S137L	ENST00000277541	NM_017617.3	137	tCg/tTg	4/34	0.584726479430311	1	FACETS	0.459	0.413	0.506	0.459	0.413	0.506	SUBCLONAL	1	TRUE	0	0.584726479430311	1		226	591	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100550	8100550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs34363744	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	130	236	0	ENST00000346208.3:c.524C>T	p.Ser175Leu	p.S175L	ENST00000346208		175	tCg/tTg	3/6	0.327513883177281	1	FACETS	0.457	0.415	0.501	0.457	0.415	0.501	INDETERMINATE	1	TRUE	0	0.584726479430311	1		236	688	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115769	8115769	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	255	439	0	ENST00000346208.3:c.1115C>T	p.Ser372Phe	p.S372F	ENST00000346208		372	tCc/tTc	6/6	0.327513883177281	1	FACETS	0.486	0.454	0.519	0.486	0.454	0.519	INDETERMINATE	1	TRUE	0	0.584726479430311	1		439	1270	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615611	43615611	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	129	223	0	ENST00000355710.3:c.2690G>C	p.Arg897Pro	p.R897P	ENST00000355710	NM_020975.4	897	cGa/cCa	15/20	0.309271077342585	1	FACETS	0.359	0.325	0.395	0.359	0.325	0.395	INDETERMINATE	1	TRUE	0	0.584726479430311	1		223	870	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912171	114912171	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	337	396	0	ENST00000543371.1:c.1241A>G	p.Tyr414Cys	p.Y414C	ENST00000543371	NM_001198531.1	414	tAc/tGc	11/14	0.309271077342585	1	FACETS	0.618	0.584	0.654	0.618	0.584	0.654	INDETERMINATE	1	TRUE	0	0.584726479430311	1		396	1319	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243237	123243237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55774317	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	164	451	0	ENST00000358487.5:c.2276G>A	p.Arg759Gln	p.R759Q	ENST00000358487	NM_000141.4	759	cGa/cAa	17/18	0.309271077342585	1	FACETS	0.374	0.343	0.407	0.374	0.343	0.407	INDETERMINATE	1	TRUE	0	0.584726479430311	1		451	1060	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200434	67200434	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	45	185	0	ENST00000312629.5:c.628C>A	p.Leu210Met	p.L210M	ENST00000312629	NM_003952.2	210	Ctg/Atg	8/15	0.333585148876551	1	FACETS	0.174	0.145	0.205	0.174	0.145	0.205	INDETERMINATE	1	TRUE	0	0.584726479430311	1		185	627	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625149	69625149	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	107	233	0	ENST00000334134.2:c.644A>C	p.Gln215Pro	p.Q215P	ENST00000334134	NM_005247.2	215	cAg/cCg	3/3	0.333585148876551	1	FACETS	0.359	0.322	0.399	0.359	0.322	0.399	INDETERMINATE	1	TRUE	0	0.584726479430311	1		233	721	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999741	100999741	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770746610	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	151	383	0	ENST00000325455.5:c.61C>T	p.Pro21Ser	p.P21S	ENST00000325455	NM_001202474.3	21	Ccc/Tcc	1/8	0.333585148876551	1	FACETS	0.358	0.327	0.391	0.358	0.327	0.391	INDETERMINATE	1	TRUE	0	0.584726479430311	1		383	1021	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375035	118375035	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	66	236	1	ENST00000534358.1:c.8428A>G	p.Ser2810Gly	p.S2810G	ENST00000534358	NM_005933.3	2810	Agc/Ggc	27/36	0.333585148876551	1	FACETS	0.293	0.254	0.334	0.293	0.254	0.334	INDETERMINATE	1	TRUE	0	0.584726479430311	1		237	546	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716364	18716364	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	122	312	1	ENST00000266497.5:c.3711A>T	p.Lys1237Asn	p.K1237N	ENST00000266497		1237	aaA/aaT	26/31	1	2	FACETS	0.454	0.409	0.5	0.454	0.409	0.5	SUBCLONAL	1	TRUE	1	0.584726479430311	2		313	920	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427405	49427405	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs557907074	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	149	281	0	ENST00000301067.7:c.11083C>T	p.Pro3695Ser	p.P3695S	ENST00000301067	NM_003482.3	3695	Cct/Tct	39/54	1	2	FACETS	0.444	0.405	0.486	0.444	0.405	0.486	SUBCLONAL	1	TRUE	1	0.584726479430311	2		281	1147	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434618	49434618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs949690934	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	133	120	0	ENST00000301067.7:c.6935C>T	p.Ser2312Leu	p.S2312L	ENST00000301067	NM_003482.3	2312	tCa/tTa	31/54	1	2	FACETS	0.962	0.88	1	0.962	0.88	1	CLONAL	1	TRUE	1	0.584726479430311	2		120	473	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438733	49438733	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1170765431	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	182	233	0	ENST00000301067.7:c.4757G>A	p.Arg1586His	p.R1586H	ENST00000301067	NM_003482.3	1586	cGc/cAc	19/54	1	2	FACETS	0.547	0.504	0.592	0.547	0.504	0.592	SUBCLONAL	1	TRUE	1	0.584726479430311	2		233	1138	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117381	115117381	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	45	316	0	ENST00000257566.3:c.793T>C	p.Tyr265His	p.Y265H	ENST00000257566	NM_016569.3	265	Tat/Cat	4/8	0.327513883177281	1	FACETS	0.131	0.109	0.155	0.131	0.109	0.155	INDETERMINATE	1	TRUE	0	0.584726479430311	1		316	834	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562870	21562870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1047262994	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	132	239	0	ENST00000382592.4:c.1049C>T	p.Pro350Leu	p.P350L	ENST00000382592	NM_014572.2	350	cCc/cTc	4/8	0.584726479430311	1	FACETS	0.489	0.444	0.535	0.489	0.444	0.535	SUBCLONAL	1	TRUE	0	0.584726479430311	1		239	654	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32905069	32905069	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	83	153	0	ENST00000380152.3:c.695A>T	p.Tyr232Phe	p.Y232F	ENST00000380152		232	tAt/tTt	9/27	0.584726479430311	1	FACETS	0.586	0.521	0.654	0.586	0.521	0.654	SUBCLONAL	1	TRUE	0	0.584726479430311	1		153	343	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134012	41134012	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	176	388	0	ENST00000379561.5:c.1616T>G	p.Leu539Arg	p.L539R	ENST00000379561	NM_002015.3	539	cTg/cGg	2/3	0.584726479430311	1	FACETS	0.481	0.443	0.521	0.481	0.443	0.521	SUBCLONAL	1	TRUE	0	0.584726479430311	1		388	885	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68292197	68292197	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1245702524	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	129	285	0	ENST00000487270.1:c.101C>T	p.Ser34Phe	p.S34F	ENST00000487270	NM_133509.3	34	tCc/tTc	3/11	0.327513883177281	1	FACETS	0.332	0.3	0.365	0.332	0.3	0.365	INDETERMINATE	1	TRUE	0	0.584726479430311	1		285	941	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028834	42028834	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	231	497	0	ENST00000219905.7:c.4372C>T	p.Pro1458Ser	p.P1458S	ENST00000219905	NM_001164273.1	1458	Cct/Tct	13/24	0.327513883177281	1	FACETS	0.473	0.44	0.507	0.473	0.44	0.507	INDETERMINATE	1	TRUE	0	0.584726479430311	1		497	1183	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354392	354392	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs928169149	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	146	299	0	ENST00000262320.3:c.1166C>T	p.Ala389Val	p.A389V	ENST00000262320	NM_003502.3	389	gCg/gTg	5/11	0.327513883177281	1	FACETS	0.357	0.325	0.39	0.357	0.325	0.39	INDETERMINATE	1	TRUE	0	0.584726479430311	1		299	991	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832856	3832856	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	126	216	0	ENST00000262367.5:c.1402A>T	p.Thr468Ser	p.T468S	ENST00000262367	NM_004380.2	468	Act/Tct	6/31	0.327513883177281	1	FACETS	0.418	0.379	0.46	0.418	0.379	0.46	INDETERMINATE	1	TRUE	0	0.584726479430311	1		216	729	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858549	9858550	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	268	316	0	ENST00000330684.3:c.2851_2852delinsAA	p.Gly951Lys	p.G951K	ENST00000330684	NM_001134407.1	951	GGg/AAg	13/13	0.327513883177281	1	FACETS	0.798	0.751	0.846	0.798	0.751	0.846	INDETERMINATE	1	TRUE	0	0.584726479430311	1		316	813	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829113	72829113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	96	225	0	ENST00000268489.5:c.7468C>T	p.Pro2490Ser	p.P2490S	ENST00000268489	NM_006885.3	2490	Cca/Tca	9/10	0.327513883177281	1	FACETS	0.344	0.306	0.384	0.344	0.306	0.384	INDETERMINATE	1	TRUE	0	0.584726479430311	1		225	676	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993320	72993320	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1224	268	459	0	ENST00000268489.5:c.725A>C	p.Lys242Thr	p.K242T	ENST00000268489	NM_006885.3	242	aAg/aCg	2/10	0.327513883177281	1	FACETS	0.435	0.406	0.464	0.435	0.406	0.464	INDETERMINATE	1	TRUE	0	0.584726479430311	1		459	1492	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72994016	72994016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs12922687	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	204	381	0	ENST00000268489.5:c.29C>T	p.Ser10Leu	p.S10L	ENST00000268489	NM_006885.3	10	tCg/tTg	2/10	0.327513883177281	1	FACETS	0.435	0.403	0.469	0.435	0.403	0.469	INDETERMINATE	1	TRUE	0	0.584726479430311	1		381	1134	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579395	7579395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	175	228	0	ENST00000269305.4:c.292C>T	p.Pro98Ser	p.P98S	ENST00000269305	NM_001126112.2	98	Cct/Tct	4/11	0.202131185010629	2	FACETS	0.779	0.719	0.842	0.39	0.359	0.421	INDETERMINATE	1	TRUE	0	0.584726479430311	2		228	768	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40376811	40376811	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	212	539	0	ENST00000293328.3:c.361C>T	p.Arg121Ter	p.R121*	ENST00000293328	NM_012448.3	121	Cga/Tga	4/19	0.202131185010629	2	FACETS	0.55	0.509	0.592	0.275	0.254	0.296	INDETERMINATE	1	TRUE	0	0.584726479430311	2		539	1319	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677945	58677945	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770413280	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	137	235	1	ENST00000305921.3:c.170C>T	p.Ala57Val	p.A57V	ENST00000305921	NM_003620.3	57	gCc/gTc	1/6	0.249084981546325	3	FACETS	0.692	0.629	0.758	0.231	0.209	0.253	INDETERMINATE	1	TRUE	0	0.584726479430311	3		236	875	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58700905	58700905	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1231	137	461	0	ENST00000305921.3:c.496G>A	p.Gly166Ser	p.G166S	ENST00000305921	NM_003620.3	166	Ggt/Agt	2/6	0.249084981546325	3	FACETS	0.443	0.401	0.487	0.148	0.133	0.163	INDETERMINATE	1	TRUE	0	0.584726479430311	3		461	1368	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732520	74732520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	57	246	0	ENST00000359995.5:c.389C>T	p.Ser130Phe	p.S130F	ENST00000359995	NM_001195427.1	130	tCc/tTc	2/3	0.249084981546325	3	FACETS	0.229	0.195	0.266	0.076	0.065	0.089	INDETERMINATE	1	TRUE	0	0.584726479430311	3		246	1100	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756697	756697	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767099976	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	133	410	0	ENST00000314574.4:c.131C>T	p.Ser44Leu	p.S44L	ENST00000314574	NM_005433.3	44	tCa/tTa	2/12	0.309271077342585	1	FACETS	0.32	0.29	0.351	0.32	0.29	0.351	INDETERMINATE	1	TRUE	0	0.584726479430311	1		410	1007	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216560	2216560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777525091	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	132	296	0	ENST00000398665.3:c.2204C>T	p.Thr735Met	p.T735M	ENST00000398665	NM_032482.2	735	aCg/aTg	20/28	1	2	FACETS	0.415	0.375	0.456	0.415	0.375	0.456	SUBCLONAL	1	TRUE	1	0.584726479430311	2		296	1089	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226845	2226845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	156	80	0	ENST00000398665.3:c.4325C>T	p.Pro1442Leu	p.P1442L	ENST00000398665	NM_032482.2	1442	cCc/cTc	27/28	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.584726479430311	2		80	424	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099309	4099309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	161	261	0	ENST00000262948.5:c.809C>T	p.Pro270Leu	p.P270L	ENST00000262948	NM_030662.3	270	cCc/cTc	7/11	1	2	FACETS	0.554	0.508	0.603	0.554	0.508	0.603	SUBCLONAL	1	TRUE	1	0.584726479430311	2		261	994	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141529	11141529	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	131	245	0	ENST00000358026.2:c.3506A>T	p.Asp1169Val	p.D1169V	ENST00000358026	NM_001128849.1	1169	gAc/gTc	25/36	1	2	FACETS	0.432	0.391	0.475	0.432	0.391	0.475	SUBCLONAL	1	TRUE	1	0.584726479430311	2		245	1038	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629158	14629158	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	53	316	0	ENST00000254322.2:c.4G>A	p.Gly2Ser	p.G2S	ENST00000254322	NM_006145.1	2	Ggt/Agt	1/3	1	2	FACETS	0.181	0.154	0.212	0.181	0.154	0.212	SUBCLONAL	1	TRUE	1	0.584726479430311	2		316	999	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271835	15271835	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748776589	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	31	71	0	ENST00000263388.2:c.6604G>A	p.Val2202Ile	p.V2202I	ENST00000263388	NM_000435.2	2202	Gtc/Atc	33/33	1	2	FACETS	0.428	0.347	0.517	0.428	0.347	0.517	SUBCLONAL	1	TRUE	1	0.584726479430311	2		71	248	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302627	15302627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768437995	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	379	331	3	ENST00000263388.2:c.731G>A	p.Arg244Gln	p.R244Q	ENST00000263388	NM_000435.2	244	cGa/cAa	5/33	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.584726479430311	2		334	1285	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942077	17942077	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	279	255	0	ENST00000458235.1:c.2938T>A	p.Tyr980Asn	p.Y980N	ENST00000458235	NM_000215.3	980	Tac/Aac	21/24	1	2	FACETS	0.952	0.896	1	0.952	0.896	1	CLONAL	1	TRUE	1	0.584726479430311	2		255	1002	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256668	19256668	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	35	132	0	ENST00000162023.5:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000162023		349	Gag/Tag	13/13	1	2	FACETS	0.242	0.198	0.292	0.242	0.198	0.292	SUBCLONAL	1	TRUE	1	0.584726479430311	2		132	494	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257856	19257856	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	48	150	0	ENST00000162023.5:c.530C>G	p.Ala177Gly	p.A177G	ENST00000162023		177	gCc/gGc	9/13	1	2	FACETS	0.26	0.219	0.305	0.26	0.219	0.305	SUBCLONAL	1	TRUE	1	0.584726479430311	2		150	632	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257863	19257863	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	49	157	0	ENST00000162023.5:c.523C>A	p.Pro175Thr	p.P175T	ENST00000162023		175	Ccc/Acc	9/13	1	2	FACETS	0.255	0.216	0.299	0.255	0.216	0.299	SUBCLONAL	1	TRUE	1	0.584726479430311	2		157	656	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258626	19258626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241841668	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	54	283	1	ENST00000162023.5:c.274G>A	p.Gly92Ser	p.G92S	ENST00000162023		92	Ggc/Agc	8/13	1	2	FACETS	0.177	0.151	0.207	0.177	0.151	0.207	SUBCLONAL	1	TRUE	1	0.584726479430311	2		284	1041	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42385026	42385026	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	171	353	1	ENST00000221972.3:c.660T>A	p.Asp220Glu	p.D220E	ENST00000221972	NM_021601.3	220	gaT/gaA	5/5	1	2	FACETS	0.496	0.455	0.538	0.496	0.455	0.538	SUBCLONAL	1	TRUE	1	0.584726479430311	2		354	1180	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910411	50910411	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762273084	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	198	364	0	ENST00000440232.2:c.1666G>A	p.Val556Ile	p.V556I	ENST00000440232	NM_002691.3	556	Gta/Ata	13/27	1	2	FACETS	0.528	0.488	0.57	0.528	0.488	0.57	SUBCLONAL	1	TRUE	1	0.584726479430311	2		364	1283	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546931	9546931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs562732119	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	88	212	0	ENST00000353224.5:c.1091C>T	p.Ser364Leu	p.S364L	ENST00000353224	NM_177990.2	364	tCg/tTg	5/10	1	2	FACETS	0.408	0.361	0.458	0.408	0.361	0.458	SUBCLONAL	1	TRUE	1	0.584726479430311	2		212	738	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561340	9561340	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	177	208	0	ENST00000353224.5:c.442G>A	p.Glu148Lys	p.E148K	ENST00000353224	NM_177990.2	148	Gag/Aag	4/10	1	2	FACETS	0.97	0.898	1	0.97	0.898	1	CLONAL	1	TRUE	1	0.584726479430311	2		208	624	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624936	9624936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760501160	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	237	333	1	ENST00000353224.5:c.41C>T	p.Pro14Leu	p.P14L	ENST00000353224	NM_177990.2	14	cCg/cTg	3/10	1	2	FACETS	0.973	0.911	1	0.973	0.911	1	CLONAL	1	TRUE	1	0.584726479430311	2		334	833	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388692	31388692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1438362757	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	154	304	0	ENST00000328111.2:c.1957G>A	p.Asp653Asn	p.D653N	ENST00000328111	NM_006892.3	653	Gat/Aat	18/23	1	2	FACETS	0.467	0.426	0.509	0.467	0.426	0.509	SUBCLONAL	1	TRUE	1	0.584726479430311	2		304	1129	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39745026	39745026	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	121	274	0	ENST00000361337.2:c.1816A>G	p.Thr606Ala	p.T606A	ENST00000361337	NM_003286.2	606	Aca/Gca	17/21	1	2	FACETS	0.456	0.412	0.504	0.456	0.412	0.504	SUBCLONAL	1	TRUE	1	0.584726479430311	2		274	907	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961521	54961521	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	221	247	0	ENST00000312783.6:c.111A>C	p.Leu37Phe	p.L37F	ENST00000312783	NM_198436.1	37	ttA/ttC	4/10	1	2	FACETS	0.846	0.788	0.905	0.846	0.788	0.905	CLONAL	1	TRUE	1	0.584726479430311	2		247	894	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206850	36206850	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	81	134	0	ENST00000300305.3:c.662T>C	p.Phe221Ser	p.F221S	ENST00000300305		221	tTt/tCt	6/8	0.390029124554369	1	FACETS	0.405	0.358	0.455	0.405	0.358	0.455	SUBCLONAL	1	TRUE	0	0.584726479430311	1		134	484	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536160	41536160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	129	245	0	ENST00000263253.7:c.1777C>T	p.Pro593Ser	p.P593S	ENST00000263253	NM_001429.3	593	Cct/Tct	9/31	0.249084981546325	3	FACETS	0.63	0.571	0.693	0.21	0.19	0.231	INDETERMINATE	1	TRUE	0	0.584726479430311	3		245	905	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914743	39914743	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	143	182	0	ENST00000378444.4:c.4619A>G	p.Asn1540Ser	p.N1540S	ENST00000378444	NM_001123385.1	1540	aAc/aGc	12/15	1	1	FACETS	0.593	0.542	0.645	0.593	0.542	0.645	SUBCLONAL	1	TRUE	0	0.584726479430311	1		182	584	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939504	76939504	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	130	142	0	ENST00000373344.5:c.1244C>T	p.Ser415Phe	p.S415F	ENST00000373344	NM_000489.3	415	tCc/tTc	9/35	1	1	FACETS	0.725	0.663	0.789	0.725	0.663	0.789	SUBCLONAL	1	TRUE	0	0.584726479430311	1		142	434	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182910	123182910	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	92	159	0	ENST00000218089.9:c.875T>C	p.Val292Ala	p.V292A	ENST00000218089	NM_001042749.1	292	gTg/gCg	10/35	1	1	FACETS	0.401	0.357	0.448	0.401	0.357	0.448	SUBCLONAL	1	TRUE	0	0.584726479430311	1		159	555	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657302	29657376	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTTTTCTCCTAGGTCAGCTGCCTATAATCTTCTGTGTGCCTTAACTTGTACCTTTAATTTAAAAATCGAGGGCCA	GTTTTCTCCTAGGTCAGCTGCCTATAATCTTCTGTGTGCCTTAACTTGTACCTTTAATTTAAAAATCGAGGGCCA	-	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	86	170	0	ENST00000356175.3:c.5547-9_5612del		p.X1849_splice	ENST00000356175	NM_000267.3	1849		38/57	0.202131185010629	2	FACETS	0.472	0.418	0.53	0.236	0.209	0.265	INDETERMINATE	1	TRUE	0	0.584726479430311	2		170	623	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905055	50905055	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	180	331	3	ENST00000440232.2:c.342del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	113	Ggg/gg	4/27	1	2	FACETS	0.515	0.474	0.558	0.515	0.474	0.558	SUBCLONAL	1	TRUE	1	0.584726479430311	2		334	1196	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663779	29663786	+	frameshift_variant	Frame_Shift_Del	DEL	AATTCCCT	AATTCCCT	-	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	290	288	0	ENST00000356175.3:c.6211_6218del	p.Asn2071Ter	p.N2071*	ENST00000356175	NM_000267.3	2071	AATTCCCTt/t	41/57	0.202131185010629	2	FACETS	1	0.992	1	0.653	0.617	0.689	INDETERMINATE	1	TRUE	0	0.584726479430311	2		288	760	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99451923	99451925	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0005159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	52	224	0	ENST00000268035.6:c.1259_1261del	p.Phe420del	p.F420del	ENST00000268035	NM_000875.3	419	tcCTTc/tcc	6/21	0.327513883177281	1	FACETS	0.193	0.164	0.226	0.193	0.164	0.226	INDETERMINATE	1	TRUE	0	0.584726479430311	1		224	651	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs786201057	NA	P-0005169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	161	371	0	ENST00000269305.4:c.374C>G	p.Thr125Arg	p.T125R	ENST00000269305	NM_001126112.2	125	aCg/aGg	4/11	0.543661623158504	1	FACETS	0.918	0.849	0.988	0.918	0.849	0.988	CLONAL	1	TRUE	0	0.543661623158504	1		371	470	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155442	99155442	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs374754606	NA	P-0005169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	55	339	1	ENST00000074304.5:c.668C>T	p.Ser223Leu	p.S223L	ENST00000074304	NM_001134224.1	223	tCg/tTg	9/26	NA	2	FACETS	0.319	0.272	0.37			1	INDETERMINATE	1	TRUE	NA	0.543661623158504	2		340	634	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020075	123020075	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	106	631	0	ENST00000355640.3:c.563G>C	p.Gly188Ala	p.G188A	ENST00000355640		188	gGa/gCa	2/7	0.301586811783481	1	FACETS	0.278	0.248	0.31	0.278	0.248	0.31	INDETERMINATE	1	TRUE	0	0.543661623158504	1		631	1021	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0005172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	93	338	1	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	0.28	2		339	562	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0005172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	71	354	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.3	1	FACETS	0.871	0.761	0.988	0.871	0.761	0.988	CLONAL	1	TRUE	0	0.28	1		355	501	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0005172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	96	578	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.241726688037467	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.28	1		579	535	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281581	198281581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139823279	NA	P-0005172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	73	464	0	ENST00000335508.6:c.550G>A	p.Val184Ile	p.V184I	ENST00000335508	NM_012433.2	184	Gtc/Atc	6/25	1	2	FACETS	0.923	0.808	1	0.923	0.808	1	CLONAL	1	TRUE	1	0.28	2		464	565	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120860	115120860	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1168678629	NA	P-0005172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	61	470	0	ENST00000257566.3:c.146A>G	p.Asn49Ser	p.N49S	ENST00000257566	NM_016569.3	49	aAc/aGc	1/8	1	2	FACETS	0.897	0.775	1	0.897	0.775	1	CLONAL	1	TRUE	1	0.28	2		470	486	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0005207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	105	205	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.366821287568641	2		205	518	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0005207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	99	338	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.894	0.799	0.994	0.894	0.799	0.994	CLONAL	1	TRUE	1	0.366821287568641	2		339	604	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0005207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	115	285	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.182902358894569	3	FACETS	0.759	0.687	0.834	0.759	0.687	0.834	INDETERMINATE	2	TRUE	1	0.366821287568641	3		285	489	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0005207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	157	728	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.182902358894569	3	FACETS	1	0.985	1	0.666	0.611	0.723	INDETERMINATE	1	TRUE	1	0.366821287568641	3		728	761	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73354982	73354982	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0005207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	57	159	0	ENST00000377767.4:c.386+2T>G		p.X129_splice	ENST00000377767	NM_014953.3	129			0.366821287568641	4	FACETS	1	0.87	1	0.337	0.29	0.388	CLONAL	1	TRUE	1	0.366821287568641	4		159	420	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402825	20402839	+	inframe_deletion	In_Frame_Del	DEL	GCGGCGGCAGCGGCG	GCGGCGGCAGCGGCG	-	novel	NA	P-0005207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	13	15	0	ENST00000346618.3:c.370_384del	p.Ser124_Gly128del	p.S124_G128del	ENST00000346618	NM_001949.4	121	cGCGGCGGCAGCGGCGgc/cgc	1/7	0.200057094617857	4	FACETS	0.914	0.672	1	0.914	0.672	1	INDETERMINATE	2	TRUE	2	0.366821287568641	4		15	53	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0005210-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	266	338	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.198744387277025	3	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.470688749863358	3		339	619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0005210-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	248	792	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	NA	2	FACETS	1	0.959	1			1	INDETERMINATE	2	TRUE	NA	0.470688749863358	2		792	518	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0005210-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	73	747	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.25523465807644	1	FACETS	0.534	0.469	0.604	0.534	0.469	0.604	INDETERMINATE	1	TRUE	0	0.470688749863358	1		747	444	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428627	49428627	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005210-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	48	648	0	ENST00000301067.7:c.10323G>T	p.Gln3441His	p.Q3441H	ENST00000301067	NM_003482.3	3441	caG/caT	35/54	0.254065671434531	1	FACETS	0.377	0.319	0.44	0.377	0.319	0.44	INDETERMINATE	1	TRUE	0	0.470688749863358	1		648	414	SUCCESS
APC	324	MSKCC	GRCh37	5	112173830	112173831	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005210-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	125	470	0	ENST00000257430.4:c.2544dup	p.Asp849ArgfsTer2	p.D849Rfs*2	ENST00000257430	NM_000038.5	847	gaa/gAaa	16/16	0.25523465807644	1	FACETS	0.875	0.798	0.956	0.875	0.798	0.956	INDETERMINATE	1	TRUE	0	0.470688749863358	1		470	464	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412095	63412095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852217	NA	P-0005210-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	160	441	2	ENST00000330258.3:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000330258	NM_152424.3	358	Cga/Tga	2/2	1	1	FACETS	0.817	0.763	0.871	1	0.992	1	CLONAL	2	TRUE	0	0.470688749863358	1		443	318	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800935	243800935	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005210-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	81	503	0	ENST00000263826.5:c.539A>T	p.Lys180Met	p.K180M	ENST00000263826	NM_005465.4	180	aAg/aTg	5/13	0.294265056549007	3	FACETS	0.63	0.555	0.71	0.315	0.277	0.355	SUBCLONAL	1	TRUE	1	0.470688749863358	3		503	675	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172265	99172265	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005210-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	22	347	0	ENST00000074304.5:c.1831A>G	p.Thr611Ala	p.T611A	ENST00000074304	NM_001134224.1	611	Acc/Gcc	17/26	1	2	FACETS	0.323	0.251	0.408	0.323	0.251	0.408	SUBCLONAL	1	TRUE	1	0.470688749863358	2		347	289	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259459	89259459	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005210-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	128	664	2	ENST00000336596.2:c.603G>T	p.Lys201Asn	p.K201N	ENST00000336596	NM_005233.5	201	aaG/aaT	3/17	1	2	FACETS	0.9	0.819	0.986	0.9	0.819	0.986	CLONAL	1	TRUE	1	0.470688749863358	2		666	604	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	338153	338153	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005210-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	37	636	0	ENST00000262320.3:c.2558A>T	p.Lys853Met	p.K853M	ENST00000262320	NM_003502.3	853	aAg/aTg	11/11	0.470688749863358	1	FACETS	0.312	0.257	0.373	0.312	0.257	0.373	SUBCLONAL	1	TRUE	0	0.470688749863358	1		636	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0005213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	49	759	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.782	0.661	0.916	0.782	0.661	0.916	CLONAL	1	TRUE	1	0.18	2		759	696	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696688	47696688	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519971	NA	P-0005213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	52	653	2	ENST00000347630.2:c.260A>G	p.Tyr87Cys	p.Y87C	ENST00000347630	NM_001007230.1	87	tAc/tGc	5/11	1	2	FACETS	0.994	0.846	1	0.994	0.846	1	CLONAL	1	TRUE	1	0.18	2		655	581	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609314	39609314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766344105	NA	P-0005213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	41	552	2	ENST00000262039.4:c.1616G>A	p.Arg539His	p.R539H	ENST00000262039	NM_002647.2	539	cGt/cAt	15/25	1	2	FACETS	0.628	0.522	0.747	0.628	0.522	0.747	SUBCLONAL	1	TRUE	1	0.18	2		554	725	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0005220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	975	585	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.595966568619582	4	FACETS	0.978	0.958	0.997	0.978	0.958	0.997	CLONAL	4	TRUE	0	0.604615817352002	4		585	1323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0005220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	735	792	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.604615817352002	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.604615817352002	2		792	1197	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063718	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0005220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	328	295	0	ENST00000412916.2:c.165+2dup		p.X55_splice	ENST00000412916		55			0.604615817352002	2	FACETS	0.97	0.929	1	0.97	0.929	1	CLONAL	2	TRUE	0	0.604615817352002	2		295	559	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094477	27094477	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	164	299	0	ENST00000324856.7:c.3185G>A	p.Gly1062Asp	p.G1062D	ENST00000324856	NM_006015.4	1062	gGt/gAt	11/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.604615817352002	2		299	470	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927457	178927457	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	990	508	4	ENST00000263967.3:c.1220G>T	p.Cys407Phe	p.C407F	ENST00000263967	NM_006218.2	407	tGc/tTc	7/21	0.595966568619582	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	4	TRUE	0	0.604615817352002	4		512	1299	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878748	151878748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778498	NA	P-0005220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	1599	427	1	ENST00000262189.6:c.6197G>A	p.Arg2066Gln	p.R2066Q	ENST00000262189	NM_170606.2	2066	cGa/cAa	36/59	0.567268731061172	1	FACETS	0.87	0.857	0.883	1	0.999	1	CLONAL	2	TRUE	0	0.604615817352002	1		428	2121	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15938210	15938210	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	293	671	2	ENST00000268712.3:c.7004C>A	p.Ser2335Tyr	p.S2335Y	ENST00000268712	NM_006311.3	2335	tCt/tAt	45/46	0.604615817352002	2	FACETS	0.889	0.837	0.943	0.445	0.418	0.472	CLONAL	1	TRUE	0	0.604615817352002	2		673	1090	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115623	8115708	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCTTGGTGTGCGAGAGCCTGTGCATTTCAGAGGCAGCAAAAAAGTAAAAAAAAAAAAAAAAAATTGATCTTTGTTTAGATTAACA	TTCTTGGTGTGCGAGAGCCTGTGCATTTCAGAGGCAGCAAAAAAGTAAAAAAAAAAAAAAAAAATTGATCTTTGTTTAGATTAACA	-	novel	NA	P-0005220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	228	105	2	ENST00000346208.3:c.1048-79_1054del		p.X350_splice	ENST00000346208		350		6/6	0.58731251094435	3	FACETS	0.895	0.851	0.937	1	0.993	1	CLONAL	3	TRUE	1	0.604615817352002	3		107	366	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	25	510	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.554	0.435	0.692	0.554	0.435	0.692	SUBCLONAL	1	TRUE	1	0.16	2		510	564	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	13	440	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.282	0.2	0.383	0.282	0.2	0.383	SUBCLONAL	1	TRUE	1	0.16	2		441	576	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	43	400	1	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.16	2		401	519	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	85	728	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.16	2		728	729	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435160	56435161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755128667	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	11	187	0	ENST00000407977.2:c.1976dup	p.Pro660SerfsTer87	p.P660Sfs*87	ENST00000407977		659	ggt/ggGt	9/10	1	2	FACETS	0.911	0.631	1	0.911	0.631	1	CLONAL	1	TRUE	1	0.16	2		187	151	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900288	101900288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111854391	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	29	541	0	ENST00000374994.4:c.722C>T	p.Ser241Leu	p.S241L	ENST00000374994	NM_004612.2	241	tCg/tTg	4/9	1	2	FACETS	0.715	0.573	0.877	0.715	0.573	0.877	SUBCLONAL	1	TRUE	1	0.16	2		541	507	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928347	69928347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	33	572	1	ENST00000352241.4:c.167G>A	p.Arg56His	p.R56H	ENST00000352241	NM_198159.2	56	cGc/cAc	2/10	1	2	FACETS	0.851	0.692	1	0.851	0.692	1	CLONAL	1	TRUE	1	0.16	2		573	485	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955112	55955112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776671822	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	26	567	0	ENST00000263923.4:c.3433G>A	p.Gly1145Arg	p.G1145R	ENST00000263923	NM_002253.2	1145	Ggg/Agg	26/30	1	2	FACETS	0.662	0.523	0.822	0.662	0.523	0.822	SUBCLONAL	1	TRUE	1	0.16	2		567	491	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442569	52442569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1298276806	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	25	446	0	ENST00000460680.1:c.176G>A	p.Arg59Gln	p.R59Q	ENST00000460680	NM_004656.3	59	cGg/cAg	4/17	1	2	FACETS	0.676	0.532	0.843	0.676	0.532	0.843	SUBCLONAL	1	TRUE	1	0.16	2		446	462	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606304	93606304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	58	617	0	ENST00000375746.1:c.124C>T	p.Arg42Cys	p.R42C	ENST00000375746	NM_001174167.1	42	Cgc/Tgc	2/14	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.16	2		617	587	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777676	9777676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	42	562	0	ENST00000377346.4:c.1012C>T	p.Arg338Trp	p.R338W	ENST00000377346	NM_005026.3	338	Cgg/Tgg	8/24	1	2	FACETS	0.802	0.668	0.951	0.802	0.668	0.951	CLONAL	1	TRUE	1	0.16	2		562	655	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257509	16257509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779755634	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	35	612	1	ENST00000375759.3:c.4774C>T	p.Arg1592Trp	p.R1592W	ENST00000375759	NM_015001.2	1592	Cgg/Tgg	11/15	1	2	FACETS	0.752	0.615	0.906	0.752	0.615	0.906	CLONAL	1	TRUE	1	0.16	2		613	582	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474086	29474086	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	31	497	0	ENST00000389048.3:c.2089A>G	p.Thr697Ala	p.T697A	ENST00000389048	NM_004304.4	697	Acc/Gcc	12/29	1	2	FACETS	0.903	0.73	1	0.903	0.73	1	CLONAL	1	TRUE	1	0.16	2		497	429	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023095	48023095	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	53	902	0	ENST00000234420.5:c.520A>T	p.Arg174Ter	p.R174*	ENST00000234420	NM_000179.2	174	Aga/Tga	3/10	1	2	FACETS	0.782	0.665	0.911	0.782	0.665	0.911	CLONAL	1	TRUE	1	0.16	2		902	847	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131412	202131412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339962485	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	36	615	0	ENST00000358485.4:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000358485	NM_001080125.1	127	cGa/cAa	2/9	1	2	FACETS	0.69	0.566	0.83	0.69	0.566	0.83	SUBCLONAL	1	TRUE	1	0.16	2		615	652	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151303	202151303	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	36	673	0	ENST00000358485.4:c.1603T>G	p.Phe535Val	p.F535V	ENST00000358485	NM_001080125.1	535	Ttc/Gtc	9/9	1	2	FACETS	0.657	0.538	0.791	0.657	0.538	0.791	SUBCLONAL	1	TRUE	1	0.16	2		673	685	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976872	55976872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs551579207	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	27	570	2	ENST00000263923.4:c.1040G>A	p.Arg347His	p.R347H	ENST00000263923	NM_002253.2	347	cGt/cAt	8/30	1	2	FACETS	0.658	0.522	0.814	0.658	0.522	0.814	SUBCLONAL	1	TRUE	1	0.16	2		572	513	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522536	187522536	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219539820	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	31	613	0	ENST00000441802.2:c.11527C>T	p.Arg3843Cys	p.R3843C	ENST00000441802	NM_005245.3	3843	Cgt/Tgt	21/27	1	2	FACETS	0.633	0.511	0.773	0.633	0.511	0.773	SUBCLONAL	1	TRUE	1	0.16	2		613	612	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540379	187540379	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375070972	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	25	432	0	ENST00000441802.2:c.7361G>A	p.Arg2454Gln	p.R2454Q	ENST00000441802	NM_005245.3	2454	cGg/cAg	10/27	1	2	FACETS	0.76	0.599	0.947	0.76	0.599	0.947	CLONAL	1	TRUE	1	0.16	2		432	411	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950532	38950532	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	27	634	0	ENST00000357387.3:c.3418G>T	p.Asp1140Tyr	p.D1140Y	ENST00000357387	NM_152756.3	1140	Gat/Tat	31/38	1	2	FACETS	0.637	0.505	0.788	0.637	0.505	0.788	SUBCLONAL	1	TRUE	1	0.16	2		634	530	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962423	38962423	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	28	417	0	ENST00000357387.3:c.1709T>C	p.Leu570Ser	p.L570S	ENST00000357387	NM_152756.3	570	tTa/tCa	19/38	1	2	FACETS	0.749	0.598	0.923	0.749	0.598	0.923	CLONAL	1	TRUE	1	0.16	2		417	467	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518038	176518038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111435837	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	43	768	1	ENST00000292408.4:c.536C>T	p.Thr179Met	p.T179M	ENST00000292408	NM_213647.1	179	aCg/aTg	5/18	1	2	FACETS	0.888	0.742	1	0.888	0.742	1	CLONAL	1	TRUE	1	0.16	2		769	605	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046703	180046703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	45	580	2	ENST00000261937.6:c.2609G>A	p.Gly870Asp	p.G870D	ENST00000261937	NM_182925.4	870	gGc/gAc	18/30	1	2	FACETS	0.846	0.709	0.997	0.846	0.709	0.997	CLONAL	1	TRUE	1	0.16	2		582	665	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911072	29911072	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	43	670	1	ENST00000376809.5:c.371G>A	p.Gly124Asp	p.G124D	ENST00000376809	NM_002116.7	124	gGc/gAc	3/8	1	2	FACETS	0.708	0.591	0.839	0.708	0.591	0.839	SUBCLONAL	1	TRUE	1	0.16	2		671	759	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200266	138200266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	25	426	0	ENST00000237289.4:c.1684C>T	p.Arg562Cys	p.R562C	ENST00000237289	NM_001270507.1	562	Cgt/Tgt	7/9	1	2	FACETS	0.661	0.52	0.824	0.661	0.52	0.824	SUBCLONAL	1	TRUE	1	0.16	2		426	473	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997756	149997756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754664378	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	29	578	0	ENST00000253339.5:c.2711G>A	p.Arg904Gln	p.R904Q	ENST00000253339		904	cGa/cAa	5/7	1	2	FACETS	0.626	0.501	0.769	0.626	0.501	0.769	SUBCLONAL	1	TRUE	1	0.16	2		578	579	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92247520	92247520	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs902137115	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	26	507	1	ENST00000265734.4:c.700G>A	p.Val234Met	p.V234M	ENST00000265734	NM_001259.6	234	Gtg/Atg	7/8	1	2	FACETS	0.658	0.52	0.817	0.658	0.52	0.817	SUBCLONAL	1	TRUE	1	0.16	2		508	494	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970981	21970981	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	45	417	0	ENST00000304494.5:c.377T>C	p.Val126Ala	p.V126A	ENST00000304494	NM_000077.4	126	gTc/gCc	2/3	1	2	FACETS	0.792	0.664	0.934	0.792	0.664	0.934	CLONAL	1	TRUE	1	0.16	2		417	710	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781193	135781193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768985094	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	58	867	2	ENST00000298552.3:c.1772C>T	p.Pro591Leu	p.P591L	ENST00000298552	NM_001162426.1	591	cCg/cTg	15/23	1	2	FACETS	0.992	0.851	1	0.992	0.851	1	CLONAL	1	TRUE	1	0.16	2		869	731	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417332	139417332	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550554578	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	40	300	2	ENST00000277541.6:c.712G>A	p.Asp238Asn	p.D238N	ENST00000277541	NM_017617.3	238	Gac/Aac	4/34	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.16	2		302	482	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106072	8106072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	22	470	0	ENST00000346208.3:c.892C>T	p.Arg298Trp	p.R298W	ENST00000346208		298	Cgg/Tgg	4/6	1	2	FACETS	0.635	0.491	0.803	0.635	0.491	0.803	SUBCLONAL	1	TRUE	1	0.16	2		470	433	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607597	43607597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs545625150	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	64	657	1	ENST00000355710.3:c.1573C>T	p.Arg525Trp	p.R525W	ENST00000355710	NM_020975.4	525	Cgg/Tgg	8/20	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.16	2		658	736	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405658	70405658	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	34	649	0	ENST00000373644.4:c.3172T>A	p.Leu1058Met	p.L1058M	ENST00000373644	NM_030625.2	1058	Ttg/Atg	4/12	1	2	FACETS	0.739	0.603	0.893	0.739	0.603	0.893	SUBCLONAL	1	TRUE	1	0.16	2		649	575	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631132	69631132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782507721	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	53	808	2	ENST00000334134.2:c.280G>A	p.Gly94Arg	p.G94R	ENST00000334134	NM_005247.2	94	Ggg/Agg	2/3	1	2	FACETS	0.941	0.801	1	0.941	0.801	1	CLONAL	1	TRUE	1	0.16	2		810	704	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374462	118374462	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	43	559	0	ENST00000534358.1:c.7855T>C	p.Tyr2619His	p.Y2619H	ENST00000534358	NM_005933.3	2619	Tat/Cat	27/36	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.16	2		559	479	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025614	1025614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200657132	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	57	537	1	ENST00000358495.3:c.761C>T	p.Thr254Met	p.T254M	ENST00000358495	NM_134424.2	254	aCg/aTg	9/12	0.3	2	FACETS	0.783	0.67	0.907			1	CLONAL	1	TRUE	NA	0.16	2		538	910	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443617	49443617	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs727503987	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	39	650	0	ENST00000301067.7:c.3754C>T	p.Arg1252Ter	p.R1252*	ENST00000301067	NM_003482.3	1252	Cga/Tga	11/54	1	2	FACETS	0.724	0.599	0.865	0.724	0.599	0.865	SUBCLONAL	1	TRUE	1	0.16	2		650	673	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202855	133202855	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057517583	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	27	622	0	ENST00000320574.5:c.6379C>T	p.Arg2127Ter	p.R2127*	ENST00000320574	NM_006231.2	2127	Cga/Tga	46/49	0.125825836573404	0	FACETS	0.537	0.426	0.664			1	SUBCLONAL	1	TRUE	0	0.16	0		622	528	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562285	21562285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749940600	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	37	486	0	ENST00000382592.4:c.1634G>A	p.Arg545His	p.R545H	ENST00000382592	NM_014572.2	545	cGt/cAt	4/8	1	2	FACETS	0.661	0.543	0.793	0.661	0.543	0.793	SUBCLONAL	1	TRUE	1	0.16	2		486	700	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954261	32954261	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55933907	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	78	685	0	ENST00000380152.3:c.9235G>A	p.Val3079Ile	p.V3079I	ENST00000380152		3079	Gtt/Att	24/27	1	2	FACETS	0.8	0.704	0.904	1	0.978	1	CLONAL	2	TRUE	1	0.16	2		685	609	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436239	110436239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771355031	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	34	217	0	ENST00000375856.3:c.2162C>T	p.Pro721Leu	p.P721L	ENST00000375856	NM_003749.2	721	cCg/cTg	1/2	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.16	2		217	332	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95579443	95579443	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs878855246	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	40	591	0	ENST00000393063.1:c.2026C>T	p.Arg676Ter	p.R676*	ENST00000393063	NM_030621.3	676	Cga/Tga	13/28	1	2	FACETS	0.864	0.717	1	0.864	0.717	1	CLONAL	1	TRUE	1	0.16	2		591	579	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473648	67473648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223736	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	32	594	0	ENST00000327367.4:c.728G>A	p.Arg243His	p.R243H	ENST00000327367	NM_005902.3	243	cGc/cAc	6/9	1	2	FACETS	0.654	0.529	0.795	0.654	0.529	0.795	SUBCLONAL	1	TRUE	1	0.16	2		594	612	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251018	99251018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	37	560	1	ENST00000268035.6:c.322G>A	p.Gly108Ser	p.G108S	ENST00000268035	NM_000875.3	108	Ggc/Agc	2/21	1	2	FACETS	0.893	0.735	1	0.893	0.735	1	CLONAL	1	TRUE	1	0.16	2		561	518	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347213	347213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767450750	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	51	442	2	ENST00000262320.3:c.1798G>A	p.Val600Met	p.V600M	ENST00000262320	NM_003502.3	600	Gtg/Atg	7/11	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.16	2		444	537	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786718	3786718	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567269945	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	39	785	0	ENST00000262367.5:c.4493G>A	p.Arg1498Gln	p.R1498Q	ENST00000262367	NM_004380.2	1498	cGa/cAa	27/31	1	2	FACETS	0.653	0.539	0.78	0.653	0.539	0.78	SUBCLONAL	1	TRUE	1	0.16	2		785	747	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862107	68862107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501244	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	39	657	0	ENST00000261769.5:c.2195G>A	p.Arg732Gln	p.R732Q	ENST00000261769	NM_004360.3	732	cGg/cAg	14/16	1	2	FACETS	0.841	0.696	1	0.841	0.696	1	CLONAL	1	TRUE	1	0.16	2		657	580	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832330	72832330	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	43	876	0	ENST00000268489.5:c.4251G>C	p.Gln1417His	p.Q1417H	ENST00000268489	NM_006885.3	1417	caG/caC	9/10	1	2	FACETS	0.835	0.697	0.988	0.835	0.697	0.988	CLONAL	1	TRUE	1	0.16	2		876	644	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992964	72992964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561634666	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	44	877	1	ENST00000268489.5:c.1081G>A	p.Gly361Arg	p.G361R	ENST00000268489	NM_006885.3	361	Gga/Aga	2/10	1	2	FACETS	0.69	0.577	0.816	0.69	0.577	0.816	SUBCLONAL	1	TRUE	1	0.16	2		878	797	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924303	11924303	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs940014479	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	16	89	0	ENST00000353533.5:c.100G>A	p.Val34Ile	p.V34I	ENST00000353533	NM_003010.3	34	Gtc/Atc	1/11	1	2	FACETS	0.917	0.679	1	0.917	0.679	1	CLONAL	1	TRUE	1	0.16	2		89	218	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016670	12016670	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	28	532	0	ENST00000353533.5:c.806A>G	p.Tyr269Cys	p.Y269C	ENST00000353533	NM_003010.3	269	tAc/tGc	7/11	1	2	FACETS	0.738	0.589	0.909	0.738	0.589	0.909	CLONAL	1	TRUE	1	0.16	2		532	474	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913471	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	33	609	0	ENST00000269571.5:c.2329G>A	p.Val777Met	p.V777M	ENST00000269571		777	Gtg/Atg	20/27	1	2	FACETS	0.674	0.548	0.817	0.674	0.548	0.817	SUBCLONAL	1	TRUE	1	0.16	2		609	612	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453322	40453322	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs753487488	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	40	1070	1	ENST00000345506.4:c.1019A>G	p.Gln340Arg	p.Q340R	ENST00000345506	NM_003152.3	340	cAg/cGg	10/20	1	2	FACETS	0.635	0.525	0.757	0.635	0.525	0.757	SUBCLONAL	1	TRUE	1	0.16	2		1071	788	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234435	41234435	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80357354	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	31	670	0	ENST00000357654.3:c.4343G>A	p.Ser1448Asn	p.S1448N	ENST00000357654	NM_007294.3	1448	aGc/aAc	12/23	1	2	FACETS	0.65	0.524	0.793	0.65	0.524	0.793	SUBCLONAL	1	TRUE	1	0.16	2		670	596	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117932	70117932	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	60	399	0	ENST00000245479.2:c.400G>T	p.Glu134Ter	p.E134*	ENST00000245479	NM_000346.3	134	Gag/Tag	1/3	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.16	2		399	550	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226926	2226926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375062102	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	21	186	0	ENST00000398665.3:c.4406C>T	p.Pro1469Leu	p.P1469L	ENST00000398665	NM_032482.2	1469	cCg/cTg	27/28	1	2	FACETS	0.628	0.483	0.798	0.628	0.483	0.798	SUBCLONAL	1	TRUE	1	0.16	2		186	418	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229645	5229645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	11	47	0	ENST00000357368.4:c.2206G>A	p.Ala736Thr	p.A736T	ENST00000357368	NM_002850.3	736	Gcc/Acc	15/38	1	2	FACETS	1	0.831	1	1	0.831	1	CLONAL	1	TRUE	1	0.16	2		47	103	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597450	10597450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200652594	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	45	667	0	ENST00000171111.5:c.1753G>A	p.Asp585Asn	p.D585N	ENST00000171111	NM_203500.1	585	Gac/Aac	6/6	1	2	FACETS	0.845	0.708	0.996	0.845	0.708	0.996	CLONAL	1	TRUE	1	0.16	2		667	666	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138624	11138624	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1057521113	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	30	508	0	ENST00000358026.2:c.3380A>G	p.Asp1127Gly	p.D1127G	ENST00000358026	NM_001128849.1	1127	gAt/gGt	24/36	1	2	FACETS	0.716	0.575	0.875	0.716	0.575	0.875	SUBCLONAL	1	TRUE	1	0.16	2		508	524	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906367	50906367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140539427	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	45	682	4	ENST00000440232.2:c.1028G>A	p.Arg343His	p.R343H	ENST00000440232	NM_002691.3	343	cGc/cAc	9/27	1	2	FACETS	0.731	0.613	0.863	0.731	0.613	0.863	SUBCLONAL	1	TRUE	1	0.16	2		686	769	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385183	41385183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1423243089	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	32	665	0	ENST00000373198.4:c.778C>T	p.Arg260Trp	p.R260W	ENST00000373198	NM_133170.3	260	Cgg/Tgg	6/32	0.202711619238885	0	FACETS	0.612	0.496	0.744			1	SUBCLONAL	1	TRUE	0	0.16	0		665	549	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145549	24145549	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	31	677	0	ENST00000263121.7:c.568C>T	p.Arg190Trp	p.R190W	ENST00000263121	NM_003073.3	190	Cgg/Tgg	5/9	1	2	FACETS	0.655	0.528	0.799	0.655	0.528	0.799	SUBCLONAL	1	TRUE	1	0.16	2		677	592	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351421	70351421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1474736821	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	30	348	0	ENST00000374080.3:c.4069C>T	p.Arg1357Cys	p.R1357C	ENST00000374080		1357	Cgc/Tgc	29/45	1	1	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	TRUE	0	0.16	1		348	326	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197819	123197819	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	42	414	0	ENST00000218089.9:c.1943A>T	p.Asn648Ile	p.N648I	ENST00000218089	NM_001042749.1	648	aAc/aTc	20/35	1	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.16	1		414	412	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027304	48027304	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	39	608	0	ENST00000234420.5:c.2184del	p.Ala729ProfsTer7	p.A729Pfs*7	ENST00000234420	NM_000179.2	728	Aaa/aa	4/10	1	2	FACETS	0.854	0.707	1	0.854	0.707	1	CLONAL	1	TRUE	1	0.16	2		608	571	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0005247-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	93	578	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.417493180927782	2	FACETS	0.887	0.802	0.975	0.887	0.802	0.975	CLONAL	2	TRUE	0	0.417493180927782	2		579	251	SUCCESS
APC	324	MSKCC	GRCh37	5	112175324	112175324	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1211642532	NA	P-0005247-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	100	474	0	ENST00000257430.4:c.4033G>T	p.Glu1345Ter	p.E1345*	ENST00000257430	NM_000038.5	1345	Gaa/Taa	16/16	0.417493180927782	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.417493180927782	3		474	247	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459758	149459758	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1029057991	NA	P-0005247-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	150	605	1	ENST00000286301.3:c.449G>A	p.Arg150His	p.R150H	ENST00000286301	NM_005211.3	150	cGc/cAc	4/22	0.417493180927782	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.417493180927782	3		606	387	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919323	48919323	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005247-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	137	400	0	ENST00000267163.4:c.488G>A	p.Ser163Asn	p.S163N	ENST00000267163	NM_000321.2	163	aGc/aAc	4/27	0.417493180927782	6	FACETS	0.912	0.842	0.983	0.73	0.674	0.787	CLONAL	4	TRUE	1	0.417493180927782	6		400	330	SUCCESS
APC	324	MSKCC	GRCh37	5	112174352	112174353	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0005247-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	28	484	1	ENST00000257430.4:c.3061_3062del	p.Leu1021ArgfsTer7	p.L1021Rfs*7	ENST00000257430	NM_000038.5	1021	CTa/a	16/16	0.417493180927782	3	FACETS	0.702	0.564	0.857	0.351	0.282	0.429	SUBCLONAL	1	TRUE	1	0.417493180927782	3		485	231	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0005253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	33	359	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.394301722231779	3	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	1	0.394301722231779	3		359	83	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527502	29527503	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0005253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	45	485	0	ENST00000356175.3:c.952_953del	p.Glu318LysfsTer11	p.E318Kfs*11	ENST00000356175	NM_000267.3	317	acAGaa/acaa	9/57	0.394301722231779	3	FACETS	1	0.953	1	0.673	0.572	0.781	CLONAL	1	TRUE	1	0.394301722231779	3		485	203	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781597	9781597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748760424	NA	P-0005253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	82	482	2	ENST00000377346.4:c.1907G>A	p.Arg636Gln	p.R636Q	ENST00000377346	NM_005026.3	636	cGg/cAg	15/24	0.341208559044771	3	FACETS	0.996	0.891	1	0.996	0.891	1	CLONAL	2	TRUE	1	0.394301722231779	3		484	250	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426806	212426806	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	17	373	0	ENST00000342788.4:c.2309T>A	p.Leu770Gln	p.L770Q	ENST00000342788	NM_005235.2	770	cTg/cAg	20/28	0.394301722231779	1	FACETS	0.558	0.421	0.718	0.558	0.421	0.718	SUBCLONAL	1	TRUE	0	0.394301722231779	1		373	124	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967228	93967228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1247358846	NA	P-0005253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	21	530	0	ENST00000369303.4:c.2124G>A	p.Met708Ile	p.M708I	ENST00000369303	NM_004440.3	708	atG/atA	12/17	0.370296521711902	1	FACETS	0.489	0.379	0.615	0.489	0.379	0.615	SUBCLONAL	1	TRUE	0	0.394301722231779	1		530	175	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481471	40481471	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	46	653	0	ENST00000264657.5:c.1238T>C	p.Leu413Pro	p.L413P	ENST00000264657	NM_139276.2	413	cTg/cCg	14/24	1	2	FACETS	0.778	0.668	0.893	1	0.967	1	SUBCLONAL	2	TRUE	1	0.394301722231779	2		653	150	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758858	41758858	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746561913	NA	P-0005253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	50	481	0	ENST00000301178.4:c.1912G>A	p.Gly638Arg	p.G638R	ENST00000301178	NM_021913.4	638	Ggg/Agg	16/20	0.394301722231779	4	FACETS	1	0.904	1	1	0.904	1	CLONAL	2	TRUE	2	0.394301722231779	4		481	167	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051610	30051610	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	17	625	0	ENST00000338641.4:c.544G>C	p.Glu182Gln	p.E182Q	ENST00000338641	NM_000268.3	182	Gaa/Caa	6/16	0.394301722231779	4	FACETS	0.497	0.371	0.646	0.248	0.185	0.323	SUBCLONAL	1	TRUE	2	0.394301722231779	4		625	242	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240838	53240838	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0005253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	41	484	1	ENST00000375401.3:c.1243-1G>T		p.X415_splice	ENST00000375401	NM_004187.3	415			0.329071362565476	0	FACETS	0.692	0.598	0.787			1	SUBCLONAL	2	TRUE	0	0.394301722231779	0		485	91	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490289	29490292	+	frameshift_variant	Frame_Shift_Del	DEL	GTGA	GTGA	-	novel	NA	P-0005253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	47	557	1	ENST00000356175.3:c.374_377del	p.Arg125GlnfsTer39	p.R125Qfs*39	ENST00000356175	NM_000267.3	125	cGTGAa/ca	4/57	0.394301722231779	3	FACETS	0.788	0.675	0.909	0.788	0.675	0.909	CLONAL	2	TRUE	1	0.394301722231779	3		558	181	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872935	35872951	+	frameshift_variant	Frame_Shift_Del	DEL	TCCCTTCACCTGGCGGA	TCCCTTCACCTGGCGGA	-	novel	NA	P-0005253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	65	658	0	ENST00000216797.5:c.281_297del	p.Ile94ArgfsTer29	p.I94Rfs*29	ENST00000216797	NM_020529.2	94	aTCCGCCAGGTGAAGGGA/a	2/6	0.394301722231779	4	FACETS	0.95	0.834	1	0.95	0.834	1	CLONAL	2	TRUE	2	0.394301722231779	4		658	242	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829109	72829110	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0005253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	25	441	1	ENST00000268489.5:c.7471_7472del	p.Gln2491ValfsTer42	p.Q2491Vfs*42	ENST00000268489	NM_006885.3	2491	CAg/g	9/10	0.394301722231779	3	FACETS	0.999	0.796	1	0.499	0.398	0.613	CLONAL	1	TRUE	1	0.394301722231779	3		442	152	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578505	7578510	+	inframe_deletion	In_Frame_Del	DEL	GGGCAG	GGGCAG	-	novel	NA	P-0005253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	92	416	0	ENST00000269305.4:c.420_425del	p.Cys141_Pro142del	p.C141_P142del	ENST00000269305	NM_001126112.2	140	acCTGCCCt/act	5/11	0.382049063783827	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	0	0.394301722231779	2		416	218	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591104	67591115	+	inframe_deletion	In_Frame_Del	DEL	TTAAACCAGACC	TTAAACCAGACC	-	novel	NA	P-0005253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	21	417	0	ENST00000274335.5:c.1700_1711del	p.Lys567_Leu570del	p.K567_L570del	ENST00000274335		566	aTTAAACCAGACCtt/att	12/15	1	2	FACETS	0.783	0.61	0.98	0.783	0.61	0.98	CLONAL	1	TRUE	1	0.394301722231779	2		417	136	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252994	36252995	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0005273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	37	413	0	ENST00000300305.3:c.367dup	p.Asp123GlyfsTer15	p.D123Gfs*15	ENST00000300305		123	gat/gGat	4/8	1	2	FACETS	0.745	0.613	0.894	0.745	0.613	0.894	SUBCLONAL	1	TRUE	1	0.17	2		413	584	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0005277-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	32	454	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		454	385	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641706	12641706	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005277-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	83	436	1	ENST00000251849.4:c.935T>A	p.Val312Glu	p.V312E	ENST00000251849	NM_002880.3	312	gTg/gAg	9/17	0.215336309651467	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		437	843	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144879	47144879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005277-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	108	475	0	ENST00000409792.3:c.4874G>A	p.Arg1625His	p.R1625H	ENST00000409792	NM_014159.6	1625	cGt/cAt	7/21	0.215336309651467	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		475	792	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909634	76909634	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005277-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	83	765	1	ENST00000373344.5:c.4271A>G	p.Lys1424Arg	p.K1424R	ENST00000373344	NM_000489.3	1424	aAa/aGa	14/35	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		766	1178	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	199	510	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.229162093166689	3	FACETS	0.773	0.717	0.83	0.773	0.717	0.83	SUBCLONAL	2	TRUE	1	0.374088043683015	3		510	817	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0005296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	316	759	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.304268256327205	2	FACETS	0.846	0.799	0.893	0.846	0.799	0.893	CLONAL	2	TRUE	0	0.374088043683015	2		759	999	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783259	9783259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005301-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	118	703	3	ENST00000377346.4:c.2503G>A	p.Ala835Thr	p.A835T	ENST00000377346	NM_005026.3	835	Gcc/Acc	20/24	1	2	FACETS	0.456	0.412	0.501	0.456	0.412	0.501	SUBCLONAL	1	TRUE	1	0.891489607012189	2		706	581	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938229	76938230	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005301-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	272	528	1	ENST00000373344.5:c.2518dup	p.Arg840LysfsTer9	p.R840Kfs*9	ENST00000373344	NM_000489.3	840	aga/aAga	9/35	0.395140191922545	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.891489607012189	0		529	710	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407508	139407508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005301-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	131	710	0	ENST00000277541.6:c.2432C>T	p.Ala811Val	p.A811V	ENST00000277541	NM_017617.3	811	gCc/gTc	15/34	0.332491146785939	1	FACETS	0.285	0.26	0.312	0.285	0.26	0.312	INDETERMINATE	1	TRUE	0	0.891489607012189	1		710	571	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942661	48942661	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0005301-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	462	420	0	ENST00000267163.4:c.1050-2A>C		p.X350_splice	ENST00000267163	NM_000321.2	350			0.891489607012189	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.891489607012189	1		420	519	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272336	15272337	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs771517374	NA	P-0005301-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	73	383	1	ENST00000263388.2:c.6102dup	p.Gly2035ArgfsTer60	p.G2035Rfs*60	ENST00000263388	NM_000435.2	2034	-/C	33/33	0.332491146785939	1	FACETS	0.276	0.243	0.311	0.276	0.243	0.311	INDETERMINATE	1	TRUE	0	0.891489607012189	1		384	329	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0005311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	82	338	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	1	0.926	1			1	INDETERMINATE	1	TRUE	NA	0.371399972539115	2		339	417	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0005311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	130	278	3	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.371399972539115	2	FACETS	0.799	0.731	0.87	0.799	0.731	0.87	SUBCLONAL	2	TRUE	0	0.371399972539115	2		281	438	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247748	59247748	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	novel	NA	P-0005311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	153	317	0	ENST00000371222.2:c.995G>C	p.Ter332SerextTer7	p.*332Sext*7	ENST00000371222	NM_002228.3	332	tGa/tCa	1/1	0.204737747752847	3	FACETS	1	0.986	1	0.696	0.638	0.756	INDETERMINATE	1	TRUE	1	0.371399972539115	3		317	702	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713812	30713812	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	163	225	0	ENST00000295754.5:c.1137C>A	p.Asp379Glu	p.D379E	ENST00000295754	NM_003242.5	379	gaC/gaA	4/7	0.336603516718131	2	FACETS	0.986	0.914	1	0.986	0.914	1	CLONAL	2	TRUE	0	0.371399972539115	2		225	445	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739909	41739909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	102	329	0	ENST00000242208.4:c.64C>T	p.Pro22Ser	p.P22S	ENST00000242208	NM_002192.2	22	Ccc/Tcc	2/3	1	2	FACETS	0.836	0.749	0.929	0.836	0.749	0.929	CLONAL	1	TRUE	1	0.371399972539115	2		329	657	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92354984	92354984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	71	281	0	ENST00000265734.4:c.493G>A	p.Gly165Ser	p.G165S	ENST00000265734	NM_001259.6	165	Ggc/Agc	4/8	1	2	FACETS	0.859	0.752	0.973	0.859	0.752	0.973	CLONAL	1	TRUE	1	0.371399972539115	2		281	445	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243756	41243756	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	59	322	0	ENST00000357654.3:c.3792G>T	p.Lys1264Asn	p.K1264N	ENST00000357654	NM_007294.3	1264	aaG/aaT	10/23	0.371399972539115	2	FACETS	0.762	0.658	0.875	0.381	0.329	0.438	SUBCLONAL	1	TRUE	0	0.371399972539115	2		322	417	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650052	206650053	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	83	285	0	ENST00000367120.3:c.575dup	p.Pro193AlafsTer112	p.P193Afs*112	ENST00000367120	NM_014002.3	191	cga/cgAa	7/22	1	2	FACETS	0.982	0.871	1	0.982	0.871	1	CLONAL	1	TRUE	1	0.371399972539115	2		285	455	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120115	70120115	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	37	33	2	ENST00000245479.2:c.1121del	p.Pro374ArgfsTer9	p.P374Rfs*9	ENST00000245479	NM_000346.3	373	Ccc/cc	3/3	0.371399972539115	2	FACETS	0.963	0.835	1	1	0.963	1	CLONAL	3	TRUE	0	0.371399972539115	2		35	69	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0005327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	314	283	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.337604143313606	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.339766657616259	2		283	859	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0005327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	317	500	0	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	0.337288737798498	2	FACETS	0.97	0.917	1	0.97	0.917	1	CLONAL	2	TRUE	0	0.339766657616259	2		500	962	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154890	2154890	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1248	244	560	0	ENST00000434045.2:c.331C>A	p.Pro111Thr	p.P111T	ENST00000434045	NM_001127598.1	111	Ccc/Acc	4/5	0.207283056708061	2	FACETS	0.963	0.897	1	0.481	0.448	0.516	CLONAL	1	TRUE	0	0.339766657616259	2		560	1492	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911235	32911235	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1859	217	951	0	ENST00000380152.3:c.2743A>C	p.Thr915Pro	p.T915P	ENST00000380152		915	Act/Cct	11/27	0.236746822188951	4	FACETS	0.824	0.763	0.889	0.412	0.381	0.445	CLONAL	1	TRUE	2	0.339766657616259	4		951	2076	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400717	56400717	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	520	910	1	ENST00000348428.3:c.1311A>T	p.Glu437Asp	p.E437D	ENST00000348428	NM_006785.3	437	gaA/gaT	11/17	0.337604143313606	2	FACETS	0.96	0.919	1	0.96	0.919	1	CLONAL	2	TRUE	0	0.339766657616259	2		911	1594	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265897	41266218	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	In_Frame_Del	DEL	GTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCA	GTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCA	-	novel	NA	P-0005327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	122	50	0	ENST00000349496.5:c.14-117_218del		p.A5_Q72del	ENST00000349496	NM_001904.3	5		3/15	0.339766657616259	4	FACETS	0.929	0.885	0.968	1	0.993	1	CLONAL	7	TRUE	1	0.339766657616259	4		50	148	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	73	192	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.989	0.887	1	0.989	0.887	1	CLONAL	1	TRUE	1	0.878881972542473	2		192	168	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982751	90982751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554564023	NA	P-0005334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	286	379	0	ENST00000265433.3:c.737G>A	p.Gly246Asp	p.G246D	ENST00000265433	NM_002485.4	246	gGt/gAt	7/16	1	2	FACETS	0.889	0.841	0.938	0.889	0.841	0.938	CLONAL	1	TRUE	1	0.878881972542473	2		379	732	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692792	89692792	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs779530981	NA	P-0005334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	184	275	0	ENST00000371953.3:c.276C>A	p.Asp92Glu	p.D92E	ENST00000371953	NM_000314.4	92	gaC/gaA	5/9	0.878881972542473	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.878881972542473	1		275	215	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425086	49425086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761717148	NA	P-0005334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	419	696	0	ENST00000301067.7:c.13402C>T	p.Arg4468Trp	p.R4468W	ENST00000301067	NM_003482.3	4468	Cgg/Tgg	39/54	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.878881972542473	2		696	844	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252919	36252919	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	337	542	0	ENST00000300305.3:c.443C>T	p.Thr148Ile	p.T148I	ENST00000300305		148	aCc/aTc	4/8	1	2	FACETS	0.974	0.927	1	0.974	0.927	1	CLONAL	1	TRUE	1	0.878881972542473	2		542	787	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0005337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	194	352	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.497733499149198	5	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.497733499149198	5		352	1170	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0005337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	308	573	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.497733499149198	5	FACETS	0.963	0.908	1			1	CLONAL	2	TRUE	NA	0.497733499149198	5		573	1122	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65312335	65312335	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	165	326	0	ENST00000342505.4:c.1984G>C	p.Glu662Gln	p.E662Q	ENST00000342505	NM_002227.2	662	Gag/Cag	14/25	0.497733499149198	5	FACETS	1	0.975	1	0.385	0.353	0.418	CLONAL	1	TRUE	2	0.497733499149198	5		326	1003	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39593419	39593419	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	107	217	0	ENST00000262039.4:c.1184A>G	p.Tyr395Cys	p.Y395C	ENST00000262039	NM_002647.2	395	tAc/tGc	11/25	0.499736169636624	3	FACETS	0.85	0.763	0.941	0.425	0.381	0.471	CLONAL	1	TRUE	1	0.497733499149198	3		217	632	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578467	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCGGACGCGGGT	GCGCGGACGCGGGT	-	novel	NA	P-0005337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	127	275	0	ENST00000269305.4:c.463_476del	p.Thr155HisfsTer21	p.T155Hfs*21	ENST00000269305	NM_001126112.2	155	ACCCGCGTCCGCGCc/c	5/11	0.438990951231927	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.497733499149198	1		275	353	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878076	48878077	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0005337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	38	76	1	ENST00000267163.4:c.30dup	p.Ala11ArgfsTer20	p.A11Rfs*20	ENST00000267163	NM_000321.2	10	gcc/gCcc	1/27	0.366238877632408	1	FACETS	0.856	0.722	0.999	0.856	0.722	0.999	CLONAL	1	TRUE	0	0.497733499149198	1		77	134	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044753	47044754	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	302	139	0	ENST00000377604.3:c.2154dup	p.Asp719Ter	p.D719*	ENST00000377604	NM_001204468.1	718	agt/agTt	19/24	0.331235479298948	3	FACETS	1	0.979	1			1	CLONAL	3	TRUE	NA	0.497733499149198	3		139	487	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740620	145740620	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1230	423	362	0	ENST00000428558.2:c.1397C>G	p.Pro466Arg	p.P466R	ENST00000428558	NM_004260.3	466	cCg/cGg	8/22	0.881268615631872	6	FACETS	0.802	0.762	0.843			1	CLONAL	2	TRUE	NA	0.881268615631872	6		362	1653	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4097290	4097290	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730880512	NA	P-0005344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	260	382	0	ENST00000262948.5:c.971A>G	p.Tyr324Cys	p.Y324C	ENST00000262948	NM_030662.3	324	tAt/tGt	8/11	1	2	FACETS	0.997	0.942	1	0.997	0.942	1	CLONAL	1	TRUE	1	0.881268615631872	2		382	592	SUCCESS
AR	367	MSKCC	GRCh37	X	66937371	66937371	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	187	229	0	ENST00000374690.3:c.2225G>T	p.Trp742Leu	p.W742L	ENST00000374690	NM_000044.3	742	tGg/tTg	5/8	1	1	FACETS	0.563	0.526	0.599	0.563	0.526	0.599	SUBCLONAL	1	TRUE	0	0.881268615631872	1		229	422	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183873	10183873	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0005354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	63	98	0	ENST00000256474.2:c.340+2T>A		p.X114_splice	ENST00000256474	NM_000551.3	114			0.466027009348333	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.500537814021062	1		98	181	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440383	52440383	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0005354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	104	226	0	ENST00000460680.1:c.669C>G	p.Tyr223Ter	p.Y223*	ENST00000460680	NM_004656.3	223	taC/taG	9/17	0.466027009348333	1	FACETS	0.983	0.891	1	0.983	0.891	1	CLONAL	1	TRUE	0	0.500537814021062	1		226	317	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522400	157522400	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	112	298	0	ENST00000346085.5:c.4672T>G	p.Ser1558Ala	p.S1558A	ENST00000346085	NM_020732.3	1558	Tcc/Gcc	18/20	0.118599171246289	4	FACETS	1	0.983	1	0.717	0.649	0.789	INDETERMINATE	1	TRUE	2	0.500537814021062	4		298	468	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359403	118359403	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	127	357	0	ENST00000534358.1:c.4407C>G	p.Asp1469Glu	p.D1469E	ENST00000534358	NM_005933.3	1469	gaC/gaG	11/36	1	2	FACETS	0.872	0.793	0.955	0.872	0.793	0.955	CLONAL	1	TRUE	1	0.500537814021062	2		357	582	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792753	33792753	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs867463920	NA	P-0005354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	15	41	0	ENST00000498907.2:c.568T>C	p.Ser190Pro	p.S190P	ENST00000498907	NM_004364.3	190	Tcg/Ccg	1/1	1	2	FACETS	0.419	0.308	0.55	0.419	0.308	0.55	SUBCLONAL	1	TRUE	1	0.500537814021062	2		41	143	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76931778	76931778	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	120	277	0	ENST00000373344.5:c.3752C>G	p.Ser1251Cys	p.S1251C	ENST00000373344	NM_000489.3	1251	tCt/tGt	10/35	1	1	FACETS	0.832	0.772	0.892	1	0.99	1	CLONAL	2	TRUE	0	0.500537814021062	1		277	216	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37665992	37665992	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2683	698	340	0	ENST00000447079.4:c.2644C>T	p.Arg882Trp	p.R882W	ENST00000447079	NM_015083.1	882	Cgg/Tgg	7/14	0.860317463478316	4	FACETS	0.888	0.853	0.924			1	CLONAL	1	FALSE	NA	0.869094160336316	4		340	3381	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931463	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622007	NA	P-0005374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1309	1193	235	0	ENST00000374690.3:c.2105T>A	p.Leu702His	p.L702H	ENST00000374690	NM_000044.3	702	cTc/cAc	4/8	0.839797363773728	2	FACETS	1	0.996	1			1	CLONAL	1	FALSE	NA	0.869094160336316	2		235	2502	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401520	401520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751008894	NA	P-0005374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1460	263	322	0	ENST00000380956.4:c.842C>T	p.Thr281Met	p.T281M	ENST00000380956	NM_001195286.1	281	aCg/aTg	7/9	NA	2	FACETS	0.351	0.328	0.376			1	INDETERMINATE	1	FALSE	NA	0.869094160336316	2		322	1723	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650653	67650653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2051	255	360	0	ENST00000264010.4:c.958C>T	p.Arg320Cys	p.R320C	ENST00000264010	NM_006565.3	320	Cgt/Tgt	5/12	0.552688606701536	3	FACETS	0.365	0.34	0.391			1	SUBCLONAL	1	FALSE	NA	0.869094160336316	3		360	2306	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646980	37646981	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	2321	364	0	ENST00000447079.4:c.2103dup	p.Pro702ThrfsTer27	p.P702Tfs*27	ENST00000447079	NM_015083.1	701	aga/agAa	3/14	0.860317463478316	4	FACETS	0.992	0.978	1			1	CLONAL	3	FALSE	NA	0.869094160336316	4		364	3354	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347204	347204	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	114	336	0	ENST00000262320.3:c.1807A>C	p.Lys603Gln	p.K603Q	ENST00000262320	NM_003502.3	603	Aaa/Caa	7/11	1	2	FACETS	0.887	0.801	0.978	0.887	0.801	0.978	CLONAL	1	TRUE	1	0.434114780074064	2		336	592	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457227	25457227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	185	336	0	ENST00000264709.3:c.2660G>A	p.Arg887Lys	p.R887K	ENST00000264709	NM_175629.2	887	aGa/aAa	23/23	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.434114780074064	2		336	829	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652562	212652770	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATGATTTCCAAAAGAGAATTAGCTAGAAGTAAAAGGTTGATCAGCCATTTGTTCTGCCATATATAACTGAACATTTCAATGAATGCAATCAAAGTTCAAAATATTAGTAATGACATAATAAGCATAACTCATTCATCGCCACATAGGGTAGAACATTTTGAGAAATTAAAAAGAATAATTCTACTTACATCCTGAACTACCATTTGTTG	ATGATTTCCAAAAGAGAATTAGCTAGAAGTAAAAGGTTGATCAGCCATTTGTTCTGCCATATATAACTGAACATTTCAATGAATGCAATCAAAGTTCAAAATATTAGTAATGACATAATAAGCATAACTCATTCATCGCCACATAGGGTAGAACATTTTGAGAAATTAAAAAGAATAATTCTACTTACATCCTGAACTACCATTTGTTG	-	novel	NA	P-0005377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	143	8	0	ENST00000342788.4:c.536_556+188del		p.X179_splice	ENST00000342788	NM_005235.2	179		4/28	1	2	FACETS	1	0.985	1	1	0.995	1	CLONAL	4	TRUE	1	0.434114780074064	2		8	158	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115875	8115880	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCTT	GCCCTT	C	novel	NA	P-0005377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	207	409	0	ENST00000346208.3:c.1221_1226delinsC	p.Pro408GlnfsTer97	p.P408Qfs*97	ENST00000346208		407	tcGCCCTTc/tcCc	6/6	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.434114780074064	2		409	851	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974792	21974792	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs141798398	NA	P-0005380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	36	184	0	ENST00000304494.5:c.35C>A	p.Ser12Ter	p.S12*	ENST00000304494	NM_000077.4	12	tCg/tAg	1/3	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.265657989879424	2		184	213	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220370	1220370	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0005380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	69	452	0	ENST00000326873.7:c.465-2A>T		p.X155_splice	ENST00000326873	NM_000455.4	155			0.265657989879424	1	FACETS	0.858	0.748	0.976	0.858	0.748	0.976	CLONAL	1	TRUE	0	0.265657989879424	1		452	525	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783241	9783241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	53	411	1	ENST00000377346.4:c.2485C>T	p.Leu829Phe	p.L829F	ENST00000377346	NM_005026.3	829	Ctc/Ttc	20/24	1	2	FACETS	0.853	0.728	0.989	0.853	0.728	0.989	CLONAL	1	TRUE	1	0.265657989879424	2		412	468	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724526	162724526	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1212499835	NA	P-0005380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	46	474	0	ENST00000367921.3:c.298G>T	p.Val100Leu	p.V100L	ENST00000367921	NM_006182.2	100	Gtg/Ttg	5/18	NA	2	FACETS	0.675	0.568	0.793			1	INDETERMINATE	1	TRUE	NA	0.265657989879424	2		474	513	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801234	1801234	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	54	342	1	ENST00000260795.2:c.363C>A	p.Phe121Leu	p.F121L	ENST00000260795		121	ttC/ttA	2/17	NA	2	FACETS	0.935	0.8	1			1	INDETERMINATE	1	TRUE	NA	0.265657989879424	2		343	435	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803660	1803660	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	65	559	1	ENST00000260795.2:c.838G>A	p.Asp280Asn	p.D280N	ENST00000260795		280	Gac/Aac	6/17	NA	2	FACETS	0.801	0.694	0.916			1	INDETERMINATE	1	TRUE	NA	0.265657989879424	2		560	611	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97897676	97897676	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	71	533	0	ENST00000289081.3:c.795G>C	p.Glu265Asp	p.E265D	ENST00000289081	NM_000136.2	265	gaG/gaC	8/15	1	2	FACETS	0.988	0.864	1	0.988	0.864	1	CLONAL	1	TRUE	1	0.265657989879424	2		533	541	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569715	95569715	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	40	355	0	ENST00000393063.1:c.4018G>C	p.Glu1340Gln	p.E1340Q	ENST00000393063	NM_030621.3	1340	Gag/Cag	22/28	0.140149046823804	3	FACETS	0.702	0.583	0.834	0.351	0.291	0.417	INDETERMINATE	1	TRUE	1	0.265657989879424	3		355	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577157	7577157	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0005380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	53	507	0	ENST00000269305.4:c.783-2A>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.206673336210647	1	FACETS	0.872	0.745	1	0.872	0.745	1	CLONAL	1	TRUE	0	0.265657989879424	1		507	397	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602335	10602335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	56	408	1	ENST00000171111.5:c.1243C>T	p.Arg415Cys	p.R415C	ENST00000171111	NM_203500.1	415	Cgc/Tgc	3/6	0.265657989879424	1	FACETS	0.823	0.707	0.95	0.823	0.707	0.95	CLONAL	1	TRUE	0	0.265657989879424	1		409	444	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795021	42795021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1275919232	NA	P-0005380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	76	469	1	ENST00000575354.2:c.2101C>T	p.Pro701Ser	p.P701S	ENST00000575354	NM_015125.3	701	Cca/Tca	10/20	1	2	FACETS	0.943	0.827	1	0.943	0.827	1	CLONAL	1	TRUE	1	0.265657989879424	2		470	607	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005390-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	94	510	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	0.205738737152988	2		510	770	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722905	49722906	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0005390-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	25	126	1	ENST00000449682.2:c.1420_1421dup	p.Asp475GlnfsTer52	p.D475Qfs*52	ENST00000449682	NM_020998.3	474	cca/ccCCa	12/18	1	2	FACETS	0.781	0.617	0.971	0.781	0.617	0.971	CLONAL	1	TRUE	1	0.205738737152988	2		127	311	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs864622237	NA	P-0005390-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	101	385	1	ENST00000269305.4:c.700T>A	p.Tyr234Asn	p.Y234N	ENST00000269305	NM_001126112.2	234	Tac/Aac	7/11	0.164700936183235	1	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	0	0.205738737152988	1		386	870	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0005393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1162	436	529	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.384692661709162	5	FACETS	1	0.989	1	0.746	0.71	0.782	CLONAL	2	TRUE	2	0.384692661709162	5		529	1598	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555525857	NA	P-0005393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	329	537	0	ENST00000269305.4:c.596G>A	p.Gly199Glu	p.G199E	ENST00000269305	NM_001126112.2	199	gGa/gAa	6/11	0.304714346146546	2	FACETS	0.903	0.856	0.951	0.903	0.856	0.951	CLONAL	2	TRUE	0	0.384692661709162	2		537	947	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996231	73996231	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	67	186	0	ENST00000318443.5:c.965A>T	p.Asn322Ile	p.N322I	ENST00000318443	NM_001024736.1	322	aAt/aTt	5/10	1	2	FACETS	0.856	0.747	0.973	0.856	0.747	0.973	CLONAL	1	TRUE	1	0.384692661709162	2		186	407	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678391	88678391	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	246	638	2	ENST00000360948.2:c.1145A>T	p.Asn382Ile	p.N382I	ENST00000360948	NM_001012338.2	382	aAc/aTc	9/19	1	2	FACETS	0.979	0.914	1	0.979	0.914	1	CLONAL	1	TRUE	1	0.384692661709162	2		640	1306	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868687	56868687	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1761	115	640	0	ENST00000308159.5:c.1779A>T	p.Arg593Ser	p.R593S	ENST00000308159	NM_014669.4	593	agA/agT	16/22	0.371711776974661	3	FACETS	0.38	0.34	0.422	0.19	0.17	0.211	SUBCLONAL	1	TRUE	1	0.384692661709162	3		640	1876	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144018	11144018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749001381	NA	P-0005393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	174	442	0	ENST00000358026.2:c.3599G>A	p.Arg1200His	p.R1200H	ENST00000358026	NM_001128849.1	1200	cGt/cAt	26/36	1	2	FACETS	0.946	0.871	1	0.946	0.871	1	CLONAL	1	TRUE	1	0.384692661709162	2		442	956	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339922	70339922	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1398	185	622	0	ENST00000374080.3:c.455C>A	p.Pro152His	p.P152H	ENST00000374080		152	cCt/cAt	4/45	0.24771054160314	3	FACETS	0.724	0.666	0.785			1	SUBCLONAL	1	TRUE	NA	0.384692661709162	3		622	1583	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70362067	70362067	+	stop_lost	Nonstop_Mutation	SNP	G	G	T	novel	NA	P-0005393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	349	589	0	ENST00000374080.3:c.6533G>T	p.Ter2178LeuextTer18	p.*2178Lext*18	ENST00000374080		2178	tGa/tTa	45/45	0.24771054160314	3	FACETS	1	0.994	1			1	CLONAL	1	TRUE	NA	0.384692661709162	3		589	1458	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023090	31023090	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005409-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	38	332	0	ENST00000375687.4:c.2576del	p.Asn859ThrfsTer8	p.N859Tfs*8	ENST00000375687	NM_015338.5	859	Aac/ac	13/13	1	2	FACETS	0.203	0.167	0.243	0.203	0.167	0.243	SUBCLONAL	1	TRUE	1	0.71245166342974	2		332	525	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0005418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	40	176	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.403	0.334	0.48	0.403	0.334	0.48	SUBCLONAL	1	TRUE	1	0.341928797330829	2		176	581	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11175466	11175466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	28	321	0	ENST00000361445.4:c.7076G>A	p.Gly2359Glu	p.G2359E	ENST00000361445	NM_004958.3	2359	gGg/gAg	51/58	0.11059136875862	0	FACETS	0.245	0.195	0.302			1	INDETERMINATE	1	TRUE	0	0.341928797330829	0		321	440	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907677	111907677	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	219	362	0	ENST00000393256.3:c.451G>C	p.Glu151Gln	p.E151Q	ENST00000393256	NM_006538.4	151	Gag/Cag	3/4	1	2	FACETS	0.778	0.725	0.833	1	0.992	1	SUBCLONAL	2	TRUE	1	0.341928797330829	2		362	823	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713568	30713568	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs751587466	NA	P-0005418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	97	213	0	ENST00000295754.5:c.893A>G	p.Asn298Ser	p.N298S	ENST00000295754	NM_003242.5	298	aAt/aGt	4/7	0.342414270541699	2	FACETS	1	0.981	1	0.729	0.655	0.807	CLONAL	1	TRUE	0	0.341928797330829	2		213	389	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477160	67477160	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs967072552	NA	P-0005418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	87	275	1	ENST00000327367.4:c.967C>T	p.Arg323Cys	p.R323C	ENST00000327367	NM_005902.3	323	Cgc/Tgc	7/9	0.11059136875862	0	FACETS	1	0.953	1			1	INDETERMINATE	1	TRUE	0	0.341928797330829	0		276	300	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575152	48575152	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	30	278	0	ENST00000342988.3:c.346C>T	p.Gln116Ter	p.Q116*	ENST00000342988	NM_005359.5	116	Cag/Tag	3/12	0.342414270541699	1	FACETS	0.271	0.218	0.332	0.271	0.218	0.332	SUBCLONAL	1	TRUE	0	0.341928797330829	1		278	536	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15378244	15378244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	109	377	1	ENST00000263377.2:c.542G>A	p.Arg181His	p.R181H	ENST00000263377	NM_058243.2	181	cGt/cAt	4/20	0.230405410851705	0	FACETS	0.889	0.803	0.979			1	CLONAL	1	TRUE	0	0.341928797330829	0		378	472	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949966	44949966	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0005418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	49	260	0	ENST00000377967.4:c.3737-2A>C		p.X1246_splice	ENST00000377967	NM_021140.2	1246			0.342414270541699	1	FACETS	0.427	0.361	0.499	0.427	0.361	0.499	SUBCLONAL	1	TRUE	0	0.341928797330829	1		260	557	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352771	70352771	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	129	474	0	ENST00000374080.3:c.4492G>T	p.Gly1498Ter	p.G1498*	ENST00000374080		1498	Gga/Tga	32/45	0.342414270541699	1	FACETS	0.951	0.874	1	1	0.991	1	CLONAL	2	TRUE	0	0.341928797330829	1		474	329	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591114	67591149	+	inframe_deletion	In_Frame_Del	DEL	CCTTATCCAGCTGAGAAAGACGAGAGACCAATACTT	CCTTATCCAGCTGAGAAAGACGAGAGACCAATACTT	-	novel	NA	P-0005418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	197	211	0	ENST00000274335.5:c.1707_1742del	p.Asp569_Leu581delinsGlu	p.D569_L581delinsE	ENST00000274335		569	gaCCTTATCCAGCTGAGAAAGACGAGAGACCAATACTTg/gag	12/15	0.341928797330829	3	FACETS	0.914	0.855	0.974	0.914	0.855	0.974	CLONAL	3	TRUE	0	0.341928797330829	3		211	492	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056542	26056542	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005425-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	48	174	0	ENST00000343677.2:c.115C>A	p.Pro39Thr	p.P39T	ENST00000343677	NM_005319.3	39	Ccg/Acg	1/1	0.789696434783577	9	FACETS	1	0.851	1			1	CLONAL	1	TRUE	NA	0.789696434783577	9		174	455	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278069	15278069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771486133	NA	P-0005425-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	95	608	1	ENST00000263388.2:c.5353C>T	p.Arg1785Cys	p.R1785C	ENST00000263388	NM_000435.2	1785	Cgt/Tgt	29/33	0.682891939417513	5	FACETS	1	0.921	1	0.346	0.308	0.385	CLONAL	1	TRUE	2	0.789696434783577	5		609	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0005435-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	134	646	4	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.705	0.64	0.774	0.705	0.64	0.774	SUBCLONAL	1	TRUE	1	0.375434688535777	2		650	1012	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0005435-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	99	529	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	1	2	FACETS	0.453	0.403	0.506	0.453	0.403	0.506	SUBCLONAL	1	TRUE	1	0.375434688535777	2		529	1165	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404818	404819	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0005441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1458	137	520	0	ENST00000399788.2:c.4375_4376del	p.Leu1459GlyfsTer18	p.L1459Gfs*18	ENST00000399788	NM_001042603.1	1459	CTg/g	26/28	0.3	8	FACETS	1	0.955	1	0.181	0.164	0.2	CLONAL	1	FALSE	2	0.3	8		520	1595	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349214	11349230	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCGCGGGCGCGCGGG	GGCCGCGGGCGCGCGGG	-	novel	NA	P-0005441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	27	47	0	ENST00000332029.2:c.106_122del	p.Pro36ValfsTer75	p.P36Vfs*75	ENST00000332029	NM_003745.1	36	CCCGCGCGCCCGCGGCCg/g	2/2	1	2	FACETS	0.811	0.658	0.978	1	0.946	1	CLONAL	2	FALSE	1	0.3	2		47	111	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627772	37627772	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005445-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	359	787	0	ENST00000447079.4:c.1687C>T	p.Gln563Ter	p.Q563*	ENST00000447079	NM_015083.1	563	Caa/Taa	2/14	1	2	FACETS	0.983	0.932	1	0.983	0.932	1	CLONAL	1	TRUE	1	0.658787600118836	2		787	1109	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618549	37618550	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005445-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	268	564	0	ENST00000447079.4:c.226dup	p.Ile76AsnfsTer4	p.I76Nfs*4	ENST00000447079	NM_015083.1	75	-/A	1/14	1	2	FACETS	0.969	0.911	1	0.969	0.911	1	CLONAL	1	TRUE	1	0.658787600118836	2		564	840	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876964	151876980	+	frameshift_variant	Frame_Shift_Del	DEL	TAGGGTCCACGCTGATC	TAGGGTCCACGCTGATC	-	novel	NA	P-0005445-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	220	561	0	ENST00000262189.6:c.7381_7397del	p.Asp2461SerfsTer3	p.D2461Sfs*3	ENST00000262189	NM_170606.2	2461	GATCAGCGTGGACCCTAt/t	37/59	0.658787600118836	3	FACETS	0.88	0.819	0.943			1	CLONAL	1	TRUE	NA	0.658787600118836	3		561	1009	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15975518	15975518	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764561903	NA	P-0005445-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	232	565	1	ENST00000268712.3:c.3836G>T	p.Arg1279Met	p.R1279M	ENST00000268712	NM_006311.3	1279	aGg/aTg	29/46	1	2	FACETS	0.877	0.82	0.936	0.877	0.82	0.936	CLONAL	1	TRUE	1	0.658787600118836	2		566	803	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724243	52724243	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005445-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	255	569	0	ENST00000322088.6:c.1375C>T	p.Arg459Cys	p.R459C	ENST00000322088	NM_014225.5	459	Cgc/Tgc	12/15	NA	2	FACETS	0.676	0.632	0.721			1	INDETERMINATE	1	TRUE	NA	0.658787600118836	2		569	1146	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	123	747	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.339468584468887	2		747	670	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900984	114900984	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778855667	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	296	802	0	ENST00000543371.1:c.598del	p.Leu200SerfsTer25	p.L200Sfs*25	ENST00000543371	NM_001198531.1	198	caC/ca	6/14	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.339468584468887	2		802	1403	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	288	592	6	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.834	0.785	0.884	1	0.995	1	CLONAL	2	FALSE	1	0.339468584468887	2		598	1017	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	208	668	11	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.339468584468887	2		679	980	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	70	158	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.87	0.769	0.976	1	0.981	1	CLONAL	2	FALSE	1	0.339468584468887	2		159	237	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738411	145738416	+	inframe_deletion	In_Frame_Del	DEL	GGTGCA	GGTGCA	-	rs548804317	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	85	447	0	ENST00000428558.2:c.2569_2574del	p.Cys857_Thr858del	p.C857_T858del	ENST00000428558	NM_004260.3	857	TGCACC/-	16/22	1	2	FACETS	0.909	0.805	1	0.909	0.805	1	CLONAL	1	FALSE	1	0.339468584468887	2		447	551	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	131	325	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.339468584468887	2		325	611	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1369	251	788	1	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.913	0.851	0.977	0.913	0.851	0.977	CLONAL	1	FALSE	1	0.339468584468887	2		789	1620	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287520	33287520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141395832	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	119	367	0	ENST00000374542.5:c.1577G>A	p.Arg526His	p.R526H	ENST00000374542	NM_001141970.1	526	cGc/cAc	6/8	1	2	FACETS	0.851	0.768	0.939	0.851	0.768	0.939	CLONAL	1	FALSE	1	0.339468584468887	2		367	824	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423601	88423601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	111	556	0	ENST00000360948.2:c.2234G>A	p.Arg745Gln	p.R745Q	ENST00000360948	NM_001012338.2	745	cGg/cAg	18/19	0.339468584468887	0	FACETS	0.732	0.66	0.808			1	SUBCLONAL	1	FALSE	0	0.339468584468887	0		556	590	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	145	613	0	ENST00000227507.2:c.859C>T	p.Pro287Ser	p.P287S	ENST00000227507	NM_053056.2	287	Ccc/Tcc	5/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.339468584468887	2		613	699	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088788	27088788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	129	576	0	ENST00000324856.7:c.2402del	p.Gly801ValfsTer32	p.G801Vfs*32	ENST00000324856	NM_006015.4	799	caG/ca	7/20	1	2	FACETS	0.976	0.885	1	0.976	0.885	1	CLONAL	1	FALSE	1	0.339468584468887	2		576	779	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533881	533881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs727503093	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	163	527	1	ENST00000451590.1:c.175G>A	p.Ala59Thr	p.A59T	ENST00000451590	NM_001130442.1	59	Gcc/Acc	3/5	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.339468584468887	2		528	822	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	88	481	1	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	0.338065134950499	0	FACETS	0.624	0.554	0.698			1	SUBCLONAL	1	FALSE	0	0.339468584468887	0		482	549	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007619	45007619	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs111482205	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	113	262	0	ENST00000558401.1:c.68-2A>G		p.X23_splice	ENST00000558401	NM_004048.2	23			0.339468584468887	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	0	0.339468584468887	1		262	478	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157488293	157488293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750810656	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	94	300	0	ENST00000346085.5:c.2999C>T	p.Ala1000Val	p.A1000V	ENST00000346085	NM_020732.3	1000	gCg/gTg	10/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.339468584468887	2		300	434	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217783	2217783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	142	535	0	ENST00000398665.3:c.2557C>T	p.Arg853Cys	p.R853C	ENST00000398665	NM_032482.2	853	Cgc/Tgc	22/28	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.339468584468887	2		535	683	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400902	72400902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1450443698	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	218	814	1	ENST00000357731.5:c.269G>A	p.Arg90Gln	p.R90Q	ENST00000357731	NM_173808.2	90	cGa/cAa	2/7	1	2	FACETS	0.967	0.898	1	0.967	0.898	1	CLONAL	1	FALSE	1	0.339468584468887	2		815	1328	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096504	178096504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1181990251	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	220	563	0	ENST00000397062.3:c.827C>T	p.Thr276Ile	p.T276I	ENST00000397062	NM_006164.4	276	aCa/aTa	5/5	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.339468584468887	2		563	1171	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097298	178097298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376926526	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	168	349	2	ENST00000397062.3:c.416C>T	p.Thr139Met	p.T139M	ENST00000397062	NM_006164.4	139	aCg/aTg	4/5	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.339468584468887	2		351	890	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150022	202150022	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	141	418	0	ENST00000358485.4:c.1463T>C	p.Leu488Pro	p.L488P	ENST00000358485	NM_001080125.1	488	cTg/cCg	8/9	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.339468584468887	2		418	633	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648431	30648431	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763085648	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	134	476	0	ENST00000295754.5:c.56G>A	p.Arg19His	p.R19H	ENST00000295754	NM_003242.5	19	cGt/cAt	1/7	1	2	FACETS	0.944	0.858	1	0.944	0.858	1	CLONAL	1	FALSE	1	0.339468584468887	2		476	836	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71064727	71064727	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	140	455	0	ENST00000318789.4:c.947T>C	p.Val316Ala	p.V316A	ENST00000318789	NM_032682.5	316	gTg/gCg	12/21	1	2	FACETS	0.981	0.893	1	0.981	0.893	1	CLONAL	1	FALSE	1	0.339468584468887	2		455	841	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407527	407527	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs908661692	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	138	517	0	ENST00000380956.4:c.1285G>A	p.Asp429Asn	p.D429N	ENST00000380956	NM_001195286.1	429	Gat/Aat	9/9	NA	2	FACETS	1	0.927	1			1	INDETERMINATE	1	FALSE	NA	0.339468584468887	2		517	797	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778012	27778012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764186127	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1506	292	1138	2	ENST00000369163.2:c.161G>A	p.Arg54His	p.R54H	ENST00000369163	NM_003536.2	54	cGc/cAc	1/1	1	2	FACETS	0.957	0.897	1	0.957	0.897	1	CLONAL	1	FALSE	1	0.339468584468887	2		1140	1798	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738446	145738446	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	83	369	0	ENST00000428558.2:c.2539C>T	p.Gln847Ter	p.Q847*	ENST00000428558	NM_004260.3	847	Cag/Tag	16/22	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	FALSE	1	0.339468584468887	2		369	461	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606365	93606365	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	82	524	0	ENST00000375746.1:c.185A>G	p.His62Arg	p.H62R	ENST00000375746	NM_001174167.1	62	cAc/cGc	2/14	1	2	FACETS	0.942	0.833	1	0.942	0.833	1	CLONAL	1	FALSE	1	0.339468584468887	2		524	513	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639968	93639968	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1480802433	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	115	432	0	ENST00000375746.1:c.1297G>A	p.Val433Met	p.V433M	ENST00000375746	NM_001174167.1	433	Gtg/Atg	10/14	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	FALSE	1	0.339468584468887	2		432	657	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622047	43622047	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1207742610	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	76	373	0	ENST00000355710.3:c.3064A>G	p.Thr1022Ala	p.T1022A	ENST00000355710	NM_020975.4	1022	Act/Gct	19/20	0.339468584468887	1	FACETS	0.812	0.714	0.916	0.812	0.714	0.916	CLONAL	1	FALSE	0	0.339468584468887	1		373	458	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691130	18691130	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	105	436	0	ENST00000266497.5:c.3241T>G	p.Phe1081Val	p.F1081V	ENST00000266497		1081	Ttt/Gtt	23/31	0.339468584468887	1	FACETS	0.715	0.641	0.794	0.715	0.641	0.794	SUBCLONAL	1	FALSE	0	0.339468584468887	1		436	718	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937670	32937670	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	75	221	0	ENST00000380152.3:c.8331G>T	p.Lys2777Asn	p.K2777N	ENST00000380152		2777	aaG/aaT	18/27	0.0905846842835603	3	FACETS	0.845	0.747	0.947	0.845	0.747	0.947	INDETERMINATE	2	FALSE	1	0.339468584468887	3		221	306	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346974	73346974	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	135	273	0	ENST00000377767.4:c.1243C>T	p.His415Tyr	p.H415Y	ENST00000377767	NM_014953.3	415	Cac/Tac	9/21	0.0905846842835603	3	FACETS	1	0.983	1	0.678	0.617	0.742	INDETERMINATE	1	FALSE	1	0.339468584468887	3		273	686	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436713	110436713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	126	452	0	ENST00000375856.3:c.1688C>T	p.Ala563Val	p.A563V	ENST00000375856	NM_003749.2	563	gCg/gTg	1/2	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.339468584468887	2		452	533	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029245	14029245	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	194	561	0	ENST00000311895.7:c.1456A>G	p.Lys486Glu	p.K486E	ENST00000311895	NM_005236.2	486	Aaa/Gaa	8/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.339468584468887	2		561	1012	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315397	30315397	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	149	538	0	ENST00000322652.5:c.1082G>A	p.Trp361Ter	p.W361*	ENST00000322652	NM_015355.2	361	tGg/tAg	10/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.339468584468887	2		538	786	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646866	37646866	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141353560	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	210	570	1	ENST00000447079.4:c.1988G>A	p.Arg663His	p.R663H	ENST00000447079	NM_015083.1	663	cGt/cAt	3/14	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.339468584468887	2		571	1013	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453375	40453375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1434706212	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	230	971	0	ENST00000345506.4:c.1072G>A	p.Gly358Arg	p.G358R	ENST00000345506	NM_003152.3	358	Ggg/Agg	10/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.339468584468887	2		971	1253	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2206734	2206734	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	173	620	0	ENST00000398665.3:c.794G>T	p.Arg265Ile	p.R265I	ENST00000398665	NM_032482.2	265	aGa/aTa	10/28	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	1	0.339468584468887	2		620	994	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214748	5214748	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	68	367	0	ENST00000357368.4:c.4319-1G>T		p.X1440_splice	ENST00000357368	NM_002850.3	1440			0.339468584468887	1	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	FALSE	0	0.339468584468887	1		367	321	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10286283	10286283	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	148	518	2	ENST00000340748.4:c.533G>A	p.Arg178Gln	p.R178Q	ENST00000340748		178	cGg/cAg	6/40	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	1	0.339468584468887	2		520	800	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123673	11123673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	126	483	0	ENST00000358026.2:c.2323G>A	p.Gly775Ser	p.G775S	ENST00000358026	NM_001128849.1	775	Ggc/Agc	16/36	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.339468584468887	2		483	650	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723007	52723007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1170466801	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	149	617	2	ENST00000322088.6:c.1192C>T	p.Arg398Trp	p.R398W	ENST00000322088	NM_014225.5	398	Cgg/Tgg	10/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.339468584468887	2		619	703	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021182	31021182	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201899433	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	142	562	0	ENST00000375687.4:c.1181G>A	p.Arg394His	p.R394H	ENST00000375687	NM_015338.5	394	cGt/cAt	12/13	1	2	FACETS	0.981	0.894	1	0.981	0.894	1	CLONAL	1	FALSE	1	0.339468584468887	2		562	853	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164725	36164725	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	162	597	0	ENST00000300305.3:c.1150C>G	p.Pro384Ala	p.P384A	ENST00000300305		384	Ccc/Gcc	8/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.339468584468887	2		597	762	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514663	44514663	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	125	472	0	ENST00000291552.4:c.493C>T	p.Arg165Ter	p.R165*	ENST00000291552	NM_006758.2	165	Cga/Tga	7/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.339468584468887	2		472	620	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342606	70342606	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	198	317	0	ENST00000374080.3:c.1367T>C	p.Val456Ala	p.V456A	ENST00000374080		456	gTa/gCa	10/45	1	1	FACETS	0.972	0.909	1	1	0.994	1	CLONAL	2	FALSE	0	0.339468584468887	1		317	498	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375194	31375194	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	112	658	0	ENST00000328111.2:c.596del	p.Gly199AlafsTer27	p.G199Afs*27	ENST00000328111	NM_006892.3	197	caG/ca	6/23	1	2	FACETS	0.828	0.745	0.916	0.828	0.745	0.916	CLONAL	1	FALSE	1	0.339468584468887	2		658	797	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391799	139391799	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1455334351	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	45	361	2	ENST00000277541.6:c.6392del	p.Gly2131AlafsTer117	p.G2131Afs*117	ENST00000277541	NM_017617.3	2131	gGc/gc	34/34	1	2	FACETS	0.715	0.602	0.838	0.715	0.602	0.838	SUBCLONAL	1	FALSE	1	0.339468584468887	2		363	371	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513282	44513287	+	inframe_deletion	In_Frame_Del	DEL	CCACCG	CCACCG	-	rs745888281	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	39	336	0	ENST00000291552.4:c.648_653del	p.Gly222_Gly223del	p.G222_G223del	ENST00000291552	NM_006758.2	216	ggCGGTGGt/ggt	8/8	1	2	FACETS	0.48	0.397	0.572	0.48	0.397	0.572	SUBCLONAL	1	FALSE	1	0.339468584468887	2		336	479	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	140	507	1	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	1	0.339468584468887	2		508	754	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098477	11098477	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	76	257	3	ENST00000358026.2:c.999del	p.Gln335SerfsTer76	p.Q335Sfs*76	ENST00000358026	NM_001128849.1	332	tCc/tc	6/36	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.339468584468887	2		260	362	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562958	29562958	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs878853890	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	196	608	1	ENST00000356175.3:c.3897del	p.Lys1299AsnfsTer10	p.K1299Nfs*10	ENST00000356175	NM_000267.3	1298	cAa/ca	29/57	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.339468584468887	2		609	1012	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067329	37067329	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	147	498	0	ENST00000231790.2:c.1240del	p.Glu414ArgfsTer77	p.E414Rfs*77	ENST00000231790	NM_000249.3	414	Gag/ag	12/19	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.339468584468887	2		498	812	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412058	63412059	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	197	472	0	ENST00000330258.3:c.1108dup	p.Glu370GlyfsTer8	p.E370Gfs*8	ENST00000330258	NM_152424.3	370	gag/gGag	2/2	0.339468584468887	0	FACETS	0.739	0.69	0.788			1	SUBCLONAL	2	FALSE	NA	0.339468584468887	0		472	519	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035140	37035142	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	novel	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	54	259	0	ENST00000231790.2:c.105_107del	p.Met35del	p.M35del	ENST00000231790	NM_000249.3	34	gaGATg/gag	1/19	1	2	FACETS	0.831	0.712	0.96	0.831	0.712	0.96	CLONAL	1	FALSE	1	0.339468584468887	2		259	383	SUCCESS
APC	324	MSKCC	GRCh37	5	112174264	112174267	+	frameshift_variant	Frame_Shift_Del	DEL	AAGT	AAGT	-	novel	NA	P-0005455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	186	531	0	ENST00000257430.4:c.2977_2980del	p.Lys993PhefsTer11	p.K993Ffs*11	ENST00000257430	NM_000038.5	991	gaAAGT/ga	16/16	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.339468584468887	2		531	849	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	50	192	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.789	0.67	0.919	0.789	0.67	0.919	CLONAL	1	TRUE	1	0.286143429284175	2		192	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0005458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	144	448	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.286143429284175	1	FACETS	0.967	0.882	1	0.967	0.882	1	CLONAL	1	TRUE	0	0.286143429284175	1		448	892	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188218	10188218	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	167	443	0	ENST00000256474.2:c.361G>T	p.Asp121Tyr	p.D121Y	ENST00000256474	NM_000551.3	121	Gat/Tat	2/3	0.286143429284175	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.286143429284175	1		443	823	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245350	53245350	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1556851765	NA	P-0005458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	140	538	0	ENST00000375401.3:c.687G>T	p.Lys229Asn	p.K229N	ENST00000375401	NM_004187.3	229	aaG/aaT	6/26	1	2	FACETS	0.804	0.73	0.882	0.804	0.73	0.882	CLONAL	1	TRUE	1	0.286143429284175	2		538	1217	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0005468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	79	338	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.851	0.749	0.96	1	0.98	1	CLONAL	2	TRUE	1	0.15	2		339	619	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0005468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	26	324	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.988	0.783	1	0.988	0.783	1	CLONAL	1	TRUE	1	0.15	2		324	351	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861129	57861129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767216717	NA	P-0005468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	114	669	1	ENST00000228682.2:c.926G>A	p.Arg309Gln	p.R309Q	ENST00000228682	NM_005269.2	309	cGg/cAg	9/12	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.15	2		670	1176	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439724	220439724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201577506	NA	P-0005468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	91	757	1	ENST00000243786.2:c.577G>A	p.Val193Ile	p.V193I	ENST00000243786	NM_002191.3	193	Gtc/Atc	2/2	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.15	2		758	1030	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057520007	NA	P-0005468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	90	644	2	ENST00000269305.4:c.614A>T	p.Tyr205Phe	p.Y205F	ENST00000269305	NM_001126112.2	205	tAt/tTt	6/11	0.0871886239611818	0	FACETS	1	0.96	1			1	INDETERMINATE	1	TRUE	0	0.15	0		646	859	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	468	510	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.226926057582645	5	FACETS	1	0.993	1	1	0.993	1	INDETERMINATE	3	TRUE	2	0.562087115729345	5		510	907	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024477	16024477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1183742719	NA	P-0005488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	35	379	0	ENST00000268712.3:c.1741C>T	p.Arg581Cys	p.R581C	ENST00000268712	NM_006311.3	581	Cgt/Tgt	16/46	0.562087115729345	2	FACETS	0.219	0.179	0.265	0.11	0.089	0.133	SUBCLONAL	1	TRUE	0	0.562087115729345	2		379	568	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630303	187630303	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774143174	NA	P-0005488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	26	345	0	ENST00000441802.2:c.679C>T	p.Arg227Cys	p.R227C	ENST00000441802	NM_005245.3	227	Cgt/Tgt	2/27	0.409633042388314	1	FACETS	0.141	0.111	0.175	0.141	0.111	0.175	SUBCLONAL	1	TRUE	0	0.562087115729345	1		345	473	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421519	32421519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	70	300	0	ENST00000332351.3:c.1073C>T	p.Thr358Met	p.T358M	ENST00000332351	NM_024426.4	358	aCg/aTg	6/10	0.183160736462897	5	FACETS	0.893	0.78	1	0.298	0.26	0.339	INDETERMINATE	1	TRUE	2	0.562087115729345	5		300	514	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695749	117695749	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	60	319	0	ENST00000369458.3:c.688G>T	p.Asp230Tyr	p.D230Y	ENST00000369458	NM_024626.3	230	Gac/Tac	4/6	0.468610614797586	3	FACETS	0.519	0.447	0.597	0.259	0.223	0.299	SUBCLONAL	1	TRUE	1	0.562087115729345	3		319	527	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650182	206650182	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0005488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	19	216	0	ENST00000367120.3:c.701+1G>T		p.X234_splice	ENST00000367120	NM_014002.3	234			0.161029167843674	4	FACETS	0.302	0.228	0.388	0.101	0.076	0.13	INDETERMINATE	1	TRUE	1	0.562087115729345	4		216	350	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495318	212495318	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	95	253	0	ENST00000342788.4:c.1948A>C	p.Thr650Pro	p.T650P	ENST00000342788	NM_005235.2	650	Act/Cct	17/28	0.562087115729345	3	FACETS	0.897	0.802	0.997	0.448	0.401	0.499	CLONAL	1	TRUE	1	0.562087115729345	3		253	483	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829272	128829272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs924171569	NA	P-0005488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	56	473	2	ENST00000249373.3:c.280G>A	p.Gly94Arg	p.G94R	ENST00000249373	NM_005631.4	94	Gga/Aga	1/12	0.155123732932532	2	FACETS	0.293	0.251	0.34	0.147	0.125	0.17	INDETERMINATE	1	TRUE	0	0.562087115729345	2		475	679	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864267	117864267	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1575	173	575	1	ENST00000297338.2:c.1390G>A	p.Asp464Asn	p.D464N	ENST00000297338	NM_006265.2	464	Gat/Aat	11/14	0.562087115729345	6	FACETS	0.748	0.686	0.814	0.187	0.171	0.204	SUBCLONAL	1	TRUE	2	0.562087115729345	6		576	1748	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980760	40980760	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	55	345	1	ENST00000373198.4:c.1726C>T	p.Pro576Ser	p.P576S	ENST00000373198	NM_133170.3	576	Ccc/Tcc	10/32	0.161029167843674	4	FACETS	0.43	0.367	0.499	0.143	0.122	0.167	INDETERMINATE	1	TRUE	1	0.562087115729345	4		346	711	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578247	7578247	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	513	529	1	ENST00000269305.4:c.602del	p.Leu201CysfsTer46	p.L201Cfs*46	ENST00000269305	NM_001126112.2	201	tTg/tg	6/11	0.562087115729345	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.562087115729345	2		530	795	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0005506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	853	454	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.630458233196429	4	FACETS	1	0.996	1			1	CLONAL	4	TRUE	NA	0.630458233196429	4		454	1047	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508535	106508535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	115	137	1	ENST00000359195.3:c.529C>T	p.Arg177Cys	p.R177C	ENST00000359195	NM_002649.2	177	Cgc/Tgc	2/11	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.630458233196429	2		138	357	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236064	108236064	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	131	495	0	ENST00000278616.4:c.9000G>C	p.Gln3000His	p.Q3000H	ENST00000278616	NM_000051.3	3000	caG/caC	63/63	0.630458233196429	1	FACETS	0.945	0.872	1	0.945	0.872	1	CLONAL	1	TRUE	0	0.630458233196429	1		495	301	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428425	49428425	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	118	564	1	ENST00000301067.7:c.10380G>C	p.Gln3460His	p.Q3460H	ENST00000301067	NM_003482.3	3460	caG/caC	36/54	NA	2	FACETS	0.938	0.854	1			1	INDETERMINATE	1	TRUE	NA	0.630458233196429	2		565	399	SUCCESS
BLM	641	MSKCC	GRCh37	15	91333942	91333942	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367543023	NA	P-0005506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	139	662	0	ENST00000355112.3:c.2887C>T	p.His963Tyr	p.H963Y	ENST00000355112	NM_000057.2	963	Cat/Tat	15/22	0.222380630741949	5	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.630458233196429	5		662	615	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095885	29095885	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0005506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	129	615	0	ENST00000328354.6:c.949A>T	p.Lys317Ter	p.K317*	ENST00000328354	NM_007194.3	317	Aaa/Taa	9/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.630458233196429	2		615	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0005516-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	445	590	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	NA	2	FACETS	0.951	0.927	0.973			1	INDETERMINATE	2	TRUE	NA	0.860504610674026	2		590	544	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245404	153245404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	185	501	0	ENST00000281708.4:c.1787C>T	p.Ser596Phe	p.S596F	ENST00000281708	NM_033632.3	596	tCt/tTt	11/12	0.463992959074761	2	FACETS	0.923	0.862	0.984	0.923	0.862	0.984	CLONAL	2	TRUE	0	0.463992959074761	2		501	432	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0005522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	335	614	0	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	0.450829106555123	2	FACETS	0.889	0.845	0.934	0.889	0.845	0.934	CLONAL	2	TRUE	0	0.463992959074761	2		614	812	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181375	185181375	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	129	723	0	ENST00000265026.3:c.1316A>C	p.Lys439Thr	p.K439T	ENST00000265026	NM_004721.4	439	aAg/aCg	8/14	1	2	FACETS	0.793	0.72	0.87	0.793	0.72	0.87	SUBCLONAL	1	TRUE	1	0.463992959074761	2		723	701	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925711	114925711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752060378	NA	P-0005522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1433	311	926	1	ENST00000543371.1:c.1789G>A	p.Val597Ile	p.V597I	ENST00000543371	NM_001198531.1	597	Gtc/Atc	14/14	1	2	FACETS	0.769	0.722	0.816	0.769	0.722	0.816	SUBCLONAL	1	TRUE	1	0.463992959074761	2		927	1744	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	298	497	0	ENST00000269305.4:c.404G>C	p.Cys135Ser	p.C135S	ENST00000269305	NM_001126112.2	135	tGc/tCc	5/11	0.463992959074761	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.463992959074761	1		497	795	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798878	135798894	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATCTGCAGGAGAAAAGG	ATCTGCAGGAGAAAAGG	-	novel	NA	P-0005522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	34	317	0	ENST00000298552.3:c.364-15_365del		p.X122_splice	ENST00000298552	NM_001162426.1	122		6/23	0.463992959074761	1	FACETS	0.536	0.441	0.64	0.536	0.441	0.64	SUBCLONAL	1	TRUE	0	0.463992959074761	1		317	210	SUCCESS
APC	324	MSKCC	GRCh37	5	112175438	112175439	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0005522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	84	405	0	ENST00000257430.4:c.4147_4148del	p.Met1383ValfsTer2	p.M1383Vfs*2	ENST00000257430	NM_000038.5	1383	ATg/g	16/16	0.463992959074761	1	FACETS	0.99	0.885	1	0.99	0.885	1	CLONAL	1	TRUE	0	0.463992959074761	1		405	281	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0005532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	124	551	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	0.747	0.674	0.825	0.747	0.674	0.825	SUBCLONAL	1	TRUE	1	0.265501754624062	2		551	1250	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123189983	123189983	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	138	503	2	ENST00000218089.9:c.1202G>T	p.Ser401Ile	p.S401I	ENST00000218089	NM_001042749.1	401	aGt/aTt	14/35	0.162890597743463	2	FACETS	0.803	0.729	0.882	0.402	0.364	0.441	CLONAL	1	TRUE	0	0.265501754624062	2		505	1294	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	415	192	0				ENST00000310581	NM_198253.2	-/1132			0.758515204097086	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.758515204097086	1		192	657	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720805	89720808	+	frameshift_variant	Frame_Shift_Del	DEL	CTTT	CTTT	-	rs398123330	NA	P-0005549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	132	141	0	ENST00000371953.3:c.956_959del	p.Thr319LysfsTer24	p.T319Kfs*24	ENST00000371953	NM_000314.4	319	aCTTTa/aa	8/9	0.758515204097086	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.758515204097086	1		141	198	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0005549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	1050	693	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.758515204097086	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.758515204097086	1		693	1575	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100375	27100375	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	745	705	0	ENST00000324856.7:c.4087C>T	p.Gln1363Ter	p.Q1363*	ENST00000324856	NM_006015.4	1363	Caa/Taa	17/20	0.758515204097086	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.758515204097086	1		705	1101	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0005549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	450	416	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.758515204097086	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.758515204097086	1		416	670	SUCCESS
APC	324	MSKCC	GRCh37	5	112173783	112173783	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs878853427	NA	P-0005549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	265	406	0	ENST00000257430.4:c.2492T>C	p.Leu831Ser	p.L831S	ENST00000257430	NM_000038.5	831	tTa/tCa	16/16	0.758515204097086	1	FACETS	0.986	0.94	1	0.986	0.94	1	CLONAL	1	TRUE	0	0.758515204097086	1		406	440	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781521	135781521	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	1225	900	2	ENST00000298552.3:c.1444A>G	p.Ile482Val	p.I482V	ENST00000298552	NM_001162426.1	482	Ata/Gta	15/23	0.758515204097086	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.758515204097086	1		902	1894	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021173	31021173	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005552-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	178	546	0	ENST00000375687.4:c.1173del	p.Glu391AspfsTer71	p.E391Dfs*71	ENST00000375687	NM_015338.5	391	gAa/ga	12/13	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.271260606238906	2		546	908	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618643	37618643	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	374	419	0	ENST00000447079.4:c.319C>G	p.Arg107Gly	p.R107G	ENST00000447079	NM_015083.1	107	Cgc/Ggc	1/14	1	2	FACETS	0.96	0.916	1	0.96	0.916	1	CLONAL	1	TRUE	1	0.872108152256915	2		419	893	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618617	37618639	+	frameshift_variant	Frame_Shift_Del	DEL	AACGTCGTGGATCAGATCGGAGC	AACGTCGTGGATCAGATCGGAGC	-	novel	NA	P-0005555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	367	389	0	ENST00000447079.4:c.293_315del	p.Glu98GlyfsTer21	p.E98Gfs*21	ENST00000447079	NM_015083.1	98	gAACGTCGTGGATCAGATCGGAGC/g	1/14	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.872108152256915	2		389	838	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627990	37627990	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	362	337	0	ENST00000447079.4:c.1905del	p.Leu635PhefsTer20	p.L635Ffs*20	ENST00000447079	NM_015083.1	635	ttA/tt	2/14	1	2	FACETS	0.969	0.923	1	0.969	0.923	1	CLONAL	1	TRUE	1	0.872108152256915	2		337	857	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56412997	56412997	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1263	496	548	0	ENST00000348428.3:c.2011del	p.Arg671AspfsTer8	p.R671Dfs*8	ENST00000348428	NM_006785.3	671	Aga/ga	16/17	0.738026132772255	3	FACETS	0.929	0.887	0.971			1	CLONAL	1	TRUE	NA	0.872108152256915	3		548	1759	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0005569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	464	759	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.67133727397575	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.67133727397575	1		759	880	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393701	139393701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763052700	NA	P-0005569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	333	340	0	ENST00000277541.6:c.5945G>A	p.Arg1982Gln	p.R1982Q	ENST00000277541	NM_017617.3	1982	cGg/cAg	32/34	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.67133727397575	2		340	958	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0005575-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	260	338	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.969	0.925	1	1	0.996	1	CLONAL	3	TRUE	1	0.429966576417146	2		339	416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0005575-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	36	792	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.397866510382081	0	FACETS	0.466	0.386	0.553			1	SUBCLONAL	1	TRUE	0	0.429966576417146	0		792	205	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38968090	38968090	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005575-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	14	448	0	ENST00000357387.3:c.1015C>G	p.Leu339Val	p.L339V	ENST00000357387	NM_152756.3	339	Cta/Gta	12/38	1	2	FACETS	0.242	0.174	0.324	0.242	0.174	0.324	SUBCLONAL	1	TRUE	1	0.429966576417146	2		448	269	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662363	117662363	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005575-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	13	348	0	ENST00000368508.3:c.5014T>G	p.Leu1672Val	p.L1672V	ENST00000368508	NM_002944.2	1672	Ttg/Gtg	30/43	1	2	FACETS	0.315	0.225	0.424	0.315	0.225	0.424	SUBCLONAL	1	TRUE	1	0.429966576417146	2		348	192	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923338	9923338	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005575-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	10	487	0	ENST00000330684.3:c.1949C>A	p.Ala650Asp	p.A650D	ENST00000330684	NM_001134407.1	650	gCt/gAt	9/13	0.381829445600894	1	FACETS	0.215	0.145	0.302	0.215	0.145	0.302	SUBCLONAL	1	TRUE	0	0.429966576417146	1		487	170	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158637098	158637098	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1426099891	NA	P-0005582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	659	738	2	ENST00000263640.3:c.82G>T	p.Val28Phe	p.V28F	ENST00000263640	NM_001105.4	28	Gtc/Ttc	4/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.8973548743863	2		740	1447	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674303	117674303	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1206111595	NA	P-0005582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	324	429	1	ENST00000368508.3:c.4171G>T	p.Asp1391Tyr	p.D1391Y	ENST00000368508	NM_002944.2	1391	Gat/Tat	26/43	1	2	FACETS	0.933	0.886	0.98	0.933	0.886	0.98	CLONAL	1	TRUE	1	0.8973548743863	2		430	774	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118365469	118365469	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	46	509	0	ENST00000534358.1:c.5350A>G	p.Lys1784Glu	p.K1784E	ENST00000534358	NM_005933.3	1784	Aaa/Gaa	18/36	0.8973548743863	1	FACETS	0.096	0.08	0.113	0.096	0.08	0.113	SUBCLONAL	1	TRUE	0	0.8973548743863	1		509	590	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039408	49039408	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	415	520	0	ENST00000267163.4:c.2394del	p.Ile799PhefsTer11	p.I799Ffs*11	ENST00000267163	NM_000321.2	798	cGg/cg	23/27	0.8973548743863	1	FACETS	0.951	0.924	0.977	0.951	0.924	0.977	CLONAL	1	TRUE	0	0.8973548743863	1		520	536	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268925	55268925	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	398	426	0	ENST00000275493.2:c.2991C>G	p.Phe997Leu	p.F997L	ENST00000275493	NM_005228.3	997	ttC/ttG	25/28	0.250634928109571	5	FACETS	0.879	0.839	0.919	0.879	0.839	0.919	INDETERMINATE	3	TRUE	2	0.615147921916073	5		426	944	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923656	39923664	+	inframe_deletion	In_Frame_Del	DEL	AGTGTGGCT	AGTGTGGCT	-	novel	NA	P-0005585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	199	530	0	ENST00000378444.4:c.3427_3435del	p.Ser1143_Thr1145del	p.S1143_T1145del	ENST00000378444	NM_001123385.1	1143	AGCCACACT/-	7/15	0.615147921916073	3	FACETS	1	0.988	1	0.647	0.602	0.693	CLONAL	1	TRUE	1	0.615147921916073	3		530	654	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944369	76944377	+	inframe_deletion	In_Frame_Del	DEL	TTGACCTGT	TTGACCTGT	-	novel	NA	P-0005585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	85	520	0	ENST00000373344.5:c.528_536del	p.Gln176_Asn179delinsHis	p.Q176_N179delinsH	ENST00000373344	NM_000489.3	176	caACAGGTCAAt/cat	7/35	0.610976123767109	2	FACETS	0.221	0.194	0.249	0.11	0.097	0.125	SUBCLONAL	1	TRUE	0	0.615147921916073	2		520	1252	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577507	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	223	398	0	ENST00000269305.4:c.774dup	p.Asp259ArgfsTer5	p.D259Rfs*5	ENST00000269305	NM_001126112.2	258	-/A	7/11	0.610976123767109	2	FACETS	0.918	0.869	0.966	0.918	0.869	0.966	CLONAL	2	TRUE	0	0.615147921916073	2		398	395	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657485	29657486	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	T	novel	NA	P-0005585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	350	228	0	ENST00000356175.3:c.5718_5719delinsT	p.Leu1906PhefsTer15	p.L1906Ffs*15	ENST00000356175	NM_000267.3	1906	ttGGaa/ttTaa	38/57	NA	2	FACETS	0.928	0.889	0.967			1	INDETERMINATE	2	TRUE	NA	0.615147921916073	2		228	613	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0005589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	113	285	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.357740233693763	1	FACETS	0.505	0.456	0.556	0.505	0.456	0.556	INDETERMINATE	1	TRUE	0	0.602375018024543	1		285	519	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0005589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	319	759	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.602375018024543	1	FACETS	0.921	0.873	0.968	0.921	0.873	0.968	CLONAL	1	TRUE	0	0.602375018024543	1		759	804	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0005589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	185	302	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.602375018024543	2		302	611	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952138	178952138	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	146	255	0	ENST00000263967.3:c.3193C>T	p.His1065Tyr	p.H1065Y	ENST00000263967	NM_006218.2	1065	Cat/Tat	21/21	0.357740233693763	1	FACETS	0.855	0.789	0.923	0.855	0.789	0.923	INDETERMINATE	1	TRUE	0	0.602375018024543	1		255	396	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920402	114920402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs927089403	NA	P-0005589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	364	633	0	ENST00000543371.1:c.1343G>A	p.Arg448Gln	p.R448Q	ENST00000543371	NM_001198531.1	448	cGg/cAg	13/14	1	2	FACETS	0.983	0.932	1	0.983	0.932	1	CLONAL	1	TRUE	1	0.602375018024543	2		633	1229	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436177	110436177	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1302515567	NA	P-0005589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	254	479	0	ENST00000375856.3:c.2224T>C	p.Tyr742His	p.Y742H	ENST00000375856	NM_003749.2	742	Tac/Cac	1/2	0.58436067967776	3	FACETS	1	0.982	1	0.56	0.525	0.597	CLONAL	1	TRUE	1	0.602375018024543	3		479	979	SUCCESS
APC	324	MSKCC	GRCh37	5	112175648	112175648	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	283	459	0	ENST00000257430.4:c.4358del	p.Pro1453LeufsTer20	p.P1453Lfs*20	ENST00000257430	NM_000038.5	1453	Cct/ct	16/16	0.357740233693763	1	FACETS	0.758	0.715	0.803	0.758	0.715	0.803	INDETERMINATE	1	TRUE	0	0.602375018024543	1		459	866	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591836	48591837	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGG	novel	NA	P-0005589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	260	450	0	ENST00000342988.3:c.1000_1003dup	p.Val335AlafsTer7	p.V335Afs*7	ENST00000342988	NM_005359.5	333	-/CAGG	9/12	0.602375018024543	1	FACETS	0.97	0.916	1	0.97	0.916	1	CLONAL	1	TRUE	0	0.602375018024543	1		450	622	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0005592-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	98	300	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.434011447084331	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.434011447084331	1		300	278	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022913	27022938	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGCCGCCGCCAGCAGCCTGGGCAA	CCCGCCGCCGCCAGCAGCCTGGGCAA	-	rs797045262	NA	P-0005592-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	23	36	0	ENST00000324856.7:c.31_56del	p.Ser11AlafsTer91	p.S11Afs*91	ENST00000324856	NM_006015.4	7	CCCGCCGCCGCCAGCAGCCTGGGCAAc/c	1/20	0.254537621911844	1	FACETS	0.783	0.622	0.962	0.783	0.622	0.962	INDETERMINATE	1	TRUE	0	0.434011447084331	1		36	106	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087911	27087911	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs757025491	NA	P-0005592-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	90	445	2	ENST00000324856.7:c.2198C>A	p.Ser733Ter	p.S733*	ENST00000324856	NM_006015.4	733	tCg/tAg	6/20	0.254537621911844	1	FACETS	0.505	0.448	0.566	0.505	0.448	0.566	INDETERMINATE	1	TRUE	0	0.434011447084331	1		447	643	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462860	120462860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755747980	NA	P-0005592-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	110	278	1	ENST00000256646.2:c.5471G>A	p.Arg1824His	p.R1824H	ENST00000256646	NM_024408.3	1824	cGt/cAt	30/34	0.254537621911844	1	FACETS	0.825	0.745	0.909	0.825	0.745	0.909	INDETERMINATE	1	TRUE	0	0.434011447084331	1		279	481	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005603-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	149	192	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.953	1			1	INDETERMINATE	1	TRUE	NA	0.810684648958296	2		192	354	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589654	67589654	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005603-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	207	266	0	ENST00000274335.5:c.1417A>C	p.Thr473Pro	p.T473P	ENST00000274335		473	Aca/Cca	10/15	0.244554336961591	4	FACETS	0.874	0.818	0.931	0.874	0.818	0.931	INDETERMINATE	2	TRUE	2	0.810684648958296	4		266	529	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265326	152265326	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005603-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	297	625	0	ENST00000206249.3:c.779G>A	p.Arg260Lys	p.R260K	ENST00000206249	NM_000125.3	260	aGa/aAa	4/8	0.244554336961591	4	FACETS	0.898	0.85	0.946	0.898	0.85	0.946	INDETERMINATE	2	TRUE	2	0.810684648958296	4		625	739	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99451968	99451968	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005603-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	240	656	0	ENST00000268035.6:c.1302G>A	p.Trp434Ter	p.W434*	ENST00000268035	NM_000875.3	434	tgG/tgA	6/21	1	2	FACETS	0.922	0.867	0.979	0.922	0.867	0.979	CLONAL	1	TRUE	1	0.810684648958296	2		656	642	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211629	46211638	+	frameshift_variant	Frame_Shift_Del	DEL	ATCATCACTT	ATCATCACTT	-	novel	NA	P-0005603-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	356	529	0	ENST00000334344.6:c.595_604del	p.Ile199TyrfsTer13	p.I199Yfs*13	ENST00000334344	NM_152641.2	199	ATCATCACTTta/ta	5/21	0.244554336961591	4	FACETS	0.811	0.77	0.852	0.811	0.77	0.852	INDETERMINATE	2	TRUE	2	0.810684648958296	4		529	981	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45423125	45423125	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0005607-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	42	254	0	ENST00000262160.6:c.3G>A	p.Met1?	p.M1?	ENST00000262160	NM_005901.5	1	atG/atA	2/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		254	296	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0005613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	735	787	1	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.654765415151548	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.66156517686671	2		788	1102	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0005617-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	41	300	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.694	0.579	0.822	0.694	0.579	0.822	SUBCLONAL	1	TRUE	1	0.306794830476156	2		300	385	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968259	2968259	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005617-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	75	450	0	ENST00000396946.4:c.1727G>A	p.Arg576His	p.R576H	ENST00000396946	NM_032415.4	576	cGc/cAc	13/25	1	2	FACETS	0.424	0.37	0.483	0.424	0.37	0.483	SUBCLONAL	1	TRUE	1	0.306794830476156	2		450	1152	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068384	26068384	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005617-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	139	430	0	ENST00000435504.4:c.106C>T	p.Gln36Ter	p.Q36*	ENST00000435504		36	Caa/Taa	2/13	1	2	FACETS	0.986	0.897	1	0.986	0.897	1	CLONAL	1	TRUE	1	0.306794830476156	2		430	919	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713171	30713171	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005617-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	28	236	0	ENST00000295754.5:c.496C>T	p.Gln166Ter	p.Q166*	ENST00000295754	NM_003242.5	166	Caa/Taa	4/7	1	2	FACETS	0.41	0.327	0.505	0.41	0.327	0.505	SUBCLONAL	1	TRUE	1	0.306794830476156	2		236	445	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005663	150005663	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005617-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	30	191	0	ENST00000253339.5:c.562C>T	p.Gln188Ter	p.Q188*	ENST00000253339		188	Cag/Tag	3/7	1	2	FACETS	0.582	0.47	0.709	0.582	0.47	0.709	SUBCLONAL	1	TRUE	1	0.306794830476156	2		191	336	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151882712	151882712	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005617-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	13	119	0	ENST00000262189.6:c.5013G>A	p.Trp1671Ter	p.W1671*	ENST00000262189	NM_170606.2	1671	tgG/tgA	34/59	1	2	FACETS	0.37	0.264	0.5	0.37	0.264	0.5	SUBCLONAL	1	TRUE	1	0.306794830476156	2		119	229	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902223	151902223	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005617-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	40	269	0	ENST00000262189.6:c.3929C>A	p.Ser1310Tyr	p.S1310Y	ENST00000262189	NM_170606.2	1310	tCt/tAt	25/59	1	2	FACETS	0.538	0.446	0.639	0.538	0.446	0.639	SUBCLONAL	1	TRUE	1	0.306794830476156	2		269	485	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994255	21994255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005617-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	46	322	0	ENST00000579755.1:c.76C>T	p.His26Tyr	p.H26Y	ENST00000579755		26	Cac/Tac	1/3	1		FACETS		0.364	0.511				SUBCLONAL	1	TRUE	1	0.306794830476156	2		322	691	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432609	49432609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005617-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	79	474	0	ENST00000301067.7:c.8530G>A	p.Glu2844Lys	p.E2844K	ENST00000301067	NM_003482.3	2844	Gaa/Aaa	34/54	1	2	FACETS	0.422	0.369	0.478	0.422	0.369	0.478	SUBCLONAL	1	TRUE	1	0.306794830476156	2		474	1221	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584430	39584430	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005617-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	67	447	0	ENST00000262039.4:c.1095G>T	p.Glu365Asp	p.E365D	ENST00000262039	NM_002647.2	365	gaG/gaT	10/25	1	2	FACETS	0.418	0.362	0.479	0.418	0.362	0.479	SUBCLONAL	1	TRUE	1	0.306794830476156	2		447	1045	SUCCESS
AR	367	MSKCC	GRCh37	X	66766240	66766261	+	frameshift_variant	Frame_Shift_Del	DEL	GGTGCAGCGGGACCCGGTTCTG	GGTGCAGCGGGACCCGGTTCTG	CCT	novel	NA	P-0005617-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	54	138	0	ENST00000374690.3:c.1252_1273delinsCCT	p.Gly418ProfsTer55	p.G418Pfs*55	ENST00000374690	NM_000044.3	418	GGTGCAGCGGGACCCGGTTCTGgg/CCTgg	1/8	0.0751919614767673	2	FACETS	1	0.924	1			1	INDETERMINATE	1	TRUE	NA	0.306794830476156	2		138	315	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	84	192	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.243126502119193	2		192	541	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0005627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	122	452	1	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.243126502119193	2		453	986	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0005627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	124	471	1	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.243126502119193	2		472	907	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145430	58145430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894340	NA	P-0005627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	91	385	1	ENST00000257904.6:c.71G>A	p.Arg24His	p.R24H	ENST00000257904	NM_000075.3	24	cGt/cAt	2/8	1	2	FACETS	0.878	0.778	0.984	0.878	0.778	0.984	CLONAL	1	TRUE	1	0.243126502119193	2		386	853	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435734	56435734	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	72	278	0	ENST00000407977.2:c.1403C>T	p.Ser468Leu	p.S468L	ENST00000407977		468	tCa/tTa	9/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.243126502119193	2		278	520	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910549	29910549	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45585732	NA	P-0005627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	13	37	2	ENST00000376809.5:c.89G>A	p.Arg30Lys	p.R30K	ENST00000376809	NM_002116.7	30	aGg/aAg	2/8	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.243126502119193	2		39	79	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254944	16254944	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747509416	NA	P-0005627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	107	346	0	ENST00000375759.3:c.2209C>T	p.Pro737Ser	p.P737S	ENST00000375759	NM_015001.2	737	Cct/Tct	11/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.243126502119193	2		346	712	SUCCESS
FH	2271	MSKCC	GRCh37	1	241671962	241671962	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs11545658	NA	P-0005627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	119	474	1	ENST00000366560.3:c.679C>T	p.Gln227Ter	p.Q227*	ENST00000366560	NM_000143.3	227	Cag/Tag	5/10	0.105521697527699	3	FACETS	0.762	0.689	0.84	0.762	0.689	0.84	INDETERMINATE	2	TRUE	1	0.243126502119193	3		475	720	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661566	227661566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1438480797	NA	P-0005627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	124	387	0	ENST00000305123.5:c.1889G>A	p.Gly630Glu	p.G630E	ENST00000305123	NM_005544.2	630	gGa/gAa	1/2	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.243126502119193	2		387	844	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144117	55144117	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	103	445	0	ENST00000257290.5:c.1946C>G	p.Thr649Ser	p.T649S	ENST00000257290	NM_006206.4	649	aCt/aGt	14/23	1	2	FACETS	0.964	0.862	1	0.964	0.862	1	CLONAL	1	TRUE	1	0.243126502119193	2		445	879	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245440	153245440	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	163	402	0	ENST00000281708.4:c.1751C>A	p.Thr584Lys	p.T584K	ENST00000281708	NM_033632.3	584	aCa/aAa	11/12	0.240602579698119	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.243126502119193	2		402	599	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294207	1294207	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	87	253	0	ENST00000310581.5:c.794C>A	p.Pro265Gln	p.P265Q	ENST00000310581	NM_198253.2	265	cCg/cAg	2/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.243126502119193	2		253	560	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163641	32163641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	52	252	0	ENST00000375023.3:c.5585G>A	p.Arg1862Gln	p.R1862Q	ENST00000375023	NM_004557.3	1862	cGg/cAg	30/30	1	2	FACETS	0.968	0.825	1	0.968	0.825	1	CLONAL	1	TRUE	1	0.243126502119193	2		252	442	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005017	150005017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1291991653	NA	P-0005627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	92	378	0	ENST00000253339.5:c.1208G>A	p.Gly403Glu	p.G403E	ENST00000253339		403	gGa/gAa	3/7	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.243126502119193	2		378	666	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468275	50468275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	95	300	0	ENST00000331340.3:c.1510G>A	p.Glu504Lys	p.E504K	ENST00000331340	NM_006060.4	504	Gag/Aag	8/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.243126502119193	2		300	669	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411579	116411579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	82	334	1	ENST00000397752.3:c.2758C>T	p.Leu920Phe	p.L920F	ENST00000397752	NM_000245.2	920	Ctt/Ttt	13/21	1	2	FACETS	0.966	0.852	1	0.966	0.852	1	CLONAL	1	TRUE	1	0.243126502119193	2		335	698	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846386	128846386	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs748959667	NA	P-0005627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	134	434	0	ENST00000249373.3:c.1222A>G	p.Ile408Val	p.I408V	ENST00000249373	NM_005631.4	408	Atc/Gtc	6/12	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.243126502119193	2		434	951	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114917788	114917788	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	51	525	1	ENST00000543371.1:c.1278G>C	p.Lys426Asn	p.K426N	ENST00000543371	NM_001198531.1	426	aaG/aaC	12/14	0.243126502119193	1	FACETS	0.405	0.342	0.473	0.405	0.342	0.473	SUBCLONAL	1	TRUE	0	0.243126502119193	1		526	911	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911201	32911201	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	59	800	1	ENST00000380152.3:c.2709A>T	p.Leu903Phe	p.L903F	ENST00000380152		903	ttA/ttT	11/27	0.211636521969365	1	FACETS	0.413	0.354	0.478	0.413	0.354	0.478	SUBCLONAL	1	TRUE	0	0.243126502119193	1		801	1032	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061459	38061459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1349901575	NA	P-0005627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	57	350	0	ENST00000250448.2:c.530C>T	p.Ser177Leu	p.S177L	ENST00000250448	NM_004496.3	177	tCg/tTg	2/2	0.211636521969365	1	FACETS	0.515	0.441	0.596	0.515	0.441	0.596	SUBCLONAL	1	TRUE	0	0.243126502119193	1		350	800	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942053	81942053	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs775355899	NA	P-0005627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1179	153	690	0	ENST00000359376.3:c.1590G>C	p.Glu530Asp	p.E530D	ENST00000359376	NM_002661.3	530	gaG/gaC	17/33	0.211636521969365	1	FACETS	0.83	0.757	0.907	0.83	0.757	0.907	CLONAL	1	TRUE	0	0.243126502119193	1		690	1332	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350623	89350623	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1472	196	1005	0	ENST00000301030.4:c.2327T>C	p.Leu776Ser	p.L776S	ENST00000301030	NM_001256183.1	776	tTa/tCa	9/13	0.211636521969365	1	FACETS	0.849	0.783	0.918	0.849	0.783	0.918	CLONAL	1	TRUE	0	0.243126502119193	1		1005	1668	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89862427	89862427	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0005627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	110	403	0	ENST00000389301.3:c.894-1G>A		p.X298_splice	ENST00000389301	NM_000135.2	298			0.211636521969365	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.243126502119193	1		403	750	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774152	56774152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1463646629	NA	P-0005627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	133	516	1	ENST00000337432.4:c.503G>A	p.Arg168Lys	p.R168K	ENST00000337432	NM_058216.2	168	aGa/aAa	3/9	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.243126502119193	2		517	937	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872366	45872366	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	167	442	0	ENST00000391945.4:c.145A>G	p.Thr49Ala	p.T49A	ENST00000391945	NM_000400.3	49	Aca/Gca	3/23	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.243126502119193	2		442	992	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42851195	42851195	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	39	355	0	ENST00000398585.3:c.698C>G	p.Ser233Cys	p.S233C	ENST00000398585	NM_001135099.1	233	tCt/tGt	7/14	1	2	FACETS	0.536	0.444	0.64	0.536	0.444	0.64	SUBCLONAL	1	TRUE	1	0.243126502119193	2		355	598	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056613	26056636	+	inframe_deletion	In_Frame_Del	DEL	GCAGGAGGCGCGGCAGCGGGAGCG	GCAGGAGGCGCGGCAGCGGGAGCG	-	novel	NA	P-0005627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	46	92	0	ENST00000343677.2:c.21_44del	p.Ala8_Ala15del	p.A8_A15del	ENST00000343677	NM_005319.3	7	gcCGCTCCCGCTGCCGCGCCTCCTGCg/gcg	1/1	0.243126502119193	4	FACETS	1	0.961	1			1	CLONAL	1	TRUE	NA	0.243126502119193	4		92	314	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922703	44922703	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	143	295	0	ENST00000377967.4:c.1565del	p.Gly522GlufsTer26	p.G522Efs*26	ENST00000377967	NM_021140.2	522	Gga/ga	16/29	1	1	FACETS	0.865	0.792	0.942	1	0.99	1	CLONAL	2	TRUE	0	0.243126502119193	1		295	597	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0005656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	100	316	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	0.874	0.792	0.959	0.874	0.792	0.959	CLONAL	1	TRUE	1	0.79725010861748	2		316	287	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440343	52440343	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	517	556	0	ENST00000460680.1:c.709del	p.Arg237AlafsTer12	p.R237Afs*12	ENST00000460680	NM_004656.3	237	Cgc/gc	9/17	0.731057028426275	1	FACETS	0.913	0.883	0.943	0.913	0.883	0.943	CLONAL	1	TRUE	0	0.79725010861748	1		556	854	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0005666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	125	585	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.911	0.827	1	0.911	0.827	1	CLONAL	1	TRUE	1	0.422089209284721	2		585	650	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012877	176012877	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	141	935	0	ENST00000367669.3:c.1499G>A	p.Gly500Glu	p.G500E	ENST00000367669	NM_022457.5	500	gGa/gAa	13/20	0.421178355176535	5	FACETS	0.965	0.877	1	0.241	0.219	0.265	CLONAL	1	TRUE	1	0.422089209284721	5		935	1131	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056314	26056314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1355795147	NA	P-0005666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	76	493	0	ENST00000343677.2:c.343G>A	p.Glu115Lys	p.E115K	ENST00000343677	NM_005319.3	115	Gaa/Aaa	1/1	0.336004053680393	5	FACETS	1	0.975	1	0.486	0.429	0.548	CLONAL	1	TRUE	2	0.422089209284721	5		493	403	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001155	150001155	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	177	957	0	ENST00000253339.5:c.2449G>A	p.Glu817Lys	p.E817K	ENST00000253339		817	Gaa/Aaa	4/7	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.422089209284721	2		957	777	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151946988	151946988	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	126	800	1	ENST00000262189.6:c.1786C>G	p.Leu596Val	p.L596V	ENST00000262189	NM_170606.2	596	Ctt/Gtt	13/59	NA	2	FACETS	0.697	0.63	0.766			1	INDETERMINATE	1	TRUE	NA	0.422089209284721	2		801	857	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151946996	151946996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	124	801	1	ENST00000262189.6:c.1778C>T	p.Ser593Leu	p.S593L	ENST00000262189	NM_170606.2	593	tCa/tTa	13/59	NA	2	FACETS	0.668	0.604	0.736			1	INDETERMINATE	1	TRUE	NA	0.422089209284721	2		802	879	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195379	102195379	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	235	1161	0	ENST00000263464.3:c.139G>C	p.Glu47Gln	p.E47Q	ENST00000263464	NM_001165.4	47	Gaa/Caa	2/9	1	2	FACETS	0.998	0.93	1	0.998	0.93	1	CLONAL	1	TRUE	1	0.422089209284721	2		1161	1116	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846135	68846135	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	96	795	0	ENST00000261769.5:c.1106A>C	p.Asn369Thr	p.N369T	ENST00000261769	NM_004360.3	369	aAc/aCc	8/16	0.422089209284721	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	0	0.422089209284721	1		795	356	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216714	7216714	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	193	1253	0	ENST00000380728.2:c.709C>T	p.Gln237Ter	p.Q237*	ENST00000380728		237	Cag/Tag	8/11	0.422089209284721	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.422089209284721	1		1253	621	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0005673-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	82	381	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.779	0.687	0.877	1	0.978	1	SUBCLONAL	2	TRUE	1	0.16	2		382	658	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476243	88476243	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005673-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	61	346	0	ENST00000360948.2:c.1889G>A	p.Arg630Lys	p.R630K	ENST00000360948	NM_001012338.2	630	aGg/aAg	15/19	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.16	2		346	737	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851285	63851285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005673-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	36	253	1	ENST00000279873.7:c.2063C>T	p.Ser688Phe	p.S688F	ENST00000279873	NM_032199.2	688	tCc/tTc	10/10	1	2	FACETS	0.755	0.619	0.908	0.755	0.619	0.908	CLONAL	1	TRUE	1	0.16	2		254	596	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456447	189456447	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005673-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	67	403	0	ENST00000264731.3:c.208C>T	p.Gln70Ter	p.Q70*	ENST00000264731	NM_003722.4	70	Cag/Tag	3/14	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.16	2		403	785	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976443	25976443	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1234284896	NA	P-0005673-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	56	541	1	ENST00000435504.4:c.1102C>T	p.Pro368Ser	p.P368S	ENST00000435504		368	Cca/Tca	11/13	1	2	FACETS	0.716	0.611	0.831	0.716	0.611	0.831	SUBCLONAL	1	TRUE	1	0.16	2		542	978	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881680	111881680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1405228237	NA	P-0005673-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	42	341	0	ENST00000393256.3:c.358C>T	p.Pro120Ser	p.P120S	ENST00000393256	NM_006538.4	120	Cct/Tct	2/4	1	2	FACETS	0.689	0.574	0.818	0.689	0.574	0.818	SUBCLONAL	1	TRUE	1	0.16	2		341	762	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553489	106553489	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005673-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	24	194	0	ENST00000369096.4:c.1454G>A	p.Arg485Lys	p.R485K	ENST00000369096	NM_001198.3	485	aGg/aAg	5/7	1	2	FACETS	0.647	0.506	0.81	0.647	0.506	0.81	SUBCLONAL	1	TRUE	1	0.16	2		194	464	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692910	89692910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005673-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	48	261	0	ENST00000371953.3:c.394G>A	p.Gly132Ser	p.G132S	ENST00000371953	NM_000314.4	132	Ggt/Agt	5/9	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.16	2		261	573	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233094	69233094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005673-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	35	391	1	ENST00000462284.1:c.959C>T	p.Pro320Leu	p.P320L	ENST00000462284	NM_002392.5	320	cCc/cTc	11/11	1	2	FACETS	0.631	0.516	0.762	0.631	0.516	0.762	SUBCLONAL	1	TRUE	1	0.16	2		392	693	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934954	9934954	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005673-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	34	263	0	ENST00000330684.3:c.1336A>G	p.Thr446Ala	p.T446A	ENST00000330684	NM_001134407.1	446	Acc/Gcc	6/13	0.3	2	FACETS	0.852	0.695	1			1	CLONAL	1	TRUE	NA	0.16	2		263	499	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249405	110249406	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0005673-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1424	79	725	2	ENST00000374672.4:c.1167_1168delinsTT	p.Arg390Trp	p.R390W	ENST00000374672	NM_004235.4	389	ccCCgg/ccTTgg	4/5	1	2	FACETS	0.657	0.575	0.746	0.657	0.575	0.746	SUBCLONAL	1	TRUE	1	0.16	2		727	1503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0005683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	161	646	4	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.351990180153773	1	FACETS	0.966	0.898	1	1	0.993	1	CLONAL	2	TRUE	0	0.351990180153773	1		650	390	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570097	212570097	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	37	311	0	ENST00000342788.4:c.1144G>T	p.Glu382Ter	p.E382*	ENST00000342788	NM_005235.2	382	Gaa/Taa	10/28	0.351990180153773	0	FACETS	0.561	0.465	0.666			1	SUBCLONAL	1	TRUE	0	0.351990180153773	0		311	243	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412946	49412946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	311	628	0	ENST00000418115.1:c.77G>A	p.Ser26Asn	p.S26N	ENST00000418115	NM_001664.2	26	aGc/aAc	2/5	0.351990180153773	3	FACETS	0.957	0.908	1	1	0.994	1	CLONAL	3	TRUE	1	0.351990180153773	3		628	724	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449521	149449521	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	95	527	0	ENST00000286301.3:c.1425G>C	p.Glu475Asp	p.E475D	ENST00000286301	NM_005211.3	475	gaG/gaC	10/22	1	2	FACETS	0.862	0.769	0.962	0.862	0.769	0.962	CLONAL	1	TRUE	1	0.351990180153773	2		527	626	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176330	24176330	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1057517825	NA	P-0005683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	175	500	0	ENST00000263121.7:c.1121G>A	p.Arg374Gln	p.R374Q	ENST00000263121	NM_003073.3	374	cGg/cAg	9/9	0.309177270761121	1	FACETS	0.795	0.738	0.854	1	0.991	1	SUBCLONAL	2	TRUE	0	0.351990180153773	1		500	515	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650367	48650367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782263736	NA	P-0005683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	149	326	0	ENST00000376670.3:c.337C>T	p.Arg113Cys	p.R113C	ENST00000376670	NM_002049.3	113	Cgc/Tgc	3/6	1	1	FACETS	0.957	0.898	1	1	0.994	1	CLONAL	3	TRUE	0	0.351990180153773	1		326	243	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245586	41245587	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs80357522	NA	P-0005683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	72	510	4	ENST00000357654.3:c.1961dup	p.Tyr655ValfsTer18	p.Y655Vfs*18	ENST00000357654	NM_007294.3	654	aag/aaAg	10/23	0.351990180153773	2	FACETS	0.773	0.677	0.877	0.387	0.338	0.439	SUBCLONAL	1	TRUE	0	0.351990180153773	2		514	529	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492732	56492732	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	562	511	1	ENST00000407977.2:c.207del	p.Phe69LeufsTer7	p.F69Lfs*7	ENST00000407977		69	ttT/tt	2/10	0.351990180153773	2	FACETS	1	0.992	1	1	0.998	1	CLONAL	4	TRUE	0	0.351990180153773	2		512	764	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125309	47125310	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005693-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	182	689	0	ENST00000409792.3:c.5960dup	p.Ser1988ValfsTer2	p.S1988Vfs*2	ENST00000409792	NM_014159.6	1987	gtg/gtTg	12/21	NA	2	FACETS	0.314	0.289	0.341			1	INDETERMINATE	1	TRUE	NA	0.912803989368627	2		689	1268	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715837	117715850	+	frameshift_variant	Frame_Shift_Del	DEL	TTTTAAAGATCTCT	TTTTAAAGATCTCT	-	novel	NA	P-0005693-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	120	412	0	ENST00000368508.3:c.908_921del	p.Lys303ThrfsTer5	p.K303Tfs*5	ENST00000368508	NM_002944.2	303	aAGAGATCTTTAAAA/a	9/43	1	2	FACETS	0.303	0.273	0.334	0.303	0.273	0.334	SUBCLONAL	1	TRUE	1	0.912803989368627	2		412	868	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	161	192	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.912	0.841	0.986	0.912	0.841	0.986	CLONAL	1	TRUE	1	0.610522795532547	2		192	578	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913233	NA	P-0005696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	35	634	0	ENST00000451590.1:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000451590	NM_001130442.1	61	cAg/cTg	3/5	1	2	FACETS	0.173	0.141	0.209	0.173	0.141	0.209	SUBCLONAL	1	TRUE	1	0.610522795532547	2		634	663	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0005696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	238	710	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.983	0.921	1	0.983	0.921	1	CLONAL	1	TRUE	1	0.610522795532547	2		710	793	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190296	32190296	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	13	338	0	ENST00000375023.3:c.443G>A	p.Gly148Glu	p.G148E	ENST00000375023	NM_004557.3	148	gGa/gAa	3/30	1	2	FACETS	0.165	0.117	0.223	0.165	0.117	0.223	SUBCLONAL	1	TRUE	1	0.610522795532547	2		338	258	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685303	89685303	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	63	287	0	ENST00000371953.3:c.198G>C	p.Lys66Asn	p.K66N	ENST00000371953	NM_000314.4	66	aaG/aaC	3/9	0.610522795532547	1	FACETS	0.806	0.711	0.904	0.806	0.711	0.904	CLONAL	1	TRUE	0	0.610522795532547	1		287	178	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915455	112915455	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121918463	NA	P-0005696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	47	743	0	ENST00000351677.2:c.854T>C	p.Phe285Ser	p.F285S	ENST00000351677	NM_002834.3	285	tTt/tCt	8/16	1	2	FACETS	0.259	0.218	0.304	0.259	0.218	0.304	SUBCLONAL	1	TRUE	1	0.610522795532547	2		743	595	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926248	112926248	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs121918468	NA	P-0005696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	78	622	0	ENST00000351677.2:c.1381G>A	p.Ala461Thr	p.A461T	ENST00000351677	NM_002834.3	461	Gct/Act	12/16	1	2	FACETS	0.449	0.395	0.507	0.449	0.395	0.507	SUBCLONAL	1	TRUE	1	0.610522795532547	2		622	569	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913514	NA	P-0005699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	37	671	0	ENST00000288135.5:c.2466T>G	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaG	17/21	0.36260042452526	1	FACETS	0.884	0.737	1	0.884	0.737	1	CLONAL	1	FALSE	0	0.36260042452526	1		671	189	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934291	39934291	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	29	547	0	ENST00000378444.4:c.308A>G	p.Glu103Gly	p.E103G	ENST00000378444	NM_001123385.1	103	gAg/gGg	4/15	0.36260042452526	2	FACETS	0.64	0.516	0.78			1	SUBCLONAL	1	FALSE	NA	0.36260042452526	2		547	250	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0005704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	146	324	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.637561783672666	3	FACETS	1	0.984	1	0.645	0.593	0.699	CLONAL	1	TRUE	1	0.637536808968726	3		324	468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577595	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0005704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	385	705	0	ENST00000269305.4:c.686_687del	p.Cys229TyrfsTer10	p.C229Yfs*10	ENST00000269305	NM_001126112.2	229	tGT/t	7/11	0.633786463007384	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.637536808968726	2		705	602	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610439	10610439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202181679	NA	P-0005704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	274	873	5	ENST00000171111.5:c.271G>A	p.Ala91Thr	p.A91T	ENST00000171111	NM_203500.1	91	Gcc/Acc	2/6	0.637536808968726	2	FACETS	0.698	0.655	0.743	0.349	0.327	0.372	SUBCLONAL	1	TRUE	0	0.637536808968726	2		878	1231	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506389	120506389	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	189	808	0	ENST00000256646.2:c.1723G>A	p.Asp575Asn	p.D575N	ENST00000256646	NM_024408.3	575	Gac/Aac	11/34	0.633786463007384	2	FACETS	0.89	0.826	0.956	0.445	0.413	0.478	CLONAL	1	TRUE	0	0.637536808968726	2		808	666	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099248	157099248	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	235	682	1	ENST00000346085.5:c.185G>T	p.Gly62Val	p.G62V	ENST00000346085	NM_020732.3	62	gGg/gTg	1/20	1	2	FACETS	0.949	0.888	1	0.949	0.888	1	CLONAL	1	TRUE	1	0.637536808968726	2		683	777	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023690	1023690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	170	785	0	ENST00000358495.3:c.874C>T	p.Pro292Ser	p.P292S	ENST00000358495	NM_134424.2	292	Ccg/Tcg	10/12	NA	2	FACETS	0.936	0.865	1			1	INDETERMINATE	1	TRUE	NA	0.637536808968726	2		785	570	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47735843	47735843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	228	976	0	ENST00000449228.1:c.17G>A	p.Gly6Glu	p.G6E	ENST00000449228	NM_001127240.2	6	gGg/gAg	1/4	1	2	FACETS	0.842	0.787	0.9	0.842	0.787	0.9	CLONAL	1	TRUE	1	0.637536808968726	2		976	849	SUCCESS
AR	367	MSKCC	GRCh37	X	66937465	66937465	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs1569314508	NA	P-0005711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	413	247	0	ENST00000374690.3:c.2318+1G>C		p.X773_splice	ENST00000374690	NM_000044.3	773			0.553515632107397	3	FACETS	0.88	0.855	0.905			1	CLONAL	4	TRUE	NA	0.553515632107397	3		247	541	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577591	7577596	+	inframe_deletion	In_Frame_Del	DEL	GGTACA	GGTACA	-	novel	NA	P-0005711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	291	533	0	ENST00000269305.4:c.685_690del	p.Cys229_Thr230del	p.C229_T230del	ENST00000269305	NM_001126112.2	229	TGTACC/-	7/11	0.553515632107397	2	FACETS	0.804	0.762	0.846	0.804	0.762	0.846	CLONAL	2	TRUE	0	0.553515632107397	2		533	654	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40498659	40498659	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	189	483	0	ENST00000264657.5:c.201G>T	p.Gln67His	p.Q67H	ENST00000264657	NM_139276.2	67	caG/caT	3/24	0.553515632107397	3	FACETS	0.904	0.835	0.975	0.452	0.417	0.488	CLONAL	1	TRUE	1	0.553515632107397	3		483	965	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577543	7577543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1019340046	NA	P-0005714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	8	678	0	ENST00000269305.4:c.738G>A	p.Met246Ile	p.M246I	ENST00000269305	NM_001126112.2	246	atG/atA	7/11	1	2	FACETS	0.304	0.196	0.445	0.304	0.196	0.445	SUBCLONAL	1	TRUE	1	0.282553577566378	2		678	186	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188164	11188164	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587777893	NA	P-0005714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	26	597	0	ENST00000361445.4:c.5930C>A	p.Thr1977Lys	p.T1977K	ENST00000361445	NM_004958.3	1977	aCa/aAa	43/58	1	2	FACETS	1	0.842	1	1	0.842	1	CLONAL	1	TRUE	1	0.282553577566378	2		597	173	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183748	10183748	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs869025619	NA	P-0005714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	24	460	0	ENST00000256474.2:c.217C>T	p.Gln73Ter	p.Q73*	ENST00000256474	NM_000551.3	73	Cag/Tag	1/3	0.282553577566378	1	FACETS	0.858	0.679	1	0.858	0.679	1	CLONAL	1	TRUE	0	0.282553577566378	1		460	170	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164717	47164717	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	21	619	0	ENST00000409792.3:c.1409C>A	p.Ser470Ter	p.S470*	ENST00000409792	NM_014159.6	470	tCa/tAa	3/21	0.282553577566378	1	FACETS	0.808	0.627	1	0.808	0.627	1	CLONAL	1	TRUE	0	0.282553577566378	1		619	158	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443592	52443592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	32	576	0	ENST00000460680.1:c.100G>T	p.Asp34Tyr	p.D34Y	ENST00000460680	NM_004656.3	34	Gac/Tac	3/17	0.282553577566378	1	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	0	0.282553577566378	1		576	174	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418409	49418409	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	35	535	1	ENST00000301067.7:c.16004C>T	p.Pro5335Leu	p.P5335L	ENST00000301067	NM_003482.3	5335	cCc/cTc	50/54	0.258324459577778	3	FACETS	0.852	0.707	1	0.852	0.707	1	CLONAL	2	TRUE	1	0.282553577566378	3		536	166	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860080	57860080	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs563340967	NA	P-0005714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	81	843	2	ENST00000228682.2:c.820G>T	p.Gly274Cys	p.G274C	ENST00000228682	NM_005269.2	274	Ggc/Tgc	8/12	0.258324459577778	3	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	1	0.282553577566378	3		845	301	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805420	1805420	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	27	519	0	ENST00000260795.2:c.932del	p.Thr311ArgfsTer11	p.T311Rfs*11	ENST00000260795		311	aCg/ag	7/17	1	2	FACETS	1	0.802	1	1	0.802	1	CLONAL	1	TRUE	1	0.282553577566378	2		519	191	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0005717-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	417	585	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.34231035285104	7	FACETS	1	0.981	1	0.841	0.803	0.88	CLONAL	4	FALSE	2	0.34231035285104	7		585	1075	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0005717-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	164	386	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.24945429359692	2	FACETS	0.823	0.76	0.889	0.823	0.76	0.889	CLONAL	2	FALSE	0	0.34231035285104	2		386	582	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102056778	102056778	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005717-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	168	457	0	ENST00000282441.5:c.718A>G	p.Met240Val	p.M240V	ENST00000282441	NM_001130145.2	240	Atg/Gtg	4/9	0.181335093974478	5	FACETS	0.951	0.876	1	0.634	0.584	0.687	INDETERMINATE	2	FALSE	2	0.34231035285104	5		457	781	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005741-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	335	510	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.515073988593507	4	FACETS	0.947	0.897	0.997			1	CLONAL	2	TRUE	NA	0.552548980494989	4		510	994	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723067	52723067	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770861676	NA	P-0005741-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	461	410	1	ENST00000322088.6:c.1252C>T	p.Arg418Trp	p.R418W	ENST00000322088	NM_014225.5	418	Cgg/Tgg	10/15	NA	2	FACETS	0.982	0.945	1			1	INDETERMINATE	2	TRUE	NA	0.552548980494989	2		411	850	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0005741-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	439	392	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.551548203485679	2	FACETS	0.954	0.916	0.991	0.954	0.916	0.991	CLONAL	2	TRUE	0	0.552548980494989	2		392	833	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845890	156845890	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750477154	NA	P-0005741-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1563	424	731	4	ENST00000524377.1:c.1520G>A	p.Arg507His	p.R507H	ENST00000524377	NM_002529.3	507	cGc/cAc	13/17	0.552548980494989	3	FACETS	0.986	0.936	1	0.493	0.468	0.519	CLONAL	1	TRUE	1	0.552548980494989	3		735	1987	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416618	49416618	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005741-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	209	395	1	ENST00000301067.7:c.16093C>T	p.Gln5365Ter	p.Q5365*	ENST00000301067	NM_003482.3	5365	Cag/Tag	51/54	0.552548980494989	2	FACETS	1	0.966	1	0.53	0.493	0.567	CLONAL	1	TRUE	0	0.552548980494989	2		396	714	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416533	49416534	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGC	novel	NA	P-0005754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	204	521	0	ENST00000301067.7:c.16175_16177dup	p.Arg5392_Thr5393insSer	p.R5392_T5393insS	ENST00000301067	NM_003482.3	5393	acc/aGCAcc	51/54	1	2	FACETS	0.966	0.895	1	0.966	0.895	1	CLONAL	1	TRUE	1	0.37	2		521	1141	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610357	81610358	+	missense_variant	Missense_Mutation	DNP	CT	CT	AC	novel	NA	P-0005754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	62	566	0	ENST00000298171.2:c.1955_1956delinsAC	p.Pro652His	p.P652H	ENST00000298171	NM_000369.2	652	cCT/cAC	10/10	1	2	FACETS	0.294	0.253	0.34	0.294	0.253	0.34	SUBCLONAL	1	TRUE	1	0.37	2		566	1138	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	93	192	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.225601143201849	2		192	563	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268766	41268766	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	104	767	0	ENST00000349496.5:c.1004A>T	p.Lys335Ile	p.K335I	ENST00000349496	NM_001904.3	335	aAa/aTa	7/15	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.225601143201849	2		767	823	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203436	NA	P-0005757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	112	571	0	ENST00000269305.4:c.487T>C	p.Tyr163His	p.Y163H	ENST00000269305	NM_001126112.2	163	Tac/Cac	5/11	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.225601143201849	2		571	951	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825386	134825386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	109	669	0	ENST00000398015.3:c.902G>A	p.Cys301Tyr	p.C301Y	ENST00000398015	NM_004441.4	301	tGc/tAc	4/16	1	2	FACETS	0.864	0.774	0.96	0.864	0.774	0.96	CLONAL	1	TRUE	1	0.225601143201849	2		669	1118	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061223	38061228	+	inframe_deletion	In_Frame_Del	DEL	TCTCGA	TCTCGA	-	novel	NA	P-0005760-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	129	394	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	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.337393356358764	2		394	573	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593582	55593587	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	AAACCC	AAACCC	-	novel	NA	P-0005780-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	392	443	1	ENST00000288135.5:c.1649_1654del	p.Lys550_Pro551del	p.K550_P551del	ENST00000288135	NM_000222.2	550	AAACCC/-	11/21	1	2	FACETS	0.98	0.935	1	0.98	0.935	1	CLONAL	1	TRUE	1	0.85	2		444	941	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0005790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	329	513	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.604031380786458	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.604031380786458	1		515	676	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884909	134884909	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	191	420	3	ENST00000398015.3:c.1685T>C	p.Val562Ala	p.V562A	ENST00000398015	NM_004441.4	562	gTc/gCc	8/16	1	2	FACETS	0.968	0.9	1	0.968	0.9	1	CLONAL	1	TRUE	1	0.604031380786458	2		423	653	SUCCESS
APC	324	MSKCC	GRCh37	5	112176263	112176263	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	98	487	0	ENST00000257430.4:c.4972A>C	p.Ser1658Arg	p.S1658R	ENST00000257430	NM_000038.5	1658	Agt/Cgt	16/16	0.604031380786458	1	FACETS	0.902	0.819	0.987	0.902	0.819	0.987	CLONAL	1	TRUE	0	0.604031380786458	1		487	251	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404935	404935	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	25	431	0	ENST00000399788.2:c.4259C>G	p.Pro1420Arg	p.P1420R	ENST00000399788	NM_001042603.1	1420	cCt/cGt	26/28	0.604031380786458	1	FACETS	0.159	0.125	0.198	0.159	0.125	0.198	SUBCLONAL	1	TRUE	0	0.604031380786458	1		431	364	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446426	49446426	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	194	454	0	ENST00000301067.7:c.1179A>C	p.Gln393His	p.Q393H	ENST00000301067	NM_003482.3	393	caA/caC	9/54	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.604031380786458	2		454	640	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599846	10599878	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCCCCGCCCCCAGGGCCTCACCAAGGACGTAG	TTCCCCGCCCCCAGGGCCTCACCAAGGACGTAG	-	novel	NA	P-0005790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	137	437	0	ENST00000171111.5:c.1698_1708+22del		p.X566_splice	ENST00000171111	NM_203500.1	566		5/6	0.604031380786458	1	FACETS	0.741	0.68	0.804	0.741	0.68	0.804	SUBCLONAL	1	TRUE	0	0.604031380786458	1		437	427	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919322	48919337	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	AGCAAATTGGAAAGGT	AGCAAATTGGAAAGGT	-	novel	NA	P-0005790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	70	289	0	ENST00000267163.4:c.488_500+3del		p.X163_splice	ENST00000267163	NM_000321.2	163		4/27	0.604031380786458	1	FACETS	0.752	0.667	0.842	0.752	0.667	0.842	SUBCLONAL	1	TRUE	0	0.604031380786458	1		289	215	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602847	10602865	+	frameshift_variant	Frame_Shift_Del	DEL	TCGGACTCGCAGCGCACGT	TCGGACTCGCAGCGCACGT	-	novel	NA	P-0005790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	87	525	0	ENST00000171111.5:c.713_731del	p.Asn238ArgfsTer33	p.N238Rfs*33	ENST00000171111	NM_203500.1	238	aACGTGCGCTGCGAGTCCGAg/ag	3/6	0.604031380786458	1	FACETS	0.48	0.427	0.536	0.48	0.427	0.536	SUBCLONAL	1	TRUE	0	0.604031380786458	1		525	419	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602574	10602575	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGT	novel	NA	P-0005790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	50	464	0	ENST00000171111.5:c.1001_1003dup	p.Tyr334dup	p.Y334dup	ENST00000171111	NM_203500.1	334	ttc/tACTtc	3/6	0.604031380786458	1	FACETS	0.363	0.31	0.422	0.363	0.31	0.422	SUBCLONAL	1	TRUE	0	0.604031380786458	1		464	318	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192544	138192551	+	frameshift_variant	Frame_Shift_Del	DEL	TCGGGAGA	TCGGGAGA	-	novel	NA	P-0005790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	279	431	0	ENST00000237289.4:c.182_189del	p.Arg61HisfsTer37	p.R61Hfs*37	ENST00000237289	NM_001270507.1	60	ttTCGGGAGAtc/tttc	2/9	0.543854034372898	3	FACETS	0.911	0.862	0.961	0.911	0.862	0.961	CLONAL	2	TRUE	1	0.604031380786458	3		431	660	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43817907	43817907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005797-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	111	646	0	ENST00000372470.3:c.1586G>A	p.Trp529Ter	p.W529*	ENST00000372470	NM_005373.2	529	tGg/tAg	11/12	1	2	FACETS	0.881	0.795	0.971	0.881	0.795	0.971	CLONAL	1	TRUE	1	0.479276158632738	2		646	526	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360558	70360558	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1265835207	NA	P-0005797-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	90	827	1	ENST00000374080.3:c.6118G>T	p.Ala2040Ser	p.A2040S	ENST00000374080		2040	Gca/Tca	42/45	1	2	FACETS	0.481	0.427	0.54	0.481	0.427	0.54	SUBCLONAL	1	TRUE	1	0.479276158632738	2		828	780	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602799	10602799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005808-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	147	635	0	ENST00000171111.5:c.779G>T	p.Arg260Leu	p.R260L	ENST00000171111	NM_203500.1	260	cGa/cTa	3/6	0.3	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	0	0.3	1		635	620	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191491	10191491	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1553620313	NA	P-0005808-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	120	527	0	ENST00000256474.2:c.484T>C	p.Cys162Arg	p.C162R	ENST00000256474	NM_000551.3	162	Tgc/Cgc	3/3	0.222679774543584	2	FACETS	1	0.984	1	0.733	0.664	0.804	CLONAL	1	FALSE	0	0.3	2		527	546	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242735	66242735	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005808-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	180	640	0	ENST00000273854.3:c.1837G>T	p.Ala613Ser	p.A613S	ENST00000273854	NM_004439.5	613	Gcc/Tcc	9/18	0.3	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	0	0.3	1		640	929	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233142	69233142	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005808-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	198	681	0	ENST00000462284.1:c.1007T>G	p.Leu336Arg	p.L336R	ENST00000462284	NM_002392.5	336	cTt/cGt	11/11	0.10503510722475	4	FACETS	1	0.989	1	0.716	0.662	0.773	INDETERMINATE	1	FALSE	2	0.3	4		681	1198	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026247	36026247	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005808-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	127	727	0	ENST00000358208.4:c.850del	p.Val284CysfsTer17	p.V284Cfs*17	ENST00000358208		283	gaG/ga	7/12	0.102947213106925	3	FACETS	0.754	0.684	0.826	0.754	0.684	0.826	INDETERMINATE	2	FALSE	1	0.3	3		727	646	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0005818-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	129	585	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.201641773474874	3	FACETS	1	0.984	1	0.709	0.643	0.778	CLONAL	1	TRUE	1	0.274511081905942	3		585	754	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0005818-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	59	284	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.201641773474874	3	FACETS	1	0.957	1	0.642	0.554	0.736	CLONAL	1	TRUE	1	0.274511081905942	3		284	381	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7152908	7152908	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005818-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	104	602	0	ENST00000302850.5:c.2060C>A	p.Pro687Gln	p.P687Q	ENST00000302850	NM_000208.2	687	cCa/cAa	10/22	0.252468018297324	0	FACETS	1	0.915	1			1	CLONAL	1	TRUE	0	0.274511081905942	0		602	539	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111452	8111453	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005818-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	93	608	0	ENST00000346208.3:c.939dup	p.Gly314ArgfsTer38	p.G314Rfs*38	ENST00000346208		313	gca/gcAa	5/6	1	2	FACETS	0.972	0.865	1	0.972	0.865	1	CLONAL	1	TRUE	1	0.274511081905942	2		608	697	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662139	227662139	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	90	644	1	ENST00000305123.5:c.1316G>A	p.Arg439Gln	p.R439Q	ENST00000305123	NM_005544.2	439	cGg/cAg	1/2	1	2	FACETS	0.239	0.211	0.269	0.239	0.211	0.269	SUBCLONAL	1	TRUE	1	0.642803902679416	2		645	1172	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005841-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	125	192	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.541435769353375	2		192	452	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0005841-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	325	525	1	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.541435769353375	2		526	1084	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447279	187447279	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005841-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	206	387	0	ENST00000232014.4:c.914G>T	p.Arg305Ile	p.R305I	ENST00000232014	NM_001130845.1	305	aGa/aTa	5/10	1	2	FACETS	0.883	0.82	0.947	0.883	0.82	0.947	CLONAL	1	TRUE	1	0.541435769353375	2		387	862	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630399	187630399	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005841-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	320	630	0	ENST00000441802.2:c.583T>G	p.Phe195Val	p.F195V	ENST00000441802	NM_005245.3	195	Ttt/Gtt	2/27	1	2	FACETS	0.952	0.898	1	0.952	0.898	1	CLONAL	1	TRUE	1	0.541435769353375	2		630	1242	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0005845-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	394	573	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.282204152237704	3	FACETS	0.904	0.861	0.948	0.904	0.861	0.948	INDETERMINATE	2	TRUE	1	0.481434099524865	3		573	1123	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937729	76937729	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005845-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	139	387	0	ENST00000373344.5:c.3019C>T	p.Gln1007Ter	p.Q1007*	ENST00000373344	NM_000489.3	1007	Caa/Taa	9/35	0.481434099524865	3	FACETS	0.908	0.827	0.993	0.454	0.413	0.497	CLONAL	1	TRUE	1	0.481434099524865	3		387	789	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0005851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	281	283	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.394610223810843	3	FACETS	0.954	0.905	1	0.954	0.905	1	CLONAL	3	TRUE	0	0.394610223810843	3		283	596	SUCCESS
APC	324	MSKCC	GRCh37	5	112177930	112177930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35540155	NA	P-0005851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	38	402	0	ENST00000257430.4:c.6639G>A	p.Met2213Ile	p.M2213I	ENST00000257430	NM_000038.5	2213	atG/atA	16/16	1	2	FACETS	0.436	0.36	0.52	0.436	0.36	0.52	SUBCLONAL	1	TRUE	1	0.394610223810843	2		402	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057519990	NA	P-0005851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	235	613	0	ENST00000269305.4:c.796G>T	p.Gly266Ter	p.G266*	ENST00000269305	NM_001126112.2	266	Gga/Tga	8/11	0.394610223810843	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.394610223810843	1		613	744	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105612	27105612	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	82	663	0	ENST00000324856.7:c.5223G>C	p.Gln1741His	p.Q1741H	ENST00000324856	NM_006015.4	1741	caG/caC	20/20	1	2	FACETS	0.501	0.441	0.565	0.501	0.441	0.565	SUBCLONAL	1	TRUE	1	0.394610223810843	2		663	830	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105712	27105712	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	92	500	0	ENST00000324856.7:c.5323G>T	p.Glu1775Ter	p.E1775*	ENST00000324856	NM_006015.4	1775	Gag/Tag	20/20	1	2	FACETS	0.665	0.591	0.744	0.665	0.591	0.744	SUBCLONAL	1	TRUE	1	0.394610223810843	2		500	701	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143189	30143189	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs748952373	NA	P-0005851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	121	288	1	ENST00000389048.3:c.337G>T	p.Gly113Cys	p.G113C	ENST00000389048	NM_004304.4	113	Ggt/Tgt	1/29	1	2	FACETS	0.765	0.697	0.835	1	0.986	1	SUBCLONAL	2	TRUE	1	0.394610223810843	2		289	401	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447778	187447778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758046316	NA	P-0005851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	209	368	1	ENST00000232014.4:c.415C>T	p.Pro139Ser	p.P139S	ENST00000232014	NM_001130845.1	139	Cct/Tct	5/10	0.340723607296223	2	FACETS	0.997	0.934	1	0.997	0.934	1	CLONAL	2	TRUE	0	0.394610223810843	2		369	531	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213800	66213800	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	31	455	1	ENST00000273854.3:c.2630G>A	p.Arg877Lys	p.R877K	ENST00000273854	NM_004439.5	877	aGa/aAa	15/18	0.394610223810843	1	FACETS	0.332	0.268	0.404	0.332	0.268	0.404	SUBCLONAL	1	TRUE	0	0.394610223810843	1		456	380	SUCCESS
APC	324	MSKCC	GRCh37	5	112176200	112176200	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	46	478	0	ENST00000257430.4:c.4909G>A	p.Asp1637Asn	p.D1637N	ENST00000257430	NM_000038.5	1637	Gat/Aat	16/16	1	2	FACETS	0.415	0.349	0.488	0.415	0.349	0.488	SUBCLONAL	1	TRUE	1	0.394610223810843	2		478	562	SUCCESS
APC	324	MSKCC	GRCh37	5	112177441	112177441	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1396748837	NA	P-0005851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	91	532	0	ENST00000257430.4:c.6150G>C	p.Lys2050Asn	p.K2050N	ENST00000257430	NM_000038.5	2050	aaG/aaC	16/16	1	2	FACETS	0.766	0.681	0.856	0.766	0.681	0.856	SUBCLONAL	1	TRUE	1	0.394610223810843	2		532	602	SUCCESS
APC	324	MSKCC	GRCh37	5	112178853	112178853	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	54	440	0	ENST00000257430.4:c.7562G>T	p.Arg2521Ile	p.R2521I	ENST00000257430	NM_000038.5	2521	aGa/aTa	16/16	1	2	FACETS	0.524	0.448	0.608	0.524	0.448	0.608	SUBCLONAL	1	TRUE	1	0.394610223810843	2		440	522	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508473	106508473	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	154	194	0	ENST00000359195.3:c.467C>A	p.Ala156Glu	p.A156E	ENST00000359195	NM_002649.2	156	gCg/gAg	2/11	0.381966575365176	4	FACETS	1	0.98	1	0.794	0.733	0.857	CLONAL	2	TRUE	1	0.394610223810843	4		194	457	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520072	106520072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	34	349	0	ENST00000359195.3:c.2500C>T	p.His834Tyr	p.H834Y	ENST00000359195	NM_002649.2	834	Cat/Tat	6/11	0.381966575365176	4	FACETS	0.437	0.356	0.528	0.146	0.118	0.176	SUBCLONAL	1	TRUE	1	0.394610223810843	4		349	550	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375990	8375990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142960593	NA	P-0005851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	67	620	1	ENST00000356435.5:c.4607G>A	p.Arg1536His	p.R1536H	ENST00000356435		1536	cGt/cAt	28/35	0.394610223810843	1	FACETS	0.541	0.471	0.616	0.541	0.471	0.616	SUBCLONAL	1	TRUE	0	0.394610223810843	1		621	504	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518118	8518118	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	98	379	0	ENST00000356435.5:c.1273C>A	p.Gln425Lys	p.Q425K	ENST00000356435		425	Cag/Aag	10/35	0.394610223810843	1	FACETS	0.949	0.852	1	0.949	0.852	1	CLONAL	1	TRUE	0	0.394610223810843	1		379	420	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811634	102811634	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	75	553	0	ENST00000307046.8:c.550A>C	p.Ser184Arg	p.S184R	ENST00000307046	NM_001111285.1	184	Agt/Cgt	4/4	0.394610223810843	1	FACETS	0.565	0.496	0.639	0.565	0.496	0.639	SUBCLONAL	1	TRUE	0	0.394610223810843	1		553	540	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133238234	133238234	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	144	538	0	ENST00000320574.5:c.2743G>A	p.Glu915Lys	p.E915K	ENST00000320574	NM_006231.2	915	Gag/Aag	24/49	NA	2	FACETS	1	0.958	1			1	INDETERMINATE	1	TRUE	NA	0.394610223810843	2		538	677	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585470	29585470	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	79	286	0	ENST00000356175.3:c.4219G>T	p.Asp1407Tyr	p.D1407Y	ENST00000356175	NM_000267.3	1407	Gat/Tat	31/57	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.394610223810843	2		286	379	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533065	63533065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376248072	NA	P-0005851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	167	548	0	ENST00000307078.5:c.1829G>A	p.Arg610Gln	p.R610Q	ENST00000307078	NM_004655.3	610	cGg/cAg	7/11	0.340723607296223	2	FACETS	0.995	0.915	1	0.497	0.457	0.539	CLONAL	1	TRUE	0	0.394610223810843	2		548	851	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368239	45368239	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	35	575	0	ENST00000262160.6:c.1363C>T	p.Gln455Ter	p.Q455*	ENST00000262160	NM_005901.5	455	Cag/Tag	11/11	0.394610223810843	1	FACETS	0.235	0.192	0.284	0.235	0.192	0.284	SUBCLONAL	1	TRUE	0	0.394610223810843	1		575	605	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343057	70343057	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	85	366	1	ENST00000374080.3:c.1598A>G	p.Gln533Arg	p.Q533R	ENST00000374080		533	cAg/cGg	11/45	0.331510070027838	0	FACETS	0.839	0.749	0.932			1	CLONAL	1	TRUE	NA	0.394610223810843	0		367	311	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430792	181430792	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	202	491	0	ENST00000325404.1:c.644C>A	p.Thr215Asn	p.T215N	ENST00000325404	NM_003106.3	215	aCc/aAc	1/1	0.515230146307418	3	FACETS	1	0.965	1	0.355	0.329	0.382	CLONAL	1	TRUE	0	0.515230146307418	3		491	926	SUCCESS
CBL	867	MSKCC	GRCh37	11	119158617	119158617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1461378431	NA	P-0005878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	66	216	0	ENST00000264033.4:c.1997C>T	p.Pro666Leu	p.P666L	ENST00000264033	NM_005188.3	666	cCt/cTt	12/16	0.160455412417758	3	FACETS	0.693	0.603	0.79	0.231	0.201	0.264	INDETERMINATE	1	TRUE	0	0.515230146307418	3		216	465	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975684	26975684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	304	499	1	ENST00000381527.3:c.1192G>A	p.Gly398Arg	p.G398R	ENST00000381527	NM_001260.1	398	Gga/Aga	12/13	0.456274332003525	3	FACETS	0.887	0.839	0.935			1	CLONAL	2	TRUE	NA	0.515230146307418	3		500	837	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430815	47430815	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	154	236	0	ENST00000377045.4:c.1781del	p.Leu594CysfsTer?	p.L594Cfs*?	ENST00000377045	NM_001654.4	594	Ttg/tg	16/16	0.515230146307418	2	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.515230146307418	2		236	450	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867167	45867168	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0005878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	65	286	0	ENST00000391945.4:c.951_952delinsTT	p.Glu317_Ala318delinsAspSer	p.E317_A318delinsDS	ENST00000391945	NM_000400.3	317	gaGGca/gaTTca	11/23	0.191703420649963	2	FACETS	0.673	0.586	0.766	0.336	0.293	0.383	INDETERMINATE	1	TRUE	0	0.515230146307418	2		286	375	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0005884-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	118	211	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	1	2	FACETS	0.905	0.82	0.993	0.905	0.82	0.993	CLONAL	1	TRUE	1	0.503658375064276	2		211	518	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675571	30675571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772732783	NA	P-0005884-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1420	288	541	0	ENST00000376406.3:c.2785G>A	p.Asp929Asn	p.D929N	ENST00000376406	NM_014641.2	929	Gat/Aat	8/15	0.503658375064276	3	FACETS	0.838	0.786	0.893	0.419	0.393	0.447	CLONAL	1	TRUE	1	0.503658375064276	3		541	1708	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972419	81972419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778251162	NA	P-0005884-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	320	573	0	ENST00000359376.3:c.3212G>A	p.Arg1071His	p.R1071H	ENST00000359376	NM_002661.3	1071	cGc/cAc	29/33	0.503658375064276	1	FACETS	0.911	0.861	0.962	0.911	0.861	0.962	CLONAL	1	TRUE	0	0.503658375064276	1		573	1044	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417580	139417580	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005898-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	302	636	0	ENST00000277541.6:c.464G>C	p.Cys155Ser	p.C155S	ENST00000277541	NM_017617.3	155	tGc/tCc	4/34	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.387631997454979	2		636	1396	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184388	7184388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765888394	NA	P-0005898-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	261	490	0	ENST00000302850.5:c.913G>A	p.Val305Ile	p.V305I	ENST00000302850	NM_000208.2	305	Gtc/Atc	3/22	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.387631997454979	2		490	1188	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803516	1803564	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTGGTGAGGGAGGGGGTGGCCCCTGAGCGTCATCTGCCCCCACAGAGC	GGTGGTGAGGGAGGGGGTGGCCCCTGAGCGTCATCTGCCCCCACAGAGC	-	novel	NA	P-0005898-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	60	172	2	ENST00000260795.2:c.740-45_743del		p.X247_splice	ENST00000260795		247		6/17	1	2	FACETS	0.718	0.62	0.824	0.718	0.62	0.824	SUBCLONAL	1	TRUE	1	0.387631997454979	2		174	431	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871987	35871988	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAT	novel	NA	P-0005898-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1393	328	805	0	ENST00000216797.5:c.623_625dup	p.Asp208dup	p.D208dup	ENST00000216797	NM_020529.2	208	gtc/gATGtc	4/6	1	2	FACETS	0.983	0.926	1	0.983	0.926	1	CLONAL	1	TRUE	1	0.387631997454979	2		805	1721	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289242	33289242	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005922-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	418	419	0	ENST00000374542.5:c.310G>T	p.Glu104Ter	p.E104*	ENST00000374542	NM_001141970.1	104	Gag/Tag	3/8	0.530619156335656	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.530619156335656	2		419	754	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151855967	151855967	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005922-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	106	388	2	ENST00000262189.6:c.11651del	p.Thr3884SerfsTer5	p.T3884Sfs*5	ENST00000262189	NM_170606.2	3884	aCg/ag	44/59	0.487648408134284	4	FACETS	0.64	0.573	0.712	0.32	0.286	0.356	SUBCLONAL	1	TRUE	2	0.530619156335656	4		390	955	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572596	64572596	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005922-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	397	464	0	ENST00000312049.6:c.1260del	p.Cys421AlafsTer24	p.C421Afs*24	ENST00000312049	NM_130799.2	420	atC/at	9/10	0.530619156335656	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.530619156335656	2		464	735	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0005932-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	22	324	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.171175508093276	5	FACETS	0.922	0.73	1	0.615	0.487	0.756	INDETERMINATE	2	TRUE	2	0.432296535009894	5		324	91	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653857	89653857	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005932-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	64	363	0	ENST00000371953.3:c.155del	p.Asp52ValfsTer2	p.D52Vfs*2	ENST00000371953	NM_000314.4	52	gAt/gt	2/9	0.432296535009894	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	2	TRUE	0	0.432296535009894	2		363	142	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178056	56178071	+	frameshift_variant	Frame_Shift_Del	DEL	TTCCCTGCAGAATACC	TTCCCTGCAGAATACC	-	novel	NA	P-0005932-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	70	271	0	ENST00000399503.3:c.3032_3047del	p.Pro1011LeufsTer66	p.P1011Lfs*66	ENST00000399503	NM_005921.1	1010	aTTCCCTGCAGAATACCt/at	14/20	0.432296535009894	6	FACETS	1	0.929	1	1	0.929	1	CLONAL	3	TRUE	3	0.432296535009894	6		271	190	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0005937-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	82	440	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.821	0.723	0.927	0.821	0.723	0.927	CLONAL	1	TRUE	1	0.229217825143507	2		441	871	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484596	57484596	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913494	NA	P-0005937-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	150	224	0	ENST00000371085.3:c.680A>T	p.Gln227Leu	p.Q227L	ENST00000371085	NM_000516.4	227	cAg/cTg	9/13	0.229217825143507	3	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	1	0.229217825143507	3		224	718	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004900	150004900	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005937-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	113	549	0	ENST00000253339.5:c.1325A>T	p.Gln442Leu	p.Q442L	ENST00000253339		442	cAg/cTg	3/7	1	2	FACETS	0.993	0.892	1	0.993	0.892	1	CLONAL	1	TRUE	1	0.229217825143507	2		549	993	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858757	9858757	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1384190116	NA	P-0005937-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	85	325	0	ENST00000330684.3:c.2644T>C	p.Ser882Pro	p.S882P	ENST00000330684	NM_001134407.1	882	Tct/Cct	13/13	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.229217825143507	2		325	715	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972428	81972428	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1341635199	NA	P-0005937-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	120	833	0	ENST00000359376.3:c.3221C>T	p.Pro1074Leu	p.P1074L	ENST00000359376	NM_002661.3	1074	cCc/cTc	29/33	1	2	FACETS	0.812	0.731	0.898	0.812	0.731	0.898	CLONAL	1	TRUE	1	0.229217825143507	2		833	1290	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262889	46262889	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005937-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	314	692	0	ENST00000371998.3:c.1062T>A	p.Asn354Lys	p.N354K	ENST00000371998		354	aaT/aaA	10/23	0.229217825143507	3	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	1	0.229217825143507	3		692	1522	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034457	47034457	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0005937-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	130	667	0	ENST00000377604.3:c.542T>A	p.Leu181Ter	p.L181*	ENST00000377604	NM_001204468.1	181	tTg/tAg	6/24	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.229217825143507	2		667	1084	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411717	63411717	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005937-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	125	703	0	ENST00000330258.3:c.1450G>T	p.Gly484Cys	p.G484C	ENST00000330258	NM_152424.3	484	Ggt/Tgt	2/2	1	2	FACETS	0.962	0.869	1	0.962	0.869	1	CLONAL	1	TRUE	1	0.229217825143507	2		703	1134	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411726	63411726	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005937-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	131	709	0	ENST00000330258.3:c.1441G>T	p.Asp481Tyr	p.D481Y	ENST00000330258	NM_152424.3	481	Gat/Tat	2/2	1	2	FACETS	0.99	0.896	1	0.99	0.896	1	CLONAL	1	TRUE	1	0.229217825143507	2		709	1155	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195123	123195123	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005937-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	130	636	1	ENST00000218089.9:c.1466C>A	p.Thr489Asn	p.T489N	ENST00000218089	NM_001042749.1	489	aCt/aAt	16/35	1	2	FACETS	0.981	0.888	1	0.981	0.888	1	CLONAL	1	TRUE	1	0.229217825143507	2		637	1156	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0005942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	383	580	1	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	NA	2	FACETS	0.84	0.797	0.883			1	INDETERMINATE	2	TRUE	NA	0.34785103098921	2		581	1311	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984084	2984084	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	66	324	0	ENST00000396946.4:c.446G>C	p.Arg149Pro	p.R149P	ENST00000396946	NM_032415.4	149	cGc/cCc	5/25	0.184081336725974	3	FACETS	0.641	0.556	0.733	0.32	0.278	0.367	INDETERMINATE	1	TRUE	1	0.34785103098921	3		324	695	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0005942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	231	554	1	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.275885521786091	3	FACETS	1	0.991	1	0.707	0.658	0.757	CLONAL	1	TRUE	1	0.34785103098921	3		555	1103	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220641	1220641	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	304	525	0	ENST00000326873.7:c.659A>C	p.Gln220Pro	p.Q220P	ENST00000326873	NM_000455.4	220	cAg/cCg	5/10	0.34785103098921	2	FACETS	0.82	0.773	0.868	0.82	0.773	0.868	CLONAL	2	TRUE	0	0.34785103098921	2		525	1066	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578378	7578379	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0005942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	84	321	0	ENST00000269305.4:c.550_551dup	p.Asp184GlufsTer64	p.D184Efs*64	ENST00000269305	NM_001126112.2	184	gat/gaGAt	5/11	0.275885521786091	3	FACETS	0.791	0.698	0.89	0.395	0.349	0.445	SUBCLONAL	1	TRUE	1	0.34785103098921	3		321	717	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735466	40735466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182388300	NA	P-0005949-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	138	546	2	ENST00000373198.4:c.3407G>A	p.Arg1136His	p.R1136H	ENST00000373198	NM_133170.3	1136	cGt/cAt	25/32	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.337957471429348	2		548	730	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259335	89259335	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750779844	NA	P-0005949-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	136	557	0	ENST00000336596.2:c.479G>A	p.Arg160His	p.R160H	ENST00000336596	NM_005233.5	160	cGt/cAt	3/17	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.337957471429348	2		557	644	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371662	55371662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005949-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	235	544	1	ENST00000297316.4:c.352G>A	p.Val118Met	p.V118M	ENST00000297316	NM_022454.3	118	Gtg/Atg	2/2	0.337957471429348	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.337957471429348	3		545	702	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112884175	112884175	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005949-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	45	355	0	ENST00000351677.2:c.110A>C	p.Asn37Thr	p.N37T	ENST00000351677	NM_002834.3	37	aAc/aCc	2/16	1	2	FACETS	0.604	0.508	0.71	0.604	0.508	0.71	SUBCLONAL	1	TRUE	1	0.337957471429348	2		355	441	SUCCESS
BLM	641	MSKCC	GRCh37	15	91295029	91295029	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005949-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	30	429	0	ENST00000355112.3:c.812A>G	p.Lys271Arg	p.K271R	ENST00000355112	NM_000057.2	271	aAg/aGg	4/22	1	2	FACETS	0.349	0.281	0.428	0.349	0.281	0.428	SUBCLONAL	1	TRUE	1	0.337957471429348	2		429	508	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16055263	16055263	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005949-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	89	480	0	ENST00000268712.3:c.839A>T	p.Lys280Met	p.K280M	ENST00000268712	NM_006311.3	280	aAg/aTg	8/46	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.337957471429348	2		480	510	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0005959-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	331	679	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	0.996	1	CLONAL	2	TRUE	1	0.256381564431403	2		679	1230	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218052	108218052	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1064794840	NA	P-0005959-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	51	559	0	ENST00000278616.4:c.8631G>C	p.Leu2877Phe	p.L2877F	ENST00000278616	NM_000051.3	2877	ttG/ttC	59/63	1	2	FACETS	0.412	0.349	0.482	0.412	0.349	0.482	SUBCLONAL	1	TRUE	1	0.256381564431403	2		559	966	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476310	88476310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760692815	NA	P-0005959-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	54	611	2	ENST00000360948.2:c.1822G>A	p.Gly608Ser	p.G608S	ENST00000360948	NM_001012338.2	608	Ggc/Agc	15/19	1	2	FACETS	0.521	0.443	0.606	0.521	0.443	0.606	SUBCLONAL	1	TRUE	1	0.256381564431403	2		613	809	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725264	49725264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142358513	NA	P-0005959-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	14	132	0	ENST00000449682.2:c.161C>T	p.Ala54Val	p.A54V	ENST00000449682	NM_020998.3	54	gCg/gTg	2/18	1	2	FACETS	0.748	0.544	0.992	0.748	0.544	0.992	CLONAL	1	TRUE	1	0.256381564431403	2		132	146	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636796	8636796	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005959-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	118	617	0	ENST00000356435.5:c.113G>T	p.Gly38Val	p.G38V	ENST00000356435		38	gGc/gTc	2/35	1	2	FACETS	0.823	0.741	0.911	0.823	0.741	0.911	CLONAL	1	TRUE	1	0.256381564431403	2		617	1118	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622074	43622074	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005959-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	42	561	1	ENST00000355710.3:c.3091G>T	p.Asp1031Tyr	p.D1031Y	ENST00000355710	NM_020975.4	1031	Gac/Tac	19/20	0.256381564431403	3	FACETS	0.471	0.392	0.559	0.235	0.196	0.28	SUBCLONAL	1	TRUE	1	0.256381564431403	3		562	785	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114679	108114679	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0005959-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	40	210	0	ENST00000278616.4:c.497-1G>T		p.X166_splice	ENST00000278616	NM_000051.3	166			1	2	FACETS	0.843	0.702	1	0.843	0.702	1	CLONAL	1	TRUE	1	0.256381564431403	2		210	370	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350270	89350270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1482994254	NA	P-0005959-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	90	966	2	ENST00000301030.4:c.2680G>A	p.Ala894Thr	p.A894T	ENST00000301030	NM_001256183.1	894	Gcc/Acc	9/13	0.256381564431403	1	FACETS	0.609	0.539	0.684	0.609	0.539	0.684	SUBCLONAL	1	TRUE	0	0.256381564431403	1		968	1005	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005965-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	22	192	0				ENST00000310581	NM_198253.2	-/1132			0.461112125954361	1	FACETS	0.326	0.253	0.408	0.326	0.253	0.408	SUBCLONAL	1	TRUE	0	0.516695799996692	1		192	194	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183787	10183787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123481	NA	P-0005965-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	30	414	0	ENST00000256474.2:c.256C>T	p.Pro86Ser	p.P86S	ENST00000256474	NM_000551.3	86	Ccc/Tcc	1/3	0.178579845471773	2	FACETS	0.523	0.424	0.634	0.262	0.212	0.317	INDETERMINATE	1	TRUE	0	0.516695799996692	2		414	222	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174395	11174395	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005965-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	47	626	0	ENST00000361445.4:c.7280T>G	p.Leu2427Arg	p.L2427R	ENST00000361445	NM_004958.3	2427	cTg/cGg	53/58	0.191571813905697	1	FACETS	0.393	0.333	0.459	0.393	0.333	0.459	INDETERMINATE	1	TRUE	0	0.516695799996692	1		626	343	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462051	120462051	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005965-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	101	592	1	ENST00000256646.2:c.5665C>G	p.Arg1889Gly	p.R1889G	ENST00000256646	NM_024408.3	1889	Cgg/Ggg	31/34	0.34404455961674	3	FACETS	1	0.964	1	0.58	0.522	0.641	CLONAL	1	TRUE	1	0.516695799996692	3		593	424	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682417	52682418	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0005965-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	85	610	0	ENST00000394830.3:c.755_756del	p.Ile252ArgfsTer11	p.I252Rfs*11	ENST00000394830	NM_018313.4	252	aTA/a	8/30	0.178579845471773	2	FACETS	0.616	0.546	0.691	0.308	0.273	0.346	INDETERMINATE	1	TRUE	0	0.516695799996692	2		610	534	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0005975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	73	283	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.909	0.797	1	0.909	0.797	1	CLONAL	1	TRUE	1	0.314829693243519	2		283	510	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144442	11144442	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0005975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	154	451	0	ENST00000358026.2:c.3775-1G>A		p.X1259_splice	ENST00000358026	NM_001128849.1	1259			0.314829693243519	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.314829693243519	1		451	670	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678783	52678784	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	84	271	0	ENST00000394830.3:c.835dup	p.Ile279AsnfsTer8	p.I279Nfs*8	ENST00000394830	NM_018313.4	279	ata/aAta	9/30	0.314829693243519	1	FACETS	0.905	0.802	1	0.905	0.802	1	CLONAL	1	TRUE	0	0.314829693243519	1		271	497	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639139	176639139	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	48	219	0	ENST00000439151.2:c.3739A>G	p.Met1247Val	p.M1247V	ENST00000439151	NM_022455.4	1247	Atg/Gtg	5/23	1	2	FACETS	0.902	0.766	1	0.902	0.766	1	CLONAL	1	TRUE	1	0.314829693243519	2		219	338	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104377169	104377169	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	143	689	0	ENST00000369902.3:c.1280A>T	p.His427Leu	p.H427L	ENST00000369902	NM_016169.3	427	cAt/cTt	10/12	1	2	FACETS	0.909	0.828	0.995	0.909	0.828	0.995	CLONAL	1	TRUE	1	0.314829693243519	2		689	999	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244838	41244838	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs80357035	NA	P-0005975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	82	389	0	ENST00000357654.3:c.2710G>T	p.Glu904Ter	p.E904*	ENST00000357654	NM_007294.3	904	Gaa/Taa	10/23	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.314829693243519	2		389	519	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853819	59853819	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	140	639	0	ENST00000259008.2:c.2040G>T	p.Leu680Phe	p.L680F	ENST00000259008	NM_032043.2	680	ttG/ttT	14/20	1	2	FACETS	0.951	0.866	1	0.951	0.866	1	CLONAL	1	TRUE	1	0.314829693243519	2		639	935	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144058	11144058	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	132	626	0	ENST00000358026.2:c.3639G>C	p.Lys1213Asn	p.K1213N	ENST00000358026	NM_001128849.1	1213	aaG/aaC	26/36	0.314829693243519	1	FACETS	0.894	0.812	0.981	0.894	0.812	0.981	CLONAL	1	TRUE	0	0.314829693243519	1		626	790	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144802	11144802	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	100	457	0	ENST00000358026.2:c.3877G>T	p.Glu1293Ter	p.E1293*	ENST00000358026	NM_001128849.1	1293	Gaa/Taa	28/36	0.314829693243519	1	FACETS	0.834	0.746	0.927	0.834	0.746	0.927	CLONAL	1	TRUE	0	0.314829693243519	1		457	642	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602280	10602280	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	97	425	0	ENST00000171111.5:c.1298del	p.Gly433AlafsTer25	p.G433Afs*25	ENST00000171111	NM_203500.1	433	gGc/gc	3/6	0.314829693243519	1	FACETS	0.876	0.782	0.975	0.876	0.782	0.975	CLONAL	1	TRUE	0	0.314829693243519	1		425	593	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207092	1207092	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555735008	NA	P-0005975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	138	588	0	ENST00000326873.7:c.180del	p.Tyr60Ter	p.Y60*	ENST00000326873	NM_000455.4	60	taC/ta	1/10	0.314829693243519	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.314829693243519	1		588	662	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0005985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	96	300	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.709791250562183	3	FACETS	1	0.976	1	0.427	0.386	0.47	CLONAL	1	TRUE	0	0.709791250562183	3		300	286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0005985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	730	290	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.69868194170366	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	4	TRUE	0	0.709791250562183	4		290	877	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0005985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	442	573	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.682453031693616	2	FACETS	1	0.996	1	0.748	0.718	0.777	CLONAL	1	TRUE	0	0.709791250562183	2		573	833	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47672732	47672732	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	492	608	0	ENST00000233146.2:c.1322C>A	p.Thr441Asn	p.T441N	ENST00000233146	NM_000251.2	441	aCt/aAt	8/16	0.664385498088206	3	FACETS	0.968	0.942	0.993	0.968	0.942	0.993	CLONAL	3	TRUE	0	0.709791250562183	3		608	647	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81574742	81574742	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	272	618	0	ENST00000298171.2:c.638T>A	p.Leu213Gln	p.L213Q	ENST00000298171	NM_000369.2	213	cTg/cAg	8/10	0.709791250562183	3	FACETS	0.9	0.853	0.947	0.9	0.853	0.947	CLONAL	2	TRUE	1	0.709791250562183	3		618	577	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312750	91312750	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759545027	NA	P-0005985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	210	594	0	ENST00000355112.3:c.2489C>T	p.Thr830Met	p.T830M	ENST00000355112	NM_000057.2	830	aCg/aTg	12/22	0.178263817918498	2	FACETS	0.789	0.735	0.845	0.394	0.367	0.423	INDETERMINATE	1	TRUE	0	0.709791250562183	2		594	750	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176464	123176464	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1539	374	712	0	ENST00000218089.9:c.431T>C	p.Ile144Thr	p.I144T	ENST00000218089	NM_001042749.1	144	aTa/aCa	7/35	0.709791250562183	6	FACETS	1	0.993	1			1	CLONAL	1	TRUE	NA	0.709791250562183	6		712	1913	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830416	72830417	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	223	572	0	ENST00000268489.5:c.6164dup	p.Pro2056AlafsTer100	p.P2056Afs*100	ENST00000268489	NM_006885.3	2055	ccg/ccCg	9/10	1	2	FACETS	0.864	0.808	0.922	0.864	0.808	0.922	CLONAL	1	TRUE	1	0.709791250562183	2		572	727	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0005995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	160	501	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.26	2		501	1138	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178569	32178569	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	117	479	0	ENST00000375023.3:c.2825G>T	p.Gly942Val	p.G942V	ENST00000375023	NM_004557.3	942	gGg/gTg	18/30	NA	2	FACETS	0.915	0.823	1			1	INDETERMINATE	1	TRUE	NA	0.26	2		479	984	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391890	139391890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	113	479	2	ENST00000277541.6:c.6301G>A	p.Ala2101Thr	p.A2101T	ENST00000277541	NM_017617.3	2101	Gca/Aca	34/34	0.12538521561635	3	FACETS	0.761	0.683	0.845			1	INDETERMINATE	1	TRUE	NA	0.26	3		481	1290	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287294	46287294	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	111	453	0	ENST00000334344.6:c.5239G>T	p.Gly1747Ter	p.G1747*	ENST00000334344	NM_152641.2	1747	Gga/Tga	19/21	1	2	FACETS	0.997	0.896	1	0.997	0.896	1	CLONAL	1	TRUE	1	0.26	2		453	856	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2218083	2218083	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1273	151	586	0	ENST00000326181.6:c.145G>T	p.Gly49Trp	p.G49W	ENST00000326181	NM_032271.2	49	Ggg/Tgg	4/21	1	2	FACETS	0.816	0.743	0.892	0.816	0.743	0.892	CLONAL	1	TRUE	1	0.26	2		586	1424	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909712	50909712	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1217	70	624	0	ENST00000440232.2:c.1432A>C	p.Ser478Arg	p.S478R	ENST00000440232	NM_002691.3	478	Agc/Cgc	12/27	0.271063867262558	1	FACETS	0.364	0.316	0.416	0.364	0.316	0.416	SUBCLONAL	1	TRUE	0	0.26	1		624	1287	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999449	100999450	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs777896116	NA	P-0005995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	160	720	1	ENST00000325455.5:c.352_353del	p.Leu118ValfsTer65	p.L118Vfs*65	ENST00000325455	NM_001202474.3	118	CTg/g	1/8	1	2	FACETS	0.948	0.867	1	0.948	0.867	1	CLONAL	1	TRUE	1	0.26	2		721	1298	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664903	138664903	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006006-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	29	92	0	ENST00000330315.3:c.662C>T	p.Ala221Val	p.A221V	ENST00000330315	NM_023067.3	221	gCg/gTg	1/1	0.212508267771794	1	FACETS	0.445	0.365	0.532	0.445	0.365	0.532	INDETERMINATE	1	TRUE	0	0.761129165638503	1		92	106	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518250	8518250	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006006-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	216	301	0	ENST00000356435.5:c.1141G>A	p.Ala381Thr	p.A381T	ENST00000356435		381	Gct/Act	10/35	0.734498852857322	3	FACETS	1	0.963	1	0.524	0.488	0.56	CLONAL	1	TRUE	1	0.761129165638503	3		301	748	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006006-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	216	360	2	ENST00000330062.3:c.515G>C	p.Arg172Thr	p.R172T	ENST00000330062	NM_002168.2	172	aGg/aCg	4/11	NA	2	FACETS	1	0.972	1			1	INDETERMINATE	1	TRUE	NA	0.761129165638503	2		362	534	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513348	44513348	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006006-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	181	335	0	ENST00000291552.4:c.587G>C	p.Arg196Thr	p.R196T	ENST00000291552	NM_006758.2	196	aGa/aCa	8/8	0.409916971643632	5	FACETS	1	0.961	1	0.355	0.327	0.384	INDETERMINATE	1	TRUE	2	0.761129165638503	5		335	956	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165331	47165344	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTTCTAAACTAT	TTCTTCTAAACTAT	-	novel	NA	P-0006006-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	230	307	1	ENST00000409792.3:c.782_795del	p.Asn261ThrfsTer8	p.N261Tfs*8	ENST00000409792	NM_014159.6	261	aATAGTTTAGAAGAA/a	3/21	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.761129165638503	2		308	600	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022302	31022302	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006006-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	269	424	1	ENST00000375687.4:c.1788del	p.Ile597SerfsTer106	p.I597Sfs*106	ENST00000375687	NM_015338.5	596	cGg/cg	13/13	0.595217701206453	4	FACETS	1	0.99	1			1	CLONAL	1	TRUE	NA	0.761129165638503	4		425	988	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056209	26056211	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs779842031	NA	P-0006006-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1321	281	341	0	ENST00000343677.2:c.446_448del	p.Lys149del	p.K149del	ENST00000343677	NM_005319.3	149	aAGAgc/agc	1/1	0.761129165638503	7	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.761129165638503	7		341	1602	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842665	68842680	+	protein_altering_variant	In_Frame_Del	DEL	CCTGTTGGTGTCTTTA	CCTGTTGGTGTCTTTA	G	novel	NA	P-0006016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	62	590	0	ENST00000261769.5:c.601_616delinsG	p.Pro201_Ile206delinsVal	p.P201_I206delinsV	ENST00000261769	NM_004360.3	201	CCTGTTGGTGTCTTTAtt/Gtt	5/16	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		590	1088	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0006019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	211	378	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.285050481202935	4	FACETS	0.895	0.838	0.953	1	0.99	1	CLONAL	3	FALSE	2	0.402300736487696	4		378	548	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0006019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	161	347	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.147118840366262	5	FACETS	1	0.967	1			1	INDETERMINATE	3	FALSE	NA	0.402300736487696	5		347	399	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578471	7578483	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCGGGGGTGTG	GGGCGGGGGTGTG	-	rs137852790	NA	P-0006019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	169	344	0	ENST00000269305.4:c.447_459del	p.Thr150AlafsTer16	p.T150Afs*16	ENST00000269305	NM_001126112.2	149	tcCACACCCCCGCCC/tc	5/11	0.147118840366262	5	FACETS	1	0.968	1			1	INDETERMINATE	3	FALSE	NA	0.402300736487696	5		344	420	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942154	81942154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	181	452	1	ENST00000359376.3:c.1691G>A	p.Arg564Gln	p.R564Q	ENST00000359376	NM_002661.3	564	cGg/cAg	17/33	1	2	FACETS	1	0.978	1	1	0.994	1	CLONAL	2	FALSE	1	0.402300736487696	2		453	407	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918896	76918903	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTTTAT	TTCTTTAT	-	novel	NA	P-0006019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	331	263	0	ENST00000373344.5:c.4088_4095del	p.His1363ArgfsTer12	p.H1363Rfs*12	ENST00000373344	NM_000489.3	1363	cATAAAGAA/c	12/35	1	1	FACETS	1	0.981	1	1	0.997	1	CLONAL	3	FALSE	0	0.402300736487696	1		263	430	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	32	338	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.175777554805858	3	FACETS	1	0.827	1	0.508	0.413	0.615	CLONAL	1	TRUE	1	0.216617540580704	3		339	322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578238	7578255	+	inframe_deletion	In_Frame_Del	DEL	TCCACACGCAAATTTCCT	TCCACACGCAAATTTCCT	-	rs1567551704	NA	P-0006056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	41	571	0	ENST00000269305.4:c.594_611del	p.Gly199_Glu204del	p.G199_E204del	ENST00000269305	NM_001126112.2	198	gaAGGAAATTTGCGTGTGGAg/gag	6/11	0.175777554805858	3	FACETS	1	0.905	1	0.562	0.469	0.665	CLONAL	1	TRUE	1	0.216617540580704	3		571	373	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123324960	123324960	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	38	596	0	ENST00000358487.5:c.368A>T	p.Asn123Ile	p.N123I	ENST00000358487	NM_000141.4	123	aAt/aTt	3/18	0.175777554805858	3	FACETS	1	0.905	1	0.572	0.474	0.681	CLONAL	1	TRUE	1	0.216617540580704	3		596	340	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513341	41513341	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	74	571	0	ENST00000263253.7:c.245C>A	p.Ser82Ter	p.S82*	ENST00000263253	NM_001429.3	82	tCa/tAa	2/31	0.15413545272141	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	0	0.216617540580704	2		571	303	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132485	11132485	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	90	624	1	ENST00000358026.2:c.2701del	p.Tyr901MetfsTer9	p.Y901Mfs*9	ENST00000358026	NM_001128849.1	901	Tat/at	19/36	0.175777554805858	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	1	0.216617540580704	3		625	412	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0006062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	376	239	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.851447317337016	3	FACETS	0.998	0.959	1	0.998	0.959	1	CLONAL	2	TRUE	1	0.851447317337016	3		239	631	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519896	NA	P-0006062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	290	515	1	ENST00000281708.4:c.1514G>T	p.Arg505Leu	p.R505L	ENST00000281708	NM_033632.3	505	cGc/cTc	10/12	0.851447317337016	2	FACETS	0.94	0.889	0.991	0.47	0.444	0.496	CLONAL	1	TRUE	0	0.851447317337016	2		516	725	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832031	72832031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144091993	NA	P-0006062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	512	779	2	ENST00000268489.5:c.4550C>T	p.Ser1517Leu	p.S1517L	ENST00000268489	NM_006885.3	1517	tCg/tTg	9/10	0.851447317337016	2	FACETS	0.943	0.904	0.981	0.471	0.452	0.491	CLONAL	1	TRUE	0	0.851447317337016	2		781	1276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	G	rs1131691039	NA	P-0006062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	1340	478	0	ENST00000269305.4:c.919+1G>C		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.851447317337016	4	FACETS	1	0.994	1			1	CLONAL	4	TRUE	NA	0.851447317337016	4		478	1449	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028638	12028638	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	1283	600	2	ENST00000353533.5:c.841C>T	p.Arg281Ter	p.R281*	ENST00000353533	NM_003010.3	281	Cga/Tga	8/11	0.364394220363833	5	FACETS	0.977	0.967	0.987			1	INDETERMINATE	5	TRUE	NA	0.851447317337016	5		602	1405	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793517	42793517	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	17	624	0	ENST00000575354.2:c.1319G>C	p.Arg440Pro	p.R440P	ENST00000575354	NM_015125.3	440	cGc/cCc	8/20	0.851447317337016	0	FACETS		NA	1			1	NA	1	TRUE	0	0.851447317337016	0		624	158	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426111	47426111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1221	438	692	0	ENST00000377045.4:c.631C>T	p.Arg211Cys	p.R211C	ENST00000377045	NM_001654.4	211	Cgc/Tgc	7/16	0.851447317337016	3	FACETS	0.884	0.841	0.928	0.442	0.42	0.464	CLONAL	1	TRUE	1	0.851447317337016	3		692	1659	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919278	48919279	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0006062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	984	434	0	ENST00000267163.4:c.444_445del	p.Met148IlefsTer8	p.M148Ifs*8	ENST00000267163	NM_000321.2	148	aTG/a	4/27	0.851447317337016	4	FACETS	0.985	0.973	0.997	0.985	0.973	0.997	CLONAL	4	TRUE	0	0.851447317337016	4		434	1086	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0006069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	96	239	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.986	0.883	1	0.986	0.883	1	CLONAL	1	TRUE	1	0.42723562220029	2		239	456	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129169	64129169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746466314	NA	P-0006069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	257	484	1	ENST00000334205.4:c.707C>T	p.Ser236Leu	p.S236L	ENST00000334205	NM_003942.2	236	tCg/tTg	7/17	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.42723562220029	2		485	851	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940100	49940100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745900173	NA	P-0006069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	355	631	2	ENST00000296474.3:c.943G>A	p.Gly315Arg	p.G315R	ENST00000296474	NM_002447.2	315	Gga/Aga	1/20	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.42723562220029	2		633	1133	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	88	510	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.252228379097723	1	FACETS	0.845	0.748	0.948	0.845	0.748	0.948	CLONAL	1	TRUE	0	0.252228379097723	1		510	722	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0006072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	154	640	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.252228379097723	1	FACETS	0.988	0.903	1	0.988	0.903	1	CLONAL	1	TRUE	0	0.252228379097723	1		640	1080	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860053	57860053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200444628	NA	P-0006072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1252	114	1078	7	ENST00000228682.2:c.793C>T	p.Arg265Trp	p.R265W	ENST00000228682	NM_005269.2	265	Cgg/Tgg	8/12	0.252228379097723	1	FACETS	0.578	0.519	0.642	0.578	0.519	0.642	SUBCLONAL	1	TRUE	0	0.252228379097723	1		1085	1366	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0006079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	180	324	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.391453445071201	3	FACETS	0.952	0.891	1	0.952	0.891	1	CLONAL	3	TRUE	0	0.391453445071201	3		324	385	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107095	27107096	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0006079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	113	350	0	ENST00000324856.7:c.6711_6712del	p.Leu2238AlafsTer39	p.L2238Afs*39	ENST00000324856	NM_006015.4	2236	CGc/c	20/20	1	2	FACETS	0.951	0.858	1	0.951	0.858	1	CLONAL	1	TRUE	1	0.391453445071201	2		350	607	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256751	16256751	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199784733	NA	P-0006079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	129	509	1	ENST00000375759.3:c.4016G>A	p.Arg1339His	p.R1339H	ENST00000375759	NM_015001.2	1339	cGt/cAt	11/15	1	2	FACETS	0.959	0.871	1	0.959	0.871	1	CLONAL	1	TRUE	1	0.391453445071201	2		510	687	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532618	46532618	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	153	580	0	ENST00000262741.5:c.460G>T	p.Val154Leu	p.V154L	ENST00000262741	NM_003629.3	154	Gtg/Ttg	4/10	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.391453445071201	2		580	781	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265654	198265654	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	130	292	0	ENST00000335508.6:c.2503G>A	p.Asp835Asn	p.D835N	ENST00000335508	NM_012433.2	835	Gat/Aat	18/25	0.350306276404976	4	FACETS	0.889	0.81	0.97	0.889	0.81	0.97	CLONAL	2	TRUE	2	0.391453445071201	4		292	520	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696229	52696229	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	321	688	0	ENST00000394830.3:c.448G>C	p.Glu150Gln	p.E150Q	ENST00000394830	NM_018313.4	150	Gag/Cag	5/30	0.249145219596282	3	FACETS	1	0.951	1			1	CLONAL	2	TRUE	NA	0.391453445071201	3		688	975	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139703	55139703	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0006079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	224	408	1	ENST00000257290.5:c.1365-1G>T		p.X455_splice	ENST00000257290	NM_006206.4	455			0.375342462192973	2	FACETS	0.91	0.852	0.968	0.91	0.852	0.968	CLONAL	2	TRUE	0	0.391453445071201	2		409	629	SUCCESS
APC	324	MSKCC	GRCh37	5	112174699	112174699	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	292	528	0	ENST00000257430.4:c.3408A>T	p.Glu1136Asp	p.E1136D	ENST00000257430	NM_000038.5	1136	gaA/gaT	16/16	0.391453445071201	2	FACETS	0.991	0.937	1	0.991	0.937	1	CLONAL	2	TRUE	0	0.391453445071201	2		528	753	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350064	81350064	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	303	526	2	ENST00000222390.5:c.1268A>G	p.His423Arg	p.H423R	ENST00000222390	NM_000601.4	423	cAt/cGt	10/18	0.311516478348504	4	FACETS	0.959	0.904	1			1	CLONAL	2	TRUE	NA	0.391453445071201	4		528	1123	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359096	81359096	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0006079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	186	449	0	ENST00000222390.5:c.866-1G>T		p.X289_splice	ENST00000222390	NM_000601.4	289			0.311516478348504	4	FACETS	0.972	0.901	1			1	CLONAL	2	TRUE	NA	0.391453445071201	4		449	680	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445352	49445352	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0006079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	156	526	0	ENST00000301067.7:c.2114C>G	p.Ser705Ter	p.S705*	ENST00000301067	NM_003482.3	705	tCa/tGa	10/54	NA	2	FACETS	0.976	0.894	1			1	INDETERMINATE	1	TRUE	NA	0.391453445071201	2		526	817	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486794	56486794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370847503	NA	P-0006079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	220	691	2	ENST00000267101.3:c.1208C>T	p.Pro403Leu	p.P403L	ENST00000267101	NM_001982.3	403	cCg/cTg	11/28	0.375342462192973	2	FACETS	1	0.976	1	0.554	0.515	0.594	CLONAL	1	TRUE	0	0.391453445071201	2		693	1014	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435299	121435299	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	141	469	0	ENST00000257555.6:c.1332G>C	p.Gln444His	p.Q444H	ENST00000257555		444	caG/caC	7/10	0.391453445071201	3	FACETS	1	0.934	1	0.515	0.469	0.563	CLONAL	1	TRUE	1	0.391453445071201	3		469	836	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005275	29005275	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	168	420	0	ENST00000282397.4:c.986A>G	p.Tyr329Cys	p.Y329C	ENST00000282397	NM_002019.4	329	tAt/tGt	7/30	0.375342462192973	2	FACETS	0.923	0.856	0.991	0.923	0.856	0.991	CLONAL	2	TRUE	0	0.391453445071201	2		420	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577123	7577123	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876660333	NA	P-0006079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	441	674	0	ENST00000269305.4:c.815T>G	p.Val272Gly	p.V272G	ENST00000269305	NM_001126112.2	272	gTg/gGg	8/11	0.375342462192973	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.391453445071201	2		674	1067	SUCCESS
AR	367	MSKCC	GRCh37	X	66765117	66765117	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	185	565	0	ENST00000374690.3:c.129G>T	p.Glu43Asp	p.E43D	ENST00000374690	NM_000044.3	43	gaG/gaT	1/8	NA	2	FACETS	1	0.934	1			1	INDETERMINATE	1	TRUE	NA	0.391453445071201	2		565	934	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	90	297	0	ENST00000397752.3:c.3028+1del		p.D1010fs	ENST00000397752	NM_000245.2	1010	Gat/at	14/21	0.283667122795037	1	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	0	0.283667122795037	1		297	541	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0006089-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	366	626	3	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.347627753461491	3	FACETS	1	0.994	1	0.816	0.782	0.849	INDETERMINATE	2	TRUE	0	0.608679206286973	3		629	641	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610455	215610455	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006089-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	203	559	0	ENST00000260947.4:c.1801G>C	p.Asp601His	p.D601H	ENST00000260947	NM_000465.2	601	Gac/Cac	8/11	NA	2	FACETS	0.834	0.785	0.883			1	INDETERMINATE	2	TRUE	NA	0.608679206286973	2		559	400	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418842	116418842	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006089-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	19	517	0	ENST00000397752.3:c.3353T>C	p.Ile1118Thr	p.I1118T	ENST00000397752	NM_000245.2	1118	aTa/aCa	17/21	NA	2	FACETS	0.201	0.152	0.258			1	INDETERMINATE	1	TRUE	NA	0.608679206286973	2		517	311	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971131	21971131	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006089-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	228	350	0	ENST00000304494.5:c.227C>G	p.Ala76Gly	p.A76G	ENST00000304494	NM_000077.4	76	gCc/gGc	2/3	0.405143003388239	6	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	3	0.608679206286973	6		350	510	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347329	89347329	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006089-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	266	1112	0	ENST00000301030.4:c.5621C>G	p.Thr1874Ser	p.T1874S	ENST00000301030	NM_001256183.1	1874	aCt/aGt	9/13	0.608679206286973	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.608679206286973	1		1112	586	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755656	39755656	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	203	646	0	ENST00000288319.7:c.1109G>C	p.Arg370Pro	p.R370P	ENST00000288319	NM_182918.3	370	cGt/cCt	10/10	1	2	FACETS	0.424	0.392	0.457	0.424	0.392	0.457	SUBCLONAL	1	TRUE	1	0.855312125130977	2		646	1120	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779837	3779838	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0006092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	434	647	0	ENST00000262367.5:c.5209_5210dup	p.Ser1737ArgfsTer8	p.S1737Rfs*8	ENST00000262367	NM_004380.2	1737	agc/agAGc	31/31	0.378914308513974	2	FACETS	0.956	0.915	0.999	0.478	0.457	0.5	INDETERMINATE	1	TRUE	0	0.855312125130977	2		647	1061	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495537	56495537	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006108-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	43	410	0	ENST00000267101.3:c.3727C>G	p.Leu1243Val	p.L1243V	ENST00000267101	NM_001982.3	1243	Ctc/Gtc	28/28	1	2	FACETS	0.873	0.728	1	0.873	0.728	1	CLONAL	1	TRUE	1	0.12	2		410	821	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	245	510	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.240651735187618	3	FACETS	0.976	0.916	1	0.651	0.611	0.691	INDETERMINATE	2	TRUE	0	0.413233908662577	3		510	733	SUCCESS
APC	324	MSKCC	GRCh37	5	112175766	112175766	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	106	334	0	ENST00000257430.4:c.4476del	p.Thr1493ArgfsTer14	p.T1493Rfs*14	ENST00000257430	NM_000038.5	1492	gCc/gc	16/16	1	2	FACETS	0.97	0.873	1	0.97	0.873	1	CLONAL	1	TRUE	1	0.413233908662577	2		334	529	SUCCESS
ALK	238	MSKCC	GRCh37	2	29436901	29436901	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	268	550	0	ENST00000389048.3:c.3692G>T	p.Arg1231Leu	p.R1231L	ENST00000389048	NM_004304.4	1231	cGg/cTg	24/29	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.413233908662577	2		550	974	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856568	111856568	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1235252492	NA	P-0006110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	46	186	2	ENST00000341259.2:c.619G>A	p.Asp207Asn	p.D207N	ENST00000341259	NM_005475.2	207	Gac/Aac	2/8	0.240651735187618	3	FACETS	0.724	0.611	0.848	0.241	0.203	0.283	INDETERMINATE	1	TRUE	0	0.413233908662577	3		188	371	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120016	70120016	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1339655148	NA	P-0006110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	33	58	0	ENST00000245479.2:c.1018C>T	p.Gln340Ter	p.Q340*	ENST00000245479	NM_000346.3	340	Cag/Tag	3/3	0.378800799129373	2	FACETS	0.929	0.782	1	0.929	0.782	1	CLONAL	2	TRUE	0	0.413233908662577	2		58	86	SUCCESS
APC	324	MSKCC	GRCh37	5	112174301	112174311	+	frameshift_variant	Frame_Shift_Del	DEL	CTAGCCCATAA	CTAGCCCATAA	-	novel	NA	P-0006110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	91	402	0	ENST00000257430.4:c.3010_3020del	p.Leu1004AsnfsTer3	p.L1004Nfs*3	ENST00000257430	NM_000038.5	1004	CTAGCCCATAAa/a	16/16	1	2	FACETS	0.639	0.568	0.716	0.639	0.568	0.716	SUBCLONAL	1	TRUE	1	0.413233908662577	2		402	689	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578248	7578249	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0006110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	285	572	0	ENST00000269305.4:c.599_600dup	p.Leu201IlefsTer47	p.L201Ifs*47	ENST00000269305	NM_001126112.2	200	-/AT	6/11	0.300547704670707	2	FACETS	1	0.993	1	0.731	0.689	0.775	CLONAL	1	TRUE	0	0.413233908662577	2		572	943	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774771	73774774	+	frameshift_variant	Frame_Shift_Del	DEL	CGAA	CGAA	-	novel	NA	P-0006110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	214	391	0	ENST00000254810.4:c.313_316del	p.Phe105LysfsTer33	p.F105Kfs*33	ENST00000254810	NM_005324.3	105	TTCGaa/aa	4/4	0.378800799129373	2	FACETS	1	0.987	1	0.625	0.582	0.67	CLONAL	1	TRUE	0	0.413233908662577	2		391	828	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0006114-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	126	381	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.986	0.897	1	0.986	0.897	1	CLONAL	1	TRUE	1	0.48575132365452	2		382	526	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779782	3779782	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006114-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	121	447	0	ENST00000262367.5:c.5266C>T	p.Gln1756Ter	p.Q1756*	ENST00000262367	NM_004380.2	1756	Cag/Tag	31/31	1	2	FACETS	0.859	0.779	0.943	0.859	0.779	0.943	CLONAL	1	TRUE	1	0.48575132365452	2		447	580	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129620	47129623	+	frameshift_variant	Frame_Shift_Del	DEL	AGGT	AGGT	-	novel	NA	P-0006114-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	169	609	0	ENST00000409792.3:c.5257_5260del	p.Thr1753ValfsTer14	p.T1753Vfs*14	ENST00000409792	NM_014159.6	1753	ACCTgt/gt	10/21	1	2	FACETS	0.861	0.793	0.932	0.861	0.793	0.932	CLONAL	1	TRUE	1	0.48575132365452	2		609	808	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988512	36988512	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006114-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	144	666	0	ENST00000354822.5:c.141G>C	p.Leu47Phe	p.L47F	ENST00000354822	NM_001079668.2	47	ttG/ttC	2/3	1	2	FACETS	0.817	0.746	0.89	0.817	0.746	0.89	CLONAL	1	TRUE	1	0.48575132365452	2		666	726	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115853	8115854	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0006137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	131	494	0	ENST00000346208.3:c.1200dup	p.Ser401ValfsTer106	p.S401Vfs*106	ENST00000346208		400	atg/atGg	6/6	1	2	FACETS	1	0.969	1	1	0.991	1	CLONAL	2	TRUE	1	0.213013832619764	2		494	540	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877154	151877154	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs767365126	NA	P-0006137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	47	346	1	ENST00000262189.6:c.7207C>T	p.Arg2403Ter	p.R2403*	ENST00000262189	NM_170606.2	2403	Cga/Tga	37/59	0.0917259726259958	3	FACETS	0.751	0.637	0.876	0.751	0.637	0.876	INDETERMINATE	2	TRUE	1	0.213013832619764	3		347	325	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900033	151900037	+	frameshift_variant	Frame_Shift_Del	DEL	GGAAA	GGAAA	-	novel	NA	P-0006137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	77	439	0	ENST00000262189.6:c.4074_4078del	p.Phe1359CysfsTer17	p.F1359Cfs*17	ENST00000262189	NM_170606.2	1358	acTTTCCct/acct	26/59	0.0917259726259958	3	FACETS	1	0.943	1	1	0.943	1	INDETERMINATE	2	TRUE	1	0.213013832619764	3		439	360	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345211	70345214	+	frameshift_variant	Frame_Shift_Del	DEL	GCAG	GCAG	-	novel	NA	P-0006137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	49	614	0	ENST00000374080.3:c.2237_2240del	p.Cys746SerfsTer33	p.C746Sfs*33	ENST00000374080		746	tGCAGc/tc	16/45	0.213013832619764	1	FACETS	0.918	0.778	1	0.918	0.778	1	CLONAL	1	TRUE	0	0.213013832619764	1		614	448	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6048644	6048644	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs763939668	NA	P-0006150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	136	396	2	ENST00000265849.7:c.7C>T	p.Arg3Ter	p.R3*	ENST00000265849	NM_000535.5	3	Cga/Tga	1/15	0.164595412265053	3	FACETS	0.871	0.791	0.955	0.871	0.791	0.955	CLONAL	2	TRUE	1	0.173581891585514	3		398	978	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927986	49927986	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372063160	NA	P-0006150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	227	580	0	ENST00000296474.3:c.3742C>T	p.Arg1248Cys	p.R1248C	ENST00000296474	NM_002447.2	1248	Cgc/Tgc	18/20	1	2	FACETS	0.944	0.878	1	1	0.994	1	CLONAL	2	TRUE	1	0.173581891585514	2		580	1385	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273029	55273029	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	148	441	0	ENST00000275493.2:c.3352G>T	p.Ala1118Ser	p.A1118S	ENST00000275493	NM_005228.3	1118	Gcg/Tcg	28/28	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.173581891585514	2		441	1205	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23635329	23635329	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs587776419	NA	P-0006150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	94	408	0	ENST00000261584.4:c.2834+1G>T		p.X945_splice	ENST00000261584	NM_024675.3	945			1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.173581891585514	2		408	967	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971198	21971199	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0006150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	48	157	0	ENST00000304494.5:c.159dup	p.Met54AspfsTer66	p.M54Dfs*66	ENST00000304494	NM_000077.4	53	-/G	2/3	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.173581891585514	2		157	372	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578458	+	missense_variant	Missense_Mutation	DNP	CG	CG	AA	novel	NA	P-0006150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	126	480	1	ENST00000269305.4:c.472_473delinsTT	p.Arg158Phe	p.R158F	ENST00000269305	NM_001126112.2	158	CGc/TTc	5/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.173581891585514	2		481	1042	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243777036	243777036	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	267	291	1	ENST00000263826.5:c.633G>T	p.Leu211Phe	p.L211F	ENST00000263826	NM_005465.4	211	ttG/ttT	7/13	1	2	FACETS	0.976	0.92	1	0.976	0.92	1	CLONAL	1	TRUE	1	0.750640489512369	2		292	729	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402466	139402466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	385	493	0	ENST00000277541.6:c.3451C>T	p.Pro1151Ser	p.P1151S	ENST00000277541	NM_017617.3	1151	Ccc/Tcc	21/34	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.750640489512369	2		493	978	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363805	118363805	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	354	397	0	ENST00000534358.1:c.5038G>T	p.Glu1680Ter	p.E1680*	ENST00000534358	NM_005933.3	1680	Gag/Tag	16/36	1	2	FACETS	0.958	0.909	1	0.958	0.909	1	CLONAL	1	TRUE	1	0.750640489512369	2		397	985	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359654	40359654	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	597	649	0	ENST00000293328.3:c.1999A>G	p.Ile667Val	p.I667V	ENST00000293328	NM_012448.3	667	Atc/Gtc	16/19	1	2	FACETS	0.948	0.911	0.985	0.948	0.911	0.985	CLONAL	1	TRUE	1	0.750640489512369	2		649	1678	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798379	42798379	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	388	380	0	ENST00000575354.2:c.4250G>T	p.Arg1417Leu	p.R1417L	ENST00000575354	NM_015125.3	1417	cGc/cTc	18/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.750640489512369	2		380	963	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006163-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	53	192	0				ENST00000310581	NM_198253.2	-/1132			0.3	0	FACETS	0.834	0.735	0.935			1	CLONAL	2	TRUE	0	0.35	0		192	118	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0006163-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	77	422	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	0.986	1	CLONAL	2	TRUE	1	0.35	2		422	208	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089775	5089775	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006163-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	41	481	0	ENST00000381652.3:c.2673C>G	p.His891Gln	p.H891Q	ENST00000381652	NM_004972.3	891	caC/caG	20/25	0.110788897927164	0	FACETS	0.982	0.833	1			1	INDETERMINATE	1	TRUE	0	0.35	0		481	155	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039327	47039327	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006163-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	73	248	0	ENST00000377604.3:c.950T>C	p.Leu317Pro	p.L317P	ENST00000377604	NM_001204468.1	317	cTg/cCg	10/24	0.3	2	FACETS	0.961	0.855	1	0.961	0.855	1	CLONAL	2	TRUE	0	0.35	2		248	217	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148725	20148726	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GC	GC	AA	novel	NA	P-0006163-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	115	206	0	ENST00000379607.5:c.338-1_338delinsTT		p.X113_splice	ENST00000379607	NM_001412.3	113		6/7	0.3	2	FACETS	0.988	0.945	1	1	0.993	1	CLONAL	5	TRUE	0	0.35	2		206	133	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587781525	NA	P-0006173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	313	520	0	ENST00000269305.4:c.842A>G	p.Asp281Gly	p.D281G	ENST00000269305	NM_001126112.2	281	gAc/gGc	8/11	0.246137254160253	2	FACETS	0.799	0.753	0.846	0.799	0.753	0.846	SUBCLONAL	2	TRUE	0	0.307749403703311	2		520	1273	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1327720	1327720	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	128	278	0	ENST00000400841.2:c.161C>G	p.Thr54Ser	p.T54S	ENST00000400841		54	aCc/aGc	2/6	1	1	FACETS	0.701	0.634	0.772	0.701	0.634	0.772	SUBCLONAL	1	TRUE	0	0.307749403703311	1		278	1004	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	54	490	1	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.835	0.715	0.966	0.835	0.715	0.966	CLONAL	1	TRUE	1	0.31	2		491	417	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857679	9857679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886042648	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	62	429	0	ENST00000330684.3:c.3722G>A	p.Arg1241Gln	p.R1241Q	ENST00000330684	NM_001134407.1	1241	cGg/cAg	13/13	1	2	FACETS	0.897	0.777	1	0.897	0.777	1	CLONAL	1	TRUE	1	0.31	2		429	446	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	68	451	2	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.801	0.697	0.912	0.801	0.697	0.912	CLONAL	1	TRUE	1	0.31	2		453	548	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1204	246	785	5	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.31	2		790	1450	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	20	109	1	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	0.3	1	FACETS	0.901	0.698	1	0.901	0.698	1	CLONAL	1	TRUE	0	0.31	1		110	121	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	85	414	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	1	2	FACETS	0.88	0.779	0.989	0.88	0.779	0.989	CLONAL	1	TRUE	1	0.31	2		414	623	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789591	3789591	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	91	411	0	ENST00000262367.5:c.4268del	p.Pro1423LeufsTer36	p.P1423Lfs*36	ENST00000262367	NM_004380.2	1423	cCt/ct	25/31	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.31	2		411	498	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578215	28578216	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	74	541	0	ENST00000241453.7:c.2955_2956del	p.Pro986AlafsTer27	p.P986Afs*27	ENST00000241453	NM_004119.2	985	tcTCcg/tccg	24/24	0.2840134187006	1	FACETS	0.796	0.698	0.9	0.796	0.698	0.9	SUBCLONAL	1	TRUE	0	0.31	1		541	507	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	96	533	3	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	0.701	0.624	0.784	0.701	0.624	0.784	SUBCLONAL	1	TRUE	1	0.31	2		536	883	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053023	180053023	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	54	511	5	ENST00000261937.6:c.1267del	p.Gln423ArgfsTer70	p.Q423Rfs*70	ENST00000261937	NM_182925.4	423	Cag/ag	10/30	1	2	FACETS	0.919	0.788	1	0.919	0.788	1	CLONAL	1	TRUE	1	0.31	2		516	379	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	43	345	1	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	0.762	0.639	0.897	0.762	0.639	0.897	SUBCLONAL	1	TRUE	1	0.31	2		346	364	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070577	67070578	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	96	508	1	ENST00000412916.2:c.207dup	p.Pro70SerfsTer13	p.P70Sfs*13	ENST00000412916		67	-/T	3/6	1	2	FACETS	0.775	0.69	0.866	0.775	0.69	0.866	SUBCLONAL	1	TRUE	1	0.31	2		509	799	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030692	48030692	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs267608092	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	83	461	0	ENST00000234420.5:c.3312del	p.Phe1104LeufsTer11	p.F1104Lfs*11	ENST00000234420	NM_000179.2	1102	acT/ac	5/10	1	2	FACETS	0.988	0.874	1	0.988	0.874	1	CLONAL	1	TRUE	1	0.31	2		461	542	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202891	16202891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910179277	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	60	503	0	ENST00000375759.3:c.599G>A	p.Arg200Gln	p.R200Q	ENST00000375759	NM_015001.2	200	cGa/cAa	3/15	1	2	FACETS	0.622	0.536	0.717	0.622	0.536	0.717	SUBCLONAL	1	TRUE	1	0.31	2		503	622	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798808	45798808	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	73	450	0	ENST00000450313.1:c.423G>T	p.Gln141His	p.Q141H	ENST00000450313	NM_012222.2	141	caG/caT	5/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.31	2		450	408	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845353	156845353	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	99	756	0	ENST00000524377.1:c.1396C>A	p.Leu466Met	p.L466M	ENST00000524377	NM_002529.3	466	Ctg/Atg	12/17	0.3	3	FACETS	1	0.951	1	0.556	0.497	0.619	CLONAL	1	TRUE	1	0.31	3		756	663	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612810	228612810	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148579172	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	171	956	2	ENST00000366696.1:c.217C>T	p.Arg73Cys	p.R73C	ENST00000366696	NM_003493.2	73	Cgc/Tgc	1/1	0.3	3	FACETS	1	0.952	1	0.526	0.483	0.572	CLONAL	1	TRUE	1	0.31	3		958	1211	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029141	26029141	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	87	503	0	ENST00000435504.4:c.209T>A	p.Ile70Asn	p.I70N	ENST00000435504		70	aTc/aAc	4/13	1	2	FACETS	0.842	0.745	0.944	0.842	0.745	0.944	CLONAL	1	TRUE	1	0.31	2		503	667	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202843	128202843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	49	368	0	ENST00000341105.2:c.877C>T	p.Arg293Trp	p.R293W	ENST00000341105	NM_032638.4	293	Cgg/Tgg	4/6	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.31	2		368	311	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467865	66467865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs939351025	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	104	421	0	ENST00000273854.3:c.404G>A	p.Arg135Gln	p.R135Q	ENST00000273854	NM_004439.5	135	cGg/cAg	3/18	1	2	FACETS	0.898	0.804	0.998	0.898	0.804	0.998	CLONAL	1	TRUE	1	0.31	2		421	747	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158647	26158647	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	15	59	0	ENST00000289316.2:c.250T>C	p.Tyr84His	p.Y84H	ENST00000289316	NM_138720.2	84	Tac/Cac	1/2	0.274278248482267	4	FACETS	1	0.841	1	0.604	0.447	0.787	CLONAL	1	TRUE	2	0.31	4		59	105	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672233	30672233	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	104	769	1	ENST00000376406.3:c.4727C>A	p.Pro1576His	p.P1576H	ENST00000376406	NM_014641.2	1576	cCt/cAt	10/15	1	2	FACETS	0.835	0.747	0.928	0.835	0.747	0.928	CLONAL	1	TRUE	1	0.31	2		770	804	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523705	148523705	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	58	359	0	ENST00000320356.2:c.748C>A	p.Gln250Lys	p.Q250K	ENST00000320356	NM_004456.4	250	Cag/Aag	8/20	1	2	FACETS	0.697	0.599	0.803	0.697	0.599	0.803	SUBCLONAL	1	TRUE	1	0.31	2		359	537	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845678	151845678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	68	406	2	ENST00000262189.6:c.13334G>A	p.Gly4445Asp	p.G4445D	ENST00000262189	NM_170606.2	4445	gGt/gAt	52/59	1	2	FACETS	0.935	0.816	1	0.935	0.816	1	CLONAL	1	TRUE	1	0.31	2		408	469	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460514	8460514	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	77	459	0	ENST00000356435.5:c.3772C>T	p.Gln1258Ter	p.Q1258*	ENST00000356435		1258	Cag/Tag	22/35	1	2	FACETS	0.785	0.689	0.888	0.785	0.689	0.888	SUBCLONAL	1	TRUE	1	0.31	2		459	633	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80343516	80343516	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	57	414	0	ENST00000286548.4:c.803C>T	p.Ser268Leu	p.S268L	ENST00000286548	NM_002072.3	268	tCg/tTg	6/7	1	2	FACETS	0.704	0.605	0.813	0.704	0.605	0.813	SUBCLONAL	1	TRUE	1	0.31	2		414	522	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636249	87636249	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	89	573	0	ENST00000277120.3:c.2414G>A	p.Cys805Tyr	p.C805Y	ENST00000277120		805	tGc/tAc	19/19	1	2	FACETS	0.886	0.786	0.993	0.886	0.786	0.993	CLONAL	1	TRUE	1	0.31	2		573	648	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123353315	123353315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3750819	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	92	603	0	ENST00000358487.5:c.17G>A	p.Arg6His	p.R6H	ENST00000358487	NM_000141.4	6	cGt/cAt	2/18	1	2	FACETS	0.92	0.818	1	0.92	0.818	1	CLONAL	1	TRUE	1	0.31	2		603	645	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998169	100998169	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1252920750	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	95	436	0	ENST00000325455.5:c.1633C>A	p.Leu545Met	p.L545M	ENST00000325455	NM_001202474.3	545	Ctg/Atg	1/8	1	2	FACETS	0.947	0.844	1	0.947	0.844	1	CLONAL	1	TRUE	1	0.31	2		436	647	SUCCESS
ATM	472	MSKCC	GRCh37	11	108168061	108168061	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1565469955	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	86	473	0	ENST00000278616.4:c.4957C>T	p.Gln1653Ter	p.Q1653*	ENST00000278616	NM_000051.3	1653	Cag/Tag	33/63	1	2	FACETS	0.878	0.777	0.985	0.878	0.777	0.985	CLONAL	1	TRUE	1	0.31	2		473	632	SUCCESS
ATM	472	MSKCC	GRCh37	11	108225561	108225561	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782149	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	86	464	0	ENST00000278616.4:c.8810T>C	p.Val2937Ala	p.V2937A	ENST00000278616	NM_000051.3	2937	gTg/gCg	61/63	1	2	FACETS	0.975	0.864	1	0.975	0.864	1	CLONAL	1	TRUE	1	0.31	2		464	569	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038875	12038875	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	102	452	0	ENST00000396373.4:c.1168A>G	p.Thr390Ala	p.T390A	ENST00000396373	NM_001987.4	390	Acc/Gcc	7/8	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.31	2		452	654	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49449088	49449088	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	25	431	1	ENST00000301067.7:c.20C>A	p.Ala7Asp	p.A7D	ENST00000301067	NM_003482.3	7	gCt/gAt	1/54	1	2	FACETS	0.344	0.27	0.429	0.344	0.27	0.429	SUBCLONAL	1	TRUE	1	0.31	2		432	469	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435210	110435210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758265068	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	61	274	1	ENST00000375856.3:c.3191C>T	p.Ser1064Leu	p.S1064L	ENST00000375856	NM_003749.2	1064	tCg/tTg	1/2	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.31	2		275	385	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9928089	9928089	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	64	461	0	ENST00000330684.3:c.1652-2A>G		p.X551_splice	ENST00000330684	NM_001134407.1	551			1	2	FACETS	0.814	0.706	0.931	0.814	0.706	0.931	CLONAL	1	TRUE	1	0.31	2		461	507	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829974	72829974	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	132	845	2	ENST00000268489.5:c.6607C>T	p.Arg2203Cys	p.R2203C	ENST00000268489	NM_006885.3	2203	Cgt/Tgt	9/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.31	2		847	770	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533696	63533696	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	63	500	0	ENST00000307078.5:c.1458G>T	p.Lys486Asn	p.K486N	ENST00000307078	NM_004655.3	486	aaG/aaT	6/11	1	2	FACETS	0.794	0.687	0.909	0.794	0.687	0.909	CLONAL	1	TRUE	1	0.31	2		500	512	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56376678	56376678	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	187	804	1	ENST00000348428.3:c.718C>A	p.Pro240Thr	p.P240T	ENST00000348428	NM_006785.3	240	Cca/Aca	5/17	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.31	2		805	1185	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317529	1317529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs755143572	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	135	579	0	ENST00000400841.2:c.536A>T	p.Lys179Met	p.K179M	ENST00000400841		179	aAg/aTg	5/6	NA	2	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.31	2		579	759	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911074	32911074	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1328	221	928	3	ENST00000380152.3:c.2588del	p.Asn863IlefsTer11	p.N863Ifs*11	ENST00000380152		861	cAa/ca	11/27	1	2	FACETS	0.92	0.854	0.99	0.92	0.854	0.99	CLONAL	1	TRUE	1	0.31	2		931	1549	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585442	29585443	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	134	502	0	ENST00000356175.3:c.4192_4193del	p.Val1398LeufsTer4	p.V1398Lfs*4	ENST00000356175	NM_000267.3	1397	atTGtc/attc	31/57	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.31	2		502	805	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023046	31023046	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	108	550	2	ENST00000375687.4:c.2535del	p.Ser846ValfsTer21	p.S846Vfs*21	ENST00000375687	NM_015338.5	844	aCc/ac	13/13	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.31	2		552	636	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786697	3786697	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	93	748	0	ENST00000262367.5:c.4514del	p.Lys1505ArgfsTer45	p.K1505Rfs*45	ENST00000262367	NM_004380.2	1505	aAg/ag	27/31	1	2	FACETS	0.832	0.74	0.931	0.832	0.74	0.931	CLONAL	1	TRUE	1	0.31	2		748	721	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131457	202131459	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	52	412	0	ENST00000358485.4:c.430_432del	p.Glu144del	p.E144del	ENST00000358485	NM_001080125.1	142	aAGGag/aag	2/9	1	2	FACETS	0.672	0.573	0.781	0.672	0.573	0.781	SUBCLONAL	1	TRUE	1	0.31	2		412	499	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522383	157522383	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	83	409	0	ENST00000346085.5:c.4657del	p.Ala1553ArgfsTer26	p.A1553Rfs*26	ENST00000346085	NM_020732.3	1552	aGg/ag	18/20	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.31	2		409	532	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515090	148515090	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1064796749	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	98	451	3	ENST00000320356.2:c.1119del	p.Thr374ProfsTer50	p.T374Pfs*50	ENST00000320356	NM_004456.4	373	ccC/cc	10/20	1	2	FACETS	0.888	0.792	0.99	0.888	0.792	0.99	CLONAL	1	TRUE	1	0.31	2		454	712	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101570	27101570	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	63	526	1	ENST00000324856.7:c.4856del	p.Pro1619GlnfsTer7	p.P1619Qfs*7	ENST00000324856	NM_006015.4	1618	Ccc/cc	18/20	1	2	FACETS	0.789	0.683	0.904	0.789	0.683	0.904	CLONAL	1	TRUE	1	0.31	2		527	515	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231357	98231358	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	59	432	0	ENST00000331920.6:c.1925dup	p.Pro643ThrfsTer11	p.P643Tfs*11	ENST00000331920	NM_000264.3	642	cca/ccCa	14/24	1	2	FACETS	0.966	0.834	1	0.966	0.834	1	CLONAL	1	TRUE	1	0.31	2		432	394	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460476	149460476	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	64	572	0	ENST00000286301.3:c.161del	p.Pro54HisfsTer58	p.P54Hfs*58	ENST00000286301	NM_005211.3	54	cCa/ca	3/22	1	2	FACETS	0.888	0.771	1	0.888	0.771	1	CLONAL	1	TRUE	1	0.31	2		572	465	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154241	2154242	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755455183	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	65	529	0	ENST00000434045.2:c.686dup	p.Glu230ArgfsTer50	p.E230Rfs*50	ENST00000434045	NM_001127598.1	229	cca/ccCa	5/5	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.31	2		529	397	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795378	42795378	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	53	424	0	ENST00000575354.2:c.2462del	p.Gly821GlufsTer103	p.G821Efs*103	ENST00000575354	NM_015125.3	820	Ggg/gg	10/20	0.3	1	FACETS	0.779	0.667	0.901	0.779	0.667	0.901	CLONAL	1	TRUE	0	0.31	1		424	371	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437474	49437474	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	106	577	0	ENST00000301067.7:c.5411del	p.Pro1804GlnfsTer48	p.P1804Qfs*48	ENST00000301067	NM_003482.3	1804	cCa/ca	23/54	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.31	2		577	523	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838210	89838211	+	missense_variant	Missense_Mutation	DNP	TG	TG	CT	novel	NA	P-0006201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	76	473	0	ENST00000389301.3:c.2026_2027delinsAG	p.Gln676Arg	p.Q676R	ENST00000389301	NM_000135.2	676	CAg/AGg	23/43	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.31	2		473	466	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589557	67589598	+	inframe_deletion	In_Frame_Del	DEL	TAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACAC	TAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACAC	-	novel	NA	P-0121560-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	31	257	0	ENST00000274335.5:c.1321_1362del	p.Asn441_Thr454del	p.N441_T454del	ENST00000274335		440	gaTAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACACt/gat	10/15	1	2	FACETS	0.862	0.717	1	0.862	0.717	1	CLONAL	1	NA	1	0.748927694022067	2		257	96	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120912	115120912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0121560-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	86	407	0	ENST00000257566.3:c.94G>A	p.Ala32Thr	p.A32T	ENST00000257566	NM_016569.3	32	Gcg/Acg	1/8	0.748927694022067	4	FACETS	0.941	0.837	1	0.314	0.279	0.351	CLONAL	1	NA	1	0.748927694022067	4		407	427	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481809	56481809	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121560-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	112	456	0	ENST00000267101.3:c.737G>T	p.Cys246Phe	p.C246F	ENST00000267101	NM_001982.3	246	tGc/tTc	7/28	0.70523454082382	3	FACETS	0.898	0.812	0.987	0.449	0.406	0.494	CLONAL	1	NA	1	0.748927694022067	3		456	458	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190656599	190656599	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121560-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	28	205	0	ENST00000441310.2:c.64G>T	p.Val22Phe	p.V22F	ENST00000441310	NM_000534.4	22	Gtc/Ttc	2/13	0.70523454082382	3	FACETS	0.704	0.57	0.852	0.352	0.285	0.426	SUBCLONAL	1	NA	1	0.748927694022067	3		205	146	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650596	48650596	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0121560-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	23	527	0	ENST00000376670.3:c.566A>T	p.Lys189Met	p.K189M	ENST00000376670	NM_002049.3	189	aAg/aTg	3/6	1	2	FACETS	0.208	0.162	0.261	0.208	0.162	0.261	SUBCLONAL	1	NA	1	0.748927694022067	2		527	295	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0006221-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	405	283	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.386311202197993	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	2	0.390469964252638	4		283	1184	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798118	45798118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200495564	NA	P-0006221-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	125	234	0	ENST00000450313.1:c.733C>T	p.Arg245Cys	p.R245C	ENST00000450313	NM_012222.2	245	Cgt/Tgt	9/16	0.280408520685169	1	FACETS	0.867	0.788	0.951	0.867	0.788	0.951	CLONAL	1	TRUE	0	0.390469964252638	1		234	594	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149036	61149036	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006221-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	92	317	1	ENST00000295025.8:c.1226C>T	p.Ser409Phe	p.S409F	ENST00000295025	NM_002908.2	409	tCt/tTt	11/11	0.367986152930178	3	FACETS	0.485	0.43	0.545	0.243	0.215	0.273	SUBCLONAL	1	TRUE	1	0.390469964252638	3		318	1161	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143519	30143519	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006221-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	72	80	0	ENST00000389048.3:c.7G>T	p.Ala3Ser	p.A3S	ENST00000389048	NM_004304.4	3	Gcc/Tcc	1/29	0.264035068824688	3	FACETS	0.885	0.784	0.991	0.885	0.784	0.991	CLONAL	2	TRUE	1	0.390469964252638	3		80	249	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662483	227662483	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006221-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	41	172	0	ENST00000305123.5:c.972C>A	p.Phe324Leu	p.F324L	ENST00000305123	NM_005544.2	324	ttC/ttA	1/2	0.369908951700278	3	FACETS	0.374	0.31	0.444	0.187	0.155	0.222	SUBCLONAL	1	TRUE	1	0.390469964252638	3		172	672	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480306	89480306	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006221-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	137	305	0	ENST00000336596.2:c.2143G>T	p.Asp715Tyr	p.D715Y	ENST00000336596	NM_005233.5	715	Gat/Tat	13/17	0.288455221981874	1	FACETS	0.64	0.581	0.701	0.64	0.581	0.701	SUBCLONAL	1	TRUE	0	0.390469964252638	1		305	883	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845550	151845550	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006221-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	140	261	0	ENST00000262189.6:c.13462G>T	p.Ala4488Ser	p.A4488S	ENST00000262189	NM_170606.2	4488	Gcc/Tcc	52/59	0.173640973014903	2	FACETS	0.846	0.77	0.925	0.423	0.385	0.463	INDETERMINATE	1	TRUE	0	0.390469964252638	2		261	848	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491478	18491478	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006221-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	200	234	0	ENST00000266497.5:c.1391G>T	p.Gly464Val	p.G464V	ENST00000266497		464	gGa/gTa	8/31	0.386311202197993	4	FACETS	1	0.988	1	0.665	0.616	0.716	CLONAL	1	TRUE	2	0.390469964252638	4		234	1071	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058564	42058564	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006221-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1328	150	545	0	ENST00000219905.7:c.8284G>C	p.Glu2762Gln	p.E2762Q	ENST00000219905	NM_001164273.1	2762	Gaa/Caa	24/24	0.390469964252638	1	FACETS	0.418	0.381	0.458	0.418	0.381	0.458	SUBCLONAL	1	TRUE	0	0.390469964252638	1		545	1478	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058645	42058645	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006221-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	137	512	0	ENST00000219905.7:c.8365G>C	p.Glu2789Gln	p.E2789Q	ENST00000219905	NM_001164273.1	2789	Gag/Cag	24/24	0.390469964252638	1	FACETS	0.438	0.397	0.481	0.438	0.397	0.481	SUBCLONAL	1	TRUE	0	0.390469964252638	1		512	1290	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73991994	73991994	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006221-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	357	325	0	ENST00000318443.5:c.14G>T	p.Arg5Leu	p.R5L	ENST00000318443	NM_001024736.1	5	cGg/cTg	2/10	0.374207164870736	2	FACETS	0.929	0.883	0.976	0.929	0.883	0.976	CLONAL	2	TRUE	0	0.390469964252638	2		325	984	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40364043	40364043	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006221-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	38	227	0	ENST00000293328.3:c.1639G>T	p.Asp547Tyr	p.D547Y	ENST00000293328	NM_012448.3	547	Gac/Tac	13/19	0.288455221981874	1	FACETS	0.301	0.248	0.36	0.301	0.248	0.36	SUBCLONAL	1	TRUE	0	0.390469964252638	1		227	521	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41247934	41247934	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006221-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	109	363	2	ENST00000357654.3:c.599G>T	p.Gly200Val	p.G200V	ENST00000357654	NM_007294.3	200	gGa/gTa	9/23	NA	2	FACETS	0.509	0.456	0.566			1	INDETERMINATE	1	TRUE	NA	0.390469964252638	2		365	1097	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527516	41527517	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCTCTTGG	novel	NA	P-0006221-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	313	291	0	ENST00000263253.7:c.1408_1415dup	p.Pro474LeufsTer7	p.P474Lfs*7	ENST00000263253	NM_001429.3	469	-/GCTCTTGG	6/31	0.367986152930178	3	FACETS	0.846	0.798	0.895	0.846	0.798	0.895	CLONAL	2	TRUE	1	0.390469964252638	3		291	1133	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	145	192	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.975	0.898	1	0.975	0.898	1	CLONAL	1	TRUE	1	0.713534646324831	2		192	417	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035169	30035169	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	677	483	2	ENST00000338641.4:c.331C>T	p.Gln111Ter	p.Q111*	ENST00000338641	NM_000268.3	111	Cag/Tag	3/16	0.67539499642802	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.713534646324831	2		485	901	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865812	57865812	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	378	674	1	ENST00000228682.2:c.3292del	p.Glu1098LysfsTer12	p.E1098Kfs*12	ENST00000228682	NM_005269.2	1097	Ggg/gg	12/12	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.713534646324831	2		675	1043	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955497	48955511	+	inframe_deletion	In_Frame_Del	DEL	CAGAAGGCAACTTGA	CAGAAGGCAACTTGA	-	novel	NA	P-0006228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	208	423	0	ENST00000267163.4:c.1615_1629del	p.Glu539_Thr543del	p.E539_T543del	ENST00000267163	NM_000321.2	538	gCAGAAGGCAACTTGAca/gca	17/27	1	2	FACETS	0.765	0.712	0.82	0.765	0.712	0.82	SUBCLONAL	1	TRUE	1	0.713534646324831	2		423	762	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0006231-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	236	609	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	0.923	0.862	0.987	1	0.995	1	CLONAL	3	TRUE	1	0.169572156299933	2		609	1005	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873066	134873066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762457030	NA	P-0006231-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	288	663	1	ENST00000398015.3:c.1370C>T	p.Pro457Leu	p.P457L	ENST00000398015	NM_004441.4	457	cCg/cTg	6/16	0.123284155891163	0	FACETS	0.787	0.739	0.836			1	SUBCLONAL	3	TRUE	0	0.169572156299933	0		664	1195	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98247998	98247998	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006231-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	223	510	0	ENST00000331920.6:c.553G>T	p.Ala185Ser	p.A185S	ENST00000331920	NM_000264.3	185	Gcc/Tcc	3/24	1	2	FACETS	0.854	0.795	0.916	1	0.995	1	CLONAL	3	TRUE	1	0.169572156299933	2		510	1026	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786197	3786197	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006231-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	253	535	0	ENST00000262367.5:c.4568del	p.Phe1523SerfsTer27	p.F1523Sfs*27	ENST00000262367	NM_004380.2	1523	tTc/tc	28/31	1	2	FACETS	0.926	0.867	0.987	1	0.996	1	CLONAL	3	TRUE	1	0.169572156299933	2		535	1074	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618688	37618689	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0006231-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	1081	768	1	ENST00000447079.4:c.364_365del	p.Leu122ThrfsTer4	p.L122Tfs*4	ENST00000447079	NM_015083.1	122	TTa/a	1/14	0.169572156299933	6	FACETS	0.984	0.961	1			1	CLONAL	10	TRUE	NA	0.169572156299933	6		769	1736	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0006234-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	134	381	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.971	0.89	1	0.971	0.89	1	CLONAL	1	TRUE	1	0.63	2		382	438	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006234-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	108	192	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.63	2		192	337	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841464	156841464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006234-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	155	432	0	ENST00000524377.1:c.767G>A	p.Ser256Asn	p.S256N	ENST00000524377	NM_002529.3	256	aGt/aAt	7/17	1	2	FACETS	0.816	0.75	0.884	0.816	0.75	0.884	CLONAL	1	TRUE	1	0.63	2		432	603	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638542	176638542	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006234-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	144	423	0	ENST00000439151.2:c.3142T>G	p.Leu1048Val	p.L1048V	ENST00000439151	NM_022455.4	1048	Tta/Gta	5/23	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.63	2		423	432	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390740	118390740	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1285242662	NA	P-0006234-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	49	495	0	ENST00000534358.1:c.11390A>G	p.Asn3797Ser	p.N3797S	ENST00000534358	NM_005933.3	3797	aAt/aGt	33/36	1	2	FACETS	0.31	0.263	0.363	0.31	0.263	0.363	SUBCLONAL	1	TRUE	1	0.63	2		495	501	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347916	73347916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139907646	NA	P-0006234-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	9	323	0	ENST00000377767.4:c.1145G>A	p.Arg382Gln	p.R382Q	ENST00000377767	NM_014953.3	382	cGa/cAa	8/21	1	2	FACETS	0.077	0.051	0.112	0.077	0.051	0.112	SUBCLONAL	1	TRUE	1	0.63	2		323	369	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0006244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	357	405	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.638183511449068	2	FACETS	0.928	0.895	0.96	0.928	0.895	0.96	CLONAL	2	TRUE	0	0.748511659014437	2		405	514	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180903	108180904	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1131691254	NA	P-0006244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	178	335	0	ENST00000278616.4:c.5784dup	p.Asn1929Ter	p.N1929*	ENST00000278616	NM_000051.3	1927	att/aTtt	39/63	0.748511659014437	1	FACETS	0.982	0.926	1	0.982	0.926	1	CLONAL	1	TRUE	0	0.748511659014437	1		335	303	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913396	NA	P-0006245-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	80	366	0	ENST00000349496.5:c.95A>T	p.Asp32Val	p.D32V	ENST00000349496	NM_001904.3	32	gAc/gTc	3/15	1	2	FACETS	0.738	0.649	0.834	0.738	0.649	0.834	SUBCLONAL	1	FALSE	1	0.290969018678664	2		366	745	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006245-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	58	192	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	FALSE	1	0.290969018678664	2		192	344	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266110	41266110	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006245-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	31	366	0	ENST00000349496.5:c.107A>C	p.His36Pro	p.H36P	ENST00000349496	NM_001904.3	36	cAt/cCt	3/15	1	2	FACETS	0.282	0.227	0.345	0.282	0.227	0.345	SUBCLONAL	1	FALSE	1	0.290969018678664	2		366	756	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023252	27023252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs571264557	NA	P-0006245-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	38	180	0	ENST00000324856.7:c.358C>T	p.Pro120Ser	p.P120S	ENST00000324856	NM_006015.4	120	Ccg/Tcg	1/20	1	2	FACETS	1	0.836	1	1	0.836	1	CLONAL	1	FALSE	1	0.290969018678664	2		180	260	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098800	178098800	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006245-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	75	390	1	ENST00000397062.3:c.245A>G	p.Glu82Gly	p.E82G	ENST00000397062	NM_006164.4	82	gAa/gGa	2/5	1	2	FACETS	0.599	0.524	0.68	0.599	0.524	0.68	SUBCLONAL	1	FALSE	1	0.290969018678664	2		391	861	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413683	138413683	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006245-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	80	268	0	ENST00000289153.2:c.1837A>T	p.Asn613Tyr	p.N613Y	ENST00000289153	NM_006219.2	613	Aac/Tac	12/22	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	1	0.290969018678664	2		268	518	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176564	56176564	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006245-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	65	303	0	ENST00000399503.3:c.2114C>A	p.Thr705Lys	p.T705K	ENST00000399503	NM_005921.1	705	aCa/aAa	12/20	1	2	FACETS	0.856	0.743	0.978	0.856	0.743	0.978	CLONAL	1	FALSE	1	0.290969018678664	2		303	522	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144620	119144620	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006245-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	59	341	0	ENST00000264033.4:c.633A>C	p.Glu211Asp	p.E211D	ENST00000264033	NM_005188.3	211	gaA/gaC	4/16	1	2	FACETS	0.615	0.529	0.71	0.615	0.529	0.71	SUBCLONAL	1	FALSE	1	0.290969018678664	2		341	659	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855801	45855801	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006245-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	127	391	0	ENST00000391945.4:c.2009G>A	p.Gly670Asp	p.G670D	ENST00000391945	NM_000400.3	670	gGc/gAc	21/23	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.290969018678664	2		391	687	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675161	30675187	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CCTGGAAACCTTCTCAGCAGCTCTGAT	CCTGGAAACCTTCTCAGCAGCTCTGAT	-	novel	NA	P-0006245-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	83	506	1	ENST00000376406.3:c.3058_3084del	p.Ile1020_Arg1028del	p.I1020_R1028del	ENST00000376406	NM_014641.2	1020	ATCAGAGCTGCTGAGAAGGTTTCCAGG/-	9/15	1	2	FACETS	0.652	0.574	0.736	0.652	0.574	0.736	SUBCLONAL	1	FALSE	1	0.290969018678664	2		507	875	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651953	36651968	+	frameshift_variant	Frame_Shift_Del	DEL	GGACAGCGAGCAGCTG	GGACAGCGAGCAGCTG	-	novel	NA	P-0006245-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	63	256	2	ENST00000244741.5:c.75_90del	p.Asp26AlafsTer7	p.D26Afs*7	ENST00000244741	NM_000389.4	25	gtGGACAGCGAGCAGCTG/gt	2/3	1	2	FACETS	0.753	0.652	0.863	0.753	0.652	0.863	SUBCLONAL	1	FALSE	1	0.290969018678664	2		258	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579348	7579348	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006247-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	128	694	0	ENST00000269305.4:c.339del	p.Leu114CysfsTer9	p.L114Cfs*9	ENST00000269305	NM_001126112.2	113	ttC/tt	4/11	0.169673197834736	2	FACETS	0.958	0.87	1	0.958	0.87	1	CLONAL	2	FALSE	0	0.202818179277867	2		694	659	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256365	46256365	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773838233	NA	P-0006248-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	1108	421	0	ENST00000371998.3:c.593G>A	p.Arg198His	p.R198H	ENST00000371998		198	cGt/cAt	7/23	0.658957325087879	4	FACETS	1	0.992	1			1	CLONAL	3	TRUE	NA	0.658957325087879	4		421	1802	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115720	8115815	+	inframe_deletion	In_Frame_Del	DEL	ATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAG	ATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAG	-	novel	NA	P-0006248-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	282	300	0	ENST00000346208.3:c.1067_1162del	p.Met356_Lys387del	p.M356_K387del	ENST00000346208		356	ATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAG/-	6/6	1	2	FACETS	0.857	0.806	0.909	0.857	0.806	0.909	CLONAL	1	TRUE	1	0.658957325087879	2		300	999	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727453	66727453	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397516790	NA	P-0006250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	25	554	0	ENST00000307102.5:c.169A>G	p.Lys57Glu	p.K57E	ENST00000307102	NM_002755.3	57	Aag/Gag	2/11	0.214499945692592	3	FACETS	0.835	0.672	1			1	CLONAL	3	TRUE	NA	0.214499945692592	3		554	103	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0006250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	20	495	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.214483807645387	1	FACETS	0.8	0.622	1	1	0.926	1	CLONAL	2	TRUE	0	0.214499945692592	1		496	104	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101267	27101268	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0006250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	20	506	1	ENST00000324856.7:c.4555dup	p.Gln1519ProfsTer13	p.Q1519Pfs*13	ENST00000324856	NM_006015.4	1517	gcc/gCcc	18/20	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.214499945692592	2		507	126	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809792	36809792	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	20	545	1	ENST00000373129.3:c.813G>T	p.Gln271His	p.Q271H	ENST00000373129	NM_032017.1	271	caG/caT	9/12	1	2	FACETS	0.942	0.733	1	1	0.938	1	CLONAL	2	TRUE	1	0.214499945692592	2		546	99	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396771	396771	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	20	451	0	ENST00000262320.3:c.255G>A	p.Trp85Ter	p.W85*	ENST00000262320	NM_003502.3	85	tgG/tgA	2/11	0.214499945692592	0	FACETS	0.788	0.614	0.982			1	CLONAL	2	TRUE	0	0.214499945692592	0		451	93	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604785	48604790	+	inframe_deletion	In_Frame_Del	DEL	TAGACG	TAGACG	-	novel	NA	P-0006250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	24	406	0	ENST00000342988.3:c.1607_1612del	p.Leu536_Glu538delinsGln	p.L536_E538delinsQ	ENST00000342988	NM_005359.5	536	cTAGACGaa/caa	12/12	0.214499945692592	2	FACETS	0.867	0.69	1	0.867	0.69	1	CLONAL	2	TRUE	0	0.214499945692592	2		406	129	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604780	48604781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	24	401	0	ENST00000342988.3:c.1602_1603insT	p.Leu535SerfsTer42	p.L535Sfs*42	ENST00000342988	NM_005359.5	534	-/T	12/12	0.214499945692592	2	FACETS	0.881	0.701	1	0.881	0.701	1	CLONAL	2	TRUE	0	0.214499945692592	2		401	127	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	285	338	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.389679467477616	4	FACETS	0.996	0.951	1	1	0.996	1	CLONAL	4	TRUE	2	0.435075781809193	4		339	472	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437605	56437605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329721997	NA	P-0006260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	195	513	0	ENST00000407977.2:c.857G>A	p.Arg286Gln	p.R286Q	ENST00000407977		286	cGg/cAg	8/10	0.435075781809193	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.435075781809193	2		513	398	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs80338963	NA	P-0006260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	70	644	0	ENST00000342988.3:c.1081C>A	p.Arg361Ser	p.R361S	ENST00000342988	NM_005359.5	361	Cgc/Agc	9/12	0.435075781809193	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.435075781809193	1		644	230	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446310	29446310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138589984	NA	P-0006260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	135	881	0	ENST00000389048.3:c.3257C>T	p.Ser1086Leu	p.S1086L	ENST00000389048	NM_004304.4	1086	tCg/tTg	20/29	0.371542933430926	4	FACETS	0.906	0.822	0.994	0.453	0.411	0.497	CLONAL	1	TRUE	2	0.435075781809193	4		881	983	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56871538	56871538	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	142	656	0	ENST00000308159.5:c.1918G>C	p.Glu640Gln	p.E640Q	ENST00000308159	NM_014669.4	640	Gag/Cag	18/22	0.389679467477616	4	FACETS	1	0.962	1	0.551	0.502	0.602	CLONAL	1	TRUE	2	0.435075781809193	4		656	850	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943399	17943399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376945173	NA	P-0006260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	126	640	1	ENST00000458235.1:c.2609G>A	p.Arg870Gln	p.R870Q	ENST00000458235	NM_000215.3	870	cGg/cAg	19/24	0.435075781809193	3	FACETS	1	0.918	1	0.507	0.459	0.556	CLONAL	1	TRUE	1	0.435075781809193	3		641	696	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920469	134920469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	229	448	0	ENST00000398015.3:c.2284G>A	p.Asp762Asn	p.D762N	ENST00000398015	NM_004441.4	762	Gac/Aac	12/16	1	2	FACETS	0.864	0.81	0.92	0.864	0.81	0.92	CLONAL	1	TRUE	1	0.80640005476439	2		448	657	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165293	47165293	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	186	319	0	ENST00000409792.3:c.833C>T	p.Ser278Phe	p.S278F	ENST00000409792	NM_014159.6	278	tCc/tTc	3/21	1	2	FACETS	0.864	0.804	0.925	0.864	0.804	0.925	CLONAL	1	TRUE	1	0.80640005476439	2		319	534	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873066	134873066	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	280	422	0	ENST00000398015.3:c.1370C>G	p.Pro457Arg	p.P457R	ENST00000398015	NM_004441.4	457	cCg/cGg	6/16	1	2	FACETS	0.946	0.894	0.999	0.946	0.894	0.999	CLONAL	1	TRUE	1	0.80640005476439	2		422	734	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807137	1807137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	274	429	0	ENST00000260795.2:c.1468G>A	p.Glu490Lys	p.E490K	ENST00000260795		490	Gag/Aag	10/17	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.80640005476439	2		429	655	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157822	106157822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	204	360	1	ENST00000380013.4:c.2723G>A	p.Gly908Asp	p.G908D	ENST00000380013	NM_001127208.2	908	gGt/gAt	3/11	1	2	FACETS	0.992	0.929	1	0.992	0.929	1	CLONAL	1	TRUE	1	0.80640005476439	2		361	510	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197629	106197629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	144	304	0	ENST00000380013.4:c.5962C>T	p.Pro1988Ser	p.P1988S	ENST00000380013	NM_001127208.2	1988	Cca/Tca	11/11	1	2	FACETS	0.95	0.877	1	0.95	0.877	1	CLONAL	1	TRUE	1	0.80640005476439	2		304	376	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517847	187517847	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202133523	NA	P-0006267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	294	362	1	ENST00000441802.2:c.12847G>A	p.Glu4283Lys	p.E4283K	ENST00000441802	NM_005245.3	4283	Gaa/Aaa	25/27	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.80640005476439	2		363	707	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752920	57752920	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0006267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	166	226	0	ENST00000274289.3:c.1009-1G>A		p.X337_splice	ENST00000274289	NM_006622.3	337			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.80640005476439	2		226	360	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168668	32168668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	742	486	0	ENST00000375023.3:c.4255G>A	p.Gly1419Arg	p.G1419R	ENST00000375023	NM_004557.3	1419	Gga/Aga	23/30	0.80640005476439	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.80640005476439	3		486	1226	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169074	32169074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	629	436	0	ENST00000375023.3:c.3959C>T	p.Ser1320Phe	p.S1320F	ENST00000375023	NM_004557.3	1320	tCc/tTc	22/30	0.80640005476439	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.80640005476439	3		436	1035	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359032	81359032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	273	432	0	ENST00000222390.5:c.929G>A	p.Gly310Glu	p.G310E	ENST00000222390	NM_000601.4	310	gGa/gAa	8/18	1	2	FACETS	0.974	0.92	1	0.974	0.92	1	CLONAL	1	TRUE	1	0.80640005476439	2		432	695	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453152	140453152	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	203	293	0	ENST00000288602.6:c.1783T>A	p.Phe595Ile	p.F595I	ENST00000288602	NM_004333.4	595	Ttt/Att	15/18	1	2	FACETS	0.938	0.877	1	0.938	0.877	1	CLONAL	1	TRUE	1	0.80640005476439	2		293	537	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528663	8528663	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	238	375	2	ENST00000356435.5:c.469A>T	p.Ile157Phe	p.I157F	ENST00000356435		157	Atc/Ttc	4/35	0.80640005476439	1	FACETS	0.99	0.945	1	0.99	0.945	1	CLONAL	1	TRUE	0	0.80640005476439	1		377	356	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63760041	63760041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	197	226	0	ENST00000279873.7:c.694C>T	p.Pro232Ser	p.P232S	ENST00000279873	NM_032199.2	232	Ccg/Tcg	4/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.80640005476439	2		226	479	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298225	123298225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	144	255	0	ENST00000358487.5:c.629G>A	p.Arg210Gln	p.R210Q	ENST00000358487	NM_000141.4	210	cGa/cAa	6/18	1	2	FACETS	0.935	0.863	1	0.935	0.863	1	CLONAL	1	TRUE	1	0.80640005476439	2		255	382	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514110	69514110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1264857484	NA	P-0006267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	233	434	2	ENST00000294312.3:c.571C>T	p.Pro191Ser	p.P191S	ENST00000294312	NM_005117.2	191	Ccc/Tcc	3/3	1	2	FACETS	0.911	0.856	0.968	0.911	0.856	0.968	CLONAL	1	TRUE	1	0.80640005476439	2		436	634	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148973	119148973	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	241	359	0	ENST00000264033.4:c.1193A>G	p.His398Arg	p.H398R	ENST00000264033	NM_005188.3	398	cAc/cGc	8/16	0.80640005476439	1	FACETS	0.988	0.944	1	0.988	0.944	1	CLONAL	1	TRUE	0	0.80640005476439	1		359	361	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793451	18793451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	243	346	0	ENST00000266497.5:c.4148C>T	p.Ser1383Phe	p.S1383F	ENST00000266497		1383	tCt/tTt	30/31	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.80640005476439	2		346	599	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425569	49425569	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779897575	NA	P-0006267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	439	653	0	ENST00000301067.7:c.12919C>T	p.Pro4307Ser	p.P4307S	ENST00000301067	NM_003482.3	4307	Ccc/Tcc	39/54	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.80640005476439	2		653	1011	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858947	57858947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	468	636	2	ENST00000228682.2:c.443C>T	p.Ser148Phe	p.S148F	ENST00000228682	NM_005269.2	148	tCc/tTc	5/12	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.80640005476439	2		638	1068	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416765	121416765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	347	490	0	ENST00000257555.6:c.194G>A	p.Gly65Glu	p.G65E	ENST00000257555		65	gGg/gAg	1/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.80640005476439	2		490	817	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435399	110435399	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1264962918	NA	P-0006267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	170	354	0	ENST00000375856.3:c.3002C>T	p.Ser1001Phe	p.S1001F	ENST00000375856	NM_003749.2	1001	tCc/tTc	1/2	1	2	FACETS	0.842	0.78	0.905	0.842	0.78	0.905	CLONAL	1	TRUE	1	0.80640005476439	2		354	501	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989106	41989106	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	396	581	0	ENST00000219905.7:c.1898G>C	p.Gly633Ala	p.G633A	ENST00000219905	NM_001164273.1	633	gGa/gCa	3/24	1	2	FACETS	0.995	0.949	1	0.995	0.949	1	CLONAL	1	TRUE	1	0.80640005476439	2		581	987	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240343	5240343	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	438	356	0	ENST00000357368.4:c.1571T>G	p.Val524Gly	p.V524G	ENST00000357368	NM_002850.3	524	gTg/gGg	12/38	0.80640005476439	3	FACETS	0.965	0.928	1	0.965	0.928	1	CLONAL	2	TRUE	1	0.80640005476439	3		356	790	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308348	15308348	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555730189	NA	P-0006267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	274	445	0	ENST00000263388.2:c.160C>T	p.Arg54Cys	p.R54C	ENST00000263388	NM_000435.2	54	Cgt/Tgt	2/33	0.80640005476439	3	FACETS	0.981	0.922	1	0.491	0.461	0.521	CLONAL	1	TRUE	1	0.80640005476439	3		445	972	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919081	50919081	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1414539977	NA	P-0006267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	199	404	0	ENST00000440232.2:c.2818G>A	p.Glu940Lys	p.E940K	ENST00000440232	NM_002691.3	940	Gag/Aag	22/27	0.314955629518168	1	FACETS	0.492	0.458	0.526	0.492	0.458	0.526	INDETERMINATE	1	TRUE	0	0.80640005476439	1		404	599	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388677	31388677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	330	452	1	ENST00000328111.2:c.1942G>A	p.Gly648Arg	p.G648R	ENST00000328111	NM_006892.3	648	Gga/Aga	18/23	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.80640005476439	2		453	810	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317569	1317569	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	223	304	0	ENST00000400841.2:c.496A>T	p.Asn166Tyr	p.N166Y	ENST00000400841		166	Aat/Tat	5/6	0.80640005476439	0	FACETS		NA	1			1	NA	1	TRUE	NA	0.80640005476439	0		304	322	SUCCESS
AR	367	MSKCC	GRCh37	X	66941716	66941716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764684648	NA	P-0006267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	289	291	0	ENST00000374690.3:c.2360G>A	p.Arg787Gln	p.R787Q	ENST00000374690	NM_000044.3	787	cGa/cAa	6/8	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.80640005476439	1		291	379	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257551	19257552	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0006267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	368	370	1	ENST00000162023.5:c.674_675delinsAT	p.Ser225Tyr	p.S225Y	ENST00000162023		225	tCC/tAT	10/13	0.80640005476439	3	FACETS	0.881	0.842	0.919	0.881	0.842	0.919	CLONAL	2	TRUE	1	0.80640005476439	3		371	727	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006270-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	125	192	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.410814300249487	2		192	490	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681461	30681461	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006270-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	137	422	0	ENST00000376406.3:c.551C>A	p.Ser184Ter	p.S184*	ENST00000376406	NM_014641.2	184	tCa/tAa	4/15	1	2	FACETS	0.857	0.78	0.938	0.857	0.78	0.938	CLONAL	1	TRUE	1	0.410814300249487	2		422	778	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117682	70117682	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006270-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	125	498	0	ENST00000245479.2:c.150G>C	p.Glu50Asp	p.E50D	ENST00000245479	NM_000346.3	50	gaG/gaC	1/3	0.397200822773254	3	FACETS	0.772	0.698	0.851	0.386	0.349	0.426	SUBCLONAL	1	TRUE	1	0.410814300249487	3		498	950	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966763	44966768	+	inframe_deletion	In_Frame_Del	DEL	TTACTG	TTACTG	-	novel	NA	P-0006270-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	176	449	0	ENST00000377967.4:c.3988_3993del	p.Tyr1330_Cys1331del	p.Y1330_C1331del	ENST00000377967	NM_021140.2	1329	caTTACTGt/cat	27/29	1	2	FACETS	0.932	0.859	1	0.932	0.859	1	CLONAL	1	TRUE	1	0.410814300249487	2		449	919	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	518	192	0				ENST00000310581	NM_198253.2	-/1132			0.489632002165093	7	FACETS	1	0.992	1	1	0.992	1	CLONAL	6	TRUE	1	0.489632002165093	7		192	741	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0006277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	625	1002	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.489632002165093	1	FACETS	0.896	0.88	0.911	1	0.998	1	CLONAL	3	TRUE	0	0.489632002165093	1		1002	717	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047527	49047527	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587778850	NA	P-0006277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	176	482	0	ENST00000267163.4:c.2520+1G>T		p.X840_splice	ENST00000267163	NM_000321.2	840			0.476871472814468	0	FACETS	0.695	0.658	0.73			1	SUBCLONAL	2	TRUE	0	0.489632002165093	0		482	264	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881632	111881632	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	122	821	0	ENST00000393256.3:c.310del	p.Ser104AlafsTer5	p.S104Afs*5	ENST00000393256	NM_006538.4	104	Agc/gc	2/4	1	2	FACETS	0.726	0.658	0.799	0.726	0.658	0.799	SUBCLONAL	1	TRUE	1	0.489632002165093	2		821	686	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0006287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	29	513	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.531689806136896	1	FACETS	0.989	0.82	1	0.989	0.82	1	CLONAL	1	TRUE	0	0.531689806136896	1		515	81	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0006287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	38	679	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	0.531689806136896	2		679	130	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845904	156845904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	26	287	1	ENST00000524377.1:c.1534C>T	p.Leu512Phe	p.L512F	ENST00000524377	NM_002529.3	512	Ctc/Ttc	13/17	0.22383418511036	1	FACETS	0.876	0.714	1	0.876	0.714	1	INDETERMINATE	1	TRUE	0	0.531689806136896	1		288	82	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157495215	157495215	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	46	202	0	ENST00000346085.5:c.3099A>C	p.Lys1033Asn	p.K1033N	ENST00000346085	NM_020732.3	1033	aaA/aaC	11/20	0.319852639451138	5	FACETS	0.984	0.844	1			1	CLONAL	2	TRUE	NA	0.531689806136896	5		202	158	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729491	41729491	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	48	336	0	ENST00000242208.4:c.1038T>G	p.His346Gln	p.H346Q	ENST00000242208	NM_002192.2	346	caT/caG	3/3	1	2	FACETS	0.687	0.585	0.797	0.687	0.585	0.797	SUBCLONAL	1	TRUE	1	0.531689806136896	2		336	263	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920448	114920448	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	48	276	0	ENST00000543371.1:c.1389C>G	p.Cys463Trp	p.C463W	ENST00000543371	NM_001198531.1	463	tgC/tgG	13/14	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.531689806136896	2		276	166	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266037	41266620	+	splice_donor_variant,splice_acceptor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	ATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTG	ATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTG	-	novel	NA	P-0006287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	33	204	0	ENST00000349496.5:c.36_419del		p.X12_splice	ENST00000349496	NM_001904.3	12	ATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTG/-	3-4/15	0.403968525016523	5	FACETS	1	0.913	1			1	CLONAL	1	TRUE	NA	0.531689806136896	5		204	187	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107222	193107222	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	18	168	0	ENST00000367435.3:c.431del	p.Glu144GlyfsTer58	p.E144Gfs*58	ENST00000367435	NM_024529.4	144	gAg/gg	6/17	0.22383418511036	1	FACETS	0.552	0.424	0.698	0.552	0.424	0.698	INDETERMINATE	1	TRUE	0	0.531689806136896	1		168	90	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71008403	71008403	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006297-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	333	289	0	ENST00000318789.4:c.2029G>C	p.Glu677Gln	p.E677Q	ENST00000318789	NM_032682.5	677	Gag/Cag	21/21	1	2	FACETS	0.967	0.92	1	0.967	0.92	1	CLONAL	1	TRUE	1	0.897947330601163	2		289	767	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911504	32911504	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006297-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	930	445	0	ENST00000380152.3:c.3015del	p.Phe1005LeufsTer38	p.F1005Lfs*38	ENST00000380152		1004	agT/ag	11/27	NA	2	FACETS	0.996	0.982	1			1	INDETERMINATE	2	TRUE	NA	0.897947330601163	2		445	1040	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057214	30057222	+	inframe_deletion	In_Frame_Del	DEL	GCTGCTTGG	GCTGCTTGG	-	novel	NA	P-0006305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	277	538	1	ENST00000338641.4:c.696_704del	p.Leu233_Gly235del	p.L233_G235del	ENST00000338641	NM_000268.3	232	ctGCTGCTTGGa/cta	8/16	0.678099045045474	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.678099045045474	1		539	478	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186791	11186791	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	270	505	0	ENST00000361445.4:c.6414G>T	p.Leu2138Phe	p.L2138F	ENST00000361445	NM_004958.3	2138	ttG/ttT	46/58	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.19	2		505	1237	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0006315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	65	300	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.736	0.644	0.834	0.736	0.644	0.834	SUBCLONAL	1	TRUE	1	0.60932105734554	2		300	290	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891686	28891686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143726778	NA	P-0006315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	151	481	0	ENST00000282397.4:c.3335G>A	p.Arg1112His	p.R1112H	ENST00000282397	NM_002019.4	1112	cGc/cAc	25/30	NA	2	FACETS	0.793	0.728	0.861			1	INDETERMINATE	1	TRUE	NA	0.60932105734554	2		481	625	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142456	119142456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	105	276	0	ENST00000264033.4:c.455C>T	p.Thr152Ile	p.T152I	ENST00000264033	NM_005188.3	152	aCc/aTc	3/16	1	2	FACETS	0.751	0.676	0.829	0.751	0.676	0.829	SUBCLONAL	1	TRUE	1	0.60932105734554	2		276	459	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849442	68849442	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	117	335	0	ENST00000261769.5:c.1345C>T	p.Gln449Ter	p.Q449*	ENST00000261769	NM_004360.3	449	Cag/Tag	10/16	0.537359224623864	1	FACETS	0.878	0.804	0.955	0.878	0.804	0.955	CLONAL	1	TRUE	0	0.60932105734554	1		335	304	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939351	76939351	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	130	440	0	ENST00000373344.5:c.1397G>T	p.Arg466Ile	p.R466I	ENST00000373344	NM_000489.3	466	aGa/aTa	9/35	1	2	FACETS	0.727	0.662	0.795	0.727	0.662	0.795	SUBCLONAL	1	TRUE	1	0.60932105734554	2		440	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	145	406	0	ENST00000269305.4:c.472C>G	p.Arg158Gly	p.R158G	ENST00000269305	NM_001126112.2	158	Cgc/Ggc	5/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.212874590729169	2		406	937	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184625	11184625	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	64	467	0	ENST00000361445.4:c.6592G>T	p.Val2198Leu	p.V2198L	ENST00000361445	NM_004958.3	2198	Gtg/Ttg	47/58	0.186420308305748	1	FACETS	0.529	0.457	0.609	0.529	0.457	0.609	SUBCLONAL	1	TRUE	0	0.212874590729169	1		467	1015	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799817	72799817	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	108	399	0	ENST00000325599.8:c.1352G>T	p.Ser451Ile	p.S451I	ENST00000325599	NM_018130.2	451	aGc/aTc	11/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.212874590729169	2		399	857	SUCCESS
ATR	545	MSKCC	GRCh37	3	142224010	142224010	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	84	493	0	ENST00000350721.4:c.5167G>T	p.Asp1723Tyr	p.D1723Y	ENST00000350721	NM_001184.3	1723	Gac/Tac	29/47	1	2	FACETS	0.761	0.67	0.859	0.761	0.67	0.859	SUBCLONAL	1	TRUE	1	0.212874590729169	2		493	1037	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430639	181430639	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	64	313	0	ENST00000325404.1:c.491A>T	p.Asn164Ile	p.N164I	ENST00000325404	NM_003106.3	164	aAc/aTc	1/1	1	2	FACETS	0.991	0.858	1	0.991	0.858	1	CLONAL	1	TRUE	1	0.212874590729169	2		313	607	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190905	185190905	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1357	73	691	2	ENST00000265026.3:c.1786A>G	p.Arg596Gly	p.R596G	ENST00000265026	NM_004721.4	596	Aga/Gga	11/14	1	2	FACETS	0.48	0.417	0.547	0.48	0.417	0.547	SUBCLONAL	1	TRUE	1	0.212874590729169	2		693	1430	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152018	55152018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs79948560	NA	P-0006341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	89	397	1	ENST00000257290.5:c.2450G>A	p.Arg817His	p.R817H	ENST00000257290	NM_006206.4	817	cGt/cAt	18/23	0.212874590729169	3	FACETS	0.821	0.726	0.923	0.41	0.363	0.462	CLONAL	1	TRUE	1	0.212874590729169	3		398	1127	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557831	187557831	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	109	433	2	ENST00000441802.2:c.3880G>T	p.Gly1294Trp	p.G1294W	ENST00000441802	NM_005245.3	1294	Ggg/Tgg	5/27	0.151183477311478	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	0	0.212874590729169	1		435	905	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287311	38287311	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	126	532	0	ENST00000425967.3:c.346G>T	p.Gly116Trp	p.G116W	ENST00000425967	NM_001174067.1	116	Ggg/Tgg	4/19	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.212874590729169	2		532	951	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81528556	81528556	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	49	330	0	ENST00000298171.2:c.235T>C	p.Ser79Pro	p.S79P	ENST00000298171	NM_000369.2	79	Tcc/Ccc	2/10	1	2	FACETS	0.743	0.628	0.869	0.743	0.628	0.869	SUBCLONAL	1	TRUE	1	0.212874590729169	2		330	620	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855998	68855998	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	74	508	0	ENST00000261769.5:c.1806C>G	p.Phe602Leu	p.F602L	ENST00000261769	NM_004360.3	602	ttC/ttG	12/16	1	2	FACETS	0.532	0.464	0.607	0.532	0.464	0.607	SUBCLONAL	1	TRUE	1	0.212874590729169	2		508	1306	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264459	30264459	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs776238079	NA	P-0006341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	118	387	0	ENST00000322652.5:c.194G>T	p.Gly65Val	p.G65V	ENST00000322652	NM_015355.2	65	gGg/gTg	1/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.212874590729169	2		387	910	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220691	1220691	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs878853247	NA	P-0006341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	93	422	0	ENST00000326873.7:c.709G>T	p.Asp237Tyr	p.D237Y	ENST00000326873	NM_000455.4	237	Gac/Tac	5/10	0.212874590729169	1	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	0	0.212874590729169	1		422	776	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944592	40944592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	66	242	0	ENST00000373198.4:c.1910G>T	p.Arg637Leu	p.R637L	ENST00000373198	NM_133170.3	637	cGg/cTg	12/32	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.212874590729169	2		242	590	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932654	39932654	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1274	148	742	2	ENST00000378444.4:c.1945C>A	p.Pro649Thr	p.P649T	ENST00000378444	NM_001123385.1	649	Cca/Aca	4/15	1	2	FACETS	0.978	0.89	1	0.978	0.89	1	CLONAL	1	TRUE	1	0.212874590729169	2		744	1422	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247530	53247530	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1255	130	625	0	ENST00000375401.3:c.279G>T	p.Trp93Cys	p.W93C	ENST00000375401	NM_004187.3	93	tgG/tgT	3/26	1	2	FACETS	0.882	0.797	0.972	0.882	0.797	0.972	CLONAL	1	TRUE	1	0.212874590729169	2		625	1385	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410853	63410853	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	62	615	0	ENST00000330258.3:c.2314G>T	p.Ala772Ser	p.A772S	ENST00000330258	NM_152424.3	772	Gcc/Tcc	2/2	0.212874590729169	1	FACETS	0.468	0.402	0.539	0.468	0.402	0.539	SUBCLONAL	1	TRUE	0	0.212874590729169	1		615	1113	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2206753	2206754	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	127	551	0	ENST00000398665.3:c.816dup	p.Ala273CysfsTer10	p.A273Cfs*10	ENST00000398665	NM_032482.2	271	-/T	10/28	0.212874590729169	1	FACETS	0.81	0.732	0.894	0.81	0.732	0.894	CLONAL	1	TRUE	0	0.212874590729169	1		551	1316	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136995	11136996	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0006341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	117	441	0	ENST00000358026.2:c.3192dup	p.Phe1065ValfsTer17	p.F1065Vfs*17	ENST00000358026	NM_001128849.1	1063	ttg/ttGg	23/36	0.212874590729169	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.212874590729169	1		441	865	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25459874	25459875	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0006341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	87	476	0	ENST00000264709.3:c.2409-1_2409delinsTT		p.X803_splice	ENST00000264709	NM_175629.2	803		21/23	1	2	FACETS	0.784	0.692	0.882	0.784	0.692	0.882	SUBCLONAL	1	TRUE	1	0.212874590729169	2		476	1043	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347552	89347552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369218399	NA	P-0006348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	135	451	0	ENST00000301030.4:c.5398G>A	p.Glu1800Lys	p.E1800K	ENST00000301030	NM_001256183.1	1800	Gag/Aag	9/13	0.522398726988437	1	FACETS	0.163	0.148	0.179	0.163	0.148	0.179	INDETERMINATE	1	TRUE	0	0.981197344980545	1		451	859	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863628	68863628	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	241	285	0	ENST00000261769.5:c.2368del	p.Thr790ProfsTer3	p.T790Pfs*3	ENST00000261769	NM_004360.3	789	ccA/cc	15/16	0.522398726988437	1	FACETS	0.34	0.318	0.361	0.34	0.318	0.361	INDETERMINATE	1	TRUE	0	0.981197344980545	1		285	737	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0006351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	60	283	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.983	0.847	1	0.983	0.847	1	CLONAL	1	TRUE	1	0.23	2		283	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0006351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	38	386	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			1	2	FACETS	0.635	0.525	0.759	0.635	0.525	0.759	SUBCLONAL	1	TRUE	1	0.23	2		386	520	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543657	29543657	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	91	527	0	ENST00000389048.3:c.1506G>T	p.Gln502His	p.Q502H	ENST00000389048	NM_004304.4	502	caG/caT	7/29	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.23	2		527	720	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629928	187629928	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	81	406	0	ENST00000441802.2:c.1054G>T	p.Val352Phe	p.V352F	ENST00000441802	NM_005245.3	352	Gtc/Ttc	2/27	0.219577733035373	1	FACETS	0.983	0.867	1	0.983	0.867	1	CLONAL	1	TRUE	0	0.23	1		406	634	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168735	56168735	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs781158252	NA	P-0006351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	44	353	1	ENST00000399503.3:c.1589G>T	p.Gly530Val	p.G530V	ENST00000399503	NM_005921.1	530	gGa/gTa	9/20	1	2	FACETS	0.656	0.55	0.775	0.656	0.55	0.775	SUBCLONAL	1	TRUE	1	0.23	2		354	583	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864521	56864521	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs769330459	NA	P-0006351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	95	557	0	ENST00000308159.5:c.1009G>T	p.Val337Leu	p.V337L	ENST00000308159	NM_014669.4	337	Gta/Tta	10/22	1	2	FACETS	0.967	0.86	1	0.967	0.86	1	CLONAL	1	TRUE	1	0.23	2		557	854	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220695	1220695	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1131690919	NA	P-0006351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	53	289	0	ENST00000326873.7:c.713T>A	p.Ile238Asn	p.I238N	ENST00000326873	NM_000455.4	238	aTc/aAc	5/10	NA	2	FACETS	0.974	0.832	1			1	INDETERMINATE	1	TRUE	NA	0.23	2		289	473	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091758	29091758	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1476312560	NA	P-0006351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	36	147	0	ENST00000328354.6:c.1199G>T	p.Gly400Val	p.G400V	ENST00000328354	NM_007194.3	400	gGg/gTg	11/15	1	2	FACETS	0.984	0.812	1	0.984	0.812	1	CLONAL	1	TRUE	1	0.23	2		147	318	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0006378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	95	483	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.354864470367116	1	FACETS	0.629	0.561	0.703	0.629	0.561	0.703	SUBCLONAL	1	TRUE	0	0.361955453694996	1		483	683	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374883	45374883	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	142	501	1	ENST00000262160.6:c.960C>A	p.Asn320Lys	p.N320K	ENST00000262160	NM_005901.5	320	aaC/aaA	8/11	0.361955453694996	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.361955453694996	1		502	627	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729089	66729100	+	frameshift_variant	Frame_Shift_Del	DEL	TCATCTGGAGAT	TCATCTGGAGAT	AG	novel	NA	P-0006378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	140	551	0	ENST00000307102.5:c.297_308delinsAG	p.His100AlafsTer10	p.H100Afs*10	ENST00000307102	NM_002755.3	99	atTCATCTGGAGATc/atAGc	3/11	1	2	FACETS	0.949	0.865	1	0.949	0.865	1	CLONAL	1	TRUE	1	0.361955453694996	2		551	815	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188321	10188321	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs869025657	NA	P-0006381-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	89	361	0	ENST00000256474.2:c.463+1G>A		p.X155_splice	ENST00000256474	NM_000551.3	155			0.45813086223798	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.45813086223798	1		361	276	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562336	21562336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765917652	NA	P-0006381-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	160	315	1	ENST00000382592.4:c.1583C>T	p.Ser528Leu	p.S528L	ENST00000382592	NM_014572.2	528	tCg/tTg	4/8	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.45813086223798	2		316	645	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456528	189456528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121908848	NA	P-0006384-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	38	496	1	ENST00000264731.3:c.289C>T	p.Arg97Cys	p.R97C	ENST00000264731	NM_003722.4	97	Cgc/Tgc	3/14	1	2	FACETS	1	0.874	1	1	0.977	1	CLONAL	3	TRUE	1	0.3	2		497	83	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988945	41989044	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAGAGGACTTGGGCAGAAAGAGAACAACTATGCTTAAGATTGCAACAGCCGCAAAGGTAGTGAATGCTAATCAGAATGCCTCTCCAAATGTCCCTGGA	AAAAGAGGACTTGGGCAGAAAGAGAACAACTATGCTTAAGATTGCAACAGCCGCAAAGGTAGTGAATGCTAATCAGAATGCCTCTCCAAATGTCCCTGGA	-	novel	NA	P-0006384-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	10	721	0	ENST00000219905.7:c.1746_1845del	p.Asp582GlufsTer6	p.D582Efs*6	ENST00000219905	NM_001164273.1	579	ggAAAAGAGGACTTGGGCAGAAAGAGAACAACTATGCTTAAGATTGCAACAGCCGCAAAGGTAGTGAATGCTAATCAGAATGCCTCTCCAAATGTCCCTGGA/gg	3/24	0.3	1	FACETS	0.525	0.358	0.731	0.525	0.358	0.731	SUBCLONAL	1	TRUE	0	0.3	1		721	108	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0006394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	352	290	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.640287724118137	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.640287724118137	2		290	492	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221161	5221161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs575201235	NA	P-0006394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	542	466	0	ENST00000357368.4:c.3305G>A	p.Arg1102His	p.R1102H	ENST00000357368	NM_002850.3	1102	cGc/cAc	20/38	0.640287724118137	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.640287724118137	3		466	1018	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175481	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0006394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	231	341	0	ENST00000257430.4:c.4192_4193del	p.Arg1399PhefsTer9	p.R1399Ffs*9	ENST00000257430	NM_000038.5	1397	GAg/g	16/16	0.271107370532185	3	FACETS	0.939	0.885	0.994	0.626	0.59	0.663	INDETERMINATE	2	TRUE	0	0.640287724118137	3		341	507	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872741	136872741	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	273	691	0	ENST00000241393.3:c.757C>A	p.Leu253Met	p.L253M	ENST00000241393	NM_003467.2	253	Ctg/Atg	2/2	0.51488341091074	3	FACETS	1	0.973	1	0.532	0.499	0.566	CLONAL	1	TRUE	1	0.640287724118137	3		691	1058	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103716	47103716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs981018402	NA	P-0006394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	481	476	0	ENST00000409792.3:c.6230G>A	p.Arg2077Gln	p.R2077Q	ENST00000409792	NM_014159.6	2077	cGa/cAa	14/21	0.640287724118137	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.640287724118137	2		476	697	SUCCESS
APC	324	MSKCC	GRCh37	5	112170788	112170789	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0006394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	132	523	0	ENST00000257430.4:c.1885_1886del	p.Leu629SerfsTer4	p.L629Sfs*4	ENST00000257430	NM_000038.5	628	acTTta/acta	15/16	0.271107370532185	3	FACETS	0.709	0.644	0.777	0.236	0.214	0.259	INDETERMINATE	1	TRUE	0	0.640287724118137	3		523	768	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0006406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	196	585	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	0.61506582948274	2		585	636	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181765	56181765	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	190	349	0	ENST00000399503.3:c.3989C>G	p.Ser1330Trp	p.S1330W	ENST00000399503	NM_005921.1	1330	tCg/tGg	17/20	1	2	FACETS	0.995	0.925	1	0.995	0.925	1	CLONAL	1	TRUE	1	0.61506582948274	2		349	621	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572261	64572261	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs104894267	NA	P-0006406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	302	566	2	ENST00000312049.6:c.1378C>T	p.Arg460Ter	p.R460*	ENST00000312049	NM_130799.2	460	Cga/Tga	10/10	0.61506582948274	1	FACETS	0.895	0.847	0.943	0.895	0.847	0.943	CLONAL	1	TRUE	0	0.61506582948274	1		568	760	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578435	7578435	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	230	403	0	ENST00000269305.4:c.495G>T	p.Gln165His	p.Q165H	ENST00000269305	NM_001126112.2	165	caG/caT	5/11	1	2	FACETS	0.945	0.884	1	0.945	0.884	1	CLONAL	1	TRUE	1	0.61506582948274	2		403	791	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661994	29661994	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs764291252	NA	P-0006406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	210	427	0	ENST00000356175.3:c.5888A>G	p.Asn1963Ser	p.N1963S	ENST00000356175	NM_000267.3	1963	aAt/aGt	39/57	1	2	FACETS	0.872	0.812	0.934	0.872	0.812	0.934	CLONAL	1	TRUE	1	0.61506582948274	2		427	783	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155721	56155722	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0006406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	190	394	0	ENST00000399503.3:c.816_817del	p.Arg273SerfsTer27	p.R273Sfs*27	ENST00000399503	NM_005921.1	271	agAAaa/agaa	3/20	1	2	FACETS	0.743	0.688	0.801	0.743	0.688	0.801	SUBCLONAL	1	TRUE	1	0.61506582948274	2		394	831	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0006410-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	918	626	3	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.798851371899467	4	FACETS	0.981	0.966	0.994	0.981	0.966	0.994	CLONAL	4	TRUE	0	0.798851371899467	4		629	1054	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814303	76814306	+	frameshift_variant	Frame_Shift_Del	DEL	ATAA	ATAA	-	novel	NA	P-0006410-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	470	266	0	ENST00000373344.5:c.6338_6341del	p.Phe2113SerfsTer9	p.F2113Sfs*9	ENST00000373344	NM_000489.3	2113	tTTATc/tc	29/35	0.588552189304874	2	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.798851371899467	2		266	558	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777134	9777134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1445282622	NA	P-0006410-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	187	479	0	ENST00000377346.4:c.898C>T	p.Arg300Cys	p.R300C	ENST00000377346	NM_005026.3	300	Cgt/Tgt	7/24	0.762138891660191	3	FACETS	0.905	0.838	0.974	0.452	0.419	0.487	CLONAL	1	TRUE	1	0.798851371899467	3		479	724	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935411	36935411	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006410-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	518	811	0	ENST00000361632.4:c.1316C>T	p.Ala439Val	p.A439V	ENST00000361632		439	gCc/gTc	10/16	0.762138891660191	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.798851371899467	3		811	891	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252156	226252156	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006410-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	57	52	0	ENST00000366813.1:c.104G>T	p.Gly35Val	p.G35V	ENST00000366813		35	gGg/gTg	1/3	0.67747787627896	3	FACETS	0.868	0.772	0.965	0.868	0.772	0.965	CLONAL	2	TRUE	1	0.798851371899467	3		52	115	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004340	150004340	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs761243837	NA	P-0006410-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	287	669	0	ENST00000253339.5:c.1885T>C	p.Ser629Pro	p.S629P	ENST00000253339		629	Tct/Cct	3/7	0.762138891660191	3	FACETS	0.98	0.922	1	0.49	0.461	0.52	CLONAL	1	TRUE	1	0.798851371899467	3		669	1026	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246890	10246890	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006410-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	116	388	0	ENST00000340748.4:c.4515C>G	p.Asn1505Lys	p.N1505K	ENST00000340748		1505	aaC/aaG	37/40	0.755829347399491	3	FACETS	0.779	0.705	0.856	0.389	0.352	0.428	SUBCLONAL	1	TRUE	1	0.798851371899467	3		388	522	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133522	55133536	+	inframe_deletion	In_Frame_Del	DEL	ACGGTCCCCGAGGCC	ACGGTCCCCGAGGCC	-	novel	NA	P-0006410-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	558	543	0	ENST00000257290.5:c.831_845del	p.Pro278_Val282del	p.P278_V282del	ENST00000257290	NM_006206.4	276	ACGGTCCCCGAGGCC/-	6/23	0.460124400791123	5	FACETS	1	0.984	1	0.772	0.746	0.798	INDETERMINATE	3	TRUE	1	0.798851371899467	5		543	995	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394851	394851	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006410-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	95	376	0	ENST00000380956.4:c.247G>T	p.Glu83Ter	p.E83*	ENST00000380956	NM_001195286.1	83	Gaa/Taa	3/9	0.762138891660191	3	FACETS	0.551	0.491	0.614	0.276	0.245	0.307	SUBCLONAL	1	TRUE	1	0.798851371899467	3		376	604	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0006422-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	33	556	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.721	0.587	0.872	0.721	0.587	0.872	SUBCLONAL	1	TRUE	1	0.22	2		556	416	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253446	226253446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006422-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	11	111	0	ENST00000366813.1:c.218G>A	p.Arg73Gln	p.R73Q	ENST00000366813		73	cGa/cAa	2/3	1	2	FACETS	1	0.705	1	1	0.705	1	CLONAL	1	TRUE	1	0.22	2		111	99	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098593	11098593	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006422-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	21	558	0	ENST00000358026.2:c.1111G>T	p.Glu371Ter	p.E371*	ENST00000358026	NM_001128849.1	371	Gag/Tag	6/36	1	2	FACETS	0.464	0.357	0.591	0.464	0.357	0.591	SUBCLONAL	1	TRUE	1	0.22	2		558	411	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715945	52715945	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006422-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	63	492	1	ENST00000322088.6:c.510C>A	p.Phe170Leu	p.F170L	ENST00000322088	NM_014225.5	170	ttC/ttA	5/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.22	2		493	389	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0006429-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	45	263	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	0.826611229846479	1	FACETS	0.343	0.292	0.398	0.343	0.292	0.398	SUBCLONAL	1	TRUE	0	0.826611229846479	1		263	186	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441213	52441213	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006429-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	46	444	0	ENST00000460680.1:c.557T>A	p.Leu186Gln	p.L186Q	ENST00000460680	NM_004656.3	186	cTg/cAg	7/17	1	2	FACETS	0.23	0.193	0.27	0.23	0.193	0.27	SUBCLONAL	1	TRUE	1	0.826611229846479	2		444	484	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966733	44966733	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006429-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	119	396	0	ENST00000377967.4:c.3957G>A	p.Trp1319Ter	p.W1319*	ENST00000377967	NM_021140.2	1319	tgG/tgA	27/29	1	1	FACETS	0.471	0.429	0.513	0.471	0.429	0.513	SUBCLONAL	1	TRUE	0	0.826611229846479	1		396	359	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	100	249	0	ENST00000397752.3:c.3028G>A	p.Asp1010Asn	p.D1010N	ENST00000397752	NM_000245.2	1010	Gat/Aat	14/21	0.207316301917147	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.223672687628691	2		249	399	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1192	188	607	1	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	0.215562657787709	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.223672687628691	1		608	1380	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371645	55371645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1420347279	NA	P-0006432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	129	532	0	ENST00000297316.4:c.335C>T	p.Ala112Val	p.A112V	ENST00000297316	NM_022454.3	112	gCg/gTg	2/2	0.223672687628691	3	FACETS	1	0.931	1	0.518	0.468	0.571	CLONAL	1	TRUE	1	0.223672687628691	3		532	1238	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955581	48955581	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0006432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	76	301	0	ENST00000267163.4:c.1695+2T>G		p.X565_splice	ENST00000267163	NM_000321.2	565			0.223672687628691	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.223672687628691	1		301	543	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0006439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	218	585	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.277848610458448	6	FACETS	1	0.982	1	0.579	0.538	0.621	CLONAL	2	TRUE	2	0.277848610458448	6		585	1054	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0006439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	72	646	4	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.125192054696104	3	FACETS	0.699	0.61	0.796	0.233	0.203	0.266	INDETERMINATE	1	TRUE	0	0.277848610458448	3		650	844	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578552	7578552	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	145	565	0	ENST00000269305.4:c.378C>A	p.Tyr126Ter	p.Y126*	ENST00000269305	NM_001126112.2	126	taC/taA	5/11	0.125192054696104	3	FACETS	0.848	0.775	0.924	0.565	0.517	0.616	INDETERMINATE	2	TRUE	0	0.277848610458448	3		565	701	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846267	156846267	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	43	591	0	ENST00000524377.1:c.1708C>T	p.Gln570Ter	p.Q570*	ENST00000524377	NM_002529.3	570	Cag/Tag	14/17	0.198402148308114	3	FACETS	0.542	0.453	0.642	0.271	0.226	0.321	SUBCLONAL	1	TRUE	1	0.277848610458448	3		591	650	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681033	117681033	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	42	593	0	ENST00000368508.3:c.3587del	p.Gly1196AspfsTer47	p.G1196Dfs*47	ENST00000368508	NM_002944.2	1196	gGa/ga	23/43	0.198402148308114	3	FACETS	0.422	0.351	0.502	0.211	0.175	0.251	SUBCLONAL	1	TRUE	1	0.277848610458448	3		593	815	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0006442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	382	759	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.343658166630511	2	FACETS	0.828	0.787	0.87	0.828	0.787	0.87	CLONAL	2	TRUE	0	0.400350048621289	2		759	1152	SUCCESS
APC	324	MSKCC	GRCh37	5	112151189	112151214	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAGGGTTCAACTACACGAATGGACCA	TAGGGTTCAACTACACGAATGGACCA	-	novel	NA	P-0006442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	86	422	0	ENST00000257430.4:c.835-2_858del		p.X279_splice	ENST00000257430	NM_000038.5	279		9/16	0.387865702446217	1	FACETS	0.7	0.621	0.783	0.7	0.621	0.783	SUBCLONAL	1	TRUE	0	0.400350048621289	1		422	491	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376240	225376246	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTACT	TTCTACT	-	novel	NA	P-0006442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	49	408	0	ENST00000264414.4:c.708_714del	p.Val237LeufsTer7	p.V237Lfs*7	ENST00000264414	NM_003590.4	236	aaAGTAGAA/aa	6/16	1	2	FACETS	0.522	0.442	0.609	0.522	0.442	0.609	SUBCLONAL	1	TRUE	1	0.400350048621289	2		408	469	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	39	192	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.85	1			1	INDETERMINATE	1	TRUE	NA	0.519350629832534	2		192	149	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593323	67593323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	74	1079	0	ENST00000274335.5:c.2069C>T	p.Ser690Phe	p.S690F	ENST00000274335		690	tCt/tTt	15/15	1	2	FACETS	0.843	0.744	0.948	0.843	0.744	0.948	CLONAL	1	TRUE	1	0.519350629832534	2		1079	338	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544646	65544646	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	22	889	0	ENST00000358664.4:c.280C>G	p.Leu94Val	p.L94V	ENST00000358664	NM_002382.4	94	Ctt/Gtt	4/5	1	2	FACETS	0.196	0.151	0.248	0.196	0.151	0.248	SUBCLONAL	1	TRUE	1	0.519350629832534	2		889	432	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716326	52716326	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	202	911	0	ENST00000322088.6:c.770G>T	p.Trp257Leu	p.W257L	ENST00000322088	NM_014225.5	257	tGg/tTg	6/15	0.447371852268921	3	FACETS	0.909	0.85	0.97	0.909	0.85	0.97	CLONAL	2	TRUE	1	0.519350629832534	3		911	539	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855952	76855952	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	88	1323	2	ENST00000373344.5:c.5648G>A	p.Trp1883Ter	p.W1883*	ENST00000373344	NM_000489.3	1883	tGg/tAg	23/35	1	2	FACETS	0.829	0.738	0.924	0.829	0.738	0.924	CLONAL	1	TRUE	1	0.519350629832534	2		1325	409	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442511	49442512	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCC	novel	NA	P-0006445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	78	1036	0	ENST00000301067.7:c.4059_4061dup	p.Glu1355dup	p.E1355dup	ENST00000301067	NM_003482.3	1355	gaa/gaGGAa	13/54	1	2	FACETS	0.905	0.802	1	0.905	0.802	1	CLONAL	1	TRUE	1	0.519350629832534	2		1036	332	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591145	67591148	+	protein_altering_variant	In_Frame_Del	DEL	TACT	TACT	A	novel	NA	P-0006445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	62	901	0	ENST00000274335.5:c.1738_1741delinsA	p.Tyr580_Leu581delinsMet	p.Y580_L581delinsM	ENST00000274335		580	TACTtg/Atg	12/15	1	2	FACETS	0.793	0.691	0.903	0.793	0.691	0.903	CLONAL	1	TRUE	1	0.519350629832534	2		901	301	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483267	120483267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	232	424	0	ENST00000256646.2:c.3094C>T	p.His1032Tyr	p.H1032Y	ENST00000256646	NM_024408.3	1032	Cat/Tat	19/34	1	2	FACETS	0.953	0.897	1	0.953	0.897	1	CLONAL	1	TRUE	1	0.9	2		424	541	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0006459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	1234	468	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.688747760270887	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.695918136490077	3		468	1530	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81558892	81558892	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	313	506	0	ENST00000298171.2:c.485C>A	p.Pro162His	p.P162H	ENST00000298171	NM_000369.2	162	cCt/cAt	6/10	0.695918136490077	3	FACETS	0.937	0.892	0.982	0.937	0.892	0.982	CLONAL	2	TRUE	1	0.695918136490077	3		506	647	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	85	407	0	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			NA	2	FACETS	0.702	0.622	0.786			1	INDETERMINATE	1	TRUE	NA	0.488425024055293	2		407	496	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	105	192	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.488425024055293	2		192	332	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298088	11298088	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	205	372	0	ENST00000361445.4:c.2020T>A	p.Cys674Ser	p.C674S	ENST00000361445	NM_004958.3	674	Tgt/Agt	13/58	0.354024776213746	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.488425024055293	1		372	462	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257432	16257432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763947168	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	288	472	0	ENST00000375759.3:c.4697C>T	p.Ser1566Phe	p.S1566F	ENST00000375759	NM_015001.2	1566	tCt/tTt	11/15	0.167585591025146	2	FACETS	1	0.994	1	0.739	0.698	0.781	INDETERMINATE	1	TRUE	0	0.488425024055293	2		472	798	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36945039	36945039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	349	599	0	ENST00000361632.4:c.59C>T	p.Pro20Leu	p.P20L	ENST00000361632		20	cCc/cTc	2/16	0.167585591025146	2	FACETS	1	0.995	1	0.732	0.695	0.77	INDETERMINATE	1	TRUE	0	0.488425024055293	2		599	976	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120460386	120460386	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	265	348	0	ENST00000256646.2:c.5930-1G>C		p.X1977_splice	ENST00000256646	NM_024408.3	1977			0.173891230042371	3	FACETS	1	0.982	1			1	INDETERMINATE	2	TRUE	NA	0.488425024055293	3		348	621	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491153	120491153	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1004494435	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	100	500	0	ENST00000256646.2:c.2636C>T	p.Ser879Phe	p.S879F	ENST00000256646	NM_024408.3	879	tCc/tTc	17/34	0.173891230042371	3	FACETS	0.51	0.454	0.569			1	INDETERMINATE	1	TRUE	NA	0.488425024055293	3		500	999	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741945	162741945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	102	555	0	ENST00000367921.3:c.1636G>A	p.Asp546Asn	p.D546N	ENST00000367921	NM_006182.2	546	Gac/Aac	13/18	0.244756689091154	1	FACETS	0.411	0.367	0.458	0.411	0.367	0.458	INDETERMINATE	1	TRUE	0	0.488425024055293	1		555	768	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243778408	243778408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	53	301	0	ENST00000263826.5:c.617C>T	p.Pro206Leu	p.P206L	ENST00000263826	NM_005465.4	206	cCc/cTc	6/13	0.244756689091154	1	FACETS	0.348	0.297	0.404	0.348	0.297	0.404	INDETERMINATE	1	TRUE	0	0.488425024055293	1		301	471	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966367	25966367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	147	508	0	ENST00000435504.4:c.2839C>T	p.Pro947Ser	p.P947S	ENST00000435504		947	Cct/Tct	13/13	1	2	FACETS	0.576	0.525	0.63	0.576	0.525	0.63	SUBCLONAL	1	TRUE	1	0.488425024055293	2		508	1045	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61724120	61724120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781425578	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	247	298	0	ENST00000401558.2:c.782G>A	p.Arg261Gln	p.R261Q	ENST00000401558	NM_003400.3	261	cGa/cAa	10/25	1	2	FACETS	0.753	0.708	0.798	1	0.993	1	SUBCLONAL	2	TRUE	1	0.488425024055293	2		298	672	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027131	71027131	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	218	405	0	ENST00000318789.4:c.1196C>T	p.Ser399Phe	p.S399F	ENST00000318789	NM_032682.5	399	tCt/tTt	15/21	0.488425024055293	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.488425024055293	1		405	572	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972912	55972913	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	118	432	0	ENST00000263923.4:c.1477_1478delinsAA	p.Gly493Lys	p.G493K	ENST00000263923	NM_002253.2	493	GGa/AAa	11/30	0.167585591025146	2	FACETS	0.644	0.581	0.711	0.322	0.29	0.356	INDETERMINATE	1	TRUE	0	0.488425024055293	2		432	750	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294416	1294417	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	69	268	0	ENST00000310581.5:c.584_585delinsAA	p.Arg195Lys	p.R195K	ENST00000310581	NM_198253.2	195	aGG/aAA	2/16	1	2	FACETS	0.65	0.568	0.737	0.65	0.568	0.737	SUBCLONAL	1	TRUE	1	0.488425024055293	2		268	435	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675553	30675553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	391	685	0	ENST00000376406.3:c.2803G>A	p.Glu935Lys	p.E935K	ENST00000376406	NM_014641.2	935	Gag/Aag	8/15	0.224244115655108	4	FACETS	0.864	0.82	0.909	0.864	0.82	0.909	INDETERMINATE	2	TRUE	2	0.488425024055293	4		685	1379	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288295	33288296	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	208	372	2	ENST00000374542.5:c.1112_1113delinsAA	p.Arg371Gln	p.R371Q	ENST00000374542	NM_001141970.1	371	cGG/cAA	4/8	0.224244115655108	4	FACETS	0.837	0.779	0.897	0.837	0.779	0.897	INDETERMINATE	2	TRUE	2	0.488425024055293	4		374	757	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004429	150004429	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	165	400	0	ENST00000253339.5:c.1796A>T	p.Asn599Ile	p.N599I	ENST00000253339		599	aAt/aTt	3/7	0.244756689091154	1	FACETS	0.893	0.824	0.963	0.893	0.824	0.963	INDETERMINATE	1	TRUE	0	0.488425024055293	1		400	572	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902253	151902253	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	84	191	0	ENST00000262189.6:c.3899G>A	p.Arg1300Lys	p.R1300K	ENST00000262189	NM_170606.2	1300	aGa/aAa	25/59	0.36367128543863	3	FACETS	1	0.962	1	0.594	0.529	0.663	CLONAL	1	TRUE	1	0.488425024055293	3		191	360	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449788	8449788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1267613597	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	102	400	0	ENST00000356435.5:c.3925G>A	p.Glu1309Lys	p.E1309K	ENST00000356435		1309	Gag/Aag	23/35	0.164505322848747	4	FACETS	0.741	0.662	0.825	0.37	0.331	0.413	INDETERMINATE	1	TRUE	2	0.488425024055293	4		400	839	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482301	87482301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	297	540	0	ENST00000277120.3:c.1588C>T	p.Pro530Ser	p.P530S	ENST00000277120		530	Ccc/Tcc	14/19	0.488425024055293	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.488425024055293	1		540	687	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242832	98242832	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	290	417	0	ENST00000331920.6:c.785T>A	p.Leu262Ter	p.L262*	ENST00000331920	NM_000264.3	262	tTg/tAg	6/24	0.488425024055293	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.488425024055293	1		417	668	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417355	139417355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1269141919	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	184	364	0	ENST00000277541.6:c.689G>A	p.Gly230Glu	p.G230E	ENST00000277541	NM_017617.3	230	gGg/gAg	4/34	0.488425024055293	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.488425024055293	1		364	428	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104264060	104264061	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	198	473	0	ENST00000369902.3:c.151_152delinsTT	p.Pro51Leu	p.P51L	ENST00000369902	NM_016169.3	51	CCg/TTg	1/12	1	2	FACETS	0.976	0.905	1	0.976	0.905	1	CLONAL	1	TRUE	1	0.488425024055293	2		473	831	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200913	67200913	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	134	404	0	ENST00000312629.5:c.901A>T	p.Lys301Ter	p.K301*	ENST00000312629	NM_003952.2	301	Aaa/Taa	10/15	1	2	FACETS	0.938	0.855	1	0.938	0.855	1	CLONAL	1	TRUE	1	0.488425024055293	2		404	585	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50481153	50481153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	185	399	0	ENST00000394963.4:c.539G>A	p.Arg180Gln	p.R180Q	ENST00000394963	NM_003076.4	180	cGg/cAg	5/13	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.488425024055293	2		399	723	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636136	28636136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	103	480	0	ENST00000241453.7:c.236C>T	p.Ala79Val	p.A79V	ENST00000241453	NM_004119.2	79	gCc/gTc	3/24	0.254048028828109	2	FACETS	0.637	0.571	0.707	0.319	0.285	0.354	INDETERMINATE	1	TRUE	0	0.488425024055293	2		480	662	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891657	28891657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	124	559	0	ENST00000282397.4:c.3364C>T	p.Pro1122Ser	p.P1122S	ENST00000282397	NM_002019.4	1122	Cct/Tct	25/30	0.254048028828109	2	FACETS	0.554	0.501	0.611	0.277	0.25	0.306	INDETERMINATE	1	TRUE	0	0.488425024055293	2		559	916	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934616	9934617	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	78	412	0	ENST00000330684.3:c.1538_1539delinsAT	p.Thr513Asn	p.T513N	ENST00000330684	NM_001134407.1	513	aCC/aAT	7/13	0.36289992968639	1	FACETS	0.388	0.341	0.439	0.388	0.341	0.439	SUBCLONAL	1	TRUE	0	0.488425024055293	1		412	622	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024723	14024723	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	135	352	0	ENST00000311895.7:c.949G>A	p.Glu317Lys	p.E317K	ENST00000311895	NM_005236.2	317	Gaa/Aaa	5/11	0.36289992968639	1	FACETS	0.725	0.662	0.791	0.725	0.662	0.791	SUBCLONAL	1	TRUE	0	0.488425024055293	1		352	576	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991961	72991961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1262542686	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	129	638	0	ENST00000268489.5:c.2084C>T	p.Pro695Leu	p.P695L	ENST00000268489	NM_006885.3	695	cCg/cTg	2/10	0.36289992968639	1	FACETS	0.5	0.454	0.549	0.5	0.454	0.549	SUBCLONAL	1	TRUE	0	0.488425024055293	1		638	798	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819661	81819661	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	145	683	1	ENST00000359376.3:c.67G>A	p.Glu23Lys	p.E23K	ENST00000359376	NM_002661.3	23	Gag/Aag	2/33	0.36289992968639	1	FACETS	0.467	0.425	0.511	0.467	0.425	0.511	SUBCLONAL	1	TRUE	0	0.488425024055293	1		684	961	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81973613	81973613	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	280	624	2	ENST00000359376.3:c.3430G>A	p.Asp1144Asn	p.D1144N	ENST00000359376	NM_002661.3	1144	Gat/Aat	30/33	0.36289992968639	1	FACETS	0.923	0.869	0.978	0.923	0.869	0.978	CLONAL	1	TRUE	0	0.488425024055293	1		626	939	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	215	513	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.488425024055293	2		513	740	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663443	29663443	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	169	470	0	ENST00000356175.3:c.6036T>A	p.Asp2012Glu	p.D2012E	ENST00000356175	NM_000267.3	2012	gaT/gaA	40/57	1	2	FACETS	0.942	0.868	1	0.942	0.868	1	CLONAL	1	TRUE	1	0.488425024055293	2		470	735	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58701083	58701083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555645770	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	348	793	0	ENST00000305921.3:c.674G>A	p.Arg225Lys	p.R225K	ENST00000305921	NM_003620.3	225	aGa/aAa	2/6	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.488425024055293	2		793	1341	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390346	56390346	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	265	681	0	ENST00000348428.3:c.1085C>A	p.Pro362His	p.P362H	ENST00000348428	NM_006785.3	362	cCt/cAt	10/17	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.488425024055293	2		681	978	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5260824	5260825	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	84	396	1	ENST00000357368.4:c.586_587delinsTT	p.Pro196Leu	p.P196L	ENST00000357368	NM_002850.3	196	CCg/TTg	7/38	1	2	FACETS	0.642	0.568	0.72	0.642	0.568	0.72	SUBCLONAL	1	TRUE	1	0.488425024055293	2		397	536	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262163	10262163	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1263023164	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	267	619	0	ENST00000340748.4:c.2128C>T	p.Pro710Ser	p.P710S	ENST00000340748		710	Cca/Tca	23/40	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.488425024055293	2		619	966	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094997	11094997	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568417458	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	182	526	0	ENST00000358026.2:c.170C>T	p.Pro57Leu	p.P57L	ENST00000358026	NM_001128849.1	57	cCc/cTc	2/36	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.488425024055293	2		526	741	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713416	40713416	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs539998222	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	139	389	0	ENST00000373198.4:c.4099C>T	p.Pro1367Ser	p.P1367S	ENST00000373198	NM_133170.3	1367	Ccc/Tcc	30/32	1	2	FACETS	0.774	0.706	0.846	0.774	0.706	0.846	SUBCLONAL	1	TRUE	1	0.488425024055293	2		389	735	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262309	46262309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	424	686	0	ENST00000371998.3:c.893G>A	p.Arg298Gln	p.R298Q	ENST00000371998		298	cGa/cAa	9/23	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.488425024055293	2		686	1259	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866442	42866442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	249	610	0	ENST00000398585.3:c.190C>T	p.Pro64Ser	p.P64S	ENST00000398585	NM_001135099.1	64	Ccc/Tcc	3/14	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.488425024055293	2		610	994	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167484	24167485	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	67	425	0	ENST00000263121.7:c.868_869delinsTT	p.Pro290Leu	p.P290L	ENST00000263121	NM_003073.3	290	CCa/TTa	7/9	0.295292500984651	1	FACETS	0.341	0.296	0.39	0.341	0.296	0.39	SUBCLONAL	1	TRUE	0	0.488425024055293	1		425	608	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44911049	44911049	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	219	474	0	ENST00000377967.4:c.748+2T>G		p.X250_splice	ENST00000377967	NM_021140.2	250			1	2	FACETS	0.973	0.906	1	0.973	0.906	1	CLONAL	1	TRUE	1	0.488425024055293	2		474	922	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422369	47422369	+	start_lost	Translation_Start_Site	SNP	G	G	T	novel	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	217	516	0	ENST00000377045.4:c.3G>T	p.Met1?	p.M1?	ENST00000377045	NM_001654.4	1	atG/atT	2/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.488425024055293	2		516	813	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412188	63412188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	286	777	0	ENST00000330258.3:c.979G>A	p.Gly327Ser	p.G327S	ENST00000330258	NM_152424.3	327	Ggt/Agt	2/2	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.488425024055293	2		777	1113	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349913	70349913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	252	610	0	ENST00000374080.3:c.3896C>T	p.Ser1299Phe	p.S1299F	ENST00000374080		1299	tCt/tTt	28/45	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.488425024055293	2		610	1000	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0006465-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	24	331	0				ENST00000310581	NM_198253.2	-/1132			0.172453557708263	3	FACETS	0.852	0.68	1	0.852	0.68	1	INDETERMINATE	2	TRUE	1	0.3	3		331	108	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916614	178916614	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0006465-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	259	529	0	ENST00000263967.3:c.1A>G	p.Met1?	p.M1?	ENST00000263967	NM_006218.2	1	Atg/Gtg	2/21	0.3	6	FACETS	1	0.984	1			1	CLONAL	5	TRUE	NA	0.3	6		529	504	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133737	55133737	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006465-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	159	358	0	ENST00000257290.5:c.950T>G	p.Ile317Ser	p.I317S	ENST00000257290	NM_006206.4	317	aTc/aGc	7/23	0.3	9	FACETS	0.933	0.862	1			1	CLONAL	5	TRUE	NA	0.3	9		358	466	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508824	106508824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226994105	NA	P-0006465-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	44	359	0	ENST00000359195.3:c.818G>A	p.Arg273His	p.R273H	ENST00000359195	NM_002649.2	273	cGc/cAc	2/11	0.3	5	FACETS	1	0.935	1	0.306	0.258	0.36	CLONAL	1	TRUE	1	0.3	5		359	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587781525	NA	P-0006472-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	322	493	1	ENST00000269305.4:c.842A>T	p.Asp281Val	p.D281V	ENST00000269305	NM_001126112.2	281	gAc/gTc	8/11	0.594451854250098	1	FACETS	0.999	0.95	1	0.999	0.95	1	CLONAL	1	TRUE	0	0.627704534052399	1		494	705	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145039	58145039	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006472-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	211	395	0	ENST00000257904.6:c.305C>A	p.Thr102Lys	p.T102K	ENST00000257904	NM_000075.3	102	aCa/aAa	3/8	1	2	FACETS	0.86	0.801	0.921	0.86	0.801	0.921	CLONAL	1	TRUE	1	0.627704534052399	2		395	782	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868209	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0006472-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	244	458	0	ENST00000269571.5:c.929_930delinsAT	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCC/tAT	8/27	1	2	FACETS	0.914	0.856	0.973	0.914	0.856	0.973	CLONAL	1	TRUE	1	0.627704534052399	2		458	851	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465395	120465395	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006475-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	33	233	0	ENST00000256646.2:c.4866A>C	p.Lys1622Asn	p.K1622N	ENST00000256646	NM_024408.3	1622	aaA/aaC	27/34	1	2	FACETS	0.698	0.568	0.846	0.698	0.568	0.846	SUBCLONAL	1	TRUE	1	0.18	2		233	525	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043407	180043407	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006475-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	43	509	0	ENST00000261937.6:c.3179G>T	p.Arg1060Leu	p.R1060L	ENST00000261937	NM_182925.4	1060	cGg/cTg	23/30	0.3	0	FACETS	0.719	0.601	0.85			1	SUBCLONAL	1	TRUE	0	0.18	0		509	545	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0006475-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	99	481	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	1	2	FACETS	0.994	0.885	1	0.994	0.885	1	CLONAL	1	TRUE	1	0.18	2		481	1107	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438216	56438216	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006475-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	66	440	0	ENST00000407977.2:c.777G>A	p.Trp259Ter	p.W259*	ENST00000407977		259	tgG/tgA	7/10	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.18	2		440	684	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845712	68845753	+	inframe_deletion	In_Frame_Del	DEL	AACAGGAACACAGGAGTCATCAGTGTGGTCACCACTGGGCTG	AACAGGAACACAGGAGTCATCAGTGTGGTCACCACTGGGCTG	-	novel	NA	P-0006475-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	132	449	0	ENST00000261769.5:c.958_999del	p.Asn320_Leu333del	p.N320_L333del	ENST00000261769	NM_004360.3	320	AACAGGAACACAGGAGTCATCAGTGTGGTCACCACTGGGCTG/-	7/16	1	2	FACETS	0.934	0.849	1	1	0.989	1	CLONAL	2	TRUE	1	0.18	2		449	785	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0006482-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	237	300	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.321533469013834	9	FACETS	1	0.973	1			1	CLONAL	3	TRUE	NA	0.321533469013834	9		300	970	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0006482-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	425	679	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.321533469013834	5	FACETS	1	0.99	1			1	CLONAL	4	TRUE	NA	0.321533469013834	5		679	890	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006482-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	164	870	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	0.222873321944045	4	FACETS	1	0.988	1	0.742	0.681	0.805	CLONAL	1	TRUE	2	0.321533469013834	4		870	909	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578529	7578529	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs780442292	NA	P-0006482-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	160	919	0	ENST00000269305.4:c.401T>G	p.Phe134Cys	p.F134C	ENST00000269305	NM_001126112.2	134	tTt/tGt	5/11	0.264543627421485	2	FACETS	0.841	0.774	0.909	0.841	0.774	0.909	CLONAL	2	TRUE	0	0.321533469013834	2		919	592	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198262815	198262815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	103	278	0	ENST00000335508.6:c.3160G>A	p.Glu1054Lys	p.E1054K	ENST00000335508	NM_012433.2	1054	Gag/Aag	22/25	NA	2	FACETS	0.584	0.524	0.648			1	INDETERMINATE	1	TRUE	NA	0.57409579602078	2		278	614	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336242	73336242	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	168	308	0	ENST00000377767.4:c.2161T>A	p.Leu721Met	p.L721M	ENST00000377767	NM_014953.3	721	Ttg/Atg	17/21	0.200287796024824	2	FACETS	1	0.976	1	0.563	0.521	0.606	INDETERMINATE	1	TRUE	0	0.57409579602078	2		308	520	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138585	11138611	+	inframe_deletion	In_Frame_Del	DEL	ATTACTTTGCGTATCGCGGCTTTAAAT	ATTACTTTGCGTATCGCGGCTTTAAAT	-	novel	NA	P-0006503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	181	473	0	ENST00000358026.2:c.3342_3368del	p.Tyr1115_Tyr1123del	p.Y1115_Y1123del	ENST00000358026	NM_001128849.1	1114	gATTACTTTGCGTATCGCGGCTTTAAATac/gac	24/36	0.57409579602078	1	FACETS	0.797	0.74	0.856	0.797	0.74	0.856	SUBCLONAL	1	TRUE	0	0.57409579602078	1		473	564	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164836	47164837	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0006503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	168	435	0	ENST00000409792.3:c.1289_1290del	p.Ser430Ter	p.S430*	ENST00000409792	NM_014159.6	430	tCT/t	3/21	0.534389314301085	1	FACETS	0.771	0.713	0.831	0.771	0.713	0.831	SUBCLONAL	1	TRUE	0	0.57409579602078	1		435	541	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30060987	30060988	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	203	404	1	ENST00000338641.4:c.822dup	p.Pro275ThrfsTer4	p.P275Tfs*4	ENST00000338641	NM_000268.3	273	-/A	9/16	0.57409579602078	1	FACETS	0.865	0.807	0.924	0.865	0.807	0.924	CLONAL	1	TRUE	0	0.57409579602078	1		405	583	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436396	52436470	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCCGCACGGAGATGTTCTGCTCCACTAGGTTGGCCAGCATGCCTGCGAAGAGGTAGAGACCCTTGAGCAGGTGCT	GCCGCACGGAGATGTTCTGCTCCACTAGGTTGGCCAGCATGCCTGCGAAGAGGTAGAGACCCTTGAGCAGGTGCT	-	novel	NA	P-0006520-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	196	506	0	ENST00000460680.1:c.2057-33_2098del		p.X686_splice	ENST00000460680	NM_004656.3	686		17/17	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		506	521	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0006546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	229	378	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.896	0.842	0.95	0.896	0.842	0.95	CLONAL	1	TRUE	1	0.929794292959247	2		378	550	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0006546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	979	640	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.929794292959247	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.929794292959247	2		640	1016	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951087	48951088	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs1131690889	NA	P-0006546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	338	491	0	ENST00000267163.4:c.1251_1252del	p.Arg418SerfsTer9	p.R418Sfs*9	ENST00000267163	NM_000321.2	417	AAa/a	13/27	0.91336566183294	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.929794292959247	1		491	369	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230432	46230432	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	346	447	0	ENST00000334344.6:c.766T>G	p.Ser256Ala	p.S256A	ENST00000334344	NM_152641.2	256	Tct/Gct	7/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.929794292959247	2		447	702	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857663	78857663	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	424	577	2	ENST00000306801.3:c.1733C>G	p.Ala578Gly	p.A578G	ENST00000306801	NM_020761.2	578	gCc/gGc	16/34	0.289349136475858	3	FACETS	1	0.995	1	0.657	0.628	0.687	INDETERMINATE	1	TRUE	1	0.929794292959247	3		579	1016	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778806	76778807	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0006546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	528	453	0	ENST00000373344.5:c.6772_6773del	p.Leu2258GlyfsTer10	p.L2258Gfs*10	ENST00000373344	NM_000489.3	2258	TTg/g	31/35	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.929794292959247	1		453	600	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870921	12870922	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0006546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	385	466	0	ENST00000228872.4:c.151_152del	p.Asp51HisfsTer73	p.D51Hfs*73	ENST00000228872	NM_004064.3	50	AGa/a	1/3	0.91208919014866	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.929794292959247	1		466	441	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165687	185165687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	98	531	0	ENST00000265026.3:c.962C>T	p.Ala321Val	p.A321V	ENST00000265026	NM_004721.4	321	gCg/gTg	5/14	1	2	FACETS	0.396	0.352	0.442	0.396	0.352	0.442	SUBCLONAL	1	TRUE	1	0.571942393187917	2		531	866	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443626	52443626	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0006553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	213	428	1	ENST00000460680.1:c.68-2A>T		p.X23_splice	ENST00000460680	NM_004656.3	23			0.506574690929955	1	FACETS	0.784	0.732	0.838	0.784	0.732	0.838	SUBCLONAL	1	TRUE	0	0.571942393187917	1		429	678	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884446	151884446	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	64	579	0	ENST00000262189.6:c.4909C>A	p.Leu1637Ile	p.L1637I	ENST00000262189	NM_170606.2	1637	Ctt/Att	33/59	1	2	FACETS	0.248	0.214	0.285	0.248	0.214	0.285	SUBCLONAL	1	TRUE	1	0.571942393187917	2		579	903	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627234	86627238	+	frameshift_variant	Frame_Shift_Del	DEL	TTATC	TTATC	-	rs1060503441	NA	P-0006553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	171	561	0	ENST00000274376.6:c.613_617del	p.Leu205LysfsTer4	p.L205Kfs*4	ENST00000274376	NM_002890.2	203	agTTATCtt/agtt	2/25	0.448945162521028	1	FACETS	0.655	0.605	0.707	0.655	0.605	0.707	SUBCLONAL	1	TRUE	0	0.571942393187917	1		561	652	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111562	8111562	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs112399242	NA	P-0006556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	204	372	0	ENST00000346208.3:c.1047+1G>A		p.X349_splice	ENST00000346208		349			1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.443824665021973	2		372	877	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404937	404937	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	225	393	0	ENST00000399788.2:c.4257del	p.Gln1419HisfsTer31	p.Q1419Hfs*31	ENST00000399788	NM_001042603.1	1419	caA/ca	26/28	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.443824665021973	2		393	985	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263728	16263729	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	183	381	0	ENST00000375759.3:c.10098dup	p.Pro3367ThrfsTer48	p.P3367Tfs*48	ENST00000375759	NM_015001.2	3366	gca/gcAa	12/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.443824665021973	2		381	747	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	85	338	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.388	0.343	0.436	0.388	0.343	0.436	SUBCLONAL	1	TRUE	1	0.770115921204816	2		339	569	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340283	116340283	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	113	340	0	ENST00000397752.3:c.1145A>G	p.Asn382Ser	p.N382S	ENST00000397752	NM_000245.2	382	aAt/aGt	2/21	1	2	FACETS	0.59	0.534	0.65	0.59	0.534	0.65	SUBCLONAL	1	TRUE	1	0.770115921204816	2		340	497	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485028	57485028	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	140	397	1	ENST00000371085.3:c.862A>T	p.Ile288Phe	p.I288F	ENST00000371085	NM_000516.4	288	Atc/Ttc	11/13	1	2	FACETS	0.496	0.452	0.542	0.496	0.452	0.542	SUBCLONAL	1	TRUE	1	0.770115921204816	2		398	733	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179488	56179514	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTAATGGCTGTTAAACAGGTAAATAT	TTTAATGGCTGTTAAACAGGTAAATAT	-	novel	NA	P-0006563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	85	345	0	ENST00000399503.3:c.3801_3819+8del		p.X1267_splice	ENST00000399503	NM_005921.1	1267		15/20	1	2	FACETS	0.418	0.37	0.469	0.418	0.37	0.469	SUBCLONAL	1	TRUE	1	0.770115921204816	2		345	528	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168811	56168811	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	86	328	0	ENST00000399503.3:c.1667del	p.Leu556Ter	p.L556*	ENST00000399503	NM_005921.1	555	gaT/ga	9/20	1	2	FACETS	0.426	0.378	0.478	0.426	0.378	0.478	SUBCLONAL	1	TRUE	1	0.770115921204816	2		328	524	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0006566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	23	300	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.793	1	1	0.793	1	CLONAL	1	TRUE	1	0.14	2		300	323	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0006566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	47	283	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.14	2		283	571	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593482	55593482	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	37	356	0	ENST00000288135.5:c.1639T>A	p.Tyr547Asn	p.Y547N	ENST00000288135	NM_000222.2	547	Tat/Aat	10/21	1	2	FACETS	0.914	0.753	1	0.914	0.753	1	CLONAL	1	TRUE	1	0.14	2		356	578	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581360	48581360	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	29	228	0	ENST00000342988.3:c.664A>T	p.Thr222Ser	p.T222S	ENST00000342988	NM_005359.5	222	Aca/Tca	5/12	1	2	FACETS	0.935	0.75	1	0.935	0.75	1	CLONAL	1	TRUE	1	0.14	2		228	443	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188219	10188219	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs5030832	NA	P-0006586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	182	406	0	ENST00000256474.2:c.362A>G	p.Asp121Gly	p.D121G	ENST00000256474	NM_000551.3	121	gAt/gGt	2/3	0.553926763647691	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	0	0.553926763647691	1		406	437	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138551	37138551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	139	331	0	ENST00000373509.5:c.85A>G	p.Lys29Glu	p.K29E	ENST00000373509	NM_002648.3	29	Aag/Gag	2/6	1	2	FACETS	0.951	0.87	1	0.951	0.87	1	CLONAL	1	FALSE	1	0.553926763647691	2		331	528	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634361	23634361	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	174	471	0	ENST00000261584.4:c.2925G>T	p.Arg975Ser	p.R975S	ENST00000261584	NM_024675.3	975	agG/agT	9/13	0.26280342337791	3	FACETS	0.825	0.76	0.894			1	INDETERMINATE	1	FALSE	NA	0.553926763647691	3		471	972	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443888	52443889	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	98	266	0	ENST00000460680.1:c.6dup	p.Lys3Ter	p.K3*	ENST00000460680	NM_004656.3	2	-/T	1/17	0.553926763647691	1	FACETS	0.859	0.776	0.944	0.859	0.776	0.944	CLONAL	1	FALSE	0	0.553926763647691	1		266	298	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0006596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	79	381	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.320975534452689	3	FACETS	0.838	0.743	0.938	0.838	0.743	0.938	CLONAL	2	TRUE	1	0.320975534452689	3		382	341	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253911	NA	P-0006596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	83	356	0	ENST00000269305.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000269305	NM_001126112.2	180	Gag/Aag	5/11	0.320975534452689	1	FACETS	0.901	0.808	0.997	1	0.985	1	CLONAL	2	TRUE	0	0.320975534452689	1		356	241	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590648	189590648	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	17	369	0	ENST00000264731.3:c.1213G>A	p.Val405Met	p.V405M	ENST00000264731	NM_003722.4	405	Gtg/Atg	10/14	0.104166333618996	1	FACETS	0.343	0.256	0.447	0.343	0.256	0.447	INDETERMINATE	1	TRUE	0	0.320975534452689	1		369	259	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163438	47163441	+	frameshift_variant	Frame_Shift_Del	DEL	AGTT	AGTT	-	novel	NA	P-0006596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	48	372	0	ENST00000409792.3:c.2685_2688del	p.Thr896SerfsTer2	p.T896Sfs*2	ENST00000409792	NM_014159.6	895	ctAACT/ct	3/21	1	2	FACETS	0.917	0.779	1	0.917	0.779	1	CLONAL	1	TRUE	1	0.320975534452689	2		372	326	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163008	47163009	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CGAATAATCTTCA	novel	NA	P-0006596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	21	425	0	ENST00000409792.3:c.3117_3118insTGAAGATTATTCG	p.Gly1040Ter	p.G1040*	ENST00000409792	NM_014159.6	1039	-/TGAAGATTATTCG	3/21	1	2	FACETS	0.507	0.391	0.642	0.507	0.391	0.642	SUBCLONAL	1	TRUE	1	0.320975534452689	2		425	258	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115457	115115458	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	48	482	0	ENST00000257566.3:c.868dup	p.Thr290AsnfsTer37	p.T290Nfs*37	ENST00000257566	NM_016569.3	290	acc/aAcc	5/8	0.326130401506856	4	FACETS	0.85	0.734	0.973	1	0.954	1	CLONAL	3	TRUE	2	0.326130401506856	4		482	153	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786928	135786928	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373454700	NA	P-0006604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	55	460	0	ENST00000298552.3:c.941C>T	p.Thr314Met	p.T314M	ENST00000298552	NM_001162426.1	314	aCg/aTg	10/23	0.251117541025646	2	FACETS	0.605	0.517	0.702	0.302	0.258	0.351	SUBCLONAL	1	TRUE	0	0.269048565438267	2		460	676	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153697	55153697	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	74	476	0	ENST00000257290.5:c.2663T>A	p.Ile888Asn	p.I888N	ENST00000257290	NM_006206.4	888	aTc/aAc	19/23	0.269048565438267	1	FACETS	0.818	0.717	0.927	0.818	0.717	0.927	CLONAL	1	TRUE	0	0.269048565438267	1		476	582	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467823	50467823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	69	332	0	ENST00000331340.3:c.1058C>T	p.Pro353Leu	p.P353L	ENST00000331340	NM_006060.4	353	cCg/cTg	8/8	1	2	FACETS	0.919	0.801	1	0.919	0.801	1	CLONAL	1	TRUE	1	0.269048565438267	2		332	558	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857209	9857209	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	83	616	0	ENST00000330684.3:c.4192G>A	p.Asp1398Asn	p.D1398N	ENST00000330684	NM_001134407.1	1398	Gac/Aac	13/13	1	2	FACETS	0.772	0.681	0.871	0.772	0.681	0.871	SUBCLONAL	1	TRUE	1	0.269048565438267	2		616	799	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006607-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	28	510	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		510	766	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0006607-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	22	990	4	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		994	752	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0006624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	734	381	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.557089802109596	4	FACETS	0.983	0.96	1	0.983	0.96	1	CLONAL	4	TRUE	0	0.588796483011901	4		382	1007	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	96	192	0				ENST00000310581	NM_198253.2	-/1132			0.27298318342509	1	FACETS	0.735	0.662	0.81	0.735	0.662	0.81	INDETERMINATE	1	TRUE	0	0.588796483011901	1		192	313	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419926	41419926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	288	520	0	ENST00000373198.4:c.395G>A	p.Gly132Glu	p.G132E	ENST00000373198	NM_133170.3	132	gGg/gAg	3/32	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.588796483011901	2		520	867	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169377	11169377	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519916	NA	P-0006624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	313	561	0	ENST00000361445.4:c.7498A>T	p.Ile2500Phe	p.I2500F	ENST00000361445	NM_004958.3	2500	Att/Ttt	56/58	1	2	FACETS	0.991	0.935	1	0.991	0.935	1	CLONAL	1	TRUE	1	0.588796483011901	2		561	1073	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812278	212812278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	230	484	1	ENST00000342788.4:c.298G>A	p.Glu100Lys	p.E100K	ENST00000342788	NM_005235.2	100	Gag/Aag	3/28	1	2	FACETS	0.985	0.921	1	0.985	0.921	1	CLONAL	1	TRUE	1	0.588796483011901	2		485	793	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873664	35873664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	183	515	0	ENST00000303115.3:c.620C>T	p.Ser207Phe	p.S207F	ENST00000303115	NM_002185.3	207	tCc/tTc	5/8	1	2	FACETS	0.783	0.724	0.844	0.783	0.724	0.844	SUBCLONAL	1	TRUE	1	0.588796483011901	2		515	794	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876208	35876208	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777033414	NA	P-0006624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	239	487	1	ENST00000303115.3:c.1000G>A	p.Glu334Lys	p.E334K	ENST00000303115	NM_002185.3	334	Gaa/Aaa	8/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.588796483011901	2		488	753	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056533	26056533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1332170864	NA	P-0006624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	108	216	0	ENST00000343677.2:c.124G>A	p.Glu42Lys	p.E42K	ENST00000343677	NM_005319.3	42	Gag/Aag	1/1	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.588796483011901	2		216	366	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412037	116412037	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	474	337	0	ENST00000397752.3:c.3022C>T	p.Pro1008Ser	p.P1008S	ENST00000397752	NM_000245.2	1008	Cca/Tca	14/21	0.343599580489446	4	FACETS	1	0.99	1	0.799	0.771	0.827	INDETERMINATE	3	TRUE	0	0.588796483011901	4		337	800	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390909	139390909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	188	436	0	ENST00000277541.6:c.7282C>T	p.His2428Tyr	p.H2428Y	ENST00000277541	NM_017617.3	2428	Cac/Tac	34/34	0.588796483011901	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.588796483011901	1		436	380	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699323	18699323	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199904184	NA	P-0006624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	191	485	1	ENST00000266497.5:c.3424C>T	p.Arg1142Cys	p.R1142C	ENST00000266497		1142	Cgt/Tgt	24/31	NA	2	FACETS	0.848	0.786	0.912			1	INDETERMINATE	1	TRUE	NA	0.588796483011901	2		486	765	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73342933	73342933	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	243	415	0	ENST00000377767.4:c.1873A>T	p.Ile625Phe	p.I625F	ENST00000377767	NM_014953.3	625	Att/Ttt	14/21	0.516101979443007	1	FACETS	0.853	0.801	0.905	0.853	0.801	0.905	CLONAL	1	TRUE	0	0.588796483011901	1		415	683	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437061	110437061	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	21	34	0	ENST00000375856.3:c.1340C>T	p.Ser447Phe	p.S447F	ENST00000375856	NM_003749.2	447	tCc/tTc	1/2	0.516101979443007	1	FACETS	0.839	0.671	1	0.839	0.671	1	CLONAL	1	TRUE	0	0.588796483011901	1		34	60	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350566	89350566	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	354	666	0	ENST00000301030.4:c.2384T>A	p.Phe795Tyr	p.F795Y	ENST00000301030	NM_001256183.1	795	tTt/tAt	9/13	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.588796483011901	2		666	1054	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763408	41763408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	345	532	0	ENST00000301178.4:c.2207G>A	p.Gly736Glu	p.G736E	ENST00000301178	NM_021913.4	736	gGg/gAg	19/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.588796483011901	2		532	999	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230884	53230884	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	181	233	2	ENST00000375401.3:c.1909C>T	p.Arg637Trp	p.R637W	ENST00000375401	NM_004187.3	637	Cgg/Tgg	14/26	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.588796483011901	1		235	341	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240747	53240747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	259	316	0	ENST00000375401.3:c.1333C>T	p.His445Tyr	p.H445Y	ENST00000375401	NM_004187.3	445	Cat/Tat	10/26	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.588796483011901	1		316	467	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721286	176721287	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0006624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	135	349	0	ENST00000439151.2:c.6917_6918delinsTT	p.Ser2306Phe	p.S2306F	ENST00000439151	NM_022455.4	2306	tCC/tTT	23/23	0.27298318342509	1	FACETS	0.68	0.622	0.74	0.68	0.622	0.74	INDETERMINATE	1	TRUE	0	0.588796483011901	1		349	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0006634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	127	369	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.3	1	FACETS	0.718	0.651	0.788	0.718	0.651	0.788	SUBCLONAL	1	TRUE	0	0.4	1		369	708	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0006634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	19	440	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	NA	2	FACETS	0.104	0.078	0.134			1	INDETERMINATE	1	TRUE	NA	0.4	2		441	917	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0006634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	129	400	1	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.755	0.685	0.83	0.755	0.685	0.83	SUBCLONAL	1	TRUE	1	0.4	2		401	854	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043449	180043449	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1460237997	NA	P-0006634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	107	364	1	ENST00000261937.6:c.3137C>T	p.Ser1046Leu	p.S1046L	ENST00000261937	NM_182925.4	1046	tCg/tTg	23/30	0.3	1	FACETS	0.686	0.616	0.759	0.686	0.616	0.759	SUBCLONAL	1	TRUE	0	0.4	1		365	624	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748533	43748533	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	229	521	0	ENST00000523873.1:c.487T>C	p.Trp163Arg	p.W163R	ENST00000523873		163	Tgg/Cgg	6/8	1	2	FACETS	0.882	0.821	0.946	0.882	0.821	0.946	CLONAL	1	TRUE	1	0.4	2		521	1298	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332895	152332895	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0006634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	94	330	1	ENST00000206249.3:c.1201A>T	p.Lys401Ter	p.K401*	ENST00000206249	NM_000125.3	401	Aag/Tag	5/8	1	2	FACETS	0.639	0.569	0.715	0.639	0.569	0.715	SUBCLONAL	1	TRUE	1	0.4	2		331	735	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243885	46243885	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0006634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	132	405	0	ENST00000334344.6:c.1979C>G	p.Ser660Ter	p.S660*	ENST00000334344	NM_152641.2	660	tCa/tGa	15/21	0.22139827013294	3	FACETS	0.88	0.798	0.966	0.44	0.399	0.483	INDETERMINATE	1	TRUE	1	0.4	3		405	900	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245592	46245592	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0006634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	174	354	0	ENST00000334344.6:c.3686C>G	p.Ser1229Ter	p.S1229*	ENST00000334344	NM_152641.2	1229	tCa/tGa	15/21	0.22139827013294	3	FACETS	1	0.982	1	0.608	0.56	0.658	INDETERMINATE	1	TRUE	1	0.4	3		354	858	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914421	32914421	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1566233568	NA	P-0006634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1383	87	646	0	ENST00000380152.3:c.5929A>G	p.Ile1977Val	p.I1977V	ENST00000380152		1977	Att/Gtt	11/27	0.279862881351137	3	FACETS	0.355	0.313	0.401	0.178	0.156	0.201	SUBCLONAL	1	TRUE	1	0.4	3		646	1470	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604777	48605475	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	CCAGCTCCTAGACGAAGTACTTCATACCATGCCGATTGCAGACCCACAACCTTTAGACTGAGGTCTTTTACCGTTGGGGCCCTTAACCTTATCAGGATGGTGGACTACAAAATACAATCCTGTTTATAATCTGAAGATATATTTCACTTTTGTTCTGCTTTATCTTTTCATAAAGGGTTGAAAATGTGTTTGCTGCCTTGCTCCTAGCAGACAGAAACTGGATTAAAACAATTTTTTTTTTCCTCTTCAGAACTTGTCAGGCATGGCTCAGAGCTTGAAGATTAGGAGAAACACATTCTTATTAATTCTTCACCTGTTATGTATGAAGGAATCATTCCAGTGCTAGAAAATTTAGCCCTTTAAAACGTCTTAGAGCCTTTTATCTGCAGAACATCGATATGTATATCATTCTACAGAATAATCCAGTATTGCTGATTTTAAAGGCAGAGAAGTTCTCAAAGTTAATTCACCTATGTTATTTTGTGTACAAGTTGTTATTGTTGAACATACTTCAAAAATAATGTGCCATGTGGGTGAGTTAATTTTACCAAGAGTAACTTTACTCTGTGTTTAAAAAGTAAGTTAATAATGTATTGTAATCTTTCATCCAAAATATTTTTTGCAAGTTATATTAGTGAAGATGGTTTCAATTCAGATTGTCTTGCAACTTCAGTTTTATTTTTGCCAAGGCAAAAAACT	CCAGCTCCTAGACGAAGTACTTCATACCATGCCGATTGCAGACCCACAACCTTTAGACTGAGGTCTTTTACCGTTGGGGCCCTTAACCTTATCAGGATGGTGGACTACAAAATACAATCCTGTTTATAATCTGAAGATATATTTCACTTTTGTTCTGCTTTATCTTTTCATAAAGGGTTGAAAATGTGTTTGCTGCCTTGCTCCTAGCAGACAGAAACTGGATTAAAACAATTTTTTTTTTCCTCTTCAGAACTTGTCAGGCATGGCTCAGAGCTTGAAGATTAGGAGAAACACATTCTTATTAATTCTTCACCTGTTATGTATGAAGGAATCATTCCAGTGCTAGAAAATTTAGCCCTTTAAAACGTCTTAGAGCCTTTTATCTGCAGAACATCGATATGTATATCATTCTACAGAATAATCCAGTATTGCTGATTTTAAAGGCAGAGAAGTTCTCAAAGTTAATTCACCTATGTTATTTTGTGTACAAGTTGTTATTGTTGAACATACTTCAAAAATAATGTGCCATGTGGGTGAGTTAATTTTACCAAGAGTAACTTTACTCTGTGTTTAAAAAGTAAGTTAATAATGTATTGTAATCTTTCATCCAAAATATTTTTTGCAAGTTATATTAGTGAAGATGGTTTCAATTCAGATTGTCTTGCAACTTCAGTTTTATTTTTGCCAAGGCAAAAAACT	-	novel	NA	P-0006634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	406	65	0	ENST00000342988.3:c.1600_*639del		p.*534*	ENST00000342988	NM_005359.5	533		12/12	0.3	1	FACETS	0.815	0.778	0.853	1	0.996	1	CLONAL	2	TRUE	0	0.4	1		65	996	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0006634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	130	346	0	ENST00000311936.3:c.34_35delinsAT	p.Gly12Ile	p.G12I	ENST00000311936	NM_004985.3	12	GGt/ATt	2/5	NA	2	FACETS	0.742	0.673	0.815			1	INDETERMINATE	1	TRUE	NA	0.4	2		346	876	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	750	338	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.21946121108811	10	FACETS	1	0.992	1			1	CLONAL	8	TRUE	NA	0.21946121108811	10		339	1511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579592	7579592	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0006637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	156	302	0	ENST00000269305.4:c.97-2A>T		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.182359919021909	2	FACETS	0.979	0.899	1	0.979	0.899	1	CLONAL	2	TRUE	0	0.21946121108811	2		302	726	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731176	162731176	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	196	393	0	ENST00000367921.3:c.1031G>T	p.Ser344Ile	p.S344I	ENST00000367921	NM_006182.2	344	aGt/aTt	9/18	0.21946121108811	3	FACETS	0.789	0.729	0.852	0.789	0.729	0.852	SUBCLONAL	2	TRUE	1	0.21946121108811	3		393	1256	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161354	55161354	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	130	417	0	ENST00000257290.5:c.3185G>T	p.Arg1062Ile	p.R1062I	ENST00000257290	NM_006206.4	1062	aGa/aTa	23/23	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.21946121108811	2		417	1037	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554844	106554844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	84	298	0	ENST00000369096.4:c.1961C>T	p.Ser654Phe	p.S654F	ENST00000369096	NM_001198.3	654	tCt/tTt	7/7	0.21946121108811	1	FACETS	0.975	0.861	1	0.975	0.861	1	CLONAL	1	TRUE	0	0.21946121108811	1		298	699	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518133	8518133	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1412991544	NA	P-0006637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	124	294	0	ENST00000356435.5:c.1258G>T	p.Ala420Ser	p.A420S	ENST00000356435		420	Gcc/Tcc	10/35	0.21946121108811	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.21946121108811	1		294	846	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416961	416961	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	100	397	0	ENST00000399788.2:c.3589C>T	p.Gln1197Ter	p.Q1197*	ENST00000399788	NM_001042603.1	1197	Caa/Taa	23/28	0.182864737793109	2	FACETS	0.853	0.76	0.952	0.426	0.38	0.476	CLONAL	1	TRUE	0	0.21946121108811	2		397	1069	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095973	11095973	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766474711	NA	P-0006637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	213	405	0	ENST00000358026.2:c.247G>A	p.Gly83Ser	p.G83S	ENST00000358026	NM_001128849.1	83	Ggc/Agc	3/36	0.182359919021909	2	FACETS	0.947	0.88	1	0.947	0.88	1	CLONAL	2	TRUE	0	0.21946121108811	2		405	1025	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223058	1223058	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	192	406	0	ENST00000326873.7:c.996del	p.Trp332CysfsTer4	p.W332Cfs*4	ENST00000326873	NM_000455.4	332	tGg/tg	8/10	0.182359919021909	2	FACETS	0.873	0.807	0.942	0.873	0.807	0.942	CLONAL	2	TRUE	0	0.21946121108811	2		406	1002	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0006647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	259	423	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	0.47435009062944	3	FACETS	0.836	0.794	0.876	0.836	0.794	0.876	CLONAL	3	TRUE	0	0.581045109488074	3		423	459	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043899	180043899	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0006647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	122	631	2	ENST00000261937.6:c.3096+1G>A		p.X1032_splice	ENST00000261937	NM_182925.4	1032			0.532043424478355	3	FACETS	0.634	0.573	0.699	0.211	0.191	0.233	SUBCLONAL	1	TRUE	0	0.581045109488074	3		633	855	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131115	55131115	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	191	558	1	ENST00000257290.5:c.658G>T	p.Ala220Ser	p.A220S	ENST00000257290	NM_006206.4	220	Gct/Tct	5/23	0.544500437780897	2	FACETS	1	0.975	1	0.552	0.513	0.591	CLONAL	1	TRUE	0	0.581045109488074	2		559	596	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123025098	123025098	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	150	316	0	ENST00000355640.3:c.988C>G	p.Leu330Val	p.L330V	ENST00000355640		330	Ctg/Gtg	4/7	0.581045109488074	2	FACETS	0.665	0.609	0.725			1	SUBCLONAL	1	TRUE	NA	0.581045109488074	2		316	776	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579481	7579487	+	frameshift_variant	Frame_Shift_Del	DEL	GCCTCTG	GCCTCTG	-	novel	NA	P-0006647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	567	557	0	ENST00000269305.4:c.200_206del	p.Pro67LeufsTer54	p.P67Lfs*54	ENST00000269305	NM_001126112.2	67	cCAGAGGCt/ct	4/11	0.522565172083615	3	FACETS	0.953	0.924	0.981	0.953	0.924	0.981	CLONAL	3	TRUE	0	0.581045109488074	3		557	881	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0006650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	128	300	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.427862594271634	3	FACETS	0.982	0.9	1	0.982	0.9	1	CLONAL	2	TRUE	1	0.427862594271634	3		300	370	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	150	376	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.427862594271634	3	FACETS	0.854	0.779	0.932	0.427	0.389	0.466	CLONAL	1	TRUE	1	0.427862594271634	3		376	997	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661705	227661705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780602110	NA	P-0006650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	194	399	0	ENST00000305123.5:c.1750G>A	p.Glu584Lys	p.E584K	ENST00000305123	NM_005544.2	584	Gag/Aag	1/2	0.427862594271634	3	FACETS	1	0.941	1	0.51	0.471	0.55	CLONAL	1	TRUE	1	0.427862594271634	3		399	1079	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440882	52440882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	197	437	2	ENST00000460680.1:c.622C>T	p.Arg208Trp	p.R208W	ENST00000460680	NM_004656.3	208	Cgg/Tgg	8/17	0.160961963433865	3	FACETS	1	0.982	1	0.591	0.547	0.636	INDETERMINATE	1	TRUE	1	0.427862594271634	3		439	946	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457087	5457087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370800260	NA	P-0006650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	97	312	0	ENST00000381577.3:c.61G>A	p.Val21Ile	p.V21I	ENST00000381577	NM_014143.3	21	Gtc/Atc	3/7	1	2	FACETS	0.851	0.761	0.946	0.851	0.761	0.946	CLONAL	1	TRUE	1	0.427862594271634	2		312	533	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740544	58740544	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	444	681	0	ENST00000305921.3:c.1451del	p.Leu484Ter	p.L484*	ENST00000305921	NM_003620.3	483	acT/ac	6/6	0.427862594271634	4	FACETS	0.989	0.943	1	0.989	0.943	1	CLONAL	2	TRUE	2	0.427862594271634	4		681	1498	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006667-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	82	192	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.483468975606544	2		192	308	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690805	89690805	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006667-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	104	181	0	ENST00000371953.3:c.212G>A	p.Cys71Tyr	p.C71Y	ENST00000371953	NM_000314.4	71	tGt/tAt	4/9	0.483468975606544	1	FACETS	0.998	0.904	1	0.998	0.904	1	CLONAL	1	TRUE	0	0.483468975606544	1		181	327	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368431	225368431	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006667-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	144	349	0	ENST00000264414.4:c.1315A>G	p.Arg439Gly	p.R439G	ENST00000264414	NM_003590.4	439	Aga/Gga	9/16	1	2	FACETS	0.76	0.694	0.829	0.76	0.694	0.829	SUBCLONAL	1	TRUE	1	0.483468975606544	2		349	784	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371779	55371779	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006667-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	55	126	0	ENST00000297316.4:c.469C>T	p.His157Tyr	p.H157Y	ENST00000297316	NM_022454.3	157	Cac/Tac	2/2	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.483468975606544	2		126	177	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0006680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	419	400	1	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.446648518207102	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.446648518207102	3		401	720	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0006680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	305	403	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.446648518207102	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.446648518207102	2		403	632	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156597	55156597	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	256	426	0	ENST00000257290.5:c.2998C>A	p.Leu1000Met	p.L1000M	ENST00000257290	NM_006206.4	1000	Ctg/Atg	22/23	0.270880859452561	2	FACETS	0.761	0.716	0.808	0.761	0.716	0.808	SUBCLONAL	2	TRUE	0	0.446648518207102	2		426	753	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871021	12871036	+	frameshift_variant	Frame_Shift_Del	DEL	GCTTGCCCGAGTTCTA	GCTTGCCCGAGTTCTA	AG	novel	NA	P-0006680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	28	297	0	ENST00000228872.4:c.248_263delinsAG	p.Ser83LysfsTer37	p.S83Kfs*37	ENST00000228872	NM_004064.3	83	aGCTTGCCCGAGTTCTAc/aAGc	1/3	0.446648518207102	2	FACETS	0.27	0.215	0.333	0.135	0.107	0.167	SUBCLONAL	1	TRUE	0	0.446648518207102	2		297	464	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0006708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	288	513	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.588732464280015	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.588732464280015	1		515	679	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0006708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	188	440	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.96	0.891	1	0.96	0.891	1	CLONAL	1	TRUE	1	0.588732464280015	2		441	665	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	206	435	1	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	NA	2	FACETS	0.947	0.881	1			1	INDETERMINATE	1	TRUE	NA	0.588732464280015	2		436	739	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139842	55139842	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	267	401	0	ENST00000257290.5:c.1503C>A	p.Cys501Ter	p.C501*	ENST00000257290	NM_006206.4	501	tgC/tgA	10/23	0.588732464280015	2	FACETS	1	0.973	1	0.53	0.499	0.563	CLONAL	1	TRUE	0	0.588732464280015	2		401	855	SUCCESS
APC	324	MSKCC	GRCh37	5	112173299	112173299	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0006708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	188	386	2	ENST00000257430.4:c.2008A>T	p.Lys670Ter	p.K670*	ENST00000257430	NM_000038.5	670	Aaa/Taa	16/16	NA	2	FACETS	1	0.947	1			1	INDETERMINATE	1	TRUE	NA	0.588732464280015	2		388	624	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437167	49437167	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	296	511	0	ENST00000301067.7:c.5512G>T	p.Glu1838Ter	p.E1838*	ENST00000301067	NM_003482.3	1838	Gag/Tag	24/54	0.202595769120427	3	FACETS	1	0.994	1	0.714	0.674	0.755	INDETERMINATE	1	TRUE	1	0.588732464280015	3		511	911	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005448	42005448	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	483	803	0	ENST00000219905.7:c.3184G>C	p.Ala1062Pro	p.A1062P	ENST00000219905	NM_001164273.1	1062	Gct/Cct	9/24	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.588732464280015	2		803	1412	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152217	11152217	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	196	393	0	ENST00000358026.2:c.4501G>T	p.Val1501Leu	p.V1501L	ENST00000358026	NM_001128849.1	1501	Gtg/Ttg	31/36	1	2	FACETS	0.922	0.857	0.99	0.922	0.857	0.99	CLONAL	1	TRUE	1	0.588732464280015	2		393	722	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271151	26271276	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	GGCTCTTAAAAGAGCCTTTTTAAGTTGGATAGAATTACTGCCCGGAAACCTCTACGCTCTCTCCCCACGAATGCGGCGAGCGAGCTGAATGTCCTTGGGCATGATAGTCACTCGCTTAGCATGGAT	GGCTCTTAAAAGAGCCTTTTTAAGTTGGATAGAATTACTGCCCGGAAACCTCTACGCTCTCTCCCCACGAATGCGGCGAGCGAGCTGAATGTCCTTGGGCATGATAGTCACTCGCTTAGCATGGAT	-	novel	NA	P-0006708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	374	427	0	ENST00000305910.3:c.337_*51del		p.*113*	ENST00000305910	NM_003534.2	113		1/1	0.567277201570506	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.588732464280015	1		427	672	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604824	+	frameshift_variant	Frame_Shift_Del	DEL	ACGAAGTACTTCATACCATGCCGATTGCAGACCCACA	ACGAAGTACTTCATACCATGCCGATTGCAGACCCACA	-	novel	NA	P-0006708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	135	468	0	ENST00000342988.3:c.1612_1648del	p.Glu538LeufsTer2	p.E538Lfs*2	ENST00000342988	NM_005359.5	537	gACGAAGTACTTCATACCATGCCGATTGCAGACCCACAa/ga	12/12	0.576422824664604	1	FACETS	0.765	0.702	0.83	0.765	0.702	0.83	SUBCLONAL	1	TRUE	0	0.588732464280015	1		468	423	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	213	338	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	0.897	0.836	0.96			1	INDETERMINATE	1	TRUE	NA	0.618611912191227	2		339	768	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0006715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	309	575	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.618611912191227	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.618611912191227	1		576	665	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0006715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	291	465	3	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.969	0.913	1	0.969	0.913	1	CLONAL	1	TRUE	1	0.618611912191227	2		468	971	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750417	57750417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	261	540	0	ENST00000274289.3:c.2051G>A	p.Cys684Tyr	p.C684Y	ENST00000274289	NM_006622.3	684	tGt/tAt	14/14	1	2	FACETS	0.916	0.86	0.974	0.916	0.86	0.974	CLONAL	1	TRUE	1	0.618611912191227	2		540	921	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763269	59763269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	307	514	0	ENST00000259008.2:c.2833G>A	p.Glu945Lys	p.E945K	ENST00000259008	NM_032043.2	945	Gaa/Aaa	19/20	1	2	FACETS	0.974	0.919	1	0.974	0.919	1	CLONAL	1	TRUE	1	0.618611912191227	2		514	1019	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348181	70348181	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	366	315	0	ENST00000374080.3:c.3245C>G	p.Thr1082Ser	p.T1082S	ENST00000374080		1082	aCc/aGc	23/45	0.618611912191227	2	FACETS	1	0.994	1			1	CLONAL	1	TRUE	NA	0.618611912191227	2		315	899	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0006718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	86	394	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.372447947996153	1	FACETS	0.79	0.701	0.883	0.79	0.701	0.883	SUBCLONAL	1	TRUE	0	0.381540236439447	1		394	462	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111957665	111957665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34677591	NA	P-0006718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	131	512	0	ENST00000375549.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000375549	NM_003002.3	12	Ggt/Agt	1/4	0.381540236439447	3	FACETS	0.996	0.904	1	0.498	0.452	0.547	CLONAL	1	TRUE	1	0.381540236439447	3		512	821	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056281	27056281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	56	378	0	ENST00000324856.7:c.1277C>T	p.Thr426Ile	p.T426I	ENST00000324856	NM_006015.4	426	aCc/aTc	2/20	1	2	FACETS	0.541	0.463	0.625	0.541	0.463	0.625	SUBCLONAL	1	TRUE	1	0.381540236439447	2		378	543	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724433	162724433	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	49	388	0	ENST00000367921.3:c.205G>T	p.Asp69Tyr	p.D69Y	ENST00000367921	NM_006182.2	69	Gat/Tat	5/18	1	2	FACETS	0.504	0.426	0.588	0.504	0.426	0.588	SUBCLONAL	1	TRUE	1	0.381540236439447	2		388	510	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525561	187525561	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	44	508	0	ENST00000441802.2:c.10518G>T	p.Lys3506Asn	p.K3506N	ENST00000441802	NM_005245.3	3506	aaG/aaT	18/27	0.172773114349535	1	FACETS	0.376	0.315	0.443	0.376	0.315	0.443	INDETERMINATE	1	TRUE	0	0.381540236439447	1		508	497	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433699	149433699	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	119	470	0	ENST00000286301.3:c.2852T>C	p.Leu951Pro	p.L951P	ENST00000286301	NM_005211.3	951	cTg/cCg	22/22	0.372447947996153	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.381540236439447	1		470	497	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020877	26020877	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375552711	NA	P-0006718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	208	991	1	ENST00000357647.3:c.160C>T	p.Arg54Cys	p.R54C	ENST00000357647	NM_003529.2	54	Cgt/Tgt	1/1	0.124969687618037	4	FACETS	1	0.989	1	0.679	0.629	0.73	INDETERMINATE	1	TRUE	2	0.381540236439447	4		992	1110	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335007	81335007	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	133	368	0	ENST00000222390.5:c.1820C>A	p.Pro607His	p.P607H	ENST00000222390	NM_000601.4	607	cCt/cAt	16/18	0.381540236439447	3	FACETS	0.849	0.776	0.925	0.849	0.776	0.925	CLONAL	2	TRUE	1	0.381540236439447	3		368	489	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346389	152346389	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs569810249	NA	P-0006718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	122	665	4	ENST00000359321.1:c.181C>A	p.Leu61Ile	p.L61I	ENST00000359321	NM_005431.1	61	Cta/Ata	3/3	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.381540236439447	2		669	587	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32449578	32449578	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	99	495	0	ENST00000332351.3:c.796C>G	p.Pro266Ala	p.P266A	ENST00000332351	NM_024426.4	266	Ccg/Gcg	3/10	0.371502245881846	1	FACETS	0.957	0.859	1	0.957	0.859	1	CLONAL	1	TRUE	0	0.381540236439447	1		495	439	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26971288	26971288	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0006718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	71	362	0	ENST00000381527.3:c.861-2A>C		p.X287_splice	ENST00000381527	NM_001260.1	287			NA	2	FACETS	1	0.904	1			1	INDETERMINATE	1	TRUE	NA	0.381540236439447	2		362	360	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586147	29586147	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs1060500293	NA	P-0006718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	54	267	0	ENST00000356175.3:c.4367G>C	p.Arg1456Thr	p.R1456T	ENST00000356175	NM_000267.3	1456	aGg/aCg	32/57	0.372447947996153	1	FACETS	0.931	0.803	1	0.931	0.803	1	CLONAL	1	TRUE	0	0.381540236439447	1		267	246	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561000	9561000	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	50	385	0	ENST00000353224.5:c.782T>A	p.Leu261Gln	p.L261Q	ENST00000353224	NM_177990.2	261	cTg/cAg	4/10	NA	2	FACETS	0.485	0.412	0.566			1	INDETERMINATE	1	TRUE	NA	0.381540236439447	2		385	540	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422721	47422721	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	96	435	0	ENST00000377045.4:c.193A>G	p.Ile65Val	p.I65V	ENST00000377045	NM_001654.4	65	Atc/Gtc	3/16	0.21321052588838	1	FACETS	0.707	0.631	0.787	0.707	0.631	0.787	INDETERMINATE	1	TRUE	0	0.381540236439447	1		435	576	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346863	73346864	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	174	328	0	ENST00000377767.4:c.1353dup	p.Leu452SerfsTer10	p.L452Sfs*10	ENST00000377767	NM_014953.3	451	-/T	9/21	0.300327988079823	3	FACETS	1	0.981	1	0.77	0.716	0.826	CLONAL	2	TRUE	0	0.381540236439447	3		328	470	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	261	192	0				ENST00000310581	NM_198253.2	-/1132			0.664599998990606	4	FACETS	0.984	0.937	1	0.984	0.937	1	CLONAL	3	TRUE	1	0.664599998990606	4		192	443	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0006725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	2122	556	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.664599998990606	11	FACETS	0.985	0.972	0.999			1	CLONAL	9	TRUE	NA	0.664599998990606	11		556	2874	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486101	8486101	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	98	601	0	ENST00000356435.5:c.2716G>A	p.Glu906Lys	p.E906K	ENST00000356435		906	Gag/Aag	17/35	0.664599998990606	1	FACETS	0.437	0.391	0.484	0.437	0.391	0.484	SUBCLONAL	1	TRUE	0	0.664599998990606	1		601	451	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24135805	24135805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	89	662	0	ENST00000263121.7:c.292G>A	p.Glu98Lys	p.E98K	ENST00000263121	NM_003073.3	98	Gag/Aag	3/9	0.353415327714414	1	FACETS	0.25	0.221	0.281	0.25	0.221	0.281	INDETERMINATE	1	TRUE	0	0.664599998990606	1		662	715	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259353	11259353	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	108	659	0	ENST00000361445.4:c.4215G>C	p.Gln1405His	p.Q1405H	ENST00000361445	NM_004958.3	1405	caG/caC	28/58	1	2	FACETS	0.427	0.383	0.473	0.427	0.383	0.473	SUBCLONAL	1	TRUE	1	0.664599998990606	2		659	762	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16174617	16174617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	73	383	0	ENST00000375759.3:c.55G>A	p.Glu19Lys	p.E19K	ENST00000375759	NM_015001.2	19	Gaa/Aaa	1/15	1	2	FACETS	0.402	0.352	0.456	0.402	0.352	0.456	SUBCLONAL	1	TRUE	1	0.664599998990606	2		383	546	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059194	27059194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	81	657	1	ENST00000324856.7:c.1831C>T	p.Gln611Ter	p.Q611*	ENST00000324856	NM_006015.4	611	Cag/Tag	4/20	1	2	FACETS	0.438	0.387	0.494	0.438	0.387	0.494	SUBCLONAL	1	TRUE	1	0.664599998990606	2		658	556	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307143	65307143	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	278	473	1	ENST00000342505.4:c.2545G>A	p.Glu849Lys	p.E849K	ENST00000342505	NM_002227.2	849	Gaa/Aaa	18/25	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.664599998990606	2		474	670	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161326473	161326473	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1227520085	NA	P-0006725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	183	462	0	ENST00000367975.2:c.248C>G	p.Ser83Cys	p.S83C	ENST00000367975	NM_003001.3	83	tCt/tGt	5/6	1	2	FACETS	0.958	0.889	1	0.958	0.889	1	CLONAL	1	TRUE	1	0.664599998990606	2		462	575	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573292	55573292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769399180	NA	P-0006725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	165	504	0	ENST00000288135.5:c.954G>A	p.Met318Ile	p.M318I	ENST00000288135	NM_000222.2	318	atG/atA	6/21	1	2	FACETS	0.925	0.855	0.997	0.925	0.855	0.997	CLONAL	1	TRUE	1	0.664599998990606	2		504	537	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967455	38967455	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	192	431	1	ENST00000357387.3:c.1135C>T	p.His379Tyr	p.H379Y	ENST00000357387	NM_152756.3	379	Cat/Tat	13/38	0.664599998990606	4	FACETS	1	0.943	1	0.341	0.315	0.368	CLONAL	1	TRUE	1	0.664599998990606	4		432	941	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873357	151873357	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	243	578	0	ENST00000262189.6:c.9181C>G	p.Gln3061Glu	p.Q3061E	ENST00000262189	NM_170606.2	3061	Caa/Gaa	38/59	NA	2	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.664599998990606	2		578	675	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873683	151873683	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0006725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	144	379	0	ENST00000262189.6:c.8855C>G	p.Ser2952Ter	p.S2952*	ENST00000262189	NM_170606.2	2952	tCa/tGa	38/59	NA	2	FACETS	0.942	0.866	1			1	INDETERMINATE	1	TRUE	NA	0.664599998990606	2		379	460	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738284	145738284	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	129	382	0	ENST00000428558.2:c.2701G>C	p.Glu901Gln	p.E901Q	ENST00000428558	NM_004260.3	901	Gag/Cag	16/22	0.640151747219206	3	FACETS	0.92	0.838	1	0.46	0.419	0.503	CLONAL	1	TRUE	1	0.664599998990606	3		382	562	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710691	114710691	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs768298443	NA	P-0006725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	297	694	1	ENST00000543371.1:c.176C>A	p.Ser59Tyr	p.S59Y	ENST00000543371	NM_001198531.1	59	tCc/tAc	1/14	0.664599998990606	2	FACETS	0.926	0.874	0.98	0.463	0.437	0.49	CLONAL	1	TRUE	0	0.664599998990606	2		695	965	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143509	108143509	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1060501687	NA	P-0006725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	95	666	4	ENST00000278616.4:c.3214G>T	p.Glu1072Ter	p.E1072*	ENST00000278616	NM_000051.3	1072	Gaa/Taa	22/63	1	2	FACETS	0.389	0.347	0.435	0.389	0.347	0.435	SUBCLONAL	1	TRUE	1	0.664599998990606	2		670	734	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188227	108188227	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587782114	NA	P-0006725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	181	496	0	ENST00000278616.4:c.6326G>A	p.Trp2109Ter	p.W2109*	ENST00000278616	NM_000051.3	2109	tGg/tAg	43/63	1	2	FACETS	0.951	0.882	1	0.951	0.882	1	CLONAL	1	TRUE	1	0.664599998990606	2		496	573	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432435	49432435	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	230	559	0	ENST00000301067.7:c.8704C>T	p.Gln2902Ter	p.Q2902*	ENST00000301067	NM_003482.3	2902	Cag/Tag	34/54	1	2	FACETS	0.946	0.885	1	0.946	0.885	1	CLONAL	1	TRUE	1	0.664599998990606	2		559	732	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608294	28608294	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	68	587	0	ENST00000241453.7:c.1762G>C	p.Glu588Gln	p.E588Q	ENST00000241453	NM_004119.2	588	Gag/Cag	14/24	0.640151747219206	3	FACETS	0.322	0.279	0.369	0.161	0.139	0.185	SUBCLONAL	1	TRUE	1	0.664599998990606	3		587	846	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954353	48954353	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	293	361	0	ENST00000267163.4:c.1474G>T	p.Glu492Ter	p.E492*	ENST00000267163	NM_000321.2	492	Gag/Tag	16/27	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	2	TRUE	NA	0.664599998990606	2		361	422	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556886	29556886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	100	286	1	ENST00000356175.3:c.2884G>A	p.Glu962Lys	p.E962K	ENST00000356175	NM_000267.3	962	Gaa/Aaa	22/57	NA	2	FACETS	0.79	0.711	0.872			1	INDETERMINATE	1	TRUE	NA	0.664599998990606	2		287	381	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667843	37667843	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1313803732	NA	P-0006725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1222	961	721	0	ENST00000447079.4:c.2728G>C	p.Glu910Gln	p.E910Q	ENST00000447079	NM_015083.1	910	Gag/Cag	8/14	0.664599998990606	8	FACETS	0.992	0.963	1			1	CLONAL	4	TRUE	NA	0.664599998990606	8		721	2183	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872138	37872138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375382055	NA	P-0006725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	2114	556	1	ENST00000269571.5:c.1459C>T	p.Arg487Trp	p.R487W	ENST00000269571		487	Cgg/Tgg	12/27	0.664599998990606	11	FACETS	0.988	0.974	1			1	CLONAL	9	TRUE	NA	0.664599998990606	11		557	2856	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619461	1619461	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	145	403	0	ENST00000344749.5:c.1180G>C	p.Glu394Gln	p.E394Q	ENST00000344749	NM_001136139.2	394	Gaa/Caa	15/19	0.309617649452752	1	FACETS	0.676	0.622	0.731	0.676	0.622	0.731	INDETERMINATE	1	TRUE	0	0.664599998990606	1		403	431	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278007	18278007	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	42	523	0	ENST00000222254.8:c.1627G>C	p.Glu543Gln	p.E543Q	ENST00000222254	NM_005027.3	543	Gag/Cag	13/16	1	2	FACETS	0.216	0.179	0.256	0.216	0.179	0.256	SUBCLONAL	1	TRUE	1	0.664599998990606	2		523	586	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39751860	39751860	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	87	608	1	ENST00000361337.2:c.2221G>T	p.Glu741Ter	p.E741*	ENST00000361337	NM_003286.2	741	Gag/Tag	21/21	0.640151747219206	3	FACETS	0.381	0.337	0.429	0.191	0.168	0.215	SUBCLONAL	1	TRUE	1	0.664599998990606	3		609	915	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040686	47040686	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	267	726	0	ENST00000377604.3:c.1321G>A	p.Asp441Asn	p.D441N	ENST00000377604	NM_001204468.1	441	Gat/Aat	13/24	1	2	FACETS	0.972	0.914	1	0.972	0.914	1	CLONAL	1	TRUE	1	0.664599998990606	2		726	827	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578541	7578562	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGGCAGGGGAGTACTGTAGGA	AGGGCAGGGGAGTACTGTAGGA	-	novel	NA	P-0006725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	181	467	1	ENST00000269305.4:c.376-8_389del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	0.664599998990606	1	FACETS	0.933	0.873	0.993	0.933	0.873	0.993	CLONAL	1	TRUE	0	0.664599998990606	1		468	390	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40384156	40384156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0006725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	199	598	0	ENST00000293328.3:c.-10-1G>A		p.X4_splice	ENST00000293328	NM_012448.3	4			1	2	FACETS	0.808	0.751	0.867	0.808	0.751	0.867	CLONAL	1	TRUE	1	0.664599998990606	2		598	741	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0006731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	332	381	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.599220353896254	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.611919299097215	4		382	844	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	162	192	0				ENST00000310581	NM_198253.2	-/1132			0.611919299097215	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.611919299097215	2		192	255	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561352	9561352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773981325	NA	P-0006731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	205	445	0	ENST00000353224.5:c.430G>A	p.Glu144Lys	p.E144K	ENST00000353224	NM_177990.2	144	Gaa/Aaa	4/10	0.599220353896254	4	FACETS	1	0.975	1	0.557	0.516	0.599	CLONAL	1	TRUE	2	0.611919299097215	4		445	970	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923318	9923318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867335598	NA	P-0006731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	183	513	0	ENST00000330684.3:c.1969G>A	p.Glu657Lys	p.E657K	ENST00000330684	NM_001134407.1	657	Gaa/Aaa	9/13	0.611919299097215	3	FACETS	1	0.951	1	0.518	0.479	0.558	CLONAL	1	TRUE	1	0.611919299097215	3		513	754	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204494660	204494660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	385	419	0	ENST00000367182.3:c.14C>T	p.Ser5Phe	p.S5F	ENST00000367182	NM_001278516.1	5	tCc/tTc	2/11	0.599220353896254	4	FACETS	0.921	0.876	0.967	0.921	0.876	0.967	CLONAL	2	TRUE	2	0.611919299097215	4		419	1101	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248500	212248500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	245	615	0	ENST00000342788.4:c.3767C>T	p.Pro1256Leu	p.P1256L	ENST00000342788	NM_005235.2	1256	cCa/cTa	28/28	0.611919299097215	3	FACETS	1	0.972	1	0.357	0.334	0.381	CLONAL	1	TRUE	0	0.611919299097215	3		615	976	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612212	189612212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764601563	NA	P-0006731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	197	400	0	ENST00000264731.3:c.1964G>A	p.Arg655Gln	p.R655Q	ENST00000264731	NM_003722.4	655	cGa/cAa	14/14	0.611919299097215	4	FACETS	1	0.971	1	0.365	0.338	0.394	CLONAL	1	TRUE	1	0.611919299097215	4		400	947	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156501	55156501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	192	399	0	ENST00000257290.5:c.2902G>A	p.Asp968Asn	p.D968N	ENST00000257290	NM_006206.4	968	Gac/Aac	22/23	0.599220353896254	4	FACETS	0.954	0.882	1	0.477	0.441	0.515	CLONAL	1	TRUE	2	0.611919299097215	4		399	1060	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161330	55161330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	191	421	2	ENST00000257290.5:c.3161C>T	p.Ser1054Phe	p.S1054F	ENST00000257290	NM_006206.4	1054	tCc/tTc	23/23	0.599220353896254	4	FACETS	0.994	0.919	1	0.497	0.459	0.537	CLONAL	1	TRUE	2	0.611919299097215	4		423	1012	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858626	57858626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367757660	NA	P-0006731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	250	593	0	ENST00000228682.2:c.364G>A	p.Gly122Ser	p.G122S	ENST00000228682	NM_005269.2	122	Ggt/Agt	4/12	1	2	FACETS	0.965	0.905	1	0.965	0.905	1	CLONAL	1	TRUE	1	0.611919299097215	2		593	847	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99472793	99472793	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6978	3796	416	0	ENST00000268035.6:c.2789A>G	p.Tyr930Cys	p.Y930C	ENST00000268035	NM_000875.3	930	tAt/tGt	14/21	0.611919299097215	40	FACETS	0.969	0.954	0.985			1	CLONAL	15	TRUE	NA	0.611919299097215	40		416	10774	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3901001	3901001	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs865788612	NA	P-0006731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	191	367	0	ENST00000262367.5:c.95C>T	p.Ser32Leu	p.S32L	ENST00000262367	NM_004380.2	32	tCa/tTa	2/31	0.611919299097215	3	FACETS	1	0.965	1	0.534	0.494	0.574	CLONAL	1	TRUE	1	0.611919299097215	3		367	764	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858558	9858558	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	197	568	0	ENST00000330684.3:c.2843C>T	p.Ser948Phe	p.S948F	ENST00000330684	NM_001134407.1	948	tCc/tTc	13/13	0.611919299097215	3	FACETS	0.974	0.903	1	0.487	0.451	0.524	CLONAL	1	TRUE	1	0.611919299097215	3		568	863	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218804	5218804	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773998457	NA	P-0006731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1353	174	446	0	ENST00000357368.4:c.3929C>T	p.Pro1310Leu	p.P1310L	ENST00000357368	NM_002850.3	1310	cCc/cTc	24/38	0.611919299097215	6	FACETS	0.828	0.76	0.9	0.276	0.253	0.3	CLONAL	1	TRUE	3	0.611919299097215	6		446	1527	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176481	123176481	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	524	590	0	ENST00000218089.9:c.448G>A	p.Glu150Lys	p.E150K	ENST00000218089	NM_001042749.1	150	Gaa/Aaa	7/35	0.55311434887229	4	FACETS	0.878	0.841	0.916	0.878	0.841	0.916	CLONAL	2	TRUE	2	0.611919299097215	4		590	1572	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217326	123217327	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0006731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	400	581	0	ENST00000218089.9:c.2980_2981delinsTT	p.Pro994Phe	p.P994F	ENST00000218089	NM_001042749.1	994	CCt/TTt	29/35	0.55311434887229	4	FACETS	0.944	0.899	0.989	0.944	0.899	0.989	CLONAL	2	TRUE	2	0.611919299097215	4		581	1116	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0006735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	325	392	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.761694219072055	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.773108016447464	1		392	476	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0006735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	173	617	2	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.41846526054425	1	FACETS	0.397	0.366	0.429	0.397	0.366	0.429	INDETERMINATE	1	TRUE	0	0.773108016447464	1		619	692	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121434595	NA	P-0006735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	338	475	0	ENST00000369535.4:c.37G>T	p.Gly13Cys	p.G13C	ENST00000369535	NM_002524.4	13	Ggt/Tgt	2/7	0.41846526054425	1	FACETS	0.824	0.787	0.861	0.824	0.787	0.861	INDETERMINATE	1	TRUE	0	0.773108016447464	1		475	651	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751020	128751020	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1580	134	323	0	ENST00000377970.2:c.557G>A	p.Cys186Tyr	p.C186Y	ENST00000377970	NM_002467.4	186	tGc/tAc	2/3	0.631855762415676	6	FACETS	0.515	0.466	0.567	0.086	0.077	0.095	SUBCLONAL	1	TRUE	0	0.773108016447464	6		323	1714	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451432	187451432	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1428	425	522	0	ENST00000232014.4:c.50A>T	p.Asp17Val	p.D17V	ENST00000232014	NM_001130845.1	17	gAt/gTt	3/10	0.560796201231226	3	FACETS	0.957	0.909	1	0.478	0.454	0.503	CLONAL	1	TRUE	1	0.6305251391203	3		522	1853	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983930	2983930	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1365	497	790	0	ENST00000396946.4:c.600C>A	p.Asp200Glu	p.D200E	ENST00000396946	NM_032415.4	200	gaC/gaA	5/25	1	2	FACETS	0.847	0.808	0.886	0.847	0.808	0.886	CLONAL	1	TRUE	1	0.6305251391203	2		790	1862	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445007	49445007	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	164	259	0	ENST00000301067.7:c.2459A>C	p.Glu820Ala	p.E820A	ENST00000301067	NM_003482.3	820	gAg/gCg	10/54	1	2	FACETS	0.767	0.706	0.83	0.767	0.706	0.83	SUBCLONAL	1	TRUE	1	0.6305251391203	2		259	678	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576397	7576978	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCGCCACTGCACTCCAGCCTGGGTGACAGAGTGAGACTCTGTCTCCAAAAAAAAAAAAAAAAAAAGCAGGCTAGGCTAAGCTATGATGTTCCTTAGATTAGGTGTATTAAATCCATTTTCAACTTACAATATTTTCAACTTACGACGAGTTTATCAGGAAGTAACACCATCGTAAGTCAAGTAGCATCTGTATCAGGCAAAGTCATAGAACCATTTTCATGCTCTCTTTAACAATTTTCTTTTTGAAAGCTGGTCTGGTCCTTTAAAATATATATTATGGTATAAGTTGGTGTTCTGAAGTTAGTTAGCTACAACCAGGAGCCATTGTCTTTGAGGCATCACTGCCCCCTGATGGCAAATGCCCCAATTGCAGGTAAAACAGTCAAGAAGAAAACGGCATTTTGAGTGTTAGACTGGAAACTTTCCACTTGATAAGAGGTCCCAAGACTTAGTACCTGAAGGGTGAAATATTCTCCATCCAGTGGTTTCTTCTTTGGCTGGGGAGAGGAGCTGGTGTTGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAAAGTGAATCTGAGGCATAACTGCA	CCCGCCACTGCACTCCAGCCTGGGTGACAGAGTGAGACTCTGTCTCCAAAAAAAAAAAAAAAAAAAGCAGGCTAGGCTAAGCTATGATGTTCCTTAGATTAGGTGTATTAAATCCATTTTCAACTTACAATATTTTCAACTTACGACGAGTTTATCAGGAAGTAACACCATCGTAAGTCAAGTAGCATCTGTATCAGGCAAAGTCATAGAACCATTTTCATGCTCTCTTTAACAATTTTCTTTTTGAAAGCTGGTCTGGTCCTTTAAAATATATATTATGGTATAAGTTGGTGTTCTGAAGTTAGTTAGCTACAACCAGGAGCCATTGTCTTTGAGGCATCACTGCCCCCTGATGGCAAATGCCCCAATTGCAGGTAAAACAGTCAAGAAGAAAACGGCATTTTGAGTGTTAGACTGGAAACTTTCCACTTGATAAGAGGTCCCAAGACTTAGTACCTGAAGGGTGAAATATTCTCCATCCAGTGGTTTCTTCTTTGGCTGGGGAGAGGAGCTGGTGTTGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAAAGTGAATCTGAGGCATAACTGCA	-	novel	NA	P-0006741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3	106	3	0	ENST00000269305.4:c.919+41_993+456del		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	0.62238903034866	1	FACETS	1	0.99	1	1	0.993	1	CLONAL	2	TRUE	0	0.6305251391203	1		3	109	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115861	8115862	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGAG	novel	NA	P-0006741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	450	667	1	ENST00000346208.3:c.1208_1211dup	p.His405GlufsTer103	p.H405Efs*103	ENST00000346208		403	ctg/cTGAGtg	6/6	1	2	FACETS	0.906	0.864	0.95	0.906	0.864	0.95	CLONAL	1	TRUE	1	0.6305251391203	2		668	1575	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371801	55371801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746536924	NA	P-0006748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	12	71	0	ENST00000297316.4:c.491C>T	p.Ala164Val	p.A164V	ENST00000297316	NM_022454.3	164	gCg/gTg	2/2	1	2	FACETS	0.837	0.591	1	0.837	0.591	1	CLONAL	1	FALSE	1	0.188560437561293	2		71	152	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971148	21971148	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs864622570	NA	P-0006748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	32	167	0	ENST00000579755.1:c.253C>T	p.Gln85Ter	p.Q85*	ENST00000579755		85	Caa/Taa	2/3	0.133025196686386	0	FACETS	0.998	0.813	1			1	CLONAL	1	FALSE	0	0.188560437561293	0		167	276	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413565	32413565	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121907903	NA	P-0006748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	43	373	0	ENST00000332351.3:c.1385G>A	p.Arg462Gln	p.R462Q	ENST00000332351	NM_024426.4	462	cGg/cAg	9/10	0.188560437561293	1	FACETS	0.499	0.416	0.591	0.499	0.416	0.591	SUBCLONAL	1	FALSE	0	0.188560437561293	1		373	828	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578457	+	frameshift_variant	Frame_Shift_Del	DEL	GCGC	GCGC	-	novel	NA	P-0006748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	44	426	0	ENST00000269305.4:c.473_476del	p.Arg158ProfsTer11	p.R158Pfs*11	ENST00000269305	NM_001126112.2	158	cGCGCc/cc	5/11	1	2	FACETS	0.551	0.46	0.652	0.551	0.46	0.652	SUBCLONAL	1	FALSE	1	0.188560437561293	2		426	847	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	74	331	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.207613634244849	2		331	619	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	36	153	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.200954409276659	1	FACETS	0.893	0.736	1	0.893	0.736	1	CLONAL	1	TRUE	0	0.207613634244849	1		153	348	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853245	68853245	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148400889	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	82	493	1	ENST00000261769.5:c.1628C>T	p.Ser543Phe	p.S543F	ENST00000261769	NM_004360.3	543	tCc/tTc	11/16	1	2	FACETS	0.656	0.576	0.742	0.656	0.576	0.742	SUBCLONAL	1	TRUE	1	0.207613634244849	2		494	1205	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169074	32169074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	74	436	0	ENST00000375023.3:c.3959C>T	p.Ser1320Phe	p.S1320F	ENST00000375023	NM_004557.3	1320	tCc/tTc	22/30	1	2	FACETS	0.682	0.595	0.776	0.682	0.595	0.776	SUBCLONAL	1	TRUE	1	0.207613634244849	2		436	1045	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	67	484	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.567	0.491	0.65	0.567	0.491	0.65	SUBCLONAL	1	TRUE	1	0.207613634244849	2		486	1138	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032404	10032404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142566406	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	17	146	0	ENST00000330684.3:c.419C>T	p.Pro140Leu	p.P140L	ENST00000330684	NM_001134407.1	140	cCg/cTg	3/13	1	2	FACETS	0.498	0.371	0.649	0.498	0.371	0.649	SUBCLONAL	1	TRUE	1	0.207613634244849	2		146	329	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453486	138453486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451809865	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1222	78	465	0	ENST00000289153.2:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000289153	NM_006219.2	321	cGa/cAa	5/22	1	2	FACETS	0.578	0.506	0.656	0.578	0.506	0.656	SUBCLONAL	1	TRUE	1	0.207613634244849	2		465	1300	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170217	32170217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	50	397	0	ENST00000375023.3:c.3391C>T	p.Pro1131Ser	p.P1131S	ENST00000375023	NM_004557.3	1131	Cct/Tct	21/30	1	2	FACETS	0.521	0.441	0.611	0.521	0.441	0.611	SUBCLONAL	1	TRUE	1	0.207613634244849	2		397	924	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790512	3790512	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	78	386	1	ENST00000262367.5:c.4021C>T	p.Arg1341Ter	p.R1341*	ENST00000262367	NM_004380.2	1341	Cga/Tga	24/31	1	2	FACETS	0.633	0.554	0.718	0.633	0.554	0.718	SUBCLONAL	1	TRUE	1	0.207613634244849	2		387	1187	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678572	88678572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1161765368	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	44	205	0	ENST00000360948.2:c.964G>A	p.Glu322Lys	p.E322K	ENST00000360948	NM_001012338.2	322	Gag/Aag	9/19	1	2	FACETS	0.715	0.599	0.844	0.715	0.599	0.844	SUBCLONAL	1	TRUE	1	0.207613634244849	2		205	593	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967209	93967209	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	62	584	0	ENST00000369303.4:c.2143G>A	p.Glu715Lys	p.E715K	ENST00000369303	NM_004440.3	715	Gaa/Aaa	12/17	0.200954409276659	1	FACETS	0.466	0.401	0.538	0.466	0.401	0.538	SUBCLONAL	1	TRUE	0	0.207613634244849	1		584	1148	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143079	7143079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138897740	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	33	245	0	ENST00000302850.5:c.2290C>T	p.Leu764Phe	p.L764F	ENST00000302850	NM_000208.2	764	Ctt/Ttt	12/22	1	2	FACETS	0.527	0.428	0.639	0.527	0.428	0.639	SUBCLONAL	1	TRUE	1	0.207613634244849	2		245	603	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184649	11184649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	100	491	0	ENST00000361445.4:c.6568G>A	p.Glu2190Lys	p.E2190K	ENST00000361445	NM_004958.3	2190	Gaa/Aaa	47/58	1	2	FACETS	0.801	0.714	0.895	0.801	0.714	0.895	CLONAL	1	TRUE	1	0.207613634244849	2		491	1202	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261091	16261091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	40	239	0	ENST00000375759.3:c.8356C>T	p.His2786Tyr	p.H2786Y	ENST00000375759	NM_015001.2	2786	Cac/Tac	11/15	1	2	FACETS	0.57	0.472	0.679	0.57	0.472	0.679	SUBCLONAL	1	TRUE	1	0.207613634244849	2		239	676	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885626	23885626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528089188	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	271	606	0	ENST00000374561.5:c.292C>T	p.Pro98Ser	p.P98S	ENST00000374561	NM_002167.4	98	Ccc/Tcc	1/3	1	2	FACETS	0.89	0.833	0.949	1	0.994	1	CLONAL	2	TRUE	1	0.207613634244849	2		606	1467	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120469121	120469121	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	136	354	0	ENST00000256646.2:c.4005+1G>C		p.X1335_splice	ENST00000256646	NM_024408.3	1335			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.207613634244849	2		354	1041	SUCCESS
ALK	238	MSKCC	GRCh37	2	29473997	29473997	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	66	426	0	ENST00000389048.3:c.2178G>A	p.Trp726Ter	p.W726*	ENST00000389048	NM_004304.4	726	tgG/tgA	12/29	1	2	FACETS	0.651	0.564	0.747	0.651	0.564	0.747	SUBCLONAL	1	TRUE	1	0.207613634244849	2		426	976	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606095	47606095	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs891924989	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	93	332	0	ENST00000263735.4:c.559G>A	p.Glu187Lys	p.E187K	ENST00000263735	NM_002354.2	187	Gag/Aag	6/9	1	2	FACETS	0.95	0.843	1	0.95	0.843	1	CLONAL	1	TRUE	1	0.207613634244849	2		332	943	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295704	212295704	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745376683	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	41	402	0	ENST00000342788.4:c.2609G>A	p.Gly870Glu	p.G870E	ENST00000342788	NM_005235.2	870	gGa/gAa	21/28	1	2	FACETS	0.535	0.444	0.637	0.535	0.444	0.637	SUBCLONAL	1	TRUE	1	0.207613634244849	2		402	738	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587251	212587251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868149408	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	47	330	1	ENST00000342788.4:c.750G>A	p.Met250Ile	p.M250I	ENST00000342788	NM_005235.2	250	atG/atA	7/28	1	2	FACETS	0.593	0.499	0.697	0.593	0.499	0.697	SUBCLONAL	1	TRUE	1	0.207613634244849	2		331	764	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729962	30729962	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs104893819	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	40	339	0	ENST00000295754.5:c.1483C>T	p.Arg495Ter	p.R495*	ENST00000295754	NM_003242.5	495	Cga/Tga	6/7	1	2	FACETS	0.563	0.467	0.671	0.563	0.467	0.671	SUBCLONAL	1	TRUE	1	0.207613634244849	2		339	684	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400051	49400051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	59	413	0	ENST00000418115.1:c.286C>T	p.Pro96Ser	p.P96S	ENST00000418115	NM_001664.2	96	Cca/Tca	4/5	1	2	FACETS	0.575	0.493	0.665	0.575	0.493	0.665	SUBCLONAL	1	TRUE	1	0.207613634244849	2		413	988	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259521	89259521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1282065699	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	43	341	1	ENST00000336596.2:c.665C>T	p.Ser222Phe	p.S222F	ENST00000336596	NM_005233.5	222	tCc/tTc	3/17	1	2	FACETS	0.609	0.508	0.721	0.609	0.508	0.721	SUBCLONAL	1	TRUE	1	0.207613634244849	2		342	680	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582310	119582310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	36	342	0	ENST00000316626.5:c.1091C>T	p.Pro364Leu	p.P364L	ENST00000316626		364	cCa/cTa	10/12	1	2	FACETS	0.518	0.424	0.623	0.518	0.424	0.623	SUBCLONAL	1	TRUE	1	0.207613634244849	2		342	670	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953926	55953926	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	70	251	0	ENST00000263923.4:c.3511-1G>A		p.X1171_splice	ENST00000263923	NM_002253.2	1171			0.200954409276659	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.207613634244849	1		251	569	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694631	176694631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	71	527	1	ENST00000439151.2:c.5215C>T	p.Pro1739Ser	p.P1739S	ENST00000439151	NM_022455.4	1739	Cct/Tct	15/23	1	2	FACETS	0.617	0.537	0.705	0.617	0.537	0.705	SUBCLONAL	1	TRUE	1	0.207613634244849	2		528	1108	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032017	26032017	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2022	127	908	0	ENST00000244661.2:c.272T>A	p.Met91Lys	p.M91K	ENST00000244661	NM_003537.3	91	aTg/aAg	1/1	1	2	FACETS	0.569	0.513	0.629	0.569	0.513	0.629	SUBCLONAL	1	TRUE	1	0.207613634244849	2		908	2149	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673196	30673196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	77	509	0	ENST00000376406.3:c.3764C>T	p.Ser1255Phe	p.S1255F	ENST00000376406	NM_014641.2	1255	tCc/tTc	10/15	1	2	FACETS	0.592	0.518	0.673	0.592	0.518	0.673	SUBCLONAL	1	TRUE	1	0.207613634244849	2		509	1253	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120631	94120631	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1321	101	758	0	ENST00000369303.4:c.420A>T	p.Glu140Asp	p.E140D	ENST00000369303	NM_004440.3	140	gaA/gaT	3/17	0.200954409276659	1	FACETS	0.613	0.546	0.685	0.613	0.546	0.685	SUBCLONAL	1	TRUE	0	0.207613634244849	1		758	1422	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686895	117686895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	49	341	2	ENST00000368508.3:c.2822C>T	p.Ser941Phe	p.S941F	ENST00000368508	NM_002944.2	941	tCc/tTc	19/43	0.200954409276659	1	FACETS	0.526	0.444	0.616	0.526	0.444	0.616	SUBCLONAL	1	TRUE	0	0.207613634244849	1		343	805	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683747	162683747	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	54	384	0	ENST00000366898.1:c.222G>A	p.Trp74Ter	p.W74*	ENST00000366898	NM_004562.2	74	tgG/tgA	3/12	NA	2	FACETS	0.55	0.468	0.641			1	INDETERMINATE	1	TRUE	NA	0.207613634244849	2		384	945	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55232991	55232991	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	71	431	1	ENST00000275493.2:c.1741C>T	p.Gln581Ter	p.Q581*	ENST00000275493	NM_005228.3	581	Cag/Tag	15/28	1	2	FACETS	0.6	0.522	0.685	0.6	0.522	0.685	SUBCLONAL	1	TRUE	1	0.207613634244849	2		432	1140	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332061	81332061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	42	335	0	ENST00000222390.5:c.2023G>A	p.Gly675Ser	p.G675S	ENST00000222390	NM_000601.4	675	Ggc/Agc	18/18	1	2	FACETS	0.572	0.476	0.679	0.572	0.476	0.679	SUBCLONAL	1	TRUE	1	0.207613634244849	2		335	707	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399985	139399985	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	112	478	1	ENST00000277541.6:c.4363C>T	p.Gln1455Ter	p.Q1455*	ENST00000277541	NM_017617.3	1455	Cag/Tag	25/34	1	2	FACETS	0.949	0.851	1	0.949	0.851	1	CLONAL	1	TRUE	1	0.207613634244849	2		479	1137	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407962	139407962	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	125	378	0	ENST00000277541.6:c.2235G>A	p.Trp745Ter	p.W745*	ENST00000277541	NM_017617.3	745	tgG/tgA	14/34	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.207613634244849	2		378	1044	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417402	139417402	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	141	502	0	ENST00000277541.6:c.642C>A	p.Asn214Lys	p.N214K	ENST00000277541	NM_017617.3	214	aaC/aaA	4/34	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.207613634244849	2		502	1304	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793323	139793323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1290	87	544	1	ENST00000247668.2:c.131C>T	p.Pro44Leu	p.P44L	ENST00000247668	NM_021138.3	44	cCc/cTc	2/11	1	2	FACETS	0.609	0.537	0.686	0.609	0.537	0.686	SUBCLONAL	1	TRUE	1	0.207613634244849	2		545	1377	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615063	43615063	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	67	466	0	ENST00000355710.3:c.2477A>T	p.Tyr826Phe	p.Y826F	ENST00000355710	NM_020975.4	826	tAc/tTc	14/20	1	2	FACETS	0.587	0.508	0.673	0.587	0.508	0.673	SUBCLONAL	1	TRUE	1	0.207613634244849	2		466	1100	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203678	94203678	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	55	337	0	ENST00000323929.3:c.976C>T	p.Pro326Ser	p.P326S	ENST00000323929	NM_005591.3	326	Cct/Tct	9/20	1	2	FACETS	0.692	0.59	0.803	0.692	0.59	0.803	SUBCLONAL	1	TRUE	1	0.207613634244849	2		337	766	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431944	49431944	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	57	352	0	ENST00000301067.7:c.9195C>G	p.Ile3065Met	p.I3065M	ENST00000301067	NM_003482.3	3065	atC/atG	34/54	1	2	FACETS	0.551	0.471	0.639	0.551	0.471	0.639	SUBCLONAL	1	TRUE	1	0.207613634244849	2		352	997	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434751	49434751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1205684726	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	111	375	0	ENST00000301067.7:c.6802G>A	p.Ala2268Thr	p.A2268T	ENST00000301067	NM_003482.3	2268	Gct/Act	31/54	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.207613634244849	2		375	973	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811664	102811664	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	61	505	1	ENST00000307046.8:c.520A>T	p.Lys174Ter	p.K174*	ENST00000307046	NM_001111285.1	174	Aag/Tag	4/4	1	2	FACETS	0.485	0.417	0.56	0.485	0.417	0.56	SUBCLONAL	1	TRUE	1	0.207613634244849	2		506	1211	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623625	28623625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1279372452	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	69	339	0	ENST00000241453.7:c.932G>A	p.Arg311Gln	p.R311Q	ENST00000241453	NM_004119.2	311	cGg/cAg	8/24	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.207613634244849	2		339	647	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900709	32900709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876659940	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	53	486	0	ENST00000380152.3:c.590C>T	p.Ser197Phe	p.S197F	ENST00000380152		197	tCt/tTt	7/27	1	2	FACETS	0.493	0.419	0.575	0.493	0.419	0.575	SUBCLONAL	1	TRUE	1	0.207613634244849	2		486	1035	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343666	343666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1281159388	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1413	189	696	1	ENST00000262320.3:c.2008C>T	p.Leu670Phe	p.L670F	ENST00000262320	NM_003502.3	670	Ctt/Ttt	8/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.207613634244849	2		697	1602	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223220	2223220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	64	485	0	ENST00000326181.6:c.832C>T	p.His278Tyr	p.H278Y	ENST00000326181	NM_032271.2	278	Cac/Tac	10/21	1	2	FACETS	0.49	0.423	0.564	0.49	0.423	0.564	SUBCLONAL	1	TRUE	1	0.207613634244849	2		485	1257	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900354	3900354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761381106	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	61	444	0	ENST00000262367.5:c.742C>T	p.Pro248Ser	p.P248S	ENST00000262367	NM_004380.2	248	Ccg/Tcg	2/31	1	2	FACETS	0.511	0.439	0.589	0.511	0.439	0.589	SUBCLONAL	1	TRUE	1	0.207613634244849	2		444	1151	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641773	23641773	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	46	312	0	ENST00000261584.4:c.1702C>G	p.Gln568Glu	p.Q568E	ENST00000261584	NM_024675.3	568	Caa/Gaa	5/13	1	2	FACETS	0.657	0.552	0.774	0.657	0.552	0.774	SUBCLONAL	1	TRUE	1	0.207613634244849	2		312	674	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56852603	56852603	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369861910	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	71	679	0	ENST00000308159.5:c.517C>T	p.Pro173Ser	p.P173S	ENST00000308159	NM_014669.4	173	Cct/Tct	6/22	1	2	FACETS	0.582	0.506	0.664	0.582	0.506	0.664	SUBCLONAL	1	TRUE	1	0.207613634244849	2		679	1176	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223335	2223335	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1229	87	530	0	ENST00000398665.3:c.3446C>T	p.Ser1149Phe	p.S1149F	ENST00000398665	NM_032482.2	1149	tCc/tTc	25/28	1	2	FACETS	0.637	0.562	0.718	0.637	0.562	0.718	SUBCLONAL	1	TRUE	1	0.207613634244849	2		530	1316	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295202	15295202	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	58	531	1	ENST00000263388.2:c.2470G>A	p.Gly824Ser	p.G824S	ENST00000263388	NM_000435.2	824	Ggt/Agt	16/33	1	2	FACETS	0.558	0.477	0.646	0.558	0.477	0.646	SUBCLONAL	1	TRUE	1	0.207613634244849	2		532	1002	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021608	31021608	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1247116484	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	34	127	0	ENST00000375687.4:c.1607C>T	p.Pro536Leu	p.P536L	ENST00000375687	NM_015338.5	536	cCc/cTc	12/13	0.207613634244849	7	FACETS	0.817	0.666	0.988			1	CLONAL	1	TRUE	NA	0.207613634244849	7		127	609	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264899	46264899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1734	183	915	3	ENST00000371998.3:c.1769G>A	p.Arg590Lys	p.R590K	ENST00000371998		590	aGa/aAa	12/23	1	2	FACETS	0.92	0.845	0.998	0.92	0.845	0.998	CLONAL	1	TRUE	1	0.207613634244849	2		918	1917	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914714	39914714	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	88	357	0	ENST00000378444.4:c.4648C>A	p.Leu1550Ile	p.L1550I	ENST00000378444	NM_001123385.1	1550	Ctc/Atc	12/15	0.129486415111193	0	FACETS	0.804	0.712	0.904			1	CLONAL	1	TRUE	NA	0.207613634244849	0		357	835	SUCCESS
AR	367	MSKCC	GRCh37	X	66943642	66943642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	63	288	0	ENST00000374690.3:c.2722C>T	p.Leu908Phe	p.L908F	ENST00000374690	NM_000044.3	908	Ctt/Ttt	8/8	0.129486415111193	0	FACETS	0.694	0.599	0.797			1	SUBCLONAL	1	TRUE	NA	0.207613634244849	0		288	693	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341625	70341625	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	79	238	0	ENST00000374080.3:c.1060C>G	p.Gln354Glu	p.Q354E	ENST00000374080		354	Cag/Gag	7/45	1	1	FACETS	0.991	0.872	1	0.991	0.872	1	CLONAL	1	TRUE	0	0.207613634244849	1		238	688	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938628	76938628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	134	302	0	ENST00000373344.5:c.2120C>T	p.Ala707Val	p.A707V	ENST00000373344	NM_000489.3	707	gCt/gTt	9/35	1	1	FACETS	0.819	0.746	0.897	1	0.988	1	CLONAL	2	TRUE	0	0.207613634244849	1		302	706	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716037	52716037	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1378	77	536	0	ENST00000322088.6:c.602del	p.Val201AlafsTer29	p.V201Afs*29	ENST00000322088	NM_014225.5	201	gTc/gc	5/15	1	2	FACETS	0.51	0.445	0.58	0.51	0.445	0.58	SUBCLONAL	1	TRUE	1	0.207613634244849	2		536	1455	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022309	31022309	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	102	263	2	ENST00000375687.4:c.1797del	p.Thr600ProfsTer103	p.T600Pfs*103	ENST00000375687	NM_015338.5	598	atC/at	13/13	0.207613634244849	7	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.207613634244849	7		265	1059	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439922	51439923	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	44	168	0	ENST00000262662.1:c.487_488delinsAA	p.Gly163Lys	p.G163K	ENST00000262662		163	GGa/AAa	4/4	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.207613634244849	2		168	346	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631414	117631415	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	44	390	0	ENST00000368508.3:c.6263_6264delinsTT	p.Ser2088Phe	p.S2088F	ENST00000368508	NM_002944.2	2088	tCC/tTT	40/43	0.200954409276659	1	FACETS	0.477	0.399	0.565	0.477	0.399	0.565	SUBCLONAL	1	TRUE	0	0.207613634244849	1		390	796	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8501020	8501021	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	37	406	0	ENST00000356435.5:c.1861_1862delinsTT	p.Pro621Leu	p.P621L	ENST00000356435		621	CCa/TTa	13/35	0.200954409276659	1	FACETS	0.464	0.382	0.557	0.464	0.382	0.557	SUBCLONAL	1	TRUE	0	0.207613634244849	1		406	688	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222336	2222337	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	59	396	2	ENST00000326181.6:c.620_621delinsTT	p.Pro207Leu	p.P207L	ENST00000326181	NM_032271.2	207	cCC/cTT	8/21	1	2	FACETS	0.604	0.518	0.698	0.604	0.518	0.698	SUBCLONAL	1	TRUE	1	0.207613634244849	2		398	941	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816248	89816249	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1191	67	527	0	ENST00000389301.3:c.3128_3129delinsTT	p.Ser1043Phe	p.S1043F	ENST00000389301	NM_000135.2	1043	tCC/tTT	32/43	1	2	FACETS	0.513	0.444	0.589	0.513	0.444	0.589	SUBCLONAL	1	TRUE	1	0.207613634244849	2		527	1258	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579415	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	93	345	1	ENST00000269305.4:c.272_273delinsAA	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tGG/tAA	4/11	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.207613634244849	2		346	889	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755530	39755531	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0006754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	79	388	1	ENST00000288319.7:c.1234_1235delinsTT	p.Pro412Phe	p.P412F	ENST00000288319	NM_182918.3	412	CCc/TTc	10/10	1	2	FACETS	0.771	0.676	0.873	0.771	0.676	0.873	SUBCLONAL	1	TRUE	1	0.207613634244849	2		389	987	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	98	510	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.787	0.702	0.879	0.787	0.702	0.879	SUBCLONAL	1	TRUE	1	0.292522644200235	2		510	851	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0006758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	110	549	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.782	0.701	0.867	0.782	0.701	0.867	SUBCLONAL	1	TRUE	1	0.292522644200235	2		549	962	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0006758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	95	626	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.759	0.675	0.849	0.759	0.675	0.849	SUBCLONAL	1	TRUE	1	0.292522644200235	2		627	856	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0006758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	125	518	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.99	0.896	1	0.99	0.896	1	CLONAL	1	TRUE	1	0.292522644200235	2		518	863	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0006758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	344	802	1	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	0.292522644200235	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.292522644200235	2		803	1046	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46736330	46736330	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs756364338	NA	P-0006758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	78	543	0	ENST00000371975.4:c.1043-1G>A		p.X348_splice	ENST00000371975	NM_003579.3	348			1	2	FACETS	0.648	0.568	0.734	0.648	0.568	0.734	SUBCLONAL	1	TRUE	1	0.292522644200235	2		543	823	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595638	55595638	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1268795324	NA	P-0006758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	54	308	0	ENST00000288135.5:c.2128A>G	p.Lys710Glu	p.K710E	ENST00000288135	NM_000222.2	710	Aag/Gag	14/21	1	2	FACETS	0.702	0.6	0.814	0.702	0.6	0.814	SUBCLONAL	1	TRUE	1	0.292522644200235	2		308	526	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157772	106157772	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	55	481	0	ENST00000380013.4:c.2673A>C	p.Gln891His	p.Q891H	ENST00000380013	NM_001127208.2	891	caA/caC	3/11	1	2	FACETS	0.435	0.371	0.505	0.435	0.371	0.505	SUBCLONAL	1	TRUE	1	0.292522644200235	2		481	865	SUCCESS
APC	324	MSKCC	GRCh37	5	112175653	112175653	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	121	709	0	ENST00000257430.4:c.4362A>T	p.Lys1454Asn	p.K1454N	ENST00000257430	NM_000038.5	1454	aaA/aaT	16/16	1	2	FACETS	0.792	0.714	0.874	0.792	0.714	0.874	SUBCLONAL	1	TRUE	1	0.292522644200235	2		709	1045	SUCCESS
APC	324	MSKCC	GRCh37	5	112175657	112175657	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0006758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	125	677	0	ENST00000257430.4:c.4366A>T	p.Lys1456Ter	p.K1456*	ENST00000257430	NM_000038.5	1456	Aaa/Taa	16/16	1	2	FACETS	0.828	0.748	0.913	0.828	0.748	0.913	CLONAL	1	TRUE	1	0.292522644200235	2		677	1032	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206829	162206829	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	63	573	0	ENST00000366898.1:c.846A>C	p.Gln282His	p.Q282H	ENST00000366898	NM_004562.2	282	caA/caC	7/12	1	2	FACETS	0.473	0.408	0.545	0.473	0.408	0.545	SUBCLONAL	1	TRUE	1	0.292522644200235	2		573	910	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233117	55233117	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	48	403	0	ENST00000275493.2:c.1867A>C	p.Asn623His	p.N623H	ENST00000275493	NM_005228.3	623	Aac/Cac	15/28	0.228294899778189	1	FACETS	0.481	0.406	0.563	0.481	0.406	0.563	SUBCLONAL	1	TRUE	0	0.292522644200235	1		403	583	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509541	106509541	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	58	601	0	ENST00000359195.3:c.1535A>C	p.Asn512Thr	p.N512T	ENST00000359195	NM_002649.2	512	aAc/aCc	2/11	1	2	FACETS	0.474	0.406	0.548	0.474	0.406	0.548	SUBCLONAL	1	TRUE	1	0.292522644200235	2		601	837	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98002947	98002947	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	59	562	0	ENST00000289081.3:c.329T>G	p.Leu110Arg	p.L110R	ENST00000289081	NM_000136.2	110	cTt/cGt	4/15	1	2	FACETS	0.437	0.375	0.505	0.437	0.375	0.505	SUBCLONAL	1	TRUE	1	0.292522644200235	2		562	923	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662360	67662360	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	128	672	0	ENST00000264010.4:c.1606C>T	p.Gln536Ter	p.Q536*	ENST00000264010	NM_006565.3	536	Cag/Tag	9/12	1	2	FACETS	0.989	0.896	1	0.989	0.896	1	CLONAL	1	TRUE	1	0.292522644200235	2		672	885	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993740	72993740	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371536462	NA	P-0006758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	140	744	0	ENST00000268489.5:c.305C>T	p.Ala102Val	p.A102V	ENST00000268489	NM_006885.3	102	gCg/gTg	2/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.292522644200235	2		744	854	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965076	15965076	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	39	367	0	ENST00000268712.3:c.5520A>C	p.Lys1840Asn	p.K1840N	ENST00000268712	NM_006311.3	1840	aaA/aaC	37/46	0.292522644200235	2	FACETS	0.436	0.36	0.52	0.218	0.18	0.26	SUBCLONAL	1	TRUE	0	0.292522644200235	2		367	612	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881441	37881441	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1429903426	NA	P-0006758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	79	474	0	ENST00000269571.5:c.2633A>G	p.His878Arg	p.H878R	ENST00000269571		878	cAt/cGt	21/27	1	2	FACETS	0.875	0.77	0.988	0.875	0.77	0.988	CLONAL	1	TRUE	1	0.292522644200235	2		474	617	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368305	45368305	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	47	624	0	ENST00000262160.6:c.1297A>C	p.Ser433Arg	p.S433R	ENST00000262160	NM_005901.5	433	Agt/Cgt	11/11	1	2	FACETS	0.346	0.291	0.408	0.346	0.291	0.408	SUBCLONAL	1	TRUE	1	0.292522644200235	2		624	928	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349999	15349999	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	54	683	0	ENST00000263377.2:c.3653A>C	p.Lys1218Thr	p.K1218T	ENST00000263377	NM_058243.2	1218	aAg/aCg	18/20	1	2	FACETS	0.463	0.394	0.538	0.463	0.394	0.538	SUBCLONAL	1	TRUE	1	0.292522644200235	2		683	798	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45854954	45854954	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	62	598	0	ENST00000391945.4:c.2216T>G	p.Leu739Arg	p.L739R	ENST00000391945	NM_000400.3	739	cTc/cGc	23/23	1	2	FACETS	0.677	0.585	0.778	0.677	0.585	0.778	SUBCLONAL	1	TRUE	1	0.292522644200235	2		598	626	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024087	31024087	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	65	581	0	ENST00000375687.4:c.3572T>G	p.Ile1191Ser	p.I1191S	ENST00000375687	NM_015338.5	1191	aTt/aGt	13/13	0.158492187058269	0	FACETS	0.425	0.368	0.487			1	INDETERMINATE	1	TRUE	0	0.292522644200235	0		581	740	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121333	29121333	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs756949505	NA	P-0006758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	102	629	0	ENST00000328354.6:c.342G>A	p.Trp114Ter	p.W114*	ENST00000328354	NM_007194.3	114	tgG/tgA	3/15	0.10965156590702	0	FACETS	0.547	0.488	0.609			1	INDETERMINATE	1	TRUE	0	0.292522644200235	0		629	902	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653830	89653830	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	223	488	0	ENST00000371953.3:c.129del	p.Gly44AlafsTer10	p.G44Afs*10	ENST00000371953	NM_000314.4	43	gAa/ga	2/9	0.237822256147404	2	FACETS	0.759	0.706	0.813	0.759	0.706	0.813	SUBCLONAL	2	TRUE	0	0.292522644200235	2		488	1005	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836302	89836319	+	inframe_deletion	In_Frame_Del	DEL	GCAGGGACAGGAAGGCCA	GCAGGGACAGGAAGGCCA	-	novel	NA	P-0006758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	114	843	0	ENST00000389301.3:c.2430_2447del	p.Gly811_Ala816del	p.G811_A816del	ENST00000389301	NM_000135.2	810	gcTGGCCTTCCTGTCCCTGCg/gcg	26/43	0.158492187058269	0	FACETS	0.59	0.53	0.653			1	INDETERMINATE	1	TRUE	0	0.292522644200235	0		843	935	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969422	44969426	+	frameshift_variant	Frame_Shift_Del	DEL	CTTGG	CTTGG	-	novel	NA	P-0006758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	177	450	0	ENST00000377967.4:c.4104_4108del	p.Asn1368LysfsTer19	p.N1368Kfs*19	ENST00000377967	NM_021140.2	1368	aaCTTGGaa/aaaa	28/29	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.292522644200235	1		450	695	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0006761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	111	759	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.94	0.844	1	0.94	0.844	1	CLONAL	1	TRUE	1	0.253402168526783	2		759	932	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372127	55372127	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	17	209	0	ENST00000297316.4:c.817C>T	p.Arg273Ter	p.R273*	ENST00000297316	NM_022454.3	273	Cga/Tga	2/2	0.253402168526783	6	FACETS	0.609	0.454	0.794	0.122	0.09	0.159	SUBCLONAL	1	TRUE	1	0.253402168526783	6		209	332	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851684	134851684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373293977	NA	P-0006761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	64	550	0	ENST00000398015.3:c.1090C>T	p.Arg364Trp	p.R364W	ENST00000398015	NM_004441.4	364	Cgg/Tgg	5/16	1	2	FACETS	0.692	0.598	0.794	0.692	0.598	0.794	SUBCLONAL	1	TRUE	1	0.253402168526783	2		550	730	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949106	151949106	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	44	600	0	ENST00000262189.6:c.1539C>G	p.Ile513Met	p.I513M	ENST00000262189	NM_170606.2	513	atC/atG	11/59	1	2	FACETS	0.466	0.389	0.551	0.466	0.389	0.551	SUBCLONAL	1	TRUE	1	0.253402168526783	2		600	746	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741636	17741636	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1441843696	NA	P-0006761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	40	286	0	ENST00000250003.3:c.307C>T	p.Arg103Cys	p.R103C	ENST00000250003	NM_002478.4	103	Cgc/Tgc	1/3	1	2	FACETS	0.809	0.674	0.96	0.809	0.674	0.96	CLONAL	1	TRUE	1	0.253402168526783	2		286	390	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005434	42005434	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	186	1049	0	ENST00000219905.7:c.3170T>A	p.Val1057Glu	p.V1057E	ENST00000219905	NM_001164273.1	1057	gTa/gAa	9/24	0.253402168526783	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.253402168526783	1		1049	1079	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992422	72992422	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs570223860	NA	P-0006761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1276	101	1123	0	ENST00000268489.5:c.1623G>C	p.Gln541His	p.Q541H	ENST00000268489	NM_006885.3	541	caG/caC	2/10	1	2	FACETS	0.579	0.515	0.647	0.579	0.515	0.647	SUBCLONAL	1	TRUE	1	0.253402168526783	2		1123	1377	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905617	50905617	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1182	103	802	0	ENST00000440232.2:c.745G>T	p.Asp249Tyr	p.D249Y	ENST00000440232	NM_002691.3	249	Gac/Tac	6/27	1	2	FACETS	0.633	0.564	0.706	0.633	0.564	0.706	SUBCLONAL	1	TRUE	1	0.253402168526783	2		802	1285	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175217	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0006761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	28	332	0	ENST00000257430.4:c.3925_3926del	p.Glu1309LysfsTer5	p.E1309Kfs*5	ENST00000257430	NM_000038.5	1309	GAa/a	16/16	1	2	FACETS	0.567	0.453	0.697	0.567	0.453	0.697	SUBCLONAL	1	TRUE	1	0.253402168526783	2		332	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0006768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	607	792	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.35482854279278	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.35482854279278	2		792	1635	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531749	46531749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1724	157	533	1	ENST00000262741.5:c.598G>A	p.Glu200Lys	p.E200K	ENST00000262741	NM_003629.3	200	Gaa/Aaa	5/10	0.35482854279278	4	FACETS	0.637	0.581	0.697			1	SUBCLONAL	1	TRUE	NA	0.35482854279278	4		534	1881	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420318	88420318	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	122	336	0	ENST00000360948.2:c.2368G>C	p.Glu790Gln	p.E790Q	ENST00000360948	NM_001012338.2	790	Gag/Cag	19/19	1	2	FACETS	0.959	0.868	1	0.959	0.868	1	CLONAL	1	TRUE	1	0.35482854279278	2		336	717	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819237	3819237	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1555	91	681	0	ENST00000262367.5:c.2998G>A	p.Glu1000Lys	p.E1000K	ENST00000262367	NM_004380.2	1000	Gag/Aag	15/31	0.345901162249105	3	FACETS	0.367	0.324	0.413	0.183	0.162	0.207	SUBCLONAL	1	TRUE	1	0.35482854279278	3		681	1646	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923647	72923647	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1425	508	805	0	ENST00000268489.5:c.3431G>T	p.Cys1144Phe	p.C1144F	ENST00000268489	NM_006885.3	1144	tGc/tTc	4/10	0.345901162249105	3	FACETS	0.872	0.833	0.912	0.872	0.833	0.912	CLONAL	2	TRUE	1	0.35482854279278	3		805	1933	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853923	59853923	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	167	512	0	ENST00000259008.2:c.1936G>T	p.Val646Phe	p.V646F	ENST00000259008	NM_032043.2	646	Gtt/Ttt	14/20	0.345901162249105	3	FACETS	0.945	0.867	1	0.472	0.433	0.514	CLONAL	1	TRUE	1	0.35482854279278	3		512	1173	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226627	1226627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781537	NA	P-0006768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	65	397	0	ENST00000326873.7:c.1283C>T	p.Ser428Leu	p.S428L	ENST00000326873	NM_000455.4	428	tCg/tTg	9/10	0.35482854279278	1	FACETS	0.55	0.477	0.629	0.55	0.477	0.629	SUBCLONAL	1	TRUE	0	0.35482854279278	1		397	548	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561234	9561234	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1228	101	551	0	ENST00000353224.5:c.548C>G	p.Ser183Cys	p.S183C	ENST00000353224	NM_177990.2	183	tCt/tGt	4/10	0.35482854279278	3	FACETS	0.504	0.449	0.564	0.252	0.224	0.282	SUBCLONAL	1	TRUE	1	0.35482854279278	3		551	1329	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250821	10250821	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	455	369	0	ENST00000340748.4:c.3659T>C	p.Leu1220Pro	p.L1220P	ENST00000340748		1220	cTg/cCg	32/40	0.384811246403154	5	FACETS	0.879	0.84	0.919	0.527	0.504	0.552	CLONAL	3	TRUE	0	0.448434845944628	5		369	1287	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40742225	40742225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2987	256	479	1	ENST00000392038.2:c.899G>A	p.Gly300Asp	p.G300D	ENST00000392038	NM_001626.4	300	gGc/gAc	10/14	0.448434845944628	10	FACETS	0.984	0.915	1			1	CLONAL	1	TRUE	NA	0.448434845944628	10		480	3243	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577107	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	496	491	0	ENST00000269305.4:c.831dup	p.Pro278SerfsTer28	p.P278Sfs*28	ENST00000269305	NM_001126112.2	277	-/T	8/11	0.396197545373509	2	FACETS	0.931	0.893	0.969	0.931	0.893	0.969	CLONAL	2	TRUE	0	0.448434845944628	2		491	1188	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332776	70332776	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	131	347	0	ENST00000373644.4:c.681del	p.Phe228SerfsTer6	p.F228Sfs*6	ENST00000373644	NM_030625.2	227	ctA/ct	2/12	0.437368056410417	3	FACETS	0.824	0.747	0.905	0.412	0.373	0.453	CLONAL	1	TRUE	1	0.448434845944628	3		347	868	SUCCESS
FH	2271	MSKCC	GRCh37	1	241683016	241683016	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs202166344	NA	P-0006788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	168	365	0	ENST00000366560.3:c.7C>G	p.Arg3Gly	p.R3G	ENST00000366560	NM_000143.3	3	Cga/Gga	1/10	1	2	FACETS	0.838	0.771	0.908	0.838	0.771	0.908	CLONAL	1	TRUE	1	0.476051666523647	2		365	842	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139573	47139573	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0006788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	143	299	0	ENST00000409792.3:c.5016-2A>C		p.X1672_splice	ENST00000409792	NM_014159.6	1672			0.476051666523647	1	FACETS	0.936	0.859	1	0.936	0.859	1	CLONAL	1	TRUE	0	0.476051666523647	1		299	489	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55962489	55962489	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	213	423	0	ENST00000263923.4:c.2635C>T	p.His879Tyr	p.H879Y	ENST00000263923	NM_002253.2	879	Cat/Tat	19/30	1	2	FACETS	0.971	0.903	1	0.971	0.903	1	CLONAL	1	TRUE	1	0.476051666523647	2		423	922	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161457	2161457	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	92	483	0	ENST00000434045.2:c.70C>A	p.Arg24Ser	p.R24S	ENST00000434045	NM_001127598.1	24	Cgc/Agc	2/5	1	2	FACETS	0.482	0.428	0.54	0.482	0.428	0.54	SUBCLONAL	1	TRUE	1	0.476051666523647	2		483	802	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490304	29490304	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876660277	NA	P-0006788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	251	462	0	ENST00000356175.3:c.389A>T	p.His130Leu	p.H130L	ENST00000356175	NM_000267.3	130	cAt/cTt	4/57	1	2	FACETS	0.907	0.848	0.969	0.907	0.848	0.969	CLONAL	1	TRUE	1	0.476051666523647	2		462	1162	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325427	1325427	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	105	463	1	ENST00000400841.2:c.248G>T	p.Gly83Val	p.G83V	ENST00000400841		83	gGg/gTg	3/6	1	1	FACETS	0.383	0.343	0.426	0.383	0.343	0.426	SUBCLONAL	1	TRUE	0	0.476051666523647	1		464	877	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230877	53230878	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0006788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	221	268	0	ENST00000375401.3:c.1915_1916del	p.Tyr639LeufsTer6	p.Y639Lfs*6	ENST00000375401	NM_004187.3	639	TAc/c	14/26	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.476051666523647	1		268	548	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183854	10183862	+	inframe_deletion	In_Frame_Del	DEL	GCATCCACA	GCATCCACA	-	novel	NA	P-0006788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	44	222	0	ENST00000256474.2:c.325_333del	p.Ile109_Ser111del	p.I109_S111del	ENST00000256474	NM_000551.3	108	cGCATCCACAgc/cgc	1/3	0.476051666523647	1	FACETS	0.423	0.356	0.497	0.423	0.356	0.497	SUBCLONAL	1	TRUE	0	0.476051666523647	1		222	333	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006794-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	33	510	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.201172748624429	2	FACETS	0.904	0.737	1	0.452	0.368	0.546	CLONAL	1	FALSE	0	0.201172748624429	2		510	363	SUCCESS
APC	324	MSKCC	GRCh37	5	112174112	112174112	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006794-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	33	577	0	ENST00000257430.4:c.2821G>T	p.Glu941Ter	p.E941*	ENST00000257430	NM_000038.5	941	Gaa/Taa	16/16	0.201172748624429	2	FACETS	0.749	0.61	0.906	0.375	0.305	0.453	CLONAL	1	FALSE	0	0.201172748624429	2		577	438	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451486	70451486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006794-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	40	673	0	ENST00000373644.4:c.6326C>T	p.Ala2109Val	p.A2109V	ENST00000373644	NM_030625.2	2109	gCa/gTa	12/12	0.201172748624429	2	FACETS	0.632	0.524	0.753	0.316	0.262	0.377	SUBCLONAL	1	FALSE	0	0.201172748624429	2		673	629	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920422	114920422	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006794-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	75	716	0	ENST00000543371.1:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000543371	NM_001198531.1	455	Cga/Tga	13/14	0.201172748624429	2	FACETS	0.982	0.86	1	0.491	0.43	0.558	CLONAL	1	FALSE	0	0.201172748624429	2		716	759	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428131	47428132	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAACATC	novel	NA	P-0006794-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	50	539	0	ENST00000377045.4:c.1092_1098dup	p.Leu367GlnfsTer22	p.L367Qfs*22	ENST00000377045	NM_001654.4	364	gtc/gtCAACATCc	11/16	0.201172748624429	4	FACETS	0.913	0.774	1	0.304	0.258	0.356	CLONAL	1	FALSE	1	0.201172748624429	4		539	654	SUCCESS
APC	324	MSKCC	GRCh37	5	112175596	112175597	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0006794-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	35	694	0	ENST00000257430.4:c.4306_4307dup	p.Ser1436ArgfsTer38	p.S1436Rfs*38	ENST00000257430	NM_000038.5	1435	-/AG	16/16	0.201172748624429	2	FACETS	0.501	0.409	0.604	0.25	0.204	0.302	SUBCLONAL	1	FALSE	0	0.201172748624429	2		694	695	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0006806-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	369	290	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.518164824225045	3	FACETS	0.956	0.919	0.991	0.956	0.919	0.991	CLONAL	3	FALSE	0	0.565312306266985	3		290	584	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774148	56774148	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006806-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	179	519	1	ENST00000337432.4:c.499G>A	p.Asp167Asn	p.D167N	ENST00000337432	NM_058216.2	167	Gat/Aat	3/9	0.565917157410219	3	FACETS	0.856	0.789	0.926	0.428	0.394	0.463	CLONAL	1	FALSE	1	0.565312306266985	3		520	949	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975471	26975472	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0006806-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	232	238	1	ENST00000381527.3:c.1098_1099del	p.Asp366GlufsTer14	p.D366Efs*14	ENST00000381527	NM_001260.1	366	gAC/g	11/13	0.171934377468078	3	FACETS	1	0.989	1			1	INDETERMINATE	2	FALSE	NA	0.565312306266985	3		239	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0006809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	332	554	1	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.523949632345666	2	FACETS	0.925	0.883	0.968	0.925	0.883	0.968	CLONAL	2	TRUE	0	0.55453595212597	2		555	647	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837954	156837954	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	115	681	0	ENST00000524377.1:c.487G>C	p.Glu163Gln	p.E163Q	ENST00000524377	NM_002529.3	163	Gag/Cag	5/17	0.343020558603209	3	FACETS	0.665	0.599	0.735			1	SUBCLONAL	1	TRUE	NA	0.55453595212597	3		681	797	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372460	55372460	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	145	765	0	ENST00000297316.4:c.1150T>G	p.Ser384Ala	p.S384A	ENST00000297316	NM_022454.3	384	Tcc/Gcc	2/2	0.424204250372891	3	FACETS	0.784	0.715	0.856			1	SUBCLONAL	1	TRUE	NA	0.55453595212597	3		765	852	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742486	17742486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	129	655	0	ENST00000250003.3:c.668G>A	p.Arg223Gln	p.R223Q	ENST00000250003	NM_002478.4	223	cGg/cAg	2/3	0.55453595212597	3	FACETS	0.762	0.691	0.836	0.381	0.345	0.418	SUBCLONAL	1	TRUE	1	0.55453595212597	3		655	780	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434166	121434166	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	634	659	1	ENST00000257555.6:c.1057C>A	p.Pro353Thr	p.P353T	ENST00000257555		353	Ccc/Acc	5/10	0.484290005259313	4	FACETS	0.979	0.953	1	0.979	0.953	1	CLONAL	4	TRUE	0	0.55453595212597	4		660	908	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781791	3781791	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	163	569	1	ENST00000262367.5:c.4876G>C	p.Glu1626Gln	p.E1626Q	ENST00000262367	NM_004380.2	1626	Gag/Cag	29/31	0.448853251479849	4	FACETS	1	0.921	1	0.502	0.46	0.545	CLONAL	1	TRUE	2	0.55453595212597	4		570	911	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858282	59858282	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	137	572	0	ENST00000259008.2:c.1713G>C	p.Leu571Phe	p.L571F	ENST00000259008	NM_032043.2	571	ttG/ttC	12/20	0.55453595212597	4	FACETS	1	0.93	1	0.256	0.233	0.28	CLONAL	1	TRUE	0	0.55453595212597	4		572	750	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117186	7117186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	194	648	1	ENST00000302850.5:c.4030G>A	p.Asp1344Asn	p.D1344N	ENST00000302850	NM_000208.2	1344	Gat/Aat	22/22	0.448853251479849	4	FACETS	1	0.955	1	0.522	0.483	0.564	CLONAL	1	TRUE	2	0.55453595212597	4		649	1041	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627390	14627390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144442851	NA	P-0006809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1298	233	1089	0	ENST00000254322.2:c.680C>T	p.Thr227Ile	p.T227I	ENST00000254322	NM_006145.1	227	aCc/aTc	2/3	0.55453595212597	4	FACETS	0.853	0.793	0.916	0.427	0.396	0.458	CLONAL	1	TRUE	2	0.55453595212597	4		1089	1531	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944486	40944486	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1303359688	NA	P-0006809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	180	754	0	ENST00000373198.4:c.2016C>A	p.Asn672Lys	p.N672K	ENST00000373198	NM_133170.3	672	aaC/aaA	12/32	0.55453595212597	3	FACETS	1	0.941	1	0.511	0.472	0.552	CLONAL	1	TRUE	1	0.55453595212597	3		754	811	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0006812-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	197	485	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.3238741783651	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.3238741783651	1		485	806	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748228	41748228	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006812-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	130	474	1	ENST00000226382.2:c.541G>T	p.Asp181Tyr	p.D181Y	ENST00000226382	NM_003924.3	181	Gac/Tac	3/3	0.3238741783651	1	FACETS	0.811	0.735	0.89	0.811	0.735	0.89	CLONAL	1	TRUE	0	0.3238741783651	1		475	830	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575671	48575672	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0006812-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	103	230	0	ENST00000342988.3:c.431_432del	p.Ser144TrpfsTer7	p.S144Wfs*7	ENST00000342988	NM_005359.5	144	tCA/t	4/12	0.3238741783651	1	FACETS	0.987	0.886	1	0.987	0.886	1	CLONAL	1	TRUE	0	0.3238741783651	1		230	540	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097609	27097609	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0006816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	98	346	0	ENST00000324856.7:c.3199-1G>A		p.X1067_splice	ENST00000324856	NM_006015.4	1067			1	2	FACETS	0.966	0.863	1	0.966	0.863	1	CLONAL	1	TRUE	1	0.321515976324353	2		346	631	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050416	128050416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1453017999	NA	P-0006816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	46	307	1	ENST00000285398.2:c.241G>A	p.Asp81Asn	p.D81N	ENST00000285398	NM_000122.1	81	Gat/Aat	3/15	1	2	FACETS	0.556	0.468	0.653	0.556	0.468	0.653	SUBCLONAL	1	TRUE	1	0.321515976324353	2		308	515	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142975	47142975	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	63	352	0	ENST00000409792.3:c.4988C>G	p.Thr1663Arg	p.T1663R	ENST00000409792	NM_014159.6	1663	aCg/aGg	8/21	0.321515976324353	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.321515976324353	1		352	291	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921555	+	missense_variant	Missense_Mutation	TNP	TGT	TGT	AGG	novel	NA	P-0006816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	63	243	0	ENST00000263967.3:c.1035_1037delinsAGG	p.Asn345_Val346delinsLysGly	p.N345_V346delinsKG	ENST00000263967	NM_006218.2	345	aaTGTa/aaAGGa	5/21	0.321515976324353	3	FACETS	0.892	0.78	1	0.892	0.78	1	CLONAL	2	TRUE	1	0.321515976324353	3		243	255	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0006816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	47	375	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.159793993984528	2	FACETS	0.71	0.6	0.83	0.355	0.3	0.415	INDETERMINATE	1	TRUE	0	0.321515976324353	2		375	412	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0006816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	89	221	0	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	0.159793993984528	2	FACETS	1	0.976	1	0.677	0.604	0.754	INDETERMINATE	1	TRUE	0	0.321515976324353	2		221	409	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371807	55371807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	17	36	0	ENST00000297316.4:c.497C>T	p.Ala166Val	p.A166V	ENST00000297316	NM_022454.3	166	gCg/gTg	2/2	1	2	FACETS	0.889	0.671	1	0.889	0.671	1	CLONAL	1	TRUE	1	0.321515976324353	2		36	119	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903772	114903772	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	285	574	0	ENST00000543371.1:c.776G>A	p.Trp259Ter	p.W259*	ENST00000543371	NM_001198531.1	259	tGg/tAg	7/14	0.287430549937056	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.321515976324353	3		574	988	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872041	35872041	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	195	605	1	ENST00000216797.5:c.572C>T	p.Ser191Phe	p.S191F	ENST00000216797	NM_020529.2	191	tCt/tTt	4/6	0.252140046252249	1	FACETS	0.915	0.846	0.987	0.915	0.846	0.987	CLONAL	1	TRUE	0	0.321515976324353	1		606	1113	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0006816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	277	536	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.319181313397686	2	FACETS	0.933	0.878	0.99	0.933	0.878	0.99	CLONAL	2	TRUE	0	0.321515976324353	2		536	923	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791995	42791995	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	103	432	0	ENST00000575354.2:c.799T>G	p.Trp267Gly	p.W267G	ENST00000575354	NM_015125.3	267	Tgg/Ggg	6/20	0.321515976324353	4	FACETS	0.715	0.637	0.797	0.238	0.212	0.266	SUBCLONAL	1	TRUE	1	0.321515976324353	4		432	1185	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950057	44950057	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	54	559	1	ENST00000377967.4:c.3826A>T	p.Asn1276Tyr	p.N1276Y	ENST00000377967	NM_021140.2	1276	Aat/Tat	26/29	1	2	FACETS	0.715	0.611	0.828	0.715	0.611	0.828	SUBCLONAL	1	TRUE	1	0.321515976324353	2		560	470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0006822-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	442	656	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.873	0.849	0.897	1	0.997	1	CLONAL	2	TRUE	1	0.870945108294929	2		657	581	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098913	47098913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006822-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	128	334	0	ENST00000409792.3:c.6361C>T	p.Arg2121Cys	p.R2121C	ENST00000409792	NM_014159.6	2121	Cgc/Tgc	15/21	1	2	FACETS	0.808	0.74	0.876	0.808	0.74	0.876	CLONAL	1	TRUE	1	0.870945108294929	2		334	364	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928398	69928398	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765235347	NA	P-0006822-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	164	326	0	ENST00000352241.4:c.218G>A	p.Arg73His	p.R73H	ENST00000352241	NM_198159.2	73	cGc/cAc	2/10	0.66268602907903	4	FACETS	1	0.923	1			1	CLONAL	1	TRUE	NA	0.870945108294929	4		326	703	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526226	189526226	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765564666	NA	P-0006822-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	242	400	1	ENST00000264731.3:c.490G>A	p.Ala164Thr	p.A164T	ENST00000264731	NM_003722.4	164	Gcc/Acc	4/14	0.736448743507217	5	FACETS	0.921	0.859	0.986	0.23	0.214	0.247	CLONAL	1	TRUE	1	0.870945108294929	5		401	1391	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158663	26158663	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006822-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	10	23	0	ENST00000289316.2:c.266C>G	p.Thr89Ser	p.T89S	ENST00000289316	NM_138720.2	89	aCc/aGc	1/2	0.800034877075093	5	FACETS	0.746	0.513	1	0.249	0.171	0.343	CLONAL	1	TRUE	2	0.870945108294929	5		23	71	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348504	89348504	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006822-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	347	618	0	ENST00000301030.4:c.4446T>A	p.Asp1482Glu	p.D1482E	ENST00000301030	NM_001256183.1	1482	gaT/gaA	9/13	0.66268602907903	4	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.870945108294929	4		618	1414	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	CC	novel	NA	P-0006822-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	288	277	0	ENST00000257430.4:c.3964delinsCC	p.Glu1322ProfsTer10	p.E1322Pfs*10	ENST00000257430	NM_000038.5	1322	Gaa/CCaa	16/16	0.738850918985306	3	FACETS	0.869	0.841	0.897	0.869	0.841	0.897	CLONAL	3	TRUE	0	0.870945108294929	3		277	364	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239419	105239419	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006829-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	221	324	0	ENST00000349310.3:c.968A>G	p.Asp323Gly	p.D323G	ENST00000349310	NM_001014432.1	323	gAc/gGc	12/15	0.127480572503663	3	FACETS	0.924	0.862	0.988			1	INDETERMINATE	1	TRUE	NA	0.815399278939523	3		324	826	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	581	160	0				ENST00000310581	NM_198253.2	-/1132			0.500717940030717	5	FACETS	0.96	0.929	0.991	0.96	0.929	0.991	CLONAL	4	TRUE	1	0.548679149715179	5		160	1005	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	1139	486	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.452374029197726	4	FACETS	0.944	0.925	0.964	0.944	0.925	0.964	CLONAL	4	TRUE	0	0.548679149715179	4		486	1702	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726624	41726624	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	461	487	0	ENST00000301178.4:c.169C>T	p.Gln57Ter	p.Q57*	ENST00000301178	NM_021913.4	57	Cag/Tag	2/20	0.548679149715179	3	FACETS	1	0.995	1	0.467	0.445	0.489	CLONAL	1	TRUE	0	0.548679149715179	3		487	1528	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045688	26045688	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1350355423	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2050	298	755	0	ENST00000540144.1:c.50C>T	p.Pro17Leu	p.P17L	ENST00000540144	NM_003531.2	17	cCg/cTg	1/1	0.131391789054127	6	FACETS	0.97	0.909	1	0.323	0.303	0.345	INDETERMINATE	1	TRUE	3	0.548679149715179	6		755	2348	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437669	52437669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	360	583	1	ENST00000460680.1:c.1492G>A	p.Glu498Lys	p.E498K	ENST00000460680	NM_004656.3	498	Gag/Aag	13/17	0.439055063296329	2	FACETS	0.886	0.838	0.935	0.443	0.419	0.468	CLONAL	1	TRUE	0	0.548679149715179	2		584	1481	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954211	48954211	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	215	318	0	ENST00000267163.4:c.1415del	p.Asn472IlefsTer6	p.N472Ifs*6	ENST00000267163	NM_000321.2	471	cAa/ca	15/27	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.548679149715179	2		318	614	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165293	47165293	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	114	363	0	ENST00000409792.3:c.833C>T	p.Ser278Phe	p.S278F	ENST00000409792	NM_014159.6	278	tCc/tTc	3/21	0.439055063296329	2	FACETS	0.824	0.746	0.907	0.412	0.373	0.454	CLONAL	1	TRUE	0	0.548679149715179	2		363	504	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17345421	17345421	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	184	453	0	ENST00000375499.3:c.798C>G	p.Ile266Met	p.I266M	ENST00000375499	NM_003000.2	266	atC/atG	8/8	0.441527279216394	3	FACETS	0.961	0.888	1	0.481	0.444	0.519	CLONAL	1	TRUE	1	0.548679149715179	3		453	889	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102084	27102084	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	517	536	1	ENST00000324856.7:c.5010G>A	p.Trp1670Ter	p.W1670*	ENST00000324856	NM_006015.4	1670	tgG/tgA	19/20	0.441527279216394	3	FACETS	0.853	0.817	0.889	0.853	0.817	0.889	CLONAL	2	TRUE	1	0.548679149715179	3		537	1408	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726530	46726530	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	242	438	0	ENST00000371975.4:c.609G>C	p.Gln203His	p.Q203H	ENST00000371975	NM_003579.3	203	caG/caC	7/18	0.441527279216394	3	FACETS	0.861	0.803	0.922	0.431	0.401	0.461	CLONAL	1	TRUE	1	0.548679149715179	3		438	1305	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204506611	204506611	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	104	453	0	ENST00000367182.3:c.397C>G	p.Gln133Glu	p.Q133E	ENST00000367182	NM_001278516.1	133	Caa/Gaa	6/11	0.441527279216394	3	FACETS	0.642	0.575	0.714	0.321	0.287	0.357	SUBCLONAL	1	TRUE	1	0.548679149715179	3		453	752	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226564946	226564946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	192	371	0	ENST00000366794.5:c.1804G>A	p.Glu602Lys	p.E602K	ENST00000366794	NM_001618.3	602	Gaa/Aaa	13/23	0.441527279216394	3	FACETS	0.837	0.774	0.904	0.419	0.387	0.452	CLONAL	1	TRUE	1	0.548679149715179	3		371	1065	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917730	29917730	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	159	414	0	ENST00000389048.3:c.938A>C	p.Lys313Thr	p.K313T	ENST00000389048	NM_004304.4	313	aAg/aCg	3/29	0.45573838996385	3	FACETS	0.67	0.613	0.729	0.223	0.204	0.243	SUBCLONAL	1	TRUE	0	0.548679149715179	3		414	1103	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439878	220439878	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1258	282	591	0	ENST00000243786.2:c.731C>G	p.Ser244Cys	p.S244C	ENST00000243786	NM_002191.3	244	tCt/tGt	2/2	0.45573838996385	3	FACETS	0.851	0.797	0.906	0.284	0.265	0.302	CLONAL	1	TRUE	0	0.548679149715179	3		591	1540	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165134	47165134	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	93	264	0	ENST00000409792.3:c.992C>T	p.Ser331Phe	p.S331F	ENST00000409792	NM_014159.6	331	tCt/tTt	3/21	0.439055063296329	2	FACETS	0.779	0.697	0.866	0.39	0.348	0.433	SUBCLONAL	1	TRUE	0	0.548679149715179	2		264	435	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165414	47165414	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	163	434	0	ENST00000409792.3:c.712C>G	p.Leu238Val	p.L238V	ENST00000409792	NM_014159.6	238	Ctg/Gtg	3/21	0.439055063296329	2	FACETS	0.764	0.702	0.828	0.382	0.351	0.414	SUBCLONAL	1	TRUE	0	0.548679149715179	2		434	778	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165518	47165518	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	339	647	0	ENST00000409792.3:c.608C>T	p.Ser203Leu	p.S203L	ENST00000409792	NM_014159.6	203	tCa/tTa	3/21	0.439055063296329	2	FACETS	0.812	0.766	0.859	0.406	0.383	0.43	CLONAL	1	TRUE	0	0.548679149715179	2		647	1522	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139714	55139714	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600186	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	106	302	0	ENST00000257290.5:c.1375G>A	p.Glu459Lys	p.E459K	ENST00000257290	NM_006206.4	459	Gaa/Aaa	10/23	0.441527279216394	3	FACETS	0.628	0.563	0.697	0.314	0.281	0.349	SUBCLONAL	1	TRUE	1	0.548679149715179	3		302	784	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947418	38947418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	90	420	2	ENST00000357387.3:c.4262C>T	p.Ser1421Leu	p.S1421L	ENST00000357387	NM_152756.3	1421	tCa/tTa	32/38	0.500717940030717	5	FACETS	0.517	0.457	0.582	0.129	0.114	0.146	SUBCLONAL	1	TRUE	1	0.548679149715179	5		422	1156	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939642	131939642	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	122	388	0	ENST00000265335.6:c.2428G>C	p.Ala810Pro	p.A810P	ENST00000265335		810	Gca/Cca	15/25	1	2	FACETS	0.613	0.554	0.674	0.613	0.554	0.674	SUBCLONAL	1	TRUE	1	0.548679149715179	2		388	726	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940578	131940578	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	159	463	0	ENST00000265335.6:c.2605G>C	p.Glu869Gln	p.E869Q	ENST00000265335		869	Gag/Cag	16/25	1	2	FACETS	0.698	0.64	0.759	0.698	0.64	0.759	SUBCLONAL	1	TRUE	1	0.548679149715179	2		463	830	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631351	117631351	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	116	426	0	ENST00000368508.3:c.6327C>G	p.Ile2109Met	p.I2109M	ENST00000368508	NM_002944.2	2109	atC/atG	40/43	0.131391789054127	6	FACETS	0.991	0.892	1	0.33	0.297	0.365	INDETERMINATE	1	TRUE	3	0.548679149715179	6		426	895	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974823	21974823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	51	110	0	ENST00000304494.5:c.4G>A	p.Glu2Lys	p.E2K	ENST00000304494	NM_000077.4	2	Gag/Aag	1/3	0.441527279216394	3	FACETS	1	0.882	1	0.515	0.442	0.593	CLONAL	1	TRUE	1	0.548679149715179	3		110	230	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998756	100998756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749674024	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	245	538	1	ENST00000325455.5:c.1046C>T	p.Ser349Leu	p.S349L	ENST00000325455	NM_001202474.3	349	tCg/tTg	1/8	0.441527279216394	3	FACETS	0.878	0.819	0.939	0.439	0.409	0.47	CLONAL	1	TRUE	1	0.548679149715179	3		539	1296	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119795	108119795	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772529339	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	154	340	0	ENST00000278616.4:c.1201C>T	p.Gln401Ter	p.Q401*	ENST00000278616	NM_000051.3	401	Cag/Tag	9/63	0.441527279216394	3	FACETS	0.788	0.721	0.858	0.394	0.36	0.429	SUBCLONAL	1	TRUE	1	0.548679149715179	3		340	908	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206578	108206578	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659942	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	99	384	0	ENST00000278616.4:c.8158G>A	p.Asp2720Asn	p.D2720N	ENST00000278616	NM_000051.3	2720	Gat/Aat	56/63	0.441527279216394	3	FACETS	0.719	0.642	0.8	0.359	0.321	0.4	SUBCLONAL	1	TRUE	1	0.548679149715179	3		384	640	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206650	108206650	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	135	504	0	ENST00000278616.4:c.8230G>T	p.Glu2744Ter	p.E2744*	ENST00000278616	NM_000051.3	2744	Gaa/Taa	56/63	0.441527279216394	3	FACETS	0.643	0.584	0.706	0.322	0.292	0.353	SUBCLONAL	1	TRUE	1	0.548679149715179	3		504	975	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	495065	495065	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	143	473	0	ENST00000399788.2:c.241G>C	p.Glu81Gln	p.E81Q	ENST00000399788	NM_001042603.1	81	Gag/Cag	2/28	0.455171738045704	3	FACETS	0.781	0.712	0.853			1	SUBCLONAL	1	TRUE	NA	0.548679149715179	3		473	851	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641487	18641487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	136	497	0	ENST00000266497.5:c.2486C>T	p.Ser829Phe	p.S829F	ENST00000266497		829	tCc/tTc	17/31	0.441527279216394	3	FACETS	0.761	0.692	0.834	0.381	0.346	0.417	SUBCLONAL	1	TRUE	1	0.548679149715179	3		497	830	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445224	49445224	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	187	364	1	ENST00000301067.7:c.2242G>A	p.Glu748Lys	p.E748K	ENST00000301067	NM_003482.3	748	Gag/Aag	10/54	0.441527279216394	3	FACETS	0.834	0.769	0.9	0.417	0.384	0.45	CLONAL	1	TRUE	1	0.548679149715179	3		365	1042	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495582	56495582	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1231170513	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	153	376	0	ENST00000267101.3:c.3772G>A	p.Glu1258Lys	p.E1258K	ENST00000267101	NM_001982.3	1258	Gaa/Aaa	28/28	0.441527279216394	3	FACETS	0.781	0.714	0.851	0.39	0.357	0.426	SUBCLONAL	1	TRUE	1	0.548679149715179	3		376	910	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26956974	26956974	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	86	294	0	ENST00000381527.3:c.480G>C	p.Met160Ile	p.M160I	ENST00000381527	NM_001260.1	160	atG/atC	5/13	0.388348654144411	5	FACETS	0.728	0.643	0.819	0.243	0.214	0.273	SUBCLONAL	1	TRUE	2	0.548679149715179	5		294	785	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134494	30134494	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	158	312	0	ENST00000263025.4:c.37G>T	p.Glu13Ter	p.E13*	ENST00000263025	NM_002746.2	13	Gag/Tag	1/9	1	2	FACETS	0.844	0.776	0.916	0.844	0.776	0.916	CLONAL	1	TRUE	1	0.548679149715179	2		312	682	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733038	74733038	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1179	190	469	2	ENST00000359995.5:c.205G>A	p.Glu69Lys	p.E69K	ENST00000359995	NM_001195427.1	69	Gag/Aag	1/3	0.548679149715179	3	FACETS	0.645	0.594	0.697	0.322	0.297	0.349	SUBCLONAL	1	TRUE	1	0.548679149715179	3		471	1369	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117593	4117593	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	338	267	0	ENST00000262948.5:c.127G>C	p.Glu43Gln	p.E43Q	ENST00000262948	NM_030662.3	43	Gag/Cag	2/11	0.548679149715179	3	FACETS	0.799	0.757	0.841	0.532	0.505	0.561	SUBCLONAL	2	TRUE	0	0.548679149715179	3		267	983	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765598	41765598	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1310	268	500	0	ENST00000301178.4:c.2474A>G	p.Asp825Gly	p.D825G	ENST00000301178	NM_021913.4	825	gAt/gGt	20/20	0.548679149715179	3	FACETS	0.789	0.738	0.842	0.263	0.246	0.281	SUBCLONAL	1	TRUE	0	0.548679149715179	3		500	1578	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795730	42795730	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	393	424	0	ENST00000575354.2:c.2719C>T	p.Gln907Ter	p.Q907*	ENST00000575354	NM_015125.3	907	Cag/Tag	11/20	0.548679149715179	3	FACETS	1	0.994	1	0.437	0.415	0.46	CLONAL	1	TRUE	0	0.548679149715179	3		424	1393	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419837	41419837	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	167	330	0	ENST00000373198.4:c.484C>G	p.Gln162Glu	p.Q162E	ENST00000373198	NM_133170.3	162	Cag/Gag	3/32	1	2	FACETS	0.877	0.808	0.949	0.877	0.808	0.949	CLONAL	1	TRUE	1	0.548679149715179	2		330	694	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922962	44922962	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1202	277	581	0	ENST00000377967.4:c.1823C>G	p.Pro608Arg	p.P608R	ENST00000377967	NM_021140.2	608	cCt/cGt	16/29	0.510542458842984	2	FACETS	0.683	0.639	0.727	0.341	0.319	0.364	SUBCLONAL	1	TRUE	0	0.548679149715179	2		581	1479	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907836	76907836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	79	191	0	ENST00000373344.5:c.4325C>T	p.Ser1442Phe	p.S1442F	ENST00000373344	NM_000489.3	1442	tCt/tTt	15/35	0.510542458842984	2	FACETS	1	0.935	1	0.535	0.477	0.597	CLONAL	1	TRUE	0	0.548679149715179	2		191	269	SUCCESS
BTK	695	MSKCC	GRCh37	X	100614317	100614317	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	227	525	1	ENST00000308731.7:c.858G>A	p.Met286Ile	p.M286I	ENST00000308731	NM_000061.2	286	atG/atA	10/19	0.510542458842984	2	FACETS	0.615	0.571	0.66	0.307	0.285	0.33	SUBCLONAL	1	TRUE	0	0.548679149715179	2		526	1346	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0006842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	1208	406	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.595487068629195	7	FACETS	0.981	0.959	1	0.981	0.959	1	CLONAL	5	TRUE	2	0.595487068629195	7		406	2059	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948705	55948705	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs765747186	NA	P-0006842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	249	291	2	ENST00000263923.4:c.3760G>C	p.Asp1254His	p.D1254H	ENST00000263923	NM_002253.2	1254	Gat/Cat	28/30	0.559618416770855	3	FACETS	0.845	0.796	0.895	0.845	0.796	0.895	CLONAL	2	TRUE	1	0.595487068629195	3		293	642	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752670	128752670	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2767	193	436	0	ENST00000377970.2:c.831C>G	p.Ile277Met	p.I277M	ENST00000377970	NM_002467.4	277	atC/atG	3/3	0.595487068629195	12	FACETS	0.871	0.801	0.945	0.079	0.072	0.086	CLONAL	1	TRUE	1	0.595487068629195	12		436	2960	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277079	18277079	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2226	249	549	0	ENST00000222254.8:c.1526T>A	p.Phe509Tyr	p.F509Y	ENST00000222254	NM_005027.3	509	tTc/tAc	12/16	0.595487068629195	8	FACETS	0.942	0.876	1			1	CLONAL	1	TRUE	NA	0.595487068629195	8		549	2475	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945240	54945240	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	148	319	0	ENST00000312783.6:c.1186A>G	p.Lys396Glu	p.K396E	ENST00000312783	NM_198436.1	396	Aaa/Gaa	10/10	0.595487068629195	6	FACETS	0.875	0.797	0.957			1	CLONAL	1	TRUE	NA	0.595487068629195	6		319	1245	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579425	7579426	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	382	432	0	ENST00000269305.4:c.261dup	p.Ala88SerfsTer61	p.A88Sfs*61	ENST00000269305	NM_001126112.2	87	-/A	4/11	0.576390559232369	2	FACETS	0.927	0.889	0.965	0.927	0.889	0.965	CLONAL	2	TRUE	0	0.595487068629195	2		432	692	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	226	586	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.297263537222281	3	FACETS	1	0.99	1	0.682	0.635	0.731	CLONAL	1	TRUE	1	0.374499061573553	3		586	1050	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884858	134884858	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	75	521	0	ENST00000398015.3:c.1634C>G	p.Ser545Trp	p.S545W	ENST00000398015	NM_004441.4	545	tCg/tGg	8/16	1	2	FACETS	0.449	0.392	0.51	0.449	0.392	0.51	SUBCLONAL	1	TRUE	1	0.374499061573553	2		521	892	SUCCESS
ATR	545	MSKCC	GRCh37	3	142232344	142232344	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	88	382	1	ENST00000350721.4:c.4640A>T	p.Glu1547Val	p.E1547V	ENST00000350721	NM_001184.3	1547	gAg/gTg	26/47	1	2	FACETS	0.52	0.46	0.585	0.52	0.46	0.585	SUBCLONAL	1	TRUE	1	0.374499061573553	2		383	903	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220707	1220707	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	155	421	1	ENST00000326873.7:c.725G>T	p.Gly242Val	p.G242V	ENST00000326873	NM_000455.4	242	gGg/gTg	5/10	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.374499061573553	2		422	622	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560503	65560503	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	212	525	1	ENST00000358664.4:c.94del	p.Glu32AsnfsTer33	p.E32Nfs*33	ENST00000358664	NM_002382.4	32	Gaa/aa	3/5	0.374499061573553	1	FACETS	0.906	0.841	0.972	0.906	0.841	0.972	CLONAL	1	TRUE	0	0.374499061573553	1		526	1016	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0006865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	150	232	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	0.423581944693997	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.423581944693997	1		232	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578513	7578549	+	frameshift_variant	Frame_Shift_Del	DEL	CTTGGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGG	CTTGGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGG	-	novel	NA	P-0006865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	46	379	0	ENST00000269305.4:c.381_417del	p.Asn131CysfsTer27	p.N131Cfs*27	ENST00000269305	NM_001126112.2	127	tcCCCTGCCCTCAACAAGATGTTTTGCCAACTGGCCAAG/tc	5/11	0.423581944693997	1	FACETS	0.301	0.253	0.355	0.301	0.253	0.355	SUBCLONAL	1	TRUE	0	0.423581944693997	1		379	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577584	7577585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTAC	novel	NA	P-0006869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	194	366	0	ENST00000269305.4:c.696_697insGTAG	p.His233ValfsTer8	p.H233Vfs*8	ENST00000269305	NM_001126112.2	232	-/GTAG	7/11	0.373956848389581	3	FACETS	1	0.981	1	0.754	0.704	0.805	CLONAL	2	FALSE	0	0.410056749627268	3		366	504	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106464	27106465	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	TT	novel	NA	P-0006869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	198	354	0	ENST00000324856.7:c.6075_6076delinsTT	p.Lys2025_Gln2026delinsAsnTer	p.K2025_Q2026delinsN*	ENST00000324856	NM_006015.4	2025	aaGCag/aaTTag	20/20	0.260715970893053	3	FACETS	0.872	0.817	0.927			1	CLONAL	3	FALSE	NA	0.410056749627268	3		354	445	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0006872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	158	203	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.486123629223969	4	FACETS	1	0.989	1	0.499	0.459	0.54	CLONAL	1	TRUE	1	0.51140214093801	4		203	624	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0006872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	289	429	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.366921480015841	2	FACETS	1	0.993	1	0.689	0.651	0.728	CLONAL	1	TRUE	0	0.51140214093801	2		429	820	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0006872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	258	431	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.368288021005534	4	FACETS	0.78	0.731	0.83	0.78	0.731	0.83	SUBCLONAL	2	TRUE	2	0.51140214093801	4		431	978	SUCCESS
APC	324	MSKCC	GRCh37	5	112175198	112175198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	151	196	1	ENST00000257430.4:c.3907C>T	p.Gln1303Ter	p.Q1303*	ENST00000257430	NM_000038.5	1303	Caa/Taa	16/16	0.368288021005534	4	FACETS	0.81	0.744	0.878	0.81	0.744	0.878	CLONAL	2	TRUE	2	0.51140214093801	4		197	551	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912173	114912173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1379	469	590	1	ENST00000543371.1:c.1243C>T	p.Pro415Ser	p.P415S	ENST00000543371	NM_001198531.1	415	Ccc/Tcc	11/14	0.291726221778545	4	FACETS	0.75	0.715	0.786	0.75	0.715	0.786	INDETERMINATE	2	TRUE	2	0.51140214093801	4		591	1848	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891674	28891674	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1763	115	479	0	ENST00000282397.4:c.3347G>C	p.Gly1116Ala	p.G1116A	ENST00000282397	NM_002019.4	1116	gGc/gCc	25/30	0.51140214093801	6	FACETS	0.484	0.434	0.538	0.097	0.086	0.108	SUBCLONAL	1	TRUE	1	0.51140214093801	6		479	1878	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0006888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	338	278	1	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.406076799822724	5	FACETS	0.893	0.85	0.936	0.893	0.85	0.936	CLONAL	4	TRUE	1	0.406076799822724	5		279	750	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0006888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	233	533	1	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	0.375486574023822	3	FACETS	0.932	0.879	0.984	0.932	0.879	0.984	CLONAL	3	TRUE	0	0.406076799822724	3		534	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0006888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	378	364	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.406076799822724	2	FACETS	0.964	0.918	1	0.964	0.918	1	CLONAL	2	TRUE	0	0.406076799822724	2		365	966	SUCCESS
APC	324	MSKCC	GRCh37	5	112174868	112174868	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085128	NA	P-0006888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	118	430	1	ENST00000257430.4:c.3577C>T	p.Gln1193Ter	p.Q1193*	ENST00000257430	NM_000038.5	1193	Cag/Tag	16/16	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.406076799822724	2		431	539	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141507	11141507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	340	562	0	ENST00000358026.2:c.3484G>A	p.Gly1162Ser	p.G1162S	ENST00000358026	NM_001128849.1	1162	Ggc/Agc	25/36	0.406076799822724	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.406076799822724	3		562	962	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270144	66270144	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs901722071	NA	P-0006888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	189	513	0	ENST00000273854.3:c.1738A>G	p.Thr580Ala	p.T580A	ENST00000273854	NM_004439.5	580	Aca/Gca	8/18	0.406076799822724	2	FACETS	1	0.934	1	0.505	0.467	0.545	CLONAL	1	TRUE	0	0.406076799822724	2		513	921	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576093	88576093	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	460	507	0	ENST00000360948.2:c.1580A>G	p.Asp527Gly	p.D527G	ENST00000360948	NM_001012338.2	527	gAc/gGc	13/19	0.406076799822724	3	FACETS	0.972	0.933	1	0.972	0.933	1	CLONAL	3	TRUE	0	0.406076799822724	3		507	935	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264341	30264341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	32	133	0	ENST00000322652.5:c.76G>A	p.Gly26Arg	p.G26R	ENST00000322652	NM_015355.2	26	Ggg/Agg	1/16	0.249809508179785	4	FACETS	0.789	0.642	0.952	0.394	0.321	0.476	CLONAL	1	TRUE	2	0.406076799822724	4		133	281	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012656	36012656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1288993928	NA	P-0006888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	149	163	0	ENST00000358208.4:c.100G>A	p.Ala34Thr	p.A34T	ENST00000358208		34	Gcc/Acc	2/12	0.406076799822724	7	FACETS	1	0.922	1	0.601	0.553	0.651	CLONAL	3	TRUE	2	0.406076799822724	7		163	492	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123040919	123040919	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	66	274	0	ENST00000355640.3:c.1382T>C	p.Val461Ala	p.V461A	ENST00000355640		461	gTt/gCt	7/7	0.385146658115437	1	FACETS	0.974	0.855	1	0.974	0.855	1	CLONAL	1	TRUE	0	0.406076799822724	1		274	266	SUCCESS
APC	324	MSKCC	GRCh37	5	112176027	112176028	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0006888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	75	388	0	ENST00000257430.4:c.4738_4739dup	p.Ser1581PhefsTer70	p.S1581Ffs*70	ENST00000257430	NM_000038.5	1579	att/atTAt	16/16	1	2	FACETS	0.73	0.641	0.825	0.73	0.641	0.825	SUBCLONAL	1	TRUE	1	0.406076799822724	2		388	506	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778072	27778089	+	inframe_deletion	In_Frame_Del	DEL	AGATCGCGCAGGACTTCA	AGATCGCGCAGGACTTCA	-	novel	NA	P-0006888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	517	1132	0	ENST00000369163.2:c.224_241del	p.Ile75_Lys80del	p.I75_K80del	ENST00000369163	NM_003536.2	74	gAGATCGCGCAGGACTTCAag/gag	1/1	0.335276097028335	3	FACETS	0.923	0.883	0.963	0.923	0.883	0.963	CLONAL	2	TRUE	1	0.406076799822724	3		1132	1660	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670432	88670434	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0006888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	503	525	1	ENST00000360948.2:c.1252_1254del	p.Pro418del	p.P418del	ENST00000360948	NM_001012338.2	418	CCT/-	11/19	0.406076799822724	3	FACETS	0.932	0.896	0.968	0.932	0.896	0.968	CLONAL	3	TRUE	0	0.406076799822724	3		526	1066	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566541	139566715	+	splice_acceptor_variant,splice_donor_variant,intron_variant	Splice_Site	DEL	GTGAGTGCCCCCACCCTCCAGAGCCCTCCTCCCGGGTCTGGGCCCAGTGGGCCTAGAGGGGCTACCCAGGCTTGGGGGTCGGGGGCGACCAAAGGCCAAGGGGCCAGTCAGATCTAGCTGGGCGGGGAGGCTGTGGGGAGCAGTGATCTCTGACCTTCGCCTCATCCAACCCTAG	GTGAGTGCCCCCACCCTCCAGAGCCCTCCTCCCGGGTCTGGGCCCAGTGGGCCTAGAGGGGCTACCCAGGCTTGGGGGTCGGGGGCGACCAAAGGCCAAGGGGCCAGTCAGATCTAGCTGGGCGGGGAGGCTGTGGGGAGCAGTGATCTCTGACCTTCGCCTCATCCAACCCTAG	-	novel	NA	P-0006888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	91	423	0	ENST00000308874.7:c.799+2_800del		p.X267_splice	ENST00000308874		267			0.406076799822724	3	FACETS	0.552	0.489	0.62	0.276	0.244	0.31	SUBCLONAL	1	TRUE	1	0.406076799822724	3		423	977	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727455	66727455	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs869025608	NA	P-0006903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	70	354	0	ENST00000307102.5:c.171G>C	p.Lys57Asn	p.K57N	ENST00000307102	NM_002755.3	57	aaG/aaC	2/11	1	2	FACETS	0.843	0.735	0.961	0.843	0.735	0.961	CLONAL	1	TRUE	1	0.25	2		354	664	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120417	70120422	+	inframe_deletion	In_Frame_Del	DEL	GCGCCC	GCGCCC	-	novel	NA	P-0006903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	136	374	0	ENST00000245479.2:c.1419_1424del	p.Gln473_Pro475delinsHis	p.Q473_P475delinsH	ENST00000245479	NM_000346.3	473	caGCGCCCc/cac	3/3	1	2	FACETS	0.837	0.763	0.914	1	0.989	1	CLONAL	2	TRUE	1	0.25	2		374	650	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094454	27094455	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	69	288	0	ENST00000324856.7:c.3163dup	p.Tyr1055LeufsTer50	p.Y1055Lfs*50	ENST00000324856	NM_006015.4	1054	-/T	11/20	0.3	2	FACETS	1	0.887	1			1	CLONAL	1	TRUE	NA	0.25	2		288	542	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0006913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	185	387	1	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.342272838443768	3	FACETS	1	0.989	1	0.718	0.663	0.774	CLONAL	1	TRUE	1	0.345465469556373	3		388	875	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006936-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	47	586	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.888	0.752	1	0.888	0.752	1	CLONAL	1	TRUE	1	0.29	2		586	365	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0006936-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	78	562	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.207034138156658	2	FACETS	1	0.973	1	0.691	0.611	0.777	CLONAL	1	TRUE	0	0.29	2		562	389	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205060	123205060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1364412973	NA	P-0006936-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	86	347	0	ENST00000218089.9:c.2420G>A	p.Arg807His	p.R807H	ENST00000218089	NM_001042749.1	807	cGt/cAt	25/35	1	1	FACETS	1	0.946	1	1	0.987	1	CLONAL	2	TRUE	0	0.29	1		347	235	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233763	133233763	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	47	548	0	ENST00000320574.5:c.3541A>G	p.Lys1181Glu	p.K1181E	ENST00000320574	NM_006231.2	1181	Aag/Gag	29/49	0.453502490651555	1	FACETS	0.369	0.311	0.432	0.369	0.311	0.432	SUBCLONAL	1	TRUE	0	0.447664374682921	1		548	442	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103513978	103513978	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	101	571	0	ENST00000355739.4:c.794A>G	p.Gln265Arg	p.Q265R	ENST00000355739	NM_000123.3	265	cAg/cGg	7/15	0.447664374682921	5	FACETS	0.844	0.753	0.94	0.281	0.251	0.314	CLONAL	1	TRUE	2	0.447664374682921	5		571	894	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266133	41266183	+	inframe_deletion	In_Frame_Del	DEL	CCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCC	CCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCC	-	novel	NA	P-0006946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	143	495	0	ENST00000349496.5:c.131_181del	p.Pro44_Ser60del	p.P44_S60del	ENST00000349496	NM_001904.3	44	CCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCC/-	3/15	0.335400758501947	4	FACETS	1	0.972	1	0.58	0.529	0.634	CLONAL	1	TRUE	2	0.447664374682921	4		495	797	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951085	17951085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	497	515	1	ENST00000458235.1:c.1208G>A	p.Arg403His	p.R403H	ENST00000458235	NM_000215.3	403	cGc/cAc	9/24	1	2	FACETS	0.974	0.935	1	0.974	0.935	1	CLONAL	1	TRUE	1	0.869198350773346	2		516	1174	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472652	88472652	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	292	246	0	ENST00000360948.2:c.1903G>C	p.Asp635His	p.D635H	ENST00000360948	NM_001012338.2	635	Gat/Cat	16/19	0.797909915275157	3	FACETS	0.966	0.91	1	0.483	0.455	0.512	CLONAL	1	TRUE	1	0.869198350773346	3		246	998	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929562	44929562	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	177	461	0	ENST00000377967.4:c.2662T>C	p.Ser888Pro	p.S888P	ENST00000377967	NM_021140.2	888	Tcc/Ccc	17/29	0.869198350773346	1	FACETS	0.416	0.386	0.448	0.416	0.386	0.448	SUBCLONAL	1	TRUE	0	0.869198350773346	1		461	553	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006972-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	173	586	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.554	0.51	0.599	0.554	0.51	0.599	SUBCLONAL	1	TRUE	1	0.816878369032753	2		586	765	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740467	58740467	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs773389405	NA	P-0006972-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	461	680	0	ENST00000305921.3:c.1372C>T	p.Arg458Ter	p.R458*	ENST00000305921	NM_003620.3	458	Cga/Tga	6/6	1	2	FACETS	0.968	0.926	1	0.968	0.926	1	CLONAL	1	TRUE	1	0.816878369032753	2		680	1166	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006989-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	145	160	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.898	0.831	0.966	0.898	0.831	0.966	CLONAL	1	TRUE	1	0.938695496161731	2		160	344	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061208	38061208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006989-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	62	268	0	ENST00000250448.2:c.781C>T	p.Arg261Cys	p.R261C	ENST00000250448	NM_004496.3	261	Cgc/Tgc	2/2	1	2	FACETS	0.323	0.28	0.37	0.323	0.28	0.37	SUBCLONAL	1	TRUE	1	0.938695496161731	2		268	409	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0006989-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	516	482	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	NA	2	FACETS	1	0.997	1			1	INDETERMINATE	1	TRUE	NA	0.938695496161731	2		482	824	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969323	44969323	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0006989-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	274	441	0	ENST00000377967.4:c.4006-1G>A		p.X1336_splice	ENST00000377967	NM_021140.2	1336			NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.938695496161731	2		441	460	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99162430	99162430	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1416263154	NA	P-0006989-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	252	339	0	ENST00000074304.5:c.950-2A>G		p.X317_splice	ENST00000074304	NM_001134224.1	317			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.938695496161731	2		339	531	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964793	15964793	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006989-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	485	607	0	ENST00000268712.3:c.5803G>T	p.Val1935Leu	p.V1935L	ENST00000268712	NM_006311.3	1935	Gtg/Ttg	37/46	1	2	FACETS	0.995	0.955	1	0.995	0.955	1	CLONAL	1	TRUE	1	0.938695496161731	2		607	1039	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872229	45872229	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006989-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	361	437	0	ENST00000391945.4:c.205A>G	p.Lys69Glu	p.K69E	ENST00000391945	NM_000400.3	69	Aaa/Gaa	4/23	1	2	FACETS	0.99	0.945	1	0.99	0.945	1	CLONAL	1	TRUE	1	0.938695496161731	2		437	777	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719113	52719113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006989-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	44	402	1	ENST00000322088.6:c.889G>A	p.Glu297Lys	p.E297K	ENST00000322088	NM_014225.5	297	Gag/Aag	7/15	1	2	FACETS	0.13	0.108	0.154	0.13	0.108	0.154	SUBCLONAL	1	TRUE	1	0.938695496161731	2		403	723	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440531	49440546	+	frameshift_variant	Frame_Shift_Del	DEL	ACTCCACACAACGCCA	ACTCCACACAACGCCA	-	novel	NA	P-0006989-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	285	431	0	ENST00000301067.7:c.4264_4279del	p.Trp1422ValfsTer79	p.W1422Vfs*79	ENST00000301067	NM_003482.3	1422	TGGCGTTGTGTGGAGTgt/gt	15/54	NA	2	FACETS	0.805	0.761	0.85			1	INDETERMINATE	1	TRUE	NA	0.938695496161731	2		431	754	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023219	27023232	+	frameshift_variant	Frame_Shift_Del	DEL	CCTAGGCCCGCCCT	CCTAGGCCCGCCCT	-	novel	NA	P-0006989-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	139	145	0	ENST00000324856.7:c.325_338del	p.Pro109GlufsTer3	p.P109Efs*3	ENST00000324856	NM_006015.4	109	CCTAGGCCCGCCCTg/g	1/20	1	2	FACETS	0.892	0.824	0.961	0.892	0.824	0.961	CLONAL	1	TRUE	1	0.938695496161731	2		145	332	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41554488	41554489	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0006989-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	256	419	0	ENST00000263253.7:c.3575dup	p.Tyr1192Ter	p.Y1192*	ENST00000263253	NM_001429.3	1192	tac/tAac	19/31	1	2	FACETS	0.689	0.647	0.731	0.689	0.647	0.731	SUBCLONAL	1	TRUE	1	0.938695496161731	2		419	792	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440525	49440526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006989-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	307	447	0	ENST00000301067.7:c.4284dup	p.Val1429CysfsTer3	p.V1429Cfs*3	ENST00000301067	NM_003482.3	1428	-/T	15/54	NA	2	FACETS	0.822	0.778	0.866			1	INDETERMINATE	1	TRUE	NA	0.938695496161731	2		447	796	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	70	160	0				ENST00000310581	NM_198253.2	-/1132			0.140490169758145	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.749775429438964	0		160	193	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0007000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	239	399	2	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.994	1	1	0.996	1	CLONAL	2	TRUE	1	0.749775429438964	2		401	280	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138729528	NA	P-0007000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	10	362	1	ENST00000269305.4:c.523C>T	p.Arg175Cys	p.R175C	ENST00000269305	NM_001126112.2	175	Cgc/Tgc	5/11	NA	2	FACETS	0.063	0.042	0.09			1	INDETERMINATE	1	TRUE	NA	0.749775429438964	2		363	422	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	186	379	0	ENST00000335508.6:c.2704G>C	p.Glu902Gln	p.E902Q	ENST00000335508	NM_012433.2	902	Gaa/Caa	18/25	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.749775429438964	2		379	466	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526179	189526179	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	382	453	0	ENST00000264731.3:c.443C>A	p.Pro148His	p.P148H	ENST00000264731	NM_003722.4	148	cCc/cAc	4/14	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.749775429438964	2		453	858	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468297	50468297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343071492	NA	P-0007000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	98	245	1	ENST00000331340.3:c.1532G>A	p.Arg511Gln	p.R511Q	ENST00000331340	NM_006060.4	511	cGa/cAa	8/8	0.140490169758145	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.749775429438964	0		246	247	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737627	145737627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771349728	NA	P-0007000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	217	464	1	ENST00000428558.2:c.3136G>A	p.Glu1046Lys	p.E1046K	ENST00000428558	NM_004260.3	1046	Gag/Aag	19/22	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.749775429438964	2		465	523	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801080	135801080	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	48	416	0	ENST00000298552.3:c.257G>T	p.Arg86Leu	p.R86L	ENST00000298552	NM_001162426.1	86	cGt/cTt	5/23	0.749775429438964	1	FACETS	0.159	0.134	0.186	0.159	0.134	0.186	SUBCLONAL	1	TRUE	0	0.749775429438964	1		416	504	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817882	3817882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757051244	NA	P-0007000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	31	397	0	ENST00000262367.5:c.3089C>T	p.Ser1030Phe	p.S1030F	ENST00000262367	NM_004380.2	1030	tCc/tTc	16/31	1	2	FACETS	0.157	0.126	0.191	0.157	0.126	0.191	SUBCLONAL	1	TRUE	1	0.749775429438964	2		397	528	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969322	44969322	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0007000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	200	468	0	ENST00000377967.4:c.4006-2A>C		p.X1336_splice	ENST00000377967	NM_021140.2	1336			0.509113375183768	1	FACETS	0.961	0.908	1	0.961	0.908	1	CLONAL	1	TRUE	0	0.749775429438964	1		468	347	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0007003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	27	551	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.802	1	1	0.802	1	CLONAL	1	TRUE	1	0.21	2		551	256	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280418	1280418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759017540	NA	P-0007003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	12	314	0	ENST00000310581.5:c.1805C>T	p.Ser602Leu	p.S602L	ENST00000310581	NM_198253.2	602	tCg/tTg	4/16	1	2	FACETS	0.563	0.396	0.768	0.563	0.396	0.768	SUBCLONAL	1	TRUE	1	0.21	2		314	203	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159748	20159748	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	42	495	0	ENST00000379607.5:c.11A>G	p.Asn4Ser	p.N4S	ENST00000379607	NM_001412.3	4	aAt/aGt	1/7	0.11946505578393	1	FACETS	1	0.926	1	1	0.926	1	INDETERMINATE	1	TRUE	0	0.21	1		495	300	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665752	29665755	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1555535032	NA	P-0007010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	328	413	0	ENST00000356175.3:c.6789_6792del	p.Tyr2264ThrfsTer5	p.Y2264Tfs*5	ENST00000356175	NM_000267.3	2263	ACTTac/ac	45/57	0.838999178816656	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.838999178816656	1		413	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577095	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519984	NA	P-0007020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	429	621	0	ENST00000269305.4:c.843C>G	p.Asp281Glu	p.D281E	ENST00000269305	NM_001126112.2	281	gaC/gaG	8/11	0.775454503196141	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.775454503196141	1		621	664	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519660	176519660	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	476	396	0	ENST00000292408.4:c.932A>G	p.Asn311Ser	p.N311S	ENST00000292408	NM_213647.1	311	aAt/aGt	8/18	0.775454503196141	2	FACETS	0.993	0.967	1	0.993	0.967	1	CLONAL	2	TRUE	0	0.775454503196141	2		396	618	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829789	76829789	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	319	701	1	ENST00000373344.5:c.6252C>A	p.Tyr2084Ter	p.Y2084*	ENST00000373344	NM_000489.3	2084	taC/taA	28/35	0.775454503196141	1	FACETS	0.549	0.52	0.579	0.549	0.52	0.579	SUBCLONAL	1	TRUE	0	0.775454503196141	1		702	917	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058534	72058535	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0007020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	1201	805	1	ENST00000357731.5:c.905dup	p.Leu303AlafsTer11	p.L303Afs*11	ENST00000357731	NM_173808.2	302	aag/aaAg	6/7	0.775454503196141	2	FACETS	0.948	0.931	0.965	0.948	0.931	0.965	CLONAL	2	TRUE	0	0.775454503196141	2		806	1634	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937086	48937094	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TAGATGAGG	TAGATGAGG	-	novel	NA	P-0007020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	423	308	0	ENST00000267163.4:c.856_861+3del		p.X286_splice	ENST00000267163	NM_000321.2	286		8/27	0.775454503196141	2	FACETS	0.921	0.892	0.95	0.921	0.892	0.95	CLONAL	2	TRUE	0	0.775454503196141	2		308	592	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807887	3807887	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	803	504	1	ENST00000262367.5:c.3532del	p.Cys1178AlafsTer72	p.C1178Afs*72	ENST00000262367	NM_004380.2	1178	Tgc/gc	18/31	0.775454503196141	3	FACETS	0.986	0.958	1	0.986	0.958	1	CLONAL	2	TRUE	1	0.775454503196141	3		505	1457	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201707	67201714	+	frameshift_variant	Frame_Shift_Del	DEL	TCTGGCCT	TCTGGCCT	-	novel	NA	P-0007020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	382	611	0	ENST00000312629.5:c.1008_1015del	p.Leu337AlafsTer20	p.L337Afs*20	ENST00000312629	NM_003952.2	336	ctTCTGGCCTgg/ctgg	12/15	1	2	FACETS	0.836	0.795	0.879	0.836	0.795	0.879	CLONAL	1	TRUE	1	0.775454503196141	2		611	1178	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120612013	120612014	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0007027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	12	53	0	ENST00000256646.2:c.7_8delinsTT	p.Ala3Phe	p.A3F	ENST00000256646	NM_024408.3	3	GCc/TTc	1/34	1	2	FACETS	0.285	0.202	0.386	0.285	0.202	0.386	SUBCLONAL	1	TRUE	1	0.786300998874185	2		53	107	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717704	89717704	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	341	336	0	ENST00000371953.3:c.731del	p.Pro244LeufsTer12	p.P244Lfs*12	ENST00000371953	NM_000314.4	243	ttC/tt	7/9	0.786300998874185	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.786300998874185	1		336	520	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007341	143007341	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	137	352	0	ENST00000262992.4:c.2443T>A	p.Ser815Thr	p.S815T	ENST00000262992	NM_001101669.1	815	Tcc/Acc	22/24	1	2	FACETS	0.442	0.402	0.484	0.442	0.402	0.484	SUBCLONAL	1	TRUE	1	0.786300998874185	2		352	789	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335724	81335724	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	278	290	0	ENST00000222390.5:c.1636G>A	p.Ala546Thr	p.A546T	ENST00000222390	NM_000601.4	546	Gct/Act	15/18	0.736630448505201	3	FACETS	0.889	0.835	0.945	0.445	0.417	0.473	CLONAL	1	TRUE	1	0.786300998874185	3		290	1108	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589146	67589148	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	novel	NA	P-0007027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	220	277	0	ENST00000274335.5:c.1134_1136del	p.Asn378del	p.N378del	ENST00000274335		378	aaCAAa/aaa	9/15	1	2	FACETS	0.768	0.717	0.82	0.768	0.717	0.82	SUBCLONAL	1	TRUE	1	0.786300998874185	2		277	729	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295173	1295173	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0007033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	33	143	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		143	166	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435202	18435202	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007043-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	121	539	2	ENST00000266497.5:c.187T>A	p.Phe63Ile	p.F63I	ENST00000266497		63	Ttt/Att	1/31	1	2	FACETS	1	0.936	1	1	0.99	1	CLONAL	2	FALSE	1	0.323626321775742	2		541	363	SUCCESS
APC	324	MSKCC	GRCh37	5	112177782	112177798	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCACGAATTCTAAAA	GCCCACGAATTCTAAAA	-	novel	NA	P-0007043-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	107	354	0	ENST00000257430.4:c.6491_6507del	p.Gly2164AlafsTer10	p.G2164Afs*10	ENST00000257430	NM_000038.5	2164	gGCCCACGAATTCTAAAA/g	16/16	0.323626321775742	0	FACETS	0.734	0.676	0.792			1	SUBCLONAL	3	FALSE	0	0.323626321775742	0		354	203	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060911	38060912	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0007043-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	112	418	0	ENST00000250448.2:c.1076_1077dup	p.Ile360ProfsTer2	p.I360Pfs*2	ENST00000250448	NM_004496.3	359	-/CC	2/2	0.247175780411004	0	FACETS	0.788	0.73	0.846			1	SUBCLONAL	3	FALSE	0	0.323626321775742	0		418	198	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279861	46279866	+	inframe_deletion	In_Frame_Del	DEL	CAGCAA	CAGCAA	-	rs748517056	NA	P-0007053-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	28	192	1	ENST00000371998.3:c.3810_3815del	p.Gln1275_Gln1276del	p.Q1275_Q1276del	ENST00000371998		1263	CAGCAA/-	20/23	0.552372357065723	3	FACETS	0.481	0.385	0.589	0.16	0.128	0.197	SUBCLONAL	1	TRUE	0	0.552372357065723	3		193	269	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	342	939	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.592420564064	4	FACETS	0.938	0.891	0.985	0.938	0.891	0.985	CLONAL	2	TRUE	2	0.740955799437711	4		940	857	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399975	139399975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374352922	NA	P-0007063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	489	437	0	ENST00000277541.6:c.4373C>T	p.Ala1458Val	p.A1458V	ENST00000277541	NM_017617.3	1458	gCg/gTg	25/34	0.642714507702913	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.740955799437711	4		437	1129	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579432	7579433	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0007063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	391	379	0	ENST00000269305.4:c.254dup	p.Ala86CysfsTer63	p.A86Cfs*63	ENST00000269305	NM_001126112.2	85	cct/ccCt	4/11	0.740955799437711	2	FACETS	0.924	0.892	0.955	0.924	0.892	0.955	CLONAL	2	TRUE	0	0.740955799437711	2		379	571	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492900	56492930	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGAGGGCAGCCAGCTGCAGCTGGTGGCCA	CCAGAGGGCAGCCAGCTGCAGCTGGTGGCCA	-	novel	NA	P-0007063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	197	162	0	ENST00000407977.2:c.9_39del	p.Gly4ProfsTer4	p.G4Pfs*4	ENST00000407977		3	ggTGGCCACCAGCTGCAGCTGGCTGCCCTCTGG/gg	2/10	0.642714507702913	4	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	2	0.740955799437711	4		162	463	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096297	178096298	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGGAGT	novel	NA	P-0007063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	475	436	0	ENST00000397062.3:c.1028_1033dup	p.Asp343_Ser344dup	p.D343_S344dup	ENST00000397062	NM_006164.4	343	ggc/gACTCCGgc	5/5	0.592420564064	4	FACETS	0.941	0.901	0.981	0.941	0.901	0.981	CLONAL	2	TRUE	2	0.740955799437711	4		436	1186	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007101-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	343	586	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.496205833492592	6	FACETS	0.952	0.908	0.997			1	CLONAL	4	TRUE	NA	0.496205833492592	6		586	723	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721063	61721063	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007101-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	121	401	0	ENST00000401558.2:c.1211C>G	p.Pro404Arg	p.P404R	ENST00000401558	NM_003400.3	404	cCc/cGc	12/25	0.338313118215433	5	FACETS	0.87	0.79	0.953	0.58	0.527	0.635	CLONAL	2	TRUE	2	0.496205833492592	5		401	489	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401636	401636	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007101-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	322	328	1	ENST00000380956.4:c.958G>T	p.Ala320Ser	p.A320S	ENST00000380956	NM_001195286.1	320	Gcc/Tcc	7/9	0.496205833492592	9	FACETS	1	0.981	1	1	0.981	1	CLONAL	6	TRUE	3	0.496205833492592	9		329	566	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190398	32190398	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007101-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	336	393	1	ENST00000375023.3:c.341G>T	p.Cys114Phe	p.C114F	ENST00000375023	NM_004557.3	114	tGc/tTc	3/30	0.496205833492592	5	FACETS	0.957	0.915	0.999			1	CLONAL	4	TRUE	NA	0.496205833492592	5		394	617	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005551	150005551	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007101-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	155	403	0	ENST00000253339.5:c.674A>T	p.Gln225Leu	p.Q225L	ENST00000253339		225	cAa/cTa	3/7	0.291800760798108	3	FACETS	1	0.938	1	0.675	0.626	0.725	INDETERMINATE	2	TRUE	0	0.496205833492592	3		403	385	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508623	106508623	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007101-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	54	245	0	ENST00000359195.3:c.617C>A	p.Pro206His	p.P206H	ENST00000359195	NM_002649.2	206	cCc/cAc	2/11	0.496205833492592	3	FACETS	0.783	0.672	0.903	0.391	0.336	0.452	CLONAL	1	TRUE	1	0.496205833492592	3		245	347	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877898	151877898	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007101-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	74	259	0	ENST00000262189.6:c.7047C>G	p.Phe2349Leu	p.F2349L	ENST00000262189	NM_170606.2	2349	ttC/ttG	36/59	0.496205833492592	3	FACETS	0.878	0.772	0.991	0.439	0.386	0.496	CLONAL	1	TRUE	1	0.496205833492592	3		259	424	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341196	8341196	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs138775068	NA	P-0007101-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	144	420	0	ENST00000356435.5:c.5020C>A	p.Arg1674Ser	p.R1674S	ENST00000356435		1674	Cgc/Agc	30/35	0.338313118215433	5	FACETS	1	0.953	1	0.702	0.644	0.761	CLONAL	2	TRUE	2	0.496205833492592	5		420	481	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376769	118376769	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007101-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	176	295	1	ENST00000534358.1:c.10162G>T	p.Ala3388Ser	p.A3388S	ENST00000534358	NM_005933.3	3388	Gct/Tct	27/36	0.496205833492592	3	FACETS	0.851	0.797	0.904	0.851	0.797	0.904	CLONAL	3	TRUE	0	0.496205833492592	3		296	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782620	NA	P-0007101-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	175	384	0	ENST00000269305.4:c.427G>A	p.Val143Met	p.V143M	ENST00000269305	NM_001126112.2	143	Gtg/Atg	5/11	0.358707386998448	3	FACETS	1	0.985	1	0.787	0.735	0.838	CLONAL	2	TRUE	0	0.496205833492592	3		384	373	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207144	1207144	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0007101-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	236	482	0	ENST00000326873.7:c.232A>T	p.Lys78Ter	p.K78*	ENST00000326873	NM_000455.4	78	Aag/Tag	1/10	0.496205833492592	2	FACETS	0.915	0.863	0.967	0.915	0.863	0.967	CLONAL	2	TRUE	0	0.496205833492592	2		482	520	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621854	1621854	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007101-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	98	444	0	ENST00000344749.5:c.938G>T	p.Gly313Val	p.G313V	ENST00000344749	NM_001136139.2	313	gGg/gTg	11/19	0.496205833492592	2	FACETS	0.902	0.822	0.982	0.902	0.822	0.982	CLONAL	2	TRUE	0	0.496205833492592	2		444	219	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0007108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	283	578	1	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	0.50197699354857	1	FACETS	0.983	0.927	1	0.983	0.927	1	CLONAL	1	TRUE	0	0.50197699354857	1		579	859	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267290	41267290	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	286	410	0	ENST00000349496.5:c.874A>G	p.Lys292Glu	p.K292E	ENST00000349496	NM_001904.3	292	Aaa/Gaa	6/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.50197699354857	2		410	1042	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287349	38287349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	96	436	1	ENST00000425967.3:c.308G>T	p.Gly103Val	p.G103V	ENST00000425967	NM_001174067.1	103	gGg/gTg	4/19	1	2	FACETS	0.379	0.337	0.424	0.379	0.337	0.424	SUBCLONAL	1	TRUE	1	0.50197699354857	2		437	1009	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760438	133760438	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	219	393	0	ENST00000318560.5:c.2761G>T	p.Glu921Ter	p.E921*	ENST00000318560	NM_005157.4	921	Gag/Tag	11/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.50197699354857	2		393	813	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945028	31945028	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs773583960	NA	P-0007108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	295	510	0	ENST00000340398.3:c.73G>T	p.Ala25Ser	p.A25S	ENST00000340398	NM_001013699.2	25	Gct/Tct	1/1	0.219462174485244	1	FACETS	0.749	0.705	0.795	0.749	0.705	0.795	INDETERMINATE	1	TRUE	0	0.50197699354857	1		510	1175	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779578	3779578	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	300	587	0	ENST00000262367.5:c.5470G>A	p.Ala1824Thr	p.A1824T	ENST00000262367	NM_004380.2	1824	Gcc/Acc	31/31	1	2	FACETS	0.91	0.856	0.966	0.91	0.856	0.966	CLONAL	1	TRUE	1	0.50197699354857	2		587	1313	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958295	11958295	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	116	172	0	ENST00000353533.5:c.205C>T	p.Gln69Ter	p.Q69*	ENST00000353533	NM_003010.3	69	Caa/Taa	2/11	0.50197699354857	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.50197699354857	1		172	324	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0007114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	146	525	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.3	2		525	972	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0007114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	140	360	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.975	0.887	1	0.975	0.887	1	CLONAL	1	TRUE	1	0.3	2		360	957	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539765	187539765	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	97	475	0	ENST00000441802.2:c.7975G>T	p.Glu2659Ter	p.E2659*	ENST00000441802	NM_005245.3	2659	Gag/Tag	10/27	1	2	FACETS	0.631	0.561	0.706	0.631	0.561	0.706	SUBCLONAL	1	TRUE	1	0.3	2		475	1025	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911973	32911973	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	304	794	0	ENST00000380152.3:c.3481G>T	p.Asp1161Tyr	p.D1161Y	ENST00000380152		1161	Gat/Tat	11/27	0.168288132289297	1	FACETS	1	0.989	1	1	0.989	1	INDETERMINATE	1	TRUE	0	0.3	1		794	1408	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134379	41134379	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1288	299	763	0	ENST00000379561.5:c.1249C>T	p.Pro417Ser	p.P417S	ENST00000379561	NM_002015.3	417	Ccc/Tcc	2/3	0.168288132289297	1	FACETS	1	0.974	1	1	0.974	1	INDETERMINATE	1	TRUE	0	0.3	1		763	1587	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637606	23637606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881890	NA	P-0007114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	90	520	1	ENST00000261584.4:c.2699C>T	p.Ala900Val	p.A900V	ENST00000261584	NM_024675.3	900	gCt/gTt	7/13	0.3	1	FACETS	0.468	0.414	0.526	0.468	0.414	0.526	SUBCLONAL	1	TRUE	0	0.3	1		521	1089	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220434	1220434	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1064794805	NA	P-0007114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	199	511	0	ENST00000326873.7:c.527A>G	p.Asp176Gly	p.D176G	ENST00000326873	NM_000455.4	176	gAc/gGc	4/10	0.3	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.3	1		511	1048	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600323	10600323	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0007114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	172	398	0	ENST00000171111.5:c.1531+1G>T		p.X511_splice	ENST00000171111	NM_203500.1	511			0.3	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.3	1		398	844	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144182	11144182	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	129	335	0	ENST00000358026.2:c.3763G>T	p.Glu1255Ter	p.E1255*	ENST00000358026	NM_001128849.1	1255	Gag/Tag	26/36	0.3	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.3	1		335	648	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156540	106156540	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1340173182	NA	P-0007118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	203	391	0	ENST00000380013.4:c.1441C>T	p.Gln481Ter	p.Q481*	ENST00000380013	NM_001127208.2	481	Cag/Tag	3/11	1	2	FACETS	0.926	0.858	0.995	0.926	0.858	0.995	CLONAL	1	TRUE	1	0.457363526684348	2		391	959	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0007118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	283	585	0	ENST00000269305.4:c.838A>T	p.Arg280Ter	p.R280*	ENST00000269305	NM_001126112.2	280	Aga/Tga	8/11	0.436974981627801	1	FACETS	0.946	0.89	1	0.946	0.89	1	CLONAL	1	TRUE	0	0.457363526684348	1		585	1009	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131447	17131447	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	127	248	0	ENST00000285071.4:c.5A>G	p.Asn2Ser	p.N2S	ENST00000285071	NM_144997.5	2	aAt/aGt	4/14	0.436974981627801	1	FACETS	0.75	0.682	0.821	0.75	0.682	0.821	SUBCLONAL	1	TRUE	0	0.457363526684348	1		248	571	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30311727	30311727	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	259	530	1	ENST00000262643.3:c.581C>A	p.Ser194Ter	p.S194*	ENST00000262643	NM_001238.2	194	tCa/tAa	7/12	0.457363526684348	1	FACETS	0.859	0.805	0.914	0.859	0.805	0.914	CLONAL	1	TRUE	0	0.457363526684348	1		531	1017	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253804	153253805	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	186	378	0	ENST00000281708.4:c.928dup	p.Tyr310LeufsTer7	p.Y310Lfs*7	ENST00000281708	NM_033632.3	310	tac/tTac	6/12	1	2	FACETS	0.798	0.737	0.862	0.798	0.737	0.862	SUBCLONAL	1	TRUE	1	0.457363526684348	2		378	1019	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880985	37880985	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	331	497	0	ENST00000269571.5:c.2314del	p.Tyr772ThrfsTer2	p.Y772Tfs*2	ENST00000269571		772	Tac/ac	20/27	0.139845258383771	3	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.457363526684348	3		497	1436	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530418	187530419	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	251	520	0	ENST00000441802.2:c.10124dup	p.Asp3376ArgfsTer11	p.D3376Rfs*11	ENST00000441802	NM_005245.3	3375	ata/atTa	16/27	1	2	FACETS	0.896	0.837	0.957	0.896	0.837	0.957	CLONAL	1	TRUE	1	0.457363526684348	2		520	1225	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0007121-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	62	565	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.3	2	FACETS	1	0.967	1			1	CLONAL	1	TRUE	NA	0.11	2		565	783	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782177	NA	P-0007121-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	74	534	0	ENST00000269305.4:c.644G>T	p.Ser215Ile	p.S215I	ENST00000269305	NM_001126112.2	215	aGt/aTt	6/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.11	2		534	1112	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158594123	158594123	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007121-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1455	111	667	1	ENST00000263640.3:c.1450G>T	p.Ala484Ser	p.A484S	ENST00000263640	NM_001105.4	484	Gca/Tca	11/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.11	2		668	1566	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522532	157522532	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1273529067	NA	P-0007121-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	55	606	0	ENST00000346085.5:c.4804A>G	p.Ile1602Val	p.I1602V	ENST00000346085	NM_020732.3	1602	Atc/Gtc	18/20	1	2	FACETS	0.923	0.787	1	0.923	0.787	1	CLONAL	1	TRUE	1	0.11	2		606	1083	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467821	50467821	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007121-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	34	318	0	ENST00000331340.3:c.1056G>T	p.Lys352Asn	p.K352N	ENST00000331340	NM_006060.4	352	aaG/aaT	8/8	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.11	2		318	530	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526687	106526687	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007121-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	49	342	0	ENST00000359195.3:c.2980G>T	p.Val994Leu	p.V994L	ENST00000359195	NM_002649.2	994	Gtg/Ttg	10/11	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.11	2		342	814	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602715	10602715	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007121-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	44	472	1	ENST00000171111.5:c.863G>T	p.Cys288Phe	p.C288F	ENST00000171111	NM_203500.1	288	tGc/tTc	3/6	1	2	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	TRUE	1	0.11	2		473	783	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152006	11152018	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGATCGAAGAG	GGAGATCGAAGAG	-	novel	NA	P-0007121-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	39	332	0	ENST00000358026.2:c.4291_4303del	p.Glu1431ArgfsTer60	p.E1431Rfs*60	ENST00000358026	NM_001128849.1	1430	gaGGAGATCGAAGAG/ga	31/36	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.11	2		332	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0007124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	380	313	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.751537356706725	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.751706360329102	3		313	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0007124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	51	1128	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.751537356706725	3	FACETS	0.454	0.387	0.528	0.151	0.129	0.176	SUBCLONAL	1	TRUE	0	0.751706360329102	3		1129	411	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556079	29556079	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886041347	NA	P-0007124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	33	270	0	ENST00000356175.3:c.2446C>T	p.Arg816Ter	p.R816*	ENST00000356175	NM_000267.3	816	Cga/Tga	21/57	0.540312187730864	0	FACETS		NA	1			1	NA	1	TRUE	0	0.751706360329102	0		270	77	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156716	55156717	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0007124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	674	248	0	ENST00000257290.5:c.3120_3121del	p.His1040GlnfsTer6	p.H1040Qfs*6	ENST00000257290	NM_006206.4	1039	agACac/agac	22/23	0.751706360329102	13	FACETS	1	0.992	1			1	CLONAL	10	TRUE	NA	0.751706360329102	13		248	890	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813013	76813014	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0007124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	183	302	0	ENST00000373344.5:c.6607_6608delinsTT	p.Glu2203Leu	p.E2203L	ENST00000373344	NM_000489.3	2203	GAg/TTg	30/35	0.504974179217567	2	FACETS	1	0.986	1			1	CLONAL	2	TRUE	NA	0.751706360329102	2		302	228	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0007134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	151	741	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.488421300564788	4	FACETS	0.939	0.865	1	0.626	0.576	0.677	CLONAL	2	FALSE	1	0.488459275232886	4		742	490	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553747	106553747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	45	481	0	ENST00000369096.4:c.1712G>A	p.Gly571Asp	p.G571D	ENST00000369096	NM_001198.3	571	gGc/gAc	5/7	0.488459275232886	5	FACETS	0.602	0.506	0.709			1	SUBCLONAL	1	FALSE	NA	0.488459275232886	5		481	530	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0007137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	19	392	1	ENST00000374080.3:c.3670C>T	p.Leu1224Phe	p.L1224F	ENST00000374080		1224	Ctc/Ttc	26/45	1	1	FACETS	0.087	0.065	0.112	0.087	0.065	0.112	SUBCLONAL	1	TRUE	0	0.446530419845366	1		393	763	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70432756	70432756	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	38	547	0	ENST00000373644.4:c.4778G>C	p.Ser1593Thr	p.S1593T	ENST00000373644	NM_030625.2	1593	aGc/aCc	8/12	1	2	FACETS	0.255	0.21	0.306	0.255	0.21	0.306	SUBCLONAL	1	TRUE	1	0.446530419845366	2		547	667	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0007140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	156	297	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.345843668747767	1	FACETS	0.445	0.407	0.485	0.445	0.407	0.485	SUBCLONAL	1	TRUE	0	0.557720350136861	1		298	906	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587780070	NA	P-0007140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	378	332	0	ENST00000269305.4:c.535C>G	p.His179Asp	p.H179D	ENST00000269305	NM_001126112.2	179	Cat/Gat	5/11	0.557720350136861	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.557720350136861	1		332	694	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0007140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	340	370	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	0.345843668747767	1	FACETS	0.746	0.706	0.788	0.746	0.706	0.788	SUBCLONAL	1	TRUE	0	0.557720350136861	1		370	1178	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913250	NA	P-0007140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	368	316	0	ENST00000369535.4:c.34G>T	p.Gly12Cys	p.G12C	ENST00000369535	NM_002524.4	12	Ggt/Tgt	2/7	0.256236656210244	1	FACETS	1	0.951	1	1	0.951	1	INDETERMINATE	1	TRUE	0	0.557720350136861	1		316	952	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166200	32166200	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1222	96	397	1	ENST00000375023.3:c.4754C>A	p.Pro1585His	p.P1585H	ENST00000375023	NM_004557.3	1585	cCt/cAt	26/30	0.138034252818479	3	FACETS	0.334	0.296	0.375	0.111	0.098	0.125	INDETERMINATE	1	TRUE	0	0.557720350136861	3		398	1318	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157454306	157454306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141030037	NA	P-0007140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	90	292	0	ENST00000346085.5:c.2516C>T	p.Thr839Ile	p.T839I	ENST00000346085	NM_020732.3	839	aCt/aTt	8/20	0.138034252818479	3	FACETS	0.409	0.361	0.459	0.136	0.12	0.153	INDETERMINATE	1	TRUE	0	0.557720350136861	3		292	1010	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435656	18435656	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757769822	NA	P-0007140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	57	260	0	ENST00000266497.5:c.641C>T	p.Pro214Leu	p.P214L	ENST00000266497		214	cCc/cTc	1/31	0.345843668747767	1	FACETS	0.212	0.181	0.245	0.212	0.181	0.245	SUBCLONAL	1	TRUE	0	0.557720350136861	1		260	696	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519865	66519865	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0007140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	53	261	0	ENST00000358598.2:c.349-1G>T		p.X117_splice	ENST00000358598	NM_212471.2	117			0.557720350136861	1	FACETS	0.181	0.153	0.211	0.181	0.153	0.211	SUBCLONAL	1	TRUE	0	0.557720350136861	1		261	759	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591808	48591808	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	182	318	0	ENST00000342988.3:c.971G>T	p.Cys324Phe	p.C324F	ENST00000342988	NM_005359.5	324	tGt/tTt	9/12	0.557720350136861	1	FACETS	0.834	0.775	0.896	0.834	0.775	0.896	CLONAL	1	TRUE	0	0.557720350136861	1		318	564	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593466	48593466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064796102	NA	P-0007140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	78	355	0	ENST00000342988.3:c.1217C>T	p.Ala406Val	p.A406V	ENST00000342988	NM_005359.5	406	gCg/gTg	10/12	0.557720350136861	1	FACETS	0.237	0.208	0.269	0.237	0.208	0.269	SUBCLONAL	1	TRUE	0	0.557720350136861	1		355	851	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161913	47161913	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0007141-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	61	414	0	ENST00000409792.3:c.4213A>T	p.Lys1405Ter	p.K1405*	ENST00000409792	NM_014159.6	1405	Aaa/Taa	3/21	0.180189696638075	3	FACETS	0.994	0.865	1	0.663	0.576	0.755	CLONAL	2	FALSE	0	0.234869182285816	3		414	292	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52661288	52661288	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0007141-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	58	570	0	ENST00000394830.3:c.1541+1G>T		p.X514_splice	ENST00000394830	NM_018313.4	514			0.180189696638075	3	FACETS	0.844	0.729	0.967	0.563	0.486	0.645	CLONAL	2	FALSE	0	0.234869182285816	3		570	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572929	7572929	+	stop_lost	Nonstop_Mutation	SNP	A	A	T	novel	NA	P-0007141-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	163	605	1	ENST00000269305.4:c.1180T>A	p.Ter394ArgextTer9	p.*394Rext*9	ENST00000269305	NM_001126112.2	394	Tga/Aga	11/11	0.234869182285816	5	FACETS	1	0.981	1	0.817	0.751	0.885	CLONAL	2	FALSE	2	0.234869182285816	5		606	766	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981509	55981509	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007141-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	49	511	0	ENST00000263923.4:c.428del	p.Asn143ThrfsTer5	p.N143Tfs*5	ENST00000263923	NM_002253.2	143	aAc/ac	4/30	0.234869182285816	3	FACETS	0.918	0.784	1	0.918	0.784	1	CLONAL	2	FALSE	1	0.234869182285816	3		511	254	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0007144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	216	332	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	1	2	FACETS	0.995	0.926	1	0.995	0.926	1	CLONAL	1	TRUE	1	0.458347897105594	2		332	947	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0007144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	296	514	0	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	0.456262348298346	1	FACETS	0.966	0.91	1	0.966	0.91	1	CLONAL	1	TRUE	0	0.458347897105594	1		514	1031	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367257	50367257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1245618829	NA	P-0007144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	129	317	1	ENST00000331340.3:c.64G>A	p.Asp22Asn	p.D22N	ENST00000331340	NM_006060.4	22	Gat/Aat	3/8	1	2	FACETS	0.72	0.653	0.79	0.72	0.653	0.79	SUBCLONAL	1	TRUE	1	0.458347897105594	2		318	782	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597394	52597394	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	233	566	0	ENST00000394830.3:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000394830	NM_018313.4	1306	Gaa/Taa	25/30	0.376931051397269	1	FACETS	0.717	0.668	0.767	0.717	0.668	0.767	SUBCLONAL	1	TRUE	0	0.458347897105594	1		566	1093	SUCCESS
ATR	545	MSKCC	GRCh37	3	142168429	142168429	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	100	309	0	ENST00000350721.4:c.7777C>A	p.Leu2593Ile	p.L2593I	ENST00000350721	NM_001184.3	2593	Ctt/Att	47/47	1	2	FACETS	0.562	0.501	0.626	0.562	0.501	0.626	SUBCLONAL	1	TRUE	1	0.458347897105594	2		309	777	SUCCESS
APC	324	MSKCC	GRCh37	5	112174602	112174602	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	298	574	0	ENST00000257430.4:c.3311C>A	p.Ser1104Ter	p.S1104*	ENST00000257430	NM_000038.5	1104	tCa/tAa	16/16	1	2	FACETS	0.953	0.896	1	0.953	0.896	1	CLONAL	1	TRUE	1	0.458347897105594	2		574	1364	SUCCESS
APC	324	MSKCC	GRCh37	5	112175642	112175642	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	350	576	0	ENST00000257430.4:c.4351G>T	p.Glu1451Ter	p.E1451*	ENST00000257430	NM_000038.5	1451	Gaa/Taa	16/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.458347897105594	2		576	1460	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866644	117866644	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1767	383	757	1	ENST00000297338.2:c.1001G>T	p.Ser334Ile	p.S334I	ENST00000297338	NM_006265.2	334	aGc/aTc	9/14	0.417921541599559	3	FACETS	0.955	0.904	1	0.478	0.452	0.505	CLONAL	1	TRUE	1	0.458347897105594	3		758	2150	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653829	89653829	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554893808	NA	P-0007144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	131	379	0	ENST00000371953.3:c.127G>T	p.Glu43Ter	p.E43*	ENST00000371953	NM_000314.4	43	Gaa/Taa	2/9	0.400666207173223	1	FACETS	0.726	0.661	0.794	0.726	0.661	0.794	SUBCLONAL	1	TRUE	0	0.458347897105594	1		379	607	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	346	598	1	ENST00000543371.1:c.1411C>A	p.Arg471Ser	p.R471S	ENST00000543371	NM_001198531.1	471	Cgc/Agc	14/14	1	2	FACETS	0.991	0.936	1	0.991	0.936	1	CLONAL	1	TRUE	1	0.458347897105594	2		599	1523	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404891	404891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	197	456	1	ENST00000399788.2:c.4303C>A	p.Leu1435Met	p.L1435M	ENST00000399788	NM_001042603.1	1435	Ctg/Atg	26/28	1	2	FACETS	0.724	0.669	0.781	0.724	0.669	0.781	SUBCLONAL	1	TRUE	1	0.458347897105594	2		457	1187	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81941323	81941323	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs772234560	NA	P-0007144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	233	585	1	ENST00000359376.3:c.1501G>T	p.Ala501Ser	p.A501S	ENST00000359376	NM_002661.3	501	Gcc/Tcc	16/33	1	2	FACETS	0.789	0.734	0.845	0.789	0.734	0.845	SUBCLONAL	1	TRUE	1	0.458347897105594	2		586	1289	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032531	12032531	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	38	264	0	ENST00000353533.5:c.967G>T	p.Gly323Ter	p.G323*	ENST00000353533	NM_003010.3	323	Gga/Tga	9/11	0.456262348298346	1	FACETS	0.233	0.192	0.279	0.233	0.192	0.279	SUBCLONAL	1	TRUE	0	0.458347897105594	1		264	548	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37882034	37882034	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	171	454	3	ENST00000269571.5:c.2800C>A	p.Leu934Met	p.L934M	ENST00000269571		934	Ctg/Atg	23/27	1	2	FACETS	0.628	0.576	0.682	0.628	0.576	0.682	SUBCLONAL	1	TRUE	1	0.458347897105594	2		457	1189	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368287	45368287	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	55	514	0	ENST00000262160.6:c.1315G>T	p.Glu439Ter	p.E439*	ENST00000262160	NM_005901.5	439	Gaa/Taa	11/11	0.458347897105594	1	FACETS	0.207	0.176	0.241	0.207	0.176	0.241	SUBCLONAL	1	TRUE	0	0.458347897105594	1		514	894	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271359	18271359	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	217	357	1	ENST00000222254.8:c.401C>T	p.Ala134Val	p.A134V	ENST00000222254	NM_005027.3	134	gCc/gTc	3/16	1	2	FACETS	0.877	0.815	0.941	0.877	0.815	0.941	CLONAL	1	TRUE	1	0.458347897105594	2		358	1080	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763458	41763458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372169583	NA	P-0007144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	345	666	0	ENST00000301178.4:c.2257G>A	p.Val753Met	p.V753M	ENST00000301178	NM_021913.4	753	Gtg/Atg	19/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.458347897105594	2		666	1401	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412596	63412596	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520610	NA	P-0007144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	223	214	0	ENST00000330258.3:c.571G>T	p.Glu191Ter	p.E191*	ENST00000330258	NM_152424.3	191	Gag/Tag	2/2	1	1	FACETS	0.833	0.786	0.881	1	0.994	1	CLONAL	2	TRUE	0	0.458347897105594	1		214	450	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250082	53250085	+	frameshift_variant	Frame_Shift_Del	DEL	AAGG	AAGG	-	novel	NA	P-0007144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	326	290	2	ENST00000375401.3:c.164_167del	p.Pro55LeufsTer17	p.P55Lfs*17	ENST00000375401	NM_004187.3	55	cCCTTt/ct	2/26	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.458347897105594	1		292	742	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0007150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	320	366	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.580669165052971	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.580669165052971	1		366	596	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412287	139412287	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	115	305	0	ENST00000277541.6:c.1358T>G	p.Val453Gly	p.V453G	ENST00000277541	NM_017617.3	453	gTc/gGc	8/34	NA	2	FACETS	0.689	0.622	0.759			1	INDETERMINATE	1	TRUE	NA	0.580669165052971	2		305	575	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354353	354353	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	41	260	0	ENST00000262320.3:c.1205C>A	p.Thr402Lys	p.T402K	ENST00000262320	NM_003502.3	402	aCg/aAg	5/11	0.40969776235855	1	FACETS	0.253	0.211	0.3	0.253	0.211	0.3	SUBCLONAL	1	TRUE	0	0.580669165052971	1		260	396	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983363	15983363	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	82	382	0	ENST00000268712.3:c.3416T>C	p.Ile1139Thr	p.I1139T	ENST00000268712	NM_006311.3	1139	aTa/aCa	26/46	0.580669165052971	1	FACETS	0.436	0.385	0.489	0.436	0.385	0.489	SUBCLONAL	1	TRUE	0	0.580669165052971	1		382	460	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936832	48936961	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATAAGTAAAAGTAGTAGAATGTTACCAAGATTATTTTTGACCTAAGTTATAGTTAGAATACTTCATTATTTTATATGATGGATGTACAATTGTTCTTATCTAATTTACCACTTTTACAGAAACAGCTGTT	ATAAGTAAAAGTAGTAGAATGTTACCAAGATTATTTTTGACCTAAGTTATAGTTAGAATACTTCATTATTTTATATGATGGATGTACAATTGTTCTTATCTAATTTACCACTTTTACAGAAACAGCTGTT	-	novel	NA	P-0007150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	209	39	0	ENST00000267163.4:c.719-116_732del		p.X240_splice	ENST00000267163	NM_000321.2	240		8/27	0.580669165052971	2	FACETS	0.996	0.964	1	1	0.995	1	CLONAL	3	TRUE	0	0.580669165052971	2		39	241	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627500	37627501	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	273	412	0	ENST00000447079.4:c.1421dup	p.Asn474LysfsTer12	p.N474Kfs*12	ENST00000447079	NM_015083.1	472	gta/gtAa	2/14	0.580669165052971	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.580669165052971	1		412	574	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0007167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	121	203	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.279597245854487	3	FACETS	1	0.984	1	0.708	0.643	0.775	CLONAL	1	TRUE	1	0.448044651427954	3		203	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0007167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	263	644	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.448044651427954	1	FACETS	0.991	0.931	1	0.991	0.931	1	CLONAL	1	TRUE	0	0.448044651427954	1		645	919	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0007167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	382	412	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.223773388011015	5	FACETS	1	0.982	1	0.713	0.677	0.75	INDETERMINATE	2	TRUE	2	0.448044651427954	5		412	1333	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0007167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	120	510	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.788	0.712	0.867	0.788	0.712	0.867	SUBCLONAL	1	TRUE	1	0.448044651427954	2		510	680	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204507421	204507421	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	132	539	0	ENST00000367182.3:c.496A>T	p.Ile166Leu	p.I166L	ENST00000367182	NM_001278516.1	166	Ata/Tta	7/11	0.448044651427954	4	FACETS	0.726	0.657	0.798	0.242	0.219	0.266	SUBCLONAL	1	TRUE	1	0.448044651427954	4		539	1176	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447260	187447260	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	277	416	0	ENST00000232014.4:c.933G>C	p.Glu311Asp	p.E311D	ENST00000232014	NM_001130845.1	311	gaG/gaC	5/10	0.279597245854487	3	FACETS	1	0.993	1	0.741	0.696	0.787	CLONAL	1	TRUE	1	0.448044651427954	3		416	1021	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176666819	176666819	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	108	511	0	ENST00000439151.2:c.4255G>C	p.Asp1419His	p.D1419H	ENST00000439151	NM_022455.4	1419	Gac/Cac	8/23	0.391440103859044	3	FACETS	0.627	0.562	0.696	0.314	0.281	0.349	SUBCLONAL	1	TRUE	1	0.448044651427954	3		511	941	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341876	8341876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	111	569	0	ENST00000356435.5:c.4764G>A	p.Met1588Ile	p.M1588I	ENST00000356435		1588	atG/atA	29/35	0.448044651427954	1	FACETS	0.655	0.59	0.723	0.655	0.59	0.723	SUBCLONAL	1	TRUE	0	0.448044651427954	1		569	587	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233093	69233093	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	132	431	0	ENST00000462284.1:c.958C>G	p.Pro320Ala	p.P320A	ENST00000462284	NM_002392.5	320	Ccc/Gcc	11/11	1	2	FACETS	0.873	0.794	0.955	0.873	0.794	0.955	CLONAL	1	TRUE	1	0.448044651427954	2		431	675	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597507	28597507	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	153	513	0	ENST00000241453.7:c.2398G>C	p.Glu800Gln	p.E800Q	ENST00000241453	NM_004119.2	800	Gaa/Caa	19/24	0.448044651427954	1	FACETS	0.708	0.648	0.769	0.708	0.648	0.769	SUBCLONAL	1	TRUE	0	0.448044651427954	1		513	749	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0007177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	105	382	0	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.497677130017942	1	FACETS	0.587	0.528	0.649	0.587	0.528	0.649	SUBCLONAL	1	TRUE	0	0.512491286509784	1		382	519	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252170	226252170	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	14	50	0	ENST00000366813.1:c.118C>A	p.His40Asn	p.H40N	ENST00000366813		40	Cat/Aat	1/3	0.398336648410756	3	FACETS	0.798	0.586	1	0.399	0.293	0.523	CLONAL	1	TRUE	1	0.512491286509784	3		50	86	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743949	41743949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199988157	NA	P-0007177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	129	395	0	ENST00000301178.4:c.884G>A	p.Arg295Gln	p.R295Q	ENST00000301178	NM_021913.4	295	cGg/cAg	7/20	1	2	FACETS	0.765	0.695	0.838	0.765	0.695	0.838	SUBCLONAL	1	TRUE	1	0.512491286509784	2		395	658	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265722	41266253	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	In_Frame_Del	DEL	TTGGTGAAATAGCAAACAAGCCACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTA	TTGGTGAAATAGCAAACAAGCCACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTA	-	novel	NA	P-0007177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	55	40	0	ENST00000349496.5:c.13+152_241+11del		p.A5_D81del	ENST00000349496	NM_001904.3	5		3/15	0.512491286509784	3	FACETS	0.946	0.847	1	0.946	0.847	1	CLONAL	3	TRUE	0	0.512491286509784	3		40	95	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127916226	127916226	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	164	447	0	ENST00000373547.4:c.418del	p.Arg140AspfsTer12	p.R140Dfs*12	ENST00000373547	NM_002721.4	140	Aga/ga	5/7	0.177594914335224	5	FACETS	0.854	0.782	0.93	0.285	0.26	0.31	INDETERMINATE	1	TRUE	2	0.512491286509784	5		447	1325	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1386	186	586	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.986	0.907	1	0.986	0.907	1	CLONAL	1	TRUE	1	0.24	2		586	1572	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637070	93637070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1837	209	483	0	ENST00000375746.1:c.1120G>A	p.Asp374Asn	p.D374N	ENST00000375746	NM_001174167.1	374	Gac/Aac	9/14	1	2	FACETS	0.851	0.787	0.919	0.851	0.787	0.919	CLONAL	1	TRUE	1	0.24	2		483	2046	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034471	47034471	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1646	256	615	0	ENST00000377604.3:c.556C>T	p.Arg186Ter	p.R186*	ENST00000377604	NM_001204468.1	186	Cga/Tga	6/24	0.277358049120492	1	FACETS	0.987	0.92	1	0.987	0.92	1	CLONAL	1	TRUE	0	0.24	1		615	1902	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	88	586	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.249397873722836	3	FACETS	1	0.898	1	1	0.898	1	CLONAL	3	TRUE	0	0.21	3		586	308	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0007215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	107	328	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	1	2	FACETS	1	0.914	1	1	0.988	1	CLONAL	2	TRUE	1	0.21	2		328	502	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984824	11984824	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	69	252	0	ENST00000353533.5:c.370A>G	p.Ser124Gly	p.S124G	ENST00000353533	NM_003010.3	124	Agt/Ggt	3/11	1	2	FACETS	1	0.944	1	1	0.984	1	CLONAL	2	TRUE	1	0.21	2		252	291	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240753	53240753	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	59	233	1	ENST00000375401.3:c.1327G>A	p.Asp443Asn	p.D443N	ENST00000375401	NM_004187.3	443	Gac/Aac	10/26	0.244214441586145	0	FACETS	0.85	0.739	0.969			1	CLONAL	2	TRUE	NA	0.21	0		234	261	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971133	21971133	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	27	174	0	ENST00000304494.5:c.225del	p.Ala76ProfsTer70	p.A76Pfs*70	ENST00000304494	NM_000077.4	75	ccC/cc	2/3	0.3	1	FACETS	0.636	0.506	0.784	0.636	0.506	0.784	SUBCLONAL	1	TRUE	0	0.21	1		174	362	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574002	7574002	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs375338359	NA	P-0007219-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	1109	713	0	ENST00000269305.4:c.1025G>C	p.Arg342Pro	p.R342P	ENST00000269305	NM_001126112.2	342	cGa/cCa	10/11	0.744498234370641	2	FACETS	0.975	0.957	0.992	0.975	0.957	0.992	CLONAL	2	TRUE	0	0.779812052116873	2		713	1459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007221-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	873	417	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.405602910395253	5	FACETS	0.947	0.925	0.969	0.947	0.925	0.969	CLONAL	5	TRUE	0	0.495346702956233	5		417	1297	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934761	49934761	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007221-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	170	439	0	ENST00000296474.3:c.2135G>C	p.Gly712Ala	p.G712A	ENST00000296474	NM_002447.2	712	gGc/gCc	7/20	NA	2	FACETS	0.749	0.689	0.812			1	INDETERMINATE	1	TRUE	NA	0.495346702956233	2		439	916	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293694	1293694	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs986886145	NA	P-0007221-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	53	236	1	ENST00000310581.5:c.1307C>T	p.Ala436Val	p.A436V	ENST00000310581	NM_198253.2	436	gCg/gTg	2/16	0.505731579509389	3	FACETS	0.703	0.601	0.813	0.351	0.3	0.407	SUBCLONAL	1	TRUE	1	0.495346702956233	3		237	380	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370941	55370941	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs745939637	NA	P-0007221-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	153	300	0	ENST00000297316.4:c.243C>G	p.Asp81Glu	p.D81E	ENST00000297316	NM_022454.3	81	gaC/gaG	1/2	0.433793357372763	4	FACETS	0.91	0.832	0.992	0.455	0.416	0.496	CLONAL	1	TRUE	2	0.495346702956233	4		300	1015	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619111	37619115	+	frameshift_variant	Frame_Shift_Del	DEL	AAGAA	AAGAA	-	novel	NA	P-0007221-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	584	394	0	ENST00000447079.4:c.790_794del	p.Lys264SerfsTer32	p.K264Sfs*32	ENST00000447079	NM_015083.1	263	AAGAAa/a	1/14	0.505731579509389	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.495346702956233	2		394	1126	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0007225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	646	536	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.641047147062176	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.641047147062176	3		536	865	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0007225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	132	415	0	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	0.641047147062176	3	FACETS	0.944	0.861	1	0.472	0.43	0.516	CLONAL	1	TRUE	1	0.641047147062176	3		415	576	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845651	63845651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	224	191	0	ENST00000279873.7:c.1390G>A	p.Ala464Thr	p.A464T	ENST00000279873	NM_032199.2	464	Gca/Aca	9/10	0.641047147062176	4	FACETS	0.902	0.852	0.951	0.902	0.852	0.951	CLONAL	3	TRUE	1	0.641047147062176	4		191	424	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973795	15973795	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs766638542	NA	P-0007225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	445	425	0	ENST00000268712.3:c.4197C>G	p.Ile1399Met	p.I1399M	ENST00000268712	NM_006311.3	1399	atC/atG	31/46	0.641047147062176	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.641047147062176	3		425	553	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276612	15276612	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	166	511	0	ENST00000263388.2:c.5653C>A	p.Gln1885Lys	p.Q1885K	ENST00000263388	NM_000435.2	1885	Cag/Aag	30/33	0.641047147062176	5	FACETS	1	0.96	1	0.269	0.246	0.292	CLONAL	1	TRUE	1	0.641047147062176	5		511	945	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0007231-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	353	399	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.625919374860098	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.625919374860098	2		399	533	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106058	8106058	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007231-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	238	323	1	ENST00000346208.3:c.878T>A	p.Met293Lys	p.M293K	ENST00000346208		293	aTg/aAg	4/6	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.625919374860098	2		324	722	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161254	56161254	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007231-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	216	329	0	ENST00000399503.3:c.1123T>G	p.Leu375Val	p.L375V	ENST00000399503	NM_005921.1	375	Tta/Gta	5/20	1	2	FACETS	0.993	0.927	1	0.993	0.927	1	CLONAL	1	TRUE	1	0.625919374860098	2		329	695	SUCCESS
ATR	545	MSKCC	GRCh37	3	142253986	142254009	+	inframe_deletion	In_Frame_Del	DEL	TGTTGAATGGCCTTCATAGAGAGC	TGTTGAATGGCCTTCATAGAGAGC	-	novel	NA	P-0007231-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	212	415	0	ENST00000350721.4:c.3858_3881del	p.Gln1286_Gln1293del	p.Q1286_Q1293del	ENST00000350721	NM_001184.3	1286	caGCTCTCTATGAAGGCCATTCAACAt/cat	21/47	1	2	FACETS	0.907	0.845	0.97	0.907	0.845	0.97	CLONAL	1	TRUE	1	0.625919374860098	2		415	747	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178385	56178397	+	frameshift_variant	Frame_Shift_Del	DEL	TGCAGATTAGATG	TGCAGATTAGATG	-	novel	NA	P-0007231-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	223	467	0	ENST00000399503.3:c.3359_3371del	p.Cys1120SerfsTer24	p.C1120Sfs*24	ENST00000399503	NM_005921.1	1120	TGCAGATTAGATGtc/tc	14/20	1	2	FACETS	0.753	0.702	0.806	0.753	0.702	0.806	SUBCLONAL	1	TRUE	1	0.625919374860098	2		467	946	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	80	939	1	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	0.21	2		940	556	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338696	70338698	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0007241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	75	209	0	ENST00000374080.3:c.94_96del	p.Lys32del	p.K32del	ENST00000374080		31	cAGAag/cag	1/45	1	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.21	1		209	441	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853105	151853105	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	43	218	0	ENST00000262189.6:c.11850del	p.Phe3951SerfsTer36	p.F3951Sfs*36	ENST00000262189	NM_170606.2	3950	ccC/cc	46/59	1	2	FACETS	0.791	0.661	0.934	0.791	0.661	0.934	CLONAL	1	TRUE	1	0.21	2		218	518	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978321	2978321	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs138920531	NA	P-0007268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	271	559	0	ENST00000396946.4:c.1009C>T	p.Arg337Ter	p.R337*	ENST00000396946	NM_032415.4	337	Cga/Tga	7/25	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.521177526883219	2		559	848	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0007271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	96	375	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.220791580809993	2		375	864	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520008	NA	P-0007271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	191	436	0	ENST00000269305.4:c.613T>C	p.Tyr205His	p.Y205H	ENST00000269305	NM_001126112.2	205	Tat/Cat	6/11	0.220791580809993	1	FACETS	0.833	0.77	0.898	1	0.992	1	CLONAL	2	TRUE	0	0.220791580809993	1		436	924	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190588	11190588	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	62	312	0	ENST00000361445.4:c.5611G>A	p.Glu1871Lys	p.E1871K	ENST00000361445	NM_004958.3	1871	Gag/Aag	39/58	0.220791580809993	1	FACETS	0.726	0.627	0.835	0.726	0.627	0.835	SUBCLONAL	1	TRUE	0	0.220791580809993	1		312	688	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36940993	36940993	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	93	542	0	ENST00000361632.4:c.346G>C	p.Glu116Gln	p.E116Q	ENST00000361632		116	Gag/Cag	3/16	0.220791580809993	1	FACETS	0.689	0.611	0.773	0.689	0.611	0.773	SUBCLONAL	1	TRUE	0	0.220791580809993	1		542	1087	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702296	47702296	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1361816581	NA	P-0007271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	182	519	0	ENST00000233146.2:c.1892G>A	p.Arg631Lys	p.R631K	ENST00000233146	NM_000251.2	631	aGa/aAa	12/16	0.220791580809993	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.220791580809993	1		519	1014	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197369	26197369	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1452	108	771	1	ENST00000356476.2:c.110A>G	p.Lys37Arg	p.K37R	ENST00000356476		37	aAg/aGg	1/1	1	2	FACETS	0.627	0.56	0.698	0.627	0.56	0.698	SUBCLONAL	1	TRUE	1	0.220791580809993	2		772	1560	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924263	11924278	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCGGCCCCGTAGGG	CCCCGGCCCCGTAGGG	-	novel	NA	P-0007271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	23	41	0	ENST00000353533.5:c.60_75del	p.Gly22ArgfsTer18	p.G22Rfs*18	ENST00000353533	NM_003010.3	20	acCCCCGGCCCCGTAGGG/ac	1/11	0.220791580809993	1	FACETS	0.874	0.694	1	1	0.942	1	CLONAL	2	TRUE	0	0.220791580809993	1		41	106	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	65	586	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.795	0.688	0.912	0.795	0.688	0.912	CLONAL	1	TRUE	1	0.207476530635401	2		586	788	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741707	145741707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543009701	NA	P-0007274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	46	628	0	ENST00000428558.2:c.796G>A	p.Glu266Lys	p.E266K	ENST00000428558	NM_004260.3	266	Gag/Aag	5/22	0.179791655796419	3	FACETS	0.869	0.731	1	0.435	0.365	0.511	CLONAL	1	TRUE	1	0.207476530635401	3		628	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786201059	NA	P-0007274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	117	1021	0	ENST00000269305.4:c.856G>C	p.Glu286Gln	p.E286Q	ENST00000269305	NM_001126112.2	286	Gaa/Caa	8/11	0.207476530635401	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.207476530635401	1		1021	978	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521711	89521711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	109	557	0	ENST00000336596.2:c.2788G>A	p.Glu930Lys	p.E930K	ENST00000336596	NM_005233.5	930	Gaa/Aaa	16/17	1	2	FACETS	0.983	0.881	1	0.983	0.881	1	CLONAL	1	TRUE	1	0.228138272003325	2		557	972	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	CT	rs121913227	NA	P-0007281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	124	360	0	ENST00000288602.6:c.1798_1799delinsAG	p.Val600Arg	p.V600R	ENST00000288602	NM_004333.4	600	GTg/AGg	15/18	0.228138272003325	3	FACETS	0.93	0.843	1	0.93	0.843	1	CLONAL	2	TRUE	1	0.228138272003325	3		360	651	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226561967	226561967	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	211	523	0	ENST00000366794.5:c.2030T>A	p.Phe677Tyr	p.F677Y	ENST00000366794	NM_001618.3	677	tTt/tAt	14/23	0.22570406642521	2	FACETS	0.901	0.836	0.967	0.901	0.836	0.967	CLONAL	2	TRUE	0	0.228138272003325	2		523	1027	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99809045	99809045	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	55	361	0	ENST00000280892.6:c.340T>A	p.Phe114Ile	p.F114I	ENST00000280892	NM_001130678.1	114	Ttt/Att	4/7	1	2	FACETS	0.823	0.704	0.953	0.823	0.704	0.953	CLONAL	1	TRUE	1	0.228138272003325	2		361	586	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127933378	127933378	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	113	656	0	ENST00000373547.4:c.157G>A	p.Asp53Asn	p.D53N	ENST00000373547	NM_002721.4	53	Gat/Aat	2/7	1	2	FACETS	0.793	0.712	0.88	0.793	0.712	0.88	SUBCLONAL	1	TRUE	1	0.228138272003325	2		656	1249	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933480	100933480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766277966	NA	P-0007281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	54	372	0	ENST00000325455.5:c.1910G>A	p.Arg637Gln	p.R637Q	ENST00000325455	NM_001202474.3	637	cGa/cAa	4/8	1	2	FACETS	0.648	0.553	0.754	0.648	0.553	0.754	SUBCLONAL	1	TRUE	1	0.228138272003325	2		372	730	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590605	95590605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	103	573	0	ENST00000393063.1:c.1304C>T	p.Pro435Leu	p.P435L	ENST00000393063	NM_030621.3	435	cCt/cTt	9/28	1	2	FACETS	0.917	0.819	1	0.917	0.819	1	CLONAL	1	TRUE	1	0.228138272003325	2		573	985	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347851	347851	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1182	142	723	0	ENST00000262320.3:c.1655C>T	p.Ala552Val	p.A552V	ENST00000262320	NM_003502.3	552	gCc/gTc	6/11	1	2	FACETS	0.94	0.854	1	0.94	0.854	1	CLONAL	1	TRUE	1	0.228138272003325	2		723	1324	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862725	9862725	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	105	524	0	ENST00000330684.3:c.2578C>T	p.Leu860Phe	p.L860F	ENST00000330684	NM_001134407.1	860	Ctc/Ttc	12/13	1	2	FACETS	0.978	0.875	1	0.978	0.875	1	CLONAL	1	TRUE	1	0.228138272003325	2		524	941	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346894	89346894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1475986671	NA	P-0007281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	129	403	0	ENST00000301030.4:c.6056C>T	p.Pro2019Leu	p.P2019L	ENST00000301030	NM_001256183.1	2019	cCc/cTc	9/13	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.228138272003325	2		403	892	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652303	48652303	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	220	439	0	ENST00000376670.3:c.974G>A	p.Gly325Glu	p.G325E	ENST00000376670	NM_002049.3	325	gGa/gAa	6/6	0.0733321183802758	0	FACETS	0.846	0.788	0.905			1	INDETERMINATE	2	TRUE	NA	0.228138272003325	0		439	880	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576926	7576942	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTAGGAAAGAGGCAAG	GCTAGGAAAGAGGCAAG	-	novel	NA	P-0007281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	98	432	0	ENST00000269305.4:c.920-16_920del		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	0.228138272003325	1	FACETS	0.94	0.838	1	0.94	0.838	1	CLONAL	1	TRUE	0	0.228138272003325	1		432	810	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375894	118375895	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0007284-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	177	410	0	ENST00000534358.1:c.9289_9290del	p.Leu3097SerfsTer15	p.L3097Sfs*15	ENST00000534358	NM_005933.3	3096	aCT/a	27/36	0.831277624903653	1	FACETS	0.905	0.856	0.952	0.905	0.856	0.952	CLONAL	1	TRUE	0	0.831277624903653	1		410	275	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217431	7217432	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0007284-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	436	729	0	ENST00000380728.2:c.364_365del	p.Val122SerfsTer26	p.V122Sfs*26	ENST00000380728		122	GTt/t	5/11	0.831277624903653	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.831277624903653	1		729	608	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	43	939	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.132923911432764	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		940	478	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0007302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	33	318	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.132923911432764	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		318	350	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595908	52595908	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	39	509	0	ENST00000394830.3:c.4007del	p.Leu1336ArgfsTer6	p.L1336Rfs*6	ENST00000394830	NM_018313.4	1336	cTg/cg	26/30	0.3	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		509	542	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0007312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	223	512	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.564482979974968	1	FACETS	0.944	0.886	1	0.944	0.886	1	CLONAL	1	TRUE	0	0.608842809263812	1		512	540	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937684	44937684	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	163	531	0	ENST00000377967.4:c.2872C>T	p.Gln958Ter	p.Q958*	ENST00000377967	NM_021140.2	958	Caa/Taa	19/29	0.608842809263812	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.608842809263812	1		531	370	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163735	72163735	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs767134486	NA	P-0007312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	191	913	0	ENST00000357731.5:c.623A>T	p.Asp208Val	p.D208V	ENST00000357731	NM_173808.2	208	gAt/gTt	4/7	1	2	FACETS	0.78	0.723	0.84	0.78	0.723	0.84	SUBCLONAL	1	TRUE	1	0.608842809263812	2		913	804	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564729	55564729	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	143	374	0	ENST00000288135.5:c.617C>A	p.Pro206Gln	p.P206Q	ENST00000288135	NM_000222.2	206	cCa/cAa	3/21	1	2	FACETS	0.925	0.848	1	0.925	0.848	1	CLONAL	1	TRUE	1	0.608842809263812	2		374	508	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001930	29001930	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0007312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	22	541	0	ENST00000282397.4:c.1235C>G	p.Ser412Ter	p.S412*	ENST00000282397	NM_002019.4	412	tCa/tGa	9/30	0.564482979974968	1	FACETS	0.147	0.113	0.185	0.147	0.113	0.185	SUBCLONAL	1	TRUE	0	0.608842809263812	1		541	343	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185200	123185200	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0007312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	216	636	0	ENST00000218089.9:c.1152T>A	p.Tyr384Ter	p.Y384*	ENST00000218089	NM_001042749.1	384	taT/taA	13/35	0.608842809263812	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.608842809263812	1		636	423	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	72	160	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.995	0.88	1	0.995	0.88	1	CLONAL	1	TRUE	1	0.54	2		160	268	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412365	139412365	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	137	386	0	ENST00000277541.6:c.1280G>A	p.Gly427Asp	p.G427D	ENST00000277541	NM_017617.3	427	gGc/gAc	8/34	1	2	FACETS	0.879	0.803	0.959	0.879	0.803	0.959	CLONAL	1	TRUE	1	0.54	2		386	577	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613406	100613406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	23	245	0	ENST00000308731.7:c.994C>T	p.Arg332Cys	p.R332C	ENST00000308731	NM_000061.2	332	Cgt/Tgt	12/19	1	1	FACETS	0.17	0.132	0.214	0.17	0.132	0.214	SUBCLONAL	1	TRUE	0	0.54	1		245	366	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589599	67589604	+	inframe_deletion	In_Frame_Del	DEL	TCAGTT	TCAGTT	-	novel	NA	P-0007339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	96	451	0	ENST00000274335.5:c.1365_1370del	p.Phe456_Gln457del	p.F456_Q457del	ENST00000274335		454	acTCAGTTt/act	10/15	1	2	FACETS	0.958	0.861	1	0.958	0.861	1	CLONAL	1	TRUE	1	0.54	2		451	371	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs28934577	NA	P-0007349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	61	291	0	ENST00000269305.4:c.770T>G	p.Leu257Arg	p.L257R	ENST00000269305	NM_001126112.2	257	cTg/cGg	7/11	0.249866334521302	0	FACETS	1	0.909	1			1	CLONAL	1	TRUE	0	0.249866334521302	0		291	345	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023676	27023676	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs867647567	NA	P-0007349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	38	216	0	ENST00000324856.7:c.782C>A	p.Ser261Ter	p.S261*	ENST00000324856	NM_006015.4	261	tCg/tAg	1/20	1	2	FACETS	0.525	0.433	0.628	0.525	0.433	0.628	SUBCLONAL	1	TRUE	1	0.249866334521302	2		216	579	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253868	153253868	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	33	209	1	ENST00000281708.4:c.865G>C	p.Ala289Pro	p.A289P	ENST00000281708	NM_033632.3	289	Gca/Cca	6/12	0.249866334521302	4	FACETS	0.719	0.585	0.87			1	SUBCLONAL	1	TRUE	NA	0.249866334521302	4		210	459	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771333	68771333	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	76	217	0	ENST00000261769.5:c.15C>A	p.Ser5Arg	p.S5R	ENST00000261769	NM_004360.3	5	agC/agA	1/16	0.184507487614174	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.249866334521302	1		217	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579370	7579370	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	116	390	0	ENST00000269305.4:c.317del	p.Ser106ThrfsTer17	p.S106Tfs*17	ENST00000269305	NM_001126112.2	106	aGc/ac	4/11	0.249866334521302	0	FACETS	0.843	0.766	0.923			1	CLONAL	2	TRUE	0	0.249866334521302	0		390	413	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798734	135798734	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0007352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	60	259	0	ENST00000298552.3:c.508+1G>T		p.X170_splice	ENST00000298552	NM_001162426.1	170			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		259	348	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573828	64573955	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGAGGCAATGCCCTGGATGGAGGTGAGGCAGAGGATCCTCAGGGAGGCAGCCCCAGCTGCCCTGCTGGCACAAATGCCCCACCAGGGCACACCCAGAAGGGGCCACAGGAAGATCCCAGGGAGTCCT	CTGAGGCAATGCCCTGGATGGAGGTGAGGCAGAGGATCCTCAGGGAGGCAGCCCCAGCTGCCCTGCTGGCACAAATGCCCCACCAGGGCACACCCAGAAGGGGCCACAGGAAGATCCCAGGGAGTCCT	-	novel	NA	P-0007355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	230	265	0	ENST00000312049.6:c.913-115_925del		p.X305_splice	ENST00000312049	NM_130799.2	305		7/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		265	383	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0007362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	77	166	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.571772151037326	2		166	238	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0007362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	400	722	0	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	0.463846712267925	3	FACETS	1	0.988	1	0.721	0.69	0.752	CLONAL	2	TRUE	0	0.571772151037326	3		722	832	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435300	110435302	+	inframe_deletion	In_Frame_Del	DEL	GGT	GGT	-	rs765493638	NA	P-0007362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	10	80	0	ENST00000375856.3:c.3099_3101del	p.Pro1036del	p.P1036del	ENST00000375856	NM_003749.2	1033	ccACCg/ccg	1/2	0.259060805174397	1	FACETS	0.133	0.09	0.187	0.133	0.09	0.187	INDETERMINATE	1	TRUE	0	0.571772151037326	1		80	188	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115750	8115750	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs104894164	NA	P-0007362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	309	643	2	ENST00000346208.3:c.1096C>T	p.Arg366Ter	p.R366*	ENST00000346208		366	Cga/Tga	6/6	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.571772151037326	2		645	952	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120671	115120671	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	261	541	0	ENST00000257566.3:c.335T>G	p.Leu112Arg	p.L112R	ENST00000257566	NM_016569.3	112	cTt/cGt	1/8	1	2	FACETS	0.911	0.854	0.969	0.911	0.854	0.969	CLONAL	1	TRUE	1	0.571772151037326	2		541	1002	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114263	115114264	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTGAGCT	novel	NA	P-0007362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	175	301	0	ENST00000257566.3:c.947_953dup	p.Leu319AlafsTer10	p.L319Afs*10	ENST00000257566	NM_016569.3	318	acc/acAGCTCACc	6/8	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.571772151037326	2		301	573	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177662	56177662	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	399	369	0	ENST00000399503.3:c.2636del	p.Gly879ValfsTer30	p.G879Vfs*30	ENST00000399503	NM_005921.1	879	Ggt/gt	14/20	0.571772151037326	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	1	0.571772151037326	3		369	730	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115965	8115968	+	frameshift_variant	Frame_Shift_Del	DEL	CATG	CATG	ATT	novel	NA	P-0007362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	53	144	0	ENST00000346208.3:c.1311_1314delinsATT	p.Ser437ArgfsTer38	p.S437Rfs*38	ENST00000346208		437	agCATG/agATT	6/6	1	2	FACETS	0.766	0.66	0.88	0.766	0.66	0.88	SUBCLONAL	1	TRUE	1	0.571772151037326	2		144	242	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0007389-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	112	429	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.259625203635036	2		429	728	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0007389-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	62	297	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.931	0.805	1	0.931	0.805	1	CLONAL	1	TRUE	1	0.259625203635036	2		298	513	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0007389-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	55	405	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.259625203635036	2		405	343	SUCCESS
APC	324	MSKCC	GRCh37	5	112175513	112175513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007389-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	55	242	0	ENST00000257430.4:c.4222G>T	p.Glu1408Ter	p.E1408*	ENST00000257430	NM_000038.5	1408	Gaa/Taa	16/16	1	2	FACETS	0.683	0.584	0.792	0.683	0.584	0.792	SUBCLONAL	1	TRUE	1	0.259625203635036	2		242	620	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449779	149449779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776196303	NA	P-0007389-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	38	222	1	ENST00000286301.3:c.1285G>A	p.Val429Met	p.V429M	ENST00000286301	NM_005211.3	429	Gtg/Atg	9/22	1	2	FACETS	0.425	0.35	0.509	0.425	0.35	0.509	SUBCLONAL	1	TRUE	1	0.259625203635036	2		223	689	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104649	209104649	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	421	460	1	ENST00000345146.2:c.929G>T	p.Gly310Val	p.G310V	ENST00000345146	NM_005896.2	310	gGg/gTg	8/10	1	2	FACETS	0.965	0.922	1	0.965	0.922	1	CLONAL	1	TRUE	1	0.85139645073447	2		461	1025	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665024	138665024	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	62	20	0	ENST00000330315.3:c.541G>T	p.Ala181Ser	p.A181S	ENST00000330315	NM_023067.3	181	Gcc/Tcc	1/1	0.456541803928567	3	FACETS	1	0.977	1			1	INDETERMINATE	2	TRUE	NA	0.85139645073447	3		20	84	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592162	55592162	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143179681	NA	P-0007400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	322	433	0	ENST00000288135.5:c.1486G>A	p.Asp496Asn	p.D496N	ENST00000288135	NM_000222.2	496	Gat/Aat	9/21	1	2	FACETS	0.892	0.846	0.939	0.892	0.846	0.939	CLONAL	1	TRUE	1	0.85139645073447	2		433	848	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280007	66280007	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	238	300	1	ENST00000273854.3:c.1682C>A	p.Pro561Gln	p.P561Q	ENST00000273854	NM_004439.5	561	cCa/cAa	7/18	1	2	FACETS	0.914	0.859	0.969	0.914	0.859	0.969	CLONAL	1	TRUE	1	0.85139645073447	2		301	612	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680746	30680746	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	375	381	0	ENST00000376406.3:c.973G>T	p.Gly325Cys	p.G325C	ENST00000376406	NM_014641.2	325	Ggc/Tgc	5/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.85139645073447	2		381	848	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652312	36652312	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	214	193	0	ENST00000244741.5:c.434C>G	p.Thr145Ser	p.T145S	ENST00000244741	NM_000389.4	145	aCc/aGc	2/3	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.85139645073447	2		193	490	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740430	145740430	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	263	180	0	ENST00000428558.2:c.1510A>G	p.Thr504Ala	p.T504A	ENST00000428558	NM_004260.3	504	Aca/Gca	9/22	0.528989424117185	3	FACETS	0.888	0.843	0.932	0.888	0.843	0.932	CLONAL	2	TRUE	1	0.85139645073447	3		180	496	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428614	49428614	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	457	443	0	ENST00000301067.7:c.10336G>T	p.Val3446Leu	p.V3446L	ENST00000301067	NM_003482.3	3446	Gtg/Ttg	35/54	1	2	FACETS	0.973	0.932	1	0.973	0.932	1	CLONAL	1	TRUE	1	0.85139645073447	2		443	1103	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579582	7579583	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	231	231	0	ENST00000269305.4:c.104dup	p.Leu35PhefsTer8	p.L35Ffs*8	ENST00000269305	NM_001126112.2	35	ttg/ttTg	4/11	0.85139645073447	1	FACETS	0.965	0.924	1	0.965	0.924	1	CLONAL	1	TRUE	0	0.85139645073447	1		231	323	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332697	153332697	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	412	473	0	ENST00000281708.4:c.259del	p.Val87Ter	p.V87*	ENST00000281708	NM_033632.3	87	Gta/ta	2/12	1	2	FACETS	0.905	0.864	0.947	0.905	0.864	0.947	CLONAL	1	TRUE	1	0.85139645073447	2		473	1069	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878102	48878103	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0007400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	521	105	0	ENST00000267163.4:c.54_55delinsTT	p.Glu19Ter	p.E19*	ENST00000267163	NM_000321.2	18	gcGGaa/gcTTaa	1/27	0.85139645073447	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.85139645073447	2		105	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0007403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	107	222	0	ENST00000269305.4:c.559+1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.276103534708663	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.276919964760147	2		222	363	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120666	94120666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1346	304	680	0	ENST00000369303.4:c.385G>A	p.Glu129Lys	p.E129K	ENST00000369303	NM_004440.3	129	Gaa/Aaa	3/17	0.252242301471553	4	FACETS	0.85	0.798	0.903	0.85	0.798	0.903	CLONAL	2	TRUE	2	0.276919964760147	4		680	1650	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670425	134670425	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	133	263	0	ENST00000398015.3:c.336G>T	p.Leu112Phe	p.L112F	ENST00000398015	NM_004441.4	112	ttG/ttT	3/16	0.252242301471553	4	FACETS	0.925	0.842	1	0.925	0.842	1	CLONAL	2	TRUE	2	0.276919964760147	4		263	663	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630456	187630456	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	168	536	0	ENST00000441802.2:c.526G>T	p.Ala176Ser	p.A176S	ENST00000441802	NM_005245.3	176	Gca/Tca	2/27	0.276919964760147	3	FACETS	1	0.974	1	0.576	0.528	0.626	CLONAL	1	TRUE	1	0.276919964760147	3		536	1199	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417398	139417398	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	82	392	0	ENST00000277541.6:c.646G>T	p.Glu216Ter	p.E216*	ENST00000277541	NM_017617.3	216	Gag/Tag	4/34	0.276919964760147	2	FACETS	0.815	0.718	0.918	0.407	0.359	0.459	CLONAL	1	TRUE	0	0.276919964760147	2		392	727	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097644	8097644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762722802	NA	P-0007403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	70	223	0	ENST00000346208.3:c.26G>A	p.Arg9His	p.R9H	ENST00000346208		9	cGc/cAc	2/6	0.276919964760147	6	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.276919964760147	6		223	526	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022393	12022393	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	299	596	0	ENST00000396373.4:c.499G>C	p.Asp167His	p.D167H	ENST00000396373	NM_001987.4	167	Gat/Cat	5/8	0.276103534708663	2	FACETS	0.878	0.826	0.931	0.878	0.826	0.931	CLONAL	2	TRUE	0	0.276919964760147	2		596	1230	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047501	49047501	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0007403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	203	362	0	ENST00000267163.4:c.2495T>A	p.Leu832Ter	p.L832*	ENST00000267163	NM_000321.2	832	tTa/tAa	24/27	0.276103534708663	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.276919964760147	2		362	710	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779094	3779094	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	145	258	0	ENST00000262367.5:c.5954G>T	p.Arg1985Leu	p.R1985L	ENST00000262367	NM_004380.2	1985	cGc/cTc	31/31	0.276919964760147	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.276919964760147	3		258	554	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220603	1220603	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	110	387	0	ENST00000326873.7:c.621C>G	p.Asp207Glu	p.D207E	ENST00000326873	NM_000455.4	207	gaC/gaG	5/10	0.243422457593059	4	FACETS	0.774	0.697	0.856			1	SUBCLONAL	2	TRUE	NA	0.276919964760147	4		387	655	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs28934577	NA	P-0007410-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	234	306	0	ENST00000269305.4:c.770T>A	p.Leu257Gln	p.L257Q	ENST00000269305	NM_001126112.2	257	cTg/cAg	7/11	0.646445420865401	2	FACETS	0.973	0.926	1	0.973	0.926	1	CLONAL	2	TRUE	0	0.646445420865401	2		306	372	SUCCESS
APC	324	MSKCC	GRCh37	5	112173278	112173278	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730881240	NA	P-0007410-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	130	278	0	ENST00000257430.4:c.1987C>T	p.Gln663Ter	p.Q663*	ENST00000257430	NM_000038.5	663	Caa/Taa	16/16	0.646445420865401	2	FACETS	0.795	0.737	0.852	0.795	0.737	0.852	SUBCLONAL	2	TRUE	0	0.646445420865401	2		278	253	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0007413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	42	536	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.40886896126463	1	FACETS	0.202	0.168	0.24	0.202	0.168	0.24	SUBCLONAL	1	TRUE	0	0.40886896126463	1		536	809	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004217	150004217	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1431439182	NA	P-0007413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	135	367	1	ENST00000253339.5:c.2008C>T	p.Arg670Trp	p.R670W	ENST00000253339		670	Cgg/Tgg	3/7	0.40886896126463	1	FACETS	0.653	0.593	0.715	0.653	0.593	0.715	SUBCLONAL	1	TRUE	0	0.40886896126463	1		368	805	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0007496-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	166	337	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.768	0.705	0.833	0.768	0.705	0.833	SUBCLONAL	1	TRUE	1	0.486520759656353	2		337	889	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577161	64577161	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886039553	NA	P-0007496-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	256	450	0	ENST00000312049.6:c.421C>T	p.Gln141Ter	p.Q141*	ENST00000312049	NM_130799.2	141	Cag/Tag	2/10	1	2	FACETS	0.896	0.838	0.955	0.896	0.838	0.955	CLONAL	1	TRUE	1	0.486520759656353	2		450	1175	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056262	27056262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007496-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	126	325	0	ENST00000324856.7:c.1258C>T	p.Gln420Ter	p.Q420*	ENST00000324856	NM_006015.4	420	Cag/Tag	2/20	1	2	FACETS	0.707	0.64	0.776	0.707	0.64	0.776	SUBCLONAL	1	TRUE	1	0.486520759656353	2		325	733	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177956	56177956	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1246045657	NA	P-0007496-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	463	492	0	ENST00000399503.3:c.2929C>T	p.Gln977Ter	p.Q977*	ENST00000399503	NM_005921.1	977	Caa/Taa	14/20	0.41982590907498	2	FACETS	0.877	0.84	0.914	0.877	0.84	0.914	CLONAL	2	TRUE	0	0.486520759656353	2		492	1085	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868915	117868915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1337089126	NA	P-0007496-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	193	354	0	ENST00000297338.2:c.784G>A	p.Asp262Asn	p.D262N	ENST00000297338	NM_006265.2	262	Gac/Aac	7/14	1	2	FACETS	0.921	0.853	0.992	0.921	0.853	0.992	CLONAL	1	TRUE	1	0.486520759656353	2		354	861	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118355658	118355658	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007496-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	178	394	0	ENST00000534358.1:c.4300T>C	p.Cys1434Arg	p.C1434R	ENST00000534358	NM_005933.3	1434	Tgc/Cgc	10/36	1	2	FACETS	0.84	0.775	0.908	0.84	0.775	0.908	CLONAL	1	TRUE	1	0.486520759656353	2		394	871	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041912	42041912	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754368991	NA	P-0007496-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	284	575	0	ENST00000219905.7:c.6107G>A	p.Cys2036Tyr	p.C2036Y	ENST00000219905	NM_001164273.1	2036	tGc/tAc	17/24	1	2	FACETS	0.867	0.814	0.922	0.867	0.814	0.922	CLONAL	1	TRUE	1	0.486520759656353	2		575	1346	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0007514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	115	406	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.224482726078626	3	FACETS	1	0.978	1	0.655	0.592	0.723	CLONAL	1	TRUE	1	0.32	3		406	636	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0007514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	95	284	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	0.32	2		284	566	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0007514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	80	329	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	0.877	0.773	0.99	0.439	0.386	0.495	CLONAL	1	TRUE	1	0.32	3		329	661	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045009	47045009	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	35	296	0	ENST00000377604.3:c.2335C>T	p.Gln779Ter	p.Q779*	ENST00000377604	NM_001204468.1	779	Cag/Tag	20/24	1	2	FACETS	0.408	0.334	0.492	0.408	0.334	0.492	SUBCLONAL	1	TRUE	1	0.32	2		296	536	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0007524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	455	368	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.417688208274746	2	FACETS	0.758	0.732	0.784	0.758	0.732	0.784	INDETERMINATE	2	TRUE	0	0.841740029515862	2		368	713	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720733	89720734	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	rs1564568350	NA	P-0007524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	19	54	0	ENST00000371953.3:c.885_886del	p.Cys296Ter	p.C296*	ENST00000371953	NM_000314.4	295	cTA/c	8/9	0.841740029515862	2	FACETS	1	0.905	1	0.61	0.495	0.724	CLONAL	1	TRUE	0	0.841740029515862	2		54	37	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188164	11188164	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587777893	NA	P-0007540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	78	324	0	ENST00000361445.4:c.5930C>A	p.Thr1977Lys	p.T1977K	ENST00000361445	NM_004958.3	1977	aCa/aAa	43/58	0.250608530390783	1	FACETS	1	0.946	1	1	0.986	1	CLONAL	2	TRUE	0	0.250608530390783	1		324	247	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183734	10183734	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs869025617	NA	P-0007540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	100	400	0	ENST00000256474.2:c.203C>A	p.Ser68Ter	p.S68*	ENST00000256474	NM_000551.3	68	tCg/tAg	1/3	0.250608530390783	1	FACETS	1	0.936	1	1	0.988	1	CLONAL	2	TRUE	0	0.250608530390783	1		400	333	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678795	52678795	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0007540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	75	349	0	ENST00000394830.3:c.824C>G	p.Ser275Ter	p.S275*	ENST00000394830	NM_018313.4	275	tCa/tGa	9/30	0.212395821597416	0	FACETS	0.869	0.772	0.971			1	CLONAL	2	TRUE	0	0.250608530390783	0		349	258	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437506	52437506	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	153	905	0	ENST00000460680.1:c.1655del	p.Asp552ValfsTer19	p.D552Vfs*19	ENST00000460680	NM_004656.3	552	gAt/gt	13/17	0.212395821597416	0	FACETS	0.899	0.828	0.972			1	CLONAL	2	TRUE	0	0.250608530390783	0		905	509	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259535	55259555	+	inframe_deletion	In_Frame_Del	DEL	GAAGAGAAAGAATACCATGCA	GAAGAGAAAGAATACCATGCA	-	novel	NA	P-0007540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	63	504	0	ENST00000275493.2:c.2597_2617del	p.Glu866_Glu872del	p.E866_E872del	ENST00000275493	NM_005228.3	865	GAAGAGAAAGAATACCATGCA/-	21/28	0.250608530390783	6	FACETS	1	0.935	1	0.285	0.246	0.328	CLONAL	1	TRUE	2	0.250608530390783	6		504	661	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43739021	43739025	+	missense_variant	Missense_Mutation	ONP	CCTTG	CCTTG	GCTTC	novel	NA	P-0007540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	63	635	0	ENST00000523873.1:c.38_42delinsGCTTC	p.Ala13_Leu14delinsGlyPhe	p.A13_L14delinsGF	ENST00000523873		13	gCCTTG/gGCTTC	1/8	0.250608530390783	5	FACETS	1	0.898	1	0.349	0.301	0.401	CLONAL	1	TRUE	2	0.250608530390783	5		635	661	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667784	37667784	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2754	795	570	2	ENST00000447079.4:c.2669G>A	p.Arg890His	p.R890H	ENST00000447079	NM_015083.1	890	cGc/cAc	8/14	0.266939884154523	167	FACETS	0.991	0.954	1			1	CLONAL	39	FALSE	NA	0.266939884154523	167		572	3549	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579372	7579373	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0007550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	24	387	0	ENST00000269305.4:c.314dup	p.Ser106GlnfsTer43	p.S106Qfs*43	ENST00000269305	NM_001126112.2	105	ggc/ggGc	4/11	0.266939884154523	2	FACETS	0.881	0.716	1	1	0.924	1	CLONAL	3	FALSE	0	0.266939884154523	2		387	68	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	290	586	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.404532274581797	4	FACETS	0.94	0.886	0.994	0.94	0.886	0.994	CLONAL	2	TRUE	2	0.513892820644169	4		586	909	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0007560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	276	370	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	0.492404487958983	4	FACETS	1	0.993	1	0.744	0.698	0.791	CLONAL	1	TRUE	2	0.513892820644169	4		370	1093	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0007560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	221	311	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.513892820644169	4	FACETS	0.95	0.895	1	0.95	0.895	1	CLONAL	3	TRUE	1	0.513892820644169	4		311	457	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0007560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	271	239	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	0.492404487958983	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	2	0.513892820644169	4		239	767	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961231	15961231	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	235	225	0	ENST00000268712.3:c.6158A>G	p.Asp2053Gly	p.D2053G	ENST00000268712	NM_006311.3	2053	gAt/gGt	39/46	0.492404487958983	4	FACETS	0.967	0.906	1	0.967	0.906	1	CLONAL	2	TRUE	2	0.513892820644169	4		225	716	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554492	63554493	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0007560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	330	291	0	ENST00000307078.5:c.246dup	p.His83ThrfsTer58	p.H83Tfs*58	ENST00000307078	NM_004655.3	82	-/A	2/11	0.492404487958983	4	FACETS	0.903	0.854	0.952	0.903	0.854	0.952	CLONAL	2	TRUE	2	0.513892820644169	4		291	1077	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0007567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	151	203	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.550174960218967	2	FACETS	0.984	0.919	1	0.984	0.919	1	CLONAL	2	TRUE	0	0.550174960218967	2		203	279	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	137	939	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.729	0.665	0.797	0.729	0.665	0.797	SUBCLONAL	1	TRUE	1	0.550174960218967	2		940	683	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0007567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	394	504	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.529576194691985	3	FACETS	0.913	0.871	0.956	0.913	0.871	0.956	CLONAL	2	TRUE	1	0.550174960218967	3		504	1000	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913351	NA	P-0007567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	212	363	0	ENST00000288602.6:c.1397G>T	p.Gly466Val	p.G466V	ENST00000288602	NM_004333.4	466	gGa/gTa	11/18	0.218008227221431	2	FACETS	0.963	0.897	1	0.482	0.448	0.516	INDETERMINATE	1	TRUE	0	0.550174960218967	2		363	800	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041117	42041117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747757361	NA	P-0007567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	280	551	3	ENST00000219905.7:c.5495G>A	p.Arg1832Gln	p.R1832Q	ENST00000219905	NM_001164273.1	1832	cGg/cAg	16/24	NA	2	FACETS	1	0.945	1			1	INDETERMINATE	1	TRUE	NA	0.550174960218967	2		554	1013	SUCCESS
APC	324	MSKCC	GRCh37	5	112174490	112174490	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854571	NA	P-0007567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	131	288	0	ENST00000257430.4:c.3199C>T	p.Gln1067Ter	p.Q1067*	ENST00000257430	NM_000038.5	1067	Caa/Taa	16/16	0.529576194691985	3	FACETS	0.924	0.841	1	0.462	0.42	0.506	CLONAL	1	TRUE	1	0.550174960218967	3		288	657	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118944	3118944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	338	635	2	ENST00000078429.4:c.628C>T	p.Arg210Trp	p.R210W	ENST00000078429	NM_002067.2	210	Cgg/Tgg	5/7	0.529576194691985	3	FACETS	0.881	0.837	0.926	0.881	0.837	0.926	CLONAL	2	TRUE	1	0.550174960218967	3		637	889	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912813	50912813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758260006	NA	P-0007567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	220	440	0	ENST00000440232.2:c.2044C>T	p.Arg682Trp	p.R682W	ENST00000440232	NM_002691.3	682	Cgg/Tgg	17/27	0.529576194691985	3	FACETS	1	0.958	1	0.52	0.484	0.558	CLONAL	1	TRUE	1	0.550174960218967	3		440	980	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0007577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	52	311	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.472072650780147	3	FACETS	0.972	0.834	1	0.486	0.417	0.561	CLONAL	1	TRUE	1	0.472591836097702	3		311	280	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120527	70120527	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0007577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	170	212	0	ENST00000245479.2:c.1529G>C	p.Ter510SerextTer49	p.*510Sext*49	ENST00000245479	NM_000346.3	510	tGa/tCa	3/3	0.336842544032737	4	FACETS	0.951	0.88	1	0.951	0.88	1	CLONAL	2	TRUE	2	0.472591836097702	4		212	557	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0007577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	151	275	1	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	0.336842544032737	4	FACETS	1	0.967	1	0.557	0.51	0.607	CLONAL	1	TRUE	2	0.472591836097702	4		276	844	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099283	157099283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	167	156	0	ENST00000346085.5:c.220G>A	p.Glu74Lys	p.E74K	ENST00000346085	NM_020732.3	74	Gaa/Aaa	1/20	0.472591836097702	2	FACETS	1	0.989	1	0.717	0.664	0.771	CLONAL	1	TRUE	0	0.472591836097702	2		156	493	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662458	227662458	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	75	150	0	ENST00000305123.5:c.997G>A	p.Glu333Lys	p.E333K	ENST00000305123	NM_005544.2	333	Gaa/Aaa	1/2	0.472591836097702	3	FACETS	1	0.922	1	0.53	0.467	0.597	CLONAL	1	TRUE	1	0.472591836097702	3		150	370	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274965	142274965	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	58	205	0	ENST00000350721.4:c.2095G>A	p.Asp699Asn	p.D699N	ENST00000350721	NM_001184.3	699	Gat/Aat	10/47	0.472072650780147	3	FACETS	0.721	0.621	0.829	0.36	0.31	0.415	SUBCLONAL	1	TRUE	1	0.472591836097702	3		205	421	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278135	142278135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	102	332	0	ENST00000350721.4:c.1690G>A	p.Asp564Asn	p.D564N	ENST00000350721	NM_001184.3	564	Gat/Aat	7/47	0.472072650780147	3	FACETS	0.806	0.722	0.896	0.403	0.361	0.448	CLONAL	1	TRUE	1	0.472591836097702	3		332	662	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586455	189586455	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	126	168	0	ENST00000264731.3:c.1079G>C	p.Arg360Thr	p.R360T	ENST00000264731	NM_003722.4	360	aGa/aCa	8/14	0.472072650780147	3	FACETS	0.974	0.883	1	0.487	0.441	0.535	CLONAL	1	TRUE	1	0.472591836097702	3		168	677	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133733	55133733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	168	413	0	ENST00000257290.5:c.946G>A	p.Glu316Lys	p.E316K	ENST00000257290	NM_006206.4	316	Gaa/Aaa	7/23	0.472591836097702	3	FACETS	0.943	0.867	1	0.314	0.289	0.341	CLONAL	1	TRUE	0	0.472591836097702	3		413	932	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851469	151851469	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	182	356	1	ENST00000262189.6:c.12022G>A	p.Glu4008Lys	p.E4008K	ENST00000262189	NM_170606.2	4008	Gag/Aag	47/59	0.472591836097702	3	FACETS	0.998	0.921	1	0.499	0.46	0.54	CLONAL	1	TRUE	1	0.472591836097702	3		357	954	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209357	98209357	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748812637	NA	P-0007577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	164	310	1	ENST00000331920.6:c.4181G>A	p.Arg1394Gln	p.R1394Q	ENST00000331920	NM_000264.3	1394	cGa/cAa	23/24	0.336842544032737	4	FACETS	1	0.974	1	0.572	0.525	0.621	CLONAL	1	TRUE	2	0.472591836097702	4		311	894	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373275	118373275	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	149	432	0	ENST00000534358.1:c.6668C>G	p.Ser2223Cys	p.S2223C	ENST00000534358	NM_005933.3	2223	tCt/tGt	27/36	0.472591836097702	4	FACETS	0.815	0.743	0.89			1	CLONAL	1	TRUE	NA	0.472591836097702	4		432	1140	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205226	46205226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	178	374	2	ENST00000334344.6:c.310C>T	p.His104Tyr	p.H104Y	ENST00000334344	NM_152641.2	104	Cat/Tat	4/21	0.412081953796127	5	FACETS	1	0.954	1	0.351	0.322	0.381	CLONAL	1	TRUE	2	0.472591836097702	5		376	1223	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861119	57861119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1580	240	441	0	ENST00000228682.2:c.916G>A	p.Glu306Lys	p.E306K	ENST00000228682	NM_005269.2	306	Gaa/Aaa	9/12	0.412081953796127	5	FACETS	0.954	0.887	1	0.318	0.295	0.341	CLONAL	1	TRUE	2	0.472591836097702	5		441	1820	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133699	2133699	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	133	245	0	ENST00000219476.3:c.3887C>G	p.Ser1296Cys	p.S1296C	ENST00000219476	NM_000548.3	1296	tCc/tGc	33/42	0.412081953796127	5	FACETS	1	0.958	1	0.366	0.332	0.401	CLONAL	1	TRUE	2	0.472591836097702	5		245	877	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348945	11348945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	80	148	0	ENST00000332029.2:c.391C>G	p.Gln131Glu	p.Q131E	ENST00000332029	NM_003745.1	131	Cag/Gag	2/2	0.412081953796127	5	FACETS	1	0.887	1	0.335	0.295	0.378	CLONAL	1	TRUE	2	0.472591836097702	5		148	575	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829319	72829319	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0007577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	272	504	0	ENST00000268489.5:c.7262C>G	p.Ser2421Ter	p.S2421*	ENST00000268489	NM_006885.3	2421	tCa/tGa	9/10	0.472591836097702	2	FACETS	0.997	0.936	1	0.499	0.468	0.531	CLONAL	1	TRUE	0	0.472591836097702	2		504	1154	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576024	29576024	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	139	310	0	ENST00000356175.3:c.3997G>T	p.Glu1333Ter	p.E1333*	ENST00000356175	NM_000267.3	1333	Gag/Tag	30/57	0.336842544032737	4	FACETS	0.985	0.897	1	0.493	0.448	0.54	CLONAL	1	TRUE	2	0.472591836097702	4		310	879	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881145	37881145	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	248	303	0	ENST00000269571.5:c.2474G>A	p.Trp825Ter	p.W825*	ENST00000269571		825	tGg/tAg	20/27	0.336842544032737	4	FACETS	0.798	0.747	0.851	0.798	0.747	0.851	SUBCLONAL	2	TRUE	2	0.472591836097702	4		303	968	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881307	37881307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	278	253	0	ENST00000269571.5:c.2499G>A	p.Met833Ile	p.M833I	ENST00000269571		833	atG/atA	21/27	0.336842544032737	4	FACETS	0.943	0.887	0.999	0.943	0.887	0.999	CLONAL	2	TRUE	2	0.472591836097702	4		253	919	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881588	37881588	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	274	317	0	ENST00000269571.5:c.2658C>G	p.Ile886Met	p.I886M	ENST00000269571		886	atC/atG	22/27	0.336842544032737	4	FACETS	0.804	0.755	0.854	0.804	0.755	0.854	CLONAL	2	TRUE	2	0.472591836097702	4		317	1062	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533019	63533019	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	165	374	0	ENST00000307078.5:c.1875G>C	p.Glu625Asp	p.E625D	ENST00000307078	NM_004655.3	625	gaG/gaC	7/11	0.336842544032737	4	FACETS	0.886	0.812	0.964	0.443	0.406	0.482	CLONAL	1	TRUE	2	0.472591836097702	4		374	1160	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265192	5265192	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	117	212	0	ENST00000357368.4:c.395C>G	p.Ser132Cys	p.S132C	ENST00000357368	NM_002850.3	132	tCt/tGt	5/38	0.472591836097702	3	FACETS	0.933	0.843	1	0.467	0.421	0.514	CLONAL	1	TRUE	1	0.472591836097702	3		212	656	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546941	9546941	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	89	188	0	ENST00000353224.5:c.1081C>G	p.Gln361Glu	p.Q361E	ENST00000353224	NM_177990.2	361	Caa/Gaa	5/10	0.402338121842498	4	FACETS	0.886	0.786	0.992	0.443	0.393	0.496	CLONAL	1	TRUE	2	0.472591836097702	4		188	626	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264072	46264072	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1327	215	508	0	ENST00000371998.3:c.1119G>C	p.Gln373His	p.Q373H	ENST00000371998		373	caG/caC	11/23	0.402338121842498	4	FACETS	0.869	0.805	0.935	0.434	0.402	0.468	CLONAL	1	TRUE	2	0.472591836097702	4		508	1542	SUCCESS
AR	367	MSKCC	GRCh37	X	66941785	66941785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	214	377	0	ENST00000374690.3:c.2429C>T	p.Ala810Val	p.A810V	ENST00000374690	NM_000044.3	810	gCa/gTa	6/8	0.208645437954674	3	FACETS	1	0.967	1	0.357	0.331	0.383	INDETERMINATE	1	TRUE	0	0.472591836097702	3		377	1046	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883676	37883869	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGGCTGCAAAGCCTCCCCACACATGACCCCAGCCCTCTACAGCGGTACAGTGAGGACCCCACAGTACCCCTGCCCTCTGAGACTGATGGCTACGTTGCCCCCCTGACCTGCAGCCCCCAGCCTGGTATGGAGTCCAGTCTAAGCAGAGAGACTGATGGGCAGGGGAGGTGGGACCTTCAGCCCAGGGTCCACT	GGGGCTGCAAAGCCTCCCCACACATGACCCCAGCCCTCTACAGCGGTACAGTGAGGACCCCACAGTACCCCTGCCCTCTGAGACTGATGGCTACGTTGCCCCCCTGACCTGCAGCCCCCAGCCTGGTATGGAGTCCAGTCTAAGCAGAGAGACTGATGGGCAGGGGAGGTGGGACCTTCAGCCCAGGGTCCACT	-	novel	NA	P-0007577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	193	344	0	ENST00000269571.5:c.3289_3412+70del		p.X1097_splice	ENST00000269571		1097		26/27	0.336842544032737	4	FACETS	1	0.975	1	0.561	0.518	0.605	CLONAL	1	TRUE	2	0.472591836097702	4		344	1072	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849569	68849570	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs876659208	NA	P-0007577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	460	497	0	ENST00000261769.5:c.1476_1477del	p.Arg492SerfsTer44	p.R492Sfs*44	ENST00000261769	NM_004360.3	491	aAG/a	10/16	0.472591836097702	2	FACETS	0.963	0.923	1	0.963	0.923	1	CLONAL	2	TRUE	0	0.472591836097702	2		497	1011	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120645	115120646	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0007577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	436	419	2	ENST00000257566.3:c.359_360dup	p.Thr121AlafsTer19	p.T121Afs*19	ENST00000257566	NM_016569.3	120	-/GC	1/8	NA	2	FACETS	0.975	0.934	1			1	INDETERMINATE	2	TRUE	NA	0.472591836097702	2		421	946	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0007608-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	346	597	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	0.312727781601298	5	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	FALSE	2	0.312727781601298	5		597	1011	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0007608-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	146	360	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	0.932	0.856	1			1	INDETERMINATE	2	FALSE	NA	0.312727781601298	2		361	501	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0007608-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	443	489	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.312727781601298	7	FACETS	0.957	0.913	1	0.957	0.913	1	CLONAL	4	FALSE	3	0.312727781601298	7		489	1319	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	322	586	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.528379612214759	3	FACETS	0.911	0.863	0.958	0.911	0.863	0.958	CLONAL	2	TRUE	1	0.528379612214759	3		586	846	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568848	212568848	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	192	450	1	ENST00000342788.4:c.1270G>T	p.Gly424Cys	p.G424C	ENST00000342788	NM_005235.2	424	Ggt/Tgt	11/28	0.528379612214759	3	FACETS	1	0.951	1	0.517	0.479	0.557	CLONAL	1	TRUE	1	0.528379612214759	3		451	888	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279190	142279190	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	383	506	1	ENST00000350721.4:c.1456G>T	p.Val486Phe	p.V486F	ENST00000350721	NM_001184.3	486	Gtt/Ttt	6/47	0.528379612214759	2	FACETS	0.945	0.904	0.986	0.945	0.904	0.986	CLONAL	2	TRUE	0	0.528379612214759	2		507	767	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178128	56178128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	170	385	0	ENST00000399503.3:c.3101C>T	p.Pro1034Leu	p.P1034L	ENST00000399503	NM_005921.1	1034	cCt/cTt	14/20	0.528379612214759	3	FACETS	1	0.95	1	0.521	0.48	0.564	CLONAL	1	TRUE	1	0.528379612214759	3		385	781	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220410	1220410	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	309	515	0	ENST00000326873.7:c.503A>T	p.His168Leu	p.H168L	ENST00000326873	NM_000455.4	168	cAt/cTt	4/10	0.528379612214759	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.528379612214759	2		515	566	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621169	1621169	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	386	553	0	ENST00000344749.5:c.977G>T	p.Gly326Val	p.G326V	ENST00000344749	NM_001136139.2	326	gGc/gTc	12/19	0.528379612214759	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.528379612214759	2		553	695	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791760	42791760	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	261	361	0	ENST00000575354.2:c.646G>T	p.Ala216Ser	p.A216S	ENST00000575354	NM_015125.3	216	Gcc/Tcc	5/20	0.528379612214759	3	FACETS	0.928	0.875	0.982	0.928	0.875	0.982	CLONAL	2	TRUE	1	0.528379612214759	3		361	673	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022589	31022589	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1478929932	NA	P-0007638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	524	527	1	ENST00000375687.4:c.2074C>T	p.Gln692Ter	p.Q692*	ENST00000375687	NM_015338.5	692	Cag/Tag	13/13	0.517765332142599	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	1	0.528379612214759	4		528	983	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934205	39934205	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	564	738	2	ENST00000378444.4:c.394G>T	p.Val132Leu	p.V132L	ENST00000378444	NM_001123385.1	132	Gtg/Ttg	4/15	0.528379612214759	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.528379612214759	3		740	1277	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044887	47044887	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	256	434	0	ENST00000377604.3:c.2213G>T	p.Ser738Ile	p.S738I	ENST00000377604	NM_001204468.1	738	aGt/aTt	20/24	0.528379612214759	3	FACETS	0.959	0.904	1	0.959	0.904	1	CLONAL	2	TRUE	1	0.528379612214759	3		434	639	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411080	63411082	+	stop_gained	Nonsense_Mutation	TNP	CTC	CTC	TTT	novel	NA	P-0007638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	205	567	0	ENST00000330258.3:c.2085_2087delinsAAA	p.Trp695_Arg696delinsTer	p.W695_R696delins*	ENST00000330258	NM_152424.3	695	tgGAGg/tgAAAg	2/2	0.528379612214759	3	FACETS	0.98	0.909	1	0.49	0.454	0.527	CLONAL	1	TRUE	1	0.528379612214759	3		567	1001	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876113	35876113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1380648416	NA	P-0007641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	36	416	0	ENST00000303115.3:c.905G>A	p.Ser302Asn	p.S302N	ENST00000303115	NM_002185.3	302	aGt/aAt	8/8	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.225720100577198	2		416	228	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938377	76938378	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	137	331	0	ENST00000373344.5:c.2370dup	p.Asp791Ter	p.D791*	ENST00000373344	NM_000489.3	790	-/T	9/35	1	1	FACETS	0.93	0.878	0.979	1	0.994	1	CLONAL	6	TRUE	0	0.225720100577198	1		331	193	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0007648-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	324	364	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.510029241083471	1	FACETS	0.961	0.911	1	0.961	0.911	1	CLONAL	1	TRUE	0	0.548026162728807	1		365	893	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0007648-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	710	387	1	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.548026162728807	4	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.548026162728807	4		388	1763	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268147	153268147	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007648-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	528	389	0	ENST00000281708.4:c.661C>T	p.Gln221Ter	p.Q221*	ENST00000281708	NM_033632.3	221	Caa/Taa	4/12	0.530786145045478	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.548026162728807	2		389	924	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245240	46245240	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007648-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	39	303	0	ENST00000334344.6:c.3334C>T	p.Gln1112Ter	p.Q1112*	ENST00000334344	NM_152641.2	1112	Cag/Tag	15/21	1	2	FACETS	0.202	0.167	0.242	0.202	0.167	0.242	SUBCLONAL	1	TRUE	1	0.548026162728807	2		303	705	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89839771	89839771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007648-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	63	462	2	ENST00000389301.3:c.1922C>T	p.Ala641Val	p.A641V	ENST00000389301	NM_000135.2	641	gCa/gTa	22/43	NA	2	FACETS	0.193	0.166	0.223			1	INDETERMINATE	1	TRUE	NA	0.548026162728807	2		464	1190	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428472	78428473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATAG	novel	NA	P-0007648-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	218	386	0	ENST00000370768.2:c.1326_1327insCTAT	p.Ile443LeufsTer49	p.I443Lfs*49	ENST00000370768	NM_003902.3	442	-/CTAT	14/20	1	2	FACETS	0.851	0.792	0.912	0.851	0.792	0.912	CLONAL	1	TRUE	1	0.548026162728807	2		386	935	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572969	7572969	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1555524108	NA	P-0007651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	42	535	0	ENST00000269305.4:c.1140del	p.His380GlnfsTer42	p.H380Qfs*42	ENST00000269305	NM_001126112.2	380	caT/ca	11/11	0.815193444946507	1	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	0	0.815193444946507	1		535	60	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0007668-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	265	460	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.599451577403887	2		460	877	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874530	155874530	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs869025191	NA	P-0007668-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1380	345	656	0	ENST00000368323.3:c.229G>A	p.Ala77Thr	p.A77T	ENST00000368323	NM_006912.5	77	Gct/Act	4/6	0.599451577403887	3	FACETS	0.867	0.818	0.918	0.434	0.409	0.459	CLONAL	1	TRUE	1	0.599451577403887	3		656	1725	SUCCESS
ATM	472	MSKCC	GRCh37	11	108137926	108137926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199875915	NA	P-0007668-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	310	502	2	ENST00000278616.4:c.2495G>A	p.Arg832His	p.R832H	ENST00000278616	NM_000051.3	832	cGt/cAt	17/63	1	2	FACETS	0.925	0.873	0.979	0.925	0.873	0.979	CLONAL	1	TRUE	1	0.599451577403887	2		504	1118	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385095	31385095	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007668-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	240	394	0	ENST00000328111.2:c.1480A>G	p.Ser494Gly	p.S494G	ENST00000328111	NM_006892.3	494	Agc/Ggc	14/23	0.599451577403887	3	FACETS	1	0.969	1	0.531	0.496	0.567	CLONAL	1	TRUE	1	0.599451577403887	3		394	980	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443751	52443754	+	frameshift_variant	Frame_Shift_Del	DEL	TGAA	TGAA	-	novel	NA	P-0007668-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	129	290	0	ENST00000460680.1:c.43_46del	p.Phe15ProfsTer56	p.F15Pfs*56	ENST00000460680	NM_004656.3	15	TTCAcc/cc	2/17	0.599451577403887	1	FACETS	0.849	0.779	0.92	0.849	0.779	0.92	CLONAL	1	TRUE	0	0.599451577403887	1		290	355	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792604	33792633	+	inframe_deletion	In_Frame_Del	DEL	GGGCGCGGGGTGCGGGCTGGGCACGGGCGT	GGGCGCGGGGTGCGGGCTGGGCACGGGCGT	-	novel	NA	P-0007668-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	26	16	0	ENST00000498907.2:c.688_717del	p.Thr230_Pro239del	p.T230_P239del	ENST00000498907	NM_004364.3	230	ACGCCCGTGCCCAGCCCGCACCCCGCGCCC/-	1/1	1	2	FACETS	0.761	0.633	0.891	1	0.948	1	SUBCLONAL	2	TRUE	1	0.599451577403887	2		16	57	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111502	8111503	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0007684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	216	508	0	ENST00000346208.3:c.990dup	p.Asn331GlufsTer21	p.N331Efs*21	ENST00000346208		330	agg/aGgg	5/6	0.102501881271445	4	FACETS	0.964	0.899	1	1	0.991	1	INDETERMINATE	3	TRUE	2	0.247030218227531	4		508	754	SUCCESS
APC	324	MSKCC	GRCh37	5	112173949	112173949	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007685-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	108	315	0	ENST00000257430.4:c.2658G>C	p.Gln886His	p.Q886H	ENST00000257430	NM_000038.5	886	caG/caC	16/16	1	2	FACETS	0.683	0.612	0.758	0.683	0.612	0.758	SUBCLONAL	1	TRUE	1	0.360766889827729	2		315	877	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425476	49425476	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007685-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1290	168	665	0	ENST00000301067.7:c.13012C>G	p.Pro4338Ala	p.P4338A	ENST00000301067	NM_003482.3	4338	Ccc/Gcc	39/54	1	2	FACETS	0.639	0.585	0.695	0.639	0.585	0.695	SUBCLONAL	1	TRUE	1	0.360766889827729	2		665	1458	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777918	3777918	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007685-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1395	179	558	1	ENST00000262367.5:c.7130C>T	p.Ser2377Leu	p.S2377L	ENST00000262367	NM_004380.2	2377	tCa/tTa	31/31	1	2	FACETS	0.63	0.579	0.684	0.63	0.579	0.684	SUBCLONAL	1	TRUE	1	0.360766889827729	2		559	1574	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0007691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	103	565	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	0.508000507004916	2		565	353	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0007691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	62	311	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.303055733218498	1	FACETS	0.859	0.753	0.97	0.859	0.753	0.97	INDETERMINATE	1	TRUE	0	0.508000507004916	1		311	212	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0007691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	95	546	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	0.508000507004916	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.508000507004916	1		546	273	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	135	586	0	ENST00000342988.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000342988	NM_005359.5	356	cCt/cTt	9/12	0.508000507004916	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.508000507004916	1		586	369	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732976	30732976	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	147	345	0	ENST00000295754.5:c.1589C>T	p.Thr530Ile	p.T530I	ENST00000295754	NM_003242.5	530	aCa/aTa	7/7	0.303055733218498	1	FACETS	1	0.979	1	1	0.979	1	INDETERMINATE	1	TRUE	0	0.508000507004916	1		345	369	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117961	70117961	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	107	160	1	ENST00000245479.2:c.429G>A	p.Trp143Ter	p.W143*	ENST00000245479	NM_000346.3	143	tgG/tgA	1/3	0.243708846109673	1	FACETS	0.888	0.804	0.974	0.888	0.804	0.974	INDETERMINATE	1	TRUE	0	0.508000507004916	1		161	354	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395663	45395664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0007691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	94	454	0	ENST00000262160.6:c.470dup	p.Asp158GlyfsTer2	p.D158Gfs*2	ENST00000262160	NM_005901.5	157	aag/aaAg	4/11	0.508000507004916	1	FACETS	0.896	0.807	0.989	0.896	0.807	0.989	CLONAL	1	TRUE	0	0.508000507004916	1		454	308	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0007694-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	752	313	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.828436211645626	4	FACETS	1	0.998	1	1	0.998	1	CLONAL	4	TRUE	0	0.828436211645626	4		313	784	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361207	66361207	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007694-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	446	353	0	ENST00000273854.3:c.965G>C	p.Cys322Ser	p.C322S	ENST00000273854	NM_004439.5	322	tGt/tCt	4/18	0.710620107906291	6	FACETS	0.989	0.954	1			1	CLONAL	4	TRUE	NA	0.828436211645626	6		353	723	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876252	35876252	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007694-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	296	352	0	ENST00000303115.3:c.1044C>G	p.Asn348Lys	p.N348K	ENST00000303115	NM_002185.3	348	aaC/aaG	8/8	0.765768461469521	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.828436211645626	4		352	614	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639905	93639905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201438493	NA	P-0007694-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	240	325	0	ENST00000375746.1:c.1234G>A	p.Ala412Thr	p.A412T	ENST00000375746	NM_001174167.1	412	Gct/Act	10/14	0.773441877076361	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.828436211645626	3		325	407	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039340	49039340	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0007694-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	353	569	0	ENST00000267163.4:c.2326-1G>T		p.X776_splice	ENST00000267163	NM_000321.2	776			0.828436211645626	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.828436211645626	2		569	406	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0007702-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	612	724	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	0.478180533745869	1	FACETS	0.659	0.638	0.679	0.659	0.638	0.679	INDETERMINATE	1	TRUE	0	0.940402562413459	1		724	1047	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89345580	89345580	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1303172994	NA	P-0007702-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	10	31	0	ENST00000301030.4:c.7370G>A	p.Cys2457Tyr	p.C2457Y	ENST00000301030	NM_001256183.1	2457	tGt/tAt	9/13	0.481387505456537	1	FACETS	0.213	0.147	0.29	0.213	0.147	0.29	INDETERMINATE	1	TRUE	0	0.940402562413459	1		31	53	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	106	160	0				ENST00000310581	NM_198253.2	-/1132			0.197107183800861	4	FACETS	0.835	0.752	0.921	1	0.974	1	CLONAL	3	TRUE	2	0.214723201649341	4		160	479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519999	NA	P-0007755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	159	296	0	ENST00000269305.4:c.716A>G	p.Asn239Ser	p.N239S	ENST00000269305	NM_001126112.2	239	aAc/aGc	7/11	1	2	FACETS	0.826	0.758	0.898	1	0.99	1	CLONAL	2	TRUE	1	0.214723201649341	2		296	896	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100081	157100092	+	inframe_deletion	In_Frame_Del	DEL	GCGGCGGCGGCC	GCGGCGGCGGCC	-	rs763063242	NA	P-0007755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	19	32	0	ENST00000346085.5:c.1029_1040del	p.Ala347_Ala350del	p.A347_A350del	ENST00000346085	NM_020732.3	340	GCGGCGGCGGCC/-	1/20	1	2	FACETS	1	0.787	1	1	0.952	1	CLONAL	3	TRUE	1	0.214723201649341	2		32	59	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	rs786202799	NA	P-0007755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	105	299	0	ENST00000269305.4:c.376-2A>T		p.X126_splice	ENST00000269305	NM_001126112.2	126			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.214723201649341	2		299	680	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681461	30681461	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	150	544	0	ENST00000376406.3:c.551C>T	p.Ser184Leu	p.S184L	ENST00000376406	NM_014641.2	184	tCa/tTa	4/15	0.214723201649341	3	FACETS	1	0.976	1	0.602	0.548	0.658	CLONAL	1	TRUE	1	0.214723201649341	3		544	1286	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527328	157527328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	169	353	0	ENST00000346085.5:c.5053G>A	p.Glu1685Lys	p.E1685K	ENST00000346085	NM_020732.3	1685	Gag/Aag	20/20	1	2	FACETS	0.946	0.871	1	1	0.992	1	CLONAL	2	TRUE	1	0.214723201649341	2		353	832	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247369	153247369	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	129	230	0	ENST00000281708.4:c.1433C>T	p.Ser478Phe	p.S478F	ENST00000281708	NM_033632.3	478	tCt/tTt	10/12	0.214723201649341	1	FACETS	0.977	0.89	1	1	0.99	1	CLONAL	2	TRUE	0	0.214723201649341	1		230	549	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428532	72428532	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	65	377	0	ENST00000477973.2:c.472C>T	p.Gln158Ter	p.Q158*	ENST00000477973	NM_012234.5	158	Cag/Tag	2/4	0.193306765436673	1	FACETS	0.652	0.564	0.748	0.652	0.564	0.748	SUBCLONAL	1	TRUE	0	0.214723201649341	1		377	829	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513469	149513469	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	58	411	0	ENST00000261799.4:c.734T>C	p.Phe245Ser	p.F245S	ENST00000261799	NM_002609.3	245	tTc/tCc	5/23	1	2	FACETS	0.604	0.517	0.699	0.604	0.517	0.699	SUBCLONAL	1	TRUE	1	0.214723201649341	2		411	895	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151919142	151919142	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	87	334	0	ENST00000262189.6:c.3443C>A	p.Ser1148Ter	p.S1148*	ENST00000262189	NM_170606.2	1148	tCa/tAa	22/59	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.214723201649341	2		334	633	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482185	87482185	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	196	479	0	ENST00000277120.3:c.1472A>G	p.Asp491Gly	p.D491G	ENST00000277120		491	gAt/gGt	14/19	1	2	FACETS	0.801	0.74	0.864	1	0.991	1	CLONAL	2	TRUE	1	0.214723201649341	2		479	1140	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900894	3900894	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0007755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	319	567	0	ENST00000262367.5:c.202A>T	p.Lys68Ter	p.K68*	ENST00000262367	NM_004380.2	68	Aaa/Taa	2/31	0.214723201649341	1	FACETS	1	0.991	1	1	0.996	1	CLONAL	2	TRUE	0	0.214723201649341	1		567	1077	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587454	29587454	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1135402862	NA	P-0007755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	77	440	0	ENST00000356175.3:c.4435A>G	p.Ser1479Gly	p.S1479G	ENST00000356175	NM_000267.3	1479	Agt/Ggt	33/57	1	2	FACETS	0.744	0.651	0.844	0.744	0.651	0.844	SUBCLONAL	1	TRUE	1	0.214723201649341	2		440	964	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637883	39637883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	150	442	2	ENST00000262039.4:c.2300G>A	p.Gly767Asp	p.G767D	ENST00000262039	NM_002647.2	767	gGt/gAt	22/25	0.214723201649341	1	FACETS	0.781	0.715	0.851	1	0.988	1	SUBCLONAL	2	TRUE	0	0.214723201649341	1		444	798	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368262	31368262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	184	314	0	ENST00000328111.2:c.133G>A	p.Glu45Lys	p.E45K	ENST00000328111	NM_006892.3	45	Gag/Aag	2/23	0.214723201649341	3	FACETS	0.929	0.861	0.999			1	CLONAL	3	TRUE	NA	0.214723201649341	3		314	681	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565505	41565505	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0007755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	200	442	0	ENST00000263253.7:c.4173-2A>G		p.X1391_splice	ENST00000263253	NM_001429.3	1391			1	2	FACETS	0.936	0.867	1	1	0.993	1	CLONAL	2	TRUE	1	0.214723201649341	2		442	995	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533500	63533526	+	inframe_deletion	In_Frame_Del	DEL	AGCAGTAATACTCGCTGCCCCCAGGGC	AGCAGTAATACTCGCTGCCCCCAGGGC	-	novel	NA	P-0007755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	145	426	1	ENST00000307078.5:c.1628_1654del	p.Cys543_Cys551del	p.C543_C551del	ENST00000307078	NM_004655.3	543	tGCCCTGGGGGCAGCGAGTATTACTGCTac/tac	6/11	0.156911587027095	3	FACETS	0.846	0.772	0.924	0.846	0.772	0.924	CLONAL	2	TRUE	1	0.214723201649341	3		427	884	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-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	162	300	0	ENST00000324856.7:c.2733-1_2744del		p.X911_splice	ENST00000324856	NM_006015.4	911		9/20	1	2	FACETS	0.94	0.863	1	1	0.991	1	CLONAL	2	TRUE	1	0.214723201649341	2		300	803	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171600	36171600	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0007759-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	32	200	0	ENST00000300305.3:c.965C>G	p.Ser322Ter	p.S322*	ENST00000300305		322	tCa/tGa	7/8	1	2	FACETS	0.653	0.529	0.793	0.653	0.529	0.793	SUBCLONAL	1	TRUE	1	0.200088492552842	2		200	490	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193219825	193219825	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007759-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	102	415	0	ENST00000367435.3:c.1579T>G	p.Ser527Ala	p.S527A	ENST00000367435	NM_024529.4	527	Tcg/Gcg	17/17	0.200088492552842	3	FACETS	0.922	0.822	1	0.461	0.411	0.515	CLONAL	1	TRUE	1	0.200088492552842	3		415	1216	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003275	143003275	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007759-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	97	466	0	ENST00000262992.4:c.2551A>C	p.Met851Leu	p.M851L	ENST00000262992	NM_001101669.1	851	Atg/Ctg	23/24	1	2	FACETS	0.781	0.694	0.875	0.781	0.694	0.875	SUBCLONAL	1	TRUE	1	0.200088492552842	2		466	1241	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0007775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	82	487	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.269338332093463	5	FACETS	1	0.966	1	0.821	0.73	0.917	CLONAL	2	TRUE	2	0.269338332093463	5		487	347	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715685	30715685	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	70	438	0	ENST00000295754.5:c.1343A>G	p.Tyr448Cys	p.Y448C	ENST00000295754	NM_003242.5	448	tAc/tGc	5/7	0.267666663458828	3	FACETS	1	0.909	1	0.692	0.61	0.78	CLONAL	2	TRUE	0	0.269338332093463	3		438	284	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285888	38285888	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	39	774	0	ENST00000425967.3:c.523G>C	p.Asp175His	p.D175H	ENST00000425967	NM_001174067.1	175	Gat/Cat	5/19	1	2	FACETS	0.908	0.755	1	0.908	0.755	1	CLONAL	1	TRUE	1	0.269338332093463	2		774	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578273	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0007775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	73	569	1	ENST00000269305.4:c.576_577delinsTT	p.Gln192_His193delinsHisTyr	p.Q192_H193delinsHY	ENST00000269305	NM_001126112.2	192	caGCat/caTTat	6/11	0.223254190539637	2	FACETS	0.941	0.832	1	0.941	0.832	1	CLONAL	2	TRUE	0	0.269338332093463	2		570	288	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827927	40827927	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536150112	NA	P-0007806-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	207	457	2	ENST00000373198.4:c.2501G>A	p.Arg834His	p.R834H	ENST00000373198	NM_133170.3	834	cGc/cAc	17/32	0.166001677001309	3	FACETS	0.749	0.693	0.807	0.25	0.231	0.269	INDETERMINATE	1	TRUE	0	0.540177395047285	3		459	1300	SUCCESS
AR	367	MSKCC	GRCh37	X	66765875	66765875	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007806-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	146	466	0	ENST00000374690.3:c.887A>G	p.Asp296Gly	p.D296G	ENST00000374690	NM_000044.3	296	gAc/gGc	1/8	1	2	FACETS	0.47	0.427	0.514	0.47	0.427	0.514	SUBCLONAL	1	TRUE	1	0.540177395047285	2		466	1151	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183862	10183864	+	missense_variant	Missense_Mutation	TNP	AGC	AGC	CCT	novel	NA	P-0007806-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	123	173	0	ENST00000256474.2:c.331_333delinsCCT	p.Ser111Pro	p.S111P	ENST00000256474	NM_000551.3	111	AGC/CCT	1/3	0.508684391689249	2	FACETS	1	0.986	1	0.703	0.644	0.763	CLONAL	1	TRUE	0	0.540177395047285	2		173	324	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0007813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	1258	565	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.3	20	FACETS	0.996	0.978	1			1	CLONAL	19	TRUE	NA	0.24	20		565	1750	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220272	55220272	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	181	372	0	ENST00000275493.2:c.662G>T	p.Gly221Val	p.G221V	ENST00000275493	NM_005228.3	221	gGg/gTg	6/28	0.180159111691631	4	FACETS	0.77	0.709	0.834	0.77	0.709	0.834	SUBCLONAL	2	TRUE	2	0.24	4		372	1214	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502187	157502187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761227259	NA	P-0007813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	105	315	0	ENST00000346085.5:c.3220G>A	p.Asp1074Asn	p.D1074N	ENST00000346085	NM_020732.3	1074	Gac/Aac	12/20	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.24	2		315	829	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945695	206945695	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	83	374	0	ENST00000423557.1:c.86G>C	p.Ser29Thr	p.S29T	ENST00000423557	NM_000572.2	29	aGc/aCc	1/5	0.3	5	FACETS	0.776	0.683	0.877	0.259	0.227	0.293	SUBCLONAL	1	TRUE	2	0.24	5		374	1212	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825442	134825442	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	91	325	0	ENST00000398015.3:c.958A>T	p.Thr320Ser	p.T320S	ENST00000398015	NM_004441.4	320	Act/Tct	4/16	0.3	3	FACETS	0.859	0.761	0.964	0.429	0.38	0.482	CLONAL	1	TRUE	1	0.24	3		325	989	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356205	66356205	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	88	366	0	ENST00000273854.3:c.1292T>C	p.Leu431Pro	p.L431P	ENST00000273854	NM_004439.5	431	cTa/cCa	5/18	0.223542077943519	3	FACETS	0.776	0.686	0.874	0.388	0.343	0.437	SUBCLONAL	1	TRUE	1	0.24	3		366	1058	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527578	157527578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142466273	NA	P-0007813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	92	290	0	ENST00000346085.5:c.5303C>T	p.Pro1768Leu	p.P1768L	ENST00000346085	NM_020732.3	1768	cCg/cTg	20/20	1	2	FACETS	0.964	0.856	1	0.964	0.856	1	CLONAL	1	TRUE	1	0.24	2		290	795	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115559	108115559	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	178	391	0	ENST00000278616.4:c.707T>G	p.Leu236Arg	p.L236R	ENST00000278616	NM_000051.3	236	cTt/cGt	7/63	1	2	FACETS	0.962	0.894	1	1	0.994	1	CLONAL	3	TRUE	1	0.24	2		391	514	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212482	133212482	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	238	360	0	ENST00000320574.5:c.5807G>C	p.Gly1936Ala	p.G1936A	ENST00000320574	NM_006231.2	1936	gGa/gCa	42/49	0.3	3	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	1	0.24	3		360	1109	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508439	29508439	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0007813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	131	396	0	ENST00000356175.3:c.587-1G>T		p.X196_splice	ENST00000356175	NM_000267.3	196			0.223542077943519	3	FACETS	0.853	0.779	0.929	1	0.981	1	CLONAL	3	TRUE	1	0.24	3		396	478	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763223	59763223	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	65	418	0	ENST00000259008.2:c.2879G>C	p.Ser960Thr	p.S960T	ENST00000259008	NM_032043.2	960	aGt/aCt	19/20	0.223542077943519	3	FACETS	1	0.939	1	0.573	0.498	0.655	CLONAL	1	TRUE	1	0.24	3		418	529	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714435	40714435	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	69	331	0	ENST00000373198.4:c.3962A>C	p.Glu1321Ala	p.E1321A	ENST00000373198	NM_133170.3	1321	gAg/gCg	29/32	NA	2	FACETS	0.654	0.568	0.747			1	INDETERMINATE	1	TRUE	NA	0.24	2		331	879	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349956	70349956	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	139	425	0	ENST00000374080.3:c.3939T>G	p.Ser1313Arg	p.S1313R	ENST00000374080		1313	agT/agG	28/45	NA	2	FACETS	0.892	0.81	0.979			1	INDETERMINATE	1	TRUE	NA	0.24	2		425	1298	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357225	70357225	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	119	280	0	ENST00000374080.3:c.5740C>G	p.Gln1914Glu	p.Q1914E	ENST00000374080		1914	Cag/Gag	39/45	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.24	2		280	788	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019988	123019989	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0007813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	221	431	0	ENST00000355640.3:c.476_477insG	p.Met160HisfsTer3	p.M160Hfs*3	ENST00000355640		159	gcc/gcGc	2/7	0.3	3	FACETS	0.752	0.698	0.808			1	SUBCLONAL	2	TRUE	NA	0.24	3		431	1372	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032188	10032190	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0007813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	69	378	0	ENST00000330684.3:c.633_635del	p.Glu211del	p.E211del	ENST00000330684	NM_001134407.1	211	gaGGAt/gat	3/13	0.223542077943519	3	FACETS	0.754	0.655	0.861	0.377	0.327	0.431	SUBCLONAL	1	TRUE	1	0.24	3		378	854	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	123	375	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.23	2		375	828	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	152	498	0	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.23	2		498	1064	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793663	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	183	829	2	ENST00000263967.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000263967	NM_006218.2	93	cGg/cAg	2/21	1	2	FACETS	0.776	0.716	0.839	1	0.99	1	SUBCLONAL	2	TRUE	1	0.23	2		831	1025	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717769	89717770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	45	148	0	ENST00000371953.3:c.800dup	p.Asp268GlyfsTer30	p.D268Gfs*30	ENST00000371953	NM_000314.4	265	cta/ctAa	7/9	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.23	2		148	280	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	112	429	0	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	0.23	2		429	785	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	134	406	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.23	2		406	834	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	90	389	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.23	2		389	639	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141523	11141523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1192589668	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	100	457	0	ENST00000358026.2:c.3500C>T	p.Ser1167Leu	p.S1167L	ENST00000358026	NM_001128849.1	1167	tCg/tTg	25/36	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.23	2		457	842	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100425	8100425	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	179	551	2	ENST00000346208.3:c.404del	p.Pro135ArgfsTer60	p.P135Rfs*60	ENST00000346208		133	taC/ta	3/6	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.23	2		553	1082	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	128	704	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	TRUE	1	0.23	2		704	891	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275290	41275290	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113411271	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	105	289	1	ENST00000349496.5:c.1456C>T	p.Arg486Cys	p.R486C	ENST00000349496	NM_001904.3	486	Cgc/Tgc	9/15	1	2	FACETS	0.8	0.718	0.885	1	0.984	1	SUBCLONAL	2	TRUE	1	0.23	2		290	571	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236087	108236087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781894	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	138	440	1	ENST00000278616.4:c.9023G>A	p.Arg3008His	p.R3008H	ENST00000278616	NM_000051.3	3008	cGt/cAt	63/63	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.23	2		441	871	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588981	67588981	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	46	291	0	ENST00000274335.5:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000274335		358	Cga/Tga	8/15	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.23	2		291	305	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	141	424	1	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	0.807	0.736	0.881	1	0.988	1	CLONAL	2	TRUE	1	0.23	2		425	760	SUCCESS
APC	324	MSKCC	GRCh37	5	112151245	112151246	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs1114167567	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	137	424	0	ENST00000257430.4:c.893_894del	p.His298LeufsTer28	p.H298Lfs*28	ENST00000257430	NM_000038.5	296	agCAca/agca	9/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.23	2		424	905	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	117	603	2	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.23	2		605	684	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828653	72828653	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777599986	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1339	298	901	3	ENST00000268489.5:c.7928G>A	p.Arg2643His	p.R2643H	ENST00000268489	NM_006885.3	2643	cGt/cAt	9/10	1	2	FACETS	0.791	0.743	0.842	1	0.994	1	SUBCLONAL	2	TRUE	1	0.23	2		904	1637	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390736	139390736	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	189	542	0	ENST00000277541.6:c.7455del	p.Ser2486ArgfsTer103	p.S2486Rfs*103	ENST00000277541	NM_017617.3	2485	ccC/cc	34/34	1	2	FACETS	0.799	0.738	0.863	1	0.991	1	SUBCLONAL	2	TRUE	1	0.23	2		542	1028	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101170	41101170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41279256	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	59	177	0	ENST00000373198.4:c.1186G>A	p.Val396Ile	p.V396I	ENST00000373198	NM_133170.3	396	Gta/Ata	8/32	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.23	2		177	392	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098363	11098363	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	162	526	0	ENST00000358026.2:c.885del	p.Thr296ArgfsTer7	p.T296Rfs*7	ENST00000358026	NM_001128849.1	294	gCc/gc	6/36	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.23	2		526	948	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100073	27100073	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs764041562	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	189	490	1	ENST00000324856.7:c.3869C>T	p.Thr1290Met	p.T1290M	ENST00000324856	NM_006015.4	1290	aCg/aTg	16/20	1	2	FACETS	0.789	0.729	0.852	1	0.991	1	SUBCLONAL	2	TRUE	1	0.23	2		491	1041	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301111	65301111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370434553	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	151	467	0	ENST00000342505.4:c.3337C>T	p.Arg1113Cys	p.R1113C	ENST00000342505	NM_002227.2	1113	Cgc/Tgc	24/25	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.23	2		467	915	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630496	47630496	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs587779102	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	162	364	1	ENST00000233146.2:c.166G>T	p.Glu56Ter	p.E56*	ENST00000233146	NM_000251.2	56	Gag/Tag	1/16	1	2	FACETS	1	0.94	1	1	0.992	1	CLONAL	2	TRUE	1	0.23	2		365	687	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705428	47705428	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs63751155	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	113	456	1	ENST00000233146.2:c.2228C>A	p.Ser743Ter	p.S743*	ENST00000233146	NM_000251.2	743	tCa/tAa	14/16	1	2	FACETS	0.785	0.708	0.866	1	0.985	1	SUBCLONAL	2	TRUE	1	0.23	2		457	626	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149483	61149483	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	128	412	0	ENST00000295025.8:c.1673A>G	p.Gln558Arg	p.Q558R	ENST00000295025	NM_002908.2	558	cAa/cGa	11/11	1	2	FACETS	0.754	0.684	0.828	1	0.986	1	SUBCLONAL	2	TRUE	1	0.23	2		412	738	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735624	204735624	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	59	139	0	ENST00000302823.3:c.425G>A	p.Gly142Asp	p.G142D	ENST00000302823	NM_005214.4	142	gGc/gAc	2/4	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.23	2		139	353	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936518	49936518	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867261592	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1225	291	789	4	ENST00000296474.3:c.1409G>A	p.Arg470His	p.R470H	ENST00000296474	NM_002447.2	470	cGt/cAt	2/20	1	2	FACETS	0.835	0.783	0.888	1	0.994	1	CLONAL	2	TRUE	1	0.23	2		793	1516	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927976	178927976	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	40	211	0	ENST00000263967.3:c.1254A>T	p.Glu418Asp	p.E418D	ENST00000263967	NM_006218.2	418	gaA/gaT	8/21	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.23	2		211	272	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431044	181431044	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	75	267	0	ENST00000325404.1:c.896A>C	p.Gln299Pro	p.Q299P	ENST00000325404	NM_003106.3	299	cAg/cCg	1/1	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.23	2		267	467	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805428	1805428	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748488719	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	154	451	0	ENST00000260795.2:c.940G>A	p.Ala314Thr	p.A314T	ENST00000260795		314	Gct/Act	7/17	1	2	FACETS	0.851	0.779	0.925	1	0.99	1	CLONAL	2	TRUE	1	0.23	2		451	787	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955593	55955593	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs373654225	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	125	627	3	ENST00000263923.4:c.3352C>T	p.Arg1118Ter	p.R1118*	ENST00000263923	NM_002253.2	1118	Cga/Tga	25/30	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.23	2		630	791	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522449	187522449	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1342860045	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	217	581	0	ENST00000441802.2:c.11614C>T	p.Arg3872Ter	p.R3872*	ENST00000441802	NM_005245.3	3872	Cga/Tga	21/27	1	2	FACETS	0.861	0.8	0.924	1	0.993	1	CLONAL	2	TRUE	1	0.23	2		581	1096	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177632	56177632	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs750250897	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	141	429	0	ENST00000399503.3:c.2605A>G	p.Ile869Val	p.I869V	ENST00000399503	NM_005921.1	869	Atc/Gtc	14/20	1	2	FACETS	0.788	0.718	0.861	1	0.988	1	SUBCLONAL	2	TRUE	1	0.23	2		429	778	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729606	41729606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	214	777	0	ENST00000242208.4:c.923G>A	p.Arg308His	p.R308H	ENST00000242208	NM_002192.2	308	cGt/cAt	3/3	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.23	2		777	1315	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211379	98211379	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	158	488	0	ENST00000331920.6:c.3776C>T	p.Thr1259Ile	p.T1259I	ENST00000331920	NM_000264.3	1259	aCa/aTa	22/24	1	2	FACETS	0.774	0.709	0.841	1	0.989	1	SUBCLONAL	2	TRUE	1	0.23	2		488	888	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250158	110250158	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	24	304	0	ENST00000374672.4:c.517T>C	p.Tyr173His	p.Y173H	ENST00000374672	NM_004235.4	173	Tat/Cat	3/5	1	2	FACETS	0.476	0.373	0.597	0.476	0.373	0.597	SUBCLONAL	1	TRUE	1	0.23	2		304	438	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750268	133750268	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	58	383	3	ENST00000318560.5:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000318560	NM_005157.4	367	Cga/Tga	7/11	1	2	FACETS	0.559	0.478	0.646	0.559	0.478	0.646	SUBCLONAL	1	TRUE	1	0.23	2		386	903	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106016	8106016	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	97	346	1	ENST00000346208.3:c.836C>T	p.Thr279Met	p.T279M	ENST00000346208		279	aCg/aTg	4/6	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.23	2		347	635	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189497	94189497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774057024	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	112	402	0	ENST00000323929.3:c.1508G>A	p.Arg503His	p.R503H	ENST00000323929	NM_005591.3	503	cGt/cAt	14/20	1	2	FACETS	0.834	0.752	0.92	1	0.986	1	CLONAL	2	TRUE	1	0.23	2		402	584	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114842	108114842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145355104	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	66	319	0	ENST00000278616.4:c.659C>T	p.Ala220Val	p.A220V	ENST00000278616	NM_000051.3	220	gCg/gTg	6/63	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.23	2		319	438	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175495	108175495	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1240167425	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	149	386	0	ENST00000278616.4:c.5590A>G	p.Thr1864Ala	p.T1864A	ENST00000278616	NM_000051.3	1864	Aca/Gca	37/63	1	2	FACETS	0.885	0.81	0.963	1	0.99	1	CLONAL	2	TRUE	1	0.23	2		386	732	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435716	49435716	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	168	548	2	ENST00000301067.7:c.6167A>G	p.Asp2056Gly	p.D2056G	ENST00000301067	NM_003482.3	2056	gAc/gGc	29/54	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.23	2		550	984	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426836	121426836	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1364708195	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	106	327	0	ENST00000257555.6:c.526+1G>A		p.X176_splice	ENST00000257555		176			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.23	2		327	642	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465432	99465432	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	137	426	1	ENST00000268035.6:c.2257C>T	p.Arg753Ter	p.R753*	ENST00000268035	NM_000875.3	753	Cga/Tga	11/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.23	2		427	875	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662384	67662384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112926498	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	212	579	0	ENST00000264010.4:c.1630C>T	p.Arg544Cys	p.R544C	ENST00000264010	NM_006565.3	544	Cgc/Tgc	9/12	1	2	FACETS	0.819	0.76	0.88	1	0.992	1	CLONAL	2	TRUE	1	0.23	2		579	1126	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347591	89347591	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	288	826	0	ENST00000301030.4:c.5359C>A	p.Leu1787Ile	p.L1787I	ENST00000301030	NM_001256183.1	1787	Ctt/Att	9/13	1	2	FACETS	0.863	0.81	0.918	1	0.994	1	CLONAL	2	TRUE	1	0.23	2		826	1451	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989483	7989483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769533529	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	103	379	0	ENST00000319144.4:c.203G>A	p.Arg68His	p.R68H	ENST00000319144	NM_001139.2	68	cGc/cAc	2/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.23	2		379	634	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15967432	15967432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1013043730	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	198	539	3	ENST00000268712.3:c.5171G>A	p.Arg1724Gln	p.R1724Q	ENST00000268712	NM_006311.3	1724	cGg/cAg	35/46	1	2	FACETS	0.785	0.726	0.846	1	0.991	1	SUBCLONAL	2	TRUE	1	0.23	2		542	1097	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118353	17118353	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	196	517	0	ENST00000285071.4:c.1484T>C	p.Leu495Pro	p.L495P	ENST00000285071	NM_144997.5	495	cTg/cCg	13/14	1	2	FACETS	0.86	0.796	0.926	1	0.992	1	CLONAL	2	TRUE	1	0.23	2		517	991	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110150	3110150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762714189	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	71	227	0	ENST00000078429.4:c.140C>T	p.Thr47Met	p.T47M	ENST00000078429	NM_002067.2	47	aCg/aTg	2/7	1	2	FACETS	0.804	0.705	0.909	1	0.977	1	CLONAL	2	TRUE	1	0.23	2		227	384	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291143	10291143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376894659	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	233	595	1	ENST00000340748.4:c.328G>A	p.Gly110Arg	p.G110R	ENST00000340748		110	Ggg/Agg	4/40	1	2	FACETS	0.811	0.755	0.869	1	0.993	1	CLONAL	2	TRUE	1	0.23	2		596	1249	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355296	15355296	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1282368628	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	26	102	0	ENST00000263377.2:c.2327C>T	p.Pro776Leu	p.P776L	ENST00000263377	NM_058243.2	776	cCg/cTg	13/20	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.23	2		102	157	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256659	19256659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	120	321	0	ENST00000162023.5:c.1054C>T	p.Arg352Trp	p.R352W	ENST00000162023		352	Cgg/Tgg	13/13	1	2	FACETS	0.875	0.793	0.962	1	0.988	1	CLONAL	2	TRUE	1	0.23	2		321	596	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023453	31023453	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs765264117	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	50	348	0	ENST00000375687.4:c.2938A>G	p.Ile980Val	p.I980V	ENST00000375687	NM_015338.5	980	Att/Gtt	13/13	1	2	FACETS	0.597	0.506	0.698	0.597	0.506	0.698	SUBCLONAL	1	TRUE	1	0.23	2		348	728	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256698	46256698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777100285	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	189	790	0	ENST00000371998.3:c.754C>T	p.Arg252Cys	p.R252C	ENST00000371998		252	Cgc/Tgc	8/23	1	2	FACETS	0.774	0.715	0.836	1	0.99	1	SUBCLONAL	2	TRUE	1	0.23	2		790	1061	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054252	30054252	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs543087642	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	120	554	0	ENST00000338641.4:c.674G>A	p.Arg225Gln	p.R225Q	ENST00000338641	NM_000268.3	225	cGg/cAg	7/16	1	2	FACETS	0.95	0.856	1	0.95	0.856	1	CLONAL	1	TRUE	1	0.23	2		554	1098	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513481	41513481	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	59	381	0	ENST00000263253.7:c.385G>A	p.Ala129Thr	p.A129T	ENST00000263253	NM_001429.3	129	Gca/Aca	2/31	1	2	FACETS	0.678	0.582	0.782	0.678	0.582	0.782	SUBCLONAL	1	TRUE	1	0.23	2		381	757	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2208958	2208958	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	156	590	0	ENST00000398665.3:c.992del	p.Asn331ThrfsTer56	p.N331Tfs*56	ENST00000398665	NM_032482.2	330	Aaa/aa	12/28	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.23	2		590	1239	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723126	49723128	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs751306787	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	167	497	0	ENST00000449682.2:c.1288_1290del	p.Glu430del	p.E430del	ENST00000449682	NM_020998.3	430	GAG/-	11/18	1	2	FACETS	0.786	0.722	0.852	1	0.99	1	SUBCLONAL	2	TRUE	1	0.23	2		497	924	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495415	56495417	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	189	518	0	ENST00000267101.3:c.3609_3611del	p.Arg1205del	p.R1205del	ENST00000267101	NM_001982.3	1202	cGGAgg/cgg	28/28	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.23	2		518	1115	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424443	49424443	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	148	463	0	ENST00000301067.7:c.13780del	p.Ala4594ProfsTer23	p.A4594Pfs*23	ENST00000301067	NM_003482.3	4594	Gcc/cc	41/54	1	2	FACETS	0.764	0.698	0.833	1	0.988	1	SUBCLONAL	2	TRUE	1	0.23	2		463	842	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007689	45007690	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	116	332	0	ENST00000558401.1:c.137_138del	p.Tyr46CysfsTer10	p.Y46Cfs*10	ENST00000558401	NM_004048.2	46	TAt/t	2/4	1	2	FACETS	0.752	0.678	0.829	1	0.984	1	SUBCLONAL	2	TRUE	1	0.23	2		332	671	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821553	72821554	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	113	442	0	ENST00000268489.5:c.10621dup	p.Glu3541GlyfsTer30	p.E3541Gfs*30	ENST00000268489	NM_006885.3	3541	gag/gGag	10/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.23	2		442	718	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40376865	40376866	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1410	272	859	0	ENST00000293328.3:c.306dup	p.Met103HisfsTer14	p.M103Hfs*14	ENST00000293328	NM_012448.3	102	-/C	4/19	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.23	2		859	1682	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020769	37020769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	71	510	0	ENST00000358127.4:c.76del	p.Val26PhefsTer3	p.V26Ffs*3	ENST00000358127	NM_001280556.1	26	Gtt/tt	2/10	1	2	FACETS	0.524	0.456	0.599	0.524	0.456	0.599	SUBCLONAL	1	TRUE	1	0.23	2		510	1178	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059170	42059170	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs756744691	NA	P-0007836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1157	289	828	3	ENST00000219905.7:c.8895del	p.Thr2966ProfsTer4	p.T2966Pfs*4	ENST00000219905	NM_001164273.1	2964	Ccc/cc	24/24	1	2	FACETS	0.869	0.815	0.924	1	0.995	1	CLONAL	2	TRUE	1	0.23	2		831	1446	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0007846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	78	399	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.982	0.862	1	0.982	0.862	1	CLONAL	1	TRUE	1	0.19	2		399	836	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041259	47041259	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	104	681	1	ENST00000377604.3:c.1687C>T	p.Gln563Ter	p.Q563*	ENST00000377604	NM_001204468.1	563	Cag/Tag	15/24	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.19	2		682	1057	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0007859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	18	791	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.404007874717997	1	FACETS	0.116	0.086	0.151	0.116	0.086	0.151	SUBCLONAL	1	TRUE	0	0.404007874717997	1		792	614	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0007859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	63	483	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.404007874717997	1	FACETS	0.621	0.539	0.709	0.621	0.539	0.709	SUBCLONAL	1	TRUE	0	0.404007874717997	1		483	401	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919683	50919683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1019032820	NA	P-0007859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	139	652	1	ENST00000440232.2:c.2851C>T	p.Pro951Ser	p.P951S	ENST00000440232	NM_002691.3	951	Ccc/Tcc	23/27	0.352873303305509	1	FACETS	0.811	0.74	0.885	0.811	0.74	0.885	CLONAL	1	TRUE	0	0.404007874717997	1		653	677	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225147	53225147	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	151	340	0	ENST00000375401.3:c.3071del	p.Glu1024GlyfsTer31	p.E1024Gfs*31	ENST00000375401	NM_004187.3	1024	gAg/gg	20/26	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.404007874717997	1		340	428	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0007870-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	157	412	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.475981477388428	4	FACETS	0.91	0.846	0.975	0.91	0.846	0.975	CLONAL	3	TRUE	1	0.471295824259916	4		412	359	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0007870-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	67	311	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.475981477388428	4	FACETS	0.89	0.775	1	0.445	0.387	0.507	CLONAL	1	TRUE	2	0.471295824259916	4		311	470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0007870-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	138	307	0	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	0.254334127155444	5	FACETS	0.966	0.891	1	0.579	0.534	0.625	INDETERMINATE	3	TRUE	0	0.471295824259916	5		307	345	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032474	12032474	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007870-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	46	320	0	ENST00000353533.5:c.910C>T	p.Arg304Ter	p.R304*	ENST00000353533	NM_003010.3	304	Cga/Tga	9/11	0.29021227290713	1	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	0	0.471295824259916	1		320	144	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867540	35867541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs869312857	NA	P-0007870-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	48	369	0	ENST00000303115.3:c.361dup	p.Ile121AsnfsTer8	p.I121Nfs*8	ENST00000303115	NM_002185.3	118	-/A	3/8	0.276013747474467	4	FACETS	0.797	0.676	0.93	0.199	0.169	0.233	INDETERMINATE	1	TRUE	0	0.471295824259916	4		369	376	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860281	151860281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007870-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	40	437	0	ENST00000262189.6:c.10381G>A	p.Asp3461Asn	p.D3461N	ENST00000262189	NM_170606.2	3461	Gat/Aat	43/59	0.471295824259916	6	FACETS	0.812	0.676	0.964	0.203	0.169	0.241	CLONAL	1	TRUE	2	0.471295824259916	6		437	406	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0007889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	61	741	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.861	0.741	0.991	0.861	0.741	0.991	CLONAL	1	TRUE	1	0.19	2		742	746	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371755	116371755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367628460	NA	P-0007889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	35	382	0	ENST00000397752.3:c.1234C>T	p.Arg412Cys	p.R412C	ENST00000397752	NM_000245.2	412	Cgc/Tgc	3/21	0.166633006856401	3	FACETS	0.84	0.688	1	0.42	0.344	0.506	CLONAL	1	TRUE	1	0.19	3		382	480	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332409	70332409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200477577	NA	P-0007889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	43	379	0	ENST00000373644.4:c.314C>T	p.Ala105Val	p.A105V	ENST00000373644	NM_030625.2	105	gCg/gTg	2/12	1	2	FACETS	0.865	0.724	1	0.865	0.724	1	CLONAL	1	TRUE	1	0.19	2		379	523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0007896-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	200	741	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	NA	2	FACETS	0.894	0.833	0.957			1	INDETERMINATE	2	TRUE	NA	0.349403464532848	2		742	640	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0007896-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	982	399	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.349403464532848	9	FACETS	1	0.98	1			1	CLONAL	8	TRUE	NA	0.349403464532848	9		399	1555	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141463	11141463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1224621923	NA	P-0007896-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	132	427	0	ENST00000358026.2:c.3440C>T	p.Ser1147Phe	p.S1147F	ENST00000358026	NM_001128849.1	1147	tCt/tTt	25/36	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.349403464532848	2		427	670	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951045	48951063	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCCTAAAGAACTGCACAG	CTCCTAAAGAACTGCACAG	-	novel	NA	P-0007896-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	31	243	0	ENST00000267163.4:c.1216-9_1225del		p.X406_splice	ENST00000267163	NM_000321.2	406		13/27	0.341819971300483	1	FACETS	0.351	0.284	0.428	0.351	0.284	0.428	SUBCLONAL	1	TRUE	0	0.349403464532848	1		243	417	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	620	939	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.596884705517916	3	FACETS	0.987	0.96	1	1	0.998	1	CLONAL	3	TRUE	1	0.596884705517916	3		940	911	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0007900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	392	495	1	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	1	2	FACETS	0.979	0.934	1	0.979	0.934	1	CLONAL	1	TRUE	1	0.820195904292884	2		496	976	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437848	110437848	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	146	124	0	ENST00000375856.3:c.553G>T	p.Gly185Trp	p.G185W	ENST00000375856	NM_003749.2	185	Ggg/Tgg	1/2	0.820195904292884	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.820195904292884	1		124	202	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849565	68849565	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	46	508	2	ENST00000261769.5:c.1468G>T	p.Glu490Ter	p.E490*	ENST00000261769	NM_004360.3	490	Gaa/Taa	10/16	0.78600816967748	1	FACETS	0.088	0.074	0.105	0.088	0.074	0.105	SUBCLONAL	1	TRUE	0	0.820195904292884	1		510	748	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578495	7578507	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCTGCACAGGG	CAGCTGCACAGGG	-	novel	NA	P-0007900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	308	361	0	ENST00000269305.4:c.423_435del	p.Pro142GlyfsTer24	p.P142Gfs*24	ENST00000269305	NM_001126112.2	141	tgCCCTGTGCAGCTG/tg	5/11	0.815620598985803	1	FACETS	0.919	0.881	0.956	0.919	0.881	0.956	CLONAL	1	TRUE	0	0.820195904292884	1		361	482	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726935	61726935	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007907-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	336	548	0	ENST00000401558.2:c.503T>C	p.Met168Thr	p.M168T	ENST00000401558	NM_003400.3	168	aTg/aCg	7/25	0.323943501609268	3	FACETS	0.906	0.857	0.956	0.906	0.857	0.956	CLONAL	2	TRUE	1	0.36730124272757	3		548	1195	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445838	49445838	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007907-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	161	596	0	ENST00000301067.7:c.1628C>A	p.Ser543Ter	p.S543*	ENST00000301067	NM_003482.3	543	tCg/tAg	10/54	0.365803920099708	3	FACETS	0.835	0.764	0.91	0.418	0.382	0.455	CLONAL	1	TRUE	1	0.36730124272757	3		596	1242	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728864	39728864	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007907-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	68	234	0	ENST00000361337.2:c.1144A>G	p.Ile382Val	p.I382V	ENST00000361337	NM_003286.2	382	Ata/Gta	12/21	1	2	FACETS	0.805	0.702	0.915	0.805	0.702	0.915	CLONAL	1	TRUE	1	0.36730124272757	2		234	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577553	+	inframe_deletion	In_Frame_Del	DEL	TGATGATGGTGAGGATGGGCCTCCGGTTCATGCCGCCCA	TGATGATGGTGAGGATGGGCCTCCGGTTCATGCCGCCCA	-	novel	NA	P-0007907-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	98	345	0	ENST00000269305.4:c.728_766del	p.Met243_Ile255del	p.M243_I255del	ENST00000269305	NM_001126112.2	243	aTGGGCGGCATGAACCGGAGGCCCATCCTCACCATCATCAca/aca	7/11	NA	2	FACETS	1	0.921	1			1	INDETERMINATE	1	TRUE	NA	0.36730124272757	2		345	516	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715979	52715979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786205227	NA	P-0007911-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	12	483	2	ENST00000322088.6:c.544C>T	p.Arg182Trp	p.R182W	ENST00000322088	NM_014225.5	182	Cgg/Tgg	5/15	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		485	578	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022535	12022535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159947	NA	P-0007911-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	308	511	0	ENST00000396373.4:c.641C>T	p.Pro214Leu	p.P214L	ENST00000396373	NM_001987.4	214	cCg/cTg	5/8	0.3	3	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	3		511	935	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239955	53239955	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007911-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	195	625	0	ENST00000375401.3:c.1486G>C	p.Gly496Arg	p.G496R	ENST00000375401	NM_004187.3	496	Ggc/Cgc	11/26	0.144152261213348	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		625	673	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007917-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	131	160	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.895	0.818	0.975			1	INDETERMINATE	1	TRUE	NA	0.632111771098555	2		160	463	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653805	89653805	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659443	NA	P-0007917-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	394	538	0	ENST00000371953.3:c.103A>G	p.Met35Val	p.M35V	ENST00000371953	NM_000314.4	35	Atg/Gtg	2/9	0.632111771098555	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.632111771098555	1		538	695	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245399	46245399	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007917-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	407	706	0	ENST00000334344.6:c.3493C>T	p.Gln1165Ter	p.Q1165*	ENST00000334344	NM_152641.2	1165	Caa/Taa	15/21	1	2	FACETS	0.985	0.937	1	0.985	0.937	1	CLONAL	1	TRUE	1	0.632111771098555	2		706	1307	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122866	2122866	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007917-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	365	712	0	ENST00000219476.3:c.2237C>G	p.Thr746Arg	p.T746R	ENST00000219476	NM_000548.3	746	aCa/aGa	21/42	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.632111771098555	2		712	1018	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577035	7577035	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	299	481	0	ENST00000269305.4:c.903del	p.Ser303AlafsTer42	p.S303Afs*42	ENST00000269305	NM_001126112.2	301	ccA/cc	8/11	NA	2	FACETS	0.921	0.871	0.971			1	INDETERMINATE	2	TRUE	NA	0.408019608521334	2		481	796	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412639	139412639	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1037236860	NA	P-0007924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	59	387	1	ENST00000277541.6:c.1205C>T	p.Ser402Leu	p.S402L	ENST00000277541	NM_017617.3	402	tCg/tTg	7/34	0.408019608521334	2	FACETS	0.426	0.366	0.492	0.213	0.183	0.246	SUBCLONAL	1	TRUE	0	0.408019608521334	2		388	679	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693852	47693852	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs63750224	NA	P-0007924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	70	544	0	ENST00000233146.2:c.1566C>G	p.Tyr522Ter	p.Y522*	ENST00000233146	NM_000251.2	522	taC/taG	10/16	0.261277791173956	4	FACETS	0.403	0.349	0.46	0.201	0.174	0.23	SUBCLONAL	1	TRUE	2	0.408019608521334	4		544	1200	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924771	49924771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs541003810	NA	P-0007924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	117	805	2	ENST00000296474.3:c.4172G>A	p.Arg1391Gln	p.R1391Q	ENST00000296474	NM_002447.2	1391	cGg/cAg	20/20	0.361604877859316	2	FACETS	0.541	0.486	0.598	0.27	0.243	0.299	SUBCLONAL	1	TRUE	0	0.408019608521334	2		807	1061	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862937	117862937	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs202084322	NA	P-0007924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	73	662	0	ENST00000297338.2:c.1540C>T	p.Gln514Ter	p.Q514*	ENST00000297338	NM_006265.2	514	Cag/Tag	12/14	0.408672663360926	3	FACETS	0.357	0.311	0.407	0.179	0.155	0.204	SUBCLONAL	1	TRUE	1	0.408019608521334	3		662	1206	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737680	145737680	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	187	341	1	ENST00000428558.2:c.3083T>A	p.Val1028Glu	p.V1028E	ENST00000428558	NM_004260.3	1028	gTg/gAg	19/22	0.408672663360926	3	FACETS	0.8	0.741	0.86	0.8	0.741	0.86	SUBCLONAL	2	TRUE	1	0.408019608521334	3		342	690	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70350017	70350017	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	245	231	0	ENST00000374080.3:c.4000G>C	p.Glu1334Gln	p.E1334Q	ENST00000374080		1334	Gag/Cag	28/45	0.408672663360926	2	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.408019608521334	2		231	488	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654553	29654553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876657714	NA	P-0007927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	177	508	2	ENST00000356175.3:c.5242C>T	p.Arg1748Ter	p.R1748*	ENST00000356175	NM_000267.3	1748	Cga/Tga	37/57	0.315460192473017	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.317921133828082	1		510	669	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577138	7577138	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587780075	NA	P-0007977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	117	509	0	ENST00000269305.4:c.800G>C	p.Arg267Pro	p.R267P	ENST00000269305	NM_001126112.2	267	cGg/cCg	8/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.188034663367519	NA		509	511	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566703	212566703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	23	408	0	ENST00000342788.4:c.1478C>T	p.Ala493Val	p.A493V	ENST00000342788	NM_005235.2	493	gCt/gTt	12/28	0.188034663367519	3	FACETS	0.693	0.54	0.871	0.347	0.27	0.436	SUBCLONAL	1	TRUE	1	0.188034663367519	3		408	386	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33290651	33290651	+	5_prime_UTR_variant	5'UTR	SNP	C	C	T	novel	NA	P-0007977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	25	444	0	ENST00000374542.5:c.-65G>A		p.*22*	ENST00000374542	NM_001141970.1	-/740		1/8	0.188034663367519	5	FACETS	0.85	0.669	1	0.283	0.223	0.353	CLONAL	1	TRUE	2	0.188034663367519	5		444	401	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066734	77066734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	60	530	0	ENST00000356341.3:c.751G>A	p.Glu251Lys	p.E251K	ENST00000356341	NM_002576.4	251	Gag/Aag	7/15	0.188034663367519	5	FACETS	0.861	0.743	0.989	0.861	0.743	0.989	CLONAL	2	TRUE	3	0.188034663367519	5		530	475	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871191	12871191	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	24	159	0	ENST00000228872.4:c.418A>C	p.Ser140Arg	p.S140R	ENST00000228872	NM_004064.3	140	Agc/Cgc	1/3	0.188034663367519	4	FACETS	1	0.885	1	0.604	0.475	0.752	CLONAL	1	TRUE	2	0.188034663367519	4		159	251	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003757	45003757	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	72	376	4	ENST00000558401.1:c.13G>A	p.Val5Met	p.V5M	ENST00000558401	NM_004048.2	5	Gtg/Atg	1/4	NA	2	FACETS	0.823	0.722	0.933			1	INDETERMINATE	2	TRUE	NA	0.188034663367519	2		380	465	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602612	10602612	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	65	325	1	ENST00000171111.5:c.966del	p.Lys323ArgfsTer5	p.K323Rfs*5	ENST00000171111	NM_203500.1	322	ccC/cc	3/6	0.188034663367519	3	FACETS	1	0.922	1	0.72	0.628	0.819	CLONAL	2	TRUE	0	0.188034663367519	3		326	350	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0007990-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	1216	278	1	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.599156635514542	7	FACETS	1	0.996	1			1	CLONAL	6	TRUE	NA	0.599156635514542	7		279	1602	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0007990-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	339	297	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.324944697345572	3	FACETS	1	0.993	1	0.798	0.764	0.833	INDETERMINATE	2	TRUE	0	0.599156635514542	3		298	614	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0007990-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	176	576	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.941	0.871	1	0.941	0.871	1	CLONAL	1	TRUE	1	0.599156635514542	2		579	624	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0007990-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	113	552	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.324944697345572	3	FACETS	0.51	0.458	0.565	0.17	0.152	0.189	INDETERMINATE	1	TRUE	0	0.599156635514542	3		552	962	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724596	724596	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777211673	NA	P-0007990-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	292	261	0	ENST00000314574.4:c.1460G>A	p.Arg487Gln	p.R487Q	ENST00000314574	NM_005433.3	487	cGa/cAa	12/12	0.340916766599867	4	FACETS	1	0.985	1			1	INDETERMINATE	2	TRUE	NA	0.599156635514542	4		261	704	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691022	NA	P-0007990-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	241	466	1	ENST00000269305.4:c.1024del	p.Arg342GlufsTer3	p.R342Efs*3	ENST00000269305	NM_001126112.2	342	Cga/ga	10/11	1	2	FACETS	0.962	0.901	1	0.962	0.901	1	CLONAL	1	TRUE	1	0.599156635514542	2		467	836	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961059	55961059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530419081	NA	P-0007990-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	188	432	0	ENST00000263923.4:c.2881C>T	p.Arg961Trp	p.R961W	ENST00000263923	NM_002253.2	961	Cgg/Tgg	21/30	1	2	FACETS	0.902	0.836	0.969	0.902	0.836	0.969	CLONAL	1	TRUE	1	0.599156635514542	2		432	696	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0008014-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	102	375	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.242557857286908	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.242557857286908	1		375	587	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555687605	NA	P-0008014-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	81	430	0	ENST00000342988.3:c.1610A>G	p.Asp537Gly	p.D537G	ENST00000342988	NM_005359.5	537	gAc/gGc	12/12	0.242557857286908	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.242557857286908	1		430	498	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980033	7980033	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008014-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	49	297	0	ENST00000319144.4:c.1304T>A	p.Val435Asp	p.V435D	ENST00000319144	NM_001139.2	435	gTc/gAc	10/15	0.242557857286908	1	FACETS	0.775	0.657	0.905	0.775	0.657	0.905	CLONAL	1	TRUE	0	0.242557857286908	1		297	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578445	7578449	+	missense_variant	Missense_Mutation	ONP	ATGGC	ATGGC	CTGGG	novel	NA	P-0008014-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	78	283	0	ENST00000269305.4:c.481_485delinsCCCAG	p.Ala161_Ile162delinsProSer	p.A161_I162delinsPS	ENST00000269305	NM_001126112.2	161	GCCATc/CCCAGc	5/11	0.242557857286908	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.242557857286908	1		283	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0008031-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	86	360	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.197848013023131	2	FACETS	1	0.979	1	0.738	0.657	0.825	CLONAL	1	TRUE	0	0.28	2		361	416	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0008031-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	48	289	1	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	1	2	FACETS	0.554	0.467	0.649	0.554	0.467	0.649	SUBCLONAL	1	TRUE	1	0.28	2		290	619	SUCCESS
APC	324	MSKCC	GRCh37	5	112174865	112174865	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0008031-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	70	352	0	ENST00000257430.4:c.3574A>T	p.Lys1192Ter	p.K1192*	ENST00000257430	NM_000038.5	1192	Aaa/Taa	16/16	1	2	FACETS	0.585	0.509	0.668	0.585	0.509	0.668	SUBCLONAL	1	TRUE	1	0.28	2		352	854	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437469	49437469	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1356371701	NA	P-0008031-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	97	522	0	ENST00000301067.7:c.5416G>A	p.Ala1806Thr	p.A1806T	ENST00000301067	NM_003482.3	1806	Gcc/Acc	23/54	1	2	FACETS	0.719	0.64	0.804	0.719	0.64	0.804	SUBCLONAL	1	TRUE	1	0.28	2		522	963	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95597889	95597889	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008031-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	100	400	0	ENST00000393063.1:c.395C>G	p.Ser132Cys	p.S132C	ENST00000393063	NM_030621.3	132	tCt/tGt	5/28	0.197848013023131	2	FACETS	0.709	0.632	0.792	0.355	0.316	0.396	SUBCLONAL	1	TRUE	0	0.28	2		400	1007	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021115	31021115	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs199846284	NA	P-0008057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	111	635	0	ENST00000375687.4:c.1114C>T	p.Gln372Ter	p.Q372*	ENST00000375687	NM_015338.5	372	Cag/Tag	12/13	0.331170519275331	5	FACETS	0.978	0.879	1	0.326	0.293	0.361	CLONAL	1	FALSE	2	0.528690449031902	5		635	770	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576862	7576930	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAAATATTCTCCATCCAGTGGTTTCTTCTTTGGCTGGGGAGAGGAGCTGGTGTTGTTGGGCAGTGCTAG	GAAATATTCTCCATCCAGTGGTTTCTTCTTTGGCTGGGGAGAGGAGCTGGTGTTGTTGGGCAGTGCTAG	-	novel	NA	P-0008057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	134	626	0	ENST00000269305.4:c.920-4_984del		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	NA	2	FACETS	1	0.922	1			1	INDETERMINATE	1	FALSE	NA	0.528690449031902	2		626	502	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416118	49416125	+	frameshift_variant	Frame_Shift_Del	DEL	ACATGTAG	ACATGTAG	-	novel	NA	P-0008057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	98	587	0	ENST00000301067.7:c.16350_16357del	p.Tyr5451ProfsTer5	p.Y5451Pfs*5	ENST00000301067	NM_003482.3	5450	atCTACATGTtc/attc	52/54	0.528690449031902	3	FACETS	0.643	0.574	0.717	0.321	0.287	0.359	SUBCLONAL	1	FALSE	1	0.528690449031902	3		587	729	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052601	42052601	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0008067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	65	701	0	ENST00000219905.7:c.7272T>G	p.Tyr2424Ter	p.Y2424*	ENST00000219905	NM_001164273.1	2424	taT/taG	20/24	0.122526279946213	0	FACETS	0.826	0.719	0.942			1	CLONAL	2	TRUE	0	0.16	0		701	413	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519436	176519436	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	26	455	0	ENST00000292408.4:c.842T>C	p.Ile281Thr	p.I281T	ENST00000292408	NM_213647.1	281	aTc/aCc	7/18	0.196526814011571	3	FACETS	1	0.82	1	0.513	0.411	0.628	INDETERMINATE	1	FALSE	1	0.373361455052204	3		455	161	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971124	21971125	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0008105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	198	241	0	ENST00000304494.5:c.233_234del	p.Leu78HisfsTer41	p.L78Hfs*41	ENST00000304494	NM_000077.4	78	cTC/c	2/3	0.484705378244219	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.491575505868539	1		241	415	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244124	153244124	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0008105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	183	434	0	ENST00000281708.4:c.2033C>G	p.Ser678Ter	p.S678*	ENST00000281708	NM_033632.3	678	tCa/tGa	12/12	0.23894813946851	4	FACETS	0.824	0.759	0.893	0.412	0.379	0.447	INDETERMINATE	1	TRUE	2	0.491575505868539	4		434	1347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0008105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	112	361	0	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	1	2	FACETS	0.842	0.76	0.928	0.842	0.76	0.928	CLONAL	1	TRUE	1	0.491575505868539	2		361	541	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261941	16261941	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	64	155	0	ENST00000375759.3:c.9206C>G	p.Ser3069Cys	p.S3069C	ENST00000375759	NM_015001.2	3069	tCc/tGc	11/15	0.480801889411186	2	FACETS	0.827	0.721	0.939	0.413	0.36	0.47	CLONAL	1	TRUE	0	0.491575505868539	2		155	315	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090594	71090594	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	50	579	0	ENST00000318789.4:c.754T>A	p.Leu252Met	p.L252M	ENST00000318789	NM_032682.5	252	Ttg/Atg	11/21	0.290314802265953	1	FACETS	0.179	0.151	0.21	0.179	0.151	0.21	INDETERMINATE	1	TRUE	0	0.491575505868539	1		579	858	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447562	187447562	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	63	377	0	ENST00000232014.4:c.631G>C	p.Glu211Gln	p.E211Q	ENST00000232014	NM_001130845.1	211	Gag/Cag	5/10	1	2	FACETS	0.415	0.359	0.477	0.415	0.359	0.477	SUBCLONAL	1	TRUE	1	0.491575505868539	2		377	617	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542861	187542861	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1340793072	NA	P-0008105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	180	457	0	ENST00000441802.2:c.4879C>T	p.Arg1627Ter	p.R1627*	ENST00000441802	NM_005245.3	1627	Cga/Tga	10/27	NA	2	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.491575505868539	2		457	694	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629184	187629184	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	186	412	1	ENST00000441802.2:c.1798C>T	p.Gln600Ter	p.Q600*	ENST00000441802	NM_005245.3	600	Cag/Tag	2/27	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.491575505868539	2		413	708	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170024	32170024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	156	516	0	ENST00000375023.3:c.3584G>A	p.Gly1195Glu	p.G1195E	ENST00000375023	NM_004557.3	1195	gGa/gAa	21/30	1	2	FACETS	0.888	0.815	0.964	0.888	0.815	0.964	CLONAL	1	TRUE	1	0.491575505868539	2		516	715	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750561	128750561	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776780683	NA	P-0008105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	361	540	0	ENST00000377970.2:c.98C>T	p.Ser33Leu	p.S33L	ENST00000377970	NM_002467.4	33	tCg/tTg	2/3	0.147492211118734	4	FACETS	0.959	0.91	1	0.959	0.91	1	INDETERMINATE	2	TRUE	2	0.491575505868539	4		540	1142	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821278	72821278	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540323473	NA	P-0008105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	236	666	0	ENST00000268489.5:c.10897C>T	p.Pro3633Ser	p.P3633S	ENST00000268489	NM_006885.3	3633	Cct/Tct	10/10	1	2	FACETS	0.897	0.836	0.959	0.897	0.836	0.959	CLONAL	1	TRUE	1	0.491575505868539	2		666	1071	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577111	+	inframe_deletion	In_Frame_Del	DEL	CCTCTGTGCGCCGGTCTCTCCCAGGACAGG	CCTCTGTGCGCCGGTCTCTCCCAGGACAGG	-	novel	NA	P-0008105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	60	517	0	ENST00000269305.4:c.827_856del	p.Ala276_Glu285del	p.A276_E285del	ENST00000269305	NM_001126112.2	276	gCCTGTCCTGGGAGAGACCGGCGCACAGAGGaa/gaa	8/11	1	2	FACETS	0.306	0.263	0.353	0.306	0.263	0.353	SUBCLONAL	1	TRUE	1	0.491575505868539	2		517	798	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	320	160	0				ENST00000310581	NM_198253.2	-/1132			0.330426818826997	4	FACETS	0.948	0.895	1	0.948	0.895	1	CLONAL	2	TRUE	2	0.402103528550728	4		160	1177	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0008106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1173	120	426	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.327904932912274	3	FACETS	0.554	0.499	0.613	0.185	0.166	0.205	SUBCLONAL	1	TRUE	0	0.402103528550728	3		426	1293	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201059	NA	P-0008106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	665	708	0	ENST00000269305.4:c.856G>T	p.Glu286Ter	p.E286*	ENST00000269305	NM_001126112.2	286	Gaa/Taa	8/11	0.327904932912274	3	FACETS	0.879	0.848	0.909	0.879	0.848	0.909	CLONAL	3	TRUE	0	0.402103528550728	3		708	1507	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432335	49432335	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0008106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1379	76	811	0	ENST00000301067.7:c.8804C>G	p.Ser2935Ter	p.S2935*	ENST00000301067	NM_003482.3	2935	tCa/tGa	34/54	1	2	FACETS	0.26	0.227	0.296	0.26	0.227	0.296	SUBCLONAL	1	TRUE	1	0.402103528550728	2		811	1455	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434732	49434732	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767236217	NA	P-0008106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1327	100	770	2	ENST00000301067.7:c.6821C>T	p.Ser2274Leu	p.S2274L	ENST00000301067	NM_003482.3	2274	tCg/tTg	31/54	1	2	FACETS	0.349	0.31	0.39	0.349	0.31	0.39	SUBCLONAL	1	TRUE	1	0.402103528550728	2		772	1427	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434435	49434435	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1345	76	736	0	ENST00000301067.7:c.7118C>G	p.Ser2373Cys	p.S2373C	ENST00000301067	NM_003482.3	2373	tCc/tGc	31/54	1	2	FACETS	0.266	0.232	0.303	0.266	0.232	0.303	SUBCLONAL	1	TRUE	1	0.402103528550728	2		736	1421	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434544	49434544	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	63	703	0	ENST00000301067.7:c.7009C>G	p.Gln2337Glu	p.Q2337E	ENST00000301067	NM_003482.3	2337	Cag/Gag	31/54	1	2	FACETS	0.251	0.216	0.289	0.251	0.216	0.289	SUBCLONAL	1	TRUE	1	0.402103528550728	2		703	1249	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942715	48942715	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	116	315	0	ENST00000267163.4:c.1102del	p.Val368Ter	p.V368*	ENST00000267163	NM_000321.2	368	Gta/ta	11/27	0.402103528550728	1	FACETS	0.886	0.803	0.974	0.886	0.803	0.974	CLONAL	1	TRUE	0	0.402103528550728	1		315	520	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421355	12421355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777334819	NA	P-0008106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	67	732	3	ENST00000287820.6:c.235G>A	p.Glu79Lys	p.E79K	ENST00000287820	NM_015869.4	79	Gaa/Aaa	2/7	0.250039153077003	3	FACETS	0.352	0.304	0.403	0.176	0.152	0.202	SUBCLONAL	1	TRUE	1	0.402103528550728	3		735	1138	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180270	32180270	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	58	519	0	ENST00000375023.3:c.2661G>C	p.Gln887His	p.Q887H	ENST00000375023	NM_004557.3	887	caG/caC	17/30	0.402103528550728	2	FACETS	0.259	0.221	0.3	0.129	0.11	0.15	SUBCLONAL	1	TRUE	0	0.402103528550728	2		519	1115	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860518	151860518	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	57	527	0	ENST00000262189.6:c.10144C>G	p.Arg3382Gly	p.R3382G	ENST00000262189	NM_170606.2	3382	Cgg/Ggg	43/59	1	2	FACETS	0.288	0.246	0.334	0.288	0.246	0.334	SUBCLONAL	1	TRUE	1	0.402103528550728	2		527	984	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205204	38205204	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	267	663	0	ENST00000317025.8:c.486G>C	p.Gln162His	p.Q162H	ENST00000317025	NM_023034.1	162	caG/caC	2/24	0.223126462342111	3	FACETS	1	0.988	1	0.407	0.381	0.435	INDETERMINATE	1	TRUE	0	0.402103528550728	3		663	1305	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089780	5089780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	77	305	1	ENST00000381652.3:c.2678G>A	p.Arg893Lys	p.R893K	ENST00000381652	NM_004972.3	893	aGa/aAa	20/25	1	2	FACETS	0.568	0.499	0.643	0.568	0.499	0.643	SUBCLONAL	1	TRUE	1	0.402103528550728	2		306	674	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874309	76874309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	107	268	0	ENST00000373344.5:c.5413C>T	p.His1805Tyr	p.H1805Y	ENST00000373344	NM_000489.3	1805	Cac/Tac	21/35	0.402103528550728	2	FACETS	0.668	0.599	0.741			1	SUBCLONAL	1	TRUE	NA	0.402103528550728	2		268	797	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176470	123176470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008139-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	211	344	0	ENST00000218089.9:c.437G>A	p.Arg146Gln	p.R146Q	ENST00000218089	NM_001042749.1	146	cGa/cAa	7/35	0.327035457370988	2	FACETS	1	0.983	1			1	CLONAL	2	TRUE	NA	0.327035457370988	2		344	565	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708994	117708994	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1290003301	NA	P-0008139-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	76	574	0	ENST00000368508.3:c.1963A>G	p.Lys655Glu	p.K655E	ENST00000368508	NM_002944.2	655	Aag/Gag	13/43	0.327035457370988	3	FACETS	0.572	0.5	0.649	0.286	0.25	0.325	SUBCLONAL	1	TRUE	1	0.327035457370988	3		574	946	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56872947	56872947	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008139-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	102	727	0	ENST00000308159.5:c.2102A>C	p.Glu701Ala	p.E701A	ENST00000308159	NM_014669.4	701	gAg/gCg	19/22	1	2	FACETS	0.552	0.492	0.615	0.552	0.492	0.615	SUBCLONAL	1	TRUE	1	0.327035457370988	2		727	1131	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0008142-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	92	203	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.446006407422355	2		203	404	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0008142-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	171	939	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.446006407422355	2		940	752	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0008142-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	135	206	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	0.442226585782433	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.446006407422355	1		206	431	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440680	56440680	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs759809905	NA	P-0008142-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	388	508	0	ENST00000407977.2:c.538C>T	p.Gln180Ter	p.Q180*	ENST00000407977		180	Caa/Taa	5/10	0.446006407422355	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.446006407422355	1		508	1041	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577589	7577590	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008142-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	191	286	0	ENST00000269305.4:c.691dup	p.Thr231AsnfsTer9	p.T231Nfs*9	ENST00000269305	NM_001126112.2	231	acc/aAcc	7/11	0.446006407422355	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.446006407422355	1		286	505	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0008148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	24	203	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		203	472	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835629	68835629	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658932	NA	P-0008148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	46	598	1	ENST00000261769.5:c.220C>T	p.Arg74Ter	p.R74*	ENST00000261769	NM_004360.3	74	Cga/Tga	3/16	0.214107323598407	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		599	918	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15379801	15379801	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	106	586	1	ENST00000263377.2:c.338G>T	p.Arg113Leu	p.R113L	ENST00000263377	NM_058243.2	113	cGc/cTc	3/20	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		587	1164	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0008158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	44	741	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.984	0.824	1	0.984	0.824	1	CLONAL	1	TRUE	1	0.15	2		742	596	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163512	47163512	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	29	211	0	ENST00000409792.3:c.2614C>T	p.Gln872Ter	p.Q872*	ENST00000409792	NM_014159.6	872	Caa/Taa	3/21	1	2	FACETS	0.719	0.575	0.882	0.719	0.575	0.882	SUBCLONAL	1	TRUE	1	0.15	2		211	538	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439922	220439922	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	63	450	0	ENST00000243786.2:c.775C>A	p.His259Asn	p.H259N	ENST00000243786	NM_002191.3	259	Cat/Aat	2/2	1	2	FACETS	0.876	0.755	1	0.876	0.755	1	CLONAL	1	TRUE	1	0.15	2		450	959	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935554	49935554	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	58	430	1	ENST00000296474.3:c.1810G>T	p.Glu604Ter	p.E604*	ENST00000296474	NM_002447.2	604	Gag/Tag	5/20	1	2	FACETS	0.79	0.676	0.914	0.79	0.676	0.914	CLONAL	1	TRUE	1	0.15	2		431	979	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232191	98232191	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	48	232	0	ENST00000331920.6:c.1751A>G	p.Asn584Ser	p.N584S	ENST00000331920	NM_000264.3	584	aAt/aGt	13/24	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.15	2		232	523	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107084	27107084	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	28	106	0	ENST00000324856.7:c.6696del	p.Arg2233GlyfsTer34	p.R2233Gfs*34	ENST00000324856	NM_006015.4	2232	cGg/cg	20/20	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.15	2		106	300	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398280	25398281	+	missense_variant	Missense_Mutation	DNP	GC	GC	CA	novel	NA	P-0008158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	29	194	0	ENST00000311936.3:c.38_39delinsTG	p.Gly13Val	p.G13V	ENST00000311936	NM_004985.3	13	gGC/gTG	2/5	1	2	FACETS	0.688	0.551	0.845	0.688	0.551	0.845	SUBCLONAL	1	TRUE	1	0.15	2		194	562	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448564	89448564	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1184230536	NA	P-0008161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	205	406	1	ENST00000336596.2:c.1528C>T	p.Arg510Ter	p.R510*	ENST00000336596	NM_005233.5	510	Cga/Tga	7/17	0.23516181416593	1	FACETS	0.732	0.677	0.788	0.732	0.677	0.788	SUBCLONAL	1	TRUE	0	0.364599312176244	1		407	1257	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165759	108165759	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	199	390	0	ENST00000278616.4:c.4882A>G	p.Met1628Val	p.M1628V	ENST00000278616	NM_000051.3	1628	Atg/Gtg	32/63	0.331274225334962	1	FACETS	0.921	0.853	0.991	0.921	0.853	0.991	CLONAL	1	TRUE	0	0.364599312176244	1		390	969	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220478	1220478	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0008161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	197	446	0	ENST00000326873.7:c.571A>T	p.Lys191Ter	p.K191*	ENST00000326873	NM_000455.4	191	Aaa/Taa	4/10	0.364599312176244	1	FACETS	0.824	0.762	0.888	0.824	0.762	0.888	CLONAL	1	TRUE	0	0.364599312176244	1		446	1073	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069331	30069332	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0008161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	76	366	1	ENST00000338641.4:c.1197_1198del	p.Gln400GlufsTer6	p.Q400Efs*6	ENST00000338641	NM_000268.3	399	gCC/g	12/16	0.331274225334962	1	FACETS	0.396	0.346	0.449	0.396	0.346	0.449	SUBCLONAL	1	TRUE	0	0.364599312176244	1		367	861	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599929	10599929	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	890	463	0	ENST00000171111.5:c.1647del	p.Met550Ter	p.M550*	ENST00000171111	NM_203500.1	549	ccC/cc	5/6	0.364599312176244	3	FACETS	0.993	0.964	1			1	CLONAL	3	TRUE	NA	0.364599312176244	3		463	1937	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101683	27101683	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	147	383	3	ENST00000324856.7:c.4965G>T	p.Gln1655His	p.Q1655H	ENST00000324856	NM_006015.4	1655	caG/caT	18/20	0.221038958612871	3	FACETS	0.793	0.724	0.866	0.793	0.724	0.866	SUBCLONAL	2	TRUE	1	0.221038958612871	3		386	931	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578260	7578260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204041	NA	P-0008168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	240	593	0	ENST00000269305.4:c.589G>A	p.Val197Met	p.V197M	ENST00000269305	NM_001126112.2	197	Gtg/Atg	6/11	0.221038958612871	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.221038958612871	2		593	1048	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696642	47696642	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519965	NA	P-0008168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	281	655	0	ENST00000347630.2:c.306C>G	p.Phe102Leu	p.F102L	ENST00000347630	NM_001007230.1	102	ttC/ttG	5/11	1	2	FACETS	0.867	0.812	0.923	1	0.994	1	CLONAL	2	TRUE	1	0.221038958612871	2		655	1467	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820555	44820556	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	274	412	0	ENST00000377967.4:c.254dup	p.Leu85PhefsTer4	p.L85Ffs*4	ENST00000377967	NM_021140.2	84	-/T	3/29	0.221038958612871	2	FACETS	0.952	0.896	1			1	CLONAL	3	TRUE	NA	0.221038958612871	2		412	868	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106843	27106855	+	frameshift_variant	Frame_Shift_Del	DEL	GTGCGCTTCCTCA	GTGCGCTTCCTCA	-	novel	NA	P-0008168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	157	321	0	ENST00000324856.7:c.6457_6469del	p.Arg2153ThrfsTer43	p.R2153Tfs*43	ENST00000324856	NM_006015.4	2152	GTGCGCTTCCTCAgt/gt	20/20	0.221038958612871	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	1	0.221038958612871	3		321	745	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112587	115112588	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTC	novel	NA	P-0008168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	66	329	0	ENST00000257566.3:c.1150_1152dup	p.Glu384dup	p.E384dup	ENST00000257566	NM_016569.3	384	-/GAG	7/8	1	2	FACETS	0.897	0.778	1	0.897	0.778	1	CLONAL	1	TRUE	1	0.221038958612871	2		329	666	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041654	47041654	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	220	275	0	ENST00000377604.3:c.1880del	p.Lys627ArgfsTer77	p.K627Rfs*77	ENST00000377604	NM_001204468.1	627	Aag/ag	17/24	0.221038958612871	2	FACETS	1	0.952	1			1	CLONAL	3	TRUE	NA	0.221038958612871	2		275	650	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0008171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	34	406	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.3	16	FACETS	0.924	0.755	1			1	CLONAL	2	TRUE	NA	0.27	16		406	394	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471047	8471047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201751722	NA	P-0008171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	48	159	0	ENST00000356435.5:c.3452G>A	p.Arg1151His	p.R1151H	ENST00000356435		1151	cGc/cAc	20/35	0.3	8	FACETS	1	0.916	1			1	CLONAL	1	TRUE	NA	0.27	8		159	568	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189835	66189835	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs55784741	NA	P-0008171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	49	99	0	ENST00000273854.3:c.3111G>T	p.Leu1037Phe	p.L1037F	ENST00000273854	NM_004439.5	1037	ttG/ttT	18/18	0.3	6	FACETS	0.838	0.709	0.981			1	CLONAL	1	TRUE	NA	0.27	6		99	667	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17125968	17125968	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	24	272	0	ENST00000285071.4:c.626A>C	p.Glu209Ala	p.E209A	ENST00000285071	NM_144997.5	209	gAg/gCg	7/14	0.3	1	FACETS	0.66	0.519	0.821	0.66	0.519	0.821	SUBCLONAL	1	TRUE	0	0.27	1		272	233	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857506	68857507	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0008171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	24	247	0	ENST00000261769.5:c.2141_2142del	p.Leu714ArgfsTer33	p.L714Rfs*33	ENST00000261769	NM_004360.3	714	cTT/c	13/16	0.3	1	FACETS	0.623	0.49	0.775	0.623	0.49	0.775	SUBCLONAL	1	TRUE	0	0.27	1		247	247	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0008174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	95	939	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.15	2		940	1254	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0008174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	42	206	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	1	2	FACETS	0.797	0.663	0.945	0.797	0.663	0.945	CLONAL	1	TRUE	1	0.15	2		206	703	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812260	212812260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751175543	NA	P-0008174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1317	74	422	0	ENST00000342788.4:c.316C>T	p.Arg106Cys	p.R106C	ENST00000342788	NM_005235.2	106	Cgt/Tgt	3/28	1	2	FACETS	0.709	0.618	0.808	0.709	0.618	0.808	SUBCLONAL	1	TRUE	1	0.15	2		422	1391	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143985	11143985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	42	251	0	ENST00000358026.2:c.3566G>A	p.Arg1189Gln	p.R1189Q	ENST00000358026	NM_001128849.1	1189	cGa/cAa	26/36	1	2	FACETS	0.719	0.598	0.853	0.719	0.598	0.853	SUBCLONAL	1	TRUE	1	0.15	2		251	779	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0008174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	56	218	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	1	2	FACETS	0.848	0.724	0.983	0.848	0.724	0.983	CLONAL	1	TRUE	1	0.15	2		218	881	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11210212	11210212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1403372273	NA	P-0008174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1301	97	466	0	ENST00000361445.4:c.4541G>A	p.Arg1514Gln	p.R1514Q	ENST00000361445	NM_004958.3	1514	cGg/cAg	31/58	1	2	FACETS	0.925	0.822	1	0.925	0.822	1	CLONAL	1	TRUE	1	0.15	2		466	1398	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034420	47034420	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	73	442	1	ENST00000377604.3:c.505C>T	p.Gln169Ter	p.Q169*	ENST00000377604	NM_001204468.1	169	Cag/Tag	6/24	1	2	FACETS	0.753	0.656	0.859	0.753	0.656	0.859	SUBCLONAL	1	TRUE	1	0.15	2		443	1292	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986534	36986535	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0008174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	209	418	0	ENST00000354822.5:c.1154dup	p.Asp386GlyfsTer53	p.D386Gfs*53	ENST00000354822	NM_001079668.2	385	tcg/tcCg	3/3	0.183766205647713	3	FACETS	0.856	0.794	0.921	1	0.987	1	CLONAL	3	TRUE	1	0.15	3		418	1166	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008179-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	83	386	0	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	0.376350067631766	2	FACETS	0.607	0.536	0.684	0.304	0.268	0.342	SUBCLONAL	1	TRUE	0	0.392057587365835	2		386	697	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233024	55233024	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144943614	NA	P-0008179-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	215	526	0	ENST00000275493.2:c.1774G>A	p.Val592Ile	p.V592I	ENST00000275493	NM_005228.3	592	Gtc/Atc	15/28	0.371098928598574	4	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	2	0.392057587365835	4		526	737	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	463304	463304	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008179-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	224	561	0	ENST00000399788.2:c.967C>G	p.Leu323Val	p.L323V	ENST00000399788	NM_001042603.1	323	Cta/Gta	8/28	0.371098928598574	4	FACETS	0.88	0.82	0.941	0.88	0.82	0.941	CLONAL	2	TRUE	2	0.392057587365835	4		561	904	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577520	7577520	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1330865474	NA	P-0008181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	56	278	0	ENST00000269305.4:c.761T>G	p.Ile254Ser	p.I254S	ENST00000269305	NM_001126112.2	254	aTc/aGc	7/11	0.3	1	FACETS	0.903	0.773	1	0.903	0.773	1	CLONAL	1	TRUE	0	0.19	1		278	591	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584607	48584607	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	48	377	0	ENST00000342988.3:c.780C>A	p.Tyr260Ter	p.Y260*	ENST00000342988	NM_005359.5	260	taC/taA	6/12	0.163420816235801	1	FACETS	0.855	0.722	1	0.855	0.722	1	CLONAL	1	TRUE	0	0.19	1		377	535	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0008181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	68	346	0	ENST00000311936.3:c.34_35delinsCT	p.Gly12Leu	p.G12L	ENST00000311936	NM_004985.3	12	GGt/CTt	2/5	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.19	2		346	698	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0008191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	132	359	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.470415117316835	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	0	0.470415117316835	3		359	214	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838341	156838341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	128	482	1	ENST00000524377.1:c.619G>A	p.Val207Met	p.V207M	ENST00000524377	NM_002529.3	207	Gtg/Atg	6/17	0.470415117316835	5	FACETS	0.972	0.912	1	1	0.991	1	CLONAL	5	TRUE	2	0.470415117316835	5		483	191	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61725837	61725837	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	23	320	0	ENST00000401558.2:c.730A>G	p.Thr244Ala	p.T244A	ENST00000401558	NM_003400.3	244	Acc/Gcc	9/25	0.188637746777554	2	FACETS	1	0.925	1	0.689	0.555	0.832	INDETERMINATE	1	TRUE	0	0.470415117316835	2		320	71	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636760	8636760	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	20	352	0	ENST00000356435.5:c.149A>G	p.Asp50Gly	p.D50G	ENST00000356435		50	gAc/gGc	2/35	0.470415117316835	1	FACETS	0.699	0.545	0.872	0.699	0.545	0.872	SUBCLONAL	1	TRUE	0	0.470415117316835	1		352	93	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244796	46244796	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	79	499	1	ENST00000334344.6:c.2890G>T	p.Gly964Ter	p.G964*	ENST00000334344	NM_152641.2	964	Gga/Tga	15/21	0.470415117316835	3	FACETS	0.894	0.799	0.992	0.894	0.799	0.992	CLONAL	2	TRUE	1	0.470415117316835	3		500	232	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0008213-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	314	486	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	NA	2	FACETS	1	0.962	1			1	INDETERMINATE	2	TRUE	NA	0.652639671249229	2		486	480	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0008213-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	436	399	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.652639671249229	7	FACETS	1	0.979	1			1	CLONAL	4	TRUE	NA	0.652639671249229	7		399	853	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912298	32912298	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008213-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	288	635	0	ENST00000380152.3:c.3806T>A	p.Val1269Asp	p.V1269D	ENST00000380152		1269	gTt/gAt	11/27	0.65661272539261	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.652639671249229	3		635	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008213-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	361	511	0	ENST00000269305.4:c.811G>C	p.Glu271Gln	p.E271Q	ENST00000269305	NM_001126112.2	271	Gag/Cag	8/11	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	2	TRUE	NA	0.652639671249229	2		511	526	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645935	67645935	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008213-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	447	369	1	ENST00000264010.4:c.863A>G	p.His288Arg	p.H288R	ENST00000264010	NM_006565.3	288	cAc/cGc	4/12	0.65661272539261	3	FACETS	1	0.982	1			1	CLONAL	3	TRUE	NA	0.652639671249229	3		370	596	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831831	72831831	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008213-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	325	667	0	ENST00000268489.5:c.4750C>T	p.Gln1584Ter	p.Q1584*	ENST00000268489	NM_006885.3	1584	Cag/Tag	9/10	NA	2	FACETS	0.845	0.808	0.883			1	INDETERMINATE	2	TRUE	NA	0.652639671249229	2		667	589	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0008229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	157	419	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.214725069956296	2		419	1290	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196213	106196213	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs370735654	NA	P-0008229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	67	266	0	ENST00000380013.4:c.4546C>T	p.Arg1516Ter	p.R1516*	ENST00000380013	NM_001127208.2	1516	Cga/Tga	11/11	0.210858458686016	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.214725069956296	1		266	517	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437701	49437701	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555194045	NA	P-0008229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1497	115	726	1	ENST00000301067.7:c.5269C>T	p.Arg1757Ter	p.R1757*	ENST00000301067	NM_003482.3	1757	Cga/Tga	22/54	1	2	FACETS	0.664	0.596	0.738	0.664	0.596	0.738	SUBCLONAL	1	TRUE	1	0.214725069956296	2		727	1612	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775915	9775915	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	83	294	0	ENST00000377346.4:c.379G>C	p.Glu127Gln	p.E127Q	ENST00000377346	NM_005026.3	127	Gag/Cag	5/24	0.147835735639795	2	FACETS	1	0.959	1	0.597	0.527	0.671	CLONAL	1	TRUE	0	0.214725069956296	2		294	648	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492581	50492581	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	64	501	0	ENST00000394963.4:c.1477C>T	p.Arg493Ter	p.R493*	ENST00000394963	NM_003076.4	493	Cga/Tga	12/13	1	2	FACETS	0.592	0.511	0.681	0.592	0.511	0.681	SUBCLONAL	1	TRUE	1	0.214725069956296	2		501	1007	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774795	73774795	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	93	587	0	ENST00000254810.4:c.292G>A	p.Glu98Lys	p.E98K	ENST00000254810	NM_005324.3	98	Gaa/Aaa	4/4	1	2	FACETS	0.724	0.641	0.812	0.724	0.641	0.812	SUBCLONAL	1	TRUE	1	0.214725069956296	2		587	1197	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017724	31017724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1005458245	NA	P-0008229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	113	325	1	ENST00000375687.4:c.586G>A	p.Asp196Asn	p.D196N	ENST00000375687	NM_015338.5	196	Gat/Aat	8/13	0.173850793784133	3	FACETS	0.866	0.78	0.956	0.866	0.78	0.956	CLONAL	2	TRUE	1	0.214725069956296	3		326	673	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839664	42839664	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	61	499	0	ENST00000398585.3:c.1575G>C	p.Met525Ile	p.M525I	ENST00000398585	NM_001135099.1	525	atG/atC	13/14	1	2	FACETS	0.681	0.586	0.785	0.681	0.586	0.785	SUBCLONAL	1	TRUE	1	0.214725069956296	2		499	834	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692953	89692953	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs786204933	NA	P-0008239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	70	457	0	ENST00000371953.3:c.437T>G	p.Leu146Ter	p.L146*	ENST00000371953	NM_000314.4	146	tTa/tGa	5/9	0.210810454136999	2	FACETS	1	0.97	1	0.694	0.607	0.787	CLONAL	1	TRUE	0	0.231467875357978	2		457	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0008239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	72	430	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.225649284474758	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.231467875357978	1		430	476	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151254	202151254	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	43	881	0	ENST00000358485.4:c.1554G>A	p.Met518Ile	p.M518I	ENST00000358485	NM_001080125.1	518	atG/atA	9/9	1	2	FACETS	0.601	0.502	0.711	0.601	0.502	0.711	SUBCLONAL	1	TRUE	1	0.231467875357978	2		881	618	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660894	227660894	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs13306470	NA	P-0008239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	83	569	1	ENST00000305123.5:c.2561G>T	p.Arg854Leu	p.R854L	ENST00000305123	NM_005544.2	854	cGc/cTc	1/2	1	2	FACETS	0.862	0.765	0.965	1	0.982	1	CLONAL	2	TRUE	1	0.231467875357978	2		570	416	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390911	89390911	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	64	559	0	ENST00000336596.2:c.977C>A	p.Pro326Gln	p.P326Q	ENST00000336596	NM_005233.5	326	cCa/cAa	5/17	0.166464173038068	2	FACETS	1	0.95	1	0.602	0.523	0.688	CLONAL	1	TRUE	0	0.231467875357978	2		559	459	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631575	119631575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	46	697	0	ENST00000316626.5:c.691G>A	p.Ala231Thr	p.A231T	ENST00000316626		231	Gcc/Acc	6/12	0.231467875357978	5	FACETS	0.753	0.633	0.887	0.251	0.211	0.296	SUBCLONAL	1	TRUE	2	0.231467875357978	5		697	711	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593414	55593414	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	47	737	1	ENST00000288135.5:c.1571C>A	p.Pro524His	p.P524H	ENST00000288135	NM_000222.2	524	cCt/cAt	10/21	0.231467875357978	4	FACETS	0.79	0.666	0.928	0.395	0.333	0.464	CLONAL	1	TRUE	2	0.231467875357978	4		738	633	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858176	27858176	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	87	854	0	ENST00000359303.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000359303	NM_003535.2	132	cGt/cTt	1/1	0.231467875357978	3	FACETS	1	0.968	1	0.632	0.559	0.709	CLONAL	1	TRUE	1	0.231467875357978	3		854	664	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910707	29910707	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	73	666	0	ENST00000376809.5:c.247T>A	p.Tyr83Asn	p.Y83N	ENST00000376809	NM_002116.7	83	Tat/Aat	2/8	0.231467875357978	3	FACETS	1	0.974	1	0.738	0.647	0.835	CLONAL	1	TRUE	1	0.231467875357978	3		666	477	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978841	13978841	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1280099827	NA	P-0008239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	68	568	0	ENST00000405192.2:c.266A>G	p.Lys89Arg	p.K89R	ENST00000405192	NM_001163147.1	89	aAg/aGg	6/12	0.143663052207732	4	FACETS	0.768	0.67	0.874	0.768	0.67	0.874	SUBCLONAL	2	TRUE	2	0.231467875357978	4		568	471	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507326	8507326	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	104	723	1	ENST00000356435.5:c.1652A>T	p.Tyr551Phe	p.Y551F	ENST00000356435		551	tAc/tTc	11/35	1	2	FACETS	0.795	0.714	0.881	1	0.984	1	SUBCLONAL	2	TRUE	1	0.231467875357978	2		724	565	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625363	69625363	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	57	614	0	ENST00000334134.2:c.430C>A	p.Arg144Ser	p.R144S	ENST00000334134	NM_005247.2	144	Cgc/Agc	3/3	0.166464173038068	2	FACETS	1	0.924	1	0.558	0.48	0.643	CLONAL	1	TRUE	0	0.231467875357978	2		614	441	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609883	81609883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	91	531	0	ENST00000298171.2:c.1481G>A	p.Cys494Tyr	p.C494Y	ENST00000298171	NM_000369.2	494	tGc/tAc	10/10	0.231467875357978	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	2	TRUE	0	0.231467875357978	2		531	387	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559089	29559089	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1131691089	NA	P-0008239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	27	103	0	ENST00000356175.3:c.3198-2A>G		p.X1066_splice	ENST00000356175	NM_000267.3	1066			0.225649284474758	1	FACETS	0.897	0.727	1	1	0.952	1	CLONAL	2	TRUE	0	0.231467875357978	1		103	115	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575219	48575219	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0008239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	73	521	0	ENST00000342988.3:c.413C>G	p.Ser138Ter	p.S138*	ENST00000342988	NM_005359.5	138	tCa/tGa	3/12	0.210810454136999	2	FACETS	0.783	0.688	0.884	0.783	0.688	0.884	SUBCLONAL	2	TRUE	0	0.231467875357978	2		521	403	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939118	76939118	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	47	692	0	ENST00000373344.5:c.1630C>G	p.His544Asp	p.H544D	ENST00000373344	NM_000489.3	544	Cat/Gat	9/35	0.135512152145551	1	FACETS	0.669	0.564	0.784	0.669	0.564	0.784	INDETERMINATE	1	TRUE	0	0.231467875357978	1		692	537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0008242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	333	364	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.946	0.898	0.995	1	0.996	1	CLONAL	2	TRUE	1	0.401325080216744	2		365	877	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0008242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	150	408	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.879	0.812	0.949	1	0.991	1	CLONAL	2	TRUE	1	0.401325080216744	2		408	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs864622237	NA	P-0008242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	240	364	0	ENST00000269305.4:c.700T>C	p.Tyr234His	p.Y234H	ENST00000269305	NM_001126112.2	234	Tac/Cac	7/11	1	2	FACETS	0.965	0.907	1	1	0.995	1	CLONAL	2	TRUE	1	0.401325080216744	2		364	620	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937611	76937615	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTT	CTTTT	-	novel	NA	P-0008242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	113	285	0	ENST00000373344.5:c.3133_3137del	p.Lys1045Ter	p.K1045*	ENST00000373344	NM_000489.3	1045	AAAAGt/t	9/35	1	1	FACETS	0.938	0.88	0.993	1	0.992	1	CLONAL	3	TRUE	0	0.401325080216744	1		285	160	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170353	32170353	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	89	318	0	ENST00000375023.3:c.3255C>G	p.Ser1085Arg	p.S1085R	ENST00000375023	NM_004557.3	1085	agC/agG	21/30	1	2	FACETS	0.838	0.745	0.937	0.838	0.745	0.937	CLONAL	1	TRUE	1	0.401325080216744	2		318	529	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510560	38510560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	80	421	1	ENST00000254066.5:c.814C>T	p.Arg272Trp	p.R272W	ENST00000254066	NM_000964.3	272	Cgg/Tgg	7/9	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	FALSE	1	0.152458612168814	2		422	960	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240039	53240039	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	70	268	0	ENST00000375401.3:c.1402G>T	p.Glu468Ter	p.E468*	ENST00000375401	NM_004187.3	468	Gag/Tag	11/26	1	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	0	0.152458612168814	1		268	590	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191528	10191529	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	166	529	0	ENST00000256474.2:c.523dup	p.Tyr175LeufsTer81	p.Y175Lfs*81	ENST00000256474	NM_000551.3	174	aat/aaTt	3/3	0.152458612168814	2	FACETS	0.999	0.916	1	0.999	0.916	1	CLONAL	2	FALSE	0	0.152458612168814	2		529	1090	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	95	160	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.732	0.659	0.809	0.732	0.659	0.809	SUBCLONAL	1	TRUE	1	0.788565915681964	2		160	329	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0008262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	278	426	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	1	2	FACETS	0.965	0.911	1	0.965	0.911	1	CLONAL	1	TRUE	1	0.788565915681964	2		426	731	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0008262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15305	1266	624	5	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.788565915681964	23	FACETS	0.899	0.87	0.928			1	CLONAL	2	TRUE	NA	0.788565915681964	23		629	16571	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721082	61721082	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	223	428	0	ENST00000401558.2:c.1192C>G	p.Gln398Glu	p.Q398E	ENST00000401558	NM_003400.3	398	Caa/Gaa	12/25	1	2	FACETS	0.882	0.826	0.94	0.882	0.826	0.94	CLONAL	1	TRUE	1	0.788565915681964	2		428	641	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340145	116340145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	312	405	0	ENST00000397752.3:c.1007G>A	p.Ser336Asn	p.S336N	ENST00000397752	NM_000245.2	336	aGc/aAc	2/21	0.788565915681964	3	FACETS	1	0.967	1	0.517	0.488	0.547	CLONAL	1	TRUE	1	0.788565915681964	3		405	1067	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223531	55223533	+	inframe_deletion	In_Frame_Del	DEL	GTG	GTG	-	novel	NA	P-0008262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9174	6107	569	0	ENST00000275493.2:c.901_903del	p.Val301del	p.V301del	ENST00000275493	NM_005228.3	300	GTG/-	8/28	0.788565915681964	23	FACETS	1	0.998	1			1	CLONAL	9	TRUE	NA	0.788565915681964	23		569	15281	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0008295-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	1015	537	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	2	TRUE	NA	0.780149900618358	2		537	1239	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600417	10600417	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008295-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	1023	584	0	ENST00000171111.5:c.1438G>T	p.Gly480Trp	p.G480W	ENST00000171111	NM_203500.1	480	Ggg/Tgg	4/6	0.780149900618358	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.780149900618358	2		584	1273	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205672	128205672	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008295-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	378	434	0	ENST00000341105.2:c.203C>A	p.Ala68Glu	p.A68E	ENST00000341105	NM_032638.4	68	gCg/gAg	2/6	0.772325084483547	3	FACETS	0.957	0.907	1	0.478	0.453	0.504	CLONAL	1	TRUE	1	0.780149900618358	3		434	1408	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335607	81335607	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008295-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	268	433	0	ENST00000222390.5:c.1753G>T	p.Ala585Ser	p.A585S	ENST00000222390	NM_000601.4	585	Gcc/Tcc	15/18	1	2	FACETS	0.849	0.799	0.9	0.849	0.799	0.9	CLONAL	1	TRUE	1	0.780149900618358	2		433	809	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94223998	94223998	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0008295-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	243	328	0	ENST00000323929.3:c.153+1G>T		p.X51_splice	ENST00000323929	NM_005591.3	51			0.696608486272272	3	FACETS	0.859	0.803	0.917			1	CLONAL	1	TRUE	NA	0.780149900618358	3		328	1008	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486068	29486068	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199474729	NA	P-0008295-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	190	291	0	ENST00000356175.3:c.245C>T	p.Ser82Phe	p.S82F	ENST00000356175	NM_000267.3	82	tCt/tTt	3/57	0.772325084483547	3	FACETS	0.812	0.752	0.874	0.406	0.376	0.437	CLONAL	1	TRUE	1	0.780149900618358	3		291	834	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0008300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	82	313	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	NA	2	FACETS	0.93	0.82	1			1	INDETERMINATE	1	TRUE	NA	0.232219920084043	2		313	759	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0008300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	240	399	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.232219920084043	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.232219920084043	3		399	1019	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78617593	78617593	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	69	318	0	ENST00000306801.3:c.331G>T	p.Glu111Ter	p.E111*	ENST00000306801	NM_020761.2	111	Gag/Tag	3/34	1	2	FACETS	0.832	0.724	0.949	0.832	0.724	0.949	CLONAL	1	TRUE	1	0.232219920084043	2		318	714	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945363	54945363	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	81	352	0	ENST00000312783.6:c.1063G>A	p.Gly355Arg	p.G355R	ENST00000312783	NM_198436.1	355	Gga/Aga	10/10	1	2	FACETS	0.86	0.757	0.971	0.86	0.757	0.971	CLONAL	1	TRUE	1	0.232219920084043	2		352	811	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480499	123480499	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs148554414	NA	P-0008300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	87	311	1	ENST00000371139.4:c.7G>T	p.Ala3Ser	p.A3S	ENST00000371139	NM_001114937.2	3	Gca/Tca	1/4	0.21738579524615	1	FACETS	0.881	0.779	0.989	0.881	0.779	0.989	CLONAL	1	TRUE	0	0.232219920084043	1		312	752	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94169023	94169054	+	frameshift_variant	Frame_Shift_Del	DEL	GAAAAATGTCTTCTTCCACATCTGATTCATCT	GAAAAATGTCTTCTTCCACATCTGATTCATCT	-	novel	NA	P-0008300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	48	506	0	ENST00000323929.3:c.1938_1969del	p.Asp647TyrfsTer28	p.D647Yfs*28	ENST00000323929	NM_005591.3	646	gtAGATGAATCAGATGTGGAAGAAGACATTTTTCct/gtct	18/20	1	2	FACETS	0.462	0.389	0.543	0.462	0.389	0.543	SUBCLONAL	1	TRUE	1	0.232219920084043	2		506	895	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197801	66197802	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0008300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	67	511	1	ENST00000273854.3:c.2897_2898delinsAA	p.Ala966Glu	p.A966E	ENST00000273854	NM_004439.5	966	gCC/gAA	17/18	1	2	FACETS	0.581	0.503	0.666	0.581	0.503	0.666	SUBCLONAL	1	TRUE	1	0.232219920084043	2		512	993	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531111	187531112	+	missense_variant	Missense_Mutation	DNP	TG	TG	CT	novel	NA	P-0008300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	54	409	0	ENST00000441802.2:c.9911_9912delinsAG	p.Thr3304Lys	p.T3304K	ENST00000441802	NM_005245.3	3304	aCA/aAG	15/27	1	2	FACETS	0.529	0.45	0.616	0.529	0.45	0.616	SUBCLONAL	1	TRUE	1	0.232219920084043	2		409	879	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276256	15276256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759704420	NA	P-0008320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	75	445	0	ENST00000263388.2:c.5738C>T	p.Ala1913Val	p.A1913V	ENST00000263388	NM_000435.2	1913	gCg/gTg	31/33	0.114347492435388	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		445	504	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0008336-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	59	399	2	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.523	0.451	0.601	0.523	0.451	0.601	SUBCLONAL	1	TRUE	1	0.49707037459425	2		401	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579415	7579415	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008336-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	162	304	0	ENST00000269305.4:c.272G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tGg/tAg	4/11	0.49707037459425	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.49707037459425	1		304	471	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493443	56493443	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008336-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	177	356	0	ENST00000267101.3:c.2851G>C	p.Asp951His	p.D951H	ENST00000267101	NM_001982.3	951	Gat/Cat	24/28	1	2	FACETS	0.905	0.835	0.977	0.905	0.835	0.977	CLONAL	1	TRUE	1	0.49707037459425	2		356	787	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126142	2126142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45517258	NA	P-0008336-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	103	472	0	ENST00000219476.3:c.2713C>T	p.Arg905Trp	p.R905W	ENST00000219476	NM_000548.3	905	Cgg/Tgg	24/42	0.49707037459425	1	FACETS	0.386	0.345	0.43	0.386	0.345	0.43	SUBCLONAL	1	TRUE	0	0.49707037459425	1		472	806	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0008343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	44	306	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.413206329596999	1	FACETS	0.947	0.813	1	0.947	0.813	1	CLONAL	1	TRUE	0	0.526579734113196	1		306	130	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240786	55240786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756870976	NA	P-0008343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	11	369	1	ENST00000275493.2:c.2030G>A	p.Arg677His	p.R677H	ENST00000275493	NM_005228.3	677	cGc/cAc	17/28	0.526579734113196	6	FACETS	0.159	0.109	0.221			1	SUBCLONAL	1	TRUE	NA	0.526579734113196	6		370	541	SUCCESS
APC	324	MSKCC	GRCh37	5	112174910	112174910	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	76	448	0	ENST00000257430.4:c.3622del	p.Thr1208ProfsTer57	p.T1208Pfs*57	ENST00000257430	NM_000038.5	1207	Aaa/aa	16/16	0.489943953979837	2	FACETS	0.869	0.783	0.957	0.869	0.783	0.957	CLONAL	2	TRUE	0	0.526579734113196	2		448	166	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085995	16085995	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	72	485	1	ENST00000281043.3:c.1171C>T	p.Arg391Cys	p.R391C	ENST00000281043	NM_005378.4	391	Cgc/Tgc	3/3	0.51629539306697	2	FACETS	1	0.945	1	0.558	0.494	0.625	CLONAL	1	TRUE	0	0.526579734113196	2		486	245	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456994	149456994	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	49	322	0	ENST00000286301.3:c.734C>A	p.Ala245Glu	p.A245E	ENST00000286301	NM_005211.3	245	gCa/gAa	6/22	0.489943953979837	2	FACETS	0.763	0.665	0.864	0.763	0.665	0.864	SUBCLONAL	2	TRUE	0	0.526579734113196	2		322	122	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023186	31023186	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774520876	NA	P-0008343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	29	577	0	ENST00000375687.4:c.2671G>A	p.Val891Ile	p.V891I	ENST00000375687	NM_015338.5	891	Gtt/Att	13/13	0.526579734113196	5	FACETS	0.38	0.304	0.466	0.095	0.076	0.117	SUBCLONAL	1	TRUE	1	0.526579734113196	5		577	519	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430441	181430441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1268	236	458	0	ENST00000325404.1:c.293G>A	p.Arg98Gln	p.R98Q	ENST00000325404	NM_003106.3	98	cGa/cAa	1/1	0.774841564618793	3	FACETS	0.562	0.523	0.603	0.187	0.174	0.201	SUBCLONAL	1	TRUE	0	0.774841564618793	3		458	1504	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821349	72821349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567505140	NA	P-0008353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	278	492	1	ENST00000268489.5:c.10826C>T	p.Ser3609Phe	p.S3609F	ENST00000268489	NM_006885.3	3609	tCc/tTc	10/10	0.622433888305268	1	FACETS	0.465	0.437	0.493	0.465	0.437	0.493	SUBCLONAL	1	TRUE	0	0.774841564618793	1		493	946	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175713	176175713	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1283	275	661	0	ENST00000367669.3:c.402C>G	p.Phe134Leu	p.F134L	ENST00000367669	NM_022457.5	134	ttC/ttG	1/20	0.518658794685981	3	FACETS	0.632	0.592	0.674	0.316	0.296	0.337	SUBCLONAL	1	TRUE	1	0.774841564618793	3		661	1558	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994346	25994346	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1663	259	550	0	ENST00000435504.4:c.467C>G	p.Ser156Cys	p.S156C	ENST00000435504		156	tCt/tGt	6/13	0.400315898332357	5	FACETS	0.752	0.701	0.805	0.251	0.233	0.269	INDETERMINATE	1	TRUE	2	0.774841564618793	5		550	1922	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176493	142176493	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1350	214	506	0	ENST00000350721.4:c.7608T>G	p.Cys2536Trp	p.C2536W	ENST00000350721	NM_001184.3	2536	tgT/tgG	45/47	0.774841564618793	3	FACETS	0.49	0.454	0.528	0.163	0.151	0.176	SUBCLONAL	1	TRUE	0	0.774841564618793	3		506	1564	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575630	55575630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1357	223	603	0	ENST00000288135.5:c.1156G>A	p.Glu386Lys	p.E386K	ENST00000288135	NM_000222.2	386	Gaa/Aaa	7/21	0.461177207015059	3	FACETS	0.505	0.469	0.544	0.168	0.156	0.182	INDETERMINATE	1	TRUE	0	0.774841564618793	3		603	1580	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979637	55979637	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	173	409	0	ENST00000263923.4:c.810G>C	p.Lys270Asn	p.K270N	ENST00000263923	NM_002253.2	270	aaG/aaC	7/30	0.461177207015059	3	FACETS	0.542	0.498	0.588	0.181	0.166	0.196	INDETERMINATE	1	TRUE	0	0.774841564618793	3		409	1143	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271408	26271408	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1259	787	988	1	ENST00000305910.3:c.205C>A	p.Gln69Lys	p.Q69K	ENST00000305910	NM_003534.2	69	Caa/Aaa	1/1	0.774841564618793	2	FACETS	0.993	0.96	1	0.496	0.48	0.513	CLONAL	1	TRUE	0	0.774841564618793	2		989	2046	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679058	117679058	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	329	457	0	ENST00000368508.3:c.3763G>C	p.Asp1255His	p.D1255H	ENST00000368508	NM_002944.2	1255	Gat/Cat	24/43	1	2	FACETS	0.883	0.836	0.93	0.883	0.836	0.93	CLONAL	1	TRUE	1	0.774841564618793	2		457	962	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729435	41729435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1616	368	794	0	ENST00000242208.4:c.1094C>T	p.Ser365Leu	p.S365L	ENST00000242208	NM_002192.2	365	tCa/tTa	3/3	0.461177207015059	3	FACETS	0.664	0.627	0.702	0.221	0.209	0.234	INDETERMINATE	1	TRUE	0	0.774841564618793	3		794	1984	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851469	151851469	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	228	500	0	ENST00000262189.6:c.12022G>C	p.Glu4008Gln	p.E4008Q	ENST00000262189	NM_170606.2	4008	Gag/Cag	47/59	NA	2	FACETS	0.662	0.618	0.708			1	INDETERMINATE	1	TRUE	NA	0.774841564618793	2		500	889	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101910003	101910003	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	309	469	0	ENST00000374994.4:c.1323G>C	p.Met441Ile	p.M441I	ENST00000374994	NM_004612.2	441	atG/atC	8/9	0.774841564618793	3	FACETS	0.807	0.759	0.855	0.269	0.253	0.285	CLONAL	1	TRUE	0	0.774841564618793	3		469	1372	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102199674	102199674	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0008353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	210	479	0	ENST00000263464.3:c.1079C>G	p.Ser360Ter	p.S360*	ENST00000263464	NM_001165.4	360	tCa/tGa	5/9	0.774841564618793	1	FACETS	0.478	0.446	0.512	0.478	0.446	0.512	SUBCLONAL	1	TRUE	0	0.774841564618793	1		479	694	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417168	417168	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	812	254	0	ENST00000399788.2:c.3382G>A	p.Ala1128Thr	p.A1128T	ENST00000399788	NM_001042603.1	1128	Gca/Aca	23/28	0.774841564618793	6	FACETS	0.95	0.924	0.976			1	CLONAL	4	TRUE	NA	0.774841564618793	6		254	1406	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246279	46246279	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0008353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	560	407	0	ENST00000334344.6:c.4373C>G	p.Ser1458Ter	p.S1458*	ENST00000334344	NM_152641.2	1458	tCa/tGa	15/21	0.386737888667029	5	FACETS	1	0.982	1			1	INDETERMINATE	2	TRUE	NA	0.774841564618793	5		407	1504	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619850	21619850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	106	306	0	ENST00000382592.4:c.316G>A	p.Glu106Lys	p.E106K	ENST00000382592	NM_014572.2	106	Gaa/Aaa	2/8	0.622433888305268	1	FACETS	0.359	0.323	0.396	0.359	0.323	0.396	SUBCLONAL	1	TRUE	0	0.774841564618793	1		306	467	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790511	3790511	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587783488	NA	P-0008353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	183	488	0	ENST00000262367.5:c.4022G>C	p.Arg1341Pro	p.R1341P	ENST00000262367	NM_004380.2	1341	cGa/cCa	24/31	0.31016761799289	3	FACETS	0.585	0.539	0.633	0.195	0.179	0.211	INDETERMINATE	1	TRUE	0	0.774841564618793	3		488	1120	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923766	72923766	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	306	811	0	ENST00000268489.5:c.3312C>G	p.Ile1104Met	p.I1104M	ENST00000268489	NM_006885.3	1104	atC/atG	4/10	0.395850180999826	1	FACETS	0.37	0.348	0.392	0.37	0.348	0.392	INDETERMINATE	1	TRUE	0	0.774841564618793	1		811	1309	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813004	89813004	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	196	429	0	ENST00000389301.3:c.3501G>T	p.Leu1167Phe	p.L1167F	ENST00000389301	NM_000135.2	1167	ttG/ttT	35/43	0.395850180999826	1	FACETS	0.363	0.336	0.391	0.363	0.336	0.391	INDETERMINATE	1	TRUE	0	0.774841564618793	1		429	853	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264375	30264375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316496668	NA	P-0008353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	108	202	0	ENST00000322652.5:c.110C>T	p.Ser37Leu	p.S37L	ENST00000322652	NM_015355.2	37	tCg/tTg	1/16	1	2	FACETS	0.583	0.526	0.643	0.583	0.526	0.643	SUBCLONAL	1	TRUE	1	0.774841564618793	2		202	478	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142826	7142826	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0008353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	106	203	0	ENST00000302850.5:c.2542+1G>T		p.X848_splice	ENST00000302850	NM_000208.2	848			1	2	FACETS	0.542	0.488	0.599	0.542	0.488	0.599	SUBCLONAL	1	TRUE	1	0.774841564618793	2		203	505	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098417	11098417	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	158	293	0	ENST00000358026.2:c.935C>G	p.Ser312Cys	p.S312C	ENST00000358026	NM_001128849.1	312	tCc/tGc	6/36	1	2	FACETS	0.622	0.571	0.674	0.622	0.571	0.674	SUBCLONAL	1	TRUE	1	0.774841564618793	2		293	656	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710530	40710530	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	120	303	0	ENST00000373198.4:c.4321G>A	p.Glu1441Lys	p.E1441K	ENST00000373198	NM_133170.3	1441	Gag/Aag	31/32	0.754103729165408	3	FACETS	0.507	0.458	0.56	0.169	0.152	0.187	SUBCLONAL	1	TRUE	0	0.774841564618793	3		303	847	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397632	139397633	+	splice_donor_variant	Splice_Site	INS	-	-	CTCTGCAC	novel	NA	P-0008353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	756	329	0	ENST00000277541.6:c.5161_5167+1dup		p.X1721_splice	ENST00000277541	NM_017617.3	1721			0.774841564618793	3	FACETS	1	0.997	1	0.823	0.803	0.843	CLONAL	2	TRUE	0	0.774841564618793	3		329	1096	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579855	7579855	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1131691018	NA	P-0008353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	394	537	0	ENST00000269305.4:c.58del	p.Ser20GlnfsTer24	p.S20Qfs*24	ENST00000269305	NM_001126112.2	20	Tca/ca	2/11	0.774841564618793	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.774841564618793	1		537	622	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0008370-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	188	406	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.99	0.918	1	0.99	0.918	1	CLONAL	1	TRUE	1	0.530334653838589	2		406	716	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0008370-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	592	390	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.530334653838589	3	FACETS	1	0.993	1			1	CLONAL	3	TRUE	NA	0.530334653838589	3		390	886	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231773	36231773	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1569061762	NA	P-0008370-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	272	501	1	ENST00000300305.3:c.611G>A	p.Arg204Gln	p.R204Q	ENST00000300305		204	cGa/cAa	5/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.530334653838589	2		502	919	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435312	56435312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139405076	NA	P-0008370-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	122	278	0	ENST00000407977.2:c.1825C>T	p.Arg609Trp	p.R609W	ENST00000407977		609	Cgg/Tgg	9/10	1	2	FACETS	0.953	0.866	1	0.953	0.866	1	CLONAL	1	TRUE	1	0.530334653838589	2		278	483	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171672	36171672	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008370-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	167	402	2	ENST00000300305.3:c.893del	p.Pro298GlnfsTer13	p.P298Qfs*13	ENST00000300305		298	cCa/ca	7/8	1	2	FACETS	0.986	0.909	1	0.986	0.909	1	CLONAL	1	TRUE	1	0.530334653838589	2		404	639	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451400	187451436	+	frameshift_variant	Frame_Shift_Del	DEL	GACTCCGGAGACGATTAAGGTTGAGAAGAACATCACT	GACTCCGGAGACGATTAAGGTTGAGAAGAACATCACT	-	novel	NA	P-0008370-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	109	437	0	ENST00000232014.4:c.46_82del	p.Ser16GlufsTer4	p.S16Efs*4	ENST00000232014	NM_001130845.1	16	AGTGATGTTCTTCTCAACCTTAATCGTCTCCGGAGTCga/ga	3/10	1	2	FACETS	0.618	0.556	0.684	0.618	0.556	0.684	SUBCLONAL	1	TRUE	1	0.530334653838589	2		437	665	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451440	187451441	+	missense_variant	Missense_Mutation	DNP	AT	AT	GC	novel	NA	P-0008370-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	111	372	0	ENST00000232014.4:c.41_42delinsGC	p.His14Arg	p.H14R	ENST00000232014	NM_001130845.1	14	cAT/cGC	3/10	1	2	FACETS	0.753	0.679	0.831	0.753	0.679	0.831	SUBCLONAL	1	TRUE	1	0.530334653838589	2		372	556	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008380-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	97	160	0				ENST00000310581	NM_198253.2	-/1132			0.295776490145119	2	FACETS	0.809	0.726	0.895	0.809	0.726	0.895	CLONAL	2	TRUE	0	0.31	2		160	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0008380-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	246	741	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.295776490145119	2	FACETS	0.835	0.782	0.891	0.835	0.782	0.891	CLONAL	2	TRUE	0	0.31	2		742	950	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720670	89720670	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786204875	NA	P-0008380-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	42	124	0	ENST00000371953.3:c.821G>A	p.Trp274Ter	p.W274*	ENST00000371953	NM_000314.4	274	tGg/tAg	8/9	0.3	2	FACETS	0.765	0.648	0.892	0.765	0.648	0.892	SUBCLONAL	2	TRUE	0	0.31	2		124	177	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453145	140453145	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913366	NA	P-0008380-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	28	616	0	ENST00000288602.6:c.1790T>G	p.Leu597Arg	p.L597R	ENST00000288602	NM_004333.4	597	cTa/cGa	15/18	0.3	2	FACETS	0.204	0.162	0.252	0.102	0.081	0.126	SUBCLONAL	1	TRUE	0	0.31	2		616	886	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106099	27106099	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008386-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	81	377	1	ENST00000324856.7:c.5710G>T	p.Glu1904Ter	p.E1904*	ENST00000324856	NM_006015.4	1904	Gaa/Taa	20/20	0.461286586787021	5	FACETS	0.906	0.82	0.992	0.906	0.82	0.992	CLONAL	3	TRUE	2	0.748806064700552	5		378	169	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111507	8111508	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0008386-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	121	518	0	ENST00000346208.3:c.994dup	p.Ala332GlyfsTer20	p.A332Gfs*20	ENST00000346208		331	-/G	5/6	0.748806064700552	6	FACETS	1	0.934	1			1	CLONAL	3	TRUE	NA	0.748806064700552	6		518	265	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539671	187539671	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008386-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	72	625	0	ENST00000441802.2:c.8069del	p.Tyr2690LeufsTer33	p.Y2690Lfs*33	ENST00000441802	NM_005245.3	2690	tAt/tt	10/27	0.693403165526636	5	FACETS	0.95	0.844	1			1	CLONAL	2	TRUE	NA	0.748806064700552	5		625	215	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008389-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	114	160	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.468785730664166	2		160	398	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0008389-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	92	166	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.837	0.747	0.932	0.837	0.747	0.932	CLONAL	1	TRUE	1	0.468785730664166	2		166	469	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0008389-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	194	432	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.968	0.897	1	0.968	0.897	1	CLONAL	1	TRUE	1	0.468785730664166	2		432	855	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908238	41908238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008389-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	101	422	2	ENST00000372991.4:c.284G>A	p.Arg95Gln	p.R95Q	ENST00000372991	NM_001760.3	95	cGa/cAa	2/5	1	2	FACETS	0.469	0.418	0.523	0.469	0.418	0.523	SUBCLONAL	1	TRUE	1	0.468785730664166	2		424	919	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940452	76940452	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008389-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	345	754	0	ENST00000373344.5:c.641A>G	p.Asp214Gly	p.D214G	ENST00000373344	NM_000489.3	214	gAt/gGt	8/35	1	2	FACETS	0.948	0.896	1	0.948	0.896	1	CLONAL	1	TRUE	1	0.468785730664166	2		754	1552	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176176108	176176109	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0008389-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	118	278	0	ENST00000367669.3:c.6_7del	p.Gly3Ter	p.G3*	ENST00000367669	NM_022457.5	2	tcTGgt/tcgt	1/20	0.468785730664166	3	FACETS	0.892	0.805	0.982	0.446	0.402	0.491	CLONAL	1	TRUE	1	0.468785730664166	3		278	697	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0008396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	500	431	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.897626176976273	4	FACETS	1	0.996	1	1	0.996	1	CLONAL	4	TRUE	0	0.897626176976273	4		431	519	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0008396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	777	644	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.897626176976273	3	FACETS	1	0.998	1	1	0.998	1	CLONAL	3	TRUE	0	0.897626176976273	3		645	794	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0008396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	213	248	2	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	0.897626176976273	7	FACETS	0.908	0.845	0.973	0.454	0.422	0.487	CLONAL	2	TRUE	3	0.897626176976273	7		250	848	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426722	212426722	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	71	558	0	ENST00000342788.4:c.2393T>G	p.Leu798Arg	p.L798R	ENST00000342788	NM_005235.2	798	cTt/cGt	20/28	0.763403230077892	4	FACETS	0.369	0.321	0.421	0.184	0.16	0.211	SUBCLONAL	1	TRUE	2	0.897626176976273	4		558	814	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783347	9783347	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148984508	NA	P-0008396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	257	533	0	ENST00000377346.4:c.2591C>T	p.Pro864Leu	p.P864L	ENST00000377346	NM_005026.3	864	cCg/cTg	20/24	0.897626176976273	3	FACETS	0.93	0.873	0.989	0.31	0.291	0.33	CLONAL	1	TRUE	0	0.897626176976273	3		533	892	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662764	227662764	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	132	495	0	ENST00000305123.5:c.691A>C	p.Thr231Pro	p.T231P	ENST00000305123	NM_005544.2	231	Acg/Ccg	1/2	0.763403230077892	4	FACETS	0.49	0.443	0.539	0.245	0.221	0.27	SUBCLONAL	1	TRUE	2	0.897626176976273	4		495	1140	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426114	138426114	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs761976401	NA	P-0008396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	39	566	0	ENST00000289153.2:c.1417T>G	p.Leu473Val	p.L473V	ENST00000289153	NM_006219.2	473	Ttg/Gtg	9/22	0.897626176976273	3	FACETS	0.302	0.25	0.36	0.151	0.125	0.18	SUBCLONAL	1	TRUE	1	0.897626176976273	3		566	417	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143181666	143181666	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	88	702	0	ENST00000262992.4:c.667A>C	p.Asn223His	p.N223H	ENST00000262992	NM_001101669.1	223	Aac/Cac	9/24	0.897626176976273	4	FACETS	0.317	0.28	0.358			1	SUBCLONAL	1	TRUE	NA	0.897626176976273	4		702	1172	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176684078	176684078	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1179	141	637	0	ENST00000439151.2:c.4892A>C	p.Lys1631Thr	p.K1631T	ENST00000439151	NM_022455.4	1631	aAg/aCg	13/23	0.897626176976273	4	FACETS	0.452	0.41	0.496	0.113	0.102	0.124	SUBCLONAL	1	TRUE	0	0.897626176976273	4		637	1320	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404656	70404656	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	237	623	2	ENST00000373644.4:c.2170G>T	p.Gly724Ter	p.G724*	ENST00000373644	NM_030625.2	724	Gga/Tga	4/12	0.897626176976273	3	FACETS	1	0.957	1	0.513	0.481	0.547	CLONAL	1	TRUE	1	0.897626176976273	3		625	745	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154238	2154238	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	254	483	0	ENST00000434045.2:c.690G>T	p.Glu230Asp	p.E230D	ENST00000434045	NM_001127598.1	230	gaG/gaT	5/5	0.303726965633239	6	FACETS	0.954	0.896	1			1	INDETERMINATE	2	TRUE	NA	0.897626176976273	6		483	829	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572633	64572633	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	270	418	0	ENST00000312049.6:c.1223A>C	p.Glu408Ala	p.E408A	ENST00000312049	NM_130799.2	408	gAg/gCg	9/10	0.897626176976273	3	FACETS	1	0.984	1	0.558	0.525	0.591	CLONAL	1	TRUE	1	0.897626176976273	3		418	781	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999455	100999455	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	390	767	0	ENST00000325455.5:c.347A>C	p.Asp116Ala	p.D116A	ENST00000325455	NM_001202474.3	116	gAc/gCc	1/8	0.742311951549913	4	FACETS	1	0.986	1	0.552	0.523	0.581	CLONAL	1	TRUE	2	0.897626176976273	4		767	1494	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257833	133257833	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs878854900	NA	P-0008396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	328	530	0	ENST00000320574.5:c.95T>G	p.Leu32Arg	p.L32R	ENST00000320574	NM_006231.2	32	cTc/cGc	2/49	NA	2	FACETS	0.994	0.946	1			1	INDETERMINATE	1	TRUE	NA	0.897626176976273	2		530	735	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385216	41385216	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2234	141	576	0	ENST00000373198.4:c.745T>C	p.Ser249Pro	p.S249P	ENST00000373198	NM_133170.3	249	Tca/Cca	6/32	0.897626176976273	7	FACETS	0.429	0.389	0.472	0.107	0.097	0.118	SUBCLONAL	1	TRUE	3	0.897626176976273	7		576	2375	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259065	16259066	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0008396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	155	421	1	ENST00000375759.3:c.6330_6331delinsTT	p.Glu2111Ter	p.E2111*	ENST00000375759	NM_015001.2	2110	ggGGag/ggTTag	11/15	0.897626176976273	3	FACETS	0.847	0.779	0.917	0.423	0.389	0.459	CLONAL	1	TRUE	1	0.897626176976273	3		422	591	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	212	160	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		160	562	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772229	68772230	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCTGCCA	novel	NA	P-0008424-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	112	411	0	ENST00000261769.5:c.84_91dup	p.Gly31AlafsTer28	p.G31Afs*28	ENST00000261769	NM_004360.3	26	-/CCCTGCCA	2/16	0.24500202520775	1	FACETS	0.807	0.725	0.895	0.807	0.725	0.895	CLONAL	1	TRUE	0	0.24500202520775	1		411	994	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	191	1128	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.354275474743604	1	FACETS	0.918	0.849	0.989	0.918	0.849	0.989	CLONAL	1	TRUE	0	0.380449441844127	1		1129	886	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837925	156837925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	156	448	0	ENST00000524377.1:c.458C>T	p.Ser153Phe	p.S153F	ENST00000524377	NM_002529.3	153	tCt/tTt	5/17	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.380449441844127	2		448	812	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521768	89521768	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	105	260	0	ENST00000336596.2:c.2845G>A	p.Asp949Asn	p.D949N	ENST00000336596	NM_005233.5	949	Gat/Aat	16/17	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.380449441844127	2		260	453	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587161	189587161	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173679499	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	123	411	0	ENST00000264731.3:c.1178G>A	p.Arg393Gln	p.R393Q	ENST00000264731	NM_003722.4	393	cGa/cAa	9/14	1	2	FACETS	0.8	0.724	0.881	0.8	0.724	0.881	SUBCLONAL	1	TRUE	1	0.380449441844127	2		411	808	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197273	106197273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	74	258	0	ENST00000380013.4:c.5606G>A	p.Gly1869Glu	p.G1869E	ENST00000380013	NM_001127208.2	1869	gGg/gAg	11/11	1	2	FACETS	0.758	0.665	0.858	0.758	0.665	0.858	SUBCLONAL	1	TRUE	1	0.380449441844127	2		258	513	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187558022	187558023	+	stop_gained	Nonsense_Mutation	DNP	CT	CT	TA	novel	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	119	305	0	ENST00000441802.2:c.3688_3689delinsTA	p.Arg1230Ter	p.R1230*	ENST00000441802	NM_005245.3	1230	AGa/TAa	5/27	0.270763661011353	1	FACETS	0.839	0.759	0.922	0.839	0.759	0.922	CLONAL	1	TRUE	0	0.380449441844127	1		305	604	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875685	35875685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	141	526	0	ENST00000303115.3:c.872G>A	p.Arg291Lys	p.R291K	ENST00000303115	NM_002185.3	291	aGa/aAa	7/8	1	2	FACETS	0.677	0.615	0.742	0.677	0.615	0.742	SUBCLONAL	1	TRUE	1	0.380449441844127	2		526	1095	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876106	35876106	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	179	472	0	ENST00000303115.3:c.898C>T	p.Pro300Ser	p.P300S	ENST00000303115	NM_002185.3	300	Cct/Tct	8/8	1	2	FACETS	0.898	0.827	0.972	0.898	0.827	0.972	CLONAL	1	TRUE	1	0.380449441844127	2		472	1048	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876397	35876397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	92	338	0	ENST00000303115.3:c.1189G>A	p.Gly397Arg	p.G397R	ENST00000303115	NM_002185.3	397	Ggg/Agg	8/8	1	2	FACETS	0.722	0.642	0.807	0.722	0.642	0.807	SUBCLONAL	1	TRUE	1	0.380449441844127	2		338	670	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964495	93964495	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	216	573	0	ENST00000369303.4:c.2402G>A	p.Arg801Lys	p.R801K	ENST00000369303	NM_004440.3	801	aGg/aAg	14/17	1	2	FACETS	0.93	0.863	0.999	0.93	0.863	0.999	CLONAL	1	TRUE	1	0.380449441844127	2		573	1221	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982107	93982107	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	191	596	0	ENST00000369303.4:c.1358G>A	p.Arg453Lys	p.R453K	ENST00000369303	NM_004440.3	453	aGa/aAa	6/17	1	2	FACETS	0.945	0.873	1	0.945	0.873	1	CLONAL	1	TRUE	1	0.380449441844127	2		596	1063	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553722	106553722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771286566	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	152	360	0	ENST00000369096.4:c.1687C>T	p.Pro563Ser	p.P563S	ENST00000369096	NM_001198.3	563	Ccc/Tcc	5/7	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.380449441844127	2		360	780	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528525	157528525	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	273	349	0	ENST00000346085.5:c.6250G>A	p.Glu2084Lys	p.E2084K	ENST00000346085	NM_020732.3	2084	Gag/Aag	20/20	0.380449441844127	2	FACETS	0.947	0.893	1	0.947	0.893	1	CLONAL	2	TRUE	0	0.380449441844127	2		349	758	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962810	2962810	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	124	344	1	ENST00000396946.4:c.2098C>A	p.Leu700Met	p.L700M	ENST00000396946	NM_032415.4	700	Ctg/Atg	16/25	1	2	FACETS	0.844	0.764	0.929	0.844	0.764	0.929	CLONAL	1	TRUE	1	0.380449441844127	2		345	772	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538835	23538835	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778496540	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	123	304	0	ENST00000380871.4:c.604G>A	p.Glu202Lys	p.E202K	ENST00000380871	NM_006167.3	202	Gag/Aag	2/2	0.354275474743604	1	FACETS	0.943	0.857	1	0.943	0.857	1	CLONAL	1	TRUE	0	0.380449441844127	1		304	555	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500831	8500831	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202068877	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	173	397	0	ENST00000356435.5:c.2051G>A	p.Arg684Gln	p.R684Q	ENST00000356435		684	cGg/cAg	13/35	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.380449441844127	2		397	831	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521361	8521361	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs966706082	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	176	386	0	ENST00000356435.5:c.877G>A	p.Asp293Asn	p.D293N	ENST00000356435		293	Gat/Aat	9/35	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.380449441844127	2		386	902	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521384	8521384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777779009	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	192	430	0	ENST00000356435.5:c.854G>A	p.Gly285Glu	p.G285E	ENST00000356435		285	gGa/gAa	9/35	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.380449441844127	2		430	975	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97876984	97876984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768508859	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	141	393	1	ENST00000289081.3:c.1081C>T	p.Arg361Trp	p.R361W	ENST00000289081	NM_000136.2	361	Cgg/Tgg	12/15	1	2	FACETS	0.913	0.832	0.998	0.913	0.832	0.998	CLONAL	1	TRUE	1	0.380449441844127	2		394	812	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596032	43596032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749390385	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	151	395	1	ENST00000355710.3:c.199C>T	p.Arg67Cys	p.R67C	ENST00000355710	NM_020975.4	67	Cgc/Tgc	2/20	0.380449441844127	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.380449441844127	1		396	622	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376112	118376112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	117	375	0	ENST00000534358.1:c.9505C>T	p.Pro3169Ser	p.P3169S	ENST00000534358	NM_005933.3	3169	Cct/Tct	27/36	0.380449441844127	1	FACETS	0.812	0.734	0.895	0.812	0.734	0.895	CLONAL	1	TRUE	0	0.380449441844127	1		375	613	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231280	46231280	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	160	329	0	ENST00000334344.6:c.1121-1G>A		p.X374_splice	ENST00000334344	NM_152641.2	374			NA	2	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.380449441844127	2		329	685	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813309	102813309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776234219	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	155	405	0	ENST00000307046.8:c.380C>T	p.Thr127Ile	p.T127I	ENST00000307046	NM_001111285.1	127	aCc/aTc	3/4	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.380449441844127	2		405	815	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623858	28623858	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	161	472	0	ENST00000241453.7:c.796G>A	p.Glu266Lys	p.E266K	ENST00000241453	NM_004119.2	266	Gaa/Aaa	7/24	0.380449441844127	1	FACETS	0.959	0.881	1	0.959	0.881	1	CLONAL	1	TRUE	0	0.380449441844127	1		472	715	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28903831	28903831	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1278121302	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	174	508	0	ENST00000282397.4:c.2628G>A	p.Met876Ile	p.M876I	ENST00000282397	NM_002019.4	876	atG/atA	19/30	0.380449441844127	1	FACETS	0.948	0.875	1	0.948	0.875	1	CLONAL	1	TRUE	0	0.380449441844127	1		508	781	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515277	103515277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs887249436	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	189	423	0	ENST00000355739.4:c.1778C>T	p.Pro593Leu	p.P593L	ENST00000355739	NM_000123.3	593	cCt/cTt	8/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.380449441844127	2		423	939	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023288	33023288	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1252	270	738	0	ENST00000300177.4:c.397A>C	p.Lys133Gln	p.K133Q	ENST00000300177	NM_001191322.1	133	Aag/Cag	2/2	1	2	FACETS	0.933	0.873	0.995	0.933	0.873	0.995	CLONAL	1	TRUE	1	0.380449441844127	2		738	1522	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058882	42058882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	238	694	0	ENST00000219905.7:c.8602C>T	p.Pro2868Ser	p.P2868S	ENST00000219905	NM_001164273.1	2868	Cct/Tct	24/24	1	2	FACETS	0.898	0.836	0.962	0.898	0.836	0.962	CLONAL	1	TRUE	1	0.380449441844127	2		694	1394	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576202	88576202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1482426106	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	146	269	1	ENST00000360948.2:c.1471C>T	p.Pro491Ser	p.P491S	ENST00000360948	NM_001012338.2	491	Ccc/Tcc	13/19	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.380449441844127	2		270	653	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678389	88678389	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	221	634	0	ENST00000360948.2:c.1147C>T	p.Pro383Ser	p.P383S	ENST00000360948	NM_001012338.2	383	Cca/Tca	9/19	1	2	FACETS	0.912	0.847	0.979	0.912	0.847	0.979	CLONAL	1	TRUE	1	0.380449441844127	2		634	1274	SUCCESS
BLM	641	MSKCC	GRCh37	15	91334068	91334068	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	105	339	0	ENST00000355112.3:c.3013A>T	p.Ile1005Leu	p.I1005L	ENST00000355112	NM_000057.2	1005	Ata/Tta	15/22	1	2	FACETS	0.898	0.806	0.995	0.898	0.806	0.995	CLONAL	1	TRUE	1	0.380449441844127	2		339	615	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828119	72828119	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs144056966	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1393	184	815	0	ENST00000268489.5:c.8462T>G	p.Val2821Gly	p.V2821G	ENST00000268489	NM_006885.3	2821	gTt/gGt	9/10	0.204637355918044	1	FACETS	0.497	0.457	0.539	0.497	0.457	0.539	INDETERMINATE	1	TRUE	0	0.380449441844127	1		815	1577	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81904516	81904516	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	233	615	0	ENST00000359376.3:c.624A>C	p.Lys208Asn	p.K208N	ENST00000359376	NM_002661.3	208	aaA/aaC	7/33	0.204637355918044	1	FACETS	0.886	0.825	0.948	0.886	0.825	0.948	INDETERMINATE	1	TRUE	0	0.380449441844127	1		615	1120	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541468	29541468	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1131691131	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	31	134	0	ENST00000356175.3:c.1393-1G>A		p.X465_splice	ENST00000356175	NM_000267.3	465			1	2	FACETS	0.78	0.635	0.94	0.78	0.635	0.94	CLONAL	1	TRUE	1	0.380449441844127	2		134	209	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553539	29553539	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1131691099	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	97	260	1	ENST00000356175.3:c.2088G>A	p.Trp696Ter	p.W696*	ENST00000356175	NM_000267.3	696	tgG/tgA	18/57	1	2	FACETS	0.822	0.734	0.916	0.822	0.734	0.916	CLONAL	1	TRUE	1	0.380449441844127	2		261	620	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39620667	39620667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1247336892	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	97	442	0	ENST00000262039.4:c.2065C>T	p.Pro689Ser	p.P689S	ENST00000262039	NM_002647.2	689	Cct/Tct	19/25	1	2	FACETS	0.611	0.544	0.682	0.611	0.544	0.682	SUBCLONAL	1	TRUE	1	0.380449441844127	2		442	835	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612320	1612320	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757572121	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	297	625	1	ENST00000344749.5:c.1699C>T	p.Arg567Trp	p.R567W	ENST00000344749	NM_001136139.2	567	Cgg/Tgg	18/19	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.380449441844127	2		626	1305	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619778	1619778	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1031123688	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	209	605	1	ENST00000344749.5:c.1167+1G>A		p.X389_splice	ENST00000344749	NM_001136139.2	389			1	2	FACETS	0.964	0.894	1	0.964	0.894	1	CLONAL	1	TRUE	1	0.380449441844127	2		606	1140	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14628990	14628990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	184	556	0	ENST00000254322.2:c.172C>T	p.Pro58Ser	p.P58S	ENST00000254322	NM_006145.1	58	Ccg/Tcg	1/3	1	2	FACETS	0.875	0.807	0.947	0.875	0.807	0.947	CLONAL	1	TRUE	1	0.380449441844127	2		556	1105	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292580	15292580	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867505691	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	138	351	0	ENST00000263388.2:c.2599G>A	p.Gly867Ser	p.G867S	ENST00000263388	NM_000435.2	867	Ggc/Agc	17/33	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.380449441844127	2		351	655	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748492	40748493	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	149	546	0	ENST00000392038.2:c.389_390delinsTT	p.Ser130Phe	p.S130F	ENST00000392038	NM_001626.4	130	tCC/tTT	5/14	1	2	FACETS	0.755	0.689	0.825	0.755	0.689	0.825	SUBCLONAL	1	TRUE	1	0.380449441844127	2		546	1037	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514563	41514563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	128	284	1	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	0.380449441844127	2		285	664	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29105996	29105996	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs774068238	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	318	410	0	ENST00000328354.6:c.844C>T	p.His282Tyr	p.H282Y	ENST00000328354	NM_007194.3	282	Cat/Tat	7/15	0.339776292153795	3	FACETS	0.978	0.925	1	0.978	0.925	1	CLONAL	2	TRUE	1	0.380449441844127	3		410	1017	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923673	39923673	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	221	513	0	ENST00000378444.4:c.3418G>A	p.Gly1140Ser	p.G1140S	ENST00000378444	NM_001123385.1	1140	Ggt/Agt	7/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.380449441844127	2		513	1066	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045784	47045784	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	151	442	1	ENST00000377604.3:c.2665G>A	p.Glu889Lys	p.E889K	ENST00000377604	NM_001204468.1	889	Gag/Aag	23/24	1	2	FACETS	0.943	0.862	1	0.943	0.862	1	CLONAL	1	TRUE	1	0.380449441844127	2		443	842	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341240	70341240	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	218	612	1	ENST00000374080.3:c.799C>T	p.Pro267Ser	p.P267S	ENST00000374080		267	Cct/Tct	6/45	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.380449441844127	2		613	1039	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348461	70348461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	217	614	0	ENST00000374080.3:c.3368C>T	p.Ser1123Phe	p.S1123F	ENST00000374080		1123	tCt/tTt	24/45	1	2	FACETS	0.968	0.899	1	0.968	0.899	1	CLONAL	1	TRUE	1	0.380449441844127	2		614	1178	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354259	70354259	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	218	547	0	ENST00000374080.3:c.4670G>T	p.Trp1557Leu	p.W1557L	ENST00000374080		1557	tGg/tTg	34/45	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.380449441844127	2		547	1144	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776888	76776888	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	149	704	0	ENST00000373344.5:c.7064C>T	p.Ser2355Leu	p.S2355L	ENST00000373344	NM_000489.3	2355	tCa/tTa	33/35	1	2	FACETS	0.705	0.643	0.77	0.705	0.643	0.77	SUBCLONAL	1	TRUE	1	0.380449441844127	2		704	1111	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849203	76849203	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	232	654	0	ENST00000373344.5:c.6073G>A	p.Glu2025Lys	p.E2025K	ENST00000373344	NM_000489.3	2025	Gaa/Aaa	26/35	1	2	FACETS	0.98	0.913	1	0.98	0.913	1	CLONAL	1	TRUE	1	0.380449441844127	2		654	1244	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939235	76939235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782164721	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	216	610	0	ENST00000373344.5:c.1513G>A	p.Glu505Lys	p.E505K	ENST00000373344	NM_000489.3	505	Gaa/Aaa	9/35	1	2	FACETS	0.869	0.807	0.935	0.869	0.807	0.935	CLONAL	1	TRUE	1	0.380449441844127	2		610	1306	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939382	76939382	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782313786	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	223	654	0	ENST00000373344.5:c.1366G>A	p.Asp456Asn	p.D456N	ENST00000373344	NM_000489.3	456	Gat/Aat	9/35	1	2	FACETS	0.834	0.774	0.896	0.834	0.774	0.896	CLONAL	1	TRUE	1	0.380449441844127	2		654	1406	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81904520	81904522	+	frameshift_variant	Frame_Shift_Del	DEL	ATG	ATG	TT	novel	NA	P-0008434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	223	619	0	ENST00000359376.3:c.628_630delinsTT	p.Met210PhefsTer53	p.M210Ffs*53	ENST00000359376	NM_002661.3	210	ATG/TT	7/33	0.204637355918044	1	FACETS	0.86	0.8	0.922	0.86	0.8	0.922	INDETERMINATE	1	TRUE	0	0.380449441844127	1		619	1104	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177584	56177584	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368201444	NA	P-0008440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	113	439	1	ENST00000399503.3:c.2557C>T	p.Arg853Cys	p.R853C	ENST00000399503	NM_005921.1	853	Cgt/Tgt	14/20	1	2	FACETS	0.697	0.627	0.772	0.697	0.627	0.772	SUBCLONAL	1	TRUE	1	0.34770802747447	2		440	932	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004775	150004775	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	139	369	0	ENST00000253339.5:c.1450A>G	p.Thr484Ala	p.T484A	ENST00000253339		484	Aca/Gca	3/7	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.34770802747447	2		369	711	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154749	2154749	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	150	512	0	ENST00000434045.2:c.472C>T	p.Pro158Ser	p.P158S	ENST00000434045	NM_001127598.1	158	Ccg/Tcg	4/5	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.34770802747447	2		512	856	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432581	49432581	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754988293	NA	P-0008440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	128	390	0	ENST00000301067.7:c.8558C>T	p.Pro2853Leu	p.P2853L	ENST00000301067	NM_003482.3	2853	cCg/cTg	34/54	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.34770802747447	2		390	724	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560088	29560088	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs878853884	NA	P-0008440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	162	437	0	ENST00000356175.3:c.3565C>T	p.Gln1189Ter	p.Q1189*	ENST00000356175	NM_000267.3	1189	Caa/Taa	27/57	1	2	FACETS	0.98	0.899	1	0.98	0.899	1	CLONAL	1	TRUE	1	0.34770802747447	2		437	951	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665764	29665764	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	143	475	0	ENST00000356175.3:c.6799C>T	p.Gln2267Ter	p.Q2267*	ENST00000356175	NM_000267.3	2267	Caa/Taa	45/57	1	2	FACETS	0.887	0.808	0.97	0.887	0.808	0.97	CLONAL	1	TRUE	1	0.34770802747447	2		475	927	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649680	48649680	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	133	643	1	ENST00000376670.3:c.164C>A	p.Ala55Asp	p.A55D	ENST00000376670	NM_002049.3	55	gCt/gAt	2/6	0.211107080224019	1	FACETS	0.692	0.628	0.76	0.692	0.628	0.76	SUBCLONAL	1	TRUE	0	0.34770802747447	1		644	913	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427974	49427974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008447-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	34	222	0	ENST00000301067.7:c.10616G>A	p.Arg3539Gln	p.R3539Q	ENST00000301067	NM_003482.3	3539	cGg/cAg	38/54	0.273078694155728	3	FACETS	0.426	0.347	0.514	0.213	0.173	0.257	SUBCLONAL	1	TRUE	1	0.387343809679505	3		222	492	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223550	55223550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	93	412	0	ENST00000275493.2:c.917C>T	p.Ser306Leu	p.S306L	ENST00000275493	NM_005228.3	306	tCg/tTg	8/28	0.156768352594289	1	FACETS	0.765	0.683	0.852	1	0.981	1	SUBCLONAL	2	TRUE	0	0.22	1		412	492	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0008467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	376	432	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.966	0.918	1	0.966	0.918	1	CLONAL	1	TRUE	1	0.713711797079105	2		432	1091	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182493	99182493	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs375661517	NA	P-0008467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	296	443	0	ENST00000074304.5:c.2296G>A	p.Asp766Asn	p.D766N	ENST00000074304	NM_001134224.1	766	Gac/Aac	22/26	1	2	FACETS	0.938	0.886	0.992	0.938	0.886	0.992	CLONAL	1	TRUE	1	0.713711797079105	2		443	884	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052632	42052632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779811318	NA	P-0008467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1246	334	848	1	ENST00000219905.7:c.7303C>T	p.Arg2435Trp	p.R2435W	ENST00000219905	NM_001164273.1	2435	Cgg/Tgg	20/24	0.365976048010821	1	FACETS	0.381	0.359	0.404	0.381	0.359	0.404	INDETERMINATE	1	TRUE	0	0.713711797079105	1		849	1580	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611131	100611131	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782338603	NA	P-0008467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	401	607	3	ENST00000308731.7:c.1475G>A	p.Arg492His	p.R492H	ENST00000308731	NM_000061.2	492	cGc/cAc	15/19	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.713711797079105	2		610	1033	SUCCESS
APC	324	MSKCC	GRCh37	5	112173257	112173258	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TAAG	novel	NA	P-0008467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	254	364	0	ENST00000257430.4:c.1967_1970dup	p.Arg657SerfsTer18	p.R657Sfs*18	ENST00000257430	NM_000038.5	656	cta/cTAAGta	16/16	NA	2	FACETS	0.752	0.705	0.801			1	INDETERMINATE	1	TRUE	NA	0.713711797079105	2		364	946	SUCCESS
APC	324	MSKCC	GRCh37	5	112175830	112175830	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	327	524	0	ENST00000257430.4:c.4539del	p.Glu1513AspfsTer10	p.E1513Dfs*10	ENST00000257430	NM_000038.5	1513	gaG/ga	16/16	NA	2	FACETS	0.901	0.853	0.95			1	INDETERMINATE	1	TRUE	NA	0.713711797079105	2		524	1017	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023844	27023844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008477-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	332	365	1	ENST00000324856.7:c.950G>A	p.Ser317Asn	p.S317N	ENST00000324856	NM_006015.4	317	aGt/aAt	1/20	1	2	FACETS	0.995	0.947	1	0.995	0.947	1	CLONAL	1	TRUE	1	0.893057943441727	2		366	747	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373568	118373568	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555046280	NA	P-0008477-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	900	466	0	ENST00000534358.1:c.6961G>A	p.Gly2321Arg	p.G2321R	ENST00000534358	NM_005933.3	2321	Gga/Aga	27/36	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	2	TRUE	NA	0.893057943441727	2		466	988	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0008481-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	69	110	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	NA	2	FACETS	0.747	0.655	0.845			1	INDETERMINATE	1	TRUE	NA	0.535388783132651	2		110	345	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842693	68842693	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008481-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	191	844	0	ENST00000261769.5:c.631del	p.Thr211GlnfsTer4	p.T211Qfs*4	ENST00000261769	NM_004360.3	210	gAa/ga	5/16	0.527498995515209	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.535388783132651	1		844	430	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45873407	45873407	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008481-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	90	680	3	ENST00000391945.4:c.89G>A	p.Arg30His	p.R30H	ENST00000391945	NM_000400.3	30	cGc/cAc	2/23	0.328903376008971	1	FACETS	0.609	0.544	0.678	0.609	0.544	0.678	SUBCLONAL	1	TRUE	0	0.535388783132651	1		683	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0008483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	93	360	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.273963431515796	2	FACETS	1	0.981	1	0.747	0.67	0.828	CLONAL	1	TRUE	0	0.346634864143557	2		361	359	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829889	72829889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1179466504	NA	P-0008483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	232	628	2	ENST00000268489.5:c.6692C>T	p.Pro2231Leu	p.P2231L	ENST00000268489	NM_006885.3	2231	cCg/cTg	9/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.346634864143557	2		630	1138	SUCCESS
APC	324	MSKCC	GRCh37	5	112162859	112162859	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	179	373	0	ENST00000257430.4:c.1464del	p.Thr489LeufsTer9	p.T489Lfs*9	ENST00000257430	NM_000038.5	488	cTt/ct	12/16	0.273963431515796	2	FACETS	1	0.989	1	0.702	0.648	0.757	CLONAL	1	TRUE	0	0.346634864143557	2		373	736	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0008490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	28	586	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.522	0.415	0.645	0.522	0.415	0.645	SUBCLONAL	1	TRUE	1	0.13	2		586	825	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481403	140481403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913357	NA	P-0008490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	31	538	0	ENST00000288602.6:c.1405G>A	p.Gly469Arg	p.G469R	ENST00000288602	NM_004333.4	469	Gga/Aga	11/18	1	2	FACETS	0.633	0.51	0.774	0.633	0.51	0.774	SUBCLONAL	1	TRUE	1	0.13	2		538	753	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629247	187629247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	38	408	0	ENST00000441802.2:c.1735C>T	p.Pro579Ser	p.P579S	ENST00000441802	NM_005245.3	579	Ccc/Tcc	2/27	0.3	2	FACETS	0.777	0.641	0.931			1	CLONAL	1	TRUE	NA	0.13	2		408	752	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482215	87482215	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	44	489	0	ENST00000277120.3:c.1502C>T	p.Ser501Phe	p.S501F	ENST00000277120		501	tCc/tTc	14/19	1	2	FACETS	0.813	0.679	0.961	0.813	0.679	0.961	CLONAL	1	TRUE	1	0.13	2		489	833	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504620	103504620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	50	399	0	ENST00000355739.4:c.241C>T	p.Pro81Ser	p.P81S	ENST00000355739	NM_000123.3	81	Cca/Tca	2/15	1	2	FACETS	0.866	0.733	1	0.866	0.733	1	CLONAL	1	TRUE	1	0.13	2		399	888	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494612	2494613	+	missense_variant	Missense_Mutation	DNP	AG	AG	GA	novel	NA	P-0008490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	35	351	0	ENST00000355716.4:c.752_753delinsGA	p.Glu251Gly	p.E251G	ENST00000355716	NM_003820.2	251	gAG/gGA	8/8	0.3	2	FACETS	0.801	0.655	0.967			1	CLONAL	1	TRUE	NA	0.13	2		351	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0008521-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	291	223	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.310290412895886	2	FACETS	0.864	0.817	0.91	1	0.992	1	CLONAL	3	FALSE	0	0.310290412895886	2		223	724	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008521-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	200	364	0	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	0.217705455696077	3	FACETS	0.858	0.796	0.922	0.858	0.796	0.922	CLONAL	2	FALSE	1	0.310290412895886	3		364	868	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0008521-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	196	499	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.146246230558911	3	FACETS	0.912	0.846	0.98	0.608	0.564	0.654	INDETERMINATE	2	FALSE	0	0.310290412895886	3		499	800	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0008521-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	126	618	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.217705455696077	3	FACETS	1	0.97	1	0.585	0.53	0.643	CLONAL	1	FALSE	1	0.310290412895886	3		618	802	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287156	33287156	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0008521-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	97	317	0	ENST00000374542.5:c.1940+1G>C		p.X647_splice	ENST00000374542	NM_001141970.1	647			0.310290412895886	3	FACETS	1	0.962	1	0.585	0.522	0.652	CLONAL	1	FALSE	1	0.310290412895886	3		317	617	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405827	157405827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373508866	NA	P-0008521-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	90	396	0	ENST00000346085.5:c.2069C>T	p.Thr690Met	p.T690M	ENST00000346085	NM_020732.3	690	aCg/aTg	6/20	0.310290412895886	3	FACETS	0.844	0.748	0.946	0.422	0.374	0.473	CLONAL	1	FALSE	1	0.310290412895886	3		396	794	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935705	13935705	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008521-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	97	269	0	ENST00000405192.2:c.1151G>T	p.Gly384Val	p.G384V	ENST00000405192	NM_001163147.1	384	gGa/gTa	12/12	0.128945585102843	4	FACETS	1	0.948	1	0.554	0.493	0.618	INDETERMINATE	1	FALSE	2	0.310290412895886	4		269	740	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14026266	14026266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008521-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	173	376	0	ENST00000405192.2:c.178G>A	p.Glu60Lys	p.E60K	ENST00000405192	NM_001163147.1	60	Gaa/Aaa	4/12	0.128945585102843	4	FACETS	0.85	0.783	0.92	0.85	0.783	0.92	INDETERMINATE	2	FALSE	2	0.310290412895886	4		376	859	SUCCESS
APC	324	MSKCC	GRCh37	5	112175036	112175037	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0008521-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	73	387	0	ENST00000257430.4:c.3746dup	p.Cys1249TrpfsTer7	p.C1249Wfs*7	ENST00000257430	NM_000038.5	1249	tgc/tGgc	16/16	0.217705455696077	3	FACETS	0.825	0.721	0.936	0.412	0.36	0.469	CLONAL	1	FALSE	1	0.310290412895886	3		387	659	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179069	123179069	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	133	459	0	ENST00000218089.9:c.518C>A	p.Ser173Tyr	p.S173Y	ENST00000218089	NM_001042749.1	173	tCc/tAc	8/35	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.22	2		459	1090	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576865	7576865	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	rs879254077	NA	P-0008538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	136	544	0	ENST00000269305.4:c.981T>G	p.Tyr327Ter	p.Y327*	ENST00000269305	NM_001126112.2	327	taT/taG	9/11	0.252841918393548	4	FACETS	1	0.977	1	0.802	0.732	0.875	CLONAL	2	TRUE	1	0.233043080487614	4		544	598	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674316	86674317	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs886041400	NA	P-0008538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	55	338	0	ENST00000274376.6:c.2450_2451del	p.Ser817TyrfsTer12	p.S817Yfs*12	ENST00000274376	NM_002890.2	816	gaCTct/gact	18/25	0.223352785508096	2	FACETS	1	0.945	1	0.608	0.522	0.702	CLONAL	1	TRUE	0	0.233043080487614	2		338	388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0008541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	403	462	1	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.388226393303905	2	FACETS	0.795	0.756	0.834	0.795	0.756	0.834	SUBCLONAL	2	TRUE	0	0.411019431929148	2		463	1234	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0008541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	90	534	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.411019431929148	2		534	426	SUCCESS
ALK	238	MSKCC	GRCh37	2	29450511	29450511	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	92	603	0	ENST00000389048.3:c.2843C>T	p.Pro948Leu	p.P948L	ENST00000389048	NM_004304.4	948	cCc/cTc	17/29	0.326830644429651	3	FACETS	0.533	0.472	0.598	0.266	0.236	0.299	SUBCLONAL	1	TRUE	1	0.411019431929148	3		603	1013	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232135	98232135	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	98	497	0	ENST00000331920.6:c.1807C>T	p.Arg603Cys	p.R603C	ENST00000331920	NM_000264.3	603	Cgc/Tgc	13/24	0.388622800675021	3	FACETS	0.82	0.732	0.914	0.273	0.244	0.305	CLONAL	1	TRUE	0	0.411019431929148	3		497	701	SUCCESS
APC	324	MSKCC	GRCh37	5	112175245	112175245	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	79	367	0	ENST00000257430.4:c.3954del	p.Pro1319LeufsTer2	p.P1319Lfs*2	ENST00000257430	NM_000038.5	1318	gaT/ga	16/16	0.378907125354243	1	FACETS	0.885	0.785	0.991	0.885	0.785	0.991	CLONAL	1	TRUE	0	0.411019431929148	1		367	345	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653796	89653798	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs1554893765	NA	P-0008548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	284	520	0	ENST00000371953.3:c.97_99del	p.Ile33del	p.I33del	ENST00000371953	NM_000314.4	32	ATT/-	2/9	0.765944708286986	1	FACETS	0.976	0.932	1	0.976	0.932	1	CLONAL	1	TRUE	0	0.765944708286986	1		520	469	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599332	55599332	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519710	NA	P-0008548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1328	36	563	0	ENST00000288135.5:c.2458G>T	p.Asp820Tyr	p.D820Y	ENST00000288135	NM_000222.2	820	Gat/Tat	17/21	0.765944708286986	3	FACETS	0.095	0.077	0.115	0.048	0.038	0.058	SUBCLONAL	1	TRUE	1	0.765944708286986	3		563	1364	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954309	48954309	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	312	410	0	ENST00000267163.4:c.1430T>G	p.Leu477Arg	p.L477R	ENST00000267163	NM_000321.2	477	cTg/cGg	16/27	0.765944708286986	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.765944708286986	1		410	492	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593640	55593660	+	inframe_deletion	In_Frame_Del	DEL	TTTACATAGACCCAACACAAC	TTTACATAGACCCAACACAAC	-	novel	NA	P-0008548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	497	626	0	ENST00000288135.5:c.1708_1728del	p.Tyr570_Leu576del	p.Y570_L576del	ENST00000288135	NM_000222.2	569	gTTTACATAGACCCAACACAACtt/gtt	11/21	0.765944708286986	3	FACETS	1	0.995	1	0.666	0.638	0.695	CLONAL	1	TRUE	1	0.765944708286986	3		626	1347	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268766	41268766	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	131	526	0	ENST00000349496.5:c.1004A>T	p.Lys335Ile	p.K335I	ENST00000349496	NM_001904.3	335	aAa/aTa	7/15	1	2	FACETS	0.969	0.885	1	0.969	0.885	1	CLONAL	1	TRUE	1	0.554963519016157	2		526	487	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65311203	65311203	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	283	459	0	ENST00000342505.4:c.2108G>T	p.Ser703Ile	p.S703I	ENST00000342505	NM_002227.2	703	aGc/aTc	15/25	1	2	FACETS	0.91	0.855	0.966	0.91	0.855	0.966	CLONAL	1	TRUE	1	0.554963519016157	2		459	1121	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0008571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	202	446	0	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	0.159923357085441	3	FACETS	1	0.989	1	0.455	0.421	0.49	INDETERMINATE	1	FALSE	0	0.3	3		446	1135	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111982979	111982979	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2673	259	428	1	ENST00000368678.4:c.1568C>T	p.Ala523Val	p.A523V	ENST00000368678		523	gCg/gTg	13/13	0.213186586602306	5	FACETS	0.854	0.795	0.915	0.285	0.265	0.305	CLONAL	1	FALSE	2	0.3	5		429	2932	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0008584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	214	375	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.532688722797229	3	FACETS	0.818	0.765	0.872	0.818	0.765	0.872	CLONAL	2	TRUE	1	0.532688722797229	3		375	622	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0008584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	257	429	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.506353084916119	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.532688722797229	2		429	462	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210692	5210692	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	134	284	0	ENST00000357368.4:c.5359C>T	p.Arg1787Trp	p.R1787W	ENST00000357368	NM_002850.3	1787	Cgg/Tgg	34/38	0.532688722797229	3	FACETS	0.967	0.881	1	0.483	0.44	0.529	CLONAL	1	TRUE	1	0.532688722797229	3		284	659	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18576896	18576897	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0008584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	124	436	0	ENST00000266497.5:c.2306dup	p.Asn769LysfsTer3	p.N769Kfs*3	ENST00000266497		768	-/A	16/31	0.532688722797229	3	FACETS	0.851	0.771	0.935	0.425	0.385	0.468	CLONAL	1	TRUE	1	0.532688722797229	3		436	693	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0008588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	99	565	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.913	0.816	1	1	0.985	1	CLONAL	2	FALSE	1	0.161096792299069	2		565	673	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468029	50468029	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	104	680	0	ENST00000331340.3:c.1264G>A	p.Ala422Thr	p.A422T	ENST00000331340	NM_006060.4	422	Gcg/Acg	8/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.161096792299069	2		680	965	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189847	11189847	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	94	842	0	ENST00000361445.4:c.5662T>A	p.Phe1888Ile	p.F1888I	ENST00000361445	NM_004958.3	1888	Ttc/Atc	40/58	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	FALSE	1	0.161096792299069	2		842	1077	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190748	108190748	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1339238483	NA	P-0008588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	38	978	4	ENST00000278616.4:c.6415G>T	p.Glu2139Ter	p.E2139*	ENST00000278616	NM_000051.3	2139	Gaa/Taa	44/63	1	2	FACETS	0.67	0.552	0.802	0.67	0.552	0.802	SUBCLONAL	1	FALSE	1	0.161096792299069	2		982	704	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203609	108203609	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	34	668	2	ENST00000278616.4:c.7909C>T	p.Gln2637Ter	p.Q2637*	ENST00000278616	NM_000051.3	2637	Cag/Tag	53/63	1	2	FACETS	0.92	0.751	1	0.92	0.751	1	CLONAL	1	FALSE	1	0.161096792299069	2		670	459	SUCCESS
APC	324	MSKCC	GRCh37	5	112173956	112173956	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	36	633	0	ENST00000257430.4:c.2667del	p.Val890SerfsTer26	p.V890Sfs*26	ENST00000257430	NM_000038.5	889	Aaa/aa	16/16	1	2	FACETS	0.685	0.562	0.825	0.685	0.562	0.825	SUBCLONAL	1	FALSE	1	0.161096792299069	2		633	652	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0008594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	72	203	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.252658097129986	3	FACETS	0.985	0.873	1			1	CLONAL	2	TRUE	NA	0.35405793877694	3		203	243	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0008594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	101	307	0	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	0.35405793877694	1	FACETS	0.947	0.85	1	0.947	0.85	1	CLONAL	1	TRUE	0	0.35405793877694	1		307	496	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0008594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	80	401	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.35405793877694	2		401	429	SUCCESS
APC	324	MSKCC	GRCh37	5	112174112	112174112	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	53	391	0	ENST00000257430.4:c.2821G>T	p.Glu941Ter	p.E941*	ENST00000257430	NM_000038.5	941	Gaa/Taa	16/16	1	2	FACETS	0.723	0.618	0.838	0.723	0.618	0.838	SUBCLONAL	1	TRUE	1	0.35405793877694	2		391	414	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549351	187549351	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	136	453	0	ENST00000441802.2:c.4767G>C	p.Lys1589Asn	p.K1589N	ENST00000441802	NM_005245.3	1589	aaG/aaC	9/27	1	2	FACETS	0.787	0.715	0.863	0.787	0.715	0.863	SUBCLONAL	1	TRUE	1	0.35405793877694	2		453	976	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729454	41729454	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1553	334	1015	0	ENST00000242208.4:c.1075G>A	p.Ala359Thr	p.A359T	ENST00000242208	NM_002192.2	359	Gca/Aca	3/3	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.35405793877694	2		1015	1887	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267223	41267235	+	protein_altering_variant	In_Frame_Del	DEL	TAAAATGGCAGTG	TAAAATGGCAGTG	A	novel	NA	P-0008594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	74	342	0	ENST00000349496.5:c.807_819delinsA	p.Lys270_Val273del	p.K270_V273del	ENST00000349496	NM_001904.3	269	gcTAAAATGGCAGTG/gcA	6/15	1	2	FACETS	0.78	0.684	0.883	0.78	0.684	0.883	SUBCLONAL	1	TRUE	1	0.35405793877694	2		342	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121912651	NA	P-0008602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	829	399	0	ENST00000269305.4:c.742C>G	p.Arg248Gly	p.R248G	ENST00000269305	NM_001126112.2	248	Cgg/Ggg	7/11	0.698029830460852	4	FACETS	0.972	0.954	0.99	0.972	0.954	0.99	CLONAL	4	TRUE	0	0.698029830460852	4		399	1037	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715389	117715389	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	86	296	0	ENST00000368508.3:c.1100G>T	p.Gly367Val	p.G367V	ENST00000368508	NM_002944.2	367	gGa/gTa	10/43	0.389048334664869	5	FACETS	0.632	0.558	0.711	0.211	0.186	0.237	INDETERMINATE	1	TRUE	2	0.698029830460852	5		296	798	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242448	55242449	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTCCCGTCGCTATCAAGG	novel	NA	P-0008602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2842	3741	290	0	ENST00000275493.2:c.2219_2236dup	p.Lys745_Glu746insValProValAlaIleLys	p.K745_E746insVPVAIK	ENST00000275493	NM_005228.3	740	att/aTTCCCGTCGCTATCAAGGtt	19/28	0.698029830460852	26	FACETS	1	0.995	1			1	CLONAL	15	TRUE	NA	0.698029830460852	26		290	6583	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0008645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	360	412	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.523846189000458	3	FACETS	0.798	0.757	0.839	0.798	0.757	0.839	SUBCLONAL	2	TRUE	1	0.527011832611903	3		412	1082	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542903	187542903	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	201	402	0	ENST00000441802.2:c.4837G>T	p.Asp1613Tyr	p.D1613Y	ENST00000441802	NM_005245.3	1613	Gat/Tat	10/27	1	2	FACETS	0.914	0.848	0.981	0.914	0.848	0.981	CLONAL	1	TRUE	1	0.527011832611903	2		402	835	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5066774	5066774	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	18	309	0	ENST00000381652.3:c.1311G>C	p.Leu437Phe	p.L437F	ENST00000381652	NM_004972.3	437	ttG/ttC	10/25	0.527011832611903	1	FACETS	0.142	0.106	0.184	0.142	0.106	0.184	SUBCLONAL	1	TRUE	0	0.527011832611903	1		309	355	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24134026	24134026	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	272	648	0	ENST00000263121.7:c.177G>C	p.Glu59Asp	p.E59D	ENST00000263121	NM_003073.3	59	gaG/gaC	2/9	1	2	FACETS	0.756	0.708	0.806	0.756	0.708	0.806	SUBCLONAL	1	TRUE	1	0.527011832611903	2		648	1365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576925	7576926	+	inframe_insertion,splice_region_variant	In_Frame_Ins	INS	-	-	GATAGGAAAGAGGCT	novel	NA	P-0008645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	125	416	0	ENST00000269305.4:c.921_922insGCCTCTTTCCTATCA	p.Ala307_Leu308insAlaSerPheLeuSer	p.A307_L308insASFLS	ENST00000269305	NM_001126112.2	307	gca/gcAGCCTCTTTCCTATCa	9/11	0.527011832611903	1	FACETS	0.643	0.585	0.705	0.643	0.585	0.705	SUBCLONAL	1	TRUE	0	0.527011832611903	1		416	543	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0008652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	98	372	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.175550441190231	1	FACETS	0.781	0.703	0.862	0.781	0.703	0.862	INDETERMINATE	1	FALSE	0	0.527961657232666	1		372	350	SUCCESS
AR	367	MSKCC	GRCh37	X	66941796	66941796	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	63	457	0	ENST00000374690.3:c.2440T>G	p.Phe814Val	p.F814V	ENST00000374690	NM_000044.3	814	Ttc/Gtc	6/8	NA	2	FACETS	0.635	0.551	0.724			1	INDETERMINATE	1	FALSE	NA	0.527961657232666	2		457	376	SUCCESS
APC	324	MSKCC	GRCh37	5	112174835	112174835	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0008652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	67	383	0	ENST00000257430.4:c.3544A>T	p.Lys1182Ter	p.K1182*	ENST00000257430	NM_000038.5	1182	Aaa/Taa	16/16	0.175550441190231	1	FACETS	0.497	0.434	0.564	0.497	0.434	0.564	INDETERMINATE	1	FALSE	0	0.527961657232666	1		383	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519991	NA	P-0008652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	111	215	0	ENST00000269305.4:c.536A>C	p.His179Pro	p.H179P	ENST00000269305	NM_001126112.2	179	cAt/cCt	5/11	0.5240220271374	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	0	0.527961657232666	1		215	289	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247985	59247986	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0008652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	64	365	0	ENST00000371222.2:c.756_757dup	p.Ile253ArgfsTer9	p.I253Rfs*9	ENST00000371222	NM_002228.3	253	atc/aGAtc	1/1	0.336197639962726	1	FACETS	0.459	0.399	0.523	0.459	0.399	0.523	SUBCLONAL	1	FALSE	0	0.527961657232666	1		365	389	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426645	47426645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	31	322	0	ENST00000377045.4:c.890G>A	p.Arg297Gln	p.R297Q	ENST00000377045	NM_001654.4	297	cGg/cAg	10/16	1	1	FACETS	0.929	0.75	1	0.929	0.75	1	CLONAL	1	TRUE	0	0.13	1		322	480	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242483	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACA	AATTAAGAGAAGCAACA	TTGCT	novel	NA	P-0008665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	43	465	0	ENST00000275493.2:c.2237_2253delinsTTGCT	p.Glu746_Thr751delinsValAla	p.E746_T751delinsVA	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACA/gTTGCT	19/28	1	2	FACETS	0.827	0.69	0.98	0.827	0.69	0.98	CLONAL	1	TRUE	1	0.13	2		465	800	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465373	120465373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008669-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	94	475	0	ENST00000256646.2:c.4888C>T	p.Arg1630Cys	p.R1630C	ENST00000256646	NM_024408.3	1630	Cgc/Tgc	27/34	1	2	FACETS	0.66	0.586	0.739	0.66	0.586	0.739	SUBCLONAL	1	FALSE	1	0.285117667820153	2		475	999	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395894	395894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1351148355	NA	P-0008669-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1310	102	716	0	ENST00000380956.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000380956	NM_001195286.1	151	Ccc/Tcc	4/9	1	2	FACETS	0.507	0.451	0.566	0.507	0.451	0.566	SUBCLONAL	1	FALSE	1	0.285117667820153	2		716	1412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0008675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	744	419	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	0.996	0.963	1	0.996	0.963	1	CLONAL	1	TRUE	1	0.838585293141997	2		419	1781	SUCCESS
APC	324	MSKCC	GRCh37	5	112173831	112173831	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	345	384	0	ENST00000257430.4:c.2544del	p.Asp849IlefsTer12	p.D849Ifs*12	ENST00000257430	NM_000038.5	847	gAa/ga	16/16	0.838585293141997	1	FACETS	0.946	0.911	0.98	0.946	0.911	0.98	CLONAL	1	TRUE	0	0.838585293141997	1		384	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579410	7579410	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567556123	NA	P-0008675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	466	364	0	ENST00000269305.4:c.277del	p.Leu93CysfsTer30	p.L93Cfs*30	ENST00000269305	NM_001126112.2	93	Ctg/tg	4/11	1	2	FACETS	0.96	0.919	1	0.96	0.919	1	CLONAL	1	TRUE	1	0.838585293141997	2		364	1158	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743931	46743931	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	371	344	0	ENST00000371975.4:c.2221G>T	p.Glu741Ter	p.E741*	ENST00000371975	NM_003579.3	741	Gag/Tag	18/18	0.838585293141997	1	FACETS	0.99	0.957	1	0.99	0.957	1	CLONAL	1	TRUE	0	0.838585293141997	1		344	519	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212522516	212522516	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	313	406	0	ENST00000342788.4:c.1909C>A	p.Pro637Thr	p.P637T	ENST00000342788	NM_005235.2	637	Cca/Aca	16/28	1	2	FACETS	0.866	0.82	0.913	0.866	0.82	0.913	CLONAL	1	TRUE	1	0.838585293141997	2		406	862	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259568	89259568	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	236	257	0	ENST00000336596.2:c.712G>T	p.Asp238Tyr	p.D238Y	ENST00000336596	NM_005233.5	238	Gat/Tat	3/17	1	2	FACETS	0.867	0.814	0.921	0.867	0.814	0.921	CLONAL	1	TRUE	1	0.838585293141997	2		257	649	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143352393	143352393	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	406	494	0	ENST00000262992.4:c.20G>T	p.Gly7Val	p.G7V	ENST00000262992	NM_001101669.1	7	gGg/gTg	2/24	1	2	FACETS	0.874	0.833	0.915	0.874	0.833	0.915	CLONAL	1	TRUE	1	0.838585293141997	2		494	1108	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627795	187627795	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs367960445	NA	P-0008675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	524	591	0	ENST00000441802.2:c.3187G>C	p.Ala1063Pro	p.A1063P	ENST00000441802	NM_005245.3	1063	Gcc/Ccc	2/27	1	2	FACETS	0.924	0.887	0.962	0.924	0.887	0.962	CLONAL	1	TRUE	1	0.838585293141997	2		591	1352	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289211	33289211	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	338	302	0	ENST00000374542.5:c.341C>G	p.Ser114Cys	p.S114C	ENST00000374542	NM_001141970.1	114	tCt/tGt	3/8	1	2	FACETS	0.942	0.895	0.989	0.942	0.895	0.989	CLONAL	1	TRUE	1	0.838585293141997	2		302	856	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340120	116340120	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	305	334	0	ENST00000397752.3:c.982C>T	p.Gln328Ter	p.Q328*	ENST00000397752	NM_000245.2	328	Cag/Tag	2/21	1	2	FACETS	0.982	0.931	1	0.982	0.931	1	CLONAL	1	TRUE	1	0.838585293141997	2		334	741	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151919103	151919103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	252	465	0	ENST00000262189.6:c.3482C>T	p.Thr1161Ile	p.T1161I	ENST00000262189	NM_170606.2	1161	aCa/aTa	22/59	1	2	FACETS	0.813	0.764	0.863	0.813	0.764	0.863	CLONAL	1	TRUE	1	0.838585293141997	2		465	739	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840625	36840625	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	382	377	0	ENST00000358127.4:c.1108T>A	p.Tyr370Asn	p.Y370N	ENST00000358127	NM_001280556.1	370	Tac/Aac	10/10	0.838585293141997	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.838585293141997	1		377	504	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98247991	98247991	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138034434	NA	P-0008675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	83	367	2	ENST00000331920.6:c.560G>A	p.Arg187His	p.R187H	ENST00000331920	NM_000264.3	187	cGt/cAt	3/24	1	2	FACETS	0.193	0.169	0.218	0.193	0.169	0.218	SUBCLONAL	1	TRUE	1	0.838585293141997	2		369	1027	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903688	114903688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	1651	884	0	ENST00000543371.1:c.692C>T	p.Pro231Leu	p.P231L	ENST00000543371	NM_001198531.1	231	cCa/cTa	7/14	0.838585293141997	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	1	0.838585293141997	3		884	2720	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226335	133226335	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	706	665	0	ENST00000320574.5:c.3723G>T	p.Glu1241Asp	p.E1241D	ENST00000320574	NM_006231.2	1241	gaG/gaT	30/49	1	2	FACETS	0.957	0.924	0.99	0.957	0.924	0.99	CLONAL	1	TRUE	1	0.838585293141997	2		665	1760	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570044	95570044	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	472	604	0	ENST00000393063.1:c.3689A>T	p.Gln1230Leu	p.Q1230L	ENST00000393063	NM_030621.3	1230	cAg/cTg	22/28	1	2	FACETS	0.912	0.872	0.951	0.912	0.872	0.951	CLONAL	1	TRUE	1	0.838585293141997	2		604	1235	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95578509	95578509	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	212	344	2	ENST00000393063.1:c.2116G>T	p.Gly706Cys	p.G706C	ENST00000393063	NM_030621.3	706	Ggc/Tgc	14/28	1	2	FACETS	0.949	0.889	1	0.949	0.889	1	CLONAL	1	TRUE	1	0.838585293141997	2		346	533	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678515	88678515	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	374	446	0	ENST00000360948.2:c.1021C>A	p.Pro341Thr	p.P341T	ENST00000360948	NM_001012338.2	341	Cct/Act	9/19	0.213778580290487	3	FACETS	1	0.993	1	0.421	0.4	0.442	INDETERMINATE	1	TRUE	0	0.838585293141997	3		446	1003	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992532	72992532	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1543	1050	1174	0	ENST00000268489.5:c.1513G>T	p.Asp505Tyr	p.D505Y	ENST00000268489	NM_006885.3	505	Gac/Tac	2/10	1	2	FACETS	0.966	0.938	0.993	0.966	0.938	0.993	CLONAL	1	TRUE	1	0.838585293141997	2		1174	2593	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602667	10602667	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	524	447	1	ENST00000171111.5:c.911T>A	p.Ile304Asn	p.I304N	ENST00000171111	NM_203500.1	304	aTc/aAc	3/6	0.838585293141997	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.838585293141997	1		448	715	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65312381	65312387	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGACC	GGAGACC	-	novel	NA	P-0008675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	58	362	0	ENST00000342505.4:c.1932_1938del	p.Gln644HisfsTer57	p.Q644Hfs*57	ENST00000342505	NM_002227.2	644	caGGTCTCC/ca	14/25	0.838585293141997	1	FACETS	0.135	0.115	0.156	0.135	0.115	0.156	SUBCLONAL	1	TRUE	0	0.838585293141997	1		362	597	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	137	162	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.918	0.84	0.999	0.918	0.84	0.999	CLONAL	1	TRUE	1	0.59	2		162	506	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	245	278	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.913	0.854	0.973	0.913	0.854	0.973	CLONAL	1	TRUE	1	0.59	2		279	910	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	157	565	1	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS	0.975	0.898	1	0.975	0.898	1	CLONAL	1	TRUE	1	0.59	2		566	546	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623896	28623896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	159	694	1	ENST00000241453.7:c.758C>T	p.Pro253Leu	p.P253L	ENST00000241453	NM_004119.2	253	cCt/cTt	7/24	1	2	FACETS	0.975	0.899	1	0.975	0.899	1	CLONAL	1	TRUE	1	0.59	2		695	553	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023732	31023732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs549552934	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	49	930	0	ENST00000375687.4:c.3217C>T	p.Arg1073Cys	p.R1073C	ENST00000375687	NM_015338.5	1073	Cgc/Tgc	13/13	1	2	FACETS	0.176	0.148	0.206	0.176	0.148	0.206	SUBCLONAL	1	TRUE	1	0.59	2		930	946	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268379	142268380	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1559984993	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	141	724	0	ENST00000350721.4:c.3112dup	p.Ser1038PhefsTer11	p.S1038Ffs*11	ENST00000350721	NM_001184.3	1038	tct/tTct	15/47	1	2	FACETS	0.827	0.757	0.9	0.827	0.757	0.9	CLONAL	1	TRUE	1	0.59	2		724	578	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210735	2210735	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1238067958	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	259	812	5	ENST00000398665.3:c.1232G>A	p.Arg411His	p.R411H	ENST00000398665	NM_032482.2	411	cGc/cAc	14/28	1	2	FACETS	0.982	0.922	1	0.982	0.922	1	CLONAL	1	TRUE	1	0.59	2		817	894	SUCCESS
AR	367	MSKCC	GRCh37	X	66931504	66931504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1340026226	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	221	442	2	ENST00000374690.3:c.2146G>A	p.Val716Met	p.V716M	ENST00000374690	NM_000044.3	716	Gtg/Atg	4/8	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.59	1		444	368	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330610	65330611	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	191	762	0	ENST00000342505.4:c.1035dup	p.Leu346ThrfsTer4	p.L346Tfs*4	ENST00000342505	NM_002227.2	345	-/A	8/25	1	2	FACETS	0.851	0.789	0.915	0.851	0.789	0.915	CLONAL	1	TRUE	1	0.59	2		762	761	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133979	41133979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149675484	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	202	752	2	ENST00000379561.5:c.1649C>T	p.Ser550Leu	p.S550L	ENST00000379561	NM_002015.3	550	tCg/tTg	2/3	1	2	FACETS	0.912	0.848	0.978	0.912	0.848	0.978	CLONAL	1	TRUE	1	0.59	2		754	751	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261065	16261065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs181891870	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	210	662	1	ENST00000375759.3:c.8330C>T	p.Ala2777Val	p.A2777V	ENST00000375759	NM_015001.2	2777	gCg/gTg	11/15	1	2	FACETS	0.991	0.924	1	0.991	0.924	1	CLONAL	1	TRUE	1	0.59	2		663	718	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65316513	65316513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755406627	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	213	601	1	ENST00000342505.4:c.1729C>T	p.Arg577Trp	p.R577W	ENST00000342505	NM_002227.2	577	Cgg/Tgg	12/25	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.59	2		602	657	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321195	65321195	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	136	549	0	ENST00000342505.4:c.1645C>T	p.Arg549Ter	p.R549*	ENST00000342505	NM_002227.2	549	Cga/Tga	11/25	1	2	FACETS	0.876	0.801	0.955	0.876	0.801	0.955	CLONAL	1	TRUE	1	0.59	2		549	526	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495657	72495657	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	144	502	0	ENST00000477973.2:c.415A>G	p.Thr139Ala	p.T139A	ENST00000477973	NM_012234.5	139	Acc/Gcc	1/4	1	2	FACETS	0.937	0.86	1	0.937	0.86	1	CLONAL	1	TRUE	1	0.59	2		502	521	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951813	2951813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377327574	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	269	629	0	ENST00000396946.4:c.3137C>T	p.Ala1046Val	p.A1046V	ENST00000396946	NM_032415.4	1046	gCc/gTc	23/25	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.59	2		629	875	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126729	5126729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774469142	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	184	815	5	ENST00000381652.3:c.3337C>T	p.Arg1113Cys	p.R1113C	ENST00000381652	NM_004972.3	1113	Cgc/Tgc	25/25	1	2	FACETS	0.976	0.905	1	0.976	0.905	1	CLONAL	1	TRUE	1	0.59	2		820	639	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840613	36840613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756710542	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	261	912	0	ENST00000358127.4:c.1120G>A	p.Ala374Thr	p.A374T	ENST00000358127	NM_001280556.1	374	Gct/Act	10/10	1	2	FACETS	0.984	0.924	1	0.984	0.924	1	CLONAL	1	TRUE	1	0.59	2		912	899	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8252001	8252001	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	262	988	0	ENST00000335790.3:c.76G>T	p.Gly26Cys	p.G26C	ENST00000335790	NM_002315.2	26	Ggc/Tgc	2/4	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.59	2		988	863	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586101	29586101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876658127	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	165	818	4	ENST00000356175.3:c.4321C>T	p.Arg1441Trp	p.R1441W	ENST00000356175	NM_000267.3	1441	Cgg/Tgg	32/57	1	2	FACETS	0.79	0.727	0.855	0.79	0.727	0.855	SUBCLONAL	1	TRUE	1	0.59	2		822	708	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510573	38510573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	215	774	0	ENST00000254066.5:c.827G>A	p.Arg276Gln	p.R276Q	ENST00000254066	NM_000964.3	276	cGg/cAg	7/9	1	2	FACETS	0.969	0.904	1	0.969	0.904	1	CLONAL	1	TRUE	1	0.59	2		774	752	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755606	39755606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	177	788	3	ENST00000288319.7:c.1159G>A	p.Ala387Thr	p.A387T	ENST00000288319	NM_182918.3	387	Gcc/Acc	10/10	1	2	FACETS	0.836	0.772	0.901	0.836	0.772	0.901	CLONAL	1	TRUE	1	0.59	2		791	718	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526212	63526215	+	frameshift_variant	Frame_Shift_Del	DEL	AAGT	AAGT	-	novel	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	175	789	0	ENST00000307078.5:c.2411_2414del	p.Tyr804SerfsTer56	p.Y804Sfs*56	ENST00000307078	NM_004655.3	804	tACTTc/tc	11/11	1	2	FACETS	0.856	0.791	0.923	0.856	0.791	0.923	CLONAL	1	TRUE	1	0.59	2		789	693	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552710	226552710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	133	473	0	ENST00000366794.5:c.2651C>T	p.Ala884Val	p.A884V	ENST00000366794	NM_001618.3	884	gCg/gTg	19/23	1	2	FACETS	0.959	0.877	1	0.959	0.877	1	CLONAL	1	TRUE	1	0.59	2		473	470	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	371	1301	4	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.98	0.93	1	0.98	0.93	1	CLONAL	1	TRUE	1	0.59	2		1305	1283	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	494	946	6	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.911	0.878	0.944	1	0.997	1	CLONAL	2	TRUE	1	0.59	2		952	919	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	324	1174	4	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.915	0.864	0.967	0.915	0.864	0.967	CLONAL	1	TRUE	1	0.59	2		1178	1200	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130337	11130337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs281875226	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	234	870	2	ENST00000358026.2:c.2576C>T	p.Thr859Met	p.T859M	ENST00000358026	NM_001128849.1	859	aCg/aTg	18/36	1	2	FACETS	0.944	0.883	1	0.944	0.883	1	CLONAL	1	TRUE	1	0.59	2		872	840	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942533	17942533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	263	1006	1	ENST00000458235.1:c.2755G>A	p.Ala919Thr	p.A919T	ENST00000458235	NM_000215.3	919	Gcg/Acg	20/24	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.59	2		1007	876	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874092	151874093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	222	984	1	ENST00000262189.6:c.8445dup	p.Ser2816IlefsTer6	p.S2816Ifs*6	ENST00000262189	NM_170606.2	2815	-/A	38/59	1	2	FACETS	0.868	0.809	0.929	0.868	0.809	0.929	CLONAL	1	TRUE	1	0.59	2		985	867	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777114	9777114	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs754116182	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	314	1061	0	ENST00000377346.4:c.883del	p.Gln295ArgfsTer39	p.Q295Rfs*39	ENST00000377346	NM_005026.3	293	gCc/gc	7/24	1	2	FACETS	0.983	0.928	1	0.983	0.928	1	CLONAL	1	TRUE	1	0.59	2		1061	1083	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28601484	28601484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	281	955	1	ENST00000253063.3:c.1169G>A	p.Arg390His	p.R390H	ENST00000253063	NM_031459.4	390	cGc/cAc	8/10	1	2	FACETS	0.986	0.928	1	0.986	0.928	1	CLONAL	1	TRUE	1	0.59	2		956	966	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111145	193111146	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	rs760591174	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	54	567	0	ENST00000367435.3:c.687_688dup	p.Val230GlufsTer28	p.V230Efs*28	ENST00000367435	NM_024529.4	226	-/AG	7/17	1	2	FACETS	0.352	0.301	0.408	0.352	0.301	0.408	SUBCLONAL	1	TRUE	1	0.59	2		567	520	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945048	31945049	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs754427138	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	258	983	0	ENST00000340398.3:c.52dup	p.Arg18ProfsTer64	p.R18Pfs*64	ENST00000340398	NM_001013699.2	18	cgc/cCgc	1/1	1	2	FACETS	0.939	0.881	0.999	0.939	0.881	0.999	CLONAL	1	TRUE	1	0.59	2		983	931	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420289	49420289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768551828	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	249	1005	0	ENST00000301067.7:c.15460C>T	p.Arg5154Trp	p.R5154W	ENST00000301067	NM_003482.3	5154	Cgg/Tgg	48/54	1	2	FACETS	0.906	0.848	0.965	0.906	0.848	0.965	CLONAL	1	TRUE	1	0.59	2		1005	932	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443799	49443799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs112236653	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	331	1226	2	ENST00000301067.7:c.3572C>T	p.Pro1191Leu	p.P1191L	ENST00000301067	NM_003482.3	1191	cCg/cTg	11/54	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.59	2		1228	1102	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830895	72830895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770650936	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	231	787	3	ENST00000268489.5:c.5686G>A	p.Ala1896Thr	p.A1896T	ENST00000268489	NM_006885.3	1896	Gcc/Acc	9/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.59	2		790	722	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526577	66526577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568703465	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	28	472	0	ENST00000358598.2:c.1133C>T	p.Ser378Leu	p.S378L	ENST00000358598	NM_212471.2	378	tCa/tTa	11/11	1	2	FACETS	0.183	0.146	0.226	0.183	0.146	0.226	SUBCLONAL	1	TRUE	1	0.59	2		472	518	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166285	7166285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555743340	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	277	1066	2	ENST00000302850.5:c.1741C>T	p.Arg581Trp	p.R581W	ENST00000302850	NM_000208.2	581	Cgg/Tgg	8/22	1	2	FACETS	0.921	0.865	0.977	0.921	0.865	0.977	CLONAL	1	TRUE	1	0.59	2		1068	1020	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40743892	40743892	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	250	845	0	ENST00000392038.2:c.815T>C	p.Val272Ala	p.V272A	ENST00000392038	NM_001626.4	272	gTa/gCa	9/14	1	2	FACETS	0.98	0.918	1	0.98	0.918	1	CLONAL	1	TRUE	1	0.59	2		845	865	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753478	42753479	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	288	1169	0	ENST00000222329.4:c.785dup	p.Gln263SerfsTer46	p.Q263Sfs*46	ENST00000222329	NM_006494.2	262	cct/ccCt	4/4	1	2	FACETS	0.891	0.838	0.945	0.891	0.838	0.945	CLONAL	1	TRUE	1	0.59	2		1169	1096	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905073	50905073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747614571	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	236	966	4	ENST00000440232.2:c.355C>T	p.Arg119Cys	p.R119C	ENST00000440232	NM_002691.3	119	Cgc/Tgc	4/27	1	2	FACETS	0.962	0.9	1	0.962	0.9	1	CLONAL	1	TRUE	1	0.59	2		970	832	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444313	50444313	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	26	488	0	ENST00000331340.3:c.245del	p.Leu82TyrfsTer11	p.L82Yfs*11	ENST00000331340	NM_006060.4	81	gaT/ga	4/8	1	2	FACETS	0.171	0.135	0.212	0.171	0.135	0.212	SUBCLONAL	1	TRUE	1	0.59	2		488	516	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450303	50450303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	232	927	3	ENST00000331340.3:c.487C>T	p.His163Tyr	p.H163Y	ENST00000331340	NM_006060.4	163	Cac/Tac	5/8	1	2	FACETS	0.941	0.879	1	0.941	0.879	1	CLONAL	1	TRUE	1	0.59	2		930	836	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846107	151846107	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	167	626	0	ENST00000262189.6:c.12905del	p.Pro4302LeufsTer24	p.P4302Lfs*24	ENST00000262189	NM_170606.2	4302	cCt/ct	52/59	1	2	FACETS	0.829	0.764	0.896	0.829	0.764	0.896	CLONAL	1	TRUE	1	0.59	2		626	683	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880210	151880210	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	211	803	3	ENST00000262189.6:c.5114G>A	p.Arg1705His	p.R1705H	ENST00000262189	NM_170606.2	1705	cGc/cAc	35/59	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.59	2		806	715	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551412	141551412	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	278	921	0	ENST00000220592.5:c.1885G>A	p.Val629Met	p.V629M	ENST00000220592	NM_012154.3	629	Gtg/Atg	15/19	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.59	2		921	872	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0008685-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1346	177	489	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.978	0.898	1	0.978	0.898	1	CLONAL	1	TRUE	1	0.23773215984512	2		489	1523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1064795203	NA	P-0008685-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	91	243	0	ENST00000269305.4:c.532C>G	p.His178Asp	p.H178D	ENST00000269305	NM_001126112.2	178	Cac/Gac	5/11	0.237957039750672	1	FACETS	0.996	0.885	1	0.996	0.885	1	CLONAL	1	TRUE	0	0.23773215984512	1		243	677	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913273	NA	P-0008685-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	51	170	0	ENST00000263967.3:c.1624G>C	p.Glu542Gln	p.E542Q	ENST00000263967	NM_006218.2	542	Gaa/Caa	10/21	1	2	FACETS	0.766	0.656	0.885	1	0.967	1	SUBCLONAL	2	TRUE	1	0.23773215984512	2		170	280	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807171	1807171	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008695-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	77	456	0	ENST00000260795.2:c.1502A>T	p.Lys501Met	p.K501M	ENST00000260795		501	aAg/aTg	10/17	0.309524171725591	5	FACETS	1	0.922	1			1	CLONAL	1	TRUE	NA	0.309524171725591	5		456	682	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16047012	16047012	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0008695-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	79	349	0	ENST00000268712.3:c.1083-2A>T		p.X361_splice	ENST00000268712	NM_006311.3	361			0.312592300717696	4	FACETS	1	0.906	1	0.259	0.227	0.292	CLONAL	1	TRUE	0	0.309524171725591	4		349	646	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191036	2191036	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008695-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	38	353	0	ENST00000398665.3:c.290A>G	p.Lys97Arg	p.K97R	ENST00000398665	NM_032482.2	97	aAg/aGg	5/28	1	2	FACETS	0.597	0.494	0.713	0.597	0.494	0.713	SUBCLONAL	1	TRUE	1	0.309524171725591	2		353	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0008726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	410	520	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.721360740677002	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.721360740677002	1		520	715	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953760	48953760	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913302	NA	P-0008726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	323	277	1	ENST00000267163.4:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000267163	NM_000321.2	455	Cga/Tga	14/27	0.721360740677002	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.721360740677002	1		278	567	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541629	120541629	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1416625402	NA	P-0008726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	535	726	4	ENST00000229340.5:c.227+1G>A		p.X76_splice	ENST00000229340	NM_006861.6	76			1	2	FACETS	0.963	0.923	1	0.963	0.923	1	CLONAL	1	TRUE	1	0.721360740677002	2		730	1541	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122880	2122880	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45517222	NA	P-0008726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	360	439	2	ENST00000219476.3:c.2251C>T	p.Arg751Ter	p.R751*	ENST00000219476	NM_000548.3	751	Cga/Tga	21/42	0.721360740677002	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.721360740677002	1		441	618	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591825	48591825	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	321	471	0	ENST00000342988.3:c.988G>C	p.Glu330Gln	p.E330Q	ENST00000342988	NM_005359.5	330	Gaa/Caa	9/12	0.721360740677002	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.721360740677002	1		471	520	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096048	11096048	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	293	353	0	ENST00000358026.2:c.326del	p.Pro109ArgfsTer194	p.P109Rfs*194	ENST00000358026	NM_001128849.1	108	Ccc/cc	3/36	0.721360740677002	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.721360740677002	1		353	514	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0008736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	164	405	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.199932336128163	4	FACETS	1	0.932	1	1	0.932	1	INDETERMINATE	2	TRUE	2	0.345438898603646	4		405	631	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0008736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	501	559	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.345438898603646	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.345438898603646	2		559	1423	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	136	533	1	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	0.945	0.86	1	0.945	0.86	1	CLONAL	1	TRUE	1	0.372316193893154	2		534	773	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	153	603	2	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.372316193893154	2		605	819	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	59	162	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.372316193893154	2		162	285	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300374	11300374	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	67	281	0	ENST00000361445.4:c.1772G>A	p.Ser591Asn	p.S591N	ENST00000361445	NM_004958.3	591	aGc/aAc	11/58	1	2	FACETS	0.723	0.629	0.824	0.723	0.629	0.824	SUBCLONAL	1	TRUE	1	0.372316193893154	2		281	498	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803818	43803818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147938568	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	225	707	0	ENST00000372470.3:c.128G>A	p.Arg43Gln	p.R43Q	ENST00000372470	NM_005373.2	43	cGa/cAa	2/12	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.372316193893154	2		707	1080	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466341	120466341	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	178	586	0	ENST00000256646.2:c.4778A>C	p.Tyr1593Ser	p.Y1593S	ENST00000256646	NM_024408.3	1593	tAt/tCt	26/34	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.372316193893154	2		586	764	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497816	120497816	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs782325711	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	98	342	0	ENST00000256646.2:c.2066A>G	p.Asn689Ser	p.N689S	ENST00000256646	NM_024408.3	689	aAt/aGt	13/34	1	2	FACETS	0.919	0.822	1	0.919	0.822	1	CLONAL	1	TRUE	1	0.372316193893154	2		342	573	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849863	156849863	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747855434	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	112	622	1	ENST00000524377.1:c.2119G>A	p.Glu707Lys	p.E707K	ENST00000524377	NM_002529.3	707	Gag/Aag	16/17	1	2	FACETS	0.582	0.522	0.645	0.582	0.522	0.645	SUBCLONAL	1	TRUE	1	0.372316193893154	2		623	1034	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111021	193111021	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	43	423	0	ENST00000367435.3:c.554T>C	p.Ile185Thr	p.I185T	ENST00000367435	NM_024529.4	185	aTc/aCc	7/17	1	2	FACETS	0.389	0.325	0.46	0.389	0.325	0.46	SUBCLONAL	1	TRUE	1	0.372316193893154	2		423	594	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143010	30143010	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	231	777	1	ENST00000389048.3:c.516G>T	p.Glu172Asp	p.E172D	ENST00000389048	NM_004304.4	172	gaG/gaT	1/29	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.372316193893154	2		778	1171	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	350	547	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.372316193893154	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.372316193893154	2		547	875	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433447	138433447	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1216567138	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	123	641	0	ENST00000289153.2:c.1165A>G	p.Ile389Val	p.I389V	ENST00000289153	NM_006219.2	389	Att/Gtt	7/22	1	2	FACETS	0.898	0.813	0.987	0.898	0.813	0.987	CLONAL	1	TRUE	1	0.372316193893154	2		641	736	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916726	178916726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772110575	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	208	1092	2	ENST00000263967.3:c.113G>A	p.Arg38His	p.R38H	ENST00000263967	NM_006218.2	38	cGt/cAt	2/21	1	2	FACETS	0.89	0.824	0.958	0.89	0.824	0.958	CLONAL	1	TRUE	1	0.372316193893154	2		1094	1256	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807506	1807506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768385286	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	248	743	0	ENST00000260795.2:c.1675G>A	p.Ala559Thr	p.A559T	ENST00000260795		559	Gcc/Acc	12/17	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.372316193893154	2		743	1036	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157674	106157674	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	48	602	0	ENST00000380013.4:c.2575A>G	p.Thr859Ala	p.T859A	ENST00000380013	NM_001127208.2	859	Acc/Gcc	3/11	1	2	FACETS	0.275	0.231	0.324	0.275	0.231	0.324	SUBCLONAL	1	TRUE	1	0.372316193893154	2		602	937	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	145	1073	2	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	0.942	0.86	1	0.942	0.86	1	CLONAL	1	TRUE	1	0.372316193893154	2		1075	827	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499641	149499641	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	129	666	0	ENST00000261799.4:c.2632A>G	p.Ser878Gly	p.S878G	ENST00000261799	NM_002609.3	878	Agc/Ggc	19/23	1	2	FACETS	0.634	0.574	0.698	0.634	0.574	0.698	SUBCLONAL	1	TRUE	1	0.372316193893154	2		666	1093	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910708	29910708	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	243	739	0	ENST00000376809.5:c.248A>G	p.Tyr83Cys	p.Y83C	ENST00000376809	NM_002116.7	83	tAt/tGt	2/8	0.339220622629437	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.372316193893154	1		739	905	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37141761	37141761	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	197	614	1	ENST00000373509.5:c.836C>A	p.Pro279Gln	p.P279Q	ENST00000373509	NM_002648.3	279	cCa/cAa	6/6	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.372316193893154	2		615	891	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016221	150016221	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	82	651	2	ENST00000253339.5:c.485G>A	p.Ser162Asn	p.S162N	ENST00000253339		162	aGc/aAc	2/7	1	2	FACETS	0.52	0.458	0.587	0.52	0.458	0.587	SUBCLONAL	1	TRUE	1	0.372316193893154	2		653	847	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976804	2976804	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	256	921	0	ENST00000396946.4:c.1208A>G	p.Tyr403Cys	p.Y403C	ENST00000396946	NM_032415.4	403	tAc/tGc	9/25	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.372316193893154	2		921	1349	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238356	98238356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	147	516	2	ENST00000331920.6:c.1688C>T	p.Ala563Val	p.A563V	ENST00000331920	NM_000264.3	563	gCg/gTg	12/24	1	2	FACETS	0.95	0.868	1	0.95	0.868	1	CLONAL	1	TRUE	1	0.372316193893154	2		518	831	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925567	114925567	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1391	218	1115	1	ENST00000543371.1:c.1645G>T	p.Ala549Ser	p.A549S	ENST00000543371	NM_001198531.1	549	Gcc/Tcc	14/14	1	2	FACETS	0.728	0.674	0.783	0.728	0.674	0.783	SUBCLONAL	1	TRUE	1	0.372316193893154	2		1116	1609	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246384	46246384	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	89	647	0	ENST00000334344.6:c.4478T>C	p.Val1493Ala	p.V1493A	ENST00000334344	NM_152641.2	1493	gTa/gCa	15/21	1	2	FACETS	0.616	0.546	0.691	0.616	0.546	0.691	SUBCLONAL	1	TRUE	1	0.372316193893154	2		647	776	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811723	102811723	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	204	891	0	ENST00000307046.8:c.461A>G	p.Lys154Arg	p.K154R	ENST00000307046	NM_001111285.1	154	aAg/aGg	4/4	1	2	FACETS	0.934	0.865	1	0.934	0.865	1	CLONAL	1	TRUE	1	0.372316193893154	2		891	1173	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112623	115112623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	33	352	0	ENST00000257566.3:c.1117G>A	p.Gly373Ser	p.G373S	ENST00000257566	NM_016569.3	373	Ggt/Agt	7/8	1	2	FACETS	0.306	0.248	0.371	0.306	0.248	0.371	SUBCLONAL	1	TRUE	1	0.372316193893154	2		352	580	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991727	72991727	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755455411	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	43	414	1	ENST00000268489.5:c.2318C>T	p.Ala773Val	p.A773V	ENST00000268489	NM_006885.3	773	gCg/gTg	2/10	1	2	FACETS	0.316	0.263	0.374	0.316	0.263	0.374	SUBCLONAL	1	TRUE	1	0.372316193893154	2		415	732	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348800	89348800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776994699	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1756	257	1489	3	ENST00000301030.4:c.4150G>A	p.Gly1384Ser	p.G1384S	ENST00000301030	NM_001256183.1	1384	Ggt/Agt	9/13	1	2	FACETS	0.686	0.639	0.734	0.686	0.639	0.734	SUBCLONAL	1	TRUE	1	0.372316193893154	2		1492	2013	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864647	37864647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756720659	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	237	719	1	ENST00000269571.5:c.299G>A	p.Arg100Gln	p.R100Q	ENST00000269571		100	cGg/cAg	3/27	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.372316193893154	2		720	1174	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40500444	40500444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	293	712	0	ENST00000264657.5:c.91C>T	p.Arg31Trp	p.R31W	ENST00000264657	NM_139276.2	31	Cgg/Tgg	2/24	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.372316193893154	2		712	1261	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56811512	56811512	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502590	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	81	620	0	ENST00000337432.4:c.1060G>A	p.Ala354Thr	p.A354T	ENST00000337432	NM_058216.2	354	Gca/Aca	9/9	1	2	FACETS	0.506	0.445	0.572	0.506	0.445	0.572	SUBCLONAL	1	TRUE	1	0.372316193893154	2		620	860	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78935253	78935253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143802144	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	238	647	0	ENST00000306801.3:c.3665G>A	p.Arg1222His	p.R1222H	ENST00000306801	NM_020761.2	1222	cGt/cAt	31/34	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.372316193893154	2		647	1031	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101040	4101040	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs999810842	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	116	329	0	ENST00000262948.5:c.682G>A	p.Val228Met	p.V228M	ENST00000262948	NM_030662.3	228	Gtg/Atg	6/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.372316193893154	2		329	520	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170774	11170774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568565786	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	109	577	0	ENST00000358026.2:c.4918C>T	p.Arg1640Trp	p.R1640W	ENST00000358026	NM_001128849.1	1640	Cgg/Tgg	35/36	1	2	FACETS	0.668	0.599	0.741	0.668	0.599	0.741	SUBCLONAL	1	TRUE	1	0.372316193893154	2		577	877	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792725	33792725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs898553101	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	199	126	1	ENST00000498907.2:c.596C>T	p.Ala199Val	p.A199V	ENST00000498907	NM_004364.3	199	gCg/gTg	1/1	0.372316193893154	4	FACETS	0.95	0.894	1	1	0.99	1	CLONAL	4	TRUE	1	0.372316193893154	4		127	386	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798142	42798142	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1467	117	696	0	ENST00000575354.2:c.4096C>T	p.Arg1366Trp	p.R1366W	ENST00000575354	NM_015125.3	1366	Cgg/Tgg	17/20	0.372316193893154	4	FACETS	0.545	0.489	0.604	0.182	0.163	0.202	SUBCLONAL	1	TRUE	1	0.372316193893154	4		696	1584	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226124	53226124	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs951268570	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	167	596	0	ENST00000375401.3:c.2725C>T	p.Arg909Trp	p.R909W	ENST00000375401	NM_004187.3	909	Cgg/Tgg	19/26	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.372316193893154	2		596	810	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944402	76944402	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	62	726	0	ENST00000373344.5:c.503T>G	p.Ile168Ser	p.I168S	ENST00000373344	NM_000489.3	168	aTt/aGt	7/35	1	2	FACETS	0.368	0.316	0.424	0.368	0.316	0.424	SUBCLONAL	1	TRUE	1	0.372316193893154	2		726	906	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845573	72845574	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1234	276	1068	2	ENST00000268489.5:c.3766dup	p.Leu1256ProfsTer25	p.L1256Pfs*25	ENST00000268489	NM_006885.3	1256	ctg/cCtg	7/10	1	2	FACETS	0.982	0.92	1	0.982	0.92	1	CLONAL	1	TRUE	1	0.372316193893154	2		1070	1510	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912302	29912303	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	46	515	0	ENST00000376809.5:c.922dup	p.Ile308AsnfsTer32	p.I308Nfs*32	ENST00000376809	NM_002116.7	307	-/A	5/8	0.339220622629437	1	FACETS	0.274	0.23	0.323	0.274	0.23	0.323	SUBCLONAL	1	TRUE	0	0.372316193893154	1		515	733	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	585	825	11	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	0.998	1	CLONAL	2	TRUE	1	0.372316193893154	2		836	1413	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239971	98239971	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	46	214	0	ENST00000331920.6:c.1361del	p.Cys454PhefsTer2	p.C454Ffs*2	ENST00000331920	NM_000264.3	454	tGt/tt	10/24	1	2	FACETS	0.563	0.474	0.66	0.563	0.474	0.66	SUBCLONAL	1	TRUE	1	0.372316193893154	2		214	439	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119781	70119781	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1274036689	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	185	525	0	ENST00000245479.2:c.788del	p.Gly263AlafsTer16	p.G263Afs*16	ENST00000245479	NM_000346.3	261	gaG/ga	3/3	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.372316193893154	2		525	983	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	151	434	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.372316193893154	2		435	689	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	169	566	0	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.372316193893154	2		566	807	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276860	15276861	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs753725730	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	129	421	2	ENST00000263388.2:c.5404dup	p.Ala1802GlyfsTer8	p.A1802Gfs*8	ENST00000263388	NM_000435.2	1802	gct/gGct	30/33	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.372316193893154	2		423	681	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097625	11097625	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	161	915	2	ENST00000358026.2:c.810del	p.Met272CysfsTer31	p.M272Cfs*31	ENST00000358026	NM_001128849.1	269	Ccc/cc	5/36	1	2	FACETS	0.715	0.654	0.779	0.715	0.654	0.779	SUBCLONAL	1	TRUE	1	0.372316193893154	2		917	1210	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643943	52643943	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	86	395	0	ENST00000394830.3:c.1953del	p.Lys651AsnfsTer5	p.K651Nfs*5	ENST00000394830	NM_018313.4	651	aaA/aa	17/30	1	2	FACETS	0.826	0.733	0.926	0.826	0.733	0.926	CLONAL	1	TRUE	1	0.372316193893154	2		395	559	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405954	157405954	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	166	588	3	ENST00000346085.5:c.2201del	p.Gly734AlafsTer11	p.G734Afs*11	ENST00000346085	NM_020732.3	732	ccG/cc	6/20	1	2	FACETS	0.957	0.879	1	0.957	0.879	1	CLONAL	1	TRUE	1	0.372316193893154	2		591	932	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0008756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	182	432	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.518795260484182	2		432	686	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945474	151945474	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0008756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	178	332	0	ENST00000262189.6:c.2045C>G	p.Ser682Ter	p.S682*	ENST00000262189	NM_170606.2	682	tCa/tGa	14/59	1	2	FACETS	0.996	0.921	1	0.996	0.921	1	CLONAL	1	TRUE	1	0.518795260484182	2		332	689	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692896	89692896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123322	NA	P-0008756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	234	395	0	ENST00000371953.3:c.380G>A	p.Gly127Glu	p.G127E	ENST00000371953	NM_000314.4	127	gGa/gAa	5/9	0.518795260484182	2	FACETS	0.985	0.931	1	0.985	0.931	1	CLONAL	2	TRUE	0	0.518795260484182	2		395	458	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084094	47084094	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	437	448	0	ENST00000409792.3:c.7195C>T	p.Arg2399Ter	p.R2399*	ENST00000409792	NM_014159.6	2399	Cga/Tga	17/21	0.496462194526875	2	FACETS	0.834	0.798	0.87	0.834	0.798	0.87	CLONAL	2	TRUE	0	0.518795260484182	2		448	1010	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815562	139815562	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs748178503	NA	P-0008756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1294	445	809	1	ENST00000247668.2:c.1033A>T	p.Met345Leu	p.M345L	ENST00000247668	NM_021138.3	345	Atg/Ttg	9/11	1	2	FACETS	0.986	0.939	1	0.986	0.939	1	CLONAL	1	TRUE	1	0.518795260484182	2		810	1739	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142099	108142099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555085210	NA	P-0008756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	210	521	0	ENST00000278616.4:c.3043C>T	p.Gln1015Ter	p.Q1015*	ENST00000278616	NM_000051.3	1015	Caa/Taa	20/63	1	2	FACETS	0.966	0.899	1	0.966	0.899	1	CLONAL	1	TRUE	1	0.518795260484182	2		521	838	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830911	72830911	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1655	531	1055	0	ENST00000268489.5:c.5670G>C	p.Gln1890His	p.Q1890H	ENST00000268489	NM_006885.3	1890	caG/caC	9/10	1	2	FACETS	0.936	0.895	0.979	0.936	0.895	0.979	CLONAL	1	TRUE	1	0.518795260484182	2		1055	2186	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590689	95590689	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008776-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	131	677	1	ENST00000393063.1:c.1220A>T	p.Asp407Val	p.D407V	ENST00000393063	NM_030621.3	407	gAt/gTt	9/28	1	2	FACETS	0.462	0.418	0.508	0.462	0.418	0.508	SUBCLONAL	1	TRUE	1	0.578763983718023	2		678	980	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0008786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	643	240	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	0.526527778300153	3	FACETS	1	0.997	1	0.698	0.673	0.722	INDETERMINATE	1	TRUE	1	0.950612801812688	3		240	1430	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200749	128200749	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0008786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	755	246	0	ENST00000341105.2:c.1056T>A	p.Cys352Ter	p.C352*	ENST00000341105	NM_032638.4	352	tgT/tgA	5/6	1	2	FACETS	0.959	0.928	0.989	0.959	0.928	0.989	CLONAL	1	TRUE	1	0.950612801812688	2		246	1657	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916756	48916756	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0008786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	383	184	0	ENST00000267163.4:c.286A>T	p.Lys96Ter	p.K96*	ENST00000267163	NM_000321.2	96	Aag/Tag	3/27	0.950612801812688	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.950612801812688	1		184	411	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725119	47725119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	419	312	0	ENST00000449228.1:c.625C>T	p.His209Tyr	p.H209Y	ENST00000449228	NM_001127240.2	209	Cat/Tat	4/4	0.485941555276202	1	FACETS	0.311	0.296	0.327	0.311	0.296	0.327	INDETERMINATE	1	TRUE	0	0.950612801812688	1		312	1486	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338668	70338668	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	1147	175	0	ENST00000374080.3:c.66del	p.Asp23MetfsTer14	p.D23Mfs*14	ENST00000374080		22	Ccc/cc	1/45	1	1	FACETS	0.982	0.969	0.993	0.982	0.969	0.993	CLONAL	1	TRUE	0	0.950612801812688	1		175	1290	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521768	89521768	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	128	260	0	ENST00000336596.2:c.2845G>A	p.Asp949Asn	p.D949N	ENST00000336596	NM_005233.5	949	Gat/Aat	16/17	0.165517917925427	3	FACETS	1	0.983	1	0.664	0.606	0.723	INDETERMINATE	1	TRUE	1	0.569781351448854	3		260	435	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244952	123244952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	313	766	0	ENST00000358487.5:c.2152G>A	p.Glu718Lys	p.E718K	ENST00000358487	NM_000141.4	718	Gaa/Aaa	16/18	0.317884585739132	1	FACETS	0.815	0.77	0.86	0.815	0.77	0.86	INDETERMINATE	1	TRUE	0	0.569781351448854	1		766	964	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205766	108205766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	246	460	0	ENST00000278616.4:c.8081G>A	p.Gly2694Glu	p.G2694E	ENST00000278616	NM_000051.3	2694	gGa/gAa	55/63	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.569781351448854	2		460	702	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466293	120466293	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866874822	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	196	408	0	ENST00000256646.2:c.4826C>T	p.Ser1609Phe	p.S1609F	ENST00000256646	NM_024408.3	1609	tCc/tTc	26/34	0.345252968897148	3	FACETS	1	0.964	1	0.531	0.492	0.571	CLONAL	1	TRUE	1	0.569781351448854	3		408	832	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432459	49432459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	307	726	1	ENST00000301067.7:c.8680C>T	p.Pro2894Ser	p.P2894S	ENST00000301067	NM_003482.3	2894	Ccg/Tcg	34/54	0.292730892184693	3	FACETS	1	0.962	1	0.515	0.484	0.546	INDETERMINATE	1	TRUE	1	0.569781351448854	3		727	1345	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015115	37015115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	368	639	0	ENST00000358127.4:c.289G>A	p.Glu97Lys	p.E97K	ENST00000358127	NM_001280556.1	97	Gaa/Aaa	3/10	0.411413365912172	1	FACETS	0.889	0.845	0.934	0.889	0.845	0.934	CLONAL	1	TRUE	0	0.569781351448854	1		639	1039	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137244	64137244	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774562817	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	187	544	2	ENST00000334205.4:c.1676C>T	p.Pro559Leu	p.P559L	ENST00000334205	NM_003942.2	559	cCg/cTg	14/17	0.323246425975591	2	FACETS	0.614	0.566	0.664	0.307	0.283	0.332	INDETERMINATE	1	TRUE	0	0.569781351448854	2		546	1069	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643951	52643951	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	77	361	0	ENST00000394830.3:c.1945C>T	p.Pro649Ser	p.P649S	ENST00000394830	NM_018313.4	649	Cct/Tct	17/30	0.165517917925427	3	FACETS	0.637	0.56	0.72	0.319	0.28	0.36	INDETERMINATE	1	TRUE	1	0.569781351448854	3		361	545	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458357	120458357	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756715170	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	243	300	0	ENST00000256646.2:c.6988C>T	p.Pro2330Ser	p.P2330S	ENST00000256646	NM_024408.3	2330	Cca/Tca	34/34	0.345252968897148	3	FACETS	0.951	0.897	1	0.951	0.897	1	CLONAL	2	TRUE	1	0.569781351448854	3		300	576	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443583	29443583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1462510005	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	102	506	1	ENST00000389048.3:c.3634C>T	p.Arg1212Cys	p.R1212C	ENST00000389048	NM_004304.4	1212	Cgc/Tgc	23/29	0.280094358423403	5	FACETS	0.539	0.48	0.601	0.108	0.096	0.121	INDETERMINATE	1	TRUE	0	0.569781351448854	5		507	1233	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143296	30143296	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	232	514	0	ENST00000389048.3:c.230C>T	p.Ser77Phe	p.S77F	ENST00000389048	NM_004304.4	77	tCc/tTc	1/29	0.280094358423403	5	FACETS	1	0.989	1	0.26	0.242	0.279	INDETERMINATE	1	TRUE	0	0.569781351448854	5		514	1162	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286754	212286754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	105	424	0	ENST00000342788.4:c.2942C>T	p.Pro981Leu	p.P981L	ENST00000342788	NM_005235.2	981	cCt/cTt	24/28	1	2	FACETS	0.499	0.447	0.554	0.499	0.447	0.554	SUBCLONAL	1	TRUE	1	0.569781351448854	2		424	739	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430902	181430902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746642730	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	455	779	0	ENST00000325404.1:c.754C>T	p.Pro252Ser	p.P252S	ENST00000325404	NM_003106.3	252	Ccc/Tcc	1/1	0.569781351448854	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.569781351448854	1		779	924	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808626	1808626	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	789	950	0	ENST00000260795.2:c.2239G>A	p.Asp747Asn	p.D747N	ENST00000260795		747	Gac/Aac	16/17	NA	2	FACETS	0.939	0.912	0.967			1	INDETERMINATE	2	TRUE	NA	0.569781351448854	2		950	1474	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628134	187628134	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	168	548	0	ENST00000441802.2:c.2848G>A	p.Glu950Lys	p.E950K	ENST00000441802	NM_005245.3	950	Gaa/Aaa	2/27	0.243626858183559	0	FACETS	0.365	0.336	0.394			1	INDETERMINATE	1	TRUE	0	0.569781351448854	0		548	696	SUCCESS
APC	324	MSKCC	GRCh37	5	112175372	112175372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	181	349	0	ENST00000257430.4:c.4081C>T	p.Pro1361Ser	p.P1361S	ENST00000257430	NM_000038.5	1361	Ccc/Tcc	16/16	0.165517917925427	3	FACETS	1	0.99	1	0.714	0.662	0.766	INDETERMINATE	1	TRUE	1	0.569781351448854	3		349	572	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401555	401555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	163	440	0	ENST00000380956.4:c.877C>T	p.Pro293Ser	p.P293S	ENST00000380956	NM_001195286.1	293	Ccc/Tcc	7/9	1	2	FACETS	0.85	0.783	0.92	0.85	0.783	0.92	CLONAL	1	TRUE	1	0.569781351448854	2		440	673	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552922	106552922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1214061937	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	70	822	3	ENST00000369096.4:c.887G>A	p.Arg296Gln	p.R296Q	ENST00000369096	NM_001198.3	296	cGg/cAg	5/7	0.411413365912172	1	FACETS	0.152	0.132	0.174	0.152	0.132	0.174	SUBCLONAL	1	TRUE	0	0.569781351448854	1		825	1157	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339916	116339916	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1463	170	675	0	ENST00000397752.3:c.778T>C	p.Tyr260His	p.Y260H	ENST00000397752	NM_000245.2	260	Tac/Cac	2/21	0.569781351448854	3	FACETS	0.47	0.43	0.511	0.235	0.215	0.256	SUBCLONAL	1	TRUE	1	0.569781351448854	3		675	1633	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925411	114925411	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	281	928	0	ENST00000543371.1:c.1489C>T	p.Pro497Ser	p.P497S	ENST00000543371	NM_001198531.1	497	Ccg/Tcg	14/14	0.317884585739132	1	FACETS	0.496	0.464	0.528	0.496	0.464	0.528	INDETERMINATE	1	TRUE	0	0.569781351448854	1		928	1423	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276880	123276880	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	286	587	0	ENST00000358487.5:c.1037A>C	p.Asn346Thr	p.N346T	ENST00000358487	NM_000141.4	346	aAt/aCt	8/18	0.317884585739132	1	FACETS	0.749	0.705	0.793	0.749	0.705	0.793	INDETERMINATE	1	TRUE	0	0.569781351448854	1		587	959	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32438054	32438054	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	151	511	0	ENST00000332351.3:c.983G>A	p.Trp328Ter	p.W328*	ENST00000332351	NM_024426.4	328	tGg/tAg	5/10	0.243626858183559	0	FACETS	0.345	0.317	0.376			1	INDETERMINATE	1	TRUE	0	0.569781351448854	0		511	660	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127687	64127687	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	307	366	1	ENST00000334205.4:c.180G>T	p.Lys60Asn	p.K60N	ENST00000334205	NM_003942.2	60	aaG/aaT	3/17	0.323246425975591	2	FACETS	1	0.994	1	0.722	0.685	0.76	INDETERMINATE	1	TRUE	0	0.569781351448854	2		367	746	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18762474	18762474	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	246	635	0	ENST00000266497.5:c.3970A>G	p.Lys1324Glu	p.K1324E	ENST00000266497		1324	Aag/Gag	29/31	NA	2	FACETS	0.835	0.781	0.891			1	INDETERMINATE	1	TRUE	NA	0.569781351448854	2		635	1034	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492745	50492745	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	155	629	0	ENST00000394963.4:c.1510C>A	p.Gln504Lys	p.Q504K	ENST00000394963	NM_003076.4	504	Caa/Aaa	13/13	0.292730892184693	3	FACETS	0.571	0.521	0.623	0.286	0.26	0.312	INDETERMINATE	1	TRUE	1	0.569781351448854	3		629	1224	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233100	69233100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867680779	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	106	532	0	ENST00000462284.1:c.965C>T	p.Pro322Leu	p.P322L	ENST00000462284	NM_002392.5	322	cCa/cTa	11/11	1	2	FACETS	0.55	0.494	0.61	0.55	0.494	0.61	SUBCLONAL	1	TRUE	1	0.569781351448854	2		532	676	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608101	28608101	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	373	666	0	ENST00000241453.7:c.1865G>A	p.Gly622Glu	p.G622E	ENST00000241453	NM_004119.2	622	gGa/gAa	15/24	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.569781351448854	2		666	1093	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626739	28626739	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	282	623	2	ENST00000241453.7:c.557C>A	p.Ser186Tyr	p.S186Y	ENST00000241453	NM_004119.2	186	tCt/tAt	5/24	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.569781351448854	2		625	917	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919595	28919595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs553261958	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	189	577	0	ENST00000282397.4:c.2342G>A	p.Arg781Gln	p.R781Q	ENST00000282397	NM_002019.4	781	cGa/cAa	16/30	1	2	FACETS	0.765	0.708	0.825	0.765	0.708	0.825	SUBCLONAL	1	TRUE	1	0.569781351448854	2		577	867	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687605	29687605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	134	737	0	ENST00000356175.3:c.8198C>T	p.Ser2733Phe	p.S2733F	ENST00000356175	NM_000267.3	2733	tCc/tTc	56/57	1	2	FACETS	0.446	0.404	0.49	0.446	0.404	0.49	SUBCLONAL	1	TRUE	1	0.569781351448854	2		737	1055	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243476	41243476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397509136	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	401	754	1	ENST00000357654.3:c.4072G>A	p.Glu1358Lys	p.E1358K	ENST00000357654	NM_007294.3	1358	Gag/Aag	10/23	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.569781351448854	2		755	1267	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243674	41243674	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	299	740	0	ENST00000357654.3:c.3874T>G	p.Ser1292Ala	p.S1292A	ENST00000357654	NM_007294.3	1292	Tct/Gct	10/23	1	2	FACETS	0.993	0.936	1	0.993	0.936	1	CLONAL	1	TRUE	1	0.569781351448854	2		740	1057	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63531763	63531763	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370503213	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	377	666	0	ENST00000307078.5:c.2218C>T	p.Pro740Ser	p.P740S	ENST00000307078	NM_004655.3	740	Cca/Tca	9/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.569781351448854	2		666	1306	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272422	15272422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	288	627	0	ENST00000263388.2:c.6017G>A	p.Arg2006Lys	p.R2006K	ENST00000263388	NM_000435.2	2006	aGg/aAg	33/33	0.165517917925427	3	FACETS	1	0.991	1	0.646	0.608	0.685	INDETERMINATE	1	TRUE	1	0.569781351448854	3		627	1005	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295759	15295759	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	351	674	0	ENST00000263388.2:c.2368C>T	p.Pro790Ser	p.P790S	ENST00000263388	NM_000435.2	790	Cct/Tct	15/33	0.165517917925427	3	FACETS	1	0.994	1	0.709	0.672	0.747	INDETERMINATE	1	TRUE	1	0.569781351448854	3		674	1116	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955043	17955043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs199602590	NA	P-0008817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	223	413	1	ENST00000458235.1:c.184G>A	p.Gly62Ser	p.G62S	ENST00000458235	NM_000215.3	62	Ggc/Agc	2/24	0.165517917925427	3	FACETS	1	0.991	1	0.711	0.665	0.759	INDETERMINATE	1	TRUE	1	0.569781351448854	3		414	707	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240017	53240017	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	53	369	1	ENST00000375401.3:c.1424A>T	p.Asn475Ile	p.N475I	ENST00000375401	NM_004187.3	475	aAc/aTc	11/26	1	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	0	0.274581448250874	1		370	235	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183729	10183730	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0008830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	126	405	0	ENST00000256474.2:c.200dup	p.Asn67LysfsTer65	p.N67Kfs*65	ENST00000256474	NM_000551.3	66	-/A	1/3	0.274581448250874	1	FACETS	0.995	0.901	1	0.995	0.901	1	CLONAL	1	FALSE	0	0.274581448250874	1		405	796	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0008840-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	27	553	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	1	2	FACETS	0.203	0.161	0.253	0.203	0.161	0.253	SUBCLONAL	1	TRUE	1	0.241553504925433	2		553	1099	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0008840-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	149	351	2	ENST00000397752.3:c.3028+1G>A		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.201830918591211	3	FACETS	1	0.971	1	0.754	0.692	0.819	CLONAL	2	TRUE	0	0.241553504925433	3		353	611	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782144	NA	P-0008840-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	87	384	0	ENST00000269305.4:c.473G>C	p.Arg158Pro	p.R158P	ENST00000269305	NM_001126112.2	158	cGc/cCc	5/11	1	2	FACETS	0.979	0.866	1	0.979	0.866	1	CLONAL	1	TRUE	1	0.241553504925433	2		384	736	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182641	38182641	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs387907272	NA	P-0008840-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	23	435	1	ENST00000396334.3:c.794T>C	p.Leu265Pro	p.L265P	ENST00000396334	NM_002468.4	265	cTg/cCg	5/5	1	2	FACETS	0.222	0.172	0.281	0.222	0.172	0.281	SUBCLONAL	1	TRUE	1	0.241553504925433	2		436	856	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527371	157527371	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1295685861	NA	P-0008840-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	113	449	0	ENST00000346085.5:c.5096T>C	p.Met1699Thr	p.M1699T	ENST00000346085	NM_020732.3	1699	aTg/aCg	20/20	1	2	FACETS	0.873	0.784	0.968	0.873	0.784	0.968	CLONAL	1	TRUE	1	0.241553504925433	2		449	1072	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358978	81358978	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs374484762	NA	P-0008840-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	257	558	0	ENST00000222390.5:c.983G>T	p.Arg328Leu	p.R328L	ENST00000222390	NM_000601.4	328	cGt/cTt	8/18	0.201830918591211	3	FACETS	1	0.976	1	0.724	0.678	0.772	CLONAL	2	TRUE	0	0.241553504925433	3		558	1098	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939078	48939078	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008840-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	89	496	0	ENST00000267163.4:c.910G>T	p.Gly304Ter	p.G304*	ENST00000267163	NM_000321.2	304	Gga/Tga	9/27	1	2	FACETS	0.813	0.72	0.914	0.813	0.72	0.914	CLONAL	1	TRUE	1	0.241553504925433	2		496	906	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0008850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	191	227	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.469978563834386	2	FACETS	0.907	0.852	0.961	0.907	0.852	0.961	CLONAL	2	TRUE	0	0.563079665141168	2		227	374	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051234	128051234	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1371919188	NA	P-0008850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	293	433	0	ENST00000285398.2:c.89C>T	p.Pro30Leu	p.P30L	ENST00000285398	NM_000122.1	30	cCg/cTg	2/15	0.453999786136196	3	FACETS	0.979	0.919	1	0.489	0.459	0.52	CLONAL	1	TRUE	1	0.563079665141168	3		433	1363	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874607	35874607	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1346	462	527	0	ENST00000303115.3:c.763C>A	p.Leu255Met	p.L255M	ENST00000303115	NM_002185.3	255	Ctg/Atg	6/8	0.563079665141168	5	FACETS	0.837	0.797	0.878	0.558	0.531	0.585	CLONAL	2	TRUE	2	0.563079665141168	5		527	1808	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602923	10602923	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	227	370	0	ENST00000171111.5:c.655G>C	p.Glu219Gln	p.E219Q	ENST00000171111	NM_203500.1	219	Gag/Cag	3/6	1	2	FACETS	0.895	0.835	0.957	0.895	0.835	0.957	CLONAL	1	TRUE	1	0.563079665141168	2		370	901	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971139	21971150	+	inframe_deletion	In_Frame_Del	DEL	GGCGCAGTTGGG	GGCGCAGTTGGG	-	novel	NA	P-0008850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	167	148	0	ENST00000304494.5:c.208_219del	p.Pro70_Ala73del	p.P70_A73del	ENST00000304494	NM_000077.4	70	CCCAACTGCGCC/-	2/3	NA	2	FACETS	0.789	0.735	0.843			1	INDETERMINATE	2	TRUE	NA	0.563079665141168	2		148	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578459	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0008850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	408	333	0	ENST00000269305.4:c.471_472insT	p.Arg158SerfsTer23	p.R158Sfs*23	ENST00000269305	NM_001126112.2	157	-/T	5/11	0.469978563834386	2	FACETS	0.76	0.726	0.794	0.76	0.726	0.794	SUBCLONAL	2	TRUE	0	0.563079665141168	2		333	953	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0008867-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	11	442	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	0.407	0.28	0.566	0.407	0.28	0.566	SUBCLONAL	1	TRUE	1	0.13	2		442	416	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398280	25398281	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0008908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	124	406	0	ENST00000311936.3:c.38_39delinsAA	p.Gly13Glu	p.G13E	ENST00000311936	NM_004985.3	13	gGC/gAA	2/5	0.292078558890348	3	FACETS	0.997	0.91	1			1	CLONAL	2	FALSE	NA	0.35542152451415	3		406	412	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015689	27015689	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	177	766	0	ENST00000335756.4:c.276G>T	p.Leu92Phe	p.L92F	ENST00000335756	NM_001809.3	92	ttG/ttT	3/5	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.35542152451415	NA		766	678	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928020	49928020	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	176	635	0	ENST00000296474.3:c.3708G>C	p.Arg1236Ser	p.R1236S	ENST00000296474	NM_002447.2	1236	agG/agC	18/20	0.35542152451415	3	FACETS	0.962	0.891	1			1	CLONAL	2	FALSE	NA	0.35542152451415	3		635	606	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138376626	138376626	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	51	475	0	ENST00000289153.2:c.2848G>T	p.Gly950Cys	p.G950C	ENST00000289153	NM_006219.2	950	Ggc/Tgc	20/22	0.181448498513559	5	FACETS	1	0.917	1			1	INDETERMINATE	1	FALSE	NA	0.35542152451415	5		475	395	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876287	35876287	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	47	306	0	ENST00000303115.3:c.1079G>T	p.Ser360Ile	p.S360I	ENST00000303115	NM_002185.3	360	aGc/aTc	8/8	0.35542152451415	4	FACETS	0.736	0.621	0.863	0.368	0.31	0.432	SUBCLONAL	1	FALSE	2	0.35542152451415	4		306	487	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350090	81350090	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	159	501	0	ENST00000222390.5:c.1242G>C	p.Met414Ile	p.M414I	ENST00000222390	NM_000601.4	414	atG/atC	10/18	0.35542152451415	5	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	FALSE	3	0.35542152451415	5		501	663	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333887	70333887	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	53	359	0	ENST00000373644.4:c.1792C>A	p.Gln598Lys	p.Q598K	ENST00000373644	NM_030625.2	598	Cag/Aag	2/12	0.292078558890348	3	FACETS	0.804	0.687	0.931			1	CLONAL	1	FALSE	NA	0.35542152451415	3		359	437	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158369	108158369	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1060501528	NA	P-0008908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	105	416	0	ENST00000278616.4:c.4036G>T	p.Glu1346Ter	p.E1346*	ENST00000278616	NM_000051.3	1346	Gag/Tag	27/63	0.287161311487059	3	FACETS	0.983	0.889	1	0.655	0.593	0.72	CLONAL	2	FALSE	0	0.35542152451415	3		416	354	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038774	47038774	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	84	128	1	ENST00000377604.3:c.781G>T	p.Gly261Cys	p.G261C	ENST00000377604	NM_001204468.1	261	Ggt/Tgt	9/24	0.342918728608526	2	FACETS	1	0.973	1			1	CLONAL	2	FALSE	NA	0.35542152451415	2		129	191	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0008911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	173	586	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.326174059466211	4	FACETS	0.902	0.836	0.969			1	CLONAL	3	TRUE	NA	0.326174059466211	4		586	520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578214	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs864309495	NA	P-0008911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	207	673	0	ENST00000269305.4:c.635_636del	p.Phe212SerfsTer3	p.F212Sfs*3	ENST00000269305	NM_001126112.2	212	tTT/t	6/11	0.326174059466211	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.326174059466211	1		673	948	SUCCESS
RET	5979	MSKCC	GRCh37	10	43572717	43572717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	78	219	1	ENST00000355710.3:c.11C>T	p.Ala4Val	p.A4V	ENST00000355710	NM_020975.4	4	gCg/gTg	1/20	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.326174059466211	2		220	451	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347217	70347217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338758	NA	P-0008911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	250	785	2	ENST00000374080.3:c.2881C>T	p.Arg961Trp	p.R961W	ENST00000374080		961	Cgg/Tgg	21/45	0.326174059466211	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.326174059466211	1		787	917	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492716	56492716	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	127	685	0	ENST00000407977.2:c.223del	p.Ile75Ter	p.I75*	ENST00000407977		75	Ata/ta	2/10	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.326174059466211	2		685	765	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0008931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	391	406	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.486795222339237	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.486795222339237	2		406	760	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577507	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	241	400	1	ENST00000269305.4:c.774dup	p.Asp259ArgfsTer5	p.D259Rfs*5	ENST00000269305	NM_001126112.2	258	-/A	7/11	0.474646670391378	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.486795222339237	1		401	731	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522476	187522476	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	347	656	0	ENST00000441802.2:c.11587T>C	p.Ser3863Pro	p.S3863P	ENST00000441802	NM_005245.3	3863	Tcc/Ccc	21/27	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.486795222339237	2		656	1257	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945382	151945382	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	94	205	0	ENST00000262189.6:c.2137del	p.Glu713AsnfsTer5	p.E713Nfs*5	ENST00000262189	NM_170606.2	713	Gaa/aa	14/59	1	2	FACETS	0.998	0.895	1	0.998	0.895	1	CLONAL	1	TRUE	1	0.486795222339237	2		205	387	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0008941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	210	249	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.42090523739776	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.42090523739776	2		249	454	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591825	48591825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767342	NA	P-0008941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	333	542	0	ENST00000342988.3:c.988G>A	p.Glu330Lys	p.E330K	ENST00000342988	NM_005359.5	330	Gaa/Aaa	9/12	0.42090523739776	2	FACETS	0.88	0.835	0.926	0.88	0.835	0.926	CLONAL	2	TRUE	0	0.42090523739776	2		542	899	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	348	454	0	ENST00000269305.4:c.430del	p.Gln144SerfsTer26	p.Q144Sfs*26	ENST00000269305	NM_001126112.2	144	Cag/ag	5/11	0.42090523739776	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.42090523739776	2		454	690	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112442	115112442	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	47	302	0	ENST00000257566.3:c.1298C>G	p.Pro433Arg	p.P433R	ENST00000257566	NM_016569.3	433	cCc/cGc	7/8	0.26228924556512	4	FACETS	0.49	0.413	0.576	0.245	0.206	0.288	SUBCLONAL	1	TRUE	2	0.42090523739776	4		302	647	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733086	74733086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	228	556	0	ENST00000359995.5:c.157G>A	p.Glu53Lys	p.E53K	ENST00000359995	NM_001195427.1	53	Gag/Aag	1/3	0.42090523739776	3	FACETS	1	0.99	1	0.45	0.419	0.481	CLONAL	1	TRUE	0	0.42090523739776	3		556	972	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245842	41245849	+	frameshift_variant	Frame_Shift_Del	DEL	TTAGGATT	TTAGGATT	-	novel	NA	P-0008941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	343	496	0	ENST00000357654.3:c.1699_1706del	p.Asn567ProfsTer16	p.N567Pfs*16	ENST00000357654	NM_007294.3	567	AATCCTAAc/c	10/23	0.42090523739776	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.42090523739776	2		496	765	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0008948-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	202	377	0	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	0.731073309345622	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.776846875942625	2		377	238	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231696	66231696	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008948-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	138	573	0	ENST00000273854.3:c.2004G>C	p.Lys668Asn	p.K668N	ENST00000273854	NM_004439.5	668	aaG/aaC	11/18	0.264531864148747	1	FACETS	0.619	0.571	0.668	0.619	0.571	0.668	INDETERMINATE	1	TRUE	0	0.776846875942625	1		573	351	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244194	153244194	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008948-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	367	585	1	ENST00000281708.4:c.1963G>T	p.Glu655Ter	p.E655*	ENST00000281708	NM_033632.3	655	Gaa/Taa	12/12	0.776846875942625	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.776846875942625	3		586	622	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041717	14041717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008948-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	131	556	0	ENST00000311895.7:c.2264C>T	p.Pro755Leu	p.P755L	ENST00000311895	NM_005236.2	755	cCc/cTc	11/11	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.776846875942625	2		556	327	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602878	10602878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008948-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	142	413	0	ENST00000171111.5:c.700C>T	p.Arg234Trp	p.R234W	ENST00000171111	NM_203500.1	234	Cgg/Tgg	3/6	0.772803528679544	2	FACETS	1	0.976	1	0.564	0.522	0.607	CLONAL	1	TRUE	0	0.776846875942625	2		413	324	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387093	31387093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143300013	NA	P-0008958-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	596	465	1	ENST00000328111.2:c.1718G>A	p.Arg573Gln	p.R573Q	ENST00000328111	NM_006892.3	573	cGg/cAg	16/23	0.526282383117601	5	FACETS	0.84	0.808	0.873	0.63	0.606	0.655	CLONAL	3	TRUE	1	0.526282383117601	5		466	1608	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0008961-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	271	576	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.458704774566337	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.458704774566337	1		579	812	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595933	52595933	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0008961-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	423	505	0	ENST00000394830.3:c.3982A>T	p.Lys1328Ter	p.K1328*	ENST00000394830	NM_018313.4	1328	Aaa/Taa	26/30	0.458704774566337	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.458704774566337	1		505	1254	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923032	44923032	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008961-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	241	433	0	ENST00000377967.4:c.1893del	p.Trp632GlyfsTer59	p.W632Gfs*59	ENST00000377967	NM_021140.2	631	ccG/cc	16/29	0.458704774566337	1	FACETS	0.854	0.799	0.911	0.854	0.799	0.911	CLONAL	1	TRUE	0	0.458704774566337	1		433	948	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0009002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	126	639	1	ENST00000269305.4:c.560-2A>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.241211630870205	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	0	0.241211630870205	1		640	839	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46714233	46714233	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	120	601	1	ENST00000371975.4:c.53G>T	p.Arg18Met	p.R18M	ENST00000371975	NM_003579.3	18	aGg/aTg	2/18	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	FALSE	1	0.241211630870205	2		602	954	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	579	160	0				ENST00000310581	NM_198253.2	-/1132			0.630431245112259	7	FACETS	0.944	0.918	0.97	1	0.996	1	CLONAL	6	TRUE	2	0.630431245112259	7		160	835	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2193750	2193750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	219	469	0	ENST00000398665.3:c.556G>A	p.Glu186Lys	p.E186K	ENST00000398665	NM_032482.2	186	Gag/Aag	6/28	0.592293768387155	3	FACETS	0.846	0.787	0.908	0.423	0.393	0.454	CLONAL	1	TRUE	1	0.630431245112259	3		469	1080	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138480	11138480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	214	375	0	ENST00000358026.2:c.3236C>T	p.Ser1079Leu	p.S1079L	ENST00000358026	NM_001128849.1	1079	tCg/tTg	24/36	0.592293768387155	3	FACETS	0.977	0.909	1	0.488	0.454	0.524	CLONAL	1	TRUE	1	0.630431245112259	3		375	914	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027189	48027189	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	225	440	0	ENST00000234420.5:c.2067C>G	p.Phe689Leu	p.F689L	ENST00000234420	NM_000179.2	689	ttC/ttG	4/10	1	2	FACETS	0.965	0.902	1	0.965	0.902	1	CLONAL	1	TRUE	1	0.630431245112259	2		440	740	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141041	55141041	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	214	472	2	ENST00000257290.5:c.1687G>A	p.Glu563Lys	p.E563K	ENST00000257290	NM_006206.4	563	Gaa/Aaa	12/23	0.630431245112259	3	FACETS	0.875	0.813	0.94	0.438	0.406	0.47	CLONAL	1	TRUE	1	0.630431245112259	3		474	1020	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971100	55971100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756721127	NA	P-0009005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	200	384	0	ENST00000263923.4:c.1697G>A	p.Ser566Asn	p.S566N	ENST00000263923	NM_002253.2	566	aGc/aAc	13/30	0.630431245112259	3	FACETS	0.877	0.812	0.943	0.438	0.406	0.472	CLONAL	1	TRUE	1	0.630431245112259	3		384	952	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137524717	137524717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	250	440	0	ENST00000367739.4:c.652G>A	p.Glu218Lys	p.E218K	ENST00000367739	NM_000416.2	218	Gaa/Aaa	5/7	0.630431245112259	3	FACETS	0.92	0.86	0.982	0.46	0.43	0.491	CLONAL	1	TRUE	1	0.630431245112259	3		440	1134	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878586	151878586	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	173	345	1	ENST00000262189.6:c.6359G>T	p.Gly2120Val	p.G2120V	ENST00000262189	NM_170606.2	2120	gGa/gTa	36/59	0.617652231135508	4	FACETS	0.924	0.851	1	0.462	0.425	0.501	CLONAL	1	TRUE	2	0.630431245112259	4		346	968	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346457	89346457	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	280	582	0	ENST00000301030.4:c.6493G>C	p.Glu2165Gln	p.E2165Q	ENST00000301030	NM_001256183.1	2165	Gag/Cag	9/13	0.630431245112259	2	FACETS	1	0.968	1	0.519	0.489	0.55	CLONAL	1	TRUE	0	0.630431245112259	2		582	855	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039666	47039666	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	454	259	0	ENST00000377604.3:c.1118A>C	p.Asp373Ala	p.D373A	ENST00000377604	NM_001204468.1	373	gAc/gCc	11/24	0.565383959866208	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.630431245112259	2		259	590	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106469	27106480	+	frameshift_variant	Frame_Shift_Del	DEL	CACCACTAACTT	CACCACTAACTT	AA	novel	NA	P-0009005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	254	382	1	ENST00000324856.7:c.6080_6091delinsAA	p.Ala2027GlufsTer12	p.A2027Efs*12	ENST00000324856	NM_006015.4	2027	gCACCACTAACTTat/gAAat	20/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.630431245112259	2		383	670	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629025	14629026	+	missense_variant	Missense_Mutation	DNP	TT	TT	AA	novel	NA	P-0009005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	216	412	1	ENST00000254322.2:c.136_137inv	p.Lys46Leu	p.K46L	ENST00000254322	NM_006145.1	46	AAg/TTg	1/3	0.592293768387155	3	FACETS	0.949	0.882	1	0.474	0.441	0.509	CLONAL	1	TRUE	1	0.630431245112259	3		413	950	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0009012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	241	405	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.155002867653717	3	FACETS	1	0.978	1	1	0.978	1	INDETERMINATE	2	FALSE	1	0.286234936958994	3		405	877	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0009012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	127	363	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.286234936958994	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	0	0.286234936958994	1		363	658	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535441	66535441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	62	150	2	ENST00000273854.3:c.20G>A	p.Arg7Gln	p.R7Q	ENST00000273854	NM_004439.5	7	cGg/cAg	1/18	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.286234936958994	2		152	350	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401004	139401004	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180096756	NA	P-0009012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	45	325	1	ENST00000277541.6:c.3989G>A	p.Arg1330His	p.R1330H	ENST00000277541	NM_017617.3	1330	cGc/cAc	24/34	1	2	FACETS	0.406	0.34	0.479	0.406	0.34	0.479	SUBCLONAL	1	FALSE	1	0.286234936958994	2		326	775	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	465607	465607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	246	438	0	ENST00000399788.2:c.769G>A	p.Asp257Asn	p.D257N	ENST00000399788	NM_001042603.1	257	Gat/Aat	6/28	NA	2	FACETS	0.784	0.733	0.837			1	INDETERMINATE	2	FALSE	NA	0.286234936958994	2		438	1096	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32890665	32890665	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs81002796	NA	P-0009012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	62	254	0	ENST00000380152.3:c.67+1G>T		p.X23_splice	ENST00000380152		23			1	2	FACETS	0.681	0.588	0.782	0.681	0.588	0.782	SUBCLONAL	1	FALSE	1	0.286234936958994	2		254	636	SUCCESS
APC	324	MSKCC	GRCh37	5	112173756	112173756	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	107	343	0	ENST00000257430.4:c.2467del	p.Ser823HisfsTer4	p.S823Hfs*4	ENST00000257430	NM_000038.5	822	cTt/ct	16/16	1	2	FACETS	0.956	0.857	1	0.956	0.857	1	CLONAL	1	FALSE	1	0.286234936958994	2		343	782	SUCCESS
APC	324	MSKCC	GRCh37	5	112175751	112175752	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1114167577	NA	P-0009012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	125	239	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	FALSE	1	0.286234936958994	2		239	776	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	525	499	1	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.864083156100017	2	FACETS	0.988	0.967	1	0.988	0.967	1	CLONAL	2	TRUE	0	0.864083156100017	2		500	615	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508487	29508487	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	256	706	0	ENST00000356175.3:c.634G>C	p.Val212Leu	p.V212L	ENST00000356175	NM_000267.3	212	Gtt/Ctt	6/57	0.857991319575395	3	FACETS	1	0.958	1	0.512	0.481	0.545	CLONAL	1	TRUE	1	0.864083156100017	3		706	828	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023996	31023996	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	267	548	0	ENST00000375687.4:c.3481A>G	p.Met1161Val	p.M1161V	ENST00000375687	NM_015338.5	1161	Atg/Gtg	13/13	0.864083156100017	3	FACETS	0.867	0.813	0.922	0.433	0.406	0.461	CLONAL	1	TRUE	1	0.864083156100017	3		548	1021	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0009048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17968	1504	326	1	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.827178946271199	16	FACETS	1	0.997	1			1	CLONAL	1	TRUE	NA	0.827178946271199	16		327	19472	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546721	9546721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	319	245	0	ENST00000353224.5:c.1301C>T	p.Ala434Val	p.A434V	ENST00000353224	NM_177990.2	434	gCg/gTg	5/10	0.827178946271199	3	FACETS	1	0.98	1	0.538	0.508	0.568	CLONAL	1	TRUE	1	0.827178946271199	3		245	1014	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0009048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4358	17981	619	0	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.827178946271199	16	FACETS	1	0.999	1			1	CLONAL	13	TRUE	NA	0.827178946271199	16		619	22339	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233012	55233012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs989939484	NA	P-0009048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	15422	344	3	ENST00000275493.2:c.1762G>A	p.Gly588Ser	p.G588S	ENST00000275493	NM_005228.3	588	Ggc/Agc	15/28	0.827178946271199	16	FACETS	1	0.999	1			1	CLONAL	15	TRUE	NA	0.827178946271199	16		347	16447	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0009058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	226	278	1	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.480103732604803	2	FACETS	0.909	0.855	0.963	0.909	0.855	0.963	CLONAL	2	TRUE	0	0.480103732604803	2		279	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0009058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	334	363	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.480103732604803	2	FACETS	0.919	0.874	0.964	0.919	0.874	0.964	CLONAL	2	TRUE	0	0.480103732604803	2		363	757	SUCCESS
APC	324	MSKCC	GRCh37	5	112175524	112175524	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	286	364	0	ENST00000257430.4:c.4233del	p.Ser1411ArgfsTer4	p.S1411Rfs*4	ENST00000257430	NM_000038.5	1411	agT/ag	16/16	0.480103732604803	2	FACETS	0.94	0.891	0.989	0.94	0.891	0.989	CLONAL	2	TRUE	0	0.480103732604803	2		364	634	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277275	41277275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	196	1120	1	ENST00000349496.5:c.1744C>T	p.Arg582Trp	p.R582W	ENST00000349496	NM_001904.3	582	Cgg/Tgg	11/15	0.435894177263831	3	FACETS	1	0.935	1	0.506	0.468	0.545	CLONAL	1	TRUE	1	0.480103732604803	3		1121	1001	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967853	93967853	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	64	816	4	ENST00000369303.4:c.2074C>A	p.Pro692Thr	p.P692T	ENST00000369303	NM_004440.3	692	Ccg/Acg	11/17	0.480103732604803	2	FACETS	0.221	0.19	0.254	0.11	0.095	0.127	SUBCLONAL	1	TRUE	0	0.480103732604803	2		820	1208	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287320	38287320	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751494167	NA	P-0009058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	416	470	1	ENST00000425967.3:c.337C>T	p.Arg113Cys	p.R113C	ENST00000425967	NM_001174067.1	113	Cgc/Tgc	4/19	0.480103732604803	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.480103732604803	3		471	1071	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569236	67569247	+	inframe_deletion	In_Frame_Del	DEL	TTGCAGAGCAGT	TTGCAGAGCAGT	-	novel	NA	P-0009058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	194	481	0	ENST00000274335.5:c.357_368del	p.Glu120_Ala123del	p.E120_A123del	ENST00000274335		118	cTTGCAGAGCAGTtt/ctt	2/15	1	2	FACETS	0.776	0.718	0.837	0.776	0.718	0.837	SUBCLONAL	1	TRUE	1	0.480103732604803	2		481	1041	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0009065-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	433	360	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.539297762252898	3	FACETS	0.897	0.865	0.929	0.897	0.865	0.929	CLONAL	3	TRUE	0	0.595853755825996	3		361	701	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630179	100630179	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009065-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	62	459	0	ENST00000308731.7:c.94T>G	p.Leu32Val	p.L32V	ENST00000308731	NM_000061.2	32	Ttg/Gtg	2/19	0.516685537952973	2	FACETS	0.215	0.185	0.248			1	SUBCLONAL	1	TRUE	NA	0.595853755825996	2		459	966	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0009068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	711	390	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.537843104395674	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.537843104395674	2		390	1219	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794527	42794527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201728833	NA	P-0009068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	339	563	1	ENST00000575354.2:c.1607C>T	p.Ala536Val	p.A536V	ENST00000575354	NM_015125.3	536	gCg/gTg	10/20	0.162601918530515	1	FACETS	0.827	0.782	0.872	0.827	0.782	0.872	INDETERMINATE	1	TRUE	0	0.537843104395674	1		564	1115	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468511	89468511	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	275	395	0	ENST00000336596.2:c.2045T>A	p.Ile682Asn	p.I682N	ENST00000336596	NM_005233.5	682	aTc/aAc	11/17	0.513744233901023	2	FACETS	0.904	0.849	0.961	0.452	0.424	0.481	CLONAL	1	TRUE	0	0.537843104395674	2		395	1131	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226573215	226573215	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	90	470	1	ENST00000366794.5:c.1001T>A	p.Val334Glu	p.V334E	ENST00000366794	NM_001618.3	334	gTa/gAa	7/23	0.342979792469972	2	FACETS	0.339	0.3	0.381	0.169	0.15	0.191	SUBCLONAL	1	TRUE	0	0.537843104395674	2		471	988	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346787	225346787	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs772355997	NA	P-0009068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	180	315	0	ENST00000264414.4:c.1851G>T	p.Gln617His	p.Q617H	ENST00000264414	NM_003590.4	617	caG/caT	14/16	1	2	FACETS	0.852	0.787	0.919	0.852	0.787	0.919	CLONAL	1	TRUE	1	0.537843104395674	2		315	786	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37058996	37058996	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs267607795	NA	P-0009068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	435	356	0	ENST00000231790.2:c.791-1G>C		p.X264_splice	ENST00000231790	NM_000249.3	264			0.537843104395674	2	FACETS	0.991	0.952	1	0.991	0.952	1	CLONAL	2	TRUE	0	0.537843104395674	2		356	816	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549779	187549779	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0009068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	148	385	0	ENST00000441802.2:c.4462A>T	p.Lys1488Ter	p.K1488*	ENST00000441802	NM_005245.3	1488	Aaa/Taa	8/27	0.267298811622957	1	FACETS	0.44	0.401	0.48	0.44	0.401	0.48	INDETERMINATE	1	TRUE	0	0.537843104395674	1		385	915	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35857110	35857110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	252	512	0	ENST00000303115.3:c.31G>A	p.Val11Ile	p.V11I	ENST00000303115	NM_002185.3	11	Gtt/Att	1/8	1	2	FACETS	0.774	0.724	0.827	0.774	0.724	0.827	SUBCLONAL	1	TRUE	1	0.537843104395674	2		512	1210	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517357	157517357	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	226	507	2	ENST00000346085.5:c.3921G>T	p.Gln1307His	p.Q1307H	ENST00000346085	NM_020732.3	1307	caG/caT	16/20	1	2	FACETS	0.73	0.679	0.782	0.73	0.679	0.782	SUBCLONAL	1	TRUE	1	0.537843104395674	2		509	1152	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066751	77066751	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs759377668	NA	P-0009068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1400	283	556	0	ENST00000356341.3:c.734A>G	p.Lys245Arg	p.K245R	ENST00000356341	NM_002576.4	245	aAg/aGg	7/15	0.537843104395674	3	FACETS	0.793	0.743	0.845	0.397	0.371	0.423	SUBCLONAL	1	TRUE	1	0.537843104395674	3		556	1683	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219106	94219106	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	224	383	0	ENST00000323929.3:c.298A>G	p.Asn100Asp	p.N100D	ENST00000323929	NM_005591.3	100	Aac/Gac	4/20	0.537843104395674	3	FACETS	0.833	0.774	0.894	0.416	0.387	0.447	CLONAL	1	TRUE	1	0.537843104395674	3		383	1269	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134286	41134286	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1342	491	878	2	ENST00000379561.5:c.1342A>T	p.Ser448Cys	p.S448C	ENST00000379561	NM_002015.3	448	Agt/Tgt	2/3	0.162601918530515	1	FACETS	0.728	0.695	0.762	0.728	0.695	0.762	INDETERMINATE	1	TRUE	0	0.537843104395674	1		880	1833	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81557432	81557432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1473074598	NA	P-0009068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	343	504	0	ENST00000298171.2:c.412C>T	p.Leu138Phe	p.L138F	ENST00000298171	NM_000369.2	138	Ctt/Ttt	5/10	1	2	FACETS	0.959	0.907	1	0.959	0.907	1	CLONAL	1	TRUE	1	0.537843104395674	2		504	1330	SUCCESS
BLM	641	MSKCC	GRCh37	15	91326105	91326105	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	289	449	2	ENST00000355112.3:c.2609A>G	p.Lys870Arg	p.K870R	ENST00000355112	NM_000057.2	870	aAg/aGg	13/22	1	2	FACETS	0.967	0.91	1	0.967	0.91	1	CLONAL	1	TRUE	1	0.537843104395674	2		451	1111	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992873	72992873	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	358	693	1	ENST00000268489.5:c.1172A>G	p.Gln391Arg	p.Q391R	ENST00000268489	NM_006885.3	391	cAg/cGg	2/10	0.301548918022607	1	FACETS	0.815	0.773	0.858	0.815	0.773	0.858	INDETERMINATE	1	TRUE	0	0.537843104395674	1		694	1194	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857238	78857238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866939416	NA	P-0009068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	286	487	0	ENST00000306801.3:c.1604C>T	p.Thr535Met	p.T535M	ENST00000306801	NM_020761.2	535	aCg/aTg	15/34	0.537843104395674	3	FACETS	0.992	0.931	1	0.496	0.465	0.528	CLONAL	1	TRUE	1	0.537843104395674	3		487	1360	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39550380	39550380	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	247	444	0	ENST00000262039.4:c.491G>T	p.Ser164Ile	p.S164I	ENST00000262039	NM_002647.2	164	aGt/aTt	4/25	0.537843104395674	3	FACETS	0.817	0.762	0.874	0.408	0.381	0.437	CLONAL	1	TRUE	1	0.537843104395674	3		444	1427	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52709302	52709302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1377540471	NA	P-0009068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	133	383	2	ENST00000322088.6:c.256G>A	p.Val86Met	p.V86M	ENST00000322088	NM_014225.5	86	Gtg/Atg	3/15	0.162601918530515	1	FACETS	0.537	0.489	0.588	0.537	0.489	0.588	INDETERMINATE	1	TRUE	0	0.537843104395674	1		385	673	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021560	31021560	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	161	281	0	ENST00000375687.4:c.1559A>G	p.Lys520Arg	p.K520R	ENST00000375687	NM_015338.5	520	aAg/aGg	12/13	1	2	FACETS	0.89	0.818	0.963	0.89	0.818	0.963	CLONAL	1	TRUE	1	0.537843104395674	2		281	673	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412341	63412341	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	376	609	1	ENST00000330258.3:c.826C>A	p.Pro276Thr	p.P276T	ENST00000330258	NM_152424.3	276	Cct/Act	2/2	0.162601918530515	1	FACETS	0.787	0.747	0.828	0.787	0.747	0.828	INDETERMINATE	1	TRUE	0	0.537843104395674	1		610	1299	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050292	13050292	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0121589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	781	656	0	ENST00000316448.5:c.244G>C	p.Glu82Gln	p.E82Q	ENST00000316448	NM_004343.3	82	Gag/Cag	3/9	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	NA	1	0.878705747545047	2		656	1757	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225940	2225940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009081-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	30	334	1	ENST00000326181.6:c.1732G>A	p.Glu578Lys	p.E578K	ENST00000326181	NM_032271.2	578	Gag/Aag	18/21	0.284246628351867	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		335	343	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0009088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	93	644	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.818	0.725	0.917	0.818	0.725	0.917	CLONAL	1	TRUE	1	0.213826988791125	2		645	1064	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100177	157100177	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1487267556	NA	P-0009088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	32	91	2	ENST00000346085.5:c.1114C>T	p.Arg372Trp	p.R372W	ENST00000346085	NM_020732.3	372	Cgg/Tgg	1/20	0.187778522824263	2	FACETS	1	0.855	1	0.529	0.431	0.639	CLONAL	1	TRUE	0	0.213826988791125	2		93	283	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434752	99434752	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	232	381	0	ENST00000268035.6:c.839A>T	p.Asp280Val	p.D280V	ENST00000268035	NM_000875.3	280	gAc/gTc	3/21	0.205430964245399	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.213826988791125	2		381	971	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134267	11134267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1180804356	NA	P-0009088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	112	394	1	ENST00000358026.2:c.2933G>A	p.Arg978Gln	p.R978Q	ENST00000358026	NM_001128849.1	978	cGa/cAa	20/36	0.213826988791125	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.213826988791125	1		395	797	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39657718	39657720	+	inframe_deletion	In_Frame_Del	DEL	ACC	ACC	-	novel	NA	P-0009088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	74	354	0	ENST00000361337.2:c.14_16del	p.His5del	p.H5del	ENST00000361337	NM_003286.2	4	gACCac/gac	1/21	0.213826988791125	3	FACETS	0.85	0.743	0.967			1	CLONAL	1	TRUE	NA	0.213826988791125	3		354	901	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	174	586	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	0.420123292372131	2		586	822	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0009098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	188	741	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.420123292372131	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.420123292372131	1		742	681	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928323	69928323	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	61	349	0	ENST00000352241.4:c.143T>C	p.Ile48Thr	p.I48T	ENST00000352241	NM_198159.2	48	aTa/aCa	2/10	1	2	FACETS	0.411	0.354	0.474	0.411	0.354	0.474	SUBCLONAL	1	TRUE	1	0.420123292372131	2		349	706	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101125	41101125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756719404	NA	P-0009098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	29	304	0	ENST00000373198.4:c.1231G>A	p.Gly411Ser	p.G411S	ENST00000373198	NM_133170.3	411	Ggc/Agc	8/32	1	2	FACETS	0.253	0.202	0.311	0.253	0.202	0.311	SUBCLONAL	1	TRUE	1	0.420123292372131	2		304	546	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938758	76938758	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	58	550	0	ENST00000373344.5:c.1990T>G	p.Leu664Val	p.L664V	ENST00000373344	NM_000489.3	664	Ttg/Gtg	9/35	0.403790658689113	1	FACETS	0.225	0.192	0.26	0.225	0.192	0.26	SUBCLONAL	1	TRUE	0	0.420123292372131	1		550	971	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555526097	NA	P-0009103-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	649	884	0	ENST00000269305.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000269305	NM_001126112.2	167	Cag/Tag	5/11	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.760129389673779	2		884	818	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484372	8484372	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009103-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	87	483	0	ENST00000356435.5:c.3160T>C	p.Tyr1054His	p.Y1054H	ENST00000356435		1054	Tat/Cat	19/35	0.760129389673779	1	FACETS	0.408	0.364	0.454	0.408	0.364	0.454	SUBCLONAL	1	TRUE	0	0.760129389673779	1		483	348	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350068	89350068	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs750887042	NA	P-0009103-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	319	959	0	ENST00000301030.4:c.2882G>T	p.Arg961Leu	p.R961L	ENST00000301030	NM_001256183.1	961	cGc/cTc	9/13	0.760129389673779	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.760129389673779	1		959	501	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937429	76937429	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009103-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	551	709	0	ENST00000373344.5:c.3319T>G	p.Cys1107Gly	p.C1107G	ENST00000373344	NM_000489.3	1107	Tgt/Ggt	9/35	0.367215805908361	5	FACETS	1	0.993	1	0.82	0.793	0.847	INDETERMINATE	3	TRUE	1	0.760129389673779	5		709	946	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260294	149260294	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761764314	NA	P-0009103-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	150	1039	2	ENST00000360632.3:c.599C>T	p.Ala200Val	p.A200V	ENST00000360632	NM_015472.4	200	gCc/gTc	4/7	0.760129389673779	1	FACETS	0.434	0.398	0.471	0.434	0.398	0.471	SUBCLONAL	1	TRUE	0	0.760129389673779	1		1041	564	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531158	187531158	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009103-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	108	457	0	ENST00000441802.2:c.9865A>T	p.Ile3289Phe	p.I3289F	ENST00000441802	NM_005245.3	3289	Atc/Ttc	15/27	0.34055193007663	1	FACETS	0.387	0.349	0.427	0.387	0.349	0.427	INDETERMINATE	1	TRUE	0	0.760129389673779	1		457	455	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591092	67591092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554051268	NA	P-0009103-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	56	468	0	ENST00000274335.5:c.1685G>A	p.Arg562His	p.R562H	ENST00000274335		562	cGt/cAt	12/15	NA	2	FACETS	0.354	0.304	0.409			1	INDETERMINATE	1	TRUE	NA	0.760129389673779	2		468	416	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	67	586	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.853	0.743	0.972	1	0.977	1	CLONAL	2	TRUE	1	0.16	2		586	491	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0009109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	59	379	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.85	0.733	0.976	1	0.974	1	CLONAL	2	TRUE	1	0.16	2		379	434	SUCCESS
ATM	472	MSKCC	GRCh37	11	108183157	108183157	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786203765	NA	P-0009109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	45	519	0	ENST00000278616.4:c.5938G>A	p.Gly1980Arg	p.G1980R	ENST00000278616	NM_000051.3	1980	Gga/Aga	40/63	1	2	FACETS	0.764	0.644	0.896	1	0.961	1	SUBCLONAL	2	TRUE	1	0.16	2		519	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0009139-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	93	424	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	FALSE	1	0.270055670791294	2		424	683	SUCCESS
APC	324	MSKCC	GRCh37	5	112163677	112163677	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0009139-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	81	626	0	ENST00000257430.4:c.1600A>T	p.Lys534Ter	p.K534*	ENST00000257430	NM_000038.5	534	Aaa/Taa	13/16	1	2	FACETS	0.743	0.654	0.839	0.743	0.654	0.839	SUBCLONAL	1	FALSE	1	0.270055670791294	2		626	807	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279464	1279464	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202123213	NA	P-0009139-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	38	457	0	ENST00000310581.5:c.2072G>A	p.Arg691His	p.R691H	ENST00000310581	NM_198253.2	691	cGc/cAc	5/16	0.220650220043603	0	FACETS	0.535	0.443	0.638			1	SUBCLONAL	1	FALSE	0	0.270055670791294	0		457	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0009142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	384	576	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.268701136381174	5	FACETS	0.929	0.882	0.976	0.619	0.588	0.651	INDETERMINATE	2	TRUE	2	0.641877519107392	5		579	1264	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0009142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	205	553	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.708	0.657	0.761	0.708	0.657	0.761	SUBCLONAL	1	TRUE	1	0.641877519107392	2		553	902	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0009142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	137	238	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.578452554738178	3	FACETS	1	0.978	1	0.6	0.549	0.652	CLONAL	1	TRUE	1	0.641877519107392	3		238	470	SUCCESS
APC	324	MSKCC	GRCh37	5	112155031	112155032	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0009142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	159	373	0	ENST00000257430.4:c.1307dup	p.Asn436LysfsTer8	p.N436Kfs*8	ENST00000257430	NM_000038.5	434	-/A	10/16	0.578452554738178	3	FACETS	0.76	0.697	0.826	0.38	0.348	0.413	SUBCLONAL	1	TRUE	1	0.641877519107392	3		373	861	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372752	81372752	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768451705	NA	P-0009142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	162	417	0	ENST00000222390.5:c.782G>A	p.Arg261His	p.R261H	ENST00000222390	NM_000601.4	261	cGc/cAc	7/18	0.60169043978366	4	FACETS	0.678	0.621	0.739	0.226	0.207	0.247	SUBCLONAL	1	TRUE	1	0.641877519107392	4		417	1222	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991306	41991306	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	298	794	0	ENST00000219905.7:c.2137G>C	p.Asp713His	p.D713H	ENST00000219905	NM_001164273.1	713	Gat/Cat	5/24	0.544342759018061	3	FACETS	0.808	0.759	0.859	0.269	0.253	0.287	CLONAL	1	TRUE	0	0.641877519107392	3		794	1518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579583	7579583	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0009142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	244	292	0	ENST00000269305.4:c.104T>A	p.Leu35Ter	p.L35*	ENST00000269305	NM_001126112.2	35	tTg/tAg	4/11	0.268701136381174	5	FACETS	0.963	0.903	1	0.642	0.602	0.683	INDETERMINATE	2	TRUE	2	0.641877519107392	5		292	775	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0009145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	314	467	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	NA	2	FACETS	0.98	0.932	1			1	INDETERMINATE	2	TRUE	NA	0.487020981313526	2		467	658	SUCCESS
APC	324	MSKCC	GRCh37	5	112175521	112175521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	135	467	0	ENST00000257430.4:c.4230C>A	p.Cys1410Ter	p.C1410*	ENST00000257430	NM_000038.5	1410	tgC/tgA	16/16	0.487020981313526	3	FACETS	1	0.911	1	0.5	0.455	0.547	CLONAL	1	TRUE	1	0.487020981313526	3		467	689	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687425	117687425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs539820527	NA	P-0009145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	94	459	0	ENST00000368508.3:c.2626G>A	p.Ala876Thr	p.A876T	ENST00000368508	NM_002944.2	876	Gca/Aca	18/43	0.487020981313526	3	FACETS	0.921	0.822	1	0.461	0.411	0.513	CLONAL	1	TRUE	1	0.487020981313526	3		459	521	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432033	49432033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1327	109	715	0	ENST00000301067.7:c.9106C>T	p.Pro3036Ser	p.P3036S	ENST00000301067	NM_003482.3	3036	Ccc/Tcc	34/54	0.438281977794297	4	FACETS	0.464	0.414	0.516	0.232	0.207	0.258	SUBCLONAL	1	TRUE	2	0.487020981313526	4		715	1436	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443478	49443478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs760144885	NA	P-0009145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	175	403	0	ENST00000301067.7:c.3893C>A	p.Ser1298Tyr	p.S1298Y	ENST00000301067	NM_003482.3	1298	tCc/tAc	11/54	0.438281977794297	4	FACETS	1	0.978	1	0.584	0.538	0.632	CLONAL	1	TRUE	2	0.487020981313526	4		403	915	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964099	28964099	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	141	626	1	ENST00000282397.4:c.1803C>A	p.His601Gln	p.H601Q	ENST00000282397	NM_002019.4	601	caC/caA	13/30	0.487020981313526	6	FACETS	1	0.947	1	0.265	0.24	0.29	CLONAL	1	TRUE	2	0.487020981313526	6		627	1079	SUCCESS
APC	324	MSKCC	GRCh37	5	112116534	112116534	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	173	597	0	ENST00000257430.4:c.580del	p.Arg194GlyfsTer11	p.R194Gfs*11	ENST00000257430	NM_000038.5	193	gcA/gc	6/16	0.487020981313526	3	FACETS	0.815	0.755	0.876	0.815	0.755	0.876	CLONAL	2	TRUE	1	0.487020981313526	3		597	542	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	240	429	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.887	0.83	0.945	0.887	0.83	0.945	CLONAL	1	TRUE	1	0.629332413921166	2		429	860	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	507	825	11	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	0.629332413921166	2		836	1460	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	428	779	1	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	NA	2	FACETS	1	0.956	1			1	INDETERMINATE	1	TRUE	NA	0.629332413921166	2		780	1355	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	159	480	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	1	2	FACETS	0.932	0.86	1	0.932	0.86	1	CLONAL	1	TRUE	1	0.629332413921166	2		480	542	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378266	225378266	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	255	724	0	ENST00000264414.4:c.629del	p.Leu210TrpfsTer16	p.L210Wfs*16	ENST00000264414	NM_003590.4	210	tTg/tg	5/16	1	2	FACETS	0.901	0.845	0.959	0.901	0.845	0.959	CLONAL	1	TRUE	1	0.629332413921166	2		724	899	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	54	661	1	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	1	2	FACETS	0.157	0.133	0.184	0.157	0.133	0.184	SUBCLONAL	1	TRUE	1	0.629332413921166	2		662	1091	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696691	176696691	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	227	658	0	ENST00000439151.2:c.5397del	p.Phe1799LeufsTer22	p.F1799Lfs*22	ENST00000439151	NM_022455.4	1798	Ttt/tt	16/23	1	2	FACETS	0.945	0.884	1	0.945	0.884	1	CLONAL	1	TRUE	1	0.629332413921166	2		658	763	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023904	27023904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1232964733	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	76	121	0	ENST00000324856.7:c.1015del	p.Ala339LeufsTer24	p.A339Lfs*24	ENST00000324856	NM_006015.4	337	tGg/tg	1/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.629332413921166	2		121	217	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294665	1294665	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	36	106	0	ENST00000310581.5:c.336del	p.Glu113ArgfsTer15	p.E113Rfs*15	ENST00000310581	NM_198253.2	112	ccC/cc	2/16	1	2	FACETS	0.5	0.414	0.594	0.5	0.414	0.594	SUBCLONAL	1	TRUE	1	0.629332413921166	2		106	229	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845901	156845901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769486223	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	464	908	0	ENST00000524377.1:c.1531G>A	p.Val511Met	p.V511M	ENST00000524377	NM_002529.3	511	Gtg/Atg	13/17	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.629332413921166	2		908	1318	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832688	3832688	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	301	558	0	ENST00000262367.5:c.1570del	p.Leu524TrpfsTer6	p.L524Wfs*6	ENST00000262367	NM_004380.2	524	Ctg/tg	6/31	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.629332413921166	2		558	854	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422384	47422384	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	355	373	0	ENST00000377045.4:c.23del	p.Pro8LeufsTer26	p.P8Lfs*26	ENST00000377045	NM_001654.4	6	ggC/gg	2/16	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.629332413921166	1		373	592	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944382	131944382	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs748536322	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	224	635	7	ENST00000265335.6:c.2801del	p.Asn934IlefsTer6	p.N934Ifs*6	ENST00000265335		932	Aaa/aa	17/25	1	2	FACETS	0.862	0.804	0.921	0.862	0.804	0.921	CLONAL	1	TRUE	1	0.629332413921166	2		642	826	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	167	491	1	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	0.616178309859873	3	FACETS	0.705	0.648	0.766	0.353	0.324	0.383	SUBCLONAL	1	TRUE	1	0.629332413921166	3		492	989	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794441	42794441	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	507	961	0	ENST00000575354.2:c.1526del	p.Pro509HisfsTer14	p.P509Hfs*14	ENST00000575354	NM_015125.3	507	cgC/cg	10/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.629332413921166	2		961	1603	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056425	26056427	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	rs774779034	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	160	324	0	ENST00000343677.2:c.230_232del	p.Asn77del	p.N77del	ENST00000343677	NM_005319.3	77	aACAgc/agc	1/1	1	2	FACETS	0.982	0.906	1	0.982	0.906	1	CLONAL	1	TRUE	1	0.629332413921166	2		324	518	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436599	49436599	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886041405	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	375	704	2	ENST00000301067.7:c.5707C>T	p.Arg1903Ter	p.R1903*	ENST00000301067	NM_003482.3	1903	Cga/Tga	26/54	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.629332413921166	2		706	1101	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	214	398	5	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.977	0.912	1	0.977	0.912	1	CLONAL	1	TRUE	1	0.629332413921166	2		403	696	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602281	10602281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	273	471	5	ENST00000171111.5:c.1297G>A	p.Gly433Ser	p.G433S	ENST00000171111	NM_203500.1	433	Ggc/Agc	3/6	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.629332413921166	2		476	842	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101117	27101117	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	359	725	0	ENST00000324856.7:c.4403del	p.Pro1468LeufsTer13	p.P1468Lfs*13	ENST00000324856	NM_006015.4	1467	Ccc/cc	18/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.629332413921166	2		725	1131	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337684	73337684	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771690280	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	304	627	5	ENST00000377767.4:c.2032del	p.Ile678PhefsTer59	p.I678Ffs*59	ENST00000377767	NM_014953.3	678	Att/tt	16/21	1	2	FACETS	0.973	0.918	1	0.973	0.918	1	CLONAL	1	TRUE	1	0.629332413921166	2		632	993	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100307	27100307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	381	734	1	ENST00000324856.7:c.4019G>A	p.Gly1340Asp	p.G1340D	ENST00000324856	NM_006015.4	1340	gGc/gAc	17/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.629332413921166	2		735	1193	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797926	45797926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782764	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	412	734	1	ENST00000450313.1:c.845C>T	p.Ala282Val	p.A282V	ENST00000450313	NM_012222.2	282	gCc/gTc	10/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.629332413921166	2		735	1267	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966231	25966231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781134057	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	363	665	1	ENST00000435504.4:c.2975C>T	p.Ala992Val	p.A992V	ENST00000435504		992	gCg/gTg	13/13	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.629332413921166	2		666	1014	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972669	25972669	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369844902	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	420	742	1	ENST00000435504.4:c.1756C>T	p.Arg586Cys	p.R586C	ENST00000435504		586	Cgt/Tgt	12/13	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.629332413921166	2		743	1258	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47600656	47600656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs538099447	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	371	855	0	ENST00000263735.4:c.131G>A	p.Arg44His	p.R44H	ENST00000263735	NM_002354.2	44	cGt/cAt	2/9	1	2	FACETS	0.948	0.899	0.997	0.948	0.899	0.997	CLONAL	1	TRUE	1	0.629332413921166	2		855	1244	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030612	48030612	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750617	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	415	905	0	ENST00000234420.5:c.3226C>T	p.Arg1076Cys	p.R1076C	ENST00000234420	NM_000179.2	1076	Cgc/Tgc	5/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.629332413921166	2		905	1303	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535336	66535336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1349494063	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	335	630	1	ENST00000273854.3:c.125C>T	p.Thr42Met	p.T42M	ENST00000273854	NM_004439.5	42	aCg/aTg	1/18	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.629332413921166	2		631	1017	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630165	187630165	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	269	450	0	ENST00000441802.2:c.817T>C	p.Tyr273His	p.Y273H	ENST00000441802	NM_005245.3	273	Tat/Cat	2/27	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.629332413921166	2		450	765	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111833	56111833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1482818434	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	11	20	0	ENST00000399503.3:c.433G>A	p.Glu145Lys	p.E145K	ENST00000399503	NM_005921.1	145	Gag/Aag	1/20	1	2	FACETS	0.794	0.598	0.991	1	0.896	1	CLONAL	2	TRUE	1	0.629332413921166	2		20	22	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012397	152012397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	239	616	0	ENST00000262189.6:c.416G>A	p.Cys139Tyr	p.C139Y	ENST00000262189	NM_170606.2	139	tGt/tAt	4/59	1	2	FACETS	0.974	0.912	1	0.974	0.912	1	CLONAL	1	TRUE	1	0.629332413921166	2		616	780	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38283760	38283760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554564353	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1209	319	547	0	ENST00000425967.3:c.718C>T	p.Arg240Cys	p.R240C	ENST00000425967	NM_001174067.1	240	Cgt/Tgt	7/19	0.629332413921166	4	FACETS	1	0.979	1	0.36	0.339	0.382	CLONAL	1	TRUE	1	0.629332413921166	4		547	1528	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971154	21971154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	71	110	0	ENST00000579755.1:c.247G>A	p.Gly83Arg	p.G83R	ENST00000579755		83	Gga/Aga	2/3	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.629332413921166	2		110	202	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537144	80537144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761634659	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	148	444	1	ENST00000286548.4:c.254C>T	p.Thr85Met	p.T85M	ENST00000286548	NM_002072.3	85	aCg/aTg	2/7	1	2	FACETS	0.956	0.879	1	0.956	0.879	1	CLONAL	1	TRUE	1	0.629332413921166	2		445	492	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396761	139396761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528703507	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	252	438	3	ENST00000277541.6:c.5347C>T	p.Arg1783Trp	p.R1783W	ENST00000277541	NM_017617.3	1783	Cgg/Tgg	28/34	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.629332413921166	2		441	792	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025901	1025901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768836719	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	481	858	0	ENST00000358495.3:c.629C>T	p.Pro210Leu	p.P210L	ENST00000358495	NM_134424.2	210	cCg/cTg	8/12	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.629332413921166	2		858	1436	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431178	49431178	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs793888512	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	326	597	3	ENST00000301067.7:c.9961C>T	p.Arg3321Ter	p.R3321*	ENST00000301067	NM_003482.3	3321	Cga/Tga	34/54	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.629332413921166	2		600	998	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218299	133218299	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777695766	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	362	626	1	ENST00000320574.5:c.5312C>T	p.Thr1771Met	p.T1771M	ENST00000320574	NM_006231.2	1771	aCg/aTg	39/49	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.629332413921166	2		627	1096	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610163	28610163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770571247	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	249	653	0	ENST00000241453.7:c.1327G>A	p.Ala443Thr	p.A443T	ENST00000241453	NM_004119.2	443	Gca/Aca	11/24	1	2	FACETS	0.915	0.857	0.974	0.915	0.857	0.974	CLONAL	1	TRUE	1	0.629332413921166	2		653	865	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472603	88472603	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	302	574	0	ENST00000360948.2:c.1952T>G	p.Leu651Arg	p.L651R	ENST00000360948	NM_001012338.2	651	cTg/cGg	16/19	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.629332413921166	2		574	906	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500390	99500390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143286842	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	91	725	0	ENST00000268035.6:c.3823C>T	p.Arg1275Trp	p.R1275W	ENST00000268035	NM_000875.3	1275	Cgg/Tgg	21/21	1	2	FACETS	0.243	0.215	0.273	0.243	0.215	0.273	SUBCLONAL	1	TRUE	1	0.629332413921166	2		725	1191	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	338194	338194	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	543	831	0	ENST00000262320.3:c.2517G>T	p.Glu839Asp	p.E839D	ENST00000262320	NM_003502.3	839	gaG/gaT	11/11	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.629332413921166	2		831	1490	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934800	9934800	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	381	916	0	ENST00000330684.3:c.1490T>G	p.Ile497Ser	p.I497S	ENST00000330684	NM_001134407.1	497	aTc/aGc	6/13	NA	2	FACETS	0.937	0.89	0.986			1	INDETERMINATE	1	TRUE	NA	0.629332413921166	2		916	1292	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993162	72993162	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778603718	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	632	1125	2	ENST00000268489.5:c.883C>T	p.Arg295Cys	p.R295C	ENST00000268489	NM_006885.3	295	Cgt/Tgt	2/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.629332413921166	2		1127	1828	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40364067	40364067	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	81	107	0	ENST00000293328.3:c.1615A>G	p.Asn539Asp	p.N539D	ENST00000293328	NM_012448.3	539	Aac/Gac	13/19	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.629332413921166	2		107	192	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435971	56435971	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780893183	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	173	332	0	ENST00000407977.2:c.1166G>A	p.Arg389His	p.R389H	ENST00000407977		389	cGc/cAc	9/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.629332413921166	2		332	489	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526085	66526085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	267	494	0	ENST00000358598.2:c.916C>T	p.Arg306Trp	p.R306W	ENST00000358598	NM_212471.2	306	Cgg/Tgg	10/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.629332413921166	2		494	801	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120245	70120245	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	470	867	0	ENST00000245479.2:c.1247A>C	p.Gln416Pro	p.Q416P	ENST00000245479	NM_000346.3	416	cAa/cCa	3/3	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.629332413921166	2		867	1342	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265583	10265583	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs865891586	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	291	566	0	ENST00000340748.4:c.1594G>A	p.Glu532Lys	p.E532K	ENST00000340748		532	Gag/Aag	19/40	1	2	FACETS	0.994	0.938	1	0.994	0.938	1	CLONAL	1	TRUE	1	0.629332413921166	2		566	930	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121091	11121091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555773256	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	378	733	0	ENST00000358026.2:c.2158G>A	p.Val720Met	p.V720M	ENST00000358026	NM_001128849.1	720	Gtg/Atg	15/36	1	2	FACETS	0.999	0.948	1	0.999	0.948	1	CLONAL	1	TRUE	1	0.629332413921166	2		733	1203	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627685	14627685	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	478	929	0	ENST00000254322.2:c.385G>A	p.Asp129Asn	p.D129N	ENST00000254322	NM_006145.1	129	Gac/Aac	2/3	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.629332413921166	2		929	1444	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281175	15281175	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	458	761	0	ENST00000263388.2:c.5081G>A	p.Arg1694Gln	p.R1694Q	ENST00000263388	NM_000435.2	1694	cGg/cAg	27/33	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.629332413921166	2		761	1278	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303224	15303224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753596637	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	359	671	1	ENST00000263388.2:c.304G>A	p.Ala102Thr	p.A102T	ENST00000263388	NM_000435.2	102	Gcc/Acc	3/33	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.629332413921166	2		672	1063	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909698	50909698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	503	820	0	ENST00000440232.2:c.1418C>T	p.Thr473Met	p.T473M	ENST00000440232	NM_002691.3	473	aCg/aTg	12/27	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.629332413921166	2		820	1480	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755585	39755585	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	351	612	1	ENST00000288319.7:c.1180G>A	p.Gly394Arg	p.G394R	ENST00000288319	NM_182918.3	394	Ggg/Agg	10/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.629332413921166	2		613	1018	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513259	44513259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	163	259	0	ENST00000291552.4:c.676C>T	p.Arg226Cys	p.R226C	ENST00000291552	NM_006758.2	226	Cgt/Tgt	8/8	1	2	FACETS	0.966	0.893	1	0.966	0.893	1	CLONAL	1	TRUE	1	0.629332413921166	2		259	536	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932255	39932255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1452619451	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	524	529	0	ENST00000378444.4:c.2344G>A	p.Asp782Asn	p.D782N	ENST00000378444	NM_001123385.1	782	Gac/Aac	4/15	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.629332413921166	1		529	842	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411480	63411480	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	469	507	0	ENST00000330258.3:c.1687A>G	p.Thr563Ala	p.T563A	ENST00000330258	NM_152424.3	563	Acc/Gcc	2/2	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.629332413921166	1		507	720	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76919038	76919038	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	313	269	1	ENST00000373344.5:c.3953del	p.Asn1318IlefsTer28	p.N1318Ifs*28	ENST00000373344	NM_000489.3	1318	aAt/at	12/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.629332413921166	1		270	528	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997825	149997826	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	76	534	0	ENST00000253339.5:c.2641dup	p.Asp881GlyfsTer40	p.D881Gfs*40	ENST00000253339		881	gat/gGat	5/7	1	2	FACETS	0.281	0.246	0.32	0.281	0.246	0.32	SUBCLONAL	1	TRUE	1	0.629332413921166	2		534	858	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657031	47657031	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1553356700	NA	P-0009152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	327	707	0	ENST00000233146.2:c.1229del	p.Gly410ValfsTer2	p.G410Vfs*2	ENST00000233146	NM_000251.2	409	caG/ca	7/16	1	2	FACETS	0.944	0.892	0.996	0.944	0.892	0.996	CLONAL	1	TRUE	1	0.629332413921166	2		707	1101	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057520007	NA	P-0009162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	299	477	0	ENST00000269305.4:c.614A>C	p.Tyr205Ser	p.Y205S	ENST00000269305	NM_001126112.2	205	tAt/tCt	6/11	0.259785912748095	2	FACETS	0.789	0.743	0.837	0.789	0.743	0.837	SUBCLONAL	2	TRUE	0	0.313147531381183	2		477	1210	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573782	41573782	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	153	450	0	ENST00000263253.7:c.6067C>T	p.Gln2023Ter	p.Q2023*	ENST00000263253	NM_001429.3	2023	Caa/Taa	31/31	0.313147531381183	1	FACETS	0.945	0.865	1	0.945	0.865	1	CLONAL	1	TRUE	0	0.313147531381183	1		450	872	SUCCESS
BTK	695	MSKCC	GRCh37	X	100625055	100625055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	76	451	2	ENST00000308731.7:c.322G>A	p.Glu108Lys	p.E108K	ENST00000308731	NM_000061.2	108	Gaa/Aaa	5/19	0.313147531381183	3	FACETS	0.685	0.599	0.777	0.342	0.299	0.389	SUBCLONAL	1	TRUE	1	0.313147531381183	3		453	820	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433879	78433879	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	111	392	0	ENST00000370768.2:c.220G>C	p.Asp74His	p.D74H	ENST00000370768	NM_003902.3	74	Gat/Cat	3/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.313147531381183	2		392	637	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258374	16258374	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	194	450	0	ENST00000375759.3:c.5639C>G	p.Ser1880Cys	p.S1880C	ENST00000375759	NM_015001.2	1880	tCt/tGt	11/15	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.313147531381183	2		450	1103	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247963	59247963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	173	380	0	ENST00000371222.2:c.780G>A	p.Met260Ile	p.M260I	ENST00000371222	NM_002228.3	260	atG/atA	1/1	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.313147531381183	2		380	1102	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699405	117699405	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0009162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	146	419	0	ENST00000369458.3:c.236T>A	p.Leu79Ter	p.L79*	ENST00000369458	NM_024626.3	79	tTg/tAg	3/6	1	2	FACETS	0.858	0.782	0.938	0.858	0.782	0.938	CLONAL	1	TRUE	1	0.313147531381183	2		419	1087	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919801	96919801	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs987656498	NA	P-0009162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	66	323	0	ENST00000258439.3:c.462C>G	p.Ile154Met	p.I154M	ENST00000258439	NM_001193304.2	154	atC/atG	4/4	0.259785912748095	2	FACETS	0.543	0.471	0.622	0.272	0.235	0.311	SUBCLONAL	1	TRUE	0	0.313147531381183	2		323	776	SUCCESS
EED	8726	MSKCC	GRCh37	11	85975233	85975233	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	54	347	0	ENST00000263360.6:c.654G>C	p.Trp218Cys	p.W218C	ENST00000263360	NM_003797.3	218	tgG/tgC	7/12	1	2	FACETS	0.589	0.502	0.683	0.589	0.502	0.683	SUBCLONAL	1	TRUE	1	0.313147531381183	2		347	586	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432359	49432359	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0009162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	121	410	0	ENST00000301067.7:c.8780C>G	p.Ser2927Ter	p.S2927*	ENST00000301067	NM_003482.3	2927	tCa/tGa	34/54	0.286585276711561	2	FACETS	0.759	0.685	0.838	0.38	0.342	0.419	SUBCLONAL	1	TRUE	0	0.313147531381183	2		410	1018	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618841	37618841	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	116	405	0	ENST00000447079.4:c.517G>T	p.Glu173Ter	p.E173*	ENST00000447079	NM_015083.1	173	Gaa/Taa	1/14	0.259785912748095	2	FACETS	0.847	0.762	0.936	0.423	0.381	0.468	CLONAL	1	TRUE	0	0.313147531381183	2		405	875	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726726	41726726	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	136	386	0	ENST00000301178.4:c.271G>C	p.Asp91His	p.D91H	ENST00000301178	NM_021913.4	91	Gat/Cat	2/20	0.297994297496716	2	FACETS	1	0.937	1	0.519	0.472	0.568	CLONAL	1	TRUE	0	0.313147531381183	2		386	837	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979322	40979322	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	102	314	0	ENST00000373198.4:c.1811A>T	p.Asp604Val	p.D604V	ENST00000373198	NM_133170.3	604	gAc/gTc	11/32	0.281571838097172	3	FACETS	0.858	0.767	0.956	0.429	0.383	0.478	CLONAL	1	TRUE	1	0.313147531381183	3		314	878	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21272519	21272519	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	140	407	0	ENST00000354336.3:c.297C>G	p.Ile99Met	p.I99M	ENST00000354336	NM_005207.3	99	atC/atG	1/3	0.313147531381183	1	FACETS	0.837	0.762	0.916	0.837	0.762	0.916	CLONAL	1	TRUE	0	0.313147531381183	1		407	901	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1206979	1206988	+	frameshift_variant	Frame_Shift_Del	DEL	GACACGTTCA	GACACGTTCA	-	novel	NA	P-0009162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	65	257	0	ENST00000326873.7:c.67_76del	p.Asp23SerfsTer25	p.D23Sfs*25	ENST00000326873	NM_000455.4	23	GACACGTTCAtc/tc	1/10	0.313147531381183	1	FACETS	0.782	0.68	0.891	0.782	0.68	0.891	SUBCLONAL	1	TRUE	0	0.313147531381183	1		257	448	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1206973	1206975	+	inframe_deletion	In_Frame_Del	DEL	GGT	GGT	-	novel	NA	P-0009162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	62	255	0	ENST00000326873.7:c.61_63del	p.Gly21del	p.G21del	ENST00000326873	NM_000455.4	21	GGT/-	1/10	0.313147531381183	1	FACETS	0.729	0.631	0.835	0.729	0.631	0.835	SUBCLONAL	1	TRUE	0	0.313147531381183	1		255	458	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	160	586	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	0.588912851882524	2		586	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0009169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	343	741	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.588912851882524	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.588912851882524	1		742	751	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440904	56440904	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1458799446	NA	P-0009169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	409	356	2	ENST00000407977.2:c.433C>T	p.Arg145Ter	p.R145*	ENST00000407977		145	Cga/Tga	4/10	0.588912851882524	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.588912851882524	1		358	866	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012465	29012465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373801409	NA	P-0009169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	159	288	0	ENST00000282397.4:c.406G>A	p.Val136Ile	p.V136I	ENST00000282397	NM_002019.4	136	Gta/Ata	4/30	0.534070896512322	3	FACETS	1	0.976	1	0.576	0.53	0.623	CLONAL	1	TRUE	1	0.588912851882524	3		288	607	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114917829	114917830	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0009169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	394	468	0	ENST00000543371.1:c.1318+2dup		p.X440_splice	ENST00000543371	NM_001198531.1	440			1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.588912851882524	2		468	1175	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398280	25398281	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0009179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	76	438	0	ENST00000311936.3:c.38_39delinsTT	p.Gly13Val	p.G13V	ENST00000311936	NM_004985.3	13	gGC/gTT	2/5	0.30594708101628	6	FACETS	0.972	0.851	1	0.243	0.212	0.276	CLONAL	1	TRUE	2	0.30594708101628	6		438	824	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667792	37667795	+	frameshift_variant	Frame_Shift_Del	DEL	ACAA	ACAA	-	novel	NA	P-0009179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	64	585	0	ENST00000447079.4:c.2682_2685del	p.Asn894LysfsTer14	p.N894Kfs*14	ENST00000447079	NM_015083.1	893	ACAAac/ac	8/14	1	2	FACETS	0.547	0.473	0.628	0.547	0.473	0.628	SUBCLONAL	1	TRUE	1	0.30594708101628	2		585	765	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0009185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	211	618	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.357931495574456	3	FACETS	0.788	0.733	0.845			1	SUBCLONAL	2	TRUE	NA	0.357931495574456	3		618	882	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587781702	NA	P-0009185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	224	429	1	ENST00000269305.4:c.920-1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.357931495574456	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	0	0.357931495574456	2		430	619	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508843	106508843	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	246	377	0	ENST00000359195.3:c.837G>T	p.Glu279Asp	p.E279D	ENST00000359195	NM_002649.2	279	gaG/gaT	2/11	0.308919797138483	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.357931495574456	4		377	860	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741886	17741886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1036774997	NA	P-0009185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	36	61	0	ENST00000250003.3:c.557C>T	p.Pro186Leu	p.P186L	ENST00000250003	NM_002478.4	186	cCg/cTg	1/3	0.357931495574456	3	FACETS	1	0.914	1	1	0.914	1	CLONAL	2	TRUE	1	0.357931495574456	3		61	105	SUCCESS
APC	324	MSKCC	GRCh37	5	112175283	112175284	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1114167544	NA	P-0009185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	172	400	0	ENST00000257430.4:c.3994dup	p.Thr1332AsnfsTer10	p.T1332Nfs*10	ENST00000257430	NM_000038.5	1331	aga/agAa	16/16	NA	2	FACETS	0.948	0.879	1			1	INDETERMINATE	2	TRUE	NA	0.357931495574456	2		400	507	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0009200-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	888	375	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.292587087003856	6	FACETS	0.909	0.886	0.932			1	INDETERMINATE	5	TRUE	NA	0.583470916393601	6		375	1451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0009200-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	628	791	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.583470916393601	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.583470916393601	2		792	1053	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022592	31022592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs373221034	NA	P-0009200-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	302	294	1	ENST00000375687.4:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000375687	NM_015338.5	693	Cga/Tga	13/13	1	2	FACETS	0.861	0.81	0.912	0.861	0.81	0.912	CLONAL	1	TRUE	1	0.583470916393601	2		295	1203	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098657	47098657	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1252670264	NA	P-0009200-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	290	289	0	ENST00000409792.3:c.6617C>T	p.Ala2206Val	p.A2206V	ENST00000409792	NM_014159.6	2206	gCt/gTt	15/21	1	2	FACETS	0.995	0.937	1	0.995	0.937	1	CLONAL	1	TRUE	1	0.583470916393601	2		289	999	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913343	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	267	1018	0	ENST00000269305.4:c.817C>A	p.Arg273Ser	p.R273S	ENST00000269305	NM_001126112.2	273	Cgt/Agt	8/11	0.249525316368845	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.25	2		1018	1052	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524321	176524321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777207919	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	104	764	0	ENST00000292408.4:c.2182G>A	p.Ala728Thr	p.A728T	ENST00000292408	NM_213647.1	728	Gca/Aca	17/18	0.246813375161169	2	FACETS	1	0.936	1	0.532	0.476	0.591	CLONAL	1	TRUE	0	0.25	2		764	782	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226564873	226564873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	207	945	1	ENST00000366794.5:c.1877G>T	p.Trp626Leu	p.W626L	ENST00000366794	NM_001618.3	626	tGg/tTg	13/23	0.246391729084993	4	FACETS	0.898	0.832	0.966	0.898	0.832	0.966	CLONAL	2	TRUE	2	0.25	4		946	1153	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47672693	47672693	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	172	766	0	ENST00000233146.2:c.1283A>T	p.His428Leu	p.H428L	ENST00000233146	NM_000251.2	428	cAc/cTc	8/16	0.246771236153903	3	FACETS	0.911	0.839	0.986	0.911	0.839	0.986	CLONAL	2	TRUE	1	0.25	3		766	850	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288604	198288604	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	98	1051	0	ENST00000335508.6:c.123G>T	p.Gln41His	p.Q41H	ENST00000335508	NM_012433.2	41	caG/caT	2/25	0.246771236153903	3	FACETS	0.762	0.678	0.853	0.381	0.339	0.427	SUBCLONAL	1	TRUE	1	0.25	3		1051	1157	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014208	70014208	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1595	407	1301	0	ENST00000394351.3:c.1069G>T	p.Gly357Trp	p.G357W	ENST00000394351	NM_000248.3	357	Ggg/Tgg	9/9	0.214032199384487	4	FACETS	1	0.961	1			1	CLONAL	2	TRUE	NA	0.25	4		1301	2002	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156957	89156957	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	204	728	1	ENST00000336596.2:c.59G>T	p.Gly20Val	p.G20V	ENST00000336596	NM_005233.5	20	gGg/gTg	1/17	0.214032199384487	4	FACETS	1	0.974	1			1	CLONAL	2	TRUE	NA	0.25	4		729	923	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204941	128204941	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	203	966	0	ENST00000341105.2:c.500G>C	p.Gly167Ala	p.G167A	ENST00000341105	NM_032638.4	167	gGc/gCc	3/6	0.246771236153903	3	FACETS	0.966	0.896	1	0.966	0.896	1	CLONAL	2	TRUE	1	0.25	3		966	946	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664718	138664718	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	39	152	0	ENST00000330315.3:c.847G>T	p.Ala283Ser	p.A283S	ENST00000330315	NM_023067.3	283	Gca/Tca	1/1	0.246771236153903	3	FACETS	0.975	0.819	1	0.975	0.819	1	CLONAL	2	TRUE	1	0.25	3		152	180	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99823049	99823049	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	84	649	0	ENST00000280892.6:c.163A>G	p.Ile55Val	p.I55V	ENST00000280892	NM_001130678.1	55	Att/Gtt	2/7	0.246771236153903	3	FACETS	1	0.926	1	0.532	0.47	0.599	CLONAL	1	TRUE	1	0.25	3		649	710	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081621	143081621	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	79	742	0	ENST00000262992.4:c.1453C>A	p.Pro485Thr	p.P485T	ENST00000262992	NM_001101669.1	485	Cca/Aca	15/24	0.246771236153903	3	FACETS	0.793	0.696	0.897	0.396	0.348	0.449	SUBCLONAL	1	TRUE	1	0.25	3		742	897	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236597	236597	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	75	263	0	ENST00000264932.6:c.1315G>T	p.Gly439Trp	p.G439W	ENST00000264932	NM_004168.2	439	Ggg/Tgg	10/15	0.300789548318359	7	FACETS	0.962	0.845	1	0.385	0.338	0.435	CLONAL	2	TRUE	2	0.25	7		263	507	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38964909	38964909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	91	468	0	ENST00000357387.3:c.1385C>T	p.Pro462Leu	p.P462L	ENST00000357387	NM_152756.3	462	cCc/cTc	16/38	0.300789548318359	10	FACETS	1	0.974	1			1	CLONAL	1	TRUE	NA	0.25	10		468	1064	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520545	176520545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770012793	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	88	626	0	ENST00000292408.4:c.1390C>T	p.Arg464Trp	p.R464W	ENST00000292408	NM_213647.1	464	Cgg/Tgg	10/18	0.246813375161169	2	FACETS	1	0.953	1	0.571	0.506	0.639	CLONAL	1	TRUE	0	0.25	2		626	617	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395873	395873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	114	877	0	ENST00000380956.4:c.430C>A	p.Pro144Thr	p.P144T	ENST00000380956	NM_001195286.1	144	Ccg/Acg	4/9	0.268290281710994	3	FACETS	0.912	0.819	1	0.456	0.409	0.506	CLONAL	1	TRUE	1	0.25	3		877	1125	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395895	395895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	120	837	0	ENST00000380956.4:c.452C>T	p.Pro151Leu	p.P151L	ENST00000380956	NM_001195286.1	151	cCc/cTc	4/9	0.268290281710994	3	FACETS	1	0.927	1	0.517	0.466	0.571	CLONAL	1	TRUE	1	0.25	3		837	1045	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163564	32163564	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	171	626	1	ENST00000375023.3:c.5662G>T	p.Ala1888Ser	p.A1888S	ENST00000375023	NM_004557.3	1888	Gcg/Tcg	30/30	0.268290281710994	3	FACETS	0.964	0.888	1	0.964	0.888	1	CLONAL	2	TRUE	1	0.25	3		627	798	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652242	36652242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753529000	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	88	545	0	ENST00000244741.5:c.364C>T	p.Arg122Cys	p.R122C	ENST00000244741	NM_000389.4	122	Cgc/Tgc	2/3	0.268290281710994	3	FACETS	1	0.94	1	0.548	0.485	0.615	CLONAL	1	TRUE	1	0.25	3		545	723	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969075	93969075	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs992785889	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	81	873	0	ENST00000369303.4:c.1921G>T	p.Ala641Ser	p.A641S	ENST00000369303	NM_004440.3	641	Gca/Tca	10/17	0.268290281710994	3	FACETS	0.767	0.674	0.867	0.383	0.337	0.434	SUBCLONAL	1	TRUE	1	0.25	3		873	951	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222598	157222598	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	181	677	2	ENST00000346085.5:c.1865A>G	p.His622Arg	p.H622R	ENST00000346085	NM_020732.3	622	cAc/cGc	4/20	0.246391729084993	4	FACETS	0.892	0.822	0.964	0.892	0.822	0.964	CLONAL	2	TRUE	2	0.25	4		679	1015	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984013	2984013	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	351	960	0	ENST00000396946.4:c.517C>A	p.Leu173Met	p.L173M	ENST00000396946	NM_032415.4	173	Ctg/Atg	5/25	0.300789548318359	5	FACETS	0.911	0.862	0.962	1	0.994	1	CLONAL	3	TRUE	3	0.25	5		960	1412	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504324	8504324	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	270	742	1	ENST00000356435.5:c.1759G>T	p.Ala587Ser	p.A587S	ENST00000356435		587	Gca/Tca	12/35	0.205269134502336	5	FACETS	1	0.943	1	1	0.943	1	CLONAL	3	TRUE	2	0.25	5		743	986	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457799	69457799	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	155	600	0	ENST00000227507.2:c.199G>C	p.Val67Leu	p.V67L	ENST00000227507	NM_053056.2	67	Gtc/Ctc	2/5	0.226049000657746	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	2	0.25	4		600	687	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999641	100999641	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1225	285	1275	0	ENST00000325455.5:c.161C>T	p.Ser54Phe	p.S54F	ENST00000325455	NM_001202474.3	54	tCc/tTc	1/8	0.226049000657746	4	FACETS	0.944	0.885	1	0.944	0.885	1	CLONAL	2	TRUE	2	0.25	4		1275	1510	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110005	115110005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs773785943	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	68	534	2	ENST00000257566.3:c.1873C>A	p.Arg625Ser	p.R625S	ENST00000257566	NM_016569.3	625	Cgc/Agc	8/8	0.300789548318359	3	FACETS	0.937	0.815	1	0.469	0.407	0.535	CLONAL	1	TRUE	1	0.25	3		536	653	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913387	28913387	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	98	939	0	ENST00000282397.4:c.2406T>A	p.Asp802Glu	p.D802E	ENST00000282397	NM_002019.4	802	gaT/gaA	17/30	1	2	FACETS	0.89	0.793	0.993	0.89	0.793	0.993	CLONAL	1	TRUE	1	0.25	2		939	881	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019548	42019548	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	263	1185	1	ENST00000219905.7:c.3601A>T	p.Lys1201Ter	p.K1201*	ENST00000219905	NM_001164273.1	1201	Aaa/Taa	10/24	0.246813375161169	2	FACETS	0.977	0.916	1	0.977	0.916	1	CLONAL	2	TRUE	0	0.25	2		1186	1077	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169040	11169040	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	216	658	0	ENST00000358026.2:c.4629+1G>T		p.X1543_splice	ENST00000358026	NM_001128849.1	1543			0.249525316368845	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.25	2		658	787	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624818	9624818	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	159	560	0	ENST00000353224.5:c.159G>T	p.Met53Ile	p.M53I	ENST00000353224	NM_177990.2	53	atG/atT	3/10	0.163214338256863	3	FACETS	0.997	0.916	1			1	CLONAL	2	TRUE	NA	0.25	3		560	718	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624833	9624833	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	200	640	1	ENST00000353224.5:c.144C>A	p.Asn48Lys	p.N48K	ENST00000353224	NM_177990.2	48	aaC/aaA	3/10	0.163214338256863	3	FACETS	1	0.967	1			1	CLONAL	2	TRUE	NA	0.25	3		641	841	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408891	41408891	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs547641233	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	294	819	0	ENST00000373198.4:c.535G>T	p.Val179Leu	p.V179L	ENST00000373198	NM_133170.3	179	Gtg/Ttg	4/32	0.300789548318359	3	FACETS	0.857	0.807	0.908	1	0.991	1	CLONAL	3	TRUE	1	0.25	3		819	1029	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231106	53231106	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	299	457	0	ENST00000375401.3:c.1796G>T	p.Arg599Leu	p.R599L	ENST00000375401	NM_004187.3	599	cGt/cTt	13/26	0.214032199384487	2	FACETS	1	0.988	1			1	CLONAL	3	TRUE	NA	0.25	2		457	698	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468028	50468029	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	107	538	0	ENST00000331340.3:c.1268_1269del	p.Arg423GlnfsTer65	p.R423Qfs*65	ENST00000331340	NM_006060.4	421	caCGcg/cacg	8/8	0.205269134502336	5	FACETS	1	0.98	1	0.476	0.427	0.529	CLONAL	1	TRUE	2	0.25	5		538	824	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725058	162725058	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	64	615	0	ENST00000367921.3:c.530del	p.Cys177LeufsTer2	p.C177Lfs*2	ENST00000367921	NM_006182.2	177	tGt/tt	6/18	0.268290281710994	3	FACETS	0.778	0.673	0.893	0.389	0.336	0.447	SUBCLONAL	1	TRUE	1	0.25	3		615	740	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845852	151845852	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	258	650	0	ENST00000262189.6:c.13160del	p.Gly4387AlafsTer26	p.G4387Afs*26	ENST00000262189	NM_170606.2	4387	gGc/gc	52/59	0.300789548318359	5	FACETS	0.968	0.908	1	0.726	0.681	0.773	CLONAL	3	TRUE	1	0.25	5		650	977	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652872	212652873	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	123	567	0	ENST00000342788.4:c.433_434delinsAT	p.Gly145Ile	p.G145I	ENST00000342788	NM_005235.2	145	GGt/ATt	4/28	0.246771236153903	3	FACETS	0.891	0.808	0.979	0.891	0.808	0.979	CLONAL	2	TRUE	1	0.25	3		567	621	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106182927	106182928	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0009223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	151	763	0	ENST00000380013.4:c.3966_3967delinsTT	p.Glu1323Ter	p.E1323*	ENST00000380013	NM_001127208.2	1322	ctGGag/ctTTag	8/11	0.246771236153903	3	FACETS	0.802	0.734	0.874	0.802	0.734	0.874	CLONAL	2	TRUE	1	0.25	3		763	847	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0009243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	354	447	1	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	0.753013227812452	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.756426773349854	2		448	448	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851850	134851850	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371710725	NA	P-0009243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	206	340	0	ENST00000398015.3:c.1256C>T	p.Pro419Leu	p.P419L	ENST00000398015	NM_004441.4	419	cCc/cTc	5/16	0.756426773349854	4	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	2	0.756426773349854	4		340	475	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985489	2985489	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	251	508	0	ENST00000396946.4:c.322G>A	p.Gly108Arg	p.G108R	ENST00000396946	NM_032415.4	108	Ggg/Agg	4/25	0.756426773349854	4	FACETS	0.894	0.842	0.947	0.894	0.842	0.947	CLONAL	2	TRUE	2	0.756426773349854	4		508	652	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273000	55273000	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	246	365	0	ENST00000275493.2:c.3323C>G	p.Pro1108Arg	p.P1108R	ENST00000275493	NM_005228.3	1108	cCt/cGt	28/28	0.756426773349854	4	FACETS	0.917	0.863	0.971	0.917	0.863	0.971	CLONAL	2	TRUE	2	0.756426773349854	4		365	623	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341806	8341806	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	247	485	0	ENST00000356435.5:c.4834G>C	p.Ala1612Pro	p.A1612P	ENST00000356435		1612	Gca/Cca	29/35	0.753159111026612	4	FACETS	0.885	0.833	0.938	0.443	0.416	0.469	CLONAL	2	TRUE	0	0.756426773349854	4		485	648	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486288	8486288	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	191	234	0	ENST00000356435.5:c.2529G>T	p.Trp843Cys	p.W843C	ENST00000356435		843	tgG/tgT	17/35	0.753159111026612	4	FACETS	0.983	0.92	1	0.492	0.46	0.524	CLONAL	2	TRUE	0	0.756426773349854	4		234	451	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741946	17741946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	28	66	0	ENST00000250003.3:c.617G>T	p.Cys206Phe	p.C206F	ENST00000250003	NM_002478.4	206	tGc/tTc	1/3	0.756426773349854	3	FACETS	0.843	0.686	1	0.422	0.343	0.508	CLONAL	1	TRUE	1	0.756426773349854	3		66	121	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245582	46245582	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	242	291	0	ENST00000334344.6:c.3676G>T	p.Gly1226Ter	p.G1226*	ENST00000334344	NM_152641.2	1226	Gga/Tga	15/21	0.499363727346613	5	FACETS	1	0.97	1	0.7	0.658	0.743	CLONAL	2	TRUE	2	0.756426773349854	5		291	650	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004236	29004236	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	343	430	0	ENST00000282397.4:c.1057T>C	p.Tyr353His	p.Y353H	ENST00000282397	NM_002019.4	353	Tac/Cac	8/30	0.755247636353362	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.756426773349854	2		430	434	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866710	37866710	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	287	377	0	ENST00000269571.5:c.877G>C	p.Ala293Pro	p.A293P	ENST00000269571		293	Gcc/Ccc	7/27	0.756426773349854	4	FACETS	0.987	0.935	1	0.987	0.935	1	CLONAL	2	TRUE	2	0.756426773349854	4		377	675	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012741	36012741	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1417751781	NA	P-0009243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	72	124	1	ENST00000358208.4:c.185A>T	p.Lys62Met	p.K62M	ENST00000358208		62	aAg/aTg	2/12	0.693436686279781	4	FACETS	0.972	0.87	1	0.972	0.87	1	CLONAL	2	TRUE	2	0.756426773349854	4		125	172	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568558	41568558	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	182	412	0	ENST00000263253.7:c.4508A>G	p.Tyr1503Cys	p.Y1503C	ENST00000263253	NM_001429.3	1503	tAt/tGt	28/31	0.67004939068845	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.756426773349854	1		412	299	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916468	39916468	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	390	502	0	ENST00000378444.4:c.4535T>C	p.Ile1512Thr	p.I1512T	ENST00000378444	NM_001123385.1	1512	aTt/aCt	11/15	0.756426773349854	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.756426773349854	2		502	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0009266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	362	536	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.315212785434485	5	FACETS	1	0.989	1	0.77	0.729	0.811	CLONAL	2	TRUE	2	0.373674919706164	5		536	1309	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460516	149460516	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	254	364	1	ENST00000286301.3:c.121C>T	p.Arg41Ter	p.R41*	ENST00000286301	NM_005211.3	41	Cga/Tga	3/22	0.369500472441153	2	FACETS	0.984	0.926	1	0.984	0.926	1	CLONAL	2	TRUE	0	0.373674919706164	2		365	691	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509973	187509973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	332	366	0	ENST00000441802.2:c.13540G>C	p.Glu4514Gln	p.E4514Q	ENST00000441802	NM_005245.3	4514	Gaa/Caa	27/27	0.373674919706164	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	0	0.373674919706164	3		366	666	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424521	49424521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	241	350	0	ENST00000301067.7:c.13702G>A	p.Ala4568Thr	p.A4568T	ENST00000301067	NM_003482.3	4568	Gct/Act	41/54	0.373674919706164	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.373674919706164	3		350	737	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992321	72992321	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	220	745	0	ENST00000268489.5:c.1724A>C	p.Glu575Ala	p.E575A	ENST00000268489	NM_006885.3	575	gAg/gCg	2/10	0.369500472441153	2	FACETS	1	0.957	1	0.52	0.483	0.558	CLONAL	1	TRUE	0	0.373674919706164	2		745	1133	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578262	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs483352697	NA	P-0009266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	290	453	0	ENST00000269305.4:c.587G>C	p.Arg196Pro	p.R196P	ENST00000269305	NM_001126112.2	196	cGa/cCa	6/11	0.315212785434485	5	FACETS	1	0.985	1	0.757	0.713	0.803	CLONAL	2	TRUE	2	0.373674919706164	5		453	1066	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045149	47045149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	288	225	0	ENST00000377604.3:c.2390C>T	p.Ser797Leu	p.S797L	ENST00000377604	NM_001204468.1	797	tCa/tTa	21/24	0.30629542241723	2	FACETS	0.892	0.848	0.936			1	CLONAL	3	TRUE	NA	0.373674919706164	2		225	576	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0009296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	23	432	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.984	0.77	1	0.984	0.77	1	CLONAL	1	TRUE	1	0.19	2		432	246	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910549	29910549	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45585732	NA	P-0009296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	37	139	3	ENST00000376809.5:c.89G>A	p.Arg30Lys	p.R30K	ENST00000376809	NM_002116.7	30	aGg/aAg	2/8	0.209048069746332	3	FACETS	1	0.896	1	1	0.896	1	CLONAL	2	TRUE	1	0.19	3		142	193	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0009304-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	71	406	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.788	0.687	0.897	0.788	0.687	0.897	SUBCLONAL	1	TRUE	1	0.247996085954515	2		406	727	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0009304-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	84	381	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.247996085954515	2		382	560	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039570	180039570	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1185976621	NA	P-0009304-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1298	159	395	0	ENST00000261937.6:c.3473C>T	p.Ala1158Val	p.A1158V	ENST00000261937	NM_182925.4	1158	gCg/gTg	26/30	1	2	FACETS	0.88	0.804	0.96	0.88	0.804	0.96	CLONAL	1	TRUE	1	0.247996085954515	2		395	1457	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061517	38061517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771653601	NA	P-0009304-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	73	109	0	ENST00000250448.2:c.472G>A	p.Asp158Asn	p.D158N	ENST00000250448	NM_004496.3	158	Gac/Aac	2/2	0.247996085954515	1	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	0	0.247996085954515	1		109	505	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857736	9857736	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009304-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1214	164	312	0	ENST00000330684.3:c.3665C>A	p.Pro1222His	p.P1222H	ENST00000330684	NM_001134407.1	1222	cCc/cAc	13/13	1	2	FACETS	0.96	0.879	1	0.96	0.879	1	CLONAL	1	TRUE	1	0.247996085954515	2		312	1378	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690822	89690822	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009304-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	20	151	1	ENST00000371953.3:c.229del	p.Asp77ThrfsTer22	p.D77Tfs*22	ENST00000371953	NM_000314.4	77	Gac/ac	4/9	0.247996085954515	1	FACETS	0.359	0.273	0.459	0.359	0.273	0.459	SUBCLONAL	1	TRUE	0	0.247996085954515	1		152	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0009307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	163	576	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.196203696024304	2	FACETS	0.78	0.716	0.847	0.78	0.716	0.847	SUBCLONAL	2	TRUE	0	0.237808642415146	2		579	879	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625219	69625219	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	70	500	0	ENST00000334134.2:c.574C>T	p.Arg192Trp	p.R192W	ENST00000334134	NM_005247.2	192	Cgg/Tgg	3/3	0.211602535666768	3	FACETS	0.595	0.517	0.68	0.298	0.258	0.34	SUBCLONAL	1	TRUE	1	0.237808642415146	3		500	1107	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	144	586	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.496077263636215	3	FACETS	0.86	0.802	0.918	0.86	0.802	0.918	CLONAL	3	TRUE	0	0.528527859431337	3		586	267	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	315	243	0	ENST00000269305.4:c.383del	p.Pro128LeufsTer42	p.P128Lfs*42	ENST00000269305	NM_001126112.2	128	cCt/ct	5/11	NA	2	FACETS	0.954	0.909	0.999			1	INDETERMINATE	2	TRUE	NA	0.528527859431337	2		243	625	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971003	21971003	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	524	236	0	ENST00000304494.5:c.355G>T	p.Glu119Ter	p.E119*	ENST00000304494	NM_000077.4	119	Gag/Tag	2/3	0.429709653761129	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.528527859431337	2		236	975	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128016961	128016961	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	78	459	1	ENST00000285398.2:c.2128C>T	p.Gln710Ter	p.Q710*	ENST00000285398	NM_000122.1	710	Cag/Tag	14/15	1	2	FACETS	0.362	0.317	0.41	0.362	0.317	0.41	SUBCLONAL	1	TRUE	1	0.528527859431337	2		460	815	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921364	178921364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	77	339	0	ENST00000263967.3:c.846G>A	p.Met282Ile	p.M282I	ENST00000263967	NM_006218.2	282	atG/atA	5/21	0.216814304113732	2	FACETS	0.578	0.509	0.652	0.289	0.254	0.326	INDETERMINATE	1	TRUE	0	0.528527859431337	2		339	504	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922760	44922760	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	116	405	0	ENST00000377967.4:c.1621C>T	p.Gln541Ter	p.Q541*	ENST00000377967	NM_021140.2	541	Cag/Tag	16/29	0.396418412374809	1	FACETS	0.866	0.788	0.946	0.866	0.788	0.946	CLONAL	1	TRUE	0	0.528527859431337	1		405	373	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197306	26197306	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	807	841	3	ENST00000356476.2:c.173C>T	p.Ser58Leu	p.S58L	ENST00000356476		58	tCg/tTg	1/1	0.775681026880198	1	FACETS	0.963	0.937	0.988	0.963	0.937	0.988	CLONAL	1	TRUE	0	0.775681026880198	1		844	1323	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074254	30074254	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	391	388	0	ENST00000338641.4:c.1516T>G	p.Ser506Ala	p.S506A	ENST00000338641	NM_000268.3	506	Tct/Gct	14/16	1	2	FACETS	0.768	0.729	0.807	0.768	0.729	0.807	SUBCLONAL	1	TRUE	1	0.775681026880198	2		388	1313	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0009330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	76	308	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.20224204121071	2		308	736	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0009330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	96	387	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.20224204121071	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.20224204121071	1		387	808	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118683	115118683	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0009330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	124	441	0	ENST00000257566.3:c.657+1G>T		p.X219_splice	ENST00000257566	NM_016569.3	219			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.20224204121071	2		441	1005	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424198	47424198	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1410667957	NA	P-0009330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	117	543	0	ENST00000377045.4:c.203G>A	p.Arg68Gln	p.R68Q	ENST00000377045	NM_001654.4	68	cGa/cAa	4/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.20224204121071	2		543	926	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255586	16255586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1412039011	NA	P-0009347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	241	424	0	ENST00000375759.3:c.2851G>A	p.Val951Met	p.V951M	ENST00000375759	NM_015001.2	951	Gtg/Atg	11/15	0.156475305188054	4	FACETS	1	0.99	1	0.688	0.641	0.737	INDETERMINATE	1	TRUE	2	0.344605837088962	4		424	1366	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966612	25966612	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	265	307	0	ENST00000435504.4:c.2594T>A	p.Ile865Lys	p.I865K	ENST00000435504		865	aTa/aAa	13/13	0.339945209030615	3	FACETS	0.868	0.814	0.923	0.868	0.814	0.923	CLONAL	2	TRUE	1	0.344605837088962	3		307	1039	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441974	52441974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	293	337	0	ENST00000460680.1:c.375G>T	p.Glu125Asp	p.E125D	ENST00000460680	NM_004656.3	125	gaG/gaT	5/17	0.219711869086499	3	FACETS	1	0.961	1	0.684	0.644	0.724	CLONAL	2	TRUE	0	0.344605837088962	3		337	972	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405120	139405120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763217096	NA	P-0009347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	187	465	0	ENST00000277541.6:c.2725G>A	p.Asp909Asn	p.D909N	ENST00000277541	NM_017617.3	909	Gac/Aac	17/34	0.174566462100689	3	FACETS	1	0.979	1	0.389	0.358	0.42	INDETERMINATE	1	TRUE	0	0.344605837088962	3		465	1091	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851957	63851957	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	49	203	0	ENST00000279873.7:c.2735A>G	p.Lys912Arg	p.K912R	ENST00000279873	NM_032199.2	912	aAg/aGg	10/10	0.344605837088962	3	FACETS	0.416	0.351	0.487	0.208	0.175	0.244	SUBCLONAL	1	TRUE	1	0.344605837088962	3		203	802	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258526	19258526	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1252	488	590	0	ENST00000162023.5:c.374T>C	p.Leu125Ser	p.L125S	ENST00000162023		125	tTg/tCg	8/13	0.174566462100689	3	FACETS	0.954	0.911	0.998	0.636	0.607	0.666	INDETERMINATE	2	TRUE	0	0.344605837088962	3		590	1740	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023789	31023789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771806916	NA	P-0009347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	419	359	0	ENST00000375687.4:c.3274G>A	p.Val1092Met	p.V1092M	ENST00000375687	NM_015338.5	1092	Gtg/Atg	13/13	0.310955757271425	4	FACETS	0.85	0.809	0.89	0.85	0.809	0.89	CLONAL	3	TRUE	1	0.344605837088962	4		359	1283	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064351	30064351	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1736	121	510	0	ENST00000338641.4:c.915T>A	p.Asp305Glu	p.D305E	ENST00000338641	NM_000268.3	305	gaT/gaA	10/16	0.156475305188054	4	FACETS	0.508	0.457	0.563	0.254	0.228	0.282	INDETERMINATE	1	TRUE	2	0.344605837088962	4		510	1857	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183804	10183804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1559426047	NA	P-0009347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	166	239	0	ENST00000256474.2:c.273del	p.Phe91LeufsTer68	p.F91Lfs*68	ENST00000256474	NM_000551.3	91	ttC/tt	1/3	0.219711869086499	3	FACETS	1	0.949	1	0.69	0.637	0.743	CLONAL	2	TRUE	0	0.344605837088962	3		239	546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578285	7578296	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGACCTAAGAG	CAGACCTAAGAG	-	novel	NA	P-0009347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	283	440	1	ENST00000269305.4:c.560-7_564del		p.X187_splice	ENST00000269305	NM_001126112.2	187		6/11	0.344605837088962	3	FACETS	0.817	0.768	0.868	0.817	0.768	0.868	CLONAL	2	TRUE	1	0.344605837088962	3		441	1178	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	449	261	0	ENST00000397752.3:c.3028G>C	p.Asp1010His	p.D1010H	ENST00000397752	NM_000245.2	1010	Gat/Cat	14/21	0.3	6	FACETS	1	0.989	1			1	CLONAL	5	TRUE	NA	0.22	6		261	1074	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435732	116435732	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1318	71	355	0	ENST00000397752.3:c.3822G>T	p.Trp1274Cys	p.W1274C	ENST00000397752	NM_000245.2	1274	tgG/tgT	20/21	0.3	6	FACETS	0.669	0.581	0.765			1	SUBCLONAL	1	TRUE	NA	0.22	6		355	1389	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626631	100626631	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1278	94	661	0	ENST00000308731.7:c.299A>T	p.Tyr100Phe	p.Y100F	ENST00000308731	NM_000061.2	100	tAt/tTt	4/19	1	2	FACETS	0.623	0.552	0.699	0.623	0.552	0.699	SUBCLONAL	1	TRUE	1	0.22	2		661	1372	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045872	47045873	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	TT	novel	NA	P-0009350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	70	481	0	ENST00000377604.3:c.2668-1_2668delinsTT		p.X890_splice	ENST00000377604	NM_001204468.1	890		24/24	1	2	FACETS	0.635	0.552	0.725	0.635	0.552	0.725	SUBCLONAL	1	TRUE	1	0.22	2		481	1002	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0009357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	30	406	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.398012464822063	3	FACETS	0.218	0.174	0.267	0.073	0.058	0.089	SUBCLONAL	1	TRUE	0	0.405555114768724	3		406	818	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0009357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	267	399	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.300390178093253	3	FACETS	1	0.991	1	0.66	0.618	0.703	CLONAL	1	TRUE	1	0.405555114768724	3		399	1200	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0009357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1359	402	619	0	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.294796994360083	4	FACETS	0.791	0.75	0.833	0.791	0.75	0.833	SUBCLONAL	2	TRUE	2	0.405555114768724	4		619	1761	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0009357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	320	461	2	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	NA	2	FACETS	0.884	0.837	0.931			1	INDETERMINATE	2	TRUE	NA	0.405555114768724	2		463	893	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987260	2987260	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	94	315	0	ENST00000396946.4:c.169G>A	p.Glu57Lys	p.E57K	ENST00000396946	NM_032415.4	57	Gaa/Aaa	3/25	0.294796994360083	4	FACETS	0.725	0.644	0.811	0.362	0.322	0.406	SUBCLONAL	1	TRUE	2	0.405555114768724	4		315	899	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0009364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	666	406	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.483197099684767	6	FACETS	0.969	0.937	1	0.969	0.937	1	CLONAL	4	TRUE	2	0.483197099684767	6		406	1398	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252994	36252995	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0009364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	112	200	0	ENST00000300305.3:c.367dup	p.Asp123GlyfsTer15	p.D123Gfs*15	ENST00000300305		123	gat/gGat	4/8	1	2	FACETS	0.958	0.866	1	0.958	0.866	1	CLONAL	1	TRUE	1	0.483197099684767	2		200	484	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163720	32163720	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	90	141	0	ENST00000375023.3:c.5506G>C	p.Glu1836Gln	p.E1836Q	ENST00000375023	NM_004557.3	1836	Gag/Cag	30/30	0.483197099684767	3	FACETS	0.797	0.709	0.892	0.399	0.354	0.446	SUBCLONAL	1	TRUE	1	0.483197099684767	3		141	580	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522551	176522551	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774571806	NA	P-0009364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	150	326	0	ENST00000292408.4:c.1648G>A	p.Val550Met	p.V550M	ENST00000292408	NM_213647.1	550	Gtg/Atg	13/18	1	2	FACETS	0.914	0.838	0.994	0.914	0.838	0.994	CLONAL	1	TRUE	1	0.483197099684767	2		326	679	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911266	29911266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41562120	NA	P-0009364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	67	79	0	ENST00000376809.5:c.565G>A	p.Val189Met	p.V189M	ENST00000376809	NM_002116.7	189	Gtg/Atg	3/8	0.483197099684767	3	FACETS	0.804	0.71	0.903	0.804	0.71	0.903	CLONAL	2	TRUE	1	0.483197099684767	3		79	214	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255388	16255388	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	217	403	0	ENST00000375759.3:c.2653G>C	p.Glu885Gln	p.E885Q	ENST00000375759	NM_015001.2	885	Gag/Cag	11/15	NA	2	FACETS	0.944	0.879	1			1	INDETERMINATE	1	TRUE	NA	0.483197099684767	2		403	951	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259513	16259513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	104	173	0	ENST00000375759.3:c.6778G>T	p.Glu2260Ter	p.E2260*	ENST00000375759	NM_015001.2	2260	Gag/Tag	11/15	NA	2	FACETS	1	0.954	1			1	INDETERMINATE	1	TRUE	NA	0.483197099684767	2		173	392	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262648	16262648	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	110	184	0	ENST00000375759.3:c.9913G>C	p.Glu3305Gln	p.E3305Q	ENST00000375759	NM_015001.2	3305	Gag/Cag	11/15	NA	2	FACETS	0.979	0.885	1			1	INDETERMINATE	1	TRUE	NA	0.483197099684767	2		184	465	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578291	226578291	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757712451	NA	P-0009364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	183	315	0	ENST00000366794.5:c.437C>T	p.Pro146Leu	p.P146L	ENST00000366794	NM_001618.3	146	cCg/cTg	4/23	0.483197099684767	5	FACETS	1	0.949	1	0.26	0.239	0.282	CLONAL	1	TRUE	1	0.483197099684767	5		315	1256	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010522	48010522	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659674	NA	P-0009364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	76	110	0	ENST00000234420.5:c.150G>C	p.Trp50Cys	p.W50C	ENST00000234420	NM_000179.2	50	tgG/tgC	1/10	0.476637853007681	3	FACETS	0.974	0.859	1	0.487	0.429	0.549	CLONAL	1	TRUE	1	0.483197099684767	3		110	401	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277586	142277586	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	149	269	0	ENST00000350721.4:c.1765G>C	p.Asp589His	p.D589H	ENST00000350721	NM_001184.3	589	Gat/Cat	8/47	0.479734608373715	4	FACETS	0.971	0.887	1	0.243	0.221	0.265	CLONAL	1	TRUE	0	0.483197099684767	4		269	942	SUCCESS
APC	324	MSKCC	GRCh37	5	112174481	112174481	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	160	352	0	ENST00000257430.4:c.3190G>A	p.Glu1064Lys	p.E1064K	ENST00000257430	NM_000038.5	1064	Gag/Aag	16/16	1	2	FACETS	0.988	0.909	1	0.988	0.909	1	CLONAL	1	TRUE	1	0.483197099684767	2		352	670	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030235	180030235	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	255	484	0	ENST00000261937.6:c.4049C>A	p.Ser1350Tyr	p.S1350Y	ENST00000261937	NM_182925.4	1350	tCc/tAc	30/30	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.483197099684767	2		484	1040	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983888	2983888	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	269	502	1	ENST00000396946.4:c.642G>C	p.Glu214Asp	p.E214D	ENST00000396946	NM_032415.4	214	gaG/gaC	5/25	0.483197099684767	3	FACETS	0.98	0.917	1	0.49	0.458	0.523	CLONAL	1	TRUE	1	0.483197099684767	3		503	1411	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970945	21970945	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	181	312	0	ENST00000304494.5:c.413G>C	p.Arg138Thr	p.R138T	ENST00000304494	NM_000077.4	138	aGa/aCa	2/3	0.483197099684767	3	FACETS	1	0.965	1	0.539	0.497	0.582	CLONAL	1	TRUE	1	0.483197099684767	3		312	863	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201692	67201692	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1636	223	524	0	ENST00000312629.5:c.993G>T	p.Met331Ile	p.M331I	ENST00000312629	NM_003952.2	331	atG/atT	12/15	0.483197099684767	6	FACETS	0.976	0.905	1			1	CLONAL	1	TRUE	NA	0.483197099684767	6		524	1859	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172469	108172469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	184	423	0	ENST00000278616.4:c.5272G>A	p.Asp1758Asn	p.D1758N	ENST00000278616	NM_000051.3	1758	Gat/Aat	35/63	0.483197099684767	2	FACETS	0.97	0.897	1	0.485	0.448	0.523	CLONAL	1	TRUE	0	0.483197099684767	2		423	785	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244959	46244959	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1499	216	445	0	ENST00000334344.6:c.3053C>T	p.Ser1018Leu	p.S1018L	ENST00000334344	NM_152641.2	1018	tCa/tTa	15/21	0.483197099684767	5	FACETS	0.899	0.833	0.968	0.3	0.277	0.323	CLONAL	1	TRUE	2	0.483197099684767	5		445	1715	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287234	46287234	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	137	268	2	ENST00000334344.6:c.5179C>A	p.Pro1727Thr	p.P1727T	ENST00000334344	NM_152641.2	1727	Cct/Act	19/21	0.483197099684767	5	FACETS	0.961	0.873	1	0.32	0.291	0.352	CLONAL	1	TRUE	2	0.483197099684767	5		270	1018	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431646	49431646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	171	310	0	ENST00000301067.7:c.9493G>A	p.Asp3165Asn	p.D3165N	ENST00000301067	NM_003482.3	3165	Gat/Aat	34/54	0.483197099684767	5	FACETS	0.918	0.842	0.997	0.306	0.28	0.333	CLONAL	1	TRUE	2	0.483197099684767	5		310	1330	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69203022	69203022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	208	370	0	ENST00000462284.1:c.49G>A	p.Asp17Asn	p.D17N	ENST00000462284	NM_002392.5	17	Gat/Aat	2/11	0.483197099684767	5	FACETS	1	0.953	1	0.347	0.321	0.374	CLONAL	1	TRUE	2	0.483197099684767	5		370	1428	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518199	103518199	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	173	296	1	ENST00000355739.4:c.2137G>A	p.Glu713Lys	p.E713K	ENST00000355739	NM_000123.3	713	Gag/Aag	9/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.483197099684767	2		297	600	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961991	41961991	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0009364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1217	358	818	0	ENST00000219905.7:c.899C>G	p.Ser300Ter	p.S300*	ENST00000219905	NM_001164273.1	300	tCa/tGa	2/24	1	2	FACETS	0.941	0.89	0.993	0.941	0.89	0.993	CLONAL	1	TRUE	1	0.483197099684767	2		818	1575	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56792452	56792452	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	230	531	0	ENST00000308159.5:c.182C>T	p.Ser61Leu	p.S61L	ENST00000308159	NM_014669.4	61	tCa/tTa	3/22	NA	2	FACETS	0.935	0.872	1			1	INDETERMINATE	1	TRUE	NA	0.483197099684767	2		531	1018	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724516	724516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	55	123	0	ENST00000314574.4:c.1540G>A	p.Asp514Asn	p.D514N	ENST00000314574	NM_005433.3	514	Gat/Aat	12/12	0.483197099684767	2	FACETS	0.746	0.643	0.858	0.373	0.321	0.429	SUBCLONAL	1	TRUE	0	0.483197099684767	2		123	305	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231438	5231438	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1313475733	NA	P-0009364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1257	241	382	0	ENST00000357368.4:c.2038C>G	p.Gln680Glu	p.Q680E	ENST00000357368	NM_002850.3	680	Cag/Gag	14/38	0.483197099684767	5	FACETS	1	0.982	1	0.383	0.356	0.41	CLONAL	1	TRUE	2	0.483197099684767	5		382	1498	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7141690	7141690	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	136	326	0	ENST00000302850.5:c.2680G>A	p.Glu894Lys	p.E894K	ENST00000302850	NM_000208.2	894	Gag/Aag	13/22	0.483197099684767	5	FACETS	0.824	0.748	0.905	0.275	0.249	0.302	CLONAL	1	TRUE	2	0.483197099684767	5		326	1178	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579709	7579710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0009364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	384	386	0	ENST00000269305.4:c.86dup	p.Asn29LysfsTer14	p.N29Kfs*14	ENST00000269305	NM_001126112.2	29	aac/aaAc	3/11	0.483197099684767	2	FACETS	0.867	0.827	0.907	0.867	0.827	0.907	CLONAL	2	TRUE	0	0.483197099684767	2		386	917	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0009367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	196	406	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.610341530440945	3	FACETS	1	0.982	1			1	CLONAL	2	TRUE	NA	0.656630264056127	3		406	359	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	135	384	1	ENST00000425967.3:c.1731C>G	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaG	13/19	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.656630264056127	2		385	406	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663730	29663730	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555534677	NA	P-0009367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	71	481	2	ENST00000356175.3:c.6162G>A	p.Trp2054Ter	p.W2054*	ENST00000356175	NM_000267.3	2054	tgG/tgA	41/57	0.656630264056127	1	FACETS	0.825	0.737	0.916	0.825	0.737	0.916	CLONAL	1	TRUE	0	0.656630264056127	1		483	176	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099271	4099271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs185999703	NA	P-0009367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	134	492	1	ENST00000262948.5:c.847G>A	p.Val283Met	p.V283M	ENST00000262948	NM_030662.3	283	Gtg/Atg	7/11	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.656630264056127	2		493	406	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863688	68863688	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786203752	NA	P-0009367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	92	248	1	ENST00000261769.5:c.2430del	p.Phe810LeufsTer6	p.F810Lfs*6	ENST00000261769	NM_004360.3	809	aaT/aa	15/16	0.600146234498112	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.656630264056127	1		249	166	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152506	56152506	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	159	373	0	ENST00000399503.3:c.564del	p.Lys188AsnfsTer2	p.K188Nfs*2	ENST00000399503	NM_005921.1	188	Aaa/aa	2/20	0.278735728935393	4	FACETS	0.981	0.909	1	0.981	0.909	1	INDETERMINATE	2	TRUE	2	0.656630264056127	4		373	409	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120756	115120756	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	198	455	1	ENST00000257566.3:c.250del	p.Gln84ArgfsTer4	p.Q84Rfs*4	ENST00000257566	NM_016569.3	84	Cag/ag	1/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.656630264056127	2		456	510	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0009370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	71	939	1	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	0.16	2		940	840	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220400	1220400	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1359582062	NA	P-0009370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	62	605	1	ENST00000326873.7:c.493G>T	p.Glu165Ter	p.E165*	ENST00000326873	NM_000455.4	165	Gag/Tag	4/10	0.3	1	FACETS	0.954	0.823	1	0.954	0.823	1	CLONAL	1	TRUE	0	0.16	1		606	747	SUCCESS
APC	324	MSKCC	GRCh37	5	112174347	112174347	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	54	378	0	ENST00000257430.4:c.3056G>C	p.Gly1019Ala	p.G1019A	ENST00000257430	NM_000038.5	1019	gGa/gCa	16/16	1	2	FACETS	0.944	0.805	1	0.944	0.805	1	CLONAL	1	TRUE	1	0.16	2		378	715	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856117	151856117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	88	516	0	ENST00000262189.6:c.11501G>A	p.Gly3834Asp	p.G3834D	ENST00000262189	NM_170606.2	3834	gGc/gAc	44/59	0.160867788805695	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.16	1		516	938	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121846	2121846	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1338802781	NA	P-0009370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	32	363	0	ENST00000219476.3:c.2008C>T	p.Pro670Ser	p.P670S	ENST00000219476	NM_000548.3	670	Cct/Tct	19/42	1	2	FACETS	0.769	0.623	0.935	0.769	0.623	0.935	CLONAL	1	TRUE	1	0.16	2		363	520	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732984	74732984	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	50	511	0	ENST00000359995.5:c.259G>T	p.Val87Leu	p.V87L	ENST00000359995	NM_001195427.1	87	Gtg/Ttg	1/3	1	2	FACETS	0.923	0.782	1	0.923	0.782	1	CLONAL	1	TRUE	1	0.16	2		511	677	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602522	10602522	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	39	375	1	ENST00000171111.5:c.1056G>A	p.Trp352Ter	p.W352*	ENST00000171111	NM_203500.1	352	tgG/tgA	3/6	0.160867788805695	1	FACETS	0.82	0.679	0.978	0.82	0.679	0.978	CLONAL	1	TRUE	0	0.16	1		376	547	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136975	11136975	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0009370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	38	459	0	ENST00000358026.2:c.3169-1G>A		p.X1057_splice	ENST00000358026	NM_001128849.1	1057			0.160867788805695	1	FACETS	0.657	0.542	0.787	0.657	0.542	0.787	SUBCLONAL	1	TRUE	0	0.16	1		459	665	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571968	64571974	+	frameshift_variant	Frame_Shift_Del	DEL	CTTCTCA	CTTCTCA	-	novel	NA	P-0009370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	54	980	1	ENST00000312049.6:c.1665_1671del	p.Ser555ArgfsTer2	p.S555Rfs*2	ENST00000312049	NM_130799.2	555	agTGAGAAG/ag	10/10	1	2	FACETS	0.696	0.592	0.81	0.696	0.592	0.81	SUBCLONAL	1	TRUE	1	0.16	2		981	970	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0009405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	215	298	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.760968555515645	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.760968555515645	1		298	336	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106279	27106279	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	279	486	1	ENST00000324856.7:c.5890G>T	p.Glu1964Ter	p.E1964*	ENST00000324856	NM_006015.4	1964	Gag/Tag	20/20	1	2	FACETS	0.86	0.81	0.91	0.86	0.81	0.91	CLONAL	1	TRUE	1	0.760968555515645	2		487	853	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293552	1293552	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	289	483	0	ENST00000310581.5:c.1449C>G	p.Asn483Lys	p.N483K	ENST00000310581	NM_198253.2	483	aaC/aaG	2/16	0.678257529212239	4	FACETS	0.949	0.891	1	0.316	0.297	0.337	CLONAL	1	TRUE	1	0.760968555515645	4		483	1409	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045873	26045873	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	471	841	0	ENST00000540144.1:c.235T>G	p.Phe79Val	p.F79V	ENST00000540144	NM_003531.2	79	Ttc/Gtc	1/1	1	2	FACETS	0.904	0.864	0.944	0.904	0.864	0.944	CLONAL	1	TRUE	1	0.760968555515645	2		841	1370	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112426	115112426	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	100	400	0	ENST00000257566.3:c.1314C>G	p.Ser438Arg	p.S438R	ENST00000257566	NM_016569.3	438	agC/agG	7/8	NA	2	FACETS	0.341	0.305	0.38			1	INDETERMINATE	1	TRUE	NA	0.760968555515645	2		400	770	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602611	10602637	+	inframe_deletion	In_Frame_Del	DEL	TGGGCGCCCGGCAGGGCATCACCTGCG	TGGGCGCCCGGCAGGGCATCACCTGCG	-	novel	NA	P-0009405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	289	440	0	ENST00000171111.5:c.941_967del	p.Thr314_Pro322del	p.T314_P322del	ENST00000171111	NM_203500.1	314	aCGCAGGTGATGCCCTGCCGGGCGCCCAag/aag	3/6	1	2	FACETS	0.88	0.83	0.931	0.88	0.83	0.931	CLONAL	1	TRUE	1	0.760968555515645	2		440	863	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660056	12660079	+	inframe_deletion	In_Frame_Del	DEL	GCTTGTCTTAGAAGGATCTGTGAG	GCTTGTCTTAGAAGGATCTGTGAG	-	novel	NA	P-0009405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	375	659	0	ENST00000251849.4:c.142_165del	p.Leu48_Ser55del	p.L48_S55del	ENST00000251849	NM_002880.3	48	CTCACAGATCCTTCTAAGACAAGC/-	2/17	0.182259947147394	3	FACETS	1	0.993	1	0.638	0.607	0.67	INDETERMINATE	1	TRUE	1	0.760968555515645	3		659	1066	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638352	117638353	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0009405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	278	547	0	ENST00000368508.3:c.6088_6089delinsTT	p.Glu2030Leu	p.E2030L	ENST00000368508	NM_002944.2	2030	GAg/TTg	38/43	0.760968555515645	1	FACETS	0.993	0.948	1	0.993	0.948	1	CLONAL	1	TRUE	0	0.760968555515645	1		547	456	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	35	160	0				ENST00000310581	NM_198253.2	-/1132			0.409370326018943	3	FACETS	0.644	0.529	0.772	0.322	0.264	0.386	SUBCLONAL	1	TRUE	1	0.409370326018943	3		160	320	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0009428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	295	706	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.409370326018943	2	FACETS	0.999	0.947	1	0.999	0.947	1	CLONAL	2	TRUE	0	0.409370326018943	2		706	721	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278049	18278049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	112	534	0	ENST00000222254.8:c.1669G>A	p.Asp557Asn	p.D557N	ENST00000222254	NM_005027.3	557	Gac/Aac	13/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.409370326018943	2		534	472	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105745	27105745	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	48	599	0	ENST00000324856.7:c.5356G>C	p.Glu1786Gln	p.E1786Q	ENST00000324856	NM_006015.4	1786	Gag/Cag	20/20	0.363519597246559	3	FACETS	0.491	0.415	0.576	0.164	0.138	0.192	SUBCLONAL	1	TRUE	0	0.409370326018943	3		599	575	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106862	27106862	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142069738	NA	P-0009428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	54	410	1	ENST00000324856.7:c.6473G>A	p.Arg2158Gln	p.R2158Q	ENST00000324856	NM_006015.4	2158	cGa/cAa	20/20	0.363519597246559	3	FACETS	0.592	0.505	0.686	0.197	0.168	0.229	SUBCLONAL	1	TRUE	0	0.409370326018943	3		411	537	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165313	47165313	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	133	674	0	ENST00000409792.3:c.813G>C	p.Leu271Phe	p.L271F	ENST00000409792	NM_014159.6	271	ttG/ttC	3/21	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.409370326018943	2		674	640	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933743	49933743	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772397266	NA	P-0009428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	146	795	0	ENST00000296474.3:c.2534G>A	p.Arg845Gln	p.R845Q	ENST00000296474	NM_002447.2	845	cGa/cAa	10/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.409370326018943	2		795	654	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182662954	182662954	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	90	362	0	ENST00000292782.4:c.708G>T	p.Trp236Cys	p.W236C	ENST00000292782	NM_020640.2	236	tgG/tgT	7/7	0.409370326018943	4	FACETS	1	0.943	1	0.365	0.324	0.408	CLONAL	1	TRUE	1	0.409370326018943	4		362	566	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524530	187524530	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	114	620	0	ENST00000441802.2:c.11150C>G	p.Ser3717Cys	p.S3717C	ENST00000441802	NM_005245.3	3717	tCt/tGt	19/27	0.398406910577173	3	FACETS	0.912	0.821	1	0.456	0.41	0.504	CLONAL	1	TRUE	1	0.409370326018943	3		620	736	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876151	35876151	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs767298556	NA	P-0009428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	47	622	0	ENST00000303115.3:c.943C>G	p.Gln315Glu	p.Q315E	ENST00000303115	NM_002185.3	315	Caa/Gaa	8/8	0.409370326018943	3	FACETS	0.297	0.25	0.35	0.149	0.125	0.175	SUBCLONAL	1	TRUE	1	0.409370326018943	3		622	930	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198296	138198296	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	123	572	0	ENST00000237289.4:c.889G>A	p.Glu297Lys	p.E297K	ENST00000237289	NM_001270507.1	297	Gag/Aag	6/9	1	2	FACETS	0.969	0.879	1	0.969	0.879	1	CLONAL	1	TRUE	1	0.409370326018943	2		572	620	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509603	106509603	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	127	568	1	ENST00000359195.3:c.1597C>T	p.Gln533Ter	p.Q533*	ENST00000359195	NM_002649.2	533	Cag/Tag	2/11	0.257577059687855	5	FACETS	1	0.972	1	0.396	0.359	0.436	CLONAL	1	TRUE	2	0.409370326018943	5		569	842	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343837	118343837	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	66	629	0	ENST00000534358.1:c.1963C>T	p.Pro655Ser	p.P655S	ENST00000534358	NM_005933.3	655	Cca/Tca	3/36	0.398406910577173	3	FACETS	0.544	0.472	0.623	0.272	0.236	0.312	SUBCLONAL	1	TRUE	1	0.409370326018943	3		629	714	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929080	32929080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358940	NA	P-0009428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	162	911	1	ENST00000380152.3:c.7090G>A	p.Glu2364Lys	p.E2364K	ENST00000380152		2364	Gaa/Aaa	14/27	0.409370326018943	1	FACETS	0.86	0.791	0.932	0.86	0.791	0.932	CLONAL	1	TRUE	0	0.409370326018943	1		912	732	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929347	32929347	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	138	1006	0	ENST00000380152.3:c.7357G>C	p.Glu2453Gln	p.E2453Q	ENST00000380152		2453	Gag/Cag	14/27	0.409370326018943	1	FACETS	0.707	0.644	0.774	0.707	0.644	0.774	SUBCLONAL	1	TRUE	0	0.409370326018943	1		1006	758	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68301900	68301900	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	103	448	0	ENST00000487270.1:c.302G>C	p.Gly101Ala	p.G101A	ENST00000487270	NM_133509.3	101	gGa/gCa	4/11	0.409370326018943	3	FACETS	0.952	0.853	1	0.317	0.284	0.352	CLONAL	1	TRUE	0	0.409370326018943	3		448	637	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40991041	40991041	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	56	654	0	ENST00000267868.3:c.85G>C	p.Glu29Gln	p.E29Q	ENST00000267868	NM_002875.4	29	Gag/Cag	2/10	0.409370326018943	1	FACETS	0.383	0.328	0.443	0.383	0.328	0.443	SUBCLONAL	1	TRUE	0	0.409370326018943	1		654	568	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644841	67644841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	58	516	0	ENST00000264010.4:c.106G>A	p.Asp36Asn	p.D36N	ENST00000264010	NM_006565.3	36	Gat/Aat	3/12	1	2	FACETS	0.479	0.412	0.553	0.479	0.412	0.553	SUBCLONAL	1	TRUE	1	0.409370326018943	2		516	591	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971319	15971319	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1305162373	NA	P-0009428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	96	517	1	ENST00000268712.3:c.4630C>T	p.His1544Tyr	p.H1544Y	ENST00000268712	NM_006311.3	1544	Cac/Tac	32/46	0.409370326018943	2	FACETS	0.923	0.826	1	0.462	0.413	0.513	CLONAL	1	TRUE	0	0.409370326018943	2		518	508	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995288	15995288	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	163	587	0	ENST00000268712.3:c.2905G>A	p.Glu969Lys	p.E969K	ENST00000268712	NM_006311.3	969	Gag/Aag	22/46	0.409370326018943	2	FACETS	1	0.977	1	0.582	0.536	0.63	CLONAL	1	TRUE	0	0.409370326018943	2		587	684	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632056	1632056	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs777156498	NA	P-0009428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	136	816	0	ENST00000344749.5:c.279C>G	p.Phe93Leu	p.F93L	ENST00000344749	NM_001136139.2	93	ttC/ttG	5/19	0.409370326018943	1	FACETS	0.919	0.839	1	0.919	0.839	1	CLONAL	1	TRUE	0	0.409370326018943	1		816	575	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243937	53243937	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	180	428	0	ENST00000375401.3:c.1056C>G	p.Phe352Leu	p.F352L	ENST00000375401	NM_004187.3	352	ttC/ttG	8/26	0.333934075628102	2	FACETS	0.778	0.722	0.836			1	SUBCLONAL	2	TRUE	NA	0.409370326018943	2		428	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0009431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	164	364	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.979	0.902	1	0.979	0.902	1	CLONAL	1	TRUE	1	0.521756581403355	2		365	642	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0009431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	429	597	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	0.500083649865809	4	FACETS	0.989	0.943	1	0.989	0.943	1	CLONAL	2	TRUE	2	0.521756581403355	4		597	1265	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0009431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	81	360	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.521756581403355	2		361	292	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0009431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	278	211	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.521756581403355	3	FACETS	0.978	0.934	1	0.978	0.934	1	CLONAL	3	TRUE	0	0.521756581403355	3		211	458	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	421	581	1	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	0.500083649865809	4	FACETS	0.993	0.946	1	0.993	0.946	1	CLONAL	2	TRUE	2	0.521756581403355	4		582	1237	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0009431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	392	439	0	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	0.521756581403355	3	FACETS	1	0.966	1	0.676	0.645	0.707	CLONAL	2	TRUE	0	0.521756581403355	3		439	934	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822585	72822586	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs764626362	NA	P-0009431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	107	358	0	ENST00000268489.5:c.9589dup	p.Gln3197ProfsTer42	p.Q3197Pfs*42	ENST00000268489	NM_006885.3	3197	cag/cCag	10/10	0.510634202320289	3	FACETS	0.82	0.736	0.907	0.41	0.368	0.454	CLONAL	1	TRUE	1	0.521756581403355	3		358	631	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850704	63850705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0009431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	338	418	0	ENST00000279873.7:c.1489dup	p.Ile497AsnfsTer31	p.I497Nfs*31	ENST00000279873	NM_032199.2	494	-/A	10/10	0.411543318520963	6	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.521756581403355	6		418	1084	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052636	42052636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1054243525	NA	P-0009431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	466	546	0	ENST00000219905.7:c.7307G>A	p.Arg2436His	p.R2436H	ENST00000219905	NM_001164273.1	2436	cGt/cAt	20/24	0.521756581403355	2	FACETS	0.985	0.947	1	0.985	0.947	1	CLONAL	2	TRUE	0	0.521756581403355	2		546	907	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009438-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	74	160	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.494071922442942	2		160	292	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183787	10183787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123481	NA	P-0009438-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	127	168	1	ENST00000256474.2:c.256C>T	p.Pro86Ser	p.P86S	ENST00000256474	NM_000551.3	86	Ccc/Tcc	1/3	0.494071922442942	1	FACETS	0.928	0.848	1	0.928	0.848	1	CLONAL	1	TRUE	0	0.494071922442942	1		169	417	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243663074	243663074	+	downstream_gene_variant	3'Flank	SNP	A	A	C	novel	NA	P-0009438-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	199	274	0				ENST00000263826	NM_005465.4	710/713			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.494071922442942	2		274	704	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566535	41566535	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009438-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	210	438	2	ENST00000263253.7:c.4412T>A	p.Leu1471His	p.L1471H	ENST00000263253	NM_001429.3	1471	cTt/cAt	27/31	1	2	FACETS	0.999	0.929	1	0.999	0.929	1	CLONAL	1	TRUE	1	0.494071922442942	2		440	851	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597506	52597506	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009438-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	120	225	0	ENST00000394830.3:c.3804del	p.Lys1268AsnfsTer20	p.K1268Nfs*20	ENST00000394830	NM_018313.4	1268	aaA/aa	25/30	0.494071922442942	1	FACETS	0.91	0.829	0.994	0.91	0.829	0.994	CLONAL	1	TRUE	0	0.494071922442942	1		225	402	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0009441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	90	311	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.406144032427619	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	0	0.40986778166488	1		311	285	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0009441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	207	424	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.406144032427619	1	FACETS	0.885	0.822	0.951	0.885	0.822	0.951	CLONAL	1	FALSE	0	0.40986778166488	1		424	907	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604715	55604715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373152714	NA	P-0009441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	65	196	0	ENST00000288135.5:c.2923G>A	p.Asp975Asn	p.D975N	ENST00000288135	NM_000222.2	975	Gat/Aat	21/21	0.14438937227699	0	FACETS	0.358	0.31	0.409			1	INDETERMINATE	1	FALSE	0	0.40986778166488	0		196	523	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453306	40453306	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1198	289	721	0	ENST00000345506.4:c.1003G>C	p.Glu335Gln	p.E335Q	ENST00000345506	NM_003152.3	335	Gag/Cag	10/20	0.40986778166488	1	FACETS	0.754	0.707	0.802	0.754	0.707	0.802	SUBCLONAL	1	FALSE	0	0.40986778166488	1		721	1487	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5258030	5258030	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	76	266	0	ENST00000357368.4:c.704G>A	p.Arg235Gln	p.R235Q	ENST00000357368	NM_002850.3	235	cGa/cAa	8/38	0.40986778166488	1	FACETS	0.523	0.459	0.591	0.523	0.459	0.591	SUBCLONAL	1	FALSE	0	0.40986778166488	1		266	564	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032094	26032095	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	G	novel	NA	P-0009441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1206	73	854	0	ENST00000244661.2:c.194_195delinsC	p.Lys65ThrfsTer26	p.K65Tfs*26	ENST00000244661	NM_003537.3	65	aAG/aC	1/1	0.406144032427619	1	FACETS	0.221	0.193	0.253	0.221	0.193	0.253	SUBCLONAL	1	FALSE	0	0.40986778166488	1		854	1279	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009451-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	104	160	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.845	0.766	0.927	0.845	0.766	0.927	CLONAL	1	TRUE	1	0.778952279529438	2		160	316	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0009451-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4309	7092	326	1	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.778952279529438	33	FACETS	0.994	0.985	1			1	CLONAL	21	TRUE	NA	0.778952279529438	33		327	11401	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882084	36882084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009451-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	310	328	0	ENST00000358127.4:c.929C>T	p.Thr310Met	p.T310M	ENST00000358127	NM_001280556.1	310	aCg/aTg	8/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.778952279529438	2		328	776	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211097	55211097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219568637	NA	P-0009451-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4244	7054	301	1	ENST00000275493.2:c.340G>A	p.Glu114Lys	p.E114K	ENST00000275493	NM_005228.3	114	Gaa/Aaa	3/28	0.778952279529438	33	FACETS	0.998	0.989	1			1	CLONAL	21	TRUE	NA	0.778952279529438	33		302	11298	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717609	89717609	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs876661024	NA	P-0009451-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	196	200	0	ENST00000371953.3:c.635-1G>T		p.X212_splice	ENST00000371953	NM_000314.4	212			0.751792030641019	1	FACETS	0.934	0.883	0.984	0.934	0.883	0.984	CLONAL	1	TRUE	0	0.778952279529438	1		200	329	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944391	76944391	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009451-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	407	188	0	ENST00000373344.5:c.514A>T	p.Thr172Ser	p.T172S	ENST00000373344	NM_000489.3	172	Act/Tct	7/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.778952279529438	1		188	537	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0009464-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	37	278	1	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.82	0.675	0.983	0.82	0.675	0.983	CLONAL	1	TRUE	1	0.16	2		279	564	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0009464-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	18	166	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.731	0.55	0.944	0.731	0.55	0.944	CLONAL	1	TRUE	1	0.16	2		166	308	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041662	47041663	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0009464-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	80	429	0	ENST00000377604.3:c.1887_1888del	p.Ala631ThrfsTer41	p.A631Tfs*41	ENST00000377604	NM_001204468.1	629	acAGgg/acgg	17/24	0.112929558327514	1	FACETS	0.883	0.779	0.994	1	0.982	1	CLONAL	2	TRUE	0	0.16	1		429	521	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746017	162746017	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009464-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	43	274	0	ENST00000367921.3:c.2140C>T	p.Arg714Ter	p.R714*	ENST00000367921	NM_006182.2	714	Cga/Tga	16/18	1	2	FACETS	0.988	0.826	1	0.988	0.826	1	CLONAL	1	TRUE	1	0.16	2		274	544	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248763	212248763	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009464-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	31	182	0	ENST00000342788.4:c.3504G>T	p.Glu1168Asp	p.E1168D	ENST00000342788	NM_005235.2	1168	gaG/gaT	28/28	0.3	4	FACETS	0.967	0.781	1			1	CLONAL	1	TRUE	NA	0.16	4		182	465	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242338	98242338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009464-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	41	285	1	ENST00000331920.6:c.980G>A	p.Cys327Tyr	p.C327Y	ENST00000331920	NM_000264.3	327	tGt/tAt	7/24	1	2	FACETS	0.965	0.803	1	0.965	0.803	1	CLONAL	1	TRUE	1	0.16	2		286	531	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591903	48591903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009464-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	62	360	0	ENST00000342988.3:c.1066C>T	p.Pro356Ser	p.P356S	ENST00000342988	NM_005359.5	356	Cct/Tct	9/12	0.112929558327514	0	FACETS	1	0.911	1			1	CLONAL	1	TRUE	0	0.16	0		360	607	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0009491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	358	565	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.299456106628657	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	0	0.299456106628657	3		565	862	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0009491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	343	419	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.292810285461776	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.299456106628657	3		419	1115	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933458	49933458	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	136	437	2	ENST00000296474.3:c.2732G>T	p.Gly911Val	p.G911V	ENST00000296474	NM_002447.2	911	gGg/gTg	11/20	0.292810285461776	3	FACETS	0.848	0.769	0.931	0.424	0.384	0.466	CLONAL	1	TRUE	1	0.299456106628657	3		439	1232	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467756	66467756	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	194	272	0	ENST00000273854.3:c.513C>A	p.Tyr171Ter	p.Y171*	ENST00000273854	NM_004439.5	171	taC/taA	3/18	0.225906184346398	3	FACETS	0.799	0.74	0.861	0.799	0.74	0.861	SUBCLONAL	2	TRUE	1	0.299456106628657	3		272	932	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507313	8507313	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	235	350	0	ENST00000356435.5:c.1665G>T	p.Glu555Asp	p.E555D	ENST00000356435		555	gaG/gaT	11/35	0.257931904684733	2	FACETS	0.849	0.793	0.907	0.849	0.793	0.907	CLONAL	2	TRUE	0	0.299456106628657	2		350	924	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248088	110248088	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	152	234	1	ENST00000374672.4:c.1384G>T	p.Asp462Tyr	p.D462Y	ENST00000374672	NM_004235.4	462	Gac/Tac	5/5	0.292810285461776	3	FACETS	0.83	0.761	0.902	0.83	0.761	0.902	CLONAL	2	TRUE	1	0.299456106628657	3		235	703	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562555	95562555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	170	240	0	ENST00000393063.1:c.4702G>A	p.Gly1568Ser	p.G1568S	ENST00000393063	NM_030621.3	1568	Ggc/Agc	24/28	0.276936209308547	4	FACETS	0.9	0.828	0.974	0.9	0.828	0.974	CLONAL	2	TRUE	2	0.299456106628657	4		240	820	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220650	1220650	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	210	290	0	ENST00000326873.7:c.668A>T	p.Glu223Val	p.E223V	ENST00000326873	NM_000455.4	223	gAg/gTg	5/10	0.257931904684733	2	FACETS	0.873	0.813	0.936	0.873	0.813	0.936	CLONAL	2	TRUE	0	0.299456106628657	2		290	803	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7141792	7141792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	229	351	0	ENST00000302850.5:c.2578G>A	p.Glu860Lys	p.E860K	ENST00000302850	NM_000208.2	860	Gaa/Aaa	13/22	0.257931904684733	2	FACETS	0.887	0.828	0.948	0.887	0.828	0.948	CLONAL	2	TRUE	0	0.299456106628657	2		351	862	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602390	10602391	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0009491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	220	426	0	ENST00000171111.5:c.1187dup	p.Tyr396Ter	p.Y396*	ENST00000171111	NM_203500.1	396	tac/taAc	3/6	0.257931904684733	2	FACETS	0.766	0.713	0.821	0.766	0.713	0.821	SUBCLONAL	2	TRUE	0	0.299456106628657	2		426	959	SUCCESS
NF2	4771	MSKCC	GRCh37	22	29999964	30000020	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	GGTCCCGGGCCTGAGCCCCGCGCCATGGCCGGGGCCATCGCTTCCCGCATGAGCTTC	GGTCCCGGGCCTGAGCCCCGCGCCATGGCCGGGGCCATCGCTTCCCGCATGAGCTTC	A	novel	NA	P-0009491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	116	166	0	ENST00000338641.4:c.-24_33delinsA		p.*8*	ENST00000338641	NM_000268.3	?-11/595		1/16	0.200654120915447	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.299456106628657	2		166	329	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0009497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	316	381	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		381	659	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156742	20156742	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0009497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	230	203	0	ENST00000379607.5:c.17-2A>G		p.X6_splice	ENST00000379607	NM_001412.3	6			1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		203	253	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923657	39923657	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	341	253	0	ENST00000378444.4:c.3434C>G	p.Thr1145Ser	p.T1145S	ENST00000378444	NM_001123385.1	1145	aCt/aGt	7/15	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		253	377	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021758	71021758	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009498-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	181	389	0	ENST00000318789.4:c.1600T>A	p.Trp534Arg	p.W534R	ENST00000318789	NM_032682.5	534	Tgg/Agg	18/21	1	2	FACETS	0.925	0.859	0.991	0.925	0.859	0.991	CLONAL	1	TRUE	1	0.747112320670615	2		389	524	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160663	56160663	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs558965285	NA	P-0009498-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	176	399	0	ENST00000399503.3:c.937C>G	p.Arg313Gly	p.R313G	ENST00000399503	NM_005921.1	313	Cgg/Ggg	4/20	1	2	FACETS	0.965	0.897	1	0.965	0.897	1	CLONAL	1	TRUE	1	0.747112320670615	2		399	488	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624294	89624295	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0009498-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	303	558	0	ENST00000371953.3:c.69dup	p.Asp24ArgfsTer20	p.D24Rfs*20	ENST00000371953	NM_000314.4	23	tta/ttAa	1/9	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.747112320670615	2		558	774	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032537	12032537	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009498-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	160	372	1	ENST00000353533.5:c.974del	p.Pro325LeufsTer4	p.P325Lfs*4	ENST00000353533	NM_003010.3	325	Cct/ct	9/11	0.747112320670615	1	FACETS	0.913	0.855	0.97	0.913	0.855	0.97	CLONAL	1	TRUE	0	0.747112320670615	1		373	294	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109322684	109322684	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009498-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	173	405	1	ENST00000436639.2:c.353A>T	p.Gln118Leu	p.Q118L	ENST00000436639	NM_014454.2	118	cAa/cTa	3/10	1	2	FACETS	0.905	0.839	0.972	0.905	0.839	0.972	CLONAL	1	TRUE	1	0.747112320670615	2		406	512	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274859	38274862	+	frameshift_variant	Frame_Shift_Del	DEL	TTCT	TTCT	-	novel	NA	P-0009498-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	44	528	0	ENST00000425967.3:c.1718_1721del	p.Lys573IlefsTer89	p.K573Ifs*89	ENST00000425967	NM_001174067.1	573	aAGAAt/at	13/19	1	2	FACETS	0.154	0.128	0.182	0.154	0.128	0.182	SUBCLONAL	1	TRUE	1	0.747112320670615	2		528	765	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	35	586	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.158332316644553	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		586	757	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119781	70119781	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1274036689	NA	P-0009519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	45	525	0	ENST00000245479.2:c.788del	p.Gly263AlafsTer16	p.G263Afs*16	ENST00000245479	NM_000346.3	261	gaG/ga	3/3	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		525	446	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0009519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	40	442	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	0.3	3	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	3		442	603	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0009519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	21	403	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.3	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		403	628	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0009519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	33	338	0	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	0.3	8	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	8		338	600	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764146326	NA	P-0009525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	646	520	0	ENST00000269305.4:c.841G>A	p.Asp281Asn	p.D281N	ENST00000269305	NM_001126112.2	281	Gac/Aac	8/11	NA	2	FACETS	0.998	0.98	1			1	INDETERMINATE	2	TRUE	NA	0.870358612445097	2		520	744	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754947	29754947	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	176	228	0	ENST00000389048.3:c.988A>G	p.Lys330Glu	p.K330E	ENST00000389048	NM_004304.4	330	Aag/Gag	4/29	0.870358612445097	3	FACETS	0.938	0.868	1	0.469	0.434	0.505	CLONAL	1	TRUE	1	0.870358612445097	3		228	619	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246803	10246814	+	inframe_deletion	In_Frame_Del	DEL	GCCCATGGGCTC	GCCCATGGGCTC	-	novel	NA	P-0009525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	178	271	0	ENST00000340748.4:c.4591_4602del	p.Glu1531_Gly1534del	p.E1531_G1534del	ENST00000340748		1531	GAGCCCATGGGC/-	37/40	0.775430517011977	4	FACETS	0.932	0.86	1	0.466	0.43	0.503	CLONAL	1	TRUE	2	0.870358612445097	4		271	821	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937062	48937062	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	416	417	0	ENST00000267163.4:c.830del	p.Leu277ProfsTer9	p.L277Pfs*9	ENST00000267163	NM_000321.2	277	cTc/cc	8/27	0.870358612445097	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.870358612445097	2		417	473	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	598	586	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.278078021559311	4	FACETS	0.876	0.844	0.909			1	CLONAL	4	TRUE	NA	0.324328101204217	4		586	1393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578177	7578177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	206	483	0	ENST00000269305.4:c.672G>C	p.Glu224Asp	p.E224D	ENST00000269305	NM_001126112.2	224	gaG/gaC	6/11	0.281969709572113	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.324328101204217	1		483	1037	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401642	401642	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210576093	NA	P-0009532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	103	318	0	ENST00000380956.4:c.964G>A	p.Asp322Asn	p.D322N	ENST00000380956	NM_001195286.1	322	Gac/Aac	7/9	0.265395533931094	3	FACETS	0.851	0.761	0.948	0.426	0.38	0.474	CLONAL	1	TRUE	1	0.324328101204217	3		318	867	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273162	198273162	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	208	483	0	ENST00000335508.6:c.1048A>T	p.Thr350Ser	p.T350S	ENST00000335508	NM_012433.2	350	Act/Tct	8/25	0.26277794246591	2	FACETS	1	0.95	1	0.516	0.478	0.556	CLONAL	1	TRUE	0	0.324328101204217	2		483	1243	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633863	86633863	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1315	290	428	0	ENST00000274376.6:c.972A>T	p.Arg324Ser	p.R324S	ENST00000274376	NM_002890.2	324	agA/agT	5/25	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.324328101204217	2		428	1605	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053028	180053028	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	129	307	0	ENST00000261937.6:c.1262C>T	p.Pro421Leu	p.P421L	ENST00000261937	NM_182925.4	421	cCc/cTc	10/30	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.324328101204217	2		307	675	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909370	41909370	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	74	130	0	ENST00000372991.4:c.18C>A	p.Cys6Ter	p.C6*	ENST00000372991	NM_001760.3	6	tgC/tgA	1/5	0.224021208614223	3	FACETS	1	0.971	1			1	CLONAL	1	TRUE	NA	0.324328101204217	3		130	387	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117874132	117874132	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1501	277	497	0	ENST00000297338.2:c.322A>T	p.Ile108Phe	p.I108F	ENST00000297338	NM_006265.2	108	Att/Ttt	4/14	0.265395533931094	3	FACETS	1	0.981	1	0.558	0.522	0.596	CLONAL	1	TRUE	1	0.324328101204217	3		497	1778	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500979	8500979	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	157	401	0	ENST00000356435.5:c.1903G>T	p.Val635Leu	p.V635L	ENST00000356435		635	Gtg/Ttg	13/35	0.281969709572113	1	FACETS	0.778	0.711	0.847	0.778	0.711	0.847	SUBCLONAL	1	TRUE	0	0.324328101204217	1		401	1043	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479292	50479292	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	90	258	0	ENST00000394963.4:c.140G>T	p.Gly47Val	p.G47V	ENST00000394963	NM_003076.4	47	gGg/gTg	1/13	1	2	FACETS	0.957	0.851	1	0.957	0.851	1	CLONAL	1	TRUE	1	0.324328101204217	2		258	580	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123204998	123204998	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0009532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	53	107	1	ENST00000218089.9:c.2359-1G>T		p.X787_splice	ENST00000218089	NM_001042749.1	787			1	1	FACETS	0.736	0.63	0.851	0.736	0.63	0.851	SUBCLONAL	1	TRUE	0	0.324328101204217	1		108	372	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0009535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1314	567	354	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.278392663517442	50	FACETS	0.978	0.938	1			1	CLONAL	17	TRUE	NA	0.278392663517442	50		354	1881	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242481	+	inframe_deletion	In_Frame_Del	DEL	AATTAAGAGAAGCAA	AATTAAGAGAAGCAA	-	rs121913425	NA	P-0009535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	1553	344	0	ENST00000275493.2:c.2237_2251del	p.Glu746_Thr751delinsAla	p.E746_T751delinsA	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAAca/gca	19/28	0.278392663517442	50	FACETS	1	0.993	1			1	CLONAL	48	TRUE	NA	0.278392663517442	50		344	1775	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352765	70352765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759105512	NA	P-0009535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	69	481	1	ENST00000374080.3:c.4486C>T	p.Arg1496Cys	p.R1496C	ENST00000374080		1496	Cgc/Tgc	32/45	0.195791539311271	3	FACETS	0.763	0.668	0.864	0.509	0.445	0.576	SUBCLONAL	2	TRUE	0	0.278392663517442	3		482	370	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020502	14020502	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1012646362	NA	P-0009535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	26	410	0	ENST00000311895.7:c.473G>A	p.Arg158His	p.R158H	ENST00000311895	NM_005236.2	158	cGt/cAt	3/11	0.171629154906647	2	FACETS	0.541	0.429	0.67	0.271	0.214	0.335	SUBCLONAL	1	TRUE	0	0.278392663517442	2		410	345	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0009542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	46	565	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.789	0.662	0.93	0.789	0.662	0.93	CLONAL	1	TRUE	1	0.12	2		565	972	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0009542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	35	379	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.63	0.514	0.761	0.63	0.514	0.761	SUBCLONAL	1	TRUE	1	0.12	2		379	926	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939043	36939043	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1511	90	553	0	ENST00000361632.4:c.666G>C	p.Met222Ile	p.M222I	ENST00000361632		222	atG/atC	5/16	1	2	FACETS	0.937	0.828	1	0.937	0.828	1	CLONAL	1	TRUE	1	0.12	2		553	1601	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857611	9857611	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1555482222	NA	P-0009542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	85	314	0	ENST00000330684.3:c.3790G>T	p.Glu1264Ter	p.E1264*	ENST00000330684	NM_001134407.1	1264	Gag/Tag	13/13	0.125156035816417	3	FACETS	1	0.969	1	0.653	0.575	0.737	CLONAL	1	TRUE	1	0.12	3		314	1150	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0009559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	452	390	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.427874084171566	6	FACETS	0.978	0.933	1	0.978	0.933	1	CLONAL	3	TRUE	3	0.427874084171566	6		390	1337	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817412	39817412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200306085	NA	P-0009559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	286	396	2	ENST00000288319.7:c.151G>A	p.Val51Ile	p.V51I	ENST00000288319	NM_182918.3	51	Gtc/Atc	2/10	0.128494475706249	5	FACETS	1	0.985	1	0.565	0.532	0.599	INDETERMINATE	2	TRUE	1	0.427874084171566	5		398	971	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281551	15281551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	764	505	2	ENST00000263388.2:c.4822G>A	p.Ala1608Thr	p.A1608T	ENST00000263388	NM_000435.2	1608	Gct/Act	26/33	0.427874084171566	5	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	2	0.427874084171566	5		507	1754	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197824	66197824	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs200305031	NA	P-0009559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	141	362	0	ENST00000273854.3:c.2875C>G	p.His959Asp	p.H959D	ENST00000273854	NM_004439.5	959	Cat/Gat	17/18	1	2	FACETS	0.753	0.686	0.824	0.753	0.686	0.824	SUBCLONAL	1	TRUE	1	0.427874084171566	2		362	875	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222982	1222982	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0009559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	198	177	0	ENST00000326873.7:c.921-2A>G		p.X307_splice	ENST00000326873	NM_000455.4	307			NA	2	FACETS	0.929	0.869	0.99			1	INDETERMINATE	2	TRUE	NA	0.427874084171566	2		177	498	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602763	10602763	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs774469695	NA	P-0009559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	376	365	1	ENST00000171111.5:c.815G>T	p.Arg272Leu	p.R272L	ENST00000171111	NM_203500.1	272	cGc/cTc	3/6	0.392722949180787	2	FACETS	0.976	0.931	1	0.976	0.931	1	CLONAL	2	TRUE	0	0.427874084171566	2		366	900	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793208	33793208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	54	32	1	ENST00000498907.2:c.113G>A	p.Gly38Asp	p.G38D	ENST00000498907	NM_004364.3	38	gGc/gAc	1/1	0.427874084171566	5	FACETS	1	0.945	1	0.78	0.678	0.888	CLONAL	2	TRUE	2	0.427874084171566	5		33	177	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181311	123181311	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs774761933	NA	P-0009559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	262	214	0	ENST00000218089.9:c.775C>T	p.Arg259Ter	p.R259*	ENST00000218089	NM_001042749.1	259	Cga/Tga	9/35	1	1	FACETS	0.783	0.739	0.826	1	0.994	1	SUBCLONAL	2	TRUE	0	0.427874084171566	1		214	615	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226642	2226642	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	278	287	0	ENST00000398665.3:c.4122del	p.Asp1374GlufsTer6	p.D1374Efs*6	ENST00000398665	NM_032482.2	1374	gaC/ga	27/28	0.392722949180787	2	FACETS	0.976	0.923	1	0.976	0.923	1	CLONAL	2	TRUE	0	0.427874084171566	2		287	666	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626013	12626013	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	novel	NA	P-0009588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	81	208	0	ENST00000251849.4:c.1947G>C	p.Ter649TyrextTer42	p.*649Yext*42	ENST00000251849	NM_002880.3	649	taG/taC	17/17	NA	2	FACETS	1	0.941	1			1	INDETERMINATE	1	TRUE	NA	0.554095086117123	2		208	270	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954971	2954971	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	72	446	0	ENST00000396946.4:c.2739G>A	p.Met913Ile	p.M913I	ENST00000396946	NM_032415.4	913	atG/atA	21/25	1	2	FACETS	0.458	0.4	0.52	0.458	0.4	0.52	SUBCLONAL	1	TRUE	1	0.554095086117123	2		446	568	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2193783	2193783	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0009588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	47	338	0	ENST00000398665.3:c.588+1G>T		p.X196_splice	ENST00000398665	NM_032482.2	196			1	2	FACETS	0.362	0.305	0.424	0.362	0.305	0.424	SUBCLONAL	1	TRUE	1	0.554095086117123	2		338	469	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0009591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	672	565	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.463172598167684	6	FACETS	1	0.97	1	1	0.97	1	CLONAL	4	TRUE	2	0.463172598167684	6		565	1393	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089463	27089463	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0009591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	108	380	0	ENST00000324856.7:c.2420-1G>C		p.X807_splice	ENST00000324856	NM_006015.4	807			1	2	FACETS	0.776	0.698	0.858	0.776	0.698	0.858	SUBCLONAL	1	TRUE	1	0.463172598167684	2		380	601	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732586	190732586	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	182	593	0	ENST00000441310.2:c.2404T>C	p.Tyr802His	p.Y802H	ENST00000441310	NM_000534.4	802	Tac/Cac	11/13	0.30573073026604	3	FACETS	0.883	0.814	0.955	0.442	0.407	0.478	CLONAL	1	TRUE	1	0.463172598167684	3		593	1096	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147534	47147534	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	124	408	0	ENST00000409792.3:c.4792C>T	p.Arg1598Ter	p.R1598*	ENST00000409792	NM_014159.6	1598	Cga/Tga	6/21	1	2	FACETS	0.723	0.654	0.795	0.723	0.654	0.795	SUBCLONAL	1	TRUE	1	0.463172598167684	2		408	741	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124445	94124445	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	213	778	0	ENST00000369303.4:c.138G>C	p.Glu46Asp	p.E46D	ENST00000369303	NM_004440.3	46	gaG/gaC	2/17	1	2	FACETS	0.737	0.683	0.793	0.737	0.683	0.793	SUBCLONAL	1	TRUE	1	0.463172598167684	2		778	1248	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545561	106545561	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	312	426	0	ENST00000359195.3:c.3038G>T	p.Cys1013Phe	p.C1013F	ENST00000359195	NM_002649.2	1013	tGt/tTt	11/11	0.30573073026604	3	FACETS	0.829	0.783	0.876	0.829	0.783	0.876	CLONAL	2	TRUE	1	0.463172598167684	3		426	1001	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910852	114910852	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	267	914	0	ENST00000543371.1:c.971C>G	p.Ser324Cys	p.S324C	ENST00000543371	NM_001198531.1	324	tCc/tGc	9/14	1	2	FACETS	0.84	0.786	0.895	0.84	0.786	0.895	CLONAL	1	TRUE	1	0.463172598167684	2		914	1373	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178627	108178627	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0009591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	111	270	0	ENST00000278616.4:c.5678C>G	p.Ser1893Ter	p.S1893*	ENST00000278616	NM_000051.3	1893	tCa/tGa	38/63	0.278470873252058	4	FACETS	0.899	0.808	0.995	0.45	0.404	0.498	CLONAL	1	TRUE	2	0.463172598167684	4		270	780	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799302	88799302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	128	554	1	ENST00000360948.2:c.83C>A	p.Ser28Tyr	p.S28Y	ENST00000360948	NM_001012338.2	28	tCc/tAc	2/19	0.319649559226275	2	FACETS	0.723	0.656	0.794	0.362	0.328	0.397	SUBCLONAL	1	TRUE	0	0.463172598167684	2		555	764	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029431	14029431	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	89	352	0	ENST00000311895.7:c.1642A>C	p.Lys548Gln	p.K548Q	ENST00000311895	NM_005236.2	548	Aaa/Caa	8/11	0.331201327559799	3	FACETS	0.671	0.595	0.753	0.336	0.297	0.377	SUBCLONAL	1	TRUE	1	0.463172598167684	3		352	705	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0009591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	237	446	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.319649559226275	2	FACETS	1	0.992	1	0.73	0.685	0.776	CLONAL	1	TRUE	0	0.463172598167684	2		446	701	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2214474	2214474	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	204	364	0	ENST00000398665.3:c.1802A>T	p.Lys601Met	p.K601M	ENST00000398665	NM_032482.2	601	aAg/aTg	19/28	0.331201327559799	3	FACETS	0.828	0.772	0.886	0.828	0.772	0.886	CLONAL	2	TRUE	1	0.463172598167684	3		364	655	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101057	4101057	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	52	193	1	ENST00000262948.5:c.665C>A	p.Ser222Tyr	p.S222Y	ENST00000262948	NM_030662.3	222	tCc/tAc	6/11	0.331201327559799	3	FACETS	0.851	0.728	0.984	0.425	0.364	0.492	CLONAL	1	TRUE	1	0.463172598167684	3		194	325	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125566	47125567	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	A	novel	NA	P-0009591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	202	589	0	ENST00000409792.3:c.5703_5704delinsT	p.Glu1901AspfsTer12	p.E1901Dfs*12	ENST00000409792	NM_014159.6	1901	gaAGgc/gaTgc	12/21	1	2	FACETS	0.825	0.764	0.888	0.825	0.764	0.888	CLONAL	1	TRUE	1	0.463172598167684	2		589	1057	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0009595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	590	939	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.626184704839332	4	FACETS	0.892	0.863	0.921	0.892	0.863	0.921	CLONAL	3	TRUE	1	0.708776537290418	4		940	1063	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023676	27023676	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs867647567	NA	P-0009595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	204	216	0	ENST00000324856.7:c.782C>A	p.Ser261Ter	p.S261*	ENST00000324856	NM_006015.4	261	tCg/tAg	1/20	0.708776537290418	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.708776537290418	1		216	355	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175420	108175420	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204751	NA	P-0009595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	177	337	0	ENST00000278616.4:c.5515C>T	p.Gln1839Ter	p.Q1839*	ENST00000278616	NM_000051.3	1839	Cag/Tag	37/63	0.702243230036152	1	FACETS	0.8	0.747	0.854	0.8	0.747	0.854	SUBCLONAL	1	TRUE	0	0.708776537290418	1		337	403	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341236	89341236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	238	363	1	ENST00000301030.4:c.7699C>T	p.Pro2567Ser	p.P2567S	ENST00000301030	NM_001256183.1	2567	Ccc/Tcc	11/13	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.708776537290418	2		364	609	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0009600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	330	408	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.762	0.724	0.8	1	0.995	1	SUBCLONAL	2	TRUE	1	0.551698415731188	2		408	785	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0009600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	619	467	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.551698415731188	2	FACETS	1	0.996	1	1	0.998	1	CLONAL	3	TRUE	0	0.551698415731188	2		467	705	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937506	76937506	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	291	297	0	ENST00000373344.5:c.3242del	p.Lys1081ArgfsTer37	p.K1081Rfs*37	ENST00000373344	NM_000489.3	1081	aAg/ag	9/35	1	1	FACETS	0.992	0.957	1	1	0.997	1	CLONAL	2	TRUE	0	0.551698415731188	1		297	385	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0009623-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	3435	399	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.606399962722973	22	FACETS	0.986	0.977	0.995			1	CLONAL	19	TRUE	NA	0.606399962722973	22		399	4272	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759361	133759361	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009623-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	217	558	0	ENST00000318560.5:c.1684C>G	p.Leu562Val	p.L562V	ENST00000318560	NM_005157.4	562	Ctg/Gtg	11/11	0.359955800947175	5	FACETS	1	0.988	1	0.437	0.406	0.469	INDETERMINATE	1	TRUE	2	0.606399962722973	5		558	1042	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158145	47158145	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009623-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	205	562	0	ENST00000409792.3:c.4554del	p.Asp1519IlefsTer8	p.D1519Ifs*8	ENST00000409792	NM_014159.6	1518	gaA/ga	4/21	0.606399962722973	3	FACETS	0.944	0.877	1	0.472	0.438	0.508	CLONAL	1	TRUE	1	0.606399962722973	3		562	933	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967202	93967203	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0009623-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	329	506	0	ENST00000369303.4:c.2149_2150delinsTT	p.Gly717Leu	p.G717L	ENST00000369303	NM_004440.3	717	GGa/TTa	12/17	0.562030983253625	5	FACETS	0.867	0.819	0.916	0.578	0.546	0.611	CLONAL	2	TRUE	2	0.606399962722973	5		506	1195	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578428	7578431	+	stop_gained	Nonsense_Mutation	ONP	GCTG	GCTG	ACTA	novel	NA	P-0009623-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	200	416	0	ENST00000269305.4:c.499_502delinsTAGT	p.Gln167_His168delinsTer	p.Q167_H168delins*	ENST00000269305	NM_001126112.2	167	CAGCac/TAGTac	5/11	0.605798362815157	2	FACETS	0.973	0.92	1	0.973	0.92	1	CLONAL	2	TRUE	0	0.606399962722973	2		416	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0009626-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	251	576	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.47444757389539	1	FACETS	0.939	0.882	0.997	0.939	0.882	0.997	CLONAL	1	FALSE	0	0.527567965936898	1		579	746	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0009633-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	141	939	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.954	0.868	1	0.954	0.868	1	CLONAL	1	TRUE	1	0.327145094885568	2		940	904	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398290	25398290	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009633-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	136	365	1	ENST00000311936.3:c.29G>T	p.Gly10Val	p.G10V	ENST00000311936	NM_004985.3	10	gGa/gTa	2/5	1	2	FACETS	0.946	0.86	1	0.946	0.86	1	CLONAL	1	TRUE	1	0.327145094885568	2		366	879	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893460	32893460	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	G	rs80358561	NA	P-0009633-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	78	258	0	ENST00000380152.3:c.314T>G	p.Leu105Ter	p.L105*	ENST00000380152		105	tTa/tGa	3/27	1	2	FACETS	0.875	0.77	0.987	0.875	0.77	0.987	CLONAL	1	TRUE	1	0.327145094885568	2		258	545	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533113	63533113	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009633-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	141	395	0	ENST00000307078.5:c.1781C>G	p.Ala594Gly	p.A594G	ENST00000307078	NM_004655.3	594	gCc/gGc	7/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.327145094885568	2		395	777	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922995	44922995	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1279060931	NA	P-0009633-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	194	599	0	ENST00000377967.4:c.1856A>G	p.His619Arg	p.H619R	ENST00000377967	NM_021140.2	619	cAt/cGt	16/29	1	2	FACETS	0.913	0.843	0.986	0.913	0.843	0.986	CLONAL	1	TRUE	1	0.327145094885568	2		599	1299	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426106	47426106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009633-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	222	590	1	ENST00000377045.4:c.626G>A	p.Arg209His	p.R209H	ENST00000377045	NM_001654.4	209	cGc/cAc	7/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.327145094885568	2		591	1178	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176338	24176338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	376	417	2	ENST00000263121.7:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000263121	NM_003073.3	377	Cgt/Tgt	9/9	0.349995318970135	2	FACETS	0.973	0.928	1	0.973	0.928	1	CLONAL	2	TRUE	0	0.446164790865835	2		419	866	SUCCESS
ATM	472	MSKCC	GRCh37	11	108225591	108225591	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555143579	NA	P-0009636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	158	457	0	ENST00000278616.4:c.8840C>A	p.Thr2947Asn	p.T2947N	ENST00000278616	NM_000051.3	2947	aCc/aAc	61/63	0.151089649966308	3	FACETS	0.924	0.846	1	0.462	0.423	0.503	INDETERMINATE	1	TRUE	1	0.446164790865835	3		457	938	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28599003	28599003	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	112	399	0	ENST00000241453.7:c.2285C>G	p.Ser762Cys	p.S762C	ENST00000241453	NM_004119.2	762	tCt/tGt	18/24	0.268290209414046	3	FACETS	0.729	0.655	0.808			1	SUBCLONAL	1	TRUE	NA	0.446164790865835	3		399	842	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276196	15276196	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs572615224	NA	P-0009636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	215	470	0	ENST00000263388.2:c.5798A>G	p.Asn1933Ser	p.N1933S	ENST00000263388	NM_000435.2	1933	aAt/aGt	31/33	0.151089649966308	3	FACETS	1	0.987	1	0.623	0.579	0.668	INDETERMINATE	1	TRUE	1	0.446164790865835	3		470	946	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023467	27023486	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGGAGCCCTACGCGGGGC	CCTGGAGCCCTACGCGGGGC	-	novel	NA	P-0009636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	722	406	0	ENST00000324856.7:c.575_594del	p.Leu192ProfsTer201	p.L192Pfs*201	ENST00000324856	NM_006015.4	191	ggCCTGGAGCCCTACGCGGGGCcc/ggcc	1/20	0.446164790865835	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	1	0.446164790865835	3		406	1685	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111495	8111496	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGGAGGA	novel	NA	P-0009636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	367	411	0	ENST00000346208.3:c.982_988dup	p.Arg330MetfsTer24	p.R330Mfs*24	ENST00000346208		327	-/TGGAGGA	5/6	0.268290209414046	3	FACETS	0.796	0.755	0.838			1	SUBCLONAL	2	TRUE	NA	0.446164790865835	3		411	1264	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120612013	120612014	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0009656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	12	53	0	ENST00000256646.2:c.7_8delinsTT	p.Ala3Phe	p.A3F	ENST00000256646	NM_024408.3	3	GCc/TTc	1/34	0.608401041699844	4	FACETS	0.484	0.342	0.657	0.242	0.171	0.329	SUBCLONAL	1	TRUE	2	0.608401041699844	4		53	131	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0009656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	61	190	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.424845865981303	1	FACETS	0.936	0.829	1	0.936	0.829	1	CLONAL	1	TRUE	0	0.608401041699844	1		190	149	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578281	7578281	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660254	NA	P-0009656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	293	610	0	ENST00000269305.4:c.568C>A	p.Pro190Thr	p.P190T	ENST00000269305	NM_001126112.2	190	Cct/Act	6/11	0.5833233162162	2	FACETS	0.944	0.901	0.987	0.944	0.901	0.987	CLONAL	2	TRUE	0	0.608401041699844	2		610	510	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426850	70426850	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009686-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	171	650	1	ENST00000373644.4:c.4510C>T	p.Gln1504Ter	p.Q1504*	ENST00000373644	NM_030625.2	1504	Cag/Tag	7/12	1	2	FACETS	0.8	0.736	0.868	0.8	0.736	0.868	SUBCLONAL	1	TRUE	1	0.42058858406867	2		651	1016	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579382	+	inframe_deletion	In_Frame_Del	DEL	CCTGGTAGG	CCTGGTAGG	-	novel	NA	P-0009686-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	145	647	0	ENST00000269305.4:c.305_313del	p.Thr102_Gly105delinsSer	p.T102_G105delinsS	ENST00000269305	NM_001126112.2	102	aCCTACCAGGgc/agc	4/11	0.42058858406867	1	FACETS	0.813	0.743	0.885	0.813	0.743	0.885	CLONAL	1	TRUE	0	0.42058858406867	1		647	670	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0009692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	330	399	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.56649362583531	2	FACETS	0.979	0.936	1	0.979	0.936	1	CLONAL	2	TRUE	0	0.56649362583531	2		399	595	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0009692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	184	426	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.56649362583531	1	FACETS	0.872	0.811	0.934	0.872	0.811	0.934	CLONAL	1	TRUE	0	0.56649362583531	1		426	534	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664465	138664465	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	136	231	0	ENST00000330315.3:c.1100C>T	p.Thr367Ile	p.T367I	ENST00000330315	NM_023067.3	367	aCc/aTc	1/1	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.56649362583531	2		231	441	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55987337	55987337	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	112	337	0	ENST00000263923.4:c.88G>C	p.Asp30His	p.D30H	ENST00000263923	NM_002253.2	30	Gat/Cat	2/30	0.56649362583531	1	FACETS	0.926	0.845	1	0.926	0.845	1	CLONAL	1	TRUE	0	0.56649362583531	1		337	306	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955087	93955087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	169	737	0	ENST00000369303.4:c.2811G>A	p.Met937Ile	p.M937I	ENST00000369303	NM_004440.3	937	atG/atA	16/17	1	2	FACETS	0.804	0.741	0.87	0.804	0.741	0.87	CLONAL	1	TRUE	1	0.56649362583531	2		737	742	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74003497	74003497	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	322	636	0	ENST00000318443.5:c.1568C>G	p.Ser523Cys	p.S523C	ENST00000318443	NM_001024736.1	523	tCt/tGt	9/10	1	2	FACETS	0.958	0.904	1	0.958	0.904	1	CLONAL	1	TRUE	1	0.56649362583531	2		636	1187	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849515	68849515	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	290	593	0	ENST00000261769.5:c.1418T>A	p.Val473Asp	p.V473D	ENST00000261769	NM_004360.3	473	gTc/gAc	10/16	0.56649362583531	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.56649362583531	1		593	733	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219316	5219322	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTACTT	CTTACTT	-	novel	NA	P-0009692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	183	442	0	ENST00000357368.4:c.3922_3923+5del		p.X1308_splice	ENST00000357368	NM_002850.3	1308		23/38	1	2	FACETS	0.953	0.883	1	0.953	0.883	1	CLONAL	1	TRUE	1	0.56649362583531	2		442	678	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779105	3779105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	95	489	0	ENST00000262367.5:c.5943G>A	p.Met1981Ile	p.M1981I	ENST00000262367	NM_004380.2	1981	atG/atA	31/31	1	2	FACETS	0.876	0.781	0.977	0.876	0.781	0.977	CLONAL	1	FALSE	1	0.3281588769024	2		489	661	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646852	37646852	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	328	903	0	ENST00000447079.4:c.1975del	p.Glu659AsnfsTer94	p.E659Nfs*94	ENST00000447079	NM_015083.1	658	aaG/aa	3/14	1	2	FACETS	0.889	0.841	0.939	1	0.995	1	CLONAL	2	FALSE	1	0.3281588769024	2		903	1124	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618700	37618701	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0009699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	155	866	0	ENST00000447079.4:c.376_377insT	p.Lys126IlefsTer31	p.K126Ifs*31	ENST00000447079	NM_015083.1	126	aaa/aTaa	1/14	1	2	FACETS	0.8	0.731	0.873	0.8	0.731	0.873	SUBCLONAL	1	FALSE	1	0.3281588769024	2		866	1181	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061202	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGCGCTTCTG	GAAGCGCTTCTG	AA	novel	NA	P-0009699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	77	262	0	ENST00000250448.2:c.787_798delinsTT	p.Gln263LeufsTer55	p.Q263Lfs*55	ENST00000250448	NM_004496.3	263	CAGAAGCGCTTC/TT	2/2	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.3281588769024	2		262	359	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0009704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	493	655	3	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.349363846358757	2	FACETS	0.937	0.897	0.978	0.937	0.897	0.978	CLONAL	2	TRUE	0	0.389320298002051	2		658	1351	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242486	+	inframe_deletion	In_Frame_Del	DEL	TTAAGAGAAGCAACATCT	TTAAGAGAAGCAACATCT	-	rs121913440	NA	P-0009704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	275	463	0	ENST00000275493.2:c.2239_2256del	p.Leu747_Ser752del	p.L747_S752del	ENST00000275493	NM_005228.3	747	TTAAGAGAAGCAACATCT/-	19/28	0.227419134392953	5	FACETS	0.804	0.753	0.856	0.536	0.502	0.571	INDETERMINATE	2	TRUE	2	0.389320298002051	5		463	1392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0009707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	65	218	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.214442207623127	2	FACETS	1	0.971	1	0.741	0.645	0.844	CLONAL	1	FALSE	0	0.214442207623127	2		218	409	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959109	2959109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767537938	NA	P-0009707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	102	365	1	ENST00000396946.4:c.2407G>A	p.Val803Ile	p.V803I	ENST00000396946	NM_032415.4	803	Gtc/Atc	18/25	0.199020478678386	3	FACETS	1	0.968	1	0.609	0.544	0.678	CLONAL	1	FALSE	1	0.214442207623127	3		366	865	SUCCESS
APC	324	MSKCC	GRCh37	5	112175707	112175707	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	74	392	0	ENST00000257430.4:c.4418del	p.Asn1473MetfsTer34	p.N1473Mfs*34	ENST00000257430	NM_000038.5	1472	gtA/gt	16/16	0.214442207623127	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	0	0.214442207623127	1		392	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0009714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	350	467	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.262542440012012	2	FACETS	0.934	0.884	0.986	0.934	0.884	0.986	CLONAL	2	TRUE	0	0.274640401042092	2		467	1364	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220469	1220469	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	413	726	0	ENST00000326873.7:c.563del	p.Gly188AlafsTer99	p.G188Afs*99	ENST00000326873	NM_000455.4	188	Ggc/gc	4/10	0.274640401042092	2	FACETS	0.921	0.875	0.969	0.921	0.875	0.969	CLONAL	2	TRUE	0	0.274640401042092	2		726	1632	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911502	134911502	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	171	499	0	ENST00000398015.3:c.1967G>T	p.Gly656Val	p.G656V	ENST00000398015	NM_004441.4	656	gGg/gTg	11/16	1	2	FACETS	0.984	0.903	1	0.984	0.903	1	CLONAL	1	TRUE	1	0.274640401042092	2		499	1265	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300456	11300456	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1301	343	546	0	ENST00000361445.4:c.1690C>A	p.Gln564Lys	p.Q564K	ENST00000361445	NM_004958.3	564	Cag/Aag	11/58	0.274640401042092	6	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.274640401042092	6		546	1644	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156848960	156848960	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1372	322	634	1	ENST00000524377.1:c.1852G>T	p.Ala618Ser	p.A618S	ENST00000524377	NM_002529.3	618	Gct/Tct	15/17	0.24741303125613	3	FACETS	0.787	0.741	0.835	0.787	0.741	0.835	SUBCLONAL	2	TRUE	1	0.274640401042092	3		635	1694	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010478	48010478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs759589301	NA	P-0009714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	109	263	3	ENST00000234420.5:c.106G>T	p.Ala36Ser	p.A36S	ENST00000234420	NM_000179.2	36	Gct/Tct	1/10	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.274640401042092	2		266	787	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505555	157505555	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	101	337	0	ENST00000346085.5:c.3536A>C	p.Gln1179Pro	p.Q1179P	ENST00000346085	NM_020732.3	1179	cAg/cCg	13/20	1	2	FACETS	0.924	0.826	1	0.924	0.826	1	CLONAL	1	TRUE	1	0.274640401042092	2		337	796	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485865	8485865	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1502	208	744	1	ENST00000356435.5:c.2952A>T	p.Leu984Phe	p.L984F	ENST00000356435		984	ttA/ttT	17/35	1	2	FACETS	0.886	0.819	0.956	0.886	0.819	0.956	CLONAL	1	TRUE	1	0.274640401042092	2		745	1710	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456447	32456447	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	189	340	1	ENST00000332351.3:c.445G>T	p.Ala149Ser	p.A149S	ENST00000332351	NM_024426.4	149	Gcg/Tcg	1/10	0.12845869664919	3	FACETS	0.972	0.9	1	0.648	0.6	0.698	INDETERMINATE	2	TRUE	0	0.274640401042092	3		341	805	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112136	115112136	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1368	162	639	2	ENST00000257566.3:c.1604C>A	p.Ala535Glu	p.A535E	ENST00000257566	NM_016569.3	535	gCg/gAg	7/8	0.274640401042092	3	FACETS	0.877	0.802	0.956	0.438	0.401	0.478	CLONAL	1	TRUE	1	0.274640401042092	3		641	1530	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118796	115118796	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1457	418	718	0	ENST00000257566.3:c.545A>G	p.Lys182Arg	p.K182R	ENST00000257566	NM_016569.3	182	aAg/aGg	2/8	0.274640401042092	3	FACETS	0.923	0.876	0.971	0.923	0.876	0.971	CLONAL	2	TRUE	1	0.274640401042092	3		718	1875	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358697	67358697	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	142	490	0	ENST00000327367.4:c.205A>T	p.Arg69Trp	p.R69W	ENST00000327367	NM_005902.3	69	Agg/Tgg	1/9	0.274640401042092	2	FACETS	1	0.941	1	0.522	0.475	0.572	CLONAL	1	TRUE	0	0.274640401042092	2		490	990	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423505	88423505	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1342	436	814	1	ENST00000360948.2:c.2330C>A	p.Thr777Lys	p.T777K	ENST00000360948	NM_001012338.2	777	aCg/aAg	18/19	0.274640401042092	2	FACETS	0.893	0.849	0.938	0.893	0.849	0.938	CLONAL	2	TRUE	0	0.274640401042092	2		815	1778	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533256	29533256	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0009714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	447	619	0	ENST00000356175.3:c.1261-2A>T		p.X421_splice	ENST00000356175	NM_000267.3	421			NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.274640401042092	2		619	1445	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453425	40453425	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2823	352	1244	0	ENST00000345506.4:c.1122C>G	p.Ile374Met	p.I374M	ENST00000345506	NM_003152.3	374	atC/atG	10/20	0.21812483852341	4	FACETS	1	0.962	1			1	CLONAL	1	TRUE	NA	0.274640401042092	4		1244	3175	SUCCESS
AXL	558	MSKCC	GRCh37	19	41737110	41737110	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1932	280	884	0	ENST00000301178.4:c.690C>A	p.Asn230Lys	p.N230K	ENST00000301178	NM_021913.4	230	aaC/aaA	6/20	0.1163541173452	3	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.274640401042092	3		884	2212	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222511	53222511	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	109	231	1	ENST00000375401.3:c.4321G>T	p.Glu1441Ter	p.E1441*	ENST00000375401	NM_004187.3	1441	Gag/Tag	26/26	1	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.274640401042092	1		232	480	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944289	206944290	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0009714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1384	363	727	0	ENST00000423557.1:c.340dup	p.Glu114GlyfsTer20	p.E114Gfs*20	ENST00000423557	NM_000572.2	114	gag/gGag	3/5	0.24741303125613	3	FACETS	0.86	0.813	0.909	0.86	0.813	0.909	CLONAL	2	TRUE	1	0.274640401042092	3		727	1747	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627317	86627317	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	216	494	0	ENST00000274376.6:c.692+1del		p.R231fs	ENST00000274376	NM_002890.2	231	aGg/ag	2/25	0.274640401042092	2	FACETS	0.819	0.762	0.878	0.819	0.762	0.878	CLONAL	2	TRUE	0	0.274640401042092	2		494	960	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256963	41256963	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	297	557	0	ENST00000357654.3:c.223del	p.Glu75LysfsTer13	p.E75Kfs*13	ENST00000357654	NM_007294.3	75	Gaa/aa	5/23	0.21812483852341	4	FACETS	0.943	0.886	1			1	CLONAL	2	TRUE	NA	0.274640401042092	4		557	1461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0009717-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	202	424	0	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	1	2	FACETS	0.969	0.899	1	0.969	0.899	1	CLONAL	1	TRUE	1	0.498868959839754	2		424	836	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615568	100615568	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009717-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	284	376	0	ENST00000308731.7:c.764G>C	p.Arg255Pro	p.R255P	ENST00000308731	NM_000061.2	255	cGa/cCa	8/19	1	1	FACETS	0.805	0.766	0.843	1	0.995	1	CLONAL	2	TRUE	0	0.498868959839754	1		376	531	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240753	53240758	+	inframe_deletion	In_Frame_Del	DEL	CAGCTC	CAGCTC	-	novel	NA	P-0009717-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	44	399	0	ENST00000375401.3:c.1322_1327del	p.Gly441_Ala442del	p.G441_A442del	ENST00000375401	NM_004187.3	441	gGAGCTGac/gac	10/26	1	1	FACETS	0.226	0.189	0.267	0.226	0.189	0.267	SUBCLONAL	1	TRUE	0	0.498868959839754	1		399	585	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183791	10183791	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009717-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	88	369	0	ENST00000256474.2:c.260del	p.Val87AspfsTer72	p.V87Dfs*72	ENST00000256474	NM_000551.3	87	gTa/ga	1/3	0.498868959839754	1	FACETS	0.863	0.773	0.956	0.863	0.773	0.956	CLONAL	1	TRUE	0	0.498868959839754	1		369	307	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578254	7578254	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551821	NA	P-0009727-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	197	474	1	ENST00000269305.4:c.595G>T	p.Gly199Ter	p.G199*	ENST00000269305	NM_001126112.2	199	Gga/Tga	6/11	NA	2	FACETS	0.835	0.781	0.889			1	INDETERMINATE	3	FALSE	NA	0.330576227093176	2		475	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0009730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	505	223	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.728522873327484	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.733958308356018	1		223	848	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524246	18524246	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs768013752	NA	P-0009730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1339	458	317	1	ENST00000266497.5:c.1757+1G>T		p.X586_splice	ENST00000266497		586			0.278717209840752	5	FACETS	1	0.996	1			1	INDETERMINATE	1	TRUE	NA	0.733958308356018	5		318	1797	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088668	27088668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1557608670	NA	P-0009730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1213	660	304	0	ENST00000324856.7:c.2277G>A	p.Met759Ile	p.M759I	ENST00000324856	NM_006015.4	759	atG/atA	7/20	1	2	FACETS	0.96	0.924	0.996	0.96	0.924	0.996	CLONAL	1	TRUE	1	0.733958308356018	2		304	1873	SUCCESS
FH	2271	MSKCC	GRCh37	1	241671983	241671983	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs747135440	NA	P-0009730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	1040	241	0	ENST00000366560.3:c.658G>T	p.Ala220Ser	p.A220S	ENST00000366560	NM_000143.3	220	Gca/Tca	5/10	0.400423829665932	4	FACETS	0.922	0.9	0.944			1	INDETERMINATE	3	TRUE	NA	0.733958308356018	4		241	1777	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156016	99156016	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1282	746	377	1	ENST00000074304.5:c.696G>T	p.Met232Ile	p.M232I	ENST00000074304	NM_001134224.1	232	atG/atT	10/26	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.733958308356018	2		378	2028	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936307	49936307	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	723	380	0	ENST00000296474.3:c.1541G>T	p.Gly514Val	p.G514V	ENST00000296474	NM_002447.2	514	gGg/gTg	3/20	0.733958308356018	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.733958308356018	1		380	1193	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217605	142217605	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1277	91	216	0	ENST00000350721.4:c.5392A>G	p.Thr1798Ala	p.T1798A	ENST00000350721	NM_001184.3	1798	Aca/Gca	32/47	0.201835530343996	3	FACETS	0.248	0.219	0.279	0.124	0.109	0.14	INDETERMINATE	1	TRUE	1	0.733958308356018	3		216	1368	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415612	152415612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	605	281	0	ENST00000206249.3:c.1462C>T	p.His488Tyr	p.H488Y	ENST00000206249	NM_000125.3	488	Cac/Tac	7/8	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.733958308356018	2		281	1634	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945082	151945082	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1239103799	NA	P-0009730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	55	102	0	ENST00000262189.6:c.2437C>A	p.Pro813Thr	p.P813T	ENST00000262189	NM_170606.2	813	Cca/Aca	14/59	0.733958308356018	1	FACETS	0.254	0.218	0.294	0.254	0.218	0.294	SUBCLONAL	1	TRUE	0	0.733958308356018	1		102	373	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425254	49425254	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	535	288	0	ENST00000301067.7:c.13234C>T	p.Gln4412Ter	p.Q4412*	ENST00000301067	NM_003482.3	4412	Caa/Taa	39/54	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.733958308356018	2		288	1442	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959085	28959085	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	1872	340	0	ENST00000282397.4:c.2053A>G	p.Asn685Asp	p.N685D	ENST00000282397	NM_002019.4	685	Aat/Gat	14/30	0.441792403562582	5	FACETS	0.884	0.869	0.9			1	CLONAL	4	TRUE	NA	0.733958308356018	5		340	3030	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039339	49039339	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0009730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	838	379	0	ENST00000267163.4:c.2326-2A>T		p.X776_splice	ENST00000267163	NM_000321.2	776			0.733958308356018	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.733958308356018	1		379	1410	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343663	343663	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1514	934	495	1	ENST00000262320.3:c.2011G>T	p.Glu671Ter	p.E671*	ENST00000262320	NM_003502.3	671	Gag/Tag	8/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.733958308356018	2		496	2448	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45423094	45423094	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	474	187	1	ENST00000262160.6:c.34G>T	p.Val12Leu	p.V12L	ENST00000262160	NM_005901.5	12	Gtg/Ttg	2/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.733958308356018	2		188	1226	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385147	41385147	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	586	310	0	ENST00000373198.4:c.814G>T	p.Asp272Tyr	p.D272Y	ENST00000373198	NM_133170.3	272	Gat/Tat	6/32	1	2	FACETS	0.948	0.91	0.986	0.948	0.91	0.986	CLONAL	1	TRUE	1	0.733958308356018	2		310	1685	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911598	39911598	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1334	661	309	0	ENST00000378444.4:c.5032C>G	p.Arg1678Gly	p.R1678G	ENST00000378444	NM_001123385.1	1678	Cgc/Ggc	15/15	1	2	FACETS	0.903	0.869	0.937	0.903	0.869	0.937	CLONAL	1	TRUE	1	0.733958308356018	2		309	1995	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921416	39921416	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	521	284	0	ENST00000378444.4:c.4404G>T	p.Gln1468His	p.Q1468H	ENST00000378444	NM_001123385.1	1468	caG/caT	10/15	1	2	FACETS	0.929	0.889	0.968	0.929	0.889	0.968	CLONAL	1	TRUE	1	0.733958308356018	2		284	1529	SUCCESS
AR	367	MSKCC	GRCh37	X	66766430	66766430	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	213	115	0	ENST00000374690.3:c.1442A>T	p.Tyr481Phe	p.Y481F	ENST00000374690	NM_000044.3	481	tAc/tTc	1/8	1	2	FACETS	0.945	0.884	1	0.945	0.884	1	CLONAL	1	TRUE	1	0.733958308356018	2		115	614	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123026617	123026617	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs112760249	NA	P-0009730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1696	870	491	0	ENST00000355640.3:c.1093A>G	p.Arg365Gly	p.R365G	ENST00000355640		365	Aga/Gga	5/7	0.136892678873237	1	FACETS	0.585	0.565	0.604	0.585	0.565	0.604	INDETERMINATE	1	TRUE	0	0.733958308356018	1		491	2566	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932538	39932539	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0009730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1318	622	408	0	ENST00000378444.4:c.2060_2061delinsAG	p.Pro687Gln	p.P687Q	ENST00000378444	NM_001123385.1	687	cCC/cAG	4/15	1	2	FACETS	0.874	0.839	0.908	0.874	0.839	0.908	CLONAL	1	TRUE	1	0.733958308356018	2		408	1940	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0009740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	478	203	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.725446027893964	4	FACETS	1	0.992	1	1	0.998	1	CLONAL	4	TRUE	1	0.725446027893964	4		203	553	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111502	8111503	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0009740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	471	508	0	ENST00000346208.3:c.990dup	p.Asn331GlufsTer21	p.N331Efs*21	ENST00000346208		330	agg/aGgg	5/6	0.137773865140979	4	FACETS	0.982	0.941	1	0.982	0.941	1	INDETERMINATE	2	TRUE	2	0.725446027893964	4		508	1141	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225687	26225687	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2063	844	1130	0	ENST00000360408.1:c.305T>G	p.Val102Gly	p.V102G	ENST00000360408	NM_003532.2	102	gTg/gGg	1/1	0.704019873093088	4	FACETS	1	0.997	1	0.46	0.444	0.477	CLONAL	1	TRUE	1	0.725446027893964	4		1130	2907	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003492	42003492	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	1162	946	0	ENST00000219905.7:c.3029C>G	p.Thr1010Arg	p.T1010R	ENST00000219905	NM_001164273.1	1010	aCa/aGa	8/24	0.725446027893964	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.725446027893964	2		946	1393	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719115	52719115	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	284	422	0	ENST00000322088.6:c.891G>T	p.Glu297Asp	p.E297D	ENST00000322088	NM_014225.5	297	gaG/gaT	7/15	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.725446027893964	2		422	698	SUCCESS
BLM	641	MSKCC	GRCh37	15	91341426	91341430	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAC	AAAAC	-	novel	NA	P-0009740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	51	526	0	ENST00000355112.3:c.3219_3223del	p.Thr1074ArgfsTer4	p.T1074Rfs*4	ENST00000355112	NM_000057.2	1073	AAAACa/a	17/22	0.725446027893964	3	FACETS	0.21	0.178	0.246	0.07	0.059	0.082	SUBCLONAL	1	TRUE	0	0.725446027893964	3		526	912	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578419	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587781845	NA	P-0009750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	192	258	0	ENST00000269305.4:c.511G>T	p.Glu171Ter	p.E171*	ENST00000269305	NM_001126112.2	171	Gag/Tag	5/11	0.59122145947557	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.7173281688747	1		258	255	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55569915	55569915	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	139	289	0	ENST00000288135.5:c.782G>T	p.Ser261Ile	p.S261I	ENST00000288135	NM_000222.2	261	aGc/aTc	5/21	0.729773299323599	1	FACETS	0.765	0.707	0.823	0.765	0.707	0.823	SUBCLONAL	1	TRUE	0	0.7173281688747	1		289	325	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86637111	86637111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759265277	NA	P-0009750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	212	235	2	ENST00000274376.6:c.1022G>A	p.Arg341Gln	p.R341Q	ENST00000274376	NM_002890.2	341	cGg/cAg	6/25	0.729773299323599	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.7173281688747	1		237	331	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394642	394642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531132523	NA	P-0009750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	482	419	0	ENST00000399788.2:c.5053G>A	p.Asp1685Asn	p.D1685N	ENST00000399788	NM_001042603.1	1685	Gat/Aat	28/28	0.375523595422918	4	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.7173281688747	4		419	1028	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0009757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	230	350	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.540863674783114	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.540863674783114	1		350	476	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372071	55372071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	51	270	0	ENST00000297316.4:c.761C>T	p.Ala254Val	p.A254V	ENST00000297316	NM_022454.3	254	gCg/gTg	2/2	0.164026475886495	2	FACETS	0.61	0.522	0.706	0.305	0.261	0.353	INDETERMINATE	1	TRUE	0	0.540863674783114	2		270	309	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971080	21971080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	105	167	1	ENST00000304494.5:c.278C>T	p.Thr93Met	p.T93M	ENST00000304494	NM_000077.4	93	aCg/aTg	2/3	0.540863674783114	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.540863674783114	1		168	279	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436055	56436055	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	189	461	0	ENST00000407977.2:c.1082del	p.Pro361LeufsTer58	p.P361Lfs*58	ENST00000407977		361	cCt/ct	9/10	0.540863674783114	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.540863674783114	1		461	497	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347578	118347578	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1085307947	NA	P-0009786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	49	542	0	ENST00000534358.1:c.3215G>T	p.Cys1072Phe	p.C1072F	ENST00000534358	NM_005933.3	1072	tGc/tTc	4/36	0.164289953727966	1	FACETS	0.375	0.317	0.44	0.375	0.317	0.44	INDETERMINATE	1	TRUE	0	0.28	1		542	802	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432041	49432041	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	75	661	0	ENST00000301067.7:c.9098C>T	p.Thr3033Ile	p.T3033I	ENST00000301067	NM_003482.3	3033	aCc/aTc	34/54	0.147715975993393	3	FACETS	0.646	0.564	0.734	0.323	0.282	0.367	INDETERMINATE	1	TRUE	1	0.28	3		661	946	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578393	7578393	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876660821	NA	P-0009787-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	82	460	0	ENST00000269305.4:c.537T>A	p.His179Gln	p.H179Q	ENST00000269305	NM_001126112.2	179	caT/caA	5/11	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	FALSE	1	0.292989672321556	2		460	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578525	7578525	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009818-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	203	355	0	ENST00000269305.4:c.405C>A	p.Cys135Ter	p.C135*	ENST00000269305	NM_001126112.2	135	tgC/tgA	5/11	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	2	FALSE	NA	0.201500528728112	2		355	875	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061208	38061209	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0009818-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	128	222	0	ENST00000250448.2:c.780dup	p.Arg261AlafsTer32	p.R261Afs*32	ENST00000250448	NM_004496.3	260	-/G	2/2	0.177116245245679	3	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	FALSE	1	0.201500528728112	3		222	686	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0009821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	625	406	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.408987328870423	5	FACETS	0.99	0.954	1			1	CLONAL	3	TRUE	NA	0.508586291878225	5		406	1459	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	432	433	0	ENST00000206249.3:c.1610A>G	p.Tyr537Cys	p.Y537C	ENST00000206249	NM_000125.3	537	tAt/tGt	8/8	0.484536124559367	3	FACETS	0.989	0.946	1	0.659	0.63	0.689	CLONAL	2	TRUE	0	0.508586291878225	3		433	1077	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900884	3900884	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1650	223	697	0	ENST00000262367.5:c.212C>T	p.Ser71Leu	p.S71L	ENST00000262367	NM_004380.2	71	tCg/tTg	2/31	0.434298741241018	5	FACETS	0.825	0.765	0.888	0.275	0.255	0.296	CLONAL	1	TRUE	2	0.508586291878225	5		697	1873	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs587781702	NA	P-0009821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	472	500	0	ENST00000269305.4:c.920-1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.460709005129449	2	FACETS	0.953	0.915	0.99	0.953	0.915	0.99	CLONAL	2	TRUE	0	0.508586291878225	2		500	974	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459212	120459212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	198	412	0	ENST00000256646.2:c.6133C>T	p.Leu2045Phe	p.L2045F	ENST00000256646	NM_024408.3	2045	Ctt/Ttt	34/34	0.508586291878225	4	FACETS	0.937	0.866	1	0.469	0.433	0.506	CLONAL	1	TRUE	2	0.508586291878225	4		412	1253	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74868226	74868226	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	114	240	0	ENST00000284811.8:c.68C>T	p.Ser23Leu	p.S23L	ENST00000284811		23	tCa/tTa	3/4	0.163097189425237	5	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.508586291878225	5		240	566	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411990	63411990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1841	207	1119	0	ENST00000330258.3:c.1177G>A	p.Glu393Lys	p.E393K	ENST00000330258	NM_152424.3	393	Gaa/Aaa	2/2	0.460709005129449	2	FACETS	0.397	0.367	0.43	0.199	0.183	0.215	SUBCLONAL	1	TRUE	0	0.508586291878225	2		1119	2048	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754353	57754354	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	GACTAAG	novel	NA	P-0009821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	155	450	0	ENST00000274289.3:c.496-5_497dup	p.Met167LeufsTer34	p.M167Lfs*34	ENST00000274289	NM_006622.3	166	tca/tcCTTAGTCa	4/14	0.505833449940397	1	FACETS	0.853	0.785	0.922	0.853	0.785	0.922	CLONAL	1	TRUE	0	0.508586291878225	1		450	533	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115750	8115750	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs104894164	NA	P-0009828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	100	643	2	ENST00000346208.3:c.1096C>T	p.Arg366Ter	p.R366*	ENST00000346208		366	Cga/Tga	6/6	0.445986763288286	12	FACETS	1	0.932	1			1	CLONAL	6	FALSE	NA	0.445986763288286	12		645	235	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0009828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	39	495	1	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.371954178448595	4	FACETS	1	0.886	1	0.771	0.666	0.877	CLONAL	3	FALSE	0	0.445986763288286	4		496	82	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72842152	72842152	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	23	438	0	ENST00000325599.8:c.1096C>G	p.His366Asp	p.H366D	ENST00000325599	NM_018130.2	366	Cac/Gac	10/11	0.445986763288286	6	FACETS	0.903	0.727	1			1	CLONAL	3	FALSE	NA	0.445986763288286	6		438	72	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356101	66356101	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	16	360	0	ENST00000273854.3:c.1396C>T	p.Gln466Ter	p.Q466*	ENST00000273854	NM_004439.5	466	Caa/Taa	5/18	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	FALSE	1	0.445986763288286	2		360	57	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245969	5245969	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	15	394	0	ENST00000357368.4:c.806T>A	p.Val269Glu	p.V269E	ENST00000357368	NM_002850.3	269	gTg/gAg	10/38	0.445986763288286	2	FACETS	1	0.889	1	0.686	0.521	0.868	CLONAL	1	FALSE	0	0.445986763288286	2		394	49	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0009831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	68	273	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	0.63	0.552	0.712	0.63	0.552	0.712	SUBCLONAL	1	TRUE	1	0.679225362987557	2		273	318	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442567	52442567	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1253151209	NA	P-0009831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	235	311	0	ENST00000460680.1:c.178C>T	p.Arg60Ter	p.R60*	ENST00000460680	NM_004656.3	60	Cga/Tga	4/17	0.369319820512923	2	FACETS	0.859	0.803	0.915	0.429	0.401	0.458	INDETERMINATE	1	TRUE	0	0.679225362987557	2		311	806	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121912651	NA	P-0009838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	205	399	0	ENST00000269305.4:c.742C>G	p.Arg248Gly	p.R248G	ENST00000269305	NM_001126112.2	248	Cgg/Ggg	7/11	0.282035409901525	2	FACETS	0.761	0.708	0.815	0.761	0.708	0.815	SUBCLONAL	2	TRUE	0	0.360326240567316	2		399	748	SUCCESS
APC	324	MSKCC	GRCh37	5	112175162	112175162	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561588104	NA	P-0009838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	72	195	0	ENST00000257430.4:c.3871C>T	p.Gln1291Ter	p.Q1291*	ENST00000257430	NM_000038.5	1291	Cag/Tag	16/16	0.282035409901525	2	FACETS	1	0.969	1	0.659	0.581	0.742	CLONAL	1	TRUE	0	0.360326240567316	2		195	303	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255346	16255346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151043425	NA	P-0009838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	343	497	0	ENST00000375759.3:c.2611C>T	p.Arg871Cys	p.R871C	ENST00000375759	NM_015001.2	871	Cgc/Tgc	11/15	0.144864228345526	4	FACETS	0.999	0.945	1	0.999	0.945	1	INDETERMINATE	2	TRUE	2	0.360326240567316	4		497	1296	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0009854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	305	503	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.3	3	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	3		503	1361	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715899	61715899	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	73	346	0	ENST00000401558.2:c.2030A>G	p.Asp677Gly	p.D677G	ENST00000401558	NM_003400.3	677	gAt/gGt	18/25	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		346	729	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604717	48604718	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0009854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	117	519	0	ENST00000342988.3:c.1540_1541del	p.Pro514LysfsTer12	p.P514Kfs*12	ENST00000342988	NM_005359.5	513	taCCca/taca	12/12	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		519	1054	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593607	55593608	+	protein_altering_variant	In_Frame_Ins	INS	-	-	TCC	novel	NA	P-0009867-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1933	1390	658	0	ENST00000288135.5:c.1673_1674insTCC	p.Lys558delinsAsnPro	p.K558delinsNP	ENST00000288135	NM_000222.2	558	aag/aaTCCg	11/21	0.539799095008329	12	FACETS	0.955	0.932	0.979			1	CLONAL	6	TRUE	NA	0.539799095008329	12		658	3323	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412110	63412110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852216	NA	P-0009871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	111	602	1	ENST00000330258.3:c.1057C>T	p.Arg353Ter	p.R353*	ENST00000330258	NM_152424.3	353	Cga/Tga	2/2	1	1	FACETS	0.523	0.469	0.58	0.523	0.469	0.58	SUBCLONAL	1	FALSE	0	0.363040988872072	1		603	957	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370796	55370796	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	103	262	3	ENST00000297316.4:c.98C>T	p.Ala33Val	p.A33V	ENST00000297316	NM_022454.3	33	gCc/gTc	1/2	0.363040988872072	3	FACETS	1	0.978	1	0.669	0.601	0.741	CLONAL	1	FALSE	1	0.363040988872072	3		265	501	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964098	28964098	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	57	692	0	ENST00000282397.4:c.1804T>G	p.Tyr602Asp	p.Y602D	ENST00000282397	NM_002019.4	602	Tac/Gac	13/30	1	2	FACETS	0.279	0.238	0.324	0.279	0.238	0.324	SUBCLONAL	1	FALSE	1	0.363040988872072	2		692	1127	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807986	3807986	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	116	488	0	ENST00000262367.5:c.3433G>T	p.Gly1145Trp	p.G1145W	ENST00000262367	NM_004380.2	1145	Ggg/Tgg	18/31	1	2	FACETS	0.641	0.577	0.709	0.641	0.577	0.709	SUBCLONAL	1	FALSE	1	0.363040988872072	2		488	997	SUCCESS
APC	324	MSKCC	GRCh37	5	112173889	112173890	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACAG	novel	NA	P-0009871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	61	509	1	ENST00000257430.4:c.2600_2603dup	p.Glu868AspfsTer45	p.E868Dfs*45	ENST00000257430	NM_000038.5	866	-/ACAG	16/16	1	2	FACETS	0.384	0.33	0.442	0.384	0.33	0.442	SUBCLONAL	1	FALSE	1	0.363040988872072	2		510	876	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910801	114910802	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0009871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1722	113	1055	0	ENST00000543371.1:c.920_921insA	p.Ile309HisfsTer19	p.I309Hfs*19	ENST00000543371	NM_001198531.1	307	acg/acAg	9/14	1	2	FACETS	0.339	0.304	0.377	0.339	0.304	0.377	SUBCLONAL	1	FALSE	1	0.363040988872072	2		1055	1835	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0009897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	31	203	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.859	0.695	1	0.859	0.695	1	CLONAL	1	TRUE	1	0.186927156711555	2		203	386	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0009897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1284	119	462	1	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.186927156711555	1	FACETS	0.823	0.74	0.911	0.823	0.74	0.911	CLONAL	1	TRUE	0	0.186927156711555	1		463	1403	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974792	21974792	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs141798398	NA	P-0009897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	29	63	0	ENST00000304494.5:c.35C>A	p.Ser12Ter	p.S12*	ENST00000304494	NM_000077.4	12	tCg/tAg	1/3	1	2	FACETS	0.664	0.532	0.815	0.664	0.532	0.815	SUBCLONAL	1	TRUE	1	0.186927156711555	2		63	467	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335121	65335121	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	81	363	1	ENST00000342505.4:c.520C>T	p.Arg174Ter	p.R174*	ENST00000342505	NM_002227.2	174	Cga/Tga	6/25	0.186927156711555	1	FACETS	0.786	0.69	0.888	0.786	0.69	0.888	SUBCLONAL	1	TRUE	0	0.186927156711555	1		364	1000	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416600	49416600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	80	348	0	ENST00000301067.7:c.16111G>A	p.Glu5371Lys	p.E5371K	ENST00000301067	NM_003482.3	5371	Gag/Aag	51/54	1	2	FACETS	0.923	0.811	1	0.923	0.811	1	CLONAL	1	TRUE	1	0.186927156711555	2		348	927	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099397	27099397	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	80	383	0	ENST00000324856.7:c.3634C>T	p.Gln1212Ter	p.Q1212*	ENST00000324856	NM_006015.4	1212	Cag/Tag	14/20	1	2	FACETS	0.778	0.683	0.881	0.778	0.683	0.881	SUBCLONAL	1	TRUE	1	0.186927156711555	2		383	1100	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184631	11184631	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	106	423	0	ENST00000361445.4:c.6586G>T	p.Glu2196Ter	p.E2196*	ENST00000361445	NM_004958.3	2196	Gag/Tag	47/58	1	2	FACETS	0.883	0.789	0.984	0.883	0.789	0.984	CLONAL	1	TRUE	1	0.186927156711555	2		423	1284	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199603	16199603	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1488988771	NA	P-0009897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	56	272	0	ENST00000375759.3:c.376G>A	p.Glu126Lys	p.E126K	ENST00000375759	NM_015001.2	126	Gaa/Aaa	2/15	1	2	FACETS	0.758	0.648	0.879	0.758	0.648	0.879	SUBCLONAL	1	TRUE	1	0.186927156711555	2		272	790	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242628	16242628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	58	378	1	ENST00000375759.3:c.1249G>A	p.Glu417Lys	p.E417K	ENST00000375759	NM_015001.2	417	Gaa/Aaa	6/15	1	2	FACETS	0.575	0.492	0.666	0.575	0.492	0.666	SUBCLONAL	1	TRUE	1	0.186927156711555	2		379	1080	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416726	29416726	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs139086136	NA	P-0009897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	52	244	0	ENST00000389048.3:c.4227G>C	p.Glu1409Asp	p.E1409D	ENST00000389048	NM_004304.4	1409	gaG/gaC	29/29	1	2	FACETS	0.751	0.638	0.875	0.751	0.638	0.875	SUBCLONAL	1	TRUE	1	0.186927156711555	2		244	741	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155681	56155681	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	60	296	0	ENST00000399503.3:c.773C>T	p.Ser258Leu	p.S258L	ENST00000399503	NM_005921.1	258	tCa/tTa	3/20	1	2	FACETS	0.64	0.55	0.739	0.64	0.55	0.739	SUBCLONAL	1	TRUE	1	0.186927156711555	2		296	1003	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637673	176637673	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	76	323	0	ENST00000439151.2:c.2273C>T	p.Ser758Leu	p.S758L	ENST00000439151	NM_022455.4	758	tCa/tTa	5/23	1	2	FACETS	0.844	0.738	0.958	0.844	0.738	0.958	CLONAL	1	TRUE	1	0.186927156711555	2		323	964	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639026	176639026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	66	282	0	ENST00000439151.2:c.3626C>T	p.Pro1209Leu	p.P1209L	ENST00000439151	NM_022455.4	1209	cCt/cTt	5/23	1	2	FACETS	0.823	0.713	0.943	0.823	0.713	0.943	CLONAL	1	TRUE	1	0.186927156711555	2		282	858	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547220	106547220	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	48	210	0	ENST00000369096.4:c.457G>A	p.Glu153Lys	p.E153K	ENST00000369096	NM_001198.3	153	Gaa/Aaa	4/7	1	2	FACETS	0.722	0.609	0.847	0.722	0.609	0.847	SUBCLONAL	1	TRUE	1	0.186927156711555	2		210	711	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771909	135771909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	49	277	0	ENST00000298552.3:c.3208G>A	p.Ala1070Thr	p.A1070T	ENST00000298552	NM_001162426.1	1070	Gcg/Acg	23/23	1	2	FACETS	0.539	0.455	0.633	0.539	0.455	0.633	SUBCLONAL	1	TRUE	1	0.186927156711555	2		277	972	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858925	57858925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1681	141	702	0	ENST00000228682.2:c.421C>T	p.His141Tyr	p.H141Y	ENST00000228682	NM_005269.2	141	Cac/Tac	5/12	1	2	FACETS	0.828	0.751	0.91	0.828	0.751	0.91	CLONAL	1	TRUE	1	0.186927156711555	2		702	1822	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028539	42028539	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1763	138	667	0	ENST00000219905.7:c.4077C>G	p.Ile1359Met	p.I1359M	ENST00000219905	NM_001164273.1	1359	atC/atG	13/24	1	2	FACETS	0.777	0.703	0.854	0.777	0.703	0.854	SUBCLONAL	1	TRUE	1	0.186927156711555	2		667	1901	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104389	2104389	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs137854406	NA	P-0009897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	80	416	0	ENST00000219476.3:c.429C>G	p.Phe143Leu	p.F143L	ENST00000219476	NM_000548.3	143	ttC/ttG	5/42	1	2	FACETS	0.709	0.622	0.803	0.709	0.622	0.803	SUBCLONAL	1	TRUE	1	0.186927156711555	2		416	1207	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835733	68835733	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1255	88	481	0	ENST00000261769.5:c.324A>C	p.Arg108Ser	p.R108S	ENST00000261769	NM_004360.3	108	agA/agC	3/16	0.186927156711555	1	FACETS	0.636	0.561	0.716	0.636	0.561	0.716	SUBCLONAL	1	TRUE	0	0.186927156711555	1		481	1343	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796353	42796353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	85	383	0	ENST00000575354.2:c.3002C>T	p.Ser1001Phe	p.S1001F	ENST00000575354	NM_015125.3	1001	tCc/tTc	12/20	1	2	FACETS	0.722	0.636	0.815	0.722	0.636	0.815	SUBCLONAL	1	TRUE	1	0.186927156711555	2		383	1260	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46271054	46271054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1601	134	571	0	ENST00000371998.3:c.3178C>T	p.Leu1060Phe	p.L1060F	ENST00000371998		1060	Ctt/Ttt	17/23	1	2	FACETS	0.826	0.748	0.91	0.826	0.748	0.91	CLONAL	1	TRUE	1	0.186927156711555	2		571	1735	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835740	68835752	+	frameshift_variant	Frame_Shift_Del	DEL	TCCACCAAAGTCA	TCCACCAAAGTCA	-	novel	NA	P-0009897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1241	82	484	0	ENST00000261769.5:c.331_343del	p.Ser111ArgfsTer2	p.S111Rfs*2	ENST00000261769	NM_004360.3	111	TCCACCAAAGTCAcg/cg	3/16	0.186927156711555	1	FACETS	0.601	0.528	0.68	0.601	0.528	0.68	SUBCLONAL	1	TRUE	0	0.186927156711555	1		484	1323	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0009902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	40	504	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.796	0.662	0.944	0.796	0.662	0.944	CLONAL	1	TRUE	1	0.242307643286783	2		504	415	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0009902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	76	618	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.871	0.769	0.979	1	0.981	1	CLONAL	2	TRUE	1	0.242307643286783	2		618	360	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295773	212295773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1299031105	NA	P-0009902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	70	492	0	ENST00000342788.4:c.2540G>A	p.Arg847His	p.R847H	ENST00000342788	NM_005235.2	847	cGt/cAt	21/28	0.185009162009308	2	FACETS	1	0.962	1	0.634	0.554	0.719	CLONAL	1	TRUE	0	0.242307643286783	2		492	456	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100451	8100451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1266983268	NA	P-0009902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	153	585	0	ENST00000346208.3:c.425C>T	p.Ser142Leu	p.S142L	ENST00000346208		142	tCg/tTg	3/6	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.242307643286783	2		585	1065	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238951	5238951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237159914	NA	P-0009902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	45	330	1	ENST00000357368.4:c.1828C>T	p.Arg610Trp	p.R610W	ENST00000357368	NM_002850.3	610	Cgg/Tgg	13/38	1	2	FACETS	0.758	0.637	0.892	0.758	0.637	0.892	SUBCLONAL	1	TRUE	1	0.242307643286783	2		331	490	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764312	39764312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751217612	NA	P-0009902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	35	304	1	ENST00000288319.7:c.800C>T	p.Thr267Met	p.T267M	ENST00000288319	NM_182918.3	267	aCg/aTg	7/10	1	2	FACETS	0.431	0.352	0.52	0.431	0.352	0.52	SUBCLONAL	1	TRUE	1	0.242307643286783	2		305	671	SUCCESS
APC	324	MSKCC	GRCh37	5	112175527	112175527	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	33	314	0	ENST00000257430.4:c.4237del	p.Met1413TrpfsTer2	p.M1413Wfs*2	ENST00000257430	NM_000038.5	1412	ggA/gg	16/16	1	2	FACETS	0.578	0.47	0.7	0.578	0.47	0.7	SUBCLONAL	1	TRUE	1	0.242307643286783	2		314	471	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0009909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	120	939	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.326598400692199	2		940	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0009909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	133	1128	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.326598400692199	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.326598400692199	1		1129	642	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869552	102869552	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766508915	NA	P-0009909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	36	188	0	ENST00000307046.8:c.89C>T	p.Ser30Leu	p.S30L	ENST00000307046	NM_001111285.1	30	tCg/tTg	2/4	0.326598400692199	3	FACETS	0.602	0.495	0.722	0.301	0.247	0.361	SUBCLONAL	1	TRUE	1	0.326598400692199	3		188	426	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976727	2976727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1298741148	NA	P-0009909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	109	449	2	ENST00000396946.4:c.1285G>A	p.Val429Ile	p.V429I	ENST00000396946	NM_032415.4	429	Gtc/Atc	9/25	0.307671998212637	1	FACETS	0.877	0.789	0.97	0.877	0.789	0.97	CLONAL	1	TRUE	0	0.326598400692199	1		451	637	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0009935-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	10	311	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.411	0.277	0.582	0.411	0.277	0.582	SUBCLONAL	1	TRUE	1	0.11	2		311	442	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500520	99500520	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009935-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	34	312	0	ENST00000268035.6:c.3953A>G	p.Asp1318Gly	p.D1318G	ENST00000268035	NM_000875.3	1318	gAc/gGc	21/21	1	2	FACETS	0.916	0.746	1	0.916	0.746	1	CLONAL	1	TRUE	1	0.11	2		312	675	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0009945-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	95	430	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.443626526047342	4	FACETS	1	0.92	1	1	0.92	1	CLONAL	3	TRUE	1	0.443626526047342	4		430	204	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519988	NA	P-0009945-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	143	526	0	ENST00000269305.4:c.808T>G	p.Phe270Val	p.F270V	ENST00000269305	NM_001126112.2	270	Ttt/Gtt	8/11	0.443626526047342	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.443626526047342	1		526	392	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573813	64573813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139936447	NA	P-0009945-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	43	250	1	ENST00000312049.6:c.940C>T	p.Arg314Trp	p.R314W	ENST00000312049	NM_130799.2	314	Cgg/Tgg	7/10	0.443626526047342	4	FACETS	1	0.937	1	0.409	0.345	0.478	CLONAL	1	TRUE	1	0.443626526047342	4		251	228	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0009948-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	129	291	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.219280844182256	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.268006829063161	1		291	780	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0009948-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	145	378	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.139139811537798	4	FACETS	1	0.98	1	0.629	0.573	0.689	INDETERMINATE	1	TRUE	2	0.268006829063161	4		378	1090	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909347	41909347	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009948-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	55	115	0	ENST00000372991.4:c.41G>T	p.Arg14Leu	p.R14L	ENST00000372991	NM_001760.3	14	cGg/cTg	1/5	0.139139811537798	4	FACETS	0.796	0.685	0.916	0.796	0.685	0.916	INDETERMINATE	2	TRUE	2	0.268006829063161	4		115	327	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374701	118374701	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009948-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	195	462	0	ENST00000534358.1:c.8094A>T	p.Glu2698Asp	p.E2698D	ENST00000534358	NM_005933.3	2698	gaA/gaT	27/36	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.268006829063161	2		462	1225	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81922859	81922859	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009948-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1395	305	696	0	ENST00000359376.3:c.848C>A	p.Pro283His	p.P283H	ENST00000359376	NM_002661.3	283	cCt/cAt	10/33	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.268006829063161	2		696	1700	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686344	30686344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	103	284	0	ENST00000295754.5:c.200G>A	p.Cys67Tyr	p.C67Y	ENST00000295754	NM_003242.5	67	tGc/tAc	2/7	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.193899816161093	2		284	1002	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600407	10600407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867398451	NA	P-0009955-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1861	187	494	0	ENST00000171111.5:c.1448G>A	p.Arg483His	p.R483H	ENST00000171111	NM_203500.1	483	cGc/cAc	4/6	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.16	2		494	2048	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0009955-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1409	171	607	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.16	2		608	1580	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	293	386	0	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	1	2	FACETS	0.985	0.928	1	0.985	0.928	1	CLONAL	1	TRUE	1	0.614741395423699	2		386	968	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969968	161969968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746215864	NA	P-0009988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	318	473	2	ENST00000366898.1:c.1001G>A	p.Arg334His	p.R334H	ENST00000366898	NM_004562.2	334	cGc/cAc	9/12	1	2	FACETS	0.983	0.929	1	0.983	0.929	1	CLONAL	1	TRUE	1	0.614741395423699	2		475	1052	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138376569	138376569	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	373	540	1	ENST00000289153.2:c.2905C>A	p.Gln969Lys	p.Q969K	ENST00000289153	NM_006219.2	969	Caa/Aaa	20/22	1	2	FACETS	0.95	0.901	0.999	0.95	0.901	0.999	CLONAL	1	TRUE	1	0.614741395423699	2		541	1278	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061219	38061219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	218	319	1	ENST00000250448.2:c.770G>A	p.Gly257Asp	p.G257D	ENST00000250448	NM_004496.3	257	gGc/gAc	2/2	1	2	FACETS	0.955	0.891	1	0.955	0.891	1	CLONAL	1	TRUE	1	0.614741395423699	2		320	743	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023308	27023308	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	37	87	0	ENST00000324856.7:c.414del	p.Ala139ProfsTer93	p.A139Pfs*93	ENST00000324856	NM_006015.4	138	tcA/tc	1/20	1	2	FACETS	0.672	0.561	0.794	0.672	0.561	0.794	SUBCLONAL	1	TRUE	1	0.614741395423699	2		87	179	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772216	68772222	+	frameshift_variant	Frame_Shift_Del	DEL	GCCAGGA	GCCAGGA	-	novel	NA	P-0009988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	292	561	2	ENST00000261769.5:c.68_74del	p.Gln23ArgfsTer31	p.Q23Rfs*31	ENST00000261769	NM_004360.3	22	tGCCAGGAg/tg	2/16	0.614741395423699	1	FACETS	0.857	0.81	0.904	0.857	0.81	0.904	CLONAL	1	TRUE	0	0.614741395423699	1		563	768	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0009998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	86	381	1				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.915	1			1	INDETERMINATE	1	TRUE	NA	0.613656669509801	2		382	274	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798770	42798770	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	126	454	0	ENST00000575354.2:c.4342G>C	p.Asp1448His	p.D1448H	ENST00000575354	NM_015125.3	1448	Gac/Cac	19/20	0.389907895828588	1	FACETS	0.563	0.512	0.615	0.563	0.512	0.615	SUBCLONAL	1	TRUE	0	0.613656669509801	1		454	506	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211805	123211805	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0009998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	195	517	0	ENST00000218089.9:c.2674-2A>G		p.X892_splice	ENST00000218089	NM_001042749.1	892			0.523046766160908	1	FACETS	0.864	0.807	0.922	0.864	0.807	0.922	CLONAL	1	TRUE	0	0.613656669509801	1		517	510	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089721	27089721	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	128	344	0	ENST00000324856.7:c.2680del	p.Thr894ProfsTer25	p.T894Pfs*25	ENST00000324856	NM_006015.4	893	Aaa/aa	8/20	1	2	FACETS	0.935	0.854	1	0.935	0.854	1	CLONAL	1	TRUE	1	0.613656669509801	2		344	446	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0010002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	103	430	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	1	2	FACETS	0.465	0.417	0.516	0.465	0.417	0.516	SUBCLONAL	1	TRUE	1	0.685709349382868	2		430	646	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517201	NA	P-0010002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	85	241	0	ENST00000263967.3:c.1637A>C	p.Gln546Pro	p.Q546P	ENST00000263967	NM_006218.2	546	cAg/cCg	10/21	1	2	FACETS	0.623	0.554	0.696	0.623	0.554	0.696	SUBCLONAL	1	TRUE	1	0.685709349382868	2		241	398	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045979	47045979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556782944	NA	P-0010002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	143	432	0	ENST00000377604.3:c.2774G>A	p.Arg925His	p.R925H	ENST00000377604	NM_001204468.1	925	cGc/cAc	24/24	1	2	FACETS	0.585	0.534	0.638	0.585	0.534	0.638	SUBCLONAL	1	TRUE	1	0.685709349382868	2		432	713	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070640	67070643	+	frameshift_variant	Frame_Shift_Del	DEL	AGAA	AGAA	-	novel	NA	P-0010002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	123	416	0	ENST00000412916.2:c.267_270del	p.Arg90LysfsTer7	p.R90Kfs*7	ENST00000412916		88	ttAGAA/tt	3/6	0.393958950675838	1	FACETS	0.373	0.338	0.41	0.373	0.338	0.41	INDETERMINATE	1	TRUE	0	0.685709349382868	1		416	632	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0010012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	249	586	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	0.995	1	CLONAL	2	TRUE	1	0.24	2		586	990	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0010012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	242	403	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	1	0.942	1	1	0.995	1	CLONAL	2	TRUE	1	0.24	2		403	1000	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112422	115112422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775182377	NA	P-0010012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	58	399	1	ENST00000257566.3:c.1318G>A	p.Ala440Thr	p.A440T	ENST00000257566	NM_016569.3	440	Gcc/Acc	7/8	1	2	FACETS	0.666	0.571	0.769	0.666	0.571	0.769	SUBCLONAL	1	TRUE	1	0.24	2		400	726	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437608	56437609	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0010012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	114	446	0	ENST00000407977.2:c.853dup	p.Leu285ProfsTer9	p.L285Pfs*9	ENST00000407977		285	cta/cCta	8/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.24	2		446	715	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974738	21974738	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	142	372	0	ENST00000304494.5:c.89del	p.Ala30GlyfsTer23	p.A30Gfs*23	ENST00000304494	NM_000077.4	30	gCg/gg	1/3	1	2	FACETS	0.86	0.785	0.938	1	0.989	1	CLONAL	2	TRUE	1	0.24	2		372	688	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438143	56438144	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0010012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	179	731	0	ENST00000407977.2:c.849_849+1delinsTT		p.X283_splice	ENST00000407977		283		7/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.24	2		731	1125	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244816	41244816	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	1056	710	0	ENST00000357654.3:c.2732del	p.Gly911GlufsTer89	p.G911Efs*89	ENST00000357654	NM_007294.3	911	gGa/ga	10/23	0.780762148093142	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	4	TRUE	0	0.789385995182347	4		710	1192	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579359	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0010035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	502	527	0	ENST00000269305.4:c.327_328dup	p.Arg110ProfsTer14	p.R110Pfs*14	ENST00000269305	NM_001126112.2	110	cgt/cCCgt	4/11	0.762468627860053	2	FACETS	0.915	0.889	0.94	0.915	0.889	0.94	CLONAL	2	TRUE	0	0.789385995182347	2		527	695	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0010042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	36	489	1	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.226380352987595	4	FACETS	0.96	0.791	1	0.48	0.395	0.574	CLONAL	1	TRUE	2	0.283034821897746	4		490	340	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951932	178951932	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1245520052	NA	P-0010042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	33	427	1	ENST00000263967.3:c.2987A>G	p.Asn996Ser	p.N996S	ENST00000263967	NM_006218.2	996	aAt/aGt	21/21	0.230343339492214	3	FACETS	1	0.884	1	0.555	0.454	0.666	CLONAL	1	TRUE	1	0.283034821897746	3		428	240	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508554	106508554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755975307	NA	P-0010042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	18	150	0	ENST00000359195.3:c.548C>T	p.Pro183Leu	p.P183L	ENST00000359195	NM_002649.2	183	cCg/cTg	2/11	0.283034821897746	6	FACETS	0.958	0.732	1			1	CLONAL	2	TRUE	NA	0.283034821897746	6		150	104	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575231	48575231	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0010042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	34	370	0	ENST00000342988.3:c.424+1G>T		p.X142_splice	ENST00000342988	NM_005359.5	142			1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.283034821897746	2		370	209	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578209	7578209	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	32	634	0	ENST00000269305.4:c.640del	p.His214IlefsTer33	p.H214Ifs*33	ENST00000269305	NM_001126112.2	214	Cat/at	6/11	1	2	FACETS	0.873	0.712	1	0.873	0.712	1	CLONAL	1	TRUE	1	0.283034821897746	2		634	259	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0010055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	783	617	1	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.755993970853294	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.755993970853294	2		618	1029	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271350	26271350	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs532386575	NA	P-0010055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	471	1123	0	ENST00000305910.3:c.263C>A	p.Ser88Tyr	p.S88Y	ENST00000305910	NM_003534.2	88	tCc/tAc	1/1	0.755993970853294	2	FACETS	0.774	0.739	0.811	0.387	0.369	0.406	SUBCLONAL	1	TRUE	0	0.755993970853294	2		1123	1609	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955385	48955385	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	40	208	0	ENST00000267163.4:c.1501A>T	p.Ser501Cys	p.S501C	ENST00000267163	NM_000321.2	501	Agt/Tgt	17/27	0.755993970853294	3	FACETS	0.704	0.591	0.828	0.235	0.197	0.276	SUBCLONAL	1	TRUE	0	0.755993970853294	3		208	207	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033815	49033859	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCCCACAGTGTATCGGCTAGCCTATCTCCGGCTAAATACACTTT	TTCCCACAGTGTATCGGCTAGCCTATCTCCGGCTAAATACACTTT	-	novel	NA	P-0010055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	461	471	0	ENST00000267163.4:c.1961-9_1996del		p.X654_splice	ENST00000267163	NM_000321.2	654		20/27	0.755993970853294	3	FACETS	0.949	0.924	0.974	0.949	0.924	0.974	CLONAL	3	TRUE	0	0.755993970853294	3		471	590	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0010058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	268	325	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	0.959	0.901	1	0.959	0.901	1	CLONAL	1	TRUE	1	0.594065929601865	2		325	941	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028178	48028178	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1270	75	493	0	ENST00000234420.5:c.3056T>A	p.Ile1019Lys	p.I1019K	ENST00000234420	NM_000179.2	1019	aTa/aAa	4/10	1	2	FACETS	0.188	0.163	0.214	0.188	0.163	0.214	SUBCLONAL	1	TRUE	1	0.594065929601865	2		493	1345	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557336	29557336	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	46	438	0	ENST00000356175.3:c.3049C>T	p.Gln1017Ter	p.Q1017*	ENST00000356175	NM_000267.3	1017	Caa/Taa	23/57	0.594065929601865	1	FACETS	0.141	0.118	0.166	0.141	0.118	0.166	SUBCLONAL	1	TRUE	0	0.594065929601865	1		438	773	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0010065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	12	524	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.148985922980704	3	FACETS	0.55	0.384	0.755	0.275	0.192	0.378	SUBCLONAL	1	TRUE	1	0.09	3		524	507	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193110982	193110982	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	22	250	0	ENST00000367435.3:c.515C>T	p.Ser172Phe	p.S172F	ENST00000367435	NM_024529.4	172	tCt/tTt	7/17	0.148985922980704	3	FACETS	1	0.887	1	0.632	0.489	0.799	CLONAL	1	TRUE	1	0.09	3		250	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0010071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	117	680	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	0.313245238014224	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	0	0.313245238014224	1		680	524	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478922	56478922	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	186	1022	0	ENST00000267101.3:c.378C>A	p.Asn126Lys	p.N126K	ENST00000267101	NM_001982.3	126	aaC/aaA	3/28	0.0482520782633067	3	FACETS	1	0.987	1	0.667	0.615	0.72	INDETERMINATE	1	FALSE	1	0.313245238014224	3		1022	1030	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164869	123164869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	215	591	1	ENST00000218089.9:c.182G>A	p.Gly61Glu	p.G61E	ENST00000218089	NM_001042749.1	61	gGa/gAa	5/35	1	1	FACETS	0.837	0.781	0.893	1	0.993	1	CLONAL	2	FALSE	0	0.313245238014224	1		592	692	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0010086-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	269	532	3	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	0.644836190906641	5	FACETS	0.94	0.884	0.997	0.627	0.589	0.665	CLONAL	2	TRUE	2	0.644836190906641	5		535	873	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105782	27105782	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0010086-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	478	652	0	ENST00000324856.7:c.5393C>G	p.Ser1798Ter	p.S1798*	ENST00000324856	NM_006015.4	1798	tCa/tGa	20/20	0.644836190906641	4	FACETS	0.995	0.96	1	0.995	0.96	1	CLONAL	3	TRUE	1	0.644836190906641	4		652	817	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211157	55211157	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010086-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	286	554	0	ENST00000275493.2:c.400G>T	p.Glu134Ter	p.E134*	ENST00000275493	NM_005228.3	134	Gag/Tag	3/28	0.601523808863288	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	2	0.644836190906641	4		554	709	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621926	1621926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010086-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	199	939	0	ENST00000344749.5:c.866C>T	p.Ser289Phe	p.S289F	ENST00000344749	NM_001136139.2	289	tCt/tTt	11/19	0.529184948686775	4	FACETS	1	0.96	1	0.527	0.488	0.568	CLONAL	1	TRUE	2	0.644836190906641	4		939	963	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256530	+	missense_variant	Missense_Mutation	DNP	TG	TG	CT	rs1057519834	NA	P-0010086-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	531	753	0	ENST00000369535.4:c.181_182delinsAG	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	CAa/AGa	3/7	0.492204647393499	5	FACETS	1	0.993	1			1	CLONAL	3	TRUE	NA	0.644836190906641	5		753	968	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0010088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	110	203	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.184516346726138	6	FACETS	1	0.976	1	0.431	0.387	0.477	INDETERMINATE	1	TRUE	3	0.40799843931098	6		203	758	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602493	10602493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	139	404	0	ENST00000171111.5:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000171111	NM_203500.1	362	cGg/cAg	3/6	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.40799843931098	2		404	601	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587175	189587175	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	180	448	0	ENST00000264731.3:c.1192G>A	p.Asp398Asn	p.D398N	ENST00000264731	NM_003722.4	398	Gat/Aat	9/14	0.184516346726138	6	FACETS	1	0.985	1	0.432	0.398	0.469	INDETERMINATE	1	TRUE	3	0.40799843931098	6		448	1235	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502404	186502405	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0010088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1947	294	899	0	ENST00000323963.5:c.131_132del	p.Leu44ProfsTer10	p.L44Pfs*10	ENST00000323963		43	TCt/t	3/11	0.184516346726138	6	FACETS	1	0.986	1	0.389	0.364	0.415	INDETERMINATE	1	TRUE	3	0.40799843931098	6		899	2241	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586422	189586422	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	120	258	0	ENST00000264731.3:c.1046G>T	p.Gly349Val	p.G349V	ENST00000264731	NM_003722.4	349	gGa/gTa	8/14	0.184516346726138	6	FACETS	1	0.981	1	0.455	0.411	0.502	INDETERMINATE	1	TRUE	3	0.40799843931098	6		258	782	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965677	93965677	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	262	857	0	ENST00000369303.4:c.2251G>C	p.Asp751His	p.D751H	ENST00000369303	NM_004440.3	751	Gat/Cat	13/17	1	2	FACETS	0.956	0.894	1	0.956	0.894	1	CLONAL	1	TRUE	1	0.40799843931098	2		857	1343	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004305	29004305	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0010088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	123	413	0	ENST00000282397.4:c.989-1G>C		p.X330_splice	ENST00000282397	NM_002019.4	330			1	2	FACETS	0.769	0.696	0.846	0.769	0.696	0.846	SUBCLONAL	1	TRUE	1	0.40799843931098	2		413	784	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217012	7217012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371474455	NA	P-0010088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	369	756	2	ENST00000380728.2:c.509C>T	p.Ala170Val	p.A170V	ENST00000380728		170	gCt/gTt	7/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.40799843931098	2		758	1519	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602939	10602939	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0010088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	155	373	0	ENST00000171111.5:c.640-1G>A		p.X214_splice	ENST00000171111	NM_203500.1	214			1	2	FACETS	0.987	0.905	1	0.987	0.905	1	CLONAL	1	TRUE	1	0.40799843931098	2		373	770	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791187	42791187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768744137	NA	P-0010088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	77	298	1	ENST00000575354.2:c.247G>A	p.Glu83Lys	p.E83K	ENST00000575354	NM_015125.3	83	Gaa/Aaa	3/20	1	2	FACETS	0.759	0.668	0.857	0.759	0.668	0.857	SUBCLONAL	1	TRUE	1	0.40799843931098	2		299	497	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860609	45860609	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1192166210	NA	P-0010088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	259	659	0	ENST00000391945.4:c.1398C>G	p.Ile466Met	p.I466M	ENST00000391945	NM_000400.3	466	atC/atG	15/23	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.40799843931098	2		659	1251	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39713132	39713132	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1213	180	558	0	ENST00000361337.2:c.538G>C	p.Asp180His	p.D180H	ENST00000361337	NM_003286.2	180	Gat/Cat	8/21	0.335491810790625	3	FACETS	0.763	0.701	0.827	0.381	0.35	0.414	SUBCLONAL	1	TRUE	1	0.40799843931098	3		558	1393	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524454	44524454	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	176	438	0	ENST00000291552.4:c.103C>G	p.Arg35Gly	p.R35G	ENST00000291552	NM_006758.2	35	Cgg/Ggg	2/8	0.335491810790625	3	FACETS	0.874	0.803	0.947	0.437	0.401	0.474	CLONAL	1	TRUE	1	0.40799843931098	3		438	1189	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0010098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	111	432	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.508781171052576	3	FACETS	0.876	0.789	0.967	0.438	0.394	0.484	CLONAL	1	TRUE	1	0.508781171052576	3		432	625	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0010098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	120	401	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.508781171052576	3	FACETS	1	0.966	1	0.568	0.515	0.623	CLONAL	1	TRUE	1	0.508781171052576	3		401	521	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0010098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	229	372	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.508781171052576	3	FACETS	0.899	0.843	0.956	0.899	0.843	0.956	CLONAL	2	TRUE	1	0.508781171052576	3		372	628	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0010098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	157	341	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.508781171052576	3	FACETS	0.946	0.877	1	0.946	0.877	1	CLONAL	2	TRUE	1	0.508781171052576	3		341	409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0010098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	402	478	1	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	0.508781171052576	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.508781171052576	2		479	725	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298032	11298032	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	200	540	0	ENST00000361445.4:c.2076C>G	p.Asn692Lys	p.N692K	ENST00000361445	NM_004958.3	692	aaC/aaG	13/58	0.502254052309443	2	FACETS	1	0.982	1	0.581	0.54	0.622	CLONAL	1	TRUE	0	0.508781171052576	2		540	677	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401091	139401091	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	58	498	0	ENST00000277541.6:c.3902G>T	p.Gly1301Val	p.G1301V	ENST00000277541	NM_017617.3	1301	gGg/gTg	24/34	0.212114580200404	3	FACETS	0.502	0.431	0.579	0.251	0.215	0.29	INDETERMINATE	1	TRUE	1	0.508781171052576	3		498	570	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597829	43597829	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	505	831	0	ENST00000355710.3:c.377T>G	p.Phe126Cys	p.F126C	ENST00000355710	NM_020975.4	126	tTc/tGc	3/20	0.508781171052576	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.508781171052576	2		831	943	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134346	41134346	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1823	281	1037	3	ENST00000379561.5:c.1282C>T	p.Gln428Ter	p.Q428*	ENST00000379561	NM_002015.3	428	Caa/Taa	2/3	0.508781171052576	5	FACETS	0.926	0.866	0.988	0.231	0.216	0.247	CLONAL	1	TRUE	1	0.508781171052576	5		1040	2104	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227017	53227017	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	235	394	0	ENST00000375401.3:c.2558T>C	p.Leu853Pro	p.L853P	ENST00000375401	NM_004187.3	853	cTc/cCc	18/26	0.204329454459049	2	FACETS	0.844	0.795	0.894			1	INDETERMINATE	2	TRUE	NA	0.508781171052576	2		394	547	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224453	123224453	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	233	443	3	ENST00000218089.9:c.3306G>T	p.Met1102Ile	p.M1102I	ENST00000218089	NM_001042749.1	1102	atG/atT	31/35	0.43622750161236	2	FACETS	1	0.99	1			1	CLONAL	1	TRUE	NA	0.508781171052576	2		446	709	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226456	133226523	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGGCCTCGGCCATCGTGACCTGGAAAGACCCAGTGAAGCCTTAAATCTCAGGATCTCGGGCTGCGCA	GAGGCCTCGGCCATCGTGACCTGGAAAGACCCAGTGAAGCCTTAAATCTCAGGATCTCGGGCTGCGCA	-	novel	NA	P-0010098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	34	512	0	ENST00000320574.5:c.3583-48_3602del		p.X1195_splice	ENST00000320574	NM_006231.2	1195		30/49	1	2	FACETS	0.234	0.191	0.283	0.234	0.191	0.283	SUBCLONAL	1	TRUE	1	0.508781171052576	2		512	571	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0010116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	79	406	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.511	0.449	0.579	0.511	0.449	0.579	SUBCLONAL	1	TRUE	1	0.357218610605768	2		406	865	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0010116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	251	525	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.217706937079863	3	FACETS	0.834	0.781	0.889	0.834	0.781	0.889	CLONAL	2	TRUE	1	0.357218610605768	3		525	993	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429977	78429978	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1200882279	NA	P-0010116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	160	493	1	ENST00000370768.2:c.901dup	p.Ile301AsnfsTer4	p.I301Nfs*4	ENST00000370768	NM_003902.3	301	ata/aAta	11/20	1	2	FACETS	0.979	0.898	1	0.979	0.898	1	CLONAL	1	TRUE	1	0.357218610605768	2		494	915	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	149	657	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.357218610605768	2		657	769	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67459125	67459125	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	232	654	0	ENST00000327367.4:c.545del	p.Pro182LeufsTer4	p.P182Lfs*4	ENST00000327367	NM_005902.3	181	Ccc/cc	4/9	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.357218610605768	2		654	1112	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	68	235	1	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	0.217706937079863	3	FACETS	0.853	0.743	0.971	0.427	0.371	0.486	CLONAL	1	TRUE	1	0.357218610605768	3		236	526	SUCCESS
APC	324	MSKCC	GRCh37	5	112175630	112175630	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	243	715	0	ENST00000257430.4:c.4339C>T	p.Gln1447Ter	p.Q1447*	ENST00000257430	NM_000038.5	1447	Caa/Taa	16/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.357218610605768	2		715	1248	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054984	176054984	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	110	735	2	ENST00000367669.3:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000367669	NM_022457.5	357	Cga/Tga	10/20	1	2	FACETS	0.513	0.459	0.57	0.513	0.459	0.57	SUBCLONAL	1	TRUE	1	0.357218610605768	2		737	1201	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542110	187542110	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	78	423	3	ENST00000441802.2:c.5630del	p.Pro1877LeufsTer20	p.P1877Lfs*20	ENST00000441802	NM_005245.3	1877	cCt/ct	10/27	1	2	FACETS	0.569	0.499	0.644	0.569	0.499	0.644	SUBCLONAL	1	TRUE	1	0.357218610605768	2		426	768	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755427	39755427	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	104	627	2	ENST00000288319.7:c.1338del	p.Phe446LeufsTer59	p.F446Lfs*59	ENST00000288319	NM_182918.3	446	ttT/tt	10/10	1	2	FACETS	0.56	0.5	0.624	0.56	0.5	0.624	SUBCLONAL	1	TRUE	1	0.357218610605768	2		629	1040	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480083	20480083	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	178	453	1	ENST00000346618.3:c.400C>T	p.Arg134Ter	p.R134*	ENST00000346618	NM_001949.4	134	Cga/Tga	2/7	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.357218610605768	2		454	827	SUCCESS
APC	324	MSKCC	GRCh37	5	112175021	112175021	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs79122263	NA	P-0010116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	150	417	2	ENST00000257430.4:c.3730C>T	p.Gln1244Ter	p.Q1244*	ENST00000257430	NM_000038.5	1244	Caa/Taa	16/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.357218610605768	2		419	692	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257321	16257321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1387656709	NA	P-0010116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	191	605	0	ENST00000375759.3:c.4586G>A	p.Arg1529His	p.R1529H	ENST00000375759	NM_015001.2	1529	cGt/cAt	11/15	1	2	FACETS	0.999	0.923	1	0.999	0.923	1	CLONAL	1	TRUE	1	0.357218610605768	2		605	1070	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012846	176012846	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	57	605	0	ENST00000367669.3:c.1530G>T	p.Gln510His	p.Q510H	ENST00000367669	NM_022457.5	510	caG/caT	13/20	1	2	FACETS	0.336	0.287	0.389	0.336	0.287	0.389	SUBCLONAL	1	TRUE	1	0.357218610605768	2		605	951	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137427	202137427	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	182	472	1	ENST00000358485.4:c.655C>A	p.Leu219Met	p.L219M	ENST00000358485	NM_001080125.1	219	Ctg/Atg	4/9	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.357218610605768	2		473	909	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960095	134960095	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	164	528	0	ENST00000398015.3:c.2452A>G	p.Met818Val	p.M818V	ENST00000398015	NM_004441.4	818	Atg/Gtg	13/16	1	2	FACETS	0.959	0.88	1	0.959	0.88	1	CLONAL	1	TRUE	1	0.357218610605768	2		528	957	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627854	187627854	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	104	650	0	ENST00000441802.2:c.3128T>C	p.Val1043Ala	p.V1043A	ENST00000441802	NM_005245.3	1043	gTg/gCg	2/27	1	2	FACETS	0.532	0.475	0.593	0.532	0.475	0.593	SUBCLONAL	1	TRUE	1	0.357218610605768	2		650	1094	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176683996	176683996	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0010116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1418	180	949	3	ENST00000439151.2:c.4810A>T	p.Lys1604Ter	p.K1604*	ENST00000439151	NM_022455.4	1604	Aaa/Taa	13/23	1	2	FACETS	0.631	0.579	0.685	0.631	0.579	0.685	SUBCLONAL	1	TRUE	1	0.357218610605768	2		952	1598	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501350	140501350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906660	NA	P-0010116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	155	298	0	ENST00000288602.6:c.722C>T	p.Thr241Met	p.T241M	ENST00000288602	NM_004333.4	241	aCg/aTg	6/18	0.217706937079863	3	FACETS	0.771	0.708	0.837	0.771	0.708	0.837	SUBCLONAL	2	TRUE	1	0.357218610605768	3		298	663	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401291	139401291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751169922	NA	P-0010116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	312	618	1	ENST00000277541.6:c.3778G>A	p.Val1260Met	p.V1260M	ENST00000277541	NM_017617.3	1260	Gtg/Atg	23/34	0.217706937079863	3	FACETS	0.913	0.862	0.966	0.913	0.862	0.966	CLONAL	2	TRUE	1	0.357218610605768	3		619	1127	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456857	32456857	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	15	149	0	ENST00000332351.3:c.35C>T	p.Pro12Leu	p.P12L	ENST00000332351	NM_024426.4	12	cCg/cTg	1/10	1	2	FACETS	0.339	0.247	0.448	0.339	0.247	0.448	SUBCLONAL	1	TRUE	1	0.357218610605768	2		149	248	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240132	41240132	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	40	88	0	ENST00000379561.5:c.218A>C	p.Asn73Thr	p.N73T	ENST00000379561	NM_002015.3	73	aAc/aCc	1/3	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.357218610605768	2		88	212	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479720	67479720	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	192	532	0	ENST00000327367.4:c.1027T>G	p.Phe343Val	p.F343V	ENST00000327367	NM_005902.3	343	Ttc/Gtc	8/9	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.357218610605768	2		532	975	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764337	39764337	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	134	364	0	ENST00000288319.7:c.775G>T	p.Ala259Ser	p.A259S	ENST00000288319	NM_182918.3	259	Gcc/Tcc	7/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.357218610605768	2		364	640	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574664	41574664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1230	282	864	0	ENST00000263253.7:c.6949C>T	p.Arg2317Trp	p.R2317W	ENST00000263253	NM_001429.3	2317	Cgg/Tgg	31/31	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.357218610605768	2		864	1512	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39725955	39725955	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	36	390	0	ENST00000361337.2:c.830del	p.Asn277IlefsTer10	p.N277Ifs*10	ENST00000361337	NM_003286.2	276	Aaa/aa	10/21	1	2	FACETS	0.281	0.23	0.338	0.281	0.23	0.338	SUBCLONAL	1	TRUE	1	0.357218610605768	2		390	718	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955562	55955562	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1297	114	827	0	ENST00000263923.4:c.3383del	p.Pro1128LeufsTer57	p.P1128Lfs*57	ENST00000263923	NM_002253.2	1128	cCt/ct	25/30	1	2	FACETS	0.452	0.406	0.502	0.452	0.406	0.502	SUBCLONAL	1	TRUE	1	0.357218610605768	2		827	1411	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023035	27023036	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0010116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	32	90	0	ENST00000324856.7:c.145dup	p.Glu49GlyfsTer62	p.E49Gfs*62	ENST00000324856	NM_006015.4	47	-/G	1/20	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.357218610605768	2		90	162	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395664	45395664	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	199	523	0	ENST00000262160.6:c.470del	p.Lys157ArgfsTer6	p.K157Rfs*6	ENST00000262160	NM_005901.5	157	aAg/ag	4/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.357218610605768	2		523	939	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0010126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	335	565	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.448197621454259	5	FACETS	0.858	0.813	0.904	0.858	0.813	0.904	CLONAL	3	TRUE	2	0.448197621454259	5		565	971	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457232	25457232	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	393	442	0	ENST00000264709.3:c.2655G>T	p.Arg885Ser	p.R885S	ENST00000264709	NM_175629.2	885	agG/agT	23/23	0.442154462489305	4	FACETS	0.881	0.836	0.926	0.881	0.836	0.926	CLONAL	2	TRUE	2	0.448197621454259	4		442	1442	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097830	8097830	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1425866094	NA	P-0010126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1745	132	771	0	ENST00000346208.3:c.212C>T	p.Thr71Met	p.T71M	ENST00000346208		71	aCg/aTg	2/6	0.253726355708124	4	FACETS	0.454	0.41	0.501	0.227	0.205	0.251	INDETERMINATE	1	TRUE	2	0.448197621454259	4		771	1877	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098551	108098551	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0010126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	153	368	0	ENST00000278616.4:c.121A>T	p.Lys41Ter	p.K41*	ENST00000278616	NM_000051.3	41	Aaa/Taa	3/63	0.448197621454259	4	FACETS	0.834	0.766	0.904			1	CLONAL	2	TRUE	NA	0.448197621454259	4		368	593	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206609	108206609	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	204	716	0	ENST00000278616.4:c.8189A>T	p.Gln2730Leu	p.Q2730L	ENST00000278616	NM_000051.3	2730	cAg/cTg	56/63	0.448197621454259	4	FACETS	0.969	0.903	1			1	CLONAL	2	TRUE	NA	0.448197621454259	4		716	680	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503145	125503145	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1234061120	NA	P-0010126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	115	707	0	ENST00000428830.2:c.512T>C	p.Leu171Ser	p.L171S	ENST00000428830	NM_001114121.2	171	tTa/tCa	6/14	0.40399393968768	4	FACETS	0.82	0.738	0.907			1	CLONAL	1	TRUE	NA	0.448197621454259	4		707	906	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514940	103514940	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1008091379	NA	P-0010126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	117	439	0	ENST00000355739.4:c.1441G>T	p.Val481Leu	p.V481L	ENST00000355739	NM_000123.3	481	Gtg/Ttg	8/15	1	2	FACETS	0.718	0.648	0.792	0.718	0.648	0.792	SUBCLONAL	1	TRUE	1	0.448197621454259	2		439	727	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606188	81606188	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	105	629	0	ENST00000298171.2:c.858T>G	p.Phe286Leu	p.F286L	ENST00000298171	NM_000369.2	286	ttT/ttG	9/10	0.433549646347752	3	FACETS	0.748	0.67	0.83	0.374	0.335	0.415	SUBCLONAL	1	TRUE	1	0.448197621454259	3		629	767	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038895	47038895	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0010126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	134	162	0	ENST00000377604.3:c.901+1G>C		p.X301_splice	ENST00000377604	NM_001204468.1	301			0.448197621454259	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.448197621454259	1		162	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0010136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	283	741	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.485082662257606	1	FACETS	0.833	0.784	0.884	0.833	0.784	0.884	CLONAL	1	TRUE	0	0.508121544498265	1		742	997	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180178	38180178	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	291	407	0	ENST00000396334.3:c.26C>T	p.Pro9Leu	p.P9L	ENST00000396334	NM_002468.4	9	cCa/cTa	1/5	0.485082662257606	1	FACETS	0.981	0.926	1	0.981	0.926	1	CLONAL	1	TRUE	0	0.508121544498265	1		407	871	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178403	56178403	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	152	434	0	ENST00000399503.3:c.3376A>G	p.Thr1126Ala	p.T1126A	ENST00000399503	NM_005921.1	1126	Aca/Gca	14/20	0.508121544498265	1	FACETS	0.764	0.702	0.829	0.764	0.702	0.829	SUBCLONAL	1	TRUE	0	0.508121544498265	1		434	584	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729297	41729297	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1652	466	792	0	ENST00000242208.4:c.1232T>C	p.Ile411Thr	p.I411T	ENST00000242208	NM_002192.2	411	aTc/aCc	3/3	1	2	FACETS	0.866	0.824	0.909	0.866	0.824	0.909	CLONAL	1	TRUE	1	0.508121544498265	2		792	2118	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392057	81392057	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	191	484	0	ENST00000222390.5:c.220T>A	p.Cys74Ser	p.C74S	ENST00000222390	NM_000601.4	74	Tgt/Agt	2/18	1	2	FACETS	0.731	0.675	0.788	0.731	0.675	0.788	SUBCLONAL	1	TRUE	1	0.508121544498265	2		484	1029	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607612	43607612	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	349	516	2	ENST00000355710.3:c.1588G>T	p.Glu530Ter	p.E530*	ENST00000355710	NM_020975.4	530	Gag/Tag	8/20	1	2	FACETS	0.989	0.935	1	0.989	0.935	1	CLONAL	1	TRUE	1	0.508121544498265	2		518	1389	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943764	9943764	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	214	308	0	ENST00000330684.3:c.1177T>C	p.Tyr393His	p.Y393H	ENST00000330684	NM_001134407.1	393	Tac/Cac	5/13	1	2	FACETS	0.844	0.784	0.906	0.844	0.784	0.906	CLONAL	1	TRUE	1	0.508121544498265	2		308	998	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637121	176637122	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1299932363	NA	P-0010136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	131	288	0	ENST00000439151.2:c.1727dup	p.Asn576LysfsTer8	p.N576Kfs*8	ENST00000439151	NM_022455.4	574	gga/ggAa	5/23	0.485082662257606	1	FACETS	0.787	0.718	0.858	0.787	0.718	0.858	SUBCLONAL	1	TRUE	0	0.508121544498265	1		288	489	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956645	93956646	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0010136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1254	320	850	1	ENST00000369303.4:c.2590_2591delinsCT	p.Gly864Leu	p.G864L	ENST00000369303	NM_004440.3	864	GGc/CTc	15/17	1	2	FACETS	0.8	0.753	0.848	0.8	0.753	0.848	SUBCLONAL	1	TRUE	1	0.508121544498265	2		851	1574	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	114	939	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.918	0.825	1	0.918	0.825	1	CLONAL	1	TRUE	1	0.248252948240534	2		940	1000	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0010146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1274	166	617	1	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.247453647649827	1	FACETS	0.813	0.745	0.886	0.813	0.745	0.886	CLONAL	1	TRUE	0	0.248252948240534	1		618	1440	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	115	388	1	ENST00000257430.4:c.3919dup	p.Ile1307AsnfsTer8	p.I1307Nfs*8	ENST00000257430	NM_000038.5	1306	gaa/gAaa	16/16	0.248252948240534	0	FACETS	0.759	0.688	0.833			1	SUBCLONAL	2	TRUE	0	0.248252948240534	0		389	459	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593504	48593504	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	95	524	3	ENST00000342988.3:c.1255G>T	p.Gly419Trp	p.G419W	ENST00000342988	NM_005359.5	419	Ggg/Tgg	10/12	0.247453647649827	1	FACETS	0.816	0.725	0.912	0.816	0.725	0.912	CLONAL	1	TRUE	0	0.248252948240534	1		527	822	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55154999	55154999	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1283	186	795	0	ENST00000257290.5:c.2708C>G	p.Ser903Cys	p.S903C	ENST00000257290	NM_006206.4	903	tCt/tGt	20/23	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.248252948240534	2		795	1469	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99802246	99802246	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	17	97	0	ENST00000280892.6:c.647G>C	p.Gly216Ala	p.G216A	ENST00000280892	NM_001130678.1	216	gGt/gCt	7/7	0.248252948240534	1	FACETS	0.674	0.505	0.872	0.674	0.505	0.872	SUBCLONAL	1	TRUE	0	0.248252948240534	1		97	178	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340928	70340928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1593	122	900	1	ENST00000374080.3:c.661C>T	p.Pro221Ser	p.P221S	ENST00000374080		221	Ccc/Tcc	5/45	0.184393610026241	3	FACETS	0.644	0.58	0.713	0.322	0.29	0.357	SUBCLONAL	1	TRUE	1	0.248252948240534	3		901	1715	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0010162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	437	432	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.931013226438866	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.935831682841553	1		432	469	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662224	227662224	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	356	415	1	ENST00000305123.5:c.1231C>T	p.Arg411Ter	p.R411*	ENST00000305123	NM_005544.2	411	Cga/Tga	1/2	0.320946277784512	2	FACETS	0.658	0.623	0.693	0.329	0.311	0.347	INDETERMINATE	1	TRUE	0	0.935831682841553	2		416	1157	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162528	47162528	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	526	362	0	ENST00000409792.3:c.3598G>T	p.Glu1200Ter	p.E1200*	ENST00000409792	NM_014159.6	1200	Gaa/Taa	3/21	0.935831682841553	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.935831682841553	2		362	553	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427939	49427939	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0010162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	711	481	0	ENST00000301067.7:c.10651A>T	p.Lys3551Ter	p.K3551*	ENST00000301067	NM_003482.3	3551	Aaa/Taa	38/54	0.546279864099134	2	FACETS	0.8	0.781	0.818	0.8	0.781	0.818	INDETERMINATE	2	TRUE	0	0.935831682841553	2		481	950	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0010195-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	35	586	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.201448211666059	3	FACETS	1	0.9	1	1	0.9	1	CLONAL	2	TRUE	1	0.26384239073307	3		586	135	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577560	7577560	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520002	NA	P-0010195-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	74	417	0	ENST00000269305.4:c.721T>C	p.Ser241Pro	p.S241P	ENST00000269305	NM_001126112.2	241	Tcc/Ccc	7/11	0.26384239073307	1	FACETS	0.982	0.871	1	1	0.984	1	CLONAL	2	TRUE	0	0.26384239073307	1		417	248	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437573	56437574	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010195-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	56	403	0	ENST00000407977.2:c.888dup	p.Asn297Ter	p.N297*	ENST00000407977		296	-/T	8/10	0.26384239073307	0	FACETS	0.836	0.728	0.949			1	CLONAL	2	TRUE	0	0.26384239073307	0		403	187	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0010207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	292	536	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.315517723654184	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.354135961163696	2		536	804	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0010207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	183	372	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.315517723654184	2	FACETS	0.851	0.79	0.915	0.851	0.79	0.915	CLONAL	2	TRUE	0	0.354135961163696	2		372	607	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495336	149495336	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	54	223	0	ENST00000261799.4:c.3311G>A	p.Ser1104Asn	p.S1104N	ENST00000261799	NM_002609.3	1104	aGc/aAc	23/23	0.354135961163696	5	FACETS	0.793	0.677	0.92	0.264	0.225	0.307	CLONAL	1	TRUE	2	0.354135961163696	5		223	589	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412164	63412164	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	449	520	1	ENST00000330258.3:c.1003C>T	p.Gln335Ter	p.Q335*	ENST00000330258	NM_152424.3	335	Cag/Tag	2/2	0.354135961163696	2	FACETS	0.907	0.87	0.944			1	CLONAL	3	TRUE	NA	0.354135961163696	2		521	932	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0010210-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	138	351	2	ENST00000397752.3:c.3028+1G>A		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.406047889435142	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.406047889435142	1		353	541	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105754	27105756	+	frameshift_variant	Frame_Shift_Ins	INS	GCC	GCC	ACCT	novel	NA	P-0010210-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	221	681	0	ENST00000324856.7:c.5365_5367delinsACCT	p.Ala1789ThrfsTer13	p.A1789Tfs*13	ENST00000324856	NM_006015.4	1789	GCC/ACCT	20/20	1	2	FACETS	0.88	0.818	0.945	0.88	0.818	0.945	CLONAL	1	TRUE	1	0.406047889435142	2		681	1237	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0010217-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	67	406	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.833	0.723	0.953	0.833	0.723	0.953	CLONAL	1	TRUE	1	0.2	2		406	804	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0010217-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	90	630	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	0.127760764776504	3	FACETS	1	0.89	1			1	CLONAL	1	TRUE	NA	0.2	3		630	985	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010217-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	75	440	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	0.989	0.866	1	0.989	0.866	1	CLONAL	1	TRUE	1	0.2	2		440	758	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0010217-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	74	554	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.804	0.702	0.915	0.804	0.702	0.915	CLONAL	1	TRUE	1	0.2	2		554	920	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717715	89717716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587782341	NA	P-0010217-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	142	358	0	ENST00000371953.3:c.741dup	p.Pro248ThrfsTer5	p.P248Tfs*5	ENST00000371953	NM_000314.4	247	tta/ttAa	7/9	0.183579846854688	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.2	2		358	666	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244664	41244664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80356955	NA	P-0010217-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	104	660	1	ENST00000357654.3:c.2884G>A	p.Glu962Lys	p.E962K	ENST00000357654	NM_007294.3	962	Gaa/Aaa	10/23	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.2	2		661	1009	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	101	939	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.638915725289232	8	FACETS	1	0.923	1			1	CLONAL	5	TRUE	NA	0.638915725289232	8		940	184	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0010223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	96	1128	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.638915725289232	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.638915725289232	2		1129	126	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210482	5210482	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs147647579	NA	P-0010223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	36	426	0	ENST00000357368.4:c.5485C>T	p.Arg1829Trp	p.R1829W	ENST00000357368	NM_002850.3	1829	Cgg/Tgg	35/38	0.638915725289232	3	FACETS	0.901	0.751	1	0.451	0.375	0.532	CLONAL	1	TRUE	1	0.638915725289232	3		426	165	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71050185	71050185	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	32	313	0	ENST00000318789.4:c.1000G>C	p.Asp334His	p.D334H	ENST00000318789	NM_032682.5	334	Gac/Cac	13/21	0.284125491577987	4	FACETS	0.864	0.722	1	0.576	0.481	0.677	INDETERMINATE	2	TRUE	1	0.638915725289232	4		313	95	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112892380	112892380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	86	625	0	ENST00000351677.2:c.538G>A	p.Asp180Asn	p.D180N	ENST00000351677	NM_002834.3	180	Gac/Aac	5/16	0.459722355801757	1	FACETS	0.804	0.75	0.852	1	0.988	1	CLONAL	2	TRUE	0	0.638915725289232	1		625	114	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936096	+	missense_variant	Missense_Mutation	DNP	AG	AG	CC	novel	NA	P-0010240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	116	257	0	ENST00000263967.3:c.1637_1638delinsCC	p.Gln546Pro	p.Q546P	ENST00000263967	NM_006218.2	546	cAG/cCC	10/21	0.249124776132455	3	FACETS	1	0.942	1	1	0.987	1	CLONAL	3	TRUE	1	0.249124776132455	3		257	335	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838408	156838408	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	165	372	0	ENST00000524377.1:c.686T>C	p.Leu229Pro	p.L229P	ENST00000524377	NM_002529.3	229	cTc/cCc	6/17	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.249124776132455	2		372	963	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348080	348080	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	149	392	0	ENST00000262320.3:c.1426C>A	p.Gln476Lys	p.Q476K	ENST00000262320	NM_003502.3	476	Cag/Aag	6/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.249124776132455	2		392	839	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44920663	44920664	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0010240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	38	273	0	ENST00000377967.4:c.1425_1425+1dup		p.Q475fs	ENST00000377967	NM_021140.2	475	cag/caGGg	14/29	0.249124776132455	0	FACETS	0.737	0.611	0.876			1	SUBCLONAL	1	TRUE	NA	0.249124776132455	0		273	311	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576901	7576901	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	134	420	0	ENST00000269305.4:c.945del	p.Gln317SerfsTer28	p.Q317Sfs*28	ENST00000269305	NM_001126112.2	315	tcT/tc	9/11	0.249124776132455	1	FACETS	0.864	0.789	0.942	1	0.989	1	CLONAL	2	TRUE	0	0.249124776132455	1		420	545	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0010243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	159	390	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.414992840981341	2	FACETS	0.861	0.801	0.921	0.861	0.801	0.921	CLONAL	2	TRUE	0	0.524652178547412	2		390	352	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0010243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	196	679	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.524652178547412	2		679	616	SUCCESS
APC	324	MSKCC	GRCh37	5	112175548	112175548	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	99	428	0	ENST00000257430.4:c.4260del	p.Ser1421ValfsTer52	p.S1421Vfs*52	ENST00000257430	NM_000038.5	1419	agC/ag	16/16	0.524652178547412	1	FACETS	0.934	0.845	1	0.934	0.845	1	CLONAL	1	TRUE	0	0.524652178547412	1		428	298	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518262	8518262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	78	394	1	ENST00000356435.5:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000356435		377	Cgc/Tgc	10/35	0.330830978691364	3	FACETS	0.704	0.62	0.794	0.352	0.31	0.397	SUBCLONAL	1	TRUE	1	0.524652178547412	3		395	533	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531912	41531912	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0010243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	149	369	0	ENST00000263253.7:c.1622+2T>C		p.X541_splice	ENST00000263253	NM_001429.3	541			0.11778594996387	4	FACETS	1	0.987	1	0.728	0.668	0.79	INDETERMINATE	1	TRUE	2	0.524652178547412	4		369	595	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0010250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	570	791	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.684571897320326	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.753486270230668	1		792	935	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100382	27100382	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	386	572	0	ENST00000324856.7:c.4094A>T	p.Gln1365Leu	p.Q1365L	ENST00000324856	NM_006015.4	1365	cAa/cTa	17/20	0.359001323495084	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.753486270230668	0		572	688	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873343	136873343	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	415	1114	0	ENST00000241393.3:c.155G>T	p.Gly52Val	p.G52V	ENST00000241393	NM_003467.2	52	gGc/gTc	2/2	0.594957429107588	1	FACETS	0.461	0.438	0.484	0.461	0.438	0.484	SUBCLONAL	1	TRUE	0	0.753486270230668	1		1114	1490	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39537666	39537666	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	294	481	0	ENST00000262039.4:c.200G>C	p.Gly67Ala	p.G67A	ENST00000262039	NM_002647.2	67	gGg/gCg	2/25	0.203929913548531	1	FACETS	0.52	0.49	0.55	0.52	0.49	0.55	INDETERMINATE	1	TRUE	0	0.753486270230668	1		481	936	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125494	7125494	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	210	705	0	ENST00000302850.5:c.3058C>G	p.Arg1020Gly	p.R1020G	ENST00000302850	NM_000208.2	1020	Cga/Gga	17/22	0.753486270230668	1	FACETS	0.421	0.391	0.451	0.421	0.391	0.451	SUBCLONAL	1	TRUE	0	0.753486270230668	1		705	826	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912843	29912859	+	frameshift_variant	Frame_Shift_Del	DEL	AGGAGGGAGTTACACTC	AGGAGGGAGTTACACTC	-	novel	NA	P-0010250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	125	334	0	ENST00000376809.5:c.1023_1039del	p.Gly342CysfsTer4	p.G342Cfs*4	ENST00000376809	NM_002116.7	340	aaAGGAGGGAGTTACACTCag/aaag	6/8	0.193910938851552	2	FACETS	0.718	0.654	0.784	0.359	0.327	0.392	INDETERMINATE	1	TRUE	0	0.753486270230668	2		334	462	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162387	47162387	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	52	348	0	ENST00000409792.3:c.3739G>T	p.Asp1247Tyr	p.D1247Y	ENST00000409792	NM_014159.6	1247	Gat/Tat	3/21	1	2	FACETS	0.768	0.654	0.894	0.768	0.654	0.894	SUBCLONAL	1	TRUE	1	0.241784202939742	2		348	560	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982020	93982020	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	81	472	0	ENST00000369303.4:c.1445A>T	p.Glu482Val	p.E482V	ENST00000369303	NM_004440.3	482	gAg/gTg	6/17	0.241784202939742	1	FACETS	0.856	0.754	0.966	0.856	0.754	0.966	CLONAL	1	TRUE	0	0.241784202939742	1		472	688	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680634	88680634	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0010253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	63	372	0	ENST00000360948.2:c.622+1G>A		p.X208_splice	ENST00000360948	NM_001012338.2	208			0.241784202939742	1	FACETS	0.745	0.644	0.854	0.745	0.644	0.854	SUBCLONAL	1	TRUE	0	0.241784202939742	1		372	615	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs878854073	NA	P-0010270-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	53	276	0	ENST00000269305.4:c.673-1G>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.194018649102084	1	FACETS	0.967	0.825	1	0.967	0.825	1	CLONAL	1	TRUE	0	0.194018649102084	1		276	510	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523342	176523342	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1199129089	NA	P-0010270-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	85	422	0	ENST00000292408.4:c.1999A>G	p.Thr667Ala	p.T667A	ENST00000292408	NM_213647.1	667	Aca/Gca	15/18	0.194018649102084	3	FACETS	1	0.924	1	0.531	0.468	0.598	CLONAL	1	TRUE	1	0.194018649102084	3		422	905	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133737	2133737	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010270-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	217	565	0	ENST00000219476.3:c.3926del	p.Pro1309LeufsTer16	p.P1309Lfs*16	ENST00000219476	NM_000548.3	1309	Cct/ct	33/42	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	2	TRUE	NA	0.194018649102084	2		565	1024	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412045	116412045	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0010273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	73	290	0	ENST00000397752.3:c.3028+2T>C		p.X1010_splice	ENST00000397752	NM_000245.2	1010			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		290	561	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0010276-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	210	551	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.946	0.878	1	0.946	0.878	1	CLONAL	1	TRUE	1	0.436885836768534	2		551	1016	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0010283-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	227	576	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.450641196383966	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.450641196383966	1		579	629	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0010283-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	187	618	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.450641196383966	2		618	822	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0010283-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	240	553	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.450641196383966	2		553	887	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928089	178928089	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010283-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	195	426	0	ENST00000263967.3:c.1367T>G	p.Leu456Arg	p.L456R	ENST00000263967	NM_006218.2	456	cTg/cGg	8/21	0.15214619519242	4	FACETS	1	0.988	1	0.682	0.632	0.735	INDETERMINATE	1	TRUE	2	0.450641196383966	4		426	920	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410970	63410970	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010283-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	115	673	0	ENST00000330258.3:c.2197C>T	p.Gln733Ter	p.Q733*	ENST00000330258	NM_152424.3	733	Caa/Taa	2/2	0.397023227681708	1	FACETS	0.47	0.423	0.519	0.47	0.423	0.519	SUBCLONAL	1	TRUE	0	0.450641196383966	1		673	842	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661449	227661452	+	frameshift_variant	Frame_Shift_Del	DEL	CCGC	CCGC	-	novel	NA	P-0010283-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	115	377	0	ENST00000305123.5:c.2003_2006del	p.Ser668MetfsTer35	p.S668Mfs*35	ENST00000305123	NM_005544.2	668	aGCGGt/at	1/2	1	2	FACETS	0.905	0.818	0.996	0.905	0.818	0.996	CLONAL	1	TRUE	1	0.450641196383966	2		377	564	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	27	203	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.963	0.769	1	0.963	0.769	1	CLONAL	1	TRUE	1	0.22	2		203	255	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	48	432	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.883	0.747	1	0.883	0.747	1	CLONAL	1	TRUE	1	0.22	2		432	494	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	59	162	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	1	0.951	1	1	0.982	1	CLONAL	2	TRUE	1	0.22	2		162	224	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	100	408	1	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.851	0.758	0.95	0.851	0.758	0.95	CLONAL	1	TRUE	1	0.22	2		409	1068	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405103	70405103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199844508	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	41	443	0	ENST00000373644.4:c.2617G>A	p.Val873Ile	p.V873I	ENST00000373644	NM_030625.2	873	Gtt/Att	4/12	1	2	FACETS	0.623	0.518	0.74	0.623	0.518	0.74	SUBCLONAL	1	TRUE	1	0.22	2		443	598	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659675	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	121	412	0	ENST00000269305.4:c.764T>C	p.Ile255Thr	p.I255T	ENST00000269305	NM_001126112.2	255	aTc/aCc	7/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.22	2		412	1032	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769886672	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	55	303	0	ENST00000405192.2:c.414dup	p.Thr139HisfsTer24	p.T139Hfs*24	ENST00000405192	NM_001163147.1	138	-/C	7/12	1	2	FACETS	0.867	0.741	1	0.867	0.741	1	CLONAL	1	TRUE	1	0.22	2		303	577	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	102	375	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.818	0.729	0.912	0.818	0.729	0.912	CLONAL	1	TRUE	1	0.22	2		375	1134	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149798	202149799	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	56	458	0	ENST00000358485.4:c.1245dup	p.Ile416TyrfsTer8	p.I416Yfs*8	ENST00000358485	NM_001080125.1	413	-/T	8/9	1	2	FACETS	0.826	0.708	0.956	0.826	0.708	0.956	CLONAL	1	TRUE	1	0.22	2		458	616	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	99	427	2	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.93	0.828	1	0.93	0.828	1	CLONAL	1	TRUE	1	0.22	2		429	968	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	81	600	4	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	1	2	FACETS	0.733	0.644	0.829	0.733	0.644	0.829	SUBCLONAL	1	TRUE	1	0.22	2		604	1004	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872461	35872461	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1834	154	803	0	ENST00000216797.5:c.442del	p.Leu148TyrfsTer16	p.L148Yfs*16	ENST00000216797	NM_020529.2	148	Cta/ta	3/6	1	2	FACETS	0.704	0.641	0.771	0.704	0.641	0.771	SUBCLONAL	1	TRUE	1	0.22	2		803	1988	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106562	27106562	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1509	129	671	0	ENST00000324856.7:c.6176del	p.Asn2059ThrfsTer76	p.N2059Tfs*76	ENST00000324856	NM_006015.4	2058	gAa/ga	20/20	1	2	FACETS	0.716	0.646	0.79	0.716	0.646	0.79	SUBCLONAL	1	TRUE	1	0.22	2		671	1638	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928976	44928976	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	68	631	0	ENST00000377967.4:c.2080del	p.Ala694LeufsTer21	p.A694Lfs*21	ENST00000377967	NM_021140.2	692	caG/ca	17/29	0.0821328898592414	0	FACETS	0.471	0.409	0.54			1	INDETERMINATE	1	TRUE	0	0.22	0		631	1023	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690401	117690401	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775074986	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	41	347	1	ENST00000369458.3:c.728C>T	p.Ser243Leu	p.S243L	ENST00000369458	NM_024626.3	243	tCg/tTg	5/6	1	2	FACETS	0.867	0.723	1	0.867	0.723	1	CLONAL	1	TRUE	1	0.22	2		348	430	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649623	206649623	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	109	325	0	ENST00000367120.3:c.458A>G	p.Tyr153Cys	p.Y153C	ENST00000367120	NM_014002.3	153	tAc/tGc	6/22	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.22	2		325	848	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253388	226253388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	36	267	0	ENST00000366813.1:c.160C>T	p.Arg54Cys	p.R54C	ENST00000366813		54	Cgt/Tgt	2/3	1	2	FACETS	0.745	0.613	0.894	0.745	0.613	0.894	SUBCLONAL	1	TRUE	1	0.22	2		267	439	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469975	25469975	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	63	335	0	ENST00000264709.3:c.1067A>G	p.Gln356Arg	p.Q356R	ENST00000264709	NM_175629.2	356	cAg/cGg	9/23	1	2	FACETS	0.6	0.518	0.691	0.6	0.518	0.691	SUBCLONAL	1	TRUE	1	0.22	2		335	954	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520241	176520241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	123	385	0	ENST00000292408.4:c.1160C>T	p.Ala387Val	p.A387V	ENST00000292408	NM_213647.1	387	gCc/gTc	9/18	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.22	2		385	932	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858507	27858507	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1381	159	650	1	ENST00000359303.2:c.64G>A	p.Ala22Thr	p.A22T	ENST00000359303	NM_003535.2	22	Gcc/Acc	1/1	1	2	FACETS	0.939	0.857	1	0.939	0.857	1	CLONAL	1	TRUE	1	0.22	2		651	1540	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015707	112015707	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	85	701	0	ENST00000368678.4:c.1135G>A	p.Glu379Lys	p.E379K	ENST00000368678		379	Gag/Aag	11/13	0.0821328898592414	0	FACETS	0.655	0.578	0.738			1	INDETERMINATE	1	TRUE	0	0.22	0		701	920	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662787	117662787	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	19	197	0	ENST00000368508.3:c.4678G>A	p.Ala1560Thr	p.A1560T	ENST00000368508	NM_002944.2	1560	Gca/Aca	29/43	0.0821328898592414	0	FACETS	0.51	0.388	0.654			1	INDETERMINATE	1	TRUE	0	0.22	0		197	264	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738373	133738373	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	49	215	0	ENST00000318560.5:c.773A>C	p.Glu258Ala	p.E258A	ENST00000318560	NM_005157.4	258	gAg/gCg	4/11	1	2	FACETS	0.781	0.661	0.914	0.781	0.661	0.914	CLONAL	1	TRUE	1	0.22	2		215	570	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1042175	1042175	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	75	425	0	ENST00000358495.3:c.50C>T	p.Ala17Val	p.A17V	ENST00000358495	NM_134424.2	17	gCt/gTt	2/12	1	2	FACETS	0.826	0.723	0.938	0.826	0.723	0.938	CLONAL	1	TRUE	1	0.22	2		425	825	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446707	49446707	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	44	252	0	ENST00000301067.7:c.1103T>G	p.Val368Gly	p.V368G	ENST00000301067	NM_003482.3	368	gTg/gGg	8/54	1	2	FACETS	0.613	0.513	0.724	0.613	0.513	0.724	SUBCLONAL	1	TRUE	1	0.22	2		252	653	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131771	2131771	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	95	357	0	ENST00000219476.3:c.3786A>C	p.Lys1262Asn	p.K1262N	ENST00000219476	NM_000548.3	1262	aaA/aaC	31/42	1	2	FACETS	0.969	0.862	1	0.969	0.862	1	CLONAL	1	TRUE	1	0.22	2		357	891	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136275	2136275	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	180	494	0	ENST00000219476.3:c.4744A>G	p.Ile1582Val	p.I1582V	ENST00000219476	NM_000548.3	1582	Atc/Gtc	37/42	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.22	2		494	1169	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857751	9857751	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1396	149	607	0	ENST00000330684.3:c.3650G>A	p.Cys1217Tyr	p.C1217Y	ENST00000330684	NM_001134407.1	1217	tGc/tAc	13/13	1	2	FACETS	0.877	0.798	0.96	0.877	0.798	0.96	CLONAL	1	TRUE	1	0.22	2		607	1545	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032525	12032525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1396947681	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	47	344	0	ENST00000353533.5:c.961G>A	p.Val321Met	p.V321M	ENST00000353533	NM_003010.3	321	Gtg/Atg	9/11	1	2	FACETS	0.917	0.774	1	0.917	0.774	1	CLONAL	1	TRUE	1	0.22	2		344	466	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350322	15350322	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	92	367	1	ENST00000263377.2:c.3457A>G	p.Lys1153Glu	p.K1153E	ENST00000263377	NM_058243.2	1153	Aag/Gag	17/20	1	2	FACETS	0.949	0.842	1	0.949	0.842	1	CLONAL	1	TRUE	1	0.22	2		368	881	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792458	33792458	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1565	150	717	1	ENST00000498907.2:c.863G>A	p.Arg288Gln	p.R288Q	ENST00000498907	NM_004364.3	288	cGg/cAg	1/1	1	2	FACETS	0.795	0.724	0.871	0.795	0.724	0.871	SUBCLONAL	1	TRUE	1	0.22	2		718	1715	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164875	36164875	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	55	276	1	ENST00000300305.3:c.1000C>T	p.Arg334Cys	p.R334C	ENST00000300305		334	Cgc/Tgc	8/8	1	2	FACETS	0.661	0.564	0.767	0.661	0.564	0.767	SUBCLONAL	1	TRUE	1	0.22	2		277	757	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248325	59248325	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	29	78	0	ENST00000371222.2:c.418del	p.Ala140GlnfsTer8	p.A140Qfs*8	ENST00000371222	NM_002228.3	140	Gca/ca	1/1	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.22	2		78	195	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539281	187539282	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	30	458	0	ENST00000441802.2:c.8458_8459del	p.Glu2820LysfsTer7	p.E2820Kfs*7	ENST00000441802	NM_005245.3	2820	GAa/a	10/27	1	2	FACETS	0.529	0.425	0.647	0.529	0.425	0.647	SUBCLONAL	1	TRUE	1	0.22	2		458	516	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615679	100615679	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1569292813	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	114	689	3	ENST00000308731.7:c.653del	p.Lys218ArgfsTer11	p.K218Rfs*11	ENST00000308731	NM_000061.2	218	aAg/ag	8/19	0.0821328898592414	0	FACETS	0.697	0.626	0.773			1	INDETERMINATE	1	TRUE	0	0.22	0		692	1159	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843236	128843237	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1248200595	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	122	389	0	ENST00000249373.3:c.349dup	p.Arg117ProfsTer19	p.R117Pfs*19	ENST00000249373	NM_005631.4	115	gcc/gCcc	2/12	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.22	2		389	1033	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932794	39932794	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1570	223	783	0	ENST00000378444.4:c.1805del	p.Pro602ArgfsTer67	p.P602Rfs*67	ENST00000378444	NM_001123385.1	602	cCg/cg	4/15	0.0821328898592414	0	FACETS	0.882	0.818	0.949			1	INDETERMINATE	1	TRUE	0	0.22	0		783	1793	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118924	70118926	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0010308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1241	156	565	0	ENST00000245479.2:c.499_501del	p.Lys167del	p.K167del	ENST00000245479	NM_000346.3	166	AAG/-	2/3	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.22	2		565	1397	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650826	48650826	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	311	672	0	ENST00000376670.3:c.695A>G	p.His232Arg	p.H232R	ENST00000376670	NM_002049.3	232	cAc/cGc	4/6	0.0993284888579325	0	FACETS	0.766	0.726	0.807			1	INDETERMINATE	1	TRUE	0	0.5	0		672	812	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881002	37881003	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCTCCCCA	rs397516982	NA	P-0010321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	254	489	0	ENST00000269571.5:c.2332_2340dup	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	-/GGCTCCCCA	20/27	0.234735308915647	3	FACETS	0.931	0.87	0.994	0.931	0.87	0.994	CLONAL	2	TRUE	1	0.234735308915647	3		489	1299	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288672	198288672	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1222778757	NA	P-0010321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	196	546	0	ENST00000335508.6:c.55C>G	p.Gln19Glu	p.Q19E	ENST00000335508	NM_012433.2	19	Caa/Gaa	2/25	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.234735308915647	2		546	1223	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847368	68847369	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	153	490	0	ENST00000261769.5:c.1292dup	p.Asn431LysfsTer15	p.N431Kfs*15	ENST00000261769	NM_004360.3	430	-/A	9/16	0.234735308915647	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.234735308915647	1		490	915	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974792	21974792	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs141798398	NA	P-0010334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	59	63	0	ENST00000304494.5:c.35C>A	p.Ser12Ter	p.S12*	ENST00000304494	NM_000077.4	12	tCg/tAg	1/3	0.465089795212396	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.465089795212396	1		63	137	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843538	156843538	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	225	434	0	ENST00000524377.1:c.964C>A	p.Leu322Ile	p.L322I	ENST00000524377	NM_002529.3	322	Ctc/Atc	8/17	0.162421663036487	3	FACETS	1	0.987	1	0.626	0.583	0.67	INDETERMINATE	1	TRUE	1	0.465089795212396	3		434	953	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47061268	47061268	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	355	762	0	ENST00000409792.3:c.7413A>C	p.Lys2471Asn	p.K2471N	ENST00000409792	NM_014159.6	2471	aaA/aaC	19/21	0.465089795212396	1	FACETS	0.949	0.899	1	0.949	0.899	1	CLONAL	1	TRUE	0	0.465089795212396	1		762	1235	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504324	186504324	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	83	400	2	ENST00000323963.5:c.661G>T	p.Val221Leu	p.V221L	ENST00000323963		221	Gtg/Ttg	7/11	0.465089795212396	3	FACETS	0.508	0.447	0.573	0.254	0.223	0.287	SUBCLONAL	1	TRUE	1	0.465089795212396	3		402	866	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0010334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	261	448	1	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.465089795212396	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.465089795212396	1		449	767	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	160	160	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.602743226509537	2		160	428	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416124	29416124	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	60	314	0	ENST00000389048.3:c.4829A>G	p.Lys1610Arg	p.K1610R	ENST00000389048	NM_004304.4	1610	aAa/aGa	29/29	1	2	FACETS	0.319	0.274	0.367	0.319	0.274	0.367	SUBCLONAL	1	TRUE	1	0.602743226509537	2		314	625	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196162	108196162	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	49	330	0	ENST00000278616.4:c.6698T>C	p.Ile2233Thr	p.I2233T	ENST00000278616	NM_000051.3	2233	aTc/aCc	46/63	1	2	FACETS	0.403	0.342	0.47	0.403	0.342	0.47	SUBCLONAL	1	TRUE	1	0.602743226509537	2		330	403	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171732	36171732	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759227406	NA	P-0010344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	277	454	0	ENST00000300305.3:c.833C>T	p.Pro278Leu	p.P278L	ENST00000300305		278	cCg/cTg	7/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.602743226509537	2		454	851	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0010345-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	41	399	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.261999267086541	3	FACETS	0.439	0.364	0.522			1	SUBCLONAL	1	TRUE	NA	0.261999267086541	3		399	807	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259441	55259442	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0010345-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	46	350	0	ENST00000275493.2:c.2499_2500delinsTT	p.Leu833_Val834delinsPheLeu	p.L833_V834delinsFL	ENST00000275493	NM_005228.3	833	ttGGtg/ttTTtg	21/28	0.261999267086541	3	FACETS	0.629	0.529	0.741			1	SUBCLONAL	1	TRUE	NA	0.261999267086541	3		350	631	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0010354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	267	408	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.964	0.91	1	0.964	0.91	1	CLONAL	1	TRUE	1	0.812081955076923	2		408	682	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909629	76909629	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs919106518	NA	P-0010354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	628	475	3	ENST00000373344.5:c.4276C>T	p.Arg1426Ter	p.R1426*	ENST00000373344	NM_000489.3	1426	Cga/Tga	14/35	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.812081955076923	1		478	781	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0010354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	596	324	0	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	1	2	FACETS	1	0.985	1	1	0.998	1	CLONAL	2	TRUE	1	0.812081955076923	2		324	728	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244814	46244815	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	100	434	0	ENST00000334344.6:c.2908_2909insT	p.Pro970LeufsTer12	p.P970Lfs*12	ENST00000334344	NM_152641.2	970	cca/cTca	15/21	1	2	FACETS	0.239	0.213	0.268	0.239	0.213	0.268	SUBCLONAL	1	TRUE	1	0.812081955076923	2		434	1029	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	217	939	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.498905412240599	5	FACETS	0.928	0.865	0.993	0.619	0.577	0.662	CLONAL	2	TRUE	2	0.5001662223548	5		940	818	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0010357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	387	430	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.5001662223548	2	FACETS	0.981	0.938	1	0.981	0.938	1	CLONAL	2	TRUE	0	0.5001662223548	2		430	789	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197101	106197101	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	96	229	0	ENST00000380013.4:c.5434G>A	p.Val1812Ile	p.V1812I	ENST00000380013	NM_001127208.2	1812	Gtc/Atc	11/11	0.5001662223548	3	FACETS	0.807	0.72	0.898	0.403	0.36	0.449	CLONAL	1	TRUE	1	0.5001662223548	3		229	595	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690814	89690814	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	108	216	0	ENST00000371953.3:c.221G>T	p.Arg74Ile	p.R74I	ENST00000371953	NM_000314.4	74	aGa/aTa	4/9	NA	2	FACETS	0.99	0.895	1			1	INDETERMINATE	1	TRUE	NA	0.5001662223548	2		216	436	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864237	57864237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	406	581	0	ENST00000228682.2:c.1714G>A	p.Glu572Lys	p.E572K	ENST00000228682	NM_005269.2	572	Gag/Aag	12/12	0.377400716835954	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.5001662223548	4		581	1193	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557619	21557619	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0010357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	141	402	1	ENST00000382592.4:c.2226C>G	p.Tyr742Ter	p.Y742*	ENST00000382592	NM_014572.2	742	taC/taG	5/8	1	2	FACETS	0.853	0.779	0.93	0.853	0.779	0.93	CLONAL	1	TRUE	1	0.5001662223548	2		403	661	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792873	33792873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	30	122	0	ENST00000498907.2:c.448G>A	p.Val150Ile	p.V150I	ENST00000498907	NM_004364.3	150	Gtc/Atc	1/1	0.486004988821453	3	FACETS	0.993	0.811	1	0.331	0.27	0.398	CLONAL	1	TRUE	0	0.5001662223548	3		122	151	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0010361-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	960	406	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.701941905696688	4	FACETS	0.877	0.859	0.895	0.877	0.859	0.895	CLONAL	4	TRUE	0	0.701941905696688	4		406	1327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0010361-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	339	360	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.673016316419438	2	FACETS	0.992	0.956	1	0.992	0.956	1	CLONAL	2	TRUE	0	0.701941905696688	2		361	487	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113243	209113243	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs758622511	NA	P-0010361-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	582	751	0	ENST00000345146.2:c.264G>T	p.Leu88Phe	p.L88F	ENST00000345146	NM_005896.2	88	ttG/ttT	4/10	0.701941905696688	2	FACETS	0.981	0.954	1	0.981	0.954	1	CLONAL	2	TRUE	0	0.701941905696688	2		751	845	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843365	128843365	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748690872	NA	P-0010361-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	166	644	0	ENST00000249373.3:c.472G>A	p.Glu158Lys	p.E158K	ENST00000249373	NM_005631.4	158	Gag/Aag	2/12	0.701941905696688	3	FACETS	0.849	0.781	0.919	0.424	0.39	0.46	CLONAL	1	TRUE	1	0.701941905696688	3		644	753	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641067	93641067	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010361-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	577	449	0	ENST00000375746.1:c.1413C>G	p.Ile471Met	p.I471M	ENST00000375746	NM_001174167.1	471	atC/atG	11/14	0.701941905696688	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.701941905696688	3		449	1026	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741220	40741220	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010361-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	533	657	0	ENST00000392038.2:c.1213G>C	p.Glu405Gln	p.E405Q	ENST00000392038	NM_001626.4	405	Gag/Cag	12/14	0.662385992713882	2	FACETS	0.986	0.957	1	0.986	0.957	1	CLONAL	2	TRUE	0	0.701941905696688	2		657	770	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873679	151873680	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTTGACACATGATTGGATGGGGATC	novel	NA	P-0010361-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	102	376	0	ENST00000262189.6:c.8858_8859insGATCCCCATCCAATCATGTGTCAAG	p.Ser2953ArgfsTer23	p.S2953Rfs*23	ENST00000262189	NM_170606.2	2953	agt/agGATCCCCATCCAATCATGTGTCAAGt	38/59	0.673016316419438	2	FACETS	0.803	0.725	0.884	0.401	0.362	0.442	CLONAL	1	TRUE	0	0.701941905696688	2		376	362	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091371	193091373	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0010361-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	357	533	0	ENST00000367435.3:c.46_48del	p.Lys16del	p.K16del	ENST00000367435	NM_024529.4	14	cAGAag/cag	1/17	0.701941905696688	5	FACETS	0.907	0.86	0.955	0.605	0.573	0.637	CLONAL	2	TRUE	2	0.701941905696688	5		533	1151	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016608	12016609	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	T	novel	NA	P-0010361-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	384	615	0	ENST00000353533.5:c.744_745delinsT	p.Gly249AlafsTer27	p.G249Afs*27	ENST00000353533	NM_003010.3	248	ttCGgc/ttTgc	7/11	0.673016316419438	2	FACETS	0.958	0.924	0.991	0.958	0.924	0.991	CLONAL	2	TRUE	0	0.701941905696688	2		615	571	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47604158	47604158	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1335312662	NA	P-0010361-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	263	677	0	ENST00000263735.4:c.497T>C	p.Leu166Pro	p.L166P	ENST00000263735	NM_002354.2	166	cTt/cCt	5/9	0.701941905696688	3	FACETS	0.87	0.815	0.927	0.435	0.407	0.464	CLONAL	1	TRUE	1	0.701941905696688	3		677	1164	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0010364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	260	362	1	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	NA	2	FACETS	0.982	0.938	1			1	INDETERMINATE	2	TRUE	NA	0.648792425673794	2		363	408	SUCCESS
APC	324	MSKCC	GRCh37	5	112174386	112174386	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0010364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	104	306	0	ENST00000257430.4:c.3095C>G	p.Ser1032Ter	p.S1032*	ENST00000257430	NM_000038.5	1032	tCa/tGa	16/16	1	2	FACETS	0.871	0.787	0.958	0.871	0.787	0.958	CLONAL	1	TRUE	1	0.648792425673794	2		306	368	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435858	56435858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	47	344	0	ENST00000407977.2:c.1279C>T	p.His427Tyr	p.H427Y	ENST00000407977		427	Cac/Tac	9/10	0.466046105535487	2	FACETS	0.292	0.246	0.342	0.146	0.123	0.171	SUBCLONAL	1	TRUE	0	0.648792425673794	2		344	497	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725035	47725035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765552886	NA	P-0010364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	261	720	0	ENST00000449228.1:c.709G>A	p.Val237Ile	p.V237I	ENST00000449228	NM_001127240.2	237	Gtc/Atc	4/4	0.608943435742712	3	FACETS	0.945	0.885	1	0.472	0.442	0.503	CLONAL	1	TRUE	1	0.648792425673794	3		720	1128	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248443	59248443	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	217	458	0	ENST00000371222.2:c.300del	p.Lys101ArgfsTer3	p.K101Rfs*3	ENST00000371222	NM_002228.3	100	ccC/cc	1/1	1	2	FACETS	0.932	0.87	0.995	0.932	0.87	0.995	CLONAL	1	TRUE	1	0.648792425673794	2		458	718	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0010380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	453	741	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.538956617192556	2	FACETS	0.916	0.88	0.952	0.916	0.88	0.952	CLONAL	2	TRUE	0	0.550228393814639	2		742	899	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0010380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	208	381	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.981	0.913	1	0.981	0.913	1	CLONAL	1	TRUE	1	0.550228393814639	2		382	771	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717756	89717756	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730882131	NA	P-0010380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	198	242	0	ENST00000371953.3:c.781C>T	p.Gln261Ter	p.Q261*	ENST00000371953	NM_000314.4	261	Cag/Tag	7/9	0.550228393814639	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.550228393814639	2		242	354	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161747	47161747	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	392	574	0	ENST00000409792.3:c.4379G>C	p.Trp1460Ser	p.W1460S	ENST00000409792	NM_014159.6	1460	tGg/tCg	3/21	0.232720530535254	3	FACETS	0.859	0.818	0.9	0.859	0.818	0.9	INDETERMINATE	2	TRUE	1	0.550228393814639	3		574	1058	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940402	49940402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760399844	NA	P-0010380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1448	570	932	4	ENST00000296474.3:c.641G>A	p.Arg214His	p.R214H	ENST00000296474	NM_002447.2	214	cGc/cAc	1/20	0.232720530535254	3	FACETS	1	0.995	1	0.655	0.627	0.683	INDETERMINATE	1	TRUE	1	0.550228393814639	3		936	2018	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039505	49039505	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs764754259	NA	P-0010380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	350	406	0	ENST00000267163.4:c.2489+1G>A		p.X830_splice	ENST00000267163	NM_000321.2	830			0.550228393814639	2	FACETS	0.954	0.912	0.995	0.954	0.912	0.995	CLONAL	2	TRUE	0	0.550228393814639	2		406	667	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874358	76874358	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	637	430	0	ENST00000373344.5:c.5364G>T	p.Gln1788His	p.Q1788H	ENST00000373344	NM_000489.3	1788	caG/caT	21/35	0.550228393814639	2	FACETS	0.872	0.85	0.894			1	CLONAL	3	TRUE	NA	0.550228393814639	2		430	885	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221995	1221995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201090	NA	P-0010397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	871	490	0	ENST00000326873.7:c.910C>T	p.Arg304Trp	p.R304W	ENST00000326873	NM_000455.4	304	Cgg/Tgg	7/10	0.527216016841929	2	FACETS	0.972	0.944	0.999	0.972	0.944	0.999	CLONAL	2	TRUE	0	0.542946004887994	2		490	1651	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248394	59248394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329490786	NA	P-0010397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	170	239	0	ENST00000371222.2:c.349G>A	p.Ala117Thr	p.A117T	ENST00000371222	NM_002228.3	117	Gcc/Acc	1/1	0.324419181855597	0	FACETS	0.282	0.259	0.306			1	INDETERMINATE	1	TRUE	0	0.542946004887994	0		239	1015	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969996	161969996	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	233	388	1	ENST00000366898.1:c.973C>A	p.Leu325Met	p.L325M	ENST00000366898	NM_004562.2	325	Ctg/Atg	9/12	1	2	FACETS	0.815	0.76	0.872	0.815	0.76	0.872	CLONAL	1	TRUE	1	0.542946004887994	2		389	1053	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118370600	118370600	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	76	353	0	ENST00000534358.1:c.6130G>A	p.Glu2044Lys	p.E2044K	ENST00000534358	NM_005933.3	2044	Gaa/Aaa	24/36	1	2	FACETS	0.47	0.412	0.532	0.47	0.412	0.532	SUBCLONAL	1	TRUE	1	0.542946004887994	2		353	596	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373799	118373799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	39	222	0	ENST00000534358.1:c.7192G>A	p.Glu2398Lys	p.E2398K	ENST00000534358	NM_005933.3	2398	Gaa/Aaa	27/36	1	2	FACETS	0.455	0.378	0.539	0.455	0.378	0.539	SUBCLONAL	1	TRUE	1	0.542946004887994	2		222	316	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216751	2216751	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	305	143	0	ENST00000398665.3:c.2395G>T	p.Glu799Ter	p.E799*	ENST00000398665	NM_032482.2	799	Gag/Tag	20/28	0.527216016841929	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.542946004887994	2		143	549	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602322	10602322	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	895	387	0	ENST00000171111.5:c.1256G>T	p.Gly419Val	p.G419V	ENST00000171111	NM_203500.1	419	gGg/gTg	3/6	0.527216016841929	2	FACETS	0.975	0.948	1	0.975	0.948	1	CLONAL	2	TRUE	0	0.542946004887994	2		387	1691	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911573	39911573	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	381	645	0	ENST00000378444.4:c.5057A>G	p.Asn1686Ser	p.N1686S	ENST00000378444	NM_001123385.1	1686	aAc/aGc	15/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.542946004887994	2		645	1338	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200084	123200084	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	500	882	3	ENST00000218089.9:c.2156G>T	p.Gly719Val	p.G719V	ENST00000218089	NM_001042749.1	719	gGa/gTa	22/35	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.542946004887994	2		885	1485	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0010402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	51	426	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	NA	2	FACETS	0.224	0.19	0.261			1	INDETERMINATE	1	FALSE	NA	0.734014714086444	2		426	621	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578277	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs1555525902	NA	P-0010402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	64	432	0	ENST00000269305.4:c.572_574del	p.Pro191del	p.P191del	ENST00000269305	NM_001126112.2	191	cCTCag/cag	6/11	0.356063987256743	3	FACETS	0.657	0.572	0.748	0.328	0.286	0.374	INDETERMINATE	1	FALSE	1	0.734014714086444	3		432	363	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427010	49427013	+	frameshift_variant	Frame_Shift_Del	DEL	CTGT	CTGT	-	rs1057519067	NA	P-0010402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	54	372	0	ENST00000301067.7:c.11475_11478del	p.Gln3826CysfsTer3	p.Q3826Cfs*3	ENST00000301067	NM_003482.3	3825	agACAG/ag	39/54	0.4397477606155	4	FACETS	0.874	0.752	1	0.437	0.376	0.503	INDETERMINATE	1	FALSE	2	0.734014714086444	4		372	292	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225572	26225572	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	124	1412	0	ENST00000360408.1:c.190C>G	p.Arg64Gly	p.R64G	ENST00000360408	NM_003532.2	64	Cgg/Ggg	1/1	0.417714415780049	4	FACETS	0.595	0.537	0.656	0.297	0.268	0.328	INDETERMINATE	1	FALSE	2	0.734014714086444	4		1412	985	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222610	69222610	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1241409542	NA	P-0010402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	100	732	0	ENST00000462284.1:c.583A>G	p.Ile195Val	p.I195V	ENST00000462284	NM_002392.5	195	Att/Gtt	8/11	0.55128041919948	4	FACETS	0.618	0.551	0.688	0.309	0.275	0.344	SUBCLONAL	1	FALSE	2	0.734014714086444	4		732	765	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166170	7166170	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	26	400	2	ENST00000302850.5:c.1856C>A	p.Ala619Asp	p.A619D	ENST00000302850	NM_000208.2	619	gCc/gAc	8/22	0.243695456186596	1	FACETS	0.17	0.135	0.21	0.17	0.135	0.21	INDETERMINATE	1	FALSE	0	0.734014714086444	1		402	264	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952066	76952066	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	103	346	1	ENST00000373344.5:c.369del	p.Gly124ValfsTer3	p.G124Vfs*3	ENST00000373344	NM_000489.3	123	aaA/aa	5/35	1	1	FACETS	0.46	0.415	0.507	0.46	0.415	0.507	SUBCLONAL	1	FALSE	0	0.734014714086444	1		347	386	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063717	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0010405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	285	160	0	ENST00000412916.2:c.165+1G>C		p.X55_splice	ENST00000412916		55			0.941987556705959	4	FACETS	0.946	0.897	0.995			1	CLONAL	2	TRUE	NA	0.941987556705959	4		160	621	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458852	120458852	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	519	394	0	ENST00000256646.2:c.6493A>G	p.Thr2165Ala	p.T2165A	ENST00000256646	NM_024408.3	2165	Aca/Gca	34/34	0.881185211133813	4	FACETS	0.991	0.953	1	0.991	0.953	1	CLONAL	2	TRUE	2	0.941987556705959	4		394	1080	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566716	212566716	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	440	387	0	ENST00000342788.4:c.1465G>T	p.Asp489Tyr	p.D489Y	ENST00000342788	NM_005235.2	489	Gac/Tac	12/28	0.854511835849115	3	FACETS	0.987	0.953	1	0.987	0.953	1	CLONAL	2	TRUE	1	0.941987556705959	3		387	696	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372356	55372356	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	276	186	0	ENST00000297316.4:c.1046G>C	p.Ser349Thr	p.S349T	ENST00000297316	NM_022454.3	349	aGt/aCt	2/2	0.926911328558777	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.941987556705959	4		186	554	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002656	37002656	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	403	366	0	ENST00000358127.4:c.593A>G	p.Lys198Arg	p.K198R	ENST00000358127	NM_001280556.1	198	aAg/aGg	5/10	0.49764198733631	4	FACETS	0.85	0.812	0.889	0.85	0.812	0.889	INDETERMINATE	2	TRUE	2	0.941987556705959	4		366	977	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407501	139407501	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1504	122	347	0	ENST00000277541.6:c.2439C>A	p.Tyr813Ter	p.Y813*	ENST00000277541	NM_017617.3	813	taC/taA	15/34	0.52248659177712	6	FACETS	0.459	0.413	0.509	0.153	0.137	0.17	INDETERMINATE	1	TRUE	3	0.941987556705959	6		347	1626	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405457	70405457	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	321	305	0	ENST00000373644.4:c.2971A>T	p.Thr991Ser	p.T991S	ENST00000373644	NM_030625.2	991	Aca/Tca	4/12	0.53740967311031	4	FACETS	1	0.994	1	0.819	0.784	0.853	INDETERMINATE	2	TRUE	1	0.941987556705959	4		305	539	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428414	49428414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	44	310	0	ENST00000301067.7:c.10391G>A	p.Gly3464Glu	p.G3464E	ENST00000301067	NM_003482.3	3464	gGg/gAg	36/54	0.529792406427593	4	FACETS	0.241	0.201	0.286	0.08	0.067	0.096	INDETERMINATE	1	TRUE	1	0.941987556705959	4		310	752	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437567	56437567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	512	304	0	ENST00000407977.2:c.895G>A	p.Val299Met	p.V299M	ENST00000407977		299	Gtg/Atg	8/10	0.607364886274124	6	FACETS	0.959	0.922	0.996	0.959	0.922	0.996	CLONAL	3	TRUE	3	0.941987556705959	6		304	1090	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867632	78867632	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1196323454	NA	P-0010405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	834	393	0	ENST00000306801.3:c.2368G>T	p.Ala790Ser	p.A790S	ENST00000306801	NM_020761.2	790	Gcc/Tcc	20/34	0.607364886274124	6	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	TRUE	3	0.941987556705959	6		393	1701	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790128	40790128	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	277	169	0	ENST00000373198.4:c.2603C>A	p.Pro868His	p.P868H	ENST00000373198	NM_133170.3	868	cCc/cAc	18/32	0.718518048027968	5	FACETS	0.865	0.821	0.908	0.865	0.821	0.908	CLONAL	3	TRUE	2	0.941987556705959	5		169	547	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862847	9862847	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	438	362	0	ENST00000330684.3:c.2456del	p.Gly819AlafsTer69	p.G819Afs*69	ENST00000330684	NM_001134407.1	819	gGc/gc	12/13	0.941987556705959	4	FACETS	0.891	0.852	0.929			1	CLONAL	2	TRUE	NA	0.941987556705959	4		362	1014	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729561	41729564	+	missense_variant	Missense_Mutation	ONP	TTAC	TTAC	ATAG	novel	NA	P-0010405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	853	843	2	ENST00000242208.4:c.965_968delinsCTAT	p.Cys322_Lys323delinsSerMet	p.C322_K323delinsSM	ENST00000242208	NM_002192.2	322	tGTAAg/tCTATg	3/3	0.881185211133813	4	FACETS	0.895	0.867	0.923	0.895	0.867	0.923	CLONAL	2	TRUE	2	0.941987556705959	4		845	1965	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286533	33286533	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0010445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	143	239	0	ENST00000374542.5:c.2210C>G	p.Ser737Ter	p.S737*	ENST00000374542	NM_001141970.1	737	tCa/tGa	8/8	0.555941483689374	1	FACETS	0.84	0.774	0.907	0.84	0.774	0.907	CLONAL	1	TRUE	0	0.602303477496249	1		239	395	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100405	2100406	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0010445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	289	515	1	ENST00000219476.3:c.143_144del	p.Leu48GlnfsTer18	p.L48Qfs*18	ENST00000219476	NM_000548.3	48	cTG/c	3/42	0.573767696714224	1	FACETS	0.892	0.843	0.941	0.892	0.843	0.941	CLONAL	1	TRUE	0	0.602303477496249	1		516	752	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575101	64575103	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-	novel	NA	P-0010445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	186	338	0	ENST00000312049.6:c.704_706del	p.Glu235del	p.E235del	ENST00000312049	NM_130799.2	235	gAGGtg/gtg	4/10	0.573767696714224	1	FACETS	0.775	0.72	0.831	0.775	0.72	0.831	SUBCLONAL	1	TRUE	0	0.602303477496249	1		338	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0010484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	192	360	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.578860661074984	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.578860661074984	1		361	421	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0010484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	86	493	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.346	0.305	0.39	0.346	0.305	0.39	SUBCLONAL	1	TRUE	1	0.578860661074984	2		493	859	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288276	33288276	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0010484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	262	480	2	ENST00000374542.5:c.1132A>T	p.Lys378Ter	p.K378*	ENST00000374542	NM_001141970.1	378	Aaa/Taa	4/8	0.578860661074984	1	FACETS	0.966	0.911	1	0.966	0.911	1	CLONAL	1	TRUE	0	0.578860661074984	1		482	666	SUCCESS
EED	8726	MSKCC	GRCh37	11	85961477	85961480	+	frameshift_variant	Frame_Shift_Del	DEL	TAAA	TAAA	-	novel	NA	P-0010484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	33	464	0	ENST00000263360.6:c.256_259del	p.Asn86ValfsTer25	p.N86Vfs*25	ENST00000263360	NM_003797.3	85	gTAAAt/gt	2/12	0.578860661074984	1	FACETS	0.163	0.132	0.198	0.163	0.132	0.198	SUBCLONAL	1	TRUE	0	0.578860661074984	1		464	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934874	NA	P-0010488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	172	430	0	ENST00000269305.4:c.451C>G	p.Pro151Ala	p.P151A	ENST00000269305	NM_001126112.2	151	Ccc/Gcc	5/11	0.551170353974682	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.551170353974682	1		430	444	SUCCESS
APC	324	MSKCC	GRCh37	5	112175328	112175328	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0010512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	190	204	0	ENST00000257430.4:c.4037C>G	p.Ser1346Ter	p.S1346*	ENST00000257430	NM_000038.5	1346	tCa/tGa	16/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.472372516957505	2		204	667	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051057	180051057	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756924526	NA	P-0010512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	59	285	0	ENST00000261937.6:c.1426C>T	p.Arg476Trp	p.R476W	ENST00000261937	NM_182925.4	476	Cgg/Tgg	11/30	1	2	FACETS	0.291	0.25	0.337	0.291	0.25	0.337	SUBCLONAL	1	TRUE	1	0.472372516957505	2		285	858	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710652	114710652	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1523	594	748	4	ENST00000543371.1:c.137C>A	p.Ser46Ter	p.S46*	ENST00000543371	NM_001198531.1	46	tCg/tAg	1/14	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.472372516957505	2		752	2117	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562432	95562432	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	306	337	2	ENST00000393063.1:c.4825A>C	p.Asn1609His	p.N1609H	ENST00000393063	NM_030621.3	1609	Aat/Cat	24/28	0.472372516957505	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.472372516957505	1		339	713	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821594	72821644	+	inframe_deletion	In_Frame_Del	DEL	GCCGCCGCCGCCGCCGCCGCCGCCACCGCCGCCGCCGCCGCCACTGCCACC	GCCGCCGCCGCCGCCGCCGCCGCCACCGCCGCCGCCGCCGCCACTGCCACC	-	novel	NA	P-0010512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	569	164	1	ENST00000268489.5:c.10531_10581del	p.Gly3511_Gly3527del	p.G3511_G3527del	ENST00000268489	NM_006885.3	3511	GGTGGCAGTGGCGGCGGCGGCGGCGGTGGCGGCGGCGGCGGCGGCGGCGGC/-	10/10	0.139822280959946	4	FACETS	0.941	0.911	0.971	1	0.998	1	INDETERMINATE	4	TRUE	2	0.472372516957505	4		165	942	SUCCESS
APC	324	MSKCC	GRCh37	5	112174134	112174135	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TATG	novel	NA	P-0010512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	223	425	0	ENST00000257430.4:c.2844_2847dup	p.Pro950TyrfsTer14	p.P950Yfs*14	ENST00000257430	NM_000038.5	948	tct/tcTATGt	16/16	1	2	FACETS	0.954	0.888	1	0.954	0.888	1	CLONAL	1	TRUE	1	0.472372516957505	2		425	990	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0010516-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	560	536	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.255463959085426	5	FACETS	0.975	0.947	1			1	CLONAL	7	FALSE	NA	0.290131428243478	5		536	812	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0010516-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	263	408	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.968	0.909	1	1	0.995	1	CLONAL	2	FALSE	1	0.290131428243478	2		408	936	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940082	76940082	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010516-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	185	399	0	ENST00000373344.5:c.666G>A	p.Trp222Ter	p.W222*	ENST00000373344	NM_000489.3	222	tgG/tgA	9/35	0.290131428243478	0	FACETS	0.762	0.708	0.818			1	SUBCLONAL	2	FALSE	0	0.290131428243478	0		399	594	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0010519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	106	203	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.441860276346271	4	FACETS	0.858	0.769	0.952	0.286	0.256	0.318	CLONAL	1	TRUE	1	0.49742925554097	4		203	744	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637555	52637555	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	284	585	0	ENST00000394830.3:c.2761C>T	p.Arg921Ter	p.R921*	ENST00000394830	NM_018313.4	921	Cga/Tga	18/30	1	2	FACETS	0.852	0.8	0.906	0.852	0.8	0.906	CLONAL	1	TRUE	1	0.49742925554097	2		585	1340	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131498	202131498	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	149	239	0	ENST00000358485.4:c.466C>G	p.Gln156Glu	p.Q156E	ENST00000358485	NM_001080125.1	156	Caa/Gaa	2/9	1	2	FACETS	0.845	0.774	0.919	0.845	0.774	0.919	CLONAL	1	TRUE	1	0.49742925554097	2		239	709	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094386	27094386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	204	346	0	ENST00000324856.7:c.3094G>A	p.Glu1032Lys	p.E1032K	ENST00000324856	NM_006015.4	1032	Gag/Aag	11/20	1	2	FACETS	0.975	0.906	1	0.975	0.906	1	CLONAL	1	TRUE	1	0.49742925554097	2		346	841	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138407755	138407755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371601853	NA	P-0010519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1390	282	428	3	ENST00000289153.2:c.2098C>T	p.Arg700Trp	p.R700W	ENST00000289153	NM_006219.2	700	Cgg/Tgg	14/22	0.441860276346271	4	FACETS	1	0.949	1	0.338	0.317	0.361	CLONAL	1	TRUE	1	0.49742925554097	4		431	1672	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146709	185146709	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	247	304	0	ENST00000265026.3:c.340G>A	p.Glu114Lys	p.E114K	ENST00000265026	NM_004721.4	114	Gaa/Aaa	2/14	0.441860276346271	4	FACETS	1	0.986	1	0.401	0.374	0.429	CLONAL	1	TRUE	1	0.49742925554097	4		304	1236	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456534	189456534	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	266	356	1	ENST00000264731.3:c.295C>T	p.Gln99Ter	p.Q99*	ENST00000264731	NM_003722.4	99	Cag/Tag	3/14	0.49742925554097	5	FACETS	1	0.991	1	0.45	0.421	0.48	CLONAL	1	TRUE	2	0.49742925554097	5		357	1384	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55603399	55603399	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	279	505	0	ENST00000288135.5:c.2755C>G	p.Gln919Glu	p.Q919E	ENST00000288135	NM_000222.2	919	Caa/Gaa	20/21	NA	2	FACETS	0.946	0.888	1			1	INDETERMINATE	1	TRUE	NA	0.49742925554097	2		505	1186	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045954	26045954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1281	1059	805	0	ENST00000540144.1:c.316G>A	p.Glu106Lys	p.E106K	ENST00000540144	NM_003531.2	106	Gaa/Aaa	1/1	0.398699468022156	3	FACETS	1	0.996	1	0.757	0.737	0.778	CLONAL	2	TRUE	0	0.49742925554097	3		805	2340	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6045613	6045613	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554306528	NA	P-0010519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	113	151	0	ENST00000265849.7:c.73C>T	p.Gln25Ter	p.Q25*	ENST00000265849	NM_000535.5	25	Cag/Tag	2/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.49742925554097	2		151	408	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40998487	40998487	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	67	432	0	ENST00000267868.3:c.338T>C	p.Leu113Pro	p.L113P	ENST00000267868	NM_002875.4	113	cTt/cCt	4/10	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.49742925554097	NA		432	1165	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799200	88799200	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	126	523	2	ENST00000360948.2:c.185C>T	p.Ser62Leu	p.S62L	ENST00000360948	NM_001012338.2	62	tCa/tTa	2/19	1	2	FACETS	0.439	0.396	0.484	0.439	0.396	0.484	SUBCLONAL	1	TRUE	1	0.49742925554097	2		525	1154	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15374297	15374297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	335	543	2	ENST00000263377.2:c.1275G>A	p.Met425Ile	p.M425I	ENST00000263377	NM_058243.2	425	atG/atA	7/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.49742925554097	2		545	1201	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61724127	61724127	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs746291979	NA	P-0010526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	225	351	0	ENST00000401558.2:c.775A>G	p.Met259Val	p.M259V	ENST00000401558	NM_003400.3	259	Atg/Gtg	10/25	0.818698956347763	2	FACETS	1	0.978	1	0.541	0.509	0.573	CLONAL	1	TRUE	0	0.818698956347763	2		351	508	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144812	58144812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763652580	NA	P-0010526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1435	302	532	0	ENST00000257904.6:c.416G>A	p.Arg139Gln	p.R139Q	ENST00000257904	NM_000075.3	139	cGa/cAa	4/8	0.758791515151777	4	FACETS	0.772	0.725	0.821	0.386	0.362	0.411	SUBCLONAL	1	TRUE	2	0.818698956347763	4		532	1737	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349326	89349326	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3018	869	1609	2	ENST00000301030.4:c.3624G>T	p.Lys1208Asn	p.K1208N	ENST00000301030	NM_001256183.1	1208	aaG/aaT	9/13	0.664521653276799	4	FACETS	0.993	0.958	1	0.497	0.479	0.515	CLONAL	1	TRUE	2	0.818698956347763	4		1611	3887	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0010529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	532	517	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	NA	2	FACETS	1	0.997	1			1	INDETERMINATE	2	FALSE	NA	0.796593490200861	2		517	603	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49929190	49929190	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs55856544	NA	P-0010529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	808	920	3	ENST00000296474.3:c.3352+1G>A		p.X1118_splice	ENST00000296474	NM_002447.2	1118			0.796593490200861	5	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	FALSE	2	0.796593490200861	5		923	1479	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927993	178927993	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	82	298	0	ENST00000263967.3:c.1271G>T	p.Trp424Leu	p.W424L	ENST00000263967	NM_006218.2	424	tGg/tTg	8/21	0.796593490200861	9	FACETS	0.817	0.719	0.923	0.136	0.119	0.154	CLONAL	1	FALSE	3	0.796593490200861	9		298	954	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346940	70346940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	264	568	0	ENST00000374080.3:c.2807G>A	p.Cys936Tyr	p.C936Y	ENST00000374080		936	tGc/tAc	20/45	0.678794048708516	3	FACETS	0.873	0.817	0.93	0.436	0.408	0.465	CLONAL	1	FALSE	1	0.678794048708516	3		568	1194	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539487	187539487	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	378	515	0	ENST00000441802.2:c.8253del	p.Phe2751LeufsTer2	p.F2751Lfs*2	ENST00000441802	NM_005245.3	2751	ttT/tt	10/27	1	2	FACETS	0.886	0.841	0.931	0.886	0.841	0.931	CLONAL	1	TRUE	1	0.695574653029433	2		515	1227	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871020	12871033	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTTGCCCGAGTT	AGCTTGCCCGAGTT	-	novel	NA	P-0010565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	276	358	0	ENST00000228872.4:c.247_260del	p.Ser83LeufsTer37	p.S83Lfs*37	ENST00000228872	NM_004064.3	83	AGCTTGCCCGAGTTc/c	1/3	0.359343429593587	1	FACETS	0.76	0.718	0.802	0.76	0.718	0.802	INDETERMINATE	1	TRUE	0	0.695574653029433	1		358	681	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0010569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	327	565	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.614128584542425	2		565	877	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0010569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	238	424	0	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	0.614128584542425	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.614128584542425	1		424	422	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0010569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	239	569	2	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.60652221702271	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.614128584542425	1		571	390	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109870	115109870	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	98	236	0	ENST00000257566.3:c.2008C>A	p.Leu670Met	p.L670M	ENST00000257566	NM_016569.3	670	Ctg/Atg	8/8	0.240652612658407	1	FACETS	0.871	0.79	0.953	0.871	0.79	0.953	INDETERMINATE	1	TRUE	0	0.614128584542425	1		236	254	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138491	11138491	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	213	525	0	ENST00000358026.2:c.3247G>T	p.Glu1083Ter	p.E1083*	ENST00000358026	NM_001128849.1	1083	Gag/Tag	24/36	0.614128584542425	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.614128584542425	1		525	376	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462896	120462896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	111	396	0	ENST00000256646.2:c.5435C>T	p.Ala1812Val	p.A1812V	ENST00000256646	NM_024408.3	1812	gCa/gTa	30/34	0.255532583364065	0	FACETS	0.351	0.318	0.386			1	INDETERMINATE	1	TRUE	0	0.614128584542425	0		396	397	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204737444	204737444	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	231	444	1	ENST00000302823.3:c.581G>T	p.Ser194Ile	p.S194I	ENST00000302823	NM_005214.4	194	aGc/aTc	4/4	0.166536216468104	5	FACETS	0.841	0.786	0.898	0.561	0.524	0.599	INDETERMINATE	2	TRUE	2	0.614128584542425	5		445	859	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248549	212248549	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	592	747	1	ENST00000342788.4:c.3718C>A	p.Pro1240Thr	p.P1240T	ENST00000342788	NM_005235.2	1240	Cct/Act	28/28	0.166536216468104	5	FACETS	1	0.99	1	0.721	0.693	0.75	INDETERMINATE	2	TRUE	2	0.614128584542425	5		748	1712	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987072	69987072	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	313	536	0	ENST00000394351.3:c.133G>T	p.Ala45Ser	p.A45S	ENST00000394351	NM_000248.3	45	Gcc/Tcc	2/9	0.614128584542425	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.614128584542425	1		536	579	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143324090	143324090	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0010569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	202	324	0	ENST00000262992.4:c.372+1G>C		p.X124_splice	ENST00000262992	NM_001101669.1	124			1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.614128584542425	2		324	540	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484171	8484171	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	338	585	0	ENST00000356435.5:c.3361G>A	p.Asp1121Asn	p.D1121N	ENST00000356435		1121	Gat/Aat	19/35	0.614128584542425	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.614128584542425	1		585	649	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239858	98239858	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	215	542	0	ENST00000331920.6:c.1474G>T	p.Gly492Ter	p.G492*	ENST00000331920	NM_000264.3	492	Gga/Tga	10/24	0.614128584542425	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.614128584542425	1		542	445	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425134	49425134	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	359	773	0	ENST00000301067.7:c.13354G>T	p.Ala4452Ser	p.A4452S	ENST00000301067	NM_003482.3	4452	Gca/Tca	39/54	0.166536216468104	5	FACETS	1	0.992	1	0.801	0.761	0.841	INDETERMINATE	2	TRUE	2	0.614128584542425	5		773	935	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858652	57858652	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0010569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	276	655	0	ENST00000228682.2:c.389+1G>T		p.X130_splice	ENST00000228682	NM_005269.2	130			0.166536216468104	5	FACETS	0.995	0.937	1	0.663	0.624	0.703	INDETERMINATE	2	TRUE	2	0.614128584542425	5		655	868	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592634	28592634	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	310	841	0	ENST00000241453.7:c.2511G>C	p.Met837Ile	p.M837I	ENST00000241453	NM_004119.2	837	atG/atC	20/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.614128584542425	2		841	909	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786036	3786036	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0010569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	155	854	0	ENST00000262367.5:c.4728+1G>T		p.X1576_splice	ENST00000262367	NM_004380.2	1576			0.392972375838953	1	FACETS	0.465	0.426	0.506	0.465	0.426	0.506	SUBCLONAL	1	TRUE	0	0.614128584542425	1		854	752	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857959	9857959	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	92	612	1	ENST00000330684.3:c.3442C>A	p.Pro1148Thr	p.P1148T	ENST00000330684	NM_001134407.1	1148	Ccg/Acg	13/13	0.392972375838953	1	FACETS	0.402	0.358	0.448	0.402	0.358	0.448	SUBCLONAL	1	TRUE	0	0.614128584542425	1		613	517	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81927361	81927361	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	151	778	0	ENST00000359376.3:c.1034A>G	p.Tyr345Cys	p.Y345C	ENST00000359376	NM_002661.3	345	tAc/tGc	12/33	0.294843125197727	0	FACETS	0.249	0.228	0.272			1	INDETERMINATE	1	TRUE	0	0.614128584542425	0		778	761	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2214566	2214566	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	150	567	1	ENST00000398665.3:c.1894G>T	p.Glu632Ter	p.E632*	ENST00000398665	NM_032482.2	632	Gag/Tag	19/28	0.501484386918337	0	FACETS	0.668	0.624	0.713			1	SUBCLONAL	1	TRUE	0	0.614128584542425	0		568	282	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142940	7142940	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	360	649	3	ENST00000302850.5:c.2429C>A	p.Ser810Tyr	p.S810Y	ENST00000302850	NM_000208.2	810	tCc/tAc	12/22	0.614128584542425	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.614128584542425	1		652	623	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602866	10602866	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	254	590	0	ENST00000171111.5:c.712A>G	p.Asn238Asp	p.N238D	ENST00000171111	NM_203500.1	238	Aac/Gac	3/6	0.614128584542425	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.614128584542425	1		590	495	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303874	30303874	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0010569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	167	502	0	ENST00000262643.3:c.112-2A>G		p.X38_splice	ENST00000262643	NM_001238.2	38			0.294843125197727	0	FACETS	0.383	0.354	0.413			1	INDETERMINATE	1	TRUE	0	0.614128584542425	0		502	548	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609983	81609984	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0010569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	183	348	1	ENST00000298171.2:c.1583_1584del	p.Arg528ProfsTer34	p.R528Pfs*34	ENST00000298171	NM_000369.2	527	atGCgc/atgc	10/10	0.25017303934262	2	FACETS	1	0.989	1	0.667	0.622	0.712	INDETERMINATE	1	TRUE	0	0.614128584542425	2		349	447	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199361	16199362	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0010569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	275	719	3	ENST00000375759.3:c.134_135delinsTT	p.Gly45Val	p.G45V	ENST00000375759	NM_015001.2	45	gGA/gTT	2/15	0.60652221702271	1	FACETS	0.804	0.758	0.851	0.804	0.758	0.851	CLONAL	1	TRUE	0	0.614128584542425	1		722	772	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060665	38060665	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010572-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	104	715	1	ENST00000250448.2:c.1324G>T	p.Ala442Ser	p.A442S	ENST00000250448	NM_004496.3	442	Gcc/Tcc	2/2	1	2	FACETS	0.459	0.41	0.511	0.459	0.41	0.511	SUBCLONAL	1	TRUE	1	0.444146054107215	2		716	1021	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627209	37627209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010572-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	68	435	0	ENST00000447079.4:c.1125del	p.Ser376ValfsTer60	p.S376Vfs*60	ENST00000447079	NM_015083.1	375	tCc/tc	2/14	1	2	FACETS	0.627	0.547	0.714	0.627	0.547	0.714	SUBCLONAL	1	TRUE	1	0.444146054107215	2		435	488	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618657	37618657	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010572-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	105	476	0	ENST00000447079.4:c.333del	p.Arg112ValfsTer12	p.R112Vfs*12	ENST00000447079	NM_015083.1	111	caT/ca	1/14	1	2	FACETS	0.654	0.586	0.726	0.654	0.586	0.726	SUBCLONAL	1	TRUE	1	0.444146054107215	2		476	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0010600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	547	485	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.784388189651839	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.807513774128125	1		485	774	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178469	56178469	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	224	392	2	ENST00000399503.3:c.3442A>G	p.Thr1148Ala	p.T1148A	ENST00000399503	NM_005921.1	1148	Act/Gct	14/20	0.41402887841961	1	FACETS	0.374	0.349	0.401	0.374	0.349	0.401	INDETERMINATE	1	TRUE	0	0.807513774128125	1		394	884	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222160	2222160	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1471	117	626	0	ENST00000398665.3:c.2992C>G	p.Leu998Val	p.L998V	ENST00000398665	NM_032482.2	998	Ctt/Gtt	24/28	0.472400256192714	2	FACETS	0.182	0.163	0.203	0.091	0.081	0.102	INDETERMINATE	1	TRUE	0	0.807513774128125	2		626	1588	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045710	47045710	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	430	587	1	ENST00000377604.3:c.2591G>T	p.Arg864Leu	p.R864L	ENST00000377604	NM_001204468.1	864	cGg/cTg	23/24	0.317478344252987	1	FACETS	0.477	0.454	0.5	0.477	0.454	0.5	INDETERMINATE	1	TRUE	0	0.807513774128125	1		588	1332	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228613001	228613001	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373549345	NA	P-0010607-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	77	685	1	ENST00000366696.1:c.26G>A	p.Arg9His	p.R9H	ENST00000366696	NM_003493.2	9	cGc/cAc	1/1	0.492785315953342	3	FACETS	0.433	0.379	0.492	0.217	0.189	0.246	SUBCLONAL	1	TRUE	1	0.492785315953342	3		686	899	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984867	55984867	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1490727992	NA	P-0010607-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	37	603	0	ENST00000263923.4:c.262C>G	p.Leu88Val	p.L88V	ENST00000263923	NM_002253.2	88	Ctc/Gtc	3/30	1	2	FACETS	0.217	0.178	0.261	0.217	0.178	0.261	SUBCLONAL	1	TRUE	1	0.492785315953342	2		603	692	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211544	98211544	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010607-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	32	463	0	ENST00000331920.6:c.3611T>C	p.Val1204Ala	p.V1204A	ENST00000331920	NM_000264.3	1204	gTg/gCg	22/24	1	2	FACETS	0.251	0.203	0.306	0.251	0.203	0.306	SUBCLONAL	1	TRUE	1	0.492785315953342	2		463	517	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250910	99250910	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010607-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	66	519	0	ENST00000268035.6:c.214A>G	p.Ser72Gly	p.S72G	ENST00000268035	NM_000875.3	72	Agc/Ggc	2/21	1	2	FACETS	0.457	0.397	0.522	0.457	0.397	0.522	SUBCLONAL	1	TRUE	1	0.492785315953342	2		519	586	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	631	939	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.576765198094252	2	FACETS	0.974	0.943	1	0.974	0.943	1	CLONAL	2	TRUE	0	0.576765198094252	2		940	1123	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0010627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	614	576	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.316192971415137	1	FACETS	1	0.996	1	1	0.996	1	INDETERMINATE	1	TRUE	0	0.576765198094252	1		579	1255	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715721	30715721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893816	NA	P-0010627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	278	439	0	ENST00000295754.5:c.1379G>A	p.Arg460His	p.R460H	ENST00000295754	NM_003242.5	460	cGc/cAc	5/7	1	2	FACETS	0.876	0.822	0.93	0.876	0.822	0.93	CLONAL	1	TRUE	1	0.576765198094252	2		439	1101	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288969	212288969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148791072	NA	P-0010627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	344	623	0	ENST00000342788.4:c.2777C>T	p.Thr926Met	p.T926M	ENST00000342788	NM_005235.2	926	aCg/aTg	23/28	NA	2	FACETS	0.994	0.941	1			1	INDETERMINATE	1	TRUE	NA	0.576765198094252	2		623	1200	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066725	94066725	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1357	560	936	1	ENST00000369303.4:c.1034C>T	p.Thr345Ile	p.T345I	ENST00000369303	NM_004440.3	345	aCc/aTc	5/17	0.287227101018543	1	FACETS	0.721	0.69	0.752	0.721	0.69	0.752	INDETERMINATE	1	TRUE	0	0.576765198094252	1		937	1917	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971110	21971110	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519881	NA	P-0010627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	169	206	0	ENST00000304494.5:c.248A>G	p.His83Arg	p.H83R	ENST00000304494	NM_000077.4	83	cAc/cGc	2/3	0.361679042455656	1	FACETS	0.821	0.76	0.883	0.821	0.76	0.883	CLONAL	1	TRUE	0	0.576765198094252	1		206	508	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527462	29527462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs76015786	NA	P-0010627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	211	413	0	ENST00000356175.3:c.911G>A	p.Arg304Gln	p.R304Q	ENST00000356175	NM_000267.3	304	cGa/cAa	9/57	1	2	FACETS	0.868	0.807	0.93	0.868	0.807	0.93	CLONAL	1	TRUE	1	0.576765198094252	2		413	843	SUCCESS
APC	324	MSKCC	GRCh37	5	112175259	112175260	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0010627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	347	445	0	ENST00000257430.4:c.3968_3969del	p.Val1323AlafsTer8	p.V1323Afs*8	ENST00000257430	NM_000038.5	1323	gTT/g	16/16	0.576765198094252	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.576765198094252	1		445	769	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925334	114925334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010628-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	87	672	0	ENST00000543371.1:c.1412G>T	p.Arg471Leu	p.R471L	ENST00000543371	NM_001198531.1	471	cGc/cTc	14/14	1	2	FACETS	0.524	0.464	0.589	0.524	0.464	0.589	SUBCLONAL	1	FALSE	1	0.462333583638006	2		672	718	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342656	118342656	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010628-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	90	310	0	ENST00000534358.1:c.782C>G	p.Ser261Cys	p.S261C	ENST00000534358	NM_005933.3	261	tCt/tGt	3/36	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	FALSE	1	0.462333583638006	2		310	371	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41011027	41011027	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010628-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	70	788	0	ENST00000267868.3:c.460G>C	p.Glu154Gln	p.E154Q	ENST00000267868	NM_002875.4	154	Gaa/Caa	6/10	0.256537838042677	0	FACETS	0.255	0.222	0.29			1	INDETERMINATE	1	FALSE	0	0.462333583638006	0		788	639	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821094	72821094	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010628-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	113	720	0	ENST00000268489.5:c.11081C>G	p.Thr3694Ser	p.T3694S	ENST00000268489	NM_006885.3	3694	aCc/aGc	10/10	1	2	FACETS	0.605	0.544	0.669	0.605	0.544	0.669	SUBCLONAL	1	FALSE	1	0.462333583638006	2		720	808	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579669	7579729	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCAGGTCCCCAGCCCAACCCTTGTCCTTACCAGAACGTTGTTTTCAGGAAGTCTGAAAGA	TCCAGGTCCCCAGCCCAACCCTTGTCCTTACCAGAACGTTGTTTTCAGGAAGTCTGAAAGA	AAC	novel	NA	P-0010628-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	204	775	3	ENST00000269305.4:c.75-8_96+31delinsGTT		p.X25_splice	ENST00000269305	NM_001126112.2	25		3/11	0.462333583638006	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	0	0.462333583638006	1		778	611	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770065	56770065	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs752608224	NA	P-0010628-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	42	573	0	ENST00000337432.4:c.61C>G	p.Pro21Ala	p.P21A	ENST00000337432	NM_058216.2	21	Cca/Gca	1/9	1	2	FACETS	0.25	0.208	0.297	0.25	0.208	0.297	SUBCLONAL	1	FALSE	1	0.462333583638006	2		573	727	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78858903	78858903	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010628-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	229	731	1	ENST00000306801.3:c.1938G>T	p.Met646Ile	p.M646I	ENST00000306801	NM_020761.2	646	atG/atT	17/34	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.462333583638006	2		732	847	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228015	36228053	+	inframe_deletion	In_Frame_Del	DEL	CCACCATGATGCTGTCATCTTCCTGGCCGAGCAGCTCCC	CCACCATGATGCTGTCATCTTCCTGGCCGAGCAGCTCCC	-	novel	NA	P-0010628-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	38	937	1	ENST00000222270.7:c.7402_7440del	p.His2468_Pro2480del	p.H2468_P2480del	ENST00000222270	NM_014727.1	2467	atCCACCATGATGCTGTCATCTTCCTGGCCGAGCAGCTCCCc/atc	33/37	0.366652303383679	1	FACETS	0.167	0.137	0.2	0.167	0.137	0.2	SUBCLONAL	1	FALSE	0	0.462333583638006	1		938	758	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656778	45656778	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010628-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	78	647	0	ENST00000407780.3:c.378G>C	p.Leu126Phe	p.L126F	ENST00000407780	NM_001283052.1	126	ttG/ttC	3/7	0.302017316137709	1	FACETS	0.405	0.355	0.458	0.405	0.355	0.458	SUBCLONAL	1	FALSE	0	0.462333583638006	1		647	641	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279423	1279423	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010628-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	238	948	3	ENST00000310581.5:c.2113G>A	p.Glu705Lys	p.E705K	ENST00000310581	NM_198253.2	705	Gag/Aag	5/16	1	2	FACETS	0.994	0.928	1	0.994	0.928	1	CLONAL	1	FALSE	1	0.462333583638006	2		951	1036	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380055	116380055	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010628-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	169	669	0	ENST00000397752.3:c.1444G>C	p.Asp482His	p.D482H	ENST00000397752	NM_000245.2	482	Gac/Cac	4/21	0.462333583638006	3	FACETS	0.913	0.839	0.99	0.456	0.419	0.495	CLONAL	1	FALSE	1	0.462333583638006	3		669	986	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045016	47045016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556782040	NA	P-0010628-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	73	1128	0	ENST00000377604.3:c.2342C>T	p.Ser781Leu	p.S781L	ENST00000377604	NM_001204468.1	781	tCa/tTa	20/24	1	2	FACETS	0.277	0.241	0.316	0.277	0.241	0.316	SUBCLONAL	1	FALSE	1	0.462333583638006	2		1128	1139	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010633-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	311	939	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.354586604326851	3	FACETS	0.822	0.778	0.866	0.822	0.778	0.866	CLONAL	2	TRUE	1	0.588056412600848	3		940	833	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	219	160	0				ENST00000310581	NM_198253.2	-/1132			0.710168674778095	3	FACETS	0.916	0.865	0.968	0.916	0.865	0.968	CLONAL	2	TRUE	1	0.777205428407213	3		160	427	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522314	157522314	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	207	429	0	ENST00000346085.5:c.4586T>C	p.Met1529Thr	p.M1529T	ENST00000346085	NM_020732.3	1529	aTg/aCg	18/20	1	2	FACETS	0.778	0.725	0.832	0.778	0.725	0.832	SUBCLONAL	1	TRUE	1	0.777205428407213	2		429	685	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805799	46805799	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	569	676	0	ENST00000290295.7:c.157C>A	p.Leu53Met	p.L53M	ENST00000290295	NM_006361.5	53	Ctg/Atg	1/2	0.493556030938979	4	FACETS	0.925	0.89	0.961			1	CLONAL	2	TRUE	NA	0.777205428407213	4		676	1406	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589196	67589205	+	frameshift_variant	Frame_Shift_Del	DEL	CATTAACCTT	CATTAACCTT	-	novel	NA	P-0010643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	213	358	0	ENST00000274335.5:c.1186_1195del	p.Leu396ValfsTer6	p.L396Vfs*6	ENST00000274335		395	cCATTAACCTTc/cc	9/15	0.710168674778095	3	FACETS	0.919	0.856	0.985	0.46	0.428	0.493	CLONAL	1	TRUE	1	0.777205428407213	3		358	828	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589579	67589596	+	inframe_deletion	In_Frame_Del	DEL	AAATTACATGAATATAAC	AAATTACATGAATATAAC	-	novel	NA	P-0010643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	226	218	0	ENST00000274335.5:c.1343_1360del	p.Lys448_Asn453del	p.K448_N453del	ENST00000274335		448	AAATTACATGAATATAAC/-	10/15	0.710168674778095	3	FACETS	0.897	0.847	0.947	0.897	0.847	0.947	CLONAL	2	TRUE	1	0.777205428407213	3		218	450	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667527	29667528	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	420	367	0	ENST00000356175.3:c.6863_6864insA	p.Pro2289AlafsTer17	p.P2289Afs*17	ENST00000356175	NM_000267.3	2288	tcg/tcAg	46/57	0.665800232264222	4	FACETS	0.972	0.929	1			1	CLONAL	2	TRUE	NA	0.777205428407213	4		367	988	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0010653-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	15	562	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.875304981014853	1	FACETS	0.03	0.021	0.04	0.03	0.021	0.04	SUBCLONAL	1	TRUE	0	0.875304981014853	1		562	645	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913409	NA	P-0010653-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	51	562	0	ENST00000349496.5:c.134C>G	p.Ser45Cys	p.S45C	ENST00000349496	NM_001904.3	45	tCt/tGt	3/15	0.875304981014853	1	FACETS	0.102	0.086	0.119	0.102	0.086	0.119	SUBCLONAL	1	TRUE	0	0.875304981014853	1		562	645	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777894	NA	P-0010660-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	301	696	0	ENST00000361445.4:c.6644C>T	p.Ser2215Phe	p.S2215F	ENST00000361445	NM_004958.3	2215	tCt/tTt	47/58	0.164816410018788	3	FACETS	1	0.992	1	0.643	0.608	0.679	INDETERMINATE	1	TRUE	1	0.777827162054711	3		696	836	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0010660-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	202	577	1	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	0.921	0.86	0.983	0.921	0.86	0.983	CLONAL	1	TRUE	1	0.777827162054711	2		578	564	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546176	41546176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010660-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	112	195	0	ENST00000263253.7:c.2791del	p.Leu931CysfsTer15	p.L931Cfs*15	ENST00000263253	NM_001429.3	931	Ctg/tg	14/31	1	2	FACETS	0.983	0.897	1	0.983	0.897	1	CLONAL	1	TRUE	1	0.777827162054711	2		195	293	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097654	27097655	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0010660-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	286	656	0	ENST00000324856.7:c.3245_3246del	p.Val1082GlyfsTer22	p.V1082Gfs*22	ENST00000324856	NM_006015.4	1081	aaTGtg/aatg	12/20	0.164816410018788	3	FACETS	1	0.988	1	0.582	0.549	0.616	INDETERMINATE	1	TRUE	1	0.777827162054711	3		656	877	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711942	89711965	+	frameshift_variant	Frame_Shift_Del	DEL	ATTATAGACCAGTGGCACTGTTGT	ATTATAGACCAGTGGCACTGTTGT	C	novel	NA	P-0010660-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	174	438	0	ENST00000371953.3:c.560_583delinsC	p.Asp187AlafsTer7	p.D187Afs*7	ENST00000371953	NM_000314.4	187	gATTATAGACCAGTGGCACTGTTGTtt/gCtt	6/9	0.677802641930416	4	FACETS	1	0.967	1	0.771	0.73	0.81	CLONAL	3	TRUE	0	0.777827162054711	4		438	258	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589581	67589596	+	protein_altering_variant	In_Frame_Del	DEL	ATTACATGAATATAAC	ATTACATGAATATAAC	T	novel	NA	P-0010660-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	70	307	0	ENST00000274335.5:c.1344_1359delinsT	p.Lys448_Tyr452del	p.K448_Y452del	ENST00000274335		448	aaATTACATGAATATAAC/aaT	10/15	0.777827162054711	3	FACETS	0.786	0.691	0.887	0.393	0.345	0.444	SUBCLONAL	1	TRUE	1	0.777827162054711	3		307	318	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0010680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	120	431	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.939	0.857	1	0.939	0.857	1	CLONAL	1	TRUE	1	0.660125554375678	2		431	387	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0010680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	324	489	1	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.544544307328764	3	FACETS	1	0.963	1			1	CLONAL	2	TRUE	NA	0.660125554375678	3		490	645	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	192	657	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.848	0.787	0.91	0.848	0.787	0.91	CLONAL	1	TRUE	1	0.660125554375678	2		657	686	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0010680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	351	514	1	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	0.660125554375678	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.660125554375678	3		515	648	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574678	41574679	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs754418509	NA	P-0010680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	449	804	0	ENST00000263253.7:c.6970dup	p.His2324ProfsTer55	p.H2324Pfs*55	ENST00000263253	NM_001429.3	2321	-/C	31/31	NA	2	FACETS	0.779	0.748	0.81			1	INDETERMINATE	2	TRUE	NA	0.660125554375678	2		804	873	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129749	108129749	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs780619951	NA	P-0010680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	432	626	1	ENST00000278616.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000278616	NM_000051.3	805	Cga/Tga	16/63	0.660125554375678	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.660125554375678	2		627	642	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953076	2953076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	464	752	1	ENST00000396946.4:c.2864G>A	p.Gly955Asp	p.G955D	ENST00000396946	NM_032415.4	955	gGc/gAc	22/25	0.644342993663983	3	FACETS	0.991	0.952	1	0.991	0.952	1	CLONAL	2	TRUE	1	0.660125554375678	3		753	943	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528558	89528558	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	115	352	1	ENST00000336596.2:c.2858A>T	p.Lys953Met	p.K953M	ENST00000336596	NM_005233.5	953	aAg/aTg	17/17	1	2	FACETS	0.898	0.816	0.983	0.898	0.816	0.983	CLONAL	1	TRUE	1	0.660125554375678	2		353	388	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751931	57751931	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55768901	NA	P-0010680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	260	619	0	ENST00000274289.3:c.1306G>A	p.Glu436Lys	p.E436K	ENST00000274289	NM_006622.3	436	Gaa/Aaa	10/14	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.660125554375678	2		619	762	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858552	57858552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143548857	NA	P-0010680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	260	682	2	ENST00000228682.2:c.290C>T	p.Thr97Met	p.T97M	ENST00000228682	NM_005269.2	97	aCg/aTg	4/12	0.660125554375678	3	FACETS	1	0.942	1	0.503	0.471	0.535	CLONAL	1	TRUE	1	0.660125554375678	3		684	1042	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46266423	46266423	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	144	574	0	ENST00000371998.3:c.2408T>A	p.Ile803Asn	p.I803N	ENST00000371998		803	aTt/aAt	13/23	0.644342993663983	3	FACETS	0.855	0.781	0.931	0.427	0.39	0.466	CLONAL	1	TRUE	1	0.660125554375678	3		574	679	SUCCESS
APC	324	MSKCC	GRCh37	5	112175645	112175645	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	117	370	0	ENST00000257430.4:c.4354del	p.Val1452TyrfsTer21	p.V1452Yfs*21	ENST00000257430	NM_000038.5	1452	Gta/ta	16/16	1	2	FACETS	0.834	0.758	0.913	0.834	0.758	0.913	CLONAL	1	TRUE	1	0.660125554375678	2		370	425	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339931	70339931	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	31	569	1	ENST00000374080.3:c.464G>T	p.Arg155Leu	p.R155L	ENST00000374080		155	cGg/cTg	4/45	0.660125554375678	2	FACETS	0.152	0.123	0.186	0.076	0.061	0.093	SUBCLONAL	1	TRUE	0	0.660125554375678	2		570	616	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102196062	102196062	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	41	375	1	ENST00000263464.3:c.822G>T	p.Glu274Asp	p.E274D	ENST00000263464	NM_001165.4	274	gaG/gaT	2/9	0.660125554375678	2	FACETS	0.314	0.261	0.372	0.157	0.13	0.186	SUBCLONAL	1	TRUE	0	0.660125554375678	2		376	396	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646921	23646921	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	38	718	2	ENST00000261584.4:c.946C>A	p.Pro316Thr	p.P316T	ENST00000261584	NM_024675.3	316	Ccc/Acc	4/13	0.660125554375678	1	FACETS	0.167	0.137	0.199	0.167	0.137	0.199	SUBCLONAL	1	TRUE	0	0.660125554375678	1		720	463	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182662958	182662958	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	28	439	0	ENST00000292782.4:c.704C>A	p.Ala235Glu	p.A235E	ENST00000292782	NM_020640.2	235	gCa/gAa	7/7	0.115246300554074	4	FACETS	0.286	0.228	0.352			1	INDETERMINATE	1	TRUE	NA	0.660125554375678	4		439	493	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859844	117859844	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	44	395	1	ENST00000297338.2:c.1791C>A	p.Phe597Leu	p.F597L	ENST00000297338	NM_006265.2	597	ttC/ttA	14/14	1	2	FACETS	0.271	0.227	0.32	0.271	0.227	0.32	SUBCLONAL	1	TRUE	1	0.660125554375678	2		396	492	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339940	70339940	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	41	566	1	ENST00000374080.3:c.473G>T	p.Trp158Leu	p.W158L	ENST00000374080		158	tGg/tTg	4/45	0.660125554375678	2	FACETS	0.201	0.167	0.239	0.101	0.083	0.12	SUBCLONAL	1	TRUE	0	0.660125554375678	2		567	618	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074279	8074279	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	95	489	0	ENST00000377482.5:c.380C>A	p.Thr127Asn	p.T127N	ENST00000377482	NM_018948.3	127	aCc/aAc	4/4	0.649824392779708	1	FACETS	0.399	0.357	0.444	0.399	0.357	0.444	SUBCLONAL	1	TRUE	0	0.660125554375678	1		489	483	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799242	45799242	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	55	492	0	ENST00000450313.1:c.191C>A	p.Ala64Asp	p.A64D	ENST00000450313	NM_012222.2	64	gCc/gAc	3/16	0.660125554375678	3	FACETS	0.333	0.284	0.387	0.167	0.142	0.194	SUBCLONAL	1	TRUE	1	0.660125554375678	3		492	665	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745954	162745954	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	41	403	0	ENST00000367921.3:c.2077C>T	p.Gln693Ter	p.Q693*	ENST00000367921	NM_006182.2	693	Caa/Taa	16/18	0.630250366923971	3	FACETS	0.352	0.293	0.418	0.176	0.146	0.209	SUBCLONAL	1	TRUE	1	0.660125554375678	3		403	469	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120795697	120795697	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	46	487	0	ENST00000257552.2:c.456C>A	p.Phe152Leu	p.F152L	ENST00000257552	NM_002442.3	152	ttC/ttA	8/15	0.630250366923971	3	FACETS	0.268	0.225	0.316	0.134	0.112	0.158	SUBCLONAL	1	TRUE	1	0.660125554375678	3		487	691	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562792	21562792	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	31	529	0	ENST00000382592.4:c.1127C>A	p.Ala376Asp	p.A376D	ENST00000382592	NM_014572.2	376	gCc/gAc	4/8	NA	2	FACETS	0.173	0.139	0.211			1	INDETERMINATE	1	TRUE	NA	0.660125554375678	2		529	544	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832067	72832067	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	22	607	1	ENST00000268489.5:c.4514C>A	p.Pro1505Gln	p.P1505Q	ENST00000268489	NM_006885.3	1505	cCa/cAa	9/10	0.649824392779708	1	FACETS	0.111	0.086	0.141	0.111	0.086	0.141	SUBCLONAL	1	TRUE	0	0.660125554375678	1		608	401	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578472	7578472	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	14	819	1	ENST00000269305.4:c.458C>A	p.Pro153His	p.P153H	ENST00000269305	NM_001126112.2	153	cCc/cAc	5/11	0.660125554375678	1	FACETS	0.048	0.034	0.065	0.048	0.034	0.065	SUBCLONAL	1	TRUE	0	0.660125554375678	1		820	592	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659804	227659804	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	25	381	0	ENST00000305123.5:c.3651C>A	p.Ser1217Arg	p.S1217R	ENST00000305123	NM_005544.2	1217	agC/agA	1/2	1	2	FACETS	0.161	0.126	0.201	0.161	0.126	0.201	SUBCLONAL	1	TRUE	1	0.660125554375678	2		381	471	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46275831	46275831	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	82	595	1	ENST00000371998.3:c.3267G>T	p.Glu1089Asp	p.E1089D	ENST00000371998		1089	gaG/gaT	18/23	0.644342993663983	3	FACETS	0.415	0.365	0.469	0.208	0.182	0.235	SUBCLONAL	1	TRUE	1	0.660125554375678	3		596	796	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119812236	119812236	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	46	523	0	ENST00000316626.5:c.46C>A	p.Pro16Thr	p.P16T	ENST00000316626		16	Ccg/Acg	1/12	1	2	FACETS	0.206	0.173	0.243	0.206	0.173	0.243	SUBCLONAL	1	TRUE	1	0.660125554375678	2		523	675	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1918616	1918616	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	25	578	0	ENST00000382891.5:c.779G>T	p.Arg260Leu	p.R260L	ENST00000382891	NM_133335.3	260	cGc/cTc	4/22	0.641116833340068	1	FACETS	0.129	0.101	0.161	0.129	0.101	0.161	SUBCLONAL	1	TRUE	0	0.660125554375678	1		578	394	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968091	55968091	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0010680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	135	517	0	ENST00000263923.4:c.2239A>T	p.Lys747Ter	p.K747*	ENST00000263923	NM_002253.2	747	Aaa/Taa	15/30	NA	2	FACETS	0.729	0.666	0.795			1	INDETERMINATE	1	TRUE	NA	0.660125554375678	2		517	561	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168754	32168754	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	46	654	1	ENST00000375023.3:c.4169C>A	p.Ser1390Tyr	p.S1390Y	ENST00000375023	NM_004557.3	1390	tCc/tAc	23/30	1	2	FACETS	0.187	0.156	0.22	0.187	0.156	0.22	SUBCLONAL	1	TRUE	1	0.660125554375678	2		655	747	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523532	106523532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	35	365	0	ENST00000359195.3:c.2684C>T	p.Thr895Ile	p.T895I	ENST00000359195	NM_002649.2	895	aCa/aTa	8/11	0.660125554375678	3	FACETS	0.251	0.205	0.303	0.126	0.102	0.152	SUBCLONAL	1	TRUE	1	0.660125554375678	3		365	561	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	109	160	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.52547375538816	2		160	352	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0010704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	239	495	1	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.52547375538816	2		496	872	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127164	22127164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057519911	NA	P-0010704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	241	502	2	ENST00000215832.6:c.964G>A	p.Glu322Lys	p.E322K	ENST00000215832	NM_002745.4	322	Gag/Aag	7/9	1	2	FACETS	0.96	0.898	1	0.96	0.898	1	CLONAL	1	TRUE	1	0.52547375538816	2		504	955	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704520	117704520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	270	551	0	ENST00000368508.3:c.2456C>T	p.Ser819Phe	p.S819F	ENST00000368508	NM_002944.2	819	tCc/tTc	16/43	1	2	FACETS	0.995	0.934	1	0.995	0.934	1	CLONAL	1	TRUE	1	0.52547375538816	2		551	1033	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056334	27056334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	86	195	0	ENST00000324856.7:c.1330G>T	p.Gly444Cys	p.G444C	ENST00000324856	NM_006015.4	444	Ggc/Tgc	2/20	1	2	FACETS	0.949	0.847	1	0.949	0.847	1	CLONAL	1	TRUE	1	0.52547375538816	2		195	345	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103717	47103717	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1205330893	NA	P-0010704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	327	614	0	ENST00000409792.3:c.6229C>T	p.Arg2077Ter	p.R2077*	ENST00000409792	NM_014159.6	2077	Cga/Tga	14/21	1	2	FACETS	0.925	0.873	0.979	0.925	0.873	0.979	CLONAL	1	TRUE	1	0.52547375538816	2		614	1345	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247211	153247211	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	297	496	0	ENST00000281708.4:c.1591G>T	p.Glu531Ter	p.E531*	ENST00000281708	NM_033632.3	531	Gaa/Taa	10/12	1	2	FACETS	0.975	0.918	1	0.975	0.918	1	CLONAL	1	TRUE	1	0.52547375538816	2		496	1159	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504349	149504349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139554380	NA	P-0010704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	163	489	3	ENST00000261799.4:c.1853C>T	p.Thr618Met	p.T618M	ENST00000261799	NM_002609.3	618	aCg/aTg	13/23	1	2	FACETS	0.86	0.792	0.932	0.86	0.792	0.932	CLONAL	1	TRUE	1	0.52547375538816	2		492	721	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730264	133730264	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	218	389	1	ENST00000318560.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000318560	NM_005157.4	110	tgG/tgA	3/11	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.52547375538816	2		390	815	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606700	43606700	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	238	617	0	ENST00000355710.3:c.1309A>T	p.Asn437Tyr	p.N437Y	ENST00000355710	NM_020975.4	437	Aac/Tac	7/20	1	2	FACETS	0.884	0.825	0.944	0.884	0.825	0.944	CLONAL	1	TRUE	1	0.52547375538816	2		617	1025	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	430180	430180	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	291	542	0	ENST00000399788.2:c.2522G>T	p.Ser841Ile	p.S841I	ENST00000399788	NM_001042603.1	841	aGc/aTc	18/28	NA	2	FACETS	0.925	0.87	0.982			1	INDETERMINATE	1	TRUE	NA	0.52547375538816	2		542	1197	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123921	46123921	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0010704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	119	266	0	ENST00000334344.6:c.186+1G>A		p.X62_splice	ENST00000334344	NM_152641.2	62			1	2	FACETS	0.705	0.638	0.776	0.705	0.638	0.776	SUBCLONAL	1	TRUE	1	0.52547375538816	2		266	642	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778882	3778882	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1254881895	NA	P-0010704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	116	281	0	ENST00000262367.5:c.6166G>A	p.Val2056Met	p.V2056M	ENST00000262367	NM_004380.2	2056	Gtg/Atg	31/31	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.52547375538816	2		281	412	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272015	15272015	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	67	172	0	ENST00000263388.2:c.6424G>T	p.Gly2142Cys	p.G2142C	ENST00000263388	NM_000435.2	2142	Ggc/Tgc	33/33	0.52547375538816	2	FACETS	0.992	0.872	1	0.496	0.436	0.56	CLONAL	1	TRUE	0	0.52547375538816	2		172	257	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026178	36026178	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	245	618	0	ENST00000358208.4:c.780G>T	p.Lys260Asn	p.K260N	ENST00000358208		260	aaG/aaT	7/12	1	2	FACETS	0.893	0.835	0.953	0.893	0.835	0.953	CLONAL	1	TRUE	1	0.52547375538816	2		618	1044	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629114	187629115	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0010704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	267	422	0	ENST00000441802.2:c.1867dup	p.Val623GlyfsTer53	p.V623Gfs*53	ENST00000441802	NM_005245.3	623	gta/gGta	2/27	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.52547375538816	2		422	1013	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631839	90631839	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519906	NA	P-0010708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	129	617	0	ENST00000330062.3:c.514A>G	p.Arg172Gly	p.R172G	ENST00000330062	NM_002168.2	172	Agg/Ggg	4/11	1	2	FACETS	0.773	0.7	0.85	0.773	0.7	0.85	SUBCLONAL	1	TRUE	1	0.35	2		617	954	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760448	133760448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	31	463	2	ENST00000318560.5:c.2771G>A	p.Gly924Glu	p.G924E	ENST00000318560	NM_005157.4	924	gGg/gAg	11/11	0.300477008229257	1	FACETS	0.255	0.206	0.312	0.255	0.206	0.312	SUBCLONAL	1	TRUE	0	0.35	1		465	572	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755766	39755766	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	26	284	0	ENST00000288319.7:c.999A>T	p.Glu333Asp	p.E333D	ENST00000288319	NM_182918.3	333	gaA/gaT	10/10	1	2	FACETS	0.313	0.247	0.389	0.313	0.247	0.389	SUBCLONAL	1	TRUE	1	0.35	2		284	474	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442085	52442085	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	110	447	0	ENST00000460680.1:c.264del	p.Asn89ThrfsTer9	p.N89Tfs*9	ENST00000460680	NM_004656.3	88	ccC/cc	5/17	0.248875724946511	1	FACETS	0.758	0.682	0.839	0.758	0.682	0.839	SUBCLONAL	1	TRUE	0	0.35	1		447	684	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517914	8517914	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	149	541	1	ENST00000356435.5:c.1477C>A	p.Leu493Met	p.L493M	ENST00000356435		493	Ctg/Atg	10/35	0.47745893237444	3	FACETS	0.702	0.64	0.767	0.234	0.213	0.256	SUBCLONAL	1	TRUE	0	0.49645102735846	3		542	1067	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426785	49426785	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	200	219	0	ENST00000301067.7:c.11703G>T	p.Gln3901His	p.Q3901H	ENST00000301067	NM_003482.3	3901	caG/caT	39/54	0.306602870206205	4	FACETS	0.938	0.873	1	0.938	0.873	1	CLONAL	2	TRUE	2	0.49645102735846	4		219	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579406	7579406	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0010711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	333	399	0	ENST00000269305.4:c.281C>G	p.Ser94Ter	p.S94*	ENST00000269305	NM_001126112.2	94	tCa/tGa	4/11	0.195531509810226	3	FACETS	1	0.993	1	0.827	0.788	0.865	INDETERMINATE	2	TRUE	0	0.49645102735846	3		399	675	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533038	63533038	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1476148267	NA	P-0010711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	445	609	0	ENST00000307078.5:c.1856T>C	p.Val619Ala	p.V619A	ENST00000307078	NM_004655.3	619	gTc/gCc	7/11	0.195531509810226	3	FACETS	0.9	0.86	0.941	0.6	0.573	0.628	INDETERMINATE	2	TRUE	0	0.49645102735846	3		609	1243	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303191	15303191	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs781622431	NA	P-0010711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	377	479	0	ENST00000263388.2:c.337C>T	p.Arg113Ter	p.R113*	ENST00000263388	NM_000435.2	113	Cga/Tga	3/33	0.195531509810226	3	FACETS	0.905	0.861	0.95	0.604	0.574	0.634	INDETERMINATE	2	TRUE	0	0.49645102735846	3		479	1047	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73343049	73343050	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0010711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	125	175	0	ENST00000377767.4:c.1756_1757delinsTT	p.Ala586Leu	p.A586L	ENST00000377767	NM_014953.3	586	GCa/TTa	14/21	0.474085984213085	2	FACETS	0.954	0.881	1	0.954	0.881	1	CLONAL	2	TRUE	0	0.49645102735846	2		175	264	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129487	152129487	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010728-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	36	127	0	ENST00000206249.3:c.440C>A	p.Pro147Gln	p.P147Q	ENST00000206249	NM_000125.3	147	cCg/cAg	1/8	0.254361203717508	3	FACETS	1	0.852	1	0.344	0.284	0.41	CLONAL	1	TRUE	0	0.33841345900263	3		127	241	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32971075	32971075	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010728-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	100	420	0	ENST00000380152.3:c.9542T>C	p.Met3181Thr	p.M3181T	ENST00000380152		3181	aTg/aCg	26/27	0.298089805203707	3	FACETS	0.804	0.718	0.897	0.402	0.359	0.449	CLONAL	1	TRUE	1	0.33841345900263	3		420	859	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152104	11152104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377573682	NA	P-0010728-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	143	421	1	ENST00000358026.2:c.4388G>A	p.Arg1463His	p.R1463H	ENST00000358026	NM_001128849.1	1463	cGc/cAc	31/36	0.33841345900263	3	FACETS	1	0.986	1	0.706	0.645	0.77	CLONAL	1	TRUE	1	0.33841345900263	3		422	700	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156686	20156686	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010728-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	153	719	0	ENST00000379607.5:c.71G>C	p.Arg24Thr	p.R24T	ENST00000379607	NM_001412.3	24	aGa/aCa	2/7	1	2	FACETS	0.799	0.729	0.872	0.799	0.729	0.872	SUBCLONAL	1	TRUE	1	0.33841345900263	2		719	1132	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795570	42795570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs754250317	NA	P-0010728-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	100	572	0	ENST00000575354.2:c.2650C>A	p.Pro884Thr	p.P884T	ENST00000575354	NM_015125.3	884	Cct/Act	10/20	1	2	FACETS	0.665	0.593	0.741	0.665	0.593	0.741	SUBCLONAL	1	TRUE	1	0.33841345900263	2		572	889	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0010734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	159	429	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.394113906766976	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.394113906766976	1		429	604	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0010734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	67	297	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.284125291131928	1	FACETS	0.421	0.366	0.481	0.421	0.366	0.481	SUBCLONAL	1	TRUE	0	0.394113906766976	1		298	648	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593466	48593466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064796102	NA	P-0010734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	228	355	0	ENST00000342988.3:c.1217C>T	p.Ala406Val	p.A406V	ENST00000342988	NM_005359.5	406	gCg/gTg	10/12	0.394113906766976	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.394113906766976	1		355	845	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0010734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	181	510	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.284125291131928	1	FACETS	0.85	0.784	0.918	0.85	0.784	0.918	CLONAL	1	TRUE	0	0.394113906766976	1		510	868	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296139	15296139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780152379	NA	P-0010734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	230	449	2	ENST00000263388.2:c.2225C>T	p.Pro742Leu	p.P742L	ENST00000263388	NM_000435.2	742	cCg/cTg	14/33	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.394113906766976	2		451	881	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426420	47426420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1020990103	NA	P-0010734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	223	290	0	ENST00000377045.4:c.763C>T	p.Arg255Trp	p.R255W	ENST00000377045	NM_001654.4	255	Cgg/Tgg	9/16	0.210492843759584	2	FACETS	0.785	0.733	0.837			1	INDETERMINATE	2	TRUE	NA	0.394113906766976	2		290	721	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412892	63412892	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	363	285	0	ENST00000330258.3:c.275del	p.Lys92ArgfsTer8	p.K92Rfs*8	ENST00000330258	NM_152424.3	92	aAg/ag	2/2	0.210492843759584	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.394113906766976	2		285	743	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0010740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	280	306	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.887996238358399	2	FACETS	0.996	0.972	1	0.996	0.972	1	CLONAL	2	TRUE	0	0.901105780347026	2		306	312	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955381	48955381	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs1258442224	NA	P-0010740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	165	148	0	ENST00000267163.4:c.1499-2A>T		p.X500_splice	ENST00000267163	NM_000321.2	500			0.88140349794735	2	FACETS	0.984	0.952	1	0.984	0.952	1	CLONAL	2	TRUE	0	0.901105780347026	2		148	186	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119666195	119666195	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1163587458	NA	P-0010740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	131	225	0	ENST00000316626.5:c.286C>T	p.Arg96Ter	p.R96*	ENST00000316626		96	Cga/Tga	3/12	0.901105780347026	6	FACETS	0.859	0.778	0.943	0.215	0.194	0.236	CLONAL	1	TRUE	2	0.901105780347026	6		225	949	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165982	118165982	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	178	308	0	ENST00000369448.3:c.492C>A	p.Asn164Lys	p.N164K	ENST00000369448	NM_017709.3	164	aaC/aaA	2/2	0.901105780347026	4	FACETS	0.954	0.881	1			1	CLONAL	1	TRUE	NA	0.901105780347026	4		308	787	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584629	187584629	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1479462211	NA	P-0010740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	1026	600	0	ENST00000441802.2:c.3404A>G	p.Asn1135Ser	p.N1135S	ENST00000441802	NM_005245.3	1135	aAt/aGt	3/27	0.901105780347026	3	FACETS	0.984	0.973	0.995	0.984	0.973	0.995	CLONAL	3	TRUE	0	0.901105780347026	3		600	1119	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14027755	14027755	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	270	387	2	ENST00000405192.2:c.89G>T	p.Arg30Met	p.R30M	ENST00000405192	NM_001163147.1	30	aGg/aTg	3/12	0.538389081325514	4	FACETS	1	0.988	1	0.399	0.375	0.424	INDETERMINATE	1	TRUE	1	0.901105780347026	4		389	952	SUCCESS
MET	4233	MSKCC	GRCh37	7	116381044	116381044	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	628	542	0	ENST00000397752.3:c.1666T>C	p.Trp556Arg	p.W556R	ENST00000397752	NM_000245.2	556	Tgg/Cgg	5/21	0.538389081325514	4	FACETS	0.868	0.842	0.893	0.868	0.842	0.893	INDETERMINATE	3	TRUE	1	0.901105780347026	4		542	1018	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771827	135771827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs118203750	NA	P-0010740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	154	614	0	ENST00000298552.3:c.3290G>A	p.Arg1097His	p.R1097H	ENST00000298552	NM_001162426.1	1097	cGt/cAt	23/23	0.337501412310113	4	FACETS	0.648	0.592	0.706	0.162	0.148	0.177	INDETERMINATE	1	TRUE	0	0.901105780347026	4		614	1003	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045686	47045686	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	397	168	0	ENST00000377604.3:c.2567T>A	p.Leu856Gln	p.L856Q	ENST00000377604	NM_001204468.1	856	cTg/cAg	23/24	0.891929309722189	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.901105780347026	2		168	416	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776367	76776367	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	366	284	1	ENST00000373344.5:c.7099G>T	p.Ala2367Ser	p.A2367S	ENST00000373344	NM_000489.3	2367	Gcc/Tcc	34/35	0.891929309722189	2	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.901105780347026	2		285	784	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095590	178095592	+	frameshift_variant	Frame_Shift_Del	DEL	ATT	ATT	G	novel	NA	P-0010740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	342	565	0	ENST00000397062.3:c.1739_1741delinsC	p.Glu580AlafsTer18	p.E580Afs*18	ENST00000397062	NM_006164.4	580	gAATac/gCac	5/5	0.538389081325514	4	FACETS	1	0.993	1	0.43	0.407	0.454	INDETERMINATE	1	TRUE	1	0.901105780347026	4		565	1118	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858738	9858738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149698593	NA	P-0010747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	76	597	2	ENST00000330684.3:c.2663C>T	p.Thr888Met	p.T888M	ENST00000330684	NM_001134407.1	888	aCg/aTg	13/13	1	2	FACETS	0.722	0.631	0.819	0.722	0.631	0.819	SUBCLONAL	1	TRUE	1	0.219209050899273	2		599	961	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844172	68844172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	109	553	0	ENST00000261769.5:c.760G>A	p.Asp254Asn	p.D254N	ENST00000261769	NM_004360.3	254	Gat/Aat	6/16	0.219209050899273	4	FACETS	1	0.937	1			1	CLONAL	1	TRUE	NA	0.219209050899273	4		553	1140	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587254	212587254	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	84	571	1	ENST00000342788.4:c.747C>A	p.Cys249Ter	p.C249*	ENST00000342788	NM_005235.2	249	tgC/tgA	7/28	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.219209050899273	2		572	729	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032275	26032275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs780546148	NA	P-0010747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	62	408	0	ENST00000244661.2:c.14A>T	p.Lys5Ile	p.K5I	ENST00000244661	NM_003537.3	5	aAa/aTa	1/1	1	2	FACETS	0.869	0.75	0.998	0.869	0.75	0.998	CLONAL	1	TRUE	1	0.219209050899273	2		408	651	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs1202793339	NA	P-0010747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	90	614	0	ENST00000269305.4:c.560-1G>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			NA	2	FACETS	0.916	0.812	1			1	INDETERMINATE	1	TRUE	NA	0.219209050899273	2		614	896	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984846	11984846	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	52	368	0	ENST00000353533.5:c.392A>G	p.Lys131Arg	p.K131R	ENST00000353533	NM_003010.3	131	aAa/aGa	3/11	0.219209050899273	1	FACETS	0.769	0.655	0.895	0.769	0.655	0.895	SUBCLONAL	1	TRUE	0	0.219209050899273	1		368	549	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593456	48593456	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	95	454	0	ENST00000342988.3:c.1207A>T	p.Ser403Cys	p.S403C	ENST00000342988	NM_005359.5	403	Agt/Tgt	10/12	0.219209050899273	4	FACETS	1	0.971	1	0.427	0.38	0.478	CLONAL	1	TRUE	1	0.219209050899273	4		454	824	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144903	47144903	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	197	343	0	ENST00000409792.3:c.4850C>T	p.Ala1617Val	p.A1617V	ENST00000409792	NM_014159.6	1617	gCc/gTc	7/21	0.691082012617021	1	FACETS	0.912	0.857	0.968	0.912	0.857	0.968	CLONAL	1	TRUE	0	0.691082012617021	1		343	409	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118355026	118355030	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TAAGG	TAAGG	-	novel	NA	P-0010757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	150	252	1	ENST00000534358.1:c.4218_4218+4del		p.X1406_splice	ENST00000534358	NM_005933.3	1406		9/36	1	2	FACETS	0.976	0.9	1	0.976	0.9	1	CLONAL	1	TRUE	1	0.691082012617021	2		253	445	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	295	939	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.19146710083191	5	FACETS	1	0.974	1	0.709	0.667	0.753	INDETERMINATE	2	TRUE	2	0.326761005081955	5		940	1265	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0010790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	305	791	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.326761005081955	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.326761005081955	2		792	897	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945176	44945178	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	novel	NA	P-0010790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	238	483	0	ENST00000377967.4:c.3505_3507del	p.Val1169del	p.V1169del	ENST00000377967	NM_021140.2	1167	tTTGtt/ttt	24/29	0.103930312209804	2	FACETS	0.95	0.89	1			1	INDETERMINATE	2	TRUE	NA	0.326761005081955	2		483	767	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121018	29121018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853009	NA	P-0010811-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	66	620	1	ENST00000328354.6:c.539G>A	p.Arg180His	p.R180H	ENST00000328354	NM_007194.3	180	cGc/cAc	4/15	1	2	FACETS	0.509	0.441	0.583	0.509	0.441	0.583	SUBCLONAL	1	TRUE	1	0.34179257019869	2		621	758	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057054	180057054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010811-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	81	580	2	ENST00000261937.6:c.565C>T	p.Arg189Trp	p.R189W	ENST00000261937	NM_182925.4	189	Cgg/Tgg	5/30	1	2	FACETS	0.609	0.536	0.688	0.609	0.536	0.688	SUBCLONAL	1	TRUE	1	0.34179257019869	2		582	778	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679810	88679810	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010811-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	113	540	0	ENST00000360948.2:c.653del	p.Asn218ThrfsTer2	p.N218Tfs*2	ENST00000360948	NM_001012338.2	218	aAc/ac	7/19	1	2	FACETS	0.853	0.768	0.943	0.853	0.768	0.943	CLONAL	1	TRUE	1	0.34179257019869	2		540	775	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0010821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	213	565	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	0.994	1	CLONAL	2	TRUE	1	0.22	2		565	837	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342150	70342150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	57	428	1	ENST00000374080.3:c.1202C>T	p.Pro401Leu	p.P401L	ENST00000374080		401	cCg/cTg	8/45	1	1	FACETS	0.965	0.829	1	0.965	0.829	1	CLONAL	1	TRUE	0	0.22	1		429	478	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115514	108115514	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0010821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	24	380	0	ENST00000278616.4:c.663-1G>A		p.X221_splice	ENST00000278616	NM_000051.3	221			1	2	FACETS	0.474	0.371	0.594	0.474	0.371	0.594	SUBCLONAL	1	TRUE	1	0.22	2		380	460	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434967	110434967	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1440534851	NA	P-0010821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	34	637	0	ENST00000375856.3:c.3434G>T	p.Arg1145Leu	p.R1145L	ENST00000375856	NM_003749.2	1145	cGc/cTc	1/2	1	2	FACETS	0.481	0.392	0.582	0.481	0.392	0.582	SUBCLONAL	1	TRUE	1	0.22	2		637	643	SUCCESS
AR	367	MSKCC	GRCh37	X	66766603	66766603	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs753693014	NA	P-0010821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	19	350	0	ENST00000374690.3:c.1615C>A	p.Arg539Ser	p.R539S	ENST00000374690	NM_000044.3	539	Cgt/Agt	1/8	1	1	FACETS	0.472	0.357	0.606	0.472	0.357	0.606	SUBCLONAL	1	TRUE	0	0.22	1		350	326	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0010828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	126	429	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	0.0990937571698226	0	FACETS	0.718	0.649	0.79			1	INDETERMINATE	1	TRUE	0	0.27	0		429	949	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255772	16255772	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776153327	NA	P-0010828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	74	375	0	ENST00000375759.3:c.3037C>T	p.Arg1013Cys	p.R1013C	ENST00000375759	NM_015001.2	1013	Cgc/Tgc	11/15	0.3	4	FACETS	0.862	0.753	0.979			1	CLONAL	1	TRUE	NA	0.27	4		375	808	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0010828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2204	262	853	2	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.787	0.733	0.843	0.787	0.733	0.843	SUBCLONAL	1	TRUE	1	0.27	2		855	2466	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156534	55156534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778597	NA	P-0010828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	84	509	0	ENST00000257290.5:c.2935C>T	p.Arg979Cys	p.R979C	ENST00000257290	NM_006206.4	979	Cgc/Tgc	22/23	0.207003170643999	0	FACETS	0.553	0.487	0.623			1	SUBCLONAL	1	TRUE	0	0.27	0		509	822	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875645	35875645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201449880	NA	P-0010828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	140	442	0	ENST00000303115.3:c.832G>A	p.Asp278Asn	p.D278N	ENST00000303115	NM_002185.3	278	Gat/Aat	7/8	0.3	5	FACETS	1	0.969	1			1	CLONAL	1	TRUE	NA	0.27	5		442	1265	SUCCESS
APC	324	MSKCC	GRCh37	5	112154703	112154703	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs730881221	NA	P-0010828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	81	346	0	ENST00000257430.4:c.974A>G	p.His325Arg	p.H325R	ENST00000257430	NM_000038.5	325	cAt/cGt	10/16	1	2	FACETS	0.882	0.777	0.995	0.882	0.777	0.995	CLONAL	1	TRUE	1	0.27	2		346	680	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846197	151846197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754010322	NA	P-0010828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	104	512	0	ENST00000262189.6:c.12815C>T	p.Thr4272Met	p.T4272M	ENST00000262189	NM_170606.2	4272	aCg/aTg	52/59	1	2	FACETS	0.91	0.814	1	0.91	0.814	1	CLONAL	1	TRUE	1	0.27	2		512	847	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900329	101900329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	90	567	0	ENST00000374994.4:c.763C>T	p.Arg255Cys	p.R255C	ENST00000374994	NM_004612.2	255	Cgt/Tgt	4/9	0.0990937571698226	0	FACETS	0.435	0.384	0.489			1	INDETERMINATE	1	TRUE	0	0.27	0		567	1120	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417329	139417329	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746827857	NA	P-0010828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	83	369	2	ENST00000277541.6:c.715G>A	p.Val239Ile	p.V239I	ENST00000277541	NM_017617.3	239	Gtc/Atc	4/34	0.0990937571698226	0	FACETS	0.87	0.77	0.977			1	INDETERMINATE	1	TRUE	0	0.27	0		371	516	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820192	139820192	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1332	244	1090	1	ENST00000247668.2:c.1345C>T	p.Pro449Ser	p.P449S	ENST00000247668	NM_021138.3	449	Ccc/Tcc	11/11	0.0990937571698226	0	FACETS	0.837	0.78	0.897			1	INDETERMINATE	1	TRUE	0	0.27	0		1091	1576	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0010828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	49	138	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.207003170643999	0	FACETS	1	0.869	1			1	CLONAL	1	TRUE	0	0.27	0		138	260	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827708	72827708	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	195	1063	0	ENST00000268489.5:c.8873T>C	p.Leu2958Pro	p.L2958P	ENST00000268489	NM_006885.3	2958	cTg/cCg	9/10	0.263726500736071	0	FACETS	0.885	0.817	0.955			1	CLONAL	1	TRUE	0	0.27	0		1063	1192	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950397	15950397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs190623603	NA	P-0010828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	114	546	0	ENST00000268712.3:c.6547C>T	p.Arg2183Cys	p.R2183C	ENST00000268712	NM_006311.3	2183	Cgc/Tgc	42/46	1	2	FACETS	0.871	0.783	0.965	0.871	0.783	0.965	CLONAL	1	TRUE	1	0.27	2		546	969	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553546	29553546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	76	336	1	ENST00000356175.3:c.2095G>A	p.Asp699Asn	p.D699N	ENST00000356175	NM_000267.3	699	Gac/Aac	18/57	1	2	FACETS	0.68	0.595	0.771	0.68	0.595	0.771	SUBCLONAL	1	TRUE	1	0.27	2		337	828	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231558	5231558	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868011195	NA	P-0010828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	66	366	2	ENST00000357368.4:c.1918C>T	p.Arg640Cys	p.R640C	ENST00000357368	NM_002850.3	640	Cgc/Tgc	14/38	0.207003170643999	0	FACETS	0.965	0.842	1			1	CLONAL	1	TRUE	0	0.27	0		368	370	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166284	7166284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747464322	NA	P-0010828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	86	730	1	ENST00000302850.5:c.1742G>A	p.Arg581Gln	p.R581Q	ENST00000302850	NM_000208.2	581	cGg/cAg	8/22	0.3	2	FACETS	0.619	0.546	0.698			1	SUBCLONAL	1	TRUE	NA	0.27	2		731	1029	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523319	9523319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1416163895	NA	P-0010828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	81	755	1	ENST00000353224.5:c.1918G>A	p.Glu640Lys	p.E640K	ENST00000353224	NM_177990.2	640	Gag/Aag	9/10	1	2	FACETS	0.55	0.483	0.623	0.55	0.483	0.623	SUBCLONAL	1	TRUE	1	0.27	2		756	1090	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42861473	42861473	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768426172	NA	P-0010828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	166	672	1	ENST00000398585.3:c.397G>A	p.Val133Met	p.V133M	ENST00000398585	NM_001135099.1	133	Gtg/Atg	4/14	0.207003170643999	0	FACETS	1	0.971	1			1	CLONAL	1	TRUE	0	0.27	0		673	802	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841145	15841145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1580	179	923	4	ENST00000307771.7:c.1229G>A	p.Arg410His	p.R410H	ENST00000307771	NM_005089.3	410	cGc/cAc	11/11	0.0990937571698226	0	FACETS	0.55	0.505	0.598			1	INDETERMINATE	1	TRUE	0	0.27	0		927	1759	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720741	89720741	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs786204884	NA	P-0010828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	10	62	0	ENST00000371953.3:c.892del	p.Gln298LysfsTer9	p.Q298Kfs*9	ENST00000371953	NM_000314.4	298	Caa/aa	8/9	0.3	2	FACETS	0.491	0.333	0.687			1	SUBCLONAL	1	TRUE	NA	0.27	2		62	151	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293075	91293075	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs367543026	NA	P-0010828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	92	363	0	ENST00000355112.3:c.582del	p.Phe194LeufsTer11	p.F194Lfs*11	ENST00000355112	NM_000057.2	193	Ttt/tt	3/22	1	2	FACETS	0.831	0.738	0.931	0.831	0.738	0.931	CLONAL	1	TRUE	1	0.27	2		363	820	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	203	527	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.84	0.78	0.903	1	0.992	1	CLONAL	2	TRUE	1	0.27	2		527	895	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348566	89348568	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs753054998	NA	P-0010828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1343	221	1461	3	ENST00000301030.4:c.4382_4384del	p.Lys1461del	p.K1461del	ENST00000301030	NM_001256183.1	1461	aAGAga/aga	9/13	0.3	1	FACETS	0.905	0.84	0.974	0.905	0.84	0.974	CLONAL	1	TRUE	0	0.27	1		1464	1564	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106885	27106906	+	frameshift_variant	Frame_Shift_Del	DEL	ATGGCTGTGGTACTGCTGGCCA	ATGGCTGTGGTACTGCTGGCCA	-	novel	NA	P-0010828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	104	479	0	ENST00000324856.7:c.6497_6518del	p.Met2166ThrfsTer27	p.M2166Tfs*27	ENST00000324856	NM_006015.4	2166	ATGGCTGTGGTACTGCTGGCCAac/ac	20/20	0.3	4	FACETS	1	0.959	1			1	CLONAL	1	TRUE	NA	0.27	4		479	855	SUCCESS
AXL	558	MSKCC	GRCh37	19	41737102	41737102	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	91	986	0	ENST00000301178.4:c.685del	p.Arg229ValfsTer21	p.R229Vfs*21	ENST00000301178	NM_021913.4	228	Ccc/cc	6/20	0.207003170643999	0	FACETS	0.426	0.377	0.479			1	SUBCLONAL	1	TRUE	0	0.27	0		986	1154	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101268	27101268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	127	609	0	ENST00000324856.7:c.4555del	p.Gln1519ArgfsTer8	p.Q1519Rfs*8	ENST00000324856	NM_006015.4	1517	gCc/gc	18/20	0.3	4	FACETS	1	0.976	1			1	CLONAL	1	TRUE	NA	0.27	4		609	961	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720814	+	inframe_deletion	In_Frame_Del	DEL	AAA	AAA	-	novel	NA	P-0010828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	69	138	0	ENST00000371953.3:c.966_968del	p.Lys322del	p.K322del	ENST00000371953	NM_000314.4	321	acAAAa/aca	8/9	0.3	2	FACETS	1	0.971	1			1	CLONAL	1	TRUE	NA	0.27	2		138	362	SUCCESS
AR	367	MSKCC	GRCh37	X	66765666	66765667	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0010828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	105	898	0	ENST00000374690.3:c.683dup	p.Thr229HisfsTer6	p.T229Hfs*6	ENST00000374690	NM_000044.3	226	-/G	1/8	0.3	0	FACETS	0.569	0.509	0.633			1	SUBCLONAL	1	TRUE	0	0.27	0		898	998	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356416	70356416	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	83	798	0	ENST00000374080.3:c.5313del	p.Lys1771AsnfsTer44	p.K1771Nfs*44	ENST00000374080		1771	Aaa/aa	37/45	0.3	0	FACETS	0.492	0.433	0.555			1	SUBCLONAL	1	TRUE	0	0.27	0		798	913	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	283	160	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	FALSE	1	0.424538681810026	2		160	570	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0010838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	587	399	2	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.404726509280494	4	FACETS	0.893	0.863	0.923			1	CLONAL	4	FALSE	NA	0.424538681810026	4		401	1103	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821373	72821373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775404633	NA	P-0010838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	347	699	0	ENST00000268489.5:c.10802C>T	p.Ser3601Leu	p.S3601L	ENST00000268489	NM_006885.3	3601	tCg/tTg	10/10	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.424538681810026	2		699	1368	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026697	6026697	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554297342	NA	P-0010838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	442	505	2	ENST00000265849.7:c.1699C>T	p.Gln567Ter	p.Q567*	ENST00000265849	NM_000535.5	567	Cag/Tag	11/15	1	2	FACETS	1	0.974	1	1	0.997	1	CLONAL	2	FALSE	1	0.424538681810026	2		507	1018	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850816	128850816	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs537683811	NA	P-0010838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1527	149	534	2	ENST00000249373.3:c.1663C>A	p.Gln555Lys	p.Q555K	ENST00000249373	NM_005631.4	555	Cag/Aag	10/12	0.207115561441794	4	FACETS	0.597	0.543	0.654			1	INDETERMINATE	1	FALSE	NA	0.424538681810026	4		536	1676	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338701	70338701	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	690	817	0	ENST00000374080.3:c.97G>C	p.Glu33Gln	p.E33Q	ENST00000374080		33	Gag/Cag	1/45	1	2	FACETS	1	0.985	1	1	0.998	1	CLONAL	2	FALSE	1	0.424538681810026	2		817	1571	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929062	44929081	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGAAACATATTGACGGTG	CAGGAAACATATTGACGGTG	-	novel	NA	P-0010838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	683	794	1	ENST00000377967.4:c.2163_2182del	p.Gly722Ter	p.G722*	ENST00000377967	NM_021140.2	721	tCAGGAAACATATTGACGGTG/t	17/29	1	2	FACETS	0.916	0.883	0.949	1	0.998	1	CLONAL	2	FALSE	1	0.424538681810026	2		795	1757	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023497	27023498	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0010845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	315	462	1	ENST00000324856.7:c.606_607del	p.His203ArgfsTer196	p.H203Rfs*196	ENST00000324856	NM_006015.4	201	aaCTct/aact	1/20	1	2	FACETS	0.955	0.905	1	0.955	0.905	1	CLONAL	1	TRUE	1	0.773279679815388	2		463	853	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0010848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	307	432	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.72476263623524	3	FACETS	0.954	0.908	0.999	0.954	0.908	0.999	CLONAL	2	TRUE	1	0.72476263623524	3		432	605	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0010848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	30	110	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.72476263623524	1	FACETS	0.825	0.697	0.955	0.825	0.697	0.955	CLONAL	1	TRUE	0	0.72476263623524	1		110	64	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0010848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	277	381	1				ENST00000310581	NM_198253.2	-/1132			0.72476263623524	3	FACETS	0.984	0.936	1	0.984	0.936	1	CLONAL	2	TRUE	1	0.72476263623524	3		382	529	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262712	16262712	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	159	302	0	ENST00000375759.3:c.9977C>T	p.Pro3326Leu	p.P3326L	ENST00000375759	NM_015001.2	3326	cCc/cTc	11/15	1	2	FACETS	0.973	0.9	1	0.973	0.9	1	CLONAL	1	TRUE	1	0.72476263623524	2		302	451	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310530	65310530	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	254	476	0	ENST00000342505.4:c.2158C>T	p.Leu720Phe	p.L720F	ENST00000342505	NM_002227.2	720	Ctc/Ttc	16/25	1	2	FACETS	0.907	0.852	0.963	0.907	0.852	0.963	CLONAL	1	TRUE	1	0.72476263623524	2		476	773	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884550	151884550	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	292	425	1	ENST00000262189.6:c.4805C>T	p.Ser1602Leu	p.S1602L	ENST00000262189	NM_170606.2	1602	tCa/tTa	33/59	0.72476263623524	3	FACETS	0.884	0.839	0.929	0.884	0.839	0.929	CLONAL	2	TRUE	1	0.72476263623524	3		426	621	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507309	8507309	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867521565	NA	P-0010848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	231	553	0	ENST00000356435.5:c.1669G>A	p.Gly557Arg	p.G557R	ENST00000356435		557	Gga/Aga	11/35	0.72476263623524	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.72476263623524	1		553	389	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518061	103518061	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	195	410	1	ENST00000355739.4:c.1999C>T	p.Gln667Ter	p.Q667*	ENST00000355739	NM_000123.3	667	Caa/Taa	9/15	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.72476263623524	2		411	523	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730805	40730805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	211	404	0	ENST00000373198.4:c.3730G>A	p.Asp1244Asn	p.D1244N	ENST00000373198	NM_133170.3	1244	Gac/Aac	27/32	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.72476263623524	2		404	516	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301150	65301150	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	228	444	1	ENST00000342505.4:c.3298del	p.Thr1100GlnfsTer6	p.T1100Qfs*6	ENST00000342505	NM_002227.2	1100	Aca/ca	24/25	1	2	FACETS	0.892	0.835	0.951	0.892	0.835	0.951	CLONAL	1	TRUE	1	0.72476263623524	2		445	705	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107022	27107023	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0010848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	176	338	0	ENST00000324856.7:c.6633_6634delinsTT	p.Gln2212Ter	p.Q2212*	ENST00000324856	NM_006015.4	2211	agCCag/agTTag	20/20	1	2	FACETS	0.993	0.923	1	0.993	0.923	1	CLONAL	1	TRUE	1	0.72476263623524	2		338	489	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961254	15961255	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0010848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	204	423	0	ENST00000268712.3:c.6134_6135delinsTT	p.Thr2045Ile	p.T2045I	ENST00000268712	NM_006311.3	2045	aCC/aTT	39/46	1	2	FACETS	0.905	0.844	0.967	0.905	0.844	0.967	CLONAL	1	TRUE	1	0.72476263623524	2		423	622	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56811537	56811538	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0010848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	225	466	0	ENST00000337432.4:c.1085_1086delinsTT	p.Ser362Phe	p.S362F	ENST00000337432	NM_058216.2	362	tCC/tTT	9/9	1	2	FACETS	0.941	0.881	1	0.941	0.881	1	CLONAL	1	TRUE	1	0.72476263623524	2		466	660	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0010858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	76	578	1	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	1	2	FACETS	0.76	0.665	0.863	0.76	0.665	0.863	SUBCLONAL	1	TRUE	1	0.2	2		579	1000	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0010858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	55	429	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.684	0.584	0.794	0.684	0.584	0.794	SUBCLONAL	1	TRUE	1	0.2	2		429	804	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0010858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	47	403	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.558	0.469	0.657	0.558	0.469	0.657	SUBCLONAL	1	TRUE	1	0.2	2		403	842	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	33	235	1	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.747	0.608	0.903	0.747	0.608	0.903	CLONAL	1	TRUE	1	0.2	2		236	442	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	63	427	2	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.916	0.791	1	0.916	0.791	1	CLONAL	1	TRUE	1	0.2	2		429	688	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0010858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	61	362	1	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	1	2	FACETS	0.944	0.814	1	0.944	0.814	1	CLONAL	1	TRUE	1	0.2	2		363	646	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	62	435	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.97	0.838	1	0.97	0.838	1	CLONAL	1	TRUE	1	0.2	2		435	639	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438584	52438584	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	56	350	0	ENST00000460680.1:c.1135G>A	p.Ala379Thr	p.A379T	ENST00000460680	NM_004656.3	379	Gca/Aca	12/17	1	2	FACETS	0.909	0.778	1	0.909	0.778	1	CLONAL	1	TRUE	1	0.2	2		350	616	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956965	2956965	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142828146	NA	P-0010858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	50	439	0	ENST00000396946.4:c.2662C>T	p.Arg888Cys	p.R888C	ENST00000396946	NM_032415.4	888	Cgt/Tgt	20/25	1	2	FACETS	0.781	0.662	0.913	0.781	0.662	0.913	CLONAL	1	TRUE	1	0.2	2		439	640	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11172938	11172938	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555337942	NA	P-0010858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	35	381	1	ENST00000361445.4:c.7337C>T	p.Thr2446Met	p.T2446M	ENST00000361445	NM_004958.3	2446	aCg/aTg	54/58	1	2	FACETS	0.501	0.41	0.605	0.501	0.41	0.605	SUBCLONAL	1	TRUE	1	0.2	2		382	698	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101612	27101612	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372335126	NA	P-0010858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	45	469	0	ENST00000324856.7:c.4894C>T	p.Pro1632Ser	p.P1632S	ENST00000324856	NM_006015.4	1632	Ccc/Tcc	18/20	1	2	FACETS	0.554	0.464	0.654	0.554	0.464	0.654	SUBCLONAL	1	TRUE	1	0.2	2		469	812	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743520	46743520	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141523334	NA	P-0010858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	51	363	0	ENST00000371975.4:c.1901G>A	p.Arg634His	p.R634H	ENST00000371975	NM_003579.3	634	cGt/cAt	17/18	1	2	FACETS	0.832	0.706	0.97	0.832	0.706	0.97	CLONAL	1	TRUE	1	0.2	2		363	613	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480397	89480397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756739935	NA	P-0010858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	82	499	0	ENST00000336596.2:c.2234G>A	p.Arg745Gln	p.R745Q	ENST00000336596	NM_005233.5	745	cGa/cAa	13/17	1	2	FACETS	0.92	0.81	1	0.92	0.81	1	CLONAL	1	TRUE	1	0.2	2		499	891	SUCCESS
ATR	545	MSKCC	GRCh37	3	142204114	142204114	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755650081	NA	P-0010858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	47	328	0	ENST00000350721.4:c.6089C>T	p.Ala2030Val	p.A2030V	ENST00000350721	NM_001184.3	2030	gCg/gTg	36/47	1	2	FACETS	0.772	0.65	0.906	0.772	0.65	0.906	CLONAL	1	TRUE	1	0.2	2		328	609	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443373	187443373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	72	407	0	ENST00000232014.4:c.1753C>T	p.Arg585Trp	p.R585W	ENST00000232014	NM_001130845.1	585	Cgg/Tgg	8/10	1	2	FACETS	0.893	0.779	1	0.893	0.779	1	CLONAL	1	TRUE	1	0.2	2		407	806	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540958	187540958	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	38	307	0	ENST00000441802.2:c.6782C>A	p.Thr2261Lys	p.T2261K	ENST00000441802	NM_005245.3	2261	aCg/aAg	10/27	1	2	FACETS	0.769	0.635	0.919	0.769	0.635	0.919	CLONAL	1	TRUE	1	0.2	2		307	494	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55219056	55219056	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1360336411	NA	P-0010858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	86	512	0	ENST00000275493.2:c.628+1G>A		p.X210_splice	ENST00000275493	NM_005228.3	210			1	2	FACETS	0.987	0.872	1	0.987	0.872	1	CLONAL	1	TRUE	1	0.2	2		512	871	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878904	151878904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	66	454	1	ENST00000262189.6:c.6041C>T	p.Ala2014Val	p.A2014V	ENST00000262189	NM_170606.2	2014	gCa/gTa	36/59	1	2	FACETS	0.988	0.857	1	0.988	0.857	1	CLONAL	1	TRUE	1	0.2	2		455	668	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154871	2154871	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773449505	NA	P-0010858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	72	596	1	ENST00000434045.2:c.350G>A	p.Arg117His	p.R117H	ENST00000434045	NM_001127598.1	117	cGt/cAt	4/5	1	2	FACETS	0.8	0.697	0.911	0.8	0.697	0.911	CLONAL	1	TRUE	1	0.2	2		597	900	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444729	49444729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199724002	NA	P-0010858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	72	455	0	ENST00000301067.7:c.2737G>A	p.Glu913Lys	p.E913K	ENST00000301067	NM_003482.3	913	Gag/Aag	10/54	1	2	FACETS	0.925	0.807	1	0.925	0.807	1	CLONAL	1	TRUE	1	0.2	2		455	778	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442738	99442738	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	85	603	2	ENST00000268035.6:c.1135G>T	p.Gly379Trp	p.G379W	ENST00000268035	NM_000875.3	379	Ggg/Tgg	5/21	0.171487338550323	1	FACETS	0.856	0.755	0.964	0.856	0.755	0.964	CLONAL	1	TRUE	0	0.2	1		605	894	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383226	31383226	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs376213530	NA	P-0010858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	64	496	0	ENST00000328111.2:c.1138C>T	p.Arg380Ter	p.R380*	ENST00000328111	NM_006892.3	380	Cga/Tga	11/23	1	2	FACETS	0.952	0.824	1	0.952	0.824	1	CLONAL	1	TRUE	1	0.2	2		496	672	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366747	40366747	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs771233237	NA	P-0010858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	38	275	0	ENST00000397332.2:c.450del	p.Asn151ThrfsTer53	p.N151Tfs*53	ENST00000397332	NM_001033082.2	150	ggG/gg	2/3	1	2	FACETS	0.987	0.817	1	0.987	0.817	1	CLONAL	1	TRUE	1	0.2	2		275	385	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017821	31017821	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	57	486	0	ENST00000375687.4:c.686del	p.Pro229ArgfsTer3	p.P229Rfs*3	ENST00000375687	NM_015338.5	228	gCc/gc	8/13	1	2	FACETS	0.806	0.691	0.933	0.806	0.691	0.933	CLONAL	1	TRUE	1	0.2	2		486	707	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425095	49425100	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	TCTGCA	TCTGCA	-	novel	NA	P-0010858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	117	554	0	ENST00000301067.7:c.13388_13393del	p.Leu4463_Lys4465delinsTer	p.L4463_K4465delins*	ENST00000301067	NM_003482.3	4463	tTGCAGAag/tag	39/54	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.2	2		554	1072	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094455	27094456	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0010858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	65	380	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	0.837	1	0.966	0.837	1	CLONAL	1	TRUE	1	0.2	2		380	673	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	178	939	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.31	2		940	886	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0010861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	209	791	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.303788356448482	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.31	1		792	1053	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0010861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	165	553	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.31	2		553	991	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638912	176638912	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs111638717	NA	P-0010861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	184	615	1	ENST00000439151.2:c.3512G>A	p.Arg1171His	p.R1171H	ENST00000439151	NM_022455.4	1171	cGt/cAt	5/23	1	2	FACETS	0.998	0.919	1	0.998	0.919	1	CLONAL	1	TRUE	1	0.31	2		616	1190	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054529	42054529	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1191	196	769	0	ENST00000219905.7:c.7713G>T	p.Leu2571Phe	p.L2571F	ENST00000219905	NM_001164273.1	2571	ttG/ttT	22/24	0.303788356448482	3	FACETS	1	0.957	1	0.527	0.486	0.569	CLONAL	1	TRUE	1	0.31	3		769	1387	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124306	2124306	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs45517237	NA	P-0010861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	217	664	0	ENST00000219476.3:c.2461A>T	p.Lys821Ter	p.K821*	ENST00000219476	NM_000548.3	821	Aag/Tag	22/42	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.31	2		664	1229	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654642	67654642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	44	669	2	ENST00000264010.4:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000264010	NM_006565.3	377	Cgt/Tgt	6/12	1	2	FACETS	0.235	0.196	0.279	0.235	0.196	0.279	SUBCLONAL	1	TRUE	1	0.31	2		671	1207	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042574	42042574	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	426	816	0	ENST00000219905.7:c.6770del	p.Pro2257LeufsTer78	p.P2257Lfs*78	ENST00000219905	NM_001164273.1	2257	Cct/ct	17/24	0.303788356448482	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.31	3		816	1479	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106534448	106534448	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	44	550	0	ENST00000369096.4:c.24del	p.Lys8AsnfsTer17	p.K8Nfs*17	ENST00000369096	NM_001198.3	7	gAa/ga	1/7	0.303788356448482	1	FACETS	0.279	0.233	0.33	0.279	0.233	0.33	SUBCLONAL	1	TRUE	0	0.31	1		550	860	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	55	551	3	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	0.303788356448482	1	FACETS	0.275	0.234	0.32	0.275	0.234	0.32	SUBCLONAL	1	TRUE	0	0.31	1		554	1091	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434074	49434074	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	35	322	0	ENST00000301067.7:c.7479del	p.Phe2494SerfsTer49	p.F2494Sfs*49	ENST00000301067	NM_003482.3	2493	ggG/gg	31/54	1	2	FACETS	0.329	0.268	0.397	0.329	0.268	0.397	SUBCLONAL	1	TRUE	1	0.31	2		322	687	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0010902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	124	406	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		406	1144	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89818580	89818580	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200022826	NA	P-0010902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	122	569	0	ENST00000389301.3:c.3032G>A	p.Arg1011His	p.R1011H	ENST00000389301	NM_000135.2	1011	cGc/cAc	31/43	0.0843506137709541	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		569	1000	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056314	26056314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1355795147	NA	P-0010912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	260	470	0	ENST00000343677.2:c.343G>A	p.Glu115Lys	p.E115K	ENST00000343677	NM_005319.3	115	Gaa/Aaa	1/1	0.625625087961341	3	FACETS	0.985	0.922	1	0.328	0.307	0.35	CLONAL	1	TRUE	0	0.625625087961341	3		470	1108	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672165	30672165	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs374205858	NA	P-0010912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	217	765	0	ENST00000376406.3:c.4795T>G	p.Cys1599Gly	p.C1599G	ENST00000376406	NM_014641.2	1599	Tgc/Ggc	10/15	0.625625087961341	3	FACETS	0.781	0.725	0.839	0.26	0.241	0.28	SUBCLONAL	1	TRUE	0	0.625625087961341	3		765	1166	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2966412	2966412	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1259	393	853	1	ENST00000396946.4:c.1768G>T	p.Asp590Tyr	p.D590Y	ENST00000396946	NM_032415.4	590	Gac/Tac	14/25	0.625625087961341	3	FACETS	0.998	0.947	1	0.499	0.473	0.526	CLONAL	1	TRUE	1	0.625625087961341	3		854	1652	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855864	45855864	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	56	571	0	ENST00000391945.4:c.1946A>G	p.Asn649Ser	p.N649S	ENST00000391945	NM_000400.3	649	aAt/aGt	21/23	0.594668897755025	2	FACETS	0.167	0.142	0.194	0.083	0.071	0.097	SUBCLONAL	1	TRUE	0	0.625625087961341	2		571	1075	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504262	186504606	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTGCTACAACATAATTTTCTCTTTTTAAGGTTGTGTTGCTTTCTGCCACAATGCCAACTGATGTGTTGGAAGTGACCAAAAAATTCATGAGAGATCCAATTCGAATTCTGGTGAAAAAGGAAGAATTGACCCTTGAAGGAATCAAACAGTTTTATATTAATGTTGAGAGAGAGGTAACTGTCTGATTGTTAGACATTATTTTACCTTCTTGTATAAGCACTGTGCTAAAATTGCAGACACTAGGACCATGTCTTGGTTTTTGCAATAATGCTAGCAGAGTACACACAAGAAGAAAAGTAACAGCACTAGATTGTAAAGACTGGGGTGGACCTCTTTCTTAATGTC	GTGCTACAACATAATTTTCTCTTTTTAAGGTTGTGTTGCTTTCTGCCACAATGCCAACTGATGTGTTGGAAGTGACCAAAAAATTCATGAGAGATCCAATTCGAATTCTGGTGAAAAAGGAAGAATTGACCCTTGAAGGAATCAAACAGTTTTATATTAATGTTGAGAGAGAGGTAACTGTCTGATTGTTAGACATTATTTTACCTTCTTGTATAAGCACTGTGCTAAAATTGCAGACACTAGGACCATGTCTTGGTTTTTGCAATAATGCTAGCAGAGTACACACAAGAAGAAAAGTAACAGCACTAGATTGTAAAGACTGGGGTGGACCTCTTTCTTAATGTC	-	novel	NA	P-0010912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	41	254	0	ENST00000323963.5:c.628-29_771+172del		p.X210_splice	ENST00000323963		210		7/11	0.595364511321785	4	FACETS	0.585	0.489	0.692	0.195	0.163	0.231	SUBCLONAL	1	TRUE	1	0.625625087961341	4		254	364	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010919-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	230	750	0	ENST00000346208.3:c.1220_1221insA	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcAg	6/6	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.39662792654093	2		750	1099	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857642	59857642	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010919-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1866	136	493	0	ENST00000259008.2:c.1915C>G	p.His639Asp	p.H639D	ENST00000259008	NM_032043.2	639	Cat/Gat	13/20	0.39662792654093	11	FACETS	0.954	0.863	1			1	CLONAL	1	TRUE	NA	0.39662792654093	11		493	2002	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	79	432	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.240464393573647	3	FACETS	1	0.958	1	0.602	0.53	0.68	CLONAL	1	FALSE	1	0.240464393573647	3		432	611	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	111	278	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.958	1	1	0.99	1	CLONAL	2	FALSE	1	0.240464393573647	2		279	418	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	126	551	3	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.240464393573647	2		554	917	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	128	340	1	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	1	FACETS	1	0.935	1	1	0.99	1	CLONAL	2	FALSE	0	0.240464393573647	1		341	455	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	19	211	1	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	1	FACETS	0.972	0.745	1	0.972	0.745	1	CLONAL	1	FALSE	0	0.240464393573647	1		212	143	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736166	204736166	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	138	591	0	ENST00000302823.3:c.529del	p.Tyr177IlefsTer10	p.Y177Ifs*10	ENST00000302823	NM_005214.4	175	Ttt/tt	3/4	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	1	0.240464393573647	2		591	1087	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	99	406	1	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	FALSE	1	0.240464393573647	2		407	771	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151289	202151290	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	79	513	0	ENST00000358485.4:c.1596dup	p.Leu533ThrfsTer6	p.L533Tfs*6	ENST00000358485	NM_001080125.1	530	aga/agAa	9/9	1	2	FACETS	0.629	0.552	0.713	0.629	0.552	0.713	SUBCLONAL	1	FALSE	1	0.240464393573647	2		513	1044	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161689	56161689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1490957244	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	83	483	1	ENST00000399503.3:c.1186C>T	p.Arg396Cys	p.R396C	ENST00000399503	NM_005921.1	396	Cgt/Tgt	6/20	1	2	FACETS	0.993	0.877	1	0.993	0.877	1	CLONAL	1	FALSE	1	0.240464393573647	2		484	695	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	67	367	5	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	0.240464393573647	3	FACETS	1	0.912	1	0.532	0.462	0.607	CLONAL	1	FALSE	1	0.240464393573647	3		372	587	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260803	16260803	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150899650	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	69	427	1	ENST00000375759.3:c.8068G>A	p.Val2690Met	p.V2690M	ENST00000375759	NM_015001.2	2690	Gtg/Atg	11/15	1	2	FACETS	0.834	0.726	0.951	0.834	0.726	0.951	CLONAL	1	FALSE	1	0.240464393573647	2		428	688	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577138	7577138	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	157	568	1	ENST00000269305.4:c.800G>T	p.Arg267Leu	p.R267L	ENST00000269305	NM_001126112.2	267	cGg/cTg	8/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.240464393573647	2		569	997	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998607	100998607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778889652	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	110	609	1	ENST00000325455.5:c.1195C>T	p.Arg399Cys	p.R399C	ENST00000325455	NM_001202474.3	399	Cgc/Tgc	1/8	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	1	0.240464393573647	2		610	875	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739410	46739410	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144207599	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	70	305	0	ENST00000371975.4:c.1601G>A	p.Arg534His	p.R534H	ENST00000371975	NM_003579.3	534	cGt/cAt	14/18	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.240464393573647	2		305	480	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310454	65310454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778407	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	102	478	1	ENST00000342505.4:c.2234C>T	p.Thr745Met	p.T745M	ENST00000342505	NM_002227.2	745	aCg/aTg	16/25	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.240464393573647	2		479	743	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165981	47165981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	80	383	0	ENST00000409792.3:c.145G>A	p.Val49Ile	p.V49I	ENST00000409792	NM_014159.6	49	Gtt/Att	3/21	1	2	FACETS	0.96	0.845	1	0.96	0.845	1	CLONAL	1	FALSE	1	0.240464393573647	2		383	693	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526170	189526170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1225645471	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	99	475	0	ENST00000264731.3:c.434C>T	p.Ala145Val	p.A145V	ENST00000264731	NM_003722.4	145	gCg/gTg	4/14	1	2	FACETS	0.852	0.759	0.952	0.852	0.759	0.952	CLONAL	1	FALSE	1	0.240464393573647	2		475	966	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439369	149439369	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	59	404	1	ENST00000286301.3:c.2026C>T	p.Arg676Ter	p.R676*	ENST00000286301	NM_005211.3	676	Cga/Tga	15/22	1	2	FACETS	0.669	0.574	0.772	0.669	0.574	0.772	SUBCLONAL	1	FALSE	1	0.240464393573647	2		405	734	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052945	180052945	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760476680	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	89	427	1	ENST00000261937.6:c.1345G>A	p.Gly449Arg	p.G449R	ENST00000261937	NM_182925.4	449	Ggg/Agg	10/30	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.240464393573647	2		428	627	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956667	93956667	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	340	682	1	ENST00000369303.4:c.2569G>A	p.Ala857Thr	p.A857T	ENST00000369303	NM_004440.3	857	Gca/Aca	15/17	0.160255612573458	3	FACETS	1	0.989	1	0.784	0.741	0.828	CLONAL	2	FALSE	0	0.240464393573647	3		683	1347	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521939	157521939	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs372833448	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	155	391	1	ENST00000346085.5:c.4211A>G	p.Tyr1404Cys	p.Y1404C	ENST00000346085	NM_020732.3	1404	tAc/tGc	18/20	0.160255612573458	3	FACETS	1	0.981	1	0.815	0.749	0.882	CLONAL	2	FALSE	0	0.240464393573647	3		392	591	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864452	151864452	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145072739	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	49	254	2	ENST00000262189.6:c.9529C>T	p.Arg3177Cys	p.R3177C	ENST00000262189	NM_170606.2	3177	Cgt/Tgt	42/59	0.240464393573647	3	FACETS	0.926	0.785	1	0.463	0.392	0.541	CLONAL	1	FALSE	1	0.240464393573647	3		256	493	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93629423	93629423	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770053469	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	166	454	3	ENST00000375746.1:c.857C>T	p.Ala286Val	p.A286V	ENST00000375746	NM_001174167.1	286	gCg/gTg	7/14	0.217703877740813	3	FACETS	0.958	0.881	1	0.958	0.881	1	CLONAL	2	FALSE	1	0.240464393573647	3		457	807	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231134	98231134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1311707136	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	54	266	1	ENST00000331920.6:c.2149G>A	p.Asp717Asn	p.D717N	ENST00000331920	NM_000264.3	717	Gac/Aac	14/24	0.217703877740813	3	FACETS	1	0.917	1	0.553	0.473	0.64	CLONAL	1	FALSE	1	0.240464393573647	3		267	455	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399309	139399309	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1166328821	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	111	451	0	ENST00000277541.6:c.4834G>A	p.Gly1612Ser	p.G1612S	ENST00000277541	NM_017617.3	1612	Ggc/Agc	26/34	0.217703877740813	3	FACETS	1	0.975	1	0.635	0.571	0.704	CLONAL	1	FALSE	1	0.240464393573647	3		451	814	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139563082	139563082	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	142	621	0	ENST00000308874.7:c.154T>A	p.Phe52Ile	p.F52I	ENST00000308874		52	Ttc/Atc	4/10	0.217703877740813	3	FACETS	1	0.983	1	0.675	0.614	0.739	CLONAL	1	FALSE	1	0.240464393573647	3		621	980	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609486	81609486	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	112	519	0	ENST00000298171.2:c.1084G>T	p.Glu362Ter	p.E362*	ENST00000298171	NM_000369.2	362	Gag/Tag	10/10	0.217703877740813	3	FACETS	1	0.957	1	0.56	0.503	0.621	CLONAL	1	FALSE	1	0.240464393573647	3		519	931	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663825	29663825	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	140	502	0	ENST00000356175.3:c.6257T>A	p.Val2086Asp	p.V2086D	ENST00000356175	NM_000267.3	2086	gTt/gAt	41/57	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.240464393573647	2		502	889	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919554	78919554	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	32	355	0	ENST00000306801.3:c.3113T>A	p.Ile1038Asn	p.I1038N	ENST00000306801	NM_020761.2	1038	aTc/aAc	26/34	1	2	FACETS	0.444	0.359	0.54	0.444	0.359	0.54	SUBCLONAL	1	FALSE	1	0.240464393573647	2		355	600	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207621	2207621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1208115143	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	157	664	1	ENST00000398665.3:c.905C>T	p.Ser302Leu	p.S302L	ENST00000398665	NM_032482.2	302	tCg/tTg	11/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.240464393573647	2		665	1079	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019447	31019447	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	66	349	0	ENST00000375687.4:c.944A>G	p.His315Arg	p.H315R	ENST00000375687	NM_015338.5	315	cAt/cGt	10/13	0.182658989537511	0	FACETS	0.602	0.522	0.688			1	SUBCLONAL	1	FALSE	0	0.240464393573647	0		349	693	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513220	44513220	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	44	186	0	ENST00000291552.4:c.715C>T	p.Arg239Ter	p.R239*	ENST00000291552	NM_006758.2	239	Cga/Tga	8/8	1	2	FACETS	0.958	0.805	1	0.958	0.805	1	CLONAL	1	FALSE	1	0.240464393573647	2		186	382	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30090766	30090766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766689587	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	123	637	1	ENST00000338641.4:c.1763G>A	p.Arg588Gln	p.R588Q	ENST00000338641	NM_000268.3	588	cGa/cAa	16/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.240464393573647	2		638	871	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851386	151851386	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	193	550	0	ENST00000262189.6:c.12105del	p.Ile4036SerfsTer47	p.I4036Sfs*47	ENST00000262189	NM_170606.2	4035	ccC/cc	47/59	0.240464393573647	3	FACETS	0.923	0.854	0.995	0.923	0.854	0.995	CLONAL	2	FALSE	1	0.240464393573647	3		550	974	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374949	45374952	+	frameshift_variant	Frame_Shift_Del	DEL	AGTG	AGTG	-	novel	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	76	372	0	ENST00000262160.6:c.891_894del	p.Thr298Ter	p.T298*	ENST00000262160	NM_005901.5	297	ctCACT/ct	8/11	1	2	FACETS	0.989	0.868	1	0.989	0.868	1	CLONAL	1	FALSE	1	0.240464393573647	2		372	639	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412940	63412940	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	151	382	0	ENST00000330258.3:c.227del	p.Gly76AspfsTer24	p.G76Dfs*24	ENST00000330258	NM_152424.3	76	gGa/ga	2/2	1	1	FACETS	0.89	0.816	0.966	1	0.991	1	CLONAL	2	FALSE	0	0.240464393573647	1		382	621	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230872	66230873	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	78	445	0	ENST00000273854.3:c.2098dup	p.Arg700LysfsTer11	p.R700Kfs*11	ENST00000273854	NM_004439.5	700	aga/aAga	12/18	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	FALSE	1	0.240464393573647	2		445	627	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683411	182683411	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	73	357	0	ENST00000292782.4:c.134del	p.Phe45SerfsTer12	p.F45Sfs*12	ENST00000292782	NM_020640.2	45	tTc/tc	2/7	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	FALSE	1	0.240464393573647	2		357	546	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426027	49426027	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	73	460	0	ENST00000301067.7:c.12461del	p.Gly4154AlafsTer7	p.G4154Afs*7	ENST00000301067	NM_003482.3	4154	gGc/gc	39/54	0.240464393573647	3	FACETS	0.907	0.792	1	0.453	0.396	0.516	CLONAL	1	FALSE	1	0.240464393573647	3		460	750	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563349	21563349	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	218	723	0	ENST00000382592.4:c.570del	p.Tyr191ThrfsTer49	p.Y191Tfs*49	ENST00000382592	NM_014572.2	190	ccC/cc	4/8	0.217703877740813	3	FACETS	0.904	0.84	0.971	0.904	0.84	0.971	CLONAL	2	FALSE	1	0.240464393573647	3		723	1123	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0010932-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	33	791	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.46	0.373	0.559	0.46	0.373	0.559	SUBCLONAL	1	TRUE	1	0.14	2		792	1025	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0010932-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	28	618	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.404	0.321	0.5	0.404	0.321	0.5	SUBCLONAL	1	TRUE	1	0.14	2		618	989	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0010932-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	35	321	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.14	2		321	458	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0010939-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	361	406	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.953	0.904	1	0.953	0.904	1	CLONAL	1	TRUE	1	0.621427815085811	2		406	1219	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995300	15995300	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0010942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	669	494	0	ENST00000268712.3:c.2893A>T	p.Lys965Ter	p.K965*	ENST00000268712	NM_006311.3	965	Aaa/Taa	22/46	0.599396790459193	2	FACETS	0.897	0.869	0.924	0.897	0.869	0.924	CLONAL	2	TRUE	0	0.638774356795502	2		494	1168	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410405	63410405	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1267	518	642	0	ENST00000330258.3:c.2762T>C	p.Leu921Pro	p.L921P	ENST00000330258	NM_152424.3	921	cTg/cCg	2/2	1	2	FACETS	0.909	0.869	0.949	0.909	0.869	0.949	CLONAL	1	TRUE	1	0.638774356795502	2		642	1785	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097821	8097822	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0010942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	316	487	0	ENST00000346208.3:c.204dup	p.Arg69GlnfsTer234	p.R69Qfs*234	ENST00000346208		68	gtc/gtCc	2/6	1	2	FACETS	0.79	0.745	0.837	0.79	0.745	0.837	SUBCLONAL	1	TRUE	1	0.638774356795502	2		487	1252	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0010979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	149	406	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.216317535522269	4	FACETS	0.946	0.865	1	0.946	0.865	1	CLONAL	2	TRUE	2	0.263636556126113	4		406	755	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021828	71021828	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0010979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	58	311	0	ENST00000318789.4:c.1531-1G>A		p.X511_splice	ENST00000318789	NM_032682.5	511			0.262431723748969	5	FACETS	1	0.936	1	0.386	0.332	0.445	CLONAL	1	TRUE	2	0.263636556126113	5		311	530	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144568	55144568	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	63	474	0	ENST00000257290.5:c.2042A>G	p.Asp681Gly	p.D681G	ENST00000257290	NM_006206.4	681	gAt/gGt	15/23	0.118658940796223	4	FACETS	0.887	0.766	1	0.443	0.383	0.509	INDETERMINATE	1	TRUE	2	0.263636556126113	4		474	681	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112315	115112316	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0010979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	31	71	0	ENST00000257566.3:c.1424dup	p.Lys476GlnfsTer216	p.K476Qfs*216	ENST00000257566	NM_016569.3	475	ggc/ggGc	7/8	0.191744788025045	4	FACETS	0.901	0.745	1	1	0.938	1	CLONAL	3	TRUE	2	0.263636556126113	4		71	110	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863660	68863661	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCTGCCAAT	novel	NA	P-0010979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	75	445	1	ENST00000261769.5:c.2403_2412dup	p.Asp805CysfsTer5	p.D805Cfs*5	ENST00000261769	NM_004360.3	800	cgc/cgCCCTGCCAATc	15/16	0.263636556126113	1	FACETS	0.97	0.852	1	0.97	0.852	1	CLONAL	1	TRUE	0	0.263636556126113	1		446	509	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0010985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	178	586	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	0.40900799946923	2		586	706	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0010985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	116	275	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.40900799946923	2		275	526	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0010985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	370	709	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.40900799946923	2		709	1343	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630194	187630194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	169	337	0	ENST00000441802.2:c.788C>T	p.Ser263Leu	p.S263L	ENST00000441802	NM_005245.3	263	tCa/tTa	2/27	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.40900799946923	2		337	668	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70432654	70432654	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs776044335	NA	P-0010985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	112	389	0	ENST00000373644.4:c.4676G>A	p.Arg1559His	p.R1559H	ENST00000373644	NM_030625.2	1559	cGt/cAt	8/12	1	2	FACETS	0.787	0.708	0.87	0.787	0.708	0.87	SUBCLONAL	1	TRUE	1	0.40900799946923	2		389	696	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368203	45368203	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	394	476	0	ENST00000262160.6:c.1399T>C	p.Ser467Pro	p.S467P	ENST00000262160	NM_005901.5	467	Tca/Cca	11/11	0.40900799946923	2	FACETS	0.844	0.809	0.879	1	0.995	1	CLONAL	3	TRUE	0	0.40900799946923	2		476	761	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589553	67589579	+	inframe_deletion	In_Frame_Del	DEL	AAGATAATATTGAAGCTGTAGGGAAAA	AAGATAATATTGAAGCTGTAGGGAAAA	-	novel	NA	P-0010985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	65	242	0	ENST00000274335.5:c.1318_1344del	p.Asp440_Lys448del	p.D440_K448del	ENST00000274335		439	gAAGATAATATTGAAGCTGTAGGGAAAAaa/gaa	10/15	1	2	FACETS	0.741	0.644	0.845	0.741	0.644	0.845	SUBCLONAL	1	TRUE	1	0.40900799946923	2		242	429	SUCCESS
APC	324	MSKCC	GRCh37	5	112174095	112174096	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0010985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	174	419	0	ENST00000257430.4:c.2805_2806del	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	tAC/t	16/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.40900799946923	2		419	680	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457291	67457292	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0010985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	216	497	0	ENST00000327367.4:c.266dup	p.Cys89TrpfsTer22	p.C89Wfs*22	ENST00000327367	NM_005902.3	89	tgc/tGgc	2/9	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.40900799946923	2		497	822	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412362	63412362	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	AT	novel	NA	P-0010985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	279	352	0	ENST00000330258.3:c.805delinsAT	p.His269IlefsTer9	p.H269Ifs*9	ENST00000330258	NM_152424.3	269	Cat/ATat	2/2	1	1	FACETS	0.959	0.91	1	1	0.996	1	CLONAL	2	TRUE	0	0.40900799946923	1		352	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010989-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	101	622	0	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	0.215917386341719	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	0	0.215759229001734	1		622	679	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145430	58145430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894340	NA	P-0010989-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	151	449	0	ENST00000257904.6:c.71G>A	p.Arg24His	p.R24H	ENST00000257904	NM_000075.3	24	cGt/cAt	2/8	0.18417251599452	2	FACETS	0.865	0.792	0.942	0.865	0.792	0.942	CLONAL	2	FALSE	0	0.215759229001734	2		449	809	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28885814	28885814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010989-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	93	604	0	ENST00000282397.4:c.3548C>T	p.Thr1183Ile	p.T1183I	ENST00000282397	NM_002019.4	1183	aCa/aTa	27/30	0.215759229001734	1	FACETS	0.852	0.756	0.954	0.852	0.756	0.954	CLONAL	1	FALSE	0	0.215759229001734	1		604	903	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010992-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	137	160	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.933	1			1	INDETERMINATE	1	TRUE	NA	0.487156412156564	2		160	549	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481403	140481403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913357	NA	P-0010992-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1296	84	538	0	ENST00000288602.6:c.1405G>A	p.Gly469Arg	p.G469R	ENST00000288602	NM_004333.4	469	Gga/Aga	11/18	0.475300562148618	3	FACETS	0.311	0.273	0.351	0.155	0.136	0.176	SUBCLONAL	1	TRUE	1	0.487156412156564	3		538	1380	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685287	89685287	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs398123316	NA	P-0010992-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	95	207	0	ENST00000371953.3:c.182A>G	p.His61Arg	p.H61R	ENST00000371953	NM_000314.4	61	cAt/cGt	3/9	0.487156412156564	1	FACETS	0.634	0.567	0.705	0.634	0.567	0.705	SUBCLONAL	1	TRUE	0	0.487156412156564	1		207	465	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52692223	52692223	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010992-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	309	580	0	ENST00000394830.3:c.637T>C	p.Ser213Pro	p.S213P	ENST00000394830	NM_018313.4	213	Tct/Cct	6/30	1	2	FACETS	0.959	0.903	1	0.959	0.903	1	CLONAL	1	TRUE	1	0.487156412156564	2		580	1323	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560019	29560019	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1555615004	NA	P-0010992-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	97	475	0	ENST00000356175.3:c.3497-1G>A		p.X1166_splice	ENST00000356175	NM_000267.3	1166			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.487156412156564	NA		475	889	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717723	89717736	+	frameshift_variant	Frame_Shift_Del	DEL	TGTGGTGATATCAA	TGTGGTGATATCAA	-	novel	NA	P-0010992-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	80	389	0	ENST00000371953.3:c.748_761del	p.Cys250SerfsTer43	p.C250Sfs*43	ENST00000371953	NM_000314.4	250	TGTGGTGATATCAAa/a	7/9	0.487156412156564	1	FACETS	0.373	0.328	0.421	0.373	0.328	0.421	SUBCLONAL	1	TRUE	0	0.487156412156564	1		389	666	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0010995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	292	654	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.318848011192627	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.318848011192627	2		654	906	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625251	69625251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782147248	NA	P-0010995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	125	683	0	ENST00000334134.2:c.542G>A	p.Arg181His	p.R181H	ENST00000334134	NM_005247.2	181	cGc/cAc	3/3	0.318848011192627	3	FACETS	0.948	0.857	1	0.474	0.428	0.522	CLONAL	1	TRUE	1	0.318848011192627	3		683	959	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360568	70360568	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779515761	NA	P-0010995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	176	665	1	ENST00000374080.3:c.6128G>A	p.Arg2043His	p.R2043H	ENST00000374080		2043	cGt/cAt	42/45	0.279247833951445	3	FACETS	1	0.976	1	0.578	0.532	0.627	CLONAL	1	TRUE	1	0.318848011192627	3		666	1107	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249020	55249022	+	missense_variant	Missense_Mutation	TNP	ACG	ACG	TCA	novel	NA	P-0010995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	223	416	0	ENST00000275493.2:c.2318_2320delinsTCA	p.His773_Val774delinsLeuMet	p.H773_V774delinsLM	ENST00000275493	NM_005228.3	773	cACGtg/cTCAtg	20/28	0.307983383136449	5	FACETS	0.974	0.906	1	0.649	0.604	0.696	CLONAL	2	TRUE	2	0.318848011192627	5		416	1062	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0011016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	320	424	0	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	0.370096379406308	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.370096379406308	1		424	991	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510329	187510329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs558459409	NA	P-0011016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	168	238	0	ENST00000441802.2:c.13184C>T	p.Pro4395Leu	p.P4395L	ENST00000441802	NM_005245.3	4395	cCg/cTg	27/27	0.370096379406308	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.370096379406308	1		238	576	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867563	35867563	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	592	169	0	ENST00000303115.3:c.377T>C	p.Ile126Thr	p.I126T	ENST00000303115	NM_002185.3	126	aTa/aCa	3/8	0.370096379406308	8	FACETS	1	0.975	1	0.867	0.837	0.896	CLONAL	6	TRUE	1	0.370096379406308	8		169	1113	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180050984	180050984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	149	599	0	ENST00000261937.6:c.1499C>T	p.Pro500Leu	p.P500L	ENST00000261937	NM_182925.4	500	cCc/cTc	11/30	1	2	FACETS	0.726	0.662	0.793	0.726	0.662	0.793	SUBCLONAL	1	TRUE	1	0.370096379406308	2		599	1109	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963931	2963931	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	359	525	0	ENST00000396946.4:c.1876G>C	p.Glu626Gln	p.E626Q	ENST00000396946	NM_032415.4	626	Gag/Cag	15/25	0.175643383452028	4	FACETS	0.909	0.86	0.959	0.909	0.86	0.959	INDETERMINATE	2	TRUE	2	0.370096379406308	4		525	1462	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492861	8492861	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0011016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	60	338	0	ENST00000356435.5:c.2467+1G>T		p.X823_splice	ENST00000356435		823			0.355514759836535	1	FACETS	0.327	0.281	0.378	0.327	0.281	0.378	SUBCLONAL	1	TRUE	0	0.370096379406308	1		338	807	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112128	115112128	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	244	471	0	ENST00000257566.3:c.1612G>T	p.Gly538Cys	p.G538C	ENST00000257566	NM_016569.3	538	Ggc/Tgc	7/8	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.370096379406308	2		471	1084	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434172	121434172	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	169	398	1	ENST00000257555.6:c.1063G>T	p.Gly355Cys	p.G355C	ENST00000257555		355	Ggc/Tgc	5/10	1	2	FACETS	0.829	0.761	0.901	0.829	0.761	0.901	CLONAL	1	TRUE	1	0.370096379406308	2		399	1101	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569794	95569794	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	311	309	0	ENST00000393063.1:c.3939G>T	p.Glu1313Asp	p.E1313D	ENST00000393063	NM_030621.3	1313	gaG/gaT	22/28	0.366741821613633	2	FACETS	0.983	0.93	1	0.983	0.93	1	CLONAL	2	TRUE	0	0.370096379406308	2		309	855	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14021929	14021929	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	99	298	0	ENST00000311895.7:c.629A>T	p.Glu210Val	p.E210V	ENST00000311895	NM_005236.2	210	gAa/gTa	4/11	NA	2	FACETS	0.574	0.511	0.641			1	INDETERMINATE	1	TRUE	NA	0.370096379406308	2		298	932	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685517	29685517	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	170	229	0	ENST00000356175.3:c.7927A>G	p.Lys2643Glu	p.K2643E	ENST00000356175	NM_000267.3	2643	Aag/Gag	54/57	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.370096379406308	2		229	701	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942703	44942703	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0011016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	284	343	0	ENST00000377967.4:c.3285-2A>T		p.X1095_splice	ENST00000377967	NM_021140.2	1095			1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.370096379406308	2		343	1115	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430798	47430798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776912006	NA	P-0011016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1366	83	601	3	ENST00000377045.4:c.1763G>A	p.Arg588His	p.R588H	ENST00000377045	NM_001654.4	588	cGc/cAc	16/16	1	2	FACETS	0.31	0.272	0.35	0.31	0.272	0.35	SUBCLONAL	1	TRUE	1	0.370096379406308	2		604	1449	SUCCESS
AR	367	MSKCC	GRCh37	X	66765917	66765917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	320	466	0	ENST00000374690.3:c.929C>T	p.Ser310Phe	p.S310F	ENST00000374690	NM_000044.3	310	tCc/tTc	1/8	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.370096379406308	2		466	1353	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340937	70340937	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	324	511	1	ENST00000374080.3:c.670C>A	p.His224Asn	p.H224N	ENST00000374080		224	Cat/Aat	5/45	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.370096379406308	2		512	1439	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953753	48953762	+	frameshift_variant	Frame_Shift_Del	DEL	GTATTACCGA	GTATTACCGA	-	novel	NA	P-0011016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	131	243	0	ENST00000267163.4:c.1359_1368del	p.Tyr453Ter	p.Y453*	ENST00000267163	NM_000321.2	452	ttGTATTACCGA/tt	14/27	0.370096379406308	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.370096379406308	1		243	547	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	210	160	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.608814039373028	2		160	633	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0011026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	1175	791	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.608814039373028	2	FACETS	0.988	0.966	1	0.988	0.966	1	CLONAL	2	TRUE	0	0.608814039373028	2		792	1953	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717661	89717661	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	425	534	0	ENST00000371953.3:c.686C>A	p.Ser229Ter	p.S229*	ENST00000371953	NM_000314.4	229	tCa/tAa	7/9	0.608814039373028	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.608814039373028	1		534	915	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964315	55964315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749143449	NA	P-0011026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	378	634	1	ENST00000263923.4:c.2498G>A	p.Arg833Gln	p.R833Q	ENST00000263923	NM_002253.2	833	cGg/cAg	17/30	1	2	FACETS	0.824	0.781	0.868	0.824	0.781	0.868	CLONAL	1	TRUE	1	0.608814039373028	2		635	1507	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0011036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	337	586	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.490214936266263	4	FACETS	0.908	0.859	0.958	0.908	0.859	0.958	CLONAL	2	TRUE	2	0.491209356406817	4		586	1127	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118944	3118944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	282	635	2	ENST00000078429.4:c.628C>T	p.Arg210Trp	p.R210W	ENST00000078429	NM_002067.2	210	Cgg/Tgg	5/7	0.491209356406817	2	FACETS	1	0.979	1	0.543	0.51	0.577	CLONAL	1	TRUE	0	0.491209356406817	2		637	1057	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650397	48650397	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	315	343	0	ENST00000376670.3:c.367G>T	p.Asp123Tyr	p.D123Y	ENST00000376670	NM_002049.3	123	Gat/Tat	3/6	1	1	FACETS	0.81	0.773	0.848	1	0.996	1	CLONAL	2	TRUE	0	0.491209356406817	1		343	597	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55124984	55124984	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1293	563	726	0	ENST00000257290.5:c.49G>A	p.Gly17Arg	p.G17R	ENST00000257290	NM_006206.4	17	Ggg/Agg	2/23	0.490214936266263	4	FACETS	0.921	0.883	0.96	0.921	0.883	0.96	CLONAL	2	TRUE	2	0.491209356406817	4		726	1856	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124424	94124424	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	157	671	1	ENST00000369303.4:c.159T>A	p.Asn53Lys	p.N53K	ENST00000369303	NM_004440.3	53	aaT/aaA	2/17	1	2	FACETS	0.92	0.845	0.998	0.92	0.845	0.998	CLONAL	1	TRUE	1	0.491209356406817	2		672	695	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869691	117869691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772999578	NA	P-0011036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1566	246	641	0	ENST00000297338.2:c.503G>A	p.Arg168His	p.R168H	ENST00000297338	NM_006265.2	168	cGt/cAt	6/14	0.491209356406817	4	FACETS	0.824	0.767	0.883	0.412	0.383	0.442	CLONAL	1	TRUE	2	0.491209356406817	4		641	1812	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456398	32456398	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	192	412	2	ENST00000332351.3:c.494C>T	p.Ser165Phe	p.S165F	ENST00000332351	NM_024426.4	165	tCc/tTc	1/10	0.490214936266263	4	FACETS	1	0.973	1	0.555	0.512	0.599	CLONAL	1	TRUE	2	0.491209356406817	4		414	1051	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205768	108205768	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1555127166	NA	P-0011036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	292	364	0	ENST00000278616.4:c.8083G>T	p.Gly2695Cys	p.G2695C	ENST00000278616	NM_000051.3	2695	Ggt/Tgt	55/63	0.491209356406817	2	FACETS	0.973	0.924	1	0.973	0.924	1	CLONAL	2	TRUE	0	0.491209356406817	2		364	611	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134105	41134105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	336	763	3	ENST00000379561.5:c.1523G>A	p.Gly508Asp	p.G508D	ENST00000379561	NM_002015.3	508	gGc/gAc	2/3	0.491209356406817	2	FACETS	1	0.974	1	0.526	0.497	0.556	CLONAL	1	TRUE	0	0.491209356406817	2		766	1300	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044713	47044713	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	252	278	4	ENST00000377604.3:c.2113G>T	p.Glu705Ter	p.E705*	ENST00000377604	NM_001204468.1	705	Gag/Tag	19/24	1	1	FACETS	0.759	0.718	0.799	1	0.994	1	SUBCLONAL	2	TRUE	0	0.491209356406817	1		282	510	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858967	243858968	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0011036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	304	488	0	ENST00000263826.5:c.97_98delinsAT	p.Gly33Ile	p.G33I	ENST00000263826	NM_005465.4	33	GGc/ATc	2/13	0.491209356406817	3	FACETS	0.909	0.86	0.959	0.909	0.86	0.959	CLONAL	2	TRUE	1	0.491209356406817	3		488	848	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124427	94124428	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0011036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	161	684	2	ENST00000369303.4:c.155_156delinsAA	p.Pro52Gln	p.P52Q	ENST00000369303	NM_004440.3	52	cCC/cAA	2/17	1	2	FACETS	0.917	0.843	0.994	0.917	0.843	0.994	CLONAL	1	TRUE	1	0.491209356406817	2		686	715	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107008	27107008	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	245	373	2	ENST00000324856.7:c.6619C>T	p.Gln2207Ter	p.Q2207*	ENST00000324856	NM_006015.4	2207	Cag/Tag	20/20	0.908425712322271	3	FACETS	1	0.974	1	0.534	0.501	0.568	CLONAL	1	TRUE	1	0.908425712322271	3		375	734	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856469	111856469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	210	373	1	ENST00000341259.2:c.520G>A	p.Ala174Thr	p.A174T	ENST00000341259	NM_005475.2	174	Gcc/Acc	2/8	0.888559648206705	3	FACETS	0.878	0.817	0.94	0.293	0.272	0.314	CLONAL	1	TRUE	0	0.908425712322271	3		374	766	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256885	41256885	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	476	469	1	ENST00000357654.3:c.301T>A	p.Tyr101Asn	p.Y101N	ENST00000357654	NM_007294.3	101	Tat/Aat	5/23	0.908425712322271	5	FACETS	0.925	0.885	0.966	0.617	0.59	0.644	CLONAL	2	TRUE	2	0.908425712322271	5		470	1338	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180504	56180505	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0011042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	510	318	0	ENST00000399503.3:c.3836dup	p.Asn1279LysfsTer5	p.N1279Kfs*5	ENST00000399503	NM_005921.1	1278	aga/agAa	16/20	0.908425712322271	5	FACETS	0.857	0.825	0.889	0.857	0.825	0.889	CLONAL	3	TRUE	2	0.908425712322271	5		318	1032	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168691	56168692	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0011042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	547	423	0	ENST00000399503.3:c.1546dup	p.Arg516LysfsTer25	p.R516Kfs*25	ENST00000399503	NM_005921.1	515	-/A	9/20	0.908425712322271	5	FACETS	0.935	0.897	0.973	0.623	0.598	0.649	CLONAL	2	TRUE	2	0.908425712322271	5		423	1522	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419921	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0011042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	224	434	0	ENST00000206249.3:c.1607_1608delinsAT	p.Leu536His	p.L536H	ENST00000206249	NM_000125.3	536	cTC/cAT	8/8	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.908425712322271	2		434	485	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0011043-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	46	405	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.170893765856744	3	FACETS	0.84	0.708	0.984	0.42	0.354	0.492	INDETERMINATE	1	FALSE	1	0.3	3		405	420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0011043-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	48	706	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	1	0.3	2		706	257	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149876	202149876	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0011043-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	19	464	0	ENST00000358485.4:c.1317T>A	p.Tyr439Ter	p.Y439*	ENST00000358485	NM_001080125.1	439	taT/taA	8/9	0.212211498352191	3	FACETS	0.569	0.432	0.729	0.285	0.216	0.365	SUBCLONAL	1	FALSE	1	0.3	3		464	256	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398235	25398235	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011043-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	53	575	0	ENST00000311936.3:c.84T>G	p.Phe28Leu	p.F28L	ENST00000311936	NM_004985.3	28	ttT/ttG	2/5	0.170893765856744	3	FACETS	0.977	0.835	1	0.488	0.417	0.566	INDETERMINATE	1	FALSE	1	0.3	3		575	416	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439919	56439919	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011043-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	12	407	0	ENST00000407977.2:c.673C>A	p.Arg225Ser	p.R225S	ENST00000407977		225	Cgc/Agc	6/10	0.170893765856744	3	FACETS	0.385	0.27	0.526	0.192	0.135	0.263	INDETERMINATE	1	FALSE	1	0.3	3		407	239	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878667	151878667	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011043-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	26	427	0	ENST00000262189.6:c.6278del	p.Pro2093HisfsTer13	p.P2093Hfs*13	ENST00000262189	NM_170606.2	2093	cCa/ca	36/59	1	2	FACETS	0.99	0.792	1	0.99	0.792	1	CLONAL	1	FALSE	1	0.3	2		427	175	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183733	10183733	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	61	430	0	ENST00000256474.2:c.202T>C	p.Ser68Pro	p.S68P	ENST00000256474	NM_000551.3	68	Tcg/Ccg	1/3	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.2	2		430	597	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098526	47098526	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	72	427	0	ENST00000409792.3:c.6748C>T	p.Gln2250Ter	p.Q2250*	ENST00000409792	NM_014159.6	2250	Caa/Taa	15/21	1	2	FACETS	0.961	0.839	1	0.961	0.839	1	CLONAL	1	TRUE	1	0.2	2		427	749	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851815	134851815	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	59	462	0	ENST00000398015.3:c.1221G>T	p.Gln407His	p.Q407H	ENST00000398015	NM_004441.4	407	caG/caT	5/16	1	2	FACETS	0.748	0.642	0.864	0.748	0.642	0.864	SUBCLONAL	1	TRUE	1	0.2	2		462	789	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197287	106197287	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	50	286	0	ENST00000380013.4:c.5620G>A	p.Glu1874Lys	p.E1874K	ENST00000380013	NM_001127208.2	1874	Gag/Aag	11/11	1	2	FACETS	0.82	0.695	0.957	0.82	0.695	0.957	CLONAL	1	TRUE	1	0.2	2		286	610	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239423	105239423	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	55	329	0	ENST00000349310.3:c.964G>C	p.Glu322Gln	p.E322Q	ENST00000349310	NM_001014432.1	322	Gag/Cag	12/15	1	2	FACETS	0.942	0.805	1	0.942	0.805	1	CLONAL	1	TRUE	1	0.2	2		329	584	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007532	62007532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762138094	NA	P-0011069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	102	696	0	ENST00000392795.3:c.335G>A	p.Gly112Asp	p.G112D	ENST00000392795	NM_001039933.1	112	gGc/gAc	3/6	1	2	FACETS	0.903	0.805	1	0.903	0.805	1	CLONAL	1	TRUE	1	0.2	2		696	1130	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793046	42793046	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	58	409	0	ENST00000575354.2:c.938C>G	p.Ser313Cys	p.S313C	ENST00000575354	NM_015125.3	313	tCt/tGt	7/20	1	2	FACETS	0.784	0.672	0.906	0.784	0.672	0.906	CLONAL	1	TRUE	1	0.2	2		409	740	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0011082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	45	403	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.721	0.605	0.851	0.721	0.605	0.851	SUBCLONAL	1	TRUE	1	0.17	2		403	734	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0011082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1278	213	881	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	1	2	FACETS	0.84	0.778	0.905	1	0.992	1	CLONAL	2	TRUE	1	0.17	2		881	1491	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945397	17945397	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199861157	NA	P-0011082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1350	95	924	0	ENST00000458235.1:c.2333A>G	p.Asn778Ser	p.N778S	ENST00000458235	NM_000215.3	778	aAt/aGt	17/24	1	2	FACETS	0.773	0.686	0.868	0.773	0.686	0.868	SUBCLONAL	1	TRUE	1	0.17	2		924	1445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0011096-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	610	655	3	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.795335927649915	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.862290935707055	1		658	732	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0011096-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	614	621	4	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	0.466939589148171	1	FACETS	0.718	0.695	0.742	0.718	0.695	0.742	INDETERMINATE	1	TRUE	0	0.862290935707055	1		625	1128	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519886	NA	P-0011096-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	231	521	0	ENST00000349496.5:c.97T>G	p.Ser33Ala	p.S33A	ENST00000349496	NM_001904.3	33	Tct/Gct	3/15	NA	2	FACETS	0.467	0.434	0.5			1	INDETERMINATE	1	TRUE	NA	0.862290935707055	2		521	1148	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830136	72830136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011096-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	351	868	2	ENST00000268489.5:c.6445C>T	p.Arg2149Cys	p.R2149C	ENST00000268489	NM_006885.3	2149	Cgc/Tgc	9/10	NA	2	FACETS	0.585	0.553	0.618			1	INDETERMINATE	1	TRUE	NA	0.862290935707055	2		870	1392	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242481	+	inframe_deletion	In_Frame_Del	DEL	AATTAAGAGAAGCAA	AATTAAGAGAAGCAA	-	rs121913425	NA	P-0011100-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	18	344	0	ENST00000275493.2:c.2237_2251del	p.Glu746_Thr751delinsAla	p.E746_T751delinsA	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAAca/gca	19/28	1	2	FACETS	0.52	0.397	0.661	0.52	0.397	0.661	SUBCLONAL	1	TRUE	1	0.640544869939225	2		344	108	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28929495	NA	P-0011107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	185	568	0	ENST00000275493.2:c.2155G>A	p.Gly719Ser	p.G719S	ENST00000275493	NM_005228.3	719	Ggc/Agc	18/28	1	2	FACETS	0.822	0.759	0.888	0.822	0.759	0.888	CLONAL	1	TRUE	1	0.466695992522773	2		568	964	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0011107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	60	418	0	ENST00000269305.4:c.673-2A>C		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.407229049741294	1	FACETS	0.379	0.327	0.436	0.379	0.327	0.436	SUBCLONAL	1	TRUE	0	0.466695992522773	1		418	520	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0011107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	198	547	0	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	1	2	FACETS	0.933	0.865	1	0.933	0.865	1	CLONAL	1	TRUE	1	0.466695992522773	2		547	909	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625282	69625282	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1262110871	NA	P-0011107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	282	894	0	ENST00000334134.2:c.511C>T	p.Arg171Cys	p.R171C	ENST00000334134	NM_005247.2	171	Cgc/Tgc	3/3	1	2	FACETS	0.969	0.91	1	0.969	0.91	1	CLONAL	1	TRUE	1	0.466695992522773	2		894	1247	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42002948	42002948	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	264	989	0	ENST00000219905.7:c.2485G>T	p.Glu829Ter	p.E829*	ENST00000219905	NM_001164273.1	829	Gaa/Taa	8/24	0.466695992522773	1	FACETS	0.738	0.691	0.786	0.738	0.691	0.786	SUBCLONAL	1	TRUE	0	0.466695992522773	1		989	1175	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890102	76890102	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	235	786	0	ENST00000373344.5:c.4792C>A	p.Leu1598Ile	p.L1598I	ENST00000373344	NM_000489.3	1598	Ctt/Att	17/35	1	2	FACETS	0.745	0.693	0.798	0.745	0.693	0.798	SUBCLONAL	1	TRUE	1	0.466695992522773	2		786	1352	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939099	76939099	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs782422536	NA	P-0011107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	168	568	0	ENST00000373344.5:c.1649G>T	p.Ser550Ile	p.S550I	ENST00000373344	NM_000489.3	550	aGt/aTt	9/35	1	2	FACETS	0.768	0.705	0.833	0.768	0.705	0.833	SUBCLONAL	1	TRUE	1	0.466695992522773	2		568	938	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858018	45858019	+	missense_variant	Missense_Mutation	DNP	CA	CA	AT	novel	NA	P-0011107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	172	715	0	ENST00000391945.4:c.1634_1635delinsAT	p.Met545Asn	p.M545N	ENST00000391945	NM_000400.3	545	aTG/aAT	17/23	1	2	FACETS	0.754	0.693	0.817	0.754	0.693	0.817	SUBCLONAL	1	TRUE	1	0.466695992522773	2		715	978	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0011110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	582	617	1	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.288269592245874	3	FACETS	1	0.992	1	0.736	0.708	0.765	CLONAL	2	TRUE	0	0.419922474289035	3		618	1518	SUCCESS
APC	324	MSKCC	GRCh37	5	112175174	112175174	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	44	195	0	ENST00000257430.4:c.3883G>T	p.Glu1295Ter	p.E1295*	ENST00000257430	NM_000038.5	1295	Gaa/Taa	16/16	1	2	FACETS	0.631	0.531	0.741	0.631	0.531	0.741	SUBCLONAL	1	TRUE	1	0.419922474289035	2		195	332	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598037	55598037	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	154	411	0	ENST00000288135.5:c.2234G>T	p.Gly745Val	p.G745V	ENST00000288135	NM_000222.2	745	gGc/gTc	16/21	1	2	FACETS	0.841	0.77	0.916	0.841	0.77	0.916	CLONAL	1	TRUE	1	0.419922474289035	2		411	872	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519988	NA	P-0011113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	269	518	0	ENST00000269305.4:c.808T>C	p.Phe270Leu	p.F270L	ENST00000269305	NM_001126112.2	270	Ttt/Ctt	8/11	0.272938013693784	2	FACETS	0.887	0.832	0.944	0.887	0.832	0.944	CLONAL	2	TRUE	0	0.274905962354691	2		518	1103	SUCCESS
CBL	867	MSKCC	GRCh37	11	119145566	119145566	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	188	480	0	ENST00000264033.4:c.772T>C	p.Trp258Arg	p.W258R	ENST00000264033	NM_005188.3	258	Tgg/Cgg	5/16	NA	2	FACETS	1	0.94	1			1	INDETERMINATE	1	TRUE	NA	0.274905962354691	2		480	1336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782177	NA	P-0011117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	34	534	0	ENST00000269305.4:c.644G>T	p.Ser215Ile	p.S215I	ENST00000269305	NM_001126112.2	215	aGt/aTt	6/11	0.129311172083458	3	FACETS	0.564	0.46	0.681	0.282	0.23	0.341	INDETERMINATE	1	TRUE	1	0.29	3		534	476	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602764	10602764	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	60	366	1	ENST00000171111.5:c.814C>T	p.Arg272Cys	p.R272C	ENST00000171111	NM_203500.1	272	Cgc/Tgc	3/6	0.233914486545258	3	FACETS	1	0.946	1			1	CLONAL	1	TRUE	NA	0.29	3		367	397	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971048	21971053	+	inframe_deletion	In_Frame_Del	DEL	GCCGCG	GCCGCG	-	novel	NA	P-0011117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	26	209	0	ENST00000304494.5:c.305_310del	p.Ala102_Leu104delinsVal	p.A102_L104delinsV	ENST00000304494	NM_000077.4	102	gCGCGGCtg/gtg	2/3	1	2	FACETS	0.858	0.684	1	0.858	0.684	1	CLONAL	1	TRUE	1	0.29	2		209	209	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0011120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	408	536	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.365658940666492	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.365658940666492	2		536	964	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0011120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	35	211	1	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	2	FACETS	0.575	0.472	0.69	0.575	0.472	0.69	SUBCLONAL	1	TRUE	1	0.365658940666492	2		212	333	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403208	213403208	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1297962291	NA	P-0011120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	212	557	2	ENST00000342788.4:c.47C>T	p.Ala16Val	p.A16V	ENST00000342788	NM_005235.2	16	gCg/gTg	1/28	0.256043175981109	4	FACETS	1	0.987	1	0.648	0.601	0.698	CLONAL	1	TRUE	2	0.365658940666492	4		559	1221	SUCCESS
APC	324	MSKCC	GRCh37	5	112175235	112175235	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0011120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	253	333	0	ENST00000257430.4:c.3944C>G	p.Ser1315Ter	p.S1315*	ENST00000257430	NM_000038.5	1315	tCa/tGa	16/16	0.365658940666492	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	0	0.365658940666492	3		333	493	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045887	180045887	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	285	319	1	ENST00000261937.6:c.2884G>A	p.Ala962Thr	p.A962T	ENST00000261937	NM_182925.4	962	Gcc/Acc	21/30	0.365658940666492	3	FACETS	0.891	0.843	0.939	0.891	0.843	0.939	CLONAL	3	TRUE	0	0.365658940666492	3		320	690	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827354	72827354	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	429	763	0	ENST00000268489.5:c.9227T>G	p.Met3076Arg	p.M3076R	ENST00000268489	NM_006885.3	3076	aTg/aGg	9/10	0.365658940666492	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.365658940666492	3		763	1296	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554551	63554551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	330	450	0	ENST00000307078.5:c.188G>A	p.Gly63Glu	p.G63E	ENST00000307078	NM_004655.3	63	gGg/gAg	2/11	0.256043175981109	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	2	0.365658940666492	4		450	995	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578448	7578448	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1064795691	NA	P-0011130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	60	290	0	ENST00000269305.4:c.482C>A	p.Ala161Asp	p.A161D	ENST00000269305	NM_001126112.2	161	gCc/gAc	5/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		290	697	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57567416	57567416	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1341162180	NA	P-0011130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	52	351	0	ENST00000316660.6:c.9del	p.Lys4ArgfsTer33	p.K4Rfs*33	ENST00000316660	NM_021127.2	3	Ggg/gg	1/2	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		351	663	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310859	123310859	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759750319	NA	P-0011163-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	179	636	1	ENST00000358487.5:c.569G>A	p.Arg190Gln	p.R190Q	ENST00000358487	NM_000141.4	190	cGg/cAg	5/18	1	2	FACETS	0.988	0.91	1	0.988	0.91	1	CLONAL	1	TRUE	1	0.327168906706214	2		637	1107	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0011176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	77	311	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.864	0.765	0.969	0.864	0.765	0.969	CLONAL	1	TRUE	1	0.532093474023838	2		311	335	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063717	+	splice_donor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0011176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	93	233	0	ENST00000412916.2:c.165+1del		p.X55_splice	ENST00000412916		55			0.532093474023838	1	FACETS	0.817	0.735	0.903	0.817	0.735	0.903	CLONAL	1	TRUE	0	0.532093474023838	1		233	314	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857523	68857533	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTGCTAAGTAA	TTGCTAAGTAA	CACTT	novel	NA	P-0011176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	68	253	0	ENST00000261769.5:c.2158_2164+4delinsCACTT		p.X720_splice	ENST00000261769	NM_004360.3	720		13/16	0.532093474023838				0.545	0.702				SUBCLONAL	1	TRUE	0	0.532093474023838	1		253	302	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0011183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	251	390	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.3	3	FACETS	0.98	0.917	1			1	CLONAL	2	TRUE	NA	0.28	3		390	1043	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0011183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	135	553	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	1	2	FACETS	0.799	0.724	0.878	0.799	0.724	0.878	SUBCLONAL	1	TRUE	1	0.28	2		553	1207	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482861	67482861	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567005581	NA	P-0011183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	99	325	0	ENST00000327367.4:c.1265C>A	p.Ser422Tyr	p.S422Y	ENST00000327367	NM_005902.3	422	tCc/tAc	9/9	1	2	FACETS	0.866	0.772	0.965	0.866	0.772	0.965	CLONAL	1	TRUE	1	0.28	2		325	817	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139650	202139650	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1271	124	509	0	ENST00000358485.4:c.811C>G	p.Pro271Ala	p.P271A	ENST00000358485	NM_001080125.1	271	Cca/Gca	6/9	0.205516258382279	3	FACETS	0.724	0.652	0.8	0.362	0.326	0.4	SUBCLONAL	1	TRUE	1	0.28	3		509	1395	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142970	47142970	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	124	480	0	ENST00000409792.3:c.4993G>T	p.Asp1665Tyr	p.D1665Y	ENST00000409792	NM_014159.6	1665	Gac/Tac	8/21	0.3	1	FACETS	0.713	0.643	0.786	0.713	0.643	0.786	SUBCLONAL	1	TRUE	0	0.28	1		480	1069	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946283	55946283	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0011183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	83	337	0	ENST00000263923.4:c.3896C>G	p.Ser1299Ter	p.S1299*	ENST00000263923	NM_002253.2	1299	tCa/tGa	30/30	1	2	FACETS	0.698	0.615	0.788	0.698	0.615	0.788	SUBCLONAL	1	TRUE	1	0.28	2		337	849	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751125	57751125	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	38	263	0	ENST00000274289.3:c.1742A>G	p.Glu581Gly	p.E581G	ENST00000274289	NM_006622.3	581	gAg/gGg	12/14	1	2	FACETS	0.373	0.307	0.447	0.373	0.307	0.447	SUBCLONAL	1	TRUE	1	0.28	2		263	728	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6439802	6439802	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	83	360	0	ENST00000356142.4:c.328G>C	p.Glu110Gln	p.E110Q	ENST00000356142	NM_018890.3	110	Gaa/Caa	5/7	0.268254725542277	3	FACETS	0.608	0.535	0.687	0.304	0.267	0.344	SUBCLONAL	1	TRUE	1	0.28	3		360	1111	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848645	151848645	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	44	291	0	ENST00000262189.6:c.12548C>G	p.Ser4183Cys	p.S4183C	ENST00000262189	NM_170606.2	4183	tCt/tGt	50/59	1	2	FACETS	0.36	0.3	0.426	0.36	0.3	0.426	SUBCLONAL	1	TRUE	1	0.28	2		291	874	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518590	69518590	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	51	189	0	ENST00000294312.3:c.55G>A	p.Ala19Thr	p.A19T	ENST00000294312	NM_005117.2	19	Gcc/Acc	1/3	1	2	FACETS	0.871	0.742	1	0.871	0.742	1	CLONAL	1	TRUE	1	0.28	2		189	418	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236087	108236087	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	70	382	0	ENST00000278616.4:c.9023G>T	p.Arg3008Leu	p.R3008L	ENST00000278616	NM_000051.3	3008	cGt/cTt	63/63	1	2	FACETS	0.489	0.425	0.559	0.489	0.425	0.559	SUBCLONAL	1	TRUE	1	0.28	2		382	1022	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641497	18641497	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	79	355	0	ENST00000266497.5:c.2496G>C	p.Gln832His	p.Q832H	ENST00000266497		832	caG/caC	17/31	0.3	3	FACETS	0.619	0.543	0.702			1	SUBCLONAL	1	TRUE	NA	0.28	3		355	1039	SUCCESS
AR	367	MSKCC	GRCh37	X	66765877	66765877	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749006575	NA	P-0011183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	95	546	0	ENST00000374690.3:c.889G>A	p.Asp297Asn	p.D297N	ENST00000374690	NM_000044.3	297	Gac/Aac	1/8	1	2	FACETS	0.574	0.509	0.643	0.574	0.509	0.643	SUBCLONAL	1	TRUE	1	0.28	2		546	1182	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545867	41545867	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1429	157	779	0	ENST00000263253.7:c.2482del	p.His828IlefsTer22	p.H828Ifs*22	ENST00000263253	NM_001429.3	828	Cat/at	14/31	1	2	FACETS	0.707	0.645	0.772	0.707	0.645	0.772	SUBCLONAL	1	TRUE	1	0.28	2		779	1586	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205334	46205340	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTAAAT	GGTAAAT	-	novel	NA	P-0011183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	79	264	1	ENST00000334344.6:c.418_418+6del		p.X140_splice	ENST00000334344	NM_152641.2	140		4/21	1	2	FACETS	0.934	0.822	1	0.934	0.822	1	CLONAL	1	TRUE	1	0.28	2		265	604	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639160	176639161	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0011183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	41	150	0	ENST00000439151.2:c.3760_3761delinsTT	p.Pro1254Phe	p.P1254F	ENST00000439151	NM_022455.4	1254	CCc/TTc	5/23	1	2	FACETS	0.805	0.672	0.951	0.805	0.672	0.951	CLONAL	1	TRUE	1	0.28	2		150	364	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947827	178947827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011193-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	311	580	0	ENST00000263967.3:c.2702G>T	p.Cys901Phe	p.C901F	ENST00000263967	NM_006218.2	901	tGt/tTt	19/21	0.399710536341008	5	FACETS	0.905	0.86	0.949	0.905	0.86	0.949	INDETERMINATE	3	TRUE	2	0.722558385553472	5		580	661	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260644	1260644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1278994586	NA	P-0011193-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	56	577	5	ENST00000310581.5:c.2915G>A	p.Arg972His	p.R972H	ENST00000310581	NM_198253.2	972	cGc/cAc	12/16	0.638558622025517	4	FACETS	0.266	0.227	0.31			1	SUBCLONAL	1	TRUE	NA	0.722558385553472	4		582	1002	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106066	8106066	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011193-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	38	300	0	ENST00000346208.3:c.886C>A	p.Gln296Lys	p.Q296K	ENST00000346208		296	Cag/Aag	4/6	0.722558385553472	3	FACETS	0.234	0.193	0.281	0.117	0.096	0.141	SUBCLONAL	1	TRUE	1	0.722558385553472	3		300	611	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610522	81610522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368452281	NA	P-0011193-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	58	610	1	ENST00000298171.2:c.2120G>A	p.Arg707Gln	p.R707Q	ENST00000298171	NM_000369.2	707	cGg/cAg	10/10	0.722558385553472	4	FACETS	0.262	0.224	0.304	0.131	0.112	0.152	SUBCLONAL	1	TRUE	2	0.722558385553472	4		611	1056	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576891	7576891	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0011201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	563	384	1	ENST00000269305.4:c.955A>T	p.Lys319Ter	p.K319*	ENST00000269305	NM_001126112.2	319	Aag/Tag	9/11	0.920159198073453	1	FACETS	0.986	0.966	1	0.986	0.966	1	CLONAL	1	TRUE	0	0.921504142669176	1		385	668	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874958	151874958	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	47	358	0	ENST00000262189.6:c.7580A>G	p.Asn2527Ser	p.N2527S	ENST00000262189	NM_170606.2	2527	aAt/aGt	38/59	0.537309918410749	1	FACETS	0.061	0.051	0.072	0.061	0.051	0.072	INDETERMINATE	1	TRUE	0	0.921504142669176	1		358	907	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900635	32900635	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs81002849	NA	P-0011201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	447	366	0	ENST00000380152.3:c.517-1G>T		p.X173_splice	ENST00000380152		173			0.920159198073453	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.921504142669176	1		366	499	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974779	15974779	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0011201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	215	486	0	ENST00000268712.3:c.4096A>T	p.Lys1366Ter	p.K1366*	ENST00000268712	NM_006311.3	1366	Aaa/Taa	30/46	0.920159198073453	1	FACETS	0.249	0.231	0.268	0.249	0.231	0.268	SUBCLONAL	1	TRUE	0	0.921504142669176	1		486	1010	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136183	11136183	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	599	427	0	ENST00000358026.2:c.3167A>T	p.Glu1056Val	p.E1056V	ENST00000358026	NM_001128849.1	1056	gAg/gTg	22/36	0.921504142669176	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.921504142669176	1		427	676	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574192	41574222	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGATGAGCCCCCAGGCTCAGCAGATGAAC	AGGGATGAGCCCCCAGGCTCAGCAGATGAAC	-	novel	NA	P-0011201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1239	89	527	0	ENST00000263253.7:c.6478_6508del	p.Gly2160Ter	p.G2160*	ENST00000263253	NM_001429.3	2159	ggAGGGATGAGCCCCCAGGCTCAGCAGATGAAC/gg	31/31	0.274721465248611	1	FACETS	0.078	0.069	0.089	0.078	0.069	0.089	INDETERMINATE	1	TRUE	0	0.921504142669176	1		527	1328	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098816	178098816	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	334	1018	0	ENST00000397062.3:c.229G>T	p.Asp77Tyr	p.D77Y	ENST00000397062	NM_006164.4	77	Gat/Tat	2/5	0.492751307641088	3	FACETS	1	0.992	1	0.623	0.591	0.655	INDETERMINATE	1	TRUE	1	0.887949282238917	3		1018	872	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451797	29451797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs79530637	NA	P-0011205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	61	993	0	ENST00000389048.3:c.2768G>A	p.Gly923Glu	p.G923E	ENST00000389048	NM_004304.4	923	gGg/gAg	16/29	0.492751307641088	3	FACETS	0.302	0.26	0.348	0.151	0.13	0.174	INDETERMINATE	1	TRUE	1	0.887949282238917	3		993	656	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264416	46264416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	62	623	1	ENST00000371998.3:c.1463G>A	p.Gly488Glu	p.G488E	ENST00000371998		488	gGg/gAg	11/23	1	2	FACETS	0.319	0.276	0.365	0.319	0.276	0.365	SUBCLONAL	1	TRUE	1	0.887949282238917	2		624	438	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961751	55961751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	50	670	0	ENST00000263923.4:c.2810C>T	p.Pro937Leu	p.P937L	ENST00000263923	NM_002253.2	937	cCc/cTc	20/30	1	2	FACETS	0.266	0.226	0.31	0.266	0.226	0.31	SUBCLONAL	1	TRUE	1	0.887949282238917	2		670	423	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214368	55214368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761795138	NA	P-0011205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	64	878	4	ENST00000275493.2:c.494G>A	p.Arg165Gln	p.R165Q	ENST00000275493	NM_005228.3	165	cGg/cAg	4/28	1	2	FACETS	0.244	0.211	0.279	0.244	0.211	0.279	SUBCLONAL	1	TRUE	1	0.887949282238917	2		882	592	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913137	44913137	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	68	463	0	ENST00000377967.4:c.812A>T	p.Gln271Leu	p.Q271L	ENST00000377967	NM_021140.2	271	cAg/cTg	10/29	1	1	FACETS	0.271	0.238	0.307	0.271	0.238	0.307	SUBCLONAL	1	TRUE	0	0.887949282238917	1		463	314	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0011221-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	242	389	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.560988136323963	1	FACETS	0.955	0.898	1	0.955	0.898	1	CLONAL	1	TRUE	0	0.560988136323963	1		389	650	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165785	118165785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1302106502	NA	P-0011221-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	155	236	0	ENST00000369448.3:c.295C>T	p.Leu99Phe	p.L99F	ENST00000369448	NM_017709.3	99	Ctt/Ttt	2/2	0.560988136323963	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.560988136323963	1		236	395	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544630	65544630	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0011221-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	238	361	0	ENST00000358664.4:c.295+1G>C		p.X99_splice	ENST00000358664	NM_002382.4	99			0.560988136323963	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.560988136323963	1		361	569	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028689	12028689	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0011221-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	252	391	0	ENST00000353533.5:c.891+1G>A		p.X297_splice	ENST00000353533	NM_003010.3	297			0.560988136323963	1	FACETS	0.988	0.931	1	0.988	0.931	1	CLONAL	1	TRUE	0	0.560988136323963	1		391	654	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098636	47098643	+	frameshift_variant	Frame_Shift_Del	DEL	GAATGTCC	GAATGTCC	-	novel	NA	P-0011221-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	279	462	0	ENST00000409792.3:c.6631_6638del	p.Gly2211TyrfsTer32	p.G2211Yfs*32	ENST00000409792	NM_014159.6	2211	GGACATTCt/t	15/21	0.560988136323963	1	FACETS	0.933	0.881	0.986	0.933	0.881	0.986	CLONAL	1	TRUE	0	0.560988136323963	1		462	767	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624296	89624298	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	novel	NA	P-0011225-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	25	281	0	ENST00000371953.3:c.70_72del	p.Asp24del	p.D24del	ENST00000371953	NM_000314.4	24	GAC/-	1/9	0.250819926928705	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		281	396	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027816	152027817	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0011225-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	18	362	0	ENST00000262189.6:c.258dup	p.Glu87ArgfsTer9	p.E87Rfs*9	ENST00000262189	NM_170606.2	86	-/A	3/59	0.175689263881827	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		362	274	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664760	138664760	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	27	137	0	ENST00000330315.3:c.805G>T	p.Gly269Cys	p.G269C	ENST00000330315	NM_023067.3	269	Ggc/Tgc	1/1	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.12	2		137	408	SUCCESS
ATR	545	MSKCC	GRCh37	3	142177921	142177921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	70	348	0	ENST00000350721.4:c.7382C>T	p.Thr2461Ile	p.T2461I	ENST00000350721	NM_001184.3	2461	aCt/aTt	44/47	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.12	2		348	1031	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021244	31021244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	51	353	0	ENST00000375687.4:c.1243G>A	p.Asp415Asn	p.D415N	ENST00000375687	NM_015338.5	415	Gat/Aat	12/13	1	2	FACETS	0.918	0.778	1	0.918	0.778	1	CLONAL	1	TRUE	1	0.12	2		353	926	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441255	52441255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011247-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	447	536	1	ENST00000460680.1:c.515G>T	p.Ser172Ile	p.S172I	ENST00000460680	NM_004656.3	172	aGc/aTc	7/17	0.661073123720234	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.684299494988781	1		537	855	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979201	93979201	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011247-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	597	683	0	ENST00000369303.4:c.1627T>G	p.Phe543Val	p.F543V	ENST00000369303	NM_004440.3	543	Ttt/Gtt	7/17	0.684299494988781	1	FACETS	0.984	0.95	1	0.984	0.95	1	CLONAL	1	TRUE	0	0.684299494988781	1		683	1167	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257169	19257169	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011247-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	229	341	0	ENST00000162023.5:c.794C>T	p.Pro265Leu	p.P265L	ENST00000162023		265	cCg/cTg	12/13	1	2	FACETS	0.886	0.829	0.945	0.886	0.829	0.945	CLONAL	1	TRUE	1	0.684299494988781	2		341	755	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928078	178928119	+	inframe_deletion	In_Frame_Del	DEL	AGAAGATTTGCTGAACCCTATTGGTGTTACTGGATCAAATCC	AGAAGATTTGCTGAACCCTATTGGTGTTACTGGATCAAATCC	-	novel	NA	P-0011247-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	352	412	0	ENST00000263967.3:c.1357_1398del	p.Glu453_Pro466del	p.E453_P466del	ENST00000263967	NM_006218.2	452	ttAGAAGATTTGCTGAACCCTATTGGTGTTACTGGATCAAATCCa/tta	8/21	0.684299494988781	3	FACETS	1	0.993	1	0.633	0.6	0.666	CLONAL	1	TRUE	1	0.684299494988781	3		412	1091	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0011254-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	200	565	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	0.389895337880059	2		565	982	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402595	20402595	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011254-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	106	312	0	ENST00000346618.3:c.132C>G	p.Phe44Leu	p.F44L	ENST00000346618	NM_001949.4	44	ttC/ttG	1/7	1	2	FACETS	0.939	0.844	1	0.939	0.844	1	CLONAL	1	TRUE	1	0.389895337880059	2		312	579	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729942	41729942	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011254-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1365	379	887	0	ENST00000242208.4:c.587G>T	p.Gly196Val	p.G196V	ENST00000242208	NM_002192.2	196	gGc/gTc	3/3	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.389895337880059	2		887	1744	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431228	49431228	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1379753637	NA	P-0011254-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	199	503	0	ENST00000301067.7:c.9911C>T	p.Pro3304Leu	p.P3304L	ENST00000301067	NM_003482.3	3304	cCc/cTc	34/54	1	2	FACETS	0.978	0.905	1	0.978	0.905	1	CLONAL	1	TRUE	1	0.389895337880059	2		503	1044	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112026	115112026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011254-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	164	374	0	ENST00000257566.3:c.1714G>T	p.Gly572Trp	p.G572W	ENST00000257566	NM_016569.3	572	Ggg/Tgg	7/8	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.389895337880059	2		374	774	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679408	29679408	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555536372	NA	P-0011254-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	149	488	0	ENST00000356175.3:c.7528C>T	p.Gln2510Ter	p.Q2510*	ENST00000356175	NM_000267.3	2510	Cag/Tag	50/57	1	2	FACETS	0.825	0.754	0.901	0.825	0.754	0.901	CLONAL	1	TRUE	1	0.389895337880059	2		488	926	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394081	31394081	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011254-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	224	426	0	ENST00000328111.2:c.2368C>G	p.Pro790Ala	p.P790A	ENST00000328111	NM_006892.3	790	Cct/Gct	22/23	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.389895337880059	2		426	982	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663380	29663381	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0011254-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	163	392	0	ENST00000356175.3:c.5974dup	p.Ser1992LysfsTer17	p.S1992Kfs*17	ENST00000356175	NM_000267.3	1991	-/A	40/57	1	2	FACETS	0.975	0.895	1	0.975	0.895	1	CLONAL	1	TRUE	1	0.389895337880059	2		392	858	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0011257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	451	408	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.99	1	1	0.998	1	CLONAL	4	TRUE	1	0.17	2		408	1190	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0011257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	598	703	1	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	1	2	FACETS	1	0.987	1	1	0.998	1	CLONAL	4	TRUE	1	0.17	2		704	1666	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939673	76939674	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0011257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	688	752	1	ENST00000373344.5:c.1074dup	p.Leu359ThrfsTer3	p.L359Tfs*3	ENST00000373344	NM_000489.3	358	-/A	9/35	0.209713047436002	1	FACETS	1	0.984	1	1	0.998	1	CLONAL	4	TRUE	0	0.17	1		753	1788	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577563	7577563	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1567549584	NA	P-0011257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	467	550	0	ENST00000269305.4:c.718A>G	p.Ser240Gly	p.S240G	ENST00000269305	NM_001126112.2	240	Agt/Ggt	7/11	1	2	FACETS	1	0.982	1	1	0.998	1	CLONAL	4	TRUE	1	0.17	2		550	1308	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778169	27778169	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2322	236	1372	0	ENST00000369163.2:c.318G>C	p.Glu106Asp	p.E106D	ENST00000369163	NM_003536.2	106	gaG/gaC	1/1	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.17	2		1372	2558	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872672	37872672	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1271	135	768	0	ENST00000269571.5:c.1632C>G	p.Cys544Trp	p.C544W	ENST00000269571		544	tgC/tgG	13/27	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.17	2		768	1406	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923853	39923853	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0011257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	109	597	0	ENST00000378444.4:c.3239-1G>A		p.X1080_splice	ENST00000378444	NM_001123385.1	1080			0.209713047436002	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.17	1		597	1049	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691039	NA	P-0011260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	227	476	1	ENST00000269305.4:c.919+1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.304056088710148	2	FACETS	0.857	0.8	0.916	0.857	0.8	0.916	CLONAL	2	TRUE	0	0.31	2		477	854	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553474	29553474	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs779546178	NA	P-0011260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	244	542	0	ENST00000356175.3:c.2023G>T	p.Gly675Ter	p.G675*	ENST00000356175	NM_000267.3	675	Gga/Tga	18/57	0.199518359352997	4	FACETS	0.783	0.73	0.838	0.783	0.73	0.838	SUBCLONAL	2	TRUE	2	0.31	4		542	1317	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069456	30069456	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	132	298	0	ENST00000338641.4:c.1321G>T	p.Ala441Ser	p.A441S	ENST00000338641	NM_000268.3	441	Gct/Tct	12/16	0.304056088710148	2	FACETS	0.885	0.809	0.964	0.885	0.809	0.964	CLONAL	2	TRUE	0	0.31	2		298	481	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935402	36935402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs948001842	NA	P-0011260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1243	141	745	0	ENST00000361632.4:c.1325C>T	p.Pro442Leu	p.P442L	ENST00000361632		442	cCt/cTt	10/16	0.304056088710148	3	FACETS	0.759	0.689	0.833	0.38	0.344	0.417	SUBCLONAL	1	TRUE	1	0.31	3		745	1384	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567289	226567289	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	208	432	0	ENST00000366794.5:c.1597G>T	p.Val533Leu	p.V533L	ENST00000366794	NM_001618.3	533	Gtg/Ttg	11/23	0.199518359352997	4	FACETS	0.913	0.847	0.98	0.913	0.847	0.98	CLONAL	2	TRUE	2	0.31	4		432	963	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671735	30671735	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	179	508	0	ENST00000376406.3:c.5225G>T	p.Cys1742Phe	p.C1742F	ENST00000376406	NM_014641.2	1742	tGc/tTc	10/15	0.274079474281936	5	FACETS	1	0.988	1	0.47	0.433	0.51	CLONAL	1	TRUE	2	0.31	5		508	1199	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433887	49433887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	178	529	0	ENST00000301067.7:c.7666C>T	p.Leu2556Phe	p.L2556F	ENST00000301067	NM_003482.3	2556	Ctc/Ttc	31/54	0.207940264506935	3	FACETS	1	0.989	1	0.734	0.676	0.793	CLONAL	1	TRUE	1	0.31	3		529	904	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560151	29560151	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	296	450	2	ENST00000356175.3:c.3628G>T	p.Glu1210Ter	p.E1210*	ENST00000356175	NM_000267.3	1210	Gaa/Taa	27/57	0.199518359352997	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.31	4		452	1123	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306560	41306560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	299	513	2	ENST00000373198.4:c.1099G>A	p.Glu367Lys	p.E367K	ENST00000373198	NM_133170.3	367	Gag/Aag	7/32	0.304056088710148	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.31	2		515	921	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913220	39913220	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1320	176	756	1	ENST00000378444.4:c.4895C>A	p.Ala1632Asp	p.A1632D	ENST00000378444	NM_001123385.1	1632	gCc/gAc	14/15	1	2	FACETS	0.759	0.697	0.824	0.759	0.697	0.824	SUBCLONAL	1	TRUE	1	0.31	2		757	1496	SUCCESS
AR	367	MSKCC	GRCh37	X	66765580	66765580	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1276699901	NA	P-0011260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	138	553	0	ENST00000374690.3:c.592C>A	p.Gln198Lys	p.Q198K	ENST00000374690	NM_000044.3	198	Cag/Aag	1/8	1	2	FACETS	0.815	0.74	0.893	0.815	0.74	0.893	CLONAL	1	TRUE	1	0.31	2		553	1093	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52685769	52685769	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	514	631	0	ENST00000394830.3:c.703del	p.Gln235ArgfsTer18	p.Q235Rfs*18	ENST00000394830	NM_018313.4	235	Cag/ag	7/30	0.293390051372566	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.31	3		631	1222	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591925	48591925	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	233	436	0	ENST00000342988.3:c.1088G>T	p.Cys363Phe	p.C363F	ENST00000342988	NM_005359.5	363	tGt/tTt	9/12	0.445040502434727	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.445040502434727	1		436	743	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986830	36986830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	23	20	0	ENST00000354822.5:c.859C>T	p.Arg287Cys	p.R287C	ENST00000354822	NM_001079668.2	287	Cgc/Tgc	3/3	1	2	FACETS	0.891	0.706	1	0.891	0.706	1	CLONAL	1	TRUE	1	0.445040502434727	2		20	116	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0011264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	215	393	1	ENST00000311936.3:c.180_181delinsAA	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggAAaa	3/5	1	2	FACETS	0.996	0.926	1	0.996	0.926	1	CLONAL	1	TRUE	1	0.445040502434727	2		394	970	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106670	27106670	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	267	380	1	ENST00000324856.7:c.6281G>T	p.Cys2094Phe	p.C2094F	ENST00000324856	NM_006015.4	2094	tGc/tTc	20/20	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.445040502434727	2		381	933	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812154	212812154	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0011264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	156	426	0	ENST00000342788.4:c.421+1G>A		p.X141_splice	ENST00000342788	NM_005235.2	141			1	2	FACETS	0.976	0.896	1	0.976	0.896	1	CLONAL	1	TRUE	1	0.445040502434727	2		426	718	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341913	8341913	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	210	401	0	ENST00000356435.5:c.4727A>G	p.Glu1576Gly	p.E1576G	ENST00000356435		1576	gAa/gGa	29/35	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.445040502434727	2		401	912	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988881	41988881	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	938	727	0	ENST00000219905.7:c.1673A>G	p.Asp558Gly	p.D558G	ENST00000219905	NM_001164273.1	558	gAc/gGc	3/24	0.433350518837726	4	FACETS	0.975	0.947	1	0.975	0.947	1	CLONAL	3	TRUE	1	0.445040502434727	4		727	2083	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942028	81942028	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs72824905	NA	P-0011264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	315	567	0	ENST00000359376.3:c.1565C>T	p.Pro522Leu	p.P522L	ENST00000359376	NM_002661.3	522	cCc/cTc	17/33	1	2	FACETS	0.998	0.94	1	0.998	0.94	1	CLONAL	1	TRUE	1	0.445040502434727	2		567	1418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579588	7579589	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0011264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	224	309	0	ENST00000269305.4:c.97_98dup	p.Leu35ProfsTer10	p.L35Pfs*10	ENST00000269305	NM_001126112.2	33	tcc/tcTCc	4/11	0.445040502434727	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.445040502434727	1		309	679	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440642	56440643	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0011264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	379	537	0	ENST00000407977.2:c.575dup	p.Ala193GlyfsTer6	p.A193Gfs*6	ENST00000407977		192	ccg/ccCg	5/10	0.445040502434727	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.445040502434727	1		537	1149	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0011280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	30	203	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.844	0.687	1	0.844	0.687	1	CLONAL	1	TRUE	1	0.38	2		203	187	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537062	41537062	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	76	724	0	ENST00000263253.7:c.1889A>G	p.Tyr630Cys	p.Y630C	ENST00000263253	NM_001429.3	630	tAc/tGc	10/31	1	2	FACETS	0.825	0.725	0.931	0.825	0.725	0.931	CLONAL	1	TRUE	1	0.38	2		724	485	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177371	56177397	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGTAATGAATGTTTTTTTCTTTCAGG	TGGTAATGAATGTTTTTTTCTTTCAGG	CCTGA	novel	NA	P-0011280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	47	579	0	ENST00000399503.3:c.2370-26_2370delinsCCTGA		p.X790_splice	ENST00000399503	NM_005921.1	790		14/20	1	2	FACETS	0.691	0.585	0.807	0.691	0.585	0.807	SUBCLONAL	1	TRUE	1	0.38	2		579	358	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0011287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	131	586	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.305074885536241	2		586	717	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0011287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	87	297	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.305074885536241	3	FACETS	1	0.966	1	0.615	0.546	0.689	CLONAL	1	TRUE	1	0.305074885536241	3		298	534	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0011287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	110	360	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.203507971123541	2	FACETS	1	0.982	1	0.713	0.643	0.786	CLONAL	1	TRUE	0	0.305074885536241	2		361	506	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0011287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	72	552	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.305074885536241	3	FACETS	0.487	0.424	0.556	0.244	0.212	0.278	SUBCLONAL	1	TRUE	1	0.305074885536241	3		552	1117	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555687605	NA	P-0011287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	154	430	0	ENST00000342988.3:c.1610A>G	p.Asp537Gly	p.D537G	ENST00000342988	NM_005359.5	537	gAc/gGc	12/12	0.203507971123541	2	FACETS	1	0.984	1	0.656	0.601	0.714	CLONAL	1	TRUE	0	0.305074885536241	2		430	769	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184989	32184989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	187	472	1	ENST00000375023.3:c.1679G>A	p.Cys560Tyr	p.C560Y	ENST00000375023	NM_004557.3	560	tGt/tAt	10/30	0.232334733998802	3	FACETS	1	0.989	1	0.731	0.675	0.789	CLONAL	1	TRUE	1	0.305074885536241	3		473	967	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160237	22160237	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	176	415	0	ENST00000215832.6:c.394C>G	p.Gln132Glu	p.Q132E	ENST00000215832	NM_002745.4	132	Cag/Gag	3/9	0.203507971123541	2	FACETS	0.759	0.701	0.82	0.759	0.701	0.82	SUBCLONAL	2	TRUE	0	0.305074885536241	2		415	760	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0011290-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	280	928	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	0.923	0.871	0.976	0.923	0.871	0.976	CLONAL	1	TRUE	1	0.763960260279361	2		928	794	SUCCESS
AR	367	MSKCC	GRCh37	X	66937372	66937372	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011290-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	453	318	0	ENST00000374690.3:c.2226G>C	p.Trp742Cys	p.W742C	ENST00000374690	NM_000044.3	742	tgG/tgC	5/8	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.763960260279361	1		318	604	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058722	47058722	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0011290-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	242	780	0	ENST00000409792.3:c.7556del	p.Lys2519ArgfsTer3	p.K2519Rfs*3	ENST00000409792	NM_014159.6	2519	aAg/ag	21/21	1	2	FACETS	0.966	0.908	1	0.966	0.908	1	CLONAL	1	TRUE	1	0.763960260279361	2		780	656	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921499	39921499	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011294-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	44	384	1	ENST00000378444.4:c.4321C>T	p.Gln1441Ter	p.Q1441*	ENST00000378444	NM_001123385.1	1441	Cag/Tag	10/15	1	1	FACETS	0.981	0.848	1	1	0.981	1	CLONAL	4	FALSE	0	0.185057394002227	1		385	110	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0011297-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	356	551	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.211017775516599	6	FACETS	0.908	0.86	0.958	0.908	0.86	0.958	CLONAL	4	TRUE	2	0.211017775516599	6		551	1321	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951813	2951813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377327574	NA	P-0011297-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	113	629	0	ENST00000396946.4:c.3137C>T	p.Ala1046Val	p.A1046V	ENST00000396946	NM_032415.4	1046	gCc/gTc	23/25	0.180463838811025	3	FACETS	1	0.973	1	0.621	0.557	0.688	CLONAL	1	TRUE	1	0.211017775516599	3		629	954	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0011297-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	52	381	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.99	0.843	1	0.99	0.843	1	CLONAL	1	TRUE	1	0.211017775516599	2		382	498	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713479	40713479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011297-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	142	416	0	ENST00000373198.4:c.4036G>A	p.Asp1346Asn	p.D1346N	ENST00000373198	NM_133170.3	1346	Gat/Aat	30/32	0.1213572273723	4	FACETS	1	0.949	1	1	0.949	1	INDETERMINATE	2	TRUE	2	0.211017775516599	4		416	771	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576114	88576115	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0011297-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	167	613	0	ENST00000360948.2:c.1558_1559delinsAA	p.Gly520Lys	p.G520K	ENST00000360948	NM_001012338.2	520	GGa/AAa	13/19	0.1213572273723	4	FACETS	0.924	0.848	1	0.924	0.848	1	INDETERMINATE	2	TRUE	2	0.211017775516599	4		613	1037	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0011302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	224	415	1	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	1	2	FACETS	0.859	0.799	0.921	0.859	0.799	0.921	CLONAL	1	TRUE	1	0.446087154299723	2		416	1169	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584787	48584787	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	365	643	2	ENST00000342988.3:c.865C>T	p.Gln289Ter	p.Q289*	ENST00000342988	NM_005359.5	289	Cag/Tag	7/12	0.446087154299723	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.446087154299723	1		645	1253	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807335	1807335	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1448843898	NA	P-0011302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	257	498	0	ENST00000260795.2:c.1584G>A	p.Met528Ile	p.M528I	ENST00000260795		528	atG/atA	11/17	1	2	FACETS	0.831	0.776	0.887	0.831	0.776	0.887	CLONAL	1	TRUE	1	0.446087154299723	2		498	1387	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317010	11317010	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	121	379	1	ENST00000361445.4:c.484G>A	p.Glu162Lys	p.E162K	ENST00000361445	NM_004958.3	162	Gag/Aag	4/58	1	2	FACETS	0.492	0.444	0.544	0.492	0.444	0.544	SUBCLONAL	1	TRUE	1	0.446087154299723	2		380	1102	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202780	16202780	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	293	563	0	ENST00000375759.3:c.488G>C	p.Arg163Thr	p.R163T	ENST00000375759	NM_015001.2	163	aGa/aCa	3/15	1	2	FACETS	0.941	0.884	1	0.941	0.884	1	CLONAL	1	TRUE	1	0.446087154299723	2		563	1396	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259202	16259202	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs142682023	NA	P-0011302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	113	294	0	ENST00000375759.3:c.6467C>G	p.Ser2156Cys	p.S2156C	ENST00000375759	NM_015001.2	2156	tCt/tGt	11/15	1	2	FACETS	0.626	0.563	0.693	0.626	0.563	0.693	SUBCLONAL	1	TRUE	1	0.446087154299723	2		294	809	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578223	226578223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	246	426	0	ENST00000366794.5:c.505G>A	p.Glu169Lys	p.E169K	ENST00000366794	NM_001618.3	169	Gag/Aag	4/23	1	2	FACETS	0.985	0.92	1	0.985	0.92	1	CLONAL	1	TRUE	1	0.446087154299723	2		426	1120	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155394	99155394	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	224	433	0	ENST00000074304.5:c.620G>C	p.Gly207Ala	p.G207A	ENST00000074304	NM_001134224.1	207	gGa/gCa	9/26	1	2	FACETS	0.897	0.834	0.961	0.897	0.834	0.961	CLONAL	1	TRUE	1	0.446087154299723	2		433	1120	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164456	47164456	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	236	506	0	ENST00000409792.3:c.1670C>G	p.Ser557Cys	p.S557C	ENST00000409792	NM_014159.6	557	tCt/tGt	3/21	0.446087154299723	1	FACETS	0.9	0.841	0.961	0.9	0.841	0.961	CLONAL	1	TRUE	0	0.446087154299723	1		506	913	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164984	47164984	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0011302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	153	265	0	ENST00000409792.3:c.1142C>G	p.Ser381Ter	p.S381*	ENST00000409792	NM_014159.6	381	tCa/tGa	3/21	0.446087154299723	1	FACETS	0.917	0.843	0.994	0.917	0.843	0.994	CLONAL	1	TRUE	0	0.446087154299723	1		265	581	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536199	106536199	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	261	478	1	ENST00000369096.4:c.166G>A	p.Glu56Lys	p.E56K	ENST00000369096	NM_001198.3	56	Gag/Aag	2/7	0.446087154299723	1	FACETS	0.937	0.879	0.997	0.937	0.879	0.997	CLONAL	1	TRUE	0	0.446087154299723	1		479	970	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513193	106513193	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	53	288	0	ENST00000359195.3:c.2097G>C	p.Leu699Phe	p.L699F	ENST00000359195	NM_002649.2	699	ttG/ttC	4/11	1	2	FACETS	0.316	0.269	0.368	0.316	0.269	0.368	SUBCLONAL	1	TRUE	1	0.446087154299723	2		288	752	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485263	8485263	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	227	453	2	ENST00000356435.5:c.3117G>C	p.Glu1039Asp	p.E1039D	ENST00000356435		1039	gaG/gaC	18/35	1	2	FACETS	0.88	0.819	0.944	0.88	0.819	0.944	CLONAL	1	TRUE	1	0.446087154299723	2		455	1156	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104375128	104375128	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	222	482	0	ENST00000369902.3:c.1126G>C	p.Glu376Gln	p.E376Q	ENST00000369902	NM_016169.3	376	Gag/Cag	9/12	1	2	FACETS	0.834	0.775	0.895	0.834	0.775	0.895	CLONAL	1	TRUE	1	0.446087154299723	2		482	1193	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170605	108170605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	124	289	0	ENST00000278616.4:c.5170G>A	p.Glu1724Lys	p.E1724K	ENST00000278616	NM_000051.3	1724	Gaa/Aaa	34/63	1	2	FACETS	0.82	0.743	0.901	0.82	0.743	0.901	CLONAL	1	TRUE	1	0.446087154299723	2		289	678	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514032	103514032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778295	NA	P-0011302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	182	333	1	ENST00000355739.4:c.848C>T	p.Ser283Phe	p.S283F	ENST00000355739	NM_000123.3	283	tCt/tTt	7/15	1	2	FACETS	0.954	0.881	1	0.954	0.881	1	CLONAL	1	TRUE	1	0.446087154299723	2		334	855	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023397	33023397	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1458654619	NA	P-0011302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1891	499	1094	0	ENST00000300177.4:c.506G>C	p.Arg169Thr	p.R169T	ENST00000300177	NM_001191322.1	169	aGa/aCa	2/2	1	2	FACETS	0.936	0.892	0.981	0.936	0.892	0.981	CLONAL	1	TRUE	1	0.446087154299723	2		1094	2390	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346918	89346918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775544970	NA	P-0011302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	56	409	0	ENST00000301030.4:c.6032C>T	p.Ser2011Leu	p.S2011L	ENST00000301030	NM_001256183.1	2011	tCg/tTg	9/13	1	2	FACETS	0.245	0.209	0.285	0.245	0.209	0.285	SUBCLONAL	1	TRUE	1	0.446087154299723	2		409	1025	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955076	17955076	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	248	430	0	ENST00000458235.1:c.151G>T	p.Glu51Ter	p.E51*	ENST00000458235	NM_000215.3	51	Gag/Tag	2/24	1	2	FACETS	0.963	0.899	1	0.963	0.899	1	CLONAL	1	TRUE	1	0.446087154299723	2		430	1155	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341246	70341246	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1485	307	545	2	ENST00000374080.3:c.805G>A	p.Glu269Lys	p.E269K	ENST00000374080		269	Gag/Aag	6/45	0.415520811999189	3	FACETS	0.939	0.882	0.998	0.47	0.441	0.499	CLONAL	1	TRUE	1	0.446087154299723	3		547	1792	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426801	47426806	+	inframe_deletion	In_Frame_Del	DEL	AGGCTT	AGGCTT	-	novel	NA	P-0011302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	472	405	0	ENST00000377045.4:c.1046_1051del	p.Gln349_Phe351delinsLeu	p.Q349_F351delinsL	ENST00000377045	NM_001654.4	349	cAGGCTTtc/ctc	10/16	0.415520811999189	3	FACETS	0.956	0.914	0.999	0.956	0.914	0.999	CLONAL	2	TRUE	1	0.446087154299723	3		405	1353	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272308	38272308	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs869320694	NA	P-0011325-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	337	544	0	ENST00000425967.3:c.2059A>G	p.Lys687Glu	p.K687E	ENST00000425967	NM_001174067.1	687	Aag/Gag	15/19	0.434965833486897	3	FACETS	0.882	0.846	0.916	1	0.993	1	CLONAL	4	TRUE	0	0.434965833486897	3		544	535	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686237	117686237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769418999	NA	P-0011325-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	110	361	0	ENST00000368508.3:c.3104G>A	p.Arg1035Gln	p.R1035Q	ENST00000368508	NM_002944.2	1035	cGa/cAa	20/43	0.253177273682545	4	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.434965833486897	4		361	520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0011328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	221	360	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.358567679183053	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.384019563751068	2		361	538	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546335	46546335	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	253	514	0	ENST00000262741.5:c.194G>A	p.Trp65Ter	p.W65*	ENST00000262741	NM_003629.3	65	tGg/tAg	2/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.384019563751068	2		514	1208	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750595	128750595	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	409	531	0	ENST00000377970.2:c.132G>T	p.Glu44Asp	p.E44D	ENST00000377970	NM_002467.4	44	gaG/gaT	2/3	0.376783150859667	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.384019563751068	4		531	1348	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404650	8404650	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	49	327	0	ENST00000356435.5:c.4097C>T	p.Pro1366Leu	p.P1366L	ENST00000356435		1366	cCt/cTt	25/35	0.380894383618213	2	FACETS	0.339	0.286	0.398	0.17	0.143	0.199	SUBCLONAL	1	TRUE	0	0.384019563751068	2		327	752	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18762502	18762502	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	178	433	0	ENST00000266497.5:c.3998A>G	p.Gln1333Arg	p.Q1333R	ENST00000266497		1333	cAg/cGg	29/31	NA	2	FACETS	0.951	0.876	1			1	INDETERMINATE	1	TRUE	NA	0.384019563751068	2		433	975	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445527	49445527	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200106242	NA	P-0011328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	403	429	1	ENST00000301067.7:c.1939C>A	p.Pro647Thr	p.P647T	ENST00000301067	NM_003482.3	647	Cca/Aca	10/54	0.306862784877586	4	FACETS	0.858	0.818	0.9	1	0.994	1	CLONAL	3	TRUE	2	0.384019563751068	4		430	1128	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828390	72828390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752003949	NA	P-0011328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	425	724	0	ENST00000268489.5:c.8191C>T	p.Arg2731Trp	p.R2731W	ENST00000268489	NM_006885.3	2731	Cgg/Tgg	9/10	1	2	FACETS	0.772	0.735	0.81	1	0.996	1	SUBCLONAL	2	TRUE	1	0.384019563751068	2		724	1434	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117935	70117935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	185	231	0	ENST00000245479.2:c.403C>T	p.Leu135Phe	p.L135F	ENST00000245479	NM_000346.3	135	Ctc/Ttc	1/3	0.340235110982721	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.384019563751068	3		231	536	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105527	11105527	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	208	273	0	ENST00000358026.2:c.1443G>T	p.Gln481His	p.Q481H	ENST00000358026	NM_001128849.1	481	caG/caT	9/36	0.384019563751068	2	FACETS	0.788	0.735	0.843	0.788	0.735	0.843	SUBCLONAL	2	TRUE	0	0.384019563751068	2		273	687	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141559	11141559	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	448	435	0	ENST00000358026.2:c.3536A>G	p.Asn1179Ser	p.N1179S	ENST00000358026	NM_001128849.1	1179	aAt/aGt	25/36	0.384019563751068	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.384019563751068	2		435	941	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056343	27056344	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0011328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	76	175	0	ENST00000324856.7:c.1341_1342del	p.Gln449AlafsTer173	p.Q449Afs*173	ENST00000324856	NM_006015.4	447	TAt/t	2/20	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.384019563751068	2		175	392	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105593	27105594	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGTG	novel	NA	P-0011328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	155	515	0	ENST00000324856.7:c.5209_5212dup	p.Asp1738GlyfsTer2	p.D1738Gfs*2	ENST00000324856	NM_006015.4	1735	gag/gaGGTGg	20/20	1	2	FACETS	0.685	0.625	0.747	0.685	0.625	0.747	SUBCLONAL	1	TRUE	1	0.384019563751068	2		515	1179	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231130	53231130	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	97	229	0	ENST00000375401.3:c.1772G>T	p.Gly591Val	p.G591V	ENST00000375401	NM_004187.3	591	gGa/gTa	13/26	1	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.267371022970581	1		229	459	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52661289	52661289	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	111	534	0	ENST00000394830.3:c.1541G>T	p.Ser514Ile	p.S514I	ENST00000394830	NM_018313.4	514	aGt/aTt	14/30	0.267371022970581	1	FACETS	0.944	0.849	1	0.944	0.849	1	CLONAL	1	TRUE	0	0.267371022970581	1		534	762	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569782	67569782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	86	340	0	ENST00000274335.5:c.443C>T	p.Thr148Ile	p.T148I	ENST00000274335		148	aCt/aTt	3/15	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.267371022970581	2		340	556	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0011341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	32	586	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.56	0.452	0.682	0.56	0.452	0.682	SUBCLONAL	1	TRUE	1	0.14	2		586	817	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0011341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	27	360	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.664	0.527	0.822	0.664	0.527	0.822	SUBCLONAL	1	TRUE	1	0.14	2		361	581	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0011361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	171	939	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.491029862518583	2		940	677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0011361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	182	391	0	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	0.491029862518583	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.491029862518583	1		391	522	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593491	48593494	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	rs80338965	NA	P-0011361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	24	323	0	ENST00000342988.3:c.1245_1248del	p.Asp415GlufsTer20	p.D415Efs*20	ENST00000342988	NM_005359.5	414	ttAGAC/tt	10/12	0.491029862518583	1	FACETS	0.186	0.145	0.233	0.186	0.145	0.233	SUBCLONAL	1	TRUE	0	0.491029862518583	1		323	397	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953760	48953760	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913302	NA	P-0011368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	147	277	1	ENST00000267163.4:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000267163	NM_000321.2	455	Cga/Tga	14/27	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.31	2		278	898	SUCCESS
AR	367	MSKCC	GRCh37	X	66937372	66937372	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	252	318	0	ENST00000374690.3:c.2226G>C	p.Trp742Cys	p.W742C	ENST00000374690	NM_000044.3	742	tgG/tgC	5/8	1	1	FACETS	0.801	0.751	0.852	1	0.994	1	CLONAL	2	TRUE	0	0.31	1		318	858	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519233	137519233	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	435	445	0	ENST00000367739.4:c.1405G>A	p.Asp469Asn	p.D469N	ENST00000367739	NM_000416.2	469	Gat/Aat	7/7	0.247101928435944	2	FACETS	0.993	0.946	1	0.993	0.946	1	CLONAL	2	TRUE	0	0.31	2		445	1413	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0011371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	63	405	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.939	0.81	1	0.939	0.81	1	CLONAL	1	TRUE	1	0.15	2		405	895	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117584	4117584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519809	NA	P-0011371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	36	360	0	ENST00000262948.5:c.136C>T	p.Leu46Phe	p.L46F	ENST00000262948	NM_030662.3	46	Ctt/Ttt	2/11	1	2	FACETS	0.787	0.645	0.946	0.787	0.645	0.946	CLONAL	1	TRUE	1	0.15	2		360	610	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149251	119149251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267606708	NA	P-0011378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	263	551	0	ENST00000264033.4:c.1259G>A	p.Arg420Gln	p.R420Q	ENST00000264033	NM_005188.3	420	cGa/cAa	9/16	NA	2	FACETS	0.784	0.735	0.834			1	INDETERMINATE	2	TRUE	NA	0.329805610902462	2		551	1017	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579366	7579366	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0011378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	202	385	0	ENST00000269305.4:c.321C>G	p.Tyr107Ter	p.Y107*	ENST00000269305	NM_001126112.2	107	taC/taG	4/11	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.329805610902462	2		385	849	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784399	9784399	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	102	517	0	ENST00000377346.4:c.2784G>T	p.Glu928Asp	p.E928D	ENST00000377346	NM_005026.3	928	gaG/gaT	22/24	1	2	FACETS	0.693	0.619	0.772	0.693	0.619	0.772	SUBCLONAL	1	TRUE	1	0.329805610902462	2		517	893	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841474	156841474	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1317408795	NA	P-0011378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	175	351	0	ENST00000524377.1:c.777C>A	p.Asn259Lys	p.N259K	ENST00000524377	NM_002529.3	259	aaC/aaA	7/17	0.263779599343133	3	FACETS	0.787	0.726	0.851	0.787	0.726	0.851	SUBCLONAL	2	TRUE	1	0.329805610902462	3		351	785	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266250	198266250	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0011378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	54	208	0	ENST00000335508.6:c.2371-1G>T		p.X791_splice	ENST00000335508	NM_012433.2	791			0.263779599343133	3	FACETS	0.833	0.713	0.964	0.416	0.356	0.482	CLONAL	1	TRUE	1	0.329805610902462	3		208	458	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741873	17741873	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	24	41	0	ENST00000250003.3:c.544G>T	p.Gly182Cys	p.G182C	ENST00000250003	NM_002478.4	182	Ggc/Tgc	1/3	0.329805610902462	3	FACETS	1	0.862	1	1	0.862	1	CLONAL	2	TRUE	1	0.329805610902462	3		41	78	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100460	102100460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	244	519	0	ENST00000282441.5:c.1304C>T	p.Pro435Leu	p.P435L	ENST00000282441	NM_001130145.2	435	cCc/cTc	9/9	0.241835658924428	2	FACETS	0.793	0.742	0.846	0.793	0.742	0.846	SUBCLONAL	2	TRUE	0	0.329805610902462	2		519	933	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121511	2121511	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs397515199	NA	P-0011378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	111	369	0	ENST00000219476.3:c.1840G>T	p.Ala614Ser	p.A614S	ENST00000219476	NM_000548.3	614	Gcc/Tcc	18/42	0.298705363488203	3	FACETS	0.816	0.732	0.905	0.408	0.366	0.453	CLONAL	1	TRUE	1	0.329805610902462	3		369	961	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044973	47044973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	196	209	0	ENST00000377604.3:c.2299C>T	p.Gln767Ter	p.Q767*	ENST00000377604	NM_001204468.1	767	Cag/Tag	20/24	0.329805610902462	2	FACETS	0.852	0.797	0.907			1	CLONAL	3	TRUE	NA	0.329805610902462	2		209	465	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0011381-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	237	724	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	0.454962787773242	4	FACETS	0.965	0.917	1	0.724	0.688	0.759	CLONAL	3	TRUE	0	0.692841485228232	4		724	400	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594258	55594258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913523	NA	P-0011381-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	81	384	0	ENST00000288135.5:c.1961T>C	p.Val654Ala	p.V654A	ENST00000288135	NM_000222.2	654	gTg/gCg	13/21	0.454962787773242	4	FACETS	0.726	0.641	0.817	0.182	0.16	0.205	SUBCLONAL	1	TRUE	0	0.692841485228232	4		384	545	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609809	117609809	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011381-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	168	752	0	ENST00000368508.3:c.6890C>A	p.Ser2297Tyr	p.S2297Y	ENST00000368508	NM_002944.2	2297	tCt/tAt	43/43	0.451292501041604	3	FACETS	0.76	0.699	0.824	0.253	0.233	0.275	SUBCLONAL	1	TRUE	0	0.692841485228232	3		752	859	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952030	178952030	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1290	469	696	0	ENST00000263967.3:c.3085G>C	p.Asp1029His	p.D1029H	ENST00000263967	NM_006218.2	1029	Gat/Cat	21/21	0.3	9	FACETS	0.907	0.864	0.95			1	CLONAL	5	TRUE	NA	0.2	9		696	1759	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	rs886039483	NA	P-0011388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	56	551	1	ENST00000269305.4:c.376T>G	p.Tyr126Asp	p.Y126D	ENST00000269305	NM_001126112.2	126	Tac/Gac	5/11	0.245099642273066	1	FACETS	0.85	0.728	0.983	0.85	0.728	0.983	CLONAL	1	TRUE	0	0.2	1		552	593	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951889	178951889	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	382	533	0	ENST00000263967.3:c.2944G>C	p.Glu982Gln	p.E982Q	ENST00000263967	NM_006218.2	982	Gag/Cag	21/21	0.3	9	FACETS	0.908	0.861	0.956			1	CLONAL	5	TRUE	NA	0.2	9		533	1430	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952078	178952078	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	471	644	0	ENST00000263967.3:c.3133G>A	p.Asp1045Asn	p.D1045N	ENST00000263967	NM_006218.2	1045	Gat/Aat	21/21	0.3	9	FACETS	0.979	0.935	1			1	CLONAL	5	TRUE	NA	0.2	9		644	1635	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797222	135797222	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs118203416	NA	P-0011388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	117	807	0	ENST00000298552.3:c.647T>C	p.Phe216Ser	p.F216S	ENST00000298552	NM_001162426.1	216	tTt/tCt	7/23	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.2	2		807	924	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244523	46244523	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	76	712	0	ENST00000334344.6:c.2617G>T	p.Ala873Ser	p.A873S	ENST00000334344	NM_152641.2	873	Gct/Tct	15/21	1	2	FACETS	0.831	0.727	0.943	0.831	0.727	0.943	CLONAL	1	TRUE	1	0.2	2		712	915	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431121	49431121	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	63	731	2	ENST00000301067.7:c.10018C>T	p.Gln3340Ter	p.Q3340*	ENST00000301067	NM_003482.3	3340	Cag/Tag	34/54	1	2	FACETS	0.912	0.788	1	0.912	0.788	1	CLONAL	1	TRUE	1	0.2	2		733	691	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952164	76952164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	83	1030	0	ENST00000373344.5:c.271G>A	p.Glu91Lys	p.E91K	ENST00000373344	NM_000489.3	91	Gaa/Aaa	5/35	1	2	FACETS	0.726	0.638	0.82	0.726	0.638	0.82	SUBCLONAL	1	TRUE	1	0.2	2		1030	1144	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0011398-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	465	559	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.709456657618244	1	FACETS	0.996	0.959	1	0.996	0.959	1	CLONAL	1	TRUE	0	0.709456657618244	1		559	849	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936983	48936983	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690863	NA	P-0011398-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	374	406	0	ENST00000267163.4:c.751C>T	p.Arg251Ter	p.R251*	ENST00000267163	NM_000321.2	251	Cga/Tga	8/27	0.709456657618244	1	FACETS	0.973	0.932	1	0.973	0.932	1	CLONAL	1	TRUE	0	0.709456657618244	1		406	699	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11175476	11175476	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011398-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1254	79	494	0	ENST00000361445.4:c.7066A>T	p.Ile2356Phe	p.I2356F	ENST00000361445	NM_004958.3	2356	Att/Ttt	51/58	1	2	FACETS	0.167	0.146	0.19	0.167	0.146	0.19	SUBCLONAL	1	TRUE	1	0.709456657618244	2		494	1333	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382151	152382151	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011398-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	298	305	0	ENST00000206249.3:c.1261A>G	p.Met421Val	p.M421V	ENST00000206249	NM_000125.3	421	Atg/Gtg	6/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.709456657618244	2		305	801	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317879	8317879	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011398-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	352	449	0	ENST00000356435.5:c.5734A>G	p.Thr1912Ala	p.T1912A	ENST00000356435		1912	Acg/Gcg	35/35	1	2	FACETS	0.955	0.906	1	0.955	0.906	1	CLONAL	1	TRUE	1	0.709456657618244	2		449	1039	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0011426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	317	406	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.425209058985374	4	FACETS	0.975	0.921	1	0.975	0.921	1	CLONAL	2	TRUE	2	0.425145854868267	4		406	1090	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023307	27023307	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0011426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	52	126	0	ENST00000324856.7:c.413C>G	p.Ser138Ter	p.S138*	ENST00000324856	NM_006015.4	138	tCa/tGa	1/20	0.424570894790271	3	FACETS	1	0.859	1	0.501	0.429	0.579	CLONAL	1	TRUE	1	0.425145854868267	3		126	296	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699360	47699360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	767	554	0	ENST00000347630.2:c.148G>A	p.Glu50Lys	p.E50K	ENST00000347630	NM_001007230.1	50	Gaa/Aaa	4/11	0.425145854868267	5	FACETS	0.946	0.917	0.976	0.946	0.917	0.976	CLONAL	4	TRUE	1	0.425145854868267	5		554	1561	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087558	27087558	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0011426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	320	446	0	ENST00000324856.7:c.2132C>G	p.Ser711Ter	p.S711*	ENST00000324856	NM_006015.4	711	tCa/tGa	5/20	0.424570894790271	3	FACETS	0.994	0.941	1	0.994	0.941	1	CLONAL	2	TRUE	1	0.425145854868267	3		446	918	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157256633	157256633	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554270809	NA	P-0011426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	189	534	0	ENST00000346085.5:c.1960C>T	p.Gln654Ter	p.Q654*	ENST00000346085	NM_020732.3	654	Caa/Taa	5/20	0.425145854868267	3	FACETS	0.918	0.847	0.992	0.306	0.282	0.331	CLONAL	1	TRUE	0	0.425145854868267	3		534	1174	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702630	52702630	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	319	366	0	ENST00000394830.3:c.268C>T	p.Gln90Ter	p.Q90*	ENST00000394830	NM_018313.4	90	Cag/Tag	4/30	0.353340907175957	3	FACETS	1	0.99	1	0.778	0.738	0.818	CLONAL	2	TRUE	0	0.425145854868267	3		366	780	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38996928	38996928	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1501	86	380	0	ENST00000357387.3:c.449T>C	p.Val150Ala	p.V150A	ENST00000357387	NM_152756.3	150	gTc/gCc	6/38	0.425145854868267	6	FACETS	0.472	0.415	0.533	0.118	0.103	0.134	SUBCLONAL	1	TRUE	2	0.425145854868267	6		380	1587	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168749	56168749	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	282	393	0	ENST00000399503.3:c.1603C>T	p.Gln535Ter	p.Q535*	ENST00000399503	NM_005921.1	535	Caa/Taa	9/20	0.424570894790271	3	FACETS	0.959	0.904	1	0.959	0.904	1	CLONAL	2	TRUE	1	0.425145854868267	3		393	839	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120699	115120699	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1374	219	651	1	ENST00000257566.3:c.307C>A	p.Pro103Thr	p.P103T	ENST00000257566	NM_016569.3	103	Ccc/Acc	1/8	0.425145854868267	5	FACETS	1	0.963	1	0.353	0.327	0.38	CLONAL	1	TRUE	2	0.425145854868267	5		652	1593	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953234	81953234	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	557	751	0	ENST00000359376.3:c.2200C>T	p.Pro734Ser	p.P734S	ENST00000359376	NM_002661.3	734	Ccc/Tcc	20/33	0.420907675806843	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.425145854868267	2		751	1308	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0011449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	391	536	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.35347606893069	2	FACETS	0.939	0.895	0.984	0.939	0.895	0.984	CLONAL	2	TRUE	0	0.410929630881351	2		536	1013	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530425	187530425	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0011449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	140	411	0	ENST00000441802.2:c.10118C>G	p.Ser3373Ter	p.S3373*	ENST00000441802	NM_005245.3	3373	tCa/tGa	16/27	0.35347606893069	2	FACETS	0.823	0.75	0.9	0.411	0.375	0.45	CLONAL	1	TRUE	0	0.410929630881351	2		411	828	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846011	151846011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs183426496	NA	P-0011449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	232	315	1	ENST00000262189.6:c.13001G>A	p.Arg4334Gln	p.R4334Q	ENST00000262189	NM_170606.2	4334	cGg/cAg	52/59	0.3642910071168	3	FACETS	0.927	0.868	0.988	0.927	0.868	0.988	CLONAL	2	TRUE	1	0.410929630881351	3		316	734	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202650	108202650	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	208	284	1	ENST00000278616.4:c.7674T>A	p.Phe2558Leu	p.F2558L	ENST00000278616	NM_000051.3	2558	ttT/ttA	52/63	0.35347606893069	2	FACETS	0.849	0.793	0.906	0.849	0.793	0.906	CLONAL	2	TRUE	0	0.410929630881351	2		285	596	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634378	23634378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	203	498	0	ENST00000261584.4:c.2908C>T	p.Leu970Phe	p.L970F	ENST00000261584	NM_024675.3	970	Ctt/Ttt	9/13	0.370971221110984	3	FACETS	0.942	0.871	1	0.314	0.29	0.339	CLONAL	1	TRUE	0	0.410929630881351	3		498	1265	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509397	46509764	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTGAGGGAGTCGTTGTGCTGAACCAAGGATGTCTGCTGGTAATGGAGCACTAGCTCCTTCAGAGAGCTGTACAGGTTGTAGGGCTCTGCAAAGCCATAGCCCCGAGCAGTGCTGTAGATCACACAGTGCTTCACTTCCCCATCGGCCCTGCAATGACAAACCACAGAAGAAATGTTAAGGTAGGTAACAATAGATAAAAGGACACTAAATGGCCAGAAGTCTGAGAGCAATTGTTATGCAAACAAGTGTTTTTTGTTAACCAGGCAAAGCTTGTGAAATTGCGTTCCCATTCCCTACAGACTTGGCCACAGATACGGGTGTTAAAACAACCACAAATGTAAGGGTTTATTTATTTCTTTTTTTTTTTT	TTGAGGGAGTCGTTGTGCTGAACCAAGGATGTCTGCTGGTAATGGAGCACTAGCTCCTTCAGAGAGCTGTACAGGTTGTAGGGCTCTGCAAAGCCATAGCCCCGAGCAGTGCTGTAGATCACACAGTGCTTCACTTCCCCATCGGCCCTGCAATGACAAACCACAGAAGAAATGTTAAGGTAGGTAACAATAGATAAAAGGACACTAAATGGCCAGAAGTCTGAGAGCAATTGTTATGCAAACAAGTGTTTTTTGTTAACCAGGCAAAGCTTGTGAAATTGCGTTCCCATTCCCTACAGACTTGGCCACAGATACGGGTGTTAAAACAACCACAAATGTAAGGGTTTATTTATTTCTTTTTTTTTTTT	-	novel	NA	P-0011449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	70	427	0	ENST00000262741.5:c.1188-221_1334del		p.X396_splice	ENST00000262741	NM_003629.3	396		10/10	0.35347606893069	2	FACETS	0.41	0.357	0.468	0.205	0.178	0.234	SUBCLONAL	1	TRUE	0	0.410929630881351	2		427	831	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720869	89720870	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0011449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	182	201	0	ENST00000371953.3:c.1022_1023del	p.Phe341Ter	p.F341*	ENST00000371953	NM_000314.4	340	aaTTtt/aatt	8/9	NA	2	FACETS	1	0.955	1			1	INDETERMINATE	2	TRUE	NA	0.410929630881351	2		201	430	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0011452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	39	467	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	1	2	FACETS	0.883	0.73	1	0.883	0.73	1	CLONAL	1	TRUE	1	0.12	2		467	736	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449796	29449796	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	56	362	0	ENST00000389048.3:c.3059C>G	p.Ser1020Cys	p.S1020C	ENST00000389048	NM_004304.4	1020	tCc/tGc	18/29	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.12	2		362	724	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100429	8100429	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	59	606	0	ENST00000346208.3:c.403C>A	p.Pro135Thr	p.P135T	ENST00000346208		135	Ccg/Acg	3/6	1	2	FACETS	0.872	0.747	1	0.872	0.747	1	CLONAL	1	TRUE	1	0.12	2		606	1128	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715770	18715770	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	49	322	0	ENST00000266497.5:c.3601A>C	p.Thr1201Pro	p.T1201P	ENST00000266497		1201	Aca/Cca	25/31	1	2	FACETS	0.845	0.713	0.991	0.845	0.713	0.991	CLONAL	1	TRUE	1	0.12	2		322	967	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486104	8486104	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	58	483	0	ENST00000356435.5:c.2713del	p.Glu905ArgfsTer4	p.E905Rfs*4	ENST00000356435		905	Gag/ag	17/35	1	2	FACETS	0.918	0.786	1	0.918	0.786	1	CLONAL	1	TRUE	1	0.12	2		483	1053	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246445	105246445	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	314	579	0	ENST00000349310.3:c.155T>G	p.Leu52Arg	p.L52R	ENST00000349310	NM_001014432.1	52	cTc/cGc	4/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.449312823876087	2		579	1235	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063321	67063321	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	126	252	0	ENST00000412916.2:c.11T>G	p.Val4Gly	p.V4G	ENST00000412916		4	gTc/gGc	1/6	0.449312823876087	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.449312823876087	1		252	416	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0011469-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	90	939	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.246294879122786	1	FACETS	0.852	0.756	0.955	0.852	0.756	0.955	CLONAL	1	TRUE	0	0.246294879122786	1		940	752	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757274881	NA	P-0011469-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	120	307	2	ENST00000269305.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	144	Cag/Tag	5/11	0.246294879122786	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.246294879122786	1		309	805	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48586235	48586235	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1555686070	NA	P-0011469-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	89	240	0	ENST00000342988.3:c.905-1G>A		p.X302_splice	ENST00000342988	NM_005359.5	302			0.230768855959434	1	FACETS	0.973	0.864	1	0.973	0.864	1	CLONAL	1	TRUE	0	0.246294879122786	1		240	651	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0011500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	349	432	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.929	0.884	0.973	0.929	0.884	0.973	CLONAL	1	TRUE	1	0.935904867705952	2		432	803	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043647	6043647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881914	NA	P-0011500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	133	375	0	ENST00000265849.7:c.206C>T	p.Ser69Leu	p.S69L	ENST00000265849	NM_000535.5	69	tCa/tTa	3/15	1	2	FACETS	0.64	0.586	0.696	0.64	0.586	0.696	SUBCLONAL	1	TRUE	1	0.935904867705952	2		375	444	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038846	47038846	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	239	121	0	ENST00000377604.3:c.853C>T	p.Gln285Ter	p.Q285*	ENST00000377604	NM_001204468.1	285	Caa/Taa	9/24	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.935904867705952	1		121	257	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0011507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	402	633	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	1	2	FACETS	0.955	0.909	1	0.955	0.909	1	CLONAL	1	TRUE	1	0.742735168014566	2		633	1134	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433650	49433650	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs794727549	NA	P-0011523-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	323	556	1	ENST00000301067.7:c.7903C>T	p.Arg2635Ter	p.R2635*	ENST00000301067	NM_003482.3	2635	Cga/Tga	31/54	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.852652201539018	2		557	729	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813334	102813334	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1430553116	NA	P-0011523-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	32	493	1	ENST00000307046.8:c.355C>T	p.Arg119Cys	p.R119C	ENST00000307046	NM_001111285.1	119	Cgc/Tgc	3/4	NA	2	FACETS	0.218	0.176	0.264			1	INDETERMINATE	1	TRUE	NA	0.852652201539018	2		494	345	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271892	15271892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011523-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	208	225	0	ENST00000263388.2:c.6547C>T	p.Pro2183Ser	p.P2183S	ENST00000263388	NM_000435.2	2183	Ccc/Tcc	33/33	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.852652201539018	2		225	374	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969322	44969322	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0011523-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	375	486	0	ENST00000377967.4:c.4006-2A>T		p.X1336_splice	ENST00000377967	NM_021140.2	1336			0.852652201539018	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.852652201539018	1		486	473	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-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	163	257	0	ENST00000263253.7:c.2132-44_2223del		p.X711_splice	ENST00000263253	NM_001429.3	711		12/31	0.672566561223074	3	FACETS	1	0.957	1			1	CLONAL	1	TRUE	NA	0.852652201539018	3		257	519	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097776	27097788	+	frameshift_variant	Frame_Shift_Del	DEL	ATTCCAAGAAGTC	ATTCCAAGAAGTC	TT	novel	NA	P-0011523-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	313	490	0	ENST00000324856.7:c.3365_3377delinsTT	p.Asp1122ValfsTer67	p.D1122Vfs*67	ENST00000324856	NM_006015.4	1122	gATTCCAAGAAGTCc/gTTc	12/20	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.852652201539018	2		490	577	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0011533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	210	586	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.380565150294789	3	FACETS	0.974	0.909	1	0.65	0.606	0.694	CLONAL	2	TRUE	0	0.380565150294789	3		586	674	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0011533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	28	203	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.274383005675471	3	FACETS	0.598	0.479	0.733	0.299	0.239	0.367	SUBCLONAL	1	TRUE	1	0.380565150294789	3		203	293	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0011533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	129	327	0	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	0.207448812924206	4	FACETS	0.792	0.72	0.866	0.792	0.72	0.866	INDETERMINATE	2	TRUE	2	0.380565150294789	4		327	591	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256439	115256439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774832953	NA	P-0011533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	144	527	0	ENST00000369535.4:c.272C>T	p.Ala91Val	p.A91V	ENST00000369535	NM_002524.4	91	gCg/gTg	3/7	0.274383005675471	3	FACETS	1	0.984	1	0.673	0.615	0.733	CLONAL	1	TRUE	1	0.380565150294789	3		527	669	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652206	48652206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1214	133	641	0	ENST00000376670.3:c.877C>T	p.Arg293Trp	p.R293W	ENST00000376670	NM_002049.3	293	Cgg/Tgg	6/6	0.196736879845633	5	FACETS	0.815	0.738	0.897	0.272	0.246	0.299	INDETERMINATE	1	TRUE	2	0.380565150294789	5		641	1347	SUCCESS
APC	324	MSKCC	GRCh37	5	112175249	112175274	+	frameshift_variant	Frame_Shift_Del	DEL	GTGAGCGAAGTTCCAGCAGTGTCACA	GTGAGCGAAGTTCCAGCAGTGTCACA	-	novel	NA	P-0011533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	74	309	0	ENST00000257430.4:c.3959_3984del	p.Val1320AlafsTer3	p.V1320Afs*3	ENST00000257430	NM_000038.5	1320	GTGAGCGAAGTTCCAGCAGTGTCACAg/g	16/16	0.207448812924206	4	FACETS	0.929	0.814	1	0.464	0.407	0.526	INDETERMINATE	1	TRUE	2	0.380565150294789	4		309	578	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249020	55249022	+	missense_variant	Missense_Mutation	TNP	ACG	ACG	TCA	novel	NA	P-0011543-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	105	416	0	ENST00000275493.2:c.2318_2320delinsTCA	p.His773_Val774delinsLeuMet	p.H773_V774delinsLM	ENST00000275493	NM_005228.3	773	cACGtg/cTCAtg	20/28	0.3	4	FACETS	0.863	0.772	0.96			1	CLONAL	2	TRUE	NA	0.14	4		416	991	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145430	58145430	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894340	NA	P-0011543-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	64	419	0	ENST00000257904.6:c.71G>T	p.Arg24Leu	p.R24L	ENST00000257904	NM_000075.3	24	cGt/cTt	2/8	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.14	2		419	902	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007706	45007707	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCATCCG	novel	NA	P-0011543-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	29	339	0	ENST00000558401.1:c.154_160dup	p.Asp54AlafsTer5	p.D54Afs*5	ENST00000558401	NM_004048.2	51	-/CCATCCG	2/4	1	2	FACETS	0.714	0.572	0.877	0.714	0.572	0.877	SUBCLONAL	1	TRUE	1	0.14	2		339	580	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578509	7578509	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519978	NA	P-0011557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	560	483	0	ENST00000269305.4:c.421T>C	p.Cys141Arg	p.C141R	ENST00000269305	NM_001126112.2	141	Tgc/Cgc	5/11	0.613670319534044	2	FACETS	0.874	0.844	0.904	0.874	0.844	0.904	CLONAL	2	TRUE	0	0.623116601029769	2		483	1028	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976415	25976415	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011560-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	104	582	0	ENST00000435504.4:c.1130A>G	p.Tyr377Cys	p.Y377C	ENST00000435504		377	tAc/tGc	11/13	1	2	FACETS	0.38	0.34	0.422	0.38	0.34	0.422	SUBCLONAL	1	TRUE	1	0.774191603220424	2		582	707	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662717	117662717	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011560-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	215	354	0	ENST00000368508.3:c.4748A>T	p.Lys1583Met	p.K1583M	ENST00000368508	NM_002944.2	1583	aAg/aTg	29/43	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.774191603220424	2		354	535	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347556	118347556	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1064797162	NA	P-0011560-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	233	413	0	ENST00000534358.1:c.3193G>T	p.Gly1065Ter	p.G1065*	ENST00000534358	NM_005933.3	1065	Gga/Tga	4/36	1	2	FACETS	0.825	0.772	0.878	0.825	0.772	0.878	CLONAL	1	TRUE	1	0.774191603220424	2		413	730	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0011566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	115	460	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		460	970	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434595	NA	P-0011566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	57	503	1	ENST00000369535.4:c.37G>A	p.Gly13Ser	p.G13S	ENST00000369535	NM_002524.4	13	Ggt/Agt	2/7	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		504	1087	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44894189	44894189	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012007-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	235	223	0	ENST00000377967.4:c.578C>T	p.Ala193Val	p.A193V	ENST00000377967	NM_021140.2	193	gCt/gTt	7/29	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.69496269530107	1		223	341	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593578	55593598	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACAGAAACCCATGTATGAAGT	ACAGAAACCCATGTATGAAGT	-	novel	NA	P-0012007-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	170	316	0	ENST00000288135.5:c.1648_1668del		p.X550_splice	ENST00000288135	NM_000222.2	550		11/21	0.691482431190808	1	FACETS	0.719	0.668	0.771	0.719	0.668	0.771	SUBCLONAL	1	TRUE	0	0.69496269530107	1		316	444	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0012010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	534	375	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.205134632120463	6	FACETS	0.922	0.886	0.959			1	CLONAL	6	TRUE	NA	0.205134632120463	6		375	1327	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0012010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	103	446	0	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.205134632120463	2		446	946	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024001	27024002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0012010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	21	103	0	ENST00000324856.7:c.1113dup	p.Gln372AlafsTer28	p.Q372Afs*28	ENST00000324856	NM_006015.4	369	-/G	1/20	1	2	FACETS	0.989	0.765	1	0.989	0.765	1	CLONAL	1	TRUE	1	0.205134632120463	2		103	207	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579321	7579322	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs587780067	NA	P-0012010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	78	284	0	ENST00000269305.4:c.365_366del	p.Val122AspfsTer26	p.V122Dfs*26	ENST00000269305	NM_001126112.2	122	gTG/g	4/11	0.198824847535602	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	0	0.205134632120463	1		284	656	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317165	11317165	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	108	509	0	ENST00000361445.4:c.329A>C	p.Tyr110Ser	p.Y110S	ENST00000361445	NM_004958.3	110	tAt/tCt	4/58	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.205134632120463	2		509	1035	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968239	134968239	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	110	421	1	ENST00000398015.3:c.2752G>A	p.Asp918Asn	p.D918N	ENST00000398015	NM_004441.4	918	Gac/Aac	15/16	NA	2	FACETS	1	0.953	1			1	INDETERMINATE	1	TRUE	NA	0.205134632120463	2		422	966	SUCCESS
APC	324	MSKCC	GRCh37	5	112116536	112116536	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200740020	NA	P-0012010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	54	277	0	ENST00000257430.4:c.581G>A	p.Arg194Lys	p.R194K	ENST00000257430	NM_000038.5	194	aGg/aAg	6/16	1	2	FACETS	0.715	0.61	0.831	0.715	0.61	0.831	SUBCLONAL	1	TRUE	1	0.205134632120463	2		277	736	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375865	118375865	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200739718	NA	P-0012010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	82	322	0	ENST00000534358.1:c.9258G>T	p.Gln3086His	p.Q3086H	ENST00000534358	NM_005933.3	3086	caG/caT	27/36	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.205134632120463	2		322	740	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713130	30713131	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0012010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	31	130	0	ENST00000295754.5:c.459_460dup	p.Asn154IlefsTer10	p.N154Ifs*10	ENST00000295754	NM_003242.5	152	gaa/gaATa	4/7	0.205134632120463	1	FACETS	0.929	0.754	1	0.929	0.754	1	CLONAL	1	TRUE	0	0.205134632120463	1		130	292	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273806	18273806	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	230	518	0	ENST00000222254.8:c.1139T>A	p.Val380Asp	p.V380D	ENST00000222254	NM_005027.3	380	gTc/gAc	10/16	1	2	FACETS	0.648	0.604	0.694	0.648	0.604	0.694	SUBCLONAL	1	TRUE	1	0.624714666710274	2		518	1136	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061196	38061197	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTT	novel	NA	P-0012030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	151	212	0	ENST00000250448.2:c.790_792dup	p.Lys264dup	p.K264dup	ENST00000250448	NM_004496.3	264	-/AAG	2/2	1	2	FACETS	0.952	0.876	1	0.952	0.876	1	CLONAL	1	TRUE	1	0.624714666710274	2		212	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0012063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	115	511	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.223153132762847	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.223153132762847	1		511	820	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645694	12645694	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs3730271	NA	P-0012063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	91	410	0	ENST00000251849.4:c.775T>C	p.Ser259Pro	p.S259P	ENST00000251849	NM_002880.3	259	Tcc/Ccc	7/17	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.223153132762847	2		410	804	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073881	8073881	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1348	87	830	1	ENST00000377482.5:c.778C>A	p.Pro260Thr	p.P260T	ENST00000377482	NM_018948.3	260	Cca/Aca	4/4	NA	2	FACETS	0.543	0.479	0.613			1	INDETERMINATE	1	TRUE	NA	0.223153132762847	2		831	1435	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259464	89259464	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	89	604	0	ENST00000336596.2:c.608C>A	p.Pro203Gln	p.P203Q	ENST00000336596	NM_005233.5	203	cCa/cAa	3/17	1	2	FACETS	0.744	0.658	0.837	0.744	0.658	0.837	SUBCLONAL	1	TRUE	1	0.223153132762847	2		604	1072	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119642260	119642260	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1388335197	NA	P-0012063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	127	462	0	ENST00000316626.5:c.437A>G	p.Tyr146Cys	p.Y146C	ENST00000316626		146	tAt/tGt	4/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.223153132762847	2		462	835	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93953207	93953207	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	113	665	1	ENST00000369303.4:c.2934G>T	p.Met978Ile	p.M978I	ENST00000369303	NM_004440.3	978	atG/atT	17/17	0.223153132762847	1	FACETS	0.886	0.795	0.981	0.886	0.795	0.981	CLONAL	1	TRUE	0	0.223153132762847	1		666	1016	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729357	41729357	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1371	74	783	0	ENST00000242208.4:c.1172G>T	p.Cys391Phe	p.C391F	ENST00000242208	NM_002192.2	391	tGt/tTt	3/3	0.161013265195219	2	FACETS	0.459	0.4	0.523	0.229	0.2	0.262	SUBCLONAL	1	TRUE	0	0.223153132762847	2		783	1445	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633395	8633395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	100	557	0	ENST00000356435.5:c.274G>A	p.Asp92Asn	p.D92N	ENST00000356435		92	Gat/Aat	3/35	1	2	FACETS	0.999	0.891	1	0.999	0.891	1	CLONAL	1	TRUE	1	0.223153132762847	2		557	897	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999731	100999731	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1365969218	NA	P-0012063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	73	694	1	ENST00000325455.5:c.71G>T	p.Gly24Val	p.G24V	ENST00000325455	NM_001202474.3	24	gGa/gTa	1/8	1	2	FACETS	0.562	0.489	0.64	0.562	0.489	0.64	SUBCLONAL	1	TRUE	1	0.223153132762847	2		695	1165	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472489	88472489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144852342	NA	P-0012063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	61	511	0	ENST00000360948.2:c.2066C>T	p.Ala689Val	p.A689V	ENST00000360948	NM_001012338.2	689	gCg/gTg	16/19	1	2	FACETS	0.592	0.509	0.683	0.592	0.509	0.683	SUBCLONAL	1	TRUE	1	0.223153132762847	2		511	923	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991344	72991344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148024459	NA	P-0012063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	70	647	0	ENST00000268489.5:c.2701G>A	p.Ala901Thr	p.A901T	ENST00000268489	NM_006885.3	901	Gcc/Acc	2/10	1	2	FACETS	0.529	0.459	0.605	0.529	0.459	0.605	SUBCLONAL	1	TRUE	1	0.223153132762847	2		647	1186	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284960	15284960	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs775797024	NA	P-0012063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	108	393	0	ENST00000263388.2:c.4655A>T	p.Gln1552Leu	p.Q1552L	ENST00000263388	NM_000435.2	1552	cAg/cTg	25/33	0.223153132762847	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.223153132762847	1		393	708	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599938	10599939	+	stop_gained	Nonsense_Mutation	DNP	GA	GA	TT	novel	NA	P-0012063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	105	585	1	ENST00000171111.5:c.1637_1638delinsAA	p.Phe546Ter	p.F546*	ENST00000171111	NM_203500.1	546	tTC/tAA	5/6	0.223153132762847	1	FACETS	0.861	0.77	0.958	0.861	0.77	0.958	CLONAL	1	TRUE	0	0.223153132762847	1		586	971	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0012066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	54	461	2	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	1	2	FACETS	0.859	0.732	0.998	0.859	0.732	0.998	CLONAL	1	TRUE	1	0.16	2		463	786	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584513	48584514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs377767334	NA	P-0012066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	53	287	0	ENST00000342988.3:c.692dup	p.Ser232GlnfsTer3	p.S232Qfs*3	ENST00000342988	NM_005359.5	229	ctg/ctGg	6/12	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.16	2		287	609	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127425	17127425	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	40	369	0	ENST00000285071.4:c.429C>A	p.Phe143Leu	p.F143L	ENST00000285071	NM_144997.5	143	ttC/ttA	6/14	1	2	FACETS	0.949	0.788	1	0.949	0.788	1	CLONAL	1	TRUE	1	0.16	2		369	527	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0012083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	163	399	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.295062370077438	5	FACETS	0.886	0.823	0.95	1	0.982	1	CLONAL	4	TRUE	2	0.344373362722328	5		399	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578206	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs886039484	NA	P-0012083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	120	724	0	ENST00000269305.4:c.643A>C	p.Ser215Arg	p.S215R	ENST00000269305	NM_001126112.2	215	Agt/Cgt	6/11	0.15526045751726	3	FACETS	0.835	0.764	0.908	0.835	0.764	0.908	INDETERMINATE	3	TRUE	0	0.344373362722328	3		724	326	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225685	26225685	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	117	1243	2	ENST00000360408.1:c.303G>T	p.Leu101Phe	p.L101F	ENST00000360408	NM_003532.2	101	ttG/ttT	1/1	0.295062370077438	5	FACETS	1	0.931	1	0.688	0.624	0.756	CLONAL	2	TRUE	2	0.344373362722328	5		1245	499	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0012111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	49	565	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.15	2		565	650	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700232	117700232	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	61	540	0	ENST00000368508.3:c.2587C>G	p.Arg863Gly	p.R863G	ENST00000368508	NM_002944.2	863	Cgg/Ggg	17/43	1	2	FACETS	0.981	0.845	1	0.981	0.845	1	CLONAL	1	TRUE	1	0.15	2		540	829	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0012134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	642	430	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.423834758371272	6	FACETS	0.916	0.886	0.946			1	CLONAL	5	TRUE	NA	0.423834758371272	6		430	1222	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs985033810	NA	P-0012134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	314	509	0	ENST00000269305.4:c.731G>T	p.Gly244Val	p.G244V	ENST00000269305	NM_001126112.2	244	gGc/gTc	7/11	0.420749315717685	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.423834758371272	2		509	684	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59770854	59770854	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	71	459	0	ENST00000259008.2:c.2512G>C	p.Asp838His	p.D838H	ENST00000259008	NM_032043.2	838	Gat/Cat	18/20	0.411033232386197	4	FACETS	0.464	0.404	0.53			1	SUBCLONAL	1	TRUE	NA	0.423834758371272	4		459	1027	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724433	162724433	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	110	418	1	ENST00000367921.3:c.205G>T	p.Asp69Tyr	p.D69Y	ENST00000367921	NM_006182.2	69	Gat/Tat	5/18	0.354945300696239	5	FACETS	0.87	0.78	0.965			1	CLONAL	1	TRUE	NA	0.423834758371272	5		419	976	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557285	29557285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367684252	NA	P-0012134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	104	430	0	ENST00000356175.3:c.2998C>T	p.Arg1000Cys	p.R1000C	ENST00000356175	NM_000267.3	1000	Cgt/Tgt	23/57	NA	2	FACETS	0.738	0.661	0.819			1	INDETERMINATE	1	TRUE	NA	0.423834758371272	2		430	665	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190744	11190744	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148876562	NA	P-0012134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	142	498	0	ENST00000361445.4:c.5455C>T	p.His1819Tyr	p.H1819Y	ENST00000361445	NM_004958.3	1819	Cat/Tat	39/58	0.405458247728916	3	FACETS	0.888	0.808	0.971	0.444	0.404	0.486	CLONAL	1	TRUE	1	0.423834758371272	3		498	915	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199310	16199310	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0012134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	81	423	3	ENST00000375759.3:c.84-1G>T		p.X28_splice	ENST00000375759	NM_015001.2	28			0.405458247728916	3	FACETS	0.564	0.496	0.637	0.282	0.248	0.319	SUBCLONAL	1	TRUE	1	0.423834758371272	3		426	821	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726606	46726606	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	73	517	0	ENST00000371975.4:c.685G>A	p.Glu229Lys	p.E229K	ENST00000371975	NM_003579.3	229	Gag/Aag	7/18	0.405458247728916	3	FACETS	0.502	0.438	0.571	0.251	0.219	0.286	SUBCLONAL	1	TRUE	1	0.423834758371272	3		517	832	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726992	46726992	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	105	666	0	ENST00000371975.4:c.826G>C	p.Glu276Gln	p.E276Q	ENST00000371975	NM_003579.3	276	Gag/Cag	8/18	0.405458247728916	3	FACETS	0.553	0.494	0.616	0.277	0.247	0.308	SUBCLONAL	1	TRUE	1	0.423834758371272	3		666	1085	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978890	25978890	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	46	361	0	ENST00000435504.4:c.1033G>T	p.Glu345Ter	p.E345*	ENST00000435504		345	Gaa/Taa	10/13	0.423834758371272	1	FACETS	0.411	0.347	0.482	0.411	0.347	0.482	SUBCLONAL	1	TRUE	0	0.423834758371272	1		361	416	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163865	47163865	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	119	566	0	ENST00000409792.3:c.2261C>T	p.Ser754Leu	p.S754L	ENST00000409792	NM_014159.6	754	tCa/tTa	3/21	0.423834758371272	1	FACETS	0.813	0.737	0.893	0.813	0.737	0.893	CLONAL	1	TRUE	0	0.423834758371272	1		566	544	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751508	57751508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	148	568	0	ENST00000274289.3:c.1483G>A	p.Glu495Lys	p.E495K	ENST00000274289	NM_006622.3	495	Gag/Aag	11/14	0.161235143941669	4	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.423834758371272	4		568	898	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5081742	5081742	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	110	352	0	ENST00000381652.3:c.2452G>A	p.Glu818Lys	p.E818K	ENST00000381652	NM_004972.3	818	Gaa/Aaa	19/25	0.327424988664099	5	FACETS	0.967	0.868	1	0.322	0.289	0.358	CLONAL	1	TRUE	2	0.423834758371272	5		352	878	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717764	89717764	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	41	228	0	ENST00000371953.3:c.789G>C	p.Lys263Asn	p.K263N	ENST00000371953	NM_000314.4	263	aaG/aaC	7/9	0.169394938871298	5	FACETS	0.763	0.636	0.903	0.254	0.212	0.301	INDETERMINATE	1	TRUE	2	0.423834758371272	5		228	415	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432932	432932	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	141	400	0	ENST00000399788.2:c.1984G>C	p.Glu662Gln	p.E662Q	ENST00000399788	NM_001042603.1	662	Gaa/Caa	15/28	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.423834758371272	2		400	617	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552696	18552696	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1023238256	NA	P-0012134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	56	611	0	ENST00000266497.5:c.2107G>A	p.Glu703Lys	p.E703K	ENST00000266497		703	Gaa/Aaa	14/31	1	2	FACETS	0.309	0.263	0.358	0.309	0.263	0.358	SUBCLONAL	1	TRUE	1	0.423834758371272	2		611	856	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235982	133235982	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	160	591	0	ENST00000320574.5:c.3174G>C	p.Lys1058Asn	p.K1058N	ENST00000320574	NM_006231.2	1058	aaG/aaC	26/49	0.371144570032166	3	FACETS	0.995	0.912	1			1	CLONAL	1	TRUE	NA	0.423834758371272	3		591	920	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910986	32910986	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1169	234	855	0	ENST00000380152.3:c.2494G>C	p.Glu832Gln	p.E832Q	ENST00000380152		832	Gag/Cag	11/27	0.423834758371272	3	FACETS	0.954	0.888	1	0.477	0.444	0.512	CLONAL	1	TRUE	1	0.423834758371272	3		855	1403	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782089	66782089	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	69	586	0	ENST00000307102.5:c.1056G>C	p.Leu352Phe	p.L352F	ENST00000307102	NM_002755.3	352	ttG/ttC	10/11	0.405458247728916	3	FACETS	0.406	0.352	0.464	0.203	0.176	0.232	SUBCLONAL	1	TRUE	1	0.423834758371272	3		586	973	SUCCESS
BLM	641	MSKCC	GRCh37	15	91341542	91341542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	61	463	0	ENST00000355112.3:c.3333G>A	p.Met1111Ile	p.M1111I	ENST00000355112	NM_000057.2	1111	atG/atA	17/22	0.405458247728916	3	FACETS	0.429	0.369	0.495	0.215	0.184	0.248	SUBCLONAL	1	TRUE	1	0.423834758371272	3		463	813	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78931424	78931424	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	54	473	0	ENST00000306801.3:c.3371G>C	p.Gly1124Ala	p.G1124A	ENST00000306801	NM_020761.2	1124	gGa/gCa	29/34	0.423834758371272	3	FACETS	0.389	0.332	0.453			1	SUBCLONAL	1	TRUE	NA	0.423834758371272	3		473	793	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520208	9520208	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	149	520	0	ENST00000353224.5:c.2061G>C	p.Gln687His	p.Q687H	ENST00000353224	NM_177990.2	687	caG/caC	10/10	0.423834758371272	3	FACETS	0.974	0.89	1	0.487	0.445	0.531	CLONAL	1	TRUE	1	0.423834758371272	3		520	875	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264401	46264401	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1475	189	893	0	ENST00000371998.3:c.1448C>G	p.Ser483Cys	p.S483C	ENST00000371998		483	tCt/tGt	11/23	0.423834758371272	3	FACETS	0.65	0.598	0.704			1	SUBCLONAL	1	TRUE	NA	0.423834758371272	3		893	1664	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536614	120536614	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0012144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	175	719	0	ENST00000229340.5:c.477+1G>T		p.X159_splice	ENST00000229340	NM_006861.6	159			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		719	755	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554311	29554311	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1567847972	NA	P-0012144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	347	578	0	ENST00000356175.3:c.2325+2T>C		p.X775_splice	ENST00000356175	NM_000267.3	775			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		578	531	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	196	939	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.831	0.77	0.894	0.831	0.77	0.894	CLONAL	1	TRUE	1	0.55373334866009	2		940	852	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978321	2978321	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs138920531	NA	P-0012147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	182	559	0	ENST00000396946.4:c.1009C>T	p.Arg337Ter	p.R337*	ENST00000396946	NM_032415.4	337	Cga/Tga	7/25	0.410654163399319	3	FACETS	0.857	0.791	0.927	0.429	0.395	0.464	CLONAL	1	TRUE	1	0.55373334866009	3		559	979	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0012147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	147	510	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.634	0.579	0.691	0.634	0.579	0.691	SUBCLONAL	1	TRUE	1	0.55373334866009	2		510	838	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175836	24175837	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555881563	NA	P-0012147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	186	617	0	ENST00000263121.7:c.1066_1067del	p.Leu356AspfsTer4	p.L356Dfs*4	ENST00000263121	NM_003073.3	355	aCT/a	8/9	1	2	FACETS	0.73	0.675	0.788	0.73	0.675	0.788	SUBCLONAL	1	TRUE	1	0.55373334866009	2		617	920	SUCCESS
APC	324	MSKCC	GRCh37	5	112128201	112128201	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0012147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	222	633	0	ENST00000257430.4:c.704T>A	p.Leu235Ter	p.L235*	ENST00000257430	NM_000038.5	235	tTa/tAa	7/16	1	2	FACETS	0.742	0.691	0.796	0.742	0.691	0.796	SUBCLONAL	1	TRUE	1	0.55373334866009	2		633	1080	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411540	63411540	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	569	902	1	ENST00000330258.3:c.1627G>T	p.Glu543Ter	p.E543*	ENST00000330258	NM_152424.3	543	Gag/Tag	2/2	0.394938456470793	3	FACETS	0.799	0.766	0.831	0.799	0.766	0.831	SUBCLONAL	2	TRUE	1	0.55373334866009	3		903	1643	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951993	178951995	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0012147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	189	550	0	ENST00000263967.3:c.3051_3053del	p.Asp1018del	p.D1018del	ENST00000263967	NM_006218.2	1016	ttTGAt/ttt	21/21	1	2	FACETS	0.705	0.652	0.761	0.705	0.652	0.761	SUBCLONAL	1	TRUE	1	0.55373334866009	2		550	968	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120139	70120140	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CG	novel	NA	P-0012147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	230	171	0	ENST00000245479.2:c.1143_1144dup	p.Leu382ArgfsTer2	p.L382Rfs*2	ENST00000245479	NM_000346.3	381	acg/aCGcg	3/3	0.55373334866009	3	FACETS	0.904	0.858	0.949	0.904	0.858	0.949	CLONAL	3	TRUE	0	0.55373334866009	3		171	391	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	160	160	0				ENST00000310581	NM_198253.2	-/1132			0.210126769756333	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.210126769756333	3		160	704	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692896	89692896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123322	NA	P-0012150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	56	395	0	ENST00000371953.3:c.380G>A	p.Gly127Glu	p.G127E	ENST00000371953	NM_000314.4	127	gGa/gAa	5/9	0.178585169316996	2	FACETS	0.919	0.793	1	0.919	0.793	1	CLONAL	2	TRUE	0	0.210126769756333	2		395	290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579366	7579366	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs770776262	NA	P-0012150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	82	741	0	ENST00000269305.4:c.321C>A	p.Tyr107Ter	p.Y107*	ENST00000269305	NM_001126112.2	107	taC/taA	4/11	0.210126769756333	1	FACETS	0.843	0.742	0.951	0.843	0.742	0.951	CLONAL	1	TRUE	0	0.210126769756333	1		741	829	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171622	32171622	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	150	961	0	ENST00000375023.3:c.3156C>A	p.Ser1052Arg	p.S1052R	ENST00000375023	NM_004557.3	1052	agC/agA	20/30	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.210126769756333	2		961	1293	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231103	46231103	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0012150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	70	679	0	ENST00000334344.6:c.1024-1G>A		p.X342_splice	ENST00000334344	NM_152641.2	342			1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.210126769756333	2		679	643	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176105668	176105668	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	132	950	0	ENST00000367669.3:c.847C>T	p.Gln283Ter	p.Q283*	ENST00000367669	NM_022457.5	283	Cag/Tag	7/20	1	2	FACETS	0.67	0.613	0.728	0.67	0.613	0.728	SUBCLONAL	1	TRUE	1	0.93	2		950	424	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781257	9781257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	306	1073	2	ENST00000377346.4:c.1762C>T	p.Pro588Ser	p.P588S	ENST00000377346	NM_005026.3	588	Ccc/Tcc	14/24	1	2	FACETS	0.611	0.576	0.647	0.611	0.576	0.647	SUBCLONAL	1	TRUE	1	0.93	2		1075	1077	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363481	40363481	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1479751948	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	242	943	2	ENST00000397332.2:c.748C>T	p.Pro250Ser	p.P250S	ENST00000397332	NM_001033082.2	250	Cca/Tca	3/3	1	2	FACETS	0.586	0.548	0.625	0.586	0.548	0.625	SUBCLONAL	1	TRUE	1	0.93	2		945	888	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439743	51439743	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	144	609	0	ENST00000262662.1:c.308G>A	p.Gly103Glu	p.G103E	ENST00000262662		103	gGg/gAg	4/4	1	2	FACETS	0.593	0.544	0.644	0.593	0.544	0.644	SUBCLONAL	1	TRUE	1	0.93	2		609	522	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459287	120459287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	150	787	0	ENST00000256646.2:c.6058G>A	p.Glu2020Lys	p.E2020K	ENST00000256646	NM_024408.3	2020	Gag/Aag	34/34	1	2	FACETS	0.558	0.512	0.606	0.558	0.512	0.606	SUBCLONAL	1	TRUE	1	0.93	2		787	578	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510762	120510762	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	253	982	0	ENST00000256646.2:c.1202G>A	p.Cys401Tyr	p.C401Y	ENST00000256646	NM_024408.3	401	tGc/tAc	7/34	1	2	FACETS	0.593	0.556	0.632	0.593	0.556	0.632	SUBCLONAL	1	TRUE	1	0.93	2		982	917	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731155	162731155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1213546369	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	200	787	0	ENST00000367921.3:c.1010C>T	p.Pro337Leu	p.P337L	ENST00000367921	NM_006182.2	337	cCt/cTt	9/18	1	2	FACETS	0.564	0.524	0.606	0.564	0.524	0.606	SUBCLONAL	1	TRUE	1	0.93	2		787	762	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450828	70450828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767467938	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	189	704	0	ENST00000373644.4:c.5668G>A	p.Gly1890Ser	p.G1890S	ENST00000373644	NM_030625.2	1890	Ggt/Agt	12/12	1	2	FACETS	0.579	0.537	0.623	0.579	0.537	0.623	SUBCLONAL	1	TRUE	1	0.93	2		704	702	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725084	89725084	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	34	283	0	ENST00000371953.3:c.1067A>G	p.Asn356Ser	p.N356S	ENST00000371953	NM_000314.4	356	aAt/aGt	9/9	1	2	FACETS	0.647	0.541	0.76	0.647	0.541	0.76	SUBCLONAL	1	TRUE	1	0.93	2		283	113	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571891	64571891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1240	394	1634	1	ENST00000312049.6:c.1748C>T	p.Ser583Leu	p.S583L	ENST00000312049	NM_130799.2	583	tCg/tTg	10/10	1	2	FACETS	0.519	0.492	0.546	0.519	0.492	0.546	SUBCLONAL	1	TRUE	1	0.93	2		1635	1634	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514067	69514067	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457646102	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	321	1135	1	ENST00000294312.3:c.614G>A	p.Gly205Glu	p.G205E	ENST00000294312	NM_005117.2	205	gGa/gAa	3/3	1	2	FACETS	0.668	0.631	0.705	0.668	0.631	0.705	SUBCLONAL	1	TRUE	1	0.93	2		1136	1034	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948625	71948625	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	312	1292	0	ENST00000298229.2:c.3337G>A	p.Val1113Met	p.V1113M	ENST00000298229	NM_001567.3	1113	Gtg/Atg	26/28	1	2	FACETS	0.59	0.556	0.624	0.59	0.556	0.624	SUBCLONAL	1	TRUE	1	0.93	2		1292	1138	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996779	100996779	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	175	1060	0	ENST00000325455.5:c.1748C>T	p.Thr583Ile	p.T583I	ENST00000325455	NM_001202474.3	583	aCc/aTc	2/8	1	2	FACETS	0.681	0.631	0.732	0.681	0.631	0.732	SUBCLONAL	1	TRUE	1	0.93	2		1060	553	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359418	118359418	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	150	652	0	ENST00000534358.1:c.4422G>A	p.Trp1474Ter	p.W1474*	ENST00000534358	NM_005933.3	1474	tgG/tgA	11/36	1	2	FACETS	0.576	0.529	0.625	0.576	0.529	0.625	SUBCLONAL	1	TRUE	1	0.93	2		652	560	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373794	118373794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	111	692	0	ENST00000534358.1:c.7187C>T	p.Pro2396Leu	p.P2396L	ENST00000534358	NM_005933.3	2396	cCa/cTa	27/36	1	2	FACETS	0.551	0.499	0.606	0.551	0.499	0.606	SUBCLONAL	1	TRUE	1	0.93	2		692	433	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103287	119103287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	162	1018	0	ENST00000264033.4:c.325C>T	p.Leu109Phe	p.L109F	ENST00000264033	NM_005188.3	109	Ctt/Ttt	2/16	1	2	FACETS	0.608	0.561	0.657	0.608	0.561	0.657	SUBCLONAL	1	TRUE	1	0.93	2		1018	573	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125499174	125499174	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	90	903	0	ENST00000428830.2:c.337C>T	p.Gln113Ter	p.Q113*	ENST00000428830	NM_001114121.2	113	Caa/Taa	4/14	1	2	FACETS	0.559	0.501	0.621	0.559	0.501	0.621	SUBCLONAL	1	TRUE	1	0.93	2		903	346	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18747498	18747498	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	76	770	0	ENST00000266497.5:c.3959A>G	p.Tyr1320Cys	p.Y1320C	ENST00000266497		1320	tAc/tGc	28/31	1	2	FACETS	0.582	0.516	0.651	0.582	0.516	0.651	SUBCLONAL	1	TRUE	1	0.93	2		770	281	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244170	46244170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	125	669	0	ENST00000334344.6:c.2264C>T	p.Thr755Ile	p.T755I	ENST00000334344	NM_152641.2	755	aCa/aTa	15/21	1	2	FACETS	0.615	0.561	0.671	0.615	0.561	0.671	SUBCLONAL	1	TRUE	1	0.93	2		669	437	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434130	49434130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	338	1177	1	ENST00000301067.7:c.7423C>T	p.Pro2475Ser	p.P2475S	ENST00000301067	NM_003482.3	2475	Cct/Tct	31/54	1	2	FACETS	0.647	0.612	0.682	0.647	0.612	0.682	SUBCLONAL	1	TRUE	1	0.93	2		1178	1124	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487950	56487950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202048840	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	271	1018	0	ENST00000267101.3:c.1681G>A	p.Gly561Ser	p.G561S	ENST00000267101	NM_001982.3	561	Ggc/Agc	14/28	1	2	FACETS	0.606	0.569	0.643	0.606	0.569	0.643	SUBCLONAL	1	TRUE	1	0.93	2		1018	962	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120783416	120783416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	284	1421	0	ENST00000257552.2:c.1067C>T	p.Ala356Val	p.A356V	ENST00000257552	NM_002442.3	356	gCc/gTc	14/15	1	2	FACETS	0.584	0.549	0.62	0.584	0.549	0.62	SUBCLONAL	1	TRUE	1	0.93	2		1421	1046	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622532	28622532	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs778216126	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	117	915	0	ENST00000241453.7:c.1085A>G	p.Asp362Gly	p.D362G	ENST00000241453	NM_004119.2	362	gAc/gGc	9/24	1	2	FACETS	0.626	0.569	0.685	0.626	0.569	0.685	SUBCLONAL	1	TRUE	1	0.93	2		915	402	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28963969	28963969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770598745	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	74	570	0	ENST00000282397.4:c.1933G>A	p.Glu645Lys	p.E645K	ENST00000282397	NM_002019.4	645	Gaa/Aaa	13/30	1	2	FACETS	0.541	0.478	0.607	0.541	0.478	0.607	SUBCLONAL	1	TRUE	1	0.93	2		570	294	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008224	29008224	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	83	676	0	ENST00000282397.4:c.647A>G	p.Tyr216Cys	p.Y216C	ENST00000282397	NM_002019.4	216	tAt/tGt	5/30	1	2	FACETS	0.591	0.527	0.658	0.591	0.527	0.658	SUBCLONAL	1	TRUE	1	0.93	2		676	302	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106214	2106214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	305	1107	1	ENST00000219476.3:c.617G>A	p.Cys206Tyr	p.C206Y	ENST00000219476	NM_000548.3	206	tGc/tAc	7/42	1	2	FACETS	0.625	0.59	0.662	0.625	0.59	0.662	SUBCLONAL	1	TRUE	1	0.93	2		1108	1049	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2115519	2115519	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs45517184	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	291	1003	0	ENST00000219476.3:c.1600-1G>A		p.X534_splice	ENST00000219476	NM_000548.3	534			1	2	FACETS	0.588	0.553	0.624	0.588	0.553	0.624	SUBCLONAL	1	TRUE	1	0.93	2		1003	1064	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129324	2129324	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	361	1221	0	ENST00000219476.3:c.3179G>A	p.Trp1060Ter	p.W1060*	ENST00000219476	NM_000548.3	1060	tGg/tAg	28/42	1	2	FACETS	0.673	0.639	0.709	0.673	0.639	0.709	SUBCLONAL	1	TRUE	1	0.93	2		1221	1153	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135288	2135288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567528890	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	370	1472	0	ENST00000219476.3:c.4627C>T	p.His1543Tyr	p.H1543Y	ENST00000219476	NM_000548.3	1543	Cac/Tac	36/42	1	2	FACETS	0.619	0.587	0.652	0.619	0.587	0.652	SUBCLONAL	1	TRUE	1	0.93	2		1472	1286	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778684	3778684	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	282	1114	0	ENST00000262367.5:c.6364C>T	p.Gln2122Ter	p.Q2122*	ENST00000262367	NM_004380.2	2122	Cag/Tag	31/31	1	2	FACETS	0.573	0.538	0.608	0.573	0.538	0.608	SUBCLONAL	1	TRUE	1	0.93	2		1114	1059	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778899	3778899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1417258350	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	190	795	1	ENST00000262367.5:c.6149G>A	p.Gly2050Glu	p.G2050E	ENST00000262367	NM_004380.2	2050	gGg/gAg	31/31	1	2	FACETS	0.591	0.548	0.635	0.591	0.548	0.635	SUBCLONAL	1	TRUE	1	0.93	2		796	691	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647089	23647089	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555461627	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	173	1393	0	ENST00000261584.4:c.778C>T	p.Gln260Ter	p.Q260*	ENST00000261584	NM_024675.3	260	Cag/Tag	4/13	1	2	FACETS	0.598	0.553	0.645	0.598	0.553	0.645	SUBCLONAL	1	TRUE	1	0.93	2		1393	622	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645096	67645096	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776556705	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	250	1323	0	ENST00000264010.4:c.361C>T	p.Pro121Ser	p.P121S	ENST00000264010	NM_006565.3	121	Cct/Tct	3/12	1	2	FACETS	0.592	0.555	0.631	0.592	0.555	0.631	SUBCLONAL	1	TRUE	1	0.93	2		1323	908	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89865595	89865595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	322	1238	0	ENST00000389301.3:c.872C>T	p.Thr291Ile	p.T291I	ENST00000389301	NM_000135.2	291	aCt/aTt	10/43	1	2	FACETS	0.613	0.579	0.648	0.613	0.579	0.648	SUBCLONAL	1	TRUE	1	0.93	2		1238	1129	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40458274	40458274	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	345	1444	0	ENST00000345506.4:c.1489G>A	p.Ala497Thr	p.A497T	ENST00000345506	NM_003152.3	497	Gcc/Acc	14/20	1	2	FACETS	0.568	0.537	0.6	0.568	0.537	0.6	SUBCLONAL	1	TRUE	1	0.93	2		1444	1306	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530121	63530121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	230	1062	0	ENST00000307078.5:c.2314G>A	p.Gly772Arg	p.G772R	ENST00000307078	NM_004655.3	772	Ggg/Agg	10/11	1	2	FACETS	0.548	0.512	0.586	0.548	0.512	0.586	SUBCLONAL	1	TRUE	1	0.93	2		1062	902	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66520200	66520200	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	145	726	0	ENST00000358598.2:c.484G>A	p.Glu162Lys	p.E162K	ENST00000358598	NM_212471.2	162	Gag/Aag	5/11	1	2	FACETS	0.563	0.516	0.611	0.563	0.516	0.611	SUBCLONAL	1	TRUE	1	0.93	2		726	554	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78938063	78938063	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	277	1164	2	ENST00000306801.3:c.3941C>T	p.Pro1314Leu	p.P1314L	ENST00000306801	NM_020761.2	1314	cCt/cTt	34/34	1	2	FACETS	0.544	0.51	0.578	0.544	0.51	0.578	SUBCLONAL	1	TRUE	1	0.93	2		1166	1096	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604803	48604803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	186	815	0	ENST00000342988.3:c.1625C>T	p.Thr542Ile	p.T542I	ENST00000342988	NM_005359.5	542	aCc/aTc	12/12	1	2	FACETS	0.614	0.57	0.66	0.614	0.57	0.66	SUBCLONAL	1	TRUE	1	0.93	2		815	651	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223242	5223242	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1263196047	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	337	1281	2	ENST00000357368.4:c.2561C>T	p.Pro854Leu	p.P854L	ENST00000357368	NM_002850.3	854	cCc/cTc	18/38	1	2	FACETS	0.62	0.587	0.655	0.62	0.587	0.655	SUBCLONAL	1	TRUE	1	0.93	2		1283	1168	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11015687	11015687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	282	997	1	ENST00000327064.4:c.281G>A	p.Gly94Asp	p.G94D	ENST00000327064	NM_199141.1	94	gGc/gAc	2/16	1	2	FACETS	0.556	0.523	0.591	0.556	0.523	0.591	SUBCLONAL	1	TRUE	1	0.93	2		998	1090	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796347	42796347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	380	1442	1	ENST00000575354.2:c.2996C>T	p.Pro999Leu	p.P999L	ENST00000575354	NM_015125.3	999	cCc/cTc	12/20	1	2	FACETS	0.63	0.598	0.663	0.63	0.598	0.663	SUBCLONAL	1	TRUE	1	0.93	2		1443	1297	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796484	42796484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780624177	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	390	1453	3	ENST00000575354.2:c.3041C>T	p.Ala1014Val	p.A1014V	ENST00000575354	NM_015125.3	1014	gCg/gTg	13/20	1	2	FACETS	0.627	0.595	0.659	0.627	0.595	0.659	SUBCLONAL	1	TRUE	1	0.93	2		1456	1338	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47730012	47730012	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	172	804	0	ENST00000449228.1:c.378-1G>A		p.X126_splice	ENST00000449228	NM_001127240.2	126			1	2	FACETS	0.556	0.513	0.6	0.556	0.513	0.6	SUBCLONAL	1	TRUE	1	0.93	2		804	665	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202123063	202123063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	177	625	0	ENST00000358485.4:c.109G>A	p.Gly37Arg	p.G37R	ENST00000358485	NM_001080125.1	37	Ggg/Agg	1/9	1	2	FACETS	0.591	0.547	0.637	0.591	0.547	0.637	SUBCLONAL	1	TRUE	1	0.93	2		625	644	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388072	31388072	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201657518	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	156	679	1	ENST00000328111.2:c.1873G>A	p.Val625Met	p.V625M	ENST00000328111	NM_006892.3	625	Gtg/Atg	17/23	1	2	FACETS	0.581	0.535	0.63	0.581	0.535	0.63	SUBCLONAL	1	TRUE	1	0.93	2		680	577	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845357	42845357	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1467695759	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	354	1124	1	ENST00000398585.3:c.905G>A	p.Gly302Glu	p.G302E	ENST00000398585	NM_001135099.1	302	gGg/gAg	9/14	1	2	FACETS	0.594	0.563	0.627	0.594	0.563	0.627	SUBCLONAL	1	TRUE	1	0.93	2		1125	1281	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572895	41572895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	306	1085	0	ENST00000263253.7:c.5180C>T	p.Pro1727Leu	p.P1727L	ENST00000263253	NM_001429.3	1727	cCa/cTa	31/31	1	2	FACETS	0.653	0.617	0.691	0.653	0.617	0.691	SUBCLONAL	1	TRUE	1	0.93	2		1085	1007	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180171	38180171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	109	562	0	ENST00000396334.3:c.19G>A	p.Glu7Lys	p.E7K	ENST00000396334	NM_002468.4	7	Gag/Aag	1/5	1	2	FACETS	0.549	0.496	0.604	0.549	0.496	0.604	SUBCLONAL	1	TRUE	1	0.93	2		562	427	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162443	47162443	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	116	675	0	ENST00000409792.3:c.3683G>A	p.Ser1228Asn	p.S1228N	ENST00000409792	NM_014159.6	1228	aGt/aAt	3/21	1	2	FACETS	0.559	0.507	0.613	0.559	0.507	0.613	SUBCLONAL	1	TRUE	1	0.93	2		675	446	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535439	66535439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	240	766	1	ENST00000273854.3:c.22G>A	p.Gly8Ser	p.G8S	ENST00000273854	NM_004439.5	8	Ggt/Agt	1/18	1	2	FACETS	0.722	0.677	0.768	0.722	0.677	0.768	SUBCLONAL	1	TRUE	1	0.93	2		767	715	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157975	106157975	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	167	618	0	ENST00000380013.4:c.2876A>G	p.Lys959Arg	p.K959R	ENST00000380013	NM_001127208.2	959	aAg/aGg	3/11	1	2	FACETS	0.604	0.557	0.651	0.604	0.557	0.651	SUBCLONAL	1	TRUE	1	0.93	2		618	595	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282604	1282604	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	361	1267	0	ENST00000310581.5:c.1709A>G	p.Lys570Arg	p.K570R	ENST00000310581	NM_198253.2	570	aAg/aGg	3/16	1	2	FACETS	0.587	0.556	0.619	0.587	0.556	0.619	SUBCLONAL	1	TRUE	1	0.93	2		1267	1322	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962441	38962441	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	49	628	0	ENST00000357387.3:c.1691A>G	p.Asn564Ser	p.N564S	ENST00000357387	NM_152756.3	564	aAc/aGc	19/38	1	2	FACETS	0.49	0.42	0.565	0.49	0.42	0.565	SUBCLONAL	1	TRUE	1	0.93	2		628	215	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38968111	38968111	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	96	866	0	ENST00000357387.3:c.994T>C	p.Tyr332His	p.Y332H	ENST00000357387	NM_152756.3	332	Tat/Cat	12/38	1	2	FACETS	0.592	0.532	0.654	0.592	0.532	0.654	SUBCLONAL	1	TRUE	1	0.93	2		866	349	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665358	176665358	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	183	602	0	ENST00000439151.2:c.4042G>A	p.Glu1348Lys	p.E1348K	ENST00000439151	NM_022455.4	1348	Gag/Aag	7/23	1	2	FACETS	0.663	0.615	0.712	0.663	0.615	0.712	SUBCLONAL	1	TRUE	1	0.93	2		602	594	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722137	176722137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1436659051	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	212	761	0	ENST00000439151.2:c.7768C>T	p.Pro2590Ser	p.P2590S	ENST00000439151	NM_022455.4	2590	Cct/Tct	23/23	1	2	FACETS	0.587	0.546	0.628	0.587	0.546	0.628	SUBCLONAL	1	TRUE	1	0.93	2		761	777	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045898	180045898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	223	899	0	ENST00000261937.6:c.2873G>A	p.Gly958Glu	p.G958E	ENST00000261937	NM_182925.4	958	gGa/gAa	21/30	1	2	FACETS	0.578	0.539	0.618	0.578	0.539	0.618	SUBCLONAL	1	TRUE	1	0.93	2		899	830	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031969	26031969	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	136	629	0	ENST00000244661.2:c.320A>G	p.Asp107Gly	p.D107G	ENST00000244661	NM_003537.3	107	gAc/gGc	1/1	1	2	FACETS	0.58	0.531	0.632	0.58	0.531	0.632	SUBCLONAL	1	TRUE	1	0.93	2		629	504	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805518	32805518	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	356	1353	1	ENST00000374899.4:c.493G>A	p.Gly165Ser	p.G165S	ENST00000374899	NM_018833.2	165	Ggt/Agt	2/12	1	2	FACETS	0.612	0.58	0.645	0.612	0.58	0.645	SUBCLONAL	1	TRUE	1	0.93	2		1354	1251	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287506	33287506	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	302	1080	0	ENST00000374542.5:c.1591T>C	p.Ser531Pro	p.S531P	ENST00000374542	NM_001141970.1	531	Tcg/Ccg	6/8	1	2	FACETS	0.613	0.578	0.649	0.613	0.578	0.649	SUBCLONAL	1	TRUE	1	0.93	2		1080	1060	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138201297	138201297	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	204	789	1	ENST00000237289.4:c.1996G>A	p.Gly666Arg	p.G666R	ENST00000237289	NM_001270507.1	666	Gga/Aga	8/9	1	2	FACETS	0.596	0.554	0.639	0.596	0.554	0.639	SUBCLONAL	1	TRUE	1	0.93	2		790	736	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505570	157505570	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs886039699	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	79	372	0	ENST00000346085.5:c.3550+1G>A		p.X1184_splice	ENST00000346085	NM_020732.3	1184			1	2	FACETS	0.572	0.508	0.639	0.572	0.508	0.639	SUBCLONAL	1	TRUE	1	0.93	2		372	297	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843327	128843327	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	324	1339	1	ENST00000249373.3:c.434C>T	p.Thr145Ile	p.T145I	ENST00000249373	NM_005631.4	145	aCc/aTc	2/12	1	2	FACETS	0.578	0.546	0.611	0.578	0.546	0.611	SUBCLONAL	1	TRUE	1	0.93	2		1340	1205	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840588	36840588	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	387	1367	0	ENST00000358127.4:c.1145C>T	p.Pro382Leu	p.P382L	ENST00000358127	NM_001280556.1	382	cCt/cTt	10/10	1	2	FACETS	0.661	0.627	0.694	0.661	0.627	0.694	SUBCLONAL	1	TRUE	1	0.93	2		1367	1260	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606361	93606361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	303	1026	1	ENST00000375746.1:c.181G>A	p.Ala61Thr	p.A61T	ENST00000375746	NM_001174167.1	61	Gca/Aca	2/14	1	2	FACETS	0.648	0.611	0.685	0.648	0.611	0.685	SUBCLONAL	1	TRUE	1	0.93	2		1027	1006	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760447	133760447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771729224	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	303	1108	1	ENST00000318560.5:c.2770G>A	p.Gly924Arg	p.G924R	ENST00000318560	NM_005157.4	924	Ggg/Agg	11/11	1	2	FACETS	0.678	0.64	0.717	0.678	0.64	0.717	SUBCLONAL	1	TRUE	1	0.93	2		1109	961	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918593	44918593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	168	892	2	ENST00000377967.4:c.1076G>A	p.Gly359Asp	p.G359D	ENST00000377967	NM_021140.2	359	gGc/gAc	12/29	1	2	FACETS	0.518	0.477	0.56	0.518	0.477	0.56	SUBCLONAL	1	TRUE	1	0.93	2		894	698	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310870	123310870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012171-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	214	823	0	ENST00000358487.5:c.558G>A	p.Met186Ile	p.M186I	ENST00000358487	NM_000141.4	186	atG/atA	5/18	1	2	FACETS	0.587	0.547	0.628	0.587	0.547	0.628	SUBCLONAL	1	TRUE	1	0.93	2		823	784	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	57	160	0				ENST00000310581	NM_198253.2	-/1132			0.161318800659938	3	FACETS	1	0.892	1	1	0.892	1	CLONAL	2	TRUE	1	0.17	3		160	350	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0012180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	31	432	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.741	0.599	0.903	0.741	0.599	0.903	CLONAL	1	TRUE	1	0.17	2		432	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0012180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	60	840	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.178220087197382	1	FACETS	0.799	0.687	0.922	0.799	0.687	0.922	CLONAL	1	TRUE	0	0.17	1		840	808	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762959	40762959	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs387906659	NA	P-0012180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	38	411	0	ENST00000392038.2:c.49G>A	p.Glu17Lys	p.E17K	ENST00000392038	NM_001626.4	17	Gaa/Aaa	3/14	1	2	FACETS	0.961	0.795	1	0.961	0.795	1	CLONAL	1	TRUE	1	0.17	2		411	465	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649065	37649065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777164311	NA	P-0012180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	49	508	0	ENST00000447079.4:c.2170G>A	p.Val724Met	p.V724M	ENST00000447079	NM_015083.1	724	Gtg/Atg	4/14	0.161318800659938	3	FACETS	0.842	0.711	0.986	0.421	0.355	0.493	CLONAL	1	TRUE	1	0.17	3		508	743	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45854924	45854924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373363992	NA	P-0012180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	55	821	2	ENST00000391945.4:c.2246C>T	p.Thr749Met	p.T749M	ENST00000391945	NM_000400.3	749	aCg/aTg	23/23	1	2	FACETS	0.878	0.75	1	0.878	0.75	1	CLONAL	1	TRUE	1	0.17	2		823	737	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	68	586	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.2	2		586	667	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0012187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	56	403	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.3	2	FACETS	0.788	0.674	0.913			1	CLONAL	1	TRUE	NA	0.2	2		403	711	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0012187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	102	477	2	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.2	2		479	846	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473729	67473729	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	62	476	0	ENST00000327367.4:c.809G>T	p.Cys270Phe	p.C270F	ENST00000327367	NM_005902.3	270	tGc/tTc	6/9	1	2	FACETS	0.838	0.723	0.963	0.838	0.723	0.963	CLONAL	1	TRUE	1	0.2	2		476	740	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604706	48604706	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	47	437	0	ENST00000342988.3:c.1528G>T	p.Gly510Ter	p.G510*	ENST00000342988	NM_005359.5	510	Gga/Tga	12/12	1	2	FACETS	0.643	0.541	0.756	0.643	0.541	0.756	SUBCLONAL	1	TRUE	1	0.2	2		437	731	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0012197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	180	607	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.622798059643483	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	FALSE	0	0.639869044883211	2		608	272	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012198-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	78	160	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.844	0.747	0.946	0.844	0.747	0.946	CLONAL	1	TRUE	1	0.525339054793423	2		160	352	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845324	156845324	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012198-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	239	948	0	ENST00000524377.1:c.1367T>A	p.Leu456Gln	p.L456Q	ENST00000524377	NM_002529.3	456	cTg/cAg	12/17	0.525339054793423	3	FACETS	0.93	0.867	0.995	0.465	0.433	0.498	CLONAL	1	TRUE	1	0.525339054793423	3		948	1236	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115739	8115739	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012198-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	261	908	0	ENST00000346208.3:c.1085A>G	p.Gln362Arg	p.Q362R	ENST00000346208		362	cAg/cGg	6/6	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.525339054793423	2		908	993	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134476	2134476	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0012198-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	218	755	0	ENST00000219476.3:c.4253C>G	p.Ser1418Ter	p.S1418*	ENST00000219476	NM_000548.3	1418	tCa/tGa	34/42	0.525339054793423	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.525339054793423	1		755	587	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459465	40459465	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750047248	NA	P-0012198-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	291	1007	1	ENST00000345506.4:c.1726G>A	p.Gly576Arg	p.G576R	ENST00000345506	NM_003152.3	576	Ggg/Agg	15/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.525339054793423	2		1008	1071	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347729	347731	+	frameshift_variant	Frame_Shift_Del	DEL	CGA	CGA	AG	novel	NA	P-0012198-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	154	499	0	ENST00000262320.3:c.1775_1777delinsCT	p.Leu592ProfsTer113	p.L592Pfs*113	ENST00000262320	NM_003502.3	592	cTCGcc/cCTcc	6/11	0.525339054793423	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.525339054793423	1		499	428	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594258	55594258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913523	NA	P-0012228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	240	384	0	ENST00000288135.5:c.1961T>C	p.Val654Ala	p.V654A	ENST00000288135	NM_000222.2	654	gTg/gCg	13/21	0.929503495711347	1	FACETS	0.577	0.546	0.608	0.577	0.546	0.608	SUBCLONAL	1	TRUE	0	0.929503495711347	1		384	479	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751145	57751145	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	57	370	0	ENST00000274289.3:c.1722C>A	p.Tyr574Ter	p.Y574*	ENST00000274289	NM_006622.3	574	taC/taA	12/14	1	2	FACETS	0.128	0.109	0.149	0.128	0.109	0.149	SUBCLONAL	1	TRUE	1	0.929503495711347	2		370	957	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796796	135796797	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	454	518	0	ENST00000298552.3:c.690_691insA	p.Pro231ThrfsTer11	p.P231Tfs*11	ENST00000298552	NM_001162426.1	230	-/A	8/23	0.929503495711347	1	FACETS	0.985	0.963	1	0.985	0.963	1	CLONAL	1	TRUE	0	0.929503495711347	1		518	531	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593587	55593604	+	inframe_deletion	In_Frame_Del	DEL	CATGTATGAAGTACAGTG	CATGTATGAAGTACAGTG	-	novel	NA	P-0012228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	394	491	0	ENST00000288135.5:c.1653_1670del	p.Met552_Trp557del	p.M552_W557del	ENST00000288135	NM_000222.2	551	ccCATGTATGAAGTACAGTGg/ccg	11/21	0.929503495711347	1	FACETS	0.968	0.943	0.99	0.968	0.943	0.99	CLONAL	1	TRUE	0	0.929503495711347	1		491	469	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878006	151878007	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0012228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	355	341	0	ENST00000262189.6:c.6938_6939del	p.Phe2313TrpfsTer8	p.F2313Wfs*8	ENST00000262189	NM_170606.2	2313	tTT/t	36/59	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.929503495711347	2		341	762	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0012229-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	155	399	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.226380560711702	5	FACETS	0.894	0.824	0.966			1	CLONAL	4	TRUE	NA	0.226380560711702	5		399	513	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	64	586	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.998	0.862	1	0.998	0.862	1	CLONAL	1	TRUE	1	0.15	2		586	855	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61705993	61705993	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	64	596	0	ENST00000401558.2:c.3178T>G	p.Phe1060Val	p.F1060V	ENST00000401558	NM_003400.3	1060	Ttt/Gtt	25/25	1	2	FACETS	0.797	0.688	0.916	0.797	0.688	0.916	CLONAL	1	TRUE	1	0.15	2		596	1071	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729917	30729917	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	47	305	1	ENST00000295754.5:c.1438G>T	p.Glu480Ter	p.E480*	ENST00000295754	NM_003242.5	480	Gag/Tag	6/7	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.15	2		306	498	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219389	1219389	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	77	544	0	ENST00000326873.7:c.443del	p.Phe148SerfsTer13	p.F148Sfs*13	ENST00000326873	NM_000455.4	147	cgT/cg	3/10	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.15	2		544	893	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0012268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	99	565	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.783	0.699	0.873	0.783	0.699	0.873	SUBCLONAL	1	TRUE	1	0.337078021589956	2		565	750	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0012268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1463	242	853	2	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.842	0.784	0.903	0.842	0.784	0.903	CLONAL	1	TRUE	1	0.337078021589956	2		855	1705	SUCCESS
APC	324	MSKCC	GRCh37	5	112174152	112174152	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0012268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	243	452	0	ENST00000257430.4:c.2861T>A	p.Leu954Ter	p.L954*	ENST00000257430	NM_000038.5	954	tTa/tAa	16/16	0.337078021589956	3	FACETS	0.838	0.783	0.895	0.838	0.783	0.895	CLONAL	2	TRUE	1	0.337078021589956	3		452	1005	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0012268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	104	353	1	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	0.783	0.701	0.87	0.783	0.701	0.87	SUBCLONAL	1	TRUE	1	0.337078021589956	2		354	788	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545855	41545855	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs867077693	NA	P-0012268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	217	653	1	ENST00000263253.7:c.2470C>T	p.Gln824Ter	p.Q824*	ENST00000263253	NM_001429.3	824	Caa/Taa	14/31	1	2	FACETS	0.936	0.868	1	0.936	0.868	1	CLONAL	1	TRUE	1	0.337078021589956	2		654	1376	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38968087	38968087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1264083148	NA	P-0012268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	116	489	2	ENST00000357387.3:c.1018C>T	p.Pro340Ser	p.P340S	ENST00000357387	NM_152756.3	340	Cct/Tct	12/38	0.337078021589956	3	FACETS	0.757	0.68	0.838	0.378	0.34	0.419	SUBCLONAL	1	TRUE	1	0.337078021589956	3		491	1063	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624269	89624269	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	59	194	0	ENST00000371953.3:c.43A>G	p.Arg15Gly	p.R15G	ENST00000371953	NM_000314.4	15	Aga/Gga	1/9	0.337078021589956	1	FACETS	0.927	0.803	1	0.927	0.803	1	CLONAL	1	TRUE	0	0.337078021589956	1		194	314	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862932	9862932	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	110	362	0	ENST00000330684.3:c.2371C>A	p.Leu791Met	p.L791M	ENST00000330684	NM_001134407.1	791	Ctg/Atg	12/13	1	2	FACETS	0.917	0.824	1	0.917	0.824	1	CLONAL	1	TRUE	1	0.337078021589956	2		362	712	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	AA	novel	NA	P-0012268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	45	243	0	ENST00000257430.4:c.3916delinsAA	p.Glu1306LysfsTer9	p.E1306Kfs*9	ENST00000257430	NM_000038.5	1306	Gaa/AAaa	16/16	0.337078021589956	3	FACETS	0.643	0.541	0.757	0.322	0.27	0.379	SUBCLONAL	1	TRUE	1	0.337078021589956	3		243	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs863224683	NA	P-0012281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	409	565	1	ENST00000269305.4:c.388C>G	p.Leu130Val	p.L130V	ENST00000269305	NM_001126112.2	130	Ctc/Gtc	5/11	0.597757618461318	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.605674879517384	2		566	665	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196896	108196896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56009889	NA	P-0012281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	373	610	1	ENST00000278616.4:c.6919C>T	p.Leu2307Phe	p.L2307F	ENST00000278616	NM_000051.3	2307	Ctt/Ttt	47/63	0.168091677979722	6	FACETS	1	0.983	1	0.721	0.684	0.758	INDETERMINATE	2	TRUE	3	0.605674879517384	6		611	1260	SUCCESS
APC	324	MSKCC	GRCh37	5	112174229	112174229	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1554084592	NA	P-0012281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	503	819	0	ENST00000257430.4:c.2938A>T	p.Lys980Ter	p.K980*	ENST00000257430	NM_000038.5	980	Aaa/Taa	16/16	0.187041812759248	3	FACETS	0.934	0.897	0.972	0.623	0.598	0.648	INDETERMINATE	2	TRUE	0	0.605674879517384	3		819	1158	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0012306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	211	429	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	NA	2	FACETS	1	0.944	1			1	INDETERMINATE	2	TRUE	NA	0.275924077291259	2		429	754	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0012306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	134	412	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.275924077291259	3	FACETS	1	0.986	1	0.742	0.675	0.812	CLONAL	1	TRUE	1	0.275924077291259	3		412	745	SUCCESS
APC	324	MSKCC	GRCh37	5	112179344	112179344	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	94	562	0	ENST00000257430.4:c.8053A>G	p.Ser2685Gly	p.S2685G	ENST00000257430	NM_000038.5	2685	Agt/Ggt	16/16	0.161800673715309	2	FACETS	0.871	0.775	0.974	0.436	0.387	0.487	INDETERMINATE	1	TRUE	0	0.275924077291259	2		562	782	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913399	NA	P-0012306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	207	555	0	ENST00000349496.5:c.100G>C	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Cga	3/15	0.275924077291259	2	FACETS	0.998	0.929	1	0.998	0.929	1	CLONAL	2	TRUE	0	0.275924077291259	2		555	752	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604673	55604673	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773828910	NA	P-0012309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	106	494	1	ENST00000288135.5:c.2881G>A	p.Gly961Ser	p.G961S	ENST00000288135	NM_000222.2	961	Ggc/Agc	21/21	1	2	FACETS	0.78	0.703	0.86	0.78	0.703	0.86	SUBCLONAL	1	FALSE	1	0.592270699066639	2		495	459	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174885	11174885	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	386	710	0	ENST00000361445.4:c.7149G>T	p.Leu2383Phe	p.L2383F	ENST00000361445	NM_004958.3	2383	ttG/ttT	52/58	1	2	FACETS	0.956	0.917	0.994	1	0.997	1	CLONAL	2	FALSE	1	0.592270699066639	2		710	682	SUCCESS
APC	324	MSKCC	GRCh37	5	112116517	112116517	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	42	360	0	ENST00000257430.4:c.562C>A	p.Gln188Lys	p.Q188K	ENST00000257430	NM_000038.5	188	Caa/Aaa	6/16	1	2	FACETS	0.565	0.475	0.663	0.565	0.475	0.663	SUBCLONAL	1	FALSE	1	0.592270699066639	2		360	251	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158579	26158579	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	58	266	0	ENST00000289316.2:c.182G>A	p.Gly61Glu	p.G61E	ENST00000289316	NM_138720.2	61	gGg/gAg	1/2	1	2	FACETS	0.725	0.629	0.828	0.725	0.629	0.828	SUBCLONAL	1	FALSE	1	0.592270699066639	2		266	270	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172130	32172130	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	161	682	0	ENST00000375023.3:c.2902G>C	p.Glu968Gln	p.E968Q	ENST00000375023	NM_004557.3	968	Gaa/Caa	19/30	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	FALSE	1	0.592270699066639	2		682	540	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185867	32185867	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	108	567	0	ENST00000375023.3:c.1529G>T	p.Cys510Phe	p.C510F	ENST00000375023	NM_004557.3	510	tGt/tTt	9/30	1	2	FACETS	0.795	0.717	0.876	0.795	0.717	0.876	SUBCLONAL	1	FALSE	1	0.592270699066639	2		567	459	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730027	41730027	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	199	1391	0	ENST00000242208.4:c.502A>T	p.Arg168Trp	p.R168W	ENST00000242208	NM_002192.2	168	Agg/Tgg	3/3	1	2	FACETS	0.775	0.719	0.833	0.775	0.719	0.833	SUBCLONAL	1	FALSE	1	0.592270699066639	2		1391	867	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376657	8376657	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	230	504	0	ENST00000356435.5:c.4456G>T	p.Asp1486Tyr	p.D1486Y	ENST00000356435		1486	Gat/Tat	27/35	1	2	FACETS	0.811	0.765	0.857	1	0.994	1	CLONAL	2	FALSE	1	0.592270699066639	2		504	479	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457388	67457388	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	111	561	0	ENST00000327367.4:c.362G>C	p.Cys121Ser	p.C121S	ENST00000327367	NM_005902.3	121	tGc/tCc	2/9	1	2	FACETS	0.732	0.661	0.807	0.732	0.661	0.807	SUBCLONAL	1	FALSE	1	0.592270699066639	2		561	512	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16005044	16005044	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	63	329	0	ENST00000268712.3:c.2210G>T	p.Ser737Ile	p.S737I	ENST00000268712	NM_006311.3	737	aGt/aTt	20/46	0.333452183164234	3	FACETS	0.788	0.685	0.898	0.263	0.228	0.3	INDETERMINATE	1	FALSE	0	0.592270699066639	3		329	350	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414850	56414850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	231	1141	3	ENST00000348428.3:c.2251C>T	p.His751Tyr	p.H751Y	ENST00000348428	NM_006785.3	751	Cac/Tac	17/17	1	2	FACETS	0.771	0.719	0.825	0.771	0.719	0.825	SUBCLONAL	1	FALSE	1	0.592270699066639	2		1144	1012	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770555	40770555	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	160	453	0	ENST00000373198.4:c.2827T>A	p.Tyr943Asn	p.Y943N	ENST00000373198	NM_133170.3	943	Tac/Aac	19/32	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	1	0.592270699066639	2		453	540	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220690	1220690	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	238	669	0	ENST00000326873.7:c.709del	p.Asp237ThrfsTer50	p.D237Tfs*50	ENST00000326873	NM_000455.4	236	gtG/gt	5/10	1	2	FACETS	0.813	0.768	0.859	1	0.994	1	CLONAL	2	FALSE	1	0.592270699066639	2		669	494	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937093	48937093	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	55	232	0	ENST00000267163.4:c.861+1del		p.E287fs	ENST00000267163	NM_000321.2	287	gaG/ga	8/27	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.592270699066639	2		232	151	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578429	7578434	+	inframe_deletion	In_Frame_Del	DEL	CTGTGA	CTGTGA	-	novel	NA	P-0012309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	192	441	0	ENST00000269305.4:c.496_501del	p.Ser166_Gln167del	p.S166_Q167del	ENST00000269305	NM_001126112.2	166	TCACAG/-	5/11	0.333452183164234	3	FACETS	0.859	0.802	0.917	0.573	0.535	0.612	INDETERMINATE	2	FALSE	0	0.592270699066639	3		441	489	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	31	160	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.914	1			1	INDETERMINATE	2	FALSE	NA	0.403205828986397	2		160	68	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248998	55248999	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCCAGCG	rs727504263	NA	P-0012312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2083	58	478	0	ENST00000275493.2:c.2300_2308dup	p.Ala767_Val769dup	p.A767_V769dup	ENST00000275493	NM_005228.3	767	atg/aTGGCCAGCGtg	20/28	0.403205828986397	56	FACETS	0.799	0.682	0.927	0.031	0.026	0.037	CLONAL	2	FALSE	5	0.403205828986397	56		478	2141	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464544	25464544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368961181	NA	P-0012312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	109	587	0	ENST00000264709.3:c.1969G>A	p.Val657Met	p.V657M	ENST00000264709	NM_175629.2	657	Gtg/Atg	17/23	0.403205828986397	6	FACETS	0.966	0.877	1			1	CLONAL	3	FALSE	NA	0.403205828986397	6		587	337	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552757	106552757	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	38	817	0	ENST00000369096.4:c.722A>C	p.Lys241Thr	p.K241T	ENST00000369096	NM_001198.3	241	aAg/aCg	5/7	0.182537393426192	5	FACETS	0.74	0.612	0.882			1	INDETERMINATE	1	FALSE	NA	0.403205828986397	5		817	409	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061208	38061208	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1292426539	NA	P-0012326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	36	339	0	ENST00000250448.2:c.781C>G	p.Arg261Gly	p.R261G	ENST00000250448	NM_004496.3	261	Cgc/Ggc	2/2	1	2	FACETS	0.321	0.263	0.385	0.321	0.263	0.385	SUBCLONAL	1	TRUE	1	0.531862563076603	2		339	422	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954957	2954957	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	88	484	0	ENST00000396946.4:c.2753G>A	p.Arg918Gln	p.R918Q	ENST00000396946	NM_032415.4	918	cGg/cAg	21/25	1	2	FACETS	0.407	0.36	0.457	0.407	0.36	0.457	SUBCLONAL	1	TRUE	1	0.531862563076603	2		484	814	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962491	100962491	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	213	533	0	ENST00000325455.5:c.1906G>T	p.Gly636Cys	p.G636C	ENST00000325455	NM_001202474.3	636	Ggt/Tgt	3/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.531862563076603	2		533	692	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205768	108205768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555127166	NA	P-0012326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	141	401	0	ENST00000278616.4:c.8083G>A	p.Gly2695Ser	p.G2695S	ENST00000278616	NM_000051.3	2695	Ggt/Agt	55/63	0.531862563076603	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.531862563076603	1		401	368	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127920632	127920647	+	frameshift_variant	Frame_Shift_Del	DEL	ACTATAGTAACCTCTG	ACTATAGTAACCTCTG	-	novel	NA	P-0012326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	77	724	0	ENST00000373547.4:c.252_267del	p.Arg85TrpfsTer10	p.R85Wfs*10	ENST00000373547	NM_002721.4	84	gaCAGAGGTTACTATAGT/ga	4/7	0.245846395853837	3	FACETS	0.474	0.416	0.537	0.237	0.208	0.269	INDETERMINATE	1	TRUE	1	0.531862563076603	3		724	773	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150377	157150377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	88	579	0	ENST00000346085.5:c.1559C>T	p.Pro520Leu	p.P520L	ENST00000346085	NM_020732.3	520	cCa/cTa	2/20	1	2	FACETS	0.868	0.773	0.968	0.868	0.773	0.968	CLONAL	1	TRUE	1	0.470488798896152	2		579	431	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984598	72984598	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0012332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	237	944	1	ENST00000268489.5:c.2986A>T	p.Lys996Ter	p.K996*	ENST00000268489	NM_006885.3	996	Aag/Tag	3/10	0.470488798896152	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.470488798896152	1		945	694	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369482	40369482	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	117	928	0	ENST00000293328.3:c.1170T>G	p.Asn390Lys	p.N390K	ENST00000293328	NM_012448.3	390	aaT/aaG	10/19	1	2	FACETS	0.683	0.616	0.754	0.683	0.616	0.754	SUBCLONAL	1	TRUE	1	0.470488798896152	2		928	728	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936066	44936067	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs886041899	NA	P-0012332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	73	412	0	ENST00000377967.4:c.2830dup	p.Tyr944LeufsTer5	p.Y944Lfs*5	ENST00000377967	NM_021140.2	943	att/aTtt	18/29	1	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.470488798896152	1		412	228	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175904	176175904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	18	40	0	ENST00000367669.3:c.211G>A	p.Ala71Thr	p.A71T	ENST00000367669	NM_022457.5	71	Gcg/Acg	1/20	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.653424347677319	2		40	49	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556879	29556880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	154	325	0	ENST00000356175.3:c.2880dup	p.Val961CysfsTer14	p.V961Cfs*14	ENST00000356175	NM_000267.3	959	-/T	22/57	0.653424347677319	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.653424347677319	1		325	314	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911597	39911597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761983121	NA	P-0012362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	168	704	1	ENST00000378444.4:c.5033G>A	p.Arg1678His	p.R1678H	ENST00000378444	NM_001123385.1	1678	cGc/cAc	15/15	0.364152488139093	1	FACETS	0.963	0.886	1	0.963	0.886	1	CLONAL	1	TRUE	0	0.364152488139093	1		705	784	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895658	28895658	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	150	695	0	ENST00000282397.4:c.3116G>A	p.Cys1039Tyr	p.C1039Y	ENST00000282397	NM_002019.4	1039	tGt/tAt	23/30	NA	2	FACETS	0.762	0.695	0.832			1	INDETERMINATE	1	TRUE	NA	0.364152488139093	2		695	1081	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849641	68849642	+	stop_gained,inframe_insertion	Nonsense_Mutation	INS	-	-	ATA	novel	NA	P-0012362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	127	490	0	ENST00000261769.5:c.1546_1547insAAT	p.Thr515_Phe516insTer	p.T515_F516ins*	ENST00000261769	NM_004360.3	515	aca/acATAa	10/16	0.364152488139093	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.364152488139093	1		490	544	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117361	115117362	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0012362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	174	774	0	ENST00000257566.3:c.812dup	p.Tyr271Ter	p.Y271*	ENST00000257566	NM_016569.3	271	tac/taAc	4/8	0.301253776670933	1	FACETS	0.794	0.73	0.86	0.794	0.73	0.86	SUBCLONAL	1	TRUE	0	0.364152488139093	1		774	985	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129423	30129423	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012369-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	268	861	0	ENST00000263025.4:c.605C>G	p.Thr202Arg	p.T202R	ENST00000263025	NM_002746.2	202	aCg/aGg	4/9	0.562273061389885	2	FACETS	0.837	0.797	0.878	0.837	0.797	0.878	CLONAL	2	TRUE	0	0.662573667923162	2		861	483	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24135796	24135796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012369-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	272	654	0	ENST00000263121.7:c.283G>A	p.Glu95Lys	p.E95K	ENST00000263121	NM_003073.3	95	Gaa/Aaa	3/9	0.550874662200323	4	FACETS	0.967	0.913	1			1	CLONAL	2	TRUE	NA	0.662573667923162	4		654	706	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043420	6043420	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012369-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	24	118	0	ENST00000265849.7:c.254T>A	p.Leu85Gln	p.L85Q	ENST00000265849	NM_000535.5	85	cTg/cAg	4/15	0.662573667923162	6	FACETS	0.834	0.658	1	0.208	0.164	0.259	CLONAL	1	TRUE	2	0.662573667923162	6		118	202	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0012372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	79	311	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.291882138772787	3	FACETS	0.817	0.723	0.915	0.817	0.723	0.915	CLONAL	2	TRUE	1	0.312453196025775	3		311	358	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527502	157527502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	195	603	0	ENST00000346085.5:c.5227G>A	p.Glu1743Lys	p.E1743K	ENST00000346085	NM_020732.3	1743	Gaa/Aaa	20/20	0.263399450314525	3	FACETS	0.853	0.79	0.918	0.853	0.79	0.918	CLONAL	2	TRUE	1	0.312453196025775	3		603	846	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711902	89711902	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	89	680	0	ENST00000371953.3:c.520T>G	p.Tyr174Asp	p.Y174D	ENST00000371953	NM_000314.4	174	Tat/Gat	6/9	1	2	FACETS	0.828	0.734	0.928	0.828	0.734	0.928	CLONAL	1	TRUE	1	0.312453196025775	2		680	688	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717723	89717724	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCAC	novel	NA	P-0012372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	72	530	0	ENST00000371953.3:c.748_749insCCAC	p.Cys250SerfsTer4	p.C250Sfs*4	ENST00000371953	NM_000314.4	250	tgt/tCCACgt	7/9	1	2	FACETS	0.769	0.673	0.874	0.769	0.673	0.874	SUBCLONAL	1	TRUE	1	0.312453196025775	2		530	599	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061250	38061250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1459219194	NA	P-0012375-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	312	718	0	ENST00000250448.2:c.739C>T	p.His247Tyr	p.H247Y	ENST00000250448	NM_004496.3	247	Cac/Tac	2/2	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.665393509234843	2		718	789	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204661	108204661	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0012375-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	268	497	0	ENST00000278616.4:c.7976T>G	p.Leu2659Ter	p.L2659*	ENST00000278616	NM_000051.3	2659	tTa/tGa	54/63	0.657605795236586	2	FACETS	0.978	0.935	1	0.978	0.935	1	CLONAL	2	TRUE	0	0.665393509234843	2		497	412	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830688	72830688	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012375-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	294	1369	2	ENST00000268489.5:c.5893C>T	p.Gln1965Ter	p.Q1965*	ENST00000268489	NM_006885.3	1965	Cag/Tag	9/10	0.665393509234843	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.665393509234843	1		1371	545	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260624	1260624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199422305	NA	P-0012382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	437	733	0	ENST00000310581.5:c.2935C>T	p.Arg979Trp	p.R979W	ENST00000310581	NM_198253.2	979	Cgg/Tgg	12/16	0.460549829072518	4	FACETS	0.915	0.873	0.957			1	CLONAL	2	TRUE	NA	0.61753251108536	4		733	1251	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575084	64575084	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	470	672	0	ENST00000312049.6:c.723T>G	p.Cys241Trp	p.C241W	ENST00000312049	NM_130799.2	241	tgT/tgG	4/10	0.606915541388687	2	FACETS	0.935	0.901	0.968	0.935	0.901	0.968	CLONAL	2	TRUE	0	0.61753251108536	2		672	814	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939105	48939105	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	rs587778843	NA	P-0012382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	180	375	0	ENST00000267163.4:c.937G>T	p.Glu313Ter	p.E313*	ENST00000267163	NM_000321.2	313	Gag/Tag	9/27	0.606915541388687	2	FACETS	0.857	0.805	0.909	0.857	0.805	0.909	CLONAL	2	TRUE	0	0.61753251108536	2		375	340	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0012392-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	37	565	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.797	0.658	0.952	0.797	0.658	0.952	CLONAL	1	FALSE	1	0.236920304020909	2		565	392	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919310	178919310	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0012395-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	48	292	1	ENST00000263967.3:c.795T>G	p.Tyr265Ter	p.Y265*	ENST00000263967	NM_006218.2	265	taT/taG	4/21	0.242134996712885	2	FACETS	0.889	0.753	1	0.445	0.376	0.52	CLONAL	1	TRUE	0	0.2498875164581	2		293	432	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101099	27101099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	253	616	1	ENST00000324856.7:c.4381C>T	p.Arg1461Ter	p.R1461*	ENST00000324856	NM_006015.4	1461	Cga/Tga	18/20	1	2	FACETS	0.96	0.898	1	0.96	0.898	1	CLONAL	1	TRUE	1	0.497748503273768	2		617	1059	SUCCESS
APC	324	MSKCC	GRCh37	5	112175273	112175273	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123121	NA	P-0012399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	107	401	0	ENST00000257430.4:c.3982C>T	p.Gln1328Ter	p.Q1328*	ENST00000257430	NM_000038.5	1328	Cag/Tag	16/16	0.352463217314376	3	FACETS	0.671	0.602	0.745	0.336	0.301	0.373	SUBCLONAL	1	TRUE	1	0.497748503273768	3		401	800	SUCCESS
APC	324	MSKCC	GRCh37	5	112170777	112170777	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876659517	NA	P-0012399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	385	633	1	ENST00000257430.4:c.1873C>T	p.Gln625Ter	p.Q625*	ENST00000257430	NM_000038.5	625	Cag/Tag	15/16	0.352463217314376	3	FACETS	0.78	0.741	0.819	0.78	0.741	0.819	SUBCLONAL	2	TRUE	1	0.497748503273768	3		634	1239	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622579	158622579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766547414	NA	P-0012399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	597	827	0	ENST00000263640.3:c.920G>A	p.Arg307Gln	p.R307Q	ENST00000263640	NM_001105.4	307	cGa/cAa	8/11	0.45245933804844	3	FACETS	1	0.972	1	0.675	0.649	0.7	CLONAL	2	TRUE	0	0.497748503273768	3		827	1480	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711026	114711026	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	209	328	0	ENST00000543371.1:c.250G>T	p.Glu84Ter	p.E84*	ENST00000543371	NM_001198531.1	84	Gaa/Taa	2/14	0.352463217314376	3	FACETS	0.825	0.77	0.881	0.825	0.77	0.881	CLONAL	2	TRUE	1	0.497748503273768	3		328	636	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363824	118363824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	222	545	1	ENST00000534358.1:c.5057G>A	p.Arg1686His	p.R1686H	ENST00000534358	NM_005933.3	1686	cGc/cAc	16/36	0.467125221894177	3	FACETS	0.965	0.897	1	0.482	0.448	0.518	CLONAL	1	TRUE	1	0.497748503273768	3		546	1155	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578376	7578376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	262	343	0	ENST00000269305.4:c.554del	p.Ser185ThrfsTer62	p.S185Tfs*62	ENST00000269305	NM_001126112.2	185	aGc/ac	5/11	0.457605415768859	2	FACETS	0.922	0.872	0.972	0.922	0.872	0.972	CLONAL	2	TRUE	0	0.497748503273768	2		343	571	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089647	27089657	+	frameshift_variant	Frame_Shift_Del	DEL	ATGGCCCTAAC	ATGGCCCTAAC	-	novel	NA	P-0012399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	182	575	1	ENST00000324856.7:c.2609_2619del	p.Pro870GlnfsTer62	p.P870Qfs*62	ENST00000324856	NM_006015.4	868	tATGGCCCTAAC/t	8/20	1	2	FACETS	0.818	0.755	0.883	0.818	0.755	0.883	CLONAL	1	TRUE	1	0.497748503273768	2		576	894	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	129	160	0				ENST00000310581	NM_198253.2	-/1132			0.449631790721168	1	FACETS	0.814	0.761	0.866	0.814	0.761	0.866	INDETERMINATE	1	TRUE	0	0.864904288445377	1		160	208	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0012407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	302	429	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.864904288445377	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.864904288445377	1		429	387	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0012407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	368	487	2	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.320729384591374	3	FACETS	1	0.985	1	0.699	0.673	0.726	INDETERMINATE	2	TRUE	0	0.864904288445377	3		489	581	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160597	56160597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	125	399	0	ENST00000399503.3:c.871C>T	p.Pro291Ser	p.P291S	ENST00000399503	NM_005921.1	291	Cct/Tct	4/20	0.449631790721168	1	FACETS	0.363	0.331	0.397	0.363	0.331	0.397	INDETERMINATE	1	TRUE	0	0.864904288445377	1		399	452	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354044	15354044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	105	143	0	ENST00000263377.2:c.2836C>T	p.Pro946Ser	p.P946S	ENST00000263377	NM_058243.2	946	Cct/Tct	14/20	0.428633331992804	1	FACETS	0.725	0.669	0.781	0.725	0.669	0.781	INDETERMINATE	1	TRUE	0	0.864904288445377	1		143	190	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076862	41076862	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs750249800	NA	P-0012407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	399	441	1	ENST00000373198.4:c.1558G>A	p.Glu520Lys	p.E520K	ENST00000373198	NM_133170.3	520	Gag/Aag	9/32	0.775092445843329	3	FACETS	0.898	0.861	0.934	0.898	0.861	0.934	CLONAL	2	TRUE	1	0.864904288445377	3		442	736	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187456	32187456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	346	520	1	ENST00000375023.3:c.1423G>A	p.Asp475Asn	p.D475N	ENST00000375023	NM_004557.3	475	Gat/Aat	8/30	0.43627394898986	1	FACETS	0.722	0.691	0.753	0.722	0.691	0.753	INDETERMINATE	1	TRUE	0	0.864904288445377	1		521	629	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967209	93967209	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	83	580	0	ENST00000369303.4:c.2143G>A	p.Glu715Lys	p.E715K	ENST00000369303	NM_004440.3	715	Gaa/Aaa	12/17	0.807988011911631	1	FACETS	0.331	0.295	0.369	0.331	0.295	0.369	SUBCLONAL	1	TRUE	0	0.864904288445377	1		580	329	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075655	8075655	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs772410037	NA	P-0012407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	453	649	0	ENST00000377482.5:c.25C>T	p.Gln9Ter	p.Q9*	ENST00000377482	NM_018948.3	9	Cag/Tag	2/4	0.320729384591374	3	FACETS	1	0.99	1	0.707	0.683	0.731	INDETERMINATE	2	TRUE	0	0.864904288445377	3		649	707	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61724021	61724021	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	147	416	0	ENST00000401558.2:c.881T>C	p.Leu294Pro	p.L294P	ENST00000401558	NM_003400.3	294	cTa/cCa	10/25	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.864904288445377	2		416	333	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582030	189582030	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	269	384	0	ENST00000264731.3:c.589G>A	p.Glu197Lys	p.E197K	ENST00000264731	NM_003722.4	197	Gaa/Aaa	5/14	0.864904288445377	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.864904288445377	1		384	329	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510099	187510099	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	127	459	1	ENST00000441802.2:c.13414G>A	p.Gly4472Ser	p.G4472S	ENST00000441802	NM_005245.3	4472	Ggt/Agt	27/27	0.483508149730433	3	FACETS	0.577	0.523	0.634	0.192	0.174	0.212	INDETERMINATE	1	TRUE	0	0.864904288445377	3		460	729	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876265	35876265	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770274946	NA	P-0012407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	268	461	1	ENST00000303115.3:c.1057G>A	p.Asp353Asn	p.D353N	ENST00000303115	NM_002185.3	353	Gat/Aat	8/8	0.449631790721168	1	FACETS	0.712	0.677	0.747	0.712	0.677	0.747	INDETERMINATE	1	TRUE	0	0.864904288445377	1		462	494	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891316	151891316	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	158	402	0	ENST00000262189.6:c.4538C>T	p.Pro1513Leu	p.P1513L	ENST00000262189	NM_170606.2	1513	cCa/cTa	30/59	0.43627394898986	1	FACETS	0.788	0.741	0.835	0.788	0.741	0.835	INDETERMINATE	1	TRUE	0	0.864904288445377	1		402	263	SUCCESS
CBL	867	MSKCC	GRCh37	11	119167720	119167720	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	346	468	0	ENST00000264033.4:c.2129C>T	p.Pro710Leu	p.P710L	ENST00000264033	NM_005188.3	710	cCt/cTt	13/16	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.864904288445377	2		468	682	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425881	49425881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764144293	NA	P-0012407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	111	484	0	ENST00000301067.7:c.12607G>A	p.Gly4203Arg	p.G4203R	ENST00000301067	NM_003482.3	4203	Gga/Aga	39/54	NA	2	FACETS	0.509	0.46	0.561			1	INDETERMINATE	1	TRUE	NA	0.864904288445377	2		484	504	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37856518	37856518	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	218	328	0	ENST00000269571.5:c.27G>A	p.Trp9Ter	p.W9*	ENST00000269571		9	tgG/tgA	1/27	1	2	FACETS	0.975	0.916	1	0.975	0.916	1	CLONAL	1	TRUE	1	0.864904288445377	2		328	517	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231606	5231606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	33	93	0	ENST00000357368.4:c.1870G>A	p.Asp624Asn	p.D624N	ENST00000357368	NM_002850.3	624	Gac/Aac	14/38	0.428633331992804	1	FACETS	0.346	0.287	0.41	0.346	0.287	0.41	INDETERMINATE	1	TRUE	0	0.864904288445377	1		93	125	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546945	9546945	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1211778979	NA	P-0012407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	244	365	0	ENST00000353224.5:c.1077A>T	p.Gln359His	p.Q359H	ENST00000353224	NM_177990.2	359	caA/caT	5/10	0.735143473445459	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.864904288445377	1		365	284	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206724	36206724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	160	307	0	ENST00000300305.3:c.788C>T	p.Pro263Leu	p.P263L	ENST00000300305		263	cCt/cTt	6/8	0.26531314205051	1	FACETS	0.452	0.417	0.487	0.452	0.417	0.487	INDETERMINATE	1	TRUE	0	0.864904288445377	1		307	465	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410673	63410673	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	150	843	0	ENST00000330258.3:c.2494G>A	p.Glu832Lys	p.E832K	ENST00000330258	NM_152424.3	832	Gaa/Aaa	2/2	0.864904288445377	1	FACETS	0.506	0.468	0.545	0.506	0.468	0.545	SUBCLONAL	1	TRUE	0	0.864904288445377	1		843	389	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332685	153332688	+	frameshift_variant	Frame_Shift_Del	DEL	AGTC	AGTC	-	novel	NA	P-0012407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	568	600	0	ENST00000281708.4:c.268_271del	p.Asp90ProfsTer78	p.D90Pfs*78	ENST00000281708	NM_033632.3	90	GACTcc/cc	2/12	0.483508149730433	3	FACETS	0.853	0.832	0.873	0.853	0.832	0.873	INDETERMINATE	3	TRUE	0	0.864904288445377	3		600	735	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945057	151945058	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	31	229	0	ENST00000262189.6:c.2461_2462delinsTT	p.Pro821Leu	p.P821L	ENST00000262189	NM_170606.2	821	CCa/TTa	14/59	0.43627394898986	1	FACETS	0.163	0.132	0.197	0.163	0.132	0.197	INDETERMINATE	1	TRUE	0	0.864904288445377	1		229	250	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223018	5223019	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	203	277	0	ENST00000357368.4:c.2784_2785delinsTT	p.Arg929Cys	p.R929C	ENST00000357368	NM_002850.3	928	ccCCgt/ccTTgt	18/38	0.428633331992804	1	FACETS	0.772	0.731	0.813	0.772	0.731	0.813	INDETERMINATE	1	TRUE	0	0.864904288445377	1		277	345	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0012413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	26	656	1	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		657	811	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	16	586	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		586	550	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268766	41268766	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	11	526	0	ENST00000349496.5:c.1004A>T	p.Lys335Ile	p.K335I	ENST00000349496	NM_001904.3	335	aAa/aTa	7/15	0.471338669674851	1	FACETS	0.08	0.054	0.112	0.08	0.054	0.112	SUBCLONAL	1	TRUE	0	0.475292408910523	1		526	442	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106445	27106445	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	149	358	0	ENST00000324856.7:c.6056A>G	p.His2019Arg	p.H2019R	ENST00000324856	NM_006015.4	2019	cAc/cGc	20/20	0.475292408910523	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.475292408910523	1		358	405	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61729409	61729409	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749929742	NA	P-0012423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	66	433	0	ENST00000401558.2:c.338C>T	p.Thr113Met	p.T113M	ENST00000401558	NM_003400.3	113	aCg/aTg	5/25	0.475292408910523	1	FACETS	0.655	0.573	0.743	0.655	0.573	0.743	SUBCLONAL	1	TRUE	0	0.475292408910523	1		433	323	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218800	66218800	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	104	561	1	ENST00000273854.3:c.2258C>T	p.Thr753Ile	p.T753I	ENST00000273854	NM_004439.5	753	aCa/aTa	13/18	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.475292408910523	2		562	391	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189389	56189389	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	203	520	1	ENST00000399503.3:c.4421C>A	p.Pro1474His	p.P1474H	ENST00000399503	NM_005921.1	1474	cCt/cAt	20/20	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.475292408910523	2		521	836	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560382	95560382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	155	307	0	ENST00000393063.1:c.5207G>A	p.Arg1736Gln	p.R1736Q	ENST00000393063	NM_030621.3	1736	cGg/cAg	25/28	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.475292408910523	2		307	642	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274104	10274104	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057521810	NA	P-0012423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	49	452	1	ENST00000330684.3:c.165G>A	p.Trp55Ter	p.W55*	ENST00000330684	NM_001134407.1	55	tgG/tgA	2/13	1	2	FACETS	0.27	0.228	0.317	0.27	0.228	0.317	SUBCLONAL	1	TRUE	1	0.475292408910523	2		453	763	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023109	31023109	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	141	440	0	ENST00000375687.4:c.2594A>G	p.Glu865Gly	p.E865G	ENST00000375687	NM_015338.5	865	gAa/gGa	13/13	1	2	FACETS	0.931	0.851	1	0.931	0.851	1	CLONAL	1	TRUE	1	0.475292408910523	2		440	637	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513329	41513330	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0012423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	189	632	0	ENST00000263253.7:c.234_235del	p.His78GlnfsTer11	p.H78Qfs*11	ENST00000263253	NM_001429.3	78	cAT/c	2/31	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.475292408910523	2		632	770	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713544	30713546	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0012423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	90	260	0	ENST00000295754.5:c.871_873del	p.Lys291del	p.K291del	ENST00000295754	NM_003242.5	290	gAGAag/gag	4/7	0.471338669674851	1	FACETS	0.934	0.838	1	0.934	0.838	1	CLONAL	1	TRUE	0	0.475292408910523	1		260	309	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0012427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	20	741	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.928	0.708	1	0.928	0.708	1	CLONAL	1	TRUE	1	0.09	2		742	479	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878116	48878116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	11	171	1	ENST00000267163.4:c.68C>T	p.Pro23Leu	p.P23L	ENST00000267163	NM_000321.2	23	cCg/cTg	1/27	1	2	FACETS	1	0.823	1	1	0.823	1	CLONAL	1	TRUE	1	0.09	2		172	185	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846377	128846377	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	29	899	2	ENST00000249373.3:c.1213C>A	p.Leu405Met	p.L405M	ENST00000249373	NM_005631.4	405	Ctg/Atg	6/12	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.09	2		901	571	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874842	151874842	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1463916448	NA	P-0012427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	23	636	0	ENST00000262189.6:c.7696C>T	p.Pro2566Ser	p.P2566S	ENST00000262189	NM_170606.2	2566	Cct/Tct	38/59	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.09	2		636	426	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430296	47430296	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	37	676	0	ENST00000377045.4:c.1571G>T	p.Arg524Leu	p.R524L	ENST00000377045	NM_001654.4	524	cGt/cTt	15/16	0.152499529861024	0	FACETS	1	0.869	1			1	CLONAL	2	TRUE	NA	0.09	0		676	352	SUCCESS
AR	367	MSKCC	GRCh37	X	66766194	66766213	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCGCAGTGCCGCTATG	GGCGGCGCAGTGCCGCTATG	-	novel	NA	P-0012427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	12	221	0	ENST00000374690.3:c.1208_1227del	p.Ala403GlyfsTer92	p.A403Gfs*92	ENST00000374690	NM_000044.3	402	gcGGCGGCGCAGTGCCGCTATGgg/gcgg	1/8	0.152499529861024	0	FACETS	1	0.841	1			1	CLONAL	1	TRUE	NA	0.09	0		221	180	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012430-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	309	939	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.383972295268438	9	FACETS	1	0.98	1			1	CLONAL	4	TRUE	NA	0.383972295268438	9		940	877	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780071	NA	P-0012430-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	128	421	0	ENST00000269305.4:c.580C>T	p.Leu194Phe	p.L194F	ENST00000269305	NM_001126112.2	194	Ctt/Ttt	6/11	0.219887987621176	3	FACETS	0.895	0.817	0.975	0.597	0.545	0.65	INDETERMINATE	2	TRUE	0	0.383972295268438	3		421	444	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974699	21974699	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012430-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	81	480	0	ENST00000304494.5:c.128del	p.Ser43IlefsTer10	p.S43Ifs*10	ENST00000304494	NM_000077.4	43	aGt/at	1/3	0.274451724292595	2	FACETS	1	0.958	1	0.586	0.52	0.656	CLONAL	1	TRUE	0	0.383972295268438	2		480	360	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092794	27092794	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012430-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	35	503	0	ENST00000324856.7:c.2815G>T	p.Gly939Cys	p.G939C	ENST00000324856	NM_006015.4	939	Ggc/Tgc	9/20	0.322400501275161	3	FACETS	0.435	0.356	0.523	0.217	0.178	0.262	SUBCLONAL	1	TRUE	1	0.383972295268438	3		503	500	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212484000	212484000	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1369649105	NA	P-0012430-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	32	359	0	ENST00000342788.4:c.2203G>T	p.Gly735Cys	p.G735C	ENST00000342788	NM_005235.2	735	Ggt/Tgt	19/28	0.383972295268438	3	FACETS	0.44	0.356	0.534	0.147	0.118	0.178	SUBCLONAL	1	TRUE	0	0.383972295268438	3		359	452	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541438	187541438	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs755378789	NA	P-0012430-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	48	389	0	ENST00000441802.2:c.6302G>T	p.Arg2101Leu	p.R2101L	ENST00000441802	NM_005245.3	2101	cGc/cTc	10/27	0.31126803517892	3	FACETS	0.662	0.56	0.774	0.331	0.28	0.387	SUBCLONAL	1	TRUE	1	0.383972295268438	3		389	450	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984081	2984081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367560107	NA	P-0012430-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	17	327	0	ENST00000396946.4:c.449G>A	p.Cys150Tyr	p.C150Y	ENST00000396946	NM_032415.4	150	tGc/tAc	5/25	1	2	FACETS	0.303	0.226	0.395	0.303	0.226	0.395	SUBCLONAL	1	TRUE	1	0.383972295268438	2		327	292	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727885	78727885	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012430-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	96	473	0	ENST00000306801.3:c.730G>T	p.Ala244Ser	p.A244S	ENST00000306801	NM_020761.2	244	Gca/Tca	6/34	0.31126803517892	3	FACETS	1	0.976	1	0.668	0.598	0.742	CLONAL	1	TRUE	1	0.383972295268438	3		473	446	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727895	78727895	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012430-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	91	461	0	ENST00000306801.3:c.740A>T	p.Glu247Val	p.E247V	ENST00000306801	NM_020761.2	247	gAg/gTg	6/34	0.31126803517892	3	FACETS	1	0.974	1	0.657	0.586	0.731	CLONAL	1	TRUE	1	0.383972295268438	3		461	430	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0012440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	64	441	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	1	2	FACETS	0.98	0.854	1	0.98	0.854	1	CLONAL	1	TRUE	1	0.387715156837556	2		441	337	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133459	55133459	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	52	453	2	ENST00000257290.5:c.763G>T	p.Gly255Cys	p.G255C	ENST00000257290	NM_006206.4	255	Ggc/Tgc	6/23	1	2	FACETS	0.731	0.625	0.847	0.731	0.625	0.847	SUBCLONAL	1	TRUE	1	0.387715156837556	2		455	367	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608238	28608239	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGAAACTCCCATTTGAGATCATATTCATATTCTCTG	novel	NA	P-0012440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1253	128	681	0	ENST00000241453.7:c.1782_1817dup	p.Tyr597_Glu608dup	p.Y597_E608dup	ENST00000241453	NM_004119.2	597	cca/ccCAGAGAATATGAATATGATCTCAAATGGGAGTTTCCa	14/24	0.387715156837556	1	FACETS	0.385	0.348	0.425	0.385	0.348	0.425	SUBCLONAL	1	TRUE	0	0.387715156837556	1		681	1381	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52649375	52649375	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	86	488	0	ENST00000394830.3:c.1916del	p.Leu639ProfsTer3	p.L639Pfs*3	ENST00000394830	NM_018313.4	639	cTc/cc	16/30	0.387715156837556	1	FACETS	0.974	0.869	1	0.974	0.869	1	CLONAL	1	TRUE	0	0.387715156837556	1		488	367	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012450-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	57	722	0	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	1	2	FACETS	0.483	0.412	0.561	0.483	0.412	0.561	SUBCLONAL	1	TRUE	1	0.192830867496465	2		722	1224	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0012450-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	157	621	2	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	1	2	FACETS	1	0.959	1	1	0.992	1	CLONAL	2	TRUE	1	0.192830867496465	2		623	760	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692900	89692900	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1114167645	NA	P-0012450-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	34	334	0	ENST00000371953.3:c.384G>C	p.Lys128Asn	p.K128N	ENST00000371953	NM_000314.4	128	aaG/aaC	5/9	1	2	FACETS	0.653	0.533	0.789	0.653	0.533	0.789	SUBCLONAL	1	TRUE	1	0.192830867496465	2		334	540	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	197	586	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.168369270421445	5	FACETS	1	0.975	1			1	CLONAL	3	TRUE	NA	0.168369270421445	5		586	877	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0012456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	71	280	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.162520004430855	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	2	TRUE	0	0.168369270421445	2		280	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578530	7578530	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	161	680	0	ENST00000269305.4:c.400T>G	p.Phe134Val	p.F134V	ENST00000269305	NM_001126112.2	134	Ttt/Gtt	5/11	0.168369270421445	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.168369270421445	2		680	875	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912306	29912306	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761593088	NA	P-0012456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	113	542	0	ENST00000376809.5:c.925G>A	p.Val309Met	p.V309M	ENST00000376809	NM_002116.7	309	Gtg/Atg	5/8	0.162520004430855	2	FACETS	0.927	0.835	1	0.927	0.835	1	CLONAL	2	TRUE	0	0.168369270421445	2		542	724	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0012504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	252	405	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.27394065926209	4	FACETS	1	0.936	1			1	CLONAL	2	TRUE	NA	0.27394065926209	4		405	1170	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578401	7578402	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCA	novel	NA	P-0012504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	96	342	0	ENST00000269305.4:c.526_528dup	p.Cys176dup	p.C176dup	ENST00000269305	NM_001126112.2	176	-/TGC	5/11	0.27394065926209	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.27394065926209	1		342	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0012514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	170	467	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.0447103301273191	3	FACETS	1	0.955	1			1	INDETERMINATE	2	TRUE	NA	0.215992198495102	3		467	828	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145430	58145430	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894340	NA	P-0012514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	90	419	0	ENST00000257904.6:c.71G>T	p.Arg24Leu	p.R24L	ENST00000257904	NM_000075.3	24	cGt/cTt	2/8	0.215992198495102	3	FACETS	1	0.969	1	0.635	0.563	0.712	CLONAL	1	TRUE	1	0.215992198495102	3		419	727	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561897	55561897	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	87	417	0	ENST00000288135.5:c.287C>A	p.Thr96Lys	p.T96K	ENST00000288135	NM_000222.2	96	aCg/aAg	2/21	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.215992198495102	2		417	787	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433967	149433967	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1390027952	NA	P-0012514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	54	441	0	ENST00000286301.3:c.2681C>T	p.Ala894Val	p.A894V	ENST00000286301	NM_005211.3	894	gCc/gTc	21/22	0.161769889584292	2	FACETS	0.639	0.544	0.743	0.319	0.272	0.372	SUBCLONAL	1	TRUE	0	0.215992198495102	2		441	783	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197301	26197301	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1609	125	925	0	ENST00000356476.2:c.178G>T	p.Glu60Ter	p.E60*	ENST00000356476		60	Gag/Tag	1/1	0.215992198495102	3	FACETS	0.74	0.666	0.817	0.247	0.222	0.273	SUBCLONAL	1	TRUE	0	0.215992198495102	3		925	1734	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672636	30672636	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	330	545	0	ENST00000376406.3:c.4324G>C	p.Val1442Leu	p.V1442L	ENST00000376406	NM_014641.2	1442	Gtg/Ctg	10/15	0.215992198495102	3	FACETS	0.974	0.92	1	0.974	0.92	1	CLONAL	3	TRUE	0	0.215992198495102	3		545	1159	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963951	2963951	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1238	132	575	0	ENST00000396946.4:c.1856C>A	p.Ser619Tyr	p.S619Y	ENST00000396946	NM_032415.4	619	tCc/tAc	15/25	0.215992198495102	5	FACETS	1	0.971	1	0.394	0.356	0.434	CLONAL	1	TRUE	2	0.215992198495102	5		575	1370	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268948	55268948	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	130	553	0	ENST00000275493.2:c.3014A>T	p.Glu1005Val	p.E1005V	ENST00000275493	NM_005228.3	1005	gAa/gTa	25/28	0.215992198495102	5	FACETS	1	0.982	1	0.459	0.415	0.506	CLONAL	1	TRUE	2	0.215992198495102	5		553	1157	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633397	8633397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	52	524	0	ENST00000356435.5:c.272G>A	p.Arg91Lys	p.R91K	ENST00000356435		91	aGg/aAg	3/35	1	2	FACETS	0.576	0.489	0.672	0.576	0.489	0.672	SUBCLONAL	1	TRUE	1	0.215992198495102	2		524	836	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983292	15983292	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	105	432	0	ENST00000268712.3:c.3487G>T	p.Gly1163Cys	p.G1163C	ENST00000268712	NM_006311.3	1163	Ggc/Tgc	26/46	0.215992198495102	5	FACETS	1	0.959	1	0.383	0.342	0.427	CLONAL	1	TRUE	2	0.215992198495102	5		432	1121	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576015	29576015	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	167	393	2	ENST00000356175.3:c.3988G>T	p.Glu1330Ter	p.E1330*	ENST00000356175	NM_000267.3	1330	Gag/Tag	30/57	0.160623642463242	3	FACETS	1	0.965	1			1	CLONAL	2	TRUE	NA	0.215992198495102	3		395	789	SUCCESS
AR	367	MSKCC	GRCh37	X	66942737	66942737	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1372	108	876	1	ENST00000374690.3:c.2518G>T	p.Asp840Tyr	p.D840Y	ENST00000374690	NM_000044.3	840	Gat/Tat	7/8	0.215801539565296	1	FACETS	0.603	0.539	0.671	0.603	0.539	0.671	SUBCLONAL	1	TRUE	0	0.215992198495102	1		877	1480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0012554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	199	360	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.351315168233154	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.360617272363356	2		361	531	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0012554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	286	432	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.346023283493264	3	FACETS	0.972	0.921	1	0.972	0.921	1	CLONAL	3	TRUE	0	0.360617272363356	3		432	642	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593431	55593431	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs72550822	NA	P-0012554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	128	678	1	ENST00000288135.5:c.1588G>A	p.Val530Ile	p.V530I	ENST00000288135	NM_000222.2	530	Gta/Ata	10/21	1	2	FACETS	0.838	0.759	0.921	0.838	0.759	0.921	CLONAL	1	TRUE	1	0.360617272363356	2		679	847	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038369	180038369	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	245	589	2	ENST00000261937.6:c.3648C>A	p.Asp1216Glu	p.D1216E	ENST00000261937	NM_182925.4	1216	gaC/gaA	27/30	0.360617272363356	3	FACETS	0.971	0.91	1	0.971	0.91	1	CLONAL	2	TRUE	1	0.360617272363356	3		591	826	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053021	180053021	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	87	516	0	ENST00000261937.6:c.1269G>T	p.Gln423His	p.Q423H	ENST00000261937	NM_182925.4	423	caG/caT	10/30	0.360617272363356	3	FACETS	0.859	0.761	0.964	0.429	0.38	0.482	CLONAL	1	TRUE	1	0.360617272363356	3		516	663	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372232	55372232	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	172	357	0	ENST00000297316.4:c.922G>A	p.Gly308Arg	p.G308R	ENST00000297316	NM_022454.3	308	Ggg/Agg	2/2	0.244323540417012	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	2	0.360617272363356	4		357	577	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285788	87285788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs76060730	NA	P-0012554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	80	651	0	ENST00000277120.3:c.125G>A	p.Arg42Gln	p.R42Q	ENST00000277120		42	cGg/cAg	2/19	0.244323540417012	4	FACETS	0.606	0.532	0.686	0.303	0.266	0.343	SUBCLONAL	1	TRUE	2	0.360617272363356	4		651	996	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66522048	66522048	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	75	229	0	ENST00000358598.2:c.703C>T	p.Leu235Phe	p.L235F	ENST00000358598	NM_212471.2	235	Ctc/Ttc	7/11	0.360617272363356	3	FACETS	1	0.922	1	0.532	0.468	0.601	CLONAL	1	TRUE	1	0.360617272363356	3		229	461	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604786	48604791	+	inframe_deletion	In_Frame_Del	DEL	AGACGA	AGACGA	-	novel	NA	P-0012554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	139	502	0	ENST00000342988.3:c.1610_1615del	p.Asp537_Glu538del	p.D537_E538del	ENST00000342988	NM_005359.5	536	ctAGACGAa/cta	12/12	0.360617272363356	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.360617272363356	1		502	580	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156187	106156187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs17253672	NA	P-0012557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	52	203	0	ENST00000380013.4:c.1088C>T	p.Pro363Leu	p.P363L	ENST00000380013	NM_001127208.2	363	cCt/cTt	3/11	0.373054757518676	3	FACETS	1	0.906	1			1	CLONAL	1	TRUE	NA	0.373054757518676	3		203	307	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	76	258	1	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	0.373054757518676	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.373054757518676	1		259	309	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705464	47705464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	22	246	0	ENST00000233146.2:c.2264C>T	p.Ser755Phe	p.S755F	ENST00000233146	NM_000251.2	755	tCt/tTt	14/16	0.296183216147804	3	FACETS	0.42	0.325	0.53	0.21	0.162	0.265	SUBCLONAL	1	TRUE	1	0.373054757518676	3		246	333	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856061	151856061	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs981195984	NA	P-0012557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	105	356	0	ENST00000262189.6:c.11557C>G	p.Arg3853Gly	p.R3853G	ENST00000262189	NM_170606.2	3853	Cgg/Ggg	44/59	0.373054757518676	3	FACETS	1	0.981	1	0.7	0.63	0.773	CLONAL	1	TRUE	1	0.373054757518676	3		356	477	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873779	151873779	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	19	173	0	ENST00000262189.6:c.8759G>A	p.Ser2920Asn	p.S2920N	ENST00000262189	NM_170606.2	2920	aGt/aAt	38/59	0.373054757518676	3	FACETS	0.398	0.301	0.511	0.199	0.15	0.256	SUBCLONAL	1	TRUE	1	0.373054757518676	3		173	304	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752872	128752872	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	29	184	0	ENST00000377970.2:c.1033G>C	p.Val345Leu	p.V345L	ENST00000377970	NM_002467.4	345	Gtc/Ctc	3/3	0.372442709537423	5	FACETS	0.851	0.685	1	0.284	0.228	0.346	CLONAL	1	TRUE	2	0.373054757518676	5		184	285	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994698	73994698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1286742863	NA	P-0012557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	47	217	0	ENST00000318443.5:c.182C>T	p.Ala61Val	p.A61V	ENST00000318443	NM_001024736.1	61	gCa/gTa	3/10	0.373054757518676	3	FACETS	1	0.943	1	0.62	0.528	0.72	CLONAL	1	TRUE	1	0.373054757518676	3		217	241	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610079	10610079	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	19	238	0	ENST00000171111.5:c.631T>A	p.Phe211Ile	p.F211I	ENST00000171111	NM_203500.1	211	Ttt/Att	2/6	0.373054757518676	1	FACETS	0.377	0.286	0.482	0.377	0.286	0.482	SUBCLONAL	1	TRUE	0	0.373054757518676	1		238	220	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724243	52724243	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	113	207	1	ENST00000322088.6:c.1375C>T	p.Arg459Cys	p.R459C	ENST00000322088	NM_014225.5	459	Cgc/Tgc	12/15	0.373054757518676	3	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	1	0.373054757518676	3		208	342	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023549	31023549	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	73	194	0	ENST00000375687.4:c.3034G>T	p.Asp1012Tyr	p.D1012Y	ENST00000375687	NM_015338.5	1012	Gac/Tac	13/13	0.373054757518676	3	FACETS	0.857	0.758	0.961	0.857	0.758	0.961	CLONAL	2	TRUE	1	0.373054757518676	3		194	271	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505016	186505235	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGAAGATGCATGCCAGAGACTTCACAGTTTCTGCTCTGGTAAGAGGTGTTCTAAAATGTCTGGATTTCCACTAAAGCAGGATTCAGACTACAATATAGCTGCTAAGTGCTGTGTTGTCGTTCCCCCTGCTTAAAATAAAGTTGTTTCTTAACTATACCTGTCTGCTATTCTCCTGTAGCAGCCAGGGACGCTTGGTCTCATACATGTTGATTAAAATTAA	AGAAGATGCATGCCAGAGACTTCACAGTTTCTGCTCTGGTAAGAGGTGTTCTAAAATGTCTGGATTTCCACTAAAGCAGGATTCAGACTACAATATAGCTGCTAAGTGCTGTGTTGTCGTTCCCCCTGCTTAAAATAAAGTTGTTTCTTAACTATACCTGTCTGCTATTCTCCTGTAGCAGCCAGGGACGCTTGGTCTCATACATGTTGATTAAAATTAA	-	novel	NA	P-0012557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	58	260	0	ENST00000323963.5:c.873_910-48del		p.X291_splice	ENST00000323963		291		8/11	0.372442709537423		FACETS		0.857	1				CLONAL	1	TRUE	2	0.373054757518676	5		260	487	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050612	49050876	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACAGGAGGATTTACAAAGAGTGGGTGTTTAATTGGGGATGGAATTAGGTAGTTATTCTGATTTTTAGATTTTTCATATCTTTTATTTGGTCCAATGAAGCAGAAAATTTAAATGAAGTTATTACCTTTGCCTGATTTTTGACACACCTCAAACTATAACTTGAGGTTGCTAACTATGAAACACTGGCATTTAATGATTTAAAGTAAAGAATTCTGTAATTTGTAGACTTCTGAGAAGTTCCAGAAAATAAATCAGATGGTATGTA	ACAGGAGGATTTACAAAGAGTGGGTGTTTAATTGGGGATGGAATTAGGTAGTTATTCTGATTTTTAGATTTTTCATATCTTTTATTTGGTCCAATGAAGCAGAAAATTTAAATGAAGTTATTACCTTTGCCTGATTTTTGACACACCTCAAACTATAACTTGAGGTTGCTAACTATGAAACACTGGCATTTAATGATTTAAAGTAAAGAATTCTGTAATTTGTAGACTTCTGAGAAGTTCCAGAAAATAAATCAGATGGTATGTA	-	novel	NA	P-0012557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3	45	8	0	ENST00000267163.4:c.2521-221_2564del		p.X841_splice	ENST00000267163	NM_000321.2	841		25/27	0.373054757518676	1	FACETS	1	0.961	1	1	0.984	1	CLONAL	4	TRUE	0	0.373054757518676	1		8	48	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578217	+	frameshift_variant	Frame_Shift_Del	DEL	TGTCGAAAAG	TGTCGAAAAG	-	novel	NA	P-0012557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	97	293	0	ENST00000269305.4:c.632_641del	p.Thr211IlefsTer33	p.T211Ifs*33	ENST00000269305	NM_001126112.2	211	aCTTTTCGACAt/at	6/11	0.266052927131569	2	FACETS	1	0.979	1	0.692	0.621	0.765	CLONAL	1	TRUE	0	0.373054757518676	2		293	376	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259456	55259478	+	frameshift_variant	Frame_Shift_Del	DEL	GGCAGCCAGGAACGTACTGGTGA	GGCAGCCAGGAACGTACTGGTGA	-	novel	NA	P-0012557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	28	180	0	ENST00000275493.2:c.2514_2536del	p.Ala839AsnfsTer50	p.A839Nfs*50	ENST00000275493	NM_005228.3	838	ctGGCAGCCAGGAACGTACTGGTGAaa/ctaa	21/28	0.373054757518676	3	FACETS	0.6	0.48	0.735	0.3	0.24	0.368	SUBCLONAL	1	TRUE	1	0.373054757518676	3		180	297	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401602	401611	+	frameshift_variant	Frame_Shift_Del	DEL	GAGCCACCTG	GAGCCACCTG	-	novel	NA	P-0012557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	42	178	0	ENST00000380956.4:c.927_936del	p.Ser309ArgfsTer72	p.S309Rfs*72	ENST00000380956	NM_001195286.1	308	ctGAGCCACCTG/ct	7/9	0.192966590417701	3	FACETS	1	0.865	1	0.344	0.289	0.404	INDETERMINATE	1	TRUE	0	0.373054757518676	3		178	259	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0012560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	404	460	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.971	0.926	1	0.971	0.926	1	CLONAL	1	TRUE	1	0.756837790286477	2		460	1099	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705581	47705581	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	386	552	0	ENST00000233146.2:c.2381T>C	p.Ile794Thr	p.I794T	ENST00000233146	NM_000251.2	794	aTa/aCa	14/16	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.580770330372226	2		552	1203	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84406166	84406166	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	260	414	0	ENST00000321945.7:c.60C>G	p.Phe20Leu	p.F20L	ENST00000321945	NM_139076.2	20	ttC/ttG	1/9	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.580770330372226	2		414	826	SUCCESS
APC	324	MSKCC	GRCh37	5	112163689	112163689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	369	492	0	ENST00000257430.4:c.1612G>A	p.Glu538Lys	p.E538K	ENST00000257430	NM_000038.5	538	Gaa/Aaa	13/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.580770330372226	2		492	1229	SUCCESS
CBL	867	MSKCC	GRCh37	11	119168188	119168188	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	217	376	0	ENST00000264033.4:c.2248T>C	p.Phe750Leu	p.F750L	ENST00000264033	NM_005188.3	750	Ttt/Ctt	14/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.580770330372226	2		376	723	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244460	46244460	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs925229355	NA	P-0012570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	314	540	0	ENST00000334344.6:c.2554C>T	p.Gln852Ter	p.Q852*	ENST00000334344	NM_152641.2	852	Cag/Tag	15/21	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.580770330372226	2		540	1080	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484291	50484291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253128772	NA	P-0012570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	374	534	0	ENST00000394963.4:c.1051C>T	p.Arg351Cys	p.R351C	ENST00000394963	NM_003076.4	351	Cgt/Tgt	9/13	1	2	FACETS	0.935	0.886	0.984	0.935	0.886	0.984	CLONAL	1	TRUE	1	0.580770330372226	2		534	1378	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526573	66526573	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	216	415	0	ENST00000358598.2:c.1129G>C	p.Val377Leu	p.V377L	ENST00000358598	NM_212471.2	377	Gtg/Ctg	11/11	0.580770330372226	3	FACETS	0.835	0.775	0.897	0.417	0.387	0.449	CLONAL	1	TRUE	1	0.580770330372226	3		415	1150	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973215	25973215	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	251	358	0	ENST00000435504.4:c.1210del	p.Thr404ProfsTer19	p.T404Pfs*19	ENST00000435504		404	Acc/cc	12/13	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.580770330372226	2		358	858	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0012577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	212	698	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.40018432472626	3	FACETS	1	0.979	1	0.57	0.529	0.613	CLONAL	1	TRUE	1	0.397474559698152	3		698	1122	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0012577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	338	604	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.40018432472626	3	FACETS	0.975	0.923	1	0.975	0.923	1	CLONAL	2	TRUE	1	0.397474559698152	3		604	1046	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0012580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	428	757	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.265444682787449	5	FACETS	1	0.963	1			1	CLONAL	5	TRUE	NA	0.265444682787449	5		758	897	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	84	766	0				ENST00000310581	NM_198253.2	-/1132			0.254557445800836	3	FACETS	1	0.978	1	0.742	0.658	0.832	CLONAL	1	TRUE	1	0.265444682787449	3		766	483	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0012580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	22	504	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.638	0.495	0.802	0.638	0.495	0.802	SUBCLONAL	1	TRUE	1	0.265444682787449	2		504	260	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578466	7578466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	220	638	0	ENST00000269305.4:c.464C>T	p.Thr155Ile	p.T155I	ENST00000269305	NM_001126112.2	155	aCc/aTc	5/11	0.213003915082617	2	FACETS	0.924	0.861	0.989	0.924	0.861	0.989	CLONAL	2	TRUE	0	0.265444682787449	2		638	897	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952139	178952139	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1560150596	NA	P-0012580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	94	429	0	ENST00000263967.3:c.3194A>T	p.His1065Leu	p.H1065L	ENST00000263967	NM_006218.2	1065	cAt/cTt	21/21	1	2	FACETS	0.879	0.787	0.975	1	0.985	1	CLONAL	2	TRUE	1	0.265444682787449	2		429	403	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863306	57863306	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	117	1061	2	ENST00000228682.2:c.1401G>A	p.Met467Ile	p.M467I	ENST00000228682	NM_005269.2	467	atG/atA	11/12	1	2	FACETS	0.707	0.636	0.784	0.707	0.636	0.784	SUBCLONAL	1	TRUE	1	0.265444682787449	2		1063	1246	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750419	39750419	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	98	655	1	ENST00000361337.2:c.2036del	p.Lys679ArgfsTer5	p.K679Rfs*5	ENST00000361337	NM_003286.2	678	gcA/gc	19/21	1	2	FACETS	0.879	0.783	0.981	0.879	0.783	0.981	CLONAL	1	TRUE	1	0.265444682787449	2		656	840	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0012587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	876	730	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.720437418682108	3	FACETS	0.991	0.974	1	0.991	0.974	1	CLONAL	3	TRUE	0	0.783321831588153	3		730	1047	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573321	41573321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	320	645	1	ENST00000263253.7:c.5606C>T	p.Pro1869Leu	p.P1869L	ENST00000263253	NM_001429.3	1869	cCc/cTc	31/31	0.726899094746585	4	FACETS	0.982	0.926	1	0.327	0.308	0.347	CLONAL	1	TRUE	1	0.783321831588153	4		646	1483	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566521	41566521	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	972	530	0	ENST00000263253.7:c.4398G>C	p.Trp1466Cys	p.W1466C	ENST00000263253	NM_001429.3	1466	tgG/tgC	27/31	0.726899094746585	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	1	0.783321831588153	4		530	1443	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916957	178916957	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1960	2145	549	0	ENST00000263967.3:c.344G>C	p.Arg115Pro	p.R115P	ENST00000263967	NM_006218.2	115	cGa/cCa	2/21	0.783321831588153	14	FACETS	0.951	0.933	0.968			1	CLONAL	8	TRUE	NA	0.783321831588153	14		549	4105	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971110	21971110	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519881	NA	P-0012587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	1145	319	0	ENST00000304494.5:c.248A>G	p.His83Arg	p.H83R	ENST00000304494	NM_000077.4	83	cAc/cGc	2/3	0.760039029790856	4	FACETS	1	0.997	1	1	0.997	1	CLONAL	4	TRUE	0	0.783321831588153	4		319	1266	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448601	89448601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775665893	NA	P-0012587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	211	451	2	ENST00000336596.2:c.1565G>A	p.Arg522His	p.R522H	ENST00000336596	NM_005233.5	522	cGc/cAc	7/17	0.783321831588153	4	FACETS	0.731	0.677	0.786			1	SUBCLONAL	1	TRUE	NA	0.783321831588153	4		453	1315	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858189	27858189	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	1175	784	3	ENST00000359303.2:c.382G>T	p.Ala128Ser	p.A128S	ENST00000359303	NM_003535.2	128	Gcg/Tcg	1/1	0.740179656784827	4	FACETS	0.966	0.952	0.979	0.966	0.952	0.979	CLONAL	4	TRUE	0	0.783321831588153	4		787	1385	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455095	50455095	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs753136483	NA	P-0012587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	184	386	0	ENST00000331340.3:c.642C>A	p.Ser214Arg	p.S214R	ENST00000331340	NM_006060.4	214	agC/agA	6/8	1	2	FACETS	0.816	0.757	0.875	0.816	0.757	0.875	CLONAL	1	TRUE	1	0.783321831588153	2		386	576	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372173	55372173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	148	201	0	ENST00000297316.4:c.863C>T	p.Ala288Val	p.A288V	ENST00000297316	NM_022454.3	288	gCg/gTg	2/2	0.756007047590519	3	FACETS	0.915	0.839	0.993	0.457	0.419	0.497	CLONAL	1	TRUE	1	0.783321831588153	3		201	575	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999111	100999111	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	724	777	0	ENST00000325455.5:c.691G>C	p.Glu231Gln	p.E231Q	ENST00000325455	NM_001202474.3	231	Gag/Cag	1/8	0.761112226528536	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.783321831588153	2		777	895	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916251	9916251	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	467	471	0	ENST00000330684.3:c.2038T>C	p.Phe680Leu	p.F680L	ENST00000330684	NM_001134407.1	680	Ttt/Ctt	10/13	0.777774988413025	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.783321831588153	3		471	819	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435749	56435749	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	315	231	0	ENST00000407977.2:c.1388C>T	p.Ala463Val	p.A463V	ENST00000407977		463	gCc/gTc	9/10	0.379117498862567	5	FACETS	1	0.991	1	0.788	0.748	0.828	INDETERMINATE	2	TRUE	2	0.783321831588153	5		231	740	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611784	100611784	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	544	283	0	ENST00000308731.7:c.1337C>A	p.Ala446Asp	p.A446D	ENST00000308731	NM_000061.2	446	gCc/gAc	14/19	0.783321831588153	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.783321831588153	2		283	629	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144134	11144141	+	frameshift_variant	Frame_Shift_Del	DEL	TCCAGCCA	TCCAGCCA	-	novel	NA	P-0012587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	586	506	0	ENST00000358026.2:c.3716_3723del	p.Ser1239Ter	p.S1239*	ENST00000358026	NM_001128849.1	1239	TCCAGCCAt/t	26/36	0.783321831588153	2	FACETS	0.991	0.967	1	0.991	0.967	1	CLONAL	2	TRUE	0	0.783321831588153	2		506	755	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0012594-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	23	751	0	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	1	2	FACETS	0.045	0.034	0.057	0.045	0.034	0.057	SUBCLONAL	1	TRUE	1	1	2		751	1026	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125499161	125499161	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012594-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	33	530	0	ENST00000428830.2:c.324G>C	p.Gln108His	p.Q108H	ENST00000428830	NM_001114121.2	108	caG/caC	4/14	1	2	FACETS	0.102	0.083	0.125	0.102	0.083	0.125	SUBCLONAL	1	TRUE	1	1	2		530	645	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894228	NA	P-0012597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	116	699	0	ENST00000451590.1:c.37G>C	p.Gly13Arg	p.G13R	ENST00000451590	NM_001130442.1	13	Ggt/Cgt	2/5	1	2	FACETS	0.995	0.897	1	0.995	0.897	1	CLONAL	1	TRUE	1	0.291728212497379	2		699	799	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0012597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	48	676	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.291728212497379	1	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	0	0.291728212497379	1		676	256	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911473	32911473	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	206	864	0	ENST00000380152.3:c.2981C>G	p.Ala994Gly	p.A994G	ENST00000380152		994	gCa/gGa	11/27	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.291728212497379	2		864	1323	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525035	9525035	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	122	488	0	ENST00000353224.5:c.1850G>C	p.Arg617Thr	p.R617T	ENST00000353224	NM_177990.2	617	aGg/aCg	8/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.291728212497379	2		488	789	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711879	89711880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	84	302	0	ENST00000371953.3:c.499dup	p.Thr167AsnfsTer13	p.T167Nfs*13	ENST00000371953	NM_000314.4	166	gta/gtAa	6/9	0.291728212497379	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.291728212497379	1		302	459	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972653	25972653	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146506022	NA	P-0012601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	33	543	0	ENST00000435504.4:c.1772G>A	p.Arg591His	p.R591H	ENST00000435504		591	cGc/cAc	12/13	0.128267744244105	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		543	749	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119023	70119024	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0012601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	27	367	0	ENST00000245479.2:c.600dup	p.Asn201GlnfsTer51	p.N201Qfs*51	ENST00000245479	NM_000346.3	199	tcc/tCcc	2/3	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		367	400	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0012625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	112	525	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.65	0.584	0.721	0.65	0.584	0.721	SUBCLONAL	1	TRUE	1	0.352522564859385	2		525	977	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577595	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0012625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	72	317	0	ENST00000269305.4:c.686_687del	p.Cys229TyrfsTer10	p.C229Yfs*10	ENST00000269305	NM_001126112.2	229	tGT/t	7/11	0.248173352763339	1	FACETS	0.65	0.568	0.737	0.65	0.568	0.737	SUBCLONAL	1	TRUE	0	0.352522564859385	1		317	518	SUCCESS
APC	324	MSKCC	GRCh37	5	112173661	112173662	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0012625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	69	342	0	ENST00000257430.4:c.2373_2374del	p.His791GlnfsTer7	p.H791Qfs*7	ENST00000257430	NM_000038.5	790	agACac/agac	16/16	1	2	FACETS	0.51	0.443	0.582	0.51	0.443	0.582	SUBCLONAL	1	TRUE	1	0.352522564859385	2		342	768	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197759	123197759	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	68	469	0	ENST00000218089.9:c.1883T>C	p.Val628Ala	p.V628A	ENST00000218089	NM_001042749.1	628	gTt/gCt	20/35	1	2	FACETS	0.3	0.259	0.344	0.3	0.259	0.344	SUBCLONAL	1	TRUE	1	0.352522564859385	2		469	1287	SUCCESS
APC	324	MSKCC	GRCh37	5	112176015	112176039	+	frameshift_variant	Frame_Shift_Del	DEL	TAGAAGAATGTATTATTTCTGCCAT	TAGAAGAATGTATTATTTCTGCCAT	-	novel	NA	P-0012625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	57	223	0	ENST00000257430.4:c.4724_4748del	p.Leu1575ArgfsTer67	p.L1575Rfs*67	ENST00000257430	NM_000038.5	1575	cTAGAAGAATGTATTATTTCTGCCATg/cg	16/16	1	2	FACETS	0.541	0.464	0.625	0.541	0.464	0.625	SUBCLONAL	1	TRUE	1	0.352522564859385	2		223	598	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	92	766	0				ENST00000310581	NM_198253.2	-/1132			0.329244977908951	3	FACETS	1	0.963	1	0.596	0.531	0.665	CLONAL	1	TRUE	1	0.329244977908951	3		766	546	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012765	36012765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	62	155	1	ENST00000358208.4:c.209C>T	p.Ser70Leu	p.S70L	ENST00000358208		70	tCg/tTg	2/12	1	2	FACETS	0.806	0.698	0.924	0.806	0.698	0.924	CLONAL	1	TRUE	1	0.329244977908951	2		156	467	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55219004	55219004	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	67	319	0	ENST00000275493.2:c.577A>G	p.Ser193Gly	p.S193G	ENST00000275493	NM_005228.3	193	Agc/Ggc	5/28	1	2	FACETS	0.41	0.355	0.47	0.41	0.355	0.47	SUBCLONAL	1	TRUE	1	0.329244977908951	2		319	993	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576876	7576904	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGTGGTTTCTTCTTTGGCTGGGGAGAG	CCAGTGGTTTCTTCTTTGGCTGGGGAGAG	-	novel	NA	P-0012628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	112	327	2	ENST00000269305.4:c.942_970del	p.Ser315TrpfsTer12	p.S315Wfs*12	ENST00000269305	NM_001126112.2	314	tcCTCTCCCCAGCCAAAGAAGAAACCACTGGat/tcat	9/11	0.329244977908951	1	FACETS	0.696	0.625	0.77	0.696	0.625	0.77	SUBCLONAL	1	TRUE	0	0.329244977908951	1		329	817	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478132	99478132	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	336	635	0	ENST00000268035.6:c.3036G>A	p.Met1012Ile	p.M1012I	ENST00000268035	NM_000875.3	1012	atG/atA	16/21	1	2	FACETS	0.877	0.83	0.926	0.877	0.83	0.926	CLONAL	1	TRUE	1	0.637228488381207	2		635	1202	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107136	27107137	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0012638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	130	270	0	ENST00000324856.7:c.6749_6750del	p.Glu2250ValfsTer27	p.E2250Vfs*27	ENST00000324856	NM_006015.4	2249	tcAGag/tcag	20/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.500632120937056	2		270	489	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571449	95571449	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs867768809	NA	P-0012638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	141	231	0	ENST00000393063.1:c.3228C>A	p.Ser1076Arg	p.S1076R	ENST00000393063	NM_030621.3	1076	agC/agA	21/28	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.500632120937056	2		231	504	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763522	41763522	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	185	448	0	ENST00000301178.4:c.2321G>T	p.Cys774Phe	p.C774F	ENST00000301178	NM_021913.4	774	tGt/tTt	19/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.500632120937056	2		448	691	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	36	840	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		840	881	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882025	NA	P-0012641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1300	35	731	0	ENST00000269305.4:c.646G>T	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ttg	6/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		731	1335	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439258	52439528	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGGCTGTGGGATGGGGCTTGTGCGCATGAACCAGCCGCCTCCTCTGCACCATCTGAGACAGGGCAAGAACACAGGCAGGACCTCCAGTAGGATCTCCAAGAAAAGCTCACAGTCTCCCCGGCCCTGTGAACCAGCACTTCCCAGAGAAGAACAGCCCAGCCAGCTGGTGCAATGGGAGTCAGCAAGCTCTAAGTCATGATCCCGCAATGAGACAGGGCAAAGAATGAGATGGGAAAAAAGAAGCAGGAAGAAAAAAAAAAAAAAAAAAAA	AGGGCTGTGGGATGGGGCTTGTGCGCATGAACCAGCCGCCTCCTCTGCACCATCTGAGACAGGGCAAGAACACAGGCAGGACCTCCAGTAGGATCTCCAAGAAAAGCTCACAGTCTCCCCGGCCCTGTGAACCAGCACTTCCCAGAGAAGAACAGCCCAGCCAGCTGGTGCAATGGGAGTCAGCAAGCTCTAAGTCATGATCCCGCAATGAGACAGGGCAAAGAATGAGATGGGAAAAAAGAAGCAGGAAGAAAAAAAAAAAAAAAAAAAA	-	novel	NA	P-0012648-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	75	595	0	ENST00000460680.1:c.932-218_984del		p.X311_splice	ENST00000460680	NM_004656.3	311		11/17	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		595	580	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	28	720	1	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		721	994	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0012658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	39	585	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		586	1109	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0012678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	827	324	1	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	0.75034465251825	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.755495735380343	2		325	1072	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907677	111907677	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1763	120	420	0	ENST00000393256.3:c.451G>C	p.Glu151Gln	p.E151Q	ENST00000393256	NM_006538.4	151	Gag/Cag	3/4	0.755495735380343	3	FACETS	0.232	0.209	0.258	0.116	0.104	0.129	SUBCLONAL	1	TRUE	1	0.755495735380343	3		420	1883	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066675	94066675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	593	467	2	ENST00000369303.4:c.1084G>A	p.Asp362Asn	p.D362N	ENST00000369303	NM_004440.3	362	Gat/Aat	5/17	0.754826417713803	2	FACETS	1	0.975	1	0.509	0.489	0.529	CLONAL	1	TRUE	0	0.755495735380343	2		469	1543	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556367	29556367	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	103	327	0	ENST00000356175.3:c.2734C>T	p.Gln912Ter	p.Q912*	ENST00000356175	NM_000267.3	912	Caa/Taa	21/57	0.75034465251825	2	FACETS	0.301	0.269	0.335	0.15	0.134	0.168	SUBCLONAL	1	TRUE	0	0.755495735380343	2		327	906	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212495	133212495	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879254168	NA	P-0012678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	290	337	0	ENST00000320574.5:c.5794C>T	p.Arg1932Cys	p.R1932C	ENST00000320574	NM_006231.2	1932	Cgt/Tgt	42/49	0.755495735380343	3	FACETS	0.872	0.82	0.926	0.436	0.41	0.463	CLONAL	1	TRUE	1	0.755495735380343	3		337	1213	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107231	193107231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	315	300	0	ENST00000367435.3:c.440G>A	p.Arg147His	p.R147H	ENST00000367435	NM_024529.4	147	cGc/cAc	6/17	1	2	FACETS	0.919	0.87	0.97	0.919	0.87	0.97	CLONAL	1	TRUE	1	0.755495735380343	2		300	907	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096669	178096669	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	272	215	0	ENST00000397062.3:c.662C>G	p.Thr221Arg	p.T221R	ENST00000397062	NM_006164.4	221	aCa/aGa	5/5	1	2	FACETS	0.972	0.917	1	0.972	0.917	1	CLONAL	1	TRUE	1	0.755495735380343	2		215	741	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683369	182683369	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1480	242	255	0	ENST00000292782.4:c.176C>A	p.Ser59Ter	p.S59*	ENST00000292782	NM_020640.2	59	tCa/tAa	2/7	0.755495735380343	7	FACETS	1	0.97	1	0.215	0.2	0.231	CLONAL	1	TRUE	2	0.755495735380343	7		255	1722	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90947833	90947833	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	79	222	0	ENST00000265433.3:c.2242C>T	p.Pro748Ser	p.P748S	ENST00000265433	NM_002485.4	748	Cct/Tct	16/16	0.755495735380343	3	FACETS	0.384	0.337	0.435	0.192	0.168	0.218	SUBCLONAL	1	TRUE	1	0.755495735380343	3		222	750	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606256	93606256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1287	107	340	0	ENST00000375746.1:c.76G>A	p.Glu26Lys	p.E26K	ENST00000375746	NM_001174167.1	26	Gaa/Aaa	2/14	0.755495735380343	3	FACETS	0.28	0.25	0.312	0.093	0.083	0.104	SUBCLONAL	1	TRUE	0	0.755495735380343	3		340	1394	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566734	139566734	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs144969763	NA	P-0012678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	989	367	0	ENST00000308874.7:c.818C>G	p.Ser273Trp	p.S273W	ENST00000308874		273	tCg/tGg	10/10	0.755495735380343	3	FACETS	1	0.995	1	0.714	0.697	0.732	CLONAL	2	TRUE	0	0.755495735380343	3		367	1683	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998327	100998327	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs753242711	NA	P-0012678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	60	50	0	ENST00000325455.5:c.1475G>C	p.Arg492Pro	p.R492P	ENST00000325455	NM_001202474.3	492	cGg/cCg	1/8	0.754487593540672	3	FACETS	0.725	0.629	0.827	0.242	0.209	0.276	SUBCLONAL	1	TRUE	0	0.755495735380343	3		50	302	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435230	18435230	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs373226538	NA	P-0012678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	90	307	0	ENST00000266497.5:c.215A>G	p.Asp72Gly	p.D72G	ENST00000266497		72	gAc/gGc	1/31	0.156094598760558	5	FACETS	0.394	0.348	0.443			1	INDETERMINATE	1	TRUE	NA	0.755495735380343	5		307	1290	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353780	68353780	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	54	246	0	ENST00000487270.1:c.615A>T	p.Lys205Asn	p.K205N	ENST00000487270	NM_133509.3	205	aaA/aaT	7/11	0.755495735380343	3	FACETS	0.271	0.231	0.316	0.136	0.115	0.158	SUBCLONAL	1	TRUE	1	0.755495735380343	3		246	726	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576129	88576129	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	407	389	0	ENST00000360948.2:c.1544A>G	p.Gln515Arg	p.Q515R	ENST00000360948	NM_001012338.2	515	cAg/cGg	13/19	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.755495735380343	2		389	1050	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858445	9858445	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	719	384	0	ENST00000330684.3:c.2956C>G	p.Leu986Val	p.L986V	ENST00000330684	NM_001134407.1	986	Ctt/Gtt	13/13	0.409737595703274	4	FACETS	1	0.996	1			1	INDETERMINATE	2	TRUE	NA	0.755495735380343	4		384	1386	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14022015	14022015	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	306	320	0	ENST00000311895.7:c.715G>C	p.Glu239Gln	p.E239Q	ENST00000311895	NM_005236.2	239	Gaa/Caa	4/11	0.409737595703274	4	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.755495735380343	4		320	1139	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024566	14024566	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0012678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	74	249	0	ENST00000311895.7:c.793-1G>C		p.X265_splice	ENST00000311895	NM_005236.2	265			0.409737595703274	4	FACETS	0.372	0.324	0.423			1	INDETERMINATE	1	TRUE	NA	0.755495735380343	4		249	925	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56875616	56875616	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0012678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	271	302	0	ENST00000308159.5:c.2221-1G>T		p.X741_splice	ENST00000308159	NM_014669.4	741			0.75034465251825	2	FACETS	0.906	0.853	0.959	0.453	0.426	0.48	CLONAL	1	TRUE	0	0.755495735380343	2		302	792	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559864	29559864	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs371544233	NA	P-0012678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	339	229	0	ENST00000356175.3:c.3461A>T	p.Asn1154Ile	p.N1154I	ENST00000356175	NM_000267.3	1154	aAt/aTt	26/57	0.75034465251825	2	FACETS	0.96	0.911	1	0.48	0.455	0.505	CLONAL	1	TRUE	0	0.755495735380343	2		229	935	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56376723	56376723	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2362	396	456	0	ENST00000348428.3:c.763A>G	p.Ile255Val	p.I255V	ENST00000348428	NM_006785.3	255	Att/Gtt	5/17	0.438072131263301	6	FACETS	0.954	0.902	1	0.318	0.3	0.336	INDETERMINATE	1	TRUE	3	0.755495735380343	6		456	2758	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627706	14627706	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1377	139	498	0	ENST00000254322.2:c.364G>T	p.Glu122Ter	p.E122*	ENST00000254322	NM_006145.1	122	Gag/Tag	2/3	0.754826417713803	2	FACETS	0.243	0.22	0.267	0.121	0.11	0.134	SUBCLONAL	1	TRUE	0	0.755495735380343	2		498	1516	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513245	41513245	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	410	344	0	ENST00000263253.7:c.149C>T	p.Ser50Phe	p.S50F	ENST00000263253	NM_001429.3	50	tCt/tTt	2/31	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.755495735380343	2		344	1058	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951082	48951086	+	frameshift_variant	Frame_Shift_Del	DEL	TACTG	TACTG	A	novel	NA	P-0012678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	400	209	0	ENST00000267163.4:c.1244_1248delinsA	p.Ile415LysfsTer4	p.I415Kfs*4	ENST00000267163	NM_000321.2	415	aTACTG/aA	13/27	0.75034465251825	2	FACETS	0.934	0.903	0.964	0.934	0.903	0.964	CLONAL	2	TRUE	0	0.755495735380343	2		209	567	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0012688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	218	762	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.20543841479975	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.20543841479975	3		762	1112	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0012688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	106	952	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.20543841479975	2		952	1013	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974695	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691187	NA	P-0012688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	75	828	0	ENST00000304494.5:c.132del	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	taC/ta	1/3	0.20543841479975	1	FACETS	0.781	0.683	0.887	0.781	0.683	0.887	SUBCLONAL	1	TRUE	0	0.20543841479975	1		828	839	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604655	48604655	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121912578	NA	P-0012688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	58	625	0	ENST00000342988.3:c.1477G>C	p.Asp493His	p.D493H	ENST00000342988	NM_005359.5	493	Gat/Cat	12/12	1	2	FACETS	0.766	0.657	0.885	0.766	0.657	0.885	SUBCLONAL	1	TRUE	1	0.20543841479975	2		625	737	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871602	35871602	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs116801398	NA	P-0012688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	83	810	1	ENST00000216797.5:c.904G>A	p.Glu302Lys	p.E302K	ENST00000216797	NM_020529.2	302	Gag/Aag	5/6	1	2	FACETS	0.879	0.774	0.992	0.879	0.774	0.992	CLONAL	1	TRUE	1	0.20543841479975	2		811	919	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434650	99434650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1297968262	NA	P-0012719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	283	471	0	ENST00000268035.6:c.737C>T	p.Thr246Met	p.T246M	ENST00000268035	NM_000875.3	246	aCg/aTg	3/21	1	2	FACETS	0.588	0.552	0.625	0.588	0.552	0.625	SUBCLONAL	1	TRUE	1	0.769248827989675	2		471	1252	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100305	27100306	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCAA	novel	NA	P-0012719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	256	566	0	ENST00000324856.7:c.4018_4022dup	p.Asn1341LysfsTer142	p.N1341Kfs*142	ENST00000324856	NM_006015.4	1339	-/GGCAA	17/20	1	2	FACETS	0.483	0.451	0.516	0.483	0.451	0.516	SUBCLONAL	1	TRUE	1	0.769248827989675	2		566	1379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0012722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	217	773	2	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.526664228398703	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.526664228398703	1		775	565	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0012722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	81	291	1	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	1	2	FACETS	0.705	0.624	0.792	0.705	0.624	0.792	SUBCLONAL	1	TRUE	1	0.526664228398703	2		292	436	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603044	48603044	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781359	NA	P-0012722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	42	257	0	ENST00000342988.3:c.1345C>T	p.Gln449Ter	p.Q449*	ENST00000342988	NM_005359.5	449	Cag/Tag	11/12	0.526664228398703	1	FACETS	0.412	0.346	0.485	0.412	0.346	0.485	SUBCLONAL	1	TRUE	0	0.526664228398703	1		257	285	SUCCESS
APC	324	MSKCC	GRCh37	5	112176030	112176030	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs886039682	NA	P-0012722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	123	366	0	ENST00000257430.4:c.4741del	p.Ser1581LeufsTer69	p.S1581Lfs*69	ENST00000257430	NM_000038.5	1580	aTt/at	16/16	1	2	FACETS	0.911	0.828	0.997	0.911	0.828	0.997	CLONAL	1	TRUE	1	0.526664228398703	2		366	513	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0012729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	86	757	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.179067743306603	2	FACETS	1	0.961	1	0.603	0.533	0.679	CLONAL	1	TRUE	0	0.179067743306603	2		758	796	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850861	128850861	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs775441067	NA	P-0012729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	142	726	0	ENST00000249373.3:c.1708G>T	p.Ala570Ser	p.A570S	ENST00000249373	NM_005631.4	570	Gcc/Tcc	10/12	0.108577051519414	4	FACETS	0.882	0.803	0.966	0.882	0.803	0.966	CLONAL	2	TRUE	2	0.179067743306603	4		726	1060	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048182	180048182	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	83	683	0	ENST00000261937.6:c.2091G>C	p.Met697Ile	p.M697I	ENST00000261937	NM_182925.4	697	atG/atC	14/30	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.179067743306603	2		683	780	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271224	26271224	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1293	168	1198	1	ENST00000305910.3:c.389G>A	p.Arg130His	p.R130H	ENST00000305910	NM_003534.2	130	cGc/cAc	1/1	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.179067743306603	2		1199	1461	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523505	106523505	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	75	378	0	ENST00000359195.3:c.2657C>G	p.Thr886Arg	p.T886R	ENST00000359195	NM_002649.2	886	aCg/aGg	8/11	0.108577051519414	4	FACETS	1	0.971	1	0.704	0.617	0.799	CLONAL	1	TRUE	2	0.179067743306603	4		378	701	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561555	9561555	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	27	375	0	ENST00000353224.5:c.227C>A	p.Pro76His	p.P76H	ENST00000353224	NM_177990.2	76	cCc/cAc	4/10	0.101401212819975	3	FACETS	0.794	0.631	0.98	0.397	0.315	0.49	INDETERMINATE	1	TRUE	1	0.179067743306603	3		375	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579394	7579394	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	96	653	0	ENST00000269305.4:c.293del	p.Pro98LeufsTer25	p.P98Lfs*25	ENST00000269305	NM_001126112.2	98	cCt/ct	4/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.179067743306603	2		653	807	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	50	720	1	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		721	969	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0012735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	45	913	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		913	1180	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0012742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	270	506	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.257360183978704	1	FACETS	0.737	0.693	0.783	0.737	0.693	0.783	INDETERMINATE	1	FALSE	0	0.56690381058212	1		506	926	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0012742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	221	763	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.359650030743711	1	FACETS	0.858	0.803	0.914	0.858	0.803	0.914	CLONAL	1	FALSE	0	0.56690381058212	1		764	651	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	104	291	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	0.257360183978704	1	FACETS	0.549	0.494	0.607	0.549	0.494	0.607	INDETERMINATE	1	FALSE	0	0.56690381058212	1		291	479	SUCCESS
APC	324	MSKCC	GRCh37	5	112175419	112175419	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0012742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	150	330	0	ENST00000257430.4:c.4128T>A	p.Tyr1376Ter	p.Y1376*	ENST00000257430	NM_000038.5	1376	taT/taA	16/16	0.257360183978704	1	FACETS	0.704	0.647	0.762	0.704	0.647	0.762	INDETERMINATE	1	FALSE	0	0.56690381058212	1		330	539	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593504	48593504	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	207	361	0	ENST00000342988.3:c.1255G>T	p.Gly419Trp	p.G419W	ENST00000342988	NM_005359.5	419	Ggg/Tgg	10/12	0.56690381058212	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	0	0.56690381058212	1		361	481	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55991403	55991403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	155	601	0	ENST00000263923.4:c.58G>A	p.Ala20Thr	p.A20T	ENST00000263923	NM_002253.2	20	Gcc/Acc	1/30	0.359650030743711	1	FACETS	0.424	0.388	0.462	0.424	0.388	0.462	SUBCLONAL	1	FALSE	0	0.56690381058212	1		601	924	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445899	49445899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	202	838	0	ENST00000301067.7:c.1567C>T	p.Pro523Ser	p.P523S	ENST00000301067	NM_003482.3	523	Ccg/Tcg	10/54	0.359650030743711	1	FACETS	0.48	0.445	0.517	0.48	0.445	0.517	SUBCLONAL	1	FALSE	0	0.56690381058212	1		838	1063	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41247905	41247905	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	151	613	0	ENST00000357654.3:c.628C>G	p.Gln210Glu	p.Q210E	ENST00000357654	NM_007294.3	210	Caa/Gaa	9/23	0.30250134143816	2	FACETS	0.483	0.44	0.527	0.241	0.22	0.264	INDETERMINATE	1	FALSE	0	0.56690381058212	2		613	1104	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439883	52439883	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	236	399	0	ENST00000460680.1:c.829C>T	p.Gln277Ter	p.Q277*	ENST00000460680	NM_004656.3	277	Caa/Taa	10/17	0.605690433105809	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.605690433105809	1		399	463	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196508	106196508	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	65	507	0	ENST00000380013.4:c.4841C>G	p.Pro1614Arg	p.P1614R	ENST00000380013	NM_001127208.2	1614	cCc/cGc	11/11	NA	2	FACETS	0.337	0.292	0.386			1	INDETERMINATE	1	TRUE	NA	0.605690433105809	2		507	637	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411649	116411649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	427	430	0	ENST00000397752.3:c.2828C>T	p.Thr943Ile	p.T943I	ENST00000397752	NM_000245.2	943	aCa/aTa	13/21	0.605690433105809	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.605690433105809	3		430	856	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027875	48027875	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	417	515	0	ENST00000234420.5:c.2753A>C	p.His918Pro	p.H918P	ENST00000234420	NM_000179.2	918	cAt/cCt	4/10	0.491562416656939	5	FACETS	0.866	0.826	0.907			1	CLONAL	3	TRUE	NA	0.491562416656939	5		515	1134	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718999	190718999	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	65	295	0	ENST00000441310.2:c.1001C>A	p.Thr334Lys	p.T334K	ENST00000441310	NM_000534.4	334	aCg/aAg	9/13	0.437173240951905	3	FACETS	0.694	0.603	0.792	0.231	0.201	0.264	SUBCLONAL	1	TRUE	0	0.491562416656939	3		295	475	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125490	47125490	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	62	728	0	ENST00000409792.3:c.5780A>T	p.Gln1927Leu	p.Q1927L	ENST00000409792	NM_014159.6	1927	cAg/cTg	12/21	0.486590857087244	2	FACETS	0.261	0.224	0.301	0.13	0.112	0.151	SUBCLONAL	1	TRUE	0	0.491562416656939	2		728	967	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879322	151879322	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	240	352	0	ENST00000262189.6:c.5623C>T	p.Gln1875Ter	p.Q1875*	ENST00000262189	NM_170606.2	1875	Cag/Tag	36/59	0.486590857087244	2	FACETS	0.948	0.895	1	0.948	0.895	1	CLONAL	2	TRUE	0	0.491562416656939	2		352	515	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456738	32456738	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs961526551	NA	P-0012785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	65	214	0	ENST00000332351.3:c.154C>G	p.Arg52Gly	p.R52G	ENST00000332351	NM_024426.4	52	Cgt/Ggt	1/10	0.491562416656939	3	FACETS	0.828	0.721	0.943	0.414	0.36	0.472	CLONAL	1	TRUE	1	0.491562416656939	3		214	398	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515220	103515220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	75	606	0	ENST00000355739.4:c.1721C>T	p.Ala574Val	p.A574V	ENST00000355739	NM_000123.3	574	gCt/gTt	8/15	0.424601290990264	5	FACETS	0.48	0.419	0.546	0.096	0.083	0.11	SUBCLONAL	1	TRUE	0	0.491562416656939	5		606	1104	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632406	1632406	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0012785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	66	556	0	ENST00000344749.5:c.146-2A>C		p.X49_splice	ENST00000344749	NM_001136139.2	49			NA	2	FACETS	0.299	0.259	0.343			1	INDETERMINATE	1	TRUE	NA	0.491562416656939	2		556	897	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572934	7572935	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0012785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	381	758	0	ENST00000269305.4:c.1174_1175del	p.Ser392ArgfsTer78	p.S392Rfs*78	ENST00000269305	NM_001126112.2	392	TCa/a	11/11	0.486590857087244	2	FACETS	0.846	0.807	0.886	0.846	0.807	0.886	CLONAL	2	TRUE	0	0.491562416656939	2		758	916	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0012792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	127	621	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.166202563549887	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	0	0.166202563549887	2		621	726	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057697	27057697	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1303	85	1009	0	ENST00000324856.7:c.1405C>A	p.Pro469Thr	p.P469T	ENST00000324856	NM_006015.4	469	Cca/Aca	3/20	0.136810522413912	1	FACETS	0.676	0.595	0.763	0.676	0.595	0.763	SUBCLONAL	1	TRUE	0	0.166202563549887	1		1009	1388	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851810	134851810	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	40	583	0	ENST00000398015.3:c.1216A>C	p.Ile406Leu	p.I406L	ENST00000398015	NM_004441.4	406	Atc/Ctc	5/16	0.166202563549887	1	FACETS	0.643	0.533	0.767	0.643	0.533	0.767	SUBCLONAL	1	TRUE	0	0.166202563549887	1		583	686	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313421	30313421	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	96	747	0	ENST00000262643.3:c.1021A>T	p.Thr341Ser	p.T341S	ENST00000262643	NM_001238.2	341	Acg/Tcg	11/12	0.166202563549887	3	FACETS	1	0.941	1	0.546	0.485	0.611	CLONAL	1	TRUE	1	0.166202563549887	3		747	1146	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0012795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	1207	525	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.935002498339331	4	FACETS	0.982	0.963	0.999	0.982	0.963	0.999	CLONAL	3	TRUE	1	0.960899215943644	4		525	1673	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557630	95557630	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	1046	613	0	ENST00000393063.1:c.5437G>C	p.Glu1813Gln	p.E1813Q	ENST00000393063	NM_030621.3	1813	Gag/Cag	26/28	0.957782599167357	2	FACETS	0.994	0.986	1	0.994	0.986	1	CLONAL	2	TRUE	0	0.960899215943644	2		613	1095	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218089	108218089	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587779874	NA	P-0012795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	277	264	0	ENST00000278616.4:c.8668C>G	p.Leu2890Val	p.L2890V	ENST00000278616	NM_000051.3	2890	Cta/Gta	59/63	0.960899215943644	1	FACETS	0.966	0.942	0.988	0.966	0.942	0.988	CLONAL	1	TRUE	0	0.960899215943644	1		264	310	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165935	47165935	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	551	604	0	ENST00000409792.3:c.191A>C	p.Asn64Thr	p.N64T	ENST00000409792	NM_014159.6	64	aAt/aCt	3/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.960899215943644	2		604	1117	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602325	28602325	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	539	623	0	ENST00000241453.7:c.2043C>A	p.Cys681Ter	p.C681*	ENST00000241453	NM_004119.2	681	tgC/tgA	16/24	1	2	FACETS	0.933	0.897	0.968	0.933	0.897	0.968	CLONAL	1	TRUE	1	0.960899215943644	2		623	1203	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0012803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	30	637	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.745561012191958	5	FACETS	0.382	0.307	0.466	0.127	0.102	0.156	SUBCLONAL	1	TRUE	2	0.789075350753471	5		637	435	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0012803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	266	733	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	0.789075350753471	3	FACETS	0.944	0.886	1	0.472	0.443	0.502	CLONAL	1	TRUE	1	0.789075350753471	3		733	996	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679835	88679835	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	78	433	0	ENST00000360948.2:c.628C>A	p.Pro210Thr	p.P210T	ENST00000360948	NM_001012338.2	210	Cct/Act	7/19	0.712271952349315	3	FACETS	0.722	0.638	0.811	0.361	0.319	0.406	SUBCLONAL	1	TRUE	1	0.789075350753471	3		433	382	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504162	123504162	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs757900199	NA	P-0012803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	140	473	0	ENST00000371139.4:c.338G>T	p.Gly113Val	p.G113V	ENST00000371139	NM_001114937.2	113	gGt/gTt	3/4	0.789075350753471	3	FACETS	0.97	0.889	1	0.485	0.444	0.527	CLONAL	1	TRUE	1	0.789075350753471	3		473	510	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176503	142176505	+	inframe_deletion	In_Frame_Del	DEL	CGA	CGA	-	novel	NA	P-0012803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	166	648	0	ENST00000350721.4:c.7596_7598del	p.Phe2532_Arg2533delinsLeu	p.F2532_R2533delinsL	ENST00000350721	NM_001184.3	2532	ttTCGa/tta	45/47	0.745561012191958	5	FACETS	0.795	0.729	0.864	0.265	0.243	0.288	SUBCLONAL	1	TRUE	2	0.789075350753471	5		648	1156	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24129433	24129567	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACATGATCGGCTCCGAGGTAGCCCGGGGCGCGTTCTCGCCCTCCCCGGGCTCGGCCCCGCGGGAGCCCCGGGGCGGGCCCATGCGCCGAGAGCGCGCGTCTCCATTCATCGGGGCGGGCGGGCGCGCGCGCGCGC	ACATGATCGGCTCCGAGGTAGCCCGGGGCGCGTTCTCGCCCTCCCCGGGCTCGGCCCCGCGGGAGCCCCGGGGCGGGCCCATGCGCCGAGAGCGCGCGTCTCCATTCATCGGGGCGGGCGGGCGCGCGCGCGCGC	-	novel	NA	P-0012813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	220	586	0	ENST00000263121.7:c.77_93+118del		p.X26_splice	ENST00000263121	NM_003073.3	26		1/9	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		586	725	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24133832	24133941	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	GGGGCCACCTCAAGGCCTGTTTGTCTGTTGCTTGATGCAGTCTGCGCCAGGACCCTCCCCTTCCCTGTGGTGCTGCGACCCTTATAATGAGCCTTCTTGCTTTACTCATA	GGGGCCACCTCAAGGCCTGTTTGTCTGTTGCTTGATGCAGTCTGCGCCAGGACCCTCCCCTTCCCTGTGGTGCTGCGACCCTTATAATGAGCCTTCTTGCTTTACTCATA	-	novel	NA	P-0012813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	90	48	0	ENST00000263121.7:c.94-109_94del		p.X32_splice	ENST00000263121	NM_003073.3	32			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		48	162	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0012816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	98	477	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.565	0.504	0.631	0.565	0.504	0.631	SUBCLONAL	1	TRUE	1	0.45076319121708	2		477	769	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996759	100996759	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	70	797	0	ENST00000325455.5:c.1768T>G	p.Phe590Val	p.F590V	ENST00000325455	NM_001202474.3	590	Ttc/Gtc	2/8	1	2	FACETS	0.281	0.244	0.322	0.281	0.244	0.322	SUBCLONAL	1	TRUE	1	0.45076319121708	2		797	1104	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591238	67591265	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTTTTTCAGGTGGTTGACTCAAAAAGG	TGTTTTTCAGGTGGTTGACTCAAAAAGG	-	novel	NA	P-0012816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	61	332	0	ENST00000274335.5:c.1746-6_1767del		p.X582_splice	ENST00000274335		582		13/15	1	2	FACETS	0.405	0.348	0.466	0.405	0.348	0.466	SUBCLONAL	1	TRUE	1	0.45076319121708	2		332	669	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692891	89692905	+	inframe_deletion	In_Frame_Del	DEL	AGCTGGAAAGGGACG	AGCTGGAAAGGGACG	-	novel	NA	P-0012816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	41	241	0	ENST00000371953.3:c.376_390del	p.Ala126_Arg130del	p.A126_R130del	ENST00000371953	NM_000314.4	125	aaAGCTGGAAAGGGACGa/aaa	5/9	1	2	FACETS	0.572	0.478	0.675	0.572	0.478	0.675	SUBCLONAL	1	TRUE	1	0.45076319121708	2		241	318	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650753	67650756	+	protein_altering_variant	In_Frame_Del	DEL	GTTC	GTTC	T	novel	NA	P-0012816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	97	524	0	ENST00000264010.4:c.1058_1061delinsT	p.Cys353_Ser354delinsPhe	p.C353_S354delinsF	ENST00000264010	NM_006565.3	353	tGTTCc/tTc	5/12	1	2	FACETS	0.457	0.406	0.511	0.457	0.406	0.511	SUBCLONAL	1	TRUE	1	0.45076319121708	2		524	942	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717705	89717713	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCAGCCG	CCTCAGCCG	T	novel	NA	P-0012816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	69	362	0	ENST00000371953.3:c.730_738delinsT	p.Pro244PhefsTer6	p.P244Ffs*6	ENST00000371953	NM_000314.4	244	CCTCAGCCG/T	7/9	1	2	FACETS	0.534	0.465	0.609	0.534	0.465	0.609	SUBCLONAL	1	TRUE	1	0.45076319121708	2		362	573	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0012823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	260	525	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.3	1	FACETS	0.863	0.81	0.916	1	0.994	1	CLONAL	2	FALSE	0	0.3	1		525	854	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743932	41743933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs778012871	NA	P-0012823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	172	712	1	ENST00000301178.4:c.874dup	p.His292ProfsTer47	p.H292Pfs*47	ENST00000301178	NM_021913.4	289	-/C	7/20	0.3	1	FACETS	0.794	0.729	0.862	0.794	0.729	0.862	SUBCLONAL	1	FALSE	0	0.3	1		713	1228	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0012823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	274	487	1	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	0.3	1	FACETS	0.881	0.829	0.934	1	0.995	1	CLONAL	2	FALSE	0	0.3	1		488	881	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0012823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	142	407	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.3	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	0	0.3	1		407	718	SUCCESS
AR	367	MSKCC	GRCh37	X	66766357	66766389	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	-	rs746853821	NA	P-0012823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	50	48	0	ENST00000374690.3:c.1388_1420del	p.Gly463_Gly473del	p.G463_G473del	ENST00000374690	NM_000044.3	457	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC/-	1/8	0.258262822416372	2	FACETS	0.833	0.717	0.958			1	CLONAL	2	FALSE	NA	0.3	2		48	200	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	330	562	0	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	0.3	1	FACETS	1	0.982	1	1	0.996	1	CLONAL	2	FALSE	0	0.3	1		562	871	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176133025	176133025	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	258	411	0	ENST00000367669.3:c.568A>G	p.Asn190Asp	p.N190D	ENST00000367669	NM_022457.5	190	Aat/Gat	4/20	0.3	1	FACETS	0.909	0.854	0.965	1	0.995	1	CLONAL	2	FALSE	0	0.3	1		411	804	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961423	54961423	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767515238	NA	P-0012823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	24	187	0	ENST00000312783.6:c.209C>T	p.Pro70Leu	p.P70L	ENST00000312783	NM_198436.1	70	cCg/cTg	4/10	0.237634433876654	1	FACETS	0.428	0.335	0.534	0.428	0.335	0.534	SUBCLONAL	1	FALSE	0	0.3	1		187	318	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913315	NA	P-0012833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	241	1039	0	ENST00000326873.7:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000326873	NM_000455.4	194	Gac/Tac	4/10	0.577183464719816	4	FACETS	1	0.984	1			1	CLONAL	4	TRUE	NA	0.888540819418321	4		1039	255	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683785	162683785	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	16	377	0	ENST00000366898.1:c.184G>C	p.Asp62His	p.D62H	ENST00000366898	NM_004562.2	62	Gat/Cat	3/12	0.888540819418321	3	FACETS	0.733	0.555	0.934	0.366	0.277	0.467	CLONAL	1	TRUE	1	0.888540819418321	3		377	71	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55960993	55960993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	56	451	0	ENST00000263923.4:c.2947C>T	p.Leu983Phe	p.L983F	ENST00000263923	NM_002253.2	983	Ctc/Ttc	21/30	0.282840816808385	3	FACETS	0.924	0.804	1	0.308	0.268	0.351	INDETERMINATE	1	TRUE	0	0.888540819418321	3		451	197	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577518	7577518	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519995	NA	P-0012833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	444	506	1	ENST00000269305.4:c.763A>T	p.Ile255Phe	p.I255F	ENST00000269305	NM_001126112.2	255	Atc/Ttc	7/11	0.888540819418321	7	FACETS	1	0.994	1			1	CLONAL	7	TRUE	NA	0.888540819418321	7		507	456	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106161	27106161	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	201	425	0	ENST00000324856.7:c.5772G>T	p.Glu1924Asp	p.E1924D	ENST00000324856	NM_006015.4	1924	gaG/gaT	20/20	0.824581647783515	5	FACETS	1	0.988	1	0.685	0.651	0.719	CLONAL	3	TRUE	0	0.888540819418321	5		425	308	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794487	242794487	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	146	365	0	ENST00000334409.5:c.455C>A	p.Pro152His	p.P152H	ENST00000334409	NM_005018.2	152	cCc/cAc	3/5	0.427257363489044	1	FACETS	1	0.993	1	1	0.993	1	INDETERMINATE	1	TRUE	0	0.888540819418321	1		365	158	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026096	71026096	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	58	419	0	ENST00000318789.4:c.1526G>T	p.Trp509Leu	p.W509L	ENST00000318789	NM_032682.5	509	tGg/tTg	17/21	0.419029966787121	3	FACETS	1	0.956	1	0.6	0.528	0.676	INDETERMINATE	1	TRUE	1	0.888540819418321	3		419	157	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140727	55140727	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	110	507	0	ENST00000257290.5:c.1588G>T	p.Ala530Ser	p.A530S	ENST00000257290	NM_006206.4	530	Gca/Tca	11/23	0.507604341129962	3	FACETS	0.832	0.766	0.897	0.832	0.766	0.897	INDETERMINATE	2	TRUE	1	0.888540819418321	3		507	215	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516919	187516919	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	115	508	1	ENST00000441802.2:c.13062G>T	p.Gln4354His	p.Q4354H	ENST00000441802	NM_005245.3	4354	caG/caT	26/27	0.835164469819927	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.888540819418321	2		509	127	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850945	128850945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762491039	NA	P-0012833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	59	312	0	ENST00000249373.3:c.1792G>A	p.Gly598Arg	p.G598R	ENST00000249373	NM_005631.4	598	Ggg/Agg	10/12	0.512124162836304	4	FACETS	1	0.949	1	1	0.949	1	INDETERMINATE	2	TRUE	2	0.888540819418321	4		312	113	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873966	151873966	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1275547808	NA	P-0012833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	41	527	0	ENST00000262189.6:c.8572G>A	p.Ala2858Thr	p.A2858T	ENST00000262189	NM_170606.2	2858	Gct/Act	38/59	0.512124162836304	4	FACETS	1	0.907	1	0.552	0.467	0.642	INDETERMINATE	1	TRUE	2	0.888540819418321	4		527	158	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097679	8097679	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	30	417	0	ENST00000346208.3:c.61G>A	p.Gly21Arg	p.G21R	ENST00000346208		21	Ggg/Agg	2/6	0.208907728876877	2	FACETS	0.759	0.63	0.895	0.379	0.315	0.448	INDETERMINATE	1	TRUE	0	0.888540819418321	2		417	89	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615015	43615015	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	35	482	1	ENST00000355710.3:c.2429G>T	p.Gly810Val	p.G810V	ENST00000355710	NM_020975.4	810	gGc/gTc	14/20	0.208907728876877	2	FACETS	0.625	0.523	0.735	0.313	0.261	0.368	INDETERMINATE	1	TRUE	0	0.888540819418321	2		483	126	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421519	32421519	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	39	389	2	ENST00000332351.3:c.1073C>A	p.Thr358Lys	p.T358K	ENST00000332351	NM_024426.4	358	aCg/aAg	6/10	0.487984652836774	1	FACETS	0.61	0.528	0.692	0.61	0.528	0.692	INDETERMINATE	1	TRUE	0	0.888540819418321	1		391	80	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486539	56486539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	157	515	0	ENST00000267101.3:c.1118G>T	p.Trp373Leu	p.W373L	ENST00000267101	NM_001982.3	373	tGg/tTg	10/28	0.850698552610187	5	FACETS	1	0.989	1	0.496	0.457	0.537	CLONAL	1	TRUE	2	0.888540819418321	5		515	554	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256177	133256177	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	107	507	0	ENST00000320574.5:c.484G>T	p.Asp162Tyr	p.D162Y	ENST00000320574	NM_006231.2	162	Gat/Tat	6/49	0.232281878396571	2	FACETS	1	0.98	1	0.608	0.561	0.655	INDETERMINATE	1	TRUE	0	0.888540819418321	2		507	198	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872356	35872356	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	144	639	0	ENST00000216797.5:c.547G>T	p.Gly183Cys	p.G183C	ENST00000216797	NM_020529.2	183	Ggc/Tgc	3/6	0.507604341129962	3	FACETS	0.907	0.832	0.985	0.454	0.416	0.493	INDETERMINATE	1	TRUE	1	0.888540819418321	3		639	516	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483854	88483854	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	20	422	0	ENST00000360948.2:c.1716G>T	p.Lys572Asn	p.K572N	ENST00000360948	NM_001012338.2	572	aaG/aaT	14/19	0.888540819418321	1	FACETS	0.472	0.377	0.573	0.472	0.377	0.573	SUBCLONAL	1	TRUE	0	0.888540819418321	1		422	53	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744382	41744382	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	130	651	0	ENST00000301178.4:c.1004del	p.Gly335AlafsTer31	p.G335Afs*31	ENST00000301178	NM_021913.4	334	ctG/ct	8/20	0.671221223514707	4	FACETS	1	0.969	1			1	CLONAL	2	TRUE	NA	0.888540819418321	4		651	255	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416650	121416652	+	missense_variant	Missense_Mutation	TNP	ATC	ATC	CTG	novel	NA	P-0012833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	56	495	0	ENST00000257555.6:c.79_81delinsCTG	p.Ile27Leu	p.I27L	ENST00000257555		27	ATC/CTG	1/10	0.232281878396571	2	FACETS	0.674	0.587	0.765	0.337	0.293	0.383	INDETERMINATE	1	TRUE	0	0.888540819418321	2		495	187	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	37	840	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.842	0.692	1	0.842	0.692	1	CLONAL	1	TRUE	1	0.14	2		840	628	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207631	2207631	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	46	968	0	ENST00000398665.3:c.915G>T	p.Trp305Cys	p.W305C	ENST00000398665	NM_032482.2	305	tgG/tgT	11/28	1	2	FACETS	0.717	0.601	0.845	0.717	0.601	0.845	SUBCLONAL	1	TRUE	1	0.14	2		968	917	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0012846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	48	671	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	1	2	FACETS	0.947	0.799	1	0.947	0.799	1	CLONAL	1	TRUE	1	0.14	2		671	724	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069291	30069291	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	35	564	0	ENST00000338641.4:c.1156G>T	p.Glu386Ter	p.E386*	ENST00000338641	NM_000268.3	386	Gaa/Taa	12/16	1	2	FACETS	0.871	0.713	1	0.871	0.713	1	CLONAL	1	TRUE	1	0.14	2		564	574	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521754	89521754	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	32	401	0	ENST00000336596.2:c.2831C>A	p.Ala944Asp	p.A944D	ENST00000336596	NM_005233.5	944	gCc/gAc	16/17	1	2	FACETS	1	0.838	1	1	0.838	1	CLONAL	1	TRUE	1	0.14	2		401	441	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729258	41729258	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	50	1029	0	ENST00000242208.4:c.1271G>T	p.Gly424Val	p.G424V	ENST00000242208	NM_002192.2	424	gGg/gTg	3/3	1	2	FACETS	0.72	0.609	0.843	0.72	0.609	0.843	SUBCLONAL	1	TRUE	1	0.14	2		1029	992	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827991	40827991	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	54	512	0	ENST00000373198.4:c.2437G>T	p.Ala813Ser	p.A813S	ENST00000373198	NM_133170.3	813	Gcc/Tcc	17/32	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.14	2		512	568	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069459	30069459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	31	436	0	ENST00000338641.4:c.1324G>A	p.Glu442Lys	p.E442K	ENST00000338641	NM_000268.3	442	Gag/Aag	12/16	1	2	FACETS	0.887	0.717	1	0.887	0.717	1	CLONAL	1	TRUE	1	0.14	2		436	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	484	702	1	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.613821491063948	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.613821491063948	1		703	954	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466022	69466022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	361	622	0	ENST00000227507.2:c.860C>T	p.Pro287Leu	p.P287L	ENST00000227507	NM_053056.2	287	cCc/cTc	5/5	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.613821491063948	2		622	1108	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967209	93967209	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	375	672	0	ENST00000369303.4:c.2143G>A	p.Glu715Lys	p.E715K	ENST00000369303	NM_004440.3	715	Gaa/Aaa	12/17	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.613821491063948	2		672	1195	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317921	8317921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150063446	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	129	493	1	ENST00000356435.5:c.5692C>T	p.Arg1898Cys	p.R1898C	ENST00000356435		1898	Cgt/Tgt	35/35	NA	2	FACETS	0.54	0.489	0.592			1	INDETERMINATE	1	TRUE	NA	0.613821491063948	2		494	779	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351871	89351872	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1478	704	1283	2	ENST00000301030.4:c.1078_1079delinsTT	p.Pro360Leu	p.P360L	ENST00000301030	NM_001256183.1	360	CCg/TTg	9/13	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.613821491063948	2		1285	2182	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495315	212495315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	192	397	0	ENST00000342788.4:c.1951C>T	p.Pro651Ser	p.P651S	ENST00000342788	NM_005235.2	651	Ccc/Tcc	17/28	1	2	FACETS	0.899	0.834	0.965	0.899	0.834	0.965	CLONAL	1	TRUE	1	0.613821491063948	2		397	696	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794430	242794430	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1246524256	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	347	706	0	ENST00000334409.5:c.512T>C	p.Val171Ala	p.V171A	ENST00000334409	NM_005018.2	171	gTt/gCt	3/5	0.613821491063948	1	FACETS	0.984	0.937	1	0.984	0.937	1	CLONAL	1	TRUE	0	0.613821491063948	1		706	796	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582147	52582147	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1436814738	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	426	599	2	ENST00000394830.3:c.4681C>T	p.Arg1561Cys	p.R1561C	ENST00000394830	NM_018313.4	1561	Cgc/Tgc	30/30	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.613821491063948	2		601	1305	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146820	185146820	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	256	340	0	ENST00000265026.3:c.451A>G	p.Thr151Ala	p.T151A	ENST00000265026	NM_004721.4	151	Act/Gct	2/14	0.613821491063948	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.613821491063948	1		340	546	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361204	66361204	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	244	370	0	ENST00000273854.3:c.968C>T	p.Pro323Leu	p.P323L	ENST00000273854	NM_004439.5	323	cCa/cTa	4/18	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.613821491063948	2		370	794	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156110	106156110	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	327	558	0	ENST00000380013.4:c.1011A>T	p.Glu337Asp	p.E337D	ENST00000380013	NM_001127208.2	337	gaA/gaT	3/11	1	2	FACETS	0.935	0.884	0.988	0.935	0.884	0.988	CLONAL	1	TRUE	1	0.613821491063948	2		558	1139	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190872	106190872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	241	359	1	ENST00000380013.4:c.4150G>A	p.Asp1384Asn	p.D1384N	ENST00000380013	NM_001127208.2	1384	Gac/Aac	9/11	1	2	FACETS	0.993	0.93	1	0.993	0.93	1	CLONAL	1	TRUE	1	0.613821491063948	2		360	791	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531139	187531139	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	275	447	0	ENST00000441802.2:c.9884A>T	p.Tyr3295Phe	p.Y3295F	ENST00000441802	NM_005245.3	3295	tAt/tTt	15/27	0.613821491063948	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.613821491063948	1		447	586	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180049799	180049799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408501130	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	510	766	6	ENST00000261937.6:c.1589C>T	p.Ala530Val	p.A530V	ENST00000261937	NM_182925.4	530	gCc/gTc	12/30	0.613821491063948	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.613821491063948	1		772	1015	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662402	117662402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs184429367	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	303	548	0	ENST00000368508.3:c.4975C>T	p.Pro1659Ser	p.P1659S	ENST00000368508	NM_002944.2	1659	Cca/Tca	30/43	1	2	FACETS	0.963	0.909	1	0.963	0.909	1	CLONAL	1	TRUE	1	0.613821491063948	2		548	1025	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704638	117704638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	345	507	1	ENST00000368508.3:c.2338G>A	p.Asp780Asn	p.D780N	ENST00000368508	NM_002944.2	780	Gac/Aac	16/43	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.613821491063948	2		508	956	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959079	2959079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542412710	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	284	566	0	ENST00000396946.4:c.2437G>A	p.Glu813Lys	p.E813K	ENST00000396946	NM_032415.4	813	Gag/Aag	18/25	1	2	FACETS	0.979	0.922	1	0.979	0.922	1	CLONAL	1	TRUE	1	0.613821491063948	2		566	945	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436018	116436018	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	432	598	1	ENST00000397752.3:c.4013C>A	p.Ser1338Ter	p.S1338*	ENST00000397752	NM_000245.2	1338	tCa/tAa	21/21	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.613821491063948	2		599	1271	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864314	151864314	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	404	736	0	ENST00000262189.6:c.9667G>T	p.Gly3223Trp	p.G3223W	ENST00000262189	NM_170606.2	3223	Ggg/Tgg	42/59	1	2	FACETS	0.997	0.949	1	0.997	0.949	1	CLONAL	1	TRUE	1	0.613821491063948	2		736	1320	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319898	8319898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	162	635	0	ENST00000356435.5:c.5603G>A	p.Gly1868Glu	p.G1868E	ENST00000356435		1868	gGa/gAa	34/35	NA	2	FACETS	0.545	0.5	0.593			1	INDETERMINATE	1	TRUE	NA	0.613821491063948	2		635	968	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404570	8404570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	325	616	0	ENST00000356435.5:c.4177G>A	p.Asp1393Asn	p.D1393N	ENST00000356435		1393	Gat/Aat	25/35	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.613821491063948	2		616	932	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966551	36966551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768417029	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	395	733	0	ENST00000358127.4:c.775G>A	p.Glu259Lys	p.E259K	ENST00000358127	NM_001280556.1	259	Gag/Aag	6/10	NA	2	FACETS	0.982	0.933	1			1	INDETERMINATE	1	TRUE	NA	0.613821491063948	2		733	1311	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864548	56864548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	547	960	1	ENST00000308159.5:c.1036G>A	p.Gly346Arg	p.G346R	ENST00000308159	NM_014669.4	346	Gga/Aga	10/22	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.613821491063948	2		961	1766	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245664	41245664	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	441	580	0	ENST00000357654.3:c.1884T>A	p.Ser628Arg	p.S628R	ENST00000357654	NM_007294.3	628	agT/agA	10/23	0.613821491063948	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.613821491063948	1		580	861	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221201	5221201	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	352	607	0	ENST00000357368.4:c.3265C>T	p.Leu1089Phe	p.L1089F	ENST00000357368	NM_002850.3	1089	Ctc/Ttc	20/38	0.613821491063948	1	FACETS	0.94	0.894	0.985	0.94	0.894	0.985	CLONAL	1	TRUE	0	0.613821491063948	1		607	846	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274350	5274350	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	276	401	0	ENST00000357368.4:c.97C>T	p.Pro33Ser	p.P33S	ENST00000357368	NM_002850.3	33	Ccc/Tcc	3/38	0.613821491063948	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.613821491063948	1		401	573	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143081	7143081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	194	333	0	ENST00000302850.5:c.2288C>T	p.Ser763Phe	p.S763F	ENST00000302850	NM_000208.2	763	tCc/tTc	12/22	0.613821491063948	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.613821491063948	1		333	426	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350050	15350050	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	405	686	0	ENST00000263377.2:c.3602C>T	p.Ser1201Phe	p.S1201F	ENST00000263377	NM_058243.2	1201	tCc/tTc	18/20	0.613821491063948	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.613821491063948	1		686	906	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852481	42852481	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759250613	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	453	759	1	ENST00000398585.3:c.605G>A	p.Arg202Lys	p.R202K	ENST00000398585	NM_001135099.1	202	aGg/aAg	6/14	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.613821491063948	2		760	1381	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545820	41545820	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1829	483	834	0	ENST00000263253.7:c.2435C>T	p.Ser812Phe	p.S812F	ENST00000263253	NM_001429.3	812	tCt/tTt	14/31	0.523196215335092	4	FACETS	1	0.987	1	0.366	0.348	0.384	CLONAL	1	TRUE	1	0.613821491063948	4		834	2312	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1331457	1331457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	372	783	0	ENST00000400841.2:c.71G>A	p.Gly24Glu	p.G24E	ENST00000400841		24	gGa/gAa	1/6	1	1	FACETS	0.617	0.585	0.65	0.617	0.585	0.65	SUBCLONAL	1	TRUE	0	0.613821491063948	1		783	1362	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1331502	1331502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	277	644	1	ENST00000400841.2:c.26G>A	p.Gly9Glu	p.G9E	ENST00000400841		9	gGa/gAa	1/6	1	1	FACETS	0.557	0.523	0.592	0.557	0.523	0.592	SUBCLONAL	1	TRUE	0	0.613821491063948	1		645	1123	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39935724	39935724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	524	375	0	ENST00000378444.4:c.148C>T	p.Pro50Ser	p.P50S	ENST00000378444	NM_001123385.1	50	Ccc/Tcc	3/15	1	1	FACETS	0.754	0.731	0.776	1	0.997	1	SUBCLONAL	2	TRUE	0	0.613821491063948	1		375	785	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245137	53245137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	513	446	1	ENST00000375401.3:c.803C>T	p.Pro268Leu	p.P268L	ENST00000375401	NM_004187.3	268	cCc/cTc	7/26	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.613821491063948	1		447	804	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937752	76937752	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	393	350	0	ENST00000373344.5:c.2996A>G	p.Lys999Arg	p.K999R	ENST00000373344	NM_000489.3	999	aAg/aGg	9/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.613821491063948	1		350	661	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937745	76937745	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	355	346	2	ENST00000373344.5:c.3003del	p.Val1002Ter	p.V1002*	ENST00000373344	NM_000489.3	1001	aaA/aa	9/35	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.613821491063948	1		348	670	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661997	29662016	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAACAGATGTACCCATCT	AAAAACAGATGTACCCATCT	-	novel	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	208	410	0	ENST00000356175.3:c.5892_5911del	p.Glu1964AspfsTer17	p.E1964Dfs*17	ENST00000356175	NM_000267.3	1964	gAAAAACAGATGTACCCATCT/g	39/57	0.613821491063948	1	FACETS	0.845	0.79	0.9	0.845	0.79	0.9	CLONAL	1	TRUE	0	0.613821491063948	1		410	556	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807508	36807509	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	274	478	0	ENST00000373129.3:c.1155_1156delinsAA	p.Ala386Thr	p.A386T	ENST00000373129	NM_032017.1	385	ctGGcc/ctAAcc	12/12	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.613821491063948	2		478	851	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202377	138202378	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0012856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	209	470	1	ENST00000237289.4:c.2294_2295delinsTT	p.Pro765Leu	p.P765L	ENST00000237289	NM_001270507.1	765	cCC/cTT	9/9	1	2	FACETS	0.844	0.785	0.904	0.844	0.785	0.904	CLONAL	1	TRUE	1	0.613821491063948	2		471	807	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519999	NA	P-0012866-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	190	655	0	ENST00000269305.4:c.716A>G	p.Asn239Ser	p.N239S	ENST00000269305	NM_001126112.2	239	aAc/aGc	7/11	0.533854639477953	1	FACETS	0.937	0.872	1	0.937	0.872	1	CLONAL	1	TRUE	0	0.533854639477953	1		655	557	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27016048	27016048	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012866-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	212	1156	1	ENST00000335756.4:c.324C>A	p.Asp108Glu	p.D108E	ENST00000335756	NM_001809.3	108	gaC/gaA	4/5	1	2	FACETS	0.679	0.63	0.731	0.679	0.63	0.731	SUBCLONAL	1	TRUE	1	0.533854639477953	2		1157	1169	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143033714	143033714	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012866-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1276	78	781	1	ENST00000262992.4:c.2257C>T	p.Gln753Ter	p.Q753*	ENST00000262992	NM_001101669.1	753	Cag/Tag	20/24	0.533854639477953	3	FACETS	0.273	0.239	0.311	0.137	0.119	0.156	SUBCLONAL	1	TRUE	1	0.533854639477953	3		782	1354	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380516	31380516	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012866-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	68	826	1	ENST00000328111.2:c.1006G>A	p.Ala336Thr	p.A336T	ENST00000328111	NM_006892.3	336	Gcc/Acc	9/23	1	2	FACETS	0.322	0.28	0.369	0.322	0.28	0.369	SUBCLONAL	1	TRUE	1	0.533854639477953	2		827	790	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101172	41101172	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012866-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	26	323	0	ENST00000373198.4:c.1184T>A	p.Ile395Asn	p.I395N	ENST00000373198	NM_133170.3	395	aTc/aAc	8/32	0.459434288105429	0	FACETS	0.203	0.161	0.25			1	SUBCLONAL	1	TRUE	0	0.533854639477953	0		323	224	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880997	37880998	+	protein_altering_variant	In_Frame_Ins	INS	-	-	TTT	rs397516979	NA	P-0012866-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	337	768	1	ENST00000269571.5:c.2326_2327insTTT	p.Gly776delinsValCys	p.G776delinsVC	ENST00000269571		776	ggt/gTTTgt	20/27	0.533854639477953	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.533854639477953	1		769	661	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0012876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	55	754	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.19	2		754	491	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	87	698	3	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.823	0.726	0.927	0.823	0.726	0.927	CLONAL	1	TRUE	1	0.19	2		701	1113	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054940	176054940	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0012876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	96	605	0	ENST00000367669.3:c.1113C>G	p.Tyr371Ter	p.Y371*	ENST00000367669	NM_022457.5	371	taC/taG	10/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.19	2		605	856	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690801	89690801	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0012876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	23	216	0	ENST00000371953.3:c.210-2A>C		p.X70_splice	ENST00000371953	NM_000314.4	70			1	2	FACETS	0.602	0.469	0.757	0.602	0.469	0.757	SUBCLONAL	1	TRUE	1	0.19	2		216	402	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657387	29657387	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	78	660	0	ENST00000356175.3:c.5620A>C	p.Thr1874Pro	p.T1874P	ENST00000356175	NM_000267.3	1874	Aca/Cca	38/57	1	2	FACETS	0.838	0.734	0.95	0.838	0.734	0.95	CLONAL	1	TRUE	1	0.19	2		660	980	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087896	27087920	+	frameshift_variant	Frame_Shift_Del	DEL	CACCCAGTGGCCAGTCGGACAGCAT	CACCCAGTGGCCAGTCGGACAGCAT	-	novel	NA	P-0012876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	67	524	0	ENST00000324856.7:c.2185_2209del	p.Pro729CysfsTer5	p.P729Cfs*5	ENST00000324856	NM_006015.4	728	cCACCCAGTGGCCAGTCGGACAGCATc/cc	6/20	1	2	FACETS	0.852	0.739	0.975	0.852	0.739	0.975	CLONAL	1	TRUE	1	0.19	2		524	828	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339306	70339334	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGTCAGCTTCAATCCTGCCAAGGTGAGAC	CGTCAGCTTCAATCCTGCCAAGGTGAGAC	-	novel	NA	P-0012876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	66	628	0	ENST00000374080.3:c.183_204+7del		p.X61_splice	ENST00000374080		61		2/45	1	2	FACETS	0.71	0.615	0.815	0.71	0.615	0.815	SUBCLONAL	1	TRUE	1	0.19	2		628	978	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591140	67591145	+	inframe_deletion	In_Frame_Del	DEL	ACCAAT	ACCAAT	-	rs751582616	NA	P-0012876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	37	379	0	ENST00000274335.5:c.1735_1740del	p.Gln579_Tyr580del	p.Q579_Y580del	ENST00000274335		578	gACCAATac/gac	12/15	1	2	FACETS	0.66	0.543	0.792	0.66	0.543	0.792	SUBCLONAL	1	TRUE	1	0.19	2		379	590	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597493	52597493	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	150	477	0	ENST00000394830.3:c.3817C>T	p.Gln1273Ter	p.Q1273*	ENST00000394830	NM_018313.4	1273	Cag/Tag	25/30	0.547750072167063	1	FACETS	0.984	0.91	1	0.984	0.91	1	CLONAL	1	TRUE	0	0.547750072167063	1		477	404	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191532	10191532	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	258	441	0	ENST00000256474.2:c.525C>A	p.Tyr175Ter	p.Y175*	ENST00000256474	NM_000551.3	175	taC/taA	3/3	0.547750072167063	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.547750072167063	1		441	577	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	178	766	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.71839124277463	2		766	461	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221743	55221743	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519829	NA	P-0012904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4592	481	887	0	ENST00000275493.2:c.787A>C	p.Thr263Pro	p.T263P	ENST00000275493	NM_005228.3	263	Acc/Ccc	7/28	0.71839124277463	14	FACETS	1	0.995	1			1	CLONAL	1	TRUE	NA	0.71839124277463	14		887	5073	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039505	49039505	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs764754259	NA	P-0012904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	184	459	0	ENST00000267163.4:c.2489+1G>A		p.X830_splice	ENST00000267163	NM_000321.2	830			0.697804505474229	1	FACETS	0.873	0.818	0.928	0.873	0.818	0.928	CLONAL	1	TRUE	0	0.71839124277463	1		459	376	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061825	38061825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1019690230	NA	P-0012904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	320	1012	0	ENST00000250448.2:c.164C>T	p.Thr55Met	p.T55M	ENST00000250448	NM_004496.3	55	aCg/aTg	2/2	1	2	FACETS	0.88	0.832	0.929	0.88	0.832	0.929	CLONAL	1	TRUE	1	0.71839124277463	2		1012	1012	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121438948	121438948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146855738	NA	P-0012914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1703	189	872	0	ENST00000257555.6:c.1849G>A	p.Val617Ile	p.V617I	ENST00000257555		617	Gtc/Atc	10/10	0.384348685513199	7	FACETS	1	0.936	1			1	CLONAL	1	FALSE	NA	0.384348685513199	7		872	1892	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180892	108180892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	161	381	0	ENST00000278616.4:c.5768C>T	p.Ser1923Phe	p.S1923F	ENST00000278616	NM_000051.3	1923	tCt/tTt	39/63	0.384348685513199	5	FACETS	1	0.963	1	0.718	0.661	0.777	CLONAL	2	FALSE	2	0.384348685513199	5		381	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0012927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	28	538	0	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	1	2	FACETS	0.476	0.38	0.586	0.476	0.38	0.586	SUBCLONAL	1	FALSE	1	0.3	2		538	392	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814139	76814139	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0012927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	23	270	0	ENST00000373344.5:c.6504+1G>C		p.X2168_splice	ENST00000373344	NM_000489.3	2168			1	1	FACETS	0.336	0.261	0.422	0.336	0.261	0.422	SUBCLONAL	1	FALSE	0	0.3	1		270	388	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657640	37657656	+	frameshift_variant	Frame_Shift_Del	DEL	AAGAATTTCCTGCATCG	AAGAATTTCCTGCATCG	-	novel	NA	P-0012930-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	170	441	0	ENST00000447079.4:c.2557_2573del	p.Lys853GlyfsTer3	p.K853Gfs*3	ENST00000447079	NM_015083.1	853	AAGAATTTCCTGCATCGg/g	6/14	1	2	FACETS	0.795	0.737	0.855	0.795	0.737	0.855	SUBCLONAL	1	TRUE	1	0.86	2		441	497	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662140	227662140	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760127800	NA	P-0012973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	466	326	0	ENST00000305123.5:c.1315C>T	p.Arg439Trp	p.R439W	ENST00000305123	NM_005544.2	439	Cgg/Tgg	1/2	0.59389005709701	3	FACETS	0.809	0.776	0.842	0.809	0.776	0.842	CLONAL	2	TRUE	1	0.767851210068581	3		326	1038	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195461	102195461	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	355	553	0	ENST00000263464.3:c.221A>T	p.Asp74Val	p.D74V	ENST00000263464	NM_001165.4	74	gAt/gTt	2/9	0.76629844233673	1	FACETS	0.969	0.93	1	0.969	0.93	1	CLONAL	1	TRUE	0	0.767851210068581	1		553	588	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126074	2126081	+	frameshift_variant	Frame_Shift_Del	DEL	ATCAGTAC	ATCAGTAC	-	novel	NA	P-0012973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	258	512	0	ENST00000219476.3:c.2648_2655del	p.Gln883ArgfsTer29	p.Q883Rfs*29	ENST00000219476	NM_000548.3	882	aATCAGTAC/a	24/42	1	2	FACETS	0.734	0.688	0.78	0.734	0.688	0.78	SUBCLONAL	1	TRUE	1	0.767851210068581	2		512	916	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119906	70119907	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0012973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	63	334	0	ENST00000245479.2:c.911dup	p.Val306GlyfsTer272	p.V306Gfs*272	ENST00000245479	NM_000346.3	303	cac/caCc	3/3	0.767851210068581	1	FACETS	0.276	0.24	0.315	0.276	0.24	0.315	SUBCLONAL	1	TRUE	0	0.767851210068581	1		334	366	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417910	32417910	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	113	589	0	ENST00000332351.3:c.1142C>A	p.Ser381Ter	p.S381*	ENST00000332351	NM_024426.4	381	tCg/tAg	7/10	1	2	FACETS	0.997	0.902	1	0.997	0.902	1	CLONAL	1	TRUE	1	0.461456009260635	2		589	491	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199926	108199926	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121434221	NA	P-0012980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	133	350	0	ENST00000278616.4:c.7268A>G	p.Glu2423Gly	p.E2423G	ENST00000278616	NM_000051.3	2423	gAa/gGa	49/63	0.409190484640033	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.461456009260635	1		350	418	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0013001-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	111	525	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.431381239612125	6	FACETS	1	0.95	1	0.431	0.39	0.474	CLONAL	2	TRUE	1	0.431381239612125	6		525	445	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599321	55599321	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913507	NA	P-0013001-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	38	537	0	ENST00000288135.5:c.2447A>T	p.Asp816Val	p.D816V	ENST00000288135	NM_000222.2	816	gAc/gTc	17/21	0.431381239612125	4	FACETS	0.985	0.819	1	0.328	0.273	0.389	CLONAL	1	TRUE	1	0.431381239612125	4		537	256	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433871	78433871	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013001-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	58	526	1	ENST00000370768.2:c.228G>T	p.Lys76Asn	p.K76N	ENST00000370768	NM_003902.3	76	aaG/aaT	3/20	0.370757469336326	4	FACETS	1	0.935	1	0.571	0.493	0.655	CLONAL	1	TRUE	2	0.431381239612125	4		527	337	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266803	198266803	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013001-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	49	528	0	ENST00000335508.6:c.2129C>A	p.Ala710Asp	p.A710D	ENST00000335508	NM_012433.2	710	gCt/gAt	15/25	0.431381239612125	3	FACETS	0.765	0.65	0.89	0.383	0.325	0.445	SUBCLONAL	1	TRUE	1	0.431381239612125	3		528	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0013011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	168	910	2	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.227378257419255	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.227378257419255	3		912	776	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221995	1221995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201090	NA	P-0013011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	206	557	0	ENST00000326873.7:c.910C>T	p.Arg304Trp	p.R304W	ENST00000326873	NM_000455.4	304	Cgg/Tgg	7/10	0.158269010938649	3	FACETS	1	0.974	1	0.736	0.683	0.79	CLONAL	2	TRUE	0	0.227378257419255	3		557	914	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809831	36809831	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	134	511	0	ENST00000373129.3:c.774G>T	p.Trp258Cys	p.W258C	ENST00000373129	NM_032017.1	258	tgG/tgT	9/12	0.227378257419255	2	FACETS	0.86	0.783	0.941	0.86	0.783	0.941	CLONAL	2	TRUE	0	0.227378257419255	2		511	685	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120493352	120493352	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs886044849	NA	P-0013011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1229	76	677	0	ENST00000256646.2:c.2474A>G	p.Tyr825Cys	p.Y825C	ENST00000256646	NM_024408.3	825	tAc/tGc	15/34	0.227378257419255	10	FACETS	0.978	0.855	1			1	CLONAL	1	TRUE	NA	0.227378257419255	10		677	1305	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193121538	193121538	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	128	599	1	ENST00000367435.3:c.936G>T	p.Met312Ile	p.M312I	ENST00000367435	NM_024529.4	312	atG/atT	10/17	0.168671336075994	5	FACETS	1	0.941	1	0.7	0.635	0.768	CLONAL	2	TRUE	2	0.227378257419255	5		600	719	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643813	52643813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777272973	NA	P-0013011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	54	507	0	ENST00000394830.3:c.2083G>A	p.Asp695Asn	p.D695N	ENST00000394830	NM_018313.4	695	Gac/Aac	17/30	0.227378257419255	2	FACETS	0.983	0.841	1	0.492	0.42	0.57	CLONAL	1	TRUE	0	0.227378257419255	2		507	483	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430230	181430230	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	42	386	2	ENST00000325404.1:c.82G>T	p.Ala28Ser	p.A28S	ENST00000325404	NM_003106.3	28	Gcg/Tcg	1/1	0.227378257419255	3	FACETS	0.883	0.737	1	0.441	0.368	0.522	CLONAL	1	TRUE	1	0.227378257419255	3		388	466	SUCCESS
APC	324	MSKCC	GRCh37	5	112162804	112162804	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs863225313	NA	P-0013011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	52	329	0	ENST00000257430.4:c.1409-1G>T		p.X470_splice	ENST00000257430	NM_000038.5	470			0.227378257419255	2	FACETS	0.781	0.669	0.901	0.781	0.669	0.901	CLONAL	2	TRUE	0	0.227378257419255	2		329	293	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983911	2983911	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1195	134	868	3	ENST00000396946.4:c.619C>A	p.Arg207Ser	p.R207S	ENST00000396946	NM_032415.4	207	Cgc/Agc	5/25	0.227378257419255	3	FACETS	0.988	0.895	1	0.494	0.447	0.543	CLONAL	1	TRUE	1	0.227378257419255	3		871	1329	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335639	81335639	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	108	555	1	ENST00000222390.5:c.1721C>A	p.Pro574His	p.P574H	ENST00000222390	NM_000601.4	574	cCt/cAt	15/18	0.227378257419255	3	FACETS	0.918	0.827	1	0.918	0.827	1	CLONAL	2	TRUE	1	0.227378257419255	3		556	576	SUCCESS
MET	4233	MSKCC	GRCh37	7	116422067	116422067	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	44	419	1	ENST00000397752.3:c.3548G>T	p.Gly1183Val	p.G1183V	ENST00000397752	NM_000245.2	1183	gGc/gTc	18/21	0.227378257419255	3	FACETS	0.704	0.59	0.832	0.352	0.295	0.416	SUBCLONAL	1	TRUE	1	0.227378257419255	3		420	612	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438686	49438686	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	162	577	0	ENST00000301067.7:c.4804A>T	p.Asn1602Tyr	p.N1602Y	ENST00000301067	NM_003482.3	1602	Aac/Tac	19/54	0.137905215121599	4	FACETS	1	0.919	1	0.668	0.613	0.725	CLONAL	2	TRUE	1	0.227378257419255	4		577	873	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622440	28622440	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	36	487	2	ENST00000241453.7:c.1177G>T	p.Glu393Ter	p.E393*	ENST00000241453	NM_004119.2	393	Gag/Tag	9/24	1	2	FACETS	0.604	0.496	0.726	0.604	0.496	0.726	SUBCLONAL	1	TRUE	1	0.227378257419255	2		489	524	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609994	81609994	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	129	329	0	ENST00000298171.2:c.1592G>T	p.Arg531Leu	p.R531L	ENST00000298171	NM_000369.2	531	cGg/cTg	10/10	0.227378257419255	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.227378257419255	3		329	557	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649083	37649083	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	58	475	0	ENST00000447079.4:c.2188A>T	p.Ile730Phe	p.I730F	ENST00000447079	NM_015083.1	730	Att/Ttt	4/14	0.227378257419255	3	FACETS	0.716	0.613	0.827	0.358	0.306	0.414	SUBCLONAL	1	TRUE	1	0.227378257419255	3		475	794	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602443	10602443	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	197	549	1	ENST00000171111.5:c.1135G>T	p.Gly379Cys	p.G379C	ENST00000171111	NM_203500.1	379	Ggc/Tgc	3/6	0.158269010938649	3	FACETS	1	0.985	1	0.813	0.755	0.874	CLONAL	2	TRUE	0	0.227378257419255	3		550	791	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546724	9546724	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	77	403	0	ENST00000353224.5:c.1298G>C	p.Arg433Pro	p.R433P	ENST00000353224	NM_177990.2	433	cGg/cCg	5/10	0.168671336075994	5	FACETS	0.977	0.86	1	0.651	0.573	0.734	CLONAL	2	TRUE	2	0.227378257419255	5		403	465	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100972	41100972	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	151	471	1	ENST00000373198.4:c.1384C>A	p.Leu462Ile	p.L462I	ENST00000373198	NM_133170.3	462	Ctc/Atc	8/32	0.168671336075994	5	FACETS	1	0.979	1	0.806	0.738	0.876	CLONAL	2	TRUE	2	0.227378257419255	5		472	737	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101151	41101151	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	93	304	0	ENST00000373198.4:c.1205A>T	p.Gln402Leu	p.Q402L	ENST00000373198	NM_133170.3	402	cAg/cTg	8/32	0.168671336075994	5	FACETS	1	0.964	1	0.793	0.709	0.883	CLONAL	2	TRUE	2	0.227378257419255	5		304	461	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225932	53225932	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	183	805	2	ENST00000375401.3:c.2917C>A	p.Leu973Met	p.L973M	ENST00000375401	NM_004187.3	973	Ctg/Atg	19/26	1	2	FACETS	0.753	0.694	0.814	1	0.99	1	SUBCLONAL	2	TRUE	1	0.227378257419255	2		807	1069	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577083	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0013011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	81	653	0	ENST00000269305.4:c.855_856delinsTT	p.Glu285_Glu286delinsAspTer	p.E285_E286delinsD*	ENST00000269305	NM_001126112.2	285	gaGGaa/gaTTaa	8/11	0.227378257419255	3	FACETS	0.733	0.644	0.829	0.366	0.322	0.415	SUBCLONAL	1	TRUE	1	0.227378257419255	3		653	1083	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003149	42003151	+	frameshift_variant	Frame_Shift_Del	DEL	CGA	CGA	T	novel	NA	P-0013011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	250	1215	0	ENST00000219905.7:c.2686_2688delinsT	p.Arg896Ter	p.R896*	ENST00000219905	NM_001164273.1	896	CGA/T	8/24	NA	2	FACETS	0.911	0.851	0.973			1	INDETERMINATE	2	TRUE	NA	0.227378257419255	2		1215	1207	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609936	43609936	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	330	1441	0	ENST00000355710.3:c.1888T>G	p.Cys630Gly	p.C630G	ENST00000355710	NM_020975.4	630	Tgc/Ggc	11/20	0.158952116969793	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		1441	1312	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013038-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	134	720	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.268146861639825	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.273728472979934	1		721	787	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0013038-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	181	1015	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.268146861639825	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.273728472979934	1		1015	1028	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581177	48581177	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013038-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	110	431	1	ENST00000342988.3:c.481G>T	p.Glu161Ter	p.E161*	ENST00000342988	NM_005359.5	161	Gaa/Taa	5/12	0.273728472979934	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.273728472979934	1		432	647	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0013041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	50	421	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.744	0.636	0.862	0.744	0.636	0.862	SUBCLONAL	1	TRUE	1	0.450773195824453	2		421	298	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	16	406	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	0.156	0.114	0.205	0.156	0.114	0.205	SUBCLONAL	1	TRUE	1	0.450773195824453	2		406	456	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117799	108117799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202160435	NA	P-0013041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	94	390	1	ENST00000278616.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000278616	NM_000051.3	337	cGt/cAt	8/63	0.450773195824453	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.450773195824453	1		391	298	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0013041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	143	595	0	ENST00000346208.3:c.1002_1003dup	p.Asp335GlyfsTer21	p.D335Gfs*21	ENST00000346208		333	-/GG	5/6	NA	2	FACETS	0.95	0.868	1			1	INDETERMINATE	1	TRUE	NA	0.450773195824453	2		595	668	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261523	16261523	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0013041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	91	404	0	ENST00000375759.3:c.8788A>T	p.Lys2930Ter	p.K2930*	ENST00000375759	NM_015001.2	2930	Aag/Tag	11/15	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.450773195824453	2		404	370	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0013054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	212	763	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.156541342973787	4	FACETS	1	0.985	1	1	0.985	1	INDETERMINATE	2	FALSE	2	0.358385245428031	4		764	675	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0013054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	263	700	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.152179632140861	3	FACETS	0.87	0.821	0.92			1	INDETERMINATE	3	FALSE	NA	0.358385245428031	3		700	663	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634644	158634644	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	225	650	0	ENST00000263640.3:c.542C>A	p.Ala181Glu	p.A181E	ENST00000263640	NM_001105.4	181	gCa/gAa	5/11	0.0884167250177761	3	FACETS	1	0.985	1	0.6	0.558	0.644	INDETERMINATE	1	FALSE	1	0.358385245428031	3		650	1233	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342677	118342677	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs943862842	NA	P-0013054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	40	359	0	ENST00000534358.1:c.803C>A	p.Thr268Lys	p.T268K	ENST00000534358	NM_005933.3	268	aCa/aAa	3/36	0.215429813919983	3	FACETS	0.95	0.794	1	0.475	0.397	0.561	CLONAL	1	FALSE	1	0.358385245428031	3		359	277	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	191	766	0				ENST00000310581	NM_198253.2	-/1132			0.377786913718349	3	FACETS	0.783	0.728	0.84	0.783	0.728	0.84	SUBCLONAL	2	TRUE	1	0.485803953915592	3		766	624	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874290	155874290	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs869025192	NA	P-0013077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	222	314	0	ENST00000368323.3:c.241G>C	p.Glu81Gln	p.E81Q	ENST00000368323	NM_006912.5	81	Gag/Cag	5/6	0.452771958018283	3	FACETS	0.924	0.865	0.983	0.924	0.865	0.983	CLONAL	2	TRUE	1	0.485803953915592	3		314	615	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266595	198266595	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	62	335	0	ENST00000335508.6:c.2241G>C	p.Leu747Phe	p.L747F	ENST00000335508	NM_012433.2	747	ttG/ttC	16/25	0.365639816244752	1	FACETS	0.477	0.413	0.546	0.477	0.413	0.546	SUBCLONAL	1	TRUE	0	0.485803953915592	1		335	405	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446247	187446247	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	250	469	3	ENST00000232014.4:c.1441C>T	p.Gln481Ter	p.Q481*	ENST00000232014	NM_001130845.1	481	Cag/Tag	6/10	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.485803953915592	2		472	696	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541522	187541522	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	179	626	2	ENST00000441802.2:c.6218A>T	p.Asp2073Val	p.D2073V	ENST00000441802	NM_005245.3	2073	gAc/gTc	10/27	1	2	FACETS	0.778	0.717	0.842	0.778	0.717	0.842	SUBCLONAL	1	TRUE	1	0.485803953915592	2		628	947	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549687	187549687	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	113	311	0	ENST00000441802.2:c.4554G>C	p.Glu1518Asp	p.E1518D	ENST00000441802	NM_005245.3	1518	gaG/gaC	8/27	1	2	FACETS	0.912	0.825	1	0.912	0.825	1	CLONAL	1	TRUE	1	0.485803953915592	2		311	510	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008975	152008975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	96	448	0	ENST00000262189.6:c.647C>T	p.Ala216Val	p.A216V	ENST00000262189	NM_170606.2	216	gCt/gTt	5/59	0.398575188743848	1	FACETS	0.581	0.519	0.646	0.581	0.519	0.646	SUBCLONAL	1	TRUE	0	0.485803953915592	1		448	515	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117870667	117870667	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1732	132	1008	0	ENST00000297338.2:c.405G>C	p.Leu135Phe	p.L135F	ENST00000297338	NM_006265.2	135	ttG/ttC	5/14	0.481515138746301	4	FACETS	0.433	0.391	0.478	0.144	0.13	0.16	SUBCLONAL	1	TRUE	1	0.485803953915592	4		1008	1864	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933314	100933314	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	368	1135	0	ENST00000325455.5:c.2076G>C	p.Met692Ile	p.M692I	ENST00000325455	NM_001202474.3	692	atG/atC	4/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.485803953915592	2		1135	1475	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114719	108114719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	51	276	0	ENST00000278616.4:c.536C>T	p.Ser179Leu	p.S179L	ENST00000278616	NM_000051.3	179	tCa/tTa	6/63	1	2	FACETS	0.515	0.438	0.598	0.515	0.438	0.598	SUBCLONAL	1	TRUE	1	0.485803953915592	2		276	408	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445980	49445980	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	116	781	0	ENST00000301067.7:c.1486C>G	p.Pro496Ala	p.P496A	ENST00000301067	NM_003482.3	496	Ccg/Gcg	10/54	1	2	FACETS	0.419	0.376	0.464	0.419	0.376	0.464	SUBCLONAL	1	TRUE	1	0.485803953915592	2		781	1140	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487175	56487175	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	105	337	0	ENST00000267101.3:c.1321C>G	p.Leu441Val	p.L441V	ENST00000267101	NM_001982.3	441	Ctg/Gtg	12/28	1	2	FACETS	0.861	0.775	0.952	0.861	0.775	0.952	CLONAL	1	TRUE	1	0.485803953915592	2		337	502	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435436	110435436	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	51	359	0	ENST00000375856.3:c.2965C>G	p.Pro989Ala	p.P989A	ENST00000375856	NM_003749.2	989	Cct/Gct	1/2	0.485803953915592	3	FACETS	0.351	0.298	0.41	0.176	0.149	0.205	SUBCLONAL	1	TRUE	1	0.485803953915592	3		359	743	SUCCESS
BLM	641	MSKCC	GRCh37	15	91326080	91326080	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	86	409	0	ENST00000355112.3:c.2584C>G	p.Leu862Val	p.L862V	ENST00000355112	NM_000057.2	862	Ctg/Gtg	13/22	0.44274690731409	1	FACETS	0.504	0.447	0.565	0.504	0.447	0.565	SUBCLONAL	1	TRUE	0	0.485803953915592	1		409	532	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807934	3807934	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148166625	NA	P-0013077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	146	400	0	ENST00000262367.5:c.3485A>G	p.Asn1162Ser	p.N1162S	ENST00000262367	NM_004380.2	1162	aAc/aGc	18/31	0.333702288907161	0	FACETS	0.712	0.656	0.77			1	SUBCLONAL	1	TRUE	0	0.485803953915592	0		400	434	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041704	14041704	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	55	598	0	ENST00000311895.7:c.2251T>C	p.Tyr751His	p.Y751H	ENST00000311895	NM_005236.2	751	Tac/Cac	11/11	0.28134814923244	5	FACETS	0.367	0.313	0.427			1	INDETERMINATE	1	TRUE	NA	0.485803953915592	5		598	1066	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348827	89348827	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1367050998	NA	P-0013077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2367	233	1831	0	ENST00000301030.4:c.4123G>C	p.Glu1375Gln	p.E1375Q	ENST00000301030	NM_001256183.1	1375	Gag/Cag	9/13	0.126481181081558	5	FACETS	0.638	0.591	0.686	0.159	0.147	0.172	INDETERMINATE	1	TRUE	1	0.485803953915592	5		1831	2600	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	80	563	0	ENST00000269305.4:c.166G>T	p.Glu56Ter	p.E56*	ENST00000269305	NM_001126112.2	56	Gaa/Taa	4/11	0.485803953915592	1	FACETS	0.48	0.423	0.54	0.48	0.423	0.54	SUBCLONAL	1	TRUE	0	0.485803953915592	1		563	520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579396	7579405	+	frameshift_variant	Frame_Shift_Del	DEL	GACAGAAGAT	GACAGAAGAT	-	novel	NA	P-0013077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	148	497	0	ENST00000269305.4:c.282_291del	p.Ser95LeufsTer25	p.S95Lfs*25	ENST00000269305	NM_001126112.2	94	tcATCTTCTGTC/tc	4/11	0.485803953915592	1	FACETS	0.859	0.789	0.931	0.859	0.789	0.931	CLONAL	1	TRUE	0	0.485803953915592	1		497	537	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	52	720	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.0977573588793603	4	FACETS	0.974	0.827	1	0.487	0.413	0.568	INDETERMINATE	1	FALSE	2	0.163516576346067	4		721	760	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0013087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	52	637	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.141675769951676	2	FACETS	0.818	0.698	0.948	0.818	0.698	0.948	CLONAL	2	FALSE	0	0.163516576346067	2		637	389	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839712	27839712	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1934	176	1770	0	ENST00000328488.2:c.382G>C	p.Ala128Pro	p.A128P	ENST00000328488	NM_003533.2	128	Gcg/Ccg	1/1	0.0977573588793603	4	FACETS	1	0.978	1	0.594	0.544	0.646	INDETERMINATE	1	FALSE	2	0.163516576346067	4		1770	2110	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117953	70117953	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	27	264	0	ENST00000245479.2:c.421A>G	p.Lys141Glu	p.K141E	ENST00000245479	NM_000346.3	141	Aag/Gag	1/3	1	2	FACETS	0.838	0.672	1	1	0.945	1	CLONAL	2	FALSE	1	0.163516576346067	2		264	197	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10292722	10292722	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	48	463	0	ENST00000340748.4:c.112G>T	p.Glu38Ter	p.E38*	ENST00000340748		38	Gaa/Taa	2/40	0.116154361731589	0	FACETS	0.934	0.789	1			1	CLONAL	1	FALSE	0	0.163516576346067	0		463	526	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045500	47045500	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	55	291	0	ENST00000377604.3:c.2467G>T	p.Glu823Ter	p.E823*	ENST00000377604	NM_001204468.1	823	Gaa/Taa	22/24	1	1	FACETS	0.914	0.786	1	1	0.975	1	CLONAL	2	FALSE	0	0.163516576346067	1		291	338	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117710	70117711	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	151	894	0	ENST00000245479.2:c.179dup	p.Lys61GlufsTer191	p.K61Efs*191	ENST00000245479	NM_000346.3	60	ctg/cTtg	1/3	1	2	FACETS	0.85	0.779	0.925	1	0.993	1	CLONAL	3	FALSE	1	0.163516576346067	2		894	724	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0013094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	543	1096	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.611758942895961	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.611758942895961	2		1097	839	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143509	108143509	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	248	743	0	ENST00000278616.4:c.3214G>A	p.Glu1072Lys	p.E1072K	ENST00000278616	NM_000051.3	1072	Gaa/Aaa	22/63	0.611758942895961	3	FACETS	0.884	0.825	0.944	0.295	0.275	0.315	CLONAL	1	TRUE	0	0.611758942895961	3		743	1198	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269047	142269047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	235	665	2	ENST00000350721.4:c.2903G>A	p.Arg968Lys	p.R968K	ENST00000350721	NM_001184.3	968	aGa/aAa	14/47	0.611758942895961	3	FACETS	0.901	0.84	0.964	0.451	0.42	0.482	CLONAL	1	TRUE	1	0.611758942895961	3		667	1113	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206842	162206842	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	229	596	0	ENST00000366898.1:c.833T>C	p.Val278Ala	p.V278A	ENST00000366898	NM_004562.2	278	gTt/gCt	7/12	0.611758942895961	2	FACETS	0.959	0.896	1	0.479	0.448	0.512	CLONAL	1	TRUE	0	0.611758942895961	2		596	781	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447006	49447006	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	334	740	0	ENST00000301067.7:c.938A>G	p.His313Arg	p.H313R	ENST00000301067	NM_003482.3	313	cAc/cGc	7/54	0.611758942895961	2	FACETS	1	0.985	1	0.551	0.522	0.581	CLONAL	1	TRUE	0	0.611758942895961	2		740	990	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273249	18273249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1595	380	873	1	ENST00000222254.8:c.1042C>T	p.Pro348Ser	p.P348S	ENST00000222254	NM_005027.3	348	Ccc/Tcc	9/16	0.58331233602907	4	FACETS	1	0.957	1	0.507	0.479	0.535	CLONAL	1	TRUE	2	0.611758942895961	4		874	1975	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128703	64128704	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GACG	novel	NA	P-0013094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	420	629	0	ENST00000334205.4:c.563_566dup	p.Glu189AspfsTer24	p.E189Dfs*24	ENST00000334205	NM_003942.2	187	ctg/ctGACGg	5/17	0.611758942895961	2	FACETS	0.889	0.854	0.924	0.889	0.854	0.924	CLONAL	2	TRUE	0	0.611758942895961	2		629	772	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937027	48937046	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	ACAACTAGAAAATGATACAA	ACAACTAGAAAATGATACAA	TTATTGAATTATT	novel	NA	P-0013094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	309	535	0	ENST00000267163.4:c.795_814delinsTTATTGAATTATT	p.Lys265AsnfsTer3	p.K265Nfs*3	ENST00000267163	NM_000321.2	265	aaACAACTAGAAAATGATACAAga/aaTTATTGAATTATTga	8/27	0.611758942895961	2	FACETS	0.853	0.813	0.893	0.853	0.813	0.893	CLONAL	2	TRUE	0	0.611758942895961	2		535	592	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0013097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	142	763	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.37254651623899	1	FACETS	0.895	0.818	0.976	0.895	0.818	0.976	CLONAL	1	TRUE	0	0.37254651623899	1		764	693	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0013097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	240	888	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.37254651623899	1	FACETS	0.848	0.791	0.908	0.848	0.791	0.908	CLONAL	1	TRUE	0	0.37254651623899	1		889	1236	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103199	119103224	+	frameshift_variant	Frame_Shift_Del	DEL	TAGCCCACCTTATATCTTAGACCTGC	TAGCCCACCTTATATCTTAGACCTGC	-	novel	NA	P-0013097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	158	514	0	ENST00000264033.4:c.239_264del	p.Ser80ThrfsTer15	p.S80Tfs*15	ENST00000264033	NM_005188.3	79	aaTAGCCCACCTTATATCTTAGACCTGCta/aata	2/16	0.37254651623899	1	FACETS	0.922	0.846	1	0.922	0.846	1	CLONAL	1	TRUE	0	0.37254651623899	1		514	749	SUCCESS
APC	324	MSKCC	GRCh37	5	112177136	112177136	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	147	595	0	ENST00000257430.4:c.5845del	p.Glu1949LysfsTer21	p.E1949Kfs*21	ENST00000257430	NM_000038.5	1949	Gaa/aa	16/16	0.37254651623899	1	FACETS	0.759	0.693	0.828	0.759	0.693	0.828	SUBCLONAL	1	TRUE	0	0.37254651623899	1		595	846	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0013105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	311	584	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.605125989548736	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.605125989548736	1		586	684	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	323	538	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.605125989548736	2		538	1035	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856020	68856020	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	463	912	0	ENST00000261769.5:c.1828C>T	p.Gln610Ter	p.Q610*	ENST00000261769	NM_004360.3	610	Cag/Tag	12/16	0.605125989548736	1	FACETS	0.94	0.9	0.981	0.94	0.9	0.981	CLONAL	1	TRUE	0	0.605125989548736	1		912	1135	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968871	15968871	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	466	674	0	ENST00000268712.3:c.4879T>G	p.Leu1627Val	p.L1627V	ENST00000268712	NM_006311.3	1627	Ttg/Gtg	33/46	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.605125989548736	NA		674	1285	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654718	67654718	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	338	630	0	ENST00000264010.4:c.1205C>T	p.Ser402Leu	p.S402L	ENST00000264010	NM_006565.3	402	tCa/tTa	6/12	0.605125989548736	1	FACETS	0.928	0.881	0.974	0.928	0.881	0.974	CLONAL	1	TRUE	0	0.605125989548736	1		630	840	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726512	46726512	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	334	537	1	ENST00000371975.4:c.591G>A	p.Met197Ile	p.M197I	ENST00000371975	NM_003579.3	197	atG/atA	7/18	0.605125989548736	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.605125989548736	1		538	757	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309819	65309819	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	349	670	0	ENST00000342505.4:c.2331G>A	p.Trp777Ter	p.W777*	ENST00000342505	NM_002227.2	777	tgG/tgA	17/25	0.605125989548736	1	FACETS	0.931	0.886	0.977	0.931	0.886	0.977	CLONAL	1	TRUE	0	0.605125989548736	1		670	864	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076716	72076716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	444	860	0	ENST00000357731.5:c.781G>A	p.Glu261Lys	p.E261K	ENST00000357731	NM_173808.2	261	Gag/Aag	5/7	0.605125989548736	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.605125989548736	1		860	981	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439909	52439909	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	270	480	0	ENST00000460680.1:c.803C>G	p.Pro268Arg	p.P268R	ENST00000460680	NM_004656.3	268	cCa/cGa	10/17	1	2	FACETS	0.977	0.919	1	0.977	0.919	1	CLONAL	1	TRUE	1	0.605125989548736	2		480	913	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518175	8518175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1354824749	NA	P-0013105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	299	611	1	ENST00000356435.5:c.1216G>A	p.Glu406Lys	p.E406K	ENST00000356435		406	Gaa/Aaa	10/35	1	2	FACETS	0.972	0.916	1	0.972	0.916	1	CLONAL	1	TRUE	1	0.605125989548736	2		612	1017	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914820	32914820	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1489	630	1100	2	ENST00000380152.3:c.6328G>A	p.Asp2110Asn	p.D2110N	ENST00000380152		2110	Gat/Aat	11/27	1	2	FACETS	0.983	0.944	1	0.983	0.944	1	CLONAL	1	TRUE	1	0.605125989548736	2		1102	2119	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968909	15968909	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0013105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	620	697	0	ENST00000268712.3:c.4841T>G	p.Leu1614Ter	p.L1614*	ENST00000268712	NM_006311.3	1614	tTa/tGa	33/46	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.605125989548736	NA		697	1495	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968933	15968933	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	626	712	0	ENST00000268712.3:c.4817T>C	p.Met1606Thr	p.M1606T	ENST00000268712	NM_006311.3	1606	aTg/aCg	33/46	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.605125989548736	NA		712	1545	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968940	15968940	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	621	724	0	ENST00000268712.3:c.4810T>A	p.Tyr1604Asn	p.Y1604N	ENST00000268712	NM_006311.3	1604	Tac/Aac	33/46	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.605125989548736	NA		724	1521	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0013115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	154	676	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.571834639675116	4	FACETS	0.971	0.897	1	0.971	0.897	1	CLONAL	2	FALSE	2	0.571834639675116	4		676	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0013115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	189	508	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	0.342075260180399	3	FACETS	1	0.964	1	0.694	0.651	0.739	INDETERMINATE	2	FALSE	0	0.571834639675116	3		508	408	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0013115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	243	474	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	0.48419755220552	3	FACETS	1	0.991	1	0.674	0.631	0.717	CLONAL	1	FALSE	1	0.571834639675116	3		474	811	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456563	29456563	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0013115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	213	629	0	ENST00000389048.3:c.2356-1G>A		p.X786_splice	ENST00000389048	NM_004304.4	786			0.137207643462456	6	FACETS	0.859	0.803	0.916	0.859	0.803	0.916	INDETERMINATE	3	FALSE	3	0.571834639675116	6		629	620	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151293	202151293	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	316	930	0	ENST00000358485.4:c.1593A>C	p.Lys531Asn	p.K531N	ENST00000358485	NM_001080125.1	531	aaA/aaC	9/9	0.533775824847002	3	FACETS	0.759	0.718	0.801	0.759	0.718	0.801	SUBCLONAL	2	FALSE	1	0.571834639675116	3		930	936	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112430	115112431	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0013115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	211	549	0	ENST00000257566.3:c.1309dup	p.His437ProfsTer2	p.H437Pfs*2	ENST00000257566	NM_016569.3	437	cat/cCat	7/8	0.113272912484793	6	FACETS	1	0.986	1	0.81	0.756	0.865	INDETERMINATE	2	FALSE	3	0.571834639675116	6		549	651	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0013141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	135	501	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.399949897858504	1	FACETS	0.887	0.809	0.968	0.887	0.809	0.968	CLONAL	1	TRUE	0	0.399949897858504	1		501	609	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120642	115120642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	198	853	0	ENST00000257566.3:c.364G>A	p.Glu122Lys	p.E122K	ENST00000257566	NM_016569.3	122	Gag/Aag	1/8	1	2	FACETS	0.906	0.838	0.976	0.906	0.838	0.976	CLONAL	1	TRUE	1	0.399949897858504	2		853	1093	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063311	67063311	+	start_lost	Translation_Start_Site	SNP	A	A	T	novel	NA	P-0013141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	78	287	0	ENST00000412916.2:c.1A>T	p.Met1?	p.M1?	ENST00000412916		1	Atg/Ttg	1/6	0.399949897858504	1	FACETS	0.987	0.876	1	0.987	0.876	1	CLONAL	1	TRUE	0	0.399949897858504	1		287	316	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845616	68845616	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	143	568	0	ENST00000261769.5:c.862G>A	p.Asp288Asn	p.D288N	ENST00000261769	NM_004360.3	288	Gac/Aac	7/16	0.399949897858504	1	FACETS	0.947	0.867	1	0.947	0.867	1	CLONAL	1	TRUE	0	0.399949897858504	1		568	604	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699247	117699247	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	185	595	0	ENST00000369458.3:c.394A>G	p.Ile132Val	p.I132V	ENST00000369458	NM_024626.3	132	Atc/Gtc	3/6	0.723920474473455	3	FACETS	0.939	0.87	1	0.47	0.435	0.506	CLONAL	1	TRUE	1	0.723920474473455	3		595	741	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414934	78414934	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	60	491	0	ENST00000370768.2:c.1832A>C	p.Tyr611Ser	p.Y611S	ENST00000370768	NM_003902.3	611	tAt/tCt	19/20	0.25762745885394	3	FACETS	0.734	0.632	0.846	0.367	0.316	0.423	SUBCLONAL	1	TRUE	1	0.265663142093288	3		491	697	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53244022	53244022	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	97	390	0	ENST00000375401.3:c.971C>A	p.Ser324Ter	p.S324*	ENST00000375401	NM_004187.3	324	tCa/tAa	8/26	0.179686064038616	2	FACETS	1	0.972	1			1	CLONAL	2	TRUE	NA	0.265663142093288	2		390	299	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183820	10183820	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	59	305	0	ENST00000256474.2:c.291del	p.Tyr98ThrfsTer61	p.Y98Tfs*61	ENST00000256474	NM_000551.3	97	Ccc/cc	1/3	0.231592541531951	3	FACETS	0.804	0.696	0.919	0.536	0.464	0.613	CLONAL	2	TRUE	0	0.265663142093288	3		305	313	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158133	47158134	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	137	781	0	ENST00000409792.3:c.4565dup	p.Asn1522LysfsTer7	p.N1522Kfs*7	ENST00000409792	NM_014159.6	1522	aat/aaAt	4/21	0.265663142093288	1	FACETS	0.855	0.782	0.931	1	0.989	1	CLONAL	2	TRUE	0	0.265663142093288	1		781	523	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990405	69990405	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	148	417	0	ENST00000394351.3:c.364G>T	p.Asp122Tyr	p.D122Y	ENST00000394351	NM_000248.3	122	Gac/Tac	4/9	0.602805423602565	4	FACETS	0.752	0.686	0.821	0.376	0.343	0.411	SUBCLONAL	1	TRUE	2	0.646519240699329	4		417	1003	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156407	106156407	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	239	563	0	ENST00000380013.4:c.1308C>A	p.His436Gln	p.H436Q	ENST00000380013	NM_001127208.2	436	caC/caA	3/11	0.646519240699329	3	FACETS	0.862	0.804	0.922	0.431	0.402	0.461	CLONAL	1	TRUE	1	0.646519240699329	3		563	1135	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	174	766	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.789	0.732	0.849	0.789	0.732	0.849	SUBCLONAL	1	FALSE	1	0.816339483874963	2		766	540	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0013181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	399	388	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.993	0.948	1	0.993	0.948	1	CLONAL	1	FALSE	1	0.816339483874963	2		389	984	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791757	42791757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568504941	NA	P-0013181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	353	545	0	ENST00000575354.2:c.643C>T	p.Arg215Trp	p.R215W	ENST00000575354	NM_015125.3	215	Cgg/Tgg	5/20	0.816339483874963	1	FACETS	0.968	0.932	1	0.968	0.932	1	CLONAL	1	FALSE	0	0.816339483874963	1		545	529	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111147	193111147	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	419	467	0	ENST00000367435.3:c.680G>T	p.Arg227Ile	p.R227I	ENST00000367435	NM_024529.4	227	aGa/aTa	7/17	1	2	FACETS	0.917	0.875	0.96	0.917	0.875	0.96	CLONAL	1	FALSE	1	0.816339483874963	2		467	1119	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381558	81381558	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773949476	NA	P-0013181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	593	614	0	ENST00000222390.5:c.503G>A	p.Arg168Gln	p.R168Q	ENST00000222390	NM_000601.4	168	cGg/cAg	5/18	1	2	FACETS	0.99	0.953	1	0.99	0.953	1	CLONAL	1	FALSE	1	0.816339483874963	2		614	1467	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249395	133249395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	96	363	0	ENST00000320574.5:c.1504G>A	p.Glu502Lys	p.E502K	ENST00000320574	NM_006231.2	502	Gag/Aag	15/49	1	2	FACETS	0.349	0.311	0.389	0.349	0.311	0.389	SUBCLONAL	1	FALSE	1	0.816339483874963	2		363	674	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993546	72993546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1276	282	852	1	ENST00000268489.5:c.499C>T	p.Pro167Ser	p.P167S	ENST00000268489	NM_006885.3	167	Ccc/Tcc	2/10	1	2	FACETS	0.443	0.415	0.473	0.443	0.415	0.473	SUBCLONAL	1	FALSE	1	0.816339483874963	2		853	1558	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163878	47163878	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	346	484	1	ENST00000409792.3:c.2248G>T	p.Glu750Ter	p.E750*	ENST00000409792	NM_014159.6	750	Gaa/Taa	3/21	1	2	FACETS	0.931	0.883	0.98	0.931	0.883	0.98	CLONAL	1	TRUE	1	0.72932987899314	2		485	1019	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589866	55589866	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0013188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	255	390	0	ENST00000288135.5:c.1346+2T>C		p.X449_splice	ENST00000288135	NM_000222.2	449			1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.72932987899314	2		390	682	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593578	55593606	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	In_Frame_Del	DEL	ACAGAAACCCATGTATGAAGTACAGTGGA	ACAGAAACCCATGTATGAAGTACAGTGGA	-	novel	NA	P-0013188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	243	497	0	ENST00000288135.5:c.1648-3_1673del		p.K550_K558del	ENST00000288135	NM_000222.2	550		11/21	1	2	FACETS	0.774	0.725	0.825	0.774	0.725	0.825	SUBCLONAL	1	TRUE	1	0.72932987899314	2		497	861	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104393	2104393	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774892845	NA	P-0013202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	345	612	0	ENST00000219476.3:c.433G>A	p.Ala145Thr	p.A145T	ENST00000219476	NM_000548.3	145	Gcc/Acc	5/42	0.437553827508669	4	FACETS	0.978	0.929	1	0.978	0.929	1	CLONAL	2	TRUE	2	0.662754481413386	4		612	885	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378590	25378590	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	320	461	0	ENST00000311936.3:c.408T>A	p.Ser136Arg	p.S136R	ENST00000311936	NM_004985.3	136	agT/agA	4/5	0.662754481413386	3	FACETS	1	0.994	1			1	CLONAL	1	TRUE	NA	0.662754481413386	3		461	889	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366252	15366252	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1489038800	NA	P-0013202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	40	828	0	ENST00000263377.2:c.1903C>T	p.His635Tyr	p.H635Y	ENST00000263377	NM_058243.2	635	Cac/Tac	10/20	1	2	FACETS	0.158	0.13	0.188	0.158	0.13	0.188	SUBCLONAL	1	TRUE	1	0.662754481413386	2		828	766	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0013216-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	468	913	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.748878804222773	1	FACETS	0.955	0.92	0.989	0.955	0.92	0.989	CLONAL	1	TRUE	0	0.748878804222773	1		913	819	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	232	840	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.971	0.911	1	0.971	0.911	1	CLONAL	1	TRUE	1	0.745408606402741	2		840	641	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845622	151845623	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0013222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	252	675	0	ENST00000262189.6:c.13389dup	p.Phe4464LeufsTer9	p.F4464Lfs*9	ENST00000262189	NM_170606.2	4463	-/C	52/59	0.541484053276413	4	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.745408606402741	4		675	1004	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577054	7577055	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	C	novel	NA	P-0013222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	414	809	0	ENST00000269305.4:c.883_884delinsG	p.Pro295ValfsTer50	p.P295Vfs*50	ENST00000269305	NM_001126112.2	295	CCt/Gt	8/11	0.741373784278019	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.745408606402741	1		809	664	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	28	766	0				ENST00000310581	NM_198253.2	-/1132			0.225224410252449	1	FACETS	0.845	0.678	1	0.845	0.678	1	CLONAL	1	TRUE	0	0.22	1		766	268	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039374	49039374	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853293	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	103	868	0	ENST00000267163.4:c.2359C>T	p.Arg787Ter	p.R787*	ENST00000267163	NM_000321.2	787	Cga/Tga	23/27	NA	2	FACETS	0.869	0.776	0.969			1	INDETERMINATE	1	TRUE	NA	0.22	2		868	1077	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132915	64132915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141809902	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	100	726	0	ENST00000334205.4:c.1049C>T	p.Pro350Leu	p.P350L	ENST00000334205	NM_003942.2	350	cCt/cTt	9/17	0.158150752320438	2	FACETS	1	0.978	1	0.69	0.617	0.767	CLONAL	1	TRUE	0	0.22	2		726	659	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041073	29041073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	70	529	0	ENST00000282397.4:c.355G>A	p.Glu119Lys	p.E119K	ENST00000282397	NM_002019.4	119	Gaa/Aaa	3/30	NA	2	FACETS	1	0.926	1			1	INDETERMINATE	1	TRUE	NA	0.22	2		529	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	88	349	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	0.158150752320438	2	FACETS	0.879	0.782	0.981	0.879	0.782	0.981	CLONAL	2	TRUE	0	0.22	2		349	455	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396238	396238	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	55	656	0	ENST00000262320.3:c.788C>T	p.Pro263Leu	p.P263L	ENST00000262320	NM_003502.3	263	cCc/cTc	2/11	0.225224410252449	1	FACETS	0.75	0.642	0.87	0.75	0.642	0.87	SUBCLONAL	1	TRUE	0	0.22	1		656	593	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456443	99456443	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	57	666	1	ENST00000268035.6:c.1760C>T	p.Thr587Ile	p.T587I	ENST00000268035	NM_000875.3	587	aCc/aTc	8/21	1	2	FACETS	0.732	0.627	0.847	0.732	0.627	0.847	SUBCLONAL	1	TRUE	1	0.22	2		667	708	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139714	55139714	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600186	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	50	492	0	ENST00000257290.5:c.1375G>A	p.Glu459Lys	p.E459K	ENST00000257290	NM_006206.4	459	Gaa/Aaa	10/23	1	2	FACETS	0.861	0.73	1	0.861	0.73	1	CLONAL	1	TRUE	1	0.22	2		492	528	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5239002	5239002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775100072	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	52	819	0	ENST00000357368.4:c.1777C>T	p.Arg593Cys	p.R593C	ENST00000357368	NM_002850.3	593	Cgc/Tgc	13/38	0.176354452714934	2	FACETS	0.636	0.54	0.742	0.318	0.27	0.371	SUBCLONAL	1	TRUE	0	0.22	2		819	743	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114126	115114126	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	104	637	0	ENST00000257566.3:c.1091A>G	p.Asn364Ser	p.N364S	ENST00000257566	NM_016569.3	364	aAc/aGc	6/8	0.295663217345086	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.22	1		637	732	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607245	189607245	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	128	840	0	ENST00000264731.3:c.1624C>T	p.Pro542Ser	p.P542S	ENST00000264731	NM_003722.4	542	Ccg/Tcg	12/14	0.299306942395776	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.22	1		840	702	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367239	50367239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1045233686	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	76	385	0	ENST00000331340.3:c.46G>A	p.Glu16Lys	p.E16K	ENST00000331340	NM_006060.4	16	Gaa/Aaa	3/8	0.158150752320438	2	FACETS	0.778	0.685	0.877	0.778	0.685	0.877	SUBCLONAL	2	TRUE	0	0.22	2		385	444	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272479	11272479	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	77	622	0	ENST00000361445.4:c.3451T>C	p.Tyr1151His	p.Y1151H	ENST00000361445	NM_004958.3	1151	Tat/Cat	23/58	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.22	2		622	617	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932227	36932227	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147017250	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	73	1033	2	ENST00000361632.4:c.2242G>A	p.Asp748Asn	p.D748N	ENST00000361632		748	Gat/Aat	16/16	1	2	FACETS	0.679	0.592	0.773	0.679	0.592	0.773	SUBCLONAL	1	TRUE	1	0.22	2		1035	978	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805178	43805178	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	56	595	2	ENST00000372470.3:c.628C>T	p.Pro210Ser	p.P210S	ENST00000372470	NM_005373.2	210	Cca/Tca	4/12	1	2	FACETS	0.934	0.801	1	0.934	0.801	1	CLONAL	1	TRUE	1	0.22	2		597	545	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248685	59248685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	112	739	0	ENST00000371222.2:c.58C>T	p.Pro20Ser	p.P20S	ENST00000371222	NM_002228.3	20	Ccg/Tcg	1/1	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.22	2		739	832	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843430	156843430	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1309829121	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	29	292	0	ENST00000524377.1:c.856G>A	p.Ala286Thr	p.A286T	ENST00000524377	NM_002529.3	286	Gcc/Acc	8/17	1	2	FACETS	0.973	0.784	1	0.973	0.784	1	CLONAL	1	TRUE	1	0.22	2		292	271	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666629	206666629	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	80	630	1	ENST00000367120.3:c.1963C>T	p.Gln655Ter	p.Q655*	ENST00000367120	NM_014002.3	655	Cag/Tag	20/22	1	2	FACETS	0.957	0.842	1	0.957	0.842	1	CLONAL	1	TRUE	1	0.22	2		631	760	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505396	25505396	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	44	672	1	ENST00000264709.3:c.362C>T	p.Ala121Val	p.A121V	ENST00000264709	NM_175629.2	121	gCa/gTa	4/23	1	2	FACETS	0.661	0.554	0.781	0.661	0.554	0.781	SUBCLONAL	1	TRUE	1	0.22	2		673	605	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498051	29498051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	93	818	2	ENST00000389048.3:c.1955C>T	p.Ser652Leu	p.S652L	ENST00000389048	NM_004304.4	652	tCa/tTa	11/29	1	2	FACETS	0.977	0.868	1	0.977	0.868	1	CLONAL	1	TRUE	1	0.22	2		820	865	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295725	212295725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	46	666	0	ENST00000342788.4:c.2588G>A	p.Gly863Glu	p.G863E	ENST00000342788	NM_005235.2	863	gGg/gAg	21/28	1	2	FACETS	0.584	0.491	0.688	0.584	0.491	0.688	SUBCLONAL	1	TRUE	1	0.22	2		666	716	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259122	89259122	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142484873	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	56	573	0	ENST00000336596.2:c.266G>A	p.Arg89Lys	p.R89K	ENST00000336596	NM_005233.5	89	aGg/aAg	3/17	0.225224410252449	1	FACETS	0.777	0.666	0.899	0.777	0.666	0.899	SUBCLONAL	1	TRUE	0	0.22	1		573	583	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286206	66286206	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138678484	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	88	749	0	ENST00000273854.3:c.1480C>T	p.Arg494Cys	p.R494C	ENST00000273854	NM_004439.5	494	Cgt/Tgt	6/18	1	2	FACETS	0.891	0.788	1	0.891	0.788	1	CLONAL	1	TRUE	1	0.22	2		749	898	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356298	66356298	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	46	615	1	ENST00000273854.3:c.1199C>T	p.Ser400Phe	p.S400F	ENST00000273854	NM_004439.5	400	tCc/tTc	5/18	1	2	FACETS	0.6	0.504	0.706	0.6	0.504	0.706	SUBCLONAL	1	TRUE	1	0.22	2		616	697	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876566	35876566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	21	283	0	ENST00000303115.3:c.1358C>T	p.Ser453Phe	p.S453F	ENST00000303115	NM_002185.3	453	tCc/tTc	8/8	0.225224410252449	1	FACETS	0.521	0.401	0.661	0.521	0.401	0.661	SUBCLONAL	1	TRUE	0	0.22	1		283	326	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176686992	176686992	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	56	686	0	ENST00000439151.2:c.4969C>T	p.Arg1657Trp	p.R1657W	ENST00000439151	NM_022455.4	1657	Cgg/Tgg	14/23	0.3	1	FACETS	0.74	0.634	0.857	0.74	0.634	0.857	SUBCLONAL	1	TRUE	0	0.22	1		686	612	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169159	32169159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	55	643	1	ENST00000375023.3:c.3874G>A	p.Glu1292Lys	p.E1292K	ENST00000375023	NM_004557.3	1292	Gag/Aag	22/30	0.202569210640114	3	FACETS	0.83	0.709	0.962	0.415	0.354	0.481	CLONAL	1	TRUE	1	0.22	3		644	669	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187545	32187545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	104	608	0	ENST00000375023.3:c.1334C>T	p.Pro445Leu	p.P445L	ENST00000375023	NM_004557.3	445	cCc/cTc	8/30	0.202569210640114	3	FACETS	0.769	0.69	0.854	0.769	0.69	0.854	SUBCLONAL	2	TRUE	1	0.22	3		608	682	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444336	50444336	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	122	537	0	ENST00000331340.3:c.266G>A	p.Gly89Glu	p.G89E	ENST00000331340	NM_006060.4	89	gGa/gAa	4/8	0.158150752320438	2	FACETS	0.819	0.742	0.901	0.819	0.742	0.901	CLONAL	2	TRUE	0	0.22	2		537	677	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381523	81381523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	109	803	0	ENST00000222390.5:c.538C>T	p.Pro180Ser	p.P180S	ENST00000222390	NM_000601.4	180	Cct/Tct	5/18	0.158150752320438	2	FACETS	1	0.955	1	0.558	0.5	0.619	CLONAL	1	TRUE	0	0.22	2		803	888	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508583	106508583	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749620239	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	67	359	0	ENST00000359195.3:c.577C>T	p.Pro193Ser	p.P193S	ENST00000359195	NM_002649.2	193	Ccc/Tcc	2/11	0.158150752320438	2	FACETS	1	0.97	1	0.708	0.618	0.806	CLONAL	1	TRUE	0	0.22	2		359	430	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242713	98242713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1197814180	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	128	616	0	ENST00000331920.6:c.904C>T	p.Pro302Ser	p.P302S	ENST00000331920	NM_000264.3	302	Cca/Tca	6/24	0.180194504940485	2	FACETS	0.83	0.753	0.91	0.83	0.753	0.91	CLONAL	2	TRUE	0	0.22	2		616	701	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420079	49420079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778198600	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	117	744	1	ENST00000301067.7:c.15670C>T	p.Arg5224Cys	p.R5224C	ENST00000301067	NM_003482.3	5224	Cgt/Tgt	48/54	0.176354452714934	2	FACETS	1	0.981	1	0.697	0.629	0.769	CLONAL	1	TRUE	0	0.22	2		745	763	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446806	49446806	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	103	701	0	ENST00000301067.7:c.1004C>T	p.Pro335Leu	p.P335L	ENST00000301067	NM_003482.3	335	cCc/cTc	8/54	0.176354452714934	2	FACETS	1	0.976	1	0.658	0.589	0.732	CLONAL	1	TRUE	0	0.22	2		701	711	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478067	99478067	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	79	684	3	ENST00000268035.6:c.2971G>T	p.Glu991Ter	p.E991*	ENST00000268035	NM_000875.3	991	Gag/Tag	16/21	1	2	FACETS	0.936	0.823	1	0.936	0.823	1	CLONAL	1	TRUE	1	0.22	2		687	767	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354425	354425	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs548567255	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	63	1363	2	ENST00000262320.3:c.1133C>T	p.Pro378Leu	p.P378L	ENST00000262320	NM_003502.3	378	cCg/cTg	5/11	0.225224410252449	1	FACETS	0.747	0.646	0.858	0.747	0.646	0.858	SUBCLONAL	1	TRUE	0	0.22	1		1365	682	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829622	72829622	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	84	1179	0	ENST00000268489.5:c.6959A>G	p.Tyr2320Cys	p.Y2320C	ENST00000268489	NM_006885.3	2320	tAc/tGc	9/10	0.225224410252449	1	FACETS	0.615	0.541	0.694	0.615	0.541	0.694	SUBCLONAL	1	TRUE	0	0.22	1		1179	1105	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665158	29665158	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1555534964	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	86	429	1	ENST00000356175.3:c.6756+1G>A		p.X2252_splice	ENST00000356175	NM_000267.3	2252			0.158150752320438	2	FACETS	1	0.978	1	0.733	0.65	0.822	CLONAL	1	TRUE	0	0.22	2		430	533	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687617	29687617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	157	824	2	ENST00000356175.3:c.8210C>T	p.Pro2737Leu	p.P2737L	ENST00000356175	NM_000267.3	2737	cCc/cTc	56/57	0.158150752320438	2	FACETS	0.786	0.72	0.855	0.786	0.72	0.855	SUBCLONAL	2	TRUE	0	0.22	2		826	908	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584479	39584479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751462355	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	63	582	0	ENST00000262039.4:c.1144G>A	p.Ala382Thr	p.A382T	ENST00000262039	NM_002647.2	382	Gcc/Acc	10/25	1	2	FACETS	0.825	0.713	0.947	0.825	0.713	0.947	CLONAL	1	TRUE	1	0.22	2		582	694	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390345	56390345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	104	996	1	ENST00000348428.3:c.1084C>T	p.Pro362Ser	p.P362S	ENST00000348428	NM_006785.3	362	Cct/Tct	10/17	1	2	FACETS	0.771	0.688	0.86	0.771	0.688	0.86	SUBCLONAL	1	TRUE	1	0.22	2		997	1226	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252870	10252870	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	37	487	0	ENST00000340748.4:c.3095C>T	p.Pro1032Leu	p.P1032L	ENST00000340748		1032	cCa/cTa	29/40	1	2	FACETS	0.496	0.408	0.596	0.496	0.408	0.596	SUBCLONAL	1	TRUE	1	0.22	2		487	678	SUCCESS
AXL	558	MSKCC	GRCh37	19	41749552	41749552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	283	1035	0	ENST00000301178.4:c.1477G>A	p.Glu493Lys	p.E493K	ENST00000301178	NM_021913.4	493	Gaa/Aaa	12/20	0.260718904533356	2	FACETS	0.857	0.806	0.909	1	0.991	1	CLONAL	3	TRUE	0	0.22	2		1035	1001	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42381388	42381388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	196	980	3	ENST00000221972.3:c.14C>T	p.Pro5Leu	p.P5L	ENST00000221972	NM_021601.3	5	cCa/cTa	1/5	0.260718904533356	2	FACETS	0.991	0.918	1	0.991	0.918	1	CLONAL	2	TRUE	0	0.22	2		983	899	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794461	42794461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756055340	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	268	1030	1	ENST00000575354.2:c.1541C>T	p.Pro514Leu	p.P514L	ENST00000575354	NM_015125.3	514	cCc/cTc	10/20	0.260718904533356	2	FACETS	0.873	0.82	0.927	1	0.991	1	CLONAL	3	TRUE	0	0.22	2		1031	930	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735443	40735443	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	73	716	0	ENST00000373198.4:c.3430A>G	p.Asn1144Asp	p.N1144D	ENST00000373198	NM_133170.3	1144	Aac/Gac	25/32	1	2	FACETS	0.821	0.717	0.934	0.821	0.717	0.934	CLONAL	1	TRUE	1	0.22	2		716	808	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101176	41101176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370385649	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	28	321	0	ENST00000373198.4:c.1180G>A	p.Glu394Lys	p.E394K	ENST00000373198	NM_133170.3	394	Gaa/Aaa	8/32	1	2	FACETS	0.701	0.561	0.861	0.701	0.561	0.861	SUBCLONAL	1	TRUE	1	0.22	2		321	363	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512374	149512391	+	inframe_deletion	In_Frame_Del	DEL	TGCGGTTGTCTTTGAACC	TGCGGTTGTCTTTGAACC	-	novel	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	73	555	0	ENST00000261799.4:c.1049_1066del	p.Trp350_Thr356delinsSer	p.W350_T356delinsS	ENST00000261799	NM_002609.3	350	tGGTTCAAAGACAACCGCAcc/tcc	7/23	0.3	1	FACETS	0.951	0.832	1	0.951	0.832	1	CLONAL	1	TRUE	0	0.22	1		555	621	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416710	121416711	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0013232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	54	639	0	ENST00000257555.6:c.139_140delinsAA	p.Gly47Lys	p.G47K	ENST00000257555		47	GGg/AAg	1/10	0.295663217345086	1	FACETS	0.747	0.638	0.867	0.747	0.638	0.867	SUBCLONAL	1	TRUE	0	0.22	1		639	585	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486049	29486050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0013242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	184	341	0	ENST00000356175.3:c.233dup	p.Asn78LysfsTer29	p.N78Kfs*29	ENST00000356175	NM_000267.3	76	gaa/gAaa	3/57	0.370921596265459	2	FACETS	0.773	0.719	0.829	0.773	0.719	0.829	SUBCLONAL	2	TRUE	0	0.436699725778818	2		341	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579409	7579410	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0013242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	296	539	0	ENST00000269305.4:c.277_278del	p.Leu93ValfsTer55	p.L93Vfs*55	ENST00000269305	NM_001126112.2	93	CTg/g	4/11	0.370921596265459	2	FACETS	0.852	0.805	0.899	0.852	0.805	0.899	CLONAL	2	TRUE	0	0.436699725778818	2		539	796	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692839	89692967	+	inframe_deletion	In_Frame_Del	DEL	TTGACCAATGGCTAAGTGAAGATGACAATCATGTTGCAGCAATTCACTGTAAAGCTGGAAAGGGACGAACTGGTGTAATGATATGTGCATATTTATTACATCGGGGCAAATTTTTAAAGGCACAAGAGG	TTGACCAATGGCTAAGTGAAGATGACAATCATGTTGCAGCAATTCACTGTAAAGCTGGAAAGGGACGAACTGGTGTAATGATATGTGCATATTTATTACATCGGGGCAAATTTTTAAAGGCACAAGAGG	-	novel	NA	P-0013242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	118	164	0	ENST00000371953.3:c.323_451del	p.Leu108_Ala151delinsPro	p.L108_A151delinsP	ENST00000371953	NM_000314.4	108	cTTGACCAATGGCTAAGTGAAGATGACAATCATGTTGCAGCAATTCACTGTAAAGCTGGAAAGGGACGAACTGGTGTAATGATATGTGCATATTTATTACATCGGGGCAAATTTTTAAAGGCACAAGAGGcc/ccc	5/9	0.370921596265459	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.436699725778818	2		164	240	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842313	151842313	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	296	621	0	ENST00000262189.6:c.14099del	p.Pro4700LeufsTer16	p.P4700Lfs*16	ENST00000262189	NM_170606.2	4700	cCt/ct	54/59	0.371528709717536	4	FACETS	0.782	0.736	0.83	0.782	0.736	0.83	SUBCLONAL	2	TRUE	2	0.436699725778818	4		621	1245	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	73	766	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.862034886991189	2		766	150	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220329	55220329	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3534	9689	452	2	ENST00000275493.2:c.719G>C	p.Cys240Ser	p.C240S	ENST00000275493	NM_005228.3	240	tGc/tCc	6/28	0.862034886991189	40	FACETS	0.985	0.978	0.991			1	CLONAL	30	TRUE	NA	0.862034886991189	40		454	13223	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3824602	3824611	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAGTGGTT	CAGAGTGGTT	-	novel	NA	P-0013259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	236	711	0	ENST00000262367.5:c.2242_2251del	p.Asn748SerfsTer3	p.N748Sfs*3	ENST00000262367	NM_004380.2	748	AACCACTCTGtc/tc	12/31	1	2	FACETS	0.925	0.87	0.981	0.925	0.87	0.981	CLONAL	1	TRUE	1	0.862034886991189	2		711	592	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711966	89711967	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0013259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	189	373	0	ENST00000371953.3:c.584_585insG	p.Phe195LeufsTer7	p.F195Lfs*7	ENST00000371953	NM_000314.4	195	ttt/ttGt	6/9	0.847749042620038	1	FACETS	0.901	0.856	0.944	0.901	0.856	0.944	CLONAL	1	TRUE	0	0.862034886991189	1		373	277	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0013262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	422	1015	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	NA	2	FACETS	0.828	0.796	0.86			1	INDETERMINATE	2	TRUE	NA	0.688575673732059	2		1015	740	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780205	9780205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781504902	NA	P-0013262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	588	806	1	ENST00000377346.4:c.1375G>A	p.Val459Met	p.V459M	ENST00000377346	NM_005026.3	459	Gtg/Atg	11/24	NA	2	FACETS	1	0.997	1			1	INDETERMINATE	1	TRUE	NA	0.688575673732059	2		807	1183	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846327	156846327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	148	760	0	ENST00000524377.1:c.1768G>A	p.Glu590Lys	p.E590K	ENST00000524377	NM_002529.3	590	Gag/Aag	14/17	1	2	FACETS	0.458	0.418	0.5	0.458	0.418	0.5	SUBCLONAL	1	TRUE	1	0.688575673732059	2		760	938	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294318	1294318	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	88	179	1	ENST00000310581.5:c.683C>A	p.Ala228Asp	p.A228D	ENST00000310581	NM_198253.2	228	gCc/gAc	2/16	NA	2	FACETS	1	0.915	1			1	INDETERMINATE	1	TRUE	NA	0.688575673732059	2		180	251	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519586	137519586	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	315	780	0	ENST00000367739.4:c.1052G>C	p.Ser351Thr	p.S351T	ENST00000367739	NM_000416.2	351	aGt/aCt	7/7	NA	2	FACETS	0.839	0.792	0.887			1	INDETERMINATE	1	TRUE	NA	0.688575673732059	2		780	1091	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134514	30134514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	159	322	0	ENST00000263025.4:c.17C>T	p.Ala6Val	p.A6V	ENST00000263025	NM_002746.2	6	gCt/gTt	1/9	0.659290554814472	4	FACETS	1	0.964	1			1	CLONAL	1	TRUE	NA	0.688575673732059	4		322	717	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971397	15971397	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	476	728	0	ENST00000268712.3:c.4552A>G	p.Lys1518Glu	p.K1518E	ENST00000268712	NM_006311.3	1518	Aaa/Gaa	32/46	0.47119468439705	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.688575673732059	1		728	806	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637011	93637011	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	150	577	0	ENST00000375746.1:c.1061del	p.Asp354AlafsTer17	p.D354Afs*17	ENST00000375746	NM_001174167.1	354	gAc/gc	9/14	0.692113391996169	1	FACETS	0.582	0.535	0.63	0.582	0.535	0.63	SUBCLONAL	1	TRUE	0	0.688575673732059	1		577	491	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419975	152419988	+	frameshift_variant	Frame_Shift_Del	DEL	CCGTGGAGGGGCAT	CCGTGGAGGGGCAT	-	novel	NA	P-0013262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	104	648	0	ENST00000206249.3:c.1671_1684del	p.Ala558AspfsTer88	p.A558Dfs*88	ENST00000206249	NM_000125.3	554	agCCGTGGAGGGGCATcc/agcc	8/8	0.692113391996169	1	FACETS	0.414	0.373	0.458	0.414	0.373	0.458	SUBCLONAL	1	TRUE	0	0.688575673732059	1		648	478	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227057	53227057	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	305	640	4	ENST00000375401.3:c.2518C>T	p.Pro840Ser	p.P840S	ENST00000375401	NM_004187.3	840	Ccc/Tcc	18/26	0.24813402260718	4	FACETS	0.786	0.74	0.833	0.786	0.74	0.833	INDETERMINATE	2	TRUE	2	0.460024586794635	4		644	1232	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691039	NA	P-0013272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	370	505	1	ENST00000269305.4:c.919+1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.442893214856128	2	FACETS	0.987	0.942	1	0.987	0.942	1	CLONAL	2	TRUE	0	0.460024586794635	2		506	815	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589599	67589604	+	inframe_deletion	In_Frame_Del	DEL	TCAGTT	TCAGTT	-	novel	NA	P-0013272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	358	359	0	ENST00000274335.5:c.1365_1370del	p.Phe456_Gln457del	p.F456_Q457del	ENST00000274335		454	acTCAGTTt/act	10/15	0.385936627804187	3	FACETS	0.869	0.83	0.909	0.869	0.83	0.909	CLONAL	3	TRUE	0	0.460024586794635	3		359	734	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249359	153249359	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0013272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	368	442	0	ENST00000281708.4:c.1418+1G>T		p.X473_splice	ENST00000281708	NM_033632.3	473			0.460024586794635	3	FACETS	0.923	0.877	0.97	0.923	0.877	0.97	CLONAL	2	TRUE	1	0.460024586794635	3		442	1066	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134471	30134472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0013272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	150	522	0	ENST00000263025.4:c.59dup	p.Gly21ArgfsTer41	p.G21Rfs*41	ENST00000263025	NM_002746.2	20	gtc/gtTc	1/9	0.416954129481509	4	FACETS	0.783	0.714	0.856	0.392	0.357	0.428	SUBCLONAL	1	TRUE	2	0.460024586794635	4		522	1216	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562285	21562285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749940600	NA	P-0013275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	290	565	1	ENST00000382592.4:c.1634G>A	p.Arg545His	p.R545H	ENST00000382592	NM_014572.2	545	cGt/cAt	4/8	0.635462108513782	1	FACETS	0.988	0.938	1	0.988	0.938	1	CLONAL	1	TRUE	0	0.635462108513782	1		566	630	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913503	NA	P-0013275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	298	598	0	ENST00000330062.3:c.515G>T	p.Arg172Met	p.R172M	ENST00000330062	NM_002168.2	172	aGg/aTg	4/11	1	2	FACETS	0.977	0.922	1	0.977	0.922	1	CLONAL	1	TRUE	1	0.635462108513782	2		598	960	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776225	135776225	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs118203705	NA	P-0013275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	235	499	0	ENST00000298552.3:c.2503-1G>T		p.X835_splice	ENST00000298552	NM_001162426.1	835			0.635462108513782	1	FACETS	0.911	0.858	0.965	0.911	0.858	0.965	CLONAL	1	TRUE	0	0.635462108513782	1		499	554	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0013292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	212	489	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.499489120578396	2		489	837	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620695	52620696	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0013292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	131	310	0	ENST00000394830.3:c.3057dup	p.Lys1020Ter	p.K1020*	ENST00000394830	NM_018313.4	1019	-/T	21/30	0.499489120578396	1	FACETS	0.898	0.822	0.978	0.898	0.822	0.978	CLONAL	1	TRUE	0	0.499489120578396	1		310	438	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0013310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	366	762	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.0630122952846799	3	FACETS	1	0.991	1	1	0.991	1	INDETERMINATE	2	TRUE	1	0.36	3		762	1023	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0013310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	99	504	0	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.3	1	FACETS	0.731	0.654	0.813	0.731	0.654	0.813	SUBCLONAL	1	TRUE	0	0.36	1		504	617	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574678	41574679	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs754418509	NA	P-0013310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	61	981	2	ENST00000263253.7:c.6970dup	p.His2324ProfsTer55	p.H2324Pfs*55	ENST00000263253	NM_001429.3	2321	-/C	31/31	1	2	FACETS	0.355	0.305	0.41	0.355	0.305	0.41	SUBCLONAL	1	TRUE	1	0.36	2		983	954	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974780	21974780	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs864622263	NA	P-0013310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	57	264	0	ENST00000304494.5:c.47T>A	p.Leu16Gln	p.L16Q	ENST00000304494	NM_000077.4	16	cTg/cAg	1/3	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.36	2		264	241	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748583	40748583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444440253	NA	P-0013310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	35	449	0	ENST00000373198.4:c.2933C>T	p.Ala978Val	p.A978V	ENST00000373198	NM_133170.3	978	gCg/gTg	21/32	0.3	1	FACETS	0.26	0.212	0.314	0.26	0.212	0.314	SUBCLONAL	1	TRUE	0	0.36	1		449	613	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857647	9857647	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	37	454	1	ENST00000330684.3:c.3754C>A	p.Gln1252Lys	p.Q1252K	ENST00000330684	NM_001134407.1	1252	Cag/Aag	13/13	NA	2	FACETS	0.169	0.139	0.203			1	INDETERMINATE	1	TRUE	NA	0.852680302469097	2		455	513	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400170	41400170	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	118	415	1	ENST00000373198.4:c.589C>T	p.Arg197Ter	p.R197*	ENST00000373198	NM_133170.3	197	Cga/Tga	5/32	0.542420216836704	1	FACETS	0.664	0.613	0.716	0.664	0.613	0.716	SUBCLONAL	1	TRUE	0	0.852680302469097	1		416	239	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595553	55595553	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs878853763	NA	P-0013313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	98	492	0	ENST00000288135.5:c.2043T>G	p.Phe681Leu	p.F681L	ENST00000288135	NM_000222.2	681	ttT/ttG	14/21	0.852680302469097	1	FACETS	0.909	0.846	0.97	0.909	0.846	0.97	CLONAL	1	TRUE	0	0.852680302469097	1		492	145	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155614	56155614	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	83	351	0	ENST00000399503.3:c.706G>T	p.Val236Phe	p.V236F	ENST00000399503	NM_005921.1	236	Gtc/Ttc	3/20	0.652436936044891	1	FACETS	0.669	0.607	0.73	0.669	0.607	0.73	SUBCLONAL	1	TRUE	0	0.852680302469097	1		351	167	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864415	57864415	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4334	1743	907	0	ENST00000228682.2:c.1892C>G	p.Pro631Arg	p.P631R	ENST00000228682	NM_005269.2	631	cCc/cGc	12/12	0.852680302469097	6	FACETS	0.91	0.888	0.932			1	CLONAL	2	TRUE	NA	0.852680302469097	6		907	6077	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556423	29556423	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs1135402832	NA	P-0013313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	111	360	0	ENST00000356175.3:c.2790T>G	p.Tyr930Ter	p.Y930*	ENST00000356175	NM_000267.3	930	taT/taG	21/57	0.427581740798982	3	FACETS	0.915	0.845	0.984	0.915	0.845	0.984	INDETERMINATE	2	TRUE	1	0.852680302469097	3		360	203	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	107	766	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.431559210709342	2		766	450	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245843	46245843	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	209	566	0	ENST00000334344.6:c.3937C>T	p.Gln1313Ter	p.Q1313*	ENST00000334344	NM_152641.2	1313	Caa/Taa	15/21	1	2	FACETS	0.93	0.863	1	0.93	0.863	1	CLONAL	1	TRUE	1	0.431559210709342	2		566	1041	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508727	148508727	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs267601394	NA	P-0013356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	192	633	0	ENST00000320356.2:c.1937A>T	p.Tyr646Phe	p.Y646F	ENST00000320356	NM_004456.4	646	tAc/tTc	16/20	1	2	FACETS	0.783	0.723	0.846	0.783	0.723	0.846	SUBCLONAL	1	TRUE	1	0.431559210709342	2		633	1136	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0013356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	212	589	1	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.431559210709342	2		590	974	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943776	9943776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1277595711	NA	P-0013356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	168	452	2	ENST00000330684.3:c.1165G>A	p.Val389Met	p.V389M	ENST00000330684	NM_001134407.1	389	Gtg/Atg	5/13	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.431559210709342	2		454	705	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100043	157100044	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGGAGC	rs747438636	NA	P-0013356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	14	98	0	ENST00000346085.5:c.992_997dup	p.Ala331_Gly332dup	p.A331_G332dup	ENST00000346085	NM_020732.3	331	gga/ggAGGAGCa	1/20	1	2	FACETS	0.403	0.292	0.536	0.403	0.292	0.536	SUBCLONAL	1	TRUE	1	0.431559210709342	2		98	161	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032197	10032197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774932381	NA	P-0013356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	199	636	1	ENST00000330684.3:c.626C>T	p.Ser209Phe	p.S209F	ENST00000330684	NM_001134407.1	209	tCc/tTc	3/13	1	2	FACETS	0.97	0.899	1	0.97	0.899	1	CLONAL	1	TRUE	1	0.431559210709342	2		637	951	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245204	46245204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	191	546	1	ENST00000334344.6:c.3298C>T	p.Gln1100Ter	p.Q1100*	ENST00000334344	NM_152641.2	1100	Cag/Tag	15/21	1	2	FACETS	0.964	0.892	1	0.964	0.892	1	CLONAL	1	TRUE	1	0.431559210709342	2		547	918	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319853	8319853	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	263	718	1	ENST00000356435.5:c.5648G>A	p.Arg1883Gln	p.R1883Q	ENST00000356435		1883	cGa/cAa	34/35	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.431559210709342	2		719	1102	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118878	61118878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	218	575	0	ENST00000295025.8:c.71G>A	p.Arg24Lys	p.R24K	ENST00000295025	NM_002908.2	24	aGa/aAa	2/11	1	2	FACETS	0.938	0.872	1	0.938	0.872	1	CLONAL	1	TRUE	1	0.431559210709342	2		575	1077	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145574	61145574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	190	595	0	ENST00000295025.8:c.686G>A	p.Gly229Asp	p.G229D	ENST00000295025	NM_002908.2	229	gGc/gAc	7/11	1	2	FACETS	0.842	0.778	0.909	0.842	0.778	0.909	CLONAL	1	TRUE	1	0.431559210709342	2		595	1046	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526134	189526134	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	194	608	0	ENST00000264731.3:c.398C>T	p.Pro133Leu	p.P133L	ENST00000264731	NM_003722.4	133	cCc/cTc	4/14	1	2	FACETS	0.946	0.876	1	0.946	0.876	1	CLONAL	1	TRUE	1	0.431559210709342	2		608	950	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923460	36923460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1464220458	NA	P-0013356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	185	580	0	ENST00000358127.4:c.802G>A	p.Ala268Thr	p.A268T	ENST00000358127	NM_001280556.1	268	Gcc/Acc	7/10	1	2	FACETS	0.971	0.897	1	0.971	0.897	1	CLONAL	1	TRUE	1	0.431559210709342	2		580	883	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409116	139409116	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	218	771	0	ENST00000277541.6:c.2053A>G	p.Asn685Asp	p.N685D	ENST00000277541	NM_017617.3	685	Aac/Gac	13/34	1	2	FACETS	0.9	0.837	0.967	0.9	0.837	0.967	CLONAL	1	TRUE	1	0.431559210709342	2		771	1122	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398035	4398035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	251	769	0	ENST00000261254.3:c.599C>T	p.Ser200Leu	p.S200L	ENST00000261254	NM_001759.3	200	tCg/tTg	4/5	1	2	FACETS	0.895	0.836	0.956	0.895	0.836	0.956	CLONAL	1	TRUE	1	0.431559210709342	2		769	1300	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719882	18719882	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0013356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	147	514	0	ENST00000266497.5:c.3780-1G>A		p.X1260_splice	ENST00000266497		1260			1	2	FACETS	0.916	0.837	0.998	0.916	0.837	0.998	CLONAL	1	TRUE	1	0.431559210709342	2		514	744	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380303	25380303	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	183	558	0	ENST00000311936.3:c.155T>G	p.Leu52Arg	p.L52R	ENST00000311936	NM_004985.3	52	cTc/cGc	3/5	1	2	FACETS	0.926	0.855	1	0.926	0.855	1	CLONAL	1	TRUE	1	0.431559210709342	2		558	916	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858597	57858597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751461298	NA	P-0013356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1263	318	940	0	ENST00000228682.2:c.335C>T	p.Ser112Leu	p.S112L	ENST00000228682	NM_005269.2	112	tCg/tTg	4/12	1	2	FACETS	0.932	0.877	0.988	0.932	0.877	0.988	CLONAL	1	TRUE	1	0.431559210709342	2		940	1581	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109819	115109819	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	170	455	0	ENST00000257566.3:c.2059G>A	p.Asp687Asn	p.D687N	ENST00000257566	NM_016569.3	687	Gac/Aac	8/8	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.431559210709342	2		455	731	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420352	88420352	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0013356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	100	291	0	ENST00000360948.2:c.2335-1G>A		p.X779_splice	ENST00000360948	NM_001012338.2	779			1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.431559210709342	2		291	447	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857638	9857638	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555482232	NA	P-0013356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	170	571	0	ENST00000330684.3:c.3763C>T	p.Gln1255Ter	p.Q1255*	ENST00000330684	NM_001134407.1	1255	Cag/Tag	13/13	1	2	FACETS	0.991	0.913	1	0.991	0.913	1	CLONAL	1	TRUE	1	0.431559210709342	2		571	795	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858706	9858706	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs796052553	NA	P-0013356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	274	738	1	ENST00000330684.3:c.2695C>T	p.Arg899Trp	p.R899W	ENST00000330684	NM_001134407.1	899	Cgg/Tgg	13/13	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.431559210709342	2		739	1109	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862887	9862887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868222927	NA	P-0013356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	254	646	1	ENST00000330684.3:c.2416G>A	p.Glu806Lys	p.E806K	ENST00000330684	NM_001134407.1	806	Gag/Aag	12/13	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.431559210709342	2		647	981	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508779	29508779	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	158	605	0	ENST00000356175.3:c.706C>T	p.Gln236Ter	p.Q236*	ENST00000356175	NM_000267.3	236	Cag/Tag	7/57	1	2	FACETS	0.815	0.747	0.887	0.815	0.747	0.887	CLONAL	1	TRUE	1	0.431559210709342	2		605	898	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274352	5274352	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	152	419	1	ENST00000357368.4:c.95C>T	p.Pro32Leu	p.P32L	ENST00000357368	NM_002850.3	32	cCc/cTc	3/38	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.431559210709342	2		420	662	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291600	15291600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	260	694	1	ENST00000263388.2:c.3034G>A	p.Gly1012Arg	p.G1012R	ENST00000263388	NM_000435.2	1012	Ggg/Agg	19/33	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.431559210709342	2		695	1165	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012653	36012653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	104	327	0	ENST00000358208.4:c.97C>T	p.Pro33Ser	p.P33S	ENST00000358208		33	Ccc/Tcc	2/12	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.431559210709342	2		327	442	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050707	30050707	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	170	483	0	ENST00000338641.4:c.509C>T	p.Pro170Leu	p.P170L	ENST00000338641	NM_000268.3	170	cCa/cTa	5/16	1	2	FACETS	0.957	0.881	1	0.957	0.881	1	CLONAL	1	TRUE	1	0.431559210709342	2		483	823	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879307	151879307	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	173	495	0	ENST00000262189.6:c.5638del	p.Gln1880LysfsTer59	p.Q1880Kfs*59	ENST00000262189	NM_170606.2	1880	Caa/aa	36/59	1	2	FACETS	0.98	0.903	1	0.98	0.903	1	CLONAL	1	TRUE	1	0.431559210709342	2		495	818	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117544	70117545	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0013356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	142	532	0	ENST00000245479.2:c.12_13delinsAA	p.Asp5Asn	p.D5N	ENST00000245479	NM_000346.3	4	ctGGac/ctAAac	1/3	1	2	FACETS	0.959	0.876	1	0.959	0.876	1	CLONAL	1	TRUE	1	0.431559210709342	2		532	686	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781428	135781429	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0013356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1318	316	1014	0	ENST00000298552.3:c.1536_1537delinsTT	p.Pro513Ser	p.P513S	ENST00000298552	NM_001162426.1	512	ctCCca/ctTTca	15/23	1	2	FACETS	0.896	0.843	0.951	0.896	0.843	0.951	CLONAL	1	TRUE	1	0.431559210709342	2		1014	1634	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0013373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	354	460	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.445664207338782	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.457037024843951	3		460	936	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440430	49440431	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0013373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	144	558	0	ENST00000301067.7:c.4379dup	p.Leu1461ThrfsTer30	p.L1461Tfs*30	ENST00000301067	NM_003482.3	1460	cca/ccCa	15/54	1	2	FACETS	0.908	0.83	0.989	0.908	0.83	0.989	CLONAL	1	TRUE	1	0.457037024843951	2		558	694	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214319	55214319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774146556	NA	P-0013373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	169	576	2	ENST00000275493.2:c.445C>T	p.Arg149Trp	p.R149W	ENST00000275493	NM_005228.3	149	Cgg/Tgg	4/28	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.457037024843951	2		578	699	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252838	36252862	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTGACAGATAACGTACCTCTTCCAC	TTGACAGATAACGTACCTCTTCCAC	-	novel	NA	P-0013373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	98	432	0	ENST00000300305.3:c.500_508+16del		p.X167_splice	ENST00000300305		167		4/8	0.134581833941893	5	FACETS	1	0.94	1			1	INDETERMINATE	1	TRUE	NA	0.457037024843951	5		432	670	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0013386-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1281	127	798	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.18	2		799	1408	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162475127	162475127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013386-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1198	67	804	0	ENST00000366898.1:c.614G>C	p.Ser205Thr	p.S205T	ENST00000366898	NM_004562.2	205	aGt/aCt	5/12	1	2	FACETS	0.588	0.509	0.675	0.588	0.509	0.675	SUBCLONAL	1	TRUE	1	0.18	2		804	1265	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730086	133730189	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTAGGAATTTGGAGATTTTTAGTAGTTACACAAGAATCAATGAAAAAGAACGAAGCTGGTTTCCAAAGCTGATATGTCTGATTTGGTTCCTTTCTTCTCAGGT	TTTAGGAATTTGGAGATTTTTAGTAGTTACACAAGAATCAATGAAAAAGAACGAAGCTGGTTTCCAAAGCTGATATGTCTGATTTGGTTCCTTTCTTCTCAGGT	-	novel	NA	P-0013386-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	20	71	0	ENST00000318560.5:c.254-102_255del		p.X85_splice	ENST00000318560	NM_005157.4	85		3/11	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.18	2		71	160	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0013396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	202	730	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	0.496087322515717	3	FACETS	1	0.967	1	0.537	0.498	0.578	CLONAL	1	TRUE	1	0.496087322515717	3		730	946	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933151	39933151	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778096	NA	P-0013396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	189	783	1	ENST00000378444.4:c.1448C>T	p.Pro483Leu	p.P483L	ENST00000378444	NM_001123385.1	483	cCg/cTg	4/15	0.496087322515717	3	FACETS	0.918	0.848	0.991	0.459	0.424	0.496	CLONAL	1	TRUE	1	0.496087322515717	3		784	1036	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	rs886039483	NA	P-0013396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	376	855	0	ENST00000269305.4:c.376T>G	p.Tyr126Asp	p.Y126D	ENST00000269305	NM_001126112.2	126	Tac/Gac	5/11	0.448789307233699	4	FACETS	0.893	0.858	0.928	0.893	0.858	0.928	CLONAL	4	TRUE	0	0.496087322515717	4		855	635	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120496249	120496249	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	194	752	0	ENST00000256646.2:c.2282del	p.Cys761SerfsTer16	p.C761Sfs*16	ENST00000256646	NM_024408.3	761	tGc/tc	14/34	0.496087322515717	2	FACETS	0.9	0.834	0.969	0.45	0.417	0.485	CLONAL	1	TRUE	0	0.496087322515717	2		752	869	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577330	64577333	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	rs587776841	NA	P-0013399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	220	784	0	ENST00000312049.6:c.249_252del	p.Ile85SerfsTer33	p.I85Sfs*33	ENST00000312049	NM_130799.2	83	ctGTCT/ct	2/10	0.510932188914901	3	FACETS	1	0.992	1	0.824	0.783	0.864	CLONAL	2	TRUE	0	0.684624367558152	3		784	349	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446884	187446884	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	175	860	0	ENST00000232014.4:c.1309G>T	p.Asp437Tyr	p.D437Y	ENST00000232014	NM_001130845.1	437	Gac/Tac	5/10	0.684624367558152	2	FACETS	0.965	0.913	1	0.965	0.913	1	CLONAL	2	TRUE	0	0.684624367558152	2		860	265	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652001	36652001	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	272	766	1	ENST00000244741.5:c.123C>A	p.Cys41Ter	p.C41*	ENST00000244741	NM_000389.4	41	tgC/tgA	2/3	0.684624367558152	3	FACETS	0.914	0.877	0.95	0.914	0.877	0.95	CLONAL	3	TRUE	0	0.684624367558152	3		767	389	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453139	140453139	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	221	643	1	ENST00000288602.6:c.1796C>A	p.Thr599Lys	p.T599K	ENST00000288602	NM_004333.4	599	aCa/aAa	15/18	0.614690983481275	4	FACETS	0.98	0.92	1	0.98	0.92	1	CLONAL	2	TRUE	2	0.684624367558152	4		644	555	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2113052	2113052	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	257	996	6	ENST00000219476.3:c.1441G>T	p.Glu481Ter	p.E481*	ENST00000219476	NM_000548.3	481	Gag/Tag	14/42	0.681380185167294	2	FACETS	0.97	0.928	1	0.97	0.928	1	CLONAL	2	TRUE	0	0.684624367558152	2		1002	387	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478626	57478626	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	332	731	2	ENST00000371085.3:c.298A>G	p.Lys100Glu	p.K100E	ENST00000371085	NM_000516.4	100	Aaa/Gaa	4/13	0.535742784861085	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.684624367558152	4		733	759	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939274	76939274	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	187	494	0	ENST00000373344.5:c.1474G>T	p.Glu492Ter	p.E492*	ENST00000373344	NM_000489.3	492	Gaa/Taa	9/35	0.619580107037957	2	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.684624367558152	2		494	226	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0013404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	113	565	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.813	0.736	0.893	0.813	0.736	0.893	CLONAL	1	TRUE	1	0.615336238507697	2		565	452	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121242	29121242	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137853007	NA	P-0013404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	206	1037	0	ENST00000328354.6:c.433C>T	p.Arg145Trp	p.R145W	ENST00000328354	NM_007194.3	145	Cgg/Tgg	3/15	0.615336238507697	1	FACETS	0.837	0.782	0.892	0.837	0.782	0.892	CLONAL	1	TRUE	0	0.615336238507697	1		1037	554	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911143	40911143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370795038	NA	P-0013404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	467	960	1	ENST00000373198.4:c.2162G>A	p.Arg721His	p.R721H	ENST00000373198	NM_133170.3	721	cGt/cAt	13/32	0.615336238507697	3	FACETS	0.926	0.888	0.964	0.926	0.888	0.964	CLONAL	2	TRUE	1	0.615336238507697	3		961	1072	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718767	190718767	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	114	533	0	ENST00000441310.2:c.925A>C	p.Asn309His	p.N309H	ENST00000441310	NM_000534.4	309	Aat/Cat	8/13	1	2	FACETS	0.965	0.877	1	0.965	0.877	1	CLONAL	1	TRUE	1	0.615336238507697	2		533	384	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492979	8492979	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	30	444	0	ENST00000356435.5:c.2350G>C	p.Asp784His	p.D784H	ENST00000356435		784	Gac/Cac	16/35	1	2	FACETS	0.176	0.141	0.216	0.176	0.141	0.216	SUBCLONAL	1	TRUE	1	0.615336238507697	2		444	553	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216469	108216469	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs1555137920	NA	P-0013404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	316	631	0	ENST00000278616.4:c.8419-1G>C		p.X2807_splice	ENST00000278616	NM_000051.3	2807			0.609007028482023	2	FACETS	0.999	0.957	1	0.999	0.957	1	CLONAL	2	TRUE	0	0.615336238507697	2		631	514	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989116	41989116	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	324	1289	0	ENST00000219905.7:c.1908A>C	p.Leu636Phe	p.L636F	ENST00000219905	NM_001164273.1	636	ttA/ttC	3/24	1	2	FACETS	0.842	0.794	0.89	0.842	0.794	0.89	CLONAL	1	TRUE	1	0.615336238507697	2		1289	1251	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351594	89351594	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	444	1408	1	ENST00000301030.4:c.1356T>A	p.Asn452Lys	p.N452K	ENST00000301030	NM_001256183.1	452	aaT/aaA	9/13	1	2	FACETS	0.891	0.849	0.935	0.891	0.849	0.935	CLONAL	1	TRUE	1	0.615336238507697	2		1409	1619	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761012	59761012	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	194	848	2	ENST00000259008.2:c.3395T>C	p.Phe1132Ser	p.F1132S	ENST00000259008	NM_032043.2	1132	tTt/tCt	20/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.615336238507697	2		850	600	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063347	67063347	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	74	394	1	ENST00000412916.2:c.37G>T	p.Glu13Ter	p.E13*	ENST00000412916		13	Gag/Tag	1/6	0.409435898174472	1	FACETS	0.279	0.244	0.315	0.279	0.244	0.315	INDETERMINATE	1	TRUE	0	0.736164979026474	1		395	456	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847167	68847249	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGCTAGCAGTCTTGGTACTTTGTAAATGACACATCTCTTTGCTCTGCAGTACAAGGGTCAGGTGCCTGAGAACGAGGCTAACG	TGCTAGCAGTCTTGGTACTTTGTAAATGACACATCTCTTTGCTCTGCAGTACAAGGGTCAGGTGCCTGAGAACGAGGCTAACG	-	novel	NA	P-0013411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	114	255	0	ENST00000261769.5:c.1138-48_1172del		p.X380_splice	ENST00000261769	NM_004360.3	380		9/16	0.409435898174472	1	FACETS	0.473	0.429	0.518	0.473	0.429	0.518	INDETERMINATE	1	TRUE	0	0.736164979026474	1		255	414	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44935950	44935951	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	126	642	0	ENST00000377967.4:c.2712dup	p.Lys905Ter	p.K905*	ENST00000377967	NM_021140.2	904	ggt/ggTt	18/29	1	2	FACETS	0.344	0.311	0.379	0.344	0.311	0.379	SUBCLONAL	1	TRUE	1	0.736164979026474	2		642	995	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577138	7577138	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587780075	NA	P-0013414-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	899	658	0	ENST00000269305.4:c.800G>C	p.Arg267Pro	p.R267P	ENST00000269305	NM_001126112.2	267	cGg/cCg	8/11	NA	2	FACETS	0.984	0.97	0.998			1	INDETERMINATE	2	TRUE	NA	0.894557603014295	2		658	1021	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653829	89653829	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554893808	NA	P-0013414-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	458	453	1	ENST00000371953.3:c.127G>T	p.Glu43Ter	p.E43*	ENST00000371953	NM_000314.4	43	Gaa/Taa	2/9	0.887124997187281	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.894557603014295	2		454	506	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033823	49033823	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0013414-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	355	524	1	ENST00000267163.4:c.1961-1G>T		p.X654_splice	ENST00000267163	NM_000321.2	654			0.894557603014295	1	FACETS	0.968	0.939	0.996	0.968	0.939	0.996	CLONAL	1	TRUE	0	0.894557603014295	1		525	453	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294058	1294058	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013414-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	274	520	0	ENST00000310581.5:c.943C>G	p.Arg315Gly	p.R315G	ENST00000310581	NM_198253.2	315	Cgt/Ggt	2/16	0.825452309090117	3	FACETS	0.727	0.681	0.773	0.363	0.34	0.387	SUBCLONAL	1	TRUE	1	0.894557603014295	3		520	1220	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250903	10250903	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013414-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	280	387	0	ENST00000340748.4:c.3577A>G	p.Ile1193Val	p.I1193V	ENST00000340748		1193	Atc/Gtc	32/40	0.874049262123089	1	FACETS	0.92	0.886	0.953	0.92	0.886	0.953	CLONAL	1	TRUE	0	0.894557603014295	1		387	376	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855288	76855288	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013414-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	298	606	0	ENST00000373344.5:c.5699G>T	p.Gly1900Val	p.G1900V	ENST00000373344	NM_000489.3	1900	gGt/gTt	24/35	0.271298308656323	1	FACETS	0.498	0.471	0.525	0.498	0.471	0.525	INDETERMINATE	1	TRUE	0	0.894557603014295	1		606	740	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171431	123171431	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013414-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	406	663	0	ENST00000218089.9:c.343C>G	p.Leu115Val	p.L115V	ENST00000218089	NM_001042749.1	115	Ctt/Gtt	6/35	0.271298308656323	1	FACETS	0.536	0.512	0.56	0.536	0.512	0.56	INDETERMINATE	1	TRUE	0	0.894557603014295	1		663	936	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190035	123190035	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0013414-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	544	673	1	ENST00000218089.9:c.1254T>A	p.Tyr418Ter	p.Y418*	ENST00000218089	NM_001042749.1	418	taT/taA	14/35	0.271298308656323	1	FACETS	0.607	0.585	0.63	0.607	0.585	0.63	INDETERMINATE	1	TRUE	0	0.894557603014295	1		674	1107	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807379	3807379	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0013414-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	596	311	0	ENST00000262367.5:c.3610-2A>T		p.X1204_splice	ENST00000262367	NM_004380.2	1204			0.886803937666368	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.894557603014295	2		311	659	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131412	202131412	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013430-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	467	471	0	ENST00000358485.4:c.380G>C	p.Arg127Pro	p.R127P	ENST00000358485	NM_001080125.1	127	cGa/cCa	2/9	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.945303947894741	2		471	915	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251912	153251912	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013430-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	620	731	0	ENST00000281708.4:c.1094G>C	p.Trp365Ser	p.W365S	ENST00000281708	NM_033632.3	365	tGg/tCg	7/12	1	2	FACETS	0.897	0.865	0.93	0.897	0.865	0.93	CLONAL	1	TRUE	1	0.945303947894741	2		731	1462	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494624	2494624	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs376143429	NA	P-0013434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	84	740	0	ENST00000355716.4:c.764T>C	p.Ile255Thr	p.I255T	ENST00000355716	NM_003820.2	255	aTt/aCt	8/8	0.469454157437898	3	FACETS	0.396	0.348	0.447	0.198	0.174	0.224	SUBCLONAL	1	TRUE	1	0.469454157437898	3		740	1117	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941741	48941741	+	splice_donor_variant	Splice_Site	SNP	T	T	A	rs41287453	NA	P-0013434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	134	325	0	ENST00000267163.4:c.1049+2T>A		p.X350_splice	ENST00000267163	NM_000321.2	350			0.45122354518875	2	FACETS	0.823	0.757	0.889	0.823	0.757	0.889	CLONAL	2	TRUE	0	0.469454157437898	2		325	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577530	7577531	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0013434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	259	659	0	ENST00000269305.4:c.750dup	p.Ile251HisfsTer13	p.I251Hfs*13	ENST00000269305	NM_001126112.2	250	-/C	7/11	0.469454157437898	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.469454157437898	1		659	705	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0013437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	188	586	0	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	0.15898799886322	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	FALSE	0	0.200823761797404	2		586	882	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0013437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	398	659	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.200823761797404	6	FACETS	1	0.985	1			1	CLONAL	4	FALSE	NA	0.200823761797404	6		659	1280	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738300	145738300	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	75	457	0	ENST00000428558.2:c.2685G>T	p.Arg895Ser	p.R895S	ENST00000428558	NM_004260.3	895	agG/agT	16/22	0.200823761797404	3	FACETS	1	0.904	1	0.52	0.454	0.59	CLONAL	1	FALSE	1	0.200823761797404	3		457	791	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226596	2226596	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	73	499	0	ENST00000398665.3:c.4076A>T	p.Lys1359Met	p.K1359M	ENST00000398665	NM_032482.2	1359	aAg/aTg	27/28	0.160458363957854	3	FACETS	1	0.931	1	0.549	0.48	0.625	CLONAL	1	FALSE	1	0.200823761797404	3		499	728	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251535	10251535	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	79	699	0	ENST00000340748.4:c.3397G>T	p.Glu1133Ter	p.E1133*	ENST00000340748		1133	Gag/Tag	31/40	0.160458363957854	3	FACETS	0.841	0.737	0.952	0.42	0.368	0.476	CLONAL	1	FALSE	1	0.200823761797404	3		699	1030	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035946	47035946	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	169	502	0	ENST00000377604.3:c.627del	p.Lys210SerfsTer56	p.K210Sfs*56	ENST00000377604	NM_001204468.1	208	gaC/ga	7/24	1	1	FACETS	1	0.967	1	1	0.993	1	CLONAL	2	FALSE	0	0.200823761797404	1		502	695	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916770	48916770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	124	408	0	ENST00000267163.4:c.301del	p.Ile101SerfsTer10	p.I101Sfs*10	ENST00000267163	NM_000321.2	100	ggA/gg	3/27	0.200823761797404	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	2	FALSE	0	0.200823761797404	2		408	616	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0013460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	107	458	1	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	1	2	FACETS	0.799	0.716	0.886	0.799	0.716	0.886	SUBCLONAL	1	TRUE	1	0.33	2		459	812	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220622	1220622	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690923	NA	P-0013460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	130	760	2	ENST00000326873.7:c.640C>T	p.Gln214Ter	p.Q214*	ENST00000326873	NM_000455.4	214	Cag/Tag	5/10	1	2	FACETS	0.948	0.86	1	0.948	0.86	1	CLONAL	1	TRUE	1	0.33	2		762	831	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220400	1220400	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1359582062	NA	P-0013460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	131	863	0	ENST00000326873.7:c.493G>T	p.Glu165Ter	p.E165*	ENST00000326873	NM_000455.4	165	Gag/Tag	4/10	1	2	FACETS	0.945	0.858	1	0.945	0.858	1	CLONAL	1	TRUE	1	0.33	2		863	840	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462324	89462324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	121	560	2	ENST00000336596.2:c.1796C>T	p.Pro599Leu	p.P599L	ENST00000336596	NM_005233.5	599	cCa/cTa	10/17	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.33	2		562	703	SUCCESS
ATR	545	MSKCC	GRCh37	3	142183956	142183956	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	116	663	0	ENST00000350721.4:c.7024A>T	p.Asn2342Tyr	p.N2342Y	ENST00000350721	NM_001184.3	2342	Aat/Tat	41/47	0.295838157926737	1	FACETS	0.815	0.735	0.9	0.815	0.735	0.9	CLONAL	1	TRUE	0	0.33	1		663	720	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180040095	180040095	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	116	850	0	ENST00000261937.6:c.3347C>G	p.Pro1116Arg	p.P1116R	ENST00000261937	NM_182925.4	1116	cCt/cGt	25/30	1	2	FACETS	0.773	0.696	0.855	0.773	0.696	0.855	SUBCLONAL	1	TRUE	1	0.33	2		850	909	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056426	180056426	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	67	394	0	ENST00000261937.6:c.818C>A	p.Ala273Glu	p.A273E	ENST00000261937	NM_182925.4	273	gCa/gAa	7/30	1	2	FACETS	0.971	0.848	1	0.971	0.848	1	CLONAL	1	TRUE	1	0.33	2		394	418	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120863	115120863	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	54	415	0	ENST00000257566.3:c.143C>A	p.Pro48His	p.P48H	ENST00000257566	NM_016569.3	48	cCc/cAc	1/8	1	2	FACETS	0.695	0.594	0.805	0.695	0.594	0.805	SUBCLONAL	1	TRUE	1	0.33	2		415	471	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940083	76940083	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	103	265	0	ENST00000373344.5:c.665G>T	p.Trp222Leu	p.W222L	ENST00000373344	NM_000489.3	222	tGg/tTg	9/35	1	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.33	1		265	403	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615579	100615579	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	181	499	0	ENST00000308731.7:c.753G>A	p.Trp251Ter	p.W251*	ENST00000308731	NM_000061.2	251	tgG/tgA	8/19	1	1	FACETS	0.836	0.776	0.897	1	0.992	1	CLONAL	2	TRUE	0	0.33	1		499	548	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013464-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	52	766	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.966	0.824	1	0.966	0.824	1	CLONAL	1	TRUE	1	0.230939693844083	2		766	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0013464-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	92	646	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.230939693844083	1	FACETS	0.83	0.737	0.93	0.83	0.737	0.93	CLONAL	1	TRUE	0	0.230939693844083	1		646	849	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013464-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	202	575	1	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	0.230939693844083	2	FACETS	0.923	0.856	0.992	0.923	0.856	0.992	CLONAL	2	TRUE	0	0.230939693844083	2		576	948	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396815	396815	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013464-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	118	701	0	ENST00000262320.3:c.211G>T	p.Glu71Ter	p.E71*	ENST00000262320	NM_003502.3	71	Gag/Tag	2/11	0.230939693844083	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.230939693844083	1		701	860	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779453	3779453	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013464-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	83	729	0	ENST00000262367.5:c.5595G>T	p.Met1865Ile	p.M1865I	ENST00000262367	NM_004380.2	1865	atG/atT	31/31	0.230939693844083	1	FACETS	0.863	0.761	0.972	0.863	0.761	0.972	CLONAL	1	TRUE	0	0.230939693844083	1		729	737	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652042	36652042	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013464-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	129	729	0	ENST00000244741.5:c.165del	p.Glu56ArgfsTer92	p.E56Rfs*92	ENST00000244741	NM_000389.4	55	aCc/ac	2/3	0.230939693844083	3	FACETS	1	0.96	1	0.557	0.504	0.614	CLONAL	1	TRUE	1	0.230939693844083	3		729	1118	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110709	2110719	+	frameshift_variant	Frame_Shift_Del	DEL	CGTCCTGTCCA	CGTCCTGTCCA	T	novel	NA	P-0013464-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	131	779	0	ENST00000219476.3:c.1014_1024delinsT	p.Val339SerfsTer21	p.V339Sfs*21	ENST00000219476	NM_000548.3	338	atCGTCCTGTCCAtc/atTtc	11/42	0.230939693844083	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.230939693844083	1		779	972	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0013484-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	380	799	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.835010098716944	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.835010098716944	2		800	432	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0013484-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	702	730	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.835010098716944	6	FACETS	1	0.972	1	0.8	0.778	0.822	CLONAL	4	TRUE	1	0.835010098716944	6		730	1122	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037877	49037877	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013484-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	264	588	1	ENST00000267163.4:c.2117G>A	p.Cys706Tyr	p.C706Y	ENST00000267163	NM_000321.2	706	tGt/tAt	21/27	0.835010098716944	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.835010098716944	2		589	302	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849822	156849822	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013484-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	365	699	0	ENST00000524377.1:c.2078G>A	p.Trp693Ter	p.W693*	ENST00000524377	NM_002529.3	693	tGg/tAg	16/17	0.835010098716944	7	FACETS	0.87	0.823	0.918	0.348	0.329	0.368	CLONAL	2	TRUE	2	0.835010098716944	7		699	1551	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519538	137519538	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs148158267	NA	P-0013484-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	116	526	0	ENST00000367739.4:c.1100C>G	p.Pro367Arg	p.P367R	ENST00000367739	NM_000416.2	367	cCg/cGg	7/7	0.828834957774621	5	FACETS	0.861	0.776	0.95	0.215	0.194	0.238	CLONAL	1	TRUE	1	0.835010098716944	5		526	727	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644916	67644916	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013484-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	311	593	0	ENST00000264010.4:c.181G>T	p.Val61Leu	p.V61L	ENST00000264010	NM_006565.3	61	Gtg/Ttg	3/12	0.816869774477958	4	FACETS	0.895	0.848	0.941	0.895	0.848	0.941	CLONAL	2	TRUE	2	0.835010098716944	4		593	764	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755745	39755745	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013484-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	329	622	0	ENST00000288319.7:c.1020G>T	p.Lys340Asn	p.K340N	ENST00000288319	NM_182918.3	340	aaG/aaT	10/10	0.835010098716944	3	FACETS	0.997	0.955	1	0.997	0.955	1	CLONAL	2	TRUE	1	0.835010098716944	3		622	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577560	7577565	+	inframe_deletion	In_Frame_Del	DEL	AACTGT	AACTGT	-	novel	NA	P-0013484-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	486	1038	0	ENST00000269305.4:c.716_721del	p.Asn239_Ser241delinsThr	p.N239_S241delinsT	ENST00000269305	NM_001126112.2	239	aACAGTTcc/acc	7/11	0.835010098716944	2	FACETS	0.978	0.955	1	0.978	0.955	1	CLONAL	2	TRUE	0	0.835010098716944	2		1038	595	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519999	NA	P-0013484-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	14	1029	0	ENST00000269305.4:c.716A>C	p.Asn239Thr	p.N239T	ENST00000269305	NM_001126112.2	239	aAc/aCc	7/11	0.835010098716944	2	FACETS	0.057	0.04	0.076	0.028	0.02	0.038	SUBCLONAL	1	TRUE	0	0.835010098716944	2		1029	593	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509434	46509434	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013484-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	194	724	1	ENST00000262741.5:c.1297C>T	p.Gln433Ter	p.Q433*	ENST00000262741	NM_003629.3	433	Cag/Tag	10/10	0.828834957774621	5	FACETS	0.962	0.889	1	0.241	0.222	0.26	CLONAL	1	TRUE	1	0.835010098716944	5		725	1088	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0013487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1210	222	458	1	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	0.170750561426717	4	FACETS	0.893	0.829	0.96	0.893	0.829	0.96	CLONAL	2	TRUE	2	0.21	4		459	1432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0013487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	250	808	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.200230629946502	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.21	2		808	1120	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593517	48593517	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	178	505	0	ENST00000342988.3:c.1268G>T	p.Gly423Val	p.G423V	ENST00000342988	NM_005359.5	423	gGa/gTa	10/12	0.199232952928983	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.21	2		505	751	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727941	41727941	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	174	719	0	ENST00000301178.4:c.566A>T	p.Gln189Leu	p.Q189L	ENST00000301178	NM_021913.4	189	cAg/cTg	4/20	0.119674402459572	4	FACETS	0.999	0.919	1	0.999	0.919	1	INDETERMINATE	2	TRUE	2	0.21	4		719	1004	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84390255	84390287	+	inframe_deletion	In_Frame_Del	DEL	GTTCAGACATGCCCAGATTGGCAACCACTAAAG	GTTCAGACATGCCCAGATTGGCAACCACTAAAG	-	novel	NA	P-0013487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	76	598	0	ENST00000321945.7:c.494_526del	p.Pro165_Glu175del	p.P165_E175del	ENST00000321945	NM_139076.2	165	cCTTTAGTGGTTGCCAATCTGGGCATGTCTGAACaa/caa	6/9	0.170750561426717	4	FACETS	0.833	0.729	0.947	0.417	0.364	0.474	CLONAL	1	TRUE	2	0.21	4		598	1051	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098807	178098807	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	178	799	0	ENST00000397062.3:c.238A>G	p.Thr80Ala	p.T80A	ENST00000397062	NM_006164.4	80	Aca/Gca	2/5	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.225121451569858	2		799	1113	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589623	67589634	+	inframe_deletion	In_Frame_Del	DEL	ATATGATAGATT	ATATGATAGATT	-	novel	NA	P-0013497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	84	353	0	ENST00000274335.5:c.1392_1403del	p.Asp464_Tyr467del	p.D464_Y467del	ENST00000274335		462	gaATATGATAGATTa/gaa	10/15	0.156575485857704	2	FACETS	1	0.971	1	0.66	0.584	0.742	CLONAL	1	TRUE	0	0.225121451569858	2		353	565	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67462907	67462907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	62	627	2	ENST00000327367.4:c.623C>T	p.Ser208Phe	p.S208F	ENST00000327367	NM_005902.3	208	tCc/tTc	5/9	1	2	FACETS	0.565	0.486	0.651	0.565	0.486	0.651	SUBCLONAL	1	TRUE	1	0.225121451569858	2		629	975	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974833	15974833	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	101	664	1	ENST00000268712.3:c.4042G>A	p.Gly1348Arg	p.G1348R	ENST00000268712	NM_006311.3	1348	Ggg/Agg	30/46	0.180769743134887	1	FACETS	0.871	0.778	0.971	0.871	0.778	0.971	CLONAL	1	TRUE	0	0.225121451569858	1		665	914	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795734	42795734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	114	695	1	ENST00000575354.2:c.2723C>T	p.Ala908Val	p.A908V	ENST00000575354	NM_015125.3	908	gCc/gTc	11/20	0.213747468279901	2	FACETS	1	0.946	1	0.54	0.485	0.598	CLONAL	1	TRUE	0	0.225121451569858	2		696	938	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650506	48650506	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	66	835	0	ENST00000376670.3:c.476C>G	p.Pro159Arg	p.P159R	ENST00000376670	NM_002049.3	159	cCc/cGc	3/6	1	2	FACETS	0.494	0.427	0.568	0.494	0.427	0.568	SUBCLONAL	1	TRUE	1	0.225121451569858	2		835	1186	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589623	67589634	+	inframe_deletion	In_Frame_Del	DEL	ATATGATAGATT	ATATGATAGATT	-	novel	NA	P-0013505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	114	353	0	ENST00000274335.5:c.1392_1403del	p.Asp464_Tyr467del	p.D464_Y467del	ENST00000274335		462	gaATATGATAGATTa/gaa	10/15	1	2	FACETS	0.753	0.679	0.832	0.753	0.679	0.832	SUBCLONAL	1	TRUE	1	0.417389491640403	2		353	725	SUCCESS
APC	324	MSKCC	GRCh37	5	112175939	112175939	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	157	447	1	ENST00000257430.4:c.4648G>T	p.Glu1550Ter	p.E1550*	ENST00000257430	NM_000038.5	1550	Gag/Tag	16/16	0.417389491640403	1	FACETS	0.91	0.837	0.987	0.91	0.837	0.987	CLONAL	1	TRUE	0	0.417389491640403	1		448	654	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325803	65325803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	169	490	1	ENST00000342505.4:c.1319G>A	p.Cys440Tyr	p.C440Y	ENST00000342505	NM_002227.2	440	tGt/tAt	9/25	0.417389491640403	1	FACETS	0.866	0.798	0.937	0.866	0.798	0.937	CLONAL	1	TRUE	0	0.417389491640403	1		491	740	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267422	198267422	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	239	589	0	ENST00000335508.6:c.1935G>T	p.Leu645Phe	p.L645F	ENST00000335508	NM_012433.2	645	ttG/ttT	14/25	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.417389491640403	2		589	1087	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74003488	74003488	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	339	824	1	ENST00000318443.5:c.1559T>C	p.Leu520Pro	p.L520P	ENST00000318443	NM_001024736.1	520	cTg/cCg	9/10	0.417389491640403	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.417389491640403	1		825	1203	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271893	18271893	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	177	448	4	ENST00000222254.8:c.496G>T	p.Asp166Tyr	p.D166Y	ENST00000222254	NM_005027.3	166	Gac/Tac	5/16	1	2	FACETS	0.877	0.808	0.949	0.877	0.808	0.949	CLONAL	1	TRUE	1	0.417389491640403	2		452	967	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923064	44923064	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0013505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	156	236	1	ENST00000377967.4:c.1923+2T>A		p.X641_splice	ENST00000377967	NM_021140.2	641			1	1	FACETS	0.754	0.699	0.811	1	0.99	1	SUBCLONAL	2	TRUE	0	0.417389491640403	1		237	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578249	7578444	+	splice_donor_variant,splice_acceptor_variant,frameshift_variant,stop_lost,intron_variant	Splice_Site	DEL	ATTTCCTTCCACTCGGATAAGATGCTGAGGAGGGGCCAGACCTAAGAGCAATCAGTGAGGAATCAGAGGCCTGGGGACCCTGGGCAACCAGCCCTGTCGTCTCTCCAGCCCCAGCTGCTCACCATCGCTATCTGAGCAGCGCTCATGGTGGGGGCAGCGCCTCACAACCTCCGTCATGTGCTGTGACTGCTTGTAG	ATTTCCTTCCACTCGGATAAGATGCTGAGGAGGGGCCAGACCTAAGAGCAATCAGTGAGGAATCAGAGGCCTGGGGACCCTGGGCAACCAGCCCTGTCGTCTCTCCAGCCCCAGCTGCTCACCATCGCTATCTGAGCAGCGCTCATGGTGGGGGCAGCGCCTCACAACCTCCGTCATGTGCTGTGACTGCTTGTAG	-	novel	NA	P-0013505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	273	701	0	ENST00000269305.4:c.486_600del		p.X162_splice	ENST00000269305	NM_001126112.2	162	atCTACAAGCAGTCACAGCACATGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCGATGGTGAGCAGCTGGGGCTGGAGAGACGACAGGGCTGGTTGCCCAGGGTCCCCAGGCCTCTGATTCCTCACTGATTGCTCTTAGGTCTGGCCCCTCCTCAGCATCTTATCCGAGTGGAAGGAAAT/at	5-6/11	0.288293993811639	1	FACETS	0.991	0.93	1	0.991	0.93	1	CLONAL	1	TRUE	0	0.417389491640403	1		701	1045	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0013511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	89	757	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.230577929105215	2		758	754	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916947	178916947	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	89	807	0	ENST00000263967.3:c.334A>T	p.Ile112Phe	p.I112F	ENST00000263967	NM_006218.2	112	Atc/Ttc	2/21	1	2	FACETS	0.717	0.634	0.806	0.717	0.634	0.806	SUBCLONAL	1	TRUE	1	0.230577929105215	2		807	1077	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857895	9857895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761399460	NA	P-0013511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	128	635	0	ENST00000330684.3:c.3506G>A	p.Arg1169Gln	p.R1169Q	ENST00000330684	NM_001134407.1	1169	cGg/cAg	13/13	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.230577929105215	2		635	900	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520017	NA	P-0013511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	147	584	0	ENST00000326873.7:c.647C>T	p.Ser216Phe	p.S216F	ENST00000326873	NM_000455.4	216	tCc/tTc	5/10	0.230577929105215	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.230577929105215	1		584	859	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519676	176519676	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	81	453	2	ENST00000292408.4:c.948G>T	p.Glu316Asp	p.E316D	ENST00000292408	NM_213647.1	316	gaG/gaT	8/18	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.230577929105215	2		455	648	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381533	81381533	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	116	718	0	ENST00000222390.5:c.528C>A	p.Tyr176Ter	p.Y176*	ENST00000222390	NM_000601.4	176	taC/taA	5/18	1	2	FACETS	0.956	0.86	1	0.956	0.86	1	CLONAL	1	TRUE	1	0.230577929105215	2		718	1052	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202233	108202233	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	73	462	0	ENST00000278616.4:c.7578A>C	p.Arg2526Ser	p.R2526S	ENST00000278616	NM_000051.3	2526	agA/agC	51/63	0.230577929105215	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.230577929105215	1		462	532	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69203005	69203005	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1442	134	553	0	ENST00000462284.1:c.32A>G	p.Asn11Ser	p.N11S	ENST00000462284	NM_002392.5	11	aAc/aGc	2/11	0.230577929105215	7	FACETS	1	0.969	1			1	CLONAL	1	TRUE	NA	0.230577929105215	7		553	1576	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828827	26828827	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	87	557	0	ENST00000381527.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000381527	NM_001260.1	17	Gag/Aag	1/13	0.230577929105215	1	FACETS	0.915	0.809	1	0.915	0.809	1	CLONAL	1	TRUE	0	0.230577929105215	1		557	730	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17941380	17941380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1443520204	NA	P-0013511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	134	519	0	ENST00000458235.1:c.3028G>A	p.Val1010Ile	p.V1010I	ENST00000458235	NM_000215.3	1010	Gtc/Atc	22/24	0.230577929105215	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.230577929105215	1		519	813	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98011546	98011546	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	74	549	0	ENST00000289081.3:c.28del	p.Cys10ValfsTer36	p.C10Vfs*36	ENST00000289081	NM_000136.2	10	Tgt/gt	2/15	1	2	FACETS	0.856	0.748	0.972	0.856	0.748	0.972	CLONAL	1	TRUE	1	0.230577929105215	2		549	750	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	461404	461405	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0013511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	118	578	0	ENST00000399788.2:c.1114_1115dup	p.Asn372LysfsTer19	p.N372Kfs*19	ENST00000399788	NM_001042603.1	372	aat/aaAAt	9/28	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.230577929105215	2		578	960	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	49	766	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.859	0.726	1	0.859	0.726	1	CLONAL	1	TRUE	1	0.16	2		766	713	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0013525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	102	621	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.814	0.728	0.906	1	0.984	1	CLONAL	2	TRUE	1	0.16	2		621	783	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781201	161781201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55830907	NA	P-0013525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	75	680	3	ENST00000366898.1:c.1204C>T	p.Arg402Cys	p.R402C	ENST00000366898	NM_004562.2	402	Cgt/Tgt	11/12	0.154885333656754	1	FACETS	0.743	0.649	0.845	0.743	0.649	0.845	SUBCLONAL	1	TRUE	0	0.16	1		683	1161	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587118	189587118	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761885185	NA	P-0013525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	51	493	1	ENST00000264731.3:c.1135C>T	p.Arg379Cys	p.R379C	ENST00000264731	NM_003722.4	379	Cgt/Tgt	9/14	1	2	FACETS	0.782	0.663	0.914	0.782	0.663	0.914	CLONAL	1	TRUE	1	0.16	2		494	815	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258815	16258815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	66	534	0	ENST00000375759.3:c.6080C>T	p.Ser2027Phe	p.S2027F	ENST00000375759	NM_015001.2	2027	tCc/tTc	11/15	1	2	FACETS	0.733	0.634	0.841	0.733	0.634	0.841	SUBCLONAL	1	TRUE	1	0.16	2		534	1126	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597835	43597835	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1362	94	915	0	ENST00000355710.3:c.383C>T	p.Ser128Leu	p.S128L	ENST00000355710	NM_020975.4	128	tCa/tTa	3/20	1	2	FACETS	0.807	0.715	0.906	0.807	0.715	0.906	CLONAL	1	TRUE	1	0.16	2		915	1456	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419070	419071	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	85	637	0	ENST00000399788.2:c.3276dup	p.Val1093SerfsTer20	p.V1093Sfs*20	ENST00000399788	NM_001042603.1	1092	-/A	22/28	1	2	FACETS	0.943	0.831	1	0.943	0.831	1	CLONAL	1	TRUE	1	0.16	2		637	1127	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804343	46804343	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1399	119	729	0	ENST00000290295.7:c.664C>T	p.Pro222Ser	p.P222S	ENST00000290295	NM_006361.5	222	Ccg/Tcg	2/2	1	2	FACETS	0.98	0.881	1	0.98	0.881	1	CLONAL	1	TRUE	1	0.16	2		729	1518	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416199	29416199	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	86	629	0	ENST00000389048.3:c.4754G>A	p.Gly1585Asp	p.G1585D	ENST00000389048	NM_004304.4	1585	gGc/gAc	29/29	1	2	FACETS	0.866	0.764	0.977	0.866	0.764	0.977	CLONAL	1	TRUE	1	0.16	2		629	1241	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248538	212248538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1275	120	811	1	ENST00000342788.4:c.3729G>A	p.Trp1243Ter	p.W1243*	ENST00000342788	NM_005235.2	1243	tgG/tgA	28/28	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.16	2		812	1395	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928736	49928736	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1226	112	774	0	ENST00000296474.3:c.3538C>T	p.Pro1180Ser	p.P1180S	ENST00000296474	NM_002447.2	1180	Ccc/Tcc	17/20	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.16	2		774	1338	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	137	840	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.783	0.713	0.856	1	0.987	1	SUBCLONAL	2	TRUE	1	0.244425907161299	2		840	716	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	84	677	1	ENST00000304494.5:c.143C>T	p.Pro48Leu	p.P48L	ENST00000304494	NM_000077.4	48	cCg/cTg	1/3	0.22873768002813	1	FACETS	0.789	0.696	0.888	0.789	0.696	0.888	SUBCLONAL	1	TRUE	0	0.244425907161299	1		678	765	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579408	7579430	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGGGCCAGGAGGGGGCTGGTG	CAGGGGCCAGGAGGGGGCTGGTG	-	rs886041861	NA	P-0013528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	47	533	0	ENST00000269305.4:c.257_279del	p.Ala86ValfsTer55	p.A86Vfs*55	ENST00000269305	NM_001126112.2	86	gCACCAGCCCCCTCCTGGCCCCTG/g	4/11	1	2	FACETS	0.703	0.593	0.825	0.703	0.593	0.825	SUBCLONAL	1	TRUE	1	0.244425907161299	2		533	547	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089710	27089711	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0013528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	49	438	0	ENST00000324856.7:c.2667dup	p.Met890HisfsTer46	p.M890Hfs*46	ENST00000324856	NM_006015.4	889	ggc/ggCc	8/20	1	2	FACETS	0.834	0.706	0.973	0.834	0.706	0.973	CLONAL	1	TRUE	1	0.244425907161299	2		438	481	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966658	44966658	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0013528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	81	361	0	ENST00000377967.4:c.3882T>G	p.Tyr1294Ter	p.Y1294*	ENST00000377967	NM_021140.2	1294	taT/taG	27/29	1	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.244425907161299	1		361	388	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0013551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	162	621	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	0.558975454648111	2		621	489	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0013551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	138	592	1	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	0.558975454648111	1	FACETS	0.903	0.83	0.977	0.903	0.83	0.977	CLONAL	1	TRUE	0	0.558975454648111	1		593	394	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213873	66213873	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1383933498	NA	P-0013551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	184	884	2	ENST00000273854.3:c.2557C>T	p.Arg853Ter	p.R853*	ENST00000273854	NM_004439.5	853	Cga/Tga	15/18	0.558975454648111	1	FACETS	0.968	0.902	1	0.968	0.902	1	CLONAL	1	TRUE	0	0.558975454648111	1		886	490	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961418	41961418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	179	1314	5	ENST00000219905.7:c.326G>A	p.Arg109His	p.R109H	ENST00000219905	NM_001164273.1	109	cGt/cAt	2/24	0.52491614420046	1	FACETS	0.731	0.677	0.787	0.731	0.677	0.787	SUBCLONAL	1	TRUE	0	0.558975454648111	1		1319	631	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947603	48947603	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0013558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	113	415	0	ENST00000267163.4:c.1190C>G	p.Ser397Ter	p.S397*	ENST00000267163	NM_000321.2	397	tCa/tGa	12/27	0.599570649594701	3	FACETS	0.907	0.85	0.962	0.907	0.85	0.962	CLONAL	3	FALSE	0	0.683601956330424	3		415	163	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252084	133252084	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	39	664	1	ENST00000320574.5:c.1126G>T	p.Ala376Ser	p.A376S	ENST00000320574	NM_006231.2	376	Gca/Tca	12/49	0.101457237980287	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.683601956330424	0		665	133	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579317	7579317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	98	448	1	ENST00000269305.4:c.370del	p.Cys124AlafsTer46	p.C124Afs*46	ENST00000269305	NM_001126112.2	124	Tgc/gc	4/11	0.626205901008798	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	FALSE	0	0.683601956330424	2		449	141	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342675	87342675	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	32	617	0	ENST00000277120.3:c.960C>A	p.Asn320Lys	p.N320K	ENST00000277120		320	aaC/aaA	9/19	NA	2	FACETS	0.8	0.663	0.947			1	INDETERMINATE	1	FALSE	NA	0.683601956330424	2		617	117	SUCCESS
AR	367	MSKCC	GRCh37	X	66931313	66931313	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	29	483	0	ENST00000374690.3:c.1955C>T	p.Pro652Leu	p.P652L	ENST00000374690	NM_000044.3	652	cCc/cTc	4/8	0.683601956330424	0	FACETS		NA	1			1	NA	1	FALSE	NA	0.683601956330424	0		483	63	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	52	720	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.206698305800553	2		721	479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0013564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	63	1096	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.206698305800553	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.206698305800553	1		1097	439	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0013564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	44	747	1	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	0.841	0.711	0.983	1	0.966	1	CLONAL	2	TRUE	1	0.206698305800553	2		748	253	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591933	48591933	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060500733	NA	P-0013564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	60	778	0	ENST00000342988.3:c.1096C>T	p.Gln366Ter	p.Q366*	ENST00000342988	NM_005359.5	366	Caa/Taa	9/12	0.206698305800553	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.206698305800553	1		778	456	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967847	93967847	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs569112388	NA	P-0013564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	68	1565	0	ENST00000369303.4:c.2080G>A	p.Val694Ile	p.V694I	ENST00000369303	NM_004440.3	694	Gtt/Att	11/17	0.206698305800553	1	FACETS	0.72	0.625	0.823	0.72	0.625	0.823	SUBCLONAL	1	TRUE	0	0.206698305800553	1		1565	819	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0013568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	189	763	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.785917971809483	4	FACETS	0.927	0.876	0.976	0.927	0.876	0.976	CLONAL	3	TRUE	1	0.785917971809483	4		764	309	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522416	176522416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519792	NA	P-0013568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	169	624	0	ENST00000292408.4:c.1605C>A	p.Asn535Lys	p.N535K	ENST00000292408	NM_213647.1	535	aaC/aaA	12/18	0.724940036085052	3	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	1	0.785917971809483	3		624	296	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729159	66729159	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	170	694	0	ENST00000307102.5:c.367T>C	p.Ser123Pro	p.S123P	ENST00000307102	NM_002755.3	123	Tct/Cct	3/11	0.785917971809483	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.785917971809483	3		694	293	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3794958	3794958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751602717	NA	P-0013568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	61	558	1	ENST00000262367.5:c.3919G>A	p.Val1307Met	p.V1307M	ENST00000262367	NM_004380.2	1307	Gtg/Atg	23/31	0.651342443312894	4	FACETS	0.966	0.841	1	0.483	0.42	0.55	CLONAL	1	TRUE	2	0.785917971809483	4		559	287	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772261	68772261	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	84	775	0	ENST00000261769.5:c.110A>G	p.Tyr37Cys	p.Y37C	ENST00000261769	NM_004360.3	37	tAc/tGc	2/16	NA	2	FACETS	0.925	0.832	1			1	INDETERMINATE	1	TRUE	NA	0.785917971809483	2		775	231	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857487	68857487	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	131	471	0	ENST00000261769.5:c.2123del	p.Pro708LeufsTer14	p.P708Lfs*14	ENST00000261769	NM_004360.3	708	Cct/ct	13/16	NA	2	FACETS	0.896	0.844	0.945			1	INDETERMINATE	2	TRUE	NA	0.785917971809483	2		471	186	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715319	61715319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	96	769	1	ENST00000401558.2:c.2294G>A	p.Arg765Gln	p.R765Q	ENST00000401558	NM_003400.3	765	cGa/cAa	19/25	0.750333496012735	3	FACETS	1	0.949	1	0.542	0.488	0.598	CLONAL	1	TRUE	1	0.785917971809483	3		770	314	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869710	117869710	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	45	861	0	ENST00000297338.2:c.484G>A	p.Asp162Asn	p.D162N	ENST00000297338	NM_006265.2	162	Gat/Aat	6/14	0.582135095796101	3	FACETS	0.848	0.723	0.983	0.283	0.241	0.328	CLONAL	1	TRUE	0	0.785917971809483	3		861	188	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611858	100611858	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	93	1143	0	ENST00000308731.7:c.1263del	p.Trp421Ter	p.W421*	ENST00000308731	NM_000061.2	421	tgG/tg	14/19	0.336693555604056	4	FACETS	1	0.945	1	0.362	0.324	0.402	INDETERMINATE	1	TRUE	1	0.785917971809483	4		1143	389	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0013584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	30	460	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.819	0.661	0.998	0.819	0.661	0.998	CLONAL	1	TRUE	1	0.22	2		460	333	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	35	1245	2	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	1	2	FACETS	0.979	0.805	1	0.979	0.805	1	CLONAL	1	TRUE	1	0.22	2		1247	325	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100640	67100640	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	57	872	0	ENST00000412916.2:c.338G>A	p.Trp113Ter	p.W113*	ENST00000412916		113	tGg/tAg	4/6	1	2	FACETS	0.983	0.844	1	0.983	0.844	1	CLONAL	1	TRUE	1	0.22	2		872	527	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850332	128850332	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	27	663	0	ENST00000249373.3:c.1595T>C	p.Met532Thr	p.M532T	ENST00000249373	NM_005631.4	532	aTg/aCg	9/12	1	2	FACETS	0.852	0.68	1	0.852	0.68	1	CLONAL	1	TRUE	1	0.22	2		663	288	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0013594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	65	676	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.723	0.63	0.821	0.723	0.63	0.821	SUBCLONAL	1	TRUE	1	0.521500796153044	2		676	345	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0013594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	180	655	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.521500796153044	1	FACETS	0.878	0.815	0.944	0.878	0.815	0.944	CLONAL	1	TRUE	0	0.521500796153044	1		655	581	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0013594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	51	534	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.521500796153044	1	FACETS	0.165	0.139	0.193	0.165	0.139	0.193	SUBCLONAL	1	TRUE	0	0.521500796153044	1		534	878	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428511	78428511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408536007	NA	P-0013594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	115	678	0	ENST00000370768.2:c.1288C>T	p.Arg430Cys	p.R430C	ENST00000370768	NM_003902.3	430	Cgt/Tgt	14/20	1	2	FACETS	0.476	0.428	0.527	0.476	0.428	0.527	SUBCLONAL	1	TRUE	1	0.521500796153044	2		678	926	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346688	89346688	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753691962	NA	P-0013594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	106	664	2	ENST00000301030.4:c.6262G>A	p.Ala2088Thr	p.A2088T	ENST00000301030	NM_001256183.1	2088	Gct/Act	9/13	0.510955261386362	1	FACETS	0.453	0.407	0.503	0.453	0.407	0.503	SUBCLONAL	1	TRUE	0	0.521500796153044	1		666	663	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662938	227662938	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	84	723	0	ENST00000305123.5:c.517C>G	p.Leu173Val	p.L173V	ENST00000305123	NM_005544.2	173	Ctg/Gtg	1/2	1	2	FACETS	0.313	0.275	0.353	0.313	0.275	0.353	SUBCLONAL	1	TRUE	1	0.521500796153044	2		723	1030	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420092	41420092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	121	370	0	ENST00000373198.4:c.229G>A	p.Val77Met	p.V77M	ENST00000373198	NM_133170.3	77	Gtg/Atg	3/32	0.481698181860471	3	FACETS	1	0.95	1	0.536	0.486	0.588	CLONAL	1	TRUE	1	0.521500796153044	3		370	546	SUCCESS
APC	324	MSKCC	GRCh37	5	112175511	112176209	+	inframe_deletion	In_Frame_Del	DEL	GTGAACCATGCAGTGGAATGGTAAGTGGCATTATAAGCCCCAGTGATCTTCCAGATAGCCCTGGACAAACCATGCCACCAAGCAGAAGTAAAACACCTCCACCACCTCCTCAAACAGCTCAAACCAAGCGAGAAGTACCTAAAAATAAAGCACCTACTGCTGAAAAGAGAGAGAGTGGACCTAAGCAAGCTGCAGTAAATGCTGCAGTTCAGAGGGTCCAGGTTCTTCCAGATGCTGATACTTTATTACATTTTGCCACGGAAAGTACTCCAGATGGATTTTCTTGTTCATCCAGCCTGAGTGCTCTGAGCCTCGATGAGCCATTTATACAGAAAGATGTGGAATTAAGAATAATGCCTCCAGTTCAGGAAAATGACAATGGGAATGAAACAGAATCAGAGCAGCCTAAAGAATCAAATGAAAACCAAGAGAAAGAGGCAGAAAAAACTATTGATTCTGAAAAGGACCTATTAGATGATTCAGATGATGATGATATTGAAATACTAGAAGAATGTATTATTTCTGCCATGCCAACAAAGTCATCACGTAAAGCAAAAAAGCCAGCCCAGACTGCTTCAAAATTACCTCCACCTGTGGCAAGGAAACCAAGTCAGCTGCCTGTGTACAAACTTCTACCATCACAAAACAGGTTGCAACCCCAAAAGCATGTTAGTTTTACACCGGGGGATGATATGCCAC	GTGAACCATGCAGTGGAATGGTAAGTGGCATTATAAGCCCCAGTGATCTTCCAGATAGCCCTGGACAAACCATGCCACCAAGCAGAAGTAAAACACCTCCACCACCTCCTCAAACAGCTCAAACCAAGCGAGAAGTACCTAAAAATAAAGCACCTACTGCTGAAAAGAGAGAGAGTGGACCTAAGCAAGCTGCAGTAAATGCTGCAGTTCAGAGGGTCCAGGTTCTTCCAGATGCTGATACTTTATTACATTTTGCCACGGAAAGTACTCCAGATGGATTTTCTTGTTCATCCAGCCTGAGTGCTCTGAGCCTCGATGAGCCATTTATACAGAAAGATGTGGAATTAAGAATAATGCCTCCAGTTCAGGAAAATGACAATGGGAATGAAACAGAATCAGAGCAGCCTAAAGAATCAAATGAAAACCAAGAGAAAGAGGCAGAAAAAACTATTGATTCTGAAAAGGACCTATTAGATGATTCAGATGATGATGATATTGAAATACTAGAAGAATGTATTATTTCTGCCATGCCAACAAAGTCATCACGTAAAGCAAAAAAGCCAGCCCAGACTGCTTCAAAATTACCTCCACCTGTGGCAAGGAAACCAAGTCAGCTGCCTGTGTACAAACTTCTACCATCACAAAACAGGTTGCAACCCCAAAAGCATGTTAGTTTTACACCGGGGGATGATATGCCAC	-	novel	NA	P-0013594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	248	503	0	ENST00000257430.4:c.4221_4919del	p.Ser1407_Pro1639del	p.S1407_P1639del	ENST00000257430	NM_000038.5	1407	aGTGAACCATGCAGTGGAATGGTAAGTGGCATTATAAGCCCCAGTGATCTTCCAGATAGCCCTGGACAAACCATGCCACCAAGCAGAAGTAAAACACCTCCACCACCTCCTCAAACAGCTCAAACCAAGCGAGAAGTACCTAAAAATAAAGCACCTACTGCTGAAAAGAGAGAGAGTGGACCTAAGCAAGCTGCAGTAAATGCTGCAGTTCAGAGGGTCCAGGTTCTTCCAGATGCTGATACTTTATTACATTTTGCCACGGAAAGTACTCCAGATGGATTTTCTTGTTCATCCAGCCTGAGTGCTCTGAGCCTCGATGAGCCATTTATACAGAAAGATGTGGAATTAAGAATAATGCCTCCAGTTCAGGAAAATGACAATGGGAATGAAACAGAATCAGAGCAGCCTAAAGAATCAAATGAAAACCAAGAGAAAGAGGCAGAAAAAACTATTGATTCTGAAAAGGACCTATTAGATGATTCAGATGATGATGATATTGAAATACTAGAAGAATGTATTATTTCTGCCATGCCAACAAAGTCATCACGTAAAGCAAAAAAGCCAGCCCAGACTGCTTCAAAATTACCTCCACCTGTGGCAAGGAAACCAAGTCAGCTGCCTGTGTACAAACTTCTACCATCACAAAACAGGTTGCAACCCCAAAAGCATGTTAGTTTTACACCGGGGGATGATATGCCACgg/agg	16/16	0.521500796153044	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.521500796153044	1		503	598	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	28	766	0				ENST00000310581	NM_198253.2	-/1132			0.234029994002042	1	FACETS	0.892	0.716	1	0.892	0.716	1	CLONAL	1	FALSE	0	0.234029994002042	1		766	237	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0013598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	380	674	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.234029994002042	6	FACETS	1	0.987	1	0.88	0.837	0.924	CLONAL	4	FALSE	1	0.234029994002042	6		674	1083	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658469	117658469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	40	378	0	ENST00000368508.3:c.5114C>T	p.Ser1705Leu	p.S1705L	ENST00000368508	NM_002944.2	1705	tCa/tTa	31/43	1	2	FACETS	0.799	0.664	0.948	0.799	0.664	0.948	CLONAL	1	FALSE	1	0.234029994002042	2		378	428	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397780	116397780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	531	868	1	ENST00000397752.3:c.2054G>A	p.Gly685Glu	p.G685E	ENST00000397752	NM_000245.2	685	gGg/gAg	8/21	0.234029994002042	6	FACETS	0.99	0.95	1	0.99	0.95	1	CLONAL	5	FALSE	1	0.234029994002042	6		869	1346	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526226	189526226	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765564666	NA	P-0013598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	139	854	2	ENST00000264731.3:c.490G>A	p.Ala164Thr	p.A164T	ENST00000264731	NM_003722.4	164	Gcc/Acc	4/14	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	FALSE	1	0.234029994002042	2		856	1188	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793456	18793456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1357943621	NA	P-0013598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	70	738	0	ENST00000266497.5:c.4153C>T	p.Pro1385Ser	p.P1385S	ENST00000266497		1385	Cca/Tca	30/31	1	2	FACETS	0.678	0.59	0.774	0.678	0.59	0.774	SUBCLONAL	1	FALSE	1	0.234029994002042	2		738	882	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393422	139393422	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1060502237	NA	P-0013598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	105	606	1	ENST00000277541.6:c.6109G>T	p.Ala2037Ser	p.A2037S	ENST00000277541	NM_017617.3	2037	Gcc/Tcc	33/34	1	2	FACETS	0.952	0.851	1	0.952	0.851	1	CLONAL	1	FALSE	1	0.234029994002042	2		607	943	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733446	85733446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1285	125	1192	3	ENST00000370580.1:c.566C>T	p.Ser189Leu	p.S189L	ENST00000370580	NM_003921.4	189	tCa/tTa	3/3	1	2	FACETS	0.758	0.683	0.837	0.758	0.683	0.837	SUBCLONAL	1	FALSE	1	0.234029994002042	2		1195	1410	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138856	64138857	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0013598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	60	443	1	ENST00000334205.4:c.2223_2224delinsTT	p.Arg742Cys	p.R742C	ENST00000334205	NM_003942.2	741	tcCCgc/tcTTgc	17/17	1	2	FACETS	0.89	0.767	1	0.89	0.767	1	CLONAL	1	FALSE	1	0.234029994002042	2		444	576	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235849	108235849	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	67	608	1	ENST00000278616.4:c.8891C>T	p.Pro2964Leu	p.P2964L	ENST00000278616	NM_000051.3	2964	cCt/cTt	62/63	0.234029994002042	1	FACETS	0.704	0.611	0.805	0.704	0.611	0.805	SUBCLONAL	1	FALSE	0	0.234029994002042	1		609	718	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112067	115112067	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	78	621	0	ENST00000257566.3:c.1673C>T	p.Ser558Phe	p.S558F	ENST00000257566	NM_016569.3	558	tCc/tTc	7/8	1	2	FACETS	0.747	0.655	0.847	0.747	0.655	0.847	SUBCLONAL	1	FALSE	1	0.234029994002042	2		621	892	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041222	29041223	+	missense_variant	Missense_Mutation	DNP	TT	TT	AA	novel	NA	P-0013598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	54	744	0	ENST00000282397.4:c.205_206inv	p.Lys69Leu	p.K69L	ENST00000282397	NM_002019.4	69	AAg/TTg	3/30	0.209916305787539	1	FACETS	0.489	0.417	0.569	0.489	0.417	0.569	SUBCLONAL	1	FALSE	0	0.234029994002042	1		744	833	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578401	7578401	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147002414	NA	P-0013598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	70	544	0	ENST00000269305.4:c.529C>T	p.Pro177Ser	p.P177S	ENST00000269305	NM_001126112.2	177	Ccc/Tcc	5/11	1	2	FACETS	0.904	0.788	1	0.904	0.788	1	CLONAL	1	FALSE	1	0.234029994002042	2		544	662	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086016	16086016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057517770	NA	P-0013598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	114	568	2	ENST00000281043.3:c.1192C>T	p.Arg398Trp	p.R398W	ENST00000281043	NM_005378.4	398	Cgg/Tgg	3/3	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.234029994002042	2		570	868	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206742	36206742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555889935	NA	P-0013598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	52	493	1	ENST00000300305.3:c.770C>T	p.Thr257Ile	p.T257I	ENST00000300305		257	aCt/aTt	6/8	1	2	FACETS	0.649	0.551	0.756	0.649	0.551	0.756	SUBCLONAL	1	FALSE	1	0.234029994002042	2		494	685	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281333	142281333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764261046	NA	P-0013598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	35	527	0	ENST00000350721.4:c.911C>T	p.Pro304Leu	p.P304L	ENST00000350721	NM_001184.3	304	cCc/cTc	4/47	1	2	FACETS	0.494	0.404	0.596	0.494	0.404	0.596	SUBCLONAL	1	FALSE	1	0.234029994002042	2		527	605	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955044	93955044	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1243004793	NA	P-0013598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	83	689	0	ENST00000369303.4:c.2854C>T	p.Leu952Phe	p.L952F	ENST00000369303	NM_004440.3	952	Ctt/Ttt	16/17	1	2	FACETS	0.875	0.771	0.986	0.875	0.771	0.986	CLONAL	1	FALSE	1	0.234029994002042	2		689	811	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372475	55372475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	82	812	1	ENST00000297316.4:c.1165C>T	p.Pro389Ser	p.P389S	ENST00000297316	NM_022454.3	389	Ccc/Tcc	2/2	1	2	FACETS	0.669	0.588	0.756	0.669	0.588	0.756	SUBCLONAL	1	FALSE	1	0.234029994002042	2		813	1048	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805087	89805088	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0013622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	15	515	0	ENST00000389301.3:c.4289_4290del	p.Pro1430ArgfsTer15	p.P1430Rfs*15	ENST00000389301	NM_000135.2	1430	cCA/c	43/43	0.271362303783301	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		515	182	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0013629-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	72	798	1	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	TRUE	1	0.15	2		799	922	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0013629-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	54	528	1	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.949	0.809	1	0.949	0.809	1	CLONAL	1	TRUE	1	0.15	2		529	759	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186742	108186742	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs532480170	NA	P-0013629-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	53	588	0	ENST00000278616.4:c.6100C>T	p.Arg2034Ter	p.R2034*	ENST00000278616	NM_000051.3	2034	Cga/Tga	42/63	1	2	FACETS	0.998	0.85	1	0.998	0.85	1	CLONAL	1	TRUE	1	0.15	2		588	708	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050708	30050708	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013629-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	35	434	0	ENST00000338641.4:c.514del	p.Arg172GlyfsTer2	p.R172Gfs*2	ENST00000338641	NM_000268.3	170	ccA/cc	5/16	1	2	FACETS	0.803	0.657	0.968	0.803	0.657	0.968	CLONAL	1	TRUE	1	0.15	2		434	581	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164838	36164839	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0013639-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	187	555	0	ENST00000300305.3:c.1036dup	p.Arg346ProfsTer254	p.R346Pfs*254	ENST00000300305		346	cgc/cCgc	8/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.275054513429582	2		555	1054	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138729528	NA	P-0013675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	176	397	0	ENST00000269305.4:c.523C>G	p.Arg175Gly	p.R175G	ENST00000269305	NM_001126112.2	175	Cgc/Ggc	5/11	0.186838098971281	2	FACETS	0.93	0.857	1	0.93	0.857	1	CLONAL	2	TRUE	0	0.213030911197084	2		397	888	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041202	47041202	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1569196077	NA	P-0013675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	176	426	0	ENST00000377604.3:c.1630C>T	p.His544Tyr	p.H544Y	ENST00000377604	NM_001204468.1	544	Cat/Tat	15/24	0.149308370513625	2	FACETS	1	0.942	1			1	CLONAL	2	TRUE	NA	0.213030911197084	2		426	806	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259516	+	missense_variant	Missense_Mutation	DNP	TG	TG	GC	novel	NA	P-0013675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	170	539	0	ENST00000275493.2:c.2573_2574delinsGC	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTG/cGC	21/28	0.186838098971281	2	FACETS	1	0.988	1	0.739	0.679	0.802	CLONAL	1	TRUE	0	0.213030911197084	2		539	1080	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0013679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	441	505	1				ENST00000310581	NM_198253.2	-/1132			0.717333071924706	3	FACETS	0.987	0.948	1	0.987	0.948	1	CLONAL	2	TRUE	1	0.717333071924706	3		506	846	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0013679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	788	581	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.628437787640852	3	FACETS	0.93	0.902	0.958			1	CLONAL	2	TRUE	NA	0.717333071924706	3		581	1605	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294163	1294163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199701877	NA	P-0013679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	330	589	3	ENST00000310581.5:c.838G>A	p.Glu280Lys	p.E280K	ENST00000310581	NM_198253.2	280	Gaa/Aaa	2/16	0.717333071924706	3	FACETS	0.939	0.887	0.993	0.47	0.443	0.497	CLONAL	1	TRUE	1	0.717333071924706	3		592	1331	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306689	41306689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868376470	NA	P-0013679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	381	657	0	ENST00000373198.4:c.970G>A	p.Glu324Lys	p.E324K	ENST00000373198	NM_133170.3	324	Gaa/Aaa	7/32	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.717333071924706	2		657	1035	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437167	49437167	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs975418578	NA	P-0013679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	542	669	0	ENST00000301067.7:c.5512G>A	p.Glu1838Lys	p.E1838K	ENST00000301067	NM_003482.3	1838	Gag/Aag	24/54	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.717333071924706	2		669	1368	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230641	46230641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	575	800	0	ENST00000334344.6:c.890C>T	p.Ser297Phe	p.S297F	ENST00000334344	NM_152641.2	297	tCc/tTc	8/21	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.717333071924706	2		800	1504	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095828	29095828	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	576	617	0	ENST00000328354.6:c.1006C>T	p.Gln336Ter	p.Q336*	ENST00000328354	NM_007194.3	336	Cag/Tag	9/15	0.175220578483815	3	FACETS	1	0.997	1	0.731	0.702	0.759	INDETERMINATE	1	TRUE	1	0.717333071924706	3		617	1493	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242662	46242662	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	305	422	0	ENST00000334344.6:c.1624C>T	p.Arg542Ter	p.R542*	ENST00000334344	NM_152641.2	542	Cga/Tga	13/21	1	2	FACETS	0.949	0.897	1	0.949	0.897	1	CLONAL	1	TRUE	1	0.717333071924706	2		422	896	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577123	7577123	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876660333	NA	P-0013679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	523	699	0	ENST00000269305.4:c.815T>G	p.Val272Gly	p.V272G	ENST00000269305	NM_001126112.2	272	gTg/gGg	8/11	0.717333071924706	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.717333071924706	1		699	882	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089694	27089694	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	355	493	0	ENST00000324856.7:c.2650T>G	p.Cys884Gly	p.C884G	ENST00000324856	NM_006015.4	884	Tgt/Ggt	8/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.717333071924706	2		493	868	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63700153	63700153	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	294	382	0	ENST00000279873.7:c.488A>T	p.Glu163Val	p.E163V	ENST00000279873	NM_032199.2	163	gAg/gTg	3/10	0.382107780802621	1	FACETS	0.814	0.772	0.856	0.814	0.772	0.856	INDETERMINATE	1	TRUE	0	0.717333071924706	1		382	646	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88635831	88635831	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	501	680	0	ENST00000372037.3:c.56C>T	p.Ser19Phe	p.S19F	ENST00000372037	NM_004329.2	19	tCt/tTt	3/13	0.382107780802621	1	FACETS	0.82	0.788	0.853	0.82	0.788	0.853	INDETERMINATE	1	TRUE	0	0.717333071924706	1		680	1092	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955422	48955422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	217	346	0	ENST00000267163.4:c.1538C>T	p.Ser513Phe	p.S513F	ENST00000267163	NM_000321.2	513	tCt/tTt	17/27	0.382107780802621	1	FACETS	0.689	0.646	0.733	0.689	0.646	0.733	INDETERMINATE	1	TRUE	0	0.717333071924706	1		346	563	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593559	48593559	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1555686624	NA	P-0013679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	194	285	0	ENST00000342988.3:c.1308+2T>C		p.X436_splice	ENST00000342988	NM_005359.5	436			0.382107780802621	1	FACETS	0.767	0.718	0.817	0.767	0.718	0.817	INDETERMINATE	1	TRUE	0	0.717333071924706	1		285	452	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744378	41744378	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	430	767	0	ENST00000301178.4:c.998C>T	p.Pro333Leu	p.P333L	ENST00000301178	NM_021913.4	333	cCc/cTc	8/20	1	2	FACETS	0.979	0.935	1	0.979	0.935	1	CLONAL	1	TRUE	1	0.717333071924706	2		767	1224	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416344	29416344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs958335893	NA	P-0013679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	590	784	0	ENST00000389048.3:c.4609G>A	p.Gly1537Arg	p.G1537R	ENST00000389048	NM_004304.4	1537	Gga/Aga	29/29	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.717333071924706	2		784	1579	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743871	40743871	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	527	591	0	ENST00000373198.4:c.3124G>A	p.Glu1042Lys	p.E1042K	ENST00000373198	NM_133170.3	1042	Gaa/Aaa	23/32	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.717333071924706	2		591	1335	SUCCESS
APC	324	MSKCC	GRCh37	5	112090657	112090657	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs145945630	NA	P-0013679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	307	510	1	ENST00000257430.4:c.70C>T	p.Arg24Ter	p.R24*	ENST00000257430	NM_000038.5	24	Cga/Tga	2/16	1	2	FACETS	0.829	0.783	0.877	0.829	0.783	0.877	CLONAL	1	TRUE	1	0.717333071924706	2		511	1032	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974390	93974390	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	529	773	0	ENST00000369303.4:c.1664T>G	p.Val555Gly	p.V555G	ENST00000369303	NM_004440.3	555	gTt/gGt	8/17	0.717333071924706	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.717333071924706	1		773	899	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240809	55240809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	245	419	1	ENST00000275493.2:c.2053G>A	p.Glu685Lys	p.E685K	ENST00000275493	NM_005228.3	685	Gag/Aag	17/28	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.717333071924706	2		420	671	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321340	1321340	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	393	604	0	ENST00000400841.2:c.415T>A	p.Ser139Thr	p.S139T	ENST00000400841		139	Tct/Act	4/6	0.717333071924706	1	FACETS	0.926	0.887	0.964	0.926	0.887	0.964	CLONAL	1	TRUE	0	0.717333071924706	1		604	759	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509960	187509963	+	missense_variant	Missense_Mutation	ONP	GGGG	GGGG	AGGC	novel	NA	P-0013679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	339	555	1	ENST00000441802.2:c.13550_13553delinsGCCT	p.Ala4517_Pro4518delinsGlyLeu	p.A4517_P4518delinsGL	ENST00000441802	NM_005245.3	4517	gCCCCt/gGCCTt	27/27	0.382107780802621	1	FACETS	0.695	0.66	0.731	0.695	0.66	0.731	INDETERMINATE	1	TRUE	0	0.717333071924706	1		556	872	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0013682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	177	763	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.204835028173415	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.207893521307253	2		764	751	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028611	12028611	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	89	568	1	ENST00000353533.5:c.814C>T	p.Pro272Ser	p.P272S	ENST00000353533	NM_003010.3	272	Cct/Tct	8/11	0.207893521307253	1	FACETS	0.95	0.841	1	0.95	0.841	1	CLONAL	1	TRUE	0	0.207893521307253	1		569	808	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514448	148514448	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	114	701	0	ENST00000320356.2:c.1276A>C	p.Lys426Gln	p.K426Q	ENST00000320356	NM_004456.4	426	Aag/Cag	11/20	0.207893521307253	3	FACETS	0.969	0.869	1	0.484	0.434	0.537	CLONAL	1	TRUE	1	0.207893521307253	3		701	1250	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877860	151877878	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGTTGGCACAGGTCCAG	GAAGTTGGCACAGGTCCAG	-	novel	NA	P-0013682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	143	547	0	ENST00000262189.6:c.7067_7085del	p.Pro2356GlnfsTer3	p.P2356Qfs*3	ENST00000262189	NM_170606.2	2356	cCTGGACCTGTGCCAACTTCa/ca	36/59	0.207893521307253	3	FACETS	0.773	0.704	0.846	0.773	0.704	0.846	SUBCLONAL	2	TRUE	1	0.207893521307253	3		547	982	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0013703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	144	411	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.189353462571964	3	FACETS	0.858	0.785	0.933	1	0.983	1	CLONAL	3	TRUE	1	0.21	3		411	589	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023513	31023513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	100	455	0	ENST00000375687.4:c.2998G>A	p.Asp1000Asn	p.D1000N	ENST00000375687	NM_015338.5	1000	Gat/Aat	13/13	0.254588817583983	3	FACETS	0.788	0.704	0.876	0.788	0.704	0.876	SUBCLONAL	2	TRUE	1	0.21	3		455	668	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711873	89711873	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs587781784	NA	P-0013703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	36	285	0	ENST00000371953.3:c.493-2A>G		p.X165_splice	ENST00000371953	NM_000314.4	165			0.189353462571964	3	FACETS	0.822	0.675	0.986	0.411	0.337	0.493	CLONAL	1	TRUE	1	0.21	3		285	461	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720819	89720837	+	frameshift_variant	Frame_Shift_Del	DEL	GATCTTGACAAAGCAAATA	GATCTTGACAAAGCAAATA	-	novel	NA	P-0013703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	38	160	1	ENST00000371953.3:c.970_988del	p.Asp324LysfsTer14	p.D324Kfs*14	ENST00000371953	NM_000314.4	324	GATCTTGACAAAGCAAATAaa/aa	8/9	0.189353462571964	3	FACETS	1	0.933	1	0.637	0.528	0.757	CLONAL	1	TRUE	1	0.21	3		161	314	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420115	49420121	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCGTA	CCTCGTA	-	novel	NA	P-0013703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	56	522	0	ENST00000301067.7:c.15628_15634del	p.Tyr5210ProfsTer31	p.Y5210Pfs*31	ENST00000301067	NM_003482.3	5210	TACGAGGcc/cc	48/54	0.189353462571964	3	FACETS	0.864	0.739	1	0.432	0.369	0.501	CLONAL	1	TRUE	1	0.21	3		522	682	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480495	57480495	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	40	347	0	ENST00000371085.3:c.490del	p.Glu164AsnfsTer8	p.E164Nfs*8	ENST00000371085	NM_000516.4	164	Gaa/aa	6/13	0.254588817583983	3	FACETS	0.75	0.623	0.893	0.375	0.311	0.447	SUBCLONAL	1	TRUE	1	0.21	3		347	561	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161746	47161746	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	90	655	0	ENST00000409792.3:c.4380G>T	p.Trp1460Cys	p.W1460C	ENST00000409792	NM_014159.6	1460	tgG/tgT	3/21	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.21	2		655	839	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163866	152163866	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	59	503	0	ENST00000206249.3:c.587A>G	p.His196Arg	p.H196R	ENST00000206249	NM_000125.3	196	cAt/cGt	2/8	0.189353462571964	3	FACETS	0.879	0.756	1	0.44	0.378	0.508	CLONAL	1	TRUE	1	0.21	3		503	706	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0013710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	82	757	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.877	0.774	0.987	0.877	0.774	0.987	CLONAL	1	TRUE	1	0.305117802024213	2		758	613	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115830	8115830	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	104	783	0	ENST00000346208.3:c.1176C>A	p.Asn392Lys	p.N392K	ENST00000346208		392	aaC/aaA	6/6	1	2	FACETS	0.659	0.588	0.734	0.659	0.588	0.734	SUBCLONAL	1	TRUE	1	0.305117802024213	2		783	1035	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021478	42021479	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	193	962	0	ENST00000219905.7:c.3775dup	p.Ser1259PhefsTer15	p.S1259Ffs*15	ENST00000219905	NM_001164273.1	1258	-/T	11/24	0.305117802024213	1	FACETS	0.987	0.912	1	0.987	0.912	1	CLONAL	1	TRUE	0	0.305117802024213	1		962	1086	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652930	29652930	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	129	545	0	ENST00000356175.3:c.4865T>A	p.Val1622Glu	p.V1622E	ENST00000356175	NM_000267.3	1622	gTg/gAg	36/57	0.305117802024213	3	FACETS	1	0.939	1			1	CLONAL	1	TRUE	NA	0.305117802024213	3		545	930	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0013723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	223	477	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.901	0.841	0.964	0.901	0.841	0.964	CLONAL	1	TRUE	1	0.572706836838436	2		477	864	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0013723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	166	754	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	0.572706836838436	2		754	535	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	216	360	0	ENST00000206249.3:c.1607T>A	p.Leu536His	p.L536H	ENST00000206249	NM_000125.3	536	cTc/cAc	8/8	1	2	FACETS	0.978	0.912	1	0.978	0.912	1	CLONAL	1	TRUE	1	0.572706836838436	2		360	771	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0013723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	205	362	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.572706836838436	2		362	705	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685281	89685281	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1060500116	NA	P-0013723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	95	176	0	ENST00000371953.3:c.176C>G	p.Ser59Ter	p.S59*	ENST00000371953	NM_000314.4	59	tCa/tGa	3/9	1	2	FACETS	0.838	0.751	0.929	0.838	0.751	0.929	CLONAL	1	TRUE	1	0.572706836838436	2		176	396	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105570	11105570	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	243	404	0	ENST00000358026.2:c.1486A>G	p.Lys496Glu	p.K496E	ENST00000358026	NM_001128849.1	496	Aaa/Gaa	9/36	1	2	FACETS	0.893	0.835	0.953	0.893	0.835	0.953	CLONAL	1	TRUE	1	0.572706836838436	2		404	950	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40743901	40743901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761347839	NA	P-0013723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	339	592	1	ENST00000392038.2:c.806G>A	p.Arg269Gln	p.R269Q	ENST00000392038	NM_001626.4	269	cGg/cAg	9/14	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.572706836838436	2		593	1146	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18762498	18762498	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	535	617	0	ENST00000266497.5:c.3994G>T	p.Val1332Leu	p.V1332L	ENST00000266497		1332	Gtg/Ttg	29/31	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.808350593648461	2		617	1279	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155821	106155821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771996203	NA	P-0013756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	430	514	1	ENST00000380013.4:c.722C>T	p.Ala241Val	p.A241V	ENST00000380013	NM_001127208.2	241	gCg/gTg	3/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.808350593648461	2		515	1037	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0013763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	368	916	1	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.227345486059766	4	FACETS	1	0.987	1			1	CLONAL	3	FALSE	NA	0.292764181906003	4		917	978	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554093	63554093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555583315	NA	P-0013763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	121	756	0	ENST00000307078.5:c.646G>A	p.Gly216Arg	p.G216R	ENST00000307078	NM_004655.3	216	Ggg/Agg	2/11	0.292764181906003	2	FACETS	0.829	0.748	0.915	0.415	0.374	0.458	CLONAL	1	FALSE	0	0.292764181906003	2		756	997	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151591	55151591	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	126	615	0	ENST00000257290.5:c.2377T>G	p.Leu793Val	p.L793V	ENST00000257290	NM_006206.4	793	Ttg/Gtg	17/23	0.292764181906003	4	FACETS	1	0.903	1	0.5	0.451	0.551	CLONAL	1	FALSE	2	0.292764181906003	4		615	1113	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197403	26197403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1321	237	972	0	ENST00000356476.2:c.76G>A	p.Ala26Thr	p.A26T	ENST00000356476		26	Gct/Act	1/1	0.292764181906003	3	FACETS	1	0.984	1	0.596	0.554	0.639	CLONAL	1	FALSE	1	0.292764181906003	3		972	1558	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013766-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	190	840	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	0.372751866985613	2		840	927	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579318	7579321	+	frameshift_variant	Frame_Shift_Del	DEL	AGTC	AGTC	-	novel	NA	P-0013766-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	147	471	0	ENST00000269305.4:c.366_369del	p.Thr123AlafsTer46	p.T123Afs*46	ENST00000269305	NM_001126112.2	122	gtGACT/gt	4/11	0.372751866985613	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.372751866985613	1		471	611	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937673	17937673	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013766-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	126	463	1	ENST00000458235.1:c.3254G>A	p.Arg1085Gln	p.R1085Q	ENST00000458235	NM_000215.3	1085	cGg/cAg	24/24	1	2	FACETS	0.872	0.79	0.959	0.872	0.79	0.959	CLONAL	1	TRUE	1	0.372751866985613	2		464	775	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713673	30713674	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0013766-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	136	404	0	ENST00000295754.5:c.1000_1001dup	p.Gln334HisfsTer5	p.Q334Hfs*5	ENST00000295754	NM_003242.5	333	cta/ctACa	4/7	0.372751866985613	1	FACETS	0.973	0.888	1	0.973	0.888	1	CLONAL	1	TRUE	0	0.372751866985613	1		404	610	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610605	52610607	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0013766-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	205	652	0	ENST00000394830.3:c.3566_3568del	p.Glu1189del	p.E1189del	ENST00000394830	NM_018313.4	1189	gAAGta/gta	23/30	0.372751866985613	1	FACETS	0.958	0.889	1	0.958	0.889	1	CLONAL	1	TRUE	0	0.372751866985613	1		652	934	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080575	5080575	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013766-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	204	628	0	ENST00000381652.3:c.2326A>C	p.Lys776Gln	p.K776Q	ENST00000381652	NM_004972.3	776	Aag/Cag	18/25	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.372751866985613	2		628	1027	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593583	55593609	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	AACCCATGTATGAAGTACAGTGGAAGG	AACCCATGTATGAAGTACAGTGGAAGG	-	novel	NA	P-0013789-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	260	607	0	ENST00000288135.5:c.1649_1675del	p.Lys550_Val559delinsIle	p.K550_V559delinsI	ENST00000288135	NM_000222.2	550	aAACCCATGTATGAAGTACAGTGGAAGGtt/att	11/21	0.466735890595981	4	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.922434170376216	4		607	829	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0013799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	200	525	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.447573354121828	3	FACETS	0.759	0.707	0.813	0.759	0.707	0.813	SUBCLONAL	2	TRUE	1	0.508545990696201	3		525	650	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0013799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	443	678	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.421643468242279	3	FACETS	1	0.995	1	0.822	0.789	0.855	CLONAL	2	TRUE	0	0.508545990696201	3		680	886	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0013799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	269	354	1	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.433106609213047	3	FACETS	1	0.991	1	0.807	0.765	0.849	CLONAL	2	TRUE	0	0.508545990696201	3		355	548	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711002	114711002	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	143	514	2	ENST00000543371.1:c.226C>T	p.Arg76Ter	p.R76*	ENST00000543371	NM_001198531.1	76	Cga/Tga	2/14	0.447573354121828	3	FACETS	0.869	0.792	0.949	0.434	0.396	0.475	CLONAL	1	TRUE	1	0.508545990696201	3		516	812	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871646	35871646	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	149	730	0	ENST00000216797.5:c.860A>T	p.Glu287Val	p.E287V	ENST00000216797	NM_020529.2	287	gAg/gTg	5/6	0.452176202728136	2	FACETS	0.61	0.557	0.666	0.305	0.278	0.333	SUBCLONAL	1	TRUE	0	0.508545990696201	2		730	961	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119745	17119745	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1386426732	NA	P-0013799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	120	581	0	ENST00000285071.4:c.1249T>G	p.Phe417Val	p.F417V	ENST00000285071	NM_144997.5	417	Ttc/Gtc	11/14	0.421643468242279	3	FACETS	0.664	0.599	0.733	0.221	0.199	0.245	SUBCLONAL	1	TRUE	0	0.508545990696201	3		581	891	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0013820-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	622	730	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.686896163386202	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.712633606622967	2		730	832	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352639	68352639	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013820-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	154	557	0	ENST00000487270.1:c.506A>G	p.Lys169Arg	p.K169R	ENST00000487270	NM_133509.3	169	aAg/aGg	6/11	0.664122314002533	2	FACETS	0.793	0.73	0.858	0.397	0.365	0.429	SUBCLONAL	1	TRUE	0	0.712633606622967	2		557	545	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119595300	119595300	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013820-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	455	686	0	ENST00000316626.5:c.869A>C	p.Glu290Ala	p.E290A	ENST00000316626		290	gAa/gCa	8/12	0.712633606622967	3	FACETS	0.944	0.907	0.982	0.944	0.907	0.982	CLONAL	2	TRUE	1	0.712633606622967	3		686	917	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	83	766	0				ENST00000310581	NM_198253.2	-/1132			0.861327821340427	3	FACETS	1	0.936	1	0.532	0.476	0.59	CLONAL	1	TRUE	1	0.861327821340427	3		766	259	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0013847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	302	621	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.967	0.917	1	0.967	0.917	1	CLONAL	1	TRUE	1	0.861327821340427	2		621	725	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733238	74733239	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0013847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	343	535	0	ENST00000359995.5:c.4_5del	p.Ser2LeufsTer67	p.S2Lfs*67	ENST00000359995	NM_001195427.1	2	AGc/c	1/3	1	2	FACETS	0.924	0.878	0.97	0.924	0.878	0.97	CLONAL	1	TRUE	1	0.861327821340427	2		535	862	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125635	47125635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	397	661	1	ENST00000409792.3:c.5635C>T	p.Arg1879Cys	p.R1879C	ENST00000409792	NM_014159.6	1879	Cgc/Tgc	12/21	1	2	FACETS	0.809	0.771	0.849	0.809	0.771	0.849	CLONAL	1	TRUE	1	0.861327821340427	2		662	1139	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0013860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	140	440	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.836	0.762	0.914	0.836	0.762	0.914	CLONAL	1	TRUE	1	0.428721227388945	2		440	781	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	17	466	0	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	0.358973962548835	2	FACETS	0.12	0.089	0.157	0.06	0.044	0.079	SUBCLONAL	1	TRUE	0	0.428721227388945	2		466	662	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920652	96920652	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	52	665	0	ENST00000258439.3:c.328G>T	p.Ala110Ser	p.A110S	ENST00000258439	NM_001193304.2	110	Gct/Tct	3/4	1	2	FACETS	0.268	0.227	0.313	0.268	0.227	0.313	SUBCLONAL	1	TRUE	1	0.428721227388945	2		665	904	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143029325	143029325	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	46	399	0	ENST00000262992.4:c.2295G>T	p.Leu765Phe	p.L765F	ENST00000262992	NM_001101669.1	765	ttG/ttT	21/24	1	2	FACETS	0.369	0.31	0.434	0.369	0.31	0.434	SUBCLONAL	1	TRUE	1	0.428721227388945	2		399	582	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249016	55249017	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCCACG	rs397517114	NA	P-0013860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	309	628	0	ENST00000275493.2:c.2315_2320dup	p.His773_Val774insAlaHis	p.H773_V774insAH	ENST00000275493	NM_005228.3	772	ccc/cCCCACGcc	20/28	0.428721227388945	3	FACETS	0.92	0.87	0.972	0.92	0.87	0.972	CLONAL	2	TRUE	1	0.428721227388945	3		628	951	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0013870-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	109	762	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.260191496129092	2		762	687	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584513	48584514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs377767334	NA	P-0013870-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	61	474	0	ENST00000342988.3:c.692dup	p.Ser232GlnfsTer3	p.S232Qfs*3	ENST00000342988	NM_005359.5	229	ctg/ctGg	6/12	0.260191496129092	1	FACETS	0.953	0.825	1	0.953	0.825	1	CLONAL	1	TRUE	0	0.260191496129092	1		474	428	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578490	7578490	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1453167097	NA	P-0013870-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	96	528	0	ENST00000269305.4:c.440T>G	p.Val147Gly	p.V147G	ENST00000269305	NM_001126112.2	147	gTt/gGt	5/11	0.214750601755825	1	FACETS	0.912	0.813	1	0.912	0.813	1	CLONAL	1	TRUE	0	0.260191496129092	1		528	704	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170729	11170729	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753578157	NA	P-0013870-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	106	613	1	ENST00000358026.2:c.4873G>A	p.Val1625Ile	p.V1625I	ENST00000358026	NM_001128849.1	1625	Gtc/Atc	35/36	0.252431801093344	1	FACETS	0.946	0.849	1	0.946	0.849	1	CLONAL	1	TRUE	0	0.260191496129092	1		614	749	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741697	17741697	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013870-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	83	459	1	ENST00000250003.3:c.368G>A	p.Ser123Asn	p.S123N	ENST00000250003	NM_002478.4	123	aGc/aAc	1/3	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.260191496129092	2		460	602	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856521	111856521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013893-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	122	374	0	ENST00000341259.2:c.572C>T	p.Pro191Leu	p.P191L	ENST00000341259	NM_005475.2	191	cCg/cTg	2/8	0.39229257729377	1	FACETS	0.931	0.847	1	0.931	0.847	1	CLONAL	1	TRUE	0	0.434516113343872	1		374	472	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81916897	81916897	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013893-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1299	261	1006	0	ENST00000359376.3:c.716C>G	p.Ser239Cys	p.S239C	ENST00000359376	NM_002661.3	239	tCt/tGt	9/33	1	2	FACETS	0.77	0.719	0.823	0.77	0.719	0.823	SUBCLONAL	1	TRUE	1	0.434516113343872	2		1006	1560	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985479	60985479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013893-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	218	851	0	ENST00000333681.4:c.421G>A	p.Gly141Arg	p.G141R	ENST00000333681		141	Ggg/Agg	2/3	0.38550748148686	1	FACETS	0.575	0.534	0.619	0.575	0.534	0.619	SUBCLONAL	1	TRUE	0	0.434516113343872	1		851	1365	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523634	148523634	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013893-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	173	439	0	ENST00000320356.2:c.819G>C	p.Gln273His	p.Q273H	ENST00000320356	NM_004456.4	273	caG/caC	8/20	0.434516113343872	3	FACETS	0.819	0.752	0.888	0.409	0.376	0.444	CLONAL	1	TRUE	1	0.434516113343872	3		439	1184	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900273	101900273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863223812	NA	P-0013893-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	258	714	0	ENST00000374994.4:c.707C>T	p.Ser236Phe	p.S236F	ENST00000374994	NM_004612.2	236	tCt/tTt	4/9	1	2	FACETS	0.822	0.768	0.878	0.822	0.768	0.878	CLONAL	1	TRUE	1	0.434516113343872	2		714	1444	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0013897-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	172	565	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.172075441854444	5	FACETS	0.942	0.867	1	0.942	0.867	1	CLONAL	3	TRUE	2	0.172075441854444	5		565	890	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0013897-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	96	607	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.172075441854444	2		607	903	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535427	66535427	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1472517358	NA	P-0013897-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	16	82	1	ENST00000273854.3:c.34C>T	p.Arg12Trp	p.R12W	ENST00000273854	NM_004439.5	12	Cgg/Tgg	1/18	1	2	FACETS	0.838	0.627	1	1	0.911	1	CLONAL	2	TRUE	1	0.172075441854444	2		83	111	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0013897-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	146	784	2	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	1	2	FACETS	0.867	0.79	0.947	1	0.989	1	CLONAL	2	TRUE	1	0.172075441854444	2		786	979	SUCCESS
APC	324	MSKCC	GRCh37	5	112175235	112175235	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0013897-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	141	360	0	ENST00000257430.4:c.3944C>G	p.Ser1315Ter	p.S1315*	ENST00000257430	NM_000038.5	1315	tCa/tGa	16/16	0.172075441854444	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	3	TRUE	0	0.172075441854444	3		360	568	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591127	67591129	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0013897-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	49	363	0	ENST00000274335.5:c.1721_1723del	p.Arg574del	p.R574del	ENST00000274335		574	AGA/-	12/15	0.172075441854444	3	FACETS	0.936	0.791	1	0.312	0.263	0.365	CLONAL	1	TRUE	0	0.172075441854444	3		363	661	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729880	30729881	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0013897-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	38	237	0	ENST00000295754.5:c.1403_1404del	p.Lys468ArgfsTer3	p.K468Rfs*3	ENST00000295754	NM_003242.5	467	gtAAaa/gtaa	6/7	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.172075441854444	2		237	301	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222726	5222726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779918003	NA	P-0013897-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	16	165	0	ENST00000357368.4:c.3077G>A	p.Arg1026His	p.R1026H	ENST00000357368	NM_002850.3	1026	cGc/cAc	18/38	0.172075441854444	1	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	0	0.172075441854444	1		165	139	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870895	12870895	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0013901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	56	356	0	ENST00000228872.4:c.122T>G	p.Leu41Ter	p.L41*	ENST00000228872	NM_004064.3	41	tTa/tGa	1/3	0.25941893453747	4	FACETS	0.783	0.67	0.908			1	CLONAL	1	FALSE	NA	0.259440623679792	4		356	694	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0013901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	81	265	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.259440623679792	2		265	494	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160679	56160680	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1169355679	NA	P-0013901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	214	611	0	ENST00000399503.3:c.954dup	p.Leu319ThrfsTer7	p.L319Tfs*7	ENST00000399503	NM_005921.1	318	tta/ttAa	4/20	1	2	FACETS	0.809	0.751	0.868	1	0.992	1	CLONAL	2	FALSE	1	0.259440623679792	2		611	1020	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871035	12871035	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	137	415	1	ENST00000228872.4:c.262del	p.Tyr88ThrfsTer31	p.Y88Tfs*31	ENST00000228872	NM_004064.3	88	Tac/ac	1/3	0.25941893453747	4	FACETS	1	0.938	1			1	CLONAL	2	FALSE	NA	0.259440623679792	4		416	643	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66781595	66781595	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	133	608	0	ENST00000307102.5:c.1003C>T	p.Gln335Ter	p.Q335*	ENST00000307102	NM_002755.3	335	Caa/Taa	9/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.259440623679792	2		608	838	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177100	56177100	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0013901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	82	225	0	ENST00000399503.3:c.2369+1G>A		p.X790_splice	ENST00000399503	NM_005921.1	790			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.259440623679792	2		225	432	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636743	8636743	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs771818096	NA	P-0013901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	46	357	0	ENST00000356435.5:c.166G>T	p.Val56Phe	p.V56F	ENST00000356435		56	Gtc/Ttc	2/35	1	2	FACETS	0.603	0.507	0.709	0.603	0.507	0.709	SUBCLONAL	1	FALSE	1	0.259440623679792	2		357	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0013908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	207	495	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.261737256043084	2	FACETS	0.784	0.73	0.84	0.784	0.73	0.84	SUBCLONAL	2	TRUE	0	0.356385698068522	2		495	741	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115903	8115904	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0013908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	118	474	0	ENST00000346208.3:c.1251dup	p.Thr418HisfsTer89	p.T418Hfs*89	ENST00000346208		417	acc/aCcc	6/6	0.334385909911757	3	FACETS	1	0.955	1	0.549	0.496	0.606	CLONAL	1	TRUE	1	0.356385698068522	3		474	710	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220678	2220678	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	269	535	0	ENST00000326181.6:c.295T>C	p.Ser99Pro	p.S99P	ENST00000326181	NM_032271.2	99	Tcc/Ccc	5/21	0.281430635079896	4	FACETS	0.973	0.913	1	0.973	0.913	1	CLONAL	2	TRUE	2	0.356385698068522	4		535	1052	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279346	18279346	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	78	401	1	ENST00000222254.8:c.1798G>A	p.Glu600Lys	p.E600K	ENST00000222254	NM_005027.3	600	Gag/Aag	14/16	0.281430635079896	4	FACETS	0.786	0.69	0.89	0.393	0.345	0.445	SUBCLONAL	1	TRUE	2	0.356385698068522	4		402	755	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098918	178098918	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	96	544	0	ENST00000397062.3:c.127C>G	p.Arg43Gly	p.R43G	ENST00000397062	NM_006164.4	43	Cgg/Ggg	2/5	1	2	FACETS	0.962	0.859	1	0.962	0.859	1	CLONAL	1	TRUE	1	0.356385698068522	2		544	560	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518299	187518299	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	40	152	0	ENST00000441802.2:c.12395C>G	p.Ser4132Cys	p.S4132C	ENST00000441802	NM_005245.3	4132	tCt/tGt	25/27	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.356385698068522	2		152	175	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952409	38952409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747782861	NA	P-0013908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	119	446	1	ENST00000357387.3:c.3016G>A	p.Asp1006Asn	p.D1006N	ENST00000357387	NM_152756.3	1006	Gat/Aat	30/38	0.350942214946057	4	FACETS	1	0.938	1	0.527	0.475	0.581	CLONAL	1	TRUE	2	0.356385698068522	4		447	860	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100115	157100115	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1015605215	NA	P-0013908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	18	25	1	ENST00000346085.5:c.1052G>C	p.Gly351Ala	p.G351A	ENST00000346085	NM_020732.3	351	gGa/gCa	1/20	0.356385698068522	7	FACETS	0.803	0.612	1			1	CLONAL	2	TRUE	NA	0.356385698068522	7		26	119	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123025137	123025137	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	222	532	0	ENST00000355640.3:c.1027C>A	p.His343Asn	p.H343N	ENST00000355640		343	Cat/Aat	4/7	0.356385698068522	2	FACETS	0.845	0.79	0.902	0.845	0.79	0.902	CLONAL	2	TRUE	0	0.356385698068522	2		532	737	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576876	7576876	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555524970	NA	P-0013918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	184	690	4	ENST00000269305.4:c.970del	p.Asp324MetfsTer21	p.D324Mfs*21	ENST00000269305	NM_001126112.2	324	Gat/at	9/11	0.174998708868749	3	FACETS	1	0.951	1			1	CLONAL	2	TRUE	NA	0.273374059577994	3		694	739	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427711	72427711	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	92	574	0	ENST00000477973.2:c.779C>A	p.Thr260Lys	p.T260K	ENST00000477973	NM_012234.5	260	aCa/aAa	4/4	0.238768267936123	2	FACETS	1	0.961	1	0.588	0.524	0.657	CLONAL	1	TRUE	0	0.273374059577994	2		574	572	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502612	149502612	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs773244332	NA	P-0013918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	44	318	0	ENST00000261799.4:c.2176C>G	p.Leu726Val	p.L726V	ENST00000261799	NM_002609.3	726	Ctg/Gtg	15/23	0.273374059577994	1	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	0	0.273374059577994	1		318	261	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0013928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	345	798	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	2	TRUE	NA	0.529280099380336	2		799	614	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94178987	94178987	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	49	559	0	ENST00000323929.3:c.1856C>G	p.Ser619Cys	p.S619C	ENST00000323929	NM_005591.3	619	tCt/tGt	16/20	0.251597104399789	4	FACETS	0.477	0.404	0.559	0.239	0.202	0.28	INDETERMINATE	1	TRUE	2	0.529280099380336	4		559	593	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267357	7267357	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	50	462	0	ENST00000302850.5:c.651A>T	p.Lys217Asn	p.K217N	ENST00000302850	NM_000208.2	217	aaA/aaT	2/22	0.202541860358523	2	FACETS	0.482	0.41	0.561	0.241	0.205	0.281	INDETERMINATE	1	TRUE	0	0.529280099380336	2		462	392	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294242	1294242	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	190	407	0	ENST00000310581.5:c.759G>T	p.Gln253His	p.Q253H	ENST00000310581	NM_198253.2	253	caG/caT	2/16	0.532660489330212	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.529280099380336	3		407	397	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	221	720	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.299100336376467	3	FACETS	0.994	0.927	1	0.994	0.927	1	CLONAL	2	TRUE	1	0.313269721499286	3		721	821	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0013931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	212	754	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.313269721499286	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.313269721499286	2		754	583	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0013931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	203	848	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	0.313269721499286	2		848	973	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591138	67591139	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0013931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	61	490	0	ENST00000274335.5:c.1732dup	p.Asp578GlyfsTer24	p.D578Gfs*24	ENST00000274335		577	-/G	12/15	1	2	FACETS	0.626	0.54	0.72	0.626	0.54	0.72	SUBCLONAL	1	TRUE	1	0.313269721499286	2		490	622	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591146	67591147	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0013931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	63	492	0	ENST00000274335.5:c.1740dup	p.Met582AspfsTer20	p.M582Dfs*20	ENST00000274335		580	tac/taCc	12/15	1	2	FACETS	0.64	0.554	0.735	0.64	0.554	0.735	SUBCLONAL	1	TRUE	1	0.313269721499286	2		492	628	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923160	48923160	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587776789	NA	P-0013934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	94	383	0	ENST00000267163.4:c.607+1G>T		p.X203_splice	ENST00000267163	NM_000321.2	203			0.721317708293583	3	FACETS	0.825	0.75	0.901	0.825	0.75	0.901	CLONAL	2	TRUE	1	0.721317708293583	3		383	215	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0013934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	520	1359	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	0.709390084900325	3	FACETS	0.938	0.913	0.963	0.938	0.913	0.963	CLONAL	3	TRUE	0	0.721317708293583	3		1359	697	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462772	69462772	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	159	555	0	ENST00000227507.2:c.585C>A	p.Phe195Leu	p.F195L	ENST00000227507	NM_053056.2	195	ttC/ttA	4/5	0.721317708293583	3	FACETS	0.844	0.775	0.915	0.422	0.387	0.458	CLONAL	1	TRUE	1	0.721317708293583	3		555	711	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870915	12870916	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0013934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	295	389	0	ENST00000228872.4:c.143_144del	p.His48LeufsTer76	p.H48Lfs*76	ENST00000228872	NM_004064.3	48	CAc/c	1/3	0.519569344655706	3	FACETS	1	0.989	1	0.74	0.707	0.773	CLONAL	2	TRUE	0	0.721317708293583	3		389	501	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198264998	198264998	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	169	493	0	ENST00000335508.6:c.2879T>C	p.Val960Ala	p.V960A	ENST00000335508	NM_012433.2	960	gTt/gCt	19/25	0.721317708293583	3	FACETS	0.893	0.823	0.965	0.446	0.411	0.483	CLONAL	1	TRUE	1	0.721317708293583	3		493	714	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468480	89468480	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	168	600	0	ENST00000336596.2:c.2014A>T	p.Ser672Cys	p.S672C	ENST00000336596	NM_005233.5	672	Agc/Tgc	11/17	0.652498794029961	4	FACETS	0.986	0.908	1	0.493	0.454	0.534	CLONAL	1	TRUE	2	0.721317708293583	4		600	813	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032278	26032278	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	201	382	0	ENST00000244661.2:c.11C>G	p.Thr4Ser	p.T4S	ENST00000244661	NM_003537.3	4	aCt/aGt	1/1	0.721317708293583	7	FACETS	0.847	0.786	0.911	0.339	0.314	0.365	CLONAL	2	TRUE	2	0.721317708293583	7		382	922	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	205	840	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.163090688837724	0	FACETS	1	0.975	1			1	CLONAL	1	TRUE	0	0.26	0		840	1047	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0013941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	85	505	1				ENST00000310581	NM_198253.2	-/1132			0.3	4	FACETS	0.837	0.743	0.938			1	CLONAL	2	TRUE	NA	0.26	4		506	492	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0013941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	255	427	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.75	0.701	0.801	1	0.992	1	SUBCLONAL	2	TRUE	1	0.26	2		427	1307	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216568	108216568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs767845728	NA	P-0013941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	62	605	0	ENST00000278616.4:c.8517C>A	p.Phe2839Leu	p.F2839L	ENST00000278616	NM_000051.3	2839	ttC/ttA	58/63	0.205901337513968	1	FACETS	0.37	0.318	0.427	0.37	0.318	0.427	SUBCLONAL	1	TRUE	0	0.26	1		605	1121	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593466	48593466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064796102	NA	P-0013941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	113	495	1	ENST00000342988.3:c.1217C>T	p.Ala406Val	p.A406V	ENST00000342988	NM_005359.5	406	gCg/gTg	10/12	1	2	FACETS	0.946	0.85	1	0.946	0.85	1	CLONAL	1	TRUE	1	0.26	2		496	919	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0013941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	69	371	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.3	0	FACETS	0.572	0.497	0.652			1	SUBCLONAL	1	TRUE	0	0.26	0		371	687	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245501	153245501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1024060344	NA	P-0013941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	65	468	2	ENST00000281708.4:c.1690C>T	p.Arg564Cys	p.R564C	ENST00000281708	NM_033632.3	564	Cgt/Tgt	11/12	0.205901337513968	1	FACETS	0.454	0.392	0.521	0.454	0.392	0.521	SUBCLONAL	1	TRUE	0	0.26	1		470	959	SUCCESS
APC	324	MSKCC	GRCh37	5	112174310	112174310	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	115	440	0	ENST00000257430.4:c.3022del	p.Ile1008TyrfsTer14	p.I1008Yfs*14	ENST00000257430	NM_000038.5	1007	Aaa/aa	16/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.26	2		440	716	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271492	26271492	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1311	470	1198	0	ENST00000305910.3:c.121C>G	p.Arg41Gly	p.R41G	ENST00000305910	NM_003534.2	41	Cgc/Ggc	1/1	0.3	0	FACETS	0.751	0.716	0.787			1	SUBCLONAL	2	TRUE	0	0.26	0		1198	1781	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44920620	44920620	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	201	669	3	ENST00000377967.4:c.1381C>T	p.Gln461Ter	p.Q461*	ENST00000377967	NM_021140.2	461	Cag/Tag	14/29	0.3	3	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.26	3		672	1348	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974698	21975012	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	ACTATTCGGTGCGTTGGGCAGCGCCCCCGCCTCCAGCAGCGCCCGCACCTCCTCTACCCGACCCCGGGCCGCGGCCGTGGCCAGCCAGTCAGCCGAAGGCTCCATGCTGCTCCCCGCCGCCGGCTCCATGCTGCTCCCCGCCGCCCGCTGCCTGCTCTCCCCCTCTCCGCAGCCGCCGAGCGCACGCGGTCCGCCCCACCCTCTGGTGACCAGCCAGCCCCTCCTCTTTCTTCCTCCGGTGCTGGCGGAAGAGCCCCCTCCGACCCTGTCCCTCAAATCCTCTGGAGGGACCGCGGTATCTTTCCAGGCAAGGGG	ACTATTCGGTGCGTTGGGCAGCGCCCCCGCCTCCAGCAGCGCCCGCACCTCCTCTACCCGACCCCGGGCCGCGGCCGTGGCCAGCCAGTCAGCCGAAGGCTCCATGCTGCTCCCCGCCGCCGGCTCCATGCTGCTCCCCGCCGCCCGCTGCCTGCTCTCCCCCTCTCCGCAGCCGCCGAGCGCACGCGGTCCGCCCCACCCTCTGGTGACCAGCCAGCCCCTCCTCTTTCTTCCTCCGGTGCTGGCGGAAGAGCCCCCTCCGACCCTGTCCCTCAAATCCTCTGGAGGGACCGCGGTATCTTTCCAGGCAAGGGG	-	novel	NA	P-0013951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	352	572	0	ENST00000304494.5:c.-186_129del		p.*62*	ENST00000304494	NM_000077.4	?-43/156		1/3	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		572	414	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685288	89685289	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0013990-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	113	318	0	ENST00000371953.3:c.188dup	p.Asn63LysfsTer11	p.N63Kfs*11	ENST00000371953	NM_000314.4	61	-/A	3/9	0.58455590792655	1	FACETS	0.97	0.887	1	0.97	0.887	1	CLONAL	1	TRUE	0	0.58455590792655	1		318	282	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549397	187549397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769656312	NA	P-0013990-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	285	824	2	ENST00000441802.2:c.4721C>T	p.Ser1574Leu	p.S1574L	ENST00000441802	NM_005245.3	1574	tCg/tTg	9/27	0.58455590792655	1	FACETS	0.999	0.945	1	0.999	0.945	1	CLONAL	1	TRUE	0	0.58455590792655	1		826	691	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	25	720	1	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		721	774	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0014005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	3328	771	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.345603406934908	21	FACETS	0.981	0.972	0.99	1	0.998	1	CLONAL	21	TRUE	1	0.345603406934908	21		771	4004	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414214	32414214	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	142	692	0	ENST00000332351.3:c.1337C>T	p.Thr446Ile	p.T446I	ENST00000332351	NM_024426.4	446	aCa/aTa	8/10	1	2	FACETS	0.647	0.588	0.709	0.647	0.588	0.709	SUBCLONAL	1	TRUE	1	0.345603406934908	2		692	1270	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059419	42059419	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1276	251	1085	0	ENST00000219905.7:c.9139G>A	p.Ala3047Thr	p.A3047T	ENST00000219905	NM_001164273.1	3047	Gca/Aca	24/24	0.315994842609339	2	FACETS	0.951	0.887	1	0.476	0.443	0.509	CLONAL	1	TRUE	0	0.345603406934908	2		1085	1527	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578501	7578502	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0014005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	181	509	0	ENST00000269305.4:c.428_429del	p.Val143AlafsTer5	p.V143Afs*5	ENST00000269305	NM_001126112.2	143	gTG/g	5/11	0.345603406934908	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.345603406934908	1		509	773	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288317	21288317	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1468	229	747	1	ENST00000354336.3:c.562G>T	p.Gly188Ter	p.G188*	ENST00000354336	NM_005207.3	188	Gga/Tga	2/3	0.254331249444945	3	FACETS	0.916	0.85	0.984	0.458	0.425	0.492	CLONAL	1	TRUE	1	0.345603406934908	3		748	1697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0014031-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	489	485	1	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.649662546280654	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.649662546280654	2		486	734	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692800	89692800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204856	NA	P-0014031-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	193	322	0	ENST00000371953.3:c.284C>T	p.Pro95Leu	p.P95L	ENST00000371953	NM_000314.4	95	cCa/cTa	5/9	0.63072184639775	2	FACETS	0.961	0.91	1	0.961	0.91	1	CLONAL	2	TRUE	0	0.649662546280654	2		322	309	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100175	27100176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0014041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	44	394	0	ENST00000324856.7:c.3977dup	p.Gln1327AlafsTer11	p.Q1327Afs*11	ENST00000324856	NM_006015.4	1324	tac/taCc	16/20	1	2	FACETS	0.739	0.619	0.872	0.739	0.619	0.872	SUBCLONAL	1	TRUE	1	0.21	2		394	567	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913250	NA	P-0014041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	56	475	0	ENST00000369535.4:c.34G>T	p.Gly12Cys	p.G12C	ENST00000369535	NM_002524.4	12	Ggt/Tgt	2/7	1	2	FACETS	0.619	0.529	0.718	0.619	0.529	0.718	SUBCLONAL	1	TRUE	1	0.21	2		475	862	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985473	2985473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	91	659	1	ENST00000396946.4:c.338G>A	p.Arg113Gln	p.R113Q	ENST00000396946	NM_032415.4	113	cGg/cAg	4/25	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.21	2		660	859	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179033	123179033	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	82	583	2	ENST00000218089.9:c.482T>C	p.Leu161Pro	p.L161P	ENST00000218089	NM_001042749.1	161	cTt/cCt	8/35	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.21	2		585	720	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0014065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	83	762	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.833	0.736	0.936	0.833	0.736	0.936	CLONAL	1	TRUE	1	0.334520350039821	2		762	596	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143579	108143579	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	72	370	0	ENST00000278616.4:c.3284G>T	p.Arg1095Ile	p.R1095I	ENST00000278616	NM_000051.3	1095	aGa/aTa	22/63	0.334520350039821	1	FACETS	0.738	0.646	0.836	0.738	0.646	0.836	SUBCLONAL	1	TRUE	0	0.334520350039821	1		370	486	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	137	766	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.867	0.797	0.939			1	INDETERMINATE	1	TRUE	NA	0.801726870689799	2		766	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0014071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	358	773	2	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.801726870689799	2		775	874	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0014071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	325	362	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	1	2	FACETS	0.967	0.918	1	0.967	0.918	1	CLONAL	1	TRUE	1	0.801726870689799	2		362	838	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0014071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	375	827	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.801726870689799	2		827	920	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294946	1294946	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1060503006	NA	P-0014071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	62	131	0	ENST00000310581.5:c.159G>C	p.Gln53His	p.Q53H	ENST00000310581	NM_198253.2	53	caG/caC	1/16	NA	2	FACETS	1	0.936	1			1	INDETERMINATE	1	TRUE	NA	0.801726870689799	2		131	143	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163806	152163806	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	359	614	0	ENST00000206249.3:c.527T>C	p.Met176Thr	p.M176T	ENST00000206249	NM_000125.3	176	aTg/aCg	2/8	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.801726870689799	2		614	860	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0014075-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	13	637	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.280752139629224	3	FACETS	0.212	0.15	0.288	0.106	0.075	0.144	SUBCLONAL	1	TRUE	1	0.336993845750205	3		637	425	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578214	28578214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778369	NA	P-0014075-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	59	600	0	ENST00000241453.7:c.2957C>T	p.Pro986Leu	p.P986L	ENST00000241453	NM_004119.2	986	cCg/cTg	24/24	1	2	FACETS	0.451	0.387	0.521	0.451	0.387	0.521	SUBCLONAL	1	TRUE	1	0.336993845750205	2		600	777	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578456	7578467	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGACGCGGGT	GCGGACGCGGGT	CC	novel	NA	P-0014075-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	266	499	2	ENST00000269305.4:c.463_474delinsGG	p.Thr155GlyfsTer12	p.T155Gfs*12	ENST00000269305	NM_001126112.2	155	ACCCGCGTCCGC/GG	5/11	0.336993845750205	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.336993845750205	2		501	713	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340015	116340015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014075-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	59	347	0	ENST00000397752.3:c.877G>A	p.Glu293Lys	p.E293K	ENST00000397752	NM_000245.2	293	Gaa/Aaa	2/21	0.336993845750205	4	FACETS	0.883	0.761	1	0.294	0.253	0.339	CLONAL	1	TRUE	1	0.336993845750205	4		347	530	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411879	116411918	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCTTTCTTTCTCTCTGTTTTAAGATCTGGGCAGTGAATT	CTCTTTCTTTCTCTCTGTTTTAAGATCTGGGCAGTGAATT	-	novel	NA	P-0014075-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	214	289	0	ENST00000397752.3:c.2888-24_2903del		p.X963_splice	ENST00000397752	NM_000245.2	963		14/21	0.336993845750205	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	1	0.336993845750205	4		289	487	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349892	70349892	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014075-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	193	337	0	ENST00000374080.3:c.3875T>A	p.Val1292Glu	p.V1292E	ENST00000374080		1292	gTa/gAa	28/45	0.244230595268058	2	FACETS	1	0.982	1			1	CLONAL	2	TRUE	NA	0.336993845750205	2		337	498	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131405	202131405	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014075-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	46	492	0	ENST00000358485.4:c.373C>A	p.Leu125Ile	p.L125I	ENST00000358485	NM_001080125.1	125	Ctc/Atc	2/9	0.137941390889727	4	FACETS	0.543	0.456	0.639	0.136	0.114	0.16	INDETERMINATE	1	TRUE	0	0.336993845750205	4		492	672	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0014091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	361	501	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.157240012608703	10	FACETS	1	0.955	1	1	0.994	1	CLONAL	8	TRUE	4	0.157240012608703	10		501	931	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0014091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1627	37	1141	1	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	0.157240012608703	10	FACETS	0.461	0.377	0.555	0.077	0.062	0.093	SUBCLONAL	1	TRUE	4	0.157240012608703	10		1142	1664	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0014091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	332	779	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.157240012608703	2	FACETS	0.919	0.874	0.964	1	0.997	1	CLONAL	6	TRUE	0	0.157240012608703	2		779	766	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350233	89350233	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763544660	NA	P-0014091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1252	144	1179	1	ENST00000301030.4:c.2717G>A	p.Arg906Gln	p.R906Q	ENST00000301030	NM_001256183.1	906	cGa/cAa	9/13	0.157240012608703	6	FACETS	0.862	0.784	0.945	0.431	0.392	0.473	CLONAL	2	TRUE	2	0.157240012608703	6		1180	1396	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003234	42003234	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	150	1002	0	ENST00000219905.7:c.2771C>T	p.Ser924Leu	p.S924L	ENST00000219905	NM_001164273.1	924	tCa/tTa	8/24	0.157240012608703	3	FACETS	0.98	0.894	1	0.98	0.894	1	CLONAL	2	TRUE	1	0.157240012608703	3		1002	1050	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932226	36932226	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014122-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	474	878	0	ENST00000361632.4:c.2243A>G	p.Asp748Gly	p.D748G	ENST00000361632		748	gAt/gGt	16/16	0.697326703482672	2	FACETS	1	0.972	1	0.511	0.488	0.533	CLONAL	1	TRUE	0	0.697326703482672	2		878	1331	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270554	10270554	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014122-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	285	435	0	ENST00000340748.4:c.1086C>A	p.Asp362Glu	p.D362E	ENST00000340748		362	gaC/gaA	15/40	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.697326703482672	2		435	786	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175813	24175813	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014122-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	319	523	0	ENST00000263121.7:c.1042del	p.Gln348SerfsTer9	p.Q348Sfs*9	ENST00000263121	NM_003073.3	347	gaC/ga	8/9	0.697326703482672	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.697326703482672	1		523	566	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850313	128850313	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014122-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	292	496	0	ENST00000249373.3:c.1576T>A	p.Phe526Ile	p.F526I	ENST00000249373	NM_005631.4	526	Ttt/Att	9/12	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.697326703482672	2		496	791	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0014129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	79	598	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.3	2	FACETS	0.878	0.771	0.993			1	CLONAL	1	TRUE	NA	0.22	2		598	818	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563077	21563077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	68	484	1	ENST00000382592.4:c.842C>T	p.Pro281Leu	p.P281L	ENST00000382592	NM_014572.2	281	cCg/cTg	4/8	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.22	2		485	615	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723122	49723122	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	53	579	0	ENST00000449682.2:c.1294T>G	p.Phe432Val	p.F432V	ENST00000449682	NM_020998.3	432	Ttc/Gtc	11/18	1	2	FACETS	0.597	0.508	0.695	0.597	0.508	0.695	SUBCLONAL	1	TRUE	1	0.22	2		579	807	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591116	67591151	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TTATCCAGCTGAGAAAGACGAGAGACCAATACTTGA	TTATCCAGCTGAGAAAGACGAGAGACCAATACTTGA	-	novel	NA	P-0014129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	29	390	0	ENST00000274335.5:c.1710_1745del	p.Ile571_Met582del	p.I571_M582del	ENST00000274335		570	cTTATCCAGCTGAGAAAGACGAGAGACCAATACTTGAtg/ctg	12/15	1	2	FACETS	0.507	0.406	0.622	0.507	0.406	0.622	SUBCLONAL	1	TRUE	1	0.22	2		390	520	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014139-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	566	840	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.449652140898687	6	FACETS	0.983	0.96	1			1	CLONAL	6	TRUE	NA	0.57251225956351	6		840	719	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0014139-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	264	478	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	0.5725164171712	3	FACETS	0.944	0.892	0.997	0.944	0.892	0.997	CLONAL	2	TRUE	1	0.57251225956351	3		478	628	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736342	243736342	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014139-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	152	524	3	ENST00000263826.5:c.705C>A	p.Phe235Leu	p.F235L	ENST00000263826	NM_005465.4	235	ttC/ttA	8/13	0.5725164171712	3	FACETS	0.906	0.83	0.985	0.453	0.415	0.493	CLONAL	1	TRUE	1	0.57251225956351	3		527	754	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150268	108150269	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014139-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	223	531	0	ENST00000278616.4:c.3338dup	p.Leu1113PhefsTer9	p.L1113Ffs*9	ENST00000278616	NM_000051.3	1112	cct/ccTt	23/63	0.5725164171712	4	FACETS	0.968	0.906	1	0.968	0.906	1	CLONAL	2	TRUE	2	0.57251225956351	4		531	633	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218092	108218092	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014139-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	136	288	0	ENST00000278616.4:c.8671G>T	p.Gly2891Cys	p.G2891C	ENST00000278616	NM_000051.3	2891	Ggt/Tgt	59/63	0.5725164171712	4	FACETS	0.986	0.906	1	0.986	0.906	1	CLONAL	2	TRUE	2	0.57251225956351	4		288	379	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636144	28636144	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014139-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	222	669	1	ENST00000241453.7:c.228C>A	p.Tyr76Ter	p.Y76*	ENST00000241453	NM_004119.2	76	taC/taA	3/24	NA	2	FACETS	0.953	0.889	1			1	INDETERMINATE	1	TRUE	NA	0.57251225956351	2		670	814	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467557	66467557	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1373753989	NA	P-0014139-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	326	584	0	ENST00000273854.3:c.712C>T	p.Arg238Ter	p.R238*	ENST00000273854	NM_004439.5	238	Cga/Tga	3/18	0.5725164171712	4	FACETS	0.885	0.837	0.933	0.885	0.837	0.933	CLONAL	2	TRUE	2	0.57251225956351	4		584	1012	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410365	63410365	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014139-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	570	544	1	ENST00000330258.3:c.2802G>C	p.Glu934Asp	p.E934D	ENST00000330258	NM_152424.3	934	gaG/gaC	2/2	0.530317359289876	2	FACETS	0.854	0.832	0.876			1	CLONAL	3	TRUE	NA	0.57251225956351	2		545	777	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0014149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	86	700	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.202860384495627	4	FACETS	0.851	0.759	0.949	1	0.971	1	CLONAL	3	TRUE	2	0.223313340906787	4		700	369	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0014149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	15	501	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.202860384495627	4	FACETS	0.227	0.165	0.302	0.113	0.082	0.151	SUBCLONAL	1	TRUE	2	0.223313340906787	4		501	725	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628470	187628470	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	67	607	1	ENST00000441802.2:c.2512C>A	p.His838Asn	p.H838N	ENST00000441802	NM_005245.3	838	Cat/Aat	2/27	0.223313340906787	1	FACETS	0.611	0.529	0.699	0.611	0.529	0.699	SUBCLONAL	1	TRUE	0	0.223313340906787	1		608	873	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0014152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	585	913	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.876802964162079	2		913	1266	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0014152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	299	388	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.866	0.819	0.913	0.866	0.819	0.913	CLONAL	1	TRUE	1	0.876802964162079	2		389	788	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0014152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	550	779	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	1	2	FACETS	0.982	0.944	1	0.982	0.944	1	CLONAL	1	TRUE	1	0.876802964162079	2		779	1278	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114709	108114709	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs375798802	NA	P-0014152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	28	256	0	ENST00000278616.4:c.526C>G	p.Leu176Val	p.L176V	ENST00000278616	NM_000051.3	176	Ctg/Gtg	6/63	0.20380981813646	3	FACETS	0.166	0.132	0.204	0.083	0.066	0.102	INDETERMINATE	1	TRUE	1	0.876802964162079	3		256	555	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523544	106523544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1343056360	NA	P-0014152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	196	449	0	ENST00000359195.3:c.2696C>T	p.Thr899Met	p.T899M	ENST00000359195	NM_002649.2	899	aCg/aTg	8/11	0.687630869639907	3	FACETS	0.645	0.597	0.695	0.323	0.298	0.348	SUBCLONAL	1	TRUE	1	0.876802964162079	3		449	997	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637295	176637295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201702515	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	153	451	1	ENST00000439151.2:c.1895G>A	p.Arg632Gln	p.R632Q	ENST00000439151	NM_022455.4	632	cGa/cAa	5/23	0.690903962674214	4	FACETS	0.932	0.854	1	0.233	0.213	0.254	CLONAL	1	TRUE	0	0.829939033821088	4		452	724	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	793	675	1	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.707793323891033	3	FACETS	0.9	0.882	0.918	0.9	0.882	0.918	CLONAL	3	TRUE	0	0.829939033821088	3		676	1001	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973811	15973811	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	370	473	0	ENST00000268712.3:c.4181C>G	p.Ser1394Ter	p.S1394*	ENST00000268712	NM_006311.3	1394	tCa/tGa	31/46	0.707793323891033	3	FACETS	0.848	0.821	0.874	0.848	0.821	0.874	CLONAL	3	TRUE	0	0.829939033821088	3		473	496	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197399	26197399	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1620	313	1244	0	ENST00000356476.2:c.80G>C	p.Arg27Pro	p.R27P	ENST00000356476		27	cGa/cCa	1/1	0.7615975349893	5	FACETS	0.876	0.823	0.931	0.292	0.274	0.311	CLONAL	1	TRUE	2	0.829939033821088	5		1244	1933	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024491	31024491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	166	606	0	ENST00000375687.4:c.3976C>T	p.Pro1326Ser	p.P1326S	ENST00000375687	NM_015338.5	1326	Cct/Tct	13/13	0.719713902276421	3	FACETS	0.842	0.776	0.911	0.421	0.388	0.456	CLONAL	1	TRUE	1	0.829939033821088	3		606	672	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174379	11174379	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1200645333	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	245	566	0	ENST00000361445.4:c.7296G>A	p.Met2432Ile	p.M2432I	ENST00000361445	NM_004958.3	2432	atG/atA	53/58	0.829939033821088	3	FACETS	1	0.978	1	0.364	0.341	0.387	CLONAL	1	TRUE	0	0.829939033821088	3		566	766	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776498	9776498	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	225	666	0	ENST00000377346.4:c.601G>C	p.Glu201Gln	p.E201Q	ENST00000377346	NM_005026.3	201	Gag/Cag	6/24	0.829939033821088	3	FACETS	0.87	0.811	0.93	0.29	0.27	0.31	CLONAL	1	TRUE	0	0.829939033821088	3		666	882	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784137	9784137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202142608	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	179	503	1	ENST00000377346.4:c.2705G>A	p.Arg902Gln	p.R902Q	ENST00000377346	NM_005026.3	902	cGa/cAa	21/24	0.829939033821088	3	FACETS	0.93	0.861	1	0.31	0.287	0.334	CLONAL	1	TRUE	0	0.829939033821088	3		504	656	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805735	43805735	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	342	798	0	ENST00000372470.3:c.791C>G	p.Ser264Cys	p.S264C	ENST00000372470	NM_005373.2	264	tCc/tGc	5/12	0.829939033821088	3	FACETS	1	0.983	1	0.361	0.342	0.381	CLONAL	1	TRUE	0	0.829939033821088	3		798	1077	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156848963	156848963	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764022882	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	370	627	0	ENST00000524377.1:c.1855C>G	p.Pro619Ala	p.P619A	ENST00000524377	NM_002529.3	619	Cca/Gca	15/17	0.829939033821088	4	FACETS	0.902	0.86	0.946	0.451	0.43	0.473	CLONAL	2	TRUE	0	0.829939033821088	4		627	904	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100630	8100630	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761929509	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	69	761	0	ENST00000346208.3:c.604C>T	p.Arg202Cys	p.R202C	ENST00000346208		202	Cgt/Tgt	3/6	0.660931897894278	3	FACETS	0.267	0.232	0.306	0.134	0.116	0.153	SUBCLONAL	1	TRUE	1	0.829939033821088	3		761	880	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623634	43623635	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	315	599	0	ENST00000355710.3:c.3262_3263delinsAA	p.Pro1088Lys	p.P1088K	ENST00000355710	NM_020975.4	1088	CCa/AAa	20/20	0.708281541398523	2	FACETS	0.808	0.776	0.838	0.808	0.776	0.838	CLONAL	2	TRUE	0	0.829939033821088	2		599	470	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247602	123247602	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	386	512	0	ENST00000358487.5:c.1889G>C	p.Arg630Thr	p.R630T	ENST00000358487	NM_000141.4	630	aGa/aCa	14/18	0.708281541398523	2	FACETS	0.873	0.844	0.9	0.873	0.844	0.9	CLONAL	2	TRUE	0	0.829939033821088	2		512	533	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518601	69518601	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	62	244	0	ENST00000294312.3:c.44G>C	p.Gly15Ala	p.G15A	ENST00000294312	NM_005117.2	15	gGc/gCc	1/3	0.829939033821088	3	FACETS	0.709	0.618	0.807	0.355	0.309	0.404	SUBCLONAL	1	TRUE	1	0.829939033821088	3		244	298	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195243	102195243	+	start_lost	Translation_Start_Site	SNP	G	G	C	novel	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	238	776	0	ENST00000263464.3:c.3G>C	p.Met1?	p.M1?	ENST00000263464	NM_001165.4	1	atG/atC	2/9	0.829939033821088	3	FACETS	0.749	0.699	0.801	0.375	0.349	0.401	SUBCLONAL	1	TRUE	1	0.829939033821088	3		776	1083	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865801	57865801	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	1026	1267	0	ENST00000228682.2:c.3278G>C	p.Arg1093Thr	p.R1093T	ENST00000228682	NM_005269.2	1093	aGa/aCa	12/12	0.707793323891033	3	FACETS	0.901	0.885	0.917	0.901	0.885	0.917	CLONAL	3	TRUE	0	0.829939033821088	3		1267	1294	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349250	11349250	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	57	166	0	ENST00000332029.2:c.86C>T	p.Ser29Phe	p.S29F	ENST00000332029	NM_003745.1	29	tCc/tTc	2/2	0.653152331723131	4	FACETS	1	0.891	1	0.515	0.447	0.588	CLONAL	1	TRUE	2	0.829939033821088	4		166	244	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56873439	56873439	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	724	1141	0	ENST00000308159.5:c.2143G>C	p.Glu715Gln	p.E715Q	ENST00000308159	NM_014669.4	715	Gag/Cag	20/22	0.653152331723131	4	FACETS	0.857	0.827	0.887	0.857	0.827	0.887	CLONAL	2	TRUE	2	0.829939033821088	4		1141	1863	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992774	72992774	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	310	1042	0	ENST00000268489.5:c.1271C>A	p.Ala424Asp	p.A424D	ENST00000268489	NM_006885.3	424	gCt/gAt	2/10	0.653152331723131	4	FACETS	0.901	0.847	0.956	0.45	0.423	0.478	CLONAL	1	TRUE	2	0.829939033821088	4		1042	1518	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075133	16075133	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	99	367	0	ENST00000268712.3:c.419C>G	p.Ser140Cys	p.S140C	ENST00000268712	NM_006311.3	140	tCt/tGt	4/46	0.707793323891033	3	FACETS	0.792	0.712	0.877	0.264	0.237	0.293	SUBCLONAL	1	TRUE	0	0.829939033821088	3		367	426	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223192	41223192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357411	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	528	585	0	ENST00000357654.3:c.4739C>T	p.Ser1580Phe	p.S1580F	ENST00000357654	NM_007294.3	1580	tCt/tTt	15/23	0.7615975349893	5	FACETS	0.928	0.894	0.962	0.928	0.894	0.962	CLONAL	3	TRUE	2	0.829939033821088	5		585	1026	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223201	41223201	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	522	560	0	ENST00000357654.3:c.4730C>G	p.Ser1577Cys	p.S1577C	ENST00000357654	NM_007294.3	1577	tCt/tGt	15/23	0.7615975349893	5	FACETS	0.949	0.915	0.983	0.949	0.915	0.983	CLONAL	3	TRUE	2	0.829939033821088	5		560	992	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761499	59761499	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	75	272	0	ENST00000259008.2:c.2908G>T	p.Asp970Tyr	p.D970Y	ENST00000259008	NM_032043.2	970	Gat/Tat	20/20	0.7615975349893	5	FACETS	0.854	0.751	0.965	0.285	0.25	0.322	CLONAL	1	TRUE	2	0.829939033821088	5		272	475	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1627384	1627384	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	305	898	0	ENST00000344749.5:c.340G>C	p.Asp114His	p.D114H	ENST00000344749	NM_001136139.2	114	Gac/Cac	6/19	0.660931897894278	3	FACETS	0.936	0.882	0.991	0.468	0.441	0.496	CLONAL	1	TRUE	1	0.829939033821088	3		898	1111	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793134	33793134	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1478	205	681	0	ENST00000498907.2:c.187G>C	p.Asp63His	p.D63H	ENST00000498907	NM_004364.3	63	Gac/Cac	1/1	0.829939033821088	6	FACETS	0.781	0.721	0.843	0.195	0.18	0.211	SUBCLONAL	1	TRUE	2	0.829939033821088	6		681	1683	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961366	54961366	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	125	368	0	ENST00000312783.6:c.266C>G	p.Ser89Cys	p.S89C	ENST00000312783	NM_198436.1	89	tCc/tGc	4/10	0.719713902276421	3	FACETS	0.949	0.865	1	0.475	0.432	0.518	CLONAL	1	TRUE	1	0.829939033821088	3		368	449	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884907	134884907	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	351	692	0	ENST00000398015.3:c.1683C>G	p.Ile561Met	p.I561M	ENST00000398015	NM_004441.4	561	atC/atG	8/16	0.670768957691183	6	FACETS	0.769	0.727	0.812	0.384	0.363	0.406	SUBCLONAL	2	TRUE	2	0.829939033821088	6		692	1463	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268415	142268415	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	105	344	0	ENST00000350721.4:c.3077G>C	p.Arg1026Thr	p.R1026T	ENST00000350721	NM_001184.3	1026	aGa/aCa	15/47	0.670768957691183	6	FACETS	0.856	0.767	0.951	0.214	0.191	0.238	CLONAL	1	TRUE	2	0.829939033821088	6		344	786	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217191	66217191	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	190	721	0	ENST00000273854.3:c.2424C>G	p.Ile808Met	p.I808M	ENST00000273854	NM_004439.5	808	atC/atG	14/18	0.695378563720975	2	FACETS	0.818	0.761	0.875	0.409	0.38	0.438	CLONAL	1	TRUE	0	0.829939033821088	2		721	560	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295098	1295098	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1166646936	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	62	111	1	ENST00000310581.5:c.7C>T	p.Arg3Cys	p.R3C	ENST00000310581	NM_198253.2	3	Cgc/Tgc	1/16	0.829939033821088	11	FACETS	1	0.939	1			1	CLONAL	1	TRUE	NA	0.829939033821088	11		112	609	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197253	26197253	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1928	454	1564	0	ENST00000356476.2:c.226G>C	p.Ala76Pro	p.A76P	ENST00000356476		76	Gcg/Ccg	1/1	0.7615975349893	5	FACETS	1	0.971	1	0.344	0.326	0.362	CLONAL	1	TRUE	2	0.829939033821088	5		1564	2382	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793641	89793641	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	373	595	0	ENST00000336032.3:c.710A>T	p.Gln237Leu	p.Q237L	ENST00000336032	NM_006813.2	237	cAg/cTg	2/2	0.604106236937789	4	FACETS	0.874	0.832	0.916	0.874	0.832	0.916	CLONAL	2	TRUE	2	0.829939033821088	4		595	941	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946340	2946340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1171346123	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	441	681	0	ENST00000396946.4:c.3397C>T	p.Arg1133Cys	p.R1133C	ENST00000396946	NM_032415.4	1133	Cgc/Tgc	25/25	0.829939033821088	3	FACETS	0.872	0.838	0.907	0.872	0.838	0.907	CLONAL	2	TRUE	1	0.829939033821088	3		681	862	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355256	81355256	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	219	767	0	ENST00000222390.5:c.1118G>T	p.Arg373Leu	p.R373L	ENST00000222390	NM_000601.4	373	cGa/cTa	9/18	0.829939033821088	3	FACETS	0.864	0.805	0.925	0.432	0.402	0.463	CLONAL	1	TRUE	1	0.829939033821088	3		767	864	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148513796	148513796	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	464	762	0	ENST00000320356.2:c.1485G>T	p.Arg495Ser	p.R495S	ENST00000320356	NM_004456.4	495	agG/agT	12/20	0.829939033821088	3	FACETS	0.899	0.865	0.933	0.899	0.865	0.933	CLONAL	2	TRUE	1	0.829939033821088	3		762	880	SUCCESS
AR	367	MSKCC	GRCh37	X	66905896	66905896	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1266872442	NA	P-0014162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	449	421	0	ENST00000374690.3:c.1813G>C	p.Asp605His	p.D605H	ENST00000374690	NM_000044.3	605	Gat/Cat	3/8	0.62297616121669	2	FACETS	0.987	0.963	1			1	CLONAL	2	TRUE	NA	0.829939033821088	2		421	548	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0014172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	155	757	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.245575514972367	4	FACETS	1	0.98	1	1	0.98	1	INDETERMINATE	2	TRUE	2	0.449329641831153	4		758	427	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	49	766	0				ENST00000310581	NM_198253.2	-/1132			0.170329614670354	4	FACETS	1	0.963	1	0.728	0.624	0.84	INDETERMINATE	1	TRUE	2	0.449329641831153	4		766	217	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0014172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	93	1068	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.446561384313164	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.449329641831153	1		1068	304	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865659	57865659	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	60	1125	0	ENST00000228682.2:c.3136C>T	p.Gln1046Ter	p.Q1046*	ENST00000228682	NM_005269.2	1046	Cag/Tag	12/12	NA	2	FACETS	0.413	0.355	0.476			1	INDETERMINATE	1	TRUE	NA	0.449329641831153	2		1125	647	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988379	36988379	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	37	195	0	ENST00000354822.5:c.274G>T	p.Gly92Cys	p.G92C	ENST00000354822	NM_001079668.2	92	Ggc/Tgc	2/3	0.208657641852196	3	FACETS	1	0.941	1	0.651	0.545	0.765	INDETERMINATE	1	TRUE	1	0.449329641831153	3		195	155	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95579509	95579509	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555372083	NA	P-0014172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	59	359	0	ENST00000393063.1:c.1960A>G	p.Arg654Gly	p.R654G	ENST00000393063	NM_030621.3	654	Aga/Gga	13/28	0.208657641852196	3	FACETS	1	0.955	1	0.621	0.539	0.708	INDETERMINATE	1	TRUE	1	0.449329641831153	3		359	259	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005382	42005382	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	82	1109	0	ENST00000219905.7:c.3118A>G	p.Ile1040Val	p.I1040V	ENST00000219905	NM_001164273.1	1040	Ata/Gta	9/24	0.316989869907413	0	FACETS	0.422	0.373	0.474			1	SUBCLONAL	1	TRUE	0	0.449329641831153	0		1109	476	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004883	16004883	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	93	606	0	ENST00000268712.3:c.2371G>C	p.Glu791Gln	p.E791Q	ENST00000268712	NM_006311.3	791	Gag/Cag	20/46	0.446561384313164	1	FACETS	0.93	0.835	1	0.93	0.835	1	CLONAL	1	TRUE	0	0.449329641831153	1		606	345	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216394	2216394	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	69	458	1	ENST00000398665.3:c.2038G>T	p.Gly680Cys	p.G680C	ENST00000398665	NM_032482.2	680	Ggc/Tgc	20/28	0.446561384313164	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.449329641831153	1		459	219	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792825	33792825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755311871	NA	P-0014172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	28	385	0	ENST00000498907.2:c.496G>A	p.Glu166Lys	p.E166K	ENST00000498907	NM_004364.3	166	Gag/Aag	1/1	0.219020965077272	2	FACETS	0.478	0.383	0.585	0.239	0.191	0.293	INDETERMINATE	1	TRUE	0	0.449329641831153	2		385	261	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714643	52714643	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	114	533	0	ENST00000322088.6:c.401G>T	p.Arg134Leu	p.R134L	ENST00000322088	NM_014225.5	134	cGg/cTg	4/15	NA	2	FACETS	0.778	0.71	0.849			1	INDETERMINATE	2	TRUE	NA	0.449329641831153	2		533	326	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523040	25523040	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	80	865	2	ENST00000264709.3:c.145G>A	p.Gly49Arg	p.G49R	ENST00000264709	NM_175629.2	49	Ggg/Agg	3/23	1	2	FACETS	0.722	0.638	0.813	0.722	0.638	0.813	SUBCLONAL	1	TRUE	1	0.449329641831153	2		867	493	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657105	215657105	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	48	568	0	ENST00000260947.4:c.280G>C	p.Asp94His	p.D94H	ENST00000260947	NM_000465.2	94	Gac/Cac	3/11	1	2	FACETS	0.573	0.486	0.668	0.573	0.486	0.668	SUBCLONAL	1	TRUE	1	0.449329641831153	2		568	373	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095859	29095859	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	101	711	0	ENST00000328354.6:c.975G>T	p.Lys325Asn	p.K325N	ENST00000328354	NM_007194.3	325	aaG/aaT	9/15	0.170329614670354	4	FACETS	0.77	0.693	0.851	0.77	0.693	0.851	INDETERMINATE	2	TRUE	2	0.449329641831153	4		711	423	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566550	41566550	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0014172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	44	631	0	ENST00000263253.7:c.4427C>G	p.Ser1476Ter	p.S1476*	ENST00000263253	NM_001429.3	1476	tCa/tGa	27/31	0.170329614670354	4	FACETS	0.573	0.481	0.676	0.287	0.24	0.338	INDETERMINATE	1	TRUE	2	0.449329641831153	4		631	495	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69998250	69998250	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	105	592	0	ENST00000394351.3:c.490C>G	p.Pro164Ala	p.P164A	ENST00000394351	NM_000248.3	164	Ccc/Gcc	5/9	0.446561384313164	1	FACETS	0.993	0.898	1	0.993	0.898	1	CLONAL	1	TRUE	0	0.449329641831153	1		592	365	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247442	71247442	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs750746668	NA	P-0014172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	105	648	0	ENST00000318789.4:c.91G>T	p.Gly31Cys	p.G31C	ENST00000318789	NM_032682.5	31	Ggt/Tgt	6/21	0.446561384313164	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.449329641831153	1		648	335	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721016	176721016	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	78	517	0	ENST00000439151.2:c.6647G>T	p.Gly2216Val	p.G2216V	ENST00000439151	NM_022455.4	2216	gGg/gTg	23/23	0.170329614670354	4	FACETS	1	0.952	1	0.577	0.509	0.649	INDETERMINATE	1	TRUE	2	0.449329641831153	4		517	436	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30674464	30675162	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTGGGAGGCTGAGGGAGGAGAGTCGCTTGAACCCGGGAGGCAGAGGTTGCAGTGAGCCAAGATCGCGCCACTGCACTCCAGCCTGGGTGACAGAGTGAGACTGTCTCAAAAAAAACAAAAAAATACACAAAAATTAGCCGGGTGACATGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGCGGCAGGAAAATTGTTTGAACCCAAGAGACGGAGGTTACAGTAAGCTGAGATCACGCCACTGCACACTCCAGCCTGGGTGACAGAGACAGACTCTGTCTCAAAAAAGAACAAAAACAAAAAATATGCTCACTGGATTTTCCTTTCTGTCTATGATCTCTCCTCCATTAGACTGGGATCTACCTGGGAAGCTACCTTTTTCCCACAGACCTGTCTCCATAATGCTACTATAGTGTTCTCCACACGTGGATGATGGTAAGGAAAAGGATGGCTGGGGCAAAGAAAGAAGAAACACGAAGGGTCTTTCTTTTGAGTCAGGTAGGAGATACAACTTAGGAAACAGATATGGAAAACAACGGGTGCCGAGGATAAAGGAATAGAAGCCAATCAAGGCGTGACAAAAATGGAAGAAAACTGAATAATGAGAAAGGAATAGATTAAAGTGAGGCTAGGTGAAAGAGCATTGGAGAAGATATAGAGATGACTTGTGGAATAGGAGGTAGAAAAAGTAGCTCTCACCC	CCTGGGAGGCTGAGGGAGGAGAGTCGCTTGAACCCGGGAGGCAGAGGTTGCAGTGAGCCAAGATCGCGCCACTGCACTCCAGCCTGGGTGACAGAGTGAGACTGTCTCAAAAAAAACAAAAAAATACACAAAAATTAGCCGGGTGACATGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGCGGCAGGAAAATTGTTTGAACCCAAGAGACGGAGGTTACAGTAAGCTGAGATCACGCCACTGCACACTCCAGCCTGGGTGACAGAGACAGACTCTGTCTCAAAAAAGAACAAAAACAAAAAATATGCTCACTGGATTTTCCTTTCTGTCTATGATCTCTCCTCCATTAGACTGGGATCTACCTGGGAAGCTACCTTTTTCCCACAGACCTGTCTCCATAATGCTACTATAGTGTTCTCCACACGTGGATGATGGTAAGGAAAAGGATGGCTGGGGCAAAGAAAGAAGAAACACGAAGGGTCTTTCTTTTGAGTCAGGTAGGAGATACAACTTAGGAAACAGATATGGAAAACAACGGGTGCCGAGGATAAAGGAATAGAAGCCAATCAAGGCGTGACAAAAATGGAAGAAAACTGAATAATGAGAAAGGAATAGATTAAAGTGAGGCTAGGTGAAAGAGCATTGGAGAAGATATAGAGATGACTTGTGGAATAGGAGGTAGAAAAAGTAGCTCTCACCC	-	novel	NA	P-0014172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	55	0	0	ENST00000376406.3:c.3083_3085-589del		p.X1028_splice	ENST00000376406	NM_014641.2	1028		9/15	0.275165544368365	6	FACETS	1	0.948	1	0.412	0.354	0.475	CLONAL	1	TRUE	3	0.449329641831153	6		0	376	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	74	720	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.412801513034675	3	FACETS	0.767	0.672	0.869	0.383	0.336	0.435	SUBCLONAL	1	TRUE	1	0.412801513034675	3		721	564	SUCCESS
APC	324	MSKCC	GRCh37	5	112173968	112173968	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs199740875	NA	P-0014182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	215	334	0	ENST00000257430.4:c.2677G>T	p.Glu893Ter	p.E893*	ENST00000257430	NM_000038.5	893	Gaa/Taa	16/16	0.412801513034675	3	FACETS	0.976	0.912	1	0.976	0.912	1	CLONAL	2	TRUE	1	0.412801513034675	3		334	644	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856093	68856093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121964878	NA	P-0014182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	210	632	0	ENST00000261769.5:c.1901C>T	p.Ala634Val	p.A634V	ENST00000261769	NM_004360.3	634	gCg/gTg	12/16	1	2	FACETS	0.97	0.9	1	0.97	0.9	1	CLONAL	1	TRUE	1	0.412801513034675	2		632	1049	SUCCESS
APC	324	MSKCC	GRCh37	5	112128142	112128142	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0014182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	68	345	0	ENST00000257430.4:c.646-1G>A		p.X216_splice	ENST00000257430	NM_000038.5	216			1	2	FACETS	0.83	0.725	0.942	0.83	0.725	0.942	CLONAL	1	TRUE	1	0.412801513034675	2		345	397	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101195	27101195	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	211	690	0	ENST00000324856.7:c.4477C>T	p.Gln1493Ter	p.Q1493*	ENST00000324856	NM_006015.4	1493	Cag/Tag	18/20	1	2	FACETS	0.994	0.923	1	0.994	0.923	1	CLONAL	1	TRUE	1	0.412801513034675	2		690	1028	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120042	70120042	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	47	62	0	ENST00000245479.2:c.1044del	p.Gln348HisfsTer35	p.Q348Hfs*35	ENST00000245479	NM_000346.3	348	caG/ca	3/3	0.15888244707072	3	FACETS	0.967	0.834	1	0.645	0.556	0.738	INDETERMINATE	2	TRUE	0	0.412801513034675	3		62	142	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917782	29917782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56077855	NA	P-0014182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1276	258	722	0	ENST00000389048.3:c.886G>A	p.Glu296Lys	p.E296K	ENST00000389048	NM_004304.4	296	Gag/Aag	3/29	0.412801513034675	3	FACETS	0.983	0.918	1	0.492	0.459	0.525	CLONAL	1	TRUE	1	0.412801513034675	3		722	1534	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532908	187532908	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	63	303	0	ENST00000441802.2:c.9485A>G	p.Tyr3162Cys	p.Y3162C	ENST00000441802	NM_005245.3	3162	tAc/tGc	14/27	1	2	FACETS	0.672	0.583	0.769	0.672	0.583	0.769	SUBCLONAL	1	TRUE	1	0.412801513034675	2		303	454	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219790	36219790	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	237	928	0	ENST00000222270.7:c.4687G>A	p.Ala1563Thr	p.A1563T	ENST00000222270	NM_014727.1	1563	Gca/Aca	20/37	1	2	FACETS	0.913	0.85	0.977	0.913	0.85	0.977	CLONAL	1	TRUE	1	0.412801513034675	2		928	1258	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0014199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	106	637	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.176271450203831	4	FACETS	0.965	0.871	1	1	0.982	1	CLONAL	3	TRUE	2	0.209959687227102	4		637	422	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0014199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	175	505	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.209959687227102	2		506	1170	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0014199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	125	827	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.209959687227102	2		827	989	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891274	101891274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	90	771	2	ENST00000374994.4:c.235C>T	p.Pro79Ser	p.P79S	ENST00000374994	NM_004612.2	79	Cct/Tct	2/9	0.209959687227102	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.209959687227102	1		773	670	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198217	185198217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	116	632	0	ENST00000265026.3:c.2699C>T	p.Ser900Phe	p.S900F	ENST00000265026	NM_004721.4	900	tCc/tTc	13/14	0.176271450203831	4	FACETS	1	0.979	1	0.674	0.606	0.746	CLONAL	1	TRUE	2	0.209959687227102	4		632	992	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0014200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	108	676	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.830722566218161	3	FACETS	0.49	0.44	0.543	0.245	0.22	0.272	SUBCLONAL	1	TRUE	1	0.858002708970396	3		676	734	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249348	110249348	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1721	519	1790	0	ENST00000374672.4:c.1225A>C	p.Lys409Gln	p.K409Q	ENST00000374672	NM_004235.4	409	Aag/Cag	4/5	1	2	FACETS	0.54	0.515	0.565	0.54	0.515	0.565	SUBCLONAL	1	TRUE	1	0.858002708970396	2		1790	2240	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041855	42041855	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	171	622	0	ENST00000219905.7:c.6050C>T	p.Ser2017Leu	p.S2017L	ENST00000219905	NM_001164273.1	2017	tCa/tTa	17/24	1	2	FACETS	0.508	0.468	0.55	0.508	0.468	0.55	SUBCLONAL	1	TRUE	1	0.858002708970396	2		622	784	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164664	36164665	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0014200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1447	332	1137	0	ENST00000300305.3:c.1210_1211insT	p.His404LeufsTer196	p.H404Lfs*196	ENST00000300305		404	cac/cTac	8/8	0.484317538439006	3	FACETS	0.622	0.585	0.659	0.311	0.292	0.33	INDETERMINATE	1	TRUE	1	0.858002708970396	3		1137	1779	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394333	162394333	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0014200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	31	321	0	ENST00000366898.1:c.734+1del		p.X245_splice	ENST00000366898	NM_004562.2	245			0.479103823474473	2	FACETS	0.175	0.141	0.213	0.087	0.07	0.107	INDETERMINATE	1	TRUE	0	0.858002708970396	2		321	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863224683	NA	P-0014203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1844	200	1400	0	ENST00000269305.4:c.388C>T	p.Leu130Phe	p.L130F	ENST00000269305	NM_001126112.2	130	Ctc/Ttc	5/11	1	2	FACETS	0.932	0.859	1	0.932	0.859	1	CLONAL	1	TRUE	1	0.21	2		1400	2044	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845624	68845632	+	inframe_deletion	In_Frame_Del	DEL	CGATGATGT	CGATGATGT	-	novel	NA	P-0014203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	187	706	0	ENST00000261769.5:c.870_878del	p.Asp290_Val293delinsGlu	p.D290_V293delinsE	ENST00000261769	NM_004360.3	290	gaCGATGATGTg/gag	7/16	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.21	2		706	1266	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1962801	1962801	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772470710	NA	P-0014203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	71	503	0	ENST00000382891.5:c.3295G>A	p.Glu1099Lys	p.E1099K	ENST00000382891	NM_133335.3	1099	Gag/Aag	18/22	1	2	FACETS	0.764	0.665	0.871	0.764	0.665	0.871	SUBCLONAL	1	TRUE	1	0.21	2		503	885	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479288	50479288	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	262	980	0	ENST00000394963.4:c.136C>G	p.Gln46Glu	p.Q46E	ENST00000394963	NM_003076.4	46	Caa/Gaa	1/13	1	2	FACETS	0.955	0.897	1	0.955	0.897	1	CLONAL	1	TRUE	1	0.589686236086178	2		980	930	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060693	38060712	+	frameshift_variant	Frame_Shift_Del	DEL	CGTAGAGCCGTAAGGCGAGT	CGTAGAGCCGTAAGGCGAGT	-	novel	NA	P-0014250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1230	149	1294	0	ENST00000250448.2:c.1277_1296del	p.Tyr426PhefsTer125	p.Y426Ffs*125	ENST00000250448	NM_004496.3	426	tACTCGCCTTACGGCTCTACG/t	2/2	1	2	FACETS	0.366	0.333	0.401	0.366	0.333	0.401	SUBCLONAL	1	TRUE	1	0.589686236086178	2		1294	1379	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61729409	61729409	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	177	554	0	ENST00000401558.2:c.338C>A	p.Thr113Lys	p.T113K	ENST00000401558	NM_003400.3	113	aCg/aAg	5/25	1	2	FACETS	0.774	0.714	0.835	0.774	0.714	0.835	SUBCLONAL	1	TRUE	1	0.589686236086178	2		554	776	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578463	7578463	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371524413	NA	P-0014253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	437	1166	0	ENST00000269305.4:c.467G>C	p.Arg156Pro	p.R156P	ENST00000269305	NM_001126112.2	156	cGc/cCc	5/11	0.550842816611915	1	FACETS	0.99	0.946	1	0.99	0.946	1	CLONAL	1	TRUE	0	0.550842816611915	1		1166	1161	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578315	226578315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779097786	NA	P-0014253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	70	514	0	ENST00000366794.5:c.413G>A	p.Arg138His	p.R138H	ENST00000366794	NM_001618.3	138	cGc/cAc	4/23	1	2	FACETS	0.359	0.313	0.41	0.359	0.313	0.41	SUBCLONAL	1	TRUE	1	0.550842816611915	2		514	707	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433291	49433291	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	52	751	1	ENST00000301067.7:c.8156G>A	p.Ser2719Asn	p.S2719N	ENST00000301067	NM_003482.3	2719	aGc/aAc	32/54	1	2	FACETS	0.237	0.201	0.276	0.237	0.201	0.276	SUBCLONAL	1	TRUE	1	0.550842816611915	2		752	798	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127364	55127364	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	77	712	0	ENST00000257290.5:c.152G>T	p.Gly51Val	p.G51V	ENST00000257290	NM_006206.4	51	gGg/gTg	3/23	0.435828115940338	1	FACETS	0.289	0.253	0.327	0.289	0.253	0.327	SUBCLONAL	1	TRUE	0	0.550842816611915	1		712	701	SUCCESS
APC	324	MSKCC	GRCh37	5	112175912	112175912	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201801	NA	P-0014253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	19	250	0	ENST00000257430.4:c.4621C>T	p.Gln1541Ter	p.Q1541*	ENST00000257430	NM_000038.5	1541	Cag/Tag	16/16	0.550842816611915	1	FACETS	0.213	0.161	0.273	0.213	0.161	0.273	SUBCLONAL	1	TRUE	0	0.550842816611915	1		250	235	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	78	693	0	ENST00000206249.3:c.1610A>G	p.Tyr537Cys	p.Y537C	ENST00000206249	NM_000125.3	537	tAt/tGt	8/8	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.259225095260902	2		693	537	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014267-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	58	538	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.190393054355321	3	FACETS	0.639	0.547	0.738	0.319	0.273	0.369	SUBCLONAL	1	TRUE	1	0.268639254047745	3		538	767	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0014267-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	126	636	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.258318246088495	4	FACETS	1	0.985	1	0.737	0.668	0.811	CLONAL	1	TRUE	2	0.268639254047745	4		636	807	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0014267-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	70	871	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.998	0.872	1	0.998	0.872	1	CLONAL	1	TRUE	1	0.268639254047745	2		871	522	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544742	65544742	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014267-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	117	658	0	ENST00000358664.4:c.184del	p.Gln62LysfsTer3	p.Q62Kfs*3	ENST00000358664	NM_002382.4	62	Caa/aa	4/5	0.148238513886063	4	FACETS	0.873	0.789	0.961	0.873	0.789	0.961	INDETERMINATE	2	TRUE	2	0.268639254047745	4		658	633	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0014293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	295	757	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.332612761538564	5	FACETS	0.901	0.854	0.948	1	0.991	1	CLONAL	4	TRUE	2	0.36116921222236	5		758	699	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	267	1011	0	ENST00000269305.4:c.472C>G	p.Arg158Gly	p.R158G	ENST00000269305	NM_001126112.2	158	Cgc/Ggc	5/11	0.223336189510287	3	FACETS	0.888	0.839	0.938	0.888	0.839	0.938	CLONAL	3	TRUE	0	0.36116921222236	3		1011	655	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537100	41537100	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	90	478	1	ENST00000263253.7:c.1927G>T	p.Glu643Ter	p.E643*	ENST00000263253	NM_001429.3	643	Gaa/Taa	10/31	0.33740629663362	4	FACETS	1	0.971	1	0.322	0.287	0.36	CLONAL	1	TRUE	0	0.36116921222236	4		479	526	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969882	81969882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	142	693	1	ENST00000359376.3:c.2951G>A	p.Arg984His	p.R984H	ENST00000359376	NM_002661.3	984	cGc/cAc	27/33	0.278514776892694	3	FACETS	0.776	0.71	0.845	0.776	0.71	0.845	SUBCLONAL	2	TRUE	1	0.36116921222236	3		694	598	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11204785	11204785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451215028	NA	P-0014293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	59	509	0	ENST00000361445.4:c.4792G>A	p.Glu1598Lys	p.E1598K	ENST00000361445	NM_004958.3	1598	Gag/Aag	34/58	NA	2	FACETS	0.774	0.668	0.889			1	INDETERMINATE	1	TRUE	NA	0.36116921222236	2		509	422	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999781	100999781	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	216	802	1	ENST00000325455.5:c.21G>T	p.Lys7Asn	p.K7N	ENST00000325455	NM_001202474.3	7	aaG/aaT	1/8	0.36116921222236	6	FACETS	1	0.946	1	0.761	0.711	0.812	CLONAL	3	TRUE	2	0.36116921222236	6		803	677	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345061	73345061	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	169	453	0	ENST00000377767.4:c.1736A>G	p.Lys579Arg	p.K579R	ENST00000377767	NM_014953.3	579	aAa/aGa	13/21	0.36116921222236	5	FACETS	1	0.983	1	0.814	0.752	0.877	CLONAL	2	TRUE	2	0.36116921222236	5		453	591	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610687	81610687	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	95	414	0	ENST00000298171.2:c.2285C>A	p.Thr762Lys	p.T762K	ENST00000298171	NM_000369.2	762	aCg/aAg	10/10	0.36116921222236	5	FACETS	0.98	0.878	1	0.653	0.585	0.724	CLONAL	2	TRUE	2	0.36116921222236	5		414	414	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676252	37676252	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	81	659	0	ENST00000447079.4:c.3007C>A	p.Leu1003Ile	p.L1003I	ENST00000447079	NM_015083.1	1003	Cta/Ata	11/14	0.36116921222236	4	FACETS	0.905	0.797	1	0.452	0.398	0.51	CLONAL	1	TRUE	2	0.36116921222236	4		659	675	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917851	29917851	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	327	961	0	ENST00000389048.3:c.817G>T	p.Glu273Ter	p.E273*	ENST00000389048	NM_004304.4	273	Gag/Tag	3/29	0.36116921222236	5	FACETS	1	0.989	1	0.858	0.815	0.902	CLONAL	3	TRUE	1	0.36116921222236	5		961	813	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605066	46605066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	135	1152	3	ENST00000263734.3:c.1283G>A	p.Gly428Asp	p.G428D	ENST00000263734	NM_001430.4	428	gGc/gAc	10/16	0.36116921222236	5	FACETS	1	0.961	1	0.277	0.251	0.305	CLONAL	1	TRUE	1	0.36116921222236	5		1155	1039	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907724	111907724	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	73	297	0	ENST00000393256.3:c.498G>T	p.Arg166Ser	p.R166S	ENST00000393256	NM_006538.4	166	agG/agT	3/4	0.313896162892636	4	FACETS	1	0.913	1	1	0.913	1	CLONAL	2	TRUE	2	0.36116921222236	4		297	265	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143129659	143129659	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	56	470	0	ENST00000262992.4:c.991A>T	p.Ser331Cys	p.S331C	ENST00000262992	NM_001101669.1	331	Agc/Tgc	12/24	0.36116921222236	5	FACETS	0.672	0.575	0.779	0.168	0.143	0.195	SUBCLONAL	1	TRUE	1	0.36116921222236	5		470	711	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135804187	135804187	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	46	391	0	ENST00000298552.3:c.73G>T	p.Val25Leu	p.V25L	ENST00000298552	NM_001162426.1	25	Gtg/Ttg	3/23	1	2	FACETS	0.809	0.684	0.945	0.809	0.684	0.945	CLONAL	1	TRUE	1	0.36116921222236	2		391	315	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	102	460	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.566	0.509	0.626	0.566	0.509	0.626	SUBCLONAL	1	TRUE	1	0.815348629394802	2		460	442	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	92	720	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.422	0.376	0.471	0.422	0.376	0.471	SUBCLONAL	1	TRUE	1	0.815348629394802	2		721	535	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984926	9984926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	179	925	1	ENST00000330684.3:c.1039G>A	p.Asp347Asn	p.D347N	ENST00000330684	NM_001134407.1	347	Gac/Aac	4/13	1	2	FACETS	0.551	0.509	0.595	0.551	0.509	0.595	SUBCLONAL	1	TRUE	1	0.815348629394802	2		926	797	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0014296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	111	736	2	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.446	0.401	0.492	0.446	0.401	0.492	SUBCLONAL	1	TRUE	1	0.815348629394802	2		738	611	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0014296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	115	248	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.603	0.546	0.662	0.603	0.546	0.662	SUBCLONAL	1	TRUE	1	0.815348629394802	2		249	468	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354414	354414	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201609463	NA	P-0014296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	248	1006	0	ENST00000262320.3:c.1144C>T	p.Arg382Cys	p.R382C	ENST00000262320	NM_003502.3	382	Cgc/Tgc	5/11	1	2	FACETS	0.546	0.51	0.583	0.546	0.51	0.583	SUBCLONAL	1	TRUE	1	0.815348629394802	2		1006	1114	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650647	67650647	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0014296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	105	498	0	ENST00000264010.4:c.953-1G>C		p.X318_splice	ENST00000264010	NM_006565.3	318			1	2	FACETS	0.467	0.419	0.517	0.467	0.419	0.517	SUBCLONAL	1	TRUE	1	0.815348629394802	2		498	552	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519039	66519039	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	145	597	0	ENST00000358598.2:c.320A>T	p.Glu107Val	p.E107V	ENST00000358598	NM_212471.2	107	gAg/gTg	3/11	1	2	FACETS	0.567	0.519	0.617	0.567	0.519	0.617	SUBCLONAL	1	TRUE	1	0.815348629394802	2		597	627	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117943	70117967	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GACGCTGGGCAAGCTCTGGAGGTAG	GACGCTGGGCAAGCTCTGGAGGTAG	-	novel	NA	P-0014296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	83	413	0	ENST00000245479.2:c.414_431+7del		p.X138_splice	ENST00000245479	NM_000346.3	138		1/3	1	2	FACETS	0.523	0.465	0.585	0.523	0.465	0.585	SUBCLONAL	1	TRUE	1	0.815348629394802	2		413	389	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251883	153251883	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0014296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	90	472	0	ENST00000281708.4:c.1122+1G>C		p.X374_splice	ENST00000281708	NM_033632.3	374			1	2	FACETS	0.556	0.496	0.619	0.556	0.496	0.619	SUBCLONAL	1	TRUE	1	0.815348629394802	2		472	397	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754079	42754080	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTGT	novel	NA	P-0014314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	306	763	0	ENST00000222329.4:c.269_272dup	p.Arg92GlnfsTer30	p.R92Qfs*30	ENST00000222329	NM_006494.2	91	aag/aaACAAg	3/4	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.7	2		763	836	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0014320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	414	1014	2	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.232654475123945	3	FACETS	1	0.973	1	0.689	0.655	0.723	CLONAL	2	TRUE	0	0.330807408313551	3		1016	1412	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112080	115112098	+	frameshift_variant	Frame_Shift_Del	DEL	AGACACCGGTGGAGGCCCC	AGACACCGGTGGAGGCCCC	-	novel	NA	P-0014320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	275	781	0	ENST00000257566.3:c.1642_1660del	p.Gly548ArgfsTer78	p.G548Rfs*78	ENST00000257566	NM_016569.3	548	GGGGCCTCCACCGGTGTCTcg/cg	7/8	0.26210819714637	4	FACETS	0.881	0.826	0.937	0.881	0.826	0.937	CLONAL	2	TRUE	2	0.330807408313551	4		781	1256	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120647	115120647	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1252	429	961	0	ENST00000257566.3:c.359del	p.Gly120AlafsTer19	p.G120Afs*19	ENST00000257566	NM_016569.3	120	gGc/gc	1/8	0.26210819714637	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.330807408313551	4		961	1681	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40742247	40742247	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	309	745	0	ENST00000392038.2:c.877G>T	p.Asp293Tyr	p.D293Y	ENST00000392038	NM_001626.4	293	Gac/Tac	10/14	0.303246697223788	4	FACETS	0.983	0.926	1	0.983	0.926	1	CLONAL	2	TRUE	2	0.330807408313551	4		745	1264	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845616	68845620	+	frameshift_variant	Frame_Shift_Del	DEL	GACGC	GACGC	-	novel	NA	P-0014324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	105	654	0	ENST00000261769.5:c.863_867del	p.Asp288GlyfsTer3	p.D288Gfs*3	ENST00000261769	NM_004360.3	288	GACGCg/g	7/16	0.256603770724719	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.23	1		654	782	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831342	72831342	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	57	299	2	ENST00000268489.5:c.5239C>T	p.Gln1747Ter	p.Q1747*	ENST00000268489	NM_006885.3	1747	Cag/Tag	9/10	0.256603770724719	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.23	1		301	343	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927985	+	inframe_deletion	In_Frame_Del	DEL	TGTCCA	TGTCCA	-	novel	NA	P-0014324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	32	258	0	ENST00000263967.3:c.1259_1264del	p.Cys420_Pro421del	p.C420_P421del	ENST00000263967	NM_006218.2	420	TGTCCA/-	8/21	1	2	FACETS	0.96	0.781	1	0.96	0.781	1	CLONAL	1	TRUE	1	0.23	2		258	290	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132815	152132815	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	97	584	2	ENST00000262189.6:c.57del	p.Glu20ArgfsTer85	p.E20Rfs*85	ENST00000262189	NM_170606.2	19	ccC/cc	1/59	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.23	2		586	824	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	377	766	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.938	0.895	0.981	1	0.997	1	CLONAL	2	TRUE	1	0.475	2		766	846	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0014367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	329	446	0	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.475	2		446	1004	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968315	15968315	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs779231258	NA	P-0014367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	180	319	0	ENST00000268712.3:c.4970A>G	p.Asn1657Ser	p.N1657S	ENST00000268712	NM_006311.3	1657	aAt/aGt	34/46	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.475	2		319	543	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	rs886039483	NA	P-0014380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	555	855	0	ENST00000269305.4:c.376T>G	p.Tyr126Asp	p.Y126D	ENST00000269305	NM_001126112.2	126	Tac/Gac	5/11	0.632245610783814	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.646095279093376	1		855	1096	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94910979	94910979	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1343181907	NA	P-0014380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	105	606	0	ENST00000536441.1:c.1151A>G	p.Asn384Ser	p.N384S	ENST00000536441	NM_144665.3	384	aAt/aGt	8/10	0.434313851416724	1	FACETS	0.333	0.298	0.369	0.333	0.298	0.369	SUBCLONAL	1	TRUE	0	0.646095279093376	1		606	661	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476802	140476802	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	203	445	0	ENST00000288602.6:c.1604C>G	p.Ser535Cys	p.S535C	ENST00000288602	NM_004333.4	535	tCc/tGc	13/18	1	2	FACETS	0.986	0.92	1	0.986	0.92	1	CLONAL	1	TRUE	1	0.646095279093376	2		445	637	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	150	720	1	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	0.439516130358427	2		721	650	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206590	108206590	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	294	319	0	ENST00000278616.4:c.8170C>A	p.Gln2724Lys	p.Q2724K	ENST00000278616	NM_000051.3	2724	Caa/Aaa	56/63	0.440626492256413	3	FACETS	0.884	0.84	0.929	0.884	0.84	0.929	CLONAL	3	TRUE	0	0.439516130358427	3		319	615	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606702	43606702	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	345	620	1	ENST00000355710.3:c.1311C>A	p.Asn437Lys	p.N437K	ENST00000355710	NM_020975.4	437	aaC/aaA	7/20	0.353066214048315	3	FACETS	0.874	0.828	0.921	0.874	0.828	0.921	CLONAL	2	TRUE	1	0.439516130358427	3		621	1095	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207197	1207198	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0014387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	423	630	3	ENST00000326873.7:c.285_286del	p.Lys96GlufsTer66	p.K96Efs*66	ENST00000326873	NM_000455.4	95	gtGAag/gtag	1/10	0.405464261809158	2	FACETS	0.855	0.816	0.894	0.855	0.816	0.894	CLONAL	2	TRUE	0	0.439516130358427	2		633	1126	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220492	1220493	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0014387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	307	465	2	ENST00000326873.7:c.585_586delinsTT	p.Gly196Cys	p.G196C	ENST00000326873	NM_000455.4	195	ctGGgc/ctTTgc	4/10	0.405464261809158	2	FACETS	0.874	0.828	0.921	0.874	0.828	0.921	CLONAL	2	TRUE	0	0.439516130358427	2		467	799	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514546	103514547	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	T	novel	NA	P-0014387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	49	233	0	ENST00000355739.4:c.1047_1048delinsT	p.Gln349HisfsTer30	p.Q349Hfs*30	ENST00000355739	NM_000123.3	349	caAGct/caTct	8/15	0.353066214048315	3	FACETS	0.677	0.574	0.788	0.338	0.287	0.394	SUBCLONAL	1	TRUE	1	0.439516130358427	3		233	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0014415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	33	760	1	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	1	2	FACETS	0.256	0.207	0.312	0.256	0.207	0.312	SUBCLONAL	1	TRUE	1	0.25	2		761	1031	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118827	115118827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745631586	NA	P-0014415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	55	457	0	ENST00000257566.3:c.514G>A	p.Val172Met	p.V172M	ENST00000257566	NM_016569.3	172	Gtg/Atg	2/8	0.138109224164484	0	FACETS	0.441	0.376	0.512			1	INDETERMINATE	1	TRUE	0	0.25	0		457	748	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435666	110435666	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs758578438	NA	P-0014415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	45	501	0	ENST00000375856.3:c.2735A>G	p.Glu912Gly	p.E912G	ENST00000375856	NM_003749.2	912	gAg/gGg	1/2	1	2	FACETS	0.423	0.354	0.5	0.423	0.354	0.5	SUBCLONAL	1	TRUE	1	0.25	2		501	851	SUCCESS
APC	324	MSKCC	GRCh37	5	112175354	112175367	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTCAGGAGCGAA	TCTTCAGGAGCGAA	-	novel	NA	P-0014415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	20	182	0	ENST00000257430.4:c.4063_4076del	p.Ser1355IlefsTer15	p.S1355Ifs*15	ENST00000257430	NM_000038.5	1355	TCTTCAGGAGCGAAa/a	16/16	1	2	FACETS	0.412	0.315	0.527	0.412	0.315	0.527	SUBCLONAL	1	TRUE	1	0.25	2		182	388	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129186	64129186	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776498965	NA	P-0014425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	62	806	0	ENST00000334205.4:c.724G>A	p.Gly242Ser	p.G242S	ENST00000334205	NM_003942.2	242	Ggc/Agc	7/17	1	2	FACETS	0.728	0.628	0.838	0.728	0.628	0.838	SUBCLONAL	1	FALSE	1	0.234154498925622	2		806	727	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662475	117662475	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0014425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	30	489	0	ENST00000368508.3:c.4903-1G>T		p.X1635_splice	ENST00000368508	NM_002944.2	1635			1	2	FACETS	0.545	0.439	0.666	0.545	0.439	0.666	SUBCLONAL	1	FALSE	1	0.234154498925622	2		489	470	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	411	460	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.752688795195337	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.752688795195337	3		460	718	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	50	693	0	ENST00000206249.3:c.1610A>G	p.Tyr537Cys	p.Y537C	ENST00000206249	NM_000125.3	537	tAt/tGt	8/8	1	2	FACETS	0.149	0.125	0.175	0.149	0.125	0.175	SUBCLONAL	1	TRUE	1	0.752688795195337	2		693	893	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061207	38061209	+	inframe_deletion	In_Frame_Del	DEL	CGC	CGC	-	novel	NA	P-0014431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	90	491	0	ENST00000250448.2:c.780_782del	p.Leu260_Arg261delinsPhe	p.L260_R261delinsF	ENST00000250448	NM_004496.3	260	ttGCGc/ttc	2/2	1	2	FACETS	0.392	0.348	0.439	0.392	0.348	0.439	SUBCLONAL	1	TRUE	1	0.752688795195337	2		491	610	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061496	38061496	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	118	311	0	ENST00000250448.2:c.493A>T	p.Ser165Cys	p.S165C	ENST00000250448	NM_004496.3	165	Agc/Tgc	2/2	1	2	FACETS	0.75	0.682	0.821	0.75	0.682	0.821	SUBCLONAL	1	TRUE	1	0.752688795195337	2		311	418	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002698	37002698	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	100	578	0	ENST00000358127.4:c.551T>A	p.Ile184Asn	p.I184N	ENST00000358127	NM_001280556.1	184	aTc/aAc	5/10	0.752688795195337	3	FACETS	0.359	0.32	0.401	0.179	0.16	0.201	SUBCLONAL	1	TRUE	1	0.752688795195337	3		578	1019	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0014451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	203	771	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.349848730144701	5	FACETS	1	0.983	1	0.859	0.804	0.915	CLONAL	3	TRUE	1	0.349848730144701	5		771	515	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574000	7574000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	161	483	0	ENST00000269305.4:c.1027G>T	p.Glu343Ter	p.E343*	ENST00000269305	NM_001126112.2	343	Gag/Tag	10/11	0.19607451103264	3	FACETS	0.888	0.824	0.953	0.888	0.824	0.953	INDETERMINATE	3	TRUE	0	0.349848730144701	3		483	406	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642785	3642785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373178144	NA	P-0014451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	52	538	1	ENST00000294008.3:c.2242G>A	p.Ala748Thr	p.A748T	ENST00000294008	NM_032444.2	748	Gcc/Acc	11/15	0.207519180977225	3	FACETS	0.723	0.616	0.84	0.362	0.308	0.42	INDETERMINATE	1	TRUE	1	0.349848730144701	3		539	483	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245967	5245967	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	80	519	1	ENST00000357368.4:c.808G>T	p.Gly270Cys	p.G270C	ENST00000357368	NM_002850.3	270	Ggc/Tgc	10/38	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.349848730144701	2		520	341	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39726879	39726879	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	25	173	0	ENST00000361337.2:c.877A>G	p.Ile293Val	p.I293V	ENST00000361337	NM_003286.2	293	Att/Gtt	11/21	0.349848730144701	6	FACETS	0.613	0.483	0.764	0.153	0.12	0.191	SUBCLONAL	1	TRUE	2	0.349848730144701	6		173	396	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268797	41268797	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	28	355	0	ENST00000349496.5:c.1035G>C	p.Lys345Asn	p.K345N	ENST00000349496	NM_001904.3	345	aaG/aaC	7/15	0.349848730144701	3	FACETS	0.577	0.462	0.708	0.192	0.154	0.236	SUBCLONAL	1	TRUE	0	0.349848730144701	3		355	326	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819812	170819812	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	37	423	0	ENST00000296930.5:c.451G>A	p.Val151Ile	p.V151I	ENST00000296930	NM_002520.6	151	Gtt/Att	5/11	0.207519180977225	3	FACETS	0.698	0.577	0.833	0.349	0.288	0.417	INDETERMINATE	1	TRUE	1	0.349848730144701	3		423	356	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2957002	2957002	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	35	366	0	ENST00000396946.4:c.2625A>C	p.Glu875Asp	p.E875D	ENST00000396946	NM_032415.4	875	gaA/gaC	20/25	0.349848730144701	5	FACETS	0.634	0.519	0.763	0.159	0.129	0.191	SUBCLONAL	1	TRUE	1	0.349848730144701	5		366	481	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508364	106508364	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	42	189	0	ENST00000359195.3:c.358G>C	p.Asp120His	p.D120H	ENST00000359195	NM_002649.2	120	Gac/Cac	2/11	0.309455115806192	5	FACETS	1	0.95	1	0.344	0.289	0.404	CLONAL	1	TRUE	1	0.349848730144701	5		189	266	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538819	23538819	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	58	257	0	ENST00000380871.4:c.620G>T	p.Arg207Leu	p.R207L	ENST00000380871	NM_006167.3	207	cGg/cTg	2/2	0.316698787824206	2	FACETS	0.829	0.723	0.94	0.829	0.723	0.94	CLONAL	2	TRUE	0	0.349848730144701	2		257	200	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617175	100617175	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	74	444	0	ENST00000308731.7:c.574C>A	p.Pro192Thr	p.P192T	ENST00000308731	NM_000061.2	192	Cct/Act	7/19	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.349848730144701	2		444	394	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0014458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	110	302	1	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.261780304774008	2		303	813	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62303948	62303948	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1363	164	436	1	ENST00000360203.5:c.739G>T	p.Val247Leu	p.V247L	ENST00000360203	NM_001283009.1	247	Gtg/Ttg	9/35	1	2	FACETS	0.821	0.751	0.894	0.821	0.751	0.894	CLONAL	1	TRUE	1	0.261780304774008	2		437	1527	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517756	187517756	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs778042377	NA	P-0014458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	45	142	0	ENST00000441802.2:c.12938C>G	p.Pro4313Arg	p.P4313R	ENST00000441802	NM_005245.3	4313	cCt/cGt	25/27	1	2	FACETS	0.934	0.787	1	0.934	0.787	1	CLONAL	1	TRUE	1	0.261780304774008	2		142	368	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176710863	176710863	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1220317485	NA	P-0014458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	116	339	0	ENST00000439151.2:c.6085A>G	p.Thr2029Ala	p.T2029A	ENST00000439151	NM_022455.4	2029	Aca/Gca	20/23	0.181731540234746	3	FACETS	0.98	0.881	1	0.49	0.44	0.542	CLONAL	1	TRUE	1	0.261780304774008	3		339	1023	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319931	8319931	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	129	244	0	ENST00000356435.5:c.5570T>A	p.Leu1857Gln	p.L1857Q	ENST00000356435		1857	cTa/cAa	34/35	0.25930232007027	2	FACETS	1	0.984	1	0.699	0.635	0.767	CLONAL	1	TRUE	0	0.261780304774008	2		244	705	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692805	89692805	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204928	NA	P-0014461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	50	298	0	ENST00000371953.3:c.289C>T	p.Gln97Ter	p.Q97*	ENST00000371953	NM_000314.4	97	Cag/Tag	5/9	1	2	FACETS	0.978	0.83	1	0.978	0.83	1	CLONAL	1	TRUE	1	0.22	2		298	465	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0014461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	25	286	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	0.295	0.231	0.369	0.295	0.231	0.369	SUBCLONAL	1	TRUE	1	0.22	2		286	771	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916644	178916644	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	41	344	2	ENST00000263967.3:c.31T>C	p.Trp11Arg	p.W11R	ENST00000263967	NM_006218.2	11	Tgg/Cgg	2/21	1	2	FACETS	0.675	0.562	0.802	0.675	0.562	0.802	SUBCLONAL	1	TRUE	1	0.22	2		346	552	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952052	178952052	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	42	370	0	ENST00000263967.3:c.3107T>C	p.Leu1036Ser	p.L1036S	ENST00000263967	NM_006218.2	1036	tTg/tCg	21/21	1	2	FACETS	0.603	0.503	0.715	0.603	0.503	0.715	SUBCLONAL	1	TRUE	1	0.22	2		370	633	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	576	460	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.504706523767984	4	FACETS	0.985	0.95	1	0.985	0.95	1	CLONAL	3	TRUE	1	0.504706523767984	4		460	1162	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0014468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	353	692	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.504706523767984	2		692	1308	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0014474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	229	700	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.508395157543058	2		700	855	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0014474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	533	777	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.508395157543058	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.508395157543058	2		777	1026	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579410	7579410	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567556123	NA	P-0014474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	277	618	0	ENST00000269305.4:c.277del	p.Leu93CysfsTer30	p.L93Cfs*30	ENST00000269305	NM_001126112.2	93	Ctg/tg	4/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.508395157543058	2		618	1001	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950776	79950776	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1258205404	NA	P-0014474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	33	193	0	ENST00000265081.6:c.230C>A	p.Pro77Gln	p.P77Q	ENST00000265081	NM_002439.4	77	cCg/cAg	1/24	1	2	FACETS	0.421	0.344	0.508	0.421	0.344	0.508	SUBCLONAL	1	TRUE	1	0.508395157543058	2		193	308	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692830	89692830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782343	NA	P-0014484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	28	181	0	ENST00000371953.3:c.314G>A	p.Cys105Tyr	p.C105Y	ENST00000371953	NM_000314.4	105	tGt/tAt	5/9	NA	2	FACETS	0.44	0.354	0.537			1	INDETERMINATE	1	TRUE	NA	0.626704854349074	2		181	203	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772299	68772321	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGCGTCCTGGGCAGAGGTGAGGG	CGCGTCCTGGGCAGAGGTGAGGG	-	novel	NA	P-0014484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	111	650	0	ENST00000261769.5:c.152_163+11del		p.X51_splice	ENST00000261769	NM_004360.3	51		2/16	0.343475795899277	1	FACETS	0.356	0.32	0.393	0.356	0.32	0.393	INDETERMINATE	1	TRUE	0	0.626704854349074	1		650	684	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268766	41268766	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	43	450	0	ENST00000349496.5:c.1004A>T	p.Lys335Ile	p.K335I	ENST00000349496	NM_001904.3	335	aAa/aTa	7/15	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		450	636	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0014494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	30	676	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		676	746	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0014506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	161	440	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.279111789609517	2	FACETS	1	0.989	1	0.731	0.674	0.789	CLONAL	1	TRUE	0	0.409511985982364	2		440	538	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0014506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	137	287	0	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	0.29274356175376	4	FACETS	0.793	0.724	0.864	0.793	0.724	0.864	SUBCLONAL	2	TRUE	2	0.409511985982364	4		287	595	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971097	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0014506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	155	397	0	ENST00000304494.5:c.261_262delinsAA	p.Glu88Lys	p.E88K	ENST00000304494	NM_000077.4	87	cgGGag/cgAAag	2/3	0.330932518870979	2	FACETS	0.843	0.779	0.909	0.843	0.779	0.909	CLONAL	2	TRUE	0	0.409511985982364	2		397	449	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636396	21636396	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	116	651	0	ENST00000421138.2:c.614A>G	p.Glu205Gly	p.E205G	ENST00000421138		205	gAg/gGg	7/16	0.29274356175376	4	FACETS	0.693	0.622	0.767	0.346	0.311	0.384	SUBCLONAL	1	TRUE	2	0.409511985982364	4		651	1153	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166772	32166772	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753820483	NA	P-0014506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	209	606	0	ENST00000375023.3:c.4466G>A	p.Arg1489Gln	p.R1489Q	ENST00000375023	NM_004557.3	1489	cGa/cAa	24/30	0.34791708659687	4	FACETS	0.772	0.717	0.829	0.386	0.358	0.415	SUBCLONAL	2	TRUE	0	0.409511985982364	4		606	932	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	226	1245	2	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.597124720963408	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.597124720963408	1		1247	481	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0014516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	263	532	0	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	0.58123592855318	1	FACETS	0.925	0.873	0.978	0.925	0.873	0.978	CLONAL	1	TRUE	0	0.597124720963408	1		532	668	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969884	81969884	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199840870	NA	P-0014519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	91	507	2	ENST00000359376.3:c.2953G>A	p.Val985Ile	p.V985I	ENST00000359376	NM_002661.3	985	Gtc/Atc	27/33	0.371607191527922	1	FACETS	0.591	0.526	0.66	0.591	0.526	0.66	SUBCLONAL	1	TRUE	0	0.441477751200587	1		509	544	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741614	145741614	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs767170672	NA	P-0014519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	84	493	0	ENST00000428558.2:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000428558	NM_004260.3	297	Gac/Tac	5/22	0.441477751200587	3	FACETS	0.724	0.639	0.814	0.362	0.319	0.407	SUBCLONAL	1	TRUE	1	0.441477751200587	3		493	642	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0014532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	63	501	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.973	0.84	1	0.973	0.84	1	CLONAL	1	TRUE	1	0.16	2		501	809	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956089	175956089	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs781050877	NA	P-0014549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	120	346	0	ENST00000367669.3:c.2123T>C	p.Leu708Pro	p.L708P	ENST00000367669	NM_022457.5	708	cTa/cCa	18/20	1	2	FACETS	0.502	0.455	0.552	0.502	0.455	0.552	SUBCLONAL	1	TRUE	1	0.878271093197057	2		346	544	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0014555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	266	248	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.702243137982823	2	FACETS	0.961	0.921	1	0.961	0.921	1	CLONAL	2	TRUE	0	0.702243137982823	2		249	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578529	7578529	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs780442292	NA	P-0014555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	1046	710	0	ENST00000269305.4:c.401T>G	p.Phe134Cys	p.F134C	ENST00000269305	NM_001126112.2	134	tTt/tGt	5/11	0.702243137982823	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.702243137982823	2		710	1470	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509447	106509447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	426	338	0	ENST00000359195.3:c.1441G>A	p.Val481Ile	p.V481I	ENST00000359195	NM_002649.2	481	Gtc/Atc	2/11	0.371892304640349	5	FACETS	1	0.992	1	0.773	0.739	0.808	INDETERMINATE	2	TRUE	2	0.702243137982823	5		338	1074	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921468	39921468	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773750414	NA	P-0014555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	57	462	0	ENST00000378444.4:c.4352C>T	p.Pro1451Leu	p.P1451L	ENST00000378444	NM_001123385.1	1451	cCg/cTg	10/15	NA	2	FACETS	0.178	0.152	0.207			1	INDETERMINATE	1	TRUE	NA	0.702243137982823	2		462	911	SUCCESS
CBL	867	MSKCC	GRCh37	11	119146799	119146799	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	195	318	0	ENST00000264033.4:c.962A>G	p.Asn321Ser	p.N321S	ENST00000264033	NM_005188.3	321	aAt/aGt	6/16	0.687020559403065	3	FACETS	0.85	0.787	0.915	0.283	0.262	0.305	CLONAL	1	TRUE	0	0.702243137982823	3		318	883	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465574	99465574	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780701626	NA	P-0014555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	233	332	2	ENST00000268035.6:c.2399G>A	p.Arg800His	p.R800H	ENST00000268035	NM_000875.3	800	cGc/cAc	11/21	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.702243137982823	2		334	662	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396839	396839	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145608130	NA	P-0014555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	161	405	0	ENST00000262320.3:c.187C>T	p.Arg63Cys	p.R63C	ENST00000262320	NM_003502.3	63	Cgc/Tgc	2/11	0.65952139836364	3	FACETS	0.578	0.529	0.629	0.193	0.176	0.21	SUBCLONAL	1	TRUE	0	0.702243137982823	3		405	1072	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754937	29754937	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	210	348	0	ENST00000389048.3:c.998T>A	p.Ile333Asn	p.I333N	ENST00000389048	NM_004304.4	333	aTc/aAc	4/29	0.686852321558761	3	FACETS	0.929	0.864	0.996	0.464	0.432	0.498	CLONAL	1	TRUE	1	0.702243137982823	3		348	870	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169625	27169625	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs775884054	NA	P-0014555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	477	372	1	ENST00000380036.4:c.626G>A	p.Arg209Gln	p.R209Q	ENST00000380036	NM_000459.3	209	cGg/cAg	4/23	0.702243137982823	3	FACETS	0.944	0.907	0.981	0.944	0.907	0.981	CLONAL	2	TRUE	1	0.702243137982823	3		373	972	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0014565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	186	913	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.224722949172737	2	FACETS	0.857	0.791	0.925	0.857	0.791	0.925	CLONAL	2	TRUE	0	0.224722949172737	2		913	966	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0014565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	89	763	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.129863002400062	3	FACETS	0.855	0.761	0.956	0.57	0.507	0.637	INDETERMINATE	2	TRUE	0	0.224722949172737	3		764	515	SUCCESS
APC	324	MSKCC	GRCh37	5	112175539	112175539	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	73	354	0	ENST00000257430.4:c.4248del	p.Ile1417LeufsTer2	p.I1417Lfs*2	ENST00000257430	NM_000038.5	1416	ggC/gg	16/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.224722949172737	2		354	458	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913080	32913080	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	104	526	0	ENST00000380152.3:c.4588A>G	p.Lys1530Glu	p.K1530E	ENST00000380152		1530	Aaa/Gaa	11/27	0.224722949172737	5	FACETS	1	0.958	1	0.753	0.676	0.834	CLONAL	2	TRUE	2	0.224722949172737	5		526	548	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646198	3646198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774683778	NA	P-0014565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	100	621	0	ENST00000294008.3:c.1880C>T	p.Pro627Leu	p.P627L	ENST00000294008	NM_032444.2	627	cCg/cTg	8/15	0.155706759744565	5	FACETS	1	0.974	1	0.437	0.39	0.488	CLONAL	1	TRUE	2	0.224722949172737	5		621	907	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190905	106190906	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0014565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	38	264	0	ENST00000380013.4:c.4182+2dup		p.X1394_splice	ENST00000380013	NM_001127208.2	1394			1	2	FACETS	0.986	0.817	1	0.986	0.817	1	CLONAL	1	TRUE	1	0.224722949172737	2		264	343	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444489	50444489	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	23	212	0	ENST00000331340.3:c.419C>A	p.Thr140Asn	p.T140N	ENST00000331340	NM_006060.4	140	aCt/aAt	4/8	0.155706759744565	5	FACETS	0.689	0.537	0.867	0.23	0.179	0.289	SUBCLONAL	1	TRUE	2	0.224722949172737	5		212	397	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0014572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	128	888	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.161976230758745	2	FACETS	1	0.982	1	0.688	0.622	0.758	CLONAL	1	TRUE	0	0.16	2		889	1163	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0014572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	252	771	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.179443951062215	5	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	2	0.16	5		771	1170	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741545	17741546	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0014572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	50	431	1	ENST00000250003.3:c.216_217delinsAA	p.Pro73Thr	p.P73T	ENST00000250003	NM_002478.4	72	gcCCcg/gcAAcg	1/3	1	2	FACETS	0.983	0.833	1	0.983	0.833	1	CLONAL	1	TRUE	1	0.16	2		432	636	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134378	41134378	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	77	367	0	ENST00000379561.5:c.1250C>G	p.Pro417Arg	p.P417R	ENST00000379561	NM_002015.3	417	cCc/cGc	2/3	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.16	2		367	793	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719287	190719287	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	22	205	0	ENST00000441310.2:c.1289A>G	p.Lys430Arg	p.K430R	ENST00000441310	NM_000534.4	430	aAa/aGa	9/13	1	2	FACETS	0.854	0.662	1	0.854	0.662	1	CLONAL	1	TRUE	1	0.16	2		205	322	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188806	32188807	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0014572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	56	564	1	ENST00000375023.3:c.747_748delinsAA	p.Cys249_Gln250delinsTer	p.C249_Q250delins*	ENST00000375023	NM_004557.3	249	tgCCag/tgAAag	4/30	1	2	FACETS	0.795	0.679	0.922	0.795	0.679	0.922	CLONAL	1	TRUE	1	0.16	2		565	881	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578551	7578551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	510	777	0	ENST00000269305.4:c.379T>C	p.Ser127Pro	p.S127P	ENST00000269305	NM_001126112.2	127	Tcc/Ccc	5/11	0.489175159932744	2	FACETS	0.878	0.845	0.91	0.878	0.845	0.91	CLONAL	2	TRUE	0	0.580478672861239	2		777	1001	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463248	25463248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754613602	NA	P-0014575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	37	455	0	ENST00000264709.3:c.2245C>T	p.Arg749Cys	p.R749C	ENST00000264709	NM_175629.2	749	Cgc/Tgc	19/23	0.451000237329782	1	FACETS	0.201	0.165	0.241	0.201	0.165	0.241	SUBCLONAL	1	TRUE	0	0.580478672861239	1		455	450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0014582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	79	649	2	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	0.33076434312442	3	FACETS	0.764	0.671	0.863	0.382	0.335	0.432	SUBCLONAL	1	FALSE	1	0.33076434312442	3		651	729	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	74	477	2	ENST00000322088.6:c.767C>A	p.Ser256Tyr	p.S256Y	ENST00000322088	NM_014225.5	256	tCc/tAc	6/15	0.195694545813301	3	FACETS	0.808	0.708	0.917	0.404	0.354	0.459	INDETERMINATE	1	FALSE	1	0.33076434312442	3		479	645	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274814	123274816	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0014582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	34	392	0	ENST00000358487.5:c.1102_1104del	p.Glu368del	p.E368del	ENST00000358487	NM_000141.4	368	GAG/-	9/18	0.195694545813301	3	FACETS	0.519	0.423	0.626	0.259	0.211	0.313	INDETERMINATE	1	FALSE	1	0.33076434312442	3		392	462	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622441	28622441	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	30	413	0	ENST00000241453.7:c.1176T>G	p.Cys392Trp	p.C392W	ENST00000241453	NM_004119.2	392	tgT/tgG	9/24	0.303667308187504	3	FACETS	0.511	0.411	0.624	0.255	0.205	0.312	SUBCLONAL	1	FALSE	1	0.33076434312442	3		413	414	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068966	30068966	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	34	541	1	ENST00000331968.5:c.1963G>T	p.Val655Leu	p.V655L	ENST00000331968	NM_002742.2	655	Gtg/Ttg	14/18	0.33076434312442	3	FACETS	0.617	0.505	0.744	0.309	0.252	0.372	SUBCLONAL	1	FALSE	1	0.33076434312442	3		542	388	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991726	72991730	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCG	CGCCG	-	novel	NA	P-0014582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	17	231	0	ENST00000268489.5:c.2315_2319del	p.Ala772GlyfsTer15	p.A772Gfs*15	ENST00000268489	NM_006885.3	772	gCGGCG/g	2/10	0.195694545813301	3	FACETS	0.406	0.303	0.529	0.203	0.151	0.265	INDETERMINATE	1	FALSE	1	0.33076434312442	3		231	295	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961086	55961086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs13129474	NA	P-0014582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	57	616	1	ENST00000263923.4:c.2854G>A	p.Val952Ile	p.V952I	ENST00000263923	NM_002253.2	952	Gtt/Att	21/30	0.33076434312442	8	FACETS	0.604	0.516	0.701			1	SUBCLONAL	1	FALSE	NA	0.33076434312442	8		617	1136	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519233	187519233	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	32	471	0	ENST00000441802.2:c.12150G>C	p.Glu4050Asp	p.E4050D	ENST00000441802	NM_005245.3	4050	gaG/gaC	23/27	1	2	FACETS	0.351	0.284	0.427	0.351	0.284	0.427	SUBCLONAL	1	FALSE	1	0.33076434312442	2		471	551	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	68	621	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA	2	FACETS	0.824	0.721	0.935			1	INDETERMINATE	1	TRUE	NA	0.443442383102963	2		621	372	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	63	423	1	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.443442383102963	2		424	282	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	166	681	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	NA	2	FACETS	0.805	0.746	0.865			1	INDETERMINATE	2	TRUE	NA	0.443442383102963	2		687	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	84	1163	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	1	2	FACETS	0.708	0.627	0.795	0.708	0.627	0.795	SUBCLONAL	1	TRUE	1	0.443442383102963	2		1163	535	SUCCESS
APC	324	MSKCC	GRCh37	5	112175675	112175676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	60	439	1	ENST00000257430.4:c.4393_4394dup	p.Ser1465ArgfsTer9	p.S1465Rfs*9	ENST00000257430	NM_000038.5	1462	aag/aAGag	16/16	0.368680881772999	1	FACETS	0.744	0.647	0.848	0.744	0.647	0.848	SUBCLONAL	1	TRUE	0	0.443442383102963	1		440	283	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	82	393	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.822	0.728	0.922	0.822	0.728	0.922	CLONAL	1	TRUE	1	0.443442383102963	2		393	450	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941831	44941831	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	46	447	0	ENST00000377967.4:c.3160del	p.Arg1054GlufsTer29	p.R1054Efs*29	ENST00000377967	NM_021140.2	1052	gAa/ga	21/29	0.443442383102963	1	FACETS	0.623	0.529	0.726	0.623	0.529	0.726	SUBCLONAL	1	TRUE	0	0.443442383102963	1		447	259	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21553889	21553889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1565941238	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	105	621	0	ENST00000382592.4:c.2713G>A	p.Glu905Lys	p.E905K	ENST00000382592	NM_014572.2	905	Gag/Aag	7/8	NA	2	FACETS	0.826	0.742	0.915			1	INDETERMINATE	1	TRUE	NA	0.443442383102963	2		621	573	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021817	71021817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs797045586	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	44	238	1	ENST00000318789.4:c.1541G>A	p.Arg514His	p.R514H	ENST00000318789	NM_032682.5	514	cGt/cAt	18/21	1	2	FACETS	0.923	0.782	1	0.923	0.782	1	CLONAL	1	TRUE	1	0.443442383102963	2		239	215	SUCCESS
ATR	545	MSKCC	GRCh37	3	142255005	142255005	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	37	342	0	ENST00000350721.4:c.3764del	p.Leu1255TyrfsTer7	p.L1255Yfs*7	ENST00000350721	NM_001184.3	1255	tTa/ta	20/47	1	2	FACETS	0.826	0.688	0.977	0.826	0.688	0.977	CLONAL	1	TRUE	1	0.443442383102963	2		342	202	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	58	339	0	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.83	0.718	0.951	0.83	0.718	0.951	CLONAL	1	TRUE	1	0.443442383102963	2		339	315	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726544	41726544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs891614619	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	85	593	0	ENST00000301178.4:c.89C>T	p.Thr30Met	p.T30M	ENST00000301178	NM_021913.4	30	aCg/aTg	2/20	1	2	FACETS	0.911	0.809	1	0.911	0.809	1	CLONAL	1	TRUE	1	0.443442383102963	2		593	421	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	59	454	5	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	0.858	0.744	0.981	0.858	0.744	0.981	CLONAL	1	TRUE	1	0.443442383102963	2		459	310	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397700	49397700	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	126	738	1	ENST00000418115.1:c.524C>T	p.Thr175Met	p.T175M	ENST00000418115	NM_001664.2	175	aCg/aTg	5/5	1	2	FACETS	0.985	0.895	1	0.985	0.895	1	CLONAL	1	TRUE	1	0.443442383102963	2		739	577	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100462	8100462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752779081	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	58	879	0	ENST00000346208.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000346208		146	Gcc/Acc	3/6	1	2	FACETS	0.516	0.444	0.595	0.516	0.444	0.595	SUBCLONAL	1	TRUE	1	0.443442383102963	2		879	507	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985583	60985583	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	57	359	0	ENST00000333681.4:c.317G>A	p.Arg106His	p.R106H	ENST00000333681		106	cGc/cAc	2/3	0.443442383102963	3	FACETS	0.949	0.819	1	0.474	0.409	0.545	CLONAL	1	TRUE	1	0.443442383102963	3		359	331	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40500498	40500498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	80	582	1	ENST00000264657.5:c.37C>T	p.Arg13Trp	p.R13W	ENST00000264657	NM_139276.2	13	Cgg/Tgg	2/24	0.375195423916783	3	FACETS	0.807	0.712	0.909	0.404	0.356	0.455	CLONAL	1	TRUE	1	0.443442383102963	3		583	546	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933594	39933594	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	63	584	1	ENST00000378444.4:c.1005del	p.Ser336ArgfsTer42	p.S336Rfs*42	ENST00000378444	NM_001123385.1	335	ccC/cc	4/15	0.443442383102963	1	FACETS	0.685	0.596	0.779	0.685	0.596	0.779	SUBCLONAL	1	TRUE	0	0.443442383102963	1		585	323	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132907	64132907	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	110	1080	2	ENST00000334205.4:c.1046del	p.Pro349HisfsTer26	p.P349Hfs*26	ENST00000334205	NM_003942.2	347	agC/ag	9/17	1	2	FACETS	0.941	0.849	1	0.941	0.849	1	CLONAL	1	TRUE	1	0.443442383102963	2		1082	527	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163356	47163356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	25	428	0	ENST00000409792.3:c.2770G>A	p.Ala924Thr	p.A924T	ENST00000409792	NM_014159.6	924	Gca/Aca	3/21	1	2	FACETS	0.387	0.306	0.481	0.387	0.306	0.481	SUBCLONAL	1	TRUE	1	0.443442383102963	2		428	291	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	152	796	11	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	0.443442383102963	2		807	536	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11227527	11227527	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	83	652	0	ENST00000361445.4:c.4301A>G	p.Glu1434Gly	p.E1434G	ENST00000361445	NM_004958.3	1434	gAa/gGa	29/58	1	2	FACETS	0.798	0.707	0.895	0.798	0.707	0.895	SUBCLONAL	1	TRUE	1	0.443442383102963	2		652	469	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78426038	78426038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770461160	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	85	569	0	ENST00000370768.2:c.1487C>T	p.Pro496Leu	p.P496L	ENST00000370768	NM_003902.3	496	cCg/cTg	15/20	1	2	FACETS	0.852	0.756	0.953	0.852	0.756	0.953	CLONAL	1	TRUE	1	0.443442383102963	2		569	450	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458957	120458957	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	108	832	0	ENST00000256646.2:c.6388A>G	p.Arg2130Gly	p.R2130G	ENST00000256646	NM_024408.3	2130	Agg/Ggg	34/34	1	2	FACETS	0.928	0.836	1	0.928	0.836	1	CLONAL	1	TRUE	1	0.443442383102963	2		832	525	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107223	193107224	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	20	360	0	ENST00000367435.3:c.437_438del	p.Val146AlafsTer3	p.V146Afs*3	ENST00000367435	NM_024529.4	144	gaGTgt/gagt	6/17	0.375195423916783	3	FACETS	0.494	0.379	0.628	0.247	0.189	0.314	SUBCLONAL	1	TRUE	1	0.443442383102963	3		360	223	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161412	2161412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303250662	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	99	673	0	ENST00000434045.2:c.115C>T	p.Arg39Cys	p.R39C	ENST00000434045	NM_001127598.1	39	Cgc/Tgc	2/5	1	2	FACETS	0.737	0.659	0.819	0.737	0.659	0.819	SUBCLONAL	1	TRUE	1	0.443442383102963	2		673	606	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112940047	112940047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	152	862	5	ENST00000351677.2:c.1699C>T	p.Pro567Ser	p.P567S	ENST00000351677	NM_002834.3	567	Cca/Tca	14/16	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.443442383102963	2		867	658	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912409	32912409	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs80358637	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	110	355	0	ENST00000380152.3:c.3917T>C	p.Val1306Ala	p.V1306A	ENST00000380152		1306	gTt/gCt	11/27	0.407536158411375	4	FACETS	0.871	0.796	0.948	0.871	0.796	0.948	CLONAL	3	TRUE	1	0.443442383102963	4		355	274	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134198	41134198	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	52	434	0	ENST00000379561.5:c.1430T>C	p.Met477Thr	p.M477T	ENST00000379561	NM_002015.3	477	aTg/aCg	2/3	0.407536158411375	4	FACETS	0.814	0.694	0.944	0.271	0.231	0.315	CLONAL	1	TRUE	1	0.443442383102963	4		434	416	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105236734	105236734	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	96	648	0	ENST00000349310.3:c.1387A>G	p.Ser463Gly	p.S463G	ENST00000349310	NM_001014432.1	463	Agc/Ggc	15/15	0.443442383102963	3	FACETS	0.869	0.775	0.968	0.434	0.387	0.484	CLONAL	1	TRUE	1	0.443442383102963	3		648	609	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41011090	41011090	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	78	475	1	ENST00000267868.3:c.523G>A	p.Ala175Thr	p.A175T	ENST00000267868	NM_002875.4	175	Gct/Act	6/10	1	2	FACETS	0.803	0.709	0.904	0.803	0.709	0.904	CLONAL	1	TRUE	1	0.443442383102963	2		476	438	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341233	89341233	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	72	573	0	ENST00000301030.4:c.7702C>A	p.Leu2568Met	p.L2568M	ENST00000301030	NM_001256183.1	2568	Ctg/Atg	11/13	1	2	FACETS	0.822	0.722	0.929	0.822	0.722	0.929	CLONAL	1	TRUE	1	0.443442383102963	2		573	395	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110174	8110174	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	98	786	0	ENST00000585124.1:c.431T>C	p.Phe144Ser	p.F144S	ENST00000585124	NM_004217.3	144	tTt/tCt	6/9	1	2	FACETS	0.785	0.702	0.873	0.785	0.702	0.873	SUBCLONAL	1	TRUE	1	0.443442383102963	2		786	563	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984727	11984727	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	43	353	0	ENST00000353533.5:c.273del	p.Glu92AsnfsTer11	p.E92Nfs*11	ENST00000353533	NM_003010.3	91	ccT/cc	3/11	1	2	FACETS	0.854	0.722	0.998	0.854	0.722	0.998	CLONAL	1	TRUE	1	0.443442383102963	2		353	227	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676176	29676176	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500372	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	79	507	0	ENST00000356175.3:c.7165G>A	p.Val2389Ile	p.V2389I	ENST00000356175	NM_000267.3	2389	Gtc/Atc	48/57	0.375195423916783	3	FACETS	1	0.978	1	0.733	0.651	0.818	CLONAL	1	TRUE	1	0.443442383102963	3		507	297	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440010	56440010	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	183	791	0	ENST00000407977.2:c.583-1G>A		p.X195_splice	ENST00000407977		195			NA	2	FACETS	0.822	0.765	0.88			1	INDETERMINATE	2	TRUE	NA	0.443442383102963	2		791	502	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59770863	59770863	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	39	471	1	ENST00000259008.2:c.2503C>T	p.His835Tyr	p.H835Y	ENST00000259008	NM_032043.2	835	Cac/Tac	18/20	0.443442383102963	3	FACETS	0.68	0.566	0.807	0.34	0.283	0.404	SUBCLONAL	1	TRUE	1	0.443442383102963	3		472	316	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774779	73774779	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	183	630	0	ENST00000254810.4:c.308G>A	p.Gly103Asp	p.G103D	ENST00000254810	NM_005324.3	103	gGt/gAt	4/4	0.443442383102963	3	FACETS	0.907	0.842	0.973	0.907	0.842	0.973	CLONAL	2	TRUE	1	0.443442383102963	3		630	556	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247875	10247875	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	99	773	1	ENST00000340748.4:c.4327G>A	p.Glu1443Lys	p.E1443K	ENST00000340748		1443	Gag/Aag	36/40	1	2	FACETS	0.846	0.757	0.939	0.846	0.757	0.939	CLONAL	1	TRUE	1	0.443442383102963	2		774	528	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300224	15300224	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	98	801	0	ENST00000263388.2:c.1052T>C	p.Leu351Pro	p.L351P	ENST00000263388	NM_000435.2	351	cTg/cCg	7/33	1	2	FACETS	0.804	0.719	0.893	0.804	0.719	0.893	CLONAL	1	TRUE	1	0.443442383102963	2		801	550	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946786	17946786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	99	708	1	ENST00000458235.1:c.1861G>A	p.Ala621Thr	p.A621T	ENST00000458235	NM_000215.3	621	Gcc/Acc	14/24	1	2	FACETS	0.775	0.694	0.862	0.775	0.694	0.862	SUBCLONAL	1	TRUE	1	0.443442383102963	2		709	576	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858052	45858052	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	117	887	2	ENST00000391945.4:c.1601G>A	p.Gly534Asp	p.G534D	ENST00000391945	NM_000400.3	534	gGc/gAc	17/23	1	2	FACETS	0.905	0.819	0.996	0.905	0.819	0.996	CLONAL	1	TRUE	1	0.443442383102963	2		889	583	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278368	39278368	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	54	788	0	ENST00000402219.2:c.781G>A	p.Gly261Ser	p.G261S	ENST00000402219	NM_005633.3	261	Ggc/Agc	6/23	0.375195423916783	3	FACETS	0.708	0.607	0.819	0.354	0.303	0.41	SUBCLONAL	1	TRUE	1	0.443442383102963	3		788	420	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027823	48027823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772514245	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	46	364	1	ENST00000234420.5:c.2701C>T	p.Arg901Cys	p.R901C	ENST00000234420	NM_000179.2	901	Cgt/Tgt	4/10	0.375195423916783	3	FACETS	0.631	0.532	0.739	0.315	0.266	0.37	SUBCLONAL	1	TRUE	1	0.443442383102963	3		365	402	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137430	202137431	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	140	505	1	ENST00000358485.4:c.660_661del	p.Arg221SerfsTer17	p.R221Sfs*17	ENST00000358485	NM_001080125.1	220	AAa/a	4/9	0.375195423916783	3	FACETS	0.877	0.805	0.95	0.877	0.805	0.95	CLONAL	2	TRUE	1	0.443442383102963	3		506	440	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732725	204732725	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	65	511	0	ENST00000302823.3:c.60G>C	p.Trp20Cys	p.W20C	ENST00000302823	NM_005214.4	20	tgG/tgC	1/4	0.375195423916783	3	FACETS	0.734	0.638	0.838	0.367	0.319	0.419	SUBCLONAL	1	TRUE	1	0.443442383102963	3		511	488	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321484	62321484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777153220	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	122	735	3	ENST00000360203.5:c.2186G>A	p.Arg729His	p.R729H	ENST00000360203	NM_001283009.1	729	cGt/cAt	25/35	1	2	FACETS	0.955	0.866	1	0.955	0.866	1	CLONAL	1	TRUE	1	0.443442383102963	2		738	576	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259068	89259068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	60	320	1	ENST00000336596.2:c.212G>A	p.Cys71Tyr	p.C71Y	ENST00000336596	NM_005233.5	71	tGc/tAc	3/17	1	2	FACETS	0.995	0.865	1	0.995	0.865	1	CLONAL	1	TRUE	1	0.443442383102963	2		321	272	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461508	138461508	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	60	601	2	ENST00000289153.2:c.513G>A	p.Trp171Ter	p.W171*	ENST00000289153	NM_006219.2	171	tgG/tgA	3/22	1	2	FACETS	0.677	0.585	0.775	0.677	0.585	0.775	SUBCLONAL	1	TRUE	1	0.443442383102963	2		603	400	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272576	142272576	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1284210638	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	70	619	0	ENST00000350721.4:c.2539G>A	p.Val847Ile	p.V847I	ENST00000350721	NM_001184.3	847	Gtc/Atc	12/47	1	2	FACETS	0.96	0.843	1	0.96	0.843	1	CLONAL	1	TRUE	1	0.443442383102963	2		619	329	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630719	187630719	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	70	682	0	ENST00000441802.2:c.263A>G	p.Tyr88Cys	p.Y88C	ENST00000441802	NM_005245.3	88	tAc/tGc	2/27	1	2	FACETS	0.81	0.709	0.917	0.81	0.709	0.917	CLONAL	1	TRUE	1	0.443442383102963	2		682	390	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627190	86627190	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	45	256	0	ENST00000274376.6:c.565A>C	p.Thr189Pro	p.T189P	ENST00000274376	NM_002890.2	189	Acg/Ccg	2/25	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.443442383102963	2		256	189	SUCCESS
APC	324	MSKCC	GRCh37	5	112176041	112176041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	79	421	1	ENST00000257430.4:c.4750C>T	p.Pro1584Ser	p.P1584S	ENST00000257430	NM_000038.5	1584	Cca/Tca	16/16	0.368680881772999	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.443442383102963	1		422	262	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456842	149456842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	116	720	1	ENST00000286301.3:c.886G>A	p.Val296Ile	p.V296I	ENST00000286301	NM_005211.3	296	Gta/Ata	6/22	1	2	FACETS	0.976	0.883	1	0.976	0.883	1	CLONAL	1	TRUE	1	0.443442383102963	2		721	536	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706866	117706866	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs761749336	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	84	481	1	ENST00000368508.3:c.2284T>C	p.Trp762Arg	p.W762R	ENST00000368508	NM_002944.2	762	Tgg/Cgg	15/43	0.181084061681876	0	FACETS	0.539	0.479	0.603			1	INDETERMINATE	1	TRUE	0	0.443442383102963	0		482	391	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829075	128829075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1247591045	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	19	39	0	ENST00000249373.3:c.88del	p.Ala30ArgfsTer25	p.A30Rfs*25	ENST00000249373	NM_005631.4	28	cGg/cg	1/12	0.344586021439986	3	FACETS	1	0.915	1	0.727	0.567	0.904	CLONAL	1	TRUE	1	0.443442383102963	3		39	72	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293493	137293493	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	117	1021	0	ENST00000481739.1:c.44T>C	p.Val15Ala	p.V15A	ENST00000481739	NM_002957.4	15	gTg/gCg	2/10	0.387059277619651	2	FACETS	0.798	0.721	0.88	0.399	0.36	0.44	SUBCLONAL	1	TRUE	0	0.443442383102963	2		1021	661	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396886	139396886	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752754662	NA	P-0014588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	111	605	1	ENST00000277541.6:c.5222C>T	p.Ala1741Val	p.A1741V	ENST00000277541	NM_017617.3	1741	gCg/gTg	28/34	0.387059277619651	2	FACETS	1	0.931	1	0.518	0.468	0.571	CLONAL	1	TRUE	0	0.443442383102963	2		606	483	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624297	89624297	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	314	762	0	ENST00000371953.3:c.71A>T	p.Asp24Val	p.D24V	ENST00000371953	NM_000314.4	24	gAc/gTc	1/9	0.624067019300166	1	FACETS	0.976	0.928	1	0.976	0.928	1	CLONAL	1	TRUE	0	0.648338671328211	1		762	671	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48921999	48921999	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	175	422	0	ENST00000267163.4:c.539C>A	p.Ser180Ter	p.S180*	ENST00000267163	NM_000321.2	180	tCg/tAg	5/27	0.620349508904592	1	FACETS	0.95	0.887	1	0.95	0.887	1	CLONAL	1	TRUE	0	0.648338671328211	1		422	384	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127259	17127259	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	227	670	0	ENST00000285071.4:c.595G>A	p.Glu199Lys	p.E199K	ENST00000285071	NM_144997.5	199	Gag/Aag	6/14	1	2	FACETS	0.93	0.869	0.992	0.93	0.869	0.992	CLONAL	1	TRUE	1	0.648338671328211	2		670	753	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	194	621	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.926	0.86	0.995	0.926	0.86	0.995	CLONAL	1	TRUE	1	0.559907775782851	2		621	748	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	69	534	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.503	0.439	0.572	0.503	0.439	0.572	SUBCLONAL	1	TRUE	1	0.559907775782851	2		534	490	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	386	681	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.942	0.902	0.981	1	0.997	1	CLONAL	2	TRUE	1	0.559907775782851	2		687	732	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132907	64132907	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	234	1080	2	ENST00000334205.4:c.1046del	p.Pro349HisfsTer26	p.P349Hfs*26	ENST00000334205	NM_003942.2	347	agC/ag	9/17	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.559907775782851	2		1082	824	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772951	135772951	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs118203724	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	132	631	0	ENST00000298552.3:c.2672del	p.Asn891ThrfsTer40	p.N891Tfs*40	ENST00000298552	NM_001162426.1	891	aAc/ac	21/23	1	2	FACETS	0.791	0.721	0.865	0.791	0.721	0.865	SUBCLONAL	1	TRUE	1	0.559907775782851	2		631	596	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181929	32181929	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	192	1069	0	ENST00000375023.3:c.2125del	p.Gln709SerfsTer22	p.Q709Sfs*22	ENST00000375023	NM_004557.3	709	Cag/ag	13/30	1	2	FACETS	0.843	0.781	0.907	0.843	0.781	0.907	CLONAL	1	TRUE	1	0.559907775782851	2		1069	814	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107258	193107258	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	103	473	0	ENST00000367435.3:c.467G>A	p.Arg156His	p.R156H	ENST00000367435	NM_024529.4	156	cGt/cAt	6/17	1	2	FACETS	0.771	0.694	0.853	0.771	0.694	0.853	SUBCLONAL	1	TRUE	1	0.559907775782851	2		473	477	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	244	812	6	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	0.559907775782851	2		818	836	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	334	677	7	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.983	1	1	0.997	1	CLONAL	2	TRUE	1	0.559907775782851	2		684	568	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969968	161969968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746215864	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	216	855	2	ENST00000366898.1:c.1001G>A	p.Arg334His	p.R334H	ENST00000366898	NM_004562.2	334	cGc/cAc	9/12	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.559907775782851	2		857	667	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007825	45007825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	143	650	0	ENST00000558401.1:c.276del	p.Thr93LeufsTer10	p.T93Lfs*10	ENST00000558401	NM_004048.2	91	aCc/ac	2/4	1	2	FACETS	0.797	0.729	0.868	0.797	0.729	0.868	SUBCLONAL	1	TRUE	1	0.559907775782851	2		650	641	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	271	876	3	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.559907775782851	2		879	936	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962854	2962854	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	201	1140	3	ENST00000396946.4:c.2054del	p.Gly685AlafsTer31	p.G685Afs*31	ENST00000396946	NM_032415.4	685	gGc/gc	16/25	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.559907775782851	2		1143	707	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955112	17955112	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755706305	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	265	1190	10	ENST00000458235.1:c.115del	p.Gln39SerfsTer108	p.Q39Sfs*108	ENST00000458235	NM_000215.3	39	Cag/ag	2/24	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.559907775782851	2		1200	913	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152104	11152104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377573682	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	225	982	0	ENST00000358026.2:c.4388G>A	p.Arg1463His	p.R1463H	ENST00000358026	NM_001128849.1	1463	cGc/cAc	31/36	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.559907775782851	2		982	725	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984672	11984672	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	114	488	0	ENST00000353533.5:c.219-1G>C		p.X73_splice	ENST00000353533	NM_003010.3	73			1	2	FACETS	0.915	0.829	1	0.915	0.829	1	CLONAL	1	TRUE	1	0.559907775782851	2		488	445	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601840	43601840	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758159521	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	165	748	0	ENST00000355710.3:c.884C>T	p.Thr295Met	p.T295M	ENST00000355710	NM_020975.4	295	aCg/aTg	5/20	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.559907775782851	2		748	569	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572113	64572113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769355346	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	206	857	2	ENST00000312049.6:c.1526G>A	p.Gly509Asp	p.G509D	ENST00000312049	NM_130799.2	509	gGt/gAt	10/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.559907775782851	2		859	697	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424138	49424138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200638996	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	257	1230	2	ENST00000301067.7:c.13924G>A	p.Val4642Ile	p.V4642I	ENST00000301067	NM_003482.3	4642	Gtc/Atc	42/54	1	2	FACETS	0.99	0.929	1	0.99	0.929	1	CLONAL	1	TRUE	1	0.559907775782851	2		1232	927	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514790	103514790	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	141	584	0	ENST00000355739.4:c.1291G>T	p.Gly431Ter	p.G431*	ENST00000355739	NM_000123.3	431	Gga/Tga	8/15	1	2	FACETS	0.97	0.889	1	0.97	0.889	1	CLONAL	1	TRUE	1	0.559907775782851	2		584	519	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007794	45007797	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	62	578	0	ENST00000558401.1:c.244_247del	p.Phe82IlefsTer20	p.F82Ifs*20	ENST00000558401	NM_004048.2	81	TCTTtc/tc	2/4	1	2	FACETS	0.367	0.317	0.422	0.367	0.317	0.422	SUBCLONAL	1	TRUE	1	0.559907775782851	2		578	603	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129065	2129066	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	86	880	0	ENST00000219476.3:c.3003dup	p.Ser1002ValfsTer4	p.S1002Vfs*4	ENST00000219476	NM_000548.3	1000	ttg/ttGg	27/42	1	2	FACETS	0.459	0.406	0.516	0.459	0.406	0.516	SUBCLONAL	1	TRUE	1	0.559907775782851	2		880	669	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17129567	17129567	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1372666497	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	281	1179	3	ENST00000285071.4:c.319G>A	p.Val107Ile	p.V107I	ENST00000285071	NM_144997.5	107	Gtc/Atc	5/14	1	2	FACETS	0.933	0.877	0.99	0.933	0.877	0.99	CLONAL	1	TRUE	1	0.559907775782851	2		1182	1076	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880988	37880988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772054394	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	184	971	0	ENST00000269571.5:c.2317G>A	p.Val773Met	p.V773M	ENST00000269571		773	Gtg/Atg	20/27	1	2	FACETS	0.86	0.796	0.927	0.86	0.796	0.927	CLONAL	1	TRUE	1	0.559907775782851	2		971	764	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288765	15288765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1317504991	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	102	263	1	ENST00000263388.2:c.3974G>A	p.Arg1325His	p.R1325H	ENST00000263388	NM_000435.2	1325	cGc/cAc	24/33	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.559907775782851	2		264	286	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210420	36210420	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1299531345	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	209	789	1	ENST00000222270.7:c.413G>A	p.Arg138His	p.R138H	ENST00000222270	NM_014727.1	138	cGc/cAc	2/37	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.559907775782851	2		790	719	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214871	36214871	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	289	1228	12	ENST00000222270.7:c.3302del	p.Pro1101LeufsTer81	p.P1101Lfs*81	ENST00000222270	NM_014727.1	1099	ggC/gg	8/37	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.559907775782851	2		1240	967	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082301	16082301	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	322	1409	0	ENST00000281043.3:c.115G>T	p.Gly39Cys	p.G39C	ENST00000281043	NM_005378.4	39	Ggc/Tgc	2/3	NA	2	FACETS	1	0.961	1			1	INDETERMINATE	1	TRUE	NA	0.559907775782851	2		1409	1127	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933437	49933438	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	217	906	0	ENST00000296474.3:c.2752dup	p.Leu918ProfsTer21	p.L918Pfs*21	ENST00000296474	NM_002447.2	918	ctg/cCtg	11/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.559907775782851	2		906	749	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998127	169998128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs753143066	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	225	1108	5	ENST00000295797.4:c.826dup	p.Thr276AsnfsTer16	p.T276Nfs*16	ENST00000295797	NM_002740.5	273	tta/ttAa	9/18	1	2	FACETS	0.745	0.693	0.798	0.745	0.693	0.798	SUBCLONAL	1	TRUE	1	0.559907775782851	2		1113	1079	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440292	187440292	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750212558	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	132	625	0	ENST00000232014.4:c.2075G>A	p.Arg692His	p.R692H	ENST00000232014	NM_001130845.1	692	cGc/cAc	10/10	1	2	FACETS	0.908	0.829	0.991	0.908	0.829	0.991	CLONAL	1	TRUE	1	0.559907775782851	2		625	519	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541459	187541459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	147	602	0	ENST00000441802.2:c.6281C>T	p.Thr2094Ile	p.T2094I	ENST00000441802	NM_005245.3	2094	aCt/aTt	10/27	1	2	FACETS	0.908	0.833	0.986	0.908	0.833	0.986	CLONAL	1	TRUE	1	0.559907775782851	2		602	578	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748510	43748510	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs774265827	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	162	646	1	ENST00000523873.1:c.464G>T	p.Arg155Leu	p.R155L	ENST00000523873		155	cGc/cTc	6/8	1	2	FACETS	0.929	0.856	1	0.929	0.856	1	CLONAL	1	TRUE	1	0.559907775782851	2		647	623	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521975	157521975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144424476	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	157	655	1	ENST00000346085.5:c.4247G>A	p.Arg1416His	p.R1416H	ENST00000346085	NM_020732.3	1416	cGc/cAc	18/20	1	2	FACETS	0.941	0.866	1	0.941	0.866	1	CLONAL	1	TRUE	1	0.559907775782851	2		656	596	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277152	38277152	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	214	1012	1	ENST00000425967.3:c.1276A>G	p.Ile426Val	p.I426V	ENST00000425967	NM_001174067.1	426	Atc/Gtc	10/19	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.559907775782851	2		1013	751	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020769	37020769	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	231	994	2	ENST00000358127.4:c.76G>T	p.Val26Phe	p.V26F	ENST00000358127	NM_001280556.1	26	Gtt/Ttt	2/10	1	2	FACETS	0.966	0.903	1	0.966	0.903	1	CLONAL	1	TRUE	1	0.559907775782851	2		996	854	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643531	52643532	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	227	682	0	ENST00000394830.3:c.2364dup	p.Val789SerfsTer7	p.V789Sfs*7	ENST00000394830	NM_018313.4	788	-/A	17/30	0.443050468575256	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.443050468575256	1		682	738	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140743	55140745	+	inframe_deletion	In_Frame_Del	DEL	TGG	TGG	-	novel	NA	P-0014636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	226	811	0	ENST00000257290.5:c.1606_1608del	p.Val536del	p.V536del	ENST00000257290	NM_006206.4	535	tTGGtg/ttg	11/23	0.227638894209697	1	FACETS	0.78	0.727	0.835	0.78	0.727	0.835	INDETERMINATE	1	TRUE	0	0.443050468575256	1		811	1018	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839757	27839757	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs747510120	NA	P-0014636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	55	676	0	ENST00000328488.2:c.337A>C	p.Ile113Leu	p.I113L	ENST00000328488	NM_003533.2	113	Att/Ctt	1/1	1	2	FACETS	0.304	0.259	0.353	0.304	0.259	0.353	SUBCLONAL	1	TRUE	1	0.443050468575256	2		676	817	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0014646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	511	714	1	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.616430063060247	2	FACETS	0.944	0.912	0.976	0.944	0.912	0.976	CLONAL	2	TRUE	0	0.616430063060247	2		715	878	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117739669	117739669	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	267	485	0	ENST00000368508.3:c.124G>A	p.Gly42Ser	p.G42S	ENST00000368508	NM_002944.2	42	Ggc/Agc	2/43	0.340686270920228	5	FACETS	0.808	0.758	0.859	0.539	0.505	0.573	INDETERMINATE	2	TRUE	2	0.616430063060247	5		485	1032	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746075	162746075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	109	445	0	ENST00000367921.3:c.2198G>A	p.Arg733Lys	p.R733K	ENST00000367921	NM_006182.2	733	aGg/aAg	16/18	0.616430063060247	5	FACETS	0.556	0.497	0.618	0.139	0.124	0.155	SUBCLONAL	1	TRUE	1	0.616430063060247	5		445	1225	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878051	48878051	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0014646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	426	334	0	ENST00000267163.4:c.3G>A	p.Met1?	p.M1?	ENST00000267163	NM_000321.2	1	atG/atA	1/27	0.596824195121887	3	FACETS	0.872	0.841	0.903	0.872	0.841	0.903	CLONAL	3	TRUE	0	0.616430063060247	3		334	691	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578423	7578423	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	550	762	0	ENST00000269305.4:c.507G>T	p.Met169Ile	p.M169I	ENST00000269305	NM_001126112.2	169	atG/atT	5/11	0.616430063060247	2	FACETS	0.962	0.931	0.994	0.962	0.931	0.994	CLONAL	2	TRUE	0	0.616430063060247	2		762	927	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671027	30671027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768568532	NA	P-0014646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1363	91	727	0	ENST00000376406.3:c.5719C>T	p.Arg1907Trp	p.R1907W	ENST00000376406	NM_014641.2	1907	Cgg/Tgg	12/15	0.364765289202991	4	FACETS	0.328	0.29	0.369	0.082	0.072	0.093	INDETERMINATE	1	TRUE	0	0.616430063060247	4		727	1454	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187987	32187987	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1395	183	854	0	ENST00000375023.3:c.1234C>T	p.Leu412Phe	p.L412F	ENST00000375023	NM_004557.3	412	Ctc/Ttc	7/30	0.364765289202991	4	FACETS	0.608	0.559	0.66	0.152	0.139	0.165	INDETERMINATE	1	TRUE	0	0.616430063060247	4		854	1578	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650056	93650056	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	217	599	0	ENST00000375746.1:c.1607T>C	p.Val536Ala	p.V536A	ENST00000375746	NM_001174167.1	536	gTc/gCc	12/14	0.616430063060247	2	FACETS	0.861	0.802	0.921	0.43	0.401	0.461	CLONAL	1	TRUE	0	0.616430063060247	2		599	818	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0014669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	190	754	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	0.575034821357292	2		754	613	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	137	448	0	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.611	0.556	0.669	0.611	0.556	0.669	SUBCLONAL	1	TRUE	1	0.575034821357292	2		448	780	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170991	56170991	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	68	220	0	ENST00000399503.3:c.1823del	p.Gly608AlafsTer48	p.G608Afs*48	ENST00000399503	NM_005921.1	607	Ggg/gg	10/20	1	2	FACETS	0.622	0.544	0.706	0.622	0.544	0.706	SUBCLONAL	1	TRUE	1	0.575034821357292	2		220	380	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519886	NA	P-0014669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	74	301	0	ENST00000349496.5:c.97T>G	p.Ser33Ala	p.S33A	ENST00000349496	NM_001904.3	33	Tct/Gct	3/15	1	2	FACETS	0.544	0.478	0.615	0.544	0.478	0.615	SUBCLONAL	1	TRUE	1	0.575034821357292	2		301	473	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720650	89720650	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1257124719	NA	P-0014669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	115	265	0	ENST00000371953.3:c.802-1G>A		p.X268_splice	ENST00000371953	NM_000314.4	268			1	2	FACETS	0.943	0.856	1	0.943	0.856	1	CLONAL	1	TRUE	1	0.575034821357292	2		265	424	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155721	56155722	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0014669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	107	350	0	ENST00000399503.3:c.816_817del	p.Arg273SerfsTer27	p.R273Sfs*27	ENST00000399503	NM_005921.1	271	agAAaa/agaa	3/20	1	2	FACETS	0.625	0.562	0.692	0.625	0.562	0.692	SUBCLONAL	1	TRUE	1	0.575034821357292	2		350	595	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0014669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	73	871	4	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.331	0.289	0.377	0.331	0.289	0.377	SUBCLONAL	1	TRUE	1	0.575034821357292	2		875	766	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089592	27089593	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0014669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	221	561	0	ENST00000324856.7:c.2549dup	p.Tyr850Ter	p.Y850*	ENST00000324856	NM_006015.4	850	tat/tAat	8/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.575034821357292	2		561	682	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903690	114903690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1369436357	NA	P-0014669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	259	637	0	ENST00000543371.1:c.694C>T	p.Arg232Trp	p.R232W	ENST00000543371	NM_001198531.1	232	Cgg/Tgg	7/14	1	2	FACETS	0.957	0.898	1	0.957	0.898	1	CLONAL	1	TRUE	1	0.575034821357292	2		637	941	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061091	38061091	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1293965921	NA	P-0014669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	16	94	0	ENST00000250448.2:c.898G>A	p.Ala300Thr	p.A300T	ENST00000250448	NM_004496.3	300	Gcc/Acc	2/2	1	2	FACETS	0.359	0.267	0.468	0.359	0.267	0.468	SUBCLONAL	1	TRUE	1	0.575034821357292	2		94	155	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219940	36219941	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCA	novel	NA	P-0014669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	238	502	0	ENST00000222270.7:c.4743_4746dup	p.Leu1583CysfsTer96	p.L1583Cfs*96	ENST00000222270	NM_014727.1	1581	tgt/tgTGCAt	21/37	1	2	FACETS	0.976	0.913	1	0.976	0.913	1	CLONAL	1	TRUE	1	0.575034821357292	2		502	848	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456660	138456660	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	125	572	0	ENST00000289153.2:c.690del	p.Lys230AsnfsTer3	p.K230Nfs*3	ENST00000289153	NM_006219.2	230	aaA/aa	4/22	0.575034821357292	3	FACETS	0.575	0.519	0.633	0.287	0.259	0.317	SUBCLONAL	1	TRUE	1	0.575034821357292	3		572	974	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589576	67589576	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1289537429	NA	P-0014669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	71	258	0	ENST00000274335.5:c.1344del	p.Lys448AsnfsTer32	p.K448Nfs*32	ENST00000274335		447	Aaa/aa	10/15	1	2	FACETS	0.561	0.491	0.636	0.561	0.491	0.636	SUBCLONAL	1	TRUE	1	0.575034821357292	2		258	440	SUCCESS
APC	324	MSKCC	GRCh37	5	112163705	112163705	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0014669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	63	238	0	ENST00000257430.4:c.1626+2T>A		p.X542_splice	ENST00000257430	NM_000038.5	542			1	2	FACETS	0.548	0.475	0.626	0.548	0.475	0.626	SUBCLONAL	1	TRUE	1	0.575034821357292	2		238	400	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341704	8341704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764664438	NA	P-0014669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	136	431	0	ENST00000356435.5:c.4936C>T	p.Leu1646Phe	p.L1646F	ENST00000356435		1646	Ctc/Ttc	29/35	1	2	FACETS	0.746	0.68	0.815	0.746	0.68	0.815	SUBCLONAL	1	TRUE	1	0.575034821357292	2		431	634	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	221	478	0	ENST00000378444.4:c.4376A>C	p.Asn1459Thr	p.N1459T	ENST00000378444	NM_001123385.1	1459	aAt/aCt	10/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.575034821357292	2		478	733	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937041	48937045	+	frameshift_variant	Frame_Shift_Del	DEL	ATACA	ATACA	TAT	novel	NA	P-0014669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	139	428	0	ENST00000267163.4:c.809_813delinsTAT	p.Asp270ValfsTer2	p.D270Vfs*2	ENST00000267163	NM_000321.2	270	gATACA/gTAT	8/27	0.575034821357292	1	FACETS	0.944	0.87	1	0.944	0.87	1	CLONAL	1	TRUE	0	0.575034821357292	1		428	365	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-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	60	256	2	ENST00000274335.5:c.1283_1299+28delinsCAAA		p.X428_splice	ENST00000274335		428		9/15	1	2	FACETS	0.64	0.555	0.732	0.64	0.555	0.732	SUBCLONAL	1	TRUE	1	0.575034821357292	2		258	326	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	119	460	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	0.28	2		460	802	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061215	38061235	+	inframe_deletion	In_Frame_Del	DEL	GCAGCCGTTCTCGAACATGTT	GCAGCCGTTCTCGAACATGTT	-	novel	NA	P-0014699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	69	384	0	ENST00000250448.2:c.754_774del	p.Asn252_Cys258del	p.N252_C258del	ENST00000250448	NM_004496.3	252	AACATGTTCGAGAACGGCTGC/-	2/2	1	2	FACETS	0.756	0.658	0.862	0.756	0.658	0.862	SUBCLONAL	1	TRUE	1	0.28	2		384	652	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857509	68857510	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0014699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	109	280	0	ENST00000261769.5:c.2145_2146del	p.Gly716AsnfsTer31	p.G716Nfs*31	ENST00000261769	NM_004360.3	715	gGA/g	13/16	0.286119460215237	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.28	1		280	617	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508342	106508342	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	55	218	0	ENST00000359195.3:c.336G>C	p.Lys112Asn	p.K112N	ENST00000359195	NM_002649.2	112	aaG/aaC	2/11	1	2	FACETS	0.757	0.648	0.876	0.757	0.648	0.876	SUBCLONAL	1	TRUE	1	0.28	2		218	519	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	27	720	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.131	0.103	0.163	0.131	0.103	0.163	SUBCLONAL	1	TRUE	1	0.52	2		721	792	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0014727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	64	711	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	1	2	FACETS	0.203	0.175	0.234	0.203	0.175	0.234	SUBCLONAL	1	TRUE	1	0.52	2		711	1211	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0014734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	33	458	1	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	1	2	FACETS	0.528	0.428	0.642	0.528	0.428	0.642	SUBCLONAL	1	TRUE	1	0.11	2		459	1137	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0014737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	96	501	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.28	2		501	677	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0014737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	75	381	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	1	2	FACETS	0.773	0.677	0.876	0.773	0.677	0.876	SUBCLONAL	1	TRUE	1	0.28	2		381	693	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111467	8111468	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0014737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	120	359	0	ENST00000346208.3:c.954dup	p.Asn319GlufsTer33	p.N319Efs*33	ENST00000346208		318	gcg/gcGg	5/6	1	2	FACETS	0.908	0.819	1	0.908	0.819	1	CLONAL	1	TRUE	1	0.28	2		359	944	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870996	12870996	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	51	280	2	ENST00000228872.4:c.223G>T	p.Glu75Ter	p.E75*	ENST00000228872	NM_004064.3	75	Gag/Tag	1/3	1	2	FACETS	0.625	0.531	0.728	0.625	0.531	0.728	SUBCLONAL	1	TRUE	1	0.28	2		282	583	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171747	36171757	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	ATCTGCCTTGT	ATCTGCCTTGT	-	novel	NA	P-0014737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	73	223	0	ENST00000300305.3:c.808_818del	p.Thr270ProfsTer326	p.T270Pfs*326	ENST00000300305		270	ACAAGGCAGATc/c	7/8	1	2	FACETS	0.921	0.807	1	0.921	0.807	1	CLONAL	1	TRUE	1	0.28	2		223	566	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	309	766	0				ENST00000310581	NM_198253.2	-/1132			0.795188544809676	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.795188544809676	1		766	450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0014760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	513	773	2	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.73030296180744	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.795188544809676	1		775	724	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43806120	43806120	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	337	550	0	ENST00000372470.3:c.916C>A	p.Gln306Lys	p.Q306K	ENST00000372470	NM_005373.2	306	Cag/Aag	6/12	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.795188544809676	2		550	831	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762439	41762439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371618406	NA	P-0014760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	48	609	0	ENST00000301178.4:c.2119C>T	p.Arg707Cys	p.R707C	ENST00000301178	NM_021913.4	707	Cgt/Tgt	18/20	1	2	FACETS	0.126	0.106	0.148	0.126	0.106	0.148	SUBCLONAL	1	TRUE	1	0.795188544809676	2		609	959	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924750	49924750	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759659890	NA	P-0014760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	364	619	0	ENST00000296474.3:c.4193G>A	p.Arg1398Gln	p.R1398Q	ENST00000296474	NM_002447.2	1398	cGg/cAg	20/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.795188544809676	2		619	834	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133814	55133814	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5511	14194	489	0	ENST00000257290.5:c.1027C>G	p.Pro343Ala	p.P343A	ENST00000257290	NM_006206.4	343	Cca/Gca	7/23	0.795188544809676	30	FACETS	0.999	0.993	1			1	CLONAL	22	TRUE	NA	0.795188544809676	30		489	19705	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589591	67589592	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0014760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	286	321	0	ENST00000274335.5:c.1355dup	p.Tyr452Ter	p.Y452*	ENST00000274335		452	tat/tAat	10/15	1	2	FACETS	0.979	0.925	1	0.979	0.925	1	CLONAL	1	TRUE	1	0.795188544809676	2		321	735	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591091	67591092	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTATGG	novel	NA	P-0014760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	256	358	0	ENST00000274335.5:c.1689_1690insGGTATG	p.Met563_Asn564insGlyMet	p.M563_N564insGM	ENST00000274335		562	cgt/cGTATGGgt	12/15	1	2	FACETS	0.886	0.833	0.939	0.886	0.833	0.939	CLONAL	1	TRUE	1	0.795188544809676	2		358	727	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115903	8115904	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0014763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	125	474	0	ENST00000346208.3:c.1251dup	p.Thr418HisfsTer89	p.T418Hfs*89	ENST00000346208		417	acc/aCcc	6/6	0.228507523354768	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.228507523354768	4		474	596	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396468	396468	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs774697501	NA	P-0014763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	88	766	0	ENST00000262320.3:c.558G>C	p.Gln186His	p.Q186H	ENST00000262320	NM_003502.3	186	caG/caC	2/11	0.228507523354768	6	FACETS	1	0.949	1			1	CLONAL	1	TRUE	NA	0.228507523354768	6		766	991	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396575	396575	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs770999059	NA	P-0014763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	66	616	1	ENST00000262320.3:c.451G>C	p.Asp151His	p.D151H	ENST00000262320	NM_003502.3	151	Gat/Cat	2/11	0.228507523354768	6	FACETS	1	0.924	1			1	CLONAL	1	TRUE	NA	0.228507523354768	6		617	767	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678747	52678747	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	54	576	0	ENST00000394830.3:c.872A>G	p.Glu291Gly	p.E291G	ENST00000394830	NM_018313.4	291	gAa/gGa	9/30	0.228507523354768	4	FACETS	0.96	0.819	1	0.48	0.409	0.557	CLONAL	1	TRUE	2	0.228507523354768	4		576	605	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527259	187527259	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201982861	NA	P-0014763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	41	521	2	ENST00000441802.2:c.10315G>A	p.Val3439Ile	p.V3439I	ENST00000441802	NM_005245.3	3439	Gtc/Atc	17/27	0.194325310788337	4	FACETS	0.816	0.679	0.969	0.408	0.339	0.485	CLONAL	1	TRUE	2	0.228507523354768	4		523	540	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217299	11217299	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519779	NA	P-0014767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	212	618	0	ENST00000361445.4:c.4379T>C	p.Leu1460Pro	p.L1460P	ENST00000361445	NM_004958.3	1460	cTt/cCt	30/58	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.345947583735706	2		618	1108	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905498	50905498	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	231	762	0	ENST00000440232.2:c.626T>C	p.Phe209Ser	p.F209S	ENST00000440232	NM_002691.3	209	tTc/tCc	6/27	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.345947583735706	2		762	1309	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130597	29130598	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCC	novel	NA	P-0014767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	118	407	0	ENST00000328354.6:c.109_112dup	p.Ile38ArgfsTer40	p.I38Rfs*40	ENST00000328354	NM_007194.3	38	ata/aGGCAta	2/15	1	2	FACETS	0.802	0.723	0.885	0.802	0.723	0.885	CLONAL	1	TRUE	1	0.345947583735706	2		407	851	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443626	52443626	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0014767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	143	408	0	ENST00000460680.1:c.68-2A>G		p.X23_splice	ENST00000460680	NM_004656.3	23			0.345947583735706	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.345947583735706	1		408	679	SUCCESS
APC	324	MSKCC	GRCh37	5	112175361	112175361	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	64	209	0	ENST00000257430.4:c.4070G>C	p.Gly1357Ala	p.G1357A	ENST00000257430	NM_000038.5	1357	gGa/gCa	16/16	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.345947583735706	2		209	367	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839775	27839775	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	118	424	0	ENST00000328488.2:c.319G>T	p.Asp107Tyr	p.D107Y	ENST00000328488	NM_003533.2	107	Gat/Tat	1/1	1	2	FACETS	0.796	0.718	0.879	0.796	0.718	0.879	SUBCLONAL	1	TRUE	1	0.345947583735706	2		424	857	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	75	766	0				ENST00000310581	NM_198253.2	-/1132			0.291646180772147	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.332417739073051	1		766	271	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0014770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	245	621	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	0.995	1	CLONAL	2	TRUE	1	0.332417739073051	2		621	693	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162113	22162113	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	220	352	0	ENST00000215832.6:c.142A>G	p.Lys48Glu	p.K48E	ENST00000215832	NM_002745.4	48	Aaa/Gaa	2/9	1	2	FACETS	0.836	0.785	0.887	1	0.995	1	CLONAL	3	TRUE	1	0.332417739073051	2		352	528	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042162	42042163	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	22	553	1	ENST00000219905.7:c.6360dup	p.Asp2121Ter	p.D2121*	ENST00000219905	NM_001164273.1	2119	-/T	17/24	0.525057111348731	1	FACETS	0.171	0.132	0.216	0.171	0.132	0.216	SUBCLONAL	1	TRUE	0	0.525057111348731	1		554	362	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527503	29527503	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	18	427	0	ENST00000356175.3:c.952G>T	p.Glu318Ter	p.E318*	ENST00000356175	NM_000267.3	318	Gaa/Taa	9/57	0.525057111348731	1	FACETS	0.168	0.126	0.218	0.168	0.126	0.218	SUBCLONAL	1	TRUE	0	0.525057111348731	1		427	301	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665760	29665763	+	frameshift_variant	Frame_Shift_Del	DEL	CAGT	CAGT	-	novel	NA	P-0014777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	18	403	0	ENST00000356175.3:c.6797_6800del	p.Ser2266LysfsTer3	p.S2266Kfs*3	ENST00000356175	NM_000267.3	2265	aaCAGT/aa	45/57	0.525057111348731	1	FACETS	0.189	0.142	0.245	0.189	0.142	0.245	SUBCLONAL	1	TRUE	0	0.525057111348731	1		403	267	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906658	50906771	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCAGGGGTGGCTGGGGTTCTAGAACATTCTGGAAGTAGGGGAATCCGAGGCAGGGCAACCACCAGGGTGACCCAATGTGCTCCCACCCCCAGGCCTGGTCCACCTTCATCCGTA	TCAGGGGTGGCTGGGGTTCTAGAACATTCTGGAAGTAGGGGAATCCGAGGCAGGGCAACCACCAGGGTGACCCAATGTGCTCCCACCCCCAGGCCTGGTCCACCTTCATCCGTA	-	novel	NA	P-0014777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	11	182	0	ENST00000440232.2:c.1138-89_1162del		p.X380_splice	ENST00000440232	NM_002691.3	380		10/27	1	2	FACETS	0.364	0.253	0.5	0.364	0.253	0.5	SUBCLONAL	1	TRUE	1	0.525057111348731	2		182	115	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020754	37020754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	43	634	2	ENST00000358127.4:c.91C>T	p.Arg31Trp	p.R31W	ENST00000358127	NM_001280556.1	31	Cgg/Tgg	2/10	0.268344802872177	3	FACETS	0.427	0.357	0.506			1	SUBCLONAL	1	TRUE	NA	0.384370642625802	3		636	624	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416680	121416680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	32	734	0	ENST00000257555.6:c.109C>T	p.Leu37Phe	p.L37F	ENST00000257555		37	Ctc/Ttc	1/10	1	2	FACETS	0.313	0.253	0.381	0.313	0.253	0.381	SUBCLONAL	1	TRUE	1	0.384370642625802	2		734	532	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520126	9520126	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	55	387	0	ENST00000353224.5:c.2143C>A	p.Gln715Lys	p.Q715K	ENST00000353224	NM_177990.2	715	Caa/Aaa	10/10	1	2	FACETS	0.69	0.591	0.796	0.69	0.591	0.796	SUBCLONAL	1	TRUE	1	0.384370642625802	2		387	415	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927018	131927018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753680691	NA	P-0014808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	97	409	0	ENST00000265335.6:c.1555C>T	p.Arg519Cys	p.R519C	ENST00000265335		519	Cgt/Tgt	10/25	0.384370642625802	3	FACETS	1	0.936	1	0.356	0.318	0.396	CLONAL	1	TRUE	0	0.384370642625802	3		409	564	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8339035	8339035	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1446928744	NA	P-0014808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	37	489	0	ENST00000356435.5:c.5266C>A	p.Gln1756Lys	p.Q1756K	ENST00000356435		1756	Caa/Aaa	32/35	0.3645815886809	4	FACETS	0.406	0.333	0.487	0.203	0.166	0.244	SUBCLONAL	1	TRUE	2	0.384370642625802	4		489	657	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0014809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	22	757	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.659	0.509	0.835	0.659	0.509	0.835	SUBCLONAL	1	TRUE	1	0.11	2		758	607	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117732	115117732	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	30	541	0	ENST00000257566.3:c.703A>T	p.Ser235Cys	p.S235C	ENST00000257566	NM_016569.3	235	Agt/Tgt	3/8	1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	1	0.11	2		541	531	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957525	1957525	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	41	827	0	ENST00000382891.5:c.2624G>C	p.Gly875Ala	p.G875A	ENST00000382891	NM_133335.3	875	gGg/gCg	14/22	1	2	FACETS	0.917	0.761	1	0.917	0.761	1	CLONAL	1	TRUE	1	0.11	2		827	813	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	188	766	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.482844332028478	2		766	555	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0014815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	466	655	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.482054751880546	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.482844332028478	2		655	852	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974730	21974730	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	181	316	0	ENST00000304494.5:c.97G>T	p.Glu33Ter	p.E33*	ENST00000304494	NM_000077.4	33	Gag/Tag	1/3	0.482844332028478	2	FACETS	0.926	0.865	0.987	0.926	0.865	0.987	CLONAL	2	TRUE	0	0.482844332028478	2		316	405	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981167	201981168	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0014815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	512	843	0	ENST00000359651.3:c.248dup	p.Asn83LysfsTer9	p.N83Kfs*9	ENST00000359651		82	-/A	2/8	0.203961171633938	5	FACETS	0.889	0.852	0.926	0.889	0.852	0.926	INDETERMINATE	3	TRUE	2	0.482844332028478	5		843	1371	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5463082	5463082	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1288445239	NA	P-0014815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	117	285	0	ENST00000381577.3:c.643G>C	p.Asp215His	p.D215H	ENST00000381577	NM_014143.3	215	Gat/Cat	4/7	0.426453215956367	5	FACETS	1	0.964	1			1	CLONAL	1	TRUE	NA	0.482844332028478	5		285	732	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781092	135781092	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	320	545	0	ENST00000298552.3:c.1873G>T	p.Glu625Ter	p.E625*	ENST00000298552	NM_001162426.1	625	Gag/Tag	15/23	0.482844332028478	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.482844332028478	2		545	598	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0014818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	136	637	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.901	0.818	0.988	0.901	0.818	0.988	CLONAL	1	TRUE	1	0.31	2		637	974	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0014818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	324	415	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.238661085631484	3	FACETS	0.838	0.794	0.884	0.838	0.794	0.884	CLONAL	3	TRUE	0	0.31	3		415	960	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911593	114911593	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	331	519	0	ENST00000543371.1:c.1111G>C	p.Glu371Gln	p.E371Q	ENST00000543371	NM_001198531.1	371	Gag/Cag	10/14	0.27926741422109	3	FACETS	0.912	0.861	0.965	0.912	0.861	0.965	CLONAL	2	TRUE	1	0.31	3		519	1352	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161293455	161293455	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	196	295	0	ENST00000367975.2:c.72C>G	p.Ile24Met	p.I24M	ENST00000367975	NM_003001.3	24	atC/atG	2/6	0.272583110986119	4	FACETS	0.843	0.781	0.909	0.422	0.39	0.455	CLONAL	2	TRUE	0	0.31	4		295	982	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739115	40739115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	281	398	0	ENST00000373198.4:c.3169G>A	p.Glu1057Lys	p.E1057K	ENST00000373198	NM_133170.3	1057	Gag/Aag	24/32	0.3	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.31	3		398	1001	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907092	32907092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	113	316	0	ENST00000380152.3:c.1477C>T	p.Pro493Ser	p.P493S	ENST00000380152		493	Cca/Tca	10/27	0.3	2	FACETS	0.959	0.864	1	0.48	0.431	0.531	CLONAL	1	TRUE	0	0.31	2		316	760	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244094	41244094	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80357175	NA	P-0014818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	138	459	0	ENST00000357654.3:c.3454G>A	p.Asp1152Asn	p.D1152N	ENST00000357654	NM_007294.3	1152	Gac/Aac	10/23	0.28767676746433	3	FACETS	0.842	0.764	0.924	0.421	0.382	0.462	CLONAL	1	TRUE	1	0.31	3		459	1222	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22413244	22413244	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326906815	NA	P-0014818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	25	37	0	ENST00000344548.3:c.371C>T	p.Ser124Phe	p.S124F	ENST00000344548	NM_001039802.1	124	tCt/tTt	6/7	0.262461412798782	2	FACETS	0.896	0.738	1	1	0.933	1	CLONAL	3	TRUE	0	0.31	2		37	60	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982319	201982319	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1354	154	638	0	ENST00000359651.3:c.698G>C	p.Arg233Pro	p.R233P	ENST00000359651		233	cGt/cCt	6/8	0.238661085631484	3	FACETS	0.761	0.694	0.832	0.254	0.231	0.278	SUBCLONAL	1	TRUE	0	0.31	3		638	1508	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982361	201982361	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755079997	NA	P-0014818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1585	179	766	0	ENST00000359651.3:c.740G>A	p.Arg247Gln	p.R247Q	ENST00000359651		247	cGa/cAa	6/8	0.238661085631484	3	FACETS	0.756	0.694	0.821	0.252	0.231	0.274	SUBCLONAL	1	TRUE	0	0.31	3		766	1764	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420471	49420471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	135	470	0	ENST00000301067.7:c.15278C>T	p.Ser5093Phe	p.S5093F	ENST00000301067	NM_003482.3	5093	tCc/tTc	48/54	0.28767676746433	3	FACETS	0.78	0.707	0.857	0.39	0.353	0.429	SUBCLONAL	1	TRUE	1	0.31	3		470	1290	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519096	103519096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	136	431	0	ENST00000355739.4:c.2434G>A	p.Asp812Asn	p.D812N	ENST00000355739	NM_000123.3	812	Gat/Aat	11/15	0.3	2	FACETS	0.888	0.807	0.974	0.444	0.403	0.487	CLONAL	1	TRUE	0	0.31	2		431	988	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519159	103519159	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	106	352	0	ENST00000355739.4:c.2497G>C	p.Glu833Gln	p.E833Q	ENST00000355739	NM_000123.3	833	Gaa/Caa	11/15	0.3	2	FACETS	0.876	0.785	0.972	0.438	0.392	0.486	CLONAL	1	TRUE	0	0.31	2		352	781	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748206	43748206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	234	510	0	ENST00000382044.4:c.2600C>T	p.Ser867Leu	p.S867L	ENST00000382044	NM_001141980.1	867	tCa/tTa	12/28	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.31	2		510	1186	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820641	3820641	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766849648	NA	P-0014818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1313	437	668	2	ENST00000262367.5:c.2810C>T	p.Pro937Leu	p.P937L	ENST00000262367	NM_004380.2	937	cCg/cTg	14/31	0.28767676746433	3	FACETS	0.93	0.885	0.977	0.93	0.885	0.977	CLONAL	2	TRUE	1	0.31	3		670	1750	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9927969	9927969	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	106	330	0	ENST00000330684.3:c.1770del	p.Ala593HisfsTer61	p.A593Hfs*61	ENST00000330684	NM_001134407.1	590	aaA/aa	8/13	0.28767676746433	3	FACETS	0.774	0.693	0.861	0.387	0.346	0.431	SUBCLONAL	1	TRUE	1	0.31	3		330	1020	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483087	29483087	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0014818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	291	443	0	ENST00000356175.3:c.147C>G	p.Tyr49Ter	p.Y49*	ENST00000356175	NM_000267.3	49	taC/taG	2/57	0.21491563471403	4	FACETS	0.995	0.935	1	0.995	0.935	1	CLONAL	2	TRUE	2	0.31	4		443	1236	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219381	1219381	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	368	593	2	ENST00000326873.7:c.433G>T	p.Glu145Ter	p.E145*	ENST00000326873	NM_000455.4	145	Gag/Tag	3/10	0.3	2	FACETS	0.877	0.831	0.924	0.877	0.831	0.924	CLONAL	2	TRUE	0	0.31	2		595	1353	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602869	10602869	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	546	747	0	ENST00000171111.5:c.709C>G	p.Leu237Val	p.L237V	ENST00000171111	NM_203500.1	237	Ctg/Gtg	3/6	0.3	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.31	2		747	1718	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646222	215646222	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	36	194	0	ENST00000260947.4:c.376G>C	p.Asp126His	p.D126H	ENST00000260947	NM_000465.2	126	Gat/Cat	4/11	0.28767676746433	3	FACETS	0.49	0.402	0.588	0.245	0.201	0.294	SUBCLONAL	1	TRUE	1	0.31	3		194	548	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523357	9523357	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	117	406	0	ENST00000353224.5:c.1880G>T	p.Trp627Leu	p.W627L	ENST00000353224	NM_177990.2	627	tGg/tTg	9/10	0.3	3	FACETS	0.819	0.737	0.906	0.409	0.368	0.453	CLONAL	1	TRUE	1	0.31	3		406	1065	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920326	134920326	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1385600362	NA	P-0014818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	90	351	0	ENST00000398015.3:c.2141G>T	p.Gly714Val	p.G714V	ENST00000398015	NM_004441.4	714	gGg/gTg	12/16	1	2	FACETS	0.848	0.752	0.949	0.848	0.752	0.949	CLONAL	1	TRUE	1	0.31	2		351	685	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198222	185198222	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs994419878	NA	P-0014818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	161	399	3	ENST00000265026.3:c.2704C>T	p.His902Tyr	p.H902Y	ENST00000265026	NM_004721.4	902	Cac/Tac	13/14	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.31	2		402	955	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332577	153332577	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	101	313	0	ENST00000281708.4:c.379C>T	p.Gln127Ter	p.Q127*	ENST00000281708	NM_033632.3	127	Cag/Tag	2/12	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.31	2		313	592	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517903	187517903	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0014818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	121	366	0	ENST00000441802.2:c.12791C>G	p.Ser4264Ter	p.S4264*	ENST00000441802	NM_005245.3	4264	tCa/tGa	25/27	1	2	FACETS	0.834	0.753	0.92	0.834	0.753	0.92	CLONAL	1	TRUE	1	0.31	2		366	936	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160720	56160720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	94	325	0	ENST00000399503.3:c.994G>A	p.Asp332Asn	p.D332N	ENST00000399503	NM_005921.1	332	Gac/Aac	4/20	0.27926741422109	3	FACETS	0.757	0.673	0.848	0.379	0.336	0.424	SUBCLONAL	1	TRUE	1	0.31	3		325	925	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751159	57751159	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	99	242	0	ENST00000274289.3:c.1708A>T	p.Thr570Ser	p.T570S	ENST00000274289	NM_006622.3	570	Acg/Tcg	12/14	0.27926741422109	3	FACETS	0.978	0.873	1	0.489	0.436	0.545	CLONAL	1	TRUE	1	0.31	3		242	754	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041017	112041017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	171	257	0	ENST00000368678.4:c.238G>A	p.Gly80Arg	p.G80R	ENST00000368678		80	Gga/Aga	3/13	0.262461412798782	2	FACETS	0.895	0.828	0.966	0.895	0.828	0.966	CLONAL	2	TRUE	0	0.31	2		257	616	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004922	150004922	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	133	298	0	ENST00000253339.5:c.1303C>G	p.Gln435Glu	p.Q435E	ENST00000253339		435	Cag/Gag	3/7	0.262461412798782	2	FACETS	1	0.985	1	0.702	0.64	0.767	CLONAL	1	TRUE	0	0.31	2		298	611	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382242	152382242	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	228	324	0	ENST00000206249.3:c.1352T>G	p.Ile451Ser	p.I451S	ENST00000206249	NM_000125.3	451	aTt/aGt	6/8	0.262461412798782	2	FACETS	0.986	0.922	1	0.986	0.922	1	CLONAL	2	TRUE	0	0.31	2		324	746	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481397	140481397	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913376	NA	P-0014818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	109	315	0	ENST00000288602.6:c.1411G>T	p.Val471Phe	p.V471F	ENST00000288602	NM_004333.4	471	Gtc/Ttc	11/18	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.31	2		315	687	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815600	139815600	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	285	522	0	ENST00000247668.2:c.1071G>T	p.Lys357Asn	p.K357N	ENST00000247668	NM_021138.3	357	aaG/aaT	9/11	0.3	2	FACETS	0.828	0.779	0.879	0.828	0.779	0.879	CLONAL	2	TRUE	0	0.31	2		522	1110	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728625	190728639	+	frameshift_variant	Frame_Shift_Del	DEL	ATTATCTAATCAACC	ATTATCTAATCAACC	G	novel	NA	P-0014818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	145	423	0	ENST00000441310.2:c.2013_2027delinsG	p.Leu672LysfsTer3	p.L672Kfs*3	ENST00000441310	NM_000534.4	671	tcATTATCTAATCAACCa/tcGa	10/13	0.28767676746433	3	FACETS	0.9	0.82	0.986	0.45	0.41	0.493	CLONAL	1	TRUE	1	0.31	3		423	1200	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0014821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	411	584	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.508326261227448	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.508326261227448	1		586	1114	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458147	120458147	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1325403451	NA	P-0014821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	371	493	0	ENST00000256646.2:c.7198C>T	p.Arg2400Ter	p.R2400*	ENST00000256646	NM_024408.3	2400	Cga/Tga	34/34	0.508326261227448	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.508326261227448	1		493	1056	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881509	48881509	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	240	284	0	ENST00000267163.4:c.232del	p.Trp78GlyfsTer33	p.W78Gfs*33	ENST00000267163	NM_000321.2	77	acT/ac	2/27	0.508326261227448	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.508326261227448	1		284	665	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843302	128843302	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1599	500	681	0	ENST00000249373.3:c.409G>C	p.Asp137His	p.D137H	ENST00000249373	NM_005631.4	137	Gac/Cac	2/12	1	2	FACETS	0.937	0.894	0.981	0.937	0.894	0.981	CLONAL	1	TRUE	1	0.508326261227448	2		681	2099	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317451	1317451	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1490	494	568	0	ENST00000400841.2:c.614A>G	p.Glu205Gly	p.E205G	ENST00000400841		205	gAg/gGg	5/6	1	2	FACETS	0.98	0.935	1	0.98	0.935	1	CLONAL	1	TRUE	1	0.508326261227448	2		568	1984	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797435	45797435	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	143	618	0	ENST00000450313.1:c.1084G>C	p.Ala362Pro	p.A362P	ENST00000450313	NM_012222.2	362	Gcc/Ccc	12/16	0.244969868999132	4	FACETS	1	0.936	1	0.519	0.471	0.568	CLONAL	1	TRUE	2	0.275139879993026	4		618	1278	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874263	155874263	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1557960039	NA	P-0014825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	145	527	0	ENST00000368323.3:c.268A>G	p.Met90Val	p.M90V	ENST00000368323	NM_006912.5	90	Atg/Gtg	5/6	0.244969868999132	4	FACETS	1	0.932	1	0.515	0.468	0.564	CLONAL	1	TRUE	2	0.275139879993026	4		527	1306	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202673	108202676	+	frameshift_variant	Frame_Shift_Del	DEL	CAAA	CAAA	-	rs1060501547	NA	P-0014825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	305	372	0	ENST00000278616.4:c.7699_7702del	p.Asn2567GlufsTer5	p.N2567Efs*5	ENST00000278616	NM_000051.3	2566	gCAAAc/gc	52/63	0.275139879993026	3	FACETS	0.929	0.878	0.981	0.929	0.878	0.981	CLONAL	3	TRUE	0	0.275139879993026	3		372	905	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59793401	59793401	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	97	448	0	ENST00000259008.2:c.2403T>A	p.Asn801Lys	p.N801K	ENST00000259008	NM_032043.2	801	aaT/aaA	17/20	0.244969868999132	4	FACETS	0.851	0.757	0.952	0.426	0.378	0.476	CLONAL	1	TRUE	2	0.275139879993026	4		448	1056	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056498	26056498	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs529286462	NA	P-0014825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	51	150	0	ENST00000343677.2:c.159G>C	p.Glu53Asp	p.E53D	ENST00000343677	NM_005319.3	53	gaG/gaC	1/1	0.278495755856892	4	FACETS	1	0.922	1	0.565	0.481	0.657	CLONAL	1	TRUE	2	0.275139879993026	4		150	418	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289010	33289010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	97	450	0	ENST00000374542.5:c.542C>T	p.Thr181Ile	p.T181I	ENST00000374542	NM_001141970.1	181	aCc/aTc	3/8	0.278495755856892	4	FACETS	0.832	0.74	0.931	0.416	0.37	0.466	CLONAL	1	TRUE	2	0.275139879993026	4		450	1080	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0014828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	64	393	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	0.672418588514468	3	FACETS	0.365	0.316	0.419	0.183	0.158	0.21	SUBCLONAL	1	FALSE	1	0.724468809065143	3		393	659	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900060	151900060	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	56	283	0	ENST00000262189.6:c.4051del	p.Arg1351GlyfsTer23	p.R1351Gfs*23	ENST00000262189	NM_170606.2	1351	Agg/gg	26/59	0.655202398452658	5	FACETS	0.405	0.346	0.47	0.101	0.086	0.118	SUBCLONAL	1	FALSE	1	0.724468809065143	5		283	797	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845959	151845959	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	72	468	2	ENST00000262189.6:c.13053del	p.Lys4351AsnfsTer5	p.K4351Nfs*5	ENST00000262189	NM_170606.2	4351	aaA/aa	52/59	0.655202398452658	5	FACETS	0.364	0.317	0.416	0.091	0.079	0.104	SUBCLONAL	1	FALSE	1	0.724468809065143	5		470	1138	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941629	48941629	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs1131690860	NA	P-0014828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	18	122	0	ENST00000267163.4:c.940-1G>T		p.X314_splice	ENST00000267163	NM_000321.2	314			0.724468809065143	3	FACETS	0.209	0.157	0.271	0.104	0.078	0.136	SUBCLONAL	1	FALSE	1	0.724468809065143	3		122	324	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115267956	115267956	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0014828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	67	383	0	ENST00000438362.2:c.1779-2A>G		p.X593_splice	ENST00000438362	NM_001242891.1	593			0.724468809065143	4	FACETS	0.346	0.3	0.397	0.173	0.15	0.199	SUBCLONAL	1	FALSE	2	0.724468809065143	4		383	921	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268841	115268841	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	175	393	0	ENST00000438362.2:c.1769del	p.Phe590SerfsTer36	p.F590Sfs*36	ENST00000438362	NM_001242891.1	590	tTc/tc	14/20	0.724468809065143	4	FACETS	0.865	0.796	0.937	0.433	0.398	0.469	CLONAL	1	FALSE	2	0.724468809065143	4		393	963	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494960	56494960	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	72	422	0	ENST00000267101.3:c.3317C>T	p.Ala1106Val	p.A1106V	ENST00000267101	NM_001982.3	1106	gCt/gTt	27/28	0.507891932823524	4	FACETS	0.417	0.363	0.475	0.139	0.121	0.159	SUBCLONAL	1	FALSE	1	0.724468809065143	4		422	822	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579533	7579534	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTCAA	novel	NA	P-0014828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	236	643	0	ENST00000269305.4:c.149_153dup	p.Gln52LeufsTer73	p.Q52Lfs*73	ENST00000269305	NM_001126112.2	51	-/TTGAA	4/11	0.672418588514468	3	FACETS	1	0.947	1	0.507	0.474	0.541	CLONAL	1	FALSE	1	0.724468809065143	3		643	875	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534449	63534449	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	91	581	0	ENST00000307078.5:c.1072C>A	p.Leu358Met	p.L358M	ENST00000307078	NM_004655.3	358	Ctg/Atg	5/11	0.724468809065143	3	FACETS	0.378	0.335	0.424	0.189	0.167	0.212	SUBCLONAL	1	FALSE	1	0.724468809065143	3		581	906	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18958620	18958620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	75	565	3	ENST00000262803.5:c.439G>A	p.Gly147Arg	p.G147R	ENST00000262803	NM_002911.3	147	Gga/Aga	3/24	0.724468809065143	3	FACETS	0.333	0.291	0.379	0.167	0.145	0.19	SUBCLONAL	1	FALSE	1	0.724468809065143	3		568	846	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47600641	47600641	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	76	486	0	ENST00000263735.4:c.116T>C	p.Phe39Ser	p.F39S	ENST00000263735	NM_002354.2	39	tTt/tCt	2/9	0.514693282836583	4	FACETS	0.472	0.414	0.536	0.236	0.207	0.268	SUBCLONAL	1	FALSE	2	0.724468809065143	4		486	766	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543874	212543874	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	114	457	0	ENST00000342788.4:c.1525A>G	p.Ser509Gly	p.S509G	ENST00000342788	NM_005235.2	509	Agt/Ggt	13/28	0.724468809065143	3	FACETS	0.516	0.464	0.571	0.258	0.232	0.286	SUBCLONAL	1	FALSE	1	0.724468809065143	3		457	831	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582243	52582243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1163354335	NA	P-0014828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	58	153	0	ENST00000394830.3:c.4585C>T	p.Arg1529Cys	p.R1529C	ENST00000394830	NM_018313.4	1529	Cgc/Tgc	30/30	0.724468809065143	3	FACETS	0.665	0.575	0.762	0.332	0.287	0.381	SUBCLONAL	1	FALSE	1	0.724468809065143	3		153	328	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294998	1294998	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	24	81	1	ENST00000310581.5:c.107G>A	p.Trp36Ter	p.W36*	ENST00000310581	NM_198253.2	36	tGg/tAg	1/16	0.724468809065143	3	FACETS	0.442	0.349	0.549	0.221	0.174	0.275	SUBCLONAL	1	FALSE	1	0.724468809065143	3		82	204	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876394	35876394	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1264	131	500	0	ENST00000303115.3:c.1186A>G	p.Asn396Asp	p.N396D	ENST00000303115	NM_002185.3	396	Aat/Gat	8/8	0.724468809065143	4	FACETS	0.447	0.404	0.493	0.149	0.134	0.165	SUBCLONAL	1	FALSE	1	0.724468809065143	4		500	1395	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177930	56177930	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	131	428	0	ENST00000399503.3:c.2903A>G	p.Asn968Ser	p.N968S	ENST00000399503	NM_005921.1	968	aAc/aGc	14/20	0.724468809065143	3	FACETS	0.559	0.506	0.613	0.279	0.253	0.307	SUBCLONAL	1	FALSE	1	0.724468809065143	3		428	882	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053239	180053239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	58	602	1	ENST00000261937.6:c.1130G>A	p.Gly377Glu	p.G377E	ENST00000261937	NM_182925.4	377	gGg/gAg	9/30	0.346435010674605	3	FACETS	0.255	0.218	0.295	0.085	0.072	0.099	INDETERMINATE	1	FALSE	0	0.724468809065143	3		603	857	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855024	76855024	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	52	406	0	ENST00000373344.5:c.5812A>G	p.Lys1938Glu	p.K1938E	ENST00000373344	NM_000489.3	1938	Aaa/Gaa	25/35	1	2	FACETS	0.321	0.274	0.373	0.321	0.274	0.373	SUBCLONAL	1	FALSE	1	0.724468809065143	2		406	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs17849781	NA	P-0014841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	356	785	0	ENST00000269305.4:c.832C>G	p.Pro278Ala	p.P278A	ENST00000269305	NM_001126112.2	278	Cct/Gct	8/11	0.632959223501974	1	FACETS	0.94	0.898	0.983	0.94	0.898	0.983	CLONAL	1	TRUE	0	0.686172851604006	1		785	725	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862206	68862217	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTGGGTTTTG	AGGTGGGTTTTG	-	novel	NA	P-0014851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	27	462	1	ENST00000261769.5:c.2295_2295+11del		p.X765_splice	ENST00000261769	NM_004360.3	765		14/16	0.358321058223763	1	FACETS	0.46	0.367	0.565	0.46	0.367	0.565	SUBCLONAL	1	TRUE	0	0.358321058223763	1		463	269	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587781702	NA	P-0014851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	73	520	0	ENST00000269305.4:c.920-1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.274576785242759	1	FACETS	0.911	0.802	1	0.911	0.802	1	CLONAL	1	TRUE	0	0.358321058223763	1		520	367	SUCCESS
ALK	238	MSKCC	GRCh37	2	29473986	29473986	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	23	528	0	ENST00000389048.3:c.2189C>T	p.Ala730Val	p.A730V	ENST00000389048	NM_004304.4	730	gCc/gTc	12/29	0.19975197472477	0	FACETS	0.194	0.151	0.245			1	INDETERMINATE	1	TRUE	0	0.358321058223763	0		528	424	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143044542	143044542	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	28	349	0	ENST00000262992.4:c.1920C>G	p.Ile640Met	p.I640M	ENST00000262992	NM_001101669.1	640	atC/atG	18/24	0.275958264421414	1	FACETS	0.415	0.332	0.509	0.415	0.332	0.509	SUBCLONAL	1	TRUE	0	0.358321058223763	1		349	309	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	121	840	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	0.287537626907749	2		840	835	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0014858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	118	715	1	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.287537626907749	1	FACETS	0.908	0.819	1	0.908	0.819	1	CLONAL	1	TRUE	0	0.287537626907749	1		716	774	SUCCESS
APC	324	MSKCC	GRCh37	5	112175351	112175352	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0014858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	158	346	0	ENST00000257430.4:c.4062_4063del	p.Ser1355PhefsTer19	p.S1355Ffs*19	ENST00000257430	NM_000038.5	1354	TTt/t	16/16	0.280637540701813	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.287537626907749	2		346	510	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259397	11259397	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	111	636	0	ENST00000361445.4:c.4171C>G	p.Arg1391Gly	p.R1391G	ENST00000361445	NM_004958.3	1391	Cga/Gga	28/58	1	2	FACETS	0.795	0.714	0.882	0.795	0.714	0.882	SUBCLONAL	1	TRUE	1	0.287537626907749	2		636	971	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246078928	246078928	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0014858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	193	538	0	ENST00000388985.4:c.717C>G	p.Tyr239Ter	p.Y239*	ENST00000388985		239	taC/taG	8/12	0.28151588689158	3	FACETS	0.848	0.785	0.914	0.848	0.785	0.914	CLONAL	2	TRUE	1	0.287537626907749	3		538	905	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67459114	67459114	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	G	novel	NA	P-0014858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	371	805	0	ENST00000327367.4:c.533-3C>G		p.X178_splice	ENST00000327367	NM_005902.3	178			0.285992928626815	3	FACETS	0.893	0.848	0.938	0.893	0.848	0.938	CLONAL	3	TRUE	0	0.287537626907749	3		805	1102	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022732	31022733	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACAGATGG	novel	NA	P-0014858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	117	717	0	ENST00000375687.4:c.2218_2225dup	p.Leu743GlnfsTer4	p.L743Qfs*4	ENST00000375687	NM_015338.5	739	-/ACAGATGG	13/13	0.286666551952651	4	FACETS	0.87	0.782	0.963	0.29	0.26	0.321	CLONAL	1	TRUE	1	0.287537626907749	4		717	1205	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0014874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	64	525	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.232022934279869	5	FACETS	0.898	0.781	1			1	CLONAL	2	FALSE	NA	0.232022934279869	5		525	414	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0014874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	36	506	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.232022934279869	5	FACETS	1	0.873	1	0.531	0.441	0.63	CLONAL	2	FALSE	1	0.232022934279869	5		506	197	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0014874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	74	772	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.232022934279869	6	FACETS	0.952	0.84	1	0.571	0.504	0.642	CLONAL	3	FALSE	1	0.232022934279869	6		772	327	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641151	3641151	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	91	1374	0	ENST00000294008.3:c.2488G>C	p.Ala830Pro	p.A830P	ENST00000294008	NM_032444.2	830	Gcg/Ccg	12/15	0.232022934279869	6	FACETS	1	0.96	1	0.584	0.52	0.651	CLONAL	2	FALSE	2	0.232022934279869	6		1374	492	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346100	89346100	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	15	121	0	ENST00000301030.4:c.6850G>A	p.Ala2284Thr	p.A2284T	ENST00000301030	NM_001256183.1	2284	Gcc/Acc	9/13	0.232022934279869	7	FACETS	0.964	0.729	1	0.771	0.583	0.979	CLONAL	4	FALSE	2	0.232022934279869	7		121	53	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40743887	40743887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774959037	NA	P-0014874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	73	759	0	ENST00000392038.2:c.820C>T	p.Arg274Cys	p.R274C	ENST00000392038	NM_001626.4	274	Cgc/Tgc	9/14	0.232022934279869	5	FACETS	1	0.94	1	1	0.94	1	CLONAL	3	FALSE	2	0.232022934279869	5		759	258	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247354	153247354	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	93	454	0	ENST00000281708.4:c.1448T>C	p.Leu483Pro	p.L483P	ENST00000281708	NM_033632.3	483	cTt/cCt	10/12	0.232022934279869	4	FACETS	0.888	0.801	0.978	1	0.968	1	CLONAL	4	FALSE	1	0.232022934279869	4		454	278	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	519	720	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.297710112094019	4	FACETS	0.857	0.821	0.893			1	CLONAL	3	TRUE	NA	0.379741143148537	4		721	1467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0014877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	275	630	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.315932452054338	2	FACETS	0.764	0.718	0.811	0.764	0.718	0.811	SUBCLONAL	2	TRUE	0	0.379741143148537	2		630	948	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0014881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	714	913	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.628315228667318	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.628315228667318	2		913	1093	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0014881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	246	505	1				ENST00000310581	NM_198253.2	-/1132			0.105231783010522	6	FACETS	1	0.979	1			1	INDETERMINATE	2	TRUE	NA	0.628315228667318	6		506	807	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685300	89685300	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs878853936	NA	P-0014881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	192	287	0	ENST00000371953.3:c.195C>A	p.Tyr65Ter	p.Y65*	ENST00000371953	NM_000314.4	65	taC/taA	3/9	0.628315228667318	2	FACETS	0.986	0.933	1	0.986	0.933	1	CLONAL	2	TRUE	0	0.628315228667318	2		287	310	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916882	178916882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	414	790	0	ENST00000263967.3:c.269G>A	p.Cys90Tyr	p.C90Y	ENST00000263967	NM_006218.2	90	tGt/tAt	2/21	0.452631877585612	3	FACETS	0.815	0.778	0.853	0.815	0.778	0.853	CLONAL	2	TRUE	1	0.628315228667318	3		790	1062	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321325	1321325	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759929605	NA	P-0014881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	583	865	1	ENST00000400841.2:c.430G>A	p.Gly144Arg	p.G144R	ENST00000400841		144	Ggg/Agg	4/6	0.502206195544897	2	FACETS	1	0.995	1			1	CLONAL	1	TRUE	NA	0.628315228667318	2		866	1500	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	4552	720	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.653870629485503	7	FACETS	0.97	0.966	0.973			1	CLONAL	8	TRUE	NA	0.653870629485503	7		721	4729	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781557	9781557	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	261	720	0	ENST00000377346.4:c.1867T>A	p.Ser623Thr	p.S623T	ENST00000377346	NM_005026.3	623	Tcc/Acc	15/24	0.313523425809342	1	FACETS	0.611	0.573	0.649	0.611	0.573	0.649	INDETERMINATE	1	TRUE	0	0.653870629485503	1		720	880	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882019	NA	P-0014894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	433	1012	0	ENST00000269305.4:c.455dup	p.Pro153AlafsTer28	p.P153Afs*28	ENST00000269305	NM_001126112.2	152	ccg/ccCg	5/11	0.710200220994144	1	FACETS	0.974	0.936	1	0.974	0.936	1	CLONAL	1	TRUE	0	0.710200220994144	1		1012	807	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871656	35871656	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	146	370	1	ENST00000216797.5:c.850G>T	p.Glu284Ter	p.E284*	ENST00000216797	NM_020529.2	284	Gag/Tag	5/6	0.710200220994144	1	FACETS	0.523	0.48	0.567	0.523	0.48	0.567	SUBCLONAL	1	TRUE	0	0.710200220994144	1		371	507	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873624	35873624	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	99	253	0	ENST00000216797.5:c.227C>G	p.Ser76Trp	p.S76W	ENST00000216797	NM_020529.2	76	tCg/tGg	1/6	0.710200220994144	1	FACETS	0.526	0.474	0.58	0.526	0.474	0.58	SUBCLONAL	1	TRUE	0	0.710200220994144	1		253	342	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37871746	37871746	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142783371	NA	P-0014894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	825	865	0	ENST00000269571.5:c.1270G>A	p.Val424Ile	p.V424I	ENST00000269571		424	Gtc/Atc	11/27	0.699997003382032	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.710200220994144	2		865	1148	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760788	59760788	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	188	571	1	ENST00000259008.2:c.3619G>T	p.Asp1207Tyr	p.D1207Y	ENST00000259008	NM_032043.2	1207	Gat/Tat	20/20	0.699997003382032	2	FACETS	0.966	0.899	1	0.483	0.449	0.518	CLONAL	1	TRUE	0	0.710200220994144	2		572	548	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950756	38950756	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199854036	NA	P-0014894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	114	326	0	ENST00000357387.3:c.3194A>G	p.Asn1065Ser	p.N1065S	ENST00000357387	NM_152756.3	1065	aAt/aGt	31/38	0.460444866915086	3	FACETS	1	0.961	1			1	CLONAL	1	TRUE	NA	0.710200220994144	3		326	393	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0014902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	107	505	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.976	1	1	0.991	1	CLONAL	2	FALSE	1	0.429842361642331	2		506	213	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2225394	2225394	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	92	756	0	ENST00000398665.3:c.3604A>G	p.Arg1202Gly	p.R1202G	ENST00000398665	NM_032482.2	1202	Aga/Gga	26/28	0.161514519758615	0	FACETS	0.862	0.777	0.951			1	INDETERMINATE	1	FALSE	0	0.429842361642331	0		756	283	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795241	42795241	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	113	887	1	ENST00000575354.2:c.2321C>A	p.Ala774Glu	p.A774E	ENST00000575354	NM_015125.3	774	gCg/gAg	10/20	1	2	FACETS	0.894	0.817	0.973	1	0.989	1	CLONAL	2	FALSE	1	0.429842361642331	2		888	294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567556006	NA	P-0014912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	279	862	0	ENST00000269305.4:c.298del	p.Gln100ArgfsTer23	p.Q100Rfs*23	ENST00000269305	NM_001126112.2	100	Cag/ag	4/11	0.635933463545296	1	FACETS	0.956	0.906	1	0.956	0.906	1	CLONAL	1	TRUE	0	0.635933463545296	1		862	626	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576102	29576142	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTCAACTTCGAAGTGTGTGCCACTGTTTATACCAGGTATG	CCTCAACTTCGAAGTGTGTGCCACTGTTTATACCAGGTATG	-	novel	NA	P-0014912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	176	609	0	ENST00000356175.3:c.4076_4110+6del		p.X1359_splice	ENST00000356175	NM_000267.3	1359		30/57	0.635933463545296	1	FACETS	0.628	0.581	0.676	0.628	0.581	0.676	SUBCLONAL	1	TRUE	0	0.635933463545296	1		609	601	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92355020	92355020	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	213	299	0	ENST00000265734.4:c.457G>C	p.Val153Leu	p.V153L	ENST00000265734	NM_001259.6	153	Gtg/Ctg	4/8	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.635933463545296	2		299	638	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549189	87549189	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	206	535	4	ENST00000277120.3:c.1746G>T	p.Lys582Asn	p.K582N	ENST00000277120		582	aaG/aaT	15/19	1	2	FACETS	0.92	0.857	0.985	0.92	0.857	0.985	CLONAL	1	TRUE	1	0.635933463545296	2		539	704	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	169	460	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.188608336730557	3	FACETS	0.867	0.799	0.936	0.867	0.799	0.936	INDETERMINATE	2	TRUE	1	0.335933468206887	3		460	678	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857317	68857317	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	138	394	0	ENST00000261769.5:c.1955del	p.Leu652Ter	p.L652*	ENST00000261769	NM_004360.3	651	aTt/at	13/16	0.335933468206887	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.335933468206887	1		394	501	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0014945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	189	1015	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.388385411446361	1	FACETS	0.966	0.894	1	0.966	0.894	1	CLONAL	1	TRUE	0	0.388385411446361	1		1015	812	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251907	153251907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	136	536	0	ENST00000281708.4:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000281708	NM_033632.3	367	Cga/Tga	7/12	1	2	FACETS	0.965	0.878	1	0.965	0.878	1	CLONAL	1	TRUE	1	0.388385411446361	2		536	726	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245617	41245617	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876658606	NA	P-0014945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	71	717	0	ENST00000357654.3:c.1931G>T	p.Cys644Phe	p.C644F	ENST00000357654	NM_007294.3	644	tGt/tTt	10/23	0.375076958113382	3	FACETS	0.362	0.314	0.413	0.181	0.157	0.207	SUBCLONAL	1	TRUE	1	0.388385411446361	3		717	1207	SUCCESS
APC	324	MSKCC	GRCh37	5	112174922	112174923	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTCT	novel	NA	P-0014945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	100	346	0	ENST00000257430.4:c.3633_3637dup	p.Ser1213CysfsTer54	p.S1213Cfs*54	ENST00000257430	NM_000038.5	1211	atg/aTGTCTtg	16/16	1	2	FACETS	0.945	0.847	1	0.945	0.847	1	CLONAL	1	TRUE	1	0.388385411446361	2		346	545	SUCCESS
APC	324	MSKCC	GRCh37	5	112176021	112176021	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	95	396	0	ENST00000257430.4:c.4731del	p.Glu1577AspfsTer73	p.E1577Dfs*73	ENST00000257430	NM_000038.5	1577	gAa/ga	16/16	1	2	FACETS	0.888	0.793	0.989	0.888	0.793	0.989	CLONAL	1	TRUE	1	0.388385411446361	2		396	551	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0014958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	127	662	1	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.492990969042694	3	FACETS	0.94	0.853	1	0.47	0.426	0.515	CLONAL	1	TRUE	1	0.506437412281543	3		663	669	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967116	25967116	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	101	441	0	ENST00000435504.4:c.2090del	p.Gly697ValfsTer102	p.G697Vfs*102	ENST00000435504		697	gGt/gt	13/13	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.506437412281543	2		441	398	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948653	71948653	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	148	711	0	ENST00000298229.2:c.3365C>A	p.Ser1122Ter	p.S1122*	ENST00000298229	NM_001567.3	1122	tCg/tAg	26/28	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.506437412281543	2		711	531	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131364	202131411	+	inframe_deletion	In_Frame_Del	DEL	GAATGTTGGAGGAAAGCAATCTGTCCTTCCTGAAGGAGCTGCTCTTCC	GAATGTTGGAGGAAAGCAATCTGTCCTTCCTGAAGGAGCTGCTCTTCC	-	novel	NA	P-0014958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	145	601	0	ENST00000358485.4:c.336_383del	p.Met112_Arg127del	p.M112_R127del	ENST00000358485	NM_001080125.1	111	aGAATGTTGGAGGAAAGCAATCTGTCCTTCCTGAAGGAGCTGCTCTTCCga/aga	2/9	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.506437412281543	2		601	561	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29106013	29106013	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	114	424	0	ENST00000328354.6:c.827T>A	p.Ile276Asn	p.I276N	ENST00000328354	NM_007194.3	276	aTt/aAt	7/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.506437412281543	2		424	403	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691947	30691947	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0014958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	93	378	0	ENST00000295754.5:c.449C>G	p.Ser150Ter	p.S150*	ENST00000295754	NM_003242.5	150	tCa/tGa	3/7	0.506437412281543	1	FACETS	0.802	0.72	0.888	0.802	0.72	0.888	CLONAL	1	TRUE	0	0.506437412281543	1		378	342	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216415	36216425	+	frameshift_variant	Frame_Shift_Del	DEL	CCCATTCTGCC	CCCATTCTGCC	GAA	novel	NA	P-0014965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	382	769	2	ENST00000222270.7:c.3678_3688delinsGAA	p.His1226GlnfsTer76	p.H1226Qfs*76	ENST00000222270	NM_014727.1	1226	caCCCATTCTGCCtg/caGAAtg	12/37	1	2	FACETS	0.957	0.909	1	0.957	0.909	1	CLONAL	1	TRUE	1	0.645511999416744	2		771	1237	SUCCESS
AXL	558	MSKCC	GRCh37	19	41737181	41737181	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	362	607	1	ENST00000301178.4:c.761C>T	p.Pro254Leu	p.P254L	ENST00000301178	NM_021913.4	254	cCc/cTc	6/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.645511999416744	2		608	1087	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111119	193111119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	23	494	0	ENST00000367435.3:c.652G>A	p.Val218Ile	p.V218I	ENST00000367435	NM_024529.4	218	Gta/Ata	7/17	1	2	FACETS	0.93	0.739	1	1	0.958	1	CLONAL	3	FALSE	1	0.155483859757385	2		494	106	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572981	7572981	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	22	522	0	ENST00000269305.4:c.1128del	p.Thr377ProfsTer45	p.T377Pfs*45	ENST00000269305	NM_001126112.2	376	tcT/tc	11/11	0.242546051053433	3	FACETS	1	0.832	1	1	0.957	1	CLONAL	5	FALSE	1	0.155483859757385	3		522	59	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285198	15285198	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	35	926	0	ENST00000263388.2:c.4417A>C	p.Lys1473Gln	p.K1473Q	ENST00000263388	NM_000435.2	1473	Aag/Cag	25/33	1	2	FACETS	1	0.883	1	1	0.976	1	CLONAL	4	FALSE	1	0.155483859757385	2		926	106	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117632219	117632219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	17	756	0	ENST00000368508.3:c.6197G>A	p.Gly2066Asp	p.G2066D	ENST00000368508	NM_002944.2	2066	gGc/gAc	39/43	0.242546051053433	3	FACETS	0.893	0.685	1	1	0.926	1	CLONAL	4	FALSE	1	0.155483859757385	3		756	66	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	69	460	0	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	0.194922771320501	2		460	657	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182641	38182641	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs387907272	NA	P-0014998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	37	291	1	ENST00000396334.3:c.794T>C	p.Leu265Pro	p.L265P	ENST00000396334	NM_002468.4	265	cTg/cCg	5/5	1	2	FACETS	0.827	0.682	0.99	0.827	0.682	0.99	CLONAL	1	TRUE	1	0.194922771320501	2		292	459	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061463	38061463	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	46	462	0	ENST00000250448.2:c.526A>G	p.Ile176Val	p.I176V	ENST00000250448	NM_004496.3	176	Atc/Gtc	2/2	1	2	FACETS	0.749	0.63	0.881	0.749	0.63	0.881	SUBCLONAL	1	TRUE	1	0.194922771320501	2		462	630	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248150	110248150	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	34	410	0	ENST00000374672.4:c.1322A>G	p.Asp441Gly	p.D441G	ENST00000374672	NM_004235.4	441	gAt/gGt	5/5	1	2	FACETS	0.533	0.434	0.645	0.533	0.434	0.645	SUBCLONAL	1	TRUE	1	0.194922771320501	2		410	654	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446493	49446493	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0014998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	43	334	0	ENST00000301067.7:c.1113-1G>A		p.X371_splice	ENST00000301067	NM_003482.3	371			1	2	FACETS	0.987	0.827	1	0.987	0.827	1	CLONAL	1	TRUE	1	0.194922771320501	2		334	447	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847285	68847285	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	73	581	1	ENST00000261769.5:c.1207del	p.Ala403ProfsTer14	p.A403Pfs*14	ENST00000261769	NM_004360.3	403	Gcc/cc	9/16	0.194922771320501	1	FACETS	0.943	0.824	1	0.943	0.824	1	CLONAL	1	TRUE	0	0.194922771320501	1		582	717	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271806	15271807	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0014998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	50	690	1	ENST00000263388.2:c.6632dup	p.Tyr2211Ter	p.Y2211*	ENST00000263388	NM_000435.2	2211	tac/taAc	33/33	0.194922771320501	1	FACETS	0.697	0.591	0.815	0.697	0.591	0.815	SUBCLONAL	1	TRUE	0	0.194922771320501	1		691	664	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0015006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	281	827	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.568036535740992	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.567969569444115	3		827	621	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020768	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs926053251	NA	P-0015006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	110	790	1	ENST00000358127.4:c.77T>G	p.Val26Gly	p.V26G	ENST00000358127	NM_001280556.1	26	gTt/gGt	2/10	0.568036535740992	3	FACETS	0.8	0.72	0.884	0.4	0.36	0.442	SUBCLONAL	1	TRUE	1	0.567969569444115	3		791	622	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0015006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	66	299	1	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	0.150027242733883	3	FACETS	1	0.922	1	0.535	0.469	0.605	INDETERMINATE	1	TRUE	1	0.567969569444115	3		300	279	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118354910	118354910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	224	524	0	ENST00000534358.1:c.4099C>T	p.Pro1367Ser	p.P1367S	ENST00000534358	NM_005933.3	1367	Ccg/Tcg	9/36	0.568036535740992	3	FACETS	0.893	0.838	0.949	0.893	0.838	0.949	CLONAL	2	TRUE	1	0.567969569444115	3		524	567	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900384	3900384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146887252	NA	P-0015006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	117	714	3	ENST00000262367.5:c.712G>A	p.Val238Met	p.V238M	ENST00000262367	NM_004380.2	238	Gtg/Atg	2/31	0.568036535740992	3	FACETS	0.992	0.899	1	0.496	0.449	0.546	CLONAL	1	TRUE	1	0.567969569444115	3		717	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578498	+	frameshift_variant	Frame_Shift_Del	DEL	CGGGGGTGTGGAATCAACCCACAGC	CGGGGGTGTGGAATCAACCCACAGC	GGGGG	novel	NA	P-0015006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	170	1148	5	ENST00000269305.4:c.432_456delinsCCCCC	p.Gln144HisfsTer30	p.Q144Hfs*30	ENST00000269305	NM_001126112.2	144	caGCTGTGGGTTGATTCCACACCCCCG/caCCCCC	5/11	0.568036535740992	3	FACETS	0.871	0.802	0.944	0.436	0.401	0.472	CLONAL	1	TRUE	1	0.567969569444115	3		1153	882	SUCCESS
APC	324	MSKCC	GRCh37	5	112173283	112173284	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0015006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	69	271	0	ENST00000257430.4:c.1993_1994del	p.Leu665IlefsTer8	p.L665Ifs*8	ENST00000257430	NM_000038.5	664	acTTta/acta	16/16	0.150027242733883	3	FACETS	1	0.91	1	0.522	0.458	0.589	INDETERMINATE	1	TRUE	1	0.567969569444115	3		271	299	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578461	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	G	novel	NA	P-0015006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	135	933	3	ENST00000269305.4:c.469_470delinsC	p.Val157ProfsTer13	p.V157Pfs*13	ENST00000269305	NM_001126112.2	157	GTc/Cc	5/11	0.568036535740992	3	FACETS	0.873	0.795	0.955	0.437	0.397	0.478	CLONAL	1	TRUE	1	0.567969569444115	3		936	699	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0015012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	278	460	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.361140555269698	5	FACETS	0.951	0.906	0.996	0.951	0.906	0.996	CLONAL	5	TRUE	0	0.361140555269698	5		460	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579533	7579533	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	442	919	0	ENST00000269305.4:c.154C>T	p.Gln52Ter	p.Q52*	ENST00000269305	NM_001126112.2	52	Caa/Taa	4/11	0.361140555269698	3	FACETS	0.901	0.866	0.935	1	0.997	1	CLONAL	4	TRUE	1	0.361140555269698	3		919	802	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100943	41100943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	144	545	1	ENST00000373198.4:c.1413G>A	p.Met471Ile	p.M471I	ENST00000373198	NM_133170.3	471	atG/atA	8/32	0.361140555269698	6	FACETS	0.884	0.807	0.964	0.442	0.403	0.482	CLONAL	2	TRUE	2	0.361140555269698	6		546	777	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263725	16263725	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	122	565	0	ENST00000375759.3:c.10094C>G	p.Pro3365Arg	p.P3365R	ENST00000375759	NM_015001.2	3365	cCt/cGt	12/15	0.0969279671586047	5	FACETS	0.964	0.876	1	0.643	0.584	0.705	INDETERMINATE	2	TRUE	2	0.361140555269698	5		565	540	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374795	118374795	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	74	432	0	ENST00000534358.1:c.8188G>T	p.Asp2730Tyr	p.D2730Y	ENST00000534358	NM_005933.3	2730	Gat/Tat	27/36	0.232261749369262	5	FACETS	1	0.974	1	0.488	0.428	0.551	CLONAL	1	TRUE	2	0.361140555269698	5		432	432	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246137	46246137	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	45	471	0	ENST00000334344.6:c.4231C>G	p.Gln1411Glu	p.Q1411E	ENST00000334344	NM_152641.2	1411	Caa/Gaa	15/21	0.361140555269698	5	FACETS	0.787	0.662	0.926	0.262	0.22	0.309	CLONAL	1	TRUE	2	0.361140555269698	5		471	488	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927057	131927059	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0015012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	69	471	0	ENST00000265335.6:c.1600_1602del	p.Thr534del	p.T534del	ENST00000265335		532	ACA/-	10/25	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.361140555269698	2		471	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0015019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	257	591	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.435829245890386	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.435829245890386	1		591	875	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737018	162737018	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0015019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	113	307	0	ENST00000367921.3:c.1163-1G>C		p.X388_splice	ENST00000367921	NM_006182.2	388			1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.435829245890386	2		307	515	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933205	49933205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1331253252	NA	P-0015019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	164	497	1	ENST00000296474.3:c.2905G>A	p.Val969Met	p.V969M	ENST00000296474	NM_002447.2	969	Gtg/Atg	12/20	1	2	FACETS	0.964	0.886	1	0.964	0.886	1	CLONAL	1	TRUE	1	0.435829245890386	2		498	781	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0015029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	270	604	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.271897694381468	5	FACETS	0.974	0.915	1	0.649	0.61	0.69	INDETERMINATE	2	TRUE	2	0.503830078369775	5		604	966	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0015029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	113	714	1	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.318895192268033	1	FACETS	0.515	0.464	0.569	0.515	0.464	0.569	SUBCLONAL	1	TRUE	0	0.503830078369775	1		715	651	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28979980	28979980	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	121	772	0	ENST00000282397.4:c.1488C>A	p.Ser496Arg	p.S496R	ENST00000282397	NM_002019.4	496	agC/agA	11/30	NA	2	FACETS	0.5	0.451	0.552			1	INDETERMINATE	1	TRUE	NA	0.503830078369775	2		772	960	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878106	48878106	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1469887040	NA	P-0015029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	91	352	0	ENST00000267163.4:c.62del	p.Pro21ArgfsTer44	p.P21Rfs*44	ENST00000267163	NM_000321.2	20	Ccc/cc	1/27	0.337371883312541	1	FACETS	0.717	0.641	0.796	0.717	0.641	0.796	SUBCLONAL	1	TRUE	0	0.503830078369775	1		352	377	SUCCESS
APC	324	MSKCC	GRCh37	5	112173600	112173600	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1060503310	NA	P-0015029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	70	421	0	ENST00000257430.4:c.2309C>G	p.Ser770Ter	p.S770*	ENST00000257430	NM_000038.5	770	tCa/tGa	16/16	0.503830078369775	1	FACETS	0.654	0.574	0.738	0.654	0.574	0.738	SUBCLONAL	1	TRUE	0	0.503830078369775	1		421	318	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0015039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	244	584	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.553439500168949	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.553439500168949	1		586	618	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909695	50909695	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	57	923	0	ENST00000440232.2:c.1415A>G	p.Tyr472Cys	p.Y472C	ENST00000440232	NM_002691.3	472	tAc/tGc	12/27	0.553439500168949	1	FACETS	0.17	0.145	0.197	0.17	0.145	0.197	SUBCLONAL	1	TRUE	0	0.553439500168949	1		923	878	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158173	47158173	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	42	653	0	ENST00000409792.3:c.4526G>C	p.Arg1509Thr	p.R1509T	ENST00000409792	NM_014159.6	1509	aGa/aCa	4/21	0.553439500168949	1	FACETS	0.144	0.119	0.171	0.144	0.119	0.171	SUBCLONAL	1	TRUE	0	0.553439500168949	1		653	763	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962421	38962421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	50	397	0	ENST00000357387.3:c.1711C>T	p.His571Tyr	p.H571Y	ENST00000357387	NM_152756.3	571	Cac/Tac	19/38	0.553439500168949	3	FACETS	0.352	0.298	0.411	0.176	0.149	0.206	SUBCLONAL	1	TRUE	1	0.553439500168949	3		397	656	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522053	157522053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	30	465	0	ENST00000346085.5:c.4325G>A	p.Gly1442Glu	p.G1442E	ENST00000346085	NM_020732.3	1442	gGa/gAa	18/20	0.337676440209576	1	FACETS	0.162	0.13	0.199	0.162	0.13	0.199	SUBCLONAL	1	TRUE	0	0.553439500168949	1		465	483	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0015049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	253	692	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.178373968568727	3	FACETS	0.912	0.853	0.972	0.912	0.853	0.972	CLONAL	2	TRUE	1	0.289352469615371	3		692	1098	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206664150	206664150	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0015049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	144	567	0	ENST00000367120.3:c.1694-2A>G		p.X565_splice	ENST00000367120	NM_014002.3	565			0.287788126934828	4	FACETS	1	0.978	1	0.409	0.372	0.448	CLONAL	1	TRUE	1	0.289352469615371	4		567	1046	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916926	178916931	+	inframe_deletion	In_Frame_Del	DEL	GTAGGC	GTAGGC	-	novel	NA	P-0015049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	393	527	0	ENST00000263967.3:c.313_318del	p.Val105_Gly106del	p.V105_G106del	ENST00000263967	NM_006218.2	105	GTAGGC/-	2/21	0.289352469615371	6	FACETS	0.972	0.929	1	0.81	0.774	0.847	CLONAL	5	TRUE	0	0.289352469615371	6		527	882	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0015052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	213	596	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.337798319527588	4	FACETS	1	0.989	1	0.686	0.637	0.737	CLONAL	1	TRUE	2	0.431025183063359	4		596	1031	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	116	548	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	0.38826403401665	3	FACETS	0.817	0.736	0.902	0.408	0.368	0.451	CLONAL	1	TRUE	1	0.431025183063359	3		548	801	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106865	27106871	+	frameshift_variant	Frame_Shift_Del	DEL	AGAACCC	AGAACCC	-	novel	NA	P-0015052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	230	479	0	ENST00000324856.7:c.6476_6482del	p.Lys2159ArgfsTer39	p.K2159Rfs*39	ENST00000324856	NM_006015.4	2159	aAGAACCCg/ag	20/20	0.38826403401665	3	FACETS	0.872	0.816	0.929	0.872	0.816	0.929	CLONAL	2	TRUE	1	0.431025183063359	3		479	744	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609732	46609732	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	226	493	0	ENST00000263734.3:c.2456T>C	p.Val819Ala	p.V819A	ENST00000263734	NM_001430.4	819	gTg/gCg	15/16	0.428302011683424	3	FACETS	0.872	0.815	0.93	0.872	0.815	0.93	CLONAL	2	TRUE	1	0.431025183063359	3		493	731	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953788	48953788	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0015065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	129	181	0	ENST00000267163.4:c.1389+2T>C		p.X463_splice	ENST00000267163	NM_000321.2	463			0.592928677014239	1	FACETS	0.928	0.853	1	0.928	0.853	1	CLONAL	1	TRUE	0	0.592928677014239	1		181	330	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593602	55593604	+	inframe_deletion	In_Frame_Del	DEL	GTG	GTG	-	novel	NA	P-0015065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	95	364	0	ENST00000288135.5:c.1669_1671del	p.Trp557del	p.W557del	ENST00000288135	NM_000222.2	556	caGTGg/cag	11/21	1	2	FACETS	0.754	0.675	0.837	0.754	0.675	0.837	SUBCLONAL	1	TRUE	1	0.592928677014239	2		364	425	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544629	65544662	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ACCTTGCTGCTCCAGAAGAGCATTCTGCCGCTTG	ACCTTGCTGCTCCAGAAGAGCATTCTGCCGCTTG	-	novel	NA	P-0015065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	374	404	0	ENST00000358664.4:c.264_295+2del		p.X88_splice	ENST00000358664	NM_002382.4	88		4/5	0.592928677014239	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.592928677014239	1		404	719	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158626	26158626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772836222	NA	P-0015072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	16	224	0	ENST00000289316.2:c.229G>A	p.Glu77Lys	p.E77K	ENST00000289316	NM_138720.2	77	Gag/Aag	1/2	0.194193707217726	3	FACETS	0.552	0.408	0.723	0.276	0.204	0.362	SUBCLONAL	1	TRUE	1	0.254421714887537	3		224	257	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101544	27101544	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	235	830	0	ENST00000324856.7:c.4826C>A	p.Ser1609Tyr	p.S1609Y	ENST00000324856	NM_006015.4	1609	tCt/tAt	18/20	0.254421714887537	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	1	0.254421714887537	3		830	1013	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107180	27107180	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	170	541	0	ENST00000324856.7:c.6791C>A	p.Ser2264Ter	p.S2264*	ENST00000324856	NM_006015.4	2264	tCa/tAa	20/20	0.254421714887537	3	FACETS	0.884	0.814	0.957	0.884	0.814	0.957	CLONAL	2	TRUE	1	0.254421714887537	3		541	852	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309851	104309851	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763813479	NA	P-0015072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	30	293	2	ENST00000369902.3:c.442G>A	p.Val148Met	p.V148M	ENST00000369902	NM_016169.3	148	Gtg/Atg	3/12	1	2	FACETS	0.639	0.515	0.78	0.639	0.515	0.78	SUBCLONAL	1	TRUE	1	0.254421714887537	2		295	369	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989023	85989023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	35	311	0	ENST00000263360.6:c.1189C>T	p.His397Tyr	p.H397Y	ENST00000263360	NM_003797.3	397	Cat/Tat	11/12	0.194193707217726	3	FACETS	0.639	0.524	0.77	0.32	0.262	0.385	SUBCLONAL	1	TRUE	1	0.254421714887537	3		311	485	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434136	49434136	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	87	724	0	ENST00000301067.7:c.7417C>T	p.Gln2473Ter	p.Q2473*	ENST00000301067	NM_003482.3	2473	Cag/Tag	31/54	0.194193707217726	3	FACETS	0.999	0.883	1	0.499	0.441	0.561	CLONAL	1	TRUE	1	0.254421714887537	3		724	772	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337248	89337248	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	67	642	0	ENST00000301030.4:c.7783G>A	p.Asp2595Asn	p.D2595N	ENST00000301030	NM_001256183.1	2595	Gat/Aat	12/13	0.194193707217726	3	FACETS	0.725	0.629	0.829	0.362	0.314	0.415	SUBCLONAL	1	TRUE	1	0.254421714887537	3		642	819	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006796	62006796	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs559091155	NA	P-0015072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	69	667	1	ENST00000392795.3:c.592G>A	p.Glu198Lys	p.E198K	ENST00000392795	NM_001039933.1	198	Gag/Aag	5/6	0.168726373677829	4	FACETS	0.818	0.711	0.934	0.409	0.355	0.467	CLONAL	1	TRUE	2	0.254421714887537	4		668	832	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302673	15302673	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	90	917	0	ENST00000263388.2:c.685G>C	p.Glu229Gln	p.E229Q	ENST00000263388	NM_000435.2	229	Gag/Cag	5/33	0.168726373677829	4	FACETS	0.759	0.671	0.853	0.379	0.335	0.427	SUBCLONAL	1	TRUE	2	0.254421714887537	4		917	1170	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181890	38181890	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	21	302	0	ENST00000396334.3:c.514G>A	p.Glu172Lys	p.E172K	ENST00000396334	NM_002468.4	172	Gag/Aag	3/5	0.194193707217726	3	FACETS	0.582	0.448	0.738	0.291	0.224	0.369	SUBCLONAL	1	TRUE	1	0.254421714887537	3		302	320	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592144	55592144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519701	NA	P-0015072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	57	553	0	ENST00000288135.5:c.1468G>A	p.Glu490Lys	p.E490K	ENST00000288135	NM_000222.2	490	Gaa/Aaa	9/21	0.194193707217726	3	FACETS	0.688	0.589	0.796	0.344	0.294	0.398	SUBCLONAL	1	TRUE	1	0.254421714887537	3		553	734	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521154	187521154	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	62	554	0	ENST00000441802.2:c.12001G>C	p.Glu4001Gln	p.E4001Q	ENST00000441802	NM_005245.3	4001	Gag/Cag	22/27	0.194193707217726	3	FACETS	0.789	0.681	0.907	0.395	0.34	0.454	CLONAL	1	TRUE	1	0.254421714887537	3		554	696	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521223	187521223	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	78	712	0	ENST00000441802.2:c.11932G>C	p.Asp3978His	p.D3978H	ENST00000441802	NM_005245.3	3978	Gac/Cac	22/27	0.194193707217726	3	FACETS	0.794	0.697	0.9	0.397	0.348	0.45	SUBCLONAL	1	TRUE	1	0.254421714887537	3		712	870	SUCCESS
APC	324	MSKCC	GRCh37	5	112177133	112177133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	41	431	1	ENST00000257430.4:c.5842G>A	p.Asp1948Asn	p.D1948N	ENST00000257430	NM_000038.5	1948	Gat/Aat	16/16	0.194193707217726	3	FACETS	0.602	0.501	0.716	0.301	0.25	0.358	SUBCLONAL	1	TRUE	1	0.254421714887537	3		432	603	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938562	76938562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	44	448	0	ENST00000373344.5:c.2186C>T	p.Ser729Leu	p.S729L	ENST00000373344	NM_000489.3	729	tCa/tTa	9/35	0.254421714887537	3	FACETS	0.647	0.541	0.763	0.323	0.27	0.382	SUBCLONAL	1	TRUE	1	0.254421714887537	3		448	603	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	23	720	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.586	0.455	0.739	0.586	0.455	0.739	SUBCLONAL	1	TRUE	1	0.12	2		721	654	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100368	27100368	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	45	599	0	ENST00000324856.7:c.4081del	p.Met1361CysfsTer120	p.M1361Cfs*120	ENST00000324856	NM_006015.4	1360	acA/ac	17/20	1	2	FACETS	0.835	0.699	0.986	0.835	0.699	0.986	CLONAL	1	TRUE	1	0.12	2		599	898	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0015493-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	57	783	0	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	1	2	FACETS	0.912	0.783	1	0.912	0.783	1	CLONAL	1	TRUE	1	0.22	2		783	568	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190320	32190320	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377458854	NA	P-0015493-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	28	587	3	ENST00000375023.3:c.419G>A	p.Arg140His	p.R140H	ENST00000375023	NM_004557.3	140	cGc/cAc	3/30	1	2	FACETS	0.769	0.615	0.944	0.769	0.615	0.944	CLONAL	1	TRUE	1	0.22	2		590	331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs786203436	NA	P-0016484-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	93	1073	0	ENST00000269305.4:c.487T>G	p.Tyr163Asp	p.Y163D	ENST00000269305	NM_001126112.2	163	Tac/Gac	5/11	0.1366233555799	3	FACETS	1	0.929	1	0.53	0.471	0.593	INDETERMINATE	1	TRUE	1	0.267938067948922	3		1073	742	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290223	15290223	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016484-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	106	1252	0	ENST00000263388.2:c.3412A>C	p.Ile1138Leu	p.I1138L	ENST00000263388	NM_000435.2	1138	Att/Ctt	21/33	1	2	FACETS	0.992	0.889	1	0.992	0.889	1	CLONAL	1	TRUE	1	0.267938067948922	2		1252	798	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495481	149495481	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016484-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	66	1555	0	ENST00000261799.4:c.3166T>A	p.Ser1056Thr	p.S1056T	ENST00000261799	NM_002609.3	1056	Tca/Aca	23/23	1	2	FACETS	0.502	0.434	0.576	0.502	0.434	0.576	SUBCLONAL	1	TRUE	1	0.267938067948922	2		1555	981	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70967599	70967599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016484-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	73	888	1	ENST00000276594.2:c.1424G>A	p.Ser475Asn	p.S475N	ENST00000276594	NM_024504.3	475	aGc/aAc	7/8	1	2	FACETS	0.679	0.592	0.772	0.679	0.592	0.772	SUBCLONAL	1	TRUE	1	0.267938067948922	2		889	803	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982735	90982735	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016484-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	52	678	3	ENST00000265433.3:c.753G>T	p.Leu251Phe	p.L251F	ENST00000265433	NM_002485.4	251	ttG/ttT	7/16	0.267938067948922	5	FACETS	0.635	0.539	0.741	0.212	0.179	0.247	SUBCLONAL	1	TRUE	2	0.267938067948922	5		681	857	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610637	10610637	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	99	783	0	ENST00000171111.5:c.73G>C	p.Glu25Gln	p.E25Q	ENST00000171111	NM_203500.1	25	Gag/Cag	2/6	0.128443411470004	4	FACETS	1	0.981	1	0.74	0.661	0.823	INDETERMINATE	1	FALSE	2	0.262866463383641	4		783	643	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692794	89692794	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121909238	NA	P-0016518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	86	496	0	ENST00000371953.3:c.278A>G	p.His93Arg	p.H93R	ENST00000371953	NM_000314.4	93	cAt/cGt	5/9	0.212858025703557	2	FACETS	0.79	0.703	0.882	0.79	0.703	0.882	SUBCLONAL	2	FALSE	0	0.262866463383641	2		496	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	132	794	0	ENST00000269305.4:c.524del	p.Arg175ProfsTer72	p.R175Pfs*72	ENST00000269305	NM_001126112.2	175	cGc/cc	5/11	0.212858025703557	2	FACETS	0.81	0.737	0.886	0.81	0.737	0.886	CLONAL	2	FALSE	0	0.262866463383641	2		794	620	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128940	64128940	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0016518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	119	759	2	ENST00000334205.4:c.571-1G>A		p.X191_splice	ENST00000334205	NM_003942.2	191			0.184325636691635	4	FACETS	0.81	0.732	0.892	0.81	0.732	0.892	CLONAL	2	FALSE	2	0.262866463383641	4		761	706	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434602	110434602	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	132	773	1	ENST00000375856.3:c.3799C>T	p.Gln1267Ter	p.Q1267*	ENST00000375856	NM_003749.2	1267	Cag/Tag	1/2	0.212858025703557	2	FACETS	0.837	0.762	0.915	0.837	0.762	0.915	CLONAL	2	FALSE	0	0.262866463383641	2		774	600	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748196	43748196	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	106	802	0	ENST00000382044.4:c.2610A>T	p.Glu870Asp	p.E870D	ENST00000382044	NM_001141980.1	870	gaA/gaT	12/28	0.247428511087801	3	FACETS	1	0.964	1	0.584	0.523	0.649	CLONAL	1	FALSE	1	0.262866463383641	3		802	781	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610601	10610601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	113	869	1	ENST00000171111.5:c.109G>A	p.Glu37Lys	p.E37K	ENST00000171111	NM_203500.1	37	Gag/Aag	2/6	0.128443411470004	4	FACETS	1	0.982	1	0.722	0.65	0.798	INDETERMINATE	1	FALSE	2	0.262866463383641	4		870	752	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272106	142272106	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs779461050	NA	P-0016518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	126	628	0	ENST00000350721.4:c.2768A>G	p.Gln923Arg	p.Q923R	ENST00000350721	NM_001184.3	923	cAa/cGa	13/47	0.184325636691635	4	FACETS	0.766	0.694	0.842	0.766	0.694	0.842	SUBCLONAL	2	FALSE	2	0.262866463383641	4		628	790	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947876	178947876	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	454	532	1	ENST00000263967.3:c.2751C>G	p.His917Gln	p.H917Q	ENST00000263967	NM_006218.2	917	caC/caG	19/21	0.262866463383641	10	FACETS	0.95	0.914	0.985			1	CLONAL	9	FALSE	NA	0.262866463383641	10		533	829	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271269	153271270	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0016518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	64	365	0	ENST00000281708.4:c.507_508dup	p.Arg170LysfsTer70	p.R170Kfs*70	ENST00000281708	NM_033632.3	170	aga/aAAga	3/12	0.212858025703557	2	FACETS	0.845	0.739	0.959	0.845	0.739	0.959	CLONAL	2	FALSE	0	0.262866463383641	2		365	288	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21968233	21968233	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	77	555	0	ENST00000304494.5:c.466del	p.Asp156IlefsTer37	p.D156Ifs*37	ENST00000304494	NM_000077.4	156	Gat/at	3/3	0.262866463383641	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	0	0.262866463383641	1		555	455	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0016638-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	199	763	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.58038152924605	2		764	673	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100585	67100585	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016638-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	156	478	0	ENST00000412916.2:c.283G>T	p.Val95Leu	p.V95L	ENST00000412916		95	Gta/Tta	4/6	0.58038152924605	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.58038152924605	1		478	336	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980034	7980034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369807670	NA	P-0016638-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	224	717	1	ENST00000319144.4:c.1303G>A	p.Val435Ile	p.V435I	ENST00000319144	NM_001139.2	435	Gtc/Atc	10/15	1	2	FACETS	0.987	0.922	1	0.987	0.922	1	CLONAL	1	TRUE	1	0.58038152924605	2		718	782	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0016638-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	161	515	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.58038152924605	2		515	528	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256412	16256416	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	novel	NA	P-0016638-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	187	681	1	ENST00000375759.3:c.3682_3686del	p.Lys1228AspfsTer7	p.K1228Dfs*7	ENST00000375759	NM_015001.2	1226	aAAAAG/a	11/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.58038152924605	2		682	618	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261081	16261082	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016638-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	198	585	0	ENST00000375759.3:c.8347dup	p.Ser2783LysfsTer30	p.S2783Kfs*30	ENST00000375759	NM_015001.2	2782	-/A	11/15	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.58038152924605	2		585	680	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804287	43804287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016638-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	258	665	0	ENST00000372470.3:c.287C>T	p.Pro96Leu	p.P96L	ENST00000372470	NM_005373.2	96	cCa/cTa	3/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.58038152924605	2		665	805	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959446	26959448	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0016638-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	134	544	0	ENST00000381527.3:c.616_618del	p.Leu206del	p.L206del	ENST00000381527	NM_001260.1	205	CTT/-	6/13	1	2	FACETS	0.866	0.791	0.945	0.866	0.791	0.945	CLONAL	1	TRUE	1	0.58038152924605	2		544	533	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0017112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	522	637	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.200270407893119	5	FACETS	1	0.993	1	0.661	0.638	0.683	INDETERMINATE	3	TRUE	0	0.765157709002652	5		637	887	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0017112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	851	937	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.751617094167551	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.765157709002652	2		939	1017	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541542	29541542	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137854557	NA	P-0017112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	20	552	0	ENST00000356175.3:c.1466A>G	p.Tyr489Cys	p.Y489C	ENST00000356175	NM_000267.3	489	tAt/tGt	13/57	NA	2	FACETS	0.323	0.248	0.408			1	INDETERMINATE	1	TRUE	NA	0.765157709002652	2		552	162	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63817051	63817051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	118	222	0	ENST00000279873.7:c.1022G>A	p.Arg341Gln	p.R341Q	ENST00000279873	NM_032199.2	341	cGa/cAa	6/10	0.765157709002652	6	FACETS	0.887	0.799	0.979	0.222	0.199	0.245	CLONAL	1	TRUE	2	0.765157709002652	6		222	880	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164182	108164182	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	154	307	0	ENST00000278616.4:c.4754G>C	p.Arg1585Thr	p.R1585T	ENST00000278616	NM_000051.3	1585	aGa/aCa	31/63	0.765157709002652	3	FACETS	1	0.96	1	0.533	0.491	0.577	CLONAL	1	TRUE	1	0.765157709002652	3		307	522	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112126	115112135	+	frameshift_variant	Frame_Shift_Del	DEL	GCCAGCGGCC	GCCAGCGGCC	-	novel	NA	P-0017112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	514	787	1	ENST00000257566.3:c.1605_1614del	p.Ala536TrpfsTer93	p.A536Wfs*93	ENST00000257566	NM_016569.3	535	gcGGCCGCTGGC/gc	7/8	0.644593581853028	4	FACETS	0.9	0.864	0.938	0.9	0.864	0.938	CLONAL	2	TRUE	2	0.765157709002652	4		788	1317	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112142	115112142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs566842835	NA	P-0017112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	537	774	1	ENST00000257566.3:c.1598G>A	p.Ser533Asn	p.S533N	ENST00000257566	NM_016569.3	533	aGc/aAc	7/8	0.644593581853028	4	FACETS	0.957	0.92	0.995	0.957	0.92	0.995	CLONAL	2	TRUE	2	0.765157709002652	4		775	1294	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160744	56160745	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	148	435	0	ENST00000399503.3:c.1019dup	p.Phe341ValfsTer44	p.F341Vfs*44	ENST00000399503	NM_005921.1	340	gtg/gTtg	4/20	1	2	FACETS	0.875	0.807	0.946	0.875	0.807	0.946	CLONAL	1	TRUE	1	0.765157709002652	2		435	442	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178091	56178091	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	137	344	0	ENST00000399503.3:c.3064C>T	p.Gln1022Ter	p.Q1022*	ENST00000399503	NM_005921.1	1022	Cag/Tag	14/20	1	2	FACETS	0.947	0.872	1	0.947	0.872	1	CLONAL	1	TRUE	1	0.765157709002652	2		344	378	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862867	117862867	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	631	561	0	ENST00000297338.2:c.1610A>C	p.Glu537Ala	p.E537A	ENST00000297338	NM_006265.2	537	gAa/gCa	12/14	0.765157709002652	5	FACETS	0.864	0.834	0.895	0.519	0.5	0.537	CLONAL	3	TRUE	0	0.765157709002652	5		561	1366	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922927	39922927	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017418-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	500	391	1	ENST00000378444.4:c.3781del	p.Arg1261GlyfsTer33	p.R1261Gfs*33	ENST00000378444	NM_001123385.1	1261	Agg/gg	8/15	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.865384749788033	1		392	614	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164962	123164962	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017418-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	222	169	0	ENST00000218089.9:c.275A>G	p.Lys92Arg	p.K92R	ENST00000218089	NM_001042749.1	92	aAg/aGg	5/35	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.865384749788033	1		169	278	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888171	81888171	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017418-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	208	627	0	ENST00000359376.3:c.316C>T	p.Leu106Phe	p.L106F	ENST00000359376	NM_002661.3	106	Ctc/Ttc	3/33	1	2	FACETS	0.507	0.471	0.545	0.507	0.471	0.545	SUBCLONAL	1	TRUE	1	0.865384749788033	2		627	948	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184754	32184754	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017418-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	435	672	1	ENST00000375023.3:c.1829C>A	p.Ala610Asp	p.A610D	ENST00000375023	NM_004557.3	610	gCc/gAc	11/30	0.865384749788033	3	FACETS	1	0.952	1	0.5	0.476	0.524	CLONAL	1	TRUE	1	0.865384749788033	3		673	1441	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265326	152265326	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017418-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	140	299	0	ENST00000206249.3:c.779G>T	p.Arg260Ile	p.R260I	ENST00000206249	NM_000125.3	260	aGa/aTa	4/8	1	2	FACETS	0.573	0.524	0.624	0.573	0.524	0.624	SUBCLONAL	1	TRUE	1	0.865384749788033	2		299	565	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779038	135779038	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017418-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	299	467	0	ENST00000298552.3:c.2208G>C	p.Met736Ile	p.M736I	ENST00000298552	NM_001162426.1	736	atG/atC	17/23	0.807306665123208	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.865384749788033	1		467	390	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44921941	44921941	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017418-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	25	327	0	ENST00000377967.4:c.1475A>T	p.Lys492Ile	p.K492I	ENST00000377967	NM_021140.2	492	aAa/aTa	15/29	1	1	FACETS	0.076	0.059	0.095	0.076	0.059	0.095	SUBCLONAL	1	TRUE	0	0.865384749788033	1		327	431	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018696-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	93	720	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.848	0.756	0.946	0.848	0.756	0.946	CLONAL	1	TRUE	1	0.393016652028332	2		721	558	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0018696-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	57	363	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.709	0.61	0.816	0.709	0.61	0.816	SUBCLONAL	1	TRUE	1	0.393016652028332	2		363	409	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492854	56492854	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018696-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	86	548	0	ENST00000407977.2:c.85G>T	p.Gly29Ter	p.G29*	ENST00000407977		29	Gga/Tga	2/10	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.393016652028332	2		548	423	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228979	36228979	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555734923	NA	P-0018696-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	122	665	1	ENST00000222270.7:c.7759C>T	p.Arg2587Ter	p.R2587*	ENST00000222270	NM_014727.1	2587	Cga/Tga	36/37	1	2	FACETS	0.91	0.824	1	0.91	0.824	1	CLONAL	1	TRUE	1	0.393016652028332	2		666	682	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434537	49434537	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1460036894	NA	P-0018696-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	111	683	0	ENST00000301067.7:c.7016A>G	p.Glu2339Gly	p.E2339G	ENST00000301067	NM_003482.3	2339	gAg/gGg	31/54	1	2	FACETS	0.868	0.781	0.959	0.868	0.781	0.959	CLONAL	1	TRUE	1	0.393016652028332	2		683	651	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66520194	66520194	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765675434	NA	P-0018696-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	114	597	2	ENST00000358598.2:c.478G>A	p.Ala160Thr	p.A160T	ENST00000358598	NM_212471.2	160	Gca/Aca	5/11	1	2	FACETS	0.809	0.729	0.894	0.809	0.729	0.894	CLONAL	1	TRUE	1	0.393016652028332	2		599	717	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221469	36221469	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018696-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	164	924	0	ENST00000222270.7:c.5228T>C	p.Leu1743Pro	p.L1743P	ENST00000222270	NM_014727.1	1743	cTg/cCg	25/37	1	2	FACETS	0.963	0.884	1	0.963	0.884	1	CLONAL	1	TRUE	1	0.393016652028332	2		924	867	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128018806	128018806	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018696-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	99	462	0	ENST00000285398.2:c.2062A>G	p.Lys688Glu	p.K688E	ENST00000285398	NM_000122.1	688	Aag/Gag	13/15	1	2	FACETS	0.951	0.851	1	0.951	0.851	1	CLONAL	1	TRUE	1	0.393016652028332	2		462	530	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715621	30715621	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018696-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	127	285	0	ENST00000295754.5:c.1279C>G	p.Pro427Ala	p.P427A	ENST00000295754	NM_003242.5	427	Cca/Gca	5/7	0.327652107088039	2	FACETS	0.855	0.783	0.929	0.855	0.783	0.929	CLONAL	2	TRUE	0	0.393016652028332	2		285	378	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422653	47422653	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1292396776	NA	P-0018696-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	108	675	0	ENST00000377045.4:c.125A>G	p.Tyr42Cys	p.Y42C	ENST00000377045	NM_001654.4	42	tAc/tGc	3/16	1	2	FACETS	0.78	0.7	0.864	0.78	0.7	0.864	SUBCLONAL	1	TRUE	1	0.393016652028332	2		675	705	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123041015	123041015	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018696-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	10	178	0	ENST00000355640.3:c.1478A>G	p.Lys493Arg	p.K493R	ENST00000355640		493	aAa/aGa	7/7	1	2	FACETS	0.275	0.186	0.387	0.275	0.186	0.387	SUBCLONAL	1	TRUE	1	0.393016652028332	2		178	185	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0018939-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	167	763	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.893	0.827	0.961	1	0.992	1	CLONAL	2	TRUE	1	0.38	2		764	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0018939-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	37	584	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.474	0.391	0.567	0.474	0.391	0.567	SUBCLONAL	1	TRUE	1	0.38	2		586	411	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929347	32929347	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018939-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	11	330	0	ENST00000380152.3:c.7357G>C	p.Glu2453Gln	p.E2453Q	ENST00000380152		2453	Gag/Cag	14/27	0.179931061722638	1	FACETS	0.27	0.186	0.373	0.27	0.186	0.373	INDETERMINATE	1	TRUE	0	0.38	1		330	174	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593269	67593269	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018939-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	18	244	0	ENST00000274335.5:c.2015T>A	p.Ile672Lys	p.I672K	ENST00000274335		672	aTa/aAa	15/15	1	2	FACETS	0.469	0.354	0.604	0.469	0.354	0.604	SUBCLONAL	1	TRUE	1	0.38	2		244	202	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11172947	11172947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759011563	NA	P-0019157-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	112	662	0	ENST00000361445.4:c.7328G>A	p.Arg2443Gln	p.R2443Q	ENST00000361445	NM_004958.3	2443	cGa/cAa	54/58	NA	2	FACETS	0.903	0.814	0.996			1	INDETERMINATE	1	TRUE	NA	0.422693871507906	2		662	587	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007719	45007719	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019157-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	114	607	0	ENST00000558401.1:c.166G>T	p.Glu56Ter	p.E56*	ENST00000558401	NM_004048.2	56	Gaa/Taa	2/4	0.422693871507906	1	FACETS	0.8	0.723	0.88	0.8	0.723	0.88	SUBCLONAL	1	TRUE	0	0.422693871507906	1		607	532	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265034	5265034	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019157-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	135	780	0	ENST00000357368.4:c.553A>C	p.Lys185Gln	p.K185Q	ENST00000357368	NM_002850.3	185	Aaa/Caa	5/38	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.422693871507906	2		780	536	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	51	766	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.786	0.68	0.897	0.786	0.68	0.897	SUBCLONAL	1	TRUE	1	0.759273962774837	2		766	171	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0020033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	100	659	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.519755709344198	4	FACETS	0.509	0.454	0.568	0.17	0.151	0.19	SUBCLONAL	1	TRUE	1	0.759273962774837	4		659	911	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653799	89653799	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	177	537	0	ENST00000371953.3:c.97A>T	p.Ile33Phe	p.I33F	ENST00000371953	NM_000314.4	33	Att/Ttt	2/9	0.759273962774837	1	FACETS	0.942	0.887	0.996	0.942	0.887	0.996	CLONAL	1	TRUE	0	0.759273962774837	1		537	307	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216718	2216718	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	147	675	0	ENST00000398665.3:c.2362G>T	p.Asp788Tyr	p.D788Y	ENST00000398665	NM_032482.2	788	Gac/Tac	20/28	1	2	FACETS	0.944	0.871	1	0.944	0.871	1	CLONAL	1	TRUE	1	0.759273962774837	2		675	410	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0020076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	228	771	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.268432467117123	6	FACETS	0.876	0.815	0.939	0.438	0.407	0.47	CLONAL	2	TRUE	2	0.381806662927678	6		771	1202	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636057	28636057	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	388	790	0	ENST00000241453.7:c.315G>C	p.Trp105Cys	p.W105C	ENST00000241453	NM_004119.2	105	tgG/tgC	3/24	0.381806662927678	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.381806662927678	2		790	994	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519988	NA	P-0020076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	277	832	0	ENST00000269305.4:c.808T>A	p.Phe270Ile	p.F270I	ENST00000269305	NM_001126112.2	270	Ttt/Att	8/11	0.310874253332051	2	FACETS	0.8	0.753	0.848	0.8	0.753	0.848	SUBCLONAL	2	TRUE	0	0.381806662927678	2		832	907	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721286	176721286	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1209039236	NA	P-0020076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	49	494	0	ENST00000439151.2:c.6917C>A	p.Ser2306Tyr	p.S2306Y	ENST00000439151	NM_022455.4	2306	tCc/tAc	23/23	0.381806662927678	3	FACETS	0.453	0.383	0.53	0.226	0.191	0.265	SUBCLONAL	1	TRUE	1	0.381806662927678	3		494	675	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020265-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	43	538	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.335	0.279	0.396	0.335	0.279	0.396	SUBCLONAL	1	TRUE	1	0.42	2		538	612	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651642	48651642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020265-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	70	650	0	ENST00000376670.3:c.808C>T	p.Arg270Trp	p.R270W	ENST00000376670	NM_002049.3	270	Cgg/Tgg	5/6	1	2	FACETS	0.386	0.335	0.44	0.386	0.335	0.44	SUBCLONAL	1	TRUE	1	0.42	2		650	864	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874011	123874013	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs780061449	NA	P-0020265-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	11	64	1	ENST00000330479.4:c.62_64del	p.Ala21del	p.A21del	ENST00000330479	NM_020382.3	14	gaGGCg/gag	2/9	1	2	FACETS	0.563	0.393	0.769	0.563	0.393	0.769	SUBCLONAL	1	TRUE	1	0.42	2		65	93	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266703	18266703	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020265-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	48	688	0	ENST00000222254.8:c.14A>T	p.Glu5Val	p.E5V	ENST00000222254	NM_005027.3	5	gAg/gTg	2/16	1	2	FACETS	0.289	0.244	0.34	0.289	0.244	0.34	SUBCLONAL	1	TRUE	1	0.42	2		688	790	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118817	61118818	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	TT	novel	NA	P-0020265-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	20	154	0	ENST00000295025.8:c.11-1_11delinsTT		p.X4_splice	ENST00000295025	NM_002908.2	4		2/11	1	2	FACETS	0.384	0.294	0.489	0.384	0.294	0.489	SUBCLONAL	1	TRUE	1	0.42	2		154	248	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292678	62292678	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020265-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	56	547	0	ENST00000360203.5:c.130A>G	p.Thr44Ala	p.T44A	ENST00000360203	NM_001283009.1	44	Acg/Gcg	3/35	0.3	4	FACETS	0.375	0.32	0.436			1	SUBCLONAL	1	TRUE	NA	0.42	4		547	1009	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0020274-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	39	654	0	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	1	2	FACETS	0.709	0.586	0.848	0.709	0.586	0.848	SUBCLONAL	1	TRUE	1	0.15	2		654	733	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199469669	NA	P-0020274-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	44	603	0	ENST00000374080.3:c.130G>T	p.Gly44Cys	p.G44C	ENST00000374080		44	Ggt/Tgt	2/45	1	2	FACETS	0.771	0.645	0.911	0.771	0.645	0.911	CLONAL	1	TRUE	1	0.15	2		603	761	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170016798	170016798	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs142234162	NA	P-0020274-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	57	585	0	ENST00000295797.4:c.1603G>C	p.Val535Leu	p.V535L	ENST00000295797	NM_002740.5	535	Gtg/Ctg	17/18	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.15	2		585	754	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881462	48881462	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	39	344	0	ENST00000267163.4:c.184C>T	p.Gln62Ter	p.Q62*	ENST00000267163	NM_000321.2	62	Cag/Tag	2/27	0.244028096991704	1	FACETS	0.769	0.639	0.914	0.769	0.639	0.914	CLONAL	1	TRUE	0	0.253039829950814	1		344	350	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843739	156843739	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	89	1049	2	ENST00000524377.1:c.1165G>A	p.Asp389Asn	p.D389N	ENST00000524377	NM_002529.3	389	Gac/Aac	8/17	1	2	FACETS	0.857	0.759	0.962	0.857	0.759	0.962	CLONAL	1	TRUE	1	0.253039829950814	2		1051	821	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0020449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	14	177	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	1	2	FACETS	0.774	0.563	1	0.774	0.563	1	CLONAL	1	TRUE	1	0.253039829950814	2		177	143	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488222	56488222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	63	666	0	ENST00000267101.3:c.1741G>A	p.Asp581Asn	p.D581N	ENST00000267101	NM_001982.3	581	Gat/Aat	15/28	1	2	FACETS	0.801	0.692	0.918	0.801	0.692	0.918	CLONAL	1	TRUE	1	0.253039829950814	2		666	622	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111435	8111435	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0020449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	33	543	2	ENST00000346208.3:c.922-1G>A		p.X308_splice	ENST00000346208		308			0.216608941357313	1	FACETS	0.54	0.439	0.653	0.54	0.439	0.653	SUBCLONAL	1	TRUE	0	0.253039829950814	1		545	422	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230594	46230598	+	frameshift_variant	Frame_Shift_Del	DEL	TGAAG	TGAAG	-	novel	NA	P-0020449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	32	608	0	ENST00000334344.6:c.843_847del	p.Ile281MetfsTer17	p.I281Mfs*17	ENST00000334344	NM_152641.2	281	atTGAAGga/atga	8/21	1	2	FACETS	0.426	0.345	0.518	0.426	0.345	0.518	SUBCLONAL	1	TRUE	1	0.253039829950814	2		608	594	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9928005	9928005	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	32	463	0	ENST00000330684.3:c.1734C>A	p.Tyr578Ter	p.Y578*	ENST00000330684	NM_001134407.1	578	taC/taA	8/13	1	2	FACETS	0.518	0.42	0.63	0.518	0.42	0.63	SUBCLONAL	1	TRUE	1	0.253039829950814	2		463	488	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89842197	89842197	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	91	808	0	ENST00000389301.3:c.1853A>G	p.Tyr618Cys	p.Y618C	ENST00000389301	NM_000135.2	618	tAc/tGc	21/43	0.216608941357313	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.253039829950814	1		808	607	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272344	15272344	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	154	1059	3	ENST00000263388.2:c.6095G>T	p.Ser2032Ile	p.S2032I	ENST00000263388	NM_000435.2	2032	aGc/aTc	33/33	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.253039829950814	2		1062	895	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378265	225378266	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	48	501	0	ENST00000264414.4:c.629dup	p.Leu210PhefsTer20	p.L210Ffs*20	ENST00000264414	NM_003590.4	210	ttg/ttTg	5/16	1	2	FACETS	0.795	0.673	0.93	0.795	0.673	0.93	CLONAL	1	TRUE	1	0.253039829950814	2		501	477	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321517	62321517	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	68	1008	1	ENST00000360203.5:c.2219A>T	p.His740Leu	p.H740L	ENST00000360203	NM_001283009.1	740	cAt/cTt	25/35	1	2	FACETS	0.668	0.58	0.763	0.668	0.58	0.763	SUBCLONAL	1	TRUE	1	0.253039829950814	2		1009	805	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149290734	149290734	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	66	783	0	ENST00000360632.3:c.485C>T	p.Pro162Leu	p.P162L	ENST00000360632	NM_015472.4	162	cCt/cTt	3/7	1	2	FACETS	0.772	0.669	0.883	0.772	0.669	0.883	SUBCLONAL	1	TRUE	1	0.253039829950814	2		783	676	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778245	27778245	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	62	589	0	ENST00000369163.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000369163	NM_003536.2	132	Cgc/Tgc	1/1	1	2	FACETS	0.869	0.751	0.997	0.869	0.751	0.997	CLONAL	1	TRUE	1	0.253039829950814	2		589	564	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711910	89711910	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs1057522285	NA	P-0020452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	149	621	0	ENST00000371953.3:c.528T>G	p.Tyr176Ter	p.Y176*	ENST00000371953	NM_000314.4	176	taT/taG	6/9	0.3563831242329	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.3563831242329	1		621	684	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849471	68849471	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	187	668	0	ENST00000261769.5:c.1374del	p.Asn458LysfsTer23	p.N458Kfs*23	ENST00000261769	NM_004360.3	458	aaT/aa	10/16	0.3563831242329	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.3563831242329	1		668	780	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	618	937	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.652050643410739	2	FACETS	0.989	0.961	1	0.989	0.961	1	CLONAL	2	TRUE	0	0.652050643410739	2		939	958	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	83	304	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.637095498615663	1	FACETS	0.933	0.843	1	0.933	0.843	1	CLONAL	1	TRUE	0	0.652050643410739	1		304	184	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251554	251554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906780	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1268	192	672	0	ENST00000264932.6:c.1765C>T	p.Arg589Trp	p.R589W	ENST00000264932	NM_004168.2	589	Cgg/Tgg	13/15	0.652050643410739	5	FACETS	0.798	0.736	0.863	0.266	0.245	0.288	SUBCLONAL	1	TRUE	2	0.652050643410739	5		672	1460	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602328	10602328	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	702	843	3	ENST00000171111.5:c.1250G>T	p.Gly417Val	p.G417V	ENST00000171111	NM_203500.1	417	gGg/gTg	3/6	0.652050643410739	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.652050643410739	2		846	1063	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007768	45007768	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	263	465	0	ENST00000558401.1:c.215C>G	p.Ser72Ter	p.S72*	ENST00000558401	NM_004048.2	72	tCa/tGa	2/4	0.652050643410739	2	FACETS	0.782	0.741	0.822	0.782	0.741	0.822	SUBCLONAL	2	TRUE	0	0.652050643410739	2		465	516	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439656	140439656	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	97	387	0	ENST00000288602.6:c.2083G>C	p.Glu695Gln	p.E695Q	ENST00000288602	NM_004333.4	695	Gag/Cag	17/18	0.652050643410739	3	FACETS	0.666	0.595	0.742	0.333	0.297	0.371	SUBCLONAL	1	TRUE	1	0.652050643410739	3		387	592	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933742	36933742	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	576	780	0	ENST00000361632.4:c.1657G>T	p.Glu553Ter	p.E553*	ENST00000361632		553	Gag/Tag	12/16	0.652050643410739	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.652050643410739	3		780	1122	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740116	162740116	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	116	474	0	ENST00000367921.3:c.1318G>A	p.Glu440Lys	p.E440K	ENST00000367921	NM_006182.2	440	Gaa/Aaa	12/18	0.652050643410739	5	FACETS	0.649	0.584	0.719	0.216	0.194	0.24	SUBCLONAL	1	TRUE	2	0.652050643410739	5		474	1084	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663871	241663871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1131691244	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	111	446	0	ENST00000366560.3:c.1256C>T	p.Ser419Leu	p.S419L	ENST00000366560	NM_000143.3	419	tCa/tTa	9/10	0.652050643410739	3	FACETS	0.789	0.712	0.871	0.395	0.356	0.436	SUBCLONAL	1	TRUE	1	0.652050643410739	3		446	572	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448360	49448360	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	47	679	0	ENST00000301067.7:c.351G>C	p.Gln117His	p.Q117H	ENST00000301067	NM_003482.3	117	caG/caC	3/54	NA	2	FACETS	0.184	0.155	0.217			1	INDETERMINATE	1	TRUE	NA	0.652050643410739	2		679	783	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112940047	112940047	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	210	845	0	ENST00000351677.2:c.1699C>G	p.Pro567Ala	p.P567A	ENST00000351677	NM_002834.3	567	Cca/Gca	14/16	0.652050643410739	3	FACETS	0.653	0.605	0.703	0.326	0.302	0.352	SUBCLONAL	1	TRUE	1	0.652050643410739	3		845	1308	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893285	32893285	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	75	540	1	ENST00000380152.3:c.139G>T	p.Ala47Ser	p.A47S	ENST00000380152		47	Gca/Tca	3/27	0.652050643410739	3	FACETS	0.566	0.497	0.64	0.283	0.248	0.32	SUBCLONAL	1	TRUE	1	0.652050643410739	3		541	539	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435067	110435067	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1328909789	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	290	861	0	ENST00000375856.3:c.3334G>A	p.Glu1112Lys	p.E1112K	ENST00000375856	NM_003749.2	1112	Gag/Aag	1/2	0.652050643410739	3	FACETS	0.911	0.856	0.968	0.455	0.428	0.484	CLONAL	1	TRUE	1	0.652050643410739	3		861	1295	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007803	45007803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	32	489	0	ENST00000558401.1:c.250C>T	p.Leu84Phe	p.L84F	ENST00000558401	NM_004048.2	84	Ctc/Ttc	2/4	0.652050643410739	2	FACETS	0.18	0.145	0.219	0.09	0.072	0.11	SUBCLONAL	1	TRUE	0	0.652050643410739	2		489	546	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788590	3788590	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	172	534	0	ENST00000262367.5:c.4364T>C	p.Ile1455Thr	p.I1455T	ENST00000262367	NM_004380.2	1455	aTt/aCt	26/31	0.632602066229165	4	FACETS	0.989	0.911	1	0.495	0.455	0.536	CLONAL	1	TRUE	2	0.652050643410739	4		534	881	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825599	50825599	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	67	436	0	ENST00000398568.2:c.2230G>A	p.Glu744Lys	p.E744K	ENST00000398568	NM_001042412.1	744	Gag/Aag	14/18	0.632602066229165	4	FACETS	0.559	0.486	0.639	0.28	0.243	0.32	SUBCLONAL	1	TRUE	2	0.652050643410739	4		436	607	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50827538	50827538	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	130	608	0	ENST00000398568.2:c.2423G>A	p.Gly808Glu	p.G808E	ENST00000398568	NM_001042412.1	808	gGa/gAa	16/18	0.632602066229165	4	FACETS	0.663	0.601	0.729	0.332	0.3	0.365	SUBCLONAL	1	TRUE	2	0.652050643410739	4		608	993	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950282	15950282	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	68	752	0	ENST00000268712.3:c.6662G>C	p.Gly2221Ala	p.G2221A	ENST00000268712	NM_006311.3	2221	gGa/gCa	42/46	0.652050643410739	2	FACETS	0.271	0.235	0.31	0.136	0.117	0.155	SUBCLONAL	1	TRUE	0	0.652050643410739	2		752	769	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950313	15950313	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	84	788	0	ENST00000268712.3:c.6631G>C	p.Glu2211Gln	p.E2211Q	ENST00000268712	NM_006311.3	2211	Gag/Cag	42/46	0.652050643410739	2	FACETS	0.324	0.286	0.365	0.162	0.143	0.183	SUBCLONAL	1	TRUE	0	0.652050643410739	2		788	795	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995257	15995257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	141	598	0	ENST00000268712.3:c.2936G>A	p.Arg979Lys	p.R979K	ENST00000268712	NM_006311.3	979	aGa/aAa	22/46	0.652050643410739	2	FACETS	0.685	0.626	0.747	0.343	0.313	0.374	SUBCLONAL	1	TRUE	0	0.652050643410739	2		598	631	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16041478	16041478	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	97	354	0	ENST00000268712.3:c.1401G>C	p.Glu467Asp	p.E467D	ENST00000268712	NM_006311.3	467	gaG/gaC	13/46	0.652050643410739	2	FACETS	0.719	0.645	0.796	0.359	0.322	0.398	SUBCLONAL	1	TRUE	0	0.652050643410739	2		354	414	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41228545	41228545	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	165	748	0	ENST00000357654.3:c.4444G>A	p.Asp1482Asn	p.D1482N	ENST00000357654	NM_007294.3	1482	Gat/Aat	13/23	0.652050643410739	3	FACETS	0.726	0.666	0.788	0.363	0.333	0.394	SUBCLONAL	1	TRUE	1	0.652050643410739	3		748	925	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699427	47699427	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	90	354	0	ENST00000347630.2:c.81C>G	p.Ile27Met	p.I27M	ENST00000347630	NM_001007230.1	27	atC/atG	4/11	0.652050643410739	3	FACETS	0.931	0.832	1	0.466	0.416	0.518	CLONAL	1	TRUE	1	0.652050643410739	3		354	393	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733140	74733140	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	75	639	0	ENST00000359995.5:c.103G>C	p.Glu35Gln	p.E35Q	ENST00000359995	NM_001195427.1	35	Gag/Cag	1/3	0.652050643410739	3	FACETS	0.269	0.235	0.306	0.134	0.117	0.153	SUBCLONAL	1	TRUE	1	0.652050643410739	3		639	1134	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7152923	7152923	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	129	520	0	ENST00000302850.5:c.2045C>G	p.Ser682Trp	p.S682W	ENST00000302850	NM_000208.2	682	tCg/tGg	10/22	0.652050643410739	2	FACETS	0.62	0.564	0.679	0.31	0.282	0.34	SUBCLONAL	1	TRUE	0	0.652050643410739	2		520	638	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905960	50905960	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	782	888	1	ENST00000440232.2:c.932G>T	p.Arg311Leu	p.R311L	ENST00000440232	NM_002691.3	311	cGc/cTc	8/27	0.652050643410739	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.652050643410739	2		889	1131	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707966	47707966	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553370439	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	109	481	0	ENST00000233146.2:c.2590G>A	p.Asp864Asn	p.D864N	ENST00000233146	NM_000251.2	864	Gat/Aat	15/16	0.652050643410739	3	FACETS	0.694	0.624	0.767	0.347	0.312	0.384	SUBCLONAL	1	TRUE	1	0.652050643410739	3		481	639	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051181	128051181	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	248	663	2	ENST00000285398.2:c.142G>C	p.Glu48Gln	p.E48Q	ENST00000285398	NM_000122.1	48	Gag/Cag	2/15	0.632602066229165	4	FACETS	0.861	0.803	0.922	0.431	0.401	0.461	CLONAL	1	TRUE	2	0.652050643410739	4		665	1459	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096202	178096202	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	153	453	0	ENST00000397062.3:c.1129G>A	p.Glu377Lys	p.E377K	ENST00000397062	NM_006164.4	377	Gaa/Aaa	5/5	0.632602066229165	4	FACETS	0.828	0.757	0.903	0.414	0.378	0.452	CLONAL	1	TRUE	2	0.652050643410739	4		453	936	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097986	178097986	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	115	464	1	ENST00000397062.3:c.394G>A	p.Asp132Asn	p.D132N	ENST00000397062	NM_006164.4	132	Gac/Aac	3/5	0.632602066229165	4	FACETS	0.773	0.696	0.854	0.386	0.348	0.427	SUBCLONAL	1	TRUE	2	0.652050643410739	4		465	754	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198299715	198299715	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1417266098	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	104	464	0	ENST00000335508.6:c.9G>T	p.Lys3Asn	p.K3N	ENST00000335508	NM_012433.2	3	aaG/aaT	1/25	0.632602066229165	4	FACETS	0.63	0.563	0.7	0.315	0.281	0.35	SUBCLONAL	1	TRUE	2	0.652050643410739	4		464	837	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209108166	209108166	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	230	389	0	ENST00000345146.2:c.683A>G	p.Gln228Arg	p.Q228R	ENST00000345146	NM_005896.2	228	cAg/cGg	6/10	0.632602066229165	4	FACETS	0.867	0.813	0.923	0.867	0.813	0.923	CLONAL	2	TRUE	2	0.652050643410739	4		389	672	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321686	62321686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777844293	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	289	769	0	ENST00000360203.5:c.2305C>T	p.Arg769Cys	p.R769C	ENST00000360203	NM_001283009.1	769	Cgt/Tgt	26/35	0.652050643410739	3	FACETS	0.963	0.905	1	0.481	0.452	0.511	CLONAL	1	TRUE	1	0.652050643410739	3		769	1221	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458338	12458338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	200	727	0	ENST00000287820.6:c.955G>A	p.Glu319Lys	p.E319K	ENST00000287820	NM_015869.4	319	Gag/Aag	6/7	1	2	FACETS	0.724	0.672	0.778	0.724	0.672	0.778	SUBCLONAL	1	TRUE	1	0.652050643410739	2		727	847	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940706	49940706	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3733136	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	155	474	0	ENST00000296474.3:c.337G>A	p.Gly113Ser	p.G113S	ENST00000296474	NM_002447.2	113	Ggc/Agc	1/20	1	2	FACETS	0.709	0.65	0.769	0.709	0.65	0.769	SUBCLONAL	1	TRUE	1	0.652050643410739	2		474	671	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651527	52651527	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	35	553	2	ENST00000394830.3:c.1569G>C	p.Met523Ile	p.M523I	ENST00000394830	NM_018313.4	523	atG/atC	15/30	1	2	FACETS	0.188	0.154	0.227	0.188	0.154	0.227	SUBCLONAL	1	TRUE	1	0.652050643410739	2		555	570	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668722	52668722	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	36	609	0	ENST00000394830.3:c.1197C>G	p.Asn399Lys	p.N399K	ENST00000394830	NM_018313.4	399	aaC/aaG	12/30	1	2	FACETS	0.195	0.159	0.234	0.195	0.159	0.234	SUBCLONAL	1	TRUE	1	0.652050643410739	2		609	567	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928074	178928074	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	54	650	0	ENST00000263967.3:c.1352G>C	p.Gly451Ala	p.G451A	ENST00000263967	NM_006218.2	451	gGa/gCa	8/21	0.512442415449752	4	FACETS	0.308	0.262	0.359	0.103	0.087	0.12	SUBCLONAL	1	TRUE	1	0.652050643410739	4		650	888	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586400	189586400	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	161	312	0	ENST00000264731.3:c.1024G>T	p.Ala342Ser	p.A342S	ENST00000264731	NM_003722.4	342	Gcc/Tcc	8/14	0.512442415449752	4	FACETS	1	0.978	1	0.392	0.36	0.425	CLONAL	1	TRUE	1	0.652050643410739	4		312	694	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213869	66213869	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	39	636	0	ENST00000273854.3:c.2561A>T	p.Lys854Met	p.K854M	ENST00000273854	NM_004439.5	854	aAg/aTg	15/18	0.20125978436801	5	FACETS	0.306	0.252	0.366			1	INDETERMINATE	1	TRUE	NA	0.652050643410739	5		636	774	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157752	106157752	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	57	274	0	ENST00000380013.4:c.2653G>T	p.Glu885Ter	p.E885*	ENST00000380013	NM_001127208.2	885	Gaa/Taa	3/11	0.652050643410739	2	FACETS	0.599	0.518	0.686	0.299	0.259	0.343	SUBCLONAL	1	TRUE	0	0.652050643410739	2		274	292	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959103	2959103	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	116	760	1	ENST00000396946.4:c.2413G>A	p.Asp805Asn	p.D805N	ENST00000396946	NM_032415.4	805	Gac/Aac	18/25	0.652050643410739	2	FACETS	0.383	0.344	0.424	0.191	0.172	0.212	SUBCLONAL	1	TRUE	0	0.652050643410739	2		761	929	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449736	8449736	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	132	596	2	ENST00000356435.5:c.3977T>C	p.Phe1326Ser	p.F1326S	ENST00000356435		1326	tTt/tCt	23/35	0.579965247169679	4	FACETS	0.654	0.593	0.719			1	SUBCLONAL	1	TRUE	NA	0.652050643410739	4		598	1022	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486135	8486135	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	178	504	0	ENST00000356435.5:c.2682G>T	p.Arg894Ser	p.R894S	ENST00000356435		894	agG/agT	17/35	0.579965247169679	4	FACETS	0.968	0.892	1			1	CLONAL	1	TRUE	NA	0.652050643410739	4		504	932	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932333	39932333	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	275	868	4	ENST00000378444.4:c.2266G>A	p.Glu756Lys	p.E756K	ENST00000378444	NM_001123385.1	756	Gag/Aag	4/15	0.652050643410739	2	FACETS	0.762	0.715	0.81	0.381	0.357	0.405	SUBCLONAL	1	TRUE	0	0.652050643410739	2		872	1107	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045943	47045943	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	228	806	0	ENST00000377604.3:c.2738C>G	p.Ser913Cys	p.S913C	ENST00000377604	NM_001204468.1	913	tCc/tGc	24/24	0.652050643410739	2	FACETS	0.728	0.679	0.779	0.364	0.339	0.39	SUBCLONAL	1	TRUE	0	0.652050643410739	2		806	960	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371751	118371751	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	148	590	0	ENST00000534358.1:c.6208T>C	p.Tyr2070His	p.Y2070H	ENST00000534358	NM_005933.3	2070	Tat/Cat	25/36	0.499509919212827	1	FACETS	0.975	0.898	1	0.975	0.898	1	CLONAL	1	TRUE	0	0.499509919212827	1		590	456	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436805	110436805	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	344	1336	0	ENST00000375856.3:c.1596C>G	p.Asp532Glu	p.D532E	ENST00000375856	NM_003749.2	532	gaC/gaG	1/2	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.499509919212827	2		1336	1263	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272209	15272209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	243	961	0	ENST00000263388.2:c.6230C>T	p.Pro2077Leu	p.P2077L	ENST00000263388	NM_000435.2	2077	cCc/cTc	33/33	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.499509919212827	2		961	956	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949753	151949765	+	frameshift_variant	Frame_Shift_Del	DEL	CCACTGAGAACTA	CCACTGAGAACTA	-	novel	NA	P-0020482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	196	893	0	ENST00000262189.6:c.1335_1347del	p.Ser446ThrfsTer5	p.S446Tfs*5	ENST00000262189	NM_170606.2	445	tcTAGTTCTCAGTGG/tc	10/59	1	2	FACETS	0.959	0.89	1	0.959	0.89	1	CLONAL	1	TRUE	1	0.499509919212827	2		893	818	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	227	720	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.354874147981976	3	FACETS	0.878	0.819	0.938	0.878	0.819	0.938	CLONAL	2	TRUE	1	0.354874147981976	3		721	858	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0020485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	169	1163	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.354874147981976	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.354874147981976	1		1163	750	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030213	180030213	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	118	1096	3	ENST00000261937.6:c.4071C>A	p.Phe1357Leu	p.F1357L	ENST00000261937	NM_182925.4	1357	ttC/ttA	30/30	1	2	FACETS	0.858	0.774	0.947	0.858	0.774	0.947	CLONAL	1	TRUE	1	0.354874147981976	2		1099	775	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	42	840	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.128387337181451	3	FACETS	0.939	0.785	1	0.469	0.392	0.555	INDETERMINATE	1	TRUE	1	0.232233450493214	3		840	430	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0020489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	24	637	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.128387337181451	3	FACETS	0.685	0.537	0.855	0.342	0.268	0.428	INDETERMINATE	1	TRUE	1	0.232233450493214	3		637	337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0020489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1623	263	1058	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.128387337181451	3	FACETS	1	0.99	1	0.67	0.625	0.717	INDETERMINATE	1	TRUE	1	0.232233450493214	3		1058	1886	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0020489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	27	761	1	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	1	2	FACETS	0.586	0.466	0.723	0.586	0.466	0.723	SUBCLONAL	1	TRUE	1	0.232233450493214	2		762	397	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11193171	11193171	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1372	134	863	1	ENST00000361445.4:c.5330G>T	p.Ser1777Ile	p.S1777I	ENST00000361445	NM_004958.3	1777	aGc/aTc	38/58	1	2	FACETS	0.766	0.694	0.843	0.766	0.694	0.843	SUBCLONAL	1	TRUE	1	0.232233450493214	2		864	1506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573010	7573010	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0020489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	115	527	1	ENST00000269305.4:c.1101-2A>T		p.X367_splice	ENST00000269305	NM_001126112.2	367			0.128387337181451	3	FACETS	1	0.974	1	0.625	0.563	0.692	INDETERMINATE	1	TRUE	1	0.232233450493214	3		528	884	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602872	10602872	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1850	431	1431	0	ENST00000171111.5:c.706G>C	p.Asp236His	p.D236H	ENST00000171111	NM_203500.1	236	Gac/Cac	3/6	0.232233450493214	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.232233450493214	1		1431	2281	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467522	25467522	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0020489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1427	115	863	0	ENST00000264709.3:c.1555-1G>T		p.X519_splice	ENST00000264709	NM_175629.2	519			1	2	FACETS	0.642	0.576	0.713	0.642	0.576	0.713	SUBCLONAL	1	TRUE	1	0.232233450493214	2		863	1542	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281653	142281653	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1258631126	NA	P-0020489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	28	838	1	ENST00000350721.4:c.591G>A	p.Met197Ile	p.M197I	ENST00000350721	NM_001184.3	197	atG/atA	4/47	0.128387337181451	3	FACETS	0.555	0.443	0.683	0.277	0.221	0.342	INDETERMINATE	1	TRUE	1	0.232233450493214	3		839	485	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68982087	68982087	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0020489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	165	1256	0	ENST00000288368.4:c.1461T>A	p.Cys487Ter	p.C487*	ENST00000288368	NM_024870.2	487	tgT/tgA	13/40	0.192372477928303	4	FACETS	1	0.979	1	0.787	0.724	0.852	CLONAL	2	TRUE	1	0.232233450493214	4		1256	742	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696688	47696688	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519971	NA	P-0020495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	162	760	0	ENST00000347630.2:c.260A>G	p.Tyr87Cys	p.Y87C	ENST00000347630	NM_001007230.1	87	tAc/tGc	5/11	1	2	FACETS	0.826	0.764	0.89	0.826	0.764	0.89	CLONAL	1	TRUE	1	0.81875706841217	2		760	479	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236235	108236235	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	novel	NA	P-0020495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	185	685	0	ENST00000278616.4:c.9171A>G	p.Ter3057TrpextTer29	p.*3057Wext*29	ENST00000278616	NM_000051.3	3057	tgA/tgG	63/63	1	2	FACETS	0.893	0.832	0.956	0.893	0.832	0.956	CLONAL	1	TRUE	1	0.81875706841217	2		685	506	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354425	354425	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs548567255	NA	P-0020503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	295	1363	2	ENST00000262320.3:c.1133C>T	p.Pro378Leu	p.P378L	ENST00000262320	NM_003502.3	378	cCg/cTg	5/11	1	2	FACETS	0.866	0.814	0.919	0.866	0.814	0.919	CLONAL	1	TRUE	1	0.553930303981047	2		1365	1230	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332607	153332607	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	98	875	0	ENST00000281708.4:c.349G>T	p.Glu117Ter	p.E117*	ENST00000281708	NM_033632.3	117	Gag/Tag	2/12	0.24838738223919	1	FACETS	0.479	0.429	0.532	0.479	0.429	0.532	INDETERMINATE	1	TRUE	0	0.553930303981047	1		875	534	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578476	7578476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767328513	NA	P-0020503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	532	1738	2	ENST00000269305.4:c.454C>T	p.Pro152Ser	p.P152S	ENST00000269305	NM_001126112.2	152	Ccg/Tcg	5/11	0.538389690699931	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.553930303981047	1		1740	1213	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949207	71949207	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	409	1750	0	ENST00000298229.2:c.3674T>C	p.Leu1225Pro	p.L1225P	ENST00000298229	NM_001567.3	1225	cTg/cCg	27/28	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.553930303981047	2		1750	1306	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863698	68863698	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	158	621	1	ENST00000261769.5:c.2437G>T	p.Glu813Ter	p.E813*	ENST00000261769	NM_004360.3	813	Gaa/Taa	15/16	1	2	FACETS	0.92	0.847	0.996	0.92	0.847	0.996	CLONAL	1	TRUE	1	0.553930303981047	2		622	620	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218467	1218467	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	331	1287	0	ENST00000326873.7:c.343del	p.Asp115MetfsTer14	p.D115Mfs*14	ENST00000326873	NM_000455.4	114	gtG/gt	2/10	0.553930303981047	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.553930303981047	1		1287	845	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610113	10610113	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	373	1328	2	ENST00000171111.5:c.597G>T	p.Leu199Phe	p.L199F	ENST00000171111	NM_203500.1	199	ttG/ttT	2/6	0.553930303981047	1	FACETS	0.996	0.948	1	0.996	0.948	1	CLONAL	1	TRUE	0	0.553930303981047	1		1330	978	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524492	187524492	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	212	1191	1	ENST00000441802.2:c.11188A>T	p.Ile3730Leu	p.I3730L	ENST00000441802	NM_005245.3	3730	Ata/Tta	19/27	0.24838738223919	1	FACETS	0.615	0.572	0.66	0.615	0.572	0.66	INDETERMINATE	1	TRUE	0	0.553930303981047	1		1192	900	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514495	149514495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760987130	NA	P-0020503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	294	1176	0	ENST00000261799.4:c.449G>A	p.Arg150Gln	p.R150Q	ENST00000261799	NM_002609.3	150	cGa/cAa	4/23	0.553930303981047	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.553930303981047	1		1176	744	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946134	13946134	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	257	1092	0	ENST00000405192.2:c.962T>C	p.Leu321Pro	p.L321P	ENST00000405192	NM_001163147.1	321	cTt/cCt	10/12	0.553930303981047	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.553930303981047	1		1092	644	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	1121	1766	0	ENST00000397752.3:c.3028G>T	p.Asp1010Tyr	p.D1010Y	ENST00000397752	NM_000245.2	1010	Gat/Tat	14/21	0.542145224413449	6	FACETS	0.998	0.98	1	0.998	0.98	1	CLONAL	6	FALSE	0	0.542145224413449	6		1766	1440	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907691	111907693	+	missense_variant	Missense_Mutation	TNP	TGG	TGG	CTT	novel	NA	P-0020513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	287	650	0	ENST00000393256.3:c.465_467delinsCTT	p.Gly156Leu	p.G156L	ENST00000393256	NM_006538.4	155	atTGGa/atCTTa	3/4	0.542145224413449	4	FACETS	0.913	0.867	0.959	0.913	0.867	0.959	CLONAL	3	FALSE	1	0.542145224413449	4		650	596	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724599	112724599	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	108	977	0	ENST00000369452.4:c.483del	p.Leu161PhefsTer8	p.L161Ffs*8	ENST00000369452	NM_007373.3	161	ttG/tt	2/9	0.542145224413449	3	FACETS	0.945	0.851	1	0.472	0.425	0.522	CLONAL	1	FALSE	1	0.542145224413449	3		977	536	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467706	66467706	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	201	753	0	ENST00000273854.3:c.563T>A	p.Leu188His	p.L188H	ENST00000273854	NM_004439.5	188	cTt/cAt	3/18	0.464657131723783	5	FACETS	1	0.98	1	0.751	0.7	0.803	CLONAL	2	FALSE	2	0.542145224413449	5		753	597	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155548	106155549	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	235	705	0	ENST00000380013.4:c.450dup	p.Val151CysfsTer11	p.V151Cfs*11	ENST00000380013	NM_001127208.2	150	tct/tcTt	3/11	0.464657131723783	5	FACETS	0.921	0.867	0.976	0.921	0.867	0.976	CLONAL	3	FALSE	2	0.542145224413449	5		705	569	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675414	30675414	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	113	852	0	ENST00000376406.3:c.2942C>T	p.Ser981Leu	p.S981L	ENST00000376406	NM_014641.2	981	tCa/tTa	8/15	0.542145224413449	5	FACETS	1	0.908	1	0.336	0.303	0.372	CLONAL	1	FALSE	2	0.542145224413449	5		852	749	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040962	47040963	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0020513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	442	1576	0	ENST00000377604.3:c.1495_1496del	p.Ala499ProfsTer18	p.A499Pfs*18	ENST00000377604	NM_001204468.1	498	CGc/c	14/24	0.542145224413449	2	FACETS	0.968	0.93	1	0.968	0.93	1	CLONAL	2	FALSE	0	0.542145224413449	2		1576	842	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814303	76814306	+	frameshift_variant	Frame_Shift_Del	DEL	ATAA	ATAA	-	novel	NA	P-0020516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	14	271	0	ENST00000373344.5:c.6338_6341del	p.Phe2113SerfsTer9	p.F2113Sfs*9	ENST00000373344	NM_000489.3	2113	tTTATc/tc	29/35	1	1	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	0	0.344232847741789	1		271	47	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161284211	161284211	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	51	605	0	ENST00000367975.2:c.16C>A	p.Leu6Met	p.L6M	ENST00000367975	NM_003001.3	6	Ctg/Atg	1/6	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.344232847741789	2		605	292	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184738	32184738	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	56	893	0	ENST00000375023.3:c.1845C>A	p.Cys615Ter	p.C615*	ENST00000375023	NM_004557.3	615	tgC/tgA	11/30	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.344232847741789	2		893	316	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164375	47164378	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	novel	NA	P-0020523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	175	672	0	ENST00000409792.3:c.1748_1751del	p.Lys583SerfsTer17	p.K583Sfs*17	ENST00000409792	NM_014159.6	583	aAACAg/ag	3/21	1	2	FACETS	0.905	0.843	0.968	0.905	0.843	0.968	CLONAL	1	TRUE	1	0.911995273440423	2		672	424	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661946	29661946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868094590	NA	P-0020546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	126	1038	4	ENST00000356175.3:c.5840G>A	p.Arg1947Gln	p.R1947Q	ENST00000356175	NM_000267.3	1947	cGa/cAa	39/57	0.220343499024619	2	FACETS	1	0.984	1	0.716	0.649	0.785	CLONAL	1	TRUE	0	0.273446837353812	2		1042	644	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713365	40713365	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	58	1308	0	ENST00000373198.4:c.4150G>A	p.Glu1384Lys	p.E1384K	ENST00000373198	NM_133170.3	1384	Gag/Aag	30/32	0.235427241544645	3	FACETS	0.502	0.43	0.581	0.251	0.215	0.291	SUBCLONAL	1	TRUE	1	0.273446837353812	3		1308	961	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980418	201980418	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	47	1161	0	ENST00000359651.3:c.154G>C	p.Glu52Gln	p.E52Q	ENST00000359651		52	Gag/Cag	1/8	0.196709157816838	3	FACETS	0.422	0.355	0.497	0.211	0.177	0.249	SUBCLONAL	1	TRUE	1	0.273446837353812	3		1161	925	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231391	46231391	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	95	872	1	ENST00000334344.6:c.1231G>C	p.Asp411His	p.D411H	ENST00000334344	NM_152641.2	411	Gat/Cat	10/21	0.196709157816838	3	FACETS	1	0.978	1	0.698	0.623	0.777	CLONAL	1	TRUE	1	0.273446837353812	3		873	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577548	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0020546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	139	1258	2	ENST00000269305.4:c.733_734delinsTT	p.Gly245Phe	p.G245F	ENST00000269305	NM_001126112.2	245	GGc/TTc	7/11	0.220343499024619	2	FACETS	1	0.968	1	0.569	0.518	0.623	CLONAL	1	TRUE	0	0.273446837353812	2		1260	893	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3094731	3094731	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	41	934	1	ENST00000078429.4:c.82C>T	p.Gln28Ter	p.Q28*	ENST00000078429	NM_002067.2	28	Cag/Tag	1/7	0.273446837353812	2	FACETS	0.416	0.345	0.495	0.208	0.172	0.248	SUBCLONAL	1	TRUE	0	0.273446837353812	2		935	721	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222841	5222841	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	52	940	1	ENST00000357368.4:c.2962G>A	p.Glu988Lys	p.E988K	ENST00000357368	NM_002850.3	988	Gag/Aag	18/38	0.273446837353812	2	FACETS	0.526	0.447	0.613	0.263	0.223	0.307	SUBCLONAL	1	TRUE	0	0.273446837353812	2		941	723	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085904	16085904	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	114	870	1	ENST00000281043.3:c.1080G>T	p.Lys360Asn	p.K360N	ENST00000281043	NM_005378.4	360	aaG/aaT	3/3	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.273446837353812	2		871	672	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710649	40710649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	39	917	0	ENST00000373198.4:c.4202G>A	p.Gly1401Glu	p.G1401E	ENST00000373198	NM_133170.3	1401	gGa/gAa	31/32	0.235427241544645	3	FACETS	0.494	0.409	0.59	0.247	0.204	0.295	SUBCLONAL	1	TRUE	1	0.273446837353812	3		917	656	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41562602	41562602	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0020546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	50	809	0	ENST00000263253.7:c.3807-1G>C		p.X1269_splice	ENST00000263253	NM_001429.3	1269			1	2	FACETS	0.532	0.451	0.622	0.532	0.451	0.622	SUBCLONAL	1	TRUE	1	0.273446837353812	2		809	687	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421280	12421280	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	49	1327	1	ENST00000287820.6:c.160G>A	p.Glu54Lys	p.E54K	ENST00000287820	NM_015869.4	54	Gaa/Aaa	2/7	0.205535137951489	2	FACETS	0.407	0.344	0.478	0.204	0.172	0.239	SUBCLONAL	1	TRUE	0	0.273446837353812	2		1328	880	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920070	1920070	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0020546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	143	1133	0	ENST00000382891.5:c.1130C>G	p.Ser377Ter	p.S377*	ENST00000382891	NM_133335.3	377	tCa/tGa	5/22	0.220343499024619	2	FACETS	1	0.98	1	0.632	0.576	0.69	CLONAL	1	TRUE	0	0.273446837353812	2		1133	828	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131951748	131951748	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	56	579	0	ENST00000265335.6:c.3090A>T	p.Glu1030Asp	p.E1030D	ENST00000265335		1030	gaA/gaT	20/25	1	2	FACETS	0.925	0.794	1	0.925	0.794	1	CLONAL	1	TRUE	1	0.273446837353812	2		579	443	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508120	106508120	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	98	379	0	ENST00000359195.3:c.114C>G	p.Ile38Met	p.I38M	ENST00000359195	NM_002649.2	38	atC/atG	2/11	0.206839593655249	5	FACETS	0.896	0.806	0.99	0.896	0.806	0.99	CLONAL	3	TRUE	2	0.273446837353812	5		379	376	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545592	106545592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	199	976	1	ENST00000359195.3:c.3069C>A	p.His1023Gln	p.H1023Q	ENST00000359195	NM_002649.2	1023	caC/caA	11/11	0.206839593655249	5	FACETS	0.863	0.801	0.927	0.863	0.801	0.927	CLONAL	3	TRUE	2	0.273446837353812	5		977	793	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273504	38273504	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1410298719	NA	P-0020546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	542	1363	3	ENST00000425967.3:c.1831G>T	p.Gly611Trp	p.G611W	ENST00000425967	NM_001174067.1	611	Ggg/Tgg	14/19	0.273446837353812	6	FACETS	0.94	0.903	0.977			1	CLONAL	5	TRUE	NA	0.273446837353812	6		1366	1305	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370789	55370789	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	146	795	0	ENST00000297316.4:c.91C>A	p.Pro31Thr	p.P31T	ENST00000297316	NM_022454.3	31	Ccc/Acc	1/2	0.273446837353812	3	FACETS	0.935	0.856	1	0.935	0.856	1	CLONAL	2	TRUE	1	0.273446837353812	3		795	649	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981456	70981456	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1250	145	1743	0	ENST00000276594.2:c.640G>C	p.Glu214Gln	p.E214Q	ENST00000276594	NM_024504.3	214	Gag/Cag	2/8	0.273446837353812	3	FACETS	0.864	0.786	0.947	0.432	0.393	0.474	CLONAL	1	TRUE	1	0.273446837353812	3		1743	1395	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563482	87563482	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1194954580	NA	P-0020546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	146	1128	0	ENST00000277120.3:c.1870G>T	p.Val624Leu	p.V624L	ENST00000277120		624	Gtg/Ttg	16/19	0.205535137951489	2	FACETS	1	0.987	1	0.747	0.683	0.814	CLONAL	1	TRUE	0	0.273446837353812	2		1128	715	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164908	123164908	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	78	284	0	ENST00000218089.9:c.221A>G	p.His74Arg	p.H74R	ENST00000218089	NM_001042749.1	74	cAc/cGc	5/35	0.273446837353812	2	FACETS	1	0.969	1			1	CLONAL	2	TRUE	NA	0.273446837353812	2		284	229	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0020556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	79	637	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.330565872663425	2		637	458	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0020556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	89	477	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.330565872663425	2		477	426	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0020556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	136	848	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	NA	2	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.330565872663425	2		848	722	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793663	NA	P-0020556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	85	1011	2	ENST00000263967.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000263967	NM_006218.2	93	cGg/cAg	2/21	1	2	FACETS	0.882	0.781	0.99	0.882	0.781	0.99	CLONAL	1	TRUE	1	0.330565872663425	2		1013	583	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121909229	NA	P-0020556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	124	717	0	ENST00000371953.3:c.389G>C	p.Arg130Pro	p.R130P	ENST00000371953	NM_000314.4	130	cGa/cCa	5/9	0.330565872663425	2	FACETS	0.982	0.898	1	0.982	0.898	1	CLONAL	2	TRUE	0	0.330565872663425	2		717	382	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112569	115112569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180836314	NA	P-0020556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	223	1235	1	ENST00000257566.3:c.1171G>A	p.Asp391Asn	p.D391N	ENST00000257566	NM_016569.3	391	Gac/Aac	7/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.330565872663425	2		1236	1101	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46254148	46254148	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	72	744	0	ENST00000371998.3:c.280G>A	p.Asp94Asn	p.D94N	ENST00000371998		94	Gat/Aat	5/23	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.330565872663425	2		744	393	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023622	27023622	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	66	398	0	ENST00000324856.7:c.728C>G	p.Ala243Gly	p.A243G	ENST00000324856	NM_006015.4	243	gCg/gGg	1/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.330565872663425	2		398	353	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108787	2108788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs137854024	NA	P-0020556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	206	1152	0	ENST00000219476.3:c.894dup	p.Val299CysfsTer39	p.V299Cfs*39	ENST00000219476	NM_000548.3	296	-/T	10/42	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.330565872663425	2		1152	1074	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023645	27023666	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCCTCCCTCCTCCAGCGCCT	CCGCCTCCCTCCTCCAGCGCCT	-	novel	NA	P-0020556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	69	500	0	ENST00000324856.7:c.759_780del	p.Ser254ArgfsTer102	p.S254Rfs*102	ENST00000324856	NM_006015.4	251	CCGCCTCCCTCCTCCAGCGCCTcc/cc	1/20	1	2	FACETS	0.989	0.865	1	0.989	0.865	1	CLONAL	1	TRUE	1	0.330565872663425	2		500	422	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087373	27087373	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	119	905	0	ENST00000324856.7:c.1950del	p.Met651TrpfsTer7	p.M651Wfs*7	ENST00000324856	NM_006015.4	649	ctC/ct	5/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.330565872663425	2		905	650	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134629	2134629	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0020556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	217	1165	1	ENST00000219476.3:c.4406C>G	p.Ser1469Ter	p.S1469*	ENST00000219476	NM_000548.3	1469	tCa/tGa	34/42	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.330565872663425	2		1166	1121	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739899	145739899	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	146	910	0	ENST00000428558.2:c.1631T>C	p.Leu544Pro	p.L544P	ENST00000428558	NM_004260.3	544	cTg/cCg	10/22	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.330565872663425	2		910	800	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293644	137293644	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	195	1401	2	ENST00000481739.1:c.195C>A	p.Phe65Leu	p.F65L	ENST00000481739	NM_002957.4	65	ttC/ttA	2/10	1	2	FACETS	0.977	0.902	1	0.977	0.902	1	CLONAL	1	TRUE	1	0.330565872663425	2		1403	1208	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0020566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	358	676	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.569125982111672	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.568892994504888	3		676	750	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0020566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	563	763	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.569125982111672	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.568892994504888	3		764	738	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167804	56167805	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0020566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	666	569	0	ENST00000399503.3:c.1370_1371del	p.Thr457SerfsTer3	p.T457Sfs*3	ENST00000399503	NM_005921.1	457	ACa/a	7/20	0.569125982111672	4	FACETS	1	0.995	1	1	0.995	1	CLONAL	4	TRUE	0	0.568892994504888	4		569	863	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0020566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	294	901	2	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.569125982111672	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.568892994504888	2		903	492	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188200	10188200	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	177	618	1	ENST00000256474.2:c.343C>A	p.His115Asn	p.H115N	ENST00000256474	NM_000551.3	115	Cac/Aac	2/3	0.422804955692644	1	FACETS	0.906	0.838	0.976	0.906	0.838	0.976	CLONAL	1	TRUE	0	0.451092108052768	1		619	671	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101073	4101073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756402608	NA	P-0020576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	97	474	1	ENST00000262948.5:c.649G>A	p.Gly217Ser	p.G217S	ENST00000262948	NM_030662.3	217	Ggc/Agc	6/11	1	2	FACETS	0.847	0.758	0.941	0.847	0.758	0.941	CLONAL	1	TRUE	1	0.451092108052768	2		475	508	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560937	9560937	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs372728080	NA	P-0020576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	92	555	1	ENST00000353224.5:c.845T>C	p.Met282Thr	p.M282T	ENST00000353224	NM_177990.2	282	aTg/aCg	4/10	0.213971431331117	1	FACETS	0.521	0.464	0.583	0.521	0.464	0.583	INDETERMINATE	1	TRUE	0	0.451092108052768	1		556	606	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440924	52440924	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0020576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	156	625	0	ENST00000460680.1:c.581-1G>C		p.X194_splice	ENST00000460680	NM_004656.3	194			0.422804955692644	1	FACETS	0.881	0.81	0.954	0.881	0.81	0.954	CLONAL	1	TRUE	0	0.451092108052768	1		625	608	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0020604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	177	621	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	0.425465223322828	2		621	691	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976624	7976624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	172	930	2	ENST00000319144.4:c.1768G>A	p.Ala590Thr	p.A590T	ENST00000319144	NM_001139.2	590	Gcc/Acc	14/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.425465223322828	2		932	753	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0020627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	296	349	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	0.75957051308416	2	FACETS	0.946	0.911	0.979	0.946	0.911	0.979	CLONAL	2	TRUE	0	0.772720831707947	2		349	405	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100631	67100631	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs868631081	NA	P-0020627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	230	888	1	ENST00000412916.2:c.329G>A	p.Trp110Ter	p.W110*	ENST00000412916		110	tGg/tAg	4/6	0.75957051308416	2	FACETS	0.945	0.905	0.983	0.945	0.905	0.983	CLONAL	2	TRUE	0	0.772720831707947	2		889	315	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11168316	11168316	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	136	763	0	ENST00000361445.4:c.7556T>C	p.Leu2519Ser	p.L2519S	ENST00000361445	NM_004958.3	2519	tTg/tCg	57/58	0.772720831707947	3	FACETS	0.935	0.855	1	0.467	0.427	0.509	CLONAL	1	TRUE	1	0.772720831707947	3		763	522	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402009	402009	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	126	733	0	ENST00000399788.2:c.4782G>C	p.Lys1594Asn	p.K1594N	ENST00000399788	NM_001042603.1	1594	aaG/aaC	27/28	0.680342513255515	4	FACETS	0.987	0.896	1	0.329	0.298	0.361	CLONAL	1	TRUE	1	0.772720831707947	4		733	586	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112910811	112910812	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0020627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	79	706	2	ENST00000351677.2:c.823_824del	p.Asn275GlnfsTer3	p.N275Qfs*3	ENST00000351677	NM_002834.3	274	AAa/a	7/16	1	2	FACETS	0.874	0.781	0.97	0.874	0.781	0.97	CLONAL	1	TRUE	1	0.772720831707947	2		708	234	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251128	99251129	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	288	828	1	ENST00000268035.6:c.437dup	p.Asn146LysfsTer3	p.N146Kfs*3	ENST00000268035	NM_000875.3	144	-/A	2/21	0.721594803305496	3	FACETS	0.934	0.889	0.98	0.934	0.889	0.98	CLONAL	2	TRUE	1	0.772720831707947	3		829	553	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15943786	15943786	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	156	612	2	ENST00000268712.3:c.6702del	p.Ile2235SerfsTer58	p.I2235Sfs*58	ENST00000268712	NM_006311.3	2234	gaG/ga	43/46	0.75957051308416	2	FACETS	0.985	0.937	1	0.985	0.937	1	CLONAL	2	TRUE	0	0.772720831707947	2		614	205	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56811509	56811509	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	111	828	0	ENST00000337432.4:c.1057T>A	p.Ser353Thr	p.S353T	ENST00000337432	NM_058216.2	353	Tct/Act	9/9	0.312133226138341	6	FACETS	0.751	0.678	0.827	0.501	0.452	0.551	INDETERMINATE	2	TRUE	3	0.772720831707947	6		828	487	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15364979	15364979	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	158	733	0	ENST00000263377.2:c.2142C>G	p.Ser714Arg	p.S714R	ENST00000263377	NM_058243.2	714	agC/agG	11/20	0.312133226138341	6	FACETS	1	0.987	1	0.465	0.426	0.504	INDETERMINATE	1	TRUE	3	0.772720831707947	6		733	747	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46271052	46271052	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	137	697	0	ENST00000371998.3:c.3176C>T	p.Thr1059Ile	p.T1059I	ENST00000371998		1059	aCt/aTt	17/23	0.312133226138341	6	FACETS	1	0.984	1	0.46	0.419	0.503	INDETERMINATE	1	TRUE	3	0.772720831707947	6		697	654	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177677	56177680	+	frameshift_variant	Frame_Shift_Del	DEL	TTCT	TTCT	-	novel	NA	P-0020627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	89	512	1	ENST00000399503.3:c.2651_2654del	p.Phe884CysfsTer24	p.F884Cfs*24	ENST00000399503	NM_005921.1	884	TTCTtg/tg	14/20	0.380652451712994	4	FACETS	1	0.929	1	0.526	0.47	0.586	INDETERMINATE	1	TRUE	2	0.772720831707947	4		513	388	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170817088	170817088	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	47	754	0	ENST00000296930.5:c.92T>G	p.Phe31Cys	p.F31C	ENST00000296930	NM_002520.6	31	tTt/tGt	2/11	0.380652451712994	4	FACETS	0.934	0.796	1	0.467	0.398	0.541	INDETERMINATE	1	TRUE	2	0.772720831707947	4		754	231	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042243	6042244	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGGCA	novel	NA	P-0020627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	146	701	0	ENST00000265849.7:c.373_377dup	p.Ser128ThrfsTer10	p.S128Tfs*10	ENST00000265849	NM_000535.5	126	cac/caTGCCAc	5/15	0.528553238389252	4	FACETS	1	0.92	1	0.503	0.46	0.548	CLONAL	1	TRUE	2	0.772720831707947	4		701	666	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187233	38188255	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCGGTTTTGGAGGCAACACTCTTTTTTGCTTGGGATAAAGCCTCTTCAGGCTGTTTATCAATGTAAATAAAAGTATACTGTTCTATTCTTTCTTCTCGAGTCATTTTCAATGCTTTCTCTGCATGGGCAATGCCAATATCCCACTGAGCACGTTCTCTCTGAGGTCGGGGTTTCCGAATCTTTAAAAAAGATAGAGATTATCAGACATGCTTTACTCTAATAGGTACATTAAAATTGATATGTATTTCCCATGTGATCCTGTTATCTTTTCAGGTCTACATAAATATCTTCAGGTTCTTTGGTCAAACAAGTGGAATGTTCTATCTCCATAATTCTGATAAAAAGATATTCGATAACATGAGGATCTACTCTCTTTTATATCCTTCCTTTGCTGATCACTCTGCTGGACAAGGTCCCCAAGAGGGAGACATCCTTCTCCTCTCATATACATAAAAAGCTAGTGATAATGAGGGAAAAGAGAACAATGATTACAGAAATGGTTATTTTCAGTGGCTAATAAAACACTAACATTAAAAATGATACCCTGAAACTCCCAATTCTCTCCCATATCTCGGGCAGAGGGCAAGTCAGGGGTGCTACAGAGATCACAACAAAGCTACTGGCAGAGTTTGAACCACAATGCATGCAGGGACAGAATGAAGTGAAAGGACAGAGCCTCAAGGAACAAATGAAAATTAACAAGACAAAGGAGAACAGGCATGGATGAGAAAAAAGGTAGACCTGAATTATAGTTTCCATAGGTCTCTAGGTCCAGAGTCAATCAGAAGACTTTGGATTGGCAAGAGGGGTAAAAATACTTTGAATAAAGATGTGTGAGATGGCCAGAGCAATTAGGAATTATCCAGGTGGCTAGACTGATGTAGCCAGAAATTAGTTAATAAAACTATGAGATAGCATATGTCAAATATTCATATATAAATCTGTAAAATGTAAGTCTCATAAAATTAATCAAAATTCTGTGATAAAATTTAGTTTTTCAAGTGTAAAAAATGACAAATTTCT	TCGGTTTTGGAGGCAACACTCTTTTTTGCTTGGGATAAAGCCTCTTCAGGCTGTTTATCAATGTAAATAAAAGTATACTGTTCTATTCTTTCTTCTCGAGTCATTTTCAATGCTTTCTCTGCATGGGCAATGCCAATATCCCACTGAGCACGTTCTCTCTGAGGTCGGGGTTTCCGAATCTTTAAAAAAGATAGAGATTATCAGACATGCTTTACTCTAATAGGTACATTAAAATTGATATGTATTTCCCATGTGATCCTGTTATCTTTTCAGGTCTACATAAATATCTTCAGGTTCTTTGGTCAAACAAGTGGAATGTTCTATCTCCATAATTCTGATAAAAAGATATTCGATAACATGAGGATCTACTCTCTTTTATATCCTTCCTTTGCTGATCACTCTGCTGGACAAGGTCCCCAAGAGGGAGACATCCTTCTCCTCTCATATACATAAAAAGCTAGTGATAATGAGGGAAAAGAGAACAATGATTACAGAAATGGTTATTTTCAGTGGCTAATAAAACACTAACATTAAAAATGATACCCTGAAACTCCCAATTCTCTCCCATATCTCGGGCAGAGGGCAAGTCAGGGGTGCTACAGAGATCACAACAAAGCTACTGGCAGAGTTTGAACCACAATGCATGCAGGGACAGAATGAAGTGAAAGGACAGAGCCTCAAGGAACAAATGAAAATTAACAAGACAAAGGAGAACAGGCATGGATGAGAAAAAAGGTAGACCTGAATTATAGTTTCCATAGGTCTCTAGGTCCAGAGTCAATCAGAAGACTTTGGATTGGCAAGAGGGGTAAAAATACTTTGAATAAAGATGTGTGAGATGGCCAGAGCAATTAGGAATTATCCAGGTGGCTAGACTGATGTAGCCAGAAATTAGTTAATAAAACTATGAGATAGCATATGTCAAATATTCATATATAAATCTGTAAAATGTAAGTCTCATAAAATTAATCAAAATTCTGTGATAAAATTTAGTTTTTCAAGTGTAAAAAATGACAAATTTCT	-	novel	NA	P-0020627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1553	109	1149	0	ENST00000317025.8:c.1065+696_1246del		p.X355_splice	ENST00000317025	NM_023034.1	355		6/24	0.772720831707947	8	FACETS	0.563	0.503	0.627	0.08	0.071	0.09	SUBCLONAL	1	TRUE	1	0.772720831707947	8		1149	1662	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372429	55372495	+	frameshift_variant	Frame_Shift_Del	DEL	TGAGATGGGCCTCCCCTACCAGGGGCATGACTCCGGTGTGAATCTCCCCGACAGCCACGGGGCCATT	TGAGATGGGCCTCCCCTACCAGGGGCATGACTCCGGTGTGAATCTCCCCGACAGCCACGGGGCCATT	-	novel	NA	P-0020627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1672	172	1264	0	ENST00000297316.4:c.1120_1186del	p.Glu374ProfsTer58	p.E374Pfs*58	ENST00000297316	NM_022454.3	373	ccTGAGATGGGCCTCCCCTACCAGGGGCATGACTCCGGTGTGAATCTCCCCGACAGCCACGGGGCCATT/cc	2/2	0.772720831707947	8	FACETS	0.801	0.734	0.872	0.114	0.104	0.125	CLONAL	1	TRUE	1	0.772720831707947	8		1264	1844	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864207	117864207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1696	101	734	0	ENST00000297338.2:c.1450G>A	p.Asp484Asn	p.D484N	ENST00000297338	NM_006265.2	484	Gac/Aac	11/14	0.772720831707947	11	FACETS	0.651	0.579	0.729	0.065	0.057	0.073	SUBCLONAL	1	TRUE	1	0.772720831707947	11		734	1797	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907792	76907792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	45	496	0	ENST00000373344.5:c.4369G>A	p.Glu1457Lys	p.E1457K	ENST00000373344	NM_000489.3	1457	Gag/Aag	15/35	0.439035251010597	1	FACETS	0.514	0.441	0.591	0.514	0.441	0.591	INDETERMINATE	1	TRUE	0	0.772720831707947	1		496	139	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41201158	41201160	+	missense_variant	Missense_Mutation	TNP	AAA	AAA	GAG	novel	NA	P-0020627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	144	1099	2	ENST00000357654.3:c.5384_5386delinsCTC	p.Leu1795_Ser1796delinsProPro	p.L1795_S1796delinsPP	ENST00000357654	NM_007294.3	1795	cTTTca/cCTCca	21/23	0.75957051308416	2	FACETS	0.956	0.882	1	0.478	0.441	0.516	CLONAL	1	TRUE	0	0.772720831707947	2		1101	390	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696689	47696689	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519972	NA	P-0020650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	293	708	1	ENST00000347630.2:c.259T>A	p.Tyr87Asn	p.Y87N	ENST00000347630	NM_001007230.1	87	Tac/Aac	5/11	1	2	FACETS	0.918	0.866	0.97	0.918	0.866	0.97	CLONAL	1	TRUE	1	0.722478165427194	2		709	884	SUCCESS
APC	324	MSKCC	GRCh37	5	112175136	112175136	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	27	281	0	ENST00000257430.4:c.3845C>A	p.Ser1282Ter	p.S1282*	ENST00000257430	NM_000038.5	1282	tCa/tAa	16/16	0.722478165427194	1	FACETS	0.213	0.17	0.262	0.213	0.17	0.262	SUBCLONAL	1	TRUE	0	0.722478165427194	1		281	224	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910429	32910429	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	42	462	0	ENST00000380152.3:c.1937G>T	p.Ser646Ile	p.S646I	ENST00000380152		646	aGc/aTc	11/27	1	2	FACETS	0.232	0.193	0.275	0.232	0.193	0.275	SUBCLONAL	1	TRUE	1	0.722478165427194	2		462	501	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061192	38061192	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	238	674	0	ENST00000250448.2:c.797T>C	p.Phe266Ser	p.F266S	ENST00000250448	NM_004496.3	266	tTc/tCc	2/2	1	2	FACETS	0.74	0.692	0.79	0.74	0.692	0.79	SUBCLONAL	1	TRUE	1	0.722478165427194	2		674	890	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061243	38061243	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	436	1029	0	ENST00000250448.2:c.746A>C	p.Asp249Ala	p.D249A	ENST00000250448	NM_004496.3	249	gAc/gCc	2/2	1	2	FACETS	0.826	0.786	0.865	0.826	0.786	0.865	CLONAL	1	TRUE	1	0.722478165427194	2		1029	1462	SUCCESS
APC	324	MSKCC	GRCh37	5	112157637	112157646	+	frameshift_variant	Frame_Shift_Del	DEL	CTAATGAAAC	CTAATGAAAC	-	novel	NA	P-0020650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	67	729	0	ENST00000257430.4:c.1357_1366del	p.Leu453PhefsTer11	p.L453Ffs*11	ENST00000257430	NM_000038.5	453	CTAATGAAACtt/tt	11/16	0.722478165427194	1	FACETS	0.284	0.248	0.323	0.284	0.248	0.323	SUBCLONAL	1	TRUE	0	0.722478165427194	1		729	417	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68984792	68984792	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	379	720	3	ENST00000288368.4:c.1556G>A	p.Trp519Ter	p.W519*	ENST00000288368	NM_024870.2	519	tGg/tAg	14/40	0.555894862978474	5	FACETS	0.915	0.875	0.956	0.915	0.875	0.956	CLONAL	3	TRUE	2	0.722478165427194	5		723	796	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0020670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	253	937	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	NA	2	FACETS	0.769	0.723	0.817			1	INDETERMINATE	2	TRUE	NA	0.432780845126003	2		939	760	SUCCESS
APC	324	MSKCC	GRCh37	5	112174916	112174916	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	60	378	0	ENST00000257430.4:c.3625G>T	p.Glu1209Ter	p.E1209*	ENST00000257430	NM_000038.5	1209	Gaa/Taa	16/16	0.432780845126003	1	FACETS	0.82	0.713	0.933	0.82	0.713	0.933	CLONAL	1	TRUE	0	0.432780845126003	1		378	265	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	59	840	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.899	0.772	1	0.899	0.772	1	CLONAL	1	TRUE	1	0.19	2		840	691	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0020680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	70	754	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	0.19	2		754	533	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0020680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	49	871	4	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.766	0.648	0.897	0.766	0.648	0.897	SUBCLONAL	1	TRUE	1	0.19	2		875	673	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653796	89653798	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs1554893765	NA	P-0020680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	40	690	0	ENST00000371953.3:c.97_99del	p.Ile33del	p.I33del	ENST00000371953	NM_000314.4	32	ATT/-	2/9	1	2	FACETS	0.917	0.762	1	0.917	0.762	1	CLONAL	1	TRUE	1	0.19	2		690	459	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100111	27100111	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	93	841	0	ENST00000324856.7:c.3910del	p.Ala1304ProfsTer177	p.A1304Pfs*177	ENST00000324856	NM_006015.4	1303	Ggg/gg	16/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.19	2		841	702	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942195	71942195	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	66	905	0	ENST00000298229.2:c.1463del	p.Gly488AlafsTer43	p.G488Afs*43	ENST00000298229	NM_001567.3	487	Ggg/gg	12/28	1	2	FACETS	0.849	0.736	0.973	0.849	0.736	0.973	CLONAL	1	TRUE	1	0.19	2		905	818	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911951	94911951	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	98	1159	0	ENST00000536441.1:c.979T>A	p.Tyr327Asn	p.Y327N	ENST00000536441	NM_144665.3	327	Tat/Aat	7/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.19	2		1159	849	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427726	49427726	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	47	949	1	ENST00000301067.7:c.10762C>G	p.His3588Asp	p.H3588D	ENST00000301067	NM_003482.3	3588	Cac/Gac	39/54	1	2	FACETS	0.698	0.587	0.82	0.698	0.587	0.82	SUBCLONAL	1	TRUE	1	0.19	2		950	709	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793525	42793525	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	48	1005	1	ENST00000575354.2:c.1327A>G	p.Ile443Val	p.I443V	ENST00000575354	NM_015125.3	443	Atc/Gtc	8/20	1	2	FACETS	0.634	0.534	0.744	0.634	0.534	0.744	SUBCLONAL	1	TRUE	1	0.19	2		1006	797	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952019	178952019	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1553826166	NA	P-0020680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	42	727	0	ENST00000263967.3:c.3074C>G	p.Thr1025Ser	p.T1025S	ENST00000263967	NM_006218.2	1025	aCc/aGc	21/21	1	2	FACETS	0.939	0.784	1	0.939	0.784	1	CLONAL	1	TRUE	1	0.19	2		727	471	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889193	76889193	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	29	824	0	ENST00000373344.5:c.4817G>T	p.Ser1606Ile	p.S1606I	ENST00000373344	NM_000489.3	1606	aGt/aTt	18/35	1	2	FACETS	0.551	0.441	0.677	0.551	0.441	0.677	SUBCLONAL	1	TRUE	1	0.19	2		824	554	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0020687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	1085	1096	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.915301080798699	2		1097	1177	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695838	117695838	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	485	949	0	ENST00000369458.3:c.599A>T	p.Glu200Val	p.E200V	ENST00000369458	NM_024626.3	200	gAg/gTg	4/6	1	2	FACETS	0.979	0.939	1	0.979	0.939	1	CLONAL	1	TRUE	1	0.915301080798699	2		949	1083	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983978	15983978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	188	628	0	ENST00000268712.3:c.3241C>T	p.Pro1081Ser	p.P1081S	ENST00000268712	NM_006311.3	1081	Ccg/Tcg	24/46	0.912459818026859	1	FACETS	0.485	0.453	0.518	0.485	0.453	0.518	SUBCLONAL	1	TRUE	0	0.915301080798699	1		628	459	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29422303	29422341	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	GCCGCCCCCCGGCCGCGGGGAGGACATGGCCGCGCACAG	GCCGCCCCCCGGCCGCGGGGAGGACATGGCCGCGCACAG	-	novel	NA	P-0020687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	388	26	0	ENST00000356175.3:c.-21_18del		p.*7*	ENST00000356175	NM_000267.3	?-5/2839		1/57	0.912459818026859	1	FACETS	0.879	0.851	0.906	0.879	0.851	0.906	CLONAL	1	TRUE	0	0.915301080798699	1		26	523	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434924	56434939	+	frameshift_variant	Frame_Shift_Del	DEL	TGTGGTTCCAGGGGCT	TGTGGTTCCAGGGGCT	-	novel	NA	P-0020687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	35	896	0	ENST00000407977.2:c.2198_2213del	p.Gln733LeufsTer89	p.Q733Lfs*89	ENST00000407977		733	cAGCCCCTGGAACCACAt/ct	9/10	0.912459818026859	1	FACETS	0.075	0.061	0.091	0.075	0.061	0.091	SUBCLONAL	1	TRUE	0	0.915301080798699	1		896	550	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755494	133755494	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	505	863	0	ENST00000318560.5:c.1465del	p.Ile489SerfsTer31	p.I489Sfs*31	ENST00000318560	NM_005157.4	488	gAa/ga	9/11	0.915301080798699	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.915301080798699	1		863	594	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231127	53231127	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	29	761	0	ENST00000375401.3:c.1775A>C	p.Glu592Ala	p.E592A	ENST00000375401	NM_004187.3	592	gAg/gCg	13/26	0.915301080798699	1	FACETS	0.061	0.048	0.076	0.061	0.048	0.076	SUBCLONAL	1	TRUE	0	0.915301080798699	1		761	562	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	82	766	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	0.923	0.812	1	0.923	0.812	1	CLONAL	1	TRUE	0	0.17	1		766	956	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526524	31526524	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0020697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1689	159	1361	0	ENST00000344624.3:c.516T>G	p.Tyr172Ter	p.Y172*	ENST00000344624		172	taT/taG	2/33	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.17	2		1361	1848	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590994	67590995	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	25	241	0	ENST00000274335.5:c.1589dup	p.Leu531ValfsTer7	p.L531Vfs*7	ENST00000274335		529	-/A	12/15	1	2	FACETS	0.819	0.646	1	0.819	0.646	1	CLONAL	1	TRUE	1	0.17	2		241	359	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591116	67591116	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	46	347	0	ENST00000274335.5:c.1709T>G	p.Leu570Arg	p.L570R	ENST00000274335		570	cTt/cGt	12/15	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.17	2		347	530	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916948	178916950	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0020718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	215	609	0	ENST00000263967.3:c.337_339del	p.Leu113del	p.L113del	ENST00000263967	NM_006218.2	112	aTCCtc/atc	2/21	0.267856470789546	4	FACETS	0.969	0.906	1	0.969	0.906	1	CLONAL	3	TRUE	1	0.314061061523843	4		609	619	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061279	38061287	+	inframe_deletion	In_Frame_Del	DEL	TTGTCCGGG	TTGTCCGGG	-	novel	NA	P-0020718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	100	859	0	ENST00000250448.2:c.702_710del	p.Asp236_Pro238del	p.D236_P238del	ENST00000250448	NM_004496.3	234	tcCCCGGACAAg/tcg	2/2	1	2	FACETS	0.899	0.804	1	0.899	0.804	1	CLONAL	1	TRUE	1	0.314061061523843	2		859	708	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	220	840	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.297244258718602	3	FACETS	1	0.968	1	0.535	0.497	0.574	CLONAL	1	TRUE	1	0.454988055457739	3		840	1110	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720649	89720649	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs587782455	NA	P-0020728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	52	283	0	ENST00000371953.3:c.802-2A>G		p.X268_splice	ENST00000371953	NM_000314.4	268			0.264607272453271	3	FACETS	0.636	0.543	0.739	0.318	0.271	0.37	INDETERMINATE	1	TRUE	1	0.454988055457739	3		283	441	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0020731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	35	621	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.851	0.697	1	0.851	0.697	1	CLONAL	1	TRUE	1	0.154836104092585	2		621	531	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0020731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	65	631	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.154836104092585	2	FACETS	0.931	0.809	1	0.931	0.809	1	CLONAL	2	TRUE	0	0.154836104092585	2		631	451	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859788	117859788	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	30	677	0	ENST00000297338.2:c.1847C>T	p.Pro616Leu	p.P616L	ENST00000297338	NM_006265.2	616	cCg/cTg	14/14	1	2	FACETS	0.758	0.61	0.927	0.758	0.61	0.927	CLONAL	1	TRUE	1	0.154836104092585	2		677	511	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256988	16256988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs938826668	NA	P-0020731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	48	1077	1	ENST00000375759.3:c.4253G>A	p.Arg1418Gln	p.R1418Q	ENST00000375759	NM_015001.2	1418	cGa/cAa	11/15	1	2	FACETS	0.771	0.65	0.905	0.771	0.65	0.905	CLONAL	1	TRUE	1	0.154836104092585	2		1078	804	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332632	65332632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	48	829	0	ENST00000342505.4:c.907C>T	p.His303Tyr	p.H303Y	ENST00000342505	NM_002227.2	303	Cat/Tat	7/25	1	2	FACETS	0.955	0.806	1	0.955	0.806	1	CLONAL	1	TRUE	1	0.154836104092585	2		829	649	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293191	212293191	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754748646	NA	P-0020731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	68	840	0	ENST00000342788.4:c.2661G>A	p.Met887Ile	p.M887I	ENST00000342788	NM_005235.2	887	atG/atA	22/28	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.154836104092585	2		840	652	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660027	227660027	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	107	860	0	ENST00000305123.5:c.3428C>T	p.Ser1143Phe	p.S1143F	ENST00000305123	NM_005544.2	1143	tCt/tTt	1/2	1	2	FACETS	0.956	0.858	1	1	0.987	1	CLONAL	2	TRUE	1	0.154836104092585	2		860	723	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067312	37067313	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0020731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	62	748	1	ENST00000231790.2:c.1223_1224delinsTT	p.Pro408Leu	p.P408L	ENST00000231790	NM_000249.3	408	cCC/cTT	12/19	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.154836104092585	2		749	631	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467840	50467841	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0020731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	42	776	0	ENST00000331340.3:c.1075_1076delinsTT	p.Pro359Leu	p.P359L	ENST00000331340	NM_006060.4	359	CCg/TTg	8/8	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.154836104092585	2		776	501	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874755	151874755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	47	744	0	ENST00000262189.6:c.7783C>T	p.Pro2595Ser	p.P2595S	ENST00000262189	NM_170606.2	2595	Ccc/Tcc	38/59	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.154836104092585	2		744	517	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971164	21971178	+	frameshift_variant	Frame_Shift_Del	DEL	AGCAGCAGCAGCTCC	AGCAGCAGCAGCTCC	TGCT	novel	NA	P-0020731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	97	968	4	ENST00000304494.5:c.180_194delinsAGCA	p.Glu61AlafsTer55	p.E61Afs*55	ENST00000304494	NM_000077.4	60	gcGGAGCTGCTGCTGCTc/gcAGCAc	2/3	1	2	FACETS	0.973	0.868	1	1	0.986	1	CLONAL	2	TRUE	1	0.154836104092585	2		972	644	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0020738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	223	913	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.360713859634435	2	FACETS	0.801	0.751	0.852	0.801	0.751	0.852	CLONAL	2	TRUE	0	0.456375327346372	2		913	610	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188192	108188193	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTTCAT	novel	NA	P-0020738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	133	670	0	ENST00000278616.4:c.6292_6297dup	p.Leu2098_His2099dup	p.L2098_H2099dup	ENST00000278616	NM_000051.3	2098	-/CTTCAT	43/63	0.456375327346372	3	FACETS	1	0.977	1	0.611	0.557	0.667	CLONAL	1	TRUE	1	0.456375327346372	3		670	586	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871147	12871148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	73	364	0	ENST00000228872.4:c.375dup	p.Glu126Ter	p.E126*	ENST00000228872	NM_004064.3	125	tct/tcTt	1/3	0.456375327346372	3	FACETS	0.936	0.822	1	0.468	0.411	0.529	CLONAL	1	TRUE	1	0.456375327346372	3		364	420	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825395	134825395	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	73	794	0	ENST00000398015.3:c.911G>C	p.Arg304Pro	p.R304P	ENST00000398015	NM_004441.4	304	cGg/cCg	4/16	NA	2	FACETS	0.563	0.493	0.639			1	INDETERMINATE	1	TRUE	NA	0.456375327346372	2		794	568	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0020747-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	101	513	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	1	2	FACETS	0.777	0.697	0.861	1	0.983	1	SUBCLONAL	2	TRUE	1	0.26	2		513	500	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200958	108200958	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020747-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	103	401	0	ENST00000278616.4:c.7325A>C	p.Gln2442Pro	p.Q2442P	ENST00000278616	NM_000051.3	2442	cAg/cCg	50/63	0.3	1	FACETS	0.929	0.839	1	1	0.987	1	CLONAL	2	TRUE	0	0.26	1		401	371	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039817	47039817	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0020747-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	160	843	0	ENST00000377604.3:c.1161-1G>T		p.X387_splice	ENST00000377604	NM_001204468.1	387			0.3	1	FACETS	0.755	0.694	0.819	1	0.989	1	SUBCLONAL	2	TRUE	0	0.26	1		843	709	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256178	133256178	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020747-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	153	612	1	ENST00000320574.5:c.483G>T	p.Glu161Asp	p.E161D	ENST00000320574	NM_006231.2	161	gaG/gaT	6/49	NA	2	FACETS	1	0.957	1			1	INDETERMINATE	2	TRUE	NA	0.26	2		613	554	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73351559	73351559	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020747-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	16	229	0	ENST00000377767.4:c.653G>A	p.Gly218Glu	p.G218E	ENST00000377767	NM_014953.3	218	gGg/gAg	4/21	0.173044803827018	0	FACETS	0.342	0.253	0.449			1	SUBCLONAL	1	TRUE	0	0.26	0		229	266	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190670474	190670474	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020747-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	72	390	0	ENST00000441310.2:c.412G>T	p.Gly138Cys	p.G138C	ENST00000441310	NM_000534.4	138	Ggt/Tgt	4/13	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.26	2		390	413	SUCCESS
ATR	545	MSKCC	GRCh37	3	142204109	142204109	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020747-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	106	549	0	ENST00000350721.4:c.6094del	p.Leu2032CysfsTer18	p.L2032Cfs*18	ENST00000350721	NM_001184.3	2032	Ctg/tg	36/47	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.26	2		549	581	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630672	187630672	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020747-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	139	643	0	ENST00000441802.2:c.310A>T	p.Asn104Tyr	p.N104Y	ENST00000441802	NM_005245.3	104	Aat/Tat	2/27	1	2	FACETS	0.787	0.718	0.859	1	0.988	1	SUBCLONAL	2	TRUE	1	0.26	2		643	679	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110091	115110098	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGACAT	GGGGACAT	-	novel	NA	P-0020747-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	37	888	0	ENST00000257566.3:c.1780_1787del	p.Met594PhefsTer95	p.M594Ffs*95	ENST00000257566	NM_016569.3	594	ATGTCCCCt/t	8/8	1	2	FACETS	0.39	0.32	0.468	0.39	0.32	0.468	SUBCLONAL	1	TRUE	1	0.26	2		888	730	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675445	30675445	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020747-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	39	574	0	ENST00000376406.3:c.2911G>T	p.Val971Leu	p.V971L	ENST00000376406	NM_014641.2	971	Gtg/Ttg	8/15	1	2	FACETS	0.576	0.477	0.687	0.576	0.477	0.687	SUBCLONAL	1	TRUE	1	0.26	2		574	521	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349018	70349018	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020747-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	49	757	0	ENST00000374080.3:c.3530T>A	p.Leu1177His	p.L1177H	ENST00000374080		1177	cTt/cAt	25/45	0.3	1	FACETS	0.449	0.379	0.526	0.449	0.379	0.526	SUBCLONAL	1	TRUE	0	0.26	1		757	731	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163313631	163313632	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATAC	novel	NA	P-0020751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	70	382	1	ENST00000271452.3:c.779_782dup	p.Val262TyrfsTer6	p.V262Yfs*6	ENST00000271452	NM_145697.2	260	gat/gATACat	10/14	0.558505802120255	6	FACETS	0.85	0.742	0.968	0.17	0.148	0.194	CLONAL	1	TRUE	1	0.558505802120255	6		383	624	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207745	102207745	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	198	676	0	ENST00000263464.3:c.1727T>G	p.Val576Gly	p.V576G	ENST00000263464	NM_001165.4	576	gTa/gGa	9/9	0.504336494551441	4	FACETS	0.961	0.896	1	0.961	0.896	1	CLONAL	2	TRUE	2	0.558505802120255	4		676	575	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748512	40748512	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1473114374	NA	P-0020751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	371	1192	0	ENST00000392038.2:c.370T>C	p.Cys124Arg	p.C124R	ENST00000392038	NM_001626.4	124	Tgt/Cgt	5/14	0.453848616850108	4	FACETS	0.998	0.949	1	0.998	0.949	1	CLONAL	2	TRUE	2	0.558505802120255	4		1192	1037	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814309	76814309	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0020751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	74	541	0	ENST00000373344.5:c.6335T>G	p.Leu2112Ter	p.L2112*	ENST00000373344	NM_000489.3	2112	tTa/tGa	29/35	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.558505802120255	2		541	263	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858045	152858045	+	synonymous_variant	Silent	SNP	G	G	A	rs369691224	NA	P-0020751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	65	569	0	ENST00000406277.2:c.570C>T	p.Ala190=	p.A190=	ENST00000406277	NM_152274.4	190	gcC/gcT	6/7	1	2	FACETS	0.763	0.667	0.866	0.763	0.667	0.866	SUBCLONAL	1	TRUE	1	0.558505802120255	2		569	305	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199400	16199400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	76	527	0	ENST00000375759.3:c.173G>A	p.Ser58Asn	p.S58N	ENST00000375759	NM_015001.2	58	aGt/aAt	2/15	0.371782270190357	4	FACETS	0.781	0.685	0.883	0.39	0.342	0.442	SUBCLONAL	1	TRUE	2	0.493689085130684	4		527	589	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551846	150551846	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	69	248	1	ENST00000369026.2:c.161G>A	p.Gly54Asp	p.G54D	ENST00000369026	NM_021960.4	54	gGc/gAc	1/3	1	2	FACETS	0.675	0.59	0.766	0.675	0.59	0.766	SUBCLONAL	1	TRUE	1	0.493689085130684	2		249	414	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163298058	163298058	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	179	861	0	ENST00000271452.3:c.240del	p.Gly81AlafsTer8	p.G81Afs*8	ENST00000271452	NM_145697.2	80	gAa/ga	4/14	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.493689085130684	2		861	598	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091355	193091355	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121434262	NA	P-0020761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	42	367	2	ENST00000367435.3:c.25C>T	p.Arg9Ter	p.R9*	ENST00000367435	NM_024529.4	9	Cga/Tga	1/17	1	2	FACETS	0.556	0.466	0.655	0.556	0.466	0.655	SUBCLONAL	1	TRUE	1	0.493689085130684	2		369	306	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206942075	206942075	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0020761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	45	492	1	ENST00000423557.1:c.445-2A>G		p.X149_splice	ENST00000423557	NM_000572.2	149			1	2	FACETS	0.527	0.444	0.618	0.527	0.444	0.618	SUBCLONAL	1	TRUE	1	0.493689085130684	2		493	346	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349393	73349393	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	117	680	1	ENST00000377767.4:c.943C>T	p.Gln315Ter	p.Q315*	ENST00000377767	NM_014953.3	315	Caa/Taa	6/21	1	2	FACETS	0.977	0.886	1	0.977	0.886	1	CLONAL	1	TRUE	1	0.493689085130684	2		681	485	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058666	42058666	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	49	284	0	ENST00000219905.7:c.8386A>T	p.Thr2796Ser	p.T2796S	ENST00000219905	NM_001164273.1	2796	Aca/Tca	24/24	0.304843608398996	2	FACETS	1	0.861	1	0.501	0.43	0.577	CLONAL	1	TRUE	0	0.493689085130684	2		284	198	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845917	72845917	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	36	548	0	ENST00000268489.5:c.3550A>G	p.Lys1184Glu	p.K1184E	ENST00000268489	NM_006885.3	1184	Aag/Gag	6/10	0.353441001398623	3	FACETS	0.512	0.422	0.613	0.171	0.14	0.205	SUBCLONAL	1	TRUE	0	0.493689085130684	3		548	355	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0020761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	192	957	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.382399377537042	2	FACETS	1	0.98	1	0.573	0.532	0.615	CLONAL	1	TRUE	0	0.493689085130684	2		957	679	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096987	11096987	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	220	988	1	ENST00000358026.2:c.478C>T	p.Gln160Ter	p.Q160*	ENST00000358026	NM_001128849.1	160	Cag/Tag	4/36	0.299067289444052	2	FACETS	0.884	0.831	0.938	0.884	0.831	0.938	CLONAL	2	TRUE	0	0.493689085130684	2		989	504	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355547	15355547	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	219	889	1	ENST00000263377.2:c.2185G>T	p.Gly729Trp	p.G729W	ENST00000263377	NM_058243.2	729	Ggg/Tgg	12/20	0.299067289444052	2	FACETS	0.807	0.757	0.857	0.807	0.757	0.857	CLONAL	2	TRUE	0	0.493689085130684	2		890	550	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18972856	18972856	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	82	649	1	ENST00000262803.5:c.2495G>A	p.Arg832His	p.R832H	ENST00000262803	NM_002911.3	832	cGc/cAc	18/24	0.299067289444052	2	FACETS	0.657	0.58	0.738	0.328	0.29	0.369	SUBCLONAL	1	TRUE	0	0.493689085130684	2		650	506	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523082	25523082	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0020761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	101	851	1	ENST00000264709.3:c.103A>T	p.Lys35Ter	p.K35*	ENST00000264709	NM_175629.2	35	Aag/Tag	3/23	0.392912082203901	3	FACETS	0.672	0.601	0.748			1	SUBCLONAL	1	TRUE	NA	0.493689085130684	3		852	759	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519815	29519815	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs75158395	NA	P-0020761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	43	805	0	ENST00000389048.3:c.1756G>T	p.Ala586Ser	p.A586S	ENST00000389048	NM_004304.4	586	Gcc/Tcc	9/29	0.498356375591908	1	FACETS	0.292	0.244	0.345	0.292	0.244	0.345	SUBCLONAL	1	TRUE	0	0.493689085130684	1		805	449	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927421	178927422	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCTTCC	novel	NA	P-0020761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	58	605	0	ENST00000263967.3:c.1187_1192dup	p.Leu396_Pro397dup	p.L396_P397dup	ENST00000263967	NM_006218.2	396	gat/gaTCTTCCt	7/21	0.473659504480229	4	FACETS	0.655	0.563	0.755	0.327	0.281	0.378	SUBCLONAL	1	TRUE	2	0.493689085130684	4		605	536	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584548	189584548	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	128	579	0	ENST00000264731.3:c.844G>T	p.Gly282Ter	p.G282*	ENST00000264731	NM_003722.4	282	Gga/Tga	6/14	0.473659504480229	4	FACETS	1	0.983	1	0.678	0.617	0.742	CLONAL	1	TRUE	2	0.493689085130684	4		579	571	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912317	29912323	+	frameshift_variant	Frame_Shift_Del	DEL	TGCTGGC	TGCTGGC	-	novel	NA	P-0020761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	226	1001	0	ENST00000376809.5:c.936_942del	p.Ala313TrpfsTer7	p.A313Wfs*7	ENST00000376809	NM_002116.7	312	atTGCTGGC/at	5/8	0.299067289444052	2	FACETS	1	0.989	1	0.645	0.603	0.687	CLONAL	1	TRUE	0	0.493689085130684	2		1001	710	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953016	2953016	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	34	858	0	ENST00000396946.4:c.2924G>T	p.Arg975Leu	p.R975L	ENST00000396946	NM_032415.4	975	cGg/cTg	22/25	0.390028741009148	1	FACETS	0.238	0.194	0.287	0.238	0.194	0.287	SUBCLONAL	1	TRUE	0	0.493689085130684	1		858	436	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5077551	5077551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	92	584	0	ENST00000381652.3:c.1963A>G	p.Lys655Glu	p.K655E	ENST00000381652	NM_004972.3	655	Aaa/Gaa	15/25	0.304843608398996	2	FACETS	1	0.959	1	0.568	0.51	0.629	CLONAL	1	TRUE	0	0.493689085130684	2		584	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0020778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	527	649	1	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.635924507916316	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.635924507916316	1		650	871	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098973	178098973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	188	352	0	ENST00000397062.3:c.72G>C	p.Trp24Cys	p.W24C	ENST00000397062	NM_006164.4	24	tgG/tgC	2/5	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.635924507916316	NA		352	507	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186007	11187029	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGAATTGCTTGAACCTGGGAGGTGGAGGTTGCAGTGAGCCAAGATTGCGCCATTATACTCCAGCCTGGGCAACAAGAGCAAAACTCTGGCTCAAAAAAAAAAAAAAAAAAAAAAAAAGCGAGAGGCCTCAAAGTGCCACCACAGCACTCAGGCCTCACTAAAACATCCCCCATAAGTAACACTCTACCCCAAGGGAAATTCCAGAGCCCACTTGCTTAACAAATCTCACTGTGAGAATCCACTTGTTCATTTTACACAATCATTTACCACAGAGACTATGATGGTAAAAAAAAAAAGAAAAAAATTTCAAGAGCCAGAAGCCCCCGTTTCAGAGGAGCTAGCACCTTCCCTGCTTGCACCCAGCTGCCTCCTCCCTGGCCTCATCAGTCTCCAACACCTGCCTTCCACTGTTACTTCTCTGCCTTGCATGCCTTTGTCATTCCCTTTATGTGTGATCATGCTTCACATAAGCCCAACTACATGAATGAACTAAGTCCTGAGGACATAATGAGAAATTTGCTTGCCCTCTATTTTCCTCTCAATGAGCATGGGAGAGATGTAGCTATGATAGGTGAGTAGTGGGAATGGCAAGCAGTAATTTCAGAAGAGGGAAGGGGTCTCAGCCAGTGTAGGAGGGAGAAGTGGGTGACAGAAGTGCACAATGGTCCTTACCCATAAGTGTCAATTTCCGGGGCCTCTGCTTGGATGTGATGACTTGCAAAGACGGTGCTATGGACTGAATGCGAATGATTGGCTGGTTGGGGTCATATGTTCCTGGCACAGCCAATTCAAGGTCCCGGCACATCAGAAGTTTTGGGGAAACATATTGCAGCTCTAAGGATGTGAGCTGTAAATAATTACCAAAGGATTTAGTGTTCTGCCTCCAGGGAAGAATTTAAACGCAATTTAAGTATTTTTCAGTGGATTGCTAATAACAATTACTTGTCCCAAAGCAGAAGTAAAACCAGATGCTTTGGAATGAGTGTTAGAACATTCATAGACAGTAAAACAGAAAGGACTATA	AGAATTGCTTGAACCTGGGAGGTGGAGGTTGCAGTGAGCCAAGATTGCGCCATTATACTCCAGCCTGGGCAACAAGAGCAAAACTCTGGCTCAAAAAAAAAAAAAAAAAAAAAAAAAGCGAGAGGCCTCAAAGTGCCACCACAGCACTCAGGCCTCACTAAAACATCCCCCATAAGTAACACTCTACCCCAAGGGAAATTCCAGAGCCCACTTGCTTAACAAATCTCACTGTGAGAATCCACTTGTTCATTTTACACAATCATTTACCACAGAGACTATGATGGTAAAAAAAAAAAGAAAAAAATTTCAAGAGCCAGAAGCCCCCGTTTCAGAGGAGCTAGCACCTTCCCTGCTTGCACCCAGCTGCCTCCTCCCTGGCCTCATCAGTCTCCAACACCTGCCTTCCACTGTTACTTCTCTGCCTTGCATGCCTTTGTCATTCCCTTTATGTGTGATCATGCTTCACATAAGCCCAACTACATGAATGAACTAAGTCCTGAGGACATAATGAGAAATTTGCTTGCCCTCTATTTTCCTCTCAATGAGCATGGGAGAGATGTAGCTATGATAGGTGAGTAGTGGGAATGGCAAGCAGTAATTTCAGAAGAGGGAAGGGGTCTCAGCCAGTGTAGGAGGGAGAAGTGGGTGACAGAAGTGCACAATGGTCCTTACCCATAAGTGTCAATTTCCGGGGCCTCTGCTTGGATGTGATGACTTGCAAAGACGGTGCTATGGACTGAATGCGAATGATTGGCTGGTTGGGGTCATATGTTCCTGGCACAGCCAATTCAAGGTCCCGGCACATCAGAAGTTTTGGGGAAACATATTGCAGCTCTAAGGATGTGAGCTGTAAATAATTACCAAAGGATTTAGTGTTCTGCCTCCAGGGAAGAATTTAAACGCAATTTAAGTATTTTTCAGTGGATTGCTAATAACAATTACTTGTCCCAAAGCAGAAGTAAAACCAGATGCTTTGGAATGAGTGTTAGAACATTCATAGACAGTAAAACAGAAAGGACTATA	-	novel	NA	P-0020778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	0	216	0	0	ENST00000361445.4:c.6351+38_6526+672del		p.X2117_splice	ENST00000361445	NM_004958.3	2117		46/58	0.298577328914974	4	FACETS	1	0.996	1	1	0.996	1	INDETERMINATE	5	TRUE	2	0.635924507916316	4		0	216	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932266	36932266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	471	684	0	ENST00000361632.4:c.2203G>A	p.Ala735Thr	p.A735T	ENST00000361632		735	Gca/Aca	16/16	0.427094672421507	3	FACETS	0.823	0.788	0.858	0.823	0.788	0.858	CLONAL	2	TRUE	1	0.635924507916316	3		684	1186	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937567	36937690	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGCCTCCCAGACCTGTTGGAGTCCTAAGCCCCGGTTTGTAGGGATCTGTTTGGACTGCGGGAGGTGTCGAGGTGGAGGGATGGCCTTCAGAGGGAGTCACCTTCCAGAACAGCTGCACTGTCCT	CGCCTCCCAGACCTGTTGGAGTCCTAAGCCCCGGTTTGTAGGGATCTGTTTGGACTGCGGGAGGTGTCGAGGTGGAGGGATGGCCTTCAGAGGGAGTCACCTTCCAGAACAGCTGCACTGTCCT	-	novel	NA	P-0020778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	51	279	0	ENST00000361632.4:c.1048_1071+100del		p.X350_splice	ENST00000361632		350		8/16	0.427094672421507	3	FACETS	0.419	0.356	0.489	0.21	0.178	0.245	SUBCLONAL	1	TRUE	1	0.635924507916316	3		279	504	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	430250	430250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1280178625	NA	P-0020778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	167	373	0	ENST00000399788.2:c.2452C>T	p.Arg818Trp	p.R818W	ENST00000399788	NM_001042603.1	818	Cgg/Tgg	18/28	0.635924507916316	1	FACETS	0.772	0.716	0.829	0.772	0.716	0.829	SUBCLONAL	1	TRUE	0	0.635924507916316	1		373	464	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431871	49431871	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	522	683	0	ENST00000301067.7:c.9268G>T	p.Glu3090Ter	p.E3090*	ENST00000301067	NM_003482.3	3090	Gag/Tag	34/54	0.635924507916316	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.635924507916316	1		683	898	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665429	138665429	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1510	428	651	0	ENST00000330315.3:c.136C>G	p.Pro46Ala	p.P46A	ENST00000330315	NM_023067.3	46	Ccg/Gcg	1/1	0.626288608923389	5	FACETS	1	0.994	1	0.339	0.322	0.357	CLONAL	1	TRUE	1	0.635924507916316	5		651	1938	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821529	32821529	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	365	688	0	ENST00000354258.4:c.65C>G	p.Ser22Trp	p.S22W	ENST00000354258	NM_000593.5	22	tCg/tGg	1/11	0.278448893221762	3	FACETS	1	0.993	1	0.638	0.605	0.672	INDETERMINATE	1	TRUE	1	0.635924507916316	3		688	1185	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873631	151873631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745471084	NA	P-0020778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	202	466	2	ENST00000262189.6:c.8907G>A	p.Met2969Ile	p.M2969I	ENST00000262189	NM_170606.2	2969	atG/atA	38/59	0.427094672421507	3	FACETS	1	0.957	1	0.521	0.483	0.559	CLONAL	1	TRUE	1	0.635924507916316	3		468	804	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090829	5090829	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	112	298	0	ENST00000381652.3:c.2977G>A	p.Gly993Arg	p.G993R	ENST00000381652	NM_004972.3	993	Gga/Aga	22/25	0.635924507916316	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.635924507916316	1		298	237	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831277	3831277	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	160	532	0	ENST00000262367.5:c.1604G>T	p.Gly535Val	p.G535V	ENST00000262367	NM_004380.2	535	gGa/gTa	7/31	NA	2	FACETS	0.953	0.876	1			1	INDETERMINATE	1	TRUE	NA	0.446444349586455	2		532	752	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607376	46607376	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	204	749	0	ENST00000263734.3:c.1565A>T	p.Asn522Ile	p.N522I	ENST00000263734	NM_001430.4	522	aAt/aTt	12/16	1	2	FACETS	0.839	0.778	0.903	0.839	0.778	0.903	CLONAL	1	TRUE	1	0.446444349586455	2		749	1089	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0020797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	471	1096	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.747270595791458	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.747270595791458	1		1097	762	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985587	2985587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064795280	NA	P-0020797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	75	706	0	ENST00000396946.4:c.224G>A	p.Arg75Gln	p.R75Q	ENST00000396946	NM_032415.4	75	cGg/cAg	4/25	1	2	FACETS	0.305	0.267	0.346	0.305	0.267	0.346	SUBCLONAL	1	TRUE	1	0.747270595791458	2		706	659	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0020809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	184	807	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	0.790143958285115	3	FACETS	0.973	0.915	1	0.973	0.915	1	CLONAL	2	TRUE	1	0.790143958285115	3		807	334	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519801	29519801	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	98	992	2	ENST00000389048.3:c.1770G>T	p.Leu590Phe	p.L590F	ENST00000389048	NM_004304.4	590	ttG/ttT	9/29	1	2	FACETS	0.943	0.855	1	0.943	0.855	1	CLONAL	1	TRUE	1	0.790143958285115	2		994	263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577054	7577054	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	703	1375	1	ENST00000269305.4:c.884del	p.Pro295LeufsTer50	p.P295Lfs*50	ENST00000269305	NM_001126112.2	295	cCt/ct	8/11	0.817369445375359	1	FACETS	0.904	0.879	0.928	0.904	0.879	0.928	CLONAL	1	TRUE	0	0.837902360003937	1		1376	1079	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420464	49420464	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	559	1072	1	ENST00000301067.7:c.15285C>G	p.Cys5095Trp	p.C5095W	ENST00000301067	NM_003482.3	5095	tgC/tgG	48/54	1	2	FACETS	0.925	0.889	0.962	0.925	0.889	0.962	CLONAL	1	TRUE	1	0.837902360003937	2		1073	1442	SUCCESS
APC	324	MSKCC	GRCh37	5	112175921	112175922	+	stop_gained	Nonsense_Mutation	DNP	GA	GA	TG	novel	NA	P-0020812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	344	451	0	ENST00000257430.4:c.4630_4631delinsTG	p.Glu1544Ter	p.E1544*	ENST00000257430	NM_000038.5	1544	GAa/TGa	16/16	0.837902360003937	2	FACETS	0.933	0.904	0.961	0.933	0.904	0.961	CLONAL	2	TRUE	0	0.837902360003937	2		451	440	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0020819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	191	1015	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	NA	2	FACETS	0.99	0.928	1			1	INDETERMINATE	2	TRUE	NA	0.462444080311013	2		1015	417	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758348	41758348	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs762510681	NA	P-0020819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	21	676	4	ENST00000301178.4:c.1804G>A	p.Gly602Ser	p.G602S	ENST00000301178	NM_021913.4	602	Ggt/Agt	15/20	1	2	FACETS	0.264	0.203	0.335	0.264	0.203	0.335	SUBCLONAL	1	TRUE	1	0.462444080311013	2		680	344	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696731	47696731	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	47	542	0	ENST00000347630.2:c.217C>A	p.Pro73Thr	p.P73T	ENST00000347630	NM_001007230.1	73	Ccc/Acc	5/11	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.462444080311013	2		542	199	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39618771	39618771	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	24	540	0	ENST00000262039.4:c.1995G>C	p.Leu665Phe	p.L665F	ENST00000262039	NM_002647.2	665	ttG/ttC	18/25	0.462444080311013	1	FACETS	0.493	0.39	0.609	0.493	0.39	0.609	SUBCLONAL	1	TRUE	0	0.462444080311013	1		540	162	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	65	766	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.868927167309295	NA		766	577	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	173	720	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.347978574293226	1	FACETS	0.466	0.433	0.501	0.466	0.433	0.501	INDETERMINATE	1	TRUE	0	0.868927167309295	1		721	483	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0020822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	151	388	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	0.868927167309295	2		389	341	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791758	42791758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1380826096	NA	P-0020822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	96	829	1	ENST00000575354.2:c.644G>A	p.Arg215Gln	p.R215Q	ENST00000575354	NM_015125.3	215	cGg/cAg	5/20	0.868927167309295	1	FACETS	0.278	0.249	0.309	0.278	0.249	0.309	SUBCLONAL	1	TRUE	0	0.868927167309295	1		830	449	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110596	8110596	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465361269	NA	P-0020822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	306	899	0	ENST00000585124.1:c.296G>A	p.Ser99Asn	p.S99N	ENST00000585124	NM_004217.3	99	aGc/aAc	5/9	1	2	FACETS	0.769	0.727	0.812	0.769	0.727	0.812	SUBCLONAL	1	TRUE	1	0.868927167309295	2		899	916	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089554	27089554	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	65	852	0	ENST00000324856.7:c.2511del	p.Gly838GlufsTer21	p.G838Efs*21	ENST00000324856	NM_006015.4	837	gCc/gc	8/20	0.868927167309295	1	FACETS	0.175	0.151	0.2	0.175	0.151	0.2	SUBCLONAL	1	TRUE	0	0.868927167309295	1		852	484	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55260505	55260505	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs987884612	NA	P-0020822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	76	897	0	ENST00000275493.2:c.2672A>G	p.Tyr891Cys	p.Y891C	ENST00000275493	NM_005228.3	891	tAt/tGt	22/28	1	2	FACETS	0.223	0.195	0.253	0.223	0.195	0.253	SUBCLONAL	1	TRUE	1	0.868927167309295	2		897	784	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0020823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	128	525	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.23	2		525	817	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600408	10600408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1412883238	NA	P-0020823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	53	859	1	ENST00000171111.5:c.1447C>T	p.Arg483Cys	p.R483C	ENST00000171111	NM_203500.1	483	Cgc/Tgc	4/6	0.23974958955852	1	FACETS	0.589	0.501	0.685	0.589	0.501	0.685	SUBCLONAL	1	TRUE	0	0.23	1		860	693	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139232	108139232	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764409952	NA	P-0020823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	67	863	1	ENST00000278616.4:c.2734C>T	p.Gln912Ter	p.Q912*	ENST00000278616	NM_000051.3	912	Cag/Tag	18/63	1	2	FACETS	0.733	0.636	0.838	0.733	0.636	0.838	SUBCLONAL	1	TRUE	1	0.23	2		864	795	SUCCESS
ATM	472	MSKCC	GRCh37	11	108213995	108213995	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	59	549	3	ENST00000278616.4:c.8315G>T	p.Gly2772Val	p.G2772V	ENST00000278616	NM_000051.3	2772	gGa/gTa	57/63	1	2	FACETS	0.954	0.821	1	0.954	0.821	1	CLONAL	1	TRUE	1	0.23	2		552	538	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219368	1219368	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	77	784	2	ENST00000326873.7:c.421del	p.Asp141ThrfsTer20	p.D141Tfs*20	ENST00000326873	NM_000455.4	140	ctG/ct	3/10	0.3	2	FACETS	1	0.931	1			1	CLONAL	1	TRUE	NA	0.23	2		786	616	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541457	187541457	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	43	591	0	ENST00000441802.2:c.6283G>C	p.Glu2095Gln	p.E2095Q	ENST00000441802	NM_005245.3	2095	Gag/Cag	10/27	1	2	FACETS	0.777	0.651	0.918	0.777	0.651	0.918	CLONAL	1	TRUE	1	0.23	2		591	481	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971149	21971192	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCT	GGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCT	-	novel	NA	P-0020823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	29	658	0	ENST00000304494.5:c.166_209del	p.Ser56GlnfsTer49	p.S56Qfs*49	ENST00000304494	NM_000077.4	56	AGCGCCCGAGTGGCGGAGCTGCTGCTGCTCCACGGCGCGGAGCCc/c	2/3	0.171324446234565	0	FACETS	0.474	0.38	0.58			1	SUBCLONAL	1	TRUE	0	0.23	0		658	410	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044578	47044579	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	70	987	0	ENST00000377604.3:c.2076dup	p.Gly693TrpfsTer27	p.G693Wfs*27	ENST00000377604	NM_001204468.1	692	gct/gcTt	18/24	1	2	FACETS	0.805	0.701	0.918	0.805	0.701	0.918	CLONAL	1	TRUE	1	0.23	2		987	756	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937067	76937067	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	66	653	0	ENST00000373344.5:c.3681G>T	p.Lys1227Asn	p.K1227N	ENST00000373344	NM_000489.3	1227	aaG/aaT	9/35	1	2	FACETS	0.866	0.751	0.99	0.866	0.751	0.99	CLONAL	1	TRUE	1	0.23	2		653	663	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	115	766	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.968	0.871	1	0.968	0.871	1	CLONAL	1	TRUE	1	0.281951813922972	2		766	843	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0020832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	194	846	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	0.281951813922972	2		846	921	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023008	27023010	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs587779737	NA	P-0020832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	11	138	1	ENST00000324856.7:c.126_128del	p.Ala45del	p.A45del	ENST00000324856	NM_006015.4	38	gaGGCg/gag	1/20	1	2	FACETS	0.413	0.285	0.571	0.413	0.285	0.571	SUBCLONAL	1	TRUE	1	0.281951813922972	2		139	189	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913136	44913136	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	129	445	3	ENST00000377967.4:c.811C>T	p.Gln271Ter	p.Q271*	ENST00000377967	NM_021140.2	271	Cag/Tag	10/29	1	2	FACETS	0.744	0.673	0.82	0.744	0.673	0.82	SUBCLONAL	1	TRUE	1	0.281951813922972	2		448	1230	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155453	47155453	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752011468	NA	P-0020832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	113	717	0	ENST00000409792.3:c.4628G>A	p.Arg1543Gln	p.R1543Q	ENST00000409792	NM_014159.6	1543	cGg/cAg	5/21	1	2	FACETS	0.797	0.716	0.883	0.797	0.716	0.883	SUBCLONAL	1	TRUE	1	0.281951813922972	2		717	1006	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106862	27106862	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	106	738	0	ENST00000324856.7:c.6473del	p.Arg2158GlnfsTer42	p.R2158Qfs*42	ENST00000324856	NM_006015.4	2158	cGa/ca	20/20	1	2	FACETS	0.774	0.693	0.861	0.774	0.693	0.861	SUBCLONAL	1	TRUE	1	0.281951813922972	2		738	971	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28600632	28600632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771504819	NA	P-0020832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	185	1062	3	ENST00000253063.3:c.983G>A	p.Arg328Gln	p.R328Q	ENST00000253063	NM_031459.4	328	cGg/cAg	7/10	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.281951813922972	2		1065	1274	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298716	46298716	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0020832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	77	536	0	ENST00000334344.6:c.5364-1G>C		p.X1788_splice	ENST00000334344	NM_152641.2	1788			1	2	FACETS	0.802	0.704	0.908	0.802	0.704	0.908	CLONAL	1	TRUE	1	0.281951813922972	2		536	681	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781317	3781317	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1390	151	1248	0	ENST00000262367.5:c.5048G>C	p.Arg1683Pro	p.R1683P	ENST00000262367	NM_004380.2	1683	cGc/cCc	30/31	1	2	FACETS	0.695	0.633	0.761	0.695	0.633	0.761	SUBCLONAL	1	TRUE	1	0.281951813922972	2		1248	1541	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524150	187524150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	107	777	1	ENST00000441802.2:c.11389G>A	p.Asp3797Asn	p.D3797N	ENST00000441802	NM_005245.3	3797	Gat/Aat	20/27	1	2	FACETS	0.817	0.732	0.908	0.817	0.732	0.908	CLONAL	1	TRUE	1	0.281951813922972	2		778	929	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525071	187525071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	116	761	0	ENST00000441802.2:c.10609G>A	p.Glu3537Lys	p.E3537K	ENST00000441802	NM_005245.3	3537	Gag/Aag	19/27	1	2	FACETS	0.868	0.781	0.96	0.868	0.781	0.96	CLONAL	1	TRUE	1	0.281951813922972	2		761	948	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138627	37138627	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0020832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1216	136	1090	0	ENST00000373509.5:c.161C>G	p.Ser54Ter	p.S54*	ENST00000373509	NM_002648.3	54	tCa/tGa	2/6	1	2	FACETS	0.714	0.647	0.784	0.714	0.647	0.784	SUBCLONAL	1	TRUE	1	0.281951813922972	2		1090	1352	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104607	69104607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs563106453	NA	P-0020832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	182	974	2	ENST00000288368.4:c.4451G>A	p.Arg1484Gln	p.R1484Q	ENST00000288368	NM_024870.2	1484	cGa/cAa	37/40	1	2	FACETS	0.937	0.862	1	0.937	0.862	1	CLONAL	1	TRUE	1	0.281951813922972	2		976	1378	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913181	44913248	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCTGGTATTTCCTCGGAAGGTGAGACTTACCAGACATTTATGTTTGATTTTGTCTATTCCAGCTAAG	TCCTGGTATTTCCTCGGAAGGTGAGACTTACCAGACATTTATGTTTGATTTTGTCTATTCCAGCTAAG	GAA	novel	NA	P-0020832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	78	913	7	ENST00000377967.4:c.856_875+48delinsGAA		p.X286_splice	ENST00000377967	NM_021140.2	286		10/29	1	2	FACETS	0.487	0.426	0.552	0.487	0.426	0.552	SUBCLONAL	1	TRUE	1	0.281951813922972	2		920	1137	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	263	766	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.956	0.902	1	0.956	0.902	1	CLONAL	1	TRUE	1	0.83229504842212	2		766	661	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0020842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	793	846	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.83229504842212	3	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.83229504842212	3		846	1174	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115955	8115956	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0020842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	300	688	0	ENST00000346208.3:c.1304_1305dup	p.Ser436ProfsTer40	p.S436Pfs*40	ENST00000346208		434	cac/caCCc	6/6	0.499435555198877	3	FACETS	1	0.993	1			1	CLONAL	1	TRUE	NA	0.83229504842212	3		688	765	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406645	70406645	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs754614889	NA	P-0020842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	269	1111	0	ENST00000373644.4:c.4159A>G	p.Thr1387Ala	p.T1387A	ENST00000373644	NM_030625.2	1387	Aca/Gca	4/12	1	2	FACETS	0.879	0.829	0.931	0.879	0.829	0.931	CLONAL	1	TRUE	1	0.83229504842212	2		1111	735	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486844	56486844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	599	802	0	ENST00000267101.3:c.1258G>A	p.Gly420Ser	p.G420S	ENST00000267101	NM_001982.3	420	Ggc/Agc	11/28	0.19567266976791	6	FACETS	0.904	0.874	0.933			1	INDETERMINATE	4	TRUE	NA	0.83229504842212	6		802	1061	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49280957	49280957	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	259	822	0	ENST00000282018.3:c.4G>C	p.Glu2Gln	p.E2Q	ENST00000282018	NM_020377.2	2	Gag/Cag	1/1	1	2	FACETS	0.892	0.84	0.944	0.892	0.84	0.944	CLONAL	1	TRUE	1	0.83229504842212	2		822	698	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472605	88472605	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	221	690	0	ENST00000360948.2:c.1950G>C	p.Glu650Asp	p.E650D	ENST00000360948	NM_001012338.2	650	gaG/gaC	16/19	1	2	FACETS	0.882	0.827	0.939	0.882	0.827	0.939	CLONAL	1	TRUE	1	0.83229504842212	2		690	602	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408885	41408885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868295248	NA	P-0020842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	319	740	0	ENST00000373198.4:c.541G>A	p.Glu181Lys	p.E181K	ENST00000373198	NM_133170.3	181	Gag/Aag	4/32	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.83229504842212	2		740	710	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	336	692	4	ENST00000263967.3:c.3012G>T	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atT	21/21	1	2	FACETS	0.929	0.882	0.976	0.929	0.882	0.976	CLONAL	1	TRUE	1	0.854992703247081	2		696	846	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629108	86629108	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853218	NA	P-0020865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	245	450	0	ENST00000274376.6:c.853C>T	p.Arg285Ter	p.R285*	ENST00000274376	NM_002890.2	285	Cga/Tga	4/25	0.854992703247081	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.854992703247081	1		450	326	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11264748	11264748	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	138	895	0	ENST00000361445.4:c.3814G>T	p.Ala1272Ser	p.A1272S	ENST00000361445	NM_004958.3	1272	Gcc/Tcc	26/58	1	2	FACETS	0.279	0.253	0.307	0.279	0.253	0.307	SUBCLONAL	1	TRUE	1	0.854992703247081	2		895	1155	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574013	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	539	888	0	ENST00000269305.4:c.1014dup	p.Glu339ArgfsTer8	p.E339Rfs*8	ENST00000269305	NM_001126112.2	338	-/C	10/11	0.854992703247081	1	FACETS	0.97	0.944	0.996	0.97	0.944	0.996	CLONAL	1	TRUE	0	0.854992703247081	1		888	744	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490300	29490306	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCATG	CAGCATG	-	novel	NA	P-0020865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	368	672	0	ENST00000356175.3:c.389_395del	p.His130LeufsTer33	p.H130Lfs*33	ENST00000356175	NM_000267.3	129	CAGCATGca/ca	4/57	0.854992703247081	1	FACETS	0.95	0.917	0.981	0.95	0.917	0.981	CLONAL	1	TRUE	0	0.854992703247081	1		672	519	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057304	180057304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140347743	NA	P-0020865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	222	966	3	ENST00000261937.6:c.434C>T	p.Thr145Met	p.T145M	ENST00000261937	NM_182925.4	145	aCg/aTg	4/30	0.854992703247081	1	FACETS	0.309	0.287	0.331	0.309	0.287	0.331	SUBCLONAL	1	TRUE	0	0.854992703247081	1		969	962	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0020875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	169	617	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	1	2	FACETS	0.996	0.921	1	0.996	0.921	1	CLONAL	1	TRUE	1	0.601675630056562	2		617	564	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0020875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	86	477	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	0.796	0.71	0.887	0.796	0.71	0.887	SUBCLONAL	1	TRUE	1	0.601675630056562	2		477	359	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0020875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	108	749	1	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	0.989	0.896	1	0.989	0.896	1	CLONAL	1	TRUE	1	0.601675630056562	2		750	363	SUCCESS
APC	324	MSKCC	GRCh37	5	112174061	112174061	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0020875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	79	506	1	ENST00000257430.4:c.2770A>T	p.Arg924Ter	p.R924*	ENST00000257430	NM_000038.5	924	Aga/Tga	16/16	1	2	FACETS	0.89	0.791	0.994	0.89	0.791	0.994	CLONAL	1	TRUE	1	0.601675630056562	2		507	295	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920435	114920435	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	199	717	1	ENST00000543371.1:c.1376G>A	p.Trp459Ter	p.W459*	ENST00000543371	NM_001198531.1	459	tGg/tAg	13/14	1	2	FACETS	0.899	0.835	0.964	0.899	0.835	0.964	CLONAL	1	TRUE	1	0.601675630056562	2		718	736	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699324	18699324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369934938	NA	P-0020875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	70	653	0	ENST00000266497.5:c.3425G>A	p.Arg1142His	p.R1142H	ENST00000266497		1142	cGt/cAt	24/31	1	2	FACETS	0.822	0.724	0.926	0.822	0.724	0.926	CLONAL	1	TRUE	1	0.601675630056562	2		653	283	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46276031	46276031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146235035	NA	P-0020875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	235	756	0	ENST00000371998.3:c.3467G>A	p.Arg1156Gln	p.R1156Q	ENST00000371998		1156	cGa/cAa	18/23	0.601675630056562	3	FACETS	0.87	0.811	0.931	0.435	0.405	0.466	CLONAL	1	TRUE	1	0.601675630056562	3		756	1168	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034395	123034395	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	70	704	0	ENST00000355640.3:c.1152C>G	p.Phe384Leu	p.F384L	ENST00000355640		384	ttC/ttG	6/7	0.601675630056562	3	FACETS	0.709	0.62	0.804	0.354	0.31	0.402	SUBCLONAL	1	TRUE	1	0.601675630056562	3		704	427	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0020885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	12	621	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.425957980058667	4	FACETS	1	0.83	1	0.623	0.447	0.829	CLONAL	1	TRUE	2	0.430387924152758	4		621	64	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0020885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	24	505	1				ENST00000310581	NM_198253.2	-/1132			0.430387924152758	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	2	TRUE	0	0.430387924152758	2		506	51	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348752	89348752	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	20	1300	0	ENST00000301030.4:c.4198G>A	p.Asp1400Asn	p.D1400N	ENST00000301030	NM_001256183.1	1400	Gat/Aat	9/13	1	2	FACETS	0.774	0.614	0.947	1	0.929	1	CLONAL	2	TRUE	1	0.430387924152758	2		1300	60	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037502	12037502	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146280653	NA	P-0020885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	15	394	3	ENST00000396373.4:c.1133G>A	p.Arg378Gln	p.R378Q	ENST00000396373	NM_001987.4	378	cGa/cAa	6/8	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.430387924152758	NA		397	54	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346880	89346880	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1272359896	NA	P-0020885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	16	337	0	ENST00000301030.4:c.6070C>T	p.Pro2024Ser	p.P2024S	ENST00000301030	NM_001256183.1	2024	Ccg/Tcg	9/13	1	2	FACETS	0.885	0.687	1	1	0.927	1	CLONAL	2	TRUE	1	0.430387924152758	2		337	42	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424972	49424972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748519188	NA	P-0020885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	10	953	0	ENST00000301067.7:c.13516C>T	p.Pro4506Ser	p.P4506S	ENST00000301067	NM_003482.3	4506	Ccc/Tcc	39/54	0.418270397399699	3	FACETS	0.672	0.461	0.931	0.336	0.23	0.466	SUBCLONAL	1	TRUE	1	0.430387924152758	3		953	84	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120535147	120535148	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	29	826	5	ENST00000229340.5:c.507_508delinsTT	p.Arg170Ter	p.R170*	ENST00000229340	NM_006861.6	169	ctCCga/ctTTga	6/6	0.418270397399699	3	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	1	0.430387924152758	3		831	68	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148529745	148529745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	15	616	1	ENST00000320356.2:c.344C>T	p.Pro115Leu	p.P115L	ENST00000320356	NM_004456.4	115	cCc/cTc	4/20	0.425957980058667	4	FACETS	1	0.874	1	1	0.874	1	CLONAL	2	TRUE	2	0.430387924152758	4		617	40	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	86	757	0	ENST00000425967.3:c.1731C>G	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaG	13/19	0.386211038690716	1	FACETS	1	0.921	1	1	0.988	1	CLONAL	2	FALSE	0	0.386211038690716	1		757	177	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894228	NA	P-0020900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	8	793	2	ENST00000451590.1:c.37G>T	p.Gly13Cys	p.G13C	ENST00000451590	NM_001130442.1	13	Ggt/Tgt	2/5	1	2	FACETS	0.115	0.073	0.169	0.115	0.073	0.169	SUBCLONAL	1	FALSE	1	0.386211038690716	2		795	361	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849261	76849261	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	74	384	0	ENST00000373344.5:c.6015del	p.Phe2005LeufsTer10	p.F2005Lfs*10	ENST00000373344	NM_000489.3	2005	ttT/tt	26/35	0.0790517449135493	2	FACETS	1	0.961	1			1	INDETERMINATE	4	FALSE	NA	0.386211038690716	2		384	92	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396893	139396893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377294245	NA	P-0020923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	221	844	0	ENST00000277541.6:c.5215G>A	p.Val1739Met	p.V1739M	ENST00000277541	NM_017617.3	1739	Gtg/Atg	28/34	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		844	831	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612157	189612157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	314	910	0	ENST00000264731.3:c.1909C>T	p.Arg637Cys	p.R637C	ENST00000264731	NM_003722.4	637	Cgt/Tgt	14/14	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		910	950	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073338	8073338	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	81	554	0	ENST00000377482.5:c.1321T>C	p.Ser441Pro	p.S441P	ENST00000377482	NM_018948.3	441	Tca/Cca	4/4	0.233937621334794	3	FACETS	0.544	0.479	0.614	0.272	0.239	0.307	INDETERMINATE	1	TRUE	1	0.515467712516679	3		554	727	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	600	756	0	ENST00000269305.4:c.644del	p.Ser215MetfsTer32	p.S215Mfs*32	ENST00000269305	NM_001126112.2	215	aGt/at	6/11	NA	2	FACETS	0.975	0.941	1			1	INDETERMINATE	2	TRUE	NA	0.515467712516679	2		756	1194	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984273	7984274	+	missense_variant	Missense_Mutation	DNP	GC	GC	CT	novel	NA	P-0020936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	218	613	1	ENST00000319144.4:c.455_456delinsAG	p.Gly152Glu	p.G152E	ENST00000319144	NM_001139.2	152	gGC/gAG	4/15	NA	2	FACETS	0.845	0.786	0.906			1	INDETERMINATE	1	TRUE	NA	0.515467712516679	2		614	1001	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033601	48033601	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1553333303	NA	P-0020936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	25	491	0	ENST00000234420.5:c.3812T>C	p.Val1271Ala	p.V1271A	ENST00000234420	NM_000179.2	1271	gTa/gCa	9/10	0.359646521542207	1	FACETS	0.29	0.229	0.36	0.29	0.229	0.36	SUBCLONAL	1	TRUE	0	0.515467712516679	1		491	248	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541891	187541891	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	254	641	1	ENST00000441802.2:c.5849T>A	p.Leu1950Gln	p.L1950Q	ENST00000441802	NM_005245.3	1950	cTa/cAa	10/27	0.515467712516679	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.515467712516679	1		642	656	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0020946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	385	1015	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.483674394812916	2	FACETS	0.966	0.923	1	0.966	0.923	1	CLONAL	2	TRUE	0	0.483674394812916	2		1015	824	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0020946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	118	607	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.483674394812916	2		607	456	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0020946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	246	869	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.483674394812916	3	FACETS	0.88	0.826	0.934	0.88	0.826	0.934	CLONAL	2	TRUE	1	0.483674394812916	3		869	718	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210733	5210733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779302415	NA	P-0020946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	190	1130	1	ENST00000357368.4:c.5318C>T	p.Ser1773Leu	p.S1773L	ENST00000357368	NM_002850.3	1773	tCg/tTg	34/38	0.308478205776014	4	FACETS	1	0.94	1	0.51	0.471	0.551	CLONAL	1	TRUE	2	0.483674394812916	4		1131	1142	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968633	55968633	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200338299	NA	P-0020946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	161	887	2	ENST00000263923.4:c.2030C>T	p.Thr677Met	p.T677M	ENST00000263923	NM_002253.2	677	aCg/aTg	14/30	0.483674394812916	3	FACETS	0.975	0.895	1	0.487	0.447	0.53	CLONAL	1	TRUE	1	0.483674394812916	3		889	848	SUCCESS
APC	324	MSKCC	GRCh37	5	112174349	112174349	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	59	404	1	ENST00000257430.4:c.3058G>T	p.Glu1020Ter	p.E1020*	ENST00000257430	NM_000038.5	1020	Gaa/Taa	16/16	NA	2	FACETS	0.935	0.812	1			1	INDETERMINATE	1	TRUE	NA	0.483674394812916	2		405	261	SUCCESS
APC	324	MSKCC	GRCh37	5	112175608	112175608	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	93	464	0	ENST00000257430.4:c.4317del	p.Pro1440HisfsTer33	p.P1440Hfs*33	ENST00000257430	NM_000038.5	1439	ccT/cc	16/16	NA	2	FACETS	1	0.937	1			1	INDETERMINATE	1	TRUE	NA	0.483674394812916	2		464	362	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830766	3830767	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	140	722	0	ENST00000262367.5:c.1789dup	p.Thr597AsnfsTer11	p.T597Nfs*11	ENST00000262367	NM_004380.2	597	act/aAct	8/31	NA	2	FACETS	1	0.935	1			1	INDETERMINATE	1	TRUE	NA	0.483674394812916	2		722	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0020956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	296	678	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.601288121892762	1	FACETS	0.994	0.942	1	0.994	0.942	1	CLONAL	1	TRUE	0	0.601288121892762	1		680	693	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	387	527	0	ENST00000397062.3:c.92G>A	p.Gly31Glu	p.G31E	ENST00000397062	NM_006164.4	31	gGa/gAa	2/5	0.599240817893404	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.601288121892762	2		527	629	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39542524	39542524	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs143755535	NA	P-0020956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	108	626	0	ENST00000262039.4:c.328A>G	p.Ile110Val	p.I110V	ENST00000262039	NM_002647.2	110	Ata/Gta	3/25	0.276116277272046	1	FACETS	0.406	0.365	0.449	0.406	0.365	0.449	INDETERMINATE	1	TRUE	0	0.601288121892762	1		626	619	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057874	27057874	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	395	1190	0	ENST00000324856.7:c.1582C>T	p.Gln528Ter	p.Q528*	ENST00000324856	NM_006015.4	528	Cag/Tag	3/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.601288121892762	2		1190	1307	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319965	8319965	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs141403124	NA	P-0020956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	53	336	0	ENST00000356435.5:c.5536G>A	p.Ala1846Thr	p.A1846T	ENST00000356435		1846	Gcg/Acg	34/35	0.595308439300505	2	FACETS	0.468	0.4	0.541	0.234	0.2	0.271	SUBCLONAL	1	TRUE	0	0.601288121892762	2		336	377	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675055	40675055	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1438983381	NA	P-0020956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	317	985	0	ENST00000249776.8:c.19C>A	p.Pro7Thr	p.P7T	ENST00000249776	NM_033286.3	7	Ccg/Acg	1/9	0.601288121892762	3	FACETS	1	0.968	1	0.346	0.326	0.367	CLONAL	1	TRUE	0	0.601288121892762	3		985	1321	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058309	42058309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	338	421	1	ENST00000219905.7:c.8029G>A	p.Asp2677Asn	p.D2677N	ENST00000219905	NM_001164273.1	2677	Gat/Aat	24/24	0.601288121892762	3	FACETS	0.987	0.94	1	0.658	0.626	0.689	CLONAL	2	TRUE	0	0.601288121892762	3		422	741	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397184	397184	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	425	591	0	ENST00000380956.4:c.569T>C	p.Ile190Thr	p.I190T	ENST00000380956	NM_001195286.1	190	aTc/aCc	5/9	0.599240817893404	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.601288121892762	2		591	677	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858084	152858084	+	synonymous_variant	Silent	SNP	A	A	G	novel	NA	P-0020956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	306	950	1	ENST00000406277.2:c.531T>C	p.His177=	p.H177=	ENST00000406277	NM_152274.4	177	caT/caC	6/7	0.389793550325501	1	FACETS	0.801	0.757	0.845	0.801	0.757	0.845	CLONAL	1	TRUE	0	0.601288121892762	1		951	889	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0020962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	53	757	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.266751826940704	1	FACETS	0.805	0.688	0.932	0.805	0.688	0.932	CLONAL	1	TRUE	0	0.266751826940704	1		758	428	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78866590	78866590	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	91	821	3	ENST00000306801.3:c.2163C>A	p.Ser721Arg	p.S721R	ENST00000306801	NM_020761.2	721	agC/agA	19/34	1	2	FACETS	0.764	0.677	0.857	0.764	0.677	0.857	SUBCLONAL	1	TRUE	1	0.266751826940704	2		824	893	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751531	57751531	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55645589	NA	P-0020962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	54	461	1	ENST00000274289.3:c.1460C>T	p.Pro487Leu	p.P487L	ENST00000274289	NM_006622.3	487	cCg/cTg	11/14	1	2	FACETS	0.748	0.639	0.868	0.748	0.639	0.868	SUBCLONAL	1	TRUE	1	0.266751826940704	2		462	541	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675571	86675571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1561325048	NA	P-0020966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	58	476	0	ENST00000274376.6:c.2513del	p.Asn838MetfsTer4	p.N838Mfs*4	ENST00000274376	NM_002890.2	836	gAa/ga	19/25	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.212079881395827	2		476	521	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288993	212288993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867944951	NA	P-0020966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	58	839	0	ENST00000342788.4:c.2753G>A	p.Gly918Glu	p.G918E	ENST00000342788	NM_005235.2	918	gGa/gAa	23/28	1	2	FACETS	0.661	0.566	0.764	0.661	0.566	0.764	SUBCLONAL	1	TRUE	1	0.212079881395827	2		839	828	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518261	8518261	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	21	444	0	ENST00000356435.5:c.1130G>T	p.Arg377Leu	p.R377L	ENST00000356435		377	cGc/cTc	10/35	0.21156135901658	1	FACETS	0.471	0.362	0.598	0.471	0.362	0.598	SUBCLONAL	1	TRUE	0	0.212079881395827	1		444	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691003	NA	P-0020966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	51	786	0	ENST00000269305.4:c.96+1G>T		p.X32_splice	ENST00000269305	NM_001126112.2	32			1	2	FACETS	0.592	0.501	0.691	0.592	0.501	0.691	SUBCLONAL	1	TRUE	1	0.212079881395827	2		786	813	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729728	162729728	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs373748687	NA	P-0020966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	104	810	0	ENST00000367921.3:c.814A>G	p.Met272Val	p.M272V	ENST00000367921	NM_006182.2	272	Atg/Gtg	8/18	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.212079881395827	2		810	771	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800975	243800975	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	79	967	0	ENST00000263826.5:c.499G>T	p.Glu167Ter	p.E167*	ENST00000263826	NM_005465.4	167	Gag/Tag	5/13	1	2	FACETS	0.691	0.606	0.783	0.691	0.606	0.783	SUBCLONAL	1	TRUE	1	0.212079881395827	2		967	1078	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649819	88649819	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	49	600	1	ENST00000372037.3:c.68G>T	p.Gly23Val	p.G23V	ENST00000372037	NM_004329.2	23	gGa/gTa	4/13	1	2	FACETS	0.774	0.655	0.905	0.774	0.655	0.905	CLONAL	1	TRUE	1	0.212079881395827	2		601	597	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998164	100998164	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0020966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	45	566	0	ENST00000325455.5:c.1637+1G>T		p.X546_splice	ENST00000325455	NM_001202474.3	546			1	2	FACETS	0.931	0.783	1	0.931	0.783	1	CLONAL	1	TRUE	1	0.212079881395827	2		566	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573976	7573976	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0020966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	84	731	1	ENST00000269305.4:c.1051A>T	p.Lys351Ter	p.K351*	ENST00000269305	NM_001126112.2	351	Aag/Tag	10/11	1	2	FACETS	0.853	0.752	0.962	0.853	0.752	0.962	CLONAL	1	TRUE	1	0.212079881395827	2		732	929	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587533	29587533	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	61	614	0	ENST00000356175.3:c.4514+1del		p.R1505fs	ENST00000356175	NM_000267.3	1505	aGg/ag	33/57	1	2	FACETS	0.957	0.826	1	0.957	0.826	1	CLONAL	1	TRUE	1	0.212079881395827	2		614	601	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440183	220440183	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	65	1047	0	ENST00000243786.2:c.1036G>T	p.Gly346Ter	p.G346*	ENST00000243786	NM_002191.3	346	Gga/Tga	2/2	1	2	FACETS	0.664	0.574	0.762	0.664	0.574	0.762	SUBCLONAL	1	TRUE	1	0.212079881395827	2		1047	923	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727156	40727156	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	55	801	2	ENST00000373198.4:c.3808C>T	p.His1270Tyr	p.H1270Y	ENST00000373198	NM_133170.3	1270	Cac/Tac	28/32	1	2	FACETS	0.67	0.572	0.778	0.67	0.572	0.778	SUBCLONAL	1	TRUE	1	0.212079881395827	2		803	774	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448520	89448520	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	79	546	0	ENST00000336596.2:c.1484C>G	p.Thr495Ser	p.T495S	ENST00000336596	NM_005233.5	495	aCc/aGc	7/17	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.212079881395827	2		546	680	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444680	187444680	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	40	449	2	ENST00000232014.4:c.1547G>T	p.Gly516Val	p.G516V	ENST00000232014	NM_001130845.1	516	gGg/gTg	7/10	1	2	FACETS	0.865	0.719	1	0.865	0.719	1	CLONAL	1	TRUE	1	0.212079881395827	2		451	436	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141005	55141005	+	splice_region_variant,intron_variant	Splice_Region	SNP	T	T	G	novel	NA	P-0020966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	41	431	0	ENST00000257290.5:c.1654-3T>G		p.X552_splice	ENST00000257290	NM_006206.4	552			0.21156135901658	1	FACETS	0.833	0.695	0.986	0.833	0.695	0.986	CLONAL	1	TRUE	0	0.212079881395827	1		431	415	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980402	55980402	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	65	591	0	ENST00000263923.4:c.689C>A	p.Pro230Gln	p.P230Q	ENST00000263923	NM_002253.2	230	cCg/cAg	6/30	0.21156135901658	1	FACETS	0.904	0.784	1	0.904	0.784	1	CLONAL	1	TRUE	0	0.212079881395827	1		591	606	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562757	176562757	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	87	810	0	ENST00000439151.2:c.653G>C	p.Arg218Thr	p.R218T	ENST00000439151	NM_022455.4	218	aGa/aCa	2/23	1	2	FACETS	0.865	0.764	0.973	0.865	0.764	0.973	CLONAL	1	TRUE	1	0.212079881395827	2		810	949	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129952	69129952	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	41	440	0	ENST00000288368.4:c.4706A>T	p.Gln1569Leu	p.Q1569L	ENST00000288368	NM_024870.2	1569	cAg/cTg	38/40	1	2	FACETS	0.916	0.764	1	0.916	0.764	1	CLONAL	1	TRUE	1	0.212079881395827	2		440	422	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484216	8484216	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	57	797	0	ENST00000356435.5:c.3316G>T	p.Asp1106Tyr	p.D1106Y	ENST00000356435		1106	Gat/Tat	19/35	0.21156135901658	1	FACETS	0.658	0.564	0.762	0.658	0.564	0.762	SUBCLONAL	1	TRUE	0	0.212079881395827	1		797	730	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197378	27197378	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	95	931	0	ENST00000380036.4:c.1690C>A	p.Gln564Lys	p.Q564K	ENST00000380036	NM_000459.3	564	Caa/Aaa	12/23	0.21156135901658	1	FACETS	0.857	0.762	0.959	0.857	0.762	0.959	CLONAL	1	TRUE	0	0.212079881395827	1		931	934	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045906	47045906	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	71	733	0	ENST00000377604.3:c.2701G>C	p.Ala901Pro	p.A901P	ENST00000377604	NM_001204468.1	901	Gca/Cca	24/24	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.212079881395827	2		733	663	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412548	63412548	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	52	656	0	ENST00000330258.3:c.619C>A	p.His207Asn	p.H207N	ENST00000330258	NM_152424.3	207	Cac/Aac	2/2	1	2	FACETS	0.815	0.693	0.948	0.815	0.693	0.948	CLONAL	1	TRUE	1	0.212079881395827	2		656	602	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338651	70338651	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	89	773	0	ENST00000374080.3:c.47G>T	p.Arg16Leu	p.R16L	ENST00000374080		16	cGg/cTg	1/45	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.212079881395827	2		773	817	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0020999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	189	525	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.825	0.764	0.888	1	0.992	1	CLONAL	2	FALSE	1	0.289335153398651	2		525	792	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473780	67473780	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730880214	NA	P-0020999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	70	766	1	ENST00000327367.4:c.860G>A	p.Arg287Gln	p.R287Q	ENST00000327367	NM_005902.3	287	cGg/cAg	6/9	1	2	FACETS	0.839	0.732	0.954	0.839	0.732	0.954	CLONAL	1	FALSE	1	0.289335153398651	2		767	577	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888267	112888267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	120	800	0	ENST00000351677.2:c.283G>A	p.Val95Ile	p.V95I	ENST00000351677	NM_002834.3	95	Gtc/Atc	3/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.289335153398651	2		800	625	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358596	67358596	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	107	822	0	ENST00000327367.4:c.104T>C	p.Val35Ala	p.V35A	ENST00000327367	NM_005902.3	35	gTc/gCc	1/9	1	2	FACETS	0.929	0.833	1	0.929	0.833	1	CLONAL	1	FALSE	1	0.289335153398651	2		822	796	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477070	67477070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	82	637	0	ENST00000327367.4:c.877G>A	p.Gly293Ser	p.G293S	ENST00000327367	NM_005902.3	293	Ggc/Agc	7/9	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	1	0.289335153398651	2		637	500	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374909	45374909	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	186	902	0	ENST00000262160.6:c.934T>C	p.Cys312Arg	p.C312R	ENST00000262160	NM_005901.5	312	Tgc/Cgc	8/11	1	2	FACETS	0.849	0.786	0.914	1	0.992	1	CLONAL	2	FALSE	1	0.289335153398651	2		902	757	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579575	7579575	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	367	896	1	ENST00000269305.4:c.112C>T	p.Gln38Ter	p.Q38*	ENST00000269305	NM_001126112.2	38	Caa/Taa	4/11	0.647358564197068	1	FACETS	0.929	0.887	0.971	0.929	0.887	0.971	CLONAL	1	TRUE	0	0.669051251458829	1		897	786	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105715	27105717	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs765246223	NA	P-0021010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	83	435	0	ENST00000324856.7:c.5334_5336del	p.Glu1780del	p.E1780del	ENST00000324856	NM_006015.4	1776	GAA/-	20/20	0.29154781185871	1	FACETS	0.36	0.318	0.404	0.36	0.318	0.404	INDETERMINATE	1	TRUE	0	0.669051251458829	1		435	459	SUCCESS
RET	5979	MSKCC	GRCh37	10	43595960	43595960	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	258	1120	3	ENST00000355710.3:c.127G>A	p.Asp43Asn	p.D43N	ENST00000355710	NM_020975.4	43	Gac/Aac	2/20	0.416679292094511	1	FACETS	0.41	0.383	0.437	0.41	0.383	0.437	SUBCLONAL	1	TRUE	0	0.669051251458829	1		1123	1253	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117747	108117747	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	78	593	0	ENST00000278616.4:c.958G>T	p.Val320Leu	p.V320L	ENST00000278616	NM_000051.3	320	Gtg/Ttg	8/63	0.453198218255444	1	FACETS	0.312	0.274	0.351	0.312	0.274	0.351	SUBCLONAL	1	TRUE	0	0.669051251458829	1		593	498	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281359	49281359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764117879	NA	P-0021010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1298	273	1177	3	ENST00000282018.3:c.406C>T	p.Arg136Cys	p.R136C	ENST00000282018	NM_020377.2	136	Cgt/Tgt	1/1	1	2	FACETS	0.519	0.486	0.554	0.519	0.486	0.554	SUBCLONAL	1	TRUE	1	0.669051251458829	2		1180	1571	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350936	89350936	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1304	225	1335	0	ENST00000301030.4:c.2014A>G	p.Ile672Val	p.I672V	ENST00000301030	NM_001256183.1	672	Ata/Gta	9/13	1	2	FACETS	0.44	0.408	0.473	0.44	0.408	0.473	SUBCLONAL	1	TRUE	1	0.669051251458829	2		1335	1529	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41247888	41247888	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	65	847	0	ENST00000357654.3:c.645A>T	p.Glu215Asp	p.E215D	ENST00000357654	NM_007294.3	215	gaA/gaT	9/23	1	2	FACETS	0.193	0.167	0.222	0.193	0.167	0.222	SUBCLONAL	1	TRUE	1	0.669051251458829	2		847	1006	SUCCESS
APC	324	MSKCC	GRCh37	5	112174384	112174384	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0021010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	101	365	0	ENST00000257430.4:c.3093T>A	p.Tyr1031Ter	p.Y1031*	ENST00000257430	NM_000038.5	1031	taT/taA	16/16	0.416679292094511	1	FACETS	0.693	0.628	0.76	0.693	0.628	0.76	SUBCLONAL	1	TRUE	0	0.669051251458829	1		365	290	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860177	151860219	+	frameshift_variant	Frame_Shift_Del	DEL	TGAATTAATTGATCCTTGTTGTATATTCTGCTGCTGTAAAACC	TGAATTAATTGATCCTTGTTGTATATTCTGCTGCTGTAAAACC	-	novel	NA	P-0021010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	57	677	0	ENST00000262189.6:c.10443_10485del	p.Gln3481HisfsTer16	p.Q3481Hfs*16	ENST00000262189	NM_170606.2	3481	caGGTTTTACAGCAGCAGAATATACAACAAGGATCAATTAATTCA/ca	43/59	1	2	FACETS	0.18	0.154	0.209	0.18	0.154	0.209	SUBCLONAL	1	TRUE	1	0.669051251458829	2		677	945	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202925	27202925	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	177	756	0	ENST00000380036.4:c.2017C>A	p.Arg673Ser	p.R673S	ENST00000380036	NM_000459.3	673	Cgt/Agt	13/23	0.426368367196315	1	FACETS	0.504	0.466	0.544	0.504	0.466	0.544	SUBCLONAL	1	TRUE	0	0.669051251458829	1		756	698	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0021043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	78	840	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	0.27	2		840	499	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0021043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	136	585	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.27	2		586	707	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0021043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	125	907	3	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.277340175262386	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.27	1		910	765	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812155	212812155	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	18	409	0	ENST00000342788.4:c.421G>T	p.Glu141Ter	p.E141*	ENST00000342788	NM_005235.2	141	Gaa/Taa	3/28	1	2	FACETS	0.425	0.319	0.549	0.425	0.319	0.549	SUBCLONAL	1	TRUE	1	0.27	2		409	314	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	84	766	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.78719481299317	2		766	208	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717730	89717730	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121909239	NA	P-0021096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	231	680	0	ENST00000371953.3:c.755A>G	p.Asp252Gly	p.D252G	ENST00000371953	NM_000314.4	252	gAt/gGt	7/9	0.78719481299317	1	FACETS	0.989	0.942	1	0.989	0.942	1	CLONAL	1	TRUE	0	0.78719481299317	1		680	360	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439701	51439701	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	183	607	0	ENST00000262662.1:c.266T>C	p.Leu89Ser	p.L89S	ENST00000262662		89	tTg/tCg	4/4	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.78719481299317	2		607	458	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231280	46231280	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0021096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	159	581	0	ENST00000334344.6:c.1121del		p.X374_splice	ENST00000334344	NM_152641.2	374			1	2	FACETS	0.955	0.885	1	0.955	0.885	1	CLONAL	1	TRUE	1	0.78719481299317	2		581	423	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538763	23538763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1279217950	NA	P-0021096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	53	461	0	ENST00000380871.4:c.676G>A	p.Val226Met	p.V226M	ENST00000380871	NM_006167.3	226	Gtg/Atg	2/2	1	2	FACETS	0.389	0.333	0.45	0.389	0.333	0.45	SUBCLONAL	1	TRUE	1	0.78719481299317	2		461	346	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97873875	97873875	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	234	986	1	ENST00000289081.3:c.1199T>A	p.Phe400Tyr	p.F400Y	ENST00000289081	NM_000136.2	400	tTc/tAc	13/15	1	2	FACETS	0.837	0.785	0.891	0.837	0.785	0.891	CLONAL	1	TRUE	1	0.78719481299317	2		987	710	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913403	NA	P-0021101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	210	527	0	ENST00000349496.5:c.110C>A	p.Ser37Tyr	p.S37Y	ENST00000349496	NM_001904.3	37	tCt/tAt	3/15	1	2	FACETS	0.906	0.85	0.963	0.906	0.85	0.963	CLONAL	1	TRUE	1	0.926894788159186	2		527	500	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134251	11134251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1218643327	NA	P-0021101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	374	980	1	ENST00000358026.2:c.2917C>T	p.Arg973Trp	p.R973W	ENST00000358026	NM_001128849.1	973	Cgg/Tgg	20/36	1	2	FACETS	0.943	0.899	0.986	0.943	0.899	0.986	CLONAL	1	TRUE	1	0.926894788159186	2		981	856	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0021127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	375	763	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.468720548230097	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.478789762966215	3		764	966	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253911	NA	P-0021127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	202	816	10	ENST00000269305.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000269305	NM_001126112.2	180	Gag/Aag	5/11	0.478789762966215	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.478789762966215	1		826	635	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508955	106508955	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759136884	NA	P-0021127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	147	534	9	ENST00000359195.3:c.949G>A	p.Glu317Lys	p.E317K	ENST00000359195	NM_002649.2	317	Gag/Aag	2/11	0.468720548230097	3	FACETS	1	0.947	1	0.524	0.479	0.571	CLONAL	1	TRUE	1	0.478789762966215	3		543	726	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226595555	226595555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	226	865	5	ENST00000366794.5:c.76G>A	p.Glu26Lys	p.E26K	ENST00000366794	NM_001618.3	26	Gag/Aag	1/23	0.468720548230097	3	FACETS	1	0.976	1	0.55	0.512	0.59	CLONAL	1	TRUE	1	0.478789762966215	3		870	1063	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131411	202131411	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs777784105	NA	P-0021127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	172	756	10	ENST00000358485.4:c.379C>T	p.Arg127Ter	p.R127*	ENST00000358485	NM_001080125.1	127	Cga/Tga	2/9	1	2	FACETS	0.999	0.922	1	0.999	0.922	1	CLONAL	1	TRUE	1	0.478789762966215	2		766	719	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665360	138665360	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	301	1272	7	ENST00000330315.3:c.205G>C	p.Glu69Gln	p.E69Q	ENST00000330315	NM_023067.3	69	Gag/Cag	1/1	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.478789762966215	2		1279	1199	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073815	8073815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	188	395	6	ENST00000377482.5:c.844G>A	p.Glu282Lys	p.E282K	ENST00000377482	NM_018948.3	282	Gag/Aag	4/4	0.478789762966215	2	FACETS	0.962	0.901	1	0.962	0.901	1	CLONAL	2	TRUE	0	0.478789762966215	2		401	408	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057733	27057733	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	699	1349	21	ENST00000324856.7:c.1441C>T	p.Gln481Ter	p.Q481*	ENST00000324856	NM_006015.4	481	Cag/Tag	3/20	0.478789762966215	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.478789762966215	2		1370	1429	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434127	49434127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	206	823	5	ENST00000301067.7:c.7426G>C	p.Glu2476Gln	p.E2476Q	ENST00000301067	NM_003482.3	2476	Gaa/Caa	31/54	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.478789762966215	2		828	828	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031990	10031990	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148531310	NA	P-0021127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	267	980	6	ENST00000330684.3:c.833C>T	p.Ser278Phe	p.S278F	ENST00000330684	NM_001134407.1	278	tCt/tTt	3/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.478789762966215	2		986	1013	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842405	68842405	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	260	886	7	ENST00000261769.5:c.466T>G	p.Trp156Gly	p.W156G	ENST00000261769	NM_004360.3	156	Tgg/Ggg	4/16	0.478789762966215	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.478789762966215	1		893	716	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805422	46805422	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	308	1090	9	ENST00000290295.7:c.534G>A	p.Trp178Ter	p.W178*	ENST00000290295	NM_006361.5	178	tgG/tgA	1/2	0.478789762966215	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.478789762966215	1		1099	889	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096402	178096402	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	176	622	4	ENST00000397062.3:c.929C>G	p.Ser310Cys	p.S310C	ENST00000397062	NM_006164.4	310	tCt/tGt	5/5	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.478789762966215	2		626	674	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55962438	55962438	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	159	809	7	ENST00000263923.4:c.2686C>G	p.Leu896Val	p.L896V	ENST00000263923	NM_002253.2	896	Ctc/Gtc	19/30	1	2	FACETS	0.85	0.781	0.923	0.85	0.781	0.923	CLONAL	1	TRUE	1	0.478789762966215	2		816	781	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227031	53227031	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	218	970	10	ENST00000375401.3:c.2544G>T	p.Met848Ile	p.M848I	ENST00000375401	NM_004187.3	848	atG/atT	18/26	1	2	FACETS	0.912	0.848	0.977	0.912	0.848	0.977	CLONAL	1	TRUE	1	0.478789762966215	2		980	999	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247157	153247157	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0021167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	175	328	0	ENST00000281708.4:c.1644+1G>A		p.X548_splice	ENST00000281708	NM_033632.3	548			1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.92	2		328	377	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842339	151842339	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0021167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	181	297	0	ENST00000262189.6:c.14073C>G	p.Tyr4691Ter	p.Y4691*	ENST00000262189	NM_170606.2	4691	taC/taG	54/59	1	2	FACETS	0.894	0.834	0.955	0.894	0.834	0.955	CLONAL	1	TRUE	1	0.92	2		297	440	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945447	151945448	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	587	1169	0	ENST00000262189.6:c.2071dup	p.Ser691PhefsTer14	p.S691Ffs*14	ENST00000262189	NM_170606.2	691	tct/tTct	14/59	1	2	FACETS	0.996	0.96	1	0.996	0.96	1	CLONAL	1	TRUE	1	0.92	2		1169	1281	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0021190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	54	762	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.392405480630038	6	FACETS	0.88	0.752	1	0.176	0.15	0.205	CLONAL	1	TRUE	1	0.392405480630038	6		762	558	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353884	68353884	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	57	840	0	ENST00000487270.1:c.719C>G	p.Ser240Cys	p.S240C	ENST00000487270	NM_133509.3	240	tCc/tGc	7/11	0.323362664121463	3	FACETS	0.919	0.792	1	0.46	0.396	0.529	CLONAL	1	TRUE	1	0.392405480630038	3		840	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577093	7577093	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882008	NA	P-0021197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	105	1075	0	ENST00000269305.4:c.845G>C	p.Arg282Pro	p.R282P	ENST00000269305	NM_001126112.2	282	cGg/cCg	8/11	0.214336468763418	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.214336468763418	1		1075	747	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692793	89692793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	29	761	0	ENST00000371953.3:c.277C>T	p.His93Tyr	p.H93Y	ENST00000371953	NM_000314.4	93	Cat/Tat	5/9	0.214336468763418	1	FACETS	0.612	0.491	0.749	0.612	0.491	0.749	SUBCLONAL	1	TRUE	0	0.214336468763418	1		761	395	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138642	37138642	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs936800231	NA	P-0021197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	88	951	0	ENST00000373509.5:c.176C>G	p.Ser59Cys	p.S59C	ENST00000373509	NM_002648.3	59	tCc/tGc	2/6	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.214336468763418	2		951	637	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503082	125503082	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	87	727	0	ENST00000428830.2:c.449G>T	p.Gly150Val	p.G150V	ENST00000428830	NM_001114121.2	150	gGc/gTc	6/14	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.214336468763418	2		727	626	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434548	110434548	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	54	900	0	ENST00000375856.3:c.3853G>T	p.Gly1285Cys	p.G1285C	ENST00000375856	NM_003749.2	1285	Ggc/Tgc	1/2	0.214336468763418	1	FACETS	0.86	0.735	0.997	0.86	0.735	0.997	CLONAL	1	TRUE	0	0.214336468763418	1		900	523	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303921	91303921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777845306	NA	P-0021197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	82	1050	0	ENST00000355112.3:c.1318G>A	p.Glu440Lys	p.E440K	ENST00000355112	NM_000057.2	440	Gag/Aag	7/22	1	2	FACETS	0.987	0.87	1	0.987	0.87	1	CLONAL	1	TRUE	1	0.214336468763418	2		1050	775	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348008	89348008	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1295892091	NA	P-0021197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	71	1253	2	ENST00000301030.4:c.4942C>G	p.Pro1648Ala	p.P1648A	ENST00000301030	NM_001256183.1	1648	Cca/Gca	9/13	1	2	FACETS	0.669	0.582	0.763	0.669	0.582	0.763	SUBCLONAL	1	TRUE	1	0.214336468763418	2		1255	991	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59886070	59886070	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	77	988	1	ENST00000259008.2:c.676A>C	p.Ser226Arg	p.S226R	ENST00000259008	NM_032043.2	226	Agt/Cgt	7/20	1	2	FACETS	0.95	0.834	1	0.95	0.834	1	CLONAL	1	TRUE	1	0.214336468763418	2		989	756	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514481	41514481	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	181	1072	0	ENST00000373198.4:c.180G>T	p.Trp60Cys	p.W60C	ENST00000373198	NM_133170.3	60	tgG/tgT	2/32	0.125169174403747	5	FACETS	0.926	0.856	1	0.695	0.642	0.75	INDETERMINATE	3	TRUE	1	0.214336468763418	5		1072	803	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651475	52651475	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0021197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	121	1130	0	ENST00000394830.3:c.1621A>T	p.Arg541Ter	p.R541*	ENST00000394830	NM_018313.4	541	Aga/Tga	15/30	0.214336468763418	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.214336468763418	1		1130	915	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851601	134851601	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	60	993	0	ENST00000398015.3:c.1007C>A	p.Thr336Lys	p.T336K	ENST00000398015	NM_004441.4	336	aCg/aAg	5/16	0.214336468763418	3	FACETS	0.932	0.802	1	0.466	0.401	0.537	CLONAL	1	TRUE	1	0.214336468763418	3		993	665	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0021231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	534	772	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.59480200351455	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.60324420104634	2		772	839	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218876	133218876	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1565936909	NA	P-0021231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	274	866	2	ENST00000320574.5:c.5060C>A	p.Ser1687Tyr	p.S1687Y	ENST00000320574	NM_006231.2	1687	tCc/tAc	38/49	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.60324420104634	2		868	854	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900635	32900635	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0021231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	161	596	0	ENST00000380152.3:c.517-1G>C		p.X173_splice	ENST00000380152		173			1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.60324420104634	2		596	530	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031863	10031863	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1555455539	NA	P-0021231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	248	925	0	ENST00000330684.3:c.960C>A	p.Cys320Ter	p.C320*	ENST00000330684	NM_001134407.1	320	tgC/tgA	3/13	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.60324420104634	2		925	802	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610172	10610172	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	281	856	1	ENST00000171111.5:c.538G>A	p.Asp180Asn	p.D180N	ENST00000171111	NM_203500.1	180	Gac/Aac	2/6	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.60324420104634	2		857	871	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47596667	47596667	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1274512381	NA	P-0021231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	176	505	0	ENST00000263735.4:c.23C>G	p.Ala8Gly	p.A8G	ENST00000263735	NM_002354.2	8	gCg/gGg	1/9	0.60324420104634	3	FACETS	1	0.97	1	0.549	0.507	0.592	CLONAL	1	TRUE	1	0.60324420104634	3		505	692	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003339	143003339	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0021231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	200	764	0	ENST00000262992.4:c.2488-1G>T		p.X830_splice	ENST00000262992	NM_001101669.1	830			1	2	FACETS	0.845	0.784	0.907	0.845	0.784	0.907	CLONAL	1	TRUE	1	0.60324420104634	2		764	785	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969933	161969933	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	198	741	2	ENST00000366898.1:c.1036G>T	p.Asp346Tyr	p.D346Y	ENST00000366898	NM_004562.2	346	Gac/Tac	9/12	1	2	FACETS	0.973	0.905	1	0.973	0.905	1	CLONAL	1	TRUE	1	0.60324420104634	2		743	675	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0021241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	130	844	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	0.854	0.774	0.937	0.854	0.774	0.937	CLONAL	1	TRUE	1	0.372385772639052	2		844	818	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0021251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	297	840	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.362863263407285	7	FACETS	0.965	0.912	1			1	CLONAL	4	TRUE	NA	0.362863263407285	7		840	809	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160588	56160588	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	101	550	0	ENST00000399503.3:c.862C>T	p.Arg288Ter	p.R288*	ENST00000399503	NM_005921.1	288	Cga/Tga	4/20	0.356250560998772	2	FACETS	0.773	0.697	0.852	0.773	0.697	0.852	SUBCLONAL	2	TRUE	0	0.362863263407285	2		550	360	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575209	48575209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767326	NA	P-0021251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	99	597	0	ENST00000342988.3:c.403C>T	p.Arg135Ter	p.R135*	ENST00000342988	NM_005359.5	135	Cga/Tga	3/12	0.356003202059441	2	FACETS	0.964	0.873	1	0.964	0.873	1	CLONAL	2	TRUE	0	0.362863263407285	2		597	283	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246216	46246216	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774475353	NA	P-0021251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	165	795	3	ENST00000334344.6:c.4310C>T	p.Ala1437Val	p.A1437V	ENST00000334344	NM_152641.2	1437	gCg/gTg	15/21	0.327841569496554	4	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	2	0.362863263407285	4		798	608	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577519	7577519	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	273	1100	2	ENST00000269305.4:c.762del	p.Ile255SerfsTer90	p.I255Sfs*90	ENST00000269305	NM_001126112.2	254	atC/at	7/11	0.356250560998772	2	FACETS	0.995	0.938	1	0.995	0.938	1	CLONAL	2	TRUE	0	0.362863263407285	2		1102	756	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	68	766	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.360481791152121	2		766	349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0021258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	162	937	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.306772098267031	3	FACETS	1	0.985	1	0.661	0.607	0.717	CLONAL	1	TRUE	1	0.360481791152121	3		939	803	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972419	81972419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778251162	NA	P-0021258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	137	661	1	ENST00000359376.3:c.3212G>A	p.Arg1071His	p.R1071H	ENST00000359376	NM_002661.3	1071	cGc/cAc	29/33	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.360481791152121	2		662	562	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274172	10274172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567354612	NA	P-0021258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	82	587	1	ENST00000330684.3:c.97G>A	p.Ala33Thr	p.A33T	ENST00000330684	NM_001134407.1	33	Gcg/Acg	2/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.360481791152121	2		588	392	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281083	49281083	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	119	958	1	ENST00000282018.3:c.130G>A	p.Val44Ile	p.V44I	ENST00000282018	NM_020377.2	44	Gta/Ata	1/1	1	2	FACETS	0.848	0.765	0.934	0.848	0.765	0.934	CLONAL	1	TRUE	1	0.360481791152121	2		959	779	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56792561	56792564	+	frameshift_variant	Frame_Shift_Del	DEL	CATT	CATT	-	novel	NA	P-0021258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	91	655	0	ENST00000308159.5:c.293_296del	p.Ile98ArgfsTer4	p.I98Rfs*4	ENST00000308159	NM_014669.4	97	gaCATT/ga	3/22	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.360481791152121	2		655	485	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878560	151878560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769422754	NA	P-0021258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	175	878	0	ENST00000262189.6:c.6385G>A	p.Asp2129Asn	p.D2129N	ENST00000262189	NM_170606.2	2129	Gac/Aac	36/59	0.293165628088566	4	FACETS	0.853	0.787	0.922	0.569	0.525	0.615	CLONAL	2	TRUE	1	0.360481791152121	4		878	774	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033245	69033245	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530869739	NA	P-0021258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	99	818	0	ENST00000288368.4:c.3685G>A	p.Val1229Ile	p.V1229I	ENST00000288368	NM_024870.2	1229	Gtc/Atc	30/40	1	2	FACETS	0.934	0.836	1	0.934	0.836	1	CLONAL	1	TRUE	1	0.360481791152121	2		818	588	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215595221	215595221	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587781376	NA	P-0021261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	85	427	0	ENST00000260947.4:c.1915T>C	p.Cys639Arg	p.C639R	ENST00000260947	NM_000465.2	639	Tgt/Cgt	10/11	1	2	FACETS	0.981	0.877	1	0.981	0.877	1	CLONAL	1	TRUE	1	0.568008078709109	2		427	305	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440916	52440916	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	148	680	1	ENST00000460680.1:c.588G>A	p.Trp196Ter	p.W196*	ENST00000460680	NM_004656.3	196	tgG/tgA	8/17	0.692331785393167	1	FACETS	0.899	0.836	0.962	0.899	0.836	0.962	CLONAL	1	TRUE	0	0.692331785393167	1		681	311	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035078	30035078	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0021264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	88	462	0	ENST00000338641.4:c.241-1G>A		p.X81_splice	ENST00000338641	NM_000268.3	81			0.692331785393167	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.692331785393167	1		462	146	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98241299	98241299	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	380	772	0	ENST00000331920.6:c.1198C>T	p.Gln400Ter	p.Q400*	ENST00000331920	NM_000264.3	400	Cag/Tag	8/24	0.670135101520847	2	FACETS	0.924	0.89	0.958	0.924	0.89	0.958	CLONAL	2	TRUE	0	0.692331785393167	2		772	594	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0021281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	143	798	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.403322899738704	1	FACETS	0.909	0.831	0.989	0.909	0.831	0.989	CLONAL	1	TRUE	0	0.403322899738704	1		799	623	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0021281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	180	565	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.35415588238349	3	FACETS	0.984	0.914	1	0.984	0.914	1	CLONAL	2	TRUE	1	0.403322899738704	3		565	545	SUCCESS
APC	324	MSKCC	GRCh37	5	112175248	112175249	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0021281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	79	320	0	ENST00000257430.4:c.3959_3960del	p.Val1320GlufsTer11	p.V1320Efs*11	ENST00000257430	NM_000038.5	1319	ccTGtg/cctg	16/16	0.403322899738704	2	FACETS	0.894	0.801	0.991	0.894	0.801	0.991	CLONAL	2	TRUE	0	0.403322899738704	2		320	219	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604707	48604707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	111	566	0	ENST00000342988.3:c.1529G>A	p.Gly510Glu	p.G510E	ENST00000342988	NM_005359.5	510	gGa/gAa	12/12	0.403322899738704	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.403322899738704	1		566	399	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166238	118166238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	27	397	1	ENST00000369448.3:c.748C>T	p.Leu250Phe	p.L250F	ENST00000369448	NM_017709.3	250	Ctt/Ttt	2/2	1	2	FACETS	0.35	0.279	0.433	0.35	0.279	0.433	SUBCLONAL	1	TRUE	1	0.403322899738704	2		398	382	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175996741	175996741	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	66	642	0	ENST00000367669.3:c.1696T>A	p.Ser566Thr	p.S566T	ENST00000367669	NM_022457.5	566	Tct/Act	15/20	1	2	FACETS	0.628	0.546	0.717	0.628	0.546	0.717	SUBCLONAL	1	TRUE	1	0.403322899738704	2		642	521	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117959	70117959	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	43	306	0	ENST00000245479.2:c.427T>C	p.Trp143Arg	p.W143R	ENST00000245479	NM_000346.3	143	Tgg/Cgg	1/3	1	2	FACETS	0.987	0.835	1	0.987	0.835	1	CLONAL	1	TRUE	1	0.403322899738704	2		306	216	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288642	33288642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	22	489	0	ENST00000374542.5:c.910C>T	p.Leu304Phe	p.L304F	ENST00000374542	NM_001141970.1	304	Ctc/Ttc	3/8	1	2	FACETS	0.259	0.2	0.327	0.259	0.2	0.327	SUBCLONAL	1	TRUE	1	0.403322899738704	2		489	422	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0021284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	57	757	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.574	0.492	0.663	0.574	0.492	0.663	SUBCLONAL	1	TRUE	1	0.350948135760758	2		758	566	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986753	36986754	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	12	116	0	ENST00000354822.5:c.935dup	p.Gln313ThrfsTer126	p.Q313Tfs*126	ENST00000354822	NM_001079668.2	312	cta/ctTa	3/3	1	2	FACETS	0.447	0.315	0.608	0.447	0.315	0.608	SUBCLONAL	1	TRUE	1	0.350948135760758	2		116	153	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987070	36987070	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	56	915	0	ENST00000354822.5:c.619G>T	p.Glu207Ter	p.E207*	ENST00000354822	NM_001079668.2	207	Gag/Tag	3/3	1	2	FACETS	0.511	0.437	0.591	0.511	0.437	0.591	SUBCLONAL	1	TRUE	1	0.350948135760758	2		915	625	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207065	1207065	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	36	913	2	ENST00000326873.7:c.157del	p.Asp53ThrfsTer11	p.D53Tfs*11	ENST00000326873	NM_000455.4	51	atG/at	1/10	1	2	FACETS	0.322	0.263	0.387	0.322	0.263	0.387	SUBCLONAL	1	TRUE	1	0.350948135760758	2		915	638	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207136	1207138	+	frameshift_variant	Frame_Shift_Del	DEL	GGG	GGG	CC	novel	NA	P-0021284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	53	1076	3	ENST00000326873.7:c.224_226delinsCC	p.Arg75ThrfsTer21	p.R75Tfs*21	ENST00000326873	NM_000455.4	75	aGGGcc/aCCcc	1/10	1	2	FACETS	0.372	0.316	0.433	0.372	0.316	0.433	SUBCLONAL	1	TRUE	1	0.350948135760758	2		1079	813	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0021291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	92	910	2	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	1	2	FACETS	0.641	0.568	0.719	0.641	0.568	0.719	SUBCLONAL	1	TRUE	1	0.287512083265535	2		912	999	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0021291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	196	770	0	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.287512083265535	2		770	982	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094386	27094386	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	269	561	0	ENST00000324856.7:c.3094G>T	p.Glu1032Ter	p.E1032*	ENST00000324856	NM_006015.4	1032	Gag/Tag	11/20	0.245025536817124	3	FACETS	0.947	0.893	1	0.947	0.893	1	CLONAL	3	TRUE	0	0.287512083265535	3		561	753	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17355135	17355135	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	299	566	0	ENST00000375499.3:c.383A>C	p.Tyr128Ser	p.Y128S	ENST00000375499	NM_003000.2	128	tAc/tCc	4/8	0.245025536817124	3	FACETS	0.949	0.897	1	0.949	0.897	1	CLONAL	3	TRUE	0	0.287512083265535	3		566	836	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944694	31944694	+	stop_lost	Nonstop_Mutation	SNP	T	T	G	novel	NA	P-0021291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	17	135	0	ENST00000340398.3:c.407A>C	p.Ter136SerextTer21	p.*136Sext*21	ENST00000340398	NM_001013699.2	136	tAa/tCa	1/1	0.287512083265535	3	FACETS	0.751	0.563	0.973			1	CLONAL	1	TRUE	NA	0.287512083265535	3		135	180	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112088	115112088	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	65	902	1	ENST00000257566.3:c.1652C>A	p.Thr551Asn	p.T551N	ENST00000257566	NM_016569.3	551	aCc/aAc	7/8	1	2	FACETS	0.462	0.399	0.53	0.462	0.399	0.53	SUBCLONAL	1	TRUE	1	0.287512083265535	2		903	979	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120789156	120789156	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	116	521	1	ENST00000257552.2:c.781G>T	p.Glu261Ter	p.E261*	ENST00000257552	NM_002442.3	261	Gag/Tag	11/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.287512083265535	2		522	623	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240982	133240982	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	59	711	0	ENST00000320574.5:c.2535G>T	p.Gln845His	p.Q845H	ENST00000320574	NM_006231.2	845	caG/caT	22/49	NA	2	FACETS	0.53	0.455	0.612			1	INDETERMINATE	1	TRUE	NA	0.287512083265535	2		711	775	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609664	28609664	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	177	585	1	ENST00000241453.7:c.1565C>A	p.Thr522Lys	p.T522K	ENST00000241453	NM_004119.2	522	aCa/aAa	12/24	0.21721678652074	2	FACETS	0.796	0.735	0.86	0.796	0.735	0.86	SUBCLONAL	2	TRUE	0	0.287512083265535	2		586	773	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231612	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0021291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	44	187	0	ENST00000357368.4:c.1864_1865del	p.Pro622SerfsTer4	p.P622Sfs*4	ENST00000357368	NM_002850.3	622	CCt/t	14/38	0.287512083265535	2	FACETS	1	0.937	1	0.612	0.517	0.715	CLONAL	1	TRUE	0	0.287512083265535	2		187	250	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660615	227660615	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1002889742	NA	P-0021291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	68	616	1	ENST00000305123.5:c.2840G>A	p.Gly947Glu	p.G947E	ENST00000305123	NM_005544.2	947	gGg/gAg	1/2	0.287512083265535	1	FACETS	0.688	0.598	0.784	0.688	0.598	0.784	SUBCLONAL	1	TRUE	0	0.287512083265535	1		617	589	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523241	9523241	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	181	644	0	ENST00000353224.5:c.1996C>A	p.Leu666Ile	p.L666I	ENST00000353224	NM_177990.2	666	Cta/Ata	9/10	NA	2	FACETS	0.838	0.775	0.904			1	INDETERMINATE	2	TRUE	NA	0.287512083265535	2		644	751	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385137	41385137	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	224	759	1	ENST00000373198.4:c.824C>A	p.Ser275Tyr	p.S275Y	ENST00000373198	NM_133170.3	275	tCt/tAt	6/32	0.287512083265535	3	FACETS	0.813	0.756	0.872	0.813	0.756	0.872	CLONAL	2	TRUE	1	0.287512083265535	3		760	1096	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419850	41419850	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	98	403	0	ENST00000373198.4:c.471G>T	p.Trp157Cys	p.W157C	ENST00000373198	NM_133170.3	157	tgG/tgT	3/32	0.287512083265535	3	FACETS	1	0.954	1	0.564	0.503	0.629	CLONAL	1	TRUE	1	0.287512083265535	3		403	691	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514823	44514823	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	166	565	0	ENST00000291552.4:c.424G>T	p.Ala142Ser	p.A142S	ENST00000291552	NM_006758.2	142	Gcc/Tcc	6/8	1	2	FACETS	0.802	0.738	0.868	1	0.99	1	CLONAL	2	TRUE	1	0.287512083265535	2		565	720	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851791	134851791	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	47	696	0	ENST00000398015.3:c.1197C>A	p.His399Gln	p.H399Q	ENST00000398015	NM_004441.4	399	caC/caA	5/16	0.157929276309416	2	FACETS	0.375	0.315	0.442	0.188	0.157	0.221	INDETERMINATE	1	TRUE	0	0.287512083265535	2		696	871	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233631	233631	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	68	262	0	ENST00000264932.6:c.935G>T	p.Arg312Leu	p.R312L	ENST00000264932	NM_004168.2	312	cGt/cTt	8/15	0.287512083265535	7	FACETS	1	0.968	1	0.232	0.202	0.265	CLONAL	1	TRUE	1	0.287512083265535	7		262	583	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977979	131977979	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	135	488	0	ENST00000265335.6:c.3862A>G	p.Arg1288Gly	p.R1288G	ENST00000265335		1288	Agg/Ggg	25/25	0.286695182205472	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.287512083265535	1		488	662	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672288	30672288	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs867585116	NA	P-0021291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	189	764	1	ENST00000376406.3:c.4672G>T	p.Gly1558Cys	p.G1558C	ENST00000376406	NM_014641.2	1558	Ggc/Tgc	10/15	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.287512083265535	2		765	956	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32182009	32182009	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	85	813	2	ENST00000375023.3:c.2045G>A	p.Gly682Asp	p.G682D	ENST00000375023	NM_004557.3	682	gGt/gAt	13/30	1	2	FACETS	0.53	0.467	0.598	0.53	0.467	0.598	SUBCLONAL	1	TRUE	1	0.287512083265535	2		815	1116	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37141746	37141746	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	87	603	0	ENST00000373509.5:c.821G>T	p.Arg274Ile	p.R274I	ENST00000373509	NM_002648.3	274	aGa/aTa	6/6	1	2	FACETS	0.717	0.634	0.806	0.717	0.634	0.806	SUBCLONAL	1	TRUE	1	0.287512083265535	2		603	844	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375991	8375991	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	141	356	0	ENST00000356435.5:c.4606C>A	p.Arg1536Ser	p.R1536S	ENST00000356435		1536	Cgt/Agt	28/35	0.287512083265535	3	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	1	0.287512083265535	3		356	550	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0021294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	446	777	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	0.861134598137539	2		777	963	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385152	41385152	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751630191	NA	P-0021294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	114	943	5	ENST00000373198.4:c.809G>A	p.Arg270His	p.R270H	ENST00000373198	NM_133170.3	270	cGc/cAc	6/32	1	2	FACETS	0.315	0.283	0.349	0.315	0.283	0.349	SUBCLONAL	1	TRUE	1	0.861134598137539	2		948	841	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831895	72831896	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACTA	novel	NA	P-0021294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	433	1100	0	ENST00000268489.5:c.4682_4685dup	p.His1563SerfsTer11	p.H1563Sfs*11	ENST00000268489	NM_006885.3	1562	gta/gtTAGTa	9/10	1	2	FACETS	0.866	0.827	0.906	0.866	0.827	0.906	CLONAL	1	TRUE	1	0.861134598137539	2		1100	1161	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0021322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	123	421	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.804	0.729	0.883	0.804	0.729	0.883	CLONAL	1	TRUE	1	0.502342490248235	2		421	609	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55143660	55143660	+	splice_donor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0021322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	35	327	0	ENST00000257290.5:c.1891+1del		p.X631_splice	ENST00000257290	NM_006206.4	631			1	2	FACETS	0.347	0.284	0.417	0.347	0.284	0.417	SUBCLONAL	1	TRUE	1	0.502342490248235	2		327	402	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158401	26158401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1336643443	NA	P-0021326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1293	161	956	0	ENST00000289316.2:c.4C>T	p.Pro2Ser	p.P2S	ENST00000289316	NM_138720.2	2	Cct/Tct	1/2	1	2	FACETS	0.286	0.261	0.312	0.286	0.261	0.312	SUBCLONAL	1	TRUE	1	0.775537082494103	2		956	1454	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0021329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	87	757	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	0.958	1	CLONAL	1	TRUE	1	0.183622048310221	2		758	801	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597402	10597402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770453522	NA	P-0021329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	147	1118	1	ENST00000171111.5:c.1801C>T	p.Arg601Trp	p.R601W	ENST00000171111	NM_203500.1	601	Cgg/Tgg	6/6	1	2	FACETS	0.754	0.687	0.824	1	0.987	1	SUBCLONAL	2	TRUE	1	0.183622048310221	2		1119	1062	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0021329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	119	882	2	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	1	2	FACETS	0.754	0.68	0.832	1	0.984	1	SUBCLONAL	2	TRUE	1	0.183622048310221	2		884	860	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414944	78414944	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	45	587	0	ENST00000370768.2:c.1822C>T	p.Gln608Ter	p.Q608*	ENST00000370768	NM_003902.3	608	Cag/Tag	19/20	1	2	FACETS	0.792	0.664	0.933	0.792	0.664	0.933	CLONAL	1	TRUE	1	0.183622048310221	2		587	619	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471665	120471665	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	46	623	0	ENST00000256646.2:c.3826G>A	p.Glu1276Lys	p.E1276K	ENST00000256646	NM_024408.3	1276	Gag/Aag	23/34	1	2	FACETS	0.756	0.635	0.889	0.756	0.635	0.889	SUBCLONAL	1	TRUE	1	0.183622048310221	2		623	663	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724445	112724445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	90	863	0	ENST00000369452.4:c.329G>A	p.Arg110Lys	p.R110K	ENST00000369452	NM_007373.3	110	aGa/aAa	2/9	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.183622048310221	2		863	817	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646846	23646846	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	79	996	0	ENST00000261584.4:c.1021G>A	p.Glu341Lys	p.E341K	ENST00000261584	NM_024675.3	341	Gaa/Aaa	4/13	1	2	FACETS	0.792	0.694	0.897	0.792	0.694	0.897	SUBCLONAL	1	TRUE	1	0.183622048310221	2		996	1087	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55704606	55704606	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	165	1016	0	ENST00000284073.2:c.670del	p.Ala224ArgfsTer76	p.A224Rfs*76	ENST00000284073	NM_138962.2	223	gtG/gt	10/14	1	2	FACETS	0.839	0.769	0.912	1	0.99	1	CLONAL	2	TRUE	1	0.183622048310221	2		1016	1071	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023307	31023307	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	81	709	1	ENST00000375687.4:c.2792A>T	p.Glu931Val	p.E931V	ENST00000375687	NM_015338.5	931	gAg/gTg	13/13	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.183622048310221	2		710	758	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851787	134851787	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	78	838	0	ENST00000398015.3:c.1193C>A	p.Ala398Asp	p.A398D	ENST00000398015	NM_004441.4	398	gCc/gAc	5/16	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.183622048310221	2		838	742	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217532	142217532	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	70	739	0	ENST00000350721.4:c.5465C>T	p.Ser1822Leu	p.S1822L	ENST00000350721	NM_001184.3	1822	tCa/tTa	32/47	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.183622048310221	2		739	751	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430807	181430807	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	67	1097	0	ENST00000325404.1:c.659C>G	p.Ser220Trp	p.S220W	ENST00000325404	NM_003106.3	220	tCg/tGg	1/1	1	2	FACETS	0.728	0.631	0.834	0.728	0.631	0.834	SUBCLONAL	1	TRUE	1	0.183622048310221	2		1097	1002	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280121	66280121	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs201024355	NA	P-0021329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	29	578	0	ENST00000273854.3:c.1568C>A	p.Thr523Lys	p.T523K	ENST00000273854	NM_004439.5	523	aCa/aAa	7/18	1	2	FACETS	0.599	0.48	0.736	0.599	0.48	0.736	SUBCLONAL	1	TRUE	1	0.183622048310221	2		578	527	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876315	35876315	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	72	647	0	ENST00000303115.3:c.1107C>G	p.Cys369Trp	p.C369W	ENST00000303115	NM_002185.3	369	tgC/tgG	8/8	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.183622048310221	2		647	614	SUCCESS
APC	324	MSKCC	GRCh37	5	112173828	112173828	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	30	472	0	ENST00000257430.4:c.2537C>A	p.Ser846Tyr	p.S846Y	ENST00000257430	NM_000038.5	846	tCt/tAt	16/16	1	2	FACETS	0.731	0.588	0.893	0.731	0.588	0.893	SUBCLONAL	1	TRUE	1	0.183622048310221	2		472	447	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180340	32180340	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	104	968	3	ENST00000375023.3:c.2591C>T	p.Pro864Leu	p.P864L	ENST00000375023	NM_004557.3	864	cCc/cTc	17/30	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.183622048310221	2		971	883	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392173	81392173	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs758790721	NA	P-0021329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	47	485	0	ENST00000222390.5:c.104G>T	p.Arg35Ile	p.R35I	ENST00000222390	NM_000601.4	35	aGa/aTa	2/18	0.132745452574092	4	FACETS	1	0.947	1	0.653	0.551	0.765	CLONAL	1	TRUE	2	0.183622048310221	4		485	464	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514388	148514388	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	114	807	0	ENST00000320356.2:c.1336A>G	p.Arg446Gly	p.R446G	ENST00000320356	NM_004456.4	446	Aga/Gga	11/20	0.132745452574092	4	FACETS	0.869	0.782	0.961	0.869	0.782	0.961	CLONAL	2	TRUE	2	0.183622048310221	4		807	846	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0021342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	440	888	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.659992916627943	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.659992916627943	1		889	858	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	363	780	0	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	0.659992916627943	1	FACETS	0.984	0.94	1	0.984	0.94	1	CLONAL	1	TRUE	0	0.659992916627943	1		780	749	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434363	121434363	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	344	941	0	ENST00000257555.6:c.1127C>A	p.Pro376His	p.P376H	ENST00000257555		376	cCc/cAc	6/10	1	2	FACETS	0.983	0.931	1	0.983	0.931	1	CLONAL	1	TRUE	1	0.659992916627943	2		941	1061	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89335055	89335055	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1213853388	NA	P-0021342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	222	480	0	ENST00000301030.4:c.7823G>A	p.Arg2608Gln	p.R2608Q	ENST00000301030	NM_001256183.1	2608	cGg/cAg	13/13	0.660296843834318	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.659992916627943	1		480	388	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946178	13946178	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	359	912	0	ENST00000405192.2:c.918C>A	p.Tyr306Ter	p.Y306*	ENST00000405192	NM_001163147.1	306	taC/taA	10/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.659992916627943	2		912	1051	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020291	123020291	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	363	435	1	ENST00000355640.3:c.779C>T	p.Pro260Leu	p.P260L	ENST00000355640		260	cCa/cTa	2/7	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.659992916627943	1		436	503	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0021345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	25	501	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.264	0.208	0.329	0.264	0.208	0.329	SUBCLONAL	1	TRUE	1	0.453649071895376	2		501	417	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376521	118376522	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	73	504	1	ENST00000534358.1:c.9915dup	p.Pro3306ThrfsTer22	p.P3306Tfs*22	ENST00000534358	NM_005933.3	3305	tta/ttAa	27/36	0.453649071895376	1	FACETS	0.918	0.812	1	0.918	0.812	1	CLONAL	1	TRUE	0	0.453649071895376	1		505	271	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553291	41553291	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	206	959	1	ENST00000263253.7:c.3380A>G	p.Asn1127Ser	p.N1127S	ENST00000263253	NM_001429.3	1127	aAt/aGt	18/31	1	2	FACETS	0.915	0.849	0.983	0.915	0.849	0.983	CLONAL	1	TRUE	1	0.453649071895376	2		960	993	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450634	70450634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747878740	NA	P-0021349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	305	656	0	ENST00000373644.4:c.5474C>T	p.Ser1825Leu	p.S1825L	ENST00000373644	NM_030625.2	1825	tCa/tTa	12/12	0.606863286678332	3	FACETS	0.945	0.891	1			1	CLONAL	1	TRUE	NA	0.802552560354624	3		656	1127	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0021349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	819	899	1	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.802552560354624	2	FACETS	0.981	0.962	1	0.981	0.962	1	CLONAL	2	TRUE	0	0.802552560354624	2		900	1040	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453132	140453132	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913365	NA	P-0021349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	1028	599	2	ENST00000288602.6:c.1803A>C	p.Lys601Asn	p.K601N	ENST00000288602	NM_004333.4	601	aaA/aaC	15/18	0.799972039408903	4	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	1	0.802552560354624	4		601	1463	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610028	81610028	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	322	433	0	ENST00000298171.2:c.1626G>A	p.Met542Ile	p.M542I	ENST00000298171	NM_000369.2	542	atG/atA	10/10	0.802552560354624	2	FACETS	0.951	0.919	0.981	0.951	0.919	0.981	CLONAL	2	TRUE	0	0.802552560354624	2		433	422	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576121	88576122	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0021349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	959	986	1	ENST00000360948.2:c.1551_1552delinsAA	p.Phe517_Arg518delinsLeuSer	p.F517_R518delinsLS	ENST00000360948	NM_001012338.2	517	ttCCgt/ttAAgt	13/19	0.445012089623774	3	FACETS	0.984	0.968	0.998			1	INDETERMINATE	3	TRUE	NA	0.802552560354624	3		987	1135	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610279	10610279	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	1045	1094	1	ENST00000171111.5:c.431C>T	p.Ser144Phe	p.S144F	ENST00000171111	NM_203500.1	144	tCc/tTc	2/6	0.802552560354624	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.802552560354624	2		1095	1267	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499433	89499433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	580	664	1	ENST00000336596.2:c.2603G>A	p.Arg868Lys	p.R868K	ENST00000336596	NM_005233.5	868	aGa/aAa	15/17	0.802552560354624	2	FACETS	0.993	0.97	1	0.993	0.97	1	CLONAL	2	TRUE	0	0.802552560354624	2		665	728	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158106	106158193	+	frameshift_variant	Frame_Shift_Del	DEL	TGGAAAAAGGTAACTAAGCAAGAGAATCCACCTGCAAGCTGTGATAATGTGCAGCAAAAGAGCATCATTGAGACCATGGAGCAGCATC	TGGAAAAAGGTAACTAAGCAAGAGAATCCACCTGCAAGCTGTGATAATGTGCAGCAAAAGAGCATCATTGAGACCATGGAGCAGCATC	-	novel	NA	P-0021349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	180	353	0	ENST00000380013.4:c.3009_3096del	p.Trp1003Ter	p.W1003*	ENST00000380013	NM_001127208.2	1003	TGGAAAAAGGTAACTAAGCAAGAGAATCCACCTGCAAGCTGTGATAATGTGCAGCAAAAGAGCATCATTGAGACCATGGAGCAGCATCtg/tg	3/11	1	2	FACETS	0.936	0.872	1	0.936	0.872	1	CLONAL	1	TRUE	1	0.802552560354624	2		353	479	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617655	39617655	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0021362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	53	468	0	ENST00000262039.4:c.1840-1G>C		p.X614_splice	ENST00000262039	NM_002647.2	614			0.384018742741049	4	FACETS	0.834	0.713	0.966	0.417	0.356	0.483	CLONAL	1	TRUE	2	0.425107588171283	4		468	426	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502264	186502264	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	146	356	1	ENST00000323963.5:c.73G>C	p.Glu25Gln	p.E25Q	ENST00000323963		25	Gag/Cag	2/11	0.425107588171283	3	FACETS	0.957	0.882	1	0.957	0.882	1	CLONAL	2	TRUE	1	0.425107588171283	3		357	435	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106882	27106882	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	237	576	1	ENST00000324856.7:c.6493G>C	p.Glu2165Gln	p.E2165Q	ENST00000324856	NM_006015.4	2165	Gag/Cag	20/20	0.425107588171283	3	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	1	0.425107588171283	3		577	667	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578551	7578552	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0021362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	433	1002	2	ENST00000269305.4:c.378dup	p.Ser127LeufsTer22	p.S127Lfs*22	ENST00000269305	NM_001126112.2	126	-/C	5/11	0.425107588171283	2	FACETS	0.901	0.86	0.941	0.901	0.86	0.941	CLONAL	2	TRUE	0	0.425107588171283	2		1004	1131	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030805	48030805	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	56	281	0	ENST00000234420.5:c.3419A>C	p.Lys1140Thr	p.K1140T	ENST00000234420	NM_000179.2	1140	aAg/aCg	5/10	0.425107588171283	3	FACETS	0.945	0.814	1	0.473	0.407	0.544	CLONAL	1	TRUE	1	0.425107588171283	3		281	338	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44935946	44935946	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	224	320	0	ENST00000377967.4:c.2707C>G	p.Leu903Val	p.L903V	ENST00000377967	NM_021140.2	903	Cta/Gta	18/29	0.425107588171283	9	FACETS	0.986	0.927	1			1	CLONAL	5	TRUE	NA	0.425107588171283	9		320	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934576	NA	P-0021372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	298	699	0	ENST00000269305.4:c.818G>C	p.Arg273Pro	p.R273P	ENST00000269305	NM_001126112.2	273	cGt/cCt	8/11	0.640323524760183	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.640323524760183	1		699	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0021375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	275	1068	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.392043939304806	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.392043939304806	1		1068	905	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591825	48591825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767342	NA	P-0021375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	79	824	0	ENST00000342988.3:c.988G>A	p.Glu330Lys	p.E330K	ENST00000342988	NM_005359.5	330	Gaa/Aaa	9/12	0.392043939304806	1	FACETS	0.606	0.534	0.683	0.606	0.534	0.683	SUBCLONAL	1	TRUE	0	0.392043939304806	1		824	535	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087558	27087558	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0021375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	342	1021	0	ENST00000324856.7:c.2132C>G	p.Ser711Ter	p.S711*	ENST00000324856	NM_006015.4	711	tCa/tGa	5/20	0.392043939304806	2	FACETS	0.985	0.935	1	0.985	0.935	1	CLONAL	2	TRUE	0	0.392043939304806	2		1021	886	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600420	10600420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	276	1172	3	ENST00000171111.5:c.1435G>A	p.Asp479Asn	p.D479N	ENST00000171111	NM_203500.1	479	Gac/Aac	4/6	0.392043939304806	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.392043939304806	1		1175	897	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597993	43597993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	222	1128	1	ENST00000355710.3:c.541C>T	p.Pro181Ser	p.P181S	ENST00000355710	NM_020975.4	181	Ccc/Tcc	3/20	0.392043939304806	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.392043939304806	1		1129	767	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90627554	90627554	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	241	985	0	ENST00000330062.3:c.1303A>G	p.Thr435Ala	p.T435A	ENST00000330062	NM_002168.2	435	Acg/Gcg	11/11	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.392043939304806	2		985	861	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61725840	61725840	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	93	815	0	ENST00000401558.2:c.727G>C	p.Glu243Gln	p.E243Q	ENST00000401558	NM_003400.3	243	Gag/Cag	9/25	1	2	FACETS	0.606	0.538	0.678	0.606	0.538	0.678	SUBCLONAL	1	TRUE	1	0.392043939304806	2		815	783	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0021382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	152	807	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		807	664	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0021385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	44	411	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.442519933852576	1	FACETS	0.437	0.368	0.514	0.437	0.368	0.514	SUBCLONAL	1	TRUE	0	0.442519933852576	1		411	354	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115969	8115970	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	137	420	0	ENST00000346208.3:c.1316dup	p.Thr440HisfsTer67	p.T440Hfs*67	ENST00000346208		439	gtc/gTtc	6/6	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.442519933852576	2		420	564	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120163	70120163	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs753584114	NA	P-0121498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	191	447	0	ENST00000245479.2:c.1165C>A	p.Pro389Thr	p.P389T	ENST00000245479	NM_000346.3	389	Ccg/Acg	3/3	0.738007966744087	5	FACETS	0.987	0.912	1	0.329	0.304	0.355	CLONAL	1	NA	2	0.738007966744087	5		447	1105	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579415	7579415	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	774	924	1	ENST00000269305.4:c.272G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tGg/tAg	4/11	0.850603613288132	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.850603613288132	2		925	867	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841230	15841231	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGCCGG	rs752736259	NA	P-0021403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	62	260	0	ENST00000307771.7:c.1338_1343dup	p.Ser447_Arg448dup	p.S447_R448dup	ENST00000307771	NM_005089.3	447	-/AGCCGG	11/11	1	1	FACETS	0.499	0.44	0.559	0.499	0.44	0.559	SUBCLONAL	1	TRUE	0	0.850603613288132	1		260	168	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781465	3781465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	183	419	0	ENST00000262367.5:c.4900G>A	p.Val1634Met	p.V1634M	ENST00000262367	NM_004380.2	1634	Gtg/Atg	30/31	0.850603613288132	2	FACETS	0.998	0.932	1	0.499	0.466	0.533	CLONAL	1	TRUE	0	0.850603613288132	2		419	431	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060928	38060928	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1319052552	NA	P-0021403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	178	675	0	ENST00000250448.2:c.1061C>G	p.Ser354Cys	p.S354C	ENST00000250448	NM_004496.3	354	tCc/tGc	2/2	0.83607849691603	3	FACETS	0.831	0.768	0.896	0.415	0.384	0.448	CLONAL	1	TRUE	1	0.850603613288132	3		675	718	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670850	134670850	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1401843217	NA	P-0021403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	223	524	0	ENST00000398015.3:c.761C>A	p.Thr254Asn	p.T254N	ENST00000398015	NM_004441.4	254	aCc/aAc	3/16	0.83607849691603	3	FACETS	1	0.946	1	0.507	0.474	0.541	CLONAL	1	TRUE	1	0.850603613288132	3		524	737	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336664	81336664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	352	566	0	ENST00000222390.5:c.1558G>A	p.Gly520Arg	p.G520R	ENST00000222390	NM_000601.4	520	Gga/Aga	14/18	0.83607849691603	3	FACETS	0.913	0.874	0.952	0.913	0.874	0.952	CLONAL	2	TRUE	1	0.850603613288132	3		566	646	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031738	69031738	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	358	933	0	ENST00000288368.4:c.3493C>A	p.Leu1165Ile	p.L1165I	ENST00000288368	NM_024870.2	1165	Ctt/Att	28/40	0.529524035561639	3	FACETS	1	0.99	1	0.581	0.551	0.611	CLONAL	1	TRUE	1	0.850603613288132	3		933	1033	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577529	7577529	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs730882027	NA	P-0021407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	234	934	1	ENST00000269305.4:c.752T>G	p.Ile251Ser	p.I251S	ENST00000269305	NM_001126112.2	251	aTc/aGc	7/11	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	2	TRUE	NA	0.727287443314547	2		935	311	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867540	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs11466445	NA	P-0021407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	10	34	0	ENST00000374994.4:c.76_78del	p.Ala26del	p.A26del	ENST00000374994	NM_004612.2	17	ctGGCg/ctg	1/9	0.438234438261393	4	FACETS	0.403	0.274	0.562			1	SUBCLONAL	1	TRUE	NA	0.727287443314547	4		34	118	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775634	9775634	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	190	806	0	ENST00000377346.4:c.177C>G	p.Phe59Leu	p.F59L	ENST00000377346	NM_005026.3	59	ttC/ttG	4/24	0.362168404018056	3	FACETS	0.856	0.802	0.911	0.856	0.802	0.911	INDETERMINATE	2	TRUE	1	0.727287443314547	3		806	416	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837937	156837937	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141021604	NA	P-0021407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	89	1085	1	ENST00000524377.1:c.470G>A	p.Arg157His	p.R157H	ENST00000524377	NM_002529.3	157	cGc/cAc	5/17	0.382930257897411	3	FACETS	0.678	0.604	0.758	0.339	0.302	0.379	INDETERMINATE	1	TRUE	1	0.727287443314547	3		1086	492	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	221	766	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.606552621540743	2		766	700	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504081	123504081	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	184	340	0	ENST00000371139.4:c.257C>T	p.Ala86Val	p.A86V	ENST00000371139	NM_001114937.2	86	gCa/gTa	3/4	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.606552621540743	1		340	305	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717715	89717716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587782341	NA	P-0021420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	195	625	1	ENST00000371953.3:c.741dup	p.Pro248ThrfsTer5	p.P248Tfs*5	ENST00000371953	NM_000314.4	247	tta/ttAa	7/9	0.606552621540743	1	FACETS	0.982	0.92	1	0.982	0.92	1	CLONAL	1	TRUE	0	0.606552621540743	1		626	456	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642470	117642470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765146445	NA	P-0021420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	256	875	2	ENST00000368508.3:c.5729G>A	p.Arg1910Gln	p.R1910Q	ENST00000368508	NM_002944.2	1910	cGa/cAa	35/43	0.606552621540743	1	FACETS	0.949	0.895	1	0.949	0.895	1	CLONAL	1	TRUE	0	0.606552621540743	1		877	620	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622476	28622476	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	256	859	0	ENST00000241453.7:c.1141T>C	p.Cys381Arg	p.C381R	ENST00000241453	NM_004119.2	381	Tgt/Cgt	9/24	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.606552621540743	2		859	828	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0021423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	328	637	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.611573800207604	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.611573800207604	3		637	632	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221955	1221958	+	frameshift_variant	Frame_Shift_Del	DEL	TGAG	TGAG	-	novel	NA	P-0021423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	576	854	3	ENST00000326873.7:c.871_874del	p.Glu291ThrfsTer44	p.E291Tfs*44	ENST00000326873	NM_000455.4	290	ctTGAG/ct	7/10	0.596468584219874	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.611573800207604	2		857	923	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288840	15288840	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	34	417	0	ENST00000263388.2:c.3899T>C	p.Val1300Ala	p.V1300A	ENST00000263388	NM_000435.2	1300	gTg/gCg	24/33	0.611573800207604	3	FACETS	0.268	0.218	0.324	0.134	0.109	0.162	SUBCLONAL	1	TRUE	1	0.611573800207604	3		417	542	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0021426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	40	926	2	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.154062162346356	2	FACETS	0.816	0.677	0.972	0.408	0.338	0.486	CLONAL	1	TRUE	0	0.154062162346356	2		928	636	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577152	7577154	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	ACC	ACC	-	rs1567548347	NA	P-0021426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	59	727	0	ENST00000269305.4:c.784_786del	p.Gly262del	p.G262del	ENST00000269305	NM_001126112.2	262	GGT/-	8/11	0.154062162346356	2	FACETS	1	0.964	1	0.7	0.603	0.806	CLONAL	1	TRUE	0	0.154062162346356	2		727	547	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994610	73994610	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	64	1047	0	ENST00000318443.5:c.94C>T	p.Gln32Ter	p.Q32*	ENST00000318443	NM_001024736.1	32	Cag/Tag	3/10	0.146347008660994	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.154062162346356	1		1047	648	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213876	66213876	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	31	876	0	ENST00000273854.3:c.2554T>G	p.Phe852Val	p.F852V	ENST00000273854	NM_004439.5	852	Ttc/Gtc	15/18	1	2	FACETS	0.915	0.739	1	0.915	0.739	1	CLONAL	1	TRUE	1	0.154062162346356	2		876	440	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349900	70349900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863223706	NA	P-0021426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	55	495	0	ENST00000374080.3:c.3883C>T	p.Arg1295Cys	p.R1295C	ENST00000374080		1295	Cgt/Tgt	28/45	0.124744273807386	2	FACETS	0.915	0.786	1			1	CLONAL	2	TRUE	NA	0.154062162346356	2		495	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519988	NA	P-0021450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	152	372	0	ENST00000269305.4:c.808T>G	p.Phe270Val	p.F270V	ENST00000269305	NM_001126112.2	270	Ttt/Gtt	8/11	0.466078651250925	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.466078651250925	1		372	482	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051642	30051642	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0021450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	79	265	0	ENST00000338641.4:c.576C>G	p.Tyr192Ter	p.Y192*	ENST00000338641	NM_000268.3	192	taC/taG	6/16	0.466078651250925	1	FACETS	0.754	0.668	0.844	0.754	0.668	0.844	SUBCLONAL	1	TRUE	0	0.466078651250925	1		265	345	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0021454-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	366	757	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.174305516603913	4	FACETS	0.879	0.836	0.923			1	INDETERMINATE	3	TRUE	NA	0.376193752664376	4		758	1015	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578415	7578415	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021454-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	205	613	2	ENST00000269305.4:c.515T>A	p.Val172Asp	p.V172D	ENST00000269305	NM_001126112.2	172	gTt/gAt	5/11	0.376193752664376	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.376193752664376	1		615	690	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377024	118377024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781919840	NA	P-0021454-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	101	394	0	ENST00000534358.1:c.10417C>T	p.Arg3473Cys	p.R3473C	ENST00000534358	NM_005933.3	3473	Cgt/Tgt	27/36	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.376193752664376	2		394	502	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199700	11199700	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021454-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	372	539	0	ENST00000361445.4:c.4888G>T	p.Val1630Leu	p.V1630L	ENST00000361445	NM_004958.3	1630	Gta/Tta	35/58	0.376193752664376	3	FACETS	0.955	0.912	0.999			1	CLONAL	3	TRUE	NA	0.376193752664376	3		539	820	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259349	11259349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021454-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	458	598	0	ENST00000361445.4:c.4219G>T	p.Gly1407Cys	p.G1407C	ENST00000361445	NM_004958.3	1407	Ggc/Tgc	28/58	0.376193752664376	3	FACETS	0.981	0.941	1			1	CLONAL	3	TRUE	NA	0.376193752664376	3		598	983	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869515	102869515	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021454-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	136	402	2	ENST00000307046.8:c.126C>A	p.Phe42Leu	p.F42L	ENST00000307046	NM_001111285.1	42	ttC/ttA	2/4	0.376193752664376	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.376193752664376	1		404	530	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543626	29543626	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021454-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	73	506	0	ENST00000389048.3:c.1537G>T	p.Asp513Tyr	p.D513Y	ENST00000389048	NM_004304.4	513	Gac/Tac	7/29	0.376193752664376	1	FACETS	0.558	0.488	0.633	0.558	0.488	0.633	SUBCLONAL	1	TRUE	0	0.376193752664376	1		506	565	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876378	35876378	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021454-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	155	565	0	ENST00000303115.3:c.1170C>A	p.Cys390Ter	p.C390*	ENST00000303115	NM_002185.3	390	tgC/tgA	8/8	NA	2	FACETS	0.982	0.9	1			1	INDETERMINATE	1	TRUE	NA	0.376193752664376	2		565	839	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617663	100617663	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021454-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	83	614	0	ENST00000308731.7:c.406A>C	p.Ser136Arg	p.S136R	ENST00000308731	NM_000061.2	136	Agt/Cgt	6/19	0.32626146703065	0	FACETS	0.495	0.438	0.557			1	SUBCLONAL	1	TRUE	0	0.376193752664376	0		614	556	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175914300	175914300	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	61	579	0	ENST00000367669.3:c.2185G>C	p.Glu729Gln	p.E729Q	ENST00000367669	NM_022457.5	729	Gaa/Caa	20/20	1	2	FACETS	0.425	0.368	0.487	0.425	0.368	0.487	SUBCLONAL	1	TRUE	1	0.712410220897769	2		579	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577016	7577090	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TACCTCGCTTAGTGCTCCCTGGGGGCAGCTCGTGGTGAGGCTCCCCTTTCTTGCGGAGATTCTCTTCCTCTGTGC	TACCTCGCTTAGTGCTCCCTGGGGGCAGCTCGTGGTGAGGCTCCCCTTTCTTGCGGAGATTCTCTTCCTCTGTGC	-	novel	NA	P-0021456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	104	889	0	ENST00000269305.4:c.848_919+3del		p.X283_splice	ENST00000269305	NM_001126112.2	283		8/11	0.712410220897769	1	FACETS	0.437	0.394	0.483	0.437	0.394	0.483	SUBCLONAL	1	TRUE	0	0.712410220897769	1		889	430	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210902	36210902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377667885	NA	P-0021456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	107	909	0	ENST00000222270.7:c.653G>A	p.Arg218Gln	p.R218Q	ENST00000222270	NM_014727.1	218	cGg/cAg	3/37	0.712410220897769	1	FACETS	0.39	0.351	0.431	0.39	0.351	0.431	SUBCLONAL	1	TRUE	0	0.712410220897769	1		909	496	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021745	71021745	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	107	609	0	ENST00000318789.4:c.1613A>C	p.Glu538Ala	p.E538A	ENST00000318789	NM_032682.5	538	gAa/gCa	18/21	NA	2	FACETS	0.52	0.467	0.575			1	INDETERMINATE	1	TRUE	NA	0.712410220897769	2		609	578	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169862	32169862	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	117	851	0	ENST00000375023.3:c.3746C>T	p.Pro1249Leu	p.P1249L	ENST00000375023	NM_004557.3	1249	cCa/cTa	21/30	1	2	FACETS	0.452	0.408	0.499	0.452	0.408	0.499	SUBCLONAL	1	TRUE	1	0.712410220897769	2		851	726	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911601	32911601	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs80358557	NA	P-0021463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	78	555	0	ENST00000380152.3:c.3109C>A	p.Gln1037Lys	p.Q1037K	ENST00000380152		1037	Caa/Aaa	11/27	1	2	FACETS	0.996	0.877	1	0.996	0.877	1	CLONAL	1	TRUE	1	0.29	2		555	540	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858337	9858337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs560057284	NA	P-0021466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	87	468	0	ENST00000330684.3:c.3064C>T	p.Arg1022Cys	p.R1022C	ENST00000330684	NM_001134407.1	1022	Cgc/Tgc	13/13	0.164852482090372	3	FACETS	0.845	0.75	0.945	0.845	0.75	0.945	CLONAL	2	TRUE	1	0.234344386361764	3		468	491	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115809	8115809	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	80	785	0	ENST00000346208.3:c.1158del	p.Lys387ArgfsTer17	p.K387Rfs*17	ENST00000346208		385	ttC/tt	6/6	1	2	FACETS	0.881	0.775	0.995	0.881	0.775	0.995	CLONAL	1	TRUE	1	0.234344386361764	2		785	775	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578199	7578199	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	125	860	0	ENST00000269305.4:c.650T>C	p.Val217Ala	p.V217A	ENST00000269305	NM_001126112.2	217	gTg/gCg	6/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.234344386361764	2		860	855	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303243	15303243	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	68	1294	0	ENST00000263388.2:c.285T>G	p.Ser95Arg	p.S95R	ENST00000263388	NM_000435.2	95	agT/agG	3/33	1	2	FACETS	0.488	0.422	0.559	0.488	0.422	0.559	SUBCLONAL	1	TRUE	1	0.234344386361764	2		1294	1190	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280234	142280234	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	54	500	0	ENST00000350721.4:c.1200G>C	p.Leu400Phe	p.L400F	ENST00000350721	NM_001184.3	400	ttG/ttC	5/47	0.164852482090372	3	FACETS	0.97	0.828	1	0.485	0.414	0.562	CLONAL	1	TRUE	1	0.234344386361764	3		500	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0021476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	518	888	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.704652828178723	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.727267291659687	1		889	879	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1039046	1039046	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	361	668	0	ENST00000358495.3:c.287T>G	p.Val96Gly	p.V96G	ENST00000358495	NM_134424.2	96	gTt/gGt	5/12	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.727267291659687	2		668	990	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945130	32945130	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs80359105	NA	P-0021476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	220	457	0	ENST00000380152.3:c.8525G>T	p.Arg2842Leu	p.R2842L	ENST00000380152		2842	cGc/cTc	20/27	0.727267291659687	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.727267291659687	1		457	378	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273878	10273878	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1830	802	876	0	ENST00000330684.3:c.391G>C	p.Ala131Pro	p.A131P	ENST00000330684	NM_001134407.1	131	Gca/Cca	2/13	0.727267291659687	4	FACETS	1	0.997	1			1	CLONAL	1	TRUE	NA	0.727267291659687	4		876	2632	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212330	36212330	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745812917	NA	P-0021476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	503	922	1	ENST00000222270.7:c.2081G>A	p.Arg694Gln	p.R694Q	ENST00000222270	NM_014727.1	694	cGg/cAg	3/37	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.727267291659687	2		923	1307	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717730	89717730	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121909239	NA	P-0021479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	229	705	0	ENST00000371953.3:c.755A>T	p.Asp252Val	p.D252V	ENST00000371953	NM_000314.4	252	gAt/gTt	7/9	0.575122999073503	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.575122999073503	1		705	552	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730858	40730858	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200227405	NA	P-0021479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	181	1019	0	ENST00000373198.4:c.3677G>A	p.Arg1226Gln	p.R1226Q	ENST00000373198	NM_133170.3	1226	cGa/cAa	27/32	1	2	FACETS	0.566	0.521	0.613	0.566	0.521	0.613	SUBCLONAL	1	TRUE	1	0.575122999073503	2		1019	1112	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696432	47696432	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519968	NA	P-0021486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	165	762	0	ENST00000347630.2:c.391T>G	p.Trp131Gly	p.W131G	ENST00000347630	NM_001007230.1	131	Tgg/Ggg	6/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.411698140605111	2		762	761	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42053959	42053959	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	37	452	0	ENST00000219905.7:c.7421T>C	p.Leu2474Pro	p.L2474P	ENST00000219905	NM_001164273.1	2474	cTa/cCa	21/24	1	2	FACETS	0.481	0.397	0.574	0.481	0.397	0.574	SUBCLONAL	1	TRUE	1	0.411698140605111	2		452	374	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89874705	89874705	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs747149073	NA	P-0021486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	177	1048	0	ENST00000389301.3:c.593A>C	p.Glu198Ala	p.E198A	ENST00000389301	NM_000135.2	198	gAa/gCa	6/43	1	2	FACETS	0.906	0.835	0.98	0.906	0.835	0.98	CLONAL	1	TRUE	1	0.411698140605111	2		1048	949	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981903	70981903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747860295	NA	P-0021486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	168	1055	3	ENST00000276594.2:c.193G>A	p.Ala65Thr	p.A65T	ENST00000276594	NM_024504.3	65	Gcc/Acc	2/8	0.39112096344329	3	FACETS	1	0.966	1	0.546	0.502	0.592	CLONAL	1	TRUE	1	0.411698140605111	3		1058	901	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0021501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	103	762	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.501	0.448	0.557	0.501	0.448	0.557	SUBCLONAL	1	TRUE	1	0.498612775237761	2		762	825	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0021501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	91	907	3	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.442	0.392	0.496	0.442	0.392	0.496	SUBCLONAL	1	TRUE	1	0.498612775237761	2		910	825	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11177083	11177084	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0021501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	98	897	0	ENST00000361445.4:c.6993dup	p.Tyr2332ValfsTer8	p.Y2332Vfs*8	ENST00000361445	NM_004958.3	2331	-/G	50/58	1	2	FACETS	0.474	0.422	0.529	0.474	0.422	0.529	SUBCLONAL	1	TRUE	1	0.498612775237761	2		897	830	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971083	21971093	+	frameshift_variant	Frame_Shift_Del	DEL	TCCAGGAAGCC	TCCAGGAAGCC	GGCT	novel	NA	P-0021501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	33	780	2	ENST00000304494.5:c.265_275delinsAGCC	p.Gly89SerfsTer55	p.G89Sfs*55	ENST00000304494	NM_000077.4	89	GGCTTCCTGGAc/AGCCc	2/3	0.24008314873162	1	FACETS	0.202	0.164	0.244	0.202	0.164	0.244	INDETERMINATE	1	TRUE	0	0.498612775237761	1		782	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0021507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	827	910	2	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.812215056515205	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.812215056515205	2		912	966	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851685	134851685	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	949	593	0	ENST00000398015.3:c.1091G>T	p.Arg364Leu	p.R364L	ENST00000398015	NM_004441.4	364	cGg/cTg	5/16	0.812215056515205	6	FACETS	1	0.992	1	1	0.992	1	CLONAL	4	TRUE	2	0.812215056515205	6		593	1479	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85742020	85742020	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	262	814	1	ENST00000370580.1:c.16C>T	p.Pro6Ser	p.P6S	ENST00000370580	NM_003921.4	6	Ccg/Tcg	1/3	0.270755651370722	4	FACETS	1	0.956	1	0.256	0.24	0.274	INDETERMINATE	1	TRUE	0	0.812215056515205	4		815	1140	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437100	121437100	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs551484245	NA	P-0021507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	748	927	0	ENST00000257555.6:c.1531C>G	p.Gln511Glu	p.Q511E	ENST00000257555		511	Cag/Gag	8/10	0.639064539003919	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.812215056515205	4		927	1610	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55607037	55607037	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	203	676	2	ENST00000284073.2:c.406G>A	p.Val136Met	p.V136M	ENST00000284073	NM_138962.2	136	Gtg/Atg	7/14	0.270755651370722	4	FACETS	1	0.987	1	0.312	0.29	0.335	INDETERMINATE	1	TRUE	0	0.812215056515205	4		678	726	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226942	2226942	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	42	743	0	ENST00000398665.3:c.4422C>A	p.Phe1474Leu	p.F1474L	ENST00000398665	NM_032482.2	1474	ttC/ttA	27/28	0.812215056515205	2	FACETS	0.133	0.11	0.158	0.067	0.055	0.079	SUBCLONAL	1	TRUE	0	0.812215056515205	2		743	777	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956565	93956565	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	521	568	0	ENST00000369303.4:c.2671G>T	p.Asp891Tyr	p.D891Y	ENST00000369303	NM_004440.3	891	Gac/Tac	15/17	0.812215056515205	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.812215056515205	3		568	590	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984000	2984000	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	748	905	0	ENST00000396946.4:c.530A>T	p.Gln177Leu	p.Q177L	ENST00000396946	NM_032415.4	177	cAg/cTg	5/25	0.812215056515205	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.812215056515205	2		905	872	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69000006	69000006	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	289	818	0	ENST00000288368.4:c.2075G>T	p.Arg692Leu	p.R692L	ENST00000288368	NM_024870.2	692	cGg/cTg	19/40	0.801283407549074	3	FACETS	0.99	0.932	1	0.495	0.466	0.525	CLONAL	1	TRUE	1	0.812215056515205	3		818	1011	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054205	30054207	+	missense_variant	Missense_Mutation	TNP	GAT	GAT	AAA	novel	NA	P-0021507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	387	618	0	ENST00000338641.4:c.627_629delinsAAA	p.Ile210Lys	p.I210K	ENST00000338641	NM_000268.3	209	aaGATa/aaAAAa	7/16	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.812215056515205	2		618	463	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0021527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	408	757	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.409501430819151	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.416838116692811	3		758	1098	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	243	766	0				ENST00000310581	NM_198253.2	-/1132			0.416838116692811	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.416838116692811	2		766	552	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416796	416796	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756725945	NA	P-0021527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	115	523	0	ENST00000399788.2:c.3754C>T	p.Arg1252Cys	p.R1252C	ENST00000399788	NM_001042603.1	1252	Cgt/Tgt	23/28	0.0915182347487201	6	FACETS	0.947	0.857	1			1	INDETERMINATE	2	TRUE	NA	0.416838116692811	6		523	534	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319959	8319959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745582718	NA	P-0021527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	61	356	0	ENST00000356435.5:c.5542G>A	p.Val1848Ile	p.V1848I	ENST00000356435		1848	Gtt/Att	34/35	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.416838116692811	NA		356	352	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976422	25976422	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	178	916	0	ENST00000435504.4:c.1123G>C	p.Glu375Gln	p.E375Q	ENST00000435504		375	Gaa/Caa	11/13	1	2	FACETS	0.992	0.915	1	0.992	0.915	1	CLONAL	1	TRUE	1	0.416838116692811	2		916	861	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982978	201982978	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	356	970	1	ENST00000359651.3:c.827G>A	p.Trp276Ter	p.W276*	ENST00000359651		276	tGg/tAg	7/8	0.416654379561134	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.416838116692811	2		971	727	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369241	118369241	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs781805661	NA	P-0021527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	88	460	2	ENST00000534358.1:c.5959G>A	p.Glu1987Lys	p.E1987K	ENST00000534358	NM_005933.3	1987	Gaa/Aaa	22/36	0.416838116692811	1	FACETS	0.989	0.884	1	0.989	0.884	1	CLONAL	1	TRUE	0	0.416838116692811	1		462	338	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28908254	28908254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	136	799	0	ENST00000282397.4:c.2501G>A	p.Gly834Glu	p.G834E	ENST00000282397	NM_002019.4	834	gGa/gAa	18/30	1	2	FACETS	0.977	0.89	1	0.977	0.89	1	CLONAL	1	TRUE	1	0.416838116692811	2		799	668	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894228	NA	P-0021547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	231	699	0	ENST00000451590.1:c.37G>C	p.Gly13Arg	p.G13R	ENST00000451590	NM_001130442.1	13	Ggt/Cgt	2/5	1	2	FACETS	0.816	0.765	0.869	1	0.993	1	CLONAL	2	TRUE	1	0.420398245360541	2		699	673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1567548223	NA	P-0021547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	162	771	3	ENST00000269305.4:c.797del	p.Gly266AspfsTer79	p.G266Dfs*79	ENST00000269305	NM_001126112.2	266	gGa/ga	8/11	0.420398245360541	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.420398245360541	1		774	606	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302250	15302250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745779705	NA	P-0021547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	205	875	0	ENST00000263388.2:c.1021C>T	p.Pro341Ser	p.P341S	ENST00000263388	NM_000435.2	341	Ccc/Tcc	6/33	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.420398245360541	2		875	788	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0021550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	163	763	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.193913532472044	5	FACETS	1	0.987	1	0.463	0.425	0.502	INDETERMINATE	1	TRUE	2	0.514534101469864	5		764	809	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578517	7578517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750600586	NA	P-0021550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	388	828	1	ENST00000269305.4:c.413C>T	p.Ala138Val	p.A138V	ENST00000269305	NM_001126112.2	138	gCc/gTc	5/11	0.306479886779969	2	FACETS	0.777	0.741	0.814	0.777	0.741	0.814	INDETERMINATE	2	TRUE	0	0.514534101469864	2		829	970	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0021550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	15	299	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	0.514534101469864	3	FACETS	0.316	0.231	0.418	0.105	0.077	0.14	SUBCLONAL	1	TRUE	0	0.514534101469864	3		299	232	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0021550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	103	296	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.514534101469864	3	FACETS	1	0.979	1	0.815	0.747	0.882	CLONAL	2	TRUE	0	0.514534101469864	3		296	206	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444951	49444951	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	61	487	0	ENST00000301067.7:c.2515G>C	p.Glu839Gln	p.E839Q	ENST00000301067	NM_003482.3	839	Gag/Cag	10/54	0.193913532472044	5	FACETS	0.562	0.484	0.647	0.187	0.161	0.216	INDETERMINATE	1	TRUE	2	0.514534101469864	5		487	748	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7132203	7132203	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	165	761	0	ENST00000302850.5:c.2808G>A	p.Trp936Ter	p.W936*	ENST00000302850	NM_000208.2	936	tgG/tgA	14/22	0.294467918041057	5	FACETS	0.921	0.844	1	0.307	0.281	0.334	INDETERMINATE	1	TRUE	2	0.514534101469864	5		761	1234	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143161	30143161	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1367800764	NA	P-0021550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	188	579	0	ENST00000389048.3:c.365C>T	p.Thr122Met	p.T122M	ENST00000389048	NM_004304.4	122	aCg/aTg	1/29	0.294467918041057	5	FACETS	0.791	0.732	0.853	0.528	0.488	0.569	INDETERMINATE	2	TRUE	2	0.514534101469864	5		579	818	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659797	227659797	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	149	422	0	ENST00000305123.5:c.3658C>G	p.Arg1220Gly	p.R1220G	ENST00000305123	NM_005544.2	1220	Cgc/Ggc	1/2	0.43482146803298	3	FACETS	0.957	0.875	1	0.478	0.437	0.521	CLONAL	1	TRUE	1	0.514534101469864	3		422	761	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047644	180047644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760931332	NA	P-0021550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	69	696	0	ENST00000261937.6:c.2371G>A	p.Val791Ile	p.V791I	ENST00000261937	NM_182925.4	791	Gtc/Atc	16/30	0.514534101469864	3	FACETS	0.369	0.32	0.421	0.123	0.106	0.141	SUBCLONAL	1	TRUE	0	0.514534101469864	3		696	915	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975366	13975366	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	295	497	0	ENST00000405192.2:c.521C>G	p.Ser174Cys	p.S174C	ENST00000405192	NM_001163147.1	174	tCc/tGc	7/12	0.362323920767404	4	FACETS	0.877	0.827	0.929	0.877	0.827	0.929	CLONAL	2	TRUE	2	0.514534101469864	4		497	990	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0021574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	358	698	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.524625357547216	3	FACETS	1	0.991	1	0.4	0.378	0.422	CLONAL	1	TRUE	0	0.570808138595541	3		698	1345	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0021574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	547	604	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.524625357547216	3	FACETS	0.845	0.816	0.873	0.845	0.816	0.873	CLONAL	3	TRUE	0	0.570808138595541	3		604	972	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864656	37864656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs950730453	NA	P-0021574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	197	803	0	ENST00000269571.5:c.308G>A	p.Arg103Gln	p.R103Q	ENST00000269571		103	cGa/cAa	3/27	0.189724181603383	1	FACETS	0.431	0.398	0.465	0.431	0.398	0.465	INDETERMINATE	1	TRUE	0	0.570808138595541	1		803	1144	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690306	117690306	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	119	513	0	ENST00000369458.3:c.823C>G	p.Leu275Val	p.L275V	ENST00000369458	NM_024626.3	275	Ctc/Gtc	5/6	0.565053908078822	1	FACETS	0.482	0.436	0.531	0.482	0.436	0.531	SUBCLONAL	1	TRUE	0	0.570808138595541	1		513	618	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112035575	112035575	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1159797492	NA	P-0021574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	136	621	0	ENST00000368678.4:c.319G>C	p.Glu107Gln	p.E107Q	ENST00000368678		107	Gaa/Caa	4/13	1	2	FACETS	0.458	0.416	0.503	0.458	0.416	0.503	SUBCLONAL	1	TRUE	1	0.570808138595541	2		621	1040	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425644	49425644	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057517992	NA	P-0021574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	155	716	0	ENST00000301067.7:c.12844C>T	p.Arg4282Ter	p.R4282*	ENST00000301067	NM_003482.3	4282	Cga/Tga	39/54	0.290482422289139	1	FACETS	0.394	0.36	0.429	0.394	0.36	0.429	INDETERMINATE	1	TRUE	0	0.570808138595541	1		716	986	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199864	138199864	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	210	487	0	ENST00000237289.4:c.1282G>C	p.Glu428Gln	p.E428Q	ENST00000237289	NM_001270507.1	428	Gag/Cag	7/9	NA	2	FACETS	0.934	0.869	1			1	INDETERMINATE	1	TRUE	NA	0.570808138595541	2		487	788	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307593	118307593	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	152	598	0	ENST00000534358.1:c.366C>G	p.Ile122Met	p.I122M	ENST00000534358	NM_005933.3	122	atC/atG	1/36	0.565053908078822	1	FACETS	0.529	0.485	0.576	0.529	0.485	0.576	SUBCLONAL	1	TRUE	0	0.570808138595541	1		598	719	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539885	187539885	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	107	532	1	ENST00000441802.2:c.7855C>A	p.Leu2619Ile	p.L2619I	ENST00000441802	NM_005245.3	2619	Ctt/Att	10/27	0.565053908078822	1	FACETS	0.489	0.44	0.541	0.489	0.44	0.541	SUBCLONAL	1	TRUE	0	0.570808138595541	1		533	548	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448173	49448173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	125	638	0	ENST00000301067.7:c.427G>A	p.Ala143Thr	p.A143T	ENST00000301067	NM_003482.3	143	Gct/Act	4/54	0.290482422289139	1	FACETS	0.332	0.3	0.366	0.332	0.3	0.366	INDETERMINATE	1	TRUE	0	0.570808138595541	1		638	942	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211836	2211836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	357	700	0	ENST00000398665.3:c.1552G>A	p.Glu518Lys	p.E518K	ENST00000398665	NM_032482.2	518	Gag/Aag	16/28	0.290482422289139	1	FACETS	0.906	0.86	0.952	0.906	0.86	0.952	INDETERMINATE	1	TRUE	0	0.570808138595541	1		700	987	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662857	227662857	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	127	647	0	ENST00000305123.5:c.598G>C	p.Glu200Gln	p.E200Q	ENST00000305123	NM_005544.2	200	Gag/Cag	1/2	0.385440506317892	1	FACETS	0.356	0.322	0.392	0.356	0.322	0.392	SUBCLONAL	1	TRUE	0	0.570808138595541	1		647	892	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497322	149497322	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs987244289	NA	P-0021574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	164	711	0	ENST00000261799.4:c.2996G>A	p.Arg999Gln	p.R999Q	ENST00000261799	NM_002609.3	999	cGa/cAa	22/23	0.290482422289139	1	FACETS	0.425	0.39	0.462	0.425	0.39	0.462	INDETERMINATE	1	TRUE	0	0.570808138595541	1		711	966	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421039	49421039	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398123721	NA	P-0021577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	80	592	1	ENST00000301067.7:c.14710C>T	p.Arg4904Ter	p.R4904*	ENST00000301067	NM_003482.3	4904	Cga/Tga	48/54	0.10380375282829	4	FACETS	0.778	0.685	0.877	0.778	0.685	0.877	INDETERMINATE	2	FALSE	2	0.20072604219012	4		593	615	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949665	151949665	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	124	592	0	ENST00000262189.6:c.1435C>T	p.Gln479Ter	p.Q479*	ENST00000262189	NM_170606.2	479	Cag/Tag	10/59	0.20072604219012	6	FACETS	0.891	0.805	0.982	0.356	0.322	0.393	CLONAL	2	FALSE	1	0.20072604219012	6		592	972	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0021593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	270	731	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.615342477478495	2		731	815	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579336	7579351	+	frameshift_variant	Frame_Shift_Del	DEL	CCCAGAATGCAAGAAG	CCCAGAATGCAAGAAG	-	novel	NA	P-0021593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	168	569	0	ENST00000269305.4:c.336_351del	p.Phe113GlnfsTer5	p.F113Qfs*5	ENST00000269305	NM_001126112.2	112	ggCTTCTTGCATTCTGGG/gg	4/11	0.615342477478495	1	FACETS	0.861	0.8	0.924	0.861	0.8	0.924	CLONAL	1	TRUE	0	0.615342477478495	1		569	439	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919252	48919252	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	88	240	0	ENST00000267163.4:c.417del	p.Asp139GlufsTer14	p.D139Efs*14	ENST00000267163	NM_000321.2	139	gaT/ga	4/27	0.615342477478495	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.615342477478495	1		240	191	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0021597-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	32	584	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.317067949902427	1	FACETS	0.467	0.379	0.565	0.467	0.379	0.565	SUBCLONAL	1	TRUE	0	0.317067949902427	1		586	364	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	57	766	0				ENST00000310581	NM_198253.2	-/1132			0.34338997779982	1	FACETS	0.99	0.874	1	1	0.981	1	CLONAL	2	TRUE	0	0.355831214902563	1		766	133	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652198	36652199	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0021608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	202	742	0	ENST00000244741.5:c.322dup	p.Glu108GlyfsTer21	p.E108Gfs*21	ENST00000244741	NM_000389.4	107	gag/gaGg	2/3	0.355831214902563	8	FACETS	1	0.981	1			1	CLONAL	3	TRUE	NA	0.355831214902563	8		742	679	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038511	47038511	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	107	355	2	ENST00000377604.3:c.673C>T	p.Gln225Ter	p.Q225*	ENST00000377604	NM_001204468.1	225	Cag/Tag	8/24	0.355831214902563	2	FACETS	1	0.96	1			1	CLONAL	2	TRUE	NA	0.355831214902563	2		357	275	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346771	91346771	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	86	496	0	ENST00000355112.3:c.3379C>T	p.Gln1127Ter	p.Q1127*	ENST00000355112	NM_000057.2	1127	Cag/Tag	18/22	0.355831214902563	4	FACETS	0.825	0.735	0.921	0.55	0.49	0.614	CLONAL	2	TRUE	1	0.355831214902563	4		496	397	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248728	212248728	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	40	486	0	ENST00000342788.4:c.3539T>A	p.Leu1180His	p.L1180H	ENST00000342788	NM_005235.2	1180	cTt/cAt	28/28	0.108909655986979	6	FACETS	0.877	0.731	1	0.877	0.731	1	CLONAL	3	TRUE	3	0.108909655986979	6		486	340	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0021628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	158	757	1	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	0.347046325074756	2		758	855	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657313	29657313	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0021628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	142	803	0	ENST00000356175.3:c.5547-1G>T		p.X1849_splice	ENST00000356175	NM_000267.3	1849			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.347046325074756	2		803	755	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78599548	78599548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	143	770	5	ENST00000306801.3:c.220G>A	p.Asp74Asn	p.D74N	ENST00000306801	NM_020761.2	74	Gat/Aat	2/34	1	2	FACETS	0.974	0.888	1	0.974	0.888	1	CLONAL	1	TRUE	1	0.347046325074756	2		775	846	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457704	149457704	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1454473722	NA	P-0021628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	200	1048	1	ENST00000286301.3:c.700G>T	p.Asp234Tyr	p.D234Y	ENST00000286301	NM_005211.3	234	Gat/Tat	5/22	0.25605294802479	3	FACETS	1	0.979	1	0.579	0.535	0.624	CLONAL	1	TRUE	1	0.347046325074756	3		1049	1169	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859424	57859424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	76	706	1	ENST00000228682.2:c.569G>T	p.Cys190Phe	p.C190F	ENST00000228682	NM_005269.2	190	tGc/tTc	6/12	1	2	FACETS	0.688	0.603	0.778	0.688	0.603	0.778	SUBCLONAL	1	TRUE	1	0.347046325074756	2		707	637	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337708	73337708	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	55	351	0	ENST00000377767.4:c.2008G>T	p.Ala670Ser	p.A670S	ENST00000377767	NM_014953.3	670	Gcc/Tcc	16/21	1	2	FACETS	0.804	0.69	0.928	0.804	0.69	0.928	CLONAL	1	TRUE	1	0.347046325074756	2		351	394	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086205	16086205	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	102	628	1	ENST00000281043.3:c.1381G>T	p.Ala461Ser	p.A461S	ENST00000281043	NM_005378.4	461	Gct/Tct	3/3	1	2	FACETS	0.861	0.77	0.956	0.861	0.77	0.956	CLONAL	1	TRUE	1	0.347046325074756	2		629	683	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324537	62324537	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs778531697	NA	P-0021628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	200	1246	0	ENST00000360203.5:c.2893G>C	p.Glu965Gln	p.E965Q	ENST00000360203	NM_001283009.1	965	Gag/Cag	30/35	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.347046325074756	2		1246	1040	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670483	134670483	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	141	696	1	ENST00000398015.3:c.394G>T	p.Ala132Ser	p.A132S	ENST00000398015	NM_004441.4	132	Gcc/Tcc	3/16	0.347046325074756	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.347046325074756	1		697	572	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664714	138664714	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	73	247	1	ENST00000330315.3:c.851C>A	p.Pro284His	p.P284H	ENST00000330315	NM_023067.3	284	cCc/cAc	1/1	0.347046325074756	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.347046325074756	1		248	280	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159135	143159135	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	66	580	0	ENST00000262992.4:c.718A>G	p.Arg240Gly	p.R240G	ENST00000262992	NM_001101669.1	240	Aga/Gga	10/24	1	2	FACETS	0.676	0.587	0.772	0.676	0.587	0.772	SUBCLONAL	1	TRUE	1	0.347046325074756	2		580	563	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2952925	2952925	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	111	812	0	ENST00000396946.4:c.3015G>T	p.Lys1005Asn	p.K1005N	ENST00000396946	NM_032415.4	1005	aaG/aaT	22/25	1	2	FACETS	0.895	0.805	0.99	0.895	0.805	0.99	CLONAL	1	TRUE	1	0.347046325074756	2		812	715	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874817	151874817	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	73	407	0	ENST00000262189.6:c.7721T>A	p.Phe2574Tyr	p.F2574Y	ENST00000262189	NM_170606.2	2574	tTc/tAc	38/59	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.347046325074756	2		407	394	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0021631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	204	637	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.37396882535609	3	FACETS	0.948	0.883	1	0.948	0.883	1	CLONAL	2	TRUE	1	0.37396882535609	3		637	683	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0021631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	88	692	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.26231252476707	1	FACETS	0.445	0.393	0.5	0.445	0.393	0.5	SUBCLONAL	1	TRUE	0	0.37396882535609	1		692	860	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053022	180053023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750808726	NA	P-0021631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	166	980	7	ENST00000261937.6:c.1267dup	p.Gln423ProfsTer4	p.Q423Pfs*4	ENST00000261937	NM_182925.4	423	cag/cCag	10/30	1	2	FACETS	0.906	0.832	0.983	0.906	0.832	0.983	CLONAL	1	TRUE	1	0.37396882535609	2		987	980	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849462	68849462	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	171	835	0	ENST00000261769.5:c.1365del	p.Val456Ter	p.V456*	ENST00000261769	NM_004360.3	455	gcA/gc	10/16	0.37396882535609	1	FACETS	0.948	0.874	1	0.948	0.874	1	CLONAL	1	TRUE	0	0.37396882535609	1		835	784	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	295	584	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.826	0.778	0.874	0.826	0.778	0.874	CLONAL	1	TRUE	1	0.728560325204789	2		586	981	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	222	565	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.938	0.878	0.999	0.938	0.878	0.999	CLONAL	1	TRUE	1	0.728560325204789	2		565	650	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	258	534	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.878	0.825	0.932	0.878	0.825	0.932	CLONAL	1	TRUE	1	0.728560325204789	2		534	807	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867540	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs11466445	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	15	34	0	ENST00000374994.4:c.76_78del	p.Ala26del	p.A26del	ENST00000374994	NM_004612.2	17	ctGGCg/ctg	1/9	1	2	FACETS	0.521	0.388	0.674	0.521	0.388	0.674	SUBCLONAL	1	TRUE	1	0.728560325204789	2		34	79	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612268	189612268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs972760958	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	169	365	0	ENST00000264731.3:c.2020C>T	p.Arg674Cys	p.R674C	ENST00000264731	NM_003722.4	674	Cgc/Tgc	14/14	0.728560325204789	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.728560325204789	1		365	285	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	223	526	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.769	0.718	0.822	0.769	0.718	0.822	SUBCLONAL	1	TRUE	1	0.728560325204789	2		528	796	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	223	459	4	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.892	0.835	0.951	0.892	0.835	0.951	CLONAL	1	TRUE	1	0.728560325204789	2		463	686	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	236	454	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	0.728560325204789	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.728560325204789	1		455	405	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056588	26056590	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs751086925	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	108	256	0	ENST00000343677.2:c.67_69del	p.Lys23del	p.K23del	ENST00000343677	NM_005319.3	23	AAG/-	1/1	1	2	FACETS	0.84	0.762	0.921	0.84	0.762	0.921	CLONAL	1	TRUE	1	0.728560325204789	2		256	353	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	303	676	0	ENST00000263967.3:c.278G>T	p.Arg93Leu	p.R93L	ENST00000263967	NM_006218.2	93	cGg/cTg	2/21	0.728560325204789	1	FACETS	0.954	0.91	0.998	0.954	0.91	0.998	CLONAL	1	TRUE	0	0.728560325204789	1		676	554	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266134	41266136	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs587776850	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	163	352	0	ENST00000349496.5:c.133_135del	p.Ser45del	p.S45del	ENST00000349496	NM_001904.3	44	cCTTct/cct	3/15	0.728560325204789	1	FACETS	0.881	0.823	0.938	0.881	0.823	0.938	CLONAL	1	TRUE	0	0.728560325204789	1		352	323	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	413	771	0	ENST00000227507.2:c.859C>T	p.Pro287Ser	p.P287S	ENST00000227507	NM_053056.2	287	Ccc/Tcc	5/5	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.728560325204789	2		771	1078	SUCCESS
EED	8726	MSKCC	GRCh37	11	85968616	85968618	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	177	355	0	ENST00000263360.6:c.615_617del	p.Leu207del	p.L207del	ENST00000263360	NM_003797.3	204	aaTCTt/aat	6/12	1	2	FACETS	0.895	0.83	0.961	0.895	0.83	0.961	CLONAL	1	TRUE	1	0.728560325204789	2		355	543	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	343	640	4	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	0.958	0.909	1	0.958	0.909	1	CLONAL	1	TRUE	1	0.728560325204789	2		644	983	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	259	442	6	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	0.728560325204789	2		448	680	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835781	68835781	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060501215	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	319	557	0	ENST00000261769.5:c.377del	p.Pro126ArgfsTer89	p.P126Rfs*89	ENST00000261769	NM_004360.3	124	cgC/cg	3/16	1	2	FACETS	0.97	0.918	1	0.97	0.918	1	CLONAL	1	TRUE	1	0.728560325204789	2		557	903	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435417	56435417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112997544	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	108	691	0	ENST00000407977.2:c.1720G>A	p.Gly574Arg	p.G574R	ENST00000407977		574	Gga/Aga	9/10	1	2	FACETS	0.293	0.262	0.325	0.293	0.262	0.325	SUBCLONAL	1	TRUE	1	0.728560325204789	2		691	1013	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226412	133226412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200114024	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	353	678	0	ENST00000320574.5:c.3646G>A	p.Gly1216Ser	p.G1216S	ENST00000320574	NM_006231.2	1216	Ggc/Agc	30/49	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.728560325204789	2		678	896	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615698	1615698	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	311	853	2	ENST00000344749.5:c.1573del	p.Arg525GlyfsTer18	p.R525Gfs*18	ENST00000344749	NM_001136139.2	525	Cgg/gg	17/19	1	2	FACETS	0.808	0.762	0.854	0.808	0.762	0.854	CLONAL	1	TRUE	1	0.728560325204789	2		855	1057	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482169	87482169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201028496	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	45	654	1	ENST00000277120.3:c.1456G>A	p.Val486Ile	p.V486I	ENST00000277120		486	Gtt/Att	14/19	1	2	FACETS	0.15	0.125	0.178	0.15	0.125	0.178	SUBCLONAL	1	TRUE	1	0.728560325204789	2		655	823	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726051	61726052	+	splice_region_variant,intron_variant	Splice_Region	DEL	AA	AA	-	rs372688892	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	164	354	0	ENST00000401558.2:c.591-4_591-3del		p.X197_splice	ENST00000401558	NM_003400.3	197			1	2	FACETS	0.866	0.8	0.933	0.866	0.8	0.933	CLONAL	1	TRUE	1	0.728560325204789	2		354	520	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190690	11190690	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	316	674	0	ENST00000361445.4:c.5509A>G	p.Thr1837Ala	p.T1837A	ENST00000361445	NM_004958.3	1837	Act/Gct	39/58	1	2	FACETS	0.962	0.91	1	0.962	0.91	1	CLONAL	1	TRUE	1	0.728560325204789	2		674	902	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101552	27101552	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	331	725	0	ENST00000324856.7:c.4837del	p.Met1613CysfsTer13	p.M1613Cfs*13	ENST00000324856	NM_006015.4	1612	Aaa/aa	18/20	1	2	FACETS	0.824	0.779	0.869	0.824	0.779	0.869	CLONAL	1	TRUE	1	0.728560325204789	2		725	1103	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981272	201981272	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1356631733	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	427	745	1	ENST00000359651.3:c.355del	p.Asp119ThrfsTer36	p.D119Tfs*36	ENST00000359651		117	ctG/ct	2/8	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.728560325204789	2		746	1152	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100727	8100728	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	205	719	0	ENST00000346208.3:c.707_708dup	p.Ser237ProfsTer29	p.S237Pfs*29	ENST00000346208		234	ttc/ttCCc	3/6	1	2	FACETS	0.664	0.617	0.713	0.664	0.617	0.713	SUBCLONAL	1	TRUE	1	0.728560325204789	2		719	847	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691190	18691190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756366407	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	225	481	0	ENST00000266497.5:c.3301C>T	p.Arg1101Cys	p.R1101C	ENST00000266497		1101	Cgt/Tgt	23/31	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.728560325204789	2		481	547	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426669	49426670	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	novel	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	95	335	0	ENST00000301067.7:c.11816_11818dup	p.Gln3939dup	p.Q3939dup	ENST00000301067	NM_003482.3	3939	ctt/cAGCtt	39/54	1	2	FACETS	0.561	0.502	0.623	0.561	0.502	0.623	SUBCLONAL	1	TRUE	1	0.728560325204789	2		335	465	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858560	57858560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760141461	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	365	754	3	ENST00000228682.2:c.298C>T	p.Arg100Cys	p.R100C	ENST00000228682	NM_005269.2	100	Cgc/Tgc	4/12	1	2	FACETS	0.969	0.921	1	0.969	0.921	1	CLONAL	1	TRUE	1	0.728560325204789	2		757	1034	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112326	115112326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1302202171	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	156	285	0	ENST00000257566.3:c.1414G>A	p.Ala472Thr	p.A472T	ENST00000257566	NM_016569.3	472	Gcg/Acg	7/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.728560325204789	2		285	390	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772316	68772316	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	367	731	2	ENST00000261769.5:c.163+2T>C		p.X55_splice	ENST00000261769	NM_004360.3	55			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.728560325204789	2		733	972	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099215	4099215	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	295	591	4	ENST00000262948.5:c.903del	p.Arg303AlafsTer24	p.R303Afs*24	ENST00000262948	NM_030662.3	301	ccC/cc	7/11	1	2	FACETS	0.973	0.92	1	0.973	0.92	1	CLONAL	1	TRUE	1	0.728560325204789	2		595	832	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027680	48027680	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	212	334	0	ENST00000234420.5:c.2558A>T	p.Lys853Met	p.K853M	ENST00000234420	NM_000179.2	853	aAg/aTg	4/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.728560325204789	2		334	536	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394129	31394129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1330224703	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	186	406	0	ENST00000328111.2:c.2416G>A	p.Glu806Lys	p.E806K	ENST00000328111	NM_006892.3	806	Gaa/Aaa	22/23	1	2	FACETS	0.962	0.895	1	0.962	0.895	1	CLONAL	1	TRUE	1	0.728560325204789	2		406	531	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397663	49397663	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	296	517	0	ENST00000418115.1:c.561del	p.Lys187AsnfsTer19	p.K187Nfs*19	ENST00000418115	NM_001664.2	187	aaA/aa	5/5	0.728560325204789	1	FACETS	0.988	0.942	1	0.988	0.942	1	CLONAL	1	TRUE	0	0.728560325204789	1		517	523	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623273	52623273	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	123	248	0	ENST00000394830.3:c.2780-2A>G		p.X927_splice	ENST00000394830	NM_018313.4	927			0.728560325204789	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.728560325204789	1		248	207	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259247	89259247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	187	472	0	ENST00000336596.2:c.391C>T	p.His131Tyr	p.H131Y	ENST00000336596	NM_005233.5	131	Cat/Tat	3/17	NA	2	FACETS	1	0.947	1			1	INDETERMINATE	1	TRUE	NA	0.728560325204789	2		472	504	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067073	143067073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	232	489	1	ENST00000262992.4:c.1640G>A	p.Gly547Asp	p.G547D	ENST00000262992	NM_001101669.1	547	gGt/gAt	16/24	1	2	FACETS	0.971	0.911	1	0.971	0.911	1	CLONAL	1	TRUE	1	0.728560325204789	2		490	656	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160580	56160580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	122	287	0	ENST00000399503.3:c.854C>T	p.Thr285Ile	p.T285I	ENST00000399503	NM_005921.1	285	aCa/aTa	4/20	1	2	FACETS	0.768	0.699	0.839	0.768	0.699	0.839	SUBCLONAL	1	TRUE	1	0.728560325204789	2		287	436	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339480	116339480	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	170	354	0	ENST00000397752.3:c.342T>A	p.Asp114Glu	p.D114E	ENST00000397752	NM_000245.2	114	gaT/gaA	2/21	1	2	FACETS	0.976	0.906	1	0.976	0.906	1	CLONAL	1	TRUE	1	0.728560325204789	2		354	478	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045165	47045165	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	305	682	0	ENST00000377604.3:c.2406A>C	p.Glu802Asp	p.E802D	ENST00000377604	NM_001204468.1	802	gaA/gaC	21/24	1	2	FACETS	0.975	0.922	1	0.975	0.922	1	CLONAL	1	TRUE	1	0.728560325204789	2		682	859	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937416	76937416	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	195	528	0	ENST00000373344.5:c.3332A>T	p.Asp1111Val	p.D1111V	ENST00000373344	NM_000489.3	1111	gAt/gTt	9/35	1	2	FACETS	0.878	0.817	0.94	0.878	0.817	0.94	CLONAL	1	TRUE	1	0.728560325204789	2		528	610	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323307	31323307	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	32	100	0	ENST00000412585.2:c.682T>A	p.Trp228Arg	p.W228R	ENST00000412585	NM_005514.6	228	Tgg/Agg	4/8	1	2	FACETS	0.582	0.479	0.694	0.582	0.479	0.694	SUBCLONAL	1	TRUE	1	0.728560325204789	2		100	151	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573976	7573976	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	385	731	1	ENST00000269305.4:c.1051A>T	p.Lys351Ter	p.K351*	ENST00000269305	NM_001126112.2	351	Aag/Tag	10/11	0.635725278929905	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.635725278929905	1		732	711	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875645	35875645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201449880	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	174	631	1	ENST00000303115.3:c.832G>A	p.Asp278Asn	p.D278N	ENST00000303115	NM_002185.3	278	Gat/Aat	7/8	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.635725278929905	2		632	508	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857692	9857692	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1389208302	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	193	345	0	ENST00000330684.3:c.3709G>A	p.Asp1237Asn	p.D1237N	ENST00000330684	NM_001134407.1	1237	Gat/Aat	13/13	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.635725278929905	2		345	565	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313222	30313222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	206	644	0	ENST00000262643.3:c.916C>T	p.His306Tyr	p.H306Y	ENST00000262643	NM_001238.2	306	Cat/Tat	10/12	1	2	FACETS	0.938	0.874	1	0.938	0.874	1	CLONAL	1	TRUE	1	0.635725278929905	2		644	691	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954188	48954188	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	98	321	0	ENST00000267163.4:c.1390-1G>A		p.X464_splice	ENST00000267163	NM_000321.2	464			1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.635725278929905	2		321	302	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39613898	39613898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	70	381	0	ENST00000262039.4:c.1816C>T	p.Pro606Ser	p.P606S	ENST00000262039	NM_002647.2	606	Ccg/Tcg	16/25	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.635725278929905	2		381	216	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175874	24175874	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	229	481	0	ENST00000263121.7:c.1102C>T	p.Gln368Ter	p.Q368*	ENST00000263121	NM_003073.3	368	Cag/Tag	8/9	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.635725278929905	2		481	690	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92252390	92252390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373488172	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	87	274	0	ENST00000265734.4:c.658C>T	p.Arg220Cys	p.R220C	ENST00000265734	NM_001259.6	220	Cgt/Tgt	6/8	1	2	FACETS	0.918	0.823	1	0.918	0.823	1	CLONAL	1	TRUE	1	0.635725278929905	2		274	298	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778251	27778251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761484168	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	229	436	0	ENST00000369163.2:c.400G>A	p.Glu134Lys	p.E134K	ENST00000369163	NM_003536.2	134	Gag/Aag	1/1	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.635725278929905	2		436	661	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436671	110436671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	490	760	1	ENST00000375856.3:c.1730C>T	p.Ser577Phe	p.S577F	ENST00000375856	NM_003749.2	577	tCc/tTc	1/2	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.635725278929905	2		761	1276	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232137	98232137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1382474804	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	191	422	2	ENST00000331920.6:c.1805G>A	p.Arg602Gln	p.R602Q	ENST00000331920	NM_000264.3	602	cGa/cAa	13/24	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.635725278929905	2		424	601	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273096	198273096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	150	438	0	ENST00000335508.6:c.1114C>T	p.Pro372Ser	p.P372S	ENST00000335508	NM_012433.2	372	Cca/Tca	8/25	1	2	FACETS	0.866	0.796	0.938	0.866	0.796	0.938	CLONAL	1	TRUE	1	0.635725278929905	2		438	545	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271633	15271633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	518	900	0	ENST00000263388.2:c.6806C>T	p.Ser2269Phe	p.S2269F	ENST00000263388	NM_000435.2	2269	tCc/tTc	33/33	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.635725278929905	2		900	1485	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730938	40730938	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	202	409	0	ENST00000373198.4:c.3598-1G>A		p.X1200_splice	ENST00000373198	NM_133170.3	1200			1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.635725278929905	2		409	614	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99169286	99169286	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	255	541	0	ENST00000074304.5:c.1216C>T	p.Gln406Ter	p.Q406*	ENST00000074304	NM_001134224.1	406	Cag/Tag	15/26	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.635725278929905	2		541	735	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45800147	45800147	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764645557	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	334	588	1	ENST00000450313.1:c.73G>A	p.Gly25Ser	p.G25S	ENST00000450313	NM_012222.2	25	Ggt/Agt	2/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.635725278929905	2		589	965	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63700047	63700048	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	101	226	1	ENST00000279873.7:c.382_383delinsTT	p.Pro128Leu	p.P128L	ENST00000279873	NM_032199.2	128	CCa/TTa	3/10	1	2	FACETS	0.94	0.849	1	0.94	0.849	1	CLONAL	1	TRUE	1	0.635725278929905	2		227	338	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446380	70446380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	213	454	0	ENST00000373644.4:c.5320G>A	p.Glu1774Lys	p.E1774K	ENST00000373644	NM_030625.2	1774	Gaa/Aaa	11/12	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.635725278929905	2		454	627	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201913	102201913	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs369562282	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	67	319	0	ENST00000263464.3:c.1265A>G	p.Asn422Ser	p.N422S	ENST00000263464	NM_001165.4	422	aAt/aGt	6/9	0.635725278929905	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.635725278929905	1		319	139	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037391	12037391	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	240	781	0	ENST00000396373.4:c.1022T>C	p.Leu341Pro	p.L341P	ENST00000396373	NM_001987.4	341	cTt/cCt	6/8	1	2	FACETS	0.966	0.905	1	0.966	0.905	1	CLONAL	1	TRUE	1	0.635725278929905	2		781	782	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244039	46244039	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	156	548	0	ENST00000334344.6:c.2133T>A	p.Cys711Ter	p.C711*	ENST00000334344	NM_152641.2	711	tgT/tgA	15/21	1	2	FACETS	0.864	0.795	0.935	0.864	0.795	0.935	CLONAL	1	TRUE	1	0.635725278929905	2		548	568	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435231	49435231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	364	587	0	ENST00000301067.7:c.6322C>T	p.Pro2108Ser	p.P2108S	ENST00000301067	NM_003482.3	2108	Ccg/Tcg	31/54	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.635725278929905	2		587	953	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447796	49447796	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	315	518	0	ENST00000301067.7:c.638T>A	p.Leu213Gln	p.L213Q	ENST00000301067	NM_003482.3	213	cTa/cAa	5/54	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.635725278929905	2		518	822	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226464	133226465	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	200	374	0	ENST00000320574.5:c.3593_3594delinsTT	p.Ala1198Val	p.A1198V	ENST00000320574	NM_006231.2	1198	gCC/gTT	30/49	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.635725278929905	2		374	600	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434487	110434487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	410	622	2	ENST00000375856.3:c.3914G>A	p.Gly1305Glu	p.G1305E	ENST00000375856	NM_003749.2	1305	gGg/gAg	1/2	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.635725278929905	2		624	1115	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872057	37872057	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	415	675	0	ENST00000269571.5:c.1378G>A	p.Glu460Lys	p.E460K	ENST00000269571		460	Gaa/Aaa	12/27	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.635725278929905	2		675	1150	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763235	59763235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761639530	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	122	652	0	ENST00000259008.2:c.2867C>T	p.Ser956Leu	p.S956L	ENST00000259008	NM_032043.2	956	tCa/tTa	19/20	1	2	FACETS	0.907	0.827	0.991	0.907	0.827	0.991	CLONAL	1	TRUE	1	0.635725278929905	2		652	423	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210483	5210484	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	261	539	1	ENST00000357368.4:c.5483_5484delinsTT	p.Ala1828Val	p.A1828V	ENST00000357368	NM_002850.3	1828	gCC/gTT	35/38	1	2	FACETS	0.925	0.868	0.982	0.925	0.868	0.982	CLONAL	1	TRUE	1	0.635725278929905	2		540	888	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42384766	42384767	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	163	441	0	ENST00000221972.3:c.528_529delinsAA	p.Asp177Asn	p.D177N	ENST00000221972	NM_021601.3	176	ttGGat/ttAAat	4/5	1	2	FACETS	0.893	0.824	0.965	0.893	0.824	0.965	CLONAL	1	TRUE	1	0.635725278929905	2		441	574	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147744	61147744	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749138316	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	96	374	0	ENST00000295025.8:c.1054G>A	p.Gly352Ser	p.G352S	ENST00000295025	NM_002908.2	352	Ggt/Agt	10/11	1	2	FACETS	0.896	0.807	0.99	0.896	0.807	0.99	CLONAL	1	TRUE	1	0.635725278929905	2		374	337	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147745	61147745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	103	377	0	ENST00000295025.8:c.1055G>A	p.Gly352Asp	p.G352D	ENST00000295025	NM_002908.2	352	gGt/gAt	10/11	1	2	FACETS	0.959	0.867	1	0.959	0.867	1	CLONAL	1	TRUE	1	0.635725278929905	2		377	338	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439851	220439851	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	365	684	0	ENST00000243786.2:c.704C>T	p.Pro235Leu	p.P235L	ENST00000243786	NM_002191.3	235	cCc/cTc	2/2	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.635725278929905	2		684	1051	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662578	227662578	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1175926903	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	257	427	0	ENST00000305123.5:c.877C>T	p.Pro293Ser	p.P293S	ENST00000305123	NM_005544.2	293	Ccg/Tcg	1/2	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.635725278929905	2		427	706	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62298874	62298874	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	389	688	1	ENST00000360203.5:c.667T>A	p.Phe223Ile	p.F223I	ENST00000360203	NM_001283009.1	223	Ttc/Atc	8/35	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.635725278929905	2		689	1097	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124431	94124431	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	64	467	2	ENST00000369303.4:c.152C>A	p.Pro51Gln	p.P51Q	ENST00000369303	NM_004440.3	51	cCa/cAa	2/17	1	2	FACETS	0.95	0.835	1	0.95	0.835	1	CLONAL	1	TRUE	1	0.635725278929905	2		469	212	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129292	152129292	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	321	570	0	ENST00000206249.3:c.245C>T	p.Pro82Leu	p.P82L	ENST00000206249	NM_000125.3	82	cCc/cTc	1/8	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.635725278929905	2		570	919	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509214	106509214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	209	586	1	ENST00000359195.3:c.1208C>T	p.Pro403Leu	p.P403L	ENST00000359195	NM_002649.2	403	cCc/cTc	2/11	1	2	FACETS	0.884	0.823	0.946	0.884	0.823	0.946	CLONAL	1	TRUE	1	0.635725278929905	2		587	744	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829108	128829108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1413825142	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	46	61	0	ENST00000249373.3:c.116C>T	p.Pro39Leu	p.P39L	ENST00000249373	NM_005631.4	39	cCt/cTt	1/12	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.635725278929905	2		61	117	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874454	151874454	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	133	386	0	ENST00000262189.6:c.8084C>T	p.Ser2695Phe	p.S2695F	ENST00000262189	NM_170606.2	2695	tCt/tTt	38/59	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.635725278929905	2		386	398	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412658	139412659	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	412	742	1	ENST00000277541.6:c.1185_1186delinsAT	p.Ala396Ser	p.A396S	ENST00000277541	NM_017617.3	395	aaGGcc/aaATcc	7/34	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.635725278929905	2		743	1233	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933557	39933557	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	379	297	0	ENST00000378444.4:c.1042C>T	p.Gln348Ter	p.Q348*	ENST00000378444	NM_001123385.1	348	Cag/Tag	4/15	1	1	FACETS	0.835	0.81	0.859	1	0.997	1	CLONAL	2	TRUE	0	0.635725278929905	1		297	487	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411168	63411169	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	265	309	0	ENST00000330258.3:c.1998_1999delinsAA	p.Ala667Thr	p.A667T	ENST00000330258	NM_152424.3	666	ctGGca/ctAAca	2/2	1	1	FACETS	0.766	0.736	0.796	1	0.995	1	SUBCLONAL	2	TRUE	0	0.635725278929905	1		309	371	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0021651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1711	456	676	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.756800024306353	11	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.756800024306353	11		676	2167	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0021651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	602	649	1	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.738395285360499	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.756800024306353	2		650	795	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87338511	87338511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs117250170	NA	P-0021651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	388	463	2	ENST00000277120.3:c.607G>A	p.Ala203Thr	p.A203T	ENST00000277120		203	Gca/Aca	7/19	0.753976319414876	2	FACETS	0.957	0.925	0.987	0.957	0.925	0.987	CLONAL	2	TRUE	0	0.756800024306353	2		465	536	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433784	49433784	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	1469	842	2	ENST00000301067.7:c.7769C>A	p.Ser2590Ter	p.S2590*	ENST00000301067	NM_003482.3	2590	tCg/tAg	31/54	0.635155014461056	6	FACETS	0.973	0.953	0.992			1	CLONAL	4	TRUE	NA	0.756800024306353	6		844	2508	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433827	49433827	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs761581210	NA	P-0021651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	1481	840	0	ENST00000301067.7:c.7726C>G	p.Gln2576Glu	p.Q2576E	ENST00000301067	NM_003482.3	2576	Caa/Gaa	31/54	0.635155014461056	6	FACETS	0.995	0.975	1			1	CLONAL	4	TRUE	NA	0.756800024306353	6		840	2471	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88428927	88428927	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	486	427	0	ENST00000360948.2:c.2173G>A	p.Glu725Lys	p.E725K	ENST00000360948	NM_001012338.2	725	Gag/Aag	17/19	0.756800024306353	3	FACETS	0.997	0.973	1	0.997	0.973	1	CLONAL	3	TRUE	0	0.756800024306353	3		427	592	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349323	89349325	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0021651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	759	918	1	ENST00000301030.4:c.3625_3627del	p.Lys1209del	p.K1209del	ENST00000301030	NM_001256183.1	1209	AAG/-	9/13	0.738395285360499	2	FACETS	0.941	0.918	0.963	0.941	0.918	0.963	CLONAL	2	TRUE	0	0.756800024306353	2		919	1066	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716209	52716209	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	233	548	0	ENST00000322088.6:c.653A>G	p.Asp218Gly	p.D218G	ENST00000322088	NM_014225.5	218	gAc/gGc	6/15	NA	2	FACETS	0.985	0.925	1			1	INDETERMINATE	1	TRUE	NA	0.756800024306353	2		548	625	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332003	81332003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	301	349	0	ENST00000222390.5:c.2081G>A	p.Gly694Asp	p.G694D	ENST00000222390	NM_000601.4	694	gGt/gAt	18/18	0.750788194263591	2	FACETS	0.975	0.94	1	0.975	0.94	1	CLONAL	2	TRUE	0	0.756800024306353	2		349	408	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482840	140482840	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	764	624	0	ENST00000288602.6:c.1295C>T	p.Ser432Leu	p.S432L	ENST00000288602	NM_004333.4	432	tCa/tTa	10/18	0.756800024306353	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	0	0.756800024306353	3		624	926	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860394	151860394	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	507	547	1	ENST00000262189.6:c.10268G>A	p.Arg3423Lys	p.R3423K	ENST00000262189	NM_170606.2	3423	aGa/aAa	43/59	0.756800024306353	3	FACETS	1	0.991	1	0.718	0.693	0.742	CLONAL	2	TRUE	0	0.756800024306353	3		548	858	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56910929	56910929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1218543185	NA	P-0021651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	266	561	1	ENST00000519728.1:c.1075G>A	p.Glu359Lys	p.E359K	ENST00000519728	NM_002350.3	359	Gag/Aag	11/13	0.757202736866383	3	FACETS	1	0.943	1			1	CLONAL	1	TRUE	NA	0.756800024306353	3		562	964	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0021658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	1051	907	3	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	NA	2	FACETS	1	0.998	1			1	INDETERMINATE	2	TRUE	NA	0.896963596137653	2		910	1125	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0021658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	66	100	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.896963596137653	2		100	126	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870777	12870777	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	170	173	0	ENST00000228872.4:c.4T>G	p.Ser2Ala	p.S2A	ENST00000228872	NM_004064.3	2	Tca/Gca	1/3	0.84828953176484	5	FACETS	0.886	0.821	0.952			1	CLONAL	2	TRUE	NA	0.896963596137653	5		173	502	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870820	12870820	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1411029555	NA	P-0021658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	214	222	0	ENST00000228872.4:c.47T>G	p.Met16Arg	p.M16R	ENST00000228872	NM_004064.3	16	aTg/aGg	1/3	0.84828953176484	5	FACETS	0.87	0.813	0.929			1	CLONAL	2	TRUE	NA	0.896963596137653	5		222	643	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140717	55140718	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTGGCTGCTGCAGTCCTGGTGCTGTTGGTGATTGTGATCATC	novel	NA	P-0021658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2056	573	824	0	ENST00000257290.5:c.1579_1620dup	p.Val527_Ile540dup	p.V527_I540dup	ENST00000257290	NM_006206.4	527	-/GTGGCTGCTGCAGTCCTGGTGCTGTTGGTGATTGTGATCATC	11/23	0.729632696284097	5	FACETS	1	0.992	1			1	CLONAL	1	TRUE	NA	0.896963596137653	5		824	2629	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938172	76938172	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	445	541	0	ENST00000373344.5:c.2576del	p.Gly859GlufsTer10	p.G859Efs*10	ENST00000373344	NM_000489.3	859	gGa/ga	9/35	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.896963596137653	1		541	515	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938173	76938173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	35	540	0	ENST00000373344.5:c.2575G>A	p.Gly859Arg	p.G859R	ENST00000373344	NM_000489.3	859	Gga/Aga	9/35	1	1	FACETS	0.083	0.068	0.101	0.083	0.068	0.101	SUBCLONAL	1	TRUE	0	0.896963596137653	1		540	517	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29115386	29115386	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	126	725	2	ENST00000328354.6:c.680G>A	p.Gly227Glu	p.G227E	ENST00000328354	NM_007194.3	227	gGa/gAa	5/15	0.394684741580656	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.370929516360774	1		727	426	SUCCESS
APC	324	MSKCC	GRCh37	5	112163662	112163662	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1428025300	NA	P-0021668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	50	510	0	ENST00000257430.4:c.1585C>T	p.Leu529Phe	p.L529F	ENST00000257430	NM_000038.5	529	Ctt/Ttt	13/16	0.228517862493566	3	FACETS	0.66	0.561	0.77	0.33	0.28	0.385	SUBCLONAL	1	TRUE	1	0.370929516360774	3		510	484	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724339	52724339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs969720045	NA	P-0021674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	262	735	0	ENST00000322088.6:c.1471G>A	p.Gly491Arg	p.G491R	ENST00000322088	NM_014225.5	491	Gga/Aga	12/15	0.369978020990309	1	FACETS	0.873	0.826	0.92	0.873	0.826	0.92	INDETERMINATE	1	TRUE	0	0.696994460600254	1		735	561	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	253	740	1	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.696994460600254	2		741	611	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721219	176721219	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	213	553	0	ENST00000439151.2:c.6850G>C	p.Glu2284Gln	p.E2284Q	ENST00000439151	NM_022455.4	2284	Gag/Cag	23/23	0.696994460600254	1	FACETS	0.665	0.622	0.709	0.665	0.622	0.709	SUBCLONAL	1	TRUE	0	0.696994460600254	1		553	599	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78420945	78420945	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	112	741	1	ENST00000370768.2:c.1775A>G	p.Lys592Arg	p.K592R	ENST00000370768	NM_003902.3	592	aAa/aGa	18/20	0.369978020990309	1	FACETS	0.358	0.323	0.395	0.358	0.323	0.395	INDETERMINATE	1	TRUE	0	0.696994460600254	1		742	585	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532555	63532555	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730881401	NA	P-0021674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	95	949	1	ENST00000307078.5:c.2024G>T	p.Arg675Leu	p.R675L	ENST00000307078	NM_004655.3	675	cGt/cTt	8/11	0.138340843385248	3	FACETS	0.46	0.409	0.514	0.153	0.136	0.172	INDETERMINATE	1	TRUE	0	0.696994460600254	3		950	799	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098967	178098967	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	161	466	0	ENST00000397062.3:c.78A>C	p.Gln26His	p.Q26H	ENST00000397062	NM_006164.4	26	caA/caC	2/5	0.696994460600254	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.696994460600254	1		466	272	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721261	176721261	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	239	534	0	ENST00000439151.2:c.6892G>C	p.Asp2298His	p.D2298H	ENST00000439151	NM_022455.4	2298	Gac/Cac	23/23	0.696994460600254	1	FACETS	0.707	0.664	0.75	0.707	0.664	0.75	SUBCLONAL	1	TRUE	0	0.696994460600254	1		534	632	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	31	460	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.906	0.734	1	0.906	0.734	1	CLONAL	1	TRUE	1	0.2	2		460	342	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0021684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	63	416	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.2	2		416	476	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0021684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	38	627	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	1	2	FACETS	0.856	0.708	1	0.856	0.708	1	CLONAL	1	TRUE	1	0.2	2		627	444	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717684	89717735	+	frameshift_variant	Frame_Shift_Del	DEL	AAGTTCATGTACTTTGAGTTCCCTCAGCCGTTACCTGTGTGTGGTGATATCA	AAGTTCATGTACTTTGAGTTCCCTCAGCCGTTACCTGTGTGTGGTGATATCA	-	novel	NA	P-0021684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	35	664	0	ENST00000371953.3:c.713_764del	p.Phe238Ter	p.F238*	ENST00000371953	NM_000314.4	237	AAGTTCATGTACTTTGAGTTCCCTCAGCCGTTACCTGTGTGTGGTGATATCAaa/aa	7/9	1	2	FACETS	0.673	0.551	0.811	0.673	0.551	0.811	SUBCLONAL	1	TRUE	1	0.2	2		664	520	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738360	133738360	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	248	465	0	ENST00000318560.5:c.760G>A	p.Gly254Arg	p.G254R	ENST00000318560	NM_005157.4	254	Ggg/Agg	4/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.902882897037414	2		465	468	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061123	38061213	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTGGCGGCGCAAGT	CCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTGGCGGCGCAAGT	GCGGCGGGGGCGGGAGCGGA	novel	NA	P-0021702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	77	555	4	ENST00000250448.2:c.776_866delinsTCCGCTCCCGCCCCCGCCGC	p.Tyr259PhefsTer10	p.Y259Ffs*10	ENST00000250448	NM_004496.3	259	tACTTGCGCCGCCAGAAGCGCTTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGCGGCGCCAAGGGc/tTCCGCTCCCGCCCCCGCCGCc	2/2	1	2	FACETS	0.838	0.736	0.949	0.838	0.736	0.949	CLONAL	1	TRUE	1	0.277446967305311	2		559	662	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658628	3658628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	206	1074	0	ENST00000294008.3:c.338C>T	p.Ser113Phe	p.S113F	ENST00000294008	NM_032444.2	113	tCt/tTt	2/15	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.277446967305311	2		1074	1218	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781409	3781409	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	107	709	0	ENST00000262367.5:c.4956del	p.Asp1653ThrfsTer91	p.D1653Tfs*91	ENST00000262367	NM_004380.2	1652	ccC/cc	30/31	1	2	FACETS	0.873	0.782	0.969	0.873	0.782	0.969	CLONAL	1	TRUE	1	0.277446967305311	2		709	884	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853057	68853193	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTATTGTTGGTTTTCAAAATAAAAACGTTGGAAGTAACCATATAACTGAAGAAGCGCTTAAGCCGTTTTCAGCTACATGTTGTTTGCTGGTCCTATTCTAAAAGCCAGAGCTTGTCCCCGTTCAGATATCGGATTT	CCTATTGTTGGTTTTCAAAATAAAAACGTTGGAAGTAACCATATAACTGAAGAAGCGCTTAAGCCGTTTTCAGCTACATGTTGTTTGCTGGTCCTATTCTAAAAGCCAGAGCTTGTCCCCGTTCAGATATCGGATTT	-	novel	NA	P-0021702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	17	69	0	ENST00000261769.5:c.1566-126_1576del		p.X522_splice	ENST00000261769	NM_004360.3	522		11/16	0.277446967305311	1	FACETS	0.838	0.644	1	1	0.922	1	CLONAL	2	TRUE	0	0.277446967305311	1		69	63	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023479	31023480	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1064796772	NA	P-0021702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	79	555	0	ENST00000375687.4:c.2966_2967del	p.Ser989Ter	p.S989*	ENST00000375687	NM_015338.5	988	gaCTct/gact	13/13	1	2	FACETS	0.973	0.857	1	0.973	0.857	1	CLONAL	1	TRUE	1	0.277446967305311	2		555	585	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152014	55152015	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0021702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	78	590	0	ENST00000257290.5:c.2447_2448del	p.His816ProfsTer2	p.H816Pfs*2	ENST00000257290	NM_006206.4	816	CAc/c	18/23	1	2	FACETS	0.953	0.838	1	0.953	0.838	1	CLONAL	1	TRUE	1	0.277446967305311	2		590	590	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541468	29541468	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1131691131	NA	P-0021709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	66	150	0	ENST00000356175.3:c.1393-1G>A		p.X465_splice	ENST00000356175	NM_000267.3	465			0.348623135183562	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	3	TRUE	0	0.348623135183562	3		150	129	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280028	66280028	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	58	406	0	ENST00000273854.3:c.1661G>A	p.Arg554Lys	p.R554K	ENST00000273854	NM_004439.5	554	aGa/aAa	7/18	1	2	FACETS	0.864	0.745	0.993	0.864	0.745	0.993	CLONAL	1	TRUE	1	0.348623135183562	2		406	385	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481403	+	missense_variant	Missense_Mutation	DNP	CC	CC	GA	rs1057519720	NA	P-0021709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	318	638	1	ENST00000288602.6:c.1405_1406delinsTC	p.Gly469Ser	p.G469S	ENST00000288602	NM_004333.4	469	GGa/TCa	11/18	0.348623135183562	5	FACETS	0.909	0.863	0.956	0.909	0.863	0.956	CLONAL	4	TRUE	1	0.348623135183562	5		639	764	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141552	11141552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	258	819	1	ENST00000358026.2:c.3529G>A	p.Asp1177Asn	p.D1177N	ENST00000358026	NM_001128849.1	1177	Gac/Aac	25/36	0.348623135183562	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.348623135183562	3		820	819	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753428	42753428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	230	912	1	ENST00000222329.4:c.836C>T	p.Pro279Leu	p.P279L	ENST00000222329	NM_006494.2	279	cCc/cTc	4/4	0.348623135183562	3	FACETS	0.836	0.78	0.893	0.836	0.78	0.893	CLONAL	2	TRUE	1	0.348623135183562	3		913	927	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508582	106508582	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	72	514	0	ENST00000359195.3:c.576C>A	p.Asp192Glu	p.D192E	ENST00000359195	NM_002649.2	192	gaC/gaA	2/11	0.348623135183562	5	FACETS	0.897	0.784	1	0.224	0.195	0.255	CLONAL	1	TRUE	1	0.348623135183562	5		514	701	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339241	87339241	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1403591514	NA	P-0021709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	264	747	1	ENST00000277120.3:c.823G>A	p.Asp275Asn	p.D275N	ENST00000277120		275	Gat/Aat	8/19	0.348623135183562	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.348623135183562	3		748	821	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	45	766	0				ENST00000310581	NM_198253.2	-/1132			0.474504214246657	1	FACETS	0.866	0.74	1	0.866	0.74	1	CLONAL	1	TRUE	0	0.474504214246657	1		766	167	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505130	149505130	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	135	821	1	ENST00000261799.4:c.1685A>G	p.Tyr562Cys	p.Y562C	ENST00000261799	NM_002609.3	562	tAc/tGc	12/23	0.42779241599413	4	FACETS	1	0.986	1	0.731	0.667	0.797	CLONAL	1	TRUE	2	0.474504214246657	4		822	574	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158050	27158050	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	207	945	0	ENST00000380036.4:c.274A>C	p.Lys92Gln	p.K92Q	ENST00000380036	NM_000459.3	92	Aag/Cag	2/23	0.287424997084491	4	FACETS	1	0.991	1	0.749	0.696	0.804	CLONAL	1	TRUE	2	0.474504214246657	4		945	859	SUCCESS
APC	324	MSKCC	GRCh37	5	112175273	112175273	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123121	NA	P-0021772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	45	377	0	ENST00000257430.4:c.3982C>T	p.Gln1328Ter	p.Q1328*	ENST00000257430	NM_000038.5	1328	Cag/Tag	16/16	0.432081078134086	1	FACETS	0.613	0.522	0.711	0.613	0.522	0.711	SUBCLONAL	1	TRUE	0	0.55937008960977	1		377	189	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579321	7579322	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs587780067	NA	P-0021772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	160	752	0	ENST00000269305.4:c.365_366del	p.Val122AspfsTer26	p.V122Dfs*26	ENST00000269305	NM_001126112.2	122	gTG/g	4/11	0.55937008960977	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.55937008960977	1		752	354	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964100	28964100	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	36	735	0	ENST00000282397.4:c.1802A>G	p.His601Arg	p.H601R	ENST00000282397	NM_002019.4	601	cAc/cGc	13/30	0.290281259847558	3	FACETS	0.415	0.341	0.497	0.138	0.113	0.166	INDETERMINATE	1	TRUE	0	0.55937008960977	3		735	397	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39535264	39535264	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	50	335	0	ENST00000262039.4:c.8A>T	p.Glu3Val	p.E3V	ENST00000262039	NM_002647.2	3	gAa/gTa	1/25	0.55937008960977	1	FACETS	0.57	0.489	0.657	0.57	0.489	0.657	SUBCLONAL	1	TRUE	0	0.55937008960977	1		335	226	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46608810	46608810	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	174	959	0	ENST00000263734.3:c.2121G>T	p.Lys707Asn	p.K707N	ENST00000263734	NM_001430.4	707	aaG/aaT	13/16	1	2	FACETS	0.991	0.916	1	0.991	0.916	1	CLONAL	1	TRUE	1	0.55937008960977	2		959	628	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751444	57751444	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	21	600	0	ENST00000274289.3:c.1547T>A	p.Phe516Tyr	p.F516Y	ENST00000274289	NM_006622.3	516	tTt/tAt	11/14	0.432081078134086	1	FACETS	0.133	0.102	0.169	0.133	0.102	0.169	SUBCLONAL	1	TRUE	0	0.55937008960977	1		600	407	SUCCESS
APC	324	MSKCC	GRCh37	5	112162826	112162827	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATTATTGCAAG	novel	NA	P-0021772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	25	626	0	ENST00000257430.4:c.1431_1441dup	p.Val481AspfsTer21	p.V481Dfs*21	ENST00000257430	NM_000038.5	477	gaa/gaATTATTGCAAGa	12/16	0.432081078134086	1	FACETS	0.212	0.167	0.263	0.212	0.167	0.263	SUBCLONAL	1	TRUE	0	0.55937008960977	1		626	304	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965672	93965672	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	27	695	0	ENST00000369303.4:c.2256G>C	p.Met752Ile	p.M752I	ENST00000369303	NM_004440.3	752	atG/atC	13/17	1	2	FACETS	0.249	0.198	0.307	0.249	0.198	0.307	SUBCLONAL	1	TRUE	1	0.55937008960977	2		695	388	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985479	2985479	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	45	748	1	ENST00000396946.4:c.332C>A	p.Pro111His	p.P111H	ENST00000396946	NM_032415.4	111	cCc/cAc	4/25	0.472751639391492	1	FACETS	0.21	0.176	0.248	0.21	0.176	0.248	SUBCLONAL	1	TRUE	0	0.55937008960977	1		749	551	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	298	766	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.874781377468291	2		766	645	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926885	112926885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507544	NA	P-0021775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	324	656	0	ENST00000351677.2:c.1505C>T	p.Ser502Leu	p.S502L	ENST00000351677	NM_002834.3	502	tCa/tTa	13/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.874781377468291	2		656	697	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259166	89259166	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	178	458	0	ENST00000336596.2:c.310C>T	p.Arg104Ter	p.R104*	ENST00000336596	NM_005233.5	104	Cga/Tga	3/17	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.874781377468291	2		458	406	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578281	7578281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	320	637	1	ENST00000269305.4:c.568C>T	p.Pro190Ser	p.P190S	ENST00000269305	NM_001126112.2	190	Cct/Tct	6/11	1	2	FACETS	0.932	0.885	0.98	0.932	0.885	0.98	CLONAL	1	TRUE	1	0.874781377468291	2		638	785	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578537	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs879254214	NA	P-0021775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	546	1095	0	ENST00000269305.4:c.393_395del	p.Asn131del	p.N131del	ENST00000269305	NM_001126112.2	131	aaCAAg/aag	5/11	1	2	FACETS	0.918	0.882	0.954	0.918	0.882	0.954	CLONAL	1	TRUE	1	0.874781377468291	2		1095	1360	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279465	1279465	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866767063	NA	P-0021775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	392	993	6	ENST00000310581.5:c.2071C>T	p.Arg691Cys	p.R691C	ENST00000310581	NM_198253.2	691	Cgc/Tgc	5/16	1	2	FACETS	0.915	0.873	0.958	0.915	0.873	0.958	CLONAL	1	TRUE	1	0.874781377468291	2		999	979	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268949	115268949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781496859	NA	P-0021775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	207	647	0	ENST00000438362.2:c.1661G>A	p.Arg554Gln	p.R554Q	ENST00000438362	NM_001242891.1	554	cGa/cAa	14/20	1	2	FACETS	0.809	0.756	0.863	0.809	0.756	0.863	CLONAL	1	TRUE	1	0.874781377468291	2		647	585	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941629	48941629	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1131690860	NA	P-0021775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	116	324	0	ENST00000267163.4:c.940-1G>A		p.X314_splice	ENST00000267163	NM_000321.2	314			0.874781377468291	1	FACETS	0.899	0.843	0.952	0.899	0.843	0.952	CLONAL	1	TRUE	0	0.874781377468291	1		324	166	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578266	7578266	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	352	698	1	ENST00000269305.4:c.583A>C	p.Ile195Leu	p.I195L	ENST00000269305	NM_001126112.2	195	Atc/Ctc	6/11	1	2	FACETS	0.893	0.849	0.938	0.893	0.849	0.938	CLONAL	1	TRUE	1	0.874781377468291	2		699	901	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0021803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	135	840	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.944	0.862	1	0.944	0.862	1	CLONAL	1	TRUE	1	0.498109138892242	2		840	574	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0021803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	95	585	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.758	0.678	0.844	0.758	0.678	0.844	SUBCLONAL	1	TRUE	1	0.498109138892242	2		586	503	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0021803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	81	501	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.893	0.793	1	0.893	0.793	1	CLONAL	1	TRUE	1	0.498109138892242	2		501	364	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0021803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	62	304	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.49063512844204	1	FACETS	0.878	0.77	0.991	0.878	0.77	0.991	CLONAL	1	TRUE	0	0.498109138892242	1		304	213	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225940	2225940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	98	821	0	ENST00000326181.6:c.1732G>A	p.Glu578Lys	p.E578K	ENST00000326181	NM_032271.2	578	Gag/Aag	18/21	1	2	FACETS	0.561	0.501	0.626	0.561	0.501	0.626	SUBCLONAL	1	TRUE	1	0.498109138892242	2		821	701	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0021803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	93	643	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.904	0.809	1	0.904	0.809	1	CLONAL	1	TRUE	1	0.498109138892242	2		643	413	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146132	38146132	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	224	792	2	ENST00000317025.8:c.3374C>T	p.Pro1125Leu	p.P1125L	ENST00000317025	NM_023034.1	1125	cCg/cTg	19/24	NA	2	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.498109138892242	2		794	810	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	403	505	1				ENST00000310581	NM_198253.2	-/1132			0.648702362607867	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	2	0.694950886112013	4		506	871	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	357	777	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.694950886112013	3	FACETS	0.932	0.882	0.984	0.466	0.441	0.492	CLONAL	1	TRUE	1	0.694950886112013	3		777	1485	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980844	40980844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1440	387	833	0	ENST00000373198.4:c.1642G>A	p.Glu548Lys	p.E548K	ENST00000373198	NM_133170.3	548	Gaa/Aaa	10/32	0.694950886112013	4	FACETS	1	0.969	1	0.344	0.326	0.363	CLONAL	1	TRUE	1	0.694950886112013	4		833	1827	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961104	55961104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371148535	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	345	820	2	ENST00000263923.4:c.2836C>T	p.Arg946Cys	p.R946C	ENST00000263923	NM_002253.2	946	Cgt/Tgt	21/30	1	2	FACETS	0.958	0.909	1	0.958	0.909	1	CLONAL	1	TRUE	1	0.694950886112013	2		822	1036	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132522	11132522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778175819	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	379	853	2	ENST00000358026.2:c.2738C>T	p.Pro913Leu	p.P913L	ENST00000358026	NM_001128849.1	913	cCg/cTg	19/36	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.694950886112013	2		855	1070	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553024	106553024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	400	842	1	ENST00000369096.4:c.989C>T	p.Pro330Leu	p.P330L	ENST00000369096	NM_001198.3	330	cCa/cTa	5/7	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.694950886112013	2		843	1134	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524329	148524329	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	150	691	0	ENST00000320356.2:c.655C>T	p.Pro219Ser	p.P219S	ENST00000320356	NM_004456.4	219	Cct/Tct	7/20	0.694950886112013	3	FACETS	0.824	0.755	0.896	0.412	0.377	0.448	CLONAL	1	TRUE	1	0.694950886112013	3		691	706	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206935	162206935	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	178	408	0	ENST00000366898.1:c.740C>T	p.Pro247Leu	p.P247L	ENST00000366898	NM_004562.2	247	cCc/cTc	7/12	1	2	FACETS	0.97	0.901	1	0.97	0.901	1	CLONAL	1	TRUE	1	0.694950886112013	2		408	528	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374909	45374909	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	323	849	0	ENST00000262160.6:c.934T>G	p.Cys312Gly	p.C312G	ENST00000262160	NM_005901.5	312	Tgc/Ggc	8/11	1	2	FACETS	0.932	0.882	0.984	0.932	0.882	0.984	CLONAL	1	TRUE	1	0.694950886112013	2		849	997	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100418	8100418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	382	950	2	ENST00000346208.3:c.392C>T	p.Ser131Phe	p.S131F	ENST00000346208		131	tCc/tTc	3/6	1	2	FACETS	0.967	0.919	1	0.967	0.919	1	CLONAL	1	TRUE	1	0.694950886112013	2		952	1137	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015732	112015732	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	279	560	0	ENST00000368678.4:c.1111-1G>A		p.X371_splice	ENST00000368678		371			1	2	FACETS	0.977	0.921	1	0.977	0.921	1	CLONAL	1	TRUE	1	0.694950886112013	2		560	822	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001963	29001963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	310	765	0	ENST00000282397.4:c.1202G>A	p.Gly401Glu	p.G401E	ENST00000282397	NM_002019.4	401	gGg/gAg	9/30	0.694950886112013	3	FACETS	0.972	0.916	1	0.486	0.458	0.515	CLONAL	1	TRUE	1	0.694950886112013	3		765	1237	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644421	18644421	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs766467454	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	158	588	0	ENST00000266497.5:c.2599T>C	p.Phe867Leu	p.F867L	ENST00000266497		867	Ttc/Ctc	18/31	1	2	FACETS	0.802	0.739	0.867	0.802	0.739	0.867	CLONAL	1	TRUE	1	0.694950886112013	2		588	567	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202340	133202340	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	367	743	1	ENST00000320574.5:c.6548C>T	p.Pro2183Leu	p.P2183L	ENST00000320574	NM_006231.2	2183	cCt/cTt	47/49	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.694950886112013	2		744	963	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28908160	28908160	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	622	778	0	ENST00000282397.4:c.2593+2T>A		p.X865_splice	ENST00000282397	NM_002019.4	865			0.694950886112013	3	FACETS	0.961	0.928	0.994	0.961	0.928	0.994	CLONAL	2	TRUE	1	0.694950886112013	3		778	1255	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037868	49037868	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	114	592	0	ENST00000267163.4:c.2108T>C	p.Ile703Thr	p.I703T	ENST00000267163	NM_000321.2	703	aTt/aCt	21/27	0.694950886112013	3	FACETS	1	0.946	1	0.53	0.481	0.581	CLONAL	1	TRUE	1	0.694950886112013	3		592	417	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435460	110435461	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	313	788	6	ENST00000375856.3:c.2940_2941delinsTT	p.Leu981Phe	p.L981F	ENST00000375856	NM_003749.2	980	aaCCtc/aaTTtc	1/2	0.694950886112013	3	FACETS	0.891	0.839	0.944	0.445	0.419	0.472	CLONAL	1	TRUE	1	0.694950886112013	3		794	1363	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73995272	73995272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372836595	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	65	24	0	ENST00000318443.5:c.578C>T	p.Ser193Leu	p.S193L	ENST00000318443	NM_001024736.1	193	tCg/tTg	4/10	0.694950886112013	6	FACETS	0.941	0.861	1	0.941	0.861	1	CLONAL	5	TRUE	1	0.694950886112013	6		24	95	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639819	3639819	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	836	910	2	ENST00000294008.3:c.3820C>T	p.Gln1274Ter	p.Q1274*	ENST00000294008	NM_032444.2	1274	Caa/Taa	12/15	0.694950886112013	2	FACETS	0.996	0.973	1	0.996	0.973	1	CLONAL	2	TRUE	0	0.694950886112013	2		912	1208	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779331	3779331	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	370	688	0	ENST00000262367.5:c.5717C>T	p.Pro1906Leu	p.P1906L	ENST00000262367	NM_004380.2	1906	cCt/cTt	31/31	0.694950886112013	2	FACETS	1	0.978	1	0.524	0.498	0.55	CLONAL	1	TRUE	0	0.694950886112013	2		688	1017	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592305	29592305	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	134	592	1	ENST00000356175.3:c.4720C>T	p.Gln1574Ter	p.Q1574*	ENST00000356175	NM_000267.3	1574	Caa/Taa	35/57	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.694950886112013	2		593	375	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805888	46805888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745392080	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	253	611	1	ENST00000290295.7:c.68G>A	p.Gly23Glu	p.G23E	ENST00000290295	NM_006361.5	23	gGg/gAg	1/2	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.694950886112013	2		612	727	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59793370	59793370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779915262	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	142	772	0	ENST00000259008.2:c.2434C>T	p.Pro812Ser	p.P812S	ENST00000259008	NM_032043.2	812	Cct/Tct	17/20	1	2	FACETS	0.892	0.82	0.967	0.892	0.82	0.967	CLONAL	1	TRUE	1	0.694950886112013	2		772	458	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265165	5265165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	460	980	2	ENST00000357368.4:c.422C>T	p.Pro141Leu	p.P141L	ENST00000357368	NM_002850.3	141	cCa/cTa	5/38	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.694950886112013	2		982	1263	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220904	36220904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	190	348	0	ENST00000222270.7:c.4954G>A	p.Gly1652Ser	p.G1652S	ENST00000222270	NM_014727.1	1652	Ggc/Agc	23/37	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.694950886112013	2		348	528	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45864839	45864839	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	503	1127	0	ENST00000391945.4:c.1180T>G	p.Phe394Val	p.F394V	ENST00000391945	NM_000400.3	394	Ttc/Gtc	12/23	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.694950886112013	2		1127	1422	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086128	16086128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	313	692	1	ENST00000281043.3:c.1304C>T	p.Ala435Val	p.A435V	ENST00000281043	NM_005378.4	435	gCc/gTc	3/3	1	2	FACETS	0.929	0.878	0.98	0.929	0.878	0.98	CLONAL	1	TRUE	1	0.694950886112013	2		693	970	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519782	29519782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	354	856	0	ENST00000389048.3:c.1789G>A	p.Val597Met	p.V597M	ENST00000389048	NM_004304.4	597	Gtg/Atg	9/29	1	2	FACETS	0.894	0.847	0.941	0.894	0.847	0.941	CLONAL	1	TRUE	1	0.694950886112013	2		856	1140	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46603879	46603880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	348	741	0	ENST00000263734.3:c.1236_1237insA	p.Ser413IlefsTer72	p.S413Ifs*72	ENST00000263734	NM_001430.4	412	-/A	9/16	1	2	FACETS	0.979	0.929	1	0.979	0.929	1	CLONAL	1	TRUE	1	0.694950886112013	2		741	1023	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419849	41419849	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	242	537	0	ENST00000373198.4:c.472C>T	p.Pro158Ser	p.P158S	ENST00000373198	NM_133170.3	158	Cca/Tca	3/32	0.694950886112013	4	FACETS	0.876	0.817	0.938	0.292	0.272	0.313	CLONAL	1	TRUE	1	0.694950886112013	4		537	1347	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637013	176637013	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	652	809	0	ENST00000439151.2:c.1613T>A	p.Ile538Asn	p.I538N	ENST00000439151	NM_022455.4	538	aTc/aAc	5/23	0.648702362607867	4	FACETS	0.952	0.918	0.987	0.952	0.918	0.987	CLONAL	2	TRUE	2	0.694950886112013	4		809	1670	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046757	180046758	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	669	772	1	ENST00000261937.6:c.2554_2555delinsAA	p.Gly852Asn	p.G852N	ENST00000261937	NM_182925.4	852	GGc/AAc	18/30	0.648702362607867	4	FACETS	0.997	0.961	1	0.997	0.961	1	CLONAL	2	TRUE	2	0.694950886112013	4		773	1637	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508701	106508701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	636	706	0	ENST00000359195.3:c.695C>T	p.Thr232Ile	p.T232I	ENST00000359195	NM_002649.2	232	aCc/aTc	2/11	0.694950886112013	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.694950886112013	3		706	1227	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341129	8341129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	220	708	0	ENST00000356435.5:c.5087G>A	p.Gly1696Glu	p.G1696E	ENST00000356435		1696	gGa/gAa	30/35	1	2	FACETS	0.951	0.889	1	0.951	0.889	1	CLONAL	1	TRUE	1	0.694950886112013	2		708	666	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486154	8486154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	309	629	0	ENST00000356435.5:c.2663G>A	p.Gly888Glu	p.G888E	ENST00000356435		888	gGa/gAa	17/35	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.694950886112013	2		629	824	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518298	8518298	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868403321	NA	P-0021846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	200	460	0	ENST00000356435.5:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000356435		365	Gaa/Aaa	10/35	1	2	FACETS	0.951	0.887	1	0.951	0.887	1	CLONAL	1	TRUE	1	0.694950886112013	2		460	605	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727829	41727829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs545028002	NA	P-0021853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	215	874	5	ENST00000301178.4:c.454G>A	p.Ala152Thr	p.A152T	ENST00000301178	NM_021913.4	152	Gcc/Acc	4/20	1	2	FACETS	0.778	0.722	0.837	1	0.992	1	SUBCLONAL	2	TRUE	1	0.216219885628886	2		879	1278	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389318	8389318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	83	763	2	ENST00000356435.5:c.4300G>A	p.Glu1434Lys	p.E1434K	ENST00000356435		1434	Gaa/Aaa	26/35	0.216219885628886	1	FACETS	0.665	0.585	0.751	0.665	0.585	0.751	SUBCLONAL	1	TRUE	0	0.216219885628886	1		765	1030	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786197	3786198	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0021853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	64	634	0	ENST00000262367.5:c.4567_4568del	p.Phe1523GlnfsTer5	p.F1523Qfs*5	ENST00000262367	NM_004380.2	1523	TTc/c	28/31	1	2	FACETS	0.578	0.499	0.665	0.578	0.499	0.665	SUBCLONAL	1	TRUE	1	0.216219885628886	2		634	1024	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578249	7578250	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	172	740	0	ENST00000269305.4:c.599dup	p.Asn200LysfsTer9	p.N200Kfs*9	ENST00000269305	NM_001126112.2	200	aat/aaAt	6/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.216219885628886	2		740	1115	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55960974	55960976	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0021853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	63	545	0	ENST00000263923.4:c.2964_2966del	p.Glu990del	p.E990del	ENST00000263923	NM_002253.2	988	gaAGAg/gag	21/30	1	2	FACETS	0.686	0.591	0.788	0.686	0.591	0.788	SUBCLONAL	1	TRUE	1	0.216219885628886	2		545	850	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197453	106197453	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	54	352	0	ENST00000380013.4:c.5786A>T	p.Glu1929Val	p.E1929V	ENST00000380013	NM_001127208.2	1929	gAg/gTg	11/11	0.126318860061739	1	FACETS	0.769	0.657	0.893	0.769	0.657	0.893	INDETERMINATE	1	TRUE	0	0.216219885628886	1		352	579	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	148	681	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.953	1	1	0.993	1	CLONAL	3	FALSE	1	0.188785535403316	2		687	497	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149671	202149671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	99	594	1	ENST00000358485.4:c.1112G>A	p.Cys371Tyr	p.C371Y	ENST00000358485	NM_001080125.1	371	tGc/tAc	8/9	1	2	FACETS	0.95	0.856	1	1	0.99	1	CLONAL	3	FALSE	1	0.188785535403316	2		595	368	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366939	15366939	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	173	1005	9	ENST00000263377.2:c.1687del	p.Ser563AlafsTer21	p.S563Afs*21	ENST00000263377	NM_058243.2	563	Agc/gc	9/20	1	2	FACETS	1	0.975	1	1	0.994	1	CLONAL	3	FALSE	1	0.188785535403316	2		1014	545	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557540	21557540	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs554244935	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	174	730	2	ENST00000382592.4:c.2305C>T	p.Arg769Trp	p.R769W	ENST00000382592	NM_014572.2	769	Cgg/Tgg	5/8	1	2	FACETS	1	0.976	1	1	0.994	1	CLONAL	3	FALSE	1	0.188785535403316	2		732	546	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	32	229	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	1	0.914	1	1	0.967	1	CLONAL	2	FALSE	1	0.188785535403316	2		229	142	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	107	514	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.994	0.906	1	1	0.992	1	CLONAL	4	FALSE	1	0.188785535403316	2		514	285	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103755	47103756	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	107	533	3	ENST00000409792.3:c.6190_6191del	p.Asp2064ProfsTer8	p.D2064Pfs*8	ENST00000409792	NM_014159.6	2064	GAc/c	14/21	1	2	FACETS	1	0.966	1	1	0.989	1	CLONAL	2	FALSE	1	0.188785535403316	2		536	488	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	81	756	0	ENST00000397062.3:c.246A>T	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaT	2/5	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.188785535403316	2		756	650	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057924	27057924	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	182	735	1	ENST00000324856.7:c.1636del	p.Gln546ArgfsTer73	p.Q546Rfs*73	ENST00000324856	NM_006015.4	544	caC/ca	3/20	1	2	FACETS	1	0.963	1	1	0.994	1	CLONAL	3	FALSE	1	0.188785535403316	2		736	607	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821956	72821956	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	66	333	0	ENST00000268489.5:c.10219del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3407	Gct/ct	10/10	1	2	FACETS	0.873	0.766	0.986	1	0.984	1	CLONAL	3	FALSE	1	0.188785535403316	2		333	267	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	95	457	2	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.994	0.9	1	1	0.991	1	CLONAL	4	FALSE	1	0.188785535403316	2		459	253	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760024	133760024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	144	783	0	ENST00000318560.5:c.2352del	p.Arg785GlyfsTer3	p.R785Gfs*3	ENST00000318560	NM_005157.4	783	Ccc/cc	11/11	1	2	FACETS	1	0.966	1	1	0.993	1	CLONAL	3	FALSE	1	0.188785535403316	2		783	464	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409036	139409036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	199	955	0	ENST00000277541.6:c.2133del	p.Thr712ProfsTer60	p.T712Pfs*60	ENST00000277541	NM_017617.3	711	ccC/cc	13/34	1	2	FACETS	0.877	0.817	0.938	1	0.995	1	CLONAL	4	FALSE	1	0.188785535403316	2		955	601	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40460202	40460202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	143	550	0	ENST00000345506.4:c.1913G>A	p.Arg638His	p.R638H	ENST00000345506	NM_003152.3	638	cGc/cAc	17/20	1	2	FACETS	0.931	0.857	1	1	0.994	1	CLONAL	4	FALSE	1	0.188785535403316	2		550	407	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572076	95572076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772243498	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	99	686	2	ENST00000393063.1:c.3032C>T	p.Ala1011Val	p.A1011V	ENST00000393063	NM_030621.3	1011	gCg/gTg	20/28	1	2	FACETS	0.896	0.806	0.991	1	0.989	1	CLONAL	3	FALSE	1	0.188785535403316	2		688	390	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591246	67591246	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	96	500	0	ENST00000274335.5:c.1746-2A>G		p.X582_splice	ENST00000274335		582			1	2	FACETS	1	0.953	1	1	0.99	1	CLONAL	3	FALSE	1	0.188785535403316	2		500	309	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	127	637	5	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	1	0.97	1	1	0.993	1	CLONAL	3	FALSE	1	0.188785535403316	2		642	396	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863054	56863054	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1266824391	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	95	646	2	ENST00000519728.1:c.327del	p.Glu110LysfsTer15	p.E110Kfs*15	ENST00000519728	NM_002350.3	107	acA/ac	5/13	1	2	FACETS	0.937	0.842	1	1	0.989	1	CLONAL	3	FALSE	1	0.188785535403316	2		648	358	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782032	9782032	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	103	580	0	ENST00000377346.4:c.2059del		p.X687_splice	ENST00000377346	NM_005026.3	687			1	2	FACETS	0.978	0.888	1	1	0.991	1	CLONAL	4	FALSE	1	0.188785535403316	2		580	279	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054920	176054920	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759451215	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	89	495	0	ENST00000367669.3:c.1133G>A	p.Arg378His	p.R378H	ENST00000367669	NM_022457.5	378	cGt/cAt	10/20	1	2	FACETS	1	0.962	1	1	0.99	1	CLONAL	3	FALSE	1	0.188785535403316	2		495	273	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497567	125497567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs537858020	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	24	400	0	ENST00000428830.2:c.131G>A	p.Arg44His	p.R44H	ENST00000428830	NM_001114121.2	44	cGt/cAt	3/14	1	2	FACETS	1	0.83	1	1	0.83	1	CLONAL	1	FALSE	1	0.188785535403316	2		400	239	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231462	46231462	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	98	411	1	ENST00000334344.6:c.1306del	p.Ile436LeufsTer4	p.I436Lfs*4	ENST00000334344	NM_152641.2	434	acA/ac	10/21	1	2	FACETS	1	0.938	1	1	0.991	1	CLONAL	4	FALSE	1	0.188785535403316	2		412	249	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421833	49421833	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758494772	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	240	730	1	ENST00000301067.7:c.14474G>A	p.Arg4825Gln	p.R4825Q	ENST00000301067	NM_003482.3	4825	cGg/cAg	46/54	1	2	FACETS	0.925	0.869	0.983	1	0.996	1	CLONAL	4	FALSE	1	0.188785535403316	2		731	687	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110086	115110086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1314719430	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	256	890	1	ENST00000257566.3:c.1792G>A	p.Gly598Arg	p.G598R	ENST00000257566	NM_016569.3	598	Gga/Aga	8/8	1	2	FACETS	1	0.964	1	1	0.996	1	CLONAL	4	FALSE	1	0.188785535403316	2		891	658	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133897	41133898	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	79	427	0	ENST00000379561.5:c.1730dup	p.Tyr578LeufsTer24	p.Y578Lfs*24	ENST00000379561	NM_002015.3	577	ggc/ggGc	2/3	1	2	FACETS	1	0.94	1	1	0.988	1	CLONAL	3	FALSE	1	0.188785535403316	2		427	258	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103525620	103525620	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149859074	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	96	472	0	ENST00000355739.4:c.2891G>A	p.Arg964Gln	p.R964Q	ENST00000355739	NM_000123.3	964	cGg/cAg	14/15	1	2	FACETS	1	0.965	1	1	0.99	1	CLONAL	3	FALSE	1	0.188785535403316	2		472	294	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435979	110435979	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	182	789	4	ENST00000375856.3:c.2422C>A	p.Arg808Ser	p.R808S	ENST00000375856	NM_003749.2	808	Cgc/Agc	1/2	1	2	FACETS	0.878	0.816	0.942	1	0.995	1	CLONAL	4	FALSE	1	0.188785535403316	2		793	549	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991731	72991731	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	74	277	1	ENST00000268489.5:c.2314del	p.Ala772ArgfsTer52	p.A772Rfs*52	ENST00000268489	NM_006885.3	772	Gcg/cg	2/10	1	2	FACETS	0.985	0.879	1	1	0.988	1	CLONAL	4	FALSE	1	0.188785535403316	2		278	199	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696638	47696638	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	118	562	2	ENST00000347630.2:c.310T>A	p.Phe104Ile	p.F104I	ENST00000347630	NM_001007230.1	104	Ttc/Atc	5/11	1	2	FACETS	0.916	0.837	0.998	1	0.992	1	CLONAL	4	FALSE	1	0.188785535403316	2		564	341	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302611	15302611	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	235	811	0	ENST00000263388.2:c.747del	p.Thr250HisfsTer122	p.T250Hfs*122	ENST00000263388	NM_000435.2	249	ggG/gg	5/33	1	2	FACETS	1	0.944	1	1	0.996	1	CLONAL	4	FALSE	1	0.188785535403316	2		811	619	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210893	36210893	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	155	675	1	ENST00000222270.7:c.649del	p.Arg217GlyfsTer22	p.R217Gfs*22	ENST00000222270	NM_014727.1	215	aCc/ac	3/37	1	2	FACETS	1	0.967	1	1	0.994	1	CLONAL	3	FALSE	1	0.188785535403316	2		676	502	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160679	56160679	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	154	494	0	ENST00000399503.3:c.953T>C	p.Leu318Ser	p.L318S	ENST00000399503	NM_005921.1	318	tTa/tCa	4/20	1	2	FACETS	0.912	0.843	0.984	1	0.994	1	CLONAL	4	FALSE	1	0.188785535403316	2		494	447	SUCCESS
APC	324	MSKCC	GRCh37	5	112178937	112178937	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199558585	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	53	386	0	ENST00000257430.4:c.7646G>A	p.Arg2549His	p.R2549H	ENST00000257430	NM_000038.5	2549	cGt/cAt	16/16	1	2	FACETS	0.871	0.752	0.997	1	0.981	1	CLONAL	3	FALSE	1	0.188785535403316	2		386	215	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793614	89793615	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	53	401	0	ENST00000336032.3:c.688dup	p.Arg230LysfsTer3	p.R230Kfs*3	ENST00000336032	NM_006813.2	228	gca/gcAa	2/2	1	2	FACETS	0.927	0.801	1	1	0.981	1	CLONAL	3	FALSE	1	0.188785535403316	2		401	202	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372755	81372755	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	121	524	0	ENST00000222390.5:c.779G>A	p.Cys260Tyr	p.C260Y	ENST00000222390	NM_000601.4	260	tGc/tAc	7/18	1	2	FACETS	0.911	0.828	0.997	1	0.991	1	CLONAL	3	FALSE	1	0.188785535403316	2		524	469	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779144	135779144	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	165	538	0	ENST00000298552.3:c.2102A>C	p.Gln701Pro	p.Q701P	ENST00000298552	NM_001162426.1	701	cAg/cCg	17/23	1	2	FACETS	0.886	0.821	0.954	1	0.994	1	CLONAL	4	FALSE	1	0.188785535403316	2		538	493	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0021872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	63	440	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.225151152953758	2		440	387	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514528	125514528	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	32	480	0	ENST00000428830.2:c.1223G>T	p.Cys408Phe	p.C408F	ENST00000428830	NM_001114121.2	408	tGt/tTt	11/14	0.225151152953758	1	FACETS	0.717	0.582	0.868	0.717	0.582	0.868	SUBCLONAL	1	FALSE	0	0.225151152953758	1		480	352	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992835	72992835	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	86	621	0	ENST00000268489.5:c.1210G>C	p.Gly404Arg	p.G404R	ENST00000268489	NM_006885.3	404	Ggc/Cgc	2/10	1	2	FACETS	0.806	0.716	0.902	1	0.981	1	CLONAL	2	FALSE	1	0.225151152953758	2		621	474	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550487	29550487	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0021872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	79	479	0	ENST00000356175.3:c.1747A>T	p.Lys583Ter	p.K583*	ENST00000356175	NM_000267.3	583	Aag/Tag	16/57	1	2	FACETS	1	0.927	1	1	0.985	1	CLONAL	2	FALSE	1	0.225151152953758	2		479	331	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652876	29652876	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	73	396	0	ENST00000356175.3:c.4811del	p.Tyr1604SerfsTer5	p.Y1604Sfs*5	ENST00000356175	NM_000267.3	1604	tAc/tc	36/57	1	2	FACETS	1	0.885	1	1	0.983	1	CLONAL	2	FALSE	1	0.225151152953758	2		396	323	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120212	70120212	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	116	771	2	ENST00000245479.2:c.1214G>T	p.Ser405Ile	p.S405I	ENST00000245479	NM_000346.3	405	aGc/aTc	3/3	1	2	FACETS	0.937	0.847	1	1	0.988	1	CLONAL	2	FALSE	1	0.225151152953758	2		773	550	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313152	30313153	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0021872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	94	735	3	ENST00000262643.3:c.846_847delinsCT	p.Leu282_Asp283delinsPheTyr	p.L282_D283delinsFY	ENST00000262643	NM_001238.2	282	ttGGat/ttCTat	10/12	1	2	FACETS	0.792	0.707	0.882	1	0.982	1	SUBCLONAL	2	FALSE	1	0.225151152953758	2		738	527	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641211	12641211	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	100	655	1	ENST00000251849.4:c.1087G>A	p.Val363Ile	p.V363I	ENST00000251849	NM_002880.3	363	Gtt/Att	10/17	1	2	FACETS	0.836	0.75	0.928	1	0.984	1	CLONAL	2	FALSE	1	0.225151152953758	2		656	531	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446891	187446891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	49	908	1	ENST00000232014.4:c.1302C>A	p.Ser434Arg	p.S434R	ENST00000232014	NM_001130845.1	434	agC/agA	5/10	1	2	FACETS	0.757	0.641	0.885	0.757	0.641	0.885	SUBCLONAL	1	FALSE	1	0.225151152953758	2		909	575	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1952907	1952907	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	106	783	0	ENST00000382891.5:c.1990G>T	p.Ala664Ser	p.A664S	ENST00000382891	NM_133335.3	664	Gcc/Tcc	10/22	1	2	FACETS	0.904	0.813	0.999	1	0.987	1	CLONAL	2	FALSE	1	0.225151152953758	2		783	521	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497343	149497343	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	119	756	0	ENST00000261799.4:c.2975del	p.Leu992CysfsTer53	p.L992Cfs*53	ENST00000261799	NM_002609.3	992	tTg/tg	22/23	1	2	FACETS	0.931	0.843	1	1	0.988	1	CLONAL	2	FALSE	1	0.225151152953758	2		756	568	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27220063	27220063	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	115	726	0	ENST00000380036.4:c.3120C>A	p.Cys1040Ter	p.C1040*	ENST00000380036	NM_000459.3	1040	tgC/tgA	21/23	1	2	FACETS	0.937	0.848	1	1	0.988	1	CLONAL	2	FALSE	1	0.225151152953758	2		726	545	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940004	76940004	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	125	837	0	ENST00000373344.5:c.744del	p.Gly249ValfsTer8	p.G249Vfs*8	ENST00000373344	NM_000489.3	248	ctT/ct	9/35	1	2	FACETS	0.966	0.877	1	1	0.989	1	CLONAL	2	FALSE	1	0.225151152953758	2		837	575	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123040881	123040881	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	105	787	1	ENST00000355640.3:c.1344G>T	p.Lys448Asn	p.K448N	ENST00000355640		448	aaG/aaT	7/7	1	2	FACETS	0.865	0.778	0.957	1	0.986	1	CLONAL	2	FALSE	1	0.225151152953758	2		788	539	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591826	48591826	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	38	578	1	ENST00000342988.3:c.989A>T	p.Glu330Val	p.E330V	ENST00000342988	NM_005359.5	330	gAa/gTa	9/12	1	2	FACETS	0.214	0.176	0.256	0.214	0.176	0.256	SUBCLONAL	1	TRUE	1	0.491112320303417	2		579	724	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0021889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	26	692	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.867	0.689	1	0.867	0.689	1	CLONAL	1	TRUE	1	0.25	2		692	240	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928072	178928098	+	inframe_deletion	In_Frame_Del	DEL	TGGATTAGAAGATTTGCTGAACCCTAT	TGGATTAGAAGATTTGCTGAACCCTAT	-	novel	NA	P-0021889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	40	677	0	ENST00000263967.3:c.1353_1379del	p.Leu452_Gly460del	p.L452_G460del	ENST00000263967	NM_006218.2	450	caTGGATTAGAAGATTTGCTGAACCCTATt/cat	8/21	0.141977751005142	5	FACETS	0.961	0.805	1	0.64	0.537	0.754	INDETERMINATE	2	TRUE	2	0.25	5		677	229	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754320	57754320	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	42	540	0	ENST00000274289.3:c.531G>C	p.Leu177Phe	p.L177F	ENST00000274289	NM_006622.3	177	ttG/ttC	4/14	0.141977751005142	5	FACETS	0.856	0.719	1	0.57	0.479	0.67	INDETERMINATE	2	TRUE	2	0.25	5		540	270	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034909	42034932	+	inframe_deletion	In_Frame_Del	DEL	CTGAGCCAGTTCAGGTGTGCAGCC	CTGAGCCAGTTCAGGTGTGCAGCC	-	novel	NA	P-0021889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	11	665	0	ENST00000219905.7:c.4754_4777del	p.Glu1585_Pro1592del	p.E1585_P1592del	ENST00000219905	NM_001164273.1	1584	tCTGAGCCAGTTCAGGTGTGCAGCCct/tct	15/24	1	2	FACETS	0.456	0.315	0.631	0.456	0.315	0.631	SUBCLONAL	1	TRUE	1	0.25	2		665	193	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577560	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0021889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	43	805	0	ENST00000269305.4:c.721_722del	p.Ser241LeufsTer22	p.S241Lfs*22	ENST00000269305	NM_001126112.2	241	TCc/c	7/11	1	2	FACETS	0.896	0.759	1	1	0.969	1	CLONAL	2	TRUE	1	0.25	2		805	192	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275810	38275810	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	18	692	0	ENST00000425967.3:c.1459A>T	p.Met487Leu	p.M487L	ENST00000425967	NM_001174067.1	487	Atg/Ttg	11/19	0.206218813699507	1	FACETS	0.681	0.515	0.875	0.681	0.515	0.875	SUBCLONAL	1	TRUE	0	0.25	1		692	185	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122246	2122247	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTT	novel	NA	P-0021917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	295	511	0	ENST00000219476.3:c.2103_2104insTTT	p.Ser701_Asp702insPhe	p.S701_D702insF	ENST00000219476	NM_000548.3	701	tct/tcTTTt	20/42	0.70205910423069	1	FACETS	0.904	0.86	0.949	0.904	0.86	0.949	CLONAL	1	TRUE	0	0.70205910423069	1		511	603	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289526	33289526	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0021917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	467	762	0	ENST00000374542.5:c.177C>G	p.Tyr59Ter	p.Y59*	ENST00000374542	NM_001141970.1	59	taC/taG	2/8	0.70205910423069	1	FACETS	0.976	0.938	1	0.976	0.938	1	CLONAL	1	TRUE	0	0.70205910423069	1		762	885	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	204	970	0	ENST00000269305.4:c.838del	p.Arg280GlufsTer65	p.R280Efs*65	ENST00000269305	NM_001126112.2	280	Aga/ga	8/11	0.385674277416111	1	FACETS	0.897	0.833	0.964	0.897	0.833	0.964	CLONAL	1	TRUE	0	0.405849700264295	1		970	893	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051638	30051638	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	124	604	0	ENST00000338641.4:c.572G>A	p.Trp191Ter	p.W191*	ENST00000338641	NM_000268.3	191	tGg/tAg	6/16	0.385674277416111	1	FACETS	0.899	0.817	0.984	0.899	0.817	0.984	CLONAL	1	TRUE	0	0.405849700264295	1		604	542	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0021927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	212	844	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	0.295302641917916	4	FACETS	0.997	0.932	1			1	CLONAL	3	TRUE	NA	0.291979344686829	4		844	627	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003747	45003747	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs1057519877	NA	P-0021927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	148	699	0	ENST00000558401.1:c.3G>A	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	atG/atA	1/4	1	2	FACETS	0.975	0.912	1	1	0.994	1	CLONAL	4	TRUE	1	0.291979344686829	2		699	260	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131486	202131486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	83	600	0	ENST00000358485.4:c.454C>T	p.Pro152Ser	p.P152S	ENST00000358485	NM_001080125.1	152	Cca/Tca	2/9	0.247186145427178	3	FACETS	1	0.925	1	1	0.925	1	CLONAL	2	TRUE	1	0.291979344686829	3		600	311	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113109	209113109	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	82	356	2	ENST00000345146.2:c.398A>G	p.His133Arg	p.H133R	ENST00000345146	NM_005896.2	133	cAt/cGt	4/10	0.247186145427178	3	FACETS	0.898	0.804	0.994	1	0.976	1	CLONAL	3	TRUE	1	0.291979344686829	3		358	239	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056617	26056617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751385999	NA	P-0021927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	113	302	0	ENST00000343677.2:c.40C>T	p.Pro14Ser	p.P14S	ENST00000343677	NM_005319.3	14	Cct/Tct	1/1	0.291979344686829	10	FACETS	1	0.946	1			1	CLONAL	5	TRUE	NA	0.291979344686829	10		302	319	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	24	766	0				ENST00000310581	NM_198253.2	-/1132			0.3	3	FACETS	0.899	0.706	1	0.449	0.353	0.56	CLONAL	1	TRUE	1	0.21	3		766	281	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579356	7579356	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	117	1002	4	ENST00000269305.4:c.331C>A	p.Leu111Met	p.L111M	ENST00000269305	NM_001126112.2	111	Ctg/Atg	4/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.21	2		1006	889	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044595	47044595	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	199	612	1	ENST00000377604.3:c.2092G>T	p.Glu698Ter	p.E698*	ENST00000377604	NM_001204468.1	698	Gag/Tag	18/24	0.169164238254144	2	FACETS	0.996	0.928	1			1	CLONAL	3	TRUE	NA	0.21	2		613	634	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268411	142268411	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	34	662	0	ENST00000350721.4:c.3081G>C	p.Glu1027Asp	p.E1027D	ENST00000350721	NM_001184.3	1027	gaG/gaC	15/47	1	2	FACETS	0.554	0.451	0.669	0.554	0.451	0.669	SUBCLONAL	1	TRUE	1	0.21	2		662	585	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916834	48916834	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	88	649	0	ENST00000267163.4:c.368del	p.Asn123ThrfsTer2	p.N123Tfs*2	ENST00000267163	NM_000321.2	122	Aaa/aa	3/27	1	2	FACETS	0.8	0.71	0.895	1	0.981	1	SUBCLONAL	2	TRUE	1	0.21	2		649	524	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536190	41536190	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	133	850	0	ENST00000263253.7:c.1807A>G	p.Arg603Gly	p.R603G	ENST00000263253	NM_001429.3	603	Aga/Gga	9/31	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.21	2		850	866	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39237845	39237845	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0021937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	86	561	0	ENST00000402219.2:c.2391-1G>A		p.X797_splice	ENST00000402219	NM_005633.3	797			1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.220476652486499	2		561	753	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163405	47163405	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	125	463	0	ENST00000409792.3:c.2721del	p.Leu908TrpfsTer5	p.L908Wfs*5	ENST00000409792	NM_014159.6	907	gtT/gt	3/21	0.170376126010556	2	FACETS	0.954	0.867	1	0.954	0.867	1	CLONAL	2	TRUE	0	0.220476652486499	2		463	594	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0021970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	285	637	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.465452181630341	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	1	0.469604921185091	4		637	558	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115435	115115437	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	rs1319662056	NA	P-0021970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	100	536	0	ENST00000257566.3:c.889_891del	p.Asn297del	p.N297del	ENST00000257566	NM_016569.3	297	AAC/-	5/8	1	2	FACETS	0.819	0.734	0.908	0.819	0.734	0.908	CLONAL	1	TRUE	1	0.469604921185091	2		536	520	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112112	115112119	+	frameshift_variant	Frame_Shift_Del	DEL	AGGAGGGG	AGGAGGGG	-	novel	NA	P-0021970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	97	598	0	ENST00000257566.3:c.1621_1628del	p.Pro541GlyfsTer148	p.P541Gfs*148	ENST00000257566	NM_016569.3	541	CCCCTCCTg/g	7/8	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.469604921185091	2		598	402	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644926	67644926	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	110	512	0	ENST00000264010.4:c.192del	p.Glu64AspfsTer10	p.E64Dfs*10	ENST00000264010	NM_006565.3	64	gAa/ga	3/12	0.469604921185091	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.469604921185091	1		512	329	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528094	157528094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	140	425	0	ENST00000346085.5:c.5819C>T	p.Ser1940Leu	p.S1940L	ENST00000346085	NM_020732.3	1940	tCg/tTg	20/20	1	2	FACETS	0.977	0.895	1	0.977	0.895	1	CLONAL	1	TRUE	1	0.546998682654852	2		425	524	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685283	89685283	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1554897262	NA	P-0021983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	94	400	0	ENST00000371953.3:c.178A>T	p.Lys60Ter	p.K60*	ENST00000371953	NM_000314.4	60	Aag/Tag	3/9	0.546998682654852	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.546998682654852	1		400	229	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636334	21636334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	42	590	0	ENST00000421138.2:c.676C>A	p.Gln226Lys	p.Q226K	ENST00000421138		226	Cag/Aag	7/16	0.546998682654852	1	FACETS	0.368	0.309	0.434	0.368	0.309	0.434	SUBCLONAL	1	TRUE	0	0.546998682654852	1		590	303	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046701	42046701	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	165	581	1	ENST00000219905.7:c.7075T>A	p.Ser2359Thr	p.S2359T	ENST00000219905	NM_001164273.1	2359	Tca/Aca	18/24	0.546998682654852	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.546998682654852	1		582	425	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72863707	72863707	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1313136028	NA	P-0021983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	194	646	0	ENST00000268489.5:c.3500A>C	p.Glu1167Ala	p.E1167A	ENST00000268489	NM_006885.3	1167	gAg/gCg	5/10	1	2	FACETS	0.928	0.861	0.998	0.928	0.861	0.998	CLONAL	1	TRUE	1	0.546998682654852	2		646	764	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579359	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGAAA	novel	NA	P-0021983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	290	659	0	ENST00000269305.4:c.324_328dup	p.Arg110LeufsTer15	p.R110Lfs*15	ENST00000269305	NM_001126112.2	110	cgt/cTTTCCgt	4/11	0.546998682654852	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.546998682654852	1		659	680	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248569	10248569	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	145	670	0	ENST00000340748.4:c.4184G>T	p.Trp1395Leu	p.W1395L	ENST00000340748		1395	tGg/tTg	35/40	1	2	FACETS	0.702	0.641	0.766	0.702	0.641	0.766	SUBCLONAL	1	TRUE	1	0.546998682654852	2		670	755	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451758	29451758	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1340992656	NA	P-0021983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	148	611	0	ENST00000389048.3:c.2807G>T	p.Gly936Val	p.G936V	ENST00000389048	NM_004304.4	936	gGa/gTa	16/29	0.546998682654852	3	FACETS	0.761	0.694	0.83	0.38	0.347	0.415	SUBCLONAL	1	TRUE	1	0.546998682654852	3		611	906	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916661	178916661	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	64	367	0	ENST00000263967.3:c.48G>A	p.Met16Ile	p.M16I	ENST00000263967	NM_006218.2	16	atG/atA	2/21	0.479287275015173	4	FACETS	1	0.891	1			1	CLONAL	1	TRUE	NA	0.546998682654852	4		367	353	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163276	32163276	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	236	773	0	ENST00000375023.3:c.5950G>T	p.Asp1984Tyr	p.D1984Y	ENST00000375023	NM_004557.3	1984	Gac/Tac	30/30	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.546998682654852	2		773	851	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0021987-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	75	621	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.24	2		621	604	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729950	47729950	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1215061428	NA	P-0021987-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	37	705	1	ENST00000449228.1:c.439G>A	p.Gly147Arg	p.G147R	ENST00000449228	NM_001127240.2	147	Ggg/Agg	3/4	1	2	FACETS	0.612	0.504	0.733	0.612	0.504	0.733	SUBCLONAL	1	TRUE	1	0.24	2		706	504	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098729	47098730	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGTT	novel	NA	P-0021987-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	64	643	0	ENST00000409792.3:c.6541_6544dup	p.Pro2182GlnfsTer3	p.P2182Qfs*3	ENST00000409792	NM_014159.6	2182	cct/cAACCct	15/21	1	2	FACETS	0.968	0.839	1	0.968	0.839	1	CLONAL	1	TRUE	1	0.24	2		643	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0021993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	274	678	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.578996006382865	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.578996006382865	2		680	471	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913396	NA	P-0021993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	99	440	0	ENST00000349496.5:c.95A>C	p.Asp32Ala	p.D32A	ENST00000349496	NM_001904.3	32	gAc/gCc	3/15	0.578996006382865	2	FACETS	0.974	0.878	1	0.487	0.439	0.537	CLONAL	1	TRUE	0	0.578996006382865	2		440	351	SUCCESS
ATR	545	MSKCC	GRCh37	3	142212147	142212147	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1175958154	NA	P-0021993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	418	508	0	ENST00000350721.4:c.5905G>A	p.Val1969Ile	p.V1969I	ENST00000350721	NM_001184.3	1969	Gtt/Att	35/47	0.578996006382865	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	0	0.578996006382865	3		508	612	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675894	30675894	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	213	899	0	ENST00000376406.3:c.2462C>T	p.Ala821Val	p.A821V	ENST00000376406	NM_014641.2	821	gCa/gTa	8/15	0.578996006382865	3	FACETS	1	0.938	1	0.505	0.469	0.542	CLONAL	1	TRUE	1	0.578996006382865	3		899	940	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76931748	76931748	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	145	717	0	ENST00000373344.5:c.3782A>C	p.Asp1261Ala	p.D1261A	ENST00000373344	NM_000489.3	1261	gAt/gCt	10/35	0.257863134736236	3	FACETS	0.929	0.85	1	0.465	0.425	0.506	INDETERMINATE	1	TRUE	1	0.578996006382865	3		717	695	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0021994-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	102	763	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.257356463717505	3	FACETS	0.844	0.76	0.933	0.844	0.76	0.933	CLONAL	2	TRUE	1	0.324189432297133	3		764	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0021994-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	77	349	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	0.324189432297133	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.324189432297133	1		349	340	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857871	57857871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760866050	NA	P-0021994-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	49	376	0	ENST00000228682.2:c.190G>A	p.Glu64Lys	p.E64K	ENST00000228682	NM_005269.2	64	Gag/Aag	3/12	1	2	FACETS	0.725	0.615	0.845	0.725	0.615	0.845	SUBCLONAL	1	TRUE	1	0.324189432297133	2		376	417	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582795	95582795	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021994-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	54	192	0	ENST00000393063.1:c.1747G>A	p.Glu583Lys	p.E583K	ENST00000393063	NM_030621.3	583	Gaa/Aaa	11/28	0.257356463717505	3	FACETS	0.831	0.718	0.952	0.831	0.718	0.952	CLONAL	2	TRUE	1	0.324189432297133	3		192	233	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018218	48018218	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021994-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	57	428	0	ENST00000234420.5:c.413C>G	p.Pro138Arg	p.P138R	ENST00000234420	NM_000179.2	138	cCa/cGa	2/10	1	2	FACETS	0.747	0.642	0.861	0.747	0.642	0.861	SUBCLONAL	1	TRUE	1	0.324189432297133	2		428	471	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739389	145739389	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs775332504	NA	P-0021994-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	72	414	0	ENST00000428558.2:c.1981G>C	p.Glu661Gln	p.E661Q	ENST00000428558	NM_004260.3	661	Gag/Cag	12/22	1	2	FACETS	0.878	0.769	0.995	0.878	0.769	0.995	CLONAL	1	TRUE	1	0.324189432297133	2		414	506	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273029	55273029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770749711	NA	P-0022014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	229	957	0	ENST00000275493.2:c.3352G>A	p.Ala1118Thr	p.A1118T	ENST00000275493	NM_005228.3	1118	Gcg/Acg	28/28	0.681401235412227	4	FACETS	1	0.936	1	0.335	0.312	0.359	CLONAL	1	TRUE	1	0.694332509770595	4		957	1112	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763239	59763239	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs587782244	NA	P-0022014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	258	857	0	ENST00000259008.2:c.2863A>C	p.Asn955His	p.N955H	ENST00000259008	NM_032043.2	955	Aat/Cat	19/20	0.697580360150413	4	FACETS	1	0.981	1	0.562	0.526	0.599	CLONAL	1	TRUE	2	0.694332509770595	4		857	1121	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25990556	25990556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1293915045	NA	P-0022014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	248	855	0	ENST00000435504.4:c.671G>A	p.Ser224Asn	p.S224N	ENST00000435504		224	aGc/aAc	8/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.694332509770595	2		855	640	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390111	89390111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	141	549	0	ENST00000336596.2:c.860G>A	p.Cys287Tyr	p.C287Y	ENST00000336596	NM_005233.5	287	tGt/tAt	4/17	0.176950920147736	5	FACETS	0.779	0.714	0.847			1	INDETERMINATE	2	TRUE	NA	0.694332509770595	5		549	532	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31483703	31483703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	118	499	0	ENST00000344624.3:c.2029C>T	p.Pro677Ser	p.P677S	ENST00000344624		677	Cca/Tca	13/33	0.533603423435388	4	FACETS	1	0.931	1	0.345	0.312	0.379	CLONAL	1	TRUE	1	0.694332509770595	4		499	557	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183764	10183764	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs5030804	NA	P-0022018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	309	573	0	ENST00000256474.2:c.233A>G	p.Asn78Ser	p.N78S	ENST00000256474	NM_000551.3	78	aAt/aGt	1/3	0.657407409863516	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.657407409863516	1		573	629	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383774	15383774	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	423	743	2	ENST00000263377.2:c.137del	p.Pro46ArgfsTer47	p.P46Rfs*47	ENST00000263377	NM_058243.2	46	cCg/cg	2/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.657407409863516	2		745	1234	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436625	52436628	+	frameshift_variant	Frame_Shift_Del	DEL	AGCC	AGCC	-	novel	NA	P-0022018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	311	856	0	ENST00000460680.1:c.2046_2049del	p.Ala683ArgfsTer8	p.A683Rfs*8	ENST00000460680	NM_004656.3	682	ctGGCT/ct	16/17	0.657407409863516	1	FACETS	0.938	0.892	0.985	0.938	0.892	0.985	CLONAL	1	TRUE	0	0.657407409863516	1		856	677	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678745	52678745	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0022018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	292	776	0	ENST00000394830.3:c.874del	p.Met292TrpfsTer8	p.M292Wfs*8	ENST00000394830	NM_018313.4	292	Atg/tg	9/30	0.657407409863516	1	FACETS	0.994	0.944	1	0.994	0.944	1	CLONAL	1	TRUE	0	0.657407409863516	1		776	600	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187956	32187956	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	390	846	2	ENST00000375023.3:c.1265C>T	p.Pro422Leu	p.P422L	ENST00000375023	NM_004557.3	422	cCt/cTt	7/30	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.657407409863516	2		848	1145	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207588	29207589	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	279	487	0	ENST00000240100.2:c.207dup	p.Asn70Ter	p.N70*	ENST00000240100	NM_001394.6	69	-/T	1/4	1	2	FACETS	0.979	0.922	1	0.979	0.922	1	CLONAL	1	TRUE	1	0.657407409863516	2		487	867	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0022021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	146	637	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.570549433468369	3	FACETS	0.918	0.84	1	0.459	0.42	0.5	CLONAL	1	TRUE	1	0.569950558619297	3		637	717	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	129	466	0	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	0.570549433468369	3	FACETS	1	0.953	1	0.536	0.488	0.586	CLONAL	1	TRUE	1	0.569950558619297	3		466	543	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0022021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	188	692	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.569950558619297	2		692	640	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061205	38061205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	136	450	0	ENST00000250448.2:c.784C>T	p.Arg262Cys	p.R262C	ENST00000250448	NM_004496.3	262	Cgc/Tgc	2/2	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.569950558619297	2		450	432	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035132	37035132	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs2020872	NA	P-0022021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	98	370	0	ENST00000231790.2:c.94A>G	p.Ile32Val	p.I32V	ENST00000231790	NM_000249.3	32	Atc/Gtc	1/19	1	2	FACETS	0.839	0.753	0.928	0.839	0.753	0.928	CLONAL	1	TRUE	1	0.569950558619297	2		370	410	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657375	29657375	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs878853904	NA	P-0022021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	368	690	0	ENST00000356175.3:c.5608C>T	p.Gln1870Ter	p.Q1870*	ENST00000356175	NM_000267.3	1870	Cag/Tag	38/57	0.569950558619297	2	FACETS	0.904	0.865	0.943	0.904	0.865	0.943	CLONAL	2	TRUE	0	0.569950558619297	2		690	714	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231771	36231774	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TTCG	TTCG	-	novel	NA	P-0022021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	223	642	1	ENST00000300305.3:c.610_613del	p.Arg204AspfsTer6	p.R204Dfs*6	ENST00000300305		204	CGAAga/ga	5/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.569950558619297	2		643	733	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936103	178936103	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	163	661	0	ENST00000263967.3:c.1645G>C	p.Asp549His	p.D549H	ENST00000263967	NM_006218.2	549	Gat/Cat	10/21	0.570549433468369	3	FACETS	0.884	0.812	0.96	0.442	0.406	0.48	CLONAL	1	TRUE	1	0.569950558619297	3		661	831	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160531	56160558	+	splice_region_variant,intron_variant	Splice_Region	DEL	ACGTACCTAATAAAAAAAAATGTTGTGA	ACGTACCTAATAAAAAAAAATGTTGTGA	G	novel	NA	P-0022021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	66	179	0	ENST00000399503.3:c.835-30_835-3delinsG		p.X279_splice	ENST00000399503	NM_005921.1	279			1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.569950558619297	2		179	217	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0022024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	350	732	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.397591517517197	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.422794156474754	1		732	1050	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0022024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	158	667	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.914	0.838	0.993	0.914	0.838	0.993	CLONAL	1	TRUE	1	0.422794156474754	2		667	818	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575102	48575102	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	78	556	2	ENST00000342988.3:c.296G>A	p.Trp99Ter	p.W99*	ENST00000342988	NM_005359.5	99	tGg/tAg	3/12	0.397591517517197	1	FACETS	0.651	0.574	0.733	0.651	0.574	0.733	SUBCLONAL	1	TRUE	0	0.422794156474754	1		558	447	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533150	533465	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGCTCAGGGCAGCTCTCCCCAAGGACCTCCGCCTTCCCCGGAGCTGTGTCGGCCCAGGACTGCAGGGCGTGAGCCCAGACCCCGGCCCTCGCCTCCCTCACTGCCCTGCCGTCCCGGGAGACTTACAGCGCGAGGGGCCGCTGGGTCACATGGGTCCCGGGGGGTCCCAGAGGGTCCCGGAGCTGGAGCTAGAGCCAGAGCGGCTGCCCTGTGTCAAGGGAGAGGGTCAGTGAGTGCTGCTCCCTGGCTGGGGCGGGGCGGGGCGGGTCCCTGGCTAGCTGTGGGGTGGAGAGCTGCCTCACCTGCCGGGTCTTG	TGGCTCAGGGCAGCTCTCCCCAAGGACCTCCGCCTTCCCCGGAGCTGTGTCGGCCCAGGACTGCAGGGCGTGAGCCCAGACCCCGGCCCTCGCCTCCCTCACTGCCCTGCCGTCCCGGGAGACTTACAGCGCGAGGGGCCGCTGGGTCACATGGGTCCCGGGGGGTCCCAGAGGGTCCCGGAGCTGGAGCTAGAGCCAGAGCGGCTGCCCTGTGTCAAGGGAGAGGGTCAGTGAGTGCTGCTCCCTGGCTGGGGCGGGGCGGGGCGGGTCCCTGGCTAGCTGTGGGGTGGAGAGCTGCCTCACCTGCCGGGTCTTG	-	novel	NA	P-0022034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	187	107	0	ENST00000451590.1:c.438_450+303del		p.X146_splice	ENST00000451590	NM_001130442.1	146		4/5	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		107	245	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073358	8073358	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	193	537	0	ENST00000377482.5:c.1301C>T	p.Ser434Leu	p.S434L	ENST00000377482	NM_018948.3	434	tCa/tTa	4/4	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.88	2		537	422	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137826	64137826	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	291	816	0	ENST00000334205.4:c.1927G>A	p.Val643Ile	p.V643I	ENST00000334205	NM_003942.2	643	Gta/Ata	15/17	1	2	FACETS	0.832	0.786	0.878	0.832	0.786	0.878	CLONAL	1	TRUE	1	0.88	2		816	795	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81574753	81574753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	108	380	0	ENST00000298171.2:c.649G>A	p.Asp217Asn	p.D217N	ENST00000298171	NM_000369.2	217	Gac/Aac	8/10	1	2	FACETS	0.937	0.856	1	0.937	0.856	1	CLONAL	1	TRUE	1	0.88	2		380	262	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292841	91292841	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	114	492	0	ENST00000355112.3:c.343C>G	p.Pro115Ala	p.P115A	ENST00000355112	NM_000057.2	115	Ccg/Gcg	3/22	1	2	FACETS	0.887	0.811	0.965	0.887	0.811	0.965	CLONAL	1	TRUE	1	0.88	2		492	292	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721015	176721015	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	28	482	0	ENST00000439151.2:c.6646G>T	p.Gly2216Trp	p.G2216W	ENST00000439151	NM_022455.4	2216	Ggg/Tgg	23/23	1	2	FACETS	0.119	0.095	0.147	0.119	0.095	0.147	SUBCLONAL	1	TRUE	1	0.88	2		482	534	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033181	69033181	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	114	537	1	ENST00000288368.4:c.3621G>T	p.Lys1207Asn	p.K1207N	ENST00000288368	NM_024870.2	1207	aaG/aaT	30/40	1	2	FACETS	0.912	0.835	0.991	0.912	0.835	0.991	CLONAL	1	TRUE	1	0.88	2		538	284	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578393	7578393	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876660821	NA	P-0022050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	56	666	0	ENST00000269305.4:c.537T>G	p.His179Gln	p.H179Q	ENST00000269305	NM_001126112.2	179	caT/caG	5/11	1	2	FACETS	0.817	0.698	0.948	0.817	0.698	0.948	CLONAL	1	TRUE	1	0.15	2		666	914	SUCCESS
APC	324	MSKCC	GRCh37	5	112173377	112173377	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	32	463	1	ENST00000257430.4:c.2086G>T	p.Glu696Ter	p.E696*	ENST00000257430	NM_000038.5	696	Gaa/Taa	16/16	1	2	FACETS	0.715	0.579	0.869	0.715	0.579	0.869	SUBCLONAL	1	TRUE	1	0.15	2		464	597	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117909	70117911	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0022050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	41	523	0	ENST00000245479.2:c.378_380del	p.Gln126_Tyr127delinsHis	p.Q126_Y127delinsH	ENST00000245479	NM_000346.3	126	cAGTac/cac	1/3	1	2	FACETS	0.797	0.662	0.947	0.797	0.662	0.947	CLONAL	1	TRUE	1	0.15	2		523	686	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	57	685	0	ENST00000269305.4:c.569del	p.Pro190LeufsTer57	p.P190Lfs*57	ENST00000269305	NM_001126112.2	190	cCt/ct	6/11	0.323983216998197	3	FACETS	0.988	0.861	1	0.988	0.861	1	CLONAL	2	TRUE	1	0.345135636299289	3		685	196	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31369165	31369165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	20	581	0	ENST00000328111.2:c.149G>A	p.Arg50Lys	p.R50K	ENST00000328111	NM_006892.3	50	aGa/aAa	3/23	0.196537235849154	3	FACETS	0.465	0.356	0.593	0.233	0.178	0.297	INDETERMINATE	1	TRUE	1	0.345135636299289	3		581	292	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964448	70964448	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	31	646	1	ENST00000276594.2:c.1580C>A	p.Ala527Glu	p.A527E	ENST00000276594	NM_024504.3	527	gCa/gAa	8/8	0.181593271096337	5	FACETS	0.96	0.779	1	0.32	0.259	0.388	INDETERMINATE	1	TRUE	2	0.345135636299289	5		647	284	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817388	39817388	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	13	598	1	ENST00000288319.7:c.175C>T	p.Gln59Ter	p.Q59*	ENST00000288319	NM_182918.3	59	Caa/Taa	2/10	0.275808629350083	1	FACETS	0.392	0.28	0.527	0.392	0.28	0.527	SUBCLONAL	1	TRUE	0	0.345135636299289	1		599	159	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913136	44913136	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	344	445	3	ENST00000377967.4:c.811C>T	p.Gln271Ter	p.Q271*	ENST00000377967	NM_021140.2	271	Cag/Tag	10/29	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.638716240940681	1		448	548	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0022074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	194	411	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.638716240940681	2		411	583	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371782	55371782	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	179	342	1	ENST00000297316.4:c.472G>A	p.Gly158Ser	p.G158S	ENST00000297316	NM_022454.3	158	Ggc/Agc	2/2	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.638716240940681	2		343	435	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	443432	443432	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	241	624	0	ENST00000399788.2:c.1465A>G	p.Ser489Gly	p.S489G	ENST00000399788	NM_001042603.1	489	Agt/Ggt	11/28	1	2	FACETS	0.969	0.908	1	0.969	0.908	1	CLONAL	1	TRUE	1	0.638716240940681	2		624	779	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871757	12871757	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0022074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	116	303	0	ENST00000228872.4:c.476-2A>C		p.X159_splice	ENST00000228872	NM_004064.3	159			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.638716240940681	2		303	325	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593488	48593488	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs730881954	NA	P-0022074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	203	507	0	ENST00000342988.3:c.1239C>A	p.Tyr413Ter	p.Y413*	ENST00000342988	NM_005359.5	413	taC/taA	10/12	0.638716240940681	1	FACETS	0.99	0.93	1	0.99	0.93	1	CLONAL	1	TRUE	0	0.638716240940681	1		507	437	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012423	152012494	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTAGTAAAAATGAAATGTAAGTCAGAGAAGGAGAAAAGTAGCTTTATTCAACTGCTTTAAGCGATAACTAT	ACTAGTAAAAATGAAATGTAAGTCAGAGAAGGAGAAAAGTAGCTTTATTCAACTGCTTTAAGCGATAACTAT	-	novel	NA	P-0022074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	121	351	0	ENST00000262189.6:c.390-71_390del		p.X130_splice	ENST00000262189	NM_170606.2	130		4/59	1	2	FACETS	0.813	0.739	0.89	0.813	0.739	0.89	CLONAL	1	TRUE	1	0.638716240940681	2		351	466	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624275	89624275	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204910	NA	P-0022093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	173	404	0	ENST00000371953.3:c.49C>T	p.Gln17Ter	p.Q17*	ENST00000371953	NM_000314.4	17	Caa/Taa	1/9	0.481528025950553	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.481528025950553	2		404	326	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932133	36932133	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	45	446	0	ENST00000361632.4:c.2336G>A	p.Gly779Asp	p.G779D	ENST00000361632		779	gGc/gAc	16/16	0.259294276531614	1	FACETS	0.424	0.357	0.496	0.424	0.357	0.496	INDETERMINATE	1	TRUE	0	0.481528025950553	1		446	335	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204620	108204620	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	21	291	1	ENST00000278616.4:c.7937del	p.Asn2646IlefsTer14	p.N2646Ifs*14	ENST00000278616	NM_000051.3	2645	atA/at	54/63	0.259294276531614	1	FACETS	0.32	0.247	0.404	0.32	0.247	0.404	INDETERMINATE	1	TRUE	0	0.481528025950553	1		292	207	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164164	47164189	+	frameshift_variant	Frame_Shift_Del	DEL	AGAGTCTAATTCCTTAATACTATCAT	AGAGTCTAATTCCTTAATACTATCAT	-	novel	NA	P-0022093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	83	364	0	ENST00000409792.3:c.1937_1962del	p.His646LeufsTer3	p.H646Lfs*3	ENST00000409792	NM_014159.6	646	cATGATAGTATTAAGGAATTAGACTCT/c	3/21	0.481528025950553	2	FACETS	0.841	0.758	0.926	0.841	0.758	0.926	CLONAL	2	TRUE	0	0.481528025950553	2		364	205	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595879	52595879	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0022093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	280	639	1	ENST00000394830.3:c.4036A>T	p.Lys1346Ter	p.K1346*	ENST00000394830	NM_018313.4	1346	Aag/Tag	26/30	0.481528025950553	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.481528025950553	2		640	574	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540586	187540597	+	inframe_deletion	In_Frame_Del	DEL	TCATTGAGGTCG	TCATTGAGGTCG	-	novel	NA	P-0022093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	83	325	0	ENST00000441802.2:c.7143_7154del	p.Asp2382_Asp2385del	p.D2382_D2385del	ENST00000441802	NM_005245.3	2381	acCGACCTCAATGAt/act	10/27	0.259294276531614	1	FACETS	0.761	0.677	0.849	0.761	0.677	0.849	INDETERMINATE	1	TRUE	0	0.481528025950553	1		325	344	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117639382	117639382	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	41	530	1	ENST00000368508.3:c.5974A>C	p.Ile1992Leu	p.I1992L	ENST00000368508	NM_002944.2	1992	Att/Ctt	37/43	0.217448817339687	0	FACETS	0.299	0.25	0.353			1	INDETERMINATE	1	TRUE	0	0.481528025950553	0		531	295	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246331	53246332	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCA	novel	NA	P-0022093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	219	282	0	ENST00000375401.3:c.647_650dup	p.Gln217HisfsTer4	p.Q217Hfs*4	ENST00000375401	NM_004187.3	217	cag/caTGCAg	5/26	0.429715348261459	2	FACETS	1	0.99	1			1	CLONAL	2	TRUE	NA	0.481528025950553	2		282	377	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	244	460	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.387970546057046	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.387970546057046	3		460	650	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061250	38061250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1459219194	NA	P-0022115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	132	756	0	ENST00000250448.2:c.739C>T	p.His247Tyr	p.H247Y	ENST00000250448	NM_004496.3	247	Cac/Tac	2/2	0.300122979820522	3	FACETS	1	0.937	1	0.519	0.472	0.57	CLONAL	1	TRUE	1	0.387970546057046	3		756	782	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662954	52662954	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	138	540	1	ENST00000394830.3:c.1399T>A	p.Ser467Thr	p.S467T	ENST00000394830	NM_018313.4	467	Tca/Aca	13/30	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.387970546057046	2		541	604	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177872	56177873	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0022115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	97	415	0	ENST00000399503.3:c.2846_2847del	p.Thr949ArgfsTer54	p.T949Rfs*54	ENST00000399503	NM_005921.1	949	ACa/a	14/20	0.300122979820522	3	FACETS	1	0.931	1	0.527	0.471	0.587	CLONAL	1	TRUE	1	0.387970546057046	3		415	566	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189432	56189433	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTAGAAC	novel	NA	P-0022115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	202	636	0	ENST00000399503.3:c.4467_4473dup	p.Gln1492ArgfsTer33	p.Q1492Rfs*33	ENST00000399503	NM_005921.1	1488	-/TTAGAAC	20/20	0.300122979820522	3	FACETS	1	0.991	1	0.743	0.69	0.798	CLONAL	1	TRUE	1	0.387970546057046	3		636	837	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0022125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	112	100	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	0.906590203586786	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.91234678265641	3		100	168	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346363	73346363	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	247	492	0	ENST00000377767.4:c.1437C>G	p.Asp479Glu	p.D479E	ENST00000377767	NM_014953.3	479	gaC/gaG	10/21	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.91234678265641	2		492	527	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916927	178916939	+	protein_altering_variant	In_Frame_Del	DEL	TAGGCAACCGTGA	TAGGCAACCGTGA	G	novel	NA	P-0022125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	127	501	0	ENST00000263967.3:c.314_326delinsG	p.Val105_Glu109delinsGly	p.V105_E109delinsG	ENST00000263967	NM_006218.2	105	gTAGGCAACCGTGAa/gGa	2/21	1	2	FACETS	0.504	0.459	0.552	0.504	0.459	0.552	SUBCLONAL	1	TRUE	1	0.91234678265641	2		501	552	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559126	29559126	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0022131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	105	268	1	ENST00000356175.3:c.3233C>G	p.Ser1078Ter	p.S1078*	ENST00000356175	NM_000267.3	1078	tCa/tGa	25/57	0.618406254103942	2	FACETS	0.923	0.852	0.992	0.923	0.852	0.992	CLONAL	2	TRUE	0	0.618406254103942	2		269	184	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164522	47164522	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs756943490	NA	P-0022131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	54	492	0	ENST00000409792.3:c.1604A>G	p.Asn535Ser	p.N535S	ENST00000409792	NM_014159.6	535	aAt/aGt	3/21	0.566992883517241	4	FACETS	0.812	0.697	0.937	0.271	0.232	0.313	CLONAL	1	TRUE	1	0.618406254103942	4		492	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577523	7577524	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	250	904	0	ENST00000269305.4:c.757dup	p.Thr253AsnfsTer11	p.T253Nfs*11	ENST00000269305	NM_001126112.2	253	acc/aAcc	7/11	0.618406254103942	2	FACETS	0.951	0.905	0.997	0.951	0.905	0.997	CLONAL	2	TRUE	0	0.618406254103942	2		904	425	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280628	41280628	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	107	693	0	ENST00000349496.5:c.2141C>A	p.Pro714His	p.P714H	ENST00000349496	NM_001904.3	714	cCt/cAt	15/15	0.566992883517241	4	FACETS	1	0.908	1	0.336	0.302	0.372	CLONAL	1	TRUE	1	0.618406254103942	4		693	555	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0022138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1237	160	994	1	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	1	2	FACETS	0.695	0.635	0.758	0.695	0.635	0.758	SUBCLONAL	1	TRUE	1	0.329618734461034	2		995	1397	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346338	73346338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	42	707	0	ENST00000377767.4:c.1462G>A	p.Asp488Asn	p.D488N	ENST00000377767	NM_014953.3	488	Gat/Aat	10/21	1	2	FACETS	0.586	0.489	0.693	0.586	0.489	0.693	SUBCLONAL	1	TRUE	1	0.329618734461034	2		707	435	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591937	48591937	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	67	632	0	ENST00000342988.3:c.1100T>C	p.Leu367Pro	p.L367P	ENST00000342988	NM_005359.5	367	cTc/cCc	9/12	0.26632920860716	1	FACETS	0.713	0.621	0.812	0.713	0.621	0.812	SUBCLONAL	1	TRUE	0	0.329618734461034	1		632	476	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0022141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	119	801	0	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	0.427326795281054	3	FACETS	1	0.905	1	0.5	0.452	0.55	CLONAL	1	TRUE	1	0.484466931359732	3		801	610	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	240	539	1	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	0.446935279830941	3	FACETS	0.991	0.941	1	0.991	0.941	1	CLONAL	3	TRUE	0	0.484466931359732	3		540	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691039	NA	P-0022141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	293	948	4	ENST00000269305.4:c.919+1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			NA	2	FACETS	1	0.974	1			1	INDETERMINATE	2	TRUE	NA	0.484466931359732	2		952	583	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793340	242793340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201540918	NA	P-0022141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	72	1262	1	ENST00000334409.5:c.737C>T	p.Thr246Met	p.T246M	ENST00000334409	NM_005018.2	246	aCg/aTg	5/5	0.485027459058798	3	FACETS	0.469	0.409	0.534	0.234	0.204	0.267	SUBCLONAL	1	TRUE	1	0.484466931359732	3		1263	788	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188085	151188085	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867628277	NA	P-0022141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	315	700	3	ENST00000262187.5:c.68C>T	p.Thr23Met	p.T23M	ENST00000262187	NM_005614.3	23	aCg/aTg	2/8	0.485027459058798	4	FACETS	0.922	0.876	0.968	0.922	0.876	0.968	CLONAL	3	TRUE	1	0.484466931359732	4		703	698	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176118212	176118212	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0022141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	31	522	0	ENST00000367669.3:c.763-2A>G		p.X255_splice	ENST00000367669	NM_022457.5	255			0.485027459058798	4	FACETS	0.446	0.36	0.543	0.223	0.18	0.272	SUBCLONAL	1	TRUE	2	0.484466931359732	4		522	426	SUCCESS
APC	324	MSKCC	GRCh37	5	112174469	112174470	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	65	402	0	ENST00000257430.4:c.3179dup	p.Gln1062ThrfsTer3	p.Q1062Tfs*3	ENST00000257430	NM_000038.5	1060	ata/aTta	16/16	0.446935279830941	3	FACETS	1	0.891	1	0.341	0.297	0.387	CLONAL	1	TRUE	0	0.484466931359732	3		402	326	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279378	38279378	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	46	1094	0	ENST00000425967.3:c.1111A>G	p.Thr371Ala	p.T371A	ENST00000425967	NM_001174067.1	371	Acg/Gcg	9/19	0.485027459058798	4	FACETS	0.313	0.262	0.369	0.156	0.131	0.185	SUBCLONAL	1	TRUE	2	0.484466931359732	4		1094	902	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0022155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	50	840	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.195146213518366	1	FACETS	0.769	0.652	0.898	0.769	0.652	0.898	SUBCLONAL	1	TRUE	0	0.200918254041812	1		840	582	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0022155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	60	659	0	ENST00000269305.4:c.782+1G>C		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.200918254041812	2		659	477	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0022158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	517	798	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.807568622587133	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.807568622587133	1		799	668	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928226	178928226	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519872	NA	P-0022158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	339	466	2	ENST00000263967.3:c.1412C>T	p.Pro471Leu	p.P471L	ENST00000263967	NM_006218.2	471	cCa/cTa	9/21	0.779028384806805	3	FACETS	0.985	0.959	1	0.985	0.959	1	CLONAL	3	TRUE	0	0.807568622587133	3		468	399	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954222	48954222	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0022158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	66	429	0	ENST00000267163.4:c.1421+2T>C		p.X474_splice	ENST00000267163	NM_000321.2	474			0.807568622587133	1	FACETS	0.492	0.435	0.552	0.492	0.435	0.552	SUBCLONAL	1	TRUE	0	0.807568622587133	1		429	198	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114760	73114760	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	41	169	1	ENST00000356692.5:c.1141G>A	p.Glu381Lys	p.E381K	ENST00000356692		381	Gaa/Aaa	9/9	0.786936497433877	2	FACETS	0.986	0.847	1	0.493	0.423	0.565	CLONAL	1	TRUE	0	0.807568622587133	2		170	103	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952085	+	missense_variant	Missense_Mutation	DNP	CA	CA	TG	novel	NA	P-0022158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	313	441	1	ENST00000263967.3:c.3139_3140inv	p.His1047Cys	p.H1047C	ENST00000263967	NM_006218.2	1047	CAt/TGt	21/21	0.779028384806805	3	FACETS	0.955	0.926	0.981	0.955	0.926	0.981	CLONAL	3	TRUE	0	0.807568622587133	3		442	380	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177807	56177807	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0022158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	145	370	1	ENST00000399503.3:c.2782del	p.Ser928LeufsTer9	p.S928Lfs*9	ENST00000399503	NM_005921.1	927	aTt/at	14/20	0.171506550605145	6	FACETS	1	0.979	1	0.785	0.724	0.847	INDETERMINATE	2	TRUE	3	0.807568622587133	6		371	399	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189392	56189393	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0022158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	318	673	0	ENST00000399503.3:c.4426_4427del	p.His1476PhefsTer46	p.H1476Ffs*46	ENST00000399503	NM_005921.1	1475	tCA/t	20/20	0.171506550605145	6	FACETS	0.847	0.803	0.891	0.847	0.803	0.891	INDETERMINATE	3	TRUE	3	0.807568622587133	6		673	811	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523169	176523169	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	434	686	3	ENST00000292408.4:c.1933A>G	p.Lys645Glu	p.K645E	ENST00000292408	NM_213647.1	645	Aaa/Gaa	14/18	0.66200063467412	3	FACETS	0.787	0.754	0.821			1	SUBCLONAL	2	TRUE	NA	0.807568622587133	3		689	958	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0022168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	126	547	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.420912984682223	2		547	571	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0022168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	337	525	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.420912984682223	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	1	0.420912984682223	4		525	721	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11168338	11168338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	241	445	0	ENST00000361445.4:c.7534G>A	p.Asp2512Asn	p.D2512N	ENST00000361445	NM_004958.3	2512	Gac/Aac	57/58	0.420912984682223	3	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.420912984682223	3		445	579	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114135	115114135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	145	597	2	ENST00000257566.3:c.1082G>A	p.Gly361Glu	p.G361E	ENST00000257566	NM_016569.3	361	gGg/gAg	6/8	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.420912984682223	2		599	657	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525068	9525068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	155	586	0	ENST00000353224.5:c.1817C>T	p.Thr606Ile	p.T606I	ENST00000353224	NM_177990.2	606	aCt/aTt	8/10	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.420912984682223	2		586	692	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0022171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	171	763	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.30966263636756	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.30966263636756	3		764	527	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0022171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	217	915	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.30966263636756	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.30966263636756	2		915	581	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593520	48593520	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	48	316	0	ENST00000342988.3:c.1271A>T	p.Asp424Val	p.D424V	ENST00000342988	NM_005359.5	424	gAt/gTt	10/12	0.150733108552741	1	FACETS	0.856	0.728	0.996	0.856	0.728	0.996	INDETERMINATE	1	TRUE	0	0.30966263636756	1		316	306	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1959713	1959713	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs548600548	NA	P-0022171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	82	395	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	0.30966263636756	2		395	365	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359091	81359091	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	34	386	0	ENST00000222390.5:c.870C>A	p.Asp290Glu	p.D290E	ENST00000222390	NM_000601.4	290	gaC/gaA	8/18	0.303909565588135	4	FACETS	0.765	0.626	0.921	0.382	0.313	0.461	CLONAL	1	TRUE	2	0.30966263636756	4		386	376	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0022174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	91	840	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		840	829	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0022174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	65	637	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.98	0.849	1	0.98	0.849	1	CLONAL	1	TRUE	1	0.18	2		637	737	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0022174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	82	838	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	1	2	FACETS	0.831	0.73	0.939	0.831	0.73	0.939	CLONAL	1	TRUE	1	0.18	2		838	1097	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023066	27023067	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0022174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	11	121	0	ENST00000324856.7:c.172_173del	p.Ser58ArgfsTer52	p.S58Rfs*52	ENST00000324856	NM_006015.4	58	AGc/c	1/20	1	2	FACETS	0.596	0.412	0.825	0.596	0.412	0.825	SUBCLONAL	1	TRUE	1	0.18	2		121	205	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101427	27101427	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	71	613	0	ENST00000324856.7:c.4709C>G	p.Ser1570Cys	p.S1570C	ENST00000324856	NM_006015.4	1570	tCt/tGt	18/20	1	2	FACETS	0.981	0.855	1	0.981	0.855	1	CLONAL	1	TRUE	1	0.18	2		613	804	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098795	47098795	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	111	803	1	ENST00000409792.3:c.6479del	p.Pro2160ArgfsTer88	p.P2160Rfs*88	ENST00000409792	NM_014159.6	2160	cCg/cg	15/21	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.18	2		804	1206	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324681	31324681	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs137854653	NA	P-0022174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	60	436	0	ENST00000412585.2:c.127G>T	p.Glu43Ter	p.E43*	ENST00000412585	NM_005514.6	43	Gag/Tag	2/8	NA	2	FACETS	0.956	0.823	1			1	INDETERMINATE	1	TRUE	NA	0.18	2		436	697	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004331	150004331	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	78	567	0	ENST00000253339.5:c.1894C>T	p.Gln632Ter	p.Q632*	ENST00000253339		632	Caa/Taa	3/7	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.18	2		567	724	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522422	157522422	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	77	797	0	ENST00000346085.5:c.4694A>T	p.Asn1565Ile	p.N1565I	ENST00000346085	NM_020732.3	1565	aAc/aTc	18/20	1	2	FACETS	0.819	0.717	0.93	0.819	0.717	0.93	CLONAL	1	TRUE	1	0.18	2		797	1044	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835937	151835937	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	64	653	0	ENST00000262189.6:c.14587G>A	p.Glu4863Lys	p.E4863K	ENST00000262189	NM_170606.2	4863	Gag/Aag	58/59	1	2	FACETS	0.882	0.763	1	0.882	0.763	1	CLONAL	1	TRUE	1	0.18	2		653	806	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846224	151846224	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0022174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	65	530	0	ENST00000262189.6:c.12788C>G	p.Ser4263Ter	p.S4263*	ENST00000262189	NM_170606.2	4263	tCa/tGa	52/59	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.18	2		530	713	SUCCESS
AR	367	MSKCC	GRCh37	X	66766134	66766135	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCCCAC	novel	NA	P-0022174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	61	629	0	ENST00000374690.3:c.1147_1152dup	p.Pro383_His384dup	p.P383_H384dup	ENST00000374690	NM_000044.3	383	-/CCCCAC	1/8	1	2	FACETS	0.725	0.623	0.836	0.725	0.623	0.836	SUBCLONAL	1	TRUE	1	0.18	2		629	935	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10267112	10267114	+	inframe_deletion	In_Frame_Del	DEL	AAA	AAA	-	novel	NA	P-0022181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	58	887	0	ENST00000340748.4:c.1304_1306del	p.Phe435del	p.F435del	ENST00000340748		435	tTTTct/tct	17/40	1	2	FACETS	0.35	0.3	0.405	0.35	0.3	0.405	SUBCLONAL	1	TRUE	1	0.455795312705346	2		887	727	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374963	149374963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	191	1215	1	ENST00000360632.3:c.131G>A	p.Arg44Gln	p.R44Q	ENST00000360632	NM_015472.4	44	cGg/cAg	2/7	1	2	FACETS	0.988	0.915	1	0.988	0.915	1	CLONAL	1	TRUE	1	0.455795312705346	2		1216	848	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430553	78430554	+	splice_donor_variant	Splice_Site	DEL	AC	AC	T	novel	NA	P-0022181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	90	565	0	ENST00000370768.2:c.735+1_735+2delinsA		p.X245_splice	ENST00000370768	NM_003902.3	245			1	2	FACETS	0.735	0.654	0.822	0.735	0.654	0.822	SUBCLONAL	1	TRUE	1	0.455795312705346	2		565	537	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164611	36164611	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	260	564	0	ENST00000300305.3:c.1264G>A	p.Glu422Lys	p.E422K	ENST00000300305		422	Gag/Aag	8/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.654987034494115	2		564	741	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801796	3801796	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	232	555	0	ENST00000262367.5:c.3710G>A	p.Cys1237Tyr	p.C1237Y	ENST00000262367	NM_004380.2	1237	tGt/tAt	20/31	1	2	FACETS	0.94	0.879	1	0.94	0.879	1	CLONAL	1	TRUE	1	0.654987034494115	2		555	754	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519130	103519130	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	112	528	0	ENST00000355739.4:c.2468G>C	p.Arg823Thr	p.R823T	ENST00000355739	NM_000123.3	823	aGa/aCa	11/15	0.158108917646602	4	FACETS	1	0.943	1	0.265	0.239	0.293	INDETERMINATE	1	TRUE	0	0.654987034494115	4		528	533	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442612	52442612	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553646045	NA	P-0022242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	108	311	0	ENST00000460680.1:c.133G>A	p.Gly45Arg	p.G45R	ENST00000460680	NM_004656.3	45	Gga/Aga	4/17	0.654987034494115	1	FACETS	0.804	0.733	0.876	0.804	0.733	0.876	CLONAL	1	TRUE	0	0.654987034494115	1		311	276	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436828	110436828	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	103	815	0	ENST00000375856.3:c.1573G>C	p.Ala525Pro	p.A525P	ENST00000375856	NM_003749.2	525	Gcg/Ccg	1/2	0.504400588486507	4	FACETS	0.802	0.718	0.89	0.401	0.359	0.445	CLONAL	1	FALSE	2	0.639216270255308	4		815	659	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149511631	149511631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375122221	NA	P-0022249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	183	630	0	ENST00000261799.4:c.1154G>A	p.Arg385His	p.R385H	ENST00000261799	NM_002609.3	385	cGc/cAc	8/23	0.639216270255308	3	FACETS	0.933	0.872	0.994	0.933	0.872	0.994	CLONAL	2	FALSE	1	0.639216270255308	3		630	405	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0022255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	15	474	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	0.522	0.38	0.695	0.522	0.38	0.695	SUBCLONAL	1	TRUE	1	0.11	2		474	522	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0022255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	14	323	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.619	0.446	0.831	0.619	0.446	0.831	SUBCLONAL	1	TRUE	1	0.11	2		323	411	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696644	47696644	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519964	NA	P-0022255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	28	498	0	ENST00000347630.2:c.304T>G	p.Phe102Val	p.F102V	ENST00000347630	NM_001007230.1	102	Ttc/Gtc	5/11	1	2	FACETS	0.989	0.789	1	0.989	0.789	1	CLONAL	1	TRUE	1	0.11	2		498	515	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76931731	76931731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	40	206	0	ENST00000373344.5:c.3799C>T	p.Pro1267Ser	p.P1267S	ENST00000373344	NM_000489.3	1267	Cct/Tct	10/35	1	1	FACETS	1	0.838	1	1	0.975	1	CLONAL	3	TRUE	0	0.11	1		206	229	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749923	162749923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022259-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	326	440	0	ENST00000367921.3:c.2455A>G	p.Ile819Val	p.I819V	ENST00000367921	NM_006182.2	819	Att/Gtt	18/18	1	2	FACETS	0.95	0.903	0.997	0.95	0.903	0.997	CLONAL	1	TRUE	1	0.922504070810389	2		440	744	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920394	134920394	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022259-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	392	444	0	ENST00000398015.3:c.2209G>C	p.Glu737Gln	p.E737Q	ENST00000398015	NM_004441.4	737	Gag/Cag	12/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.922504070810389	2		444	838	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561327	9561327	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1369133982	NA	P-0022289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	19	584	0	ENST00000353224.5:c.455A>G	p.Tyr152Cys	p.Y152C	ENST00000353224	NM_177990.2	152	tAt/tGt	4/10	0.291632380489564	1	FACETS	0.288	0.218	0.37	0.288	0.218	0.37	SUBCLONAL	1	TRUE	0	0.323495037517099	1		584	342	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437818	52437818	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0022289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	88	796	1	ENST00000460680.1:c.1343T>A	p.Leu448Ter	p.L448*	ENST00000460680	NM_004656.3	448	tTg/tAg	13/17	0.323495037517099	1	FACETS	0.925	0.823	1	0.925	0.823	1	CLONAL	1	TRUE	0	0.323495037517099	1		797	493	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0022303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	113	586	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.183936159043738	3	FACETS	1	0.981	1	0.699	0.631	0.771	INDETERMINATE	1	TRUE	1	0.31601577523117	3		586	592	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640758	3640758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	110	601	0	ENST00000294008.3:c.2881C>T	p.Pro961Ser	p.P961S	ENST00000294008	NM_032444.2	961	Cct/Tct	12/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.31601577523117	2		601	530	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493607	56493660	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CACCTATCGATATAGAGAGAGAGTGGGCCTGGAATAGCCCCTGGGCCAGAGCCC	CACCTATCGATATAGAGAGAGAGTGGGCCTGGAATAGCCCCTGGGCCAGAGCCC	-	novel	NA	P-0022310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	70	304	0	ENST00000267101.3:c.2938-13_2978del		p.X980_splice	ENST00000267101	NM_001982.3	980		25/28	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		304	305	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0022313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	196	825	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.229320601516013	2	FACETS	0.907	0.843	0.973	0.907	0.843	0.973	CLONAL	2	TRUE	0	0.320573721563403	2		825	674	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199365	11199365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587777895	NA	P-0022313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	66	495	1	ENST00000361445.4:c.5126G>A	p.Arg1709His	p.R1709H	ENST00000361445	NM_004958.3	1709	cGc/cAc	36/58	0.246235168290164	2	FACETS	0.947	0.824	1	0.473	0.412	0.539	CLONAL	1	TRUE	0	0.320573721563403	2		496	435	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711958	89711958	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	73	526	0	ENST00000371953.3:c.576del	p.Leu193CysfsTer6	p.L193Cfs*6	ENST00000371953	NM_000314.4	192	gcA/gc	6/9	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.320573721563403	2		526	419	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115801	8115801	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	120	649	0	ENST00000346208.3:c.1147G>C	p.Glu383Gln	p.E383Q	ENST00000346208		383	Gag/Cag	6/6	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.320573721563403	2		649	672	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342776	118342776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781978595	NA	P-0022313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	27	293	0	ENST00000534358.1:c.902G>A	p.Arg301Gln	p.R301Q	ENST00000534358	NM_005933.3	301	cGa/cAa	3/36	0.320573721563403	4	FACETS	0.737	0.587	0.907	0.246	0.195	0.303	CLONAL	1	TRUE	1	0.320573721563403	4		293	302	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915155	32915155	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	26	657	1	ENST00000380152.3:c.6663C>G	p.Asn2221Lys	p.N2221K	ENST00000380152		2221	aaC/aaG	11/27	1	2	FACETS	0.429	0.34	0.532	0.429	0.34	0.532	SUBCLONAL	1	TRUE	1	0.320573721563403	2		658	378	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827756	72827756	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	36	563	0	ENST00000268489.5:c.8825A>G	p.Asp2942Gly	p.D2942G	ENST00000268489	NM_006885.3	2942	gAt/gGt	9/10	1	2	FACETS	0.506	0.416	0.607	0.506	0.416	0.607	SUBCLONAL	1	TRUE	1	0.320573721563403	2		563	444	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989672	15989682	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGTGGCCT	GGCGGTGGCCT	-	novel	NA	P-0022313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	83	393	0	ENST00000268712.3:c.3091_3101del	p.Arg1031ProfsTer36	p.R1031Pfs*36	ENST00000268712	NM_006311.3	1031	AGGCCACCGCCc/c	23/46	0.229320601516013	2	FACETS	0.759	0.676	0.847	0.759	0.676	0.847	SUBCLONAL	2	TRUE	0	0.320573721563403	2		393	341	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754828	29754828	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	77	505	0	ENST00000389048.3:c.1107C>A	p.Asn369Lys	p.N369K	ENST00000389048	NM_004304.4	369	aaC/aaA	4/29	0.320573721563403	3	FACETS	1	0.929	1	0.54	0.475	0.61	CLONAL	1	TRUE	1	0.320573721563403	3		505	516	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715845	61715846	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0022313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	97	606	0	ENST00000401558.2:c.2083_2084del	p.Asn695CysfsTer24	p.N695Cfs*24	ENST00000401558	NM_003400.3	695	AAt/t	18/25	0.320573721563403	3	FACETS	1	0.972	1	0.636	0.568	0.707	CLONAL	1	TRUE	1	0.320573721563403	3		606	552	SUCCESS
APC	324	MSKCC	GRCh37	5	112170737	112170741	+	frameshift_variant	Frame_Shift_Del	DEL	TGCAC	TGCAC	-	rs1554083160	NA	P-0022313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	59	653	0	ENST00000257430.4:c.1834_1838del	p.Ala612CysfsTer20	p.A612Cfs*20	ENST00000257430	NM_000038.5	611	ggTGCACtt/ggtt	15/16	1	2	FACETS	0.754	0.65	0.868	0.754	0.65	0.868	SUBCLONAL	1	TRUE	1	0.320573721563403	2		653	488	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146975	38146976	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0022313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	85	977	0	ENST00000317025.8:c.3166_3167del	p.Glu1056LysfsTer2	p.E1056Kfs*2	ENST00000317025	NM_023034.1	1056	GAa/a	18/24	0.320573721563403	1	FACETS	0.808	0.716	0.907	0.808	0.716	0.907	CLONAL	1	TRUE	0	0.320573721563403	1		977	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0022323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	359	1096	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	NA	2	FACETS	0.936	0.897	0.974			1	INDETERMINATE	2	TRUE	NA	0.619722507814811	2		1097	619	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0022323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	240	699	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.460942266391967	4	FACETS	0.858	0.805	0.913			1	CLONAL	2	TRUE	NA	0.619722507814811	4		699	731	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21639506	21639506	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	99	420	2	ENST00000421138.2:c.408del	p.Ile137PhefsTer4	p.I137Ffs*4	ENST00000421138		136	gtC/gt	6/16	0.619722824473504	3	FACETS	1	0.959	1	0.564	0.508	0.623	CLONAL	1	TRUE	1	0.619722507814811	3		422	371	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274136	18274136	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	52	837	1	ENST00000222254.8:c.1354C>T	p.Gln452Ter	p.Q452*	ENST00000222254	NM_005027.3	452	Cag/Tag	11/16	0.619722824473504	3	FACETS	0.254	0.215	0.297	0.127	0.107	0.149	SUBCLONAL	1	TRUE	1	0.619722507814811	3		838	866	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096078	178096078	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	241	538	0	ENST00000397062.3:c.1253A>C	p.His418Pro	p.H418P	ENST00000397062	NM_006164.4	418	cAt/cCt	5/5	0.514199573554902	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.619722507814811	4		538	544	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40789991	40789991	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0022323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	334	595	0	ENST00000373198.4:c.2739+1G>T		p.X913_splice	ENST00000373198	NM_133170.3	913			0.619722507814811	6	FACETS	1	0.951	1	1	0.951	1	CLONAL	3	TRUE	3	0.619722507814811	6		595	804	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977884	131977884	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786203127	NA	P-0022323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	36	474	1	ENST00000265335.6:c.3767G>A	p.Arg1256His	p.R1256H	ENST00000265335		1256	cGc/cAc	25/25	0.514199573554902	4	FACETS	0.344	0.282	0.414	0.172	0.141	0.207	SUBCLONAL	1	TRUE	2	0.619722507814811	4		475	547	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727455	66727455	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs869025608	NA	P-0022336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	199	755	0	ENST00000307102.5:c.171G>T	p.Lys57Asn	p.K57N	ENST00000307102	NM_002755.3	57	aaG/aaT	2/11	0.419853021568519	2	FACETS	0.812	0.759	0.867	0.812	0.759	0.867	CLONAL	2	TRUE	0	0.463156054472694	2		755	529	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978868	13978868	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	224	506	0	ENST00000405192.2:c.239C>A	p.Ala80Asp	p.A80D	ENST00000405192	NM_001163147.1	80	gCt/gAt	6/12	0.411737242682775	5	FACETS	0.89	0.834	0.947	0.89	0.834	0.947	CLONAL	3	TRUE	2	0.463156054472694	5		506	614	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325081	123325081	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs765682593	NA	P-0022336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	134	845	0	ENST00000358487.5:c.247A>G	p.Asn83Asp	p.N83D	ENST00000358487	NM_000141.4	83	Aat/Gat	3/18	0.463156054472694	3	FACETS	0.967	0.88	1	0.483	0.44	0.53	CLONAL	1	TRUE	1	0.463156054472694	3		845	737	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660594	227660594	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	252	760	0	ENST00000305123.5:c.2861G>T	p.Trp954Leu	p.W954L	ENST00000305123	NM_005544.2	954	tGg/tTg	1/2	0.463156054472694	4	FACETS	1	0.982	1			1	CLONAL	2	TRUE	NA	0.463156054472694	4		760	715	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056388	26056388	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1399375725	NA	P-0022336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	339	508	0	ENST00000343677.2:c.269A>C	p.Lys90Thr	p.K90T	ENST00000343677	NM_005319.3	90	aAg/aCg	1/1	0.463156054472694	4	FACETS	0.941	0.902	0.98	0.941	0.902	0.98	CLONAL	4	TRUE	0	0.463156054472694	4		508	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0022343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	140	907	3	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.366032225770785	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.366032225770785	1		910	601	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937067	48937067	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	49	363	0	ENST00000267163.4:c.837del	p.Glu280AsnfsTer6	p.E280Nfs*6	ENST00000267163	NM_000321.2	279	Aaa/aa	8/27	0.87440907022979	1	FACETS	0.876	0.79	0.956	0.876	0.79	0.956	CLONAL	1	TRUE	0	0.87440907022979	1		363	72	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678491	88678491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	152	573	1	ENST00000360948.2:c.1045C>T	p.His349Tyr	p.H349Y	ENST00000360948	NM_001012338.2	349	Cat/Tat	9/19	1	2	FACETS	0.968	0.898	1	0.968	0.898	1	CLONAL	1	TRUE	1	0.87440907022979	2		574	359	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248998	55248999	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCCAGCG	rs727504263	NA	P-0022353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	25	540	0	ENST00000275493.2:c.2300_2308dup	p.Ala767_Val769dup	p.A767_V769dup	ENST00000275493	NM_005228.3	767	atg/aTGGCCAGCGtg	20/28	1	2	FACETS	0.706	0.555	0.88	0.706	0.555	0.88	SUBCLONAL	1	TRUE	1	0.15	2		540	472	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214862	36214862	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	36	999	1	ENST00000222270.7:c.3288G>T	p.Glu1096Asp	p.E1096D	ENST00000222270	NM_014727.1	1096	gaG/gaT	8/37	0.119963709374287	0	FACETS	0.628	0.515	0.755			1	SUBCLONAL	1	TRUE	0	0.15	0		1000	650	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915952	127915952	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs865855853	NA	P-0022376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	205	713	0	ENST00000373547.4:c.529C>T	p.Arg177Ter	p.R177*	ENST00000373547	NM_002721.4	177	Cga/Tga	6/7	1	2	FACETS	0.89	0.829	0.951	0.89	0.829	0.951	CLONAL	1	TRUE	1	0.706932330146928	2		713	652	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2107104	2107104	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0022376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	59	930	0	ENST00000219476.3:c.775-2A>G		p.X259_splice	ENST00000219476	NM_000548.3	259			0.706932330146928	1	FACETS	0.186	0.16	0.215	0.186	0.16	0.215	SUBCLONAL	1	TRUE	0	0.706932330146928	1		930	579	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578541	7578542	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	753	1078	0	ENST00000269305.4:c.388_389insA	p.Leu130HisfsTer19	p.L130Hfs*19	ENST00000269305	NM_001126112.2	130	ctc/cAtc	5/11	0.639328033923359	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.706932330146928	2		1078	1064	SUCCESS
APC	324	MSKCC	GRCh37	5	112111356	112111357	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0022376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	111	389	0	ENST00000257430.4:c.454_455del	p.Glu152LysfsTer15	p.E152Kfs*15	ENST00000257430	NM_000038.5	151	gaAGaa/gaaa	5/16	0.706932330146928	1	FACETS	0.898	0.826	0.97	0.898	0.826	0.97	CLONAL	1	TRUE	0	0.706932330146928	1		389	226	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133751	2133752	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	A	novel	NA	P-0022376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	252	968	1	ENST00000219476.3:c.3939_3940delinsA	p.Pro1315GlnfsTer10	p.P1315Qfs*10	ENST00000219476	NM_000548.3	1313	gaGCcc/gaAcc	33/42	0.706932330146928	1	FACETS	0.749	0.707	0.793	0.749	0.707	0.793	SUBCLONAL	1	TRUE	0	0.706932330146928	1		969	615	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397675	139397675	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs886043624	NA	P-0022410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	199	934	0	ENST00000277541.6:c.5126T>C	p.Leu1709Pro	p.L1709P	ENST00000277541	NM_017617.3	1709	cTg/cCg	27/34	0.294978451171776	3	FACETS	0.973	0.905	1	0.486	0.452	0.521	INDETERMINATE	1	TRUE	1	0.87	3		934	675	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949104	71949104	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	224	873	0	ENST00000298229.2:c.3571G>C	p.Gly1191Arg	p.G1191R	ENST00000298229	NM_001567.3	1191	Ggg/Cgg	27/28	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.87	NA		873	500	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94910989	94910989	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	124	1016	1	ENST00000536441.1:c.1141A>T	p.Met381Leu	p.M381L	ENST00000536441	NM_144665.3	381	Atg/Ttg	8/10	1	2	FACETS	0.429	0.389	0.472	0.429	0.389	0.472	SUBCLONAL	1	TRUE	1	0.87	2		1017	664	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052721	42052722	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	97	776	1	ENST00000219905.7:c.7393dup	p.Thr2465AsnfsTer6	p.T2465Nfs*6	ENST00000219905	NM_001164273.1	2464	-/A	20/24	1	2	FACETS	0.411	0.368	0.458	0.411	0.368	0.458	SUBCLONAL	1	TRUE	1	0.87	2		777	542	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788588	3788588	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	72	637	1	ENST00000262367.5:c.4366G>T	p.Gly1456Ter	p.G1456*	ENST00000262367	NM_004380.2	1456	Gga/Tga	26/31	1	2	FACETS	0.44	0.387	0.497	0.44	0.387	0.497	SUBCLONAL	1	TRUE	1	0.87	2		638	376	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3827649	3827649	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	57	688	0	ENST00000262367.5:c.2123del	p.Leu708ArgfsTer5	p.L708Rfs*5	ENST00000262367	NM_004380.2	708	cTg/cg	11/31	1	2	FACETS	0.315	0.271	0.363	0.315	0.271	0.363	SUBCLONAL	1	TRUE	1	0.87	2		688	416	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843384	3843385	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	A	novel	NA	P-0022410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	66	432	0	ENST00000262367.5:c.1216+2dup		p.X406_splice	ENST00000262367	NM_004380.2	406			1	2	FACETS	0.446	0.39	0.507	0.446	0.39	0.507	SUBCLONAL	1	TRUE	1	0.87	2		432	340	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499822	8499822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758558790	NA	P-0022410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	222	670	1	ENST00000356435.5:c.2147G>A	p.Arg716His	p.R716H	ENST00000356435		716	cGc/cAc	14/35	0.3	5	FACETS	0.758	0.708	0.81	0.379	0.354	0.405	INDETERMINATE	2	TRUE	1	0.87	5		671	776	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390880	139390881	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	TCTCCACTCAGGAA	novel	NA	P-0022410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	231	1151	0	ENST00000277541.6:c.7297_7310dup	p.Glu2437AspfsTer3	p.E2437Dfs*3	ENST00000277541	NM_017617.3	2437	gag/gaTTCCTGAGTGGAGAg	34/34	0.294978451171776	3	FACETS	1	0.977	1	0.546	0.511	0.581	INDETERMINATE	1	TRUE	1	0.87	3		1151	698	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395191	139395191	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	134	1321	0	ENST00000277541.6:c.5747A>G	p.Gln1916Arg	p.Q1916R	ENST00000277541	NM_017617.3	1916	cAg/cGg	31/34	0.294978451171776	3	FACETS	0.555	0.505	0.609	0.278	0.252	0.305	INDETERMINATE	1	TRUE	1	0.87	3		1321	796	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399359	139399360	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0022410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	76	1169	0	ENST00000277541.6:c.4782_4783dup	p.Glu1595GlyfsTer22	p.E1595Gfs*22	ENST00000277541	NM_017617.3	1595	gag/gGGag	26/34	0.294978451171776	3	FACETS	0.341	0.299	0.387	0.171	0.149	0.194	INDETERMINATE	1	TRUE	1	0.87	3		1169	735	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44733216	44733216	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0022410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	112	817	1	ENST00000377967.4:c.208A>T	p.Lys70Ter	p.K70*	ENST00000377967	NM_021140.2	70	Aag/Tag	2/29	1	2	FACETS	0.481	0.434	0.53	0.481	0.434	0.53	SUBCLONAL	1	TRUE	1	0.87	2		818	535	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0022424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	231	771	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.448547494101657	3	FACETS	1	0.993	1	0.748	0.701	0.796	CLONAL	1	TRUE	1	0.571235128760884	3		771	695	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572926	7572929	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	GTCA	GTCA	-	novel	NA	P-0022424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	600	241	2	ENST00000269305.4:c.1180_*1del		p.*394*	ENST00000269305	NM_001126112.2	394		11/11	0.571235128760884	2	FACETS	0.875	0.853	0.896	1	0.997	1	CLONAL	3	TRUE	0	0.571235128760884	2		243	800	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55130059	55130059	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	243	724	0	ENST00000257290.5:c.593T>G	p.Phe198Cys	p.F198C	ENST00000257290	NM_006206.4	198	tTc/tGc	4/23	0.571235128760884	4	FACETS	1	0.993	1			1	CLONAL	1	TRUE	NA	0.571235128760884	4		724	895	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	95	676	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.865	0.778	0.955	0.865	0.778	0.955	CLONAL	1	TRUE	1	0.671920745607869	2		676	327	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	202	505	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.942	0.878	1	0.942	0.878	1	CLONAL	1	TRUE	1	0.671920745607869	2		506	638	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163297	32163297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1239036035	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	326	1013	0	ENST00000375023.3:c.5929G>A	p.Glu1977Lys	p.E1977K	ENST00000375023	NM_004557.3	1977	Gag/Aag	30/30	1	2	FACETS	0.869	0.822	0.918	0.869	0.822	0.918	CLONAL	1	TRUE	1	0.671920745607869	2		1013	1116	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	167	711	4	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	0.785	0.724	0.848	0.785	0.724	0.848	SUBCLONAL	1	TRUE	1	0.671920745607869	2		715	633	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249510	153249510	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1157879635	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	149	780	0	ENST00000281708.4:c.1268G>T	p.Gly423Val	p.G423V	ENST00000281708	NM_033632.3	423	gGa/gTa	9/12	1	2	FACETS	0.757	0.694	0.821	0.757	0.694	0.821	SUBCLONAL	1	TRUE	1	0.671920745607869	2		780	586	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750924	128750924	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	229	712	0	ENST00000377970.2:c.461C>T	p.Ser154Leu	p.S154L	ENST00000377970	NM_002467.4	154	tCg/tTg	2/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.671920745607869	2		712	640	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874261	155874261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352822	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	251	726	0	ENST00000368323.3:c.270G>A	p.Met90Ile	p.M90I	ENST00000368323	NM_006912.5	90	atG/atA	5/6	1	2	FACETS	0.904	0.849	0.962	0.904	0.849	0.962	CLONAL	1	TRUE	1	0.671920745607869	2		726	826	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663346	227663346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024227751	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	221	598	0	ENST00000305123.5:c.109G>A	p.Glu37Lys	p.E37K	ENST00000305123	NM_005544.2	37	Gag/Aag	1/2	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.671920745607869	2		598	637	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855277	76855277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	15	306	0	ENST00000373344.5:c.5710G>A	p.Glu1904Lys	p.E1904K	ENST00000373344	NM_000489.3	1904	Gaa/Aaa	24/35	1	1	FACETS	0.174	0.128	0.23	0.174	0.128	0.23	SUBCLONAL	1	TRUE	0	0.671920745607869	1		306	170	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678029	58678029	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567962294	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	130	397	0	ENST00000305921.3:c.254C>T	p.Ser85Leu	p.S85L	ENST00000305921	NM_003620.3	85	tCg/tTg	1/6	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.671920745607869	2		397	370	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	495124	495124	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	148	574	0	ENST00000399788.2:c.182T>C	p.Phe61Ser	p.F61S	ENST00000399788	NM_001042603.1	61	tTt/tCt	2/28	1	2	FACETS	0.966	0.89	1	0.966	0.89	1	CLONAL	1	TRUE	1	0.671920745607869	2		574	456	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871218	12871218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771553626	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	97	325	0	ENST00000228872.4:c.445G>A	p.Ala149Thr	p.A149T	ENST00000228872	NM_004064.3	149	Gca/Aca	1/3	1	2	FACETS	0.834	0.751	0.921	0.834	0.751	0.921	CLONAL	1	TRUE	1	0.671920745607869	2		325	346	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986776	36986776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1409463722	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	99	271	0	ENST00000354822.5:c.913C>T	p.Pro305Ser	p.P305S	ENST00000354822	NM_001079668.2	305	Ccc/Tcc	3/3	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.671920745607869	2		271	264	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023151	33023151	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	200	678	0	ENST00000300177.4:c.260A>C	p.Lys87Thr	p.K87T	ENST00000300177	NM_001191322.1	87	aAa/aCa	2/2	1	2	FACETS	0.907	0.845	0.972	0.907	0.845	0.972	CLONAL	1	TRUE	1	0.671920745607869	2		678	656	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293279	91293279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	129	524	0	ENST00000355112.3:c.781C>T	p.His261Tyr	p.H261Y	ENST00000355112	NM_000057.2	261	Cat/Tat	3/22	1	2	FACETS	0.865	0.79	0.942	0.865	0.79	0.942	CLONAL	1	TRUE	1	0.671920745607869	2		524	444	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832829	3832829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	236	759	0	ENST00000262367.5:c.1429G>A	p.Asp477Asn	p.D477N	ENST00000262367	NM_004380.2	477	Gac/Aac	6/31	1	2	FACETS	0.908	0.85	0.967	0.908	0.85	0.967	CLONAL	1	TRUE	1	0.671920745607869	2		759	774	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831423	89831423	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	252	853	0	ENST00000389301.3:c.2653G>A	p.Glu885Lys	p.E885K	ENST00000389301	NM_000135.2	885	Gag/Aag	28/43	1	2	FACETS	0.941	0.884	1	0.941	0.884	1	CLONAL	1	TRUE	1	0.671920745607869	2		853	797	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774181	56774181	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555594861	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	195	682	0	ENST00000337432.4:c.532C>T	p.Gln178Ter	p.Q178*	ENST00000337432	NM_058216.2	178	Cag/Tag	3/9	1	2	FACETS	0.947	0.881	1	0.947	0.881	1	CLONAL	1	TRUE	1	0.671920745607869	2		682	613	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118890	70118890	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs137853129	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	255	807	0	ENST00000245479.2:c.462C>G	p.Phe154Leu	p.F154L	ENST00000245479	NM_000346.3	154	ttC/ttG	2/3	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.671920745607869	2		807	749	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39537549	39537549	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	109	477	0	ENST00000262039.4:c.83G>C	p.Gly28Ala	p.G28A	ENST00000262039	NM_002647.2	28	gGg/gCg	2/25	1	2	FACETS	0.98	0.891	1	0.98	0.891	1	CLONAL	1	TRUE	1	0.671920745607869	2		477	331	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211624	36211624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs574808075	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	198	639	0	ENST00000222270.7:c.1375C>T	p.Pro459Ser	p.P459S	ENST00000222270	NM_014727.1	459	Cct/Tct	3/37	1	2	FACETS	0.933	0.868	0.998	0.933	0.868	0.998	CLONAL	1	TRUE	1	0.671920745607869	2		639	632	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218827	36218827	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	338	984	1	ENST00000222270.7:c.4438G>A	p.Glu1480Lys	p.E1480K	ENST00000222270	NM_014727.1	1480	Gag/Aag	18/37	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.671920745607869	2		985	995	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855787	45855787	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	259	812	0	ENST00000391945.4:c.2023G>T	p.Gly675Cys	p.G675C	ENST00000391945	NM_000400.3	675	Ggc/Tgc	21/23	1	2	FACETS	0.917	0.861	0.974	0.917	0.861	0.974	CLONAL	1	TRUE	1	0.671920745607869	2		812	841	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470018	25470018	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	179	569	0	ENST00000264709.3:c.1024G>A	p.Glu342Lys	p.E342K	ENST00000264709	NM_175629.2	342	Gag/Aag	9/23	1	2	FACETS	0.943	0.875	1	0.943	0.875	1	CLONAL	1	TRUE	1	0.671920745607869	2		569	565	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994311	25994311	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	184	574	0	ENST00000435504.4:c.502C>T	p.Gln168Ter	p.Q168*	ENST00000435504		168	Cag/Tag	6/13	1	2	FACETS	0.933	0.866	1	0.933	0.866	1	CLONAL	1	TRUE	1	0.671920745607869	2		574	587	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022319	26022322	+	frameshift_variant	Frame_Shift_Del	DEL	TTCT	TTCT	-	novel	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	263	728	0	ENST00000435504.4:c.335_338del	p.Glu112AlafsTer54	p.E112Afs*54	ENST00000435504		112	gAGAAc/gc	5/13	1	2	FACETS	0.859	0.807	0.913	0.859	0.807	0.913	CLONAL	1	TRUE	1	0.671920745607869	2		728	911	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456548	29456577	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GATTAACTGGTTTGTCTGTAGAAACAAAAA	GATTAACTGGTTTGTCTGTAGAAACAAAAA	-	novel	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	159	821	0	ENST00000389048.3:c.2356-15_2370del		p.X786_splice	ENST00000389048	NM_004304.4	786		14/29	1	2	FACETS	0.641	0.589	0.696	0.641	0.589	0.696	SUBCLONAL	1	TRUE	1	0.671920745607869	2		821	738	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707902	47707902	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	132	687	0	ENST00000233146.2:c.2526G>C	p.Glu842Asp	p.E842D	ENST00000233146	NM_000251.2	842	gaG/gaC	15/16	1	2	FACETS	0.747	0.682	0.815	0.747	0.682	0.815	SUBCLONAL	1	TRUE	1	0.671920745607869	2		687	526	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727078	40727078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs896375033	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	215	745	2	ENST00000373198.4:c.3886G>A	p.Glu1296Lys	p.E1296K	ENST00000373198	NM_133170.3	1296	Gag/Aag	28/32	1	2	FACETS	0.932	0.87	0.995	0.932	0.87	0.995	CLONAL	1	TRUE	1	0.671920745607869	2		747	687	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200780	128200780	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143554523	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	263	725	1	ENST00000341105.2:c.1025C>T	p.Ala342Val	p.A342V	ENST00000341105	NM_032638.4	342	gCc/gTc	5/6	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.671920745607869	2		726	714	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502778	186502778	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	227	635	1	ENST00000323963.5:c.236C>T	p.Ser79Leu	p.S79L	ENST00000323963		79	tCa/tTa	4/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.671920745607869	2		636	634	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902968	1902968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	209	679	0	ENST00000382891.5:c.587C>T	p.Ser196Leu	p.S196L	ENST00000382891	NM_133335.3	196	tCa/tTa	2/22	1	2	FACETS	0.858	0.799	0.918	0.858	0.799	0.918	CLONAL	1	TRUE	1	0.671920745607869	2		679	725	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754303	57754303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	203	694	1	ENST00000274289.3:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000274289	NM_006622.3	183	cGa/cAa	4/14	1	2	FACETS	0.947	0.883	1	0.947	0.883	1	CLONAL	1	TRUE	1	0.671920745607869	2		695	638	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925402	131925402	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	82	351	0	ENST00000265335.6:c.1325T>C	p.Ile442Thr	p.I442T	ENST00000265335		442	aTa/aCa	9/25	1	2	FACETS	0.918	0.82	1	0.918	0.82	1	CLONAL	1	TRUE	1	0.671920745607869	2		351	266	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170817130	170817130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	131	497	0	ENST00000296930.5:c.134G>A	p.Arg45Lys	p.R45K	ENST00000296930	NM_002520.6	45	aGa/aAa	2/11	1	2	FACETS	0.944	0.865	1	0.944	0.865	1	CLONAL	1	TRUE	1	0.671920745607869	2		497	413	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324127	31324127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41561814	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	140	468	0	ENST00000412585.2:c.436G>A	p.Asp146Asn	p.D146N	ENST00000412585	NM_005514.6	146	Gat/Aat	3/8	1	2	FACETS	0.856	0.785	0.929	0.856	0.785	0.929	CLONAL	1	TRUE	1	0.671920745607869	2		468	487	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001329	150001329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	145	867	1	ENST00000253339.5:c.2275G>A	p.Glu759Lys	p.E759K	ENST00000253339		759	Gaa/Aaa	4/7	1	2	FACETS	0.788	0.722	0.855	0.788	0.722	0.855	SUBCLONAL	1	TRUE	1	0.671920745607869	2		868	548	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845511	151845511	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs773633131	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	294	807	0	ENST00000262189.6:c.13501A>G	p.Met4501Val	p.M4501V	ENST00000262189	NM_170606.2	4501	Atg/Gtg	52/59	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.671920745607869	2		807	870	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942741	44942741	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	239	361	0	ENST00000377967.4:c.3321del	p.Ala1108LeufsTer12	p.A1108Lfs*12	ENST00000377967	NM_021140.2	1107	ccT/cc	23/29	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.671920745607869	1		361	366	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942846	44942846	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	245	398	0	ENST00000377967.4:c.3426A>C	p.Arg1142Ser	p.R1142S	ENST00000377967	NM_021140.2	1142	agA/agC	23/29	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.671920745607869	1		398	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0022450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	31	913	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.713	0.574	0.871	0.713	0.574	0.871	SUBCLONAL	1	TRUE	1	0.11	2		913	791	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037474	12037474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	12	549	0	ENST00000396373.4:c.1105C>T	p.Arg369Trp	p.R369W	ENST00000396373	NM_001987.4	369	Cgg/Tgg	6/8	1	2	FACETS	0.37	0.259	0.51	0.37	0.259	0.51	SUBCLONAL	1	TRUE	1	0.11	2		549	589	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453136	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	rs397516897	NA	P-0022450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	47	702	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	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.11	2		702	622	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971153	21971153	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913383	NA	P-0022457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	70	716	0	ENST00000304494.5:c.205G>T	p.Glu69Ter	p.E69*	ENST00000304494	NM_000077.4	69	Gag/Tag	2/3	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.21	2		716	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912664	NA	P-0022457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	103	959	0	ENST00000269305.4:c.1010G>C	p.Arg337Pro	p.R337P	ENST00000269305	NM_001126112.2	337	cGc/cCc	10/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.21	2		959	843	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	54	738	2	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	1	2	FACETS	0.794	0.677	0.922	0.794	0.677	0.922	CLONAL	1	TRUE	1	0.21	2		740	648	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610285	10610285	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	143	1123	1	ENST00000171111.5:c.425C>T	p.Thr142Met	p.T142M	ENST00000171111	NM_203500.1	142	aCg/aTg	2/6	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.21	2		1124	1014	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522741	67522741	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	42	527	1	ENST00000274335.5:c.244del	p.Ile82SerfsTer32	p.I82Sfs*32	ENST00000274335		80	Aaa/aa	1/15	1	2	FACETS	0.941	0.787	1	0.941	0.787	1	CLONAL	1	TRUE	1	0.21	2		528	425	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356382	66356382	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	41	771	0	ENST00000273854.3:c.1115G>T	p.Ser372Ile	p.S372I	ENST00000273854	NM_004439.5	372	aGt/aTt	5/18	1	2	FACETS	0.578	0.481	0.688	0.578	0.481	0.688	SUBCLONAL	1	TRUE	1	0.21	2		771	675	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120478211	120478211	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	61	679	0	ENST00000256646.2:c.3539A>T	p.Gln1180Leu	p.Q1180L	ENST00000256646	NM_024408.3	1180	cAg/cTg	22/34	1	2	FACETS	0.98	0.845	1	0.98	0.845	1	CLONAL	1	TRUE	1	0.21	2		679	593	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667492	241667492	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs766441385	NA	P-0022457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	29	549	1	ENST00000366560.3:c.958G>T	p.Ala320Ser	p.A320S	ENST00000366560	NM_000143.3	320	Gct/Tct	7/10	1	2	FACETS	0.598	0.479	0.733	0.598	0.479	0.733	SUBCLONAL	1	TRUE	1	0.21	2		550	462	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325200	123325200	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	53	924	0	ENST00000358487.5:c.128A>T	p.Gln43Leu	p.Q43L	ENST00000358487	NM_000141.4	43	cAa/cTa	3/18	1	2	FACETS	0.713	0.607	0.83	0.713	0.607	0.83	SUBCLONAL	1	TRUE	1	0.21	2		924	708	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941285	71941285	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	48	1044	1	ENST00000298229.2:c.1060G>A	p.Glu354Lys	p.E354K	ENST00000298229	NM_001567.3	354	Gag/Aag	9/28	1	2	FACETS	0.478	0.403	0.562	0.478	0.403	0.562	SUBCLONAL	1	TRUE	1	0.21	2		1045	956	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345933	73345933	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs201039391	NA	P-0022457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	50	628	0	ENST00000377767.4:c.1605G>T	p.Lys535Asn	p.K535N	ENST00000377767	NM_014953.3	535	aaG/aaT	11/21	1	2	FACETS	0.99	0.841	1	0.99	0.841	1	CLONAL	1	TRUE	1	0.21	2		628	481	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108041	30108041	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	64	953	0	ENST00000331968.5:c.766C>A	p.Pro256Thr	p.P256T	ENST00000331968	NM_002742.2	256	Cca/Aca	5/18	1	2	FACETS	0.75	0.648	0.861	0.75	0.648	0.861	SUBCLONAL	1	TRUE	1	0.21	2		953	813	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119928	70119928	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs138423956	NA	P-0022457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	35	735	0	ENST00000245479.2:c.930C>A	p.His310Gln	p.H310Q	ENST00000245479	NM_000346.3	310	caC/caA	3/3	1	2	FACETS	0.483	0.395	0.583	0.483	0.395	0.583	SUBCLONAL	1	TRUE	1	0.21	2		735	690	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094931	11094931	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	126	936	0	ENST00000358026.2:c.104C>A	p.Ser35Ter	p.S35*	ENST00000358026	NM_001128849.1	35	tCg/tAg	2/36	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.21	2		936	835	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276310	15276310	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs369768722	NA	P-0022457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	111	1083	1	ENST00000263388.2:c.5684G>T	p.Arg1895Leu	p.R1895L	ENST00000263388	NM_000435.2	1895	cGc/cTc	31/33	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.21	2		1084	915	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281917	39281917	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	40	714	0	ENST00000402219.2:c.558A>T	p.Leu186Phe	p.L186F	ENST00000402219	NM_005633.3	186	ttA/ttT	5/23	1	2	FACETS	0.615	0.51	0.733	0.615	0.51	0.733	SUBCLONAL	1	TRUE	1	0.21	2		714	619	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225343063	225343063	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0022457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	37	796	1	ENST00000264414.4:c.2030-1G>T		p.X677_splice	ENST00000264414	NM_003590.4	677			1	2	FACETS	0.482	0.396	0.579	0.482	0.396	0.579	SUBCLONAL	1	TRUE	1	0.21	2		797	731	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793308	242793308	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	88	1118	0	ENST00000334409.5:c.769A>G	p.Met257Val	p.M257V	ENST00000334409	NM_005018.2	257	Atg/Gtg	5/5	1	2	FACETS	0.861	0.761	0.969	0.861	0.761	0.969	CLONAL	1	TRUE	1	0.21	2		1118	973	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873709	35873709	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs901925052	NA	P-0022457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	68	712	0	ENST00000303115.3:c.665C>A	p.Pro222Gln	p.P222Q	ENST00000303115	NM_002185.3	222	cCa/cAa	5/8	1	2	FACETS	0.943	0.82	1	0.943	0.82	1	CLONAL	1	TRUE	1	0.21	2		712	687	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876121	35876121	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	76	787	3	ENST00000303115.3:c.913G>T	p.Asp305Tyr	p.D305Y	ENST00000303115	NM_002185.3	305	Gac/Tac	8/8	1	2	FACETS	0.859	0.752	0.974	0.859	0.752	0.974	CLONAL	1	TRUE	1	0.21	2		790	843	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359075	81359075	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1289926169	NA	P-0022457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	48	659	0	ENST00000222390.5:c.886A>G	p.Thr296Ala	p.T296A	ENST00000222390	NM_000601.4	296	Act/Gct	8/18	1	2	FACETS	0.73	0.616	0.856	0.73	0.616	0.856	SUBCLONAL	1	TRUE	1	0.21	2		659	626	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850853	128850853	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1180041451	NA	P-0022457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	97	1064	0	ENST00000249373.3:c.1700A>G	p.Lys567Arg	p.K567R	ENST00000249373	NM_005631.4	567	aAg/aGg	10/12	1	2	FACETS	0.939	0.835	1	0.939	0.835	1	CLONAL	1	TRUE	1	0.21	2		1064	984	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850951	128850951	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs767352128	NA	P-0022457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	74	720	0	ENST00000249373.3:c.1798G>T	p.Val600Leu	p.V600L	ENST00000249373	NM_005631.4	600	Gtg/Ttg	10/12	1	2	FACETS	0.961	0.841	1	0.961	0.841	1	CLONAL	1	TRUE	1	0.21	2		720	733	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205323	38205323	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	71	1409	0	ENST00000317025.8:c.367G>C	p.Glu123Gln	p.E123Q	ENST00000317025	NM_023034.1	123	Gaa/Caa	2/24	1	2	FACETS	0.567	0.493	0.648	0.567	0.493	0.648	SUBCLONAL	1	TRUE	1	0.21	2		1409	1192	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933439	39933439	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	79	966	0	ENST00000378444.4:c.1160G>T	p.Arg387Met	p.R387M	ENST00000378444	NM_001123385.1	387	aGg/aTg	4/15	1	2	FACETS	0.884	0.776	1	0.884	0.776	1	CLONAL	1	TRUE	1	0.21	2		966	851	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360548	70360548	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	50	969	0	ENST00000374080.3:c.6108G>T	p.Gln2036His	p.Q2036H	ENST00000374080		2036	caG/caT	42/45	1	2	FACETS	0.508	0.43	0.595	0.508	0.43	0.595	SUBCLONAL	1	TRUE	1	0.21	2		969	937	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	1316	766	0				ENST00000310581	NM_198253.2	-/1132			0.836114852031594	8	FACETS	0.962	0.947	0.976	0.962	0.947	0.976	CLONAL	7	TRUE	1	0.836114852031594	8		766	1640	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020337	123020337	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	195	392	0	ENST00000355640.3:c.825G>T	p.Trp275Cys	p.W275C	ENST00000355640		275	tgG/tgT	2/7	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.836114852031594	2		392	454	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120134	70120134	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	119	179	1	ENST00000245479.2:c.1136C>T	p.Ala379Val	p.A379V	ENST00000245479	NM_000346.3	379	gCg/gTg	3/3	0.767726324098193	3	FACETS	1	0.944	1	0.524	0.478	0.572	CLONAL	1	TRUE	1	0.836114852031594	3		180	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579410	7579410	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567556123	NA	P-0022470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	603	618	0	ENST00000269305.4:c.277del	p.Leu93CysfsTer30	p.L93Cfs*30	ENST00000269305	NM_001126112.2	93	Ctg/tg	4/11	0.570729265824749	1	FACETS	0.975	0.94	1	0.975	0.94	1	CLONAL	1	FALSE	0	0.628141856406381	1		618	1351	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120478157	120478161	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTG	TTCTG	-	novel	NA	P-0022470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	450	413	0	ENST00000256646.2:c.3589_3593del	p.Gln1197TrpfsTer6	p.Q1197Wfs*6	ENST00000256646	NM_024408.3	1197	CAGAAt/t	22/34	1	2	FACETS	0.877	0.836	0.92	0.877	0.836	0.92	CLONAL	1	FALSE	1	0.628141856406381	2		413	1633	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	46	460	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.290497470442057	3	FACETS	0.945	0.798	1	0.473	0.399	0.553	CLONAL	1	TRUE	1	0.29826592502588	3		460	375	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0022477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	125	525	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.290497470442057	3	FACETS	0.874	0.794	0.957	0.874	0.794	0.957	CLONAL	2	TRUE	1	0.29826592502588	3		525	551	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0022477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	126	340	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.29826592502588	3	FACETS	0.865	0.792	0.941	0.865	0.792	0.941	CLONAL	3	TRUE	0	0.29826592502588	3		340	374	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519934	NA	P-0022477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	36	380	0	ENST00000263967.3:c.333G>C	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaC	2/21	0.290497470442057	3	FACETS	0.715	0.588	0.857	0.357	0.294	0.429	SUBCLONAL	1	TRUE	1	0.29826592502588	3		380	388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579413	7579413	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	46	684	0	ENST00000269305.4:c.274C>T	p.Pro92Ser	p.P92S	ENST00000269305	NM_001126112.2	92	Ccc/Tcc	4/11	0.290497470442057	3	FACETS	0.42	0.352	0.495	0.21	0.176	0.248	SUBCLONAL	1	TRUE	1	0.29826592502588	3		684	844	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913315	NA	P-0022505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	76	1039	0	ENST00000326873.7:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000326873	NM_000455.4	194	Gac/Tac	4/10	0.221200093091631	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.221200093091631	1		1039	495	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600323	10600323	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0022505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	64	789	0	ENST00000171111.5:c.1531+1G>T		p.X511_splice	ENST00000171111	NM_203500.1	511			0.221200093091631	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.221200093091631	1		789	413	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847224	68847232	+	inframe_deletion	In_Frame_Del	DEL	TCAGGTGCC	TCAGGTGCC	-	novel	NA	P-0022521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	107	712	0	ENST00000261769.5:c.1147_1155del	p.Gln383_Pro385del	p.Q383_P385del	ENST00000261769	NM_004360.3	382	ggTCAGGTGCCt/ggt	9/16	0.446997550742757	1	FACETS	0.956	0.864	1	0.956	0.864	1	CLONAL	1	TRUE	0	0.446997550742757	1		712	389	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881002	37881003	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCTCCCCC	novel	NA	P-0022521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	197	1153	0	ENST00000269571.5:c.2339_2340insCGGCTCCCC	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	-/GGCTCCCCC	20/27	1	2	FACETS	0.93	0.861	1	0.93	0.861	1	CLONAL	1	TRUE	1	0.446997550742757	2		1153	948	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171628	36171628	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	87	516	0	ENST00000300305.3:c.937del	p.Leu313SerfsTer15	p.L313Sfs*15	ENST00000300305		313	Ctc/tc	7/8	1	2	FACETS	0.92	0.819	1	0.92	0.819	1	CLONAL	1	TRUE	1	0.446997550742757	2		516	423	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0022525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	96	763	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.385741833251641	1	FACETS	0.915	0.82	1	0.915	0.82	1	CLONAL	1	TRUE	0	0.404521436139168	1		764	414	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814632	43814632	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs867968333	NA	P-0022525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	93	855	0	ENST00000372470.3:c.1427C>A	p.Ser476Ter	p.S476*	ENST00000372470	NM_005373.2	476	tCg/tAg	9/12	0.385741833251641	1	FACETS	0.794	0.709	0.883	0.794	0.709	0.883	SUBCLONAL	1	TRUE	0	0.404521436139168	1		855	462	SUCCESS
FH	2271	MSKCC	GRCh37	1	241672019	241672020	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0022525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	116	748	0	ENST00000366560.3:c.621dup	p.Leu208ValfsTer9	p.L208Vfs*9	ENST00000366560	NM_000143.3	207	-/G	5/10	0.404521436139168	3	FACETS	0.892	0.804	0.985	0.446	0.402	0.493	CLONAL	1	TRUE	1	0.404521436139168	3		748	773	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93607715	93607715	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0022525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	37	354	1	ENST00000375746.1:c.418-1G>A		p.X140_splice	ENST00000375746	NM_001174167.1	140			1	2	FACETS	0.706	0.586	0.84	0.706	0.586	0.84	SUBCLONAL	1	TRUE	1	0.404521436139168	2		355	259	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295458	1295459	+	upstream_gene_variant	5'Flank	DEL	CG	CG	-	rs34764648	NA	P-0022538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	23	13	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		13	44	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772850	135772850	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	259	635	0	ENST00000298552.3:c.2773G>T	p.Glu925Ter	p.E925*	ENST00000298552	NM_001162426.1	925	Gaa/Taa	21/23	0.679021920961185	1	FACETS	0.775	0.731	0.82	0.775	0.731	0.82	SUBCLONAL	1	TRUE	0	0.679021920961185	1		635	650	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724625	43724625	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	426	809	0	ENST00000382044.4:c.3442T>A	p.Leu1148Met	p.L1148M	ENST00000382044	NM_001141980.1	1148	Ttg/Atg	17/28	1	2	FACETS	0.965	0.92	1	0.965	0.92	1	CLONAL	1	TRUE	1	0.679021920961185	2		809	1300	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183712	10183713	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0022541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	482	828	0	ENST00000256474.2:c.181_182insG	p.Pro61ArgfsTer71	p.P61Rfs*71	ENST00000256474	NM_000551.3	61	ccc/cGcc	1/3	0.679021920961185	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.679021920961185	1		828	891	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437596	52437596	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	306	656	0	ENST00000460680.1:c.1565del	p.Pro522LeufsTer49	p.P522Lfs*49	ENST00000460680	NM_004656.3	522	cCt/ct	13/17	0.679021920961185	1	FACETS	0.847	0.804	0.89	0.847	0.804	0.89	CLONAL	1	TRUE	0	0.679021920961185	1		656	703	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199822	138199822	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	266	414	0	ENST00000237289.4:c.1240A>C	p.Asn414His	p.N414H	ENST00000237289	NM_001270507.1	414	Aat/Cat	7/9	0.679021920961185	1	FACETS	0.951	0.902	1	0.951	0.902	1	CLONAL	1	TRUE	0	0.679021920961185	1		414	544	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022542-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	149	766	0				ENST00000310581	NM_198253.2	-/1132			0.372173946119883	3	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	1	0.399134750270203	3		766	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0022542-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	308	916	1	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.399134750270203	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.399134750270203	2		917	745	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0022542-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	148	547	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.399134750270203	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.399134750270203	2		547	348	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729163	66729163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516792	NA	P-0022542-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	154	998	4	ENST00000307102.5:c.371C>T	p.Pro124Leu	p.P124L	ENST00000307102	NM_002755.3	124	cCg/cTg	3/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.399134750270203	2		1002	695	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022542-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	120	776	1	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	0.399134750270203	3	FACETS	1	0.935	1	0.522	0.472	0.575	CLONAL	1	TRUE	1	0.399134750270203	3		777	691	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	CT	rs121913227	NA	P-0022542-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	151	708	1	ENST00000288602.6:c.1798_1799delinsAG	p.Val600Arg	p.V600R	ENST00000288602	NM_004333.4	600	GTg/AGg	15/18	0.372173946119883	3	FACETS	0.93	0.857	1	0.93	0.857	1	CLONAL	2	TRUE	1	0.399134750270203	3		709	488	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798597	45798597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780087	NA	P-0022542-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	285	965	1	ENST00000450313.1:c.497C>T	p.Ser166Phe	p.S166F	ENST00000450313	NM_012222.2	166	tCc/tTc	6/16	0.324654092151703	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.399134750270203	4		966	861	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871011	12871011	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022542-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	61	441	1	ENST00000228872.4:c.238G>T	p.Glu80Ter	p.E80*	ENST00000228872	NM_004064.3	80	Gag/Tag	1/3	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.399134750270203	2		442	271	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524125	18524125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1391898033	NA	P-0022542-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	56	475	1	ENST00000266497.5:c.1637C>T	p.Pro546Leu	p.P546L	ENST00000266497		546	cCc/cTc	11/31	1	2	FACETS	0.869	0.749	0.998	0.869	0.749	0.998	CLONAL	1	TRUE	1	0.399134750270203	2		476	323	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444248	49444248	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1025261494	NA	P-0022542-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	172	1224	1	ENST00000301067.7:c.3123G>T	p.Gln1041His	p.Q1041H	ENST00000301067	NM_003482.3	1041	caG/caT	11/54	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.399134750270203	2		1225	796	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445842	49445842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1472465711	NA	P-0022542-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	248	1442	0	ENST00000301067.7:c.1624G>A	p.Ala542Thr	p.A542T	ENST00000301067	NM_003482.3	542	Gca/Aca	10/54	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.399134750270203	2		1442	1014	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110100	115110100	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1458110040	NA	P-0022542-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	147	1189	1	ENST00000257566.3:c.1778C>T	p.Ala593Val	p.A593V	ENST00000257566	NM_016569.3	593	gCc/gTc	8/8	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.399134750270203	2		1190	707	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012392	29012392	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022542-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	186	864	0	ENST00000282397.4:c.479T>G	p.Val160Gly	p.V160G	ENST00000282397	NM_002019.4	160	gTt/gGt	4/30	0.324654092151703	4	FACETS	0.965	0.894	1	0.965	0.894	1	CLONAL	2	TRUE	2	0.399134750270203	4		864	676	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224181	36224182	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0022542-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	256	914	2	ENST00000222270.7:c.6731_6732delinsTT	p.Pro2244Leu	p.P2244L	ENST00000222270	NM_014727.1	2244	cCC/cTT	28/37	0.399134750270203	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.399134750270203	3		916	679	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085833	16085833	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022542-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	99	584	1	ENST00000281043.3:c.1009C>T	p.Pro337Ser	p.P337S	ENST00000281043	NM_005378.4	337	Ccc/Tcc	3/3	0.399134750270203	3	FACETS	1	0.967	1	0.6	0.538	0.666	CLONAL	1	TRUE	1	0.399134750270203	3		585	496	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919748	96919748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022542-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	197	705	0	ENST00000258439.3:c.515C>T	p.Thr172Ile	p.T172I	ENST00000258439	NM_001193304.2	172	aCc/aTc	4/4	0.324654092151703	4	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	2	0.399134750270203	4		705	678	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807174	1807174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022542-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	307	958	0	ENST00000260795.2:c.1505C>T	p.Pro502Leu	p.P502L	ENST00000260795		502	cCt/cTt	10/17	0.399134750270203	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.399134750270203	3		958	754	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920127	1920127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022542-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	277	961	1	ENST00000382891.5:c.1187C>T	p.Pro396Leu	p.P396L	ENST00000382891	NM_133335.3	396	cCc/cTc	5/22	0.399134750270203	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.399134750270203	3		962	759	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541804	187541804	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022542-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	79	614	0	ENST00000441802.2:c.5936T>G	p.Phe1979Cys	p.F1979C	ENST00000441802	NM_005245.3	1979	tTt/tGt	10/27	0.399134750270203	3	FACETS	0.926	0.816	1	0.463	0.408	0.522	CLONAL	1	TRUE	1	0.399134750270203	3		614	513	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509636	106509636	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs867282260	NA	P-0022542-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	79	642	2	ENST00000359195.3:c.1630C>T	p.Arg544Ter	p.R544*	ENST00000359195	NM_002649.2	544	Cga/Tga	2/11	0.372173946119883	3	FACETS	0.938	0.828	1	0.469	0.414	0.529	CLONAL	1	TRUE	1	0.399134750270203	3		644	506	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98011465	98011465	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022542-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	212	879	0	ENST00000289081.3:c.109C>T	p.His37Tyr	p.H37Y	ENST00000289081	NM_000136.2	37	Cac/Tac	2/15	0.399134750270203	2	FACETS	0.865	0.809	0.923	0.865	0.809	0.923	CLONAL	2	TRUE	0	0.399134750270203	2		879	614	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772057	135772058	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0022542-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	161	648	2	ENST00000298552.3:c.3059_3060delinsTT	p.Thr1020Ile	p.T1020I	ENST00000298552	NM_001162426.1	1020	aCC/aTT	23/23	0.399134750270203	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	0	0.399134750270203	2		650	399	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139565449	139565449	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022542-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	204	708	0	ENST00000308874.7:c.619G>A	p.Val207Met	p.V207M	ENST00000308874		207	Gtg/Atg	8/10	0.399134750270203	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.399134750270203	2		708	463	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441252	52441252	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	48	445	0	ENST00000460680.1:c.518A>G	p.Tyr173Cys	p.Y173C	ENST00000460680	NM_004656.3	173	tAt/tGt	7/17	0.268703766759387	1	FACETS	0.74	0.627	0.864	0.74	0.627	0.864	SUBCLONAL	1	TRUE	0	0.268703766759387	1		445	418	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469672	NA	P-0022551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	226	692	2	ENST00000374080.3:c.131G>A	p.Gly44Asp	p.G44D	ENST00000374080		44	gGt/gAt	2/45	0.540435625552665	1	FACETS	0.484	0.453	0.517	0.484	0.453	0.517	SUBCLONAL	1	TRUE	0	0.799800741282319	1		694	700	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577102	7577102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793881	NA	P-0022551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	621	786	2	ENST00000269305.4:c.836G>A	p.Gly279Glu	p.G279E	ENST00000269305	NM_001126112.2	279	gGg/gAg	8/11	0.539996086266761	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.799800741282319	1		788	847	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951075	48951075	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	172	363	0	ENST00000267163.4:c.1237G>T	p.Glu413Ter	p.E413*	ENST00000267163	NM_000321.2	413	Gaa/Taa	13/27	0.734899202419481	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.799800741282319	1		363	242	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	193	1036	0	ENST00000267101.3:c.310G>C	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ctg	3/28	1	2	FACETS	0.825	0.762	0.89	0.825	0.762	0.89	CLONAL	1	TRUE	1	0.432936509001852	2		1036	1081	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203543	108203543	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	140	553	0	ENST00000278616.4:c.7843C>T	p.Gln2615Ter	p.Q2615*	ENST00000278616	NM_000051.3	2615	Cag/Tag	53/63	0.283192539941117	2	FACETS	1	0.973	1	0.575	0.526	0.626	CLONAL	1	TRUE	0	0.432936509001852	2		553	562	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092922	27093718	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTGAGAATTTTTTTCTCTTTTACAGGGATGGCAGCCAGCCCAGAGATGATGGGCCTTGGGGATGTAAAGTTAACTCCAGCCACCAAAATGAACAACAAGGCAGATGGGACACCCAAGACAGAATCCAAATCCAAGGTAGTGATTTTTGTCTTGACTCCTTTCAACTTTGTGTCCTATCTTTTTCAGTGATAGGAAGGAAAAAGAAAAGAGAGTGACAAGATCCCAGCCTTTTATGACACCGGACTAGATAGTCTCTGAAAAAGCTGCTGTTGCCTCCTCTTATCATGAAAGGTCCCAGAATAATAGCTCAGTGAGTTGGGTCTGGGTTGGTCTAAGGGATCCTGGTAAATAACATAATATTCTCACAGCTGTTTGTTATGGGGGAAATGCCAGACACTGCAGCATCAAACTCTCTGTACTGTTTGGCTGGTGCCCTCTGTGAAACCGTGCCTCCTATACTCAAGCATTGATAGATGGGGTGTGCCATGGGCAACTAGTTGCTCTTCTCTTCCTGAACCTTACTCATAGCAGCAGGAATGGTACCCTGTGTTCTGTAAAGAAGGAGATAAGGCAGATGAGGCTTGAGTCCTTGGCTTCCCTTAGGTTGGTCCTGGGTGTACTGTTAGGCTGTGCGGTAGTAAAGGGTCCTACTCAGCATTTGGGTCATTTGTAATATTTCTGTCCTTGGCCATACCTCACTTTCCCTATCTGTATACATAGGGAAAATAAAAATCATAGCTGTTAATTCCTGTGAGTCTTCACCTCTGGCTCCCAGCCCTTTTGACCACGTTCCTGT	CTTGAGAATTTTTTTCTCTTTTACAGGGATGGCAGCCAGCCCAGAGATGATGGGCCTTGGGGATGTAAAGTTAACTCCAGCCACCAAAATGAACAACAAGGCAGATGGGACACCCAAGACAGAATCCAAATCCAAGGTAGTGATTTTTGTCTTGACTCCTTTCAACTTTGTGTCCTATCTTTTTCAGTGATAGGAAGGAAAAAGAAAAGAGAGTGACAAGATCCCAGCCTTTTATGACACCGGACTAGATAGTCTCTGAAAAAGCTGCTGTTGCCTCCTCTTATCATGAAAGGTCCCAGAATAATAGCTCAGTGAGTTGGGTCTGGGTTGGTCTAAGGGATCCTGGTAAATAACATAATATTCTCACAGCTGTTTGTTATGGGGGAAATGCCAGACACTGCAGCATCAAACTCTCTGTACTGTTTGGCTGGTGCCCTCTGTGAAACCGTGCCTCCTATACTCAAGCATTGATAGATGGGGTGTGCCATGGGCAACTAGTTGCTCTTCTCTTCCTGAACCTTACTCATAGCAGCAGGAATGGTACCCTGTGTTCTGTAAAGAAGGAGATAAGGCAGATGAGGCTTGAGTCCTTGGCTTCCCTTAGGTTGGTCCTGGGTGTACTGTTAGGCTGTGCGGTAGTAAAGGGTCCTACTCAGCATTTGGGTCATTTGTAATATTTCTGTCCTTGGCCATACCTCACTTTCCCTATCTGTATACATAGGGAAAATAAAAATCATAGCTGTTAATTCCTGTGAGTCTTCACCTCTGGCTCCCAGCCCTTTTGACCACGTTCCTGT	-	novel	NA	P-0022558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	41	421	0	ENST00000324856.7:c.2879-22_2989-559del		p.X960_splice	ENST00000324856	NM_006015.4	960		10/20	0.413127586953709	1	FACETS	0.442	0.369	0.522	0.442	0.369	0.522	SUBCLONAL	1	TRUE	0	0.432936509001852	1		421	336	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0022564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	267	814	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.560300997665961	2		814	792	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591246	67591246	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0022578-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	425	765	1	ENST00000274335.5:c.1746-2A>T		p.X582_splice	ENST00000274335		582			0.576307067503615	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.576307067503615	3		766	884	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41209135	41209135	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022578-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	43	1032	1	ENST00000357654.3:c.5211A>T	p.Arg1737Ser	p.R1737S	ENST00000357654	NM_007294.3	1737	agA/agT	19/23	1	2	FACETS	0.409	0.343	0.482	0.409	0.343	0.482	SUBCLONAL	1	TRUE	1	0.576307067503615	2		1033	365	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391279	139391279	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022578-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	43	1235	1	ENST00000277541.6:c.6912G>T	p.Leu2304Phe	p.L2304F	ENST00000277541	NM_017617.3	2304	ttG/ttT	34/34	0.215945175217377	2	FACETS	0.424	0.356	0.499	0.212	0.178	0.25	INDETERMINATE	1	TRUE	0	0.576307067503615	2		1236	352	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0022581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	37	678	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.718205852969106	3	FACETS	0.968	0.813	1	0.484	0.406	0.567	CLONAL	1	TRUE	1	0.766655395353628	3		680	138	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0022581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	28	367	0	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	0.766655395353628	3	FACETS	1	0.928	1	0.64	0.528	0.757	CLONAL	1	TRUE	1	0.766655395353628	3		367	79	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913255	NA	P-0022581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	104	745	0	ENST00000369535.4:c.183A>C	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caC	3/7	0.273348946085313	5	FACETS	0.938	0.85	1	0.625	0.567	0.685	INDETERMINATE	2	TRUE	2	0.766655395353628	5		745	311	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168682	32168682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs935064991	NA	P-0022581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	21	808	1	ENST00000375023.3:c.4241C>T	p.Ala1414Val	p.A1414V	ENST00000375023	NM_004557.3	1414	gCg/gTg	23/30	0.423501735740814	3	FACETS	0.433	0.335	0.545	0.217	0.167	0.273	INDETERMINATE	1	TRUE	1	0.766655395353628	3		809	175	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0022588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	245	1359	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	0.327632349666741	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.327632349666741	1		1359	1065	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098964	178098975	+	inframe_deletion	In_Frame_Del	DEL	ATCTTGCCTCCA	ATCTTGCCTCCA	-	novel	NA	P-0022588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	81	511	0	ENST00000397062.3:c.70_81del	p.Trp24_Asp27del	p.W24_D27del	ENST00000397062	NM_006164.4	24	TGGAGGCAAGAT/-	2/5	0.212586848131079	1	FACETS	0.931	0.824	1	0.931	0.824	1	CLONAL	1	TRUE	0	0.327632349666741	1		511	444	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485766	57485766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	41	612	0	ENST00000371085.3:c.1067G>A	p.Arg356His	p.R356H	ENST00000371085	NM_000516.4	356	cGt/cAt	13/13	1	2	FACETS	0.4	0.333	0.476	0.4	0.333	0.476	SUBCLONAL	1	TRUE	1	0.327632349666741	2		612	625	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426181	49426181	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	100	970	2	ENST00000301067.7:c.12307C>T	p.Gln4103Ter	p.Q4103*	ENST00000301067	NM_003482.3	4103	Cag/Tag	39/54	1	2	FACETS	0.637	0.567	0.71	0.637	0.567	0.71	SUBCLONAL	1	TRUE	1	0.327632349666741	2		972	959	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193181230	193181230	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	159	621	0	ENST00000367435.3:c.1066G>A	p.Gly356Arg	p.G356R	ENST00000367435	NM_024529.4	356	Gga/Aga	12/17	0.207774974999705	2	FACETS	1	0.987	1	0.699	0.643	0.758	CLONAL	1	TRUE	0	0.327632349666741	2		621	694	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600477	43600477	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	233	1187	1	ENST00000355710.3:c.703G>T	p.Glu235Ter	p.E235*	ENST00000355710	NM_020975.4	235	Gag/Tag	4/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.327632349666741	2		1188	1090	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446874	18446874	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	123	771	0	ENST00000266497.5:c.959A>C	p.His320Pro	p.H320P	ENST00000266497		320	cAt/cCt	4/31	1	2	FACETS	0.989	0.895	1	0.989	0.895	1	CLONAL	1	TRUE	1	0.327632349666741	2		771	759	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556086	29556086	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	80	406	1	ENST00000356175.3:c.2453C>A	p.Ser818Tyr	p.S818Y	ENST00000356175	NM_000267.3	818	tCc/tAc	21/57	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.327632349666741	2		407	431	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873027	134873027	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1185	132	1040	0	ENST00000398015.3:c.1331G>T	p.Ser444Ile	p.S444I	ENST00000398015	NM_004441.4	444	aGt/aTt	6/16	0.251016735595587	4	FACETS	0.812	0.735	0.894			1	CLONAL	1	TRUE	NA	0.327632349666741	4		1040	1317	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968562	55968562	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	131	944	0	ENST00000263923.4:c.2101T>G	p.Phe701Val	p.F701V	ENST00000263923	NM_002253.2	701	Ttt/Gtt	14/30	0.130014629465006	5	FACETS	1	0.972	1	0.297	0.269	0.326	INDETERMINATE	1	TRUE	1	0.327632349666741	5		944	1005	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407462	407462	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	33	492	0	ENST00000380956.4:c.1220C>G	p.Pro407Arg	p.P407R	ENST00000380956	NM_001195286.1	407	cCt/cGt	9/9	0.256452183877186	2	FACETS	0.311	0.253	0.378	0.156	0.126	0.189	SUBCLONAL	1	TRUE	0	0.327632349666741	2		492	647	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971178	21971179	+	stop_gained	Nonsense_Mutation	DNP	CG	CG	AT	novel	NA	P-0022588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	143	871	1	ENST00000579755.1:c.222_223delinsAT	p.Gly75Ter	p.G75*	ENST00000579755		74	ggCGga/ggATga	2/3	0.327632349666741	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.327632349666741	1		872	712	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239846	98239846	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	123	1105	0	ENST00000331920.6:c.1486A>T	p.Asn496Tyr	p.N496Y	ENST00000331920	NM_000264.3	496	Aac/Tac	10/24	1	2	FACETS	0.73	0.659	0.805	0.73	0.659	0.805	SUBCLONAL	1	TRUE	1	0.327632349666741	2		1105	1029	SUCCESS
AR	367	MSKCC	GRCh37	X	66765719	66765719	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1614	211	2025	0	ENST00000374690.3:c.731C>G	p.Ser244Trp	p.S244W	ENST00000374690	NM_000044.3	244	tCg/tGg	1/8	1	2	FACETS	0.706	0.653	0.761	0.706	0.653	0.761	SUBCLONAL	1	TRUE	1	0.327632349666741	2		2025	1825	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184144	123184144	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	44	705	0	ENST00000218089.9:c.1002G>T	p.Trp334Cys	p.W334C	ENST00000218089	NM_001042749.1	334	tgG/tgT	11/35	1	2	FACETS	0.436	0.365	0.515	0.436	0.365	0.515	SUBCLONAL	1	TRUE	1	0.327632349666741	2		705	616	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000095	30000095	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0022609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	210	777	0	ENST00000338641.4:c.109del	p.Cys37AlafsTer3	p.C37Afs*3	ENST00000338641	NM_000268.3	36	aaT/aa	1/16	0.833825571746889	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.833825571746889	1		777	269	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0022612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	96	757	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.546563701860723	2	FACETS	0.815	0.73	0.904	0.408	0.365	0.452	CLONAL	1	TRUE	0	0.546563701860723	2		758	431	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0022612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	208	784	2	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	0.535971552184945	2	FACETS	1	0.99	1	0.675	0.631	0.719	CLONAL	1	TRUE	0	0.546563701860723	2		786	564	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840607	36840607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528158465	NA	P-0022612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	172	914	0	ENST00000358127.4:c.1126G>A	p.Ala376Thr	p.A376T	ENST00000358127	NM_001280556.1	376	Gcc/Acc	10/10	0.535971552184945	2	FACETS	1	0.938	1	0.508	0.47	0.548	CLONAL	1	TRUE	0	0.546563701860723	2		914	619	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100550	8100550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs34363744	NA	P-0022612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	162	915	1	ENST00000346208.3:c.524C>T	p.Ser175Leu	p.S175L	ENST00000346208		175	tCg/tTg	3/6	0.46291820671975	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.546563701860723	1		916	428	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952054	178952054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	92	443	0	ENST00000263967.3:c.3109G>A	p.Glu1037Lys	p.E1037K	ENST00000263967	NM_006218.2	1037	Gag/Aag	21/21	0.4736985304812	3	FACETS	1	0.968	1	0.402	0.36	0.446	CLONAL	1	TRUE	0	0.546563701860723	3		443	355	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332435	70332435	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	319	793	0	ENST00000373644.4:c.340C>T	p.Arg114Ter	p.R114*	ENST00000373644	NM_030625.2	114	Cga/Tga	2/12	0.535971552184945	2	FACETS	0.971	0.927	1	0.971	0.927	1	CLONAL	2	TRUE	0	0.546563701860723	2		793	601	SUCCESS
APC	324	MSKCC	GRCh37	5	112174620	112174620	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0022612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	161	452	0	ENST00000257430.4:c.3329C>G	p.Ser1110Ter	p.S1110*	ENST00000257430	NM_000038.5	1110	tCa/tGa	16/16	0.535971552184945	2	FACETS	0.963	0.901	1	0.963	0.901	1	CLONAL	2	TRUE	0	0.546563701860723	2		452	306	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198246	138198246	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200840068	NA	P-0022612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	50	448	2	ENST00000237289.4:c.839G>A	p.Arg280Gln	p.R280Q	ENST00000237289	NM_001270507.1	280	cGg/cAg	6/9	0.4736985304812	3	FACETS	0.604	0.513	0.702	0.201	0.171	0.234	SUBCLONAL	1	TRUE	0	0.546563701860723	3		450	386	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576858	7576875	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTGAAATATTCTCCAT	GGGTGAAATATTCTCCAT	A	novel	NA	P-0022612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	175	779	0	ENST00000269305.4:c.971_988delinsT	p.Asp324ValfsTer7	p.D324Vfs*7	ENST00000269305	NM_001126112.2	324	gATGGAGAATATTTCACCCtt/gTtt	9/11	0.513640393729373	2	FACETS	1	0.99	1	0.728	0.677	0.779	CLONAL	1	TRUE	0	0.546563701860723	2		779	440	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233681	233681	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs771328239	NA	P-0121554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	230	412	3	ENST00000264932.6:c.985C>T	p.Arg329Ter	p.R329*	ENST00000264932	NM_004168.2	329	Cga/Tga	8/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	NA	1	0.721709345186934	2		415	566	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740733	58740733	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0121554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	586	630	1	ENST00000305921.3:c.1638del	p.Met547Ter	p.M547*	ENST00000305921	NM_003620.3	546	ctG/ct	6/6	0.685560017827052	3	FACETS	0.998	0.964	1	0.998	0.964	1	CLONAL	2	NA	1	0.721709345186934	3		631	1107	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0022655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	58	621	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		621	201	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220307	98220308	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTCCA	novel	NA	P-0022665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	458	361	0	ENST00000331920.6:c.3151_3155dup	p.Ala1053GlyfsTer7	p.A1053Gfs*7	ENST00000331920	NM_000264.3	1052	acg/acTGGACg	18/24	0.906165240722809	2	FACETS	0.887	0.864	0.908	0.887	0.864	0.908	CLONAL	2	TRUE	0	0.906165240722809	2		361	570	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	49	720	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	TRUE	1	0.12	2		721	814	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0022675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	28	700	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	1	2	FACETS	0.614	0.489	0.758	0.614	0.489	0.758	SUBCLONAL	1	TRUE	1	0.12	2		700	760	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891162	101891162	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	35	428	0	ENST00000374994.4:c.123T>G	p.Cys41Trp	p.C41W	ENST00000374994	NM_004612.2	41	tgT/tgG	2/9	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.12	2		428	533	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010560	48010560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	18	642	1	ENST00000234420.5:c.188C>T	p.Ser63Phe	p.S63F	ENST00000234420	NM_000179.2	63	tCc/tTc	1/10	0.102986413330876	0	FACETS	0.149	0.112	0.193			1	INDETERMINATE	1	FALSE	0	0.408595092294554	0		643	350	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324896	31324896	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	81	560	1	ENST00000412585.2:c.40T>C	p.Ser14Pro	p.S14P	ENST00000412585	NM_005514.6	14	Tcg/Ccg	1/8	0.408595092294554	7	FACETS	0.82	0.724	0.921	0.41	0.362	0.461	CLONAL	2	FALSE	3	0.408595092294554	7		561	489	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0022756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	48	840	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.91	0.769	1	0.91	0.769	1	CLONAL	1	TRUE	1	0.189306581371703	2		840	557	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0022756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	93	747	1	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.189306581371703	1	FACETS	0.992	0.88	1	0.992	0.88	1	CLONAL	1	TRUE	0	0.189306581371703	1		748	897	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0022756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	111	1068	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.189306581371703	1	FACETS	0.957	0.859	1	0.957	0.859	1	CLONAL	1	TRUE	0	0.189306581371703	1		1068	1109	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152009026	152009026	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	23	381	0	ENST00000262189.6:c.596del	p.Arg199HisfsTer7	p.R199Hfs*7	ENST00000262189	NM_170606.2	199	cGa/ca	5/59	1	2	FACETS	0.713	0.555	0.894	0.713	0.555	0.894	SUBCLONAL	1	TRUE	1	0.189306581371703	2		381	341	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0022759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	284	777	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.430730269295653	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.558962526938488	4		777	699	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0022759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	170	937	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.558962526938488	1	FACETS	0.963	0.895	1	0.963	0.895	1	CLONAL	1	TRUE	0	0.558962526938488	1		939	455	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875645	35875645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201449880	NA	P-0022759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	58	631	1	ENST00000303115.3:c.832G>A	p.Asp278Asn	p.D278N	ENST00000303115	NM_002185.3	278	Gat/Aat	7/8	0.558962526938488	2	FACETS	0.631	0.545	0.723	0.315	0.272	0.362	SUBCLONAL	1	TRUE	0	0.558962526938488	2		632	329	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041554	14041554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772728961	NA	P-0022759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	110	632	0	ENST00000311895.7:c.2101C>T	p.Arg701Cys	p.R701C	ENST00000311895	NM_005236.2	701	Cgt/Tgt	11/11	1	2	FACETS	0.944	0.854	1	0.944	0.854	1	CLONAL	1	TRUE	1	0.558962526938488	2		632	417	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680722	88680722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	157	875	0	ENST00000360948.2:c.535G>A	p.Glu179Lys	p.E179K	ENST00000360948	NM_001012338.2	179	Gag/Aag	6/19	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.558962526938488	2		875	530	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0022759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	92	601	2				ENST00000310581	NM_198253.2	-/1132			0.558962526938488	2	FACETS	1	0.977	1	0.648	0.585	0.713	CLONAL	1	TRUE	0	0.558962526938488	2		603	254	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716366	18716366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs935135637	NA	P-0022759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	75	615	0	ENST00000266497.5:c.3713C>T	p.Ser1238Leu	p.S1238L	ENST00000266497		1238	tCa/tTa	26/31	1	2	FACETS	0.803	0.71	0.903	0.803	0.71	0.903	CLONAL	1	TRUE	1	0.558962526938488	2		615	334	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443979	49443979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201623566	NA	P-0022759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	152	917	0	ENST00000301067.7:c.3392C>T	p.Pro1131Leu	p.P1131L	ENST00000301067	NM_003482.3	1131	cCg/cTg	11/54	1	2	FACETS	0.978	0.899	1	0.978	0.899	1	CLONAL	1	TRUE	1	0.558962526938488	2		917	556	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258592	16258592	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	99	657	0	ENST00000375759.3:c.5857C>T	p.Pro1953Ser	p.P1953S	ENST00000375759	NM_015001.2	1953	Cct/Tct	11/15	0.430730269295653	4	FACETS	0.899	0.804	1	0.45	0.402	0.5	CLONAL	1	TRUE	2	0.558962526938488	4		657	614	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443637	49443637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	148	755	2	ENST00000301067.7:c.3734C>T	p.Ser1245Phe	p.S1245F	ENST00000301067	NM_003482.3	1245	tCt/tTt	11/54	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.558962526938488	2		757	516	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489525	56489525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	147	750	0	ENST00000267101.3:c.1990C>T	p.Leu664Phe	p.L664F	ENST00000267101	NM_001982.3	664	Ctc/Ttc	17/28	1	2	FACETS	0.969	0.889	1	0.969	0.889	1	CLONAL	1	TRUE	1	0.558962526938488	2		750	543	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622468	28622468	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	57	804	0	ENST00000241453.7:c.1149G>A	p.Trp383Ter	p.W383*	ENST00000241453	NM_004119.2	383	tgG/tgA	9/24	0.417250438937254	2	FACETS	0.662	0.572	0.759	0.331	0.286	0.38	SUBCLONAL	1	TRUE	0	0.558962526938488	2		804	308	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166227	7166227	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745372291	NA	P-0022759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	146	833	1	ENST00000302850.5:c.1799C>T	p.Ser600Leu	p.S600L	ENST00000302850	NM_000208.2	600	tCg/tTg	8/22	1	2	FACETS	0.967	0.888	1	0.967	0.888	1	CLONAL	1	TRUE	1	0.558962526938488	2		834	540	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209103942	209103942	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	130	543	0	ENST00000345146.2:c.1007G>A	p.Trp336Ter	p.W336*	ENST00000345146	NM_005896.2	336	tGg/tAg	9/10	0.543591431641723	3	FACETS	0.918	0.845	0.993	0.918	0.845	0.993	CLONAL	2	TRUE	1	0.558962526938488	3		543	324	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151576	55151576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536062496	NA	P-0022759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	87	777	0	ENST00000257290.5:c.2362G>A	p.Glu788Lys	p.E788K	ENST00000257290	NM_006206.4	788	Gaa/Aaa	17/23	1	2	FACETS	0.884	0.789	0.984	0.884	0.789	0.984	CLONAL	1	TRUE	1	0.558962526938488	2		777	352	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981193	55981193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	50	570	0	ENST00000263923.4:c.506G>A	p.Arg169Lys	p.R169K	ENST00000263923	NM_002253.2	169	aGa/aAa	5/30	1	2	FACETS	0.881	0.758	1	0.881	0.758	1	CLONAL	1	TRUE	1	0.558962526938488	2		570	203	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155686	56155686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201539021	NA	P-0022759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	94	578	0	ENST00000399503.3:c.778C>T	p.Arg260Cys	p.R260C	ENST00000399503	NM_005921.1	260	Cgc/Tgc	3/20	0.558962526938488	2	FACETS	0.763	0.682	0.847	0.381	0.341	0.424	SUBCLONAL	1	TRUE	0	0.558962526938488	2		578	441	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339185	87339185	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1236700381	NA	P-0022759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	109	702	0	ENST00000277120.3:c.767C>T	p.Ser256Leu	p.S256L	ENST00000277120		256	tCa/tTa	8/19	1	2	FACETS	0.975	0.883	1	0.975	0.883	1	CLONAL	1	TRUE	1	0.558962526938488	2		702	400	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0022779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	164	915	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.449832016246576	2	FACETS	0.897	0.844	0.949	1	0.991	1	CLONAL	3	TRUE	0	0.449832016246576	2		915	271	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0022779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	921	925	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.449832016246576	16	FACETS	0.997	0.977	1			1	CLONAL	14	TRUE	NA	0.449832016246576	16		925	1217	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117409	115117410	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	91	692	0	ENST00000257566.3:c.764dup	p.Arg256LysfsTer4	p.R256Kfs*4	ENST00000257566	NM_016569.3	255	gta/gtTa	4/8	0.292939439019637	4	FACETS	1	0.92	1	1	0.92	1	CLONAL	2	TRUE	2	0.449832016246576	4		692	286	SUCCESS
APC	324	MSKCC	GRCh37	5	112175459	112175459	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	88	524	0	ENST00000257430.4:c.4168G>C	p.Val1390Leu	p.V1390L	ENST00000257430	NM_000038.5	1390	Gtc/Ctc	16/16	0.449832016246576	4	FACETS	1	0.919	1	1	0.919	1	CLONAL	2	TRUE	2	0.449832016246576	4		524	276	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	45	766	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.756	0.648	0.87	1	0.965	1	SUBCLONAL	2	TRUE	1	0.399417814704045	2		766	149	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0022796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	40	676	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.399417814704045	2		676	140	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0022796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	45	621	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.399417814704045	2		621	162	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466799	25466799	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751562376	NA	P-0022796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	8	1095	3	ENST00000264709.3:c.1904G>A	p.Arg635Gln	p.R635Q	ENST00000264709	NM_175629.2	635	cGg/cAg	16/23	1	2	FACETS	0.113	0.072	0.167	0.113	0.072	0.167	SUBCLONAL	1	TRUE	1	0.399417814704045	2		1098	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0022800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	162	1081	1	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	1	2	FACETS	0.809	0.741	0.881	1	0.989	1	CLONAL	2	TRUE	1	0.17	2		1082	1178	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949125	71949125	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	66	879	0	ENST00000298229.2:c.3592G>C	p.Glu1198Gln	p.E1198Q	ENST00000298229	NM_001567.3	1198	Gag/Cag	27/28	1	2	FACETS	0.717	0.62	0.823	0.717	0.62	0.823	SUBCLONAL	1	TRUE	1	0.17	2		879	1083	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369196	118369196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	58	723	1	ENST00000534358.1:c.5914G>A	p.Asp1972Asn	p.D1972N	ENST00000534358	NM_005933.3	1972	Gat/Aat	22/36	0.3	3	FACETS	0.93	0.797	1			1	CLONAL	1	TRUE	NA	0.17	3		724	796	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373923	118373923	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	31	525	0	ENST00000534358.1:c.7316C>G	p.Thr2439Ser	p.T2439S	ENST00000534358	NM_005933.3	2439	aCt/aGt	27/36	0.3	3	FACETS	0.658	0.531	0.803			1	SUBCLONAL	1	TRUE	NA	0.17	3		525	601	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95597878	95597878	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs768445477	NA	P-0022800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	70	924	0	ENST00000393063.1:c.406G>C	p.Glu136Gln	p.E136Q	ENST00000393063	NM_030621.3	136	Gag/Cag	5/28	1	2	FACETS	0.819	0.712	0.935	0.819	0.712	0.935	CLONAL	1	TRUE	1	0.17	2		924	1006	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686937	37686937	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	87	813	0	ENST00000447079.4:c.3841C>G	p.Leu1281Val	p.L1281V	ENST00000447079	NM_015083.1	1281	Ctg/Gtg	14/14	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.17	2		813	898	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804398	46804398	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1343659361	NA	P-0022800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	71	641	1	ENST00000290295.7:c.609C>A	p.Ser203Arg	p.S203R	ENST00000290295	NM_006361.5	203	agC/agA	2/2	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.17	2		642	695	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591966	48591966	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	29	565	0	ENST00000342988.3:c.1129G>T	p.Glu377Ter	p.E377*	ENST00000342988	NM_005359.5	377	Gag/Tag	9/12	0.181908659134007	1	FACETS	0.64	0.512	0.785	0.64	0.512	0.785	SUBCLONAL	1	TRUE	0	0.17	1		565	488	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600475	10600475	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	92	946	1	ENST00000171111.5:c.1380G>T	p.Arg460Ser	p.R460S	ENST00000171111	NM_203500.1	460	agG/agT	4/6	0.181908659134007	1	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	0	0.17	1		947	977	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221474	36221474	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1280	104	1181	1	ENST00000222270.7:c.5233G>T	p.Asp1745Tyr	p.D1745Y	ENST00000222270	NM_014727.1	1745	Gat/Tat	25/37	0.157989979260731	2	FACETS	0.884	0.789	0.986	0.442	0.394	0.493	CLONAL	1	TRUE	0	0.17	2		1182	1384	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786892	135786892	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	77	780	0	ENST00000298552.3:c.977del	p.Leu326HisfsTer5	p.L326Hfs*5	ENST00000298552	NM_001162426.1	326	cTa/ca	10/23	0.181908659134007	1	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	0	0.17	1		780	804	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939639	76939639	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	74	536	0	ENST00000373344.5:c.1109A>G	p.Tyr370Cys	p.Y370C	ENST00000373344	NM_000489.3	370	tAt/tGt	9/35	1	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.17	1		536	553	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0022817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	44	762	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.7	0.584	0.829	0.7	0.584	0.829	SUBCLONAL	1	TRUE	1	0.12	2		762	1048	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0022824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	256	1089	2	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.142131745593213	1	FACETS	1	0.991	1	1	0.991	1	INDETERMINATE	1	TRUE	0	0.485949204580356	1		1091	619	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780956	9780956	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	31	866	0	ENST00000377346.4:c.1678G>A	p.Asp560Asn	p.D560N	ENST00000377346	NM_005026.3	560	Gat/Aat	13/24	0.485949204580356	1	FACETS	0.263	0.213	0.32	0.263	0.213	0.32	SUBCLONAL	1	TRUE	0	0.485949204580356	1		866	367	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65349077	65349077	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	145	1013	3	ENST00000342505.4:c.88G>T	p.Glu30Ter	p.E30*	ENST00000342505	NM_002227.2	30	Gag/Tag	3/25	0.485949204580356	1	FACETS	0.963	0.886	1	0.963	0.886	1	CLONAL	1	TRUE	0	0.485949204580356	1		1016	469	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	401923	401923	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0022824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	31	476	0	ENST00000399788.2:c.4866+2T>C		p.X1622_splice	ENST00000399788	NM_001042603.1	1622			NA	2	FACETS	0.325	0.263	0.396			1	INDETERMINATE	1	TRUE	NA	0.485949204580356	2		476	392	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119298	3119298	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	33	1215	0	ENST00000078429.4:c.830A>T	p.Asp277Val	p.D277V	ENST00000078429	NM_002067.2	277	gAc/gTc	6/7	0.485949204580356	1	FACETS	0.204	0.166	0.247	0.204	0.166	0.247	SUBCLONAL	1	TRUE	0	0.485949204580356	1		1215	504	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665339	117665339	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	60	841	1	ENST00000368508.3:c.4408C>G	p.Leu1470Val	p.L1470V	ENST00000368508	NM_002944.2	1470	Ctg/Gtg	27/43	1	2	FACETS	0.854	0.742	0.974	0.854	0.742	0.974	CLONAL	1	TRUE	1	0.485949204580356	2		842	289	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864293	151864293	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	93	1014	0	ENST00000262189.6:c.9688G>C	p.Asp3230His	p.D3230H	ENST00000262189	NM_170606.2	3230	Gat/Cat	42/59	0.405331669323985	1	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	0	0.485949204580356	1		1014	286	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730334	133730334	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	152	878	2	ENST00000318560.5:c.400C>T	p.Arg134Cys	p.R134C	ENST00000318560	NM_005157.4	134	Cgc/Tgc	3/11	0.485949204580356	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.485949204580356	1		880	421	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	71	766	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.28	2		766	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	119	969	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	NA	2	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.28	2		970	723	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610608	81610608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	74	571	0	ENST00000298171.2:c.2206G>A	p.Glu736Lys	p.E736K	ENST00000298171	NM_000369.2	736	Gaa/Aaa	10/10	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.28	2		571	503	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528489	29528489	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764079291	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	106	678	0	ENST00000356175.3:c.1246C>T	p.Arg416Ter	p.R416*	ENST00000356175	NM_000267.3	416	Cga/Tga	11/57	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.28	2		678	636	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230691	46230691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424958105	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	80	734	2	ENST00000334344.6:c.940C>T	p.Arg314Cys	p.R314C	ENST00000334344	NM_152641.2	314	Cgt/Tgt	8/21	1	2	FACETS	0.959	0.845	1	0.959	0.845	1	CLONAL	1	TRUE	1	0.28	2		736	596	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813307	102813307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764732420	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	86	677	1	ENST00000307046.8:c.382G>A	p.Asp128Asn	p.D128N	ENST00000307046	NM_001111285.1	128	Gac/Aac	3/4	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.28	2		678	606	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584500	189584500	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	34	523	3	ENST00000264731.3:c.796C>T	p.Arg266Ter	p.R266*	ENST00000264731	NM_003722.4	266	Cga/Tga	6/14	1	2	FACETS	0.54	0.441	0.651	0.54	0.441	0.651	SUBCLONAL	1	TRUE	1	0.28	2		526	450	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78811795	78811795	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	83	639	0	ENST00000306801.3:c.1210C>T	p.Arg404Trp	p.R404W	ENST00000306801	NM_020761.2	404	Cgg/Tgg	10/34	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.28	2		639	501	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205756	108205756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531980488	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	70	613	0	ENST00000278616.4:c.8071C>T	p.Arg2691Cys	p.R2691C	ENST00000278616	NM_000051.3	2691	Cgc/Tgc	55/63	1	2	FACETS	0.954	0.833	1	0.954	0.833	1	CLONAL	1	TRUE	1	0.28	2		613	524	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153703	55153703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	94	754	0	ENST00000257290.5:c.2669C>T	p.Ser890Phe	p.S890F	ENST00000257290	NM_006206.4	890	tCc/tTc	19/23	0.273363061831606	3	FACETS	1	0.965	1	0.602	0.536	0.672	CLONAL	1	TRUE	1	0.28	3		754	636	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265323	152265323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866869178	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	59	454	0	ENST00000206249.3:c.776G>A	p.Arg259Gln	p.R259Q	ENST00000206249	NM_000125.3	259	cGa/cAa	4/8	1	2	FACETS	0.976	0.842	1	0.976	0.842	1	CLONAL	1	TRUE	1	0.28	2		454	432	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509849	106509849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426277818	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	137	814	0	ENST00000359195.3:c.1843G>A	p.Glu615Lys	p.E615K	ENST00000359195	NM_002649.2	615	Gaa/Aaa	2/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.28	2		814	746	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69000044	69000044	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	89	765	0	ENST00000288368.4:c.2113G>A	p.Gly705Arg	p.G705R	ENST00000288368	NM_024870.2	705	Gga/Aga	19/40	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.28	2		765	576	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106940	27106940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1179332640	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	70	634	1	ENST00000324856.7:c.6551C>T	p.Ala2184Val	p.A2184V	ENST00000324856	NM_006015.4	2184	gCc/gTc	20/20	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.28	2		635	499	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937970	36937970	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	83	994	0	ENST00000361632.4:c.866C>T	p.Ala289Val	p.A289V	ENST00000361632		289	gCc/gTc	7/16	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.28	2		994	590	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226566857	226566857	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	88	688	0	ENST00000366794.5:c.1731C>A	p.Asp577Glu	p.D577E	ENST00000366794	NM_001618.3	577	gaC/gaA	12/23	1	2	FACETS	0.945	0.838	1	0.945	0.838	1	CLONAL	1	TRUE	1	0.28	2		688	665	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720717	89720717	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	24	148	1	ENST00000371953.3:c.868G>A	p.Val290Ile	p.V290I	ENST00000371953	NM_000314.4	290	Gta/Ata	8/9	1	2	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	TRUE	1	0.28	2		149	158	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194164	94194164	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	140	802	1	ENST00000323929.3:c.1264T>A	p.Ser422Thr	p.S422T	ENST00000323929	NM_005591.3	422	Tca/Aca	12/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.28	2		803	812	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112383	115112383	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	71	572	0	ENST00000257566.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000257566	NM_016569.3	453	Gag/Aag	7/8	1	2	FACETS	0.857	0.748	0.974	0.857	0.748	0.974	CLONAL	1	TRUE	1	0.28	2		572	592	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923459	9923459	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	63	789	0	ENST00000330684.3:c.1828G>A	p.Gly610Ser	p.G610S	ENST00000330684	NM_001134407.1	610	Ggc/Agc	9/13	1	2	FACETS	0.785	0.679	0.9	0.785	0.679	0.9	SUBCLONAL	1	TRUE	1	0.28	2		789	573	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992171	72992171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	86	827	0	ENST00000268489.5:c.1874C>T	p.Ser625Phe	p.S625F	ENST00000268489	NM_006885.3	625	tCc/tTc	2/10	0.285647155547406	1	FACETS	0.933	0.827	1	0.933	0.827	1	CLONAL	1	TRUE	0	0.28	1		827	566	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619810	1619810	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1302173832	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	111	913	0	ENST00000344749.5:c.1136C>T	p.Ser379Leu	p.S379L	ENST00000344749	NM_001136139.2	379	tCg/tTg	14/19	1	2	FACETS	0.918	0.824	1	0.918	0.824	1	CLONAL	1	TRUE	1	0.28	2		913	864	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226908	2226908	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	77	476	0	ENST00000398665.3:c.4388C>T	p.Ser1463Phe	p.S1463F	ENST00000398665	NM_032482.2	1463	tCc/tTc	27/28	1	2	FACETS	0.98	0.862	1	0.98	0.862	1	CLONAL	1	TRUE	1	0.28	2		476	561	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276875	15276875	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	100	943	0	ENST00000263388.2:c.5390C>T	p.Ser1797Phe	p.S1797F	ENST00000263388	NM_000435.2	1797	tCc/tTc	30/33	1	2	FACETS	0.924	0.825	1	0.924	0.825	1	CLONAL	1	TRUE	1	0.28	2		943	773	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291056	15291056	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	130	940	0	ENST00000263388.2:c.3154G>A	p.Glu1052Lys	p.E1052K	ENST00000263388	NM_000435.2	1052	Gag/Aag	20/33	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.28	2		940	846	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313039	30313039	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	75	683	0	ENST00000262643.3:c.840+2T>G		p.X280_splice	ENST00000262643	NM_001238.2	280			1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.28	2		683	497	SUCCESS
ALK	238	MSKCC	GRCh37	2	29419721	29419721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1215186876	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	64	599	0	ENST00000389048.3:c.4079G>A	p.Arg1360Gln	p.R1360Q	ENST00000389048	NM_004304.4	1360	cGg/cAg	28/29	1	2	FACETS	0.867	0.752	0.992	0.867	0.752	0.992	CLONAL	1	TRUE	1	0.28	2		599	527	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609599	46609599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	122	989	1	ENST00000263734.3:c.2323C>T	p.His775Tyr	p.H775Y	ENST00000263734	NM_001430.4	775	Cat/Tat	15/16	1	2	FACETS	0.973	0.878	1	0.973	0.878	1	CLONAL	1	TRUE	1	0.28	2		990	896	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158637091	158637091	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	98	761	0	ENST00000263640.3:c.89C>T	p.Pro30Leu	p.P30L	ENST00000263640	NM_001105.4	30	cCc/cTc	4/11	1	2	FACETS	0.976	0.871	1	0.976	0.871	1	CLONAL	1	TRUE	1	0.28	2		761	717	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31381354	31381354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766544393	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	115	688	1	ENST00000328111.2:c.1079C>T	p.Ser360Leu	p.S360L	ENST00000328111	NM_006892.3	360	tCg/tTg	10/23	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.28	2		689	686	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980865	40980865	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs746154941	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	85	708	0	ENST00000373198.4:c.1621A>G	p.Lys541Glu	p.K541E	ENST00000373198	NM_133170.3	541	Aaa/Gaa	10/32	1	2	FACETS	0.976	0.864	1	0.976	0.864	1	CLONAL	1	TRUE	1	0.28	2		708	622	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447519	12447519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	92	850	2	ENST00000287820.6:c.758C>T	p.Ser253Phe	p.S253F	ENST00000287820	NM_015869.4	253	tCc/tTc	5/7	1	2	FACETS	0.981	0.872	1	0.981	0.872	1	CLONAL	1	TRUE	1	0.28	2		852	670	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144868	47144868	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	122	816	0	ENST00000409792.3:c.4885C>T	p.His1629Tyr	p.H1629Y	ENST00000409792	NM_014159.6	1629	Cac/Tac	7/21	1	2	FACETS	0.993	0.897	1	0.993	0.897	1	CLONAL	1	TRUE	1	0.28	2		816	878	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934214	49934214	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	85	970	2	ENST00000296474.3:c.2293C>T	p.Gln765Ter	p.Q765*	ENST00000296474	NM_002447.2	765	Cag/Tag	8/20	1	2	FACETS	0.933	0.825	1	0.933	0.825	1	CLONAL	1	TRUE	1	0.28	2		972	651	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149465980	149465980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	118	928	1	ENST00000286301.3:c.11G>A	p.Gly4Glu	p.G4E	ENST00000286301	NM_005211.3	4	gGa/gAa	2/22	0.284778407618985	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.28	1		929	683	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057251	180057251	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	90	886	0	ENST00000261937.6:c.487C>T	p.Pro163Ser	p.P163S	ENST00000261937	NM_182925.4	163	Ccc/Tcc	4/30	0.284778407618985	1	FACETS	0.991	0.881	1	0.991	0.881	1	CLONAL	1	TRUE	0	0.28	1		886	558	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271294	26271295	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	68	704	2	ENST00000305910.3:c.318_319delinsAA	p.Asp107Asn	p.D107N	ENST00000305910	NM_003534.2	106	gaGGat/gaAAat	1/1	1	2	FACETS	0.798	0.694	0.91	0.798	0.694	0.91	CLONAL	1	TRUE	1	0.28	2		706	609	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93973602	93973602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	71	682	0	ENST00000369303.4:c.1774G>A	p.Gly592Ser	p.G592S	ENST00000369303	NM_004440.3	592	Ggc/Agc	9/17	1	2	FACETS	0.959	0.838	1	0.959	0.838	1	CLONAL	1	TRUE	1	0.28	2		682	529	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555353	106555353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	68	525	1	ENST00000369096.4:c.2470G>A	p.Asp824Asn	p.D824N	ENST00000369096	NM_001198.3	824	Gat/Aat	7/7	1	2	FACETS	0.975	0.85	1	0.975	0.85	1	CLONAL	1	TRUE	1	0.28	2		526	498	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521965	157521965	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	92	636	0	ENST00000346085.5:c.4237G>A	p.Gly1413Ser	p.G1413S	ENST00000346085	NM_020732.3	1413	Ggc/Agc	18/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.28	2		636	518	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249088	55249088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754426793	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	96	835	1	ENST00000275493.2:c.2386G>A	p.Gly796Ser	p.G796S	ENST00000275493	NM_005228.3	796	Ggc/Agc	20/28	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.28	2		836	571	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058515	69058515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	101	958	1	ENST00000288368.4:c.4159C>T	p.His1387Tyr	p.H1387Y	ENST00000288368	NM_024870.2	1387	Cat/Tat	34/40	1	2	FACETS	0.813	0.726	0.906	0.813	0.726	0.906	CLONAL	1	TRUE	1	0.28	2		959	887	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980602	70980602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	68	661	0	ENST00000276594.2:c.775G>A	p.Val259Met	p.V259M	ENST00000276594	NM_024504.3	259	Gtg/Atg	4/8	1	2	FACETS	0.857	0.746	0.976	0.857	0.746	0.976	CLONAL	1	TRUE	1	0.28	2		661	567	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492876	8492876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	87	697	0	ENST00000356435.5:c.2453C>T	p.Ser818Phe	p.S818F	ENST00000356435		818	tCc/tTc	16/35	0.303753239114201	1	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	0	0.28	1		697	523	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209493	98209493	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	94	819	0	ENST00000331920.6:c.4045C>T	p.Pro1349Ser	p.P1349S	ENST00000331920	NM_000264.3	1349	Cct/Tct	23/24	0.303753239114201	1	FACETS	0.966	0.861	1	0.966	0.861	1	CLONAL	1	TRUE	0	0.28	1		819	598	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589655	69589655	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	110	196	0	ENST00000168712.1:c.198G>C	p.Glu66Asp	p.E66D	ENST00000168712	NM_002007.2	66	gaG/gaC	1/3	0.528502355133602	5	FACETS	0.896	0.804	0.993			1	CLONAL	1	TRUE	NA	0.528502355133602	5		196	833	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431013	49431013	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	121	633	0	ENST00000301067.7:c.10126G>C	p.Val3376Leu	p.V3376L	ENST00000301067	NM_003482.3	3376	Gtg/Ctg	34/54	1	2	FACETS	0.786	0.711	0.865	1	0.986	1	SUBCLONAL	2	TRUE	1	0.22	2		633	700	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098436	47098437	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1322967408	NA	P-0022840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	146	632	0	ENST00000409792.3:c.6837dup	p.Val2280CysfsTer89	p.V2280Cfs*89	ENST00000409792	NM_014159.6	2279	-/T	15/21	0.295415212935549	1	FACETS	1	0.955	1	1	0.992	1	CLONAL	2	TRUE	0	0.22	1		632	557	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437816	52437816	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	182	714	0	ENST00000460680.1:c.1345G>C	p.Ala449Pro	p.A449P	ENST00000460680	NM_004656.3	449	Gct/Cct	13/17	0.295415212935549	1	FACETS	1	0.963	1	1	0.993	1	CLONAL	2	TRUE	0	0.22	1		714	691	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163902	152163925	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTTCAAGAGAAGTATTCAAGGTA	TCTTCAAGAGAAGTATTCAAGGTA	-	novel	NA	P-0022840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	77	519	0	ENST00000206249.3:c.623_643+3del		p.X208_splice	ENST00000206249	NM_000125.3	208		2/8	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.22	2		519	577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0022844-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	212	675	1	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.409538761599519	2		676	864	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514254	69514254	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022844-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	188	631	0	ENST00000294312.3:c.427G>T	p.Val143Phe	p.V143F	ENST00000294312	NM_005117.2	143	Gtc/Ttc	3/3	0.409538761599519	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.409538761599519	1		631	675	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724457	43724457	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022844-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	108	813	0	ENST00000382044.4:c.3610G>C	p.Glu1204Gln	p.E1204Q	ENST00000382044	NM_001141980.1	1204	Gag/Cag	17/28	0.172737172712668	0	FACETS	0.326	0.292	0.362			1	INDETERMINATE	1	TRUE	0	0.409538761599519	0		813	956	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577556	+	frameshift_variant	Frame_Shift_Del	DEL	CCATGC	CCATGC	AA	novel	NA	P-0022844-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	175	680	5	ENST00000269305.4:c.725_730delinsTT	p.Cys242PhefsTer4	p.C242Ffs*4	ENST00000269305	NM_001126112.2	242	tGCATGGgc/tTTgc	7/11	NA	2	FACETS	1	0.928	1			1	INDETERMINATE	1	TRUE	NA	0.409538761599519	2		685	849	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207175	1207190	+	frameshift_variant	Frame_Shift_Del	DEL	TCCCCAACGGGGAGGC	TCCCCAACGGGGAGGC	-	novel	NA	P-0022844-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	180	725	0	ENST00000326873.7:c.263_278del	p.Ile88ThrfsTer3	p.I88Tfs*3	ENST00000326873	NM_000455.4	88	aTCCCCAACGGGGAGGCc/ac	1/10	0.409538761599519	1	FACETS	0.98	0.907	1	0.98	0.907	1	CLONAL	1	TRUE	0	0.409538761599519	1		725	713	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602487	10602487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022844-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	105	496	0	ENST00000171111.5:c.1091G>A	p.Gly364Asp	p.G364D	ENST00000171111	NM_203500.1	364	gGc/gAc	3/6	0.409538761599519	1	FACETS	0.86	0.775	0.95	0.86	0.775	0.95	CLONAL	1	TRUE	0	0.409538761599519	1		496	474	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376275	225376275	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022844-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	101	331	0	ENST00000264414.4:c.679G>T	p.Glu227Ter	p.E227*	ENST00000264414	NM_003590.4	227	Gaa/Taa	6/16	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.409538761599519	2		331	461	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817444	39817444	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022844-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	171	500	0	ENST00000288319.7:c.119A>T	p.Asp40Val	p.D40V	ENST00000288319	NM_182918.3	40	gAc/gTc	2/10	0.409538761599519	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.409538761599519	1		500	586	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165814	47165822	+	inframe_deletion	In_Frame_Del	DEL	TGGAGGGTT	TGGAGGGTT	-	novel	NA	P-0022844-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	143	483	0	ENST00000409792.3:c.304_312del	p.Asn102_Pro104del	p.N102_P104del	ENST00000409792	NM_014159.6	102	AACCCTCCA/-	3/21	0.351028949226791	1	FACETS	0.864	0.79	0.941	0.864	0.79	0.941	CLONAL	1	TRUE	0	0.409538761599519	1		483	643	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196420	106196420	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022844-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	115	464	0	ENST00000380013.4:c.4753A>T	p.Thr1585Ser	p.T1585S	ENST00000380013	NM_001127208.2	1585	Act/Tct	11/11	0.351028949226791	1	FACETS	0.849	0.768	0.934	0.849	0.768	0.934	CLONAL	1	TRUE	0	0.409538761599519	1		464	526	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521307	187521307	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022844-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	175	578	0	ENST00000441802.2:c.11848G>T	p.Val3950Leu	p.V3950L	ENST00000441802	NM_005245.3	3950	Gtg/Ttg	22/27	0.351028949226791	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.409538761599519	1		578	678	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370910	55370910	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022844-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	138	713	1	ENST00000297316.4:c.212C>A	p.Pro71Gln	p.P71Q	ENST00000297316	NM_022454.3	71	cCg/cAg	1/2	0.409538761599519	3	FACETS	0.867	0.788	0.949	0.433	0.394	0.475	CLONAL	1	TRUE	1	0.409538761599519	3		714	937	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401195	139401195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372348365	NA	P-0022844-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	179	667	0	ENST00000277541.6:c.3874C>T	p.His1292Tyr	p.H1292Y	ENST00000277541	NM_017617.3	1292	Cac/Tac	23/34	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.409538761599519	2		667	764	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	51	1098	0	ENST00000269305.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	336	Gag/Tag	10/11	1	2	FACETS	0.602	0.51	0.704	0.602	0.51	0.704	SUBCLONAL	1	TRUE	1	0.17	2		1098	997	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380276	+	missense_variant	Missense_Mutation	DNP	TT	TT	CA	novel	NA	P-0022883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	61	891	3	ENST00000311936.3:c.182_183delinsTG	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAA/cTG	3/5	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.17	2		894	701	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	74	766	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.948	1			1	INDETERMINATE	1	TRUE	NA	0.632736152144612	2		766	211	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0022890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	238	621	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.252619467393114	4	FACETS	0.933	0.876	0.991	0.933	0.876	0.991	INDETERMINATE	2	TRUE	2	0.632736152144612	4		621	658	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610104	81610104	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	282	597	0	ENST00000298171.2:c.1702A>G	p.Ile568Val	p.I568V	ENST00000298171	NM_000369.2	568	Atc/Gtc	10/10	0.500801559281112	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	2	0.632736152144612	4		597	619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0022908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	832	1096	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.879565396407606	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.879565396407606	2		1097	924	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0022908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	158	388	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.879565396407606	2		389	357	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150505	157150505	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1203546101	NA	P-0022908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	39	657	0	ENST00000346085.5:c.1687C>T	p.Gln563Ter	p.Q563*	ENST00000346085	NM_020732.3	563	Cag/Tag	2/20	1	2	FACETS	0.165	0.136	0.197	0.165	0.136	0.197	SUBCLONAL	1	TRUE	1	0.879565396407606	2		657	539	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939214	76939214	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	399	677	0	ENST00000373344.5:c.1534del	p.Asp512IlefsTer2	p.D512Ifs*2	ENST00000373344	NM_000489.3	512	Gat/at	9/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.879565396407606	1		677	454	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061156	38061192	+	protein_altering_variant	In_Frame_Del	DEL	CCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGA	CCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGA	GCCGGCG	novel	NA	P-0022911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	40	754	3	ENST00000250448.2:c.797_833delinsCGCCGGC	p.Phe266_Gly278delinsSerProAla	p.F266_G278delinsSPA	ENST00000250448	NM_004496.3	266	tTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGc/tCGCCGGCc	2/2	1	2	FACETS	0.966	0.802	1	0.966	0.802	1	CLONAL	1	TRUE	1	0.15	2		757	552	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822242	72822242	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	45	1223	0	ENST00000268489.5:c.9933del	p.Phe3311LeufsTer42	p.F3311Lfs*42	ENST00000268489	NM_006885.3	3311	ttT/tt	10/10	1	2	FACETS	0.676	0.566	0.798	0.676	0.566	0.798	SUBCLONAL	1	TRUE	1	0.15	2		1223	888	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	88	766	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.607774410697067	2		766	261	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs104886003	NA	P-0022918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	28	922	0	ENST00000263967.3:c.1633G>C	p.Glu545Gln	p.E545Q	ENST00000263967	NM_006218.2	545	Gag/Cag	10/21	1	2	FACETS	0.182	0.145	0.225	0.182	0.145	0.225	SUBCLONAL	1	TRUE	1	0.607774410697067	2		922	505	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665752	29665755	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1555535032	NA	P-0022918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	89	573	0	ENST00000356175.3:c.6789_6792del	p.Tyr2264ThrfsTer5	p.Y2264Tfs*5	ENST00000356175	NM_000267.3	2263	ACTTac/ac	45/57	0.603080735379871	1	FACETS	0.962	0.871	1	0.962	0.871	1	CLONAL	1	TRUE	0	0.607774410697067	1		573	212	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034879	42034879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	184	741	0	ENST00000219905.7:c.4721C>T	p.Pro1574Leu	p.P1574L	ENST00000219905	NM_001164273.1	1574	cCa/cTa	15/24	0.194596092578702	1	FACETS	0.825	0.768	0.883	0.825	0.768	0.883	INDETERMINATE	1	TRUE	0	0.607774410697067	1		741	511	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103513953	103513953	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	35	611	0	ENST00000355739.4:c.769C>T	p.Gln257Ter	p.Q257*	ENST00000355739	NM_000123.3	257	Caa/Taa	7/15	0.424398473134315	1	FACETS	0.238	0.195	0.286	0.238	0.195	0.286	SUBCLONAL	1	TRUE	0	0.607774410697067	1		611	337	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412283	139412285	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	novel	NA	P-0022918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	192	1220	0	ENST00000277541.6:c.1360_1362del	p.Asn454del	p.N454del	ENST00000277541	NM_017617.3	454	AAC/-	8/34	0.607774410697067	1	FACETS	0.962	0.9	1	0.962	0.9	1	CLONAL	1	TRUE	0	0.607774410697067	1		1220	457	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0022921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	380	840	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.296470244294632	3	FACETS	0.896	0.853	0.939			1	INDETERMINATE	2	TRUE	NA	0.540388095346359	3		840	997	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0022921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	105	501	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.936	0.845	1	0.936	0.845	1	CLONAL	1	TRUE	1	0.540388095346359	2		501	415	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0022921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	106	427	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.996	0.9	1	0.996	0.9	1	CLONAL	1	TRUE	1	0.540388095346359	2		427	394	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440373	52440373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	159	691	0	ENST00000460680.1:c.679C>T	p.Arg227Cys	p.R227C	ENST00000460680	NM_004656.3	227	Cgc/Tgc	9/17	1	2	FACETS	0.921	0.847	0.997	0.921	0.847	0.997	CLONAL	1	TRUE	1	0.540388095346359	2		691	639	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513309	44513309	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568949835	NA	P-0022921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	91	1006	0	ENST00000291552.4:c.626G>A	p.Arg209His	p.R209H	ENST00000291552	NM_006758.2	209	cGt/cAt	8/8	1	2	FACETS	0.341	0.302	0.383	0.341	0.302	0.383	SUBCLONAL	1	TRUE	1	0.540388095346359	2		1006	987	SUCCESS
APC	324	MSKCC	GRCh37	5	112174119	112174119	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1554084512	NA	P-0022921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	113	484	1	ENST00000257430.4:c.2828C>A	p.Ser943Ter	p.S943*	ENST00000257430	NM_000038.5	943	tCa/tAa	16/16	1	2	FACETS	0.955	0.865	1	0.955	0.865	1	CLONAL	1	TRUE	1	0.540388095346359	2		485	438	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679418	29679418	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	130	540	0	ENST00000356175.3:c.7538C>G	p.Thr2513Ser	p.T2513S	ENST00000356175	NM_000267.3	2513	aCt/aGt	50/57	1	2	FACETS	0.88	0.801	0.961	0.88	0.801	0.961	CLONAL	1	TRUE	1	0.540388095346359	2		540	547	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598227	28598227	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	259	1047	1	ENST00000253063.3:c.199C>A	p.Leu67Met	p.L67M	ENST00000253063	NM_031459.4	67	Ctg/Atg	3/10	1	2	FACETS	0.985	0.924	1	0.985	0.924	1	CLONAL	1	TRUE	1	0.540388095346359	2		1048	973	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358699	67358699	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0022921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	221	481	0	ENST00000327367.4:c.206+1G>A		p.X69_splice	ENST00000327367	NM_005902.3	69			0.522499672022351	2	FACETS	0.921	0.869	0.973	0.921	0.869	0.973	CLONAL	2	TRUE	0	0.540388095346359	2		481	444	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374908	45374908	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs797044882	NA	P-0022921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	409	825	0	ENST00000262160.6:c.935G>C	p.Cys312Ser	p.C312S	ENST00000262160	NM_005901.5	312	tGc/tCc	8/11	0.530167565150356	2	FACETS	0.983	0.943	1	0.983	0.943	1	CLONAL	2	TRUE	0	0.540388095346359	2		825	770	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942771	44942773	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs398122829	NA	P-0022921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	472	463	0	ENST00000377967.4:c.3354_3356del	p.Leu1119del	p.L1119del	ENST00000377967	NM_021140.2	1117	aaTCTt/aat	23/29	0.540077218956837	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.540388095346359	2		463	731	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	84	766	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.467802602071791	2		766	317	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0022924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	141	755	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.467802602071791	2		755	600	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797278	42797278	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs968289754	NA	P-0022924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	27	937	1	ENST00000575354.2:c.3640C>T	p.Arg1214Ter	p.R1214*	ENST00000575354	NM_015125.3	1214	Cga/Tga	15/20	0.467802602071791	1	FACETS	0.203	0.161	0.251	0.203	0.161	0.251	SUBCLONAL	1	TRUE	0	0.467802602071791	1		938	435	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434596	99434596	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs757968524	NA	P-0022924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	135	710	0	ENST00000268035.6:c.683A>G	p.Asn228Ser	p.N228S	ENST00000268035	NM_000875.3	228	aAt/aGt	3/21	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.467802602071791	2		710	532	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608359	43608359	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	61	1171	0	ENST00000355710.3:c.1707C>G	p.His569Gln	p.H569Q	ENST00000355710	NM_020975.4	569	caC/caG	9/20	1	2	FACETS	0.31	0.267	0.358	0.31	0.267	0.358	SUBCLONAL	1	TRUE	1	0.467802602071791	2		1171	840	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796496	42796508	+	frameshift_variant	Frame_Shift_Del	DEL	GTACCAGCCCTGC	GTACCAGCCCTGC	-	novel	NA	P-0022924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	36	1056	0	ENST00000575354.2:c.3055_3067del	p.Thr1019ProfsTer16	p.T1019Pfs*16	ENST00000575354	NM_015125.3	1018	gGTACCAGCCCTGCg/gg	13/20	0.467802602071791	1	FACETS	0.205	0.168	0.246	0.205	0.168	0.246	SUBCLONAL	1	TRUE	0	0.467802602071791	1		1056	576	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0022931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	401	604	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.321247382919808	6	FACETS	0.942	0.9	0.983			1	CLONAL	5	TRUE	NA	0.321247382919808	6		604	871	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577064	7577064	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0022931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	205	789	1	ENST00000269305.4:c.874A>T	p.Lys292Ter	p.K292*	ENST00000269305	NM_001126112.2	292	Aaa/Taa	8/11	0.270830156095639	2	FACETS	0.88	0.819	0.943	0.88	0.819	0.943	CLONAL	2	TRUE	0	0.321247382919808	2		790	725	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366921	40366921	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	47	687	0	ENST00000397332.2:c.276G>T	p.Glu92Asp	p.E92D	ENST00000397332	NM_001033082.2	92	gaG/gaT	2/3	0.203392707289595	2	FACETS	0.563	0.475	0.66	0.281	0.237	0.33	SUBCLONAL	1	TRUE	0	0.321247382919808	2		687	520	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158626939	158626939	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	51	634	2	ENST00000263640.3:c.731C>A	p.Ser244Ter	p.S244*	ENST00000263640	NM_001105.4	244	tCa/tAa	7/11	1	2	FACETS	0.47	0.398	0.548	0.47	0.398	0.548	SUBCLONAL	1	TRUE	1	0.321247382919808	2		636	676	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	257	460	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.256454925219716	5	FACETS	0.846	0.799	0.894	0.846	0.799	0.894	INDETERMINATE	3	TRUE	2	0.704571439053665	5		460	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0022967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	395	798	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.704571439053665	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.704571439053665	1		799	631	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164602	36164617	+	frameshift_variant	Frame_Shift_Del	DEL	GCGAGCGCTCGCCGCC	GCGAGCGCTCGCCGCC	CT	novel	NA	P-0022967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	855	608	3	ENST00000300305.3:c.1258_1273delinsAG	p.Gly420SerfsTer175	p.G420Sfs*175	ENST00000300305		420	GGCGGCGAGCGCTCGCcg/AGcg	8/8	0.704571439053665	3	FACETS	1	0.998	1	1	0.998	1	CLONAL	3	TRUE	0	0.704571439053665	3		611	992	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027121	71027121	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	211	537	0	ENST00000318789.4:c.1206C>G	p.Ser402Arg	p.S402R	ENST00000318789	NM_032682.5	402	agC/agG	15/21	0.326964227392469	3	FACETS	1	0.984	1	0.585	0.546	0.626	INDETERMINATE	1	TRUE	1	0.704571439053665	3		537	692	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282583	1282583	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1311034283	NA	P-0022967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	98	678	1	ENST00000310581.5:c.1730G>A	p.Arg577Gln	p.R577Q	ENST00000310581	NM_198253.2	577	cGg/cAg	3/16	NA	2	FACETS	0.328	0.292	0.367			1	INDETERMINATE	1	TRUE	NA	0.704571439053665	2		679	847	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851369	151851369	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	205	557	0	ENST00000262189.6:c.12122del	p.Pro4041LeufsTer42	p.P4041Lfs*42	ENST00000262189	NM_170606.2	4041	cCt/ct	47/59	0.326964227392469	3	FACETS	1	0.977	1	0.557	0.519	0.597	INDETERMINATE	1	TRUE	1	0.704571439053665	3		557	706	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0022971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	35	757	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.919	0.753	1	0.919	0.753	1	CLONAL	1	TRUE	1	0.16	2		758	476	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0022971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	19	504	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.705	0.534	0.905	0.705	0.534	0.905	CLONAL	1	TRUE	1	0.16	2		504	337	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584513	48584514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs377767334	NA	P-0022971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	35	474	0	ENST00000342988.3:c.692dup	p.Ser232GlnfsTer3	p.S232Qfs*3	ENST00000342988	NM_005359.5	229	ctg/ctGg	6/12	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.16	2		474	369	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0022971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	34	692	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.866	0.707	1	0.866	0.707	1	CLONAL	1	TRUE	1	0.16	2		692	491	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988357	41988357	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	23	682	0	ENST00000219905.7:c.1150del	p.Glu384AsnfsTer3	p.E384Nfs*3	ENST00000219905	NM_001164273.1	383	gaG/ga	3/24	1	2	FACETS	0.639	0.497	0.804	0.639	0.497	0.804	SUBCLONAL	1	TRUE	1	0.16	2		682	450	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641610	23641610	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs753012991	NA	P-0022971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	43	710	0	ENST00000261584.4:c.1865T>C	p.Leu622Pro	p.L622P	ENST00000261584	NM_024675.3	622	cTt/cCt	5/13	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.16	2		710	516	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512411	38512411	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	31	797	3	ENST00000254066.5:c.1322C>T	p.Pro441Leu	p.P441L	ENST00000254066	NM_000964.3	441	cCa/cTa	9/9	1	2	FACETS	0.676	0.546	0.825	0.676	0.546	0.825	SUBCLONAL	1	TRUE	1	0.16	2		800	573	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0022974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	58	421	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.162403145823983	3	FACETS	1	0.911	1	0.538	0.464	0.617	INDETERMINATE	1	TRUE	1	0.33916897655174	3		421	372	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167804	56167805	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0022974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	77	569	0	ENST00000399503.3:c.1370_1371del	p.Thr457SerfsTer3	p.T457Sfs*3	ENST00000399503	NM_005921.1	457	ACa/a	7/20	1	2	FACETS	0.897	0.79	1	0.897	0.79	1	CLONAL	1	TRUE	1	0.33916897655174	2		569	506	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720649	89720649	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs587782455	NA	P-0022974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	45	283	0	ENST00000371953.3:c.802-2A>G		p.X268_splice	ENST00000371953	NM_000314.4	268			1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.33916897655174	2		283	238	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176991	56177009	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTTGGCCGCCTTTGTCT	TTCTTGGCCGCCTTTGTCT	-	novel	NA	P-0022974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	69	529	0	ENST00000399503.3:c.2262_2280del	p.Leu755Ter	p.L755*	ENST00000399503	NM_005921.1	754	cTTCTTGGCCGCCTTTGTCTt/ct	13/20	1	2	FACETS	0.829	0.723	0.942	0.829	0.723	0.942	CLONAL	1	TRUE	1	0.33916897655174	2		529	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0022984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	489	769	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.605083706658754	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.605083706658754	2		769	776	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519922	NA	P-0022984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	205	888	1	ENST00000397062.3:c.235G>A	p.Glu79Lys	p.E79K	ENST00000397062	NM_006164.4	79	Gag/Aag	2/5	0.520196019853942	5	FACETS	1	0.978	1	0.284	0.263	0.306	CLONAL	1	TRUE	1	0.605083706658754	5		889	1137	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519704	176519704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143108014	NA	P-0022984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	211	838	1	ENST00000292408.4:c.976G>A	p.Glu326Lys	p.E326K	ENST00000292408	NM_213647.1	326	Gag/Aag	8/18	0.332828891721936	3	FACETS	1	0.971	1	0.54	0.502	0.579	INDETERMINATE	1	TRUE	1	0.605083706658754	3		839	841	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023405	27023405	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	252	636	0	ENST00000324856.7:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000324856	NM_006015.4	171	Caa/Taa	1/20	0.496832553934886	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.605083706658754	1		636	560	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444127	49444127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	487	870	1	ENST00000301067.7:c.3244G>T	p.Glu1082Ter	p.E1082*	ENST00000301067	NM_003482.3	1082	Gaa/Taa	11/54	0.454279753354045	3	FACETS	1	0.995	1	0.817	0.788	0.846	CLONAL	2	TRUE	0	0.605083706658754	3		871	855	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609982	81609982	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	88	373	0	ENST00000298171.2:c.1580T>A	p.Met527Lys	p.M527K	ENST00000298171	NM_000369.2	527	aTg/aAg	10/10	0.595101356348515	3	FACETS	0.957	0.853	1	0.319	0.284	0.356	CLONAL	1	TRUE	0	0.605083706658754	3		373	396	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639233	3639233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759045352	NA	P-0022984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	270	956	0	ENST00000294008.3:c.4406C>T	p.Ser1469Phe	p.S1469F	ENST00000294008	NM_032444.2	1469	tCc/tTc	12/15	0.171463596785867	3	FACETS	1	0.991	1	0.641	0.602	0.68	INDETERMINATE	1	TRUE	1	0.605083706658754	3		956	907	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499367	89499368	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0022984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	752	520	2	ENST00000336596.2:c.2537_2538delinsAA	p.Pro846Gln	p.P846Q	ENST00000336596	NM_005233.5	846	cCC/cAA	15/17	0.605083706658754	7	FACETS	1	0.993	1	0.881	0.858	0.905	CLONAL	5	TRUE	1	0.605083706658754	7		522	1181	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151947020	151947021	+	missense_variant	Missense_Mutation	DNP	TC	TC	GT	novel	NA	P-0022984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	15	692	2	ENST00000262189.6:c.1753_1754delinsAC	p.Glu585Thr	p.E585T	ENST00000262189	NM_170606.2	585	GAa/ACa	13/59	0.515660286344504	3	FACETS	0.248	0.181	0.329	0.124	0.09	0.165	SUBCLONAL	1	TRUE	1	0.605083706658754	3		694	260	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69050700	69050701	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0022984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	128	767	2	ENST00000288368.4:c.4035_4036delinsTT	p.Leu1345_Glu1346delinsPheTer	p.L1345_E1346delinsF*	ENST00000288368	NM_024870.2	1345	ttGGaa/ttTTaa	33/40	0.57114531902821	6	FACETS	0.953	0.876	1	0.715	0.657	0.774	CLONAL	3	TRUE	2	0.605083706658754	6		769	327	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	32	339	0	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.905	0.734	1	0.905	0.734	1	CLONAL	1	TRUE	1	0.14	2		339	505	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023904	27023904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1232964733	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	14	144	0	ENST00000324856.7:c.1015del	p.Ala339LeufsTer24	p.A339Lfs*24	ENST00000324856	NM_006015.4	337	tGg/tg	1/20	1	2	FACETS	0.791	0.571	1	0.791	0.571	1	CLONAL	1	TRUE	1	0.14	2		144	253	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	43	483	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.81	0.676	0.96	0.81	0.676	0.96	CLONAL	1	TRUE	1	0.14	2		484	758	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	47	500	4	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.14	2		504	628	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149728	202149728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	58	661	0	ENST00000358485.4:c.1173del	p.Ile392SerfsTer4	p.I392Sfs*4	ENST00000358485	NM_001080125.1	390	gCc/gc	8/9	1	2	FACETS	0.953	0.817	1	0.953	0.817	1	CLONAL	1	TRUE	1	0.14	2		661	869	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513234	44513234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780011533	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	49	384	1	ENST00000291552.4:c.701G>A	p.Arg234His	p.R234H	ENST00000291552	NM_006758.2	234	cGt/cAt	8/8	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.14	2		385	604	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	44	543	2	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.898	0.751	1	0.898	0.751	1	CLONAL	1	TRUE	1	0.14	2		545	700	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874637	35874637	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	56	450	4	ENST00000303115.3:c.799del	p.Arg267GlyfsTer28	p.R267Gfs*28	ENST00000303115	NM_002185.3	265	Aaa/aa	6/8	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.14	2		454	694	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310208	91310208	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs747341586	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	46	553	4	ENST00000355112.3:c.2268del	p.Asp757ThrfsTer4	p.D757Tfs*4	ENST00000355112	NM_000057.2	754	tcA/tc	10/22	1	2	FACETS	0.985	0.828	1	0.985	0.828	1	CLONAL	1	TRUE	1	0.14	2		557	667	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354353	354353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142097791	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	66	703	3	ENST00000262320.3:c.1205C>T	p.Thr402Met	p.T402M	ENST00000262320	NM_003502.3	402	aCg/aTg	5/11	1	2	FACETS	0.881	0.762	1	0.881	0.762	1	CLONAL	1	TRUE	1	0.14	2		706	1070	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156936	106156936	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs763386429	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	37	412	0	ENST00000380013.4:c.1842del	p.Leu615SerfsTer24	p.L615Sfs*24	ENST00000380013	NM_001127208.2	613	Ggg/gg	3/11	1	2	FACETS	0.921	0.758	1	0.921	0.758	1	CLONAL	1	TRUE	1	0.14	2		412	574	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167562	24167562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769023941	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	57	621	1	ENST00000263121.7:c.946C>T	p.Arg316Trp	p.R316W	ENST00000263121	NM_003073.3	316	Cgg/Tgg	7/9	1	2	FACETS	0.935	0.8	1	0.935	0.8	1	CLONAL	1	TRUE	1	0.14	2		622	871	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905579	50905579	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	81	875	0	ENST00000440232.2:c.707T>C	p.Leu236Pro	p.L236P	ENST00000440232	NM_002691.3	236	cTg/cCg	6/27	1	2	FACETS	0.963	0.845	1	0.963	0.845	1	CLONAL	1	TRUE	1	0.14	2		875	1202	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78422338	78422338	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1244295456	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	46	433	0	ENST00000370768.2:c.1624G>A	p.Ala542Thr	p.A542T	ENST00000370768	NM_003902.3	542	Gct/Act	17/20	1	2	FACETS	0.944	0.793	1	0.944	0.793	1	CLONAL	1	TRUE	1	0.14	2		433	696	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599233	28599234	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	74	759	1	ENST00000253063.3:c.685dup	p.Gln229ProfsTer7	p.Q229Pfs*7	ENST00000253063	NM_031459.4	227	gcc/gCcc	5/10	1	2	FACETS	0.976	0.852	1	0.976	0.852	1	CLONAL	1	TRUE	1	0.14	2		760	1083	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273209	115273209	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs990081919	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	51	565	0	ENST00000438362.2:c.1249C>T	p.Arg417Cys	p.R417C	ENST00000438362	NM_001242891.1	417	Cgt/Tgt	11/20	1	2	FACETS	0.819	0.694	0.957	0.819	0.694	0.957	CLONAL	1	TRUE	1	0.14	2		565	890	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998275	100998275	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	28	290	0	ENST00000325455.5:c.1527del	p.Ala510ArgfsTer36	p.A510Rfs*36	ENST00000325455	NM_001202474.3	509	ccC/cc	1/8	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.14	2		290	370	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420234	49420234	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	65	713	0	ENST00000301067.7:c.15515del	p.Gly5172GlufsTer71	p.G5172Efs*71	ENST00000301067	NM_003482.3	5172	gGa/ga	48/54	1	2	FACETS	0.857	0.741	0.985	0.857	0.741	0.985	CLONAL	1	TRUE	1	0.14	2		713	1083	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481915	56481915	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	64	735	0	ENST00000267101.3:c.843G>C	p.Gln281His	p.Q281H	ENST00000267101	NM_001982.3	281	caG/caC	7/28	1	2	FACETS	0.816	0.704	0.938	0.816	0.704	0.938	CLONAL	1	TRUE	1	0.14	2		735	1121	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856119	111856119	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	104	584	1	ENST00000341259.2:c.170C>A	p.Pro57Gln	p.P57Q	ENST00000341259	NM_005475.2	57	cCg/cAg	2/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.14	2		585	1048	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218312	133218312	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs915396081	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	52	717	0	ENST00000320574.5:c.5299G>A	p.Glu1767Lys	p.E1767K	ENST00000320574	NM_006231.2	1767	Gag/Aag	39/49	1	2	FACETS	0.757	0.642	0.884	0.757	0.642	0.884	SUBCLONAL	1	TRUE	1	0.14	2		717	981	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436791	110436793	+	inframe_deletion	In_Frame_Del	DEL	CCG	CCG	-	rs769193882	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	74	831	3	ENST00000375856.3:c.1608_1610del	p.Gly537del	p.G537del	ENST00000375856	NM_003749.2	536	ggCGGt/ggt	1/2	1	2	FACETS	0.95	0.829	1	0.95	0.829	1	CLONAL	1	TRUE	1	0.14	2		834	1113	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059410	42059410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	37	423	0	ENST00000219905.7:c.9130C>T	p.Pro3044Ser	p.P3044S	ENST00000219905	NM_001164273.1	3044	Cct/Tct	24/24	1	2	FACETS	0.764	0.628	0.917	0.764	0.628	0.917	CLONAL	1	TRUE	1	0.14	2		423	692	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619133	37619133	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	51	602	0	ENST00000447079.4:c.809C>T	p.Ser270Leu	p.S270L	ENST00000447079	NM_015083.1	270	tCg/tTg	1/14	1	2	FACETS	0.901	0.763	1	0.901	0.763	1	CLONAL	1	TRUE	1	0.14	2		602	809	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650797	37650797	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	78	687	0	ENST00000447079.4:c.2269A>G	p.Lys757Glu	p.K757E	ENST00000447079	NM_015083.1	757	Aag/Gag	5/14	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.14	2		687	1054	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271812	15271813	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	77	780	0	ENST00000263388.2:c.6626dup	p.Pro2210AlafsTer32	p.P2210Afs*32	ENST00000263388	NM_000435.2	2209	ccg/ccCg	33/33	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.14	2		780	1083	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212375	36212375	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	62	772	1	ENST00000222270.7:c.2126C>A	p.Pro709His	p.P709H	ENST00000222270	NM_014727.1	709	cCt/cAt	3/37	1	2	FACETS	0.81	0.697	0.933	0.81	0.697	0.933	CLONAL	1	TRUE	1	0.14	2		773	1094	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216122	36216122	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	33	507	1	ENST00000222270.7:c.3530A>G	p.Glu1177Gly	p.E1177G	ENST00000222270	NM_014727.1	1177	gAg/gGg	11/37	1	2	FACETS	0.748	0.608	0.908	0.748	0.608	0.908	CLONAL	1	TRUE	1	0.14	2		508	630	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218836	36218836	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	66	755	1	ENST00000222270.7:c.4447G>T	p.Glu1483Ter	p.E1483*	ENST00000222270	NM_014727.1	1483	Gag/Tag	18/37	1	2	FACETS	0.803	0.695	0.922	0.803	0.695	0.922	CLONAL	1	TRUE	1	0.14	2		756	1174	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204618	128204618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	57	783	1	ENST00000341105.2:c.823G>A	p.Ala275Thr	p.A275T	ENST00000341105	NM_032638.4	275	Gcc/Acc	3/6	1	2	FACETS	0.869	0.743	1	0.869	0.743	1	CLONAL	1	TRUE	1	0.14	2		784	937	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665403	138665403	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	62	783	0	ENST00000330315.3:c.162G>T	p.Lys54Asn	p.K54N	ENST00000330315	NM_023067.3	54	aaG/aaT	1/1	1	2	FACETS	0.856	0.737	0.986	0.856	0.737	0.986	CLONAL	1	TRUE	1	0.14	2		783	1035	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294138	1294138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774657340	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	77	892	1	ENST00000310581.5:c.863C>T	p.Ala288Val	p.A288V	ENST00000310581	NM_198253.2	288	gCg/gTg	2/16	1	2	FACETS	0.935	0.818	1	0.935	0.818	1	CLONAL	1	TRUE	1	0.14	2		893	1177	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206869	162206869	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	45	510	0	ENST00000366898.1:c.806T>C	p.Val269Ala	p.V269A	ENST00000366898	NM_004562.2	269	gTg/gCg	7/12	1	2	FACETS	0.741	0.621	0.876	0.741	0.621	0.876	SUBCLONAL	1	TRUE	1	0.14	2		510	867	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945650	151945650	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	60	900	0	ENST00000262189.6:c.1869del	p.Asp624IlefsTer5	p.D624Ifs*5	ENST00000262189	NM_170606.2	623	gtT/gt	14/59	1	2	FACETS	0.737	0.632	0.852	0.737	0.632	0.852	SUBCLONAL	1	TRUE	1	0.14	2		900	1163	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740546	145740546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746417965	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	49	660	1	ENST00000428558.2:c.1471C>T	p.Arg491Trp	p.R491W	ENST00000428558	NM_004260.3	491	Cgg/Tgg	8/22	1	2	FACETS	0.789	0.666	0.925	0.789	0.666	0.925	CLONAL	1	TRUE	1	0.14	2		661	887	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966566	36966566	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	69	685	0	ENST00000358127.4:c.760G>T	p.Glu254Ter	p.E254*	ENST00000358127	NM_001280556.1	254	Gag/Tag	6/10	1	2	FACETS	0.976	0.848	1	0.976	0.848	1	CLONAL	1	TRUE	1	0.14	2		685	1010	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732813	44732813	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	51	667	0	ENST00000377967.4:c.16G>A	p.Val6Met	p.V6M	ENST00000377967	NM_021140.2	6	Gtg/Atg	1/29	1	2	FACETS	0.788	0.668	0.922	0.788	0.668	0.922	CLONAL	1	TRUE	1	0.14	2		667	924	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413565	32413565	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121907903	NA	P-0023008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	14	574	0	ENST00000332351.3:c.1385G>A	p.Arg462Gln	p.R462Q	ENST00000332351	NM_024426.4	462	cGg/cAg	9/10	1	2	FACETS	0.29	0.209	0.39	0.29	0.209	0.39	SUBCLONAL	1	FALSE	1	0.246540709083169	2		574	391	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273974	10273974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773569899	NA	P-0023008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	81	1013	2	ENST00000330684.3:c.295G>A	p.Val99Met	p.V99M	ENST00000330684	NM_001134407.1	99	Gtg/Atg	2/13	1	2	FACETS	0.913	0.804	1	0.913	0.804	1	CLONAL	1	FALSE	1	0.246540709083169	2		1015	720	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	163	720	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.954	0.876	1	0.954	0.876	1	CLONAL	1	TRUE	1	0.418446840355652	2		721	817	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781504	NA	P-0023011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	235	821	2	ENST00000269305.4:c.314G>A	p.Gly105Asp	p.G105D	ENST00000269305	NM_001126112.2	105	gGc/gAc	4/11	0.418446840355652	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.418446840355652	1		823	768	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	91	425	0	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	0.418446840355652	1	FACETS	0.805	0.719	0.896	0.805	0.719	0.896	CLONAL	1	TRUE	0	0.418446840355652	1		425	427	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124202	2124202	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs796053511	NA	P-0023011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	132	652	0	ENST00000219476.3:c.2357G>A	p.Arg786His	p.R786H	ENST00000219476	NM_000548.3	786	cGc/cAc	22/42	0.418446840355652	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.418446840355652	1		652	486	SUCCESS
APC	324	MSKCC	GRCh37	5	112155044	112155044	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	C	rs863225311	NA	P-0023011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	240	458	0	ENST00000257430.4:c.1312+3A>C		p.X438_splice	ENST00000257430	NM_000038.5	438			0.412252494689656	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.418446840355652	2		458	541	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519721	137519721	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0023015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	114	365	0	ENST00000367739.4:c.917C>G	p.Ser306Ter	p.S306*	ENST00000367739	NM_000416.2	306	tCa/tGa	7/7	0.605316679897756	1	FACETS	0.837	0.763	0.911	0.837	0.763	0.911	CLONAL	1	TRUE	0	0.605316679897756	1		365	314	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31431733	31431733	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	235	649	0	ENST00000344624.3:c.3095G>C	p.Arg1032Thr	p.R1032T	ENST00000344624		1032	aGa/aCa	23/33	1	2	FACETS	0.947	0.886	1	0.947	0.886	1	CLONAL	1	TRUE	1	0.605316679897756	2		649	820	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106612	27106612	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	271	709	0	ENST00000324856.7:c.6223C>G	p.Pro2075Ala	p.P2075A	ENST00000324856	NM_006015.4	2075	Cca/Gca	20/20	0.602668631570874	3	FACETS	1	0.942	1	0.502	0.471	0.535	CLONAL	1	TRUE	1	0.605316679897756	3		709	1161	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568503	41568503	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	202	485	0	ENST00000263253.7:c.4453G>A	p.Asp1485Asn	p.D1485N	ENST00000263253	NM_001429.3	1485	Gat/Aat	28/31	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.605316679897756	2		485	650	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49724666	49724666	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	235	506	1	ENST00000449682.2:c.523G>T	p.Asp175Tyr	p.D175Y	ENST00000449682	NM_020998.3	175	Gat/Tat	5/18	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.605316679897756	2		507	653	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188354	142188354	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	666	641	0	ENST00000350721.4:c.6377T>G	p.Ile2126Ser	p.I2126S	ENST00000350721	NM_001184.3	2126	aTc/aGc	38/47	0.605316679897756	4	FACETS	0.966	0.936	0.996	0.966	0.936	0.996	CLONAL	3	TRUE	1	0.605316679897756	4		641	1219	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317089	87317089	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	106	527	0	ENST00000277120.3:c.228G>C	p.Gln76His	p.Q76H	ENST00000277120		76	caG/caC	3/19	1	2	FACETS	0.461	0.413	0.512	0.461	0.413	0.512	SUBCLONAL	1	TRUE	1	0.605316679897756	2		527	760	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106812	27106815	+	frameshift_variant	Frame_Shift_Del	DEL	CAGC	CAGC	AGT	novel	NA	P-0023015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	274	680	1	ENST00000324856.7:c.6423_6426delinsAGT	p.Phe2141LeufsTer59	p.F2141Lfs*59	ENST00000324856	NM_006015.4	2141	ttCAGC/ttAGT	20/20	0.602668631570874	3	FACETS	1	0.951	1	0.508	0.476	0.54	CLONAL	1	TRUE	1	0.605316679897756	3		681	1161	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0023048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	115	460	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.98	0.887	1	0.98	0.887	1	CLONAL	1	TRUE	1	0.487149769028463	2		460	482	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	246	1245	2	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.487149769028463	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.487149769028463	1		1247	680	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0023048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	170	796	0	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	1	2	FACETS	0.947	0.873	1	0.947	0.873	1	CLONAL	1	TRUE	1	0.487149769028463	2		796	737	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25462012	25462012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766564570	NA	P-0023048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	155	730	0	ENST00000264709.3:c.2395C>T	p.Pro799Ser	p.P799S	ENST00000264709	NM_175629.2	799	Ccc/Tcc	20/23	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.487149769028463	2		730	635	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932558	39932558	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	227	1155	2	ENST00000378444.4:c.2041C>T	p.Pro681Ser	p.P681S	ENST00000378444	NM_001123385.1	681	Cct/Tct	4/15	NA	2	FACETS	0.983	0.917	1			1	INDETERMINATE	1	TRUE	NA	0.487149769028463	2		1157	948	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	159	766	0				ENST00000310581	NM_198253.2	-/1132			0.319322054584155	1	FACETS	0.789	0.727	0.853	0.789	0.727	0.853	SUBCLONAL	1	FALSE	0	0.521845682870484	1		766	571	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0023058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1853	6699	1052	4	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.521845682870484	23	FACETS	1	0.998	1			1	CLONAL	19	FALSE	NA	0.521845682870484	23		1056	8552	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165662	118165662	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768091631	NA	P-0023058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	99	391	0	ENST00000369448.3:c.172C>T	p.Arg58Trp	p.R58W	ENST00000369448	NM_017709.3	58	Cgg/Tgg	2/2	1	2	FACETS	0.91	0.818	1	0.91	0.818	1	CLONAL	1	FALSE	1	0.521845682870484	2		391	417	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720823	89720823	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1114167654	NA	P-0023058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	197	596	0	ENST00000371953.3:c.974T>C	p.Leu325Pro	p.L325P	ENST00000371953	NM_000314.4	325	cTt/cCt	8/9	0.521845682870484	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	FALSE	0	0.521845682870484	1		596	552	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998998	11998998	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	122	446	0	ENST00000353533.5:c.500C>T	p.Ala167Val	p.A167V	ENST00000353533	NM_003010.3	167	gCa/gTa	4/11	1	2	FACETS	0.842	0.764	0.924	0.842	0.764	0.924	CLONAL	1	FALSE	1	0.521845682870484	2		446	555	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176496	123176496	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0023058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	146	189	0	ENST00000218089.9:c.462+1G>C		p.X154_splice	ENST00000218089	NM_001042749.1	154			1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	0	0.521845682870484	1		189	297	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0023071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	81	567	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	0.520519769092385	1	FACETS	0.423	0.373	0.476	0.423	0.373	0.476	SUBCLONAL	1	TRUE	0	0.520519769092385	1		567	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0023071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	185	444	1	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.520519769092385	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.520519769092385	1		445	415	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640428	3640428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	105	798	0	ENST00000294008.3:c.3211C>T	p.Pro1071Ser	p.P1071S	ENST00000294008	NM_032444.2	1071	Cca/Tca	12/15	0.353542380212664	0	FACETS	0.29	0.259	0.321			1	SUBCLONAL	1	TRUE	0	0.520519769092385	0		798	668	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249463	153249463	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	233	510	0	ENST00000281708.4:c.1315A>G	p.Thr439Ala	p.T439A	ENST00000281708	NM_033632.3	439	Aca/Gca	9/12	0.286119535035863	1	FACETS	0.814	0.761	0.868	0.814	0.761	0.868	INDETERMINATE	1	TRUE	0	0.520519769092385	1		510	814	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107191	27107191	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	249	522	0	ENST00000324856.7:c.6803del	p.Asn2268ThrfsTer14	p.N2268Tfs*14	ENST00000324856	NM_006015.4	2268	Aac/ac	20/20	0.377910669508823	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.520519769092385	1		522	673	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828047	72828048	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	144	835	0	ENST00000268489.5:c.8533dup	p.Thr2845AsnfsTer11	p.T2845Nfs*11	ENST00000268489	NM_006885.3	2845	acc/aAcc	9/10	0.474233585946865	1	FACETS	0.485	0.442	0.53	0.485	0.442	0.53	SUBCLONAL	1	TRUE	0	0.520519769092385	1		835	844	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268225	153268225	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0023071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	69	122	0	ENST00000281708.4:c.585-2A>G		p.X195_splice	ENST00000281708	NM_033632.3	195			0.286119535035863	1	FACETS	0.966	0.857	1	0.966	0.857	1	INDETERMINATE	1	TRUE	0	0.520519769092385	1		122	203	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591232	67591253	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAAAACTGTTTTTCAGGTGGTT	CAAAACTGTTTTTCAGGTGGTT	GAA	novel	NA	P-0023071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	70	342	1	ENST00000274335.5:c.1746-16_1751delinsGAA		p.X582_splice	ENST00000274335		582		13/15	0.344033181537419	1	FACETS	0.463	0.405	0.525	0.463	0.405	0.525	SUBCLONAL	1	TRUE	0	0.520519769092385	1		343	430	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	186	693	0	ENST00000206249.3:c.1610A>G	p.Tyr537Cys	p.Y537C	ENST00000206249	NM_000125.3	537	tAt/tGt	8/8	0.81889736375427	3	FACETS	0.962	0.892	1	0.481	0.446	0.517	CLONAL	1	TRUE	1	0.852651583183804	3		693	647	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0023091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	985	920	3	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.852651583183804	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.852651583183804	3		923	1079	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	186	680	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.781518867521629	4	FACETS	1	0.972	1	0.367	0.34	0.395	CLONAL	1	TRUE	1	0.852651583183804	4		680	734	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681095	37681095	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5699	302	569	1	ENST00000447079.4:c.3264G>T	p.Gln1088His	p.Q1088H	ENST00000447079	NM_015083.1	1088	caG/caT	12/14	0.852651583183804	32	FACETS	0.814	0.761	0.869			1	CLONAL	2	TRUE	NA	0.852651583183804	32		570	6001	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629094	86629094	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	145	400	0	ENST00000274376.6:c.839A>G	p.Asp280Gly	p.D280G	ENST00000274376	NM_002890.2	280	gAt/gGt	4/25	0.48624176918982	5	FACETS	1	0.956	1	0.7	0.647	0.754	INDETERMINATE	2	TRUE	2	0.852651583183804	5		400	369	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591109	+	missense_variant	Missense_Mutation	ONP	AAAC	AAAC	GAAG	novel	NA	P-0023091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	217	408	0	ENST00000274335.5:c.1699_1702delinsGAAG	p.Lys567_Pro568delinsGluAla	p.K567_P568delinsEA	ENST00000274335		567	AAACca/GAAGca	12/15	0.48624176918982	5	FACETS	0.934	0.882	0.986	0.934	0.882	0.986	INDETERMINATE	3	TRUE	2	0.852651583183804	5		408	414	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041923	14041923	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	32	380	0	ENST00000311895.7:c.2470G>A	p.Asp824Asn	p.D824N	ENST00000311895	NM_005236.2	824	Gat/Aat	11/11	1	2	FACETS	0.466	0.378	0.565	0.466	0.378	0.565	SUBCLONAL	1	TRUE	1	0.339157066489022	2		380	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578242	7578242	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882003	NA	P-0023102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	110	771	0	ENST00000269305.4:c.607G>T	p.Val203Leu	p.V203L	ENST00000269305	NM_001126112.2	203	Gtg/Ttg	6/11	0.339157066489022	1	FACETS	0.94	0.847	1	0.94	0.847	1	CLONAL	1	TRUE	0	0.339157066489022	1		771	573	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902419	1902420	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1324457447	NA	P-0023102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	170	778	0	ENST00000382891.5:c.40_41del	p.Ser14CysfsTer42	p.S14Cfs*42	ENST00000382891	NM_133335.3	13	cAG/c	2/22	0.339157066489022	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.339157066489022	1		778	609	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259516	+	missense_variant	Missense_Mutation	DNP	TG	TG	GT	rs1057519848	NA	P-0023102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	2465	723	0	ENST00000275493.2:c.2573_2574delinsGT	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTG/cGT	21/28	0.339157066489022	23	FACETS	0.987	0.977	0.998			1	CLONAL	22	TRUE	NA	0.339157066489022	23		723	3052	SUCCESS
APC	324	MSKCC	GRCh37	5	112154723	112154723	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775126020	NA	P-0023109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	77	695	1	ENST00000257430.4:c.994C>T	p.Arg332Ter	p.R332*	ENST00000257430	NM_000038.5	332	Cga/Tga	10/16	0.582914819481194	1	FACETS	0.828	0.739	0.92	0.828	0.739	0.92	CLONAL	1	TRUE	0	0.582914819481194	1		696	226	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs864622237	NA	P-0023109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	160	849	0	ENST00000269305.4:c.700T>G	p.Tyr234Asp	p.Y234D	ENST00000269305	NM_001126112.2	234	Tac/Gac	7/11	0.582914819481194	3	FACETS	0.974	0.895	1	0.487	0.447	0.528	CLONAL	1	TRUE	1	0.582914819481194	3		849	728	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0023109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	238	681	1	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.582914819481194	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	1	0.582914819481194	3		682	524	SUCCESS
APC	324	MSKCC	GRCh37	5	112175944	112175945	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0023109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	35	385	0	ENST00000257430.4:c.4655_4656del	p.Glu1552GlyfsTer6	p.E1552Gfs*6	ENST00000257430	NM_000038.5	1551	aaAGag/aaag	16/16	0.582914819481194	1	FACETS	0.66	0.551	0.776	0.66	0.551	0.776	SUBCLONAL	1	TRUE	0	0.582914819481194	1		385	129	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112769049	112769049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	241	738	0	ENST00000369452.4:c.1328G>A	p.Gly443Asp	p.G443D	ENST00000369452	NM_007373.3	443	gGt/gAt	7/9	0.582914819481194	3	FACETS	0.872	0.821	0.925	0.872	0.821	0.925	CLONAL	2	TRUE	1	0.582914819481194	3		738	612	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215722	133215724	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs1060500844	NA	P-0023109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	186	563	0	ENST00000320574.5:c.5539_5541del	p.Lys1847del	p.K1847del	ENST00000320574	NM_006231.2	1847	AAG/-	40/49	0.582914819481194	5	FACETS	0.993	0.923	1	0.662	0.615	0.711	CLONAL	2	TRUE	2	0.582914819481194	5		563	602	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210784	36210784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747042157	NA	P-0023109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	324	1004	3	ENST00000222270.7:c.535C>T	p.Arg179Trp	p.R179W	ENST00000222270	NM_014727.1	179	Cgg/Tgg	3/37	0.480547007524627	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	2	0.582914819481194	4		1007	710	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979543	2979543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148083162	NA	P-0023109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	175	682	1	ENST00000396946.4:c.704G>A	p.Arg235Gln	p.R235Q	ENST00000396946	NM_032415.4	235	cGg/cAg	6/25	0.520548235902674	6	FACETS	0.942	0.871	1	0.471	0.435	0.508	CLONAL	2	TRUE	2	0.582914819481194	6		683	690	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317094	87317094	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs771127404	NA	P-0023109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	89	648	0	ENST00000277120.3:c.233G>T	p.Arg78Met	p.R78M	ENST00000277120		78	aGg/aTg	3/19	NA	2	FACETS	0.763	0.681	0.85			1	INDETERMINATE	1	TRUE	NA	0.582914819481194	2		648	400	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437989	49437989	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370969225	NA	P-0023129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	184	755	0	ENST00000301067.7:c.5182G>A	p.Asp1728Asn	p.D1728N	ENST00000301067	NM_003482.3	1728	Gac/Aac	21/54	NA	2	FACETS	0.987	0.918	1			1	INDETERMINATE	1	TRUE	NA	0.691732417348433	2		755	539	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597613	28597613	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	181	707	1	ENST00000241453.7:c.2292T>A	p.Asp764Glu	p.D764E	ENST00000241453	NM_004119.2	764	gaT/gaA	19/24	0.691732417348433	1	FACETS	0.923	0.865	0.981	0.923	0.865	0.981	CLONAL	1	TRUE	0	0.691732417348433	1		708	371	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577493	7577497	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CCTGA	CCTGA	-	rs1567548832	NA	P-0023129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	182	760	1	ENST00000269305.4:c.782+2_782+6del		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.691732417348433	1	FACETS	0.935	0.877	0.994	0.935	0.877	0.994	CLONAL	1	TRUE	0	0.691732417348433	1		761	368	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291852	15291852	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	180	938	0	ENST00000263388.2:c.2914C>G	p.Leu972Val	p.L972V	ENST00000263388	NM_000435.2	972	Cta/Gta	18/33	1	2	FACETS	0.848	0.786	0.912	0.848	0.786	0.912	CLONAL	1	TRUE	1	0.691732417348433	2		938	614	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143022	30143022	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	217	864	1	ENST00000389048.3:c.504C>A	p.Phe168Leu	p.F168L	ENST00000389048	NM_004304.4	168	ttC/ttA	1/29	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.691732417348433	2		865	618	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821195	32821196	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CAGGCCCCCAGCCAGAGCACGGCCCAGCGGCT	novel	NA	P-0023129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	174	777	0	ENST00000354258.4:c.367_398dup	p.Cys133Ter	p.C133*	ENST00000354258	NM_000593.5	133	tgc/tgAGCCGCTGGGCCGTGCTCTGGCTGGGGGCCTGc	1/11	0.329399678804707	3	FACETS	0.82	0.755	0.886	0.41	0.377	0.443	INDETERMINATE	1	TRUE	1	0.691732417348433	3		777	826	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0023136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	134	505	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.964	0.886	1	0.964	0.886	1	CLONAL	1	TRUE	1	0.749650892967138	2		506	371	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742679	39742679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	133	466	3	ENST00000361337.2:c.1522C>T	p.Arg508Cys	p.R508C	ENST00000361337	NM_003286.2	508	Cgt/Tgt	15/21	1	2	FACETS	0.972	0.894	1	0.972	0.894	1	CLONAL	1	TRUE	1	0.749650892967138	2		469	365	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619333	23619333	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	96	438	0	ENST00000261584.4:c.3202G>A	p.Gly1068Arg	p.G1068R	ENST00000261584	NM_024675.3	1068	Ggg/Agg	12/13	1	2	FACETS	0.818	0.738	0.902	0.818	0.738	0.902	CLONAL	1	TRUE	1	0.749650892967138	2		438	313	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983275	149983275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	298	720	2	ENST00000253339.5:c.2983C>T	p.Arg995Cys	p.R995C	ENST00000253339		995	Cgc/Tgc	7/7	0.732555133647501	2	FACETS	0.986	0.951	1	0.986	0.951	1	CLONAL	2	TRUE	0	0.749650892967138	2		722	403	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55603353	55603353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	100	445	0	ENST00000288135.5:c.2709G>A	p.Met903Ile	p.M903I	ENST00000288135	NM_000222.2	903	atG/atA	20/21	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.749650892967138	2		445	259	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765672	41765672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	208	710	0	ENST00000301178.4:c.2548G>A	p.Asp850Asn	p.D850N	ENST00000301178	NM_021913.4	850	Gat/Aat	20/20	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.749650892967138	2		710	550	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2220182	2220182	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	224	843	0	ENST00000398665.3:c.2767C>T	p.His923Tyr	p.H923Y	ENST00000398665	NM_032482.2	923	Cac/Tac	23/28	1	2	FACETS	0.946	0.886	1	0.946	0.886	1	CLONAL	1	TRUE	1	0.749650892967138	2		843	632	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913236	39913236	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774089771	NA	P-0023136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	174	655	0	ENST00000378444.4:c.4879G>A	p.Asp1627Asn	p.D1627N	ENST00000378444	NM_001123385.1	1627	Gat/Aat	14/15	1	2	FACETS	0.967	0.898	1	0.967	0.898	1	CLONAL	1	TRUE	1	0.749650892967138	2		655	480	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444311	50444311	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778251001	NA	P-0023136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	94	332	0	ENST00000331340.3:c.241G>A	p.Asp81Asn	p.D81N	ENST00000331340	NM_006060.4	81	Gat/Aat	4/8	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.749650892967138	2		332	229	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636826	8636826	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1353675904	NA	P-0023136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	242	548	0	ENST00000356435.5:c.83G>A	p.Arg28Gln	p.R28Q	ENST00000356435		28	cGa/cAa	2/35	0.73975894193465	3	FACETS	0.85	0.803	0.898	0.85	0.803	0.898	CLONAL	2	TRUE	1	0.749650892967138	3		548	522	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690374	117690374	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	172	663	0	ENST00000369458.3:c.755A>G	p.Gln252Arg	p.Q252R	ENST00000369458	NM_024626.3	252	cAg/cGg	5/6	1	2	FACETS	0.964	0.895	1	0.964	0.895	1	CLONAL	1	TRUE	1	0.749650892967138	2		663	476	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117027	193117027	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	139	508	1	ENST00000367435.3:c.760C>T	p.Gln254Ter	p.Q254*	ENST00000367435	NM_024529.4	254	Caa/Taa	8/17	1	2	FACETS	0.911	0.838	0.986	0.911	0.838	0.986	CLONAL	1	TRUE	1	0.749650892967138	2		509	407	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939439	71939444	+	inframe_deletion	In_Frame_Del	DEL	CATCGG	CATCGG	-	novel	NA	P-0023136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	321	941	0	ENST00000298229.2:c.295_300del	p.Ile99_Gly100del	p.I99_G100del	ENST00000298229	NM_001567.3	98	ctCATCGGc/ctc	3/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.749650892967138	2		941	805	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150268	108150268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064795850	NA	P-0023136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	132	611	0	ENST00000278616.4:c.3335C>T	p.Pro1112Leu	p.P1112L	ENST00000278616	NM_000051.3	1112	cCt/cTt	23/63	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.749650892967138	2		611	343	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487938	56487938	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	209	733	0	ENST00000267101.3:c.1669C>T	p.Gln557Ter	p.Q557*	ENST00000267101	NM_001982.3	557	Caa/Taa	14/28	1	2	FACETS	0.952	0.89	1	0.952	0.89	1	CLONAL	1	TRUE	1	0.749650892967138	2		733	586	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563350	21563351	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0023136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	285	966	3	ENST00000382592.4:c.568_569delinsTT	p.Pro190Phe	p.P190F	ENST00000382592	NM_014572.2	190	CCc/TTc	4/8	1	2	FACETS	0.919	0.867	0.972	0.919	0.867	0.972	CLONAL	1	TRUE	1	0.749650892967138	2		969	827	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420216	88420216	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	178	573	0	ENST00000360948.2:c.2470C>T	p.Leu824Phe	p.L824F	ENST00000360948	NM_001012338.2	824	Ctc/Ttc	19/19	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.749650892967138	2		573	471	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313035	30313035	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	104	517	0	ENST00000262643.3:c.838G>A	p.Glu280Lys	p.E280K	ENST00000262643	NM_001238.2	280	Gag/Aag	9/12	1	2	FACETS	0.802	0.725	0.881	0.802	0.725	0.881	CLONAL	1	TRUE	1	0.749650892967138	2		517	346	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172125	99172125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	142	573	0	ENST00000074304.5:c.1691C>T	p.Pro564Leu	p.P564L	ENST00000074304	NM_001134224.1	564	cCc/cTc	17/26	1	2	FACETS	0.893	0.822	0.967	0.893	0.822	0.967	CLONAL	1	TRUE	1	0.749650892967138	2		573	424	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566839	212566839	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	79	324	0	ENST00000342788.4:c.1342C>T	p.Gln448Ter	p.Q448*	ENST00000342788	NM_005235.2	448	Cag/Tag	12/28	1	2	FACETS	0.958	0.858	1	0.958	0.858	1	CLONAL	1	TRUE	1	0.749650892967138	2		324	220	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440115	220440115	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	220	758	0	ENST00000243786.2:c.968G>C	p.Gly323Ala	p.G323A	ENST00000243786	NM_002191.3	323	gGg/gCg	2/2	1	2	FACETS	0.938	0.878	0.999	0.938	0.878	0.999	CLONAL	1	TRUE	1	0.749650892967138	2		758	626	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31448661	31448661	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	177	692	0	ENST00000344624.3:c.2875C>T	p.Pro959Ser	p.P959S	ENST00000344624		959	Ccc/Tcc	20/33	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.749650892967138	2		692	465	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8497265	8497266	+	stop_gained,splice_region_variant	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0023136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	153	436	1	ENST00000356435.5:c.2325_2326delinsAA	p.Trp775_Glu776delinsTer	p.W775_E776delins*	ENST00000356435		775	tgGGaa/tgAAaa	15/35	0.73975894193465	3	FACETS	0.968	0.904	1	0.968	0.904	1	CLONAL	2	TRUE	1	0.749650892967138	3		437	290	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239043	98239043	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	119	449	0	ENST00000331920.6:c.1600G>T	p.Glu534Ter	p.E534*	ENST00000331920	NM_000264.3	534	Gag/Tag	11/24	1	2	FACETS	0.918	0.838	0.999	0.918	0.838	0.999	CLONAL	1	TRUE	1	0.749650892967138	2		449	346	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240459	98240459	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	119	424	0	ENST00000331920.6:c.1225C>T	p.Gln409Ter	p.Q409*	ENST00000331920	NM_000264.3	409	Cag/Tag	9/24	1	2	FACETS	0.84	0.766	0.917	0.84	0.766	0.917	CLONAL	1	TRUE	1	0.749650892967138	2		424	378	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878094	48878094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	12	183	1	ENST00000267163.4:c.46G>A	p.Ala16Thr	p.A16T	ENST00000267163	NM_000321.2	16	Gcc/Acc	1/27	1	2	FACETS	0.161	0.113	0.22	0.161	0.113	0.22	SUBCLONAL	1	TRUE	1	0.749650892967138	2		184	199	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1060501197	NA	P-0023152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	102	853	1	ENST00000269305.4:c.716del	p.Asn239ThrfsTer8	p.N239Tfs*8	ENST00000269305	NM_001126112.2	239	aAc/ac	7/11	0.230734215710903	1	FACETS	0.867	0.776	0.965	0.867	0.776	0.965	CLONAL	1	TRUE	0	0.26892746892957	1		854	757	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044850	47044850	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	112	491	0	ENST00000377604.3:c.2176C>T	p.Arg726Ter	p.R726*	ENST00000377604	NM_001204468.1	726	Cga/Tga	20/24	1	1	FACETS	0.779	0.704	0.856	1	0.985	1	SUBCLONAL	2	TRUE	0	0.26892746892957	1		491	463	SUCCESS
AR	367	MSKCC	GRCh37	X	66937372	66937372	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	114	385	0	ENST00000374690.3:c.2226G>C	p.Trp742Cys	p.W742C	ENST00000374690	NM_000044.3	742	tgG/tgC	5/8	1	1	FACETS	0.904	0.82	0.99	1	0.988	1	CLONAL	2	TRUE	0	0.26892746892957	1		385	406	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106492	27106492	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	141	880	0	ENST00000324856.7:c.6103G>T	p.Glu2035Ter	p.E2035*	ENST00000324856	NM_006015.4	2035	Gag/Tag	20/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.26892746892957	2		880	727	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316389	14316389	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	129	870	2	ENST00000256196.4:c.216A>T	p.Gln72His	p.Q72H	ENST00000256196		72	caA/caT	3/6	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.26892746892957	2		872	675	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971088	21971089	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	79	665	0	ENST00000304494.5:c.269dup	p.Leu91ProfsTer29	p.L91Pfs*29	ENST00000304494	NM_000077.4	90	ttc/ttTc	2/3	0.26892746892957	1	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	0	0.26892746892957	1		665	500	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949160	44949161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	66	320	0	ENST00000377967.4:c.3723dup	p.Gly1242TrpfsTer9	p.G1242Wfs*9	ENST00000377967	NM_021140.2	1241	gtt/gTtt	25/29	1	1	FACETS	0.802	0.703	0.905	1	0.977	1	CLONAL	2	TRUE	0	0.26892746892957	1		320	265	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519975	NA	P-0001196-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	206	923	0	ENST00000269305.4:c.403T>C	p.Cys135Arg	p.C135R	ENST00000269305	NM_001126112.2	135	Tgc/Cgc	5/11	0.0944008044030267	3	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.420006729698777	3		923	504	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948775	55948775	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001196-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	163	636	0	ENST00000263923.4:c.3690G>C	p.Lys1230Asn	p.K1230N	ENST00000263923	NM_002253.2	1230	aaG/aaC	28/30	0.324393454470961	3	FACETS	1	0.985	1	0.82	0.762	0.878	CLONAL	2	TRUE	0	0.420006729698777	3		636	382	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524597	103524597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765051569	NA	P-0001196-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	51	320	1	ENST00000355739.4:c.2728C>T	p.His910Tyr	p.H910Y	ENST00000355739	NM_000123.3	910	Cat/Tat	13/15	0.420006729698777	3	FACETS	1	0.891	1	0.35	0.299	0.404	CLONAL	1	TRUE	0	0.420006729698777	3		321	280	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349239	11349239	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001196-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	43	206	0	ENST00000332029.2:c.97C>T	p.Pro33Ser	p.P33S	ENST00000332029	NM_003745.1	33	Ccc/Tcc	2/2	0.416385346885858	2	FACETS	1	0.955	1	0.683	0.582	0.789	CLONAL	1	TRUE	0	0.420006729698777	2		206	150	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120296	94120319	+	protein_altering_variant	In_Frame_Del	DEL	GCACTGCAGTGCATCCTGGGGGCG	GCACTGCAGTGCATCCTGGGGGCG	TCC	novel	NA	P-0001196-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	44	329	3	ENST00000369303.4:c.732_755delinsGGA	p.Asn244_Ala252delinsLysGlu	p.N244_A252delinsKE	ENST00000369303	NM_004440.3	244	aaCGCCCCCAGGATGCACTGCAGTGCa/aaGGAa	3/17	0.370941209554841	4	FACETS	0.988	0.833	1	0.494	0.416	0.579	CLONAL	1	TRUE	2	0.420006729698777	4		332	301	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542172	141542172	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001196-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	85	618	0	ENST00000220592.5:c.2551G>A	p.Asp851Asn	p.D851N	ENST00000220592	NM_012154.3	851	Gac/Aac	19/19	0.204711187656799	3	FACETS	1	0.971	1	0.643	0.572	0.717	INDETERMINATE	1	TRUE	1	0.420006729698777	3		618	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001242-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	297	547	0	ENST00000269305.4:c.736del	p.Met246Ter	p.M246*	ENST00000269305	NM_001126112.2	246	Atg/tg	7/11	0.367722696293875	3	FACETS	1	0.99	1	0.782	0.742	0.823	CLONAL	2	TRUE	0	0.448391458154402	3		547	691	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670327	134670327	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373140258	NA	P-0001242-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	96	339	1	ENST00000398015.3:c.238C>T	p.Arg80Trp	p.R80W	ENST00000398015	NM_004441.4	80	Cgg/Tgg	3/16	0.448391458154402	7	FACETS	1	0.968	1	0.309	0.275	0.345	CLONAL	1	TRUE	3	0.448391458154402	7		340	735	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371995	55371995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001242-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1455	116	554	0	ENST00000297316.4:c.685G>A	p.Gly229Ser	p.G229S	ENST00000297316	NM_022454.3	229	Ggc/Agc	2/2	0.448391458154402	10	FACETS	0.92	0.826	1			1	CLONAL	1	TRUE	NA	0.448391458154402	10		554	1571	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983229	149983229	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001242-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	64	397	0	ENST00000253339.5:c.3029T>G	p.Phe1010Cys	p.F1010C	ENST00000253339		1010	tTt/tGt	7/7	0.426191325558916	4	FACETS	0.49	0.423	0.563	0.163	0.141	0.188	SUBCLONAL	1	TRUE	1	0.448391458154402	4		397	844	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0002917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	336	606	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.265973868847319	3	FACETS	1	0.988	1	0.757	0.717	0.798	CLONAL	2	TRUE	0	0.338433660053961	3		606	1022	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149324	61149324	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	52	374	0	ENST00000295025.8:c.1514G>A	p.Ser505Asn	p.S505N	ENST00000295025	NM_002908.2	505	aGc/aAc	11/11	1	2	FACETS	0.563	0.479	0.655	0.563	0.479	0.655	SUBCLONAL	1	TRUE	1	0.338433660053961	2		374	546	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459632	149459632	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs751557861	NA	P-0002917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	387	630	0	ENST00000286301.3:c.575G>T	p.Arg192Leu	p.R192L	ENST00000286301	NM_005211.3	192	cGg/cTg	4/22	0.265973868847319	3	FACETS	0.845	0.804	0.886	0.845	0.804	0.886	CLONAL	3	TRUE	0	0.338433660053961	3		630	1055	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207198	1207198	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0002917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	228	630	0	ENST00000326873.7:c.286A>T	p.Lys96Ter	p.K96*	ENST00000326873	NM_000455.4	96	Aag/Tag	1/10	0.338433660053961	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.338433660053961	1		630	978	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120457997	120457997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	75	563	0	ENST00000256646.2:c.7348G>A	p.Gly2450Arg	p.G2450R	ENST00000256646	NM_024408.3	2450	Gga/Aga	34/34	0.338433660053961	1	FACETS	0.503	0.44	0.571	0.503	0.44	0.571	SUBCLONAL	1	TRUE	0	0.338433660053961	1		563	732	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842316	151842316	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	136	342	0	ENST00000262189.6:c.14096T>C	p.Leu4699Pro	p.L4699P	ENST00000262189	NM_170606.2	4699	cTt/cCt	54/59	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.338433660053961	2		342	618	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0002940-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	24	364	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.858	0.678	1	0.858	0.678	1	CLONAL	1	TRUE	1	0.29585755026798	2		364	189	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028875	47028875	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002940-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	73	266	0	ENST00000377604.3:c.179C>A	p.Ser60Ter	p.S60*	ENST00000377604	NM_001204468.1	60	tCa/tAa	3/24	0.180419853790449	0	FACETS	0.673	0.596	0.754			1	SUBCLONAL	2	TRUE	NA	0.29585755026798	0		266	258	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003958-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	84	439	0	ENST00000206249.3:c.1610A>G	p.Tyr537Cys	p.Y537C	ENST00000206249	NM_000125.3	537	tAt/tGt	8/8	0.196743904869107	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.196743904869107	1		439	668	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100613	67100613	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003958-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	82	533	0	ENST00000412916.2:c.311A>G	p.Asn104Ser	p.N104S	ENST00000412916		104	aAt/aGt	4/6	0.196743904869107	1	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	0	0.196743904869107	1		533	726	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842343	68842344	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0003958-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	80	383	0	ENST00000261769.5:c.406dup	p.Gln136ProfsTer32	p.Q136Pfs*32	ENST00000261769	NM_004360.3	135	atc/atCc	4/16	0.196743904869107	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.196743904869107	1		383	674	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639197	176639197	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0003958-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	59	305	0	ENST00000439151.2:c.3796+1G>C		p.X1266_splice	ENST00000439151	NM_022455.4	1266			1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.196743904869107	2		305	592	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0005742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	92	510	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	0.370290351763737	2		510	465	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5465595	5465595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148141792	NA	P-0005742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	345	710	2	ENST00000381577.3:c.779G>A	p.Arg260His	p.R260H	ENST00000381577	NM_014143.3	260	cGt/cAt	5/7	0.370290351763737	2	FACETS	0.913	0.866	0.961	0.913	0.866	0.961	CLONAL	2	TRUE	0	0.370290351763737	2		712	1020	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0005742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	98	430	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.702	0.626	0.783	0.702	0.626	0.783	SUBCLONAL	1	TRUE	1	0.370290351763737	2		430	754	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577069	7577069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55819519	NA	P-0005742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	41	724	0	ENST00000269305.4:c.869G>A	p.Arg290His	p.R290H	ENST00000269305	NM_001126112.2	290	cGc/cAc	8/11	1	2	FACETS	0.259	0.215	0.309	0.259	0.215	0.309	SUBCLONAL	1	TRUE	1	0.370290351763737	2		724	854	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175951	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	115	365	1	ENST00000257430.4:c.4660del	p.Glu1554LysfsTer11	p.E1554Kfs*11	ENST00000257430	NM_000038.5	1554	Gaa/aa	16/16	1	2	FACETS	0.962	0.868	1	0.962	0.868	1	CLONAL	1	TRUE	1	0.370290351763737	2		366	646	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243045	105243045	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	129	1022	1	ENST00000349310.3:c.238T>C	p.Trp80Arg	p.W80R	ENST00000349310	NM_001014432.1	80	Tgg/Cgg	5/15	1	2	FACETS	0.748	0.678	0.823	0.748	0.678	0.823	SUBCLONAL	1	TRUE	1	0.370290351763737	2		1023	931	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	17	721	0	ENST00000269305.4:c.775G>C	p.Asp259His	p.D259H	ENST00000269305	NM_001126112.2	259	Gac/Cac	7/11	1	2	FACETS	0.12	0.088	0.157	0.12	0.088	0.157	SUBCLONAL	1	TRUE	1	0.370290351763737	2		721	767	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0005742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	163	327	1	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.370290351763737	2		328	708	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520274	176520274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1562071377	NA	P-0005742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	53	436	0	ENST00000292408.4:c.1193G>A	p.Arg398Gln	p.R398Q	ENST00000292408	NM_213647.1	398	cGg/cAg	9/18	1	2	FACETS	0.802	0.687	0.927	0.802	0.687	0.927	CLONAL	1	TRUE	1	0.370290351763737	2		436	357	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713609	30713609	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	103	366	0	ENST00000295754.5:c.934G>T	p.Glu312Ter	p.E312*	ENST00000295754	NM_003242.5	312	Gag/Tag	4/7	1	2	FACETS	0.946	0.849	1	0.946	0.849	1	CLONAL	1	TRUE	1	0.370290351763737	2		366	588	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217536	142217536	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780593003	NA	P-0005742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	179	514	2	ENST00000350721.4:c.5461G>A	p.Asp1821Asn	p.D1821N	ENST00000350721	NM_001184.3	1821	Gac/Aac	32/47	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.370290351763737	2		516	946	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741837	17741837	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199584989	NA	P-0005742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	42	239	1	ENST00000250003.3:c.508G>A	p.Ala170Thr	p.A170T	ENST00000250003	NM_002478.4	170	Gcg/Acg	1/3	1	2	FACETS	0.918	0.773	1	0.918	0.773	1	CLONAL	1	TRUE	1	0.370290351763737	2		240	247	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0005860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	129	606	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.3	5	FACETS	0.938	0.855	1	0.938	0.855	1	CLONAL	3	TRUE	2	0.23	5		606	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0005860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	45	819	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.23	2		819	287	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089562	27089562	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	55	783	0	ENST00000324856.7:c.2518C>T	p.Gln840Ter	p.Q840*	ENST00000324856	NM_006015.4	840	Caa/Taa	8/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.23	2		783	381	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204864	NA	P-0006424-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	45	580	1	ENST00000371953.3:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000371953	NM_000314.4	171	Cag/Tag	6/9	0.310805094180735	1	FACETS	0.271	0.228	0.319	0.271	0.228	0.319	INDETERMINATE	1	TRUE	0	0.537457622908123	1		581	452	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056160	27056160	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006424-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	86	451	0	ENST00000324856.7:c.1156C>T	p.Gln386Ter	p.Q386*	ENST00000324856	NM_006015.4	386	Cag/Tag	2/20	NA	2	FACETS	0.334	0.294	0.376			1	INDETERMINATE	1	TRUE	NA	0.537457622908123	2		451	959	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412958	49412958	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006424-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1543	205	780	0	ENST00000418115.1:c.65T>G	p.Leu22Arg	p.L22R	ENST00000418115	NM_001664.2	22	cTc/cGc	2/5	1	2	FACETS	0.436	0.403	0.471	0.436	0.403	0.471	SUBCLONAL	1	TRUE	1	0.537457622908123	2		780	1748	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100584	67100584	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0006424-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	127	474	0	ENST00000412916.2:c.283-1G>A		p.X95_splice	ENST00000412916		95			0.310805094180735	1	FACETS	0.435	0.394	0.479	0.435	0.394	0.479	INDETERMINATE	1	TRUE	0	0.537457622908123	1		474	794	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862203	68862204	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0006424-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	159	526	0	ENST00000261769.5:c.2293dup	p.Gln765ProfsTer4	p.Q765Pfs*4	ENST00000261769	NM_004360.3	764	gac/gaCc	14/16	0.310805094180735	1	FACETS	0.434	0.397	0.472	0.434	0.397	0.472	INDETERMINATE	1	TRUE	0	0.537457622908123	1		526	997	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273093	18273093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006424-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1354	209	653	0	ENST00000222254.8:c.983C>T	p.Ala328Val	p.A328V	ENST00000222254	NM_005027.3	328	gCt/gTt	8/16	1	2	FACETS	0.498	0.46	0.537	0.498	0.46	0.537	SUBCLONAL	1	TRUE	1	0.537457622908123	2		653	1563	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0006572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	200	702	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.175722705152103	3	FACETS	1	0.973	1	0.734	0.68	0.791	CLONAL	2	TRUE	0	0.193277159189178	3		702	1030	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251991	8251991	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760736132	NA	P-0006572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	61	679	0	ENST00000335790.3:c.86G>A	p.Arg29His	p.R29H	ENST00000335790	NM_002315.2	29	cGc/cAc	2/4	0.193277159189178	3	FACETS	0.63	0.541	0.727	0.315	0.27	0.364	SUBCLONAL	1	TRUE	1	0.193277159189178	3		679	1099	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610265	10610265	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	190	716	0	ENST00000171111.5:c.445G>T	p.Glu149Ter	p.E149*	ENST00000171111	NM_203500.1	149	Gag/Tag	2/6	0.162778054325504	2	FACETS	0.91	0.841	0.983	0.91	0.841	0.983	CLONAL	2	TRUE	0	0.193277159189178	2		716	1080	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041349	47041349	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0006572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	92	344	0	ENST00000377604.3:c.1694-1G>A		p.X565_splice	ENST00000377604	NM_001204468.1	565			1	1	FACETS	0.874	0.78	0.974	1	0.984	1	CLONAL	2	TRUE	0	0.193277159189178	1		344	492	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394795	394795	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	84	516	0	ENST00000399788.2:c.4900G>A	p.Glu1634Lys	p.E1634K	ENST00000399788	NM_001042603.1	1634	Gag/Aag	28/28	0.175722705152103	3	FACETS	0.911	0.803	1	0.304	0.267	0.343	CLONAL	1	TRUE	0	0.193277159189178	3		516	1046	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646430	23646430	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	57	539	0	ENST00000261584.4:c.1437G>C	p.Gln479His	p.Q479H	ENST00000261584	NM_024675.3	479	caG/caC	4/13	1	2	FACETS	0.654	0.559	0.758	0.654	0.559	0.758	SUBCLONAL	1	TRUE	1	0.193277159189178	2		539	902	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578460	+	inframe_deletion	In_Frame_Del	DEL	CCATGGCGCGGA	CCATGGCGCGGA	-	novel	NA	P-0006572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	169	652	0	ENST00000269305.4:c.470_481del	p.Val157_Met160del	p.V157_M160del	ENST00000269305	NM_001126112.2	157	gTCCGCGCCATGGcc/gcc	5/11	1	2	FACETS	0.867	0.797	0.941	1	0.991	1	CLONAL	2	TRUE	1	0.193277159189178	2		652	1008	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220436	1220436	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	937	718	0	ENST00000326873.7:c.529A>T	p.Ile177Phe	p.I177F	ENST00000326873	NM_000455.4	177	Atc/Ttc	4/10	0.193277159189178	10	FACETS	0.978	0.952	1			1	CLONAL	10	TRUE	NA	0.193277159189178	10		718	1757	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152045	55152045	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	104	582	0	ENST00000257290.5:c.2477T>A	p.Leu826Gln	p.L826Q	ENST00000257290	NM_006206.4	826	cTg/cAg	18/23	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.193277159189178	2		582	1011	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729935	41729935	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	53	649	0	ENST00000242208.4:c.594G>T	p.Lys198Asn	p.K198N	ENST00000242208	NM_002192.2	198	aaG/aaT	3/3	0.162778054325504	2	FACETS	0.568	0.482	0.662	0.284	0.241	0.331	SUBCLONAL	1	TRUE	0	0.193277159189178	2		649	966	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0006767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	60	579	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	1	2	FACETS	0.396	0.339	0.458	0.396	0.339	0.458	SUBCLONAL	1	TRUE	1	0.271189364565718	2		579	1118	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715721	30715721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893816	NA	P-0006767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	100	487	0	ENST00000295754.5:c.1379G>A	p.Arg460His	p.R460H	ENST00000295754	NM_003242.5	460	cGc/cAc	5/7	0.229716953175172	1	FACETS	0.741	0.661	0.826	0.741	0.661	0.826	SUBCLONAL	1	TRUE	0	0.271189364565718	1		487	860	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852409	63852409	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376805718	NA	P-0006767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	141	511	0	ENST00000279873.7:c.3187G>A	p.Gly1063Arg	p.G1063R	ENST00000279873	NM_032199.2	1063	Ggg/Agg	10/10	0.252182426639087	3	FACETS	1	0.971	1			1	CLONAL	1	TRUE	NA	0.271189364565718	3		511	1018	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943598	17943598	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0006767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	98	617	0	ENST00000458235.1:c.2490+1G>C		p.X830_splice	ENST00000458235	NM_000215.3	830			1	2	FACETS	0.767	0.683	0.857	0.767	0.683	0.857	SUBCLONAL	1	TRUE	1	0.271189364565718	2		617	942	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15378313	15378315	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0006767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	143	557	0	ENST00000263377.2:c.471_473del	p.Phe157del	p.F157del	ENST00000263377	NM_058243.2	157	ttCTTg/ttg	4/20	1	2	FACETS	0.989	0.901	1	0.989	0.901	1	CLONAL	1	TRUE	1	0.271189364565718	2		557	1066	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11019811	11019811	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006801-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	52	285	0	ENST00000327064.4:c.486G>C	p.Met162Ile	p.M162I	ENST00000327064	NM_199141.1	162	atG/atC	4/16	1	2	FACETS	0.569	0.489	0.655	0.569	0.489	0.655	SUBCLONAL	1	TRUE	1	0.758181544581963	2		285	241	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324562	62324562	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006801-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	27	411	0	ENST00000360203.5:c.2918G>C	p.Gly973Ala	p.G973A	ENST00000360203	NM_001283009.1	973	gGa/gCa	30/35	0.758181544581963	3	FACETS	0.263	0.209	0.325	0.132	0.104	0.163	SUBCLONAL	1	TRUE	1	0.758181544581963	3		411	373	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435202	18435202	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007043-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	184	359	0	ENST00000266497.5:c.187T>A	p.Phe63Ile	p.F63I	ENST00000266497		63	Ttt/Att	1/31	1	2	FACETS	0.905	0.843	0.968	0.905	0.843	0.968	CLONAL	1	TRUE	1	0.829752977555208	2		359	490	SUCCESS
APC	324	MSKCC	GRCh37	5	112177782	112177798	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCACGAATTCTAAAA	GCCCACGAATTCTAAAA	-	novel	NA	P-0007043-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	169	332	0	ENST00000257430.4:c.6491_6507del	p.Gly2164AlafsTer10	p.G2164Afs*10	ENST00000257430	NM_000038.5	2164	gGCCCACGAATTCTAAAA/g	16/16	0.803084558339981	1	FACETS	0.927	0.877	0.976	0.927	0.877	0.976	CLONAL	1	TRUE	0	0.829752977555208	1		332	257	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060909	38060911	+	frameshift_variant	Frame_Shift_Ins	INS	TAT	TAT	ATGG	novel	NA	P-0007043-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	196	346	1	ENST00000250448.2:c.1078_1080delinsCCAT	p.Ile360ProfsTer2	p.I360Pfs*2	ENST00000250448	NM_004496.3	360	ATA/CCAT	2/2	0.829752977555208	1	FACETS	0.833	0.787	0.878	0.833	0.787	0.878	CLONAL	1	TRUE	0	0.829752977555208	1		347	332	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183873	10183873	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0008137-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	119	601	0	ENST00000256474.2:c.340+2T>A		p.X114_splice	ENST00000256474	NM_000551.3	114			0.319612635357061	3	FACETS	0.942	0.861	1	0.628	0.574	0.683	CLONAL	2	TRUE	0	0.464853304598929	3		601	335	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474041	29474041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs78723472	NA	P-0008137-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	73	898	0	ENST00000389048.3:c.2134G>A	p.Val712Met	p.V712M	ENST00000389048	NM_004304.4	712	Gtg/Atg	12/29	0.464853304598929	3	FACETS	0.734	0.643	0.832	0.367	0.321	0.416	SUBCLONAL	1	TRUE	1	0.464853304598929	3		898	527	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003742	45003813	+	splice_donor_variant,coding_sequence_variant,5_prime_UTR_variant	Splice_Site	DEL	GAGATGTCTCGCTCCGTGGCCTTAGCTGTGCTCGCGCTACTCTCTCTTTCTGGCCTGGAGGCTATCCAGCGT	GAGATGTCTCGCTCCGTGGCCTTAGCTGTGCTCGCGCTACTCTCTCTTTCTGGCCTGGAGGCTATCCAGCGT	-	novel	NA	P-0008137-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	26	491	0	ENST00000558401.1:c.1_67+5del		p.X1_splice	ENST00000558401	NM_004048.2	1		1/4	0.309904714600828	3	FACETS	0.325	0.257	0.403	0.163	0.128	0.202	SUBCLONAL	1	TRUE	1	0.464853304598929	3		491	424	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010785-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	1387	606	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.722515698196625	6	FACETS	1	0.997	1			1	CLONAL	5	TRUE	NA	0.853822284454932	6		606	1676	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577575	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782289	NA	P-0010785-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	326	630	0	ENST00000269305.4:c.706T>C	p.Tyr236His	p.Y236H	ENST00000269305	NM_001126112.2	236	Tac/Cac	7/11	0.810496971485697	1	FACETS	0.927	0.893	0.961	0.927	0.893	0.961	CLONAL	1	TRUE	0	0.853822284454932	1		630	472	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837972	156837972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367836863	NA	P-0010785-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	395	764	1	ENST00000524377.1:c.505G>A	p.Gly169Arg	p.G169R	ENST00000524377	NM_002529.3	169	Gga/Aga	5/17	1	2	FACETS	0.945	0.902	0.989	0.945	0.902	0.989	CLONAL	1	TRUE	1	0.853822284454932	2		765	979	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663682	117663682	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs770437430	NA	P-0010785-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	184	477	0	ENST00000368508.3:c.4550T>C	p.Ile1517Thr	p.I1517T	ENST00000368508	NM_002944.2	1517	aTt/aCt	28/43	0.853822284454932	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.853822284454932	1		477	223	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971116	21971117	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0010785-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	199	410	0	ENST00000304494.5:c.240_241dup	p.Pro81HisfsTer66	p.P81Hfs*66	ENST00000304494	NM_000077.4	81	ccc/cACcc	2/3	0.853822284454932	1	FACETS	0.812	0.769	0.855	0.812	0.769	0.855	CLONAL	1	TRUE	0	0.853822284454932	1		410	329	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141568667	141569434	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAGACCTGGGGACACAGAACACAGGCATCGGCATCGGGGCTGTCCCGACCTGAGTGCAGGCGCCACTTGCGAGAATCAGTTTTCATAGGAATGTGGCTGGGGACCCAAGTTATGGGGGGCTGCAGGGCTCCCCTAGGGAGGGTGACCCACAGGTCACCCCCAGGCCACCCCAGCCGGGTCCGTCTCACCTACAAGAGTACCACGTGGTGGAGGGGAGGCTCAGCTTAGAGCATGGGGTGTCCACCCTCGTGCTGTTCTGCGCCCCCCATGGGTCATCGTGATAACACGGGGTACGGTGGATGGCCCTGCAAATGGCCTTCCAAAAGGACGGGTTCAGCGGGCAGGGCTTGTGGAGCCAGGGGTGGGCCCCCCATTCTGTTGCTGATGGGCAGAAGGACCCCGGGTAAGTCCTAGACCCCCCCCAATCTGAGTTTCTTGGAGTAGAAAGCAGGCTGACTGGGTACAGACACCTGCCGGGCTGTGTAAGGATTAAATGAAGACAAAAGAAAACGCATCCTAGGTTCCAGCGTTAGGAAATGCTGATCACAGCCACGCTGCTGCTTCTAGTCCTGAGATCATGACTCAGACGTGACTGACTCCCCAACCTCATCCTCACCCCATGGGGTTGTATTTATTTAGGAAACCCCCACTCCCGCTCTGGGAAATGGATCTAACTCATCTCCATGCTACCTCATCTGATGGCTACATTCTGCCACCCCCACCTCCCCAAATGCGCACAAGAACCAGAACTGCAAAATGCGGTCCCGG	TAGACCTGGGGACACAGAACACAGGCATCGGCATCGGGGCTGTCCCGACCTGAGTGCAGGCGCCACTTGCGAGAATCAGTTTTCATAGGAATGTGGCTGGGGACCCAAGTTATGGGGGGCTGCAGGGCTCCCCTAGGGAGGGTGACCCACAGGTCACCCCCAGGCCACCCCAGCCGGGTCCGTCTCACCTACAAGAGTACCACGTGGTGGAGGGGAGGCTCAGCTTAGAGCATGGGGTGTCCACCCTCGTGCTGTTCTGCGCCCCCCATGGGTCATCGTGATAACACGGGGTACGGTGGATGGCCCTGCAAATGGCCTTCCAAAAGGACGGGTTCAGCGGGCAGGGCTTGTGGAGCCAGGGGTGGGCCCCCCATTCTGTTGCTGATGGGCAGAAGGACCCCGGGTAAGTCCTAGACCCCCCCCAATCTGAGTTTCTTGGAGTAGAAAGCAGGCTGACTGGGTACAGACACCTGCCGGGCTGTGTAAGGATTAAATGAAGACAAAAGAAAACGCATCCTAGGTTCCAGCGTTAGGAAATGCTGATCACAGCCACGCTGCTGCTTCTAGTCCTGAGATCATGACTCAGACGTGACTGACTCCCCAACCTCATCCTCACCCCATGGGGTTGTATTTATTTAGGAAACCCCCACTCCCGCTCTGGGAAATGGATCTAACTCATCTCCATGCTACCTCATCTGATGGCTACATTCTGCCACCCCCACCTCCCCAAATGCGCACAAGAACCAGAACTGCAAAATGCGGTCCCGG	-	novel	NA	P-0011092-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	167	571	0	ENST00000220592.5:c.790+60_795del		p.X264_splice	ENST00000220592	NM_012154.3	264		7/19	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		571	683	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231707	66231707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1211795184	NA	P-0012128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	196	462	0	ENST00000273854.3:c.1993G>A	p.Glu665Lys	p.E665K	ENST00000273854	NM_004439.5	665	Gaa/Aaa	11/18	0.305087309760354	5	FACETS	1	0.98	1			1	CLONAL	3	TRUE	NA	0.418324866100237	5		462	457	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879794	37879794	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	315	350	0	ENST00000269571.5:c.2089G>C	p.Val697Leu	p.V697L	ENST00000269571		697	Gtg/Ctg	18/27	0.411533875304018	4	FACETS	1	0.952	1			1	CLONAL	3	TRUE	NA	0.418324866100237	4		350	711	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584593	48584593	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	128	352	0	ENST00000342988.3:c.766C>T	p.Gln256Ter	p.Q256*	ENST00000342988	NM_005359.5	256	Cag/Tag	6/12	0.418324866100237	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.418324866100237	1		352	482	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935426	36935426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	146	523	0	ENST00000361632.4:c.1301G>A	p.Arg434Lys	p.R434K	ENST00000361632		434	aGa/aAa	10/16	1	2	FACETS	0.884	0.807	0.964	0.884	0.807	0.964	CLONAL	1	TRUE	1	0.418324866100237	2		523	790	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440882	52440882	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	131	529	0	ENST00000460680.1:c.622C>G	p.Arg208Gly	p.R208G	ENST00000460680	NM_004656.3	208	Cgg/Ggg	8/17	1	2	FACETS	0.914	0.831	1	0.914	0.831	1	CLONAL	1	TRUE	1	0.418324866100237	2		529	685	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523654	176523654	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	170	586	0	ENST00000292408.4:c.2065C>T	p.Pro689Ser	p.P689S	ENST00000292408	NM_213647.1	689	Ccg/Tcg	16/18	1	2	FACETS	0.951	0.875	1	0.951	0.875	1	CLONAL	1	TRUE	1	0.418324866100237	2		586	855	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672972	30672972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	139	579	0	ENST00000376406.3:c.3988C>T	p.Pro1330Ser	p.P1330S	ENST00000376406	NM_014641.2	1330	Cct/Tct	10/15	1	2	FACETS	0.789	0.719	0.864	0.789	0.719	0.864	SUBCLONAL	1	TRUE	1	0.418324866100237	2		579	842	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673742	30673742	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	128	446	0	ENST00000376406.3:c.3218C>T	p.Ser1073Phe	p.S1073F	ENST00000376406	NM_014641.2	1073	tCt/tTt	10/15	1	2	FACETS	0.944	0.858	1	0.944	0.858	1	CLONAL	1	TRUE	1	0.418324866100237	2		446	648	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984943	9984943	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	248	393	0	ENST00000330684.3:c.1022T>C	p.Val341Ala	p.V341A	ENST00000330684	NM_001134407.1	341	gTt/gCt	4/13	0.418324866100237	3	FACETS	0.956	0.897	1	0.956	0.897	1	CLONAL	2	TRUE	1	0.418324866100237	3		393	750	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775629	39775629	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	62	196	1	ENST00000288319.7:c.391C>T	p.Pro131Ser	p.P131S	ENST00000288319	NM_182918.3	131	Cct/Tct	4/10	1	2	FACETS	0.852	0.74	0.972	0.852	0.74	0.972	CLONAL	1	TRUE	1	0.418324866100237	2		197	348	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491662	120491663	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs312262800	NA	P-0012128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	105	246	0	ENST00000256646.2:c.2566_2567del	p.Ser856LeufsTer17	p.S856Lfs*17	ENST00000256646	NM_024408.3	856	AGt/t	16/34	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.418324866100237	2		246	489	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640578	3640578	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138344471	NA	P-0012128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	160	570	0	ENST00000294008.3:c.3061C>T	p.Arg1021Cys	p.R1021C	ENST00000294008	NM_032444.2	1021	Cgc/Tgc	12/15	1	2	FACETS	0.86	0.789	0.935	0.86	0.789	0.935	CLONAL	1	TRUE	1	0.418324866100237	2		570	889	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578232	7578234	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	AAA	AAA	-	novel	NA	P-0012128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	158	575	0	ENST00000269305.4:c.615_617del	p.Tyr205_Leu206delinsTer	p.Y205_L206delins*	ENST00000269305	NM_001126112.2	205	taTTTg/tag	6/11	0.393883117154657	1	FACETS	0.888	0.816	0.962	0.888	0.816	0.962	CLONAL	1	TRUE	0	0.418324866100237	1		575	673	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0017977-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3740	181	402	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.559700881034081	22	FACETS	1	0.963	1	0.054	0.049	0.06	CLONAL	1	TRUE	2	0.559700881034081	22		402	3921	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098816	178098816	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017977-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	181	587	0	ENST00000397062.3:c.229G>C	p.Asp77His	p.D77H	ENST00000397062	NM_006164.4	77	Gat/Cat	2/5	0.534525186658078	3	FACETS	0.914	0.843	0.987	0.457	0.421	0.494	CLONAL	1	TRUE	1	0.559700881034081	3		587	906	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577101	7577101	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017977-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	241	733	1	ENST00000269305.4:c.837del	p.Arg280GlufsTer65	p.R280Efs*65	ENST00000269305	NM_001126112.2	279	ggG/gg	8/11	0.504834063221836	1	FACETS	0.984	0.926	1	0.984	0.926	1	CLONAL	1	TRUE	0	0.559700881034081	1		734	630	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749964	162749964	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017977-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	173	504	0	ENST00000367921.3:c.2496G>C	p.Trp832Cys	p.W832C	ENST00000367921	NM_006182.2	832	tgG/tgC	18/18	0.559700881034081	3	FACETS	1	0.931	1	0.505	0.466	0.546	CLONAL	1	TRUE	1	0.559700881034081	3		504	783	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713543	30713543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017977-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	136	379	0	ENST00000295754.5:c.868G>A	p.Glu290Lys	p.E290K	ENST00000295754	NM_003242.5	290	Gag/Aag	4/7	0.559700881034081	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.559700881034081	1		379	343	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250047	53250047	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017977-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	139	517	0	ENST00000375401.3:c.202C>T	p.Arg68Ter	p.R68*	ENST00000375401	NM_004187.3	68	Cga/Tga	2/26	0.559700881034081	1	FACETS	0.766	0.702	0.832	0.766	0.702	0.832	SUBCLONAL	1	TRUE	0	0.559700881034081	1		517	467	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56798169	56798172	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	ATTA	ATTA	-	novel	NA	P-0017977-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	103	375	0	ENST00000337432.4:c.900_903del	p.Leu301GlyfsTer12	p.L301Gfs*12	ENST00000337432	NM_058216.2	300	gcATTA/gc	6/9	0.559700881034081	4	FACETS	0.747	0.669	0.831	0.249	0.223	0.277	SUBCLONAL	1	TRUE	1	0.559700881034081	4		375	768	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0020119-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	98	402	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		402	872	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577093	7577093	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882008	NA	P-0020119-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	62	579	0	ENST00000269305.4:c.845G>C	p.Arg282Pro	p.R282P	ENST00000269305	NM_001126112.2	282	cGg/cCg	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		579	1171	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916831	48916831	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020119-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	35	439	1	ENST00000267163.4:c.361C>T	p.Gln121Ter	p.Q121*	ENST00000267163	NM_000321.2	121	Cag/Tag	3/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		440	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0020722-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	66	501	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	1	2	FACETS	0.642	0.556	0.737	0.642	0.556	0.737	SUBCLONAL	1	FALSE	1	0.219029298439366	2		501	938	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115711	8115778	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCTGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAATCCAAAAAGTG	CCCCTGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAATCCAAAAAGTG	-	novel	NA	P-0020722-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	110	335	0	ENST00000346208.3:c.1058_1125del	p.Pro353GlnfsTer5	p.P353Qfs*5	ENST00000346208		353	CCCCTGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAATCCAAAAAGTGc/c	6/6	0.15461683644317	3	FACETS	0.878	0.79	0.97	0.878	0.79	0.97	CLONAL	2	FALSE	1	0.219029298439366	3		335	635	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221951	1221955	+	frameshift_variant	Frame_Shift_Del	DEL	TGCTT	TGCTT	-	novel	NA	P-0020722-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	64	507	0	ENST00000326873.7:c.866_870del	p.Met289ArgfsTer27	p.M289Rfs*27	ENST00000326873	NM_000455.4	289	aTGCTT/a	7/10	1	2	FACETS	0.676	0.584	0.776	0.676	0.584	0.776	SUBCLONAL	1	FALSE	1	0.219029298439366	2		507	865	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115859	8115875	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTGAGCCACATCTCG	CCCTGAGCCACATCTCG	-	novel	NA	P-0021199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	35	531	0	ENST00000346208.3:c.1209_1225del	p.Ser404GlnfsTer97	p.S404Qfs*97	ENST00000346208		402	tCCCTGAGCCACATCTCG/t	6/6	1	2	FACETS	0.566	0.462	0.682	0.566	0.462	0.682	SUBCLONAL	1	TRUE	1	0.197004165542773	2		531	628	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247124	53247124	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	49	358	0	ENST00000375401.3:c.376G>T	p.Glu126Ter	p.E126*	ENST00000375401	NM_004187.3	126	Gaa/Taa	4/26	0.197004165542773	1	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	0	0.197004165542773	1		358	431	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	172	314	0				ENST00000310581	NM_198253.2	-/1132			0.64796948842084	4	FACETS	0.803	0.746	0.861	0.803	0.746	0.861	CLONAL	2	FALSE	2	0.88280122388181	4		314	457	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11193150	11193150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764395301	NA	P-0022532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	57	507	0	ENST00000361445.4:c.5351G>A	p.Arg1784His	p.R1784H	ENST00000361445	NM_004958.3	1784	cGc/cAc	38/58	0.529980348266641	5	FACETS	0.322	0.275	0.373	0.107	0.091	0.125	SUBCLONAL	1	FALSE	2	0.88280122388181	5		507	933	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953730	48953730	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs3092891	NA	P-0022532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	394	371	2	ENST00000267163.4:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000267163	NM_000321.2	445	Cga/Tga	14/27	0.390028645043218	4	FACETS	1	0.986	1			1	INDETERMINATE	4	FALSE	NA	0.88280122388181	4		373	419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573983	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0022532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	486	730	1	ENST00000269305.4:c.1044_1045delinsTT	p.Leu348_Glu349delinsPheTer	p.L348_E349delinsF*	ENST00000269305	NM_001126112.2	348	ttGGaa/ttTTaa	10/11	0.881845430371928	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	FALSE	0	0.88280122388181	2		731	538	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651944	36651945	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0022532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1403	344	504	0	ENST00000244741.5:c.68dup	p.Val25SerfsTer11	p.V25Sfs*11	ENST00000244741	NM_000389.4	22	-/G	2/3	0.88280122388181	6	FACETS	1	0.991	1	0.247	0.232	0.261	CLONAL	1	FALSE	1	0.88280122388181	6		504	1747	SUCCESS
MET	4233	MSKCC	GRCh37	7	116409697	116409697	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0022532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	45	162	0	ENST00000397752.3:c.2584-2A>G		p.X862_splice	ENST00000397752	NM_000245.2	862			0.64796948842084	4	FACETS	0.648	0.548	0.758	0.324	0.274	0.379	SUBCLONAL	1	FALSE	2	0.88280122388181	4		162	296	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577537	7577538	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0022966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	238	575	2	ENST00000269305.4:c.743_744delinsAA	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGG/cAA	7/11	0.304718990218389	2	FACETS	0.895	0.838	0.954	0.895	0.838	0.954	CLONAL	2	TRUE	0	0.32	2		577	831	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933252	100933252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	73	590	0	ENST00000325455.5:c.2138C>T	p.Ser713Phe	p.S713F	ENST00000325455	NM_001202474.3	713	tCt/tTt	4/8	1	2	FACETS	0.673	0.588	0.764	0.673	0.588	0.764	SUBCLONAL	1	TRUE	1	0.32	2		590	678	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801795	3801795	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	238	479	0	ENST00000262367.5:c.3711T>G	p.Cys1237Trp	p.C1237W	ENST00000262367	NM_004380.2	1237	tgT/tgG	20/31	0.280446689436312	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.32	2		479	689	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808247	99808247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	184	603	0	ENST00000280892.6:c.442C>T	p.Arg148Cys	p.R148C	ENST00000280892	NM_001130678.1	148	Cgc/Tgc	5/7	0.0772253440286708	4	FACETS	0.795	0.734	0.858	0.795	0.734	0.858	INDETERMINATE	2	TRUE	2	0.32	4		603	955	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932275	36932276	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0022966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	73	593	0	ENST00000361632.4:c.2193_2194delinsAA	p.Asp732Asn	p.D732N	ENST00000361632		731	ggGGac/ggAAac	16/16	0.0772253440286708	4	FACETS	0.695	0.607	0.791	0.348	0.303	0.396	INDETERMINATE	1	TRUE	2	0.32	4		593	866	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925406	114925406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs77673441	NA	P-0022966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	231	544	1	ENST00000543371.1:c.1484C>T	p.Pro495Leu	p.P495L	ENST00000543371	NM_001198531.1	495	cCc/cTc	14/14	0.0609775351847013	3	FACETS	0.883	0.824	0.944			1	INDETERMINATE	2	TRUE	NA	0.32	3		545	948	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136985	11136985	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	91	580	0	ENST00000358026.2:c.3178T>C	p.Ser1060Pro	p.S1060P	ENST00000358026	NM_001128849.1	1060	Tcc/Ccc	23/36	1	2	FACETS	0.781	0.694	0.875	0.781	0.694	0.875	SUBCLONAL	1	TRUE	1	0.32	2		580	728	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916831	178916831	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	166	613	0	ENST00000263967.3:c.218T>C	p.Val73Ala	p.V73A	ENST00000263967	NM_006218.2	73	gTt/gCt	2/21	0.251449102527219	5	FACETS	1	0.988	1	0.487	0.447	0.529	CLONAL	1	TRUE	2	0.32	5		613	1051	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99812391	99812391	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	54	450	0	ENST00000280892.6:c.278G>C	p.Trp93Ser	p.W93S	ENST00000280892	NM_001130678.1	93	tGg/tCg	3/7	0.0772253440286708	4	FACETS	0.579	0.493	0.673	0.289	0.246	0.337	INDETERMINATE	1	TRUE	2	0.32	4		450	770	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724369	117724369	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	200	543	0	ENST00000368508.3:c.510G>A	p.Trp170Ter	p.W170*	ENST00000368508	NM_002944.2	170	tgG/tgA	6/43	0.304718990218389	2	FACETS	0.851	0.791	0.913	0.851	0.791	0.913	CLONAL	2	TRUE	0	0.32	2		543	734	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157454315	157454315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs527698870	NA	P-0022966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	48	399	0	ENST00000346085.5:c.2525C>T	p.Pro842Leu	p.P842L	ENST00000346085	NM_020732.3	842	cCa/cTa	8/20	0.304718990218389	2	FACETS	0.699	0.592	0.817	0.35	0.296	0.409	SUBCLONAL	1	TRUE	0	0.32	2		399	429	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930154	68930154	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0022966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	160	348	0	ENST00000288368.4:c.213+2T>G		p.X71_splice	ENST00000288368	NM_024870.2	71			0.304718990218389	6	FACETS	1	0.975	1	0.461	0.424	0.5	CLONAL	2	TRUE	1	0.32	6		348	711	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970898	70970898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	94	444	0	ENST00000276594.2:c.1363C>T	p.His455Tyr	p.H455Y	ENST00000276594	NM_024504.3	455	Cat/Tat	6/8	0.304718990218389	6	FACETS	0.916	0.813	1	0.183	0.162	0.206	CLONAL	1	TRUE	1	0.32	6		444	1052	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	52	559	1	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	1	2	FACETS	0.486	0.413	0.566	0.486	0.413	0.566	SUBCLONAL	1	FALSE	1	0.324249887009447	2		560	660	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	161	781	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	FALSE	1	0.324249887009447	2		786	973	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	72	491	0	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.872	0.764	0.989	0.872	0.764	0.989	CLONAL	1	FALSE	1	0.324249887009447	2		491	509	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	161	375	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.31312234418511	2	FACETS	0.933	0.862	1	0.933	0.862	1	CLONAL	2	FALSE	0	0.324249887009447	2		375	532	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37055939	37055939	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	160	422	0	ENST00000231790.2:c.694G>T	p.Gly232Ter	p.G232*	ENST00000231790	NM_000249.3	232	Gga/Tga	9/19	0.31312234418511	2	FACETS	0.933	0.861	1	0.933	0.861	1	CLONAL	2	FALSE	0	0.324249887009447	2		422	529	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469128	25469128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	151	889	1	ENST00000264709.3:c.1330G>A	p.Glu444Lys	p.E444K	ENST00000264709	NM_175629.2	444	Gag/Aag	11/23	1	2	FACETS	0.846	0.772	0.924	0.846	0.772	0.924	CLONAL	1	FALSE	1	0.324249887009447	2		890	1101	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665144	29665144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs562367786	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	119	778	2	ENST00000356175.3:c.6743G>A	p.Arg2248His	p.R2248H	ENST00000356175	NM_000267.3	2248	cGt/cAt	44/57	1	2	FACETS	0.952	0.86	1	0.952	0.86	1	CLONAL	1	FALSE	1	0.324249887009447	2		780	771	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923087	39923087	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	67	816	6	ENST00000378444.4:c.3621del	p.Lys1207AsnfsTer31	p.K1207Nfs*31	ENST00000378444	NM_001123385.1	1207	aaA/aa	8/15	1	2	FACETS	0.401	0.347	0.46	0.401	0.347	0.46	SUBCLONAL	1	FALSE	1	0.324249887009447	2		822	1030	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248633	59248634	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	137	696	7	ENST00000371222.2:c.109_110del	p.Ser37HisfsTer69	p.S37Hfs*69	ENST00000371222	NM_002228.3	37	AGc/c	1/1	1	2	FACETS	0.701	0.636	0.769	0.701	0.636	0.769	SUBCLONAL	1	FALSE	1	0.324249887009447	2		703	1206	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	93	533	1	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	1	2	FACETS	0.964	0.859	1	0.964	0.859	1	CLONAL	1	FALSE	1	0.324249887009447	2		534	595	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	221	413	1	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.975	0.911	1	1	0.994	1	CLONAL	2	FALSE	1	0.324249887009447	2		414	699	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007825	45007825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	38	584	2	ENST00000558401.1:c.276del	p.Thr93LeufsTer10	p.T93Lfs*10	ENST00000558401	NM_004048.2	91	aCc/ac	2/4	1	2	FACETS	0.327	0.269	0.392	0.327	0.269	0.392	SUBCLONAL	1	FALSE	1	0.324249887009447	2		586	717	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471739	120471739	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138832326	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	95	633	0	ENST00000256646.2:c.3752G>A	p.Arg1251His	p.R1251H	ENST00000256646	NM_024408.3	1251	cGc/cAc	23/34	1	2	FACETS	0.896	0.799	1	0.896	0.799	1	CLONAL	1	FALSE	1	0.324249887009447	2		633	654	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981586	101981586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1319669560	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	55	351	0	ENST00000282441.5:c.7C>T	p.Pro3Ser	p.P3S	ENST00000282441	NM_001130145.2	3	Ccc/Tcc	1/9	1	2	FACETS	0.776	0.665	0.897	0.776	0.665	0.897	SUBCLONAL	1	FALSE	1	0.324249887009447	2		351	437	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17354304	17354306	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs1173714647	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	44	670	0	ENST00000375499.3:c.478_480del	p.Lys160del	p.K160del	ENST00000375499	NM_003000.2	160	AAG/-	5/8	1	2	FACETS	0.315	0.263	0.373	0.315	0.263	0.373	SUBCLONAL	1	FALSE	1	0.324249887009447	2		670	862	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445124	49445124	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	168	985	0	ENST00000301067.7:c.2342C>T	p.Ala781Val	p.A781V	ENST00000301067	NM_003482.3	781	gCt/gTt	10/54	1	2	FACETS	0.988	0.907	1	0.988	0.907	1	CLONAL	1	FALSE	1	0.324249887009447	2		985	1049	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885263	111885263	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1179360058	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	122	772	0	ENST00000341259.2:c.1151A>G	p.Asp384Gly	p.D384G	ENST00000341259	NM_005475.2	384	gAt/gGt	6/8	1	2	FACETS	0.911	0.823	1	0.911	0.823	1	CLONAL	1	FALSE	1	0.324249887009447	2		772	826	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506715	103506715	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	36	277	0	ENST00000355739.4:c.462del	p.Lys154AsnfsTer16	p.K154Nfs*16	ENST00000355739	NM_000123.3	153	gAa/ga	4/15	1	2	FACETS	0.705	0.581	0.843	0.705	0.581	0.843	SUBCLONAL	1	FALSE	1	0.324249887009447	2		277	315	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95563045	95563045	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1555367927	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	55	303	0	ENST00000393063.1:c.4212del	p.Asp1405ThrfsTer23	p.D1405Tfs*23	ENST00000393063	NM_030621.3	1404	aaA/aa	24/28	1	2	FACETS	0.863	0.741	0.996	0.863	0.741	0.996	CLONAL	1	FALSE	1	0.324249887009447	2		303	393	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729115	66729115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504819	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	115	820	2	ENST00000307102.5:c.323G>A	p.Arg108Gln	p.R108Q	ENST00000307102	NM_002755.3	108	cGg/cAg	3/11	1	2	FACETS	0.678	0.61	0.751	0.678	0.61	0.751	SUBCLONAL	1	FALSE	1	0.324249887009447	2		822	1046	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964756	15964756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1452521115	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	155	721	3	ENST00000268712.3:c.5840C>T	p.Ala1947Val	p.A1947V	ENST00000268712	NM_006311.3	1947	gCg/gTg	37/46	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.324249887009447	2		724	921	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211658	36211658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	93	644	0	ENST00000222270.7:c.1409G>A	p.Gly470Asp	p.G470D	ENST00000222270	NM_014727.1	470	gGc/gAc	3/37	1	2	FACETS	0.956	0.852	1	0.956	0.852	1	CLONAL	1	FALSE	1	0.324249887009447	2		644	600	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440151	220440151	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs140659175	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	157	930	0	ENST00000243786.2:c.1004T>C	p.Met335Thr	p.M335T	ENST00000243786	NM_002191.3	335	aTg/aCg	2/2	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	FALSE	1	0.324249887009447	2		930	963	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662289	227662289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1372054385	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	125	721	0	ENST00000305123.5:c.1166C>T	p.Pro389Leu	p.P389L	ENST00000305123	NM_005544.2	389	cCg/cTg	1/2	1	2	FACETS	0.881	0.797	0.97	0.881	0.797	0.97	CLONAL	1	FALSE	1	0.324249887009447	2		721	875	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125266	47125266	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	122	631	0	ENST00000409792.3:c.6004A>G	p.Thr2002Ala	p.T2002A	ENST00000409792	NM_014159.6	2002	Aca/Gca	12/21	0.31312234418511	2	FACETS	0.986	0.892	1	0.493	0.446	0.543	CLONAL	1	FALSE	0	0.324249887009447	2		631	763	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70005638	70005638	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	106	669	0	ENST00000394351.3:c.667C>A	p.Arg223Ser	p.R223S	ENST00000394351	NM_000248.3	223	Cgc/Agc	7/9	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	1	0.324249887009447	2		669	592	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205035	128205035	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs770243533	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	117	842	0	ENST00000341105.2:c.406G>T	p.Gly136Cys	p.G136C	ENST00000341105	NM_032638.4	136	Ggc/Tgc	3/6	1	2	FACETS	0.827	0.745	0.913	0.827	0.745	0.913	CLONAL	1	FALSE	1	0.324249887009447	2		842	873	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403485	138403485	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	37	635	0	ENST00000289153.2:c.2297T>C	p.Val766Ala	p.V766A	ENST00000289153	NM_006219.2	766	gTt/gCt	15/22	1	2	FACETS	0.319	0.262	0.383	0.319	0.262	0.383	SUBCLONAL	1	FALSE	1	0.324249887009447	2		635	716	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455575	189455575	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs147340040	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	101	793	2	ENST00000264731.3:c.109C>T	p.Arg37Ter	p.R37*	ENST00000264731	NM_003722.4	37	Cga/Tga	2/14	1	2	FACETS	0.84	0.75	0.934	0.84	0.75	0.934	CLONAL	1	FALSE	1	0.324249887009447	2		795	742	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953579	38953579	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	57	496	0	ENST00000357387.3:c.2774C>T	p.Ala925Val	p.A925V	ENST00000357387	NM_152756.3	925	gCa/gTa	28/38	1	2	FACETS	0.739	0.635	0.852	0.739	0.635	0.852	SUBCLONAL	1	FALSE	1	0.324249887009447	2		496	476	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564417	86564417	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	46	636	0	ENST00000274376.6:c.149C>A	p.Pro50His	p.P50H	ENST00000274376	NM_002890.2	50	cCt/cAt	1/25	1	2	FACETS	0.423	0.355	0.498	0.423	0.355	0.498	SUBCLONAL	1	FALSE	1	0.324249887009447	2		636	671	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187959	32187959	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs373411879	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	155	938	0	ENST00000375023.3:c.1262A>G	p.Gln421Arg	p.Q421R	ENST00000375023	NM_004557.3	421	cAg/cGg	7/30	1	2	FACETS	0.977	0.893	1	0.977	0.893	1	CLONAL	1	FALSE	1	0.324249887009447	2		938	979	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138552	37138554	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs942893612	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	98	614	0	ENST00000373509.5:c.88_90del	p.Glu30del	p.E30del	ENST00000373509	NM_002648.3	29	aAGGag/aag	2/6	1	2	FACETS	0.888	0.792	0.989	0.888	0.792	0.989	CLONAL	1	FALSE	1	0.324249887009447	2		614	681	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873690	151873690	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	87	658	0	ENST00000262189.6:c.8848C>G	p.His2950Asp	p.H2950D	ENST00000262189	NM_170606.2	2950	Cat/Gat	38/59	1	2	FACETS	0.73	0.646	0.82	0.73	0.646	0.82	SUBCLONAL	1	FALSE	1	0.324249887009447	2		658	735	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738369	133738369	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	39	601	0	ENST00000318560.5:c.769T>C	p.Tyr257His	p.Y257H	ENST00000318560	NM_005157.4	257	Tac/Cac	4/11	1	2	FACETS	0.366	0.302	0.437	0.366	0.302	0.437	SUBCLONAL	1	FALSE	1	0.324249887009447	2		601	658	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139440219	139440219	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	26	120	0	ENST00000277541.6:c.20C>A	p.Pro7His	p.P7H	ENST00000277541	NM_017617.3	7	cCc/cAc	1/34	1	2	FACETS	0.756	0.603	0.931	0.756	0.603	0.931	CLONAL	1	FALSE	1	0.324249887009447	2		120	212	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	130	314	0				ENST00000310581	NM_198253.2	-/1132			0.168290065067877	5	FACETS	1	0.956	1	1	0.956	1	CLONAL	3	FALSE	2	0.168290065067877	5		314	596	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057988	27057988	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	127	746	0	ENST00000324856.7:c.1696C>T	p.Gln566Ter	p.Q566*	ENST00000324856	NM_006015.4	566	Cag/Tag	3/20	0.168290065067877	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	FALSE	1	0.168290065067877	3		746	753	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941720	48941720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	57	545	0	ENST00000267163.4:c.1030C>T	p.Gln344Ter	p.Q344*	ENST00000267163	NM_000321.2	344	Cag/Tag	10/27	0.130791136923163	1	FACETS	0.886	0.764	1	1	0.975	1	CLONAL	2	FALSE	0	0.168290065067877	1		545	350	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0023185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	162	1014	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.168290065067877	3	FACETS	0.902	0.826	0.982			1	CLONAL	2	FALSE	NA	0.168290065067877	3		1014	1157	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578551	7578558	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTACTGT	AGTACTGT	-	novel	NA	P-0023185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	272	990	0	ENST00000269305.4:c.376-4_379del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	0.168290065067877	3	FACETS	1	0.965	1	1	0.994	1	CLONAL	3	FALSE	1	0.168290065067877	3		990	1123	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482552	56482552	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1439217874	NA	P-0023185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	118	702	0	ENST00000267101.3:c.1009G>C	p.Gly337Arg	p.G337R	ENST00000267101	NM_001982.3	337	Ggg/Cgg	9/28	0.159847337894656	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	2	FALSE	0	0.168290065067877	2		702	690	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023204	33023204	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	71	749	2	ENST00000300177.4:c.313G>A	p.Glu105Lys	p.E105K	ENST00000300177	NM_001191322.1	105	Gag/Aag	2/2	0.168290065067877	3	FACETS	1	0.943	1	0.575	0.501	0.656	CLONAL	1	FALSE	1	0.168290065067877	3		751	795	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856356	45856356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	170	858	0	ENST00000391945.4:c.1816G>A	p.Glu606Lys	p.E606K	ENST00000391945	NM_000400.3	606	Gag/Aag	19/23	0.168290065067877	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	FALSE	1	0.168290065067877	3		858	894	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096412	178096412	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	41	482	0	ENST00000397062.3:c.919C>A	p.His307Asn	p.H307N	ENST00000397062	NM_006164.4	307	Cat/Aat	5/5	0.168290065067877	3	FACETS	1	0.872	1	0.528	0.44	0.627	CLONAL	1	FALSE	1	0.168290065067877	3		482	500	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164633	36164635	+	frameshift_variant	Frame_Shift_Del	DEL	GTA	GTA	CT	novel	NA	P-0023185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	74	790	1	ENST00000300305.3:c.1240_1242delinsAG	p.Tyr414SerfsTer180	p.Y414Sfs*180	ENST00000300305		414	TAC/AG	8/8	0.168290065067877	3	FACETS	1	0.9	1	0.518	0.452	0.589	CLONAL	1	FALSE	1	0.168290065067877	3		791	921	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638416	117638416	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	63	529	0	ENST00000368508.3:c.6025A>G	p.Ile2009Val	p.I2009V	ENST00000368508	NM_002944.2	2009	Att/Gtt	38/43	1	2	FACETS	0.849	0.736	0.97	1	0.976	1	CLONAL	2	FALSE	1	0.168290065067877	2		529	441	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200335	138200335	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs190199205	NA	P-0023185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	49	554	1	ENST00000237289.4:c.1753G>A	p.Asp585Asn	p.D585N	ENST00000237289	NM_001270507.1	585	Gac/Aac	7/9	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	FALSE	1	0.168290065067877	2		555	564	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026886	6026886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	35	479	0	ENST00000265849.7:c.1510G>A	p.Glu504Lys	p.E504K	ENST00000265849	NM_000535.5	504	Gag/Aag	11/15	0.168290065067877	6	FACETS	0.919	0.752	1	0.306	0.25	0.37	CLONAL	1	FALSE	3	0.168290065067877	6		479	605	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859445	151859445	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	46	650	0	ENST00000262189.6:c.11217G>C	p.Gln3739His	p.Q3739H	ENST00000262189	NM_170606.2	3739	caG/caC	43/59	0.168290065067877	3	FACETS	1	0.881	1	0.528	0.444	0.621	CLONAL	1	FALSE	1	0.168290065067877	3		650	561	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0023189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	174	656	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.456111917162847	2		656	630	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189466	56189467	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0023189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	61	687	0	ENST00000399503.3:c.4502_4503del	p.Glu1501AlafsTer21	p.E1501Afs*21	ENST00000399503	NM_005921.1	1500	AGa/a	20/20	1	2	FACETS	0.41	0.353	0.471	0.41	0.353	0.471	SUBCLONAL	1	TRUE	1	0.456111917162847	2		687	653	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309141	137309141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767968089	NA	P-0023189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	178	944	3	ENST00000481739.1:c.748G>A	p.Val250Met	p.V250M	ENST00000481739	NM_002957.4	250	Gtg/Atg	5/10	1	2	FACETS	0.849	0.783	0.918	0.849	0.783	0.918	CLONAL	1	TRUE	1	0.456111917162847	2		947	919	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112447	115112448	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCTTTGTCCAGCCG	novel	NA	P-0023192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	441	794	0	ENST00000257566.3:c.1279_1292dup	p.Ser432GlyfsTer205	p.S432Gfs*205	ENST00000257566	NM_016569.3	431	gcg/gcCGGCTGGACAAAGCg	7/8	0.634631355615058	3	FACETS	1	0.996	1	0.728	0.695	0.761	CLONAL	1	TRUE	1	0.693109462328546	3		794	1177	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0023195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	36	574	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.617	0.505	0.743	0.617	0.505	0.743	SUBCLONAL	1	TRUE	1	0.15	2		574	778	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57470685	57470685	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	40	419	0	ENST00000371085.3:c.158A>C	p.Lys53Thr	p.K53T	ENST00000371085	NM_000516.4	53	aAa/aCa	2/13	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.15	2		419	464	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249457	153249457	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	53	797	0	ENST00000281708.4:c.1321C>G	p.Arg441Gly	p.R441G	ENST00000281708	NM_033632.3	441	Cgg/Ggg	9/12	1	2	FACETS	0.848	0.722	0.988	0.848	0.722	0.988	CLONAL	1	TRUE	1	0.15	2		797	833	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0023207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	95	495	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.2	2		495	716	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120776	115120776	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs770004469	NA	P-0023226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	40	721	0	ENST00000257566.3:c.230C>G	p.Pro77Arg	p.P77R	ENST00000257566	NM_016569.3	77	cCg/cGg	1/8	0.219092402473935	1	FACETS	0.48	0.399	0.571	0.48	0.399	0.571	SUBCLONAL	1	FALSE	0	0.3	1		721	472	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120808	115120839	+	frameshift_variant	Frame_Shift_Del	DEL	ATCCATGATCGGCTTGGCCAGGGCGCCCGGCA	ATCCATGATCGGCTTGGCCAGGGCGCCCGGCA	-	novel	NA	P-0023226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	34	610	0	ENST00000257566.3:c.167_198del	p.Leu56ProfsTer44	p.L56Pfs*44	ENST00000257566	NM_016569.3	56	cTGCCGGGCGCCCTGGCCAAGCCGATCATGGAT/c	1/8	0.219092402473935	1	FACETS	0.546	0.447	0.657	0.546	0.447	0.657	SUBCLONAL	1	FALSE	0	0.3	1		610	353	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252990	36252991	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACACCCCC	novel	NA	P-0023226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	49	528	0	ENST00000300305.3:c.371_372insGGGGGTGT	p.Pro125GlyfsTer11	p.P125Gfs*11	ENST00000300305		124	gtt/gtGGGGGTGTt	4/8	1	2	FACETS	0.571	0.483	0.668	0.571	0.483	0.668	SUBCLONAL	1	FALSE	1	0.3	2		528	572	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43772110	43772110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756804341	NA	P-0023273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	381	1023	1	ENST00000382044.4:c.605C>T	p.Ser202Leu	p.S202L	ENST00000382044	NM_001141980.1	202	tCa/tTa	6/28	0.59535779195513	1	FACETS	0.664	0.631	0.697	0.664	0.631	0.697	SUBCLONAL	1	TRUE	0	0.682693417257072	1		1024	1107	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0023276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	270	769	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.167948287213715	0	FACETS	0.892	0.84	0.944			1	CLONAL	4	FALSE	0	0.167782860832475	0		770	751	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905944	50905944	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755457889	NA	P-0023276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	189	961	1	ENST00000440232.2:c.916C>T	p.Arg306Cys	p.R306C	ENST00000440232	NM_002691.3	306	Cgc/Tgc	8/27	1	2	FACETS	1	0.984	1	1	0.994	1	CLONAL	2	FALSE	1	0.167782860832475	2		962	916	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0023314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7012	243	539	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.659105200686122	20	FACETS	0.705	0.653	0.759			1	SUBCLONAL	1	TRUE	NA	0.659105200686122	20		539	7255	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063372	67063372	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	218	308	0	ENST00000412916.2:c.62T>G	p.Leu21Arg	p.L21R	ENST00000412916		21	cTg/cGg	1/6	0.640805448875033	1	FACETS	0.942	0.886	0.997	0.942	0.886	0.997	CLONAL	1	TRUE	0	0.659105200686122	1		308	471	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844175	68844175	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	306	592	0	ENST00000261769.5:c.763C>T	p.Gln255Ter	p.Q255*	ENST00000261769	NM_004360.3	255	Cag/Tag	6/16	0.640805448875033	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.659105200686122	1		592	599	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117408	115117408	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	235	428	1	ENST00000257566.3:c.766del	p.Arg256GlufsTer6	p.R256Efs*6	ENST00000257566	NM_016569.3	256	Aga/ga	4/8	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.659105200686122	2		429	684	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579865	7579868	+	frameshift_variant	Frame_Shift_Del	DEL	CTGA	CTGA	-	novel	NA	P-0023314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	287	660	0	ENST00000269305.4:c.45_48del	p.Ser15ArgfsTer28	p.S15Rfs*28	ENST00000269305	NM_001126112.2	15	agTCAG/ag	2/11	0.626385377500523	1	FACETS	0.896	0.849	0.943	0.896	0.849	0.943	CLONAL	1	TRUE	0	0.659105200686122	1		660	652	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788651	3788651	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	181	705	0	ENST00000262367.5:c.4303G>T	p.Asp1435Tyr	p.D1435Y	ENST00000262367	NM_004380.2	1435	Gat/Tat	26/31	0.465438041621604	3	FACETS	1	0.982	1	0.759	0.71	0.809	CLONAL	2	TRUE	0	0.492798013374609	3		705	402	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738308	190738308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	52	652	0	ENST00000441310.2:c.2560C>T	p.Leu854Phe	p.L854F	ENST00000441310	NM_000534.4	854	Ctt/Ttt	12/13	0.411264673886951	5	FACETS	0.528	0.449	0.616	0.176	0.149	0.206	SUBCLONAL	1	TRUE	2	0.492798013374609	5		652	695	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391330	139391331	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCA	novel	NA	P-0023320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	380	999	0	ENST00000277541.6:c.6857_6860dup	p.Ser2288GlyfsTer67	p.S2288Gfs*67	ENST00000277541	NM_017617.3	2287	ggc/ggTGGGc	34/34	0.502264796979763	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	4	TRUE	0	0.492798013374609	4		999	560	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942703	44942703	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0023320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	131	578	0	ENST00000377967.4:c.3285-2A>G		p.X1095_splice	ENST00000377967	NM_021140.2	1095			0.343167775844798	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.492798013374609	1		578	299	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	354	1119	0	ENST00000269305.4:c.388del	p.Leu130SerfsTer40	p.L130Sfs*40	ENST00000269305	NM_001126112.2	130	Ctc/tc	5/11	0.455814413775784	2	FACETS	0.972	0.926	1	0.972	0.926	1	CLONAL	2	TRUE	0	0.455814413775784	2		1119	799	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602329	10602329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	175	1074	0	ENST00000171111.5:c.1249G>A	p.Gly417Arg	p.G417R	ENST00000171111	NM_203500.1	417	Ggg/Agg	3/6	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.455814413775784	2		1074	728	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226049	133226049	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	145	912	5	ENST00000320574.5:c.3848C>A	p.Ala1283Asp	p.A1283D	ENST00000320574	NM_006231.2	1283	gCc/gAc	31/49	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.455814413775784	2		917	576	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350234	89350234	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	75	1101	2	ENST00000301030.4:c.2716C>T	p.Arg906Ter	p.R906*	ENST00000301030	NM_001256183.1	906	Cga/Tga	9/13	0.455814413775784	1	FACETS	0.351	0.307	0.399	0.351	0.307	0.399	SUBCLONAL	1	TRUE	0	0.455814413775784	1		1103	723	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627730	37627730	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	346	1169	0	ENST00000447079.4:c.1649del	p.Pro550LeufsTer60	p.P550Lfs*60	ENST00000447079	NM_015083.1	549	Ccc/cc	2/14	0.452764016878459	2	FACETS	0.933	0.887	0.978	0.933	0.887	0.978	CLONAL	2	TRUE	0	0.455814413775784	2		1169	814	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610264	10610264	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	129	985	2	ENST00000171111.5:c.446A>T	p.Glu149Val	p.E149V	ENST00000171111	NM_203500.1	149	gAg/gTg	2/6	1	2	FACETS	0.76	0.689	0.834	0.76	0.689	0.834	SUBCLONAL	1	TRUE	1	0.455814413775784	2		987	745	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965421	18965421	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	108	540	2	ENST00000262803.5:c.1168G>T	p.Glu390Ter	p.E390*	ENST00000262803	NM_002911.3	390	Gag/Tag	9/24	1	2	FACETS	0.989	0.893	1	0.989	0.893	1	CLONAL	1	TRUE	1	0.455814413775784	2		542	479	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422454	225422456	+	inframe_deletion	In_Frame_Del	DEL	ATA	ATA	-	novel	NA	P-0023324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	112	969	0	ENST00000264414.4:c.184_186del	p.Tyr62del	p.Y62del	ENST00000264414	NM_003590.4	62	TAT/-	2/16	1	2	FACETS	0.907	0.819	0.999	0.907	0.819	0.999	CLONAL	1	TRUE	1	0.455814413775784	2		969	542	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958055	54958055	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	89	484	0	ENST00000312783.6:c.552A>G	p.Ile184Met	p.I184M	ENST00000312783	NM_198436.1	184	atA/atG	6/10	1	2	FACETS	0.847	0.754	0.945	0.847	0.754	0.945	CLONAL	1	TRUE	1	0.455814413775784	2		484	461	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42843882	42843882	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	88	838	1	ENST00000398585.3:c.1037C>A	p.Thr346Lys	p.T346K	ENST00000398585	NM_001135099.1	346	aCg/aAg	10/14	1	2	FACETS	0.705	0.626	0.789	0.705	0.626	0.789	SUBCLONAL	1	TRUE	1	0.455814413775784	2		839	548	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277511	142277511	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1278516813	NA	P-0023324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	83	652	0	ENST00000350721.4:c.1840G>A	p.Ala614Thr	p.A614T	ENST00000350721	NM_001184.3	614	Gcc/Acc	8/47	0.455814413775784	4	FACETS	0.76	0.67	0.855			1	SUBCLONAL	1	TRUE	NA	0.455814413775784	4		652	698	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950414	38950414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	124	759	0	ENST00000357387.3:c.3536G>A	p.Gly1179Glu	p.G1179E	ENST00000357387	NM_152756.3	1179	gGa/gAa	31/38	0.40702176104546	3	FACETS	1	0.934	1	0.519	0.47	0.57	CLONAL	1	TRUE	1	0.455814413775784	3		759	644	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459432	50459432	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	58	422	0	ENST00000331340.3:c.721A>G	p.Lys241Glu	p.K241E	ENST00000331340	NM_006060.4	241	Aaa/Gaa	7/8	1	2	FACETS	0.764	0.66	0.876	0.764	0.66	0.876	SUBCLONAL	1	TRUE	1	0.455814413775784	2		422	333	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207387	29207387	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	79	648	0	ENST00000240100.2:c.409C>A	p.Arg137Ser	p.R137S	ENST00000240100	NM_001394.6	137	Cgc/Agc	1/4	1	2	FACETS	0.749	0.661	0.842	0.749	0.661	0.842	SUBCLONAL	1	TRUE	1	0.455814413775784	2		648	463	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371820	55371820	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1180015365	NA	P-0023324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	17	138	0	ENST00000297316.4:c.510G>C	p.Glu170Asp	p.E170D	ENST00000297316	NM_022454.3	170	gaG/gaC	2/2	1	2	FACETS	0.811	0.616	1	0.811	0.616	1	CLONAL	1	TRUE	1	0.455814413775784	2		138	92	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870205	44870205	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0023324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	47	470	0	ENST00000377967.4:c.385-1G>C		p.X129_splice	ENST00000377967	NM_021140.2	129			1	1	FACETS	0.658	0.56	0.764	0.658	0.56	0.764	SUBCLONAL	1	TRUE	0	0.455814413775784	1		470	242	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971185	21971185	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	289	662	0	ENST00000304494.5:c.173G>C	p.Arg58Pro	p.R58P	ENST00000304494	NM_000077.4	58	cGa/cCa	2/3	0.432805687079514	3	FACETS	0.952	0.907	0.998	0.952	0.907	0.998	CLONAL	3	TRUE	0	0.455814413775784	3		662	545	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971185	21971185	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	AG	novel	NA	P-0023324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	275	662	0	ENST00000304494.5:c.173delinsCT	p.Arg58ProfsTer62	p.R58Pfs*62	ENST00000304494	NM_000077.4	58	cGa/cCTa	2/3	0.432805687079514				0.86	0.952				CLONAL	3	TRUE	0	0.455814413775784	3		662	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0023340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	34	646	1	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	1	2	FACETS	0.145	0.118	0.177	0.145	0.118	0.177	SUBCLONAL	1	TRUE	1	0.39	2		647	1200	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727455	66727455	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs869025608	NA	P-0023340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	45	635	0	ENST00000307102.5:c.171G>C	p.Lys57Asn	p.K57N	ENST00000307102	NM_002755.3	57	aaG/aaC	2/11	1	2	FACETS	0.319	0.267	0.376	0.319	0.267	0.376	SUBCLONAL	1	TRUE	1	0.39	2		635	724	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31431749	31431749	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	42	719	0	ENST00000344624.3:c.3079G>T	p.Gly1027Trp	p.G1027W	ENST00000344624		1027	Ggg/Tgg	23/33	1	2	FACETS	0.315	0.262	0.374	0.315	0.262	0.374	SUBCLONAL	1	TRUE	1	0.39	2		719	683	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202218	138202218	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0023340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	49	660	0	ENST00000237289.4:c.2135C>G	p.Ser712Ter	p.S712*	ENST00000237289	NM_001270507.1	712	tCa/tGa	9/9	1	2	FACETS	0.34	0.287	0.398	0.34	0.287	0.398	SUBCLONAL	1	TRUE	1	0.39	2		660	740	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0023347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12465	796	676	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.470912704583547	56	FACETS	1	0.994	1			1	CLONAL	3	TRUE	NA	0.470912704583547	56		676	13261	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0023347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	392	573	1	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.470912704583547	2	FACETS	0.935	0.893	0.978	0.935	0.893	0.978	CLONAL	2	TRUE	0	0.470912704583547	2		574	890	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885833	59885833	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0023347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	213	614	0	ENST00000259008.2:c.913A>T	p.Lys305Ter	p.K305*	ENST00000259008	NM_032043.2	305	Aaa/Taa	7/20	0.470912704583547	3	FACETS	0.891	0.833	0.951	0.891	0.833	0.951	CLONAL	2	TRUE	1	0.470912704583547	3		614	627	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094907	143094907	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	51	828	0	ENST00000262992.4:c.1237G>T	p.Val413Phe	p.V413F	ENST00000262992	NM_001101669.1	413	Gtt/Ttt	14/24	0.470912704583547	2	FACETS	0.349	0.296	0.408	0.175	0.148	0.204	SUBCLONAL	1	TRUE	0	0.470912704583547	2		828	620	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74868215	74868215	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	100	309	0	ENST00000284811.8:c.79del	p.His27MetfsTer5	p.H27Mfs*5	ENST00000284811		27	Cat/at	3/4	0.13902019607696	3	FACETS	0.849	0.768	0.933			1	INDETERMINATE	2	TRUE	NA	0.470912704583547	3		309	309	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041164	47041165	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	339	527	0	ENST00000377604.3:c.1592_1593insT	p.Pro532ThrfsTer7	p.P532Tfs*7	ENST00000377604	NM_001204468.1	531	tca/tcTa	15/24	0.470912704583547	2	FACETS	0.835	0.8	0.869			1	CLONAL	3	TRUE	NA	0.470912704583547	2		527	575	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0023350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	31	327	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.72	0.582	0.877	0.72	0.582	0.877	SUBCLONAL	1	TRUE	1	0.19	2		327	453	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115441	115115443	+	inframe_deletion	In_Frame_Del	DEL	GTC	GTC	-	novel	NA	P-0023350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	78	875	0	ENST00000257566.3:c.883_885del	p.Asp295del	p.D295del	ENST00000257566	NM_016569.3	295	GAC/-	5/8	1	2	FACETS	0.921	0.808	1	0.921	0.808	1	CLONAL	1	TRUE	1	0.19	2		875	891	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842331	68842331	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	35	717	0	ENST00000261769.5:c.392C>G	p.Ser131Cys	p.S131C	ENST00000261769	NM_004360.3	131	tCc/tGc	4/16	1	2	FACETS	0.758	0.621	0.912	0.758	0.621	0.912	CLONAL	1	TRUE	1	0.19	2		717	486	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842340	68842396	+	protein_altering_variant	In_Frame_Del	DEL	GAATCCAAGCAGAATTGCTCACATTTCCCAACTCCTCTCCTGGCCTCAGAAGACAGA	GAATCCAAGCAGAATTGCTCACATTTCCCAACTCCTCTCCTGGCCTCAGAAGACAGA	AAAGCCAGG	novel	NA	P-0023350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	52	1008	5	ENST00000261769.5:c.401_457delinsAAAGCCAGG	p.Gly134_Lys153delinsGluSerGlnGlu	p.G134_K153delinsESQE	ENST00000261769	NM_004360.3	134	gGAATCCAAGCAGAATTGCTCACATTTCCCAACTCCTCTCCTGGCCTCAGAAGACAGAag/gAAAGCCAGGag	4/16	1	2	FACETS	0.849	0.722	0.988	0.849	0.722	0.988	CLONAL	1	TRUE	1	0.19	2		1013	645	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004984	150004984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	45	583	0	ENST00000253339.5:c.1241G>A	p.Arg414Lys	p.R414K	ENST00000253339		414	aGa/aAa	3/7	1	2	FACETS	0.892	0.749	1	0.892	0.749	1	CLONAL	1	TRUE	1	0.19	2		583	531	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0023354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	81	606	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	0.27270782204146	2		606	532	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278106	41278106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	41	573	0	ENST00000349496.5:c.1982G>A	p.Arg661Gln	p.R661Q	ENST00000349496	NM_001904.3	661	cGa/cAa	13/15	1	2	FACETS	0.674	0.562	0.799	0.674	0.562	0.799	SUBCLONAL	1	TRUE	1	0.27270782204146	2		573	446	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578401	7578401	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147002414	NA	P-0023354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	122	828	0	ENST00000269305.4:c.529C>T	p.Pro177Ser	p.P177S	ENST00000269305	NM_001126112.2	177	Ccc/Tcc	5/11	0.27270782204146	1	FACETS	0.756	0.687	0.828	1	0.986	1	SUBCLONAL	2	TRUE	0	0.27270782204146	1		828	511	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593397	48593397	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs377767355	NA	P-0023354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	62	432	0	ENST00000342988.3:c.1148T>A	p.Ile383Lys	p.I383K	ENST00000342988	NM_005359.5	383	aTa/aAa	10/12	0.27270782204146	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.27270782204146	1		432	328	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295211	1295211	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0023354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	35	453	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.913	0.752	1	0.913	0.752	1	CLONAL	1	TRUE	1	0.27270782204146	2		454	281	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929266	44929267	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TAACAATGTG	novel	NA	P-0023354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	89	912	0	ENST00000377967.4:c.2367_2376dup	p.Gly793Ter	p.G793*	ENST00000377967	NM_021140.2	789	aat/aaTAACAATGTGt	17/29	0.27270782204146	1	FACETS	0.906	0.804	1	0.906	0.804	1	CLONAL	1	TRUE	0	0.27270782204146	1		912	622	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0023357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	100	278	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.918	0.828	1	0.918	0.828	1	CLONAL	1	TRUE	1	0.621004560673661	2		278	351	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625159	69625159	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554980306	NA	P-0023357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	104	744	3	ENST00000334134.2:c.634C>T	p.Arg212Trp	p.R212W	ENST00000334134	NM_005247.2	212	Cgg/Tgg	3/3	1	2	FACETS	0.575	0.516	0.637	0.575	0.516	0.637	SUBCLONAL	1	TRUE	1	0.621004560673661	2		747	583	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414854	78414854	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	107	395	0	ENST00000370768.2:c.1912C>T	p.Pro638Ser	p.P638S	ENST00000370768	NM_003902.3	638	Cct/Tct	19/20	1	2	FACETS	0.838	0.758	0.923	0.838	0.758	0.923	CLONAL	1	TRUE	1	0.621004560673661	2		395	411	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849652	68849652	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	160	514	0	ENST00000261769.5:c.1555C>T	p.Gln519Ter	p.Q519*	ENST00000261769	NM_004360.3	519	Cag/Tag	10/16	0.617806423612604	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.621004560673661	1		514	334	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571975	64571975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224527	NA	P-0023360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	253	726	0	ENST00000312049.6:c.1664G>A	p.Ser555Asn	p.S555N	ENST00000312049	NM_130799.2	555	aGt/aAt	10/10	0.665791199758631	1	FACETS	0.973	0.921	1	0.973	0.921	1	CLONAL	1	TRUE	0	0.665791199758631	1		726	521	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32968894	32968894	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	120	401	0	ENST00000380152.3:c.9325C>A	p.Leu3109Ile	p.L3109I	ENST00000380152		3109	Ctt/Att	25/27	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.665791199758631	2		401	358	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0023367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	91	364	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.678880392741316	2		364	243	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	147	669	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.678880392741316	2		669	401	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0023367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	82	336	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.926	0.827	1	0.926	0.827	1	CLONAL	1	TRUE	1	0.678880392741316	2		336	261	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023423	27023423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	106	538	1	ENST00000324856.7:c.529C>T	p.Gln177Ter	p.Q177*	ENST00000324856	NM_006015.4	177	Caa/Taa	1/20	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.678880392741316	2		539	293	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339326	70339334	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTGAGAC	AGGTGAGAC	-	novel	NA	P-0023367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	105	458	0	ENST00000374080.3:c.204_204+8del		p.X68_splice	ENST00000374080		68		2/45	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.678880392741316	2		458	264	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0023383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	352	670	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.699199999274759	2	FACETS	0.954	0.921	0.985	0.954	0.921	0.985	CLONAL	2	TRUE	0	0.759254157943864	2		671	486	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	543	781	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	1	0.940963697009302	2		786	774	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	448	656	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	NA	2	FACETS	0.844	0.822	0.865			1	INDETERMINATE	2	TRUE	NA	0.940963697009302	2		656	564	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	159	255	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.876	0.813	0.939	0.876	0.813	0.939	CLONAL	1	TRUE	1	0.940963697009302	2		255	386	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	239	655	2	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	1	2	FACETS	0.855	0.805	0.906	0.855	0.805	0.906	CLONAL	1	TRUE	1	0.940963697009302	2		657	594	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743932	41743933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs778012871	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	424	1072	5	ENST00000301178.4:c.874dup	p.His292ProfsTer47	p.H292Pfs*47	ENST00000301178	NM_021913.4	289	-/C	7/20	1	2	FACETS	0.857	0.819	0.896	0.857	0.819	0.896	CLONAL	1	TRUE	1	0.940963697009302	2		1077	1051	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514495	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	307	670	1	ENST00000269305.4:c.542G>A	p.Arg181His	p.R181H	ENST00000269305	NM_001126112.2	181	cGc/cAc	5/11	1	2	FACETS	0.968	0.92	1	0.968	0.92	1	CLONAL	1	TRUE	1	0.940963697009302	2		671	674	SUCCESS
AR	367	MSKCC	GRCh37	X	66943543	66943543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852581	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	51	297	0	ENST00000374690.3:c.2623C>T	p.His875Tyr	p.H875Y	ENST00000374690	NM_000044.3	875	Cat/Tat	8/8	1	1	FACETS	0.227	0.194	0.262	0.227	0.194	0.262	SUBCLONAL	1	TRUE	0	0.940963697009302	1		297	253	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716217	52716217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1173183954	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	282	634	0	ENST00000322088.6:c.661C>T	p.Arg221Trp	p.R221W	ENST00000322088	NM_014225.5	221	Cgg/Tgg	6/15	1	2	FACETS	0.979	0.929	1	0.979	0.929	1	CLONAL	1	TRUE	1	0.940963697009302	2		634	612	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100425	8100425	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	155	913	4	ENST00000346208.3:c.404del	p.Pro135ArgfsTer60	p.P135Rfs*60	ENST00000346208		133	taC/ta	3/6	1	2	FACETS	0.37	0.339	0.403	0.37	0.339	0.403	SUBCLONAL	1	TRUE	1	0.940963697009302	2		917	890	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138319	2138319	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373365980	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	318	737	0	ENST00000219476.3:c.5252G>A	p.Arg1751His	p.R1751H	ENST00000219476	NM_000548.3	1751	cGc/cAc	41/42	1	2	FACETS	0.899	0.853	0.945	0.899	0.853	0.945	CLONAL	1	TRUE	1	0.940963697009302	2		737	752	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907683	111907683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146318804	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	259	501	0	ENST00000393256.3:c.457C>T	p.Arg153Trp	p.R153W	ENST00000393256	NM_006538.4	153	Cgg/Tgg	3/4	1	2	FACETS	0.967	0.915	1	0.967	0.915	1	CLONAL	1	TRUE	1	0.940963697009302	2		501	569	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214591	5214591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770889503	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	47	839	1	ENST00000357368.4:c.4475G>A	p.Arg1492Gln	p.R1492Q	ENST00000357368	NM_002850.3	1492	cGg/cAg	29/38	1	2	FACETS	0.115	0.096	0.136	0.115	0.096	0.136	SUBCLONAL	1	TRUE	1	0.940963697009302	2		840	867	SUCCESS
AR	367	MSKCC	GRCh37	X	66931504	66931504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1340026226	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	105	416	0	ENST00000374690.3:c.2146G>A	p.Val716Met	p.V716M	ENST00000374690	NM_000044.3	716	Gtg/Atg	4/8	1	1	FACETS	0.386	0.35	0.423	0.386	0.35	0.423	SUBCLONAL	1	TRUE	0	0.940963697009302	1		416	306	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217230	11217230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786205165	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	309	433	0	ENST00000361445.4:c.4448G>A	p.Cys1483Tyr	p.C1483Y	ENST00000361445	NM_004958.3	1483	tGc/tAc	30/58	1	2	FACETS	0.926	0.879	0.974	0.926	0.879	0.974	CLONAL	1	TRUE	1	0.940963697009302	2		433	709	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713738	30713738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893813	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	202	536	0	ENST00000295754.5:c.1063G>A	p.Ala355Thr	p.A355T	ENST00000295754	NM_003242.5	355	Gcc/Acc	4/7	1	2	FACETS	0.982	0.923	1	0.982	0.923	1	CLONAL	1	TRUE	1	0.940963697009302	2		536	437	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684342	29684342	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	58	800	0	ENST00000356175.3:c.7862A>G	p.Tyr2621Cys	p.Y2621C	ENST00000356175	NM_000267.3	2621	tAc/tGc	53/57	1	2	FACETS	0.368	0.318	0.422	0.368	0.318	0.422	SUBCLONAL	1	TRUE	1	0.940963697009302	2		800	335	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252757	10252757	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	116	765	0	ENST00000340748.4:c.3208G>A	p.Glu1070Lys	p.E1070K	ENST00000340748		1070	Gag/Aag	29/40	1	2	FACETS	0.303	0.272	0.335	0.303	0.272	0.335	SUBCLONAL	1	TRUE	1	0.940963697009302	2		765	815	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270529	98270530	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs751977093	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	59	403	2	ENST00000331920.6:c.114dup	p.Leu39AlafsTer51	p.L39Afs*51	ENST00000331920	NM_000264.3	38	-/G	1/24	1	2	FACETS	0.274	0.236	0.316	0.274	0.236	0.316	SUBCLONAL	1	TRUE	1	0.940963697009302	2		405	457	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465448	99465448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773205989	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	265	600	0	ENST00000268035.6:c.2273C>T	p.Thr758Met	p.T758M	ENST00000268035	NM_000875.3	758	aCg/aTg	11/21	1	2	FACETS	0.966	0.914	1	0.966	0.914	1	CLONAL	1	TRUE	1	0.940963697009302	2		600	583	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138135	2138135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201206500	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	367	903	1	ENST00000219476.3:c.5155G>A	p.Ala1719Thr	p.A1719T	ENST00000219476	NM_000548.3	1719	Gca/Aca	40/42	1	2	FACETS	0.985	0.94	1	0.985	0.94	1	CLONAL	1	TRUE	1	0.940963697009302	2		904	792	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421541	32421541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	332	791	0	ENST00000332351.3:c.1051G>A	p.Gly351Arg	p.G351R	ENST00000332351	NM_024426.4	351	Gga/Aga	6/10	1	2	FACETS	0.941	0.895	0.987	0.941	0.895	0.987	CLONAL	1	TRUE	1	0.940963697009302	2		791	750	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622516	158622516	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs387906589	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	180	688	2	ENST00000263640.3:c.983G>T	p.Gly328Val	p.G328V	ENST00000263640	NM_001105.4	328	gGg/gTg	8/11	1	2	FACETS	0.922	0.861	0.984	0.922	0.861	0.984	CLONAL	1	TRUE	1	0.940963697009302	2		690	415	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492897	8492897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs544419494	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	281	656	0	ENST00000356435.5:c.2432G>A	p.Arg811His	p.R811H	ENST00000356435		811	cGc/cAc	16/35	1	2	FACETS	0.956	0.906	1	0.956	0.906	1	CLONAL	1	TRUE	1	0.940963697009302	2		656	625	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	849	1111	2	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.894	0.879	0.909	1	0.999	1	CLONAL	2	TRUE	1	0.940963697009302	2		1113	1009	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52725368	52725368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	268	640	0	ENST00000322088.6:c.1535G>A	p.Cys512Tyr	p.C512Y	ENST00000322088	NM_014225.5	512	tGt/tAt	13/15	1	2	FACETS	0.951	0.9	1	0.951	0.9	1	CLONAL	1	TRUE	1	0.940963697009302	2		640	599	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	113	542	0	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.256	0.23	0.284	0.256	0.23	0.284	SUBCLONAL	1	TRUE	1	0.940963697009302	2		542	939	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	168	885	1	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.39	0.358	0.423	0.39	0.358	0.423	SUBCLONAL	1	TRUE	1	0.940963697009302	2		886	915	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40874872	40874874	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	241	991	0	ENST00000428826.2:c.426_428del	p.Glu142del	p.E142del	ENST00000428826		142	gaAGAt/gat	6/21	1	2	FACETS	0.897	0.845	0.95	0.897	0.845	0.95	CLONAL	1	TRUE	1	0.940963697009302	2		991	571	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	388	570	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.926	0.884	0.968	0.926	0.884	0.968	CLONAL	1	TRUE	1	0.940963697009302	2		570	891	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456798	32456798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1397886023	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	329	712	1	ENST00000332351.3:c.94G>A	p.Gly32Arg	p.G32R	ENST00000332351	NM_024426.4	32	Gga/Aga	1/10	1	2	FACETS	0.899	0.854	0.944	0.899	0.854	0.944	CLONAL	1	TRUE	1	0.940963697009302	2		713	778	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	179	711	35	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.940963697009302	2		746	373	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43746203	43746203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs114262569	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	43	755	2	ENST00000523873.1:c.322C>T	p.Arg108Trp	p.R108W	ENST00000523873		108	Cgg/Tgg	4/8	1	2	FACETS	0.137	0.114	0.163	0.137	0.114	0.163	SUBCLONAL	1	TRUE	1	0.940963697009302	2		757	666	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060955	38060955	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	29	516	0	ENST00000250448.2:c.1034del	p.Gly345AlafsTer5	p.G345Afs*5	ENST00000250448	NM_004496.3	345	gGc/gc	2/2	1	2	FACETS	0.139	0.111	0.171	0.139	0.111	0.171	SUBCLONAL	1	TRUE	1	0.940963697009302	2		516	444	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992720	68992721	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs764112302	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	150	808	3	ENST00000288368.4:c.1693dup	p.Ser565PhefsTer3	p.S565Ffs*3	ENST00000288368	NM_024870.2	562	cgt/cgTt	16/40	1	2	FACETS	0.781	0.722	0.842	0.781	0.722	0.842	SUBCLONAL	1	TRUE	1	0.940963697009302	2		811	408	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602565	10602565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	312	820	0	ENST00000171111.5:c.1013C>T	p.Ser338Leu	p.S338L	ENST00000171111	NM_203500.1	338	tCg/tTg	3/6	1	2	FACETS	0.835	0.792	0.879	0.835	0.792	0.879	CLONAL	1	TRUE	1	0.940963697009302	2		820	794	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432738	49432738	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555191203	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	360	855	1	ENST00000301067.7:c.8401C>T	p.Arg2801Ter	p.R2801*	ENST00000301067	NM_003482.3	2801	Cga/Tga	34/54	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.940963697009302	2		856	751	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11181406	11181406	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	54	939	0	ENST00000361445.4:c.6830A>G	p.His2277Arg	p.H2277R	ENST00000361445	NM_004958.3	2277	cAc/cGc	49/58	1	2	FACETS	0.141	0.12	0.164	0.141	0.12	0.164	SUBCLONAL	1	TRUE	1	0.940963697009302	2		939	815	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182071	11182073	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs1196560364	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	166	736	0	ENST00000361445.4:c.6773_6775del	p.Lys2258del	p.K2258del	ENST00000361445	NM_004958.3	2258	aAGAtc/atc	48/58	1	2	FACETS	0.581	0.536	0.628	0.581	0.536	0.628	SUBCLONAL	1	TRUE	1	0.940963697009302	2		736	607	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255986	16255986	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	209	628	0	ENST00000375759.3:c.3251T>C	p.Leu1084Pro	p.L1084P	ENST00000375759	NM_015001.2	1084	cTa/cCa	11/15	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.940963697009302	2		628	437	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262695	16262696	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	29	564	0	ENST00000375759.3:c.9967_9968del	p.Thr3323SerfsTer24	p.T3323Sfs*24	ENST00000375759	NM_015001.2	3320	ctCAca/ctca	11/15	1	2	FACETS	0.107	0.086	0.132	0.107	0.086	0.132	SUBCLONAL	1	TRUE	1	0.940963697009302	2		564	574	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726435	46726435	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142433634	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	198	569	0	ENST00000371975.4:c.514C>T	p.Arg172Cys	p.R172C	ENST00000371975	NM_003579.3	172	Cgc/Tgc	7/18	1	2	FACETS	0.843	0.789	0.899	0.843	0.789	0.899	CLONAL	1	TRUE	1	0.940963697009302	2		569	499	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471713	120471713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	239	561	1	ENST00000256646.2:c.3778C>T	p.Arg1260Cys	p.R1260C	ENST00000256646	NM_024408.3	1260	Cgt/Tgt	23/34	1	2	FACETS	0.925	0.872	0.979	0.925	0.872	0.979	CLONAL	1	TRUE	1	0.940963697009302	2		562	549	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195544	102195544	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs922637067	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	167	677	1	ENST00000263464.3:c.304G>A	p.Val102Ile	p.V102I	ENST00000263464	NM_001165.4	102	Gtt/Att	2/9	1	2	FACETS	0.872	0.811	0.934	0.872	0.811	0.934	CLONAL	1	TRUE	1	0.940963697009302	2		678	407	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374498	118374498	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	173	514	0	ENST00000534358.1:c.7896del	p.Phe2632LeufsTer9	p.F2632Lfs*9	ENST00000534358	NM_005933.3	2631	Ttt/tt	27/36	1	2	FACETS	0.832	0.774	0.891	0.832	0.774	0.891	CLONAL	1	TRUE	1	0.940963697009302	2		514	442	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230734	46230734	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	119	473	1	ENST00000334344.6:c.983G>A	p.Arg328Lys	p.R328K	ENST00000334344	NM_152641.2	328	aGg/aAg	8/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.940963697009302	2		474	242	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425047	49425047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778628310	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	386	918	0	ENST00000301067.7:c.13441G>A	p.Glu4481Lys	p.E4481K	ENST00000301067	NM_003482.3	4481	Gag/Aag	39/54	1	2	FACETS	0.918	0.876	0.96	0.918	0.876	0.96	CLONAL	1	TRUE	1	0.940963697009302	2		918	894	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871609	35871610	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	129	394	0	ENST00000216797.5:c.896_897del	p.Thr299ArgfsTer7	p.T299Rfs*7	ENST00000216797	NM_020529.2	299	aCA/a	5/6	1	2	FACETS	0.87	0.801	0.941	0.87	0.801	0.941	CLONAL	1	TRUE	1	0.940963697009302	2		394	315	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631620	90631620	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745751309	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	409	797	2	ENST00000330062.3:c.649G>A	p.Val217Met	p.V217M	ENST00000330062	NM_002168.2	217	Gtg/Atg	5/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.940963697009302	2		799	845	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658800	3658800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746769352	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	112	836	0	ENST00000294008.3:c.166G>A	p.Ala56Thr	p.A56T	ENST00000294008	NM_032444.2	56	Gct/Act	2/15	1	2	FACETS	0.403	0.364	0.445	0.403	0.364	0.445	SUBCLONAL	1	TRUE	1	0.940963697009302	2		836	590	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644818	67644818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773609766	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	210	580	1	ENST00000264010.4:c.83G>A	p.Arg28His	p.R28H	ENST00000264010	NM_006565.3	28	cGc/cAc	3/12	0.89923737931934	2	FACETS	0.926	0.869	0.983	0.463	0.434	0.492	CLONAL	1	TRUE	0	0.940963697009302	2		581	482	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831525	72831526	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	590	751	0	ENST00000268489.5:c.5055_5056del	p.Ser1687CysfsTer86	p.S1687Cfs*86	ENST00000268489	NM_006885.3	1685	acTGag/acag	9/10	0.89923737931934	2	FACETS	0.929	0.912	0.945	0.929	0.912	0.945	CLONAL	2	TRUE	0	0.940963697009302	2		751	675	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348338	89348338	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1161378737	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	66	1185	0	ENST00000301030.4:c.4612G>A	p.Ala1538Thr	p.A1538T	ENST00000301030	NM_001256183.1	1538	Gca/Aca	9/13	0.89923737931934	2	FACETS	0.135	0.117	0.155	0.068	0.058	0.078	SUBCLONAL	1	TRUE	0	0.940963697009302	2		1185	1038	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577071	7577072	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	397	886	0	ENST00000269305.4:c.866_867del	p.Leu289ProfsTer16	p.L289Pfs*16	ENST00000269305	NM_001126112.2	289	cTC/c	8/11	1	2	FACETS	0.905	0.865	0.947	0.905	0.865	0.947	CLONAL	1	TRUE	1	0.940963697009302	2		886	932	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222049	2222049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769178549	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	469	959	1	ENST00000398665.3:c.2881G>A	p.Glu961Lys	p.E961K	ENST00000398665	NM_032482.2	961	Gag/Aag	24/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.940963697009302	2		960	985	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300159	15300159	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1435305678	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	390	964	2	ENST00000263388.2:c.1117G>A	p.Gly373Ser	p.G373S	ENST00000263388	NM_000435.2	373	Ggc/Agc	7/33	1	2	FACETS	0.924	0.882	0.966	0.924	0.882	0.966	CLONAL	1	TRUE	1	0.940963697009302	2		966	897	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731545	47731545	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	55	47	0	ENST00000449228.1:c.247del	p.Arg83AlafsTer146	p.R83Afs*146	ENST00000449228	NM_001127240.2	83	Cgc/gc	2/4	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.940963697009302	2		47	95	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519794	29519794	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	45	738	0	ENST00000389048.3:c.1777T>C	p.Trp593Arg	p.W593R	ENST00000389048	NM_004304.4	593	Tgg/Cgg	9/29	1	2	FACETS	0.13	0.109	0.154	0.13	0.109	0.154	SUBCLONAL	1	TRUE	1	0.940963697009302	2		738	733	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657008	47657008	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63751412	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	130	487	0	ENST00000233146.2:c.1204C>T	p.Gln402Ter	p.Q402*	ENST00000233146	NM_000251.2	402	Caa/Taa	7/16	1	2	FACETS	0.915	0.844	0.987	0.915	0.844	0.987	CLONAL	1	TRUE	1	0.940963697009302	2		487	302	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702188	47702188	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	190	554	0	ENST00000233146.2:c.1784T>C	p.Leu595Pro	p.L595P	ENST00000233146	NM_000251.2	595	cTc/cCc	12/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.940963697009302	2		554	385	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026992	48026992	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868760377	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	99	479	0	ENST00000234420.5:c.1870G>A	p.Gly624Ser	p.G624S	ENST00000234420	NM_000179.2	624	Ggc/Agc	4/10	1	2	FACETS	0.859	0.781	0.938	0.859	0.781	0.938	CLONAL	1	TRUE	1	0.940963697009302	2		479	245	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99203949	99203949	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1370549873	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	121	452	2	ENST00000074304.5:c.2812C>T	p.Arg938Ter	p.R938*	ENST00000074304	NM_001134224.1	938	Cga/Tga	26/26	1	2	FACETS	0.872	0.8	0.944	0.872	0.8	0.944	CLONAL	1	TRUE	1	0.940963697009302	2		454	295	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095665	178095666	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	22	662	0	ENST00000397062.3:c.1665dup	p.Gln556ThrfsTer15	p.Q556Tfs*15	ENST00000397062	NM_006164.4	555	-/A	5/5	1	2	FACETS	0.146	0.113	0.184	0.146	0.113	0.184	SUBCLONAL	1	TRUE	1	0.940963697009302	2		662	321	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478756	57478757	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	29	480	1	ENST00000371085.3:c.348dup	p.Val117ArgfsTer23	p.V117Rfs*23	ENST00000371085	NM_000516.4	114	-/C	5/13	1	2	FACETS	0.125	0.1	0.154	0.125	0.1	0.154	SUBCLONAL	1	TRUE	1	0.940963697009302	2		481	492	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050333	37050333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763992299	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	157	574	1	ENST00000231790.2:c.482C>T	p.Thr161Met	p.T161M	ENST00000231790	NM_000249.3	161	aCg/aTg	6/19	1	2	FACETS	0.94	0.874	1	0.94	0.874	1	CLONAL	1	TRUE	1	0.940963697009302	2		575	355	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665081	138665081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	122	299	0	ENST00000330315.3:c.484C>T	p.Pro162Ser	p.P162S	ENST00000330315	NM_023067.3	162	Ccc/Tcc	1/1	1	2	FACETS	0.776	0.711	0.844	0.776	0.711	0.844	SUBCLONAL	1	TRUE	1	0.940963697009302	2		299	334	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607190	189607190	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	53	928	1	ENST00000264731.3:c.1569G>T	p.Gln523His	p.Q523H	ENST00000264731	NM_003722.4	523	caG/caT	12/14	1	2	FACETS	0.112	0.095	0.131	0.112	0.095	0.131	SUBCLONAL	1	TRUE	1	0.940963697009302	2		929	1003	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133797	55133797	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	35	636	0	ENST00000257290.5:c.1010T>C	p.Val337Ala	p.V337A	ENST00000257290	NM_006206.4	337	gTa/gCa	7/23	1	2	FACETS	0.152	0.124	0.183	0.152	0.124	0.183	SUBCLONAL	1	TRUE	1	0.940963697009302	2		636	491	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332934	153332934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	21	445	0	ENST00000281708.4:c.22G>A	p.Val8Met	p.V8M	ENST00000281708	NM_033632.3	8	Gtg/Atg	2/12	1	2	FACETS	0.108	0.083	0.138	0.108	0.083	0.138	SUBCLONAL	1	TRUE	1	0.940963697009302	2		445	413	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293848	1293848	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	493	1070	3	ENST00000310581.5:c.1153C>T	p.Arg385Cys	p.R385C	ENST00000310581	NM_198253.2	385	Cgc/Tgc	2/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.940963697009302	2		1073	1017	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871259	35871259	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs200233367	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	158	541	0	ENST00000303115.3:c.481A>G	p.Lys161Glu	p.K161E	ENST00000303115	NM_002185.3	161	Aaa/Gaa	4/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.940963697009302	2		541	312	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057753	180057753	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761266143	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	137	684	0	ENST00000261937.6:c.202C>T	p.Pro68Ser	p.P68S	ENST00000261937	NM_182925.4	68	Cca/Tca	3/30	1	2	FACETS	0.378	0.344	0.414	0.378	0.344	0.414	SUBCLONAL	1	TRUE	1	0.940963697009302	2		684	770	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32814922	32814922	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs375324960	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	362	906	1	ENST00000354258.4:c.2143C>T	p.Arg715Ter	p.R715*	ENST00000354258	NM_000593.5	715	Cga/Tga	10/11	1	2	FACETS	0.873	0.832	0.916	0.873	0.832	0.916	CLONAL	1	TRUE	1	0.940963697009302	2		907	881	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286573	33286573	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	252	559	0	ENST00000374542.5:c.2170G>T	p.Val724Leu	p.V724L	ENST00000374542	NM_001141970.1	724	Gtg/Ttg	8/8	1	2	FACETS	0.903	0.852	0.955	0.903	0.852	0.955	CLONAL	1	TRUE	1	0.940963697009302	2		559	593	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845572	128845572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775852783	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	297	666	2	ENST00000249373.3:c.869G>A	p.Arg290His	p.R290H	ENST00000249373	NM_005631.4	290	cGc/cAc	4/12	1	2	FACETS	0.997	0.947	1	0.997	0.947	1	CLONAL	1	TRUE	1	0.940963697009302	2		668	633	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285509	38285509	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	346	878	0	ENST00000425967.3:c.644del	p.Pro215GlnfsTer8	p.P215Qfs*8	ENST00000425967	NM_001174067.1	215	cCa/ca	6/19	1	2	FACETS	0.945	0.9	0.99	0.945	0.9	0.99	CLONAL	1	TRUE	1	0.940963697009302	2		878	778	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500885	8500885	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	229	745	0	ENST00000356435.5:c.1997C>A	p.Pro666His	p.P666H	ENST00000356435		666	cCt/cAt	13/35	1	2	FACETS	0.962	0.906	1	0.962	0.906	1	CLONAL	1	TRUE	1	0.940963697009302	2		745	506	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405155	139405155	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	127	950	2	ENST00000277541.6:c.2690C>T	p.Ala897Val	p.A897V	ENST00000277541	NM_017617.3	897	gCc/gTc	17/34	1	2	FACETS	0.291	0.263	0.321	0.291	0.263	0.321	SUBCLONAL	1	TRUE	1	0.940963697009302	2		952	927	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	198	726	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.677916910264776	2		726	577	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061240	38061240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	211	846	0	ENST00000250448.2:c.749C>T	p.Ser250Phe	p.S250F	ENST00000250448	NM_004496.3	250	tCc/tTc	2/2	1	2	FACETS	0.987	0.922	1	0.987	0.922	1	CLONAL	1	TRUE	1	0.677916910264776	2		846	631	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097836	8097836	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	190	729	0	ENST00000346208.3:c.218A>T	p.Gln73Leu	p.Q73L	ENST00000346208		73	cAg/cTg	2/6	1	2	FACETS	0.966	0.899	1	0.966	0.899	1	CLONAL	1	TRUE	1	0.677916910264776	2		729	580	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265247	16265247	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	171	626	0	ENST00000375759.3:c.10739C>A	p.Pro3580His	p.P3580H	ENST00000375759	NM_015001.2	3580	cCc/cAc	14/15	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.677916910264776	2		626	497	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829584	72829585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	90	820	0	ENST00000268489.5:c.6996dup	p.Cys2333MetfsTer2	p.C2333Mfs*2	ENST00000268489	NM_006885.3	2332	-/A	9/10	1	2	FACETS	0.421	0.373	0.471	0.421	0.373	0.471	SUBCLONAL	1	TRUE	1	0.677916910264776	2		820	631	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169005	11169005	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	36	826	0	ENST00000358026.2:c.4595T>A	p.Leu1532His	p.L1532H	ENST00000358026	NM_001128849.1	1532	cTc/cAc	32/36	1	2	FACETS	0.155	0.127	0.187	0.155	0.127	0.187	SUBCLONAL	1	TRUE	1	0.677916910264776	2		826	686	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214163	36214163	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0023421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	287	891	1	ENST00000222270.7:c.2989A>T	p.Lys997Ter	p.K997*	ENST00000222270	NM_014727.1	997	Aag/Tag	6/37	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.677916910264776	2		892	768	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548281	41548281	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	139	494	0	ENST00000263253.7:c.3072del	p.Glu1025ArgfsTer34	p.E1025Rfs*34	ENST00000263253	NM_001429.3	1023	atA/at	16/31	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.677916910264776	2		494	391	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846308	156846308	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	246	989	2	ENST00000524377.1:c.1753del	p.Leu585CysfsTer73	p.L585Cfs*73	ENST00000524377	NM_002529.3	583	cgC/cg	14/17	0.70828967816419	4	FACETS	0.844	0.794	0.895	0.844	0.794	0.895	CLONAL	2	TRUE	2	0.76384883436071	4		991	673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781504	NA	P-0023438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	642	953	0	ENST00000269305.4:c.314G>T	p.Gly105Val	p.G105V	ENST00000269305	NM_001126112.2	105	gGc/gTc	4/11	0.697411174312903	4	FACETS	1	0.986	1			1	CLONAL	4	TRUE	NA	0.76384883436071	4		953	738	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494693	2494693	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	272	909	1	ENST00000355716.4:c.833G>T	p.Gly278Val	p.G278V	ENST00000355716	NM_003820.2	278	gGg/gTg	8/8	0.76384883436071	3	FACETS	0.99	0.942	1	0.99	0.942	1	CLONAL	2	TRUE	1	0.76384883436071	3		910	497	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161326608	161326608	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	294	836	0	ENST00000367975.2:c.384del	p.Trp129GlyfsTer7	p.W129Gfs*7	ENST00000367975	NM_003001.3	128	aCc/ac	5/6	0.70828967816419	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.76384883436071	4		836	660	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226553675	226553675	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	174	578	0	ENST00000366794.5:c.2485T>A	p.Tyr829Asn	p.Y829N	ENST00000366794	NM_001618.3	829	Tat/Aat	18/23	0.76384883436071	7	FACETS	0.866	0.799	0.936	0.347	0.319	0.375	CLONAL	2	TRUE	2	0.76384883436071	7		578	765	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759948	63759948	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	82	368	0	ENST00000279873.7:c.601A>G	p.Ile201Val	p.I201V	ENST00000279873	NM_032199.2	201	Att/Gtt	4/10	0.76384883436071	3	FACETS	0.817	0.726	0.914	0.409	0.363	0.457	CLONAL	1	TRUE	1	0.76384883436071	3		368	363	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359457	118359457	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	185	508	0	ENST00000534358.1:c.4461G>T	p.Arg1487Ser	p.R1487S	ENST00000534358	NM_005933.3	1487	agG/agT	11/36	0.438730910243782	4	FACETS	1	0.978	1			1	INDETERMINATE	2	TRUE	NA	0.76384883436071	4		508	390	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169145	119169145	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	119	724	1	ENST00000264033.4:c.2329C>A	p.Pro777Thr	p.P777T	ENST00000264033	NM_005188.3	777	Cca/Aca	15/16	0.438730910243782	4	FACETS	1	0.962	1			1	INDETERMINATE	1	TRUE	NA	0.76384883436071	4		725	492	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118824	115118824	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	549	719	0	ENST00000257566.3:c.517G>C	p.Ala173Pro	p.A173P	ENST00000257566	NM_016569.3	173	Gct/Cct	2/8	0.76384883436071	4	FACETS	0.994	0.974	1	0.994	0.974	1	CLONAL	4	TRUE	0	0.76384883436071	4		719	638	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680637	88680637	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	98	588	0	ENST00000360948.2:c.620G>A	p.Cys207Tyr	p.C207Y	ENST00000360948	NM_001012338.2	207	tGt/tAt	6/19	1	2	FACETS	0.961	0.871	1	0.961	0.871	1	CLONAL	1	TRUE	1	0.76384883436071	2		588	267	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220371	1220371	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0023438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	249	747	0	ENST00000326873.7:c.465del		p.X155_splice	ENST00000326873	NM_000455.4	155			NA	2	FACETS	0.973	0.935	1			1	INDETERMINATE	2	TRUE	NA	0.76384883436071	2		747	335	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610311	10610311	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	369	1192	0	ENST00000171111.5:c.399G>T	p.Met133Ile	p.M133I	ENST00000171111	NM_203500.1	133	atG/atT	2/6	0.736980486832315	2	FACETS	0.947	0.916	0.978	0.947	0.916	0.978	CLONAL	2	TRUE	0	0.76384883436071	2		1192	510	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264391	46264391	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	97	575	0	ENST00000371998.3:c.1438A>T	p.Ile480Phe	p.I480F	ENST00000371998		480	Atc/Ttc	11/23	0.76384883436071	5	FACETS	0.587	0.523	0.656	0.196	0.174	0.219	SUBCLONAL	1	TRUE	2	0.76384883436071	5		575	928	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527633	41527634	+	stop_gained,inframe_insertion	Nonsense_Mutation	INS	-	-	ATGAGTAAGTTTGTGTCATCCTAATAACATGGTATTGGTTGTGTCAGTAAATGACATCTA	novel	NA	P-0023438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	89	535	0	ENST00000263253.7:c.1525_1528+56dup		p.-508MSKFVSS**HGIGCVSK*HL	ENST00000263253	NM_001429.3	508	-/ATGAGTAAGTTTGTGTCATCCTAATAACATGGTATTGGTTGTGTCAGTAAATGACATCTA	6/31	0.723293412341929	3	FACETS	0.647	0.575	0.722	0.216	0.191	0.241	SUBCLONAL	1	TRUE	0	0.76384883436071	3		535	498	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498496	89498496	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	141	393	0	ENST00000336596.2:c.2468G>T	p.Arg823Ile	p.R823I	ENST00000336596	NM_005233.5	823	aGa/aTa	14/17	0.742154818838636	2	FACETS	0.942	0.891	0.99	0.942	0.891	0.99	CLONAL	2	TRUE	0	0.76384883436071	2		393	196	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046086	180046086	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	58	575	0	ENST00000261937.6:c.2785T>G	p.Phe929Val	p.F929V	ENST00000261937	NM_182925.4	929	Ttc/Gtc	20/30	0.723293412341929	3	FACETS	0.999	0.871	1	0.333	0.29	0.379	CLONAL	1	TRUE	0	0.76384883436071	3		575	210	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945048	151945048	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	41	848	0	ENST00000262189.6:c.2471G>C	p.Gly824Ala	p.G824A	ENST00000262189	NM_170606.2	824	gGc/gCc	14/59	0.751220462743169	4	FACETS	0.391	0.326	0.464	0.13	0.108	0.155	SUBCLONAL	1	TRUE	1	0.76384883436071	4		848	484	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76953125	76953125	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0023438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	283	352	1	ENST00000373344.5:c.190-2A>T		p.X64_splice	ENST00000373344	NM_000489.3	64			0.695095879870772	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.76384883436071	2		353	326	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0023441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	127	442	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	0.426070523536797	3	FACETS	1	0.956	1	0.544	0.494	0.597	CLONAL	1	TRUE	1	0.462606053902248	3		442	621	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519938	NA	P-0023448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	121	528	0	ENST00000263967.3:c.1034A>T	p.Asn345Ile	p.N345I	ENST00000263967	NM_006218.2	345	aAt/aTt	5/21	1	2	FACETS	0.938	0.851	1	0.938	0.851	1	CLONAL	1	TRUE	1	0.440058255282745	2		528	586	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	109	543	0	ENST00000342988.3:c.1610A>T	p.Asp537Val	p.D537V	ENST00000342988	NM_005359.5	537	gAc/gTc	12/12	0.440058255282745	1	FACETS	0.849	0.767	0.935	0.849	0.767	0.935	CLONAL	1	TRUE	0	0.440058255282745	1		543	455	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398220	25398220	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	327	721	0	ENST00000311936.3:c.99T>A	p.Asp33Glu	p.D33E	ENST00000311936	NM_004985.3	33	gaT/gaA	2/5	0.440058255282745	3	FACETS	0.923	0.874	0.973	0.923	0.874	0.973	CLONAL	2	TRUE	1	0.440058255282745	3		721	982	SUCCESS
APC	324	MSKCC	GRCh37	5	112175147	112175147	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	226	231	0	ENST00000257430.4:c.3856G>T	p.Glu1286Ter	p.E1286*	ENST00000257430	NM_000038.5	1286	Gaa/Taa	16/16	0.440058255282745	3	FACETS	0.91	0.859	0.961	0.91	0.859	0.961	CLONAL	3	TRUE	0	0.440058255282745	3		231	459	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437573	56437574	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	195	803	1	ENST00000407977.2:c.888dup	p.Asn297Ter	p.N297*	ENST00000407977		296	-/T	8/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.440058255282745	2		804	782	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760879	133760879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749413196	NA	P-0023448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	205	984	0	ENST00000318560.5:c.3202G>A	p.Val1068Met	p.V1068M	ENST00000318560	NM_005157.4	1068	Gtg/Atg	11/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.440058255282745	2		984	885	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251805	212251805	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1176367181	NA	P-0023448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	107	527	0	ENST00000342788.4:c.3254C>A	p.Thr1085Asn	p.T1085N	ENST00000342788	NM_005235.2	1085	aCt/aAt	27/28	1	2	FACETS	0.914	0.823	1	0.914	0.823	1	CLONAL	1	TRUE	1	0.440058255282745	2		527	532	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38981967	38981967	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0023448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	122	573	0	ENST00000357387.3:c.753+2T>C		p.X251_splice	ENST00000357387	NM_152756.3	251			0.362932522352809	3	FACETS	1	0.942	1	0.527	0.477	0.579	CLONAL	1	TRUE	1	0.440058255282745	3		573	642	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865848	56865848	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	22	428	0	ENST00000308159.5:c.1180A>G	p.Ile394Val	p.I394V	ENST00000308159	NM_014669.4	394	Att/Gtt	11/22	0.269253648713912	1	FACETS	0.343	0.265	0.434	0.343	0.265	0.434	SUBCLONAL	1	TRUE	0	0.269253648713912	1		428	412	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742865	145742865	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1432766447	NA	P-0023458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	29	596	0	ENST00000428558.2:c.146A>G	p.Lys49Arg	p.K49R	ENST00000428558	NM_004260.3	49	aAg/aGg	3/22	1	2	FACETS	0.506	0.405	0.62	0.506	0.405	0.62	SUBCLONAL	1	TRUE	1	0.269253648713912	2		596	426	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0023464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	258	702	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.289861191647371	3	FACETS	0.78	0.732	0.831	0.78	0.732	0.831	SUBCLONAL	2	TRUE	1	0.408263693269834	3		702	975	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939673	76939674	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	140	1111	1	ENST00000373344.5:c.1074dup	p.Leu359ThrfsTer3	p.L359Tfs*3	ENST00000373344	NM_000489.3	358	-/A	9/35	NA	2	FACETS	0.628	0.571	0.688			1	INDETERMINATE	1	TRUE	NA	0.408263693269834	2		1112	1092	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139519	47139519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	132	868	0	ENST00000409792.3:c.5068G>A	p.Gly1690Arg	p.G1690R	ENST00000409792	NM_014159.6	1690	Gga/Aga	9/21	1	2	FACETS	0.723	0.655	0.793	0.723	0.655	0.793	SUBCLONAL	1	TRUE	1	0.408263693269834	2		868	895	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369223	118369223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	70	587	0	ENST00000534358.1:c.5941C>T	p.Arg1981Trp	p.R1981W	ENST00000534358	NM_005933.3	1981	Cgg/Tgg	22/36	0.243340227943299	4	FACETS	0.703	0.612	0.801	0.351	0.306	0.401	INDETERMINATE	1	TRUE	2	0.408263693269834	4		587	687	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609796	28609796	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	224	753	0	ENST00000241453.7:c.1433T>C	p.Ile478Thr	p.I478T	ENST00000241453	NM_004119.2	478	aTc/aCc	12/24	0.289861191647371	3	FACETS	0.777	0.725	0.831	0.777	0.725	0.831	SUBCLONAL	2	TRUE	1	0.408263693269834	3		753	850	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435149	56435149	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	265	825	0	ENST00000407977.2:c.1988C>T	p.Pro663Leu	p.P663L	ENST00000407977		663	cCc/cTc	9/10	0.310945985661273	5	FACETS	0.844	0.79	0.899	0.563	0.527	0.6	CLONAL	2	TRUE	2	0.408263693269834	5		825	1240	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285196	198285196	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	114	865	1	ENST00000335508.6:c.371G>T	p.Arg124Leu	p.R124L	ENST00000335508	NM_012433.2	124	cGg/cTg	4/25	0.289861191647371	3	FACETS	0.729	0.656	0.807	0.365	0.328	0.404	SUBCLONAL	1	TRUE	1	0.408263693269834	3		866	922	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643770	52643770	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	119	877	0	ENST00000394830.3:c.2126T>A	p.Ile709Asn	p.I709N	ENST00000394830	NM_018313.4	709	aTt/aAt	17/30	1	2	FACETS	0.683	0.616	0.754	0.683	0.616	0.754	SUBCLONAL	1	TRUE	1	0.408263693269834	2		877	853	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001284	150001284	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	103	903	0	ENST00000253339.5:c.2320G>T	p.Asp774Tyr	p.D774Y	ENST00000253339		774	Gat/Tat	4/7	0.289861191647371	3	FACETS	0.623	0.556	0.694	0.311	0.278	0.347	SUBCLONAL	1	TRUE	1	0.408263693269834	3		903	976	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636347	87636347	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	112	791	0	ENST00000277120.3:c.2512G>T	p.Gly838Cys	p.G838C	ENST00000277120		838	Ggc/Tgc	19/19	0.276332587296406	3	FACETS	0.707	0.635	0.784	0.354	0.317	0.392	SUBCLONAL	1	TRUE	1	0.408263693269834	3		791	934	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039372	47039372	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	138	888	1	ENST00000377604.3:c.995G>T	p.Arg332Leu	p.R332L	ENST00000377604	NM_001204468.1	332	cGc/cTc	10/24	0.391308352703755	1	FACETS	0.735	0.67	0.803	0.735	0.67	0.803	SUBCLONAL	1	TRUE	0	0.408263693269834	1		889	732	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722761	49722761	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs62262682	NA	P-0023474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	12	33	0	ENST00000449682.2:c.1478G>T	p.Arg493Leu	p.R493L	ENST00000449682	NM_020998.3	493	cGt/cTt	13/18	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.353029407141553	2		33	49	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412045	116412045	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0023474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	670	1054	2	ENST00000397752.3:c.3028+2T>C		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.344735858736219	4	FACETS	0.973	0.941	1	0.973	0.941	1	CLONAL	4	TRUE	0	0.353029407141553	4		1056	1320	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624974	9624974	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0023474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	50	320	0	ENST00000353224.5:c.3G>A	p.Met1?	p.M1?	ENST00000353224	NM_177990.2	1	atG/atA	3/10	0.353029407141553	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.353029407141553	1		320	209	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644389	18644389	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	55	511	0	ENST00000266497.5:c.2567T>A	p.Val856Glu	p.V856E	ENST00000266497		856	gTa/gAa	18/31	0.336113936164882	3	FACETS	0.765	0.655	0.885	0.383	0.327	0.443	SUBCLONAL	1	TRUE	1	0.353029407141553	3		511	479	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872440	35872440	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	129	702	0	ENST00000216797.5:c.463G>T	p.Gly155Cys	p.G155C	ENST00000216797	NM_020529.2	155	Ggc/Tgc	3/6	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.353029407141553	2		702	702	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618716	37618716	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1567669192	NA	P-0023474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	104	732	0	ENST00000447079.4:c.397del	p.Ser133AlafsTer11	p.S133Afs*11	ENST00000447079	NM_015083.1	131	gAa/ga	1/14	1	2	FACETS	0.86	0.771	0.955	0.86	0.771	0.955	CLONAL	1	TRUE	1	0.353029407141553	2		732	685	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034426	123034426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	55	669	0	ENST00000355640.3:c.1183G>A	p.Glu395Lys	p.E395K	ENST00000355640		395	Gaa/Aaa	6/7	0.202786003507957	1	FACETS	0.983	0.842	1	0.983	0.842	1	CLONAL	1	TRUE	0	0.202786003507957	1		669	496	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934954	9934954	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	30	484	0	ENST00000330684.3:c.1336A>G	p.Thr446Ala	p.T446A	ENST00000330684	NM_001134407.1	446	Acc/Gcc	6/13	0.202786003507957	3	FACETS	0.886	0.714	1	0.443	0.357	0.54	CLONAL	1	TRUE	1	0.202786003507957	3		484	368	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724365	52724365	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	52	566	0	ENST00000322088.6:c.1497G>A	p.Met499Ile	p.M499I	ENST00000322088	NM_014225.5	499	atG/atA	12/15	0.202786003507957	2	FACETS	1	0.941	1	0.606	0.517	0.703	CLONAL	1	TRUE	0	0.202786003507957	2		566	423	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273515	38273515	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	114	860	0	ENST00000425967.3:c.1820G>T	p.Arg607Leu	p.R607L	ENST00000425967	NM_001174067.1	607	cGg/cTg	14/19	0.202786003507957	2	FACETS	0.911	0.822	1	0.911	0.822	1	CLONAL	2	TRUE	0	0.202786003507957	2		860	617	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501249	140501249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	57	752	0	ENST00000288602.6:c.823G>A	p.Glu275Lys	p.E275K	ENST00000288602	NM_004333.4	275	Gaa/Aaa	6/18	0.144459563160582	4	FACETS	0.954	0.817	1	0.477	0.408	0.552	CLONAL	1	TRUE	2	0.202786003507957	4		752	709	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206646616	206646616	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	125	960	0	ENST00000367120.3:c.46G>C	p.Gly16Arg	p.G16R	ENST00000367120	NM_014002.3	16	Ggg/Cgg	3/22	0.102340650009886	4	FACETS	0.865	0.783	0.952	0.865	0.783	0.952	INDETERMINATE	2	TRUE	2	0.202786003507957	4		960	857	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575473	64575473	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	135	804	1	ENST00000312049.6:c.544G>T	p.Ala182Ser	p.A182S	ENST00000312049	NM_130799.2	182	Gcc/Tcc	3/10	0.202786003507957	3	FACETS	0.991	0.902	1	0.991	0.902	1	CLONAL	2	TRUE	1	0.202786003507957	3		805	740	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77085399	77085399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	49	573	2	ENST00000356341.3:c.451G>A	p.Glu151Lys	p.E151K	ENST00000356341	NM_002576.4	151	Gag/Aag	5/15	0.202786003507957	3	FACETS	0.963	0.815	1	0.481	0.407	0.563	CLONAL	1	TRUE	1	0.202786003507957	3		575	553	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656271	18656271	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	70	691	0	ENST00000266497.5:c.2950G>T	p.Gly984Ter	p.G984*	ENST00000266497		984	Gga/Tga	21/31	0.116839648264797	3	FACETS	1	0.971	1	0.717	0.626	0.815	INDETERMINATE	1	TRUE	1	0.202786003507957	3		691	530	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445116	49445116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	116	739	0	ENST00000301067.7:c.2350G>A	p.Glu784Lys	p.E784K	ENST00000301067	NM_003482.3	784	Gag/Aag	10/54	0.116839648264797	3	FACETS	1	0.938	1	1	0.938	1	INDETERMINATE	2	TRUE	1	0.202786003507957	3		739	600	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885460	111885460	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	85	608	0	ENST00000341259.2:c.1237C>A	p.His413Asn	p.H413N	ENST00000341259	NM_005475.2	413	Cac/Aac	7/8	0.116839648264797	3	FACETS	0.842	0.746	0.945	0.842	0.746	0.945	INDETERMINATE	2	TRUE	1	0.202786003507957	3		608	548	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432200	121432200	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	92	716	0	ENST00000257555.6:c.947A>T	p.Lys316Met	p.K316M	ENST00000257555		316	aAg/aTg	4/10	0.116839648264797	3	FACETS	0.927	0.826	1	0.927	0.826	1	INDETERMINATE	2	TRUE	1	0.202786003507957	3		716	539	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237658	133237658	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	77	915	0	ENST00000320574.5:c.2957A>T	p.Gln986Leu	p.Q986L	ENST00000320574	NM_006231.2	986	cAa/cTa	25/49	0.116839648264797	3	FACETS	0.996	0.873	1	0.498	0.436	0.564	INDETERMINATE	1	TRUE	1	0.202786003507957	3		915	840	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527780	103527780	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	62	498	0	ENST00000355739.4:c.3088G>T	p.Ala1030Ser	p.A1030S	ENST00000355739	NM_000123.3	1030	Gca/Tca	15/15	0.116839648264797	3	FACETS	1	0.953	1	0.621	0.537	0.713	INDETERMINATE	1	TRUE	1	0.202786003507957	3		498	542	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094776	2094776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757412628	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	67	861	0	ENST00000219066.1:c.404C>T	p.Ser135Leu	p.S135L	ENST00000219066	NM_002528.5	135	tCa/tTa	3/6	0.202786003507957	3	FACETS	1	0.894	1	0.517	0.449	0.591	CLONAL	1	TRUE	1	0.202786003507957	3		861	704	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662326	67662327	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	307	566	0	ENST00000264010.4:c.1573dup	p.Cys525LeufsTer6	p.C525Lfs*6	ENST00000264010	NM_006565.3	524	-/T	9/12	0.202786003507957	7	FACETS	0.93	0.88	0.98	0.93	0.88	0.98	CLONAL	6	TRUE	1	0.202786003507957	7		566	818	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40384139	40384139	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	104	573	0	ENST00000293328.3:c.7G>T	p.Val3Leu	p.V3L	ENST00000293328	NM_012448.3	3	Gtg/Ttg	2/19	0.144459563160582	4	FACETS	0.886	0.794	0.984	0.886	0.794	0.984	CLONAL	2	TRUE	2	0.202786003507957	4		573	696	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244453	41244453	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	118	790	0	ENST00000357654.3:c.3095G>C	p.Arg1032Thr	p.R1032T	ENST00000357654	NM_007294.3	1032	aGa/aCa	10/23	0.144459563160582	4	FACETS	0.905	0.817	0.999	0.905	0.817	0.999	CLONAL	2	TRUE	2	0.202786003507957	4		790	773	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214867	36214867	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	91	924	0	ENST00000222270.7:c.3293G>T	p.Gly1098Val	p.G1098V	ENST00000222270	NM_014727.1	1098	gGg/gTg	8/37	0.202786003507957	2	FACETS	1	0.955	1	0.575	0.51	0.644	CLONAL	1	TRUE	0	0.202786003507957	2		924	781	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223235	36223235	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	222	1185	0	ENST00000222270.7:c.5785G>T	p.Ala1929Ser	p.A1929S	ENST00000222270	NM_014727.1	1929	Gcc/Tcc	28/37	0.202786003507957	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.202786003507957	2		1185	941	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989623	212989623	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	58	370	0	ENST00000342788.4:c.88G>T	p.Ala30Ser	p.A30S	ENST00000342788	NM_005235.2	30	Gca/Tca	2/28	0.102340650009886	4	FACETS	1	0.871	1	1	0.871	1	INDETERMINATE	2	TRUE	2	0.202786003507957	4		370	341	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376116	225376116	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	149	900	0	ENST00000264414.4:c.838G>T	p.Glu280Ter	p.E280*	ENST00000264414	NM_003590.4	280	Gag/Tag	6/16	0.102340650009886	4	FACETS	1	0.916	1	1	0.916	1	INDETERMINATE	2	TRUE	2	0.202786003507957	4		900	881	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225449678	225449678	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	69	527	0	ENST00000264414.4:c.49C>G	p.Arg17Gly	p.R17G	ENST00000264414	NM_003590.4	17	Cgg/Ggg	1/16	0.102340650009886	4	FACETS	0.828	0.723	0.942	0.828	0.723	0.942	INDETERMINATE	2	TRUE	2	0.202786003507957	4		527	494	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443586	52443586	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	121	566	0	ENST00000460680.1:c.106C>T	p.Gln36Ter	p.Q36*	ENST00000460680	NM_004656.3	36	Cag/Tag	3/17	0.202786003507957	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.202786003507957	2		566	491	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499365	89499366	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	96	565	0	ENST00000336596.2:c.2535_2536delinsAA	p.Pro846Thr	p.P846T	ENST00000336596	NM_005233.5	845	ccCCcc/ccAAcc	15/17	0.102340650009886	4	FACETS	0.938	0.837	1	0.938	0.837	1	INDETERMINATE	2	TRUE	2	0.202786003507957	4		565	607	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138383941	138383941	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	132	705	0	ENST00000289153.2:c.2609T>C	p.Val870Ala	p.V870A	ENST00000289153	NM_006219.2	870	gTg/gCg	18/22	0.102340650009886	4	FACETS	0.908	0.824	0.997	0.908	0.824	0.997	INDETERMINATE	2	TRUE	2	0.202786003507957	4		705	862	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180817	106180817	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs904812983	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	78	473	0	ENST00000380013.4:c.3845G>T	p.Gly1282Val	p.G1282V	ENST00000380013	NM_001127208.2	1282	gGt/gTt	7/11	0.202786003507957	3	FACETS	0.925	0.816	1	0.925	0.816	1	CLONAL	2	TRUE	1	0.202786003507957	3		473	458	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120525	94120525	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	40	646	0	ENST00000369303.4:c.526C>A	p.Pro176Thr	p.P176T	ENST00000369303	NM_004440.3	176	Cct/Act	3/17	0.202786003507957	2	FACETS	0.958	0.797	1	0.479	0.398	0.568	CLONAL	1	TRUE	0	0.202786003507957	2		646	412	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201860	152201860	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	80	619	0	ENST00000206249.3:c.714G>T	p.Gln238His	p.Q238H	ENST00000206249	NM_000125.3	238	caG/caT	3/8	0.202786003507957	2	FACETS	0.887	0.784	0.996	0.887	0.784	0.996	CLONAL	2	TRUE	0	0.202786003507957	2		619	445	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346669	81346669	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	46	385	0	ENST00000222390.5:c.1284G>T	p.Trp428Cys	p.W428C	ENST00000222390	NM_000601.4	428	tgG/tgT	11/18	0.144459563160582	4	FACETS	0.895	0.757	1	0.895	0.757	1	CLONAL	2	TRUE	2	0.202786003507957	4		385	305	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92355085	92355085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369264969	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	28	390	0	ENST00000265734.4:c.392G>A	p.Arg131Gln	p.R131Q	ENST00000265734	NM_001259.6	131	cGa/cAa	4/8	0.144459563160582	4	FACETS	0.797	0.636	0.98	0.398	0.318	0.49	CLONAL	1	TRUE	2	0.202786003507957	4		390	417	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128848667	128848667	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	134	774	2	ENST00000249373.3:c.1332G>T	p.Lys444Asn	p.K444N	ENST00000249373	NM_005631.4	444	aaG/aaT	7/12	0.144459563160582	4	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	2	0.202786003507957	4		776	730	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484218	8484218	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	126	760	1	ENST00000356435.5:c.3314C>A	p.Pro1105Gln	p.P1105Q	ENST00000356435		1105	cCa/cAa	19/35	0.202786003507957	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	1	0.202786003507957	3		761	636	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563491	87563491	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs201553907	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	59	816	0	ENST00000277120.3:c.1879G>T	p.Asp627Tyr	p.D627Y	ENST00000277120		627	Gac/Tac	16/19	0.202786003507957	3	FACETS	0.852	0.732	0.984	0.426	0.366	0.492	CLONAL	1	TRUE	1	0.202786003507957	3		816	752	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209239	98209239	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	64	843	0	ENST00000331920.6:c.4299G>T	p.Gln1433His	p.Q1433H	ENST00000331920	NM_000264.3	1433	caG/caT	23/24	0.202786003507957	3	FACETS	1	0.899	1	0.523	0.453	0.6	CLONAL	1	TRUE	1	0.202786003507957	3		843	664	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390623	139390623	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554826328	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	69	979	2	ENST00000277541.6:c.7568C>T	p.Ser2523Leu	p.S2523L	ENST00000277541	NM_017617.3	2523	tCg/tTg	34/34	0.202786003507957	3	FACETS	0.935	0.813	1	0.467	0.406	0.534	CLONAL	1	TRUE	1	0.202786003507957	3		981	802	SUCCESS
BTK	695	MSKCC	GRCh37	X	100612539	100612539	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	42	739	1	ENST00000308731.7:c.1135C>T	p.Gln379Ter	p.Q379*	ENST00000308731	NM_000061.2	379	Caa/Taa	13/19	0.202786003507957	1	FACETS	0.719	0.6	0.851	0.719	0.6	0.851	SUBCLONAL	1	TRUE	0	0.202786003507957	1		740	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0023522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	26	605	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.653308821940878	1	FACETS	0.084	0.065	0.104	0.084	0.065	0.104	SUBCLONAL	1	TRUE	0	0.675720361759355	1		605	610	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	263	708	6	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.675720361759355	2		714	762	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0023522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	443	628	11	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	0.675720361759355	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.675720361759355	2		639	634	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446283	70446284	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	238	657	7	ENST00000373644.4:c.5230dup	p.Arg1744LysfsTer26	p.R1744Kfs*26	ENST00000373644	NM_030625.2	1741	-/A	11/12	1	2	FACETS	0.976	0.915	1	0.976	0.915	1	CLONAL	1	TRUE	1	0.675720361759355	2		664	722	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201671	66201671	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773217274	NA	P-0023522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	247	620	5	ENST00000273854.3:c.2831C>T	p.Thr944Met	p.T944M	ENST00000273854	NM_004439.5	944	aCg/aTg	16/18	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.675720361759355	2		625	674	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922294	100922294	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1315135533	NA	P-0023522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	158	474	2	ENST00000325455.5:c.2218C>T	p.Arg740Ter	p.R740*	ENST00000325455	NM_001202474.3	740	Cga/Tga	5/8	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.675720361759355	2		476	448	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246350	46246350	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1275863291	NA	P-0023522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	159	492	5	ENST00000334344.6:c.4444C>T	p.Gln1482Ter	p.Q1482*	ENST00000334344	NM_152641.2	1482	Caa/Taa	15/21	1	2	FACETS	0.93	0.859	1	0.93	0.859	1	CLONAL	1	TRUE	1	0.675720361759355	2		497	506	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500901	8500901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	208	682	12	ENST00000356435.5:c.1981G>A	p.Glu661Lys	p.E661K	ENST00000356435		661	Gag/Aag	13/35	1	2	FACETS	0.885	0.824	0.946	0.885	0.824	0.946	CLONAL	1	TRUE	1	0.675720361759355	2		694	696	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031708	36031708	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	305	845	11	ENST00000358208.4:c.1537G>A	p.Glu513Lys	p.E513K	ENST00000358208		513	Gag/Aag	12/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.675720361759355	2		856	860	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117823	108117823	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	233	616	1	ENST00000278616.4:c.1034T>G	p.Leu345Trp	p.L345W	ENST00000278616	NM_000051.3	345	tTg/tGg	8/63	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.675720361759355	2		617	661	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212248	5212248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776677741	NA	P-0023522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	203	629	5	ENST00000357368.4:c.4783C>T	p.Arg1595Cys	p.R1595C	ENST00000357368	NM_002850.3	1595	Cgc/Tgc	32/38	1	2	FACETS	0.982	0.916	1	0.982	0.916	1	CLONAL	1	TRUE	1	0.675720361759355	2		634	612	SUCCESS
APC	324	MSKCC	GRCh37	5	112175535	112175536	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0023522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	277	368	1	ENST00000257430.4:c.4245_4246del	p.Ser1415ArgfsTer7	p.S1415Rfs*7	ENST00000257430	NM_000038.5	1415	aGT/a	16/16	0.675720361759355	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.675720361759355	2		369	410	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039171	49039188	+	frameshift_variant	Frame_Shift_Del	DEL	ATTCTATTATAGTATTCT	ATTCTATTATAGTATTCT	G	novel	NA	P-0023522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	99	528	2	ENST00000267163.4:c.2249_2266delinsG	p.Asp750GlyfsTer2	p.D750Gfs*2	ENST00000267163	NM_000321.2	750	gATTCTATTATAGTATTCTat/gGat	22/27	0.657362946974374	1	FACETS	0.554	0.499	0.611	0.554	0.499	0.611	SUBCLONAL	1	TRUE	0	0.675720361759355	1		530	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0023546-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	312	708	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.312906745345313	2	FACETS	1	0.972	1	1	0.997	1	CLONAL	4	TRUE	0	0.312906745345313	2		708	490	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913396	NA	P-0023546-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	47	390	0	ENST00000349496.5:c.95A>C	p.Asp32Ala	p.D32A	ENST00000349496	NM_001904.3	32	gAc/gCc	3/15	0.312906745345313	6	FACETS	1	0.944	1	0.422	0.357	0.493	CLONAL	1	TRUE	3	0.312906745345313	6		390	386	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106519962	106519962	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0023546-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	20	243	1	ENST00000359195.3:c.2392-2A>T		p.X798_splice	ENST00000359195	NM_002649.2	798			0.312906745345313	3	FACETS	0.711	0.546	0.902	0.355	0.273	0.451	CLONAL	1	TRUE	1	0.312906745345313	3		244	208	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0023549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	246	694	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	0.865488597091397	2		694	675	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0023588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	118	478	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.795	0.717	0.878	0.795	0.717	0.878	SUBCLONAL	1	FALSE	1	0.340839152768407	2		478	871	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0023588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	126	510	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	FALSE	1	0.340839152768407	2		510	729	SUCCESS
APC	324	MSKCC	GRCh37	5	112175751	112175752	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1114167577	NA	P-0023588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	68	511	1	ENST00000257430.4:c.4463dup	p.Leu1488PhefsTer26	p.L1488Ffs*26	ENST00000257430	NM_000038.5	1487	act/acTt	16/16	1	2	FACETS	0.833	0.726	0.948	0.833	0.726	0.948	CLONAL	1	FALSE	1	0.340839152768407	2		512	479	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395686	45395686	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	113	739	2	ENST00000262160.6:c.448G>T	p.Glu150Ter	p.E150*	ENST00000262160	NM_005901.5	150	Gaa/Taa	4/11	0.293025093571588	1	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	FALSE	0	0.340839152768407	1		741	547	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127460	55127460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779332376	NA	P-0023588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	100	934	3	ENST00000257290.5:c.248C>T	p.Thr83Met	p.T83M	ENST00000257290	NM_006206.4	83	aCg/aTg	3/23	1	2	FACETS	0.872	0.78	0.97	0.872	0.78	0.97	CLONAL	1	FALSE	1	0.340839152768407	2		937	673	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156540	106156540	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1340173182	NA	P-0023592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	39	425	0	ENST00000380013.4:c.1441C>T	p.Gln481Ter	p.Q481*	ENST00000380013	NM_001127208.2	481	Cag/Tag	3/11	1	2	FACETS	0.606	0.502	0.722	0.606	0.502	0.722	SUBCLONAL	1	TRUE	1	0.27336104178775	2		425	471	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166280	118166280	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	86	413	0	ENST00000369448.3:c.793del	p.Thr265LeufsTer2	p.T265Lfs*2	ENST00000369448	NM_017709.3	264	Aaa/aa	2/2	0.23768014043536	2	FACETS	0.777	0.691	0.867	0.777	0.691	0.867	SUBCLONAL	2	TRUE	0	0.27336104178775	2		413	405	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343276	118343276	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	64	418	0	ENST00000534358.1:c.1402C>T	p.His468Tyr	p.H468Y	ENST00000534358	NM_005933.3	468	Cac/Tac	3/36	1	2	FACETS	0.942	0.817	1	0.942	0.817	1	CLONAL	1	TRUE	1	0.27336104178775	2		418	497	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426782	121426782	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	53	683	0	ENST00000257555.6:c.473A>C	p.Lys158Thr	p.K158T	ENST00000257555		158	aAg/aCg	2/10	0.190119781613758	1	FACETS	0.53	0.451	0.616	0.53	0.451	0.616	SUBCLONAL	1	TRUE	0	0.27336104178775	1		683	632	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43769806	43769806	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	68	647	0	ENST00000382044.4:c.940C>T	p.Gln314Ter	p.Q314*	ENST00000382044	NM_001141980.1	314	Cag/Tag	8/28	0.27336104178775	1	FACETS	0.792	0.69	0.903	0.792	0.69	0.903	CLONAL	1	TRUE	0	0.27336104178775	1		647	542	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530166	63530166	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	105	558	1	ENST00000307078.5:c.2269C>T	p.His757Tyr	p.H757Y	ENST00000307078	NM_004655.3	757	Cac/Tac	10/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.27336104178775	2		559	631	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223175	36223175	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	88	820	0	ENST00000222270.7:c.5725C>G	p.Pro1909Ala	p.P1909A	ENST00000222270	NM_014727.1	1909	Ccc/Gcc	28/37	1	2	FACETS	0.585	0.517	0.659	0.585	0.517	0.659	SUBCLONAL	1	TRUE	1	0.27336104178775	2		820	1100	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045687	26045687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	37	286	0	ENST00000540144.1:c.49C>T	p.Pro17Ser	p.P17S	ENST00000540144	NM_003531.2	17	Ccg/Tcg	1/1	0.195448633601511	3	FACETS	0.81	0.668	0.967	0.405	0.334	0.484	CLONAL	1	TRUE	1	0.27336104178775	3		286	380	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924280	11924280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	14	131	1	ENST00000353533.5:c.77C>T	p.Ser26Phe	p.S26F	ENST00000353533	NM_003010.3	26	tCc/tTc	1/11	0.145030966673976	1	FACETS	0.702	0.511	0.928	0.702	0.511	0.928	INDETERMINATE	1	TRUE	0	0.27336104178775	1		132	126	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0023603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	426	637	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.363279425428984	3	FACETS	0.842	0.807	0.877	0.842	0.807	0.877	CLONAL	3	TRUE	0	0.473885995407501	3		637	880	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974782	21974783	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CAGT	novel	NA	P-0023603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	101	204	0	ENST00000304494.5:c.41_44dup	p.Trp15Ter	p.W15*	ENST00000304494	NM_000077.4	15	tgg/tgACTGg	1/3	0.421742993430433	2	FACETS	0.753	0.683	0.825	0.753	0.683	0.825	SUBCLONAL	2	TRUE	0	0.473885995407501	2		204	283	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518112	8518112	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs533774328	NA	P-0023603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	139	470	0	ENST00000356435.5:c.1279C>T	p.Arg427Ter	p.R427*	ENST00000356435		427	Cga/Tga	10/35	0.280781965514341	1	FACETS	1	0.958	1	1	0.958	1	INDETERMINATE	1	TRUE	0	0.473885995407501	1		470	420	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827900	40827900	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	94	590	0	ENST00000373198.4:c.2528C>A	p.Ser843Tyr	p.S843Y	ENST00000373198	NM_133170.3	843	tCt/tAt	17/32	0.241845605761631	6	FACETS	0.709	0.629	0.795			1	INDETERMINATE	1	TRUE	NA	0.473885995407501	6		590	1090	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784122	120784122	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	127	620	1	ENST00000257552.2:c.863C>T	p.Ser288Phe	p.S288F	ENST00000257552	NM_002442.3	288	tCt/tTt	13/15	0.140355168617739	5	FACETS	1	0.932	1	0.259	0.234	0.285	INDETERMINATE	1	TRUE	1	0.473885995407501	5		621	885	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457757	149457757	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	76	497	0	ENST00000286301.3:c.647G>T	p.Arg216Leu	p.R216L	ENST00000286301	NM_005211.3	216	cGa/cTa	5/22	0.191089706536085	5	FACETS	0.606	0.531	0.688	0.202	0.177	0.23	INDETERMINATE	1	TRUE	2	0.473885995407501	5		497	905	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444346	50444346	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	173	367	0	ENST00000331340.3:c.276G>T	p.Met92Ile	p.M92I	ENST00000331340	NM_006060.4	92	atG/atT	4/8	0.473885995407501	5	FACETS	1	0.988	1	0.361	0.332	0.391	CLONAL	1	TRUE	1	0.473885995407501	5		367	865	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851955	128851955	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	92	662	0	ENST00000249373.3:c.2027G>T	p.Arg676Met	p.R676M	ENST00000249373	NM_005631.4	676	aGg/aTg	12/12	0.355153025039293	2	FACETS	0.577	0.513	0.645	0.288	0.256	0.323	SUBCLONAL	1	TRUE	0	0.473885995407501	2		662	673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0023626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	114	466	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.316985541448612	1	FACETS	0.979	0.884	1	0.979	0.884	1	CLONAL	1	TRUE	0	0.316985541448612	1		466	618	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126097	2126119	+	frameshift_variant	Frame_Shift_Del	DEL	CATCACGTCATAGCCATGTGGTT	CATCACGTCATAGCCATGTGGTT	-	novel	NA	P-0023626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	108	671	0	ENST00000219476.3:c.2673_2695del	p.His891GlnfsTer16	p.H891Qfs*16	ENST00000219476	NM_000548.3	890	CATCACGTCATAGCCATGTGGTTc/c	24/42	0.316985541448612	1	FACETS	0.799	0.717	0.885	0.799	0.717	0.885	SUBCLONAL	1	TRUE	0	0.316985541448612	1		671	718	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660625	227660626	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0023626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	177	527	0	ENST00000305123.5:c.2829dup	p.Met944AspfsTer31	p.M944Dfs*31	ENST00000305123	NM_005544.2	943	-/G	1/2	0.29636052870507	2	FACETS	0.889	0.823	0.957	0.889	0.823	0.957	CLONAL	2	TRUE	0	0.316985541448612	2		527	628	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	201	314	0				ENST00000310581	NM_198253.2	-/1132			0.42170684684218	4	FACETS	0.879	0.822	0.937	0.879	0.822	0.937	CLONAL	3	TRUE	1	0.42170684684218	4		314	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555526097	NA	P-0023636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	119	653	0	ENST00000269305.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000269305	NM_001126112.2	167	Cag/Tag	5/11	1	2	FACETS	0.906	0.82	0.996	0.906	0.82	0.996	CLONAL	1	TRUE	1	0.42170684684218	2		653	623	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438046	49438047	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	rs886043506	NA	P-0023636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	140	607	0	ENST00000301067.7:c.5124_5125del	p.Arg1709HisfsTer25	p.R1709Hfs*25	ENST00000301067	NM_003482.3	1708	acACgc/acgc	21/54	0.139236127039668	3	FACETS	1	0.976	1	0.597	0.545	0.652	INDETERMINATE	1	TRUE	1	0.42170684684218	3		607	673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579446	7579452	+	frameshift_variant	Frame_Shift_Del	DEL	TAGGAGC	TAGGAGC	-	novel	NA	P-0023636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	162	620	0	ENST00000269305.4:c.235_241del	p.Ala79HisfsTer42	p.A79Hfs*42	ENST00000269305	NM_001126112.2	79	GCTCCTAca/ca	4/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.42170684684218	2		620	711	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	32	314	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		314	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579362	7579362	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057523496	NA	P-0023669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	126	734	0	ENST00000269305.4:c.325T>G	p.Phe109Val	p.F109V	ENST00000269305	NM_001126112.2	109	Ttc/Gtc	4/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.364545107938036	2		734	612	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577555	7577556	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0023669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	86	596	1	ENST00000269305.4:c.725_726delinsTT	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGC/tTT	7/11	1	2	FACETS	0.85	0.754	0.953	0.85	0.754	0.953	CLONAL	1	TRUE	1	0.364545107938036	2		597	555	SUCCESS
AR	367	MSKCC	GRCh37	X	66765304	66765304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	17	322	0	ENST00000374690.3:c.316G>A	p.Gly106Ser	p.G106S	ENST00000374690	NM_000044.3	106	Ggc/Agc	1/8	1	1	FACETS	0.276	0.206	0.36	0.276	0.206	0.36	SUBCLONAL	1	TRUE	0	0.364545107938036	1		322	276	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063321	67063321	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	128	440	0	ENST00000412916.2:c.11T>G	p.Val4Gly	p.V4G	ENST00000412916		4	gTc/gGc	1/6	0.45218900516728	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.45218900516728	1		440	422	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0023676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	148	674	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.976	0.893	1	0.976	0.893	1	CLONAL	1	TRUE	1	0.45218900516728	2		674	671	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0023679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	190	672	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	1	2	FACETS	0.885	0.82	0.953	0.885	0.82	0.953	CLONAL	1	TRUE	1	0.551709752199591	2		672	778	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845366	151845366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	183	857	1	ENST00000262189.6:c.13646G>A	p.Arg4549His	p.R4549H	ENST00000262189	NM_170606.2	4549	cGc/cAc	52/59	1	2	FACETS	0.978	0.906	1	0.978	0.906	1	CLONAL	1	TRUE	1	0.551709752199591	2		858	678	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061466	38061466	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs751849657	NA	P-0023679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	163	707	0	ENST00000250448.2:c.523T>A	p.Tyr175Asn	p.Y175N	ENST00000250448	NM_004496.3	175	Tac/Aac	2/2	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.551709752199591	2		707	570	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675074	40675074	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	199	909	0	ENST00000249776.8:c.38T>G	p.Phe13Cys	p.F13C	ENST00000249776	NM_033286.3	13	tTc/tGc	1/9	1	2	FACETS	0.976	0.907	1	0.976	0.907	1	CLONAL	1	TRUE	1	0.551709752199591	2		909	739	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422410	225422410	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	147	898	0	ENST00000264414.4:c.230T>C	p.Leu77Pro	p.L77P	ENST00000264414	NM_003590.4	77	cTa/cCa	2/16	1	2	FACETS	0.797	0.729	0.867	0.797	0.729	0.867	SUBCLONAL	1	TRUE	1	0.551709752199591	2		898	669	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161230	56161230	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	153	771	0	ENST00000399503.3:c.1099del	p.Gln367AsnfsTer2	p.Q367Nfs*2	ENST00000399503	NM_005921.1	367	Caa/aa	5/20	1	2	FACETS	0.842	0.772	0.914	0.842	0.772	0.914	CLONAL	1	TRUE	1	0.551709752199591	2		771	659	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177693	56177693	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	84	487	0	ENST00000399503.3:c.2667del	p.Asn891ThrfsTer18	p.N891Tfs*18	ENST00000399503	NM_005921.1	889	gTt/gt	14/20	1	2	FACETS	0.83	0.738	0.926	0.83	0.738	0.926	CLONAL	1	TRUE	1	0.551709752199591	2		487	367	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977857	134977857	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	89	518	0	ENST00000398015.3:c.2850C>A	p.Asp950Glu	p.D950E	ENST00000398015	NM_004441.4	950	gaC/gaA	16/16	1	2	FACETS	0.906	0.807	1	0.906	0.807	1	CLONAL	1	TRUE	1	0.424405178643767	2		518	463	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0023714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	1228	715	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.441486181289636	6	FACETS	1	0.994	1			1	CLONAL	5	TRUE	NA	0.441486181289636	6		715	2010	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845621	72845621	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	212	576	0	ENST00000268489.5:c.3719T>C	p.Val1240Ala	p.V1240A	ENST00000268489	NM_006885.3	1240	gTg/gCg	7/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.441486181289636	2		576	870	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917723	29917723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	249	655	0	ENST00000389048.3:c.945G>A	p.Met315Ile	p.M315I	ENST00000389048	NM_004304.4	315	atG/atA	3/29	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.441486181289636	2		655	979	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101909998	101909999	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAAA	novel	NA	P-0023714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	89	385	0	ENST00000374994.4:c.1321_1322insAAAA	p.Met441LysfsTer8	p.M441Kfs*8	ENST00000374994	NM_004612.2	440	gaa/gAAAAaa	8/9	0.441486181289636	1	FACETS	0.979	0.877	1	0.979	0.877	1	CLONAL	1	TRUE	0	0.441486181289636	1		385	321	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123691	11123691	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023752-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	438	662	3	ENST00000358026.2:c.2341A>T	p.Met781Leu	p.M781L	ENST00000358026	NM_001128849.1	781	Atg/Ttg	16/36	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.850907251184661	2		665	964	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934027	39934027	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023752-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	448	304	0	ENST00000378444.4:c.572G>A	p.Trp191Ter	p.W191*	ENST00000378444	NM_001123385.1	191	tGg/tAg	4/15	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.850907251184661	1		304	516	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184083	56184084	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0023757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	58	313	0	ENST00000399503.3:c.4289dup	p.Cys1430TrpfsTer2	p.C1430Wfs*2	ENST00000399503	NM_005921.1	1430	tgt/tGgt	19/20	0.506270245531703	1	FACETS	0.764	0.665	0.869	0.764	0.665	0.869	SUBCLONAL	1	TRUE	0	0.506270245531703	1		313	224	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	131	552	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.432939331261912	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.460242289805675	4		552	357	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435578	18435578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747513676	NA	P-0023780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	67	178	0	ENST00000266497.5:c.563C>T	p.Pro188Leu	p.P188L	ENST00000266497		188	cCg/cTg	1/31	0.432939331261912	4	FACETS	1	0.923	1	1	0.923	1	CLONAL	2	TRUE	2	0.460242289805675	4		178	201	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281837	39281837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374761537	NA	P-0023780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	52	342	0	ENST00000402219.2:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000402219	NM_005633.3	213	cGa/cAa	5/23	0.405531532809198	4	FACETS	0.904	0.773	1	0.452	0.386	0.524	CLONAL	1	TRUE	2	0.460242289805675	4		342	365	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667359	241667359	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	126	256	0	ENST00000366560.3:c.1091G>A	p.Gly364Glu	p.G364E	ENST00000366560	NM_000143.3	364	gGa/gAa	7/10	0.33766590494578	5	FACETS	0.921	0.845	0.998	0.921	0.845	0.998	CLONAL	3	TRUE	2	0.460242289805675	5		256	335	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202678	108202679	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs759965045	NA	P-0023780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	74	212	0	ENST00000278616.4:c.7705_7706del	p.Asp2569Ter	p.D2569*	ENST00000278616	NM_000051.3	2568	AGa/a	52/63	0.431379909145433	2	FACETS	0.777	0.693	0.864	0.777	0.693	0.864	SUBCLONAL	2	TRUE	0	0.460242289805675	2		212	207	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40384142	40384142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113461014	NA	P-0023780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	98	286	0	ENST00000293328.3:c.4G>A	p.Ala2Thr	p.A2T	ENST00000293328	NM_012448.3	2	Gct/Act	2/19	0.432939331261912	4	FACETS	0.891	0.802	0.983	0.891	0.802	0.983	CLONAL	2	TRUE	2	0.460242289805675	4		286	349	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138375112	138375112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138462760	NA	P-0023793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	80	236	0	ENST00000289153.2:c.2947C>T	p.Arg983Cys	p.R983C	ENST00000289153	NM_006219.2	983	Cgc/Tgc	21/22	0.183842458201618	3	FACETS	0.795	0.715	0.877	0.795	0.715	0.877	INDETERMINATE	2	TRUE	1	0.681228203974979	3		236	198	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62008748	62008748	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	94	265	0	ENST00000392795.3:c.68C>A	p.Ala23Glu	p.A23E	ENST00000392795	NM_001039933.1	23	gCa/gAa	2/6	0.268127916535117	6	FACETS	1	0.949	1	0.543	0.489	0.599	INDETERMINATE	2	TRUE	2	0.681228203974979	6		265	300	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827997	40827997	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1306080663	NA	P-0023793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	73	260	0	ENST00000373198.4:c.2431A>G	p.Ser811Gly	p.S811G	ENST00000373198	NM_133170.3	811	Agt/Ggt	17/32	0.268127916535117	6	FACETS	0.917	0.811	1	0.459	0.405	0.515	INDETERMINATE	2	TRUE	2	0.681228203974979	6		260	276	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980379	1980379	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	284	425	0	ENST00000382891.5:c.3841C>G	p.Pro1281Ala	p.P1281A	ENST00000382891	NM_133335.3	1281	Cct/Gct	22/22	0.681228203974979	6	FACETS	0.883	0.834	0.932			1	CLONAL	3	TRUE	NA	0.681228203974979	6		425	744	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0023805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	155	670	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.603102401420095	1	FACETS	0.891	0.825	0.958	0.891	0.825	0.958	CLONAL	1	TRUE	0	0.603102401420095	1		671	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0023805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	169	463	0	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	0.603102401420095	1	FACETS	0.967	0.9	1	0.967	0.9	1	CLONAL	1	TRUE	0	0.603102401420095	1		463	405	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1918644	1918644	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	193	603	0	ENST00000382891.5:c.807C>A	p.Asp269Glu	p.D269E	ENST00000382891	NM_133335.3	269	gaC/gaA	4/22	NA	2	FACETS	0.718	0.664	0.773			1	INDETERMINATE	1	TRUE	NA	0.603102401420095	2		603	892	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	36	314	0				ENST00000310581	NM_198253.2	-/1132			0.361732741912297	3	FACETS	0.853	0.706	1	0.427	0.353	0.508	CLONAL	1	TRUE	1	0.409916947776813	3		314	248	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130436	29130436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555932172	NA	P-0023821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	216	384	0	ENST00000328354.6:c.274C>T	p.Pro92Ser	p.P92S	ENST00000328354	NM_007194.3	92	Ccc/Tcc	2/15	0.409916947776813	6	FACETS	1	0.943	1	1	0.943	1	CLONAL	4	TRUE	2	0.409916947776813	6		384	478	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976861	55976861	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	105	379	1	ENST00000263923.4:c.1051C>T	p.Pro351Ser	p.P351S	ENST00000263923	NM_002253.2	351	Cct/Tct	8/30	0.370350998610338	4	FACETS	0.866	0.781	0.954	0.866	0.781	0.954	CLONAL	2	TRUE	2	0.409916947776813	4		380	417	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832595	72832595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	25	180	0	ENST00000268489.5:c.3986G>A	p.Gly1329Glu	p.G1329E	ENST00000268489	NM_006885.3	1329	gGa/gAa	9/10	0.393726922560059	4	FACETS	0.882	0.7	1	0.294	0.233	0.363	CLONAL	1	TRUE	1	0.409916947776813	4		180	195	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553668	106553668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1261004652	NA	P-0023821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	38	225	0	ENST00000369096.4:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000369096	NM_001198.3	545	Gaa/Aaa	5/7	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.409916947776813	2		225	176	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783244	9783244	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554743340	NA	P-0023821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	55	367	1	ENST00000377346.4:c.2488C>T	p.Arg830Cys	p.R830C	ENST00000377346	NM_005026.3	830	Cgt/Tgt	20/24	0.361732741912297	3	FACETS	0.785	0.673	0.906	0.392	0.336	0.453	CLONAL	1	TRUE	1	0.409916947776813	3		368	412	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73333994	73333994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	36	336	0	ENST00000377767.4:c.2816C>T	p.Thr939Ile	p.T939I	ENST00000377767	NM_014953.3	939	aCt/aTt	21/21	0.370350998610338	4	FACETS	1	0.839	1	0.507	0.42	0.604	CLONAL	1	TRUE	2	0.409916947776813	4		336	244	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7978981	7978981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145046775	NA	P-0023821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	61	406	0	ENST00000319144.4:c.1586G>A	p.Gly529Asp	p.G529D	ENST00000319144	NM_001139.2	529	gGt/gAt	12/15	0.370350998610338	4	FACETS	0.945	0.818	1	0.473	0.409	0.542	CLONAL	1	TRUE	2	0.409916947776813	4		406	444	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291560	15291560	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	157	432	0	ENST00000263388.2:c.3074C>T	p.Pro1025Leu	p.P1025L	ENST00000263388	NM_000435.2	1025	cCc/cTc	19/33	0.370350998610338	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.409916947776813	4		432	482	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860532	45860532	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	156	389	1	ENST00000391945.4:c.1475C>T	p.Pro492Leu	p.P492L	ENST00000391945	NM_000400.3	492	cCt/cTt	15/23	0.336489393298288	5	FACETS	1	0.969	1			1	CLONAL	2	TRUE	NA	0.409916947776813	5		390	557	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742733	39742733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	66	319	1	ENST00000361337.2:c.1576G>A	p.Glu526Lys	p.E526K	ENST00000361337	NM_003286.2	526	Gag/Aag	15/21	0.409916947776813	5	FACETS	0.795	0.695	0.902	0.53	0.463	0.601	CLONAL	2	TRUE	2	0.409916947776813	5		320	327	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197767	123197767	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	97	376	0	ENST00000218089.9:c.1891G>A	p.Ala631Thr	p.A631T	ENST00000218089	NM_001042749.1	631	Gca/Aca	20/35	0.409916947776813	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.409916947776813	2		376	208	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50815298	50815298	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	143	310	0	ENST00000398568.2:c.1651C>T	p.Gln551Ter	p.Q551*	ENST00000398568	NM_001042412.1	551	Cag/Tag	9/18	0.361180415518446	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.74812749162121	0		310	253	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243777021	243777021	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	147	373	0	ENST00000263826.5:c.648G>C	p.Gln216His	p.Q216H	ENST00000263826	NM_005465.4	216	caG/caC	7/13	1	2	FACETS	0.916	0.844	0.99	0.916	0.844	0.99	CLONAL	1	TRUE	1	0.74812749162121	2		373	429	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934515	9934515	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	136	320	0	ENST00000330684.3:c.1640C>G	p.Ser547Cys	p.S547C	ENST00000330684	NM_001134407.1	547	tCt/tGt	7/13	1	2	FACETS	0.993	0.914	1	0.993	0.914	1	CLONAL	1	TRUE	1	0.74812749162121	2		320	366	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	33	314	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.582	0.478	0.697	0.582	0.478	0.697	SUBCLONAL	1	TRUE	1	0.572318587307022	2		314	198	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911514	131911514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143802516	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	82	266	0	ENST00000265335.6:c.259C>T	p.Arg87Cys	p.R87C	ENST00000265335		87	Cgt/Tgt	3/25	0.232269115951369	3	FACETS	1	0.905	1	0.51	0.453	0.571	INDETERMINATE	1	TRUE	1	0.572318587307022	3		266	361	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935508	13935508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536563766	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	105	153	0	ENST00000405192.2:c.1348G>A	p.Glu450Lys	p.E450K	ENST00000405192	NM_001163147.1	450	Gaa/Aaa	12/12	0.572318587307022	3	FACETS	0.814	0.74	0.89			1	CLONAL	2	TRUE	NA	0.572318587307022	3		153	290	SUCCESS
AR	367	MSKCC	GRCh37	X	66863145	66863145	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	77	188	0	ENST00000374690.3:c.1664C>T	p.Pro555Leu	p.P555L	ENST00000374690	NM_000044.3	555	cCa/cTa	2/8	1	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.572318587307022	1		188	154	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274115	10274115	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555491518	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	71	383	2	ENST00000330684.3:c.154C>T	p.Arg52Ter	p.R52*	ENST00000330684	NM_001134407.1	52	Cga/Tga	2/13	1	2	FACETS	0.922	0.814	1	0.922	0.814	1	CLONAL	1	TRUE	1	0.572318587307022	2		385	269	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913338	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	15	273	0	ENST00000288602.6:c.1781A>C	p.Asp594Ala	p.D594A	ENST00000288602	NM_004333.4	594	gAt/gCt	15/18	0.572318587307022	3	FACETS	0.158	0.115	0.21	0.079	0.057	0.105	SUBCLONAL	1	TRUE	1	0.572318587307022	3		273	427	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561263	9561263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769939031	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	61	274	0	ENST00000353224.5:c.519G>A	p.Met173Ile	p.M173I	ENST00000353224	NM_177990.2	173	atG/atA	4/10	1	2	FACETS	0.738	0.642	0.84	0.738	0.642	0.84	SUBCLONAL	1	TRUE	1	0.572318587307022	2		274	289	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294370	1294370	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	141	409	0	ENST00000310581.5:c.631G>A	p.Gly211Arg	p.G211R	ENST00000310581	NM_198253.2	211	Ggg/Agg	2/16	1	2	FACETS	0.785	0.727	0.843	1	0.99	1	SUBCLONAL	2	TRUE	1	0.572318587307022	2		409	314	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052693	42052693	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	101	341	0	ENST00000219905.7:c.7364C>T	p.Ser2455Phe	p.S2455F	ENST00000219905	NM_001164273.1	2455	tCt/tTt	20/24	1	2	FACETS	0.821	0.738	0.907	0.821	0.738	0.907	CLONAL	1	TRUE	1	0.572318587307022	2		341	430	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285666	46285666	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	110	263	0	ENST00000334344.6:c.5026C>T	p.Gln1676Ter	p.Q1676*	ENST00000334344	NM_152641.2	1676	Cag/Tag	17/21	0.232269115951369	3	FACETS	1	0.977	1	0.629	0.57	0.691	INDETERMINATE	1	TRUE	1	0.572318587307022	3		263	393	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231149	46231149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	85	298	0	ENST00000334344.6:c.1069C>T	p.His357Tyr	p.H357Y	ENST00000334344	NM_152641.2	357	Cat/Tat	9/21	0.232269115951369	3	FACETS	1	0.928	1	0.528	0.47	0.589	INDETERMINATE	1	TRUE	1	0.572318587307022	3		298	362	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47700145	47700145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752686914	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	91	256	0	ENST00000347630.2:c.28C>T	p.Pro10Ser	p.P10S	ENST00000347630	NM_001007230.1	10	Ccg/Tcg	3/11	0.572318587307022	3	FACETS	1	0.955	1	0.563	0.504	0.625	CLONAL	1	TRUE	1	0.572318587307022	3		256	363	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955074	93955074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	143	220	0	ENST00000369303.4:c.2824G>A	p.Asp942Asn	p.D942N	ENST00000369303	NM_004440.3	942	Gat/Aat	16/17	0.389204901491873	3	FACETS	1	0.978	1	0.754	0.702	0.807	CLONAL	2	TRUE	0	0.572318587307022	3		220	284	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811603	102811603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	97	380	0	ENST00000307046.8:c.581G>A	p.Gly194Glu	p.G194E	ENST00000307046	NM_001111285.1	194	gGa/gAa	4/4	0.232269115951369	3	FACETS	1	0.953	1	0.553	0.497	0.612	INDETERMINATE	1	TRUE	1	0.572318587307022	3		380	394	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980769	40980769	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	68	305	0	ENST00000373198.4:c.1717G>A	p.Gly573Ser	p.G573S	ENST00000373198	NM_133170.3	573	Ggc/Agc	10/32	0.512153593809406	1	FACETS	0.707	0.623	0.795	0.707	0.623	0.795	SUBCLONAL	1	TRUE	0	0.572318587307022	1		305	240	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231189	46231189	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	74	265	0	ENST00000334344.6:c.1109T>G	p.Leu370Ter	p.L370*	ENST00000334344	NM_152641.2	370	tTa/tGa	9/21	0.232269115951369	3	FACETS	1	0.94	1	0.551	0.486	0.618	INDETERMINATE	1	TRUE	1	0.572318587307022	3		265	302	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099959	27099959	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	100	402	0	ENST00000324856.7:c.3838C>T	p.Pro1280Ser	p.P1280S	ENST00000324856	NM_006015.4	1280	Ccc/Tcc	15/20	1	2	FACETS	0.955	0.861	1	0.955	0.861	1	CLONAL	1	TRUE	1	0.572318587307022	2		402	366	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439578	51439578	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	81	197	0	ENST00000262662.1:c.143G>A	p.Gly48Glu	p.G48E	ENST00000262662		48	gGa/gAa	4/4	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.572318587307022	2		197	266	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241948	72241948	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	66	232	0	ENST00000357731.5:c.442A>C	p.Met148Leu	p.M148L	ENST00000357731	NM_173808.2	148	Atg/Ctg	3/7	1	2	FACETS	0.815	0.714	0.922	0.815	0.714	0.922	CLONAL	1	TRUE	1	0.572318587307022	2		232	283	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148992	119148993	+	missense_variant	Missense_Mutation	DNP	TC	TC	GG	novel	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	88	330	0	ENST00000264033.4:c.1212_1213delinsGG	p.Cys404_Leu405delinsTrpVal	p.C404_L405delinsWV	ENST00000264033	NM_005188.3	404	tgTCtt/tgGGtt	8/16	1	2	FACETS	0.881	0.787	0.979	0.881	0.787	0.979	CLONAL	1	TRUE	1	0.572318587307022	2		330	349	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149244	119149244	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs745896960	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	81	312	0	ENST00000264033.4:c.1252T>G	p.Phe418Val	p.F418V	ENST00000264033	NM_005188.3	418	Ttc/Gtc	9/16	1	2	FACETS	0.795	0.706	0.889	0.795	0.706	0.889	SUBCLONAL	1	TRUE	1	0.572318587307022	2		312	356	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800819	18800819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868545833	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	55	200	0	ENST00000266497.5:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000266497		1399	Gat/Aat	31/31	0.56710722149497	4	FACETS	0.83	0.713	0.957	0.277	0.237	0.319	CLONAL	1	TRUE	1	0.572318587307022	4		200	364	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836990	89836990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	111	426	0	ENST00000389301.3:c.2204G>A	p.Ser735Asn	p.S735N	ENST00000389301	NM_000135.2	735	aGt/aAt	24/43	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.572318587307022	2		426	358	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560082	29560082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	60	194	0	ENST00000356175.3:c.3559C>T	p.Leu1187Phe	p.L1187F	ENST00000356175	NM_000267.3	1187	Ctt/Ttt	27/57	0.512153593809406	1	FACETS	0.924	0.814	1	0.924	0.814	1	CLONAL	1	TRUE	0	0.572318587307022	1		194	162	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59886117	59886117	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs140097800	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	74	191	0	ENST00000259008.2:c.629C>T	p.Pro210Leu	p.P210L	ENST00000259008	NM_032043.2	210	cCc/cTc	7/20	0.572318587307022	3	FACETS	1	0.954	1	0.579	0.512	0.65	CLONAL	1	TRUE	1	0.572318587307022	3		191	287	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284915	15284915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	75	430	0	ENST00000263388.2:c.4700C>T	p.Pro1567Leu	p.P1567L	ENST00000263388	NM_000435.2	1567	cCc/cTc	25/33	1	2	FACETS	0.904	0.8	1	0.904	0.8	1	CLONAL	1	TRUE	1	0.572318587307022	2		430	290	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943709	17943709	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	83	338	0	ENST00000458235.1:c.2380G>C	p.Gly794Arg	p.G794R	ENST00000458235	NM_000215.3	794	Ggt/Cgt	18/24	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.572318587307022	2		338	272	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279551	18279552	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	91	310	1	ENST00000222254.8:c.1824_1825delinsAA	p.Met608_Glu609delinsIleLys	p.M608_E609delinsIK	ENST00000222254	NM_005027.3	608	atGGag/atAAag	15/16	1	2	FACETS	0.901	0.807	0.999	0.901	0.807	0.999	CLONAL	1	TRUE	1	0.572318587307022	2		311	353	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456450	29456450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	151	481	0	ENST00000389048.3:c.2468G>A	p.Gly823Glu	p.G823E	ENST00000389048	NM_004304.4	823	gGa/gAa	14/29	0.572318587307022	3	FACETS	1	0.979	1	0.595	0.547	0.646	CLONAL	1	TRUE	1	0.572318587307022	3		481	570	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561525	9561525	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs918236421	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	97	366	0	ENST00000353224.5:c.257T>C	p.Leu86Pro	p.L86P	ENST00000353224	NM_177990.2	86	cTa/cCa	4/10	1	2	FACETS	0.963	0.867	1	0.963	0.867	1	CLONAL	1	TRUE	1	0.572318587307022	2		366	352	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012753	36012753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	56	185	2	ENST00000358208.4:c.197G>A	p.Gly66Asp	p.G66D	ENST00000358208		66	gGc/gAc	2/12	1	2	FACETS	0.964	0.838	1	0.964	0.838	1	CLONAL	1	TRUE	1	0.572318587307022	2		187	203	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057249	30057249	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	82	341	0	ENST00000338641.4:c.731A>T	p.Tyr244Phe	p.Y244F	ENST00000338641	NM_000268.3	244	tAt/tTt	8/16	0.571105317547253	5	FACETS	0.837	0.739	0.943	0.209	0.184	0.236	CLONAL	1	TRUE	1	0.572318587307022	5		341	636	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627290	12627290	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	107	272	0	ENST00000251849.4:c.1426C>T	p.Leu476Phe	p.L476F	ENST00000251849	NM_002880.3	476	Ctc/Ttc	14/17	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.572318587307022	2		272	322	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144843	47144843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	131	368	0	ENST00000409792.3:c.4910C>T	p.Thr1637Ile	p.T1637I	ENST00000409792	NM_014159.6	1637	aCc/aTc	7/21	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.572318587307022	2		368	452	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405928	49405928	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	128	403	2	ENST00000418115.1:c.210G>T	p.Arg70Ser	p.R70S	ENST00000418115	NM_001664.2	70	agG/agT	3/5	1	2	FACETS	0.99	0.904	1	0.99	0.904	1	CLONAL	1	TRUE	1	0.572318587307022	2		405	452	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584539	189584539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	76	260	0	ENST00000264731.3:c.835C>T	p.Pro279Ser	p.P279S	ENST00000264731	NM_003722.4	279	Ccc/Tcc	6/14	1	2	FACETS	0.929	0.823	1	0.929	0.823	1	CLONAL	1	TRUE	1	0.572318587307022	2		260	286	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030331	180030331	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	76	393	0	ENST00000261937.6:c.3953G>A	p.Arg1318Lys	p.R1318K	ENST00000261937	NM_182925.4	1318	aGg/aAg	30/30	1	2	FACETS	0.942	0.835	1	0.942	0.835	1	CLONAL	1	TRUE	1	0.572318587307022	2		393	282	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553017	106553017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1175567617	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	209	423	0	ENST00000369096.4:c.982C>T	p.Pro328Ser	p.P328S	ENST00000369096	NM_001198.3	328	Ccc/Tcc	5/7	0.389204901491873	3	FACETS	1	0.982	1	0.74	0.697	0.784	CLONAL	2	TRUE	0	0.572318587307022	3		423	423	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978383	2978383	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	176	502	0	ENST00000396946.4:c.947G>A	p.Arg316Lys	p.R316K	ENST00000396946	NM_032415.4	316	aGg/aAg	7/25	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.572318587307022	2		502	433	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371874	55371874	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1050774871	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	35	192	0	ENST00000297316.4:c.564C>A	p.Phe188Leu	p.F188L	ENST00000297316	NM_022454.3	188	ttC/ttA	2/2	0.558399888353989	1	FACETS	0.909	0.768	1	0.909	0.768	1	CLONAL	1	TRUE	0	0.572318587307022	1		192	96	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80343439	80343439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	88	196	0	ENST00000286548.4:c.880G>A	p.Glu294Lys	p.E294K	ENST00000286548	NM_002072.3	294	Gaa/Aaa	6/7	0.572318587307022	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.572318587307022	1		196	180	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937338	76937338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	119	199	0	ENST00000373344.5:c.3410G>A	p.Arg1137Lys	p.R1137K	ENST00000373344	NM_000489.3	1137	aGa/aAa	9/35	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.572318587307022	1		199	224	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0023861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	124	466	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.625493777050589	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.625493777050589	1		466	255	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	221	552	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.986	0.921	1	0.986	0.921	1	CLONAL	1	TRUE	1	0.625493777050589	2		552	717	SUCCESS
APC	324	MSKCC	GRCh37	5	112175651	112175651	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	254	459	0	ENST00000257430.4:c.4364del	p.Asn1455IlefsTer18	p.N1455Ifs*18	ENST00000257430	NM_000038.5	1454	Aaa/aa	16/16	0.499107002110757	3	FACETS	1	0.992	1	0.83	0.79	0.87	CLONAL	2	TRUE	0	0.625493777050589	3		459	428	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274195	10274195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542256226	NA	P-0023861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	74	435	0	ENST00000330684.3:c.74C>T	p.Ala25Val	p.A25V	ENST00000330684	NM_001134407.1	25	gCg/gTg	2/13	NA	2	FACETS	1	0.925	1			1	INDETERMINATE	1	TRUE	NA	0.625493777050589	2		435	225	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201037	108201037	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	144	566	0	ENST00000278616.4:c.7404A>C	p.Glu2468Asp	p.E2468D	ENST00000278616	NM_000051.3	2468	gaA/gaC	50/63	1	2	FACETS	0.967	0.889	1	0.967	0.889	1	CLONAL	1	TRUE	1	0.625493777050589	2		566	476	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517874	187517874	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs983524169	NA	P-0023861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	102	636	0	ENST00000441802.2:c.12820G>A	p.Glu4274Lys	p.E4274K	ENST00000441802	NM_005245.3	4274	Gaa/Aaa	25/27	0.625493777050589	1	FACETS	0.721	0.653	0.791	0.721	0.653	0.791	SUBCLONAL	1	TRUE	0	0.625493777050589	1		636	311	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151947971	151947971	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145240734	NA	P-0023861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	182	796	0	ENST00000262189.6:c.1702G>A	p.Gly568Ser	p.G568S	ENST00000262189	NM_170606.2	568	Ggt/Agt	12/59	1	2	FACETS	0.851	0.788	0.916	0.851	0.788	0.916	CLONAL	1	TRUE	1	0.625493777050589	2		796	684	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0023874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	24	466	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.809	1	1	0.809	1	CLONAL	1	TRUE	1	0.13	2		466	357	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003150	42003150	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	28	437	0	ENST00000219905.7:c.2687G>A	p.Arg896Gln	p.R896Q	ENST00000219905	NM_001164273.1	896	cGa/cAa	8/24	1	2	FACETS	0.941	0.751	1	0.941	0.751	1	CLONAL	1	TRUE	1	0.13	2		437	458	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467509	66467509	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	14	222	0	ENST00000273854.3:c.760C>T	p.Gln254Ter	p.Q254*	ENST00000273854	NM_004439.5	254	Caa/Taa	3/18	1	2	FACETS	1	0.745	1	1	0.745	1	CLONAL	1	TRUE	1	0.13	2		222	209	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202753	16202753	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1159912329	NA	P-0023880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	18	342	0	ENST00000375759.3:c.461G>A	p.Arg154Gln	p.R154Q	ENST00000375759	NM_015001.2	154	cGg/cAg	3/15	0.100735512132648	3	FACETS	0.363	0.274	0.468			1	INDETERMINATE	1	TRUE	NA	0.629080417652545	3		342	207	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210432	2210432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761437945	NA	P-0023880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	146	391	0	ENST00000398665.3:c.1039C>T	p.Arg347Cys	p.R347C	ENST00000398665	NM_032482.2	347	Cgc/Tgc	13/28	0.461417131233348	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	2	0.629080417652545	4		391	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757274881	NA	P-0023897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	217	560	0	ENST00000269305.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	144	Cag/Tag	5/11	0.296820300869516	0	FACETS	0.561	0.527	0.595			1	INDETERMINATE	1	TRUE	0	0.614759329942698	0		560	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912657	NA	P-0023902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	238	550	0	ENST00000269305.4:c.814G>C	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ctg	8/11	0.519120182845381	2	FACETS	0.95	0.9	1	0.95	0.9	1	CLONAL	2	TRUE	0	0.564164934825044	2		550	444	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242470	+	missense_variant	Missense_Mutation	DNP	TT	TT	CC	rs397517096	NA	P-0023902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	405	382	0	ENST00000275493.2:c.2239_2240delinsCC	p.Leu747Pro	p.L747P	ENST00000275493	NM_005228.3	747	TTa/CCa	19/28	0.564164934825044	7	FACETS	0.923	0.886	0.96	0.923	0.886	0.96	CLONAL	5	TRUE	2	0.564164934825044	7		382	750	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021452	31021452	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	69	365	0	ENST00000375687.4:c.1451A>T	p.Glu484Val	p.E484V	ENST00000375687	NM_015338.5	484	gAg/gTg	12/13	0.492871210214566	4	FACETS	0.886	0.774	1	0.295	0.258	0.335	CLONAL	1	TRUE	1	0.564164934825044	4		365	432	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	54	314	0				ENST00000310581	NM_198253.2	-/1132			0.106145791945191	1	FACETS	0.545	0.476	0.616	0.545	0.476	0.616	INDETERMINATE	1	TRUE	0	0.802378286846382	1		314	148	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267698	198267698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	208	563	0	ENST00000335508.6:c.1781G>A	p.Arg594Gln	p.R594Q	ENST00000335508	NM_012433.2	594	cGa/cAa	13/25	1	2	FACETS	0.943	0.882	1	0.943	0.882	1	CLONAL	1	TRUE	1	0.802378286846382	2		563	550	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5258035	5258035	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	68	498	2	ENST00000357368.4:c.699C>A	p.Tyr233Ter	p.Y233*	ENST00000357368	NM_002850.3	233	taC/taA	8/38	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.544441699092083	2		500	193	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107010	11107010	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	62	671	0	ENST00000358026.2:c.1715A>T	p.Lys572Met	p.K572M	ENST00000358026	NM_001128849.1	572	aAg/aTg	10/36	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.544441699092083	2		671	193	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191480	10191481	+	missense_variant	Missense_Mutation	DNP	TG	TG	CA	novel	NA	P-0023955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	54	524	1	ENST00000256474.2:c.473_474inv	p.Leu158Pro	p.L158P	ENST00000256474	NM_000551.3	158	cTG/cCA	3/3	0.544441699092083	1	FACETS	0.722	0.626	0.824	0.722	0.626	0.824	SUBCLONAL	1	TRUE	0	0.544441699092083	1		525	200	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142952	47142953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	76	528	0	ENST00000409792.3:c.5010dup	p.Tyr1671IlefsTer41	p.Y1671Ifs*41	ENST00000409792	NM_014159.6	1670	-/A	8/21	0.544441699092083	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.544441699092083	1		528	191	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682418	52682418	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1468547899	NA	P-0023955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	79	652	0	ENST00000394830.3:c.755T>C	p.Ile252Thr	p.I252T	ENST00000394830	NM_018313.4	252	aTa/aCa	8/30	0.544441699092083	1	FACETS	0.926	0.828	1	0.926	0.828	1	CLONAL	1	TRUE	0	0.544441699092083	1		652	228	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150004	202150004	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	378	910	0	ENST00000358485.4:c.1445A>T	p.Gln482Leu	p.Q482L	ENST00000358485	NM_001080125.1	482	cAg/cTg	8/9	0.560043989520545	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.560043989520545	4		910	975	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223483	53223488	+	inframe_deletion	In_Frame_Del	DEL	GGCGCG	GGCGCG	-	novel	NA	P-0023961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	129	385	0	ENST00000375401.3:c.3871_3876del	p.Ala1292_Arg1293del	p.A1292_R1293del	ENST00000375401	NM_004187.3	1291	CGCGCC/-	23/26	0.560043989520545	2	FACETS	1	0.969	1			1	CLONAL	1	TRUE	NA	0.560043989520545	2		385	409	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328377	137328382	+	missense_variant	Missense_Mutation	ONP	CTCTTC	CTCTTC	ATCTTG	novel	NA	P-0023961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1595	390	1127	2	ENST00000481739.1:c.1306_1311delinsATCTTG	p.Leu436_Phe437delinsIleLeu	p.L436_F437delinsIL	ENST00000481739	NM_002957.4	436	CTCTTC/ATCTTG	10/10	0.560043989520545	8	FACETS	0.94	0.89	0.992			1	CLONAL	2	TRUE	NA	0.560043989520545	8		1129	1985	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121912666	NA	P-0023971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	403	869	0	ENST00000269305.4:c.659A>C	p.Tyr220Ser	p.Y220S	ENST00000269305	NM_001126112.2	220	tAt/tCt	6/11	0.36634361786532	5	FACETS	1	0.969	1	1	0.969	1	CLONAL	5	TRUE	0	0.36634361786532	5		869	676	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431799	49431805	+	frameshift_variant	Frame_Shift_Del	DEL	CAGATGC	CAGATGC	-	novel	NA	P-0023971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	156	682	1	ENST00000301067.7:c.9334_9340del	p.Ala3112CysfsTer5	p.A3112Cfs*5	ENST00000301067	NM_003482.3	3112	GCATCTGtg/tg	34/54	0.36634361786532	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.36634361786532	3		683	478	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129191	2129191	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs745731000	NA	P-0023971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	135	850	0	ENST00000219476.3:c.3125C>G	p.Pro1042Arg	p.P1042R	ENST00000219476	NM_000548.3	1042	cCg/cGg	27/42	0.36634361786532	3	FACETS	1	0.985	1	0.711	0.649	0.777	CLONAL	1	TRUE	1	0.36634361786532	3		850	613	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935517	13935517	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	48	452	0	ENST00000405192.2:c.1339C>A	p.Pro447Thr	p.P447T	ENST00000405192	NM_001163147.1	447	Ccc/Acc	12/12	0.36634361786532	4	FACETS	0.846	0.717	0.989	0.282	0.239	0.33	CLONAL	1	TRUE	1	0.36634361786532	4		452	423	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139440227	139440228	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	12	77	0	ENST00000277541.6:c.11dup	p.Leu5ProfsTer25	p.L5Pfs*25	ENST00000277541	NM_017617.3	4	ctc/ctTc	1/34	0.36634361786532	3	FACETS	0.775	0.562	1	0.775	0.562	1	CLONAL	2	TRUE	1	0.36634361786532	3		77	50	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627919	37627919	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	205	898	1	ENST00000447079.4:c.1834C>T	p.Gln612Ter	p.Q612*	ENST00000447079	NM_015083.1	612	Caa/Taa	2/14	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.479489035846944	2		899	855	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061188	38061205	+	inframe_deletion	In_Frame_Del	DEL	CTTGAAGCGCTTCTGGCG	CTTGAAGCGCTTCTGGCG	-	novel	NA	P-0023988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	557	644	0	ENST00000250448.2:c.784_801del	p.Arg262_Lys267del	p.R262_K267del	ENST00000250448	NM_004496.3	262	CGCCAGAAGCGCTTCAAG/-	2/2	0.479489035846944	6	FACETS	1	0.99	1			1	CLONAL	5	TRUE	NA	0.479489035846944	6		644	867	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649101	37649101	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	136	709	0	ENST00000447079.4:c.2206G>C	p.Gly736Arg	p.G736R	ENST00000447079	NM_015083.1	736	Gga/Cga	4/14	1	2	FACETS	0.921	0.84	1	0.921	0.84	1	CLONAL	1	TRUE	1	0.479489035846944	2		709	616	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0023995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	104	400	0	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.341132765519907	2	FACETS	1	0.981	1	0.671	0.609	0.734	CLONAL	1	TRUE	0	0.52564168534936	2		400	295	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561490	9561490	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	52	720	0	ENST00000353224.5:c.292A>G	p.Asn98Asp	p.N98D	ENST00000353224	NM_177990.2	98	Aac/Gac	4/10	0.19870121641391	5	FACETS	0.668	0.568	0.776	0.223	0.189	0.259	INDETERMINATE	1	TRUE	2	0.52564168534936	5		720	530	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959241	2959241	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	64	687	0	ENST00000396946.4:c.2275C>G	p.Arg759Gly	p.R759G	ENST00000396946	NM_032415.4	759	Cgg/Ggg	18/25	0.52564168534936	1	FACETS	0.911	0.803	1	0.911	0.803	1	CLONAL	1	TRUE	0	0.52564168534936	1		687	197	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938089	76938090	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0024029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	269	406	0	ENST00000373344.5:c.2658_2659del	p.Glu886AspfsTer10	p.E886Dfs*10	ENST00000373344	NM_000489.3	886	gaGAct/gact	9/35	1	1	FACETS	1	0.993	1	1	0.997	1	CLONAL	3	FALSE	0	0.367344573411614	1		406	349	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0024029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	122	288	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.967	1	1	0.991	1	CLONAL	2	FALSE	1	0.367344573411614	2		288	301	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432040	121432040	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771108132	NA	P-0024029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	358	944	1	ENST00000257555.6:c.787C>T	p.Arg263Cys	p.R263C	ENST00000257555		263	Cgt/Tgt	4/10	0.104422869228453	3	FACETS	1	0.991	1	1	0.991	1	INDETERMINATE	2	FALSE	1	0.367344573411614	3		945	981	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527568	29527569	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555610903	NA	P-0024029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	91	595	0	ENST00000356175.3:c.1019_1020del	p.Ser340CysfsTer12	p.S340Cfs*12	ENST00000356175	NM_000267.3	339	aaCTct/aact	9/57	0.33258735538079	0	FACETS	0.736	0.667	0.805			1	SUBCLONAL	2	FALSE	0	0.367344573411614	0		595	213	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519996	NA	P-0024029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	832	972	2	ENST00000269305.4:c.395A>T	p.Lys132Met	p.K132M	ENST00000269305	NM_001126112.2	132	aAg/aTg	5/11	0.367344573411614	2	FACETS	0.915	0.899	0.93	1	0.999	1	CLONAL	5	FALSE	0	0.367344573411614	2		974	990	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589625	67589627	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	novel	NA	P-0024029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	124	441	0	ENST00000274335.5:c.1390_1392del	p.Asp464del	p.D464del	ENST00000274335		463	tATGat/tat	10/15	1	2	FACETS	0.97	0.888	1	1	0.99	1	CLONAL	2	FALSE	1	0.367344573411614	2		441	348	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954161	32954161	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	252	529	0	ENST00000380152.3:c.9135A>T	p.Leu3045Phe	p.L3045F	ENST00000380152		3045	ttA/ttT	24/27	0.367344573411614	3	FACETS	1	0.989	1	1	0.995	1	CLONAL	3	FALSE	1	0.367344573411614	3		529	466	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919282	48919283	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0024029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	153	388	0	ENST00000267163.4:c.447_448del	p.Arg150ThrfsTer6	p.R150Tfs*6	ENST00000267163	NM_000321.2	149	tcAAga/tcga	4/27	0.367344573411614	1	FACETS	1	0.969	1	1	0.994	1	CLONAL	3	FALSE	0	0.367344573411614	1		388	219	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303101	15303101	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	66	1033	1	ENST00000263388.2:c.349T>A	p.Cys117Ser	p.C117S	ENST00000263388	NM_000435.2	117	Tgc/Agc	4/33	1	2	FACETS	0.419	0.362	0.48	0.419	0.362	0.48	SUBCLONAL	1	FALSE	1	0.367344573411614	2		1034	858	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339230	70339232	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0024029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	25	338	0	ENST00000374080.3:c.107_109del	p.Leu36_Thr37delinsPro	p.L36_T37delinsP	ENST00000374080		36	cTGAcg/ccg	2/45	1	1	FACETS	0.273	0.215	0.34	0.273	0.215	0.34	SUBCLONAL	1	FALSE	0	0.367344573411614	1		338	407	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125838	47125838	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	130	385	0	ENST00000409792.3:c.5432C>T	p.Thr1811Ile	p.T1811I	ENST00000409792	NM_014159.6	1811	aCt/aTt	12/21	1	2	FACETS	0.99	0.914	1	0.99	0.914	1	CLONAL	1	TRUE	1	0.884025656926387	2		385	297	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	67	314	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.276624860164955	2		314	399	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0024039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	50	364	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.863	0.734	1	0.863	0.734	1	CLONAL	1	TRUE	1	0.276624860164955	2		364	419	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	58	510	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.844	0.726	0.972	0.844	0.726	0.972	CLONAL	1	TRUE	1	0.276624860164955	2		510	497	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0024039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	71	357	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.87	0.76	0.989	0.87	0.76	0.989	CLONAL	1	TRUE	1	0.276624860164955	2		357	590	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285938	38285938	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913473	NA	P-0024039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	63	724	0	ENST00000425967.3:c.473C>T	p.Ser158Leu	p.S158L	ENST00000425967	NM_001174067.1	158	tCg/tTg	5/19	1	2	FACETS	0.89	0.77	1	0.89	0.77	1	CLONAL	1	TRUE	1	0.276624860164955	2		724	512	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923060	44923060	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	81	833	0	ENST00000377967.4:c.1921C>T	p.Gln641Ter	p.Q641*	ENST00000377967	NM_021140.2	641	Cag/Tag	16/29	1	2	FACETS	0.915	0.807	1	0.915	0.807	1	CLONAL	1	TRUE	1	0.276624860164955	2		833	640	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115963	8115964	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0024039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	43	534	0	ENST00000346208.3:c.1310_1311dup	p.Met438AlafsTer38	p.M438Afs*38	ENST00000346208		437	agc/aGCgc	6/6	1	2	FACETS	0.718	0.601	0.847	0.718	0.601	0.847	SUBCLONAL	1	TRUE	1	0.276624860164955	2		534	433	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748660	43748660	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	125	1264	0	ENST00000382044.4:c.2146G>C	p.Glu716Gln	p.E716Q	ENST00000382044	NM_001141980.1	716	Gaa/Caa	12/28	1	2	FACETS	0.935	0.845	1	0.935	0.845	1	CLONAL	1	TRUE	1	0.276624860164955	2		1264	967	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748786	43748786	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	92	1116	0	ENST00000382044.4:c.2020G>C	p.Glu674Gln	p.E674Q	ENST00000382044	NM_001141980.1	674	Gag/Cag	12/28	1	2	FACETS	0.778	0.69	0.872	0.778	0.69	0.872	SUBCLONAL	1	TRUE	1	0.276624860164955	2		1116	855	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439427	220439427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	51	494	0	ENST00000243786.2:c.280G>A	p.Glu94Lys	p.E94K	ENST00000243786	NM_002191.3	94	Gag/Aag	2/2	0.276624860164955	1	FACETS	0.946	0.808	1	0.946	0.808	1	CLONAL	1	TRUE	0	0.276624860164955	1		494	336	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180462	38180462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	73	781	0	ENST00000396334.3:c.310G>A	p.Glu104Lys	p.E104K	ENST00000396334	NM_002468.4	104	Gag/Aag	1/5	1	2	FACETS	0.912	0.798	1	0.912	0.798	1	CLONAL	1	TRUE	1	0.276624860164955	2		781	579	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651941	36651942	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	171	756	0	ENST00000244741.5:c.65dup	p.Gly23ArgfsTer13	p.G23Rfs*13	ENST00000244741	NM_000389.4	21	-/T	2/3	0.242211800142709	2	FACETS	0.898	0.829	0.97	0.898	0.829	0.97	CLONAL	2	TRUE	0	0.276624860164955	2		756	688	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	135	314	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.87	0.801	0.941	0.87	0.801	0.941	CLONAL	1	TRUE	1	0.85230797546121	2		314	364	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0024042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14846	504	548	0	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.85230797546121	45	FACETS	1	0.995	1			1	CLONAL	1	TRUE	NA	0.85230797546121	45		548	15350	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685307	89685307	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123317	NA	P-0024042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	212	569	0	ENST00000371953.3:c.202T>C	p.Tyr68His	p.Y68H	ENST00000371953	NM_000314.4	68	Tac/Cac	3/9	0.85230797546121	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.85230797546121	1		569	267	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195617	102195617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1173728754	NA	P-0024042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	185	639	2	ENST00000263464.3:c.377C>T	p.Pro126Leu	p.P126L	ENST00000263464	NM_001165.4	126	cCg/cTg	2/9	1	2	FACETS	0.881	0.82	0.942	0.881	0.82	0.942	CLONAL	1	TRUE	1	0.85230797546121	2		641	493	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0024045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	184	329	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.319574896624753	4	FACETS	0.835	0.772	0.9	0.835	0.772	0.9	CLONAL	2	TRUE	2	0.399487598904825	4		329	772	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0024045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	303	1132	3	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.319404650303991	2	FACETS	0.762	0.719	0.806	0.762	0.719	0.806	SUBCLONAL	2	TRUE	0	0.399487598904825	2		1135	995	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631979	90631979	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	238	631	0	ENST00000330062.3:c.374A>G	p.Glu125Gly	p.E125G	ENST00000330062	NM_002168.2	125	gAg/gGg	4/11	0.319574896624753	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.399487598904825	4		631	777	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0024047-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	80	478	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	0.16	2		478	780	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0024047-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	43	606	2	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.689	0.575	0.816	0.689	0.575	0.816	SUBCLONAL	1	TRUE	1	0.16	2		608	780	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461967	120461967	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024047-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	24	433	0	ENST00000256646.2:c.5749G>T	p.Ala1917Ser	p.A1917S	ENST00000256646	NM_024408.3	1917	Gca/Tca	31/34	1	2	FACETS	0.885	0.694	1	0.885	0.694	1	CLONAL	1	TRUE	1	0.16	2		433	339	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799670	72799670	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024047-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	51	594	0	ENST00000325599.8:c.1499G>T	p.Ser500Ile	p.S500I	ENST00000325599	NM_018130.2	500	aGt/aTt	11/11	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.16	2		594	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0024059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	237	466	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.48262635985077	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.48262635985077	1		466	685	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106946	11106946	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	48	833	0	ENST00000358026.2:c.1651G>C	p.Ala551Pro	p.A551P	ENST00000358026	NM_001128849.1	551	Gcc/Ccc	10/36	0.48262635985077	1	FACETS	0.176	0.148	0.207	0.176	0.148	0.207	SUBCLONAL	1	TRUE	0	0.48262635985077	1		833	858	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0024069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	179	769	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.473655280268967	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.486482141779721	1		770	460	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0024069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	15	364	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.283	0.207	0.374	0.283	0.207	0.374	SUBCLONAL	1	TRUE	1	0.486482141779721	2		364	218	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0024069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	25	319	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.203579278947647	2	FACETS	0.511	0.405	0.632	0.256	0.202	0.316	INDETERMINATE	1	TRUE	0	0.486482141779721	2		319	201	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729094	66729099	+	inframe_deletion	In_Frame_Del	DEL	TGGAGA	TGGAGA	-	novel	NA	P-0024069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	97	720	0	ENST00000307102.5:c.303_308del	p.Glu102_Ile103del	p.E102_I103del	ENST00000307102	NM_002755.3	101	cTGGAGAtc/ctc	3/11	0.236652381959911	1	FACETS	0.961	0.867	1	0.961	0.867	1	INDETERMINATE	1	TRUE	0	0.486482141779721	1		720	314	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216546	108216546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529296539	NA	P-0024069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	45	550	0	ENST00000278616.4:c.8495G>A	p.Arg2832His	p.R2832H	ENST00000278616	NM_000051.3	2832	cGt/cAt	58/63	0.175321367360551	2	FACETS	0.566	0.477	0.663	0.283	0.238	0.332	INDETERMINATE	1	TRUE	0	0.486482141779721	2		550	327	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609902	117609902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781588795	NA	P-0024069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	79	693	0	ENST00000368508.3:c.6797C>T	p.Thr2266Met	p.T2266M	ENST00000368508	NM_002944.2	2266	aCg/aTg	43/43	0.194666676857619	3	FACETS	1	0.975	1	0.689	0.612	0.769	INDETERMINATE	1	TRUE	1	0.486482141779721	3		693	293	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344159	70344159	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199582086	NA	P-0024069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	50	596	4	ENST00000374080.3:c.1895G>A	p.Arg632Gln	p.R632Q	ENST00000374080		632	cGg/cAg	13/45	0.316836356868403	1	FACETS	0.416	0.354	0.484	0.416	0.354	0.484	SUBCLONAL	1	TRUE	0	0.486482141779721	1		600	374	SUCCESS
APC	324	MSKCC	GRCh37	5	112173578	112173578	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	42	423	0	ENST00000257430.4:c.2287G>T	p.Glu763Ter	p.E763*	ENST00000257430	NM_000038.5	763	Gaa/Taa	16/16	0.203579278947647	2	FACETS	1	0.931	1	0.587	0.5	0.681	INDETERMINATE	1	TRUE	0	0.486482141779721	2		423	147	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514030	125514030	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	42	687	1	ENST00000428830.2:c.968C>T	p.Thr323Ile	p.T323I	ENST00000428830	NM_001114121.2	323	aCa/aTa	10/14	0.175321367360551	2	FACETS	0.702	0.59	0.823	0.351	0.295	0.412	INDETERMINATE	1	TRUE	0	0.486482141779721	2		688	246	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250778	26250778	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	27	440	0	ENST00000446824.2:c.56A>T	p.Lys19Met	p.K19M	ENST00000446824	NM_021018.2	19	aAg/aTg	1/1	0.194666676857619	3	FACETS	0.5	0.399	0.615	0.25	0.199	0.308	INDETERMINATE	1	TRUE	1	0.486482141779721	3		440	276	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015133	37015133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223489007	NA	P-0024080-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	479	687	0	ENST00000358127.4:c.271G>A	p.Ala91Thr	p.A91T	ENST00000358127	NM_001280556.1	91	Gcc/Acc	3/10	0.604626952532649	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	2	0.611964963374812	4		687	1240	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060783	38060794	+	inframe_deletion	In_Frame_Del	DEL	GATGGAGAACGG	GATGGAGAACGG	-	novel	NA	P-0024080-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1420	206	975	0	ENST00000250448.2:c.1195_1206del	p.Pro399_Ile402del	p.P399_I402del	ENST00000250448	NM_004496.3	399	CCGTTCTCCATC/-	2/2	0.611964963374812	4	FACETS	0.667	0.617	0.72	0.334	0.308	0.36	SUBCLONAL	1	TRUE	2	0.611964963374812	4		975	1626	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061152	38061202	+	inframe_deletion	In_Frame_Del	DEL	CCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTG	CCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTG	-	novel	NA	P-0024080-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	344	201	0	ENST00000250448.2:c.787_837del	p.Gln263_Gly279del	p.Q263_G279del	ENST00000250448	NM_004496.3	263	CAGAAGCGCTTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGG/-	2/2	0.611964963374812	4	FACETS	0.995	0.953	1	1	0.996	1	CLONAL	3	TRUE	2	0.611964963374812	4		201	607	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0024085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	178	255	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.386754739022754	3	FACETS	0.854	0.791	0.92	0.854	0.791	0.92	CLONAL	2	TRUE	1	0.386754739022754	3		255	643	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371830	55371830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1457048078	NA	P-0024095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	83	150	0	ENST00000297316.4:c.520G>A	p.Val174Met	p.V174M	ENST00000297316	NM_022454.3	174	Gtg/Atg	2/2	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.673138309553187	2		150	211	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406599	70406599	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	361	794	0	ENST00000373644.4:c.4113T>G	p.Ser1371Arg	p.S1371R	ENST00000373644	NM_030625.2	1371	agT/agG	4/12	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.673138309553187	2		794	1031	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267535	198267535	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	154	426	0	ENST00000335508.6:c.1822A>G	p.Thr608Ala	p.T608A	ENST00000335508	NM_012433.2	608	Act/Gct	14/25	1	2	FACETS	0.94	0.866	1	0.94	0.866	1	CLONAL	1	TRUE	1	0.673138309553187	2		426	487	SUCCESS
APC	324	MSKCC	GRCh37	5	112176427	112176428	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	102	319	0	ENST00000257430.4:c.5138dup	p.Leu1713PhefsTer3	p.L1713Ffs*3	ENST00000257430	NM_000038.5	1712	-/T	16/16	0.634493886888564	1	FACETS	0.824	0.751	0.898	0.824	0.751	0.898	CLONAL	1	TRUE	0	0.673138309553187	1		319	244	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0024113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	257	606	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.895	0.84	0.951	0.895	0.84	0.951	CLONAL	1	TRUE	1	0.669576164978459	2		606	858	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0024113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	319	847	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.646134140937754	1	FACETS	0.998	0.951	1	0.998	0.951	1	CLONAL	1	TRUE	0	0.669576164978459	1		849	635	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0024113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	203	375	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.669576164978459	2		375	592	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411678	63411678	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	740	386	0	ENST00000330258.3:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000330258	NM_152424.3	497	Cga/Tga	2/2	0.666079709296754	2	FACETS		NA	1			1	NA	3	TRUE	NA	0.669576164978459	2		386	884	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012410	29012410	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	887	585	0	ENST00000282397.4:c.461T>G	p.Leu154Arg	p.L154R	ENST00000282397	NM_002019.4	154	cTc/cGc	4/30	0.669576164978459	4	FACETS	0.982	0.957	1	0.982	0.957	1	CLONAL	3	TRUE	1	0.669576164978459	4		585	1501	SUCCESS
APC	324	MSKCC	GRCh37	5	112176030	112176030	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs886039682	NA	P-0024113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	166	363	0	ENST00000257430.4:c.4741del	p.Ser1581LeufsTer69	p.S1581Lfs*69	ENST00000257430	NM_000038.5	1580	aTt/at	16/16	1	2	FACETS	0.858	0.792	0.926	0.858	0.792	0.926	CLONAL	1	TRUE	1	0.669576164978459	2		363	578	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120351	70120352	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	367	818	0	ENST00000245479.2:c.1354dup	p.Tyr452LeufsTer126	p.Y452Lfs*126	ENST00000245479	NM_000346.3	451	-/T	3/3	1	2	FACETS	0.882	0.836	0.928	0.882	0.836	0.928	CLONAL	1	TRUE	1	0.669576164978459	2		818	1243	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541582	187541582	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	185	427	0	ENST00000441802.2:c.6158T>C	p.Val2053Ala	p.V2053A	ENST00000441802	NM_005245.3	2053	gTg/gCg	10/27	0.365066695851464	1	FACETS	0.743	0.692	0.794	0.743	0.692	0.794	INDETERMINATE	1	TRUE	0	0.669576164978459	1		427	495	SUCCESS
APC	324	MSKCC	GRCh37	5	112174600	112174600	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	194	449	1	ENST00000257430.4:c.3309G>T	p.Arg1103Ser	p.R1103S	ENST00000257430	NM_000038.5	1103	agG/agT	16/16	1	2	FACETS	0.967	0.901	1	0.967	0.901	1	CLONAL	1	TRUE	1	0.669576164978459	2		450	599	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	413	510	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.6212500421259	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.6212500421259	3		510	822	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40367050	40367050	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	258	764	0	ENST00000397332.2:c.147C>G	p.Phe49Leu	p.F49L	ENST00000397332	NM_001033082.2	49	ttC/ttG	2/3	1	2	FACETS	0.915	0.858	0.973	0.915	0.858	0.973	CLONAL	1	TRUE	1	0.6212500421259	2		764	908	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934194	48934194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	222	757	3	ENST00000267163.4:c.649C>T	p.Gln217Ter	p.Q217*	ENST00000267163	NM_000321.2	217	Cag/Tag	7/27	0.6212500421259	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.6212500421259	1		760	481	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060904	38060904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	171	522	0	ENST00000250448.2:c.1085C>T	p.Ser362Phe	p.S362F	ENST00000250448	NM_004496.3	362	tCc/tTc	2/2	1	2	FACETS	0.971	0.898	1	0.971	0.898	1	CLONAL	1	TRUE	1	0.6212500421259	2		522	567	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639984	3639984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	69	867	0	ENST00000294008.3:c.3655G>A	p.Glu1219Lys	p.E1219K	ENST00000294008	NM_032444.2	1219	Gag/Aag	12/15	1	2	FACETS	0.245	0.212	0.28	0.245	0.212	0.28	SUBCLONAL	1	TRUE	1	0.6212500421259	2		867	908	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934874	NA	P-0024123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	301	965	0	ENST00000269305.4:c.451C>G	p.Pro151Ala	p.P151A	ENST00000269305	NM_001126112.2	151	Ccc/Gcc	5/11	0.6212500421259	1	FACETS	0.953	0.904	1	0.953	0.904	1	CLONAL	1	TRUE	0	0.6212500421259	1		965	701	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016673	12016674	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0024123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	190	578	2	ENST00000353533.5:c.809_810insA	p.Met270IlefsTer4	p.M270Ifs*4	ENST00000353533	NM_003010.3	270	atg/atAg	7/11	0.6212500421259	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.6212500421259	1		580	390	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221626	36221626	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	313	872	0	ENST00000222270.7:c.5295G>A	p.Trp1765Ter	p.W1765*	ENST00000222270	NM_014727.1	1765	tgG/tgA	26/37	1	2	FACETS	0.996	0.941	1	0.996	0.941	1	CLONAL	1	TRUE	1	0.6212500421259	2		872	1012	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983034	111983034	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	316	932	2	ENST00000368678.4:c.1513G>A	p.Glu505Lys	p.E505K	ENST00000368678		505	Gaa/Aaa	13/13	0.618567250006322	1	FACETS	0.973	0.924	1	0.973	0.924	1	CLONAL	1	TRUE	0	0.6212500421259	1		934	721	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0024126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	300	810	3	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.905	0.859	0.951	0.905	0.859	0.951	CLONAL	1	TRUE	1	1	2		813	663	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	60	552	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.19	2		552	630	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0024133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	58	637	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.19	2		638	590	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0024137-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	58	327	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.2	2		327	544	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772290	68772290	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024137-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	67	597	0	ENST00000261769.5:c.139G>T	p.Glu47Ter	p.E47*	ENST00000261769	NM_004360.3	47	Gag/Tag	2/16	0.214744733825317	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.2	1		597	562	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070555	67070555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024137-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	43	376	1	ENST00000412916.2:c.179C>T	p.Thr60Ile	p.T60I	ENST00000412916		60	aCa/aTa	3/6	0.214744733825317	1	FACETS	0.777	0.65	0.918	0.777	0.65	0.918	CLONAL	1	TRUE	0	0.2	1		377	498	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577129	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519986	NA	P-0024138-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	239	611	0	ENST00000269305.4:c.809T>G	p.Phe270Cys	p.F270C	ENST00000269305	NM_001126112.2	270	tTt/tGt	8/11	0.254753118197127	4	FACETS	0.888	0.834	0.943	1	0.987	1	CLONAL	4	TRUE	1	0.254753118197127	4		611	663	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219461	133219461	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024138-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	179	784	0	ENST00000320574.5:c.4673A>G	p.Glu1558Gly	p.E1558G	ENST00000320574	NM_006231.2	1558	gAa/gGa	36/49	0.254753118197127	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.254753118197127	2		784	621	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562750	21562750	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024138-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	184	400	0	ENST00000382592.4:c.1169del	p.Pro390ArgfsTer43	p.P390Rfs*43	ENST00000382592	NM_014572.2	390	cCg/cg	4/8	0.254753118197127	5	FACETS	0.924	0.863	0.986			1	CLONAL	5	TRUE	NA	0.254753118197127	5		400	432	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213995	2213995	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs778008287	NA	P-0024138-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	133	581	0	ENST00000326181.6:c.74C>A	p.Thr25Asn	p.T25N	ENST00000326181	NM_032271.2	25	aCc/aAc	2/21	0.254753118197127	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.254753118197127	2		581	464	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871984	45871985	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0024138-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	117	559	0	ENST00000391945.4:c.263_264delinsTT	p.Arg88Leu	p.R88L	ENST00000391945	NM_000400.3	88	cGA/cTT	5/23	0.254753118197127	4	FACETS	0.916	0.828	1	0.916	0.828	1	CLONAL	2	TRUE	2	0.254753118197127	4		559	629	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873163	136873164	+	missense_variant	Missense_Mutation	DNP	AC	AC	TA	novel	NA	P-0024138-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	65	295	0	ENST00000241393.3:c.334_335delinsTA	p.Val112Tyr	p.V112Y	ENST00000241393	NM_003467.2	112	GTc/TAc	2/2	0.226210136581188	4	FACETS	0.783	0.681	0.892	0.783	0.681	0.892	SUBCLONAL	2	TRUE	2	0.254753118197127	4		295	409	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023570	31023570	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760148910	NA	P-0024138-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	103	382	0	ENST00000375687.4:c.3055A>G	p.Arg1019Gly	p.R1019G	ENST00000375687	NM_015338.5	1019	Aga/Gga	13/13	0.254753118197127	4	FACETS	0.893	0.801	0.99	0.893	0.801	0.99	CLONAL	2	TRUE	2	0.254753118197127	4		382	568	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978617	70978617	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024138-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	328	693	0	ENST00000276594.2:c.1036G>C	p.Gly346Arg	p.G346R	ENST00000276594	NM_024504.3	346	Ggg/Cgg	5/8	0.254753118197127	5	FACETS	0.903	0.855	0.952	1	0.991	1	CLONAL	4	TRUE	2	0.254753118197127	5		693	985	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393429	139393429	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024138-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	172	639	2	ENST00000277541.6:c.6102G>A	p.Trp2034Ter	p.W2034*	ENST00000277541	NM_017617.3	2034	tgG/tgA	33/34	0.238937242505513	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.254753118197127	2		641	614	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857642	9857642	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024138-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	28	339	0	ENST00000330684.3:c.3759G>T	p.Met1253Ile	p.M1253I	ENST00000330684	NM_001134407.1	1253	atG/atT	13/13	0.254753118197127	2	FACETS	0.544	0.435	0.669	0.272	0.217	0.335	SUBCLONAL	1	TRUE	0	0.254753118197127	2		339	404	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372782	81372783	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0024138-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	49	356	0	ENST00000222390.5:c.751_752delinsAA	p.Pro251Asn	p.P251N	ENST00000222390	NM_000601.4	251	CCc/AAc	7/18	0.254753118197127	4	FACETS	1	0.92	1	0.567	0.481	0.661	CLONAL	1	TRUE	2	0.254753118197127	4		356	426	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650258	48650258	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024138-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	78	583	0	ENST00000376670.3:c.228G>C	p.Gln76His	p.Q76H	ENST00000376670	NM_002049.3	76	caG/caC	3/6	0.226210136581188	4	FACETS	1	0.969	1	0.661	0.582	0.747	CLONAL	1	TRUE	2	0.254753118197127	4		583	581	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0024143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	433	769	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.395138093566865	2	FACETS	0.825	0.789	0.862	0.825	0.789	0.862	CLONAL	2	TRUE	0	0.484596629819055	2		770	1083	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120796810	120796810	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	214	859	0	ENST00000257552.2:c.449G>A	p.Arg150Gln	p.R150Q	ENST00000257552	NM_002442.3	150	cGa/cAa	7/15	0.375296687380662	3	FACETS	0.869	0.806	0.934	0.434	0.403	0.467	CLONAL	1	TRUE	1	0.484596629819055	3		859	1263	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127632	2127632	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	214	856	0	ENST00000219476.3:c.2871G>C	p.Leu957Phe	p.L957F	ENST00000219476	NM_000548.3	957	ttG/ttC	26/42	0.375296687380662	3	FACETS	0.891	0.827	0.958	0.446	0.413	0.479	CLONAL	1	TRUE	1	0.484596629819055	3		856	1231	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407569	407569	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	121	673	0	ENST00000380956.4:c.1327T>G	p.Ser443Ala	p.S443A	ENST00000380956	NM_001195286.1	443	Tct/Gct	9/9	0.439118291342763	3	FACETS	0.769	0.694	0.847			1	SUBCLONAL	1	TRUE	NA	0.484596629819055	3		673	807	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324917	31324917	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs776780353	NA	P-0024143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	128	855	1	ENST00000412585.2:c.19C>T	p.Arg7Ter	p.R7*	ENST00000412585	NM_005514.6	7	Cga/Tga	1/8	0.432977061719771	3	FACETS	0.568	0.514	0.626	0.284	0.257	0.313	SUBCLONAL	1	TRUE	1	0.484596629819055	3		856	1155	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295246	1295247	+	upstream_gene_variant	5'Flank	DNP	CC	CC	TT	novel	NA	P-0024156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	102	520	2				ENST00000310581	NM_198253.2	-/1132			0.374364722899557	2	FACETS	0.955	0.856	1	0.477	0.428	0.53	CLONAL	1	TRUE	0	0.374922889731522	2		522	570	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958386	90958386	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	126	674	0	ENST00000265433.3:c.2052T>A	p.Asn684Lys	p.N684K	ENST00000265433	NM_002485.4	684	aaT/aaA	13/16	0.168474350869454	1	FACETS	0.824	0.747	0.904	0.824	0.747	0.904	INDETERMINATE	1	TRUE	0	0.374922889731522	1		674	663	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0024166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	61	403	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.91	0.785	1	0.91	0.785	1	CLONAL	1	TRUE	1	0.233592140662258	2		403	574	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0024166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	273	643	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.233592140662258	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.233592140662258	3		643	1131	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230641	46230641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	24	485	0	ENST00000334344.6:c.890C>T	p.Ser297Phe	p.S297F	ENST00000334344	NM_152641.2	297	tCc/tTc	8/21	1	2	FACETS	0.239	0.187	0.301	0.239	0.187	0.301	SUBCLONAL	1	TRUE	1	0.233592140662258	2		485	858	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459558	50459558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	64	308	0	ENST00000331340.3:c.847C>T	p.Leu283Phe	p.L283F	ENST00000331340	NM_006060.4	283	Ctt/Ttt	7/8	1	2	FACETS	0.972	0.842	1	0.972	0.842	1	CLONAL	1	TRUE	1	0.233592140662258	2		308	564	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610162	43610162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	108	779	1	ENST00000355710.3:c.2114C>T	p.Ser705Phe	p.S705F	ENST00000355710	NM_020975.4	705	tCc/tTc	11/20	0.233592140662258	1	FACETS	0.986	0.885	1	0.986	0.885	1	CLONAL	1	TRUE	0	0.233592140662258	1		780	828	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086130	16086130	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs984467548	NA	P-0024166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	104	526	0	ENST00000281043.3:c.1306G>A	p.Glu436Lys	p.E436K	ENST00000281043	NM_005378.4	436	Gag/Aag	3/3	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.233592140662258	2		526	813	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668786	52668786	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	53	381	0	ENST00000394830.3:c.1133C>T	p.Ser378Phe	p.S378F	ENST00000394830	NM_018313.4	378	tCc/tTc	12/30	1	2	FACETS	0.653	0.556	0.76	0.653	0.556	0.76	SUBCLONAL	1	TRUE	1	0.233592140662258	2		381	695	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956771	68956771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774302685	NA	P-0024166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	115	615	0	ENST00000288368.4:c.889C>T	p.Arg297Cys	p.R297C	ENST00000288368	NM_024870.2	297	Cgt/Tgt	8/40	1	2	FACETS	0.902	0.81	0.999	0.902	0.81	0.999	CLONAL	1	TRUE	1	0.233592140662258	2		615	1092	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643953	52643953	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	62	411	0	ENST00000394830.3:c.1943C>T	p.Ser648Phe	p.S648F	ENST00000394830	NM_018313.4	648	tCt/tTt	17/30	1	2	FACETS	0.762	0.657	0.875	0.762	0.657	0.875	SUBCLONAL	1	TRUE	1	0.233592140662258	2		411	697	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46527611	46527611	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	116	567	0	ENST00000262741.5:c.754G>A	p.Glu252Lys	p.E252K	ENST00000262741	NM_003629.3	252	Gag/Aag	6/10	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.233592140662258	2		567	918	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858952	243858952	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	108	568	0	ENST00000263826.5:c.113A>T	p.Tyr38Phe	p.Y38F	ENST00000263826	NM_005465.4	38	tAt/tTt	2/13	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.233592140662258	2		568	755	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14303170	14303171	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0024166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	95	547	3	ENST00000256196.4:c.504_505delinsTT	p.His169Tyr	p.H169Y	ENST00000256196		168	ttCCat/ttTTat	5/6	0.233592140662258	1	FACETS	0.884	0.786	0.988	0.884	0.786	0.988	CLONAL	1	TRUE	0	0.233592140662258	1		550	813	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575571	64575572	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0024166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	65	404	1	ENST00000312049.6:c.446-1_446delinsAA		p.X149_splice	ENST00000312049	NM_130799.2	149		3/10	0.233592140662258	1	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	0	0.233592140662258	1		405	462	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913362	28913362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	149	659	1	ENST00000282397.4:c.2431G>A	p.Glu811Lys	p.E811K	ENST00000282397	NM_002019.4	811	Gag/Aag	17/30	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.233592140662258	2		660	1147	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872421	35872421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1344072314	NA	P-0024166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	124	601	0	ENST00000216797.5:c.482G>A	p.Gly161Glu	p.G161E	ENST00000216797	NM_020529.2	161	gGa/gAa	3/6	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.233592140662258	2		601	977	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213931	2213931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	113	692	0	ENST00000326181.6:c.10G>A	p.Gly4Ser	p.G4S	ENST00000326181	NM_032271.2	4	Ggc/Agc	2/21	1	2	FACETS	0.996	0.895	1	0.996	0.895	1	CLONAL	1	TRUE	1	0.233592140662258	2		692	971	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857077	9857077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	47	321	0	ENST00000330684.3:c.4324C>T	p.Pro1442Ser	p.P1442S	ENST00000330684	NM_001134407.1	1442	Ccc/Tcc	13/13	1	2	FACETS	0.811	0.685	0.951	0.811	0.685	0.951	CLONAL	1	TRUE	1	0.233592140662258	2		321	496	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274073	10274073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	126	689	0	ENST00000330684.3:c.196G>A	p.Asp66Asn	p.D66N	ENST00000330684	NM_001134407.1	66	Gac/Aac	2/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.233592140662258	2		689	889	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39251184	39251185	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	78	709	0	ENST00000402219.2:c.1168dup	p.Ile390AsnfsTer4	p.I390Nfs*4	ENST00000402219	NM_005633.3	390	ata/aAta	9/23	1	2	FACETS	0.618	0.541	0.701	0.618	0.541	0.701	SUBCLONAL	1	TRUE	1	0.233592140662258	2		709	1081	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422908	12422908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267599576	NA	P-0024166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	96	598	0	ENST00000287820.6:c.398C>T	p.Ser133Phe	p.S133F	ENST00000287820	NM_015869.4	133	tCc/tTc	3/7	1	2	FACETS	0.803	0.713	0.898	0.803	0.713	0.898	CLONAL	1	TRUE	1	0.233592140662258	2		598	1024	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960002	134960002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	78	378	3	ENST00000398015.3:c.2359C>T	p.Pro787Ser	p.P787S	ENST00000398015	NM_004441.4	787	Cct/Tct	13/16	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.233592140662258	2		381	613	SUCCESS
APC	324	MSKCC	GRCh37	5	112175093	112175093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	34	212	0	ENST00000257430.4:c.3802C>T	p.Pro1268Ser	p.P1268S	ENST00000257430	NM_000038.5	1268	Cca/Tca	16/16	1	2	FACETS	0.829	0.679	0.998	0.829	0.679	0.998	CLONAL	1	TRUE	1	0.233592140662258	2		212	351	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187067	38187067	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	134	703	0	ENST00000317025.8:c.1410G>A	p.Trp470Ter	p.W470*	ENST00000317025	NM_023034.1	470	tgG/tgA	6/24	1	2	FACETS	0.966	0.875	1	0.966	0.875	1	CLONAL	1	TRUE	1	0.233592140662258	2		703	1188	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611838	100611838	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	103	350	0	ENST00000308731.7:c.1283C>T	p.Ala428Val	p.A428V	ENST00000308731	NM_000061.2	428	gCc/gTc	14/19	1	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.233592140662258	1		350	569	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78923245	78923245	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	51	717	0	ENST00000306801.3:c.3268G>A	p.Asp1090Asn	p.D1090N	ENST00000306801	NM_020761.2	1090	Gat/Aat	28/34	0.575561653606064	3	FACETS	0.419	0.356	0.488	0.209	0.178	0.244	SUBCLONAL	1	TRUE	1	0.654119062100682	3		717	494	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828372	72828372	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	66	633	0	ENST00000268489.5:c.8209G>T	p.Glu2737Ter	p.E2737*	ENST00000268489	NM_006885.3	2737	Gaa/Taa	9/10	0.382242819831471	1	FACETS	0.388	0.339	0.441	0.388	0.339	0.441	INDETERMINATE	1	TRUE	0	0.654119062100682	1		633	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578264	7578265	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0024214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	156	793	0	ENST00000269305.4:c.583_584dup	p.Arg196SerfsTer52	p.R196Sfs*52	ENST00000269305	NM_001126112.2	195	atc/atATc	6/11	0.642611699256731	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.654119062100682	1		793	314	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0024230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	141	304	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	0.211638396905306	1	FACETS	0.87	0.796	0.948	0.87	0.796	0.948	INDETERMINATE	1	TRUE	0	0.429122531832665	1		304	593	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913274	NA	P-0024230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	42	762	0	ENST00000263967.3:c.1634A>T	p.Glu545Val	p.E545V	ENST00000263967	NM_006218.2	545	gAg/gTg	10/21	0.211638396905306	1	FACETS	0.299	0.249	0.354	0.299	0.249	0.354	INDETERMINATE	1	TRUE	0	0.429122531832665	1		762	514	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	60	314	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.852	0.745	0.966	0.852	0.745	0.966	CLONAL	1	TRUE	1	0.648707415100649	2		314	217	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0024237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	169	439	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.648707415100649	2		439	420	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0024237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	228	566	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.648707415100649	2		566	698	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685314	89685315	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TG	TG	-	rs1564826836	NA	P-0024237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	170	481	0	ENST00000371953.3:c.209+1_209+2del		p.X70_splice	ENST00000371953	NM_000314.4	70		3/9	0.618900413415524	1	FACETS	0.965	0.901	1	0.965	0.901	1	CLONAL	1	TRUE	0	0.648707415100649	1		481	367	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259447	16259447	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	116	568	0	ENST00000375759.3:c.6712C>A	p.Pro2238Thr	p.P2238T	ENST00000375759	NM_015001.2	2238	Cct/Act	11/15	1	2	FACETS	0.838	0.76	0.918	0.838	0.76	0.918	CLONAL	1	TRUE	1	0.648707415100649	2		568	427	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126129	2126129	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	72	1093	0	ENST00000219476.3:c.2700C>G	p.Cys900Trp	p.C900W	ENST00000219476	NM_000548.3	900	tgC/tgG	24/42	0.618900413415524	1	FACETS	0.288	0.252	0.327	0.288	0.252	0.327	SUBCLONAL	1	TRUE	0	0.648707415100649	1		1093	521	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130350	2130350	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	42	988	1	ENST00000219476.3:c.3582G>A	p.Trp1194Ter	p.W1194*	ENST00000219476	NM_000548.3	1194	tgG/tgA	30/42	0.618900413415524	1	FACETS	0.198	0.165	0.235	0.198	0.165	0.235	SUBCLONAL	1	TRUE	0	0.648707415100649	1		989	441	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0024240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	75	676	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.451996564694992	7	FACETS	0.998	0.915	1	1	0.975	1	CLONAL	6	TRUE	2	0.451996564694992	7		676	118	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579379	7579397	+	frameshift_variant	Frame_Shift_Del	DEL	TAGGTTTTCTGGGAAGGGA	TAGGTTTTCTGGGAAGGGA	-	novel	NA	P-0024240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	55	1115	0	ENST00000269305.4:c.290_308del	p.Val97AlafsTer20	p.V97Afs*20	ENST00000269305	NM_001126112.2	97	gTCCCTTCCCAGAAAACCTAc/gc	4/11	0.391850863696744	4	FACETS	1	0.953	1	1	0.979	1	CLONAL	4	TRUE	1	0.451996564694992	4		1115	81	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0024244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	57	606	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.786	0.674	0.909	0.786	0.674	0.909	CLONAL	1	TRUE	1	0.224042700941683	2		606	647	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0024244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	96	569	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.224042700941683	2		569	807	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15374266	15374266	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	40	554	0	ENST00000263377.2:c.1306G>C	p.Asp436His	p.D436H	ENST00000263377	NM_058243.2	436	Gac/Cac	7/20	0.134472452494801	3	FACETS	0.625	0.518	0.745	0.208	0.172	0.249	SUBCLONAL	1	TRUE	0	0.224042700941683	3		554	635	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15374304	15374304	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	54	768	0	ENST00000263377.2:c.1268G>C	p.Arg423Pro	p.R423P	ENST00000263377	NM_058243.2	423	cGa/cCa	7/20	0.134472452494801	3	FACETS	0.602	0.513	0.701	0.201	0.171	0.234	SUBCLONAL	1	TRUE	0	0.224042700941683	3		768	890	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15374317	15374317	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	53	824	1	ENST00000263377.2:c.1255G>A	p.Gly419Ser	p.G419S	ENST00000263377	NM_058243.2	419	Ggt/Agt	7/20	0.134472452494801	3	FACETS	0.597	0.507	0.695	0.199	0.169	0.232	SUBCLONAL	1	TRUE	0	0.224042700941683	3		825	882	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15374332	15374332	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	58	809	0	ENST00000263377.2:c.1240G>A	p.Asp414Asn	p.D414N	ENST00000263377	NM_058243.2	414	Gat/Aat	7/20	0.134472452494801	3	FACETS	0.652	0.559	0.755	0.217	0.186	0.252	SUBCLONAL	1	TRUE	0	0.224042700941683	3		809	883	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15374353	15374353	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs201905395	NA	P-0024244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	50	750	0	ENST00000263377.2:c.1219C>G	p.Leu407Val	p.L407V	ENST00000263377	NM_058243.2	407	Ctg/Gtg	7/20	0.134472452494801	3	FACETS	0.623	0.527	0.729	0.208	0.175	0.243	SUBCLONAL	1	TRUE	0	0.224042700941683	3		750	797	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974795	21974795	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	11	194	0	ENST00000304494.5:c.32del	p.Pro11LeufsTer15	p.P11Lfs*15	ENST00000304494	NM_000077.4	11	cCt/ct	1/3	0.224042700941683	1	FACETS	0.538	0.373	0.743	0.538	0.373	0.743	SUBCLONAL	1	TRUE	0	0.224042700941683	1		194	162	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44948998	44949002	+	frameshift_variant	Frame_Shift_Del	DEL	AATTT	AATTT	-	novel	NA	P-0024244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	27	251	0	ENST00000377967.4:c.3559_3563del	p.Asn1187ProfsTer10	p.N1187Pfs*10	ENST00000377967	NM_021140.2	1187	AATTTc/c	25/29	1	1	FACETS	0.982	0.786	1	0.982	0.786	1	CLONAL	1	TRUE	0	0.224042700941683	1		251	218	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	22	510	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.172	0.133	0.219	0.172	0.133	0.219	SUBCLONAL	1	TRUE	1	0.33	2		510	774	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916248	9916248	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397518472	NA	P-0024247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	61	527	1	ENST00000330684.3:c.2041C>T	p.Arg681Ter	p.R681*	ENST00000330684	NM_001134407.1	681	Cga/Tga	10/13	1	2	FACETS	0.478	0.412	0.551	0.478	0.412	0.551	SUBCLONAL	1	TRUE	1	0.33	2		528	773	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	33	703	0	ENST00000397062.3:c.246A>T	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaT	2/5	1	2	FACETS	0.165	0.133	0.201	0.165	0.133	0.201	SUBCLONAL	1	TRUE	1	0.33	2		703	1211	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692815	89692815	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	80	298	0	ENST00000371953.3:c.299T>C	p.Leu100Pro	p.L100P	ENST00000371953	NM_000314.4	100	cTt/cCt	5/9	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.33	2		298	434	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106873	27106874	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0024247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	93	580	1	ENST00000324856.7:c.6487_6488del	p.Cys2163ProfsTer61	p.C2163Pfs*61	ENST00000324856	NM_006015.4	2162	GTg/g	20/20	1	2	FACETS	0.71	0.631	0.794	0.71	0.631	0.794	SUBCLONAL	1	TRUE	1	0.33	2		581	794	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650783	67650783	+	splice_donor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0024247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	136	520	0	ENST00000264010.4:c.1086+2del		p.X362_splice	ENST00000264010	NM_006565.3	362			1	2	FACETS	0.951	0.864	1	0.951	0.864	1	CLONAL	1	TRUE	1	0.33	2		520	867	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674238	86674242	+	frameshift_variant	Frame_Shift_Del	DEL	CACAA	CACAA	-	novel	NA	P-0024247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	99	471	0	ENST00000274376.6:c.2373_2377del	p.Thr792CysfsTer36	p.T792Cfs*36	ENST00000274376	NM_002890.2	790	gcCACAAca/gcca	18/25	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.33	2		471	527	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0024260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	423	478	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.52291765523648	3	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.52291765523648	3		478	932	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0024260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	488	637	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.52291765523648	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.52291765523648	2		638	864	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0024260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	85	375	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	0.52291765523648	1	FACETS	0.87	0.779	0.965	0.87	0.779	0.965	CLONAL	1	TRUE	0	0.52291765523648	1		375	276	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1485978447	NA	P-0024260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	140	613	2	ENST00000324856.7:c.5164C>T	p.Arg1722Ter	p.R1722*	ENST00000324856	NM_006015.4	1722	Cga/Tga	20/20	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.52291765523648	2		615	523	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789621	3789621	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	210	607	0	ENST00000262367.5:c.4238A>G	p.His1413Arg	p.H1413R	ENST00000262367	NM_004380.2	1413	cAc/cGc	25/31	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.52291765523648	2		607	723	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120132	70120133	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0024260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	196	226	0	ENST00000245479.2:c.1137_1138dup	p.His380ArgfsTer4	p.H380Rfs*4	ENST00000245479	NM_000346.3	378	-/GC	3/3	0.512052229342522	4	FACETS	0.984	0.936	1	0.984	0.936	1	CLONAL	4	TRUE	0	0.52291765523648	4		226	290	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940077	76940077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	141	583	1	ENST00000373344.5:c.671C>T	p.Ala224Val	p.A224V	ENST00000373344	NM_000489.3	224	gCg/gTg	9/35	1	2	FACETS	0.827	0.756	0.902	0.827	0.756	0.902	CLONAL	1	TRUE	1	0.52291765523648	2		584	652	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	108	314	0				ENST00000310581	NM_198253.2	-/1132			0.3	3	FACETS	0.946	0.863	1	0.946	0.863	1	CLONAL	3	TRUE	0	0.32	3		314	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0024263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	126	819	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.205501440000915	2	FACETS	0.81	0.738	0.885	0.81	0.738	0.885	CLONAL	2	TRUE	0	0.32	2		819	486	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148513825	148513825	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	26	656	1	ENST00000320356.2:c.1456C>T	p.Pro486Ser	p.P486S	ENST00000320356	NM_004456.4	486	Ccc/Tcc	12/20	1	2	FACETS	0.371	0.293	0.46	0.371	0.293	0.46	SUBCLONAL	1	TRUE	1	0.32	2		657	438	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256676	16256676	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	38	603	0	ENST00000375759.3:c.3941C>A	p.Ser1314Tyr	p.S1314Y	ENST00000375759	NM_015001.2	1314	tCt/tAt	11/15	1	2	FACETS	0.487	0.402	0.581	0.487	0.402	0.581	SUBCLONAL	1	TRUE	1	0.32	2		603	488	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089629	27089629	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	90	706	2	ENST00000324856.7:c.2586del	p.Met863TrpfsTer28	p.M863Wfs*28	ENST00000324856	NM_006015.4	862	tCc/tc	8/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.32	2		708	453	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66781559	66781559	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1301109791	NA	P-0024263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	30	616	0	ENST00000307102.5:c.967C>G	p.Pro323Ala	p.P323A	ENST00000307102	NM_002755.3	323	Cca/Gca	9/11	1	2	FACETS	0.456	0.367	0.557	0.456	0.367	0.557	SUBCLONAL	1	TRUE	1	0.32	2		616	411	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987049	69987049	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	97	739	0	ENST00000394351.3:c.110C>G	p.Ser37Cys	p.S37C	ENST00000394351	NM_000248.3	37	tCt/tGt	2/9	0.178290493647498	4	FACETS	1	0.981	1	0.748	0.669	0.832	INDETERMINATE	1	TRUE	2	0.32	4		739	535	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403478	139403478	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	73	1020	0	ENST00000277541.6:c.3015C>A	p.Phe1005Leu	p.F1005L	ENST00000277541	NM_017617.3	1005	ttC/ttA	19/34	1	2	FACETS	0.877	0.769	0.994	0.877	0.769	0.994	CLONAL	1	TRUE	1	0.32	2		1020	520	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0024267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	92	606	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.801	0.711	0.898	1	0.981	1	CLONAL	2	TRUE	1	0.13	2		606	883	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0024267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	49	778	2	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	1	2	FACETS	0.695	0.586	0.815	0.695	0.586	0.815	SUBCLONAL	1	TRUE	1	0.13	2		780	1085	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426901	70426901	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	58	634	0	ENST00000373644.4:c.4561G>T	p.Val1521Leu	p.V1521L	ENST00000373644	NM_030625.2	1521	Gtg/Ttg	7/12	0.170083783631542	3	FACETS	1	0.965	1			1	CLONAL	1	TRUE	NA	0.13	3		634	657	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244278	5244279	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0024267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	54	1014	2	ENST00000357368.4:c.1203_1204delinsTT	p.Trp401_Val402delinsCysLeu	p.W401_V402delinsCL	ENST00000357368	NM_002850.3	401	tgGGtg/tgTTtg	11/38	1	2	FACETS	0.891	0.759	1	0.891	0.759	1	CLONAL	1	TRUE	1	0.13	2		1016	932	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7120714	7120714	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	58	1190	1	ENST00000302850.5:c.3576A>T	p.Lys1192Asn	p.K1192N	ENST00000302850	NM_000208.2	1192	aaA/aaT	20/22	1	2	FACETS	0.934	0.8	1	0.934	0.8	1	CLONAL	1	TRUE	1	0.13	2		1191	955	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197198	26197198	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	41	752	0	ENST00000356476.2:c.281A>T	p.Gln94Leu	p.Q94L	ENST00000356476		94	cAg/cTg	1/1	1	2	FACETS	0.89	0.739	1	0.89	0.739	1	CLONAL	1	TRUE	1	0.13	2		752	709	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509581	106509581	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	48	770	1	ENST00000359195.3:c.1575C>A	p.His525Gln	p.H525Q	ENST00000359195	NM_002649.2	525	caC/caA	2/11	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.13	2		771	712	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0024270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	67	605	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.401	0.347	0.46	0.401	0.347	0.46	SUBCLONAL	1	TRUE	1	0.345793455859244	2		605	966	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931589	NA	P-0024270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	33	485	1	ENST00000349496.5:c.101G>A	p.Gly34Glu	p.G34E	ENST00000349496	NM_001904.3	34	gGa/gAa	3/15	1	2	FACETS	0.381	0.31	0.462	0.381	0.31	0.462	SUBCLONAL	1	TRUE	1	0.345793455859244	2		486	501	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405948	49405948	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	52	823	1	ENST00000418115.1:c.190G>A	p.Glu64Lys	p.E64K	ENST00000418115	NM_001664.2	64	Gaa/Aaa	3/5	1	2	FACETS	0.327	0.277	0.381	0.327	0.277	0.381	SUBCLONAL	1	TRUE	1	0.345793455859244	2		824	921	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692983	89692983	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	47	577	0	ENST00000371953.3:c.467G>T	p.Gly156Val	p.G156V	ENST00000371953	NM_000314.4	156	gGg/gTg	5/9	1	2	FACETS	0.423	0.356	0.497	0.423	0.356	0.497	SUBCLONAL	1	TRUE	1	0.345793455859244	2		577	642	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525554	137525554	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	62	862	0	ENST00000367739.4:c.461G>C	p.Gly154Ala	p.G154A	ENST00000367739	NM_000416.2	154	gGa/gCa	4/7	1	2	FACETS	0.384	0.33	0.442	0.384	0.33	0.442	SUBCLONAL	1	TRUE	1	0.345793455859244	2		862	935	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685310	86685310	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	46	230	0	ENST00000274376.6:c.3026T>G	p.Leu1009Arg	p.L1009R	ENST00000274376	NM_002890.2	1009	cTt/cGt	24/25	0.8211179391361	1	FACETS	0.41	0.352	0.471	0.41	0.352	0.471	SUBCLONAL	1	TRUE	0	0.872248232220203	1		230	145	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0024318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	430	391	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	NA	2	FACETS	0.95	0.926	0.972			1	INDETERMINATE	2	TRUE	NA	0.872248232220203	2		391	519	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196214	106196214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777692532	NA	P-0024321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	145	254	0	ENST00000380013.4:c.4547G>A	p.Arg1516Gln	p.R1516Q	ENST00000380013	NM_001127208.2	1516	cGa/cAa	11/11	0.570913087986697	3	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	1	0.570913087986697	3		254	317	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	413	552	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.412476055236628	3	FACETS	0.845	0.806	0.884	0.845	0.806	0.884	CLONAL	2	TRUE	1	0.565592741352618	3		552	1109	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0024328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	118	483	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.565592741352618	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.565592741352618	1		483	298	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575203	48575203	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	178	419	0	ENST00000342988.3:c.397T>A	p.Tyr133Asn	p.Y133N	ENST00000342988	NM_005359.5	133	Tac/Aac	3/12	0.48478504102386	1	FACETS	0.918	0.853	0.983	0.918	0.853	0.983	CLONAL	1	TRUE	0	0.565592741352618	1		419	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0024331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	254	562	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.470890936698243	1	FACETS	0.771	0.729	0.813	1	0.994	1	SUBCLONAL	2	TRUE	0	0.470890936698243	1		563	535	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805527	46805527	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	121	921	0	ENST00000290295.7:c.429C>A	p.Tyr143Ter	p.Y143*	ENST00000290295	NM_006361.5	143	taC/taA	1/2	0.470890936698243	1	FACETS	0.599	0.542	0.659	0.599	0.542	0.659	SUBCLONAL	1	TRUE	0	0.470890936698243	1		921	656	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954586	17954586	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs774202259	NA	P-0024331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	50	701	2	ENST00000458235.1:c.308G>A	p.Arg103His	p.R103H	ENST00000458235	NM_000215.3	103	cGc/cAc	3/24	0.190578826778271	2	FACETS	0.365	0.309	0.426	0.182	0.154	0.213	INDETERMINATE	1	TRUE	0	0.470890936698243	2		703	582	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923784	39923784	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	140	875	0	ENST00000378444.4:c.3307G>C	p.Glu1103Gln	p.E1103Q	ENST00000378444	NM_001123385.1	1103	Gag/Cag	7/15	NA	2	FACETS	0.918	0.838	1			1	INDETERMINATE	1	TRUE	NA	0.470890936698243	2		875	648	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717715	89717716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587782341	NA	P-0024338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	34	528	0	ENST00000371953.3:c.741dup	p.Pro248ThrfsTer5	p.P248Tfs*5	ENST00000371953	NM_000314.4	247	tta/ttAa	7/9	0.848457471770649	1	FACETS	0.143	0.117	0.173	0.143	0.117	0.173	SUBCLONAL	1	TRUE	0	0.848457471770649	1		528	322	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577481	64577481	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	262	466	0	ENST00000312049.6:c.101T>G	p.Leu34Arg	p.L34R	ENST00000312049	NM_130799.2	34	cTg/cGg	2/10	0.848457471770649	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.848457471770649	1		466	340	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288570	33288570	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	94	508	0	ENST00000374542.5:c.982C>G	p.Arg328Gly	p.R328G	ENST00000374542	NM_001141970.1	328	Cgt/Ggt	3/8	0.848457471770649	1	FACETS	0.267	0.238	0.297	0.267	0.238	0.297	SUBCLONAL	1	TRUE	0	0.848457471770649	1		508	478	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288945	33288945	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	185	434	0	ENST00000374542.5:c.607del	p.Arg203GlyfsTer26	p.R203Gfs*26	ENST00000374542	NM_001141970.1	203	Cgg/gg	3/8	0.848457471770649	1	FACETS	0.766	0.721	0.809	0.766	0.721	0.809	SUBCLONAL	1	TRUE	0	0.848457471770649	1		434	328	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813098	76813098	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	28	654	0	ENST00000373344.5:c.6523A>C	p.Ile2175Leu	p.I2175L	ENST00000373344	NM_000489.3	2175	Att/Ctt	30/35	0.848457471770649	1	FACETS	0.089	0.071	0.11	0.089	0.071	0.11	SUBCLONAL	1	TRUE	0	0.848457471770649	1		654	427	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0024344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	43	810	3	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.42	0.35	0.498	0.42	0.35	0.498	SUBCLONAL	1	FALSE	1	0.247445074511197	2		813	828	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0024344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	42	403	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	FALSE	1	0.247445074511197	2		403	301	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587161	189587161	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173679499	NA	P-0024344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	39	680	1	ENST00000264731.3:c.1178G>A	p.Arg393Gln	p.R393Q	ENST00000264731	NM_003722.4	393	cGa/cAa	9/14	1	2	FACETS	0.502	0.415	0.599	0.502	0.415	0.599	SUBCLONAL	1	FALSE	1	0.247445074511197	2		681	628	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431747	49431747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	43	696	0	ENST00000301067.7:c.9392C>T	p.Pro3131Leu	p.P3131L	ENST00000301067	NM_003482.3	3131	cCt/cTt	34/54	1	2	FACETS	0.623	0.521	0.736	0.623	0.521	0.736	SUBCLONAL	1	FALSE	1	0.247445074511197	2		696	558	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438728	49438728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1290729871	NA	P-0024344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	61	725	0	ENST00000301067.7:c.4762G>A	p.Glu1588Lys	p.E1588K	ENST00000301067	NM_003482.3	1588	Gaa/Aaa	19/54	1	2	FACETS	0.563	0.485	0.65	0.563	0.485	0.65	SUBCLONAL	1	FALSE	1	0.247445074511197	2		725	875	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55704619	55704619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567945640	NA	P-0024344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	72	793	0	ENST00000284073.2:c.682C>T	p.Arg228Cys	p.R228C	ENST00000284073	NM_138962.2	228	Cgt/Tgt	10/14	1	2	FACETS	0.655	0.571	0.747	0.655	0.571	0.747	SUBCLONAL	1	FALSE	1	0.247445074511197	2		793	888	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57569920	57569920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	47	430	1	ENST00000316660.6:c.100G>A	p.Asp34Asn	p.D34N	ENST00000316660	NM_021127.2	34	Gac/Aac	2/2	1	2	FACETS	0.767	0.648	0.899	0.767	0.648	0.899	SUBCLONAL	1	FALSE	1	0.247445074511197	2		431	495	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610200	10610201	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0024344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	104	766	0	ENST00000171111.5:c.509_510delinsTT	p.Ala170Val	p.A170V	ENST00000171111	NM_203500.1	170	gCC/gTT	2/6	1	2	FACETS	0.954	0.853	1	0.954	0.853	1	CLONAL	1	FALSE	1	0.247445074511197	2		766	881	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224086	36224087	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0024344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	51	702	0	ENST00000222270.7:c.6641dup	p.Val2215SerfsTer88	p.V2215Sfs*88	ENST00000222270	NM_014727.1	2212	-/C	28/37	1	2	FACETS	0.577	0.489	0.673	0.577	0.489	0.673	SUBCLONAL	1	FALSE	1	0.247445074511197	2		702	715	SUCCESS
REL	5966	MSKCC	GRCh37	2	61128131	61128131	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	43	505	0	ENST00000295025.8:c.307C>T	p.Gln103Ter	p.Q103*	ENST00000295025	NM_002908.2	103	Caa/Taa	4/11	1	2	FACETS	0.492	0.411	0.583	0.492	0.411	0.583	SUBCLONAL	1	FALSE	1	0.247445074511197	2		505	706	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155399	99155399	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1559033620	NA	P-0024344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	41	516	0	ENST00000074304.5:c.625C>T	p.Arg209Ter	p.R209*	ENST00000074304	NM_001134224.1	209	Cga/Tga	9/26	1	2	FACETS	0.491	0.408	0.584	0.491	0.408	0.584	SUBCLONAL	1	FALSE	1	0.247445074511197	2		516	675	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187219	38187219	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	73	903	2	ENST00000317025.8:c.1258C>T	p.Arg420Ter	p.R420*	ENST00000317025	NM_023034.1	420	Cga/Tga	6/24	1	2	FACETS	0.512	0.446	0.584	0.512	0.446	0.584	SUBCLONAL	1	FALSE	1	0.247445074511197	2		905	1152	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205605	38205605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	49	823	0	ENST00000317025.8:c.85C>T	p.Arg29Cys	p.R29C	ENST00000317025	NM_023034.1	29	Cgt/Tgt	2/24	1	2	FACETS	0.439	0.37	0.515	0.439	0.37	0.515	SUBCLONAL	1	FALSE	1	0.247445074511197	2		823	903	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370867	55370868	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0024344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	31	444	0	ENST00000297316.4:c.169_170delinsAA	p.Gly57Lys	p.G57K	ENST00000297316	NM_022454.3	57	GGg/AAg	1/2	1	2	FACETS	0.58	0.469	0.706	0.58	0.469	0.706	SUBCLONAL	1	FALSE	1	0.247445074511197	2		444	432	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606356	93606356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	57	637	0	ENST00000375746.1:c.176G>A	p.Arg59Lys	p.R59K	ENST00000375746	NM_001174167.1	59	aGg/aAg	2/14	1	2	FACETS	0.769	0.66	0.889	0.769	0.66	0.889	SUBCLONAL	1	FALSE	1	0.247445074511197	2		637	599	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933691	39933691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	34	317	0	ENST00000378444.4:c.908C>T	p.Ala303Val	p.A303V	ENST00000378444	NM_001123385.1	303	gCc/gTc	4/15	1	1	FACETS	0.845	0.693	1	0.845	0.693	1	CLONAL	1	FALSE	0	0.247445074511197	1		317	285	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0024348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	80	454	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	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.404589348717167	2		454	351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0024351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	431	569	2	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.794392102007135	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.794392102007135	1		571	653	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954299	48954299	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs1395304450	NA	P-0024351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	226	528	1	ENST00000267163.4:c.1422-2A>T		p.X474_splice	ENST00000267163	NM_000321.2	474			0.794392102007135	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.794392102007135	1		529	327	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	459866	459866	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	67	980	0	ENST00000399788.2:c.1229G>A	p.Gly410Glu	p.G410E	ENST00000399788	NM_001042603.1	410	gGa/gAa	10/28	NA	2	FACETS	0.149	0.129	0.172			1	INDETERMINATE	1	TRUE	NA	0.794392102007135	2		980	1129	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65568266	65568266	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	173	420	1	ENST00000358664.4:c.61G>T	p.Ala21Ser	p.A21S	ENST00000358664	NM_002382.4	21	Gcg/Tcg	2/5	1	2	FACETS	0.939	0.872	1	0.939	0.872	1	CLONAL	1	TRUE	1	0.794392102007135	2		421	464	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274137	10274137	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	302	694	0	ENST00000330684.3:c.132C>A	p.His44Gln	p.H44Q	ENST00000330684	NM_001134407.1	44	caC/caA	2/13	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.794392102007135	2		694	740	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347060	89347060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	312	686	0	ENST00000301030.4:c.5890G>A	p.Gly1964Arg	p.G1964R	ENST00000301030	NM_001256183.1	1964	Ggg/Agg	9/13	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.794392102007135	2		686	785	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1976588	1976588	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0024351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	355	790	0	ENST00000382891.5:c.3373-2A>T		p.X1125_splice	ENST00000382891	NM_133335.3	1125			0.794392102007135	1	FACETS	0.981	0.944	1	0.981	0.944	1	CLONAL	1	TRUE	0	0.794392102007135	1		790	549	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0024364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	74	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.936	0.821	1	0.936	0.821	1	CLONAL	1	TRUE	1	0.325469084401501	2		326	486	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070527	67070543	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGATTTTTCTAAAAGGC	TGATTTTTCTAAAAGGC	-	novel	NA	P-0024364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	40	216	0	ENST00000412916.2:c.166-14_168del		p.X56_splice	ENST00000412916		56		3/6	0.325469084401501	1	FACETS	0.785	0.657	0.927	0.785	0.657	0.927	CLONAL	1	TRUE	0	0.325469084401501	1		216	262	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326168	62326168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773397014	NA	P-0024364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	113	598	0	ENST00000360203.5:c.3184G>A	p.Ala1062Thr	p.A1062T	ENST00000360203	NM_001283009.1	1062	Gcc/Acc	32/35	1	2	FACETS	0.778	0.7	0.862	0.778	0.7	0.862	SUBCLONAL	1	TRUE	1	0.325469084401501	2		598	892	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928067	178928067	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	97	536	0	ENST00000263967.3:c.1345C>G	p.Pro449Ala	p.P449A	ENST00000263967	NM_006218.2	449	Cct/Gct	8/21	1	2	FACETS	0.849	0.757	0.947	0.849	0.757	0.947	CLONAL	1	TRUE	1	0.325469084401501	2		536	702	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873376	151873377	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0024364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	82	320	0	ENST00000262189.6:c.9161_9162insC	p.Leu3055SerfsTer32	p.L3055Sfs*32	ENST00000262189	NM_170606.2	3054	ctt/ctCt	38/59	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.325469084401501	2		320	459	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0024371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	99	288	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.580400646758575	2		288	333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578502	7578502	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	299	820	0	ENST00000269305.4:c.428T>C	p.Val143Ala	p.V143A	ENST00000269305	NM_001126112.2	143	gTg/gCg	5/11	0.564905814732631	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.580400646758575	1		820	725	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541941	187541948	+	frameshift_variant	Frame_Shift_Del	DEL	AGTCTTGT	AGTCTTGT	-	novel	NA	P-0024371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	203	479	0	ENST00000441802.2:c.5792_5799del	p.Tyr1931TrpfsTer20	p.Y1931Wfs*20	ENST00000441802	NM_005245.3	1931	tACAAGACT/t	10/27	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.580400646758575	2		479	651	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888812	76888812	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	178	292	0	ENST00000373344.5:c.5017C>T	p.Gln1673Ter	p.Q1673*	ENST00000373344	NM_000489.3	1673	Caa/Taa	19/35	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.580400646758575	1		292	295	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579865	7579868	+	frameshift_variant	Frame_Shift_Del	DEL	CTGA	CTGA	-	novel	NA	P-0024394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	82	660	0	ENST00000269305.4:c.45_48del	p.Ser15ArgfsTer28	p.S15Rfs*28	ENST00000269305	NM_001126112.2	15	agTCAG/ag	2/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		660	689	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0024397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	148	304	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	0.191388750595099	3	FACETS	0.785	0.725	0.847	0.785	0.725	0.847	INDETERMINATE	2	TRUE	1	0.604801509930085	3		304	406	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106037	8106050	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGCGGGCTCTAT	CCTGCGGGCTCTAT	-	novel	NA	P-0024397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	141	373	0	ENST00000346208.3:c.858_871del	p.Cys287GlnfsTer11	p.C287Qfs*11	ENST00000346208		286	gCCTGCGGGCTCTAT/g	4/6	1	2	FACETS	0.952	0.873	1	0.952	0.873	1	CLONAL	1	TRUE	1	0.604801509930085	2		373	490	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119682	70119683	+	splice_acceptor_variant	Splice_Site	INS	-	-	G	novel	NA	P-0024397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	177	479	0	ENST00000245479.2:c.687dup		p.X229_splice	ENST00000245479	NM_000346.3	229			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.604801509930085	2		479	540	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827919	40827919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	30	486	1	ENST00000373198.4:c.2509G>A	p.Glu837Lys	p.E837K	ENST00000373198	NM_133170.3	837	Gaa/Aaa	17/32	1	2	FACETS	0.178	0.143	0.218	0.178	0.143	0.218	SUBCLONAL	1	TRUE	1	0.604801509930085	2		487	558	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098414	47098414	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	78	430	0	ENST00000409792.3:c.6860C>G	p.Ser2287Cys	p.S2287C	ENST00000409792	NM_014159.6	2287	tCt/tGt	15/21	1	2	FACETS	0.532	0.469	0.599	0.532	0.469	0.599	SUBCLONAL	1	TRUE	1	0.604801509930085	2		430	485	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862958	117862958	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	25	446	1	ENST00000297338.2:c.1519G>A	p.Glu507Lys	p.E507K	ENST00000297338	NM_006265.2	507	Gaa/Aaa	12/14	1	2	FACETS	0.184	0.144	0.23	0.184	0.144	0.23	SUBCLONAL	1	TRUE	1	0.604801509930085	2		447	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0024406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	372	573	1	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.441938765343875	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.441938765343875	2		574	808	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753454	42753454	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	129	597	0	ENST00000222329.4:c.810G>C	p.Met270Ile	p.M270I	ENST00000222329	NM_006494.2	270	atG/atC	4/4	0.271279479166975	4	FACETS	0.743	0.672	0.818	0.371	0.336	0.409	SUBCLONAL	1	TRUE	2	0.441938765343875	4		597	1133	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146544	55146544	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	55	331	0	ENST00000257290.5:c.2218A>G	p.Thr740Ala	p.T740A	ENST00000257290	NM_006206.4	740	Aca/Gca	16/23	0.436851276975179	2	FACETS	0.473	0.405	0.548	0.237	0.202	0.274	SUBCLONAL	1	TRUE	0	0.441938765343875	2		331	526	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0024421-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	32	478	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.58	0.469	0.705	0.58	0.469	0.705	SUBCLONAL	1	TRUE	1	0.2	2		478	552	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610211	10610211	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024421-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	79	727	0	ENST00000171111.5:c.499G>T	p.Val167Phe	p.V167F	ENST00000171111	NM_203500.1	167	Gtt/Ttt	2/6	1	2	FACETS	0.871	0.764	0.986	0.871	0.764	0.986	CLONAL	1	TRUE	1	0.2	2		727	907	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170384	119170384	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024421-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	51	428	3	ENST00000264033.4:c.2614C>T	p.Gln872Ter	p.Q872*	ENST00000264033	NM_005188.3	872	Cag/Tag	16/16	1	2	FACETS	0.917	0.779	1	0.917	0.779	1	CLONAL	1	TRUE	1	0.2	2		431	556	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662760	227662760	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024421-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	73	794	0	ENST00000305123.5:c.695G>T	p.Gly232Val	p.G232V	ENST00000305123	NM_005544.2	232	gGg/gTg	1/2	1	2	FACETS	0.745	0.65	0.848	0.745	0.65	0.848	SUBCLONAL	1	TRUE	1	0.2	2		794	980	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447202	187447202	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024421-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	67	697	0	ENST00000232014.4:c.991C>G	p.Pro331Ala	p.P331A	ENST00000232014	NM_001130845.1	331	Cca/Gca	5/10	1	2	FACETS	0.83	0.72	0.95	0.83	0.72	0.95	CLONAL	1	TRUE	1	0.2	2		697	807	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294750	1294750	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024421-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	50	622	0	ENST00000310581.5:c.251T>A	p.Val84Glu	p.V84E	ENST00000310581	NM_198253.2	84	gTg/gAg	2/16	1	2	FACETS	0.734	0.622	0.858	0.734	0.622	0.858	SUBCLONAL	1	TRUE	1	0.2	2		622	681	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428192	47428192	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024421-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	81	696	1	ENST00000377045.4:c.1152G>T	p.Trp384Cys	p.W384C	ENST00000377045	NM_001654.4	384	tgG/tgT	11/16	1	2	FACETS	0.865	0.761	0.978	0.865	0.761	0.978	CLONAL	1	TRUE	1	0.2	2		697	936	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121193	11121194	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	A	novel	NA	P-0024421-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	68	649	2	ENST00000358026.2:c.2260_2261delinsA	p.Leu754ThrfsTer20	p.L754Tfs*20	ENST00000358026	NM_001128849.1	754	CTc/Ac	15/36	1	2	FACETS	0.852	0.74	0.974	0.852	0.74	0.974	CLONAL	1	TRUE	1	0.2	2		651	798	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882019	NA	P-0024445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	142	751	0	ENST00000269305.4:c.455dup	p.Pro153AlafsTer28	p.P153Afs*28	ENST00000269305	NM_001126112.2	152	ccg/ccCg	5/11	0.576986519756023	3	FACETS	0.866	0.791	0.945	0.433	0.395	0.473	CLONAL	1	TRUE	1	0.576986519756023	3		751	732	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920413	114920413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767830105	NA	P-0024445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	277	497	1	ENST00000543371.1:c.1354G>A	p.Gly452Arg	p.G452R	ENST00000543371	NM_001198531.1	452	Ggg/Agg	13/14	0.576986519756023	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.576986519756023	2		498	447	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508082	106508082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	73	202	0	ENST00000359195.3:c.76C>T	p.Arg26Cys	p.R26C	ENST00000359195	NM_002649.2	26	Cgc/Tgc	2/11	0.311585350214204	5	FACETS	1	0.902	1	0.678	0.602	0.758	INDETERMINATE	2	TRUE	2	0.576986519756023	5		202	232	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648329	206648329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55721947	NA	P-0024445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	98	600	1	ENST00000367120.3:c.350G>A	p.Arg117His	p.R117H	ENST00000367120	NM_014002.3	117	cGc/cAc	5/22	0.531267855283776	4	FACETS	0.765	0.683	0.853	0.383	0.341	0.427	SUBCLONAL	1	TRUE	2	0.576986519756023	4		601	700	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578383	7578383	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	258	529	0	ENST00000269305.4:c.547del	p.Ser183GlnfsTer64	p.S183Qfs*64	ENST00000269305	NM_001126112.2	183	Tca/ca	5/11	0.576986519756023	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.576986519756023	3		529	540	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793481	42793481	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs532264982	NA	P-0024445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	279	651	3	ENST00000575354.2:c.1283G>A	p.Arg428His	p.R428H	ENST00000575354	NM_015125.3	428	cGt/cAt	8/20	0.576986519756023	3	FACETS	0.956	0.904	1	0.956	0.904	1	CLONAL	2	TRUE	1	0.576986519756023	3		654	652	SUCCESS
APC	324	MSKCC	GRCh37	5	112175208	112175208	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	111	243	0	ENST00000257430.4:c.3919del	p.Ile1307Ter	p.I1307*	ENST00000257430	NM_000038.5	1306	gAa/ga	16/16	0.576986519756023	3	FACETS	0.908	0.843	0.971	0.908	0.843	0.971	CLONAL	3	TRUE	0	0.576986519756023	3		243	182	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739012	145739012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373292946	NA	P-0024445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	77	618	0	ENST00000428558.2:c.2143C>T	p.Arg715Trp	p.R715W	ENST00000428558	NM_004260.3	715	Cgg/Tgg	13/22	0.576986519756023	6	FACETS	0.582	0.51	0.661	0.146	0.127	0.166	SUBCLONAL	1	TRUE	2	0.576986519756023	6		618	987	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0024488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	47	655	2	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	1	2	FACETS	0.668	0.564	0.783	0.668	0.564	0.783	SUBCLONAL	1	TRUE	1	0.29	2		657	485	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0024488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	27	668	2	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	0.127092843737836	1	FACETS	0.365	0.29	0.451	0.365	0.29	0.451	INDETERMINATE	1	TRUE	0	0.29	1		670	436	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212208	5212208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148739536	NA	P-0024488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	98	812	0	ENST00000357368.4:c.4823G>A	p.Arg1608Gln	p.R1608Q	ENST00000357368	NM_002850.3	1608	cGg/cAg	32/38	1	2	FACETS	0.772	0.692	0.855	1	0.983	1	SUBCLONAL	2	TRUE	1	0.29	2		812	438	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0024488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	46	450	2	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.29	2		452	315	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690817	89690819	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs1554897864	NA	P-0024488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	18	526	0	ENST00000371953.3:c.226_228del	p.Tyr76del	p.Y76del	ENST00000371953	NM_000314.4	75	cATTat/cat	4/9	0.127092843737836	1	FACETS	0.297	0.223	0.385	0.297	0.223	0.385	INDETERMINATE	1	TRUE	0	0.29	1		526	357	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827732	72827732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241554729	NA	P-0024488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	39	645	2	ENST00000268489.5:c.8849G>A	p.Arg2950His	p.R2950H	ENST00000268489	NM_006885.3	2950	cGc/cAc	9/10	1	2	FACETS	0.492	0.407	0.587	0.492	0.407	0.587	SUBCLONAL	1	TRUE	1	0.29	2		647	547	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916726	178916726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772110575	NA	P-0024488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	35	494	0	ENST00000263967.3:c.113G>A	p.Arg38His	p.R38H	ENST00000263967	NM_006218.2	38	cGt/cAt	2/21	1	2	FACETS	0.524	0.429	0.63	0.524	0.429	0.63	SUBCLONAL	1	TRUE	1	0.29	2		494	461	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753187	128753187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779123478	NA	P-0024488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	24	362	0	ENST00000377970.2:c.1348C>T	p.Arg450Trp	p.R450W	ENST00000377970	NM_002467.4	450	Cgg/Tgg	3/3	1	2	FACETS	0.465	0.364	0.581	0.465	0.364	0.581	SUBCLONAL	1	TRUE	1	0.29	2		362	356	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054978	176054978	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	53	825	1	ENST00000367669.3:c.1075C>T	p.Arg359Ter	p.R359*	ENST00000367669	NM_022457.5	359	Cga/Tga	10/20	1	2	FACETS	0.538	0.458	0.626	0.538	0.458	0.626	SUBCLONAL	1	TRUE	1	0.29	2		826	679	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256321	16256321	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	34	737	0	ENST00000375759.3:c.3591del	p.Asp1198MetfsTer2	p.D1198Mfs*2	ENST00000375759	NM_015001.2	1196	Aaa/aa	11/15	1	2	FACETS	0.393	0.32	0.475	0.393	0.32	0.475	SUBCLONAL	1	TRUE	1	0.29	2		737	597	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68290283	68290283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867530891	NA	P-0024488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	33	681	0	ENST00000487270.1:c.23G>A	p.Arg8Gln	p.R8Q	ENST00000487270	NM_133509.3	8	cGa/cAa	2/11	1	2	FACETS	0.473	0.385	0.573	0.473	0.385	0.573	SUBCLONAL	1	TRUE	1	0.29	2		681	481	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0024488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	107	840	0	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.29	2		840	705	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228979	36228979	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555734923	NA	P-0024488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	27	647	0	ENST00000222270.7:c.7759C>T	p.Arg2587Ter	p.R2587*	ENST00000222270	NM_014727.1	2587	Cga/Tga	36/37	1	2	FACETS	0.345	0.273	0.427	0.345	0.273	0.427	SUBCLONAL	1	TRUE	1	0.29	2		647	540	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856595	111856595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1454335466	NA	P-0024488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	23	205	1	ENST00000341259.2:c.646C>T	p.Arg216Cys	p.R216C	ENST00000341259	NM_005475.2	216	Cgc/Tgc	2/8	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.29	2		206	128	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654616	67654616	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1259610303	NA	P-0024488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	51	720	0	ENST00000264010.4:c.1103G>A	p.Arg368His	p.R368H	ENST00000264010	NM_006565.3	368	cGt/cAt	6/12	1	2	FACETS	0.606	0.515	0.707	0.606	0.515	0.707	SUBCLONAL	1	TRUE	1	0.29	2		720	580	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265331	16265331	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs889756630	NA	P-0024488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	30	812	1	ENST00000375759.3:c.10823C>T	p.Ala3608Val	p.A3608V	ENST00000375759	NM_015001.2	3608	gCg/gTg	14/15	1	2	FACETS	0.371	0.298	0.455	0.371	0.298	0.455	SUBCLONAL	1	TRUE	1	0.29	2		813	557	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106025	27106025	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371595717	NA	P-0024488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	50	541	0	ENST00000324856.7:c.5636G>A	p.Arg1879Gln	p.R1879Q	ENST00000324856	NM_006015.4	1879	cGg/cAg	20/20	0.3	1	FACETS	0.752	0.64	0.875	0.752	0.64	0.875	SUBCLONAL	1	TRUE	0	0.29	1		541	392	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100591	8100591	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	43	752	0	ENST00000346208.3:c.568del	p.Leu190CysfsTer5	p.L190Cfs*5	ENST00000346208		189	Ccc/cc	3/6	1	2	FACETS	0.548	0.458	0.648	0.548	0.458	0.648	SUBCLONAL	1	TRUE	1	0.29	2		752	541	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417801	32417801	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0024488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	20	502	1	ENST00000332351.3:c.1249+2T>A		p.X417_splice	ENST00000332351	NM_024426.4	417			1	2	FACETS	0.351	0.268	0.449	0.351	0.268	0.449	SUBCLONAL	1	TRUE	1	0.29	2		503	393	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022454	12022454	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753079378	NA	P-0024488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	133	966	0	ENST00000396373.4:c.560C>T	p.Thr187Met	p.T187M	ENST00000396373	NM_001987.4	187	aCg/aTg	5/8	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.29	2		966	819	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218405	133218405	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770181299	NA	P-0024488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	94	946	6	ENST00000320574.5:c.5206G>A	p.Val1736Ile	p.V1736I	ENST00000320574	NM_006231.2	1736	Gtc/Atc	39/49	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.29	2		952	536	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3634827	3634827	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs543847606	NA	P-0024488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	64	946	2	ENST00000294008.3:c.4682C>T	p.Thr1561Met	p.T1561M	ENST00000294008	NM_032444.2	1561	aCg/aTg	13/15	1	2	FACETS	0.645	0.558	0.74	0.645	0.558	0.74	SUBCLONAL	1	TRUE	1	0.29	2		948	684	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78933944	78933944	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1389264031	NA	P-0024488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	74	896	3	ENST00000306801.3:c.3544G>A	p.Val1182Met	p.V1182M	ENST00000306801	NM_020761.2	1182	Gtg/Atg	30/34	1	2	FACETS	0.945	0.829	1	0.945	0.829	1	CLONAL	1	TRUE	1	0.29	2		899	540	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912867	50912867	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868562435	NA	P-0024488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	51	1006	0	ENST00000440232.2:c.2098G>A	p.Val700Ile	p.V700I	ENST00000440232	NM_002691.3	700	Gta/Ata	17/27	1	2	FACETS	0.667	0.567	0.777	0.667	0.567	0.777	SUBCLONAL	1	TRUE	1	0.29	2		1006	527	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427720	72427720	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	60	467	0	ENST00000477973.2:c.770T>G	p.Val257Gly	p.V257G	ENST00000477973	NM_012234.5	257	gTc/gGc	4/4	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.29	2		467	385	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417822	138417822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs547624936	NA	P-0024488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	28	659	1	ENST00000289153.2:c.1697G>A	p.Arg566Gln	p.R566Q	ENST00000289153	NM_006219.2	566	cGa/cAa	11/22	1	2	FACETS	0.352	0.281	0.435	0.352	0.281	0.435	SUBCLONAL	1	TRUE	1	0.29	2		660	548	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879277	151879277	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs956673837	NA	P-0024488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	25	607	2	ENST00000262189.6:c.5668C>T	p.Arg1890Ter	p.R1890*	ENST00000262189	NM_170606.2	1890	Cga/Tga	36/59	1	2	FACETS	0.372	0.293	0.464	0.372	0.293	0.464	SUBCLONAL	1	TRUE	1	0.29	2		609	463	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187222	38187222	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	59	526	3	ENST00000317025.8:c.1255del	p.Thr419ProfsTer8	p.T419Pfs*8	ENST00000317025	NM_023034.1	419	Acc/cc	6/24	1	2	FACETS	0.42	0.36	0.486	0.42	0.36	0.486	SUBCLONAL	1	TRUE	1	0.29	2		529	968	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405602	139405602	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0024488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	46	922	0	ENST00000277541.6:c.2587+2T>C		p.X863_splice	ENST00000277541	NM_017617.3	863			1	2	FACETS	0.583	0.491	0.685	0.583	0.491	0.685	SUBCLONAL	1	TRUE	1	0.29	2		922	544	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922270	39922270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	28	243	0	ENST00000378444.4:c.3902C>T	p.Ala1301Val	p.A1301V	ENST00000378444	NM_001123385.1	1301	gCa/gTa	9/15	1	1	FACETS	0.772	0.62	0.941	0.772	0.62	0.941	CLONAL	1	TRUE	0	0.29	1		243	214	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228288	53228288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1569264240	NA	P-0024488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	21	408	0	ENST00000375401.3:c.2114G>A	p.Arg705His	p.R705H	ENST00000375401	NM_004187.3	705	cGc/cAc	15/26	1	1	FACETS	0.413	0.318	0.523	0.413	0.318	0.523	SUBCLONAL	1	TRUE	0	0.29	1		408	300	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0024516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	46	336	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.313664338052699	3	FACETS	0.841	0.71	0.984	0.42	0.355	0.492	CLONAL	1	TRUE	1	0.330364011166754	3		336	386	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437115	110437115	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1450781846	NA	P-0024516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	83	103	0	ENST00000375856.3:c.1286G>T	p.Arg429Leu	p.R429L	ENST00000375856	NM_003749.2	429	cGc/cTc	1/2	0.330364011166754	4	FACETS	1	0.92	1	1	0.92	1	CLONAL	3	TRUE	1	0.330364011166754	4		103	217	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579716	7579716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1192416464	NA	P-0024516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	316	624	0	ENST00000269305.4:c.80del	p.Pro27LeufsTer17	p.P27Lfs*17	ENST00000269305	NM_001126112.2	27	cCt/ct	3/11	0.330364011166754	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	1	0.330364011166754	4		624	784	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584754	48584754	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	142	536	0	ENST00000342988.3:c.833del	p.Pro278LeufsTer58	p.P278Lfs*58	ENST00000342988	NM_005359.5	278	Cct/ct	7/12	0.199755165309687	3	FACETS	1	0.959	1			1	CLONAL	2	TRUE	NA	0.330364011166754	3		536	467	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185819	32185819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145916093	NA	P-0024516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	314	692	0	ENST00000375023.3:c.1577C>T	p.Ala526Val	p.A526V	ENST00000375023	NM_004557.3	526	gCg/gTg	9/30	0.330364011166754	6	FACETS	1	0.981	1	0.811	0.767	0.856	CLONAL	3	TRUE	2	0.330364011166754	6		692	973	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0024516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	221	496	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.330364011166754	8	FACETS	0.884	0.822	0.947	0.663	0.617	0.71	CLONAL	3	TRUE	4	0.330364011166754	8		496	1005	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412044	63412044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	148	777	0	ENST00000330258.3:c.1123C>T	p.Pro375Ser	p.P375S	ENST00000330258	NM_152424.3	375	Cca/Tca	2/2	0.189471834911923	4	FACETS	0.836	0.765	0.91	0.836	0.765	0.91	INDETERMINATE	2	TRUE	2	0.330364011166754	4		777	713	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0024523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	18	656	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.112	0.083	0.145	0.112	0.083	0.145	SUBCLONAL	1	TRUE	1	0.576369022163296	2		656	560	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0024523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	147	364	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.814	0.745	0.884	0.814	0.745	0.884	CLONAL	1	TRUE	1	0.576369022163296	2		364	627	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115928	8115929	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0024523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	37	542	1	ENST00000346208.3:c.1275dup	p.Ser426IlefsTer81	p.S426Ifs*81	ENST00000346208		425	cca/ccAa	6/6	1	2	FACETS	0.242	0.199	0.291	0.242	0.199	0.291	SUBCLONAL	1	TRUE	1	0.576369022163296	2		543	530	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939260	71939260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	150	885	2	ENST00000298229.2:c.209G>A	p.Arg70His	p.R70H	ENST00000298229	NM_001567.3	70	cGc/cAc	2/28	1	2	FACETS	0.703	0.644	0.766	0.703	0.644	0.766	SUBCLONAL	1	TRUE	1	0.576369022163296	2		887	740	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780705	9780705	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	106	724	0	ENST00000377346.4:c.1507G>A	p.Val503Ile	p.V503I	ENST00000377346	NM_005026.3	503	Gtc/Atc	12/24	1	2	FACETS	0.646	0.581	0.715	0.646	0.581	0.715	SUBCLONAL	1	TRUE	1	0.576369022163296	2		724	569	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061215	38061215	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	155	593	0	ENST00000250448.2:c.774C>G	p.Cys258Trp	p.C258W	ENST00000250448	NM_004496.3	258	tgC/tgG	2/2	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.576369022163296	2		593	506	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646192	23646192	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555461154	NA	P-0024523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	27	470	0	ENST00000261584.4:c.1675C>T	p.Gln559Ter	p.Q559*	ENST00000261584	NM_024675.3	559	Caa/Taa	4/13	1	2	FACETS	0.186	0.147	0.23	0.186	0.147	0.23	SUBCLONAL	1	TRUE	1	0.576369022163296	2		470	504	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651591	48651591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557020430	NA	P-0024523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	190	674	0	ENST00000376670.3:c.757C>T	p.Arg253Trp	p.R253W	ENST00000376670	NM_002049.3	253	Cgg/Tgg	5/6	0.262568969512333	1	FACETS	0.808	0.751	0.865	0.808	0.751	0.865	INDETERMINATE	1	TRUE	0	0.576369022163296	1		674	581	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0024526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	232	478	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.996	0.935	1	0.996	0.935	1	CLONAL	1	TRUE	1	0.724295726148624	2		478	643	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0024526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	84	255	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.935	0.839	1	0.935	0.839	1	CLONAL	1	TRUE	1	0.724295726148624	2		255	248	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792362	33792362	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	291	931	0	ENST00000498907.2:c.959A>T	p.Asp320Val	p.D320V	ENST00000498907	NM_004364.3	320	gAc/gTc	1/1	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.724295726148624	2		931	749	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289023	33289023	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	254	542	0	ENST00000374542.5:c.529C>T	p.Gln177Ter	p.Q177*	ENST00000374542	NM_001141970.1	177	Cag/Tag	3/8	0.713977801172049	1	FACETS	0.921	0.872	0.969	0.921	0.872	0.969	CLONAL	1	TRUE	0	0.713977801172049	1		542	497	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852271	128852271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	258	795	0	ENST00000249373.3:c.2343G>A	p.Met781Ile	p.M781I	ENST00000249373	NM_005631.4	781	atG/atA	12/12	1	2	FACETS	0.925	0.87	0.982	0.925	0.87	0.982	CLONAL	1	TRUE	1	0.713977801172049	2		795	781	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0024566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	164	792	54	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.378810222168965	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.378810222168965	1		846	570	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	44	573	1	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	1	2	FACETS	0.456	0.382	0.538	0.456	0.382	0.538	SUBCLONAL	1	TRUE	1	0.378810222168965	2		574	509	SUCCESS
APC	324	MSKCC	GRCh37	5	112170683	112170683	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554083132	NA	P-0024566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	112	803	0	ENST00000257430.4:c.1779G>A	p.Trp593Ter	p.W593*	ENST00000257430	NM_000038.5	593	tgG/tgA	15/16	0.352835958652127	2	FACETS	0.756	0.686	0.829	0.756	0.686	0.829	SUBCLONAL	2	TRUE	0	0.378810222168965	2		803	391	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716227	243716227	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	72	867	0	ENST00000263826.5:c.967T>C	p.Tyr323His	p.Y323H	ENST00000263826	NM_005465.4	323	Tat/Cat	10/13	1	2	FACETS	0.787	0.689	0.892	0.787	0.689	0.892	SUBCLONAL	1	TRUE	1	0.378810222168965	2		867	483	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25368412	25368412	+	intron_variant	Intron	SNP	G	G	A	novel	NA	P-0024566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	34	782	0	ENST00000311936.3:c.451-5567C>T		p.*151*	ENST00000311936	NM_004985.3	178/189			1	2	FACETS	0.439	0.359	0.529	0.439	0.359	0.529	SUBCLONAL	1	TRUE	1	0.378810222168965	2		782	409	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100465	2100465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	102	876	0	ENST00000219476.3:c.203C>T	p.Ala68Val	p.A68V	ENST00000219476	NM_000548.3	68	gCa/gTa	3/42	1	2	FACETS	0.928	0.832	1	0.928	0.832	1	CLONAL	1	TRUE	1	0.378810222168965	2		876	580	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960137	134960137	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	56	897	0	ENST00000398015.3:c.2494G>T	p.Asp832Tyr	p.D832Y	ENST00000398015	NM_004441.4	832	Gat/Tat	13/16	1	2	FACETS	0.699	0.6	0.806	0.699	0.6	0.806	SUBCLONAL	1	TRUE	1	0.378810222168965	2		897	423	SUCCESS
AR	367	MSKCC	GRCh37	X	66863204	66863204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	175	458	0	ENST00000374690.3:c.1723C>T	p.Leu575Phe	p.L575F	ENST00000374690	NM_000044.3	575	Ctc/Ttc	2/8	0.378810222168965	2	FACETS	0.933	0.876	0.99			1	CLONAL	3	TRUE	NA	0.378810222168965	2		458	330	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630193	100630193	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	210	473	0	ENST00000308731.7:c.80A>T	p.Lys27Met	p.K27M	ENST00000308731	NM_000061.2	27	aAg/aTg	2/19	0.378810222168965	2	FACETS	0.922	0.869	0.974			1	CLONAL	3	TRUE	NA	0.378810222168965	2		473	401	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	46	314	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.8	0.68	0.929	0.8	0.68	0.929	CLONAL	1	TRUE	1	0.491638986590732	2		314	234	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131505	202131505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	103	519	0	ENST00000358485.4:c.473C>T	p.Ser158Phe	p.S158F	ENST00000358485	NM_001080125.1	158	tCt/tTt	2/9	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.491638986590732	2		519	364	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0024576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	116	598	0	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	0.16444721743671	4	FACETS	0.815	0.74	0.893			1	INDETERMINATE	2	TRUE	NA	0.491638986590732	4		598	432	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584501	189584501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908849	NA	P-0024576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	92	486	2	ENST00000264731.3:c.797G>A	p.Arg266Gln	p.R266Q	ENST00000264731	NM_003722.4	266	cGa/cAa	6/14	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.491638986590732	2		488	341	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137450	202137450	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	83	574	1	ENST00000358485.4:c.678C>G	p.Ile226Met	p.I226M	ENST00000358485	NM_001080125.1	226	atC/atG	4/9	1	2	FACETS	0.872	0.775	0.976	0.872	0.775	0.976	CLONAL	1	TRUE	1	0.491638986590732	2		575	387	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211903	123211903	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	72	304	0	ENST00000218089.9:c.2770C>T	p.Gln924Ter	p.Q924*	ENST00000218089	NM_001042749.1	924	Caa/Taa	27/35	1	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.491638986590732	1		304	157	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987147	69987147	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760770591	NA	P-0024576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	47	634	0	ENST00000394351.3:c.208G>A	p.Ala70Thr	p.A70T	ENST00000394351	NM_000248.3	70	Gca/Aca	2/9	0.491638986590732	2	FACETS	0.409	0.345	0.48	0.205	0.172	0.24	SUBCLONAL	1	TRUE	0	0.491638986590732	2		634	467	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255049	16255049	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	86	423	0	ENST00000375759.3:c.2314C>G	p.Pro772Ala	p.P772A	ENST00000375759	NM_015001.2	772	Cca/Gca	11/15	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.491638986590732	2		423	350	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178697	108178697	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	99	388	0	ENST00000278616.4:c.5748G>A	p.Met1916Ile	p.M1916I	ENST00000278616	NM_000051.3	1916	atG/atA	38/63	0.491638986590732	2	FACETS	0.85	0.773	0.927	0.85	0.773	0.927	CLONAL	2	TRUE	0	0.491638986590732	2		388	237	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645517	215645519	+	frameshift_variant	Frame_Shift_Del	DEL	CAG	CAG	AT	novel	NA	P-0024576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	30	731	3	ENST00000260947.4:c.1079_1081delinsAT	p.Pro360HisfsTer40	p.P360Hfs*40	ENST00000260947	NM_000465.2	360	cCTGaa/cATaa	4/11	1	2	FACETS	0.279	0.225	0.341	0.279	0.225	0.341	SUBCLONAL	1	TRUE	1	0.491638986590732	2		734	437	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79965929	79965929	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs766194502	NA	P-0024576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	54	644	0	ENST00000265081.6:c.593T>C	p.Phe198Ser	p.F198S	ENST00000265081	NM_002439.4	198	tTt/tCt	4/24	1	2	FACETS	0.646	0.554	0.745	0.646	0.554	0.745	SUBCLONAL	1	TRUE	1	0.491638986590732	2		644	340	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205062	38205062	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	442	809	0	ENST00000317025.8:c.628G>A	p.Glu210Lys	p.E210K	ENST00000317025	NM_023034.1	210	Gag/Aag	2/24	0.193841131872402	7	FACETS	1	0.988	1	1	0.988	1	CLONAL	5	TRUE	2	0.193841131872402	7		809	1241	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0024598-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	323	365	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.751442903116408	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.75301824693795	1		365	533	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273216	18273216	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0024598-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	37	362	0	ENST00000222254.8:c.1011-2A>T		p.X337_splice	ENST00000222254	NM_005027.3	337			1	2	FACETS	0.14	0.115	0.168	0.14	0.115	0.168	SUBCLONAL	1	TRUE	1	0.75301824693795	2		362	702	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73992051	73992051	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1414351122	NA	P-0024599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	149	827	0	ENST00000318443.5:c.71G>T	p.Cys24Phe	p.C24F	ENST00000318443	NM_001024736.1	24	tGc/tTc	2/10	1	2	FACETS	0.609	0.557	0.664	0.609	0.557	0.664	SUBCLONAL	1	TRUE	1	0.648487236536234	2		827	754	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145567	24145567	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	267	668	1	ENST00000263121.7:c.586G>T	p.Asp196Tyr	p.D196Y	ENST00000263121	NM_003073.3	196	Gat/Tat	5/9	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.648487236536234	2		669	761	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005263	150005263	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	167	444	0	ENST00000253339.5:c.962G>T	p.Ser321Ile	p.S321I	ENST00000253339		321	aGt/aTt	3/7	1	2	FACETS	0.983	0.91	1	0.983	0.91	1	CLONAL	1	TRUE	1	0.648487236536234	2		444	524	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526735	106526735	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	136	382	0	ENST00000359195.3:c.3028C>T	p.Gln1010Ter	p.Q1010*	ENST00000359195	NM_002649.2	1010	Cag/Tag	10/11	0.348674412314653	1	FACETS	0.826	0.762	0.892	0.826	0.762	0.892	INDETERMINATE	1	TRUE	0	0.648487236536234	1		382	343	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	147	552	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.469141729328725	2		552	510	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0024604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	83	319	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.469141729328725	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.469141729328725	1		319	248	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248067	59248067	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0024604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	31	259	0	ENST00000371222.2:c.676A>T	p.Lys226Ter	p.K226*	ENST00000371222	NM_002228.3	226	Aag/Tag	1/1	0.221265456340685	1	FACETS	0.328	0.266	0.399	0.328	0.266	0.399	INDETERMINATE	1	TRUE	0	0.469141729328725	1		259	308	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607597	43607597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs545625150	NA	P-0024604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	148	641	0	ENST00000355710.3:c.1573C>T	p.Arg525Trp	p.R525W	ENST00000355710	NM_020975.4	525	Cgg/Tgg	8/20	1	2	FACETS	0.807	0.738	0.879	0.807	0.738	0.879	CLONAL	1	TRUE	1	0.469141729328725	2		641	782	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741684	17741684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1384940737	NA	P-0024604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	120	401	1	ENST00000250003.3:c.355C>T	p.Arg119Trp	p.R119W	ENST00000250003	NM_002478.4	119	Cgg/Tgg	1/3	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.469141729328725	2		402	490	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362615	118362615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	44	313	0	ENST00000534358.1:c.4976C>T	p.Thr1659Ile	p.T1659I	ENST00000534358	NM_005933.3	1659	aCt/aTt	15/36	1	2	FACETS	0.357	0.299	0.421	0.357	0.299	0.421	SUBCLONAL	1	TRUE	1	0.469141729328725	2		313	526	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457294	67457294	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1085307496	NA	P-0024604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	139	517	0	ENST00000327367.4:c.268C>T	p.Arg90Cys	p.R90C	ENST00000327367	NM_005902.3	90	Cgc/Tgc	2/9	0.469141729328725	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.469141729328725	1		517	439	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530154	212530154	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	22	362	0	ENST00000342788.4:c.1765T>G	p.Cys589Gly	p.C589G	ENST00000342788	NM_005235.2	589	Tgt/Ggt	15/28	1	2	FACETS	0.233	0.18	0.295	0.233	0.18	0.295	SUBCLONAL	1	TRUE	1	0.469141729328725	2		362	402	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045845	143045845	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	46	369	1	ENST00000262992.4:c.1789C>T	p.Arg597Ter	p.R597*	ENST00000262992	NM_001101669.1	597	Cga/Tga	17/24	0.469141729328725	1	FACETS	0.344	0.29	0.404	0.344	0.29	0.404	SUBCLONAL	1	TRUE	0	0.469141729328725	1		370	436	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965569	93965569	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	38	361	0	ENST00000369303.4:c.2359C>G	p.Pro787Ala	p.P787A	ENST00000369303	NM_004440.3	787	Cca/Gca	13/17	1	2	FACETS	0.399	0.33	0.476	0.399	0.33	0.476	SUBCLONAL	1	TRUE	1	0.469141729328725	2		361	406	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724358	117724358	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772261492	NA	P-0024604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	146	467	2	ENST00000368508.3:c.521C>T	p.Ala174Val	p.A174V	ENST00000368508	NM_002944.2	174	gCg/gTg	6/43	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.469141729328725	2		469	581	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412647	63412648	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0024604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	103	476	0	ENST00000330258.3:c.519dup	p.Ser174Ter	p.S174*	ENST00000330258	NM_152424.3	173	-/T	2/2	1	2	FACETS	0.777	0.697	0.861	0.777	0.697	0.861	SUBCLONAL	1	TRUE	1	0.469141729328725	2		476	565	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0024614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	687	329	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.3	11	FACETS	0.963	0.932	0.994			1	CLONAL	8	FALSE	NA	0.3	11		329	1397	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs967461896	NA	P-0024614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	129	597	0	ENST00000269305.4:c.526T>C	p.Cys176Arg	p.C176R	ENST00000269305	NM_001126112.2	176	Tgc/Cgc	5/11	0.191343139367916	2	FACETS	1	0.976	1	0.613	0.556	0.672	CLONAL	1	FALSE	0	0.3	2		597	702	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039399	49039399	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	37	728	2	ENST00000267163.4:c.2384C>A	p.Ser795Ter	p.S795*	ENST00000267163	NM_000321.2	795	tCa/tAa	23/27	0.191343139367916	2	FACETS	0.351	0.288	0.421	0.175	0.144	0.211	SUBCLONAL	1	FALSE	0	0.3	2		730	703	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0024630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	621	769	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.804379119779336	3	FACETS	0.997	0.978	1	0.997	0.978	1	CLONAL	3	FALSE	0	0.804379119779336	3		770	724	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881462	48881462	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	303	336	1	ENST00000267163.4:c.184C>T	p.Gln62Ter	p.Q62*	ENST00000267163	NM_000321.2	62	Cag/Tag	2/27	0.804228054048661	5	FACETS	0.961	0.936	0.983	0.961	0.936	0.983	CLONAL	5	FALSE	0	0.804379119779336	5		337	346	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557835	21557835	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	479	808	0	ENST00000382592.4:c.2010G>T	p.Lys670Asn	p.K670N	ENST00000382592	NM_014572.2	670	aaG/aaT	5/8	0.804228054048661	5	FACETS	0.985	0.949	1	0.591	0.569	0.613	CLONAL	3	FALSE	0	0.804379119779336	5		808	889	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281353	15281353	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	361	694	0	ENST00000263388.2:c.4903G>C	p.Glu1635Gln	p.E1635Q	ENST00000263388	NM_000435.2	1635	Gag/Cag	27/33	0.706100810596559	6	FACETS	0.845	0.804	0.886	0.845	0.804	0.886	CLONAL	3	FALSE	3	0.804379119779336	6		694	924	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39251175	39251175	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	132	738	0	ENST00000402219.2:c.1178A>T	p.Lys393Ile	p.K393I	ENST00000402219	NM_005633.3	393	aAa/aTa	9/23	0.220768981908377	3	FACETS	1	0.966	1	0.552	0.505	0.6	INDETERMINATE	1	FALSE	1	0.804379119779336	3		738	417	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023199	31023199	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs767583580	NA	P-0024630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	109	796	1	ENST00000375687.4:c.2684C>G	p.Ser895Cys	p.S895C	ENST00000375687	NM_015338.5	895	tCt/tGt	13/13	0.690244808242899	6	FACETS	0.701	0.628	0.778	0.234	0.209	0.26	SUBCLONAL	1	FALSE	3	0.804379119779336	6		797	1009	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156430	106156430	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	84	400	0	ENST00000380013.4:c.1331C>A	p.Thr444Lys	p.T444K	ENST00000380013	NM_001127208.2	444	aCa/aAa	3/11	0.608695969516636	4	FACETS	1	0.976	1	0.683	0.611	0.758	CLONAL	1	FALSE	2	0.804379119779336	4		400	276	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5055702	5055702	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	152	424	2	ENST00000381652.3:c.970A>G	p.Ile324Val	p.I324V	ENST00000381652	NM_004972.3	324	Att/Gtt	8/25	0.108859671712107	6	FACETS	1	0.971	1			1	INDETERMINATE	3	FALSE	NA	0.804379119779336	6		426	305	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933118	39933118	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	120	458	1	ENST00000378444.4:c.1481G>T	p.Cys494Phe	p.C494F	ENST00000378444	NM_001123385.1	494	tGt/tTt	4/15	0.56499332353331	2	FACETS	0.73	0.664	0.797			1	SUBCLONAL	1	FALSE	NA	0.804379119779336	2		459	409	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0024631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	14	364	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.095	0.068	0.129	0.095	0.068	0.129	SUBCLONAL	1	TRUE	1	0.539545247284189	2		364	544	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867376	68867378	+	frameshift_variant	Frame_Shift_Del	DEL	ATG	ATG	T	novel	NA	P-0024631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	153	444	0	ENST00000261769.5:c.2623_2625delinsT	p.Met875LeufsTer39	p.M875Lfs*39	ENST00000261769	NM_004360.3	875	ATG/T	16/16	0.528832945460024	1	FACETS	0.974	0.901	1	0.974	0.901	1	CLONAL	1	TRUE	0	0.539545247284189	1		444	425	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0024637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	10	660	4	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	0.077	0.051	0.109	0.077	0.051	0.109	SUBCLONAL	1	TRUE	1	0.776124599334051	2		664	335	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066796	30066796	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201010570	NA	P-0024637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	33	585	0	ENST00000331968.5:c.2335G>A	p.Gly779Ser	p.G779S	ENST00000331968	NM_002742.2	779	Ggc/Agc	16/18	0.246069329169552	3	FACETS	0.227	0.185	0.276	0.114	0.092	0.138	INDETERMINATE	1	TRUE	1	0.776124599334051	3		585	519	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440808	52440896	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCAGAGAGTAGAACAGGGCAGGCACAGGGCCCTTACCCTGCAGTGGCGAGGCCGATACGCTCCATGATGACCCGCCGGGCCTTGTCTG	TCCAGAGAGTAGAACAGGGCAGGCACAGGGCCCTTACCCTGCAGTGGCGAGGCCGATACGCTCCATGATGACCCGCCGGGCCTTGTCTG	-	novel	NA	P-0024643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	131	501	0	ENST00000460680.1:c.608_659+37del		p.X203_splice	ENST00000460680	NM_004656.3	203		8/17	1	2	FACETS	0.78	0.712	0.85	0.78	0.712	0.85	SUBCLONAL	1	TRUE	1	0.702750023427444	2		501	478	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442539	52442540	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	224	751	0	ENST00000460680.1:c.205dup	p.Thr69AsnfsTer5	p.T69Nfs*5	ENST00000460680	NM_004656.3	69	acg/aAcg	4/17	1	2	FACETS	0.827	0.772	0.883	0.827	0.772	0.883	CLONAL	1	TRUE	1	0.702750023427444	2		751	771	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0024644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	207	605	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.193838288176586	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	0	0.193838288176586	2		605	1060	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0024644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	144	585	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.193838288176586	2	FACETS	0.945	0.863	1	0.945	0.863	1	CLONAL	2	TRUE	0	0.193838288176586	2		585	786	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141426	11141426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	193	835	0	ENST00000358026.2:c.3403C>T	p.Arg1135Trp	p.R1135W	ENST00000358026	NM_001128849.1	1135	Cgg/Tgg	25/36	0.156545186630871	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.193838288176586	4		835	1094	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219344	1219345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTGT	novel	NA	P-0024644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	198	935	0	ENST00000326873.7:c.400_403dup	p.Gly135ValfsTer29	p.G135Vfs*29	ENST00000326873	NM_000455.4	132	-/GTGT	3/10	0.193838288176586	2	FACETS	0.928	0.858	1	0.928	0.858	1	CLONAL	2	TRUE	0	0.193838288176586	2		935	1101	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0024645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	201	365	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	0.297062721619464	3	FACETS	0.869	0.813	0.925	0.869	0.813	0.925	INDETERMINATE	2	TRUE	1	0.608386323329222	3		365	496	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7163179	7163180	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0024645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	263	955	1	ENST00000302850.5:c.1892dup	p.Ser632ValfsTer2	p.S632Vfs*2	ENST00000302850	NM_000208.2	631	gtg/gtTg	9/22	1	2	FACETS	0.915	0.859	0.973	0.915	0.859	0.973	CLONAL	1	TRUE	1	0.608386323329222	2		956	945	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105745	27105745	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	178	477	1	ENST00000324856.7:c.5356G>T	p.Glu1786Ter	p.E1786*	ENST00000324856	NM_006015.4	1786	Gag/Tag	20/20	0.608386323329222	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.608386323329222	1		478	371	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0024646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	456	847	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.663585021692388	2	FACETS	0.841	0.815	0.866	0.841	0.815	0.866	CLONAL	2	TRUE	0	0.842374192126593	2		849	644	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0024646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	276	387	2	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	0.689535382388294	4	FACETS	1	0.993	1	0.853	0.823	0.881	CLONAL	3	TRUE	0	0.842374192126593	4		389	354	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023603	27023625	+	frameshift_variant	Frame_Shift_Del	DEL	GGCACTCCGGGCTCCGGCGCGGC	GGCACTCCGGGCTCCGGCGCGGC	-	novel	NA	P-0024646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	693	781	1	ENST00000324856.7:c.712_734del	p.Thr238GlyfsTer154	p.T238Gfs*154	ENST00000324856	NM_006015.4	237	GGCACTCCGGGCTCCGGCGCGGCg/g	1/20	0.73453436626784	3	FACETS	0.886	0.867	0.904	0.886	0.867	0.904	CLONAL	3	TRUE	0	0.842374192126593	3		782	880	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913277	NA	P-0024646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	286	407	0	ENST00000263967.3:c.3145G>A	p.Gly1049Ser	p.G1049S	ENST00000263967	NM_006218.2	1049	Ggt/Agt	21/21	0.64965415842898	6	FACETS	0.913	0.871	0.955	0.913	0.871	0.955	CLONAL	4	TRUE	2	0.842374192126593	6		407	499	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324202	31324202	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs41556417	NA	P-0024646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	10	8	0	ENST00000412585.2:c.361A>T	p.Ser121Cys	p.S121C	ENST00000412585	NM_005514.6	121	Agc/Tgc	3/8	0.842374192126593	7	FACETS	0.91	0.655	1	0.683	0.491	0.891	CLONAL	3	TRUE	3	0.842374192126593	7		8	27	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940110	31940110	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1891	195	1001	0	ENST00000375333.2:c.252C>A	p.Cys84Ter	p.C84*	ENST00000375333	NM_032454.1	84	tgC/tgA	2/8	0.842374192126593	7	FACETS	0.689	0.635	0.747	0.172	0.158	0.187	SUBCLONAL	1	TRUE	3	0.842374192126593	7		1001	2086	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0024647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	156	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.271039630734513	2	FACETS	0.784	0.73	0.837	0.784	0.73	0.837	INDETERMINATE	2	TRUE	0	0.614451603545265	2		326	324	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0024647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	31	631	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.271039630734513	2	FACETS	0.176	0.142	0.216	0.088	0.071	0.108	INDETERMINATE	1	TRUE	0	0.614451603545265	2		632	572	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115710	8115711	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0024647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	94	445	0	ENST00000346208.3:c.1060dup	p.Leu354ProfsTer17	p.L354Pfs*17	ENST00000346208		352	-/C	6/6	1	2	FACETS	0.85	0.763	0.941	0.85	0.763	0.941	CLONAL	1	TRUE	1	0.614451603545265	2		445	360	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070605	67070605	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	83	390	0	ENST00000412916.2:c.229C>T	p.Gln77Ter	p.Q77*	ENST00000412916		77	Cag/Tag	3/6	0.613739826876975	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.614451603545265	1		390	178	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0024649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	600	582	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	0.842793357476403	4	FACETS	1	0.985	1			1	CLONAL	3	TRUE	NA	0.862101858238123	4		582	849	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491740	120491740	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	182	415	1	ENST00000256646.2:c.2489G>T	p.Cys830Phe	p.C830F	ENST00000256646	NM_024408.3	830	tGt/tTt	16/34	1	2	FACETS	0.947	0.883	1	0.947	0.883	1	CLONAL	1	TRUE	1	0.862101858238123	2		416	446	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857674	78857674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748286798	NA	P-0024649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	371	934	0	ENST00000306801.3:c.1744G>A	p.Gly582Ser	p.G582S	ENST00000306801	NM_020761.2	582	Ggc/Agc	16/34	NA	2	FACETS	0.975	0.929	1			1	INDETERMINATE	1	TRUE	NA	0.862101858238123	2		934	883	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221313	1221314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0024649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	671	824	0	ENST00000326873.7:c.836_837insA	p.Leu282AlafsTer3	p.L282Afs*3	ENST00000326873	NM_000455.4	279	ggc/ggAc	6/10	0.862101858238123	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.862101858238123	2		824	761	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602290	10602290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	702	927	2	ENST00000171111.5:c.1288G>A	p.Gly430Ser	p.G430S	ENST00000171111	NM_203500.1	430	Ggc/Agc	3/6	0.862101858238123	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.862101858238123	2		929	793	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	539	781	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.915	0.886	0.943	1	0.998	1	CLONAL	2	TRUE	1	0.68354782830273	2		786	862	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	718	1111	2	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.926	0.901	0.951	1	0.998	1	CLONAL	2	TRUE	1	0.68354782830273	2		1113	1134	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	299	562	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.992	0.937	1	0.992	0.937	1	CLONAL	1	TRUE	1	0.68354782830273	2		563	882	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	336	623	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.978	0.927	1	0.978	0.927	1	CLONAL	1	TRUE	1	0.68354782830273	2		624	1005	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	134	338	1	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.68354782830273	2		339	392	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	212	584	0	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.95	0.887	1	0.95	0.887	1	CLONAL	1	TRUE	1	0.68354782830273	2		584	653	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100324	8100324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs904307886	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	181	955	0	ENST00000346208.3:c.298G>A	p.Gly100Ser	p.G100S	ENST00000346208		100	Ggc/Agc	3/6	1	2	FACETS	0.514	0.474	0.556	0.514	0.474	0.556	SUBCLONAL	1	TRUE	1	0.68354782830273	2		955	1030	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	242	661	20	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.779	0.729	0.831	0.779	0.729	0.831	SUBCLONAL	1	TRUE	1	0.68354782830273	2		681	909	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	270	809	0	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	0.68354782830273	3	FACETS	0.973	0.913	1			1	CLONAL	1	TRUE	NA	0.68354782830273	3		809	1089	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721436	176721436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780750393	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	297	675	1	ENST00000439151.2:c.7067C>T	p.Thr2356Met	p.T2356M	ENST00000439151	NM_022455.4	2356	aCg/aTg	23/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.68354782830273	2		676	836	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796926	78796926	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	278	683	0	ENST00000306801.3:c.1039T>C	p.Phe347Leu	p.F347L	ENST00000306801	NM_020761.2	347	Ttt/Ctt	9/34	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.68354782830273	2		683	802	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976476	25976476	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	262	732	0	ENST00000435504.4:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000435504		357	Cga/Tga	11/13	0.68354782830273	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.68354782830273	1		732	475	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687471	37687472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs760014508	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	94	407	3	ENST00000447079.4:c.4382dup	p.Thr1463AsnfsTer50	p.T1463Nfs*50	ENST00000447079	NM_015083.1	1459	tgg/tGgg	14/14	1	2	FACETS	0.696	0.624	0.772	0.696	0.624	0.772	SUBCLONAL	1	TRUE	1	0.68354782830273	2		410	395	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394349	162394349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137853054	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	203	548	0	ENST00000366898.1:c.719C>T	p.Thr240Met	p.T240M	ENST00000366898	NM_004562.2	240	aCg/aTg	6/12	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.68354782830273	2		548	593	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	139	400	7	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	1	2	FACETS	0.882	0.809	0.957	0.882	0.809	0.957	CLONAL	1	TRUE	1	0.68354782830273	2		407	461	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803183	1803183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764712450	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	373	1003	1	ENST00000260795.2:c.535G>A	p.Ala179Thr	p.A179T	ENST00000260795		179	Gct/Act	4/17	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.68354782830273	2		1004	987	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533939	63533940	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs771001164	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	134	226	0	ENST00000307078.5:c.1214_1215del	p.Glu405GlyfsTer56	p.E405Gfs*56	ENST00000307078	NM_004655.3	405	gAG/g	6/11	1	2	FACETS	0.79	0.723	0.861	0.79	0.723	0.861	SUBCLONAL	1	TRUE	1	0.68354782830273	2		226	496	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057937	27057937	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	300	942	0	ENST00000324856.7:c.1650del	p.Tyr551ThrfsTer68	p.Y551Tfs*68	ENST00000324856	NM_006015.4	549	Ccc/cc	3/20	1	2	FACETS	0.879	0.829	0.93	0.879	0.829	0.93	CLONAL	1	TRUE	1	0.68354782830273	2		942	999	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428299	33428299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368914740	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	262	732	3	ENST00000345365.6:c.824G>A	p.Arg275Gln	p.R275Q	ENST00000345365	NM_002878.3	275	cGg/cAg	9/10	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.68354782830273	2		735	760	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976706	2976706	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1044557293	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	281	813	1	ENST00000396946.4:c.1306C>T	p.Arg436Trp	p.R436W	ENST00000396946	NM_032415.4	436	Cgg/Tgg	9/25	0.68354782830273	3	FACETS	1	0.968	1			1	CLONAL	1	TRUE	NA	0.68354782830273	3		814	1057	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257366	19257366	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	280	917	4	ENST00000162023.5:c.767del	p.Pro256GlnfsTer?	p.P256Qfs*?	ENST00000162023		256	cCa/ca	11/13	1	2	FACETS	0.861	0.811	0.913	0.861	0.811	0.913	CLONAL	1	TRUE	1	0.68354782830273	2		921	951	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5465595	5465595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148141792	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	134	710	2	ENST00000381577.3:c.779G>A	p.Arg260His	p.R260H	ENST00000381577	NM_014143.3	260	cGt/cAt	5/7	0.477156901313844	3	FACETS	0.974	0.89	1	0.487	0.445	0.531	CLONAL	1	TRUE	1	0.68354782830273	3		712	540	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390736	139390736	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	339	1118	4	ENST00000277541.6:c.7455del	p.Ser2486ArgfsTer103	p.S2486Rfs*103	ENST00000277541	NM_017617.3	2485	ccC/cc	34/34	0.477156901313844	3	FACETS	0.98	0.926	1	0.49	0.463	0.518	CLONAL	1	TRUE	1	0.68354782830273	3		1122	1358	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209298	133209298	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060500809	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	85	907	1	ENST00000320574.5:c.6088del	p.Ala2030ProfsTer18	p.A2030Pfs*18	ENST00000320574	NM_006231.2	2030	Gcc/cc	44/49	1	2	FACETS	0.255	0.225	0.288	0.255	0.225	0.288	SUBCLONAL	1	TRUE	1	0.68354782830273	2		908	975	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497358	149497358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35731372	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	289	747	0	ENST00000261799.4:c.2960G>A	p.Arg987Gln	p.R987Q	ENST00000261799	NM_002609.3	987	cGg/cAg	22/23	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.68354782830273	2		747	792	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615698	1615698	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	424	1119	2	ENST00000344749.5:c.1573del	p.Arg525GlyfsTer18	p.R525Gfs*18	ENST00000344749	NM_001136139.2	525	Cgg/gg	17/19	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.68354782830273	2		1121	1191	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907653	111907653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	208	451	1	ENST00000393256.3:c.427C>T	p.Arg143Cys	p.R143C	ENST00000393256	NM_006538.4	143	Cgc/Tgc	3/4	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.68354782830273	2		452	590	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513268	44513268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761081553	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	311	787	1	ENST00000291552.4:c.667G>A	p.Gly223Arg	p.G223R	ENST00000291552	NM_006758.2	223	Gga/Aga	8/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.68354782830273	2		788	842	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722149	176722149	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146010779	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	35	661	1	ENST00000439151.2:c.7780G>A	p.Ala2594Thr	p.A2594T	ENST00000439151	NM_022455.4	2594	Gcc/Acc	23/23	1	2	FACETS	0.163	0.133	0.197	0.163	0.133	0.197	SUBCLONAL	1	TRUE	1	0.68354782830273	2		662	629	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245501	153245501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1024060344	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	218	623	0	ENST00000281708.4:c.1690C>T	p.Arg564Cys	p.R564C	ENST00000281708	NM_033632.3	564	Cgt/Tgt	11/12	1	2	FACETS	0.939	0.878	1	0.939	0.878	1	CLONAL	1	TRUE	1	0.68354782830273	2		623	679	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025857	48025857	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs267608041	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	145	407	1	ENST00000234420.5:c.741del	p.Lys247AsnfsTer32	p.K247Nfs*32	ENST00000234420	NM_000179.2	245	atA/at	4/10	0.68354782830273	1	FACETS	0.997	0.929	1	0.997	0.929	1	CLONAL	1	TRUE	0	0.68354782830273	1		408	280	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7132271	7132271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	56	716	1	ENST00000302850.5:c.2740C>T	p.Arg914Cys	p.R914C	ENST00000302850	NM_000208.2	914	Cgt/Tgt	14/22	1	2	FACETS	0.193	0.164	0.224	0.193	0.164	0.224	SUBCLONAL	1	TRUE	1	0.68354782830273	2		717	850	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210417	2210417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	263	789	0	ENST00000398665.3:c.1024C>T	p.Arg342Trp	p.R342W	ENST00000398665	NM_032482.2	342	Cgg/Tgg	13/28	1	2	FACETS	0.904	0.85	0.96	0.904	0.85	0.96	CLONAL	1	TRUE	1	0.68354782830273	2		789	851	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589576	67589576	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1289537429	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	104	402	0	ENST00000274335.5:c.1344del	p.Lys448AsnfsTer32	p.K448Nfs*32	ENST00000274335		447	Aaa/aa	10/15	1	2	FACETS	0.831	0.751	0.915	0.831	0.751	0.915	CLONAL	1	TRUE	1	0.68354782830273	2		402	366	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445500	49445500	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs886042284	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	131	980	1	ENST00000301067.7:c.1966del	p.Leu656CysfsTer274	p.L656Cfs*274	ENST00000301067	NM_003482.3	656	Ctg/tg	10/54	0.102915690291119	4	FACETS	0.539	0.488	0.593	0.27	0.244	0.297	INDETERMINATE	1	TRUE	2	0.68354782830273	4		981	1197	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368253	45368253	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	443	668	0	ENST00000262160.6:c.1349A>G	p.Asp450Gly	p.D450G	ENST00000262160	NM_005901.5	450	gAc/gGc	11/11	0.68354782830273	2	FACETS	0.959	0.926	0.99	0.959	0.926	0.99	CLONAL	2	TRUE	0	0.68354782830273	2		668	676	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948208	71948209	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs749079348	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	314	1128	2	ENST00000298229.2:c.2927dup	p.Pro977ThrfsTer7	p.P977Tfs*7	ENST00000298229	NM_001567.3	974	gcc/gCcc	26/28	0.68354782830273	1	FACETS	0.784	0.744	0.825	0.784	0.744	0.825	SUBCLONAL	1	TRUE	0	0.68354782830273	1		1130	771	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953258	81953258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776768909	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	79	360	1	ENST00000359376.3:c.2224C>T	p.Arg742Cys	p.R742C	ENST00000359376	NM_002661.3	742	Cgc/Tgc	20/33	1	2	FACETS	0.596	0.527	0.669	0.596	0.527	0.669	SUBCLONAL	1	TRUE	1	0.68354782830273	2		361	388	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873105	134873105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749312347	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	228	698	0	ENST00000398015.3:c.1409G>A	p.Arg470Gln	p.R470Q	ENST00000398015	NM_004441.4	470	cGg/cAg	6/16	1	2	FACETS	0.94	0.879	1	0.94	0.879	1	CLONAL	1	TRUE	1	0.68354782830273	2		698	710	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444377	49444377	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1057519595	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	280	724	1	ENST00000301067.7:c.2994del	p.Met999Ter	p.M999*	ENST00000301067	NM_003482.3	998	ccT/cc	11/54	0.102915690291119	4	FACETS	0.764	0.719	0.809	0.764	0.719	0.809	INDETERMINATE	2	TRUE	2	0.68354782830273	4		725	903	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619163	43619163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	252	755	1	ENST00000355710.3:c.2846G>A	p.Gly949Glu	p.G949E	ENST00000355710	NM_020975.4	949	gGa/gAa	17/20	1	2	FACETS	0.894	0.839	0.95	0.894	0.839	0.95	CLONAL	1	TRUE	1	0.68354782830273	2		756	825	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778282	3778282	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	276	815	2	ENST00000262367.5:c.6766del	p.Leu2256SerfsTer46	p.L2256Sfs*46	ENST00000262367	NM_004380.2	2256	Ctc/tc	31/31	1	2	FACETS	0.942	0.887	0.998	0.942	0.887	0.998	CLONAL	1	TRUE	1	0.68354782830273	2		817	857	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210893	36210893	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	319	908	2	ENST00000222270.7:c.649del	p.Arg217GlyfsTer22	p.R217Gfs*22	ENST00000222270	NM_014727.1	215	aCc/ac	3/37	1	2	FACETS	0.952	0.901	1	0.952	0.901	1	CLONAL	1	TRUE	1	0.68354782830273	2		910	980	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274710	123274710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753437208	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	253	753	1	ENST00000358487.5:c.1208C>T	p.Thr403Met	p.T403M	ENST00000358487	NM_000141.4	403	aCg/aTg	9/18	1	2	FACETS	0.988	0.929	1	0.988	0.929	1	CLONAL	1	TRUE	1	0.68354782830273	2		754	749	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307173	65307173	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs181919006	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	214	646	0	ENST00000342505.4:c.2515C>T	p.Arg839Ter	p.R839*	ENST00000342505	NM_002227.2	839	Cga/Tga	18/25	1	2	FACETS	0.953	0.89	1	0.953	0.89	1	CLONAL	1	TRUE	1	0.68354782830273	2		646	657	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041668	14041668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765235917	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	228	562	1	ENST00000311895.7:c.2215G>A	p.Gly739Ser	p.G739S	ENST00000311895	NM_005236.2	739	Ggc/Agc	11/11	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.68354782830273	2		563	664	SUCCESS
CBL	867	MSKCC	GRCh37	11	119167717	119167717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770667508	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	272	709	1	ENST00000264033.4:c.2126G>A	p.Arg709Gln	p.R709Q	ENST00000264033	NM_005188.3	709	cGg/cAg	13/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.68354782830273	2		710	763	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023034	27023034	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	28	129	0	ENST00000324856.7:c.140G>C	p.Arg47Pro	p.R47P	ENST00000324856	NM_006015.4	47	cGc/cCc	1/20	1	2	FACETS	0.519	0.419	0.629	0.519	0.419	0.629	SUBCLONAL	1	TRUE	1	0.68354782830273	2		129	158	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805098	43805098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137952228	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	288	823	2	ENST00000372470.3:c.548C>T	p.Thr183Met	p.T183M	ENST00000372470	NM_005373.2	183	aCg/aTg	4/12	1	2	FACETS	0.958	0.903	1	0.958	0.903	1	CLONAL	1	TRUE	1	0.68354782830273	2		825	880	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619190	43619190	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	244	731	0	ENST00000355710.3:c.2873A>C	p.Glu958Ala	p.E958A	ENST00000355710	NM_020975.4	958	gAg/gCg	17/20	1	2	FACETS	0.889	0.833	0.946	0.889	0.833	0.946	CLONAL	1	TRUE	1	0.68354782830273	2		731	803	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197341	94197341	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780134	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	302	804	0	ENST00000323929.3:c.1163G>A	p.Arg388Gln	p.R388Q	ENST00000323929	NM_005591.3	388	cGg/cAg	11/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.68354782830273	2		804	819	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172463	108172463	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	191	592	0	ENST00000278616.4:c.5266A>G	p.Thr1756Ala	p.T1756A	ENST00000278616	NM_000051.3	1756	Aca/Gca	35/63	1	2	FACETS	0.938	0.872	1	0.938	0.872	1	CLONAL	1	TRUE	1	0.68354782830273	2		592	596	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362638	118362638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555042614	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	202	488	0	ENST00000534358.1:c.4999C>T	p.Arg1667Trp	p.R1667W	ENST00000534358	NM_005933.3	1667	Cgg/Tgg	15/36	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.68354782830273	2		488	577	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424138	49424138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200638996	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	394	912	2	ENST00000301067.7:c.13924G>A	p.Val4642Ile	p.V4642I	ENST00000301067	NM_003482.3	4642	Gtc/Atc	42/54	0.102915690291119	4	FACETS	0.922	0.878	0.966	0.922	0.878	0.966	INDETERMINATE	2	TRUE	2	0.68354782830273	4		914	1053	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433394	49433394	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783727	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	53	957	0	ENST00000301067.7:c.8053C>T	p.Arg2685Ter	p.R2685*	ENST00000301067	NM_003482.3	2685	Cga/Tga	32/54	0.102915690291119	4	FACETS	0.254	0.216	0.297	0.127	0.108	0.149	INDETERMINATE	1	TRUE	2	0.68354782830273	4		957	1027	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30103628	30103628	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763394987	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	265	713	0	ENST00000331968.5:c.1310C>T	p.Thr437Met	p.T437M	ENST00000331968	NM_002742.2	437	aCg/aTg	8/18	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.68354782830273	2		713	735	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031880	10031880	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765104792	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	280	844	1	ENST00000330684.3:c.943G>A	p.Glu315Lys	p.E315K	ENST00000330684	NM_001134407.1	315	Gag/Aag	3/13	1	2	FACETS	0.986	0.929	1	0.986	0.929	1	CLONAL	1	TRUE	1	0.68354782830273	2		845	831	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351703	89351703	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773132293	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	329	1017	2	ENST00000301030.4:c.1247C>T	p.Ala416Val	p.A416V	ENST00000301030	NM_001256183.1	416	gCg/gTg	9/13	1	2	FACETS	0.936	0.886	0.987	0.936	0.886	0.987	CLONAL	1	TRUE	1	0.68354782830273	2		1019	1028	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435956	56435956	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	71	512	0	ENST00000407977.2:c.1181C>T	p.Ala394Val	p.A394V	ENST00000407977		394	gCa/gTa	9/10	1	2	FACETS	0.404	0.353	0.459	0.404	0.353	0.459	SUBCLONAL	1	TRUE	1	0.68354782830273	2		512	514	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107209	11107209	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	148	752	0	ENST00000358026.2:c.1801C>T	p.Pro601Ser	p.P601S	ENST00000358026	NM_001128849.1	601	Ccg/Tcg	11/36	1	2	FACETS	0.512	0.467	0.558	0.512	0.467	0.558	SUBCLONAL	1	TRUE	1	0.68354782830273	2		752	846	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379649	17379651	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs748337921	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	147	504	6	ENST00000359435.4:c.45_47del	p.Glu18del	p.E18del	ENST00000359435	NM_001033549.1	12	GAG/-	2/9	1	2	FACETS	0.813	0.747	0.882	0.813	0.747	0.882	CLONAL	1	TRUE	1	0.68354782830273	2		510	529	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260206	19260206	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	381	972	1	ENST00000162023.5:c.87G>T	p.Met29Ile	p.M29I	ENST00000162023		29	atG/atT	7/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.68354782830273	2		973	1034	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724289	52724289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	272	653	0	ENST00000322088.6:c.1421G>A	p.Gly474Glu	p.G474E	ENST00000322088	NM_014225.5	474	gGg/gAg	12/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.68354782830273	2		653	749	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432680	29432680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	40	750	1	ENST00000389048.3:c.3808G>A	p.Asp1270Asn	p.D1270N	ENST00000389048	NM_004304.4	1270	Gac/Aac	25/29	0.68354782830273	1	FACETS	0.142	0.117	0.169	0.142	0.117	0.169	SUBCLONAL	1	TRUE	0	0.68354782830273	1		751	543	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561222	9561222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	45	634	0	ENST00000353224.5:c.560C>T	p.Pro187Leu	p.P187L	ENST00000353224	NM_177990.2	187	cCt/cTt	4/10	1	2	FACETS	0.206	0.172	0.243	0.206	0.172	0.243	SUBCLONAL	1	TRUE	1	0.68354782830273	2		634	639	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031742	36031742	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1358694181	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	348	840	0	ENST00000358208.4:c.1571C>T	p.Thr524Met	p.T524M	ENST00000358208		524	aCg/aTg	12/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.68354782830273	2		840	953	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546129	41546129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748820220	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	181	509	1	ENST00000263253.7:c.2744G>A	p.Arg915His	p.R915H	ENST00000263253	NM_001429.3	915	cGc/cAc	14/31	1	2	FACETS	0.981	0.911	1	0.981	0.911	1	CLONAL	1	TRUE	1	0.68354782830273	2		510	540	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41558730	41558733	+	frameshift_variant	Frame_Shift_Del	DEL	AATA	AATA	-	novel	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	208	603	1	ENST00000263253.7:c.3681_3684del	p.Asn1227LysfsTer49	p.N1227Kfs*49	ENST00000263253	NM_001429.3	1225	acAATA/ac	21/31	1	2	FACETS	0.887	0.827	0.949	0.887	0.827	0.949	CLONAL	1	TRUE	1	0.68354782830273	2		604	686	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574029	41574029	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	226	625	0	ENST00000263253.7:c.6314G>A	p.Gly2105Asp	p.G2105D	ENST00000263253	NM_001429.3	2105	gGc/gAc	31/31	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.68354782830273	2		625	607	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188239	10188239	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553619956	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	305	874	1	ENST00000256474.2:c.382C>T	p.Leu128Phe	p.L128F	ENST00000256474	NM_000551.3	128	Ctt/Ttt	2/3	1	2	FACETS	0.909	0.858	0.961	0.909	0.858	0.961	CLONAL	1	TRUE	1	0.68354782830273	2		875	982	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180849	106180849	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	167	477	0	ENST00000380013.4:c.3877A>C	p.Met1293Leu	p.M1293L	ENST00000380013	NM_001127208.2	1293	Atg/Ctg	7/11	1	2	FACETS	0.962	0.891	1	0.962	0.891	1	CLONAL	1	TRUE	1	0.68354782830273	2		477	508	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111581	56111581	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	120	215	1	ENST00000399503.3:c.181C>T	p.Gln61Ter	p.Q61*	ENST00000399503	NM_005921.1	61	Cag/Tag	1/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.68354782830273	2		216	314	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178071	56178071	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	161	465	0	ENST00000399503.3:c.3044C>A	p.Pro1015His	p.P1015H	ENST00000399503	NM_005921.1	1015	cCt/cAt	14/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.68354782830273	2		465	449	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288600	33288600	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	188	489	0	ENST00000374542.5:c.952C>G	p.Arg318Gly	p.R318G	ENST00000374542	NM_001141970.1	318	Cga/Gga	3/8	1	2	FACETS	0.928	0.862	0.995	0.928	0.862	0.995	CLONAL	1	TRUE	1	0.68354782830273	2		489	593	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249387	110249387	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	379	1163	0	ENST00000374672.4:c.1186del	p.His396ThrfsTer48	p.H396Tfs*48	ENST00000374672	NM_004235.4	396	Cac/ac	4/5	0.477156901313844	3	FACETS	0.953	0.903	1	0.476	0.451	0.502	CLONAL	1	TRUE	1	0.68354782830273	3		1163	1562	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577542	+	frameshift_variant	Frame_Shift_Del	DEL	CGGTT	CGGTT	-	novel	NA	P-0024652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	296	793	1	ENST00000269305.4:c.739_743del	p.Asn247GlufsTer15	p.N247Efs*15	ENST00000269305	NM_001126112.2	247	AACCGg/g	7/11	0.366397871730945	3	FACETS	1	0.991	1	0.818	0.774	0.863	CLONAL	2	TRUE	0	0.366397871730945	3		794	779	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426767	212426768	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0024652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	62	621	0	ENST00000342788.4:c.2347_2348del	p.Leu783AlafsTer31	p.L783Afs*31	ENST00000342788	NM_005235.2	783	TTg/g	20/28	1	2	FACETS	0.614	0.531	0.705	0.614	0.531	0.705	SUBCLONAL	1	TRUE	1	0.366397871730945	2		621	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0024655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	230	792	54	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.657124025780682	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.657124025780682	1		846	445	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0024655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	215	430	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.469003662600741	3	FACETS	0.859	0.807	0.912	0.859	0.807	0.912	CLONAL	2	TRUE	1	0.657124025780682	3		430	506	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0024655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	62	192	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.657124025780682	1	FACETS	0.807	0.714	0.902	0.807	0.714	0.902	CLONAL	1	TRUE	0	0.657124025780682	1		192	157	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	111	452	13	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	0.657124025780682	1	FACETS	0.969	0.891	1	0.969	0.891	1	CLONAL	1	TRUE	0	0.657124025780682	1		465	234	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5246048	5246048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781664688	NA	P-0024655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	34	455	0	ENST00000357368.4:c.727G>A	p.Val243Met	p.V243M	ENST00000357368	NM_002850.3	243	Gtg/Atg	10/38	0.494267642434125	1	FACETS	0.286	0.235	0.343	0.286	0.235	0.343	SUBCLONAL	1	TRUE	0	0.657124025780682	1		455	243	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967975	93967975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776394413	NA	P-0024655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	214	654	32	ENST00000369303.4:c.1952G>A	p.Arg651His	p.R651H	ENST00000369303	NM_004440.3	651	cGt/cAt	11/17	0.466846446300361	3	FACETS	0.966	0.909	1	0.966	0.909	1	CLONAL	2	TRUE	1	0.657124025780682	3		686	448	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724579	724579	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	431	654	54	ENST00000314574.4:c.1477T>C	p.Cys493Arg	p.C493R	ENST00000314574	NM_005433.3	493	Tgc/Cgc	12/12	0.247094138023003	6	FACETS	0.913	0.882	0.944			1	INDETERMINATE	5	TRUE	NA	0.657124025780682	6		708	665	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	299	781	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.932	0.88	0.985	0.932	0.88	0.985	CLONAL	1	TRUE	1	0.689359876629614	2		786	931	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991757	72991758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760959844	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	213	421	1	ENST00000268489.5:c.2287dup	p.Glu763GlyfsTer26	p.E763Gfs*26	ENST00000268489	NM_006885.3	763	gag/gGag	2/10	1	2	FACETS	0.938	0.876	1	0.938	0.876	1	CLONAL	1	TRUE	1	0.689359876629614	2		422	659	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	236	646	5	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.892	0.835	0.95	0.892	0.835	0.95	CLONAL	1	TRUE	1	0.689359876629614	2		651	768	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	354	458	10	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.913	0.866	0.961	0.913	0.866	0.961	CLONAL	1	TRUE	1	0.689359876629614	2		468	1125	SUCCESS
APC	324	MSKCC	GRCh37	5	112178879	112178879	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881265	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	209	405	1	ENST00000257430.4:c.7588C>T	p.Arg2530Trp	p.R2530W	ENST00000257430	NM_000038.5	2530	Cgg/Tgg	16/16	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.689359876629614	2		406	586	SUCCESS
AR	367	MSKCC	GRCh37	X	66943552	66943552	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137852578	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	194	289	0	ENST00000374690.3:c.2632A>G	p.Thr878Ala	p.T878A	ENST00000374690	NM_000044.3	878	Act/Gct	8/8	1	1	FACETS	0.956	0.898	1	0.956	0.898	1	CLONAL	1	TRUE	0	0.689359876629614	1		289	386	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532517	63532517	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	313	843	0	ENST00000307078.5:c.2062del	p.Leu688Ter	p.L688*	ENST00000307078	NM_004655.3	688	Ctg/tg	8/11	1	2	FACETS	0.957	0.905	1	0.957	0.905	1	CLONAL	1	TRUE	1	0.689359876629614	2		843	949	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039609	180039609	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs954889734	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	256	816	0	ENST00000261937.6:c.3434G>A	p.Arg1145His	p.R1145H	ENST00000261937	NM_182925.4	1145	cGc/cAc	26/30	1	2	FACETS	0.975	0.916	1	0.975	0.916	1	CLONAL	1	TRUE	1	0.689359876629614	2		816	762	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	261	621	1	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	0.965	0.907	1	0.965	0.907	1	CLONAL	1	TRUE	1	0.689359876629614	2		622	785	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	76	897	5	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	0.242	0.212	0.275	0.242	0.212	0.275	SUBCLONAL	1	TRUE	1	0.689359876629614	2		902	910	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244133	133244133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759398253	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	284	717	1	ENST00000320574.5:c.2275C>T	p.Arg759Cys	p.R759C	ENST00000320574	NM_006231.2	759	Cgt/Tgt	20/49	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.689359876629614	2		718	819	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11206807	11206807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202187935	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	323	757	1	ENST00000361445.4:c.4612C>T	p.Arg1538Trp	p.R1538W	ENST00000361445	NM_004958.3	1538	Cgg/Tgg	32/58	1	2	FACETS	0.975	0.923	1	0.975	0.923	1	CLONAL	1	TRUE	1	0.689359876629614	2		758	961	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549230	21549230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113238499	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	426	1083	4	ENST00000382592.4:c.3046G>A	p.Glu1016Lys	p.E1016K	ENST00000382592	NM_014572.2	1016	Gaa/Aaa	8/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.689359876629614	2		1087	1180	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182749	38182749	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	66	706	0	ENST00000396334.3:c.902G>A	p.Arg301His	p.R301H	ENST00000396334	NM_002468.4	301	cGc/cAc	5/5	1	2	FACETS	0.243	0.21	0.278	0.243	0.21	0.278	SUBCLONAL	1	TRUE	1	0.689359876629614	2		706	789	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	135	965	2	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	1	2	FACETS	0.317	0.287	0.349	0.317	0.287	0.349	SUBCLONAL	1	TRUE	1	0.689359876629614	2		967	1234	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249857	110249857	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	96	759	3	ENST00000374672.4:c.818C>T	p.Thr273Met	p.T273M	ENST00000374672	NM_004235.4	273	aCg/aTg	3/5	0.647450340272318	3	FACETS	0.33	0.293	0.37	0.165	0.146	0.185	SUBCLONAL	1	TRUE	1	0.689359876629614	3		762	1134	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447396	12447396	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553647989	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	288	628	1	ENST00000287820.6:c.635G>A	p.Arg212Gln	p.R212Q	ENST00000287820	NM_015869.4	212	cGg/cAg	5/7	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.689359876629614	2		629	803	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217350	11217350	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	77	634	0	ENST00000361445.4:c.4330-2A>C		p.X1444_splice	ENST00000361445	NM_004958.3	1444			1	2	FACETS	0.311	0.273	0.353	0.311	0.273	0.353	SUBCLONAL	1	TRUE	1	0.689359876629614	2		634	718	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262753	16262753	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	49	428	0	ENST00000375759.3:c.10018G>T	p.Ala3340Ser	p.A3340S	ENST00000375759	NM_015001.2	3340	Gct/Tct	11/15	1	2	FACETS	0.326	0.276	0.381	0.326	0.276	0.381	SUBCLONAL	1	TRUE	1	0.689359876629614	2		428	436	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264114	16264114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	68	831	0	ENST00000375759.3:c.10483C>T	p.Pro3495Ser	p.P3495S	ENST00000375759	NM_015001.2	3495	Ccc/Tcc	12/15	1	2	FACETS	0.209	0.181	0.24	0.209	0.181	0.24	SUBCLONAL	1	TRUE	1	0.689359876629614	2		831	942	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439771	51439771	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	161	350	0	ENST00000262662.1:c.336A>C	p.Lys112Asn	p.K112N	ENST00000262662		112	aaA/aaC	4/4	1	2	FACETS	0.781	0.72	0.845	0.781	0.72	0.845	SUBCLONAL	1	TRUE	1	0.689359876629614	2		350	598	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846235	156846235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201564883	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	269	762	1	ENST00000524377.1:c.1676G>A	p.Arg559His	p.R559H	ENST00000524377	NM_002529.3	559	cGt/cAt	14/17	1	2	FACETS	0.889	0.836	0.943	0.889	0.836	0.943	CLONAL	1	TRUE	1	0.689359876629614	2		763	878	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949100	71949100	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	57	645	1	ENST00000298229.2:c.3567G>T	p.Gln1189His	p.Q1189H	ENST00000298229	NM_001567.3	1189	caG/caT	27/28	1	2	FACETS	0.259	0.222	0.3	0.259	0.222	0.3	SUBCLONAL	1	TRUE	1	0.689359876629614	2		646	638	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201111	108201111	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	65	456	0	ENST00000278616.4:c.7478A>G	p.Glu2493Gly	p.E2493G	ENST00000278616	NM_000051.3	2493	gAa/gGa	50/63	1	2	FACETS	0.244	0.211	0.28	0.244	0.211	0.28	SUBCLONAL	1	TRUE	1	0.689359876629614	2		456	774	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953539	32953539	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397508014	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	222	576	0	ENST00000380152.3:c.8842del	p.Ile2948LeufsTer28	p.I2948Lfs*28	ENST00000380152		2947	gAa/ga	22/27	1	2	FACETS	0.888	0.83	0.948	0.888	0.83	0.948	CLONAL	1	TRUE	1	0.689359876629614	2		576	725	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058412	42058412	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	58	539	0	ENST00000219905.7:c.8132T>C	p.Val2711Ala	p.V2711A	ENST00000219905	NM_001164273.1	2711	gTg/gCg	24/24	1	2	FACETS	0.224	0.192	0.26	0.224	0.192	0.26	SUBCLONAL	1	TRUE	1	0.689359876629614	2		539	750	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714075	43714075	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs773155828	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	338	794	0	ENST00000382044.4:c.4078C>T	p.Arg1360Ter	p.R1360*	ENST00000382044	NM_001141980.1	1360	Cga/Tga	19/28	1	2	FACETS	0.979	0.928	1	0.979	0.928	1	CLONAL	1	TRUE	1	0.689359876629614	2		794	1002	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472537	88472537	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	162	724	0	ENST00000360948.2:c.2018A>G	p.Gln673Arg	p.Q673R	ENST00000360948	NM_001012338.2	673	cAg/cGg	16/19	1	2	FACETS	0.514	0.472	0.559	0.514	0.472	0.559	SUBCLONAL	1	TRUE	1	0.689359876629614	2		724	914	SUCCESS
BLM	641	MSKCC	GRCh37	15	91295140	91295140	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	50	513	0	ENST00000355112.3:c.923T>G	p.Ile308Ser	p.I308S	ENST00000355112	NM_000057.2	308	aTt/aGt	4/22	1	2	FACETS	0.195	0.165	0.229	0.195	0.165	0.229	SUBCLONAL	1	TRUE	1	0.689359876629614	2		513	743	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789688	3789688	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	41	579	0	ENST00000262367.5:c.4171T>C	p.Tyr1391His	p.Y1391H	ENST00000262367	NM_004380.2	1391	Tat/Cat	25/31	1	2	FACETS	0.169	0.14	0.202	0.169	0.14	0.202	SUBCLONAL	1	TRUE	1	0.689359876629614	2		579	703	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862737	9862737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201072838	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	249	566	0	ENST00000330684.3:c.2566C>T	p.Arg856Trp	p.R856W	ENST00000330684	NM_001134407.1	856	Cgg/Tgg	12/13	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.689359876629614	2		566	693	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56870517	56870517	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	205	422	0	ENST00000308159.5:c.1787G>A	p.Gly596Glu	p.G596E	ENST00000308159	NM_014669.4	596	gGa/gAa	17/22	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.689359876629614	2		422	585	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625629	1625629	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	334	1116	0	ENST00000344749.5:c.445T>C	p.Tyr149His	p.Y149H	ENST00000344749	NM_001136139.2	149	Tac/Cac	7/19	1	2	FACETS	0.953	0.902	1	0.953	0.902	1	CLONAL	1	TRUE	1	0.689359876629614	2		1116	1017	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10259560	10259560	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	71	741	0	ENST00000340748.4:c.2672A>G	p.Lys891Arg	p.K891R	ENST00000340748		891	aAa/aGa	26/40	1	2	FACETS	0.247	0.215	0.281	0.247	0.215	0.281	SUBCLONAL	1	TRUE	1	0.689359876629614	2		741	835	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599936	10599936	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	83	894	0	ENST00000171111.5:c.1640T>C	p.Val547Ala	p.V547A	ENST00000171111	NM_203500.1	547	gTa/gCa	5/6	1	2	FACETS	0.252	0.222	0.285	0.252	0.222	0.285	SUBCLONAL	1	TRUE	1	0.689359876629614	2		894	955	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387338	17387338	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs896136975	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	354	1021	0	ENST00000359435.4:c.604G>A	p.Val202Met	p.V202M	ENST00000359435	NM_001033549.1	202	Gtg/Atg	7/9	1	2	FACETS	0.94	0.891	0.989	0.94	0.891	0.989	CLONAL	1	TRUE	1	0.689359876629614	2		1021	1093	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793223	42793223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775303325	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	337	890	0	ENST00000575354.2:c.1115C>T	p.Ala372Val	p.A372V	ENST00000575354	NM_015125.3	372	gCg/gTg	7/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.689359876629614	2		890	941	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868418	45868418	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	86	765	0	ENST00000391945.4:c.361-2A>G		p.X121_splice	ENST00000391945	NM_000400.3	121			1	2	FACETS	0.289	0.255	0.325	0.289	0.255	0.325	SUBCLONAL	1	TRUE	1	0.689359876629614	2		765	864	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714643	52714643	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	306	793	1	ENST00000322088.6:c.401G>A	p.Arg134Gln	p.R134Q	ENST00000322088	NM_014225.5	134	cGg/cAg	4/15	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.689359876629614	2		794	883	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022394	26022394	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377317571	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	80	576	0	ENST00000435504.4:c.263C>T	p.Pro88Leu	p.P88L	ENST00000435504		88	cCg/cTg	5/13	1	2	FACETS	0.289	0.254	0.327	0.289	0.254	0.327	SUBCLONAL	1	TRUE	1	0.689359876629614	2		576	802	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149666	61149666	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	16	178	0	ENST00000295025.8:c.1856T>C	p.Val619Ala	p.V619A	ENST00000295025	NM_002908.2	619	gTa/gCa	11/11	1	2	FACETS	0.163	0.12	0.215	0.163	0.12	0.215	SUBCLONAL	1	TRUE	1	0.689359876629614	2		178	284	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339039	225339039	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752958265	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	93	582	0	ENST00000264414.4:c.2230C>T	p.Arg744Cys	p.R744C	ENST00000264414	NM_003590.4	744	Cgt/Tgt	16/16	1	2	FACETS	0.31	0.275	0.348	0.31	0.275	0.348	SUBCLONAL	1	TRUE	1	0.689359876629614	2		582	870	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326202	62326202	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	307	912	3	ENST00000360203.5:c.3218C>T	p.Ser1073Phe	p.S1073F	ENST00000360203	NM_001283009.1	1073	tCc/tTc	32/35	1	2	FACETS	0.97	0.917	1	0.97	0.917	1	CLONAL	1	TRUE	1	0.689359876629614	2		915	918	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656975	45656975	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	117	939	0	ENST00000407780.3:c.181A>C	p.Thr61Pro	p.T61P	ENST00000407780	NM_001283052.1	61	Acc/Ccc	3/7	NA	2	FACETS	0.303	0.272	0.335			1	INDETERMINATE	1	TRUE	NA	0.689359876629614	2		939	1122	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573329	41573329	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	55	985	0	ENST00000263253.7:c.5614A>G	p.Thr1872Ala	p.T1872A	ENST00000263253	NM_001429.3	1872	Act/Gct	31/31	1	2	FACETS	0.156	0.132	0.182	0.156	0.132	0.182	SUBCLONAL	1	TRUE	1	0.689359876629614	2		985	1024	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645660	12645660	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	33	242	0	ENST00000251849.4:c.809T>C	p.Leu270Pro	p.L270P	ENST00000251849	NM_002880.3	270	cTg/cCg	7/17	1	2	FACETS	0.251	0.204	0.304	0.251	0.204	0.304	SUBCLONAL	1	TRUE	1	0.689359876629614	2		242	381	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940409	49940409	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	41	780	0	ENST00000296474.3:c.634A>G	p.Ser212Gly	p.S212G	ENST00000296474	NM_002447.2	212	Agc/Ggc	1/20	1	2	FACETS	0.145	0.12	0.173	0.145	0.12	0.173	SUBCLONAL	1	TRUE	1	0.689359876629614	2		780	819	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440372	52440372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	110	665	3	ENST00000460680.1:c.680G>A	p.Arg227His	p.R227H	ENST00000460680	NM_004656.3	227	cGc/cAc	9/17	1	2	FACETS	0.496	0.446	0.549	0.496	0.446	0.549	SUBCLONAL	1	TRUE	1	0.689359876629614	2		668	643	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751533	57751533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	238	427	0	ENST00000274289.3:c.1458G>A	p.Met486Ile	p.M486I	ENST00000274289	NM_006622.3	486	atG/atA	11/14	1	2	FACETS	0.96	0.901	1	0.96	0.901	1	CLONAL	1	TRUE	1	0.689359876629614	2		427	719	SUCCESS
APC	324	MSKCC	GRCh37	5	112174392	112174392	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	51	234	0	ENST00000257430.4:c.3101A>G	p.Glu1034Gly	p.E1034G	ENST00000257430	NM_000038.5	1034	gAg/gGg	16/16	1	2	FACETS	0.374	0.318	0.434	0.374	0.318	0.434	SUBCLONAL	1	TRUE	1	0.689359876629614	2		234	396	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32189104	32189104	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	42	447	0	ENST00000375023.3:c.452-2A>G		p.X151_splice	ENST00000375023	NM_004557.3	151			1	2	FACETS	0.262	0.219	0.31	0.262	0.219	0.31	SUBCLONAL	1	TRUE	1	0.689359876629614	2		447	465	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120400	94120400	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	203	346	0	ENST00000369303.4:c.651T>A	p.Asp217Glu	p.D217E	ENST00000369303	NM_004440.3	217	gaT/gaA	3/17	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.689359876629614	2		346	589	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553714	106553714	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	71	493	0	ENST00000369096.4:c.1679A>G	p.Lys560Arg	p.K560R	ENST00000369096	NM_001198.3	560	aAg/aGg	5/7	1	2	FACETS	0.292	0.254	0.333	0.292	0.254	0.333	SUBCLONAL	1	TRUE	1	0.689359876629614	2		493	705	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099473	157099473	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	156	482	0	ENST00000346085.5:c.410A>T	p.Asn137Ile	p.N137I	ENST00000346085	NM_020732.3	137	aAc/aTc	1/20	1	2	FACETS	0.791	0.728	0.856	0.791	0.728	0.856	SUBCLONAL	1	TRUE	1	0.689359876629614	2		482	572	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395451	116395451	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	269	581	0	ENST00000397752.3:c.1744A>G	p.Thr582Ala	p.T582A	ENST00000397752	NM_000245.2	582	Acc/Gcc	6/21	1	2	FACETS	0.936	0.881	0.992	0.936	0.881	0.992	CLONAL	1	TRUE	1	0.689359876629614	2		581	834	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128849177	128849177	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	95	832	0	ENST00000249373.3:c.1405T>C	p.Cys469Arg	p.C469R	ENST00000249373	NM_005631.4	469	Tgc/Cgc	8/12	1	2	FACETS	0.293	0.26	0.328	0.293	0.26	0.328	SUBCLONAL	1	TRUE	1	0.689359876629614	2		832	940	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141568626	141568626	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	82	826	0	ENST00000220592.5:c.836A>G	p.Tyr279Cys	p.Y279C	ENST00000220592	NM_012154.3	279	tAc/tGc	7/19	0.689359876629614	3	FACETS	0.259	0.227	0.293	0.13	0.113	0.147	SUBCLONAL	1	TRUE	1	0.689359876629614	3		826	1235	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069097	5069099	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs1371743120	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	242	470	1	ENST00000381652.3:c.1407_1409del	p.Lys469del	p.K469del	ENST00000381652	NM_004972.3	468	AAG/-	11/25	0.689359876629614	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.689359876629614	1		471	453	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915900	127915900	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	90	635	0	ENST00000373547.4:c.581T>A	p.Leu194Gln	p.L194Q	ENST00000373547	NM_002721.4	194	cTg/cAg	6/7	0.647450340272318	3	FACETS	0.293	0.258	0.329	0.146	0.129	0.165	SUBCLONAL	1	TRUE	1	0.689359876629614	3		635	1200	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915910	127915910	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	79	637	0	ENST00000373547.4:c.571T>C	p.Phe191Leu	p.F191L	ENST00000373547	NM_002721.4	191	Ttt/Ctt	6/7	0.647450340272318	3	FACETS	0.26	0.227	0.295	0.13	0.113	0.148	SUBCLONAL	1	TRUE	1	0.689359876629614	3		637	1186	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133729579	133729579	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	78	716	0	ENST00000318560.5:c.208T>C	p.Tyr70His	p.Y70H	ENST00000318560	NM_005157.4	70	Tat/Cat	2/11	0.647450340272318	3	FACETS	0.251	0.219	0.285	0.125	0.109	0.143	SUBCLONAL	1	TRUE	1	0.689359876629614	3		716	1214	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730449	133730449	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	53	497	0	ENST00000318560.5:c.515A>G	p.Tyr172Cys	p.Y172C	ENST00000318560	NM_005157.4	172	tAc/tGc	3/11	0.647450340272318	3	FACETS	0.267	0.227	0.311	0.134	0.113	0.156	SUBCLONAL	1	TRUE	1	0.689359876629614	3		497	774	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417577	139417577	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	303	1177	0	ENST00000277541.6:c.467T>C	p.Leu156Pro	p.L156P	ENST00000277541	NM_017617.3	156	cTg/cCg	4/34	0.661653357942956	3	FACETS	0.889	0.837	0.944	0.445	0.418	0.472	CLONAL	1	TRUE	1	0.689359876629614	3		1177	1329	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195619	123195619	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	78	72	0	ENST00000218089.9:c.1535-2A>G		p.X512_splice	ENST00000218089	NM_001042749.1	512			1	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.689359876629614	1		72	108	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195621	123195621	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	83	86	0	ENST00000218089.9:c.1535C>A	p.Ala512Glu	p.A512E	ENST00000218089	NM_001042749.1	512	gCa/gAa	17/35	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.689359876629614	1		86	117	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579321	7579322	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs587780067	NA	P-0024661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	279	577	0	ENST00000269305.4:c.365_366del	p.Val122AspfsTer26	p.V122Dfs*26	ENST00000269305	NM_001126112.2	122	gTG/g	4/11	0.828776725694818	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.828776725694818	1		577	370	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554622	29554622	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1567848213	NA	P-0024661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	162	350	0	ENST00000356175.3:c.2407C>T	p.Gln803Ter	p.Q803*	ENST00000356175	NM_000267.3	803	Cag/Tag	20/57	0.828776725694818	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.828776725694818	1		350	229	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1023835002	NA	P-0024663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	29	549	0	ENST00000558401.1:c.1A>G	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Gtg	1/4	0.252182959003186	1	FACETS	0.246	0.197	0.301	0.246	0.197	0.301	INDETERMINATE	1	TRUE	0	0.485831997402114	1		549	368	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622179	162622179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781608005	NA	P-0024663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	70	487	0	ENST00000366898.1:c.518C>T	p.Thr173Met	p.T173M	ENST00000366898	NM_004562.2	173	aCg/aTg	4/12	NA	2	FACETS	0.689	0.603	0.781			1	INDETERMINATE	1	TRUE	NA	0.485831997402114	2		487	418	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881414	48881414	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0024663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	30	210	0	ENST00000267163.4:c.138-2A>G		p.X46_splice	ENST00000267163	NM_000321.2	46			0.252182959003186	1	FACETS	0.748	0.614	0.894	0.748	0.614	0.894	INDETERMINATE	1	TRUE	0	0.485831997402114	1		210	125	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144122	11144122	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	51	974	2	ENST00000358026.2:c.3703G>T	p.Asp1235Tyr	p.D1235Y	ENST00000358026	NM_001128849.1	1235	Gac/Tac	26/36	0.268804176064509	0	FACETS	0.228	0.194	0.266			1	INDETERMINATE	1	TRUE	0	0.485831997402114	0		976	473	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243675647	243675647	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	45	611	0	ENST00000263826.5:c.1333A>C	p.Thr445Pro	p.T445P	ENST00000263826	NM_005465.4	445	Aca/Cca	12/13	NA	2	FACETS	0.577	0.487	0.676			1	INDETERMINATE	1	TRUE	NA	0.485831997402114	2		611	321	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121799	108121799	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	37	468	0	ENST00000278616.4:c.1607G>T	p.Cys536Phe	p.C536F	ENST00000278616	NM_000051.3	536	tGt/tTt	10/63	1	2	FACETS	0.614	0.509	0.73	0.614	0.509	0.73	SUBCLONAL	1	TRUE	1	0.485831997402114	2		468	248	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954220	48954220	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1555286575	NA	P-0024663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	47	487	0	ENST00000267163.4:c.1421G>T	p.Ser474Ile	p.S474I	ENST00000267163	NM_000321.2	474	aGc/aTc	15/27	0.252182959003186	1	FACETS	0.476	0.403	0.554	0.476	0.403	0.554	INDETERMINATE	1	TRUE	0	0.485831997402114	1		487	308	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562725	95562725	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	23	495	0	ENST00000393063.1:c.4532A>G	p.Tyr1511Cys	p.Y1511C	ENST00000393063	NM_030621.3	1511	tAt/tGt	24/28	0.252182959003186	1	FACETS	0.263	0.205	0.329	0.263	0.205	0.329	INDETERMINATE	1	TRUE	0	0.485831997402114	1		495	273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578396	7578397	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0024663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	85	731	0	ENST00000269305.4:c.533_534del	p.His178ProfsTer2	p.H178Pfs*2	ENST00000269305	NM_001126112.2	178	cAC/c	5/11	0.485831997402114	1	FACETS	0.674	0.6	0.753	0.674	0.6	0.753	SUBCLONAL	1	TRUE	0	0.485831997402114	1		731	393	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873196	136873196	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	61	397	0	ENST00000241393.3:c.302A>G	p.Asn101Ser	p.N101S	ENST00000241393	NM_003467.2	101	aAc/aGc	2/2	1	2	FACETS	0.713	0.619	0.815	0.713	0.619	0.815	SUBCLONAL	1	TRUE	1	0.485831997402114	2		397	352	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275153	41275153	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs781731106	NA	P-0024663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	21	502	0	ENST00000349496.5:c.1319A>G	p.Gln440Arg	p.Q440R	ENST00000349496	NM_001904.3	440	cAa/cGa	9/15	1	2	FACETS	0.266	0.204	0.338	0.266	0.204	0.338	SUBCLONAL	1	TRUE	1	0.485831997402114	2		502	325	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589009	67589023	+	protein_altering_variant	In_Frame_Del	DEL	ATTATACTCTTACAC	ATTATACTCTTACAC	GTG	novel	NA	P-0024663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	47	375	1	ENST00000274335.5:c.1100_1114delinsGTG	p.Asp367_Leu372delinsGlyVal	p.D367_L372delinsGV	ENST00000274335		367	gATTATACTCTTACACta/gGTGta	8/15	0.168008237565865	3	FACETS	1	0.901	1	0.358	0.305	0.415	INDETERMINATE	1	TRUE	0	0.485831997402114	3		376	224	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106573	27106573	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	AT	novel	NA	P-0024663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	91	938	0	ENST00000324856.7:c.6184delinsAT	p.Val2062IlefsTer37	p.V2062Ifs*37	ENST00000324856	NM_006015.4	2062	Gtt/ATtt	20/20	0.485831997402114	1	FACETS	0.663	0.592	0.738	0.663	0.592	0.738	SUBCLONAL	1	TRUE	0	0.485831997402114	1		938	428	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0024664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	104	578	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.40985256348542	4	FACETS	1	0.976	1	0.822	0.747	0.9	CLONAL	2	FALSE	1	0.40985256348542	4		578	290	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0024664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	26	357	2	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.23301323395474	3	FACETS	0.813	0.649	0.998	0.407	0.324	0.499	INDETERMINATE	1	FALSE	1	0.40985256348542	3		359	188	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40864438	40864438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139326526	NA	P-0024664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	34	916	2	ENST00000428826.2:c.1270G>A	p.Val424Ile	p.V424I	ENST00000428826		424	Gta/Ata	12/21	NA	2	FACETS	0.542	0.444	0.652			1	INDETERMINATE	1	FALSE	NA	0.40985256348542	2		918	306	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390402	118390407	+	frameshift_variant	Frame_Shift_Del	DEL	GTGCCA	GTGCCA	CT	novel	NA	P-0024664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	30	600	1	ENST00000534358.1:c.11216_11221delinsCT	p.Gly3739AlafsTer22	p.G3739Afs*22	ENST00000534358	NM_005933.3	3739	gGTGCCAag/gCTag	32/36	0.23301323395474	3	FACETS	0.681	0.551	0.827	0.341	0.275	0.414	INDETERMINATE	1	FALSE	1	0.40985256348542	3		601	259	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270147	66270147	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	20	431	1	ENST00000273854.3:c.1735G>T	p.Val579Leu	p.V579L	ENST00000273854	NM_004439.5	579	Gtg/Ttg	8/18	0.23301323395474	3	FACETS	0.579	0.445	0.735	0.29	0.222	0.368	INDETERMINATE	1	FALSE	1	0.40985256348542	3		432	203	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245462	153245462	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	62	680	0	ENST00000281708.4:c.1729T>G	p.Leu577Val	p.L577V	ENST00000281708	NM_033632.3	577	Tta/Gta	11/12	0.23301323395474	3	FACETS	1	0.949	1	0.596	0.518	0.678	INDETERMINATE	1	FALSE	1	0.40985256348542	3		680	306	SUCCESS
APC	324	MSKCC	GRCh37	5	112175171	112175172	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0024664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	20	239	0	ENST00000257430.4:c.3881dup	p.Glu1295GlyfsTer6	p.E1295Gfs*6	ENST00000257430	NM_000038.5	1294	cag/cAag	16/16	0.23301323395474	3	FACETS	0.878	0.678	1	0.439	0.339	0.553	INDETERMINATE	1	FALSE	1	0.40985256348542	3		239	134	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468061	50468061	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	10	416	0	ENST00000331340.3:c.1296C>G	p.His432Gln	p.H432Q	ENST00000331340	NM_006060.4	432	caC/caG	8/8	0.237139829662617	5	FACETS	0.48	0.326	0.674	0.16	0.108	0.225	INDETERMINATE	1	FALSE	2	0.40985256348542	5		416	164	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0024665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	247	400	0	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.373112306245381	2	FACETS	0.9	0.848	0.953	0.9	0.848	0.953	CLONAL	2	TRUE	0	0.460349077618812	2		400	596	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0024665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	76	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.128773245233929	5	FACETS	1	0.944	1	0.282	0.248	0.319	INDETERMINATE	1	TRUE	1	0.460349077618812	5		326	495	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724632	162724632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767283136	NA	P-0024665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	154	361	0	ENST00000367921.3:c.404G>A	p.Arg135His	p.R135H	ENST00000367921	NM_006182.2	135	cGt/cAt	5/18	0.216471560352928	5	FACETS	1	0.922	1	0.668	0.615	0.724	INDETERMINATE	2	TRUE	2	0.460349077618812	5		361	564	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244197	5244197	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754224013	NA	P-0024665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	61	347	0	ENST00000357368.4:c.1285G>A	p.Ala429Thr	p.A429T	ENST00000357368	NM_002850.3	429	Gcg/Acg	11/38	0.460349077618812	1	FACETS	0.604	0.524	0.689	0.604	0.524	0.689	SUBCLONAL	1	TRUE	0	0.460349077618812	1		347	338	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719888	52719888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	101	511	0	ENST00000322088.6:c.1100C>T	p.Pro367Leu	p.P367L	ENST00000322088	NM_014225.5	367	cCc/cTc	9/15	0.205420759583818	3	FACETS	0.694	0.62	0.772	0.347	0.31	0.386	INDETERMINATE	1	TRUE	1	0.460349077618812	3		511	778	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	364	552	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.549746802992076	3	FACETS	0.903	0.859	0.947	0.903	0.859	0.947	CLONAL	2	TRUE	1	0.549746802992076	3		552	935	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579534	7579535	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0024666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	439	623	0	ENST00000269305.4:c.152_153del	p.Glu51AlafsTer5	p.E51Afs*5	ENST00000269305	NM_001126112.2	51	gAA/g	4/11	NA	2	FACETS	0.934	0.897	0.971			1	INDETERMINATE	2	TRUE	NA	0.549746802992076	2		623	855	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440543	49440543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	942	647	0	ENST00000301067.7:c.4267C>T	p.Arg1423Cys	p.R1423C	ENST00000301067	NM_003482.3	1423	Cgt/Tgt	15/54	0.466294315674875	5	FACETS	0.972	0.948	0.997			1	CLONAL	4	TRUE	NA	0.549746802992076	5		647	1608	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	77	314	0				ENST00000310581	NM_198253.2	-/1132			0.589585557323992	5	FACETS	0.906	0.797	1	0.226	0.199	0.256	CLONAL	1	FALSE	1	0.613633084083	5		314	532	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945129	32945129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80359104	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	97	415	0	ENST00000380152.3:c.8524C>T	p.Arg2842Cys	p.R2842C	ENST00000380152		2842	Cgc/Tgc	20/27	0.613633084083	3	FACETS	0.879	0.787	0.976	0.44	0.393	0.488	CLONAL	1	FALSE	1	0.613633084083	3		415	470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	385	904	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.61177567626795	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	FALSE	0	0.613633084083	2		904	624	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134479	30134479	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	326	554	0	ENST00000263025.4:c.52G>C	p.Glu18Gln	p.E18Q	ENST00000263025	NM_002746.2	18	Gag/Cag	1/9	0.613633084083	3	FACETS	0.948	0.912	0.984	0.948	0.912	0.984	CLONAL	3	FALSE	0	0.613633084083	3		554	488	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278050	18278050	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	155	878	0	ENST00000222254.8:c.1670A>G	p.Asp557Gly	p.D557G	ENST00000222254	NM_005027.3	557	gAc/gGc	13/16	0.192673738289677	3	FACETS	0.897	0.823	0.974	0.299	0.274	0.325	INDETERMINATE	1	FALSE	0	0.613633084083	3		878	736	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687370	37687370	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	117	601	0	ENST00000447079.4:c.4274G>A	p.Gly1425Glu	p.G1425E	ENST00000447079	NM_015083.1	1425	gGa/gAa	14/14	0.425642353978197	4	FACETS	0.924	0.835	1	0.462	0.417	0.509	CLONAL	1	FALSE	2	0.613633084083	4		601	666	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635601	47635603	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs267607919	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	207	785	0	ENST00000233146.2:c.279_281del	p.Leu94del	p.L94del	ENST00000233146	NM_000251.2	91	gaTCTt/gat	2/16	0.613633084083	3	FACETS	0.991	0.92	1	0.495	0.46	0.532	CLONAL	1	FALSE	1	0.613633084083	3		785	890	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730858	40730858	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200227405	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	214	903	0	ENST00000373198.4:c.3677G>A	p.Arg1226Gln	p.R1226Q	ENST00000373198	NM_133170.3	1226	cGa/cAa	27/32	0.425642353978197	4	FACETS	1	0.972	1	0.544	0.505	0.584	CLONAL	1	FALSE	2	0.613633084083	4		903	1035	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217348	11217348	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	143	675	0	ENST00000361445.4:c.4330G>A	p.Glu1444Lys	p.E1444K	ENST00000361445	NM_004958.3	1444	Gag/Aag	30/58	0.370764199632386	1	FACETS	0.758	0.698	0.821	0.758	0.698	0.821	SUBCLONAL	1	FALSE	0	0.613633084083	1		675	426	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434129	49434129	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1182599084	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	335	794	2	ENST00000301067.7:c.7424del	p.Pro2475LeufsTer10	p.P2475Lfs*10	ENST00000301067	NM_003482.3	2475	cCt/ct	31/54	0.589095118661978	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	FALSE	2	0.613633084083	4		796	856	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445170	49445170	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	421	949	2	ENST00000301067.7:c.2296G>T	p.Glu766Ter	p.E766*	ENST00000301067	NM_003482.3	766	Gag/Tag	10/54	0.589095118661978	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	FALSE	2	0.613633084083	4		951	1091	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50482350	50482350	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	189	784	0	ENST00000394963.4:c.701C>G	p.Ser234Cys	p.S234C	ENST00000394963	NM_003076.4	234	tCt/tGt	6/13	0.589095118661978	4	FACETS	0.986	0.911	1	0.493	0.455	0.532	CLONAL	1	FALSE	2	0.613633084083	4		784	1008	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856517	111856517	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	93	430	0	ENST00000341259.2:c.568G>A	p.Glu190Lys	p.E190K	ENST00000341259	NM_005475.2	190	Gag/Aag	2/8	0.589095118661978	4	FACETS	0.858	0.765	0.957	0.429	0.382	0.479	CLONAL	1	FALSE	2	0.613633084083	4		430	570	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115428	115115429	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	376	881	1	ENST00000257566.3:c.897dup	p.Ala300CysfsTer27	p.A300Cfs*27	ENST00000257566	NM_016569.3	299	-/T	5/8	0.425642353978197	4	FACETS	0.9	0.856	0.946	0.9	0.856	0.946	CLONAL	2	FALSE	2	0.613633084083	4		882	1098	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042695	42042695	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	50	601	0	ENST00000219905.7:c.6890C>A	p.Thr2297Asn	p.T2297N	ENST00000219905	NM_001164273.1	2297	aCt/aAt	17/24	0.613633084083	3	FACETS	0.376	0.318	0.439	0.188	0.159	0.22	SUBCLONAL	1	FALSE	1	0.613633084083	3		601	567	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779313	3779313	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	268	659	0	ENST00000262367.5:c.5735C>G	p.Ser1912Ter	p.S1912*	ENST00000262367	NM_004380.2	1912	tCa/tGa	31/31	0.613633084083	3	FACETS	0.981	0.929	1	0.654	0.619	0.689	CLONAL	2	FALSE	0	0.613633084083	3		659	582	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14026115	14026115	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	104	424	0	ENST00000311895.7:c.1075G>C	p.Glu359Gln	p.E359Q	ENST00000311895	NM_005236.2	359	Gaa/Caa	6/11	0.613633084083	3	FACETS	0.933	0.839	1	0.311	0.279	0.344	CLONAL	1	FALSE	0	0.613633084083	3		424	475	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351104	89351104	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	169	758	0	ENST00000301030.4:c.1846G>C	p.Glu616Gln	p.E616Q	ENST00000301030	NM_001256183.1	616	Gag/Cag	9/13	0.613633084083	2	FACETS	0.998	0.923	1	0.499	0.461	0.538	CLONAL	1	FALSE	0	0.613633084083	2		758	552	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864610	37864610	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	185	746	0	ENST00000269571.5:c.262C>G	p.His88Asp	p.H88D	ENST00000269571		88	Cac/Gac	3/27	0.425642353978197	4	FACETS	1	0.975	1	0.564	0.521	0.609	CLONAL	1	FALSE	2	0.613633084083	4		746	862	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879888	37879888	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	187	971	0	ENST00000269571.5:c.2183C>G	p.Ser728Cys	p.S728C	ENST00000269571		728	tCt/tGt	18/27	0.425642353978197	4	FACETS	1	0.925	1	0.501	0.462	0.541	CLONAL	1	FALSE	2	0.613633084083	4		971	982	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57569912	57569912	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	103	432	0	ENST00000316660.6:c.92G>C	p.Arg31Thr	p.R31T	ENST00000316660	NM_021127.2	31	aGa/aCa	2/2	0.613633084083	3	FACETS	1	0.927	1	0.517	0.466	0.571	CLONAL	1	FALSE	1	0.613633084083	3		432	424	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597480	10597480	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568395805	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	168	778	1	ENST00000171111.5:c.1723C>T	p.His575Tyr	p.H575Y	ENST00000171111	NM_203500.1	575	Cac/Tac	6/6	0.192673738289677	3	FACETS	0.907	0.835	0.982	0.302	0.278	0.328	INDETERMINATE	1	FALSE	0	0.613633084083	3		779	789	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944611	40944611	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	101	441	0	ENST00000373198.4:c.1891G>A	p.Glu631Lys	p.E631K	ENST00000373198	NM_133170.3	631	Gag/Aag	12/32	0.425642353978197	4	FACETS	1	0.948	1	0.544	0.488	0.603	CLONAL	1	FALSE	2	0.613633084083	4		441	488	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29099531	29099531	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	112	531	0	ENST00000328354.6:c.870C>G	p.Asn290Lys	p.N290K	ENST00000328354	NM_007194.3	290	aaC/aaG	8/15	0.153872913788016	3	FACETS	0.892	0.805	0.982	0.297	0.268	0.328	INDETERMINATE	1	FALSE	0	0.613633084083	3		531	535	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573711	41573711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1417305999	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	190	892	1	ENST00000263253.7:c.5996G>A	p.Gly1999Glu	p.G1999E	ENST00000263253	NM_001429.3	1999	gGa/gAa	31/31	0.153872913788016	3	FACETS	1	0.966	1	0.357	0.331	0.385	INDETERMINATE	1	FALSE	0	0.613633084083	3		893	755	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928503	69928503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	232	935	0	ENST00000352241.4:c.323C>T	p.Ser108Phe	p.S108F	ENST00000352241	NM_198159.2	108	tCt/tTt	2/10	0.613633084083	3	FACETS	0.993	0.926	1	0.497	0.463	0.531	CLONAL	1	FALSE	1	0.613633084083	3		935	995	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231757	66231757	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	91	497	0	ENST00000273854.3:c.1943G>C	p.Arg648Thr	p.R648T	ENST00000273854	NM_004439.5	648	aGa/aCa	11/18	0.613633084083	3	FACETS	0.777	0.692	0.866	0.388	0.346	0.433	SUBCLONAL	1	FALSE	1	0.613633084083	3		497	499	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910593	29910593	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199474365	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	308	911	1	ENST00000376809.5:c.133C>T	p.Arg45Cys	p.R45C	ENST00000376809	NM_002116.7	45	Cgc/Tgc	2/8	0.589095118661978	4	FACETS	0.909	0.86	0.959	0.909	0.86	0.959	CLONAL	2	FALSE	2	0.613633084083	4		912	891	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169057	32169057	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	406	930	0	ENST00000375023.3:c.3976G>C	p.Gly1326Arg	p.G1326R	ENST00000375023	NM_004557.3	1326	Gga/Cga	22/30	0.589095118661978	4	FACETS	0.972	0.927	1	0.972	0.927	1	CLONAL	2	FALSE	2	0.613633084083	4		930	1098	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120402	94120402	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	197	389	0	ENST00000369303.4:c.649G>A	p.Asp217Asn	p.D217N	ENST00000369303	NM_004440.3	217	Gat/Aat	3/17	0.613633084083	3	FACETS	0.863	0.807	0.92	0.863	0.807	0.92	CLONAL	2	FALSE	1	0.613633084083	3		389	486	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715411	117715411	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	50	635	0	ENST00000368508.3:c.1078A>T	p.Arg360Ter	p.R360*	ENST00000368508	NM_002944.2	360	Aga/Tga	10/43	0.613633084083	3	FACETS	0.294	0.248	0.344	0.147	0.124	0.172	SUBCLONAL	1	FALSE	1	0.613633084083	3		635	725	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527475	157527475	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	124	472	0	ENST00000346085.5:c.5200G>C	p.Asp1734His	p.D1734H	ENST00000346085	NM_020732.3	1734	Gat/Cat	20/20	NA	2	FACETS	1	0.93	1			1	INDETERMINATE	1	FALSE	NA	0.613633084083	2		472	396	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211168	55211168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	119	487	1	ENST00000275493.2:c.411G>A	p.Met137Ile	p.M137I	ENST00000275493	NM_005228.3	137	atG/atA	3/28	0.589095118661978	4	FACETS	0.762	0.688	0.841	0.381	0.344	0.421	SUBCLONAL	1	FALSE	2	0.613633084083	4		488	821	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398615	116398615	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	187	690	0	ENST00000397752.3:c.2205C>G	p.Ile735Met	p.I735M	ENST00000397752	NM_000245.2	735	atC/atG	9/21	0.613633084083	3	FACETS	0.988	0.914	1	0.494	0.457	0.533	CLONAL	1	FALSE	1	0.613633084083	3		690	806	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873393	151873393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs76034210	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	213	433	0	ENST00000262189.6:c.9145G>A	p.Glu3049Lys	p.E3049K	ENST00000262189	NM_170606.2	3049	Gaa/Aaa	38/59	0.613633084083	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	FALSE	1	0.613633084083	3		433	450	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877972	151877972	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	87	408	0	ENST00000262189.6:c.6973C>T	p.Gln2325Ter	p.Q2325*	ENST00000262189	NM_170606.2	2325	Cag/Tag	36/59	0.613633084083	3	FACETS	0.825	0.734	0.922	0.413	0.367	0.461	CLONAL	1	FALSE	1	0.613633084083	3		408	449	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900124	151900125	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	94	454	0	ENST00000262189.6:c.3986_3987del	p.Thr1329IlefsTer3	p.T1329Ifs*3	ENST00000262189	NM_170606.2	1329	aCT/a	26/59	0.613633084083	3	FACETS	0.807	0.721	0.898	0.404	0.36	0.449	CLONAL	1	FALSE	1	0.613633084083	3		454	496	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902229	151902229	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	151	664	0	ENST00000262189.6:c.3923C>G	p.Ser1308Ter	p.S1308*	ENST00000262189	NM_170606.2	1308	tCa/tGa	25/59	0.613633084083	3	FACETS	0.919	0.842	0.999	0.459	0.421	0.5	CLONAL	1	FALSE	1	0.613633084083	3		664	700	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90947835	90947835	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs766237464	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	225	432	0	ENST00000265433.3:c.2240A>G	p.Asn747Ser	p.N747S	ENST00000265433	NM_002485.4	747	aAt/aGt	16/16	0.613633084083	6	FACETS	1	0.976	1	0.545	0.509	0.582	CLONAL	2	FALSE	2	0.613633084083	6		432	749	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123199756	123199756	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	118	287	0	ENST00000218089.9:c.2056C>T	p.Gln686Ter	p.Q686*	ENST00000218089	NM_001042749.1	686	Cag/Tag	21/35	0.554073603098965	2	FACETS	1	0.945	1			1	CLONAL	1	FALSE	NA	0.613633084083	2		287	366	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202465	123202465	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	152	379	0	ENST00000218089.9:c.2317C>T	p.Gln773Ter	p.Q773*	ENST00000218089	NM_001042749.1	773	Caa/Taa	24/35	0.554073603098965	2	FACETS	1	0.968	1			1	CLONAL	1	FALSE	NA	0.613633084083	2		379	454	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245832	46245832	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0024669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	100	545	0	ENST00000334344.6:c.3926C>G	p.Ser1309Ter	p.S1309*	ENST00000334344	NM_152641.2	1309	tCa/tGa	15/21	0.515029567455524	2	FACETS	0.53	0.473	0.59	0.265	0.236	0.295	SUBCLONAL	1	TRUE	0	0.515029567455524	2		545	733	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753745	42753746	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0024669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1326	350	1059	1	ENST00000222329.4:c.518dup	p.Ser174LeufsTer15	p.S174Lfs*15	ENST00000222329	NM_006494.2	173	ttc/ttTc	4/4	0.419378901263113	3	FACETS	1	0.96	1	0.51	0.481	0.539	CLONAL	1	TRUE	1	0.515029567455524	3		1060	1676	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453132	140453132	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913365	NA	P-0024673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	26	426	0	ENST00000288602.6:c.1803A>T	p.Lys601Asn	p.K601N	ENST00000288602	NM_004333.4	601	aaA/aaT	15/18	1	2	FACETS	0.628	0.495	0.781	0.628	0.495	0.781	SUBCLONAL	1	TRUE	1	0.12	2		426	690	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	89	593	0	ENST00000397062.3:c.246A>C	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaC	2/5	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.12	2		593	1035	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503187	125503187	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	36	334	0	ENST00000428830.2:c.554A>T	p.His185Leu	p.H185L	ENST00000428830	NM_001114121.2	185	cAt/cTt	6/14	1	2	FACETS	1	0.84	1	1	0.84	1	CLONAL	1	TRUE	1	0.12	2		334	585	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562721	29562721	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	51	477	0	ENST00000356175.3:c.3802del	p.Ala1268GlnfsTer17	p.A1268Qfs*17	ENST00000356175	NM_000267.3	1267	ttG/tt	28/57	1	2	FACETS	0.975	0.826	1	0.975	0.826	1	CLONAL	1	TRUE	1	0.12	2		477	872	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0024683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	191	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.904	0.844	0.965	0.904	0.844	0.965	CLONAL	1	TRUE	1	0.867703663271863	2		326	487	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741694	17741694	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	588	294	0	ENST00000250003.3:c.365T>G	p.Leu122Arg	p.L122R	ENST00000250003	NM_002478.4	122	cTg/cGg	1/3	0.851293542937157	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.867703663271863	2		294	656	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277037	18277037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	76	760	0	ENST00000222254.8:c.1484G>A	p.Gly495Asp	p.G495D	ENST00000222254	NM_005027.3	495	gGc/gAc	12/16	0.367237141625432	3	FACETS	0.478	0.418	0.543	0.239	0.209	0.272	SUBCLONAL	1	TRUE	1	0.367237141625432	3		760	1025	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435104	56435104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	79	634	1	ENST00000407977.2:c.2033G>A	p.Cys678Tyr	p.C678Y	ENST00000407977		678	tGc/tAc	9/10	1	2	FACETS	0.504	0.443	0.571	0.504	0.443	0.571	SUBCLONAL	1	TRUE	1	0.367237141625432	2		635	853	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821324	32821324	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	82	736	0	ENST00000354258.4:c.270del	p.Ala91ProfsTer32	p.A91Pfs*32	ENST00000354258	NM_000593.5	90	ctC/ct	1/11	0.118328600593443	4	FACETS	0.744	0.655	0.839	0.372	0.327	0.42	INDETERMINATE	1	TRUE	2	0.367237141625432	4		736	821	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6027051	6027051	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs876661256	NA	P-0024686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	87	682	1	ENST00000265849.7:c.1345C>T	p.Gln449Ter	p.Q449*	ENST00000265849	NM_000535.5	449	Cag/Tag	11/15	0.24991860230554	3	FACETS	0.702	0.621	0.789	0.234	0.207	0.263	SUBCLONAL	1	TRUE	0	0.367237141625432	3		683	799	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0024721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	155	891	1	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.648943934508518	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.648943934508518	1		892	281	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348763	118348763	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	51	422	0	ENST00000534358.1:c.3416A>G	p.Lys1139Arg	p.K1139R	ENST00000534358	NM_005933.3	1139	aAg/aGg	5/36	0.648943934508518	1	FACETS	0.425	0.364	0.49	0.425	0.364	0.49	SUBCLONAL	1	TRUE	0	0.648943934508518	1		422	250	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557844	21557844	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	142	775	0	ENST00000382592.4:c.2001G>C	p.Met667Ile	p.M667I	ENST00000382592	NM_014572.2	667	atG/atC	5/8	0.306620256225438	1	FACETS	0.776	0.715	0.838	0.776	0.715	0.838	INDETERMINATE	1	TRUE	0	0.648943934508518	1		775	381	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657475	29657508	+	frameshift_variant	Frame_Shift_Del	DEL	TAGAATTTTTGGAAGAGTGTATTTCTGGATTTAG	TAGAATTTTTGGAAGAGTGTATTTCTGGATTTAG	-	novel	NA	P-0024721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	209	568	0	ENST00000356175.3:c.5708_5741del	p.Leu1903SerfsTer7	p.L1903Sfs*7	ENST00000356175	NM_000267.3	1903	tTAGAATTTTTGGAAGAGTGTATTTCTGGATTTAGc/tc	38/57	0.628462025284991	2	FACETS	0.815	0.769	0.861	0.815	0.769	0.861	CLONAL	2	TRUE	0	0.648943934508518	2		568	395	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151893052	151893085	+	frameshift_variant	Frame_Shift_Del	DEL	TGTTTAAAACTTCAGAAATATCAGCTAATGGGTC	TGTTTAAAACTTCAGAAATATCAGCTAATGGGTC	-	novel	NA	P-0024721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	41	631	0	ENST00000262189.6:c.4285_4318del	p.Asp1429GlnfsTer8	p.D1429Qfs*8	ENST00000262189	NM_170606.2	1429	GACCCATTAGCTGATATTTCTGAAGTTTTAAACAca/ca	28/59	0.307373057464549	1	FACETS	0.191	0.158	0.226	0.191	0.158	0.226	INDETERMINATE	1	TRUE	0	0.648943934508518	1		631	448	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486128	8486155	+	frameshift_variant	Frame_Shift_Del	DEL	CTGAGAGCCTGAAGACGTATGATGCTCC	CTGAGAGCCTGAAGACGTATGATGCTCC	-	novel	NA	P-0024721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	63	504	0	ENST00000356435.5:c.2662_2689del	p.Gly888ProfsTer12	p.G888Pfs*12	ENST00000356435		888	GGAGCATCATACGTCTTCAGGCTCTCAGcc/cc	17/35	0.628462025284991	2	FACETS	0.503	0.437	0.574	0.252	0.218	0.287	SUBCLONAL	1	TRUE	0	0.648943934508518	2		504	386	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930282	39930282	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	82	781	1	ENST00000378444.4:c.3182A>T	p.Lys1061Met	p.K1061M	ENST00000378444	NM_001123385.1	1061	aAg/aTg	6/15	0.454980258613502	1	FACETS	0.402	0.356	0.45	0.402	0.356	0.45	SUBCLONAL	1	TRUE	0	0.648943934508518	1		782	425	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271883	15271896	+	frameshift_variant	Frame_Shift_Del	DEL	GGAACGAGGGGCCT	GGAACGAGGGGCCT	-	novel	NA	P-0024721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	87	651	0	ENST00000263388.2:c.6543_6556del	p.Gly2182AlafsTer55	p.G2182Afs*55	ENST00000263388	NM_000435.2	2181	ccAGGCCCCTCGTTCCtg/cctg	33/33	0.524004595900913	1	FACETS	0.745	0.671	0.822	0.745	0.671	0.822	SUBCLONAL	1	TRUE	0	0.648943934508518	1		651	243	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0024724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	369	569	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.620116041303522	1	FACETS	0.965	0.92	1	0.965	0.92	1	CLONAL	1	TRUE	0	0.620116041303522	1		569	851	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526314	189526314	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	186	239	0	ENST00000264731.3:c.578C>T	p.Thr193Met	p.T193M	ENST00000264731	NM_003722.4	193	aCg/aTg	4/14	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.620116041303522	2		239	567	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420070	49420073	+	frameshift_variant	Frame_Shift_Del	DEL	AGCA	AGCA	-	novel	NA	P-0024724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	268	807	0	ENST00000301067.7:c.15676_15679del	p.Cys5226AlafsTer16	p.C5226Afs*16	ENST00000301067	NM_003482.3	5226	TGCTgc/gc	48/54	1	2	FACETS	0.971	0.913	1	0.971	0.913	1	CLONAL	1	TRUE	1	0.620116041303522	2		807	890	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245009	41245009	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555589446	NA	P-0024724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	323	946	0	ENST00000357654.3:c.2539A>G	p.Met847Val	p.M847V	ENST00000357654	NM_007294.3	847	Atg/Gtg	10/23	1	2	FACETS	0.868	0.82	0.918	0.868	0.82	0.918	CLONAL	1	TRUE	1	0.620116041303522	2		946	1200	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910364	29910378	+	inframe_deletion	In_Frame_Del	DEL	CTACTCTCGGGGGCC	CTACTCTCGGGGGCC	-	novel	NA	P-0024724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	229	495	0	ENST00000376809.5:c.36_50del	p.Leu13_Leu17del	p.L13_L17del	ENST00000376809	NM_002116.7	12	CTACTCTCGGGGGCC/-	1/8	0.620116041303522	1	FACETS	0.731	0.685	0.779	0.731	0.685	0.779	SUBCLONAL	1	TRUE	0	0.620116041303522	1		495	697	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323185	31323187	+	inframe_deletion	In_Frame_Del	DEL	CCA	CCA	-	novel	NA	P-0024724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	292	769	0	ENST00000412585.2:c.802_804del	p.Trp268del	p.W268del	ENST00000412585	NM_005514.6	268	TGG/-	4/8	0.620116041303522	1	FACETS	0.944	0.895	0.994	0.944	0.895	0.994	CLONAL	1	TRUE	0	0.620116041303522	1		769	688	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390601	139390610	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGACGTTG	GGAGACGTTG	-	novel	NA	P-0024724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	354	1106	0	ENST00000277541.6:c.7581_7590del	p.Asn2528ThrfsTer58	p.N2528Tfs*58	ENST00000277541	NM_017617.3	2527	tcCAACGTCTCC/tc	34/34	1	2	FACETS	0.851	0.805	0.897	0.851	0.805	0.897	CLONAL	1	TRUE	1	0.620116041303522	2		1106	1342	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626680	100626680	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	244	370	0	ENST00000308731.7:c.250del	p.Glu84LysfsTer37	p.E84Kfs*37	ENST00000308731	NM_000061.2	84	Gaa/aa	4/19	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.620116041303522	1		370	411	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52621421	52621428	+	frameshift_variant	Frame_Shift_Del	DEL	TTGTAATA	TTGTAATA	-	novel	NA	P-0024724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	259	759	0	ENST00000394830.3:c.2989_2996del	p.Tyr997GlnfsTer5	p.Y997Qfs*5	ENST00000394830	NM_018313.4	997	TATTACAAc/c	20/30	1	2	FACETS	0.84	0.788	0.894	0.84	0.788	0.894	CLONAL	1	TRUE	1	0.620116041303522	2		759	994	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0024724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	381	569	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.241137074258897	2	FACETS	0.927	0.879	0.975	0.927	0.879	0.975	CLONAL	2	TRUE	0	0.309656477557496	2		569	1328	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526314	189526314	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	167	239	0	ENST00000264731.3:c.578C>T	p.Thr193Met	p.T193M	ENST00000264731	NM_003722.4	193	aCg/aTg	4/14	0.309656477557496	3	FACETS	0.925	0.853	1	0.925	0.853	1	CLONAL	2	TRUE	1	0.309656477557496	3		239	673	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910364	29910378	+	inframe_deletion	In_Frame_Del	DEL	CTACTCTCGGGGGCC	CTACTCTCGGGGGCC	-	novel	NA	P-0024724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	118	495	0	ENST00000376809.5:c.36_50del	p.Leu13_Leu17del	p.L13_L17del	ENST00000376809	NM_002116.7	12	CTACTCTCGGGGGCC/-	1/8	0.241137074258897	2	FACETS	0.656	0.59	0.726	0.328	0.295	0.363	SUBCLONAL	1	TRUE	0	0.309656477557496	2		495	1162	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438647	49438647	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	173	491	0	ENST00000301067.7:c.4843C>T	p.Arg1615Ter	p.R1615*	ENST00000301067	NM_003482.3	1615	Cga/Tga	19/54	1	2	FACETS	0.97	0.891	1	0.97	0.891	1	CLONAL	1	TRUE	1	0.309656477557496	2		491	1152	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254587	16254587	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	55	334	0	ENST00000375759.3:c.1852G>C	p.Glu618Gln	p.E618Q	ENST00000375759	NM_015001.2	618	Gag/Cag	11/15	1	2	FACETS	0.583	0.498	0.676	0.583	0.498	0.676	SUBCLONAL	1	TRUE	1	0.309656477557496	2		334	609	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255053	16255053	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	88	230	0	ENST00000375759.3:c.2318G>C	p.Arg773Thr	p.R773T	ENST00000375759	NM_015001.2	773	aGa/aCa	11/15	1	2	FACETS	0.923	0.818	1	0.923	0.818	1	CLONAL	1	TRUE	1	0.309656477557496	2		230	616	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151882665	151882665	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0024724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	57	434	0	ENST00000262189.6:c.5060C>G	p.Ser1687Ter	p.S1687*	ENST00000262189	NM_170606.2	1687	tCa/tGa	34/59	0.244690717004837	1	FACETS	0.54	0.463	0.624	0.54	0.463	0.624	SUBCLONAL	1	TRUE	0	0.309656477557496	1		434	576	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0024729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	209	606	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.968	0.906	1	0.968	0.906	1	CLONAL	1	TRUE	1	0.792593449101727	2		606	545	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0024729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	226	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.753930395090713	2	FACETS	0.967	0.928	1	0.967	0.928	1	CLONAL	2	TRUE	0	0.792593449101727	2		326	295	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307188	65307188	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	132	640	1	ENST00000342505.4:c.2500C>T	p.Gln834Ter	p.Q834*	ENST00000342505	NM_002227.2	834	Cag/Tag	18/25	0.775428536207975	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.792593449101727	1		641	195	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871865	12871865	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	94	285	0	ENST00000228872.4:c.583del	p.Arg195AspfsTer30	p.R195Dfs*30	ENST00000228872	NM_004064.3	194	agA/ag	2/3	1	2	FACETS	0.953	0.862	1	0.953	0.862	1	CLONAL	1	TRUE	1	0.792593449101727	2		285	249	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43730585	43730585	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	113	636	0	ENST00000382044.4:c.3128G>A	p.Cys1043Tyr	p.C1043Y	ENST00000382044	NM_001141980.1	1043	tGt/tAt	16/28	1	2	FACETS	0.88	0.802	0.96	0.88	0.802	0.96	CLONAL	1	TRUE	1	0.792593449101727	2		636	324	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581171	48581171	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0024729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	131	426	2	ENST00000342988.3:c.475A>T	p.Lys159Ter	p.K159*	ENST00000342988	NM_005359.5	159	Aag/Tag	5/12	0.775428536207975	1	FACETS	0.955	0.894	1	0.955	0.894	1	CLONAL	1	TRUE	0	0.792593449101727	1		428	209	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56411723	56411723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	14	545	3	ENST00000348428.3:c.1907C>T	p.Pro636Leu	p.P636L	ENST00000348428	NM_006785.3	636	cCa/cTa	15/17	0.775428536207975	1	FACETS	0.084	0.06	0.113	0.084	0.06	0.113	SUBCLONAL	1	TRUE	0	0.792593449101727	1		548	253	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419834	41419834	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0024729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	75	441	0	ENST00000373198.4:c.486+1G>A		p.X162_splice	ENST00000373198	NM_133170.3	162			0.19639336951122	1	FACETS	0.499	0.444	0.556	0.499	0.444	0.556	INDETERMINATE	1	TRUE	0	0.792593449101727	1		441	229	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032034	26032034	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	182	434	0	ENST00000244661.2:c.255C>A	p.Phe85Leu	p.F85L	ENST00000244661	NM_003537.3	85	ttC/ttA	1/1	0.527269765222681	5	FACETS	1	0.985	1			1	CLONAL	2	TRUE	NA	0.792593449101727	5		434	423	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627780	14627781	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0024730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	123	609	0	ENST00000254322.2:c.289_290del	p.Asp97ProfsTer7	p.D97Pfs*7	ENST00000254322	NM_006145.1	97	GAc/c	2/3	0.765943218014056	1	FACETS	0.962	0.896	1	0.962	0.896	1	CLONAL	1	TRUE	0	0.765943218014056	1		609	206	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177457	56177457	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	125	398	0	ENST00000399503.3:c.2431del	p.Met811TrpfsTer11	p.M811Wfs*11	ENST00000399503	NM_005921.1	810	tcA/tc	14/20	1	2	FACETS	0.952	0.872	1	0.952	0.872	1	CLONAL	1	TRUE	1	0.765943218014056	2		398	343	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	38	552	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	FALSE	1	0.11982060894099	2		552	591	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	95	630	5	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	0.104237012992629	3	FACETS	1	0.978	1	0.729	0.648	0.817	CLONAL	1	FALSE	1	0.11982060894099	3		635	1152	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0024733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	29	356	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.96	0.77	1	0.96	0.77	1	CLONAL	1	FALSE	1	0.11982060894099	2		356	504	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755670	57755670	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1427	107	945	2	ENST00000274289.3:c.117del	p.Glu40ArgfsTer60	p.E40Rfs*60	ENST00000274289	NM_006622.3	39	ccC/cc	1/14	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.11982060894099	2		947	1534	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752960	128752960	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	45	532	0	ENST00000377970.2:c.1121A>G	p.His374Arg	p.H374R	ENST00000377970	NM_002467.4	374	cAc/cGc	3/3	1	2	FACETS	0.885	0.741	1	0.885	0.741	1	CLONAL	1	FALSE	1	0.11982060894099	2		532	849	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0024733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1260	74	644	5	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	0.926	0.807	1	0.926	0.807	1	CLONAL	1	FALSE	1	0.11982060894099	2		649	1334	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627818	187627818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149283579	NA	P-0024733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	69	817	1	ENST00000441802.2:c.3164C>T	p.Thr1055Met	p.T1055M	ENST00000441802	NM_005245.3	1055	aCg/aTg	2/27	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	FALSE	1	0.11982060894099	2		818	1087	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204992	128204992	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	82	745	0	ENST00000341105.2:c.449del	p.Gly150GlufsTer68	p.G150Efs*68	ENST00000341105	NM_032638.4	150	gGa/ga	3/6	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.11982060894099	2		745	1119	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022647	31022647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	73	754	1	ENST00000375687.4:c.2132C>T	p.Thr711Ile	p.T711I	ENST00000375687	NM_015338.5	711	aCt/aTt	13/13	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.11982060894099	2		755	989	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197294	106197294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	37	387	1	ENST00000380013.4:c.5627C>T	p.Ala1876Val	p.A1876V	ENST00000380013	NM_001127208.2	1876	gCa/gTa	11/11	1	2	FACETS	1	0.844	1	1	0.844	1	CLONAL	1	FALSE	1	0.11982060894099	2		388	601	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45800110	45800110	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1192	72	823	2	ENST00000450313.1:c.110A>G	p.Gln37Arg	p.Q37R	ENST00000450313	NM_012222.2	37	cAg/cGg	2/16	1	2	FACETS	0.951	0.828	1	0.951	0.828	1	CLONAL	1	FALSE	1	0.11982060894099	2		825	1264	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845618	63845618	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	41	330	0	ENST00000279873.7:c.1359del	p.Glu454LysfsTer25	p.E454Kfs*25	ENST00000279873	NM_032199.2	453	Aaa/aa	9/10	0.104237012992629	3	FACETS	0.813	0.678	0.964	0.813	0.678	0.964	CLONAL	2	FALSE	1	0.11982060894099	3		330	446	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692842	89692875	+	frameshift_variant	Frame_Shift_Del	DEL	ACCAATGGCTAAGTGAAGATGACAATCATGTTGC	ACCAATGGCTAAGTGAAGATGACAATCATGTTGC	-	novel	NA	P-0024733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	18	229	0	ENST00000371953.3:c.327_360del	p.Asp109GlufsTer14	p.D109Efs*14	ENST00000371953	NM_000314.4	109	gACCAATGGCTAAGTGAAGATGACAATCATGTTGCa/ga	5/9	0.104237012992629	3	FACETS	0.829	0.627	1	0.829	0.627	1	CLONAL	2	FALSE	1	0.11982060894099	3		229	192	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124388	2124388	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	99	955	0	ENST00000219476.3:c.2543C>T	p.Ser848Phe	p.S848F	ENST00000219476	NM_000548.3	848	tCc/tTc	22/42	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.11982060894099	2		955	1292	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2132501	2132501	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	79	850	0	ENST00000219476.3:c.3879G>T	p.Trp1293Cys	p.W1293C	ENST00000219476	NM_000548.3	1293	tgG/tgT	32/42	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	1	0.11982060894099	2		850	1230	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821629	72821629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755941465	NA	P-0024733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	11	69	0	ENST00000268489.5:c.10546G>A	p.Gly3516Ser	p.G3516S	ENST00000268489	NM_006885.3	3516	Ggc/Agc	10/10	1	2	FACETS	0.785	0.546	1	1	0.864	1	CLONAL	2	FALSE	1	0.11982060894099	2		69	117	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821673	72821673	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	36	288	0	ENST00000268489.5:c.10502T>C	p.Val3501Ala	p.V3501A	ENST00000268489	NM_006885.3	3501	gTg/gCg	10/10	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	FALSE	1	0.11982060894099	2		288	454	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78829348	78829348	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0024733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	49	597	0	ENST00000306801.3:c.1398+1G>A		p.X466_splice	ENST00000306801	NM_020761.2	466			1	2	FACETS	0.904	0.763	1	0.904	0.763	1	CLONAL	1	FALSE	1	0.11982060894099	2		597	905	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948745	17948745	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1332	94	938	0	ENST00000458235.1:c.1697T>C	p.Met566Thr	p.M566T	ENST00000458235	NM_000215.3	566	aTg/aCg	12/24	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	FALSE	1	0.11982060894099	2		938	1426	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976261	18976261	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0024733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	73	747	0	ENST00000262803.5:c.3019+2T>C		p.X1007_splice	ENST00000262803	NM_002911.3	1007			1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	1	0.11982060894099	2		747	1034	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745201	41745201	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	77	696	0	ENST00000301178.4:c.1267C>A	p.Leu423Met	p.L423M	ENST00000301178	NM_021913.4	423	Ctg/Atg	9/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.11982060894099	2		696	1020	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50143253	50143253	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	90	488	0	ENST00000246792.3:c.103G>A	p.Val35Met	p.V35M	ENST00000246792	NM_006270.3	35	Gtg/Atg	1/6	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.11982060894099	2		488	1026	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716281	52716281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1177432332	NA	P-0024733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1212	81	768	0	ENST00000322088.6:c.725C>T	p.Ala242Val	p.A242V	ENST00000322088	NM_014225.5	242	gCc/gTc	6/15	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	FALSE	1	0.11982060894099	2		768	1293	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031209	36031209	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1205	74	883	1	ENST00000358208.4:c.1328C>G	p.Thr443Ser	p.T443S	ENST00000358208		443	aCc/aGc	11/12	1	2	FACETS	0.966	0.842	1	0.966	0.842	1	CLONAL	1	FALSE	1	0.11982060894099	2		884	1279	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42861488	42861488	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	58	731	2	ENST00000398585.3:c.382C>A	p.Leu128Met	p.L128M	ENST00000398585	NM_001135099.1	128	Ctg/Atg	4/14	1	2	FACETS	0.901	0.772	1	0.901	0.772	1	CLONAL	1	FALSE	1	0.11982060894099	2		733	1074	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950138	38950138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573790456	NA	P-0024733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	41	597	0	ENST00000357387.3:c.3812C>T	p.Thr1271Met	p.T1271M	ENST00000357387	NM_152756.3	1271	aCg/aTg	31/38	1	2	FACETS	0.884	0.734	1	0.884	0.734	1	CLONAL	1	FALSE	1	0.11982060894099	2		597	774	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527739	157527739	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1218816452	NA	P-0024733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	57	613	2	ENST00000346085.5:c.5464G>A	p.Gly1822Ser	p.G1822S	ENST00000346085	NM_020732.3	1822	Ggc/Agc	20/20	0.0763807093970386	4	FACETS	1	0.91	1	0.544	0.465	0.631	CLONAL	1	FALSE	2	0.11982060894099	4		615	979	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937159	76937159	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	37	672	1	ENST00000373344.5:c.3589C>T	p.Gln1197Ter	p.Q1197*	ENST00000373344	NM_000489.3	1197	Caa/Taa	9/35	0.11982060894099	1	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	FALSE	0	0.11982060894099	1		673	543	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0024744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	49	478	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.352123955276733	3	FACETS	0.791	0.681	0.908	0.791	0.681	0.908	CLONAL	2	TRUE	1	0.429990465004974	3		478	175	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584560	48584560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	70	496	0	ENST00000342988.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000342988	NM_005359.5	245	Cag/Tag	6/12	0.372086676733624	2	FACETS	0.857	0.762	0.954	0.857	0.762	0.954	CLONAL	2	TRUE	0	0.429990465004974	2		496	190	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	99	438	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	0.429990465004974	3	FACETS	0.919	0.841	0.997	0.919	0.841	0.997	CLONAL	3	TRUE	0	0.429990465004974	3		438	203	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473779	67473779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906850	NA	P-0024744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	24	442	0	ENST00000327367.4:c.859C>T	p.Arg287Trp	p.R287W	ENST00000327367	NM_005902.3	287	Cgg/Tgg	6/9	0.366333660275654	2	FACETS	0.677	0.535	0.836	0.338	0.267	0.418	SUBCLONAL	1	TRUE	0	0.429990465004974	2		442	165	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150217	108150217	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0024744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	16	414	1	ENST00000278616.4:c.3285-1G>T		p.X1095_splice	ENST00000278616	NM_000051.3	1095			0.204437628893088	5	FACETS	0.881	0.656	1	0.294	0.218	0.382	INDETERMINATE	1	TRUE	2	0.429990465004974	5		415	139	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0024764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	104	814	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.346184698331925	1	FACETS	0.688	0.616	0.764	0.688	0.616	0.764	SUBCLONAL	1	TRUE	0	0.346184698331925	1		814	722	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0024764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	257	605	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.346184698331925	2		605	1004	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656969	47656969	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779075	NA	P-0024764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	73	409	1	ENST00000233146.2:c.1165C>T	p.Arg389Ter	p.R389*	ENST00000233146	NM_000251.2	389	Cga/Tga	7/16	0.175182219062368	1	FACETS	0.478	0.417	0.543	0.478	0.417	0.543	INDETERMINATE	1	TRUE	0	0.346184698331925	1		410	730	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78425869	78425869	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	38	374	0	ENST00000370768.2:c.1576G>A	p.Ala526Thr	p.A526T	ENST00000370768	NM_003902.3	526	Gct/Act	16/20	1	2	FACETS	0.305	0.251	0.366	0.305	0.251	0.366	SUBCLONAL	1	TRUE	1	0.346184698331925	2		374	719	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528119	103528119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55798001	NA	P-0024764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	33	361	0	ENST00000355739.4:c.3427G>A	p.Ala1143Thr	p.A1143T	ENST00000355739	NM_000123.3	1143	Gcg/Acg	15/15	1	2	FACETS	0.321	0.26	0.389	0.321	0.26	0.389	SUBCLONAL	1	TRUE	1	0.346184698331925	2		361	594	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41962101	41962101	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	101	416	0	ENST00000219905.7:c.1009G>A	p.Asp337Asn	p.D337N	ENST00000219905	NM_001164273.1	337	Gat/Aat	2/24	0.320175498870961	1	FACETS	0.757	0.678	0.842	0.757	0.678	0.842	SUBCLONAL	1	TRUE	0	0.346184698331925	1		416	637	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212170	5212170	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1242977508	NA	P-0024764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	114	623	0	ENST00000357368.4:c.4861G>T	p.Val1621Leu	p.V1621L	ENST00000357368	NM_002850.3	1621	Gtg/Ttg	32/38	1	2	FACETS	0.8	0.72	0.885	0.8	0.72	0.885	SUBCLONAL	1	TRUE	1	0.346184698331925	2		623	823	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299124	15299124	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	155	563	0	ENST00000263388.2:c.1414G>C	p.Glu472Gln	p.E472Q	ENST00000263388	NM_000435.2	472	Gag/Cag	9/33	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.346184698331925	2		563	825	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971733	18971733	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	102	529	1	ENST00000262803.5:c.2399G>T	p.Arg800Leu	p.R800L	ENST00000262803	NM_002911.3	800	cGc/cTc	17/24	1	2	FACETS	0.929	0.833	1	0.929	0.833	1	CLONAL	1	TRUE	1	0.346184698331925	2		530	634	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391150	89391150	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	91	455	1	ENST00000336596.2:c.1216A>T	p.Thr406Ser	p.T406S	ENST00000336596	NM_005233.5	406	Acc/Tcc	5/17	0.248412296037544	2	FACETS	0.59	0.523	0.662	0.295	0.261	0.331	SUBCLONAL	1	TRUE	0	0.346184698331925	2		456	891	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270140	66270140	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	162	415	0	ENST00000273854.3:c.1742T>C	p.Val581Ala	p.V581A	ENST00000273854	NM_004439.5	581	gTg/gCg	8/18	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.346184698331925	2		415	765	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553742	106553742	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	52	442	1	ENST00000369096.4:c.1707G>T	p.Gln569His	p.Q569H	ENST00000369096	NM_001198.3	569	caG/caT	5/7	1	2	FACETS	0.405	0.344	0.473	0.405	0.344	0.473	SUBCLONAL	1	TRUE	1	0.346184698331925	2		443	741	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372722	81372722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	73	419	0	ENST00000222390.5:c.812G>A	p.Cys271Tyr	p.C271Y	ENST00000222390	NM_000601.4	271	tGc/tAc	7/18	1	2	FACETS	0.662	0.579	0.752	0.662	0.579	0.752	SUBCLONAL	1	TRUE	1	0.346184698331925	2		419	637	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396497	139396497	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	86	608	0	ENST00000277541.6:c.5428C>T	p.Gln1810Ter	p.Q1810*	ENST00000277541	NM_017617.3	1810	Cag/Tag	29/34	0.175182219062368	1	FACETS	0.548	0.484	0.616	0.548	0.484	0.616	INDETERMINATE	1	TRUE	0	0.346184698331925	1		608	750	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0024765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	191	430	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.209219605140835	3	FACETS	1	0.99	1	0.731	0.677	0.787	INDETERMINATE	1	TRUE	1	0.392745353304308	3		430	796	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0024765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	177	535	2	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.392745353304308	1	FACETS	0.994	0.918	1	0.994	0.918	1	CLONAL	1	TRUE	0	0.392745353304308	1		537	729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0024765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	295	637	0	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	0.330704168097726	2	FACETS	0.847	0.799	0.895	0.847	0.799	0.895	CLONAL	2	TRUE	0	0.392745353304308	2		637	887	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052632	42052632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779811318	NA	P-0024765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	183	524	2	ENST00000219905.7:c.7303C>T	p.Arg2435Trp	p.R2435W	ENST00000219905	NM_001164273.1	2435	Cgg/Tgg	20/24	1	2	FACETS	0.998	0.921	1	0.998	0.921	1	CLONAL	1	TRUE	1	0.392745353304308	2		526	934	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037403	12037403	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	245	623	0	ENST00000396373.4:c.1034T>C	p.Val345Ala	p.V345A	ENST00000396373	NM_001987.4	345	gTc/gCc	6/8	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.392745353304308	2		623	1193	SUCCESS
AR	367	MSKCC	GRCh37	X	66766444	66766444	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	25	327	0	ENST00000374690.3:c.1456C>A	p.Pro486Thr	p.P486T	ENST00000374690	NM_000044.3	486	Ccc/Acc	1/8	0.392745353304308	1	FACETS	0.265	0.208	0.33	0.265	0.208	0.33	SUBCLONAL	1	TRUE	0	0.392745353304308	1		327	386	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286540	33286540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	156	518	0	ENST00000374542.5:c.2203G>A	p.Val735Met	p.V735M	ENST00000374542	NM_001141970.1	735	Gtg/Atg	8/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.547873416445305	2		518	524	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663151	227663151	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377203122	NA	P-0024766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	97	669	1	ENST00000305123.5:c.304G>A	p.Glu102Lys	p.E102K	ENST00000305123	NM_005544.2	102	Gag/Aag	1/2	0.547873416445305	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.547873416445305	1		670	230	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541334	187541334	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	112	445	0	ENST00000441802.2:c.6406del	p.Ser2136HisfsTer2	p.S2136Hfs*2	ENST00000441802	NM_005245.3	2136	Tca/ca	10/27	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.547873416445305	2		445	406	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324486	31324486	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs41540113	NA	P-0024766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	104	697	0	ENST00000412585.2:c.322T>G	p.Tyr108Asp	p.Y108D	ENST00000412585	NM_005514.6	108	Tac/Gac	2/8	1	2	FACETS	0.855	0.77	0.944	0.855	0.77	0.944	CLONAL	1	TRUE	1	0.547873416445305	2		697	444	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68973000	68973000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1261578482	NA	P-0024766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	98	447	0	ENST00000288368.4:c.1325G>A	p.Gly442Glu	p.G442E	ENST00000288368	NM_024870.2	442	gGa/gAa	11/40	0.547873416445305	3	FACETS	0.902	0.808	1	0.451	0.404	0.501	CLONAL	1	TRUE	1	0.547873416445305	3		447	505	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240726	53240726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	163	369	0	ENST00000375401.3:c.1354G>A	p.Gly452Ser	p.G452S	ENST00000375401	NM_004187.3	452	Ggt/Agt	10/26	1	1	FACETS	0.828	0.78	0.874	1	0.993	1	CLONAL	2	TRUE	0	0.547873416445305	1		369	261	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0024767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	108	439	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.423732905736346	0	FACETS		NA	1			1	NA	3	FALSE	0	0.423732905736346	0		439	145	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606262	93606262	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	121	503	0	ENST00000375746.1:c.82T>G	p.Tyr28Asp	p.Y28D	ENST00000375746	NM_001174167.1	28	Tac/Gac	2/14	0.118595330379816	1	FACETS	0.753	0.691	0.816	1	0.987	1	INDETERMINATE	2	FALSE	0	0.423732905736346	1		503	299	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	47	510	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.987	0.835	1	0.987	0.835	1	CLONAL	1	TRUE	1	0.242270745735088	2		510	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0024768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	94	466	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.219853168769256	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.242270745735088	1		466	542	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0024768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	49	430	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.874	0.741	1	0.874	0.741	1	CLONAL	1	TRUE	1	0.242270745735088	2		430	463	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444317	50444317	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	51	278	0	ENST00000331340.3:c.247C>T	p.Arg83Ter	p.R83*	ENST00000331340	NM_006060.4	83	Cga/Tga	4/8	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.242270745735088	2		278	418	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0024768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	61	298	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.242270745735088	2		298	474	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574678	41574679	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs754418509	NA	P-0024768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	84	553	4	ENST00000263253.7:c.6970dup	p.His2324ProfsTer55	p.H2324Pfs*55	ENST00000263253	NM_001429.3	2321	-/C	31/31	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.242270745735088	2		557	657	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829788	76829788	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	55	254	0	ENST00000373344.5:c.6253C>T	p.Arg2085Cys	p.R2085C	ENST00000373344	NM_000489.3	2085	Cgt/Tgt	28/35	1	1	FACETS	0.762	0.657	0.873	1	0.969	1	SUBCLONAL	2	TRUE	0	0.242270745735088	1		254	262	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832068	72832073	+	inframe_deletion	In_Frame_Del	DEL	GGCTCT	GGCTCT	-	novel	NA	P-0024768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	71	433	0	ENST00000268489.5:c.4508_4513del	p.Gln1503_Ser1504del	p.Q1503_S1504del	ENST00000268489	NM_006885.3	1503	cAGAGCCca/cca	9/10	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.242270745735088	2		433	572	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78519586	78519586	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	40	321	0	ENST00000306801.3:c.157G>T	p.Asp53Tyr	p.D53Y	ENST00000306801	NM_020761.2	53	Gat/Tat	1/34	1	2	FACETS	0.786	0.654	0.933	0.786	0.654	0.933	CLONAL	1	TRUE	1	0.242270745735088	2		321	420	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281237	142281237	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	41	431	0	ENST00000350721.4:c.1007G>T	p.Arg336Leu	p.R336L	ENST00000350721	NM_001184.3	336	cGg/cTg	4/47	1	2	FACETS	0.639	0.531	0.758	0.639	0.531	0.758	SUBCLONAL	1	TRUE	1	0.242270745735088	2		431	530	SUCCESS
APC	324	MSKCC	GRCh37	5	112174223	112174223	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	49	346	0	ENST00000257430.4:c.2932del	p.Gln978LysfsTer2	p.Q978Kfs*2	ENST00000257430	NM_000038.5	978	Caa/aa	16/16	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.242270745735088	2		346	395	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0024769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	43	810	3	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	FALSE	1	0.409051032715401	2		813	191	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0024769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	48	403	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.886	0.754	1	0.886	0.754	1	CLONAL	1	FALSE	1	0.409051032715401	2		403	265	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221708	22221709	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCG	rs751880548	NA	P-0024769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	23	118	4	ENST00000215832.6:c.20_22dup	p.Ala7dup	p.A7dup	ENST00000215832	NM_002745.4	7	ggc/gCGGgc	1/9	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	FALSE	1	0.409051032715401	2		122	96	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579589	7579589	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	52	570	1	ENST00000269305.4:c.98C>T	p.Ser33Phe	p.S33F	ENST00000269305	NM_001126112.2	33	tCc/tTc	4/11	1	2	FACETS	0.689	0.589	0.798	0.689	0.589	0.798	SUBCLONAL	1	FALSE	1	0.409051032715401	2		571	369	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8338947	8338947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	12	565	0	ENST00000356435.5:c.5354G>A	p.Arg1785Lys	p.R1785K	ENST00000356435		1785	aGg/aAg	32/35	1	2	FACETS	0.422	0.298	0.573	0.422	0.298	0.573	SUBCLONAL	1	FALSE	1	0.409051032715401	2		565	139	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199583	16199583	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	61	511	1	ENST00000375759.3:c.356C>T	p.Pro119Leu	p.P119L	ENST00000375759	NM_015001.2	119	cCa/cTa	2/15	1	2	FACETS	0.722	0.625	0.827	0.722	0.625	0.827	SUBCLONAL	1	FALSE	1	0.409051032715401	2		512	413	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472664	88472664	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs56300182	NA	P-0024769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	50	333	0	ENST00000360948.2:c.1891G>A	p.Ala631Thr	p.A631T	ENST00000360948	NM_001012338.2	631	Gcc/Acc	16/19	1	2	FACETS	0.867	0.741	1	0.867	0.741	1	CLONAL	1	FALSE	1	0.409051032715401	2		333	282	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108869	2108869	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	130	719	0	ENST00000219476.3:c.970T>C	p.Tyr324His	p.Y324H	ENST00000219476	NM_000548.3	324	Tac/Cac	10/42	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	FALSE	1	0.409051032715401	2		719	627	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72863699	72863699	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	88	724	0	ENST00000268489.5:c.3508G>T	p.Ala1170Ser	p.A1170S	ENST00000268489	NM_006885.3	1170	Gct/Tct	5/10	1	2	FACETS	0.809	0.718	0.905	0.809	0.718	0.905	CLONAL	1	FALSE	1	0.409051032715401	2		724	532	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265615	10265616	+	missense_variant	Missense_Mutation	DNP	TC	TC	GT	novel	NA	P-0024769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	89	658	0	ENST00000340748.4:c.1561_1562delinsAC	p.Asp521Thr	p.D521T	ENST00000340748		521	GAc/ACc	19/40	1	2	FACETS	0.91	0.81	1	0.91	0.81	1	CLONAL	1	FALSE	1	0.409051032715401	2		658	478	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354020	15354020	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	12	302	1	ENST00000263377.2:c.2860C>A	p.Pro954Thr	p.P954T	ENST00000263377	NM_058243.2	954	Ccc/Acc	14/20	1	2	FACETS	0.249	0.174	0.34	0.249	0.174	0.34	SUBCLONAL	1	FALSE	1	0.409051032715401	2		303	236	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306628	41306628	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	79	738	0	ENST00000373198.4:c.1031A>G	p.Asn344Ser	p.N344S	ENST00000373198	NM_133170.3	344	aAc/aGc	7/32	1	2	FACETS	0.905	0.799	1	0.905	0.799	1	CLONAL	1	FALSE	1	0.409051032715401	2		738	427	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965332	68965332	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	16	481	0	ENST00000288368.4:c.944C>T	p.Ala315Val	p.A315V	ENST00000288368	NM_024870.2	315	gCt/gTt	9/40	1	2	FACETS	0.889	0.669	1	0.889	0.669	1	CLONAL	1	FALSE	1	0.409051032715401	2		481	88	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265615	10265615	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	87	648	0	ENST00000340748.4:c.1562A>C	p.Asp521Ala	p.D521A	ENST00000340748		521	gAc/gCc	19/40	1	2	FACETS	0.896	0.796	1	0.896	0.796	1	CLONAL	1	FALSE	1	0.409051032715401	2		648	475	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265616	10265616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767797868	NA	P-0024769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	89	658	0	ENST00000340748.4:c.1561G>A	p.Asp521Asn	p.D521N	ENST00000340748		521	Gac/Aac	19/40	1	2	FACETS	0.91	0.81	1	0.91	0.81	1	CLONAL	1	FALSE	1	0.409051032715401	2		658	478	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835794	68835794	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	141	523	1	ENST00000261769.5:c.385C>T	p.Gln129Ter	p.Q129*	ENST00000261769	NM_004360.3	129	Cag/Tag	3/16	0.479229909733233	1	FACETS	0.753	0.699	0.808	1	0.99	1	SUBCLONAL	2	TRUE	0	0.479229909733233	1		524	297	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884834	111884834	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs181079548	NA	P-0024773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	27	413	2	ENST00000341259.2:c.923G>A	p.Arg308Gln	p.R308Q	ENST00000341259	NM_005475.2	308	cGa/cAa	4/8	0.45474753302292	3	FACETS	0.55	0.439	0.676	0.183	0.146	0.226	SUBCLONAL	1	TRUE	0	0.479229909733233	3		415	254	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs878854073	NA	P-0024775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	132	318	0	ENST00000269305.4:c.673-1G>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.280385702310547	1	FACETS	0.818	0.742	0.897	0.818	0.742	0.897	CLONAL	1	TRUE	0	0.321340390278214	1		318	843	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121913370	NA	P-0024775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	63	340	0	ENST00000288602.6:c.1742A>G	p.Asn581Ser	p.N581S	ENST00000288602	NM_004333.4	581	aAt/aGt	15/18	1	2	FACETS	0.834	0.723	0.954	0.834	0.723	0.954	CLONAL	1	TRUE	1	0.321340390278214	2		340	470	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25462022	25462022	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	186	604	1	ENST00000264709.3:c.2385G>T	p.Trp795Cys	p.W795C	ENST00000264709	NM_175629.2	795	tgG/tgT	20/23	NA	2	FACETS	1	0.962	1			1	INDETERMINATE	1	TRUE	NA	0.321340390278214	2		605	1084	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526161	189526161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	217	615	0	ENST00000264731.3:c.425G>A	p.Ser142Asn	p.S142N	ENST00000264731	NM_003722.4	142	aGc/aAc	4/14	0.227876713664793	3	FACETS	1	0.98	1	0.573	0.532	0.617	CLONAL	1	TRUE	1	0.321340390278214	3		615	1367	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970901	21970901	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs45476696	NA	P-0024775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	151	750	0	ENST00000304494.5:c.457G>T	p.Asp153Tyr	p.D153Y	ENST00000304494	NM_000077.4	153	Gac/Tac	2/3	0.321340390278214	1	FACETS	0.733	0.669	0.8	0.733	0.669	0.8	SUBCLONAL	1	TRUE	0	0.321340390278214	1		750	1076	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589841	69589841	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	10	79	0	ENST00000168712.1:c.12del	p.Thr6ArgfsTer4	p.T6Rfs*4	ENST00000168712	NM_002007.2	4	ccC/cc	1/3	1	2	FACETS	0.506	0.344	0.707	0.506	0.344	0.707	SUBCLONAL	1	TRUE	1	0.321340390278214	2		79	123	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347353	89347353	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	209	713	1	ENST00000301030.4:c.5597A>T	p.His1866Leu	p.H1866L	ENST00000301030	NM_001256183.1	1866	cAc/cTc	9/13	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.321340390278214	2		714	1248	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989502	212989502	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	67	445	1	ENST00000342788.4:c.209A>T	p.His70Leu	p.H70L	ENST00000342788	NM_005235.2	70	cAc/cTc	2/28	0.321340390278214	1	FACETS	0.448	0.388	0.512	0.448	0.388	0.512	SUBCLONAL	1	TRUE	0	0.321340390278214	1		446	782	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023946	31023946	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs758535168	NA	P-0024775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	160	579	0	ENST00000375687.4:c.3431A>G	p.His1144Arg	p.H1144R	ENST00000375687	NM_015338.5	1144	cAt/cGt	13/13	0.150895230440793	3	FACETS	1	0.923	1			1	INDETERMINATE	1	TRUE	NA	0.321340390278214	3		579	1146	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851759	134851759	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	116	558	0	ENST00000398015.3:c.1165T>A	p.Cys389Ser	p.C389S	ENST00000398015	NM_004441.4	389	Tgc/Agc	5/16	0.227876713664793	3	FACETS	0.807	0.726	0.893	0.404	0.363	0.447	CLONAL	1	TRUE	1	0.321340390278214	3		558	1038	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224590	224590	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	151	553	1	ENST00000264932.6:c.266G>T	p.Cys89Phe	p.C89F	ENST00000264932	NM_004168.2	89	tGt/tTt	3/15	0.227876713664793	3	FACETS	0.917	0.837	1	0.459	0.418	0.501	CLONAL	1	TRUE	1	0.321340390278214	3		554	1189	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617629	100617629	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	157	745	0	ENST00000308731.7:c.440G>T	p.Trp147Leu	p.W147L	ENST00000308731	NM_000061.2	147	tGg/tTg	6/19	0.321340390278214	1	FACETS	0.808	0.739	0.88	0.808	0.739	0.88	CLONAL	1	TRUE	0	0.321340390278214	1		745	1015	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0024775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	370	814	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.408017673957409	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.409510741237879	2		814	858	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047507	49047507	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0024775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	160	462	0	ENST00000267163.4:c.2501C>G	p.Ser834Ter	p.S834*	ENST00000267163	NM_000321.2	834	tCa/tGa	24/27	0.397641646948618	3	FACETS	0.937	0.873	1	0.937	0.873	1	CLONAL	3	TRUE	0	0.409510741237879	3		462	335	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561289	9561289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985722631	NA	P-0024775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	38	521	0	ENST00000353224.5:c.493G>A	p.Ala165Thr	p.A165T	ENST00000353224	NM_177990.2	165	Gca/Aca	4/10	0.409510741237879	3	FACETS	0.376	0.31	0.45	0.188	0.155	0.225	SUBCLONAL	1	TRUE	1	0.409510741237879	3		521	594	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670364	246670364	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	94	461	0	ENST00000388985.4:c.156C>G	p.Cys52Trp	p.C52W	ENST00000388985		52	tgC/tgG	1/12	0.409510741237879	5	FACETS	0.974	0.866	1	0.325	0.288	0.363	CLONAL	1	TRUE	2	0.409510741237879	5		461	761	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112910760	112910760	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	96	528	0	ENST00000351677.2:c.769C>A	p.Gln257Lys	p.Q257K	ENST00000351677	NM_002834.3	257	Cag/Aag	7/16	0.409510741237879	3	FACETS	0.962	0.859	1	0.481	0.429	0.536	CLONAL	1	TRUE	1	0.409510741237879	3		528	587	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560479	65560505	+	inframe_deletion	In_Frame_Del	DEL	TGATGTGGTCCCTACGTTTTCGTTCCA	TGATGTGGTCCCTACGTTTTCGTTCCA	-	novel	NA	P-0024775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	196	500	0	ENST00000358664.4:c.92_118del	p.Leu31_Lys40delinsGln	p.L31_K40delinsQ	ENST00000358664	NM_002382.4	31	cTGGAACGAAAACGTAGGGACCACATCAaa/caa	3/5	0.409510741237879	3	FACETS	1	0.958	1	0.691	0.645	0.739	CLONAL	2	TRUE	0	0.409510741237879	3		500	556	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562683	29562683	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060500308	NA	P-0024775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	176	636	0	ENST00000356175.3:c.3763C>T	p.Gln1255Ter	p.Q1255*	ENST00000356175	NM_000267.3	1255	Caa/Taa	28/57	0.409510741237879	4	FACETS	0.848	0.784	0.915	0.848	0.784	0.915	CLONAL	2	TRUE	2	0.409510741237879	4		636	714	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685497	29685497	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0024775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	51	314	0	ENST00000356175.3:c.7908-1G>C		p.X2636_splice	ENST00000356175	NM_000267.3	2636			0.409510741237879	4	FACETS	0.86	0.741	0.988	0.86	0.741	0.988	CLONAL	2	TRUE	2	0.409510741237879	4		314	204	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127382	55127382	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	196	714	2	ENST00000257290.5:c.170G>A	p.Trp57Ter	p.W57*	ENST00000257290	NM_006206.4	57	tGg/tAg	3/23	0.25108831363196	5	FACETS	0.914	0.848	0.983	0.61	0.565	0.656	CLONAL	2	TRUE	2	0.409510741237879	5		716	845	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400267	139400267	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	247	796	1	ENST00000277541.6:c.4081G>A	p.Gly1361Ser	p.G1361S	ENST00000277541	NM_017617.3	1361	Ggc/Agc	25/34	0.409510741237879	5	FACETS	0.78	0.728	0.834	0.52	0.485	0.556	SUBCLONAL	2	TRUE	2	0.409510741237879	5		797	1248	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409899	63409899	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	66	367	0	ENST00000330258.3:c.3268G>T	p.Val1090Phe	p.V1090F	ENST00000330258	NM_152424.3	1090	Gtc/Ttc	2/2	0.409510741237879	3	FACETS	0.781	0.679	0.891	0.391	0.339	0.446	SUBCLONAL	1	TRUE	1	0.409510741237879	3		367	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0024776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	69	671	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.28344326072033	1	FACETS	0.528	0.46	0.602	0.528	0.46	0.602	SUBCLONAL	1	TRUE	0	0.371217232300648	1		671	573	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444975	49444975	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	26	554	0	ENST00000301067.7:c.2491T>A	p.Ser831Thr	p.S831T	ENST00000301067	NM_003482.3	831	Tca/Aca	10/54	1	2	FACETS	0.373	0.295	0.462	0.373	0.295	0.462	SUBCLONAL	1	TRUE	1	0.371217232300648	2		554	376	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236601	236602	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCC	novel	NA	P-0024776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	17	237	0	ENST00000264932.6:c.1321_1324dup	p.Ala442GlyfsTer40	p.A442Gfs*40	ENST00000264932	NM_004168.2	440	gag/gaGGCCg	10/15	1	2	FACETS	0.422	0.315	0.548	0.422	0.315	0.548	SUBCLONAL	1	TRUE	1	0.371217232300648	2		237	217	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672321	30672321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	57	709	0	ENST00000376406.3:c.4639G>A	p.Val1547Ile	p.V1547I	ENST00000376406	NM_014641.2	1547	Gtc/Atc	10/15	1	2	FACETS	0.486	0.416	0.562	0.486	0.416	0.562	SUBCLONAL	1	TRUE	1	0.371217232300648	2		709	632	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183626	185183626	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	26	612	0	ENST00000265026.3:c.1480G>C	p.Glu494Gln	p.E494Q	ENST00000265026	NM_004721.4	494	Gaa/Caa	9/14	1	2	FACETS	0.567	0.448	0.703	0.567	0.448	0.703	SUBCLONAL	1	TRUE	1	0.208042329819177	2		612	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0024786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	389	708	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.38326435115443	2	FACETS	0.967	0.922	1	0.967	0.922	1	CLONAL	2	TRUE	0	0.415160495014856	2		708	969	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458612	120458612	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	158	577	0	ENST00000256646.2:c.6733del	p.His2245IlefsTer10	p.H2245Ifs*10	ENST00000256646	NM_024408.3	2245	Cat/at	34/34	1	2	FACETS	0.995	0.913	1	0.995	0.913	1	CLONAL	1	TRUE	1	0.415160495014856	2		577	765	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798142	32798142	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	164	629	0	ENST00000374899.4:c.1537G>C	p.Ala513Pro	p.A513P	ENST00000374899	NM_018833.2	513	Gct/Cct	9/12	1	2	FACETS	0.948	0.871	1	0.948	0.871	1	CLONAL	1	TRUE	1	0.415160495014856	2		629	833	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601945	43601945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80236571	NA	P-0024788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	30	648	1	ENST00000355710.3:c.989G>A	p.Arg330Gln	p.R330Q	ENST00000355710	NM_020975.4	330	cGg/cAg	5/20	0.419543031138296	1	FACETS	0.207	0.166	0.254	0.207	0.166	0.254	SUBCLONAL	1	TRUE	0	0.419543031138296	1		649	546	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680651	88680651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	72	487	1	ENST00000360948.2:c.606G>A	p.Met202Ile	p.M202I	ENST00000360948	NM_001012338.2	202	atG/atA	6/19	0.123732866796914	3	FACETS	0.693	0.606	0.787	0.231	0.202	0.263	INDETERMINATE	1	TRUE	0	0.419543031138296	3		488	599	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610174	10610174	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	109	670	0	ENST00000171111.5:c.536T>G	p.Leu179Arg	p.L179R	ENST00000171111	NM_203500.1	179	cTg/cGg	2/6	0.403295854811473	0	FACETS	0.491	0.442	0.543			1	SUBCLONAL	1	TRUE	0	0.419543031138296	0		670	614	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046481	69046481	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	40	621	0	ENST00000288368.4:c.3954T>G	p.Phe1318Leu	p.F1318L	ENST00000288368	NM_024870.2	1318	ttT/ttG	32/40	1	2	FACETS	0.296	0.245	0.353	0.296	0.245	0.353	SUBCLONAL	1	TRUE	1	0.419543031138296	2		621	644	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0024789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	58	392	0	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	0.755546259473365	2	FACETS	0.401	0.346	0.461	0.2	0.173	0.231	SUBCLONAL	1	FALSE	0	0.755546259473365	2		392	383	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231238	98231238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1366288601	NA	P-0024789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	107	578	0	ENST00000331920.6:c.2045G>A	p.Arg682His	p.R682H	ENST00000331920	NM_000264.3	682	cGc/cAc	14/24	0.723089522656272	3	FACETS	0.604	0.543	0.669	0.201	0.181	0.223	SUBCLONAL	1	FALSE	0	0.755546259473365	3		578	646	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439793	52439793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	89	530	1	ENST00000460680.1:c.919G>A	p.Gly307Ser	p.G307S	ENST00000460680	NM_004656.3	307	Ggc/Agc	10/17	0.755546259473365	2	FACETS	0.455	0.404	0.508	0.227	0.202	0.254	SUBCLONAL	1	FALSE	0	0.755546259473365	2		531	518	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137540398	137540398	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	165	441	0	ENST00000367739.4:c.67G>T	p.Asp23Tyr	p.D23Y	ENST00000367739	NM_000416.2	23	Gat/Tat	1/7	0.720083613650324	3	FACETS	0.802	0.747	0.858	0.535	0.498	0.572	CLONAL	2	FALSE	0	0.755546259473365	3		441	375	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050713	30050713	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	87	297	0	ENST00000338641.4:c.516+1del		p.R172fs	ENST00000338641	NM_000268.3	172	aGg/ag	5/16	0.639563554019165	1	FACETS	0.935	0.847	1	0.935	0.847	1	CLONAL	1	TRUE	0	0.639563554019165	1		297	198	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	40	314	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.991	0.827	1	0.991	0.827	1	CLONAL	1	TRUE	1	0.27	2		314	299	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	67	510	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	0.27	2		510	456	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806092	1806092	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913484	NA	P-0024795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	57	554	0	ENST00000260795.2:c.1111A>T	p.Ser371Cys	p.S371C	ENST00000260795		371	Agt/Tgt	8/17	1	2	FACETS	0.865	0.743	0.998	0.865	0.743	0.998	CLONAL	1	TRUE	1	0.27	2		554	488	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519893	NA	P-0024795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	70	649	0	ENST00000267101.3:c.310G>T	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ttg	3/28	1	2	FACETS	0.823	0.718	0.937	0.823	0.718	0.937	CLONAL	1	TRUE	1	0.27	2		649	630	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566488	41566488	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	55	543	0	ENST00000263253.7:c.4365G>C	p.Gln1455His	p.Q1455H	ENST00000263253	NM_001429.3	1455	caG/caC	27/31	1	2	FACETS	0.886	0.759	1	0.886	0.759	1	CLONAL	1	TRUE	1	0.27	2		543	460	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969327	44969327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	64	420	0	ENST00000377967.4:c.4009G>A	p.Glu1337Lys	p.E1337K	ENST00000377967	NM_021140.2	1337	Gag/Aag	28/29	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.27	2		420	384	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790455	3790455	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783490	NA	P-0024795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	66	497	0	ENST00000262367.5:c.4078C>T	p.Arg1360Ter	p.R1360*	ENST00000262367	NM_004380.2	1360	Cga/Tga	24/31	1	2	FACETS	0.98	0.852	1	0.98	0.852	1	CLONAL	1	TRUE	1	0.27	2		497	499	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200024	123200024	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0024795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	29	165	0	ENST00000218089.9:c.2097-1G>A		p.X699_splice	ENST00000218089	NM_001042749.1	699			1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.27	2		165	155	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214596	5214596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	60	498	2	ENST00000357368.4:c.4470G>A	p.Met1490Ile	p.M1490I	ENST00000357368	NM_002850.3	1490	atG/atA	29/38	1	2	FACETS	0.884	0.762	1	0.884	0.762	1	CLONAL	1	TRUE	1	0.27	2		500	503	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976852	18976852	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0024795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	41	455	0	ENST00000262803.5:c.3238-1G>C		p.X1080_splice	ENST00000262803	NM_002911.3	1080			1	2	FACETS	0.868	0.725	1	0.868	0.725	1	CLONAL	1	TRUE	1	0.27	2		455	350	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1940242	1940242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746362705	NA	P-0024795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	62	367	2	ENST00000382891.5:c.1739C>T	p.Ser580Leu	p.S580L	ENST00000382891	NM_133335.3	580	tCg/tTg	8/22	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.27	2		369	375	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519130	187519130	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	64	421	0	ENST00000441802.2:c.12253C>T	p.Gln4085Ter	p.Q4085*	ENST00000441802	NM_005245.3	4085	Cag/Tag	23/27	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.27	2		421	463	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539973	187539973	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	42	452	0	ENST00000441802.2:c.7767C>G	p.Asp2589Glu	p.D2589E	ENST00000441802	NM_005245.3	2589	gaC/gaG	10/27	1	2	FACETS	0.804	0.672	0.949	0.804	0.672	0.949	CLONAL	1	TRUE	1	0.27	2		452	387	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966782	44966782	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0024795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	68	615	0	ENST00000377967.4:c.4005+1G>A		p.X1335_splice	ENST00000377967	NM_021140.2	1335			1	2	FACETS	0.95	0.828	1	0.95	0.828	1	CLONAL	1	TRUE	1	0.27	2		615	530	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260483	16260483	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	164	332	0	ENST00000375759.3:c.7749del	p.Glu2584LysfsTer7	p.E2584Kfs*7	ENST00000375759	NM_015001.2	2583	gAa/ga	11/15	1	2	FACETS	0.881	0.819	0.944	0.881	0.819	0.944	CLONAL	1	TRUE	1	0.954624924598631	2		332	390	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115920	8115920	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	410	363	0	ENST00000346208.3:c.1266del	p.Met422IlefsTer53	p.M422Ifs*53	ENST00000346208		422	atG/at	6/6	0.954624924598631	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.954624924598631	3		363	600	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572583	64572583	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	236	587	0	ENST00000312049.6:c.1273G>T	p.Glu425Ter	p.E425*	ENST00000312049	NM_130799.2	425	Gag/Tag	9/10	0.932458273615569	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.954624924598631	1		587	252	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011115	12011115	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0024796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	242	423	0	ENST00000353533.5:c.522T>A	p.Cys174Ter	p.C174*	ENST00000353533	NM_003010.3	174	tgT/tgA	5/11	0.917624529781117	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.954624924598631	1		423	253	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20153856	20153857	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	252	402	0	ENST00000379607.5:c.203dup	p.Val69GlyfsTer19	p.V69Gfs*19	ENST00000379607	NM_001412.3	68	aag/aaAg	3/7	1	2	FACETS	0.895	0.844	0.946	0.895	0.844	0.946	CLONAL	1	TRUE	1	0.954624924598631	2		402	590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579440	7579440	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs867725248	NA	P-0024798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	478	515	0	ENST00000269305.4:c.247del	p.Ala83ArgfsTer40	p.A83Rfs*40	ENST00000269305	NM_001126112.2	83	Gcg/cg	4/11	0.929100315422868	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.929100315422868	1		515	536	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374783	118374783	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	238	344	0	ENST00000534358.1:c.8176G>T	p.Gly2726Trp	p.G2726W	ENST00000534358	NM_005933.3	2726	Ggg/Tgg	27/36	1	2	FACETS	0.976	0.921	1	0.976	0.921	1	CLONAL	1	TRUE	1	0.929100315422868	2		344	525	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497570	125497570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs760734978	NA	P-0024798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	340	316	0	ENST00000428830.2:c.134C>A	p.Ala45Asp	p.A45D	ENST00000428830	NM_001114121.2	45	gCc/gAc	3/14	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.929100315422868	2		316	641	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428447	72428447	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	502	566	1	ENST00000477973.2:c.557A>T	p.Glu186Val	p.E186V	ENST00000477973	NM_012234.5	186	gAa/gTa	2/4	0.929100315422868	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.929100315422868	1		567	559	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158417	106158417	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	228	255	0	ENST00000380013.4:c.3318G>T	p.Glu1106Asp	p.E1106D	ENST00000380013	NM_001127208.2	1106	gaG/gaT	3/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.929100315422868	2		255	481	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293958	1293958	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	1071	624	2	ENST00000310581.5:c.1043G>T	p.Ser348Ile	p.S348I	ENST00000310581	NM_198253.2	348	aGc/aTc	2/16	0.929100315422868	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.929100315422868	3		626	1663	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674347	86674347	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	17	297	0	ENST00000274376.6:c.2479T>C	p.Ser827Pro	p.S827P	ENST00000274376	NM_002890.2	827	Tct/Cct	18/25	0.929100315422868	1	FACETS	0.066	0.049	0.086	0.066	0.049	0.086	SUBCLONAL	1	TRUE	0	0.929100315422868	1		297	297	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057770	180057770	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	322	342	0	ENST00000261937.6:c.185C>A	p.Pro62Gln	p.P62Q	ENST00000261937	NM_182925.4	62	cCa/cAa	3/30	0.929100315422868	1	FACETS	0.995	0.969	1	0.995	0.969	1	CLONAL	1	TRUE	0	0.929100315422868	1		342	373	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0024799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	18	364	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.203036743996442	5	FACETS	0.841	0.657	1	0.841	0.657	1	INDETERMINATE	3	TRUE	2	0.41210516746777	5		364	56	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0024799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	32	212	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	0.399663931577716	3	FACETS	0.9	0.782	1	1	0.944	1	CLONAL	4	TRUE	0	0.41210516746777	3		212	52	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139220	108139221	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	30	489	0	ENST00000278616.4:c.2723dup	p.Thr909AsnfsTer11	p.T909Nfs*11	ENST00000278616	NM_000051.3	908	gta/gTta	18/63	0.41210516746777	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	2	TRUE	0	0.41210516746777	2		489	62	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578525	7578525	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519976	NA	P-0024800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	128	583	0	ENST00000269305.4:c.405C>G	p.Cys135Trp	p.C135W	ENST00000269305	NM_001126112.2	135	tgC/tgG	5/11	1	2	FACETS	0.459	0.415	0.505	0.459	0.415	0.505	SUBCLONAL	1	FALSE	1	0.588519422845118	2		583	948	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466420	120466420	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs552225415	NA	P-0024800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	34	473	1	ENST00000256646.2:c.4699C>T	p.Arg1567Trp	p.R1567W	ENST00000256646	NM_024408.3	1567	Cgg/Tgg	26/34	1	2	FACETS	0.173	0.14	0.209	0.173	0.14	0.209	SUBCLONAL	1	FALSE	1	0.588519422845118	2		474	669	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383273	4383273	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	31	383	0	ENST00000261254.3:c.67G>C	p.Asp23His	p.D23H	ENST00000261254	NM_001759.3	23	Gac/Cac	1/5	1	2	FACETS	0.2	0.161	0.245	0.2	0.161	0.245	SUBCLONAL	1	FALSE	1	0.588519422845118	2		383	526	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226090	2226090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316961587	NA	P-0024800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	84	579	0	ENST00000326181.6:c.1787C>T	p.Thr596Met	p.T596M	ENST00000326181	NM_032271.2	596	aCg/aTg	19/21	1	2	FACETS	0.301	0.265	0.34	0.301	0.265	0.34	SUBCLONAL	1	FALSE	1	0.588519422845118	2		579	948	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0024803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	47	364	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.369553095558752	4	FACETS	1	0.886	1	0.352	0.298	0.411	CLONAL	1	TRUE	1	0.369553095558752	4		364	330	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0024803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	130	585	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.220727606267792	4	FACETS	1	0.937	1	0.688	0.628	0.75	INDETERMINATE	2	TRUE	1	0.369553095558752	4		585	467	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0024803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	106	268	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.369553095558752	6	FACETS	0.906	0.82	0.996	0.68	0.615	0.747	CLONAL	3	TRUE	2	0.369553095558752	6		268	367	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247294	153247294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	65	294	1	ENST00000281708.4:c.1508C>T	p.Ala503Val	p.A503V	ENST00000281708	NM_033632.3	503	gCa/gTa	10/12	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.369553095558752	2		295	299	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720669	89720669	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	87	204	0	ENST00000371953.3:c.820T>G	p.Trp274Gly	p.W274G	ENST00000371953	NM_000314.4	274	Tgg/Ggg	8/9	0.369553095558752	4	FACETS	0.907	0.817	1	0.907	0.817	1	CLONAL	3	TRUE	1	0.369553095558752	4		204	237	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150336	108150336	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0024803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	40	292	1	ENST00000278616.4:c.3402+1G>A		p.X1134_splice	ENST00000278616	NM_000051.3	1134			1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.369553095558752	2		293	199	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0024804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	220	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.378027287848689	7	FACETS	0.957	0.901	1	0.798	0.751	0.845	CLONAL	5	TRUE	1	0.378027287848689	7		326	473	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0024804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	61	423	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.378027287848689	3	FACETS	0.957	0.829	1	0.478	0.414	0.548	CLONAL	1	TRUE	1	0.378027287848689	3		423	401	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256320	16256321	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0024804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	35	411	0	ENST00000375759.3:c.3591dup	p.Asp1198ArgfsTer4	p.D1198Rfs*4	ENST00000375759	NM_015001.2	1195	-/A	11/15	1	2	FACETS	0.688	0.567	0.823	0.688	0.567	0.823	SUBCLONAL	1	TRUE	1	0.378027287848689	2		411	269	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066617	94066617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	127	427	0	ENST00000369303.4:c.1142C>T	p.Pro381Leu	p.P381L	ENST00000369303	NM_004440.3	381	cCc/cTc	5/17	0.346829018510349	3	FACETS	1	0.971	1	0.388	0.353	0.425	CLONAL	1	TRUE	0	0.500482200406425	3		427	545	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541024	187541024	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	86	392	0	ENST00000441802.2:c.6716T>A	p.Ile2239Lys	p.I2239K	ENST00000441802	NM_005245.3	2239	aTa/aAa	10/27	1	2	FACETS	0.878	0.781	0.979	0.878	0.781	0.979	CLONAL	1	TRUE	1	0.5	2		392	392	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0024822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	326	585	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.538564406857434	4	FACETS	0.966	0.918	1	0.966	0.918	1	CLONAL	2	TRUE	2	0.80252589578454	4		585	758	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36208923	36208925	+	start_lost,inframe_deletion	Translation_Start_Site	DEL	GGC	GGC	-	rs898578503	NA	P-0024822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	10	36	0	ENST00000222270.7:c.14_16del	p.Ala5?	p.A5?	ENST00000222270	NM_014727.1	1	atGGCg/atg	1/37	0.783565617887572	3	FACETS	0.309	0.21	0.431	0.103	0.07	0.144	SUBCLONAL	1	TRUE	0	0.80252589578454	3		36	113	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432129	49432129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1440	340	803	0	ENST00000301067.7:c.9010G>A	p.Glu3004Lys	p.E3004K	ENST00000301067	NM_003482.3	3004	Gag/Aag	34/54	0.538564406857434	4	FACETS	0.858	0.809	0.909	0.429	0.404	0.455	CLONAL	1	TRUE	2	0.80252589578454	4		803	1780	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023598	31023598	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200702600	NA	P-0024822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	186	612	2	ENST00000375687.4:c.3083C>T	p.Ser1028Leu	p.S1028L	ENST00000375687	NM_015338.5	1028	tCg/tTg	13/13	0.607961324993371	4	FACETS	0.701	0.646	0.758	0.35	0.323	0.379	SUBCLONAL	1	TRUE	2	0.80252589578454	4		614	1192	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602767	10602767	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	1306	937	0	ENST00000171111.5:c.811G>C	p.Val271Leu	p.V271L	ENST00000171111	NM_203500.1	271	Gtg/Ctg	3/6	0.783565617887572	3	FACETS	0.938	0.924	0.952	0.938	0.924	0.952	CLONAL	3	TRUE	0	0.80252589578454	3		937	1620	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821594	72821626	+	inframe_deletion	In_Frame_Del	DEL	GCCGCCGCCGCCGCCGCCGCCGCCACCGCCGCC	GCCGCCGCCGCCGCCGCCGCCGCCACCGCCGCC	-	novel	NA	P-0024822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	24	137	0	ENST00000268489.5:c.10549_10581del	p.Gly3517_Gly3527del	p.G3517_G3527del	ENST00000268489	NM_006885.3	3517	GGCGGCGGTGGCGGCGGCGGCGGCGGCGGCGGC/-	10/10	0.607961324993371	4	FACETS	0.305	0.239	0.382	0.153	0.119	0.191	SUBCLONAL	1	TRUE	2	0.80252589578454	4		137	353	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972490	81972490	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	293	555	0	ENST00000359376.3:c.3283G>T	p.Asp1095Tyr	p.D1095Y	ENST00000359376	NM_002661.3	1095	Gac/Tac	29/33	0.607961324993371	4	FACETS	1	0.94	1	0.5	0.47	0.531	CLONAL	1	TRUE	2	0.80252589578454	4		555	1316	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10266621	10266621	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	49	538	0	ENST00000340748.4:c.1352G>T	p.Gly451Val	p.G451V	ENST00000340748		451	gGt/gTt	18/40	0.783565617887572	3	FACETS	0.198	0.167	0.233	0.066	0.055	0.078	SUBCLONAL	1	TRUE	0	0.80252589578454	3		538	863	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029204	26029204	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	26	389	0	ENST00000435504.4:c.146G>A	p.Gly49Glu	p.G49E	ENST00000435504		49	gGg/gAg	4/13	0.80252589578454	3	FACETS	0.219	0.173	0.272	0.109	0.086	0.136	SUBCLONAL	1	TRUE	1	0.80252589578454	3		389	415	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114184	73114184	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	135	529	0	ENST00000356692.5:c.820G>A	p.Gly274Arg	p.G274R	ENST00000356692		274	Gga/Aga	8/9	0.80252589578454	3	FACETS	0.629	0.573	0.689	0.315	0.286	0.345	SUBCLONAL	1	TRUE	1	0.80252589578454	3		529	749	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146582	185146582	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	248	597	0	ENST00000265026.3:c.213C>A	p.Ser71Arg	p.S71R	ENST00000265026	NM_004721.4	71	agC/agA	2/14	0.80252589578454	3	FACETS	0.927	0.868	0.988	0.464	0.434	0.494	CLONAL	1	TRUE	1	0.80252589578454	3		597	934	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0024823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	144	810	3	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.17906173580813	1	FACETS	0.822	0.749	0.899	0.822	0.749	0.899	INDETERMINATE	1	TRUE	0	0.313322527885605	1		813	943	SUCCESS
APC	324	MSKCC	GRCh37	5	112174152	112174152	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0024823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	43	427	0	ENST00000257430.4:c.2861T>A	p.Leu954Ter	p.L954*	ENST00000257430	NM_000038.5	954	tTa/tAa	16/16	0.17906173580813	1	FACETS	0.423	0.354	0.5	0.423	0.354	0.5	INDETERMINATE	1	TRUE	0	0.313322527885605	1		427	547	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517201	NA	P-0024823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	186	840	0	ENST00000263967.3:c.1637A>C	p.Gln546Pro	p.Q546P	ENST00000263967	NM_006218.2	546	cAg/cCg	10/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.313322527885605	2		840	992	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579390	7579393	+	frameshift_variant	Frame_Shift_Del	DEL	GGAA	GGAA	-	rs730882015	NA	P-0024823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	106	788	1	ENST00000269305.4:c.294_297del	p.Ser99ArgfsTer23	p.S99Rfs*23	ENST00000269305	NM_001126112.2	98	ccTTCC/cc	4/11	0.289517324753693	1	FACETS	0.708	0.634	0.786	0.708	0.634	0.786	SUBCLONAL	1	TRUE	0	0.313322527885605	1		789	806	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216505	2216505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	100	867	1	ENST00000398665.3:c.2149G>A	p.Ala717Thr	p.A717T	ENST00000398665	NM_032482.2	717	Gct/Act	20/28	1	2	FACETS	0.582	0.518	0.65	0.582	0.518	0.65	SUBCLONAL	1	TRUE	1	0.313322527885605	2		868	1097	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426007	138426007	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	58	581	0	ENST00000289153.2:c.1524C>A	p.Phe508Leu	p.F508L	ENST00000289153	NM_006219.2	508	ttC/ttA	9/22	1	2	FACETS	0.455	0.39	0.527	0.455	0.39	0.527	SUBCLONAL	1	TRUE	1	0.313322527885605	2		581	813	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161347	185161347	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	86	731	0	ENST00000265026.3:c.774C>G	p.Asp258Glu	p.D258E	ENST00000265026	NM_004721.4	258	gaC/gaG	4/14	1	2	FACETS	0.567	0.5	0.639	0.567	0.5	0.639	SUBCLONAL	1	TRUE	1	0.313322527885605	2		731	968	SUCCESS
APC	324	MSKCC	GRCh37	5	112174179	112174179	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	50	461	0	ENST00000257430.4:c.2888G>C	p.Ser963Thr	p.S963T	ENST00000257430	NM_000038.5	963	aGt/aCt	16/16	0.17906173580813	1	FACETS	0.468	0.397	0.547	0.468	0.397	0.547	INDETERMINATE	1	TRUE	0	0.313322527885605	1		461	575	SUCCESS
APC	324	MSKCC	GRCh37	5	112175620	112175621	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAAACAGC	novel	NA	P-0024823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	74	349	0	ENST00000257430.4:c.4330_4337dup	p.Gln1447LysfsTer29	p.Q1447Kfs*29	ENST00000257430	NM_000038.5	1443	-/CAAACAGC	16/16	0.17906173580813	1	FACETS	0.832	0.73	0.94	0.832	0.73	0.94	INDETERMINATE	1	TRUE	0	0.313322527885605	1		349	479	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0024824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	84	430	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.0907940657779731	4	FACETS	1	0.955	1	1	0.955	1	INDETERMINATE	2	TRUE	2	0.167498029983875	4		430	505	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419986	41419986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372989163	NA	P-0024824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	46	425	1	ENST00000373198.4:c.335G>A	p.Arg112His	p.R112H	ENST00000373198	NM_133170.3	112	cGt/cAt	3/32	0.167498029983875	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.167498029983875	1		426	358	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0024824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	48	192	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.167498029983875	6	FACETS	0.977	0.833	1	0.733	0.624	0.85	CLONAL	3	TRUE	2	0.167498029983875	6		192	261	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0024824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	34	356	2	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.167498029983875	6	FACETS	1	0.934	1	0.337	0.275	0.406	CLONAL	1	TRUE	2	0.167498029983875	6		358	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782082	NA	P-0024824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	122	476	0	ENST00000269305.4:c.745A>T	p.Arg249Trp	p.R249W	ENST00000269305	NM_001126112.2	249	Agg/Tgg	7/11	0.167498029983875	2	FACETS	1	0.965	1	1	0.988	1	CLONAL	3	TRUE	0	0.167498029983875	2		476	433	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575696	48575696	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0024824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	136	553	1	ENST00000342988.3:c.454+2T>A		p.X152_splice	ENST00000342988	NM_005359.5	152			0.167498029983875	2	FACETS	0.913	0.833	0.996	1	0.984	1	CLONAL	3	TRUE	0	0.167498029983875	2		554	593	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98244444	98244444	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	61	499	0	ENST00000331920.6:c.626T>G	p.Leu209Arg	p.L209R	ENST00000331920	NM_000264.3	209	cTt/cGt	4/24	0.167498029983875	3	FACETS	0.769	0.664	0.883	0.769	0.664	0.883	SUBCLONAL	2	TRUE	1	0.167498029983875	3		499	513	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246481	105246481	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	92	539	0	ENST00000349310.3:c.119A>C	p.Glu40Ala	p.E40A	ENST00000349310	NM_001014432.1	40	gAg/gCg	4/15	NA	3	FACETS	0.987	0.883	1			1	INDETERMINATE	3	TRUE	NA	0.167498029983875	3		539	402	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123704	11123704	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	137	460	0	ENST00000358026.2:c.2354A>C	p.Lys785Thr	p.K785T	ENST00000358026	NM_001128849.1	785	aAg/aCg	16/36	0.167498029983875	2	FACETS	0.929	0.853	1	1	0.99	1	CLONAL	4	TRUE	0	0.167498029983875	2		460	440	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485449	57485449	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	56	275	0	ENST00000371085.3:c.1031A>C	p.Glu344Ala	p.E344A	ENST00000371085	NM_000516.4	344	gAg/gCg	12/13	0.167498029983875	6	FACETS	1	0.931	1	0.571	0.491	0.658	CLONAL	2	TRUE	2	0.167498029983875	6		275	391	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925501	131925501	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	75	304	0	ENST00000265335.6:c.1424T>G	p.Leu475Arg	p.L475R	ENST00000265335		475	cTt/cGt	9/25	0.167498029983875	6	FACETS	1	0.906	1	0.774	0.682	0.872	CLONAL	3	TRUE	2	0.167498029983875	6		304	386	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509250	106509250	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	66	449	0	ENST00000359195.3:c.1244A>G	p.Glu415Gly	p.E415G	ENST00000359195	NM_002649.2	415	gAg/gGg	2/11	0.167498029983875	8	FACETS	1	0.888	1	0.512	0.445	0.585	CLONAL	2	TRUE	4	0.167498029983875	8		449	578	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0024824-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	72	578	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.834	0.727	0.951	0.834	0.727	0.951	CLONAL	1	TRUE	1	0.186360633413917	2		578	926	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0024824-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	88	430	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.996	0.881	1	0.996	0.881	1	CLONAL	1	TRUE	1	0.186360633413917	2		430	948	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419986	41419986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372989163	NA	P-0024824-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	114	425	1	ENST00000373198.4:c.335G>A	p.Arg112His	p.R112H	ENST00000373198	NM_133170.3	112	cGt/cAt	3/32	0.186360633413917	3	FACETS	1	0.961	1	0.571	0.512	0.633	CLONAL	1	TRUE	1	0.186360633413917	3		426	1172	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0024824-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	53	192	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.186360633413917	2		192	498	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0024824-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	84	356	2	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	0.186360633413917	2		358	772	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007871	45007872	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0024824-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	135	546	0	ENST00000558401.1:c.319_320del	p.Leu107ValfsTer7	p.L107Vfs*7	ENST00000558401	NM_004048.2	106	acTTtg/actg	2/4	0.186360633413917	1	FACETS	0.793	0.721	0.869	1	0.987	1	SUBCLONAL	2	TRUE	0	0.186360633413917	1		546	828	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782082	NA	P-0024824-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	171	476	0	ENST00000269305.4:c.745A>T	p.Arg249Trp	p.R249W	ENST00000269305	NM_001126112.2	249	Agg/Tgg	7/11	0.186360633413917	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.186360633413917	1		476	1287	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575696	48575696	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0024824-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	96	553	1	ENST00000342988.3:c.454+2T>A		p.X152_splice	ENST00000342988	NM_005359.5	152			0.186360633413917	1	FACETS	0.91	0.809	1	0.91	0.809	1	CLONAL	1	TRUE	0	0.186360633413917	1		554	1027	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432129	49432129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024824-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1411	162	803	0	ENST00000301067.7:c.9010G>A	p.Glu3004Lys	p.E3004K	ENST00000301067	NM_003482.3	3004	Gag/Aag	34/54	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.186360633413917	2		803	1573	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412904	49412904	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024824-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1329	148	825	0	ENST00000418115.1:c.119A>G	p.Glu40Gly	p.E40G	ENST00000418115	NM_001664.2	40	gAg/gGg	2/5	0.186360633413917	1	FACETS	0.975	0.888	1	0.975	0.888	1	CLONAL	1	TRUE	0	0.186360633413917	1		825	1477	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526253	189526253	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024824-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	130	722	0	ENST00000264731.3:c.517G>T	p.Gly173Cys	p.G173C	ENST00000264731	NM_003722.4	173	Ggc/Tgc	4/14	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.186360633413917	2		722	1241	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555526097	NA	P-0024825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	122	653	0	ENST00000269305.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000269305	NM_001126112.2	167	Cag/Tag	5/11	0.241483148843499	2	FACETS	1	0.98	1	0.646	0.587	0.708	CLONAL	1	TRUE	0	0.378435367711126	2		653	499	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248633	59248634	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0024827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	71	696	7	ENST00000371222.2:c.109_110del	p.Ser37HisfsTer69	p.S37Hfs*69	ENST00000371222	NM_002228.3	37	AGc/c	1/1	1	2	FACETS	0.736	0.64	0.84	0.736	0.64	0.84	SUBCLONAL	1	TRUE	1	0.182956971675176	2		703	1055	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	33	314	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.182956971675176	2		314	342	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023348	27023348	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	45	228	1	ENST00000324856.7:c.454C>T	p.Gln152Ter	p.Q152*	ENST00000324856	NM_006015.4	152	Caa/Taa	1/20	1	2	FACETS	1	0.876	1	1	0.973	1	CLONAL	2	TRUE	1	0.182956971675176	2		229	237	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305439	65305439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	37	448	0	ENST00000342505.4:c.2689G>A	p.Glu897Lys	p.E897K	ENST00000342505	NM_002227.2	897	Gaa/Aaa	20/25	1	2	FACETS	0.625	0.514	0.75	0.625	0.514	0.75	SUBCLONAL	1	TRUE	1	0.182956971675176	2		448	647	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94211960	94211960	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	50	579	0	ENST00000323929.3:c.485T>A	p.Ile162Lys	p.I162K	ENST00000323929	NM_005591.3	162	aTa/aAa	6/20	0.182956971675176	3	FACETS	0.72	0.609	0.842	0.36	0.304	0.421	SUBCLONAL	1	TRUE	1	0.182956971675176	3		579	829	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	75	415	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	0.169948088082716	2	FACETS	1	0.965	1	0.648	0.567	0.734	CLONAL	1	TRUE	0	0.182956971675176	2		415	633	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801794	3801794	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	39	505	0	ENST00000262367.5:c.3712G>T	p.Glu1238Ter	p.E1238*	ENST00000262367	NM_004380.2	1238	Gag/Tag	20/31	0.0660697976143243	1	FACETS	0.607	0.502	0.725	0.607	0.502	0.725	INDETERMINATE	1	TRUE	0	0.182956971675176	1		505	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0024827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	149	533	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.115137205264896	1	FACETS	1	0.93	1	1	0.991	1	CLONAL	2	TRUE	0	0.182956971675176	1		533	727	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652034	36652035	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0024827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	119	654	0	ENST00000244741.5:c.158_159dup	p.Val54LeufsTer95	p.V54Lfs*95	ENST00000244741	NM_000389.4	52	-/TT	2/3	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.182956971675176	2		654	891	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0024828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	196	606	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.975	0.907	1	1	0.993	1	CLONAL	2	TRUE	1	0.323237953125255	2		606	622	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0024828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	55	605	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.306778256090715	1	FACETS	0.66	0.566	0.763	0.66	0.566	0.763	SUBCLONAL	1	TRUE	0	0.323237953125255	1		605	432	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243512	41243512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80357407	NA	P-0024828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	116	731	1	ENST00000357654.3:c.4036G>A	p.Glu1346Lys	p.E1346K	ENST00000357654	NM_007294.3	1346	Gaa/Aaa	10/23	0.180545076604033	3	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.323237953125255	3		732	628	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971102	21971102	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	55	395	0	ENST00000304494.5:c.256del	p.Ala86ProfsTer60	p.A86Pfs*60	ENST00000304494	NM_000077.4	86	Gcc/cc	2/3	0.323237953125255	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.323237953125255	1		395	249	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908852	101908852	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	73	600	0	ENST00000374994.4:c.1217del	p.Leu406Ter	p.L406*	ENST00000374994	NM_004612.2	406	Tta/ta	7/9	0.323237953125255	1	FACETS	0.887	0.779	1	0.887	0.779	1	CLONAL	1	TRUE	0	0.323237953125255	1		600	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0024829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	253	466	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.481703861774181	1	FACETS	0.896	0.84	0.953	0.896	0.84	0.953	CLONAL	1	TRUE	0	0.481703861774181	1		466	890	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0024829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	177	623	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.481703861774181	1	FACETS	0.516	0.474	0.559	0.516	0.474	0.559	SUBCLONAL	1	TRUE	0	0.481703861774181	1		624	1082	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625164	69625164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115452181	NA	P-0024829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	97	330	0	ENST00000334134.2:c.629G>A	p.Arg210Gln	p.R210Q	ENST00000334134	NM_005247.2	210	cGg/cAg	3/3	1	2	FACETS	0.393	0.349	0.439	0.393	0.349	0.439	SUBCLONAL	1	TRUE	1	0.481703861774181	2		330	1026	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168978	11168978	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	128	388	0	ENST00000358026.2:c.4568G>T	p.Arg1523Leu	p.R1523L	ENST00000358026	NM_001128849.1	1523	cGa/cTa	32/36	1	2	FACETS	0.6	0.543	0.66	0.6	0.543	0.66	SUBCLONAL	1	TRUE	1	0.481703861774181	2		388	886	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284906	15284906	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1469453455	NA	P-0024829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	346	439	0	ENST00000263388.2:c.4709G>A	p.Arg1570His	p.R1570H	ENST00000263388	NM_000435.2	1570	cGt/cAt	25/33	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.481703861774181	2		439	1250	SUCCESS
APC	324	MSKCC	GRCh37	5	112174787	112174788	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0024829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	156	222	0	ENST00000257430.4:c.3497dup	p.Tyr1166Ter	p.Y1166*	ENST00000257430	NM_000038.5	1166	tat/tAat	16/16	0.464030265867653	2	FACETS	0.912	0.848	0.977	0.912	0.848	0.977	CLONAL	2	TRUE	0	0.481703861774181	2		222	355	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133322	38133322	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0024829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	1095	356	0	ENST00000317025.8:c.4151C>G	p.Ser1384Ter	p.S1384*	ENST00000317025	NM_023034.1	1384	tCa/tGa	24/24	0.481703861774181	11	FACETS	0.944	0.922	0.966			1	CLONAL	8	TRUE	NA	0.481703861774181	11		356	1907	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133950	38133950	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	2825	558	0	ENST00000317025.8:c.3936C>G	p.Ile1312Met	p.I1312M	ENST00000317025	NM_023034.1	1312	atC/atG	23/24	0.481703861774181	11	FACETS	0.962	0.95	0.973			1	CLONAL	10	TRUE	NA	0.481703861774181	11		558	3864	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970924	70970924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1277239045	NA	P-0024829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	392	451	0	ENST00000276594.2:c.1337G>A	p.Arg446Gln	p.R446Q	ENST00000276594	NM_024504.3	446	cGg/cAg	6/8	0.201565545580491	5	FACETS	1	0.984	1	0.721	0.685	0.758	INDETERMINATE	2	TRUE	2	0.481703861774181	5		451	1296	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0024830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	133	403	0				ENST00000310581	NM_198253.2	-/1132			0.376536246163611	3	FACETS	0.79	0.723	0.859	0.79	0.723	0.859	SUBCLONAL	2	TRUE	1	0.4655966648238	3		403	446	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0024830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	169	428	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.4655966648238	5	FACETS	0.844	0.782	0.907	0.844	0.782	0.907	CLONAL	3	TRUE	2	0.4655966648238	5		428	487	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105676	27105678	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs753766136	NA	P-0024830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	58	344	0	ENST00000324856.7:c.5299_5301del	p.Glu1767del	p.E1767del	ENST00000324856	NM_006015.4	1763	GAA/-	20/20	0.391430260855427	3	FACETS	0.994	0.86	1	0.497	0.43	0.569	CLONAL	1	TRUE	1	0.4655966648238	3		344	309	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074171	8074171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	71	304	0	ENST00000377482.5:c.488C>T	p.Ser163Phe	p.S163F	ENST00000377482	NM_018948.3	163	tCt/tTt	4/4	0.391430260855427	3	FACETS	0.974	0.855	1	0.487	0.427	0.551	CLONAL	1	TRUE	1	0.4655966648238	3		304	386	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858001	9858001	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs748967552	NA	P-0024830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	77	501	0	ENST00000330684.3:c.3400C>A	p.Gln1134Lys	p.Q1134K	ENST00000330684	NM_001134407.1	1134	Cag/Aag	13/13	0.264873767613082	4	FACETS	0.741	0.651	0.839	0.371	0.325	0.42	INDETERMINATE	1	TRUE	2	0.4655966648238	4		501	654	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156135	99156135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	184	445	0	ENST00000074304.5:c.815C>T	p.Ala272Val	p.A272V	ENST00000074304	NM_001134224.1	272	gCc/gTc	10/26	0.223442749426765	3	FACETS	0.887	0.825	0.951	0.887	0.825	0.951	INDETERMINATE	2	TRUE	1	0.4655966648238	3		445	549	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0024832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	57	606	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.225612682341758	4	FACETS	0.803	0.689	0.927	0.402	0.344	0.464	CLONAL	1	TRUE	2	0.351286891360408	4		606	546	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374389	31374389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371009965	NA	P-0024832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	94	569	0	ENST00000328111.2:c.388C>T	p.Arg130Cys	p.R130C	ENST00000328111	NM_006892.3	130	Cgc/Tgc	5/23	0.306307912879173	5	FACETS	0.922	0.82	1	0.307	0.273	0.344	CLONAL	1	TRUE	2	0.351286891360408	5		569	886	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936201	71936201	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	85	373	0	ENST00000298229.2:c.173T>C	p.Leu58Pro	p.L58P	ENST00000298229	NM_001567.3	58	cTc/cCc	1/28	0.351286891360408	3	FACETS	1	0.979	1	0.741	0.659	0.827	CLONAL	1	TRUE	1	0.351286891360408	3		373	384	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965421	25965421	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	85	689	0	ENST00000435504.4:c.3785C>G	p.Ala1262Gly	p.A1262G	ENST00000435504		1262	gCc/gGc	13/13	0.351286891360408	3	FACETS	0.661	0.583	0.744	0.33	0.291	0.372	SUBCLONAL	1	TRUE	1	0.351286891360408	3		689	861	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248725	212248725	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	51	345	0	ENST00000342788.4:c.3542A>G	p.Gln1181Arg	p.Q1181R	ENST00000342788	NM_005235.2	1181	cAa/cGa	28/28	0.351286891360408	3	FACETS	0.799	0.681	0.929	0.4	0.34	0.465	CLONAL	1	TRUE	1	0.351286891360408	3		345	427	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247168	153247168	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	26	323	0	ENST00000281708.4:c.1634A>T	p.Tyr545Phe	p.Y545F	ENST00000281708	NM_033632.3	545	tAt/tTt	10/12	0.225612682341758	4	FACETS	0.563	0.446	0.698	0.282	0.223	0.349	SUBCLONAL	1	TRUE	2	0.351286891360408	4		323	355	SUCCESS
APC	324	MSKCC	GRCh37	5	112174252	112174252	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	46	409	0	ENST00000257430.4:c.2961del	p.Glu988LysfsTer17	p.E988Kfs*17	ENST00000257430	NM_000038.5	987	tcT/tc	16/16	0.351286891360408	3	FACETS	0.74	0.624	0.868	0.37	0.312	0.434	SUBCLONAL	1	TRUE	1	0.351286891360408	3		409	416	SUCCESS
APC	324	MSKCC	GRCh37	5	112175087	112175087	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	36	279	0	ENST00000257430.4:c.3796G>A	p.Asp1266Asn	p.D1266N	ENST00000257430	NM_000038.5	1266	Gat/Aat	16/16	0.351286891360408	3	FACETS	0.782	0.645	0.935	0.391	0.322	0.468	CLONAL	1	TRUE	1	0.351286891360408	3		279	308	SUCCESS
APC	324	MSKCC	GRCh37	5	112175540	112175541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0024832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	21	280	0	ENST00000257430.4:c.4250_4251dup	p.Ile1418LeufsTer2	p.I1418Lfs*2	ENST00000257430	NM_000038.5	1417	att/aTTtt	16/16	0.351286891360408	3	FACETS	0.343	0.263	0.436	0.171	0.131	0.218	SUBCLONAL	1	TRUE	1	0.351286891360408	3		280	410	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372264	55372264	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	81	552	0	ENST00000297316.4:c.954G>T	p.Gln318His	p.Q318H	ENST00000297316	NM_022454.3	318	caG/caT	2/2	0.316188516867475	4	FACETS	0.916	0.807	1	0.458	0.403	0.517	CLONAL	1	TRUE	2	0.351286891360408	4		552	680	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37006485	37006485	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	35	372	0	ENST00000358127.4:c.460T>G	p.Ser154Ala	p.S154A	ENST00000358127	NM_001280556.1	154	Tcc/Gcc	4/10	0.351286891360408	3	FACETS	0.537	0.44	0.646			1	SUBCLONAL	1	TRUE	NA	0.351286891360408	3		372	436	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	88	552	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.925	0.821	1	0.925	0.821	1	CLONAL	1	TRUE	1	0.331428571243021	2		552	574	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965586	93965586	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs372024057	NA	P-0024833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	77	424	0	ENST00000369303.4:c.2342G>T	p.Arg781Leu	p.R781L	ENST00000369303	NM_004440.3	781	cGa/cTa	13/17	0.262719865150587	1	FACETS	0.948	0.836	1	0.948	0.836	1	CLONAL	1	TRUE	0	0.331428571243021	1		424	409	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0024834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	214	606	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.899	0.842	0.956	1	0.995	1	CLONAL	3	TRUE	1	0.286033854024387	2		606	555	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741689	17741689	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	20	410	0	ENST00000250003.3:c.361del	p.Arg121AlafsTer2	p.R121Afs*2	ENST00000250003	NM_002478.4	120	cgC/cg	1/3	0.286033854024387	1	FACETS	0.67	0.515	0.848	0.67	0.515	0.848	SUBCLONAL	1	TRUE	0	0.286033854024387	1		410	179	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194145	94194145	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	56	515	0	ENST00000323929.3:c.1283G>T	p.Arg428Met	p.R428M	ENST00000323929	NM_005591.3	428	aGg/aTg	12/20	0.286033854024387	1	FACETS	0.869	0.748	1	0.869	0.748	1	CLONAL	1	TRUE	0	0.286033854024387	1		515	386	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200991	108200991	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587781361	NA	P-0024834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	45	397	0	ENST00000278616.4:c.7358G>C	p.Arg2453Pro	p.R2453P	ENST00000278616	NM_000051.3	2453	cGt/cCt	50/63	0.286033854024387	1	FACETS	0.93	0.786	1	0.93	0.786	1	CLONAL	1	TRUE	0	0.286033854024387	1		397	290	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143235878	143235878	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs377514187	NA	P-0024834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	37	360	0	ENST00000262992.4:c.410C>A	p.Pro137Gln	p.P137Q	ENST00000262992	NM_001101669.1	137	cCg/cAg	6/24	0.174451254395114	1	FACETS	0.752	0.622	0.895	0.752	0.622	0.895	SUBCLONAL	1	TRUE	0	0.286033854024387	1		360	295	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221249	1221249	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	TAC	novel	NA	P-0024834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	61	626	0	ENST00000326873.7:c.772delinsTAC	p.Asp258TyrfsTer30	p.D258Yfs*30	ENST00000326873	NM_000455.4	258	Gac/TACac	6/10	0.286033854024387	1	FACETS	0.964	0.836	1	0.964	0.836	1	CLONAL	1	TRUE	0	0.286033854024387	1		626	379	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0024837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	336	327	1	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	0.315967682545249	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	0	0.334824032753814	3		328	735	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	213	735	1	ENST00000269305.4:c.476C>A	p.Ala159Asp	p.A159D	ENST00000269305	NM_001126112.2	159	gCc/gAc	5/11	0.334824032753814	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.334824032753814	1		736	938	SUCCESS
APC	324	MSKCC	GRCh37	5	112164604	112164605	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0024837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	81	328	0	ENST00000257430.4:c.1681_1682del	p.Lys561AspfsTer19	p.K561Dfs*19	ENST00000257430	NM_000038.5	560	AAa/a	14/16	0.334824032753814	1	FACETS	0.995	0.881	1	0.995	0.881	1	CLONAL	1	TRUE	0	0.334824032753814	1		328	405	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	81	510	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.43196968118525	2	FACETS	0.591	0.521	0.665	0.295	0.26	0.333	SUBCLONAL	1	TRUE	0	0.491333040400083	2		510	558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0024838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	197	637	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.491333040400083	1	FACETS	0.985	0.917	1	0.985	0.917	1	CLONAL	1	TRUE	0	0.491333040400083	1		638	614	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	114	573	1	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	1	2	FACETS	0.884	0.799	0.973	0.884	0.799	0.973	CLONAL	1	TRUE	1	0.491333040400083	2		574	525	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0024838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	103	585	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.483499239087755	3	FACETS	0.712	0.637	0.791	0.356	0.318	0.396	SUBCLONAL	1	TRUE	1	0.491333040400083	3		585	734	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0024838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	67	357	2	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.735	0.642	0.835	0.735	0.642	0.835	SUBCLONAL	1	TRUE	1	0.491333040400083	2		359	371	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175481	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0024838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	60	274	0	ENST00000257430.4:c.4192_4193del	p.Arg1399PhefsTer9	p.R1399Ffs*9	ENST00000257430	NM_000038.5	1397	GAg/g	16/16	1	2	FACETS	0.708	0.613	0.81	0.708	0.613	0.81	SUBCLONAL	1	TRUE	1	0.491333040400083	2		274	345	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281926	49281926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	72	623	1	ENST00000282018.3:c.973C>T	p.Pro325Ser	p.P325S	ENST00000282018	NM_020377.2	325	Cca/Tca	1/1	0.491333040400083	5	FACETS	0.421	0.366	0.481	0.14	0.122	0.161	SUBCLONAL	1	TRUE	2	0.491333040400083	5		624	1209	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245389	153245389	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	126	574	1	ENST00000281708.4:c.1802C>T	p.Ser601Phe	p.S601F	ENST00000281708	NM_033632.3	601	tCt/tTt	11/12	1	2	FACETS	0.883	0.802	0.967	0.883	0.802	0.967	CLONAL	1	TRUE	1	0.491333040400083	2		575	581	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0024839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	16	676	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.540401704050746	4	FACETS	1	0.861	1	0.606	0.461	0.768	CLONAL	1	TRUE	2	0.741340773842244	4		676	62	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0024839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	17	608	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.540401704050746	4	FACETS	0.733	0.554	0.939	0.366	0.277	0.47	CLONAL	1	TRUE	2	0.741340773842244	4		609	109	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929134	32929134	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	18	566	2	ENST00000380152.3:c.7147del	p.Tyr2383IlefsTer11	p.Y2383Ifs*11	ENST00000380152		2382	Ttt/tt	14/27	0.36712851976128	1	FACETS	0.695	0.55	0.845	0.695	0.55	0.845	INDETERMINATE	1	TRUE	0	0.741340773842244	1		568	44	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851406	151851406	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	19	640	0	ENST00000262189.6:c.12085C>G	p.Pro4029Ala	p.P4029A	ENST00000262189	NM_170606.2	4029	Cca/Gca	47/59	0.379022297363139	4	FACETS	0.842	0.666	1	0.842	0.666	1	INDETERMINATE	2	TRUE	2	0.741340773842244	4		640	53	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538964	23538964	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	103	562	0	ENST00000380871.4:c.475A>G	p.Lys159Glu	p.K159E	ENST00000380871	NM_006167.3	159	Aag/Gag	2/2	0.741340773842244	3	FACETS	1	0.96	1	0.709	0.655	0.763	CLONAL	2	TRUE	0	0.741340773842244	3		562	179	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748939	43748939	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	11	958	0	ENST00000382044.4:c.1867del	p.Asp623IlefsTer25	p.D623Ifs*25	ENST00000382044	NM_001141980.1	623	Gat/at	12/28	0.741340773842244	1	FACETS	0.34	0.24	0.456	0.34	0.24	0.456	SUBCLONAL	1	TRUE	0	0.741340773842244	1		958	55	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0024840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	212	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.964	0.901	1	0.964	0.901	1	CLONAL	1	TRUE	1	0.711839310568367	2		326	618	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120675	115120676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	549	685	1	ENST00000257566.3:c.330dup	p.Glu111ArgfsTer27	p.E111Rfs*27	ENST00000257566	NM_016569.3	110	-/A	1/8	1	2	FACETS	0.999	0.958	1	0.999	0.958	1	CLONAL	1	TRUE	1	0.711839310568367	2		686	1544	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097173	11097173	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	360	504	0	ENST00000358026.2:c.664C>A	p.Pro222Thr	p.P222T	ENST00000358026	NM_001128849.1	222	Cca/Aca	4/36	1	2	FACETS	0.986	0.936	1	0.986	0.936	1	CLONAL	1	TRUE	1	0.711839310568367	2		504	1026	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431637	6431637	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	313	443	0	ENST00000356142.4:c.190T>C	p.Tyr64His	p.Y64H	ENST00000356142	NM_018890.3	64	Tat/Cat	3/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.711839310568367	2		443	833	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411886	116411904	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTCTCTCTGTTTTAAGAT	TTTCTCTCTGTTTTAAGAT	-	novel	NA	P-0024841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1415	137	765	0	ENST00000397752.3:c.2888-17_2889del		p.X963_splice	ENST00000397752	NM_000245.2	963		14/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		765	1552	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115727	108115727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747727055	NA	P-0024842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	24	217	1	ENST00000278616.4:c.875C>T	p.Pro292Leu	p.P292L	ENST00000278616	NM_000051.3	292	cCg/cTg	7/63	0.499546862902037	1	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	0	0.527043210559979	1		218	64	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448310	56448310	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567880628	NA	P-0024842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	18	501	1	ENST00000407977.2:c.337C>T	p.Arg113Ter	p.R113*	ENST00000407977		113	Cga/Tga	3/10	1	2	FACETS	0.248	0.187	0.321	0.248	0.187	0.321	SUBCLONAL	1	TRUE	1	0.527043210559979	2		502	275	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62009593	62009593	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	38	455	0	ENST00000392795.3:c.29C>A	p.Pro10His	p.P10H	ENST00000392795	NM_001039933.1	10	cCc/cAc	1/6	1	2	FACETS	0.665	0.554	0.785	0.665	0.554	0.785	SUBCLONAL	1	TRUE	1	0.527043210559979	2		455	217	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512406	149512406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201250234	NA	P-0024842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	104	428	0	ENST00000261799.4:c.1034C>T	p.Pro345Leu	p.P345L	ENST00000261799	NM_002609.3	345	cCg/cTg	7/23	1	2	FACETS	0.78	0.711	0.85	1	0.986	1	SUBCLONAL	2	TRUE	1	0.527043210559979	2		428	253	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112769094	112769094	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	36	502	0	ENST00000369452.4:c.1373A>G	p.Asn458Ser	p.N458S	ENST00000369452	NM_007373.3	458	aAc/aGc	7/9	1	2	FACETS	0.849	0.708	1	0.849	0.708	1	CLONAL	1	TRUE	1	0.527043210559979	2		502	161	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219323	1219323	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1421605142	NA	P-0024842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	50	480	0	ENST00000326873.7:c.375G>A	p.Met125Ile	p.M125I	ENST00000326873	NM_000455.4	125	atG/atA	3/10	1	2	FACETS	0.648	0.553	0.75	0.648	0.553	0.75	SUBCLONAL	1	TRUE	1	0.527043210559979	2		480	293	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219722	36219722	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	78	675	0	ENST00000222270.7:c.4619A>G	p.Tyr1540Cys	p.Y1540C	ENST00000222270	NM_014727.1	1540	tAt/tGt	20/37	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.527043210559979	2		675	275	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940022	76940022	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	21	531	1	ENST00000373344.5:c.726A>T	p.Lys242Asn	p.K242N	ENST00000373344	NM_000489.3	242	aaA/aaT	9/35	0.105054490672959	0	FACETS	0.237	0.184	0.298			1	INDETERMINATE	1	TRUE	0	0.527043210559979	0		532	159	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630149	100630149	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	22	441	0	ENST00000308731.7:c.124T>C	p.Tyr42His	p.Y42H	ENST00000308731	NM_000061.2	42	Tat/Cat	2/19	0.105054490672959	0	FACETS	0.272	0.213	0.34			1	INDETERMINATE	1	TRUE	0	0.527043210559979	0		441	145	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479218	50479218	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	28	331	0	ENST00000394963.4:c.68del	p.Gly23AlafsTer47	p.G23Afs*47	ENST00000394963	NM_003076.4	22	gcG/gc	1/13	0.330161900206168	1	FACETS	0.447	0.359	0.546	0.447	0.359	0.546	SUBCLONAL	1	TRUE	0	0.452872219859833	1		331	214	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480132	50480132	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0024843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	26	364	0	ENST00000394963.4:c.365+1G>A		p.X122_splice	ENST00000394963	NM_003076.4	122			0.330161900206168	1	FACETS	0.292	0.231	0.361	0.292	0.231	0.361	SUBCLONAL	1	TRUE	0	0.452872219859833	1		364	304	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106833	27106833	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0024846-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	192	613	0	ENST00000324856.7:c.6444T>G	p.Tyr2148Ter	p.Y2148*	ENST00000324856	NM_006015.4	2148	taT/taG	20/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.891194544400839	2		613	403	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436880	49436880	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024846-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	240	782	0	ENST00000301067.7:c.5623T>G	p.Leu1875Val	p.L1875V	ENST00000301067	NM_003482.3	1875	Tta/Gta	25/54	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.891194544400839	2		782	508	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950397	68950397	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024846-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	136	443	0	ENST00000288368.4:c.709T>A	p.Ser237Thr	p.S237T	ENST00000288368	NM_024870.2	237	Tcc/Acc	7/40	1	2	FACETS	0.954	0.881	1	0.954	0.881	1	CLONAL	1	TRUE	1	0.891194544400839	2		443	320	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199655	11199655	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	336	427	0	ENST00000361445.4:c.4933A>G	p.Ser1645Gly	p.S1645G	ENST00000361445	NM_004958.3	1645	Agc/Ggc	35/58	0.897109602721385	2	FACETS	0.892	0.847	0.937	0.446	0.423	0.469	CLONAL	1	TRUE	0	0.897109602721385	2		427	840	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579340	7579340	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	708	494	0	ENST00000269305.4:c.347del	p.Ser116LeufsTer7	p.S116Lfs*7	ENST00000269305	NM_001126112.2	116	tCt/tt	4/11	0.897109602721385	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.897109602721385	2		494	781	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629816	187629816	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	73	509	1	ENST00000441802.2:c.1166T>C	p.Val389Ala	p.V389A	ENST00000441802	NM_005245.3	389	gTa/gCa	2/27	0.897109602721385	2	FACETS	0.14	0.121	0.159	0.07	0.06	0.08	SUBCLONAL	1	TRUE	0	0.897109602721385	2		510	1166	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100304	8100304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	84	556	2	ENST00000346208.3:c.278C>T	p.Ser93Phe	p.S93F	ENST00000346208		93	tCc/tTc	3/6	1	2	FACETS	0.791	0.7	0.889	0.791	0.7	0.889	SUBCLONAL	1	TRUE	1	0.36056264510696	2		558	589	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023356	27023356	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	20	276	0	ENST00000324856.7:c.462del	p.Tyr154Ter	p.Y154*	ENST00000324856	NM_006015.4	154	taC/ta	1/20	0.119916740063065	1	FACETS	0.377	0.289	0.48	0.377	0.289	0.48	INDETERMINATE	1	TRUE	0	0.36056264510696	1		276	241	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344648	118344658	+	frameshift_variant	Frame_Shift_Del	DEL	CTTCTGCCAAA	CTTCTGCCAAA	-	novel	NA	P-0024850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	95	461	1	ENST00000534358.1:c.2774_2784del	p.Ser925Ter	p.S925*	ENST00000534358	NM_005933.3	925	tCTTCTGCCAAA/t	3/36	0.333234720448253	1	FACETS	0.9	0.805	1	0.9	0.805	1	CLONAL	1	TRUE	0	0.36056264510696	1		462	480	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	92	314	0				ENST00000310581	NM_198253.2	-/1132			0.235695385583554	4	FACETS	0.857	0.77	0.947	0.857	0.77	0.947	INDETERMINATE	2	TRUE	2	0.535123973002016	4		314	308	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0024855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	181	327	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.535123973002016	3	FACETS	0.93	0.867	0.994	0.93	0.867	0.994	CLONAL	2	TRUE	1	0.535123973002016	3		327	461	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0024855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	389	672	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.493089893799132	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.535123973002016	3		672	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0024855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	120	472	3	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.477691554575454	1	FACETS	0.939	0.857	1	0.939	0.857	1	CLONAL	1	TRUE	0	0.535123973002016	1		475	350	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188995	32188995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753307747	NA	P-0024855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	151	733	2	ENST00000375023.3:c.559G>A	p.Glu187Lys	p.E187K	ENST00000375023	NM_004557.3	187	Gag/Aag	4/30	0.342632285219961	5	FACETS	0.988	0.909	1	0.658	0.606	0.713	CLONAL	2	TRUE	2	0.535123973002016	5		735	515	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221729	36221729	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	145	795	0	ENST00000222270.7:c.5398G>T	p.Glu1800Ter	p.E1800*	ENST00000222270	NM_014727.1	1800	Gag/Tag	26/37	0.476289276619765	3	FACETS	1	0.983	1	0.646	0.592	0.701	CLONAL	1	TRUE	1	0.535123973002016	3		795	532	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430515	181430515	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	90	658	0	ENST00000325404.1:c.367G>C	p.Asp123His	p.D123H	ENST00000325404	NM_003106.3	123	Gat/Cat	1/1	0.535123973002016	3	FACETS	0.806	0.717	0.9	0.403	0.358	0.45	CLONAL	1	TRUE	1	0.535123973002016	3		658	529	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183318	56183330	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGGGACAATTG	CTGGGGACAATTG	-	novel	NA	P-0024855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	187	459	0	ENST00000399503.3:c.4229_4241del	p.Leu1410HisfsTer8	p.L1410Hfs*8	ENST00000399503	NM_005921.1	1410	CTGGGGACAATTGca/ca	18/20	0.369758874874372	3	FACETS	1	0.965	1	0.698	0.653	0.744	CLONAL	2	TRUE	0	0.535123973002016	3		459	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs17849781	NA	P-0024858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	339	631	1	ENST00000269305.4:c.832C>A	p.Pro278Thr	p.P278T	ENST00000269305	NM_001126112.2	278	Cct/Act	8/11	0.313010697156295	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.318959411154819	2		632	1045	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572194	64572194	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	129	405	0	ENST00000312049.6:c.1445G>T	p.Gly482Val	p.G482V	ENST00000312049	NM_130799.2	482	gGc/gTc	10/10	NA	2	FACETS	1	0.934	1			1	INDETERMINATE	1	TRUE	NA	0.318959411154819	2		405	780	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624296	89624296	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786201995	NA	P-0024858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	114	552	0	ENST00000371953.3:c.70G>T	p.Asp24Tyr	p.D24Y	ENST00000371953	NM_000314.4	24	Gac/Tac	1/9	0.318959411154819	1	FACETS	0.847	0.764	0.936	0.847	0.764	0.936	CLONAL	1	TRUE	0	0.318959411154819	1		552	709	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255464	16255464	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	62	484	0	ENST00000375759.3:c.2729C>A	p.Ser910Tyr	p.S910Y	ENST00000375759	NM_015001.2	910	tCt/tAt	11/15	1	2	FACETS	0.464	0.4	0.535	0.464	0.4	0.535	SUBCLONAL	1	TRUE	1	0.318959411154819	2		484	837	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980874	40980874	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	125	503	1	ENST00000373198.4:c.1612C>T	p.Gln538Ter	p.Q538*	ENST00000373198	NM_133170.3	538	Cag/Tag	10/32	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.318959411154819	2		504	731	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62312038	62312038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371141081	NA	P-0024858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	183	659	2	ENST00000360203.5:c.1157C>T	p.Thr386Met	p.T386M	ENST00000360203	NM_001283009.1	386	aCg/aTg	14/35	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.318959411154819	2		661	1065	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0024859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	132	527	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.587435122137101	1	FACETS	0.848	0.779	0.919	0.848	0.779	0.919	CLONAL	1	TRUE	0	0.5968771449517	1		527	366	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398279	25398279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894365	NA	P-0024859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	14	662	2	ENST00000311936.3:c.40G>A	p.Val14Ile	p.V14I	ENST00000311936	NM_004985.3	14	Gta/Ata	2/5	0.239156268413661	3	FACETS	0.091	0.065	0.123	0.03	0.021	0.041	INDETERMINATE	1	TRUE	0	0.5968771449517	3		664	669	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965476	68965476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751712561	NA	P-0024859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	132	648	0	ENST00000288368.4:c.1088G>A	p.Arg363Gln	p.R363Q	ENST00000288368	NM_024870.2	363	cGg/cAg	9/40	0.167888725753643	0	FACETS	0.409	0.374	0.445			1	INDETERMINATE	1	TRUE	0	0.5968771449517	0		648	436	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112764364	112764364	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	28	354	0	ENST00000369452.4:c.973A>C	p.Ser325Arg	p.S325R	ENST00000369452	NM_007373.3	325	Agt/Cgt	5/9	0.580843305925172	2	FACETS	0.349	0.279	0.427	0.174	0.139	0.214	SUBCLONAL	1	TRUE	0	0.5968771449517	2		354	269	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196476	67196476	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	75	610	0	ENST00000312629.5:c.102G>C	p.Leu34Phe	p.L34F	ENST00000312629	NM_003952.2	34	ttG/ttC	2/15	0.235734866783768	1	FACETS	0.191	0.166	0.217	0.191	0.166	0.217	INDETERMINATE	1	TRUE	0	0.5968771449517	1		610	924	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248369	212248369	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1325370392	NA	P-0024859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	24	226	0	ENST00000342788.4:c.3898C>T	p.Pro1300Ser	p.P1300S	ENST00000342788	NM_005235.2	1300	Cct/Tct	28/28	1	2	FACETS	0.512	0.405	0.633	0.512	0.405	0.633	SUBCLONAL	1	TRUE	1	0.5968771449517	2		226	157	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143044475	143044475	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	16	453	0	ENST00000262992.4:c.1987G>C	p.Val663Leu	p.V663L	ENST00000262992	NM_001101669.1	663	Gta/Cta	18/24	0.591638820034191	1	FACETS	0.177	0.131	0.232	0.177	0.131	0.232	SUBCLONAL	1	TRUE	0	0.5968771449517	1		453	212	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778107	27778107	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	55	691	0	ENST00000369163.2:c.256C>T	p.Gln86Ter	p.Q86*	ENST00000369163	NM_003536.2	86	Cag/Tag	1/1	0.5968771449517	7	FACETS	0.476	0.406	0.554	0.119	0.101	0.139	SUBCLONAL	1	TRUE	3	0.5968771449517	7		691	964	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520006	NA	P-0024867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	314	488	0	ENST00000269305.4:c.821T>G	p.Val274Gly	p.V274G	ENST00000269305	NM_001126112.2	274	gTt/gGt	8/11	0.816166914387707	1	FACETS	0.959	0.921	0.996	0.959	0.921	0.996	CLONAL	1	TRUE	0	0.816166914387707	1		488	475	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424159	49424181	+	frameshift_variant	Frame_Shift_Del	DEL	GCACCGATGGGGGTGGGGTGGGG	GCACCGATGGGGGTGGGGTGGGG	-	novel	NA	P-0024867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	240	434	0	ENST00000301067.7:c.13881_13903del	p.Pro4628AlafsTer11	p.P4628Afs*11	ENST00000301067	NM_003482.3	4627	ccCCCCACCCCACCCCCATCGGTGCag/ccag	42/54	NA	2	FACETS	0.934	0.878	0.99			1	INDETERMINATE	1	TRUE	NA	0.816166914387707	2		434	630	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225449704	225449705	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0024867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	112	267	0	ENST00000264414.4:c.22_23del	p.Thr8GlyfsTer19	p.T8Gfs*19	ENST00000264414	NM_003590.4	8	ACg/g	1/16	NA	2	FACETS	0.8	0.728	0.875			1	INDETERMINATE	1	TRUE	NA	0.816166914387707	2		267	343	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794482	242794482	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	279	497	0	ENST00000334409.5:c.460G>T	p.Ala154Ser	p.A154S	ENST00000334409	NM_005018.2	154	Gcc/Tcc	3/5	0.816166914387707	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.816166914387707	1		497	398	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671579	30671579	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	316	411	1	ENST00000376406.3:c.5381C>A	p.Ala1794Glu	p.A1794E	ENST00000376406	NM_014641.2	1794	gCa/gAa	10/15	1	2	FACETS	0.964	0.914	1	0.964	0.914	1	CLONAL	1	TRUE	1	0.816166914387707	2		412	803	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720876	89720876	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0024876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	107	370	0	ENST00000371953.3:c.1026+1G>T		p.X342_splice	ENST00000371953	NM_000314.4	342			0.159444169433383	2	FACETS	1	0.97	1	0.604	0.543	0.669	INDETERMINATE	1	TRUE	0	0.28209706619565	2		370	628	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209504	98209504	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766315655	NA	P-0024876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	41	554	1	ENST00000331920.6:c.4034G>A	p.Arg1345His	p.R1345H	ENST00000331920	NM_000264.3	1345	cGt/cAt	23/24	0.28209706619565	1	FACETS	0.413	0.343	0.49	0.413	0.343	0.49	SUBCLONAL	1	TRUE	0	0.28209706619565	1		555	605	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0024876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	77	538	0	ENST00000269305.4:c.673-2A>C		p.X225_splice	ENST00000269305	NM_001126112.2	225			1	2	FACETS	0.764	0.67	0.864	0.764	0.67	0.864	SUBCLONAL	1	TRUE	1	0.28209706619565	2		538	715	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203704	94203704	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	33	374	0	ENST00000323929.3:c.950A>T	p.His317Leu	p.H317L	ENST00000323929	NM_005591.3	317	cAt/cTt	9/20	1	2	FACETS	0.384	0.312	0.466	0.384	0.312	0.466	SUBCLONAL	1	TRUE	1	0.28209706619565	2		374	609	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912264	32912264	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782720	NA	P-0024876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	85	523	0	ENST00000380152.3:c.3772A>G	p.Ile1258Val	p.I1258V	ENST00000380152		1258	Ata/Gta	11/27	1	2	FACETS	0.722	0.637	0.813	0.722	0.637	0.813	SUBCLONAL	1	TRUE	1	0.28209706619565	2		523	835	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121783	2121783	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0024876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	121	655	0	ENST00000219476.3:c.1947-2A>T		p.X649_splice	ENST00000219476	NM_000548.3	649			1	2	FACETS	0.922	0.832	1	0.922	0.832	1	CLONAL	1	TRUE	1	0.28209706619565	2		655	930	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715673	30715673	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	30	333	1	ENST00000295754.5:c.1331A>T	p.Gln444Leu	p.Q444L	ENST00000295754	NM_003242.5	444	cAg/cTg	5/7	1	2	FACETS	0.454	0.366	0.556	0.454	0.366	0.556	SUBCLONAL	1	TRUE	1	0.28209706619565	2		334	468	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169993053	169993053	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	98	478	0	ENST00000295797.4:c.683A>G	p.Asp228Gly	p.D228G	ENST00000295797	NM_002740.5	228	gAt/gGt	8/18	0.114708505456361	3	FACETS	0.843	0.75	0.941	0.421	0.375	0.471	INDETERMINATE	1	TRUE	1	0.28209706619565	3		478	941	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557391	187557391	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0024876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	87	340	0	ENST00000441802.2:c.3973-2A>T		p.X1325_splice	ENST00000441802	NM_005245.3	1325			0.159444169433383	2	FACETS	1	0.971	1	0.647	0.574	0.723	INDETERMINATE	1	TRUE	0	0.28209706619565	2		340	477	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001028	150001028	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	32	393	0	ENST00000253339.5:c.2576C>T	p.Ser859Phe	p.S859F	ENST00000253339		859	tCt/tTt	4/7	1	2	FACETS	0.373	0.302	0.454	0.373	0.302	0.454	SUBCLONAL	1	TRUE	1	0.28209706619565	2		393	608	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0024878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	115	702	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.872	0.79	0.957	0.872	0.79	0.957	CLONAL	1	TRUE	1	0.564734330331497	2		702	467	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814532	43814532	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	66	193	0	ENST00000372470.3:c.1330del	p.Ala444ProfsTer52	p.A444Pfs*52	ENST00000372470	NM_005373.2	443	Ggg/gg	9/12	1	2	FACETS	0.902	0.792	1	0.902	0.792	1	CLONAL	1	TRUE	1	0.564734330331497	2		193	259	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28908183	28908183	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	126	338	0	ENST00000282397.4:c.2572G>T	p.Val858Leu	p.V858L	ENST00000282397	NM_002019.4	858	Gtg/Ttg	18/30	1	2	FACETS	0.892	0.813	0.975	0.892	0.813	0.975	CLONAL	1	TRUE	1	0.564734330331497	2		338	500	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005287	29005287	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	110	324	0	ENST00000282397.4:c.974C>A	p.Ser325Ter	p.S325*	ENST00000282397	NM_002019.4	325	tCa/tAa	7/30	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.564734330331497	2		324	365	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502250	186502250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778995582	NA	P-0024878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	65	181	1	ENST00000323963.5:c.59C>T	p.Pro20Leu	p.P20L	ENST00000323963		20	cCc/cTc	2/11	1	2	FACETS	0.882	0.773	0.997	0.882	0.773	0.997	CLONAL	1	TRUE	1	0.564734330331497	2		182	261	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098954	178098954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553488015	NA	P-0024886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	252	298	0	ENST00000397062.3:c.91G>A	p.Gly31Arg	p.G31R	ENST00000397062	NM_006164.4	31	Gga/Aga	2/5	0.578460280961858	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.578460280961858	3		298	499	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207168	1207168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520039	NA	P-0024886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	244	461	1	ENST00000326873.7:c.256C>T	p.Arg86Ter	p.R86*	ENST00000326873	NM_000455.4	86	Cga/Tga	1/10	0.578460280961858	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.578460280961858	1		462	489	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945060	38945060	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	243	383	0	ENST00000357387.3:c.4744C>T	p.Gln1582Ter	p.Q1582*	ENST00000357387	NM_152756.3	1582	Caa/Taa	35/38	0.578460280961858	5	FACETS	0.823	0.77	0.878	0.412	0.385	0.439	CLONAL	2	TRUE	1	0.578460280961858	5		383	953	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836778	151836778	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	152	430	0	ENST00000262189.6:c.14442G>C	p.Glu4814Asp	p.E4814D	ENST00000262189	NM_170606.2	4814	gaG/gaC	56/59	1	2	FACETS	0.882	0.81	0.956	0.882	0.81	0.956	CLONAL	1	TRUE	1	0.578460280961858	2		430	596	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862756	9862756	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	170	373	0	ENST00000330684.3:c.2547C>A	p.Phe849Leu	p.F849L	ENST00000330684	NM_001134407.1	849	ttC/ttA	12/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.578460280961858	2		373	504	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645681	12645681	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397516830	NA	P-0024886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	224	237	0	ENST00000251849.4:c.788T>G	p.Val263Gly	p.V263G	ENST00000251849	NM_002880.3	263	gTc/gGc	7/17	0.578460280961858	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.578460280961858	2		237	353	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836825	151836825	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	193	492	1	ENST00000262189.6:c.14395G>A	p.Glu4799Lys	p.E4799K	ENST00000262189	NM_170606.2	4799	Gag/Aag	56/59	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.578460280961858	2		493	631	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041674	47041674	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	251	243	0	ENST00000377604.3:c.1899del	p.Lys634ArgfsTer70	p.K634Rfs*70	ENST00000377604	NM_001204468.1	633	tcG/tc	17/24	1	1	FACETS	0.871	0.835	0.906	1	0.996	1	CLONAL	2	TRUE	0	0.578460280961858	1		243	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519996	NA	P-0024887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	143	775	0	ENST00000269305.4:c.395A>C	p.Lys132Thr	p.K132T	ENST00000269305	NM_001126112.2	132	aAg/aCg	5/11	0.330386895502503	1	FACETS	0.962	0.879	1	0.962	0.879	1	CLONAL	1	TRUE	0	0.3584563600977	1		775	681	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347917	73347917	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs202067860	NA	P-0024887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	8	373	1	ENST00000377767.4:c.1144C>T	p.Arg382Ter	p.R382*	ENST00000377767	NM_014953.3	382	Cga/Tga	8/21	0.3584563600977	1	FACETS	0.116	0.074	0.17	0.116	0.074	0.17	SUBCLONAL	1	TRUE	0	0.3584563600977	1		374	317	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161984	47161984	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	31	333	0	ENST00000409792.3:c.4142del	p.Leu1381Ter	p.L1381*	ENST00000409792	NM_014159.6	1381	tTa/ta	3/21	0.231088504240117	1	FACETS	1	0.911	1	1	0.911	1	INDETERMINATE	1	TRUE	0	0.482478121242195	1		333	85	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468318	50468318	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	25	287	0	ENST00000331340.3:c.1553T>C	p.Met518Thr	p.M518T	ENST00000331340	NM_006060.4	518	aTg/aCg	8/8	1	2	FACETS	0.551	0.437	0.68	0.551	0.437	0.68	SUBCLONAL	1	TRUE	1	0.482478121242195	2		287	188	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115903	8115904	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0024889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	229	532	0	ENST00000346208.3:c.1251dup	p.Thr418HisfsTer89	p.T418Hfs*89	ENST00000346208		417	acc/aCcc	6/6	0.31040358216473	3	FACETS	1	0.987	1	0.604	0.565	0.644	INDETERMINATE	1	TRUE	1	0.691860130310183	3		532	738	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490377	56490377	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	126	469	1	ENST00000267101.3:c.2146G>T	p.Gly716Cys	p.G716C	ENST00000267101	NM_001982.3	716	Ggc/Tgc	18/28	0.664452207968746	5	FACETS	1	0.928	1	0.257	0.233	0.283	CLONAL	1	TRUE	1	0.691860130310183	5		470	722	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121152	3121152	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs376124717	NA	P-0024889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	37	619	0	ENST00000078429.4:c.1055A>G	p.Asn352Ser	p.N352S	ENST00000078429	NM_002067.2	352	aAc/aGc	7/7	0.691860130310183	1	FACETS	0.167	0.138	0.201	0.167	0.138	0.201	SUBCLONAL	1	TRUE	0	0.691860130310183	1		619	418	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55219010	55219010	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	25	481	0	ENST00000275493.2:c.583C>T	p.Pro195Ser	p.P195S	ENST00000275493	NM_005228.3	195	Ccc/Tcc	5/28	0.691860130310183	3	FACETS	0.213	0.167	0.266	0.107	0.083	0.133	SUBCLONAL	1	TRUE	1	0.691860130310183	3		481	456	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27168535	27168535	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	133	726	0	ENST00000380036.4:c.407G>A	p.Gly136Glu	p.G136E	ENST00000380036	NM_000459.3	136	gGa/gAa	3/23	0.277094574347477	2	FACETS	0.634	0.578	0.693	0.317	0.289	0.347	INDETERMINATE	1	TRUE	0	0.691860130310183	2		726	606	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27168582	27168582	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	129	731	0	ENST00000380036.4:c.454G>A	p.Asp152Asn	p.D152N	ENST00000380036	NM_000459.3	152	Gat/Aat	3/23	0.277094574347477	2	FACETS	0.6	0.545	0.657	0.3	0.272	0.329	INDETERMINATE	1	TRUE	0	0.691860130310183	2		731	622	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156720	20156720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	81	568	1	ENST00000379607.5:c.37C>T	p.Arg13Cys	p.R13C	ENST00000379607	NM_001412.3	13	Cgc/Tgc	2/7	1	2	FACETS	0.534	0.469	0.604	0.534	0.469	0.604	SUBCLONAL	1	TRUE	1	0.322315659883041	2		569	941	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793008	33793010	+	inframe_deletion	In_Frame_Del	DEL	CGC	CGC	-	rs780345232	NA	P-0024890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	11	113	1	ENST00000498907.2:c.311_313del	p.Gly104del	p.G104del	ENST00000498907	NM_004364.3	104	gGCGac/gac	1/1	1	2	FACETS	0.446	0.309	0.615	0.446	0.309	0.615	SUBCLONAL	1	TRUE	1	0.322315659883041	2		114	153	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130389	29130389	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs587782401	NA	P-0024890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	51	478	0	ENST00000328354.6:c.319+2T>C		p.X107_splice	ENST00000328354	NM_007194.3	107			1	2	FACETS	0.524	0.445	0.611	0.524	0.445	0.611	SUBCLONAL	1	TRUE	1	0.322315659883041	2		478	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0024892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	131	630	0	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	0.478402278826356	3	FACETS	1	0.979	1	0.626	0.57	0.684	CLONAL	1	TRUE	1	0.473106167473247	3		630	547	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249029	55249029	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	8	507	1	ENST00000275493.2:c.2327G>T	p.Arg776Leu	p.R776L	ENST00000275493	NM_005228.3	776	cGc/cTc	20/28	0.394061987520253	3	FACETS	0.116	0.074	0.171	0.058	0.037	0.086	SUBCLONAL	1	TRUE	1	0.473106167473247	3		508	361	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920422	114920422	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	58	560	2	ENST00000543371.1:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000543371	NM_001198531.1	455	Cga/Tga	13/14	0.478402278826356	3	FACETS	0.785	0.677	0.902	0.393	0.338	0.451	CLONAL	1	TRUE	1	0.473106167473247	3		562	386	SUCCESS
APC	324	MSKCC	GRCh37	5	112174484	112174484	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	67	261	1	ENST00000257430.4:c.3193C>T	p.Gln1065Ter	p.Q1065*	ENST00000257430	NM_000038.5	1065	Caa/Taa	16/16	0.478402278826356	4	FACETS	0.944	0.833	1	0.629	0.555	0.707	CLONAL	2	TRUE	1	0.473106167473247	4		262	221	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119823	70119823	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	143	688	0	ENST00000245479.2:c.825del	p.Ile275MetfsTer4	p.I275Mfs*4	ENST00000245479	NM_000346.3	275	atC/at	3/3	0.341433049605598	4	FACETS	0.985	0.906	1	0.985	0.906	1	CLONAL	2	TRUE	2	0.473106167473247	4		688	452	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692988	89692988	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	28	443	0	ENST00000371953.3:c.472G>C	p.Val158Leu	p.V158L	ENST00000371953	NM_000314.4	158	Gta/Cta	5/9	0.478402278826356	3	FACETS	0.477	0.382	0.585	0.238	0.191	0.293	SUBCLONAL	1	TRUE	1	0.473106167473247	3		443	307	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052635	42052635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	61	526	1	ENST00000219905.7:c.7306C>T	p.Arg2436Cys	p.R2436C	ENST00000219905	NM_001164273.1	2436	Cgt/Tgt	20/24	0.341285104395187	4	FACETS	0.621	0.535	0.714			1	SUBCLONAL	1	TRUE	NA	0.473106167473247	4		527	612	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740695	58740696	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	rs755988177	NA	P-0024892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	37	504	0	ENST00000305921.3:c.1601_1602del	p.Phe534Ter	p.F534*	ENST00000305921	NM_003620.3	534	TTt/t	6/6	0.341433049605598	4	FACETS	0.5	0.412	0.598	0.25	0.206	0.299	SUBCLONAL	1	TRUE	2	0.473106167473247	4		504	461	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125428	7125428	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	125	797	0	ENST00000302850.5:c.3124G>T	p.Ala1042Ser	p.A1042S	ENST00000302850	NM_000208.2	1042	Gcc/Tcc	17/22	0.392437364299427	4	FACETS	1	0.98	1	0.653	0.593	0.716	CLONAL	1	TRUE	2	0.473106167473247	4		797	596	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252867	10252867	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758882865	NA	P-0024892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	116	539	0	ENST00000340748.4:c.3098C>T	p.Ala1033Val	p.A1033V	ENST00000340748		1033	gCg/gTg	29/40	0.392437364299427	4	FACETS	1	0.953	1	0.546	0.493	0.603	CLONAL	1	TRUE	2	0.473106167473247	4		539	661	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495321	212495321	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0024892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	19	434	1	ENST00000342788.4:c.1947-2A>G		p.X649_splice	ENST00000342788	NM_005235.2	649			0.314869021360953	1	FACETS	0.288	0.219	0.368	0.288	0.219	0.368	SUBCLONAL	1	TRUE	0	0.473106167473247	1		435	213	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029318	14029318	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	66	280	0	ENST00000311895.7:c.1529del	p.Val510AlafsTer9	p.V510Afs*9	ENST00000311895	NM_005236.2	510	gTc/gc	8/11	1	2	FACETS	0.938	0.818	1	0.938	0.818	1	CLONAL	1	TRUE	1	0.331755191306655	2		280	424	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183832	10183832	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	95	500	0	ENST00000256474.2:c.301del	p.Leu101CysfsTer58	p.L101Cfs*58	ENST00000256474	NM_000551.3	101	Ctg/tg	1/3	0.331755191306655	1	FACETS	0.905	0.808	1	0.905	0.808	1	CLONAL	1	TRUE	0	0.331755191306655	1		500	528	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610567	52610567	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	102	455	0	ENST00000394830.3:c.3606del	p.Cys1203ValfsTer41	p.C1203Vfs*41	ENST00000394830	NM_018313.4	1202	acA/ac	23/30	0.331755191306655	1	FACETS	0.977	0.877	1	0.977	0.877	1	CLONAL	1	TRUE	0	0.331755191306655	1		455	525	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940407	31940408	+	missense_variant	Missense_Mutation	DNP	GC	GC	TA	novel	NA	P-0024894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	99	537	2	ENST00000375333.2:c.440_441delinsTA	p.Arg147Leu	p.R147L	ENST00000375333	NM_032454.1	147	cGC/cTA	3/8	1	2	FACETS	0.893	0.798	0.994	0.893	0.798	0.994	CLONAL	1	TRUE	1	0.331755191306655	2		539	668	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182108	99182108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	28	351	0	ENST00000074304.5:c.2173G>A	p.Glu725Lys	p.E725K	ENST00000074304	NM_001134224.1	725	Gag/Aag	21/26	1	2	FACETS	0.812	0.649	0.997	0.812	0.649	0.997	CLONAL	1	TRUE	1	0.19	2		351	363	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0024900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	93	562	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.401	0.355	0.45	0.401	0.355	0.45	SUBCLONAL	1	TRUE	1	0.431777938496386	2		563	1075	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368476	225368476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	62	706	0	ENST00000264414.4:c.1270G>A	p.Glu424Lys	p.E424K	ENST00000264414	NM_003590.4	424	Gaa/Aaa	9/16	1	2	FACETS	0.245	0.211	0.283	0.245	0.211	0.283	SUBCLONAL	1	TRUE	1	0.431777938496386	2		706	1171	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575194	48575194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555685186	NA	P-0024900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	66	337	0	ENST00000342988.3:c.388C>T	p.Pro130Ser	p.P130S	ENST00000342988	NM_005359.5	130	Cca/Tca	3/12	1	2	FACETS	0.525	0.456	0.6	0.525	0.456	0.6	SUBCLONAL	1	TRUE	1	0.431777938496386	2		337	582	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1040463	1040463	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	180	797	4	ENST00000358495.3:c.109C>A	p.Gln37Lys	p.Q37K	ENST00000358495	NM_134424.2	37	Cag/Aag	3/12	1	2	FACETS	0.695	0.64	0.753	0.695	0.64	0.753	SUBCLONAL	1	TRUE	1	0.431777938496386	2		801	1199	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66525014	66525014	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	128	256	0	ENST00000358598.2:c.773C>T	p.Ser258Phe	p.S258F	ENST00000358598	NM_212471.2	258	tCt/tTt	9/11	0.295369708917823	5	FACETS	0.777	0.706	0.851			1	SUBCLONAL	2	TRUE	NA	0.431777938496386	5		256	629	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61722610	61722610	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	66	444	0	ENST00000401558.2:c.1027C>G	p.Leu343Val	p.L343V	ENST00000401558	NM_003400.3	343	Ctc/Gtc	11/25	1	2	FACETS	0.444	0.385	0.508	0.444	0.385	0.508	SUBCLONAL	1	TRUE	1	0.431777938496386	2		444	689	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-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	722	869	4	ENST00000397752.3:c.3024_3028+3delinsTG		p.X1008_splice	ENST00000397752	NM_000245.2	1008		14/21	0.220149130286332	5	FACETS	0.993	0.959	1			1	INDETERMINATE	3	TRUE	NA	0.431777938496386	5		873	1849	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	122	552	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	0.169310815574899	2		552	1108	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518388	8518388	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	37	274	0	ENST00000356435.5:c.1003A>G	p.Thr335Ala	p.T335A	ENST00000356435		335	Aca/Gca	10/35	1	2	FACETS	0.963	0.794	1	0.963	0.794	1	CLONAL	1	TRUE	1	0.169310815574899	2		274	454	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544630	65544630	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs786203385	NA	P-0024901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	84	559	0	ENST00000358664.4:c.295+1G>A		p.X99_splice	ENST00000358664	NM_002382.4	99			0.169310815574899	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.169310815574899	1		559	869	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647272	2647272	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	122	592	1	ENST00000342085.4:c.1550A>T	p.His517Leu	p.H517L	ENST00000342085	NM_002613.4	517	cAc/cTc	13/14	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.169310815574899	2		593	1055	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128036800	128036800	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	85	612	0	ENST00000285398.2:c.1679T>G	p.Val560Gly	p.V560G	ENST00000285398	NM_000122.1	560	gTc/gGc	10/15	1	2	FACETS	0.861	0.759	0.972	0.861	0.759	0.972	CLONAL	1	TRUE	1	0.169310815574899	2		612	1166	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117874180	117874180	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0024901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	84	366	2	ENST00000297338.2:c.275-1G>T		p.X92_splice	ENST00000297338	NM_006265.2	92			0.169310815574899	3	FACETS	0.751	0.663	0.845	0.751	0.663	0.845	SUBCLONAL	2	TRUE	1	0.169310815574899	3		368	717	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695938	117695938	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142973937	NA	P-0024903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	43	499	0	ENST00000369458.3:c.499C>T	p.Arg167Trp	p.R167W	ENST00000369458	NM_024626.3	167	Cgg/Tgg	4/6	1	2	FACETS	0.482	0.403	0.572	0.482	0.403	0.572	SUBCLONAL	1	TRUE	1	0.25	2		499	713	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152093	55152093	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121908585	NA	P-0024904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	276	685	0	ENST00000257290.5:c.2525A>T	p.Asp842Val	p.D842V	ENST00000257290	NM_006206.4	842	gAc/gTc	18/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.627026885634022	2		685	835	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592705	28592705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201208287	NA	P-0024904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	135	528	1	ENST00000241453.7:c.2440G>A	p.Ala814Thr	p.A814T	ENST00000241453	NM_004119.2	814	Gcc/Acc	20/24	1	2	FACETS	0.671	0.611	0.733	0.671	0.611	0.733	SUBCLONAL	1	TRUE	1	0.627026885634022	2		529	642	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0024905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	195	364	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.718071181690659	3	FACETS	1	0.982	1	0.583	0.542	0.625	CLONAL	1	FALSE	1	0.709623188429185	3		364	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577505	7577505	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs745425759	NA	P-0024905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	455	618	0	ENST00000269305.4:c.776A>T	p.Asp259Val	p.D259V	ENST00000269305	NM_001126112.2	259	gAc/gTc	7/11	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	2	FALSE	NA	0.709623188429185	2		618	550	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117755	70117755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	182	561	0	ENST00000245479.2:c.223G>A	p.Glu75Lys	p.E75K	ENST00000245479	NM_000346.3	75	Gag/Aag	1/3	0.718071181690659	3	FACETS	1	0.935	1	0.505	0.467	0.544	CLONAL	1	FALSE	1	0.709623188429185	3		561	688	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720808	89720808	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1114167667	NA	P-0024905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	193	247	0	ENST00000371953.3:c.959T>A	p.Leu320Ter	p.L320*	ENST00000371953	NM_000314.4	320	tTa/tAa	8/9	0.215658119008087	1	FACETS		NA	1	1	0.995	1	INDETERMINATE	2	FALSE	0	0.709623188429185	1		247	231	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041390	42041390	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	134	637	0	ENST00000219905.7:c.5585C>T	p.Ser1862Phe	p.S1862F	ENST00000219905	NM_001164273.1	1862	tCt/tTt	17/24	0.303550903146486	5	FACETS	0.713	0.646	0.783			1	INDETERMINATE	1	FALSE	NA	0.709623188429185	5		637	1094	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160595	56160595	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	278	341	0	ENST00000399503.3:c.872del	p.Pro291LeufsTer21	p.P291Lfs*21	ENST00000399503	NM_005921.1	290	gCc/gc	4/20	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	2	FALSE	NA	0.709623188429185	2		341	324	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197187	26197187	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	210	502	2	ENST00000356476.2:c.292G>T	p.Glu98Ter	p.E98*	ENST00000356476		98	Gag/Tag	1/1	0.718071181690659	5	FACETS	1	0.986	1			1	CLONAL	1	FALSE	NA	0.709623188429185	5		504	985	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443613	29443613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519783	NA	P-0024907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	158	855	0	ENST00000389048.3:c.3604G>A	p.Gly1202Arg	p.G1202R	ENST00000389048	NM_004304.4	1202	Gga/Aga	23/29	0.515687368816743	3	FACETS	0.871	0.798	0.947	0.436	0.399	0.474	CLONAL	1	TRUE	1	0.515418358113169	3		855	885	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374320	81374320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	110	313	0	ENST00000222390.5:c.742G>A	p.Glu248Lys	p.E248K	ENST00000222390	NM_000601.4	248	Gaa/Aaa	6/18	0.512946942299238	4	FACETS	1	0.944	1	0.535	0.482	0.592	CLONAL	1	TRUE	2	0.515418358113169	4		313	604	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141499	11141499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	335	718	0	ENST00000358026.2:c.3476G>A	p.Gly1159Glu	p.G1159E	ENST00000358026	NM_001128849.1	1159	gGg/gAg	25/36	0.515418358113169	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.515418358113169	2		718	645	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443631	29443631	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519784	NA	P-0024907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	185	855	3	ENST00000389048.3:c.3586C>A	p.Leu1196Met	p.L1196M	ENST00000389048	NM_004304.4	1196	Ctg/Atg	23/29	0.515687368816743	3	FACETS	0.951	0.878	1	0.476	0.439	0.514	CLONAL	1	TRUE	1	0.515418358113169	3		858	949	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256919	41256919	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	433	840	1	ENST00000357654.3:c.267del	p.Ile90PhefsTer29	p.I90Ffs*29	ENST00000357654	NM_007294.3	89	atC/at	5/23	0.515687368816743	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.515418358113169	3		841	1047	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469139	25469139	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs773260349	NA	P-0024907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	439	883	1	ENST00000264709.3:c.1319G>A	p.Trp440Ter	p.W440*	ENST00000264709	NM_175629.2	440	tGg/tAg	11/23	0.515687368816743	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.515418358113169	3		884	1022	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038203	128038203	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	174	612	0	ENST00000285398.2:c.1347G>C	p.Lys449Asn	p.K449N	ENST00000285398	NM_000122.1	449	aaG/aaC	9/15	0.515687368816743	3	FACETS	1	0.925	1	0.502	0.462	0.543	CLONAL	1	TRUE	1	0.515418358113169	3		612	846	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0024908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	257	606	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.265817716375633	3	FACETS	0.812	0.759	0.867	0.812	0.759	0.867	CLONAL	2	TRUE	1	0.265817716375633	3		606	1349	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832409	72832409	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	80	345	0	ENST00000268489.5:c.4172T>A	p.Leu1391Gln	p.L1391Q	ENST00000268489	NM_006885.3	1391	cTg/cAg	9/10	0.265817716375633	3	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.265817716375633	3		345	480	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911371	39911371	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	99	184	0	ENST00000378444.4:c.5259C>G	p.Asn1753Lys	p.N1753K	ENST00000378444	NM_001123385.1	1753	aaC/aaG	15/15	0.0957695198726776	2	FACETS	1	0.97	1			1	INDETERMINATE	2	TRUE	NA	0.265817716375633	2		184	313	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593603	55593603	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913235	NA	P-0024909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	364	421	0	ENST00000288135.5:c.1669T>C	p.Trp557Arg	p.W557R	ENST00000288135	NM_000222.2	557	Tgg/Cgg	11/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.954775998138525	2		421	755	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	29	510	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.182292469658432	4	FACETS	0.617	0.494	0.758	0.206	0.164	0.253	SUBCLONAL	1	TRUE	1	0.207987402160057	4		510	546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0024910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	341	847	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.207987402160057	2	FACETS	0.961	0.913	1	1	0.996	1	CLONAL	4	TRUE	0	0.207987402160057	2		849	853	SUCCESS
APC	324	MSKCC	GRCh37	5	112174784	112174784	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0024910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	71	361	0	ENST00000257430.4:c.3493A>T	p.Lys1165Ter	p.K1165*	ENST00000257430	NM_000038.5	1165	Aaa/Taa	16/16	1	2	FACETS	0.908	0.797	1	1	0.98	1	CLONAL	2	TRUE	1	0.207987402160057	2		361	376	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0024910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	118	466	0	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	1	2	FACETS	0.985	0.892	1	1	0.989	1	CLONAL	2	TRUE	1	0.207987402160057	2		466	576	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154797	2154797	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	155	761	0	ENST00000434045.2:c.424A>T	p.Thr142Ser	p.T142S	ENST00000434045	NM_001127598.1	142	Acc/Tcc	4/5	0.207987402160057	5	FACETS	0.868	0.793	0.946	0.434	0.396	0.473	CLONAL	2	TRUE	1	0.207987402160057	5		761	1127	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987106	36987106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	394	650	1	ENST00000354822.5:c.583C>T	p.Arg195Trp	p.R195W	ENST00000354822	NM_001079668.2	195	Cgg/Tgg	3/3	0.207987402160057	2	FACETS	0.905	0.866	0.945	1	0.997	1	CLONAL	5	TRUE	0	0.207987402160057	2		651	837	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175213	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0024910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	55	228	0	ENST00000257430.4:c.3923_3924del	p.Lys1308ArgfsTer6	p.K1308Rfs*6	ENST00000257430	NM_000038.5	1307	atAAaa/ataa	16/16	1	2	FACETS	0.816	0.702	0.939	1	0.971	1	CLONAL	2	TRUE	1	0.207987402160057	2		228	324	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965617	93965617	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	120	585	0	ENST00000369303.4:c.2311G>C	p.Val771Leu	p.V771L	ENST00000369303	NM_004440.3	771	Gtt/Ctt	13/17	0.207987402160057	5	FACETS	0.899	0.812	0.991	0.599	0.541	0.661	CLONAL	2	TRUE	2	0.207987402160057	5		585	842	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103384	77103385	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	70	424	1	ENST00000356341.3:c.181_182delinsAA	p.Gly61Lys	p.G61K	ENST00000356341	NM_002576.4	61	GGa/AAa	2/15	0.704949832105686	4	FACETS	0.741	0.648	0.84			1	SUBCLONAL	1	TRUE	NA	0.768648572437714	4		425	435	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103457	77103457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs997423059	NA	P-0024919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	92	542	1	ENST00000356341.3:c.109G>A	p.Gly37Ser	p.G37S	ENST00000356341	NM_002576.4	37	Ggt/Agt	2/15	0.704949832105686	4	FACETS	0.766	0.682	0.854			1	SUBCLONAL	1	TRUE	NA	0.768648572437714	4		543	553	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121912	2121912	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201769220	NA	P-0024919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	364	986	3	ENST00000219476.3:c.2074G>A	p.Val692Ile	p.V692I	ENST00000219476	NM_000548.3	692	Gtc/Atc	19/42	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.768648572437714	2		989	447	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211679	5211679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	62	929	1	ENST00000357368.4:c.5156G>A	p.Ser1719Asn	p.S1719N	ENST00000357368	NM_002850.3	1719	aGc/aAc	33/38	0.616193111866915	4	FACETS	0.332	0.286	0.382			1	SUBCLONAL	1	TRUE	NA	0.768648572437714	4		930	860	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0024927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	9	255	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.441	0.291	0.634	0.441	0.291	0.634	SUBCLONAL	1	TRUE	1	0.12	2		255	340	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727455	66727455	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs869025608	NA	P-0024927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	21	419	1	ENST00000307102.5:c.171G>T	p.Lys57Asn	p.K57N	ENST00000307102	NM_002755.3	57	aaG/aaT	2/11	1	2	FACETS	1	0.797	1	1	0.797	1	CLONAL	1	TRUE	1	0.12	2		420	337	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0024927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	12	347	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.573	0.401	0.786	0.573	0.401	0.786	SUBCLONAL	1	TRUE	1	0.12	2		347	349	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757438	40757438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	48	613	0	ENST00000373198.4:c.2860G>A	p.Asp954Asn	p.D954N	ENST00000373198	NM_133170.3	954	Gat/Aat	20/32	1	2	FACETS	0.763	0.645	0.893	1	0.962	1	SUBCLONAL	2	TRUE	1	0.12	2		613	524	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138570	55138570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	38	462	0	ENST00000257290.5:c.1247C>T	p.Ser416Phe	p.S416F	ENST00000257290	NM_006206.4	416	tCc/tTc	9/23	0.121642350105681	3	FACETS	1	0.94	1	0.677	0.559	0.808	CLONAL	1	TRUE	1	0.12	3		462	496	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	544	781	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.246460164747443	3	FACETS	1	0.962	1			1	CLONAL	17	TRUE	1	0.05	3		786	1311	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	193	661	20	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	1	0.951	1	1	0.995	1	CLONAL	7	TRUE	1	0.05	2		681	1063	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163554	32163554	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1392	310	543	1	ENST00000375023.3:c.5672del	p.Gly1891AlafsTer13	p.G1891Afs*13	ENST00000375023	NM_004557.3	1891	gGc/gc	30/30	0.366257023076068	4	FACETS	0.956	0.899	1	1	0.997	1	CLONAL	8	TRUE	2	0.05	4		544	1702	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	62	428	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	1	0.909	1	1	0.987	1	CLONAL	7	TRUE	1	0.05	2		428	335	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	46	430	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.974	0.831	1	1	0.983	1	CLONAL	10	TRUE	1	0.05	2		430	189	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	96	354	5	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.995	0.893	1	1	0.992	1	CLONAL	10	TRUE	1	0.05	2		359	386	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	85	458	10	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.959	0.853	1	1	0.991	1	CLONAL	9	TRUE	1	0.05	2		468	394	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	94	389	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	0.153160942734435	4	FACETS	0.985	0.88	1	1	0.99	1	CLONAL	8	TRUE	2	0.05	4		389	501	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	150	425	2	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.246460164747443	3	FACETS	1	0.954	1	1	0.993	1	CLONAL	6	TRUE	1	0.05	3		427	961	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	26	347	3	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	0.0819512859152139	0	FACETS	0.941	0.754	1			1	CLONAL	7	TRUE	0	0.05	0		350	150	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221709	22221714	+	inframe_deletion	In_Frame_Del	DEL	CCGCCG	CCGCCG	-	rs751880548	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	53	161	3	ENST00000215832.6:c.17_22del	p.Ala6_Ala7del	p.A6_A7del	ENST00000215832	NM_002745.4	6	gCGGCGGgc/ggc	1/9	0.153160942734435	3	FACETS	1	0.869	1	1	0.979	1	CLONAL	5	TRUE	1	0.05	3		164	427	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	90	436	2	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	0.246460164747443	3	FACETS	0.988	0.88	1	1	0.99	1	CLONAL	8	TRUE	1	0.05	3		438	467	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913253	39913253	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	262	287	0	ENST00000378444.4:c.4862del	p.Pro1621GlnfsTer53	p.P1621Qfs*53	ENST00000378444	NM_001123385.1	1621	cCa/ca	14/15	0.3	2	FACETS	1	0.955	1	1	0.997	1	CLONAL	20	TRUE	0	0.05	2		287	520	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882049	36882050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs780753361	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	240	732	5	ENST00000358127.4:c.963dup	p.Ala322ArgfsTer19	p.A322Rfs*19	ENST00000358127	NM_001280556.1	321	-/C	8/10	1	2	FACETS	1	0.969	1	1	0.996	1	CLONAL	7	TRUE	1	0.05	2		737	1287	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794441	42794441	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1758	411	894	0	ENST00000575354.2:c.1526del	p.Pro509HisfsTer14	p.P509Hfs*14	ENST00000575354	NM_015125.3	507	cgC/cg	10/20	0.366257023076068	3	FACETS	0.971	0.921	1	1	0.997	1	CLONAL	8	TRUE	0	0.05	3		894	2169	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	61	506	8	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	1	0.872	1	1	0.987	1	CLONAL	8	TRUE	1	0.05	2		514	304	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332471	70332471	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	124	585	0	ENST00000373644.4:c.380del	p.Lys127ArgfsTer8	p.K127Rfs*8	ENST00000373644	NM_030625.2	126	Aaa/aa	2/12	0.153160942734435	3	FACETS	0.969	0.878	1	1	0.992	1	CLONAL	8	TRUE	1	0.05	3		585	656	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983877	2983877	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	188	740	0	ENST00000396946.4:c.653C>T	p.Ala218Val	p.A218V	ENST00000396946	NM_032415.4	218	gCg/gTg	5/25	1	2	FACETS	1	0.951	1	1	0.995	1	CLONAL	7	TRUE	1	0.05	2		740	1034	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248394	59248394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329490786	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	84	395	0	ENST00000371222.2:c.349G>A	p.Ala117Thr	p.A117T	ENST00000371222	NM_002228.3	117	Gcc/Acc	1/1	0.246460164747443	3	FACETS	0.925	0.815	1	1	0.983	1	CLONAL	4	TRUE	1	0.05	3		395	931	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992721	68992721	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs764112302	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	23	695	4	ENST00000288368.4:c.1693del	p.Ser565ArgfsTer10	p.S565Rfs*10	ENST00000288368	NM_024870.2	562	cgT/cg	16/40	0.0819512859152139	0	FACETS	1	0.827	1			1	CLONAL	5	TRUE	0	0.05	0		699	165	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262102	10262102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1210	89	691	1	ENST00000340748.4:c.2189G>A	p.Arg730His	p.R730H	ENST00000340748		730	cGc/cAc	23/40	0.153160942734435	4	FACETS	0.959	0.847	1	1	0.976	1	CLONAL	3	TRUE	2	0.05	4		692	1299	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047659	180047659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1006377301	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	207	651	3	ENST00000261937.6:c.2356G>A	p.Ala786Thr	p.A786T	ENST00000261937	NM_182925.4	786	Gct/Act	16/30	0.153160942734435	0	FACETS	0.978	0.908	1			1	CLONAL	8	TRUE	0	0.05	0		654	1005	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421039	49421039	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398123721	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	82	483	3	ENST00000301067.7:c.14710C>T	p.Arg4904Ter	p.R4904*	ENST00000301067	NM_003482.3	4904	Cga/Tga	48/54	0.366257023076068	4	FACETS	1	0.911	1	1	0.978	1	CLONAL	3	TRUE	2	0.05	4		486	1099	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435199	49435199	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	74	530	1	ENST00000301067.7:c.6354del	p.Ala2119LeufsTer25	p.A2119Lfs*25	ENST00000301067	NM_003482.3	2118	ccC/cc	31/54	0.366257023076068	4	FACETS	0.896	0.783	1	1	0.98	1	CLONAL	4	TRUE	2	0.05	4		531	867	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291084	10291084	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	261	644	1	ENST00000340748.4:c.387del	p.Lys130AsnfsTer129	p.K130Nfs*129	ENST00000340748		129	ccC/cc	4/40	0.153160942734435	4	FACETS	1	0.969	1	1	0.996	1	CLONAL	8	TRUE	2	0.05	4		645	1296	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624390	21624390	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	61	565	1	ENST00000421138.2:c.1639G>A	p.Ala547Thr	p.A547T	ENST00000421138		547	Gca/Aca	14/16	0.153160942734435	0	FACETS	0.923	0.802	1			1	CLONAL	8	TRUE	0	0.05	0		566	314	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209267	133209267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs5745021	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	243	609	1	ENST00000320574.5:c.6119C>T	p.Ala2040Val	p.A2040V	ENST00000320574	NM_006231.2	2040	gCg/gTg	44/49	1	2	FACETS	0.959	0.896	1	1	0.996	1	CLONAL	9	TRUE	1	0.05	2		610	1126	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67459188	67459188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760091844	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	216	511	0	ENST00000327367.4:c.604G>A	p.Ala202Thr	p.A202T	ENST00000327367	NM_005902.3	202	Gca/Aca	4/9	1	2	FACETS	1	0.952	1	1	0.996	1	CLONAL	9	TRUE	1	0.05	2		511	933	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581192	48581193	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	98	404	0	ENST00000342988.3:c.497_498del	p.Phe166Ter	p.F166*	ENST00000342988	NM_005359.5	166	TTt/t	5/12	1	2	FACETS	1	0.905	1	1	0.992	1	CLONAL	9	TRUE	1	0.05	2		404	432	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306664	41306664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	156	649	0	ENST00000373198.4:c.995G>A	p.Gly332Asp	p.G332D	ENST00000373198	NM_133170.3	332	gGc/gAc	7/32	0.3	0	FACETS	1	0.923	1			1	CLONAL	7	TRUE	0	0.05	0		649	840	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056175	26056175	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61742489	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	288	448	0	ENST00000343677.2:c.482C>T	p.Pro161Leu	p.P161L	ENST00000343677	NM_005319.3	161	cCg/cTg	1/1	0.3	8	FACETS	1	0.95	1			1	CLONAL	9	TRUE	NA	0.05	8		448	1452	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188975	11188975	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	60	666	0	ENST00000361445.4:c.5748G>A	p.Trp1916Ter	p.W1916*	ENST00000361445	NM_004958.3	1916	tgG/tgA	41/58	0.246460164747443	3	FACETS	0.929	0.8	1	1	0.976	1	CLONAL	4	TRUE	1	0.05	3		666	662	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255619	16255619	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	150	469	0	ENST00000375759.3:c.2884A>G	p.Lys962Glu	p.K962E	ENST00000375759	NM_015001.2	962	Aag/Gag	11/15	0.246460164747443	3	FACETS	1	0.95	1	1	0.994	1	CLONAL	8	TRUE	1	0.05	3		469	731	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261278	115261278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	219	559	0	ENST00000438362.2:c.2443C>T	p.Arg815Cys	p.R815C	ENST00000438362	NM_001242891.1	815	Cgc/Tgc	19/20	0.246460164747443	3	FACETS	0.97	0.903	1	1	0.996	1	CLONAL	9	TRUE	1	0.05	3		559	1028	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551942	150551942	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1341	277	467	0	ENST00000369026.2:c.65G>T	p.Gly22Val	p.G22V	ENST00000369026	NM_021960.4	22	gGg/gTg	1/3	0.246460164747443	3	FACETS	1	0.939	1	1	0.996	1	CLONAL	7	TRUE	1	0.05	3		467	1618	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800808	18800808	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1434167120	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	22	352	0	ENST00000266497.5:c.4186-2A>G		p.X1396_splice	ENST00000266497		1396			0.153160942734435	0	FACETS	0.984	0.781	1			1	CLONAL	10	TRUE	0	0.05	0		352	85	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859570	57859570	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1566559716	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	65	467	0	ENST00000228682.2:c.625-1G>A		p.X209_splice	ENST00000228682	NM_005269.2	209			0.366257023076068	4	FACETS	0.97	0.839	1	1	0.969	1	CLONAL	3	TRUE	2	0.05	4		467	938	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349139	11349139	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	211	357	1	ENST00000332029.2:c.197G>A	p.Arg66His	p.R66H	ENST00000332029	NM_003745.1	66	cGc/cAc	2/2	0.246460164747443	3	FACETS	1	0.958	1	1	0.995	1	CLONAL	8	TRUE	1	0.05	3		358	1035	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830964	72830964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	112	477	2	ENST00000268489.5:c.5617C>T	p.His1873Tyr	p.H1873Y	ENST00000268489	NM_006885.3	1873	Cac/Tac	9/10	0.153160942734435	4	FACETS	1	0.937	1	1	0.991	1	CLONAL	7	TRUE	2	0.05	4		479	638	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983223	7983225	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs1302782570	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	292	558	0	ENST00000319144.4:c.789_791del	p.Phe264del	p.F264del	ENST00000319144	NM_001139.2	263	ttCTTt/ttt	7/15	0.246460164747443	3	FACETS	1	0.958	1	1	0.997	1	CLONAL	8	TRUE	1	0.05	3		558	1458	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155436	99155436	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	113	355	0	ENST00000074304.5:c.662T>C	p.Leu221Pro	p.L221P	ENST00000074304	NM_001134224.1	221	cTg/cCg	9/26	0.0819512859152139	0	FACETS	0.958	0.866	1			1	CLONAL	8	TRUE	0	0.05	0		355	560	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523513	41523513	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	169	459	0	ENST00000263253.7:c.929T>C	p.Val310Ala	p.V310A	ENST00000263253	NM_001429.3	310	gTc/gCc	4/31	0.153160942734435	3	FACETS	0.993	0.914	1	1	0.994	1	CLONAL	8	TRUE	1	0.05	3		459	872	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026124	71026127	+	frameshift_variant	Frame_Shift_Del	DEL	CAAA	CAAA	-	novel	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	150	444	0	ENST00000318789.4:c.1495_1498del	p.Phe499LeufsTer27	p.F499Lfs*27	ENST00000318789	NM_032682.5	499	TTTGct/ct	17/21	0.246460164747443	3	FACETS	0.949	0.869	1	1	0.994	1	CLONAL	9	TRUE	1	0.05	3		444	720	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461564	138461564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202220571	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	66	514	1	ENST00000289153.2:c.457C>T	p.Arg153Cys	p.R153C	ENST00000289153	NM_006219.2	153	Cgc/Tgc	3/22	0.0819512859152139	0	FACETS	1	0.879	1			1	CLONAL	9	TRUE	0	0.05	0		515	278	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516975	187516975	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	59	378	0	ENST00000441802.2:c.13006G>A	p.Val4336Met	p.V4336M	ENST00000441802	NM_005245.3	4336	Gtg/Atg	26/27	0.3	5	FACETS	0.947	0.815	1			1	CLONAL	5	TRUE	NA	0.05	5		378	536	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323214	31323214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	254	503	0	ENST00000412585.2:c.775C>T	p.Pro259Ser	p.P259S	ENST00000412585	NM_005514.6	259	Cca/Tca	4/8	0.366257023076068	4	FACETS	0.989	0.924	1	1	0.996	1	CLONAL	8	TRUE	2	0.05	4		503	1348	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350151	81350151	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	17	378	0	ENST00000222390.5:c.1181G>T	p.Gly394Val	p.G394V	ENST00000222390	NM_000601.4	394	gGg/gTg	10/18	1	2	FACETS	1	0.769	1	1	0.943	1	CLONAL	3	TRUE	1	0.05	2		378	220	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929028	44929028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1358181248	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	28	218	0	ENST00000377967.4:c.2128C>T	p.Gln710Ter	p.Q710*	ENST00000377967	NM_021140.2	710	Caa/Taa	17/29	0.3	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	2	TRUE	0	0.05	2		218	499	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412123	63412124	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0024928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	257	455	0	ENST00000330258.3:c.1043dup	p.Gln349ProfsTer29	p.Q349Pfs*29	ENST00000330258	NM_152424.3	348	ggc/ggGc	2/2	1	1	FACETS	0.971	0.916	1	1	0.997	1	CLONAL	16	TRUE	0	0.05	1		455	645	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0024930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	275	670	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.274801307147004	3	FACETS	1	0.983	1			1	CLONAL	3	TRUE	NA	0.274801307147004	3		671	691	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7978975	7978975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769562383	NA	P-0024930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	210	563	0	ENST00000319144.4:c.1592C>T	p.Pro531Leu	p.P531L	ENST00000319144	NM_001139.2	531	cCg/cTg	12/15	0.274801307147004	3	FACETS	0.951	0.889	1			1	CLONAL	3	TRUE	NA	0.274801307147004	3		563	609	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0024930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	75	359	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	0.149203583026994	2	FACETS	0.775	0.684	0.872	0.775	0.684	0.872	INDETERMINATE	2	TRUE	0	0.274801307147004	2		359	352	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106408	27106434	+	inframe_deletion	In_Frame_Del	DEL	CTGCTGCTCATCCTGGGCAAGCTGATC	CTGCTGCTCATCCTGGGCAAGCTGATC	-	novel	NA	P-0024930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	100	441	0	ENST00000324856.7:c.6026_6052del	p.Leu2009_Leu2017del	p.L2009_L2017del	ENST00000324856	NM_006015.4	2007	CTGCTGCTCATCCTGGGCAAGCTGATC/-	20/20	0.274801307147004	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.274801307147004	1		441	447	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823913	3823913	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057520652	NA	P-0024930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	65	546	0	ENST00000262367.5:c.2302C>T	p.Arg768Ter	p.R768*	ENST00000262367	NM_004380.2	768	Cga/Tga	13/31	1	2	FACETS	0.879	0.763	1	0.879	0.763	1	CLONAL	1	TRUE	1	0.274801307147004	2		546	538	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056594	26056594	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	16	180	0	ENST00000343677.2:c.63G>T	p.Lys21Asn	p.K21N	ENST00000343677	NM_005319.3	21	aaG/aaT	1/1	1	2	FACETS	0.518	0.383	0.678	0.518	0.383	0.678	SUBCLONAL	1	TRUE	1	0.274801307147004	2		180	225	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0024932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	128	496	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.375956328106323	3	FACETS	0.86	0.785	0.938	0.86	0.785	0.938	CLONAL	2	TRUE	1	0.3929096214084	3		496	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0024932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	93	671	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.344937415115354	1	FACETS	0.926	0.828	1	0.926	0.828	1	CLONAL	1	TRUE	0	0.3929096214084	1		671	411	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145743003	145743003	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	66	216	0	ENST00000428558.2:c.101C>T	p.Ala34Val	p.A34V	ENST00000428558	NM_004260.3	34	gCg/gTg	2/22	0.3929096214084	3	FACETS	1	0.94	1	0.377	0.329	0.429	CLONAL	1	TRUE	0	0.3929096214084	3		216	355	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271393	26271393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	52	499	0	ENST00000305910.3:c.220G>A	p.Glu74Lys	p.E74K	ENST00000305910	NM_003534.2	74	Gaa/Aaa	1/1	0.253300378405001	4	FACETS	0.745	0.635	0.866			1	SUBCLONAL	1	TRUE	NA	0.3929096214084	4		499	495	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105258937	105258937	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	44	733	0	ENST00000349310.3:c.44G>C	p.Arg15Pro	p.R15P	ENST00000349310	NM_001014432.1	15	cGa/cCa	3/15	0.292008510522982	2	FACETS	0.456	0.382	0.538	0.228	0.191	0.269	SUBCLONAL	1	TRUE	0	0.3929096214084	2		733	491	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673761	30673761	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	85	395	0	ENST00000376406.3:c.3199C>G	p.Leu1067Val	p.L1067V	ENST00000376406	NM_014641.2	1067	Ctt/Gtt	10/15	1	2	FACETS	0.857	0.76	0.96	0.857	0.76	0.96	CLONAL	1	TRUE	1	0.3929096214084	2		395	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0024933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	140	562	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	NA	2	FACETS	0.836	0.763	0.912			1	INDETERMINATE	2	TRUE	NA	0.250234468226322	2		563	669	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0024933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	299	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.250234468226322	6	FACETS	1	0.977	1	1	0.977	1	CLONAL	5	TRUE	1	0.250234468226322	6		326	683	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278344	39278344	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	68	706	0	ENST00000402219.2:c.805A>G	p.Met269Val	p.M269V	ENST00000402219	NM_005633.3	269	Atg/Gtg	6/23	0.169805435696543	3	FACETS	0.748	0.649	0.854	0.374	0.324	0.427	SUBCLONAL	1	TRUE	1	0.250234468226322	3		706	818	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984079	2984079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	65	358	0	ENST00000396946.4:c.451G>A	p.Glu151Lys	p.E151K	ENST00000396946	NM_032415.4	151	Gag/Aag	5/25	0.169805435696543	3	FACETS	1	0.965	1	0.675	0.587	0.77	CLONAL	1	TRUE	1	0.250234468226322	3		358	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0024935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	378	587	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	1	2	FACETS	0.875	0.846	0.904	1	0.997	1	CLONAL	2	TRUE	1	0.810079364490095	2		587	533	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800941	243800941	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	148	520	0	ENST00000263826.5:c.533T>A	p.Ile178Asn	p.I178N	ENST00000263826	NM_005465.4	178	aTt/aAt	5/13	0.526900206984762	4	FACETS	0.868	0.794	0.946	0.289	0.264	0.316	CLONAL	1	TRUE	1	0.810079364490095	4		520	762	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754681	42754681	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	74	389	0	ENST00000222329.4:c.59C>A	p.Ser20Ter	p.S20*	ENST00000222329	NM_006494.2	20	tCg/tAg	2/4	1	2	FACETS	0.293	0.256	0.332	0.293	0.256	0.332	SUBCLONAL	1	TRUE	1	0.823706666987089	2		389	614	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933329	39933330	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	382	366	0	ENST00000378444.4:c.1269dup	p.Pro424ThrfsTer16	p.P424Tfs*16	ENST00000378444	NM_001123385.1	423	-/A	4/15	1	1	FACETS	0.813	0.78	0.845	0.813	0.78	0.845	CLONAL	1	TRUE	0	0.823706666987089	1		366	671	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115898	8115899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0024947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	64	583	0	ENST00000346208.3:c.1245dup	p.Leu416AlafsTer91	p.L416Afs*91	ENST00000346208		415	atg/atGg	6/6	0.240540001202493	1	FACETS	0.482	0.417	0.553	0.482	0.417	0.553	SUBCLONAL	1	TRUE	0	0.347665831078466	1		583	631	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438424	52438499	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATCCGAAGCACCTAGAACCTGGTAGCCTTAGAAAGCTGGGCTGACCTAAGGGCAGAGTTGGTGTTCTGCACGTCAT	ATCCGAAGCACCTAGAACCTGGTAGCCTTAGAAAGCTGGGCTGACCTAAGGGCAGAGTTGGTGTTCTGCACGTCAT	-	novel	NA	P-0024948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	133	218	0	ENST00000460680.1:c.1220_1250+45del		p.X407_splice	ENST00000460680	NM_004656.3	407		12/17	0.869160983778426	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.869160983778426	1		218	165	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486310	8486310	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	64	268	0	ENST00000356435.5:c.2507T>G	p.Met836Arg	p.M836R	ENST00000356435		836	aTg/aGg	17/35	0.869160983778426	1	FACETS	0.362	0.317	0.409	0.362	0.317	0.409	SUBCLONAL	1	TRUE	0	0.869160983778426	1		268	230	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0024949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	84	478	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.969	0.861	1	0.969	0.861	1	CLONAL	1	TRUE	1	0.429128804149024	2		478	404	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355283	81355283	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	49	381	0	ENST00000222390.5:c.1091G>T	p.Trp364Leu	p.W364L	ENST00000222390	NM_000601.4	364	tGg/tTg	9/18	0.147553325603078	4	FACETS	1	0.919	1	0.561	0.478	0.651	INDETERMINATE	1	TRUE	2	0.429128804149024	4		381	291	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274723	123274723	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1441011501	NA	P-0024949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	88	495	1	ENST00000358487.5:c.1195C>T	p.Arg399Ter	p.R399*	ENST00000358487	NM_000141.4	399	Cga/Tga	9/18	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.429128804149024	2		496	374	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164163	108164164	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs864622164	NA	P-0024949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	86	370	0	ENST00000278616.4:c.4741dup	p.Ile1581AsnfsTer5	p.I1581Nfs*5	ENST00000278616	NM_000051.3	1579	caa/cAaa	31/63	0.429128804149024	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.429128804149024	1		370	275	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649605	48649605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	18	673	0	ENST00000376670.3:c.89C>T	p.Ser30Leu	p.S30L	ENST00000376670	NM_002049.3	30	tCa/tTa	2/6	0.166180929539257	1	FACETS	0.196	0.147	0.253	0.196	0.147	0.253	INDETERMINATE	1	TRUE	0	0.429128804149024	1		673	337	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156848936	156848936	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	180	568	0	ENST00000524377.1:c.1828C>A	p.Leu610Met	p.L610M	ENST00000524377	NM_002529.3	610	Ctg/Atg	15/17	0.429128804149024	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.429128804149024	3		568	434	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70432717	70432717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	95	616	1	ENST00000373644.4:c.4739C>T	p.Ser1580Leu	p.S1580L	ENST00000373644	NM_030625.2	1580	tCa/tTa	8/12	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.429128804149024	2		617	374	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076762	102076764	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0024949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	21	557	0	ENST00000282441.5:c.943_945del	p.Lys315del	p.K315del	ENST00000282441	NM_001130145.2	314	gAGAag/gag	5/9	1	2	FACETS	0.233	0.179	0.297	0.233	0.179	0.297	SUBCLONAL	1	TRUE	1	0.429128804149024	2		557	420	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066811	30066811	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	51	495	0	ENST00000331968.5:c.2320T>C	p.Tyr774His	p.Y774H	ENST00000331968	NM_002742.2	774	Tat/Cat	16/18	0.429128804149024	6	FACETS	0.731	0.621	0.853			1	SUBCLONAL	1	TRUE	NA	0.429128804149024	6		495	604	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260251	10260251	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	45	506	0	ENST00000340748.4:c.2416G>T	p.Gly806Trp	p.G806W	ENST00000340748		806	Ggg/Tgg	25/40	0.166180929539257	1	FACETS	0.472	0.398	0.553	0.472	0.398	0.553	INDETERMINATE	1	TRUE	0	0.429128804149024	1		506	349	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463289	25463289	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	63	441	1	ENST00000264709.3:c.2204A>T	p.Tyr735Phe	p.Y735F	ENST00000264709	NM_175629.2	735	tAc/tTc	19/23	0.166180929539257	1	FACETS	0.821	0.716	0.932	0.821	0.716	0.932	INDETERMINATE	1	TRUE	0	0.429128804149024	1		442	281	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164090	47164090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750308104	NA	P-0024949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	79	381	0	ENST00000409792.3:c.2036C>T	p.Ala679Val	p.A679V	ENST00000409792	NM_014159.6	679	gCa/gTa	3/21	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.429128804149024	2		381	348	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-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	95	381	3	ENST00000265433.3:c.38-4_45delinsATAAAT		p.X13_splice	ENST00000265433	NM_002485.4	13		2/16	0.429128804149024	3	FACETS	1	0.98	1	0.708	0.635	0.784	CLONAL	1	TRUE	1	0.429128804149024	3		384	380	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752987	128752987	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	34	352	0	ENST00000377970.2:c.1148A>T	p.Asn383Ile	p.N383I	ENST00000377970	NM_002467.4	383	aAc/aTc	3/3	0.429128804149024	3	FACETS	0.4	0.326	0.483	0.2	0.163	0.242	SUBCLONAL	1	TRUE	1	0.429128804149024	3		352	481	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47004897	47004897	+	intron_variant	Intron	SNP	G	G	T	rs1251032975	NA	P-0024949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	55	412	0	ENST00000377604.3:c.-126+13G>T		p.*42*	ENST00000377604	NM_001204468.1	-/163			0.166180929539257	1	FACETS	0.822	0.71	0.941	0.822	0.71	0.941	INDETERMINATE	1	TRUE	0	0.429128804149024	1		412	245	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040675	47040675	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	62	634	0	ENST00000377604.3:c.1310A>G	p.Tyr437Cys	p.Y437C	ENST00000377604	NM_001204468.1	437	tAc/tGc	13/24	0.166180929539257	1	FACETS	0.723	0.629	0.823	0.723	0.629	0.823	INDETERMINATE	1	TRUE	0	0.429128804149024	1		634	314	SUCCESS
AR	367	MSKCC	GRCh37	X	66931426	66931426	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	95	580	0	ENST00000374690.3:c.2068C>A	p.His690Asn	p.H690N	ENST00000374690	NM_000044.3	690	Cac/Aac	4/8	0.166180929539257	1	FACETS	0.906	0.813	1	0.906	0.813	1	INDETERMINATE	1	TRUE	0	0.429128804149024	1		580	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0024950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	63	569	2	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	NA	2	FACETS	0.771	0.666	0.884			1	INDETERMINATE	1	FALSE	NA	0.270675004530508	2		571	604	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170774	11170774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568565786	NA	P-0024950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	35	627	0	ENST00000358026.2:c.4918C>T	p.Arg1640Trp	p.R1640W	ENST00000358026	NM_001128849.1	1640	Cgg/Tgg	35/36	0.227659793030458	0	FACETS	0.297	0.243	0.358			1	SUBCLONAL	1	FALSE	0	0.270675004530508	0		627	635	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712836	43712836	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1566921088	NA	P-0024950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	87	738	2	ENST00000382044.4:c.4348G>T	p.Asp1450Tyr	p.D1450Y	ENST00000382044	NM_001141980.1	1450	Gac/Tac	21/28	1	2	FACETS	0.731	0.646	0.823	0.731	0.646	0.823	SUBCLONAL	1	FALSE	1	0.270675004530508	2		740	879	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916178	9916178	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	34	547	0	ENST00000330684.3:c.2111A>T	p.Tyr704Phe	p.Y704F	ENST00000330684	NM_001134407.1	704	tAc/tTc	10/13	1	2	FACETS	0.413	0.336	0.499	0.413	0.336	0.499	SUBCLONAL	1	FALSE	1	0.270675004530508	2		547	609	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135057	11135057	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	61	645	2	ENST00000358026.2:c.3024C>A	p.Tyr1008Ter	p.Y1008*	ENST00000358026	NM_001128849.1	1008	taC/taA	21/36	0.227659793030458	0	FACETS	0.585	0.505	0.672			1	SUBCLONAL	1	FALSE	0	0.270675004530508	0		647	562	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795216	42795216	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	155	634	2	ENST00000575354.2:c.2296G>T	p.Gly766Cys	p.G766C	ENST00000575354	NM_015125.3	766	Ggc/Tgc	10/20	0.270675004530508	4	FACETS	0.968	0.887	1			1	CLONAL	2	FALSE	NA	0.270675004530508	4		636	752	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215903	142215903	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	37	440	0	ENST00000350721.4:c.5690A>T	p.Lys1897Met	p.K1897M	ENST00000350721	NM_001184.3	1897	aAg/aTg	33/47	1	2	FACETS	0.431	0.354	0.517	0.431	0.354	0.517	SUBCLONAL	1	FALSE	1	0.270675004530508	2		440	635	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56432330	56432330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771349279	NA	P-0024951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	102	459	0	ENST00000407977.2:c.2326G>A	p.Glu776Lys	p.E776K	ENST00000407977		776	Gag/Aag	10/10	1	2	FACETS	0.983	0.883	1	0.983	0.883	1	CLONAL	1	TRUE	1	0.40751378475517	2		459	509	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430371	78430371	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	109	586	1	ENST00000370768.2:c.797A>G	p.Asn266Ser	p.N266S	ENST00000370768	NM_003902.3	266	aAt/aGt	10/20	0.389599618811566	1	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	0	0.40751378475517	1		587	426	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0024952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	83	606	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.95	0.839	1	0.95	0.839	1	CLONAL	1	TRUE	1	0.2799267362777	2		606	624	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524486	44524486	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	38	312	0	ENST00000291552.4:c.71T>C	p.Ile24Thr	p.I24T	ENST00000291552	NM_006758.2	24	aTt/aCt	2/8	0.2799267362777	3	FACETS	0.806	0.667	0.96			1	CLONAL	1	TRUE	NA	0.2799267362777	3		312	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579336	7579337	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0024952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	75	624	0	ENST00000269305.4:c.350_351del	p.Gly117AspfsTer31	p.G117Dfs*31	ENST00000269305	NM_001126112.2	117	gGG/g	4/11	0.229825270675695	1	FACETS	0.86	0.755	0.972	0.86	0.755	0.972	CLONAL	1	TRUE	0	0.2799267362777	1		624	536	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435540	110435540	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1255216533	NA	P-0024953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	158	346	3	ENST00000375856.3:c.2861C>T	p.Pro954Leu	p.P954L	ENST00000375856	NM_003749.2	954	cCg/cTg	1/2	0.690238765448483	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.690238765448483	1		349	267	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134386	2134393	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCCGAG	CTCCCGAG	-	novel	NA	P-0024953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	225	529	2	ENST00000219476.3:c.4165_4172del	p.Pro1389AlafsTer22	p.P1389Afs*22	ENST00000219476	NM_000548.3	1388	tCTCCCGAG/t	34/42	0.690238765448483	1	FACETS	0.949	0.896	1	0.949	0.896	1	CLONAL	1	TRUE	0	0.690238765448483	1		531	450	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711879	89711879	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1554900515	NA	P-0024954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	79	448	0	ENST00000371953.3:c.497T>A	p.Val166Glu	p.V166E	ENST00000371953	NM_000314.4	166	gTa/gAa	6/9	0.386161618177233	1	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	0	0.386161618177233	1		448	323	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665157	29665157	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	85	603	0	ENST00000356175.3:c.6756G>C	p.Lys2252Asn	p.K2252N	ENST00000356175	NM_000267.3	2252	aaG/aaC	44/57	0.386161618177233	1	FACETS	0.815	0.724	0.911	0.815	0.724	0.911	CLONAL	1	TRUE	0	0.386161618177233	1		603	436	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	126	314	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.778	0.713	0.845	0.778	0.713	0.845	SUBCLONAL	1	TRUE	1	0.909414680434915	2		314	356	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0024956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	135	288	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.973	0.9	1	0.973	0.9	1	CLONAL	1	TRUE	1	0.909414680434915	2		288	305	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	169	319	0	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	0.909414680434915	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.909414680434915	1		319	198	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413070	139413072	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0024956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	106	497	0	ENST00000277541.6:c.1070_1072del	p.Phe357del	p.F357del	ENST00000277541	NM_017617.3	357	tTCTac/tac	6/34	0.495255282158957	1	FACETS	0.22	0.197	0.244	0.22	0.197	0.244	INDETERMINATE	1	TRUE	0	0.909414680434915	1		497	578	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794440	42794441	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0024956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	37	729	0	ENST00000575354.2:c.1526dup	p.Leu510ThrfsTer4	p.L510Tfs*4	ENST00000575354	NM_015125.3	507	cgc/cgCc	10/20	0.909414680434915	1	FACETS	0.098	0.08	0.118	0.098	0.08	0.118	SUBCLONAL	1	TRUE	0	0.909414680434915	1		729	453	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791718	42791718	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1344635105	NA	P-0024956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	32	453	0	ENST00000575354.2:c.604C>T	p.Arg202Trp	p.R202W	ENST00000575354	NM_015125.3	202	Cgg/Tgg	5/20	0.909414680434915	1	FACETS	0.1	0.081	0.122	0.1	0.081	0.122	SUBCLONAL	1	TRUE	0	0.909414680434915	1		453	382	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795609	42795609	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	78	706	2	ENST00000575354.2:c.2694del	p.Ala900ProfsTer24	p.A900Pfs*24	ENST00000575354	NM_015125.3	897	Ccc/cc	10/20	0.909414680434915	1	FACETS	0.226	0.2	0.255	0.226	0.2	0.255	SUBCLONAL	1	TRUE	0	0.909414680434915	1		708	413	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439888	51439889	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0024956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	22	243	0	ENST00000262662.1:c.454_455dup	p.Val153LeufsTer4	p.V153Lfs*4	ENST00000262662		151	-/GT	4/4	0.909414680434915	1	FACETS	0.162	0.126	0.203	0.162	0.126	0.203	SUBCLONAL	1	TRUE	0	0.909414680434915	1		243	163	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793215	42793218	+	frameshift_variant	Frame_Shift_Del	DEL	CAGT	CAGT	-	novel	NA	P-0024956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	145	675	0	ENST00000575354.2:c.1110_1113del	p.Ser370ArgfsTer6	p.S370Rfs*6	ENST00000575354	NM_015125.3	369	gaCAGT/ga	7/20	0.909414680434915	1	FACETS	0.381	0.35	0.413	0.381	0.35	0.413	SUBCLONAL	1	TRUE	0	0.909414680434915	1		675	456	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796982	42796982	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	60	738	0	ENST00000575354.2:c.3443del	p.Pro1148ArgfsTer13	p.P1148Rfs*13	ENST00000575354	NM_015125.3	1147	gCc/gc	14/20	0.909414680434915	1	FACETS	0.135	0.116	0.156	0.135	0.116	0.156	SUBCLONAL	1	TRUE	0	0.909414680434915	1		738	533	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907100	101907101	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024963-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	58	449	0	ENST00000374994.4:c.1061dup	p.Ala355GlyfsTer5	p.A355Gfs*5	ENST00000374994	NM_004612.2	354	ctg/cTtg	6/9	1	2	FACETS	0.851	0.732	0.98	0.851	0.732	0.98	CLONAL	1	TRUE	1	0.278155081159904	2		449	490	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720699	89720699	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs786202840	NA	P-0024966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	11	79	0	ENST00000371953.3:c.850G>T	p.Glu284Ter	p.E284*	ENST00000371953	NM_000314.4	284	Gag/Tag	8/9	0.400479327516028	1	FACETS	0.494	0.345	0.673	0.494	0.345	0.673	SUBCLONAL	1	TRUE	0	0.400479327516028	1		79	89	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662939	52662939	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	130	563	0	ENST00000394830.3:c.1414C>T	p.Arg472Ter	p.R472*	ENST00000394830	NM_018313.4	472	Cga/Tga	13/30	0.400479327516028	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.400479327516028	1		563	517	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091838	29091838	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	54	258	1	ENST00000328354.6:c.1119G>T	p.Lys373Asn	p.K373N	ENST00000328354	NM_007194.3	373	aaG/aaT	11/15	0.291872891751367	1	FACETS	0.888	0.766	1	0.888	0.766	1	CLONAL	1	TRUE	0	0.400479327516028	1		259	243	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755740	39755740	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747083136	NA	P-0024966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	49	438	2	ENST00000288319.7:c.1025C>T	p.Thr342Met	p.T342M	ENST00000288319	NM_182918.3	342	aCg/aTg	10/10	1	2	FACETS	0.457	0.387	0.535	0.457	0.387	0.535	SUBCLONAL	1	TRUE	1	0.400479327516028	2		440	535	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191545	10191545	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	133	467	0	ENST00000256474.2:c.538del	p.Ile180SerfsTer22	p.I180Sfs*22	ENST00000256474	NM_000551.3	180	Atc/tc	3/3	0.400479327516028	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.400479327516028	1		467	467	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240705	53240705	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0024966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	64	298	0	ENST00000375401.3:c.1375A>T	p.Lys459Ter	p.K459*	ENST00000375401	NM_004187.3	459	Aaa/Taa	10/26	1	1	FACETS	0.772	0.673	0.878	0.772	0.673	0.878	SUBCLONAL	1	TRUE	0	0.400479327516028	1		298	331	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0024967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	52	606	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.222962538913328	3	FACETS	1	0.957	1	0.675	0.577	0.781	CLONAL	1	TRUE	1	0.242031490469207	3		606	357	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217230	11217230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786205165	NA	P-0024967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	130	433	0	ENST00000361445.4:c.4448G>A	p.Cys1483Tyr	p.C1483Y	ENST00000361445	NM_004958.3	1483	tGc/tAc	30/58	0.190469958713245	2	FACETS	0.858	0.78	0.939	0.858	0.78	0.939	CLONAL	2	TRUE	0	0.242031490469207	2		433	626	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	24	510	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.701	0.55	0.874	0.701	0.55	0.874	SUBCLONAL	1	TRUE	1	0.242031490469207	2		510	283	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872557	37872557	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	65	277	0	ENST00000269571.5:c.1517G>T	p.Gly506Val	p.G506V	ENST00000269571		506	gGc/gTc	13/27	0.222962538913328	3	FACETS	0.839	0.731	0.954	0.839	0.731	0.954	CLONAL	2	TRUE	1	0.242031490469207	3		277	359	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118864	70118864	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	84	263	0	ENST00000245479.2:c.436del	p.Leu146Ter	p.L146*	ENST00000245479	NM_000346.3	146	Ctg/tg	2/3	0.222962538913328	3	FACETS	0.863	0.765	0.966	0.863	0.765	0.966	CLONAL	2	TRUE	1	0.242031490469207	3		263	451	SUCCESS
APC	324	MSKCC	GRCh37	5	112174405	112174406	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0024967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	17	202	0	ENST00000257430.4:c.3116dup	p.Arg1040LysfsTer8	p.R1040Kfs*8	ENST00000257430	NM_000038.5	1038	-/G	16/16	0.222483701610881	1	FACETS	0.928	0.699	1	0.928	0.699	1	CLONAL	1	TRUE	0	0.242031490469207	1		202	133	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0024968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	69	375	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.786	0.687	0.892	0.786	0.687	0.892	SUBCLONAL	1	TRUE	1	0.4	2		375	439	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	568	781	5	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	0.644287679417334	2		786	830	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	171	304	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	0.925	0.856	0.996	0.925	0.856	0.996	CLONAL	1	TRUE	1	0.644287679417334	2		304	574	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	176	430	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.855	0.791	0.921	0.855	0.791	0.921	CLONAL	1	TRUE	1	0.644287679417334	2		430	639	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	216	432	2	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.644287679417334	2		434	621	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	305	458	10	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.897	0.846	0.949	0.897	0.846	0.949	CLONAL	1	TRUE	1	0.644287679417334	2		468	1056	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	216	447	2	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.835	0.778	0.894	0.835	0.778	0.894	CLONAL	1	TRUE	1	0.644287679417334	2		449	803	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	333	579	1	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.644287679417334	2		580	1006	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460401	149460401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	244	535	2	ENST00000286301.3:c.236C>T	p.Thr79Met	p.T79M	ENST00000286301	NM_005211.3	79	aCg/aTg	3/22	1	2	FACETS	0.895	0.839	0.953	0.895	0.839	0.953	CLONAL	1	TRUE	1	0.644287679417334	2		537	846	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451784	29451784	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs772809305	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	320	638	5	ENST00000389048.3:c.2781del	p.Cys928AlafsTer11	p.C928Afs*11	ENST00000389048	NM_004304.4	927	ggG/gg	16/29	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.644287679417334	2		643	975	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	533	553	13	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	0.916	0.886	0.946	1	0.998	1	CLONAL	2	TRUE	1	0.644287679417334	2		566	903	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733513	85733513	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs387906350	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	205	552	3	ENST00000370580.1:c.499del	p.Ser167LeufsTer6	p.S167Lfs*6	ENST00000370580	NM_003921.4	167	Tct/ct	3/3	1	2	FACETS	0.851	0.792	0.912	0.851	0.792	0.912	CLONAL	1	TRUE	1	0.644287679417334	2		555	748	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1039289	1039289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11571421	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	273	534	0	ENST00000358495.3:c.208C>T	p.Arg70Trp	p.R70W	ENST00000358495	NM_134424.2	70	Cgg/Tgg	4/12	NA	2	FACETS	0.93	0.875	0.987			1	INDETERMINATE	1	TRUE	NA	0.644287679417334	2		534	911	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118924	70118926	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	302	611	0	ENST00000245479.2:c.499_501del	p.Lys167del	p.K167del	ENST00000245479	NM_000346.3	166	AAG/-	2/3	1	2	FACETS	0.932	0.879	0.986	0.932	0.879	0.986	CLONAL	1	TRUE	1	0.644287679417334	2		611	1006	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939674	76939674	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	258	737	2	ENST00000373344.5:c.1074del	p.Lys358AsnfsTer2	p.K358Nfs*2	ENST00000373344	NM_000489.3	358	aaA/aa	9/35	1	2	FACETS	0.814	0.763	0.866	0.814	0.763	0.866	CLONAL	1	TRUE	1	0.644287679417334	2		739	984	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206909	162206909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150562946	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	188	410	1	ENST00000366898.1:c.766C>T	p.Arg256Cys	p.R256C	ENST00000366898	NM_004562.2	256	Cgc/Tgc	7/12	1	2	FACETS	0.961	0.893	1	0.961	0.893	1	CLONAL	1	TRUE	1	0.644287679417334	2		411	607	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781402	3781402	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	283	546	0	ENST00000262367.5:c.4963del	p.Leu1655CysfsTer89	p.L1655Cfs*89	ENST00000262367	NM_004380.2	1655	Ctg/tg	30/31	1	2	FACETS	0.997	0.94	1	0.997	0.94	1	CLONAL	1	TRUE	1	0.644287679417334	2		546	881	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459100	120459100	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	292	587	0	ENST00000256646.2:c.6245C>T	p.Pro2082Leu	p.P2082L	ENST00000256646	NM_024408.3	2082	cCt/cTt	34/34	1	2	FACETS	0.956	0.901	1	0.956	0.901	1	CLONAL	1	TRUE	1	0.644287679417334	2		587	948	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216512	108216512	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876660081	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	394	444	2	ENST00000278616.4:c.8461A>G	p.Met2821Val	p.M2821V	ENST00000278616	NM_000051.3	2821	Atg/Gtg	58/63	0.644287679417334	2	FACETS	0.947	0.911	0.982	0.947	0.911	0.982	CLONAL	2	TRUE	0	0.644287679417334	2		446	646	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307495	118307500	+	inframe_deletion	In_Frame_Del	DEL	TCGTCT	TCGTCT	-	novel	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	187	477	0	ENST00000534358.1:c.279_284del	p.Ser97_Ser98del	p.S97_S98del	ENST00000534358	NM_005933.3	90	TCGTCT/-	1/36	0.644287679417334	2	FACETS	0.833	0.772	0.896	0.416	0.386	0.448	CLONAL	1	TRUE	0	0.644287679417334	2		477	697	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125507403	125507403	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	199	463	0	ENST00000428830.2:c.783del	p.Asp262IlefsTer42	p.D262Ifs*42	ENST00000428830	NM_001114121.2	260	Aaa/aa	8/14	0.644287679417334	2	FACETS	0.902	0.839	0.967	0.451	0.419	0.484	CLONAL	1	TRUE	0	0.644287679417334	2		463	685	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864218	57864218	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	245	525	4	ENST00000228682.2:c.1700del	p.Pro567LeufsTer46	p.P567Lfs*46	ENST00000228682	NM_005269.2	565	ttC/tt	12/12	1	2	FACETS	0.98	0.919	1	0.98	0.919	1	CLONAL	1	TRUE	1	0.644287679417334	2		529	776	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32971138	32971138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507432	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	188	589	2	ENST00000380152.3:c.9605C>T	p.Pro3202Leu	p.P3202L	ENST00000380152		3202	cCg/cTg	26/27	1	2	FACETS	0.876	0.813	0.941	0.876	0.813	0.941	CLONAL	1	TRUE	1	0.644287679417334	2		591	666	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504501	103504501	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	118	343	0	ENST00000355739.4:c.122G>T	p.Gly41Val	p.G41V	ENST00000355739	NM_000123.3	41	gGa/gTa	2/15	1	2	FACETS	0.745	0.675	0.817	0.745	0.675	0.817	SUBCLONAL	1	TRUE	1	0.644287679417334	2		343	492	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103520471	103520471	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778290	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	120	294	0	ENST00000355739.4:c.2542C>T	p.Arg848Trp	p.R848W	ENST00000355739	NM_000123.3	848	Cgg/Tgg	12/15	1	2	FACETS	0.885	0.805	0.967	0.885	0.805	0.967	CLONAL	1	TRUE	1	0.644287679417334	2		294	421	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348864	11348864	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	102	156	0	ENST00000332029.2:c.472C>G	p.Pro158Ala	p.P158A	ENST00000332029	NM_003745.1	158	Ccg/Gcg	2/2	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.644287679417334	2		156	257	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346520	89346520	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555525685	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	236	590	0	ENST00000301030.4:c.6430C>T	p.Gln2144Ter	p.Q2144*	ENST00000301030	NM_001256183.1	2144	Cag/Tag	9/13	1	2	FACETS	0.985	0.923	1	0.985	0.923	1	CLONAL	1	TRUE	1	0.644287679417334	2		590	744	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682564	37682564	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	160	289	0	ENST00000447079.4:c.3755C>T	p.Ala1252Val	p.A1252V	ENST00000447079	NM_015083.1	1252	gCa/gTa	13/14	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.644287679417334	2		289	491	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463271	25463271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770568549	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	260	457	3	ENST00000264709.3:c.2222C>T	p.Ala741Val	p.A741V	ENST00000264709	NM_175629.2	741	gCg/gTg	19/23	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.644287679417334	2		460	755	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41554418	41554418	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	260	429	0	ENST00000263253.7:c.3504G>T	p.Leu1168Phe	p.L1168F	ENST00000263253	NM_001429.3	1168	ttG/ttT	19/31	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.644287679417334	2		429	759	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1795767	1795767	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	122	302	1	ENST00000260795.2:c.106G>A	p.Ala36Thr	p.A36T	ENST00000260795		36	Gca/Aca	1/17	1	2	FACETS	0.827	0.752	0.904	0.827	0.752	0.904	CLONAL	1	TRUE	1	0.644287679417334	2		303	458	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542812	187542812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	194	510	0	ENST00000441802.2:c.4928G>A	p.Gly1643Asp	p.G1643D	ENST00000441802	NM_005245.3	1643	gGc/gAc	10/27	1	2	FACETS	0.854	0.793	0.917	0.854	0.793	0.917	CLONAL	1	TRUE	1	0.644287679417334	2		510	705	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176666844	176666844	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	216	470	0	ENST00000439151.2:c.4280G>T	p.Gly1427Val	p.G1427V	ENST00000439151	NM_022455.4	1427	gGg/gTg	8/23	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.644287679417334	2		470	659	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912275	29912275	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	330	694	0	ENST00000376809.5:c.896-2A>G		p.X299_splice	ENST00000376809	NM_002116.7	299			1	2	FACETS	0.929	0.878	0.98	0.929	0.878	0.98	CLONAL	1	TRUE	1	0.644287679417334	2		694	1103	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860048	151860048	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	169	341	0	ENST00000262189.6:c.10614T>A	p.Asn3538Lys	p.N3538K	ENST00000262189	NM_170606.2	3538	aaT/aaA	43/59	1	2	FACETS	0.94	0.87	1	0.94	0.87	1	CLONAL	1	TRUE	1	0.644287679417334	2		341	558	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372037	55372037	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1217255052	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	269	506	1	ENST00000297316.4:c.727G>A	p.Gly243Arg	p.G243R	ENST00000297316	NM_022454.3	243	Ggg/Agg	2/2	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.644287679417334	2		507	781	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978659	70978659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370561462	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	301	653	0	ENST00000276594.2:c.994C>T	p.Arg332Cys	p.R332C	ENST00000276594	NM_024504.3	332	Cgc/Tgc	5/8	1	2	FACETS	0.948	0.894	1	0.948	0.894	1	CLONAL	1	TRUE	1	0.644287679417334	2		653	986	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211521	98211521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559827048	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	275	464	0	ENST00000331920.6:c.3634G>A	p.Gly1212Ser	p.G1212S	ENST00000331920	NM_000264.3	1212	Ggc/Agc	22/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.644287679417334	2		464	759	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409753	139409753	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs576030298	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	298	595	2	ENST00000277541.6:c.2003C>T	p.Pro668Leu	p.P668L	ENST00000277541	NM_017617.3	668	cCg/cTg	12/34	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.644287679417334	2		597	875	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44910997	44910997	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	238	490	0	ENST00000377967.4:c.698A>G	p.Gln233Arg	p.Q233R	ENST00000377967	NM_021140.2	233	cAg/cGg	9/29	1	2	FACETS	0.94	0.88	1	0.94	0.88	1	CLONAL	1	TRUE	1	0.644287679417334	2		490	786	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966655	44966655	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	109	348	1	ENST00000377967.4:c.3879G>T	p.Lys1293Asn	p.K1293N	ENST00000377967	NM_021140.2	1293	aaG/aaT	27/29	1	2	FACETS	0.808	0.73	0.888	0.808	0.73	0.888	CLONAL	1	TRUE	1	0.644287679417334	2		349	419	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0024974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	68	387	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.454042482430796	1	FACETS	0.629	0.55	0.713	0.629	0.55	0.713	SUBCLONAL	1	TRUE	0	0.462049026152461	1		387	360	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428038	49428038	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	93	308	0	ENST00000301067.7:c.10552C>T	p.Gln3518Ter	p.Q3518*	ENST00000301067	NM_003482.3	3518	Cag/Tag	38/54	1	2	FACETS	0.797	0.711	0.888	0.797	0.711	0.888	SUBCLONAL	1	TRUE	1	0.462049026152461	2		308	505	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2113043	2113043	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121964862	NA	P-0024974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	116	285	1	ENST00000219476.3:c.1432C>T	p.Gln478Ter	p.Q478*	ENST00000219476	NM_000548.3	478	Cag/Tag	14/42	0.454042482430796	1	FACETS	0.99	0.9	1	0.99	0.9	1	CLONAL	1	TRUE	0	0.462049026152461	1		286	390	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2137864	2137864	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	95	291	0	ENST00000219476.3:c.4990G>A	p.Gly1664Ser	p.G1664S	ENST00000219476	NM_000548.3	1664	Ggc/Agc	39/42	0.454042482430796	1	FACETS	0.735	0.659	0.816	0.735	0.659	0.816	SUBCLONAL	1	TRUE	0	0.462049026152461	1		291	430	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0024974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	122	393	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			1	2	FACETS	0.734	0.664	0.808	0.734	0.664	0.808	SUBCLONAL	1	TRUE	1	0.462049026152461	2		393	719	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946003	17946003	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771020913	NA	P-0024974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	136	358	0	ENST00000458235.1:c.1936G>A	p.Gly646Ser	p.G646S	ENST00000458235	NM_000215.3	646	Ggc/Agc	15/24	1	2	FACETS	0.93	0.848	1	0.93	0.848	1	CLONAL	1	TRUE	1	0.462049026152461	2		358	633	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902188	50902189	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGT	novel	NA	P-0024974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	76	286	0	ENST00000440232.2:c.82_83insTTG	p.Asp27_Ala28insVal	p.D27_A28insV	ENST00000440232	NM_002691.3	27	gat/gaTGTt	2/27	1	2	FACETS	0.661	0.581	0.746	0.661	0.581	0.746	SUBCLONAL	1	TRUE	1	0.462049026152461	2		286	498	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1959703	1959703	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	74	215	0	ENST00000382891.5:c.2925G>C	p.Gln975His	p.Q975H	ENST00000382891	NM_133335.3	975	caG/caC	16/22	0.185498779432779	4	FACETS	0.866	0.759	0.98			1	INDETERMINATE	1	TRUE	NA	0.462049026152461	4		215	541	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247268	153247278	+	frameshift_variant	Frame_Shift_Del	DEL	TGCCATCATAT	TGCCATCATAT	-	novel	NA	P-0024974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	93	319	0	ENST00000281708.4:c.1524_1534del	p.Tyr509GlufsTer4	p.Y509Efs*4	ENST00000281708	NM_033632.3	508	caATATGATGGCAgg/cagg	10/12	0.454042482430796	1	FACETS	0.774	0.693	0.859	0.774	0.693	0.859	SUBCLONAL	1	TRUE	0	0.462049026152461	1		319	400	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911102	29911103	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0024974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	213	310	0	ENST00000376809.5:c.403dup	p.Arg135ProfsTer42	p.R135Pfs*42	ENST00000376809	NM_002116.7	134	ctc/ctCc	3/8	0.405715616066023	2	FACETS	0.772	0.722	0.823	0.772	0.722	0.823	SUBCLONAL	2	TRUE	0	0.462049026152461	2		310	597	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93973624	93973628	+	frameshift_variant	Frame_Shift_Del	DEL	ACCAC	ACCAC	CCAA	novel	NA	P-0024974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	58	401	0	ENST00000369303.4:c.1748_1752delinsTTGG	p.Cys583PhefsTer46	p.C583Ffs*46	ENST00000369303	NM_004440.3	583	tGTGGT/tTTGG	9/17	0.454042482430796	1	FACETS	0.641	0.555	0.734	0.641	0.555	0.734	SUBCLONAL	1	TRUE	0	0.462049026152461	1		401	301	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69012017	69012017	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	125	492	0	ENST00000288368.4:c.2654T>C	p.Phe885Ser	p.F885S	ENST00000288368	NM_024870.2	885	tTc/tCc	23/40	1	2	FACETS	0.956	0.869	1	0.956	0.869	1	CLONAL	1	TRUE	1	0.462049026152461	2		492	566	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0024974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	92	184	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.454042482430796	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.462049026152461	1		184	292	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0024977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	212	478	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.250928760973774	6	FACETS	1	0.971	1			1	INDETERMINATE	3	TRUE	NA	0.634826505302175	6		478	479	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0024977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	172	226	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.634826505302175	4	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	2	0.634826505302175	4		226	439	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0024977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	289	379	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.622512266951901	2	FACETS	0.969	0.926	1	0.969	0.926	1	CLONAL	2	TRUE	0	0.634826505302175	2		379	470	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494873	56494873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752248295	NA	P-0024977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	190	337	0	ENST00000267101.3:c.3230G>A	p.Arg1077Gln	p.R1077Q	ENST00000267101	NM_001982.3	1077	cGg/cAg	27/28	0.634826505302175	6	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.634826505302175	6		337	1075	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989602	15989602	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	94	242	0	ENST00000268712.3:c.3171C>G	p.Ile1057Met	p.I1057M	ENST00000268712	NM_006311.3	1057	atC/atG	23/46	0.622512266951901	2	FACETS	1	0.957	1	0.555	0.501	0.61	CLONAL	1	TRUE	0	0.634826505302175	2		242	267	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257557	16257557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	84	321	0	ENST00000375759.3:c.4822G>A	p.Glu1608Lys	p.E1608K	ENST00000375759	NM_015001.2	1608	Gag/Aag	11/15	0.469896878097763	4	FACETS	1	0.946	1	0.553	0.492	0.618	CLONAL	1	TRUE	2	0.634826505302175	4		321	391	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164717	47164717	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0024977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	66	290	0	ENST00000409792.3:c.1409C>G	p.Ser470Ter	p.S470*	ENST00000409792	NM_014159.6	470	tCa/tGa	3/21	0.634826505302175	3	FACETS	0.881	0.771	0.998	0.44	0.385	0.499	CLONAL	1	TRUE	1	0.634826505302175	3		290	311	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257779	16257779	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	102	321	0	ENST00000375759.3:c.5044G>C	p.Glu1682Gln	p.E1682Q	ENST00000375759	NM_015001.2	1682	Gaa/Caa	11/15	0.469896878097763	4	FACETS	1	0.95	1	0.546	0.491	0.605	CLONAL	1	TRUE	2	0.634826505302175	4		321	481	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746135	162746135	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	207	211	0	ENST00000367921.3:c.2258G>A	p.Trp753Ter	p.W753*	ENST00000367921	NM_006182.2	753	tGg/tAg	16/18	0.496816464011509	5	FACETS	0.976	0.917	1			1	CLONAL	3	TRUE	NA	0.634826505302175	5		211	435	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609046	43609046	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	252	304	0	ENST00000355710.3:c.1802G>T	p.Gly601Val	p.G601V	ENST00000355710	NM_020975.4	601	gGg/gTg	10/20	0.634826505302175	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.634826505302175	4		304	584	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443843	18443843	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	57	363	0	ENST00000266497.5:c.816G>T	p.Trp272Cys	p.W272C	ENST00000266497		272	tgG/tgT	3/31	0.427525567213372	3	FACETS	0.946	0.838	1			1	CLONAL	2	TRUE	NA	0.634826505302175	3		363	125	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109709	115109709	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	147	420	0	ENST00000257566.3:c.2169C>A	p.Ser723Arg	p.S723R	ENST00000257566	NM_016569.3	723	agC/agA	8/8	0.634826505302175	3	FACETS	0.862	0.788	0.938	0.431	0.394	0.469	CLONAL	1	TRUE	1	0.634826505302175	3		420	708	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216899	7216899	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	137	295	0	ENST00000380728.2:c.622C>G	p.Gln208Glu	p.Q208E	ENST00000380728		208	Cag/Gag	7/11	0.622512266951901	2	FACETS	0.963	0.883	1	0.482	0.441	0.523	CLONAL	1	TRUE	0	0.634826505302175	2		295	448	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012099	16012099	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0024977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	180	334	0	ENST00000268712.3:c.2182+1G>T		p.X728_splice	ENST00000268712	NM_006311.3	728			0.622512266951901	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.634826505302175	2		334	280	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349643	15349643	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	123	328	0	ENST00000263377.2:c.3931C>T	p.Gln1311Ter	p.Q1311*	ENST00000263377	NM_058243.2	1311	Cag/Tag	19/20	0.634826505302175	3	FACETS	1	0.917	1	0.504	0.458	0.552	CLONAL	1	TRUE	1	0.634826505302175	3		328	506	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353711	15353711	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	316	395	0	ENST00000263377.2:c.3169G>T	p.Gly1057Cys	p.G1057C	ENST00000263377	NM_058243.2	1057	Ggt/Tgt	14/20	0.634826505302175	3	FACETS	0.931	0.885	0.978	0.931	0.885	0.978	CLONAL	2	TRUE	1	0.634826505302175	3		395	704	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791335	42791335	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	130	366	0	ENST00000575354.2:c.395C>T	p.Ser132Phe	p.S132F	ENST00000575354	NM_015125.3	132	tCc/tTc	3/20	0.117723002817527	3	FACETS	1	0.98	1	0.623	0.57	0.678	INDETERMINATE	1	TRUE	1	0.634826505302175	3		366	433	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096264	178096264	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	105	298	0	ENST00000397062.3:c.1067C>T	p.Ser356Leu	p.S356L	ENST00000397062	NM_006164.4	356	tCa/tTa	5/5	0.634826505302175	3	FACETS	0.84	0.755	0.929	0.42	0.377	0.465	CLONAL	1	TRUE	1	0.634826505302175	3		298	519	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096291	178096291	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0024977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	111	335	0	ENST00000397062.3:c.1040C>G	p.Ser347Ter	p.S347*	ENST00000397062	NM_006164.4	347	tCa/tGa	5/5	0.634826505302175	3	FACETS	0.818	0.738	0.903	0.409	0.369	0.452	CLONAL	1	TRUE	1	0.634826505302175	3		335	563	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790069	40790070	+	missense_variant	Missense_Mutation	DNP	TG	TG	AT	novel	NA	P-0024977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	115	426	1	ENST00000373198.4:c.2661_2662delinsAT	p.Ile888Phe	p.I888F	ENST00000373198	NM_133170.3	887	gcCAtc/gcATtc	18/32	0.634826505302175	3	FACETS	0.884	0.799	0.972	0.442	0.399	0.486	CLONAL	1	TRUE	1	0.634826505302175	3		427	540	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845291	42845291	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs764393597	NA	P-0024977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	111	354	0	ENST00000398585.3:c.971C>A	p.Thr324Asn	p.T324N	ENST00000398585	NM_001135099.1	324	aCc/aAc	9/14	0.634826505302175	4	FACETS	0.793	0.713	0.877	0.396	0.356	0.439	SUBCLONAL	1	TRUE	2	0.634826505302175	4		354	721	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280104	66280104	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	172	303	1	ENST00000273854.3:c.1585G>T	p.Gly529Cys	p.G529C	ENST00000273854	NM_004439.5	529	Ggc/Tgc	7/18	0.634826505302175	3	FACETS	0.978	0.914	1	0.978	0.914	1	CLONAL	2	TRUE	1	0.634826505302175	3		304	365	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067138	143067138	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs376698756	NA	P-0024977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	100	320	0	ENST00000262992.4:c.1575G>C	p.Trp525Cys	p.W525C	ENST00000262992	NM_001101669.1	525	tgG/tgC	16/24	0.634826505302175	3	FACETS	1	0.953	1	0.549	0.494	0.606	CLONAL	1	TRUE	1	0.634826505302175	3		320	378	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31422936	31422936	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	254	551	4	ENST00000344624.3:c.3377G>T	p.Arg1126Met	p.R1126M	ENST00000344624		1126	aGg/aTg	26/33	0.567421986044866	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.634826505302175	4		555	590	SUCCESS
APC	324	MSKCC	GRCh37	5	112177449	112177449	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	96	276	0	ENST00000257430.4:c.6158C>T	p.Pro2053Leu	p.P2053L	ENST00000257430	NM_000038.5	2053	cCt/cTt	16/16	0.567421986044866	4	FACETS	0.827	0.746	0.911	0.827	0.746	0.911	CLONAL	2	TRUE	2	0.634826505302175	4		276	299	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435856	149435856	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	341	445	1	ENST00000286301.3:c.2368C>A	p.His790Asn	p.H790N	ENST00000286301	NM_005211.3	790	Cat/Aat	18/22	0.567421986044866	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.634826505302175	4		446	842	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977593	2977593	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	286	384	0	ENST00000396946.4:c.1091G>T	p.Arg364Leu	p.R364L	ENST00000396946	NM_032415.4	364	cGc/cTc	8/25	0.567421986044866	4	FACETS	0.987	0.933	1	0.987	0.933	1	CLONAL	2	TRUE	2	0.634826505302175	4		384	746	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97887388	97887388	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	111	362	0	ENST00000289081.3:c.976C>G	p.Leu326Val	p.L326V	ENST00000289081	NM_000136.2	326	Ctg/Gtg	10/15	1	2	FACETS	0.868	0.786	0.952	0.868	0.786	0.952	CLONAL	1	TRUE	1	0.634826505302175	2		362	403	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229503	98229503	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1215737141	NA	P-0024977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	118	376	0	ENST00000331920.6:c.2455C>T	p.Leu819Phe	p.L819F	ENST00000331920	NM_000264.3	819	Ctt/Ttt	15/24	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.634826505302175	2		376	361	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802689	135802689	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	52	248	0	ENST00000298552.3:c.109del	p.Arg37ValfsTer6	p.R37Vfs*6	ENST00000298552	NM_001162426.1	37	Cgt/gt	4/23	1	2	FACETS	0.7	0.602	0.805	0.7	0.602	0.805	SUBCLONAL	1	TRUE	1	0.634826505302175	2		248	234	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790069	40790069	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	115	420	0	ENST00000373198.4:c.2662A>T	p.Ile888Phe	p.I888F	ENST00000373198	NM_133170.3	888	Atc/Ttc	18/32	0.634826505302175	3	FACETS	0.884	0.799	0.972	0.442	0.399	0.486	CLONAL	1	TRUE	1	0.634826505302175	3		420	540	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	72	314	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.721094894424702	2		314	194	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717650	89717650	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs1057520900	NA	P-0024978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	177	409	0	ENST00000371953.3:c.675T>G	p.Tyr225Ter	p.Y225*	ENST00000371953	NM_000314.4	225	taT/taG	7/9	0.721094894424702	1	FACETS	0.966	0.908	1	0.966	0.908	1	CLONAL	1	TRUE	0	0.721094894424702	1		409	325	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097616	27097616	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0024978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	87	327	0	ENST00000324856.7:c.3205A>T	p.Lys1069Ter	p.K1069*	ENST00000324856	NM_006015.4	1069	Aag/Tag	12/20	1	2	FACETS	0.605	0.539	0.675	0.605	0.539	0.675	SUBCLONAL	1	TRUE	1	0.721094894424702	2		327	399	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	116	314	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.878	0.803	0.955	0.878	0.803	0.955	CLONAL	1	TRUE	1	0.868961386588015	2		314	304	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0024983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	239	467	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.963	0.907	1	0.963	0.907	1	CLONAL	1	TRUE	1	0.868961386588015	2		467	571	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0024983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11721	617	472	0	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.868961386588015	24	FACETS	1	0.994	1			1	CLONAL	1	TRUE	NA	0.868961386588015	24		472	12338	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054984	176054984	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	101	507	3	ENST00000367669.3:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000367669	NM_022457.5	357	Cga/Tga	10/20	1	2	FACETS	0.379	0.339	0.421	0.379	0.339	0.421	SUBCLONAL	1	TRUE	1	0.868961386588015	2		510	614	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653851	89653851	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1554893824	NA	P-0024983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	136	342	0	ENST00000371953.3:c.149T>C	p.Ile50Thr	p.I50T	ENST00000371953	NM_000314.4	50	aTt/aCt	2/9	0.868961386588015	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.868961386588015	1		342	176	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775612	9775612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772851443	NA	P-0024983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	244	380	0	ENST00000377346.4:c.155G>A	p.Arg52His	p.R52H	ENST00000377346	NM_005026.3	52	cGc/cAc	4/24	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.868961386588015	2		380	561	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098540	108098540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	161	331	0	ENST00000278616.4:c.110C>T	p.Pro37Leu	p.P37L	ENST00000278616	NM_000051.3	37	cCt/cTt	3/63	1	2	FACETS	0.945	0.878	1	0.945	0.878	1	CLONAL	1	TRUE	1	0.868961386588015	2		331	392	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248549	8248549	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373424725	NA	P-0024985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	68	403	2	ENST00000335790.3:c.338G>A	p.Cys113Tyr	p.C113Y	ENST00000335790	NM_002315.2	113	tGc/tAc	3/4	0.227764704943742	4	FACETS	0.666	0.578	0.762	0.333	0.289	0.381	SUBCLONAL	1	TRUE	2	0.329778885920075	4		405	823	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465310	120465310	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	98	431	0	ENST00000256646.2:c.4951G>T	p.Ala1651Ser	p.A1651S	ENST00000256646	NM_024408.3	1651	Gcc/Tcc	27/34	1	2	FACETS	0.41	0.365	0.457	0.41	0.365	0.457	SUBCLONAL	1	TRUE	1	0.653594997536087	2		431	732	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	176	552	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.277969325063285	2	FACETS	1	0.99	1	0.735	0.682	0.789	INDETERMINATE	1	TRUE	0	0.469490924569783	2		552	510	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0024987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	208	847	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.430192414976633	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	0	0.469490924569783	2		849	442	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100430	8100430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770601456	NA	P-0024987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	52	490	0	ENST00000346208.3:c.404C>T	p.Pro135Leu	p.P135L	ENST00000346208		135	cCg/cTg	3/6	0.270061651344983	3	FACETS	0.526	0.448	0.612	0.263	0.224	0.306	INDETERMINATE	1	TRUE	1	0.469490924569783	3		490	520	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117407	115117408	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	154	447	0	ENST00000257566.3:c.766dup	p.Arg256LysfsTer4	p.R256Kfs*4	ENST00000257566	NM_016569.3	256	aga/aAga	4/8	0.277969325063285	2	FACETS	1	0.987	1	0.688	0.634	0.743	INDETERMINATE	1	TRUE	0	0.469490924569783	2		447	477	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348839	89348839	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	179	705	0	ENST00000301030.4:c.4111G>C	p.Ala1371Pro	p.A1371P	ENST00000301030	NM_001256183.1	1371	Gcc/Ccc	9/13	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.469490924569783	2		705	720	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438274	56438275	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0024987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	36	401	0	ENST00000407977.2:c.718_719insGA	p.Ile240ArgfsTer180	p.I240Rfs*180	ENST00000407977		240	atc/aGAtc	7/10	0.277969325063285	2	FACETS	0.352	0.289	0.422	0.176	0.144	0.211	INDETERMINATE	1	TRUE	0	0.469490924569783	2		401	436	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604748	48604748	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	114	400	0	ENST00000342988.3:c.1570T>C	p.Trp524Arg	p.W524R	ENST00000342988	NM_005359.5	524	Tgg/Cgg	12/12	0.469490924569783	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.469490924569783	1		400	318	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278094	41278094	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	88	376	0	ENST00000349496.5:c.1970C>A	p.Ala657Asp	p.A657D	ENST00000349496	NM_001904.3	657	gCt/gAt	13/15	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.469490924569783	2		376	372	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0024988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	158	403	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.781945548289125	2		403	390	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711892	89711892	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	216	447	0	ENST00000371953.3:c.510T>G	p.Ser170Arg	p.S170R	ENST00000371953	NM_000314.4	170	agT/agG	6/9	0.781945548289125	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.781945548289125	1		447	333	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174459	11174460	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0024988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	321	581	2	ENST00000361445.4:c.7215_7216delinsCT	p.Glu2405_Val2406delinsAspLeu	p.E2405_V2406delinsDL	ENST00000361445	NM_004958.3	2405	gaGGtg/gaCTtg	53/58	0.781945548289125	1	FACETS	0.979	0.938	1	0.979	0.938	1	CLONAL	1	TRUE	0	0.781945548289125	1		583	511	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248007	59248007	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	19	460	2	ENST00000371222.2:c.736G>A	p.Asp246Asn	p.D246N	ENST00000371222	NM_002228.3	246	Gac/Aac	1/1	0.781945548289125	1	FACETS	0.081	0.061	0.105	0.081	0.061	0.105	SUBCLONAL	1	TRUE	0	0.781945548289125	1		462	364	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs878854073	NA	P-0024993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	280	318	0	ENST00000269305.4:c.673-1G>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.506801323681685	2	FACETS	0.902	0.855	0.948	0.902	0.855	0.948	CLONAL	2	TRUE	0	0.521087932748342	2		318	596	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440430	49440431	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0024993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	177	456	0	ENST00000301067.7:c.4379dup	p.Leu1461ThrfsTer30	p.L1461Tfs*30	ENST00000301067	NM_003482.3	1460	cca/ccCa	15/54	1	2	FACETS	0.793	0.731	0.857	0.793	0.731	0.857	SUBCLONAL	1	TRUE	1	0.521087932748342	2		456	857	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465988	69465988	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	253	397	0	ENST00000227507.2:c.826G>T	p.Glu276Ter	p.E276*	ENST00000227507	NM_053056.2	276	Gag/Tag	5/5	0.521087932748342	7	FACETS	0.799	0.746	0.854			1	SUBCLONAL	2	TRUE	NA	0.521087932748342	7		397	1400	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296160	15296160	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772203584	NA	P-0024993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	172	420	0	ENST00000263388.2:c.2204G>A	p.Arg735Gln	p.R735Q	ENST00000263388	NM_000435.2	735	cGa/cAa	14/33	1	2	FACETS	0.903	0.833	0.976	0.903	0.833	0.976	CLONAL	1	TRUE	1	0.521087932748342	2		420	731	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257144	16257144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775010663	NA	P-0024993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	233	347	1	ENST00000375759.3:c.4409G>A	p.Arg1470Gln	p.R1470Q	ENST00000375759	NM_015001.2	1470	cGa/cAa	11/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.521087932748342	2		348	858	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798793	45798793	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	206	438	0	ENST00000450313.1:c.438C>G	p.Ile146Met	p.I146M	ENST00000450313	NM_012222.2	146	atC/atG	5/16	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.521087932748342	2		438	785	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457888	69457888	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs148113872	NA	P-0024993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1330	124	357	0	ENST00000227507.2:c.288G>C	p.Lys96Asn	p.K96N	ENST00000227507	NM_053056.2	96	aaG/aaC	2/5	0.521087932748342	7	FACETS	0.754	0.679	0.833			1	SUBCLONAL	1	TRUE	NA	0.521087932748342	7		357	1454	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679969	30679969	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	122	294	0	ENST00000376406.3:c.1750G>T	p.Gly584Cys	p.G584C	ENST00000376406	NM_014641.2	584	Ggc/Tgc	5/15	1	2	FACETS	0.95	0.863	1	0.95	0.863	1	CLONAL	1	TRUE	1	0.521087932748342	2		294	493	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852125	128852125	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	198	390	0	ENST00000249373.3:c.2197G>T	p.Val733Phe	p.V733F	ENST00000249373	NM_005631.4	733	Gtc/Ttc	12/12	0.51621549686978	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.521087932748342	1		390	496	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399470	139399471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	478	331	0	ENST00000277541.6:c.4672_4673insA	p.Gly1558GlufsTer52	p.G1558Efs*52	ENST00000277541	NM_017617.3	1558	ggg/gAgg	26/34	0.510514307320479	3	FACETS	0.914	0.881	0.947	0.914	0.881	0.947	CLONAL	3	TRUE	0	0.521087932748342	3		331	843	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	85	314	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.898	0.798	1	0.898	0.798	1	CLONAL	1	TRUE	1	0.479441308669333	2		314	395	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546847	9546847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	139	407	0	ENST00000353224.5:c.1175C>T	p.Ser392Leu	p.S392L	ENST00000353224	NM_177990.2	392	tCg/tTg	5/10	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.479441308669333	2		407	573	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873660	35873660	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs201559094	NA	P-0024995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	121	461	0	ENST00000303115.3:c.616C>T	p.Arg206Ter	p.R206*	ENST00000303115	NM_002185.3	206	Cga/Tga	5/8	1	2	FACETS	0.869	0.787	0.954	0.869	0.787	0.954	CLONAL	1	TRUE	1	0.479441308669333	2		461	581	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0024995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	119	438	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.479441308669333	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.479441308669333	1		438	361	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643768	52643768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	185	636	2	ENST00000394830.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000394830	NM_018313.4	710	Cga/Tga	17/30	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.479441308669333	2		638	695	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381466	81381466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	93	351	1	ENST00000222390.5:c.595G>A	p.Glu199Lys	p.E199K	ENST00000222390	NM_000601.4	199	Gaa/Aaa	5/18	1	2	FACETS	0.771	0.688	0.859	0.771	0.688	0.859	SUBCLONAL	1	TRUE	1	0.479441308669333	2		352	503	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858732	9858732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	113	394	0	ENST00000330684.3:c.2669C>T	p.Ser890Phe	p.S890F	ENST00000330684	NM_001134407.1	890	tCc/tTc	13/13	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.479441308669333	2		394	426	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52663035	52663035	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	108	299	0	ENST00000394830.3:c.1318C>T	p.Gln440Ter	p.Q440*	ENST00000394830	NM_018313.4	440	Caa/Taa	13/30	1	2	FACETS	0.977	0.882	1	0.977	0.882	1	CLONAL	1	TRUE	1	0.479441308669333	2		299	461	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109319805	109319805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	177	581	1	ENST00000436639.2:c.883C>T	p.Pro295Ser	p.P295S	ENST00000436639	NM_014454.2	295	Cct/Tct	5/10	1	2	FACETS	0.947	0.874	1	0.947	0.874	1	CLONAL	1	TRUE	1	0.479441308669333	2		582	780	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39311683	39311683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	227	764	0	ENST00000373001.3:c.976C>T	p.Leu326Phe	p.L326F	ENST00000373001	NM_022157.3	326	Ctt/Ttt	6/7	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.479441308669333	2		764	905	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549155	21549155	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	195	691	0	ENST00000382592.4:c.3121A>T	p.Thr1041Ser	p.T1041S	ENST00000382592	NM_014572.2	1041	Acc/Tcc	8/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.479441308669333	2		691	750	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81528557	81528557	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	128	421	0	ENST00000298171.2:c.236C>T	p.Ser79Phe	p.S79F	ENST00000298171	NM_000369.2	79	tCc/tTc	2/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.479441308669333	2		421	500	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214669	36214669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	130	509	0	ENST00000222270.7:c.3095C>T	p.Ser1032Phe	p.S1032F	ENST00000222270	NM_014727.1	1032	tCc/tTc	8/37	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.479441308669333	2		509	511	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254497	1254497	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	120	665	0	ENST00000310581.5:c.3281G>A	p.Gly1094Glu	p.G1094E	ENST00000310581	NM_198253.2	1094	gGg/gAg	15/16	1	2	FACETS	0.894	0.81	0.981	0.894	0.81	0.981	CLONAL	1	TRUE	1	0.479441308669333	2		665	560	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194925	29194925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771553603	NA	P-0024995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	191	645	1	ENST00000240100.2:c.803C>T	p.Ala268Val	p.A268V	ENST00000240100	NM_001394.6	268	gCc/gTc	4/4	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.479441308669333	2		646	671	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220521	123220521	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs146561651	NA	P-0024995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	159	343	0	ENST00000218089.9:c.3178A>G	p.Ile1060Val	p.I1060V	ENST00000218089	NM_001042749.1	1060	Att/Gtt	30/35	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.479441308669333	1		343	374	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711927	89711928	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554900593	NA	P-0024996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	41	556	0	ENST00000371953.3:c.548dup	p.Asn184GlufsTer6	p.N184Efs*6	ENST00000371953	NM_000314.4	182	tta/ttAa	6/9	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.185304056610188	2		556	346	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354442	91354442	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	25	408	0	ENST00000355112.3:c.3882C>G	p.Asp1294Glu	p.D1294E	ENST00000355112	NM_000057.2	1294	gaC/gaG	21/22	1	2	FACETS	0.849	0.669	1	0.849	0.669	1	CLONAL	1	TRUE	1	0.185304056610188	2		408	318	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022061	5022061	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	34	696	0	ENST00000381652.3:c.76del	p.Ser26LeufsTer7	p.S26Lfs*7	ENST00000381652	NM_004972.3	25	aTt/at	3/25	1	2	FACETS	0.946	0.773	1	0.946	0.773	1	CLONAL	1	TRUE	1	0.185304056610188	2		696	388	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0024997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	754	702	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.517745917948161	6	FACETS	0.978	0.951	1			1	CLONAL	5	TRUE	NA	0.517745917948161	6		702	1213	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0024997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	409	579	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	0.517745917948161	5	FACETS	0.965	0.922	1	0.965	0.922	1	CLONAL	3	TRUE	2	0.517745917948161	5		579	970	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577095	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519984	NA	P-0024997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	338	645	0	ENST00000269305.4:c.843C>G	p.Asp281Glu	p.D281E	ENST00000269305	NM_001126112.2	281	gaC/gaG	8/11	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	2	TRUE	NA	0.517745917948161	2		645	622	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15374334	15374334	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201883209	NA	P-0024997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	111	545	2	ENST00000263377.2:c.1238G>A	p.Arg413His	p.R413H	ENST00000263377	NM_058243.2	413	cGt/cAt	7/20	0.517745917948161	3	FACETS	0.916	0.826	1	0.458	0.413	0.506	CLONAL	1	TRUE	1	0.517745917948161	3		547	589	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716328	52716328	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	118	571	0	ENST00000322088.6:c.772C>G	p.Arg258Gly	p.R258G	ENST00000322088	NM_014225.5	258	Cgc/Ggc	6/15	NA	2	FACETS	0.946	0.858	1			1	INDETERMINATE	1	TRUE	NA	0.517745917948161	2		571	482	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0024998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	95	336	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.829	0.746	0.915	0.829	0.746	0.915	CLONAL	1	TRUE	1	0.720663190144136	2		336	318	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0024998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	8	428	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.07	0.044	0.103	0.07	0.044	0.103	SUBCLONAL	1	TRUE	1	0.720663190144136	2		428	319	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158677	26158677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1177142438	NA	P-0024998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	11	40	0	ENST00000289316.2:c.280G>A	p.Glu94Lys	p.E94K	ENST00000289316	NM_138720.2	94	Gag/Aag	1/2	1	2	FACETS	1	0.809	1	1	0.809	1	CLONAL	1	TRUE	1	0.720663190144136	2		40	27	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	36	552	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	0.19	2		552	376	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879657	37879657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377979176	NA	P-0024999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	38	444	0	ENST00000269571.5:c.2032C>T	p.Arg678Trp	p.R678W	ENST00000269571		678	Cgg/Tgg	17/27	0.0818219496113449	0	FACETS	0.9	0.746	1			1	INDETERMINATE	1	TRUE	0	0.19	0		444	360	SUCCESS
APC	324	MSKCC	GRCh37	5	112179255	112179255	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	32	342	0	ENST00000257430.4:c.7964A>C	p.Glu2655Ala	p.E2655A	ENST00000257430	NM_000038.5	2655	gAg/gCg	16/16	1	2	FACETS	0.918	0.746	1	0.918	0.746	1	CLONAL	1	TRUE	1	0.19	2		342	367	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965646	93965646	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	30	417	0	ENST00000369303.4:c.2282C>T	p.Ala761Val	p.A761V	ENST00000369303	NM_004440.3	761	gCt/gTt	13/17	1	2	FACETS	0.907	0.732	1	0.907	0.732	1	CLONAL	1	TRUE	1	0.19	2		417	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs879253911	NA	P-0025000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	243	504	0	ENST00000269305.4:c.538G>T	p.Glu180Ter	p.E180*	ENST00000269305	NM_001126112.2	180	Gag/Tag	5/11	0.410512556087099	2	FACETS	0.982	0.925	1	0.982	0.925	1	CLONAL	2	TRUE	0	0.409654549552077	2		504	604	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781465	3781465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	89	328	0	ENST00000262367.5:c.4900G>A	p.Val1634Met	p.V1634M	ENST00000262367	NM_004380.2	1634	Gtg/Atg	30/31	0.410512556087099	3	FACETS	1	0.963	1	0.594	0.529	0.662	CLONAL	1	TRUE	1	0.409654549552077	3		328	441	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608378	43608378	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	103	776	0	ENST00000355710.3:c.1726C>G	p.Gln576Glu	p.Q576E	ENST00000355710	NM_020975.4	576	Caa/Gaa	9/20	0.218154712440705	3	FACETS	0.662	0.592	0.737			1	INDETERMINATE	1	TRUE	NA	0.409654549552077	3		776	915	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443645	49443645	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	172	564	0	ENST00000301067.7:c.3726G>C	p.Leu1242Phe	p.L1242F	ENST00000301067	NM_003482.3	1242	ttG/ttC	11/54	0.401272723427241	5	FACETS	1	0.988	1	0.469	0.431	0.508	CLONAL	1	TRUE	2	0.409654549552077	5		564	964	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69210658	69210658	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	147	485	1	ENST00000462284.1:c.241G>T	p.Val81Leu	p.V81L	ENST00000462284	NM_002392.5	81	Gta/Tta	4/11	0.401272723427241	5	FACETS	1	0.937	1	0.345	0.314	0.378	CLONAL	1	TRUE	2	0.409654549552077	5		486	1119	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40998481	40998481	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760517215	NA	P-0025000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	145	587	0	ENST00000267868.3:c.332A>G	p.Lys111Arg	p.K111R	ENST00000267868	NM_002875.4	111	aAa/aGa	4/10	0.410512556087099	2	FACETS	0.951	0.869	1	0.476	0.434	0.519	CLONAL	1	TRUE	0	0.409654549552077	2		587	744	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270105	198270105	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1294	136	533	0	ENST00000335508.6:c.1331del	p.Phe444SerfsTer10	p.F444Sfs*10	ENST00000335508	NM_012433.2	444	tTc/tc	10/25	0.409654549552077	8	FACETS	1	0.932	1			1	CLONAL	1	TRUE	NA	0.409654549552077	8		533	1430	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945567	54945567	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	163	615	0	ENST00000312783.6:c.1003C>G	p.Gln335Glu	p.Q335E	ENST00000312783	NM_198436.1	335	Caa/Gaa	9/10	0.410512556087099	3	FACETS	1	0.948	1	0.522	0.479	0.567	CLONAL	1	TRUE	1	0.409654549552077	3		615	918	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503760	186503760	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	120	491	0	ENST00000323963.5:c.441del	p.Lys147AsnfsTer21	p.K147Nfs*21	ENST00000323963		146	cAa/ca	5/11	0.409654549552077	6	FACETS	0.858	0.773	0.949	0.172	0.154	0.19	CLONAL	1	TRUE	1	0.409654549552077	6		491	1242	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979269	93979269	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	256	498	1	ENST00000369303.4:c.1559C>T	p.Ala520Val	p.A520V	ENST00000369303	NM_004440.3	520	gCt/gTt	7/17	0.410512556087099	3	FACETS	0.978	0.927	1	0.978	0.927	1	CLONAL	3	TRUE	0	0.409654549552077	3		499	513	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0025001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	110	670	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.328219334940268	1	FACETS	0.91	0.82	1	0.91	0.82	1	CLONAL	1	TRUE	0	0.348564183778541	1		671	573	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473732	67473732	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	176	595	0	ENST00000327367.4:c.812T>G	p.Leu271Arg	p.L271R	ENST00000327367	NM_005902.3	271	cTa/cGa	6/9	0.348564183778541	2	FACETS	0.918	0.851	0.987	0.918	0.851	0.987	CLONAL	2	TRUE	0	0.348564183778541	2		595	550	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15984031	15984031	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	86	373	0	ENST00000268712.3:c.3188G>A	p.Gly1063Asp	p.G1063D	ENST00000268712	NM_006311.3	1063	gGc/gAc	24/46	0.328219334940268	1	FACETS	0.991	0.882	1	0.991	0.882	1	CLONAL	1	TRUE	0	0.348564183778541	1		373	411	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321760	62321774	+	inframe_deletion	In_Frame_Del	DEL	CCTGCATGTCCCCAG	CCTGCATGTCCCCAG	-	novel	NA	P-0025001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	47	565	0	ENST00000360203.5:c.2383_2397del	p.His795_Leu799del	p.H795_L799del	ENST00000360203	NM_001283009.1	793	gaCCTGCATGTCCCCAGc/gac	26/35	0.339142947584218	4	FACETS	0.606	0.511	0.712	0.202	0.17	0.238	SUBCLONAL	1	TRUE	1	0.348564183778541	4		565	600	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729447	41729447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	98	622	2	ENST00000242208.4:c.1082C>T	p.Thr361Met	p.T361M	ENST00000242208	NM_002192.2	361	aCg/aTg	3/3	1	2	FACETS	0.968	0.865	1	0.968	0.865	1	CLONAL	1	TRUE	1	0.348564183778541	2		624	581	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184621	185184621	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	82	317	1	ENST00000265026.3:c.1513C>T	p.Gln505Ter	p.Q505*	ENST00000265026	NM_004721.4	505	Caa/Taa	10/14	0.506287286184341	3	FACETS	0.916	0.812	1	0.458	0.406	0.514	CLONAL	1	TRUE	1	0.506287286184341	3		318	443	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938476	44938488	+	frameshift_variant	Frame_Shift_Del	DEL	AGATGAAAACTGG	AGATGAAAACTGG	-	novel	NA	P-0025002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	84	250	0	ENST00000377967.4:c.3024_3036del	p.Asp1009IlefsTer35	p.D1009Ifs*35	ENST00000377967	NM_021140.2	1008	gcAGATGAAAACTGG/gc	20/29	1	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.506287286184341	1		250	239	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	187	542	0	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.597948764992754	2		542	604	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0025003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	121	631	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.778	0.706	0.853	0.778	0.706	0.853	SUBCLONAL	1	TRUE	1	0.597948764992754	2		632	520	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023904	27023904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1232964733	NA	P-0025003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	36	89	0	ENST00000324856.7:c.1015del	p.Ala339LeufsTer24	p.A339Lfs*24	ENST00000324856	NM_006015.4	337	tGg/tg	1/20	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.597948764992754	2		89	103	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306996	65306997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	80	396	2	ENST00000342505.4:c.2580dup	p.Pro861ThrfsTer4	p.P861Tfs*4	ENST00000342505	NM_002227.2	860	-/A	19/25	1	2	FACETS	0.789	0.7	0.883	0.789	0.7	0.883	SUBCLONAL	1	TRUE	1	0.597948764992754	2		398	339	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339110	65339111	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	97	480	6	ENST00000342505.4:c.425dup	p.Ile143AspfsTer9	p.I143Dfs*9	ENST00000342505	NM_002227.2	142	aag/aaAg	5/25	1	2	FACETS	0.716	0.642	0.795	0.716	0.642	0.795	SUBCLONAL	1	TRUE	1	0.597948764992754	2		486	453	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852118	63852118	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	120	478	1	ENST00000279873.7:c.2901del	p.Lys967AsnfsTer15	p.K967Nfs*15	ENST00000279873	NM_032199.2	966	Aaa/aa	10/10	0.597948764992754	3	FACETS	0.916	0.83	1	0.458	0.415	0.503	CLONAL	1	TRUE	1	0.597948764992754	3		479	569	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0025003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	54	364	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.597948764992754	3	FACETS	0.69	0.592	0.796	0.345	0.296	0.398	SUBCLONAL	1	TRUE	1	0.597948764992754	3		364	340	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717730	89717731	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	171	422	0	ENST00000371953.3:c.756dup	p.Ile253TyrfsTer45	p.I253Yfs*45	ENST00000371953	NM_000314.4	252	gat/gaTt	7/9	0.597948764992754	3	FACETS	0.897	0.835	0.96	0.897	0.835	0.96	CLONAL	2	TRUE	1	0.597948764992754	3		422	414	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363830	118363830	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	120	427	0	ENST00000534358.1:c.5067del	p.Glu1690LysfsTer20	p.E1690Kfs*20	ENST00000534358	NM_005933.3	1688	tCc/tc	16/36	1	2	FACETS	0.852	0.774	0.933	0.852	0.774	0.933	CLONAL	1	TRUE	1	0.597948764992754	2		427	471	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0025003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	105	429	5	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	0.493585843442929	3	FACETS	1	0.972	1	0.402	0.363	0.443	CLONAL	1	TRUE	0	0.597948764992754	3		434	378	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0025003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	279	500	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.978	0.933	1	1	0.996	1	CLONAL	2	TRUE	1	0.597948764992754	2		500	477	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112919885	112919885	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	30	204	0	ENST00000351677.2:c.1100G>A	p.Cys367Tyr	p.C367Y	ENST00000351677	NM_002834.3	367	tGt/tAt	10/16	1	2	FACETS	1	0.845	1	1	0.845	1	CLONAL	1	TRUE	1	0.597948764992754	2		204	98	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954022	32954023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs397507419	NA	P-0025003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	83	523	5	ENST00000380152.3:c.9097dup	p.Thr3033AsnfsTer11	p.T3033Nfs*11	ENST00000380152		3030	aca/acAa	23/27	1	2	FACETS	0.734	0.652	0.821	0.734	0.652	0.821	SUBCLONAL	1	TRUE	1	0.597948764992754	2		528	378	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052726	42052744	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGTAAGTGTTCTGTGTAA	GAGTAAGTGTTCTGTGTAA	-	novel	NA	P-0025003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	43	405	0	ENST00000219905.7:c.7397_7398+17del		p.X2466_splice	ENST00000219905	NM_001164273.1	2466		20/24	1	2	FACETS	0.432	0.363	0.508	0.432	0.363	0.508	SUBCLONAL	1	TRUE	1	0.597948764992754	2		405	333	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2113050	2113050	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	160	469	1	ENST00000219476.3:c.1439A>G	p.Tyr480Cys	p.Y480C	ENST00000219476	NM_000548.3	480	tAt/tGt	14/42	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.597948764992754	2		470	505	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655481	67655481	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs34679888	NA	P-0025003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	65	469	2	ENST00000264010.4:c.1348del	p.Ser450ValfsTer61	p.S450Vfs*61	ENST00000264010	NM_006565.3	448	cgA/cg	7/12	1	2	FACETS	0.616	0.537	0.7	0.616	0.537	0.7	SUBCLONAL	1	TRUE	1	0.597948764992754	2		471	353	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991757	72991758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760959844	NA	P-0025003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	82	421	1	ENST00000268489.5:c.2287dup	p.Glu763GlyfsTer26	p.E763Gfs*26	ENST00000268489	NM_006885.3	763	gag/gGag	2/10	1	2	FACETS	0.807	0.717	0.901	0.807	0.717	0.901	CLONAL	1	TRUE	1	0.597948764992754	2		422	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572991	7572991	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	105	409	0	ENST00000269305.4:c.1118del	p.Lys373ArgfsTer49	p.K373Rfs*49	ENST00000269305	NM_001126112.2	373	aAg/ag	11/11	1	2	FACETS	0.733	0.66	0.81	0.733	0.66	0.81	SUBCLONAL	1	TRUE	1	0.597948764992754	2		409	479	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118940	70118941	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	153	519	0	ENST00000245479.2:c.514dup	p.Tyr172LeufsTer80	p.Y172Lfs*80	ENST00000245479	NM_000346.3	171	gat/gaTt	2/3	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.597948764992754	2		519	508	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18975039	18975039	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759670824	NA	P-0025003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	84	315	0	ENST00000262803.5:c.2836G>A	p.Val946Ile	p.V946I	ENST00000262803	NM_002911.3	946	Gtc/Atc	20/24	1	2	FACETS	0.854	0.761	0.951	0.854	0.761	0.951	CLONAL	1	TRUE	1	0.597948764992754	2		315	329	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068421	26068421	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	104	449	0	ENST00000435504.4:c.69del	p.Lys23AsnfsTer7	p.K23Nfs*7	ENST00000435504		23	aaA/aa	2/13	0.597948764992754	3	FACETS	0.937	0.844	1	0.469	0.422	0.518	CLONAL	1	TRUE	1	0.597948764992754	3		449	482	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368395	225368395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	85	522	1	ENST00000264414.4:c.1351G>A	p.Glu451Lys	p.E451K	ENST00000264414	NM_003590.4	451	Gaa/Aaa	9/16	0.597948764992754	3	FACETS	0.737	0.654	0.826	0.369	0.327	0.413	SUBCLONAL	1	TRUE	1	0.597948764992754	3		523	501	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022697	31022697	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	94	420	1	ENST00000375687.4:c.2182G>A	p.Glu728Lys	p.E728K	ENST00000375687	NM_015338.5	728	Gaa/Aaa	13/13	1	2	FACETS	0.836	0.75	0.927	0.836	0.75	0.927	CLONAL	1	TRUE	1	0.597948764992754	2		421	376	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735488	40735488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	161	489	1	ENST00000373198.4:c.3385G>A	p.Val1129Met	p.V1129M	ENST00000373198	NM_133170.3	1129	Gtg/Atg	25/32	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.597948764992754	2		490	516	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845309	42845309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	157	469	1	ENST00000398585.3:c.953G>A	p.Cys318Tyr	p.C318Y	ENST00000398585	NM_001135099.1	318	tGc/tAc	9/14	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.597948764992754	2		470	492	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155487	47155487	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	74	373	0	ENST00000409792.3:c.4594C>T	p.Arg1532Trp	p.R1532W	ENST00000409792	NM_014159.6	1532	Cgg/Tgg	5/21	1	2	FACETS	0.938	0.831	1	0.938	0.831	1	CLONAL	1	TRUE	1	0.597948764992754	2		373	264	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928080	178928080	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	96	521	0	ENST00000263967.3:c.1358A>G	p.Glu453Gly	p.E453G	ENST00000263967	NM_006218.2	453	gAa/gGa	8/21	1	2	FACETS	0.72	0.645	0.799	0.72	0.645	0.799	SUBCLONAL	1	TRUE	1	0.597948764992754	2		521	446	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591054	67591056	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0025003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	51	266	0	ENST00000274335.5:c.1651_1653del	p.Lys551del	p.K551del	ENST00000274335		549	ttGAAg/ttg	12/15	1	2	FACETS	0.755	0.649	0.868	0.755	0.649	0.868	SUBCLONAL	1	TRUE	1	0.597948764992754	2		266	226	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79974821	79974821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143211109	NA	P-0025003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	177	462	0	ENST00000265081.6:c.1249C>T	p.Arg417Trp	p.R417W	ENST00000265081	NM_002439.4	417	Cgg/Tgg	8/24	1	2	FACETS	0.961	0.89	1	0.961	0.89	1	CLONAL	1	TRUE	1	0.597948764992754	2		462	616	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852017	128852018	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0025003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	108	464	0	ENST00000249373.3:c.2094dup	p.Ser699GlnfsTer118	p.S699Qfs*118	ENST00000249373	NM_005631.4	697	gcc/gCcc	12/12	1	2	FACETS	0.742	0.669	0.818	0.742	0.669	0.818	SUBCLONAL	1	TRUE	1	0.597948764992754	2		464	487	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482927	140482927	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	117	557	1	ENST00000288602.6:c.1208del	p.Pro403LeufsTer8	p.P403Lfs*8	ENST00000288602	NM_004333.4	403	cCt/ct	10/18	1	2	FACETS	0.927	0.843	1	0.927	0.843	1	CLONAL	1	TRUE	1	0.597948764992754	2		558	422	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226007	53226007	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	162	533	0	ENST00000375401.3:c.2842G>A	p.Ala948Thr	p.A948T	ENST00000375401	NM_004187.3	948	Gct/Act	19/26	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.597948764992754	2		533	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	143	552	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.274295043818428	2		552	996	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622211	117622211	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs760646608	NA	P-0025005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	40	500	0	ENST00000368508.3:c.6659A>T	p.Asn2220Ile	p.N2220I	ENST00000368508	NM_002944.2	2220	aAt/aTt	42/43	1	2	FACETS	0.425	0.352	0.506	0.425	0.352	0.506	SUBCLONAL	1	TRUE	1	0.274295043818428	2		500	687	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224375	36224375	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	200	648	0	ENST00000222270.7:c.6925G>T	p.Asp2309Tyr	p.D2309Y	ENST00000222270	NM_014727.1	2309	Gat/Tat	28/37	0.132901786518221	3	FACETS	1	0.989	1	0.471	0.435	0.508	INDETERMINATE	1	TRUE	0	0.274295043818428	3		648	1174	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	92	606	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	0.237903227930743	2		606	752	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484780	57484780	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	67	457	0	ENST00000371085.3:c.760A>G	p.Asn254Asp	p.N254D	ENST00000371085	NM_000516.4	254	Aac/Gac	10/13	1	2	FACETS	0.922	0.801	1	0.922	0.801	1	CLONAL	1	TRUE	1	0.237903227930743	2		457	611	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933576	39933579	+	frameshift_variant	Frame_Shift_Del	DEL	GGGT	GGGT	-	novel	NA	P-0025008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	94	432	0	ENST00000378444.4:c.1020_1023del	p.Pro341GlufsTer36	p.P341Efs*36	ENST00000378444	NM_001123385.1	340	tcACCC/tc	4/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.237903227930743	2		432	546	SUCCESS
AR	367	MSKCC	GRCh37	X	66931310	66931310	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	53	445	0	ENST00000374690.3:c.1952G>T	p.Ser651Ile	p.S651I	ENST00000374690	NM_000044.3	651	aGc/aTc	4/8	1	2	FACETS	0.745	0.635	0.866	0.745	0.635	0.866	SUBCLONAL	1	TRUE	1	0.237903227930743	2		445	598	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0025012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	166	367	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.852973932245502	2	FACETS	0.993	0.925	1	0.497	0.462	0.532	CLONAL	1	TRUE	0	0.868127793155095	2		367	385	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260803	16260803	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150899650	NA	P-0025012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	212	543	1	ENST00000375759.3:c.8068G>A	p.Val2690Met	p.V2690M	ENST00000375759	NM_015001.2	2690	Gtg/Atg	11/15	0.852975683993052	2	FACETS	1	0.944	1	0.502	0.472	0.534	CLONAL	1	TRUE	0	0.868127793155095	2		544	486	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574538	64574538	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	208	622	0	ENST00000312049.6:c.857T>C	p.Leu286Pro	p.L286P	ENST00000312049	NM_130799.2	286	cTa/cCa	6/10	0.868127793155095	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.868127793155095	1		622	270	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063332	67063332	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	91	258	0	ENST00000412916.2:c.22C>A	p.Gln8Lys	p.Q8K	ENST00000412916		8	Cag/Aag	1/6	0.841495496707281	4	FACETS	0.948	0.847	1	0.474	0.423	0.528	CLONAL	1	TRUE	2	0.868127793155095	4		258	413	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0025013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	117	391	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.224626290143934	2		391	715	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0025013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	49	226	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.796	0.674	0.931	0.796	0.674	0.931	CLONAL	1	FALSE	1	0.224626290143934	2		226	548	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426722	212426722	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	38	524	0	ENST00000342788.4:c.2393T>G	p.Leu798Arg	p.L798R	ENST00000342788	NM_005235.2	798	cTt/cGt	20/28	1	2	FACETS	0.506	0.417	0.606	0.506	0.417	0.606	SUBCLONAL	1	FALSE	1	0.224626290143934	2		524	669	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858746	9858746	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	26	279	0	ENST00000330684.3:c.2655C>A	p.Phe885Leu	p.F885L	ENST00000330684	NM_001134407.1	885	ttC/ttA	13/13	0.224626290143934	0	FACETS	0.637	0.505	0.786			1	SUBCLONAL	1	FALSE	0	0.224626290143934	0		279	282	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0025014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	256	552	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.621072411916079	2		552	669	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0025014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	187	462	1	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	0.37485101166574	1	FACETS	0.744	0.692	0.797	0.744	0.692	0.797	SUBCLONAL	1	TRUE	0	0.621072411916079	1		463	558	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696404	47696404	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	250	479	0	ENST00000347630.2:c.419A>G	p.Asp140Gly	p.D140G	ENST00000347630	NM_001007230.1	140	gAt/gGt	6/11	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.621072411916079	2		479	571	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	124	314	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		314	552	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0025016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	186	478	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.248526416207408	5	FACETS	1	0.983	1	0.805	0.744	0.868	CLONAL	2	TRUE	2	0.248526416207408	5		478	851	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0025016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	53	321	1	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	0.240741566572937	2	FACETS	0.751	0.645	0.865	0.751	0.645	0.865	SUBCLONAL	2	TRUE	0	0.248526416207408	2		322	284	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576863	7576863	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	125	506	0	ENST00000269305.4:c.983del	p.Phe328SerfsTer17	p.F328Sfs*17	ENST00000269305	NM_001126112.2	328	tTc/tc	9/11	0.240741566572937	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.248526416207408	2		506	454	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245316	46245316	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	104	316	0	ENST00000334344.6:c.3410C>A	p.Ser1137Ter	p.S1137*	ENST00000334344	NM_152641.2	1137	tCa/tAa	15/21	0.248526416207408	3	FACETS	1	0.973	1	0.813	0.734	0.895	CLONAL	2	TRUE	0	0.248526416207408	3		316	386	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599909	28599909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239081741	NA	P-0025016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	41	378	1	ENST00000253063.3:c.791G>A	p.Arg264His	p.R264H	ENST00000253063	NM_031459.4	264	cGc/cAc	6/10	0.248526416207408	3	FACETS	0.994	0.83	1	0.497	0.415	0.588	CLONAL	1	TRUE	1	0.248526416207408	3		379	373	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180585	94180585	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	68	332	0	ENST00000323929.3:c.1583C>G	p.Ala528Gly	p.A528G	ENST00000323929	NM_005591.3	528	gCa/gGa	15/20	0.248526416207408	4	FACETS	0.835	0.73	0.948	0.835	0.73	0.948	CLONAL	2	TRUE	2	0.248526416207408	4		332	409	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207693	102207693	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	131	330	1	ENST00000263464.3:c.1675G>T	p.Val559Leu	p.V559L	ENST00000263464	NM_001165.4	559	Gtg/Ttg	9/9	0.248526416207408	4	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	2	0.248526416207408	4		331	605	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950888	32950888	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	118	427	0	ENST00000380152.3:c.8714A>T	p.Tyr2905Phe	p.Y2905F	ENST00000380152		2905	tAt/tTt	21/27	0.226684888829862	3	FACETS	0.903	0.817	0.993	0.903	0.817	0.993	CLONAL	2	TRUE	1	0.248526416207408	3		427	591	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024730	14024730	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	111	334	0	ENST00000311895.7:c.956C>A	p.Ala319Asp	p.A319D	ENST00000311895	NM_005236.2	319	gCt/gAt	5/11	0.240741566572937	2	FACETS	0.874	0.789	0.963	0.874	0.789	0.963	CLONAL	2	TRUE	0	0.248526416207408	2		334	511	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665090	29665100	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTTGGGTGT	TCTTTGGGTGT	-	novel	NA	P-0025016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	117	445	0	ENST00000356175.3:c.6689_6699del	p.Val2230AspfsTer2	p.V2230Dfs*2	ENST00000356175	NM_000267.3	2230	gTCTTTGGGTGT/g	44/57	0.248526416207408	3	FACETS	0.814	0.736	0.897	0.814	0.736	0.897	CLONAL	2	TRUE	1	0.248526416207408	3		445	650	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610375	10610375	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	98	467	0	ENST00000171111.5:c.335C>A	p.Thr112Asn	p.T112N	ENST00000171111	NM_203500.1	112	aCc/aAc	2/6	0.248526416207408	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	0	0.248526416207408	2		467	380	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147711	61147711	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	110	290	0	ENST00000295025.8:c.1022del	p.Asn341IlefsTer33	p.N341Ifs*33	ENST00000295025	NM_002908.2	341	Aat/at	10/11	0.248526416207408	3	FACETS	0.893	0.805	0.986	0.893	0.805	0.986	CLONAL	2	TRUE	1	0.248526416207408	3		290	557	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274706	198274706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	83	280	0	ENST00000335508.6:c.692G>A	p.Arg231Lys	p.R231K	ENST00000335508	NM_012433.2	231	aGa/aAa	7/25	0.248526416207408	4	FACETS	1	0.918	1	1	0.918	1	CLONAL	2	TRUE	2	0.248526416207408	4		280	400	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959350	38959350	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0025016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	133	422	0	ENST00000357387.3:c.2125A>T	p.Arg709Ter	p.R709*	ENST00000357387	NM_152756.3	709	Aga/Tga	22/38	0.248526416207408	4	FACETS	0.835	0.759	0.915	0.835	0.759	0.915	CLONAL	2	TRUE	2	0.248526416207408	4		422	800	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405889	157405889	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	28	302	0	ENST00000346085.5:c.2131G>T	p.Asp711Tyr	p.D711Y	ENST00000346085	NM_020732.3	711	Gat/Tat	6/20	0.248526416207408	3	FACETS	0.736	0.589	0.904	0.368	0.294	0.452	CLONAL	1	TRUE	1	0.248526416207408	3		302	344	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151167739	151167739	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0025016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	37	263	0	ENST00000262187.5:c.381-1G>T		p.X127_splice	ENST00000262187	NM_005614.3	127			0.248526416207408	3	FACETS	0.744	0.613	0.89	0.372	0.306	0.445	SUBCLONAL	1	TRUE	1	0.248526416207408	3		263	450	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370727	55370727	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	71	347	0	ENST00000297316.4:c.29G>A	p.Ser10Asn	p.S10N	ENST00000297316	NM_022454.3	10	aGt/aAt	1/2	0.248526416207408	5	FACETS	0.892	0.786	1	0.892	0.786	1	CLONAL	3	TRUE	2	0.248526416207408	5		347	293	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989697	68989697	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	41	409	0	ENST00000288368.4:c.1635G>T	p.Met545Ile	p.M545I	ENST00000288368	NM_024870.2	545	atG/atT	15/40	0.248526416207408	5	FACETS	0.88	0.732	1	0.293	0.244	0.348	CLONAL	1	TRUE	2	0.248526416207408	5		409	515	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485834	8485834	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	65	276	0	ENST00000356435.5:c.2983C>A	p.Arg995Ser	p.R995S	ENST00000356435		995	Cgt/Agt	17/35	0.240741566572937	2	FACETS	0.802	0.7	0.911	0.802	0.7	0.911	CLONAL	2	TRUE	0	0.248526416207408	2		276	326	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518141	8518141	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	68	319	0	ENST00000356435.5:c.1250C>A	p.Pro417Gln	p.P417Q	ENST00000356435		417	cCa/cAa	10/35	0.240741566572937	2	FACETS	0.819	0.718	0.927	0.819	0.718	0.927	CLONAL	2	TRUE	0	0.248526416207408	2		319	334	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971024	21971024	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660436	NA	P-0025016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	65	307	0	ENST00000304494.5:c.334C>A	p.Arg112Ser	p.R112S	ENST00000304494	NM_000077.4	112	Cgt/Agt	2/3	0.240741566572937	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	2	TRUE	0	0.248526416207408	2		307	251	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637689	52637689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	28	580	1	ENST00000394830.3:c.2627G>A	p.Arg876His	p.R876H	ENST00000394830	NM_018313.4	876	cGt/cAt	18/30	0.392698317730051	1	FACETS	0.266	0.212	0.327	0.266	0.212	0.327	SUBCLONAL	1	TRUE	0	0.392698317730051	1		581	431	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552797	226552797	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	348	547	0	ENST00000366794.5:c.2564A>G	p.His855Arg	p.H855R	ENST00000366794	NM_001618.3	855	cAt/cGt	19/23	0.392698317730051	3	FACETS	0.991	0.939	1	0.991	0.939	1	CLONAL	2	TRUE	1	0.392698317730051	3		547	1070	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631667	90631668	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0025019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	164	616	1	ENST00000330062.3:c.601_602delinsTT	p.Gly201Phe	p.G201F	ENST00000330062	NM_002168.2	201	GGc/TTc	5/11	1	2	FACETS	0.873	0.801	0.948	0.873	0.801	0.948	CLONAL	1	TRUE	1	0.392698317730051	2		617	957	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292998	91292998	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	135	583	0	ENST00000355112.3:c.500A>G	p.Lys167Arg	p.K167R	ENST00000355112	NM_000057.2	167	aAa/aGa	3/22	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.392698317730051	2		583	594	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183808	10183808	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131690964	NA	P-0025019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	133	508	0	ENST00000256474.2:c.278del	p.Gly93AlafsTer66	p.G93Afs*66	ENST00000256474	NM_000551.3	93	Ggc/gc	1/3	0.392698317730051	1	FACETS	0.885	0.806	0.967	0.885	0.806	0.967	CLONAL	1	TRUE	0	0.392698317730051	1		508	615	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0025020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	277	328	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.523569474467589	3	FACETS	0.967	0.934	0.998			1	CLONAL	3	TRUE	NA	0.741956049072371	3		328	353	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661904	29661904	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0025020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	277	395	0	ENST00000356175.3:c.5798C>G	p.Ser1933Ter	p.S1933*	ENST00000356175	NM_000267.3	1933	tCa/tGa	39/57	0.589666289291881	2	FACETS	0.985	0.948	1	0.985	0.948	1	CLONAL	2	TRUE	0	0.741956049072371	2		395	379	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480494	57480494	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	157	226	0	ENST00000371085.3:c.489C>A	p.Tyr163Ter	p.Y163*	ENST00000371085	NM_000516.4	163	taC/taA	6/13	0.656059060455228	4	FACETS	0.847	0.784	0.912	0.847	0.784	0.912	CLONAL	2	TRUE	2	0.741956049072371	4		226	435	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322280	31322280	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	167	231	0	ENST00000412585.2:c.1069G>C	p.Asp357His	p.D357H	ENST00000412585	NM_005514.6	357	Gat/Cat	7/8	0.656059060455228	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.741956049072371	4		231	350	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0025022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	377	781	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.784228230024395	1	FACETS	0.958	0.921	0.994	0.958	0.921	0.994	CLONAL	1	TRUE	0	0.784228230024395	1		786	610	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306996	65306997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	115	396	2	ENST00000342505.4:c.2580dup	p.Pro861ThrfsTer4	p.P861Tfs*4	ENST00000342505	NM_002227.2	860	-/A	19/25	0.784228230024395	1	FACETS	0.33	0.298	0.363	0.33	0.298	0.363	SUBCLONAL	1	TRUE	0	0.784228230024395	1		398	541	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0025022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	377	425	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.784228230024395	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.784228230024395	1		425	583	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0025022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	34	306	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	0.784228230024395	1	FACETS	0.152	0.124	0.184	0.152	0.124	0.184	SUBCLONAL	1	TRUE	0	0.784228230024395	1		306	346	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	358	447	2	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	0.784228230024395	1	FACETS	0.91	0.873	0.947	0.91	0.873	0.947	CLONAL	1	TRUE	0	0.784228230024395	1		449	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0025022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	19	568	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.784228230024395	1	FACETS	0.042	0.031	0.055	0.042	0.031	0.055	SUBCLONAL	1	TRUE	0	0.784228230024395	1		568	701	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711883	89711884	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0025022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	77	445	0	ENST00000371953.3:c.502_503del	p.Ile168SerfsTer11	p.I168Sfs*11	ENST00000371953	NM_000314.4	167	acTAtt/actt	6/9	0.784228230024395	1	FACETS	0.322	0.284	0.362	0.322	0.284	0.362	SUBCLONAL	1	TRUE	0	0.784228230024395	1		445	371	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0025022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	111	196	6	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	0.784228230024395	1	FACETS	0.967	0.899	1	0.967	0.899	1	CLONAL	1	TRUE	0	0.784228230024395	1		202	178	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693002	89693003	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0025022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	14	322	0	ENST00000371953.3:c.491dup	p.Val166SerfsTer14	p.V166Sfs*14	ENST00000371953	NM_000314.4	162	-/A	5/9	0.784228230024395	1	FACETS	0.086	0.062	0.115	0.086	0.062	0.115	SUBCLONAL	1	TRUE	0	0.784228230024395	1		322	253	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0025022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	45	345	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.784228230024395	1	FACETS	0.217	0.183	0.254	0.217	0.183	0.254	SUBCLONAL	1	TRUE	0	0.784228230024395	1		345	322	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512402	38512402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	92	497	6	ENST00000254066.5:c.1319del	p.Pro440ArgfsTer203	p.P440Rfs*203	ENST00000254066	NM_000964.3	438	gCc/gc	9/9	0.784228230024395	1	FACETS	0.25	0.222	0.28	0.25	0.222	0.28	SUBCLONAL	1	TRUE	0	0.784228230024395	1		503	570	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463182	25463182	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs779626155	NA	P-0025022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	84	465	0	ENST00000264709.3:c.2311C>T	p.Arg771Ter	p.R771*	ENST00000264709	NM_175629.2	771	Cga/Tga	19/23	0.784228230024395	1	FACETS	0.238	0.21	0.268	0.238	0.21	0.268	SUBCLONAL	1	TRUE	0	0.784228230024395	1		465	547	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436092	116436092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45578433	NA	P-0025022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	139	527	0	ENST00000397752.3:c.4087G>A	p.Ala1363Thr	p.A1363T	ENST00000397752	NM_000245.2	1363	Gct/Act	21/21	1	2	FACETS	0.353	0.32	0.387	0.353	0.32	0.387	SUBCLONAL	1	TRUE	1	0.784228230024395	2		527	1005	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556378	29556379	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0025022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	343	489	0	ENST00000356175.3:c.2747dup	p.Asn916LysfsTer3	p.N916Kfs*3	ENST00000356175	NM_000267.3	915	-/A	21/57	0.784228230024395	1	FACETS	0.985	0.946	1	0.985	0.946	1	CLONAL	1	TRUE	0	0.784228230024395	1		489	540	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698151	47698151	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	224	434	0	ENST00000233146.2:c.1709del	p.Tyr570LeufsTer20	p.Y570Lfs*20	ENST00000233146	NM_000251.2	570	tAt/tt	11/16	0.784228230024395	1	FACETS	0.962	0.914	1	0.962	0.914	1	CLONAL	1	TRUE	0	0.784228230024395	1		434	361	SUCCESS
AR	367	MSKCC	GRCh37	X	66765121	66765121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	112	365	3	ENST00000374690.3:c.133G>A	p.Ala45Thr	p.A45T	ENST00000374690	NM_000044.3	45	Gcg/Acg	1/8	1	2	FACETS	0.416	0.374	0.46	0.416	0.374	0.46	SUBCLONAL	1	TRUE	1	0.784228230024395	2		368	687	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	349	696	2	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.678464037627128	2		698	978	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829040	128829042	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	rs570242755	NA	P-0025023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	13	98	0	ENST00000249373.3:c.67_69del	p.Leu23del	p.L23del	ENST00000249373	NM_005631.4	16	ggGCTg/ggg	1/12	0.67827354107197	3	FACETS	0.253	0.18	0.341	0.126	0.09	0.171	SUBCLONAL	1	TRUE	1	0.678464037627128	3		98	203	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799050	42799050	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2070	458	794	1	ENST00000575354.2:c.4534C>T	p.Arg1512Cys	p.R1512C	ENST00000575354	NM_015125.3	1512	Cgt/Tgt	20/20	0.67827354107197	5	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.678464037627128	5		795	2528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0025023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	268	488	0	ENST00000269305.4:c.375+1G>T		p.X125_splice	ENST00000269305	NM_001126112.2	125			1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.678464037627128	2		488	690	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860126	57860126	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1302	348	657	0	ENST00000228682.2:c.866T>G	p.Val289Gly	p.V289G	ENST00000228682	NM_005269.2	289	gTg/gGg	8/12	0.60669545219964	4	FACETS	1	0.971	1			1	CLONAL	1	TRUE	NA	0.678464037627128	4		657	1650	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032554	47032554	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	1012	327	2	ENST00000377604.3:c.460G>T	p.Val154Leu	p.V154L	ENST00000377604	NM_001204468.1	154	Gtg/Ttg	5/24	0.678464037627128	3	FACETS	1	0.998	1			1	CLONAL	3	TRUE	NA	0.678464037627128	3		329	1142	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154263	2154263	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1341	354	599	0	ENST00000434045.2:c.665C>G	p.Pro222Arg	p.P222R	ENST00000434045	NM_001127598.1	222	cCc/cGc	5/5	0.672499529638623	4	FACETS	1	0.967	1	0.517	0.488	0.546	CLONAL	1	TRUE	2	0.678464037627128	4		599	1695	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32438072	32438072	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	519	517	0	ENST00000332351.3:c.965G>T	p.Ser322Ile	p.S322I	ENST00000332351	NM_024426.4	322	aGc/aTc	5/10	0.672499529638623	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.678464037627128	4		517	1265	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373754	118373754	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	189	461	0	ENST00000534358.1:c.7147G>T	p.Asp2383Tyr	p.D2383Y	ENST00000534358	NM_005933.3	2383	Gac/Tac	27/36	0.67827354107197	4	FACETS	0.861	0.795	0.93			1	CLONAL	1	TRUE	NA	0.678464037627128	4		461	1086	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21626516	21626516	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs755294309	NA	P-0025023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	1040	691	2	ENST00000421138.2:c.1416C>A	p.Asn472Lys	p.N472K	ENST00000421138		472	aaC/aaA	13/16	0.67827354107197	4	FACETS	0.98	0.963	0.996	0.98	0.963	0.996	CLONAL	4	TRUE	0	0.678464037627128	4		693	1313	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864856	57864856	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	703	703	1	ENST00000228682.2:c.2333A>T	p.Glu778Val	p.E778V	ENST00000228682	NM_005269.2	778	gAa/gTa	12/12	0.60669545219964	4	FACETS	0.999	0.964	1			1	CLONAL	2	TRUE	NA	0.678464037627128	4		704	1741	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281477	49281477	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	286	650	0	ENST00000282018.3:c.524A>C	p.Asp175Ala	p.D175A	ENST00000282018	NM_020377.2	175	gAc/gCc	1/1	0.67827354107197	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.678464037627128	1		650	484	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034992	42034992	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	697	614	0	ENST00000219905.7:c.4834G>T	p.Val1612Leu	p.V1612L	ENST00000219905	NM_001164273.1	1612	Gtg/Ttg	15/24	0.67827354107197	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.678464037627128	2		614	996	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16052833	16052833	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0025023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	124	461	0	ENST00000268712.3:c.843-2A>G		p.X281_splice	ENST00000268712	NM_006311.3	281			1	2	FACETS	0.872	0.796	0.952	0.872	0.796	0.952	CLONAL	1	TRUE	1	0.678464037627128	2		461	419	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486081	29486081	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	403	624	2	ENST00000356175.3:c.258A>G	p.Ile86Met	p.I86M	ENST00000356175	NM_000267.3	86	atA/atG	3/57	0.67827354107197	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.678464037627128	2		626	592	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40364198	40364198	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	421	880	1	ENST00000293328.3:c.1484del	p.Pro495HisfsTer19	p.P495Hfs*19	ENST00000293328	NM_012448.3	495	cCa/ca	13/19	0.67827354107197	3	FACETS	1	0.989	1	0.375	0.356	0.393	CLONAL	1	TRUE	0	0.678464037627128	3		881	1479	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584501	48584501	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	201	429	0	ENST00000342988.3:c.674C>T	p.Pro225Leu	p.P225L	ENST00000342988	NM_005359.5	225	cCt/cTt	6/12	0.67827354107197	4	FACETS	1	0.928	1	0.334	0.309	0.36	CLONAL	1	TRUE	1	0.678464037627128	4		429	993	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488736	212488736	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	1029	602	0	ENST00000342788.4:c.2113C>T	p.Pro705Ser	p.P705S	ENST00000342788	NM_005235.2	705	Ccc/Tcc	18/28	0.641680965490578	5	FACETS	0.972	0.95	0.993	0.972	0.95	0.993	CLONAL	4	TRUE	1	0.678464037627128	5		602	1574	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180195	38180195	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	939	429	0	ENST00000396334.3:c.43G>T	p.Ala15Ser	p.A15S	ENST00000396334	NM_002468.4	15	Gct/Tct	1/5	0.67827354107197	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	4	TRUE	0	0.678464037627128	4		429	1139	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391022	89391022	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	533	645	0	ENST00000336596.2:c.1088G>T	p.Cys363Phe	p.C363F	ENST00000336596	NM_005233.5	363	tGt/tTt	5/17	0.67827354107197	2	FACETS	0.992	0.962	1	0.992	0.962	1	CLONAL	2	TRUE	0	0.678464037627128	2		645	792	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968600	55968600	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	700	703	2	ENST00000263923.4:c.2063G>C	p.Cys688Ser	p.C688S	ENST00000263923	NM_002253.2	688	tGc/tCc	14/30	0.67827354107197	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.678464037627128	2		705	986	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168671	56168671	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	451	500	0	ENST00000399503.3:c.1525G>C	p.Val509Leu	p.V509L	ENST00000399503	NM_005921.1	509	Gtg/Ctg	9/20	0.67827354107197	2	FACETS	0.992	0.96	1	0.992	0.96	1	CLONAL	2	TRUE	0	0.678464037627128	2		500	670	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407507	407507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	468	663	1	ENST00000380956.4:c.1265G>A	p.Gly422Glu	p.G422E	ENST00000380956	NM_001195286.1	422	gGa/gAa	9/9	0.664322113226857	5	FACETS	1	0.991	1	0.748	0.716	0.781	CLONAL	2	TRUE	2	0.678464037627128	5		664	1240	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509676	106509676	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	282	535	0	ENST00000359195.3:c.1670C>A	p.Ala557Glu	p.A557E	ENST00000359195	NM_002649.2	557	gCg/gAg	2/11	0.67827354107197	3	FACETS	1	0.978	1	0.54	0.508	0.574	CLONAL	1	TRUE	1	0.678464037627128	3		535	1030	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524689	106524689	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	373	447	0	ENST00000359195.3:c.2850C>A	p.Asp950Glu	p.D950E	ENST00000359195	NM_002649.2	950	gaC/gaA	9/11	0.67827354107197	3	FACETS	0.979	0.936	1	0.979	0.936	1	CLONAL	2	TRUE	1	0.678464037627128	3		447	752	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69143594	69143594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	210	459	0	ENST00000288368.4:c.4802C>T	p.Pro1601Leu	p.P1601L	ENST00000288368	NM_024870.2	1601	cCc/cTc	40/40	0.67827354107197	3	FACETS	1	0.935	1	0.502	0.467	0.539	CLONAL	1	TRUE	1	0.678464037627128	3		459	825	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864889	117864889	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	457	643	1	ENST00000297338.2:c.1220G>T	p.Gly407Val	p.G407V	ENST00000297338	NM_006265.2	407	gGa/gTa	10/14	0.475882454277314	6	FACETS	1	0.96	1	0.504	0.48	0.528	CLONAL	2	TRUE	2	0.678464037627128	6		644	1575	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412371	63412371	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	677	433	0	ENST00000330258.3:c.796G>T	p.Ala266Ser	p.A266S	ENST00000330258	NM_152424.3	266	Gcc/Tcc	2/2	0.60669545219964	2	FACETS	1	0.998	1			1	CLONAL	2	TRUE	NA	0.678464037627128	2		433	817	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0025024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	225	329	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.354550893716852	3	FACETS	0.871	0.812	0.931	0.871	0.812	0.931	CLONAL	2	TRUE	1	0.354550893716852	3		329	858	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317878	8317878	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151311972	NA	P-0025024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	100	321	0	ENST00000356435.5:c.5735C>T	p.Thr1912Met	p.T1912M	ENST00000356435		1912	aCg/aTg	35/35	0.188955943185401	1	FACETS	0.787	0.704	0.874	0.787	0.704	0.874	INDETERMINATE	1	TRUE	0	0.354550893716852	1		321	590	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625456	69625456	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	28	254	0	ENST00000334134.2:c.337G>T	p.Ala113Ser	p.A113S	ENST00000334134	NM_005247.2	113	Gcc/Tcc	3/3	0.188955943185401	1	FACETS	0.255	0.203	0.315	0.255	0.203	0.315	INDETERMINATE	1	TRUE	0	0.354550893716852	1		254	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579397	7579397	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	223	344	0	ENST00000269305.4:c.290del	p.Val97AlafsTer26	p.V97Afs*26	ENST00000269305	NM_001126112.2	97	gTc/gc	4/11	0.262544576629741	2	FACETS	0.835	0.78	0.892	0.835	0.78	0.892	CLONAL	2	TRUE	0	0.354550893716852	2		344	753	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0025027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	33	637	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.487	0.396	0.589	0.487	0.396	0.589	SUBCLONAL	1	FALSE	1	0.3	2		638	452	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162669	47162669	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	37	453	0	ENST00000409792.3:c.3457del	p.Ile1153Ter	p.I1153*	ENST00000409792	NM_014159.6	1153	Ata/ta	3/21	1	2	FACETS	0.563	0.464	0.674	0.563	0.464	0.674	SUBCLONAL	1	FALSE	1	0.3	2		453	438	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753187	128753187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779123478	NA	P-0025030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	63	362	0	ENST00000377970.2:c.1348C>T	p.Arg450Trp	p.R450W	ENST00000377970	NM_002467.4	450	Cgg/Tgg	3/3	1	2	FACETS	0.78	0.676	0.893	0.78	0.676	0.893	SUBCLONAL	1	TRUE	1	0.331493593038343	2		362	487	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531066	187531066	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	155	568	0	ENST00000441802.2:c.9957del	p.Thr3320LeufsTer2	p.T3320Lfs*2	ENST00000441802	NM_005245.3	3319	gcC/gc	15/27	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.331493593038343	2		568	832	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574000	7574000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	263	781	0	ENST00000269305.4:c.1027G>T	p.Glu343Ter	p.E343*	ENST00000269305	NM_001126112.2	343	Gag/Tag	10/11	0.719361590128561	1	FACETS	0.943	0.899	0.986	0.943	0.899	0.986	CLONAL	1	TRUE	0	0.782444351445343	1		781	434	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168519	56168528	+	frameshift_variant	Frame_Shift_Del	DEL	GATCTAAGTG	GATCTAAGTG	-	novel	NA	P-0025031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	151	485	0	ENST00000399503.3:c.1477_1486del	p.Ser493AspfsTer61	p.S493Dfs*61	ENST00000399503	NM_005921.1	492	aGATCTAAGTGg/ag	8/20	0.719361590128561	1	FACETS	0.854	0.799	0.91	0.854	0.799	0.91	CLONAL	1	TRUE	0	0.782444351445343	1		485	275	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855984	68855984	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121964877	NA	P-0025043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	44	726	2	ENST00000261769.5:c.1792C>T	p.Arg598Ter	p.R598*	ENST00000261769	NM_004360.3	598	Cga/Tga	12/16	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		728	655	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861143	57861143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772799269	NA	P-0025044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	342	563	0	ENST00000228682.2:c.940C>T	p.Arg314Cys	p.R314C	ENST00000228682	NM_005269.2	314	Cgc/Tgc	9/12	1	2	FACETS	0.944	0.897	0.993	0.944	0.897	0.993	CLONAL	1	TRUE	1	0.787253242363475	2		563	920	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576851	7576851	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0025044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	380	624	0	ENST00000269305.4:c.993+2T>G		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.787253242363475	1	FACETS	0.984	0.947	1	0.984	0.947	1	CLONAL	1	TRUE	0	0.787253242363475	1		624	595	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26021117	26021117	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	223	371	0	ENST00000357647.3:c.400G>C	p.Glu134Gln	p.E134Q	ENST00000357647	NM_003529.2	134	Gag/Cag	1/1	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.787253242363475	2		371	562	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	228	606	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.951	0.887	1	0.951	0.887	1	CLONAL	1	TRUE	1	0.523682867048913	2		606	916	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0025046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	237	778	2	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.523682867048913	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.523682867048913	1		780	596	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0025046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	100	425	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.832	0.747	0.921	0.832	0.747	0.921	CLONAL	1	TRUE	1	0.523682867048913	2		425	459	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355121	15355121	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	35	736	0	ENST00000263377.2:c.2502G>C	p.Glu834Asp	p.E834D	ENST00000263377	NM_058243.2	834	gaG/gaC	13/20	0.523682867048913	1	FACETS	0.201	0.164	0.242	0.201	0.164	0.242	SUBCLONAL	1	TRUE	0	0.523682867048913	1		736	491	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	151	606	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.60694067850724	2		606	485	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	85	255	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.737	0.656	0.823	0.737	0.656	0.823	SUBCLONAL	1	TRUE	1	0.60694067850724	2		255	380	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	111	304	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	0.818	0.74	0.9	0.818	0.74	0.9	CLONAL	1	TRUE	1	0.60694067850724	2		304	447	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	88	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.85	0.76	0.945	0.85	0.76	0.945	CLONAL	1	TRUE	1	0.60694067850724	2		326	341	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187222	38187222	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	45	526	3	ENST00000317025.8:c.1255del	p.Thr419ProfsTer8	p.T419Pfs*8	ENST00000317025	NM_023034.1	419	Acc/cc	6/24	1	2	FACETS	0.225	0.188	0.266	0.225	0.188	0.266	SUBCLONAL	1	TRUE	1	0.60694067850724	2		529	659	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533939	63533940	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs771001164	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	74	226	0	ENST00000307078.5:c.1214_1215del	p.Glu405GlyfsTer56	p.E405Gfs*56	ENST00000307078	NM_004655.3	405	gAG/g	6/11	1	2	FACETS	0.818	0.723	0.918	0.818	0.723	0.918	CLONAL	1	TRUE	1	0.60694067850724	2		226	298	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850705	63850705	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs201178069	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	27	311	0	ENST00000279873.7:c.1489del	p.Ile497Ter	p.I497*	ENST00000279873	NM_032199.2	495	Aaa/aa	10/10	1	2	FACETS	0.24	0.19	0.296	0.24	0.19	0.296	SUBCLONAL	1	TRUE	1	0.60694067850724	2		311	371	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053023	180053023	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	81	388	4	ENST00000261937.6:c.1267del	p.Gln423ArgfsTer70	p.Q423Rfs*70	ENST00000261937	NM_182925.4	423	Cag/ag	10/30	1	2	FACETS	0.902	0.803	1	0.902	0.803	1	CLONAL	1	TRUE	1	0.60694067850724	2		392	296	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	11	224	0	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	1	1	FACETS	0.121	0.083	0.168	0.121	0.083	0.168	SUBCLONAL	1	TRUE	0	0.60694067850724	1		224	208	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	83	458	10	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.453	0.4	0.509	0.453	0.4	0.509	SUBCLONAL	1	TRUE	1	0.60694067850724	2		468	604	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	150	234	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	0.566943391591376	2	FACETS	0.951	0.89	1	0.951	0.89	1	CLONAL	2	TRUE	0	0.60694067850724	2		234	260	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106514	27106514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	68	397	0	ENST00000324856.7:c.6125G>A	p.Ser2042Asn	p.S2042N	ENST00000324856	NM_006015.4	2042	aGc/aAc	20/20	1	2	FACETS	0.522	0.456	0.594	0.522	0.456	0.594	SUBCLONAL	1	TRUE	1	0.60694067850724	2		397	429	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838408	156838408	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	104	366	0	ENST00000524377.1:c.686T>C	p.Leu229Pro	p.L229P	ENST00000524377	NM_002529.3	229	cTc/cCc	6/17	1	2	FACETS	0.99	0.896	1	0.99	0.896	1	CLONAL	1	TRUE	1	0.60694067850724	2		366	346	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163307849	163307849	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	92	296	0	ENST00000271452.3:c.475C>G	p.His159Asp	p.H159D	ENST00000271452	NM_145697.2	159	Cac/Gac	7/14	1	2	FACETS	0.844	0.757	0.936	0.844	0.757	0.936	CLONAL	1	TRUE	1	0.60694067850724	2		296	359	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163313577	163313577	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	30	331	0	ENST00000271452.3:c.724A>G	p.Thr242Ala	p.T242A	ENST00000271452	NM_145697.2	242	Aca/Gca	10/14	1	2	FACETS	0.218	0.175	0.267	0.218	0.175	0.267	SUBCLONAL	1	TRUE	1	0.60694067850724	2		331	453	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450787	70450787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	36	305	0	ENST00000373644.4:c.5627G>A	p.Ser1876Asn	p.S1876N	ENST00000373644	NM_030625.2	1876	aGc/aAc	12/12	1	2	FACETS	0.28	0.23	0.337	0.28	0.23	0.337	SUBCLONAL	1	TRUE	1	0.60694067850724	2		305	423	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457951	69457951	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	14	277	0	ENST00000227507.2:c.355del	p.Leu119Ter	p.L119*	ENST00000227507	NM_053056.2	117	atC/at	2/5	1	2	FACETS	0.169	0.122	0.226	0.169	0.122	0.226	SUBCLONAL	1	TRUE	1	0.60694067850724	2		277	273	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939522	71939522	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	30	420	0	ENST00000298229.2:c.377C>A	p.Pro126Gln	p.P126Q	ENST00000298229	NM_001567.3	126	cCg/cAg	3/28	1	2	FACETS	0.246	0.198	0.3	0.246	0.198	0.3	SUBCLONAL	1	TRUE	1	0.60694067850724	2		420	402	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94179003	94179003	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747646574	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	29	350	0	ENST00000323929.3:c.1840G>A	p.Ala614Thr	p.A614T	ENST00000323929	NM_005591.3	614	Gca/Aca	16/20	1	2	FACETS	0.22	0.176	0.27	0.22	0.176	0.27	SUBCLONAL	1	TRUE	1	0.60694067850724	2		350	435	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912676	100912676	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	28	276	0	ENST00000325455.5:c.2646T>A	p.Asp882Glu	p.D882E	ENST00000325455	NM_001202474.3	882	gaT/gaA	7/8	1	2	FACETS	0.231	0.184	0.285	0.231	0.184	0.285	SUBCLONAL	1	TRUE	1	0.60694067850724	2		276	399	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114816	108114817	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	149	485	1	ENST00000278616.4:c.640dup	p.Ser214PhefsTer40	p.S214Ffs*40	ENST00000278616	NM_000051.3	211	-/T	6/63	1	2	FACETS	0.926	0.851	1	0.926	0.851	1	CLONAL	1	TRUE	1	0.60694067850724	2		486	530	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344369	118344369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	23	216	0	ENST00000534358.1:c.2495C>T	p.Pro832Leu	p.P832L	ENST00000534358	NM_005933.3	832	cCt/cTt	3/36	1	2	FACETS	0.222	0.172	0.279	0.222	0.172	0.279	SUBCLONAL	1	TRUE	1	0.60694067850724	2		216	342	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1036341	1036341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775265125	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	43	374	1	ENST00000358495.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000358495	NM_134424.2	146	gCg/gTg	6/12	1	2	FACETS	0.328	0.274	0.387	0.328	0.274	0.387	SUBCLONAL	1	TRUE	1	0.60694067850724	2		375	432	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21627877	21627877	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1295951241	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	157	548	0	ENST00000421138.2:c.1253A>G	p.Tyr418Cys	p.Y418C	ENST00000421138		418	tAc/tGc	12/16	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.60694067850724	2		548	493	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859434	57859434	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	23	391	0	ENST00000228682.2:c.579A>C	p.Glu193Asp	p.E193D	ENST00000228682	NM_005269.2	193	gaA/gaC	6/12	1	2	FACETS	0.186	0.144	0.234	0.186	0.144	0.234	SUBCLONAL	1	TRUE	1	0.60694067850724	2		391	408	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953514	32953514	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	138	331	0	ENST00000380152.3:c.8815A>G	p.Lys2939Glu	p.K2939E	ENST00000380152		2939	Aag/Gag	22/27	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.60694067850724	2		331	432	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878069	48878069	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	20	160	0	ENST00000267163.4:c.25del	p.Thr9ArgfsTer56	p.T9Rfs*56	ENST00000267163	NM_000321.2	7	cgA/cg	1/27	1	2	FACETS	0.42	0.323	0.531	0.42	0.323	0.531	SUBCLONAL	1	TRUE	1	0.60694067850724	2		160	157	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524683	103524683	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	36	310	0	ENST00000355739.4:c.2814A>C	p.Lys938Asn	p.K938N	ENST00000355739	NM_000123.3	938	aaA/aaC	13/15	1	2	FACETS	0.287	0.236	0.345	0.287	0.236	0.345	SUBCLONAL	1	TRUE	1	0.60694067850724	2		310	413	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701932	43701933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	24	209	0	ENST00000382044.4:c.5312dup	p.Leu1771PhefsTer24	p.L1771Ffs*24	ENST00000382044	NM_001141980.1	1771	ttg/ttTg	25/28	1	2	FACETS	0.348	0.274	0.433	0.348	0.274	0.433	SUBCLONAL	1	TRUE	1	0.60694067850724	2		209	227	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483932	88483932	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	133	425	1	ENST00000360948.2:c.1638G>T	p.Glu546Asp	p.E546D	ENST00000360948	NM_001012338.2	546	gaG/gaT	14/19	1	2	FACETS	0.985	0.902	1	0.985	0.902	1	CLONAL	1	TRUE	1	0.60694067850724	2		426	445	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631704	90631704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	59	354	0	ENST00000330062.3:c.565G>A	p.Ala189Thr	p.A189T	ENST00000330062	NM_002168.2	189	Gcc/Acc	5/11	1	2	FACETS	0.512	0.442	0.587	0.512	0.442	0.587	SUBCLONAL	1	TRUE	1	0.60694067850724	2		354	380	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778882	3778882	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1254881895	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	30	282	0	ENST00000262367.5:c.6166G>A	p.Val2056Met	p.V2056M	ENST00000262367	NM_004380.2	2056	Gtg/Atg	31/31	1	2	FACETS	0.3	0.242	0.366	0.3	0.242	0.366	SUBCLONAL	1	TRUE	1	0.60694067850724	2		282	329	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650720	67650720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	147	424	0	ENST00000264010.4:c.1025G>A	p.Arg342His	p.R342H	ENST00000264010	NM_006565.3	342	cGt/cAt	5/12	1	2	FACETS	0.941	0.864	1	0.941	0.864	1	CLONAL	1	TRUE	1	0.60694067850724	2		424	515	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830807	72830807	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	26	386	0	ENST00000268489.5:c.5774del	p.Gly1925ValfsTer72	p.G1925Vfs*72	ENST00000268489	NM_006885.3	1925	gGt/gt	9/10	1	2	FACETS	0.191	0.151	0.237	0.191	0.151	0.237	SUBCLONAL	1	TRUE	1	0.60694067850724	2		386	449	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942828	15942828	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	125	363	0	ENST00000268712.3:c.6874G>A	p.Val2292Ile	p.V2292I	ENST00000268712	NM_006311.3	2292	Gta/Ata	44/46	1	2	FACETS	0.905	0.825	0.988	0.905	0.825	0.988	CLONAL	1	TRUE	1	0.60694067850724	2		363	455	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15952280	15952280	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	38	359	0	ENST00000268712.3:c.6415A>G	p.Arg2139Gly	p.R2139G	ENST00000268712	NM_006311.3	2139	Agg/Ggg	41/46	1	2	FACETS	0.294	0.243	0.351	0.294	0.243	0.351	SUBCLONAL	1	TRUE	1	0.60694067850724	2		359	426	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983295	15983295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1355823096	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	129	357	0	ENST00000268712.3:c.3484C>T	p.Arg1162Trp	p.R1162W	ENST00000268712	NM_006311.3	1162	Cgg/Tgg	26/46	1	2	FACETS	0.947	0.865	1	0.947	0.865	1	CLONAL	1	TRUE	1	0.60694067850724	2		357	449	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119725	17119725	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	90	288	0	ENST00000285071.4:c.1269del	p.His423GlnfsTer45	p.H423Qfs*45	ENST00000285071	NM_144997.5	423	caC/ca	11/14	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.60694067850724	2		288	277	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687228	37687228	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	31	334	0	ENST00000447079.4:c.4132G>T	p.Gly1378Cys	p.G1378C	ENST00000447079	NM_015083.1	1378	Ggc/Tgc	14/14	1	2	FACETS	0.261	0.211	0.318	0.261	0.211	0.318	SUBCLONAL	1	TRUE	1	0.60694067850724	2		334	391	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453399	40453399	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs759027671	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	153	534	9	ENST00000345506.4:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000345506	NM_003152.3	366	Ccc/cc	10/20	1	2	FACETS	0.918	0.845	0.994	0.918	0.845	0.994	CLONAL	1	TRUE	1	0.60694067850724	2		543	549	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119978	70119978	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	11	140	0	ENST00000245479.2:c.983del	p.Pro328ArgfsTer55	p.P328Rfs*55	ENST00000245479	NM_000346.3	327	aCc/ac	3/3	1	2	FACETS	0.243	0.168	0.336	0.243	0.168	0.336	SUBCLONAL	1	TRUE	1	0.60694067850724	2		140	149	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78923342	78923342	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749994413	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	81	255	0	ENST00000306801.3:c.3365C>T	p.Thr1122Met	p.T1122M	ENST00000306801	NM_020761.2	1122	aCg/aTg	28/34	1	2	FACETS	0.974	0.869	1	0.974	0.869	1	CLONAL	1	TRUE	1	0.60694067850724	2		255	274	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210583	5210583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253335014	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	26	363	1	ENST00000357368.4:c.5384C>T	p.Pro1795Leu	p.P1795L	ENST00000357368	NM_002850.3	1795	cCg/cTg	35/38	1	2	FACETS	0.245	0.194	0.303	0.245	0.194	0.303	SUBCLONAL	1	TRUE	1	0.60694067850724	2		364	350	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276729	15276729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	134	416	1	ENST00000263388.2:c.5536G>A	p.Ala1846Thr	p.A1846T	ENST00000263388	NM_000435.2	1846	Gct/Act	30/33	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.60694067850724	2		417	438	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290893	15290893	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	52	442	0	ENST00000263388.2:c.3317A>G	p.Tyr1106Cys	p.Y1106C	ENST00000263388	NM_000435.2	1106	tAc/tGc	20/33	1	2	FACETS	0.361	0.307	0.419	0.361	0.307	0.419	SUBCLONAL	1	TRUE	1	0.60694067850724	2		442	475	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15374311	15374311	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	29	389	0	ENST00000263377.2:c.1261G>A	p.Asp421Asn	p.D421N	ENST00000263377	NM_058243.2	421	Gac/Aac	7/20	1	2	FACETS	0.221	0.177	0.271	0.221	0.177	0.271	SUBCLONAL	1	TRUE	1	0.60694067850724	2		389	433	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273026	18273026	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	120	376	0	ENST00000222254.8:c.921del	p.Lys308ArgfsTer33	p.K308Rfs*33	ENST00000222254	NM_005027.3	306	Ccc/cc	8/16	1	2	FACETS	0.92	0.837	1	0.92	0.837	1	CLONAL	1	TRUE	1	0.60694067850724	2		376	430	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258545	19258545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368616462	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	25	401	0	ENST00000162023.5:c.355G>A	p.Glu119Lys	p.E119K	ENST00000162023		119	Gaa/Aaa	8/13	1	2	FACETS	0.193	0.151	0.241	0.193	0.151	0.241	SUBCLONAL	1	TRUE	1	0.60694067850724	2		401	427	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224734	36224735	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	129	477	1	ENST00000222270.7:c.7120_7121insA	p.Pro2374HisfsTer6	p.P2374Hfs*6	ENST00000222270	NM_014727.1	2374	cca/cAca	30/37	1	2	FACETS	0.859	0.783	0.937	0.859	0.783	0.937	CLONAL	1	TRUE	1	0.60694067850724	2		478	495	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	62	201	1	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	1	2	FACETS	0.824	0.72	0.934	0.824	0.72	0.934	CLONAL	1	TRUE	1	0.60694067850724	2		202	248	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912080	50912080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	149	406	0	ENST00000440232.2:c.1814C>T	p.Ser605Leu	p.S605L	ENST00000440232	NM_002691.3	605	tCg/tTg	15/27	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.60694067850724	2		406	437	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	107	375	1	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.685	0.617	0.756	0.685	0.617	0.756	SUBCLONAL	1	TRUE	1	0.60694067850724	2		376	515	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128030506	128030506	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs770925947	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	57	418	0	ENST00000285398.2:c.1762del	p.Glu588LysfsTer23	p.E588Kfs*23	ENST00000285398	NM_000122.1	588	Gaa/aa	11/15	1	2	FACETS	0.456	0.392	0.525	0.456	0.392	0.525	SUBCLONAL	1	TRUE	1	0.60694067850724	2		418	412	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617542	158617543	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	22	351	0	ENST00000263640.3:c.1113dup	p.Asn372GlufsTer18	p.N372Efs*18	ENST00000263640	NM_001105.4	371	-/G	9/11	1	2	FACETS	0.186	0.143	0.235	0.186	0.143	0.235	SUBCLONAL	1	TRUE	1	0.60694067850724	2		351	390	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437288	220437288	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1190141661	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	124	420	0	ENST00000243786.2:c.197del	p.Gly66AlafsTer61	p.G66Afs*61	ENST00000243786	NM_002191.3	64	ctG/ct	1/2	1	2	FACETS	0.92	0.839	1	0.92	0.839	1	CLONAL	1	TRUE	1	0.60694067850724	2		420	444	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022358	31022358	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1230703370	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	16	197	0	ENST00000375687.4:c.1843G>A	p.Ala615Thr	p.A615T	ENST00000375687	NM_015338.5	615	Gca/Aca	13/13	1	2	FACETS	0.193	0.142	0.254	0.193	0.142	0.254	SUBCLONAL	1	TRUE	1	0.60694067850724	2		197	273	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385153	41385153	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776806194	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	134	409	0	ENST00000373198.4:c.808C>T	p.Arg270Cys	p.R270C	ENST00000373198	NM_133170.3	270	Cgc/Tgc	6/32	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.60694067850724	2		409	408	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633207	12633207	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs730880382	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	122	349	0	ENST00000251849.4:c.1193G>T	p.Arg398Leu	p.R398L	ENST00000251849	NM_002880.3	398	cGc/cTc	11/17	1	2	FACETS	0.905	0.824	0.99	0.905	0.824	0.99	CLONAL	1	TRUE	1	0.60694067850724	2		349	444	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200691	128200691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	103	342	2	ENST00000341105.2:c.1114G>A	p.Ala372Thr	p.A372T	ENST00000341105	NM_032638.4	372	Gcc/Acc	5/6	1	2	FACETS	0.992	0.898	1	0.992	0.898	1	CLONAL	1	TRUE	1	0.60694067850724	2		344	342	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451336	187451336	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	86	253	0	ENST00000232014.4:c.146T>C	p.Val49Ala	p.V49A	ENST00000232014	NM_001130845.1	49	gTc/gCc	3/10	1	2	FACETS	0.861	0.769	0.958	0.861	0.769	0.958	CLONAL	1	TRUE	1	0.60694067850724	2		253	329	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920318	1920318	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	41	427	5	ENST00000382891.5:c.1382del	p.Leu461TrpfsTer12	p.L461Wfs*12	ENST00000382891	NM_133335.3	460	Ttt/tt	5/22	1	2	FACETS	0.29	0.241	0.344	0.29	0.241	0.344	SUBCLONAL	1	TRUE	1	0.60694067850724	2		432	466	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1955117	1955117	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	60	436	1	ENST00000382891.5:c.2204G>A	p.Cys735Tyr	p.C735Y	ENST00000382891	NM_133335.3	735	tGt/tAt	12/22	1	2	FACETS	0.391	0.337	0.449	0.391	0.337	0.449	SUBCLONAL	1	TRUE	1	0.60694067850724	2		437	506	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152018	55152018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs79948560	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	128	338	0	ENST00000257290.5:c.2450G>A	p.Arg817His	p.R817H	ENST00000257290	NM_006206.4	817	cGt/cAt	18/23	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.60694067850724	2		338	410	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554836	187554836	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	20	232	0	ENST00000441802.2:c.4323+2T>C		p.X1441_splice	ENST00000441802	NM_005245.3	1441			1	2	FACETS	0.215	0.164	0.274	0.215	0.164	0.274	SUBCLONAL	1	TRUE	1	0.60694067850724	2		232	307	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449396	31449396	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	44	353	0	ENST00000344624.3:c.2813G>A	p.Arg938Gln	p.R938Q	ENST00000344624		938	cGg/cAg	19/33	1	2	FACETS	0.371	0.311	0.436	0.371	0.311	0.436	SUBCLONAL	1	TRUE	1	0.60694067850724	2		353	391	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177039	56177039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777628678	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	34	294	0	ENST00000399503.3:c.2309C>T	p.Ala770Val	p.A770V	ENST00000399503	NM_005921.1	770	gCt/gTt	13/20	1	2	FACETS	0.251	0.204	0.303	0.251	0.204	0.303	SUBCLONAL	1	TRUE	1	0.60694067850724	2		294	447	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750808	57750808	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	48	346	0	ENST00000274289.3:c.1796G>T	p.Arg599Leu	p.R599L	ENST00000274289	NM_006622.3	599	cGg/cTg	13/14	1	2	FACETS	0.37	0.313	0.432	0.37	0.313	0.432	SUBCLONAL	1	TRUE	1	0.60694067850724	2		346	428	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515217	149515217	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	83	391	0	ENST00000261799.4:c.265A>G	p.Asn89Asp	p.N89D	ENST00000261799	NM_002609.3	89	Aac/Gac	3/23	1	2	FACETS	0.57	0.504	0.639	0.57	0.504	0.639	SUBCLONAL	1	TRUE	1	0.60694067850724	2		391	480	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046289	180046289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	23	294	0	ENST00000261937.6:c.2725G>A	p.Val909Met	p.V909M	ENST00000261937	NM_182925.4	909	Gtg/Atg	19/30	1	2	FACETS	0.259	0.202	0.325	0.259	0.202	0.325	SUBCLONAL	1	TRUE	1	0.60694067850724	2		294	293	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31946776	31946776	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	30	405	0	ENST00000375333.2:c.664G>T	p.Val222Leu	p.V222L	ENST00000375333	NM_032454.1	222	Gta/Tta	4/8	0.566943391591376	2	FACETS	0.227	0.183	0.278	0.114	0.091	0.139	SUBCLONAL	1	TRUE	0	0.60694067850724	2		405	435	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	206	387	0	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	0.566943391591376	2	FACETS	0.861	0.812	0.911	0.861	0.812	0.911	CLONAL	2	TRUE	0	0.60694067850724	2		387	394	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109309771	109309771	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	145	475	0	ENST00000436639.2:c.1544G>A	p.Trp515Ter	p.W515*	ENST00000436639	NM_014454.2	515	tGg/tAg	9/10	1	2	FACETS	0.864	0.792	0.938	0.864	0.792	0.938	CLONAL	1	TRUE	1	0.60694067850724	2		475	553	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835931	151835931	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	111	378	0	ENST00000262189.6:c.14593G>T	p.Gly4865Ter	p.G4865*	ENST00000262189	NM_170606.2	4865	Gga/Tga	58/59	1	2	FACETS	0.867	0.785	0.952	0.867	0.785	0.952	CLONAL	1	TRUE	1	0.60694067850724	2		378	422	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891639	151891639	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1383716454	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	21	248	0	ENST00000262189.6:c.4393A>G	p.Thr1465Ala	p.T1465A	ENST00000262189	NM_170606.2	1465	Act/Gct	29/59	1	2	FACETS	0.21	0.162	0.267	0.21	0.162	0.267	SUBCLONAL	1	TRUE	1	0.60694067850724	2		248	329	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346202	152346202	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	46	367	0	ENST00000359321.1:c.368G>A	p.Ser123Asn	p.S123N	ENST00000359321	NM_005431.1	123	aGc/aAc	3/3	1	2	FACETS	0.292	0.245	0.343	0.292	0.245	0.343	SUBCLONAL	1	TRUE	1	0.60694067850724	2		367	520	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	77	272	2	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	0.881	0.782	0.985	0.881	0.782	0.985	CLONAL	1	TRUE	1	0.60694067850724	2		274	288	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741985	145741985	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	115	331	0	ENST00000428558.2:c.518A>G	p.Gln173Arg	p.Q173R	ENST00000428558	NM_004260.3	173	cAg/cGg	5/22	1	2	FACETS	0.992	0.902	1	0.992	0.902	1	CLONAL	1	TRUE	1	0.60694067850724	2		331	382	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212729	27212729	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	87	477	0	ENST00000380036.4:c.2711A>G	p.Tyr904Cys	p.Y904C	ENST00000380036	NM_000459.3	904	tAc/tGc	17/23	1	2	FACETS	0.553	0.491	0.62	0.553	0.491	0.62	SUBCLONAL	1	TRUE	1	0.60694067850724	2		477	518	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391896	139391896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766745955	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	39	367	1	ENST00000277541.6:c.6295G>A	p.Asp2099Asn	p.D2099N	ENST00000277541	NM_017617.3	2099	Gac/Aac	34/34	1	2	FACETS	0.344	0.285	0.409	0.344	0.285	0.409	SUBCLONAL	1	TRUE	1	0.60694067850724	2		368	374	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407473	139407473	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	52	373	0	ENST00000277541.6:c.2467G>T	p.Gly823Cys	p.G823C	ENST00000277541	NM_017617.3	823	Ggt/Tgt	15/34	1	2	FACETS	0.515	0.44	0.595	0.515	0.44	0.595	SUBCLONAL	1	TRUE	1	0.60694067850724	2		373	333	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422384	47422384	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	89	154	0	ENST00000377045.4:c.23del	p.Pro8LeufsTer26	p.P8Lfs*26	ENST00000377045	NM_001654.4	6	ggC/gg	2/16	1	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.60694067850724	1		154	159	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426420	47426420	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	50	193	0	ENST00000377045.4:c.763C>G	p.Arg255Gly	p.R255G	ENST00000377045	NM_001654.4	255	Cgg/Ggg	9/16	1	1	FACETS	0.638	0.55	0.731	0.638	0.55	0.731	SUBCLONAL	1	TRUE	0	0.60694067850724	1		193	180	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652397	48652397	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	18	164	0	ENST00000376670.3:c.1073del	p.Pro358GlnfsTer74	p.P358Qfs*74	ENST00000376670	NM_002049.3	356	ggC/gg	6/6	1	1	FACETS	0.203	0.153	0.261	0.203	0.153	0.261	SUBCLONAL	1	TRUE	0	0.60694067850724	1		164	204	SUCCESS
AR	367	MSKCC	GRCh37	X	66931518	66931519	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	100	189	0	ENST00000374690.3:c.2162dup	p.Ala722GlyfsTer47	p.A722Gfs*47	ENST00000374690	NM_000044.3	720	-/A	4/8	1	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.60694067850724	1		189	187	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617162	100617162	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	12	209	0	ENST00000308731.7:c.587A>C	p.Gln196Pro	p.Q196P	ENST00000308731	NM_000061.2	196	cAg/cCg	7/19	1	1	FACETS	0.126	0.088	0.172	0.126	0.088	0.172	SUBCLONAL	1	TRUE	0	0.60694067850724	1		209	219	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	170	781	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.433124314108431	2	FACETS	1	0.984	1	0.619	0.572	0.668	CLONAL	1	TRUE	0	0.433124314108431	2		786	634	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	100	413	1	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.433124314108431	2		414	458	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	150	570	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.433124314108431	2		570	668	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722761	49722761	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs62262682	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	10	33	0	ENST00000449682.2:c.1478G>T	p.Arg493Leu	p.R493L	ENST00000449682	NM_020998.3	493	cGt/cTt	13/18	1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	1	0.433124314108431	2		33	36	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	182	655	3	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.433124314108431	2		658	688	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	146	430	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.433124314108431	2		430	649	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444317	50444317	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	97	278	0	ENST00000331340.3:c.247C>T	p.Arg83Ter	p.R83*	ENST00000331340	NM_006060.4	83	Cga/Tga	4/8	1	2	FACETS	0.924	0.827	1	0.924	0.827	1	CLONAL	1	TRUE	1	0.433124314108431	2		278	485	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102033228	102033228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	162	573	6	ENST00000282441.5:c.614C>T	p.Ala205Val	p.A205V	ENST00000282441	NM_001130145.2	205	gCc/gTc	3/9	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.433124314108431	2		579	693	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	188	458	10	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.948	0.876	1	0.948	0.876	1	CLONAL	1	TRUE	1	0.433124314108431	2		468	916	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804953	43804953	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	62	315	1	ENST00000372470.3:c.408del	p.Ser137ValfsTer29	p.S137Vfs*29	ENST00000372470	NM_005373.2	135	Ccc/cc	4/12	1	2	FACETS	0.884	0.768	1	0.884	0.768	1	CLONAL	1	TRUE	1	0.433124314108431	2		316	324	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779211	3779211	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783507	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	21	276	1	ENST00000262367.5:c.5837del	p.Pro1946HisfsTer30	p.P1946Hfs*30	ENST00000262367	NM_004380.2	1946	cCa/ca	31/31	1	2	FACETS	0.328	0.252	0.415	0.328	0.252	0.415	SUBCLONAL	1	TRUE	1	0.433124314108431	2		277	296	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	77	367	0	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	0.909	0.803	1	0.909	0.803	1	CLONAL	1	TRUE	1	0.433124314108431	2		367	391	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	291	541	1	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	0.433124314108431	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.433124314108431	2		542	616	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	124	510	2	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.907	0.823	0.996	0.907	0.823	0.996	CLONAL	1	TRUE	1	0.433124314108431	2		512	631	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874637	35874637	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	33	448	4	ENST00000303115.3:c.799del	p.Arg267GlyfsTer28	p.R267Gfs*28	ENST00000303115	NM_002185.3	265	Aaa/aa	6/8	1	2	FACETS	0.297	0.241	0.36	0.297	0.241	0.36	SUBCLONAL	1	TRUE	1	0.433124314108431	2		452	513	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822585	72822586	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs764626362	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	31	325	1	ENST00000268489.5:c.9589dup	p.Gln3197ProfsTer42	p.Q3197Pfs*42	ENST00000268489	NM_006885.3	3197	cag/cCag	10/10	1	2	FACETS	0.315	0.254	0.383	0.315	0.254	0.383	SUBCLONAL	1	TRUE	1	0.433124314108431	2		326	455	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347983	347983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760961378	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	133	507	5	ENST00000262320.3:c.1523del	p.Gly508ValfsTer197	p.G508Vfs*197	ENST00000262320	NM_003502.3	508	gGt/gt	6/11	1	2	FACETS	0.987	0.899	1	0.987	0.899	1	CLONAL	1	TRUE	1	0.433124314108431	2		512	622	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864938	117864938	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1259968025	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	89	336	0	ENST00000297338.2:c.1171C>T	p.Arg391Cys	p.R391C	ENST00000297338	NM_006265.2	391	Cgc/Tgc	10/14	1	2	FACETS	0.876	0.78	0.978	0.876	0.78	0.978	CLONAL	1	TRUE	1	0.433124314108431	2		336	469	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347930	347930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141148118	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	63	557	2	ENST00000262320.3:c.1576G>A	p.Ala526Thr	p.A526T	ENST00000262320	NM_003502.3	526	Gcg/Acg	6/11	1	2	FACETS	0.453	0.391	0.52	0.453	0.391	0.52	SUBCLONAL	1	TRUE	1	0.433124314108431	2		559	642	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	137	633	3	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	0.973	0.888	1	0.973	0.888	1	CLONAL	1	TRUE	1	0.433124314108431	2		636	650	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371645	55371645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1420347279	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	30	498	0	ENST00000297316.4:c.335C>T	p.Ala112Val	p.A112V	ENST00000297316	NM_022454.3	112	gCg/gTg	2/2	1	2	FACETS	0.251	0.202	0.308	0.251	0.202	0.308	SUBCLONAL	1	TRUE	1	0.433124314108431	2		498	551	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244155	153244156	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	150	611	0	ENST00000281708.4:c.2001dup	p.Ser668GlufsTer26	p.S668Efs*26	ENST00000281708	NM_033632.3	667	-/G	12/12	1	2	FACETS	0.951	0.871	1	0.951	0.871	1	CLONAL	1	TRUE	1	0.433124314108431	2		611	728	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199945	138199945	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	57	362	2	ENST00000237289.4:c.1368del	p.Pro457LeufsTer20	p.P457Lfs*20	ENST00000237289	NM_001270507.1	455	Ggg/gg	7/9	1	2	FACETS	0.608	0.523	0.7	0.608	0.523	0.7	SUBCLONAL	1	TRUE	1	0.433124314108431	2		364	433	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740171	162740171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs189206909	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	153	540	0	ENST00000367921.3:c.1373G>A	p.Arg458His	p.R458H	ENST00000367921	NM_006182.2	458	cGc/cAc	12/18	1	2	FACETS	0.968	0.887	1	0.968	0.887	1	CLONAL	1	TRUE	1	0.433124314108431	2		540	730	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654856	29654856	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1049849034	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	32	295	0	ENST00000356175.3:c.5545C>T	p.Arg1849Trp	p.R1849W	ENST00000356175	NM_000267.3	1849	Cgg/Tgg	37/57	1	2	FACETS	0.374	0.303	0.454	0.374	0.303	0.454	SUBCLONAL	1	TRUE	1	0.433124314108431	2		295	395	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905288	50905288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376236497	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	42	692	1	ENST00000440232.2:c.496C>T	p.Arg166Trp	p.R166W	ENST00000440232	NM_002691.3	166	Cgg/Tgg	5/27	1	2	FACETS	0.245	0.204	0.291	0.245	0.204	0.291	SUBCLONAL	1	TRUE	1	0.433124314108431	2		693	791	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906603	32906603	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359777	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	42	409	0	ENST00000380152.3:c.994del	p.Ile332PhefsTer17	p.I332Ffs*17	ENST00000380152		330	Aaa/aa	10/27	1	2	FACETS	0.352	0.293	0.417	0.352	0.293	0.417	SUBCLONAL	1	TRUE	1	0.433124314108431	2		409	551	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572092	64572093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs767319284	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	126	511	1	ENST00000312049.6:c.1546dup	p.Arg516ProfsTer15	p.R516Pfs*15	ENST00000312049	NM_130799.2	516	cgg/cCgg	10/10	1	2	FACETS	0.955	0.868	1	0.955	0.868	1	CLONAL	1	TRUE	1	0.433124314108431	2		512	609	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522741	67522741	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	31	279	2	ENST00000274335.5:c.244del	p.Ile82SerfsTer32	p.I82Sfs*32	ENST00000274335		80	Aaa/aa	1/15	1	2	FACETS	0.361	0.291	0.439	0.361	0.291	0.439	SUBCLONAL	1	TRUE	1	0.433124314108431	2		281	397	SUCCESS
AR	367	MSKCC	GRCh37	X	66765598	66765598	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	137	694	0	ENST00000374690.3:c.610G>A	p.Glu204Lys	p.E204K	ENST00000374690	NM_000044.3	204	Gaa/Aaa	1/8	1	2	FACETS	0.882	0.804	0.964	0.882	0.804	0.964	CLONAL	1	TRUE	1	0.433124314108431	2		694	717	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226899	2226899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762029066	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	51	415	2	ENST00000398665.3:c.4379C>T	p.Thr1460Met	p.T1460M	ENST00000398665	NM_032482.2	1460	aCg/aTg	27/28	1	2	FACETS	0.533	0.453	0.62	0.533	0.453	0.62	SUBCLONAL	1	TRUE	1	0.433124314108431	2		417	442	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480010	50480010	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	121	572	0	ENST00000394963.4:c.249del	p.Asn84ThrfsTer79	p.N84Tfs*79	ENST00000394963	NM_003076.4	82	Ggg/gg	2/13	1	2	FACETS	0.883	0.799	0.97	0.883	0.799	0.97	CLONAL	1	TRUE	1	0.433124314108431	2		572	633	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396234	396234	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	130	575	5	ENST00000262320.3:c.792del	p.Gly265GlufsTer149	p.G265Efs*149	ENST00000262320	NM_003502.3	264	ccC/cc	2/11	1	2	FACETS	0.957	0.871	1	0.957	0.871	1	CLONAL	1	TRUE	1	0.433124314108431	2		580	627	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426737	47426737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200106543	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	71	524	1	ENST00000377045.4:c.982C>T	p.Arg328Trp	p.R328W	ENST00000377045	NM_001654.4	328	Cgg/Tgg	10/16	1	2	FACETS	0.489	0.427	0.557	0.489	0.427	0.557	SUBCLONAL	1	TRUE	1	0.433124314108431	2		525	670	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646467	23646467	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881906	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	75	625	0	ENST00000261584.4:c.1400G>A	p.Gly467Asp	p.G467D	ENST00000261584	NM_024675.3	467	gGc/gAc	4/13	1	2	FACETS	0.43	0.376	0.488	0.43	0.376	0.488	SUBCLONAL	1	TRUE	1	0.433124314108431	2		625	806	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484206	8484206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768568228	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	123	592	1	ENST00000356435.5:c.3326G>A	p.Arg1109His	p.R1109H	ENST00000356435		1109	cGt/cAt	19/35	1	2	FACETS	0.836	0.758	0.919	0.836	0.758	0.919	CLONAL	1	TRUE	1	0.433124314108431	2		593	679	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599251	28599251	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1416314446	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	163	635	0	ENST00000253063.3:c.701del	p.Pro234LeufsTer13	p.P234Lfs*13	ENST00000253063	NM_031459.4	233	Ccc/cc	5/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.433124314108431	2		635	702	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048145	180048145	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758234191	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	70	670	1	ENST00000261937.6:c.2128G>A	p.Val710Met	p.V710M	ENST00000261937	NM_182925.4	710	Gtg/Atg	14/30	1	2	FACETS	0.469	0.409	0.535	0.469	0.409	0.535	SUBCLONAL	1	TRUE	1	0.433124314108431	2		671	689	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166275	32166275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs967436228	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	42	550	0	ENST00000375023.3:c.4679C>T	p.Ala1560Val	p.A1560V	ENST00000375023	NM_004557.3	1560	gCg/gTg	26/30	1	2	FACETS	0.306	0.255	0.364	0.306	0.255	0.364	SUBCLONAL	1	TRUE	1	0.433124314108431	2		550	633	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241923	72241923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	103	508	0	ENST00000357731.5:c.467T>C	p.Val156Ala	p.V156A	ENST00000357731	NM_173808.2	156	gTc/gCc	3/7	1	2	FACETS	0.802	0.719	0.889	0.802	0.719	0.889	CLONAL	1	TRUE	1	0.433124314108431	2		508	593	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302611	15302611	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	62	673	1	ENST00000263388.2:c.747del	p.Thr250HisfsTer122	p.T250Hfs*122	ENST00000263388	NM_000435.2	249	ggG/gg	5/33	1	2	FACETS	0.418	0.36	0.481	0.418	0.36	0.481	SUBCLONAL	1	TRUE	1	0.433124314108431	2		674	685	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775608	9775608	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	51	460	2	ENST00000377346.4:c.151C>T	p.His51Tyr	p.H51Y	ENST00000377346	NM_005026.3	51	Cac/Tac	4/24	1	2	FACETS	0.472	0.401	0.55	0.472	0.401	0.55	SUBCLONAL	1	TRUE	1	0.433124314108431	2		462	499	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115252284	115252284	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	94	552	0	ENST00000369535.4:c.356A>T	p.Asp119Val	p.D119V	ENST00000369535	NM_002524.4	119	gAt/gTt	4/7	1	2	FACETS	0.65	0.578	0.726	0.65	0.578	0.726	SUBCLONAL	1	TRUE	1	0.433124314108431	2		552	668	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266563	115266564	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	137	600	0	ENST00000438362.2:c.1951dup	p.Leu651ProfsTer5	p.L651Pfs*5	ENST00000438362	NM_001242891.1	651	ctg/cCtg	16/20	1	2	FACETS	0.832	0.758	0.91	0.832	0.758	0.91	CLONAL	1	TRUE	1	0.433124314108431	2		600	760	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235837	108235837	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1131691149	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	86	473	0	ENST00000278616.4:c.8879G>A	p.Trp2960Ter	p.W2960*	ENST00000278616	NM_000051.3	2960	tGg/tAg	62/63	1	2	FACETS	0.647	0.573	0.726	0.647	0.573	0.726	SUBCLONAL	1	TRUE	1	0.433124314108431	2		473	614	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307394	118307394	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	11	36	0	ENST00000534358.1:c.173del	p.Pro58ArgfsTer92	p.P58Rfs*92	ENST00000534358	NM_005933.3	56	tCc/tc	1/36	1	2	FACETS	1	0.722	1	1	0.722	1	CLONAL	1	TRUE	1	0.433124314108431	2		36	50	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243938	46243938	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	41	555	1	ENST00000334344.6:c.2032G>T	p.Ala678Ser	p.A678S	ENST00000334344	NM_152641.2	678	Gca/Tca	15/21	1	2	FACETS	0.33	0.274	0.392	0.33	0.274	0.392	SUBCLONAL	1	TRUE	1	0.433124314108431	2		556	574	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123889578	123889578	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	18	201	0	ENST00000330479.4:c.805G>T	p.Gly269Cys	p.G269C	ENST00000330479	NM_020382.3	269	Ggc/Tgc	7/9	1	2	FACETS	0.301	0.227	0.389	0.301	0.227	0.389	SUBCLONAL	1	TRUE	1	0.433124314108431	2		201	276	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563390	21563390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745776774	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	160	678	2	ENST00000382592.4:c.529G>A	p.Gly177Ser	p.G177S	ENST00000382592	NM_014572.2	177	Ggc/Agc	4/8	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.433124314108431	2		680	727	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911476	32911476	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397507299	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	49	452	0	ENST00000380152.3:c.2984G>C	p.Gly995Ala	p.G995A	ENST00000380152		995	gGa/gCa	11/27	1	2	FACETS	0.373	0.316	0.437	0.373	0.316	0.437	SUBCLONAL	1	TRUE	1	0.433124314108431	2		452	606	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225330	2225330	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	38	544	0	ENST00000326181.6:c.1415T>C	p.Val472Ala	p.V472A	ENST00000326181	NM_032271.2	472	gTg/gCg	16/21	1	2	FACETS	0.266	0.219	0.319	0.266	0.219	0.319	SUBCLONAL	1	TRUE	1	0.433124314108431	2		544	659	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862754	9862754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060503230	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	28	478	0	ENST00000330684.3:c.2549C>T	p.Thr850Met	p.T850M	ENST00000330684	NM_001134407.1	850	aCg/aTg	12/13	1	2	FACETS	0.231	0.184	0.285	0.231	0.184	0.285	SUBCLONAL	1	TRUE	1	0.433124314108431	2		478	559	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56872935	56872935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	32	471	0	ENST00000308159.5:c.2090C>T	p.Thr697Ile	p.T697I	ENST00000308159	NM_014669.4	697	aCc/aTc	19/22	1	2	FACETS	0.25	0.202	0.305	0.25	0.202	0.305	SUBCLONAL	1	TRUE	1	0.433124314108431	2		471	590	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832599	72832599	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	33	291	0	ENST00000268489.5:c.3982C>A	p.Leu1328Met	p.L1328M	ENST00000268489	NM_006885.3	1328	Ctg/Atg	9/10	1	2	FACETS	0.434	0.354	0.524	0.434	0.354	0.524	SUBCLONAL	1	TRUE	1	0.433124314108431	2		291	351	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805352	89805352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745882980	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	47	528	0	ENST00000389301.3:c.4198C>T	p.Arg1400Cys	p.R1400C	ENST00000389301	NM_000135.2	1400	Cgt/Tgt	42/43	1	2	FACETS	0.327	0.275	0.385	0.327	0.275	0.385	SUBCLONAL	1	TRUE	1	0.433124314108431	2		528	663	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622324	1622325	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	103	546	0	ENST00000344749.5:c.639dup	p.Phe214LeufsTer40	p.F214Lfs*40	ENST00000344749	NM_001136139.2	213	-/C	9/19	1	2	FACETS	0.704	0.63	0.781	0.704	0.63	0.781	SUBCLONAL	1	TRUE	1	0.433124314108431	2		546	676	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215323	5215323	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1379973129	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	40	540	2	ENST00000357368.4:c.4295G>A	p.Arg1432His	p.R1432H	ENST00000357368	NM_002850.3	1432	cGt/cAt	28/38	1	2	FACETS	0.297	0.246	0.354	0.297	0.246	0.354	SUBCLONAL	1	TRUE	1	0.433124314108431	2		542	621	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231557	5231557	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150939732	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	40	376	2	ENST00000357368.4:c.1919G>A	p.Arg640His	p.R640H	ENST00000357368	NM_002850.3	640	cGc/cAc	14/38	1	2	FACETS	0.389	0.323	0.462	0.389	0.323	0.462	SUBCLONAL	1	TRUE	1	0.433124314108431	2		378	475	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7167979	7167979	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs201978448	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	147	530	0	ENST00000302850.5:c.1610C>T	p.Ala537Val	p.A537V	ENST00000302850	NM_000208.2	537	gCc/gTc	7/22	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.433124314108431	2		530	605	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626843	14626843	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377564300	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	174	641	1	ENST00000254322.2:c.932G>A	p.Arg311His	p.R311H	ENST00000254322	NM_006145.1	311	cGt/cAt	3/3	1	2	FACETS	0.939	0.865	1	0.939	0.865	1	CLONAL	1	TRUE	1	0.433124314108431	2		642	856	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741245	40741245	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	47	506	0	ENST00000392038.2:c.1188del	p.Ser398AlafsTer177	p.S398Afs*177	ENST00000392038	NM_001626.4	396	ggG/gg	12/14	1	2	FACETS	0.341	0.287	0.4	0.341	0.287	0.4	SUBCLONAL	1	TRUE	1	0.433124314108431	2		506	637	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964998	25964998	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772369923	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	50	436	1	ENST00000435504.4:c.4208G>A	p.Arg1403His	p.R1403H	ENST00000435504		1403	cGc/cAc	13/13	1	2	FACETS	0.395	0.334	0.461	0.395	0.334	0.461	SUBCLONAL	1	TRUE	1	0.433124314108431	2		437	585	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39746892	39746892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	39	319	1	ENST00000361337.2:c.1906C>T	p.Pro636Ser	p.P636S	ENST00000361337	NM_003286.2	636	Cca/Tca	18/21	1	2	FACETS	0.534	0.444	0.634	0.534	0.444	0.634	SUBCLONAL	1	TRUE	1	0.433124314108431	2		320	337	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30090766	30090766	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	42	574	2	ENST00000338641.4:c.1763G>T	p.Arg588Leu	p.R588L	ENST00000338641	NM_000268.3	588	cGa/cTa	16/16	1	2	FACETS	0.289	0.24	0.343	0.289	0.24	0.343	SUBCLONAL	1	TRUE	1	0.433124314108431	2		576	672	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650320	12650320	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	43	687	0	ENST00000251849.4:c.526T>C	p.Cys176Arg	p.C176R	ENST00000251849	NM_002880.3	176	Tgt/Cgt	5/17	1	2	FACETS	0.26	0.217	0.309	0.26	0.217	0.309	SUBCLONAL	1	TRUE	1	0.433124314108431	2		687	763	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713806	30713806	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	132	539	0	ENST00000295754.5:c.1131del	p.His377GlnfsTer11	p.H377Qfs*11	ENST00000295754	NM_003242.5	377	caC/ca	4/7	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.433124314108431	2		539	587	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713679	52713679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764436452	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	84	500	0	ENST00000394830.3:c.49G>A	p.Gly17Arg	p.G17R	ENST00000394830	NM_018313.4	17	Ggg/Agg	2/30	1	2	FACETS	0.618	0.546	0.694	0.618	0.546	0.694	SUBCLONAL	1	TRUE	1	0.433124314108431	2		500	628	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186894	142186894	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	45	469	0	ENST00000350721.4:c.6569G>A	p.Arg2190His	p.R2190H	ENST00000350721	NM_001184.3	2190	cGt/cAt	39/47	1	2	FACETS	0.351	0.294	0.414	0.351	0.294	0.414	SUBCLONAL	1	TRUE	1	0.433124314108431	2		469	592	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374711	149374711	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1485853361	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	75	507	2	ENST00000360632.3:c.383del	p.Pro128ArgfsTer5	p.P128Rfs*5	ENST00000360632	NM_015472.4	128	cCg/cg	2/7	1	2	FACETS	0.586	0.514	0.664	0.586	0.514	0.664	SUBCLONAL	1	TRUE	1	0.433124314108431	2		509	591	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155832	106155832	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	42	440	0	ENST00000380013.4:c.733A>C	p.Thr245Pro	p.T245P	ENST00000380013	NM_001127208.2	245	Acc/Ccc	3/11	1	2	FACETS	0.346	0.289	0.411	0.346	0.289	0.411	SUBCLONAL	1	TRUE	1	0.433124314108431	2		440	560	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226110	226110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	107	510	0	ENST00000264932.6:c.569G>A	p.Cys190Tyr	p.C190Y	ENST00000264932	NM_004168.2	190	tGc/tAc	5/15	1	2	FACETS	0.884	0.795	0.977	0.884	0.795	0.977	CLONAL	1	TRUE	1	0.433124314108431	2		510	559	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958784	38958784	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	93	446	0	ENST00000357387.3:c.2328A>T	p.Glu776Asp	p.E776D	ENST00000357387	NM_152756.3	776	gaA/gaT	23/38	1	2	FACETS	0.898	0.802	1	0.898	0.802	1	CLONAL	1	TRUE	1	0.433124314108431	2		446	478	SUCCESS
APC	324	MSKCC	GRCh37	5	112170727	112170727	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	156	598	1	ENST00000257430.4:c.1823C>T	p.Ala608Val	p.A608V	ENST00000257430	NM_000038.5	608	gCt/gTt	15/16	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.433124314108431	2		599	718	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777858	27777858	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	44	253	1	ENST00000369163.2:c.7C>T	p.Arg3Cys	p.R3C	ENST00000369163	NM_003536.2	3	Cgt/Tgt	1/1	1	2	FACETS	0.71	0.599	0.832	0.71	0.599	0.832	SUBCLONAL	1	TRUE	1	0.433124314108431	2		254	286	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211028	55211028	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	38	560	0	ENST00000275493.2:c.271A>G	p.Ile91Val	p.I91V	ENST00000275493	NM_005228.3	91	Att/Gtt	3/28	1	2	FACETS	0.285	0.235	0.342	0.285	0.235	0.342	SUBCLONAL	1	TRUE	1	0.433124314108431	2		560	615	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411644	116411644	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	169	643	0	ENST00000397752.3:c.2823A>G	p.Ile941Met	p.I941M	ENST00000397752	NM_000245.2	941	atA/atG	13/21	1	2	FACETS	0.956	0.88	1	0.956	0.88	1	CLONAL	1	TRUE	1	0.433124314108431	2		643	816	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69143599	69143599	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	45	404	0	ENST00000288368.4:c.4807G>T	p.Ala1603Ser	p.A1603S	ENST00000288368	NM_024870.2	1603	Gct/Tct	40/40	1	2	FACETS	0.38	0.319	0.448	0.38	0.319	0.448	SUBCLONAL	1	TRUE	1	0.433124314108431	2		404	547	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518282	8518282	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	44	342	2	ENST00000356435.5:c.1109T>A	p.Ile370Asn	p.I370N	ENST00000356435		370	aTt/aAt	10/35	1	2	FACETS	0.438	0.367	0.516	0.438	0.367	0.516	SUBCLONAL	1	TRUE	1	0.433124314108431	2		344	464	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206713	27206713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	77	528	0	ENST00000380036.4:c.2498G>A	p.Gly833Asp	p.G833D	ENST00000380036	NM_000459.3	833	gGc/gAc	15/23	1	2	FACETS	0.473	0.414	0.536	0.473	0.414	0.536	SUBCLONAL	1	TRUE	1	0.433124314108431	2		528	752	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27220141	27220141	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	119	474	0	ENST00000380036.4:c.3198G>T	p.Glu1066Asp	p.E1066D	ENST00000380036	NM_000459.3	1066	gaG/gaT	21/23	1	2	FACETS	0.99	0.897	1	0.99	0.897	1	CLONAL	1	TRUE	1	0.433124314108431	2		474	555	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137325984	137325984	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753474465	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	56	512	0	ENST00000481739.1:c.1172C>T	p.Ala391Val	p.A391V	ENST00000481739	NM_002957.4	391	gCg/gTg	9/10	1	2	FACETS	0.423	0.362	0.49	0.423	0.362	0.49	SUBCLONAL	1	TRUE	1	0.433124314108431	2		512	611	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227751	53227751	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	55	597	0	ENST00000375401.3:c.2437C>T	p.Gln813Ter	p.Q813*	ENST00000375401	NM_004187.3	813	Cag/Tag	17/26	1	2	FACETS	0.324	0.276	0.376	0.324	0.276	0.376	SUBCLONAL	1	TRUE	1	0.433124314108431	2		597	785	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0025051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	122	552	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.333189781075952	2	FACETS	0.479	0.433	0.528	0.24	0.216	0.264	INDETERMINATE	1	TRUE	0	0.592218413144639	2		552	860	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485288	8485288	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	192	629	0	ENST00000356435.5:c.3092A>C	p.Lys1031Thr	p.K1031T	ENST00000356435		1031	aAg/aCg	18/35	1	2	FACETS	0.937	0.87	1	0.937	0.87	1	CLONAL	1	TRUE	1	0.592218413144639	2		629	692	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763098116	NA	P-0025051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	84	685	1	ENST00000269305.4:c.830G>A	p.Cys277Tyr	p.C277Y	ENST00000269305	NM_001126112.2	277	tGt/tAt	8/11	1	2	FACETS	0.316	0.278	0.356	0.316	0.278	0.356	SUBCLONAL	1	TRUE	1	0.592218413144639	2		686	899	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926270	112926270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918457	NA	P-0025051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	185	666	0	ENST00000351677.2:c.1403C>T	p.Thr468Met	p.T468M	ENST00000351677	NM_002834.3	468	aCg/aTg	12/16	1	2	FACETS	0.755	0.698	0.815	0.755	0.698	0.815	SUBCLONAL	1	TRUE	1	0.592218413144639	2		666	827	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729399	41729399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	52	592	0	ENST00000242208.4:c.1130G>A	p.Arg377His	p.R377H	ENST00000242208	NM_002192.2	377	cGc/cAc	3/3	0.123726691729158	3	FACETS	0.275	0.233	0.321	0.092	0.077	0.107	INDETERMINATE	1	TRUE	0	0.592218413144639	3		592	828	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323991	31323991	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1050692	NA	P-0025051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	10	116	1	ENST00000412585.2:c.572G>C	p.Trp191Ser	p.W191S	ENST00000412585	NM_005514.6	191	tGg/tCg	3/8	0.294739992561855	2	FACETS	0.241	0.164	0.338	0.121	0.082	0.169	INDETERMINATE	1	TRUE	0	0.592218413144639	2		117	140	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290896	15290896	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	255	808	0	ENST00000263388.2:c.3314del	p.Gly1105AlafsTer167	p.G1105Afs*167	ENST00000263388	NM_000435.2	1105	gGc/gc	20/33	1	2	FACETS	0.961	0.901	1	0.961	0.901	1	CLONAL	1	TRUE	1	0.592218413144639	2		808	896	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856545	111856545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1157707616	NA	P-0025051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	32	472	1	ENST00000341259.2:c.596C>T	p.Ala199Val	p.A199V	ENST00000341259	NM_005475.2	199	gCg/gTg	2/8	1	2	FACETS	0.204	0.165	0.248	0.204	0.165	0.248	SUBCLONAL	1	TRUE	1	0.592218413144639	2		473	531	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107186	27107219	+	frameshift_variant	Frame_Shift_Del	DEL	TGATGAACTCATTGGTTTCACAAGTCATTTGTGA	TGATGAACTCATTGGTTTCACAAGTCATTTGTGA	-	novel	NA	P-0025051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	171	578	1	ENST00000324856.7:c.6799_6832del	p.Met2267TyrfsTer4	p.M2267Yfs*4	ENST00000324856	NM_006015.4	2266	tTGATGAACTCATTGGTTTCACAAGTCATTTGTGAt/tt	20/20	1	2	FACETS	0.79	0.728	0.854	0.79	0.728	0.854	SUBCLONAL	1	TRUE	1	0.592218413144639	2		579	731	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46733215	46733215	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	209	713	0	ENST00000371975.4:c.976A>G	p.Thr326Ala	p.T326A	ENST00000371975	NM_003579.3	326	Act/Gct	9/18	1	2	FACETS	0.829	0.771	0.889	0.829	0.771	0.889	CLONAL	1	TRUE	1	0.592218413144639	2		713	851	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162750028	162750028	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771898787	NA	P-0025051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	211	545	1	ENST00000367921.3:c.2560G>A	p.Asp854Asn	p.D854N	ENST00000367921	NM_006182.2	854	Gac/Aac	18/18	1	2	FACETS	0.999	0.932	1	0.999	0.932	1	CLONAL	1	TRUE	1	0.592218413144639	2		546	713	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982974	201982974	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	267	727	0	ENST00000359651.3:c.823C>A	p.Leu275Met	p.L275M	ENST00000359651		275	Ctg/Atg	7/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.592218413144639	2		727	849	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230740	46230740	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0025051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	142	513	0	ENST00000334344.6:c.989T>G	p.Leu330Ter	p.L330*	ENST00000334344	NM_152641.2	330	tTa/tGa	8/21	0.333189781075952	2	FACETS	0.985	0.904	1	0.492	0.452	0.534	INDETERMINATE	1	TRUE	0	0.592218413144639	2		513	487	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50483768	50483768	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	261	581	0	ENST00000394963.4:c.873G>C	p.Gln291His	p.Q291H	ENST00000394963	NM_003076.4	291	caG/caC	7/13	0.333189781075952	2	FACETS	1	0.992	1	0.653	0.615	0.691	INDETERMINATE	1	TRUE	0	0.592218413144639	2		581	675	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578209	28578209	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs74041526	NA	P-0025051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	82	636	0	ENST00000241453.7:c.2962G>T	p.Ala988Ser	p.A988S	ENST00000241453	NM_004119.2	988	Gct/Tct	24/24	1	2	FACETS	0.316	0.278	0.357	0.316	0.278	0.357	SUBCLONAL	1	TRUE	1	0.592218413144639	2		636	877	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252983	36252991	+	inframe_deletion	In_Frame_Del	DEL	CATCTGGAA	CATCTGGAA	-	novel	NA	P-0025051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	95	559	0	ENST00000300305.3:c.371_379del	p.Val124_Asp126del	p.V124_D126del	ENST00000300305		124	gTTCCAGATGgc/ggc	4/8	0.444918138705662	2	FACETS	0.485	0.432	0.541	0.242	0.216	0.271	SUBCLONAL	1	TRUE	0	0.592218413144639	2		559	662	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0025062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	64	364	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.727	0.629	0.834	0.727	0.629	0.834	SUBCLONAL	1	TRUE	1	0.241549804631807	2		364	729	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217662	7217662	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	69	428	0	ENST00000380728.2:c.265C>T	p.Gln89Ter	p.Q89*	ENST00000380728		89	Cag/Tag	4/11	NA	2	FACETS	0.983	0.857	1			1	INDETERMINATE	1	TRUE	NA	0.241549804631807	2		428	581	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206759	36206771	+	frameshift_variant	Frame_Shift_Del	DEL	GGCACGAGGGTTG	GGCACGAGGGTTG	-	novel	NA	P-0025062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	79	611	0	ENST00000300305.3:c.741_753del	p.Asn248ProfsTer2	p.N248Pfs*2	ENST00000300305		247	ccCAACCCTCGTGCC/cc	6/8	1	2	FACETS	0.934	0.822	1	0.934	0.822	1	CLONAL	1	TRUE	1	0.241549804631807	2		611	700	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426064	49426064	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	56	449	1	ENST00000301067.7:c.12424G>T	p.Gly4142Trp	p.G4142W	ENST00000301067	NM_003482.3	4142	Ggg/Tgg	39/54	0.573789434999288	4	FACETS	0.96	0.828	1	0.48	0.414	0.552	CLONAL	1	TRUE	2	0.573789434999288	4		450	320	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645025	67645025	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	54	516	2	ENST00000264010.4:c.290C>T	p.Thr97Ile	p.T97I	ENST00000264010	NM_006565.3	97	aCt/aTt	3/12	1	2	FACETS	0.946	0.82	1	0.946	0.82	1	CLONAL	1	TRUE	1	0.573789434999288	2		518	199	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309805	65309805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747502464	NA	P-0025066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	50	626	1	ENST00000342505.4:c.2345C>T	p.Thr782Met	p.T782M	ENST00000342505	NM_002227.2	782	aCg/aTg	17/25	0.46606598194946	3	FACETS	0.392	0.332	0.458	0.196	0.166	0.229	SUBCLONAL	1	TRUE	1	0.518771271857714	3		627	619	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426867	49426867	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	103	419	0	ENST00000301067.7:c.11621C>G	p.Ser3874Cys	p.S3874C	ENST00000301067	NM_003482.3	3874	tCc/tGc	39/54	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.518771271857714	2		419	347	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863233	57863233	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	141	480	0	ENST00000228682.2:c.1328G>T	p.Gly443Val	p.G443V	ENST00000228682	NM_005269.2	443	gGg/gTg	11/12	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.518771271857714	2		480	447	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039210	49039228	+	frameshift_variant	Frame_Shift_Del	DEL	GACTGAAAACAAATATTTT	GACTGAAAACAAATATTTT	-	novel	NA	P-0025066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	84	571	2	ENST00000267163.4:c.2289_2307del	p.Arg763SerfsTer41	p.R763Sfs*41	ENST00000267163	NM_000321.2	763	aGACTGAAAACAAATATTTTg/ag	22/27	0.513778267305035	2	FACETS	1	0.957	1	0.57	0.51	0.633	CLONAL	1	TRUE	0	0.518771271857714	2		573	284	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710644	117710644	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs760234329	NA	P-0025066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	207	350	0	ENST00000368508.3:c.1628G>C	p.Gly543Ala	p.G543A	ENST00000368508	NM_002944.2	543	gGt/gCt	12/43	0.48317075638215	3	FACETS	0.936	0.885	0.986	0.936	0.885	0.986	CLONAL	3	TRUE	0	0.518771271857714	3		350	358	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317553	1317553	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs373430886	NA	P-0025066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	54	589	0	ENST00000400841.2:c.512C>A	p.Thr171Asn	p.T171N	ENST00000400841		171	aCc/aAc	5/6	0.337455615497269	1	FACETS	0.463	0.397	0.534	0.463	0.397	0.534	SUBCLONAL	1	TRUE	0	0.518771271857714	1		589	333	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695893	117695893	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	109	581	1	ENST00000369458.3:c.544G>T	p.Ala182Ser	p.A182S	ENST00000369458	NM_024626.3	182	Gca/Tca	4/6	0.312278486315368	4	FACETS	1	0.946	1	0.361	0.324	0.401	CLONAL	1	TRUE	1	0.311489871644726	4		582	847	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421614	49421614	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	110	636	0	ENST00000301067.7:c.14615A>G	p.Gln4872Arg	p.Q4872R	ENST00000301067	NM_003482.3	4872	cAa/cGa	47/54	0.312278486315368	3	FACETS	0.877	0.787	0.973	0.438	0.393	0.487	CLONAL	1	TRUE	1	0.311489871644726	3		636	931	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923159	48923159	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	159	436	0	ENST00000267163.4:c.607+1del		p.G203fs	ENST00000267163	NM_000321.2	203	Ggg/gg	6/27	0.312278486315368	2	FACETS	0.891	0.827	0.955	1	0.988	1	CLONAL	3	TRUE	0	0.311489871644726	2		436	382	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831080	72831080	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	72	307	0	ENST00000268489.5:c.5501A>G	p.Asp1834Gly	p.D1834G	ENST00000268489	NM_006885.3	1834	gAt/gGt	9/10	1	2	FACETS	0.994	0.871	1	0.994	0.871	1	CLONAL	1	TRUE	1	0.311489871644726	2		307	465	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125305	47125305	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	121	533	0	ENST00000409792.3:c.5965G>C	p.Asp1989His	p.D1989H	ENST00000409792	NM_014159.6	1989	Gat/Cat	12/21	0.219825445825858	3	FACETS	1	0.967	1	0.578	0.522	0.637	CLONAL	1	TRUE	1	0.311489871644726	3		533	777	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845328	151845328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	57	415	0	ENST00000262189.6:c.13684C>T	p.Leu4562Phe	p.L4562F	ENST00000262189	NM_170606.2	4562	Ctt/Ttt	52/59	0.242348584978676	3	FACETS	0.652	0.559	0.754			1	SUBCLONAL	1	TRUE	NA	0.311489871644726	3		415	649	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738104	145738105	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCCAGTGGTGTGGGTGCAGCTCCAGGTAGCA	novel	NA	P-0025071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	89	684	0	ENST00000428558.2:c.2773_2805dup	p.Cys925_Leu935dup	p.C925_L935dup	ENST00000428558	NM_004260.3	925	-/TGCTACCTGGAGCTGCACCCACACCACTGGCTG	17/22	0.312278486315368	3	FACETS	0.631	0.558	0.71	0.21	0.186	0.237	SUBCLONAL	1	TRUE	0	0.311489871644726	3		684	1046	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	103	606	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.16736618925937	1	FACETS	0.777	0.705	0.851	0.777	0.705	0.851	INDETERMINATE	1	TRUE	0	0.621783410648045	1		606	294	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115972	8115973	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0025072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	72	193	0	ENST00000346208.3:c.1320dup	p.Ala441ArgfsTer66	p.A441Rfs*66	ENST00000346208		440	acc/aCcc	6/6	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.621783410648045	2		193	219	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	154	606	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	0.992	1	CLONAL	2	TRUE	1	0.21	2		606	668	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	24	510	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.469	0.367	0.588	0.469	0.367	0.588	SUBCLONAL	1	TRUE	1	0.21	2		510	487	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	62	319	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.21	2		319	418	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	39	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.922	0.765	1	0.922	0.765	1	CLONAL	1	TRUE	1	0.21	2		326	403	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	24	317	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.527	0.412	0.659	0.527	0.412	0.659	SUBCLONAL	1	TRUE	1	0.21	2		318	434	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	32	586	2	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.679	0.55	0.824	0.679	0.55	0.824	SUBCLONAL	1	TRUE	1	0.21	2		588	449	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26911760	26911760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	53	488	0	ENST00000381527.3:c.185C>T	p.Ser62Leu	p.S62L	ENST00000381527	NM_001260.1	62	tCg/tTg	2/13	1	2	FACETS	0.886	0.755	1	0.886	0.755	1	CLONAL	1	TRUE	1	0.21	2		488	570	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254637	10254637	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	27	380	0	ENST00000340748.4:c.2873G>A	p.Arg958His	p.R958H	ENST00000340748		958	cGc/cAc	28/40	1	2	FACETS	0.624	0.496	0.771	0.624	0.496	0.771	SUBCLONAL	1	TRUE	1	0.21	2		380	412	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533881	533881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs727503093	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	90	567	1	ENST00000451590.1:c.175G>A	p.Ala59Thr	p.A59T	ENST00000451590	NM_001130442.1	59	Gcc/Acc	3/5	1	2	FACETS	0.76	0.676	0.849	1	0.98	1	SUBCLONAL	2	TRUE	1	0.21	2		568	564	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236087	108236087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781894	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	57	455	3	ENST00000278616.4:c.9023G>A	p.Arg3008His	p.R3008H	ENST00000278616	NM_000051.3	3008	cGt/cAt	63/63	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.21	2		458	531	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	22	430	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.54	0.418	0.682	0.54	0.418	0.682	SUBCLONAL	1	TRUE	1	0.21	2		430	388	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56852600	56852600	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	52	456	1	ENST00000308159.5:c.518del	p.Pro173LeufsTer25	p.P173Lfs*25	ENST00000308159	NM_014669.4	172	Ccc/cc	6/22	1	2	FACETS	0.894	0.761	1	0.894	0.761	1	CLONAL	1	TRUE	1	0.21	2		457	554	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319406	11319406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149221273	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	29	497	1	ENST00000361445.4:c.61G>A	p.Val21Ile	p.V21I	ENST00000361445	NM_004958.3	21	Gtc/Atc	2/58	1	2	FACETS	0.551	0.441	0.677	0.551	0.441	0.677	SUBCLONAL	1	TRUE	1	0.21	2		498	501	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962930	2962930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1349831751	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	31	709	2	ENST00000396946.4:c.1978C>T	p.Arg660Trp	p.R660W	ENST00000396946	NM_032415.4	660	Cgg/Tgg	16/25	1	2	FACETS	0.565	0.456	0.688	0.565	0.456	0.688	SUBCLONAL	1	TRUE	1	0.21	2		711	523	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630605	187630605	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	44	616	0	ENST00000441802.2:c.377del	p.Asn126IlefsTer20	p.N126Ifs*20	ENST00000441802	NM_005245.3	126	aAt/at	2/27	1	2	FACETS	0.576	0.482	0.681	0.576	0.482	0.681	SUBCLONAL	1	TRUE	1	0.21	2		616	727	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163554	32163554	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	41	543	1	ENST00000375023.3:c.5672del	p.Gly1891AlafsTer13	p.G1891Afs*13	ENST00000375023	NM_004557.3	1891	gGc/gc	30/30	1	2	FACETS	0.923	0.77	1	0.923	0.77	1	CLONAL	1	TRUE	1	0.21	2		544	423	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251725	212251725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144311212	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	30	344	0	ENST00000342788.4:c.3334C>T	p.Arg1112Cys	p.R1112C	ENST00000342788	NM_005235.2	1112	Cgc/Tgc	27/28	1	2	FACETS	0.787	0.635	0.96	0.787	0.635	0.96	CLONAL	1	TRUE	1	0.21	2		344	363	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	36	655	3	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.642	0.527	0.771	0.642	0.527	0.771	SUBCLONAL	1	TRUE	1	0.21	2		658	534	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324892	31324892	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs765875917	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	15	152	0	ENST00000412585.2:c.44del	p.Ala15GlyfsTer5	p.A15Gfs*5	ENST00000412585	NM_005514.6	15	gCg/gg	1/8	1	2	FACETS	1	0.78	1	1	0.78	1	CLONAL	1	TRUE	1	0.21	2		152	134	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128420047	128420047	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	65	585	5	ENST00000265960.3:c.381del	p.Lys127AsnfsTer20	p.K127Nfs*20	ENST00000265960	NM_001006617.1	127	aaA/aa	4/12	1	2	FACETS	0.939	0.814	1	0.939	0.814	1	CLONAL	1	TRUE	1	0.21	2		590	659	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793430	42793430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144065857	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	20	466	1	ENST00000575354.2:c.1232C>T	p.Ala411Val	p.A411V	ENST00000575354	NM_015125.3	411	gCg/gTg	8/20	1	2	FACETS	0.519	0.396	0.663	0.519	0.396	0.663	SUBCLONAL	1	TRUE	1	0.21	2		467	367	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641560	47641560	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	T	rs193922376	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	27	134	0	ENST00000233146.2:c.942+3A>T		p.X314_splice	ENST00000233146	NM_000251.2	314			1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.21	2		134	238	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221060	5221060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140049694	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	21	422	3	ENST00000357368.4:c.3406G>A	p.Gly1136Ser	p.G1136S	ENST00000357368	NM_002850.3	1136	Ggc/Agc	20/38	1	2	FACETS	0.519	0.399	0.66	0.519	0.399	0.66	SUBCLONAL	1	TRUE	1	0.21	2		425	385	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434054	49434054	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369604891	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	32	444	0	ENST00000301067.7:c.7499C>T	p.Ala2500Val	p.A2500V	ENST00000301067	NM_003482.3	2500	gCg/gTg	31/54	1	2	FACETS	0.68	0.552	0.826	0.68	0.552	0.826	SUBCLONAL	1	TRUE	1	0.21	2		444	448	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980402	201980402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	63	634	1	ENST00000359651.3:c.142del	p.Gln48ArgfsTer107	p.Q48Rfs*107	ENST00000359651		46	aaC/aa	1/8	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.21	2		635	572	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226573320	226573320	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374381502	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	48	459	0	ENST00000366794.5:c.896C>T	p.Ser299Leu	p.S299L	ENST00000366794	NM_001618.3	299	tCg/tTg	7/23	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.21	2		459	410	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940202	71940202	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	57	562	0	ENST00000298229.2:c.587C>T	p.Ala196Val	p.A196V	ENST00000298229	NM_001567.3	196	gCt/gTt	5/28	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.21	NA		562	564	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926866	112926866	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	72	680	0	ENST00000351677.2:c.1486A>T	p.Met496Leu	p.M496L	ENST00000351677	NM_002834.3	496	Atg/Ttg	13/16	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.21	2		680	648	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3799644	3799644	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	42	587	0	ENST00000262367.5:c.3820A>G	p.Thr1274Ala	p.T1274A	ENST00000262367	NM_004380.2	1274	Acc/Gcc	21/31	1	2	FACETS	0.574	0.478	0.681	0.574	0.478	0.681	SUBCLONAL	1	TRUE	1	0.21	2		587	697	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883774	37883774	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	35	665	2	ENST00000269571.5:c.3391del	p.Leu1131Ter	p.L1131*	ENST00000269571		1129	gCc/gc	26/27	1	2	FACETS	0.603	0.493	0.726	0.603	0.493	0.726	SUBCLONAL	1	TRUE	1	0.21	2		667	553	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78519468	78519468	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	46	441	0	ENST00000306801.3:c.43del	p.Glu15ArgfsTer17	p.E15Rfs*17	ENST00000306801	NM_020761.2	13	ctG/ct	1/34	1	2	FACETS	0.954	0.804	1	0.954	0.804	1	CLONAL	1	TRUE	1	0.21	2		441	459	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4094485	4094485	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	43	632	0	ENST00000262948.5:c.1058A>G	p.Asn353Ser	p.N353S	ENST00000262948	NM_030662.3	353	aAc/aGc	10/11	1	2	FACETS	0.811	0.678	0.958	0.811	0.678	0.958	CLONAL	1	TRUE	1	0.21	2		632	505	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097014	11097014	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	27	555	0	ENST00000358026.2:c.505C>A	p.Pro169Thr	p.P169T	ENST00000358026	NM_001128849.1	169	Cca/Aca	4/36	1	2	FACETS	0.579	0.46	0.716	0.579	0.46	0.716	SUBCLONAL	1	TRUE	1	0.21	2		555	444	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976139	18976139	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	38	597	0	ENST00000262803.5:c.2899G>T	p.Gly967Cys	p.G967C	ENST00000262803	NM_002911.3	967	Ggc/Tgc	21/24	1	2	FACETS	0.678	0.56	0.81	0.678	0.56	0.81	SUBCLONAL	1	TRUE	1	0.21	2		597	534	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256742	19256742	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	63	414	0	ENST00000162023.5:c.971C>A	p.Ser324Tyr	p.S324Y	ENST00000162023		324	tCt/tAt	13/13	1	2	FACETS	0.769	0.668	0.878	1	0.972	1	SUBCLONAL	2	TRUE	1	0.21	2		414	390	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703507	47703507	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	rs63751123	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	71	418	0	ENST00000233146.2:c.2010del	p.Asn671IlefsTer14	p.N671Ifs*14	ENST00000233146	NM_000251.2	669	ggC/gg	13/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.21	2		418	479	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044543	128044543	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754010782	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	38	440	0	ENST00000285398.2:c.1078C>T	p.Arg360Cys	p.R360C	ENST00000285398	NM_000122.1	360	Cgc/Tgc	8/15	1	2	FACETS	0.693	0.572	0.829	0.693	0.572	0.829	SUBCLONAL	1	TRUE	1	0.21	2		440	522	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719073	190719073	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	41	300	0	ENST00000441310.2:c.1075G>T	p.Val359Phe	p.V359F	ENST00000441310	NM_000534.4	359	Gtt/Ttt	9/13	1	2	FACETS	0.847	0.706	1	0.847	0.706	1	CLONAL	1	TRUE	1	0.21	2		300	461	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212252701	212252701	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	32	220	0	ENST00000342788.4:c.3152G>T	p.Ser1051Ile	p.S1051I	ENST00000342788	NM_005235.2	1051	aGc/aTc	26/28	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.21	2		220	262	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866377	42866377	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	49	526	1	ENST00000398585.3:c.255del	p.Val86CysfsTer9	p.V86Cfs*9	ENST00000398585	NM_001135099.1	85	ccC/cc	3/14	1	2	FACETS	0.899	0.762	1	0.899	0.762	1	CLONAL	1	TRUE	1	0.21	2		527	519	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513265	44513265	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1189536714	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	37	473	1	ENST00000291552.4:c.670C>T	p.Arg224Trp	p.R224W	ENST00000291552	NM_006758.2	224	Cgg/Tgg	8/8	1	2	FACETS	0.653	0.537	0.782	0.653	0.537	0.782	SUBCLONAL	1	TRUE	1	0.21	2		474	540	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553224	41553224	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	65	570	0	ENST00000263253.7:c.3313A>G	p.Lys1105Glu	p.K1105E	ENST00000263253	NM_001429.3	1105	Aag/Gag	18/31	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.21	2		570	572	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924823	49924823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772336656	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	42	684	1	ENST00000296474.3:c.4120C>T	p.Arg1374Cys	p.R1374C	ENST00000296474	NM_002447.2	1374	Cgt/Tgt	20/20	1	2	FACETS	0.787	0.657	0.932	0.787	0.657	0.932	CLONAL	1	TRUE	1	0.21	2		685	508	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586505	189586505	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs576449010	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	23	313	0	ENST00000264731.3:c.1129C>T	p.Pro377Ser	p.P377S	ENST00000264731	NM_003722.4	377	Ccg/Tcg	8/14	1	2	FACETS	0.597	0.465	0.75	0.597	0.465	0.75	SUBCLONAL	1	TRUE	1	0.21	2		313	367	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38955721	38955721	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	37	372	0	ENST00000357387.3:c.2585A>G	p.Asn862Ser	p.N862S	ENST00000357387	NM_152756.3	862	aAc/aGc	26/38	1	2	FACETS	0.833	0.687	0.996	0.833	0.687	0.996	CLONAL	1	TRUE	1	0.21	2		372	423	SUCCESS
APC	324	MSKCC	GRCh37	5	112170759	112170772	+	frameshift_variant	Frame_Shift_Del	DEL	ACTCTTACTTACCG	ACTCTTACTTACCG	-	novel	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	80	593	0	ENST00000257430.4:c.1855_1868del	p.Thr619GlufsTer10	p.T619Efs*10	ENST00000257430	NM_000038.5	619	ACTCTTACTTACCGg/g	15/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.21	2		593	554	SUCCESS
AR	367	MSKCC	GRCh37	X	66931404	66931404	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	108	568	1	ENST00000374690.3:c.2046G>T	p.Glu682Asp	p.E682D	ENST00000374690	NM_000044.3	682	gaG/gaT	4/8	1	2	FACETS	0.904	0.814	0.999	1	0.987	1	CLONAL	2	TRUE	1	0.21	2		569	569	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748517	40748517	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs201717577	NA	P-0025074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	273	643	0	ENST00000392038.2:c.365A>G	p.Tyr122Cys	p.Y122C	ENST00000392038	NM_001626.4	122	tAc/tGc	5/14	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.491358302116039	2		643	1095	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0025075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	54	510	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.197657035399052	3	FACETS	0.808	0.69	0.936	0.404	0.345	0.468	CLONAL	1	TRUE	1	0.293831557528766	3		510	522	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691871	30691871	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	87	455	0	ENST00000295754.5:c.373G>T	p.Glu125Ter	p.E125*	ENST00000295754	NM_003242.5	125	Gaa/Taa	3/7	0.187712293523312	2	FACETS	1	0.923	1	0.526	0.466	0.589	CLONAL	1	TRUE	0	0.293831557528766	2		455	563	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90976656	90976656	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121908973	NA	P-0025075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	119	533	0	ENST00000265433.3:c.976C>G	p.Gln326Glu	p.Q326E	ENST00000265433	NM_002485.4	326	Cag/Gag	8/16	0.11889850595495	4	FACETS	0.753	0.68	0.829	0.753	0.68	0.829	INDETERMINATE	2	TRUE	2	0.293831557528766	4		533	696	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	59	314	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.644722681363834	2		314	172	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0025079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	75	357	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.644722681363834	2		357	230	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696428	47696428	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	79	486	0	ENST00000347630.2:c.395G>A	p.Gly132Glu	p.G132E	ENST00000347630	NM_001007230.1	132	gGa/gAa	6/11	1	2	FACETS	0.848	0.754	0.946	0.848	0.754	0.946	CLONAL	1	TRUE	1	0.644722681363834	2		486	289	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808919	1808920	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGAC	novel	NA	P-0025079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	81	474	0	ENST00000260795.2:c.2353_2356dup	p.Asp786GlyfsTer32	p.D786Gfs*32	ENST00000260795		784	ggg/ggGGACg	17/17	1	2	FACETS	0.746	0.662	0.833	0.746	0.662	0.833	SUBCLONAL	1	TRUE	1	0.644722681363834	2		474	337	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	90	606	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.829	0.734	0.93	0.829	0.734	0.93	CLONAL	1	TRUE	1	0.235580502188689	2		606	922	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0025082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	121	466	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.235580502188689	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.235580502188689	1		466	754	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575108	48575108	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	83	425	0	ENST00000342988.3:c.302G>T	p.Trp101Leu	p.W101L	ENST00000342988	NM_005359.5	101	tGg/tTg	3/12	0.205715408602512	1	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	0	0.235580502188689	1		425	616	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227113	2227114	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0025082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	85	613	0	ENST00000398665.3:c.4595dup	p.Thr1533HisfsTer5	p.T1533Hfs*5	ENST00000398665	NM_032482.2	1531	-/G	27/28	1	2	FACETS	0.87	0.768	0.98	0.87	0.768	0.98	CLONAL	1	TRUE	1	0.235580502188689	2		613	829	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044417	128044417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1805162	NA	P-0025082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	115	567	1	ENST00000285398.2:c.1204G>A	p.Gly402Ser	p.G402S	ENST00000285398	NM_000122.1	402	Ggc/Agc	8/15	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.235580502188689	2		568	909	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119585452	119585452	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	81	416	0	ENST00000316626.5:c.933C>A	p.Phe311Leu	p.F311L	ENST00000316626		311	ttC/ttA	9/12	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.235580502188689	2		416	673	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526250	31526250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201911246	NA	P-0025082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	280	801	1	ENST00000344624.3:c.790C>T	p.Arg264Trp	p.R264W	ENST00000344624		264	Cgg/Tgg	2/33	0.235580502188689	3	FACETS	0.994	0.933	1	0.994	0.933	1	CLONAL	2	TRUE	1	0.235580502188689	3		802	1336	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	178	781	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.981	0.911	1	1	0.993	1	CLONAL	2	TRUE	1	0.336521892236027	2		786	539	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	42	533	1	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	0.29129087525776	3	FACETS	0.81	0.678	0.956	0.405	0.339	0.478	CLONAL	1	TRUE	1	0.336521892236027	3		534	360	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	77	552	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.336521892236027	2		552	394	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685314	89685315	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TG	TG	-	rs1564826836	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	32	481	0	ENST00000371953.3:c.209+1_209+2del		p.X70_splice	ENST00000371953	NM_000314.4	70		3/9	1	2	FACETS	0.764	0.623	0.921	0.764	0.623	0.921	CLONAL	1	TRUE	1	0.336521892236027	2		481	249	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	43	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.29129087525776	3	FACETS	1	0.894	1	0.541	0.455	0.635	CLONAL	1	TRUE	1	0.336521892236027	3		326	276	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228979	36228979	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555734923	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	113	647	0	ENST00000222270.7:c.7759C>T	p.Arg2587Ter	p.R2587*	ENST00000222270	NM_014727.1	2587	Cga/Tga	36/37	1	2	FACETS	0.983	0.886	1	0.983	0.886	1	CLONAL	1	TRUE	1	0.336521892236027	2		647	683	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227057	53227057	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	24	450	0	ENST00000375401.3:c.2518C>T	p.Pro840Ser	p.P840S	ENST00000375401	NM_004187.3	840	Ccc/Tcc	18/26	0.336521892236027	1	FACETS	0.258	0.202	0.324	0.258	0.202	0.324	SUBCLONAL	1	TRUE	0	0.336521892236027	1		450	459	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	25	258	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	0.774	0.614	0.955	0.774	0.614	0.955	CLONAL	1	TRUE	1	0.336521892236027	2		258	192	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	49	630	5	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	1	2	FACETS	0.758	0.644	0.883	0.758	0.644	0.883	SUBCLONAL	1	TRUE	1	0.336521892236027	2		635	384	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480122	50480122	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	75	485	0	ENST00000394963.4:c.356G>A	p.Arg119Gln	p.R119Q	ENST00000394963	NM_003076.4	119	cGa/cAa	2/13	1	2	FACETS	0.843	0.74	0.953	0.843	0.74	0.953	CLONAL	1	TRUE	1	0.336521892236027	2		485	529	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523009	25523009	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	127	612	1	ENST00000264709.3:c.176del	p.Pro59ArgfsTer13	p.P59Rfs*13	ENST00000264709	NM_175629.2	59	cCg/cg	3/23	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.336521892236027	2		613	681	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	65	354	5	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.336521892236027	2		359	377	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	96	541	0	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	1	2	FACETS	0.979	0.874	1	0.979	0.874	1	CLONAL	1	TRUE	1	0.336521892236027	2		541	583	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196880	108196880	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	71	488	0	ENST00000278616.4:c.6908del	p.Lys2303ArgfsTer7	p.K2303Rfs*7	ENST00000278616	NM_000051.3	2301	gcA/gc	47/63	1	2	FACETS	0.979	0.858	1	0.979	0.858	1	CLONAL	1	TRUE	1	0.336521892236027	2		488	431	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	115	224	0	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	0.336521892236027	1	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	0	0.336521892236027	1		224	564	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226589969	226589969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770918209	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	103	556	2	ENST00000366794.5:c.232C>T	p.Arg78Trp	p.R78W	ENST00000366794	NM_001618.3	78	Cgg/Tgg	2/23	1	2	FACETS	0.945	0.847	1	0.945	0.847	1	CLONAL	1	TRUE	1	0.336521892236027	2		558	648	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100727	8100728	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs771019738	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	92	714	0	ENST00000346208.3:c.708dup	p.Ser237GlnfsTer66	p.S237Qfs*66	ENST00000346208		234	ttc/ttCc	3/6	1	2	FACETS	0.892	0.794	0.996	0.892	0.794	0.996	CLONAL	1	TRUE	1	0.336521892236027	2		714	613	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404809	70404809	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	31	543	0	ENST00000373644.4:c.2328del	p.Lys776AsnfsTer19	p.K776Nfs*19	ENST00000373644	NM_030625.2	775	Aaa/aa	4/12	1	2	FACETS	0.642	0.521	0.778	0.642	0.521	0.778	SUBCLONAL	1	TRUE	1	0.336521892236027	2		543	287	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	91	458	10	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	0.956	1	CLONAL	1	TRUE	1	0.336521892236027	2		468	474	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612801	228612801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369460992	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	114	692	1	ENST00000366696.1:c.226G>A	p.Ala76Thr	p.A76T	ENST00000366696	NM_003493.2	76	Gct/Act	1/1	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.336521892236027	2		693	589	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752695	42752695	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1366176199	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	77	692	8	ENST00000222329.4:c.1569del	p.Leu525SerfsTer6	p.L525Sfs*6	ENST00000222329	NM_006494.2	523	ggG/gg	4/4	1	2	FACETS	0.846	0.744	0.955	0.846	0.744	0.955	CLONAL	1	TRUE	1	0.336521892236027	2		700	541	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437166	110437166	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	12	31	1	ENST00000375856.3:c.1235G>A	p.Arg412His	p.R412H	ENST00000375856	NM_003749.2	412	cGc/cAc	1/2	0.29129087525776	3	FACETS	1	0.855	1	0.683	0.491	0.906	CLONAL	1	TRUE	1	0.336521892236027	3		32	61	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	154	837	5	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.336521892236027	2		842	824	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609942	43609942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767407	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	123	815	2	ENST00000355710.3:c.1894G>A	p.Glu632Lys	p.E632K	ENST00000355710	NM_020975.4	632	Gag/Aag	11/20	1	2	FACETS	0.934	0.845	1	0.934	0.845	1	CLONAL	1	TRUE	1	0.336521892236027	2		817	783	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905585	50905585	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs553342844	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	122	772	0	ENST00000440232.2:c.713C>T	p.Thr238Met	p.T238M	ENST00000440232	NM_002691.3	238	aCg/aTg	6/27	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.336521892236027	2		772	689	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186724	11186724	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	101	620	0	ENST00000361445.4:c.6481C>T	p.Gln2161Ter	p.Q2161*	ENST00000361445	NM_004958.3	2161	Caa/Taa	46/58	1	2	FACETS	0.915	0.819	1	0.915	0.819	1	CLONAL	1	TRUE	1	0.336521892236027	2		620	656	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087486	27087487	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	116	781	0	ENST00000324856.7:c.2060_2061insA	p.His688SerfsTer129	p.H688Sfs*129	ENST00000324856	NM_006015.4	687	cct/ccAt	5/20	1	2	FACETS	0.95	0.857	1	0.95	0.857	1	CLONAL	1	TRUE	1	0.336521892236027	2		781	726	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27098991	27098991	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs375417370	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	88	496	0	ENST00000324856.7:c.3407C>T	p.Ala1136Val	p.A1136V	ENST00000324856	NM_006015.4	1136	gCg/gTg	13/20	1	2	FACETS	0.913	0.81	1	0.913	0.81	1	CLONAL	1	TRUE	1	0.336521892236027	2		496	573	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932041	36932041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs567871402	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	78	573	0	ENST00000361632.4:c.2428G>A	p.Asp810Asn	p.D810N	ENST00000361632		810	Gac/Aac	16/16	1	2	FACETS	0.775	0.682	0.875	0.775	0.682	0.875	SUBCLONAL	1	TRUE	1	0.336521892236027	2		573	598	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46725734	46725734	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	90	471	0	ENST00000371975.4:c.374del	p.Pro125ArgfsTer2	p.P125Rfs*2	ENST00000371975	NM_003579.3	124	Ccc/cc	5/18	1	2	FACETS	0.987	0.878	1	0.987	0.878	1	CLONAL	1	TRUE	1	0.336521892236027	2		471	542	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65304162	65304162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367582687	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	43	606	1	ENST00000342505.4:c.2953G>A	p.Val985Ile	p.V985I	ENST00000342505	NM_002227.2	985	Gtt/Att	21/25	1	2	FACETS	0.543	0.454	0.641	0.543	0.454	0.641	SUBCLONAL	1	TRUE	1	0.336521892236027	2		607	471	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097749	8097749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1215707952	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	145	628	3	ENST00000346208.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000346208		44	cCg/cTg	2/6	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.336521892236027	2		631	695	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342866	118342866	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148514018	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	49	307	0	ENST00000534358.1:c.992G>A	p.Arg331Gln	p.R331Q	ENST00000534358	NM_005933.3	331	cGg/cAg	3/36	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.336521892236027	2		307	282	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246489	46246489	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	37	287	0	ENST00000334344.6:c.4583C>T	p.Ala1528Val	p.A1528V	ENST00000334344	NM_152641.2	1528	gCa/gTa	15/21	1	2	FACETS	0.873	0.724	1	0.873	0.724	1	CLONAL	1	TRUE	1	0.336521892236027	2		287	252	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120801	115120801	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	92	550	0	ENST00000257566.3:c.205G>A	p.Val69Met	p.V69M	ENST00000257566	NM_016569.3	69	Gtg/Atg	1/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.336521892236027	2		550	438	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913456	32913456	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	45	589	0	ENST00000380152.3:c.4964A>G	p.Tyr1655Cys	p.Y1655C	ENST00000380152		1655	tAc/tGc	11/27	0.29129087525776	3	FACETS	0.835	0.704	0.98	0.418	0.352	0.49	CLONAL	1	TRUE	1	0.336521892236027	3		589	374	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49280993	49280993	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200402832	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	61	707	0	ENST00000282018.3:c.40G>A	p.Val14Ile	p.V14I	ENST00000282018	NM_020377.2	14	Gta/Ata	1/1	0.29129087525776	3	FACETS	0.795	0.686	0.912	0.397	0.343	0.456	CLONAL	1	TRUE	1	0.336521892236027	3		707	533	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436236	110436236	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778015136	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	52	400	0	ENST00000375856.3:c.2165C>T	p.Ala722Val	p.A722V	ENST00000375856	NM_003749.2	722	gCg/gTg	1/2	0.29129087525776	3	FACETS	0.948	0.81	1	0.474	0.405	0.549	CLONAL	1	TRUE	1	0.336521892236027	3		400	381	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986616	36986616	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	48	273	0	ENST00000354822.5:c.1073C>A	p.Pro358Gln	p.P358Q	ENST00000354822	NM_001079668.2	358	cCg/cAg	3/3	0.336521892236027	2	FACETS	0.991	0.843	1	0.495	0.421	0.576	CLONAL	1	TRUE	0	0.336521892236027	2		273	288	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994829	73994829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751833994	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	37	288	2	ENST00000318443.5:c.313G>A	p.Ala105Thr	p.A105T	ENST00000318443	NM_001024736.1	105	Gca/Aca	3/10	1	2	FACETS	0.894	0.742	1	0.894	0.742	1	CLONAL	1	TRUE	1	0.336521892236027	2		290	246	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129042	30129042	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745793573	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	136	718	3	ENST00000263025.4:c.724C>T	p.Arg242Trp	p.R242W	ENST00000263025	NM_002746.2	242	Cgg/Tgg	5/9	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.336521892236027	2		721	730	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50784069	50784069	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	75	657	1	ENST00000398568.2:c.460G>A	p.Ala154Thr	p.A154T	ENST00000398568	NM_001042412.1	154	Gca/Aca	3/18	1	2	FACETS	0.824	0.723	0.932	0.824	0.723	0.932	CLONAL	1	TRUE	1	0.336521892236027	2		658	541	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122373	17122373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375352888	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	185	564	1	ENST00000285071.4:c.1022G>A	p.Arg341Gln	p.R341Q	ENST00000285071	NM_144997.5	341	cGg/cAg	9/14	1	2	FACETS	1	0.967	1	1	0.994	1	CLONAL	2	TRUE	1	0.336521892236027	2		565	516	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687394	37687394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1265551180	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	76	508	1	ENST00000447079.4:c.4298C>T	p.Ala1433Val	p.A1433V	ENST00000447079	NM_015083.1	1433	gCa/gTa	14/14	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.336521892236027	2		509	451	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736865	736865	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	91	837	0	ENST00000314574.4:c.1234del	p.Ile412Ter	p.I412*	ENST00000314574	NM_005433.3	412	Ata/ta	10/12	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.336521892236027	2		837	539	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210855	36210856	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	131	833	0	ENST00000222270.7:c.610dup	p.Gln204ProfsTer9	p.Q204Pfs*9	ENST00000222270	NM_014727.1	202	-/C	3/37	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.336521892236027	2		833	664	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218337	36218337	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	117	705	0	ENST00000222270.7:c.4118-2A>G		p.X1373_splice	ENST00000222270	NM_014727.1	1373			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.336521892236027	2		705	636	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223698	36223698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768089106	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	131	800	2	ENST00000222270.7:c.6248C>T	p.Thr2083Met	p.T2083M	ENST00000222270	NM_014727.1	2083	aCg/aTg	28/37	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.336521892236027	2		802	764	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607784	46607784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs112301187	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	123	776	1	ENST00000263734.3:c.1973G>A	p.Arg658His	p.R658H	ENST00000263734	NM_001430.4	658	cGc/cAc	12/16	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.336521892236027	2		777	723	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268352	198268352	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	47	467	0	ENST00000335508.6:c.1676T>C	p.Ile559Thr	p.I559T	ENST00000335508	NM_012433.2	559	aTa/aCa	12/25	1	2	FACETS	0.814	0.69	0.951	0.814	0.69	0.951	CLONAL	1	TRUE	1	0.336521892236027	2		467	343	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22142659	22142659	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	46	378	0	ENST00000215832.6:c.743C>A	p.Ser248Ter	p.S248*	ENST00000215832	NM_002745.4	248	tCa/tAa	6/9	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.336521892236027	2		378	244	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430327	181430327	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	61	387	1	ENST00000325404.1:c.179C>T	p.Ala60Val	p.A60V	ENST00000325404	NM_003106.3	60	gCc/gTc	1/1	0.29129087525776	3	FACETS	1	0.958	1	0.638	0.554	0.728	CLONAL	1	TRUE	1	0.336521892236027	3		388	332	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514306	148514325	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TATCTTACCTGTCTACATGT	TATCTTACCTGTCTACATGT	-	novel	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	37	426	0	ENST00000320356.2:c.1399_1410+8del		p.X467_splice	ENST00000320356	NM_004456.4	467		11/20	1	2	FACETS	0.811	0.672	0.965	0.811	0.672	0.965	CLONAL	1	TRUE	1	0.336521892236027	2		426	271	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187104	38187104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758646155	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	130	736	0	ENST00000317025.8:c.1373C>T	p.Ala458Val	p.A458V	ENST00000317025	NM_023034.1	458	gCg/gTg	6/24	0.29129087525776	3	FACETS	1	0.947	1	0.532	0.482	0.585	CLONAL	1	TRUE	1	0.336521892236027	3		736	848	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129919	69129919	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	65	397	0	ENST00000288368.4:c.4673A>G	p.Tyr1558Cys	p.Y1558C	ENST00000288368	NM_024870.2	1558	tAc/tGc	38/40	0.330654727918966	5	FACETS	0.856	0.742	0.98	0.285	0.247	0.327	CLONAL	1	TRUE	2	0.336521892236027	5		397	679	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342800	87342800	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	34	487	0	ENST00000277120.3:c.1085T>A	p.Ile362Lys	p.I362K	ENST00000277120		362	aTa/aAa	9/19	1	2	FACETS	0.466	0.38	0.562	0.466	0.38	0.562	SUBCLONAL	1	TRUE	1	0.336521892236027	2		487	434	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738235	133738235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs909306692	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	89	605	1	ENST00000318560.5:c.635C>T	p.Thr212Met	p.T212M	ENST00000318560	NM_005157.4	212	aCg/aTg	4/11	1	2	FACETS	0.893	0.793	1	0.893	0.793	1	CLONAL	1	TRUE	1	0.336521892236027	2		606	592	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781304	135781304	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	66	652	1	ENST00000298552.3:c.1661C>A	p.Pro554His	p.P554H	ENST00000298552	NM_001162426.1	554	cCc/cAc	15/23	1	2	FACETS	0.606	0.526	0.693	0.606	0.526	0.693	SUBCLONAL	1	TRUE	1	0.336521892236027	2		653	647	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328348	137328348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	110	777	0	ENST00000481739.1:c.1277G>A	p.Arg426His	p.R426H	ENST00000481739	NM_002957.4	426	cGc/cAc	10/10	1	2	FACETS	0.751	0.674	0.832	0.751	0.674	0.832	SUBCLONAL	1	TRUE	1	0.336521892236027	2		777	871	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	75	314	0				ENST00000310581	NM_198253.2	-/1132			0.272424925336194	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.272424925336194	2		314	238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0025084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	60	493	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.195377812133082	3	FACETS	1	0.889	1	0.517	0.446	0.594	CLONAL	1	TRUE	1	0.272424925336194	3		493	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0025084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	89	517	0	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	0.195377812133082	3	FACETS	0.8	0.712	0.893	0.8	0.712	0.893	SUBCLONAL	2	TRUE	1	0.272424925336194	3		517	464	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625189	69625189	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	181	436	2	ENST00000334134.2:c.604C>A	p.Pro202Thr	p.P202T	ENST00000334134	NM_005247.2	202	Cct/Act	3/3	0.237497645330154	5	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	2	0.272424925336194	5		438	569	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372393	118372393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	81	452	0	ENST00000534358.1:c.6326C>T	p.Ser2109Leu	p.S2109L	ENST00000534358	NM_005933.3	2109	tCa/tTa	26/36	0.272424925336194	2	FACETS	0.772	0.685	0.865	0.772	0.685	0.865	SUBCLONAL	2	TRUE	0	0.272424925336194	2		452	385	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456545	32456545	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	13	34	0	ENST00000332351.3:c.347A>G	p.Tyr116Cys	p.Y116C	ENST00000332351	NM_024426.4	116	tAc/tGc	1/10	0.237497645330154	5	FACETS	0.82	0.594	1	0.547	0.396	0.723	CLONAL	2	TRUE	2	0.272424925336194	5		34	82	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436285	110436285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750160363	NA	P-0025084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	39	164	0	ENST00000375856.3:c.2116G>A	p.Gly706Arg	p.G706R	ENST00000375856	NM_003749.2	706	Ggg/Agg	1/2	0.242735524099564	3	FACETS	1	0.955	1	0.497	0.416	0.587	CLONAL	1	TRUE	0	0.272424925336194	3		164	218	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125302	7125302	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	37	354	0	ENST00000302850.5:c.3250del	p.His1084IlefsTer19	p.H1084Ifs*19	ENST00000302850	NM_000208.2	1084	Cat/at	17/22	0.272424925336194	2	FACETS	0.882	0.73	1	0.441	0.365	0.526	CLONAL	1	TRUE	0	0.272424925336194	2		354	308	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627521	14627521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	105	429	1	ENST00000254322.2:c.549G>A	p.Met183Ile	p.M183I	ENST00000254322	NM_006145.1	183	atG/atA	2/3	0.272424925336194	2	FACETS	0.996	0.9	1	0.996	0.9	1	CLONAL	2	TRUE	0	0.272424925336194	2		430	387	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713670	52713670	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	30	376	0	ENST00000394830.3:c.58G>C	p.Asp20His	p.D20H	ENST00000394830	NM_018313.4	20	Gat/Cat	2/30	0.272424925336194	2	FACETS	0.608	0.49	0.742	0.304	0.245	0.371	SUBCLONAL	1	TRUE	0	0.272424925336194	2		376	362	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806669	1806669	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	65	562	0	ENST00000260795.2:c.1385A>G	p.Asp462Gly	p.D462G	ENST00000260795		462	gAc/gGc	9/17	NA	2	FACETS	1	0.893	1			1	INDETERMINATE	1	TRUE	NA	0.272424925336194	2		562	463	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201089	108201089	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	76	489	0	ENST00000278616.4:c.7456C>G	p.Arg2486Gly	p.R2486G	ENST00000278616	NM_000051.3	2486	Cga/Gga	50/63	0.513487189559503	1	FACETS	0.574	0.507	0.646	0.574	0.507	0.646	SUBCLONAL	1	TRUE	0	0.513487189559503	1		489	383	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665248	176665248	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs760426933	NA	P-0025086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	38	306	0	ENST00000439151.2:c.3932G>T	p.Arg1311Leu	p.R1311L	ENST00000439151	NM_022455.4	1311	cGc/cTc	7/23	1	2	FACETS	0.288	0.237	0.344	0.288	0.237	0.344	SUBCLONAL	1	TRUE	1	0.513487189559503	2		306	514	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696449	47696449	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	270	454	0	ENST00000347630.2:c.374T>G	p.Phe125Cys	p.F125C	ENST00000347630	NM_001007230.1	125	tTt/tGt	6/11	1	2	FACETS	0.956	0.9	1	0.956	0.9	1	CLONAL	1	TRUE	1	0.702680386034449	2		454	804	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	225	606	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	0.697489526480164	2		606	608	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593519	48593519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	180	315	0	ENST00000342988.3:c.1270G>A	p.Asp424Asn	p.D424N	ENST00000342988	NM_005359.5	424	Gat/Aat	10/12	0.697489526480164	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.697489526480164	1		315	313	SUCCESS
APC	324	MSKCC	GRCh37	5	112175213	112175213	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0025088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	256	249	0	ENST00000257430.4:c.3922A>T	p.Lys1308Ter	p.K1308*	ENST00000257430	NM_000038.5	1308	Aaa/Taa	16/16	0.694105999193259	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.697489526480164	2		249	346	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604774	48604782	+	inframe_deletion	In_Frame_Del	DEL	CCTCCAGCT	CCTCCAGCT	-	novel	NA	P-0025088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	278	446	1	ENST00000342988.3:c.1599_1607del	p.Gln534_Leu536del	p.Q534_L536del	ENST00000342988	NM_005359.5	532	gcCCTCCAGCTc/gcc	12/12	0.697489526480164	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.697489526480164	1		447	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0025089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	116	466	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.301152791282367	1	FACETS	0.967	0.874	1	0.967	0.874	1	CLONAL	1	TRUE	0	0.33	1		466	607	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0025089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	72	585	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.811	0.71	0.92	0.811	0.71	0.92	CLONAL	1	TRUE	1	0.33	2		585	538	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0025089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	79	567	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.33	2		567	468	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589306	28589306	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	72	372	0	ENST00000241453.7:c.2741C>A	p.Ala914Asp	p.A914D	ENST00000241453	NM_004119.2	914	gCt/gAt	22/24	1	2	FACETS	0.778	0.68	0.883	0.778	0.68	0.883	SUBCLONAL	1	TRUE	1	0.33	2		372	561	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465609	99465609	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	84	371	0	ENST00000268035.6:c.2434A>G	p.Lys812Glu	p.K812E	ENST00000268035	NM_000875.3	812	Aag/Gag	11/21	0.301152791282367	1	FACETS	0.861	0.762	0.965	0.861	0.762	0.965	CLONAL	1	TRUE	0	0.33	1		371	494	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384741	17384741	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	166	548	1	ENST00000359435.4:c.373C>A	p.Gln125Lys	p.Q125K	ENST00000359435	NM_001033549.1	125	Cag/Aag	4/9	0.301152791282367	1	FACETS	0.988	0.908	1	0.988	0.908	1	CLONAL	1	TRUE	0	0.33	1		549	850	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219029	36219029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748191051	NA	P-0025089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	144	488	1	ENST00000222270.7:c.4528G>A	p.Ala1510Thr	p.A1510T	ENST00000222270	NM_014727.1	1510	Gcc/Acc	19/37	1	2	FACETS	0.953	0.869	1	0.953	0.869	1	CLONAL	1	TRUE	1	0.33	2		489	916	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965872	25965872	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	125	446	0	ENST00000435504.4:c.3334G>T	p.Gly1112Cys	p.G1112C	ENST00000435504		1112	Ggc/Tgc	13/13	0.244787726096619	1	FACETS	0.918	0.832	1	0.918	0.832	1	CLONAL	1	TRUE	0	0.33	1		446	689	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972977	25972977	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	66	275	0	ENST00000435504.4:c.1448C>A	p.Pro483Gln	p.P483Q	ENST00000435504		483	cCa/cAa	12/13	0.244787726096619	1	FACETS	0.872	0.761	0.991	0.872	0.761	0.991	CLONAL	1	TRUE	0	0.33	1		275	383	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755829	39755829	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	31	184	0	ENST00000288319.7:c.936G>T	p.Gln312His	p.Q312H	ENST00000288319	NM_182918.3	312	caG/caT	10/10	0.274302070607841	3	FACETS	0.725	0.588	0.879	0.362	0.294	0.44	SUBCLONAL	1	TRUE	1	0.33	3		184	302	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982069	38982069	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	40	487	0	ENST00000357387.3:c.653G>T	p.Cys218Phe	p.C218F	ENST00000357387	NM_152756.3	218	tGc/tTc	8/38	0.280426762071563	4	FACETS	0.473	0.392	0.564			1	SUBCLONAL	1	TRUE	NA	0.33	4		487	681	SUCCESS
APC	324	MSKCC	GRCh37	5	112175969	112175969	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	35	234	0	ENST00000257430.4:c.4678G>T	p.Glu1560Ter	p.E1560*	ENST00000257430	NM_000038.5	1560	Gaa/Taa	16/16	0.301152791282367	1	FACETS	0.681	0.561	0.814	0.681	0.561	0.814	SUBCLONAL	1	TRUE	0	0.33	1		234	260	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468167	50468167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	145	332	0	ENST00000331340.3:c.1402C>T	p.Arg468Trp	p.R468W	ENST00000331340	NM_006060.4	468	Cgg/Tgg	8/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.33	2		332	709	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020205	123020205	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	90	298	0	ENST00000355640.3:c.693G>T	p.Leu231Phe	p.L231F	ENST00000355640		231	ttG/ttT	2/7	1	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.33	1		298	356	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241873	72241873	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1252345844	NA	P-0025091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	57	348	0	ENST00000357731.5:c.517C>T	p.Arg173Ter	p.R173*	ENST00000357731	NM_173808.2	173	Cga/Tga	3/7	1	2	FACETS	0.823	0.706	0.951	0.823	0.706	0.951	CLONAL	1	TRUE	1	0.234249658217297	2		348	591	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845623	68845623	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	232	518	0	ENST00000261769.5:c.869A>T	p.Asp290Val	p.D290V	ENST00000261769	NM_004360.3	290	gAc/gTc	7/16	0.234249658217297	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.234249658217297	2		518	942	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578499	7578499	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs786203071	NA	P-0025091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	31	722	0	ENST00000269305.4:c.431A>C	p.Gln144Pro	p.Q144P	ENST00000269305	NM_001126112.2	144	cAg/cCg	5/11	1	2	FACETS	0.254	0.204	0.31	0.254	0.204	0.31	SUBCLONAL	1	TRUE	1	0.234249658217297	2		722	1044	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501279	140501279	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs397516905	NA	P-0025091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	69	358	0	ENST00000288602.6:c.793G>C	p.Gly265Arg	p.G265R	ENST00000288602	NM_004333.4	265	Ggt/Cgt	6/18	0.234249658217297	3	FACETS	1	0.953	1	0.602	0.524	0.685	CLONAL	1	TRUE	1	0.234249658217297	3		358	547	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907043	101907043	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	33	329	0	ENST00000374994.4:c.1003A>G	p.Lys335Glu	p.K335E	ENST00000374994	NM_004612.2	335	Aaa/Gaa	6/9	0.195923118723503	3	FACETS	0.72	0.586	0.871	0.36	0.293	0.436	SUBCLONAL	1	TRUE	1	0.234249658217297	3		329	437	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248450	212248450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1480034665	NA	P-0025092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	91	278	1	ENST00000342788.4:c.3817C>T	p.Arg1273Trp	p.R1273W	ENST00000342788	NM_005235.2	1273	Cgg/Tgg	28/28	0.178849443937911	2	FACETS	1	0.962	1	0.577	0.518	0.638	INDETERMINATE	1	TRUE	0	0.509108372393441	2		279	310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0025092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	302	486	1	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.509108372393441	2	FACETS	0.955	0.908	1	0.955	0.908	1	CLONAL	2	TRUE	0	0.509108372393441	2		487	621	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024001	27024002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0025094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	30	92	0	ENST00000324856.7:c.1113dup	p.Gln372AlafsTer28	p.Q372Afs*28	ENST00000324856	NM_006015.4	369	-/G	1/20	1	2	FACETS	1	0.822	1	1	0.822	1	CLONAL	1	TRUE	1	0.517493791780171	2		92	116	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221947	1221947	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs863224448	NA	P-0025094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	157	643	0	ENST00000326873.7:c.863-1G>A		p.X288_splice	ENST00000326873	NM_000455.4	288			0.517493791780171	1	FACETS	0.949	0.876	1	0.949	0.876	1	CLONAL	1	TRUE	0	0.517493791780171	1		643	474	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982989	201982990	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0025094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	187	628	0	ENST00000359651.3:c.841dup	p.Asp281GlyfsTer20	p.D281Gfs*20	ENST00000359651		280	cgg/cGgg	7/8	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.517493791780171	2		628	685	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998279	100998285	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGCCC	GCCGCCC	-	novel	NA	P-0025094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	34	170	0	ENST00000325455.5:c.1517_1523del	p.Gly506AlafsTer38	p.G506Afs*38	ENST00000325455	NM_001202474.3	506	gGGGCGGCc/gc	1/8	0.461110386474876	3	FACETS	0.803	0.662	0.959	0.401	0.331	0.48	CLONAL	1	TRUE	1	0.517493791780171	3		170	206	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243094	105243094	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1566818959	NA	P-0025096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	298	619	1	ENST00000349310.3:c.189G>A	p.Met63Ile	p.M63I	ENST00000349310	NM_001014432.1	63	atG/atA	5/15	1	2	FACETS	0.935	0.882	0.989	0.935	0.882	0.989	CLONAL	1	TRUE	1	0.638100163343765	2		620	999	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858237	27858238	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs763163035	NA	P-0025096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	315	474	0	ENST00000359303.2:c.333_334del	p.Ala112TyrfsTer11	p.A112Yfs*11	ENST00000359303	NM_003535.2	111	tgTGct/tgct	1/1	0.297661326707675	2	FACETS	1	0.994	1	0.684	0.649	0.718	INDETERMINATE	1	TRUE	0	0.638100163343765	2		474	722	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243054	105243055	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCGGATGATGAAGGTGTTGGGCCGGGGCCGCAC	novel	NA	P-0025096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	271	770	0	ENST00000349310.3:c.228_229insGTGCGGCCCCGGCCCAACACCTTCATCATCCGC	p.Arg76_Cys77insValArgProArgProAsnThrPheIleIleArg	p.R76_C77insVRPRPNTFIIR	ENST00000349310	NM_001014432.1	76	-/GTGCGGCCCCGGCCCAACACCTTCATCATCCGC	5/15	1	2	FACETS	0.654	0.612	0.697	0.654	0.612	0.697	SUBCLONAL	1	TRUE	1	0.638100163343765	2		770	1299	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0025098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	206	512	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		512	579	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0025099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	46	364	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.804	0.679	0.941	0.804	0.679	0.941	CLONAL	1	TRUE	1	0.31	2		364	369	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0025099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	62	552	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.746	0.645	0.856	0.746	0.645	0.856	SUBCLONAL	1	TRUE	1	0.31	2		552	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0025099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	83	506	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.302029910887728	1	FACETS	0.925	0.819	1	0.925	0.819	1	CLONAL	1	TRUE	0	0.31	1		506	489	SUCCESS
APC	324	MSKCC	GRCh37	5	112174094	112174095	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs863225332	NA	P-0025099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	42	296	0	ENST00000257430.4:c.2804dup	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	tac/tAac	16/16	1	2	FACETS	0.772	0.646	0.91	0.772	0.646	0.91	CLONAL	1	TRUE	1	0.31	2		296	351	SUCCESS
APC	324	MSKCC	GRCh37	5	112175720	112175720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	48	227	0	ENST00000257430.4:c.4429C>T	p.Gln1477Ter	p.Q1477*	ENST00000257430	NM_000038.5	1477	Cag/Tag	16/16	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.31	2		227	305	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962304	2962304	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs895009948	NA	P-0025099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	46	583	0	ENST00000396946.4:c.2233G>A	p.Gly745Ser	p.G745S	ENST00000396946	NM_032415.4	745	Ggc/Agc	17/25	1	2	FACETS	0.604	0.509	0.71	0.604	0.509	0.71	SUBCLONAL	1	TRUE	1	0.31	2		583	491	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047894	180047894	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	83	663	0	ENST00000261937.6:c.2281G>A	p.Ala761Thr	p.A761T	ENST00000261937	NM_182925.4	761	Gcc/Acc	15/30	1	2	FACETS	0.997	0.882	1	0.997	0.882	1	CLONAL	1	TRUE	1	0.31	2		663	537	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31495463	31495463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	73	432	0	ENST00000344624.3:c.1685G>A	p.Arg562His	p.R562H	ENST00000344624		562	cGt/cAt	9/33	1	2	FACETS	0.818	0.716	0.927	0.818	0.716	0.927	CLONAL	1	TRUE	1	0.31	2		432	576	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753836	42753836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1250639908	NA	P-0025099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	97	650	4	ENST00000222329.4:c.428G>A	p.Arg143His	p.R143H	ENST00000222329	NM_006494.2	143	cGc/cAc	4/4	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.31	2		654	576	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920434	114920434	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	82	476	0	ENST00000543371.1:c.1375T>C	p.Trp459Arg	p.W459R	ENST00000543371	NM_001198531.1	459	Tgg/Cgg	13/14	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.31	2		476	523	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622118	1622131	+	frameshift_variant	Frame_Shift_Del	DEL	TACCGGGCGGGAGG	TACCGGGCGGGAGG	-	novel	NA	P-0025099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	67	579	0	ENST00000344749.5:c.744_757del	p.Leu249ArgfsTer95	p.L249Rfs*95	ENST00000344749	NM_001136139.2	248	ccCCTCCCGCCCGGTAgc/ccgc	10/19	1	2	FACETS	0.969	0.845	1	0.969	0.845	1	CLONAL	1	TRUE	1	0.31	2		579	446	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274910	41274910	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	73	414	0	ENST00000349496.5:c.1160A>T	p.Asn387Ile	p.N387I	ENST00000349496	NM_001904.3	387	aAt/aTt	8/15	1	2	FACETS	0.959	0.841	1	0.959	0.841	1	CLONAL	1	TRUE	1	0.31	2		414	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0025102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	350	486	1	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.389493029530389	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.389493029530389	2		487	768	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317099	11317099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201093943	NA	P-0025102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	126	483	2	ENST00000361445.4:c.395G>A	p.Arg132His	p.R132H	ENST00000361445	NM_004958.3	132	cGt/cAt	4/58	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.389493029530389	2		485	645	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435692	110435700	+	inframe_deletion	In_Frame_Del	DEL	GCTGGGCAG	GCTGGGCAG	-	rs752700578	NA	P-0025102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	42	367	0	ENST00000375856.3:c.2701_2709del	p.Leu901_Ser903del	p.L901_S903del	ENST00000375856	NM_003749.2	901	CTGCCCAGC/-	1/2	0.389493029530389	6	FACETS	0.489	0.407	0.581			1	SUBCLONAL	1	TRUE	NA	0.389493029530389	6		367	784	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202123070	202123070	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	51	278	0	ENST00000358485.4:c.116C>G	p.Ser39Trp	p.S39W	ENST00000358485	NM_001080125.1	39	tCg/tGg	1/9	0.220395087517992	3	FACETS	0.839	0.715	0.973	0.419	0.357	0.487	INDETERMINATE	1	TRUE	1	0.389493029530389	3		278	373	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	80	314	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.405476466222787	2		314	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578513	7578513	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	19	922	0	ENST00000269305.4:c.417G>C	p.Lys139Asn	p.K139N	ENST00000269305	NM_001126112.2	139	aaG/aaC	5/11	0.337768591738505	1	FACETS	0.081	0.061	0.105	0.081	0.061	0.105	SUBCLONAL	1	TRUE	0	0.405476466222787	1		922	924	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913355	NA	P-0025107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	133	463	0	ENST00000288602.6:c.1406G>T	p.Gly469Val	p.G469V	ENST00000288602	NM_004333.4	469	gGa/gTa	11/18	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.405476466222787	2		463	588	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119842	70119842	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	227	742	0	ENST00000245479.2:c.844G>A	p.Val282Ile	p.V282I	ENST00000245479	NM_000346.3	282	Gtc/Atc	3/3	0.405476466222787	3	FACETS	1	0.991	1	0.716	0.668	0.766	CLONAL	1	TRUE	1	0.405476466222787	3		742	940	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs878854073	NA	P-0025107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	100	318	0	ENST00000269305.4:c.673-1G>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.337768591738505	1	FACETS	0.736	0.66	0.817	0.736	0.66	0.817	SUBCLONAL	1	TRUE	0	0.405476466222787	1		318	534	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519027	103519027	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	180	486	0	ENST00000355739.4:c.2365G>A	p.Glu789Lys	p.E789K	ENST00000355739	NM_000123.3	789	Gaa/Aaa	11/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.405476466222787	2		486	685	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033734	48033734	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	113	372	0	ENST00000234420.5:c.3947del	p.Gly1316AspfsTer11	p.G1316Dfs*11	ENST00000234420	NM_000179.2	1315	aaG/aa	9/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.405476466222787	2		372	525	SUCCESS
APC	324	MSKCC	GRCh37	5	112179224	112179224	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1114167605	NA	P-0025107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	119	378	0	ENST00000257430.4:c.7933T>A	p.Tyr2645Asn	p.Y2645N	ENST00000257430	NM_000038.5	2645	Tat/Aat	16/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.405476466222787	2		378	490	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	63	314	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.682	0.594	0.776	0.682	0.594	0.776	SUBCLONAL	1	TRUE	1	0.601647985467438	2		314	307	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0025108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24107	519	571	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.601647985467438	50	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.601647985467438	50		571	24626	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400932	72400932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	106	485	0	ENST00000357731.5:c.239C>T	p.Ala80Val	p.A80V	ENST00000357731	NM_173808.2	80	gCg/gTg	2/7	1	2	FACETS	0.883	0.798	0.972	0.883	0.798	0.972	CLONAL	1	TRUE	1	0.601647985467438	2		485	399	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717723	89717723	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	194	550	0	ENST00000371953.3:c.748del	p.Cys250ValfsTer6	p.C250Vfs*6	ENST00000371953	NM_000314.4	250	Tgt/gt	7/9	0.601647985467438	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.601647985467438	1		550	376	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940392	13940392	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	125	444	1	ENST00000405192.2:c.1114T>A	p.Tyr372Asn	p.Y372N	ENST00000405192	NM_001163147.1	372	Tat/Aat	11/12	0.601647985467438	3	FACETS	0.902	0.819	0.989	0.451	0.409	0.495	CLONAL	1	TRUE	1	0.601647985467438	3		445	599	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524646	106524646	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	95	370	0	ENST00000359195.3:c.2807G>C	p.Cys936Ser	p.C936S	ENST00000359195	NM_002649.2	936	tGt/tCt	9/11	0.601647985467438	3	FACETS	0.927	0.83	1	0.464	0.415	0.515	CLONAL	1	TRUE	1	0.601647985467438	3		370	443	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26970430	26970443	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGAAGATATAAA	TGGGAAGATATAAA	-	novel	NA	P-0025110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	11	273	0	ENST00000381527.3:c.799_812del	p.Trp267LysfsTer4	p.W267Kfs*4	ENST00000381527	NM_001260.1	267	TGGGAAGATATAAAa/a	8/13	1	2	FACETS	0.445	0.308	0.616	0.445	0.308	0.616	SUBCLONAL	1	TRUE	1	0.26	2		273	190	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551316	141551316	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	146	729	0	ENST00000220592.5:c.1981C>G	p.Pro661Ala	p.P661A	ENST00000220592	NM_012154.3	661	Ccc/Gcc	15/19	1	2	FACETS	0.843	0.772	0.918	1	0.989	1	CLONAL	2	TRUE	1	0.26	2		729	666	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	199	606	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.819307196919792	3	FACETS	0.781	0.734	0.829	0.781	0.734	0.829	SUBCLONAL	2	TRUE	1	0.882644818560227	3		606	416	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699371	47699371	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	74	542	0	ENST00000347630.2:c.137A>G	p.Glu46Gly	p.E46G	ENST00000347630	NM_001007230.1	46	gAg/gGg	4/11	1	2	FACETS	0.71	0.631	0.793	0.71	0.631	0.793	SUBCLONAL	1	TRUE	1	0.882644818560227	2		542	236	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719271	61719271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	174	476	0	ENST00000401558.2:c.1786C>T	p.Arg596Cys	p.R596C	ENST00000401558	NM_003400.3	596	Cgc/Tgc	16/25	0.756634869044255	3	FACETS	0.8	0.749	0.852	0.8	0.749	0.852	SUBCLONAL	2	TRUE	1	0.882644818560227	3		476	355	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022384	31022393	+	frameshift_variant	Frame_Shift_Del	DEL	GGTCCGAGGG	GGTCCGAGGG	-	novel	NA	P-0025111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	63	307	0	ENST00000375687.4:c.1870_1879del	p.Val624ArgfsTer76	p.V624Rfs*76	ENST00000375687	NM_015338.5	623	caGGTCCGAGGG/ca	13/13	1	2	FACETS	0.816	0.72	0.915	0.816	0.72	0.915	CLONAL	1	TRUE	1	0.882644818560227	2		307	175	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247295	153247295	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	175	367	1	ENST00000281708.4:c.1507G>A	p.Ala503Thr	p.A503T	ENST00000281708	NM_033632.3	503	Gca/Aca	10/12	0.718042501552573	2	FACETS	0.787	0.747	0.825	0.787	0.747	0.825	SUBCLONAL	2	TRUE	0	0.882644818560227	2		368	252	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0025112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	115	574	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.923	0.834	1	0.923	0.834	1	CLONAL	1	TRUE	1	0.42293318680398	2		574	589	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0025112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	192	466	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.42293318680398	1	FACETS	0.956	0.886	1	0.956	0.886	1	CLONAL	1	TRUE	0	0.42293318680398	1		466	749	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600446	10600446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	251	690	0	ENST00000171111.5:c.1409G>A	p.Arg470His	p.R470H	ENST00000171111	NM_203500.1	470	cGt/cAt	4/6	0.42293318680398	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.42293318680398	1		690	909	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041205	47041205	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	255	804	0	ENST00000377604.3:c.1634del	p.Pro545LeufsTer159	p.P545Lfs*159	ENST00000377604	NM_001204468.1	545	Cct/ct	15/24	1	2	FACETS	0.927	0.866	0.99	0.927	0.866	0.99	CLONAL	1	TRUE	1	0.42293318680398	2		804	1301	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799180	42799180	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	222	659	0	ENST00000575354.2:c.4664G>T	p.Gly1555Val	p.G1555V	ENST00000575354	NM_015125.3	1555	gGg/gTg	20/20	0.42293318680398	2	FACETS	0.98	0.912	1	0.49	0.456	0.526	CLONAL	1	TRUE	0	0.42293318680398	2		659	1071	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159750	20159750	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	161	497	1	ENST00000379607.5:c.9G>T	p.Lys3Asn	p.K3N	ENST00000379607	NM_001412.3	3	aaG/aaT	1/7	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.42293318680398	2		498	712	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974788	21974796	+	frameshift_variant	Frame_Shift_Del	DEL	AGCCGAAGG	AGCCGAAGG	C	novel	NA	P-0025112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	52	189	0	ENST00000304494.5:c.31_39delinsG	p.Pro11GlyfsTer30	p.P11Gfs*30	ENST00000304494	NM_000077.4	11	CCTTCGGCT/G	1/3	0.42293318680398	1	FACETS	0.889	0.767	1	0.889	0.767	1	CLONAL	1	TRUE	0	0.42293318680398	1		189	218	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027685	152027685	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0025116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	130	557	0	ENST00000262189.6:c.389+1G>C		p.X130_splice	ENST00000262189	NM_170606.2	130			1	2	FACETS	0.812	0.737	0.89	0.812	0.737	0.89	CLONAL	1	TRUE	1	0.427725386378055	2		557	749	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76919042	76919042	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0025116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	94	114	0	ENST00000373344.5:c.3949A>T	p.Lys1317Ter	p.K1317*	ENST00000373344	NM_000489.3	1317	Aaa/Taa	12/35	1	1	FACETS	0.831	0.756	0.906	1	0.986	1	CLONAL	2	TRUE	0	0.427725386378055	1		114	208	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	125	314	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.415303552612844	2		314	554	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624257	89624270	+	frameshift_variant	Frame_Shift_Del	DEL	AGAAACAAAAGGAG	AGAAACAAAAGGAG	-	novel	NA	P-0025118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	124	254	0	ENST00000371953.3:c.32_45del	p.Arg11IlefsTer28	p.R11Ifs*28	ENST00000371953	NM_000314.4	11	AGAAACAAAAGGAGa/a	1/9	0.415303552612844	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.415303552612844	1		254	379	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907171	101907171	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0025118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	111	318	0	ENST00000374994.4:c.1130+1G>C		p.X377_splice	ENST00000374994	NM_004612.2	377			0.415303552612844	1	FACETS	0.99	0.896	1	0.99	0.896	1	CLONAL	1	TRUE	0	0.415303552612844	1		318	428	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0025119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	294	466	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.372344770723394	2	FACETS	0.82	0.776	0.865	0.82	0.776	0.865	CLONAL	2	FALSE	0	0.468489952594816	2		466	765	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0025119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	335	552	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.327024382078059	5	FACETS	1	0.989	1	0.776	0.735	0.818	CLONAL	2	FALSE	2	0.468489952594816	5		552	1046	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857925	9857925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs534440095	NA	P-0025119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	190	479	1	ENST00000330684.3:c.3476G>A	p.Arg1159His	p.R1159H	ENST00000330684	NM_001134407.1	1159	cGc/cAc	13/13	0.185824509563987	5	FACETS	0.817	0.756	0.88	0.545	0.504	0.587	INDETERMINATE	2	FALSE	2	0.468489952594816	5		480	845	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584497	48584497	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	142	315	1	ENST00000342988.3:c.670C>T	p.Gln224Ter	p.Q224*	ENST00000342988	NM_005359.5	224	Cag/Tag	6/12	0.258870146986071	3	FACETS	0.928	0.855	1	0.619	0.57	0.669	INDETERMINATE	2	FALSE	0	0.468489952594816	3		316	403	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030329	180030329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142322370	NA	P-0025119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	518	596	1	ENST00000261937.6:c.3955C>T	p.Arg1319Trp	p.R1319W	ENST00000261937	NM_182925.4	1319	Cgg/Tgg	30/30	0.290558150905024	3	FACETS	0.877	0.845	0.91			1	CLONAL	3	FALSE	NA	0.468489952594816	3		597	1037	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371912	55371912	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	160	344	0	ENST00000297316.4:c.602G>C	p.Gly201Ala	p.G201A	ENST00000297316	NM_022454.3	201	gGc/gCc	2/2	0.31020284081381	6	FACETS	0.756	0.693	0.822	0.378	0.346	0.411	SUBCLONAL	2	FALSE	2	0.468489952594816	6		344	875	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781074	135781077	+	frameshift_variant	Frame_Shift_Del	DEL	CTTT	CTTT	-	rs118203595	NA	P-0025119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	119	531	0	ENST00000298552.3:c.1888_1891del	p.Lys630GlnfsTer22	p.K630Qfs*22	ENST00000298552	NM_001162426.1	630	AAAGca/ca	15/23	0.391855074309882	3	FACETS	0.73	0.658	0.806	0.365	0.329	0.403	SUBCLONAL	1	FALSE	1	0.468489952594816	3		531	859	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	39	314	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.979	0.818	1	0.979	0.818	1	CLONAL	1	TRUE	1	0.329149167410618	2		314	242	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057874	27057874	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	89	479	0	ENST00000324856.7:c.1582C>T	p.Gln528Ter	p.Q528*	ENST00000324856	NM_006015.4	528	Cag/Tag	3/20	1	2	FACETS	0.939	0.834	1	0.939	0.834	1	CLONAL	1	TRUE	1	0.329149167410618	2		479	576	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781440	135781440	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203542	NA	P-0025120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	63	293	0	ENST00000298552.3:c.1525C>T	p.Arg509Ter	p.R509*	ENST00000298552	NM_001162426.1	509	Cga/Tga	15/23	0.329149167410618	1	FACETS	0.987	0.86	1	0.987	0.86	1	CLONAL	1	TRUE	0	0.329149167410618	1		293	324	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740727	58740727	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	65	391	1	ENST00000305921.3:c.1636del	p.Leu546Ter	p.L546*	ENST00000305921	NM_003620.3	544	ggC/gg	6/6	0.329149167410618	3	FACETS	0.849	0.736	0.97	0.424	0.368	0.485	CLONAL	1	TRUE	1	0.329149167410618	3		392	542	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891275	101891275	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	94	444	1	ENST00000374994.4:c.236C>A	p.Pro79His	p.P79H	ENST00000374994	NM_004612.2	79	cCt/cAt	2/9	0.329149167410618	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.329149167410618	1		445	379	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0025127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	1516	402	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.642914755207875	11	FACETS	1	0.992	1			1	CLONAL	8	TRUE	NA	0.642914755207875	11		402	2256	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576889	7576890	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	310	752	2	ENST00000269305.4:c.956dup	p.Lys320GlufsTer17	p.K320Efs*17	ENST00000269305	NM_001126112.2	319	aag/aaAg	9/11	0.642914755207875	1	FACETS	0.919	0.873	0.966	0.919	0.873	0.966	CLONAL	1	TRUE	0	0.642914755207875	1		754	712	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206647713	206647713	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1285749873	NA	P-0025127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	328	513	0	ENST00000367120.3:c.127A>G	p.Thr43Ala	p.T43A	ENST00000367120	NM_014002.3	43	Acc/Gcc	4/22	0.642914755207875	3	FACETS	1	0.985	1	0.558	0.527	0.59	CLONAL	1	TRUE	1	0.642914755207875	3		513	1208	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58142981	58142981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	52	749	0	ENST00000257904.6:c.803G>A	p.Gly268Glu	p.G268E	ENST00000257904	NM_000075.3	268	gGa/gAa	7/8	0.642914755207875	1	FACETS	0.127	0.108	0.149	0.127	0.108	0.149	SUBCLONAL	1	TRUE	0	0.642914755207875	1		749	863	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822544	72822544	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747010178	NA	P-0025127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	47	509	0	ENST00000268489.5:c.9631C>T	p.Pro3211Ser	p.P3211S	ENST00000268489	NM_006885.3	3211	Ccc/Tcc	10/10	1	2	FACETS	0.26	0.219	0.305	0.26	0.219	0.305	SUBCLONAL	1	TRUE	1	0.642914755207875	2		509	563	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15943793	15943793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	28	516	0	ENST00000268712.3:c.6695G>A	p.Gly2232Glu	p.G2232E	ENST00000268712	NM_006311.3	2232	gGa/gAa	43/46	0.642914755207875	1	FACETS	0.153	0.122	0.188	0.153	0.122	0.188	SUBCLONAL	1	TRUE	0	0.642914755207875	1		516	387	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245963	41245963	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	76	920	0	ENST00000357654.3:c.1585C>G	p.Pro529Ala	p.P529A	ENST00000357654	NM_007294.3	529	Cct/Gct	10/23	0.161696272335665	2	FACETS	0.219	0.191	0.249	0.11	0.095	0.125	INDETERMINATE	1	TRUE	0	0.642914755207875	2		920	1079	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170755	7170755	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	61	697	0	ENST00000302850.5:c.1276T>G	p.Ser426Ala	p.S426A	ENST00000302850	NM_000208.2	426	Tcc/Gcc	6/22	0.374232193835321	1	FACETS	0.156	0.134	0.18	0.156	0.134	0.18	INDETERMINATE	1	TRUE	0	0.642914755207875	1		697	825	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097128	178097128	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	21	305	0	ENST00000397062.3:c.586G>C	p.Glu196Gln	p.E196Q	ENST00000397062	NM_006164.4	196	Gag/Cag	4/5	0.642914755207875	1	FACETS	0.154	0.119	0.196	0.154	0.119	0.196	SUBCLONAL	1	TRUE	0	0.642914755207875	1		305	287	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817505	39817505	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	50	580	0	ENST00000288319.7:c.58G>C	p.Glu20Gln	p.E20Q	ENST00000288319	NM_182918.3	20	Gag/Cag	2/10	1	2	FACETS	0.179	0.151	0.209	0.179	0.151	0.209	SUBCLONAL	1	TRUE	1	0.642914755207875	2		580	871	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911454	39911454	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	50	688	0	ENST00000378444.4:c.5176C>G	p.Leu1726Val	p.L1726V	ENST00000378444	NM_001123385.1	1726	Ctg/Gtg	15/15	1	2	FACETS	0.175	0.148	0.205	0.175	0.148	0.205	SUBCLONAL	1	TRUE	1	0.642914755207875	2		688	888	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0025128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	165	403	0				ENST00000310581	NM_198253.2	-/1132			0.203720174192467	5	FACETS	0.922	0.854	0.99	1	0.99	1	CLONAL	5	TRUE	2	0.203720174192467	5		403	459	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	53	525	0	ENST00000335508.6:c.2704G>A	p.Glu902Lys	p.E902K	ENST00000335508	NM_012433.2	902	Gaa/Aaa	18/25	0.167183751687839	3	FACETS	1	0.963	1	0.724	0.619	0.838	CLONAL	1	TRUE	1	0.203720174192467	3		525	396	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401291	139401291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751169922	NA	P-0025128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	60	906	1	ENST00000277541.6:c.3778G>A	p.Val1260Met	p.V1260M	ENST00000277541	NM_017617.3	1260	Gtg/Atg	23/34	1	2	FACETS	0.844	0.726	0.972	0.844	0.726	0.972	CLONAL	1	TRUE	1	0.203720174192467	2		907	698	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020196	123020196	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	62	364	0	ENST00000355640.3:c.684C>G	p.Phe228Leu	p.F228L	ENST00000355640		228	ttC/ttG	2/7	0.0741927634613373	2	FACETS	1	0.888	1			1	INDETERMINATE	2	TRUE	NA	0.203720174192467	2		364	298	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094345	27094346	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	136	545	0	ENST00000324856.7:c.3054dup	p.Glu1019Ter	p.E1019*	ENST00000324856	NM_006015.4	1018	cct/ccTt	11/20	0.0283417472787151	4	FACETS	0.896	0.818	0.977	1	0.983	1	INDETERMINATE	3	TRUE	2	0.203720174192467	4		545	598	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115961	8115972	+	inframe_deletion	In_Frame_Del	DEL	CCAGCATGGTCA	CCAGCATGGTCA	-	novel	NA	P-0025128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	166	411	0	ENST00000346208.3:c.1309_1320del	p.Ser437_Thr440del	p.S437_T440del	ENST00000346208		436	tCCAGCATGGTCAcc/tcc	6/6	0.203720174192467	3	FACETS	0.914	0.847	0.984	1	0.992	1	CLONAL	4	TRUE	1	0.203720174192467	3		411	491	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450780	70450780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	26	507	0	ENST00000373644.4:c.5620G>A	p.Glu1874Lys	p.E1874K	ENST00000373644	NM_030625.2	1874	Gaa/Aaa	12/12	0.203720174192467	3	FACETS	0.544	0.43	0.676	0.272	0.215	0.338	SUBCLONAL	1	TRUE	1	0.203720174192467	3		507	517	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196068	67196068	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs756293976	NA	P-0025128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	43	589	0	ENST00000312629.5:c.52G>T	p.Glu18Ter	p.E18*	ENST00000312629	NM_003952.2	18	Gag/Tag	1/15	1	2	FACETS	0.739	0.618	0.874	0.739	0.618	0.874	SUBCLONAL	1	TRUE	1	0.203720174192467	2		589	571	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438190	56438190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	79	780	1	ENST00000407977.2:c.803C>T	p.Ser268Leu	p.S268L	ENST00000407977		268	tCa/tTa	7/10	0.0283417472787151	4	FACETS	1	0.973	1	0.705	0.62	0.796	INDETERMINATE	1	TRUE	2	0.203720174192467	4		781	662	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220184	36220184	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	59	612	0	ENST00000222270.7:c.4904G>A	p.Arg1635Gln	p.R1635Q	ENST00000222270	NM_014727.1	1635	cGa/cAa	22/37	0.203720174192467	7	FACETS	1	0.959	1	0.267	0.229	0.308	CLONAL	1	TRUE	2	0.203720174192467	7		612	656	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164691	36164691	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	43	806	0	ENST00000300305.3:c.1184del	p.Pro395ArgfsTer199	p.P395Rfs*199	ENST00000300305		395	cCg/cg	8/8	0.149879998330695	2	FACETS	0.645	0.539	0.764	0.323	0.269	0.382	SUBCLONAL	1	TRUE	0	0.203720174192467	2		806	654	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925491	131925491	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	41	322	0	ENST00000265335.6:c.1414G>C	p.Asp472His	p.D472H	ENST00000265335		472	Gac/Cac	9/25	0.167183751687839	3	FACETS	1	0.94	1	0.647	0.54	0.764	CLONAL	1	TRUE	1	0.203720174192467	3		322	343	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163297	32163297	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	56	966	0	ENST00000375023.3:c.5929G>C	p.Glu1977Gln	p.E1977Q	ENST00000375023	NM_004557.3	1977	Gag/Cag	30/30	0.203720174192467	5	FACETS	0.717	0.612	0.832	0.179	0.153	0.208	SUBCLONAL	1	TRUE	1	0.203720174192467	5		966	1001	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106543497	106543497	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	26	311	0	ENST00000369096.4:c.299G>C	p.Gly100Ala	p.G100A	ENST00000369096	NM_001198.3	100	gGa/gCa	3/7	1	2	FACETS	0.892	0.708	1	0.892	0.708	1	CLONAL	1	TRUE	1	0.203720174192467	2		311	286	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035212	6035212	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	41	587	0	ENST00000265849.7:c.856G>A	p.Asp286Asn	p.D286N	ENST00000265849	NM_000535.5	286	Gac/Aac	8/15	0.203720174192467	3	FACETS	0.875	0.728	1	0.437	0.364	0.519	CLONAL	1	TRUE	1	0.203720174192467	3		587	507	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020270	123020270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	53	330	0	ENST00000355640.3:c.758C>T	p.Ser253Leu	p.S253L	ENST00000355640		253	tCa/tTa	2/7	0.0741927634613373	2	FACETS	1	0.896	1			1	INDETERMINATE	2	TRUE	NA	0.203720174192467	2		330	248	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211837	123211837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	40	197	0	ENST00000218089.9:c.2704G>A	p.Glu902Lys	p.E902K	ENST00000218089	NM_001042749.1	902	Gaa/Aaa	27/35	0.0741927634613373	2	FACETS	1	0.854	1			1	INDETERMINATE	2	TRUE	NA	0.203720174192467	2		197	193	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996276	73996276	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	14	27	0	ENST00000318443.5:c.1010G>C	p.Ser337Thr	p.S337T	ENST00000318443	NM_001024736.1	337	aGc/aCc	5/10	1	2	FACETS	1	0.774	1	1	0.942	1	CLONAL	4	TRUE	1	0.203720174192467	2		27	34	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0025129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	17	672	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.153269399940583	3	FACETS	0.941	0.702	1	0.471	0.351	0.614	CLONAL	1	TRUE	1	0.12	3		672	319	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0025129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	8	679	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	0.153269399940583	3	FACETS	0.516	0.331	0.757	0.258	0.165	0.379	SUBCLONAL	1	TRUE	1	0.12	3		679	274	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6442009	6442009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	10	313	0	ENST00000356142.4:c.568G>A	p.Glu190Lys	p.E190K	ENST00000356142	NM_018890.3	190	Gaa/Aaa	7/7	0.220609339958316	4	FACETS	1	0.745	1	0.559	0.379	0.784	CLONAL	1	TRUE	2	0.12	4		313	167	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0025130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	714	670	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	0.781053635539226	2		671	913	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266714	198266714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	175	502	0	ENST00000335508.6:c.2218G>A	p.Gly740Arg	p.G740R	ENST00000335508	NM_012433.2	740	Gga/Aga	15/25	1	2	FACETS	0.96	0.892	1	0.96	0.892	1	CLONAL	1	TRUE	1	0.781053635539226	2		502	467	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	120	314	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.321538887042699	2		314	586	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0025133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	57	299	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.321538887042699	1	FACETS	0.705	0.607	0.812	0.705	0.607	0.812	SUBCLONAL	1	TRUE	0	0.321538887042699	1		299	422	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853918	59853918	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786202760	NA	P-0025133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	98	425	0	ENST00000259008.2:c.1941G>C	p.Trp647Cys	p.W647C	ENST00000259008	NM_032043.2	647	tgG/tgC	14/20	1	2	FACETS	0.875	0.781	0.974	0.875	0.781	0.974	CLONAL	1	TRUE	1	0.321538887042699	2		425	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0025136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	606	670	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.863579250763507	2	FACETS	0.967	0.951	0.982	0.967	0.951	0.982	CLONAL	2	TRUE	0	0.928212561039886	2		670	675	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	749	511	0	ENST00000425967.3:c.1731C>G	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaG	13/19	0.928216338092819	4	FACETS	0.843	0.819	0.866			1	CLONAL	3	TRUE	NA	0.928212561039886	4		511	1231	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514020	103514020	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	237	522	0	ENST00000355739.4:c.836G>T	p.Arg279Met	p.R279M	ENST00000355739	NM_000123.3	279	aGg/aTg	7/15	0.838505944972721	4	FACETS	1	0.943	1	0.337	0.314	0.36	CLONAL	1	TRUE	1	0.928212561039886	4		522	974	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577050	7577050	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	372	873	1	ENST00000269305.4:c.888C>A	p.His296Gln	p.H296Q	ENST00000269305	NM_001126112.2	296	caC/caA	8/11	0.863579250763507	2	FACETS	0.868	0.827	0.91	0.434	0.413	0.455	CLONAL	1	TRUE	0	0.928212561039886	2		874	923	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196951	108196951	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs200940211	NA	P-0025137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	20	317	0	ENST00000278616.4:c.6974C>T	p.Ala2325Val	p.A2325V	ENST00000278616	NM_000051.3	2325	gCg/gTg	47/63	0.516478728861224	5	FACETS	0.271	0.207	0.347	0.09	0.069	0.116	INDETERMINATE	1	TRUE	2	0.939956745494614	5		317	378	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123875214	123875214	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	121	360	0	ENST00000330479.4:c.170A>G	p.Tyr57Cys	p.Y57C	ENST00000330479	NM_020382.3	57	tAc/tGc	3/9	0.939956745494614	3	FACETS	1	0.933	1	0.513	0.468	0.559	CLONAL	1	TRUE	1	0.939956745494614	3		360	369	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26927919	26927919	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	220	447	0	ENST00000381527.3:c.358C>G	p.Pro120Ala	p.P120A	ENST00000381527	NM_001260.1	120	Cca/Gca	4/13	0.871519964492735	4	FACETS	0.906	0.852	0.961	0.906	0.852	0.961	CLONAL	2	TRUE	2	0.939956745494614	4		447	501	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56878466	56878466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764588936	NA	P-0025138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	95	566	1	ENST00000308159.5:c.2405G>A	p.Arg802Gln	p.R802Q	ENST00000308159	NM_014669.4	802	cGa/cAa	22/22	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.19	2		567	803	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799129	42799129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139613152	NA	P-0025139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	340	487	0	ENST00000575354.2:c.4613C>T	p.Pro1538Leu	p.P1538L	ENST00000575354	NM_015125.3	1538	cCg/cTg	20/20	0.834467741078298	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.834467741078298	1		487	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579702	7579702	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	345	560	0	ENST00000269305.4:c.94del	p.Leu32CysfsTer12	p.L32Cfs*12	ENST00000269305	NM_001126112.2	32	Ctg/tg	3/11	0.7967474772781	1	FACETS	0.943	0.908	0.977	0.943	0.908	0.977	CLONAL	1	TRUE	0	0.834467741078298	1		560	511	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642558	117642558	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0025139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	441	682	0	ENST00000368508.3:c.5642-1G>T		p.X1881_splice	ENST00000368508	NM_002944.2	1881			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.834467741078298	2		682	1045	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0025140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	26	820	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	1	2	FACETS	0.616	0.486	0.766	0.616	0.486	0.766	SUBCLONAL	1	TRUE	1	0.14	2		820	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578502	7578502	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555526241	NA	P-0025140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	26	1127	0	ENST00000269305.4:c.428T>G	p.Val143Gly	p.V143G	ENST00000269305	NM_001126112.2	143	gTg/gGg	5/11	1	2	FACETS	0.559	0.441	0.695	0.559	0.441	0.695	SUBCLONAL	1	TRUE	1	0.14	2		1127	665	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431642	6431642	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	21	613	0	ENST00000356142.4:c.195C>A	p.Asp65Glu	p.D65E	ENST00000356142	NM_018890.3	65	gaC/gaA	3/7	0.3	2	FACETS	0.758	0.582	0.962			1	CLONAL	1	TRUE	NA	0.14	2		613	396	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0025143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	427	454	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	0.846003802395002	3	FACETS	0.956	0.92	0.992	0.956	0.92	0.992	CLONAL	2	TRUE	1	0.846003802395002	3		454	751	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303766	65303766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	207	468	13	ENST00000342505.4:c.2989C>T	p.Arg997Trp	p.R997W	ENST00000342505	NM_002227.2	997	Cgg/Tgg	22/25	1	2	FACETS	0.952	0.892	1	0.952	0.892	1	CLONAL	1	TRUE	1	0.846003802395002	2		481	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578196	7578196	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	288	817	0	ENST00000269305.4:c.653T>A	p.Val218Glu	p.V218E	ENST00000269305	NM_001126112.2	218	gTg/gAg	6/11	0.367329368055138	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.367329368055138	2		817	770	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523292	176523292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1172824038	NA	P-0025144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	201	780	0	ENST00000292408.4:c.1949G>A	p.Arg650His	p.R650H	ENST00000292408	NM_213647.1	650	cGc/cAc	15/18	0.367329368055138	3	FACETS	1	0.988	1	0.671	0.622	0.722	CLONAL	1	TRUE	1	0.367329368055138	3		780	965	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813248	89813248	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs369979902	NA	P-0025144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	48	663	0	ENST00000389301.3:c.3399C>G	p.His1133Gln	p.H1133Q	ENST00000389301	NM_000135.2	1133	caC/caG	34/43	0.353655992514152	2	FACETS	0.359	0.303	0.421	0.179	0.151	0.211	SUBCLONAL	1	TRUE	0	0.367329368055138	2		663	728	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157827	106157827	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs967732016	NA	P-0025144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	143	320	0	ENST00000380013.4:c.2728C>A	p.Gln910Lys	p.Q910K	ENST00000380013	NM_001127208.2	910	Caa/Aaa	3/11	0.353549811025664	3	FACETS	0.868	0.802	0.935	0.868	0.802	0.935	CLONAL	3	TRUE	0	0.367329368055138	3		320	354	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231462	46231462	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	311	339	0	ENST00000334344.6:c.1306del	p.Ile436LeufsTer4	p.I436Lfs*4	ENST00000334344	NM_152641.2	434	acA/ac	10/21	0.616564963244146	3	FACETS	0.88	0.835	0.926	0.88	0.835	0.926	CLONAL	2	TRUE	1	0.616564963244146	3		339	750	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981116	201981117	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	278	657	0	ENST00000359651.3:c.197dup	p.Trp67LeufsTer25	p.W67Lfs*25	ENST00000359651		65	-/T	2/8	1	2	FACETS	0.875	0.822	0.929	0.875	0.822	0.929	CLONAL	1	TRUE	1	0.616564963244146	2		657	1031	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918430	94918430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758607294	NA	P-0025145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	81	472	0	ENST00000536441.1:c.752G>A	p.Ser251Asn	p.S251N	ENST00000536441	NM_144665.3	251	aGc/aAc	5/10	1	2	FACETS	0.327	0.288	0.37	0.327	0.288	0.37	SUBCLONAL	1	TRUE	1	0.616564963244146	2		472	803	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378559	25378559	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs387907206	NA	P-0025145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	458	506	0	ENST00000311936.3:c.439A>G	p.Lys147Glu	p.K147E	ENST00000311936	NM_004985.3	147	Aag/Gag	4/5	0.0764674508249954	6	FACETS	1	0.965	1			1	INDETERMINATE	3	TRUE	NA	0.616564963244146	6		506	1096	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29002006	29002006	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	339	514	0	ENST00000282397.4:c.1159G>A	p.Gly387Ser	p.G387S	ENST00000282397	NM_002019.4	387	Ggc/Agc	9/30	0.379582067694886	3	FACETS	1	0.993	1	0.666	0.631	0.702	CLONAL	1	TRUE	1	0.616564963244146	3		514	1080	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532474	63532474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757100957	NA	P-0025145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	369	665	1	ENST00000307078.5:c.2105G>A	p.Arg702His	p.R702H	ENST00000307078	NM_004655.3	702	cGc/cAc	8/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.616564963244146	2		666	1117	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522726	67522726	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	106	221	0	ENST00000274335.5:c.223G>T	p.Glu75Ter	p.E75*	ENST00000274335		75	Gaa/Taa	1/15	1	2	FACETS	0.849	0.767	0.935	0.849	0.767	0.935	CLONAL	1	TRUE	1	0.616564963244146	2		221	405	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591108	67591134	+	inframe_deletion	In_Frame_Del	DEL	ACCAGACCTTATCCAGCTGAGAAAGAC	ACCAGACCTTATCCAGCTGAGAAAGAC	-	novel	NA	P-0025145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	96	305	0	ENST00000274335.5:c.1701_1727del	p.Pro568_Thr576del	p.P568_T576del	ENST00000274335		567	aaACCAGACCTTATCCAGCTGAGAAAGACg/aag	12/15	1	2	FACETS	0.639	0.572	0.711	0.639	0.572	0.711	SUBCLONAL	1	TRUE	1	0.616564963244146	2		305	487	SUCCESS
APC	324	MSKCC	GRCh37	5	112175236	112175237	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	C	novel	NA	P-0025145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	234	235	0	ENST00000257430.4:c.3945_3946delinsC	p.Ala1316LeufsTer5	p.A1316Lfs*5	ENST00000257430	NM_000038.5	1315	tcAGct/tcCct	16/16	0.561664016221274	2	FACETS	0.906	0.859	0.952	0.906	0.859	0.952	CLONAL	2	TRUE	0	0.616564963244146	2		235	419	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121541	2121541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334081822	NA	P-0025146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	59	793	2	ENST00000219476.3:c.1870G>A	p.Asp624Asn	p.D624N	ENST00000219476	NM_000548.3	624	Gac/Aac	18/42	0.24552081317637	4	FACETS	0.614	0.526	0.71			1	SUBCLONAL	1	FALSE	NA	0.244409382928698	4		795	979	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0025149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	45	403	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.294451974403565	2		403	208	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0025149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	311	567	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.259990122271972	3	FACETS	0.886	0.838	0.935	0.886	0.838	0.935	CLONAL	3	TRUE	0	0.294451974403565	3		567	912	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0025149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	110	400	2	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.294451974403565	2		402	501	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858279	27858279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	119	451	0	ENST00000359303.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000359303	NM_003535.2	98	Gag/Aag	1/1	0.130817549565845	3	FACETS	1	0.974	1	0.612	0.552	0.674	INDETERMINATE	1	TRUE	1	0.294451974403565	3		451	758	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873782	151873782	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0025149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	89	356	0	ENST00000262189.6:c.8756C>G	p.Ser2919Ter	p.S2919*	ENST00000262189	NM_170606.2	2919	tCa/tGa	38/59	0.10285822537676	4	FACETS	1	0.967	1	0.622	0.552	0.697	INDETERMINATE	1	TRUE	2	0.294451974403565	4		356	629	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627392	14627392	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	233	652	0	ENST00000254322.2:c.678G>C	p.Gln226His	p.Q226H	ENST00000254322	NM_006145.1	226	caG/caC	2/3	0.169234573257999	2	FACETS	1	0.991	1	0.707	0.659	0.757	INDETERMINATE	1	TRUE	0	0.294451974403565	2		652	1119	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437213	52437213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	144	660	0	ENST00000460680.1:c.1831G>A	p.Glu611Lys	p.E611K	ENST00000460680	NM_004656.3	611	Gag/Aag	14/17	0.155641284378649	4	FACETS	1	0.984	1	0.688	0.627	0.752	INDETERMINATE	1	TRUE	2	0.294451974403565	4		660	920	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001452	150001452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	171	636	0	ENST00000253339.5:c.2152G>A	p.Glu718Lys	p.E718K	ENST00000253339		718	Gaa/Aaa	4/7	0.130817549565845	3	FACETS	1	0.982	1	0.619	0.569	0.672	INDETERMINATE	1	TRUE	1	0.294451974403565	3		636	1076	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578496	7578496	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782197	NA	P-0025150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	261	953	0	ENST00000269305.4:c.434T>C	p.Leu145Pro	p.L145P	ENST00000269305	NM_001126112.2	145	cTg/cCg	5/11	0.569162063949943	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.569162063949943	1		953	627	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878877	117878877	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	94	536	0	ENST00000297338.2:c.92A>G	p.His31Arg	p.H31R	ENST00000297338	NM_006265.2	31	cAt/cGt	2/14	0.382197107341321	1	FACETS	0.459	0.409	0.511	0.459	0.409	0.511	SUBCLONAL	1	TRUE	0	0.569162063949943	1		536	515	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0025151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	53	493	1	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	1	2	FACETS	0.898	0.767	1	0.898	0.767	1	CLONAL	1	TRUE	1	0.23	2		494	513	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0025152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3907	700	676	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.506109536578193	25	FACETS	1	0.976	1			1	CLONAL	4	TRUE	NA	0.506109536578193	25		676	4607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577587	7577587	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	264	692	2	ENST00000269305.4:c.694A>T	p.Ile232Phe	p.I232F	ENST00000269305	NM_001126112.2	232	Atc/Ttc	7/11	0.301645575591899	3	FACETS	1	0.981	1	0.723	0.683	0.763	INDETERMINATE	2	TRUE	0	0.506109536578193	3		694	603	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514515	103514515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	49	312	0	ENST00000355739.4:c.1016C>T	p.Pro339Leu	p.P339L	ENST00000355739	NM_000123.3	339	cCt/cTt	8/15	0.486959726423825	3	FACETS	0.707	0.602	0.823	0.354	0.301	0.412	SUBCLONAL	1	TRUE	1	0.506109536578193	3		312	343	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162249	47162249	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	205	588	1	ENST00000409792.3:c.3877T>A	p.Tyr1293Asn	p.Y1293N	ENST00000409792	NM_014159.6	1293	Tat/Aat	3/21	0.438329424201151	5	FACETS	0.876	0.815	0.94	0.584	0.543	0.627	CLONAL	2	TRUE	2	0.506109536578193	5		589	813	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197184	106197187	+	frameshift_variant	Frame_Shift_Del	DEL	TGCA	TGCA	-	novel	NA	P-0025152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	218	384	0	ENST00000380013.4:c.5517_5520del	p.Ala1840ArgfsTer46	p.A1840Rfs*46	ENST00000380013	NM_001127208.2	1839	ggTGCA/gg	11/11	0.455776869107297	4	FACETS	1	0.988	1	0.612	0.574	0.65	CLONAL	2	TRUE	0	0.506109536578193	4		384	530	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618954	37618954	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	444	621	0	ENST00000447079.4:c.630C>A	p.Tyr210Ter	p.Y210*	ENST00000447079	NM_015083.1	210	taC/taA	1/14	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.770850717574635	2		621	913	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619371	37619371	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0025153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	169	323	1	ENST00000447079.4:c.1046+1G>T		p.X349_splice	ENST00000447079	NM_015083.1	349			1	2	FACETS	0.893	0.828	0.96	0.893	0.828	0.96	CLONAL	1	TRUE	1	0.770850717574635	2		324	491	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631557	119631562	+	inframe_deletion	In_Frame_Del	DEL	TAGAGG	TAGAGG	-	novel	NA	P-0025153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	226	360	0	ENST00000316626.5:c.704_709del	p.Thr235_Ser236del	p.T235_S236del	ENST00000316626		235	aCCTCTAgt/agt	6/12	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.770850717574635	2		360	569	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31946709	31946709	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	371	702	0	ENST00000375333.2:c.597A>T	p.Arg199Ser	p.R199S	ENST00000375333	NM_032454.1	199	agA/agT	4/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.770850717574635	2		702	893	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0025154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	37	552	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.527	0.433	0.633	0.527	0.433	0.633	SUBCLONAL	1	TRUE	1	0.19	2		552	739	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266713	198266713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776846119	NA	P-0025154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	46	470	0	ENST00000335508.6:c.2219G>A	p.Gly740Glu	p.G740E	ENST00000335508	NM_012433.2	740	gGa/gAa	15/25	1	2	FACETS	0.703	0.591	0.827	0.703	0.591	0.827	SUBCLONAL	1	TRUE	1	0.19	2		470	689	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242474	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGA	GAATTAAGA	-	rs121913436	NA	P-0025155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	85	586	0	ENST00000275493.2:c.2239_2247del	p.Leu747_Glu749del	p.L747_E749del	ENST00000275493	NM_005228.3	746	GAATTAAGA/-	19/28	0.290519697051959	5	FACETS	0.76	0.673	0.852	0.506	0.448	0.568	SUBCLONAL	2	TRUE	2	0.290519697051959	5		586	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579316	7579317	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0025156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	279	579	0	ENST00000269305.4:c.370dup	p.Cys124LeufsTer25	p.C124Lfs*25	ENST00000269305	NM_001126112.2	124	tgc/tTgc	4/11	0.473910159906035	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.492653696334234	4		579	823	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374298	138374298	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	153	681	0	ENST00000289153.2:c.3146T>G	p.Leu1049Arg	p.L1049R	ENST00000289153	NM_006219.2	1049	cTc/cGc	22/22	0.492653696334234	4	FACETS	0.994	0.909	1	0.248	0.227	0.271	CLONAL	1	TRUE	0	0.492653696334234	4		681	933	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567555939	NA	P-0025156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	360	768	0	ENST00000269305.4:c.310del	p.Gln104ArgfsTer19	p.Q104Rfs*19	ENST00000269305	NM_001126112.2	104	Cag/ag	4/11	0.473910159906035	4	FACETS	0.971	0.922	1	0.971	0.922	1	CLONAL	2	TRUE	2	0.492653696334234	4		768	1123	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038330	180038330	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0025156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	117	475	0	ENST00000261937.6:c.3686+1G>T		p.X1229_splice	ENST00000261937	NM_182925.4	1229			0.470408927226754	4	FACETS	1	0.956	1	0.367	0.331	0.405	CLONAL	1	TRUE	1	0.492653696334234	4		475	644	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163836	32163836	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	129	491	0	ENST00000375023.3:c.5390A>T	p.Asp1797Val	p.D1797V	ENST00000375023	NM_004557.3	1797	gAc/gTc	30/30	0.492653696334234	4	FACETS	1	0.928	1	0.342	0.31	0.376	CLONAL	1	TRUE	1	0.492653696334234	4		491	762	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0025157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	338	466	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.89099570133166	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.915159062353927	1		466	377	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727455	66727455	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs869025608	NA	P-0025157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	206	419	1	ENST00000307102.5:c.171G>T	p.Lys57Asn	p.K57N	ENST00000307102	NM_002755.3	57	aaG/aaT	2/11	0.462578118144624	3	FACETS	1	0.987	1	0.61	0.57	0.65	INDETERMINATE	1	TRUE	1	0.915159062353927	3		420	538	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0025157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	239	443	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.286546486707524	2	FACETS	1	0.993	1	0.643	0.611	0.675	INDETERMINATE	1	TRUE	0	0.915159062353927	2		444	406	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953650	32953650	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	580	426	0	ENST00000380152.3:c.8951C>T	p.Ser2984Leu	p.S2984L	ENST00000380152		2984	tCa/tTa	22/27	0.915159062353927	5	FACETS	1	0.996	1	0.614	0.592	0.636	CLONAL	2	TRUE	1	0.915159062353927	5		426	1225	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557411	95557411	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	330	555	1	ENST00000393063.1:c.5563C>T	p.Arg1855Ter	p.R1855*	ENST00000393063	NM_030621.3	1855	Cga/Tga	27/28	0.261921907352781	4	FACETS	0.904	0.859	0.949	0.904	0.859	0.949	INDETERMINATE	2	TRUE	2	0.915159062353927	4		556	764	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584538	48584539	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	315	542	0	ENST00000342988.3:c.713dup	p.Leu238PhefsTer26	p.L238Ffs*26	ENST00000342988	NM_005359.5	237	-/T	6/12	0.915159062353927	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.915159062353927	1		542	359	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721513	49721513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1409047630	NA	P-0025157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	319	638	0	ENST00000449682.2:c.2126C>T	p.Thr709Met	p.T709M	ENST00000449682	NM_020998.3	709	aCg/aTg	18/18	0.226539619959105	4	FACETS	0.934	0.888	0.98	0.934	0.888	0.98	INDETERMINATE	2	TRUE	2	0.915159062353927	4		638	715	SUCCESS
APC	324	MSKCC	GRCh37	5	112175610	112175619	+	frameshift_variant	Frame_Shift_Del	DEL	CACCACCTCC	CACCACCTCC	AACACCTCG	novel	NA	P-0025157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	98	362	0	ENST00000257430.4:c.4319_4328delinsAACACCTCG	p.Pro1440GlnfsTer33	p.P1440Qfs*33	ENST00000257430	NM_000038.5	1440	cCACCACCTCCt/cAACACCTCGt	16/16	0.286546486707524	2	FACETS	0.588	0.529	0.65	0.294	0.264	0.325	INDETERMINATE	1	TRUE	0	0.915159062353927	2		362	364	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649566	206649566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1464747771	NA	P-0025158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	87	474	0	ENST00000367120.3:c.401G>A	p.Arg134His	p.R134H	ENST00000367120	NM_014002.3	134	cGc/cAc	6/22	0.295711498603949	5	FACETS	0.914	0.814	1	0.61	0.542	0.68	CLONAL	2	TRUE	2	0.339530230221559	5		474	423	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	97	234	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	0.339530230221559	5	FACETS	1	0.942	1	0.715	0.642	0.792	CLONAL	2	TRUE	2	0.339530230221559	5		234	402	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933445	39933445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1177018779	NA	P-0025158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	44	507	4	ENST00000378444.4:c.1154C>T	p.Ala385Val	p.A385V	ENST00000378444	NM_001123385.1	385	gCg/gTg	4/15	0.299148476186129	0	FACETS	0.984	0.838	1			1	CLONAL	1	TRUE	0	0.339530230221559	0		511	174	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428521	72428530	+	frameshift_variant	Frame_Shift_Del	DEL	GGTGGCATAC	GGTGGCATAC	-	novel	NA	P-0025158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	107	472	0	ENST00000477973.2:c.472_481del	p.Gln158HisfsTer47	p.Q158Hfs*47	ENST00000477973	NM_012234.5	158	caGTATGCCACC/ca	2/4	0.219744863498206	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.339530230221559	2		472	297	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630252	187630252	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	53	523	0	ENST00000441802.2:c.730A>G	p.Thr244Ala	p.T244A	ENST00000441802	NM_005245.3	244	Acg/Gcg	2/27	0.343420805512775	1	FACETS	0.922	0.793	1	0.922	0.793	1	CLONAL	1	TRUE	0	0.339530230221559	1		523	281	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964492	93964492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	63	560	0	ENST00000369303.4:c.2405G>A	p.Trp802Ter	p.W802*	ENST00000369303	NM_004440.3	802	tGg/tAg	14/17	0.275492357397397	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.339530230221559	1		560	284	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412301	63412301	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	25	807	0	ENST00000330258.3:c.866C>A	p.Thr289Lys	p.T289K	ENST00000330258	NM_152424.3	289	aCa/aAa	2/2	0.299148476186129	0	FACETS	0.41	0.324	0.508			1	SUBCLONAL	1	TRUE	0	0.339530230221559	0		807	237	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	44	460	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	0.419177184530816	3	FACETS	0.853	0.739	0.97	0.853	0.739	0.97	CLONAL	2	TRUE	1	0.65146803354085	3		460	105	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106932	11106933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0025159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	66	621	0	ENST00000358026.2:c.1639dup	p.Asp547GlyfsTer17	p.D547Gfs*17	ENST00000358026	NM_001128849.1	546	aag/aaGg	10/36	0.65146803354085	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.65146803354085	1		621	122	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0025160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	325	672	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	1	2	FACETS	0.969	0.916	1	0.969	0.916	1	CLONAL	1	TRUE	1	0.649469347278524	2		672	1033	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0025160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	613	895	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	0.649469347278524	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.649469347278524	2		895	899	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482425	56482425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	234	618	0	ENST00000267101.3:c.973G>A	p.Gly325Arg	p.G325R	ENST00000267101	NM_001982.3	325	Gga/Aga	8/28	0.649469347278524	2	FACETS	1	0.956	1	0.513	0.48	0.546	CLONAL	1	TRUE	0	0.649469347278524	2		618	703	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900288	101900288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111854391	NA	P-0025160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	151	601	1	ENST00000374994.4:c.722C>T	p.Ser241Leu	p.S241L	ENST00000374994	NM_004612.2	241	tCg/tTg	4/9	1	2	FACETS	0.898	0.826	0.972	0.898	0.826	0.972	CLONAL	1	TRUE	1	0.649469347278524	2		602	518	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023873	27023873	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0025160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	88	149	1	ENST00000324856.7:c.979A>T	p.Lys327Ter	p.K327*	ENST00000324856	NM_006015.4	327	Aag/Tag	1/20	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.649469347278524	2		150	269	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094744	2094744	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	408	987	2	ENST00000219066.1:c.436G>T	p.Val146Leu	p.V146L	ENST00000219066	NM_002528.5	146	Gtg/Ttg	3/6	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.649469347278524	2		989	1177	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266041	41266672	+	splice_donor_variant,splice_acceptor_variant,stop_lost,protein_altering_variant,intron_variant	Splice_Site	DEL	CCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCAAGATGATGCAGAACTTGCCACACGTGCAATCCCTGAACTGA	CCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCAAGATGATGCAGAACTTGCCACACGTGCAATCCCTGAACTGA	-	novel	NA	P-0025160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	89	344	0	ENST00000349496.5:c.39_470del		p.X13_splice	ENST00000349496	NM_001904.3	13	gCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCAAGATGATGCAGAACTTGCCACACGTGCAATCCCTGAACTGAca/gca	3-4/15	1	2	FACETS	0.719	0.642	0.8	0.719	0.642	0.8	SUBCLONAL	1	TRUE	1	0.649469347278524	2		344	381	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70005682	70005682	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1559749017	NA	P-0025160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	121	545	3	ENST00000394351.3:c.710+1G>A		p.X237_splice	ENST00000394351	NM_000248.3	237			1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.649469347278524	2		548	355	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908891	101908891	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	223	741	0	ENST00000374994.4:c.1255G>C	p.Gly419Arg	p.G419R	ENST00000374994	NM_004612.2	419	Gga/Cga	7/9	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.649469347278524	2		741	681	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	28	606	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.148	0.118	0.184	0.148	0.118	0.184	SUBCLONAL	1	TRUE	1	0.466827096381028	2		606	808	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0025161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	94	510	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.797	0.712	0.888	0.797	0.712	0.888	SUBCLONAL	1	TRUE	1	0.466827096381028	2		510	505	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0025161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	184	552	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.976	0.902	1	0.976	0.902	1	CLONAL	1	TRUE	1	0.466827096381028	2		552	808	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0025161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	15	428	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.466827096381028	1	FACETS	0.1	0.073	0.134	0.1	0.073	0.134	SUBCLONAL	1	TRUE	0	0.466827096381028	1		428	491	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0025161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	11	229	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	1	FACETS	0.083	0.057	0.117	0.083	0.057	0.117	SUBCLONAL	1	TRUE	0	0.466827096381028	1		229	433	SUCCESS
APC	324	MSKCC	GRCh37	5	112175536	112175536	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	135	257	0	ENST00000257430.4:c.4245del	p.Ser1415ArgfsTer4	p.S1415Rfs*4	ENST00000257430	NM_000038.5	1415	agT/ag	16/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.466827096381028	2		257	432	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0025161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	138	423	0	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	0.389393143620071	1	FACETS	0.896	0.82	0.974	0.896	0.82	0.974	CLONAL	1	TRUE	0	0.466827096381028	1		423	506	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16056703	16056704	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	100	459	0	ENST00000268712.3:c.738dup	p.Ala247SerfsTer6	p.A247Sfs*6	ENST00000268712	NM_006311.3	246	-/A	7/46	0.42853486593215	1	FACETS	0.803	0.722	0.888	0.803	0.722	0.888	CLONAL	1	TRUE	0	0.466827096381028	1		459	409	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004982	16004982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	73	564	0	ENST00000268712.3:c.2272G>A	p.Glu758Lys	p.E758K	ENST00000268712	NM_006311.3	758	Gaa/Aaa	20/46	0.42853486593215	1	FACETS	0.336	0.293	0.382	0.336	0.293	0.382	SUBCLONAL	1	TRUE	0	0.466827096381028	1		564	714	SUCCESS
APC	324	MSKCC	GRCh37	5	112163688	112163688	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	129	345	0	ENST00000257430.4:c.1611del	p.Ser537ArgfsTer12	p.S537Rfs*12	ENST00000257430	NM_000038.5	537	agT/ag	13/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.466827096381028	2		345	493	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938121	76938121	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	306	332	0	ENST00000373344.5:c.2627C>G	p.Ser876Cys	p.S876C	ENST00000373344	NM_000489.3	876	tCt/tGt	9/35	1	1	FACETS	0.945	0.902	0.986	1	0.996	1	CLONAL	2	TRUE	0	0.466827096381028	1		332	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	454	670	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.935102023624223	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	0	0.935102023624223	1		671	509	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245843	46245843	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	384	404	0	ENST00000334344.6:c.3937C>T	p.Gln1313Ter	p.Q1313*	ENST00000334344	NM_152641.2	1313	Caa/Taa	15/21	0.935102023624223	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	FALSE	0	0.935102023624223	1		404	421	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980844	40980844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	272	565	0	ENST00000373198.4:c.1642G>A	p.Glu548Lys	p.E548K	ENST00000373198	NM_133170.3	548	Gaa/Aaa	10/32	0.416951776675601	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.935102023624223	0		565	602	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	444	428	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.935102023624223	2		428	917	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	132	218	0				ENST00000310581	NM_198253.2	-/1132			0.173017593797929	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.935102023624223	0		218	229	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346589	81346589	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	380	514	1	ENST00000222390.5:c.1364G>A	p.Gly455Glu	p.G455E	ENST00000222390	NM_000601.4	455	gGa/gAa	11/18	1	2	FACETS	0.98	0.936	1	0.98	0.936	1	CLONAL	1	FALSE	1	0.935102023624223	2		515	829	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2952942	2952942	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	285	675	0	ENST00000396946.4:c.2998G>A	p.Glu1000Lys	p.E1000K	ENST00000396946	NM_032415.4	1000	Gag/Aag	22/25	0.716416601097479	1	FACETS	0.556	0.528	0.584	0.556	0.528	0.584	SUBCLONAL	1	FALSE	0	0.935102023624223	1		675	584	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509612	106509612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	385	580	0	ENST00000359195.3:c.1606C>T	p.Pro536Ser	p.P536S	ENST00000359195	NM_002649.2	536	Cct/Tct	2/11	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	FALSE	NA	0.935102023624223	2		580	807	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484270	8484270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867884876	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	459	606	1	ENST00000356435.5:c.3262C>T	p.Arg1088Cys	p.R1088C	ENST00000356435		1088	Cgt/Tgt	19/35	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	1	FALSE	NA	0.935102023624223	2		607	823	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729162	66729163	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	465	821	3	ENST00000307102.5:c.370_371delinsTT	p.Pro124Leu	p.P124L	ENST00000307102	NM_002755.3	124	CCg/TTg	3/11	1	2	FACETS	0.91	0.872	0.948	0.91	0.872	0.948	CLONAL	1	FALSE	1	0.935102023624223	2		824	1093	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367234	50367234	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	130	365	0	ENST00000331340.3:c.41G>A	p.Gly14Glu	p.G14E	ENST00000331340	NM_006060.4	14	gGg/gAg	3/8	0.348971092045809	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.935102023624223	0		365	336	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624541	93624541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	233	510	0	ENST00000375746.1:c.632G>A	p.Gly211Glu	p.G211E	ENST00000375746	NM_001174167.1	211	gGg/gAg	4/14	1	2	FACETS	0.975	0.919	1	0.975	0.919	1	CLONAL	1	FALSE	1	0.935102023624223	2		510	511	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612807	228612807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	424	670	0	ENST00000366696.1:c.220G>A	p.Glu74Lys	p.E74K	ENST00000366696	NM_003493.2	74	Gag/Aag	1/1	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.935102023624223	2		670	850	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717705	89717705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064794675	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	445	541	1	ENST00000371953.3:c.730C>T	p.Pro244Ser	p.P244S	ENST00000371953	NM_000314.4	244	Cct/Tct	7/9	1	2	FACETS	0.981	0.941	1	0.981	0.941	1	CLONAL	1	FALSE	1	0.935102023624223	2		542	970	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249881	110249881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	314	477	1	ENST00000374672.4:c.794C>T	p.Pro265Leu	p.P265L	ENST00000374672	NM_004235.4	265	cCc/cTc	3/5	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.935102023624223	2		478	631	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546694	9546694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs942131023	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	189	307	0	ENST00000353224.5:c.1328G>A	p.Gly443Glu	p.G443E	ENST00000353224	NM_177990.2	443	gGa/gAa	5/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.935102023624223	2		307	375	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710750	117710750	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	265	425	0	ENST00000368508.3:c.1522G>A	p.Asp508Asn	p.D508N	ENST00000368508	NM_002944.2	508	Gac/Aac	12/43	NA	2	FACETS	1	0.963	1			1	INDETERMINATE	1	FALSE	NA	0.935102023624223	2		425	555	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911493	32911493	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	438	492	0	ENST00000380152.3:c.3001T>C	p.Ser1001Pro	p.S1001P	ENST00000380152		1001	Tca/Cca	11/27	NA	2	FACETS	0.864	0.826	0.902			1	INDETERMINATE	1	FALSE	NA	0.935102023624223	2		492	1084	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961969	41961969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1306489330	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	509	495	1	ENST00000219905.7:c.877C>T	p.Arg293Cys	p.R293C	ENST00000219905	NM_001164273.1	293	Cgt/Tgt	2/24	1	2	FACETS	0.997	0.958	1	0.997	0.958	1	CLONAL	1	FALSE	1	0.935102023624223	2		496	1092	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745117	41745117	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	390	753	0	ENST00000301178.4:c.1183G>A	p.Gly395Arg	p.G395R	ENST00000301178	NM_021913.4	395	Ggg/Agg	9/20	1	2	FACETS	0.949	0.906	0.992	0.949	0.906	0.992	CLONAL	1	FALSE	1	0.935102023624223	2		753	879	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868119	45868119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373346316	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	509	862	2	ENST00000391945.4:c.571C>T	p.Pro191Ser	p.P191S	ENST00000391945	NM_000400.3	191	Cca/Tca	7/23	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.935102023624223	2		864	1071	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384996	31384996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1169940446	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	300	513	1	ENST00000328111.2:c.1381C>T	p.Arg461Cys	p.R461C	ENST00000328111	NM_006892.3	461	Cgc/Tgc	14/23	1	2	FACETS	0.977	0.927	1	0.977	0.927	1	CLONAL	1	FALSE	1	0.935102023624223	2		514	657	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419877	41419878	+	missense_variant	Missense_Mutation	DNP	CT	CT	TA	novel	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	234	544	1	ENST00000373198.4:c.443_444delinsTA	p.Lys148Ile	p.K148I	ENST00000373198	NM_133170.3	148	aAG/aTA	3/32	0.416951776675601	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.935102023624223	0		545	528	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62293236	62293236	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	525	681	0	ENST00000360203.5:c.335C>A	p.Ala112Asp	p.A112D	ENST00000360203	NM_001283009.1	112	gCc/gAc	4/35	NA	2	FACETS	0.999	0.961	1			1	INDETERMINATE	1	FALSE	NA	0.935102023624223	2		681	1124	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12393114	12393114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	416	700	0	ENST00000287820.6:c.23C>T	p.Ser8Phe	p.S8F	ENST00000287820	NM_015869.4	8	tCt/tTt	1/7	1	2	FACETS	0.952	0.91	0.993	0.952	0.91	0.993	CLONAL	1	FALSE	1	0.935102023624223	2		700	935	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69788756	69788757	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	323	409	1	ENST00000352241.4:c.8_9delinsTT	p.Ser3Phe	p.S3F	ENST00000352241	NM_198159.2	3	tCC/tTT	1/10	0.20073132092614	3	FACETS	1	0.995	1	0.749	0.713	0.785	INDETERMINATE	1	FALSE	1	0.935102023624223	3		410	677	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629805	187629805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773408982	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	678	785	1	ENST00000441802.2:c.1177C>T	p.Pro393Ser	p.P393S	ENST00000441802	NM_005245.3	393	Cct/Tct	2/27	0.935102023624223	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	FALSE	0	0.935102023624223	1		786	729	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876230	35876230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753614229	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	291	496	0	ENST00000303115.3:c.1022G>A	p.Gly341Glu	p.G341E	ENST00000303115	NM_002185.3	341	gGa/gAa	8/8	NA	2	FACETS	1	0.953	1			1	INDETERMINATE	1	FALSE	NA	0.935102023624223	2		496	620	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911302	29911302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41546018	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	90	495	0	ENST00000376809.5:c.601G>A	p.Glu201Lys	p.E201K	ENST00000376809	NM_002116.7	201	Gag/Aag	3/8	NA	2	FACETS	0.39	0.347	0.435			1	INDETERMINATE	1	FALSE	NA	0.935102023624223	2		495	494	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183063	32183063	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	518	1003	4	ENST00000375023.3:c.1961G>A	p.Gly654Glu	p.G654E	ENST00000375023	NM_004557.3	654	gGa/gAa	12/30	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.935102023624223	2		1007	1056	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965572	93965572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	371	559	0	ENST00000369303.4:c.2356G>A	p.Asp786Asn	p.D786N	ENST00000369303	NM_004440.3	786	Gat/Aat	13/17	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.935102023624223	2		559	770	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129330	152129330	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	201	436	2	ENST00000206249.3:c.283G>A	p.Gly95Arg	p.G95R	ENST00000206249	NM_000125.3	95	Ggg/Agg	1/8	0.20073132092614	3	FACETS	1	0.989	1	0.639	0.598	0.68	INDETERMINATE	1	FALSE	1	0.935102023624223	3		438	494	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528952	157528952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1263114512	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	369	492	0	ENST00000346085.5:c.6677C>T	p.Ser2226Leu	p.S2226L	ENST00000346085	NM_020732.3	2226	tCg/tTg	20/20	0.20073132092614	3	FACETS	1	0.995	1	0.717	0.684	0.75	INDETERMINATE	1	FALSE	1	0.935102023624223	3		492	808	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415001	116415001	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1201989602	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	600	722	1	ENST00000397752.3:c.3095C>T	p.Ser1032Phe	p.S1032F	ENST00000397752	NM_000245.2	1032	tCc/tTc	15/21	NA	2	FACETS	0.955	0.92	0.99			1	INDETERMINATE	1	FALSE	NA	0.935102023624223	2		723	1344	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845361	151845362	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	362	611	1	ENST00000262189.6:c.13650_13651delinsAA	p.Gly4551Ser	p.G4551S	ENST00000262189	NM_170606.2	4550	gtGGgt/gtAAgt	52/59	1	2	FACETS	0.867	0.825	0.909	0.867	0.825	0.909	CLONAL	1	FALSE	1	0.935102023624223	2		612	893	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863061	56863061	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	23	699	0	ENST00000519728.1:c.328del	p.Glu110LysfsTer15	p.E110Kfs*15	ENST00000519728	NM_002350.3	110	Gaa/aa	5/13	0.935102023624223	1	FACETS	0.059	0.046	0.075	0.059	0.046	0.075	SUBCLONAL	1	FALSE	0	0.935102023624223	1		699	442	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863061	56863061	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	368	699	0	ENST00000519728.1:c.328G>A	p.Glu110Lys	p.E110K	ENST00000519728	NM_002350.3	110	Gaa/Aaa	5/13	0.935102023624223	1	FACETS	0.948	0.923	0.972	0.948	0.923	0.972	CLONAL	1	FALSE	0	0.935102023624223	1		699	442	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970993	70970993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	500	828	0	ENST00000276594.2:c.1268C>T	p.Pro423Leu	p.P423L	ENST00000276594	NM_024504.3	423	cCc/cTc	6/8	0.935102023624223	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	0	0.935102023624223	1		828	566	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27173277	27173277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1364054872	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	548	792	0	ENST00000380036.4:c.818G>A	p.Gly273Glu	p.G273E	ENST00000380036	NM_000459.3	273	gGa/gAa	6/23	1	2	FACETS	0.952	0.916	0.988	0.952	0.916	0.988	CLONAL	1	FALSE	1	0.935102023624223	2		792	1231	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285689	87285689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	296	545	0	ENST00000277120.3:c.26G>A	p.Gly9Glu	p.G9E	ENST00000277120		9	gGa/gAa	2/19	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.935102023624223	2		545	630	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637113	93637113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	305	520	0	ENST00000375746.1:c.1163G>A	p.Gly388Asp	p.G388D	ENST00000375746	NM_001174167.1	388	gGc/gAc	9/14	1	2	FACETS	0.997	0.948	1	0.997	0.948	1	CLONAL	1	FALSE	1	0.935102023624223	2		520	654	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613674	100613674	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	324	235	0	ENST00000308731.7:c.905G>A	p.Gly302Glu	p.G302E	ENST00000308731	NM_000061.2	302	gGa/gAa	11/19	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	0	0.935102023624223	1		235	358	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711873	89711873	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs587781784	NA	P-0025165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	83	498	0	ENST00000371953.3:c.493-2A>G		p.X165_splice	ENST00000371953	NM_000314.4	165			0.291323525000714	2	FACETS	1	0.957	1	0.582	0.517	0.651	CLONAL	1	TRUE	0	0.370526350317011	2		498	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579359	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0025165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	110	616	0	ENST00000269305.4:c.328dup	p.Arg110ProfsTer39	p.R110Pfs*39	ENST00000269305	NM_001126112.2	110	cgt/cCgt	4/11	0.291323525000714	2	FACETS	0.777	0.704	0.853	0.777	0.704	0.853	SUBCLONAL	2	TRUE	0	0.370526350317011	2		616	382	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113179	209113179	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775517144	NA	P-0025165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	29	466	0	ENST00000345146.2:c.328G>A	p.Glu110Lys	p.E110K	ENST00000345146	NM_005896.2	110	Gaa/Aaa	4/10	0.291323525000714	2	FACETS	0.36	0.288	0.441	0.18	0.144	0.221	SUBCLONAL	1	TRUE	0	0.370526350317011	2		466	435	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0025168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	672	364	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.490585665587959	6	FACETS	1	0.969	1	1	0.969	1	CLONAL	4	TRUE	2	0.490585665587959	6		364	1354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0025168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	494	917	4	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.4791543614668	2	FACETS	0.989	0.951	1	0.989	0.951	1	CLONAL	2	TRUE	0	0.490585665587959	2		921	1018	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727072	243727072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773474217	NA	P-0025168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	196	641	4	ENST00000263826.5:c.898G>A	p.Ala300Thr	p.A300T	ENST00000263826	NM_005465.4	300	Gca/Aca	9/13	0.417435945384424	4	FACETS	0.972	0.898	1	0.486	0.449	0.525	CLONAL	1	TRUE	2	0.490585665587959	4		645	1225	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214674	133214674	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	168	652	2	ENST00000320574.5:c.5604C>A	p.Phe1868Leu	p.F1868L	ENST00000320574	NM_006231.2	1868	ttC/ttA	41/49	0.490585665587959	3	FACETS	1	0.974	1	0.568	0.523	0.615	CLONAL	1	TRUE	1	0.490585665587959	3		654	751	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62311258	62311258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs761998383	NA	P-0025168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	117	503	1	ENST00000360203.5:c.1094T>C	p.Ile365Thr	p.I365T	ENST00000360203	NM_001283009.1	365	aTc/aCc	13/35	0.488497471274509	3	FACETS	0.95	0.859	1	0.475	0.429	0.523	CLONAL	1	TRUE	1	0.490585665587959	3		504	625	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0025169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	329	552	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.446349364810959	2	FACETS	0.814	0.778	0.849	0.814	0.778	0.849	CLONAL	2	TRUE	0	0.692446853681058	2		552	584	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683697	162683697	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528661586	NA	P-0025169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	65	601	0	ENST00000366898.1:c.272C>T	p.Ala91Val	p.A91V	ENST00000366898	NM_004562.2	91	gCg/gTg	3/12	0.189757498030504	4	FACETS	0.885	0.772	1	0.443	0.386	0.503	INDETERMINATE	1	TRUE	2	0.692446853681058	4		601	359	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248450	212248450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1480034665	NA	P-0025169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	53	278	1	ENST00000342788.4:c.3817C>T	p.Arg1273Trp	p.R1273W	ENST00000342788	NM_005235.2	1273	Cgg/Tgg	28/28	0.278555912458106	3	FACETS	0.612	0.524	0.706	0.204	0.174	0.236	INDETERMINATE	1	TRUE	0	0.692446853681058	3		279	337	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982409	201982409	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	143	780	0	ENST00000359651.3:c.788G>A	p.Gly263Asp	p.G263D	ENST00000359651		263	gGc/gAc	6/8	0.692446853681058	5	FACETS	0.765	0.697	0.838	0.191	0.174	0.21	SUBCLONAL	1	TRUE	1	0.692446853681058	5		780	1100	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711314	114711314	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	152	454	0	ENST00000543371.1:c.329A>T	p.Asp110Val	p.D110V	ENST00000543371	NM_001198531.1	110	gAc/gTc	3/14	0.310483930367723	2	FACETS	1	0.99	1	0.72	0.671	0.769	INDETERMINATE	1	TRUE	0	0.692446853681058	2		454	305	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215712	133215712	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs185498408	NA	P-0025169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	136	369	0	ENST00000320574.5:c.5551C>T	p.Gln1851Ter	p.Q1851*	ENST00000320574	NM_006231.2	1851	Cag/Tag	40/49	0.345586040791439	2	FACETS	0.786	0.731	0.839	0.786	0.731	0.839	INDETERMINATE	2	TRUE	0	0.692446853681058	2		369	250	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913337	28913337	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1257	71	770	0	ENST00000282397.4:c.2456A>T	p.Lys819Met	p.K819M	ENST00000282397	NM_002019.4	819	aAg/aTg	17/30	0.692446853681058	6	FACETS	0.368	0.32	0.421	0.092	0.08	0.106	SUBCLONAL	1	TRUE	2	0.692446853681058	6		770	1328	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728803	39728803	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	54	454	1	ENST00000361337.2:c.1083C>A	p.Phe361Leu	p.F361L	ENST00000361337	NM_003286.2	361	ttC/ttA	12/21	0.692446853681058	3	FACETS	0.367	0.313	0.426	0.184	0.156	0.213	SUBCLONAL	1	TRUE	1	0.692446853681058	3		455	572	SUCCESS
APC	324	MSKCC	GRCh37	5	112175924	112175924	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	38	250	0	ENST00000257430.4:c.4633T>C	p.Ser1545Pro	p.S1545P	ENST00000257430	NM_000038.5	1545	Tca/Cca	16/16	0.278555912458106	3	FACETS	0.803	0.672	0.946	0.268	0.224	0.316	INDETERMINATE	1	TRUE	0	0.692446853681058	3		250	184	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279363	38279363	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	104	835	1	ENST00000425967.3:c.1126A>G	p.Asn376Asp	p.N376D	ENST00000425967	NM_001174067.1	376	Aac/Gac	9/19	0.400663294741281	1	FACETS	0.418	0.376	0.462	0.418	0.376	0.462	INDETERMINATE	1	TRUE	0	0.692446853681058	1		836	470	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0025170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	237	496	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.318694424304102	4	FACETS	0.93	0.881	0.98	0.93	0.881	0.98	CLONAL	4	TRUE	0	0.396053586118482	4		496	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578204	7578204	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520001	NA	P-0025170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	201	669	0	ENST00000269305.4:c.645T>G	p.Ser215Arg	p.S215R	ENST00000269305	NM_001126112.2	215	agT/agG	6/11	0.30716823882503	3	FACETS	1	0.963	1	0.698	0.651	0.745	CLONAL	2	TRUE	0	0.396053586118482	3		669	581	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593431	55593431	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs72550822	NA	P-0025170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	24	397	1	ENST00000288135.5:c.1588G>A	p.Val530Ile	p.V530I	ENST00000288135	NM_000222.2	530	Gta/Ata	10/21	0.30088161991018	3	FACETS	0.382	0.299	0.478	0.127	0.099	0.16	SUBCLONAL	1	TRUE	0	0.396053586118482	3		398	380	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796941	45796941	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	73	568	0	ENST00000450313.1:c.1389G>C	p.Gln463His	p.Q463H	ENST00000450313	NM_012222.2	463	caG/caC	14/16	0.163117644477538	3	FACETS	0.981	0.861	1	0.327	0.287	0.37	INDETERMINATE	1	TRUE	0	0.396053586118482	3		568	450	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952148	178952158	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	ACTGAAAAGAT	ACTGAAAAGAT	-	novel	NA	P-0025170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	225	13	0	ENST00000263967.3:c.3204_*7del		p.*1068*	ENST00000263967	NM_006218.2	1068		21/21	0.287539892277928	2	FACETS	1	0.971	1	1	0.994	1	CLONAL	3	TRUE	0	0.396053586118482	2		13	367	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636869	176636869	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	75	421	0	ENST00000439151.2:c.1469A>G	p.Lys490Arg	p.K490R	ENST00000439151	NM_022455.4	490	aAg/aGg	5/23	0.13695946834342	4	FACETS	0.867	0.767	0.972	0.867	0.767	0.972	INDETERMINATE	2	TRUE	2	0.396053586118482	4		421	305	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191590	10191590	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs5030825	NA	P-0025173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	119	664	2	ENST00000256474.2:c.583C>T	p.Gln195Ter	p.Q195*	ENST00000256474	NM_000551.3	195	Cag/Tag	3/3	0.536957593678935	1	FACETS	0.775	0.705	0.847	0.775	0.705	0.847	SUBCLONAL	1	TRUE	0	0.548893360820827	1		666	406	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18496295	18496295	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs376605293	NA	P-0025173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	63	434	0	ENST00000266497.5:c.1429+1G>C		p.X477_splice	ENST00000266497		477			1	2	FACETS	0.643	0.559	0.733	0.643	0.559	0.733	SUBCLONAL	1	TRUE	1	0.548893360820827	2		434	357	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968312	18968312	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	70	850	0	ENST00000262803.5:c.2152G>A	p.Glu718Lys	p.E718K	ENST00000262803	NM_002911.3	718	Gag/Aag	15/24	1	2	FACETS	0.325	0.283	0.371	0.325	0.283	0.371	SUBCLONAL	1	TRUE	1	0.548893360820827	2		850	784	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	18	314	0				ENST00000310581	NM_198253.2	-/1132			0.419277611161566	0	FACETS	0.792	0.614	0.987			1	CLONAL	1	FALSE	0	0.411559961967576	0		314	65	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0025174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	190	683	2	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.419277611161566	3	FACETS	0.856	0.795	0.919	0.856	0.795	0.919	CLONAL	2	FALSE	1	0.411559961967576	3		685	650	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903746	41903746	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200046302	NA	P-0025174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	100	660	0	ENST00000372991.4:c.811C>T	p.Arg271Trp	p.R271W	ENST00000372991	NM_001760.3	271	Cgg/Tgg	5/5	0.411559961967576	7	FACETS	0.913	0.818	1	0.456	0.409	0.507	CLONAL	2	FALSE	3	0.411559961967576	7		660	540	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919281	48919281	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs587778870	NA	P-0025174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	86	370	0	ENST00000267163.4:c.446C>G	p.Ser149Ter	p.S149*	ENST00000267163	NM_000321.2	149	tCa/tGa	4/27	0.402372141783394	5	FACETS	0.82	0.73	0.916	0.547	0.486	0.611	CLONAL	2	FALSE	2	0.411559961967576	5		370	412	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95596409	95596409	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs763801533	NA	P-0025174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	77	474	0	ENST00000393063.1:c.559C>T	p.Arg187Ter	p.R187*	ENST00000393063	NM_030621.3	187	Cga/Tga	6/28	0.310795021048563	4	FACETS	1	0.896	1	0.51	0.448	0.576	CLONAL	1	FALSE	2	0.411559961967576	4		474	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0025175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	642	847	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.614485071680146	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.614485071680146	2		849	889	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922875	39922875	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1381182530	NA	P-0025175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	248	343	0	ENST00000378444.4:c.3833G>C	p.Ser1278Thr	p.S1278T	ENST00000378444	NM_001123385.1	1278	aGt/aCt	8/15	0.608350436971351	2	FACETS	1	0.993	1			1	CLONAL	1	TRUE	NA	0.614485071680146	2		343	567	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058596	72058596	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	327	632	0	ENST00000357731.5:c.844C>G	p.Leu282Val	p.L282V	ENST00000357731	NM_173808.2	282	Ctc/Gtc	6/7	0.614485071680146	2	FACETS	0.93	0.89	0.97	0.93	0.89	0.97	CLONAL	2	TRUE	0	0.614485071680146	2		632	572	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195910	102195910	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	142	441	0	ENST00000263464.3:c.670G>C	p.Glu224Gln	p.E224Q	ENST00000263464	NM_001165.4	224	Gaa/Caa	2/9	0.614485071680146	4	FACETS	0.954	0.87	1	0.477	0.435	0.521	CLONAL	1	TRUE	2	0.614485071680146	4		441	782	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195999	102195999	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	151	412	0	ENST00000263464.3:c.759G>C	p.Gln253His	p.Q253H	ENST00000263464	NM_001165.4	253	caG/caC	2/9	0.614485071680146	4	FACETS	1	0.973	1	0.573	0.525	0.623	CLONAL	1	TRUE	2	0.614485071680146	4		412	692	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986971	36986971	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	611	392	0	ENST00000354822.5:c.718C>T	p.Gln240Ter	p.Q240*	ENST00000354822	NM_001079668.2	240	Cag/Tag	3/3	0.614485071680146	2	FACETS	0.853	0.833	0.872	1	0.998	1	CLONAL	3	TRUE	0	0.614485071680146	2		392	777	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748800	41748800	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	317	777	0	ENST00000301178.4:c.1325C>T	p.Ser442Leu	p.S442L	ENST00000301178	NM_021913.4	442	tCa/tTa	11/20	0.614485071680146	3	FACETS	1	0.968	1	0.519	0.489	0.55	CLONAL	1	TRUE	1	0.614485071680146	3		777	1299	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198273	185198273	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	514	545	0	ENST00000265026.3:c.2755C>G	p.Gln919Glu	p.Q919E	ENST00000265026	NM_004721.4	919	Cag/Gag	13/14	0.282832170542238	5	FACETS	0.935	0.899	0.972	0.935	0.899	0.972	INDETERMINATE	3	TRUE	2	0.614485071680146	5		545	1146	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120745	94120745	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	344	604	0	ENST00000369303.4:c.306G>C	p.Leu102Phe	p.L102F	ENST00000369303	NM_004440.3	102	ttG/ttC	3/17	0.614485071680146	3	FACETS	0.992	0.945	1	0.992	0.945	1	CLONAL	2	TRUE	1	0.614485071680146	3		604	738	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026633	6026633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	653	1196	2	ENST00000265849.7:c.1763C>T	p.Ser588Phe	p.S588F	ENST00000265849	NM_000535.5	588	tCt/tTt	11/15	0.5439645427519	4	FACETS	0.973	0.937	1	0.973	0.937	1	CLONAL	2	TRUE	2	0.614485071680146	4		1198	1764	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148507497	148507497	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	318	516	1	ENST00000320356.2:c.1957C>T	p.Gln653Ter	p.Q653*	ENST00000320356	NM_004456.4	653	Caa/Taa	17/20	0.614485071680146	2	FACETS	0.997	0.955	1	0.997	0.955	1	CLONAL	2	TRUE	0	0.614485071680146	2		517	519	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148507506	148507506	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	273	472	0	ENST00000320356.2:c.1948A>T	p.Ile650Phe	p.I650F	ENST00000320356	NM_004456.4	650	Att/Ttt	17/20	0.614485071680146	2	FACETS	0.968	0.923	1	0.968	0.923	1	CLONAL	2	TRUE	0	0.614485071680146	2		472	459	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260743	16260743	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	44	367	0	ENST00000375759.3:c.8008G>C	p.Gly2670Arg	p.G2670R	ENST00000375759	NM_015001.2	2670	Ggc/Cgc	11/15	0.582728728014998	2	FACETS	0.367	0.308	0.432	0.184	0.154	0.216	SUBCLONAL	1	TRUE	0	0.582856083497925	2		367	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577544	+	inframe_deletion	In_Frame_Del	DEL	GGTTCA	GGTTCA	-	novel	NA	P-0025177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	237	454	0	ENST00000269305.4:c.737_742del	p.Met246_Asn247del	p.M246_N247del	ENST00000269305	NM_001126112.2	246	aTGAACCgg/agg	7/11	0.582856083497925	2	FACETS	0.968	0.919	1	0.968	0.919	1	CLONAL	2	TRUE	0	0.582856083497925	2		454	420	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56879250	56879407	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCCCGCCTTCTTTTTTCTTCCTAGGTTACTATAACAACAGTACCAAGGTGGCTGTGAAAACCCTGAAGCCAGGAACTATGTCTGTGCAAGCCTTCCTGGAAGAAGCCAACCTCATGAAGACCCTGCAGCATGACAAGCTCGTGAGGCTCTACGCTGTG	GCCCGCCTTCTTTTTTCTTCCTAGGTTACTATAACAACAGTACCAAGGTGGCTGTGAAAACCCTGAAGCCAGGAACTATGTCTGTGCAAGCCTTCCTGGAAGAAGCCAACCTCATGAAGACCCTGCAGCATGACAAGCTCGTGAGGCTCTACGCTGTG	-	novel	NA	P-0025177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	77	344	0	ENST00000519728.1:c.791-23_925del		p.X264_splice	ENST00000519728	NM_002350.3	264		9/13	0.582911384189665	5	FACETS	0.736	0.646	0.833	0.245	0.215	0.278	SUBCLONAL	1	TRUE	2	0.582856083497925	5		344	673	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0025178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	293	574	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.486021634174342	2	FACETS	0.96	0.912	1	0.96	0.912	1	CLONAL	2	TRUE	0	0.492148446439081	2		574	620	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0025178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	309	566	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	0.486021634174342	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.492148446439081	2		566	623	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598115	55598115	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	154	533	0	ENST00000288135.5:c.2312G>T	p.Ser771Ile	p.S771I	ENST00000288135	NM_000222.2	771	aGc/aTc	16/21	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.492148446439081	2		533	604	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0025185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	222	442	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	0.937	0.877	0.997	1	0.994	1	CLONAL	2	TRUE	1	0.382950891756841	2		442	619	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919758	50919758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750457028	NA	P-0025185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	272	351	0	ENST00000440232.2:c.2926G>A	p.Glu976Lys	p.E976K	ENST00000440232	NM_002691.3	976	Gag/Aag	23/27	0.382950891756841	9	FACETS	1	0.98	1			1	CLONAL	2	TRUE	NA	0.382950891756841	9		351	1492	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919689	50919689	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1451	323	432	0	ENST00000440232.2:c.2857G>C	p.Asp953His	p.D953H	ENST00000440232	NM_002691.3	953	Gac/Cac	23/27	0.382950891756841	9	FACETS	1	0.983	1			1	CLONAL	2	TRUE	NA	0.382950891756841	9		432	1774	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919707	50919707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1411727570	NA	P-0025185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1419	302	399	1	ENST00000440232.2:c.2875G>A	p.Glu959Lys	p.E959K	ENST00000440232	NM_002691.3	959	Gag/Aag	23/27	0.382950891756841	9	FACETS	1	0.975	1			1	CLONAL	2	TRUE	NA	0.382950891756841	9		400	1721	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919872	50919872	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs985679759	NA	P-0025185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	225	319	0	ENST00000440232.2:c.2959G>A	p.Asp987Asn	p.D987N	ENST00000440232	NM_002691.3	987	Gac/Aac	24/27	0.382950891756841	9	FACETS	1	0.958	1			1	CLONAL	2	TRUE	NA	0.382950891756841	9		319	1320	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871129	12871129	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	57	246	0	ENST00000228872.4:c.357del	p.Ile119MetfsTer26	p.I119Mfs*26	ENST00000228872	NM_004064.3	119	aTt/at	1/3	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	FALSE	1	0.320163486595054	2		246	329	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924320	11924320	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0025187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	84	142	0	ENST00000353533.5:c.115+2T>A		p.X39_splice	ENST00000353533	NM_003010.3	39			0.320163486595054	0	FACETS	0.679	0.616	0.743			1	SUBCLONAL	3	FALSE	0	0.320163486595054	0		142	175	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62323146	62323146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	442	436	0	ENST00000360203.5:c.2608G>A	p.Glu870Lys	p.E870K	ENST00000360203	NM_001283009.1	870	Gaa/Aaa	28/35	0.320163486595054	10	FACETS	1	0.974	1	0.514	0.491	0.538	CLONAL	5	FALSE	0	0.320163486595054	10		436	1225	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168964	32168964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	67	619	0	ENST00000375023.3:c.4069C>T	p.Pro1357Ser	p.P1357S	ENST00000375023	NM_004557.3	1357	Ccc/Tcc	22/30	1	2	FACETS	0.781	0.679	0.89	0.781	0.679	0.89	SUBCLONAL	1	FALSE	1	0.320163486595054	2		619	536	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871129	12871129	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025187-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	178	246	0	ENST00000228872.4:c.357del	p.Ile119MetfsTer26	p.I119Mfs*26	ENST00000228872	NM_004064.3	119	aTt/at	1/3	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.754861601113669	2		246	446	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924320	11924320	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0025187-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	86	142	0	ENST00000353533.5:c.115+2T>A		p.X39_splice	ENST00000353533	NM_003010.3	39			0.751679550194228	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.754861601113669	1		142	119	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62323146	62323146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025187-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1488	1173	436	0	ENST00000360203.5:c.2608G>A	p.Glu870Lys	p.E870K	ENST00000360203	NM_001283009.1	870	Gaa/Aaa	28/35	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.754861601113669	NA		436	2661	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0025188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	115	552	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.18938895009578	3	FACETS	0.948	0.855	1	0.474	0.427	0.524	INDETERMINATE	1	TRUE	1	0.376102806937588	3		552	766	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0025188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	237	623	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.297267817104864	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.376102806937588	1		624	938	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0025188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	40	425	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.277	0.229	0.33	0.277	0.229	0.33	SUBCLONAL	1	TRUE	1	0.376102806937588	2		425	769	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0025188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	119	467	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.371881234498123	1	FACETS	0.859	0.778	0.945	0.859	0.778	0.945	CLONAL	1	TRUE	0	0.376102806937588	1		467	598	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107000	11107000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141090393	NA	P-0025188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	146	439	0	ENST00000358026.2:c.1705C>T	p.Arg569Trp	p.R569W	ENST00000358026	NM_001128849.1	569	Cgg/Tgg	10/36	1	2	FACETS	0.872	0.796	0.952	0.872	0.796	0.952	CLONAL	1	TRUE	1	0.376102806937588	2		439	890	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481454	20481455	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0025188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	89	331	0	ENST00000346618.3:c.529dup	p.Thr177AsnfsTer4	p.T177Nfs*4	ENST00000346618	NM_001949.4	175	gaa/gAaa	3/7	1	2	FACETS	0.872	0.775	0.975	0.872	0.775	0.975	CLONAL	1	TRUE	1	0.376102806937588	2		331	543	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106016	8106016	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	100	446	1	ENST00000346208.3:c.836C>T	p.Thr279Met	p.T279M	ENST00000346208		279	aCg/aTg	4/6	1	2	FACETS	0.653	0.583	0.728	0.653	0.583	0.728	SUBCLONAL	1	TRUE	1	0.376102806937588	2		447	814	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772005	135772005	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs768443391	NA	P-0025188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	36	367	0	ENST00000298552.3:c.3112A>G	p.Ser1038Gly	p.S1038G	ENST00000298552	NM_001162426.1	1038	Agc/Ggc	23/23	1	2	FACETS	0.316	0.259	0.38	0.316	0.259	0.38	SUBCLONAL	1	TRUE	1	0.376102806937588	2		367	606	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434356	121434356	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	185	522	1	ENST00000257555.6:c.1124del	p.Gly375AlafsTer9	p.G375Afs*9	ENST00000257555		374	Ggg/gg	6/10	0.376102806937588	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.376102806937588	1		523	725	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300569	11300569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1363405074	NA	P-0025188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	98	569	1	ENST00000361445.4:c.1577G>A	p.Arg526His	p.R526H	ENST00000361445	NM_004958.3	526	cGt/cAt	11/58	1	2	FACETS	0.539	0.48	0.602	0.539	0.48	0.602	SUBCLONAL	1	TRUE	1	0.376102806937588	2		570	967	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794950	42794950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141594034	NA	P-0025188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	140	629	0	ENST00000575354.2:c.2030G>A	p.Arg677Gln	p.R677Q	ENST00000575354	NM_015125.3	677	cGg/cAg	10/20	1	2	FACETS	0.802	0.73	0.878	0.802	0.73	0.878	CLONAL	1	TRUE	1	0.376102806937588	2		629	928	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105746	27105746	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	104	336	0	ENST00000324856.7:c.5357A>C	p.Glu1786Ala	p.E1786A	ENST00000324856	NM_006015.4	1786	gAg/gCg	20/20	1	2	FACETS	0.995	0.893	1	0.995	0.893	1	CLONAL	1	TRUE	1	0.376102806937588	2		336	556	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850865	63850865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	154	392	0	ENST00000279873.7:c.1643C>T	p.Ala548Val	p.A548V	ENST00000279873	NM_032199.2	548	gCc/gTc	10/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.376102806937588	2		392	672	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77064624	77064624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1392857529	NA	P-0025188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	180	538	1	ENST00000356341.3:c.793G>A	p.Asp265Asn	p.D265N	ENST00000356341	NM_002576.4	265	Gat/Aat	8/15	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.376102806937588	2		539	775	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433950	49433950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780306423	NA	P-0025188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	215	574	0	ENST00000301067.7:c.7603C>T	p.Arg2535Cys	p.R2535C	ENST00000301067	NM_003482.3	2535	Cgt/Tgt	31/54	0.18938895009578	3	FACETS	1	0.991	1	0.729	0.678	0.781	INDETERMINATE	1	TRUE	1	0.376102806937588	3		574	932	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435254	49435254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199761931	NA	P-0025188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	229	592	2	ENST00000301067.7:c.6299C>T	p.Pro2100Leu	p.P2100L	ENST00000301067	NM_003482.3	2100	cCg/cTg	31/54	0.18938895009578	3	FACETS	0.77	0.718	0.823	0.77	0.718	0.823	INDETERMINATE	2	TRUE	1	0.376102806937588	3		594	940	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033822	49033822	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0025188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	202	385	0	ENST00000267163.4:c.1961-2A>C		p.X654_splice	ENST00000267163	NM_000321.2	654			0.321948107279629	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	0	0.376102806937588	2		385	535	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827589	72827589	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343025200	NA	P-0025188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	147	561	0	ENST00000268489.5:c.8992C>T	p.Arg2998Trp	p.R2998W	ENST00000268489	NM_006885.3	2998	Cgg/Tgg	9/10	1	2	FACETS	0.823	0.751	0.899	0.823	0.751	0.899	CLONAL	1	TRUE	1	0.376102806937588	2		561	950	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857732	78857732	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	132	561	0	ENST00000306801.3:c.1802A>G	p.His601Arg	p.H601R	ENST00000306801	NM_020761.2	601	cAt/cGt	16/34	1	2	FACETS	0.848	0.77	0.93	0.848	0.77	0.93	CLONAL	1	TRUE	1	0.376102806937588	2		561	828	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222835	5222835	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	112	592	0	ENST00000357368.4:c.2968G>A	p.Gly990Ser	p.G990S	ENST00000357368	NM_002850.3	990	Ggc/Agc	18/38	1	2	FACETS	0.679	0.61	0.752	0.679	0.61	0.752	SUBCLONAL	1	TRUE	1	0.376102806937588	2		592	877	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030687	48030688	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0025188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	258	413	0	ENST00000234420.5:c.3301_3302del	p.Lys1101AspfsTer6	p.K1101Dfs*6	ENST00000234420	NM_000179.2	1101	AAg/g	5/10	0.376102806937588	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.376102806937588	2		413	657	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566457	41566457	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	112	454	0	ENST00000263253.7:c.4334A>G	p.Asp1445Gly	p.D1445G	ENST00000263253	NM_001429.3	1445	gAt/gGt	27/31	1	2	FACETS	0.869	0.783	0.961	0.869	0.783	0.961	CLONAL	1	TRUE	1	0.376102806937588	2		454	685	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678790	52678790	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0025188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	152	350	0	ENST00000394830.3:c.829A>T	p.Lys277Ter	p.K277*	ENST00000394830	NM_018313.4	277	Aaa/Taa	9/30	0.18938895009578	3	FACETS	0.772	0.709	0.838	0.772	0.709	0.838	INDETERMINATE	2	TRUE	1	0.376102806937588	3		350	622	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937422	178937422	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	36	205	0	ENST00000263967.3:c.1810T>C	p.Cys604Arg	p.C604R	ENST00000263967	NM_006218.2	604	Tgt/Cgt	12/21	0.18938895009578	3	FACETS	0.79	0.652	0.943	0.395	0.326	0.472	INDETERMINATE	1	TRUE	1	0.376102806937588	3		205	288	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225652	225652	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	259	518	0	ENST00000264932.6:c.431A>T	p.Glu144Val	p.E144V	ENST00000264932	NM_004168.2	144	gAg/gTg	4/15	0.18938895009578	3	FACETS	0.801	0.751	0.853	0.801	0.751	0.853	INDETERMINATE	2	TRUE	1	0.376102806937588	3		518	1021	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372112	55372112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1385441707	NA	P-0025188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	45	512	0	ENST00000297316.4:c.802G>A	p.Gly268Ser	p.G268S	ENST00000297316	NM_022454.3	268	Ggt/Agt	2/2	1	2	FACETS	0.314	0.263	0.371	0.314	0.263	0.371	SUBCLONAL	1	TRUE	1	0.376102806937588	2		512	762	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376665	8376665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753080783	NA	P-0025188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	94	565	1	ENST00000356435.5:c.4448C>T	p.Thr1483Met	p.T1483M	ENST00000356435		1483	aCg/aTg	27/35	1	2	FACETS	0.536	0.476	0.6	0.536	0.476	0.6	SUBCLONAL	1	TRUE	1	0.376102806937588	2		566	933	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	223	606	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.260880672734642	2	FACETS	1	0.992	1	0.742	0.692	0.795	CLONAL	1	TRUE	0	0.32653254840947	2		606	920	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610162	43610163	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AG	novel	NA	P-0025189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	66	581	4	ENST00000355710.3:c.2114_2115delinsAG	p.Ser705Ter	p.S705*	ENST00000355710	NM_020975.4	705	tCC/tAG	11/20	0.295227058413314	2	FACETS	0.623	0.54	0.712	0.311	0.27	0.356	SUBCLONAL	1	TRUE	0	0.32653254840947	2		585	649	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444755	49444755	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	243	709	0	ENST00000301067.7:c.2711G>A	p.Gly904Glu	p.G904E	ENST00000301067	NM_003482.3	904	gGg/gAg	10/54	0.260880672734642	2	FACETS	0.927	0.869	0.986	0.927	0.869	0.986	CLONAL	2	TRUE	0	0.32653254840947	2		709	803	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28880827	28880827	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368266056	NA	P-0025189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	181	588	1	ENST00000282397.4:c.3803C>T	p.Ser1268Leu	p.S1268L	ENST00000282397	NM_002019.4	1268	tCg/tTg	29/30	0.260880672734642	2	FACETS	0.839	0.777	0.903	0.839	0.777	0.903	CLONAL	2	TRUE	0	0.32653254840947	2		589	661	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640904	3640904	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	37	716	0	ENST00000294008.3:c.2735del	p.Gly912GlufsTer89	p.G912Efs*89	ENST00000294008	NM_032444.2	912	gGa/ga	12/15	1	2	FACETS	0.33	0.271	0.397	0.33	0.271	0.397	SUBCLONAL	1	TRUE	1	0.32653254840947	2		716	686	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835650	68835650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501225	NA	P-0025189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	145	537	0	ENST00000261769.5:c.241G>A	p.Gly81Ser	p.G81S	ENST00000261769	NM_004360.3	81	Ggt/Agt	3/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.32653254840947	2		537	756	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0025189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	250	607	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.303160108240919	2	FACETS	0.959	0.9	1	0.959	0.9	1	CLONAL	2	TRUE	0	0.32653254840947	2		607	798	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952239	17952239	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1396599867	NA	P-0025189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	76	545	0	ENST00000458235.1:c.1101G>T	p.Arg367Ser	p.R367S	ENST00000458235	NM_000215.3	367	agG/agT	8/24	1	2	FACETS	0.786	0.69	0.889	0.786	0.69	0.889	SUBCLONAL	1	TRUE	1	0.32653254840947	2		545	592	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953399	17953399	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	91	565	0	ENST00000458235.1:c.587C>A	p.Pro196Gln	p.P196Q	ENST00000458235	NM_000215.3	196	cCa/cAa	6/24	1	2	FACETS	0.845	0.75	0.945	0.845	0.75	0.945	CLONAL	1	TRUE	1	0.32653254840947	2		565	660	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464512	25464512	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	106	595	0	ENST00000264709.3:c.2001G>T	p.Glu667Asp	p.E667D	ENST00000264709	NM_175629.2	667	gaG/gaT	17/23	0.32653254840947	3	FACETS	0.864	0.774	0.96	0.432	0.387	0.48	CLONAL	1	TRUE	1	0.32653254840947	3		595	874	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098815	178098815	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	127	610	0	ENST00000397062.3:c.230A>T	p.Asp77Val	p.D77V	ENST00000397062	NM_006164.4	77	gAt/gTt	2/5	0.32653254840947	3	FACETS	0.843	0.762	0.929			1	CLONAL	1	TRUE	NA	0.32653254840947	3		610	1073	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794118	242794118	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs758277335	NA	P-0025189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	90	582	1	ENST00000334409.5:c.610C>A	p.Arg204Ser	p.R204S	ENST00000334409	NM_005018.2	204	Cgc/Agc	4/5	NA	2	FACETS	0.791	0.702	0.886			1	INDETERMINATE	1	TRUE	NA	0.32653254840947	2		583	697	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69998286	69998286	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	108	461	2	ENST00000394351.3:c.526G>T	p.Ala176Ser	p.A176S	ENST00000394351	NM_000248.3	176	Gcc/Tcc	5/9	0.32653254840947	1	FACETS	0.943	0.849	1	0.943	0.849	1	CLONAL	1	TRUE	0	0.32653254840947	1		463	587	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134514485	134514485	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	78	480	0	ENST00000398015.3:c.12T>A	p.Asp4Glu	p.D4E	ENST00000398015	NM_004441.4	4	gaT/gaA	1/16	0.151673414819323	2	FACETS	0.821	0.722	0.927	0.41	0.361	0.464	INDETERMINATE	1	TRUE	0	0.32653254840947	2		480	582	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140703	55140703	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs974033003	NA	P-0025189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	91	486	0	ENST00000257290.5:c.1564C>T	p.Arg522Cys	p.R522C	ENST00000257290	NM_006206.4	522	Cgt/Tgt	11/23	0.32653254840947	3	FACETS	0.733	0.649	0.822	0.366	0.324	0.411	SUBCLONAL	1	TRUE	1	0.32653254840947	3		486	885	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225654	225654	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	92	537	0	ENST00000264932.6:c.433C>A	p.Gln145Lys	p.Q145K	ENST00000264932	NM_004168.2	145	Cag/Aag	4/15	0.32653254840947	3	FACETS	0.851	0.756	0.953	0.426	0.378	0.477	CLONAL	1	TRUE	1	0.32653254840947	3		537	770	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441149	149441149	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	64	541	0	ENST00000286301.3:c.1763T>A	p.Leu588His	p.L588H	ENST00000286301	NM_005211.3	588	cTc/cAc	13/22	1	2	FACETS	0.813	0.706	0.93	0.813	0.706	0.93	CLONAL	1	TRUE	1	0.32653254840947	2		541	482	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481435	20481435	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs753339943	NA	P-0025189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	38	276	0	ENST00000346618.3:c.506-2A>T		p.X169_splice	ENST00000346618	NM_001949.4	169			1	2	FACETS	0.578	0.478	0.689	0.578	0.478	0.689	SUBCLONAL	1	TRUE	1	0.32653254840947	2		276	403	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168916	32168916	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	71	631	0	ENST00000375023.3:c.4117G>T	p.Glu1373Ter	p.E1373*	ENST00000375023	NM_004557.3	1373	Gag/Tag	22/30	1	2	FACETS	0.659	0.575	0.75	0.659	0.575	0.75	SUBCLONAL	1	TRUE	1	0.32653254840947	2		631	660	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012244	152012244	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	215	479	0	ENST00000262189.6:c.569G>C	p.Arg190Pro	p.R190P	ENST00000262189	NM_170606.2	190	cGa/cCa	4/59	0.318459242509973	4	FACETS	0.908	0.844	0.974	0.605	0.563	0.649	CLONAL	2	TRUE	1	0.32653254840947	4		479	962	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8523526	8523526	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0025189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	125	343	0	ENST00000356435.5:c.680-2A>T		p.X227_splice	ENST00000356435		227			0.295227058413314	2	FACETS	0.809	0.737	0.884	0.809	0.737	0.884	CLONAL	2	TRUE	0	0.32653254840947	2		343	473	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570280	87570280	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	74	447	0	ENST00000277120.3:c.2020C>G	p.Gln674Glu	p.Q674E	ENST00000277120		674	Cag/Gag	17/19	1	2	FACETS	0.906	0.795	1	0.906	0.795	1	CLONAL	1	TRUE	1	0.32653254840947	2		447	500	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849320	76849320	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0025189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	91	436	1	ENST00000373344.5:c.5957-1G>T		p.X1986_splice	ENST00000373344	NM_000489.3	1986			0.32653254840947	1	FACETS	0.986	0.879	1	0.986	0.879	1	CLONAL	1	TRUE	0	0.32653254840947	1		437	473	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0025190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	148	364	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.693200946568078	2		364	385	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0025190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	108	425	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.693200946568078	2		425	286	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063718	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0025190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	45	104	0	ENST00000412916.2:c.165+2dup		p.X55_splice	ENST00000412916		55			0.693200946568078	1	FACETS	0.953	0.835	1	0.953	0.835	1	CLONAL	1	TRUE	0	0.693200946568078	1		104	89	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16005024	16005024	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs760547329	NA	P-0025190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	200	413	0	ENST00000268712.3:c.2230C>T	p.Arg744Ter	p.R744*	ENST00000268712	NM_006311.3	744	Cga/Tga	20/46	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.693200946568078	2		413	516	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554253	29554253	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	20	203	0	ENST00000356175.3:c.2272del	p.Arg758GlufsTer2	p.R758Efs*2	ENST00000356175	NM_000267.3	757	Aaa/aa	19/57	0.693200946568078	1	FACETS	0.277	0.214	0.35	0.277	0.214	0.35	SUBCLONAL	1	TRUE	0	0.693200946568078	1		203	136	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167742	56167743	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGATGAG	novel	NA	P-0025190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	114	243	0	ENST00000399503.3:c.1313_1314insGGGATGA	p.Glu439GlyfsTer2	p.E439Gfs*2	ENST00000399503	NM_005921.1	436	aag/aaGGATGAGg	7/20	1	2	FACETS	0.911	0.829	0.996	0.911	0.829	0.996	CLONAL	1	TRUE	1	0.693200946568078	2		243	361	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168550	56168550	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0025190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	163	248	0	ENST00000399503.3:c.1505+1G>T		p.X502_splice	ENST00000399503	NM_005921.1	502			1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.693200946568078	2		248	469	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0025192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	97	278	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.869	0.783	0.958	0.869	0.783	0.958	CLONAL	1	TRUE	1	0.699947871394761	2		278	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0025192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	203	472	3	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.648898615240869	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.699947871394761	1		475	329	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0025192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	119	285	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	0.872	0.794	0.952	0.872	0.794	0.952	CLONAL	1	TRUE	1	0.699947871394761	2		285	390	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591925	48591925	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	101	386	3	ENST00000342988.3:c.1088G>T	p.Cys363Phe	p.C363F	ENST00000342988	NM_005359.5	363	tGt/tTt	9/12	0.69990125311719	1	FACETS	0.525	0.474	0.579	0.525	0.474	0.579	SUBCLONAL	1	TRUE	0	0.699947871394761	1		389	357	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380283	25380283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913528	NA	P-0025192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	138	439	0	ENST00000311936.3:c.175G>A	p.Ala59Thr	p.A59T	ENST00000311936	NM_004985.3	59	Gca/Aca	3/5	0.169051310769173	2	FACETS	0.707	0.646	0.77	0.353	0.323	0.385	INDETERMINATE	1	TRUE	0	0.699947871394761	2		439	558	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480459	89480459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	124	257	3	ENST00000336596.2:c.2296G>A	p.Gly766Arg	p.G766R	ENST00000336596	NM_005233.5	766	Gga/Aga	13/17	1	2	FACETS	0.879	0.803	0.958	0.879	0.803	0.958	CLONAL	1	TRUE	1	0.699947871394761	2		260	403	SUCCESS
APC	324	MSKCC	GRCh37	5	112175530	112175530	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	111	249	0	ENST00000257430.4:c.4240del	p.Val1414Ter	p.V1414*	ENST00000257430	NM_000038.5	1413	atG/at	16/16	1	2	FACETS	0.964	0.877	1	0.964	0.877	1	CLONAL	1	TRUE	1	0.699947871394761	2		249	329	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031883	26031884	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs758780418	NA	P-0025192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	105	161	2	ENST00000244661.2:c.405_406del	p.Arg135SerfsTer12	p.R135Sfs*12	ENST00000244661	NM_003537.3	135	agAGcg/agcg	1/1	0.169051310769173	2	FACETS	1	0.954	1	0.54	0.491	0.59	INDETERMINATE	1	TRUE	0	0.699947871394761	2		163	278	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964358	55964358	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	172	407	0	ENST00000263923.4:c.2455C>T	p.Arg819Ter	p.R819*	ENST00000263923	NM_002253.2	819	Cga/Tga	17/30	0.20702066007797	1	FACETS	0.652	0.605	0.7	0.652	0.605	0.7	INDETERMINATE	1	TRUE	0	0.699947871394761	1		407	490	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603007	48603007	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0025192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	100	264	0	ENST00000342988.3:c.1309-1G>T		p.X437_splice	ENST00000342988	NM_005359.5	437			0.69990125311719	1	FACETS	0.579	0.523	0.637	0.579	0.523	0.637	SUBCLONAL	1	TRUE	0	0.699947871394761	1		264	321	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188153	11188153	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	190	408	0	ENST00000361445.4:c.5941A>G	p.Lys1981Glu	p.K1981E	ENST00000361445	NM_004958.3	1981	Aag/Gag	43/58	1	2	FACETS	0.969	0.902	1	0.969	0.902	1	CLONAL	1	TRUE	1	0.699947871394761	2		408	560	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870872	12870873	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0025192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	84	159	0	ENST00000228872.4:c.101dup	p.Val36GlyfsTer89	p.V36Gfs*89	ENST00000228872	NM_004064.3	33	-/G	1/3	0.169051310769173	2	FACETS	1	0.971	1	0.606	0.547	0.666	INDETERMINATE	1	TRUE	0	0.699947871394761	2		159	198	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059226	47059226	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	37	290	0	ENST00000409792.3:c.7435T>C	p.Ser2479Pro	p.S2479P	ENST00000409792	NM_014159.6	2479	Tcc/Ccc	20/21	0.49798929150184	1	FACETS	0.205	0.169	0.245	0.205	0.169	0.245	SUBCLONAL	1	TRUE	0	0.699947871394761	1		290	335	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481391	140481392	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTA	novel	NA	P-0025192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	96	354	0	ENST00000288602.6:c.1414_1416dup	p.Tyr472dup	p.Y472dup	ENST00000288602	NM_004333.4	472	-/TAC	11/18	0.630767171940678	4	FACETS	0.72	0.642	0.802	0.24	0.214	0.268	SUBCLONAL	1	TRUE	1	0.699947871394761	4		354	648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0025193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	339	528	1	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	0.766289993888122	2	FACETS	0.975	0.943	1	0.975	0.943	1	CLONAL	2	TRUE	0	0.77397383862369	2		529	449	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513521	41513521	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	166	458	1	ENST00000263253.7:c.425G>T	p.Gly142Val	p.G142V	ENST00000263253	NM_001429.3	142	gGa/gTa	2/31	0.757498163488112	3	FACETS	0.982	0.906	1	0.327	0.302	0.354	CLONAL	1	TRUE	0	0.77397383862369	3		459	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0025194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	286	847	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.578647895217951	3	FACETS	0.945	0.906	0.984	0.945	0.906	0.984	CLONAL	3	TRUE	0	0.608933778638242	3		849	432	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0025194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	171	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.609891734717151	3	FACETS	0.982	0.917	1	0.982	0.917	1	CLONAL	2	TRUE	1	0.608933778638242	3		326	373	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585361	29585361	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1555618492	NA	P-0025194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	279	445	0	ENST00000356175.3:c.4111-1G>A		p.X1371_splice	ENST00000356175	NM_000267.3	1371			0.578647895217951	3	FACETS	0.906	0.866	0.944	0.906	0.866	0.944	CLONAL	3	TRUE	0	0.608933778638242	3		445	440	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540958	187540958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs189912205	NA	P-0025194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	122	319	0	ENST00000441802.2:c.6782C>T	p.Thr2261Met	p.T2261M	ENST00000441802	NM_005245.3	2261	aCg/aTg	10/27	0.595892684751352	4	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	2	0.608933778638242	4		319	310	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404903	404903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	213	584	2	ENST00000399788.2:c.4291G>A	p.Glu1431Lys	p.E1431K	ENST00000399788	NM_001042603.1	1431	Gaa/Aaa	26/28	0.449702462788966	3	FACETS	0.858	0.804	0.912			1	CLONAL	2	TRUE	NA	0.608933778638242	3		586	532	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913250	NA	P-0025197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	310	299	0	ENST00000369535.4:c.34G>A	p.Gly12Ser	p.G12S	ENST00000369535	NM_002524.4	12	Ggt/Agt	2/7	0.507310947187838	6	FACETS	0.9	0.86	0.94	0.9	0.86	0.94	CLONAL	5	FALSE	1	0.507310947187838	6		299	547	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727490	88727490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1222179640	NA	P-0025197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	19	361	0	ENST00000360948.2:c.289G>A	p.Val97Met	p.V97M	ENST00000360948	NM_001012338.2	97	Gtg/Atg	3/19	0.198734574735702	5	FACETS	0.396	0.3	0.509	0.132	0.1	0.17	INDETERMINATE	1	FALSE	2	0.507310947187838	5		361	333	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991700	72991700	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	40	205	0	ENST00000268489.5:c.2345del	p.Ala782GlyfsTer42	p.A782Gfs*42	ENST00000268489	NM_006885.3	782	gCg/gg	2/10	0.441811182353577	3	FACETS	0.979	0.822	1	0.489	0.411	0.575	CLONAL	1	FALSE	1	0.507310947187838	3		205	202	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0025201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	473	466	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.632016244962451	3	FACETS	0.987	0.96	1	0.987	0.96	1	CLONAL	3	TRUE	0	0.677647498237134	3		466	631	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171645	32171645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	71	568	1	ENST00000375023.3:c.3133G>A	p.Val1045Met	p.V1045M	ENST00000375023	NM_004557.3	1045	Gtg/Atg	20/30	0.648919939458063	4	FACETS	0.348	0.303	0.398	0.116	0.101	0.133	SUBCLONAL	1	TRUE	1	0.677647498237134	4		569	1009	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561756	55561756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376469897	NA	P-0025201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	281	466	0	ENST00000288135.5:c.146G>A	p.Arg49His	p.R49H	ENST00000288135	NM_000222.2	49	cGc/cAc	2/21	0.647194425786399	2	FACETS	0.94	0.9	0.98	0.94	0.9	0.98	CLONAL	2	TRUE	0	0.677647498237134	2		466	441	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434836	110434836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1397766674	NA	P-0025201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1474	220	629	0	ENST00000375856.3:c.3565G>A	p.Gly1189Ser	p.G1189S	ENST00000375856	NM_003749.2	1189	Ggc/Agc	1/2	0.677647498237134	7	FACETS	1	0.951	1	0.207	0.191	0.223	CLONAL	1	TRUE	2	0.677647498237134	7		629	1694	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371707	89371707	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	83	599	0	ENST00000301030.4:c.133G>A	p.Gly45Ser	p.G45S	ENST00000301030	NM_001256183.1	45	Ggc/Agc	4/13	0.677647498237134	3	FACETS	0.373	0.328	0.421	0.124	0.109	0.141	SUBCLONAL	1	TRUE	0	0.677647498237134	3		599	880	SUCCESS
APC	324	MSKCC	GRCh37	5	112174375	112174384	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTAAATAT	TCTTAAATAT	-	novel	NA	P-0025201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	303	357	0	ENST00000257430.4:c.3086_3095del	p.Leu1029GlnfsTer5	p.L1029Qfs*5	ENST00000257430	NM_000038.5	1028	agTCTTAAATAT/ag	16/16	0.672193684016878	3	FACETS	0.909	0.874	0.943			1	CLONAL	3	TRUE	NA	0.677647498237134	3		357	439	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	86	314	0				ENST00000310581	NM_198253.2	-/1132			0.519192937499554	3	FACETS	0.775	0.695	0.859	0.775	0.695	0.859	SUBCLONAL	2	TRUE	1	0.516922381832285	3		314	270	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0025203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	352	391	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.519192937499554	1	FACETS	1	0.996	1	1	0.997	1	CLONAL	2	TRUE	0	0.516922381832285	1		391	422	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0025203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	75	432	2	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	0.519192937499554	1	FACETS	0.992	0.884	1	0.992	0.884	1	CLONAL	1	TRUE	0	0.516922381832285	1		434	217	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439724	220439724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201577506	NA	P-0025203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	115	379	0	ENST00000243786.2:c.577G>A	p.Val193Ile	p.V193I	ENST00000243786	NM_002191.3	193	Gtc/Atc	2/2	0.519192937499554	1	FACETS	0.914	0.832	0.999	0.914	0.832	0.999	CLONAL	1	TRUE	0	0.516922381832285	1		379	361	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653780	89653781	+	splice_acceptor_variant	Splice_Site	DEL	AG	AG	-	rs1554893747	NA	P-0025203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	26	397	0	ENST00000371953.3:c.80-1_80del		p.X27_splice	ENST00000371953	NM_000314.4	27			0.516922381832285	1	FACETS	0.379	0.302	0.465	0.379	0.302	0.465	SUBCLONAL	1	TRUE	0	0.516922381832285	1		397	197	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693815	47693816	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0025203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	38	364	0	ENST00000233146.2:c.1530_1531del	p.Gln510HisfsTer2	p.Q510Hfs*2	ENST00000233146	NM_000251.2	510	cAG/c	10/16	0.496059443871854	1	FACETS	0.476	0.396	0.563	0.476	0.396	0.563	SUBCLONAL	1	TRUE	0	0.516922381832285	1		364	229	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155989	99155990	+	splice_acceptor_variant	Splice_Site	DEL	AG	AG	-	novel	NA	P-0025203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	76	317	0	ENST00000074304.5:c.671-2_671-1del		p.X224_splice	ENST00000074304	NM_001134224.1	224			0.355866208872572	1	FACETS	0.747	0.662	0.836	0.747	0.662	0.836	SUBCLONAL	1	TRUE	0	0.516922381832285	1		317	292	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342636	70342637	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0025203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	104	478	0	ENST00000374080.3:c.1398_1399del	p.His466GlnfsTer3	p.H466Qfs*3	ENST00000374080		466	cAT/c	10/45	1	2	FACETS	0.89	0.802	0.983	0.89	0.802	0.983	CLONAL	1	TRUE	1	0.516922381832285	2		478	452	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	99	314	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.837	0.761	0.915	0.837	0.761	0.915	CLONAL	1	TRUE	1	0.973293021231173	2		314	243	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436952	49436952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748653082	NA	P-0025204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	250	573	2	ENST00000301067.7:c.5551G>A	p.Val1851Met	p.V1851M	ENST00000301067	NM_003482.3	1851	Gtg/Atg	25/54	1	2	FACETS	0.846	0.798	0.895	0.846	0.798	0.895	CLONAL	1	TRUE	1	0.973293021231173	2		575	607	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160239	22160239	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	231	391	0	ENST00000215832.6:c.392A>G	p.Tyr131Cys	p.Y131C	ENST00000215832	NM_002745.4	131	tAc/tGc	3/9	1	2	FACETS	0.969	0.914	1	0.969	0.914	1	CLONAL	1	TRUE	1	0.973293021231173	2		391	490	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159017	24159017	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	317	662	0	ENST00000263121.7:c.689C>G	p.Pro230Arg	p.P230R	ENST00000263121	NM_003073.3	230	cCg/cGg	6/9	1	2	FACETS	0.936	0.89	0.982	0.936	0.89	0.982	CLONAL	1	TRUE	1	0.973293021231173	2		662	696	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0025207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	166	847	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.393501876702188	2		849	749	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430403	78430412	+	frameshift_variant	Frame_Shift_Del	DEL	AATTAACTCT	AATTAACTCT	-	novel	NA	P-0025207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	29	566	0	ENST00000370768.2:c.756_765del	p.Leu252PhefsTer18	p.L252Ffs*18	ENST00000370768	NM_003902.3	252	ttAGAGTTAATT/tt	10/20	0.250894262457229	3	FACETS	0.511	0.411	0.626	0.256	0.205	0.313	SUBCLONAL	1	TRUE	1	0.393501876702188	3		566	345	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108802	2108821	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTCTCTGGGGAGCCCACC	GGCTCTCTGGGGAGCCCACC	-	rs137854012	NA	P-0025207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	50	605	0	ENST00000219476.3:c.909_928del	p.Trp304PhefsTer27	p.W304Ffs*27	ENST00000219476	NM_000548.3	301	atGGCTCTCTGGGGAGCCCACCgg/atgg	10/42	1	2	FACETS	0.281	0.237	0.329	0.281	0.237	0.329	SUBCLONAL	1	TRUE	1	0.393501876702188	2		605	904	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322675	30322675	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	105	585	0	ENST00000322652.5:c.1688G>A	p.Arg563His	p.R563H	ENST00000322652	NM_015355.2	563	cGt/cAt	14/16	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.393501876702188	2		585	482	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508177	38508177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749735817	NA	P-0025207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	61	401	0	ENST00000254066.5:c.485G>A	p.Arg162Gln	p.R162Q	ENST00000254066	NM_000964.3	162	cGa/cAa	5/9	1	2	FACETS	0.481	0.414	0.553	0.481	0.414	0.553	SUBCLONAL	1	TRUE	1	0.393501876702188	2		401	645	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605072	46605072	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1281194175	NA	P-0025207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	93	677	0	ENST00000263734.3:c.1289C>A	p.Ala430Asp	p.A430D	ENST00000263734	NM_001430.4	430	gCc/gAc	10/16	1	2	FACETS	0.554	0.492	0.621	0.554	0.492	0.621	SUBCLONAL	1	TRUE	1	0.393501876702188	2		677	853	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196508	106196508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	34	471	0	ENST00000380013.4:c.4841C>T	p.Pro1614Leu	p.P1614L	ENST00000380013	NM_001127208.2	1614	cCc/cTc	11/11	1	2	FACETS	0.497	0.406	0.598	0.497	0.406	0.598	SUBCLONAL	1	TRUE	1	0.393501876702188	2		471	348	SUCCESS
APC	324	MSKCC	GRCh37	5	112175198	112175199	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0025207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	75	293	0	ENST00000257430.4:c.3910dup	p.Ile1304AsnfsTer11	p.I1304Nfs*11	ENST00000257430	NM_000038.5	1303	caa/cAaa	16/16	0.294688286081948	3	FACETS	1	0.932	1	0.707	0.631	0.787	CLONAL	2	TRUE	0	0.393501876702188	3		293	215	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197087	26197087	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	62	446	0	ENST00000356476.2:c.392T>A	p.Ile131Asn	p.I131N	ENST00000356476		131	aTt/aAt	1/1	0.348039281834122	3	FACETS	0.536	0.462	0.616	0.179	0.154	0.206	SUBCLONAL	1	TRUE	0	0.393501876702188	3		446	704	SUCCESS
AR	367	MSKCC	GRCh37	X	66765382	66765382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770661499	NA	P-0025207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	74	261	0	ENST00000374690.3:c.394G>A	p.Val132Ile	p.V132I	ENST00000374690	NM_000044.3	132	Gtc/Atc	1/8	0.393501876702188	2	FACETS	1	0.96	1			1	CLONAL	1	TRUE	NA	0.393501876702188	2		261	311	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0025208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	289	605	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.526818696689709	1	FACETS	0.8	0.763	0.837	1	0.995	1	SUBCLONAL	2	TRUE	0	0.526818696689709	1		605	505	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0025208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	182	510	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.526818696689709	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.526818696689709	2		510	307	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575096	48575096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555685159	NA	P-0025208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	89	419	1	ENST00000342988.3:c.290G>A	p.Arg97His	p.R97H	ENST00000342988	NM_005359.5	97	cGt/cAt	3/12	0.526818696689709	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.526818696689709	1		420	244	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288489	15288489	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	33	171	1	ENST00000263388.2:c.4250G>A	p.Cys1417Tyr	p.C1417Y	ENST00000263388	NM_000435.2	1417	tGc/tAc	24/33	0.368506050722838	3	FACETS	0.768	0.631	0.92	0.384	0.315	0.46	CLONAL	1	TRUE	1	0.526818696689709	3		172	206	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613119	52613119	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	138	425	1	ENST00000394830.3:c.3409G>A	p.Asp1137Asn	p.D1137N	ENST00000394830	NM_018313.4	1137	Gac/Aac	22/30	0.413294905987532	4	FACETS	1	0.925	1	0.509	0.463	0.557	CLONAL	1	TRUE	2	0.526818696689709	4		426	786	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803144	1803144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219348193	NA	P-0025208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	137	412	1	ENST00000260795.2:c.496G>A	p.Val166Met	p.V166M	ENST00000260795		166	Gtg/Atg	4/17	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.526818696689709	2		413	434	SUCCESS
APC	324	MSKCC	GRCh37	5	112175264	112175301	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGTGTCACAGCACCCTAGAACCAAATCCAGCAGACT	GCAGTGTCACAGCACCCTAGAACCAAATCCAGCAGACT	-	novel	NA	P-0025208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	105	289	0	ENST00000257430.4:c.3977_4014del	p.Val1326GlyfsTer3	p.V1326Gfs*3	ENST00000257430	NM_000038.5	1325	GCAGTGTCACAGCACCCTAGAACCAAATCCAGCAGACTg/g	16/16	0.526818696689709	2	FACETS	0.81	0.74	0.882	0.81	0.74	0.882	CLONAL	2	TRUE	0	0.526818696689709	2		289	246	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056080	26056118	+	inframe_deletion	In_Frame_Del	DEL	CAGCCTTAGCAGCACTTTTGGCAGCTTTCTTGGGCTTCG	CAGCCTTAGCAGCACTTTTGGCAGCTTTCTTGGGCTTCG	-	novel	NA	P-0025208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	51	347	0	ENST00000343677.2:c.539_577del	p.Ala180_Ala192del	p.A180_A192del	ENST00000343677	NM_005319.3	180	gCGAAGCCCAAGAAAGCTGCCAAAAGTGCTGCTAAGGCTGtg/gtg	1/1	1	2	FACETS	0.59	0.504	0.684	0.59	0.504	0.684	SUBCLONAL	1	TRUE	1	0.526818696689709	2		347	328	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777655	9777655	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	80	526	0	ENST00000377346.4:c.991A>T	p.Ser331Cys	p.S331C	ENST00000377346	NM_005026.3	331	Agc/Tgc	8/24	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		526	676	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0025218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	24	369	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	0.391	0.306	0.49	0.391	0.306	0.49	SUBCLONAL	1	FALSE	1	0.245550752895065	2		369	500	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0025218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	15	585	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.146435761051002	0	FACETS	0.275	0.2	0.365			1	INDETERMINATE	1	FALSE	0	0.245550752895065	0		585	335	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056342	27056343	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0025218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	33	347	0	ENST00000324856.7:c.1338_1339del	p.Gln449AlafsTer173	p.Q449Afs*173	ENST00000324856	NM_006015.4	446	tcTTat/tcat	2/20	1	2	FACETS	0.517	0.42	0.626	0.517	0.42	0.626	SUBCLONAL	1	FALSE	1	0.245550752895065	2		347	520	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604765	48604766	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0025218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	30	473	2	ENST00000342988.3:c.1589_1590del	p.His530ProfsTer46	p.H530Pfs*46	ENST00000342988	NM_005359.5	529	ttACac/ttac	12/12	0.146435761051002	0	FACETS	0.339	0.272	0.415			1	INDETERMINATE	1	FALSE	0	0.245550752895065	0		475	544	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522551	176522551	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	328	579	0	ENST00000292408.4:c.1648G>C	p.Val550Leu	p.V550L	ENST00000292408	NM_213647.1	550	Gtg/Ctg	13/18	0.7103057976203	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.7103057976203	3		579	619	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16005023	16005023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775391836	NA	P-0025219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	197	610	1	ENST00000268712.3:c.2231G>A	p.Arg744Gln	p.R744Q	ENST00000268712	NM_006311.3	744	cGa/cAa	20/46	1	2	FACETS	0.987	0.921	1	0.987	0.921	1	CLONAL	1	TRUE	1	0.7103057976203	2		611	562	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685311	89685312	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0025222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	129	333	0	ENST00000371953.3:c.208_209dup	p.Cys71PhefsTer29	p.C71Ffs*29	ENST00000371953	NM_000314.4	69	aat/aaTCt	3/9	0.632548980228366	1	FACETS	0.797	0.733	0.863	0.797	0.733	0.863	SUBCLONAL	1	TRUE	0	0.659422841171134	1		333	329	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112892446	112892446	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	126	419	0	ENST00000351677.2:c.604A>G	p.Met202Val	p.M202V	ENST00000351677	NM_002834.3	202	Atg/Gtg	5/16	1	2	FACETS	0.998	0.913	1	0.998	0.913	1	CLONAL	1	TRUE	1	0.659422841171134	2		419	383	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579372	7579393	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCTGGTAGGTTTTCTGGGAA	GCCCTGGTAGGTTTTCTGGGAA	-	novel	NA	P-0025222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	99	506	0	ENST00000269305.4:c.294_315del	p.Ser99AlafsTer17	p.S99Afs*17	ENST00000269305	NM_001126112.2	98	ccTTCCCAGAAAACCTACCAGGGC/cc	4/11	0.659422841171134	1	FACETS	0.802	0.728	0.877	0.802	0.728	0.877	CLONAL	1	TRUE	0	0.659422841171134	1		506	251	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858254	59858254	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	143	460	0	ENST00000259008.2:c.1741C>G	p.Arg581Gly	p.R581G	ENST00000259008	NM_032043.2	581	Cga/Gga	12/20	1	2	FACETS	0.995	0.915	1	0.995	0.915	1	CLONAL	1	TRUE	1	0.659422841171134	2		460	436	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971042	21971042	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	111	264	2	ENST00000304494.5:c.316G>A	p.Val106Met	p.V106M	ENST00000304494	NM_000077.4	106	Gtg/Atg	2/3	0.659422841171134	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.659422841171134	1		266	163	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0025224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	72	603	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.0751642073143368	4	FACETS	0.877	0.771	0.99	0.877	0.771	0.99	INDETERMINATE	2	FALSE	2	0.285121663604361	4		603	370	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165213	47165213	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	62	477	0	ENST00000409792.3:c.913del	p.Thr305GlnfsTer35	p.T305Qfs*35	ENST00000409792	NM_014159.6	305	Aca/ca	3/21	0.135338342525162	4	FACETS	1	0.97	1	0.489	0.424	0.559	INDETERMINATE	1	FALSE	1	0.285121663604361	4		477	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882025	NA	P-0025224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	224	752	0	ENST00000269305.4:c.646G>T	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ttg	6/11	0.285121663604361	4	FACETS	1	0.976	1	1	0.993	1	CLONAL	4	FALSE	1	0.285121663604361	4		752	474	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247812	59247813	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0025224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	289	884	0	ENST00000371222.2:c.930_931del	p.Lys311SerfsTer6	p.K311Sfs*6	ENST00000371222	NM_002228.3	310	caGAaa/caaa	1/1	0.285121663604361	5	FACETS	1	0.975	1	1	0.994	1	CLONAL	4	FALSE	2	0.285121663604361	5		884	690	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347934	73347934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	28	375	1	ENST00000377767.4:c.1127C>T	p.Ala376Val	p.A376V	ENST00000377767	NM_014953.3	376	gCt/gTt	8/21	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.285121663604361	NA		376	232	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325047	123325047	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	47	653	0	ENST00000358487.5:c.281T>A	p.Ile94Lys	p.I94K	ENST00000358487	NM_000141.4	94	aTa/aAa	3/18	0.285121663604361	5	FACETS	1	0.948	1	0.435	0.368	0.508	CLONAL	1	FALSE	2	0.285121663604361	5		653	361	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437172	110437172	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	10	53	0	ENST00000375856.3:c.1229G>T	p.Gly410Val	p.G410V	ENST00000375856	NM_003749.2	410	gGc/gTc	1/2	0.285121663604361	5	FACETS	1	0.711	1	0.681	0.474	0.925	CLONAL	2	FALSE	2	0.285121663604361	5		53	49	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726706	88726706	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	66	539	0	ENST00000360948.2:c.338C>A	p.Ser113Ter	p.S113*	ENST00000360948	NM_001012338.2	113	tCa/tAa	4/19	0.148877750654521	4	FACETS	1	0.948	1	1	0.948	1	INDETERMINATE	2	FALSE	2	0.285121663604361	4		539	258	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012675	36012675	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	11	195	0	ENST00000358208.4:c.119A>G	p.Lys40Arg	p.K40R	ENST00000358208		40	aAg/aGg	2/12	0.285121663604361	5	FACETS	0.715	0.496	0.986	0.238	0.165	0.329	CLONAL	1	FALSE	2	0.285121663604361	5		195	154	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691806	30691806	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	31	548	0	ENST00000295754.5:c.308A>G	p.Asp103Gly	p.D103G	ENST00000295754	NM_003242.5	103	gAc/gGc	3/7	0.135338342525162	4	FACETS	0.622	0.503	0.758	0.207	0.167	0.253	INDETERMINATE	1	FALSE	1	0.285121663604361	4		548	449	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541666	187541666	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	41	428	0	ENST00000441802.2:c.6074T>C	p.Ile2025Thr	p.I2025T	ENST00000441802	NM_005245.3	2025	aTa/aCa	10/27	0.0751642073143368	4	FACETS	0.829	0.697	0.973	0.829	0.697	0.973	INDETERMINATE	2	FALSE	2	0.285121663604361	4		428	223	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638030	176638030	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs746793939	NA	P-0025224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	228	754	0	ENST00000439151.2:c.2630G>T	p.Ser877Ile	p.S877I	ENST00000439151	NM_022455.4	877	aGt/aTt	5/23	0.285121663604361	6	FACETS	0.983	0.926	1			1	CLONAL	5	FALSE	NA	0.285121663604361	6		754	511	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001188	150001188	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	74	664	0	ENST00000253339.5:c.2416C>T	p.Arg806Ter	p.R806*	ENST00000253339		806	Cga/Tga	4/7	0.190164093368689	4	FACETS	1	0.973	1	0.477	0.419	0.54	CLONAL	1	FALSE	1	0.285121663604361	4		664	466	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946077	13946077	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	42	416	0	ENST00000405192.2:c.1019T>G	p.Phe340Cys	p.F340C	ENST00000405192	NM_001163147.1	340	tTt/tGt	10/12	0.285121663604361	5	FACETS	0.983	0.821	1	0.328	0.273	0.387	CLONAL	1	FALSE	2	0.285121663604361	5		416	428	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543672	148544220	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GATTGGAACTAAACATACTCTTAAAAAAAAAAATGAAGGAGAGGAAAGGAGAAATTGTTCATTGTTAGAAAATGTATAACACCTGTAAAGCAGGTTAAAAATCTAGTGTATCCTCAAAAATATCAAGAACATTTTCTTAGGTGCATATAGATTTTACACTATAGTTTCCCACATTCAAATAATACAAAAACACCACATCTGTTATTTTATTGCAAGTGGTTAGAGAACAGGAAACGATTGCCATCCTTTCTTTGTTGACTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATTTTTTTTTTTAATCACAATGACTTTAGAAACATAAAATCATGAAATGCATCCCTTTATATTTAGGGAGGCATTTCTGCAGCTGCATATGCAAATAAAAGTATACTAAACAAAGACTGATTAATGTGCATGGTATAATGTTAAGACAGATCAAGAACCTAAGCTTCCAAGTATTCACTCATCTTATTGTAAATACAAACTTGGCTAGAATTATTTTAAATAAAAACTTATTGAACTTAGGAGGG	GATTGGAACTAAACATACTCTTAAAAAAAAAAATGAAGGAGAGGAAAGGAGAAATTGTTCATTGTTAGAAAATGTATAACACCTGTAAAGCAGGTTAAAAATCTAGTGTATCCTCAAAAATATCAAGAACATTTTCTTAGGTGCATATAGATTTTACACTATAGTTTCCCACATTCAAATAATACAAAAACACCACATCTGTTATTTTATTGCAAGTGGTTAGAGAACAGGAAACGATTGCCATCCTTTCTTTGTTGACTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATTTTTTTTTTTAATCACAATGACTTTAGAAACATAAAATCATGAAATGCATCCCTTTATATTTAGGGAGGCATTTCTGCAGCTGCATATGCAAATAAAAGTATACTAAACAAAGACTGATTAATGTGCATGGTATAATGTTAAGACAGATCAAGAACCTAAGCTTCCAAGTATTCACTCATCTTATTGTAAATACAAACTTGGCTAGAATTATTTTAAATAAAAACTTATTGAACTTAGGAGGG	-	novel	NA	P-0025224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	62	433	0	ENST00000320356.2:c.117+54_136del		p.X39_splice	ENST00000320356	NM_004456.4	39		3/20	0.226713734192132	3	FACETS	1	0.965	1	0.453	0.393	0.517	CLONAL	1	FALSE	0	0.285121663604361	3		433	366	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0025225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	94	463	0	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	0.212998760684642	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.212998760684642	1		463	683	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0025225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	165	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.212998760684642	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.212998760684642	3		326	714	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740573	145740573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573164516	NA	P-0025225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	91	563	1	ENST00000428558.2:c.1444C>T	p.Arg482Cys	p.R482C	ENST00000428558	NM_004260.3	482	Cgc/Tgc	8/22	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.212998760684642	2		564	605	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230895	53230895	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	93	506	0	ENST00000375401.3:c.1898A>G	p.Tyr633Cys	p.Y633C	ENST00000375401	NM_004187.3	633	tAc/tGc	14/26	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.212998760684642	2		506	684	SUCCESS
ALK	238	MSKCC	GRCh37	2	29436860	29436860	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs281864720	NA	P-0121448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	24	323	0	ENST00000389048.3:c.3733T>G	p.Phe1245Val	p.F1245V	ENST00000389048	NM_004304.4	1245	Ttc/Gtc	24/29	0.788289087500626	3	FACETS	0.316	0.248	0.394	0.158	0.124	0.197	SUBCLONAL	1	NA	1	0.857737462095488	3		323	253	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0025238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	118	670	1	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	0.338174011091612	2		671	590	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0025238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	259	552	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.300590570066291	4	FACETS	1	0.983	1			1	CLONAL	3	TRUE	NA	0.338174011091612	4		552	621	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786862	135786862	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514808	NA	P-0025238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	83	439	0	ENST00000298552.3:c.1007G>A	p.Arg336Gln	p.R336Q	ENST00000298552	NM_001162426.1	336	cGg/cAg	10/23	0.332625497334919	2	FACETS	0.883	0.781	0.992	0.441	0.39	0.496	CLONAL	1	TRUE	0	0.338174011091612	2		439	556	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436257	110436257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1316736634	NA	P-0025239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	19	287	0	ENST00000375856.3:c.2144C>T	p.Ala715Val	p.A715V	ENST00000375856	NM_003749.2	715	gCg/gTg	1/2	1	2	FACETS	0.741	0.565	0.945	0.741	0.565	0.945	CLONAL	1	TRUE	1	0.272794996517457	2		287	188	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90976637	90976637	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0025239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	238	508	0	ENST00000265433.3:c.994+1del		p.X332_splice	ENST00000265433	NM_002485.4	332			0.272794996517457	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	1	0.272794996517457	4		508	683	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	166	255	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.997	0.925	1	1	0.993	1	CLONAL	2	TRUE	1	0.376636194905119	2		255	442	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	156	655	3	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.376636194905119	2		658	806	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	88	621	1	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	2	FACETS	0.774	0.686	0.867	0.774	0.686	0.867	SUBCLONAL	1	TRUE	1	0.376636194905119	2		622	604	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	61	467	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.782	0.677	0.896	0.782	0.677	0.896	SUBCLONAL	1	TRUE	1	0.376636194905119	2		467	414	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	105	306	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.961	0.874	1	1	0.988	1	CLONAL	2	TRUE	1	0.376636194905119	2		306	290	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112154	115112154	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	110	567	0	ENST00000257566.3:c.1586del	p.Gly529AlafsTer103	p.G529Afs*103	ENST00000257566	NM_016569.3	529	gGc/gc	7/8	1	2	FACETS	0.951	0.857	1	0.951	0.857	1	CLONAL	1	TRUE	1	0.376636194905119	2		567	614	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182575	99182575	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1231375445	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	86	530	0	ENST00000074304.5:c.2378G>A	p.Arg793Gln	p.R793Q	ENST00000074304	NM_001134224.1	793	cGa/cAa	22/26	1	2	FACETS	0.862	0.764	0.965	0.862	0.764	0.965	CLONAL	1	TRUE	1	0.376636194905119	2		530	530	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654642	67654642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	156	542	1	ENST00000264010.4:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000264010	NM_006565.3	377	Cgt/Tgt	6/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.376636194905119	2		543	667	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850705	63850705	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs201178069	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	44	311	0	ENST00000279873.7:c.1489del	p.Ile497Ter	p.I497*	ENST00000279873	NM_032199.2	495	Aaa/aa	10/10	1	2	FACETS	0.715	0.602	0.838	0.715	0.602	0.838	SUBCLONAL	1	TRUE	1	0.376636194905119	2		311	327	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088788	27088788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	83	570	3	ENST00000324856.7:c.2402del	p.Gly801ValfsTer32	p.G801Vfs*32	ENST00000324856	NM_006015.4	799	caG/ca	7/20	1	2	FACETS	0.964	0.855	1	0.964	0.855	1	CLONAL	1	TRUE	1	0.376636194905119	2		573	457	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053023	180053023	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	101	388	4	ENST00000261937.6:c.1267del	p.Gln423ArgfsTer70	p.Q423Rfs*70	ENST00000261937	NM_182925.4	423	Cag/ag	10/30	1	2	FACETS	0.851	0.762	0.946	0.851	0.762	0.946	CLONAL	1	TRUE	1	0.376636194905119	2		392	630	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468185	120468185	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	125	618	3	ENST00000256646.2:c.4254del	p.Ser1419AlafsTer8	p.S1419Afs*8	ENST00000256646	NM_024408.3	1418	ccC/cc	25/34	1	2	FACETS	0.948	0.86	1	0.948	0.86	1	CLONAL	1	TRUE	1	0.376636194905119	2		621	700	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885145	111885145	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs892433462	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	107	529	0	ENST00000341259.2:c.1038del	p.Leu347CysfsTer26	p.L347Cfs*26	ENST00000341259	NM_005475.2	345	Ggg/gg	6/8	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.376636194905119	2		529	511	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	67	319	0	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.376636194905119	2		319	307	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155721	56155722	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	74	353	0	ENST00000399503.3:c.816_817del	p.Arg273SerfsTer27	p.R273Sfs*27	ENST00000399503	NM_005921.1	271	agAAaa/agaa	3/20	1	2	FACETS	0.958	0.843	1	0.958	0.843	1	CLONAL	1	TRUE	1	0.376636194905119	2		353	410	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217557	142217557	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1268253442	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	80	548	0	ENST00000350721.4:c.5440del	p.Arg1814GlufsTer10	p.R1814Efs*10	ENST00000350721	NM_001184.3	1814	Aga/ga	32/47	1	2	FACETS	0.904	0.798	1	0.904	0.798	1	CLONAL	1	TRUE	1	0.376636194905119	2		548	470	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434595	110434595	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs555841746	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	59	543	1	ENST00000375856.3:c.3806A>C	p.Gln1269Pro	p.Q1269P	ENST00000375856	NM_003749.2	1269	cAg/cCg	1/2	1	2	FACETS	0.52	0.447	0.599	0.52	0.447	0.599	SUBCLONAL	1	TRUE	1	0.376636194905119	2		544	603	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790819	89790819	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	92	673	1	ENST00000336032.3:c.211del	p.Gln71SerfsTer112	p.Q71Sfs*112	ENST00000336032	NM_006813.2	69	aCc/ac	1/2	1	2	FACETS	0.809	0.72	0.904	0.809	0.72	0.904	CLONAL	1	TRUE	1	0.376636194905119	2		674	604	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955111	17955112	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755706305	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	90	698	0	ENST00000458235.1:c.115dup	p.Gln39ProfsTer13	p.Q39Pfs*13	ENST00000458235	NM_000215.3	39	cag/cCag	2/24	1	2	FACETS	0.666	0.59	0.746	0.666	0.59	0.746	SUBCLONAL	1	TRUE	1	0.376636194905119	2		698	718	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696461	47696461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	72	459	0	ENST00000347630.2:c.362G>A	p.Arg121Gln	p.R121Q	ENST00000347630	NM_001007230.1	121	cGg/cAg	6/11	1	2	FACETS	0.993	0.872	1	0.993	0.872	1	CLONAL	1	TRUE	1	0.376636194905119	2		459	385	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188294	32188295	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs766348245	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	76	756	5	ENST00000375023.3:c.1046dup	p.Thr350HisfsTer4	p.T350Hfs*4	ENST00000375023	NM_004557.3	349	ggc/ggGc	6/30	1	2	FACETS	0.6	0.526	0.679	0.6	0.526	0.679	SUBCLONAL	1	TRUE	1	0.376636194905119	2		761	673	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86668014	86668014	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	36	298	0	ENST00000274376.6:c.1776+2T>C		p.X592_splice	ENST00000274376	NM_002890.2	592			1	2	FACETS	0.724	0.598	0.863	0.724	0.598	0.863	SUBCLONAL	1	TRUE	1	0.376636194905119	2		298	264	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813432	102813432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751304020	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	89	535	1	ENST00000307046.8:c.257C>T	p.Ala86Val	p.A86V	ENST00000307046	NM_001111285.1	86	gCg/gTg	3/4	1	2	FACETS	0.742	0.658	0.831	0.742	0.658	0.831	SUBCLONAL	1	TRUE	1	0.376636194905119	2		536	637	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929412	44929415	+	frameshift_variant	Frame_Shift_Del	DEL	ACAA	ACAA	-	rs786205676	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	108	674	0	ENST00000377967.4:c.2515_2518del	p.Asn839ValfsTer27	p.N839Vfs*27	ENST00000377967	NM_021140.2	838	ACAAac/ac	17/29	1	2	FACETS	0.84	0.754	0.93	0.84	0.754	0.93	CLONAL	1	TRUE	1	0.376636194905119	2		674	683	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	106	646	5	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.376636194905119	2		651	555	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944121	71944123	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	107	622	0	ENST00000298229.2:c.1960_1962del	p.Glu654del	p.E654del	ENST00000298229	NM_001567.3	652	GAG/-	17/28	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.376636194905119	2		622	553	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38631981	38631981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1255149646	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	106	654	7	ENST00000299084.4:c.471del	p.Gln158SerfsTer16	p.Q158Sfs*16	ENST00000299084	NM_152594.2	156	cTt/ct	5/7	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.376636194905119	2		661	506	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260223	19260223	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767499551	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	127	749	0	ENST00000162023.5:c.70C>T	p.Arg24Trp	p.R24W	ENST00000162023		24	Cgg/Tgg	7/13	1	2	FACETS	0.942	0.854	1	0.942	0.854	1	CLONAL	1	TRUE	1	0.376636194905119	2		749	716	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948376	71948376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746017563	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	161	865	2	ENST00000298229.2:c.3088C>T	p.Arg1030Trp	p.R1030W	ENST00000298229	NM_001567.3	1030	Cgg/Tgg	26/28	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.376636194905119	2		867	820	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073803	8073804	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	54	298	0	ENST00000377482.5:c.855dup	p.Arg286GlnfsTer7	p.R286Qfs*7	ENST00000377482	NM_018948.3	285	-/C	4/4	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.376636194905119	2		298	248	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248576	8248577	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	120	718	0	ENST00000335790.3:c.310dup	p.Ala104GlyfsTer40	p.A104Gfs*40	ENST00000335790	NM_002315.2	104	gcc/gGcc	3/4	1	2	FACETS	0.908	0.821	0.999	0.908	0.821	0.999	CLONAL	1	TRUE	1	0.376636194905119	2		718	702	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942052	71942053	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1326136034	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	98	672	2	ENST00000298229.2:c.1322dup	p.Asn441LysfsTer25	p.N441Kfs*25	ENST00000298229	NM_001567.3	439	cca/ccAa	12/28	1	2	FACETS	0.772	0.689	0.86	0.772	0.689	0.86	SUBCLONAL	1	TRUE	1	0.376636194905119	2		674	674	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192633	94192633	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747832587	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	120	672	0	ENST00000323929.3:c.1441del	p.Thr481HisfsTer43	p.T481Hfs*43	ENST00000323929	NM_005591.3	481	Aca/ca	13/20	1	2	FACETS	0.961	0.87	1	0.961	0.87	1	CLONAL	1	TRUE	1	0.376636194905119	2		672	663	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102874150	102874150	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	48	420	0	ENST00000307046.8:c.10del	p.Ile4SerfsTer17	p.I4Sfs*17	ENST00000307046	NM_001111285.1	4	Atc/tc	1/4	1	2	FACETS	0.671	0.569	0.783	0.671	0.569	0.783	SUBCLONAL	1	TRUE	1	0.376636194905119	2		420	380	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252024	133252024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	128	667	0	ENST00000320574.5:c.1186del	p.Glu396SerfsTer16	p.E396Sfs*16	ENST00000320574	NM_006231.2	396	Gag/ag	12/49	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.376636194905119	2		667	666	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563246	21563246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	122	768	0	ENST00000382592.4:c.673G>A	p.Gly225Ser	p.G225S	ENST00000382592	NM_014572.2	225	Ggc/Agc	4/8	1	2	FACETS	0.896	0.811	0.986	0.896	0.811	0.986	CLONAL	1	TRUE	1	0.376636194905119	2		768	723	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566120	95566120	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	50	312	0	ENST00000393063.1:c.4203A>C	p.Glu1401Asp	p.E1401D	ENST00000393063	NM_030621.3	1401	gaA/gaC	23/28	1	2	FACETS	0.843	0.719	0.977	0.843	0.719	0.977	CLONAL	1	TRUE	1	0.376636194905119	2		312	315	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994788	73994788	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs368957019	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	90	585	0	ENST00000318443.5:c.272A>G	p.Asn91Ser	p.N91S	ENST00000318443	NM_001024736.1	91	aAc/aGc	3/10	1	2	FACETS	0.883	0.786	0.987	0.883	0.786	0.987	CLONAL	1	TRUE	1	0.376636194905119	2		585	541	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679189	88679189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200596109	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	76	575	1	ENST00000360948.2:c.848C>T	p.Thr283Met	p.T283M	ENST00000360948	NM_001012338.2	283	aCg/aTg	8/19	1	2	FACETS	0.645	0.566	0.73	0.645	0.566	0.73	SUBCLONAL	1	TRUE	1	0.376636194905119	2		576	626	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862948	9862948	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	85	418	0	ENST00000330684.3:c.2357-2A>G		p.X786_splice	ENST00000330684	NM_001134407.1	786			1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.376636194905119	2		418	443	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992483	72992483	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	127	804	0	ENST00000268489.5:c.1562del	p.Lys521ArgfsTer15	p.K521Rfs*15	ENST00000268489	NM_006885.3	521	aAg/ag	2/10	1	2	FACETS	0.91	0.825	0.999	0.91	0.825	0.999	CLONAL	1	TRUE	1	0.376636194905119	2		804	741	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578521	7578521	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	177	857	0	ENST00000269305.4:c.409C>G	p.Leu137Val	p.L137V	ENST00000269305	NM_001126112.2	137	Ctg/Gtg	5/11	1	2	FACETS	0.98	0.903	1	0.98	0.903	1	CLONAL	1	TRUE	1	0.376636194905119	2		857	959	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667845	37667845	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	101	484	0	ENST00000447079.4:c.2730G>T	p.Glu910Asp	p.E910D	ENST00000447079	NM_015083.1	910	gaG/gaT	8/14	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.376636194905119	2		484	482	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804366	46804366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1466480316	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	113	466	3	ENST00000290295.7:c.641G>A	p.Arg214His	p.R214H	ENST00000290295	NM_006361.5	214	cGt/cAt	2/2	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.376636194905119	2		469	511	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55334496	55334496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	62	413	0	ENST00000284073.2:c.100C>T	p.Pro34Ser	p.P34S	ENST00000284073	NM_138962.2	34	Cca/Tca	2/14	1	2	FACETS	0.88	0.764	1	0.88	0.764	1	CLONAL	1	TRUE	1	0.376636194905119	2		413	374	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101901	11101901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	166	704	0	ENST00000358026.2:c.1321C>T	p.Arg441Cys	p.R441C	ENST00000358026	NM_001128849.1	441	Cgc/Tgc	8/36	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.376636194905119	2		704	825	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289671	15289671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	123	828	2	ENST00000263388.2:c.3800C>A	p.Pro1267His	p.P1267H	ENST00000263388	NM_000435.2	1267	cCt/cAt	23/33	1	2	FACETS	0.823	0.744	0.906	0.823	0.744	0.906	CLONAL	1	TRUE	1	0.376636194905119	2		830	794	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752930	42752930	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs768716522	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	143	765	0	ENST00000222329.4:c.1334A>G	p.Asp445Gly	p.D445G	ENST00000222329	NM_006494.2	445	gAt/gGt	4/4	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.376636194905119	2		765	732	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537911	212537911	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	78	611	0	ENST00000342788.4:c.1694G>C	p.Gly565Ala	p.G565A	ENST00000342788	NM_005235.2	565	gGc/gCc	14/28	1	2	FACETS	0.77	0.678	0.868	0.77	0.678	0.868	SUBCLONAL	1	TRUE	1	0.376636194905119	2		611	538	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37056033	37056033	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	86	421	0	ENST00000231790.2:c.788A>T	p.Asn263Ile	p.N263I	ENST00000231790	NM_000249.3	263	aAc/aTc	9/19	0.376489163442811	2	FACETS	0.865	0.776	0.957	0.865	0.776	0.957	CLONAL	2	TRUE	0	0.376636194905119	2		421	264	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515612	31515613	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	70	519	0	ENST00000344624.3:c.1006dup	p.Glu336GlyfsTer4	p.E336Gfs*4	ENST00000344624		336	gag/gGag	4/33	1	2	FACETS	0.839	0.734	0.952	0.839	0.734	0.952	CLONAL	1	TRUE	1	0.376636194905119	2		519	443	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86676377	86676377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	43	351	0	ENST00000274376.6:c.2655G>A	p.Trp885Ter	p.W885*	ENST00000274376	NM_002890.2	885	tgG/tgA	20/25	1	2	FACETS	0.852	0.718	0.999	0.852	0.718	0.999	CLONAL	1	TRUE	1	0.376636194905119	2		351	268	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176662911	176662911	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	65	377	0	ENST00000439151.2:c.3891del	p.Lys1297AsnfsTer12	p.K1297Nfs*12	ENST00000439151	NM_022455.4	1296	Aaa/aa	6/23	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.376636194905119	2		377	325	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670915	30670915	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	121	721	0	ENST00000376406.3:c.5831del	p.Gly1944GlufsTer27	p.G1944Efs*27	ENST00000376406	NM_014641.2	1944	gGa/ga	12/15	1	2	FACETS	0.852	0.77	0.938	0.852	0.77	0.938	CLONAL	1	TRUE	1	0.376636194905119	2		721	754	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099899	157099899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	117	615	1	ENST00000346085.5:c.836G>A	p.Ser279Asn	p.S279N	ENST00000346085	NM_020732.3	279	aGc/aAc	1/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.376636194905119	2		616	581	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521969	157521969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs530430137	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	85	448	2	ENST00000346085.5:c.4241C>T	p.Pro1414Leu	p.P1414L	ENST00000346085	NM_020732.3	1414	cCg/cTg	18/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.376636194905119	2		450	394	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467614	50467614	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	50	245	0	ENST00000331340.3:c.851-2A>G		p.X284_splice	ENST00000331340	NM_006060.4	284			1	2	FACETS	0.942	0.805	1	0.942	0.805	1	CLONAL	1	TRUE	1	0.376636194905119	2		245	282	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346037	152346037	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	91	547	0	ENST00000359321.1:c.533A>G	p.Gln178Arg	p.Q178R	ENST00000359321	NM_005431.1	178	cAg/cGg	3/3	1	2	FACETS	0.924	0.823	1	0.924	0.823	1	CLONAL	1	TRUE	1	0.376636194905119	2		547	523	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559360	141559360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	123	609	1	ENST00000220592.5:c.1441G>A	p.Ala481Thr	p.A481T	ENST00000220592	NM_012154.3	481	Gcc/Acc	12/19	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.376636194905119	2		610	653	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595382	141595382	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	80	668	0	ENST00000220592.5:c.51del	p.Ile18SerfsTer121	p.I18Sfs*121	ENST00000220592	NM_012154.3	17	ccC/cc	2/19	1	2	FACETS	0.613	0.539	0.692	0.613	0.539	0.692	SUBCLONAL	1	TRUE	1	0.376636194905119	2		668	693	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760801	133760801	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746810970	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	98	585	1	ENST00000318560.5:c.3124G>A	p.Ala1042Thr	p.A1042T	ENST00000318560	NM_005157.4	1042	Gcc/Acc	11/11	1	2	FACETS	0.875	0.782	0.973	0.875	0.782	0.973	CLONAL	1	TRUE	1	0.376636194905119	2		586	595	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403420	139403420	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	127	790	1	ENST00000277541.6:c.3073T>C	p.Cys1025Arg	p.C1025R	ENST00000277541	NM_017617.3	1025	Tgc/Cgc	19/34	1	2	FACETS	0.9	0.816	0.989	0.9	0.816	0.989	CLONAL	1	TRUE	1	0.376636194905119	2		791	749	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870210	44870210	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746630730	NA	P-0025240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	51	562	0	ENST00000377967.4:c.389C>T	p.Ala130Val	p.A130V	ENST00000377967	NM_021140.2	130	gCt/gTt	5/29	1	2	FACETS	0.672	0.573	0.781	0.672	0.573	0.781	SUBCLONAL	1	TRUE	1	0.376636194905119	2		562	403	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0025242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	139	336	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.943	0.864	1	0.943	0.864	1	CLONAL	1	TRUE	1	0.57	2		336	517	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023904	27023904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1232964733	NA	P-0025242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	15	89	0	ENST00000324856.7:c.1015del	p.Ala339LeufsTer24	p.A339Lfs*24	ENST00000324856	NM_006015.4	337	tGg/tg	1/20	1	2	FACETS	0.702	0.524	0.905	0.702	0.524	0.905	CLONAL	1	TRUE	1	0.57	2		89	75	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0025242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	121	510	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.847	0.77	0.929	0.847	0.77	0.929	CLONAL	1	TRUE	1	0.57	2		510	501	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0025242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	126	306	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.998	0.911	1	0.998	0.911	1	CLONAL	1	TRUE	1	0.57	2		306	443	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	168	339	0	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.922	0.851	0.996	0.922	0.851	0.996	CLONAL	1	TRUE	1	0.57	2		339	639	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116263	209116263	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	87	344	0	ENST00000345146.2:c.13del	p.Ile5SerfsTer7	p.I5Sfs*7	ENST00000345146	NM_005896.2	5	Atc/tc	3/10	1	2	FACETS	0.694	0.617	0.775	0.694	0.617	0.775	SUBCLONAL	1	TRUE	1	0.57	2		344	440	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435136	110435136	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs780127725	NA	P-0025242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	153	457	0	ENST00000375856.3:c.3265G>C	p.Ala1089Pro	p.A1089P	ENST00000375856	NM_003749.2	1089	Gcc/Ccc	1/2	1	2	FACETS	0.835	0.766	0.906	0.835	0.766	0.906	CLONAL	1	TRUE	1	0.57	2		457	643	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067432	37067433	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs587778906	NA	P-0025242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	172	389	0	ENST00000231790.2:c.1348dup	p.Asp450GlyfsTer29	p.D450Gfs*29	ENST00000231790	NM_000249.3	448	gag/gaGg	12/19	1	2	FACETS	0.914	0.845	0.987	0.914	0.845	0.987	CLONAL	1	TRUE	1	0.57	2		389	660	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618676	37618676	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1021200845	NA	P-0025242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	205	392	0	ENST00000447079.4:c.352C>T	p.Arg118Cys	p.R118C	ENST00000447079	NM_015083.1	118	Cgt/Tgt	1/14	1	2	FACETS	0.915	0.851	0.981	0.915	0.851	0.981	CLONAL	1	TRUE	1	0.57	2		392	786	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58701089	58701089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	44	516	0	ENST00000305921.3:c.680G>A	p.Arg227Gln	p.R227Q	ENST00000305921	NM_003620.3	227	cGa/cAa	2/6	1	2	FACETS	0.204	0.17	0.241	0.204	0.17	0.241	SUBCLONAL	1	TRUE	1	0.57	2		516	758	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942053	71942053	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	228	590	2	ENST00000298229.2:c.1322del	p.Asn441ThrfsTer2	p.N441Tfs*2	ENST00000298229	NM_001567.3	439	ccA/cc	12/28	1	2	FACETS	0.94	0.878	1	0.94	0.878	1	CLONAL	1	TRUE	1	0.57	2		592	851	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109969	115109969	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	205	454	1	ENST00000257566.3:c.1909C>T	p.Arg637Trp	p.R637W	ENST00000257566	NM_016569.3	637	Cgg/Tgg	8/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.57	2		455	668	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561417	141561417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1487711892	NA	P-0025242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	133	246	0	ENST00000220592.5:c.1388C>T	p.Thr463Met	p.T463M	ENST00000220592	NM_012154.3	463	aCg/aTg	11/19	1	2	FACETS	0.952	0.87	1	0.952	0.87	1	CLONAL	1	TRUE	1	0.57	2		246	490	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0025242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	220	625	0	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	1	2	FACETS	0.813	0.757	0.871	0.813	0.757	0.871	CLONAL	1	TRUE	1	0.57	2		625	949	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366609	40366609	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0025242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	202	469	0	ENST00000397332.2:c.586+2T>C		p.X196_splice	ENST00000397332	NM_001033082.2	196			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.57	2		469	634	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851288	156851288	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	216	517	1	ENST00000524377.1:c.2245C>A	p.Pro749Thr	p.P749T	ENST00000524377	NM_002529.3	749	Cca/Aca	17/17	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.57	2		518	739	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983022	201983022	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	242	608	0	ENST00000359651.3:c.871G>T	p.Gly291Cys	p.G291C	ENST00000359651		291	Ggc/Tgc	7/8	1	2	FACETS	0.927	0.867	0.988	0.927	0.867	0.988	CLONAL	1	TRUE	1	0.57	2		608	916	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948484	71948484	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	232	649	0	ENST00000298229.2:c.3201del	p.Ser1068AlafsTer63	p.S1068Afs*63	ENST00000298229	NM_001567.3	1066	Ccc/cc	26/28	1	2	FACETS	0.905	0.846	0.967	0.905	0.846	0.967	CLONAL	1	TRUE	1	0.57	2		649	899	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856139	111856139	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	23	336	0	ENST00000341259.2:c.190T>C	p.Ser64Pro	p.S64P	ENST00000341259	NM_005475.2	64	Tcg/Ccg	2/8	1	2	FACETS	0.197	0.153	0.248	0.197	0.153	0.248	SUBCLONAL	1	TRUE	1	0.57	2		336	410	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257722	133257722	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0025242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	194	412	0	ENST00000320574.5:c.204+2T>A		p.X68_splice	ENST00000320574	NM_006231.2	68			1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.57	2		412	676	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061157	38061157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	88	168	0	ENST00000250448.2:c.832G>A	p.Gly278Ser	p.G278S	ENST00000250448	NM_004496.3	278	Ggc/Agc	2/2	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.57	2		168	279	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219068	36219068	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	188	469	1	ENST00000222270.7:c.4567C>T	p.Pro1523Ser	p.P1523S	ENST00000222270	NM_014727.1	1523	Cca/Tca	19/37	1	2	FACETS	0.938	0.87	1	0.938	0.87	1	CLONAL	1	TRUE	1	0.57	2		470	703	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053501	37053501	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0025242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	194	422	0	ENST00000231790.2:c.589-1G>A		p.X197_splice	ENST00000231790	NM_000249.3	197			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.57	2		422	589	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143226690	143226690	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs1330358087	NA	P-0025242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	111	330	0	ENST00000262992.4:c.424C>T	p.Arg142Ter	p.R142*	ENST00000262992	NM_001101669.1	142	Cga/Tga	7/24	1	2	FACETS	0.788	0.712	0.868	0.788	0.712	0.868	SUBCLONAL	1	TRUE	1	0.57	2		330	494	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162475200	162475200	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs755495887	NA	P-0025242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	151	403	0	ENST00000366898.1:c.541T>C	p.Ser181Pro	p.S181P	ENST00000366898	NM_004562.2	181	Tct/Cct	5/12	1	2	FACETS	0.979	0.901	1	0.979	0.901	1	CLONAL	1	TRUE	1	0.57	2		403	541	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346567	81346567	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	30	328	0	ENST00000222390.5:c.1386T>A	p.Asp462Glu	p.D462E	ENST00000222390	NM_000601.4	462	gaT/gaA	11/18	1	2	FACETS	0.251	0.202	0.307	0.251	0.202	0.307	SUBCLONAL	1	TRUE	1	0.57	2		328	419	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537132	80537132	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	206	494	0	ENST00000286548.4:c.266C>T	p.Ala89Val	p.A89V	ENST00000286548	NM_002072.3	89	gCc/gTc	2/7	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.57	2		494	714	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417553	139417553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	284	609	1	ENST00000277541.6:c.491G>A	p.Cys164Tyr	p.C164Y	ENST00000277541	NM_017617.3	164	tGc/tAc	4/34	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.57	2		610	906	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092815	27092815	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	64	582	0	ENST00000324856.7:c.2840del	p.Pro947HisfsTer21	p.P947Hfs*21	ENST00000324856	NM_006015.4	946	Ccc/cc	9/20	1	2	FACETS	0.353	0.305	0.406	0.353	0.305	0.406	SUBCLONAL	1	TRUE	1	0.434363131399993	2		582	834	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10286283	10286283	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	135	649	0	ENST00000340748.4:c.533G>A	p.Arg178Gln	p.R178Q	ENST00000340748		178	cGg/cAg	6/40	1	2	FACETS	0.713	0.648	0.781	0.713	0.648	0.781	SUBCLONAL	1	TRUE	1	0.434363131399993	2		649	872	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514015	103514015	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	36	558	0	ENST00000355739.4:c.831G>C	p.Glu277Asp	p.E277D	ENST00000355739	NM_000123.3	277	gaG/gaC	7/15	1	2	FACETS	0.279	0.228	0.335	0.279	0.228	0.335	SUBCLONAL	1	TRUE	1	0.434363131399993	2		558	595	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201920	102201920	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	73	316	0	ENST00000263464.3:c.1272A>T	p.Glu424Asp	p.E424D	ENST00000263464	NM_001165.4	424	gaA/gaT	6/9	1	2	FACETS	0.715	0.627	0.809	0.715	0.627	0.809	SUBCLONAL	1	TRUE	1	0.434363131399993	2		316	470	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914982	32914982	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397507860	NA	P-0025243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	103	581	2	ENST00000380152.3:c.6490C>T	p.Gln2164Ter	p.Q2164*	ENST00000380152		2164	Cag/Tag	11/27	0.376170857212406	1	FACETS	0.7	0.629	0.776	0.7	0.629	0.776	SUBCLONAL	1	TRUE	0	0.434363131399993	1		583	530	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303080	15303080	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	63	1052	0	ENST00000263388.2:c.370C>G	p.Leu124Val	p.L124V	ENST00000263388	NM_000435.2	124	Ctc/Gtc	4/33	1	2	FACETS	0.373	0.322	0.429	0.373	0.322	0.429	SUBCLONAL	1	TRUE	1	0.434363131399993	2		1052	777	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158636950	158636950	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	136	564	0	ENST00000263640.3:c.230G>T	p.Gly77Val	p.G77V	ENST00000263640	NM_001105.4	77	gGa/gTa	4/11	1	2	FACETS	0.858	0.781	0.938	0.858	0.781	0.938	CLONAL	1	TRUE	1	0.434363131399993	2		564	730	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968305	134968305	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	66	712	1	ENST00000398015.3:c.2818C>A	p.Leu940Ile	p.L940I	ENST00000398015	NM_004441.4	940	Ctc/Atc	15/16	0.434363131399993	3	FACETS	0.435	0.376	0.498	0.217	0.188	0.249	SUBCLONAL	1	TRUE	1	0.434363131399993	3		713	851	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56171055	56171055	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0025243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	34	337	0	ENST00000399503.3:c.1883C>G	p.Ser628Ter	p.S628*	ENST00000399503	NM_005921.1	628	tCa/tGa	10/20	1	2	FACETS	0.305	0.248	0.368	0.305	0.248	0.368	SUBCLONAL	1	TRUE	1	0.434363131399993	2		337	514	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679939	30679939	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	86	454	0	ENST00000376406.3:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000376406	NM_014641.2	594	Gat/Aat	5/15	1	2	FACETS	0.642	0.568	0.72	0.642	0.568	0.72	SUBCLONAL	1	TRUE	1	0.434363131399993	2		454	617	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517444	157517444	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	47	526	2	ENST00000346085.5:c.4008C>A	p.Asp1336Glu	p.D1336E	ENST00000346085	NM_020732.3	1336	gaC/gaA	16/20	1	2	FACETS	0.328	0.276	0.386	0.328	0.276	0.386	SUBCLONAL	1	TRUE	1	0.434363131399993	2		528	659	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339257	87339273	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ACCTCACTGTGCATTGT	ACCTCACTGTGCATTGT	-	novel	NA	P-0025243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	51	618	0	ENST00000277120.3:c.841_853+4del		p.X281_splice	ENST00000277120		281		8/19	1	2	FACETS	0.346	0.293	0.404	0.346	0.293	0.404	SUBCLONAL	1	TRUE	1	0.434363131399993	2		618	679	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0025244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	183	364	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.465927227065059	2		364	781	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0025244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	462	637	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.465927227065059	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.465927227065059	2		637	924	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0025244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	363	578	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.465927227065059	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.465927227065059	3		578	928	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001366	29001366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779189056	NA	P-0025244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	571	391	0	ENST00000282397.4:c.1366G>A	p.Ala456Thr	p.A456T	ENST00000282397	NM_002019.4	456	Gca/Aca	10/30	0.401901822957614	5	FACETS	0.936	0.903	0.969			1	CLONAL	4	TRUE	NA	0.465927227065059	5		391	1112	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281699	49281699	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1287	309	855	0	ENST00000282018.3:c.746T>C	p.Ile249Thr	p.I249T	ENST00000282018	NM_020377.2	249	aTc/aCc	1/1	0.465927227065059	3	FACETS	1	0.959	1	0.512	0.481	0.544	CLONAL	1	TRUE	1	0.465927227065059	3		855	1596	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198260834	198260834	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	187	642	0	ENST00000335508.6:c.3485G>C	p.Gly1162Ala	p.G1162A	ENST00000335508	NM_012433.2	1162	gGa/gCa	23/25	0.465927227065059	3	FACETS	0.896	0.827	0.969	0.448	0.413	0.485	CLONAL	1	TRUE	1	0.465927227065059	3		642	1104	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539348	187539348	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	138	487	0	ENST00000441802.2:c.8392C>G	p.Gln2798Glu	p.Q2798E	ENST00000441802	NM_005245.3	2798	Caa/Gaa	10/27	1	2	FACETS	0.942	0.86	1	0.942	0.86	1	CLONAL	1	TRUE	1	0.465927227065059	2		487	629	SUCCESS
APC	324	MSKCC	GRCh37	5	112175784	112175799	+	frameshift_variant	Frame_Shift_Del	DEL	ATGGATTTTCTTGTTC	ATGGATTTTCTTGTTC	-	novel	NA	P-0025244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	184	346	0	ENST00000257430.4:c.4495_4510del	p.Gly1499ProfsTer3	p.G1499Pfs*3	ENST00000257430	NM_000038.5	1498	gATGGATTTTCTTGTTCa/ga	16/16	0.465927227065059	3	FACETS	1	0.946	1	0.678	0.631	0.725	CLONAL	2	TRUE	0	0.465927227065059	3		346	479	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	163	495	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.400122162899187	1	FACETS	0.956	0.88	1	0.956	0.88	1	CLONAL	1	TRUE	0	0.400122162899187	1		495	682	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	258	562	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.400122162899187	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.400122162899187	1		563	751	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189867	11189867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	161	476	2	ENST00000361445.4:c.5642C>T	p.Thr1881Met	p.T1881M	ENST00000361445	NM_004958.3	1881	aCg/aTg	40/58	0.400122162899187	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.400122162899187	1		478	601	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	110	617	1	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	0.400122162899187	1	FACETS	0.516	0.463	0.572	0.516	0.463	0.572	SUBCLONAL	1	TRUE	0	0.400122162899187	1		618	852	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491731	120491731	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	65	364	0	ENST00000256646.2:c.2498T>C	p.Val833Ala	p.V833A	ENST00000256646	NM_024408.3	833	gTa/gCa	16/34	0.400122162899187	1	FACETS	0.564	0.49	0.643	0.564	0.49	0.643	SUBCLONAL	1	TRUE	0	0.400122162899187	1		364	461	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874572	155874572	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	101	595	1	ENST00000368323.3:c.187C>T	p.Arg63Cys	p.R63C	ENST00000368323	NM_006912.5	63	Cgt/Tgt	4/6	0.400122162899187	1	FACETS	0.498	0.445	0.555	0.498	0.445	0.555	SUBCLONAL	1	TRUE	0	0.400122162899187	1		596	811	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70412277	70412277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	42	303	0	ENST00000373644.4:c.4387G>A	p.Ala1463Thr	p.A1463T	ENST00000373644	NM_030625.2	1463	Gca/Aca	6/12	0.400122162899187	1	FACETS	0.474	0.397	0.56	0.474	0.397	0.56	SUBCLONAL	1	TRUE	0	0.400122162899187	1		303	354	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571907	64571907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	331	653	0	ENST00000312049.6:c.1732C>T	p.Gln578Ter	p.Q578*	ENST00000312049	NM_130799.2	578	Caa/Taa	10/10	0.400122162899187	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.400122162899187	1		653	981	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625281	69625281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35983315	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	97	438	0	ENST00000334134.2:c.512G>A	p.Arg171His	p.R171H	ENST00000334134	NM_005247.2	171	cGc/cAc	3/3	0.400122162899187	1	FACETS	0.592	0.528	0.66	0.592	0.528	0.66	SUBCLONAL	1	TRUE	0	0.400122162899187	1		438	655	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948668	71948668	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	98	438	1	ENST00000298229.2:c.3380C>A	p.Ala1127Asp	p.A1127D	ENST00000298229	NM_001567.3	1127	gCc/gAc	26/28	0.400122162899187	1	FACETS	0.661	0.591	0.735	0.661	0.591	0.735	SUBCLONAL	1	TRUE	0	0.400122162899187	1		439	593	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102033228	102033228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	105	573	6	ENST00000282441.5:c.614C>T	p.Ala205Val	p.A205V	ENST00000282441	NM_001130145.2	205	gCc/gTc	3/9	0.400122162899187	1	FACETS	0.608	0.545	0.674	0.608	0.545	0.674	SUBCLONAL	1	TRUE	0	0.400122162899187	1		579	691	SUCCESS
ATM	472	MSKCC	GRCh37	11	108099951	108099951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878853493	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	35	314	0	ENST00000278616.4:c.232G>A	p.Ala78Thr	p.A78T	ENST00000278616	NM_000051.3	78	Gca/Aca	4/63	0.400122162899187	1	FACETS	0.436	0.358	0.523	0.436	0.358	0.523	SUBCLONAL	1	TRUE	0	0.400122162899187	1		314	321	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348837	118348837	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	85	311	0	ENST00000534358.1:c.3490C>A	p.Pro1164Thr	p.P1164T	ENST00000534358	NM_005933.3	1164	Cct/Act	5/36	0.400122162899187	1	FACETS	0.719	0.637	0.805	0.719	0.637	0.805	SUBCLONAL	1	TRUE	0	0.400122162899187	1		311	473	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	131	599	3	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	0.400122162899187	1	FACETS	0.669	0.607	0.734	0.669	0.607	0.734	SUBCLONAL	1	TRUE	0	0.400122162899187	1		602	783	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856574	111856574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	46	132	0	ENST00000341259.2:c.625G>A	p.Ala209Thr	p.A209T	ENST00000341259	NM_005475.2	209	Gcc/Acc	2/8	0.400122162899187	1	FACETS	0.748	0.635	0.87	0.748	0.635	0.87	SUBCLONAL	1	TRUE	0	0.400122162899187	1		132	246	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022911	33022911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1280677560	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	68	338	0	ENST00000300177.4:c.20C>T	p.Thr7Met	p.T7M	ENST00000300177	NM_001191322.1	7	aCg/aTg	2/2	0.400122162899187	1	FACETS	0.634	0.553	0.72	0.634	0.553	0.72	SUBCLONAL	1	TRUE	0	0.400122162899187	1		338	429	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991059	41991059	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	102	365	0	ENST00000219905.7:c.2014-2A>G		p.X672_splice	ENST00000219905	NM_001164273.1	672			0.400122162899187	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.400122162899187	1		365	357	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996790	73996790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775147523	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	52	209	1	ENST00000318443.5:c.1346C>T	p.Ala449Val	p.A449V	ENST00000318443	NM_001024736.1	449	gCg/gTg	6/10	0.400122162899187	1	FACETS	0.634	0.542	0.733	0.634	0.542	0.733	SUBCLONAL	1	TRUE	0	0.400122162899187	1		210	328	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830751	3830751	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	28	359	0	ENST00000262367.5:c.1805G>A	p.Ser602Asn	p.S602N	ENST00000262367	NM_004380.2	602	aGc/aAc	8/31	0.400122162899187	1	FACETS	0.215	0.171	0.266	0.215	0.171	0.266	SUBCLONAL	1	TRUE	0	0.400122162899187	1		359	520	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868072	56868072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771065608	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	57	330	1	ENST00000308159.5:c.1570C>T	p.Arg524Trp	p.R524W	ENST00000308159	NM_014669.4	524	Cgg/Tgg	14/22	0.400122162899187	1	FACETS	0.421	0.361	0.486	0.421	0.361	0.486	SUBCLONAL	1	TRUE	0	0.400122162899187	1		331	542	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950271	15950271	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	199	714	0	ENST00000268712.3:c.6673G>C	p.Asp2225His	p.D2225H	ENST00000268712	NM_006311.3	2225	Gat/Cat	42/46	0.400122162899187	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.400122162899187	1		714	772	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441504	40441504	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	126	463	0	ENST00000345506.4:c.75C>G	p.His25Gln	p.H25Q	ENST00000345506	NM_003152.3	25	caC/caG	3/20	0.400122162899187	1	FACETS	0.73	0.662	0.802	0.73	0.662	0.802	SUBCLONAL	1	TRUE	0	0.400122162899187	1		463	690	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244694	41244694	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	109	684	0	ENST00000357654.3:c.2854T>G	p.Phe952Val	p.F952V	ENST00000357654	NM_007294.3	952	Ttt/Gtt	10/23	0.400122162899187	1	FACETS	0.64	0.575	0.708	0.64	0.575	0.708	SUBCLONAL	1	TRUE	0	0.400122162899187	1		684	681	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245027	41245027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1800709	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	105	724	1	ENST00000357654.3:c.2521C>T	p.Arg841Trp	p.R841W	ENST00000357654	NM_007294.3	841	Cgg/Tgg	10/23	0.400122162899187	1	FACETS	0.555	0.497	0.617	0.555	0.497	0.617	SUBCLONAL	1	TRUE	0	0.400122162899187	1		725	756	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63545678	63545678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	120	416	2	ENST00000307078.5:c.916G>A	p.Ala306Thr	p.A306T	ENST00000307078	NM_004655.3	306	Gcg/Acg	3/11	0.400122162899187	1	FACETS	0.758	0.686	0.834	0.758	0.686	0.834	SUBCLONAL	1	TRUE	0	0.400122162899187	1		418	633	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857261	78857261	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1046298474	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	37	405	3	ENST00000306801.3:c.1627G>A	p.Val543Ile	p.V543I	ENST00000306801	NM_020761.2	543	Gtc/Atc	15/34	0.400122162899187	1	FACETS	0.249	0.205	0.299	0.249	0.205	0.299	SUBCLONAL	1	TRUE	0	0.400122162899187	1		408	593	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867611	78867611	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	99	578	0	ENST00000306801.3:c.2347A>C	p.Thr783Pro	p.T783P	ENST00000306801	NM_020761.2	783	Acc/Ccc	20/34	0.400122162899187	1	FACETS	0.524	0.467	0.584	0.524	0.467	0.584	SUBCLONAL	1	TRUE	0	0.400122162899187	1		578	756	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226986	2226986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1418469674	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	107	363	0	ENST00000398665.3:c.4466C>T	p.Ala1489Val	p.A1489V	ENST00000398665	NM_032482.2	1489	gCc/gTc	27/28	0.400122162899187	1	FACETS	0.636	0.571	0.704	0.636	0.571	0.704	SUBCLONAL	1	TRUE	0	0.400122162899187	1		363	673	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208010	5208010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	124	472	1	ENST00000357368.4:c.5701C>T	p.Arg1901Trp	p.R1901W	ENST00000357368	NM_002850.3	1901	Cgg/Tgg	37/38	0.400122162899187	1	FACETS	0.679	0.615	0.747	0.679	0.615	0.747	SUBCLONAL	1	TRUE	0	0.400122162899187	1		473	730	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138614	11138614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	215	511	0	ENST00000358026.2:c.3370C>T	p.Leu1124Phe	p.L1124F	ENST00000358026	NM_001128849.1	1124	Ctc/Ttc	24/36	0.400122162899187	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.400122162899187	1		511	699	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257144	19257144	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	59	350	0	ENST00000162023.5:c.819del	p.Thr274ProfsTer?	p.T274Pfs*?	ENST00000162023		273	ccC/cc	12/13	0.400122162899187	1	FACETS	0.51	0.439	0.586	0.51	0.439	0.586	SUBCLONAL	1	TRUE	0	0.400122162899187	1		350	463	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211850	36211850	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1379320589	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	148	597	1	ENST00000222270.7:c.1601C>T	p.Ala534Val	p.A534V	ENST00000222270	NM_014727.1	534	gCc/gTc	3/37	0.400122162899187	1	FACETS	0.663	0.606	0.724	0.663	0.606	0.724	SUBCLONAL	1	TRUE	0	0.400122162899187	1		598	892	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798428	42798428	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	126	560	1	ENST00000575354.2:c.4303del	p.Asp1435ThrfsTer19	p.D1435Tfs*19	ENST00000575354	NM_015125.3	1433	gaG/ga	18/20	0.400122162899187	1	FACETS	0.554	0.501	0.609	0.554	0.501	0.609	SUBCLONAL	1	TRUE	0	0.400122162899187	1		561	910	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799131	42799131	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	157	454	1	ENST00000575354.2:c.4620del	p.Thr1541LeufsTer79	p.T1541Lfs*79	ENST00000575354	NM_015125.3	1539	Ccc/cc	20/20	0.400122162899187	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.400122162899187	1		455	530	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140100	50140100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1358894507	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	109	510	0	ENST00000246792.3:c.325G>A	p.Ala109Thr	p.A109T	ENST00000246792	NM_006270.3	109	Gcc/Acc	3/6	0.400122162899187	1	FACETS	0.622	0.559	0.688	0.622	0.559	0.688	SUBCLONAL	1	TRUE	0	0.400122162899187	1		510	701	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213243	39213243	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	152	714	2	ENST00000402219.2:c.3724del	p.Ser1242ValfsTer37	p.S1242Vfs*37	ENST00000402219	NM_005633.3	1242	Agt/gt	23/23	0.400122162899187	1	FACETS	0.734	0.672	0.799	0.734	0.672	0.799	SUBCLONAL	1	TRUE	0	0.400122162899187	1		716	828	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657066	47657066	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	90	310	0	ENST00000233146.2:c.1262T>G	p.Leu421Arg	p.L421R	ENST00000233146	NM_000251.2	421	cTg/cGg	7/16	0.400122162899187	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.400122162899187	1		310	334	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62325821	62325821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756579704	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	92	406	0	ENST00000360203.5:c.3089C>T	p.Ser1030Leu	p.S1030L	ENST00000360203	NM_001283009.1	1030	tCg/tTg	31/35	0.400122162899187	1	FACETS	0.638	0.567	0.712	0.638	0.567	0.712	SUBCLONAL	1	TRUE	0	0.400122162899187	1		406	577	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42842590	42842590	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs771443342	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	114	547	5	ENST00000398585.3:c.1267del	p.Ala423ProfsTer12	p.A423Pfs*12	ENST00000398585	NM_001135099.1	423	Gcc/cc	11/14	0.400122162899187	1	FACETS	0.638	0.574	0.704	0.638	0.574	0.704	SUBCLONAL	1	TRUE	0	0.400122162899187	1		552	715	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139542	47139542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	97	428	1	ENST00000409792.3:c.5045C>T	p.Ser1682Leu	p.S1682L	ENST00000409792	NM_014159.6	1682	tCa/tTa	9/21	0.400122162899187	1	FACETS	0.733	0.656	0.815	0.733	0.656	0.815	SUBCLONAL	1	TRUE	0	0.400122162899187	1		429	529	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928867	49928867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1320258189	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	111	560	0	ENST00000296474.3:c.3499G>A	p.Gly1167Ser	p.G1167S	ENST00000296474	NM_002447.2	1167	Ggt/Agt	16/20	0.400122162899187	1	FACETS	0.653	0.587	0.722	0.653	0.587	0.722	SUBCLONAL	1	TRUE	0	0.400122162899187	1		560	680	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932759	49932759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751488352	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	157	712	0	ENST00000296474.3:c.3112G>A	p.Ala1038Thr	p.A1038T	ENST00000296474	NM_002447.2	1038	Gca/Aca	14/20	0.400122162899187	1	FACETS	0.703	0.644	0.765	0.703	0.644	0.765	SUBCLONAL	1	TRUE	0	0.400122162899187	1		712	893	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169985727	169985727	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369872734	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	127	546	0	ENST00000295797.4:c.389G>A	p.Arg130His	p.R130H	ENST00000295797	NM_002740.5	130	cGc/cAc	5/18	0.400122162899187	1	FACETS	0.671	0.608	0.737	0.671	0.608	0.737	SUBCLONAL	1	TRUE	0	0.400122162899187	1		546	757	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947803	178947803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	38	325	0	ENST00000263967.3:c.2678C>T	p.Ala893Val	p.A893V	ENST00000263967	NM_006218.2	893	gCc/gTc	19/21	0.400122162899187	1	FACETS	0.435	0.361	0.518	0.435	0.361	0.518	SUBCLONAL	1	TRUE	0	0.400122162899187	1		325	349	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260644	1260644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1278994586	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	153	501	1	ENST00000310581.5:c.2915G>A	p.Arg972His	p.R972H	ENST00000310581	NM_198253.2	972	cGc/cAc	12/16	1	2	FACETS	0.797	0.729	0.869	0.797	0.729	0.869	SUBCLONAL	1	TRUE	1	0.400122162899187	2		502	959	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508827	31508827	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	171	554	0	ENST00000344624.3:c.1488C>G	p.Ser496Arg	p.S496R	ENST00000344624		496	agC/agG	7/33	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.400122162899187	2		554	756	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38981989	38981989	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	49	497	0	ENST00000357387.3:c.733C>T	p.Arg245Ter	p.R245*	ENST00000357387	NM_152756.3	245	Cga/Tga	8/38	1	2	FACETS	0.432	0.365	0.505	0.432	0.365	0.505	SUBCLONAL	1	TRUE	1	0.400122162899187	2		497	567	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183208	56183208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	63	309	2	ENST00000399503.3:c.4118C>T	p.Ala1373Val	p.A1373V	ENST00000399503	NM_005921.1	1373	gCc/gTc	18/20	1	2	FACETS	0.662	0.573	0.757	0.662	0.573	0.757	SUBCLONAL	1	TRUE	1	0.400122162899187	2		311	476	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753013	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	86	301	0	ENST00000274289.3:c.1003_1004del	p.Leu335AlafsTer11	p.L335Afs*11	ENST00000274289	NM_006622.3	335	TTg/g	7/14	1	2	FACETS	0.981	0.872	1	0.981	0.872	1	CLONAL	1	TRUE	1	0.400122162899187	2		301	438	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593301	67593301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	165	267	0	ENST00000274335.5:c.2047G>A	p.Glu683Lys	p.E683K	ENST00000274335		683	Gag/Aag	15/15	1	2	FACETS	0.813	0.752	0.876	1	0.991	1	CLONAL	2	TRUE	1	0.400122162899187	2		267	507	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	58	251	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	1	2	FACETS	0.848	0.732	0.972	0.848	0.732	0.972	CLONAL	1	TRUE	1	0.400122162899187	2		251	342	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166736	32166736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867581638	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	330	605	0	ENST00000375023.3:c.4502G>A	p.Arg1501Gln	p.R1501Q	ENST00000375023	NM_004557.3	1501	cGg/cAg	24/30	0.400122162899187	1	FACETS	0.763	0.724	0.802	1	0.995	1	SUBCLONAL	2	TRUE	0	0.400122162899187	1		605	865	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715470	117715470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	132	497	1	ENST00000368508.3:c.1019C>T	p.Ser340Phe	p.S340F	ENST00000368508	NM_002944.2	340	tCt/tTt	10/43	0.400122162899187	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.400122162899187	1		498	398	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129085	152129085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767166523	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	117	446	4	ENST00000206249.3:c.38C>T	p.Ala13Val	p.A13V	ENST00000206249	NM_000125.3	13	gCc/gTc	1/8	0.400122162899187	1	FACETS	0.743	0.671	0.818	0.743	0.671	0.818	SUBCLONAL	1	TRUE	0	0.400122162899187	1		450	630	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572622	141572622	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772067763	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	102	478	0	ENST00000220592.5:c.448C>T	p.Arg150Trp	p.R150W	ENST00000220592	NM_012154.3	150	Cgg/Tgg	4/19	0.400122162899187	2	FACETS	0.682	0.61	0.758	0.341	0.305	0.379	SUBCLONAL	1	TRUE	0	0.400122162899187	2		478	748	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971053	21971053	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137854598	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	85	237	0	ENST00000304494.5:c.305C>T	p.Ala102Val	p.A102V	ENST00000304494	NM_000077.4	102	gCg/gTg	2/3	0.400122162899187	1	FACETS	0.914	0.813	1	0.914	0.813	1	CLONAL	1	TRUE	0	0.400122162899187	1		237	372	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399386	139399386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201360886	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	105	424	0	ENST00000277541.6:c.4757G>A	p.Arg1586His	p.R1586H	ENST00000277541	NM_017617.3	1586	cGc/cAc	26/34	0.400122162899187	1	FACETS	0.718	0.645	0.795	0.718	0.645	0.795	SUBCLONAL	1	TRUE	0	0.400122162899187	1		424	585	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404305	139404305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777658333	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	126	530	1	ENST00000277541.6:c.2849C>T	p.Ala950Val	p.A950V	ENST00000277541	NM_017617.3	950	gCc/gTc	18/34	0.400122162899187	1	FACETS	0.716	0.649	0.786	0.716	0.649	0.786	SUBCLONAL	1	TRUE	0	0.400122162899187	1		531	704	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916463	39916463	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	129	320	0	ENST00000378444.4:c.4540C>T	p.Arg1514Ter	p.R1514*	ENST00000378444	NM_001123385.1	1514	Cga/Tga	11/15	0.290494668030017	0	FACETS	0.91	0.832	0.991			1	CLONAL	1	TRUE	NA	0.400122162899187	0		320	425	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416406	29416406	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	348	779	1	ENST00000389048.3:c.4547C>A	p.Thr1516Asn	p.T1516N	ENST00000389048	NM_004304.4	1516	aCc/aAc	29/29	0.722683555806384	3	FACETS	0.909	0.86	0.96	0.455	0.43	0.48	CLONAL	1	TRUE	1	0.740031946636151	3		780	1417	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713692	52713696	+	frameshift_variant	Frame_Shift_Del	DEL	GGAAG	GGAAG	-	novel	NA	P-0025246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	148	491	0	ENST00000394830.3:c.32_36del	p.Pro11GlnfsTer8	p.P11Qfs*8	ENST00000394830	NM_018313.4	11	cCTTCC/c	2/30	1	2	FACETS	0.693	0.636	0.753	0.693	0.636	0.753	SUBCLONAL	1	TRUE	1	0.740031946636151	2		491	577	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0025247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	170	288	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.857	0.797	0.918	1	0.992	1	CLONAL	2	TRUE	1	0.46337438555018	2		288	428	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0025247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	421	569	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	0.979	0.937	1	1	0.997	1	CLONAL	2	TRUE	1	0.46337438555018	2		569	928	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	420	858	0	ENST00000269305.4:c.833del	p.Pro278LeufsTer67	p.P278Lfs*67	ENST00000269305	NM_001126112.2	278	cCt/ct	8/11	1	2	FACETS	0.957	0.916	0.999	1	0.997	1	CLONAL	2	TRUE	1	0.46337438555018	2		858	947	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412252	139412252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057523819	NA	P-0025247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	59	904	1	ENST00000277541.6:c.1393G>A	p.Ala465Thr	p.A465T	ENST00000277541	NM_017617.3	465	Gcc/Acc	8/34	0.26438059050385	1	FACETS	0.227	0.194	0.263	0.227	0.194	0.263	INDETERMINATE	1	TRUE	0	0.46337438555018	1		905	862	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940978	49940978	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140992621	NA	P-0025247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	339	642	0	ENST00000296474.3:c.65C>T	p.Ala22Val	p.A22V	ENST00000296474	NM_002447.2	22	gCg/gTg	1/20	1	2	FACETS	0.985	0.938	1	1	0.996	1	CLONAL	2	TRUE	1	0.46337438555018	2		642	743	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938056	76938057	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	403	373	0	ENST00000373344.5:c.2691dup	p.Asp898ArgfsTer13	p.D898Rfs*13	ENST00000373344	NM_000489.3	897	-/A	9/35	1	1	FACETS	0.911	0.887	0.933	1	0.998	1	CLONAL	3	TRUE	0	0.46337438555018	1		373	489	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0025254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	1047	792	54	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	NA	2	FACETS	0.995	0.979	1			1	INDETERMINATE	2	TRUE	NA	0.810407610601532	2		846	1298	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0025254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	956	792	1	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.810407610601532	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.810407610601532	2		793	1161	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0025254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	361	593	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	0.788944690140408	1	FACETS	0.989	0.953	1	0.989	0.953	1	CLONAL	1	TRUE	0	0.810407610601532	1		593	536	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	333	576	0	ENST00000342988.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000342988	NM_005359.5	356	cCt/cTt	9/12	0.788944690140408	1	FACETS	0.998	0.96	1	0.998	0.96	1	CLONAL	1	TRUE	0	0.810407610601532	1		576	490	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40743886	40743886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434593	NA	P-0025254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	767	652	0	ENST00000392038.2:c.821G>A	p.Arg274His	p.R274H	ENST00000392038	NM_001626.4	274	cGc/cAc	9/14	0.704359040333256	4	FACETS	0.977	0.945	1	0.977	0.945	1	CLONAL	2	TRUE	2	0.810407610601532	4		652	1754	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243859004	243859004	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	232	451	0	ENST00000263826.5:c.61A>C	p.Asn21His	p.N21H	ENST00000263826	NM_005465.4	21	Aac/Cac	2/13	1	2	FACETS	0.972	0.914	1	0.972	0.914	1	CLONAL	1	TRUE	1	0.810407610601532	2		451	589	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857463	68857464	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0025254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1213	386	679	1	ENST00000261769.5:c.2098_2099delinsAA	p.Pro700Asn	p.P700N	ENST00000261769	NM_004360.3	700	CCt/AAt	13/16	0.381051882248481	5	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.810407610601532	5		680	1599	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295698	212295698	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	353	657	0	ENST00000342788.4:c.2615A>G	p.Glu872Gly	p.E872G	ENST00000342788	NM_005235.2	872	gAa/gGa	21/28	0.810407610601532	3	FACETS	0.979	0.927	1			1	CLONAL	1	TRUE	NA	0.810407610601532	3		657	1250	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566842	212566842	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	392	305	1	ENST00000342788.4:c.1339T>C	p.Phe447Leu	p.F447L	ENST00000342788	NM_005235.2	447	Ttc/Ctc	12/28	NA	2	FACETS	0.981	0.954	1			1	INDETERMINATE	2	TRUE	NA	0.810407610601532	2		306	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0025255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	222	769	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.391048801377221	2	FACETS	0.907	0.85	0.966	0.907	0.85	0.966	CLONAL	2	TRUE	0	0.393454353381212	2		770	622	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748041	72748041	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1313981698	NA	P-0025255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	235	726	0	ENST00000357731.5:c.137A>G	p.Asp46Gly	p.D46G	ENST00000357731	NM_173808.2	46	gAc/gGc	1/7	0.393454353381212	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.393454353381212	2		726	571	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37865585	37865585	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	58	730	0	ENST00000269571.5:c.454G>A	p.Gly152Arg	p.G152R	ENST00000269571		152	Ggg/Agg	4/27	0.291953891477847	3	FACETS	0.518	0.444	0.599	0.259	0.222	0.3	SUBCLONAL	1	TRUE	1	0.393454353381212	3		730	681	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213906	66213906	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1363376793	NA	P-0025255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	22	554	0	ENST00000273854.3:c.2524A>G	p.Ile842Val	p.I842V	ENST00000273854	NM_004439.5	842	Atc/Gtc	15/18	0.209544985837784	1	FACETS	0.25	0.193	0.315	0.25	0.193	0.315	INDETERMINATE	1	TRUE	0	0.393454353381212	1		554	360	SUCCESS
APC	324	MSKCC	GRCh37	5	112174559	112174559	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	104	544	1	ENST00000257430.4:c.3268C>T	p.Gln1090Ter	p.Q1090*	ENST00000257430	NM_000038.5	1090	Caa/Taa	16/16	0.393454353381212	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.393454353381212	1		545	366	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0025256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	140	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.500871873232475	3	FACETS	0.897	0.818	0.981	0.449	0.409	0.491	CLONAL	1	TRUE	1	0.500871873232475	3		326	779	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0025256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	428	570	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.494139153547119	2	FACETS	0.966	0.926	1	0.966	0.926	1	CLONAL	2	TRUE	0	0.500871873232475	2		570	885	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108652	8108652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777705809	NA	P-0025256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	292	708	1	ENST00000585124.1:c.743G>A	p.Arg248His	p.R248H	ENST00000585124	NM_004217.3	248	cGc/cAc	8/9	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.500871873232475	2		709	1086	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293475	1293475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554042799	NA	P-0025256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	235	782	1	ENST00000310581.5:c.1526C>T	p.Thr509Met	p.T509M	ENST00000310581	NM_198253.2	509	aCg/aTg	2/16	0.367434399859579	3	FACETS	0.88	0.82	0.943			1	CLONAL	1	TRUE	NA	0.500871873232475	3		783	1333	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061701	38061701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	122	337	1	ENST00000250448.2:c.288G>A	p.Met96Ile	p.M96I	ENST00000250448	NM_004496.3	96	atG/atA	2/2	0.500871873232475	3	FACETS	1	0.907	1	0.5	0.453	0.549	CLONAL	1	TRUE	1	0.500871873232475	3		338	609	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870298	155870298	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	242	629	0	ENST00000368323.3:c.541G>A	p.Glu181Lys	p.E181K	ENST00000368323	NM_006912.5	181	Gag/Aag	6/6	0.500871873232475	3	FACETS	1	0.951	1	0.511	0.477	0.547	CLONAL	1	TRUE	1	0.500871873232475	3		629	1182	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675422	241675422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	130	402	0	ENST00000366560.3:c.400G>A	p.Asp134Asn	p.D134N	ENST00000366560	NM_000143.3	134	Gat/Aat	4/10	0.499260946862703	4	FACETS	1	0.949	1			1	CLONAL	1	TRUE	NA	0.500871873232475	4		402	731	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446449	49446449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760762714	NA	P-0025256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	225	573	0	ENST00000301067.7:c.1156G>A	p.Asp386Asn	p.D386N	ENST00000301067	NM_003482.3	386	Gat/Aat	9/54	0.500871873232475	4	FACETS	1	0.97	1	0.359	0.333	0.385	CLONAL	1	TRUE	1	0.500871873232475	4		573	1252	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46252829	46252829	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0025256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1237	68	234	0	ENST00000371998.3:c.256+2T>C		p.X86_splice	ENST00000371998		86			0.500871873232475	13	FACETS	0.781	0.677	0.895			1	SUBCLONAL	1	TRUE	NA	0.500871873232475	13		234	1305	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551083	41551083	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	263	727	0	ENST00000263253.7:c.3227G>C	p.Arg1076Pro	p.R1076P	ENST00000263253	NM_001429.3	1076	cGt/cCt	17/31	0.48981382518073	3	FACETS	0.961	0.899	1	0.32	0.299	0.342	CLONAL	1	TRUE	0	0.500871873232475	3		727	1366	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265533	152265533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	214	587	0	ENST00000206249.3:c.986C>T	p.Ser329Phe	p.S329F	ENST00000206249	NM_000125.3	329	tCc/tTc	4/8	0.494139153547119	2	FACETS	0.98	0.912	1	0.49	0.456	0.525	CLONAL	1	TRUE	0	0.500871873232475	2		587	872	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0025257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	156	403	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.839035663272892	2		403	321	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0025257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	529	478	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	0.839035663272892	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.839035663272892	2		478	591	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163019	47163026	+	frameshift_variant	Frame_Shift_Del	DEL	TCATGAAC	TCATGAAC	-	novel	NA	P-0025257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	70	460	0	ENST00000409792.3:c.3100_3107del	p.Val1034ArgfsTer7	p.V1034Rfs*7	ENST00000409792	NM_014159.6	1034	GTTCATGAa/a	3/21	1	2	FACETS	0.455	0.398	0.515	0.455	0.398	0.515	SUBCLONAL	1	TRUE	1	0.839035663272892	2		460	367	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0025258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	92	510	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.333152531692828	5	FACETS	1	0.916	1	0.259	0.23	0.291	CLONAL	1	TRUE	1	0.333152531692828	5		510	798	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46252683	46252683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372533478	NA	P-0025258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	38	366	2	ENST00000371998.3:c.112C>T	p.Arg38Trp	p.R38W	ENST00000371998		38	Cgg/Tgg	4/23	1	2	FACETS	0.758	0.629	0.901	0.758	0.629	0.901	CLONAL	1	TRUE	1	0.333152531692828	2		368	301	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687112	176687112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	101	674	0	ENST00000439151.2:c.5089C>T	p.Arg1697Trp	p.R1697W	ENST00000439151	NM_022455.4	1697	Cgg/Tgg	14/23	0.333152531692828	1	FACETS	0.896	0.803	0.994	0.896	0.803	0.994	CLONAL	1	TRUE	0	0.333152531692828	1		674	564	SUCCESS
FH	2271	MSKCC	GRCh37	1	241661199	241661199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201115573	NA	P-0025259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	125	792	3	ENST00000366560.3:c.1462G>A	p.Glu488Lys	p.E488K	ENST00000366560	NM_000143.3	488	Gaa/Aaa	10/10	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		795	1010	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0025264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	157	675	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	0.807358547730222	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.807358547730222	1		675	219	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707599	176707599	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	261	512	0	ENST00000439151.2:c.5656A>C	p.Thr1886Pro	p.T1886P	ENST00000439151	NM_022455.4	1886	Act/Cct	18/23	NA	2	FACETS	0.971	0.916	1			1	INDETERMINATE	1	TRUE	NA	0.807358547730222	2		512	666	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0025266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	120	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.269712122632621	3	FACETS	0.863	0.782	0.948	0.863	0.782	0.948	CLONAL	2	TRUE	1	0.269712122632621	3		326	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577507	7577507	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	201	715	0	ENST00000269305.4:c.774A>C	p.Glu258Asp	p.E258D	ENST00000269305	NM_001126112.2	258	gaA/gaC	7/11	0.269712122632621	2	FACETS	0.978	0.909	1	0.978	0.909	1	CLONAL	2	TRUE	0	0.269712122632621	2		715	762	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0025267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	466	825	6	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	1	2	FACETS	0.952	0.912	0.994	0.952	0.912	0.994	CLONAL	1	TRUE	1	0.828554099919983	2		831	1181	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218538	5218538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767763908	NA	P-0025267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1246	153	854	1	ENST00000357368.4:c.3941G>A	p.Arg1314His	p.R1314H	ENST00000357368	NM_002850.3	1314	cGc/cAc	25/38	0.322892083296691	3	FACETS	0.373	0.34	0.408	0.187	0.17	0.204	INDETERMINATE	1	TRUE	1	0.828554099919983	3		855	1399	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508683	106508683	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	371	557	2	ENST00000359195.3:c.677G>T	p.Arg226Leu	p.R226L	ENST00000359195	NM_002649.2	226	cGc/cTc	2/11	1	2	FACETS	0.974	0.928	1	0.974	0.928	1	CLONAL	1	TRUE	1	0.828554099919983	2		559	919	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039195	49039195	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	323	592	1	ENST00000267163.4:c.2273C>A	p.Ser758Ter	p.S758*	ENST00000267163	NM_000321.2	758	tCg/tAg	22/27	0.828554099919983	1	FACETS	0.997	0.961	1	0.997	0.961	1	CLONAL	1	TRUE	0	0.828554099919983	1		593	458	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458576	120458576	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	392	651	3	ENST00000256646.2:c.6769A>G	p.Met2257Val	p.M2257V	ENST00000256646	NM_024408.3	2257	Atg/Gtg	34/34	0.822003596797411	3	FACETS	1	0.962	1	0.507	0.482	0.533	CLONAL	1	TRUE	1	0.828554099919983	3		654	1319	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778377	3778377	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	367	787	1	ENST00000262367.5:c.6671del	p.Gly2224AlafsTer78	p.G2224Afs*78	ENST00000262367	NM_004380.2	2224	gGc/gc	31/31	0.828554099919983	1	FACETS	0.954	0.919	0.987	0.954	0.919	0.987	CLONAL	1	TRUE	0	0.828554099919983	1		788	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578450	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0025267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	460	801	3	ENST00000269305.4:c.480_481delinsTT	p.Met160_Ala161delinsIleSer	p.M160_A161delinsIS	ENST00000269305	NM_001126112.2	160	atGGcc/atTTcc	5/11	1	2	FACETS	0.978	0.937	1	0.978	0.937	1	CLONAL	1	TRUE	1	0.828554099919983	2		804	1135	SUCCESS
ATR	545	MSKCC	GRCh37	3	142222256	142222256	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	823	472	9	ENST00000350721.4:c.5236C>G	p.Leu1746Val	p.L1746V	ENST00000350721	NM_001184.3	1746	Ctt/Gtt	30/47	0.688640377005141	4	FACETS	0.916	0.892	0.939	0.916	0.892	0.939	CLONAL	3	TRUE	1	0.828554099919983	4		481	1322	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430344	47430344	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	215	859	3	ENST00000377045.4:c.1619A>G	p.Lys540Arg	p.K540R	ENST00000377045	NM_001654.4	540	aAg/aGg	15/16	0.504435625819372	1	FACETS	0.324	0.301	0.348	0.324	0.301	0.348	SUBCLONAL	1	TRUE	0	0.828554099919983	1		862	937	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0025269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	138	510	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.878	0.8	0.959	0.878	0.8	0.959	CLONAL	1	TRUE	1	0.437794294672947	2		510	718	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938967	76938967	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782774889	NA	P-0025269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	109	757	0	ENST00000373344.5:c.1781C>T	p.Ser594Phe	p.S594F	ENST00000373344	NM_000489.3	594	tCc/tTc	9/35	1	2	FACETS	0.526	0.472	0.584	0.526	0.472	0.584	SUBCLONAL	1	TRUE	1	0.437794294672947	2		757	946	SUCCESS
CBL	867	MSKCC	GRCh37	11	119077192	119077192	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	70	412	0	ENST00000264033.4:c.65C>T	p.Ser22Leu	p.S22L	ENST00000264033	NM_005188.3	22	tCg/tTg	1/16	0.437794294672947	1	FACETS	0.523	0.457	0.593	0.523	0.457	0.593	SUBCLONAL	1	TRUE	0	0.437794294672947	1		412	478	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243496	46243496	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	123	445	0	ENST00000334344.6:c.1849G>C	p.Val617Leu	p.V617L	ENST00000334344	NM_152641.2	617	Gtt/Ctt	14/21	1	2	FACETS	0.806	0.73	0.886	0.806	0.73	0.886	CLONAL	1	TRUE	1	0.437794294672947	2		445	697	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243509	46243509	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1300885277	NA	P-0025269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	123	435	0	ENST00000334344.6:c.1862T>C	p.Val621Ala	p.V621A	ENST00000334344	NM_152641.2	621	gTt/gCt	14/21	1	2	FACETS	0.859	0.779	0.944	0.859	0.779	0.944	CLONAL	1	TRUE	1	0.437794294672947	2		435	654	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73334685	73334685	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	126	440	0	ENST00000377767.4:c.2775G>C	p.Met925Ile	p.M925I	ENST00000377767	NM_014953.3	925	atG/atC	20/21	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.437794294672947	2		440	549	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795072	42795072	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1568515919	NA	P-0025269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	173	693	3	ENST00000575354.2:c.2152C>A	p.Pro718Thr	p.P718T	ENST00000575354	NM_015125.3	718	Cct/Act	10/20	1	2	FACETS	0.921	0.848	0.997	0.921	0.848	0.997	CLONAL	1	TRUE	1	0.437794294672947	2		696	858	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940088	31940088	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs746708221	NA	P-0025269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	161	498	1	ENST00000375333.2:c.230C>G	p.Pro77Arg	p.P77R	ENST00000375333	NM_032454.1	77	cCc/cGc	2/8	1	2	FACETS	0.99	0.91	1	0.99	0.91	1	CLONAL	1	TRUE	1	0.437794294672947	2		499	743	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924226	11924249	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGCGGCGGCTCCGGGGGCGGCA	GCGGCGGCGGCTCCGGGGGCGGCA	C	novel	NA	P-0025269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	21	6	0	ENST00000353533.5:c.23_46delinsC	p.Gly8AlafsTer25	p.G8Afs*25	ENST00000353533	NM_003010.3	8	gGCGGCGGCGGCTCCGGGGGCGGCAgc/gCgc	1/11	0.437794294672947	1	FACETS	0.861	0.737	0.968	1	0.962	1	CLONAL	3	TRUE	0	0.437794294672947	1		6	29	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0025272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	244	574	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.268901257267225	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.286305363756431	2		574	768	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578441	7578441	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1567553246	NA	P-0025272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1269	190	725	1	ENST00000269305.4:c.489C>G	p.Tyr163Ter	p.Y163*	ENST00000269305	NM_001126112.2	163	taC/taG	5/11	0.245844176304174	1	FACETS	0.779	0.718	0.843	0.779	0.718	0.843	SUBCLONAL	1	TRUE	0	0.286305363756431	1		726	1459	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911934	32911934	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397507667	NA	P-0025272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	268	580	0	ENST00000380152.3:c.3442C>T	p.Gln1148Ter	p.Q1148*	ENST00000380152		1148	Cag/Tag	11/27	NA	2	FACETS	1	0.969	1			1	INDETERMINATE	2	TRUE	NA	0.286305363756431	2		580	894	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482869	67482869	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	275	438	0	ENST00000327367.4:c.1273T>G	p.Ser425Ala	p.S425A	ENST00000327367	NM_005902.3	425	Tct/Gct	9/9	0.268901257267225	2	FACETS	0.944	0.887	1	0.944	0.887	1	CLONAL	2	TRUE	0	0.286305363756431	2		438	1017	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	54	606	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.864	0.735	1	0.864	0.735	1	CLONAL	1	TRUE	1	0.12	2		606	1042	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940077	76940077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	56	583	1	ENST00000373344.5:c.671C>T	p.Ala224Val	p.A224V	ENST00000373344	NM_000489.3	224	gCg/gTg	9/35	1	2	FACETS	0.922	0.787	1	0.922	0.787	1	CLONAL	1	TRUE	1	0.12	2		584	1012	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0025273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	45	328	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	0.855	0.716	1	0.855	0.716	1	CLONAL	1	TRUE	1	0.12	2		328	877	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012324	152012324	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	75	537	0	ENST00000262189.6:c.489G>A	p.Trp163Ter	p.W163*	ENST00000262189	NM_170606.2	163	tgG/tgA	4/59	1	2	FACETS	0.758	0.664	0.861	1	0.975	1	SUBCLONAL	2	TRUE	1	0.12	2		537	824	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293544	137293544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761885700	NA	P-0025273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	66	686	0	ENST00000481739.1:c.95C>T	p.Ser32Leu	p.S32L	ENST00000481739	NM_002957.4	32	tCg/tTg	2/10	1	2	FACETS	0.966	0.835	1	0.966	0.835	1	CLONAL	1	TRUE	1	0.12	2		686	1139	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519998	NA	P-0025279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	247	686	0	ENST00000269305.4:c.581T>C	p.Leu194Pro	p.L194P	ENST00000269305	NM_001126112.2	194	cTt/cCt	6/11	0.131792294912102	6	FACETS	0.991	0.949	1			1	INDETERMINATE	5	FALSE	NA	0.649708650204438	6		686	353	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843482	156843482	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	87	575	0	ENST00000524377.1:c.908T>A	p.Phe303Tyr	p.F303Y	ENST00000524377	NM_002529.3	303	tTc/tAc	8/17	0.623554881233487	5	FACETS	1	0.952	1			1	CLONAL	1	FALSE	NA	0.649708650204438	5		575	468	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184535	7184535	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs781007453	NA	P-0025279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	102	525	0	ENST00000302850.5:c.766C>G	p.Arg256Gly	p.R256G	ENST00000302850	NM_000208.2	256	Cgc/Ggc	3/22	0.553819008372831	6	FACETS	1	0.958	1	0.284	0.254	0.316	CLONAL	1	FALSE	2	0.649708650204438	6		525	635	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39234270	39234270	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	51	616	0	ENST00000402219.2:c.2575C>A	p.Leu859Ile	p.L859I	ENST00000402219	NM_005633.3	859	Cta/Ata	16/23	0.604632907927013	4	FACETS	0.89	0.762	1	0.297	0.254	0.343	CLONAL	1	FALSE	1	0.649708650204438	4		616	291	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024146	31024146	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	97	705	0	ENST00000375687.4:c.3631G>C	p.Asp1211His	p.D1211H	ENST00000375687	NM_015338.5	1211	Gac/Cac	13/13	0.616062473103174	4	FACETS	1	0.934	1	0.352	0.315	0.391	CLONAL	1	FALSE	1	0.649708650204438	4		705	466	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540399	187540399	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	53	441	0	ENST00000441802.2:c.7341C>G	p.Ile2447Met	p.I2447M	ENST00000441802	NM_005245.3	2447	atC/atG	10/27	0.649708650204438	3	FACETS	0.865	0.744	0.993	0.432	0.372	0.497	CLONAL	1	FALSE	1	0.649708650204438	3		441	250	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750748	57750748	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	36	427	0	ENST00000274289.3:c.1856G>C	p.Gly619Ala	p.G619A	ENST00000274289	NM_006622.3	619	gGc/gCc	13/14	0.649708650204438	3	FACETS	0.972	0.812	1	0.486	0.406	0.573	CLONAL	1	FALSE	1	0.649708650204438	3		427	151	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158491	26158491	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	78	534	0	ENST00000289316.2:c.94C>G	p.Arg32Gly	p.R32G	ENST00000289316	NM_138720.2	32	Cgc/Ggc	1/2	0.649708650204438	6	FACETS	1	0.928	1	0.215	0.189	0.243	CLONAL	1	FALSE	1	0.649708650204438	6		534	513	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0025280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	1348	767	1	ENST00000397752.3:c.3028+1G>A		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.515139028503205	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	4	TRUE	0	0.515139028503205	4		768	1959	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577567	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1567549651	NA	P-0025280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	320	627	0	ENST00000269305.4:c.714dup	p.Asn239Ter	p.N239*	ENST00000269305	NM_001126112.2	238	-/T	7/11	0.37433412902618	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.515139028503205	1		627	756	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953826	131953826	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs368980595	NA	P-0025280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	72	431	0	ENST00000265335.6:c.3229C>T	p.Arg1077Ter	p.R1077*	ENST00000265335		1077	Cga/Tga	21/25	0.249281293498152	3	FACETS	0.499	0.435	0.567	0.166	0.145	0.189	INDETERMINATE	1	TRUE	0	0.515139028503205	3		431	705	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573146	41573155	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAAGCTCC	CAGAAGCTCC	-	novel	NA	P-0025280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	115	637	0	ENST00000263253.7:c.5431_5440del	p.Gln1811GlyfsTer92	p.Q1811Gfs*92	ENST00000263253	NM_001429.3	1811	CAGAAGCTCCgg/gg	31/31	1	2	FACETS	0.497	0.447	0.55	0.497	0.447	0.55	SUBCLONAL	1	TRUE	1	0.515139028503205	2		637	899	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971133	13971133	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	87	222	1	ENST00000405192.2:c.796G>A	p.Asp266Asn	p.D266N	ENST00000405192	NM_001163147.1	266	Gac/Aac	8/12	0.515139028503205	4	FACETS	1	0.908	1	0.256	0.227	0.287	CLONAL	1	TRUE	0	0.515139028503205	4		223	499	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	272	314	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.923	0.87	0.977	0.923	0.87	0.977	CLONAL	1	TRUE	1	0.779395115668651	2		314	756	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919526	78919526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	321	496	0	ENST00000306801.3:c.3085G>A	p.Val1029Met	p.V1029M	ENST00000306801	NM_020761.2	1029	Gtg/Atg	26/34	1	2	FACETS	0.945	0.895	0.995	0.945	0.895	0.995	CLONAL	1	TRUE	1	0.779395115668651	2		496	872	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383686	15383686	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	316	598	0	ENST00000263377.2:c.225G>A	p.Trp75Ter	p.W75*	ENST00000263377	NM_058243.2	75	tgG/tgA	2/20	0.779395115668651	3	FACETS	0.874	0.823	0.925	0.437	0.411	0.463	CLONAL	1	TRUE	1	0.779395115668651	3		598	1290	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0025281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	29314	779	21	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.779395115668651	18	FACETS	1	0.999	1			1	CLONAL	18	TRUE	NA	0.779395115668651	18		800	30184	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169019	32169019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	174	722	0	ENST00000375023.3:c.4014G>A	p.Met1338Ile	p.M1338I	ENST00000375023	NM_004557.3	1338	atG/atA	22/30	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.310343179072881	2		722	936	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248980	55248981	+	splice_region_variant,intron_variant	In_Frame_Ins	INS	-	-	TCCAGGAAGCCT	rs397517106	NA	P-0025284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1418	82	375	0	ENST00000275493.2:c.2284-5_2290dup		p.A763_Y764insFQEA	ENST00000275493	NM_005228.3	763			0.310343179072881	11	FACETS	0.844	0.741	0.956	0.084	0.074	0.096	CLONAL	1	TRUE	1	0.310343179072881	11		375	1500	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873717	151873717	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	140	541	0	ENST00000262189.6:c.8821C>A	p.Pro2941Thr	p.P2941T	ENST00000262189	NM_170606.2	2941	Cca/Aca	38/59	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.310343179072881	2		541	823	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981861	101981863	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0025285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	34	672	0	ENST00000282441.5:c.286_288del	p.Phe96del	p.F96del	ENST00000282441	NM_001130145.2	94	tcCTTc/tcc	1/9	1	2	FACETS	0.927	0.755	1	0.927	0.755	1	CLONAL	1	TRUE	1	0.11	2		672	667	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884510	151884510	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	26	446	0	ENST00000262189.6:c.4845G>A	p.Trp1615Ter	p.W1615*	ENST00000262189	NM_170606.2	1615	tgG/tgA	33/59	1	2	FACETS	0.916	0.724	1	0.916	0.724	1	CLONAL	1	TRUE	1	0.11	2		446	516	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0025286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	118	454	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	1	2	FACETS	0.908	0.826	0.992	0.908	0.826	0.992	CLONAL	1	TRUE	1	0.651496746049066	2		454	399	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913514	NA	P-0025286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	16	436	0	ENST00000288135.5:c.2466T>A	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaA	17/21	1	2	FACETS	0.096	0.07	0.127	0.096	0.07	0.127	SUBCLONAL	1	TRUE	1	0.651496746049066	2		436	510	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913514	NA	P-0025286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	37	436	0	ENST00000288135.5:c.2466T>G	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaG	17/21	1	2	FACETS	0.223	0.183	0.267	0.223	0.183	0.267	SUBCLONAL	1	TRUE	1	0.651496746049066	2		436	510	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599341	55599341	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519761	NA	P-0025286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	15	433	0	ENST00000288135.5:c.2467T>G	p.Tyr823Asp	p.Y823D	ENST00000288135	NM_000222.2	823	Tat/Gat	17/21	1	2	FACETS	0.091	0.066	0.122	0.091	0.066	0.122	SUBCLONAL	1	TRUE	1	0.651496746049066	2		433	505	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594258	55594258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913523	NA	P-0025286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	59	420	0	ENST00000288135.5:c.1961T>C	p.Val654Ala	p.V654A	ENST00000288135	NM_000222.2	654	gTg/gCg	13/21	1	2	FACETS	0.367	0.316	0.423	0.367	0.316	0.423	SUBCLONAL	1	TRUE	1	0.651496746049066	2		420	493	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602664	55602664	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs1057519713	NA	P-0025286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	24	272	0	ENST00000288135.5:c.2485G>C	p.Ala829Pro	p.A829P	ENST00000288135	NM_000222.2	829	Gct/Cct	18/21	1	2	FACETS	0.241	0.189	0.301	0.241	0.189	0.301	SUBCLONAL	1	TRUE	1	0.651496746049066	2		272	306	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89811418	89811418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780078373	NA	P-0025286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	235	567	2	ENST00000389301.3:c.3575C>T	p.Pro1192Leu	p.P1192L	ENST00000389301	NM_000135.2	1192	cCg/cTg	36/43	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.651496746049066	2		569	637	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0025287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	104	403	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.794906352557024	2		403	252	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692836	89692836	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786204858	NA	P-0025287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	87	173	0	ENST00000371953.3:c.320A>G	p.Asp107Gly	p.D107G	ENST00000371953	NM_000314.4	107	gAt/gGt	5/9	0.779850765809458	1	FACETS	0.999	0.924	1	0.999	0.924	1	CLONAL	1	TRUE	0	0.794906352557024	1		173	132	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0025287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7465	2335	687	3	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.794906352557024	23	FACETS	0.934	0.914	0.954			1	CLONAL	6	TRUE	NA	0.794906352557024	23		690	9800	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs149840192	NA	P-0025287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7502	2298	686	4	ENST00000275493.2:c.866C>A	p.Ala289Asp	p.A289D	ENST00000275493	NM_005228.3	289	gCc/gAc	7/28	0.794906352557024	23	FACETS	0.919	0.899	0.939			1	CLONAL	6	TRUE	NA	0.794906352557024	23		690	9800	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	35	314	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.981	0.807	1	0.981	0.807	1	CLONAL	1	TRUE	1	0.231638626259617	2		314	308	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692993	89692993	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519724	NA	P-0025288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	38	342	0	ENST00000371953.3:c.477G>T	p.Arg159Ser	p.R159S	ENST00000371953	NM_000314.4	159	agG/agT	5/9	0.231638626259617	1	FACETS	0.753	0.624	0.898	0.753	0.624	0.898	SUBCLONAL	1	TRUE	0	0.231638626259617	1		342	385	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444317	50444317	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	44	278	0	ENST00000331340.3:c.247C>T	p.Arg83Ter	p.R83*	ENST00000331340	NM_006060.4	83	Cga/Tga	4/8	0.231638626259617	3	FACETS	0.966	0.811	1	0.483	0.405	0.569	CLONAL	1	TRUE	1	0.231638626259617	3		278	439	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828410	72828410	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745311893	NA	P-0025288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	81	408	0	ENST00000268489.5:c.8171C>T	p.Thr2724Ile	p.T2724I	ENST00000268489	NM_006885.3	2724	aCt/aTt	9/10	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.231638626259617	2		408	621	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524692	106524694	+	inframe_deletion	In_Frame_Del	DEL	TAT	TAT	-	novel	NA	P-0025288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	48	315	0	ENST00000359195.3:c.2856_2858del	p.Ile952del	p.I952del	ENST00000359195	NM_002649.2	951	aaTATt/aat	9/11	0.231638626259617	3	FACETS	0.997	0.843	1	0.498	0.421	0.583	CLONAL	1	TRUE	1	0.231638626259617	3		315	464	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0025290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	83	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.635	0.562	0.711	0.635	0.562	0.711	SUBCLONAL	1	TRUE	1	0.583767965759039	2		326	448	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0025290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	117	585	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.539	0.487	0.595	0.539	0.487	0.595	SUBCLONAL	1	TRUE	1	0.583767965759039	2		585	743	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0025290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	100	407	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.644	0.577	0.715	0.644	0.577	0.715	SUBCLONAL	1	TRUE	1	0.583767965759039	2		407	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs864622237	NA	P-0025290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	133	562	0	ENST00000269305.4:c.700T>C	p.Tyr234His	p.Y234H	ENST00000269305	NM_001126112.2	234	Tac/Cac	7/11	1	2	FACETS	0.567	0.515	0.622	0.567	0.515	0.622	SUBCLONAL	1	TRUE	1	0.583767965759039	2		562	803	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107231	193107231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	53	292	0	ENST00000367435.3:c.440G>A	p.Arg147His	p.R147H	ENST00000367435	NM_024529.4	147	cGc/cAc	6/17	1	2	FACETS	0.528	0.452	0.61	0.528	0.452	0.61	SUBCLONAL	1	TRUE	1	0.583767965759039	2		292	344	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712013	89712014	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1114167663	NA	P-0025290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	74	219	0	ENST00000371953.3:c.632dup	p.Cys211TrpfsTer32	p.C211Wfs*32	ENST00000371953	NM_000314.4	211	tgc/tGgc	6/9	0.337916976225168	2	FACETS	1	0.902	1	0.509	0.452	0.569	INDETERMINATE	1	TRUE	0	0.583767965759039	2		219	249	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448103	49448103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	117	461	2	ENST00000301067.7:c.497C>T	p.Ser166Leu	p.S166L	ENST00000301067	NM_003482.3	166	tCa/tTa	4/54	1	2	FACETS	0.59	0.533	0.651	0.59	0.533	0.651	SUBCLONAL	1	TRUE	1	0.583767965759039	2		463	679	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129381	64129381	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	69	580	0	ENST00000334205.4:c.813C>G	p.Asp271Glu	p.D271E	ENST00000334205	NM_003942.2	271	gaC/gaG	8/17	1	2	FACETS	0.309	0.268	0.353	0.309	0.268	0.353	SUBCLONAL	1	TRUE	1	0.583767965759039	2		580	765	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434530	110434530	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	133	499	1	ENST00000375856.3:c.3871G>T	p.Gly1291Trp	p.G1291W	ENST00000375856	NM_003749.2	1291	Ggg/Tgg	1/2	1	2	FACETS	0.671	0.611	0.734	0.671	0.611	0.734	SUBCLONAL	1	TRUE	1	0.583767965759039	2		500	679	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058342	42058342	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201470885	NA	P-0025290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	72	276	0	ENST00000219905.7:c.8062G>A	p.Val2688Ile	p.V2688I	ENST00000219905	NM_001164273.1	2688	Gtc/Atc	24/24	1	2	FACETS	0.5	0.438	0.567	0.5	0.438	0.567	SUBCLONAL	1	TRUE	1	0.583767965759039	2		276	493	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713262	30713263	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0025290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	97	368	0	ENST00000295754.5:c.588dup	p.Leu197AlafsTer27	p.L197Afs*27	ENST00000295754	NM_003242.5	196	aag/aaGg	4/7	1	2	FACETS	0.592	0.529	0.659	0.592	0.529	0.659	SUBCLONAL	1	TRUE	1	0.583767965759039	2		368	561	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332628	153332628	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	119	443	0	ENST00000281708.4:c.328G>T	p.Glu110Ter	p.E110*	ENST00000281708	NM_033632.3	110	Gag/Tag	2/12	1	2	FACETS	0.62	0.56	0.682	0.62	0.56	0.682	SUBCLONAL	1	TRUE	1	0.583767965759039	2		443	658	SUCCESS
APC	324	MSKCC	GRCh37	5	112176016	112176016	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	73	298	0	ENST00000257430.4:c.4725del	p.Glu1576LysfsTer74	p.E1576Kfs*74	ENST00000257430	NM_000038.5	1575	ctA/ct	16/16	1	2	FACETS	0.562	0.493	0.636	0.562	0.493	0.636	SUBCLONAL	1	TRUE	1	0.583767965759039	2		298	445	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673712	176673712	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751194525	NA	P-0025290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	90	396	1	ENST00000439151.2:c.4412G>A	p.Arg1471Gln	p.R1471Q	ENST00000439151	NM_022455.4	1471	cGa/cAa	10/23	1	2	FACETS	0.503	0.447	0.563	0.503	0.447	0.563	SUBCLONAL	1	TRUE	1	0.583767965759039	2		397	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0025293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	175	466	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.676841949439701	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.714129471659221	2		466	242	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0025293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	24	299	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.705064625867939	2	FACETS	0.851	0.687	1	0.425	0.343	0.514	CLONAL	1	TRUE	0	0.714129471659221	2		299	79	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144049	11144051	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0025293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	197	608	0	ENST00000358026.2:c.3634_3636del	p.Glu1212del	p.E1212del	ENST00000358026	NM_001128849.1	1210	gtGGAg/gtg	26/36	0.656470562430483	2	FACETS	0.876	0.83	0.921	0.876	0.83	0.921	CLONAL	2	TRUE	0	0.714129471659221	2		608	315	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942129	71942129	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	89	727	0	ENST00000298229.2:c.1393G>T	p.Asp465Tyr	p.D465Y	ENST00000298229	NM_001567.3	465	Gac/Tac	12/28	0.676841949439701	2	FACETS	0.704	0.629	0.782	0.352	0.314	0.391	SUBCLONAL	1	TRUE	0	0.714129471659221	2		727	354	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942138	71942138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	108	735	0	ENST00000298229.2:c.1402G>A	p.Val468Ile	p.V468I	ENST00000298229	NM_001567.3	468	Gtc/Atc	12/28	0.676841949439701	2	FACETS	0.79	0.715	0.867	0.395	0.357	0.434	SUBCLONAL	1	TRUE	0	0.714129471659221	2		735	383	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061909	38061909	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	183	539	0	ENST00000250448.2:c.80C>G	p.Ser27Cys	p.S27C	ENST00000250448	NM_004496.3	27	tCc/tGc	2/2	0.686929233264332	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.714129471659221	2		539	232	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226169	2226169	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	164	666	0	ENST00000326181.6:c.1867del	p.Arg623GlyfsTer11	p.R623Gfs*11	ENST00000326181	NM_032271.2	622	gaC/ga	19/21	0.706423641863971	4	FACETS	0.856	0.793	0.92	0.856	0.793	0.92	CLONAL	2	TRUE	2	0.714129471659221	4		666	460	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621912	1621914	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs748560717	NA	P-0025293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	36	620	0	ENST00000344749.5:c.878_880del	p.Phe293del	p.F293del	ENST00000344749	NM_001136139.2	293	tTCTcc/tcc	11/19	0.656470562430483	2	FACETS	0.375	0.309	0.447	0.187	0.154	0.224	SUBCLONAL	1	TRUE	0	0.714129471659221	2		620	269	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064436	30064436	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0025293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	174	451	0	ENST00000338641.4:c.999+1G>T		p.X333_splice	ENST00000338641	NM_000268.3	333			0.690292746961777	2	FACETS	0.941	0.891	0.988	0.941	0.891	0.988	CLONAL	2	TRUE	0	0.714129471659221	2		451	259	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592098	67592099	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGAGGGAAGCGAGATGGCACTTTTCTTGTC	novel	NA	P-0025293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	159	269	0	ENST00000274335.5:c.1917_1946dup	p.Gly640_Arg649dup	p.G640_R649dup	ENST00000274335		640	-/CGAGGGAAGCGAGATGGCACTTTTCTTGTC	14/15	0.612149645842534	3	FACETS	0.927	0.865	0.989	0.618	0.576	0.66	CLONAL	2	TRUE	0	0.714129471659221	3		269	326	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80071512	80071512	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0025293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	187	397	0	ENST00000265081.6:c.2254-1G>C		p.X752_splice	ENST00000265081	NM_002439.4	752			0.612149645842534	3	FACETS	0.855	0.812	0.897	0.855	0.812	0.897	CLONAL	3	TRUE	0	0.714129471659221	3		397	277	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613300	100613300	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	148	476	0	ENST00000308731.7:c.1100C>T	p.Ala367Val	p.A367V	ENST00000308731	NM_000061.2	367	gCa/gTa	12/19	0.714129471659221	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.714129471659221	2		476	200	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0025305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	309	466	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.513810985298122	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.531905869685672	1		466	801	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0025305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	165	570	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.350542718381744	1	FACETS	0.53	0.487	0.575	0.53	0.487	0.575	SUBCLONAL	1	TRUE	0	0.531905869685672	1		570	859	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56415048	56415048	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781745181	NA	P-0025305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	33	331	0	ENST00000348428.3:c.2449G>A	p.Asp817Asn	p.D817N	ENST00000348428	NM_006785.3	817	Gac/Aac	17/17	0.507111492407426	2	FACETS	0.189	0.153	0.23	0.095	0.076	0.115	SUBCLONAL	1	TRUE	0	0.531905869685672	2		331	655	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048118	180048118	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	301	659	0	ENST00000261937.6:c.2155G>C	p.Glu719Gln	p.E719Q	ENST00000261937	NM_182925.4	719	Gag/Cag	14/30	1	2	FACETS	0.899	0.846	0.953	0.899	0.846	0.953	CLONAL	1	TRUE	1	0.531905869685672	2		659	1259	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412753	63412753	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	131	480	0	ENST00000330258.3:c.414G>T	p.Glu138Asp	p.E138D	ENST00000330258	NM_152424.3	138	gaG/gaT	2/2	0.231428960038518	1	FACETS	0.405	0.367	0.445	0.405	0.367	0.445	INDETERMINATE	1	TRUE	0	0.531905869685672	1		480	893	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778777	76778777	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	147	486	0	ENST00000373344.5:c.6802G>A	p.Glu2268Lys	p.E2268K	ENST00000373344	NM_000489.3	2268	Gaa/Aaa	31/35	0.231428960038518	1	FACETS	0.618	0.565	0.672	0.618	0.565	0.672	INDETERMINATE	1	TRUE	0	0.531905869685672	1		486	657	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0025307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	322	467	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.29505150731781	4	FACETS	0.853	0.807	0.899	0.853	0.807	0.899	CLONAL	3	TRUE	1	0.35	4		467	971	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0025307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	147	503	0	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.299577452580231	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.35	1		503	690	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540689	187540689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs544202909	NA	P-0025307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	108	340	0	ENST00000441802.2:c.7051G>A	p.Glu2351Lys	p.E2351K	ENST00000441802	NM_005245.3	2351	Gag/Aag	10/27	1	2	FACETS	0.991	0.891	1	0.991	0.891	1	CLONAL	1	TRUE	1	0.35	2		340	623	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0025307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	226	357	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	0.29505150731781	4	FACETS	1	0.983	1	0.766	0.716	0.817	CLONAL	2	TRUE	1	0.35	4		357	759	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562748	21562748	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1225626637	NA	P-0025307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	250	470	1	ENST00000382592.4:c.1171C>T	p.Arg391Cys	p.R391C	ENST00000382592	NM_014572.2	391	Cgc/Tgc	4/8	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.35	2		471	960	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798863	42798863	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1256197247	NA	P-0025307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	108	595	0	ENST00000575354.2:c.4435C>G	p.Gln1479Glu	p.Q1479E	ENST00000575354	NM_015125.3	1479	Cag/Gag	19/20	1	2	FACETS	0.588	0.527	0.654	0.588	0.527	0.654	SUBCLONAL	1	TRUE	1	0.35	2		595	1049	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221084	5221084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371881792	NA	P-0025307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	84	456	0	ENST00000357368.4:c.3382G>A	p.Val1128Ile	p.V1128I	ENST00000357368	NM_002850.3	1128	Gtc/Atc	20/38	1	2	FACETS	0.582	0.513	0.656	0.582	0.513	0.656	SUBCLONAL	1	TRUE	1	0.35	2		456	825	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351104	89351104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	184	516	0	ENST00000301030.4:c.1846G>A	p.Glu616Lys	p.E616K	ENST00000301030	NM_001256183.1	616	Gag/Aag	9/13	0.299577452580231	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.35	1		516	713	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444729	49444729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199724002	NA	P-0025307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1252	239	756	0	ENST00000301067.7:c.2737G>A	p.Glu913Lys	p.E913K	ENST00000301067	NM_003482.3	913	Gag/Aag	10/54	0.22036344989394	4	FACETS	1	0.987	1	0.618	0.575	0.663	CLONAL	1	TRUE	2	0.35	4		756	1491	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851203	63851203	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	112	476	0	ENST00000279873.7:c.1981G>C	p.Asp661His	p.D661H	ENST00000279873	NM_032199.2	661	Gac/Cac	10/10	1	2	FACETS	0.716	0.643	0.793	0.716	0.643	0.793	SUBCLONAL	1	TRUE	1	0.35	2		476	894	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851498	63851498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	96	396	0	ENST00000279873.7:c.2276G>A	p.Arg759Lys	p.R759K	ENST00000279873	NM_032199.2	759	aGa/aAa	10/10	1	2	FACETS	0.729	0.649	0.813	0.729	0.649	0.813	SUBCLONAL	1	TRUE	1	0.35	2		396	753	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427237	49427237	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	195	506	0	ENST00000301067.7:c.11251del	p.Val3751TrpfsTer79	p.V3751Wfs*79	ENST00000301067	NM_003482.3	3751	Gtg/tg	39/54	0.22036344989394	4	FACETS	1	0.989	1	0.694	0.642	0.749	CLONAL	1	TRUE	2	0.35	4		506	1083	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115443	115115444	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	206	545	0	ENST00000257566.3:c.882dup	p.Asp295ArgfsTer32	p.D295Rfs*32	ENST00000257566	NM_016569.3	294	-/A	5/8	NA	2	FACETS	0.786	0.731	0.842			1	INDETERMINATE	2	TRUE	NA	0.35	2		545	749	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954237	32954237	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	139	565	0	ENST00000380152.3:c.9211G>C	p.Glu3071Gln	p.E3071Q	ENST00000380152		3071	Gag/Cag	24/27	1	2	FACETS	0.862	0.785	0.944	0.862	0.785	0.944	CLONAL	1	TRUE	1	0.35	2		565	921	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853208	68853222	+	inframe_deletion	In_Frame_Del	DEL	AACTGGCTGGAGATT	AACTGGCTGGAGATT	-	novel	NA	P-0025307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	128	449	0	ENST00000261769.5:c.1593_1607del	p.Trp532_Asn536del	p.W532_N536del	ENST00000261769	NM_004360.3	531	AACTGGCTGGAGATT/-	11/16	0.299577452580231	1	FACETS	0.862	0.782	0.946	0.862	0.782	0.946	CLONAL	1	TRUE	0	0.35	1		449	700	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660640	190660640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778185859	NA	P-0025307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	141	324	0	ENST00000441310.2:c.278G>A	p.Arg93His	p.R93H	ENST00000441310	NM_000534.4	93	cGt/cAt	3/13	0.166255081687169	3	FACETS	0.862	0.789	0.938	0.862	0.789	0.938	INDETERMINATE	2	TRUE	1	0.35	3		324	549	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750508	57750508	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	79	504	0	ENST00000274289.3:c.1960A>T	p.Thr654Ser	p.T654S	ENST00000274289	NM_006622.3	654	Act/Tct	14/14	1	2	FACETS	0.64	0.563	0.724	0.64	0.563	0.724	SUBCLONAL	1	TRUE	1	0.35	2		504	705	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517506	176517506	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	199	681	0	ENST00000292408.4:c.207G>T	p.Glu69Asp	p.E69D	ENST00000292408	NM_213647.1	69	gaG/gaT	3/18	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.35	2		681	1065	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43752282	43752282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	78	479	0	ENST00000523873.1:c.682G>A	p.Asp228Asn	p.D228N	ENST00000523873		228	Gac/Aac	8/8	1	2	FACETS	0.613	0.538	0.694	0.613	0.538	0.694	SUBCLONAL	1	TRUE	1	0.35	2		479	727	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336663	81336663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	68	357	0	ENST00000222390.5:c.1559G>A	p.Gly520Glu	p.G520E	ENST00000222390	NM_000601.4	520	gGa/gAa	14/18	0.166255081687169	3	FACETS	0.906	0.79	1	0.453	0.395	0.516	INDETERMINATE	1	TRUE	1	0.35	3		357	504	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916752	48916753	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0025308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	219	444	0	ENST00000267163.4:c.287dup	p.Glu97GlyfsTer13	p.E97Gfs*13	ENST00000267163	NM_000321.2	94	-/A	3/27	0.504774036320576	2	FACETS	0.943	0.89	0.997	0.943	0.89	0.997	CLONAL	2	TRUE	0	0.534879573329362	2		444	434	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865065	57865065	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	391	870	1	ENST00000228682.2:c.2542T>C	p.Phe848Leu	p.F848L	ENST00000228682	NM_005269.2	848	Ttt/Ctt	12/12	0.482434445284191	4	FACETS	0.898	0.854	0.944	0.898	0.854	0.944	CLONAL	2	TRUE	2	0.534879573329362	4		871	1249	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917083	50917083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747996611	NA	P-0025308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	68	954	1	ENST00000440232.2:c.2335G>A	p.Ala779Thr	p.A779T	ENST00000440232	NM_002691.3	779	Gcg/Acg	19/27	0.532992539265976	4	FACETS	0.366	0.317	0.419	0.091	0.079	0.105	SUBCLONAL	1	TRUE	0	0.534879573329362	4		955	1067	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070927	30070927	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	259	539	2	ENST00000338641.4:c.1443C>A	p.Tyr481Ter	p.Y481*	ENST00000338641	NM_000268.3	481	taC/taA	13/16	0.495294292892825	2	FACETS	0.984	0.934	1	0.984	0.934	1	CLONAL	2	TRUE	0	0.534879573329362	2		541	492	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692790	89692790	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554898067	NA	P-0025309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	150	410	0	ENST00000371953.3:c.274G>T	p.Asp92Tyr	p.D92Y	ENST00000371953	NM_000314.4	92	Gac/Tac	5/9	0.616075143473942	2	FACETS	0.978	0.918	1	0.978	0.918	1	CLONAL	2	TRUE	0	0.616075143473942	2		410	249	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056343	27056344	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0025309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	227	284	0	ENST00000324856.7:c.1341_1342del	p.Gln449AlafsTer173	p.Q449Afs*173	ENST00000324856	NM_006015.4	447	TAt/t	2/20	0.303389959976521	3	FACETS	0.926	0.882	0.968	0.926	0.882	0.968	INDETERMINATE	3	TRUE	0	0.616075143473942	3		284	347	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750686	128750686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	164	425	0	ENST00000377970.2:c.223C>T	p.Pro75Ser	p.P75S	ENST00000377970	NM_002467.4	75	Ccc/Tcc	2/3	1	2	FACETS	0.803	0.74	0.869	0.803	0.74	0.869	CLONAL	1	TRUE	1	0.616075143473942	2		425	663	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764303	39764303	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1414795545	NA	P-0025309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	281	652	0	ENST00000288319.7:c.809C>T	p.Ser270Leu	p.S270L	ENST00000288319	NM_182918.3	270	tCg/tTg	7/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.616075143473942	2		652	835	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916940	178916957	+	inframe_deletion	In_Frame_Del	DEL	AGAAAAGATCCTCAATCG	AGAAAAGATCCTCAATCG	-	novel	NA	P-0025309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	70	397	0	ENST00000263967.3:c.332_349del	p.Lys111_Glu116del	p.K111_E116del	ENST00000263967	NM_006218.2	109	gaAGAAAAGATCCTCAATCGa/gaa	2/21	1	2	FACETS	0.697	0.612	0.787	0.697	0.612	0.787	SUBCLONAL	1	TRUE	1	0.616075143473942	2		397	326	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0025315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	8326	548	0	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.837604323945268	22	FACETS	0.982	0.98	0.985			1	CLONAL	22	TRUE	NA	0.837604323945268	22		548	8624	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0025315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	848	793	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	NA	2	FACETS	1	0.997	1			1	INDETERMINATE	2	TRUE	NA	0.837604323945268	2		793	950	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2220125	2220125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542823835	NA	P-0025315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	369	769	0	ENST00000398665.3:c.2710G>A	p.Val904Met	p.V904M	ENST00000398665	NM_032482.2	904	Gtg/Atg	23/28	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.837604323945268	2		769	867	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39629522	39629527	+	inframe_deletion	In_Frame_Del	DEL	TTGGAG	TTGGAG	-	novel	NA	P-0025315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	213	456	1	ENST00000262039.4:c.2222_2227del	p.Val741_Gly742del	p.V741_G742del	ENST00000262039	NM_002647.2	739	cTTGGAGtt/ctt	21/25	1	2	FACETS	0.859	0.804	0.916	0.859	0.804	0.916	CLONAL	1	TRUE	1	0.837604323945268	2		457	592	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814226	76814226	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	317	465	0	ENST00000373344.5:c.6418A>C	p.Asn2140His	p.N2140H	ENST00000373344	NM_000489.3	2140	Aat/Cat	29/35	0.837604323945268	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.837604323945268	1		465	392	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0025318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	30	364	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.449292095860686	4	FACETS	0.194	0.155	0.238	0.048	0.038	0.06	SUBCLONAL	1	TRUE	0	0.449292095860686	4		364	999	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0025318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	134	369	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	0.935	0.852	1	0.935	0.852	1	CLONAL	1	TRUE	1	0.449292095860686	2		369	638	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588651	28588651	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770630954	NA	P-0025318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	160	497	1	ENST00000241453.7:c.2797C>T	p.Arg933Trp	p.R933W	ENST00000241453	NM_004119.2	933	Cgg/Tgg	23/24	NA	2	FACETS	0.942	0.865	1			1	INDETERMINATE	1	TRUE	NA	0.449292095860686	2		498	756	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40678685	40678685	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1312244817	NA	P-0025318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	113	383	0	ENST00000249776.8:c.427C>T	p.Arg143Ter	p.R143*	ENST00000249776	NM_033286.3	143	Cga/Tga	3/9	1	2	FACETS	0.805	0.726	0.888	0.805	0.726	0.888	CLONAL	1	TRUE	1	0.449292095860686	2		383	625	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0025319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	156	569	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	1	0.979	1	1	0.993	1	CLONAL	2	FALSE	1	0.272924730166436	2		569	488	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733236	74733236	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	93	231	0	ENST00000359995.5:c.7T>A	p.Tyr3Asn	p.Y3N	ENST00000359995	NM_001195427.1	3	Tac/Aac	1/3	1	2	FACETS	0.944	0.846	1	1	0.986	1	CLONAL	2	FALSE	1	0.272924730166436	2		231	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0025326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	294	569	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.541215592041309	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.55283652406999	1		569	761	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262604	16262604	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	32	346	0	ENST00000375759.3:c.9869C>A	p.Thr3290Asn	p.T3290N	ENST00000375759	NM_015001.2	3290	aCc/aAc	11/15	0.55283652406999	1	FACETS	0.214	0.173	0.259	0.214	0.173	0.259	SUBCLONAL	1	TRUE	0	0.55283652406999	1		346	392	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0025328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	203	595	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	0.376120602625893	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.376120602625893	1		595	649	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0025328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	591	802	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.376120602625893	2		802	1467	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775805	9775805	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	64	749	0	ENST00000377346.4:c.348G>T	p.Gln116His	p.Q116H	ENST00000377346	NM_005026.3	116	caG/caT	4/24	0.376120602625893	1	FACETS	0.274	0.237	0.316	0.274	0.237	0.316	SUBCLONAL	1	TRUE	0	0.376120602625893	1		749	1007	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910476	32910476	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	65	547	0	ENST00000380152.3:c.1984T>A	p.Ser662Thr	p.S662T	ENST00000380152		662	Tct/Act	11/27	0.233253001158906	1	FACETS	0.404	0.35	0.463	0.404	0.35	0.463	SUBCLONAL	1	TRUE	0	0.376120602625893	1		547	694	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40740954	40740954	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs778976738	NA	P-0025328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	250	788	0	ENST00000392038.2:c.1364G>T	p.Arg455Leu	p.R455L	ENST00000392038	NM_001626.4	455	cGc/cTc	13/14	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.376120602625893	2		788	1162	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480502	89480502	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	125	333	0	ENST00000336596.2:c.2339C>G	p.Thr780Arg	p.T780R	ENST00000336596	NM_005233.5	780	aCa/aGa	13/17	0.367725760785122	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.376120602625893	1		333	470	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249011	55249011	+	protein_altering_variant	In_Frame_Ins	INS	A	A	GCGGCAC	novel	NA	P-0025328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	502	589	0	ENST00000275493.2:c.2309delinsGCGGCAC	p.Asp770delinsGlyGlyThr	p.D770delinsGGT	ENST00000275493	NM_005228.3	770	gAc/gGCGGCACc	20/28	0.376120602625893	7	FACETS	0.964	0.924	1			1	CLONAL	4	TRUE	NA	0.376120602625893	7		589	1343	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820827	36820827	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	77	491	0	ENST00000373129.3:c.550G>C	p.Val184Leu	p.V184L	ENST00000373129	NM_032017.1	184	Gtg/Ctg	6/12	1	2	FACETS	0.868	0.762	0.984	0.868	0.762	0.984	CLONAL	1	TRUE	1	0.23	2		491	771	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061178	38061185	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	GCTTCTCG	GCTTCTCG	-	novel	NA	P-0025329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	90	405	1	ENST00000250448.2:c.804_811del	p.Cys268Ter	p.C268*	ENST00000250448	NM_004496.3	268	tgCGAGAAGCag/tgag	2/2	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.23	2		406	727	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696434	47696434	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	112	591	0	ENST00000347630.2:c.389A>T	p.Asp130Val	p.D130V	ENST00000347630	NM_001007230.1	130	gAc/gTc	6/11	1	2	FACETS	0.919	0.825	1	0.919	0.825	1	CLONAL	1	TRUE	1	0.23	2		591	1060	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0025330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	115	702	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	0.978	1	CLONAL	1	TRUE	1	0.16	2		702	1080	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0025330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	68	825	6	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	1	2	FACETS	0.925	0.803	1	0.925	0.803	1	CLONAL	1	TRUE	1	0.16	2		831	919	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226550845	226550845	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	45	521	0	ENST00000366794.5:c.2803G>T	p.Ala935Ser	p.A935S	ENST00000366794	NM_001618.3	935	Gct/Tct	21/23	1	2	FACETS	0.665	0.557	0.785	0.665	0.557	0.785	SUBCLONAL	1	TRUE	1	0.16	2		521	846	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332872	70332872	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	63	585	0	ENST00000373644.4:c.777A>T	p.Lys259Asn	p.K259N	ENST00000373644	NM_030625.2	259	aaA/aaT	2/12	1	2	FACETS	0.84	0.724	0.966	0.84	0.724	0.966	CLONAL	1	TRUE	1	0.16	2		585	938	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420190	49420190	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	46	638	0	ENST00000301067.7:c.15559G>T	p.Ala5187Ser	p.A5187S	ENST00000301067	NM_003482.3	5187	Gcc/Tcc	48/54	1	2	FACETS	0.716	0.601	0.844	0.716	0.601	0.844	SUBCLONAL	1	TRUE	1	0.16	2		638	803	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992183	72992183	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	56	605	0	ENST00000268489.5:c.1862A>T	p.Gln621Leu	p.Q621L	ENST00000268489	NM_006885.3	621	cAg/cTg	2/10	1	2	FACETS	0.78	0.666	0.904	0.78	0.666	0.904	CLONAL	1	TRUE	1	0.16	2		605	898	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426725	47426725	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	87	560	0	ENST00000377045.4:c.970G>T	p.Val324Leu	p.V324L	ENST00000377045	NM_001654.4	324	Gtg/Ttg	10/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.16	2		560	959	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411696	63411696	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	87	715	0	ENST00000330258.3:c.1471C>A	p.Arg491Ser	p.R491S	ENST00000330258	NM_152424.3	491	Cgc/Agc	2/2	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.16	2		715	1035	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357717	70357717	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	81	738	0	ENST00000374080.3:c.5968C>A	p.His1990Asn	p.H1990N	ENST00000374080		1990	Cac/Aac	41/45	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.16	2		738	968	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0025330-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	30	478	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.51	0.409	0.626	0.51	0.409	0.626	SUBCLONAL	1	TRUE	1	0.13	2		478	905	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0025330-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	17	226	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.413	0.307	0.541	0.413	0.307	0.541	SUBCLONAL	1	TRUE	1	0.13	2		226	633	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913495	NA	P-0025330-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	82	516	1	ENST00000371085.3:c.602G>T	p.Arg201Leu	p.R201L	ENST00000371085	NM_000516.4	201	cGt/cTt	8/13	0.225707958441316	3	FACETS	1	0.975	1	0.722	0.636	0.816	CLONAL	1	TRUE	1	0.13	3		517	930	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212824	27212824	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025330-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	68	661	0	ENST00000380036.4:c.2806C>A	p.Leu936Met	p.L936M	ENST00000380036	NM_000459.3	936	Ctg/Atg	17/23	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.13	2		661	990	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0025330-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	214	646	1	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	NA	2	FACETS	0.881	0.819	0.945			1	INDETERMINATE	2	TRUE	NA	0.248961767098064	2		647	976	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602748	10602748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025330-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	400	640	1	ENST00000171111.5:c.830C>T	p.Thr277Met	p.T277M	ENST00000171111	NM_203500.1	277	aCg/aTg	3/6	0.236876750523899	3	FACETS	0.961	0.914	1	0.961	0.914	1	CLONAL	3	TRUE	0	0.248961767098064	3		641	1253	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36934797	36934797	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025330-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	191	683	0	ENST00000361632.4:c.1536G>T	p.Met512Ile	p.M512I	ENST00000361632		512	atG/atT	11/16	0.227971020255339	3	FACETS	0.964	0.892	1	0.964	0.892	1	CLONAL	2	TRUE	1	0.248961767098064	3		683	895	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888102	81888102	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025330-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	78	494	0	ENST00000359376.3:c.247G>T	p.Glu83Ter	p.E83*	ENST00000359376	NM_002661.3	83	Gag/Tag	3/33	0.248961767098064	3	FACETS	0.866	0.76	0.98	0.433	0.38	0.49	CLONAL	1	TRUE	1	0.248961767098064	3		494	814	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244550	41244550	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs80357124	NA	P-0025330-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	83	649	0	ENST00000357654.3:c.2998G>C	p.Glu1000Gln	p.E1000Q	ENST00000357654	NM_007294.3	1000	Gag/Cag	10/23	0.244698404944094	4	FACETS	1	0.882	1	0.334	0.294	0.377	CLONAL	1	TRUE	1	0.248961767098064	4		649	832	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015126	37015126	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025330-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	116	674	0	ENST00000358127.4:c.278C>G	p.Pro93Arg	p.P93R	ENST00000358127	NM_001280556.1	93	cCc/cGc	3/10	0.227971020255339	3	FACETS	0.992	0.893	1	0.496	0.446	0.549	CLONAL	1	TRUE	1	0.248961767098064	3		674	1056	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615080	100615080	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025330-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	138	666	0	ENST00000308731.7:c.835T>C	p.Tyr279His	p.Y279H	ENST00000308731	NM_000061.2	279	Tat/Cat	9/19	0.246770326505703	2	FACETS	0.824	0.751	0.899	0.824	0.751	0.899	CLONAL	2	TRUE	0	0.248961767098064	2		666	673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0025331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	967	769	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.998	1			1	CLONAL	4	TRUE	1	0.424842290044904	2		770	1071	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0025331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	181	288	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.282366050956343	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.424842290044904	1		288	491	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855014	76855017	+	frameshift_variant	Frame_Shift_Del	DEL	CTAT	CTAT	-	novel	NA	P-0025331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	339	341	0	ENST00000373344.5:c.5819_5822del	p.Asp1940ValfsTer14	p.D1940Vfs*14	ENST00000373344	NM_000489.3	1940	gATAGt/gt	25/35	1	1	FACETS	0.993	0.963	1	1	0.997	1	CLONAL	3	TRUE	0	0.424842290044904	1		341	422	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859932	117859932	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0025331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	36	245	0	ENST00000297338.2:c.1705-2A>G		p.X569_splice	ENST00000297338	NM_006265.2	569			0.424842290044904	4	FACETS	0.393	0.322	0.472	0.196	0.161	0.236	SUBCLONAL	1	TRUE	2	0.424842290044904	4		245	615	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0025333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	144	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.953	0.87	1	0.953	0.87	1	CLONAL	1	TRUE	1	0.396788302896256	2		326	762	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170291	119170291	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	28	317	1	ENST00000264033.4:c.2521C>T	p.Gln841Ter	p.Q841*	ENST00000264033	NM_005188.3	841	Cag/Tag	16/16	0.323356816834065	1	FACETS	0.228	0.182	0.281	0.228	0.182	0.281	SUBCLONAL	1	TRUE	0	0.396788302896256	1		318	496	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870982	12870992	+	frameshift_variant	Frame_Shift_Del	DEL	TAGAGGGCAAG	TAGAGGGCAAG	-	novel	NA	P-0025333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	116	364	0	ENST00000228872.4:c.211_221del	p.Glu71ArgfsTer50	p.E71Rfs*50	ENST00000228872	NM_004064.3	70	cTAGAGGGCAAG/c	1/3	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.396788302896256	2		364	575	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0025334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	85	510	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.869	0.768	0.978	0.869	0.768	0.978	CLONAL	1	TRUE	1	0.263183004357364	2		510	743	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164754	36164773	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGAGCCCATGGCCGACAT	GCCGAGCCCATGGCCGACAT	-	novel	NA	P-0025334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	89	385	0	ENST00000300305.3:c.1102_1121del	p.Met368HisfsTer225	p.M368Hfs*225	ENST00000300305		368	ATGTCGGCCATGGGCTCGGCc/c	8/8	1	2	FACETS	0.95	0.842	1	0.95	0.842	1	CLONAL	1	TRUE	1	0.263183004357364	2		385	712	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0025335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	132	423	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	0.279899378928273	2		423	838	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	107	314	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.697950572574595	2		314	234	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85742008	85742008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1403156514	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	254	469	0	ENST00000370580.1:c.28G>A	p.Glu10Lys	p.E10K	ENST00000370580	NM_003921.4	10	Gag/Aag	1/3	0.439006586154508	3	FACETS	0.852	0.805	0.9	0.852	0.805	0.9	CLONAL	2	TRUE	1	0.697950572574595	3		469	576	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982975	201982975	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	251	481	0	ENST00000359651.3:c.824T>C	p.Leu275Pro	p.L275P	ENST00000359651		275	cTg/cCg	7/8	0.439006586154508	3	FACETS	1	0.993	1	0.725	0.682	0.769	CLONAL	1	TRUE	1	0.697950572574595	3		481	669	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610019	43610019	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	285	569	0	ENST00000355710.3:c.1971C>G	p.Ile657Met	p.I657M	ENST00000355710	NM_020975.4	657	atC/atG	11/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.697950572574595	2		569	728	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8246213	8246213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	162	447	0	ENST00000335790.3:c.421G>A	p.Asp141Asn	p.D141N	ENST00000335790	NM_002315.2	141	Gac/Aac	4/4	0.122425547622982	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.697950572574595	0		447	431	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205233	61205233	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	226	568	0	ENST00000301761.2:c.173G>C	p.Arg58Thr	p.R58T	ENST00000301761	NM_017841.2	58	aGa/aCa	2/4	1	2	FACETS	0.941	0.881	1	0.941	0.881	1	CLONAL	1	TRUE	1	0.697950572574595	2		568	688	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50488271	50488271	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	216	625	0	ENST00000394963.4:c.1185A>C	p.Glu395Asp	p.E395D	ENST00000394963	NM_003076.4	395	gaA/gaC	10/13	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.697950572574595	2		625	595	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218378	69218378	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1225544458	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	260	568	0	ENST00000462284.1:c.470A>G	p.His157Arg	p.H157R	ENST00000462284	NM_002392.5	157	cAt/cGt	7/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.697950572574595	2		568	724	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112303	115112303	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	66	148	0	ENST00000257566.3:c.1437C>A	p.Phe479Leu	p.F479L	ENST00000257566	NM_016569.3	479	ttC/ttA	7/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.697950572574595	2		148	153	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914857	32914857	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	187	538	0	ENST00000380152.3:c.6365T>C	p.Met2122Thr	p.M2122T	ENST00000380152		2122	aTg/aCg	11/27	0.352141664605972	1	FACETS	0.823	0.77	0.876	0.823	0.77	0.876	INDETERMINATE	1	TRUE	0	0.697950572574595	1		538	424	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335933	73335933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	219	378	1	ENST00000377767.4:c.2362C>T	p.His788Tyr	p.H788Y	ENST00000377767	NM_014953.3	788	Cat/Tat	18/21	0.352141664605972	1	FACETS	0.807	0.759	0.856	0.807	0.759	0.856	INDETERMINATE	1	TRUE	0	0.697950572574595	1		379	506	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023120	33023120	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	84	328	0	ENST00000300177.4:c.229A>G	p.Ser77Gly	p.S77G	ENST00000300177	NM_001191322.1	77	Agc/Ggc	2/2	0.393901402576263	1	FACETS	0.448	0.398	0.5	0.448	0.398	0.5	INDETERMINATE	1	TRUE	0	0.697950572574595	1		328	350	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654704	67654717	+	frameshift_variant	Frame_Shift_Del	DEL	CATGAGAACCCATT	CATGAGAACCCATT	-	novel	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	164	531	0	ENST00000264010.4:c.1193_1206del	p.Met398ArgfsTer6	p.M398Rfs*6	ENST00000264010	NM_006565.3	397	caCATGAGAACCCATTca/caca	6/12	1	2	FACETS	0.829	0.765	0.895	0.829	0.765	0.895	CLONAL	1	TRUE	1	0.697950572574595	2		531	567	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217617	7217617	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	215	408	0	ENST00000380728.2:c.310G>T	p.Glu104Ter	p.E104*	ENST00000380728		104	Gaa/Taa	4/11	0.697950572574595	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.697950572574595	1		408	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578522	7578522	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs758781593	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	340	575	0	ENST00000269305.4:c.408A>C	p.Gln136His	p.Q136H	ENST00000269305	NM_001126112.2	136	caA/caC	5/11	0.697950572574595	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.697950572574595	1		575	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578539	7578539	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	327	569	0	ENST00000269305.4:c.391A>G	p.Asn131Asp	p.N131D	ENST00000269305	NM_001126112.2	131	Aac/Gac	5/11	0.697950572574595	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.697950572574595	1		569	508	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760725	59760725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	605	760	0	ENST00000259008.2:c.3682G>A	p.Glu1228Lys	p.E1228K	ENST00000259008	NM_032043.2	1228	Gaa/Aaa	20/20	0.697950572574595	3	FACETS	0.992	0.958	1	0.992	0.958	1	CLONAL	2	TRUE	1	0.697950572574595	3		760	1179	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050425	13050425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536586990	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	209	433	0	ENST00000316448.5:c.377C>T	p.Ser126Leu	p.S126L	ENST00000316448	NM_004343.3	126	tCa/tTa	3/9	0.439006586154508	3	FACETS	1	0.983	1	0.582	0.542	0.623	CLONAL	1	TRUE	1	0.697950572574595	3		433	694	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274088	18274088	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	206	444	0	ENST00000222254.8:c.1306G>C	p.Glu436Gln	p.E436Q	ENST00000222254	NM_005027.3	436	Gag/Cag	11/16	0.439006586154508	3	FACETS	1	0.979	1	0.565	0.526	0.605	CLONAL	1	TRUE	1	0.697950572574595	3		444	705	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45873425	45873425	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	180	451	0	ENST00000391945.4:c.71A>G	p.Tyr24Cys	p.Y24C	ENST00000391945	NM_000400.3	24	tAc/tGc	2/23	0.439006586154508	3	FACETS	1	0.982	1	0.594	0.55	0.638	CLONAL	1	TRUE	1	0.697950572574595	3		451	586	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921148	50921148	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	317	493	0	ENST00000440232.2:c.3268G>A	p.Glu1090Lys	p.E1090K	ENST00000440232	NM_002691.3	1090	Gaa/Aaa	27/27	0.439006586154508	3	FACETS	0.91	0.866	0.955	0.91	0.866	0.955	CLONAL	2	TRUE	1	0.697950572574595	3		493	673	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143370	30143370	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	191	353	0	ENST00000389048.3:c.156G>C	p.Lys52Asn	p.K52N	ENST00000389048	NM_004304.4	52	aaG/aaC	1/29	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.697950572574595	2		353	473	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262364	39262364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	163	559	0	ENST00000402219.2:c.1063G>A	p.Glu355Lys	p.E355K	ENST00000402219	NM_005633.3	355	Gaa/Aaa	8/23	1	2	FACETS	0.781	0.72	0.844	0.781	0.72	0.844	SUBCLONAL	1	TRUE	1	0.697950572574595	2		559	598	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270190	198270190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	169	313	0	ENST00000335508.6:c.1246C>T	p.Pro416Ser	p.P416S	ENST00000335508	NM_012433.2	416	Cct/Tct	10/25	0.393901402576263	1	FACETS	0.841	0.784	0.898	0.841	0.784	0.898	INDETERMINATE	1	TRUE	0	0.697950572574595	1		313	375	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587193	212587193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	112	511	0	ENST00000342788.4:c.808C>T	p.Pro270Ser	p.P270S	ENST00000342788	NM_005235.2	270	Cca/Tca	7/28	0.393901402576263	1	FACETS	0.363	0.328	0.401	0.363	0.328	0.401	INDETERMINATE	1	TRUE	0	0.697950572574595	1		511	575	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661578	227661578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770397566	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	253	496	0	ENST00000305123.5:c.1877G>A	p.Arg626Gln	p.R626Q	ENST00000305123	NM_005544.2	626	cGa/cAa	1/2	0.393901402576263	1	FACETS	0.904	0.856	0.953	0.904	0.856	0.953	INDETERMINATE	1	TRUE	0	0.697950572574595	1		496	522	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39708750	39708750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	208	648	0	ENST00000361337.2:c.361G>A	p.Glu121Lys	p.E121K	ENST00000361337	NM_003286.2	121	Gaa/Aaa	6/21	0.352203283460722	3	FACETS	1	0.991	1	0.719	0.673	0.767	INDETERMINATE	1	TRUE	1	0.697950572574595	3		648	559	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162107	22162107	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	197	407	0	ENST00000215832.6:c.148C>G	p.Arg50Gly	p.R50G	ENST00000215832	NM_002745.4	50	Cga/Gga	2/9	0.520413088979886	1	FACETS	0.833	0.781	0.886	0.833	0.781	0.886	CLONAL	1	TRUE	0	0.697950572574595	1		407	441	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051631	30051648	+	inframe_deletion	In_Frame_Del	DEL	ACTGCTTGGTACGCAGAG	ACTGCTTGGTACGCAGAG	-	novel	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	49	412	0	ENST00000338641.4:c.565_582del	p.Thr189_Glu194del	p.T189_E194del	ENST00000338641	NM_000268.3	189	ACTGCTTGGTACGCAGAG/-	6/16	0.520413088979886	1	FACETS	0.203	0.172	0.237	0.203	0.172	0.237	SUBCLONAL	1	TRUE	0	0.697950572574595	1		412	450	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074296	30074296	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	194	436	2	ENST00000338641.4:c.1558G>T	p.Glu520Ter	p.E520*	ENST00000338641	NM_000268.3	520	Gag/Tag	14/16	0.520413088979886	1	FACETS	0.876	0.822	0.931	0.876	0.822	0.931	CLONAL	1	TRUE	0	0.697950572574595	1		438	413	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	162	392	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	0.697950572574595	2		392	462	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119642300	119642300	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	212	574	0	ENST00000316626.5:c.397G>C	p.Asp133His	p.D133H	ENST00000316626		133	Gac/Cac	4/12	1	2	FACETS	0.999	0.934	1	0.999	0.934	1	CLONAL	1	TRUE	1	0.697950572574595	2		574	608	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186501400	186501400	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs571299759	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	110	282	0	ENST00000323963.5:c.1A>G	p.Met1?	p.M1?	ENST00000323963		1	Atg/Gtg	1/11	1	2	FACETS	0.843	0.764	0.924	0.843	0.764	0.924	CLONAL	1	TRUE	1	0.697950572574595	2		282	374	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247252	153247252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	118	452	0	ENST00000281708.4:c.1550G>A	p.Gly517Glu	p.G517E	ENST00000281708	NM_033632.3	517	gGa/gAa	10/12	0.393901402576263	1	FACETS	0.447	0.406	0.491	0.447	0.406	0.491	INDETERMINATE	1	TRUE	0	0.697950572574595	1		452	492	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509431	149509431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	175	516	0	ENST00000261799.4:c.1468G>A	p.Glu490Lys	p.E490K	ENST00000261799	NM_002609.3	490	Gag/Aag	10/23	1	2	FACETS	0.922	0.855	0.991	0.922	0.855	0.991	CLONAL	1	TRUE	1	0.697950572574595	2		516	544	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169159	32169159	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	94	478	0	ENST00000375023.3:c.3874G>C	p.Glu1292Gln	p.E1292Q	ENST00000375023	NM_004557.3	1292	Gag/Cag	22/30	0.352141664605972	1	FACETS	0.402	0.36	0.447	0.402	0.36	0.447	INDETERMINATE	1	TRUE	0	0.697950572574595	1		478	436	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043660	6043660	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	110	451	0	ENST00000265849.7:c.193C>T	p.Leu65Phe	p.L65F	ENST00000265849	NM_000535.5	65	Ctt/Ttt	3/15	0.697950572574595	1	FACETS	0.866	0.795	0.938	0.866	0.795	0.938	CLONAL	1	TRUE	0	0.697950572574595	1		451	237	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249028	55249028	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	37	435	0	ENST00000275493.2:c.2326C>G	p.Arg776Gly	p.R776G	ENST00000275493	NM_005228.3	776	Cgc/Ggc	20/28	0.697950572574595	1	FACETS	0.187	0.154	0.223	0.187	0.154	0.223	SUBCLONAL	1	TRUE	0	0.697950572574595	1		435	370	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833957	44833957	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	232	323	0	ENST00000377967.4:c.381G>A	p.Trp127Ter	p.W127*	ENST00000377967	NM_021140.2	127	tgG/tgA	4/29	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.697950572574595	1		323	315	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858416	89858416	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs769718381	NA	P-0025336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	209	522	0	ENST00000389301.3:c.1144C>T	p.Gln382Ter	p.Q382*	ENST00000389301	NM_000135.2	382	Cag/Tag	13/43	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.697950572574595	2		522	571	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0025342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	189	552	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	0.308004233141359	2		552	1125	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575209	48575209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767326	NA	P-0025342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	119	355	0	ENST00000342988.3:c.403C>T	p.Arg135Ter	p.R135*	ENST00000342988	NM_005359.5	135	Cga/Tga	3/12	0.282541751053932	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.308004233141359	1		355	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0025343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1345	98	785	1	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	1	2	FACETS	0.321	0.285	0.359	0.321	0.285	0.359	SUBCLONAL	1	TRUE	1	0.423760405636481	2		786	1443	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874287	155874287	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs869025194	NA	P-0025343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	74	604	0	ENST00000368323.3:c.244T>C	p.Phe82Leu	p.F82L	ENST00000368323	NM_006912.5	82	Ttt/Ctt	5/6	1	2	FACETS	0.301	0.262	0.343	0.301	0.262	0.343	SUBCLONAL	1	TRUE	1	0.423760405636481	2		604	1160	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0025346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	69	510	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.640817297616111	3	FACETS	0.242	0.21	0.277	0.121	0.105	0.139	SUBCLONAL	1	TRUE	1	0.640817297616111	3		510	1175	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0025346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	41	554	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.34808999509211	1	FACETS	0.11	0.091	0.132	0.11	0.091	0.132	INDETERMINATE	1	TRUE	0	0.640817297616111	1		554	788	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0025349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	238	442	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.587271341410574	2		442	771	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101054	27101054	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	195	487	0	ENST00000324856.7:c.4336C>T	p.Arg1446Ter	p.R1446*	ENST00000324856	NM_006015.4	1446	Cga/Tga	18/20	0.128652370718861	0	FACETS	0.428	0.398	0.459			1	INDETERMINATE	1	TRUE	0	0.587271341410574	0		487	640	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097737	27097737	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	216	427	0	ENST00000324856.7:c.3326G>T	p.Arg1109Leu	p.R1109L	ENST00000324856	NM_006015.4	1109	cGg/cTg	12/20	0.128652370718861	0	FACETS	0.472	0.441	0.504			1	INDETERMINATE	1	TRUE	0	0.587271341410574	0		427	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0025350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	383	569	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.564002838889735	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.564002838889735	1		569	889	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555526097	NA	P-0025351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	235	653	0	ENST00000269305.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000269305	NM_001126112.2	167	Cag/Tag	5/11	0.492451016405038	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.492451016405038	1		653	626	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885793	111885793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	165	635	0	ENST00000341259.2:c.1415G>A	p.Cys472Tyr	p.C472Y	ENST00000341259	NM_005475.2	472	tGc/tAc	8/8	1	2	FACETS	0.903	0.831	0.978	0.903	0.831	0.978	CLONAL	1	TRUE	1	0.492451016405038	2		635	742	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0025352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	170	430	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		430	420	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942562	71942562	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	118	488	0	ENST00000298229.2:c.1518G>A	p.Trp506Ter	p.W506*	ENST00000298229	NM_001567.3	506	tgG/tgA	13/28	0.469642828271998	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.469642828271998	1		488	382	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996111	73996111	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1418436632	NA	P-0025353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	47	689	0	ENST00000318443.5:c.845A>G	p.Asn282Ser	p.N282S	ENST00000318443	NM_001024736.1	282	aAc/aGc	5/10	0.25904475025952	1	FACETS	0.334	0.281	0.391	0.334	0.281	0.391	INDETERMINATE	1	TRUE	0	0.469642828271998	1		689	459	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849663	68849663	+	splice_donor_variant	Splice_Site	DEL	G	G	-	rs1064795267	NA	P-0025353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	127	421	0	ENST00000261769.5:c.1565+1del		p.X522_splice	ENST00000261769	NM_004360.3	522			0.469642828271998	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.469642828271998	1		421	389	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0025354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	198	478	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.280724678253948	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.438915747950759	1		478	638	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0025354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	103	616	0	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.280724678253948	1	FACETS	0.489	0.438	0.544	0.489	0.438	0.544	SUBCLONAL	1	TRUE	0	0.438915747950759	1		616	749	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098975	178098975	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1328994103	NA	P-0025354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	75	382	0	ENST00000397062.3:c.70T>C	p.Trp24Arg	p.W24R	ENST00000397062	NM_006164.4	24	Tgg/Cgg	2/5	1	2	FACETS	0.883	0.778	0.995	0.883	0.778	0.995	CLONAL	1	TRUE	1	0.438915747950759	2		382	387	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731172	162731172	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	260	449	3	ENST00000367921.3:c.1027G>T	p.Ala343Ser	p.A343S	ENST00000367921	NM_006182.2	343	Gcc/Tcc	9/18	0.218284159204354	3	FACETS	0.871	0.819	0.925	0.871	0.819	0.925	INDETERMINATE	2	TRUE	1	0.438915747950759	3		452	829	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589632	69589633	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0025354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	69	334	1	ENST00000168712.1:c.220_221delinsTT	p.Gly74Phe	p.G74F	ENST00000168712	NM_002007.2	74	GGc/TTc	1/3	0.280724678253948	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	0	0.438915747950759	1		335	238	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909941	100909941	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	51	606	0	ENST00000325455.5:c.2708T>C	p.Val903Ala	p.V903A	ENST00000325455	NM_001202474.3	903	gTt/gCt	8/8	0.280724678253948	1	FACETS	0.423	0.36	0.492	0.423	0.36	0.492	SUBCLONAL	1	TRUE	0	0.438915747950759	1		606	429	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335854	73335854	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	133	510	0	ENST00000377767.4:c.2441G>T	p.Cys814Phe	p.C814F	ENST00000377767	NM_014953.3	814	tGt/tTt	18/21	0.152747108279559	0	FACETS	0.585	0.533	0.639			1	INDETERMINATE	1	TRUE	0	0.438915747950759	0		510	581	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220405	1220405	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0025354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	181	643	0	ENST00000326873.7:c.498C>G	p.Tyr166Ter	p.Y166*	ENST00000326873	NM_000455.4	166	taC/taG	4/10	0.280724678253948	1	FACETS	0.886	0.819	0.954	0.886	0.819	0.954	CLONAL	1	TRUE	0	0.438915747950759	1		643	727	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447492	187447492	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	87	583	0	ENST00000232014.4:c.701G>T	p.Ser234Ile	p.S234I	ENST00000232014	NM_001130845.1	234	aGt/aTt	5/10	0.218325299049557	0	FACETS	0.363	0.321	0.407			1	INDETERMINATE	1	TRUE	0	0.438915747950759	0		583	613	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730127	41730127	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	128	359	0	ENST00000242208.4:c.402G>T	p.Lys134Asn	p.K134N	ENST00000242208	NM_002192.2	134	aaG/aaT	3/3	0.438915747950759	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.438915747950759	1		359	416	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484168	8484168	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	192	575	1	ENST00000356435.5:c.3364G>T	p.Gly1122Cys	p.G1122C	ENST00000356435		1122	Ggc/Tgc	19/35	0.280724678253948	1	FACETS	0.952	0.884	1	0.952	0.884	1	CLONAL	1	TRUE	0	0.438915747950759	1		576	717	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813110	76813110	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	85	536	0	ENST00000373344.5:c.6511A>C	p.Met2171Leu	p.M2171L	ENST00000373344	NM_000489.3	2171	Atg/Ctg	30/35	0.280724678253948	1	FACETS	0.613	0.544	0.687	0.613	0.544	0.687	SUBCLONAL	1	TRUE	0	0.438915747950759	1		536	493	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739581	145739581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375100228	NA	P-0025355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	314	552	0	ENST00000428558.2:c.1870G>A	p.Val624Ile	p.V624I	ENST00000428558	NM_004260.3	624	Gtc/Atc	11/22	1	2	FACETS	0.936	0.884	0.989	0.936	0.884	0.989	CLONAL	1	TRUE	1	0.632397572261982	2		552	1061	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577128	7577128	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	340	508	0	ENST00000269305.4:c.810T>A	p.Phe270Leu	p.F270L	ENST00000269305	NM_001126112.2	270	ttT/ttA	8/11	0.620483373664373	1	FACETS	0.951	0.905	0.997	0.951	0.905	0.997	CLONAL	1	TRUE	0	0.632397572261982	1		508	773	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126587	2126587	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs45517271	NA	P-0025355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	315	371	0	ENST00000219476.3:c.2837+1G>T		p.X946_splice	ENST00000219476	NM_000548.3	946			0.632397572261982	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.632397572261982	1		371	631	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829040	128829045	+	inframe_deletion	In_Frame_Del	DEL	GCTGCT	GCTGCT	-	rs570242755	NA	P-0025355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	15	52	0	ENST00000249373.3:c.64_69del	p.Leu22_Leu23del	p.L22_L23del	ENST00000249373	NM_005631.4	16	ggGCTGCTg/ggg	1/12	1	2	FACETS	0.431	0.319	0.563	0.431	0.319	0.563	SUBCLONAL	1	TRUE	1	0.632397572261982	2		52	110	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	209	314	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.922	0.86	0.986	0.922	0.86	0.986	CLONAL	1	TRUE	1	0.661555486414807	2		314	685	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123691	11123691	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	347	704	0	ENST00000358026.2:c.2341A>G	p.Met781Val	p.M781V	ENST00000358026	NM_001128849.1	781	Atg/Gtg	16/36	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.661555486414807	2		704	989	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843521	3843523	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0025357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	331	576	1	ENST00000262367.5:c.1080_1082del	p.Leu362del	p.L362del	ENST00000262367	NM_004380.2	360	ctACTg/ctg	4/31	1	2	FACETS	0.94	0.89	0.992	0.94	0.89	0.992	CLONAL	1	TRUE	1	0.661555486414807	2		577	1064	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0025361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	263	552	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.324814051651435	3	FACETS	0.798	0.749	0.849	0.798	0.749	0.849	SUBCLONAL	2	TRUE	1	0.397440156799217	3		552	994	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0025361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	251	847	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.308714423492571	2	FACETS	0.787	0.739	0.837	0.787	0.739	0.837	SUBCLONAL	2	TRUE	0	0.397440156799217	2		849	802	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280099	115280099	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	146	590	1	ENST00000438362.2:c.533G>T	p.Arg178Leu	p.R178L	ENST00000438362	NM_001242891.1	178	cGt/cTt	5/20	0.324814051651435	3	FACETS	0.845	0.77	0.924	0.423	0.385	0.462	CLONAL	1	TRUE	1	0.397440156799217	3		591	1042	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400157	41400157	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	201	611	0	ENST00000373198.4:c.602T>C	p.Val201Ala	p.V201A	ENST00000373198	NM_133170.3	201	gTg/gCg	5/32	0.262144150397295	4	FACETS	1	0.99	1	0.706	0.654	0.76	CLONAL	1	TRUE	2	0.397440156799217	4		611	1001	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0025362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	89	810	3	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.474866387024977	3	FACETS	0.415	0.366	0.466	0.138	0.122	0.156	SUBCLONAL	1	TRUE	0	0.500239630090058	3		813	1073	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0025362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	439	439	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.995	0.955	1	1	0.997	1	CLONAL	2	TRUE	1	0.500239630090058	2		439	882	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0025362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	272	578	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.4008097564575	4	FACETS	0.944	0.888	1	0.944	0.888	1	CLONAL	2	TRUE	2	0.500239630090058	4		578	864	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733279	40733279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201275244	NA	P-0025362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	72	611	0	ENST00000373198.4:c.3527G>A	p.Arg1176His	p.R1176H	ENST00000373198	NM_133170.3	1176	cGt/cAt	26/32	0.438533035783763	3	FACETS	0.335	0.292	0.383	0.168	0.146	0.192	SUBCLONAL	1	TRUE	1	0.500239630090058	3		611	1073	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396925	139396925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766358616	NA	P-0025362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	44	384	3	ENST00000277541.6:c.5183C>T	p.Pro1728Leu	p.P1728L	ENST00000277541	NM_017617.3	1728	cCg/cTg	28/34	0.158725028258605	5	FACETS	0.48	0.402	0.568	0.16	0.134	0.19	INDETERMINATE	1	TRUE	2	0.500239630090058	5		387	641	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528647	89528647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536144760	NA	P-0025362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	38	235	0	ENST00000336596.2:c.2947G>A	p.Val983Met	p.V983M	ENST00000336596	NM_005233.5	983	Gtg/Atg	17/17	0.351811662113784	3	FACETS	0.546	0.452	0.65	0.273	0.226	0.325	SUBCLONAL	1	TRUE	1	0.500239630090058	3		235	348	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159747	20159747	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	69	441	0	ENST00000379607.5:c.12T>A	p.Asn4Lys	p.N4K	ENST00000379607	NM_001412.3	4	aaT/aaA	1/7	NA	2	FACETS	0.48	0.418	0.546			1	INDETERMINATE	1	TRUE	NA	0.500239630090058	2		441	575	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325123	123325123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371714070	NA	P-0025362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	60	671	1	ENST00000358487.5:c.205G>A	p.Val69Met	p.V69M	ENST00000358487	NM_000141.4	69	Gtg/Atg	3/18	0.500239630090058	3	FACETS	0.305	0.261	0.352	0.152	0.13	0.176	SUBCLONAL	1	TRUE	1	0.500239630090058	3		672	984	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39721179	39721179	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	430	710	0	ENST00000361337.2:c.682G>T	p.Ala228Ser	p.A228S	ENST00000361337	NM_003286.2	228	Gcc/Tcc	9/21	0.281622826539143	6	FACETS	0.917	0.875	0.96	0.688	0.656	0.72	INDETERMINATE	3	TRUE	2	0.500239630090058	6		710	1250	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696281	52696283	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0025362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	301	549	0	ENST00000394830.3:c.394_396del	p.Pro132del	p.P132del	ENST00000394830	NM_018313.4	132	CCT/-	5/30	0.466629899991055	2	FACETS	0.919	0.872	0.965	0.919	0.872	0.965	CLONAL	2	TRUE	0	0.500239630090058	2		549	655	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193892	106193892	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1049545383	NA	P-0025364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	152	320	1	ENST00000380013.4:c.4354C>T	p.Arg1452Ter	p.R1452*	ENST00000380013	NM_001127208.2	1452	Cga/Tga	10/11	NA	2	FACETS	0.873	0.803	0.947			1	INDETERMINATE	1	FALSE	NA	0.608450911861672	2		321	572	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152853898	152853898	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	187	282	0	ENST00000406277.2:c.666C>A	p.Asp222Glu	p.D222E	ENST00000406277	NM_152274.4	222	gaC/gaA	7/7	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	0	0.608450911861672	1		282	327	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572594	64572594	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs386134249	NA	P-0025365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	122	589	1	ENST00000312049.6:c.1262G>A	p.Cys421Tyr	p.C421Y	ENST00000312049	NM_130799.2	421	tGc/tAc	9/10	0.305265281722286	1	FACETS	0.845	0.763	0.93	0.845	0.763	0.93	CLONAL	1	TRUE	0	0.305265281722286	1		590	802	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050653	30050653	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	111	454	0	ENST00000338641.4:c.455del	p.Asp152AlafsTer22	p.D152Afs*22	ENST00000338641	NM_000268.3	152	gAc/gc	5/16	0.304898559172983	1	FACETS	0.941	0.847	1	0.941	0.847	1	CLONAL	1	TRUE	0	0.305265281722286	1		454	655	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631289	117631290	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	119	566	0	ENST00000368508.3:c.6388_6389insA	p.Pro2130HisfsTer14	p.P2130Hfs*14	ENST00000368508	NM_002944.2	2130	cca/cAca	40/43	0.304898559172983	1	FACETS	0.928	0.838	1	0.928	0.838	1	CLONAL	1	TRUE	0	0.305265281722286	1		566	712	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246445	105246445	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	425	565	0	ENST00000349310.3:c.155T>G	p.Leu52Arg	p.L52R	ENST00000349310	NM_001014432.1	52	cTc/cGc	4/15	0.644251371207237	2	FACETS	0.998	0.963	1	0.998	0.963	1	CLONAL	2	TRUE	0	0.644251371207237	2		565	661	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663317	67663317	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	246	590	0	ENST00000264010.4:c.1718A>G	p.His573Arg	p.H573R	ENST00000264010	NM_006565.3	573	cAt/cGt	10/12	0.644251371207237	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.644251371207237	1		590	498	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111511	8111511	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	259	698	0	ENST00000346208.3:c.998del	p.Asn333MetfsTer22	p.N333Mfs*22	ENST00000346208		333	Aat/at	5/6	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.644251371207237	2		698	790	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231830	36231830	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1569061888	NA	P-0025367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	265	642	0	ENST00000300305.3:c.554A>C	p.Gln185Pro	p.Q185P	ENST00000300305		185	cAa/cCa	5/8	1	2	FACETS	0.97	0.912	1	0.97	0.912	1	CLONAL	1	TRUE	1	0.644251371207237	2		642	848	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540213	23540214	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTCTGG	rs754270608	NA	P-0025367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	55	287	0	ENST00000380871.4:c.184_189dup	p.Pro62_Glu63dup	p.P62_E63dup	ENST00000380871	NM_006167.3	62	-/CCAGAG	1/2	1	2	FACETS	0.547	0.471	0.63	0.547	0.471	0.63	SUBCLONAL	1	TRUE	1	0.644251371207237	2		287	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0025387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	49	605	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.806	0.682	0.943	0.806	0.682	0.943	CLONAL	1	TRUE	1	0.2	2		605	608	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0025387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	33	552	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.771	0.628	0.932	0.771	0.628	0.932	CLONAL	1	TRUE	1	0.2	2		552	428	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62325754	62325754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145335410	NA	P-0025387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	68	500	0	ENST00000360203.5:c.3022G>A	p.Val1008Met	p.V1008M	ENST00000360203	NM_001283009.1	1008	Gtg/Atg	31/35	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.2	2		500	572	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039620	47039620	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	48	256	1	ENST00000377604.3:c.1072C>T	p.Gln358Ter	p.Q358*	ENST00000377604	NM_001204468.1	358	Cag/Tag	11/24	1	1	FACETS	0.834	0.711	0.967	1	0.969	1	CLONAL	2	TRUE	0	0.2	1		257	259	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	60	364	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.483347010718902	3	FACETS	1	0.88	1	0.507	0.44	0.579	CLONAL	1	TRUE	1	0.483347010718902	3		364	304	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	209	670	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.967	0.899	1	0.967	0.899	1	CLONAL	1	TRUE	1	0.483347010718902	2		671	894	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961538	54961538	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1338142196	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	209	570	0	ENST00000312783.6:c.94C>T	p.Pro32Ser	p.P32S	ENST00000312783	NM_198436.1	32	Cct/Tct	4/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.483347010718902	2		570	818	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549095	87549095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	158	519	1	ENST00000277120.3:c.1652G>A	p.Arg551Gln	p.R551Q	ENST00000277120		551	cGa/cAa	15/19	1	2	FACETS	0.991	0.911	1	0.991	0.911	1	CLONAL	1	TRUE	1	0.483347010718902	2		520	660	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710903	117710903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	144	568	0	ENST00000368508.3:c.1369G>A	p.Asp457Asn	p.D457N	ENST00000368508	NM_002944.2	457	Gac/Aac	12/43	1	2	FACETS	0.87	0.795	0.948	0.87	0.795	0.948	CLONAL	1	TRUE	1	0.483347010718902	2		568	685	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998556	100998556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1474172577	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	189	535	0	ENST00000325455.5:c.1246G>A	p.Asp416Asn	p.D416N	ENST00000325455	NM_001202474.3	416	Gat/Aat	1/8	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.483347010718902	2		535	695	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995569	68995569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775560862	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	140	807	1	ENST00000288368.4:c.1973C>T	p.Ser658Leu	p.S658L	ENST00000288368	NM_024870.2	658	tCg/tTg	18/40	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.483347010718902	2		808	571	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569662	41569662	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	83	372	0	ENST00000263253.7:c.4653G>C	p.Lys1551Asn	p.K1551N	ENST00000263253	NM_001429.3	1551	aaG/aaC	29/31	1	2	FACETS	0.899	0.799	1	0.899	0.799	1	CLONAL	1	TRUE	1	0.483347010718902	2		372	382	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101557	27101557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	253	739	3	ENST00000324856.7:c.4839G>A	p.Met1613Ile	p.M1613I	ENST00000324856	NM_006015.4	1613	atG/atA	18/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.483347010718902	2		742	990	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11206746	11206746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	199	613	2	ENST00000361445.4:c.4673C>T	p.Ser1558Phe	p.S1558F	ENST00000361445	NM_004958.3	1558	tCc/tTc	32/58	1	2	FACETS	0.94	0.872	1	0.94	0.872	1	CLONAL	1	TRUE	1	0.483347010718902	2		615	876	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256058	16256059	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	229	665	0	ENST00000375759.3:c.3323_3324delinsTT	p.Pro1108Leu	p.P1108L	ENST00000375759	NM_015001.2	1108	cCC/cTT	11/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.483347010718902	2		665	911	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807416	36807416	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	307	665	0	ENST00000373129.3:c.1248C>A	p.Asp416Glu	p.D416E	ENST00000373129	NM_032017.1	416	gaC/gaA	12/12	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.483347010718902	2		665	1088	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805683	43805683	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	219	616	2	ENST00000372470.3:c.739C>T	p.Gln247Ter	p.Q247*	ENST00000372470	NM_005373.2	247	Cag/Tag	5/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.483347010718902	2		618	808	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518493	204518493	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	144	440	0	ENST00000367182.3:c.1156T>C	p.Phe386Leu	p.F386L	ENST00000367182	NM_001278516.1	386	Ttt/Ctt	11/11	1	2	FACETS	0.881	0.806	0.96	0.881	0.806	0.96	CLONAL	1	TRUE	1	0.483347010718902	2		440	676	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246518365	246518365	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	169	520	0	ENST00000388985.4:c.196C>G	p.Arg66Gly	p.R66G	ENST00000388985		66	Cgc/Ggc	2/12	1	2	FACETS	0.957	0.882	1	0.957	0.882	1	CLONAL	1	TRUE	1	0.483347010718902	2		520	731	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606886	43606886	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	298	853	0	ENST00000355710.3:c.1495C>A	p.Gln499Lys	p.Q499K	ENST00000355710	NM_020975.4	499	Cag/Aag	7/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.483347010718902	2		853	1050	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332570	70332570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	174	626	0	ENST00000373644.4:c.475C>T	p.Pro159Ser	p.P159S	ENST00000373644	NM_030625.2	159	Cca/Tca	2/12	1	2	FACETS	0.966	0.892	1	0.966	0.892	1	CLONAL	1	TRUE	1	0.483347010718902	2		626	745	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533853	533853	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	237	742	3	ENST00000451590.1:c.203G>T	p.Arg68Leu	p.R68L	ENST00000451590	NM_001130442.1	68	cGg/cTg	3/5	0.483347010718902	1	FACETS	0.976	0.914	1	0.976	0.914	1	CLONAL	1	TRUE	0	0.483347010718902	1		745	762	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428059	49428059	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	206	599	1	ENST00000301067.7:c.10531G>T	p.Glu3511Ter	p.E3511*	ENST00000301067	NM_003482.3	3511	Gag/Tag	38/54	1	2	FACETS	0.996	0.925	1	0.996	0.925	1	CLONAL	1	TRUE	1	0.483347010718902	2		600	856	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861964	57861964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	200	564	1	ENST00000228682.2:c.1265C>T	p.Pro422Leu	p.P422L	ENST00000228682	NM_005269.2	422	cCc/cTc	10/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.483347010718902	2		565	768	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354529	91354530	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	178	544	0	ENST00000355112.3:c.3969_3970delinsTT	p.His1324Tyr	p.H1324Y	ENST00000355112	NM_000057.2	1323	tcCCac/tcTTac	21/22	1	2	FACETS	0.931	0.86	1	0.931	0.86	1	CLONAL	1	TRUE	1	0.483347010718902	2		544	791	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900857	3900857	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	402	564	0	ENST00000262367.5:c.239C>T	p.Ser80Phe	p.S80F	ENST00000262367	NM_004380.2	80	tCt/tTt	2/31	NA	2	FACETS	0.992	0.95	1			1	INDETERMINATE	2	TRUE	NA	0.483347010718902	2		564	838	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56873432	56873432	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	202	592	0	ENST00000308159.5:c.2137-1G>T		p.X713_splice	ENST00000308159	NM_014669.4	713			1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.483347010718902	2		592	831	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577608	7577609	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	181	582	0	ENST00000269305.4:c.673-1_673delinsAA		p.X225_splice	ENST00000269305	NM_001126112.2	225		7/11	1	2	FACETS	0.93	0.86	1	0.93	0.86	1	CLONAL	1	TRUE	1	0.483347010718902	2		582	805	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858033	40858033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	230	643	0	ENST00000428826.2:c.1831C>T	p.Leu611Phe	p.L611F	ENST00000428826		611	Ctt/Ttt	16/21	0.483347010718902	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.483347010718902	1		643	715	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438202	56438202	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372132623	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	420	715	0	ENST00000407977.2:c.791G>A	p.Ser264Asn	p.S264N	ENST00000407977		264	aGc/aAc	7/10	0.340295776956533	5	FACETS	1	0.99	1	0.754	0.718	0.791	CLONAL	2	TRUE	2	0.483347010718902	5		715	1325	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438212	56438212	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	405	680	0	ENST00000407977.2:c.781G>A	p.Asp261Asn	p.D261N	ENST00000407977		261	Gac/Aac	7/10	0.340295776956533	5	FACETS	1	0.989	1	0.748	0.711	0.785	CLONAL	2	TRUE	2	0.483347010718902	5		680	1289	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772370	56772370	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	322	634	0	ENST00000337432.4:c.224A>G	p.Tyr75Cys	p.Y75C	ENST00000337432	NM_058216.2	75	tAt/tGt	2/9	0.340295776956533	5	FACETS	1	0.958	1	0.678	0.64	0.717	CLONAL	2	TRUE	2	0.483347010718902	5		634	1130	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121050	3121050	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	231	728	0	ENST00000078429.4:c.953C>T	p.Pro318Leu	p.P318L	ENST00000078429	NM_002067.2	318	cCc/cTc	7/7	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.483347010718902	2		728	936	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379830	17379831	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	238	865	0	ENST00000359435.4:c.215_216delinsTT	p.Ser72Phe	p.S72F	ENST00000359435	NM_001033549.1	72	tCC/tTT	2/9	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.483347010718902	2		865	978	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213370	36213370	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	306	874	1	ENST00000222270.7:c.2567C>T	p.Pro856Leu	p.P856L	ENST00000222270	NM_014727.1	856	cCc/cTc	4/37	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.483347010718902	2		875	1041	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440219	220440219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	243	743	0	ENST00000243786.2:c.1072C>T	p.Leu358Phe	p.L358F	ENST00000243786	NM_002191.3	358	Ctt/Ttt	2/2	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.483347010718902	2		743	989	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485825	57485825	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	212	520	0	ENST00000371085.3:c.1126T>C	p.Phe376Leu	p.F376L	ENST00000371085	NM_000516.4	376	Ttc/Ctc	13/13	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.483347010718902	2		520	811	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564739	41564739	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	199	712	1	ENST00000263253.7:c.4040G>T	p.Gly1347Val	p.G1347V	ENST00000263253	NM_001429.3	1347	gGa/gTa	25/31	1	2	FACETS	0.95	0.881	1	0.95	0.881	1	CLONAL	1	TRUE	1	0.483347010718902	2		713	867	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149245664	149245664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	195	805	1	ENST00000360632.3:c.864G>A	p.Met288Ile	p.M288I	ENST00000360632	NM_015472.4	288	atG/atA	5/7	0.483347010718902	3	FACETS	0.835	0.771	0.901	0.417	0.385	0.451	CLONAL	1	TRUE	1	0.483347010718902	3		806	1200	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449635	187449636	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	158	568	0	ENST00000232014.4:c.244_245delinsAA	p.Gly82Lys	p.G82K	ENST00000232014	NM_001130845.1	82	GGa/AAa	4/10	0.483347010718902	3	FACETS	0.905	0.829	0.984	0.452	0.414	0.492	CLONAL	1	TRUE	1	0.483347010718902	3		568	897	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155044	55155044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	180	580	0	ENST00000257290.5:c.2753C>T	p.Pro918Leu	p.P918L	ENST00000257290	NM_006206.4	918	cCt/cTt	20/23	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.483347010718902	2		580	726	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970866	55970866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	193	612	0	ENST00000263923.4:c.1931C>T	p.Ala644Val	p.A644V	ENST00000263923	NM_002253.2	644	gCt/gTt	13/30	1	2	FACETS	0.985	0.913	1	0.985	0.913	1	CLONAL	1	TRUE	1	0.483347010718902	2		612	811	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526702	31526702	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	274	749	0	ENST00000344624.3:c.338T>C	p.Val113Ala	p.V113A	ENST00000344624		113	gTt/gCt	2/33	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.483347010718902	2		749	1072	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057762	180057762	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	137	533	1	ENST00000261937.6:c.193C>T	p.Gln65Ter	p.Q65*	ENST00000261937	NM_182925.4	65	Cag/Tag	3/30	1	2	FACETS	0.809	0.737	0.884	0.809	0.737	0.884	CLONAL	1	TRUE	1	0.483347010718902	2		534	701	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178628	32178628	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	292	741	0	ENST00000375023.3:c.2766C>A	p.Phe922Leu	p.F922L	ENST00000375023	NM_004557.3	922	ttC/ttA	18/30	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.483347010718902	2		741	962	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099170	157099170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1455171423	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	118	396	1	ENST00000346085.5:c.107C>T	p.Ser36Phe	p.S36F	ENST00000346085	NM_020732.3	36	tCc/tTc	1/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.483347010718902	2		397	446	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835888	151835888	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	187	596	0	ENST00000262189.6:c.14636G>C	p.Gly4879Ala	p.G4879A	ENST00000262189	NM_170606.2	4879	gGa/gCa	58/59	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.483347010718902	2		596	697	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956812	68956813	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	181	592	1	ENST00000288368.4:c.930_931delinsAT	p.Asp311Tyr	p.D311Y	ENST00000288368	NM_024870.2	310	gtGGat/gtATat	8/40	1	2	FACETS	0.987	0.912	1	0.987	0.912	1	CLONAL	1	TRUE	1	0.483347010718902	2		593	759	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250213	110250213	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	195	655	0	ENST00000374672.4:c.462C>G	p.Ile154Met	p.I154M	ENST00000374672	NM_004235.4	154	atC/atG	3/5	1	2	FACETS	0.936	0.867	1	0.936	0.867	1	CLONAL	1	TRUE	1	0.483347010718902	2		655	862	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411167	63411167	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	174	635	0	ENST00000330258.3:c.2000C>A	p.Ala667Glu	p.A667E	ENST00000330258	NM_152424.3	667	gCa/gAa	2/2	0.414403246784051	1	FACETS	0.666	0.614	0.72	0.666	0.614	0.72	SUBCLONAL	1	TRUE	0	0.483347010718902	1		635	820	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342397	70342397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	431	716	2	ENST00000374080.3:c.1288G>A	p.Glu430Lys	p.E430K	ENST00000374080		430	Gag/Aag	9/45	0.270544421843698	4	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.483347010718902	4		718	1111	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923132	48923133	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	A	novel	NA	P-0025389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	131	620	0	ENST00000267163.4:c.580_581delinsA	p.Ser194IlefsTer7	p.S194Ifs*7	ENST00000267163	NM_000321.2	194	TCt/At	6/27	0.47993440276891	2	FACETS	0.922	0.851	0.993	0.922	0.851	0.993	CLONAL	2	TRUE	0	0.483347010718902	2		620	294	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0025392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	83	414	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.924	0.823	1	0.924	0.823	1	CLONAL	1	TRUE	1	0.558174763673007	2		414	322	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112035608	112035608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	117	630	1	ENST00000368678.4:c.286C>T	p.Arg96Trp	p.R96W	ENST00000368678		96	Cgg/Tgg	4/13	1	2	FACETS	0.84	0.761	0.922	0.84	0.761	0.922	CLONAL	1	TRUE	1	0.558174763673007	2		631	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0025394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	562	891	1	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.371892680932902	2	FACETS	0.997	0.96	1	0.997	0.96	1	CLONAL	2	TRUE	0	0.454738580221563	2		892	1240	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0025394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	158	472	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	0.958	0.88	1	0.958	0.88	1	CLONAL	1	TRUE	1	0.454738580221563	2		472	725	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974776	21974776	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	33	292	0	ENST00000304494.5:c.51del	p.Thr18ArgfsTer8	p.T18Rfs*8	ENST00000304494	NM_000077.4	17	gcC/gc	1/3	0.371892680932902	2	FACETS	0.326	0.265	0.395	0.163	0.132	0.198	SUBCLONAL	1	TRUE	0	0.454738580221563	2		292	445	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807390	36807390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769273778	NA	P-0025394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	125	860	2	ENST00000373129.3:c.1274C>T	p.Thr425Met	p.T425M	ENST00000373129	NM_032017.1	425	aCg/aTg	12/12	NA	2	FACETS	0.452	0.408	0.499			1	INDETERMINATE	1	TRUE	NA	0.454738580221563	2		862	1216	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541636	187541636	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	75	460	0	ENST00000441802.2:c.6104C>A	p.Thr2035Asn	p.T2035N	ENST00000441802	NM_005245.3	2035	aCt/aAt	10/27	NA	2	FACETS	0.382	0.334	0.434			1	INDETERMINATE	1	TRUE	NA	0.454738580221563	2		460	863	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995602	68995602	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	194	694	0	ENST00000288368.4:c.2006T>C	p.Leu669Pro	p.L669P	ENST00000288368	NM_024870.2	669	cTt/cCt	18/40	0.203742755506755	2	FACETS	0.878	0.812	0.946	0.439	0.406	0.473	INDETERMINATE	1	TRUE	0	0.454738580221563	2		694	972	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909656	76909656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1557118764	NA	P-0025394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	116	310	2	ENST00000373344.5:c.4249C>T	p.Arg1417Trp	p.R1417W	ENST00000373344	NM_000489.3	1417	Cgg/Tgg	14/35	0.279622006997032	2	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.454738580221563	2		312	426	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0025395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	286	552	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.173215598584255	2	FACETS	1	0.992	1	0.691	0.649	0.734	INDETERMINATE	1	TRUE	0	0.36342626796337	2		552	1139	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579378	7579378	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0025395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	197	696	0	ENST00000269305.4:c.309C>G	p.Tyr103Ter	p.Y103*	ENST00000269305	NM_001126112.2	103	taC/taG	4/11	0.36342626796337	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.36342626796337	1		696	883	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	152	698	1	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.457858961756151	1	FACETS	0.992	0.913	1	0.992	0.913	1	CLONAL	1	TRUE	0	0.460011545787629	1		699	513	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592335	29592335	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	81	629	0	ENST00000356175.3:c.4750A>T	p.Ile1584Phe	p.I1584F	ENST00000356175	NM_000267.3	1584	Att/Ttt	35/57	0.457858961756151	1	FACETS	0.798	0.708	0.891	0.798	0.708	0.891	SUBCLONAL	1	TRUE	0	0.460011545787629	1		629	340	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022486	31022486	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	38	373	0	ENST00000375687.4:c.1973del	p.Gly658GlufsTer45	p.G658Efs*45	ENST00000375687	NM_015338.5	657	gaG/ga	13/13	0.406365656386203	3	FACETS	0.445	0.367	0.531	0.222	0.183	0.266	SUBCLONAL	1	TRUE	1	0.460011545787629	3		373	457	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0025398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	42	329	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	0.437	0.364	0.519	0.437	0.364	0.519	SUBCLONAL	1	TRUE	1	0.25	2		329	769	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0025401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	59	478	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.814	0.7	0.939	0.814	0.7	0.939	CLONAL	1	TRUE	1	0.225018388822309	2		478	644	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100575	8100575	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	157	732	0	ENST00000346208.3:c.549C>A	p.Cys183Ter	p.C183*	ENST00000346208		183	tgC/tgA	3/6	0.225018388822309	3	FACETS	0.922	0.845	1	0.922	0.845	1	CLONAL	2	TRUE	1	0.225018388822309	3		732	842	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431750	49431750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	78	710	1	ENST00000301067.7:c.9389C>T	p.Ser3130Phe	p.S3130F	ENST00000301067	NM_003482.3	3130	tCt/tTt	34/54	1	2	FACETS	0.898	0.788	1	0.898	0.788	1	CLONAL	1	TRUE	1	0.225018388822309	2		711	772	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278040	18278040	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	91	794	0	ENST00000222254.8:c.1660A>G	p.Arg554Gly	p.R554G	ENST00000222254	NM_005027.3	554	Aga/Gga	13/16	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.225018388822309	2		794	774	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549412	187549412	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	81	785	0	ENST00000441802.2:c.4706G>T	p.Gly1569Val	p.G1569V	ENST00000441802	NM_005245.3	1569	gGg/gTg	9/27	1	2	FACETS	0.981	0.864	1	0.981	0.864	1	CLONAL	1	TRUE	1	0.225018388822309	2		785	734	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0025402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	44	518	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	1	2	FACETS	0.22	0.183	0.26	0.22	0.183	0.26	SUBCLONAL	1	TRUE	1	0.470521894809257	2		518	851	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0025406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	150	562	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.902	0.823	0.985	0.902	0.823	0.985	CLONAL	1	FALSE	1	0.306684330274174	2		563	1084	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0025406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	122	322	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.263675055202286	2	FACETS	0.82	0.746	0.898	0.82	0.746	0.898	CLONAL	2	FALSE	0	0.306684330274174	2		322	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0025406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	181	816	3	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	FALSE	1	0.306684330274174	2		819	1173	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128020	30128020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376745934	NA	P-0025406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1452	137	734	0	ENST00000263025.4:c.1109G>A	p.Arg370His	p.R370H	ENST00000263025	NM_002746.2	370	cGc/cAc	8/9	0.306684330274174	4	FACETS	0.735	0.666	0.808			1	SUBCLONAL	1	FALSE	NA	0.306684330274174	4		734	1589	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561534	9561534	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1007888461	NA	P-0025406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	178	709	0	ENST00000353224.5:c.248A>G	p.Asn83Ser	p.N83S	ENST00000353224	NM_177990.2	83	aAc/aGc	4/10	0.306684330274174	6	FACETS	1	0.987	1	0.467	0.429	0.507	CLONAL	1	FALSE	3	0.306684330274174	6		709	1337	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	216	314	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.886	0.831	0.942	0.886	0.831	0.942	CLONAL	1	TRUE	1	0.909555722830723	2		314	536	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983013	201983014	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	392	791	0	ENST00000359651.3:c.863dup	p.Asn289GlnfsTer12	p.N289Qfs*12	ENST00000359651		288	ctc/cTtc	7/8	1	2	FACETS	0.931	0.908	0.952	1	0.997	1	CLONAL	2	TRUE	1	0.909555722830723	2		791	463	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589788	69589788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1462632542	NA	P-0025407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	5246	118	0	ENST00000168712.1:c.65C>T	p.Pro22Leu	p.P22L	ENST00000168712	NM_002007.2	22	cCc/cTc	1/3	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.909555722830723	NA		118	5596	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711878	89711879	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	31	411	1	ENST00000371953.3:c.497dup	p.Thr167AsnfsTer13	p.T167Nfs*13	ENST00000371953	NM_000314.4	166	gta/gTta	6/9	1	2	FACETS	0.761	0.617	0.922	0.761	0.617	0.922	CLONAL	1	TRUE	1	0.289048843278818	2		412	282	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717662	89717663	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0025408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	71	520	0	ENST00000371953.3:c.687_688del	p.Gly230ThrfsTer12	p.G230Tfs*12	ENST00000371953	NM_000314.4	229	tcAGga/tcga	7/9	1	2	FACETS	0.965	0.844	1	0.965	0.844	1	CLONAL	1	TRUE	1	0.289048843278818	2		520	509	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435097	110435097	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	257	464	0	ENST00000375856.3:c.3304A>G	p.Thr1102Ala	p.T1102A	ENST00000375856	NM_003749.2	1102	Acg/Gcg	1/2	0.289048843278818	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.289048843278818	1		464	1113	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0025408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	265	535	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.289048843278818	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.289048843278818	1		535	1163	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094956	11094956	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	164	493	0	ENST00000358026.2:c.129G>C	p.Met43Ile	p.M43I	ENST00000358026	NM_001128849.1	43	atG/atC	2/36	0.0578460880630502	3	FACETS	1	0.986	1	0.674	0.618	0.732	INDETERMINATE	1	TRUE	1	0.289048843278818	3		493	964	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	61	523	0	ENST00000263967.3:c.3012G>T	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atT	21/21	1	2	FACETS	0.938	0.811	1	0.938	0.811	1	CLONAL	1	TRUE	1	0.289048843278818	2		523	450	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503971	186503974	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	novel	NA	P-0025408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	23	285	0	ENST00000323963.5:c.541_544del	p.Val181TrpfsTer8	p.V181Wfs*8	ENST00000323963		179	aTGTTt/at	6/11	1	2	FACETS	0.723	0.566	0.903	0.723	0.566	0.903	CLONAL	1	TRUE	1	0.289048843278818	2		285	220	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0025409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	79	574	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.794	0.698	0.896	0.794	0.698	0.896	SUBCLONAL	1	TRUE	1	0.31	2		574	642	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729740	162729740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	67	511	0	ENST00000367921.3:c.826G>A	p.Asp276Asn	p.D276N	ENST00000367921	NM_006182.2	276	Gac/Aac	8/18	1	2	FACETS	0.808	0.703	0.921	0.808	0.703	0.921	CLONAL	1	TRUE	1	0.31	2		511	535	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619837	21619837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	69	342	0	ENST00000382592.4:c.329C>T	p.Ala110Val	p.A110V	ENST00000382592	NM_014572.2	110	gCa/gTa	2/8	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.31	2		342	422	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986876	36986877	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0025409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	37	143	0	ENST00000354822.5:c.812dup	p.Thr272HisfsTer167	p.T272Hfs*167	ENST00000354822	NM_001079668.2	271	ggc/ggGc	3/3	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.31	2		143	164	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986961	36986961	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	44	325	2	ENST00000354822.5:c.728G>T	p.Arg243Leu	p.R243L	ENST00000354822	NM_001079668.2	243	cGc/cTc	3/3	1	2	FACETS	0.879	0.74	1	0.879	0.74	1	CLONAL	1	TRUE	1	0.31	2		327	323	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821865	59821865	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	71	644	0	ENST00000259008.2:c.2185G>T	p.Gly729Ter	p.G729*	ENST00000259008	NM_032043.2	729	Gga/Tga	15/20	1	2	FACETS	0.667	0.581	0.759	0.667	0.581	0.759	SUBCLONAL	1	TRUE	1	0.31	2		644	687	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759495	133759496	+	stop_gained	Nonsense_Mutation	DNP	GA	GA	TT	novel	NA	P-0025409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	65	497	1	ENST00000318560.5:c.1818_1819delinsTT	p.Lys606_Lys607delinsAsnTer	p.K606_K607delinsN*	ENST00000318560	NM_005157.4	606	aaGAag/aaTTag	11/11	1	2	FACETS	0.872	0.757	0.995	0.872	0.757	0.995	CLONAL	1	TRUE	1	0.31	2		498	481	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858363	89858375	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGACAACCAGG	GCAGACAACCAGG	-	novel	NA	P-0025410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	233	644	0	ENST00000389301.3:c.1185_1197del	p.Leu396PhefsTer15	p.L396Ffs*15	ENST00000389301	NM_000135.2	395	gcCCTGGTTGTCTGC/gc	13/43	0.258077392785163	1	FACETS	0.751	0.701	0.801	0.751	0.701	0.801	INDETERMINATE	1	TRUE	0	0.529968402764174	1		644	861	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976267	7976267	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1366953758	NA	P-0025410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	105	420	0	ENST00000319144.4:c.1928G>A	p.Arg643Gln	p.R643Q	ENST00000319144	NM_001139.2	643	cGg/cAg	15/15	0.124744854408099	1	FACETS	0.405	0.362	0.449	0.405	0.362	0.449	INDETERMINATE	1	TRUE	0	0.529968402764174	1		420	720	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0025411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	28	585	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.133449596375671	1	FACETS	0.382	0.305	0.469	0.382	0.305	0.469	INDETERMINATE	1	FALSE	0	0.305481348645292	1		585	407	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1131691035	NA	P-0025411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	48	628	1	ENST00000269305.4:c.592del	p.Glu198LysfsTer49	p.E198Kfs*49	ENST00000269305	NM_001126112.2	198	Gaa/aa	6/11	1	2	FACETS	0.537	0.454	0.629	0.537	0.454	0.629	SUBCLONAL	1	FALSE	1	0.305481348645292	2		629	585	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602909	55602909	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs766036617	NA	P-0025411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	32	496	0	ENST00000288135.5:c.2619G>T	p.Met873Ile	p.M873I	ENST00000288135	NM_000222.2	873	atG/atT	19/21	1	2	FACETS	0.427	0.346	0.518	0.427	0.346	0.518	SUBCLONAL	1	FALSE	1	0.305481348645292	2		496	491	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100403	8100403	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	45	549	0	ENST00000346208.3:c.377C>A	p.Ser126Tyr	p.S126Y	ENST00000346208		126	tCc/tAc	3/6	1	2	FACETS	0.571	0.48	0.672	0.571	0.48	0.672	SUBCLONAL	1	FALSE	1	0.305481348645292	2		549	516	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613426	100613426	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0025411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	29	498	0	ENST00000308731.7:c.975-1G>T		p.X325_splice	ENST00000308731	NM_000061.2	325			1	2	FACETS	0.392	0.314	0.481	0.392	0.314	0.481	SUBCLONAL	1	FALSE	1	0.305481348645292	2		498	484	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942195	71942195	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	55	544	0	ENST00000298229.2:c.1463del	p.Gly488AlafsTer43	p.G488Afs*43	ENST00000298229	NM_001567.3	487	Ggg/gg	12/28	1	2	FACETS	0.623	0.533	0.722	0.623	0.533	0.722	SUBCLONAL	1	FALSE	1	0.305481348645292	2		544	578	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355246	81355246	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	31	466	0	ENST00000222390.5:c.1128C>A	p.Tyr376Ter	p.Y376*	ENST00000222390	NM_000601.4	376	taC/taA	9/18	1	2	FACETS	0.471	0.38	0.573	0.471	0.38	0.573	SUBCLONAL	1	FALSE	1	0.305481348645292	2		466	431	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748153	72748153	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	33	377	0	ENST00000357731.5:c.25G>T	p.Gly9Cys	p.G9C	ENST00000357731	NM_173808.2	9	Ggt/Tgt	1/7	1	2	FACETS	0.537	0.438	0.65	0.537	0.438	0.65	SUBCLONAL	1	FALSE	1	0.305481348645292	2		377	402	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625222	69625222	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	49	531	0	ENST00000334134.2:c.571G>T	p.Val191Leu	p.V191L	ENST00000334134	NM_005247.2	191	Gtg/Ttg	3/3	1	2	FACETS	0.554	0.469	0.648	0.554	0.469	0.648	SUBCLONAL	1	FALSE	1	0.305481348645292	2		531	579	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039144	49039144	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs764520289	NA	P-0025411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	14	344	1	ENST00000267163.4:c.2222G>T	p.Arg741Leu	p.R741L	ENST00000267163	NM_000321.2	741	cGt/cTt	22/27	1	2	FACETS	0.364	0.263	0.486	0.364	0.263	0.486	SUBCLONAL	1	FALSE	1	0.305481348645292	2		345	252	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004886	16004886	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	50	535	0	ENST00000268712.3:c.2368G>T	p.Ala790Ser	p.A790S	ENST00000268712	NM_006311.3	790	Gct/Tct	20/46	1	2	FACETS	0.497	0.421	0.582	0.497	0.421	0.582	SUBCLONAL	1	FALSE	1	0.305481348645292	2		535	658	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604780	48604780	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	26	439	0	ENST00000342988.3:c.1602G>T	p.Gln534His	p.Q534H	ENST00000342988	NM_005359.5	534	caG/caT	12/12	1	2	FACETS	0.354	0.279	0.44	0.354	0.279	0.44	SUBCLONAL	1	FALSE	1	0.305481348645292	2		439	481	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662653	227662653	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	28	444	0	ENST00000305123.5:c.802A>T	p.Ser268Cys	p.S268C	ENST00000305123	NM_005544.2	268	Agc/Tgc	1/2	1	2	FACETS	0.386	0.308	0.475	0.386	0.308	0.475	SUBCLONAL	1	FALSE	1	0.305481348645292	2		444	475	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252986	36252986	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	39	459	0	ENST00000300305.3:c.376G>T	p.Asp126Tyr	p.D126Y	ENST00000300305		126	Gat/Tat	4/8	1	2	FACETS	0.484	0.4	0.577	0.484	0.4	0.577	SUBCLONAL	1	FALSE	1	0.305481348645292	2		459	528	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143352400	143352400	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	39	577	1	ENST00000262992.4:c.13G>T	p.Glu5Ter	p.E5*	ENST00000262992	NM_001101669.1	5	Gag/Tag	2/24	1	2	FACETS	0.461	0.381	0.55	0.461	0.381	0.55	SUBCLONAL	1	FALSE	1	0.305481348645292	2		578	554	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30682891	30682891	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	45	636	0	ENST00000376406.3:c.62G>T	p.Ser21Ile	p.S21I	ENST00000376406	NM_014641.2	21	aGt/aTt	2/15	1	2	FACETS	0.485	0.406	0.571	0.485	0.406	0.571	SUBCLONAL	1	FALSE	1	0.305481348645292	2		636	608	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2952954	2952954	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	37	533	0	ENST00000396946.4:c.2986G>C	p.Gly996Arg	p.G996R	ENST00000396946	NM_032415.4	996	Gga/Cga	22/25	1	2	FACETS	0.404	0.332	0.485	0.404	0.332	0.485	SUBCLONAL	1	FALSE	1	0.305481348645292	2		533	599	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38196095	38196095	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	28	707	1	ENST00000317025.8:c.706G>T	p.Glu236Ter	p.E236*	ENST00000317025	NM_023034.1	236	Gaa/Taa	3/24	1	2	FACETS	0.381	0.304	0.469	0.381	0.304	0.469	SUBCLONAL	1	FALSE	1	0.305481348645292	2		708	481	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27203009	27203009	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	39	607	0	ENST00000380036.4:c.2101G>T	p.Gly701Cys	p.G701C	ENST00000380036	NM_000459.3	701	Ggc/Tgc	13/23	1	2	FACETS	0.449	0.371	0.535	0.449	0.371	0.535	SUBCLONAL	1	FALSE	1	0.305481348645292	2		607	569	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039305	47039305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	38	570	0	ENST00000377604.3:c.928C>T	p.His310Tyr	p.H310Y	ENST00000377604	NM_001204468.1	310	Cac/Tac	10/24	1	2	FACETS	0.456	0.377	0.546	0.456	0.377	0.546	SUBCLONAL	1	FALSE	1	0.305481348645292	2		570	545	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044482	47044482	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	33	532	0	ENST00000377604.3:c.1979G>C	p.Arg660Pro	p.R660P	ENST00000377604	NM_001204468.1	660	cGc/cCc	18/24	1	2	FACETS	0.408	0.331	0.494	0.408	0.331	0.494	SUBCLONAL	1	FALSE	1	0.305481348645292	2		532	530	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0025412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	41	428	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.713	0.592	0.848	0.713	0.592	0.848	SUBCLONAL	1	TRUE	1	0.16	2		428	719	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226064	53226064	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs782405999	NA	P-0025412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	66	472	2	ENST00000375401.3:c.2785C>T	p.Arg929Ter	p.R929*	ENST00000375401	NM_004187.3	929	Cga/Tga	19/26	1	2	FACETS	0.783	0.677	0.898	0.783	0.677	0.898	SUBCLONAL	1	TRUE	1	0.16	2		474	1054	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015133	37015133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223489007	NA	P-0025412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	75	687	0	ENST00000358127.4:c.271G>A	p.Ala91Thr	p.A91T	ENST00000358127	NM_001280556.1	91	Gcc/Acc	3/10	1	2	FACETS	0.881	0.77	1	0.881	0.77	1	CLONAL	1	TRUE	1	0.16	2		687	1064	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068321	30068321	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs756900091	NA	P-0025412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	31	341	0	ENST00000331968.5:c.2078C>A	p.Ala693Asp	p.A693D	ENST00000331968	NM_002742.2	693	gCt/gAt	15/18	1	2	FACETS	0.633	0.511	0.773	0.633	0.511	0.773	SUBCLONAL	1	TRUE	1	0.16	2		341	612	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498394	89498394	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	35	354	0	ENST00000336596.2:c.2366G>C	p.Arg789Thr	p.R789T	ENST00000336596	NM_005233.5	789	aGg/aCg	14/17	1	2	FACETS	0.809	0.662	0.974	0.809	0.662	0.974	CLONAL	1	TRUE	1	0.16	2		354	541	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474026	29474026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147858673	NA	P-0025413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	206	797	0	ENST00000389048.3:c.2149G>A	p.Glu717Lys	p.E717K	ENST00000389048	NM_004304.4	717	Gag/Aag	12/29	1	2	FACETS	0.943	0.875	1	0.943	0.875	1	CLONAL	1	TRUE	1	0.446948335044833	2		797	978	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348879	11348879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1197896613	NA	P-0025413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	107	305	0	ENST00000332029.2:c.457C>T	p.His153Tyr	p.H153Y	ENST00000332029	NM_003745.1	153	Cac/Tac	2/2	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.446948335044833	2		305	417	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201319	133201319	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	161	752	0	ENST00000320574.5:c.6825G>C	p.Glu2275Asp	p.E2275D	ENST00000320574	NM_006231.2	2275	gaG/gaC	49/49	1	2	FACETS	0.756	0.693	0.822	0.756	0.693	0.822	SUBCLONAL	1	TRUE	1	0.446948335044833	2		752	953	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041582	42041582	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0025413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	205	697	0	ENST00000219905.7:c.5777C>G	p.Ser1926Ter	p.S1926*	ENST00000219905	NM_001164273.1	1926	tCa/tGa	17/24	1	2	FACETS	0.891	0.826	0.958	0.891	0.826	0.958	CLONAL	1	TRUE	1	0.446948335044833	2		697	1030	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207169	1207169	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	194	818	1	ENST00000326873.7:c.257G>A	p.Arg86Gln	p.R86Q	ENST00000326873	NM_000455.4	86	cGa/cAa	1/10	1	2	FACETS	0.743	0.686	0.802	0.743	0.686	0.802	SUBCLONAL	1	TRUE	1	0.446948335044833	2		819	1169	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271962	18271962	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	103	383	0	ENST00000222254.8:c.565G>T	p.Glu189Ter	p.E189*	ENST00000222254	NM_005027.3	189	Gag/Tag	5/16	1	2	FACETS	0.888	0.798	0.983	0.888	0.798	0.983	CLONAL	1	TRUE	1	0.446948335044833	2		383	519	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149395	61149395	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	118	575	0	ENST00000295025.8:c.1585G>C	p.Asp529His	p.D529H	ENST00000295025	NM_002908.2	529	Gac/Cac	11/11	1	2	FACETS	0.698	0.629	0.769	0.698	0.629	0.769	SUBCLONAL	1	TRUE	1	0.446948335044833	2		575	757	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149488	61149488	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1460557137	NA	P-0025413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	120	521	0	ENST00000295025.8:c.1678G>C	p.Asp560His	p.D560H	ENST00000295025	NM_002908.2	560	Gat/Cat	11/11	1	2	FACETS	0.705	0.637	0.777	0.705	0.637	0.777	SUBCLONAL	1	TRUE	1	0.446948335044833	2		521	762	SUCCESS
APC	324	MSKCC	GRCh37	5	112176595	112176595	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	111	471	0	ENST00000257430.4:c.5304G>C	p.Lys1768Asn	p.K1768N	ENST00000257430	NM_000038.5	1768	aaG/aaC	16/16	1	2	FACETS	0.729	0.656	0.806	0.729	0.656	0.806	SUBCLONAL	1	TRUE	1	0.446948335044833	2		471	681	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519380	137519380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1470644923	NA	P-0025413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	61	320	0	ENST00000367739.4:c.1258G>A	p.Glu420Lys	p.E420K	ENST00000367739	NM_000416.2	420	Gaa/Aaa	7/7	0.446948335044833	1	FACETS	0.549	0.476	0.628	0.549	0.476	0.628	SUBCLONAL	1	TRUE	0	0.446948335044833	1		320	386	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859576	151859576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	141	670	0	ENST00000262189.6:c.11086C>T	p.Gln3696Ter	p.Q3696*	ENST00000262189	NM_170606.2	3696	Caa/Taa	43/59	0.446948335044833	1	FACETS	0.693	0.632	0.756	0.693	0.632	0.756	SUBCLONAL	1	TRUE	0	0.446948335044833	1		670	707	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061215	38061235	+	inframe_deletion	In_Frame_Del	DEL	GCAGCCGTTCTCGAACATGTT	GCAGCCGTTCTCGAACATGTT	-	novel	NA	P-0025414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	409	522	0	ENST00000250448.2:c.754_774del	p.Asn252_Cys258del	p.N252_C258del	ENST00000250448	NM_004496.3	252	AACATGTTCGAGAACGGCTGC/-	2/2	0.243048147866674	3	FACETS	0.871	0.831	0.911			1	INDETERMINATE	2	TRUE	NA	0.589328565478059	3		522	1032	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199949	108199949	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0025414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	178	288	0	ENST00000278616.4:c.7291A>T	p.Lys2431Ter	p.K2431*	ENST00000278616	NM_000051.3	2431	Aaa/Taa	49/63	0.589328565478059	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.589328565478059	1		288	404	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752815	42752826	+	inframe_deletion	In_Frame_Del	DEL	GCGTAGCTTGAG	GCGTAGCTTGAG	-	novel	NA	P-0025414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1216	122	767	0	ENST00000222329.4:c.1438_1449del	p.Leu480_Arg483del	p.L480_R483del	ENST00000222329	NM_006494.2	480	CTCAAGCTACGC/-	4/4	1	2	FACETS	0.309	0.278	0.342	0.309	0.278	0.342	SUBCLONAL	1	TRUE	1	0.589328565478059	2		767	1338	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940465	76940465	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	380	385	0	ENST00000373344.5:c.628A>T	p.Ser210Cys	p.S210C	ENST00000373344	NM_000489.3	210	Agc/Tgc	8/35	1	1	FACETS	0.75	0.722	0.778	1	0.996	1	SUBCLONAL	2	TRUE	0	0.589328565478059	1		385	606	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0025416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	56	403	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.781	0.667	0.905	0.781	0.667	0.905	CLONAL	1	TRUE	1	0.189798814936446	2		403	756	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0025416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	59	430	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.839	0.721	0.968	0.839	0.721	0.968	CLONAL	1	TRUE	1	0.189798814936446	2		430	741	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587781525	NA	P-0025416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	91	672	0	ENST00000269305.4:c.842A>G	p.Asp281Gly	p.D281G	ENST00000269305	NM_001126112.2	281	gAc/gGc	8/11	1	2	FACETS	0.799	0.707	0.898	0.799	0.707	0.898	SUBCLONAL	1	TRUE	1	0.189798814936446	2		672	1200	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774148	56774148	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	68	738	2	ENST00000337432.4:c.499G>T	p.Asp167Tyr	p.D167Y	ENST00000337432	NM_058216.2	167	Gat/Tat	3/9	1	2	FACETS	0.678	0.588	0.776	0.678	0.588	0.776	SUBCLONAL	1	TRUE	1	0.189798814936446	2		740	1057	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051617	30051617	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	66	527	1	ENST00000338641.4:c.551G>T	p.Trp184Leu	p.W184L	ENST00000338641	NM_000268.3	184	tGg/tTg	6/16	1	2	FACETS	0.794	0.687	0.91	0.794	0.687	0.91	CLONAL	1	TRUE	1	0.189798814936446	2		528	876	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0025436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	83	442	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	0.779	0.688	0.878	0.779	0.688	0.878	SUBCLONAL	1	TRUE	1	0.31	2		442	687	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980007	7980007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147992320	NA	P-0025436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	107	524	1	ENST00000319144.4:c.1330G>A	p.Val444Ile	p.V444I	ENST00000319144	NM_001139.2	444	Gtt/Att	10/15	1	2	FACETS	0.97	0.87	1	0.97	0.87	1	CLONAL	1	TRUE	1	0.31	2		525	712	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871129	12871129	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	37	246	0	ENST00000228872.4:c.357del	p.Ile119MetfsTer26	p.I119Mfs*26	ENST00000228872	NM_004064.3	119	aTt/at	1/3	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.31	2		246	213	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106352	27106352	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	90	413	0	ENST00000324856.7:c.5963T>G	p.Ile1988Ser	p.I1988S	ENST00000324856	NM_006015.4	1988	aTt/aGt	20/20	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.31	2		413	566	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761072	59761072	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	121	501	0	ENST00000259008.2:c.3335A>T	p.Asp1112Val	p.D1112V	ENST00000259008	NM_032043.2	1112	gAt/gTt	20/20	0.302521970033238	6	FACETS	1	0.958	1			1	CLONAL	1	TRUE	NA	0.31	6		501	1134	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702178	47702178	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs371614039	NA	P-0025436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	68	327	0	ENST00000233146.2:c.1774A>G	p.Met592Val	p.M592V	ENST00000233146	NM_000251.2	592	Atg/Gtg	12/16	1	2	FACETS	0.874	0.762	0.995	0.874	0.762	0.995	CLONAL	1	TRUE	1	0.31	2		327	502	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	51	606	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.898	0.76	1	0.898	0.76	1	CLONAL	1	TRUE	1	0.12	2		606	947	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0025438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	35	395	2	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.736	0.601	0.888	0.736	0.601	0.888	SUBCLONAL	1	TRUE	1	0.12	2		397	793	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0025438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	43	387	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	0.976	0.815	1	0.976	0.815	1	CLONAL	1	TRUE	1	0.12	2		387	734	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0025438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	31	392	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	1	2	FACETS	0.921	0.743	1	0.921	0.743	1	CLONAL	1	TRUE	1	0.12	2		392	561	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962298	2962298	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769577430	NA	P-0025438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	55	695	1	ENST00000396946.4:c.2239G>A	p.Val747Ile	p.V747I	ENST00000396946	NM_032415.4	747	Gtc/Atc	17/25	1	2	FACETS	0.943	0.804	1	0.943	0.804	1	CLONAL	1	TRUE	1	0.12	2		696	972	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439874	51439874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs955574509	NA	P-0025440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	54	260	0	ENST00000262662.1:c.439T>C	p.Tyr147His	p.Y147H	ENST00000262662		147	Tat/Cat	4/4	0.240516899021315	4	FACETS	0.736	0.629	0.853	0.368	0.314	0.427	INDETERMINATE	1	TRUE	2	0.428557219244811	4		260	489	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	164	314	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.972	1			1	INDETERMINATE	1	TRUE	NA	0.661304641555009	2		314	452	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0025441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	302	510	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	0.661304641555009	2		510	882	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453135	140453136	+	missense_variant	Missense_Mutation	DNP	CA	CA	TT	rs121913377	NA	P-0025441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	227	514	0	ENST00000288602.6:c.1799_1800delinsAA	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTG/gAA	15/18	1	2	FACETS	0.907	0.848	0.967	0.907	0.848	0.967	CLONAL	1	TRUE	1	0.661304641555009	2		514	757	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050277	13050277	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1328767759	NA	P-0025441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	280	481	0	ENST00000316448.5:c.229C>G	p.Leu77Val	p.L77V	ENST00000316448	NM_004343.3	77	Ctg/Gtg	3/9	1	2	FACETS	0.955	0.899	1	0.955	0.899	1	CLONAL	1	TRUE	1	0.661304641555009	2		481	887	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	22	606	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.64	0.495	0.808	0.64	0.495	0.808	SUBCLONAL	1	TRUE	1	0.19	2		606	362	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0025443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	15	430	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.434	0.316	0.576	0.434	0.316	0.576	SUBCLONAL	1	TRUE	1	0.19	2		430	364	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912660	NA	P-0025443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	96	714	0	ENST00000269305.4:c.839G>T	p.Arg280Ile	p.R280I	ENST00000269305	NM_001126112.2	280	aGa/aTa	8/11	1	2	FACETS	0.876	0.779	0.981	0.876	0.779	0.981	CLONAL	1	TRUE	1	0.19	2		714	1153	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723440	52723440	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0025443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	72	512	2	ENST00000322088.6:c.1303-2A>T		p.X435_splice	ENST00000322088	NM_014225.5	435			1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.19	2		514	725	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191326	185191326	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	73	471	1	ENST00000265026.3:c.2207G>T	p.Arg736Met	p.R736M	ENST00000265026	NM_004721.4	736	aGg/aTg	11/14	1	2	FACETS	0.86	0.75	0.978	0.86	0.75	0.978	CLONAL	1	TRUE	1	0.19	2		472	894	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535412	66535412	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	22	204	0	ENST00000273854.3:c.49G>T	p.Gly17Cys	p.G17C	ENST00000273854	NM_004439.5	17	Ggc/Tgc	1/18	1	2	FACETS	0.591	0.457	0.746	0.591	0.457	0.746	SUBCLONAL	1	TRUE	1	0.19	2		204	392	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681090	30681090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61754764	NA	P-0025443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	58	397	2	ENST00000376406.3:c.629C>T	p.Pro210Leu	p.P210L	ENST00000376406	NM_014641.2	210	cCg/cTg	5/15	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.19	2		399	567	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372038	55372038	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	51	407	0	ENST00000297316.4:c.728G>T	p.Gly243Val	p.G243V	ENST00000297316	NM_022454.3	243	gGg/gTg	2/2	1	2	FACETS	0.71	0.602	0.829	0.71	0.602	0.829	SUBCLONAL	1	TRUE	1	0.19	2		407	756	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015085	37015085	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	124	649	0	ENST00000358127.4:c.319C>A	p.Pro107Thr	p.P107T	ENST00000358127	NM_001280556.1	107	Ccc/Acc	3/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.19	2		649	1143	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435972	110435972	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1171816938	NA	P-0025447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	98	473	0	ENST00000375856.3:c.2429A>G	p.Tyr810Cys	p.Y810C	ENST00000375856	NM_003749.2	810	tAc/tGc	1/2	1	2	FACETS	0.914	0.823	1	0.914	0.823	1	CLONAL	1	TRUE	1	0.614296175089543	2		473	349	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073904	8073904	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	42	309	0	ENST00000377482.5:c.755G>T	p.Gly252Val	p.G252V	ENST00000377482	NM_018948.3	252	gGa/gTa	4/4	0.614296175089543	1	FACETS	0.37	0.311	0.435	0.37	0.311	0.435	SUBCLONAL	1	TRUE	0	0.614296175089543	1		309	256	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074022	8074022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	27	261	0	ENST00000377482.5:c.637G>A	p.Asp213Asn	p.D213N	ENST00000377482	NM_018948.3	213	Gat/Aat	4/4	0.614296175089543	1	FACETS	0.271	0.216	0.332	0.271	0.216	0.332	SUBCLONAL	1	TRUE	0	0.614296175089543	1		261	225	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057652	27057653	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0025447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	113	357	0	ENST00000324856.7:c.1361dup	p.Tyr454Ter	p.Y454*	ENST00000324856	NM_006015.4	454	tat/tAat	3/20	0.614296175089543	1	FACETS	0.992	0.91	1	0.992	0.91	1	CLONAL	1	TRUE	0	0.614296175089543	1		357	257	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643710	38643710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	199	523	1	ENST00000299084.4:c.1180G>A	p.Asp394Asn	p.D394N	ENST00000299084	NM_152594.2	394	Gac/Aac	7/7	0.614296175089543	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.614296175089543	1		524	431	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191563	10191563	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	147	375	0	ENST00000256474.2:c.556del	p.Glu186LysfsTer16	p.E186Kfs*16	ENST00000256474	NM_000551.3	186	Gaa/aa	3/3	0.604474369299894	1	FACETS	0.97	0.898	1	0.97	0.898	1	CLONAL	1	TRUE	0	0.614296175089543	1		375	342	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597490	52597490	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0025447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	140	313	0	ENST00000394830.3:c.3820A>T	p.Lys1274Ter	p.K1274*	ENST00000394830	NM_018313.4	1274	Aag/Tag	25/30	0.604474369299894	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.614296175089543	1		313	270	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967185	93967185	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	137	476	0	ENST00000369303.4:c.2167C>G	p.Leu723Val	p.L723V	ENST00000369303	NM_004440.3	723	Ctc/Gtc	12/17	1	2	FACETS	0.937	0.858	1	0.937	0.858	1	CLONAL	1	TRUE	1	0.614296175089543	2		476	476	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0025448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	59	510	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.532	0.459	0.611	0.532	0.459	0.611	SUBCLONAL	1	TRUE	1	0.528076552661181	2		510	420	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155725	56155726	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0025448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	40	401	0	ENST00000399503.3:c.819_820del	p.Arg273SerfsTer27	p.R273Sfs*27	ENST00000399503	NM_005921.1	273	AGa/a	3/20	1	2	FACETS	0.357	0.297	0.424	0.357	0.297	0.424	SUBCLONAL	1	TRUE	1	0.528076552661181	2		401	424	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063684	67063684	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	12	297	1	ENST00000412916.2:c.133C>T	p.Gln45Ter	p.Q45*	ENST00000412916		45	Cag/Tag	2/6	0.225937458833519	1	FACETS	0.18	0.126	0.246	0.18	0.126	0.246	INDETERMINATE	1	TRUE	0	0.528076552661181	1		298	186	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161703	56161704	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0025448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	49	585	0	ENST00000399503.3:c.1203dup	p.Ala402SerfsTer5	p.A402Sfs*5	ENST00000399503	NM_005921.1	400	-/A	6/20	1	2	FACETS	0.335	0.283	0.392	0.335	0.283	0.392	SUBCLONAL	1	TRUE	1	0.528076552661181	2		585	554	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	446	606	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.609059881075888	4	FACETS	0.865	0.826	0.904	0.865	0.826	0.904	CLONAL	2	TRUE	2	0.722169442840845	4		606	1230	SUCCESS
APC	324	MSKCC	GRCh37	5	112175147	112175147	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	349	231	0	ENST00000257430.4:c.3856G>T	p.Glu1286Ter	p.E1286*	ENST00000257430	NM_000038.5	1286	Gaa/Taa	16/16	0.668042873339995	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	0	0.722169442840845	3		231	435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0025610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	673	623	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.717206500887982	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.722169442840845	2		624	876	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0025610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	368	425	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.56671674285013	5	FACETS	0.992	0.943	1			1	CLONAL	2	TRUE	NA	0.722169442840845	5		425	1070	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30133009	30133009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760058972	NA	P-0025610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	459	518	3	ENST00000331968.5:c.592G>A	p.Gly198Ser	p.G198S	ENST00000331968	NM_002742.2	198	Ggt/Agt	4/18	0.382389743888381	6	FACETS	1	0.991	1	0.574	0.548	0.6	INDETERMINATE	2	TRUE	2	0.722169442840845	6		521	1354	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732724	204732724	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000509-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	145	504	0	ENST00000302823.3:c.59G>A	p.Trp20Ter	p.W20*	ENST00000302823	NM_005214.4	20	tGg/tAg	1/4	1	2	FACETS	0.785	0.72	0.854	0.785	0.72	0.854	SUBCLONAL	1	TRUE	1	0.637637389650513	2		504	579	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474637	138474651	+	inframe_deletion	In_Frame_Del	DEL	CCTGGGTCACAACTT	CCTGGGTCACAACTT	-	novel	NA	P-0000509-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	137	598	0	ENST00000289153.2:c.342_356del	p.Ser115_Gly119del	p.S115_G119del	ENST00000289153	NM_006219.2	114	agAAGTTGTGACCCAGGg/agg	2/22	1	2	FACETS	0.865	0.791	0.94	0.865	0.791	0.94	CLONAL	1	TRUE	1	0.637637389650513	2		598	497	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859653	151859653	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000509-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	147	333	0	ENST00000262189.6:c.11009A>C	p.Asn3670Thr	p.N3670T	ENST00000262189	NM_170606.2	3670	aAt/aCt	43/59	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.637637389650513	2		333	450	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0000913-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	118	607	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.271194926743321	5	FACETS	0.891	0.803	0.984	0.297	0.267	0.328	INDETERMINATE	1	TRUE	2	0.510932792198778	5		607	916	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0000913-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	186	514	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.271194926743321	5	FACETS	0.838	0.776	0.903	0.559	0.517	0.602	INDETERMINATE	2	TRUE	2	0.510932792198778	5		514	767	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0000913-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	361	654	0	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	0.504873537047998	2	FACETS	0.98	0.937	1	0.98	0.937	1	CLONAL	2	TRUE	0	0.510932792198778	2		654	721	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422464	225422464	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000913-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	33	538	0	ENST00000264414.4:c.176G>C	p.Arg59Thr	p.R59T	ENST00000264414	NM_003590.4	59	aGa/aCa	2/16	0.292484920541919	1	FACETS	0.197	0.16	0.238	0.197	0.16	0.238	INDETERMINATE	1	TRUE	0	0.510932792198778	1		538	489	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937034	48937035	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000913-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	161	370	2	ENST00000267163.4:c.806dup	p.Asn269LysfsTer2	p.N269Kfs*2	ENST00000267163	NM_000321.2	268	gaa/gAaa	8/27	0.47871725333854	2	FACETS	1	0.99	1	0.747	0.692	0.802	CLONAL	1	TRUE	0	0.510932792198778	2		372	422	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81528560	81528560	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000913-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	50	313	1	ENST00000298171.2:c.239G>A	p.Arg80Lys	p.R80K	ENST00000298171	NM_000369.2	80	aGa/aAa	2/10	0.510932792198778	7	FACETS	0.529	0.447	0.619			1	SUBCLONAL	1	TRUE	NA	0.510932792198778	7		314	843	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789696	3789696	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs761058155	NA	P-0000913-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	175	426	0	ENST00000262367.5:c.4163C>G	p.Ser1388Cys	p.S1388C	ENST00000262367	NM_004380.2	1388	tCt/tGt	25/31	0.210587361523424	4	FACETS	0.827	0.765	0.891	0.413	0.382	0.446	INDETERMINATE	2	TRUE	0	0.510932792198778	4		426	626	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376368	15376368	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000913-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	233	928	0	ENST00000263377.2:c.646C>A	p.Pro216Thr	p.P216T	ENST00000263377	NM_058243.2	216	Cct/Act	5/20	0.504873537047998	2	FACETS	0.827	0.771	0.885	0.413	0.385	0.443	CLONAL	1	TRUE	0	0.510932792198778	2		928	1103	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187951	32187951	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000913-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	59	604	1	ENST00000375023.3:c.1270T>A	p.Tyr424Asn	p.Y424N	ENST00000375023	NM_004557.3	424	Tat/Aat	7/30	0.31305660324433	4	FACETS	0.402	0.345	0.465	0.201	0.172	0.233	SUBCLONAL	1	TRUE	2	0.510932792198778	4		605	867	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163733	152163733	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000913-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	60	406	0	ENST00000206249.3:c.454C>A	p.Pro152Thr	p.P152T	ENST00000206249	NM_000125.3	152	Cca/Aca	2/8	1	2	FACETS	0.605	0.523	0.694	0.605	0.523	0.694	SUBCLONAL	1	TRUE	1	0.510932792198778	2		406	388	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035204	6035207	+	frameshift_variant	Frame_Shift_Del	DEL	CTGT	CTGT	-	rs267608154	NA	P-0000913-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	96	472	0	ENST00000265849.7:c.861_864del	p.Arg287SerfsTer19	p.R287Sfs*19	ENST00000265849	NM_000535.5	287	agACAG/ag	8/15	0.271194926743321	5	FACETS	0.715	0.635	0.799	0.238	0.211	0.267	INDETERMINATE	1	TRUE	2	0.510932792198778	5		472	929	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027806	48027807	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1553414010	NA	P-0001625-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	81	399	0	ENST00000234420.5:c.2690dup	p.Asn897LysfsTer3	p.N897Kfs*3	ENST00000234420	NM_000179.2	895	aca/acAa	4/10	1	2	FACETS	0.799	0.706	0.898	0.799	0.706	0.898	SUBCLONAL	1	TRUE	1	0.407971094683563	2		399	497	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241722	55241722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1051753269	NA	P-0001625-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	228	464	2	ENST00000275493.2:c.2170G>A	p.Gly724Ser	p.G724S	ENST00000275493	NM_005228.3	724	Ggc/Agc	18/28	0.339176504645954	4	FACETS	0.945	0.882	1	0.63	0.588	0.673	CLONAL	2	TRUE	1	0.407971094683563	4		466	833	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0001625-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	221	518	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	0.339176504645954	4	FACETS	1	0.967	1	0.703	0.657	0.751	CLONAL	2	TRUE	1	0.407971094683563	4		518	723	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0002133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	198	588	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.454832005184195	5	FACETS	0.893	0.839	0.947	0.893	0.839	0.947	INDETERMINATE	3	TRUE	2	0.798555820438282	5		588	407	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101468	27101468	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	428	546	0	ENST00000324856.7:c.4750C>T	p.Gln1584Ter	p.Q1584*	ENST00000324856	NM_006015.4	1584	Cag/Tag	18/20	0.751483901756613	3	FACETS	0.928	0.903	0.951	0.928	0.903	0.951	CLONAL	3	TRUE	0	0.798555820438282	3		546	539	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867305	68867306	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0002133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	288	398	0	ENST00000261769.5:c.2553dup	p.Glu852ArgfsTer9	p.E852Rfs*9	ENST00000261769	NM_004360.3	851	tca/tcAa	16/16	0.781041003457005	2	FACETS	0.952	0.918	0.984	0.952	0.918	0.984	CLONAL	2	TRUE	0	0.798555820438282	2		398	379	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221961	1221961	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	170	580	1	ENST00000326873.7:c.876C>A	p.Tyr292Ter	p.Y292*	ENST00000326873	NM_000455.4	292	taC/taA	7/10	0.771591972118657	2	FACETS	0.995	0.925	1	0.497	0.462	0.533	CLONAL	1	TRUE	0	0.798555820438282	2		581	428	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0002587-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	312	400	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.202921055839845	7	FACETS	1	0.953	1	1	0.953	1	CLONAL	5	TRUE	2	0.202921055839845	7		400	919	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0002587-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	300	389	0	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	0.202921055839845	5	FACETS	1	0.973	1	1	0.995	1	CLONAL	5	TRUE	2	0.202921055839845	5		389	740	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057947	27057947	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0002587-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	307	335	0	ENST00000324856.7:c.1655C>G	p.Ser552Ter	p.S552*	ENST00000324856	NM_006015.4	552	tCa/tGa	3/20	0.169503941933988	4	FACETS	0.955	0.909	1	1	0.996	1	CLONAL	6	TRUE	1	0.202921055839845	4		335	635	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8339022	8339022	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002587-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	207	348	0	ENST00000356435.5:c.5279C>A	p.Ala1760Glu	p.A1760E	ENST00000356435		1760	gCa/gAa	32/35	0.194644540942417	2	FACETS	0.945	0.888	1	1	0.995	1	CLONAL	5	TRUE	0	0.202921055839845	2		348	432	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720678	89720679	+	stop_gained	Nonsense_Mutation	DNP	AC	AC	TA	novel	NA	P-0002587-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	67	72	0	ENST00000371953.3:c.829_830delinsTA	p.Thr277Ter	p.T277*	ENST00000371953	NM_000314.4	277	ACa/TAa	8/9	0.202921055839845	5	FACETS	0.941	0.835	1	1	0.978	1	CLONAL	5	TRUE	2	0.202921055839845	5		72	183	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099974	27099975	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0002587-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	208	327	0	ENST00000324856.7:c.3854dup	p.Tyr1285Ter	p.Y1285*	ENST00000324856	NM_006015.4	1285	tat/tAat	15/20	0.169503941933988	4	FACETS	0.957	0.893	1	1	0.988	1	CLONAL	4	TRUE	1	0.202921055839845	4		327	644	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819954	170819956	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	rs751654967	NA	P-0002587-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	337	255	0	ENST00000296930.5:c.504_506del	p.Asp168del	p.D168del	ENST00000296930	NM_002520.6	166	GAT/-	6/11	0.19444208286361	5	FACETS	0.972	0.928	1	1	0.995	1	CLONAL	7	TRUE	0	0.202921055839845	5		255	637	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0003573-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	25	607	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.3	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		607	971	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0003573-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	40	514	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.3	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		514	893	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003591-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	61	774	2	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.38371350176417	2	FACETS	0.99	0.86	1	0.495	0.43	0.565	CLONAL	1	TRUE	0	0.383806934605329	2		776	321	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805422	46805422	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003591-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	81	874	0	ENST00000290295.7:c.534G>A	p.Trp178Ter	p.W178*	ENST00000290295	NM_006361.5	178	tgG/tgA	1/2	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.383806934605329	2		874	391	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459959	99459959	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003591-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	43	607	0	ENST00000268035.6:c.2055G>C	p.Glu685Asp	p.E685D	ENST00000268035	NM_000875.3	685	gaG/gaC	10/21	1	2	FACETS	0.749	0.63	0.88	0.749	0.63	0.88	SUBCLONAL	1	TRUE	1	0.383806934605329	2		607	299	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587138	212587138	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003591-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	43	535	0	ENST00000342788.4:c.863T>A	p.Phe288Tyr	p.F288Y	ENST00000342788	NM_005235.2	288	tTc/tAc	7/28	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.383806934605329	2		535	219	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799159	45799159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	63	743	1	ENST00000450313.1:c.274G>A	p.Glu92Lys	p.E92K	ENST00000450313	NM_012222.2	92	Gaa/Aaa	3/16	0.237313581164608	1	FACETS	0.198	0.17	0.228	0.198	0.17	0.228	INDETERMINATE	1	TRUE	0	0.438153741006558	1		744	1135	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874036	123874036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1244784020	NA	P-0003882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	15	38	0	ENST00000330479.4:c.67G>A	p.Ala23Thr	p.A23T	ENST00000330479	NM_020382.3	23	Gca/Aca	2/9	NA	2	FACETS	0.571	0.421	0.746			1	INDETERMINATE	1	TRUE	NA	0.438153741006558	2		38	120	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061360	38061360	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	88	660	0	ENST00000250448.2:c.629A>G	p.Asn210Ser	p.N210S	ENST00000250448	NM_004496.3	210	aAc/aGc	2/2	1	2	FACETS	0.412	0.364	0.463	0.412	0.364	0.463	SUBCLONAL	1	TRUE	1	0.438153741006558	2		660	976	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729083	66729083	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	208	617	0	ENST00000307102.5:c.292-1G>A		p.X98_splice	ENST00000307102	NM_002755.3	98			0.237313581164608	1	FACETS	0.814	0.756	0.874	0.814	0.756	0.874	INDETERMINATE	1	TRUE	0	0.438153741006558	1		617	911	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120527	70120527	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0003882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1404	88	865	0	ENST00000245479.2:c.1529G>C	p.Ter510SerextTer49	p.*510Sext*49	ENST00000245479	NM_000346.3	510	tGa/tCa	3/3	0.187465425607726	3	FACETS	0.328	0.289	0.37	0.109	0.096	0.124	INDETERMINATE	1	TRUE	0	0.438153741006558	3		865	1492	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229339	36229339	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	116	672	0	ENST00000222270.7:c.8029C>G	p.Leu2677Val	p.L2677V	ENST00000222270	NM_014727.1	2677	Ctg/Gtg	37/37	0.31083025043157	1	FACETS	0.436	0.392	0.482	0.436	0.392	0.482	SUBCLONAL	1	TRUE	0	0.438153741006558	1		672	949	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082599	16082599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	29	279	1	ENST00000281043.3:c.413G>A	p.Arg138His	p.R138H	ENST00000281043	NM_005378.4	138	cGc/cAc	2/3	0.237313581164608	1	FACETS	0.25	0.2	0.307	0.25	0.2	0.307	INDETERMINATE	1	TRUE	0	0.438153741006558	1		280	413	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086067	16086067	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs766297977	NA	P-0003882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	56	651	0	ENST00000281043.3:c.1243G>C	p.Glu415Gln	p.E415Q	ENST00000281043	NM_005378.4	415	Gag/Cag	3/3	0.237313581164608	1	FACETS	0.217	0.185	0.252	0.217	0.185	0.252	INDETERMINATE	1	TRUE	0	0.438153741006558	1		651	919	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966511	25966511	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	73	652	0	ENST00000435504.4:c.2695C>G	p.Leu899Val	p.L899V	ENST00000435504		899	Ctt/Gtt	13/13	0.237313581164608	1	FACETS	0.236	0.205	0.269	0.236	0.205	0.269	INDETERMINATE	1	TRUE	0	0.438153741006558	1		652	1103	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514857	44514859	+	frameshift_variant	Frame_Shift_Ins	INS	CAA	CAA	TTAT	novel	NA	P-0003882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	59	509	1	ENST00000291552.4:c.388_390delinsATAA	p.Leu130IlefsTer3	p.L130Ifs*3	ENST00000291552	NM_006758.2	130	TTG/ATAA	6/8	1	2	FACETS	0.266	0.228	0.308	0.266	0.228	0.308	SUBCLONAL	1	TRUE	1	0.438153741006558	2		510	1012	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021828	71021828	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0003882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	20	229	0	ENST00000318789.4:c.1531-1G>C		p.X511_splice	ENST00000318789	NM_032682.5	511			0.376247532137658	1	FACETS	0.242	0.185	0.308	0.242	0.185	0.308	SUBCLONAL	1	TRUE	0	0.438153741006558	1		229	295	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149243913	149243913	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0003882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	83	539	0	ENST00000360632.3:c.906-1G>T		p.X302_splice	ENST00000360632	NM_015472.4	302			0.438153741006558	3	FACETS	0.442	0.389	0.5	0.221	0.194	0.25	SUBCLONAL	1	TRUE	1	0.438153741006558	3		539	1044	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80150054	80150054	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	64	637	0	ENST00000265081.6:c.2919C>G	p.Ile973Met	p.I973M	ENST00000265081	NM_002439.4	973	atC/atG	21/24	0.192515778000178	2	FACETS	0.249	0.215	0.287	0.125	0.107	0.144	INDETERMINATE	1	TRUE	0	0.438153741006558	2		637	1171	SUCCESS
APC	324	MSKCC	GRCh37	5	112176087	112176087	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	47	414	1	ENST00000257430.4:c.4796C>A	p.Ser1599Ter	p.S1599*	ENST00000257430	NM_000038.5	1599	tCa/tAa	16/16	0.192515778000178	2	FACETS	0.3	0.253	0.353	0.15	0.126	0.177	INDETERMINATE	1	TRUE	0	0.438153741006558	2		415	714	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508765	148508765	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs751723382	NA	P-0003882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	51	480	0	ENST00000320356.2:c.1899C>G	p.Ile633Met	p.I633M	ENST00000320356	NM_004456.4	633	atC/atG	16/20	1	2	FACETS	0.238	0.201	0.278	0.238	0.201	0.278	SUBCLONAL	1	TRUE	1	0.438153741006558	2		480	980	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210187	123210187	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	50	537	0	ENST00000218089.9:c.2539C>T	p.Gln847Ter	p.Q847*	ENST00000218089	NM_001042749.1	847	Cag/Tag	26/35	0.423136086909275	1	FACETS	0.196	0.165	0.23	0.196	0.165	0.23	SUBCLONAL	1	TRUE	0	0.438153741006558	1		537	910	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969465	44969470	+	inframe_deletion	In_Frame_Del	DEL	CTGATG	CTGATG	-	novel	NA	P-0004138-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	149	289	0	ENST00000377967.4:c.4148_4153del	p.Leu1383_Met1384del	p.L1383_M1384del	ENST00000377967	NM_021140.2	1383	CTGATG/-	28/29	0.430003164420602	2	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.482621396059156	2		289	248	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343359	118343360	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0004138-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	149	359	0	ENST00000534358.1:c.1485_1486delinsAT	p.Ile496Phe	p.I496F	ENST00000534358	NM_005933.3	495	gaGAtt/gaATtt	3/36	0.482621396059156	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.482621396059156	2		359	274	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111886036	111886036	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004138-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	155	581	0	ENST00000341259.2:c.1658C>A	p.Ser553Ter	p.S553*	ENST00000341259	NM_005475.2	553	tCg/tAg	8/8	0.482621396059156	3	FACETS	1	0.988	1	0.709	0.653	0.768	CLONAL	1	TRUE	1	0.482621396059156	3		581	562	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0004488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	305	802	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.305030716247397	5	FACETS	0.913	0.861	0.966	0.913	0.861	0.966	CLONAL	3	TRUE	2	0.305030716247397	5		802	1064	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220715	1220715	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	188	218	0	ENST00000326873.7:c.733C>T	p.Leu245Phe	p.L245F	ENST00000326873	NM_000455.4	245	Ctc/Ttc	5/10	0.23308534554311	4	FACETS	0.935	0.875	0.996			1	CLONAL	4	TRUE	NA	0.305030716247397	4		218	430	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307277	65307277	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	121	175	0	ENST00000342505.4:c.2411G>C	p.Arg804Thr	p.R804T	ENST00000342505	NM_002227.2	804	aGa/aCa	18/25	0.305030716247397	3	FACETS	0.863	0.789	0.94	0.863	0.789	0.94	CLONAL	3	TRUE	0	0.305030716247397	3		175	353	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14027744	14027744	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	189	327	0	ENST00000405192.2:c.100T>A	p.Phe34Ile	p.F34I	ENST00000405192	NM_001163147.1	34	Ttc/Atc	3/12	0.175967691098202	5	FACETS	0.915	0.845	0.987	0.61	0.563	0.658	INDETERMINATE	2	TRUE	2	0.305030716247397	5		327	987	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350086	81350086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	234	324	1	ENST00000222390.5:c.1246G>A	p.Asp416Asn	p.D416N	ENST00000222390	NM_000601.4	416	Gac/Aac	10/18	0.175967691098202	5	FACETS	1	0.961	1	0.696	0.649	0.745	INDETERMINATE	2	TRUE	2	0.305030716247397	5		325	1071	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819261	3819261	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	136	302	0	ENST00000262367.5:c.2974G>T	p.Val992Leu	p.V992L	ENST00000262367	NM_004380.2	992	Gta/Tta	15/31	0.141679037334277	3	FACETS	0.916	0.837	0.999			1	INDETERMINATE	2	TRUE	NA	0.305030716247397	3		302	561	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56852603	56852603	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	169	448	0	ENST00000308159.5:c.517C>A	p.Pro173Thr	p.P173T	ENST00000308159	NM_014669.4	173	Cct/Act	6/22	0.218569840066382	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.305030716247397	1		448	799	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548916	29548916	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	63	194	0	ENST00000356175.3:c.1690G>T	p.Asp564Tyr	p.D564Y	ENST00000356175	NM_000267.3	564	Gat/Tat	15/57	0.175967691098202	5	FACETS	1	0.938	1	0.382	0.331	0.438	INDETERMINATE	1	TRUE	2	0.305030716247397	5		194	525	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143973	11143973	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	98	223	0	ENST00000358026.2:c.3554A>G	p.Gln1185Arg	p.Q1185R	ENST00000358026	NM_001128849.1	1185	cAa/cGa	26/36	0.232008219019086	1	FACETS	0.838	0.756	0.923	1	0.985	1	CLONAL	2	TRUE	0	0.305030716247397	1		223	325	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602762	10602763	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0004488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	144	297	0	ENST00000171111.5:c.815_816del	p.Arg272LeufsTer77	p.R272Lfs*77	ENST00000171111	NM_203500.1	272	cGC/c	3/6	0.232008219019086	1	FACETS	0.879	0.809	0.952	1	0.99	1	CLONAL	2	TRUE	0	0.305030716247397	1		297	455	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966033	25966033	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	400	480	0	ENST00000435504.4:c.3173T>C	p.Leu1058Pro	p.L1058P	ENST00000435504		1058	cTa/cCa	13/13	0.831243923653211	3	FACETS	0.951	0.904	1	0.476	0.452	0.5	CLONAL	1	TRUE	1	0.831243923653211	3		480	1432	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445211	29445211	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	665	438	0	ENST00000389048.3:c.3514A>G	p.Ser1172Gly	p.S1172G	ENST00000389048	NM_004304.4	1172	Agc/Ggc	22/29	0.831243923653211	3	FACETS	0.945	0.915	0.974	0.945	0.915	0.974	CLONAL	2	TRUE	1	0.831243923653211	3		438	1199	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439841	220439841	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	461	580	0	ENST00000243786.2:c.694C>A	p.Arg232Ser	p.R232S	ENST00000243786	NM_002191.3	232	Cgc/Agc	2/2	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.831243923653211	2		580	1081	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448599	89448599	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs776808297	NA	P-0004787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	30	523	0	ENST00000336596.2:c.1563C>A	p.Ser521Arg	p.S521R	ENST00000336596	NM_005233.5	521	agC/agA	7/17	0.790606461364223	1	FACETS	0.071	0.056	0.087	0.071	0.056	0.087	SUBCLONAL	1	TRUE	0	0.831243923653211	1		523	598	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847333	68847333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	371	636	0	ENST00000261769.5:c.1255G>A	p.Asp419Asn	p.D419N	ENST00000261769	NM_004360.3	419	Gat/Aat	9/16	0.831243923653211	2	FACETS	0.707	0.67	0.744	0.353	0.335	0.372	SUBCLONAL	1	TRUE	0	0.831243923653211	2		636	1263	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827523	72827523	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	872	715	0	ENST00000268489.5:c.9058G>T	p.Glu3020Ter	p.E3020*	ENST00000268489	NM_006885.3	3020	Gag/Tag	9/10	0.831243923653211	2	FACETS	0.958	0.94	0.975	0.958	0.94	0.975	CLONAL	2	TRUE	0	0.831243923653211	2		715	1095	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021262	31021262	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0004787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1255	358	407	0	ENST00000375687.4:c.1261A>T	p.Arg421Ter	p.R421*	ENST00000375687	NM_015338.5	421	Aga/Tga	12/13	0.831243923653211	3	FACETS	0.756	0.715	0.798	0.378	0.357	0.399	SUBCLONAL	1	TRUE	1	0.831243923653211	3		407	1613	SUCCESS
AR	367	MSKCC	GRCh37	X	66766427	66766427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	121	176	0	ENST00000374690.3:c.1439C>T	p.Pro480Leu	p.P480L	ENST00000374690	NM_000044.3	480	cCc/cTc	1/8	NA	2	FACETS	1	0.962	1			1	INDETERMINATE	1	TRUE	NA	0.831243923653211	2		176	270	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436931	110436945	+	inframe_deletion	In_Frame_Del	DEL	GCCCGAGGCGGAGGC	GCCCGAGGCGGAGGC	-	novel	NA	P-0004787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	59	87	0	ENST00000375856.3:c.1456_1470del	p.Ala486_Gly490del	p.A486_G490del	ENST00000375856	NM_003749.2	486	GCCTCCGCCTCGGGC/-	1/2	0.831243923653211	3	FACETS	0.943	0.823	1	0.314	0.274	0.357	CLONAL	1	TRUE	0	0.831243923653211	3		87	213	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11292527	11292535	+	inframe_deletion	In_Frame_Del	DEL	ATGTCCATG	ATGTCCATG	-	novel	NA	P-0004787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	268	429	0	ENST00000361445.4:c.2472_2480del	p.Ile824_Asp826del	p.I824_D826del	ENST00000361445	NM_004958.3	824	atCATGGACATg/atg	16/58	0.827024670220806	1	FACETS	0.655	0.62	0.69	0.655	0.62	0.69	SUBCLONAL	1	TRUE	0	0.831243923653211	1		429	575	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033825	49033825	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	723	354	0	ENST00000267163.4:c.1962del	p.Tyr655IlefsTer3	p.Y655Ifs*3	ENST00000267163	NM_000321.2	654	gtG/gt	20/27	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	2	TRUE	NA	0.831243923653211	2		354	863	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166356	7166356	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762498057	NA	P-0004854-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	170	627	0	ENST00000302850.5:c.1670C>T	p.Thr557Met	p.T557M	ENST00000302850	NM_000208.2	557	aCg/aTg	8/22	1	2	FACETS	0.854	0.793	0.916	0.854	0.793	0.916	CLONAL	1	TRUE	1	0.859903828530018	2		627	463	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295211	15295211	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004854-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	28	826	0	ENST00000263388.2:c.2461G>C	p.Gly821Arg	p.G821R	ENST00000263388	NM_000435.2	821	Ggc/Cgc	16/33	1	2	FACETS	0.119	0.095	0.148	0.119	0.095	0.148	SUBCLONAL	1	TRUE	1	0.859903828530018	2		826	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577579	7577579	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0121438-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	216	716	0	ENST00000269305.4:c.702C>A	p.Tyr234Ter	p.Y234*	ENST00000269305	NM_001126112.2	234	taC/taA	7/11	0.527573247824368	2	FACETS	0.904	0.851	0.957	0.904	0.851	0.957	CLONAL	2	NA	0	0.527573247824368	2		716	453	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80150103	80150103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0121438-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	150	712	0	ENST00000265081.6:c.2968G>A	p.Ala990Thr	p.A990T	ENST00000265081	NM_002439.4	990	Gcc/Acc	21/24	1	2	FACETS	0.967	0.888	1	0.967	0.888	1	CLONAL	1	NA	1	0.527573247824368	2		712	588	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0005618-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	57	547	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.698	0.6	0.806	0.698	0.6	0.806	SUBCLONAL	1	TRUE	1	0.326490522912315	2		547	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0005618-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	155	418	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	0.326490522912315	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.326490522912315	1		418	630	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783196	9783196	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005618-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	48	334	0	ENST00000377346.4:c.2440G>T	p.Gly814Cys	p.G814C	ENST00000377346	NM_005026.3	814	Ggc/Tgc	20/24	0.326490522912315	1	FACETS	0.429	0.362	0.503	0.429	0.362	0.503	SUBCLONAL	1	TRUE	0	0.326490522912315	1		334	573	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442009	52442009	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761048859	NA	P-0005618-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	218	380	1	ENST00000460680.1:c.340C>T	p.Arg114Cys	p.R114C	ENST00000460680	NM_004656.3	114	Cgc/Tgc	5/17	0.326490522912315	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.326490522912315	1		381	749	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911254	29911254	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs41541015	NA	P-0005618-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	149	290	0	ENST00000376809.5:c.553G>C	p.Asp185His	p.D185H	ENST00000376809	NM_002116.7	185	Gat/Cat	3/8	0.326490522912315	3	FACETS	0.909	0.834	0.987	0.909	0.834	0.987	CLONAL	2	TRUE	1	0.326490522912315	3		290	584	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117629971	117629971	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005618-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	207	313	0	ENST00000368508.3:c.6555T>G	p.Asn2185Lys	p.N2185K	ENST00000368508	NM_002944.2	2185	aaT/aaG	41/43	0.150393667532818	3	FACETS	0.969	0.902	1			1	INDETERMINATE	2	TRUE	NA	0.326490522912315	3		313	761	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729753	41729753	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005618-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	130	561	0	ENST00000242208.4:c.776A>C	p.Lys259Thr	p.K259T	ENST00000242208	NM_002192.2	259	aAg/aCg	3/3	1	2	FACETS	0.681	0.616	0.75	0.681	0.616	0.75	SUBCLONAL	1	TRUE	1	0.326490522912315	2		561	1169	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984909	101984909	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005618-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	71	290	0	ENST00000282441.5:c.356C>G	p.Thr119Ser	p.T119S	ENST00000282441	NM_001130145.2	119	aCt/aGt	2/9	1	2	FACETS	0.683	0.596	0.777	0.683	0.596	0.777	SUBCLONAL	1	TRUE	1	0.326490522912315	2		290	637	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432236	49432236	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750788651	NA	P-0005618-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	235	578	2	ENST00000301067.7:c.8903C>T	p.Pro2968Leu	p.P2968L	ENST00000301067	NM_003482.3	2968	cCg/cTg	34/54	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.326490522912315	2		580	969	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910400	29910437	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCGGGTGAGTGCGGGGTCGGGAGGGAAACCGCCTCTGC	GCGGGTGAGTGCGGGGTCGGGAGGGAAACCGCCTCTGC	-	novel	NA	P-0005618-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	100	337	0	ENST00000376809.5:c.71_73+35del		p.X24_splice	ENST00000376809	NM_002116.7	24		1/8	0.326490522912315	3	FACETS	0.718	0.64	0.802	0.359	0.32	0.401	SUBCLONAL	1	TRUE	1	0.326490522912315	3		337	992	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102134	27102143	+	frameshift_variant	Frame_Shift_Del	DEL	CATTAGATAC	CATTAGATAC	-	novel	NA	P-0005618-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	210	438	0	ENST00000324856.7:c.5063_5072del	p.Leu1688SerfsTer12	p.L1688Sfs*12	ENST00000324856	NM_006015.4	1687	gCATTAGATACc/gc	19/20	0.28021390973166	1	FACETS	0.753	0.702	0.805	1	0.992	1	SUBCLONAL	2	TRUE	0	0.326490522912315	1		438	715	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0005730-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	171	430	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	0.394337521363777	2		430	650	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0005730-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	31	234	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.308428913110392	2	FACETS	1	0.9	1	0.574	0.471	0.686	CLONAL	1	TRUE	0	0.394337521363777	2		234	137	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467835	50467835	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs751623054	NA	P-0005730-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	30	193	0	ENST00000331340.3:c.1070G>T	p.Gly357Val	p.G357V	ENST00000331340	NM_006060.4	357	gGc/gTc	8/8	0.124937861970655	3	FACETS	0.753	0.61	0.913	0.251	0.203	0.305	INDETERMINATE	1	TRUE	0	0.394337521363777	3		193	242	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857656	9857656	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754286517	NA	P-0005730-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	17	226	0	ENST00000330684.3:c.3745G>A	p.Asp1249Asn	p.D1249N	ENST00000330684	NM_001134407.1	1249	Gat/Aat	13/13	0.0706070072694653	3	FACETS	0.776	0.585	0.999	0.388	0.292	0.5	INDETERMINATE	1	TRUE	1	0.394337521363777	3		226	133	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0005813-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	391	472	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.4848516321812	5	FACETS	1	0.992	1	0.794	0.756	0.832	CLONAL	2	TRUE	2	0.585786722742288	5		472	1053	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0005813-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	382	607	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.4848516321812	5	FACETS	0.92	0.874	0.968	0.614	0.582	0.646	CLONAL	2	TRUE	2	0.585786722742288	5		607	1331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0005813-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	506	773	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.585786722742288	2	FACETS	0.984	0.95	1	0.984	0.95	1	CLONAL	2	TRUE	0	0.585786722742288	2		773	878	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039377	49039378	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCCTTACAAGTTTCCTAGTTC	novel	NA	P-0005813-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	423	739	1	ENST00000267163.4:c.2363_2384dup	p.Arg798GlnfsTer4	p.R798Qfs*4	ENST00000267163	NM_000321.2	788	agc/aGCCCTTACAAGTTTCCTAGTTCgc	23/27	0.585786722742288	2	FACETS	1	0.995	1	0.67	0.64	0.701	CLONAL	1	TRUE	0	0.585786722742288	2		740	1077	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	128	855	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	0.469945988515127	2		855	543	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271835	15271835	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748776589	NA	P-0006009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	64	925	1	ENST00000263388.2:c.6604G>A	p.Val2202Ile	p.V2202I	ENST00000263388	NM_000435.2	2202	Gtc/Atc	33/33	1	2	FACETS	0.523	0.453	0.598	0.523	0.453	0.598	SUBCLONAL	1	TRUE	1	0.469945988515127	2		926	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0006197-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	279	844	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.587831872045782	1	FACETS	0.99	0.936	1	0.99	0.936	1	CLONAL	1	TRUE	0	0.587831872045782	1		844	677	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441465	52441477	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	ATATCCTTTGCTC	ATATCCTTTGCTC	T	novel	NA	P-0006197-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	163	497	0	ENST00000460680.1:c.376-1_387delinsA		p.X126_splice	ENST00000460680	NM_004656.3	126		6/17	0.587831872045782	1	FACETS	0.853	0.79	0.917	0.853	0.79	0.917	CLONAL	1	TRUE	0	0.587831872045782	1		497	459	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165346	47165347	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0006197-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	172	397	0	ENST00000409792.3:c.779dup	p.Asn261Ter	p.N261*	ENST00000409792	NM_014159.6	260	tct/tcCt	3/21	0.587831872045782	1	FACETS	0.877	0.815	0.941	0.877	0.815	0.941	CLONAL	1	TRUE	0	0.587831872045782	1		397	471	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035172	30035258	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGATCACACAACATTTATTCTTCTTACAGGTACATCAGTCAAGGCTACCCCCCAGTTCTGAGAGAACTTGCCCAGGAGTGGTTGCA	GAGATCACACAACATTTATTCTTCTTACAGGTACATCAGTCAAGGCTACCCCCCAGTTCTGAGAGAACTTGCCCAGGAGTGGTTGCA	-	novel	NA	P-0006197-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	114	595	0	ENST00000338641.4:c.337_363+60del		p.X113_splice	ENST00000338641	NM_000268.3	113		3/16	0.587831872045782	1	FACETS	0.624	0.565	0.685	0.624	0.565	0.685	SUBCLONAL	1	TRUE	0	0.587831872045782	1		595	439	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0006677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	201	802	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.274596693660738	1	FACETS	0.796	0.74	0.855	1	0.992	1	SUBCLONAL	2	TRUE	0	0.274596693660738	1		802	793	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162267	47162267	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	68	425	0	ENST00000409792.3:c.3859C>T	p.Gln1287Ter	p.Q1287*	ENST00000409792	NM_014159.6	1287	Cag/Tag	3/21	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.274596693660738	2		425	438	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165518	118165519	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0006677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	42	395	1	ENST00000369448.3:c.28_29delinsTT	p.Asp10Phe	p.D10F	ENST00000369448	NM_017709.3	10	GAt/TTt	2/2	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.274596693660738	2		396	281	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606638	29606638	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	76	786	0	ENST00000389048.3:c.1242G>T	p.Leu414Phe	p.L414F	ENST00000389048	NM_004304.4	414	ttG/ttT	5/29	1	2	FACETS	0.983	0.864	1	0.983	0.864	1	CLONAL	1	TRUE	1	0.274596693660738	2		786	563	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757417	40757417	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	71	835	0	ENST00000373198.4:c.2881T>A	p.Tyr961Asn	p.Y961N	ENST00000373198	NM_133170.3	961	Tac/Aac	20/32	0.274596693660738	1	FACETS	0.937	0.82	1	0.937	0.82	1	CLONAL	1	TRUE	0	0.274596693660738	1		835	476	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265554	152265554	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	51	680	0	ENST00000206249.3:c.1007C>A	p.Pro336His	p.P336H	ENST00000206249	NM_000125.3	336	cCc/cAc	4/8	0.159752964929568	1	FACETS	0.67	0.57	0.78	0.67	0.57	0.78	INDETERMINATE	1	TRUE	0	0.274596693660738	1		680	478	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040801	47040801	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0006677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	79	795	1	ENST00000377604.3:c.1435+1G>T		p.X479_splice	ENST00000377604	NM_001204468.1	479			1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.274596693660738	2		796	532	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247085	53247085	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	40	737	0	ENST00000375401.3:c.415C>T	p.Gln139Ter	p.Q139*	ENST00000375401	NM_004187.3	139	Cag/Tag	4/26	1	2	FACETS	0.624	0.518	0.741	0.624	0.518	0.741	SUBCLONAL	1	TRUE	1	0.274596693660738	2		737	467	SUCCESS
AR	367	MSKCC	GRCh37	X	66765297	66765297	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	76	868	0	ENST00000374690.3:c.312del	p.Thr105GlnfsTer70	p.T105Qfs*70	ENST00000374690	NM_000044.3	103	ggC/gg	1/8	1	2	FACETS	0.966	0.848	1	0.966	0.848	1	CLONAL	1	TRUE	1	0.274596693660738	2		868	573	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0007371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	481	426	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.620488367867469	3	FACETS	0.873	0.844	0.902	1	0.996	1	CLONAL	3	TRUE	1	0.633772168628751	3		426	763	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947827	178947827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	277	493	0	ENST00000263967.3:c.2702G>T	p.Cys901Phe	p.C901F	ENST00000263967	NM_006218.2	901	tGt/tTt	19/21	0.618081579305639	3	FACETS	0.845	0.799	0.892	0.845	0.799	0.892	CLONAL	2	TRUE	1	0.633772168628751	3		493	681	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692792	89692792	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs779530981	NA	P-0007371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	146	286	0	ENST00000371953.3:c.276C>A	p.Asp92Glu	p.D92E	ENST00000371953	NM_000314.4	92	gaC/gaA	5/9	0.60610477049239	5	FACETS	0.822	0.754	0.892	0.548	0.502	0.595	CLONAL	2	TRUE	2	0.633772168628751	5		286	547	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370985	55370985	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	219	384	1	ENST00000297316.4:c.287C>G	p.Ala96Gly	p.A96G	ENST00000297316	NM_022454.3	96	gCc/gGc	1/2	0.618081579305639	3	FACETS	0.983	0.926	1	0.983	0.926	1	CLONAL	2	TRUE	1	0.633772168628751	3		385	463	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720761	89720761	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	12	62	0	ENST00000371953.3:c.912del	p.Cys304Ter	p.C304*	ENST00000371953	NM_000314.4	304	tgC/tg	8/9	0.60610477049239	5	FACETS	0.717	0.509	0.968	0.239	0.169	0.323	CLONAL	1	TRUE	2	0.633772168628751	5		62	103	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058052	27058052	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	47	133	0	ENST00000324856.7:c.1762del	p.Gln588SerfsTer31	p.Q588Sfs*31	ENST00000324856	NM_006015.4	587	tCc/tc	3/20	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.633772168628751	2		133	145	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779601	3779605	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCC	CAGCC	-	novel	NA	P-0007371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	295	404	0	ENST00000262367.5:c.5443_5447del	p.Gly1815ProfsTer149	p.G1815Pfs*149	ENST00000262367	NM_004380.2	1815	GGCTGc/c	31/31	0.633396980825036	5	FACETS	1	0.99	1	0.597	0.564	0.629	CLONAL	2	TRUE	1	0.633772168628751	5		404	761	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012928	176012928	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007375-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	227	528	0	ENST00000367669.3:c.1448A>G	p.Lys483Arg	p.K483R	ENST00000367669	NM_022457.5	483	aAg/aGg	13/20	0.381895916182053	2	FACETS	0.859	0.804	0.915	0.859	0.804	0.915	CLONAL	2	TRUE	0	0.385254695565976	2		528	686	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2105462	2105462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007375-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	153	451	0	ENST00000219476.3:c.541G>A	p.Val181Met	p.V181M	ENST00000219476	NM_000548.3	181	Gtg/Atg	6/42	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.385254695565976	2		451	763	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675423	241675427	+	frameshift_variant	Frame_Shift_Del	DEL	ATTTA	ATTTA	-	rs863223995	NA	P-0007375-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	193	458	0	ENST00000366560.3:c.395_399del	p.Leu132Ter	p.L132*	ENST00000366560	NM_000143.3	132	tTAAAT/t	4/10	0.381895916182053	2	FACETS	0.899	0.838	0.962	0.899	0.838	0.962	CLONAL	2	TRUE	0	0.385254695565976	2		458	557	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566494	41566495	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTAT	novel	NA	P-0007375-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	109	438	0	ENST00000263253.7:c.4372_4373insTATC	p.Pro1458LeufsTer16	p.P1458Lfs*16	ENST00000263253	NM_001429.3	1457	-/CTAT	27/31	0.293457563635268	1	FACETS	0.686	0.617	0.759	0.686	0.617	0.759	SUBCLONAL	1	TRUE	0	0.385254695565976	1		438	666	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929155	32929155	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007633-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	59	649	0	ENST00000380152.3:c.7165A>G	p.Arg2389Gly	p.R2389G	ENST00000380152		2389	Aga/Gga	14/27	1	2	FACETS	0.29	0.248	0.335	0.29	0.248	0.335	SUBCLONAL	1	TRUE	1	0.36	2		649	1132	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098925	47098926	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0007633-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	109	384	0	ENST00000409792.3:c.6348_6349insA	p.Ser2117IlefsTer10	p.S2117Ifs*10	ENST00000409792	NM_014159.6	2116	-/A	15/21	1	2	FACETS	0.759	0.681	0.841	0.759	0.681	0.841	SUBCLONAL	1	TRUE	1	0.36	2		384	798	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163371	47163373	+	frameshift_variant	Frame_Shift_Del	DEL	CTG	CTG	A	novel	NA	P-0007633-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	41	339	0	ENST00000409792.3:c.2753_2755delinsT	p.Ser918LeufsTer16	p.S918Lfs*16	ENST00000409792	NM_014159.6	918	tCAGag/tTag	3/21	NA	2	FACETS	0.29	0.24	0.345			1	INDETERMINATE	1	TRUE	NA	0.36	2		339	786	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0008481-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	48	174	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.210443985475929	2	FACETS	1	0.96	1	0.723	0.614	0.841	CLONAL	1	TRUE	0	0.216351703922753	2		174	307	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271495	26271495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008481-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	41	387	0	ENST00000305910.3:c.118C>T	p.His40Tyr	p.H40Y	ENST00000305910	NM_003534.2	40	Cat/Tat	1/1	0.216351703922753	5	FACETS	0.872	0.725	1	0.291	0.241	0.345	CLONAL	1	TRUE	2	0.216351703922753	5		387	576	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842693	68842693	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008481-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	126	636	0	ENST00000261769.5:c.631del	p.Thr211GlnfsTer4	p.T211Qfs*4	ENST00000261769	NM_004360.3	210	gAa/ga	5/16	0.216351703922753	2	FACETS	0.791	0.717	0.869	0.791	0.717	0.869	SUBCLONAL	2	TRUE	0	0.216351703922753	2		636	736	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45873407	45873407	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008481-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	90	537	2	ENST00000391945.4:c.89G>A	p.Arg30His	p.R30H	ENST00000391945	NM_000400.3	30	cGc/cAc	2/23	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.216351703922753	2		539	598	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456741	32456741	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008481-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	41	356	0	ENST00000332351.3:c.151G>T	p.Glu51Ter	p.E51*	ENST00000332351	NM_024426.4	51	Gaa/Taa	1/10	0.216351703922753	4	FACETS	0.904	0.753	1	0.452	0.376	0.536	CLONAL	1	TRUE	2	0.216351703922753	4		356	510	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577083	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0008481-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	19	751	1	ENST00000269305.4:c.855_856delinsAA	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	285	gaGGaa/gaAAaa	8/11	0.210443985475929	2	FACETS	0.218	0.164	0.282	0.109	0.082	0.141	SUBCLONAL	1	TRUE	0	0.216351703922753	2		752	805	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213485	36213485	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008481-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	99	810	0	ENST00000222270.7:c.2587G>A	p.Val863Met	p.V863M	ENST00000222270	NM_014727.1	863	Gtg/Atg	5/37	1	2	FACETS	0.992	0.884	1	0.992	0.884	1	CLONAL	1	TRUE	1	0.216351703922753	2		810	923	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561735	55561735	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs746856550	NA	P-0008481-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	54	379	0	ENST00000288135.5:c.125G>C	p.Gly42Ala	p.G42A	ENST00000288135	NM_000222.2	42	gGa/gCa	2/21	0.216351703922753	2	FACETS	1	0.947	1	0.619	0.53	0.716	CLONAL	1	TRUE	0	0.216351703922753	2		379	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0009403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	283	873	3	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.39395590936966	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.4187466214879	2		876	644	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0009403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	416	570	1	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	0.385452516535071	3	FACETS	0.995	0.955	1	0.995	0.955	1	CLONAL	3	TRUE	0	0.4187466214879	3		571	805	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105895	27105895	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	238	358	0	ENST00000324856.7:c.5506G>T	p.Glu1836Ter	p.E1836*	ENST00000324856	NM_006015.4	1836	Gag/Tag	20/20	0.419258797807369	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.4187466214879	3		358	599	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851342	156851342	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	207	495	0	ENST00000524377.1:c.2299G>T	p.Glu767Ter	p.E767*	ENST00000524377	NM_002529.3	767	Gag/Tag	17/17	0.4187466214879	6	FACETS	0.959	0.891	1	0.48	0.445	0.515	CLONAL	2	TRUE	2	0.4187466214879	6		495	947	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487547	56487547	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0009403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	229	372	0	ENST00000267101.3:c.1481-1G>T		p.X494_splice	ENST00000267101	NM_001982.3	494			0.385452516535071	3	FACETS	0.952	0.899	1	0.952	0.899	1	CLONAL	3	TRUE	0	0.4187466214879	3		372	463	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117764	115117764	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	40	407	0	ENST00000257566.3:c.671C>G	p.Pro224Arg	p.P224R	ENST00000257566	NM_016569.3	224	cCa/cGa	3/8	0.4187466214879	2	FACETS	0.401	0.333	0.477	0.201	0.166	0.239	SUBCLONAL	1	TRUE	0	0.4187466214879	2		407	476	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953453	32953453	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0009403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	143	332	0	ENST00000380152.3:c.8755-1G>T		p.X2919_splice	ENST00000380152		2919			0.39395590936966	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	0	0.4187466214879	2		332	335	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40483518	40483518	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	361	473	0	ENST00000264657.5:c.1081C>A	p.Gln361Lys	p.Q361K	ENST00000264657	NM_139276.2	361	Cag/Aag	11/24	0.419258797807369	4	FACETS	0.942	0.897	0.987	0.942	0.897	0.987	CLONAL	3	TRUE	1	0.4187466214879	4		473	866	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804217	46804217	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	141	535	0	ENST00000290295.7:c.790T>A	p.Phe264Ile	p.F264I	ENST00000290295	NM_006361.5	264	Ttt/Att	2/2	0.419258797807369	4	FACETS	1	0.94	1	0.347	0.316	0.38	CLONAL	1	TRUE	1	0.4187466214879	4		535	918	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209108239	209108239	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	251	629	0	ENST00000345146.2:c.610G>C	p.Gly204Arg	p.G204R	ENST00000345146	NM_005896.2	204	Ggt/Cgt	6/10	0.342901479596316	4	FACETS	0.99	0.928	1	0.99	0.928	1	CLONAL	2	TRUE	2	0.4187466214879	4		629	859	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031173	36031173	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	223	517	0	ENST00000358208.4:c.1292G>T	p.Trp431Leu	p.W431L	ENST00000358208		431	tGg/tTg	11/12	0.39395590936966	2	FACETS	0.953	0.894	1	0.953	0.894	1	CLONAL	2	TRUE	0	0.4187466214879	2		517	559	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144835	47144835	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0009403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	382	618	0	ENST00000409792.3:c.4917+1G>C		p.X1639_splice	ENST00000409792	NM_014159.6	1639			0.316922055137904	3	FACETS	0.964	0.922	1			1	CLONAL	3	TRUE	NA	0.4187466214879	3		618	763	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526433	31526433	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	160	817	0	ENST00000344624.3:c.607C>G	p.His203Asp	p.H203D	ENST00000344624		203	Cat/Gat	2/33	0.261531047085854	4	FACETS	0.913	0.835	0.994	0.456	0.417	0.497	CLONAL	1	TRUE	2	0.4187466214879	4		817	1188	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526614	31526614	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1209326010	NA	P-0009403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	76	427	0	ENST00000344624.3:c.426C>G	p.Phe142Leu	p.F142L	ENST00000344624		142	ttC/ttG	2/33	0.261531047085854	4	FACETS	0.846	0.742	0.957	0.423	0.371	0.479	CLONAL	1	TRUE	2	0.4187466214879	4		427	609	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509092	106509092	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	228	418	0	ENST00000359195.3:c.1086G>C	p.Arg362Ser	p.R362S	ENST00000359195	NM_002649.2	362	agG/agC	2/11	0.38794645540195	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.4187466214879	3		418	636	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339158	87339158	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	212	406	0	ENST00000277120.3:c.740A>T	p.Gln247Leu	p.Q247L	ENST00000277120		247	cAg/cTg	8/19	0.419258797807369	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.4187466214879	3		406	569	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732822	44732822	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	63	304	0	ENST00000377967.4:c.25G>C	p.Ala9Pro	p.A9P	ENST00000377967	NM_021140.2	9	Gct/Cct	1/29	0.419258797807369	3	FACETS	0.731	0.633	0.836	0.365	0.316	0.418	SUBCLONAL	1	TRUE	1	0.4187466214879	3		304	498	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360624	70360629	+	inframe_deletion	In_Frame_Del	DEL	CAGCAG	CAGCAG	-	rs754533796	NA	P-0009403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	36	297	0	ENST00000374080.3:c.6195_6200del	p.Gln2075_Gln2076del	p.Q2075_Q2076del	ENST00000374080		2062	CAGCAG/-	42/45	0.419258797807369	5	FACETS	0.477	0.391	0.573	0.159	0.13	0.191	SUBCLONAL	1	TRUE	2	0.4187466214879	5		297	587	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912297	29912329	+	inframe_deletion	In_Frame_Del	DEL	ATCCCCATCGTGGGCATCATTGCTGGCCTGGTT	ATCCCCATCGTGGGCATCATTGCTGGCCTGGTT	-	novel	NA	P-0009403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	139	676	0	ENST00000376809.5:c.916_948del	p.Ile306_Val316del	p.I306_V316del	ENST00000376809	NM_002116.7	306	ATCCCCATCGTGGGCATCATTGCTGGCCTGGTT/-	5/8	0.419258797807369	1	FACETS	0.926	0.847	1	0.926	0.847	1	CLONAL	1	TRUE	0	0.4187466214879	1		676	567	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221313	1221314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs121913321	NA	P-0010403-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	31	607	0	ENST00000326873.7:c.842dup	p.Leu282AlafsTer3	p.L282Afs*3	ENST00000326873	NM_000455.4	279	ggc/ggCc	6/10	1	2	FACETS	0.716	0.578	0.873	0.716	0.578	0.873	SUBCLONAL	1	TRUE	1	0.16	2		607	541	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435300	110435302	+	inframe_deletion	In_Frame_Del	DEL	GGT	GGT	-	rs765493638	NA	P-0010403-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	10	172	1	ENST00000375856.3:c.3099_3101del	p.Pro1036del	p.P1036del	ENST00000375856	NM_003749.2	1033	ccACCg/ccg	1/2	1	2	FACETS	0.744	0.505	1	0.744	0.505	1	CLONAL	1	TRUE	1	0.16	2		173	168	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715678	30715678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039551	NA	P-0010403-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	28	354	0	ENST00000295754.5:c.1336G>A	p.Asp446Asn	p.D446N	ENST00000295754	NM_003242.5	446	Gat/Aat	5/7	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.16	2		354	308	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100999	41100999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1371429276	NA	P-0010403-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	36	568	0	ENST00000373198.4:c.1357C>T	p.Arg453Cys	p.R453C	ENST00000373198	NM_133170.3	453	Cgc/Tgc	8/32	1	2	FACETS	0.846	0.694	1	0.846	0.694	1	CLONAL	1	TRUE	1	0.16	2		568	532	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602374	10602374	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010403-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	62	816	1	ENST00000171111.5:c.1204C>T	p.Gln402Ter	p.Q402*	ENST00000171111	NM_203500.1	402	Cag/Tag	3/6	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.16	2		817	751	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37876056	37876056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010403-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	39	702	0	ENST00000269571.5:c.1915G>A	p.Asp639Asn	p.D639N	ENST00000269571		639	Gac/Aac	16/27	1	2	FACETS	0.808	0.669	0.965	0.808	0.669	0.965	CLONAL	1	TRUE	1	0.16	2		702	603	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2193709	2193709	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010403-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	47	775	0	ENST00000398665.3:c.515A>T	p.Gln172Leu	p.Q172L	ENST00000398665	NM_032482.2	172	cAg/cTg	6/28	1	2	FACETS	0.958	0.808	1	0.958	0.808	1	CLONAL	1	TRUE	1	0.16	2		775	613	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660967	227660967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010403-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	40	525	0	ENST00000305123.5:c.2488C>T	p.Pro830Ser	p.P830S	ENST00000305123	NM_005544.2	830	Cca/Tca	1/2	1	2	FACETS	0.952	0.791	1	0.952	0.791	1	CLONAL	1	TRUE	1	0.16	2		525	525	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662127	227662127	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs745943416	NA	P-0010403-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	33	543	0	ENST00000305123.5:c.1328G>T	p.Arg443Leu	p.R443L	ENST00000305123	NM_005544.2	443	cGc/cTc	1/2	1	2	FACETS	0.786	0.639	0.952	0.786	0.639	0.952	CLONAL	1	TRUE	1	0.16	2		543	525	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662281	227662281	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1438378264	NA	P-0010403-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	35	599	0	ENST00000305123.5:c.1174C>G	p.Leu392Val	p.L392V	ENST00000305123	NM_005544.2	392	Ctg/Gtg	1/2	1	2	FACETS	0.772	0.631	0.93	0.772	0.631	0.93	CLONAL	1	TRUE	1	0.16	2		599	567	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149245626	149245626	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010403-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	34	671	0	ENST00000360632.3:c.902A>G	p.Asn301Ser	p.N301S	ENST00000360632	NM_015472.4	301	aAt/aGt	5/7	1	2	FACETS	0.678	0.552	0.82	0.678	0.552	0.82	SUBCLONAL	1	TRUE	1	0.16	2		671	627	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860756	151860756	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010403-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	34	495	0	ENST00000262189.6:c.9906del	p.Thr3303ProfsTer58	p.T3303Pfs*58	ENST00000262189	NM_170606.2	3302	ccC/cc	43/59	1	2	FACETS	0.93	0.76	1	0.93	0.76	1	CLONAL	1	TRUE	1	0.16	2		495	457	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110251321	110251321	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010403-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	31	418	0	ENST00000374672.4:c.16G>T	p.Gly6Cys	p.G6C	ENST00000374672	NM_004235.4	6	Ggc/Tgc	2/5	1	2	FACETS	0.925	0.748	1	0.925	0.748	1	CLONAL	1	TRUE	1	0.16	2		418	419	SUCCESS
FH	2271	MSKCC	GRCh37	1	241669329	241669329	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1553341157	NA	P-0010963-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	204	394	0	ENST00000366560.3:c.878T>A	p.Val293Asp	p.V293D	ENST00000366560	NM_000143.3	293	gTt/gAt	6/10	0.424754447021021	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.424754447021021	2		394	451	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28929495	NA	P-0011107-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	175	721	0	ENST00000275493.2:c.2155G>A	p.Gly719Ser	p.G719S	ENST00000275493	NM_005228.3	719	Ggc/Agc	18/28	1	2	FACETS	0.982	0.909	1	0.982	0.909	1	CLONAL	1	TRUE	1	0.595759072356845	2		721	598	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0011107-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	167	645	0	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.595759072356845	2		645	555	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259442	55259442	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397517127	NA	P-0011107-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	132	527	0	ENST00000275493.2:c.2500G>T	p.Val834Leu	p.V834L	ENST00000275493	NM_005228.3	834	Gtg/Ttg	21/28	1	2	FACETS	0.901	0.823	0.982	0.901	0.823	0.982	CLONAL	1	TRUE	1	0.595759072356845	2		527	492	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625282	69625282	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1262110871	NA	P-0011107-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	336	857	0	ENST00000334134.2:c.511C>T	p.Arg171Cys	p.R171C	ENST00000334134	NM_005247.2	171	Cgc/Tgc	3/3	0.595759072356845	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.595759072356845	3		857	713	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42002948	42002948	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011107-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	237	657	0	ENST00000219905.7:c.2485G>T	p.Glu829Ter	p.E829*	ENST00000219905	NM_001164273.1	829	Gaa/Taa	8/24	0.595759072356845	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.595759072356845	1		657	475	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890102	76890102	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011107-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	205	648	0	ENST00000373344.5:c.4792C>A	p.Leu1598Ile	p.L1598I	ENST00000373344	NM_000489.3	1598	Ctt/Att	17/35	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.595759072356845	2		648	659	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939099	76939099	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs782422536	NA	P-0011107-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	184	611	0	ENST00000373344.5:c.1649G>T	p.Ser550Ile	p.S550I	ENST00000373344	NM_000489.3	550	aGt/aTt	9/35	1	2	FACETS	0.891	0.826	0.959	0.891	0.826	0.959	CLONAL	1	TRUE	1	0.595759072356845	2		611	693	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858018	45858019	+	missense_variant	Missense_Mutation	DNP	CA	CA	AT	novel	NA	P-0011107-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	144	800	1	ENST00000391945.4:c.1634_1635delinsAT	p.Met545Asn	p.M545N	ENST00000391945	NM_000400.3	545	aTG/aAT	17/23	1	2	FACETS	0.955	0.877	1	0.955	0.877	1	CLONAL	1	TRUE	1	0.595759072356845	2		801	506	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713759	30713759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011107-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	150	575	1	ENST00000295754.5:c.1084C>T	p.His362Tyr	p.H362Y	ENST00000295754	NM_003242.5	362	Cac/Tac	4/7	0.595759072356845	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.595759072356845	1		576	341	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020504	69020504	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011107-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	421	748	2	ENST00000288368.4:c.2876G>A	p.Gly959Asp	p.G959D	ENST00000288368	NM_024870.2	959	gGt/gAt	24/40	0.595759072356845	3	FACETS	0.961	0.92	1	0.961	0.92	1	CLONAL	2	TRUE	1	0.595759072356845	3		750	954	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77064606	77064607	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0011256-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	86	798	0	ENST00000356341.3:c.810_811del	p.Arg272ValfsTer2	p.R272Vfs*2	ENST00000356341	NM_002576.4	270	taTAca/taca	8/15	1	2	FACETS	0.218	0.193	0.246	0.218	0.193	0.246	SUBCLONAL	1	TRUE	1	0.93999692814314	2		798	838	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907695	111907695	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011392-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	504	596	0	ENST00000393256.3:c.469G>A	p.Asp157Asn	p.D157N	ENST00000393256	NM_006538.4	157	Gac/Aac	3/4	1	2	FACETS	0.932	0.893	0.972	0.932	0.893	0.972	CLONAL	1	TRUE	1	0.791020454639453	2		596	1367	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795860	42795860	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011392-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	463	610	0	ENST00000575354.2:c.2849C>T	p.Ser950Leu	p.S950L	ENST00000575354	NM_015125.3	950	tCa/tTa	11/20	1	2	FACETS	0.966	0.924	1	0.966	0.924	1	CLONAL	1	TRUE	1	0.791020454639453	2		610	1212	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059225	27059234	+	frameshift_variant	Frame_Shift_Del	DEL	GTAAGGGAGG	GTAAGGGAGG	-	novel	NA	P-0011392-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	349	583	0	ENST00000324856.7:c.1863_1872del	p.Gly623LysfsTer3	p.G623Kfs*3	ENST00000324856	NM_006015.4	621	aGTAAGGGAGGg/ag	4/20	1	2	FACETS	0.68	0.643	0.717	0.68	0.643	0.717	SUBCLONAL	1	TRUE	1	0.791020454639453	2		583	1298	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325019	123325039	+	inframe_deletion	In_Frame_Del	DEL	GCCGGAGTCTCTAGGCGTGGC	GCCGGAGTCTCTAGGCGTGGC	-	novel	NA	P-0011392-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	482	566	0	ENST00000358487.5:c.289_309del	p.Ala97_Gly103del	p.A97_G103del	ENST00000358487	NM_000141.4	97	GCCACGCCTAGAGACTCCGGC/-	3/18	0.791020454639453	1	FACETS	0.971	0.938	1	0.971	0.938	1	CLONAL	1	TRUE	0	0.791020454639453	1		566	759	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0013820-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	27	482	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	1	2	FACETS	0.912	0.726	1	0.912	0.726	1	CLONAL	1	TRUE	1	0.154174148419856	2		482	384	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352639	68352639	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013820-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	34	470	0	ENST00000487270.1:c.506A>G	p.Lys169Arg	p.K169R	ENST00000487270	NM_133509.3	169	aAg/aGg	6/11	1	2	FACETS	0.847	0.691	1	0.847	0.691	1	CLONAL	1	TRUE	1	0.154174148419856	2		470	521	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119595300	119595300	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013820-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	36	428	0	ENST00000316626.5:c.869A>C	p.Glu290Ala	p.E290A	ENST00000316626		290	gAa/gCa	8/12	0.154174148419856	3	FACETS	1	0.826	1	0.503	0.413	0.604	CLONAL	1	TRUE	1	0.154174148419856	3		428	500	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013926-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	66	571	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.660561788860083	2		571	171	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795353	39795353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs187337793	NA	P-0013926-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	118	878	0	ENST00000288319.7:c.367C>T	p.Arg123Cys	p.R123C	ENST00000288319	NM_182918.3	123	Cgc/Tgc	3/10	1	2	FACETS	0.76	0.69	0.833	0.76	0.69	0.833	SUBCLONAL	1	TRUE	1	0.660561788860083	2		878	470	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692979	89692979	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123325	NA	P-0013926-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	117	664	0	ENST00000371953.3:c.463T>C	p.Tyr155His	p.Y155H	ENST00000371953	NM_000314.4	155	Tat/Cat	5/9	0.660561788860083	1	FACETS	0.721	0.658	0.785	0.721	0.658	0.785	SUBCLONAL	1	TRUE	0	0.660561788860083	1		664	329	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279667	18279667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013926-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	137	774	1	ENST00000222254.8:c.1940G>A	p.Arg647His	p.R647H	ENST00000222254	NM_005027.3	647	cGc/cAc	15/16	0.585835444098862	3	FACETS	0.973	0.889	1	0.487	0.444	0.531	CLONAL	1	TRUE	1	0.660561788860083	3		775	567	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47672748	47672748	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013926-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	43	837	0	ENST00000233146.2:c.1338C>A	p.Asp446Glu	p.D446E	ENST00000233146	NM_000251.2	446	gaC/gaA	8/16	1	2	FACETS	0.181	0.151	0.215	0.181	0.151	0.215	SUBCLONAL	1	TRUE	1	0.660561788860083	2		837	720	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111493	56111512	+	frameshift_variant	Frame_Shift_Del	DEL	CAAGGCGAGCAGCGCGCCCG	CAAGGCGAGCAGCGCGCCCG	-	novel	NA	P-0013926-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	10	143	0	ENST00000399503.3:c.94_113del	p.Lys32GlyfsTer37	p.K32Gfs*37	ENST00000399503	NM_005921.1	31	ctCAAGGCGAGCAGCGCGCCCGcg/ctcg	1/20	1	2	FACETS	0.481	0.332	0.66	0.481	0.332	0.66	SUBCLONAL	1	TRUE	1	0.660561788860083	2		143	63	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	261	790	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.367039288607444	3	FACETS	0.861	0.808	0.916	0.861	0.808	0.916	CLONAL	2	FALSE	1	0.367039288607444	3		790	977	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	69	588	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.805	0.703	0.915	0.805	0.703	0.915	CLONAL	1	FALSE	1	0.367039288607444	2		588	467	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602757	10602757	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	173	786	0	ENST00000171111.5:c.821A>T	p.His274Leu	p.H274L	ENST00000171111	NM_203500.1	274	cAc/cTc	3/6	1	2	FACETS	0.893	0.821	0.968	0.893	0.821	0.968	CLONAL	1	FALSE	1	0.367039288607444	2		786	1056	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230538	46230538	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	72	460	1	ENST00000334344.6:c.787G>T	p.Glu263Ter	p.E263*	ENST00000334344	NM_152641.2	263	Gaa/Taa	8/21	0.367039288607444	3	FACETS	0.675	0.589	0.767	0.337	0.294	0.384	SUBCLONAL	1	FALSE	1	0.367039288607444	3		461	688	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670811	134670811	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	98	442	0	ENST00000398015.3:c.722A>G	p.Asn241Ser	p.N241S	ENST00000398015	NM_004441.4	241	aAc/aGc	3/16	1	2	FACETS	0.996	0.892	1	0.996	0.892	1	CLONAL	1	FALSE	1	0.367039288607444	2		442	536	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133813	55133813	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	110	501	0	ENST00000257290.5:c.1028del	p.Pro343HisfsTer8	p.P343Hfs*8	ENST00000257290	NM_006206.4	342	taC/ta	7/23	1	2	FACETS	0.871	0.784	0.964	0.871	0.784	0.964	CLONAL	1	FALSE	1	0.367039288607444	2		501	688	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388023	81388023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	78	623	1	ENST00000222390.5:c.352C>T	p.Leu118Phe	p.L118F	ENST00000222390	NM_000601.4	118	Ctc/Ttc	3/18	1	2	FACETS	0.737	0.648	0.832	0.737	0.648	0.832	SUBCLONAL	1	FALSE	1	0.367039288607444	2		624	577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577508	7577508	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1060501201	NA	P-0014497-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	755	617	0	ENST00000269305.4:c.773A>C	p.Glu258Ala	p.E258A	ENST00000269305	NM_001126112.2	258	gAa/gCa	7/11	0.634337727779336	3	FACETS	0.963	0.94	0.986	0.963	0.94	0.986	CLONAL	3	TRUE	0	0.640663195339466	3		617	1077	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0014497-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	415	529	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	0.348691302220476	6	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.640663195339466	6		529	1323	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686283	117686283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014497-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	194	434	0	ENST00000368508.3:c.3058C>T	p.Pro1020Ser	p.P1020S	ENST00000368508	NM_002944.2	1020	Cct/Tct	20/43	0.640663195339466	3	FACETS	0.966	0.895	1	0.483	0.447	0.52	CLONAL	1	TRUE	1	0.640663195339466	3		434	828	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811690	102811690	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1347715435	NA	P-0014497-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	433	813	0	ENST00000307046.8:c.494C>A	p.Thr165Lys	p.T165K	ENST00000307046	NM_001111285.1	165	aCa/aAa	4/4	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.640663195339466	2		813	1281	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127622	2127622	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014497-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	380	702	0	ENST00000219476.3:c.2861A>T	p.Lys954Ile	p.K954I	ENST00000219476	NM_000548.3	954	aAa/aTa	26/42	0.61485247807776	3	FACETS	0.775	0.737	0.812	0.516	0.491	0.542	SUBCLONAL	2	TRUE	0	0.640663195339466	3		702	1011	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526205	189526205	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014497-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	697	708	0	ENST00000264731.3:c.469G>T	p.Asp157Tyr	p.D157Y	ENST00000264731	NM_003722.4	157	Gat/Tat	4/14	0.640663195339466	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.640663195339466	3		708	1329	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057792	180057792	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014497-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	211	373	1	ENST00000261937.6:c.163C>T	p.His55Tyr	p.H55Y	ENST00000261937	NM_182925.4	55	Cac/Tac	3/30	0.26791370450269	3	FACETS	0.754	0.705	0.803	0.754	0.705	0.803	INDETERMINATE	2	TRUE	1	0.640663195339466	3		374	577	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087928	27087928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1351664579	NA	P-0014497-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	363	632	0	ENST00000324856.7:c.2215C>T	p.Pro739Ser	p.P739S	ENST00000324856	NM_006015.4	739	Cct/Tct	6/20	0.640663195339466	4	FACETS	1	0.994	1	0.478	0.453	0.504	CLONAL	1	TRUE	1	0.640663195339466	4		632	1297	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099124	27099124	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0014968-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	24	657	0	ENST00000324856.7:c.3539+1G>T		p.X1180_splice	ENST00000324856	NM_006015.4	1180			1	2	FACETS	0.639	0.5	0.798	0.639	0.5	0.798	SUBCLONAL	1	TRUE	1	0.200421575001365	2		657	375	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797895	42797895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014968-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	34	958	0	ENST00000575354.2:c.3947G>A	p.Gly1316Glu	p.G1316E	ENST00000575354	NM_015125.3	1316	gGg/gAg	16/20	0.106699337632249	4	FACETS	0.75	0.612	0.906	0.375	0.306	0.453	INDETERMINATE	1	TRUE	2	0.200421575001365	4		958	543	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578231	226578231	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1297847926	NA	P-0015146-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	48	652	0	ENST00000366794.5:c.497A>G	p.Asn166Ser	p.N166S	ENST00000366794	NM_001618.3	166	aAc/aGc	4/23	0.182860485617874	2	FACETS	0.518	0.438	0.606	0.259	0.219	0.303	INDETERMINATE	1	TRUE	0	0.352441282524789	2		652	526	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446245	70446245	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015146-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	95	561	0	ENST00000373644.4:c.5185A>G	p.Ile1729Val	p.I1729V	ENST00000373644	NM_030625.2	1729	Atc/Gtc	11/12	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.352441282524789	2		561	490	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244872	46244872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766470086	NA	P-0015146-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	106	745	0	ENST00000334344.6:c.2966C>T	p.Ser989Leu	p.S989L	ENST00000334344	NM_152641.2	989	tCg/tTg	15/21	0.193918190525083	2	FACETS	0.815	0.731	0.904	0.408	0.365	0.452	INDETERMINATE	1	TRUE	0	0.352441282524789	2		745	738	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0015146-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	280	622	0	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.352441282524789	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	0	0.352441282524789	3		622	592	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233083	66233083	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015146-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	69	569	0	ENST00000273854.3:c.1916A>C	p.Asn639Thr	p.N639T	ENST00000273854	NM_004439.5	639	aAt/aCt	10/18	0.303115063028518	2	FACETS	0.844	0.737	0.959	0.422	0.368	0.48	CLONAL	1	TRUE	0	0.352441282524789	2		569	464	SUCCESS
APC	324	MSKCC	GRCh37	5	112175513	112175513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015146-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	91	428	0	ENST00000257430.4:c.4222G>T	p.Glu1408Ter	p.E1408*	ENST00000257430	NM_000038.5	1408	Gaa/Taa	16/16	0.336073520214834	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.352441282524789	1		428	325	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390743	139390743	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015146-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	126	869	5	ENST00000277541.6:c.7448C>T	p.Thr2483Met	p.T2483M	ENST00000277541	NM_017617.3	2483	aCg/aTg	34/34	0.346851705851748	2	FACETS	1	0.984	1	0.705	0.642	0.771	CLONAL	1	TRUE	0	0.352441282524789	2		874	507	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	129	855	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.234666062098503	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.244021114470531	1		855	883	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0015701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	145	971	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.219178658140175	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.244021114470531	1		973	873	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0018522-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	45	174	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.439793751308592	1	FACETS	0.401	0.339	0.469	0.401	0.339	0.469	SUBCLONAL	1	FALSE	0	0.56314213337224	1		174	286	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772228	68772262	+	frameshift_variant	Frame_Shift_Del	DEL	AGCCCTGCCACCCTGGCTTTGACGCCGAGAGCTAC	AGCCCTGCCACCCTGGCTTTGACGCCGAGAGCTAC	-	novel	NA	P-0018522-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	188	540	0	ENST00000261769.5:c.78_112del	p.Glu26AspfsTer21	p.E26Dfs*21	ENST00000261769	NM_004360.3	26	gAGCCCTGCCACCCTGGCTTTGACGCCGAGAGCTAC/g	2/16	0.56314213337224	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	0	0.56314213337224	1		540	468	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891006	112891006	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018522-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	45	263	0	ENST00000351677.2:c.340C>T	p.His114Tyr	p.H114Y	ENST00000351677	NM_002834.3	114	Cat/Tat	4/16	0.135769480939328	0	FACETS	0.113	0.094	0.133			1	INDETERMINATE	1	FALSE	0	0.56314213337224	0		263	620	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11554273	NA	P-0018543-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	54	575	0	ENST00000371085.3:c.601C>A	p.Arg201Ser	p.R201S	ENST00000371085	NM_000516.4	201	Cgt/Agt	8/13	1	2	FACETS	0.438	0.373	0.51	0.438	0.373	0.51	SUBCLONAL	1	TRUE	1	0.3	2		575	822	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435852	110435853	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCTGGCTGGGC	novel	NA	P-0018588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	96	523	0	ENST00000375856.3:c.2538_2548dup	p.Ala850GlyfsTer20	p.A850Gfs*20	ENST00000375856	NM_003749.2	850	gcg/gGCCCAGCCAGGcg	1/2	0.733709025377772	4	FACETS	0.547	0.487	0.611			1	SUBCLONAL	1	TRUE	NA	0.822538877364146	4		523	778	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646930	37646931	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0018588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	310	992	0	ENST00000447079.4:c.2055_2056del	p.Pro686ArgfsTer13	p.P686Rfs*13	ENST00000447079	NM_015083.1	684	gaCTct/gact	3/14	1	2	FACETS	0.69	0.651	0.73	0.69	0.651	0.73	SUBCLONAL	1	TRUE	1	0.822538877364146	2		992	1092	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676216	37676217	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0018588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	421	658	0	ENST00000447079.4:c.2972_2973del	p.Ser991CysfsTer4	p.S991Cfs*4	ENST00000447079	NM_015083.1	991	TCt/t	11/14	0.822538877364146	3	FACETS	0.913	0.877	0.949			1	CLONAL	2	TRUE	NA	0.822538877364146	3		658	791	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018719-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	99	611	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.362977375858703	6	FACETS	1	0.98	1	0.472	0.423	0.523	INDETERMINATE	1	TRUE	3	0.788778809018166	6		611	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs967461896	NA	P-0018719-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	163	621	1	ENST00000269305.4:c.526T>C	p.Cys176Arg	p.C176R	ENST00000269305	NM_001126112.2	176	Tgc/Cgc	5/11	NA	2	FACETS	0.939	0.893	0.983			1	INDETERMINATE	2	TRUE	NA	0.788778809018166	2		622	220	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117642	70117642	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018719-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	77	583	0	ENST00000245479.2:c.110C>A	p.Ser37Ter	p.S37*	ENST00000245479	NM_000346.3	37	tCg/tAg	1/3	0.672354341925881	3	FACETS	1	0.977	1	0.458	0.41	0.507	CLONAL	1	TRUE	0	0.788778809018166	3		583	198	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917835	29917835	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018719-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	105	674	0	ENST00000389048.3:c.833C>A	p.Pro278His	p.P278H	ENST00000389048	NM_004304.4	278	cCt/cAt	3/29	0.750185671616708	2	FACETS	0.986	0.898	1	0.493	0.449	0.538	CLONAL	1	TRUE	0	0.788778809018166	2		674	270	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165175	47165175	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018719-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	178	378	0	ENST00000409792.3:c.951C>G	p.Ile317Met	p.I317M	ENST00000409792	NM_014159.6	317	atC/atG	3/21	0.531254372594812	4	FACETS	1	0.983	1	0.76	0.712	0.808	CLONAL	2	TRUE	1	0.788778809018166	4		378	354	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165290	47165290	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0018719-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	201	444	0	ENST00000409792.3:c.836C>G	p.Ser279Ter	p.S279*	ENST00000409792	NM_014159.6	279	tCa/tGa	3/21	0.531254372594812	4	FACETS	1	0.989	1	0.821	0.775	0.868	CLONAL	2	TRUE	1	0.788778809018166	4		444	370	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139213	37139213	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018719-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	63	525	1	ENST00000373509.5:c.553A>G	p.Ile185Val	p.I185V	ENST00000373509	NM_002648.3	185	Atc/Gtc	4/6	0.788778809018166	5	FACETS	0.753	0.653	0.862	0.251	0.217	0.288	SUBCLONAL	1	TRUE	2	0.788778809018166	5		526	463	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522571	157522571	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018719-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	134	693	2	ENST00000346085.5:c.4843G>T	p.Ala1615Ser	p.A1615S	ENST00000346085	NM_020732.3	1615	Gca/Tca	18/20	0.362977375858703	6	FACETS	1	0.985	1	0.466	0.425	0.51	INDETERMINATE	1	TRUE	3	0.788778809018166	6		695	626	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215809	98215809	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018719-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	120	655	0	ENST00000331920.6:c.3400C>G	p.Leu1134Val	p.L1134V	ENST00000331920	NM_000264.3	1134	Ctg/Gtg	20/24	0.757862013295904	3	FACETS	1	0.939	1	0.347	0.315	0.379	CLONAL	1	TRUE	0	0.788778809018166	3		655	408	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0019281-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	77	174	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.813590817109579	1	FACETS	0.884	0.808	0.958	0.884	0.808	0.958	CLONAL	1	TRUE	0	0.813590817109579	1		174	127	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578214	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs864309495	NA	P-0019281-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	236	651	0	ENST00000269305.4:c.635_636del	p.Phe212SerfsTer3	p.F212Sfs*3	ENST00000269305	NM_001126112.2	212	tTT/t	6/11	0.772911582366351	1	FACETS	0.887	0.844	0.93	0.887	0.844	0.93	CLONAL	1	TRUE	0	0.813590817109579	1		651	388	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577222	64577224	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs794728657	NA	P-0019281-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	246	671	1	ENST00000312049.6:c.358_360del	p.Lys120del	p.K120del	ENST00000312049	NM_130799.2	120	AAG/-	2/10	0.769036283325156	1	FACETS	0.877	0.835	0.919	0.877	0.835	0.919	CLONAL	1	TRUE	0	0.813590817109579	1		672	409	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923680	39923681	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	rs1555915763	NA	P-0019281-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	215	602	0	ENST00000378444.4:c.3410_3411del	p.Lys1137SerfsTer4	p.K1137Sfs*4	ENST00000378444	NM_001123385.1	1137	aAA/a	7/15	1	2	FACETS	0.927	0.868	0.987	0.927	0.868	0.987	CLONAL	1	TRUE	1	0.813590817109579	2		602	570	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104325	2104327	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs1342475885	NA	P-0019281-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	176	552	0	ENST00000219476.3:c.369_371del	p.Phe124del	p.F124del	ENST00000219476	NM_000548.3	122	cTCTtc/ctc	5/42	0.813590817109579	1	FACETS	0.987	0.936	1	0.987	0.936	1	CLONAL	1	TRUE	0	0.813590817109579	1		552	260	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633289	12633291	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0019281-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	146	531	0	ENST00000251849.4:c.1109_1111del	p.Gly370del	p.G370del	ENST00000251849	NM_002880.3	370	gGAGat/gat	11/17	0.813590817109579	1	FACETS	0.848	0.794	0.902	0.848	0.794	0.902	CLONAL	1	TRUE	0	0.813590817109579	1		531	251	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286872	33286873	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0019281-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	235	608	0	ENST00000374542.5:c.2064_2065del	p.Pro689GlnfsTer51	p.P689Qfs*51	ENST00000374542	NM_001141970.1	688	tcTCcc/tccc	7/8	0.75203116362788	1	FACETS	0.828	0.785	0.87	0.828	0.785	0.87	CLONAL	1	TRUE	0	0.813590817109579	1		608	414	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16235871	16235871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140552804	NA	P-0019281-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	205	519	0	ENST00000375759.3:c.937G>A	p.Ala313Thr	p.A313T	ENST00000375759	NM_015001.2	313	Gca/Aca	4/15	0.813590817109579	1	FACETS	0.993	0.946	1	0.993	0.946	1	CLONAL	1	TRUE	0	0.813590817109579	1		519	301	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0019439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	49	484	0	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	1	2	FACETS	0.792	0.675	0.92	0.792	0.675	0.92	CLONAL	1	TRUE	1	0.393830926855091	2		484	314	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0019451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	78	629	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.332665572832838	5	FACETS	0.886	0.778	1	0.295	0.259	0.335	CLONAL	1	TRUE	2	0.381775000911306	5		629	725	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0019451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	517	802	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.381775000911306	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.381775000911306	3		802	986	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782329	NA	P-0019451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	209	861	3	ENST00000269305.4:c.746G>A	p.Arg249Lys	p.R249K	ENST00000269305	NM_001126112.2	249	aGg/aAg	7/11	0.381775000911306	3	FACETS	0.925	0.868	0.982	1	0.992	1	CLONAL	3	TRUE	1	0.381775000911306	3		864	470	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856097	111856097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1013978345	NA	P-0019451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	41	616	4	ENST00000341259.2:c.148C>T	p.Arg50Trp	p.R50W	ENST00000341259	NM_005475.2	50	Cgg/Tgg	2/8	0.381775000911306	3	FACETS	0.752	0.629	0.889	0.251	0.209	0.297	SUBCLONAL	1	TRUE	0	0.381775000911306	3		620	340	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041041	42041041	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	219	893	1	ENST00000219905.7:c.5419C>T	p.Gln1807Ter	p.Q1807*	ENST00000219905	NM_001164273.1	1807	Cag/Tag	16/24	0.230261151657158	3	FACETS	1	0.981	1	0.748	0.7	0.796	CLONAL	2	TRUE	0	0.381775000911306	3		894	609	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123122	5123122	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0019451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	217	610	0	ENST00000381652.3:c.3177+1G>T		p.X1059_splice	ENST00000381652	NM_004972.3	1059			0.381775000911306	3	FACETS	1	0.978	1	0.734	0.687	0.782	CLONAL	2	TRUE	0	0.381775000911306	3		610	615	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950328	17950328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1438576059	NA	P-0019451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	155	902	0	ENST00000458235.1:c.1399G>A	p.Val467Met	p.V467M	ENST00000458235	NM_000215.3	467	Gtg/Atg	10/24	0.381775000911306	2	FACETS	0.886	0.819	0.956	0.886	0.819	0.956	CLONAL	2	TRUE	0	0.381775000911306	2		902	458	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434182	12434182	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	144	730	0	ENST00000287820.6:c.550A>G	p.Lys184Glu	p.K184E	ENST00000287820	NM_015869.4	184	Aaa/Gaa	4/7	0.332665572832838	5	FACETS	1	0.985	1	0.466	0.425	0.51	CLONAL	1	TRUE	2	0.381775000911306	5		730	848	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475403	12475403	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	118	758	0	ENST00000287820.6:c.1277C>A	p.Pro426Gln	p.P426Q	ENST00000287820	NM_015869.4	426	cCa/cAa	7/7	0.332665572832838	5	FACETS	1	0.984	1	0.49	0.442	0.539	CLONAL	1	TRUE	2	0.381775000911306	5		758	662	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629259	187629259	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	81	817	0	ENST00000441802.2:c.1723G>A	p.Glu575Lys	p.E575K	ENST00000441802	NM_005245.3	575	Gaa/Aaa	2/27	0.381775000911306	3	FACETS	0.873	0.77	0.983			1	CLONAL	1	TRUE	NA	0.381775000911306	3		817	579	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187192	38187192	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1401	106	1058	0	ENST00000317025.8:c.1285C>G	p.Gln429Glu	p.Q429E	ENST00000317025	NM_023034.1	429	Cag/Gag	6/24	0.381775000911306	7	FACETS	0.72	0.643	0.803			1	SUBCLONAL	1	TRUE	NA	0.381775000911306	7		1058	1507	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0019726-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	65	586	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.472538798018042	1	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	0	0.472538798018042	1		586	208	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0019726-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	88	759	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.4347919313103	2	FACETS	1	0.982	1	0.742	0.668	0.819	CLONAL	1	TRUE	0	0.472538798018042	2		759	251	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0019726-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	111	436	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	0.308252152593934	4	FACETS	1	0.929	1	1	0.987	1	CLONAL	3	TRUE	2	0.472538798018042	4		436	228	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845465	151845465	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0019726-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	134	734	0	ENST00000262189.6:c.13547T>G	p.Leu4516Ter	p.L4516*	ENST00000262189	NM_170606.2	4516	tTa/tGa	52/59	0.376120526941971	2	FACETS	0.873	0.805	0.942	0.873	0.805	0.942	CLONAL	2	TRUE	0	0.472538798018042	2		734	325	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981878	201981879	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0019796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	118	932	0	ENST00000359651.3:c.591dup	p.Thr198HisfsTer19	p.T198Hfs*19	ENST00000359651		197	tcc/tCcc	4/8	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.252302515699714	2		932	883	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347106	347106	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	102	991	1	ENST00000262320.3:c.1905G>A	p.Trp635Ter	p.W635*	ENST00000262320	NM_003502.3	635	tgG/tgA	7/11	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.252302515699714	2		992	791	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839724	27839724	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	57	662	0	ENST00000328488.2:c.370G>C	p.Asp124His	p.D124H	ENST00000328488	NM_003533.2	124	Gac/Cac	1/1	0.252302515699714	10	FACETS	1	0.944	1	0.243	0.208	0.282	CLONAL	1	TRUE	5	0.252302515699714	10		662	747	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019935-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	120	571	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.944	0.861	1	0.944	0.861	1	CLONAL	1	TRUE	1	0.646786594523796	2		571	393	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509060	106509060	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019935-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	171	514	2	ENST00000359195.3:c.1054G>A	p.Val352Met	p.V352M	ENST00000359195	NM_002649.2	352	Gtg/Atg	2/11	0.319120492669675	3	FACETS	1	0.974	1	0.374	0.345	0.403	INDETERMINATE	1	TRUE	0	0.646786594523796	3		516	624	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0019967-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	57	917	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.284951944467792	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.23	1		918	321	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371984	55371984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019967-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	83	503	0	ENST00000297316.4:c.674C>T	p.Ser225Phe	p.S225F	ENST00000297316	NM_022454.3	225	tCc/tTc	2/2	0.3	3	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	1	0.23	3		503	367	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578204	7578204	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	229	501	1	ENST00000269305.4:c.645T>A	p.Ser215Arg	p.S215R	ENST00000269305	NM_001126112.2	215	agT/agA	6/11	0.549178496102849	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.549178496102849	2		502	387	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	218	446	0	ENST00000304494.5:c.143C>T	p.Pro48Leu	p.P48L	ENST00000304494	NM_000077.4	48	cCg/cTg	1/3	0.549178496102849	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.549178496102849	2		446	326	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740157	162740157	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	240	376	1	ENST00000367921.3:c.1359G>T	p.Met453Ile	p.M453I	ENST00000367921	NM_006182.2	453	atG/atT	12/18	0.517032798733245	5	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	2	0.549178496102849	5		377	497	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431570	49431597	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCCCGTGGCCCCAAAGGAGGCCTTCT	CCTCCCGTGGCCCCAAAGGAGGCCTTCT	TCG	novel	NA	P-0020569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	71	437	2	ENST00000301067.7:c.9542_9569delinsCGA	p.Glu3181AlafsTer8	p.E3181Afs*8	ENST00000301067	NM_003482.3	3181	gAGAAGGCCTCCTTTGGGGCCACGGGAGGa/gCGAa	34/54	0.549178496102849	4	FACETS	0.813	0.711	0.922	0.271	0.237	0.308	CLONAL	1	TRUE	1	0.549178496102849	4		439	493	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443512	49443512	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	245	333	3	ENST00000301067.7:c.3859del	p.Glu1287ArgfsTer43	p.E1287Rfs*43	ENST00000301067	NM_003482.3	1287	Gag/ag	11/54	0.549178496102849	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	3	TRUE	1	0.549178496102849	4		336	449	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911691	32911691	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203711	NA	P-0020569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	136	383	0	ENST00000380152.3:c.3199A>G	p.Thr1067Ala	p.T1067A	ENST00000380152		1067	Act/Gct	11/27	0.549178496102849	3	FACETS	0.977	0.902	1	0.977	0.902	1	CLONAL	2	TRUE	1	0.549178496102849	3		383	323	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635645	47635645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41295286	NA	P-0020569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	90	494	0	ENST00000233146.2:c.317G>A	p.Arg106Lys	p.R106K	ENST00000233146	NM_000251.2	106	aGa/aAa	2/16	0.549178496102849	3	FACETS	0.904	0.806	1	0.452	0.403	0.504	CLONAL	1	TRUE	1	0.549178496102849	3		494	462	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602970	55602970	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141126803	NA	P-0020569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	106	282	0	ENST00000288135.5:c.2680C>T	p.His894Tyr	p.H894Y	ENST00000288135	NM_000222.2	894	Cac/Tac	19/21	0.549178496102849	3	FACETS	0.915	0.834	0.997	0.915	0.834	0.997	CLONAL	2	TRUE	1	0.549178496102849	3		282	269	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629127	86629127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	86	237	0	ENST00000274376.6:c.872C>T	p.Thr291Ile	p.T291I	ENST00000274376	NM_002890.2	291	aCa/aTa	4/25	0.549178496102849	2	FACETS	0.979	0.894	1	0.979	0.894	1	CLONAL	2	TRUE	0	0.549178496102849	2		237	160	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520479	176520479	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	151	592	0	ENST00000292408.4:c.1324G>T	p.Gly442Cys	p.G442C	ENST00000292408	NM_213647.1	442	Ggc/Tgc	10/18	0.549178496102849	2	FACETS	1	0.979	1	0.589	0.543	0.636	CLONAL	1	TRUE	0	0.549178496102849	2		592	467	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978741	70978741	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0020569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	165	297	0	ENST00000276594.2:c.913-1G>T		p.X305_splice	ENST00000276594	NM_024504.3	305			0.549178496102849	6	FACETS	0.922	0.854	0.99	0.691	0.641	0.743	CLONAL	3	TRUE	2	0.549178496102849	6		297	456	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944878	31944878	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs141415515	NA	P-0020569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	38	301	0	ENST00000340398.3:c.223G>C	p.Ala75Pro	p.A75P	ENST00000340398	NM_001013699.2	75	Gcg/Ccg	1/1	0.549178496102849	4	FACETS	0.627	0.519	0.746	0.209	0.173	0.249	SUBCLONAL	1	TRUE	1	0.549178496102849	4		301	342	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966635	36966635	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	225	819	2	ENST00000358127.4:c.691C>A	p.Gln231Lys	p.Q231K	ENST00000358127	NM_001280556.1	231	Cag/Aag	6/10	1	2	FACETS	0.747	0.697	0.798	0.747	0.697	0.798	SUBCLONAL	1	TRUE	1	0.727019161195683	2		821	829	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	294	795	9	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.993	0.936	1	0.993	0.936	1	CLONAL	1	TRUE	1	0.618408150183184	2		804	958	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	345	1035	7	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	0.954	1	CLONAL	1	TRUE	1	0.618408150183184	2		1042	1107	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121909229	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	335	814	3	ENST00000371953.3:c.389G>T	p.Arg130Leu	p.R130L	ENST00000371953	NM_000314.4	130	cGa/cTa	5/9	0.618408150183184	3	FACETS	0.952	0.906	0.998	0.952	0.906	0.998	CLONAL	2	TRUE	1	0.618408150183184	3		817	745	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	340	604	2	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.837	0.799	0.874	1	0.996	1	CLONAL	2	TRUE	1	0.618408150183184	2		606	657	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075570	8075570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1289050189	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	251	783	1	ENST00000377482.5:c.110G>A	p.Arg37His	p.R37H	ENST00000377482	NM_018948.3	37	cGc/cAc	2/4	1	2	FACETS	0.957	0.898	1	0.957	0.898	1	CLONAL	1	TRUE	1	0.618408150183184	2		784	848	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	282	682	5	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.96	0.904	1	0.96	0.904	1	CLONAL	1	TRUE	1	0.618408150183184	2		687	950	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087346	27087346	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	173	693	3	ENST00000324856.7:c.1921-1G>T		p.X641_splice	ENST00000324856	NM_006015.4	641			1	2	FACETS	0.876	0.809	0.944	0.876	0.809	0.944	CLONAL	1	TRUE	1	0.618408150183184	2		696	639	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649922	88649922	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786201038	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	214	783	1	ENST00000372037.3:c.176del	p.Leu59Ter	p.L59*	ENST00000372037	NM_004329.2	57	ccT/cc	4/13	0.618408150183184	3	FACETS	0.925	0.859	0.992	0.462	0.429	0.496	CLONAL	1	TRUE	1	0.618408150183184	3		784	980	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624294	89624295	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	309	916	2	ENST00000371953.3:c.69dup	p.Asp24ArgfsTer20	p.D24Rfs*20	ENST00000371953	NM_000314.4	23	tta/ttAa	1/9	0.618408150183184	3	FACETS	1	0.983	1	0.554	0.522	0.587	CLONAL	1	TRUE	1	0.618408150183184	3		918	1180	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	236	758	10	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.618408150183184	3	FACETS	1	0.968	1	0.529	0.494	0.565	CLONAL	1	TRUE	1	0.618408150183184	3		768	945	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	352	1031	6	ENST00000227507.2:c.859C>G	p.Pro287Ala	p.P287A	ENST00000227507	NM_053056.2	287	Ccc/Gcc	5/5	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.618408150183184	2		1037	1016	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180454	94180454	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852761	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	250	898	4	ENST00000323929.3:c.1714C>T	p.Arg572Ter	p.R572*	ENST00000323929	NM_005591.3	572	Cga/Tga	15/20	1	2	FACETS	0.94	0.881	1	0.94	0.881	1	CLONAL	1	TRUE	1	0.618408150183184	2		902	860	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	463	765	9	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	0.906	0.873	0.94	1	0.997	1	CLONAL	2	TRUE	1	0.618408150183184	2		774	826	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	259	857	7	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.945	0.887	1	0.945	0.887	1	CLONAL	1	TRUE	1	0.618408150183184	2		864	886	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654642	67654642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	350	952	6	ENST00000264010.4:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000264010	NM_006565.3	377	Cgt/Tgt	6/12	1	2	FACETS	0.805	0.769	0.841	1	0.996	1	CLONAL	2	TRUE	1	0.618408150183184	2		958	703	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357478	89357478	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	317	1004	1	ENST00000301030.4:c.340C>T	p.Arg114Cys	p.R114C	ENST00000301030	NM_001256183.1	114	Cgc/Tgc	5/13	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.618408150183184	2		1005	958	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883240	37883240	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749539903	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	331	1007	1	ENST00000269571.5:c.3143G>A	p.Arg1048His	p.R1048H	ENST00000269571		1048	cGc/cAc	25/27	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.618408150183184	2		1008	1028	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47700144	47700144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767367200	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	221	742	0	ENST00000347630.2:c.29C>T	p.Pro10Leu	p.P10L	ENST00000347630	NM_001007230.1	10	cCg/cTg	3/11	1	2	FACETS	0.928	0.867	0.992	0.928	0.867	0.992	CLONAL	1	TRUE	1	0.618408150183184	2		742	770	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584772	48584773	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	236	809	0	ENST00000342988.3:c.854dup	p.Asn285LysfsTer23	p.N285Kfs*23	ENST00000342988	NM_005359.5	284	caa/cAaa	7/12	1	2	FACETS	0.912	0.853	0.972	0.912	0.853	0.972	CLONAL	1	TRUE	1	0.618408150183184	2		809	837	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354227	15354227	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769217775	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	116	1082	2	ENST00000263377.2:c.2653G>A	p.Ala885Thr	p.A885T	ENST00000263377	NM_058243.2	885	Gcc/Acc	14/20	1	2	FACETS	0.336	0.302	0.373	0.336	0.302	0.373	SUBCLONAL	1	TRUE	1	0.618408150183184	2		1084	1115	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45854955	45854955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	302	1020	1	ENST00000391945.4:c.2215C>T	p.Leu739Phe	p.L739F	ENST00000391945	NM_000400.3	739	Ctc/Ttc	23/23	1	2	FACETS	0.948	0.894	1	0.948	0.894	1	CLONAL	1	TRUE	1	0.618408150183184	2		1021	1030	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637476	47637476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750574	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	40	738	0	ENST00000233146.2:c.610G>A	p.Gly204Arg	p.G204R	ENST00000233146	NM_000251.2	204	Gga/Aga	3/16	1	2	FACETS	0.187	0.155	0.223	0.187	0.155	0.223	SUBCLONAL	1	TRUE	1	0.618408150183184	2		738	692	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096099	178096099	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	68	584	1	ENST00000397062.3:c.1232A>G	p.Gln411Arg	p.Q411R	ENST00000397062	NM_006164.4	411	cAg/cGg	5/5	1	2	FACETS	0.309	0.268	0.353	0.309	0.268	0.353	SUBCLONAL	1	TRUE	1	0.618408150183184	2		585	712	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732726	204732726	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	234	742	1	ENST00000302823.3:c.61C>A	p.Pro21Thr	p.P21T	ENST00000302823	NM_005214.4	21	Ccc/Acc	1/4	1	2	FACETS	0.883	0.825	0.942	0.883	0.825	0.942	CLONAL	1	TRUE	1	0.618408150183184	2		743	857	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735608	204735608	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	40	675	0	ENST00000302823.3:c.409C>G	p.Pro137Ala	p.P137A	ENST00000302823	NM_005214.4	137	Ccg/Gcg	2/4	1	2	FACETS	0.195	0.162	0.233	0.195	0.162	0.233	SUBCLONAL	1	TRUE	1	0.618408150183184	2		675	662	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62305435	62305435	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	273	845	3	ENST00000360203.5:c.912del	p.Ser305AlafsTer4	p.S305Afs*4	ENST00000360203	NM_001283009.1	303	tCc/tc	10/35	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.618408150183184	2		848	881	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645687	12645687	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	134	466	1	ENST00000251849.4:c.782C>A	p.Pro261His	p.P261H	ENST00000251849	NM_002880.3	261	cCt/cAt	7/17	1	2	FACETS	0.922	0.844	1	0.922	0.844	1	CLONAL	1	TRUE	1	0.618408150183184	2		467	470	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913400	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	180	616	0	ENST00000349496.5:c.98C>A	p.Ser33Tyr	p.S33Y	ENST00000349496	NM_001904.3	33	tCt/tAt	3/15	1	2	FACETS	0.926	0.857	0.996	0.926	0.857	0.996	CLONAL	1	TRUE	1	0.618408150183184	2		616	629	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584583	52584583	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	271	896	0	ENST00000394830.3:c.4430del	p.Pro1477LeufsTer12	p.P1477Lfs*12	ENST00000394830	NM_018313.4	1477	cCt/ct	29/30	1	2	FACETS	0.894	0.84	0.95	0.894	0.84	0.95	CLONAL	1	TRUE	1	0.618408150183184	2		896	980	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156921	89156921	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	242	1012	0	ENST00000336596.2:c.23T>C	p.Leu8Pro	p.L8P	ENST00000336596	NM_005233.5	8	cTc/cCc	1/17	1	2	FACETS	0.894	0.837	0.953	0.894	0.837	0.953	CLONAL	1	TRUE	1	0.618408150183184	2		1012	875	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413710	138413710	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	210	752	3	ENST00000289153.2:c.1810del	p.Arg604GlyfsTer4	p.R604Gfs*4	ENST00000289153	NM_006219.2	604	Cgg/gg	12/22	1	2	FACETS	0.974	0.909	1	0.974	0.909	1	CLONAL	1	TRUE	1	0.618408150183184	2		755	697	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664761	138664761	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs797044528	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	179	571	0	ENST00000330315.3:c.804del	p.Gly269AlafsTer2	p.G269Afs*2	ENST00000330315	NM_023067.3	268	ccC/cc	1/1	1	2	FACETS	0.882	0.817	0.95	0.882	0.817	0.95	CLONAL	1	TRUE	1	0.618408150183184	2		571	656	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916927	178916947	+	inframe_deletion	In_Frame_Del	DEL	TAGGCAACCGTGAAGAAAAGA	TAGGCAACCGTGAAGAAAAGA	-	novel	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	156	830	3	ENST00000263967.3:c.315_335del	p.Gly106_Ile112del	p.G106_I112del	ENST00000263967	NM_006218.2	105	gTAGGCAACCGTGAAGAAAAGAtc/gtc	2/21	1	2	FACETS	0.775	0.712	0.84	0.775	0.712	0.84	SUBCLONAL	1	TRUE	1	0.618408150183184	2		833	651	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638817	176638818	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	54	887	0	ENST00000439151.2:c.3418_3419del	p.Val1140AsnfsTer4	p.V1140Nfs*4	ENST00000439151	NM_022455.4	1139	tcTGta/tcta	5/23	1	2	FACETS	0.196	0.167	0.228	0.196	0.167	0.228	SUBCLONAL	1	TRUE	1	0.618408150183184	2		887	891	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707573	176707573	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	72	936	0	ENST00000439151.2:c.5630G>T	p.Arg1877Leu	p.R1877L	ENST00000439151	NM_022455.4	1877	cGt/cTt	18/23	1	2	FACETS	0.25	0.218	0.286	0.25	0.218	0.286	SUBCLONAL	1	TRUE	1	0.618408150183184	2		936	930	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671630	30671630	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	337	927	1	ENST00000376406.3:c.5330A>C	p.Gln1777Pro	p.Q1777P	ENST00000376406	NM_014641.2	1777	cAg/cCg	10/15	0.618408150183184	3	FACETS	1	0.962	1	0.512	0.483	0.541	CLONAL	1	TRUE	1	0.618408150183184	3		928	1394	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940403	31940403	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	342	835	0	ENST00000375333.2:c.436G>A	p.Ala146Thr	p.A146T	ENST00000375333	NM_032454.1	146	Gcg/Acg	3/8	0.618408150183184	3	FACETS	1	0.983	1	0.546	0.516	0.577	CLONAL	1	TRUE	1	0.618408150183184	3		835	1326	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527816	157527817	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs35441529	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	391	735	2	ENST00000346085.5:c.5547dup	p.Ser1851LysfsTer5	p.S1851Kfs*5	ENST00000346085	NM_020732.3	1847	-/C	20/20	0.618408150183184	3	FACETS	0.954	0.911	0.996	0.954	0.911	0.996	CLONAL	2	TRUE	1	0.618408150183184	3		737	868	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874149	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	253	1040	1	ENST00000262189.6:c.8389_8390del	p.Lys2797GlyfsTer11	p.K2797Gfs*11	ENST00000262189	NM_170606.2	2797	AAg/g	38/59	1	2	FACETS	0.84	0.787	0.895	0.84	0.787	0.895	CLONAL	1	TRUE	1	0.618408150183184	2		1041	974	SUCCESS
AR	367	MSKCC	GRCh37	X	66765159	66765200	+	inframe_deletion	In_Frame_Del	DEL	GCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA	GCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA	-	rs3032358	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	89	320	0	ENST00000374690.3:c.198_239del	p.Gln67_Gln80del	p.Q67_Q80del	ENST00000374690	NM_000044.3	57	ctGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAg/ctg	1/8	1	2	FACETS	0.757	0.676	0.843	0.757	0.676	0.843	SUBCLONAL	1	TRUE	1	0.618408150183184	2		320	380	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352366	70352366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	247	815	1	ENST00000374080.3:c.4393C>T	p.Arg1465Cys	p.R1465C	ENST00000374080		1465	Cgt/Tgt	31/45	1	2	FACETS	0.984	0.923	1	0.984	0.923	1	CLONAL	1	TRUE	1	0.618408150183184	2		816	812	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0021321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	1260	756	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.523583590029256	4	FACETS	1	0.998	1	1	0.999	1	CLONAL	3	TRUE	2	0.672160020447133	4		756	1861	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593491	48593494	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	rs80338965	NA	P-0021321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	236	425	0	ENST00000342988.3:c.1245_1248del	p.Asp415GlufsTer20	p.D415Efs*20	ENST00000342988	NM_005359.5	414	ttAGAC/tt	10/12	0.644666796765884	2	FACETS	0.944	0.899	0.988	0.944	0.899	0.988	CLONAL	2	TRUE	0	0.672160020447133	2		425	372	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578224	7578224	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1429743956	NA	P-0021321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	443	864	0	ENST00000269305.4:c.625A>T	p.Arg209Ter	p.R209*	ENST00000269305	NM_001126112.2	209	Aga/Tga	6/11	0.631692780210503	2	FACETS	0.893	0.861	0.925	0.893	0.861	0.925	CLONAL	2	TRUE	0	0.672160020447133	2		864	738	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813599	50813599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	351	634	0	ENST00000398568.2:c.1153C>T	p.Leu385Phe	p.L385F	ENST00000398568	NM_001042412.1	385	Ctt/Ttt	8/18	0.672160020447133	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.672160020447133	3		634	689	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030862	36030862	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	162	528	0	ENST00000358208.4:c.1141G>A	p.Glu381Lys	p.E381K	ENST00000358208		381	Gag/Aag	10/12	0.546130356668677	5	FACETS	1	0.954	1	0.353	0.323	0.383	CLONAL	1	TRUE	2	0.672160020447133	5		528	915	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974691	21974732	+	inframe_deletion	In_Frame_Del	DEL	GACCGTAACTATTCGGTGCGTTGGGCAGCGCCCCCGCCTCCA	GACCGTAACTATTCGGTGCGTTGGGCAGCGCCCCCGCCTCCA	-	novel	NA	P-0021321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	200	559	0	ENST00000304494.5:c.95_136del	p.Leu32_Gly45del	p.L32_G45del	ENST00000304494	NM_000077.4	32	cTGGAGGCGGGGGCGCTGCCCAACGCACCGAATAGTTACGGTCgg/cgg	1/3	0.672160020447133	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.672160020447133	1		559	357	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820620	44820632	+	frameshift_variant	Frame_Shift_Del	DEL	TGGAAGATTATCC	TGGAAGATTATCC	-	novel	NA	P-0021321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	307	721	0	ENST00000377967.4:c.317_329del	p.Leu106Ter	p.L106*	ENST00000377967	NM_021140.2	106	tTGGAAGATTATCCa/ta	3/29	0.206112305131622	3	FACETS	0.761	0.721	0.802	0.507	0.48	0.535	INDETERMINATE	2	TRUE	0	0.672160020447133	3		721	802	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	742	571	0				ENST00000310581	NM_198253.2	-/1132			0.829074691821462	5	FACETS	0.928	0.9	0.956	0.928	0.9	0.956	CLONAL	3	TRUE	2	0.866102689945641	5		571	1415	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226576371	226576371	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	697	1064	0	ENST00000366794.5:c.703G>C	p.Glu235Gln	p.E235Q	ENST00000366794	NM_001618.3	235	Gaa/Caa	5/23	0.699114684045372	4	FACETS	0.956	0.924	0.988	0.956	0.924	0.988	CLONAL	2	TRUE	2	0.866102689945641	4		1064	1571	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48921987	48921987	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	448	745	0	ENST00000267163.4:c.528del	p.Gln176HisfsTer10	p.Q176Hfs*10	ENST00000267163	NM_000321.2	176	cAa/ca	5/27	0.864125154085729	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.866102689945641	2		745	513	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781324	3781326	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs587783502	NA	P-0021348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	1146	1493	1	ENST00000262367.5:c.5039_5041del	p.Ser1680del	p.S1680del	ENST00000262367	NM_004380.2	1680	tCCTtg/ttg	30/31	0.54007434611127	4	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.866102689945641	4		1494	2092	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843624	3843624	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	280	730	2	ENST00000262367.5:c.979C>T	p.Gln327Ter	p.Q327*	ENST00000262367	NM_004380.2	327	Cag/Tag	4/31	0.54007434611127	4	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.866102689945641	4		732	1024	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216947	7216947	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	377	847	0	ENST00000380728.2:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000380728		192	Cag/Tag	7/11	0.866102689945641	2	FACETS	0.892	0.865	0.918	0.892	0.865	0.918	CLONAL	2	TRUE	0	0.866102689945641	2		847	488	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547926	41547926	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	715	905	0	ENST00000263253.7:c.2907G>C	p.Glu969Asp	p.E969D	ENST00000263253	NM_001429.3	969	gaG/gaC	15/31	0.866102689945641	3	FACETS	0.978	0.95	1	0.978	0.95	1	CLONAL	2	TRUE	1	0.866102689945641	3		905	1210	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564858	41564858	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	365	929	2	ENST00000263253.7:c.4159C>T	p.Pro1387Ser	p.P1387S	ENST00000263253	NM_001429.3	1387	Cca/Tca	25/31	0.866102689945641	3	FACETS	0.973	0.923	1	0.487	0.461	0.513	CLONAL	1	TRUE	1	0.866102689945641	3		931	1241	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948295	31948295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	450	1143	2	ENST00000375333.2:c.883G>A	p.Ala295Thr	p.A295T	ENST00000375333	NM_032454.1	295	Gct/Act	6/8	0.81470956693621	3	FACETS	0.942	0.898	0.987	0.471	0.449	0.494	CLONAL	1	TRUE	1	0.866102689945641	3		1145	1581	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624394	140624394	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1390903353	NA	P-0021348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	458	417	1	ENST00000288602.6:c.110C>T	p.Ser37Leu	p.S37L	ENST00000288602	NM_004333.4	37	tCg/tTg	1/18	0.866102689945641	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.866102689945641	3		418	735	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089839	5089839	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	267	486	0	ENST00000381652.3:c.2737T>G	p.Tyr913Asp	p.Y913D	ENST00000381652	NM_004972.3	913	Tac/Gac	20/25	0.81470956693621	3	FACETS	0.962	0.917	1	0.962	0.917	1	CLONAL	2	TRUE	1	0.866102689945641	3		486	459	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300892	137300892	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs755685635	NA	P-0021348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1277	593	1211	0	ENST00000481739.1:c.537T>G	p.Ile179Met	p.I179M	ENST00000481739	NM_002957.4	179	atT/atG	4/10	0.866102689945641	3	FACETS	1	0.985	1	0.525	0.503	0.546	CLONAL	1	TRUE	1	0.866102689945641	3		1211	1870	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0021485-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	34	773	0	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		773	499	SUCCESS
APC	324	MSKCC	GRCh37	5	112173441	112173441	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	28	396	0	ENST00000257430.4:c.2150T>C	p.Met717Thr	p.M717T	ENST00000257430	NM_000038.5	717	aTg/aCg	16/16	0.222191977180046	4	FACETS	0.928	0.753	1	0.928	0.753	1	CLONAL	2	TRUE	2	0.285197781401083	4		396	136	SUCCESS
APC	324	MSKCC	GRCh37	5	112178040	112178040	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1247815306	NA	P-0021530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	30	478	1	ENST00000257430.4:c.6749G>T	p.Gly2250Val	p.G2250V	ENST00000257430	NM_000038.5	2250	gGc/gTc	16/16	0.222191977180046	4	FACETS	1	0.919	1	0.635	0.515	0.769	CLONAL	1	TRUE	2	0.285197781401083	4		479	213	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202788	133202788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201165149	NA	P-0021540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	130	712	1	ENST00000320574.5:c.6446G>A	p.Arg2149His	p.R2149H	ENST00000320574	NM_006231.2	2149	cGc/cAc	46/49	0.202197701663465	1	FACETS	0.89	0.814	0.968	1	0.992	1	CLONAL	3	TRUE	0	0.202197701663465	1		713	433	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255014	16255014	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0021540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	18	412	0	ENST00000375759.3:c.2279C>G	p.Ser760Ter	p.S760*	ENST00000375759	NM_015001.2	760	tCa/tGa	11/15	0.146550582012469	4	FACETS	0.704	0.53	0.91			1	CLONAL	1	TRUE	NA	0.202197701663465	4		412	304	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262240	115262240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	180	646	1	ENST00000438362.2:c.2314C>T	p.Arg772Cys	p.R772C	ENST00000438362	NM_001242891.1	772	Cgc/Tgc	18/20	1	2	FACETS	1	0.98	1	1	0.993	1	CLONAL	2	TRUE	1	0.202197701663465	2		647	761	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	33	571	0				ENST00000310581	NM_198253.2	-/1132			0.114627623834377	0	FACETS	0.39	0.316	0.473			1	INDETERMINATE	1	TRUE	0	0.208560277981514	0		571	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780071	NA	P-0021676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	70	866	0	ENST00000269305.4:c.580C>T	p.Leu194Phe	p.L194F	ENST00000269305	NM_001126112.2	194	Ctt/Ttt	6/11	1	2	FACETS	0.839	0.73	0.957	0.839	0.73	0.957	CLONAL	1	TRUE	1	0.208560277981514	2		866	800	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114799874	114799874	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1305520561	NA	P-0021676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	93	760	2	ENST00000543371.1:c.541G>A	p.Ala181Thr	p.A181T	ENST00000543371	NM_001198531.1	181	Gca/Aca	5/14	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.208560277981514	2		762	792	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933047	39933047	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	118	465	2	ENST00000378444.4:c.1552G>T	p.Glu518Ter	p.E518*	ENST00000378444	NM_001123385.1	518	Gaa/Taa	4/15	1	1	FACETS	0.908	0.822	0.998	1	0.988	1	CLONAL	2	TRUE	0	0.208560277981514	1		467	558	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797242	32797242	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771932254	NA	P-0021676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	87	1028	1	ENST00000374899.4:c.1867C>T	p.Arg623Ter	p.R623*	ENST00000374899	NM_018833.2	623	Cga/Tga	11/12	NA	2	FACETS	0.756	0.668	0.852			1	INDETERMINATE	1	TRUE	NA	0.208560277981514	2		1029	1103	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984448	201984449	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	76	651	0	ENST00000359651.3:c.1114dup	p.Ter372LeufsTer99	p.*372Lfs*99	ENST00000359651		371	-/T	8/8	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.208560277981514	2		651	692	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333405	70333405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	100	992	0	ENST00000373644.4:c.1310C>T	p.Pro437Leu	p.P437L	ENST00000373644	NM_030625.2	437	cCa/cTa	2/12	1	2	FACETS	0.912	0.813	1	0.912	0.813	1	CLONAL	1	TRUE	1	0.208560277981514	2		992	1051	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231201	46231201	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0021676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	51	480	1	ENST00000334344.6:c.1120+1G>A		p.X374_splice	ENST00000334344	NM_152641.2	374			0.173047727476059	3	FACETS	0.818	0.699	0.948	0.818	0.699	0.948	CLONAL	2	TRUE	1	0.208560277981514	3		481	330	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244433	46244433	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	48	693	0	ENST00000334344.6:c.2527C>T	p.Gln843Ter	p.Q843*	ENST00000334344	NM_152641.2	843	Caa/Taa	15/21	0.173047727476059	3	FACETS	0.678	0.571	0.795	0.339	0.285	0.398	SUBCLONAL	1	TRUE	1	0.208560277981514	3		693	750	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508715	38508715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758973243	NA	P-0021676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	48	821	2	ENST00000254066.5:c.763G>A	p.Ala255Thr	p.A255T	ENST00000254066	NM_000964.3	255	Gcc/Acc	6/9	1	2	FACETS	0.483	0.407	0.568	0.483	0.407	0.568	SUBCLONAL	1	TRUE	1	0.208560277981514	2		823	953	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028007	69028007	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1176717959	NA	P-0021676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	22	602	0	ENST00000288368.4:c.3166T>C	p.Tyr1056His	p.Y1056H	ENST00000288368	NM_024870.2	1056	Tat/Cat	26/40	0.173047727476059	3	FACETS	0.653	0.505	0.824	0.326	0.252	0.412	SUBCLONAL	1	TRUE	1	0.208560277981514	3		602	357	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636715	8636715	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	77	374	1	ENST00000356435.5:c.194G>A	p.Ser65Asn	p.S65N	ENST00000356435		65	aGc/aAc	2/35	0.208560277981514	3	FACETS	0.957	0.844	1			1	CLONAL	2	TRUE	NA	0.208560277981514	3		375	426	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797325	135797325	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	36	407	0	ENST00000298552.3:c.544G>C	p.Ala182Pro	p.A182P	ENST00000298552	NM_001162426.1	182	Gcc/Ccc	7/23	0.208560277981514	1	FACETS	0.926	0.763	1	0.926	0.763	1	CLONAL	1	TRUE	0	0.208560277981514	1		407	334	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0021682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	51	855	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.108992609039892	3	FACETS	0.749	0.636	0.872	0.374	0.318	0.436	INDETERMINATE	1	FALSE	1	0.285003747180339	3		855	546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579533	7579533	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	51	1086	0	ENST00000269305.4:c.154C>T	p.Gln52Ter	p.Q52*	ENST00000269305	NM_001126112.2	52	Caa/Taa	4/11	1	2	FACETS	0.702	0.597	0.817	0.702	0.597	0.817	SUBCLONAL	1	FALSE	1	0.285003747180339	2		1086	510	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050909	49050909	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	64	675	0	ENST00000267163.4:c.2593G>T	p.Gly865Ter	p.G865*	ENST00000267163	NM_000321.2	865	Gga/Tga	25/27	1	2	FACETS	0.824	0.714	0.943	0.824	0.714	0.943	CLONAL	1	FALSE	1	0.285003747180339	2		675	545	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965103	25965103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	35	710	0	ENST00000435504.4:c.4103C>T	p.Pro1368Leu	p.P1368L	ENST00000435504		1368	cCt/cTt	13/13	1	2	FACETS	0.606	0.497	0.729	0.606	0.497	0.729	SUBCLONAL	1	FALSE	1	0.285003747180339	2		710	405	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686884	37686884	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	84	389	0	ENST00000447079.4:c.3788A>C	p.Glu1263Ala	p.E1263A	ENST00000447079	NM_015083.1	1263	gAg/gCg	14/14	0.249876453174064	1	FACETS	0.482	0.426	0.542	0.482	0.426	0.542	INDETERMINATE	1	TRUE	0	0.445192427205815	1		389	609	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577505	7577505	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs745425759	NA	P-0021908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	247	827	0	ENST00000269305.4:c.776A>T	p.Asp259Val	p.D259V	ENST00000269305	NM_001126112.2	259	gAc/gTc	7/11	NA	2	FACETS	0.929	0.872	0.988			1	INDETERMINATE	2	TRUE	NA	0.346529045741992	2		827	767	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134487	41134487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1340321845	NA	P-0021908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	91	670	0	ENST00000379561.5:c.1141C>T	p.Leu381Phe	p.L381F	ENST00000379561	NM_002015.3	381	Ctc/Ttc	2/3	0.346533815043066	3	FACETS	0.739	0.655	0.828	0.369	0.327	0.414	SUBCLONAL	1	TRUE	1	0.346529045741992	3		670	834	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958474	90958474	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	74	632	0	ENST00000265433.3:c.1964del	p.Leu655TyrfsTer2	p.L655Yfs*2	ENST00000265433	NM_002485.4	655	tTa/ta	13/16	0.250144375406872	5	FACETS	0.718	0.627	0.816	0.239	0.209	0.272	SUBCLONAL	1	TRUE	2	0.346529045741992	5		632	904	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	224	571	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.83561288227099	2		571	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0021911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	1224	971	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.282568422565198	3	FACETS	0.994	0.981	1			1	INDETERMINATE	3	TRUE	NA	0.83561288227099	3		973	1393	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925397	114925397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773530340	NA	P-0021911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	485	902	3	ENST00000543371.1:c.1475C>T	p.Ser492Leu	p.S492L	ENST00000543371	NM_001198531.1	492	tCg/tTg	14/14	0.83343269070393	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.83561288227099	1		905	668	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023348	27023348	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	107	197	0	ENST00000324856.7:c.454del	p.Gln152AsnfsTer80	p.Q152Nfs*80	ENST00000324856	NM_006015.4	152	Caa/aa	1/20	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.83561288227099	2		197	244	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369084	118369084	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0021911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	185	429	0	ENST00000534358.1:c.5803-1G>T		p.X1935_splice	ENST00000534358	NM_005933.3	1935			0.835654350547806	1	FACETS	0.958	0.911	1	0.958	0.911	1	CLONAL	1	TRUE	0	0.83561288227099	1		429	269	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287220	46287220	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757492254	NA	P-0021911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	148	504	1	ENST00000334344.6:c.5165G>A	p.Gly1722Asp	p.G1722D	ENST00000334344	NM_152641.2	1722	gGc/gAc	19/21	0.410921323118922	1	FACETS	0.391	0.359	0.424	0.391	0.359	0.424	INDETERMINATE	1	TRUE	0	0.83561288227099	1		505	528	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037920	49037923	+	frameshift_variant	Frame_Shift_Del	DEL	ATTC	ATTC	-	novel	NA	P-0021911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	272	621	2	ENST00000267163.4:c.2161_2164del	p.Phe721LysfsTer4	p.F721Kfs*4	ENST00000267163	NM_000321.2	720	aaATTC/aa	21/27	0.735092648119371	1	FACETS	0.952	0.913	0.99	0.952	0.913	0.99	CLONAL	1	TRUE	0	0.83561288227099	1		623	398	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660088	12660088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	335	631	2	ENST00000251849.4:c.133G>A	p.Asp45Asn	p.D45N	ENST00000251849	NM_002880.3	45	Gat/Aat	2/17	0.410921323118922	1	FACETS	0.685	0.654	0.717	0.685	0.654	0.717	INDETERMINATE	1	TRUE	0	0.83561288227099	1		633	681	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031926	26031926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	233	519	2	ENST00000244661.2:c.363G>A	p.Met121Ile	p.M121I	ENST00000244661	NM_003537.3	121	atG/atA	1/1	NA	2	FACETS	0.929	0.873	0.986			1	INDETERMINATE	1	TRUE	NA	0.83561288227099	2		521	600	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0021912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	251	971	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.488292209561239	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.488292209561239	1		973	770	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	178	729	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	1	2	FACETS	0.97	0.896	1	0.97	0.896	1	CLONAL	1	TRUE	1	0.488292209561239	2		729	752	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89842197	89842197	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	204	697	0	ENST00000389301.3:c.1853A>C	p.Tyr618Ser	p.Y618S	ENST00000389301	NM_000135.2	618	tAc/tCc	21/43	0.488292209561239	1	FACETS	0.984	0.917	1	0.984	0.917	1	CLONAL	1	TRUE	0	0.488292209561239	1		697	642	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158192	47158192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771882570	NA	P-0021912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	179	590	1	ENST00000409792.3:c.4507C>T	p.Pro1503Ser	p.P1503S	ENST00000409792	NM_014159.6	1503	Cct/Tct	4/21	0.488292209561239	1	FACETS	0.96	0.891	1	0.96	0.891	1	CLONAL	1	TRUE	0	0.488292209561239	1		591	577	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945483	151945490	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGATAC	CTGGATAC	-	novel	NA	P-0021912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	193	1106	0	ENST00000262189.6:c.2029_2036del	p.Val677ArgfsTer25	p.V677Rfs*25	ENST00000262189	NM_170606.2	677	GTATCCAGa/a	14/59	1	2	FACETS	0.62	0.572	0.669	0.62	0.572	0.669	SUBCLONAL	1	TRUE	1	0.488292209561239	2		1106	1276	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845757	68845757	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587780784	NA	P-0021913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	82	415	0	ENST00000261769.5:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000261769	NM_004360.3	335	Cga/Tga	7/16	0.377124536269026	1	FACETS	0.991	0.881	1	0.991	0.881	1	CLONAL	1	TRUE	0	0.377124536269026	1		415	356	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846204	156846204	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	95	687	0	ENST00000524377.1:c.1645G>A	p.Ala549Thr	p.A549T	ENST00000524377	NM_002529.3	549	Gcg/Acg	14/17	0.161111324141407	2	FACETS	0.73	0.65	0.815	0.365	0.325	0.408	INDETERMINATE	1	TRUE	0	0.377124536269026	2		687	690	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987418	2987421	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CCTC	CCTC	-	novel	NA	P-0021913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	45	682	0	ENST00000396946.4:c.8_11del	p.Gly3GlufsTer12	p.G3Efs*12	ENST00000396946	NM_032415.4	3	gGAGGa/ga	3/25	1	2	FACETS	0.389	0.326	0.459	0.389	0.326	0.459	SUBCLONAL	1	TRUE	1	0.377124536269026	2		682	613	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937596	76937600	+	frameshift_variant	Frame_Shift_Del	DEL	TCTCT	TCTCT	-	novel	NA	P-0021914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	141	493	0	ENST00000373344.5:c.3148_3152del	p.Arg1050Ter	p.R1050*	ENST00000373344	NM_000489.3	1050	AGAGAt/t	9/35	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.288712780182152	2		493	700	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220443	1220443	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	228	786	0	ENST00000326873.7:c.536C>G	p.Pro179Arg	p.P179R	ENST00000326873	NM_000455.4	179	cCg/cGg	4/10	0.604660668052525	1	FACETS	0.843	0.791	0.896	0.843	0.791	0.896	CLONAL	1	TRUE	0	0.604660668052525	1		786	624	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526287	189526287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	581	467	0	ENST00000264731.3:c.551C>T	p.Ser184Leu	p.S184L	ENST00000264731	NM_003722.4	184	tCg/tTg	4/14	0.5822303342034	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	1	0.604660668052525	4		467	1014	SUCCESS
ALK	238	MSKCC	GRCh37	2	29473981	29473981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768366852	NA	P-0021915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	267	727	1	ENST00000389048.3:c.2194G>A	p.Asp732Asn	p.D732N	ENST00000389048	NM_004304.4	732	Gac/Aac	12/29	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.604660668052525	2		728	877	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130378	11130378	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs866236389	NA	P-0021915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	447	632	0	ENST00000358026.2:c.2616+1G>A		p.X872_splice	ENST00000358026	NM_001128849.1	872			0.604660668052525	3	FACETS	0.975	0.935	1	0.975	0.935	1	CLONAL	2	TRUE	1	0.604660668052525	3		632	987	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18943136	18943136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	27	296	0	ENST00000262803.5:c.118C>T	p.Leu40Phe	p.L40F	ENST00000262803	NM_002911.3	40	Ctt/Ttt	1/24	1	2	FACETS	0.214	0.17	0.265	0.214	0.17	0.265	SUBCLONAL	1	TRUE	1	0.604660668052525	2		296	417	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841892	151841892	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	138	408	0	ENST00000262189.6:c.14249A>T	p.Tyr4750Phe	p.Y4750F	ENST00000262189	NM_170606.2	4750	tAt/tTt	55/59	0.604660668052525	1	FACETS	0.842	0.776	0.911	0.842	0.776	0.911	CLONAL	1	TRUE	0	0.604660668052525	1		408	378	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606265	93606265	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	230	678	0	ENST00000375746.1:c.85C>G	p.Leu29Val	p.L29V	ENST00000375746	NM_001174167.1	29	Ctg/Gtg	2/14	1	2	FACETS	0.879	0.821	0.939	0.879	0.821	0.939	CLONAL	1	TRUE	1	0.604660668052525	2		678	865	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763927	76763927	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	193	319	0	ENST00000373344.5:c.7381C>T	p.Gln2461Ter	p.Q2461*	ENST00000373344	NM_000489.3	2461	Cag/Tag	35/35	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.604660668052525	1		319	379	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99486217	99486217	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	197	717	0	ENST00000268035.6:c.3525del	p.Val1176CysfsTer69	p.V1176Cfs*69	ENST00000268035	NM_000875.3	1175	Ccc/cc	19/21	1	2	FACETS	0.952	0.884	1	0.952	0.884	1	CLONAL	1	TRUE	1	0.550188958035189	2		717	752	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032808	30032808	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	45	436	0	ENST00000338641.4:c.183del	p.Phe62LeufsTer61	p.F62Lfs*61	ENST00000338641	NM_000268.3	61	ttC/tt	2/16	0.467084589446901	0	FACETS	0.233	0.196	0.273			1	SUBCLONAL	1	TRUE	0	0.550188958035189	0		436	316	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0021918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	42	128	0	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	0.225666332122562	2	FACETS	0.859	0.735	0.988			1	INDETERMINATE	2	TRUE	NA	0.400906547900737	2		128	122	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949351	71949351	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1464980666	NA	P-0021918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	122	694	0	ENST00000298229.2:c.3731C>G	p.Pro1244Arg	p.P1244R	ENST00000298229	NM_001567.3	1244	cCg/cGg	28/28	0.251365088220737	4	FACETS	0.769	0.693	0.849	0.384	0.346	0.425	SUBCLONAL	1	TRUE	2	0.400906547900737	4		694	1109	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50830261	50830261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	160	487	1	ENST00000398568.2:c.2704C>T	p.Gln902Ter	p.Q902*	ENST00000398568	NM_001042412.1	902	Caa/Taa	18/18	0.400906547900737	2	FACETS	0.871	0.806	0.938	0.871	0.806	0.938	CLONAL	2	TRUE	0	0.400906547900737	2		488	458	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687562	29687562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555537228	NA	P-0021918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	219	636	3	ENST00000356175.3:c.8155G>A	p.Asp2719Asn	p.D2719N	ENST00000356175	NM_000267.3	2719	Gac/Aac	56/57	0.251365088220737	4	FACETS	0.862	0.803	0.923	0.862	0.803	0.923	CLONAL	2	TRUE	2	0.400906547900737	4		639	888	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325453	1325453	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0021918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1487	229	578	0	ENST00000400841.2:c.222C>G	p.Tyr74Ter	p.Y74*	ENST00000400841		74	taC/taG	3/6	0.400906547900737	5	FACETS	1	0.966	1			1	CLONAL	1	TRUE	NA	0.400906547900737	5		578	1716	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0021923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	78	625	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.498368468085046	3	FACETS	1	0.919	1	0.524	0.463	0.589	CLONAL	1	TRUE	1	0.498368468085046	3		625	373	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853326	68853326	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1555516592	NA	P-0021923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	228	810	0	ENST00000261769.5:c.1709A>G	p.Asn570Ser	p.N570S	ENST00000261769	NM_004360.3	570	aAt/aGt	11/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.498368468085046	2		810	804	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525934	148525934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	279	908	0	ENST00000320356.2:c.523G>A	p.Val175Met	p.V175M	ENST00000320356	NM_004456.4	175	Gtg/Atg	6/20	NA	2	FACETS	1	0.953	1			1	INDETERMINATE	2	TRUE	NA	0.498368468085046	2		908	558	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426836	121426836	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1364708195	NA	P-0021924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	122	442	1	ENST00000257555.6:c.526+1G>A		p.X176_splice	ENST00000257555		176			0.712009318630582	3	FACETS	0.776	0.704	0.851	0.259	0.234	0.284	SUBCLONAL	1	TRUE	0	0.780371942287665	3		443	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579491	7579491	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	459	766	0	ENST00000269305.4:c.196del	p.Met66CysfsTer57	p.M66Cfs*57	ENST00000269305	NM_001126112.2	66	Atg/tg	4/11	0.690693901468915	2	FACETS	0.897	0.869	0.924	0.897	0.869	0.924	CLONAL	2	TRUE	0	0.780371942287665	2		766	656	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342741	118342741	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	38	322	0	ENST00000534358.1:c.867G>C	p.Lys289Asn	p.K289N	ENST00000534358	NM_005933.3	289	aaG/aaC	3/36	0.780371942287665	3	FACETS	0.478	0.397	0.568	0.239	0.198	0.284	SUBCLONAL	1	TRUE	1	0.780371942287665	3		322	283	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188116	32188262	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCTCCTGGTGCTTCTCTCACCCTCCTTCTCTACCTCCCACCTCCTGATACCCTCTACCCCCATACCTGTGCGTCCAGGTGGGCAGAGGCAGGAGAAAGAGCCCACCCGGTCAATGCAGGTGGATCCCGGGGCACAGGTGGCAGCAA	TCCTCCTGGTGCTTCTCTCACCCTCCTTCTCTACCTCCCACCTCCTGATACCCTCTACCCCCATACCTGTGCGTCCAGGTGGGCAGAGGCAGGAGAAAGAGCCCACCCGGTCAATGCAGGTGGATCCCGGGGCACAGGTGGCAGCAA	-	novel	NA	P-0021924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	123	382	0	ENST00000375023.3:c.1079_1160-55del		p.X360_splice	ENST00000375023	NM_004557.3	360		6/30	0.780371942287665	5	FACETS	0.958	0.868	1	0.24	0.217	0.264	CLONAL	1	TRUE	1	0.780371942287665	5		382	714	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869547	117869547	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	123	590	0	ENST00000297338.2:c.647A>C	p.Lys216Thr	p.K216T	ENST00000297338	NM_006265.2	216	aAg/aCg	6/14	0.780371942287665	7	FACETS	0.825	0.744	0.91	0.206	0.186	0.228	CLONAL	1	TRUE	3	0.780371942287665	7		590	1128	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932825	39932825	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	200	711	0	ENST00000378444.4:c.1774C>A	p.Pro592Thr	p.P592T	ENST00000378444	NM_001123385.1	592	Cca/Aca	4/15	0.352391746794595	5	FACETS	1	0.977	1	0.376	0.348	0.405	INDETERMINATE	1	TRUE	2	0.780371942287665	5		711	986	SUCCESS
AR	367	MSKCC	GRCh37	X	66943552	66943552	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137852578	NA	P-0021928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	311	316	0	ENST00000374690.3:c.2632A>G	p.Thr878Ala	p.T878A	ENST00000374690	NM_000044.3	878	Act/Gct	8/8	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.850645346212477	1		316	371	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829761	72829761	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	480	897	0	ENST00000268489.5:c.6820C>T	p.Gln2274Ter	p.Q2274*	ENST00000268489	NM_006885.3	2274	Caa/Taa	9/10	0.850645346212477	1	FACETS	0.959	0.931	0.987	0.959	0.931	0.987	CLONAL	1	TRUE	0	0.850645346212477	1		897	676	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506954	186506954	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	203	354	0	ENST00000323963.5:c.1120A>G	p.Ile374Val	p.I374V	ENST00000323963		374	Ata/Gta	11/11	1	2	FACETS	0.996	0.934	1	0.996	0.934	1	CLONAL	1	TRUE	1	0.850645346212477	2		354	479	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922894	44922894	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	341	324	0	ENST00000377967.4:c.1757del	p.Gly586GlufsTer7	p.G586Efs*7	ENST00000377967	NM_021140.2	585	ctG/ct	16/29	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.850645346212477	1		324	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0021932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	353	808	3	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.354875875881435	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.354875875881435	2		811	912	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067884	30067884	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	157	805	0	ENST00000338641.4:c.1069G>T	p.Glu357Ter	p.E357*	ENST00000338641	NM_000268.3	357	Gag/Tag	11/16	0.354875875881435	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.354875875881435	1		805	699	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590736	189590736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558374141	NA	P-0022048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	67	645	2	ENST00000264731.3:c.1301C>T	p.Thr434Met	p.T434M	ENST00000264731	NM_003722.4	434	aCg/aTg	10/14	1	2	FACETS	0.537	0.469	0.61	0.537	0.469	0.61	SUBCLONAL	1	TRUE	1	0.63507765145649	2		647	393	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0022048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	53	337	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.818	0.707	0.936	0.818	0.707	0.936	CLONAL	1	TRUE	1	0.63507765145649	2		337	204	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022913	27022938	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGCCGCCGCCAGCAGCCTGGGCAA	CCCGCCGCCGCCAGCAGCCTGGGCAA	-	rs797045262	NA	P-0022048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	58	46	0	ENST00000324856.7:c.31_56del	p.Ser11AlafsTer91	p.S11Afs*91	ENST00000324856	NM_006015.4	7	CCCGCCGCCGCCAGCAGCCTGGGCAAc/c	1/20	0.149681237543191	2	FACETS	1	0.961	1	0.621	0.547	0.697	INDETERMINATE	1	TRUE	0	0.63507765145649	2		46	147	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0022048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	199	697	3	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.63507765145649	2		700	422	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244689	46244689	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	179	661	1	ENST00000334344.6:c.2783T>C	p.Ile928Thr	p.I928T	ENST00000334344	NM_152641.2	928	aTt/aCt	15/21	0.583953779135426	3	FACETS	0.785	0.731	0.841	0.523	0.487	0.561	SUBCLONAL	2	TRUE	0	0.63507765145649	3		662	473	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112406	115112406	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	173	519	0	ENST00000257566.3:c.1334G>C	p.Ser445Thr	p.S445T	ENST00000257566	NM_016569.3	445	aGc/aCc	7/8	0.583953779135426	3	FACETS	0.841	0.774	0.91	0.28	0.258	0.304	CLONAL	1	TRUE	0	0.63507765145649	3		519	854	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117423	115117471	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGGCTGGTATTTGTGCATGGAGTTCAATATAGTCTGCAGGGGCAGGGA	GGGGCTGGTATTTGTGCATGGAGTTCAATATAGTCTGCAGGGGCAGGGA	-	novel	NA	P-0022048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	122	488	0	ENST00000257566.3:c.718-15_751del		p.X240_splice	ENST00000257566	NM_016569.3	240		4/8	0.583953779135426	3	FACETS	1	0.98	1	0.781	0.725	0.836	CLONAL	2	TRUE	0	0.63507765145649	3		488	216	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134317	41134317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1200027367	NA	P-0022048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	91	557	2	ENST00000379561.5:c.1311G>A	p.Met437Ile	p.M437I	ENST00000379561	NM_002015.3	437	atG/atA	2/3	0.159786624127027	2	FACETS	1	0.948	1	0.541	0.487	0.596	INDETERMINATE	1	TRUE	0	0.63507765145649	2		559	265	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78921071	78921071	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs766428272	NA	P-0022048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	85	697	1	ENST00000306801.3:c.3185A>G	p.Asn1062Ser	p.N1062S	ENST00000306801	NM_020761.2	1062	aAt/aGt	27/34	0.63507765145649	3	FACETS	0.477	0.421	0.537	0.239	0.21	0.269	SUBCLONAL	1	TRUE	1	0.63507765145649	3		698	739	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313428	30313428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	138	624	1	ENST00000262643.3:c.1028G>A	p.Ser343Asn	p.S343N	ENST00000262643	NM_001238.2	343	aGc/aAc	11/12	1	2	FACETS	0.983	0.902	1	0.983	0.902	1	CLONAL	1	TRUE	1	0.63507765145649	2		625	442	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026807	48026807	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	122	526	0	ENST00000234420.5:c.1685A>C	p.Asp562Ala	p.D562A	ENST00000234420	NM_000179.2	562	gAt/gCt	4/10	0.159786624127027	2	FACETS	1	0.98	1	0.614	0.563	0.666	INDETERMINATE	1	TRUE	0	0.63507765145649	2		526	313	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952075	+	missense_variant	Missense_Mutation	DNP	GA	GA	TC	novel	NA	P-0022048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	11	437	1	ENST00000263967.3:c.3129_3130inv	p.Met1043_Asn1044delinsIleHis	p.M1043_N1044delinsIH	ENST00000263967	NM_006218.2	1043	atGAat/atTCat	21/21	1	2	FACETS	0.182	0.126	0.252	0.182	0.126	0.252	SUBCLONAL	1	TRUE	1	0.63507765145649	2		438	190	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960118	151960119	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	108	574	0	ENST00000262189.6:c.1281_1282insT	p.Asn428Ter	p.N428*	ENST00000262189	NM_170606.2	427	-/T	9/59	0.549294010761595	3	FACETS	1	0.984	1	0.714	0.649	0.78	CLONAL	1	TRUE	1	0.63507765145649	3		574	314	SUCCESS
APC	324	MSKCC	GRCh37	5	112175858	112175858	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0022114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	61	349	0	ENST00000257430.4:c.4567A>T	p.Arg1523Ter	p.R1523*	ENST00000257430	NM_000038.5	1523	Aga/Tga	16/16	0.566858717491573	1	FACETS	0.842	0.752	0.932	0.842	0.752	0.932	CLONAL	1	TRUE	0	0.744921966077962	1		349	122	SUCCESS
APC	324	MSKCC	GRCh37	5	112175875	112175905	+	frameshift_variant	Frame_Shift_Del	DEL	TCAGGAAAATGACAATGGGAATGAAACAGAA	TCAGGAAAATGACAATGGGAATGAAACAGAA	-	novel	NA	P-0022114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	44	325	0	ENST00000257430.4:c.4588_4618del	p.Glu1530SerfsTer25	p.E1530Sfs*25	ENST00000257430	NM_000038.5	1528	gtTCAGGAAAATGACAATGGGAATGAAACAGAA/gt	16/16	0.566858717491573	1	FACETS	0.713	0.618	0.81	0.713	0.618	0.81	SUBCLONAL	1	TRUE	0	0.744921966077962	1		325	104	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671946	30671946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	269	1071	3	ENST00000376406.3:c.5014C>A	p.Pro1672Thr	p.P1672T	ENST00000376406	NM_014641.2	1672	Cct/Act	10/15	0.102734689336981	4	FACETS	0.762	0.717	0.808	0.762	0.717	0.808	INDETERMINATE	2	TRUE	2	0.744921966077962	4		1074	827	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180900	106180900	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	16	500	0	ENST00000380013.4:c.3928A>G	p.Lys1310Glu	p.K1310E	ENST00000380013	NM_001127208.2	1310	Aag/Gag	7/11	1	2	FACETS	0.174	0.128	0.228	0.174	0.128	0.228	SUBCLONAL	1	TRUE	1	0.744921966077962	2		500	247	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0022245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	376	790	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.382838310574519	5	FACETS	1	0.957	1	1	0.995	1	CLONAL	4	TRUE	2	0.382838310574519	5		790	772	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0022245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	136	678	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.360081636644121	4	FACETS	1	0.909	1	0.5	0.454	0.549	CLONAL	1	TRUE	2	0.382838310574519	4		678	982	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0022245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	270	698	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.382838310574519	2	FACETS	0.945	0.891	1	0.945	0.891	1	CLONAL	2	TRUE	0	0.382838310574519	2		698	746	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462327	89462327	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	82	526	0	ENST00000336596.2:c.1799A>T	p.His600Leu	p.H600L	ENST00000336596	NM_005233.5	600	cAt/cTt	10/17	0.167702439264558	3	FACETS	1	0.953	1	0.382	0.338	0.429	INDETERMINATE	1	TRUE	0	0.382838310574519	3		526	445	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619221	37619221	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	104	595	0	ENST00000447079.4:c.897G>C	p.Gln299His	p.Q299H	ENST00000447079	NM_015083.1	299	caG/caC	1/14	0.421598986695733	2	FACETS	0.764	0.687	0.846	0.382	0.343	0.423	SUBCLONAL	1	TRUE	0	0.496542750152103	2		595	548	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070829	30070829	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0022359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	171	570	0	ENST00000338641.4:c.1345A>T	p.Lys449Ter	p.K449*	ENST00000338641	NM_000268.3	449	Aaa/Taa	13/16	0.421598986695733	2	FACETS	0.832	0.774	0.89	0.832	0.774	0.89	CLONAL	2	TRUE	0	0.496542750152103	2		570	414	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914747	39914747	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	77	318	0	ENST00000378444.4:c.4615G>C	p.Glu1539Gln	p.E1539Q	ENST00000378444	NM_001123385.1	1539	Gag/Cag	12/15	0.496542750152103	2	FACETS	0.857	0.757	0.962			1	CLONAL	1	TRUE	NA	0.496542750152103	2		318	362	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0022361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	40	629	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.546	0.452	0.651	0.546	0.452	0.651	SUBCLONAL	1	TRUE	1	0.17	2		629	862	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757274881	NA	P-0022361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1267	68	794	3	ENST00000269305.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	144	Cag/Tag	5/11	1	2	FACETS	0.599	0.519	0.687	0.599	0.519	0.687	SUBCLONAL	1	TRUE	1	0.17	2		797	1335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	rs886039483	NA	P-0022361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1185	76	707	0	ENST00000269305.4:c.376T>G	p.Tyr126Asp	p.Y126D	ENST00000269305	NM_001126112.2	126	Tac/Gac	5/11	1	2	FACETS	0.709	0.619	0.806	0.709	0.619	0.806	SUBCLONAL	1	TRUE	1	0.17	2		707	1261	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274217	5274217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	51	686	1	ENST00000357368.4:c.230G>A	p.Arg77His	p.R77H	ENST00000357368	NM_002850.3	77	cGc/cAc	3/38	1	2	FACETS	0.684	0.58	0.8	0.684	0.58	0.8	SUBCLONAL	1	TRUE	1	0.17	2		687	877	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420868	49420868	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	71	594	0	ENST00000301067.7:c.14881C>G	p.Pro4961Ala	p.P4961A	ENST00000301067	NM_003482.3	4961	Ccc/Gcc	48/54	1	2	FACETS	0.93	0.81	1	0.93	0.81	1	CLONAL	1	TRUE	1	0.17	2		594	898	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295434	1295435	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0022361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	13	36	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.944	0.694	1	1	0.928	1	CLONAL	3	TRUE	1	0.17	2		36	54	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0022400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	39	533	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.875	0.723	1	0.875	0.723	1	CLONAL	1	TRUE	1	0.14	2		534	637	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0022400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	34	808	3	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.551	0.449	0.668	0.551	0.449	0.668	SUBCLONAL	1	TRUE	1	0.14	2		811	881	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971029	21971029	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519852	NA	P-0022400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	74	551	0	ENST00000304494.5:c.329G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tGg/tAg	2/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.14	2		551	737	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0022400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	29	776	0	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	1	2	FACETS	0.499	0.399	0.614	0.499	0.399	0.614	SUBCLONAL	1	TRUE	1	0.14	2		776	830	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	19	424	2	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	0.665	0.504	0.856	0.665	0.504	0.856	SUBCLONAL	1	TRUE	1	0.14	2		426	408	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760960	133760960	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750196179	NA	P-0022400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	46	873	1	ENST00000318560.5:c.3283C>T	p.Arg1095Trp	p.R1095W	ENST00000318560	NM_005157.4	1095	Cgg/Tgg	11/11	1	2	FACETS	0.737	0.618	0.868	0.737	0.618	0.868	SUBCLONAL	1	TRUE	1	0.14	2		874	892	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546724	9546724	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	20	404	0	ENST00000353224.5:c.1298G>T	p.Arg433Leu	p.R433L	ENST00000353224	NM_177990.2	433	cGg/cTg	5/10	1	2	FACETS	0.754	0.576	0.963	0.754	0.576	0.963	CLONAL	1	TRUE	1	0.14	2		404	379	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532539	187532539	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0022400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	25	547	0	ENST00000441802.2:c.9853+1G>A		p.X3285_splice	ENST00000441802	NM_005245.3	3285			1	2	FACETS	0.815	0.642	1	0.815	0.642	1	CLONAL	1	TRUE	1	0.14	2		547	438	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151871289	151871289	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs754722659	NA	P-0022435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	50	752	0	ENST00000262189.6:c.9301A>G	p.Met3101Val	p.M3101V	ENST00000262189	NM_170606.2	3101	Atg/Gtg	39/59	NA	2	FACETS	0.41	0.347	0.48			1	INDETERMINATE	1	TRUE	NA	0.29	2		752	841	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510209	120510209	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022510-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	34	459	0	ENST00000256646.2:c.1300G>T	p.Val434Leu	p.V434L	ENST00000256646	NM_024408.3	434	Gtg/Ttg	8/34	1	2	FACETS	0.306	0.249	0.37	0.306	0.249	0.37	SUBCLONAL	1	TRUE	1	0.410233981930232	2		459	542	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022510-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	57	418	0	ENST00000256196.4:c.68G>C	p.Gly23Ala	p.G23A	ENST00000256196		23	gGc/gCc	1/6	0.206074958977841	1	FACETS	0.535	0.46	0.616	0.535	0.46	0.616	INDETERMINATE	1	TRUE	0	0.410233981930232	1		418	413	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435358	110435358	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022510-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	43	589	0	ENST00000375856.3:c.3043C>G	p.Pro1015Ala	p.P1015A	ENST00000375856	NM_003749.2	1015	Ccg/Gcg	1/2	0.410233981930232	1	FACETS	0.395	0.331	0.466	0.395	0.331	0.466	SUBCLONAL	1	TRUE	0	0.410233981930232	1		589	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578435	7578435	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022510-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	166	655	0	ENST00000269305.4:c.495del	p.Gln165HisfsTer5	p.Q165Hfs*5	ENST00000269305	NM_001126112.2	165	caG/ca	5/11	0.410233981930232	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.410233981930232	1		655	582	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268422	198268422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022510-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	212	422	0	ENST00000335508.6:c.1606C>T	p.Leu536Phe	p.L536F	ENST00000335508	NM_012433.2	536	Ctt/Ttt	12/25	0.235722849794674	4	FACETS	1	0.98	1			1	INDETERMINATE	2	TRUE	NA	0.410233981930232	4		422	651	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121332	29121332	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1060502695	NA	P-0022510-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	62	730	0	ENST00000328354.6:c.343T>A	p.Phe115Ile	p.F115I	ENST00000328354	NM_007194.3	115	Ttt/Att	3/15	1	2	FACETS	0.344	0.296	0.396	0.344	0.296	0.396	SUBCLONAL	1	TRUE	1	0.410233981930232	2		730	879	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437505	52437505	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022510-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	33	555	0	ENST00000460680.1:c.1656T>G	p.Asp552Glu	p.D552E	ENST00000460680	NM_004656.3	552	gaT/gaG	13/17	0.410233981930232	1	FACETS	0.255	0.207	0.309	0.255	0.207	0.309	SUBCLONAL	1	TRUE	0	0.410233981930232	1		555	501	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139873	55139873	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs866988382	NA	P-0022510-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	76	345	0	ENST00000257290.5:c.1534C>T	p.Arg512Ter	p.R512*	ENST00000257290	NM_006206.4	512	Cga/Tga	10/23	1	2	FACETS	0.98	0.865	1	0.98	0.865	1	CLONAL	1	TRUE	1	0.410233981930232	2		345	378	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156079	106156079	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022510-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	77	353	0	ENST00000380013.4:c.980C>A	p.Ser327Ter	p.S327*	ENST00000380013	NM_001127208.2	327	tCa/tAa	3/11	0.410233981930232	1	FACETS	0.904	0.8	1	0.904	0.8	1	CLONAL	1	TRUE	0	0.410233981930232	1		353	330	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249456	153249456	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022510-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	145	519	0	ENST00000281708.4:c.1322G>C	p.Arg441Pro	p.R441P	ENST00000281708	NM_033632.3	441	cGg/cCg	9/12	0.410233981930232	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.410233981930232	1		519	524	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86642524	86642524	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022510-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	28	430	0	ENST00000274376.6:c.1085A>T	p.Tyr362Phe	p.Y362F	ENST00000274376	NM_002890.2	362	tAt/tTt	7/25	0.410233981930232	1	FACETS	0.238	0.19	0.293	0.238	0.19	0.293	SUBCLONAL	1	TRUE	0	0.410233981930232	1		430	456	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032275	26032275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs780546148	NA	P-0022510-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	59	226	0	ENST00000244661.2:c.14A>T	p.Lys5Ile	p.K5I	ENST00000244661	NM_003537.3	5	aAa/aTa	1/1	0.279066313092424	1	FACETS	0.907	0.789	1	0.907	0.789	1	CLONAL	1	TRUE	0	0.410233981930232	1		226	252	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508067	106508067	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771734598	NA	P-0022510-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	51	182	0	ENST00000359195.3:c.61C>T	p.Arg21Trp	p.R21W	ENST00000359195	NM_002649.2	21	Cgg/Tgg	2/11	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.410233981930232	2		182	245	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5073735	5073735	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022510-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	105	403	0	ENST00000381652.3:c.1814C>G	p.Ser605Cys	p.S605C	ENST00000381652	NM_004972.3	605	tCt/tGt	14/25	0.410233981930232	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.410233981930232	1		403	373	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091793	29091793	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs758677815	NA	P-0022510-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	44	546	0	ENST00000328354.6:c.1164del	p.Thr389ProfsTer25	p.T389Pfs*25	ENST00000328354	NM_007194.3	388	ccC/cc	11/15	1	2	FACETS	0.346	0.289	0.409	0.346	0.289	0.409	SUBCLONAL	1	TRUE	1	0.410233981930232	2		546	620	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	111	855	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.3	3	FACETS	0.992	0.892	1	0.496	0.446	0.549	CLONAL	1	TRUE	1	0.37	3		855	717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0022534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	74	665	1	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	1	2	FACETS	0.365	0.318	0.416	0.365	0.318	0.416	SUBCLONAL	1	TRUE	1	0.37	2		666	1095	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	79	446	0	ENST00000304494.5:c.143C>T	p.Pro48Leu	p.P48L	ENST00000304494	NM_000077.4	48	cCg/cTg	1/3	1	2	FACETS	0.456	0.4	0.517	0.456	0.4	0.517	SUBCLONAL	1	TRUE	1	0.37	2		446	936	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057730	27057730	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1442	131	825	1	ENST00000324856.7:c.1438C>T	p.Gln480Ter	p.Q480*	ENST00000324856	NM_006015.4	480	Cag/Tag	3/20	1	2	FACETS	0.45	0.407	0.496	0.45	0.407	0.496	SUBCLONAL	1	TRUE	1	0.37	2		826	1573	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817863	3817864	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0022534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	86	701	0	ENST00000262367.5:c.3107_3108insG	p.Asp1037ArgfsTer14	p.D1037Rfs*14	ENST00000262367	NM_004380.2	1036	aca/acGa	16/31	1	2	FACETS	0.489	0.432	0.551	0.489	0.432	0.551	SUBCLONAL	1	TRUE	1	0.37	2		701	950	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39347524	39347524	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	67	546	0	ENST00000402219.2:c.40G>T	p.Glu14Ter	p.E14*	ENST00000402219	NM_005633.3	14	Gag/Tag	1/23	1	2	FACETS	0.416	0.361	0.477	0.416	0.361	0.477	SUBCLONAL	1	TRUE	1	0.37	2		546	870	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435289	18435289	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022548-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	329	445	0	ENST00000266497.5:c.277del	p.Ser93AlafsTer38	p.S93Afs*38	ENST00000266497		92	Aaa/aa	1/31	0.661515769612267	3	FACETS	0.882	0.84	0.925	0.882	0.84	0.925	CLONAL	2	TRUE	1	0.726020784656439	3		445	700	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613121	52613122	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0022548-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	230	571	0	ENST00000394830.3:c.3406_3407delinsTA	p.Gly1136Tyr	p.G1136Y	ENST00000394830	NM_018313.4	1136	GGc/TAc	22/30	1	2	FACETS	0.881	0.825	0.939	0.881	0.825	0.939	CLONAL	1	TRUE	1	0.726020784656439	2		571	719	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022617-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	394	571	0				ENST00000310581	NM_198253.2	-/1132			0.862714517266129	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.862714517266129	2		571	456	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259730	16259730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764509266	NA	P-0022617-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	556	565	1	ENST00000375759.3:c.6995G>A	p.Arg2332His	p.R2332H	ENST00000375759	NM_015001.2	2332	cGc/cAc	11/15	0.862714517266129	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.862714517266129	2		566	614	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322585	39322585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022617-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	355	768	0	ENST00000373001.3:c.407del	p.Gly136GlufsTer5	p.G136Efs*5	ENST00000373001	NM_022157.3	136	gGa/ga	2/7	0.862714517266129	2	FACETS	0.979	0.932	1	0.489	0.466	0.513	CLONAL	1	TRUE	0	0.862714517266129	2		768	841	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711922	89711922	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022617-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	589	611	1	ENST00000371953.3:c.540C>A	p.Tyr180Ter	p.Y180*	ENST00000371953	NM_000314.4	180	taC/taA	6/9	0.862714517266129	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.862714517266129	2		612	657	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293060	91293060	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0022617-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	306	576	0	ENST00000355112.3:c.562A>T	p.Lys188Ter	p.K188*	ENST00000355112	NM_000057.2	188	Aag/Tag	3/22	0.862714517266129	2	FACETS	1	0.962	1	0.508	0.482	0.534	CLONAL	1	TRUE	0	0.862714517266129	2		576	698	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654681	29654683	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0022617-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	486	511	0	ENST00000356175.3:c.5371_5373del	p.Phe1791del	p.F1791del	ENST00000356175	NM_000267.3	1790	acCTTc/acc	37/57	0.862714517266129	2	FACETS	0.99	0.969	1	0.99	0.969	1	CLONAL	2	TRUE	0	0.862714517266129	2		511	569	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285039	15285039	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022617-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	333	663	1	ENST00000263388.2:c.4576C>A	p.Arg1526Ser	p.R1526S	ENST00000263388	NM_000435.2	1526	Cgt/Agt	25/33	0.862714517266129	2	FACETS	1	0.976	1	0.521	0.496	0.546	CLONAL	1	TRUE	0	0.862714517266129	2		664	741	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117684026	117684026	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022617-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	217	503	0	ENST00000368508.3:c.3121C>A	p.Pro1041Thr	p.P1041T	ENST00000368508	NM_002944.2	1041	Cca/Aca	21/43	0.862714517266129	2	FACETS	1	0.943	1	0.502	0.472	0.533	CLONAL	1	TRUE	0	0.862714517266129	2		503	501	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022642-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	47	571	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		571	101	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0022671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	176	790	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.539848547912535	3	FACETS	0.9	0.837	0.964	0.9	0.837	0.964	CLONAL	2	TRUE	1	0.539848547912535	3		790	460	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602619	10602619	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1239985410	NA	P-0022671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	560	1045	0	ENST00000171111.5:c.959G>T	p.Arg320Leu	p.R320L	ENST00000171111	NM_203500.1	320	cGg/cTg	3/6	0.164498069677637	4	FACETS	1	0.988	1	1	0.988	1	INDETERMINATE	2	TRUE	2	0.539848547912535	4		1045	1494	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435378	110435378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs934565701	NA	P-0022671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1753	681	781	0	ENST00000375856.3:c.3023C>T	p.Pro1008Leu	p.P1008L	ENST00000375856	NM_003749.2	1008	cCc/cTc	1/2	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.539848547912535	2		781	2434	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042598	42042598	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0022671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	44	509	1	ENST00000219905.7:c.6793A>T	p.Arg2265Ter	p.R2265*	ENST00000219905	NM_001164273.1	2265	Aga/Tga	17/24	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.539848547912535	2		510	161	SUCCESS
BLM	641	MSKCC	GRCh37	15	91298157	91298157	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	27	293	0	ENST00000355112.3:c.1076C>A	p.Thr359Lys	p.T359K	ENST00000355112	NM_000057.2	359	aCa/aAa	5/22	1	2	FACETS	0.8	0.647	0.969	0.8	0.647	0.969	CLONAL	1	TRUE	1	0.539848547912535	2		293	125	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817720	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	83	469	1	ENST00000262367.5:c.3250dup	p.Ile1084AsnfsTer3	p.I1084Nfs*3	ENST00000262367	NM_004380.2	1084	atc/aAtc		0.164498069677637	4	FACETS	1	0.965	1	0.612	0.543	0.684	INDETERMINATE	1	TRUE	2	0.539848547912535	4		470	387	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223021	1223022	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	327	678	0	ENST00000326873.7:c.959dup	p.Pro321AlafsTer39	p.P321Afs*39	ENST00000326873	NM_000455.4	320	gtg/gTtg	8/10	0.539848547912535	1	FACETS	0.931	0.882	0.981	0.931	0.882	0.981	CLONAL	1	TRUE	0	0.539848547912535	1		678	950	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051264	13051264	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	69	332	1	ENST00000316448.5:c.700G>A	p.Glu234Lys	p.E234K	ENST00000316448	NM_004343.3	234	Gag/Aag	5/9	0.164498069677637	4	FACETS	1	0.975	1	0.743	0.654	0.836	INDETERMINATE	1	TRUE	2	0.539848547912535	4		333	265	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091814	29091814	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	73	671	0	ENST00000328354.6:c.1143G>C	p.Met381Ile	p.M381I	ENST00000328354	NM_007194.3	381	atG/atC	11/15	0.201962179856875	1	FACETS	0.721	0.637	0.808	0.721	0.637	0.808	INDETERMINATE	1	TRUE	0	0.539848547912535	1		671	274	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333864	70333864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528233201	NA	P-0022678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	52	514	2	ENST00000373644.4:c.1769G>A	p.Arg590Gln	p.R590Q	ENST00000373644	NM_030625.2	590	cGa/cAa	2/12	1	2	FACETS	0.671	0.57	0.782	0.671	0.57	0.782	SUBCLONAL	1	TRUE	1	0.228326265623557	2		516	679	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578166	7578183	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCAAACCAGACCTCAGGC	GCAAACCAGACCTCAGGC	-	novel	NA	P-0022678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	75	748	2	ENST00000269305.4:c.666_672+11del		p.X222_splice	ENST00000269305	NM_001126112.2	222		6/11	1	2	FACETS	0.547	0.478	0.623	0.547	0.478	0.623	SUBCLONAL	1	TRUE	1	0.228326265623557	2		750	1200	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0022805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	75	630	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.18	2		630	808	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482607	56482607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs993665271	NA	P-0022805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	87	875	2	ENST00000267101.3:c.1064C>T	p.Thr355Ile	p.T355I	ENST00000267101	NM_001982.3	355	aCc/aTc	9/28	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.18	2		877	891	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701295	43701295	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0022805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	51	490	0	ENST00000382044.4:c.5401-1G>A		p.X1801_splice	ENST00000382044	NM_001141980.1	1801			1	2	FACETS	0.991	0.842	1	0.991	0.842	1	CLONAL	1	TRUE	1	0.18	2		490	572	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167765	56167765	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	50	496	0	ENST00000399503.3:c.1331del	p.Pro444LeufsTer43	p.P444Lfs*43	ENST00000399503	NM_005921.1	444	Cct/ct	7/20	1	2	FACETS	0.864	0.732	1	0.864	0.732	1	CLONAL	1	TRUE	1	0.18	2		496	643	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419916	152419916	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	58	712	0	ENST00000206249.3:c.1603C>T	p.Pro535Ser	p.P535S	ENST00000206249	NM_000125.3	535	Ccc/Tcc	8/8	1	2	FACETS	0.822	0.705	0.95	0.822	0.705	0.95	CLONAL	1	TRUE	1	0.18	2		712	784	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177852	56177852	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs200778337	NA	P-0022805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	42	430	0	ENST00000399503.3:c.2825C>A	p.Thr942Lys	p.T942K	ENST00000399503	NM_005921.1	942	aCa/aAa	14/20	1	2	FACETS	0.858	0.716	1	0.858	0.716	1	CLONAL	1	TRUE	1	0.18	2		430	544	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	155	855	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.934	0.859	1	0.934	0.859	1	CLONAL	1	TRUE	1	0.53517142510622	2		855	620	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519999	NA	P-0022828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	156	726	1	ENST00000269305.4:c.716A>G	p.Asn239Ser	p.N239S	ENST00000269305	NM_001126112.2	239	aAc/aGc	7/11	0.53517142510622	1	FACETS	0.868	0.801	0.937	0.868	0.801	0.937	CLONAL	1	TRUE	0	0.53517142510622	1		727	492	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	171	695	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	0.888	0.819	0.959	0.888	0.819	0.959	CLONAL	1	TRUE	1	0.53517142510622	2		695	720	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911579	101911579	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	164	688	0	ENST00000374994.4:c.1507del	p.Met503CysfsTer44	p.M503Cfs*44	ENST00000374994	NM_004612.2	502	Aaa/aa	9/9	0.53517142510622	1	FACETS	0.963	0.892	1	0.963	0.892	1	CLONAL	1	TRUE	0	0.53517142510622	1		688	466	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0022950-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	56	633	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	0.7	0.599	0.812	0.7	0.599	0.812	SUBCLONAL	1	TRUE	1	0.22	2		633	727	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0022950-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	44	862	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	1	2	FACETS	0.538	0.45	0.636	0.538	0.45	0.636	SUBCLONAL	1	TRUE	1	0.22	2		862	744	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0023017-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	915	598	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.292722234959893	2	FACETS	0.948	0.923	0.973	1	0.998	1	CLONAL	4	TRUE	0	0.292722234959893	2		598	1648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0023017-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	468	778	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.279749085917799	2	FACETS	0.961	0.916	1	0.961	0.916	1	CLONAL	2	TRUE	0	0.292722234959893	2		778	1664	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279562	123279562	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121918499	NA	P-0023349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	197	980	0	ENST00000358487.5:c.870G>C	p.Trp290Cys	p.W290C	ENST00000358487	NM_000141.4	290	tgG/tgC	7/18	0.173270768308946	1	FACETS	0.911	0.842	0.982	0.911	0.842	0.982	INDETERMINATE	1	TRUE	0	0.332716468099296	1		980	1084	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105813	27105814	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0023349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	141	627	0	ENST00000324856.7:c.5426_5427dup	p.Asp1810LeufsTer6	p.D1810Lfs*6	ENST00000324856	NM_006015.4	1808	-/TT	20/20	0.332716468099296	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.332716468099296	1		627	626	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870235	155870235	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	203	974	0	ENST00000368323.3:c.604del	p.Ser202ValfsTer6	p.S202Vfs*6	ENST00000368323	NM_006912.5	202	Agt/gt	6/6	0.173270768308946	1	FACETS	0.984	0.912	1	0.984	0.912	1	INDETERMINATE	1	TRUE	0	0.332716468099296	1		974	1034	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0023369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	94	419	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	0.219579934567642	1	FACETS	0.766	0.685	0.852	0.766	0.685	0.852	INDETERMINATE	1	TRUE	0	0.416860654850427	1		419	466	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988976	85988976	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	93	268	1	ENST00000263360.6:c.1142A>G	p.Asn381Ser	p.N381S	ENST00000263360	NM_003797.3	381	aAt/aGt	11/12	0.219579934567642	1	FACETS	0.843	0.754	0.936	0.843	0.754	0.936	INDETERMINATE	1	TRUE	0	0.416860654850427	1		269	419	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872008	35872008	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	126	348	0	ENST00000216797.5:c.605T>C	p.Leu202Ser	p.L202S	ENST00000216797	NM_020529.2	202	tTg/tCg	4/6	0.416860654850427	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.416860654850427	1		348	474	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221236	1221236	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	204	590	0	ENST00000326873.7:c.762del	p.Phe255SerfsTer32	p.F255Sfs*32	ENST00000326873	NM_000455.4	253	taC/ta	6/10	0.416860654850427	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.416860654850427	1		590	725	SUCCESS
AR	367	MSKCC	GRCh37	X	66766343	66766343	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	23	186	1	ENST00000374690.3:c.1355G>A	p.Gly452Asp	p.G452D	ENST00000374690	NM_000044.3	452	gGt/gAt	1/8	1	2	FACETS	0.45	0.352	0.563	0.45	0.352	0.563	SUBCLONAL	1	TRUE	1	0.416860654850427	2		187	245	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577280	64577280	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	56	1032	0	ENST00000312049.6:c.302T>A	p.Val101Asp	p.V101D	ENST00000312049	NM_130799.2	101	gTc/gAc	2/10	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.148093913028626	2		1032	623	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139310	108139310	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	55	1055	0	ENST00000278616.4:c.2813del	p.Pro938LeufsTer11	p.P938Lfs*11	ENST00000278616	NM_000051.3	938	Cct/ct	18/63	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.148093913028626	2		1055	658	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220549	98220549	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	23	669	0	ENST00000331920.6:c.2914del	p.Ala972ProfsTer23	p.A972Pfs*23	ENST00000331920	NM_000264.3	972	Gcc/cc	18/24	1	2	FACETS	0.75	0.584	0.943	0.75	0.584	0.943	CLONAL	1	TRUE	1	0.148093913028626	2		669	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0023476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	288	885	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	NA	2	FACETS	1	0.967	1			1	INDETERMINATE	3	TRUE	NA	0.273774384543625	2		885	682	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691025	NA	P-0023567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	134	649	6	ENST00000269305.4:c.785G>T	p.Gly262Val	p.G262V	ENST00000269305	NM_001126112.2	262	gGt/gTt	8/11	0.173097604571545	3	FACETS	1	0.977	1	0.811	0.739	0.885	CLONAL	2	TRUE	0	0.205217014001705	3		655	592	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244226	46244226	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	43	532	0	ENST00000334344.6:c.2320C>G	p.Pro774Ala	p.P774A	ENST00000334344	NM_152641.2	774	Cca/Gca	15/21	0.205217014001705	2	FACETS	0.955	0.8	1	0.477	0.4	0.563	CLONAL	1	TRUE	0	0.205217014001705	2		532	439	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602379	10602379	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	61	808	5	ENST00000171111.5:c.1199C>G	p.Thr400Ser	p.T400S	ENST00000171111	NM_203500.1	400	aCc/aGc	3/6	0.205217014001705	2	FACETS	0.869	0.749	1	0.435	0.374	0.5	CLONAL	1	TRUE	0	0.205217014001705	2		813	684	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0023585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	122	790	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.246973527959662	1	FACETS	0.905	0.817	0.998	0.905	0.817	0.998	CLONAL	1	TRUE	0	0.247146041767646	1		790	956	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0023585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	121	971	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.247146041767646	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.247146041767646	1		973	753	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0023586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	45	732	1	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.30923462196041	1	FACETS	0.324	0.271	0.382	0.324	0.271	0.382	SUBCLONAL	1	TRUE	0	0.30923462196041	1		733	760	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665728	29665728	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	65	341	0	ENST00000356175.3:c.6763G>T	p.Glu2255Ter	p.E2255*	ENST00000356175	NM_000267.3	2255	Gag/Tag	45/57	0.30923462196041	1	FACETS	0.836	0.727	0.953	0.836	0.727	0.953	CLONAL	1	TRUE	0	0.30923462196041	1		341	425	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181953	38181953	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201772694	NA	P-0023586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	40	622	1	ENST00000396334.3:c.577C>T	p.Arg193Trp	p.R193W	ENST00000396334	NM_002468.4	193	Cgg/Tgg	3/5	0.308822406216703	2	FACETS	0.384	0.318	0.458	0.192	0.159	0.229	SUBCLONAL	1	TRUE	0	0.30923462196041	2		623	673	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971205	21971217	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GACCTGCCAGAGA	GACCTGCCAGAGA	-	novel	NA	P-0023586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	38	578	0	ENST00000304494.5:c.151-10_153del		p.X51_splice	ENST00000304494	NM_000077.4	51		2/3	0.30923462196041	1	FACETS	0.471	0.389	0.562	0.471	0.389	0.562	SUBCLONAL	1	TRUE	0	0.30923462196041	1		578	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0023591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	380	785	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.128047611888155	3	FACETS	1	0.995	1	0.683	0.651	0.715	INDETERMINATE	1	TRUE	1	0.844681401218263	3		786	937	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578277	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs1555525902	NA	P-0023591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	297	644	1	ENST00000269305.4:c.572_574del	p.Pro191del	p.P191del	ENST00000269305	NM_001126112.2	191	cCTCag/cag	6/11	0.128047611888155	3	FACETS	1	0.994	1	0.713	0.676	0.751	INDETERMINATE	1	TRUE	1	0.844681401218263	3		645	701	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469672	NA	P-0023591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	349	680	0	ENST00000374080.3:c.131G>A	p.Gly44Asp	p.G44D	ENST00000374080		44	gGt/gAt	2/45	NA	2	FACETS	1	0.958	1			1	INDETERMINATE	1	TRUE	NA	0.844681401218263	2		680	821	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14303257	14303257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	316	809	0	ENST00000256196.4:c.418G>A	p.Glu140Lys	p.E140K	ENST00000256196		140	Gaa/Aaa	5/6	0.844681401218263	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.844681401218263	1		809	410	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549163	87549163	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	88	614	0	ENST00000277120.3:c.1720T>A	p.Tyr574Asn	p.Y574N	ENST00000277120		574	Tat/Aat	15/19	0.128047611888155	3	FACETS	0.445	0.394	0.499	0.222	0.197	0.25	INDETERMINATE	1	TRUE	1	0.844681401218263	3		614	666	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931811	39931811	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	316	732	1	ENST00000378444.4:c.2788C>A	p.Pro930Thr	p.P930T	ENST00000378444	NM_001123385.1	930	Cca/Aca	4/15	NA	2	FACETS	0.995	0.945	1			1	INDETERMINATE	1	TRUE	NA	0.844681401218263	2		733	752	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871758	12871758	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0023592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	73	190	0	ENST00000228872.4:c.476-1G>C		p.X159_splice	ENST00000228872	NM_004064.3	159			0.468671065524469	1	FACETS	0.723	0.642	0.808	0.723	0.642	0.808	SUBCLONAL	1	TRUE	0	0.599267546744725	1		190	236	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624296	89624296	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs786201995	NA	P-0023592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	151	478	0	ENST00000371953.3:c.70G>C	p.Asp24His	p.D24H	ENST00000371953	NM_000314.4	24	Gac/Cac	1/9	0.522249022499572	1	FACETS	0.642	0.59	0.695	0.642	0.59	0.695	SUBCLONAL	1	TRUE	0	0.599267546744725	1		478	550	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745986	745986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371352602	NA	P-0023592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	183	562	2	ENST00000314574.4:c.536G>A	p.Arg179Gln	p.R179Q	ENST00000314574	NM_005433.3	179	cGa/cAa	5/12	NA	2	FACETS	0.651	0.601	0.703			1	INDETERMINATE	1	TRUE	NA	0.599267546744725	2		564	938	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0023592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	139	475	1	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.522249022499572	1	FACETS	0.696	0.638	0.755	0.696	0.638	0.755	SUBCLONAL	1	TRUE	0	0.599267546744725	1		476	467	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047495	49047495	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0023592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	152	398	0	ENST00000267163.4:c.2490-1G>C		p.X830_splice	ENST00000267163	NM_000321.2	830			0.53712574186722	2	FACETS	0.972	0.894	1	0.486	0.447	0.526	CLONAL	1	TRUE	0	0.599267546744725	2		398	522	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166280	118166280	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	122	335	0	ENST00000369448.3:c.793del	p.Thr265LeufsTer2	p.T265Lfs*2	ENST00000369448	NM_017709.3	264	Aaa/aa	2/2	0.599267546744725	1	FACETS	0.859	0.787	0.933	0.859	0.787	0.933	CLONAL	1	TRUE	0	0.599267546744725	1		335	332	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343276	118343276	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	158	361	0	ENST00000534358.1:c.1402C>T	p.His468Tyr	p.H468Y	ENST00000534358	NM_005933.3	468	Cac/Tac	3/36	NA	2	FACETS	0.947	0.872	1			1	INDETERMINATE	1	TRUE	NA	0.599267546744725	2		361	557	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426782	121426782	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	62	521	0	ENST00000257555.6:c.473A>C	p.Lys158Thr	p.K158T	ENST00000257555		158	aAg/aCg	2/10	0.21267849093977	1	FACETS	0.186	0.16	0.214	0.186	0.16	0.214	INDETERMINATE	1	TRUE	0	0.599267546744725	1		521	779	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43769806	43769806	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	47	541	1	ENST00000382044.4:c.940C>T	p.Gln314Ter	p.Q314*	ENST00000382044	NM_001141980.1	314	Cag/Tag	8/28	0.599267546744725	1	FACETS	0.202	0.17	0.238	0.202	0.17	0.238	SUBCLONAL	1	TRUE	0	0.599267546744725	1		542	543	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347549	89347549	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs938676909	NA	P-0023592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	211	566	1	ENST00000301030.4:c.5401G>A	p.Glu1801Lys	p.E1801K	ENST00000301030	NM_001256183.1	1801	Gaa/Aaa	9/13	0.453958912427517	1	FACETS	0.733	0.684	0.783	0.733	0.684	0.783	SUBCLONAL	1	TRUE	0	0.599267546744725	1		567	673	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530166	63530166	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	231	472	0	ENST00000307078.5:c.2269C>T	p.His757Tyr	p.H757Y	ENST00000307078	NM_004655.3	757	Cac/Tac	10/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.599267546744725	2		472	714	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632383	1632383	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0023592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	209	619	0	ENST00000344749.5:c.167C>G	p.Ser56Ter	p.S56*	ENST00000344749	NM_001136139.2	56	tCa/tGa	4/19	0.414921207100131	1	FACETS	0.65	0.606	0.697	0.65	0.606	0.697	SUBCLONAL	1	TRUE	0	0.599267546744725	1		619	751	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11019791	11019791	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs779696123	NA	P-0023592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	126	402	0	ENST00000327064.4:c.466C>G	p.Leu156Val	p.L156V	ENST00000327064	NM_199141.1	156	Ctg/Gtg	4/16	0.414921207100131	1	FACETS	0.569	0.517	0.622	0.569	0.517	0.622	SUBCLONAL	1	TRUE	0	0.599267546744725	1		402	518	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11019874	11019874	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	147	483	0	ENST00000327064.4:c.549C>G	p.Phe183Leu	p.F183L	ENST00000327064	NM_199141.1	183	ttC/ttG	4/16	0.414921207100131	1	FACETS	0.539	0.494	0.587	0.539	0.494	0.587	SUBCLONAL	1	TRUE	0	0.599267546744725	1		483	637	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223175	36223175	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	79	782	0	ENST00000222270.7:c.5725C>G	p.Pro1909Ala	p.P1909A	ENST00000222270	NM_014727.1	1909	Ccc/Gcc	28/37	1	2	FACETS	0.227	0.199	0.258	0.227	0.199	0.258	SUBCLONAL	1	TRUE	1	0.599267546744725	2		782	1159	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130170	143130170	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	119	491	0	ENST00000262992.4:c.846G>C	p.Glu282Asp	p.E282D	ENST00000262992	NM_001101669.1	282	gaG/gaC	11/24	0.124824834690319	0	FACETS	0.264	0.239	0.291			1	INDETERMINATE	1	TRUE	0	0.599267546744725	0		491	602	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045687	26045687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	46	248	1	ENST00000540144.1:c.49C>T	p.Pro17Ser	p.P17S	ENST00000540144	NM_003531.2	17	Ccg/Tcg	1/1	0.322435643684682	3	FACETS	0.522	0.441	0.612	0.261	0.22	0.306	INDETERMINATE	1	TRUE	1	0.599267546744725	3		249	382	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411944	116411944	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	226	703	0	ENST00000397752.3:c.2929A>T	p.Thr977Ser	p.T977S	ENST00000397752	NM_000245.2	977	Act/Tct	14/21	0.599267546744725	1	FACETS	0.76	0.711	0.81	0.76	0.711	0.81	SUBCLONAL	1	TRUE	0	0.599267546744725	1		703	695	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971292	13971292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772105404	NA	P-0023594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	306	697	2	ENST00000405192.2:c.637C>T	p.Arg213Cys	p.R213C	ENST00000405192	NM_001163147.1	213	Cgc/Tgc	8/12	0.378603958230567	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.378603958230567	3		699	836	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874092	151874093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	367	843	0	ENST00000262189.6:c.8445dup	p.Ser2816IlefsTer6	p.S2816Ifs*6	ENST00000262189	NM_170606.2	2815	-/A	38/59	0.378603958230567	3	FACETS	0.965	0.915	1	0.965	0.915	1	CLONAL	2	TRUE	1	0.378603958230567	3		843	1195	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856545	111856545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1157707616	NA	P-0023594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	124	429	0	ENST00000341259.2:c.596C>T	p.Ala199Val	p.A199V	ENST00000341259	NM_005475.2	199	gCg/gTg	2/8	0.180890490258254	3	FACETS	1	0.984	1	0.71	0.644	0.777	INDETERMINATE	1	TRUE	1	0.378603958230567	3		429	549	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572942	7572942	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs749817236	NA	P-0023594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	177	756	0	ENST00000269305.4:c.1167del	p.Pro390LeufsTer32	p.P390Lfs*32	ENST00000269305	NM_001126112.2	389	ggG/gg	11/11	0.378603958230567	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.378603958230567	1		756	625	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470500	25470500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	218	925	0	ENST00000264709.3:c.974C>T	p.Thr325Ile	p.T325I	ENST00000264709	NM_175629.2	325	aCc/aTc	8/23	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.378603958230567	2		925	995	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519999	NA	P-0023596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	71	726	1	ENST00000269305.4:c.716A>G	p.Asn239Ser	p.N239S	ENST00000269305	NM_001126112.2	239	aAc/aGc	7/11	0.252915381596	3	FACETS	1	0.966	1	0.812	0.725	0.902	CLONAL	2	TRUE	0	0.383677714160153	3		727	181	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249017	55249018	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCA	rs1554350381	NA	P-0023596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	329	700	2	ENST00000275493.2:c.2317_2319dup	p.His773dup	p.H773dup	ENST00000275493	NM_005228.3	773	ccc/ccCCAc	20/28	0.383677714160153	16	FACETS	1	0.976	1			1	CLONAL	12	TRUE	NA	0.383677714160153	16		702	515	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16097825	16097825	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs73281920	NA	P-0023596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	18	626	0	ENST00000268712.3:c.59A>C	p.Tyr20Ser	p.Y20S	ENST00000268712	NM_006311.3	20	tAt/tCt	2/46	0.252915381596	3	FACETS	0.766	0.581	0.98	0.255	0.193	0.327	CLONAL	1	TRUE	0	0.383677714160153	3		626	146	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054402	42054402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752413385	NA	P-0023596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	13	490	1	ENST00000219905.7:c.7586G>A	p.Arg2529Lys	p.R2529K	ENST00000219905	NM_001164273.1	2529	aGa/aAa	22/24	0.305171415683619	2	FACETS	0.32	0.228	0.431	0.16	0.114	0.216	SUBCLONAL	1	TRUE	0	0.383677714160153	2		491	212	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132468	11132468	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	11	713	0	ENST00000358026.2:c.2684A>T	p.Gln895Leu	p.Q895L	ENST00000358026	NM_001128849.1	895	cAg/cTg	19/36	0.383677714160153	1	FACETS	0.333	0.231	0.459	0.333	0.231	0.459	SUBCLONAL	1	TRUE	0	0.383677714160153	1		713	139	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16097870	16097870	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs76145228	NA	P-0023596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	17	260	0	ENST00000268712.3:c.14G>T	p.Gly5Val	p.G5V	ENST00000268712	NM_006311.3	5	gGt/gTt	2/46	0.252915381596	3	FACETS	1	0.904	1	0.482	0.369	0.61	CLONAL	1	TRUE	0	0.383677714160153	3		260	73	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197240	26197240	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	13	479	1	ENST00000356476.2:c.239A>G	p.Lys80Arg	p.K80R	ENST00000356476		80	aAg/aGg	1/1	0.309171359707509	2	FACETS	1	0.847	1	0.627	0.461	0.817	CLONAL	1	TRUE	0	0.383677714160153	2		480	54	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0023597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	549	796	1	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.641375880795414	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.641375880795414	2		797	826	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157406018	157406018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs974267163	NA	P-0023597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	100	605	1	ENST00000346085.5:c.2260A>G	p.Ile754Val	p.I754V	ENST00000346085	NM_020732.3	754	Atc/Gtc	6/20	0.606254489894529	3	FACETS	0.561	0.501	0.625	0.281	0.25	0.313	SUBCLONAL	1	TRUE	1	0.641375880795414	3		606	734	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750789	128750789	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	1013	654	0	ENST00000377970.2:c.326C>G	p.Ser109Cys	p.S109C	ENST00000377970	NM_002467.4	109	tCc/tGc	2/3	0.641375880795414	5	FACETS	1	0.994	1	1	0.998	1	CLONAL	4	TRUE	2	0.641375880795414	5		654	1480	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317539	1317539	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	338	711	0	ENST00000400841.2:c.526G>T	p.Asp176Tyr	p.D176Y	ENST00000400841		176	Gat/Tat	5/6	0.366887961718703	4	FACETS	0.803	0.76	0.847	0.803	0.76	0.847	INDETERMINATE	2	TRUE	2	0.641375880795414	4		711	1077	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058331	42058331	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023650-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	63	389	0	ENST00000219905.7:c.8051T>C	p.Leu2684Pro	p.L2684P	ENST00000219905	NM_001164273.1	2684	cTg/cCg	24/24	1	2	FACETS	0.907	0.786	1	0.907	0.786	1	CLONAL	1	FALSE	1	0.3	2		389	463	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231497	5231497	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200771602	NA	P-0023801-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	185	826	0	ENST00000357368.4:c.1979C>T	p.Pro660Leu	p.P660L	ENST00000357368	NM_002850.3	660	cCg/cTg	14/38	1	2	FACETS	0.442	0.407	0.478	0.442	0.407	0.478	SUBCLONAL	1	TRUE	1	0.754773666078804	2		826	1109	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76931719	76931719	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0023801-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	129	662	0	ENST00000373344.5:c.3809+2T>A		p.X1270_splice	ENST00000373344	NM_000489.3	1270			1	2	FACETS	0.418	0.379	0.459	0.418	0.379	0.459	SUBCLONAL	1	TRUE	1	0.754773666078804	2		662	818	SUCCESS
AR	367	MSKCC	GRCh37	X	66765182	66765182	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023839-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	15	131	0	ENST00000374690.3:c.194A>T	p.Gln65Leu	p.Q65L	ENST00000374690	NM_000044.3	65	cAg/cTg	1/8	0.3	6	FACETS	0.702	0.513	0.93	0.117	0.085	0.155	CLONAL	1	TRUE	0	0.21	6		131	289	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058201	42058201	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0023839-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	29	252	0	ENST00000219905.7:c.7922-1G>A		p.X2641_splice	ENST00000219905	NM_001164273.1	2641			1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.21	2		252	245	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170723	11170723	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1303089960	NA	P-0023839-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	64	755	2	ENST00000358026.2:c.4867C>T	p.Arg1623Trp	p.R1623W	ENST00000358026	NM_001128849.1	1623	Cgg/Tgg	35/36	1	2	FACETS	0.762	0.658	0.875	0.762	0.658	0.875	SUBCLONAL	1	TRUE	1	0.21	2		757	800	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128201287	128201287	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023839-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	61	607	0	ENST00000265960.3:c.1448A>C	p.Asn483Thr	p.N483T	ENST00000265960	NM_001006617.1	483	aAc/aCc	12/12	1	2	FACETS	0.868	0.748	0.999	0.868	0.748	0.999	CLONAL	1	TRUE	1	0.21	2		607	669	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937238	36937251	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGGCACTGGCTGT	GGGGCACTGGCTGT	-	novel	NA	P-0023849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	10	861	0	ENST00000361632.4:c.1072-4_1081del		p.X358_splice	ENST00000361632		358		9/16	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		861	119	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128016871	128016871	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0023850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	17	300	0	ENST00000285398.2:c.2217+1G>A		p.X739_splice	ENST00000285398	NM_000122.1	739			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		300	275	SUCCESS
APC	324	MSKCC	GRCh37	5	112162804	112162804	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs863225313	NA	P-0023903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	18	331	0	ENST00000257430.4:c.1409-1G>A		p.X470_splice	ENST00000257430	NM_000038.5	470			0.315290083060508	2	FACETS	1	0.809	1	1	0.809	1	CLONAL	2	TRUE	0	0.315290083060508	2		331	55	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs967461896	NA	P-0023903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	23	560	0	ENST00000269305.4:c.526T>G	p.Cys176Gly	p.C176G	ENST00000269305	NM_001126112.2	176	Tgc/Ggc	5/11	0.315290083060508	3	FACETS	1	0.895	1	1	0.895	1	CLONAL	2	TRUE	1	0.315290083060508	3		560	71	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356200	66356200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770587480	NA	P-0023903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	10	525	0	ENST00000273854.3:c.1297G>A	p.Ala433Thr	p.A433T	ENST00000273854	NM_004439.5	433	Gct/Act	5/18	0.177807742144316	1	FACETS	0.712	0.49	0.983	0.712	0.49	0.983	INDETERMINATE	1	TRUE	0	0.315290083060508	1		525	75	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	175	533	1				ENST00000310581	NM_198253.2	-/1132			0.45484770348293	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	0	0.45484770348293	2		534	384	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608604	189608604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	165	885	2	ENST00000264731.3:c.1679C>T	p.Ser560Leu	p.S560L	ENST00000264731	NM_003722.4	560	tCa/tTa	13/14	0.382231542449055	4	FACETS	1	0.988	1	0.705	0.648	0.763	CLONAL	1	TRUE	2	0.45484770348293	4		887	749	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	553	785	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.442311493571151	5	FACETS	0.966	0.937	0.995	0.966	0.937	0.995	CLONAL	5	TRUE	0	0.45484770348293	5		786	847	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845912	156845912	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	88	889	0	ENST00000524377.1:c.1542G>A	p.Trp514Ter	p.W514*	ENST00000524377	NM_002529.3	514	tgG/tgA	13/17	0.457567084656107	3	FACETS	0.647	0.573	0.726	0.324	0.286	0.363	SUBCLONAL	1	TRUE	1	0.45484770348293	3		889	734	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041073	29041073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	203	660	0	ENST00000282397.4:c.355G>A	p.Glu119Lys	p.E119K	ENST00000282397	NM_002019.4	119	Gaa/Aaa	3/30	0.457567084656107	3	FACETS	0.938	0.876	1	0.938	0.876	1	CLONAL	2	TRUE	1	0.45484770348293	3		660	584	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275648	41275648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397514554	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	163	635	1	ENST00000349496.5:c.1543C>T	p.Arg515Ter	p.R515*	ENST00000349496	NM_001904.3	515	Cga/Tga	10/15	0.382231542449055	4	FACETS	0.821	0.756	0.888	0.821	0.756	0.888	CLONAL	2	TRUE	2	0.45484770348293	4		636	635	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857158	9857158	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	154	579	0	ENST00000330684.3:c.4243G>A	p.Asp1415Asn	p.D1415N	ENST00000330684	NM_001134407.1	1415	Gac/Aac	13/13	0.457567084656107	4	FACETS	0.892	0.821	0.966	0.892	0.821	0.966	CLONAL	2	TRUE	2	0.45484770348293	4		579	552	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285570	46285570	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs78222561	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	167	381	0	ENST00000334344.6:c.4930C>T	p.Gln1644Ter	p.Q1644*	ENST00000334344	NM_152641.2	1644	Cag/Tag	17/21	0.457567084656107	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.45484770348293	4		381	490	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020539	69020539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	111	716	0	ENST00000288368.4:c.2911G>A	p.Asp971Asn	p.D971N	ENST00000288368	NM_024870.2	971	Gat/Aat	24/40	0.319800568301483	3	FACETS	1	0.96	1	0.562	0.507	0.62	CLONAL	1	TRUE	1	0.45484770348293	3		716	533	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347750	89347750	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	206	699	0	ENST00000301030.4:c.5200G>A	p.Asp1734Asn	p.D1734N	ENST00000301030	NM_001256183.1	1734	Gac/Aac	9/13	0.400401016454565	4	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	2	0.45484770348293	4		699	647	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747137	40747138	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	71	584	2	ENST00000373198.4:c.2944_2945delinsTT	p.Pro982Leu	p.P982L	ENST00000373198	NM_133170.3	982	CCg/TTg	22/32	0.457567084656107	3	FACETS	0.779	0.681	0.884	0.389	0.34	0.442	SUBCLONAL	1	TRUE	1	0.45484770348293	3		586	492	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670364	134670364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	111	546	0	ENST00000398015.3:c.275C>T	p.Thr92Ile	p.T92I	ENST00000398015	NM_004441.4	92	aCt/aTt	3/16	0.382231542449055	4	FACETS	1	0.979	1	0.669	0.603	0.737	CLONAL	1	TRUE	2	0.45484770348293	4		546	531	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117004	193117004	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267598258	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	254	538	0	ENST00000367435.3:c.737C>T	p.Ser246Phe	p.S246F	ENST00000367435	NM_024529.4	246	tCc/tTc	8/17	0.457567084656107	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.45484770348293	3		538	597	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163816	72163816	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1383099540	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	249	483	4	ENST00000357731.5:c.542C>T	p.Pro181Leu	p.P181L	ENST00000357731	NM_173808.2	181	cCa/cTa	4/7	0.448749058270197	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	1	0.45484770348293	4		487	487	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400982	72400982	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	59	475	0	ENST00000357731.5:c.189A>C	p.Glu63Asp	p.E63D	ENST00000357731	NM_173808.2	63	gaA/gaC	2/7	0.448749058270197	4	FACETS	0.854	0.737	0.981	0.285	0.245	0.327	CLONAL	1	TRUE	1	0.45484770348293	4		475	442	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435131	49435131	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	235	573	0	ENST00000301067.7:c.6422G>A	p.Gly2141Glu	p.G2141E	ENST00000301067	NM_003482.3	2141	gGg/gAg	31/54	0.457567084656107	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.45484770348293	4		573	657	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495603	56495603	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369300309	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	269	670	1	ENST00000267101.3:c.3793C>T	p.Arg1265Trp	p.R1265W	ENST00000267101	NM_001982.3	1265	Cgg/Tgg	28/28	0.457567084656107	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	2	0.45484770348293	4		671	723	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28971123	28971123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141906217	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	104	637	0	ENST00000282397.4:c.1634G>A	p.Gly545Glu	p.G545E	ENST00000282397	NM_002019.4	545	gGa/gAa	12/30	0.457567084656107	3	FACETS	0.981	0.881	1	0.491	0.44	0.544	CLONAL	1	TRUE	1	0.45484770348293	3		637	572	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005278	29005278	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	149	602	1	ENST00000282397.4:c.983T>A	p.Ile328Lys	p.I328K	ENST00000282397	NM_002019.4	328	aTa/aAa	7/30	0.457567084656107	3	FACETS	0.852	0.784	0.921	0.852	0.784	0.921	CLONAL	2	TRUE	1	0.45484770348293	3		603	472	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345041	73345042	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	GT	novel	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	66	516	0	ENST00000377767.4:c.1755_1755+1delinsAC		p.X585_splice	ENST00000377767	NM_014953.3	585		13/21	0.457567084656107	3	FACETS	0.651	0.566	0.744	0.326	0.283	0.372	SUBCLONAL	1	TRUE	1	0.45484770348293	3		516	547	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527856	103527856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	92	549	0	ENST00000355739.4:c.3164C>T	p.Thr1055Ile	p.T1055I	ENST00000355739	NM_000123.3	1055	aCc/aTc	15/15	0.457567084656107	3	FACETS	0.921	0.821	1	0.461	0.41	0.514	CLONAL	1	TRUE	1	0.45484770348293	3		549	539	SUCCESS
BLM	641	MSKCC	GRCh37	15	91295158	91295158	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751438275	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	249	527	0	ENST00000355112.3:c.941C>T	p.Ser314Phe	p.S314F	ENST00000355112	NM_000057.2	314	tCc/tTc	4/22	0.457567084656107	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	2	0.45484770348293	4		527	745	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129414	2129414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	202	601	0	ENST00000219476.3:c.3269C>T	p.Ser1090Phe	p.S1090F	ENST00000219476	NM_000548.3	1090	tCc/tTc	28/42	0.457567084656107	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	2	0.45484770348293	4		601	587	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632558	3632558	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	252	834	0	ENST00000294008.3:c.5290C>T	p.Pro1764Ser	p.P1764S	ENST00000294008	NM_032444.2	1764	Ccg/Tcg	15/15	0.457567084656107	4	FACETS	0.909	0.852	0.967	0.909	0.852	0.967	CLONAL	2	TRUE	2	0.45484770348293	4		834	887	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81954870	81954870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	227	825	0	ENST00000359376.3:c.2303C>T	p.Ser768Phe	p.S768F	ENST00000359376	NM_002661.3	768	tCc/tTc	21/33	0.400401016454565	4	FACETS	0.945	0.884	1	0.945	0.884	1	CLONAL	2	TRUE	2	0.45484770348293	4		825	768	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664601	29664601	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1060500345	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	342	536	0	ENST00000356175.3:c.6579+1G>A		p.X2193_splice	ENST00000356175	NM_000267.3	2193			0.442311493571151	5	FACETS	0.908	0.872	0.944	0.908	0.872	0.944	CLONAL	5	TRUE	0	0.45484770348293	5		536	557	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919517	78919517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	436	686	0	ENST00000306801.3:c.3076C>T	p.Pro1026Ser	p.P1026S	ENST00000306801	NM_020761.2	1026	Ccc/Tcc	26/34	0.45484770348293	6	FACETS	1	0.968	1	1	0.968	1	CLONAL	4	TRUE	2	0.45484770348293	6		686	906	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622127	1622127	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	253	726	0	ENST00000344749.5:c.748C>T	p.Pro250Ser	p.P250S	ENST00000344749	NM_001136139.2	250	Ccg/Tcg	10/19	0.457567084656107	4	FACETS	0.999	0.938	1	0.999	0.938	1	CLONAL	2	TRUE	2	0.45484770348293	4		726	810	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632090	1632090	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	230	779	1	ENST00000344749.5:c.245C>T	p.Thr82Ile	p.T82I	ENST00000344749	NM_001136139.2	82	aCt/aTt	5/19	0.457567084656107	4	FACETS	0.913	0.853	0.974	0.913	0.853	0.974	CLONAL	2	TRUE	2	0.45484770348293	4		780	806	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945496	17945496	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776106625	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	238	722	0	ENST00000458235.1:c.2234C>T	p.Pro745Leu	p.P745L	ENST00000458235	NM_000215.3	745	cCg/cTg	17/24	0.457567084656107	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.45484770348293	3		722	589	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765567	41765567	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	295	782	0	ENST00000301178.4:c.2443G>A	p.Glu815Lys	p.E815K	ENST00000301178	NM_021913.4	815	Gag/Aag	20/20	0.457567084656107	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.45484770348293	3		782	691	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47607010	47607010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	219	737	1	ENST00000263735.4:c.760G>A	p.Glu254Lys	p.E254K	ENST00000263735	NM_002354.2	254	Gaa/Aaa	7/9	0.339398744408833	6	FACETS	1	0.985	1	0.788	0.735	0.842	CLONAL	2	TRUE	3	0.45484770348293	6		738	778	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488655	212488655	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	325	581	0	ENST00000342788.4:c.2194G>A	p.Val732Ile	p.V732I	ENST00000342788	NM_005235.2	732	Gtt/Att	18/28	0.45484770348293	6	FACETS	0.908	0.863	0.954	0.908	0.863	0.954	CLONAL	4	TRUE	2	0.45484770348293	6		581	751	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523297	9523297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1229227713	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	212	703	0	ENST00000353224.5:c.1940C>T	p.Pro647Leu	p.P647L	ENST00000353224	NM_177990.2	647	cCt/cTt	9/10	0.457567084656107	3	FACETS	0.957	0.895	1	0.957	0.895	1	CLONAL	2	TRUE	1	0.45484770348293	3		703	598	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546802	9546803	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	87	399	1	ENST00000353224.5:c.1219_1220delinsAA	p.Ser407Lys	p.S407K	ENST00000353224	NM_177990.2	407	TCa/AAa	5/10	0.457567084656107	3	FACETS	1	0.973	1	0.652	0.582	0.726	CLONAL	1	TRUE	1	0.45484770348293	3		400	360	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69788803	69788803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	148	563	1	ENST00000352241.4:c.55G>A	p.Glu19Lys	p.E19K	ENST00000352241	NM_198159.2	19	Gaa/Aaa	1/10	0.382231542449055	4	FACETS	0.968	0.891	1	0.968	0.891	1	CLONAL	2	TRUE	2	0.45484770348293	4		564	489	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876280	35876280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	117	651	0	ENST00000303115.3:c.1072C>T	p.Pro358Ser	p.P358S	ENST00000303115	NM_002185.3	358	Cca/Tca	8/8	0.457567084656107	3	FACETS	1	0.952	1	0.542	0.491	0.597	CLONAL	1	TRUE	1	0.45484770348293	3		651	582	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187372	32187372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	211	649	0	ENST00000375023.3:c.1507C>T	p.Pro503Ser	p.P503S	ENST00000375023	NM_004557.3	503	Cca/Tca	8/30	0.45484770348293	6	FACETS	0.972	0.904	1	0.486	0.452	0.522	CLONAL	2	TRUE	2	0.45484770348293	6		649	911	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965690	93965690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	182	608	0	ENST00000369303.4:c.2238G>A	p.Met746Ile	p.M746I	ENST00000369303	NM_004440.3	746	atG/atA	13/17	0.45484770348293	6	FACETS	0.931	0.86	1	0.465	0.43	0.502	CLONAL	2	TRUE	2	0.45484770348293	6		608	821	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552828	106552828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1385182753	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	535	781	0	ENST00000369096.4:c.793G>A	p.Asp265Asn	p.D265N	ENST00000369096	NM_001198.3	265	Gac/Aac	5/7	0.45484770348293	6	FACETS	0.989	0.952	1	0.989	0.952	1	CLONAL	4	TRUE	2	0.45484770348293	6		781	1136	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724329	117724329	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	467	713	2	ENST00000368508.3:c.550C>T	p.Pro184Ser	p.P184S	ENST00000368508	NM_002944.2	184	Ccc/Tcc	6/43	0.45484770348293	6	FACETS	0.971	0.931	1	0.971	0.931	1	CLONAL	4	TRUE	2	0.45484770348293	6		715	1010	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950436	68950436	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	103	704	0	ENST00000288368.4:c.748G>A	p.Gly250Arg	p.G250R	ENST00000288368	NM_024870.2	250	Gga/Aga	7/40	0.319800568301483	3	FACETS	1	0.944	1	0.539	0.484	0.596	CLONAL	1	TRUE	1	0.45484770348293	3		704	516	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982640	90982640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	105	513	0	ENST00000265433.3:c.848C>T	p.Pro283Leu	p.P283L	ENST00000265433	NM_002485.4	283	cCt/cTt	7/16	0.319800568301483	3	FACETS	1	0.971	1	0.607	0.546	0.67	CLONAL	1	TRUE	1	0.45484770348293	3		513	467	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090508	5090508	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	115	593	1	ENST00000381652.3:c.2824C>T	p.Gln942Ter	p.Q942*	ENST00000381652	NM_004972.3	942	Caa/Taa	21/25	0.457567084656107	4	FACETS	1	0.969	1	0.588	0.53	0.648	CLONAL	1	TRUE	2	0.45484770348293	4		594	626	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202914	27202914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	254	673	0	ENST00000380036.4:c.2006C>T	p.Ser669Phe	p.S669F	ENST00000380036	NM_000459.3	669	tCt/tTt	13/23	0.45484770348293	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.45484770348293	2		673	542	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786038	135786038	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	264	880	0	ENST00000298552.3:c.1183C>T	p.Pro395Ser	p.P395S	ENST00000298552	NM_001162426.1	395	Cct/Tct	12/23	0.457567084656107	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.45484770348293	3		880	679	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401010	139401010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	237	768	0	ENST00000277541.6:c.3983C>T	p.Thr1328Ile	p.T1328I	ENST00000277541	NM_017617.3	1328	aCc/aTc	24/34	0.457567084656107	3	FACETS	0.985	0.925	1	0.985	0.925	1	CLONAL	2	TRUE	1	0.45484770348293	3		768	649	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426731	47426731	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1452639448	NA	P-0023923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	273	371	1	ENST00000377045.4:c.976C>T	p.Arg326Ter	p.R326*	ENST00000377045	NM_001654.4	326	Cga/Tga	10/16	0.457567084656107	2	FACETS	0.95	0.909	0.991			1	CLONAL	3	TRUE	NA	0.45484770348293	2		372	421	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	191	571	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.992	0.927	1	0.992	0.927	1	CLONAL	1	TRUE	1	0.814310008080723	2		571	473	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220274	55220274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	8270	906	1	ENST00000275493.2:c.664C>T	p.Arg222Cys	p.R222C	ENST00000275493	NM_005228.3	222	Cgc/Tgc	6/28	0.814310008080723	25	FACETS	1	0.999	1	0.936	0.932	0.941	CLONAL	22	TRUE	1	0.814310008080723	25		907	9369	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	443429	443429	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	196	692	1	ENST00000399788.2:c.1468T>A	p.Tyr490Asn	p.Y490N	ENST00000399788	NM_001042603.1	490	Tat/Aat	11/28	NA	2	FACETS	1	0.967	1			1	INDETERMINATE	1	TRUE	NA	0.814310008080723	2		693	458	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56798159	56798159	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs143026267	NA	P-0023927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	241	858	0	ENST00000337432.4:c.890T>G	p.Leu297Arg	p.L297R	ENST00000337432	NM_058216.2	297	cTt/cGt	6/9	1	2	FACETS	0.885	0.831	0.939	0.885	0.831	0.939	CLONAL	1	TRUE	1	0.814310008080723	2		858	669	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752679	42752679	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200428259	NA	P-0023927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	217	826	1	ENST00000222329.4:c.1585C>T	p.Arg529Trp	p.R529W	ENST00000222329	NM_006494.2	529	Cgg/Tgg	4/4	0.814310008080723	3	FACETS	0.942	0.878	1	0.471	0.439	0.504	CLONAL	1	TRUE	1	0.814310008080723	3		827	796	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591054	67591056	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0023927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	123	455	0	ENST00000274335.5:c.1651_1653del	p.Lys551del	p.K551del	ENST00000274335		549	ttGAAg/ttg	12/15	1	2	FACETS	0.839	0.767	0.913	0.839	0.767	0.913	CLONAL	1	TRUE	1	0.814310008080723	2		455	360	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061224	38061237	+	protein_altering_variant	In_Frame_Del	DEL	CTCGAACATGTTGC	CTCGAACATGTTGC	ATGTT	novel	NA	P-0023928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	166	728	4	ENST00000250448.2:c.752_765delinsAACAT	p.Gly251_Glu255delinsGluHis	p.G251_E255delinsEH	ENST00000250448	NM_004496.3	251	gGCAACATGTTCGAG/gAACAT	2/2	1	2	FACETS	0.813	0.75	0.877	1	0.991	1	CLONAL	2	TRUE	1	0.335439663041882	2		732	609	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619285	37619286	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0023928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	171	607	0	ENST00000447079.4:c.962_963del	p.Gly321AlafsTer29	p.G321Afs*29	ENST00000447079	NM_015083.1	321	GGg/g	1/14	1	2	FACETS	0.883	0.817	0.952	1	0.992	1	CLONAL	2	TRUE	1	0.335439663041882	2		607	577	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627616	37627616	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	204	705	0	ENST00000447079.4:c.1531G>T	p.Glu511Ter	p.E511*	ENST00000447079	NM_015083.1	511	Gag/Tag	2/14	1	2	FACETS	0.827	0.77	0.887	1	0.992	1	CLONAL	2	TRUE	1	0.335439663041882	2		705	735	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	363	855	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.118124835433903	5	FACETS	1	0.99	1			1	INDETERMINATE	3	TRUE	NA	0.319379352423915	5		855	973	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0023931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	99	853	1	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.319379352423915	1	FACETS	0.94	0.842	1	0.94	0.842	1	CLONAL	1	TRUE	0	0.319379352423915	1		854	554	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575065	48575065	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	75	543	1	ENST00000342988.3:c.259C>T	p.Arg87Trp	p.R87W	ENST00000342988	NM_005359.5	87	Cgg/Tgg	3/12	0.319379352423915	1	FACETS	0.821	0.721	0.927	0.821	0.721	0.927	CLONAL	1	TRUE	0	0.319379352423915	1		544	481	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420183	49420183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	71	763	0	ENST00000301067.7:c.15566G>A	p.Gly5189Glu	p.G5189E	ENST00000301067	NM_003482.3	5189	gGa/gAa	48/54	1	2	FACETS	0.862	0.753	0.978	0.862	0.753	0.978	CLONAL	1	TRUE	1	0.319379352423915	2		763	516	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808911	3808911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	113	813	0	ENST00000262367.5:c.3313G>A	p.Asp1105Asn	p.D1105N	ENST00000262367	NM_004380.2	1105	Gac/Aac	17/31	1	2	FACETS	0.94	0.846	1	0.94	0.846	1	CLONAL	1	TRUE	1	0.319379352423915	2		813	753	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149498369	149498369	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	98	837	1	ENST00000261799.4:c.2845C>T	p.Pro949Ser	p.P949S	ENST00000261799	NM_002609.3	949	Ccc/Tcc	21/23	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.319379352423915	2		838	610	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs770248150	NA	P-0023932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	722	750	0	ENST00000311936.3:c.351A>C	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaC	4/5	0.711746532505477	7	FACETS	1	0.996	1	1	0.996	1	CLONAL	6	TRUE	1	0.711746532505477	7		750	889	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666644	206666644	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	151	822	1	ENST00000367120.3:c.1978G>A	p.Gly660Arg	p.G660R	ENST00000367120	NM_014002.3	660	Ggg/Agg	20/22	0.686914443210855	5	FACETS	1	0.97	1	0.283	0.259	0.308	CLONAL	1	TRUE	1	0.711746532505477	5		823	775	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258530	19258530	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	174	859	0	ENST00000162023.5:c.370G>C	p.Ala124Pro	p.A124P	ENST00000162023		124	Gcc/Ccc	8/13	0.711746532505477	3	FACETS	1	0.965	1	0.537	0.497	0.579	CLONAL	1	TRUE	1	0.711746532505477	3		859	617	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217556	142217556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	52	759	0	ENST00000350721.4:c.5441G>A	p.Arg1814Lys	p.R1814K	ENST00000350721	NM_001184.3	1814	aGa/aAa	32/47	1	2	FACETS	0.323	0.275	0.376	0.323	0.275	0.376	SUBCLONAL	1	TRUE	1	0.711746532505477	2		759	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0023933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	126	683	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	0.786	0.718	0.858			1	INDETERMINATE	2	TRUE	NA	0.37	2		683	433	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0023933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	119	732	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.37	2		732	542	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0023933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	98	536	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.256014383732014	2	FACETS	1	0.98	1	0.695	0.625	0.768	CLONAL	1	TRUE	0	0.37	2		536	381	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546721	9546721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	62	391	0	ENST00000353224.5:c.1301C>T	p.Ala434Val	p.A434V	ENST00000353224	NM_177990.2	434	gCg/gTg	5/10	0.259918168383452	4	FACETS	1	0.963	1	0.667	0.58	0.761	CLONAL	1	TRUE	2	0.37	4		391	344	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604764	48604764	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0023933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	27	575	0	ENST00000342988.3:c.1586T>G	p.Leu529Ter	p.L529*	ENST00000342988	NM_005359.5	529	tTa/tGa	12/12	0.3	1	FACETS	0.386	0.308	0.476	0.386	0.308	0.476	SUBCLONAL	1	TRUE	0	0.37	1		575	308	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096009	178096009	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	61	583	0	ENST00000397062.3:c.1322T>C	p.Phe441Ser	p.F441S	ENST00000397062	NM_006164.4	441	tTc/tCc	5/5	1	2	FACETS	0.767	0.663	0.879	0.767	0.663	0.879	SUBCLONAL	1	TRUE	1	0.37	2		583	430	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275120	41275120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	95	460	1	ENST00000349496.5:c.1286G>A	p.Cys429Tyr	p.C429Y	ENST00000349496	NM_001904.3	429	tGc/tAc	9/15	0.3	3	FACETS	1	0.975	1	0.66	0.59	0.733	CLONAL	1	TRUE	1	0.37	3		461	461	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851674	134851675	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	102	609	0	ENST00000398015.3:c.1085dup	p.Cys363ValfsTer12	p.C363Vfs*12	ENST00000398015	NM_004441.4	360	-/A	5/16	0.3	3	FACETS	1	0.983	1	0.746	0.671	0.824	CLONAL	1	TRUE	1	0.37	3		609	438	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69103959	69103959	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	48	770	0	ENST00000288368.4:c.4349C>A	p.Ala1450Glu	p.A1450E	ENST00000288368	NM_024870.2	1450	gCa/gAa	36/40	0.3	3	FACETS	0.587	0.496	0.687	0.293	0.248	0.344	SUBCLONAL	1	TRUE	1	0.37	3		770	524	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577255	64577276	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTCGAGGATAGAGGGACAGG	TTCTCGAGGATAGAGGGACAGG	-	novel	NA	P-0023934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	72	732	0	ENST00000312049.6:c.306_327del	p.Asp102GlufsTer10	p.D102Efs*10	ENST00000312049	NM_130799.2	102	gaCCTGTCCCTCTATCCTCGAGAA/ga	2/10	0.17937020670781	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.15	1		732	827	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339425	116339425	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	47	493	1	ENST00000397752.3:c.287T>A	p.Phe96Tyr	p.F96Y	ENST00000397752	NM_000245.2	96	tTc/tAc	2/21	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.15	2		494	586	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350485	15350485	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200957651	NA	P-0023936-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	63	736	0	ENST00000263377.2:c.3430G>A	p.Val1144Ile	p.V1144I	ENST00000263377	NM_058243.2	1144	Gtc/Atc	16/20	1	2	FACETS	0.772	0.673	0.877	0.772	0.673	0.877	SUBCLONAL	1	TRUE	1	0.555311029322223	2		736	294	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118368666	118368667	+	protein_altering_variant	In_Frame_Ins	INS	-	-	CTA	novel	NA	P-0023939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	142	489	0	ENST00000534358.1:c.5680_5681insCTA	p.Leu1894delinsProIle	p.L1894delinsPI	ENST00000534358	NM_005933.3	1894	cta/cCTAta	21/36	0.60162094166668	3	FACETS	0.836	0.763	0.912	0.418	0.381	0.456	CLONAL	1	TRUE	1	0.628038294516313	3		489	711	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931485	131931485	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	131	441	0	ENST00000265335.6:c.2192del	p.Gly731AspfsTer5	p.G731Dfs*5	ENST00000265335		730	ctG/ct	13/25	0.628038294516313	2	FACETS	0.944	0.863	1	0.472	0.431	0.514	CLONAL	1	TRUE	0	0.628038294516313	2		441	442	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016208	150016208	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0023939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	247	399	0	ENST00000253339.5:c.496+2T>C		p.X166_splice	ENST00000253339		166			0.622109371723972	2	FACETS	0.962	0.915	1	0.962	0.915	1	CLONAL	2	TRUE	0	0.628038294516313	2		399	409	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	115	571	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.679011774718693	2		571	265	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0023940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	162	966	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.679011774718693	2		967	416	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610290	81610290	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	163	513	0	ENST00000298171.2:c.1888A>C	p.Ile630Leu	p.I630L	ENST00000298171	NM_000369.2	630	Atc/Ctc	10/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.679011774718693	2		513	445	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041598	47041598	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	207	370	0	ENST00000377604.3:c.1823G>A	p.Trp608Ter	p.W608*	ENST00000377604	NM_001204468.1	608	tGg/tAg	17/24	1	1	FACETS		NA	1	1	0.995	1	NA	2	TRUE	0	0.679011774718693	1		370	263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0023943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	288	887	3	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.400341904775614	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.400341904775614	1		890	823	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	93	424	2	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.400341904775614	2		426	455	SUCCESS
APC	324	MSKCC	GRCh37	5	112174253	112174253	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	104	530	4	ENST00000257430.4:c.2962G>T	p.Glu988Ter	p.E988*	ENST00000257430	NM_000038.5	988	Gaa/Taa	16/16	1	2	FACETS	0.921	0.827	1	0.921	0.827	1	CLONAL	1	TRUE	1	0.400341904775614	2		534	564	SUCCESS
APC	324	MSKCC	GRCh37	5	112175569	112175569	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	94	413	0	ENST00000257430.4:c.4280del	p.Pro1427LeufsTer46	p.P1427Lfs*46	ENST00000257430	NM_000038.5	1426	agC/ag	16/16	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.400341904775614	2		413	460	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0023944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	100	588	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.249276186260968	3	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	1	0.249276186260968	3		588	435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0023944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	109	844	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.249276186260968	2		844	586	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0023946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	171	598	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.538759159933278	2		598	569	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551334	150551334	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	240	749	2	ENST00000369026.2:c.673G>A	p.Glu225Lys	p.E225K	ENST00000369026	NM_021960.4	225	Gag/Aag	1/3	0.532495661972733	4	FACETS	0.989	0.922	1	0.33	0.307	0.353	CLONAL	1	TRUE	1	0.538759159933278	4		751	1386	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518660	204518660	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	148	485	0	ENST00000367182.3:c.1323G>C	p.Glu441Asp	p.E441D	ENST00000367182	NM_001278516.1	441	gaG/gaC	11/11	0.532495661972733	4	FACETS	0.991	0.905	1	0.33	0.301	0.361	CLONAL	1	TRUE	1	0.538759159933278	4		485	853	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943946	71943946	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	208	738	0	ENST00000298229.2:c.1879G>A	p.Glu627Lys	p.E627K	ENST00000298229	NM_001567.3	627	Gag/Aag	16/28	1	2	FACETS	0.927	0.862	0.994	0.927	0.862	0.994	CLONAL	1	TRUE	1	0.538759159933278	2		738	833	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944526	71944526	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	205	730	0	ENST00000298229.2:c.2082G>C	p.Trp694Cys	p.W694C	ENST00000298229	NM_001567.3	694	tgG/tgC	18/28	1	2	FACETS	0.952	0.885	1	0.952	0.885	1	CLONAL	1	TRUE	1	0.538759159933278	2		730	799	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119687	108119687	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	98	294	0	ENST00000278616.4:c.1093G>C	p.Glu365Gln	p.E365Q	ENST00000278616	NM_000051.3	365	Gag/Cag	9/63	1	2	FACETS	0.842	0.756	0.933	0.842	0.756	0.933	CLONAL	1	TRUE	1	0.538759159933278	2		294	432	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49419971	49419971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	142	511	0	ENST00000301067.7:c.15778C>T	p.Pro5260Ser	p.P5260S	ENST00000301067	NM_003482.3	5260	Ccc/Tcc	48/54	1	2	FACETS	0.973	0.891	1	0.973	0.891	1	CLONAL	1	TRUE	1	0.538759159933278	2		511	542	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420020	49420020	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	168	610	0	ENST00000301067.7:c.15729C>G	p.Ile5243Met	p.I5243M	ENST00000301067	NM_003482.3	5243	atC/atG	48/54	1	2	FACETS	0.945	0.872	1	0.945	0.872	1	CLONAL	1	TRUE	1	0.538759159933278	2		610	660	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061839	38061839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752132466	NA	P-0023946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	221	709	0	ENST00000250448.2:c.150G>A	p.Met50Ile	p.M50I	ENST00000250448	NM_004496.3	50	atG/atA	2/2	1	2	FACETS	0.71	0.66	0.762	0.71	0.66	0.762	SUBCLONAL	1	TRUE	1	0.538759159933278	2		709	1155	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347590	91347590	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0023946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	141	473	0	ENST00000355112.3:c.3751+1G>T		p.X1251_splice	ENST00000355112	NM_000057.2	1251			1	2	FACETS	0.947	0.867	1	0.947	0.867	1	CLONAL	1	TRUE	1	0.538759159933278	2		473	553	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639546	3639546	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1233948411	NA	P-0023946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	186	776	1	ENST00000294008.3:c.4093G>A	p.Asp1365Asn	p.D1365N	ENST00000294008	NM_032444.2	1365	Gac/Aac	12/15	0.430775589991664	3	FACETS	0.931	0.86	1	0.466	0.43	0.503	CLONAL	1	TRUE	1	0.538759159933278	3		777	941	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	167	627	1	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.538759159933278	1	FACETS	0.881	0.816	0.948	0.881	0.816	0.948	CLONAL	1	TRUE	0	0.538759159933278	1		628	514	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821842	72821842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	167	526	0	ENST00000268489.5:c.10333G>A	p.Glu3445Lys	p.E3445K	ENST00000268489	NM_006885.3	3445	Gaa/Aaa	10/10	0.538759159933278	1	FACETS	0.886	0.821	0.954	0.886	0.821	0.954	CLONAL	1	TRUE	0	0.538759159933278	1		526	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0023946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	222	684	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	0.538759159933278	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.538759159933278	1		684	593	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961849	15961860	+	frameshift_variant	Frame_Shift_Del	DEL	AGGTGAGCTGGC	AGGTGAGCTGGC	TG	novel	NA	P-0023946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	197	591	3	ENST00000268712.3:c.5935_5946delinsCA	p.Ala1979GlnfsTer67	p.A1979Qfs*67	ENST00000268712	NM_006311.3	1979	GCCAGCTCACCT/CA	38/46	0.538759159933278	1	FACETS	0.942	0.879	1	0.942	0.879	1	CLONAL	1	TRUE	0	0.538759159933278	1		594	567	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667571	29667571	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691073	NA	P-0023946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	226	664	0	ENST00000356175.3:c.6907C>T	p.Gln2303Ter	p.Q2303*	ENST00000356175	NM_000267.3	2303	Cag/Tag	46/57	0.538759159933278	1	FACETS	0.968	0.908	1	0.968	0.908	1	CLONAL	1	TRUE	0	0.538759159933278	1		664	633	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368223	45368223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	175	551	1	ENST00000262160.6:c.1379C>T	p.Ser460Leu	p.S460L	ENST00000262160	NM_005901.5	460	tCa/tTa	11/11	0.538759159933278	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.538759159933278	1		552	468	SUCCESS
REL	5966	MSKCC	GRCh37	2	61121620	61121620	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	206	557	0	ENST00000295025.8:c.242G>C	p.Gly81Ala	p.G81A	ENST00000295025	NM_002908.2	81	gGa/gCa	3/11	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.538759159933278	2		557	755	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252947	36252948	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0023946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	162	527	1	ENST00000300305.3:c.414_415insC	p.Asn139GlnfsTer5	p.N139Qfs*5	ENST00000300305		138	-/C	4/8	1	2	FACETS	0.984	0.907	1	0.984	0.907	1	CLONAL	1	TRUE	1	0.538759159933278	2		528	611	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252987	36252993	+	frameshift_variant	Frame_Shift_Del	DEL	TGGAACA	TGGAACA	-	novel	NA	P-0023946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	150	523	0	ENST00000300305.3:c.369_375del	p.Asp123GlufsTer8	p.D123Efs*8	ENST00000300305		123	gaTGTTCCA/ga	4/8	1	2	FACETS	0.882	0.809	0.958	0.882	0.809	0.958	CLONAL	1	TRUE	1	0.538759159933278	2		523	631	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825328	134825328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	109	507	0	ENST00000398015.3:c.844G>A	p.Glu282Lys	p.E282K	ENST00000398015	NM_004441.4	282	Gaa/Aaa	4/16	1	2	FACETS	0.848	0.766	0.935	0.848	0.766	0.935	CLONAL	1	TRUE	1	0.538759159933278	2		507	477	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151855971	151855971	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	206	640	0	ENST00000262189.6:c.11647G>A	p.Asp3883Asn	p.D3883N	ENST00000262189	NM_170606.2	3883	Gac/Aac	44/59	1	2	FACETS	0.996	0.926	1	0.996	0.926	1	CLONAL	1	TRUE	1	0.538759159933278	2		640	768	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873626	151873626	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	184	588	0	ENST00000262189.6:c.8912C>G	p.Ser2971Cys	p.S2971C	ENST00000262189	NM_170606.2	2971	tCt/tGt	38/59	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.538759159933278	2		588	602	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949162	151949162	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	166	545	0	ENST00000262189.6:c.1483G>C	p.Glu495Gln	p.E495Q	ENST00000262189	NM_170606.2	495	Gag/Cag	11/59	1	2	FACETS	0.852	0.785	0.922	0.852	0.785	0.922	CLONAL	1	TRUE	1	0.538759159933278	2		545	723	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223591	53223591	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	108	525	1	ENST00000375401.3:c.3768G>T	p.Glu1256Asp	p.E1256D	ENST00000375401	NM_004187.3	1256	gaG/gaT	23/26	1	2	FACETS	0.842	0.76	0.929	0.842	0.76	0.929	CLONAL	1	TRUE	1	0.538759159933278	2		526	476	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098975	178098975	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1328994103	NA	P-0023948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	38	355	0	ENST00000397062.3:c.70T>C	p.Trp24Arg	p.W24R	ENST00000397062	NM_006164.4	24	Tgg/Cgg	2/5	0.228122289171886	3	FACETS	0.777	0.642	0.928	0.389	0.321	0.464	CLONAL	1	TRUE	1	0.232692923471165	3		355	469	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106917	27106917	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	80	519	0	ENST00000324856.7:c.6532del	p.Asp2178ThrfsTer22	p.D2178Tfs*22	ENST00000324856	NM_006015.4	2176	caG/ca	20/20	0.182345715722622	2	FACETS	0.773	0.683	0.868	0.773	0.683	0.868	SUBCLONAL	2	TRUE	0	0.232692923471165	2		519	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0023948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	67	576	0	ENST00000269305.4:c.96+1G>A		p.X32_splice	ENST00000269305	NM_001126112.2	32			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.232692923471165	2		576	438	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971053	21971053	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs137854598	NA	P-0023948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	74	377	0	ENST00000304494.5:c.305C>A	p.Ala102Glu	p.A102E	ENST00000304494	NM_000077.4	102	gCg/gAg	2/3	0.192663634307814	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	2	TRUE	0	0.232692923471165	2		377	305	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261836	16261836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	102	601	0	ENST00000375759.3:c.9101C>T	p.Ser3034Phe	p.S3034F	ENST00000375759	NM_015001.2	3034	tCc/tTc	11/15	0.182345715722622	2	FACETS	0.913	0.821	1	0.913	0.821	1	CLONAL	2	TRUE	0	0.232692923471165	2		601	480	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518636	69518636	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	33	523	0	ENST00000294312.3:c.9C>G	p.Ser3Arg	p.S3R	ENST00000294312	NM_005117.2	3	agC/agG	1/3	0.228122289171886	3	FACETS	0.75	0.611	0.907	0.375	0.305	0.454	CLONAL	1	TRUE	1	0.232692923471165	3		523	422	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588171	69588171	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	61	747	0	ENST00000168712.1:c.527G>T	p.Gly176Val	p.G176V	ENST00000168712	NM_002007.2	176	gGc/gTc	3/3	0.228122289171886	3	FACETS	0.994	0.857	1	0.497	0.428	0.571	CLONAL	1	TRUE	1	0.232692923471165	3		747	589	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206728	102206728	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	49	610	0	ENST00000263464.3:c.1357del	p.Ala453HisfsTer6	p.A453Hfs*6	ENST00000263464	NM_001165.4	452	atG/at	7/9	0.228122289171886	3	FACETS	0.952	0.807	1	0.476	0.403	0.556	CLONAL	1	TRUE	1	0.232692923471165	3		610	494	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426943	49426944	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0023948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	66	568	0	ENST00000301067.7:c.11544_11545delinsTT	p.Met3848_Gly3849delinsIleTer	p.M3848_G3849delinsI*	ENST00000301067	NM_003482.3	3848	atGGga/atTTga	39/54	0.182345715722622	2	FACETS	1	0.969	1	0.702	0.612	0.799	CLONAL	1	TRUE	0	0.232692923471165	2		568	404	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858312	9858312	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	49	482	0	ENST00000330684.3:c.3089C>A	p.Pro1030Gln	p.P1030Q	ENST00000330684	NM_001134407.1	1030	cCa/cAa	13/13	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.232692923471165	2		482	370	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46602969	46602969	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	100	717	0	ENST00000263734.3:c.1027G>T	p.Val343Phe	p.V343F	ENST00000263734	NM_001430.4	343	Gtc/Ttc	8/16	0.228122289171886	3	FACETS	0.82	0.734	0.911	0.82	0.734	0.911	CLONAL	2	TRUE	1	0.232692923471165	3		717	585	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248390	212248390	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	44	387	0	ENST00000342788.4:c.3877G>T	p.Gly1293Cys	p.G1293C	ENST00000342788	NM_005235.2	1293	Ggc/Tgc	28/28	0.182345715722622	2	FACETS	1	0.926	1	0.589	0.496	0.691	CLONAL	1	TRUE	0	0.232692923471165	2		387	321	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022323	31022323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	27	498	0	ENST00000375687.4:c.1808C>T	p.Ser603Phe	p.S603F	ENST00000375687	NM_015338.5	603	tCc/tTc	13/13	1	2	FACETS	0.574	0.457	0.709	0.574	0.457	0.709	SUBCLONAL	1	TRUE	1	0.232692923471165	2		498	404	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439302	52439302	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	59	660	3	ENST00000460680.1:c.940G>T	p.Glu314Ter	p.E314*	ENST00000460680	NM_004656.3	314	Gag/Tag	11/17	0.210336139956376	1	FACETS	0.998	0.861	1	0.998	0.861	1	CLONAL	1	TRUE	0	0.232692923471165	1		663	449	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590364	67590364	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	14	195	0	ENST00000274335.5:c.1426G>A	p.Glu476Lys	p.E476K	ENST00000274335		476	Gaa/Aaa	11/15	1	2	FACETS	0.692	0.501	0.92	0.692	0.501	0.92	SUBCLONAL	1	TRUE	1	0.232692923471165	2		195	174	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048171	180048171	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	49	789	0	ENST00000261937.6:c.2102T>A	p.Val701Glu	p.V701E	ENST00000261937	NM_182925.4	701	gTg/gAg	14/30	1	2	FACETS	0.798	0.675	0.932	0.798	0.675	0.932	CLONAL	1	TRUE	1	0.232692923471165	2		789	528	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032314	42032314	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	172	788	1	ENST00000219905.7:c.4499del	p.Asn1500IlefsTer19	p.N1500Ifs*19	ENST00000219905	NM_001164273.1	1500	Aat/at	14/24	1	2	FACETS	0.858	0.795	0.921	0.858	0.795	0.921	CLONAL	1	TRUE	1	0.788085211958324	2		789	509	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921591	39921595	+	frameshift_variant	Frame_Shift_Del	DEL	GACAG	GACAG	A	novel	NA	P-0023949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	77	796	0	ENST00000378444.4:c.4225_4229delinsT	p.Leu1409TyrfsTer74	p.L1409Yfs*74	ENST00000378444	NM_001123385.1	1409	CTGTCa/Ta	10/15	1	2	FACETS	0.359	0.315	0.405	0.359	0.315	0.405	SUBCLONAL	1	TRUE	1	0.788085211958324	2		796	545	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	69	571	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.542275680174078	2		571	248	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826593	50826593	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	119	438	0	ENST00000398568.2:c.2318A>G	p.Asn773Ser	p.N773S	ENST00000398568	NM_001042412.1	773	aAt/aGt	15/18	0.542275680174078	3	FACETS	0.822	0.743	0.905	0.411	0.371	0.453	CLONAL	1	TRUE	1	0.542275680174078	3		438	679	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376433	15376433	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	232	875	1	ENST00000263377.2:c.581C>A	p.Ser194Tyr	p.S194Y	ENST00000263377	NM_058243.2	194	tCc/tAc	5/20	1	2	FACETS	0.959	0.896	1	0.959	0.896	1	CLONAL	1	TRUE	1	0.542275680174078	2		876	892	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0023951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	143	909	1	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.563326432705982	2	FACETS	1	0.967	1	0.548	0.504	0.593	CLONAL	1	TRUE	0	0.60734531933997	2		910	430	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375486	40375486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138255473	NA	P-0023951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	74	778	1	ENST00000293328.3:c.464C>T	p.Thr155Met	p.T155M	ENST00000293328	NM_012448.3	155	aCg/aTg	5/19	0.563326432705982	2	FACETS	0.563	0.494	0.636	0.281	0.247	0.318	SUBCLONAL	1	TRUE	0	0.60734531933997	2		779	433	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38996982	38996982	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	109	651	0	ENST00000357387.3:c.395G>T	p.Cys132Phe	p.C132F	ENST00000357387	NM_152756.3	132	tGc/tTc	6/38	0.385135592392498	5	FACETS	1	0.937	1	0.352	0.317	0.39	CLONAL	1	TRUE	2	0.60734531933997	5		651	649	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875866	76875866	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	57	310	1	ENST00000373344.5:c.5269G>A	p.Glu1757Lys	p.E1757K	ENST00000373344	NM_000489.3	1757	Gag/Aag	20/35	0.554250744855784	2	FACETS	0.688	0.595	0.787			1	SUBCLONAL	1	TRUE	NA	0.60734531933997	2		311	273	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	186	855	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.497020980273864	3	FACETS	0.961	0.897	1	0.961	0.897	1	CLONAL	2	TRUE	1	0.530211292712221	3		855	462	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0023952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	91	234	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.431880618080283	4	FACETS	1	0.981	1	0.74	0.662	0.821	CLONAL	1	TRUE	2	0.530211292712221	4		234	355	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872498	136872498	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs104893624	NA	P-0023952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	202	348	1	ENST00000241393.3:c.1000C>T	p.Arg334Ter	p.R334*	ENST00000241393	NM_003467.2	334	Cga/Tga	2/2	0.52023885025459	2	FACETS	0.982	0.925	1	0.982	0.925	1	CLONAL	2	TRUE	0	0.530211292712221	2		349	388	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903759	114903760	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0023952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	151	541	0	ENST00000543371.1:c.763_764del	p.His255SerfsTer72	p.H255Sfs*72	ENST00000543371	NM_001198531.1	255	CAt/t	7/14	1	2	FACETS	0.959	0.881	1	0.959	0.881	1	CLONAL	1	TRUE	1	0.530211292712221	2		541	594	SUCCESS
APC	324	MSKCC	GRCh37	5	112174759	112174760	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs786203020	NA	P-0023952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	111	402	0	ENST00000257430.4:c.3473_3474del	p.Arg1158ThrfsTer5	p.R1158Tfs*5	ENST00000257430	NM_000038.5	1156	gaAGag/gaag	16/16	0.431880618080283	4	FACETS	0.89	0.808	0.974	0.89	0.808	0.974	CLONAL	2	TRUE	2	0.530211292712221	4		402	360	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0023953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	123	726	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.374763587752161	1	FACETS	0.849	0.77	0.933	0.849	0.77	0.933	CLONAL	1	TRUE	0	0.374763587752161	1		726	628	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121610	2121610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45509392	NA	P-0023953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	120	647	0	ENST00000219476.3:c.1939G>A	p.Asp647Asn	p.D647N	ENST00000219476	NM_000548.3	647	Gac/Aac	18/42	1	2	FACETS	0.855	0.773	0.942	0.855	0.773	0.942	CLONAL	1	TRUE	1	0.374763587752161	2		647	749	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0023956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	59	714	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	0.167908173787223	7	FACETS	0.95	0.834	1			1	CLONAL	6	FALSE	NA	0.167908173787223	7		714	175	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38148170	38148170	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	67	643	0	ENST00000317025.8:c.2941C>A	p.Pro981Thr	p.P981T	ENST00000317025	NM_023034.1	981	Ccc/Acc	17/24	1	2	FACETS	1	0.923	1	1	0.988	1	CLONAL	5	FALSE	1	0.167908173787223	2		643	153	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436431	110436431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	285	780	0	ENST00000375856.3:c.1970C>T	p.Thr657Met	p.T657M	ENST00000375856	NM_003749.2	657	aCg/aTg	1/2	1	2	FACETS	0.802	0.753	0.853	0.802	0.753	0.853	CLONAL	1	TRUE	1	0.525492450584668	2		780	1352	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255832	16255832	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	150	615	0	ENST00000375759.3:c.3097G>A	p.Gly1033Arg	p.G1033R	ENST00000375759	NM_015001.2	1033	Gga/Aga	11/15	0.524332313722154	1	FACETS	0.952	0.878	1	0.952	0.878	1	CLONAL	1	TRUE	0	0.525492450584668	1		615	442	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720876	89720876	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs786201041	NA	P-0023959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	81	386	0	ENST00000371953.3:c.1026+1G>C		p.X342_splice	ENST00000371953	NM_000314.4	342			0.525492450584668	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.525492450584668	1		386	192	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526594	31526594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	187	701	0	ENST00000344624.3:c.446C>T	p.Pro149Leu	p.P149L	ENST00000344624		149	cCc/cTc	2/33	1	2	FACETS	0.926	0.857	0.996	0.926	0.857	0.996	CLONAL	1	TRUE	1	0.525492450584668	2		701	769	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858153	152858153	+	synonymous_variant	Silent	SNP	C	C	T	novel	NA	P-0023959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	221	830	1	ENST00000406277.2:c.462G>A	p.Leu154=	p.L154=	ENST00000406277	NM_152274.4	154	ctG/ctA	6/7	1	2	FACETS	0.881	0.82	0.943	0.881	0.82	0.943	CLONAL	1	TRUE	1	0.525492450584668	2		831	955	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0023962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	252	839	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.721422871813944	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.721422871813944	1		841	426	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974751	21974751	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	77	419	0	ENST00000304494.5:c.76G>T	p.Glu26Ter	p.E26*	ENST00000304494	NM_000077.4	26	Gag/Tag	1/3	0.721422871813944	1	FACETS	0.853	0.77	0.936	0.853	0.77	0.936	CLONAL	1	TRUE	0	0.721422871813944	1		419	160	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729775	41729775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	135	500	1	ENST00000242208.4:c.754G>A	p.Ala252Thr	p.A252T	ENST00000242208	NM_002192.2	252	Gcc/Acc	3/3	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.721422871813944	2		501	373	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108093	30108093	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	66	760	0	ENST00000331968.5:c.714G>C	p.Glu238Asp	p.E238D	ENST00000331968	NM_002742.2	238	gaG/gaC	5/18	1	2	FACETS	0.341	0.296	0.389	0.341	0.296	0.389	SUBCLONAL	1	TRUE	1	0.721422871813944	2		760	537	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420333	88420333	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	168	536	0	ENST00000360948.2:c.2353C>G	p.Gln785Glu	p.Q785E	ENST00000360948	NM_001012338.2	785	Caa/Gaa	19/19	0.721422871813944	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.721422871813944	1		536	290	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022668	31022668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754554150	NA	P-0023962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	114	809	0	ENST00000375687.4:c.2153G>A	p.Arg718Lys	p.R718K	ENST00000375687	NM_015338.5	718	aGa/aAa	13/13	NA	2	FACETS	0.533	0.481	0.588			1	INDETERMINATE	1	TRUE	NA	0.721422871813944	2		809	593	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0023963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	92	602	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.781	0.696	0.872	0.781	0.696	0.872	SUBCLONAL	1	TRUE	1	0.41995758758546	2		603	561	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188297	32188297	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs753855314	NA	P-0023963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	113	875	2	ENST00000375023.3:c.1044del	p.Gly349AlafsTer49	p.G349Afs*49	ENST00000375023	NM_004557.3	348	ggC/gg	6/30	0.388406022412826	1	FACETS	0.81	0.732	0.892	0.81	0.732	0.892	CLONAL	1	TRUE	0	0.41995758758546	1		877	525	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0023963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	230	728	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.939	0.883	0.997	1	0.994	1	CLONAL	2	TRUE	1	0.41995758758546	2		730	583	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	64	757	1	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	2	FACETS	0.57	0.494	0.652	0.57	0.494	0.652	SUBCLONAL	1	TRUE	1	0.41995758758546	2		758	535	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045000	47045000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556782020	NA	P-0023963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	106	1067	0	ENST00000377604.3:c.2326C>T	p.Arg776Trp	p.R776W	ENST00000377604	NM_001204468.1	776	Cgg/Tgg	20/24	1	2	FACETS	0.796	0.715	0.882	0.796	0.715	0.882	SUBCLONAL	1	TRUE	1	0.41995758758546	2		1067	634	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422384	47422384	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	67	580	3	ENST00000377045.4:c.23del	p.Pro8LeufsTer26	p.P8Lfs*26	ENST00000377045	NM_001654.4	6	ggC/gg	2/16	1	2	FACETS	0.765	0.667	0.87	0.765	0.667	0.87	SUBCLONAL	1	TRUE	1	0.41995758758546	2		583	417	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860556	45860556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	95	958	3	ENST00000391945.4:c.1451C>T	p.Thr484Met	p.T484M	ENST00000391945	NM_000400.3	484	aCg/aTg	15/23	1	2	FACETS	0.88	0.786	0.979	0.88	0.786	0.979	CLONAL	1	TRUE	1	0.41995758758546	2		961	514	SUCCESS
APC	324	MSKCC	GRCh37	5	112179788	112179788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201459013	NA	P-0023963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	63	407	0	ENST00000257430.4:c.8497C>T	p.Arg2833Cys	p.R2833C	ENST00000257430	NM_000038.5	2833	Cgc/Tgc	16/16	0.382218553766581	3	FACETS	0.81	0.703	0.926			1	CLONAL	1	TRUE	NA	0.41995758758546	3		407	448	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628072	90628072	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781481805	NA	P-0023963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	141	848	4	ENST00000330062.3:c.1247C>T	p.Ala416Val	p.A416V	ENST00000330062	NM_002168.2	416	gCg/gTg	10/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.41995758758546	2		852	606	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223175	36223175	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	87	938	3	ENST00000222270.7:c.5730del	p.Arg1911AspfsTer23	p.R1911Dfs*23	ENST00000222270	NM_014727.1	1909	Ccc/cc	28/37	1	2	FACETS	0.683	0.605	0.765	0.683	0.605	0.765	SUBCLONAL	1	TRUE	1	0.41995758758546	2		941	607	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202265	138202265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373799889	NA	P-0023963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	100	692	0	ENST00000237289.4:c.2182C>T	p.Arg728Cys	p.R728C	ENST00000237289	NM_001270507.1	728	Cgc/Tgc	9/9	1	2	FACETS	0.802	0.718	0.891	0.802	0.718	0.891	CLONAL	1	TRUE	1	0.41995758758546	2		692	594	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0023963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	125	792	6	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.768	0.695	0.845	0.768	0.695	0.845	SUBCLONAL	1	TRUE	1	0.41995758758546	2		798	775	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798511	32798511	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs765335850	NA	P-0023963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	143	878	1	ENST00000374899.4:c.1345C>T	p.Arg449Ter	p.R449*	ENST00000374899	NM_018833.2	449	Cga/Tga	8/12	0.388406022412826	1	FACETS	0.897	0.821	0.976	0.897	0.821	0.976	CLONAL	1	TRUE	0	0.41995758758546	1		879	600	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272238	15272238	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs760917811	NA	P-0023963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	61	753	2	ENST00000263388.2:c.6201del	p.Lys2069ArgfsTer16	p.K2069Rfs*16	ENST00000263388	NM_000435.2	2067	ccC/cc	33/33	1	2	FACETS	0.669	0.579	0.767	0.669	0.579	0.767	SUBCLONAL	1	TRUE	1	0.41995758758546	2		755	434	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672317	86672317	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	139	691	1	ENST00000274376.6:c.2119C>T	p.Arg707Cys	p.R707C	ENST00000274376	NM_002890.2	707	Cgt/Tgt	16/25	0.388406022412826	1	FACETS	0.88	0.805	0.959	0.88	0.805	0.959	CLONAL	1	TRUE	0	0.41995758758546	1		692	594	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864391	57864391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753413155	NA	P-0023963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1536	96	807	0	ENST00000228682.2:c.1868G>A	p.Arg623Gln	p.R623Q	ENST00000228682	NM_005269.2	623	cGa/cAa	12/12	0.41995758758546	11	FACETS	0.81	0.718	0.908			1	CLONAL	1	TRUE	NA	0.41995758758546	11		807	1632	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987063	36987063	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760880632	NA	P-0023963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	102	752	1	ENST00000354822.5:c.626G>A	p.Arg209His	p.R209H	ENST00000354822	NM_001079668.2	209	cGc/cAc	3/3	1	2	FACETS	0.917	0.823	1	0.917	0.823	1	CLONAL	1	TRUE	1	0.41995758758546	2		753	530	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222522	2222523	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs750035555	NA	P-0023963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	104	812	1	ENST00000326181.6:c.722dup	p.Leu242AlafsTer55	p.L242Afs*55	ENST00000326181	NM_032271.2	239	tgc/tgCc	9/21	0.141218371112762	0	FACETS	0.548	0.493	0.607			1	INDETERMINATE	1	TRUE	0	0.41995758758546	0		813	524	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845236	89845236	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775917892	NA	P-0023963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	102	771	1	ENST00000389301.3:c.1799G>A	p.Arg600His	p.R600H	ENST00000389301	NM_000135.2	600	cGt/cAt	20/43	1	2	FACETS	0.966	0.867	1	0.966	0.867	1	CLONAL	1	TRUE	1	0.41995758758546	2		772	503	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276747	15276747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	99	830	0	ENST00000263388.2:c.5518G>A	p.Glu1840Lys	p.E1840K	ENST00000263388	NM_000435.2	1840	Gag/Aag	30/33	1	2	FACETS	0.854	0.765	0.949	0.854	0.765	0.949	CLONAL	1	TRUE	1	0.41995758758546	2		830	552	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220070	36220070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	94	756	0	ENST00000222270.7:c.4790G>A	p.Arg1597Gln	p.R1597Q	ENST00000222270	NM_014727.1	1597	cGg/cAg	22/37	1	2	FACETS	0.995	0.89	1	0.995	0.89	1	CLONAL	1	TRUE	1	0.41995758758546	2		756	450	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719299	190719299	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs969471436	NA	P-0023963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	81	529	1	ENST00000441310.2:c.1301A>G	p.Asn434Ser	p.N434S	ENST00000441310	NM_000534.4	434	aAt/aGt	9/13	1	2	FACETS	0.704	0.621	0.792	0.704	0.621	0.792	SUBCLONAL	1	TRUE	1	0.41995758758546	2		530	548	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413712	138413712	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	115	586	0	ENST00000289153.2:c.1808C>A	p.Pro603His	p.P603H	ENST00000289153	NM_006219.2	603	cCc/cAc	12/22	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.41995758758546	2		586	537	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032249	26032249	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	95	388	0	ENST00000244661.2:c.40G>T	p.Gly14Cys	p.G14C	ENST00000244661	NM_003537.3	14	Ggt/Tgt	1/1	0.281986827333285	4	FACETS	1	0.98	1	0.717	0.642	0.796	CLONAL	1	TRUE	2	0.41995758758546	4		388	448	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877842	151877842	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	93	532	0	ENST00000262189.6:c.7103A>G	p.Gln2368Arg	p.Q2368R	ENST00000262189	NM_170606.2	2368	cAg/cGg	36/59	0.371653885589031	1	FACETS	0.792	0.708	0.88	0.792	0.708	0.88	SUBCLONAL	1	TRUE	0	0.41995758758546	1		532	442	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090508	5090509	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	101	571	0	ENST00000381652.3:c.2829dup	p.His944ThrfsTer2	p.H944Tfs*2	ENST00000381652	NM_004972.3	942	caa/cAaa	21/25	0.403692717712312	1	FACETS	0.833	0.749	0.922	0.833	0.749	0.922	CLONAL	1	TRUE	0	0.41995758758546	1		571	456	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044971	47044971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	60	991	1	ENST00000377604.3:c.2297G>A	p.Arg766His	p.R766H	ENST00000377604	NM_001204468.1	766	cGc/cAc	20/24	1	2	FACETS	0.472	0.407	0.544	0.472	0.407	0.544	SUBCLONAL	1	TRUE	1	0.41995758758546	2		992	605	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410771	63410771	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	83	723	0	ENST00000330258.3:c.2396del	p.Asn799ThrfsTer9	p.N799Tfs*9	ENST00000330258	NM_152424.3	799	aAc/ac	2/2	1	2	FACETS	0.8	0.708	0.898	0.8	0.708	0.898	SUBCLONAL	1	TRUE	1	0.41995758758546	2		723	494	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0023964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	660	790	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.516465863320968	4	FACETS	0.94	0.909	0.972	0.94	0.909	0.972	CLONAL	3	TRUE	1	0.516465863320968	4		790	1374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659675	NA	P-0023964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	249	690	0	ENST00000269305.4:c.764T>C	p.Ile255Thr	p.I255T	ENST00000269305	NM_001126112.2	255	aTc/aCc	7/11	0.516465863320968	1	FACETS	0.951	0.893	1	0.951	0.893	1	CLONAL	1	TRUE	0	0.516465863320968	1		690	752	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672323	86672323	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554049422	NA	P-0023964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	182	491	0	ENST00000274376.6:c.2125C>T	p.Arg709Ter	p.R709*	ENST00000274376	NM_002890.2	709	Cga/Tga	16/25	1	2	FACETS	0.976	0.903	1	0.976	0.903	1	CLONAL	1	TRUE	1	0.516465863320968	2		491	722	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0023964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	149	436	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.516465863320968	2		436	442	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0023964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	170	460	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.516465863320968	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.516465863320968	1		460	461	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726691	41726691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776776986	NA	P-0023964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	271	748	4	ENST00000301178.4:c.236C>T	p.Ala79Val	p.A79V	ENST00000301178	NM_021913.4	79	gCg/gTg	2/20	1	2	FACETS	0.961	0.902	1	0.961	0.902	1	CLONAL	1	TRUE	1	0.516465863320968	2		752	1092	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942713	44942714	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0023964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	156	479	0	ENST00000377967.4:c.3294dup	p.Gln1099AlafsTer4	p.Q1099Afs*4	ENST00000377967	NM_021140.2	1098	ttg/ttGg	23/29	0.516465863320968	1	FACETS	0.894	0.825	0.966	0.894	0.825	0.966	CLONAL	1	TRUE	0	0.516465863320968	1		479	501	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0023966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	200	966	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.587031797846215	2		967	621	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0023966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	359	772	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.587031797846215	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.587031797846215	2		772	597	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168695	32168695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143103753	NA	P-0023966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	191	889	1	ENST00000375023.3:c.4228C>T	p.Arg1410Cys	p.R1410C	ENST00000375023	NM_004557.3	1410	Cgc/Tgc	23/30	0.556725561814183	2	FACETS	0.884	0.831	0.937	0.884	0.831	0.937	CLONAL	2	TRUE	0	0.587031797846215	2		890	368	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481412	140481412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913353	NA	P-0023966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	52	697	2	ENST00000288602.6:c.1396G>A	p.Gly466Arg	p.G466R	ENST00000288602	NM_004333.4	466	Gga/Aga	11/18	NA	2	FACETS	0.35	0.298	0.407			1	INDETERMINATE	1	TRUE	NA	0.587031797846215	2		699	506	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641487	18641487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	147	687	2	ENST00000266497.5:c.2486C>T	p.Ser829Phe	p.S829F	ENST00000266497		829	tCc/tTc	17/31	0.318229054946446	1	FACETS	0.91	0.84	0.98	0.91	0.84	0.98	INDETERMINATE	1	TRUE	0	0.587031797846215	1		689	389	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295230	+	upstream_gene_variant	5'Flank	TNP	GGG	GGG	AGA	novel	NA	P-0023966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	102	551	0				ENST00000310581	NM_198253.2	-/1132			0.417184687669611	3	FACETS	0.861	0.783	0.941	0.861	0.783	0.941	CLONAL	2	TRUE	1	0.587031797846215	3		551	261	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138513	11138513	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	151	859	0	ENST00000358026.2:c.3269C>T	p.Pro1090Leu	p.P1090L	ENST00000358026	NM_001128849.1	1090	cCc/cTc	24/36	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.587031797846215	2		859	481	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257084	16257084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	157	790	0	ENST00000375759.3:c.4349G>A	p.Arg1450Lys	p.R1450K	ENST00000375759	NM_015001.2	1450	aGa/aAa	11/15	1	2	FACETS	0.91	0.837	0.985	0.91	0.837	0.985	CLONAL	1	TRUE	1	0.587031797846215	2		790	588	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404750	70404750	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	197	691	0	ENST00000373644.4:c.2264C>T	p.Thr755Ile	p.T755I	ENST00000373644	NM_030625.2	755	aCc/aTc	4/12	0.318229054946446	1	FACETS	0.915	0.855	0.977	0.915	0.855	0.977	INDETERMINATE	1	TRUE	0	0.587031797846215	1		691	518	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989155	41989156	+	missense_variant	Missense_Mutation	DNP	CT	CT	TC	novel	NA	P-0023966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	161	858	1	ENST00000219905.7:c.1947_1948delinsTC	p.Phe650Leu	p.F650L	ENST00000219905	NM_001164273.1	649	acCTtt/acTCtt	3/24	0.216122746201994	1	FACETS	0.744	0.687	0.802	0.744	0.687	0.802	INDETERMINATE	1	TRUE	0	0.587031797846215	1		859	521	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880995	37880995	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	161	922	0	ENST00000269571.5:c.2324C>T	p.Ala775Val	p.A775V	ENST00000269571		775	gCt/gTt	20/27	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.587031797846215	2		922	513	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10292744	10292744	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	148	743	0	ENST00000340748.4:c.90T>G	p.Asp30Glu	p.D30E	ENST00000340748		30	gaT/gaG	2/40	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.587031797846215	2		743	468	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762890	40762890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	186	938	0	ENST00000392038.2:c.118G>A	p.Glu40Lys	p.E40K	ENST00000392038	NM_001626.4	40	Gag/Aag	3/14	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.587031797846215	2		938	525	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758808	41758808	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	178	843	1	ENST00000301178.4:c.1862C>T	p.Pro621Leu	p.P621L	ENST00000301178	NM_021913.4	621	cCt/cTt	16/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.587031797846215	2		844	564	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753611	42753611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761263189	NA	P-0023966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	183	811	0	ENST00000222329.4:c.653G>A	p.Arg218Gln	p.R218Q	ENST00000222329	NM_006494.2	218	cGa/cAa	4/4	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.587031797846215	2		811	535	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798813	42798813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	143	873	0	ENST00000575354.2:c.4385C>T	p.Ser1462Phe	p.S1462F	ENST00000575354	NM_015125.3	1462	tCc/tTc	19/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.587031797846215	2		873	434	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661455	227661455	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	184	700	0	ENST00000305123.5:c.2000C>T	p.Pro667Leu	p.P667L	ENST00000305123	NM_005544.2	667	cCc/cTc	1/2	0.556725561814183	2	FACETS	0.922	0.867	0.976	0.922	0.867	0.976	CLONAL	2	TRUE	0	0.587031797846215	2		700	340	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979334	40979334	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	194	780	0	ENST00000373198.4:c.1799T>C	p.Leu600Ser	p.L600S	ENST00000373198	NM_133170.3	600	tTg/tCg	11/32	0.333599191550004	4	FACETS	0.886	0.825	0.949	0.886	0.825	0.949	INDETERMINATE	2	TRUE	2	0.587031797846215	4		780	592	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499408	89499408	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	137	606	0	ENST00000336596.2:c.2578T>C	p.Cys860Arg	p.C860R	ENST00000336596	NM_005233.5	860	Tgc/Cgc	15/17	1	2	FACETS	0.995	0.912	1	0.995	0.912	1	CLONAL	1	TRUE	1	0.587031797846215	2		606	469	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665464	138665540	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCTCGGCGGCGGCCCTTCTGGCTCCTTGACTGTGCGACCGGTCTCTGGGGCCAGCAGGGCCCCCGCCGCGTCCTC	GGGCTCGGCGGCGGCCCTTCTGGCTCCTTGACTGTGCGACCGGTCTCTGGGGCCAGCAGGGCCCCCGCCGCGTCCTC	-	novel	NA	P-0023966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	30	741	0	ENST00000330315.3:c.25_101del	p.Glu9ArgfsTer61	p.E9Rfs*61	ENST00000330315	NM_023067.3	9	GAGGACGCGGCGGGGGCCCTGCTGGCCCCAGAGACCGGTCGCACAGTCAAGGAGCCAGAAGGGCCGCCGCCGAGCCCa/a	1/1	1	2	FACETS	0.265	0.214	0.324	0.265	0.214	0.324	SUBCLONAL	1	TRUE	1	0.587031797846215	2		741	385	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861092	35861092	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	153	478	0	ENST00000303115.3:c.221G>A	p.Cys74Tyr	p.C74Y	ENST00000303115	NM_002185.3	74	tGt/tAt	2/8	0.417184687669611	3	FACETS	0.816	0.755	0.879	0.816	0.755	0.879	CLONAL	2	TRUE	1	0.587031797846215	3		478	413	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665629	86665629	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0023966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	47	412	0	ENST00000274376.6:c.1611-1G>A		p.X537_splice	ENST00000274376	NM_002890.2	537			0.318229054946446	1	FACETS	0.378	0.321	0.441	0.378	0.321	0.441	INDETERMINATE	1	TRUE	0	0.587031797846215	1		412	299	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510178	149510178	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	191	870	0	ENST00000261799.4:c.1291G>A	p.Glu431Lys	p.E431K	ENST00000261799	NM_002609.3	431	Gaa/Aaa	9/23	0.318229054946446	1	FACETS	0.974	0.91	1	0.974	0.91	1	INDETERMINATE	1	TRUE	0	0.587031797846215	1		870	472	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509072	106509072	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372885634	NA	P-0023966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	309	711	0	ENST00000359195.3:c.1066G>A	p.Asp356Asn	p.D356N	ENST00000359195	NM_002649.2	356	Gac/Aac	2/11	0.389755996450873	3	FACETS	1	0.993	1	0.828	0.791	0.865	CLONAL	2	TRUE	0	0.587031797846215	3		711	548	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982059	70982059	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760440697	NA	P-0023966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	116	743	1	ENST00000276594.2:c.37G>A	p.Asp13Asn	p.D13N	ENST00000276594	NM_024504.3	13	Gac/Aac	2/8	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.587031797846215	2		744	386	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155149	106155149	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	35	449	0	ENST00000380013.4:c.50T>G	p.Phe17Cys	p.F17C	ENST00000380013	NM_001127208.2	17	tTc/tGc	3/11	1	2	FACETS	0.545	0.446	0.655	0.545	0.446	0.655	SUBCLONAL	1	TRUE	1	0.283753688239868	2		449	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0023969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	73	622	0	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.24	2		622	603	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0023969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	34	463	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	0.8	0.655	0.963	0.8	0.655	0.963	CLONAL	1	TRUE	1	0.24	2		463	354	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088787	27088788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0023969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	58	625	0	ENST00000324856.7:c.2402dup	p.Gln802SerfsTer15	p.Q802Sfs*15	ENST00000324856	NM_006015.4	799	cag/caGg	7/20	1	2	FACETS	0.727	0.624	0.839	0.727	0.624	0.839	SUBCLONAL	1	TRUE	1	0.24	2		625	665	SUCCESS
APC	324	MSKCC	GRCh37	5	112174760	112174760	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	18	400	1	ENST00000257430.4:c.3469G>A	p.Glu1157Lys	p.E1157K	ENST00000257430	NM_000038.5	1157	Gag/Aag	16/16	1	2	FACETS	0.426	0.32	0.552	0.426	0.32	0.552	SUBCLONAL	1	TRUE	1	0.24	2		401	352	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467437	66467437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749830045	NA	P-0023969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	51	398	1	ENST00000273854.3:c.832G>A	p.Ala278Thr	p.A278T	ENST00000273854	NM_004439.5	278	Gcc/Acc	3/18	1	2	FACETS	0.926	0.788	1	0.926	0.788	1	CLONAL	1	TRUE	1	0.24	2		399	459	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0023969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	55	400	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.88	0.753	1	0.88	0.753	1	CLONAL	1	TRUE	1	0.24	2		400	521	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716327	52716327	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	77	677	0	ENST00000322088.6:c.771G>T	p.Trp257Cys	p.W257C	ENST00000322088	NM_014225.5	257	tgG/tgT	6/15	1	2	FACETS	0.968	0.85	1	0.968	0.85	1	CLONAL	1	TRUE	1	0.24	2		677	663	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866417	37866417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	182	688	1	ENST00000269571.5:c.722C>T	p.Ala241Val	p.A241V	ENST00000269571		241	gCt/gTt	6/27	1	2	FACETS	0.995	0.92	1	1	0.993	1	CLONAL	2	TRUE	1	0.24	2		689	762	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0023972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	410	909	1	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.3	3	FACETS	0.963	0.919	1	0.963	0.919	1	CLONAL	3	FALSE	0	0.3	3		910	1088	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120493418	120493418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	92	827	0	ENST00000256646.2:c.2408C>T	p.Pro803Leu	p.P803L	ENST00000256646	NM_024408.3	803	cCa/cTa	15/34	0.268636688879081	3	FACETS	0.779	0.691	0.874	0.39	0.345	0.437	SUBCLONAL	1	FALSE	1	0.3	3		827	905	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967215	134967216	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0023972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	68	712	3	ENST00000398015.3:c.2554_2555delinsTT	p.Ala852Phe	p.A852F	ENST00000398015	NM_004441.4	852	GCt/TTt	14/16	0.297220234579535	5	FACETS	0.764	0.663	0.874	0.255	0.221	0.292	SUBCLONAL	1	FALSE	2	0.3	5		715	860	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561547	9561547	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	125	581	1	ENST00000353224.5:c.235G>A	p.Glu79Lys	p.E79K	ENST00000353224	NM_177990.2	79	Gaa/Aaa	4/10	1	2	FACETS	0.915	0.828	1	0.915	0.828	1	CLONAL	1	TRUE	1	0.34952563085858	2		582	782	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456447	189456447	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	36	488	0	ENST00000264731.3:c.208C>T	p.Gln70Ter	p.Q70*	ENST00000264731	NM_003722.4	70	Cag/Tag	3/14	0.13221337107539	3	FACETS	0.391	0.32	0.47	0.195	0.16	0.235	INDETERMINATE	1	TRUE	1	0.34952563085858	3		488	619	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0023973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	82	445	0	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	1	2	FACETS	0.967	0.856	1	0.967	0.856	1	CLONAL	1	TRUE	1	0.34952563085858	2		445	485	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061141	38061141	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	27	180	0	ENST00000250448.2:c.848G>A	p.Gly283Glu	p.G283E	ENST00000250448	NM_004496.3	283	gGg/gAg	2/2	0.13221337107539	3	FACETS	1	0.818	1	0.51	0.409	0.623	INDETERMINATE	1	TRUE	1	0.34952563085858	3		180	178	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176504	142176504	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1196005889	NA	P-0023973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	107	533	0	ENST00000350721.4:c.7597C>T	p.Arg2533Ter	p.R2533*	ENST00000350721	NM_001184.3	2533	Cga/Tga	45/47	1	2	FACETS	0.854	0.766	0.947	0.854	0.766	0.947	CLONAL	1	TRUE	1	0.34952563085858	2		533	717	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944959	31944959	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	41	549	0	ENST00000340398.3:c.142C>T	p.Leu48Phe	p.L48F	ENST00000340398	NM_001013699.2	48	Ctt/Ttt	1/1	0.13221337107539	3	FACETS	0.457	0.38	0.543	0.229	0.19	0.272	INDETERMINATE	1	TRUE	1	0.34952563085858	3		549	603	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426270	49426270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1028956623	NA	P-0023973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	153	929	1	ENST00000301067.7:c.12218C>T	p.Ser4073Leu	p.S4073L	ENST00000301067	NM_003482.3	4073	tCa/tTa	39/54	0.13221337107539	3	FACETS	1	0.94	1	0.518	0.473	0.565	INDETERMINATE	1	TRUE	1	0.34952563085858	3		930	993	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926255	112926255	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	128	630	0	ENST00000351677.2:c.1388T>A	p.Ile463Asn	p.I463N	ENST00000351677	NM_002834.3	463	aTt/aAt	12/16	0.34952563085858	1	FACETS	0.944	0.858	1	0.944	0.858	1	CLONAL	1	TRUE	0	0.34952563085858	1		630	640	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857388	9857388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754258505	NA	P-0023973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	95	582	1	ENST00000330684.3:c.4013G>A	p.Gly1338Glu	p.G1338E	ENST00000330684	NM_001134407.1	1338	gGg/gAg	13/13	1	2	FACETS	0.832	0.742	0.929	0.832	0.742	0.929	CLONAL	1	TRUE	1	0.34952563085858	2		583	653	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23625323	23625323	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0023973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	134	714	1	ENST00000261584.4:c.3201+2T>A		p.X1067_splice	ENST00000261584	NM_024675.3	1067			1	2	FACETS	0.854	0.775	0.936	0.854	0.775	0.936	CLONAL	1	TRUE	1	0.34952563085858	2		715	898	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577544	7577544	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587780074	NA	P-0023973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	142	756	0	ENST00000269305.4:c.737T>G	p.Met246Arg	p.M246R	ENST00000269305	NM_001126112.2	246	aTg/aGg	7/11	0.348180817950222	1	FACETS	0.952	0.87	1	0.952	0.87	1	CLONAL	1	TRUE	0	0.34952563085858	1		756	704	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313215	30313216	+	missense_variant	Missense_Mutation	DNP	CT	CT	TA	novel	NA	P-0023973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	153	884	0	ENST00000262643.3:c.909_910delinsTA	p.Leu304Met	p.L304M	ENST00000262643	NM_001238.2	303	gcCTtg/gcTAtg	10/12	1	2	FACETS	0.994	0.909	1	0.994	0.909	1	CLONAL	1	TRUE	1	0.34952563085858	2		884	881	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566859	212566859	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	43	373	0	ENST00000342788.4:c.1322G>A	p.Gly441Asp	p.G441D	ENST00000342788	NM_005235.2	441	gGc/gAc	12/28	0.34952563085858	1	FACETS	0.501	0.42	0.591	0.501	0.42	0.591	SUBCLONAL	1	TRUE	0	0.34952563085858	1		373	405	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827885	40827885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	107	611	2	ENST00000373198.4:c.2543G>A	p.Gly848Glu	p.G848E	ENST00000373198	NM_133170.3	848	gGa/gAa	17/32	1	2	FACETS	0.93	0.836	1	0.93	0.836	1	CLONAL	1	TRUE	1	0.34952563085858	2		613	658	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62294198	62294237	+	frameshift_variant	Frame_Shift_Del	DEL	AGAAGGTGGCAAGTCGCTCCTGTCATTTCTACAACAACGT	AGAAGGTGGCAAGTCGCTCCTGTCATTTCTACAACAACGT	-	novel	NA	P-0023973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	46	721	0	ENST00000360203.5:c.501_538+2del		p.KKVASRSCHFYNNV165fs	ENST00000360203	NM_001283009.1	165	aAGAAGGTGGCAAGTCGCTCCTGTCATTTCTACAACAACGTa/aa	6/35	1	2	FACETS	0.35	0.294	0.412	0.35	0.294	0.412	SUBCLONAL	1	TRUE	1	0.34952563085858	2		721	752	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1978301	1978301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774737951	NA	P-0023973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	160	777	3	ENST00000382891.5:c.3721G>A	p.Glu1241Lys	p.E1241K	ENST00000382891	NM_133335.3	1241	Gag/Aag	21/22	0.219294184995159	3	FACETS	0.983	0.9	1	0.492	0.45	0.535	CLONAL	1	TRUE	1	0.34952563085858	3		780	1094	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131193	55131193	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	127	581	0	ENST00000257290.5:c.736C>T	p.Gln246Ter	p.Q246*	ENST00000257290	NM_006206.4	246	Caa/Taa	5/23	0.219294184995159	3	FACETS	0.985	0.892	1	0.492	0.446	0.542	CLONAL	1	TRUE	1	0.34952563085858	3		581	867	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673241	30673241	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	87	515	0	ENST00000376406.3:c.3719C>T	p.Pro1240Leu	p.P1240L	ENST00000376406	NM_014641.2	1240	cCt/cTt	10/15	0.2955287997944	4	FACETS	0.819	0.724	0.921	0.41	0.362	0.461	CLONAL	1	TRUE	2	0.34952563085858	4		515	820	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878620	151878620	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	127	697	2	ENST00000262189.6:c.6325T>A	p.Phe2109Ile	p.F2109I	ENST00000262189	NM_170606.2	2109	Ttt/Att	36/59	1	2	FACETS	0.812	0.735	0.893	0.812	0.735	0.893	CLONAL	1	TRUE	1	0.34952563085858	2		699	895	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020458	69020458	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	136	784	0	ENST00000288368.4:c.2830G>A	p.Glu944Lys	p.E944K	ENST00000288368	NM_024870.2	944	Gaa/Aaa	24/40	1	2	FACETS	0.799	0.726	0.876	0.799	0.726	0.876	SUBCLONAL	1	TRUE	1	0.34952563085858	2		784	974	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90960096	90960096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs962092255	NA	P-0023973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	52	411	1	ENST00000265433.3:c.1870C>T	p.Arg624Cys	p.R624C	ENST00000265433	NM_002485.4	624	Cgt/Tgt	12/16	1	2	FACETS	0.554	0.472	0.645	0.554	0.472	0.645	SUBCLONAL	1	TRUE	1	0.34952563085858	2		412	537	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90960110	90960110	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	45	346	1	ENST00000265433.3:c.1856A>T	p.Glu619Val	p.E619V	ENST00000265433	NM_002485.4	619	gAa/gTa	12/16	1	2	FACETS	0.555	0.466	0.653	0.555	0.466	0.653	SUBCLONAL	1	TRUE	1	0.34952563085858	2		347	464	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128321935	128321936	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0023973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	120	650	1	ENST00000265960.3:c.824_825delinsTT	p.Ser275Phe	p.S275F	ENST00000265960	NM_001006617.1	275	tCC/tTT	6/12	0.0852044236543317	3	FACETS	1	0.941	1			1	INDETERMINATE	1	TRUE	NA	0.34952563085858	3		651	763	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15833834	15833834	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	132	680	0	ENST00000307771.7:c.592C>T	p.Pro198Ser	p.P198S	ENST00000307771	NM_005089.3	198	Cct/Tct	8/11	1	2	FACETS	0.935	0.849	1	0.935	0.849	1	CLONAL	1	TRUE	1	0.34952563085858	2		680	808	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045731	47045731	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	71	831	0	ENST00000377604.3:c.2612G>T	p.Trp871Leu	p.W871L	ENST00000377604	NM_001204468.1	871	tGg/tTg	23/24	1	2	FACETS	0.474	0.413	0.541	0.474	0.413	0.541	SUBCLONAL	1	TRUE	1	0.34952563085858	2		831	857	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410945	63410945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	149	748	1	ENST00000330258.3:c.2222C>T	p.Pro741Leu	p.P741L	ENST00000330258	NM_152424.3	741	cCc/cTc	2/2	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.34952563085858	2		749	811	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778830	76778830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	139	707	0	ENST00000373344.5:c.6749G>A	p.Gly2250Glu	p.G2250E	ENST00000373344	NM_000489.3	2250	gGa/gAa	31/35	1	2	FACETS	0.908	0.826	0.994	0.908	0.826	0.994	CLONAL	1	TRUE	1	0.34952563085858	2		707	876	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	142	855	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.563524972825096	1	FACETS	0.71	0.652	0.771	0.71	0.652	0.771	SUBCLONAL	1	TRUE	0	0.581980981028148	1		855	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0023974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	271	885	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.581980981028148	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.581980981028148	1		885	609	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0023974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	175	602	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.581980981028148	3	FACETS	0.876	0.807	0.948	0.438	0.403	0.474	CLONAL	1	TRUE	1	0.581980981028148	3		603	886	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100916	27100916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267598526	NA	P-0023974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	199	716	0	ENST00000324856.7:c.4198C>T	p.Pro1400Ser	p.P1400S	ENST00000324856	NM_006015.4	1400	Cct/Tct	18/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.581980981028148	2		716	667	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881513	48881513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	263	507	0	ENST00000267163.4:c.235G>T	p.Glu79Ter	p.E79*	ENST00000267163	NM_000321.2	79	Gag/Tag	2/27	0.581980981028148	2	FACETS	0.9	0.855	0.946	0.9	0.855	0.946	CLONAL	2	TRUE	0	0.581980981028148	2		507	502	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591846	48591846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	267	720	0	ENST00000342988.3:c.1009G>A	p.Glu337Lys	p.E337K	ENST00000342988	NM_005359.5	337	Gag/Aag	9/12	0.581980981028148	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.581980981028148	1		720	490	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169953061	169953061	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	228	664	0	ENST00000295797.4:c.145G>A	p.Gly49Ser	p.G49S	ENST00000295797	NM_002740.5	49	Ggc/Agc	2/18	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.581980981028148	2		664	767	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0023976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	11	790	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.555	0.383	0.771	0.555	0.383	0.771	SUBCLONAL	1	TRUE	1	0.14	2		790	283	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0023976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	13	365	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	1	2	FACETS	0.915	0.653	1	0.915	0.653	1	CLONAL	1	TRUE	1	0.14	2		365	203	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039468	49039468	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	28	682	0	ENST00000267163.4:c.2453G>T	p.Gly818Val	p.G818V	ENST00000267163	NM_000321.2	818	gGt/gTt	23/27	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.14	2		682	318	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955419	48955419	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0023984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	42	518	0	ENST00000267163.4:c.1535T>A	p.Leu512Ter	p.L512*	ENST00000267163	NM_000321.2	512	tTg/tAg	17/27	0.546628908823878	1	FACETS	0.247	0.206	0.292	0.247	0.206	0.292	SUBCLONAL	1	TRUE	0	0.557269482324567	1		518	441	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936983	48936983	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690863	NA	P-0023984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	51	545	1	ENST00000267163.4:c.751C>T	p.Arg251Ter	p.R251*	ENST00000267163	NM_000321.2	251	Cga/Tga	8/27	0.546628908823878	1	FACETS	0.258	0.219	0.301	0.258	0.219	0.301	SUBCLONAL	1	TRUE	0	0.557269482324567	1		546	511	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806119	1806119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931614	NA	P-0023984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	11	784	0	ENST00000260795.2:c.1138G>A	p.Gly380Arg	p.G380R	ENST00000260795		380	Ggg/Agg	8/17	0.557269482324567	1	FACETS	0.064	0.044	0.09	0.064	0.044	0.09	SUBCLONAL	1	TRUE	0	0.557269482324567	1		784	443	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027147	49027148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	60	580	0	ENST00000267163.4:c.1716dup	p.Ile573TyrfsTer2	p.I573Yfs*2	ENST00000267163	NM_000321.2	572	ctt/cTtt	18/27	0.546628908823878	1	FACETS	0.282	0.243	0.325	0.282	0.243	0.325	SUBCLONAL	1	TRUE	0	0.557269482324567	1		580	550	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037966	49037966	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	177	560	0	ENST00000267163.4:c.2206C>T	p.Gln736Ter	p.Q736*	ENST00000267163	NM_000321.2	736	Cag/Tag	21/27	0.789472883560932	1	FACETS	0.89	0.838	0.941	0.89	0.838	0.941	CLONAL	1	TRUE	0	0.789472883560932	1		560	305	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587782529	NA	P-0023987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	262	785	0	ENST00000269305.4:c.1009C>G	p.Arg337Gly	p.R337G	ENST00000269305	NM_001126112.2	337	Cgc/Ggc	10/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.789472883560932	2		785	644	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577095	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519984	NA	P-0023987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	230	742	1	ENST00000269305.4:c.843C>A	p.Asp281Glu	p.D281E	ENST00000269305	NM_001126112.2	281	gaC/gaA	8/11	1	2	FACETS	0.822	0.769	0.875	0.822	0.769	0.875	CLONAL	1	TRUE	1	0.789472883560932	2		743	709	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	30	682	5	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	0.336035434009016	4	FACETS	0.761	0.615	0.926	0.38	0.307	0.463	CLONAL	1	TRUE	2	0.356561672460695	4		687	300	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716212	52716212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555791268	NA	P-0023989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	23	650	1	ENST00000322088.6:c.656C>T	p.Ser219Leu	p.S219L	ENST00000322088	NM_014225.5	219	tCg/tTg	6/15	NA	2	FACETS	0.683	0.536	0.85			1	INDETERMINATE	1	TRUE	NA	0.356561672460695	2		651	189	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087961	27087961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	59	748	0	ENST00000324856.7:c.2248C>T	p.Arg750Ter	p.R750*	ENST00000324856	NM_006015.4	750	Cga/Tga	6/20	0.336035434009016	4	FACETS	1	0.939	1	0.58	0.501	0.665	CLONAL	1	TRUE	2	0.356561672460695	4		748	387	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519757	NA	P-0023989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	42	374	0	ENST00000274335.5:c.1126G>C	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Cga	9/15	0.356561672460695	4	FACETS	0.921	0.771	1	0.46	0.385	0.543	CLONAL	1	TRUE	2	0.356561672460695	4		374	347	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589309	67589309	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	40	401	1	ENST00000274335.5:c.1297C>T	p.Gln433Ter	p.Q433*	ENST00000274335		433	Cag/Tag	9/15	0.356561672460695	4	FACETS	0.805	0.67	0.955	0.403	0.335	0.478	CLONAL	1	TRUE	2	0.356561672460695	4		402	378	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5462929	5462929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146495642	NA	P-0023989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	20	402	1	ENST00000381577.3:c.490G>A	p.Glu164Lys	p.E164K	ENST00000381577	NM_014143.3	164	Gaa/Aaa	4/7	1	2	FACETS	0.394	0.301	0.502	0.394	0.301	0.502	SUBCLONAL	1	TRUE	1	0.356561672460695	2		403	285	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0023990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	686	732	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.587313750504406	6	FACETS	0.987	0.956	1	0.987	0.956	1	CLONAL	4	TRUE	2	0.587313750504406	6		732	1287	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882019	NA	P-0023990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	392	872	1	ENST00000269305.4:c.455dup	p.Pro153AlafsTer28	p.P153Afs*28	ENST00000269305	NM_001126112.2	152	ccg/ccCg	5/11	NA	2	FACETS	0.907	0.869	0.944			1	INDETERMINATE	2	TRUE	NA	0.587313750504406	2		873	736	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241873	72241873	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1252345844	NA	P-0023990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	103	534	0	ENST00000357731.5:c.517C>T	p.Arg173Ter	p.R173*	ENST00000357731	NM_173808.2	173	Cga/Tga	3/7	0.587313750504406	3	FACETS	0.953	0.857	1	0.477	0.428	0.527	CLONAL	1	TRUE	1	0.587313750504406	3		534	476	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307510	118307511	+	missense_variant	Missense_Mutation	DNP	TC	TC	GT	novel	NA	P-0023990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	358	785	1	ENST00000534358.1:c.283_284delinsGT	p.Ser95Val	p.S95V	ENST00000534358	NM_005933.3	95	TCa/GTa	1/36	0.556017751055761	4	FACETS	0.929	0.882	0.976	0.929	0.882	0.976	CLONAL	2	TRUE	2	0.587313750504406	4		786	1042	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643689	38643689	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	415	882	0	ENST00000299084.4:c.1159T>A	p.Phe387Ile	p.F387I	ENST00000299084	NM_152594.2	387	Ttt/Att	7/7	0.587313750504406	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.587313750504406	3		882	883	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117803	70117803	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	175	714	0	ENST00000245479.2:c.271A>G	p.Met91Val	p.M91V	ENST00000245479	NM_000346.3	91	Atg/Gtg	1/3	0.587313750504406	3	FACETS	1	0.926	1	0.502	0.463	0.542	CLONAL	1	TRUE	1	0.587313750504406	3		714	768	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0023991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	27	588	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.345	0.273	0.426	0.345	0.273	0.426	SUBCLONAL	1	TRUE	1	0.321109576382314	2		588	488	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813761	50813762	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0023991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	113	908	0	ENST00000398568.2:c.1317_1318dup	p.Gln440ProfsTer4	p.Q440Pfs*4	ENST00000398568	NM_001042412.1	439	gcc/gCCcc	8/18	0.321109576382314	1	FACETS	0.95	0.857	1	0.95	0.857	1	CLONAL	1	TRUE	0	0.321109576382314	1		908	622	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199742	138199934	+	frameshift_variant	Frame_Shift_Del	DEL	GTGAAACGCCCAACTGCCCCTTCTTCATGTCTGTGAACACCCAGCCTTTATGCCATGAGTGCTCAGAGAGGCGGCAAAAGAATCAAAACAAACTCCCAAAGCTGAACTCCAAGCCGGGCCCTGAGGGGCTCCCTGGCATGGCGCTCGGGGCCTCTCGGGGAGAAGCCTATGAGCCCTTGGCGTGGAACCCTGA	GTGAAACGCCCAACTGCCCCTTCTTCATGTCTGTGAACACCCAGCCTTTATGCCATGAGTGCTCAGAGAGGCGGCAAAAGAATCAAAACAAACTCCCAAAGCTGAACTCCAAGCCGGGCCCTGAGGGGCTCCCTGGCATGGCGCTCGGGGCCTCTCGGGGAGAAGCCTATGAGCCCTTGGCGTGGAACCCTGA	-	novel	NA	P-0023991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	97	757	0	ENST00000237289.4:c.1161_1353del	p.Cys387TrpfsTer26	p.C387Wfs*26	ENST00000237289	NM_001270507.1	387	tGTGAAACGCCCAACTGCCCCTTCTTCATGTCTGTGAACACCCAGCCTTTATGCCATGAGTGCTCAGAGAGGCGGCAAAAGAATCAAAACAAACTCCCAAAGCTGAACTCCAAGCCGGGCCCTGAGGGGCTCCCTGGCATGGCGCTCGGGGCCTCTCGGGGAGAAGCCTATGAGCCCTTGGCGTGGAACCCTGAg/tg	7/9	0.321109576382314	1	FACETS	0.833	0.744	0.927	0.833	0.744	0.927	CLONAL	1	TRUE	0	0.321109576382314	1		757	609	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	196	774	2	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.859	0.797	0.923	0.859	0.797	0.923	CLONAL	1	FALSE	1	0.575275515070965	2		776	793	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189845	11189845	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	269	819	1	ENST00000361445.4:c.5664C>A	p.Phe1888Leu	p.F1888L	ENST00000361445	NM_004958.3	1888	ttC/ttA	40/58	0.575275515070965	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	0	0.575275515070965	1		820	607	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	357	774	2	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.45529858671483	6	FACETS	1	0.983	1			1	CLONAL	3	FALSE	NA	0.45529858671483	6		776	931	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	90	855	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.808	0.718	0.903	0.808	0.718	0.903	CLONAL	1	TRUE	1	0.382276901341516	2		855	583	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0024023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	91	611	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.892	0.794	0.995	0.892	0.794	0.995	CLONAL	1	TRUE	1	0.382276901341516	2		611	534	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0024023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	93	473	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.925	0.825	1	0.925	0.825	1	CLONAL	1	TRUE	1	0.382276901341516	2		473	526	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440680	56440680	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs759809905	NA	P-0024023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	176	872	2	ENST00000407977.2:c.538C>T	p.Gln180Ter	p.Q180*	ENST00000407977		180	Caa/Taa	5/10	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.382276901341516	2		874	893	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627284	12627284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	157	568	0	ENST00000251849.4:c.1432G>A	p.Glu478Lys	p.E478K	ENST00000251849	NM_002880.3	478	Gaa/Aaa	14/17	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.382276901341516	2		568	574	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440892	56440892	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	174	847	1	ENST00000407977.2:c.445G>T	p.Glu149Ter	p.E149*	ENST00000407977		149	Gag/Tag	4/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.382276901341516	2		848	845	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686398	30686399	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0024023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	24	427	0	ENST00000295754.5:c.255_256dup	p.Ala86GlyfsTer11	p.A86Gfs*11	ENST00000295754	NM_003242.5	85	gtg/gtGGg	2/7	1	2	FACETS	0.289	0.226	0.362	0.289	0.226	0.362	SUBCLONAL	1	TRUE	1	0.382276901341516	2		427	435	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729898	30729899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	135	452	0	ENST00000295754.5:c.1422dup	p.Gly475TrpfsTer41	p.G475Wfs*41	ENST00000295754	NM_003242.5	473	-/T	6/7	1	2	FACETS	0.755	0.691	0.821	1	0.987	1	SUBCLONAL	2	TRUE	1	0.382276901341516	2		452	468	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041404	47041405	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0024023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	151	463	0	ENST00000377604.3:c.1753dup	p.Gln585ProfsTer7	p.Q585Pfs*7	ENST00000377604	NM_001204468.1	583	gac/gaCc	16/24	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.382276901341516	1		463	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0024024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	20	754	1	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	1	2	FACETS	0.051	0.038	0.066	0.051	0.038	0.066	SUBCLONAL	1	TRUE	1	0.97	2		755	808	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0024025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	73	386	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	0.58717062916102	3	FACETS	0.883	0.779	0.993	0.294	0.259	0.331	CLONAL	1	TRUE	0	0.72103262900946	3		386	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0024025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	622	839	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.594435555527537	4	FACETS	0.887	0.865	0.908	0.887	0.865	0.908	CLONAL	4	TRUE	0	0.72103262900946	4		841	837	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528711	8528711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774617096	NA	P-0024025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	82	435	0	ENST00000356435.5:c.421C>T	p.Arg141Cys	p.R141C	ENST00000356435		141	Cgc/Tgc	4/35	0.594435555527537	4	FACETS	0.792	0.701	0.89	0.198	0.175	0.223	SUBCLONAL	1	TRUE	0	0.72103262900946	4		435	494	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242486	+	inframe_deletion	In_Frame_Del	DEL	TTAAGAGAAGCAACATCT	TTAAGAGAAGCAACATCT	-	rs121913440	NA	P-0024025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	382	527	0	ENST00000275493.2:c.2239_2256del	p.Leu747_Ser752del	p.L747_S752del	ENST00000275493	NM_005228.3	747	TTAAGAGAAGCAACATCT/-	19/28	0.708925222415477	4	FACETS	1	0.993	1	0.829	0.8	0.857	CLONAL	3	TRUE	0	0.72103262900946	4		527	550	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242713	16242713	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	138	624	0	ENST00000375759.3:c.1334T>A	p.Leu445His	p.L445H	ENST00000375759	NM_015001.2	445	cTt/cAt	6/15	0.478827181203216	3	FACETS	0.899	0.822	0.98			1	CLONAL	1	TRUE	NA	0.72103262900946	3		624	579	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743346	162743346	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	86	446	0	ENST00000367921.3:c.1816G>T	p.Ala606Ser	p.A606S	ENST00000367921	NM_006182.2	606	Gct/Tct	14/18	0.72103262900946	6	FACETS	0.754	0.666	0.847	0.188	0.166	0.212	SUBCLONAL	1	TRUE	2	0.72103262900946	6		446	773	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28901634	28901634	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	98	574	0	ENST00000282397.4:c.2761C>G	p.Leu921Val	p.L921V	ENST00000282397	NM_002019.4	921	Ctc/Gtc	20/30	0.58717062916102	3	FACETS	0.681	0.609	0.757	0.227	0.203	0.253	SUBCLONAL	1	TRUE	0	0.72103262900946	3		574	543	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934546	9934546	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	95	562	0	ENST00000330684.3:c.1609G>T	p.Val537Phe	p.V537F	ENST00000330684	NM_001134407.1	537	Gtt/Ttt	7/13	0.510447303410636	5	FACETS	0.736	0.655	0.822	0.245	0.218	0.274	SUBCLONAL	1	TRUE	2	0.72103262900946	5		562	745	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39708741	39708741	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	54	599	0	ENST00000361337.2:c.352G>C	p.Asp118His	p.D118H	ENST00000361337	NM_003286.2	118	Gat/Cat	6/21	0.630100887716079	5	FACETS	0.523	0.446	0.607	0.174	0.148	0.203	SUBCLONAL	1	TRUE	2	0.72103262900946	5		599	596	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177575	56177575	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	33	429	0	ENST00000399503.3:c.2548A>T	p.Thr850Ser	p.T850S	ENST00000399503	NM_005921.1	850	Acc/Tcc	14/20	0.575372844834283	4	FACETS	0.358	0.291	0.433	0.09	0.072	0.109	SUBCLONAL	1	TRUE	0	0.72103262900946	4		429	440	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170827161	170827161	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	183	305	0	ENST00000296930.5:c.529G>T	p.Asp177Tyr	p.D177Y	ENST00000296930	NM_002520.6	177	Gat/Tat	7/11	0.72103262900946	4	FACETS	1	0.979	1	0.554	0.519	0.59	CLONAL	2	TRUE	0	0.72103262900946	4		305	394	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268918	55268918	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	140	797	0	ENST00000275493.2:c.2984C>T	p.Ser995Phe	p.S995F	ENST00000275493	NM_005228.3	995	tCc/tTc	25/28	0.708925222415477	4	FACETS	0.719	0.655	0.788	0.18	0.163	0.197	SUBCLONAL	1	TRUE	0	0.72103262900946	4		797	929	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209600	98209600	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	81	672	0	ENST00000331920.6:c.3938C>G	p.Pro1313Arg	p.P1313R	ENST00000331920	NM_000264.3	1313	cCa/cGa	23/24	0.569706422964594	3	FACETS	0.711	0.629	0.798	0.237	0.209	0.266	SUBCLONAL	1	TRUE	0	0.72103262900946	3		672	430	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0024026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	268	654	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.386240202549046	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.386240202549046	2		654	594	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940403	13940403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1274578649	NA	P-0024026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	58	569	0	ENST00000405192.2:c.1103G>A	p.Arg368His	p.R368H	ENST00000405192	NM_001163147.1	368	cGt/cAt	11/12	0.225917648482172	4	FACETS	0.624	0.536	0.721	0.312	0.268	0.361	INDETERMINATE	1	TRUE	2	0.386240202549046	4		569	667	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155921	106155921	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs777145283	NA	P-0024026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	94	463	2	ENST00000380013.4:c.822del	p.Asn275IlefsTer18	p.N275Ifs*18	ENST00000380013	NM_001127208.2	274	atC/at	3/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.386240202549046	2		465	420	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272347	15272347	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779314594	NA	P-0024026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	101	1064	5	ENST00000263388.2:c.6092G>A	p.Arg2031His	p.R2031H	ENST00000263388	NM_000435.2	2031	cGc/cAc	33/33	0.167004935315423	4	FACETS	0.626	0.558	0.699	0.313	0.279	0.35	INDETERMINATE	1	TRUE	2	0.386240202549046	4		1069	1158	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349024	89349024	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779550492	NA	P-0024026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	91	1062	1	ENST00000301030.4:c.3926C>T	p.Thr1309Met	p.T1309M	ENST00000301030	NM_001256183.1	1309	aCg/aTg	9/13	0.204783496541229	3	FACETS	0.565	0.5	0.634	0.283	0.25	0.317	INDETERMINATE	1	TRUE	1	0.386240202549046	3		1063	995	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65349035	65349035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	176	678	0	ENST00000342505.4:c.130G>A	p.Asp44Asn	p.D44N	ENST00000342505	NM_002227.2	44	Gac/Aac	3/25	0.169843804510613	4	FACETS	0.866	0.8	0.935	0.866	0.8	0.935	INDETERMINATE	2	TRUE	2	0.386240202549046	4		678	729	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40490751	40490751	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	178	704	0	ENST00000264657.5:c.548G>C	p.Gly183Ala	p.G183A	ENST00000264657	NM_139276.2	183	gGa/gCa	6/24	0.223028535046105	2	FACETS	1	0.989	1	0.703	0.65	0.757	INDETERMINATE	1	TRUE	0	0.386240202549046	2		704	656	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118597	11118597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747463080	NA	P-0024026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	55	575	0	ENST00000358026.2:c.2021C>T	p.Pro674Leu	p.P674L	ENST00000358026	NM_001128849.1	674	cCg/cTg	14/36	0.167004935315423	4	FACETS	0.687	0.587	0.795	0.343	0.293	0.398	INDETERMINATE	1	TRUE	2	0.386240202549046	4		575	575	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921181	50921181	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs761614971	NA	P-0024026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	81	979	2	ENST00000440232.2:c.3305del	p.Pro1102LeufsTer22	p.P1102Lfs*22	ENST00000440232	NM_002691.3	1101	Ccc/cc	27/27	0.167004935315423	4	FACETS	0.543	0.477	0.614	0.271	0.238	0.307	INDETERMINATE	1	TRUE	2	0.386240202549046	4		981	1071	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156204	106156204	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	101	468	0	ENST00000380013.4:c.1105C>G	p.Arg369Gly	p.R369G	ENST00000380013	NM_001127208.2	369	Cgg/Ggg	3/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.386240202549046	2		468	428	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156445	106156445	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	47	476	0	ENST00000380013.4:c.1346T>A	p.Val449Glu	p.V449E	ENST00000380013	NM_001127208.2	449	gTg/gAg	3/11	1	2	FACETS	0.544	0.46	0.638	0.544	0.46	0.638	SUBCLONAL	1	TRUE	1	0.386240202549046	2		476	447	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994186	21994187	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0024026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	259	822	0	ENST00000579755.1:c.144dup	p.Leu49AlafsTer14	p.L49Afs*14	ENST00000579755		48	-/G	1/3	0.386240202549046				0.893	1				CLONAL	2	TRUE	0	0.386240202549046	2		822	707	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139818323	139818323	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0024026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	457	773	0	ENST00000247668.2:c.1158C>G	p.Tyr386Ter	p.Y386*	ENST00000247668	NM_021138.3	386	taC/taG	10/11	0.386240202549046	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.386240202549046	3		773	871	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0024030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	107	865	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.192436842285518	2	FACETS	1	0.982	1	0.734	0.66	0.812	CLONAL	1	TRUE	0	0.256100781344074	2		865	569	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0024030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	50	509	3	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.256100781344074	2		512	369	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983134	201983150	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AGCTGAGCCGGGCCATG	AGCTGAGCCGGGCCATG	-	novel	NA	P-0024030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	29	698	0	ENST00000359651.3:c.985_1001del	p.Leu329ValfsTer136	p.L329Vfs*136	ENST00000359651		328	aAGCTGAGCCGGGCCATG/a	7/8	0.151220904261715	4	FACETS	0.598	0.479	0.733	0.299	0.239	0.367	INDETERMINATE	1	TRUE	2	0.256100781344074	4		698	476	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753342	42753342	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375702097	NA	P-0024031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	148	1060	1	ENST00000222329.4:c.922G>A	p.Glu308Lys	p.E308K	ENST00000222329	NM_006494.2	308	Gag/Aag	4/4	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.340696787158099	2		1061	865	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428023	49428023	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	146	726	2	ENST00000301067.7:c.10567A>T	p.Met3523Leu	p.M3523L	ENST00000301067	NM_003482.3	3523	Atg/Ttg	38/54	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		728	567	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835576	68835577	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	56	510	0	ENST00000261769.5:c.171dup	p.Glu58Ter	p.E58*	ENST00000261769	NM_004360.3	56	aat/aaTt	3/16	0.413973710286529	1	FACETS	0.627	0.54	0.721	0.627	0.54	0.721	SUBCLONAL	1	TRUE	0	0.43526911864268	1		510	321	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251870	212251870	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	22	272	0	ENST00000342788.4:c.3189G>T	p.Gln1063His	p.Q1063H	ENST00000342788	NM_005235.2	1063	caG/caT	27/28	1	2	FACETS	0.416	0.323	0.523	0.416	0.323	0.523	SUBCLONAL	1	TRUE	1	0.43526911864268	2		272	243	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522485	187522485	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	55	725	0	ENST00000441802.2:c.11578A>G	p.Arg3860Gly	p.R3860G	ENST00000441802	NM_005245.3	3860	Aga/Gga	21/27	1	2	FACETS	0.551	0.472	0.637	0.551	0.472	0.637	SUBCLONAL	1	TRUE	1	0.43526911864268	2		725	459	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	78	855	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	0.306494383920388	2		855	474	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717724	89717724	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	100	655	0	ENST00000371953.3:c.749G>T	p.Cys250Phe	p.C250F	ENST00000371953	NM_000314.4	250	tGt/tTt	7/9	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.306494383920388	2		655	458	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999728	100999728	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	63	966	0	ENST00000325455.5:c.74C>A	p.Ser25Tyr	p.S25Y	ENST00000325455	NM_001202474.3	25	tCc/tAc	1/8	1	2	FACETS	0.86	0.745	0.984	0.86	0.745	0.984	CLONAL	1	TRUE	1	0.306494383920388	2		966	478	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577537	7577538	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0024035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	58	861	2	ENST00000269305.4:c.743_744delinsTT	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGG/cTT	7/11	1	2	FACETS	0.852	0.734	0.981	0.852	0.734	0.981	CLONAL	1	TRUE	1	0.306494383920388	2		863	444	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295678	212295678	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	31	591	0	ENST00000342788.4:c.2635G>C	p.Gly879Arg	p.G879R	ENST00000342788	NM_005235.2	879	Gga/Cga	21/28	1	2	FACETS	0.634	0.514	0.77	0.634	0.514	0.77	SUBCLONAL	1	TRUE	1	0.306494383920388	2		591	319	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091749	29091749	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1435731482	NA	P-0024035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	27	411	0	ENST00000328354.6:c.1208G>T	p.Gly403Val	p.G403V	ENST00000328354	NM_007194.3	403	gGg/gTg	11/15	0.262915875960139	1	FACETS	0.646	0.516	0.792	0.646	0.516	0.792	SUBCLONAL	1	TRUE	0	0.306494383920388	1		411	231	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371883	55371883	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	21	353	0	ENST00000297316.4:c.575del	p.Pro192ArgfsTer195	p.P192Rfs*195	ENST00000297316	NM_022454.3	191	ggC/gg	2/2	1	2	FACETS	0.908	0.705	1	0.908	0.705	1	CLONAL	1	TRUE	1	0.306494383920388	2		353	151	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518349	8518349	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	15	410	0	ENST00000356435.5:c.1042C>A	p.Pro348Thr	p.P348T	ENST00000356435		348	Cct/Act	10/35	1	2	FACETS	0.346	0.252	0.458	0.346	0.252	0.458	SUBCLONAL	1	TRUE	1	0.306494383920388	2		410	283	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184090	123184090	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	27	611	0	ENST00000218089.9:c.948G>T	p.Met316Ile	p.M316I	ENST00000218089	NM_001042749.1	316	atG/atT	11/35	1	2	FACETS	0.511	0.406	0.63	0.511	0.406	0.63	SUBCLONAL	1	TRUE	1	0.306494383920388	2		611	345	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0024037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	306	802	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.289752908129244	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.289752908129244	3		802	997	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0024037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	35	405	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.476	0.389	0.573	0.476	0.389	0.573	SUBCLONAL	1	TRUE	1	0.289752908129244	2		405	508	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220410	1220410	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	400	896	1	ENST00000326873.7:c.503A>T	p.His168Leu	p.H168L	ENST00000326873	NM_000455.4	168	cAt/cTt	4/10	0.289752908129244	2	FACETS	0.842	0.802	0.882	1	0.994	1	CLONAL	3	TRUE	0	0.289752908129244	2		897	1093	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038562	47038562	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	167	883	0	ENST00000377604.3:c.724G>T	p.Glu242Ter	p.E242*	ENST00000377604	NM_001204468.1	242	Gag/Tag	8/24	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.289752908129244	2		883	964	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032204	10032204	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	278	825	0	ENST00000330684.3:c.619G>T	p.Asp207Tyr	p.D207Y	ENST00000330684	NM_001134407.1	207	Gac/Tac	3/13	0.160085502340659	2	FACETS	1	0.956	1	1	0.956	1	INDETERMINATE	2	TRUE	0	0.289752908129244	2		825	942	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880864	134880864	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	210	619	0	ENST00000398015.3:c.1427A>G	p.His476Arg	p.H476R	ENST00000398015	NM_004441.4	476	cAc/cGc	7/16	0.257171649431287	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.289752908129244	3		619	731	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355323	81355323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	46	439	0	ENST00000222390.5:c.1051G>A	p.Glu351Lys	p.E351K	ENST00000222390	NM_000601.4	351	Gaa/Aaa	9/18	0.230570722692268	1	FACETS	0.595	0.502	0.699	0.595	0.502	0.699	SUBCLONAL	1	TRUE	0	0.289752908129244	1		439	456	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635179	87635179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	159	645	0	ENST00000277120.3:c.2231G>A	p.Arg744Lys	p.R744K	ENST00000277120		744	aGg/aAg	18/19	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.289752908129244	2		645	735	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411537	63411537	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	132	942	0	ENST00000330258.3:c.1630C>G	p.Pro544Ala	p.P544A	ENST00000330258	NM_152424.3	544	Ccc/Gcc	2/2	0.163193653955621	2	FACETS	0.892	0.809	0.981	0.446	0.404	0.491	INDETERMINATE	1	TRUE	0	0.289752908129244	2		942	1021	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76931746	76931746	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	77	732	0	ENST00000373344.5:c.3784G>T	p.Asp1262Tyr	p.D1262Y	ENST00000373344	NM_000489.3	1262	Gat/Tat	10/35	0.163193653955621	2	FACETS	0.617	0.541	0.7	0.309	0.27	0.35	INDETERMINATE	1	TRUE	0	0.289752908129244	2		732	861	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121912666	NA	P-0024038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	113	939	0	ENST00000269305.4:c.659A>C	p.Tyr220Ser	p.Y220S	ENST00000269305	NM_001126112.2	220	tAt/tCt	6/11	0.3	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.2	1		939	878	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0024040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	83	696	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.266897903772937	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.266897903772937	1		696	481	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0024040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	47	502	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.266897903772937	1	FACETS	0.898	0.76	1	0.898	0.76	1	CLONAL	1	TRUE	0	0.266897903772937	1		502	340	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455179	29455179	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148001139	NA	P-0024040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	59	550	4	ENST00000389048.3:c.2623G>A	p.Gly875Arg	p.G875R	ENST00000389048	NM_004304.4	875	Gga/Aga	15/29	0.266897903772937	3	FACETS	0.868	0.747	1	0.434	0.373	0.501	CLONAL	1	TRUE	1	0.266897903772937	3		554	577	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	155	571	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.909	0.843	0.976	0.909	0.843	0.976	CLONAL	1	TRUE	1	0.907050282882766	2		571	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0024044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	644	782	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.907050282882766	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.907050282882766	2		782	706	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692768	89692768	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0024044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	221	622	0	ENST00000371953.3:c.254-2A>C		p.X85_splice	ENST00000371953	NM_000314.4	85			0.907050282882766	1	FACETS	0.994	0.959	1	0.994	0.959	1	CLONAL	1	TRUE	0	0.907050282882766	1		622	268	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0024047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	84	722	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.284938715419766	11	FACETS	1	0.941	1	0.111	0.098	0.126	CLONAL	1	FALSE	1	0.284938715419766	11		722	1207	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0024047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	79	726	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.284938715419766	2		726	443	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023280	27023284	+	frameshift_variant	Frame_Shift_Del	DEL	GCGAT	GCGAT	-	novel	NA	P-0024047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	18	164	0	ENST00000324856.7:c.387_391del	p.Ser129ArgfsTer269	p.S129Rfs*269	ENST00000324856	NM_006015.4	129	aGCGAT/a	1/20	1	2	FACETS	0.648	0.49	0.833	0.648	0.49	0.833	SUBCLONAL	1	FALSE	1	0.284938715419766	2		164	195	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383231	4383231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	11	484	0	ENST00000261254.3:c.25G>A	p.Asp9Asn	p.D9N	ENST00000261254	NM_001759.3	9	Gac/Aac	1/5	0.284938715419766	1	FACETS	0.305	0.21	0.423	0.305	0.21	0.423	SUBCLONAL	1	FALSE	0	0.284938715419766	1		484	217	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517753	187517753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	15	300	1	ENST00000441802.2:c.12941C>T	p.Ser4314Leu	p.S4314L	ENST00000441802	NM_005245.3	4314	tCa/tTa	25/27	1	2	FACETS	0.537	0.394	0.709	0.537	0.394	0.709	SUBCLONAL	1	FALSE	1	0.284938715419766	2		301	196	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0024047-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1828	148	722	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.224905446942395	20	FACETS	1	0.915	1	0.112	0.101	0.123	CLONAL	2	TRUE	2	0.224905446942395	20		722	1976	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0024047-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	156	726	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	NA	2	FACETS	0.988	0.907	1			1	INDETERMINATE	2	TRUE	NA	0.224905446942395	2		726	702	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023280	27023284	+	frameshift_variant	Frame_Shift_Del	DEL	GCGAT	GCGAT	-	novel	NA	P-0024047-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	16	164	0	ENST00000324856.7:c.387_391del	p.Ser129ArgfsTer269	p.S129Rfs*269	ENST00000324856	NM_006015.4	129	aGCGAT/a	1/20	0.189439003836938	3	FACETS	0.606	0.448	0.795	0.303	0.224	0.398	SUBCLONAL	1	TRUE	1	0.224905446942395	3		164	261	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383231	4383231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024047-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	38	484	0	ENST00000261254.3:c.25G>A	p.Asp9Asn	p.D9N	ENST00000261254	NM_001759.3	9	Gac/Aac	1/5	0.175004852009779	1	FACETS	0.903	0.749	1	0.903	0.749	1	CLONAL	1	TRUE	0	0.224905446942395	1		484	332	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517753	187517753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024047-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	28	300	1	ENST00000441802.2:c.12941C>T	p.Ser4314Leu	p.S4314L	ENST00000441802	NM_005245.3	4314	tCa/tTa	25/27	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.224905446942395	2		301	223	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562363	95562363	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs545392797	NA	P-0024047-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	29	453	0	ENST00000393063.1:c.4894T>C	p.Ser1632Pro	p.S1632P	ENST00000393063	NM_030621.3	1632	Tct/Cct	24/28	1	2	FACETS	0.559	0.448	0.686	0.559	0.448	0.686	SUBCLONAL	1	TRUE	1	0.224905446942395	2		453	461	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923207	39923207	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0024047-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	32	485	0	ENST00000378444.4:c.3503-2A>G		p.X1168_splice	ENST00000378444	NM_001123385.1	1168			0.143532192331018	3	FACETS	0.666	0.54	0.809			1	SUBCLONAL	1	TRUE	NA	0.224905446942395	3		485	475	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0024047-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2281	256	722	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.410331120541916	16	FACETS	0.952	0.887	1	0.136	0.126	0.146	CLONAL	2	TRUE	2	0.410331120541916	16		722	2537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0024047-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	240	726	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	NA	2	FACETS	1	0.949	1			1	INDETERMINATE	2	TRUE	NA	0.410331120541916	2		726	580	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023280	27023284	+	frameshift_variant	Frame_Shift_Del	DEL	GCGAT	GCGAT	-	novel	NA	P-0024047-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	18	164	0	ENST00000324856.7:c.387_391del	p.Ser129ArgfsTer269	p.S129Rfs*269	ENST00000324856	NM_006015.4	129	aGCGAT/a	1/20	0.349029928802465	3	FACETS	0.833	0.634	1	0.416	0.317	0.531	CLONAL	1	TRUE	1	0.410331120541916	3		164	127	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383231	4383231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024047-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	79	484	0	ENST00000261254.3:c.25G>A	p.Asp9Asn	p.D9N	ENST00000261254	NM_001759.3	9	Gac/Aac	1/5	0.410331120541916	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.410331120541916	1		484	269	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517753	187517753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024047-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	50	300	1	ENST00000441802.2:c.12941C>T	p.Ser4314Leu	p.S4314L	ENST00000441802	NM_005245.3	4314	tCa/tTa	25/27	0.349029928802465	3	FACETS	1	0.87	1	0.51	0.435	0.591	CLONAL	1	TRUE	1	0.410331120541916	3		301	288	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923207	39923207	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0024047-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	49	485	0	ENST00000378444.4:c.3503-2A>G		p.X1168_splice	ENST00000378444	NM_001123385.1	1168			0.410331120541916	3	FACETS	0.501	0.423	0.586			1	SUBCLONAL	1	TRUE	NA	0.410331120541916	3		485	575	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998922	11998922	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024047-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	68	481	0	ENST00000353533.5:c.424del	p.Gln142LysfsTer10	p.Q142Kfs*10	ENST00000353533	NM_003010.3	142	Caa/aa	4/11	0.349029928802465	3	FACETS	0.607	0.528	0.693	0.304	0.264	0.347	SUBCLONAL	1	TRUE	1	0.410331120541916	3		481	658	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998922	11998931	+	frameshift_variant	Frame_Shift_Del	DEL	CAAAAACAAC	CAAAAACAAC	AAAAAAAAA	novel	NA	P-0024047-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	88	504	1	ENST00000353533.5:c.424_433delinsAAAAAAAAA	p.Gln142LysfsTer10	p.Q142Kfs*10	ENST00000353533	NM_003010.3	142	CAAAAACAACtt/AAAAAAAAAtt	4/11	0.349029928802465	3	FACETS	0.769	0.682	0.863	0.385	0.341	0.432	SUBCLONAL	1	TRUE	1	0.410331120541916	3		505	672	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	31	629	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.816	0.659	0.993	0.816	0.659	0.993	CLONAL	1	TRUE	1	0.17	2		629	447	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960098	151960099	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	A	novel	NA	P-0024049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	36	481	0	ENST00000262189.6:c.1299+2dup		p.X433_splice	ENST00000262189	NM_170606.2	433			1	2	FACETS	1	0.833	1	1	0.833	1	CLONAL	1	TRUE	1	0.17	2		481	418	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070642	67070642	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	21	268	0	ENST00000412916.2:c.268del	p.Arg90GlufsTer8	p.R90Efs*8	ENST00000412916		89	gAa/ga	3/6	0.157265118976656	1	FACETS	1	0.79	1	1	0.79	1	CLONAL	1	TRUE	0	0.17	1		268	221	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178136	56178137	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0024049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	29	465	0	ENST00000399503.3:c.3110_3111del	p.Lys1037ArgfsTer4	p.K1037Rfs*4	ENST00000399503	NM_005921.1	1037	AAa/a	14/20	1	2	FACETS	0.93	0.747	1	0.93	0.747	1	CLONAL	1	TRUE	1	0.17	2		465	367	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	49	629	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.668	0.565	0.78	0.668	0.565	0.78	SUBCLONAL	1	TRUE	1	0.292450172390433	2		629	502	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942739	44942739	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	35	497	0	ENST00000377967.4:c.3320del	p.Pro1107LeufsTer13	p.P1107Lfs*13	ENST00000377967	NM_021140.2	1107	Cct/ct	23/29	1	2	FACETS	0.519	0.425	0.625	0.519	0.425	0.625	SUBCLONAL	1	TRUE	1	0.292450172390433	2		497	461	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115749	8115749	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	50	510	2	ENST00000346208.3:c.1096del	p.Arg366GlufsTer38	p.R366Efs*38	ENST00000346208		365	aaC/aa	6/6	1	2	FACETS	0.74	0.629	0.862	0.74	0.629	0.862	SUBCLONAL	1	TRUE	1	0.292450172390433	2		512	462	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070637	67070638	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	13	204	0	ENST00000412916.2:c.263dup	p.Leu88PhefsTer28	p.L88Ffs*28	ENST00000412916		87	-/T	3/6	0.272844900143623	1	FACETS	0.356	0.254	0.481	0.356	0.254	0.481	SUBCLONAL	1	TRUE	0	0.292450172390433	1		204	213	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0024051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	79	690	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.321897174932881	2		690	470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0024051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	102	773	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.293831710244965	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.321897174932881	1		773	506	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939160	36939160	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	78	780	0	ENST00000361632.4:c.549G>C	p.Gln183His	p.Q183H	ENST00000361632		183	caG/caC	5/16	1	2	FACETS	0.943	0.831	1	0.943	0.831	1	CLONAL	1	TRUE	1	0.321897174932881	2		780	514	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570039	95570039	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	115	589	0	ENST00000393063.1:c.3694A>T	p.Ser1232Cys	p.S1232C	ENST00000393063	NM_030621.3	1232	Agc/Tgc	22/28	0.321897174932881	2	FACETS	0.921	0.837	1	0.921	0.837	1	CLONAL	2	TRUE	0	0.321897174932881	2		589	388	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274266	10274266	+	start_lost	Translation_Start_Site	SNP	C	C	A	novel	NA	P-0024051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	32	295	0	ENST00000330684.3:c.3G>T	p.Met1?	p.M1?	ENST00000330684	NM_001134407.1	1	atG/atT	2/13	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.321897174932881	2		295	182	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127276	55127276	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	47	484	0	ENST00000257290.5:c.64C>G	p.Leu22Val	p.L22V	ENST00000257290	NM_006206.4	22	Ctc/Gtc	3/23	1	2	FACETS	0.827	0.7	0.966	0.827	0.7	0.966	CLONAL	1	TRUE	1	0.321897174932881	2		484	353	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86658399	86658400	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0024051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	19	243	0	ENST00000274376.6:c.1364_1365del	p.Asp455GlyfsTer6	p.D455Gfs*6	ENST00000274376	NM_002890.2	455	gAT/g	10/25	0.313988762820971	1	FACETS	0.611	0.467	0.778	0.611	0.467	0.778	SUBCLONAL	1	TRUE	0	0.321897174932881	1		243	162	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227928	123227928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	55	774	0	ENST00000218089.9:c.3639G>A	p.Met1213Ile	p.M1213I	ENST00000218089	NM_001042749.1	1213	atG/atA	33/35	NA	2	FACETS	0.706	0.605	0.817			1	INDETERMINATE	1	TRUE	NA	0.321897174932881	2		774	484	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	287	629	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.436569126116718	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.44013975119367	3		629	753	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	340	716	0	ENST00000263967.3:c.3012G>A	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atA	21/21	0.436569126116718	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.44013975119367	3		716	894	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0024054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	408	765	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	0.44013975119367	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.44013975119367	2		765	868	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0024054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	159	536	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	0.44013975119367	2		536	568	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729875	30729875	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1553631693	NA	P-0024054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	107	377	0	ENST00000295754.5:c.1397-1G>A		p.X466_splice	ENST00000295754	NM_003242.5	466			1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.44013975119367	2		377	469	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138857	64138857	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779234584	NA	P-0024054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	204	595	0	ENST00000334205.4:c.2224C>T	p.Arg742Cys	p.R742C	ENST00000334205	NM_003942.2	742	Cgc/Tgc	17/17	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.44013975119367	2		595	725	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249427	153249427	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	184	759	0	ENST00000281708.4:c.1351G>T	p.Gly451Ter	p.G451*	ENST00000281708	NM_033632.3	451	Gga/Tga	9/12	0.44013975119367	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.44013975119367	1		759	593	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137437	202137438	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0024054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	134	542	0	ENST00000358485.4:c.666_667del	p.Ala224ProfsTer14	p.A224Pfs*14	ENST00000358485	NM_001080125.1	222	gTC/g	4/9	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.44013975119367	2		542	579	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535448	66535448	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	121	358	0	ENST00000273854.3:c.13G>T	p.Gly5Trp	p.G5W	ENST00000273854	NM_004439.5	5	Ggg/Tgg	1/18	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.44013975119367	2		358	444	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911071	29911072	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	TATA	novel	NA	P-0024054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	186	823	0	ENST00000376809.5:c.370_371insTATA	p.Gly124ValfsTer2	p.G124Vfs*2	ENST00000376809	NM_002116.7	124	ggc/gTATAgc	3/8	1	2	FACETS	0.99	0.915	1	0.99	0.915	1	CLONAL	1	TRUE	1	0.44013975119367	2		823	854	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0024063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	126	533	1				ENST00000310581	NM_198253.2	-/1132			0.38751334801514	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.412205180003141	1		534	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0024063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	222	727	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	0.296637127494095	2	FACETS	1	0.991	1	0.699	0.652	0.746	CLONAL	1	TRUE	0	0.412205180003141	2		727	771	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988395	41988395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	85	579	0	ENST00000219905.7:c.1187G>A	p.Cys396Tyr	p.C396Y	ENST00000219905	NM_001164273.1	396	tGc/tAc	3/24	1	2	FACETS	0.667	0.59	0.75	0.667	0.59	0.75	SUBCLONAL	1	TRUE	1	0.412205180003141	2		579	618	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715980	52715980	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	110	603	1	ENST00000322088.6:c.545G>A	p.Arg182Gln	p.R182Q	ENST00000322088	NM_014225.5	182	cGg/cAg	5/15	1	2	FACETS	0.665	0.597	0.736	0.665	0.597	0.736	SUBCLONAL	1	TRUE	1	0.412205180003141	2		604	803	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89444996	89444996	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	73	539	0	ENST00000336596.2:c.1316C>G	p.Pro439Arg	p.P439R	ENST00000336596	NM_005233.5	439	cCt/cGt	6/17	0.30003930721603	2	FACETS	0.724	0.635	0.82	0.362	0.317	0.41	SUBCLONAL	1	TRUE	0	0.412205180003141	2		539	489	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806568	1806576	+	inframe_deletion	In_Frame_Del	DEL	CGCGTCCAT	CGCGTCCAT	-	novel	NA	P-0024063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	88	631	0	ENST00000260795.2:c.1284_1292del	p.Asn428_Met431delinsLys	p.N428_M431delinsK	ENST00000260795		428	aaCGCGTCCATg/aag	9/17	0.296637127494095	2	FACETS	0.419	0.37	0.472	0.21	0.185	0.236	SUBCLONAL	1	TRUE	0	0.412205180003141	2		631	1018	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148661	20148661	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	168	579	0	ENST00000379607.5:c.402del	p.Ile134MetfsTer32	p.I134Mfs*32	ENST00000379607	NM_001412.3	134	atT/at	6/7	0.412205180003141	3	FACETS	0.836	0.772	0.902	0.557	0.515	0.601	CLONAL	2	TRUE	0	0.412205180003141	3		579	588	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019721	123019721	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	219	704	0	ENST00000355640.3:c.209T>A	p.Val70Glu	p.V70E	ENST00000355640		70	gTa/gAa	2/7	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.412205180003141	2		704	860	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0024064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	10	625	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		625	39	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	634	855	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.568685301929073	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.659020402791867	4		855	1516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0024065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	599	698	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.659020402791867	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.659020402791867	2		698	875	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207092	1207092	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555735008	NA	P-0024065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	723	837	0	ENST00000326873.7:c.180del	p.Tyr60Ter	p.Y60*	ENST00000326873	NM_000455.4	60	taC/ta	1/10	0.659020402791867	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.659020402791867	2		837	1060	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226120	2226120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759516773	NA	P-0024065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	50	649	2	ENST00000326181.6:c.1817C>T	p.Ala606Val	p.A606V	ENST00000326181	NM_032271.2	606	gCg/gTg	19/21	1	2	FACETS	0.165	0.139	0.193	0.165	0.139	0.193	SUBCLONAL	1	TRUE	1	0.659020402791867	2		651	921	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971029	21971032	+	frameshift_variant	Frame_Shift_Del	DEL	CAGG	CAGG	-	novel	NA	P-0024065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	361	421	0	ENST00000304494.5:c.326_329del	p.Ala109GlyfsTer36	p.A109Gfs*36	ENST00000304494	NM_000077.4	109	gCCTGg/gg	2/3	0.659020402791867	2	FACETS	0.978	0.941	1	0.978	0.941	1	CLONAL	2	TRUE	0	0.659020402791867	2		421	560	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860109	152860109	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	128	376	0	ENST00000406277.2:c.319G>T	p.Glu107Ter	p.E107*	ENST00000406277	NM_152274.4	107	Gaa/Taa	5/7	1		FACETS		0.987	1				CLONAL	1	TRUE	0	0.373685174276997	1		376	378	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	166	588	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.907	0.838	0.977	0.907	0.838	0.977	CLONAL	1	TRUE	1	0.676651413722949	2		588	541	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	282	971	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.676323535183932	1	FACETS	0.98	0.931	1	0.98	0.931	1	CLONAL	1	TRUE	0	0.676651413722949	1		973	563	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	245	728	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.676651413722949	2		730	722	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263973	104263974	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776579	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	66	232	1	ENST00000369902.3:c.71dup	p.Ala25GlyfsTer23	p.A25Gfs*23	ENST00000369902	NM_016169.3	22	gcc/gCcc	1/12	1	2	FACETS	0.72	0.631	0.814	0.72	0.631	0.814	SUBCLONAL	1	TRUE	1	0.676651413722949	2		233	271	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70441157	70441157	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	rs764225020	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	204	509	0	ENST00000373644.4:c.4832del	p.Asn1611ThrfsTer13	p.N1611Tfs*13	ENST00000373644	NM_030625.2	1609	gAa/ga	9/12	1	2	FACETS	0.988	0.922	1	0.988	0.922	1	CLONAL	1	TRUE	1	0.676651413722949	2		509	610	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490382	29490382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754096545	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	231	433	0	ENST00000356175.3:c.467G>A	p.Arg156His	p.R156H	ENST00000356175	NM_000267.3	156	cGc/cAc	4/57	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.676651413722949	2		433	683	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284907	15284907	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs551991530	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	241	687	1	ENST00000263388.2:c.4708C>T	p.Arg1570Cys	p.R1570C	ENST00000263388	NM_000435.2	1570	Cgt/Tgt	25/33	0.676651413722949	1	FACETS	0.964	0.911	1	0.964	0.911	1	CLONAL	1	TRUE	0	0.676651413722949	1		688	489	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574678	41574679	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs754418509	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	253	758	3	ENST00000263253.7:c.6970dup	p.His2324ProfsTer55	p.H2324Pfs*55	ENST00000263253	NM_001429.3	2321	-/C	31/31	0.676651413722949	1	FACETS	0.832	0.785	0.879	0.832	0.785	0.879	CLONAL	1	TRUE	0	0.676651413722949	1		761	595	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	271	733	4	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	1	2	FACETS	0.941	0.886	0.998	0.941	0.886	0.998	CLONAL	1	TRUE	1	0.676651413722949	2		737	851	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99452113	99452113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	129	341	0	ENST00000268035.6:c.1447G>A	p.Gly483Arg	p.G483R	ENST00000268035	NM_000875.3	483	Ggg/Agg	6/21	1	2	FACETS	0.968	0.886	1	0.968	0.886	1	CLONAL	1	TRUE	1	0.676651413722949	2		341	394	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781122	161781122	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	243	545	4	ENST00000366898.1:c.1283del	p.Asn428MetfsTer7	p.N428Mfs*7	ENST00000366898	NM_004562.2	428	aAt/at	11/12	1	2	FACETS	0.967	0.907	1	0.967	0.907	1	CLONAL	1	TRUE	1	0.676651413722949	2		549	743	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	227	564	8	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.95	0.889	1	0.95	0.889	1	CLONAL	1	TRUE	1	0.676651413722949	2		572	706	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87322770	87322770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781137734	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	222	558	0	ENST00000277120.3:c.371G>A	p.Arg124Gln	p.R124Q	ENST00000277120		124	cGa/cAa	5/19	0.676651413722949	1	FACETS	0.973	0.919	1	0.973	0.919	1	CLONAL	1	TRUE	0	0.676651413722949	1		558	446	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661663	227661664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761880048	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	111	378	11	ENST00000305123.5:c.1791dup	p.His598AlafsTer13	p.H598Afs*13	ENST00000305123	NM_005544.2	597	-/G	1/2	1	2	FACETS	0.833	0.755	0.914	0.833	0.755	0.914	CLONAL	1	TRUE	1	0.676651413722949	2		389	394	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521525	46521525	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	304	727	2	ENST00000262741.5:c.883del	p.Met295Ter	p.M295*	ENST00000262741	NM_003629.3	295	Atg/tg	7/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.676651413722949	2		729	868	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760447	133760447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771729224	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	193	588	0	ENST00000318560.5:c.2770G>A	p.Gly924Arg	p.G924R	ENST00000318560	NM_005157.4	924	Ggg/Agg	11/11	1	2	FACETS	0.941	0.876	1	0.941	0.876	1	CLONAL	1	TRUE	1	0.676651413722949	2		588	606	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427522	49427522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201283589	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	203	531	0	ENST00000301067.7:c.10966C>T	p.Arg3656Cys	p.R3656C	ENST00000301067	NM_003482.3	3656	Cgc/Tgc	39/54	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.676651413722949	2		531	594	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218918	193218918	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	156	372	0	ENST00000367435.3:c.1476G>A	p.Trp492Ter	p.W492*	ENST00000367435	NM_024529.4	492	tgG/tgA	16/17	1	2	FACETS	0.939	0.867	1	0.939	0.867	1	CLONAL	1	TRUE	1	0.676651413722949	2		372	491	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518485	69518485	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1005963395	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	123	364	1	ENST00000294312.3:c.160G>A	p.Gly54Arg	p.G54R	ENST00000294312	NM_005117.2	54	Ggg/Agg	1/3	1	2	FACETS	0.983	0.898	1	0.983	0.898	1	CLONAL	1	TRUE	1	0.676651413722949	2		365	370	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865788	57865788	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	272	682	0	ENST00000228682.2:c.3265A>G	p.Ser1089Gly	p.S1089G	ENST00000228682	NM_005269.2	1089	Agt/Ggt	12/12	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.676651413722949	2		682	781	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233172	69233172	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	171	346	0	ENST00000462284.1:c.1037A>G	p.Glu346Gly	p.E346G	ENST00000462284	NM_002392.5	346	gAa/gGa	11/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.676651413722949	2		346	490	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541630	120541630	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	216	430	0	ENST00000229340.5:c.227C>T	p.Thr76Met	p.T76M	ENST00000229340	NM_006861.6	76	aCg/aTg	3/6	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.676651413722949	2		430	571	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023091	33023091	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	131	361	0	ENST00000300177.4:c.200C>A	p.Ala67Asp	p.A67D	ENST00000300177	NM_001191322.1	67	gCc/gAc	2/2	1	2	FACETS	0.926	0.848	1	0.926	0.848	1	CLONAL	1	TRUE	1	0.676651413722949	2		361	418	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749223	43749223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	273	757	0	ENST00000382044.4:c.1583G>A	p.Ser528Asn	p.S528N	ENST00000382044	NM_001141980.1	528	aGt/aAt	12/28	1	2	FACETS	0.959	0.903	1	0.959	0.903	1	CLONAL	1	TRUE	1	0.676651413722949	2		757	841	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808053	3808054	+	splice_region_variant,intron_variant	Splice_Region	DEL	AA	AA	-	rs75459669	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	154	329	5	ENST00000262367.5:c.3370-5_3370-4del		p.X1124_splice	ENST00000262367	NM_004380.2	1124			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.676651413722949	2		334	404	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78519431	78519431	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	175	381	0	ENST00000306801.3:c.2T>C	p.Met1?	p.M1?	ENST00000306801	NM_020761.2	1	aTg/aCg	1/34	1	2	FACETS	0.97	0.9	1	0.97	0.9	1	CLONAL	1	TRUE	1	0.676651413722949	2		381	533	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218447	1218447	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs886041996	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	276	736	0	ENST00000326873.7:c.326del	p.Asn109MetfsTer20	p.N109Mfs*20	ENST00000326873	NM_000455.4	108	Aaa/aa	2/10	0.676651413722949	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.676651413722949	1		736	534	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966216	25966216	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753665572	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	263	615	0	ENST00000435504.4:c.2990A>G	p.Asn997Ser	p.N997S	ENST00000435504		997	aAc/aGc	13/13	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.676651413722949	2		615	742	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295770	212295770	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	214	591	0	ENST00000342788.4:c.2543A>G	p.Asn848Ser	p.N848S	ENST00000342788	NM_005235.2	848	aAt/aGt	21/28	1	2	FACETS	0.941	0.879	1	0.941	0.879	1	CLONAL	1	TRUE	1	0.676651413722949	2		591	672	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231776	36231776	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	254	638	1	ENST00000300305.3:c.608C>A	p.Pro203His	p.P203H	ENST00000300305		203	cCt/cAt	5/8	0.642658104241801	2	FACETS	0.993	0.933	1	0.497	0.466	0.527	CLONAL	1	TRUE	0	0.676651413722949	2		639	756	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170015155	170015155	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	292	657	0	ENST00000295797.4:c.1561T>C	p.Phe521Leu	p.F521L	ENST00000295797	NM_002740.5	521	Ttc/Ctc	16/18	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.676651413722949	2		657	858	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430759	181430759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	238	585	1	ENST00000325404.1:c.611C>T	p.Ala204Val	p.A204V	ENST00000325404	NM_003106.3	204	gCc/gTc	1/1	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.676651413722949	2		586	673	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356239	66356239	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370503988	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	241	578	0	ENST00000273854.3:c.1258G>A	p.Gly420Ser	p.G420S	ENST00000273854	NM_004439.5	420	Ggc/Agc	5/18	0.676651413722949	1	FACETS	0.917	0.866	0.968	0.917	0.866	0.968	CLONAL	1	TRUE	0	0.676651413722949	1		578	514	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672864	30672864	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	589	785	0	ENST00000376406.3:c.4096A>G	p.Thr1366Ala	p.T1366A	ENST00000376406	NM_014641.2	1366	Act/Gct	10/15	0.642658104241801	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.676651413722949	2		785	863	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894954	101894954	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	177	366	0	ENST00000374994.4:c.510del	p.Phe170LeufsTer8	p.F170Lfs*8	ENST00000374994	NM_004612.2	169	ccT/cc	3/9	0.676651413722949	1	FACETS	0.946	0.885	1	0.946	0.885	1	CLONAL	1	TRUE	0	0.676651413722949	1		366	366	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412664	63412664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1176557852	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	247	575	0	ENST00000330258.3:c.503G>A	p.Gly168Asp	p.G168D	ENST00000330258	NM_152424.3	168	gGc/gAc	2/2	0.676651413722949	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.676651413722949	1		575	477	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360589	70360591	+	inframe_deletion	In_Frame_Del	DEL	AGC	AGC	-	rs769857818	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	165	522	11	ENST00000374080.3:c.6165_6167del	p.Gln2076del	p.Q2076del	ENST00000374080		2050	gAGCag/gag	42/45	0.676651413722949	1	FACETS	0.75	0.696	0.805	0.75	0.696	0.805	SUBCLONAL	1	TRUE	0	0.676651413722949	1		533	430	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123022517	123022517	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	257	620	0	ENST00000355640.3:c.926A>G	p.Asp309Gly	p.D309G	ENST00000355640		309	gAt/gGt	3/7	NA	2	FACETS	0.775	0.726	0.825			1	INDETERMINATE	1	TRUE	NA	0.676651413722949	2		620	980	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0024073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	147	651	1	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	1	2	FACETS	0.94	0.857	1	0.94	0.857	1	CLONAL	1	TRUE	1	0.3313941065918	2		652	944	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354161	15354161	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	120	648	2	ENST00000263377.2:c.2719C>T	p.Gln907Ter	p.Q907*	ENST00000263377	NM_058243.2	907	Caa/Taa	14/20	1	2	FACETS	0.843	0.761	0.93	0.843	0.761	0.93	CLONAL	1	TRUE	1	0.3313941065918	2		650	859	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29197620	29197620	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	444	737	0	ENST00000240100.2:c.574G>C	p.Asp192His	p.D192H	ENST00000240100	NM_001394.6	192	Gac/Cac	2/4	0.165439031210939	6	FACETS	0.899	0.858	0.941	0.899	0.858	0.941	INDETERMINATE	3	TRUE	3	0.487971065968126	6		737	1333	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619281	37619281	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0024076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	171	503	0	ENST00000447079.4:c.957C>G	p.Tyr319Ter	p.Y319*	ENST00000447079	NM_015083.1	319	taC/taG	1/14	0.188119878493336	3	FACETS	0.837	0.772	0.904	1	0.984	1	CLONAL	3	TRUE	1	0.21	3		503	717	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618522	37618523	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0024076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	318	660	0	ENST00000447079.4:c.199dup	p.Ile67AsnfsTer8	p.I67Nfs*8	ENST00000447079	NM_015083.1	66	-/A	1/14	0.188119878493336	3	FACETS	0.878	0.831	0.926	1	0.995	1	CLONAL	4	TRUE	1	0.21	3		660	953	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593590	55593607	+	inframe_deletion	In_Frame_Del	DEL	GTATGAAGTACAGTGGAA	GTATGAAGTACAGTGGAA	-	novel	NA	P-0024077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	133	474	0	ENST00000288135.5:c.1657_1674del	p.Tyr553_Lys558del	p.Y553_K558del	ENST00000288135	NM_000222.2	552	atGTATGAAGTACAGTGGAAg/atg	11/21	0.691300443131266	3	FACETS	0.86	0.794	0.926	0.86	0.794	0.926	CLONAL	2	TRUE	1	0.691300443131266	3		474	301	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	422344	422344	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	76	490	0	ENST00000399788.2:c.2914G>A	p.Ala972Thr	p.A972T	ENST00000399788	NM_001042603.1	972	Gca/Aca	20/28	0.510852006074696	4	FACETS	0.855	0.753	0.964			1	CLONAL	1	TRUE	NA	0.691300443131266	4		490	435	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913499	NA	P-0024078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	151	329	0	ENST00000345146.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000345146	NM_005896.2	132	Cgt/Ggt	4/10	1	2	FACETS	0.829	0.762	0.898	0.829	0.762	0.898	CLONAL	1	TRUE	1	0.677448776420757	2		329	538	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0024078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	673	694	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.628099365919972	2	FACETS	0.96	0.933	0.986	0.96	0.933	0.986	CLONAL	2	TRUE	0	0.677448776420757	2		694	1035	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813101	76813101	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	331	353	0	ENST00000373344.5:c.6520A>G	p.Lys2174Glu	p.K2174E	ENST00000373344	NM_000489.3	2174	Aag/Gag	30/35	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.677448776420757	1		353	505	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015133	37015133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223489007	NA	P-0024080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	381	886	1	ENST00000358127.4:c.271G>A	p.Ala91Thr	p.A91T	ENST00000358127	NM_001280556.1	91	Gcc/Acc	3/10	0.482622665646283	1	FACETS	0.514	0.489	0.539	0.514	0.489	0.539	INDETERMINATE	1	TRUE	0	0.825674869940612	1		887	1055	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060783	38060794	+	inframe_deletion	In_Frame_Del	DEL	GATGGAGAACGG	GATGGAGAACGG	-	novel	NA	P-0024080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1284	360	1096	0	ENST00000250448.2:c.1195_1206del	p.Pro399_Ile402del	p.P399_I402del	ENST00000250448	NM_004496.3	399	CCGTTCTCCATC/-	2/2	1	2	FACETS	0.53	0.501	0.56	0.53	0.501	0.56	SUBCLONAL	1	TRUE	1	0.825674869940612	2		1096	1644	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061152	38061202	+	inframe_deletion	In_Frame_Del	DEL	CCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTG	CCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTG	-	novel	NA	P-0024080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	398	296	0	ENST00000250448.2:c.787_837del	p.Gln263_Gly279del	p.Q263_G279del	ENST00000250448	NM_004496.3	263	CAGAAGCGCTTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGG/-	2/2	1	2	FACETS	0.793	0.765	0.821	1	0.997	1	SUBCLONAL	2	TRUE	1	0.825674869940612	2		296	608	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926270	112926271	+	missense_variant	Missense_Mutation	DNP	CG	CG	TT	novel	NA	P-0024082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	340	621	3	ENST00000351677.2:c.1403_1404delinsTT	p.Thr468Ile	p.T468I	ENST00000351677	NM_002834.3	468	aCG/aTT	12/16	0.393701644568306	2	FACETS	0.852	0.807	0.897	0.852	0.807	0.897	CLONAL	2	TRUE	0	0.393701644568306	2		624	1014	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483000	29483000	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs1263745475	NA	P-0024082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	178	364	0	ENST00000356175.3:c.61-1G>T		p.X21_splice	ENST00000356175	NM_000267.3	21			0.279067772212275	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.393701644568306	2		364	397	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40491367	40491367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	229	833	0	ENST00000264657.5:c.433G>A	p.Glu145Lys	p.E145K	ENST00000264657	NM_139276.2	145	Gag/Aag	5/24	0.351484015198525	2	FACETS	0.907	0.843	0.972	0.453	0.421	0.486	CLONAL	1	TRUE	0	0.393701644568306	2		833	1283	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219336	1219370	+	protein_altering_variant	In_Frame_Del	DEL	GAGTACTGCGTGTGTGGCATGCAGGAAATGCTGGA	GAGTACTGCGTGTGTGGCATGCAGGAAATGCTGGA	CATGC	novel	NA	P-0024082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	352	869	4	ENST00000326873.7:c.388_422delinsCATGC	p.Glu130_Asp141delinsHisAla	p.E130_D141delinsHA	ENST00000326873	NM_000455.4	130	GAGTACTGCGTGTGTGGCATGCAGGAAATGCTGGAc/CATGCc	3/10	0.351484015198525	2	FACETS	1	0.993	1	0.674	0.638	0.711	CLONAL	1	TRUE	0	0.393701644568306	2		873	1326	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7152896	7152896	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	349	733	0	ENST00000302850.5:c.2072C>G	p.Ser691Cys	p.S691C	ENST00000302850	NM_000208.2	691	tCt/tGt	10/22	0.351484015198525	2	FACETS	0.807	0.765	0.85	0.807	0.765	0.85	CLONAL	2	TRUE	0	0.393701644568306	2		733	1098	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610277	10610278	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0024082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	509	961	0	ENST00000171111.5:c.432dup	p.Ile145HisfsTer29	p.I145Hfs*29	ENST00000171111	NM_203500.1	144	-/C	2/6	0.351484015198525	2	FACETS	0.898	0.86	0.936	0.898	0.86	0.936	CLONAL	2	TRUE	0	0.393701644568306	2		961	1440	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890222	72890223	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1470466800	NA	P-0024082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	168	679	0	ENST00000325599.8:c.459dup	p.Arg154ThrfsTer11	p.R154Tfs*11	ENST00000325599	NM_018130.2	153	-/A	4/11	0.393701644568306	2	FACETS	0.909	0.835	0.986	0.454	0.417	0.493	CLONAL	1	TRUE	0	0.393701644568306	2		679	939	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622243	162622243	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	152	625	2	ENST00000366898.1:c.454G>T	p.Gly152Cys	p.G152C	ENST00000366898	NM_004562.2	152	Ggc/Tgc	4/12	0.348403972894191	1	FACETS	0.911	0.835	0.989	0.911	0.835	0.989	CLONAL	1	TRUE	0	0.393701644568306	1		627	681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0024083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	413	589	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.765465888354712	2	FACETS	0.992	0.963	1	0.992	0.963	1	CLONAL	2	TRUE	0	0.765465888354712	2		589	544	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256416	16256416	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1234631776	NA	P-0024083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	184	560	0	ENST00000375759.3:c.3681G>C	p.Lys1227Asn	p.K1227N	ENST00000375759	NM_015001.2	1227	aaG/aaC	11/15	1	2	FACETS	0.823	0.764	0.884	0.823	0.764	0.884	CLONAL	1	TRUE	1	0.765465888354712	2		560	584	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936091	71936091	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	29	100	0	ENST00000298229.2:c.63G>A	p.Trp21Ter	p.W21*	ENST00000298229	NM_001567.3	21	tgG/tgA	1/28	0.139637478848939	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.765465888354712	0		100	74	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416347	29416347	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs752701859	NA	P-0024083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	56	800	1	ENST00000389048.3:c.4606G>C	p.Glu1536Gln	p.E1536Q	ENST00000389048	NM_004304.4	1536	Gag/Cag	29/29	NA	2	FACETS	0.27	0.231	0.312			1	INDETERMINATE	1	TRUE	NA	0.765465888354712	2		801	542	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149793	202149793	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs773127303	NA	P-0024083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	249	642	0	ENST00000358485.4:c.1234A>G	p.Lys412Glu	p.K412E	ENST00000358485	NM_001080125.1	412	Aaa/Gaa	8/9	0.280125246034228	3	FACETS	1	0.976	1	0.54	0.506	0.575	INDETERMINATE	1	TRUE	1	0.765465888354712	3		642	833	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096093	71096093	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	35	254	0	ENST00000318789.4:c.664G>A	p.Gly222Ser	p.G222S	ENST00000318789	NM_032682.5	222	Ggc/Agc	10/21	NA	2	FACETS	0.324	0.267	0.388			1	INDETERMINATE	1	TRUE	NA	0.765465888354712	2		254	282	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0024084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	70	533	1				ENST00000310581	NM_198253.2	-/1132			0.192076134059485	1	FACETS	1	0.885	1	1	0.982	1	CLONAL	2	TRUE	0	0.192076134059485	1		534	327	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0024084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	85	428	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	0.106286907863805	3	FACETS	0.891	0.793	0.993	1	0.974	1	INDETERMINATE	3	TRUE	1	0.192076134059485	3		428	363	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56911041	56911041	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	172	612	0	ENST00000519728.1:c.1187A>G	p.Glu396Gly	p.E396G	ENST00000519728	NM_002350.3	396	gAg/gGg	11/13	1	2	FACETS	0.953	0.878	1	0.953	0.878	1	CLONAL	1	TRUE	1	0.437590502762565	2		612	825	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0024089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	119	790	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	0.376679868010616	2		790	566	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0024089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	77	588	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.376679868010616	2		588	396	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685281	89685281	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1060500116	NA	P-0024089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	214	521	0	ENST00000371953.3:c.176C>G	p.Ser59Ter	p.S59*	ENST00000371953	NM_000314.4	59	tCa/tGa	3/9	0.376679868010616	3	FACETS	0.954	0.897	1	0.954	0.897	1	CLONAL	3	TRUE	0	0.376679868010616	3		521	472	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100175	27100176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0024089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	100	600	1	ENST00000324856.7:c.3977dup	p.Gln1327AlafsTer11	p.Q1327Afs*11	ENST00000324856	NM_006015.4	1324	tac/taCc	16/20	1	2	FACETS	0.931	0.834	1	0.931	0.834	1	CLONAL	1	TRUE	1	0.376679868010616	2		601	570	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426027	49426049	+	frameshift_variant	Frame_Shift_Del	DEL	CCCAGAAGGTTCTGGGTCATGGA	CCCAGAAGGTTCTGGGTCATGGA	-	novel	NA	P-0024089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	94	757	0	ENST00000301067.7:c.12439_12461del	p.Ser4147ProfsTer13	p.S4147Pfs*13	ENST00000301067	NM_003482.3	4147	TCCATGACCCAGAACCTTCTGGGc/c	39/54	1	2	FACETS	0.675	0.601	0.755	0.675	0.601	0.755	SUBCLONAL	1	TRUE	1	0.376679868010616	2		757	739	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247294	153247294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	105	498	0	ENST00000281708.4:c.1508C>T	p.Ala503Val	p.A503V	ENST00000281708	NM_033632.3	503	gCa/gTa	10/12	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.376679868010616	2		498	547	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0024090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1369	52	790	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.665	0.564	0.778	0.665	0.564	0.778	SUBCLONAL	1	TRUE	1	0.11	2		790	1421	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987025	36987025	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1555349209	NA	P-0024090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	52	630	0	ENST00000354822.5:c.664G>T	p.Glu222Ter	p.E222*	ENST00000354822	NM_001079668.2	222	Gag/Tag	3/3	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.11	2		630	909	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987031	36987031	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	47	628	0	ENST00000354822.5:c.658G>C	p.Glu220Gln	p.E220Q	ENST00000354822	NM_001079668.2	220	Gag/Cag	3/3	1	2	FACETS	0.954	0.802	1	0.954	0.802	1	CLONAL	1	TRUE	1	0.11	2		628	896	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0024093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	127	547	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.263122802301165	2	FACETS	0.868	0.79	0.95	0.868	0.79	0.95	CLONAL	2	TRUE	0	0.263122802301165	2		547	556	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007794	45007794	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	67	433	0	ENST00000558401.1:c.241T>G	p.Ser81Ala	p.S81A	ENST00000558401	NM_004048.2	81	Tct/Gct	2/4	1	2	FACETS	0.892	0.776	1	0.892	0.776	1	CLONAL	1	TRUE	1	0.263122802301165	2		433	571	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469996	25469997	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	AGCTC	novel	NA	P-0024093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	82	534	0	ENST00000264709.3:c.1041_1045dup	p.Ser349Ter	p.S349*	ENST00000264709	NM_175629.2	349	tcg/tGAGCTcg	9/23	0.263122802301165	3	FACETS	1	0.953	1	0.58	0.512	0.653	CLONAL	1	TRUE	1	0.263122802301165	3		534	608	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089778	27089778	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0024096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	105	585	0	ENST00000324856.7:c.2732+2T>G		p.X911_splice	ENST00000324856	NM_006015.4	911			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		585	752	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216753	7216753	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs745671551	NA	P-0024097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	51	525	0	ENST00000380728.2:c.670C>T	p.Gln224Ter	p.Q224*	ENST00000380728		224	Cag/Tag	8/11	0.281197902177442	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.281197902177442	1		525	241	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574005	7574006	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	ACATCTCGAAGCGCTCACGCCC	novel	NA	P-0024097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	67	817	2	ENST00000269305.4:c.1000_1021dup	p.Phe341TrpfsTer3	p.F341Wfs*3	ENST00000269305	NM_001126112.2	341	ttc/tGGGCGTGAGCGCTTCGAGATGTtc	10/11	0.281197902177442	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	0	0.281197902177442	1		819	391	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856047	151856049	+	missense_variant	Missense_Mutation	TNP	CGT	CGT	AGA	novel	NA	P-0024097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	28	620	0	ENST00000262189.6:c.11569_11571delinsTCT	p.Thr3857Ser	p.T3857S	ENST00000262189	NM_170606.2	3857	ACG/TCT	44/59	1	2	FACETS	0.687	0.55	0.842	0.687	0.55	0.842	SUBCLONAL	1	TRUE	1	0.281197902177442	2		620	290	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0024099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	10	320	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.549	0.375	0.764	0.549	0.375	0.764	SUBCLONAL	1	TRUE	1	0.350382898725642	2		320	104	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030387	49030387	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373601944	NA	P-0024099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	43	555	1	ENST00000267163.4:c.1862G>A	p.Arg621His	p.R621H	ENST00000267163	NM_000321.2	621	cGt/cAt	19/27	0.177368221148694	3	FACETS	0.925	0.787	1	0.925	0.787	1	INDETERMINATE	2	TRUE	1	0.350382898725642	3		556	156	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041026	112041026	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746134687	NA	P-0024099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	27	418	1	ENST00000368678.4:c.229C>T	p.Arg77Cys	p.R77C	ENST00000368678		77	Cgt/Tgt	3/13	0.350382898725642	1	FACETS	0.558	0.446	0.684	0.558	0.446	0.684	SUBCLONAL	1	TRUE	0	0.350382898725642	1		419	228	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623545	28623545	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	28	541	0	ENST00000241453.7:c.1012C>G	p.Gln338Glu	p.Q338E	ENST00000241453	NM_004119.2	338	Caa/Gaa	8/24	0.177368221148694	3	FACETS	0.944	0.76	1	0.472	0.38	0.575	INDETERMINATE	1	TRUE	1	0.350382898725642	3		541	199	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883606	37883608	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0024099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	67	764	1	ENST00000269571.5:c.3219_3221del	p.Pro1074del	p.P1074del	ENST00000269571		1073	tCTCca/tca	26/27	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.350382898725642	2		765	359	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441274	52441274	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	65	546	0	ENST00000460680.1:c.496G>T	p.Glu166Ter	p.E166*	ENST00000460680	NM_004656.3	166	Gag/Tag	7/17	0.350382898725642	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.350382898725642	1		546	218	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650051	206650051	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs782081148	NA	P-0024105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	118	736	1	ENST00000367120.3:c.571C>T	p.Arg191Ter	p.R191*	ENST00000367120	NM_014002.3	191	Cga/Tga	7/22	1	2	FACETS	0.566	0.511	0.625	0.566	0.511	0.625	SUBCLONAL	1	TRUE	1	0.539178953008953	2		737	773	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934574	NA	P-0024105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	698	783	0	ENST00000269305.4:c.844C>G	p.Arg282Gly	p.R282G	ENST00000269305	NM_001126112.2	282	Cgg/Ggg	8/11	0.539178953008953	3	FACETS	0.934	0.907	0.961			1	CLONAL	3	TRUE	NA	0.539178953008953	3		783	1173	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211652	5211652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369364998	NA	P-0024105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	180	808	2	ENST00000357368.4:c.5183G>A	p.Arg1728Gln	p.R1728Q	ENST00000357368	NM_002850.3	1728	cGg/cAg	33/38	1	2	FACETS	0.905	0.836	0.975	0.905	0.836	0.975	CLONAL	1	TRUE	1	0.539178953008953	2		810	738	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072577	5072577	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1902	117	663	0	ENST00000381652.3:c.1727C>T	p.Thr576Ile	p.T576I	ENST00000381652	NM_004972.3	576	aCa/aTa	13/25	0.539178953008953	15	FACETS	0.968	0.869	1	0.069	0.062	0.077	CLONAL	1	TRUE	1	0.539178953008953	15		663	2019	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0024106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	41	657	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.148071378557222	0	FACETS	0.863	0.745	0.984			1	CLONAL	4	TRUE	0	0.2	0		657	95	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0024106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	20	348	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	1	0.778	1	1	0.941	1	CLONAL	2	TRUE	1	0.2	2		348	100	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0024106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	27	728	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.831	1	1	0.956	1	CLONAL	2	TRUE	1	0.2	2		730	131	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0024106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	34	493	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.977	0.826	1	1	0.975	1	CLONAL	4	TRUE	1	0.2	2		495	87	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0024106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	35	214	0	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	0.569466868018321	2	FACETS	0.951	0.805	1	1	0.967	1	CLONAL	4	TRUE	0	0.2	2		214	92	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	48	455	1	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.984	0.855	1	1	0.982	1	CLONAL	4	TRUE	1	0.2	2		456	122	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0024106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	13	355	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	0.148071378557222	3	FACETS	0.941	0.683	1	0.941	0.683	1	CLONAL	2	TRUE	1	0.2	3		355	76	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0024106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	38	561	0	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	0.107438520537902	3	FACETS	1	0.917	1	1	0.917	1	INDETERMINATE	2	TRUE	1	0.2	3		561	180	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0024106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	59	247	0	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	0.107438520537902	3	FACETS	0.887	0.777	1	1	0.978	1	INDETERMINATE	4	TRUE	1	0.2	3		247	183	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522741	67522741	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	35	256	0	ENST00000274335.5:c.244del	p.Ile82SerfsTer32	p.I82Sfs*32	ENST00000274335		80	Aaa/aa	1/15	0.3	5	FACETS	1	0.852	1			1	CLONAL	4	TRUE	NA	0.2	5		256	112	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0024106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	26	592	3	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	0.224459228597688	4	FACETS	0.963	0.778	1	1	0.934	1	CLONAL	3	TRUE	2	0.2	4		595	108	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696462	47696462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	36	380	0	ENST00000347630.2:c.361C>T	p.Arg121Trp	p.R121W	ENST00000347630	NM_001007230.1	121	Cgg/Tgg	6/11	1	2	FACETS	0.882	0.746	1	1	0.976	1	CLONAL	4	TRUE	1	0.2	2		380	102	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900080	151900081	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	32	431	0	ENST00000262189.6:c.4030dup	p.Ile1344AsnfsTer11	p.I1344Nfs*11	ENST00000262189	NM_170606.2	1344	ata/aAta	26/59	1	2	FACETS	0.78	0.639	0.938	1	0.949	1	CLONAL	2	TRUE	1	0.2	2		431	205	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023247	27023248	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0024106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	46	120	0	ENST00000324856.7:c.353_354del	p.Thr118ArgfsTer281	p.T118Rfs*281	ENST00000324856	NM_006015.4	118	aCG/a	1/20	0.107438520537902	3	FACETS	1	0.874	1	1	0.976	1	INDETERMINATE	4	TRUE	1	0.2	3		120	125	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717690	89717691	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	118	421	0	ENST00000371953.3:c.716dup	p.Met239IlefsTer4	p.M239Ifs*4	ENST00000371953	NM_000314.4	239	atg/aTtg	7/9	0.569466868018321	2	FACETS	0.98	0.919	1	1	0.993	1	CLONAL	7	TRUE	0	0.2	2		421	172	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258104	123258104	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	11	484	0	ENST00000358487.5:c.1577A>C	p.Lys526Thr	p.K526T	ENST00000358487	NM_000141.4	526	aAa/aCa	12/18	0.3	6	FACETS	0.901	0.623	1			1	CLONAL	1	TRUE	NA	0.2	6		484	171	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118778	115118778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751907473	NA	P-0024106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	29	520	0	ENST00000257566.3:c.563C>T	p.Pro188Leu	p.P188L	ENST00000257566	NM_016569.3	188	cCg/cTg	2/8	1	2	FACETS	0.848	0.694	1	1	0.965	1	CLONAL	3	TRUE	1	0.2	2		520	114	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929161	32929162	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs397507899	NA	P-0024106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	10	406	0	ENST00000380152.3:c.7177dup	p.Met2393AsnfsTer19	p.M2393Nfs*19	ENST00000380152		2391	gaa/gAaa	14/27	0.148071378557222	3	FACETS	0.797	0.542	1	0.399	0.271	0.558	CLONAL	1	TRUE	1	0.2	3		406	138	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226098	2226098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	42	581	0	ENST00000326181.6:c.1795G>A	p.Val599Met	p.V599M	ENST00000326181	NM_032271.2	599	Gtg/Atg	19/21	1	2	FACETS	1	0.903	1	1	0.978	1	CLONAL	3	TRUE	1	0.2	2		581	130	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435168	56435168	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	10	510	0	ENST00000407977.2:c.1969del	p.Arg657GlyfsTer43	p.R657Gfs*43	ENST00000407977		657	Cgg/gg	9/10	1	2	FACETS	0.73	0.496	1	0.73	0.496	1	CLONAL	1	TRUE	1	0.2	2		510	137	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243975	5243975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1488811231	NA	P-0024106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	14	500	2	ENST00000357368.4:c.1507G>A	p.Ala503Thr	p.A503T	ENST00000357368	NM_002850.3	503	Gcc/Acc	11/38	0.148071378557222	0	FACETS	1	0.737	1			1	CLONAL	1	TRUE	0	0.2	0		502	111	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965931	25965931	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	28	508	0	ENST00000435504.4:c.3275A>G	p.His1092Arg	p.H1092R	ENST00000435504		1092	cAc/cGc	13/13	1	2	FACETS	0.946	0.766	1	1	0.954	1	CLONAL	2	TRUE	1	0.2	2		508	148	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180350	38180350	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	26	540	0	ENST00000396334.3:c.198G>T	p.Glu66Asp	p.E66D	ENST00000396334	NM_002468.4	66	gaG/gaT	1/5	0.186217644427432	4	FACETS	0.821	0.655	1	0.821	0.655	1	CLONAL	2	TRUE	2	0.2	4		540	190	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181768	56181768	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	56	305	0	ENST00000399503.3:c.3992T>A	p.Val1331Glu	p.V1331E	ENST00000399503	NM_005921.1	1331	gTg/gAg	17/20	0.3	5	FACETS	1	0.925	1			1	CLONAL	5	TRUE	NA	0.2	5		305	136	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514435	149514435	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	26	524	0	ENST00000261799.4:c.509C>A	p.Pro170His	p.P170H	ENST00000261799	NM_002609.3	170	cCt/cAt	4/23	1	2	FACETS	0.875	0.709	1	1	0.962	1	CLONAL	3	TRUE	1	0.2	2		524	99	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843383	128843383	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761169486	NA	P-0024106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	34	487	0	ENST00000249373.3:c.490C>T	p.Pro164Ser	p.P164S	ENST00000249373	NM_005631.4	164	Cct/Tct	2/12	1	2	FACETS	1	0.904	1	1	0.976	1	CLONAL	4	TRUE	1	0.2	2		487	78	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56882315	56882315	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	62	468	0	ENST00000519728.1:c.1013A>G	p.Lys338Arg	p.K338R	ENST00000519728	NM_002350.3	338	aAa/aGa	10/13	1	2	FACETS	1	0.924	1	1	0.985	1	CLONAL	3	TRUE	1	0.2	2		468	193	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566407	139566407	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	26	495	0	ENST00000308874.7:c.666del	p.His222GlnfsTer32	p.H222Qfs*32	ENST00000308874		222	caC/ca	9/10	1	2	FACETS	1	0.896	1	1	0.959	1	CLONAL	2	TRUE	1	0.2	2		495	110	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0024107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	176	588	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.109901522333241	4	FACETS	0.808	0.746	0.871	0.808	0.746	0.871	INDETERMINATE	2	TRUE	2	0.448362364584427	4		588	704	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879854	37879854	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	416	961	0	ENST00000269571.5:c.2149G>A	p.Glu717Lys	p.E717K	ENST00000269571		717	Gag/Aag	18/27	0.448362364584427	7	FACETS	0.999	0.951	1			1	CLONAL	3	TRUE	NA	0.448362364584427	7		961	1313	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980383	201980394	+	inframe_deletion	In_Frame_Del	DEL	TGGTACTGACCC	TGGTACTGACCC	-	novel	NA	P-0024107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	184	1156	2	ENST00000359651.3:c.121_132del	p.Val41_Leu44del	p.V41_L44del	ENST00000359651		40	tTGGTACTGACCCtg/ttg	1/8	0.448362364584427	3	FACETS	0.951	0.877	1	0.475	0.438	0.514	CLONAL	1	TRUE	1	0.448362364584427	3		1158	1057	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112590	115112590	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	182	983	1	ENST00000257566.3:c.1150G>T	p.Glu384Ter	p.E384*	ENST00000257566	NM_016569.3	384	Gag/Tag	7/8	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.448362364584427	2		984	630	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061349	38061349	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	222	881	0	ENST00000250448.2:c.640T>A	p.Trp214Arg	p.W214R	ENST00000250448	NM_004496.3	214	Tgg/Agg	2/2	0.214077750024309	4	FACETS	0.946	0.884	1	0.946	0.884	1	INDETERMINATE	2	TRUE	2	0.448362364584427	4		881	758	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881329	37881329	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	430	984	0	ENST00000269571.5:c.2521C>A	p.Leu841Ile	p.L841I	ENST00000269571		841	Ctc/Atc	21/27	0.448362364584427	7	FACETS	0.936	0.892	0.982			1	CLONAL	3	TRUE	NA	0.448362364584427	7		984	1448	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259171	36259171	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	148	767	0	ENST00000300305.3:c.320G>T	p.Arg107Leu	p.R107L	ENST00000300305		107	cGc/cTc	3/8	0.448362364584427	3	FACETS	0.998	0.912	1	0.499	0.456	0.544	CLONAL	1	TRUE	1	0.448362364584427	3		767	810	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220349	55220349	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	280	876	4	ENST00000275493.2:c.739G>T	p.Asp247Tyr	p.D247Y	ENST00000275493	NM_005228.3	247	Gac/Tac	6/28	0.309772699662668	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.448362364584427	4		880	816	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860665	151860690	+	frameshift_variant	Frame_Shift_Del	DEL	GTAAACTGGGCATTCTAACAGGGCTA	GTAAACTGGGCATTCTAACAGGGCTA	-	novel	NA	P-0024107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	293	841	0	ENST00000262189.6:c.9972_9997del	p.Ser3325TrpfsTer17	p.S3325Wfs*17	ENST00000262189	NM_170606.2	3324	acTAGCCCTGTTAGAATGCCCAGTTTACct/acct	43/59	NA	2	FACETS	0.948	0.899	0.999			1	INDETERMINATE	2	TRUE	NA	0.448362364584427	2		841	689	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969953	81969953	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	238	564	0	ENST00000359376.3:c.3022C>T	p.Gln1008Ter	p.Q1008*	ENST00000359376	NM_002661.3	1008	Cag/Tag	27/33	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.802280444469909	2		564	563	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957451	175957452	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0024108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	282	690	1	ENST00000367669.3:c.1944_1945delinsTT	p.Ala649Ser	p.A649S	ENST00000367669	NM_022457.5	648	ctGGct/ctTTct	17/20	1	2	FACETS	0.929	0.877	0.981	0.929	0.877	0.981	CLONAL	1	TRUE	1	0.802280444469909	2		691	757	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	287	850	0	ENST00000269305.4:c.734del	p.Gly245AlafsTer2	p.G245Afs*2	ENST00000269305	NM_001126112.2	245	gGc/gc	7/11	0.802280444469909	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.802280444469909	1		850	403	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207059	1208081	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTGATGGGGGACCTGCTGGGGGAAGGCTCTTACGGCAAGGTGAAGGAGGTGCTGGACTCGGAGACGCTGTGCAGGAGGGCCGTCAAGATCCTCAAGAAGAAGAAGTTGCGAAGGATCCCCAACGGGGAGGCCAACGTGAAGAAGTAAGTATGGCTTGCTGGGGTCGGGGCCGGGCCGGGCCAGTCACGGTGCTGATGGTTCTGTCTTCCTTCCTTCTCTCCTCCCTCCCTCCCTTACTTCCTCTTAACACCCTGAGCTGGACCCGTCTGGCGCCTGTGTCCTCCGTGCCAGGGAGAGCGTGGTTGGGGGCCTGCGTTACGGACTTTCACTCAGGCAAGGCCAGTTGTCGCAGCGGGGCGTGCGTTTGCATGGGCTCTTGGACTCCAGTTAAAATGCCCTGGTAGCGAAACCCTCCTGAGAAGGGAGCGGCCCCCAATCCCCTAAGACTAGCCCCTTGGCTCCCCCAGCTGTCCAAGGAGCAGAGGCGCCCAGTGGAATCAGCCTGTGTTTGTTTGGGCCCCGAGAGTTTGTGTGCGGCCGCCAACACGTTTTCTGCGCAGTGTGTGGCCGTTACCGGGGCCAGGCGAAATGTGATTTGTTTATCCTGTCAGAGGGGAACCCTGGGCTGCCAAAAATAACTGTTTGCACCGGCTTATCAGTCAGCAGGAGGGAAACGTAGCCTTTCCTCATTTGCCAGGGATGTGACGCTGGAAGCATCCCTGGCCCCCGGGGCTGGAAGCCCTGCCCGAGGGGGACTGTGCCTCCCTCCCGAATTGCATCCGGAAGACCTTACTTTTCCAACTGACTTCTTCAGGCACGGGGCTGCCGCTGGGCATCCCGGACGCCTCTGCATCTGTGCGCGGAGAAGCTCCTACCTAGGGCAGCACTGGCCGGCCTGAGCCTCTCCCAGCTGGTGGGGGTGGCCGGGGGTGTCCCTGCCTTATCGCAGCCAGACACGCTGCACCTGCCGCCGCCTGGCGGGCCCTGCCCAGGCCCTGCTCCTTTCCCAGCCTTCTTAACTT	CCTGATGGGGGACCTGCTGGGGGAAGGCTCTTACGGCAAGGTGAAGGAGGTGCTGGACTCGGAGACGCTGTGCAGGAGGGCCGTCAAGATCCTCAAGAAGAAGAAGTTGCGAAGGATCCCCAACGGGGAGGCCAACGTGAAGAAGTAAGTATGGCTTGCTGGGGTCGGGGCCGGGCCGGGCCAGTCACGGTGCTGATGGTTCTGTCTTCCTTCCTTCTCTCCTCCCTCCCTCCCTTACTTCCTCTTAACACCCTGAGCTGGACCCGTCTGGCGCCTGTGTCCTCCGTGCCAGGGAGAGCGTGGTTGGGGGCCTGCGTTACGGACTTTCACTCAGGCAAGGCCAGTTGTCGCAGCGGGGCGTGCGTTTGCATGGGCTCTTGGACTCCAGTTAAAATGCCCTGGTAGCGAAACCCTCCTGAGAAGGGAGCGGCCCCCAATCCCCTAAGACTAGCCCCTTGGCTCCCCCAGCTGTCCAAGGAGCAGAGGCGCCCAGTGGAATCAGCCTGTGTTTGTTTGGGCCCCGAGAGTTTGTGTGCGGCCGCCAACACGTTTTCTGCGCAGTGTGTGGCCGTTACCGGGGCCAGGCGAAATGTGATTTGTTTATCCTGTCAGAGGGGAACCCTGGGCTGCCAAAAATAACTGTTTGCACCGGCTTATCAGTCAGCAGGAGGGAAACGTAGCCTTTCCTCATTTGCCAGGGATGTGACGCTGGAAGCATCCCTGGCCCCCGGGGCTGGAAGCCCTGCCCGAGGGGGACTGTGCCTCCCTCCCGAATTGCATCCGGAAGACCTTACTTTTCCAACTGACTTCTTCAGGCACGGGGCTGCCGCTGGGCATCCCGGACGCCTCTGCATCTGTGCGCGGAGAAGCTCCTACCTAGGGCAGCACTGGCCGGCCTGAGCCTCTCCCAGCTGGTGGGGGTGGCCGGGGGTGTCCCTGCCTTATCGCAGCCAGACACGCTGCACCTGCCGCCGCCTGGCGGGCCCTGCCCAGGCCCTGCTCCTTTCCCAGCCTTCTTAACTT	-	novel	NA	P-0024108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	311	863	0	ENST00000326873.7:c.147_290+879del		p.X49_splice	ENST00000326873	NM_000455.4	49		1/10	0.792676589587551	2	FACETS	0.832	0.799	0.864	0.832	0.799	0.864	CLONAL	2	TRUE	0	0.802280444469909	2		863	466	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238932	5238932	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	99	222	0	ENST00000357368.4:c.1847C>A	p.Ser616Tyr	p.S616Y	ENST00000357368	NM_002850.3	616	tCc/tAc	13/38	0.792676589587551	2	FACETS	1	0.962	1	0.551	0.502	0.6	CLONAL	1	TRUE	0	0.802280444469909	2		222	224	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597401	10597401	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	384	985	1	ENST00000171111.5:c.1802G>A	p.Arg601Gln	p.R601Q	ENST00000171111	NM_203500.1	601	cGg/cAg	6/6	0.802280444469909	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.802280444469909	1		986	543	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410000	139410000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369522885	NA	P-0024108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	271	758	1	ENST00000277541.6:c.1838G>A	p.Arg613His	p.R613H	ENST00000277541	NM_017617.3	613	cGc/cAc	11/34	0.246370747259195	1	FACETS	0.679	0.643	0.715	0.679	0.643	0.715	INDETERMINATE	1	TRUE	0	0.802280444469909	1		759	596	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	448	855	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.451595030952037	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.451595030952037	3		855	1176	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0024112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	130	838	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.30564509204253	2		838	637	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0024113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	70	790	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	0.316686442182098	2		790	393	SUCCESS
APC	324	MSKCC	GRCh37	5	112176030	112176030	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs886039682	NA	P-0024113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	51	363	0	ENST00000257430.4:c.4741del	p.Ser1581LeufsTer69	p.S1581Lfs*69	ENST00000257430	NM_000038.5	1580	aTt/at	16/16	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.316686442182098	2		363	302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0024113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	68	917	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.316686442182098	1	FACETS	0.763	0.665	0.867	0.763	0.665	0.867	SUBCLONAL	1	TRUE	0	0.316686442182098	1		918	474	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0024113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	51	375	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.316686442182098	2		375	311	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411678	63411678	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	126	386	0	ENST00000330258.3:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000330258	NM_152424.3	497	Cga/Tga	2/2	1	1	FACETS	1	0.965	1	1	0.991	1	CLONAL	2	TRUE	0	0.316686442182098	1		386	307	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012410	29012410	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	251	585	0	ENST00000282397.4:c.461T>G	p.Leu154Arg	p.L154R	ENST00000282397	NM_002019.4	154	cTc/cGc	4/30	0.316686442182098	5	FACETS	1	0.968	1	1	0.968	1	CLONAL	4	TRUE	1	0.316686442182098	5		585	564	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120351	70120352	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	78	818	0	ENST00000245479.2:c.1354dup	p.Tyr452LeufsTer126	p.Y452Lfs*126	ENST00000245479	NM_000346.3	451	-/T	3/3	1	2	FACETS	0.719	0.632	0.813	0.719	0.632	0.813	SUBCLONAL	1	TRUE	1	0.316686442182098	2		818	685	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541582	187541582	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	46	427	0	ENST00000441802.2:c.6158T>C	p.Val2053Ala	p.V2053A	ENST00000441802	NM_005245.3	2053	gTg/gCg	10/27	1	2	FACETS	0.7	0.59	0.821	0.7	0.59	0.821	SUBCLONAL	1	TRUE	1	0.316686442182098	2		427	415	SUCCESS
APC	324	MSKCC	GRCh37	5	112174600	112174600	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	49	449	1	ENST00000257430.4:c.3309G>T	p.Arg1103Ser	p.R1103S	ENST00000257430	NM_000038.5	1103	agG/agT	16/16	1	2	FACETS	0.927	0.788	1	0.927	0.788	1	CLONAL	1	TRUE	1	0.316686442182098	2		450	334	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	121	571	0				ENST00000310581	NM_198253.2	-/1132			0.817938510933905	3	FACETS	0.906	0.839	0.973	0.906	0.839	0.973	CLONAL	2	TRUE	1	0.817938510933905	3		571	230	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0024114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	323	548	1	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	0.817938510933905	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.817938510933905	1		549	405	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486037	8486037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	168	417	0	ENST00000356435.5:c.2780C>T	p.Ser927Leu	p.S927L	ENST00000356435		927	tCa/tTa	17/35	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.817938510933905	2		417	408	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934194	48934194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	148	468	0	ENST00000267163.4:c.649C>T	p.Gln217Ter	p.Q217*	ENST00000267163	NM_000321.2	217	Cag/Tag	7/27	1	2	FACETS	0.828	0.763	0.895	0.828	0.763	0.895	CLONAL	1	TRUE	1	0.817938510933905	2		468	437	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44910953	44910953	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0024114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	118	153	0	ENST00000377967.4:c.655-1G>A		p.X219_splice	ENST00000377967	NM_021140.2	219			1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.817938510933905	1		153	145	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969322	44969322	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0024114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	128	150	0	ENST00000377967.4:c.4006-2A>T		p.X1336_splice	ENST00000377967	NM_021140.2	1336			1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.817938510933905	1		150	151	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933731	36933731	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	257	516	0	ENST00000361632.4:c.1668G>C	p.Lys556Asn	p.K556N	ENST00000361632		556	aaG/aaC	12/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.817938510933905	2		516	607	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720847	89720847	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	112	223	0	ENST00000371953.3:c.999del	p.Asn334ThrfsTer10	p.N334Tfs*10	ENST00000371953	NM_000314.4	333	gCc/gc	8/9	0.817938510933905	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.817938510933905	1		223	154	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466961	18466961	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	157	407	0	ENST00000266497.5:c.1100A>T	p.Gln367Leu	p.Q367L	ENST00000266497		367	cAg/cTg	5/31	1	2	FACETS	0.965	0.894	1	0.965	0.894	1	CLONAL	1	TRUE	1	0.817938510933905	2		407	398	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233062	69233062	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	104	248	0	ENST00000462284.1:c.927G>T	p.Trp309Cys	p.W309C	ENST00000462284	NM_002392.5	309	tgG/tgT	11/11	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.817938510933905	2		248	243	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48921999	48921999	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	rs1131690871	NA	P-0024114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	164	401	0	ENST00000267163.4:c.539del	p.Ser180Ter	p.S180*	ENST00000267163	NM_000321.2	180	tCg/tg	5/27	1	2	FACETS	0.966	0.897	1	0.966	0.897	1	CLONAL	1	TRUE	1	0.817938510933905	2		401	415	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866609	37866609	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs769870618	NA	P-0024114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	199	431	0	ENST00000269571.5:c.776A>G	p.Asn259Ser	p.N259S	ENST00000269571		259	aAc/aGc	7/27	1	2	FACETS	0.971	0.908	1	0.971	0.908	1	CLONAL	1	TRUE	1	0.817938510933905	2		431	501	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358974	81358974	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	180	433	1	ENST00000222390.5:c.987G>A	p.Trp329Ter	p.W329*	ENST00000222390	NM_000601.4	329	tgG/tgA	8/18	1	2	FACETS	0.991	0.924	1	0.991	0.924	1	CLONAL	1	TRUE	1	0.817938510933905	2		434	444	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69039620	69039620	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	25	515	1	ENST00000288368.4:c.3732G>T	p.Lys1244Asn	p.K1244N	ENST00000288368	NM_024870.2	1244	aaG/aaT	31/40	1	2	FACETS	0.132	0.103	0.165	0.132	0.103	0.165	SUBCLONAL	1	TRUE	1	0.817938510933905	2		516	463	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938307	76938307	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1557139647	NA	P-0024114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	194	243	0	ENST00000373344.5:c.2441C>G	p.Ser814Cys	p.S814C	ENST00000373344	NM_000489.3	814	tCt/tGt	9/35	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.817938510933905	1		243	232	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0024118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	579	642	1	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	0.864035116245446	3	FACETS	0.989	0.975	1	0.989	0.975	1	CLONAL	3	FALSE	0	0.917126742156548	3		643	621	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656878	45656878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1306205252	NA	P-0024118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	169	602	0	ENST00000407780.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000407780	NM_001283052.1	93	cGg/cAg	3/7	0.854226354328437	3	FACETS	0.94	0.869	1	0.47	0.434	0.507	CLONAL	1	FALSE	1	0.917126742156548	3		602	572	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248494	59248513	+	frameshift_variant	Frame_Shift_Del	DEL	GGACTGGATTATCAGGCGCT	GGACTGGATTATCAGGCGCT	AGACTGCGCG	novel	NA	P-0024118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	407	586	2	ENST00000371222.2:c.230_249delinsCGCGCAGTCT	p.Glu77AlafsTer24	p.E77Afs*24	ENST00000371222	NM_002228.3	77	gAGCGCCTGATAATCCAGTCC/gCGCGCAGTCT	1/1	0.582269108707352	3	FACETS	1	0.982	1	0.686	0.662	0.71	CLONAL	2	FALSE	0	0.917126742156548	3		588	629	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005541	42005541	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	342	637	0	ENST00000219905.7:c.3278del	p.Gly1093AspfsTer40	p.G1093Dfs*40	ENST00000219905	NM_001164273.1	1093	Gga/ga	9/24	0.853649745840923	3	FACETS	0.973	0.934	1	0.973	0.934	1	CLONAL	2	FALSE	1	0.917126742156548	3		637	559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0024120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	62	683	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.179034222705394	2		683	517	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796465	42796465	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	31	1167	2	ENST00000575354.2:c.3022C>T	p.Gln1008Ter	p.Q1008*	ENST00000575354	NM_015125.3	1008	Cag/Tag	13/20	1	2	FACETS	0.613	0.494	0.748	0.613	0.494	0.748	SUBCLONAL	1	FALSE	1	0.179034222705394	2		1169	565	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949994	44949994	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1450363794	NA	P-0024120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	50	794	3	ENST00000377967.4:c.3763C>T	p.Arg1255Trp	p.R1255W	ENST00000377967	NM_021140.2	1255	Cgg/Tgg	26/29	NA	2	FACETS	1	0.954	1			1	INDETERMINATE	1	FALSE	NA	0.179034222705394	2		797	416	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675346	241675346	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	57	1071	1	ENST00000366560.3:c.476A>G	p.Asn159Ser	p.N159S	ENST00000366560	NM_000143.3	159	aAt/aGt	4/10	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	1	0.179034222705394	2		1072	524	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981766	201981766	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs879040508	NA	P-0024120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	40	1058	0	ENST00000359651.3:c.479-2A>T		p.X160_splice	ENST00000359651		160			1	2	FACETS	0.937	0.778	1	0.937	0.778	1	CLONAL	1	FALSE	1	0.179034222705394	2		1058	477	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981792	70981792	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	44	1261	1	ENST00000276594.2:c.304T>C	p.Tyr102His	p.Y102H	ENST00000276594	NM_024504.3	102	Tac/Cac	2/8	1	2	FACETS	0.861	0.721	1	0.861	0.721	1	CLONAL	1	FALSE	1	0.179034222705394	2		1262	571	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349688	70349688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	28	907	0	ENST00000374080.3:c.3850C>T	p.Arg1284Cys	p.R1284C	ENST00000374080		1284	Cgc/Tgc	27/45	0.179034222705394	1	FACETS	0.558	0.445	0.688	0.558	0.445	0.688	SUBCLONAL	1	FALSE	0	0.179034222705394	1		907	510	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0024122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	146	509	3	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.305000338126238	1	FACETS	0.875	0.802	0.952	0.875	0.802	0.952	CLONAL	1	TRUE	0	0.423984921942367	1		512	620	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0024122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	280	692	1	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.423984921942367	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.423984921942367	1		693	798	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39709868	39709870	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs748165145	NA	P-0024122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	109	371	0	ENST00000361337.2:c.504_506del	p.Glu169del	p.E169del	ENST00000361337	NM_003286.2	165	ctAGAa/cta	7/21	0.423984921942367	3	FACETS	0.74	0.664	0.821			1	SUBCLONAL	1	TRUE	NA	0.423984921942367	3		371	842	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245486	153245486	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	157	603	3	ENST00000281708.4:c.1705G>T	p.Glu569Ter	p.E569*	ENST00000281708	NM_033632.3	569	Gag/Tag	11/12	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.423984921942367	2		606	738	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245521	153245521	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	120	484	0	ENST00000281708.4:c.1670G>T	p.Gly557Val	p.G557V	ENST00000281708	NM_033632.3	557	gGa/gTa	11/12	1	2	FACETS	0.998	0.905	1	0.998	0.905	1	CLONAL	1	TRUE	1	0.423984921942367	2		484	567	SUCCESS
APC	324	MSKCC	GRCh37	5	112175358	112175359	+	stop_gained,inframe_insertion	Nonsense_Mutation	INS	-	-	TTA	novel	NA	P-0024122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	39	350	0	ENST00000257430.4:c.4067_4068insTTA	p.Ser1356_Gly1357insTer	p.S1356_G1357ins*	ENST00000257430	NM_000038.5	1356	tca/tcTTAa	16/16	0.305000338126238	1	FACETS	0.4	0.332	0.476	0.4	0.332	0.476	SUBCLONAL	1	TRUE	0	0.423984921942367	1		350	362	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	27	571	0				ENST00000310581	NM_198253.2	-/1132			0.188383421168972	1	FACETS	1	0.918	1	1	0.918	1	INDETERMINATE	1	TRUE	0	0.471176281496894	1		571	72	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0024124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	81	625	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.98	0.87	1	0.98	0.87	1	CLONAL	1	TRUE	1	0.471176281496894	2		625	351	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428218	47428218	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	67	838	1	ENST00000377045.4:c.1178A>T	p.His393Leu	p.H393L	ENST00000377045	NM_001654.4	393	cAc/cTc	11/16	0.11708338045252	0	FACETS	0.44	0.384	0.499			1	INDETERMINATE	1	TRUE	0	0.471176281496894	0		839	342	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	263	869	0	ENST00000397752.3:c.3028G>A	p.Asp1010Asn	p.D1010N	ENST00000397752	NM_000245.2	1010	Gat/Aat	14/21	1	2	FACETS	0.605	0.566	0.645	0.605	0.566	0.645	SUBCLONAL	1	TRUE	1	0.694153271580016	2		869	1252	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391966	139391967	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	69	700	0	ENST00000277541.6:c.6224dup	p.Thr2076AspfsTer192	p.T2076Dfs*192	ENST00000277541	NM_017617.3	2075	gag/gaAg	34/34	1	2	FACETS	0.226	0.196	0.259	0.226	0.196	0.259	SUBCLONAL	1	TRUE	1	0.694153271580016	2		700	878	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405615	139405615	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199505287	NA	P-0024125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	386	731	2	ENST00000277541.6:c.2576C>T	p.Thr859Met	p.T859M	ENST00000277541	NM_017617.3	859	aCg/aTg	16/34	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.694153271580016	2		733	1008	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145588	11145588	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs1308562238	NA	P-0024127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	282	510	9	ENST00000358026.2:c.3952-2A>T		p.X1318_splice	ENST00000358026	NM_001128849.1	1318			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		519	358	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0024128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	123	790	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.997	0.904	1	0.997	0.904	1	CLONAL	1	TRUE	1	0.41	2		790	602	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	92	629	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	0.41	2		629	428	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0024128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	61	611	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.673	0.582	0.772	0.673	0.582	0.772	SUBCLONAL	1	TRUE	1	0.41	2		611	442	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752961	128752962	+	inframe_insertion	In_Frame_Ins	INS	-	-	AACGTCTTGGAGCGCCAGAGGAGG	novel	NA	P-0024128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	34	663	0	ENST00000377970.2:c.1127_1150dup	p.Val376_Asn383dup	p.V376_N383dup	ENST00000377970	NM_002467.4	376	-/AACGTCTTGGAGCGCCAGAGGAGG	3/3	1	2	FACETS	0.315	0.257	0.381	0.315	0.257	0.381	SUBCLONAL	1	TRUE	1	0.41	2		663	526	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0024129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	484	511	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	0.7183941985232	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	0	0.7183941985232	3		511	607	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653842	89653842	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1114167670	NA	P-0024129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	440	546	0	ENST00000371953.3:c.141del	p.Asn48ThrfsTer6	p.N48Tfs*6	ENST00000371953	NM_000314.4	47	aGg/ag	2/9	0.7183941985232	2	FACETS	0.994	0.964	1	0.994	0.964	1	CLONAL	2	TRUE	0	0.7183941985232	2		546	616	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260316	149260316	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	479	698	4	ENST00000360632.3:c.577C>A	p.His193Asn	p.H193N	ENST00000360632	NM_015472.4	193	Cac/Aac	4/7	0.7183941985232	2	FACETS	0.992	0.963	1	0.992	0.963	1	CLONAL	2	TRUE	0	0.7183941985232	2		702	672	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	163	678	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.480035213576637	2		678	552	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88672134	88672134	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	184	628	0	ENST00000372037.3:c.668C>T	p.Pro223Leu	p.P223L	ENST00000372037	NM_004329.2	223	cCt/cTt	8/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.480035213576637	2		628	626	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281980	49281980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777806801	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	80	706	1	ENST00000282018.3:c.1027G>A	p.Glu343Lys	p.E343K	ENST00000282018	NM_020377.2	343	Gaa/Aaa	1/1	1	2	FACETS	0.536	0.472	0.604	0.536	0.472	0.604	SUBCLONAL	1	TRUE	1	0.480035213576637	2		707	622	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254672	16254672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	187	658	0	ENST00000375759.3:c.1937C>T	p.Ser646Phe	p.S646F	ENST00000375759	NM_015001.2	646	tCc/tTc	11/15	0.23521458083245	1	FACETS	0.944	0.877	1	0.944	0.877	1	INDETERMINATE	1	TRUE	0	0.480035213576637	1		658	627	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818207	43818207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	117	641	0	ENST00000372470.3:c.1672G>A	p.Asp558Asn	p.D558N	ENST00000372470	NM_005373.2	558	Gat/Aat	12/12	1	2	FACETS	0.961	0.871	1	0.961	0.871	1	CLONAL	1	TRUE	1	0.480035213576637	2		641	507	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120508075	120508076	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	85	402	0	ENST00000256646.2:c.1681_1681+1delinsAA		p.X561_splice	ENST00000256646	NM_024408.3	561		10/34	1	2	FACETS	0.853	0.758	0.954	0.853	0.758	0.954	CLONAL	1	TRUE	1	0.480035213576637	2		402	415	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162742024	162742024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	105	532	0	ENST00000367921.3:c.1715G>A	p.Gly572Glu	p.G572E	ENST00000367921	NM_006182.2	572	gGa/gAa	13/18	1	2	FACETS	0.886	0.797	0.979	0.886	0.797	0.979	CLONAL	1	TRUE	1	0.480035213576637	2		532	494	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193121567	193121567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	48	460	0	ENST00000367435.3:c.965C>T	p.Ser322Phe	p.S322F	ENST00000367435	NM_024529.4	322	tCt/tTt	10/17	1	2	FACETS	0.392	0.331	0.459	0.392	0.331	0.459	SUBCLONAL	1	TRUE	1	0.480035213576637	2		460	510	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649611	206649611	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	135	679	1	ENST00000367120.3:c.446G>A	p.Gly149Glu	p.G149E	ENST00000367120	NM_014002.3	149	gGg/gAg	6/22	1	2	FACETS	0.973	0.888	1	0.973	0.888	1	CLONAL	1	TRUE	1	0.480035213576637	2		680	578	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612629	228612629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	132	580	0	ENST00000366696.1:c.398G>A	p.Gly133Glu	p.G133E	ENST00000366696	NM_003493.2	133	gGg/gAg	1/1	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.480035213576637	2		580	502	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246021924	246021924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	185	865	0	ENST00000388985.4:c.950C>T	p.Ser317Phe	p.S317F	ENST00000388985		317	tCt/tTt	10/12	1	2	FACETS	0.971	0.898	1	0.971	0.898	1	CLONAL	1	TRUE	1	0.480035213576637	2		865	794	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405581	70405582	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	211	696	1	ENST00000373644.4:c.3095_3096delinsTT	p.Ser1032Phe	p.S1032F	ENST00000373644	NM_030625.2	1032	tCC/tTT	4/12	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.480035213576637	2		697	744	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112769505	112769505	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	94	704	1	ENST00000369452.4:c.1457T>A	p.Leu486His	p.L486H	ENST00000369452	NM_007373.3	486	cTt/cAt	8/9	1	2	FACETS	0.639	0.569	0.713	0.639	0.569	0.713	SUBCLONAL	1	TRUE	1	0.480035213576637	2		705	613	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047325	77047325	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	44	492	0	ENST00000356341.3:c.1219G>T	p.Asp407Tyr	p.D407Y	ENST00000356341	NM_002576.4	407	Gac/Tac	13/15	0.243091940582013	2	FACETS	0.421	0.354	0.496	0.211	0.177	0.248	INDETERMINATE	1	TRUE	0	0.480035213576637	2		492	435	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909855	100909855	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	114	304	0	ENST00000325455.5:c.2794A>T	p.Lys932Ter	p.K932*	ENST00000325455	NM_001202474.3	932	Aaa/Taa	8/8	0.243091940582013	2	FACETS	1	0.986	1	0.74	0.675	0.807	INDETERMINATE	1	TRUE	0	0.480035213576637	2		304	321	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192078	108192078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200431631	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	242	650	0	ENST00000278616.4:c.6503C>T	p.Ser2168Leu	p.S2168L	ENST00000278616	NM_000051.3	2168	tCg/tTg	45/63	0.243091940582013	2	FACETS	0.751	0.706	0.798	0.751	0.706	0.798	INDETERMINATE	2	TRUE	0	0.480035213576637	2		650	671	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342452	118342452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	57	416	0	ENST00000534358.1:c.578C>T	p.Pro193Leu	p.P193L	ENST00000534358	NM_005933.3	193	cCa/cTa	3/36	0.243091940582013	2	FACETS	0.568	0.489	0.654	0.284	0.244	0.327	INDETERMINATE	1	TRUE	0	0.480035213576637	2		416	418	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390342	118390342	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	175	557	0	ENST00000534358.1:c.11156G>C	p.Gly3719Ala	p.G3719A	ENST00000534358	NM_005933.3	3719	gGt/gCt	32/36	0.243091940582013	2	FACETS	1	0.99	1	0.731	0.678	0.784	INDETERMINATE	1	TRUE	0	0.480035213576637	2		557	499	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420955	49420955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	113	593	2	ENST00000301067.7:c.14794C>T	p.Pro4932Ser	p.P4932S	ENST00000301067	NM_003482.3	4932	Ccc/Tcc	48/54	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.480035213576637	2		595	448	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434804	49434804	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	157	872	1	ENST00000301067.7:c.6749C>T	p.Pro2250Leu	p.P2250L	ENST00000301067	NM_003482.3	2250	cCc/cTc	31/54	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.480035213576637	2		873	652	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28979939	28979939	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	156	738	1	ENST00000282397.4:c.1529C>A	p.Ala510Glu	p.A510E	ENST00000282397	NM_002019.4	510	gCa/gAa	11/30	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.480035213576637	2		739	565	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100220	30100220	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866059930	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	117	450	0	ENST00000331968.5:c.1400C>T	p.Pro467Leu	p.P467L	ENST00000331968	NM_002742.2	467	cCt/cTt	10/18	1	2	FACETS	0.927	0.839	1	0.927	0.839	1	CLONAL	1	TRUE	1	0.480035213576637	2		450	526	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560227	95560227	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	101	425	0	ENST00000393063.1:c.5362G>T	p.Glu1788Ter	p.E1788*	ENST00000393063	NM_030621.3	1788	Gag/Tag	25/28	1	2	FACETS	0.903	0.811	0.999	0.903	0.811	0.999	CLONAL	1	TRUE	1	0.480035213576637	2		425	466	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675068	40675068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	129	752	1	ENST00000249776.8:c.32G>A	p.Arg11Lys	p.R11K	ENST00000249776	NM_033286.3	11	aGa/aAa	1/9	0.23521458083245	1	FACETS	0.638	0.58	0.699	0.638	0.58	0.699	INDETERMINATE	1	TRUE	0	0.480035213576637	1		753	640	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675103	40675103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	194	828	1	ENST00000249776.8:c.67G>A	p.Asp23Asn	p.D23N	ENST00000249776	NM_033286.3	23	Gat/Aat	1/9	0.23521458083245	1	FACETS	0.913	0.848	0.979	0.913	0.848	0.979	INDETERMINATE	1	TRUE	0	0.480035213576637	1		829	673	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961963	41961963	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs753015602	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	137	570	0	ENST00000219905.7:c.871C>G	p.Arg291Gly	p.R291G	ENST00000219905	NM_001164273.1	291	Cgg/Ggg	2/24	0.23521458083245	1	FACETS	0.837	0.766	0.911	0.837	0.766	0.911	INDETERMINATE	1	TRUE	0	0.480035213576637	1		570	518	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713232	43713232	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	173	798	2	ENST00000382044.4:c.4241C>T	p.Thr1414Ile	p.T1414I	ENST00000382044	NM_001141980.1	1414	aCt/aTt	20/28	0.23521458083245	1	FACETS	0.881	0.814	0.949	0.881	0.814	0.949	INDETERMINATE	1	TRUE	0	0.480035213576637	1		800	622	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724691	43724691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	110	795	0	ENST00000382044.4:c.3376G>A	p.Val1126Met	p.V1126M	ENST00000382044	NM_001141980.1	1126	Gtg/Atg	17/28	0.23521458083245	1	FACETS	0.553	0.498	0.611	0.553	0.498	0.611	INDETERMINATE	1	TRUE	0	0.480035213576637	1		795	630	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032279	10032279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	134	687	0	ENST00000330684.3:c.544G>A	p.Glu182Lys	p.E182K	ENST00000330684	NM_001134407.1	182	Gaa/Aaa	3/13	1	2	FACETS	0.985	0.898	1	0.985	0.898	1	CLONAL	1	TRUE	1	0.480035213576637	2		687	567	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133274	30133275	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	131	741	1	ENST00000263025.4:c.223_224delinsTT	p.Pro75Phe	p.P75F	ENST00000263025	NM_002746.2	75	CCc/TTc	2/9	1	2	FACETS	0.911	0.83	0.996	0.911	0.83	0.996	CLONAL	1	TRUE	1	0.480035213576637	2		742	599	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827964	72827964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768307205	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	171	781	3	ENST00000268489.5:c.8617G>A	p.Glu2873Lys	p.E2873K	ENST00000268489	NM_006885.3	2873	Gaa/Aaa	9/10	0.247240523561742	1	FACETS	0.771	0.711	0.833	0.771	0.711	0.833	INDETERMINATE	1	TRUE	0	0.480035213576637	1		784	702	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828755	72828755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	59	608	0	ENST00000268489.5:c.7826C>T	p.Ser2609Phe	p.S2609F	ENST00000268489	NM_006885.3	2609	tCc/tTc	9/10	0.247240523561742	1	FACETS	0.432	0.373	0.497	0.432	0.373	0.497	INDETERMINATE	1	TRUE	0	0.480035213576637	1		608	432	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81979779	81979780	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	106	505	1	ENST00000359376.3:c.3482-1_3482delinsAA		p.X1161_splice	ENST00000359376	NM_002661.3	1161		31/33	0.247240523561742	1	FACETS	0.803	0.725	0.884	0.803	0.725	0.884	INDETERMINATE	1	TRUE	0	0.480035213576637	1		506	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	155	759	0	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	0.480035213576637	2		759	542	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110133	8110133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	144	676	1	ENST00000585124.1:c.472C>T	p.Pro158Ser	p.P158S	ENST00000585124	NM_004217.3	158	Ccc/Tcc	6/9	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.480035213576637	2		677	510	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012211	16012211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1391053845	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	130	517	2	ENST00000268712.3:c.2071C>T	p.Arg691Cys	p.R691C	ENST00000268712	NM_006311.3	691	Cgt/Tgt	19/46	1	2	FACETS	0.964	0.878	1	0.964	0.878	1	CLONAL	1	TRUE	1	0.480035213576637	2		519	562	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245740	41245740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	84	843	2	ENST00000357654.3:c.1808C>T	p.Ser603Leu	p.S603L	ENST00000357654	NM_007294.3	603	tCa/tTa	10/23	1	2	FACETS	0.485	0.428	0.546	0.485	0.428	0.546	SUBCLONAL	1	TRUE	1	0.480035213576637	2		845	722	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245861	41245861	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs80356898	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	165	716	3	ENST00000357654.3:c.1687C>T	p.Gln563Ter	p.Q563*	ENST00000357654	NM_007294.3	563	Cag/Tag	10/23	1	2	FACETS	0.938	0.863	1	0.938	0.863	1	CLONAL	1	TRUE	1	0.480035213576637	2		719	733	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435090	56435090	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	144	717	0	ENST00000407977.2:c.2047C>T	p.His683Tyr	p.H683Y	ENST00000407977		683	Cat/Tat	9/10	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.480035213576637	2		717	587	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774769	73774769	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	98	437	0	ENST00000254810.4:c.318A>T	p.Glu106Asp	p.E106D	ENST00000254810	NM_005324.3	106	gaA/gaT	4/4	1	2	FACETS	0.936	0.84	1	0.936	0.84	1	CLONAL	1	TRUE	1	0.480035213576637	2		437	436	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621863	1621864	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	47	666	2	ENST00000344749.5:c.928_929delinsTT	p.Pro310Phe	p.P310F	ENST00000344749	NM_001136139.2	310	CCt/TTt	11/19	0.289113259006451	2	FACETS	0.422	0.356	0.495	0.211	0.178	0.248	SUBCLONAL	1	TRUE	0	0.480035213576637	2		668	464	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222055	2222055	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	55	738	0	ENST00000398665.3:c.2887G>A	p.Ala963Thr	p.A963T	ENST00000398665	NM_032482.2	963	Gcc/Acc	24/28	0.289113259006451	2	FACETS	0.481	0.412	0.557	0.241	0.206	0.279	SUBCLONAL	1	TRUE	0	0.480035213576637	2		738	476	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222277	2222277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	64	750	0	ENST00000398665.3:c.3109C>T	p.Pro1037Ser	p.P1037S	ENST00000398665	NM_032482.2	1037	Cct/Tct	24/28	0.289113259006451	2	FACETS	0.461	0.399	0.528	0.23	0.199	0.264	SUBCLONAL	1	TRUE	0	0.480035213576637	2		750	579	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226643	2226643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269354910	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	161	679	1	ENST00000398665.3:c.4123G>A	p.Gly1375Ser	p.G1375S	ENST00000398665	NM_032482.2	1375	Ggc/Agc	27/28	0.289113259006451	2	FACETS	1	0.989	1	0.729	0.675	0.785	CLONAL	1	TRUE	0	0.480035213576637	2		680	460	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118977	3118977	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	182	796	0	ENST00000078429.4:c.661G>A	p.Glu221Lys	p.E221K	ENST00000078429	NM_002067.2	221	Gag/Aag	5/7	0.289113259006451	2	FACETS	1	0.988	1	0.672	0.624	0.722	CLONAL	1	TRUE	0	0.480035213576637	2		796	564	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223192	5223192	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	54	713	1	ENST00000357368.4:c.2611G>A	p.Gly871Ser	p.G871S	ENST00000357368	NM_002850.3	871	Ggc/Agc	18/38	0.289113259006451	2	FACETS	0.446	0.381	0.517	0.223	0.19	0.259	SUBCLONAL	1	TRUE	0	0.480035213576637	2		714	504	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117082	7117083	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	45	688	1	ENST00000302850.5:c.4133_4134delinsAA	p.Arg1378Gln	p.R1378Q	ENST00000302850	NM_000208.2	1378	cGG/cAA	22/22	0.289113259006451	2	FACETS	0.34	0.285	0.401	0.17	0.142	0.201	SUBCLONAL	1	TRUE	0	0.480035213576637	2		689	551	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051148	13051148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	63	629	1	ENST00000316448.5:c.584C>T	p.Ser195Phe	p.S195F	ENST00000316448	NM_004343.3	195	tCc/tTc	5/9	0.289113259006451	2	FACETS	0.501	0.434	0.574	0.25	0.217	0.287	SUBCLONAL	1	TRUE	0	0.480035213576637	2		630	524	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271561	15271561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	67	875	1	ENST00000263388.2:c.6878C>T	p.Pro2293Leu	p.P2293L	ENST00000263388	NM_000435.2	2293	cCc/cTc	33/33	0.289113259006451	2	FACETS	0.491	0.426	0.56	0.245	0.213	0.28	SUBCLONAL	1	TRUE	0	0.480035213576637	2		876	569	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291528	15291528	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	179	595	0	ENST00000263388.2:c.3106C>T	p.Arg1036Ter	p.R1036*	ENST00000263388	NM_000435.2	1036	Cga/Tga	19/33	0.289113259006451	2	FACETS	0.788	0.734	0.844	0.788	0.734	0.844	SUBCLONAL	2	TRUE	0	0.480035213576637	2		595	473	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384937	17384937	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	40	838	2	ENST00000359435.4:c.487C>T	p.Pro163Ser	p.P163S	ENST00000359435	NM_001033549.1	163	Ccc/Tcc	5/9	0.289113259006451	2	FACETS	0.306	0.253	0.364	0.153	0.126	0.182	SUBCLONAL	1	TRUE	0	0.480035213576637	2		840	545	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943518	17943518	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	38	623	0	ENST00000458235.1:c.2491-1G>C		p.X831_splice	ENST00000458235	NM_000215.3	831			0.289113259006451	2	FACETS	0.353	0.291	0.421	0.176	0.145	0.211	SUBCLONAL	1	TRUE	0	0.480035213576637	2		623	449	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274165	18274166	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	194	715	2	ENST00000222254.8:c.1383_1384delinsTT	p.Gln462Ter	p.Q462*	ENST00000222254	NM_005027.3	461	gaCCag/gaTTag	11/16	0.289113259006451	2	FACETS	0.764	0.713	0.816	0.764	0.713	0.816	SUBCLONAL	2	TRUE	0	0.480035213576637	2		717	529	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867730	45867730	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	202	806	1	ENST00000391945.4:c.670G>A	p.Glu224Lys	p.E224K	ENST00000391945	NM_000400.3	224	Gaa/Aaa	8/23	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.480035213576637	2		807	618	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902172	50902172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779418268	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	172	681	0	ENST00000440232.2:c.64C>T	p.Leu22Phe	p.L22F	ENST00000440232	NM_002691.3	22	Ctc/Ttc	2/27	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.480035213576637	2		681	518	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143035	30143036	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	251	772	1	ENST00000389048.3:c.490_491delinsAA	p.Gly164Lys	p.G164K	ENST00000389048	NM_004304.4	164	GGg/AAg	1/29	0.480035213576637	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.480035213576637	3		773	635	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222264	39222264	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1281786941	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	107	525	0	ENST00000402219.2:c.3346A>G	p.Ser1116Gly	p.S1116G	ENST00000402219	NM_005633.3	1116	Agc/Ggc	20/23	0.480035213576637	3	FACETS	0.771	0.692	0.855	0.385	0.346	0.428	SUBCLONAL	1	TRUE	1	0.480035213576637	3		525	717	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426669	212426669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	209	658	1	ENST00000342788.4:c.2446G>A	p.Gly816Arg	p.G816R	ENST00000342788	NM_005235.2	816	Gga/Aga	20/28	0.452457603979769	2	FACETS	0.854	0.8	0.908	0.854	0.8	0.908	CLONAL	2	TRUE	0	0.480035213576637	2		659	510	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566709	212566709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	172	423	1	ENST00000342788.4:c.1472G>A	p.Arg491Lys	p.R491K	ENST00000342788	NM_005235.2	491	aGa/aAa	12/28	0.452457603979769	2	FACETS	0.855	0.796	0.915	0.855	0.796	0.915	CLONAL	2	TRUE	0	0.480035213576637	2		424	419	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546694	9546694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs942131023	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	161	483	0	ENST00000353224.5:c.1328G>A	p.Gly443Glu	p.G443E	ENST00000353224	NM_177990.2	443	gGa/gAa	5/10	0.401387118714908	3	FACETS	0.894	0.828	0.963	0.894	0.828	0.963	CLONAL	2	TRUE	1	0.480035213576637	3		483	465	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39706274	39706274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	98	313	0	ENST00000361337.2:c.332C>T	p.Ser111Phe	p.S111F	ENST00000361337	NM_003286.2	111	tCt/tTt	5/21	0.401387118714908	3	FACETS	1	0.958	1	0.566	0.508	0.628	CLONAL	1	TRUE	1	0.480035213576637	3		313	447	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714425	40714426	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	147	645	2	ENST00000373198.4:c.3971_3972delinsTT	p.Ser1324Phe	p.S1324F	ENST00000373198	NM_133170.3	1324	tCC/tTT	29/32	0.401387118714908	3	FACETS	1	0.98	1	0.616	0.565	0.67	CLONAL	1	TRUE	1	0.480035213576637	3		647	616	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288281	21288281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	86	768	0	ENST00000354336.3:c.526C>T	p.Pro176Ser	p.P176S	ENST00000354336	NM_005207.3	176	Cct/Tct	2/3	0.283599775903748	3	FACETS	0.577	0.51	0.649	0.289	0.255	0.325	INDETERMINATE	1	TRUE	1	0.480035213576637	3		768	770	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29083962	29083962	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs200432447	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	23	113	1	ENST00000328354.6:c.1555C>T	p.Arg519Ter	p.R519*	ENST00000328354	NM_007194.3	519	Cga/Tga	15/15	0.283599775903748	3	FACETS	0.958	0.758	1	0.479	0.379	0.592	INDETERMINATE	1	TRUE	1	0.480035213576637	3		114	124	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47079163	47079163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	136	719	1	ENST00000409792.3:c.7343C>T	p.Pro2448Leu	p.P2448L	ENST00000409792	NM_014159.6	2448	cCc/cTc	18/21	0.247240523561742	1	FACETS	0.77	0.704	0.84	0.77	0.704	0.84	INDETERMINATE	1	TRUE	0	0.480035213576637	1		720	559	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162908	47162908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	156	555	2	ENST00000409792.3:c.3218C>T	p.Pro1073Leu	p.P1073L	ENST00000409792	NM_014159.6	1073	cCa/cTa	3/21	0.247240523561742	1	FACETS	0.85	0.782	0.92	0.85	0.782	0.92	INDETERMINATE	1	TRUE	0	0.480035213576637	1		557	581	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163793	47163793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	77	638	1	ENST00000409792.3:c.2333C>T	p.Pro778Leu	p.P778L	ENST00000409792	NM_014159.6	778	cCa/cTa	3/21	0.247240523561742	1	FACETS	0.451	0.397	0.51	0.451	0.397	0.51	INDETERMINATE	1	TRUE	0	0.480035213576637	1		639	540	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199890	128199890	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779338723	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	82	487	0	ENST00000341105.2:c.1415C>T	p.Pro472Leu	p.P472L	ENST00000341105	NM_032638.4	472	cCg/cTg	6/6	1	2	FACETS	0.883	0.783	0.988	0.883	0.783	0.988	CLONAL	1	TRUE	1	0.480035213576637	2		487	387	SUCCESS
ATR	545	MSKCC	GRCh37	3	142254994	142254994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	82	444	0	ENST00000350721.4:c.3775C>T	p.Pro1259Ser	p.P1259S	ENST00000350721	NM_001184.3	1259	Cca/Tca	20/47	1	2	FACETS	0.758	0.671	0.85	0.758	0.671	0.85	SUBCLONAL	1	TRUE	1	0.480035213576637	2		444	451	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683491	182683491	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	98	666	1	ENST00000292782.4:c.54C>A	p.Phe18Leu	p.F18L	ENST00000292782	NM_020640.2	18	ttC/ttA	2/7	0.23521458083245	1	FACETS	0.413	0.368	0.461	0.413	0.368	0.461	INDETERMINATE	1	TRUE	0	0.480035213576637	1		667	751	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801486	1801486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766911583	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	64	758	0	ENST00000260795.2:c.392C>T	p.Ser131Leu	p.S131L	ENST00000260795		131	tCg/tTg	3/17	0.247240523561742	1	FACETS	0.351	0.304	0.402	0.351	0.304	0.402	INDETERMINATE	1	TRUE	0	0.480035213576637	1		758	577	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127487	55127487	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759729258	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	160	628	0	ENST00000257290.5:c.275C>T	p.Ala92Val	p.A92V	ENST00000257290	NM_006206.4	92	gCg/gTg	3/23	0.247240523561742	1	FACETS	0.889	0.819	0.961	0.889	0.819	0.961	INDETERMINATE	1	TRUE	0	0.480035213576637	1		628	570	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161339	55161339	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	56	590	0	ENST00000257290.5:c.3170C>T	p.Ser1057Phe	p.S1057F	ENST00000257290	NM_006206.4	1057	tCc/tTc	23/23	0.247240523561742	1	FACETS	0.398	0.342	0.46	0.398	0.342	0.46	INDETERMINATE	1	TRUE	0	0.480035213576637	1		590	445	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564515	55564515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754738766	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	65	565	0	ENST00000288135.5:c.403C>T	p.Arg135Cys	p.R135C	ENST00000288135	NM_000222.2	135	Cgc/Tgc	3/21	0.247240523561742	1	FACETS	0.452	0.393	0.516	0.452	0.393	0.516	INDETERMINATE	1	TRUE	0	0.480035213576637	1		565	455	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602982	55602982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	112	446	0	ENST00000288135.5:c.2692G>A	p.Glu898Lys	p.E898K	ENST00000288135	NM_000222.2	898	Gaa/Aaa	19/21	0.247240523561742	1	FACETS	0.861	0.78	0.945	0.861	0.78	0.945	INDETERMINATE	1	TRUE	0	0.480035213576637	1		446	412	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972864	55972864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866807777	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	122	573	1	ENST00000263923.4:c.1526G>A	p.Gly509Glu	p.G509E	ENST00000263923	NM_002253.2	509	gGa/gAa	11/30	0.247240523561742	1	FACETS	0.77	0.699	0.843	0.77	0.699	0.843	INDETERMINATE	1	TRUE	0	0.480035213576637	1		574	502	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213909	66213909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	41	554	0	ENST00000273854.3:c.2521C>T	p.Pro841Ser	p.P841S	ENST00000273854	NM_004439.5	841	Cca/Tca	15/18	0.247240523561742	1	FACETS	0.321	0.267	0.38	0.321	0.267	0.38	INDETERMINATE	1	TRUE	0	0.480035213576637	1		554	405	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213917	66213917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	42	521	0	ENST00000273854.3:c.2513G>A	p.Gly838Glu	p.G838E	ENST00000273854	NM_004439.5	838	gGa/gAa	15/18	0.247240523561742	1	FACETS	0.347	0.29	0.41	0.347	0.29	0.41	INDETERMINATE	1	TRUE	0	0.480035213576637	1		521	383	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467380	66467380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	28	272	0	ENST00000273854.3:c.889G>A	p.Glu297Lys	p.E297K	ENST00000273854	NM_004439.5	297	Gag/Aag	3/18	0.480035213576637	1	FACETS	0.428	0.344	0.522	0.428	0.344	0.522	SUBCLONAL	1	TRUE	0	0.480035213576637	1		272	207	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467661	66467661	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	66	549	0	ENST00000273854.3:c.608G>A	p.Gly203Glu	p.G203E	ENST00000273854	NM_004439.5	203	gGa/gAa	3/18	0.480035213576637	1	FACETS	0.495	0.431	0.564	0.495	0.431	0.564	SUBCLONAL	1	TRUE	0	0.480035213576637	1		549	422	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156918	106156918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778708	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	103	525	1	ENST00000380013.4:c.1819G>A	p.Gly607Arg	p.G607R	ENST00000380013	NM_001127208.2	607	Gga/Aga	3/11	0.480035213576637	1	FACETS	0.801	0.722	0.884	0.801	0.722	0.884	CLONAL	1	TRUE	0	0.480035213576637	1		526	407	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057081	180057081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139378654	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	103	678	0	ENST00000261937.6:c.538G>A	p.Gly180Arg	p.G180R	ENST00000261937	NM_182925.4	180	Ggg/Agg	5/30	1	2	FACETS	0.833	0.749	0.922	0.833	0.749	0.922	CLONAL	1	TRUE	1	0.480035213576637	2		678	515	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056296	26056296	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	60	543	1	ENST00000343677.2:c.361A>T	p.Lys121Ter	p.K121*	ENST00000343677	NM_005319.3	121	Aaa/Taa	1/1	0.23521458083245	1	FACETS	0.434	0.374	0.498	0.434	0.374	0.498	INDETERMINATE	1	TRUE	0	0.480035213576637	1		544	438	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672308	30672308	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767273130	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	68	726	0	ENST00000376406.3:c.4652C>T	p.Pro1551Leu	p.P1551L	ENST00000376406	NM_014641.2	1551	cCc/cTc	10/15	0.23521458083245	1	FACETS	0.421	0.367	0.48	0.421	0.367	0.48	INDETERMINATE	1	TRUE	0	0.480035213576637	1		726	511	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188823	32188823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs8192585	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	115	675	2	ENST00000375023.3:c.731C>T	p.Ser244Leu	p.S244L	ENST00000375023	NM_004557.3	244	tCg/tTg	4/30	0.23521458083245	1	FACETS	0.826	0.749	0.906	0.826	0.749	0.906	INDETERMINATE	1	TRUE	0	0.480035213576637	1		677	441	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798504	32798505	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	229	779	3	ENST00000374899.4:c.1351_1352delinsTT	p.Pro451Leu	p.P451L	ENST00000374899	NM_018833.2	451	CCa/TTa	8/12	0.243091940582013	2	FACETS	0.799	0.75	0.849	0.799	0.75	0.849	INDETERMINATE	2	TRUE	0	0.480035213576637	2		782	597	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964384	93964384	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	65	582	0	ENST00000369303.4:c.2513G>A	p.Trp838Ter	p.W838*	ENST00000369303	NM_004440.3	838	tGg/tAg	14/17	0.4267182063471	1	FACETS	0.517	0.45	0.589	0.517	0.45	0.589	SUBCLONAL	1	TRUE	0	0.480035213576637	1		582	398	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982061	93982061	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	73	569	0	ENST00000369303.4:c.1404T>A	p.His468Gln	p.H468Q	ENST00000369303	NM_004440.3	468	caT/caA	6/17	0.4267182063471	1	FACETS	0.561	0.493	0.634	0.561	0.493	0.634	SUBCLONAL	1	TRUE	0	0.480035213576637	1		569	412	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117632225	117632225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	61	726	0	ENST00000368508.3:c.6191C>T	p.Ser2064Leu	p.S2064L	ENST00000368508	NM_002944.2	2064	tCa/tTa	39/43	0.296789673485966	0	FACETS	0.292	0.252	0.335			1	SUBCLONAL	1	TRUE	0	0.480035213576637	0		726	453	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662429	117662429	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	68	652	1	ENST00000368508.3:c.4948C>T	p.Pro1650Ser	p.P1650S	ENST00000368508	NM_002944.2	1650	Cct/Tct	30/43	0.296789673485966	0	FACETS	0.353	0.308	0.402			1	SUBCLONAL	1	TRUE	0	0.480035213576637	0		653	417	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678055	117678055	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	61	526	0	ENST00000368508.3:c.3878C>T	p.Ser1293Phe	p.S1293F	ENST00000368508	NM_002944.2	1293	tCc/tTc	25/43	0.296789673485966	0	FACETS	0.366	0.317	0.419			1	SUBCLONAL	1	TRUE	0	0.480035213576637	0		526	361	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725462	117725462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	67	641	0	ENST00000368508.3:c.419G>A	p.Gly140Glu	p.G140E	ENST00000368508	NM_002944.2	140	gGa/gAa	5/43	0.296789673485966	0	FACETS	0.349	0.304	0.397			1	SUBCLONAL	1	TRUE	0	0.480035213576637	0		641	416	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415612	152415612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	71	709	1	ENST00000206249.3:c.1462C>T	p.His488Tyr	p.H488Y	ENST00000206249	NM_000125.3	488	Cac/Tac	7/8	0.161953543143707	0	FACETS	0.36	0.315	0.408			1	INDETERMINATE	1	TRUE	0	0.480035213576637	0		710	427	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522553	157522553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	94	810	1	ENST00000346085.5:c.4825C>T	p.Pro1609Ser	p.P1609S	ENST00000346085	NM_020732.3	1609	Cct/Tct	18/20	NA	2	FACETS	0.55	0.489	0.615			1	INDETERMINATE	1	TRUE	NA	0.480035213576637	2		811	712	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984094	2984094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	125	536	0	ENST00000396946.4:c.436G>A	p.Asp146Asn	p.D146N	ENST00000396946	NM_032415.4	146	Gac/Aac	5/25	0.401387118714908	3	FACETS	1	0.98	1	0.639	0.582	0.699	CLONAL	1	TRUE	1	0.480035213576637	3		536	505	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729807	41729807	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756546726	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	126	393	0	ENST00000242208.4:c.722G>A	p.Arg241Gln	p.R241Q	ENST00000242208	NM_002192.2	241	cGg/cAg	3/3	0.401387118714908	3	FACETS	1	0.986	1	0.731	0.667	0.798	CLONAL	1	TRUE	1	0.480035213576637	3		393	445	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367239	50367239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1045233686	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	118	440	0	ENST00000331340.3:c.46G>A	p.Glu16Lys	p.E16K	ENST00000331340	NM_006060.4	16	Gaa/Aaa	3/8	0.401387118714908	3	FACETS	0.824	0.751	0.899	0.824	0.751	0.899	CLONAL	2	TRUE	1	0.480035213576637	3		440	370	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851483	151851483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	245	545	1	ENST00000262189.6:c.12008C>T	p.Pro4003Leu	p.P4003L	ENST00000262189	NM_170606.2	4003	cCc/cTc	47/59	0.480035213576637	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.480035213576637	3		546	571	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874754	151874754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775427298	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	265	512	0	ENST00000262189.6:c.7784C>T	p.Pro2595Leu	p.P2595L	ENST00000262189	NM_170606.2	2595	cCc/cTc	38/59	0.480035213576637	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.480035213576637	3		512	557	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879204	151879204	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	64	658	0	ENST00000262189.6:c.5741T>C	p.Phe1914Ser	p.F1914S	ENST00000262189	NM_170606.2	1914	tTt/tCt	36/59	0.480035213576637	3	FACETS	0.552	0.478	0.632	0.276	0.239	0.316	SUBCLONAL	1	TRUE	1	0.480035213576637	3		658	599	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285602	38285602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	100	440	0	ENST00000425967.3:c.551C>T	p.Pro184Leu	p.P184L	ENST00000425967	NM_001174067.1	184	cCa/cTa	6/19	0.23521458083245	1	FACETS	0.822	0.741	0.908	0.822	0.741	0.908	INDETERMINATE	1	TRUE	0	0.480035213576637	1		440	385	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950469	68950469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	88	633	1	ENST00000288368.4:c.781C>T	p.Gln261Ter	p.Q261*	ENST00000288368	NM_024870.2	261	Caa/Taa	7/40	0.283599775903748	3	FACETS	0.645	0.571	0.724	0.322	0.285	0.362	INDETERMINATE	1	TRUE	1	0.480035213576637	3		634	705	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542592	141542593	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	171	686	0	ENST00000220592.5:c.2393_2394delinsTT	p.Ser798Phe	p.S798F	ENST00000220592	NM_012154.3	798	tCC/tTT	18/19	0.283599775903748	3	FACETS	1	0.988	1	0.687	0.634	0.741	INDETERMINATE	1	TRUE	1	0.480035213576637	3		686	643	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006089	22006089	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376104829	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	97	508	0	ENST00000276925.6:c.314G>A	p.Arg105Gln	p.R105Q	ENST00000276925	NM_004936.3	105	cGg/cAg	2/2	0.480035213576637	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.480035213576637	1		508	295	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606448	93606448	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	62	776	1	ENST00000375746.1:c.268C>T	p.His90Tyr	p.H90Y	ENST00000375746	NM_001174167.1	90	Cac/Tac	2/14	0.23521458083245	1	FACETS	0.419	0.362	0.48	0.419	0.362	0.48	INDETERMINATE	1	TRUE	0	0.480035213576637	1		777	469	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238318	98238318	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	104	420	0	ENST00000331920.6:c.1726C>T	p.Gln576Ter	p.Q576*	ENST00000331920	NM_000264.3	576	Cag/Tag	12/24	0.23521458083245	1	FACETS	0.995	0.901	1	0.995	0.901	1	INDETERMINATE	1	TRUE	0	0.480035213576637	1		420	331	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242871	98242871	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	39	382	0	ENST00000331920.6:c.747-1G>A		p.X249_splice	ENST00000331920	NM_000264.3	249			0.23521458083245	1	FACETS	0.328	0.272	0.391	0.328	0.272	0.391	INDETERMINATE	1	TRUE	0	0.480035213576637	1		382	376	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249984	110249984	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs61749200	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	120	557	0	ENST00000374672.4:c.691C>G	p.Leu231Val	p.L231V	ENST00000374672	NM_004235.4	231	Ctg/Gtg	3/5	0.23521458083245	1	FACETS	1	0.947	1	1	0.947	1	INDETERMINATE	1	TRUE	0	0.480035213576637	1		557	361	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128322026	128322026	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	175	733	0	ENST00000265960.3:c.734T>C	p.Phe245Ser	p.F245S	ENST00000265960	NM_001006617.1	245	tTc/tCc	6/12	0.23521458083245	1	FACETS	0.989	0.917	1	0.989	0.917	1	INDETERMINATE	1	TRUE	0	0.480035213576637	1		733	560	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417634	139417634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749786734	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	110	697	2	ENST00000277541.6:c.410C>T	p.Ser137Leu	p.S137L	ENST00000277541	NM_017617.3	137	tCg/tTg	4/34	0.23521458083245	1	FACETS	0.803	0.726	0.882	0.803	0.726	0.882	INDETERMINATE	1	TRUE	0	0.480035213576637	1		699	434	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314906	1314906	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	73	491	0	ENST00000400841.2:c.755G>A	p.Trp252Ter	p.W252*	ENST00000400841		252	tGg/tAg	6/6	1	1	FACETS	0.642	0.565	0.724	0.642	0.565	0.724	SUBCLONAL	1	TRUE	0	0.480035213576637	1		491	360	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0024131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	180	722	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.341481544578962	3	FACETS	0.861	0.796	0.928	0.861	0.796	0.928	CLONAL	2	TRUE	1	0.341481544578962	3		722	717	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717615	89717615	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909227	NA	P-0024131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	27	496	0	ENST00000371953.3:c.640C>T	p.Gln214Ter	p.Q214*	ENST00000371953	NM_000314.4	214	Cag/Tag	7/9	0.228837243040247	1	FACETS	0.278	0.22	0.344	0.278	0.22	0.344	SUBCLONAL	1	TRUE	0	0.341481544578962	1		496	472	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041734	42041734	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	82	520	0	ENST00000219905.7:c.5929C>T	p.Gln1977Ter	p.Q1977*	ENST00000219905	NM_001164273.1	1977	Cag/Tag	17/24	0.114194203409823	1	FACETS	0.716	0.633	0.806	0.716	0.633	0.806	INDETERMINATE	1	TRUE	0	0.341481544578962	1		520	556	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509627	106509627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	39	572	1	ENST00000359195.3:c.1621G>A	p.Asp541Asn	p.D541N	ENST00000359195	NM_002649.2	541	Gac/Aac	2/11	1	2	FACETS	0.342	0.282	0.409	0.342	0.282	0.409	SUBCLONAL	1	TRUE	1	0.341481544578962	2		573	668	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0024132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	327	872	1	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.741284646271402	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.750125309597389	1		873	515	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458120	120458120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	212	686	1	ENST00000256646.2:c.7225C>T	p.Gln2409Ter	p.Q2409*	ENST00000256646	NM_024408.3	2409	Cag/Tag	34/34	0.428199460188658	1	FACETS	0.787	0.74	0.834	0.787	0.74	0.834	INDETERMINATE	1	TRUE	0	0.750125309597389	1		687	449	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038260	30038260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1185977513	NA	P-0024132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	110	628	1	ENST00000338641.4:c.433G>A	p.Ala145Thr	p.A145T	ENST00000338641	NM_000268.3	145	Gcc/Acc	4/16	NA	2	FACETS	0.606	0.547	0.668			1	INDETERMINATE	1	TRUE	NA	0.750125309597389	2		629	484	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78599548	78599548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	127	630	2	ENST00000306801.3:c.220G>A	p.Asp74Asn	p.D74N	ENST00000306801	NM_020761.2	74	Gat/Aat	2/34	0.741284646271402	1	FACETS	0.519	0.474	0.565	0.519	0.474	0.565	SUBCLONAL	1	TRUE	0	0.750125309597389	1		632	408	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759398	133759398	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779869434	NA	P-0024132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	85	792	0	ENST00000318560.5:c.1721G>A	p.Arg574Gln	p.R574Q	ENST00000318560	NM_005157.4	574	cGa/cAa	11/11	0.385613575275651	1	FACETS	0.245	0.217	0.275	0.245	0.217	0.275	INDETERMINATE	1	TRUE	0	0.750125309597389	1		792	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0024134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	110	683	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.209763175507598	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	0	0.20994052455187	2		683	494	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716070	243716070	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	98	813	0	ENST00000263826.5:c.1124C>A	p.Ser375Ter	p.S375*	ENST00000263826	NM_005465.4	375	tCa/tAa	10/13	0.20994052455187	5	FACETS	0.892	0.796	0.994	0.595	0.531	0.663	CLONAL	2	TRUE	2	0.20994052455187	5		813	688	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436109	49436109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755573725	NA	P-0024134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	24	335	0	ENST00000301067.7:c.5872C>T	p.Arg1958Cys	p.R1958C	ENST00000301067	NM_003482.3	1958	Cgc/Tgc	28/54	0.20994052455187	3	FACETS	1	0.877	1	0.588	0.463	0.73	CLONAL	1	TRUE	1	0.20994052455187	3		335	215	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243048	105243049	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGGCAGCGGATGATGAAGGTGTTGGGCCGGGGCCGCTCCGT	novel	NA	P-0024135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	63	902	0	ENST00000349310.3:c.193_234dup	p.Thr65_Leu78dup	p.T65_L78dup	ENST00000349310	NM_001014432.1	65	-/ACGGAGCGGCCCCGGCCCAACACCTTCATCATCCGCTGCCTG	5/15	1	2	FACETS	0.642	0.554	0.739	0.642	0.554	0.739	SUBCLONAL	1	TRUE	1	0.215101943606015	2		902	912	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177027	56177031	+	frameshift_variant	Frame_Shift_Del	DEL	TGGAA	TGGAA	-	novel	NA	P-0024135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	69	674	0	ENST00000399503.3:c.2298_2302del	p.Leu766PhefsTer4	p.L766Ffs*4	ENST00000399503	NM_005921.1	766	tTGGAA/t	13/20	1	2	FACETS	0.79	0.687	0.902	0.79	0.687	0.902	CLONAL	1	TRUE	1	0.215101943606015	2		674	812	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177549	56177552	+	frameshift_variant	Frame_Shift_Del	DEL	TGAG	TGAG	-	novel	NA	P-0024135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	52	618	0	ENST00000399503.3:c.2524_2527del	p.Ser842PhefsTer14	p.S842Ffs*14	ENST00000399503	NM_005921.1	841	cTGAGt/ct	14/20	1	2	FACETS	0.797	0.678	0.927	0.797	0.678	0.927	CLONAL	1	TRUE	1	0.215101943606015	2		618	607	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249037	55249038	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0024136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	179	740	1	ENST00000275493.2:c.2335_2336delinsTT	p.Gly779Phe	p.G779F	ENST00000275493	NM_005228.3	779	GGc/TTc	20/28	0.351471088078651	3	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	1	0.351471088078651	3		741	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0024136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	241	842	0	ENST00000269305.4:c.560-1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.216194861230981	3	FACETS	0.922	0.868	0.976			1	CLONAL	3	TRUE	NA	0.351471088078651	3		842	583	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425787	49425788	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0024136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	79	725	0	ENST00000301067.7:c.12700_12701del	p.Gln4235GlyfsTer98	p.Q4235Gfs*98	ENST00000301067	NM_003482.3	4234	AGt/t	39/54	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.351471088078651	2		725	400	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222519	39222520	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	23	778	0	ENST00000402219.2:c.3090dup	p.Tyr1031IlefsTer2	p.Y1031Ifs*2	ENST00000402219	NM_005633.3	1030	-/A	20/23	1	2	FACETS	0.288	0.223	0.362	0.288	0.223	0.362	SUBCLONAL	1	TRUE	1	0.351471088078651	2		778	455	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631626	90631626	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	98	823	0	ENST00000330062.3:c.643G>T	p.Gly215Cys	p.G215C	ENST00000330062	NM_002168.2	215	Ggc/Tgc	5/11	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.351471088078651	2		823	531	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257909	19257909	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	223	944	1	ENST00000162023.5:c.477A>T	p.Glu159Asp	p.E159D	ENST00000162023		159	gaA/gaT	9/13	0.12149036001137	4	FACETS	0.895	0.838	0.953	1	0.991	1	INDETERMINATE	3	TRUE	2	0.351471088078651	4		945	639	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716214	52716214	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	106	746	0	ENST00000322088.6:c.658G>T	p.Val220Leu	p.V220L	ENST00000322088	NM_014225.5	220	Gtg/Ttg	6/15	0.351471088078651	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.351471088078651	1		746	407	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445090	89445090	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	42	583	0	ENST00000336596.2:c.1410C>A	p.Tyr470Ter	p.Y470*	ENST00000336596	NM_005233.5	470	taC/taA	6/17	1	2	FACETS	0.671	0.562	0.792	0.671	0.562	0.792	SUBCLONAL	1	TRUE	1	0.351471088078651	2		583	356	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411722	116411722	+	intron_variant	Intron	SNP	A	A	T	novel	NA	P-0024136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	188	1279	2	ENST00000397752.3:c.2887+14A>T		p.*963*	ENST00000397752	NM_000245.2	-/1390			0.12149036001137	4	FACETS	0.798	0.738	0.861	0.798	0.738	0.861	INDETERMINATE	2	TRUE	2	0.351471088078651	4		1281	906	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191756	123191756	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	94	643	0	ENST00000218089.9:c.1345A>G	p.Lys449Glu	p.K449E	ENST00000218089	NM_001042749.1	449	Aaa/Gaa	15/35	0.351471088078651	3	FACETS	0.994	0.885	1			1	CLONAL	1	TRUE	NA	0.351471088078651	3		643	633	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217320	123217320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	70	993	0	ENST00000218089.9:c.2974C>A	p.His992Asn	p.H992N	ENST00000218089	NM_001042749.1	992	Cat/Aat	29/35	0.351471088078651	3	FACETS	0.71	0.618	0.808			1	SUBCLONAL	1	TRUE	NA	0.351471088078651	3		993	660	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692820	89692820	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587782641	NA	P-0024137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	16	320	0	ENST00000371953.3:c.306del	p.Lys102AsnfsTer11	p.K102Nfs*11	ENST00000371953	NM_000314.4	102	Aaa/aa	5/9	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		320	207	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577129	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519986	NA	P-0024138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	293	686	0	ENST00000269305.4:c.809T>G	p.Phe270Cys	p.F270C	ENST00000269305	NM_001126112.2	270	tTt/tGt	8/11	0.306266119732062	2	FACETS	0.817	0.771	0.863	0.817	0.771	0.863	CLONAL	2	TRUE	0	0.425032447804567	2		686	844	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219461	133219461	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	183	780	0	ENST00000320574.5:c.4673A>G	p.Glu1558Gly	p.E1558G	ENST00000320574	NM_006231.2	1558	gAa/gGa	36/49	0.39725570078869	1	FACETS	0.962	0.891	1	0.962	0.891	1	CLONAL	1	TRUE	0	0.425032447804567	1		780	705	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562750	21562750	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	57	492	0	ENST00000382592.4:c.1169del	p.Pro390ArgfsTer43	p.P390Rfs*43	ENST00000382592	NM_014572.2	390	cCg/cg	4/8	0.235227401489239	1	FACETS	0.409	0.351	0.473	0.409	0.351	0.473	INDETERMINATE	1	TRUE	0	0.425032447804567	1		492	516	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213995	2213995	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs778008287	NA	P-0024138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	237	673	1	ENST00000326181.6:c.74C>A	p.Thr25Asn	p.T25N	ENST00000326181	NM_032271.2	25	aCc/aAc	2/21	0.425032447804567	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.425032447804567	1		674	697	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871984	45871985	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0024138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	125	567	1	ENST00000391945.4:c.263_264delinsTT	p.Arg88Leu	p.R88L	ENST00000391945	NM_000400.3	88	cGA/cTT	5/23	1	2	FACETS	0.772	0.699	0.849	0.772	0.699	0.849	SUBCLONAL	1	TRUE	1	0.425032447804567	2		568	762	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278347	39278347	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	58	763	0	ENST00000402219.2:c.802G>C	p.Glu268Gln	p.E268Q	ENST00000402219	NM_005633.3	268	Gaa/Caa	6/23	0.384340662261448	3	FACETS	0.315	0.27	0.366	0.158	0.135	0.183	SUBCLONAL	1	TRUE	1	0.425032447804567	3		763	1049	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873163	136873164	+	missense_variant	Missense_Mutation	DNP	AC	AC	TA	novel	NA	P-0024138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	97	447	0	ENST00000241393.3:c.334_335delinsTA	p.Val112Tyr	p.V112Y	ENST00000241393	NM_003467.2	112	GTc/TAc	2/2	1	2	FACETS	0.839	0.75	0.933	0.839	0.75	0.933	CLONAL	1	TRUE	1	0.425032447804567	2		447	544	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023570	31023570	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760148910	NA	P-0024138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	124	525	0	ENST00000375687.4:c.3055A>G	p.Arg1019Gly	p.R1019G	ENST00000375687	NM_015338.5	1019	Aga/Gga	13/13	1	2	FACETS	0.852	0.772	0.936	0.852	0.772	0.936	CLONAL	1	TRUE	1	0.425032447804567	2		525	685	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978617	70978617	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	405	702	0	ENST00000276594.2:c.1036G>C	p.Gly346Arg	p.G346R	ENST00000276594	NM_024504.3	346	Ggg/Cgg	5/8	0.374409350871544	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.425032447804567	3		702	1092	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393429	139393429	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	175	655	1	ENST00000277541.6:c.6102G>A	p.Trp2034Ter	p.W2034*	ENST00000277541	NM_017617.3	2034	tgG/tgA	33/34	0.425032447804567	1	FACETS	0.875	0.808	0.945	0.875	0.808	0.945	CLONAL	1	TRUE	0	0.425032447804567	1		656	741	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555525857	NA	P-0024140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	117	754	1	ENST00000269305.4:c.596G>A	p.Gly199Glu	p.G199E	ENST00000269305	NM_001126112.2	199	gGa/gAa	6/11	0.476952454714411	1	FACETS	0.87	0.792	0.951	0.87	0.792	0.951	CLONAL	1	TRUE	0	0.513666408789987	1		755	389	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0024141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	293	547	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.567772218936338	4	FACETS	0.854	0.813	0.895	0.854	0.813	0.895	CLONAL	3	TRUE	1	0.691896485486396	4		547	559	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0024141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	27	476	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.567772218936338	4	FACETS	0.328	0.261	0.406	0.109	0.087	0.136	SUBCLONAL	1	TRUE	1	0.691896485486396	4		476	402	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0024151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	159	1116	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	1	2	FACETS	0.294	0.268	0.321	0.294	0.268	0.321	SUBCLONAL	1	TRUE	1	0.81	2		1116	1336	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921510	39921510	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0024151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	650	602	0	ENST00000378444.4:c.4310C>G	p.Ser1437Ter	p.S1437*	ENST00000378444	NM_001123385.1	1437	tCa/tGa	10/15	0.128704344928765	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.81	2		602	788	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845586	63845586	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	327	516	0	ENST00000279873.7:c.1325A>T	p.Lys442Ile	p.K442I	ENST00000279873	NM_032199.2	442	aAa/aTa	9/10	0.3	4	FACETS	0.948	0.901	0.995			1	INDETERMINATE	2	TRUE	NA	0.81	4		516	771	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267306	41267306	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	338	792	0	ENST00000349496.5:c.890C>G	p.Thr297Arg	p.T297R	ENST00000349496	NM_001904.3	297	aCg/aGg	6/15	1	2	FACETS	0.955	0.907	1	0.955	0.907	1	CLONAL	1	TRUE	1	0.81	2		792	874	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0024153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	247	774	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.595	0.558	0.634	0.595	0.558	0.634	SUBCLONAL	1	TRUE	1	0.976527684043249	2		774	850	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63662029	63662030	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0024153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	240	511	0	ENST00000279873.7:c.134_135del	p.Arg45MetfsTer29	p.R45Mfs*29	ENST00000279873	NM_032199.2	45	AGa/a	2/10	1	2	FACETS	0.611	0.572	0.65	0.611	0.572	0.65	SUBCLONAL	1	TRUE	1	0.976527684043249	2		511	805	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	71	629	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.251551125977017	4	FACETS	0.763	0.668	0.865	0.763	0.668	0.865	SUBCLONAL	2	TRUE	2	0.270465208765855	4		629	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0024155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	161	914	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.270465208765855	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	TRUE	0	0.270465208765855	3		914	414	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163325165	163325165	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	94	581	0	ENST00000271452.3:c.1301A>G	p.His434Arg	p.H434R	ENST00000271452	NM_145697.2	434	cAc/cGc	14/14	0.301982463026696	3	FACETS	0.865	0.774	0.962	0.865	0.774	0.962	CLONAL	2	TRUE	1	0.270465208765855	3		581	456	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265672	41266192	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTTGTCAGGCTACCTTTTGCTCCATTTTCTGCTCACTCCTCCTAATGGCTTGGTGAAATAGCAAACAAGCCACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTG	ACTTGTCAGGCTACCTTTTGCTCCATTTTCTGCTCACTCCTCCTAATGGCTTGGTGAAATAGCAAACAAGCCACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTG	-	novel	NA	P-0024155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	132	219	0	ENST00000349496.5:c.13+100_189del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.270465208765855	3	FACETS	0.901	0.837	0.964	1	0.99	1	CLONAL	5	TRUE	0	0.270465208765855	3		219	246	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793765	89793765	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	118	685	0	ENST00000336032.3:c.834T>A	p.Asn278Lys	p.N278K	ENST00000336032	NM_006813.2	278	aaT/aaA	2/2	0.291499170040066	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	2	0.270465208765855	4		685	510	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0024160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	95	659	0	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	1	2	FACETS	0.826	0.735	0.923	0.826	0.735	0.923	CLONAL	1	TRUE	1	0.29	2		659	793	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	115	723	0	ENST00000263967.3:c.3012G>T	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atT	21/21	1	2	FACETS	0.822	0.739	0.91	0.822	0.739	0.91	CLONAL	1	TRUE	1	0.29	2		723	965	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221226	1221226	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876661238	NA	P-0024160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	113	860	1	ENST00000326873.7:c.749C>T	p.Thr250Met	p.T250M	ENST00000326873	NM_000455.4	250	aCg/aTg	6/10	1	2	FACETS	0.793	0.712	0.878	0.793	0.712	0.878	SUBCLONAL	1	TRUE	1	0.29	2		861	983	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196441	106196450	+	frameshift_variant	Frame_Shift_Del	DEL	ACCAGCCCTA	ACCAGCCCTA	-	novel	NA	P-0024160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	89	659	0	ENST00000380013.4:c.4774_4783del	p.Thr1592Ter	p.T1592*	ENST00000380013	NM_001127208.2	1592	ACCAGCCCTAtg/tg	11/11	1	2	FACETS	0.796	0.705	0.893	0.796	0.705	0.893	SUBCLONAL	1	TRUE	1	0.29	2		659	771	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223533	53223533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	72	257	0	ENST00000375401.3:c.3826G>A	p.Glu1276Lys	p.E1276K	ENST00000375401	NM_004187.3	1276	Gag/Aag	23/26	1	1	FACETS	0.801	0.708	0.899	1	0.979	1	CLONAL	2	TRUE	0	0.29	1		257	265	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	184	629	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.875	0.811	0.94	0.875	0.811	0.94	CLONAL	1	TRUE	1	0.666754462184467	2		629	631	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0024162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	262	811	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.666754462184467	1	FACETS	0.936	0.886	0.986	0.936	0.886	0.986	CLONAL	1	TRUE	0	0.666754462184467	1		812	560	SUCCESS
APC	324	MSKCC	GRCh37	5	112175193	112175193	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1064794042	NA	P-0024162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	129	298	0	ENST00000257430.4:c.3904del	p.Leu1302CysfsTer3	p.L1302Cfs*3	ENST00000257430	NM_000038.5	1301	aCc/ac	16/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.666754462184467	2		298	351	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031864	10031864	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	408	819	3	ENST00000330684.3:c.959G>T	p.Cys320Phe	p.C320F	ENST00000330684	NM_001134407.1	320	tGc/tTc	3/13	0.666754462184467	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.666754462184467	2		822	609	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30302723	30302723	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	121	549	0	ENST00000322652.5:c.814G>T	p.Glu272Ter	p.E272*	ENST00000322652	NM_015355.2	272	Gaa/Taa	7/16	0.666754462184467	3	FACETS	0.632	0.571	0.696	0.316	0.285	0.348	SUBCLONAL	1	TRUE	1	0.666754462184467	3		549	766	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554281	63554281	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	293	859	0	ENST00000307078.5:c.458C>G	p.Thr153Ser	p.T153S	ENST00000307078	NM_004655.3	153	aCc/aGc	2/11	0.666754462184467	3	FACETS	0.927	0.872	0.984	0.464	0.436	0.492	CLONAL	1	TRUE	1	0.666754462184467	3		859	1264	SUCCESS
APC	324	MSKCC	GRCh37	5	112174372	112174372	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	94	370	0	ENST00000257430.4:c.3081del	p.Tyr1027Ter	p.Y1027*	ENST00000257430	NM_000038.5	1027	taT/ta	16/16	1	2	FACETS	0.953	0.858	1	0.953	0.858	1	CLONAL	1	TRUE	1	0.666754462184467	2		370	296	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358998	81358998	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	162	737	0	ENST00000222390.5:c.963G>A	p.Trp321Ter	p.W321*	ENST00000222390	NM_000601.4	321	tgG/tgA	8/18	0.666754462184467	3	FACETS	0.812	0.746	0.881	0.406	0.373	0.441	CLONAL	1	TRUE	1	0.666754462184467	3		737	798	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	177	629	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	0.335098591536409	2		629	779	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164786	47164786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs998524208	NA	P-0024163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	79	746	0	ENST00000409792.3:c.1340C>T	p.Ser447Phe	p.S447F	ENST00000409792	NM_014159.6	447	tCt/tTt	3/21	1	2	FACETS	0.627	0.551	0.709	0.627	0.551	0.709	SUBCLONAL	1	TRUE	1	0.335098591536409	2		746	752	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650647	67650647	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0024163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	78	699	0	ENST00000264010.4:c.953-1G>C		p.X318_splice	ENST00000264010	NM_006565.3	318			1	2	FACETS	0.724	0.636	0.818	0.724	0.636	0.818	SUBCLONAL	1	TRUE	1	0.335098591536409	2		699	643	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149453003	149453003	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756763314	NA	P-0024163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	43	924	0	ENST00000286301.3:c.943G>A	p.Val315Met	p.V315M	ENST00000286301	NM_005211.3	315	Gtg/Atg	7/22	1	2	FACETS	0.37	0.309	0.439	0.37	0.309	0.439	SUBCLONAL	1	TRUE	1	0.335098591536409	2		924	693	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641058	3641058	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1223	148	1495	0	ENST00000294008.3:c.2581C>T	p.Gln861Ter	p.Q861*	ENST00000294008	NM_032444.2	861	Cag/Tag	12/15	1	2	FACETS	0.644	0.586	0.705	0.644	0.586	0.705	SUBCLONAL	1	TRUE	1	0.335098591536409	2		1495	1371	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821812	59821812	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	122	1131	0	ENST00000259008.2:c.2238C>G	p.Ile746Met	p.I746M	ENST00000259008	NM_032043.2	746	atC/atG	15/20	1	2	FACETS	0.639	0.576	0.705	0.639	0.576	0.705	SUBCLONAL	1	TRUE	1	0.335098591536409	2		1131	1140	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229363	36229363	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	110	926	1	ENST00000222270.7:c.8053G>T	p.Glu2685Ter	p.E2685*	ENST00000222270	NM_014727.1	2685	Gag/Tag	37/37	1	2	FACETS	0.748	0.671	0.829	0.748	0.671	0.829	SUBCLONAL	1	TRUE	1	0.335098591536409	2		927	878	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164142	47164142	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	78	868	0	ENST00000409792.3:c.1984C>T	p.Gln662Ter	p.Q662*	ENST00000409792	NM_014159.6	662	Caa/Taa	3/21	1	2	FACETS	0.523	0.459	0.593	0.523	0.459	0.593	SUBCLONAL	1	TRUE	1	0.335098591536409	2		868	890	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164366	47164366	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	88	766	0	ENST00000409792.3:c.1760C>G	p.Ser587Cys	p.S587C	ENST00000409792	NM_014159.6	587	tCt/tGt	3/21	1	2	FACETS	0.61	0.54	0.686	0.61	0.54	0.686	SUBCLONAL	1	TRUE	1	0.335098591536409	2		766	861	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839674	27839683	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	TAGGAATATT	TAGGAATATT	-	novel	NA	P-0024163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	551	46	0	ENST00000328488.2:c.411_*9del		p.*137*	ENST00000328488	NM_003533.2	137		1/1	1	2	FACETS	1	0.978	1	1	0.998	1	CLONAL	3	TRUE	1	0.335098591536409	2		46	1076	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168991	32168991	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	108	1237	0	ENST00000375023.3:c.4042G>C	p.Glu1348Gln	p.E1348Q	ENST00000375023	NM_004557.3	1348	Gaa/Caa	22/30	1	2	FACETS	0.554	0.496	0.616	0.554	0.496	0.616	SUBCLONAL	1	TRUE	1	0.335098591536409	2		1237	1163	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	29	571	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.839	1	1	0.839	1	CLONAL	1	TRUE	1	0.825740175123453	2		571	70	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0024164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	138	481	5	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.921	0.848	0.995	0.921	0.848	0.995	CLONAL	1	TRUE	1	0.825740175123453	2		486	363	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791820	42791820	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	164	997	0	ENST00000575354.2:c.706G>T	p.Glu236Ter	p.E236*	ENST00000575354	NM_015125.3	236	Gag/Tag	5/20	0.822888668566948	1	FACETS	0.813	0.763	0.862	0.813	0.763	0.862	CLONAL	1	TRUE	0	0.825740175123453	1		997	287	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628748	187628748	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	247	1133	0	ENST00000441802.2:c.2234A>G	p.Asp745Gly	p.D745G	ENST00000441802	NM_005245.3	745	gAc/gGc	2/27	1	2	FACETS	0.992	0.935	1	0.992	0.935	1	CLONAL	1	TRUE	1	0.825740175123453	2		1133	603	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412663	139412663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	63	1086	2	ENST00000277541.6:c.1181G>A	p.Gly394Asp	p.G394D	ENST00000277541	NM_017617.3	394	gGc/gAc	7/34	1	2	FACETS	0.296	0.256	0.339	0.296	0.256	0.339	SUBCLONAL	1	TRUE	1	0.825740175123453	2		1088	516	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484218	8484218	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	44	536	2	ENST00000356435.5:c.3314C>A	p.Pro1105Gln	p.P1105Q	ENST00000356435		1105	cCa/cAa	19/35	1	2	FACETS	0.716	0.601	0.844	0.716	0.601	0.844	SUBCLONAL	1	TRUE	1	0.27	2		538	455	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0024170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	109	588	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.47515290054617	3	FACETS	1	0.943	1	0.533	0.48	0.588	CLONAL	1	TRUE	1	0.47515290054617	3		588	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579473	7579473	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782769	NA	P-0024170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	157	886	0	ENST00000269305.4:c.214C>T	p.Pro72Ser	p.P72S	ENST00000269305	NM_001126112.2	72	Ccc/Tcc	4/11	0.47515290054617	3	FACETS	0.951	0.871	1	0.475	0.435	0.517	CLONAL	1	TRUE	1	0.47515290054617	3		886	860	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116115	67116115	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0024170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	195	523	1	ENST00000412916.2:c.400-1G>A		p.X134_splice	ENST00000412916		134			0.47515290054617	2	FACETS	0.937	0.878	0.997	0.937	0.878	0.997	CLONAL	2	TRUE	0	0.47515290054617	2		524	438	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271807	15271808	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0024170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	291	856	0	ENST00000263388.2:c.6631_6632insC	p.Tyr2211SerfsTer31	p.Y2211Sfs*31	ENST00000263388	NM_000435.2	2211	tac/tCac	33/33	0.462328583702379	3	FACETS	0.966	0.913	1	0.966	0.913	1	CLONAL	2	TRUE	1	0.47515290054617	3		856	785	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25462085	25462085	+	splice_acceptor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0024170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	126	622	0	ENST00000264709.3:c.2323-1del		p.X775_splice	ENST00000264709	NM_175629.2	775			1	2	FACETS	0.97	0.882	1	0.97	0.882	1	CLONAL	1	TRUE	1	0.47515290054617	2		622	547	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467083	25467083	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs568207978	NA	P-0024177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	156	592	3	ENST00000264709.3:c.1792C>T	p.Arg598Ter	p.R598*	ENST00000264709	NM_175629.2	598	Cga/Tga	15/23	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.45	2		595	554	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305319	65305319	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	56	655	0	ENST00000342505.4:c.2809A>T	p.Ile937Phe	p.I937F	ENST00000342505	NM_002227.2	937	Att/Ttt	20/25	1	2	FACETS	0.372	0.318	0.431	0.372	0.318	0.431	SUBCLONAL	1	TRUE	1	0.45	2		655	669	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210847	133210847	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	31	717	3	ENST00000320574.5:c.5929G>T	p.Glu1977Ter	p.E1977*	ENST00000320574	NM_006231.2	1977	Gaa/Taa	43/49	1	2	FACETS	0.227	0.182	0.277	0.227	0.182	0.277	SUBCLONAL	1	TRUE	1	0.45	2		720	608	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469986	25469987	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTGCAAAAC	novel	NA	P-0024177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	125	564	0	ENST00000264709.3:c.1047_1055dup	p.Cys351_Ser352insArgPheCys	p.C351_S352insRFC	ENST00000264709	NM_175629.2	352	agt/agGTTTTGCAGt	9/23	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.45	2		564	526	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942030	44942030	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	78	403	0	ENST00000377967.4:c.3284del	p.Lys1095SerfsTer9	p.K1095Sfs*9	ENST00000377967	NM_021140.2	1094	Aaa/aa	22/29	1	2	FACETS	0.722	0.637	0.814	0.722	0.637	0.814	SUBCLONAL	1	TRUE	1	0.45	2		403	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0024178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	217	651	0	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.310820981702656	4	FACETS	0.924	0.869	0.98			1	CLONAL	4	TRUE	NA	0.310820981702656	4		651	495	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0024178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	859	722	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.310820981702656	18	FACETS	1	0.99	1	0.96	0.937	0.982	CLONAL	15	TRUE	2	0.310820981702656	18		722	1255	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44896902	44896902	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	35	648	0	ENST00000377967.4:c.622C>T	p.Gln208Ter	p.Q208*	ENST00000377967	NM_021140.2	208	Caa/Taa	8/29	0.264168367704603	4	FACETS	0.46	0.376	0.555	0.23	0.188	0.278	SUBCLONAL	1	TRUE	2	0.310820981702656	4		648	642	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101699	27101699	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1286058909	NA	P-0024178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	42	760	0	ENST00000324856.7:c.4981A>G	p.Met1661Val	p.M1661V	ENST00000324856	NM_006015.4	1661	Atg/Gtg	18/20	0.310820981702656	4	FACETS	0.592	0.494	0.702	0.296	0.247	0.351	SUBCLONAL	1	TRUE	2	0.310820981702656	4		760	598	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78599506	78599506	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	64	497	0	ENST00000306801.3:c.178G>A	p.Val60Ile	p.V60I	ENST00000306801	NM_020761.2	60	Gtt/Att	2/34	0.310820981702656	3	FACETS	1	0.903	1	0.524	0.455	0.599	CLONAL	1	TRUE	1	0.310820981702656	3		497	454	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267862	46267862	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773852491	NA	P-0024178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	66	650	0	ENST00000371998.3:c.2623G>A	p.Ala875Thr	p.A875T	ENST00000371998		875	Gct/Act	14/23	0.310820981702656	4	FACETS	0.905	0.786	1	0.453	0.393	0.518	CLONAL	1	TRUE	2	0.310820981702656	4		650	615	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468251	50468251	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	413	610	0	ENST00000331340.3:c.1486G>T	p.Gly496Cys	p.G496C	ENST00000331340	NM_006060.4	496	Ggc/Tgc	8/8	0.310820981702656	8	FACETS	0.963	0.924	1			1	CLONAL	7	TRUE	NA	0.310820981702656	8		610	762	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412344	63412344	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	98	686	0	ENST00000330258.3:c.823G>C	p.Ala275Pro	p.A275P	ENST00000330258	NM_152424.3	275	Gcc/Ccc	2/2	0.264168367704603	4	FACETS	0.787	0.705	0.874	0.787	0.705	0.874	SUBCLONAL	2	TRUE	2	0.310820981702656	4		686	525	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	77	571	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.942	0.838	1	0.942	0.838	1	CLONAL	1	FALSE	1	0.651384777705483	2		571	251	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0024180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	390	618	1	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.651384777705483	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	FALSE	0	0.651384777705483	2		619	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579357	7579358	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGGAAAC	rs1131691004	NA	P-0024183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	47	767	0	ENST00000269305.4:c.323_329dup	p.Leu111PhefsTer40	p.L111Ffs*40	ENST00000269305	NM_001126112.2	110	cgt/cgGTTTCCGt	4/11	1	2	FACETS	0.99	0.833	1	0.99	0.833	1	CLONAL	1	TRUE	1	0.12	2		767	791	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251977	153251978	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	TTTATTAC	novel	NA	P-0024183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	58	731	0	ENST00000281708.4:c.1021_1028dup	p.Pro344Ter	p.P344*	ENST00000281708	NM_033632.3	343	aaa/aaGTAATAAAa	7/12	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.12	2		731	754	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	118	571	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.897	0.815	0.983	0.897	0.815	0.983	CLONAL	1	TRUE	1	0.583450919431136	2		571	451	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573894	18573894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759658584	NA	P-0024188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	151	540	2	ENST00000266497.5:c.2212C>T	p.Arg738Cys	p.R738C	ENST00000266497		738	Cgt/Tgt	15/31	1	2	FACETS	0.926	0.851	1	0.926	0.851	1	CLONAL	1	TRUE	1	0.583450919431136	2		542	559	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0024188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	473	755	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.567122351550351	2	FACETS	0.935	0.9	0.97	0.935	0.9	0.97	CLONAL	2	TRUE	0	0.583450919431136	2		755	867	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862896	9862896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1198247451	NA	P-0024188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	241	701	1	ENST00000330684.3:c.2407G>A	p.Glu803Lys	p.E803K	ENST00000330684	NM_001134407.1	803	Gag/Aag	12/13	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.583450919431136	2		702	821	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355048	15355048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	281	786	0	ENST00000263377.2:c.2575C>T	p.Pro859Ser	p.P859S	ENST00000263377	NM_058243.2	859	Cct/Tct	13/20	1	2	FACETS	0.98	0.922	1	0.98	0.922	1	CLONAL	1	TRUE	1	0.583450919431136	2		786	983	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713470	40713470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318044562	NA	P-0024188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	196	715	1	ENST00000373198.4:c.4045C>T	p.Arg1349Cys	p.R1349C	ENST00000373198	NM_133170.3	1349	Cgt/Tgt	30/32	1	2	FACETS	0.923	0.857	0.991	0.923	0.857	0.991	CLONAL	1	TRUE	1	0.583450919431136	2		716	728	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498444	89498444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	173	527	3	ENST00000336596.2:c.2416G>A	p.Asp806Asn	p.D806N	ENST00000336596	NM_005233.5	806	Gat/Aat	14/17	1	2	FACETS	0.917	0.847	0.988	0.917	0.847	0.988	CLONAL	1	TRUE	1	0.583450919431136	2		530	647	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69230522	69230522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	161	541	0	ENST00000462284.1:c.911C>T	p.Ser304Phe	p.S304F	ENST00000462284	NM_002392.5	304	tCc/tTc	10/11	1	2	FACETS	0.911	0.839	0.985	0.911	0.839	0.985	CLONAL	1	TRUE	1	0.583450919431136	2		541	606	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14317346	14317346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	258	720	0	ENST00000256196.4:c.164G>A	p.Cys55Tyr	p.C55Y	ENST00000256196		55	tGt/tAt	2/6	1	2	FACETS	0.929	0.871	0.988	0.929	0.871	0.988	CLONAL	1	TRUE	1	0.583450919431136	2		720	952	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514080	69514080	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141765810	NA	P-0024188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	260	721	2	ENST00000294312.3:c.601G>A	p.Gly201Arg	p.G201R	ENST00000294312	NM_005117.2	201	Ggg/Agg	3/3	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.583450919431136	2		723	823	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536951	120536951	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	204	600	1	ENST00000229340.5:c.235C>T	p.Arg79Trp	p.R79W	ENST00000229340	NM_006861.6	79	Cgg/Tgg	4/6	1	2	FACETS	0.953	0.886	1	0.953	0.886	1	CLONAL	1	TRUE	1	0.583450919431136	2		601	734	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396856	396856	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs574168909	NA	P-0024188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	231	652	1	ENST00000262320.3:c.170C>T	p.Ser57Leu	p.S57L	ENST00000262320	NM_003502.3	57	tCg/tTg	2/11	1	2	FACETS	0.962	0.899	1	0.962	0.899	1	CLONAL	1	TRUE	1	0.583450919431136	2		653	823	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677263	29677263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	207	560	1	ENST00000356175.3:c.7321C>T	p.Leu2441Phe	p.L2441F	ENST00000356175	NM_000267.3	2441	Ctt/Ttt	49/57	0.226238448103778	3	FACETS	1	0.991	1	0.715	0.667	0.764	INDETERMINATE	1	TRUE	1	0.583450919431136	3		561	641	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857657	59857657	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	185	481	0	ENST00000259008.2:c.1900C>T	p.Gln634Ter	p.Q634*	ENST00000259008	NM_032043.2	634	Cag/Tag	13/20	0.226238448103778	3	FACETS	1	0.981	1	0.586	0.543	0.631	INDETERMINATE	1	TRUE	1	0.583450919431136	3		481	699	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097212	11097235	+	inframe_deletion	In_Frame_Del	DEL	GGCCCTGGCCCCGGCCCGGGTCCC	GGCCCTGGCCCCGGCCCGGGTCCC	-	novel	NA	P-0024188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	263	639	0	ENST00000358026.2:c.708_731del	p.Gly237_Pro244del	p.G237_P244del	ENST00000358026	NM_001128849.1	235	GGCCCTGGCCCCGGCCCGGGTCCC/-	4/36	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.583450919431136	2		639	806	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462550	29462550	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	179	543	0	ENST00000389048.3:c.2351C>T	p.Pro784Leu	p.P784L	ENST00000389048	NM_004304.4	784	cCc/cTc	13/29	1	2	FACETS	0.914	0.846	0.985	0.914	0.846	0.985	CLONAL	1	TRUE	1	0.583450919431136	2		543	671	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827991	40827991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	204	533	0	ENST00000373198.4:c.2437G>A	p.Ala813Thr	p.A813T	ENST00000373198	NM_133170.3	813	Gcc/Acc	17/32	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.583450919431136	2		533	681	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070358	37070358	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	174	558	0	ENST00000231790.2:c.1493G>A	p.Arg498Lys	p.R498K	ENST00000231790	NM_000249.3	498	aGa/aAa	13/19	0.583450919431136	3	FACETS	0.889	0.819	0.961	0.444	0.409	0.481	CLONAL	1	TRUE	1	0.583450919431136	3		558	867	SUCCESS
APC	324	MSKCC	GRCh37	5	112155002	112155002	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	219	687	1	ENST00000257430.4:c.1273G>A	p.Glu425Lys	p.E425K	ENST00000257430	NM_000038.5	425	Gaa/Aaa	10/16	1	2	FACETS	0.849	0.791	0.909	0.849	0.791	0.909	CLONAL	1	TRUE	1	0.583450919431136	2		688	884	SUCCESS
APC	324	MSKCC	GRCh37	5	112155005	112155005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200598389	NA	P-0024188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	213	675	2	ENST00000257430.4:c.1276G>T	p.Ala426Ser	p.A426S	ENST00000257430	NM_000038.5	426	Gct/Tct	10/16	1	2	FACETS	0.845	0.786	0.906	0.845	0.786	0.906	CLONAL	1	TRUE	1	0.583450919431136	2		677	864	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180035999	180035999	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775663376	NA	P-0024188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	306	804	1	ENST00000261937.6:c.3862G>A	p.Glu1288Lys	p.E1288K	ENST00000261937	NM_182925.4	1288	Gag/Aag	29/30	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.583450919431136	2		805	1017	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117717362	117717362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	150	504	0	ENST00000368508.3:c.845C>T	p.Ser282Leu	p.S282L	ENST00000368508	NM_002944.2	282	tCa/tTa	8/43	0.583450919431136	1	FACETS	0.8	0.738	0.865	0.8	0.738	0.865	SUBCLONAL	1	TRUE	0	0.583450919431136	1		504	455	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718148	117718148	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs747794595	NA	P-0024188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	237	653	1	ENST00000368508.3:c.709C>T	p.Gln237Ter	p.Q237*	ENST00000368508	NM_002944.2	237	Caa/Taa	7/43	0.583450919431136	1	FACETS	0.908	0.853	0.963	0.908	0.853	0.963	CLONAL	1	TRUE	0	0.583450919431136	1		654	634	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972955	68972955	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141759315	NA	P-0024188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	198	564	0	ENST00000288368.4:c.1280G>A	p.Arg427Lys	p.R427K	ENST00000288368	NM_024870.2	427	aGg/aAg	11/40	1	2	FACETS	0.963	0.895	1	0.963	0.895	1	CLONAL	1	TRUE	1	0.583450919431136	2		564	705	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046405	69046405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	235	691	0	ENST00000288368.4:c.3878G>A	p.Ser1293Asn	p.S1293N	ENST00000288368	NM_024870.2	1293	aGc/aAc	32/40	1	2	FACETS	0.968	0.906	1	0.968	0.906	1	CLONAL	1	TRUE	1	0.583450919431136	2		691	832	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139818414	139818415	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	211	676	2	ENST00000247668.2:c.1249_1250delinsTT	p.Pro417Leu	p.P417L	ENST00000247668	NM_021138.3	417	CCg/TTg	10/11	0.499530973639147	3	FACETS	1	0.969	1	0.537	0.499	0.576	CLONAL	1	TRUE	1	0.583450919431136	3		678	870	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0024189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	36	562	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.245	0.201	0.294	0.245	0.201	0.294	SUBCLONAL	1	TRUE	1	0.707529243907265	2		562	415	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0024189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	670	755	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.707529243907265	4	FACETS	0.976	0.947	1			1	CLONAL	3	TRUE	NA	0.707529243907265	4		755	1105	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436296	110436296	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1175038077	NA	P-0024189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	25	179	0	ENST00000375856.3:c.2105T>C	p.Val702Ala	p.V702A	ENST00000375856	NM_003749.2	702	gTg/gCg	1/2	1	2	FACETS	0.512	0.409	0.628	0.512	0.409	0.628	SUBCLONAL	1	TRUE	1	0.707529243907265	2		179	138	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0024193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	99	547	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.240716452904566	1	FACETS	0.368	0.329	0.41	0.368	0.329	0.41	INDETERMINATE	1	TRUE	0	0.607763751093293	1		547	616	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0024193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	39	657	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.125267354246183	5	FACETS	0.268	0.221	0.32			1	INDETERMINATE	1	TRUE	NA	0.607763751093293	5		657	917	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955419	48955419	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0024193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	260	518	0	ENST00000267163.4:c.1535T>A	p.Leu512Ter	p.L512*	ENST00000267163	NM_000321.2	512	tTg/tAg	17/27	0.394251941883794	2	FACETS	0.821	0.778	0.864	0.821	0.778	0.864	CLONAL	2	TRUE	0	0.607763751093293	2		518	521	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916843	48916843	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	54	540	0	ENST00000267163.4:c.373G>T	p.Glu125Ter	p.E125*	ENST00000267163	NM_000321.2	125	Gaa/Taa	3/27	0.394251941883794	2	FACETS	0.332	0.283	0.385	0.166	0.141	0.193	SUBCLONAL	1	TRUE	0	0.607763751093293	2		540	536	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038831	47038831	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	478	971	1	ENST00000377604.3:c.838G>T	p.Gly280Ter	p.G280*	ENST00000377604	NM_001204468.1	280	Gga/Tga	9/24	0.125267354246183	5	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.607763751093293	5		972	1219	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480396	89480396	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs369276620	NA	P-0024193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	26	382	0	ENST00000336596.2:c.2233C>T	p.Arg745Ter	p.R745*	ENST00000336596	NM_005233.5	745	Cga/Tga	13/17	0.240716452904566	1	FACETS	0.157	0.124	0.195	0.157	0.124	0.195	INDETERMINATE	1	TRUE	0	0.607763751093293	1		382	380	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098419	11098419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	60	683	0	ENST00000358026.2:c.937C>T	p.Pro313Ser	p.P313S	ENST00000358026	NM_001128849.1	313	Ccc/Tcc	6/36	0.199379311535314	2	FACETS	0.26	0.224	0.301	0.13	0.112	0.151	INDETERMINATE	1	TRUE	0	0.607763751093293	2		683	758	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410310	63410310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374610712	NA	P-0024193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	255	911	1	ENST00000330258.3:c.2857C>T	p.Pro953Ser	p.P953S	ENST00000330258	NM_152424.3	953	Cca/Tca	2/2	0.205765832269729	3	FACETS	0.987	0.923	1	0.329	0.307	0.351	INDETERMINATE	1	TRUE	0	0.607763751093293	3		912	1109	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834145	156834145	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0024193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	231	895	1	ENST00000524377.1:c.213-1G>T		p.X71_splice	ENST00000524377	NM_002529.3	71			0.549186341745316	4	FACETS	0.926	0.861	0.993	0.309	0.287	0.331	CLONAL	1	TRUE	1	0.607763751093293	4		896	1320	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725507	162725507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773159664	NA	P-0024193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	348	710	0	ENST00000367921.3:c.619G>A	p.Gly207Ser	p.G207S	ENST00000367921	NM_006182.2	207	Ggt/Agt	7/18	0.549186341745316	4	FACETS	0.954	0.906	1	0.636	0.604	0.669	CLONAL	2	TRUE	1	0.607763751093293	4		710	965	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148875	119148876	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	TT	novel	NA	P-0024193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	185	323	0	ENST00000264033.4:c.1096-1_1096delinsTT		p.X366_splice	ENST00000264033	NM_005188.3	366		8/16	0.604312199743422	2	FACETS	0.917	0.863	0.97	0.917	0.863	0.97	CLONAL	2	TRUE	0	0.607763751093293	2		323	332	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250160	133250161	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0024193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	109	616	1	ENST00000320574.5:c.1359_1359+1delinsTT		p.X453_splice	ENST00000320574	NM_006231.2	453		13/49	0.199379311535314	2	FACETS	0.604	0.543	0.667	0.302	0.271	0.334	INDETERMINATE	1	TRUE	0	0.607763751093293	2		617	594	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626681	28626681	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0024193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	65	503	0	ENST00000241453.7:c.614+1G>T		p.X205_splice	ENST00000241453	NM_004119.2	205			0.394251941883794	2	FACETS	0.327	0.283	0.375	0.164	0.141	0.188	SUBCLONAL	1	TRUE	0	0.607763751093293	2		503	654	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436248	110436248	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	199	419	0	ENST00000375856.3:c.2153G>C	p.Arg718Thr	p.R718T	ENST00000375856	NM_003749.2	718	aGg/aCg	1/2	0.394251941883794	2	FACETS	1	0.991	1	0.706	0.661	0.751	CLONAL	1	TRUE	0	0.607763751093293	2		419	464	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422175	81422175	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	39	603	1	ENST00000298171.2:c.151C>T	p.Pro51Ser	p.P51S	ENST00000298171	NM_000369.2	51	Ccg/Tcg	1/10	0.171433158538303	2	FACETS	0.189	0.156	0.226	0.095	0.078	0.113	INDETERMINATE	1	TRUE	0	0.607763751093293	2		604	678	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989067	41989067	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0024193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	110	708	0	ENST00000219905.7:c.1859T>A	p.Leu620Ter	p.L620*	ENST00000219905	NM_001164273.1	620	tTg/tAg	3/24	0.607763751093293	1	FACETS	0.679	0.616	0.745	0.679	0.616	0.745	SUBCLONAL	1	TRUE	0	0.607763751093293	1		708	371	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857306	9857306	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	83	622	1	ENST00000330684.3:c.4095C>A	p.Asn1365Lys	p.N1365K	ENST00000330684	NM_001134407.1	1365	aaC/aaA	13/13	0.171433158538303	2	FACETS	0.416	0.367	0.468	0.208	0.183	0.234	INDETERMINATE	1	TRUE	0	0.607763751093293	2		623	657	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732954	74732954	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	61	444	0	ENST00000359995.5:c.289G>T	p.Asp97Tyr	p.D97Y	ENST00000359995	NM_001195427.1	97	Gac/Tac	1/3	0.101527925212257	5	FACETS	0.761	0.658	0.874	0.19	0.164	0.219	INDETERMINATE	1	TRUE	1	0.607763751093293	5		444	504	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78921077	78921078	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	56	915	0	ENST00000306801.3:c.3191_3192insT	p.Arg1066SerfsTer36	p.R1066Sfs*36	ENST00000306801	NM_020761.2	1064	aac/aaTc	27/34	0.101527925212257	5	FACETS	0.382	0.326	0.443	0.095	0.081	0.111	INDETERMINATE	1	TRUE	1	0.607763751093293	5		915	923	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291775	15291775	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	83	904	0	ENST00000263388.2:c.2991C>A	p.Cys997Ter	p.C997*	ENST00000263388	NM_000435.2	997	tgC/tgA	18/33	0.199379311535314	2	FACETS	0.294	0.259	0.332	0.147	0.129	0.166	INDETERMINATE	1	TRUE	0	0.607763751093293	2		904	929	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954643	17954643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201067961	NA	P-0024193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	141	1034	2	ENST00000458235.1:c.251C>T	p.Pro84Leu	p.P84L	ENST00000458235	NM_000215.3	84	cCg/cTg	3/24	0.199379311535314	2	FACETS	0.461	0.419	0.505	0.23	0.209	0.253	INDETERMINATE	1	TRUE	0	0.607763751093293	2		1036	1007	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795736	42795744	+	inframe_deletion	In_Frame_Del	DEL	CCGCCCCCG	CCGCCCCCG	-	novel	NA	P-0024193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	89	1057	0	ENST00000575354.2:c.2725_2733del	p.Pro909_Pro911del	p.P909_P911del	ENST00000575354	NM_015125.3	909	CCGCCCCCG/-	11/20	0.199379311535314	2	FACETS	0.271	0.239	0.305	0.135	0.119	0.153	INDETERMINATE	1	TRUE	0	0.607763751093293	2		1057	1082	SUCCESS
ATR	545	MSKCC	GRCh37	3	142243041	142243042	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0024193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	52	378	0	ENST00000350721.4:c.3946-1_3946delinsTT		p.X1316_splice	ENST00000350721	NM_001184.3	1316		22/47	0.240716452904566	1	FACETS	0.331	0.283	0.383	0.331	0.283	0.383	INDETERMINATE	1	TRUE	0	0.607763751093293	1		378	360	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003320	143003320	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	71	714	1	ENST00000262992.4:c.2506G>C	p.Gly836Arg	p.G836R	ENST00000262992	NM_001101669.1	836	Ggt/Cgt	23/24	1	2	FACETS	0.278	0.242	0.317	0.278	0.242	0.317	SUBCLONAL	1	TRUE	1	0.607763751093293	2		715	841	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495352	149495352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	283	813	0	ENST00000261799.4:c.3295G>A	p.Ala1099Thr	p.A1099T	ENST00000261799	NM_002609.3	1099	Gcg/Acg	23/23	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.607763751093293	2		813	873	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355311	81355311	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	48	424	0	ENST00000222390.5:c.1063C>G	p.Arg355Gly	p.R355G	ENST00000222390	NM_000601.4	355	Cga/Gga	9/18	0.607763751093293	3	FACETS	0.33	0.278	0.387	0.165	0.139	0.194	SUBCLONAL	1	TRUE	1	0.607763751093293	3		424	625	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913545	39913545	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	65	828	2	ENST00000378444.4:c.4783A>T	p.Ser1595Cys	p.S1595C	ENST00000378444	NM_001123385.1	1595	Agt/Tgt	13/15	0.125267354246183	5	FACETS	0.391	0.338	0.449			1	INDETERMINATE	1	TRUE	NA	0.607763751093293	5		830	1046	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006880	47006880	+	5_prime_UTR_variant	5'UTR	SNP	C	C	A	novel	NA	P-0024193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1256	93	983	1	ENST00000377604.3:c.-1C>A		p.*1*	ENST00000377604	NM_001204468.1	-/852		2/24	0.125267354246183	5	FACETS	0.434	0.384	0.487			1	INDETERMINATE	1	TRUE	NA	0.607763751093293	5		984	1349	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410728	63410728	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	80	866	0	ENST00000330258.3:c.2439T>A	p.Asp813Glu	p.D813E	ENST00000330258	NM_152424.3	813	gaT/gaA	2/2	0.205765832269729	3	FACETS	0.371	0.326	0.421	0.124	0.108	0.141	INDETERMINATE	1	TRUE	0	0.607763751093293	3		866	924	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345950	70345951	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	109	790	0	ENST00000374080.3:c.2490dup	p.Ala831CysfsTer2	p.A831Cfs*2	ENST00000374080		829	-/T	18/45	0.205765832269729	3	FACETS	0.469	0.42	0.521	0.156	0.14	0.174	INDETERMINATE	1	TRUE	0	0.607763751093293	3		790	997	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349973	70349973	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	122	831	0	ENST00000374080.3:c.3956G>T	p.Arg1319Leu	p.R1319L	ENST00000374080		1319	cGc/cTc	28/45	0.205765832269729	3	FACETS	0.537	0.484	0.592	0.179	0.161	0.198	INDETERMINATE	1	TRUE	0	0.607763751093293	3		831	975	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202423	123202423	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	44	630	0	ENST00000218089.9:c.2275C>A	p.Leu759Met	p.L759M	ENST00000218089	NM_001042749.1	759	Ctg/Atg	24/35	0.205765832269729	3	FACETS	0.228	0.19	0.27	0.076	0.063	0.09	INDETERMINATE	1	TRUE	0	0.607763751093293	3		630	829	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	206	571	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.864	0.806	0.924	1	0.993	1	CLONAL	2	TRUE	1	0.363846872581737	2		571	655	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0024194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	196	625	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.815	0.758	0.874	1	0.992	1	CLONAL	2	TRUE	1	0.363846872581737	2		625	661	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0024194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	70	436	1	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.865	0.756	0.981	0.865	0.756	0.981	CLONAL	1	TRUE	1	0.363846872581737	2		437	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0024197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	238	839	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.350443598686785	2	FACETS	0.949	0.89	1	0.949	0.89	1	CLONAL	2	TRUE	0	0.356185064198304	2		841	704	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242486	+	protein_altering_variant	In_Frame_Del	DEL	ATTAAGAGAAGCAACATCT	ATTAAGAGAAGCAACATCT	GCAA	novel	NA	P-0024197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	1834	644	2	ENST00000275493.2:c.2238_2256delinsGCAA	p.Leu747_Ser752delinsGln	p.L747_S752delinsQ	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACATCT/gaGCAA	19/28	0.356185064198304	34	FACETS	1	0.995	1	0.92	0.908	0.932	CLONAL	29	TRUE	2	0.356185064198304	34		646	2343	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489230	2489230	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	130	944	3	ENST00000355716.4:c.135C>A	p.Asp45Glu	p.D45E	ENST00000355716	NM_003820.2	45	gaC/gaA	2/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.356185064198304	2		947	625	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022750	12022750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	54	646	0	ENST00000396373.4:c.856G>T	p.Asp286Tyr	p.D286Y	ENST00000396373	NM_001987.4	286	Gat/Tat	5/8	0.356185064198304	5	FACETS	0.815	0.696	0.945	0.204	0.174	0.237	CLONAL	1	TRUE	1	0.356185064198304	5		646	571	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018075	48018075	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	91	743	0	ENST00000234420.5:c.270C>G	p.Phe90Leu	p.F90L	ENST00000234420	NM_000179.2	90	ttC/ttG	2/10	0.356185064198304	3	FACETS	0.959	0.852	1	0.479	0.426	0.536	CLONAL	1	TRUE	1	0.356185064198304	3		743	628	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157519964	157519964	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554234963	NA	P-0024197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	209	857	3	ENST00000346085.5:c.4033C>T	p.Gln1345Ter	p.Q1345*	ENST00000346085	NM_020732.3	1345	Cag/Tag	17/20	0.356185064198304	3	FACETS	0.972	0.906	1	0.972	0.906	1	CLONAL	2	TRUE	1	0.356185064198304	3		860	711	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373255	118373255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	24	628	0	ENST00000534358.1:c.6648G>A	p.Met2216Ile	p.M2216I	ENST00000534358	NM_005933.3	2216	atG/atA	27/36	0.245104948102531	1	FACETS	0.507	0.397	0.633	0.507	0.397	0.633	SUBCLONAL	1	TRUE	0	0.245104948102531	1		628	339	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945066	31945066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	36	929	0	ENST00000340398.3:c.35C>T	p.Thr12Ile	p.T12I	ENST00000340398	NM_001013699.2	12	aCc/aTc	1/1	1	2	FACETS	0.7	0.575	0.841	0.7	0.575	0.841	SUBCLONAL	1	TRUE	1	0.196912566746555	2		929	522	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587778720	NA	P-0024199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	62	966	0	ENST00000269305.4:c.638G>C	p.Arg213Pro	p.R213P	ENST00000269305	NM_001126112.2	213	cGa/cCa	6/11	0.196912566746555	1	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	0	0.196912566746555	1		966	552	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193181563	193181564	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0024199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	23	733	0	ENST00000367435.3:c.1111_1112del	p.Leu371AsnfsTer5	p.L371Nfs*5	ENST00000367435	NM_024529.4	370	tcTTta/tcta	13/17	0.128587628594246	3	FACETS	0.601	0.468	0.756	0.3	0.234	0.378	SUBCLONAL	1	TRUE	1	0.196912566746555	3		733	427	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610298	10610298	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	40	1286	1	ENST00000171111.5:c.412G>A	p.Glu138Lys	p.E138K	ENST00000171111	NM_203500.1	138	Gaa/Aaa	2/6	0.196912566746555	1	FACETS	0.68	0.564	0.808	0.68	0.564	0.808	SUBCLONAL	1	TRUE	0	0.196912566746555	1		1287	539	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637261	47637261	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1486720679	NA	P-0024199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	46	774	0	ENST00000233146.2:c.395A>T	p.Glu132Val	p.E132V	ENST00000233146	NM_000251.2	132	gAa/gTa	3/16	1	2	FACETS	0.952	0.802	1	0.952	0.802	1	CLONAL	1	TRUE	1	0.196912566746555	2		774	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0024201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	197	935	2	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	0.3	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.29	1		937	861	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0024201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	67	465	4	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.93	0.81	1	0.93	0.81	1	CLONAL	1	TRUE	1	0.29	2		469	497	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251907	153251907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	167	669	1	ENST00000281708.4:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000281708	NM_033632.3	367	Cga/Tga	7/12	0.23769906417593	2	FACETS	0.924	0.853	0.998	0.924	0.853	0.998	CLONAL	2	TRUE	0	0.29	2		670	623	SUCCESS
APC	324	MSKCC	GRCh37	5	112175282	112175282	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0024201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	57	337	0	ENST00000257430.4:c.3991A>T	p.Arg1331Ter	p.R1331*	ENST00000257430	NM_000038.5	1331	Aga/Tga	16/16	1	2	FACETS	0.927	0.798	1	0.927	0.798	1	CLONAL	1	TRUE	1	0.29	2		337	424	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494163	140494163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	272	961	0	ENST00000288602.6:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000288602	NM_004333.4	362	cGa/cAa	8/18	0.3	3	FACETS	0.909	0.853	0.968	0.909	0.853	0.968	CLONAL	2	TRUE	1	0.29	3		961	1181	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0024202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	381	602	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.420071194565263	5	FACETS	0.943	0.903	0.983	0.943	0.903	0.983	CLONAL	4	TRUE	1	0.462294493317891	5		603	740	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0024202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	313	755	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.462294493317891	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.462294493317891	3		755	733	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347499	91347499	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	112	803	0	ENST00000355112.3:c.3661G>T	p.Glu1221Ter	p.E1221*	ENST00000355112	NM_000057.2	1221	Gaa/Taa	19/22	0.462294493317891	6	FACETS	0.754	0.676	0.838	0.251	0.225	0.28	SUBCLONAL	1	TRUE	3	0.462294493317891	6		803	1236	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500778	149500778	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755218503	NA	P-0024202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	66	734	2	ENST00000261799.4:c.2452G>A	p.Ala818Thr	p.A818T	ENST00000261799	NM_002609.3	818	Gcc/Acc	17/23	0.443334821178209	3	FACETS	0.462	0.4	0.529	0.231	0.2	0.265	SUBCLONAL	1	TRUE	1	0.462294493317891	3		736	761	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602619	10602619	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1239985410	NA	P-0024203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	805	1045	0	ENST00000171111.5:c.959G>T	p.Arg320Leu	p.R320L	ENST00000171111	NM_203500.1	320	cGg/cTg	3/6	0.633997036089058	3	FACETS	0.994	0.971	1	0.994	0.971	1	CLONAL	3	TRUE	0	0.633997036089058	3		1045	1122	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974792	21974792	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs141798398	NA	P-0024203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	242	235	2	ENST00000304494.5:c.35C>A	p.Ser12Ter	p.S12*	ENST00000304494	NM_000077.4	12	tCg/tAg	1/3	0.633997036089058	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.633997036089058	3		237	304	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574030	7574030	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	676	866	0	ENST00000269305.4:c.997del	p.Arg333ValfsTer12	p.R333Vfs*12	ENST00000269305	NM_001126112.2	333	Cgt/gt	10/11	0.633997036089058	3	FACETS	0.976	0.951	1	0.976	0.951	1	CLONAL	3	TRUE	0	0.633997036089058	3		866	959	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023741	27023741	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	398	683	1	ENST00000324856.7:c.848del	p.Gly283AlafsTer80	p.G283Afs*80	ENST00000324856	NM_006015.4	283	Ggc/gc	1/20	0.633997036089058	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.633997036089058	2		684	604	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599185	28599185	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	624	1173	2	ENST00000253063.3:c.631G>T	p.Val211Leu	p.V211L	ENST00000253063	NM_031459.4	211	Gtg/Ttg	5/10	0.633997036089058	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.633997036089058	2		1175	960	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464883	120464883	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	199	569	0	ENST00000256646.2:c.5189T>A	p.Val1730Glu	p.V1730E	ENST00000256646	NM_024408.3	1730	gTg/gAg	28/34	0.633997036089058	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.633997036089058	1		569	361	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479225	50479225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	204	767	2	ENST00000394963.4:c.73G>A	p.Ala25Thr	p.A25T	ENST00000394963	NM_003076.4	25	Gct/Act	1/13	0.581021951039868	4	FACETS	0.94	0.871	1	0.313	0.29	0.338	CLONAL	1	TRUE	1	0.633997036089058	4		769	1119	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959403	26959403	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	404	755	0	ENST00000381527.3:c.570G>C	p.Leu190Phe	p.L190F	ENST00000381527	NM_001260.1	190	ttG/ttC	6/13	0.633997036089058	2	FACETS	0.991	0.955	1	0.991	0.955	1	CLONAL	2	TRUE	0	0.633997036089058	2		755	643	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014044	14014044	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	210	641	1	ENST00000311895.7:c.22C>T	p.Arg8Ter	p.R8*	ENST00000311895	NM_005236.2	8	Cga/Tga	1/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.633997036089058	2		642	609	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677825	47677825	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	222	671	0	ENST00000347630.2:c.1040A>T	p.His347Leu	p.H347L	ENST00000347630	NM_001007230.1	347	cAc/cTc	11/11	0.633997036089058	4	FACETS	1	0.961	1	0.35	0.325	0.375	CLONAL	1	TRUE	1	0.633997036089058	4		671	1091	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1646372	1646372	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	916	1126	2	ENST00000344749.5:c.127G>T	p.Ala43Ser	p.A43S	ENST00000344749	NM_001136139.2	43	Gcg/Tcg	3/19	0.633997036089058	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.633997036089058	3		1128	1229	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46597045	46597045	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777687956	NA	P-0024203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	192	758	2	ENST00000263734.3:c.859G>A	p.Glu287Lys	p.E287K	ENST00000263734	NM_001430.4	287	Gag/Aag	7/16	0.598612212352174	4	FACETS	0.975	0.901	1	0.488	0.45	0.526	CLONAL	1	TRUE	2	0.633997036089058	4		760	1015	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526279	31526279	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	625	1179	0	ENST00000344624.3:c.761G>C	p.Arg254Pro	p.R254P	ENST00000344624		254	cGc/cCc	2/33	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	2	TRUE	NA	0.633997036089058	2		1179	961	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503852	149503852	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	417	873	0	ENST00000261799.4:c.1984C>A	p.Leu662Met	p.L662M	ENST00000261799	NM_002609.3	662	Ctg/Atg	14/23	0.633997036089058	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.633997036089058	2		873	647	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683719	162683719	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	456	903	1	ENST00000366898.1:c.250G>T	p.Gly84Ter	p.G84*	ENST00000366898	NM_004562.2	84	Gga/Tga	3/12	0.633997036089058	3	FACETS	0.956	0.917	0.995	0.956	0.917	0.995	CLONAL	2	TRUE	1	0.633997036089058	3		904	991	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132748	152132748	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0024203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	204	703	0	ENST00000262189.6:c.124A>T	p.Lys42Ter	p.K42*	ENST00000262189	NM_170606.2	42	Aaa/Taa	1/59	0.633997036089058	3	FACETS	1	0.953	1	0.517	0.48	0.555	CLONAL	1	TRUE	1	0.633997036089058	3		703	820	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132788	152132788	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	238	922	0	ENST00000262189.6:c.84C>G	p.Ser28Arg	p.S28R	ENST00000262189	NM_170606.2	28	agC/agG	1/59	0.633997036089058	3	FACETS	0.986	0.921	1	0.493	0.46	0.527	CLONAL	1	TRUE	1	0.633997036089058	3		922	1003	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989639	68989639	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	201	689	0	ENST00000288368.4:c.1577G>T	p.Cys526Phe	p.C526F	ENST00000288368	NM_024870.2	526	tGc/tTc	15/40	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.633997036089058	2		689	600	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0024205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	219	656	2	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.453891034077024	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.453891034077024	1		658	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0024205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	529	947	0	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.453891034077024	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.453891034077024	2		947	1066	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858929	243858929	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	152	753	0	ENST00000263826.5:c.136G>T	p.Asp46Tyr	p.D46Y	ENST00000263826	NM_005465.4	46	Gat/Tat	2/13	1	2	FACETS	0.937	0.859	1	0.937	0.859	1	CLONAL	1	TRUE	1	0.453891034077024	2		753	715	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89478289	89478289	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	166	697	1	ENST00000336596.2:c.2108A>G	p.Glu703Gly	p.E703G	ENST00000336596	NM_005233.5	703	gAg/gGg	12/17	1	2	FACETS	0.956	0.88	1	0.956	0.88	1	CLONAL	1	TRUE	1	0.453891034077024	2		698	765	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155960	106155960	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1247817772	NA	P-0024205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	121	435	1	ENST00000380013.4:c.861G>T	p.Lys287Asn	p.K287N	ENST00000380013	NM_001127208.2	287	aaG/aaT	3/11	0.453891034077024	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.453891034077024	1		436	403	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226576395	226576395	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758314341	NA	P-0024205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	197	859	0	ENST00000366794.5:c.679G>A	p.Glu227Lys	p.E227K	ENST00000366794	NM_001618.3	227	Gaa/Aaa	5/23	1	2	FACETS	0.927	0.859	0.998	0.927	0.859	0.998	CLONAL	1	TRUE	1	0.453891034077024	2		859	936	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0024206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	126	839	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.22373784974293	2	FACETS	1	0.975	1	0.609	0.553	0.668	CLONAL	1	TRUE	0	0.320633491574603	2		841	645	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284985	15284985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	67	880	4	ENST00000263388.2:c.4630C>T	p.Arg1544Cys	p.R1544C	ENST00000263388	NM_000435.2	1544	Cgc/Tgc	25/33	0.165720251632028	3	FACETS	0.726	0.63	0.829	0.363	0.315	0.415	INDETERMINATE	1	TRUE	1	0.320633491574603	3		884	668	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649942	88649942	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0024206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	95	777	0	ENST00000372037.3:c.191C>G	p.Ser64Ter	p.S64*	ENST00000372037	NM_004329.2	64	tCa/tGa	4/13	0.219943466633448	2	FACETS	0.785	0.699	0.877	0.392	0.349	0.439	SUBCLONAL	1	TRUE	0	0.320633491574603	2		777	755	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88651978	88651978	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	90	417	0	ENST00000372037.3:c.325C>G	p.Gln109Glu	p.Q109E	ENST00000372037	NM_004329.2	109	Cag/Gag	5/13	0.219943466633448	2	FACETS	1	0.975	1	0.67	0.598	0.746	CLONAL	1	TRUE	0	0.320633491574603	2		417	419	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572020	64572020	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780844361	NA	P-0024206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	61	911	0	ENST00000312049.6:c.1619C>T	p.Pro540Leu	p.P540L	ENST00000312049	NM_130799.2	540	cCc/cTc	10/10	0.219943466633448	2	FACETS	0.38	0.327	0.439	0.19	0.163	0.22	SUBCLONAL	1	TRUE	0	0.320633491574603	2		911	1000	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434271	49434271	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555192218	NA	P-0024206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	76	1248	0	ENST00000301067.7:c.7282del	p.Arg2428GlyfsTer57	p.R2428Gfs*57	ENST00000301067	NM_003482.3	2428	Cgg/gg	31/54	0.16114465246685	2	FACETS	0.547	0.479	0.621	0.274	0.239	0.311	INDETERMINATE	1	TRUE	0	0.320633491574603	2		1248	866	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42026780	42026780	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	44	473	0	ENST00000219905.7:c.3904G>C	p.Asp1302His	p.D1302H	ENST00000219905	NM_001164273.1	1302	Gat/Cat	12/24	0.165720251632028	3	FACETS	0.517	0.433	0.611	0.258	0.216	0.306	INDETERMINATE	1	TRUE	1	0.320633491574603	3		473	616	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094750	2094750	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	87	981	0	ENST00000219066.1:c.430G>C	p.Asp144His	p.D144H	ENST00000219066	NM_002528.5	144	Gac/Cac	3/6	0.0588970510436657	3	FACETS	0.716	0.632	0.805	0.358	0.316	0.403	INDETERMINATE	1	TRUE	1	0.320633491574603	3		981	880	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63545662	63545662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	54	699	0	ENST00000307078.5:c.932C>A	p.Ser311Tyr	p.S311Y	ENST00000307078	NM_004655.3	311	tCc/tAc	3/11	0.222925658537989	2	FACETS	0.604	0.515	0.7	0.302	0.257	0.35	SUBCLONAL	1	TRUE	0	0.320633491574603	2		699	558	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937605	17937605	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	64	991	0	ENST00000458235.1:c.3322C>G	p.His1108Asp	p.H1108D	ENST00000458235	NM_000215.3	1108	Cat/Gat	24/24	0.165720251632028	3	FACETS	0.603	0.521	0.692	0.302	0.26	0.346	INDETERMINATE	1	TRUE	1	0.320633491574603	3		991	768	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47730006	47730006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	44	590	0	ENST00000449228.1:c.383C>T	p.Ser128Leu	p.S128L	ENST00000449228	NM_001127240.2	128	tCa/tTa	3/4	0.165720251632028	3	FACETS	0.658	0.552	0.775	0.329	0.276	0.388	INDETERMINATE	1	TRUE	1	0.320633491574603	3		590	484	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39283950	39283950	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	68	672	0	ENST00000402219.2:c.403G>C	p.Glu135Gln	p.E135Q	ENST00000402219	NM_005633.3	135	Gaa/Caa	4/23	0.165720251632028	3	FACETS	0.625	0.542	0.714	0.312	0.271	0.357	INDETERMINATE	1	TRUE	1	0.320633491574603	3		672	788	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61710143	61710143	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	51	629	0	ENST00000401558.2:c.2761G>C	p.Asp921His	p.D921H	ENST00000401558	NM_003400.3	921	Gat/Cat	22/25	0.165720251632028	3	FACETS	0.575	0.488	0.671	0.287	0.244	0.336	INDETERMINATE	1	TRUE	1	0.320633491574603	3		629	642	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61710168	61710168	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	52	627	1	ENST00000401558.2:c.2736G>C	p.Gln912His	p.Q912H	ENST00000401558	NM_003400.3	912	caG/caC	22/25	0.165720251632028	3	FACETS	0.536	0.455	0.625	0.268	0.227	0.313	INDETERMINATE	1	TRUE	1	0.320633491574603	3		628	702	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144072	55144072	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	56	620	0	ENST00000257290.5:c.1901G>A	p.Arg634Lys	p.R634K	ENST00000257290	NM_006206.4	634	aGa/aAa	14/23	0.16114465246685	2	FACETS	0.664	0.569	0.768	0.332	0.284	0.384	INDETERMINATE	1	TRUE	0	0.320633491574603	2		620	526	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995543	68995543	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	93	862	0	ENST00000288368.4:c.1947C>G	p.Phe649Leu	p.F649L	ENST00000288368	NM_024870.2	649	ttC/ttG	18/40	0.320633491574603	3	FACETS	0.605	0.537	0.679	0.202	0.179	0.227	SUBCLONAL	1	TRUE	0	0.320633491574603	3		862	1112	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50821726	50821729	+	missense_variant	Missense_Mutation	ONP	CATC	CATC	TATT	novel	NA	P-0024206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	79	645	0	ENST00000398568.2:c.2062_2065delinsTATT	p.His688_His689delinsTyrTyr	p.H688_H689delinsYY	ENST00000398568	NM_001042412.1	688	CATCat/TATTat	13/18	0.0588970510436657	3	FACETS	0.725	0.637	0.82	0.362	0.318	0.41	INDETERMINATE	1	TRUE	1	0.320633491574603	3		645	789	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0024213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	111	750	3	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.249182999696768	3	FACETS	1	0.958	1	0.739	0.668	0.813	CLONAL	2	TRUE	0	0.249182999696768	3		753	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	530	773	1	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.554384287533214	2	FACETS	0.91	0.878	0.941	0.91	0.878	0.941	CLONAL	2	TRUE	0	0.6165157646815	2		774	945	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979562	7979562	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	421	681	0	ENST00000319144.4:c.1463G>T	p.Arg488Leu	p.R488L	ENST00000319144	NM_001139.2	488	cGt/cTt	11/15	0.554384287533214	2	FACETS	0.801	0.767	0.834	0.801	0.767	0.834	CLONAL	2	TRUE	0	0.6165157646815	2		681	853	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245466	41245466	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	719	896	0	ENST00000357654.3:c.2082del	p.Ser694ArgfsTer7	p.S694Rfs*7	ENST00000357654	NM_007294.3	694	agC/ag	10/23	0.556282738923501	2	FACETS	0.892	0.865	0.919	0.892	0.865	0.919	CLONAL	2	TRUE	0	0.6165157646815	2		896	1307	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46276090	46276090	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	139	571	2	ENST00000371998.3:c.3526C>T	p.Gln1176Ter	p.Q1176*	ENST00000371998		1176	Cag/Tag	18/23	1	2	FACETS	0.585	0.533	0.639	0.585	0.533	0.639	SUBCLONAL	1	TRUE	1	0.6165157646815	2		573	771	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685281	89685281	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1060500116	NA	P-0024216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	53	521	0	ENST00000371953.3:c.176C>G	p.Ser59Ter	p.S59*	ENST00000371953	NM_000314.4	59	tCa/tGa	3/9	0.299847341599388	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.29	1		521	270	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674233	86674233	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1463885690	NA	P-0024216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	71	451	0	ENST00000274376.6:c.2365C>T	p.Arg789Ter	p.R789*	ENST00000274376	NM_002890.2	789	Cga/Tga	18/25	0.299847341599388	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.29	1		451	347	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037480	12037480	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	70	413	0	ENST00000396373.4:c.1111G>C	p.Val371Leu	p.V371L	ENST00000396373	NM_001987.4	371	Gtg/Ctg	6/8	0.102999289206097	3	FACETS	1	0.959	1	0.618	0.541	0.701	INDETERMINATE	1	TRUE	1	0.29	3		413	447	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441780	49441780	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555195442	NA	P-0024216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	146	606	0	ENST00000301067.7:c.4204C>T	p.Gln1402Ter	p.Q1402*	ENST00000301067	NM_003482.3	1402	Cag/Tag	14/54	0.299847341599388	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.29	1		606	627	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919215	48919215	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0024216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	28	212	0	ENST00000267163.4:c.381-1G>T		p.X127_splice	ENST00000267163	NM_000321.2	127			0.299847341599388	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.29	1		212	115	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43733737	43733737	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	30	596	0	ENST00000382044.4:c.3085G>C	p.Glu1029Gln	p.E1029Q	ENST00000382044	NM_001141980.1	1029	Gag/Cag	15/28	0.299847341599388	1	FACETS	0.338	0.271	0.413	0.338	0.271	0.413	SUBCLONAL	1	TRUE	0	0.29	1		596	524	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320350	30320350	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	56	391	0	ENST00000322652.5:c.1291C>T	p.Gln431Ter	p.Q431*	ENST00000322652	NM_015355.2	431	Cag/Tag	11/16	0.299847341599388	1	FACETS	0.995	0.857	1	0.995	0.857	1	CLONAL	1	TRUE	0	0.29	1		391	332	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211381	36211381	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768486033	NA	P-0024216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	81	818	0	ENST00000222270.7:c.1132G>A	p.Gly378Arg	p.G378R	ENST00000222270	NM_014727.1	378	Gga/Aga	3/37	1	2	FACETS	0.767	0.676	0.866	0.767	0.676	0.866	SUBCLONAL	1	TRUE	1	0.29	2		818	728	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587167	189587167	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	74	591	0	ENST00000264731.3:c.1184C>G	p.Ser395Cys	p.S395C	ENST00000264731	NM_003722.4	395	tCc/tGc	9/14	0.299847341599388	3	FACETS	0.938	0.821	1	0.469	0.41	0.532	CLONAL	1	TRUE	1	0.29	3		591	623	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978658	70978658	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	153	892	3	ENST00000276594.2:c.995G>A	p.Arg332His	p.R332H	ENST00000276594	NM_024504.3	332	cGc/cAc	5/8	0.102999289206097	3	FACETS	1	0.981	1	0.627	0.573	0.683	INDETERMINATE	1	TRUE	1	0.29	3		895	964	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8338966	8338966	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	58	630	0	ENST00000356435.5:c.5335A>T	p.Met1779Leu	p.M1779L	ENST00000356435		1779	Atg/Ttg	32/35	1	2	FACETS	0.719	0.618	0.83	0.719	0.618	0.83	SUBCLONAL	1	TRUE	1	0.29	2		630	556	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405632	139405632	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	69	1016	0	ENST00000277541.6:c.2559C>G	p.Phe853Leu	p.F853L	ENST00000277541	NM_017617.3	853	ttC/ttG	16/34	1	2	FACETS	0.5	0.434	0.571	0.5	0.434	0.571	SUBCLONAL	1	TRUE	1	0.29	2		1016	952	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200039	123200039	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0024216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	28	206	0	ENST00000218089.9:c.2111C>G	p.Ser704Ter	p.S704*	ENST00000218089	NM_001042749.1	704	tCa/tGa	22/35	0.228802329924673	0	FACETS	1	0.887	1			1	CLONAL	1	TRUE	NA	0.29	0		206	121	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578276	7578312	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGAGGGGCCAGACCTAAGAGCAATCAGTGAGGAATC	AGGAGGGGCCAGACCTAAGAGCAATCAGTGAGGAATC	-	novel	NA	P-0024217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	75	587	0	ENST00000269305.4:c.560-23_573del		p.X187_splice	ENST00000269305	NM_001126112.2	187		6/11	0.203201838484051	1	FACETS	0.861	0.759	0.968	1	0.98	1	CLONAL	2	FALSE	0	0.214364495242506	1		587	363	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762871	40762871	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	129	602	0	ENST00000392038.2:c.137A>T	p.Asp46Val	p.D46V	ENST00000392038	NM_001626.4	46	gAt/gTt	3/14	0.214364495242506	1	FACETS	1	0.962	1	1	0.991	1	CLONAL	2	FALSE	0	0.214364495242506	1		602	488	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157335	106157336	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0024217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	48	385	0	ENST00000380013.4:c.2241dup	p.Leu748IlefsTer6	p.L748Ifs*6	ENST00000380013	NM_001127208.2	746	caa/cAaa	3/11	1	2	FACETS	0.8	0.681	0.929	1	0.967	1	CLONAL	2	FALSE	1	0.214364495242506	2		385	280	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359909	87359909	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs777294894	NA	P-0024218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	283	423	0	ENST00000277120.3:c.1217A>G	p.Asp406Gly	p.D406G	ENST00000277120		406	gAc/gGc	11/19	0.375713503976074	4	FACETS	0.92	0.869	0.971	1	0.993	1	CLONAL	3	TRUE	2	0.398451828889822	4		423	720	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0024220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	145	997	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	0.353862118454559	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.353862118454559	1		997	591	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247784	10247784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745789285	NA	P-0024220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	133	1036	1	ENST00000340748.4:c.4418G>A	p.Arg1473His	p.R1473H	ENST00000340748		1473	cGt/cAt	36/40	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.353862118454559	2		1037	727	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0024222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	86	653	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.324416481652131	1	FACETS	0.743	0.658	0.833	0.743	0.658	0.833	SUBCLONAL	1	FALSE	0	0.324416481652131	1		653	598	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0024222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	79	611	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	0.969	1	CLONAL	1	FALSE	1	0.324416481652131	2		611	378	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921551	178921551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	41	486	0	ENST00000263967.3:c.1033A>G	p.Asn345Asp	p.N345D	ENST00000263967	NM_006218.2	345	Aat/Gat	5/21	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	FALSE	1	0.324416481652131	2		486	245	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354205	15354205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	94	785	0	ENST00000263377.2:c.2675C>T	p.Pro892Leu	p.P892L	ENST00000263377	NM_058243.2	892	cCa/cTa	14/20	0.297926648825286	4	FACETS	0.907	0.806	1			1	CLONAL	1	FALSE	NA	0.324416481652131	4		785	846	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118498	17118498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs755959303	NA	P-0024225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	26	685	1	ENST00000285071.4:c.1432+1G>A		p.X478_splice	ENST00000285071	NM_144997.5	478			0.398980588648095	1	FACETS	0.235	0.186	0.292	0.235	0.186	0.292	SUBCLONAL	1	TRUE	0	0.448906471937841	1		686	382	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682537	37682537	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	27	393	0	ENST00000447079.4:c.3728G>T	p.Arg1243Ile	p.R1243I	ENST00000447079	NM_015083.1	1243	aGa/aTa	13/14	0.41552569768757	4	FACETS	0.338	0.268	0.418			1	SUBCLONAL	1	TRUE	NA	0.448906471937841	4		393	516	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866444	37866445	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	125	877	0	ENST00000269571.5:c.750dup	p.Asp251Ter	p.D251*	ENST00000269571		250	tct/tcTt	6/27	0.41552569768757	4	FACETS	0.989	0.895	1			1	CLONAL	1	TRUE	NA	0.448906471937841	4		877	816	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0024226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	118	632	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	0.608765979734736	1	FACETS	0.859	0.786	0.934	0.859	0.786	0.934	CLONAL	1	TRUE	0	0.608765979734736	1		632	314	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0024226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	187	683	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	0.608765979734736	1	FACETS	0.879	0.82	0.94	0.879	0.82	0.94	CLONAL	1	TRUE	0	0.608765979734736	1		683	486	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732969	30732969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893810	NA	P-0024226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	137	391	1	ENST00000295754.5:c.1582C>T	p.Arg528Cys	p.R528C	ENST00000295754	NM_003242.5	528	Cgt/Tgt	7/7	0.608765979734736	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.608765979734736	1		392	276	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412946	49412946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	277	869	1	ENST00000418115.1:c.77G>A	p.Ser26Asn	p.S26N	ENST00000418115	NM_001664.2	26	aGc/aAc	2/5	0.608765979734736	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.608765979734736	1		870	591	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061469	38061469	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	132	600	0	ENST00000250448.2:c.520T>G	p.Ser174Ala	p.S174A	ENST00000250448	NM_004496.3	174	Tcg/Gcg	2/2	0.608765979734736	1	FACETS	0.996	0.919	1	0.996	0.919	1	CLONAL	1	TRUE	0	0.608765979734736	1		600	303	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068393	26068394	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	33	614	0	ENST00000435504.4:c.96dup	p.Glu33ArgfsTer35	p.E33Rfs*35	ENST00000435504		32	-/A	2/13	0.608765979734736	1	FACETS	0.122	0.099	0.148	0.122	0.099	0.148	SUBCLONAL	1	TRUE	0	0.608765979734736	1		614	619	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	87	571	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.904	1			1	INDETERMINATE	1	TRUE	NA	0.724979587300209	2		571	239	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349513	89349513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150325340	NA	P-0024227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	121	831	0	ENST00000301030.4:c.3437C>T	p.Thr1146Met	p.T1146M	ENST00000301030	NM_001256183.1	1146	aCg/aTg	9/13	1	2	FACETS	0.491	0.444	0.54	0.491	0.444	0.54	SUBCLONAL	1	TRUE	1	0.724979587300209	2		831	680	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0024228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	40	802	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	0.344491379059026	2		802	183	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0024228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	14	436	1	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.661	0.482	0.874	0.661	0.482	0.874	SUBCLONAL	1	TRUE	1	0.344491379059026	2		437	123	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741886	17741886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1036774997	NA	P-0024228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	42	176	1	ENST00000250003.3:c.557C>T	p.Pro186Leu	p.P186L	ENST00000250003	NM_002478.4	186	cCg/cTg	1/3	1	2	FACETS	0.787	0.66	0.926	0.787	0.66	0.926	CLONAL	1	TRUE	1	0.344491379059026	2		177	310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs878854073	NA	P-0024228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	71	722	0	ENST00000269305.4:c.673-1G>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.344491379059026	2		722	365	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193172955	193172955	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs779180488	NA	P-0024228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	20	663	0	ENST00000367435.3:c.1003C>G	p.Pro335Ala	p.P335A	ENST00000367435	NM_024529.4	335	Cct/Gct	11/17	0.344491379059026	3	FACETS	0.443	0.339	0.566	0.222	0.169	0.283	SUBCLONAL	1	TRUE	1	0.344491379059026	3		663	307	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194805	30194805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	33	965	0	ENST00000331968.5:c.340C>T	p.Leu114Phe	p.L114F	ENST00000331968	NM_002742.2	114	Ctt/Ttt	2/18	1	2	FACETS	0.689	0.563	0.83	0.689	0.563	0.83	SUBCLONAL	1	TRUE	1	0.344491379059026	2		965	278	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609973	81609973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	34	369	0	ENST00000298171.2:c.1571C>G	p.Thr524Ser	p.T524S	ENST00000298171	NM_000369.2	524	aCc/aGc	10/10	1	2	FACETS	0.619	0.507	0.744	0.619	0.507	0.744	SUBCLONAL	1	TRUE	1	0.344491379059026	2		369	319	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486083	29486083	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0024228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	10	752	0	ENST00000356175.3:c.260T>A	p.Leu87Ter	p.L87*	ENST00000356175	NM_000267.3	87	tTg/tAg	3/57	1	2	FACETS	0.358	0.243	0.503	0.358	0.243	0.503	SUBCLONAL	1	TRUE	1	0.344491379059026	2		752	162	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289753	15289753	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0024228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	188	998	1	ENST00000263388.2:c.3719-1G>A		p.X1240_splice	ENST00000263388	NM_000435.2	1240			1	2	FACETS	0.988	0.912	1	0.988	0.912	1	CLONAL	1	TRUE	1	0.344491379059026	2		999	1105	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17940999	17940999	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	206	1193	1	ENST00000458235.1:c.3125G>A	p.Arg1042Gln	p.R1042Q	ENST00000458235	NM_000215.3	1042	cGg/cAg	23/24	1	2	FACETS	0.939	0.869	1	0.939	0.869	1	CLONAL	1	TRUE	1	0.344491379059026	2		1194	1274	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155399	99155399	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	38	581	0	ENST00000074304.5:c.625C>G	p.Arg209Gly	p.R209G	ENST00000074304	NM_001134224.1	209	Cga/Gga	9/26	1	2	FACETS	0.845	0.703	1	0.845	0.703	1	CLONAL	1	TRUE	1	0.344491379059026	2		581	261	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715604	30715604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	10	330	0	ENST00000295754.5:c.1262C>T	p.Thr421Ile	p.T421I	ENST00000295754	NM_003242.5	421	aCt/aTt	5/7	1	2	FACETS	0.652	0.447	0.905	0.652	0.447	0.905	SUBCLONAL	1	TRUE	1	0.344491379059026	2		330	89	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467380	66467380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	24	272	0	ENST00000273854.3:c.889G>A	p.Glu297Lys	p.E297K	ENST00000273854	NM_004439.5	297	Gag/Aag	3/18	0.440678127301345	3	FACETS	0.858	0.679	1	0.429	0.339	0.53	CLONAL	1	TRUE	1	0.440678127301345	3		272	155	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	122	883	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.374265654998114	2	FACETS	0.92	0.844	0.996	0.92	0.844	0.996	CLONAL	2	TRUE	0	0.440678127301345	2		883	301	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982036	93982036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1165179670	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	41	523	0	ENST00000369303.4:c.1429G>A	p.Glu477Lys	p.E477K	ENST00000369303	NM_004440.3	477	Gaa/Aaa	6/17	0.440678127301345	4	FACETS	0.934	0.782	1	0.467	0.391	0.551	CLONAL	1	TRUE	2	0.440678127301345	4		523	287	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209264	98209264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778630	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	78	721	1	ENST00000331920.6:c.4274C>T	p.Ser1425Leu	p.S1425L	ENST00000331920	NM_000264.3	1425	tCg/tTg	23/24	0.268660092954013	5	FACETS	0.772	0.682	0.867	0.514	0.455	0.578	SUBCLONAL	2	TRUE	2	0.440678127301345	5		722	381	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027128	49027128	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs794727199	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	39	432	0	ENST00000267163.4:c.1696-1G>A		p.X566_splice	ENST00000267163	NM_000321.2	566			0.440678127301345	1	FACETS	0.914	0.771	1	0.914	0.771	1	CLONAL	1	TRUE	0	0.440678127301345	1		432	151	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681547	117681547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151330473	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	110	459	0	ENST00000368508.3:c.3403G>A	p.Gly1135Arg	p.G1135R	ENST00000368508	NM_002944.2	1135	Ggg/Agg	22/43	0.195452871959919	4	FACETS	1	0.914	1	1	0.914	1	INDETERMINATE	2	TRUE	2	0.440678127301345	4		459	357	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7218299	7218299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	103	654	0	ENST00000380728.2:c.73G>A	p.Glu25Lys	p.E25K	ENST00000380728		25	Gag/Aag	2/11	0.374265654998114	2	FACETS	0.982	0.896	1	0.982	0.896	1	CLONAL	2	TRUE	0	0.440678127301345	2		654	238	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100093	27100093	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	52	667	0	ENST00000324856.7:c.3889G>C	p.Glu1297Gln	p.E1297Q	ENST00000324856	NM_006015.4	1297	Gag/Cag	16/20	0.440678127301345	4	FACETS	0.81	0.691	0.939	0.405	0.345	0.47	CLONAL	1	TRUE	2	0.440678127301345	4		667	420	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231731	66231731	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388138471	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	104	667	1	ENST00000273854.3:c.1969G>A	p.Glu657Lys	p.E657K	ENST00000273854	NM_004439.5	657	Gag/Aag	11/18	0.440678127301345	3	FACETS	0.85	0.769	0.933	0.85	0.769	0.933	CLONAL	2	TRUE	1	0.440678127301345	3		668	339	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255463	16255465	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	117	555	0	ENST00000375759.3:c.2731_2733del	p.Ser911del	p.S911del	ENST00000375759	NM_015001.2	910	TCT/-	11/15	0.440678127301345	4	FACETS	0.944	0.859	1	0.944	0.859	1	CLONAL	2	TRUE	2	0.440678127301345	4		555	405	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599275	28599275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	114	862	0	ENST00000253063.3:c.721C>T	p.Pro241Ser	p.P241S	ENST00000253063	NM_031459.4	241	Cca/Tca	5/10	0.440678127301345	4	FACETS	0.918	0.833	1	0.918	0.833	1	CLONAL	2	TRUE	2	0.440678127301345	4		862	406	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733497	85733497	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	47	622	0	ENST00000370580.1:c.515T>G	p.Leu172Arg	p.L172R	ENST00000370580	NM_003921.4	172	cTg/cGg	3/3	0.440678127301345	4	FACETS	0.75	0.634	0.877	0.375	0.317	0.439	SUBCLONAL	1	TRUE	2	0.440678127301345	4		622	410	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458899	120458899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	50	822	0	ENST00000256646.2:c.6446C>T	p.Ser2149Phe	p.S2149F	ENST00000256646	NM_024408.3	2149	tCc/tTc	34/34	0.440678127301345	4	FACETS	0.906	0.771	1	0.453	0.385	0.526	CLONAL	1	TRUE	2	0.440678127301345	4		822	361	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226549703	226549703	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1216944456	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	57	574	0	ENST00000366794.5:c.2930C>G	p.Ser977Cys	p.S977C	ENST00000366794	NM_001618.3	977	tCt/tGt	22/23	0.440678127301345	4	FACETS	1	0.91	1	0.537	0.463	0.617	CLONAL	1	TRUE	2	0.440678127301345	4		574	347	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226573363	226573363	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	39	531	0	ENST00000366794.5:c.853G>A	p.Asp285Asn	p.D285N	ENST00000366794	NM_001618.3	285	Gat/Aat	7/23	0.440678127301345	4	FACETS	0.748	0.621	0.888	0.374	0.31	0.444	SUBCLONAL	1	TRUE	2	0.440678127301345	4		531	341	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405785	70405785	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1388958746	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	63	610	0	ENST00000373644.4:c.3299T>C	p.Val1100Ala	p.V1100A	ENST00000373644	NM_030625.2	1100	gTt/gCt	4/12	1	2	FACETS	0.976	0.851	1	0.976	0.851	1	CLONAL	1	TRUE	1	0.440678127301345	2		610	293	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154309	2154309	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747266091	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	62	875	0	ENST00000434045.2:c.619G>A	p.Glu207Lys	p.E207K	ENST00000434045	NM_001127598.1	207	Gag/Aag	5/5	1	2	FACETS	0.974	0.848	1	0.974	0.848	1	CLONAL	1	TRUE	1	0.440678127301345	2		875	289	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456374	32456374	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	62	848	0	ENST00000332351.3:c.518G>A	p.Gly173Glu	p.G173E	ENST00000332351	NM_024426.4	173	gGa/gAa	1/10	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.440678127301345	2		848	251	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307502	118307502	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs782112520	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	50	592	0	ENST00000534358.1:c.275C>G	p.Ser92Trp	p.S92W	ENST00000534358	NM_005933.3	92	tCg/tGg	1/36	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.440678127301345	2		592	221	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118370083	118370083	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	48	460	0	ENST00000534358.1:c.6027G>C	p.Leu2009Phe	p.L2009F	ENST00000534358	NM_005933.3	2009	ttG/ttC	23/36	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.440678127301345	2		460	216	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444816	49444816	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1316716261	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	44	929	1	ENST00000301067.7:c.2650C>T	p.Pro884Ser	p.P884S	ENST00000301067	NM_003482.3	884	Cct/Tct	10/54	1	2	FACETS	0.693	0.585	0.812	0.693	0.585	0.812	SUBCLONAL	1	TRUE	1	0.440678127301345	2		930	288	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201321	133201321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	61	643	1	ENST00000320574.5:c.6823G>A	p.Glu2275Lys	p.E2275K	ENST00000320574	NM_006231.2	2275	Gag/Aag	49/49	1	2	FACETS	0.884	0.769	1	0.884	0.769	1	CLONAL	1	TRUE	1	0.440678127301345	2		644	313	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939102	48939102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	59	461	0	ENST00000267163.4:c.934C>T	p.Pro312Ser	p.P312S	ENST00000267163	NM_000321.2	312	Cca/Tca	9/27	0.440678127301345	1	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	0	0.440678127301345	1		461	198	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194858	30194858	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771807174	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	89	594	0	ENST00000331968.5:c.287G>A	p.Gly96Glu	p.G96E	ENST00000331968	NM_002742.2	96	gGa/gAa	2/18	0.440678127301345	3	FACETS	0.862	0.774	0.953	0.862	0.774	0.953	CLONAL	2	TRUE	1	0.440678127301345	3		594	286	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675056	40675056	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs753817858	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	69	788	0	ENST00000249776.8:c.20C>A	p.Pro7Gln	p.P7Q	ENST00000249776	NM_033286.3	7	cCg/cAg	1/9	1	2	FACETS	0.9	0.789	1	0.9	0.789	1	CLONAL	1	TRUE	1	0.440678127301345	2		788	348	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988724	41988724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	67	540	1	ENST00000219905.7:c.1516G>A	p.Glu506Lys	p.E506K	ENST00000219905	NM_001164273.1	506	Gaa/Aaa	3/24	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.440678127301345	2		541	278	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042099	42042100	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	54	660	1	ENST00000219905.7:c.6294_6295delinsTT	p.Gln2099Ter	p.Q2099*	ENST00000219905	NM_001164273.1	2098	gtCCaa/gtTTaa	17/24	1	2	FACETS	0.798	0.686	0.919	0.798	0.686	0.919	CLONAL	1	TRUE	1	0.440678127301345	2		661	307	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779332	3779332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	58	643	1	ENST00000262367.5:c.5716C>T	p.Pro1906Ser	p.P1906S	ENST00000262367	NM_004380.2	1906	Cct/Tct	31/31	0.440678127301345	1	FACETS	0.786	0.682	0.897	0.786	0.682	0.897	SUBCLONAL	1	TRUE	0	0.440678127301345	1		644	261	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243613	41243613	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	74	782	1	ENST00000357654.3:c.3935C>T	p.Thr1312Ile	p.T1312I	ENST00000357654	NM_007294.3	1312	aCc/aTc	10/23	0.440678127301345	2	FACETS	0.941	0.829	1	0.47	0.414	0.53	CLONAL	1	TRUE	0	0.440678127301345	2		783	357	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383082	42383082	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	45	496	0	ENST00000221972.3:c.102G>A	p.Trp34Ter	p.W34*	ENST00000221972	NM_021601.3	34	tgG/tgA	2/5	0.336877322744135	3	FACETS	1	0.899	1	0.539	0.457	0.628	CLONAL	1	TRUE	1	0.440678127301345	3		496	231	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39744079	39744079	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	84	499	0	ENST00000361337.2:c.1707T>G	p.Asn569Lys	p.N569K	ENST00000361337	NM_003286.2	569	aaT/aaG	16/21	0.325400570201404	4	FACETS	0.912	0.815	1	0.912	0.815	1	CLONAL	2	TRUE	2	0.440678127301345	4		499	301	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817520	39817520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	67	655	0	ENST00000288319.7:c.43G>A	p.Asp15Asn	p.D15N	ENST00000288319	NM_182918.3	15	Gac/Aac	2/10	0.440678127301345	4	FACETS	1	0.922	1	0.54	0.471	0.613	CLONAL	1	TRUE	2	0.440678127301345	4		655	406	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441310	52441310	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	50	575	0	ENST00000460680.1:c.460G>C	p.Glu154Gln	p.E154Q	ENST00000460680	NM_004656.3	154	Gag/Cag	7/17	0.440678127301345	3	FACETS	0.882	0.752	1	0.441	0.376	0.512	CLONAL	1	TRUE	1	0.440678127301345	3		575	314	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651407	52651407	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	66	770	1	ENST00000394830.3:c.1689G>T	p.Leu563Phe	p.L563F	ENST00000394830	NM_018313.4	563	ttG/ttT	15/30	0.440678127301345	3	FACETS	0.935	0.815	1	0.467	0.407	0.532	CLONAL	1	TRUE	1	0.440678127301345	3		771	391	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281172	142281172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866710163	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	56	509	0	ENST00000350721.4:c.1072C>T	p.Pro358Ser	p.P358S	ENST00000350721	NM_001184.3	358	Cca/Tca	4/47	0.440678127301345	3	FACETS	0.972	0.838	1	0.486	0.419	0.559	CLONAL	1	TRUE	1	0.440678127301345	3		509	319	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149498335	149498335	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748647567	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	68	843	0	ENST00000261799.4:c.2879G>A	p.Arg960Lys	p.R960K	ENST00000261799	NM_002609.3	960	aGa/aAa	21/23	0.440678127301345	2	FACETS	1	0.922	1	0.534	0.469	0.603	CLONAL	1	TRUE	0	0.440678127301345	2		843	289	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490518	20490518	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1379633990	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	117	656	1	ENST00000346618.3:c.1255G>A	p.Glu419Lys	p.E419K	ENST00000346618	NM_001949.4	419	Gaa/Aaa	7/7	0.440678127301345	5	FACETS	1	0.972	1	0.78	0.71	0.852	CLONAL	2	TRUE	2	0.440678127301345	5		657	377	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117632183	117632183	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	51	667	0	ENST00000368508.3:c.6233G>A	p.Arg2078Lys	p.R2078K	ENST00000368508	NM_002944.2	2078	aGg/aAg	39/43	0.195452871959919	4	FACETS	0.864	0.737	1	0.432	0.368	0.502	INDETERMINATE	1	TRUE	2	0.440678127301345	4		667	386	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997784	149997784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	113	634	0	ENST00000253339.5:c.2683G>A	p.Glu895Lys	p.E895K	ENST00000253339		895	Gag/Aag	5/7	0.440678127301345	4	FACETS	0.947	0.86	1	0.947	0.86	1	CLONAL	2	TRUE	2	0.440678127301345	4		634	390	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394422	162394422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	61	564	2	ENST00000366898.1:c.646C>T	p.Pro216Ser	p.P216S	ENST00000366898	NM_004562.2	216	Ccc/Tcc	6/12	0.440678127301345	4	FACETS	1	0.93	1	0.557	0.483	0.637	CLONAL	1	TRUE	2	0.440678127301345	4		566	358	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508580	106508580	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs796052174	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	70	373	1	ENST00000359195.3:c.574G>A	p.Asp192Asn	p.D192N	ENST00000359195	NM_002649.2	192	Gac/Aac	2/11	0.440678127301345	4	FACETS	0.995	0.88	1	0.995	0.88	1	CLONAL	2	TRUE	2	0.440678127301345	4		374	230	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545758	106545758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	110	798	0	ENST00000359195.3:c.3235G>A	p.Gly1079Arg	p.G1079R	ENST00000359195	NM_002649.2	1079	Gga/Aga	11/11	0.440678127301345	4	FACETS	0.842	0.762	0.926	0.842	0.762	0.926	CLONAL	2	TRUE	2	0.440678127301345	4		798	427	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922494	56922494	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	46	476	0	ENST00000519728.1:c.1364C>T	p.Ala455Val	p.A455V	ENST00000519728	NM_002350.3	455	gCc/gTc	13/13	0.440678127301345	4	FACETS	0.798	0.674	0.934	0.266	0.224	0.312	CLONAL	1	TRUE	1	0.440678127301345	4		476	377	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970964	70970964	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868518861	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	250	825	0	ENST00000276594.2:c.1297C>T	p.Pro433Ser	p.P433S	ENST00000276594	NM_024504.3	433	Ccc/Tcc	6/8	0.440678127301345	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	1	0.440678127301345	4		825	487	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737696	145737696	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	66	715	0	ENST00000428558.2:c.3067G>C	p.Gly1023Arg	p.G1023R	ENST00000428558	NM_004260.3	1023	Ggg/Cgg	19/22	0.440678127301345	7	FACETS	1	0.893	1	0.258	0.224	0.295	CLONAL	1	TRUE	3	0.440678127301345	7		715	610	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457304	5457304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	50	319	0	ENST00000381577.3:c.278C>T	p.Ser93Phe	p.S93F	ENST00000381577	NM_014143.3	93	tCc/tTc	3/7	0.440678127301345	4	FACETS	1	0.927	1	0.572	0.488	0.662	CLONAL	1	TRUE	2	0.440678127301345	4		319	286	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197324	27197324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	118	622	0	ENST00000380036.4:c.1636C>T	p.Pro546Ser	p.P546S	ENST00000380036	NM_000459.3	546	Cca/Tca	12/23	0.440678127301345	4	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	2	0.440678127301345	4		622	367	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206751	27206751	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779255150	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	120	559	0	ENST00000380036.4:c.2536G>A	p.Asp846Asn	p.D846N	ENST00000380036	NM_000459.3	846	Gat/Aat	15/23	0.440678127301345	4	FACETS	1	0.923	1	1	0.923	1	CLONAL	2	TRUE	2	0.440678127301345	4		559	387	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229538	98229538	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	46	583	1	ENST00000331920.6:c.2420C>T	p.Thr807Ile	p.T807I	ENST00000331920	NM_000264.3	807	aCc/aTc	15/24	0.268660092954013	5	FACETS	0.925	0.781	1	0.308	0.26	0.361	CLONAL	1	TRUE	2	0.440678127301345	5		584	375	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396249	139396250	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	106	842	2	ENST00000277541.6:c.5588_5589delinsTT	p.Pro1863Leu	p.P1863L	ENST00000277541	NM_017617.3	1863	cCC/cTT	30/34	0.268660092954013	5	FACETS	1	0.958	1	0.736	0.666	0.808	CLONAL	2	TRUE	2	0.440678127301345	5		844	362	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411276	63411276	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	118	428	0	ENST00000330258.3:c.1891C>G	p.Arg631Gly	p.R631G	ENST00000330258	NM_152424.3	631	Cga/Gga	2/2	0.3670709204001	2	FACETS	0.834	0.773	0.895			1	CLONAL	3	TRUE	NA	0.440678127301345	2		428	214	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411987	63411987	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	61	392	0	ENST00000330258.3:c.1180G>C	p.Glu394Gln	p.E394Q	ENST00000330258	NM_152424.3	394	Gaa/Caa	2/2	0.3670709204001	2	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.440678127301345	2		392	189	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665721	29665721	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0024233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	395	331	0	ENST00000356175.3:c.6757-1G>A		p.X2253_splice	ENST00000356175	NM_000267.3	2253			0.671551705598426	3	FACETS	0.986	0.956	1	0.986	0.956	1	CLONAL	3	FALSE	0	0.671551705598426	3		331	531	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138651	55138651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	490	558	0	ENST00000257290.5:c.1328C>T	p.Pro443Leu	p.P443L	ENST00000257290	NM_006206.4	443	cCt/cTt	9/23	0.558843046480463	3	FACETS	1	0.994	1			1	CLONAL	2	FALSE	NA	0.671551705598426	3		558	853	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0024234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	239	841	5	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.258491901987089	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.267194662373434	2		846	811	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743862	46743862	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs981989748	NA	P-0024234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	210	712	2	ENST00000371975.4:c.2152G>A	p.Glu718Lys	p.E718K	ENST00000371975	NM_003579.3	718	Gag/Aag	18/18	0.0835403935084302	4	FACETS	1	0.976	1	1	0.976	1	INDETERMINATE	2	TRUE	2	0.267194662373434	4		714	895	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610476	81610477	+	missense_variant	Missense_Mutation	DNP	CT	CT	AC	novel	NA	P-0024234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	62	509	0	ENST00000298171.2:c.2074_2075delinsAC	p.Leu692Thr	p.L692T	ENST00000298171	NM_000369.2	692	CTa/ACa	10/10	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.267194662373434	2		509	463	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042016	42042016	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	112	684	4	ENST00000219905.7:c.6211G>C	p.Ala2071Pro	p.A2071P	ENST00000219905	NM_001164273.1	2071	Gct/Cct	17/24	0.0835403935084302	4	FACETS	0.807	0.727	0.892	0.807	0.727	0.892	INDETERMINATE	2	TRUE	2	0.267194662373434	4		688	658	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579337	7579338	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TA	novel	NA	P-0024234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	144	868	4	ENST00000269305.4:c.349_350delinsTA	p.Gly117Ter	p.G117*	ENST00000269305	NM_001126112.2	117	GGg/TAg	4/11	0.248076324711437	2	FACETS	0.82	0.75	0.893	0.82	0.75	0.893	CLONAL	2	TRUE	0	0.267194662373434	2		872	657	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486068	29486068	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	37	720	2	ENST00000356175.3:c.245C>A	p.Ser82Tyr	p.S82Y	ENST00000356175	NM_000267.3	82	tCt/tAt	3/57	0.241655294319075	3	FACETS	0.787	0.649	0.94	0.393	0.324	0.47	CLONAL	1	TRUE	1	0.267194662373434	3		722	399	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600000	10600000	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	267	956	2	ENST00000171111.5:c.1576G>T	p.Asp526Tyr	p.D526Y	ENST00000171111	NM_203500.1	526	Gat/Tat	5/6	0.258491901987089	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.267194662373434	2		958	982	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132638	11132638	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	212	881	0	ENST00000358026.2:c.2854G>T	p.Glu952Ter	p.E952*	ENST00000358026	NM_001128849.1	952	Gaa/Taa	19/36	0.258491901987089	2	FACETS	0.955	0.889	1	0.955	0.889	1	CLONAL	2	TRUE	0	0.267194662373434	2		881	831	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546781	9546781	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	27	405	2	ENST00000353224.5:c.1241C>A	p.Pro414His	p.P414H	ENST00000353224	NM_177990.2	414	cCc/cAc	5/10	0.0835403935084302	4	FACETS	0.764	0.609	0.942	0.382	0.304	0.471	INDETERMINATE	1	TRUE	2	0.267194662373434	4		407	335	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090041	37090041	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793400	NA	P-0024234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	179	863	3	ENST00000231790.2:c.1930G>A	p.Asp644Asn	p.D644N	ENST00000231790	NM_000249.3	644	Gac/Aac	17/19	0.2488528215085	3	FACETS	0.906	0.836	0.979	0.906	0.836	0.979	CLONAL	2	TRUE	1	0.267194662373434	3		866	838	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671546	30671546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	583	898	6	ENST00000376406.3:c.5414C>T	p.Pro1805Leu	p.P1805L	ENST00000376406	NM_014641.2	1805	cCt/cTt	10/15	0.267194662373434	7	FACETS	0.99	0.952	1	0.99	0.952	1	CLONAL	5	TRUE	2	0.267194662373434	7		904	1471	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866538	56866538	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	127	1022	0	ENST00000519728.1:c.785G>T	p.Trp262Leu	p.W262L	ENST00000519728	NM_002350.3	262	tGg/tTg	8/13	0.224682367196976	4	FACETS	0.936	0.845	1	0.312	0.281	0.344	CLONAL	1	TRUE	1	0.267194662373434	4		1022	1287	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585361	29585361	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0024236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	169	625	1	ENST00000356175.3:c.4111-1G>T		p.X1371_splice	ENST00000356175	NM_000267.3	1371			0.362068899645722	2	FACETS	0.805	0.744	0.867	0.805	0.744	0.867	CLONAL	2	TRUE	0	0.371779071042856	2		626	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0024236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	291	971	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.254888647755863	2	FACETS	0.911	0.86	0.963	0.911	0.86	0.963	CLONAL	2	TRUE	0	0.371779071042856	2		973	859	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910349	29910349	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	234	1122	0	ENST00000376809.5:c.19C>T	p.Arg7Ter	p.R7*	ENST00000376809	NM_002116.7	7	Cga/Tga	1/8	0.167902002321712	3	FACETS	1	0.992	1	0.488	0.455	0.522	INDETERMINATE	1	TRUE	0	0.371779071042856	3		1122	1020	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592128	55592128	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	45	750	0	ENST00000288135.5:c.1452G>T	p.Lys484Asn	p.K484N	ENST00000288135	NM_000222.2	484	aaG/aaT	9/21	0.371779071042856	3	FACETS	0.335	0.28	0.395	0.112	0.093	0.132	SUBCLONAL	1	TRUE	0	0.371779071042856	3		750	858	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444486	50444486	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	111	395	0	ENST00000331340.3:c.416A>G	p.His139Arg	p.H139R	ENST00000331340	NM_006060.4	139	cAc/cGc	4/8	0.263345985919283	4	FACETS	1	0.983	1	0.741	0.668	0.817	CLONAL	1	TRUE	2	0.371779071042856	4		395	553	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851944	63851944	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	100	614	0	ENST00000279873.7:c.2722C>A	p.Leu908Met	p.L908M	ENST00000279873	NM_032199.2	908	Ctg/Atg	10/10	1	2	FACETS	0.838	0.749	0.932	0.838	0.749	0.932	CLONAL	1	TRUE	1	0.371779071042856	2		614	642	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003461	42003461	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	65	641	1	ENST00000219905.7:c.2998G>A	p.Asp1000Asn	p.D1000N	ENST00000219905	NM_001164273.1	1000	Gac/Aac	8/24	0.30273145584741	2	FACETS	0.55	0.476	0.629	0.275	0.238	0.315	SUBCLONAL	1	TRUE	0	0.371779071042856	2		642	636	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993758	72993758	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	127	525	0	ENST00000268489.5:c.287A>G	p.Glu96Gly	p.E96G	ENST00000268489	NM_006885.3	96	gAg/gGg	2/10	0.321990567520937	2	FACETS	0.806	0.736	0.878	0.806	0.736	0.878	CLONAL	2	TRUE	0	0.371779071042856	2		525	424	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130265	11130265	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0024236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	179	461	0	ENST00000358026.2:c.2506-2A>C		p.X836_splice	ENST00000358026	NM_001128849.1	836			0.362068899645722	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.371779071042856	2		461	459	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376221	225376221	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	207	685	0	ENST00000264414.4:c.733A>G	p.Ile245Val	p.I245V	ENST00000264414	NM_003590.4	245	Ata/Gta	6/16	0.362068899645722	2	FACETS	0.884	0.825	0.944	0.884	0.825	0.944	CLONAL	2	TRUE	0	0.371779071042856	2		685	630	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513574	41513574	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	154	642	0	ENST00000263253.7:c.478C>T	p.Gln160Ter	p.Q160*	ENST00000263253	NM_001429.3	160	Cag/Tag	2/31	0.321990567520937	2	FACETS	0.837	0.771	0.904	0.837	0.771	0.904	CLONAL	2	TRUE	0	0.371779071042856	2		642	495	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670848	134670848	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	77	450	0	ENST00000398015.3:c.759C>A	p.Cys253Ter	p.C253*	ENST00000398015	NM_004441.4	253	tgC/tgA	3/16	0.216279204085771	3	FACETS	1	0.968	1	0.646	0.571	0.727	INDETERMINATE	1	TRUE	1	0.371779071042856	3		450	380	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247384	153247384	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0024236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	78	305	1	ENST00000281708.4:c.1419-1G>C		p.X473_splice	ENST00000281708	NM_033632.3	473			0.321990567520937	2	FACETS	0.795	0.707	0.886	0.795	0.707	0.886	SUBCLONAL	2	TRUE	0	0.371779071042856	2		306	264	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665310	176665310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758774947	NA	P-0024236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	85	512	1	ENST00000439151.2:c.3994G>A	p.Glu1332Lys	p.E1332K	ENST00000439151	NM_022455.4	1332	Gag/Aag	7/23	0.180843059175507	4	FACETS	1	0.921	1	0.526	0.466	0.591	INDETERMINATE	1	TRUE	2	0.371779071042856	4		513	596	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554318	106554318	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	171	531	1	ENST00000369096.4:c.1846G>T	p.Ala616Ser	p.A616S	ENST00000369096	NM_001198.3	616	Gcc/Tcc	6/7	0.321990567520937	2	FACETS	0.814	0.753	0.877	0.814	0.753	0.877	CLONAL	2	TRUE	0	0.371779071042856	2		532	565	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374373	81374373	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	156	516	0	ENST00000222390.5:c.689A>T	p.Lys230Met	p.K230M	ENST00000222390	NM_000601.4	230	aAg/aTg	6/18	0.180843059175507	4	FACETS	0.909	0.836	0.986	0.909	0.836	0.986	INDETERMINATE	2	TRUE	2	0.371779071042856	4		516	633	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971117	21971117	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1334828764	NA	P-0024236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	114	502	0	ENST00000304494.5:c.241C>A	p.Pro81Thr	p.P81T	ENST00000304494	NM_000077.4	81	Ccc/Acc	2/3	0.371779071042856	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.371779071042856	1		502	419	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0024238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	58	790	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.895	0.768	1	0.895	0.768	1	CLONAL	1	TRUE	1	0.2	2		790	648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0024238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	58	811	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.163028065784102	1	FACETS	0.817	0.701	0.943	0.817	0.701	0.943	CLONAL	1	TRUE	0	0.2	1		812	639	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107175	27107175	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	61	700	0	ENST00000324856.7:c.6787del	p.Val2263TyrfsTer4	p.V2263Yfs*4	ENST00000324856	NM_006015.4	2262	tcG/tc	20/20	0.163028065784102	1	FACETS	0.865	0.745	0.994	0.865	0.745	0.994	CLONAL	1	TRUE	0	0.2	1		700	635	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606082	81606082	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	66	774	0	ENST00000298171.2:c.752A>C	p.Glu251Ala	p.E251A	ENST00000298171	NM_000369.2	251	gAa/gCa	9/10	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.2	2		774	650	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0024241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	711	808	3	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.7120087448194	2	FACETS	0.954	0.93	0.976	0.954	0.93	0.976	CLONAL	2	TRUE	0	0.747036452474827	2		811	998	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	148	795	9	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.961	0.878	1	0.961	0.878	1	CLONAL	1	FALSE	1	0.346054829512729	2		804	890	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	264	728	2	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	FALSE	1	0.346054829512729	2		730	730	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911514	131911514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143802516	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	120	594	1	ENST00000265335.6:c.259C>T	p.Arg87Cys	p.R87C	ENST00000265335		87	Cgt/Tgt	3/25	1	2	FACETS	0.923	0.834	1	0.923	0.834	1	CLONAL	1	FALSE	1	0.346054829512729	2		595	751	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106336	27106337	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	53	682	0	ENST00000324856.7:c.5952_5953del	p.Ser1985GlnfsTer13	p.S1985Qfs*13	ENST00000324856	NM_006015.4	1983	TGt/t	20/20	0.135660765740359	3	FACETS	0.397	0.337	0.463	0.199	0.168	0.232	INDETERMINATE	1	FALSE	1	0.346054829512729	3		682	905	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	82	725	5	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	0.817	0.721	0.919	0.817	0.721	0.919	CLONAL	1	FALSE	1	0.346054829512729	2		730	580	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641389	18641389	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1229278001	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	52	337	0	ENST00000266497.5:c.2393del	p.Asn798MetfsTer16	p.N798Mfs*16	ENST00000266497		796	ctA/ct	17/31	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.346054829512729	2		337	231	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	120	787	4	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	0.346054829512729	1	FACETS	0.832	0.753	0.916	0.832	0.753	0.916	CLONAL	1	FALSE	0	0.346054829512729	1		791	689	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932018	39932018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367736022	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	84	790	1	ENST00000378444.4:c.2581C>T	p.Arg861Cys	p.R861C	ENST00000378444	NM_001123385.1	861	Cgc/Tgc	4/15	NA	2	FACETS	0.61	0.538	0.687			1	INDETERMINATE	1	FALSE	NA	0.346054829512729	2		791	796	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	96	959	1	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	NA	2	FACETS	0.702	0.625	0.784			1	INDETERMINATE	1	FALSE	NA	0.346054829512729	2		960	790	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977554	2977554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs992263343	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	70	696	0	ENST00000396946.4:c.1130G>A	p.Arg377Gln	p.R377Q	ENST00000396946	NM_032415.4	377	cGg/cAg	8/25	0.346054829512729	1	FACETS	0.548	0.477	0.623	0.548	0.477	0.623	SUBCLONAL	1	FALSE	0	0.346054829512729	1		696	611	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302456	15302456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749561286	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	132	818	3	ENST00000263388.2:c.815C>T	p.Thr272Met	p.T272M	ENST00000263388	NM_000435.2	272	aCg/aTg	6/33	1	2	FACETS	0.977	0.887	1	0.977	0.887	1	CLONAL	1	FALSE	1	0.346054829512729	2		821	781	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900171	101900171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564161322	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	44	360	1	ENST00000374994.4:c.605C>T	p.Ala202Val	p.A202V	ENST00000374994	NM_004612.2	202	gCg/gTg	4/9	0.135660765740359	3	FACETS	0.616	0.517	0.726	0.308	0.258	0.363	INDETERMINATE	1	FALSE	1	0.346054829512729	3		361	484	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023045	150023045	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1175780468	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	152	756	0	ENST00000253339.5:c.218C>T	p.Thr73Met	p.T73M	ENST00000253339		73	aCg/aTg	1/7	0.135660765740359	3	FACETS	1	0.972	1	0.572	0.523	0.624	INDETERMINATE	1	FALSE	1	0.346054829512729	3		756	900	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	136	771	4	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.986	0.897	1	0.986	0.897	1	CLONAL	1	FALSE	1	0.346054829512729	2		775	797	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007332	143007332	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	106	540	2	ENST00000262992.4:c.2452del	p.Arg818GlufsTer4	p.R818Efs*4	ENST00000262992	NM_001101669.1	818	Aga/ga	22/24	1	2	FACETS	0.966	0.868	1	0.966	0.868	1	CLONAL	1	FALSE	1	0.346054829512729	2		542	634	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741573	17741573	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1285231710	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	34	400	0	ENST00000250003.3:c.244C>T	p.Arg82Cys	p.R82C	ENST00000250003	NM_002478.4	82	Cgc/Tgc	1/3	0.21563428650872	0	FACETS	0.42	0.344	0.505			1	SUBCLONAL	1	FALSE	0	0.346054829512729	0		400	306	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	101	804	4	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	0.346054829512729	1	FACETS	0.681	0.609	0.757	0.681	0.609	0.757	SUBCLONAL	1	FALSE	0	0.346054829512729	1		808	709	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63537616	63537616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	152	792	1	ENST00000307078.5:c.1016G>A	p.Arg339His	p.R339H	ENST00000307078	NM_004655.3	339	cGc/cAc	4/11	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	FALSE	1	0.346054829512729	2		793	865	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107135	27107136	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	155	657	0	ENST00000324856.7:c.6747dup	p.Glu2250ArgfsTer28	p.E2250Rfs*28	ENST00000324856	NM_006015.4	2249	tca/tcAa	20/20	0.135660765740359	3	FACETS	1	0.974	1	0.579	0.53	0.631	INDETERMINATE	1	FALSE	1	0.346054829512729	3		657	907	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588108	69588108	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	107	713	0	ENST00000168712.1:c.590T>C	p.Met197Thr	p.M197T	ENST00000168712	NM_002007.2	197	aTg/aCg	3/3	1	2	FACETS	0.899	0.807	0.996	0.899	0.807	0.996	CLONAL	1	FALSE	1	0.346054829512729	2		713	688	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163554	32163554	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	115	595	3	ENST00000375023.3:c.5672del	p.Gly1891AlafsTer13	p.G1891Afs*13	ENST00000375023	NM_004557.3	1891	gGc/gc	30/30	0.0861254152743449	4	FACETS	1	0.974	1	0.62	0.559	0.685	INDETERMINATE	1	FALSE	2	0.346054829512729	4		598	721	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966872	25966873	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	70	599	0	ENST00000435504.4:c.2333dup	p.Val779SerfsTer25	p.V779Sfs*25	ENST00000435504		778	cca/ccCa	13/13	0.346054829512729	1	FACETS	0.638	0.557	0.726	0.638	0.557	0.726	SUBCLONAL	1	FALSE	0	0.346054829512729	1		599	524	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891137	101891137	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1554698880	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	101	321	0	ENST00000374994.4:c.98C>T	p.Ala33Val	p.A33V	ENST00000374994	NM_004612.2	33	gCg/gTg	2/9	0.135660765740359	3	FACETS	0.813	0.732	0.899	0.813	0.732	0.899	INDETERMINATE	2	FALSE	1	0.346054829512729	3		321	421	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979986	7979987	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs746723399	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	119	744	1	ENST00000319144.4:c.1350dup	p.Leu451AlafsTer27	p.L451Afs*27	ENST00000319144	NM_001139.2	450	-/G	10/15	0.288816487563555	3	FACETS	0.917	0.827	1	0.458	0.413	0.506	CLONAL	1	FALSE	1	0.346054829512729	3		745	880	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88677065	88677065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765530074	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	140	755	5	ENST00000372037.3:c.850C>T	p.Arg284Cys	p.R284C	ENST00000372037	NM_004329.2	284	Cgc/Tgc	9/13	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	1	0.346054829512729	2		760	772	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204992	128204992	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	79	713	0	ENST00000341105.2:c.449del	p.Gly150GlufsTer68	p.G150Efs*68	ENST00000341105	NM_032638.4	150	gGa/ga	3/6	0.230823783673698	0	FACETS	0.576	0.508	0.65			1	SUBCLONAL	1	FALSE	0	0.346054829512729	0		713	518	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73352418	73352418	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	135	704	3	ENST00000377767.4:c.487del	p.Met163CysfsTer12	p.M163Cfs*12	ENST00000377767	NM_014953.3	163	Atg/tg	3/21	1	2	FACETS	0.919	0.835	1	0.919	0.835	1	CLONAL	1	FALSE	1	0.346054829512729	2		707	849	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265446	152265446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371610514	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	55	602	0	ENST00000206249.3:c.899G>A	p.Arg300His	p.R300H	ENST00000206249	NM_000125.3	300	cGc/cAc	4/8	0.135660765740359	3	FACETS	0.694	0.594	0.804	0.347	0.297	0.402	INDETERMINATE	1	FALSE	1	0.346054829512729	3		602	537	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106539	27106539	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	161	888	0	ENST00000324856.7:c.6150G>A	p.Trp2050Ter	p.W2050*	ENST00000324856	NM_006015.4	2050	tgG/tgA	20/20	0.135660765740359	3	FACETS	0.989	0.905	1	0.494	0.452	0.538	INDETERMINATE	1	FALSE	1	0.346054829512729	3		888	1104	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248394	59248394	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	97	474	0	ENST00000371222.2:c.349G>T	p.Ala117Ser	p.A117S	ENST00000371222	NM_002228.3	117	Gcc/Tcc	1/1	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.346054829512729	2		474	439	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434561	49434562	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	75	769	0	ENST00000301067.7:c.6991dup	p.Leu2331ProfsTer46	p.L2331Pfs*46	ENST00000301067	NM_003482.3	2331	ctg/cCtg	31/54	0.0861254152743449	4	FACETS	0.727	0.636	0.825	0.363	0.318	0.413	INDETERMINATE	1	FALSE	2	0.346054829512729	4		769	803	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112323	115112324	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	rs1381943852	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	46	233	0	ENST00000257566.3:c.1416_1417del	p.Leu473ProfsTer218	p.L473Pfs*218	ENST00000257566	NM_016569.3	472	gcGCtc/gctc	7/8	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	FALSE	1	0.346054829512729	2		233	242	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483867	88483867	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	102	799	0	ENST00000360948.2:c.1703T>C	p.Leu568Pro	p.L568P	ENST00000360948	NM_001012338.2	568	cTt/cCt	14/19	0.346054829512729	1	FACETS	0.795	0.713	0.883	0.795	0.713	0.883	SUBCLONAL	1	FALSE	0	0.346054829512729	1		799	613	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830138	72830138	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	71	634	1	ENST00000268489.5:c.6443C>A	p.Pro2148His	p.P2148H	ENST00000268489	NM_006885.3	2148	cCt/cAt	9/10	0.21563428650872	0	FACETS	0.47	0.41	0.534			1	SUBCLONAL	1	FALSE	0	0.346054829512729	0		635	571	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857686	59857686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781321	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	147	553	1	ENST00000259008.2:c.1871C>T	p.Ser624Leu	p.S624L	ENST00000259008	NM_032043.2	624	tCg/tTg	13/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.346054829512729	2		554	724	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681710	78681710	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	122	671	0	ENST00000306801.3:c.418A>G	p.Asn140Asp	p.N140D	ENST00000306801	NM_020761.2	140	Aac/Gac	4/34	1	2	FACETS	0.917	0.829	1	0.917	0.829	1	CLONAL	1	FALSE	1	0.346054829512729	2		671	769	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085768	16085768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	48	641	0	ENST00000281043.3:c.944C>T	p.Ser315Phe	p.S315F	ENST00000281043	NM_005378.4	315	tCc/tTc	3/3	0.346054829512729	1	FACETS	0.566	0.48	0.661	0.566	0.48	0.661	SUBCLONAL	1	FALSE	0	0.346054829512729	1		641	405	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46611745	46611745	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	170	782	0	ENST00000263734.3:c.2559C>A	p.Ser853Arg	p.S853R	ENST00000263734	NM_001430.4	853	agC/agA	16/16	0.346054829512729	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	0	0.346054829512729	1		782	685	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017757	31017757	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1318312862	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	88	735	0	ENST00000375687.4:c.619A>G	p.Ser207Gly	p.S207G	ENST00000375687	NM_015338.5	207	Agc/Ggc	8/13	1	2	FACETS	0.809	0.717	0.906	0.809	0.717	0.906	CLONAL	1	FALSE	1	0.346054829512729	2		735	629	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022281	31022281	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	72	481	0	ENST00000375687.4:c.1766C>A	p.Pro589His	p.P589H	ENST00000375687	NM_015338.5	589	cCc/cAc	13/13	1	2	FACETS	0.738	0.645	0.837	0.738	0.645	0.837	SUBCLONAL	1	FALSE	1	0.346054829512729	2		481	564	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267849	46267849	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	106	738	0	ENST00000371998.3:c.2615del	p.Asn872IlefsTer20	p.N872Ifs*20	ENST00000371998		870	gtA/gt	14/23	1	2	FACETS	0.709	0.635	0.788	0.709	0.635	0.788	SUBCLONAL	1	FALSE	1	0.346054829512729	2		738	864	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070868	30070868	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771143279	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	127	728	0	ENST00000338641.4:c.1384C>T	p.Arg462Cys	p.R462C	ENST00000338641	NM_000268.3	462	Cgc/Tgc	13/16	0.0861254152743449	4	FACETS	1	0.977	1	0.627	0.568	0.689	INDETERMINATE	1	FALSE	2	0.346054829512729	4		728	788	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911071	29911071	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199474487	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	237	1143	1	ENST00000376809.5:c.370G>T	p.Gly124Cys	p.G124C	ENST00000376809	NM_002116.7	124	Ggc/Tgc	3/8	0.0861254152743449	4	FACETS	1	0.99	1	0.692	0.644	0.741	INDETERMINATE	1	FALSE	2	0.346054829512729	4		1144	1332	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820974	32820974	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	239	1045	1	ENST00000354258.4:c.620C>T	p.Ala207Val	p.A207V	ENST00000354258	NM_000593.5	207	gCa/gTa	1/11	0.0861254152743449	4	FACETS	1	0.989	1	0.661	0.615	0.708	INDETERMINATE	1	FALSE	2	0.346054829512729	4		1046	1407	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528355	157528355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	115	832	0	ENST00000346085.5:c.6080C>T	p.Thr2027Met	p.T2027M	ENST00000346085	NM_020732.3	2027	aCg/aTg	20/20	0.135660765740359	3	FACETS	0.776	0.698	0.859	0.388	0.349	0.43	INDETERMINATE	1	FALSE	1	0.346054829512729	3		832	1005	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528564	157528564	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	171	802	0	ENST00000346085.5:c.6289G>C	p.Asp2097His	p.D2097H	ENST00000346085	NM_020732.3	2097	Gac/Cac	20/20	0.135660765740359	3	FACETS	1	0.984	1	0.637	0.586	0.69	INDETERMINATE	1	FALSE	1	0.346054829512729	3		802	910	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528628	157528628	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	120	817	0	ENST00000346085.5:c.6353A>G	p.Tyr2118Cys	p.Y2118C	ENST00000346085	NM_020732.3	2118	tAc/tGc	20/20	0.135660765740359	3	FACETS	0.975	0.881	1	0.488	0.44	0.538	INDETERMINATE	1	FALSE	1	0.346054829512729	3		817	834	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979408	2979408	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	99	709	4	ENST00000396946.4:c.839del	p.Asn280ThrfsTer86	p.N280Tfs*86	ENST00000396946	NM_032415.4	280	aAc/ac	6/25	0.346054829512729	1	FACETS	0.704	0.629	0.784	0.704	0.629	0.784	SUBCLONAL	1	FALSE	0	0.346054829512729	1		713	672	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212783	27212783	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754385594	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	128	910	3	ENST00000380036.4:c.2765C>T	p.Thr922Met	p.T922M	ENST00000380036	NM_000459.3	922	aCg/aTg	17/23	0.346054829512729	2	FACETS	0.823	0.745	0.905	0.411	0.372	0.453	CLONAL	1	FALSE	0	0.346054829512729	2		913	899	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222750	53222750	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782171515	NA	P-0024243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	108	987	3	ENST00000375401.3:c.4186C>T	p.Arg1396Trp	p.R1396W	ENST00000375401	NM_004187.3	1396	Cgg/Tgg	25/26	0.346054829512729	1	FACETS	0.622	0.558	0.69	0.622	0.558	0.69	SUBCLONAL	1	FALSE	0	0.346054829512729	1		990	830	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0024245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	516	683	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.904089230749732	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.904089230749732	1		683	612	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932373	36932373	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	572	917	0	ENST00000361632.4:c.2096T>A	p.Leu699Gln	p.L699Q	ENST00000361632		699	cTg/cAg	16/16	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.904089230749732	2		917	1244	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434324	49434324	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	628	1067	0	ENST00000301067.7:c.7229G>T	p.Arg2410Leu	p.R2410L	ENST00000301067	NM_003482.3	2410	cGa/cTa	31/54	1	2	FACETS	0.969	0.935	1	0.969	0.935	1	CLONAL	1	TRUE	1	0.904089230749732	2		1067	1433	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881543	48881543	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0024245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	136	416	0	ENST00000267163.4:c.264+1G>C		p.X88_splice	ENST00000267163	NM_000321.2	88			0.904089230749732	1	FACETS	0.975	0.93	1	0.975	0.93	1	CLONAL	1	TRUE	0	0.904089230749732	1		416	169	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268828	41268828	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	266	658	0	ENST00000349496.5:c.1066G>T	p.Ala356Ser	p.A356S	ENST00000349496	NM_001904.3	356	Gct/Tct	7/15	0.904089230749732	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.904089230749732	1		658	320	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038452	180038452	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs744282	NA	P-0024245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	477	901	0	ENST00000261937.6:c.3565C>A	p.Arg1189Ser	p.R1189S	ENST00000261937	NM_182925.4	1189	Cgc/Agc	27/30	1	2	FACETS	0.899	0.861	0.937	0.899	0.861	0.937	CLONAL	1	TRUE	1	0.904089230749732	2		901	1174	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521944	157521944	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	369	631	1	ENST00000346085.5:c.4216C>A	p.Gln1406Lys	p.Q1406K	ENST00000346085	NM_020732.3	1406	Cag/Aag	18/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.904089230749732	2		632	808	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987145	36987145	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	31	854	0	ENST00000354822.5:c.544A>T	p.Asn182Tyr	p.N182Y	ENST00000354822	NM_001079668.2	182	Aac/Tac	3/3	0.3	1	FACETS	0.373	0.301	0.454	0.373	0.301	0.454	SUBCLONAL	1	TRUE	0	0.28	1		854	511	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692896	89692896	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs398123322	NA	P-0024249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	262	646	0	ENST00000371953.3:c.380G>T	p.Gly127Val	p.G127V	ENST00000371953	NM_000314.4	127	gGa/gTa	5/9	0.644227259118967	2	FACETS	0.945	0.902	0.987	0.945	0.902	0.987	CLONAL	2	TRUE	0	0.655507957026543	2		646	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057520000	NA	P-0024249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	761	1145	0	ENST00000269305.4:c.452C>G	p.Pro151Arg	p.P151R	ENST00000269305	NM_001126112.2	151	cCc/cGc	5/11	0.632949414052406	4	FACETS	0.961	0.94	0.981	0.961	0.94	0.981	CLONAL	4	TRUE	0	0.655507957026543	4		1145	1000	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262293	16262294	+	missense_variant	Missense_Mutation	DNP	GC	GC	CT	novel	NA	P-0024249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	21	320	0	ENST00000375759.3:c.9558_9559delinsCT	p.His3187Tyr	p.H3187Y	ENST00000375759	NM_015001.2	3186	ctGCac/ctCTac	11/15	0.530727386404512	5	FACETS	0.318	0.244	0.404	0.106	0.081	0.135	SUBCLONAL	1	TRUE	2	0.655507957026543	5		320	400	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930652	32930652	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881557	NA	P-0024249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	289	608	1	ENST00000380152.3:c.7523G>A	p.Gly2508Asp	p.G2508D	ENST00000380152		2508	gGc/gAc	15/27	0.655507957026543	2	FACETS	0.922	0.881	0.963	0.922	0.881	0.963	CLONAL	2	TRUE	0	0.655507957026543	2		609	478	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709079	117709079	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs776365305	NA	P-0024249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	46	803	0	ENST00000368508.3:c.1878C>G	p.Phe626Leu	p.F626L	ENST00000368508	NM_002944.2	626	ttC/ttG	13/43	0.655507957026543	3	FACETS	0.241	0.202	0.284	0.121	0.101	0.142	SUBCLONAL	1	TRUE	1	0.655507957026543	3		803	773	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0024251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	209	780	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.509066483392368	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.509066483392368	1		780	591	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675607	86675607	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	109	435	0	ENST00000274376.6:c.2543T>C	p.Leu848Pro	p.L848P	ENST00000274376	NM_002890.2	848	cTa/cCa	19/25	1	2	FACETS	0.879	0.794	0.969	0.879	0.794	0.969	CLONAL	1	TRUE	1	0.509066483392368	2		435	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0024258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	283	917	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.544822814359026	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.544822814359026	1		918	566	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953214	81953214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369516453	NA	P-0024258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	176	484	2	ENST00000359376.3:c.2180G>A	p.Arg727Gln	p.R727Q	ENST00000359376	NM_002661.3	727	cGa/cAa	20/33	0.500900846829519	3	FACETS	0.983	0.917	1	0.983	0.917	1	CLONAL	2	TRUE	1	0.544822814359026	3		486	418	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248501	59248502	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	215	839	0	ENST00000371222.2:c.241dup	p.Ile81AsnfsTer26	p.I81Nfs*26	ENST00000371222	NM_002228.3	81	atc/aAtc	1/1	0.544822814359026	2	FACETS	1	0.981	1	0.566	0.528	0.605	CLONAL	1	TRUE	0	0.544822814359026	2		839	697	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844393	156844395	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs768558242	NA	P-0024258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	190	1135	0	ENST00000524377.1:c.1231_1233del	p.Lys411del	p.K411del	ENST00000524377	NM_002529.3	409	gAGAag/gag	10/17	0.544822814359026	3	FACETS	0.819	0.756	0.884	0.409	0.378	0.442	CLONAL	1	TRUE	1	0.544822814359026	3		1135	1084	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492582	50492582	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	204	911	2	ENST00000394963.4:c.1478G>A	p.Arg493Gln	p.R493Q	ENST00000394963	NM_003076.4	493	cGa/cAa	12/13	0.544822814359026	3	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.544822814359026	3		913	808	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267451	7267451	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	74	689	0	ENST00000302850.5:c.557G>T	p.Cys186Phe	p.C186F	ENST00000302850	NM_000208.2	186	tGt/tTt	2/22	0.343697236112279	2	FACETS	0.534	0.468	0.604	0.267	0.234	0.302	SUBCLONAL	1	TRUE	0	0.544822814359026	2		689	509	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466897	57466897	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	76	372	0	ENST00000371085.3:c.116C>T	p.Ala39Val	p.A39V	ENST00000371085	NM_000516.4	39	gCc/gTc	1/13	0.461623260843729	4	FACETS	0.726	0.637	0.821	0.363	0.318	0.411	SUBCLONAL	1	TRUE	2	0.544822814359026	4		372	594	SUCCESS
ATR	545	MSKCC	GRCh37	3	142257420	142257420	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024259-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	149	660	0	ENST00000350721.4:c.3629C>T	p.Ser1210Phe	p.S1210F	ENST00000350721	NM_001184.3	1210	tCc/tTc	19/47	0.261509592071414	2	FACETS	1	0.988	1	0.739	0.678	0.802	CLONAL	1	FALSE	0	0.351221713908414	2		660	574	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485783	57485783	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024259-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	55	606	1	ENST00000371085.3:c.1084C>A	p.His362Asn	p.H362N	ENST00000371085	NM_000516.4	362	Cat/Aat	13/13	0.351221713908414	4	FACETS	0.491	0.419	0.57	0.123	0.104	0.143	SUBCLONAL	1	FALSE	0	0.351221713908414	4		607	862	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37628894	37628923	+	inframe_deletion	In_Frame_Del	DEL	TGTCCCACAGCCCCAGGTTCACTGGCTTGC	TGTCCCACAGCCCCAGGTTCACTGGCTTGC	-	novel	NA	P-0024259-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	331	1007	2	ENST00000249071.6:c.143_172del	p.Ser48_Asp57del	p.S48_D57del	ENST00000249071	NM_002872.4	48	aGCAAGCCAGTGAACCTGGGGCTGTGGGACAct/act	3/7	0.351221713908414	3	FACETS	0.808	0.763	0.855	0.808	0.763	0.855	CLONAL	2	FALSE	1	0.351221713908414	3		1009	1371	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185195165	185195165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024259-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	86	540	1	ENST00000265026.3:c.2482G>A	p.Glu828Lys	p.E828K	ENST00000265026	NM_004721.4	828	Gaa/Aaa	12/14	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.351221713908414	NA		541	625	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185195184	185195184	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024259-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	74	493	0	ENST00000265026.3:c.2501G>A	p.Arg834Lys	p.R834K	ENST00000265026	NM_004721.4	834	aGg/aAg	12/14	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.351221713908414	NA		493	575	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908225	41908225	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024259-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1229	91	1122	0	ENST00000372991.4:c.297G>T	p.Leu99Phe	p.L99F	ENST00000372991	NM_001760.3	99	ttG/ttT	2/5	1	2	FACETS	0.393	0.347	0.442	0.393	0.347	0.442	SUBCLONAL	1	FALSE	1	0.351221713908414	2		1122	1320	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870225	44870225	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024259-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	152	905	0	ENST00000377967.4:c.404G>T	p.Gly135Val	p.G135V	ENST00000377967	NM_021140.2	135	gGt/gTt	5/29	0.351221713908414	1	FACETS	0.854	0.781	0.929	0.854	0.781	0.929	CLONAL	1	FALSE	0	0.351221713908414	1		905	836	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106818	27106818	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	106	679	0	ENST00000324856.7:c.6430del	p.Leu2144TrpfsTer56	p.L2144Wfs*56	ENST00000324856	NM_006015.4	2143	cgC/cg	20/20	0.332611572866876	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.362019092967407	1		679	464	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273009	115273010	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	113	861	0	ENST00000438362.2:c.1363dup	p.Arg455LysfsTer3	p.R455Kfs*3	ENST00000438362	NM_001242891.1	455	agg/aAgg	12/20	0.332611572866876	1	FACETS	0.961	0.868	1	0.961	0.868	1	CLONAL	1	TRUE	0	0.362019092967407	1		861	532	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514278	69514278	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	113	725	0	ENST00000294312.3:c.403C>T	p.Arg135Ter	p.R135*	ENST00000294312	NM_005117.2	135	Cga/Tga	3/3	1	2	FACETS	0.944	0.851	1	0.944	0.851	1	CLONAL	1	TRUE	1	0.362019092967407	2		725	661	SUCCESS
APC	324	MSKCC	GRCh37	5	112175889	112175889	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	57	325	0	ENST00000257430.4:c.4598A>G	p.Asn1533Ser	p.N1533S	ENST00000257430	NM_000038.5	1533	aAt/aGt	16/16	0.332611572866876	1	FACETS	0.996	0.863	1	0.996	0.863	1	CLONAL	1	TRUE	0	0.362019092967407	1		325	259	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	146	855	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	0.309386584991003	2		855	850	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0024268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	156	846	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.309386584991003	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.309386584991003	1		847	778	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	200	855	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.0664065661214521	4	FACETS	1	0.936	1			1	INDETERMINATE	2	TRUE	NA	0.490440775257583	4		855	605	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0024286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	441	971	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.488496688114168	2	FACETS	0.965	0.925	1	0.965	0.925	1	CLONAL	2	TRUE	0	0.490440775257583	2		973	932	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0024286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	118	234	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.460761616170745	3	FACETS	0.868	0.802	0.934	0.868	0.802	0.934	CLONAL	3	TRUE	0	0.490440775257583	3		234	230	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852409	63852409	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376805718	NA	P-0024286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	328	635	0	ENST00000279873.7:c.3187G>A	p.Gly1063Arg	p.G1063R	ENST00000279873	NM_032199.2	1063	Ggg/Agg	10/10	0.490440775257583	2	FACETS	0.972	0.926	1	0.972	0.926	1	CLONAL	2	TRUE	0	0.490440775257583	2		635	688	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120612018	120612018	+	start_lost	Translation_Start_Site	SNP	C	C	G	rs56159748	NA	P-0024286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	12	90	0	ENST00000256646.2:c.3G>C	p.Met1?	p.M1?	ENST00000256646	NM_024408.3	1	atG/atC	1/34	0.490440775257583	3	FACETS	0.628	0.446	0.846	0.314	0.223	0.423	SUBCLONAL	1	TRUE	1	0.490440775257583	3		90	97	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416332	29416332	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	163	873	1	ENST00000389048.3:c.4621G>T	p.Val1541Phe	p.V1541F	ENST00000389048	NM_004304.4	1541	Gtc/Ttc	29/29	0.490440775257583	3	FACETS	0.851	0.78	0.924	0.425	0.39	0.462	CLONAL	1	TRUE	1	0.490440775257583	3		874	973	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99181178	99181178	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	149	614	0	ENST00000074304.5:c.2119T>G	p.Tyr707Asp	p.Y707D	ENST00000074304	NM_001134224.1	707	Tac/Gac	20/26	0.490440775257583	3	FACETS	0.896	0.819	0.977	0.448	0.409	0.489	CLONAL	1	TRUE	1	0.490440775257583	3		614	844	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560085	29560085	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	113	351	0	ENST00000356175.3:c.3562C>T	p.Gln1188Ter	p.Q1188*	ENST00000356175	NM_000267.3	1188	Caa/Taa	27/57	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.536200831981451	2		351	398	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50811826	50811826	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs886040872	NA	P-0024287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	142	677	0	ENST00000398568.2:c.1103C>A	p.Ser368Ter	p.S368*	ENST00000398568	NM_001042412.1	368	tCa/tAa	7/18	0.536200831981451	1	FACETS	0.934	0.86	1	0.934	0.86	1	CLONAL	1	TRUE	0	0.536200831981451	1		677	415	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664535	29664536	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	rs1131691084	NA	P-0024287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	177	600	0	ENST00000356175.3:c.6522_6523del	p.Glu2174AspfsTer46	p.E2174Dfs*46	ENST00000356175	NM_000267.3	2172	GAg/g	42/57	1	2	FACETS	0.953	0.881	1	0.953	0.881	1	CLONAL	1	TRUE	1	0.536200831981451	2		600	693	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375177	31375177	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs7354578	NA	P-0024287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	162	762	0	ENST00000328111.2:c.574G>T	p.Ala192Ser	p.A192S	ENST00000328111	NM_006892.3	192	Gcc/Tcc	6/23	1	2	FACETS	0.956	0.881	1	0.956	0.881	1	CLONAL	1	TRUE	1	0.536200831981451	2		762	632	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	290	622	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.703776103751158	2		622	725	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	198	795	9	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.748	0.695	0.803	0.748	0.695	0.803	SUBCLONAL	1	TRUE	1	0.703776103751158	2		804	752	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	365	1035	7	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.884	0.838	0.93	0.884	0.838	0.93	CLONAL	1	TRUE	1	0.703776103751158	2		1042	1174	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	174	693	2	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.636	0.587	0.688	0.636	0.587	0.688	SUBCLONAL	1	TRUE	1	0.703776103751158	2		695	777	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	192	516	3	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.828	0.769	0.888	0.828	0.769	0.888	CLONAL	1	TRUE	1	0.703776103751158	2		519	659	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	206	604	2	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.703776103751158	2		606	543	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	201	728	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.735	0.683	0.789	0.735	0.683	0.789	SUBCLONAL	1	TRUE	1	0.703776103751158	2		730	777	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	48	493	0	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	0.206	0.174	0.242	0.206	0.174	0.242	SUBCLONAL	1	TRUE	1	0.703776103751158	2		493	661	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749415085	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	191	411	0	ENST00000263967.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000263967	NM_006218.2	38	Cgt/Tgt	2/21	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.703776103751158	2		411	537	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	257	354	0	ENST00000397062.3:c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	NM_006164.4	34	Cga/Gga	2/5	0.169861373716029	3	FACETS	0.801	0.756	0.847	0.801	0.756	0.847	INDETERMINATE	2	TRUE	1	0.703776103751158	3		354	616	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851754	134851754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56396912	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	189	515	0	ENST00000398015.3:c.1160C>T	p.Thr387Met	p.T387M	ENST00000398015	NM_004441.4	387	aCg/aTg	5/16	1	2	FACETS	0.79	0.733	0.849	0.79	0.733	0.849	SUBCLONAL	1	TRUE	1	0.703776103751158	2		515	680	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	232	742	2	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.679	0.633	0.726	0.679	0.633	0.726	SUBCLONAL	1	TRUE	1	0.703776103751158	2		744	971	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	64	538	0	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	0.253	0.218	0.29	0.253	0.218	0.29	SUBCLONAL	1	TRUE	1	0.703776103751158	2		538	719	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101417	27101417	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	178	454	0	ENST00000324856.7:c.4703del	p.Pro1568LeufsTer44	p.P1568Lfs*44	ENST00000324856	NM_006015.4	1567	Ccc/cc	18/20	1	2	FACETS	0.831	0.769	0.894	0.831	0.769	0.894	CLONAL	1	TRUE	1	0.703776103751158	2		454	609	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176683975	176683975	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	59	586	0	ENST00000439151.2:c.4789A>T	p.Lys1597Ter	p.K1597*	ENST00000439151	NM_022455.4	1597	Aag/Tag	13/23	1	2	FACETS	0.204	0.175	0.236	0.204	0.175	0.236	SUBCLONAL	1	TRUE	1	0.703776103751158	2		586	821	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349754	89349755	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	272	869	0	ENST00000301030.4:c.3195dup	p.His1066ThrfsTer2	p.H1066Tfs*2	ENST00000301030	NM_001256183.1	1065	-/A	9/13	1	2	FACETS	0.74	0.694	0.786	0.74	0.694	0.786	SUBCLONAL	1	TRUE	1	0.703776103751158	2		869	1045	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	181	493	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.784	0.726	0.844	0.784	0.726	0.844	SUBCLONAL	1	TRUE	1	0.703776103751158	2		495	656	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874011	123874013	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs780061449	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	16	54	0	ENST00000330479.4:c.62_64del	p.Ala21del	p.A21del	ENST00000330479	NM_020382.3	14	gaGGCg/gag	2/9	1	2	FACETS	0.429	0.321	0.554	0.429	0.321	0.554	SUBCLONAL	1	TRUE	1	0.703776103751158	2		54	106	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030877	36030877	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751005087	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	48	509	1	ENST00000358208.4:c.1156G>A	p.Val386Ile	p.V386I	ENST00000358208		386	Gtc/Atc	10/12	1	2	FACETS	0.197	0.166	0.232	0.197	0.166	0.232	SUBCLONAL	1	TRUE	1	0.703776103751158	2		510	692	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591611	38591611	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121434313	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	199	494	0	ENST00000299084.4:c.70C>T	p.Arg24Ter	p.R24*	ENST00000299084	NM_152594.2	24	Cga/Tga	2/7	1	2	FACETS	0.824	0.767	0.884	0.824	0.767	0.884	CLONAL	1	TRUE	1	0.703776103751158	2		494	686	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660475	67660475	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	230	421	0	ENST00000264010.4:c.1375C>T	p.Gln459Ter	p.Q459*	ENST00000264010	NM_006565.3	459	Cag/Tag	8/12	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.703776103751158	2		421	610	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574081	41574081	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	29	453	0	ENST00000263253.7:c.6370del	p.Val2124SerfsTer10	p.V2124Sfs*10	ENST00000263253	NM_001429.3	2122	caG/ca	31/31	1	2	FACETS	0.149	0.119	0.183	0.149	0.119	0.183	SUBCLONAL	1	TRUE	1	0.703776103751158	2		453	553	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884833	111884833	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1174628091	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	52	399	0	ENST00000341259.2:c.922C>T	p.Arg308Ter	p.R308*	ENST00000341259	NM_005475.2	308	Cga/Tga	4/8	1	2	FACETS	0.338	0.288	0.393	0.338	0.288	0.393	SUBCLONAL	1	TRUE	1	0.703776103751158	2		399	437	SUCCESS
AXL	558	MSKCC	GRCh37	19	41749571	41749571	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200850031	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	57	634	0	ENST00000301178.4:c.1496G>A	p.Arg499His	p.R499H	ENST00000301178	NM_021913.4	499	cGc/cAc	12/20	1	2	FACETS	0.206	0.176	0.239	0.206	0.176	0.239	SUBCLONAL	1	TRUE	1	0.703776103751158	2		634	785	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871940	45871940	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142462393	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	48	669	0	ENST00000391945.4:c.308C>T	p.Pro103Leu	p.P103L	ENST00000391945	NM_000400.3	103	cCg/cTg	5/23	1	2	FACETS	0.159	0.134	0.187	0.159	0.134	0.187	SUBCLONAL	1	TRUE	1	0.703776103751158	2		669	858	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027807	48027807	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	136	412	2	ENST00000234420.5:c.2690del	p.Asn897IlefsTer9	p.N897Ifs*9	ENST00000234420	NM_000179.2	895	acA/ac	4/10	0.169861373716029	3	FACETS	0.862	0.787	0.941	0.431	0.393	0.471	INDETERMINATE	1	TRUE	1	0.703776103751158	3		414	606	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229306	36229306	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	46	674	2	ENST00000222270.7:c.7996G>A	p.Val2666Met	p.V2666M	ENST00000222270	NM_014727.1	2666	Gtg/Atg	37/37	1	2	FACETS	0.159	0.133	0.188	0.159	0.133	0.188	SUBCLONAL	1	TRUE	1	0.703776103751158	2		676	821	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953259	81953259	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756480279	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	20	291	0	ENST00000359376.3:c.2225G>A	p.Arg742His	p.R742H	ENST00000359376	NM_002661.3	742	cGc/cAc	20/33	1	2	FACETS	0.147	0.112	0.189	0.147	0.112	0.189	SUBCLONAL	1	TRUE	1	0.703776103751158	2		291	386	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120529701	120529701	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	53	468	0	ENST00000256646.2:c.756del	p.Phe252LeufsTer144	p.F252Lfs*144	ENST00000256646	NM_024408.3	252	ttT/tt	5/34	1	2	FACETS	0.264	0.225	0.307	0.264	0.225	0.307	SUBCLONAL	1	TRUE	1	0.703776103751158	2		468	570	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246490633	246490633	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	191	362	1	ENST00000388985.4:c.401A>T	p.Asn134Ile	p.N134I	ENST00000388985		134	aAc/aTc	5/12	0.703776103751158	3	FACETS	0.992	0.92	1	0.496	0.46	0.533	CLONAL	1	TRUE	1	0.703776103751158	3		363	740	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692896	89692897	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	398	378	0	ENST00000371953.3:c.383dup	p.Arg130ThrfsTer50	p.R130Tfs*50	ENST00000371953	NM_000314.4	127	gga/ggAa	5/9	0.703776103751158	2	FACETS	0.957	0.924	0.989	0.957	0.924	0.989	CLONAL	2	TRUE	0	0.703776103751158	2		378	591	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941843	71941843	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514511	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	214	537	2	ENST00000298229.2:c.1201C>T	p.Arg401Trp	p.R401W	ENST00000298229	NM_001567.3	401	Cgg/Tgg	11/28	1	2	FACETS	0.952	0.889	1	0.952	0.889	1	CLONAL	1	TRUE	1	0.703776103751158	2		539	639	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924704	94924704	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	453	816	0	ENST00000536441.1:c.206C>T	p.Ser69Phe	p.S69F	ENST00000536441	NM_144665.3	69	tCc/tTc	3/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.703776103751158	2		816	1149	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343580	118343580	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1368855534	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	206	545	0	ENST00000534358.1:c.1706C>T	p.Pro569Leu	p.P569L	ENST00000534358	NM_005933.3	569	cCg/cTg	3/36	1	2	FACETS	0.875	0.816	0.936	0.875	0.816	0.936	CLONAL	1	TRUE	1	0.703776103751158	2		545	669	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493997	56493997	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	204	629	0	ENST00000267101.3:c.3169A>G	p.Met1057Val	p.M1057V	ENST00000267101	NM_001982.3	1057	Atg/Gtg	26/28	1	2	FACETS	0.701	0.651	0.752	0.701	0.651	0.752	SUBCLONAL	1	TRUE	1	0.703776103751158	2		629	827	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623674	28623674	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	258	507	0	ENST00000241453.7:c.883G>A	p.Gly295Ser	p.G295S	ENST00000241453	NM_004119.2	295	Ggc/Agc	8/24	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.703776103751158	2		507	715	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557704	95557704	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	191	467	0	ENST00000393063.1:c.5365-2A>G		p.X1789_splice	ENST00000393063	NM_030621.3	1789			1	2	FACETS	0.761	0.706	0.818	0.761	0.706	0.818	SUBCLONAL	1	TRUE	1	0.703776103751158	2		467	713	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38545388	38545388	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	256	488	0	ENST00000299084.4:c.2T>C	p.Met1?	p.M1?	ENST00000299084	NM_152594.2	1	aTg/aCg	1/7	1	2	FACETS	0.917	0.862	0.974	0.917	0.862	0.974	CLONAL	1	TRUE	1	0.703776103751158	2		488	793	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003136	42003137	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	89	686	0	ENST00000219905.7:c.2678dup	p.Val894CysfsTer19	p.V894Cfs*19	ENST00000219905	NM_001164273.1	891	-/C	8/24	1	2	FACETS	0.279	0.247	0.314	0.279	0.247	0.314	SUBCLONAL	1	TRUE	1	0.703776103751158	2		686	905	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821142	72821142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147553973	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	324	666	3	ENST00000268489.5:c.11033C>T	p.Pro3678Leu	p.P3678L	ENST00000268489	NM_006885.3	3678	cCg/cTg	10/10	1	2	FACETS	0.963	0.912	1	0.963	0.912	1	CLONAL	1	TRUE	1	0.703776103751158	2		669	956	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821344	72821344	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	105	297	1	ENST00000268489.5:c.10831del	p.His3611ThrfsTer83	p.H3611Tfs*83	ENST00000268489	NM_006885.3	3611	Cac/ac	10/10	1	2	FACETS	0.628	0.566	0.694	0.628	0.566	0.694	SUBCLONAL	1	TRUE	1	0.703776103751158	2		298	475	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832056	72832056	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	48	540	0	ENST00000268489.5:c.4525G>A	p.Asp1509Asn	p.D1509N	ENST00000268489	NM_006885.3	1509	Gac/Aac	9/10	1	2	FACETS	0.198	0.166	0.232	0.198	0.166	0.232	SUBCLONAL	1	TRUE	1	0.703776103751158	2		540	690	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992952	72992952	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	263	834	2	ENST00000268489.5:c.1093del	p.Tyr365MetfsTer31	p.Y365Mfs*31	ENST00000268489	NM_006885.3	365	Tat/at	2/10	1	2	FACETS	0.688	0.645	0.733	0.688	0.645	0.733	SUBCLONAL	1	TRUE	1	0.703776103751158	2		836	1086	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89345525	89345525	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	90	346	0	ENST00000301030.4:c.7425del	p.Tyr2476ThrfsTer15	p.Y2476Tfs*15	ENST00000301030	NM_001256183.1	2475	tcC/tc	9/13	1	2	FACETS	0.737	0.66	0.818	0.737	0.66	0.818	SUBCLONAL	1	TRUE	1	0.703776103751158	2		346	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578452	7578452	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs377274728	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	229	729	0	ENST00000269305.4:c.478A>G	p.Met160Val	p.M160V	ENST00000269305	NM_001126112.2	160	Atg/Gtg	5/11	1	2	FACETS	0.715	0.667	0.764	0.715	0.667	0.764	SUBCLONAL	1	TRUE	1	0.703776103751158	2		729	910	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	147	642	0	ENST00000307078.5:c.1993_1994dup	p.Asn666AlafsTer24	p.N666Afs*24	ENST00000307078	NM_004655.3	665	ggc/ggGGc	8/11	1	2	FACETS	0.502	0.458	0.548	0.502	0.458	0.548	SUBCLONAL	1	TRUE	1	0.703776103751158	2		642	832	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371819	45371819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	42	433	0	ENST00000262160.6:c.1172C>T	p.Ala391Val	p.A391V	ENST00000262160	NM_005901.5	391	gCt/gTt	10/11	1	2	FACETS	0.183	0.152	0.217	0.183	0.152	0.217	SUBCLONAL	1	TRUE	1	0.703776103751158	2		433	652	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950343	17950343	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	310	701	0	ENST00000458235.1:c.1384C>A	p.Leu462Met	p.L462M	ENST00000458235	NM_000215.3	462	Ctg/Atg	10/24	1	2	FACETS	0.961	0.908	1	0.961	0.908	1	CLONAL	1	TRUE	1	0.703776103751158	2		701	917	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967707	18967707	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	156	566	3	ENST00000262803.5:c.1846A>G	p.Thr616Ala	p.T616A	ENST00000262803	NM_002911.3	616	Aca/Gca	14/24	1	2	FACETS	0.617	0.566	0.67	0.617	0.566	0.67	SUBCLONAL	1	TRUE	1	0.703776103751158	2		569	718	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223795	36223795	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	137	890	0	ENST00000222270.7:c.6348del	p.Phe2116LeufsTer3	p.F2116Lfs*3	ENST00000222270	NM_014727.1	2115	gaT/ga	28/37	1	2	FACETS	0.375	0.34	0.412	0.375	0.34	0.412	SUBCLONAL	1	TRUE	1	0.703776103751158	2		890	1038	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763510	41763510	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	209	453	0	ENST00000301178.4:c.2309A>G	p.Gln770Arg	p.Q770R	ENST00000301178	NM_021913.4	770	cAg/cGg	19/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.703776103751158	2		453	590	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905530	50905530	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749052483	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	226	768	1	ENST00000440232.2:c.658G>A	p.Val220Met	p.V220M	ENST00000440232	NM_002691.3	220	Gtg/Atg	6/27	1	2	FACETS	0.724	0.675	0.774	0.724	0.675	0.774	SUBCLONAL	1	TRUE	1	0.703776103751158	2		769	887	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439679	220439679	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372427524	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	223	698	1	ENST00000243786.2:c.532G>A	p.Val178Met	p.V178M	ENST00000243786	NM_002191.3	178	Gtg/Atg	2/2	0.169861373716029	3	FACETS	0.975	0.909	1	0.487	0.454	0.522	INDETERMINATE	1	TRUE	1	0.703776103751158	3		699	879	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39706276	39706276	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	27	240	0	ENST00000361337.2:c.334A>G	p.Ser112Gly	p.S112G	ENST00000361337	NM_003286.2	112	Agt/Ggt	5/21	1	2	FACETS	0.2	0.159	0.247	0.2	0.159	0.247	SUBCLONAL	1	TRUE	1	0.703776103751158	2		240	384	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292848	62292848	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	63	210	0	ENST00000360203.5:c.300A>G	p.Ile100Met	p.I100M	ENST00000360203	NM_001283009.1	100	atA/atG	3/35	1	2	FACETS	0.806	0.707	0.911	0.806	0.707	0.911	CLONAL	1	TRUE	1	0.703776103751158	2		210	222	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191606	10191606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754016774	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	42	522	0	ENST00000256474.2:c.599G>A	p.Arg200Gln	p.R200Q	ENST00000256474	NM_000551.3	200	cGg/cAg	3/3	1	2	FACETS	0.161	0.133	0.191	0.161	0.133	0.191	SUBCLONAL	1	TRUE	1	0.703776103751158	2		522	743	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668640	52668640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	265	583	0	ENST00000394830.3:c.1279C>T	p.Pro427Ser	p.P427S	ENST00000394830	NM_018313.4	427	Ccc/Tcc	12/30	1	2	FACETS	0.886	0.833	0.94	0.886	0.833	0.94	CLONAL	1	TRUE	1	0.703776103751158	2		583	850	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430639	181430639	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	160	501	1	ENST00000325404.1:c.491A>G	p.Asn164Ser	p.N164S	ENST00000325404	NM_003106.3	164	aAc/aGc	1/1	1	2	FACETS	0.641	0.589	0.695	0.641	0.589	0.695	SUBCLONAL	1	TRUE	1	0.703776103751158	2		502	709	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294400	1294400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765833936	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	176	570	4	ENST00000310581.5:c.601C>T	p.Arg201Trp	p.R201W	ENST00000310581	NM_198253.2	201	Cgg/Tgg	2/16	NA	2	FACETS	0.627	0.578	0.677			1	INDETERMINATE	1	TRUE	NA	0.703776103751158	2		574	798	SUCCESS
APC	324	MSKCC	GRCh37	5	112177642	112177643	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs587780602	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	96	354	0	ENST00000257430.4:c.6363_6365dup	p.Ala2122dup	p.A2122dup	ENST00000257430	NM_000038.5	2122	-/GCT	16/16	1	2	FACETS	0.608	0.544	0.674	0.608	0.544	0.674	SUBCLONAL	1	TRUE	1	0.703776103751158	2		354	449	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504305	149504305	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780819031	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	212	791	1	ENST00000261799.4:c.1897G>A	p.Val633Ile	p.V633I	ENST00000261799	NM_002609.3	633	Gtc/Atc	13/23	1	2	FACETS	0.71	0.661	0.761	0.71	0.661	0.761	SUBCLONAL	1	TRUE	1	0.703776103751158	2		792	848	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687121	176687121	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784137	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	66	491	1	ENST00000439151.2:c.5098C>T	p.Arg1700Ter	p.R1700*	ENST00000439151	NM_022455.4	1700	Cga/Tga	14/23	1	2	FACETS	0.234	0.203	0.269	0.234	0.203	0.269	SUBCLONAL	1	TRUE	1	0.703776103751158	2		492	800	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045854	180045854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1400281005	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	55	588	0	ENST00000261937.6:c.2917C>T	p.Arg973Trp	p.R973W	ENST00000261937	NM_182925.4	973	Cgg/Tgg	21/30	1	2	FACETS	0.24	0.204	0.278	0.24	0.204	0.278	SUBCLONAL	1	TRUE	1	0.703776103751158	2		588	652	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190474	32190474	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	189	753	0	ENST00000375023.3:c.265G>T	p.Gly89Trp	p.G89W	ENST00000375023	NM_004557.3	89	Ggg/Tgg	3/30	1	2	FACETS	0.618	0.572	0.666	0.618	0.572	0.666	SUBCLONAL	1	TRUE	1	0.703776103751158	2		753	869	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099445	157099450	+	inframe_deletion	In_Frame_Del	DEL	CAGCAA	CAGCAA	-	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	72	359	0	ENST00000346085.5:c.390_395del	p.Gln130_Gln131del	p.Q130_Q131del	ENST00000346085	NM_020732.3	128	CAGCAA/-	1/20	1	2	FACETS	0.331	0.289	0.376	0.331	0.289	0.376	SUBCLONAL	1	TRUE	1	0.703776103751158	2		359	619	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214387	55214388	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	228	715	1	ENST00000275493.2:c.516dup	p.Leu173SerfsTer19	p.L173Sfs*19	ENST00000275493	NM_005228.3	171	-/T	4/28	1	2	FACETS	0.762	0.712	0.814	0.762	0.712	0.814	SUBCLONAL	1	TRUE	1	0.703776103751158	2		716	850	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476734	140476734	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	62	408	1	ENST00000288602.6:c.1672C>T	p.Arg558Ter	p.R558*	ENST00000288602	NM_004333.4	558	Cga/Tga	13/18	1	2	FACETS	0.285	0.245	0.327	0.285	0.245	0.327	SUBCLONAL	1	TRUE	1	0.703776103751158	2		409	619	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56882275	56882275	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	208	519	0	ENST00000519728.1:c.974-1G>T		p.X325_splice	ENST00000519728	NM_002350.3	325			1	2	FACETS	0.809	0.753	0.866	0.809	0.753	0.866	CLONAL	1	TRUE	1	0.703776103751158	2		519	731	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27168574	27168576	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	222	559	0	ENST00000380036.4:c.453_455del	p.Glu151del	p.E151del	ENST00000380036	NM_000459.3	149	aAAGaa/aaa	3/23	1	2	FACETS	0.701	0.653	0.75	0.701	0.653	0.75	SUBCLONAL	1	TRUE	1	0.703776103751158	2		559	900	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636209	87636209	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201902834	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	74	407	0	ENST00000277120.3:c.2374C>T	p.Arg792Cys	p.R792C	ENST00000277120		792	Cgc/Tgc	19/19	1	2	FACETS	0.397	0.348	0.449	0.397	0.348	0.449	SUBCLONAL	1	TRUE	1	0.703776103751158	2		407	530	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940082	76940082	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	186	475	0	ENST00000373344.5:c.666G>C	p.Trp222Cys	p.W222C	ENST00000373344	NM_000489.3	222	tgG/tgC	9/35	1	2	FACETS	0.716	0.663	0.771	0.716	0.663	0.771	SUBCLONAL	1	TRUE	1	0.703776103751158	2		475	738	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	54	571	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.21	2		571	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	85	699	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.21	2		699	770	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106492	108106492	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587781688	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	27	332	0	ENST00000278616.4:c.427A>G	p.Asn143Asp	p.N143D	ENST00000278616	NM_000051.3	143	Aac/Gac	5/63	1	2	FACETS	0.84	0.67	1	0.84	0.67	1	CLONAL	1	TRUE	1	0.21	2		332	306	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612975	228612975	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	47	366	0	ENST00000366696.1:c.52C>A	p.Arg18Ser	p.R18S	ENST00000366696	NM_003493.2	18	Cgc/Agc	1/1	0.179600992113038	3	FACETS	0.851	0.718	0.999	0.426	0.359	0.5	CLONAL	1	TRUE	1	0.21	3		366	581	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105565	27105565	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	52	578	0	ENST00000324856.7:c.5176G>T	p.Glu1726Ter	p.E1726*	ENST00000324856	NM_006015.4	1726	Gag/Tag	20/20	1	2	FACETS	0.831	0.707	0.967	0.831	0.707	0.967	CLONAL	1	TRUE	1	0.21	2		578	596	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609051	43609051	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	43	578	0	ENST00000355710.3:c.1807A>T	p.Lys603Ter	p.K603*	ENST00000355710	NM_020975.4	603	Aaa/Taa	10/20	0.179600992113038	3	FACETS	0.603	0.503	0.714	0.301	0.251	0.357	SUBCLONAL	1	TRUE	1	0.21	3		578	751	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514115	69514115	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	59	671	1	ENST00000294312.3:c.566C>T	p.Ser189Phe	p.S189F	ENST00000294312	NM_005117.2	189	tCt/tTt	3/3	1	2	FACETS	0.703	0.604	0.812	0.703	0.604	0.812	SUBCLONAL	1	TRUE	1	0.21	2		672	799	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376847	118376847	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	43	341	0	ENST00000534358.1:c.10240A>T	p.Thr3414Ser	p.T3414S	ENST00000534358	NM_005933.3	3414	Aca/Tca	27/36	1	2	FACETS	0.92	0.771	1	0.92	0.771	1	CLONAL	1	TRUE	1	0.21	2		341	445	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871757	12871757	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	35	220	1	ENST00000228872.4:c.476-2A>T		p.X159_splice	ENST00000228872	NM_004064.3	159			1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.21	2		221	302	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214642	133214642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145621558	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	101	484	1	ENST00000320574.5:c.5636G>A	p.Arg1879His	p.R1879H	ENST00000320574	NM_006231.2	1879	cGt/cAt	41/49	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.21	2		485	694	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281048	49281048	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	36	714	0	ENST00000282018.3:c.95C>G	p.Thr32Arg	p.T32R	ENST00000282018	NM_020377.2	32	aCa/aGa	1/1	1	2	FACETS	0.57	0.467	0.685	0.57	0.467	0.685	SUBCLONAL	1	TRUE	1	0.21	2		714	602	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65568292	65568292	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	29	180	0	ENST00000358664.4:c.37-2A>T		p.X13_splice	ENST00000358664	NM_002382.4	13			1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.21	2		180	229	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472474	88472474	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	62	625	0	ENST00000360948.2:c.2081A>T	p.Lys694Met	p.K694M	ENST00000360948	NM_001012338.2	694	aAg/aTg	16/19	1	2	FACETS	0.795	0.685	0.914	0.795	0.685	0.914	CLONAL	1	TRUE	1	0.21	2		625	743	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476354	88476354	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	78	649	0	ENST00000360948.2:c.1778C>G	p.Thr593Ser	p.T593S	ENST00000360948	NM_001012338.2	593	aCc/aGc	15/19	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.21	2		649	724	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857140	9857140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	29	385	0	ENST00000330684.3:c.4261G>A	p.Asp1421Asn	p.D1421N	ENST00000330684	NM_001134407.1	1421	Gat/Aat	13/13	1	2	FACETS	0.672	0.539	0.823	0.672	0.539	0.823	SUBCLONAL	1	TRUE	1	0.21	2		385	411	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857358	9857358	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	46	426	0	ENST00000330684.3:c.4043T>A	p.Leu1348Gln	p.L1348Q	ENST00000330684	NM_001134407.1	1348	cTg/cAg	13/13	1	2	FACETS	0.887	0.747	1	0.887	0.747	1	CLONAL	1	TRUE	1	0.21	2		426	494	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660575	67660575	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	61	644	0	ENST00000264010.4:c.1475A>G	p.Glu492Gly	p.E492G	ENST00000264010	NM_006565.3	492	gAg/gGg	8/12	1	2	FACETS	0.891	0.768	1	0.891	0.768	1	CLONAL	1	TRUE	1	0.21	2		644	652	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855902	68855902	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	23	359	0	ENST00000261769.5:c.1712-2A>G		p.X571_splice	ENST00000261769	NM_004360.3	571			1	2	FACETS	0.644	0.502	0.809	0.644	0.502	0.809	SUBCLONAL	1	TRUE	1	0.21	2		359	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573966	7573966	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	66	650	1	ENST00000269305.4:c.1061A>T	p.Gln354Leu	p.Q354L	ENST00000269305	NM_001126112.2	354	cAg/cTg	10/11	1	2	FACETS	0.817	0.708	0.936	0.817	0.708	0.936	CLONAL	1	TRUE	1	0.21	2		651	769	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805639	46805639	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs771674803	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	67	712	0	ENST00000290295.7:c.317T>G	p.Leu106Arg	p.L106R	ENST00000290295	NM_006361.5	106	cTg/cGg	1/2	1	2	FACETS	0.646	0.56	0.741	0.646	0.56	0.741	SUBCLONAL	1	TRUE	1	0.21	2		712	987	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602560	10602560	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	66	659	0	ENST00000171111.5:c.1018A>T	p.Ser340Cys	p.S340C	ENST00000171111	NM_203500.1	340	Agc/Tgc	3/6	1	2	FACETS	0.806	0.698	0.923	0.806	0.698	0.923	CLONAL	1	TRUE	1	0.21	2		659	780	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933459	49933459	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	99	708	0	ENST00000296474.3:c.2731G>A	p.Gly911Arg	p.G911R	ENST00000296474	NM_002447.2	911	Ggg/Agg	11/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.21	2		708	774	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013714	170013714	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	80	555	0	ENST00000295797.4:c.1433A>C	p.Gln478Pro	p.Q478P	ENST00000295797	NM_002740.5	478	cAa/cCa	15/18	0.179600992113038	3	FACETS	0.829	0.731	0.933	0.829	0.731	0.933	CLONAL	2	TRUE	1	0.21	3		555	508	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161267	185161267	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	124	665	0	ENST00000265026.3:c.694A>G	p.Ile232Val	p.I232V	ENST00000265026	NM_004721.4	232	Atc/Gtc	4/14	0.179600992113038	3	FACETS	0.828	0.749	0.911	0.828	0.749	0.911	CLONAL	2	TRUE	1	0.21	3		665	788	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144657	55144657	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs756055115	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	28	381	0	ENST00000257290.5:c.2131A>G	p.Asn711Asp	p.N711D	ENST00000257290	NM_006206.4	711	Aac/Gac	15/23	1	2	FACETS	0.696	0.556	0.856	0.696	0.556	0.856	SUBCLONAL	1	TRUE	1	0.21	2		381	383	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146542	55146542	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	37	424	0	ENST00000257290.5:c.2216C>A	p.Thr739Asn	p.T739N	ENST00000257290	NM_006206.4	739	aCt/aAt	16/23	1	2	FACETS	0.866	0.714	1	0.866	0.714	1	CLONAL	1	TRUE	1	0.21	2		424	407	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218794	66218794	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs764118898	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	31	459	0	ENST00000273854.3:c.2264A>G	p.Tyr755Cys	p.Y755C	ENST00000273854	NM_004439.5	755	tAt/tGt	13/18	1	2	FACETS	0.802	0.649	0.975	0.802	0.649	0.975	CLONAL	1	TRUE	1	0.21	2		459	368	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197269	106197269	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	32	281	0	ENST00000380013.4:c.5602C>A	p.His1868Asn	p.H1868N	ENST00000380013	NM_001127208.2	1868	Cat/Aat	11/11	1	2	FACETS	0.806	0.655	0.977	0.806	0.655	0.977	CLONAL	1	TRUE	1	0.21	2		281	378	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79966066	79966066	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	68	621	0	ENST00000265081.6:c.730A>G	p.Lys244Glu	p.K244E	ENST00000265081	NM_002439.4	244	Aaa/Gaa	4/24	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.21	2		621	533	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681904	30681904	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	64	496	0	ENST00000376406.3:c.193G>T	p.Ala65Ser	p.A65S	ENST00000376406	NM_014641.2	65	Gcc/Tcc	3/15	1	2	FACETS	0.948	0.821	1	0.948	0.821	1	CLONAL	1	TRUE	1	0.21	2		496	643	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168942	32168942	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	74	900	2	ENST00000375023.3:c.4091C>A	p.Ala1364Asp	p.A1364D	ENST00000375023	NM_004557.3	1364	gCc/gAc	22/30	1	2	FACETS	0.771	0.673	0.877	0.771	0.673	0.877	SUBCLONAL	1	TRUE	1	0.21	2		902	914	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171618	32171618	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	73	741	0	ENST00000375023.3:c.3160C>A	p.Pro1054Thr	p.P1054T	ENST00000375023	NM_004557.3	1054	Ccc/Acc	20/30	1	2	FACETS	0.829	0.723	0.943	0.829	0.723	0.943	CLONAL	1	TRUE	1	0.21	2		741	839	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965572	93965572	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	34	465	0	ENST00000369303.4:c.2356G>T	p.Asp786Tyr	p.D786Y	ENST00000369303	NM_004440.3	786	Gat/Tat	13/17	1	2	FACETS	0.707	0.577	0.853	0.707	0.577	0.853	SUBCLONAL	1	TRUE	1	0.21	2		465	458	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679015	117679015	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	42	584	0	ENST00000368508.3:c.3806A>C	p.His1269Pro	p.H1269P	ENST00000368508	NM_002944.2	1269	cAc/cCc	24/43	1	2	FACETS	0.813	0.679	0.962	0.813	0.679	0.962	CLONAL	1	TRUE	1	0.21	2		584	492	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418967	116418967	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	51	350	0	ENST00000397752.3:c.3478A>T	p.Met1160Leu	p.M1160L	ENST00000397752	NM_000245.2	1160	Atg/Ttg	17/21	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.21	2		350	474	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151855974	151855974	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	54	575	0	ENST00000262189.6:c.11644A>G	p.Thr3882Ala	p.T3882A	ENST00000262189	NM_170606.2	3882	Act/Gct	44/59	1	2	FACETS	0.78	0.666	0.906	0.78	0.666	0.906	CLONAL	1	TRUE	1	0.21	2		575	659	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70967578	70967578	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	113	661	2	ENST00000276594.2:c.1445T>C	p.Val482Ala	p.V482A	ENST00000276594	NM_024504.3	482	gTc/gCc	7/8	0.274375417082605	3	FACETS	0.789	0.71	0.872	0.789	0.71	0.872	SUBCLONAL	2	TRUE	1	0.21	3		663	754	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015037	37015037	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	81	507	0	ENST00000358127.4:c.367del	p.Val123CysfsTer36	p.V123Cfs*36	ENST00000358127	NM_001280556.1	123	Gtg/tg	3/10	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.21	2		507	654	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128268624	128268624	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs367600280	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	96	701	0	ENST00000265960.3:c.1031A>G	p.Gln344Arg	p.Q344R	ENST00000265960	NM_001006617.1	344	cAg/cGg	8/12	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.21	2		701	899	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796771	135796771	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	53	320	0	ENST00000298552.3:c.716A>T	p.Asp239Val	p.D239V	ENST00000298552	NM_001162426.1	239	gAc/gTc	8/23	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.21	2		320	396	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390651	139390651	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	107	771	0	ENST00000277541.6:c.7540C>G	p.Pro2514Ala	p.P2514A	ENST00000277541	NM_017617.3	2514	Cct/Gct	34/34	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.21	2		771	940	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923198	39923198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	52	247	0	ENST00000378444.4:c.3510G>A	p.Trp1170Ter	p.W1170*	ENST00000378444	NM_001123385.1	1170	tgG/tgA	8/15	0.3	2	FACETS	0.934	0.802	1	0.934	0.802	1	CLONAL	2	TRUE	0	0.21	2		247	265	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937398	76937398	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	58	255	0	ENST00000373344.5:c.3350T>A	p.Met1117Lys	p.M1117K	ENST00000373344	NM_000489.3	1117	aTg/aAg	9/35	0.3	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.21	2		255	228	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611248	100611248	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	54	203	0	ENST00000308731.7:c.1358C>G	p.Ser453Cys	p.S453C	ENST00000308731	NM_000061.2	453	tCc/tGc	15/19	0.3	2	FACETS	0.956	0.824	1	0.956	0.824	1	CLONAL	2	TRUE	0	0.21	2		203	269	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0024294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	50	533	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.86	0.731	1	0.86	0.731	1	CLONAL	1	TRUE	1	0.29	2		534	401	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562738	29562739	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555615472	NA	P-0024294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	83	461	0	ENST00000356175.3:c.3822_3823del	p.Phe1275ProfsTer8	p.F1275Pfs*8	ENST00000356175	NM_000267.3	1273	aCT/a	28/57	1	2	FACETS	0.909	0.802	1	0.909	0.802	1	CLONAL	1	TRUE	1	0.29	2		461	630	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717720	89717720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	72	505	1	ENST00000371953.3:c.745G>A	p.Val249Met	p.V249M	ENST00000371953	NM_000314.4	249	Gtg/Atg	7/9	0.245079480360738	1	FACETS	0.766	0.67	0.87	0.766	0.67	0.87	SUBCLONAL	1	TRUE	0	0.29	1		506	554	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984450	72984450	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	98	591	0	ENST00000268489.5:c.3134G>T	p.Cys1045Phe	p.C1045F	ENST00000268489	NM_006885.3	1045	tGt/tTt	3/10	1	2	FACETS	0.911	0.813	1	0.911	0.813	1	CLONAL	1	TRUE	1	0.29	2		591	742	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324656	31324656	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	34	217	0	ENST00000412585.2:c.152del	p.Tyr51SerfsTer8	p.Y51Sfs*8	ENST00000412585	NM_005514.6	51	tAc/tc	2/8	1	2	FACETS	1	0.831	1	1	0.831	1	CLONAL	1	TRUE	1	0.29	2		217	232	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0024295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	85	549	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			1	2	FACETS	0.837	0.738	0.944	0.837	0.738	0.944	CLONAL	1	TRUE	1	0.21	2		549	967	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971068	21971068	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	59	325	1	ENST00000304494.5:c.290T>A	p.Leu97Gln	p.L97Q	ENST00000304494	NM_000077.4	97	cTg/cAg	2/3	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.21	2		326	549	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0024296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	441	391	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.758741643083924	6	FACETS	0.953	0.917	0.988	0.953	0.917	0.988	CLONAL	4	TRUE	2	0.758741643083924	6		391	768	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497824	25497824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	254	574	0	ENST00000264709.3:c.625C>T	p.Arg209Cys	p.R209C	ENST00000264709	NM_175629.2	209	Cgc/Tgc	6/23	0.758741643083924	3	FACETS	0.914	0.866	0.962	0.914	0.866	0.962	CLONAL	2	TRUE	1	0.758741643083924	3		574	505	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482606	56482606	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	406	697	1	ENST00000267101.3:c.1063A>G	p.Thr355Ala	p.T355A	ENST00000267101	NM_001982.3	355	Acc/Gcc	9/28	0.758741643083924	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.758741643083924	3		698	728	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924617	94924617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1433012201	NA	P-0024296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	32	613	0	ENST00000536441.1:c.293G>A	p.Arg98His	p.R98H	ENST00000536441	NM_144665.3	98	cGc/cAc	3/10	0.758741643083924	3	FACETS	0.182	0.147	0.222	0.091	0.073	0.111	SUBCLONAL	1	TRUE	1	0.758741643083924	3		613	639	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118940	115118940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	125	263	0	ENST00000257566.3:c.401C>T	p.Pro134Leu	p.P134L	ENST00000257566	NM_016569.3	134	cCt/cTt	2/8	0.758741643083924	3	FACETS	1	0.978	1	0.608	0.556	0.661	CLONAL	1	TRUE	1	0.758741643083924	3		263	374	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0024297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	115	802	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.957	1	1	0.989	1	CLONAL	2	TRUE	1	0.146741931562539	2		802	705	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220701	1220701	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs730881976	NA	P-0024297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	96	594	1	ENST00000326873.7:c.719C>A	p.Ser240Ter	p.S240*	ENST00000326873	NM_000455.4	240	tCg/tAg	5/10	0.146741931562539	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.146741931562539	1		595	887	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502264	186502264	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	55	264	0	ENST00000323963.5:c.73G>C	p.Glu25Gln	p.E25Q	ENST00000323963		25	Gag/Cag	2/11	1	2	FACETS	0.757	0.648	0.876	1	0.967	1	SUBCLONAL	2	TRUE	1	0.146741931562539	2		264	495	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268927	55268927	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1289194907	NA	P-0024297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	65	643	0	ENST00000275493.2:c.2993A>G	p.Tyr998Cys	p.Y998C	ENST00000275493	NM_005228.3	998	tAc/tGc	25/28	1	2	FACETS	0.928	0.802	1	0.928	0.802	1	CLONAL	1	TRUE	1	0.146741931562539	2		643	955	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600531	10600531	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0024297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	86	441	0	ENST00000171111.5:c.1326-2A>T		p.X442_splice	ENST00000171111	NM_203500.1	442			0.146741931562539	1	FACETS	0.785	0.694	0.882	1	0.98	1	SUBCLONAL	2	TRUE	0	0.146741931562539	1		441	692	SUCCESS
APC	324	MSKCC	GRCh37	5	112178286	112178286	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	38	411	0	ENST00000257430.4:c.6995G>T	p.Gly2332Val	p.G2332V	ENST00000257430	NM_000038.5	2332	gGt/gTt	16/16	1	2	FACETS	0.857	0.707	1	0.857	0.707	1	CLONAL	1	TRUE	1	0.146741931562539	2		411	604	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69032484	69032484	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	61	580	0	ENST00000288368.4:c.3558C>A	p.Asp1186Glu	p.D1186E	ENST00000288368	NM_024870.2	1186	gaC/gaA	29/40	1	2	FACETS	0.957	0.823	1	0.957	0.823	1	CLONAL	1	TRUE	1	0.146741931562539	2		580	869	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0024298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	71	256	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.190926779008324	3	FACETS	1	0.933	1	0.547	0.481	0.617	INDETERMINATE	1	TRUE	1	0.477154313729133	3		256	337	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0024298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	97	314	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	0.190926779008324	3	FACETS	1	0.981	1	0.717	0.645	0.792	INDETERMINATE	1	TRUE	1	0.477154313729133	3		314	351	SUCCESS
APC	324	MSKCC	GRCh37	5	112154723	112154723	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775126020	NA	P-0024298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	117	484	0	ENST00000257430.4:c.994C>T	p.Arg332Ter	p.R332*	ENST00000257430	NM_000038.5	332	Cga/Tga	10/16	0.190926779008324	3	FACETS	1	0.936	1	0.523	0.473	0.575	INDETERMINATE	1	TRUE	1	0.477154313729133	3		484	581	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577544	7577544	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587780074	NA	P-0024298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	390	713	0	ENST00000269305.4:c.737T>C	p.Met246Thr	p.M246T	ENST00000269305	NM_001126112.2	246	aTg/aCg	7/11	0.477154313729133	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.477154313729133	2		713	780	SUCCESS
AR	367	MSKCC	GRCh37	X	66765176	66765176	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs62636527	NA	P-0024298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	13	217	1	ENST00000374690.3:c.188A>T	p.Gln63Leu	p.Q63L	ENST00000374690	NM_000044.3	63	cAg/cTg	1/8	0.477154313729133	2	FACETS	0.347	0.248	0.466	0.174	0.124	0.233	SUBCLONAL	1	TRUE	0	0.477154313729133	2		218	157	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944250	81944250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147396004	NA	P-0024298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	331	748	0	ENST00000359376.3:c.1859C>T	p.Thr620Met	p.T620M	ENST00000359376	NM_002661.3	620	aCg/aTg	18/33	0.472376623452182	3	FACETS	0.97	0.92	1	0.97	0.92	1	CLONAL	2	TRUE	1	0.477154313729133	3		748	886	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279578	1279578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs890242322	NA	P-0024298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	60	829	1	ENST00000310581.5:c.1958G>A	p.Arg653His	p.R653H	ENST00000310581	NM_198253.2	653	cGt/cAt	5/16	0.472376623452182	3	FACETS	0.307	0.263	0.355	0.153	0.131	0.178	SUBCLONAL	1	TRUE	1	0.477154313729133	3		830	1015	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0024299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	648	722	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.843045836722715	2	FACETS	0.994	0.975	1	0.994	0.975	1	CLONAL	2	TRUE	0	0.843045836722715	2		722	773	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0024299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	230	405	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.843045836722715	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.843045836722715	1		405	292	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882019	NA	P-0024299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	807	849	0	ENST00000269305.4:c.455del	p.Pro152ArgfsTer18	p.P152Rfs*18	ENST00000269305	NM_001126112.2	152	cCg/cg	5/11	0.843045836722715	2	FACETS	0.955	0.937	0.973	0.955	0.937	0.973	CLONAL	2	TRUE	0	0.843045836722715	2		849	1002	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483288	120483288	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	243	429	2	ENST00000256646.2:c.3073G>A	p.Glu1025Lys	p.E1025K	ENST00000256646	NM_024408.3	1025	Gag/Aag	19/34	0.843045836722715	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.843045836722715	1		431	325	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246091319	246091319	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	117	413	0	ENST00000388985.4:c.616C>G	p.His206Asp	p.H206D	ENST00000388985		206	Cac/Gac	7/12	0.843045836722715	3	FACETS	0.484	0.436	0.535	0.242	0.218	0.268	SUBCLONAL	1	TRUE	1	0.843045836722715	3		413	815	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715649	18715649	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	159	338	0	ENST00000266497.5:c.3480A>C	p.Glu1160Asp	p.E1160D	ENST00000266497		1160	gaA/gaC	25/31	0.843045836722715	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.843045836722715	1		338	214	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955282	48955492	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AACCTTTCTACTGTTTTCTTTGTCTGATAATAACTTCCAAAAAAATACCTAGCTCAAGGGTTAATATTTCATAAATAGTTACTTTTTTTTTTCATTTTTAGGAAGTACATCTCAGAATCTTGATTCTGGAACAGATTTGTCTTTCCCATGGATTCTGAATGTGCTTAATTTAAAAGCCTTTGATTTTTACAAAGTGATCGAAAGTTTTATC	AACCTTTCTACTGTTTTCTTTGTCTGATAATAACTTCCAAAAAAATACCTAGCTCAAGGGTTAATATTTCATAAATAGTTACTTTTTTTTTTCATTTTTAGGAAGTACATCTCAGAATCTTGATTCTGGAACAGATTTGTCTTTCCCATGGATTCTGAATGTGCTTAATTTAAAAGCCTTTGATTTTTACAAAGTGATCGAAAGTTTTATC	-	novel	NA	P-0024299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4	136	40	1	ENST00000267163.4:c.1499-99_1610del		p.X500_splice	ENST00000267163	NM_000321.2	500		17/27	0.843045836722715	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.843045836722715	1		41	140	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50821744	50821745	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0024299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	105	530	1	ENST00000398568.2:c.2080_2081delinsTT	p.Glu694Leu	p.E694L	ENST00000398568	NM_001042412.1	694	GAa/TTa	13/18	0.814081262226112	1	FACETS	0.435	0.394	0.478	0.435	0.394	0.478	SUBCLONAL	1	TRUE	0	0.843045836722715	1		531	331	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777910	27777911	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0024299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	174	372	0	ENST00000369163.2:c.59_60del	p.Gln20ProfsTer54	p.Q20Pfs*54	ENST00000369163	NM_003536.2	20	cAG/c	1/1	0.843045836722715	2	FACETS	0.752	0.697	0.809	0.376	0.348	0.405	SUBCLONAL	1	TRUE	0	0.843045836722715	2		372	549	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752723	128752724	+	missense_variant	Missense_Mutation	DNP	GA	GA	TG	novel	NA	P-0024299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1279	157	289	1	ENST00000377970.2:c.884_885delinsTG	p.Gly295Val	p.G295V	ENST00000377970	NM_002467.4	295	gGA/gTG	3/3	0.843045836722715	8	FACETS	0.915	0.836	0.999			1	CLONAL	1	TRUE	NA	0.843045836722715	8		290	1436	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750437	133750437	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	320	585	1	ENST00000318560.5:c.1268G>A	p.Trp423Ter	p.W423*	ENST00000318560	NM_005157.4	423	tGg/tAg	7/11	0.843045836722715	2	FACETS	0.924	0.876	0.972	0.462	0.438	0.486	CLONAL	1	TRUE	0	0.843045836722715	2		586	822	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0024301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	124	403	0				ENST00000310581	NM_198253.2	-/1132			0.370428545841921	1	FACETS	0.747	0.684	0.812	0.747	0.684	0.812	INDETERMINATE	1	TRUE	0	0.646890120587488	1		403	347	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623860	28623860	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	236	614	0	ENST00000241453.7:c.794G>A	p.Gly265Glu	p.G265E	ENST00000241453	NM_004119.2	265	gGg/gAg	7/24	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.646890120587488	2		614	726	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379701	17379701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	290	745	0	ENST00000359435.4:c.86C>T	p.Ser29Phe	p.S29F	ENST00000359435	NM_001033549.1	29	tCc/tTc	2/9	1	2	FACETS	0.99	0.933	1	0.99	0.933	1	CLONAL	1	TRUE	1	0.646890120587488	2		745	906	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337632	73337632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1176301061	NA	P-0024301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	165	387	0	ENST00000377767.4:c.2084C>T	p.Pro695Leu	p.P695L	ENST00000377767	NM_014953.3	695	cCt/cTt	16/21	1	2	FACETS	0.928	0.857	1	0.928	0.857	1	CLONAL	1	TRUE	1	0.646890120587488	2		387	550	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272142	18272142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1359242480	NA	P-0024301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	10	42	0	ENST00000222254.8:c.652C>T	p.Arg218Cys	p.R218C	ENST00000222254	NM_005027.3	218	Cgc/Tgc	6/16	1	2	FACETS	0.515	0.356	0.706	0.515	0.356	0.706	SUBCLONAL	1	TRUE	1	0.646890120587488	2		42	60	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127933383	127933383	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	137	653	0	ENST00000373547.4:c.152G>A	p.Cys51Tyr	p.C51Y	ENST00000373547	NM_002721.4	51	tGt/tAt	2/7	0.646890120587488	1	FACETS	0.487	0.444	0.531	0.487	0.444	0.531	SUBCLONAL	1	TRUE	0	0.646890120587488	1		653	589	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220443	1220443	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	44	786	0	ENST00000326873.7:c.536C>G	p.Pro179Arg	p.P179R	ENST00000326873	NM_000455.4	179	cCg/cGg	4/10	1	2	FACETS	0.859	0.718	1	0.859	0.718	1	CLONAL	1	TRUE	1	0.14	2		786	732	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888736	76888736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	40	691	2	ENST00000373344.5:c.5093G>A	p.Arg1698Gln	p.R1698Q	ENST00000373344	NM_000489.3	1698	cGg/cAg	19/35	1	2	FACETS	0.728	0.603	0.868	0.728	0.603	0.868	SUBCLONAL	1	TRUE	1	0.14	2		693	785	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602785	10602785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	57	855	1	ENST00000171111.5:c.793C>T	p.Gln265Ter	p.Q265*	ENST00000171111	NM_203500.1	265	Cag/Tag	3/6	1	2	FACETS	0.981	0.84	1	0.981	0.84	1	CLONAL	1	TRUE	1	0.14	2		856	830	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446889	18446889	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1172811749	NA	P-0024303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	34	565	0	ENST00000266497.5:c.974A>G	p.Asp325Gly	p.D325G	ENST00000266497		325	gAc/gGc	4/31	1	2	FACETS	0.745	0.607	0.901	0.745	0.607	0.901	CLONAL	1	TRUE	1	0.14	2		565	652	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728722	190728722	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs756580931	NA	P-0024303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	29	403	0	ENST00000441310.2:c.2110A>G	p.Lys704Glu	p.K704E	ENST00000441310	NM_000534.4	704	Aaa/Gaa	10/13	1	2	FACETS	0.723	0.579	0.888	0.723	0.579	0.888	SUBCLONAL	1	TRUE	1	0.14	2		403	573	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0024305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	124	533	1				ENST00000310581	NM_198253.2	-/1132			0.317135886116825	1	FACETS	0.814	0.753	0.874	0.814	0.753	0.874	INDETERMINATE	1	TRUE	0	0.770894214646981	1		534	243	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399191	139399191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1243453790	NA	P-0024305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	235	578	0	ENST00000277541.6:c.4952C>T	p.Ser1651Leu	p.S1651L	ENST00000277541	NM_017617.3	1651	tCg/tTg	26/34	0.231964669744613	3	FACETS	0.784	0.738	0.829	0.784	0.738	0.829	INDETERMINATE	2	TRUE	1	0.770894214646981	3		578	539	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500886	8500886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	256	621	0	ENST00000356435.5:c.1996C>T	p.Pro666Ser	p.P666S	ENST00000356435		666	Cct/Tct	13/35	0.770894214646981	1	FACETS	0.96	0.915	1	0.96	0.915	1	CLONAL	1	TRUE	0	0.770894214646981	1		621	425	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641144	117641144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866970127	NA	P-0024305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	290	674	0	ENST00000368508.3:c.5827G>A	p.Glu1943Lys	p.E1943K	ENST00000368508	NM_002944.2	1943	Gaa/Aaa	36/43	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.770894214646981	2		674	706	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0024305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	566	512	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.770894214646981	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.770894214646981	3		512	667	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176561	142176561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	338	554	0	ENST00000350721.4:c.7540C>T	p.Arg2514Cys	p.R2514C	ENST00000350721	NM_001184.3	2514	Cgc/Tgc	45/47	0.770894214646981	3	FACETS	0.948	0.905	0.99	0.948	0.905	0.99	CLONAL	2	TRUE	1	0.770894214646981	3		554	641	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866442	42866442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	126	847	0	ENST00000398585.3:c.190C>T	p.Pro64Ser	p.P64S	ENST00000398585	NM_001135099.1	64	Ccc/Tcc	3/14	0.421920053330581	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.770894214646981	0		847	485	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547004	9547004	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	93	273	0	ENST00000353224.5:c.1018C>T	p.Leu340Phe	p.L340F	ENST00000353224	NM_177990.2	340	Ctc/Ttc	5/10	1	2	FACETS	0.865	0.78	0.953	0.865	0.78	0.953	CLONAL	1	TRUE	1	0.770894214646981	2		273	279	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674200	117674200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	282	741	0	ENST00000368508.3:c.4274G>A	p.Arg1425Lys	p.R1425K	ENST00000368508	NM_002944.2	1425	aGg/aAg	26/43	NA	2	FACETS	1	0.953	1			1	INDETERMINATE	1	TRUE	NA	0.770894214646981	2		741	725	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228066	53228066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	189	313	0	ENST00000375401.3:c.2248C>T	p.Arg750Trp	p.R750W	ENST00000375401	NM_004187.3	750	Cgg/Tgg	16/26	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.770894214646981	1		313	240	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258764	16258764	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530603850	NA	P-0024305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	34	460	0	ENST00000375759.3:c.6029G>A	p.Arg2010His	p.R2010H	ENST00000375759	NM_015001.2	2010	cGt/cAt	11/15	0.770894214646981	1	FACETS	0.159	0.13	0.192	0.159	0.13	0.192	SUBCLONAL	1	TRUE	0	0.770894214646981	1		460	340	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8105964	8105964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	142	480	0	ENST00000346208.3:c.784G>A	p.Glu262Lys	p.E262K	ENST00000346208		262	Gag/Aag	4/6	1	2	FACETS	0.873	0.803	0.945	0.873	0.803	0.945	CLONAL	1	TRUE	1	0.770894214646981	2		480	422	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37671991	37671991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	228	551	0	ENST00000447079.4:c.2776C>T	p.Leu926Phe	p.L926F	ENST00000447079	NM_015083.1	926	Ctt/Ttt	9/14	1	2	FACETS	0.92	0.862	0.979	0.92	0.862	0.979	CLONAL	1	TRUE	1	0.770894214646981	2		551	643	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223423	2223424	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	novel	NA	P-0024305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	134	541	1	ENST00000398665.3:c.3534_3535delinsTT	p.His1179Tyr	p.H1179Y	ENST00000398665	NM_032482.2	1178	gcACac/gcTTac	25/28	0.429799612232628	1	FACETS	0.645	0.595	0.697	0.645	0.595	0.697	INDETERMINATE	1	TRUE	0	0.770894214646981	1		542	331	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292564	15292564	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	123	684	0	ENST00000263388.2:c.2615C>T	p.Ser872Phe	p.S872F	ENST00000263388	NM_000435.2	872	tCc/tTc	17/33	0.429799612232628	1	FACETS	0.409	0.371	0.447	0.409	0.371	0.447	INDETERMINATE	1	TRUE	0	0.770894214646981	1		684	480	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792394	33792394	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	119	801	0	ENST00000498907.2:c.927G>C	p.Glu309Asp	p.E309D	ENST00000498907	NM_004364.3	309	gaG/gaC	1/1	0.429799612232628	1	FACETS	0.367	0.333	0.403	0.367	0.333	0.403	INDETERMINATE	1	TRUE	0	0.770894214646981	1		801	517	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211667	36211667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1199792737	NA	P-0024305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	61	484	0	ENST00000222270.7:c.1418C>T	p.Pro473Leu	p.P473L	ENST00000222270	NM_014727.1	473	cCc/cTc	3/37	0.429799612232628	1	FACETS	0.329	0.285	0.375	0.329	0.285	0.375	INDETERMINATE	1	TRUE	0	0.770894214646981	1		484	296	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799250	42799251	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	68	572	1	ENST00000575354.2:c.4734_4735delinsTT	p.Pro1579Ser	p.P1579S	ENST00000575354	NM_015125.3	1578	ccCCca/ccTTca	20/20	0.429799612232628	1	FACETS	0.35	0.306	0.396	0.35	0.306	0.396	INDETERMINATE	1	TRUE	0	0.770894214646981	1		573	310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0024306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	175	712	1	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	0.19	2		713	1264	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0024306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	81	761	1	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.937	0.824	1	0.937	0.824	1	CLONAL	1	TRUE	1	0.19	2		762	910	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588876	29588876	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0024306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	48	327	0	ENST00000356175.3:c.4661+1G>T		p.X1554_splice	ENST00000356175	NM_000267.3	1554			1	2	FACETS	0.828	0.699	0.971	0.828	0.699	0.971	CLONAL	1	TRUE	1	0.19	2		327	610	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570448	95570448	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	37	345	0	ENST00000393063.1:c.3285C>G	p.Asp1095Glu	p.D1095E	ENST00000393063	NM_030621.3	1095	gaC/gaG	22/28	1	2	FACETS	0.651	0.536	0.781	0.651	0.536	0.781	SUBCLONAL	1	TRUE	1	0.19	2		345	598	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991674	72991674	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	31	362	0	ENST00000268489.5:c.2371G>T	p.Gly791Trp	p.G791W	ENST00000268489	NM_006885.3	791	Ggg/Tgg	2/10	1	2	FACETS	0.572	0.462	0.698	0.572	0.462	0.698	SUBCLONAL	1	TRUE	1	0.19	2		362	570	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599958	10599958	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	107	702	1	ENST00000171111.5:c.1618G>T	p.Glu540Ter	p.E540*	ENST00000171111	NM_203500.1	540	Gaa/Taa	5/6	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.19	2		703	1114	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015209	71015209	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0024306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	30	250	0	ENST00000318789.4:c.1723-2A>T		p.X575_splice	ENST00000318789	NM_032682.5	575			1	2	FACETS	0.853	0.688	1	0.853	0.688	1	CLONAL	1	TRUE	1	0.19	2		250	370	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976840	55976840	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	61	526	0	ENST00000263923.4:c.1072C>G	p.Pro358Ala	p.P358A	ENST00000263923	NM_002253.2	358	Cca/Gca	8/30	1	2	FACETS	0.625	0.537	0.721	0.625	0.537	0.721	SUBCLONAL	1	TRUE	1	0.19	2		526	1028	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971092	21971092	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137854599	NA	P-0024306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	73	362	0	ENST00000304494.5:c.266G>A	p.Gly89Asp	p.G89D	ENST00000304494	NM_000077.4	89	gGc/gAc	2/3	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.19	2		362	643	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907097	101907097	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	64	566	1	ENST00000374994.4:c.1057G>A	p.Gly353Arg	p.G353R	ENST00000374994	NM_004612.2	353	Gga/Aga	6/9	1	2	FACETS	0.923	0.798	1	0.923	0.798	1	CLONAL	1	TRUE	1	0.19	2		567	730	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412971	63412971	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1221	139	815	1	ENST00000330258.3:c.196A>T	p.Ile66Phe	p.I66F	ENST00000330258	NM_152424.3	66	Atc/Ttc	2/2	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.19	2		816	1360	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366981	15366981	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1485	365	551	0	ENST00000263377.2:c.1645G>C	p.Glu549Gln	p.E549Q	ENST00000263377	NM_058243.2	549	Gaa/Caa	9/20	0.578361604105456	4	FACETS	0.98	0.926	1			1	CLONAL	1	TRUE	NA	0.674348560802005	4		551	1850	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111499	8111499	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	410	534	0	ENST00000346208.3:c.985A>G	p.Arg329Gly	p.R329G	ENST00000346208		329	Agg/Ggg	5/6	1	2	FACETS	0.987	0.94	1	0.987	0.94	1	CLONAL	1	TRUE	1	0.674348560802005	2		534	1232	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	463273	463273	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	357	424	0	ENST00000399788.2:c.998G>C	p.Gly333Ala	p.G333A	ENST00000399788	NM_001042603.1	333	gGa/gCa	8/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.674348560802005	2		424	1005	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784122	120784122	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	388	627	0	ENST00000257552.2:c.863C>G	p.Ser288Cys	p.S288C	ENST00000257552	NM_002442.3	288	tCt/tGt	13/15	1	2	FACETS	0.995	0.946	1	0.995	0.946	1	CLONAL	1	TRUE	1	0.674348560802005	2		627	1157	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028640	42028640	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	347	538	0	ENST00000219905.7:c.4178C>A	p.Ser1393Tyr	p.S1393Y	ENST00000219905	NM_001164273.1	1393	tCt/tAt	13/24	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.674348560802005	2		538	1029	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058571	42058571	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	223	292	0	ENST00000219905.7:c.8291G>C	p.Arg2764Thr	p.R2764T	ENST00000219905	NM_001164273.1	2764	aGa/aCa	24/24	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.674348560802005	2		292	652	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647602	23647602	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs769790850	NA	P-0024308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	320	488	0	ENST00000261584.4:c.265G>C	p.Asp89His	p.D89H	ENST00000261584	NM_024675.3	89	Gat/Cat	4/13	NA	2	FACETS	0.964	0.912	1			1	INDETERMINATE	1	TRUE	NA	0.674348560802005	2		488	984	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849484	68849484	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	355	461	0	ENST00000261769.5:c.1387G>C	p.Glu463Gln	p.E463Q	ENST00000261769	NM_004360.3	463	Gag/Cag	10/16	0.674348560802005	1	FACETS	0.973	0.93	1	0.973	0.93	1	CLONAL	1	TRUE	0	0.674348560802005	1		461	717	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528481	29528481	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	352	467	0	ENST00000356175.3:c.1238C>A	p.Ser413Ter	p.S413*	ENST00000356175	NM_000267.3	413	tCa/tAa	11/57	0.674348560802005	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.674348560802005	1		467	674	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137313599	137313599	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	404	616	0	ENST00000481739.1:c.858C>G	p.Ile286Met	p.I286M	ENST00000481739	NM_002957.4	286	atC/atG	6/10	0.674348560802005	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.674348560802005	1		616	754	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390923	139390923	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0024308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	339	601	0	ENST00000277541.6:c.7268C>G	p.Ser2423Ter	p.S2423*	ENST00000277541	NM_017617.3	2423	tCa/tGa	34/34	0.674348560802005	1	FACETS	0.963	0.919	1	0.963	0.919	1	CLONAL	1	TRUE	0	0.674348560802005	1		601	692	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	407	855	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.587083971879135	3	FACETS	0.945	0.903	0.987	0.945	0.903	0.987	CLONAL	2	TRUE	1	0.587083971879135	3		855	949	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0024312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	25	419	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	0.22498440828267	1	FACETS	0.149	0.117	0.185	0.149	0.117	0.185	INDETERMINATE	1	TRUE	0	0.587083971879135	1		419	405	SUCCESS
APC	324	MSKCC	GRCh37	5	112175466	112175466	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786204170	NA	P-0024312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	277	348	0	ENST00000257430.4:c.4175C>A	p.Ser1392Ter	p.S1392*	ENST00000257430	NM_000038.5	1392	tCa/tAa	16/16	0.587083971879135	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.587083971879135	2		348	450	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114760	73114760	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	16	177	0	ENST00000356692.5:c.1141G>A	p.Glu381Lys	p.E381K	ENST00000356692		381	Gaa/Aaa	9/9	0.22498440828267	1	FACETS	0.225	0.167	0.294	0.225	0.167	0.294	INDETERMINATE	1	TRUE	0	0.587083971879135	1		177	171	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40367512	40367512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1334492695	NA	P-0024312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	16	37	0	ENST00000397332.2:c.49G>A	p.Gly17Ser	p.G17S	ENST00000397332	NM_001033082.2	17	Ggt/Agt	1/3	0.587083971879135	1	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	0	0.587083971879135	1		37	33	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920446	114920446	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	176	545	0	ENST00000543371.1:c.1387T>C	p.Cys463Arg	p.C463R	ENST00000543371	NM_001198531.1	463	Tgc/Cgc	13/14	0.587083971879135	1	FACETS	0.971	0.905	1	0.971	0.905	1	CLONAL	1	TRUE	0	0.587083971879135	1		545	436	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86682685	86682685	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0024312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	86	399	1	ENST00000274376.6:c.2890A>T	p.Lys964Ter	p.K964*	ENST00000274376	NM_002890.2	964	Aaa/Taa	23/25	0.587083971879135	2	FACETS	0.718	0.639	0.802	0.359	0.319	0.401	SUBCLONAL	1	TRUE	0	0.587083971879135	2		400	408	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989672	68989672	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs757775649	NA	P-0024312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	271	708	0	ENST00000288368.4:c.1610T>C	p.Val537Ala	p.V537A	ENST00000288368	NM_024870.2	537	gTt/gCt	15/40	1	2	FACETS	0.758	0.717	0.799	1	0.994	1	SUBCLONAL	2	TRUE	1	0.587083971879135	2		708	609	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938212	76938212	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	146	727	0	ENST00000373344.5:c.2536G>A	p.Asp846Asn	p.D846N	ENST00000373344	NM_000489.3	846	Gat/Aat	9/35	0.479275494635457	1	FACETS	0.408	0.372	0.445	0.408	0.372	0.445	SUBCLONAL	1	TRUE	0	0.587083971879135	1		727	862	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443599	52443601	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0024314-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	110	515	0	ENST00000460680.1:c.91_93del	p.Glu31del	p.E31del	ENST00000460680	NM_004656.3	31	GAG/-	3/17	0.237085975394572	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	2	TRUE	0	0.237085975394572	2		515	458	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070904	30070917	+	frameshift_variant	Frame_Shift_Del	DEL	GAGATTGCCACCAA	GAGATTGCCACCAA	-	novel	NA	P-0024314-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	109	588	0	ENST00000338641.4:c.1421_1434del	p.Glu474AlafsTer16	p.E474Afs*16	ENST00000338641	NM_000268.3	474	GAGATTGCCACCAAg/g	13/16	0.237085975394572	2	FACETS	0.783	0.705	0.865	0.783	0.705	0.865	SUBCLONAL	2	TRUE	0	0.237085975394572	2		588	587	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	62	855	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	FALSE	1	0.184088808298188	2		855	660	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0024315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	79	773	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.165592171408183	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	FALSE	0	0.184088808298188	1		773	703	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061904	38061904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	83	783	0	ENST00000250448.2:c.85G>A	p.Val29Ile	p.V29I	ENST00000250448	NM_004496.3	29	Gtc/Atc	2/2	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.184088808298188	2		783	770	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467865	66467865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs939351025	NA	P-0024315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	34	414	0	ENST00000273854.3:c.404G>A	p.Arg135Gln	p.R135Q	ENST00000273854	NM_004439.5	135	cGg/cAg	3/18	1	2	FACETS	0.669	0.546	0.809	0.669	0.546	0.809	SUBCLONAL	1	FALSE	1	0.184088808298188	2		414	552	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533790	63533790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	53	609	1	ENST00000307078.5:c.1364C>T	p.Pro455Leu	p.P455L	ENST00000307078	NM_004655.3	455	cCa/cTa	6/11	1	2	FACETS	0.858	0.731	0.998	0.858	0.731	0.998	CLONAL	1	FALSE	1	0.184088808298188	2		610	671	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144147	11144147	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064795161	NA	P-0024315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	336	722	1	ENST00000358026.2:c.3728G>A	p.Arg1243Gln	p.R1243Q	ENST00000358026	NM_001128849.1	1243	cGg/cAg	26/36	0.184088808298188	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	4	FALSE	0	0.184088808298188	4		723	995	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0024316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	109	846	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.15	2		847	1049	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371708	225371708	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	50	612	0	ENST00000264414.4:c.896T>G	p.Met299Arg	p.M299R	ENST00000264414	NM_003590.4	299	aTg/aGg	7/16	1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	1	0.15	2		612	666	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264486	30264486	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	46	545	0	ENST00000322652.5:c.221C>A	p.Pro74Gln	p.P74Q	ENST00000322652	NM_015355.2	74	cCg/cAg	1/16	1	2	FACETS	0.868	0.729	1	0.868	0.729	1	CLONAL	1	TRUE	1	0.15	2		545	707	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879498	151879498	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	56	516	0	ENST00000262189.6:c.5447del	p.Asn1816MetfsTer33	p.N1816Mfs*33	ENST00000262189	NM_170606.2	1816	aAt/at	36/59	0.0825720002065595	3	FACETS	1	0.947	1	0.619	0.53	0.717	INDETERMINATE	1	TRUE	1	0.15	3		516	648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578520	7578520	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	458	876	0	ENST00000269305.4:c.410T>A	p.Leu137Gln	p.L137Q	ENST00000269305	NM_001126112.2	137	cTg/cAg	5/11	0.394345284885566	4	FACETS	0.972	0.937	1			1	CLONAL	4	TRUE	NA	0.450299134928923	4		876	759	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439886	220439886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758448367	NA	P-0024317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	177	746	0	ENST00000243786.2:c.739C>T	p.Arg247Cys	p.R247C	ENST00000243786	NM_002191.3	247	Cgc/Tgc	2/2	0.443043987519042	4	FACETS	0.911	0.843	0.98	0.911	0.843	0.98	CLONAL	2	TRUE	2	0.450299134928923	4		746	626	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294097	1294106	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCCCAC	GGCGGCCCAC	-	novel	NA	P-0024317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	180	896	0	ENST00000310581.5:c.895_904del	p.Val299SerfsTer49	p.V299Sfs*49	ENST00000310581	NM_198253.2	299	GTGGGCCGCCag/ag	2/16	0.443043987519042	4	FACETS	0.882	0.817	0.95	0.882	0.817	0.95	CLONAL	2	TRUE	2	0.450299134928923	4		896	657	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971142	21971142	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	76	389	0	ENST00000304494.5:c.216C>A	p.Cys72Ter	p.C72*	ENST00000304494	NM_000077.4	72	tgC/tgA	2/3	0.431259435966664	2	FACETS	0.781	0.697	0.868	0.781	0.697	0.868	SUBCLONAL	2	TRUE	0	0.450299134928923	2		389	216	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100198	27100198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	101	396	1	ENST00000324856.7:c.3994C>T	p.Gln1332Ter	p.Q1332*	ENST00000324856	NM_006015.4	1332	Cag/Tag	16/20	1	2	FACETS	0.706	0.637	0.778	0.706	0.637	0.778	SUBCLONAL	1	TRUE	1	0.805633201096972	2		397	355	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514495	149514495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760987130	NA	P-0024323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	86	594	0	ENST00000261799.4:c.449G>A	p.Arg150Gln	p.R150Q	ENST00000261799	NM_002609.3	150	cGa/cAa	4/23	1	2	FACETS	0.485	0.431	0.543	0.485	0.431	0.543	SUBCLONAL	1	TRUE	1	0.805633201096972	2		594	440	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936072	44936072	+	splice_donor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0024323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	133	431	0	ENST00000377967.4:c.2832+1del		p.X944_splice	ENST00000377967	NM_021140.2	944			0.795489662071022	1	FACETS	0.996	0.936	1	0.996	0.936	1	CLONAL	1	TRUE	0	0.805633201096972	1		431	198	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023516	27023517	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCAACCACCAGTACAA	novel	NA	P-0024323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	28	496	0	ENST00000324856.7:c.624_639dup	p.Ser214GlnfsTer191	p.S214Qfs*191	ENST00000324856	NM_006015.4	208	ccc/cCCAACCACCAGTACAAcc	1/20	1	2	FACETS	0.206	0.164	0.253	0.206	0.164	0.253	SUBCLONAL	1	TRUE	1	0.805633201096972	2		496	338	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101109	27101110	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0024323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	29	644	0	ENST00000324856.7:c.4394_4395del	p.Ser1465CysfsTer25	p.S1465Cfs*25	ENST00000324856	NM_006015.4	1464	gTC/g	18/20	1	2	FACETS	0.158	0.126	0.194	0.158	0.126	0.194	SUBCLONAL	1	TRUE	1	0.805633201096972	2		644	456	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265970	41266028	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGG	AGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGG	-	novel	NA	P-0024323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	36	114	0	ENST00000349496.5:c.14-44_28del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	1	2	FACETS	0.577	0.481	0.68	0.577	0.481	0.68	SUBCLONAL	1	TRUE	1	0.805633201096972	2		114	155	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103730	47103734	+	frameshift_variant	Frame_Shift_Del	DEL	TTTAT	TTTAT	-	novel	NA	P-0024323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	30	479	0	ENST00000409792.3:c.6212_6216del	p.Asn2071ArgfsTer17	p.N2071Rfs*17	ENST00000409792	NM_014159.6	2071	aATAAA/a	14/21	1	2	FACETS	0.14	0.112	0.171	0.14	0.112	0.171	SUBCLONAL	1	TRUE	1	0.805633201096972	2		479	533	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278106	41278106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	168	513	1	ENST00000349496.5:c.1982G>A	p.Arg661Gln	p.R661Q	ENST00000349496	NM_001904.3	661	cGa/cAa	13/15	1	2	FACETS	0.492	0.453	0.533	0.492	0.453	0.533	SUBCLONAL	1	TRUE	1	0.890122870252328	2		514	767	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100198	27100198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	252	396	1	ENST00000324856.7:c.3994C>T	p.Gln1332Ter	p.Q1332*	ENST00000324856	NM_006015.4	1332	Cag/Tag	16/20	1	2	FACETS	0.971	0.917	1	0.971	0.917	1	CLONAL	1	TRUE	1	0.890122870252328	2		397	583	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514495	149514495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760987130	NA	P-0024323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	168	594	0	ENST00000261799.4:c.449G>A	p.Arg150Gln	p.R150Q	ENST00000261799	NM_002609.3	150	cGa/cAa	4/23	1	2	FACETS	0.439	0.403	0.476	0.439	0.403	0.476	SUBCLONAL	1	TRUE	1	0.890122870252328	2		594	860	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936072	44936072	+	splice_donor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0024323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	201	431	0	ENST00000377967.4:c.2832+1del		p.X944_splice	ENST00000377967	NM_021140.2	944			0.890122870252328	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.890122870252328	1		431	249	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367271	50367271	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1284126054	NA	P-0024323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	58	496	0	ENST00000331340.3:c.78G>C	p.Glu26Asp	p.E26D	ENST00000331340	NM_006060.4	26	gaG/gaC	3/8	1	2	FACETS	0.22	0.189	0.254	0.22	0.189	0.254	SUBCLONAL	1	TRUE	1	0.890122870252328	2		496	592	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0024327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	31	533	1				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.834	0.695	0.981			1	INDETERMINATE	1	TRUE	NA	0.816764677597145	2		534	91	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0024327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	164	419	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.938	0.871	1	0.938	0.871	1	CLONAL	1	TRUE	1	0.816764677597145	2		419	428	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248599	212248599	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1281587425	NA	P-0024329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	46	804	1	ENST00000342788.4:c.3668A>G	p.Lys1223Arg	p.K1223R	ENST00000342788	NM_005235.2	1223	aAg/aGg	28/28	0.223066259633516	2	FACETS	0.267	0.224	0.314	0.133	0.112	0.157	INDETERMINATE	1	TRUE	0	0.653955480304837	2		805	527	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40738999	40738999	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	54	696	0	ENST00000373198.4:c.3285A>C	p.Glu1095Asp	p.E1095D	ENST00000373198	NM_133170.3	1095	gaA/gaC	24/32	0.653600061132901	1	FACETS	0.234	0.2	0.272	0.234	0.2	0.272	SUBCLONAL	1	TRUE	0	0.653955480304837	1		696	474	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046509	30046509	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	49	783	0	ENST00000331968.5:c.2674A>T	p.Ser892Cys	p.S892C	ENST00000331968	NM_002742.2	892	Agt/Tgt	18/18	0.163226282106763	3	FACETS	0.36	0.305	0.421	0.12	0.101	0.141	INDETERMINATE	1	TRUE	0	0.653955480304837	3		783	552	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678391	88678391	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	42	1025	1	ENST00000360948.2:c.1145A>C	p.Asn382Thr	p.N382T	ENST00000360948	NM_001012338.2	382	aAc/aCc	9/19	0.619561602871165	1	FACETS	0.134	0.111	0.159	0.134	0.111	0.159	SUBCLONAL	1	TRUE	0	0.653955480304837	1		1026	645	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857929	9857929	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	58	784	0	ENST00000330684.3:c.3472T>G	p.Phe1158Val	p.F1158V	ENST00000330684	NM_001134407.1	1158	Ttc/Gtc	13/13	0.103361903139446	3	FACETS	0.35	0.3	0.405	0.175	0.15	0.203	INDETERMINATE	1	TRUE	1	0.653955480304837	3		784	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574006	7574021	+	frameshift_variant	Frame_Shift_Del	DEL	ACATCTCGAAGCGCTC	ACATCTCGAAGCGCTC	-	novel	NA	P-0024329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	340	970	0	ENST00000269305.4:c.1006_1021del	p.Glu336SerfsTer4	p.E336Sfs*4	ENST00000269305	NM_001126112.2	336	GAGCGCTTCGAGATGTtc/tc	10/11	0.64527009754324	3	FACETS	1	0.977	1	0.691	0.659	0.722	CLONAL	2	TRUE	0	0.653955480304837	3		970	666	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732902	74732902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs908674875	NA	P-0024329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	35	120	0	ENST00000359995.5:c.341G>A	p.Gly114Asp	p.G114D	ENST00000359995	NM_001195427.1	114	gGc/gAc	1/3	0.309018295631615	0	FACETS	0.276	0.23	0.326			1	INDETERMINATE	1	TRUE	0	0.653955480304837	0		120	134	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587179	212587179	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	56	758	0	ENST00000342788.4:c.822A>T	p.Gln274His	p.Q274H	ENST00000342788	NM_005235.2	274	caA/caT	7/28	0.223066259633516	2	FACETS	0.337	0.289	0.39	0.169	0.144	0.195	INDETERMINATE	1	TRUE	0	0.653955480304837	2		758	508	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989604	212989604	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	24	462	0	ENST00000342788.4:c.107T>G	p.Leu36Arg	p.L36R	ENST00000342788	NM_005235.2	36	cTg/cGg	2/28	0.223066259633516	2	FACETS	0.247	0.194	0.309	0.124	0.097	0.155	INDETERMINATE	1	TRUE	0	0.653955480304837	2		462	297	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727077	40727077	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	54	700	0	ENST00000373198.4:c.3887A>C	p.Glu1296Ala	p.E1296A	ENST00000373198	NM_133170.3	1296	gAg/gCg	28/32	0.653600061132901	1	FACETS	0.194	0.165	0.225	0.194	0.165	0.225	SUBCLONAL	1	TRUE	0	0.653955480304837	1		700	573	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42838060	42838070	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	CCATGTGGATT	CCATGTGGATT	-	novel	NA	P-0024329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	698	61	0	ENST00000398585.3:c.1589_*9del		p.*530*	ENST00000398585	NM_001135099.1	530		14/14	0.567708469186515	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.653955480304837	1		61	1114	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920431	134920431	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	121	821	0	ENST00000398015.3:c.2246A>T	p.Asn749Ile	p.N749I	ENST00000398015	NM_004441.4	749	aAc/aTc	12/16	0.442759143972518	2	FACETS	0.654	0.593	0.718	0.327	0.296	0.359	SUBCLONAL	1	TRUE	0	0.653955480304837	2		821	566	SUCCESS
APC	324	MSKCC	GRCh37	5	112176594	112176594	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	37	493	0	ENST00000257430.4:c.5303A>C	p.Lys1768Thr	p.K1768T	ENST00000257430	NM_000038.5	1768	aAg/aCg	16/16	0.177818114815223	3	FACETS	0.4	0.33	0.479	0.133	0.11	0.16	INDETERMINATE	1	TRUE	0	0.653955480304837	3		493	375	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965571	93965571	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	48	675	1	ENST00000369303.4:c.2357A>G	p.Asp786Gly	p.D786G	ENST00000369303	NM_004440.3	786	gAt/gGt	13/17	0.177818114815223	3	FACETS	0.43	0.364	0.503	0.143	0.121	0.168	INDETERMINATE	1	TRUE	0	0.653955480304837	3		676	453	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441599	6441599	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs5828	NA	P-0024329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	44	455	0	ENST00000356142.4:c.446A>G	p.Lys149Arg	p.K149R	ENST00000356142	NM_018890.3	149	aAg/aGg	6/7	0.564599862509961	4	FACETS	0.411	0.345	0.486			1	SUBCLONAL	1	TRUE	NA	0.653955480304837	4		455	541	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946161	13946161	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	356	835	0	ENST00000405192.2:c.935T>G	p.Leu312Arg	p.L312R	ENST00000405192	NM_001163147.1	312	cTt/cGt	10/12	0.564599862509961	4	FACETS	0.896	0.851	0.942			1	CLONAL	2	TRUE	NA	0.653955480304837	4		835	1005	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27217717	27217717	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	63	785	0	ENST00000380036.4:c.3023A>G	p.Glu1008Gly	p.E1008G	ENST00000380036	NM_000459.3	1008	gAg/gGg	19/23	0.176846822526163	2	FACETS	0.265	0.229	0.305	0.133	0.114	0.153	INDETERMINATE	1	TRUE	0	0.653955480304837	2		785	727	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044491	47044491	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	66	424	2	ENST00000377604.3:c.1988A>G	p.Asn663Ser	p.N663S	ENST00000377604	NM_001204468.1	663	aAc/aGc	18/24	0.468167454230352	2	FACETS	0.524	0.457	0.596			1	SUBCLONAL	1	TRUE	NA	0.653955480304837	2		426	385	SUCCESS
AR	367	MSKCC	GRCh37	X	66931370	66931370	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	65	448	0	ENST00000374690.3:c.2012A>T	p.Gln671Leu	p.Q671L	ENST00000374690	NM_000044.3	671	cAg/cTg	4/8	0.468167454230352	2	FACETS	0.593	0.518	0.674			1	SUBCLONAL	1	TRUE	NA	0.653955480304837	2		448	335	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	163	774	2	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.525809656046311	1	FACETS	0.791	0.731	0.852	0.791	0.731	0.852	SUBCLONAL	1	TRUE	0	0.580655818662638	1		776	504	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0024333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	221	830	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.580813215266701	6	FACETS	1	0.97	1	0.788	0.74	0.836	CLONAL	3	TRUE	2	0.580813215266701	6		830	522	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0024333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	54	551	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.543492612285607	2	FACETS	0.877	0.759	1	0.439	0.379	0.501	CLONAL	1	TRUE	0	0.580813215266701	2		551	212	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015003	37015003	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	90	750	0	ENST00000358127.4:c.401C>T	p.Ser134Phe	p.S134F	ENST00000358127	NM_001280556.1	134	tCc/tTc	3/10	0.443429490877815	4	FACETS	0.736	0.653	0.824			1	SUBCLONAL	1	TRUE	NA	0.600771146927305	4		750	652	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600369	10600369	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs549967865	NA	P-0024336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	50	1138	1	ENST00000171111.5:c.1486G>A	p.Glu496Lys	p.E496K	ENST00000171111	NM_203500.1	496	Gag/Aag	4/6	NA	2	FACETS	0.248	0.209	0.29			1	INDETERMINATE	1	TRUE	NA	0.600771146927305	2		1139	672	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137727	64137727	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	62	1204	2	ENST00000334205.4:c.1828C>T	p.Gln610Ter	p.Q610*	ENST00000334205	NM_003942.2	610	Cag/Tag	15/17	NA	2	FACETS	0.326	0.281	0.375			1	INDETERMINATE	1	TRUE	NA	0.600771146927305	2		1206	633	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772315	68772315	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0024336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	353	984	1	ENST00000261769.5:c.163+1G>T		p.X55_splice	ENST00000261769	NM_004360.3	55			0.600771146927305	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.600771146927305	2		985	547	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265342	46265342	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	107	519	0	ENST00000371998.3:c.2212C>G	p.Leu738Val	p.L738V	ENST00000371998		738	Ctt/Gtt	12/23	0.600771146927305	6	FACETS	1	0.908	1	0.253	0.227	0.281	CLONAL	1	TRUE	2	0.600771146927305	6		519	774	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319396	62319396	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	204	1137	0	ENST00000360203.5:c.1588G>C	p.Asp530His	p.D530H	ENST00000360203	NM_001283009.1	530	Gac/Cac	18/35	0.600771146927305	6	FACETS	1	0.965	1	0.268	0.248	0.29	CLONAL	1	TRUE	2	0.600771146927305	6		1137	1393	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655395	45655395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	63	1125	1	ENST00000407780.3:c.457G>A	p.Glu153Lys	p.E153K	ENST00000407780	NM_001283052.1	153	Gag/Aag	4/7	0.600771146927305	3	FACETS	0.304	0.262	0.35	0.152	0.131	0.175	SUBCLONAL	1	TRUE	1	0.600771146927305	3		1126	898	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178098	142178098	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	176	601	0	ENST00000350721.4:c.7320del	p.Leu2441Ter	p.L2441*	ENST00000350721	NM_001184.3	2440	ttT/tt	43/47	0.600771146927305	3	FACETS	0.884	0.824	0.945	0.884	0.824	0.945	CLONAL	2	TRUE	1	0.600771146927305	3		601	431	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430992	181430992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	55	978	2	ENST00000325404.1:c.844G>A	p.Glu282Lys	p.E282K	ENST00000325404	NM_003106.3	282	Gag/Aag	1/1	0.600771146927305	3	FACETS	0.329	0.281	0.382	0.165	0.14	0.191	SUBCLONAL	1	TRUE	1	0.600771146927305	3		980	723	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80083442	80083442	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	166	1210	2	ENST00000265081.6:c.2494G>T	p.Asp832Tyr	p.D832Y	ENST00000265081	NM_002439.4	832	Gac/Tac	18/24	0.600771146927305	4	FACETS	0.875	0.803	0.95	0.437	0.401	0.475	CLONAL	1	TRUE	2	0.600771146927305	4		1212	1011	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317273	87317273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	39	598	0	ENST00000277120.3:c.298G>A	p.Asp100Asn	p.D100N	ENST00000277120		100	Gat/Aat	4/19	1	2	FACETS	0.75	0.62	0.896	0.75	0.62	0.896	SUBCLONAL	1	TRUE	1	0.14	2		598	743	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	15	403	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	1	0.795	1	1	0.795	1	CLONAL	1	TRUE	0	0.14	1		403	181	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944947	31944947	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868835690	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	21	403	0	ENST00000340398.3:c.154C>T	p.Arg52Cys	p.R52C	ENST00000340398	NM_001013699.2	52	Cgt/Tgt	1/1	1	2	FACETS	0.826	0.636	1	0.826	0.636	1	CLONAL	1	TRUE	1	0.14	2		403	363	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435399	110435399	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1264962918	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	29	525	0	ENST00000375856.3:c.3002C>T	p.Ser1001Phe	p.S1001F	ENST00000375856	NM_003749.2	1001	tCc/tTc	1/2	1	2	FACETS	0.876	0.702	1	0.876	0.702	1	CLONAL	1	TRUE	1	0.14	2		525	473	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26046038	26046038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867056701	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	27	290	0	ENST00000540144.1:c.400G>A	p.Glu134Lys	p.E134K	ENST00000540144	NM_003531.2	134	Gaa/Aaa	1/1	0.3	3	FACETS	1	0.834	1			1	CLONAL	1	TRUE	NA	0.14	3		290	391	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509849	106509849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426277818	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	39	618	0	ENST00000359195.3:c.1843G>A	p.Glu615Lys	p.E615K	ENST00000359195	NM_002649.2	615	Gaa/Aaa	2/11	1	2	FACETS	0.795	0.657	0.949	0.795	0.657	0.949	CLONAL	1	TRUE	1	0.14	2		618	701	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426121	47426121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519786	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	30	754	0	ENST00000377045.4:c.641C>T	p.Ser214Phe	p.S214F	ENST00000377045	NM_001654.4	214	tCc/tTc	7/16	1	2	FACETS	0.668	0.536	0.818	0.668	0.536	0.818	SUBCLONAL	1	TRUE	1	0.14	2		754	642	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915055	131915055	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786203485	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	36	599	1	ENST00000265335.6:c.412C>T	p.Arg138Ter	p.R138*	ENST00000265335		138	Cga/Tga	4/25	1	2	FACETS	0.778	0.638	0.936	0.778	0.638	0.936	CLONAL	1	TRUE	1	0.14	2		600	661	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714448	117714448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775340905	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	42	589	0	ENST00000368508.3:c.1201G>A	p.Glu401Lys	p.E401K	ENST00000368508	NM_002944.2	401	Gag/Aag	11/43	1	2	FACETS	1	0.835	1	1	0.835	1	CLONAL	1	TRUE	1	0.14	2		589	599	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180050958	180050958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781305649	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	32	790	0	ENST00000261937.6:c.1525G>A	p.Glu509Lys	p.E509K	ENST00000261937	NM_182925.4	509	Gag/Aag	11/30	0.3	1	FACETS	0.729	0.59	0.887	0.729	0.59	0.887	SUBCLONAL	1	TRUE	0	0.14	1		790	583	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031699	69031699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	37	692	1	ENST00000288368.4:c.3454C>T	p.His1152Tyr	p.H1152Y	ENST00000288368	NM_024870.2	1152	Cat/Tat	28/40	1	2	FACETS	0.805	0.662	0.965	0.805	0.662	0.965	CLONAL	1	TRUE	1	0.14	2		693	657	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222510	39222510	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167317994	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	34	565	1	ENST00000402219.2:c.3100C>T	p.Pro1034Ser	p.P1034S	ENST00000402219	NM_005633.3	1034	Ccc/Tcc	20/23	1	2	FACETS	0.753	0.614	0.911	0.753	0.614	0.911	CLONAL	1	TRUE	1	0.14	2		566	645	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164709	36164709	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1350744261	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	30	609	1	ENST00000300305.3:c.1166C>T	p.Ser389Leu	p.S389L	ENST00000300305		389	tCg/tTg	8/8	1	2	FACETS	0.743	0.597	0.909	0.743	0.597	0.909	CLONAL	1	TRUE	1	0.14	2		610	577	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937048	36937048	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	54	502	0	ENST00000361632.4:c.1271T>C	p.Phe424Ser	p.F424S	ENST00000361632		424	tTc/tCc	9/16	1	2	FACETS	0.828	0.708	0.958	1	0.97	1	CLONAL	2	TRUE	1	0.14	2		502	466	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851402	156851402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	32	701	0	ENST00000524377.1:c.2359G>A	p.Ala787Thr	p.A787T	ENST00000524377	NM_002529.3	787	Gca/Aca	17/17	1	2	FACETS	0.794	0.643	0.965	0.794	0.643	0.965	CLONAL	1	TRUE	1	0.14	2		701	576	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344275	118344275	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375240261	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	24	508	0	ENST00000534358.1:c.2401C>T	p.His801Tyr	p.H801Y	ENST00000534358	NM_005933.3	801	Cat/Tat	3/36	1	2	FACETS	0.728	0.569	0.912	0.728	0.569	0.912	CLONAL	1	TRUE	1	0.14	2		508	471	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375782	118375782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782150443	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	31	563	1	ENST00000534358.1:c.9175C>T	p.Pro3059Ser	p.P3059S	ENST00000534358	NM_005933.3	3059	Ccg/Tcg	27/36	1	2	FACETS	0.792	0.639	0.966	0.792	0.639	0.966	CLONAL	1	TRUE	1	0.14	2		564	559	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444382	49444382	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	28	648	0	ENST00000301067.7:c.2989C>T	p.Pro997Ser	p.P997S	ENST00000301067	NM_003482.3	997	Ccc/Tcc	11/54	1	2	FACETS	0.768	0.612	0.946	0.768	0.612	0.946	CLONAL	1	TRUE	1	0.14	2		648	521	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608279	28608279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	39	722	1	ENST00000241453.7:c.1777G>A	p.Asp593Asn	p.D593N	ENST00000241453	NM_004119.2	593	Gat/Aat	14/24	1	2	FACETS	0.781	0.646	0.933	0.781	0.646	0.933	CLONAL	1	TRUE	1	0.14	2		723	713	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683996	29683996	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	36	674	0	ENST00000356175.3:c.7694C>A	p.Ser2565Ter	p.S2565*	ENST00000356175	NM_000267.3	2565	tCa/tAa	52/57	1	2	FACETS	0.751	0.615	0.903	0.751	0.615	0.903	CLONAL	1	TRUE	1	0.14	2		674	685	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858208	59858208	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs864622155	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	36	551	0	ENST00000259008.2:c.1787C>T	p.Pro596Leu	p.P596L	ENST00000259008	NM_032043.2	596	cCa/cTa	12/20	1	2	FACETS	0.829	0.68	0.997	0.829	0.68	0.997	CLONAL	1	TRUE	1	0.14	2		551	620	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796963	78796963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	34	569	0	ENST00000306801.3:c.1076C>T	p.Ser359Leu	p.S359L	ENST00000306801	NM_020761.2	359	tCg/tTg	9/34	1	2	FACETS	0.805	0.657	0.974	0.805	0.657	0.974	CLONAL	1	TRUE	1	0.14	2		569	603	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794728	42794728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769275790	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	34	666	0	ENST00000575354.2:c.1808C>T	p.Pro603Leu	p.P603L	ENST00000575354	NM_015125.3	603	cCc/cTc	10/20	1	2	FACETS	0.872	0.711	1	0.872	0.711	1	CLONAL	1	TRUE	1	0.14	2		666	557	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721066	61721066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	41	607	0	ENST00000401558.2:c.1208C>T	p.Pro403Leu	p.P403L	ENST00000401558	NM_003400.3	403	cCt/cTt	12/25	1	2	FACETS	0.915	0.761	1	0.915	0.761	1	CLONAL	1	TRUE	1	0.14	2		607	640	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265010	198265010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	57	429	0	ENST00000335508.6:c.2867C>T	p.Ser956Phe	p.S956F	ENST00000335508	NM_012433.2	956	tCt/tTt	19/25	1	2	FACETS	0.786	0.675	0.907	1	0.97	1	CLONAL	2	TRUE	1	0.14	2		429	518	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732774	204732774	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	35	460	0	ENST00000302823.3:c.109G>A	p.Ala37Thr	p.A37T	ENST00000302823	NM_005214.4	37	Gca/Aca	1/4	1	2	FACETS	0.882	0.721	1	0.882	0.721	1	CLONAL	1	TRUE	1	0.14	2		460	567	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645955	215645955	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	41	563	0	ENST00000260947.4:c.643A>C	p.Asn215His	p.N215H	ENST00000260947	NM_000465.2	215	Aac/Cac	4/11	1	2	FACETS	0.79	0.657	0.94	0.79	0.657	0.94	CLONAL	1	TRUE	1	0.14	2		563	741	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793358	242793358	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	36	734	1	ENST00000334409.5:c.719C>T	p.Pro240Leu	p.P240L	ENST00000334409	NM_005018.2	240	cCc/cTc	5/5	0.3	1	FACETS	0.783	0.642	0.941	0.783	0.642	0.941	CLONAL	1	TRUE	0	0.14	1		735	611	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525099	9525099	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	31	645	0	ENST00000353224.5:c.1786G>A	p.Glu596Lys	p.E596K	ENST00000353224	NM_177990.2	596	Gag/Aag	8/10	1	2	FACETS	0.743	0.599	0.907	0.743	0.599	0.907	CLONAL	1	TRUE	1	0.14	2		645	596	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076880	41076880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	29	556	1	ENST00000373198.4:c.1540G>A	p.Gly514Arg	p.G514R	ENST00000373198	NM_133170.3	514	Ggg/Agg	9/32	0.3	1	FACETS	0.712	0.57	0.874	0.712	0.57	0.874	SUBCLONAL	1	TRUE	0	0.14	1		557	541	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433429	138433429	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	48	687	1	ENST00000289153.2:c.1183C>T	p.Pro395Ser	p.P395S	ENST00000289153	NM_006219.2	395	Cca/Tca	7/22	1	2	FACETS	0.884	0.745	1	0.884	0.745	1	CLONAL	1	TRUE	1	0.14	2		688	776	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191494	185191494	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	38	752	0	ENST00000265026.3:c.2375C>T	p.Thr792Ile	p.T792I	ENST00000265026	NM_004721.4	792	aCc/aTc	11/14	1	2	FACETS	0.766	0.631	0.917	0.766	0.631	0.917	CLONAL	1	TRUE	1	0.14	2		752	709	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805462	1805462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	33	744	1	ENST00000260795.2:c.974C>T	p.Ser325Phe	p.S325F	ENST00000260795		325	tCc/tTc	7/17	1	2	FACETS	0.837	0.681	1	0.837	0.681	1	CLONAL	1	TRUE	1	0.14	2		745	563	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188788	32188788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1036330983	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	28	704	0	ENST00000375023.3:c.766G>A	p.Asp256Asn	p.D256N	ENST00000375023	NM_004557.3	256	Gac/Aac	4/30	1	2	FACETS	0.714	0.569	0.88	0.714	0.569	0.88	SUBCLONAL	1	TRUE	1	0.14	2		704	560	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402812	139402812	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771739312	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	41	710	1	ENST00000277541.6:c.3197C>T	p.Ser1066Leu	p.S1066L	ENST00000277541	NM_017617.3	1066	tCg/tTg	20/34	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.14	2		711	558	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921577	39921577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771281786	NA	P-0024339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	38	653	0	ENST00000378444.4:c.4243G>A	p.Glu1415Lys	p.E1415K	ENST00000378444	NM_001123385.1	1415	Gag/Aag	10/15	1	2	FACETS	0.957	0.79	1	0.957	0.79	1	CLONAL	1	TRUE	1	0.14	2		653	567	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	30	571	0				ENST00000310581	NM_198253.2	-/1132			0.201981166502575	1	FACETS	1	0.938	1	1	0.938	1	INDETERMINATE	1	TRUE	0	0.405768507598956	1		571	88	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981529	201981530	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0024340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	88	828	0	ENST00000359651.3:c.445dup	p.Ala149GlyfsTer12	p.A149Gfs*12	ENST00000359651		148	atg/atGg	3/8	0.276889496373989	3	FACETS	0.815	0.73	0.905	0.815	0.73	0.905	CLONAL	2	TRUE	1	0.405768507598956	3		828	320	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914486	32914486	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	70	816	0	ENST00000380152.3:c.5994A>T	p.Gln1998His	p.Q1998H	ENST00000380152		1998	caA/caT	11/27	0.34800883250915	3	FACETS	0.641	0.559	0.731	0.321	0.279	0.366	SUBCLONAL	1	TRUE	1	0.405768507598956	3		816	647	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993165	72993165	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs202133340	NA	P-0024340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	53	855	0	ENST00000268489.5:c.880G>T	p.Val294Phe	p.V294F	ENST00000268489	NM_006885.3	294	Gtc/Ttc	2/10	0.188090796045496	1	FACETS	0.362	0.308	0.42	0.362	0.308	0.42	INDETERMINATE	1	TRUE	0	0.405768507598956	1		855	576	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370323	40370323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs983871904	NA	P-0024340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	97	956	1	ENST00000293328.3:c.1015C>T	p.Pro339Ser	p.P339S	ENST00000293328	NM_012448.3	339	Cct/Tct	9/19	0.276889496373989	3	FACETS	1	0.914	1	0.513	0.458	0.57	CLONAL	1	TRUE	1	0.405768507598956	3		957	561	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52725463	52725463	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	31	726	0	ENST00000322088.6:c.1630C>G	p.Leu544Val	p.L544V	ENST00000322088	NM_014225.5	544	Ctg/Gtg	13/15	1	2	FACETS	0.344	0.278	0.419	0.344	0.278	0.419	SUBCLONAL	1	TRUE	1	0.405768507598956	2		726	444	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754827	29754827	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	39	600	0	ENST00000389048.3:c.1108G>T	p.Glu370Ter	p.E370*	ENST00000389048	NM_004304.4	370	Gag/Tag	4/29	0.188090796045496	1	FACETS	0.494	0.411	0.586	0.494	0.411	0.586	INDETERMINATE	1	TRUE	0	0.405768507598956	1		600	310	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268483	46268483	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs778964948	NA	P-0024340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	127	484	0	ENST00000371998.3:c.2870C>G	p.Ser957Cys	p.S957C	ENST00000371998		957	tCt/tGt	15/23	0.34800883250915	3	FACETS	0.951	0.87	1	0.951	0.87	1	CLONAL	2	TRUE	1	0.405768507598956	3		484	396	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170002311	170002311	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	51	231	0	ENST00000295797.4:c.1130G>A	p.Arg377Lys	p.R377K	ENST00000295797	NM_002740.5	377	aGa/aAa	12/18	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.405768507598956	2		231	206	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69050743	69050743	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	26	494	0	ENST00000288368.4:c.4078C>G	p.Leu1360Val	p.L1360V	ENST00000288368	NM_024870.2	1360	Ctg/Gtg	33/40	0.197058357882082	1	FACETS	0.291	0.23	0.361	0.291	0.23	0.361	INDETERMINATE	1	TRUE	0	0.405768507598956	1		494	351	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0024341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	230	622	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.313847621707651	5	FACETS	0.987	0.942	1	0.79	0.753	0.825	INDETERMINATE	4	TRUE	0	0.684449463448119	5		622	345	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0024341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	58	706	1	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.684449463448119	2		707	116	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715619	30715619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730880224	NA	P-0024341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	30	413	0	ENST00000295754.5:c.1277C>T	p.Ala426Val	p.A426V	ENST00000295754	NM_003242.5	426	gCt/gTt	5/7	0.684449463448119	1	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	0	0.684449463448119	1		413	54	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012465	29012465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373801409	NA	P-0024341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	35	683	0	ENST00000282397.4:c.406G>A	p.Val136Ile	p.V136I	ENST00000282397	NM_002019.4	136	Gta/Ata	4/30	0.684449463448119	7	FACETS	1	0.908	1	0.194	0.16	0.232	CLONAL	1	TRUE	1	0.684449463448119	7		683	238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578250	7578250	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1131691011	NA	P-0024341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	43	880	0	ENST00000269305.4:c.599del	p.Asn200IlefsTer47	p.N200Ifs*47	ENST00000269305	NM_001126112.2	200	aAt/at	6/11	0.672951335534524	1	FACETS	0.908	0.79	1	0.908	0.79	1	CLONAL	1	TRUE	0	0.684449463448119	1		880	91	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730910	40730910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370873414	NA	P-0024341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	34	666	3	ENST00000373198.4:c.3625C>T	p.Arg1209Trp	p.R1209W	ENST00000373198	NM_133170.3	1209	Cgg/Tgg	27/32	0.282677218840978	1	FACETS	0.641	0.538	0.749	0.641	0.538	0.749	INDETERMINATE	1	TRUE	0	0.684449463448119	1		669	102	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446262	70446262	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	38	631	0	ENST00000373644.4:c.5202C>G	p.Ile1734Met	p.I1734M	ENST00000373644	NM_030625.2	1734	atC/atG	11/12	1	2	FACETS	0.841	0.71	0.981	0.841	0.71	0.981	CLONAL	1	TRUE	1	0.684449463448119	2		631	132	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021251	31021251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769921728	NA	P-0024341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	34	648	0	ENST00000375687.4:c.1250G>A	p.Arg417Gln	p.R417Q	ENST00000375687	NM_015338.5	417	cGa/cAa	12/13	0.282677218840978	1	FACETS	0.499	0.415	0.589	0.499	0.415	0.589	INDETERMINATE	1	TRUE	0	0.684449463448119	1		648	131	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111420	56111420	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs776502274	NA	P-0024341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	93	399	0	ENST00000399503.3:c.20A>G	p.Asn7Ser	p.N7S	ENST00000399503	NM_005921.1	7	aAt/aGt	1/20	1	2	FACETS	0.95	0.856	1	0.95	0.856	1	CLONAL	1	TRUE	1	0.684449463448119	2		399	286	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	359972	359972	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0024343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	324	739	15	ENST00000262320.3:c.1116+1G>A		p.X372_splice	ENST00000262320	NM_003502.3	372			0.650486480271988	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.650486480271988	1		754	642	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647182	23647182	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	431	1089	3	ENST00000261584.4:c.685C>G	p.Pro229Ala	p.P229A	ENST00000261584	NM_024675.3	229	Cca/Gca	4/13	0.650486480271988	1	FACETS	0.931	0.892	0.971	0.931	0.892	0.971	CLONAL	1	TRUE	0	0.650486480271988	1		1092	960	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176336	24176336	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	378	926	12	ENST00000263121.7:c.1127G>C	p.Arg376Thr	p.R376T	ENST00000263121	NM_003073.3	376	aGg/aCg	9/9	1	2	FACETS	0.996	0.946	1	0.996	0.946	1	CLONAL	1	TRUE	1	0.650486480271988	2		938	1167	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0024345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	139	683	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.405576251594828	0	FACETS	0.676	0.617	0.737			1	SUBCLONAL	1	FALSE	0	0.405576251594828	0		683	603	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0024345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	196	732	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	FALSE	1	0.405576251594828	2		732	895	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629094	86629094	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	68	478	0	ENST00000274376.6:c.839A>G	p.Asp280Gly	p.D280G	ENST00000274376	NM_002890.2	280	gAt/gGt	4/25	0.405576251594828	0	FACETS	0.357	0.31	0.407			1	SUBCLONAL	1	FALSE	0	0.405576251594828	0		478	559	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439784	51439784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1321555751	NA	P-0024345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	89	482	0	ENST00000262662.1:c.349C>T	p.Arg117Trp	p.R117W	ENST00000262662		117	Cgg/Tgg	4/4	0.405576251594828	0	FACETS	0.535	0.476	0.597			1	SUBCLONAL	1	FALSE	0	0.405576251594828	0		482	488	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752974	42752974	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	139	800	0	ENST00000222329.4:c.1290C>G	p.Ile430Met	p.I430M	ENST00000222329	NM_006494.2	430	atC/atG	4/4	0.405576251594828	0	FACETS	0.53	0.483	0.579			1	SUBCLONAL	1	FALSE	0	0.405576251594828	0		800	769	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	57	571	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.503612069740187	2		571	177	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717777	89717777	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0024346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	114	527	0	ENST00000371953.3:c.801+1G>T		p.X267_splice	ENST00000371953	NM_000314.4	267			0.503612069740187	1	FACETS	0.951	0.866	1	0.951	0.866	1	CLONAL	1	TRUE	0	0.503612069740187	1		527	356	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945731	206945731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	145	840	0	ENST00000423557.1:c.50G>A	p.Arg17Lys	p.R17K	ENST00000423557	NM_000572.2	17	aGg/aAg	1/5	1	2	FACETS	0.976	0.894	1	0.976	0.894	1	CLONAL	1	TRUE	1	0.503612069740187	2		840	590	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966664	36966664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142210825	NA	P-0024346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	140	802	0	ENST00000358127.4:c.662G>A	p.Arg221Gln	p.R221Q	ENST00000358127	NM_001280556.1	221	cGg/cAg	6/10	0.503612069740187	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.503612069740187	1		802	349	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921551	178921551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	20	486	0	ENST00000263967.3:c.1033A>G	p.Asn345Asp	p.N345D	ENST00000263967	NM_006218.2	345	Aat/Gat	5/21	1	2	FACETS	0.102	0.077	0.131	0.102	0.077	0.131	SUBCLONAL	1	TRUE	1	0.649269663045625	2		486	605	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0024347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	59	588	1	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.232	0.198	0.268	0.232	0.198	0.268	SUBCLONAL	1	TRUE	1	0.649269663045625	2		589	785	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11177096	11177096	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878855328	NA	P-0024347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	269	582	0	ENST00000361445.4:c.6981G>A	p.Met2327Ile	p.M2327I	ENST00000361445	NM_004958.3	2327	atG/atA	50/58	1	2	FACETS	0.976	0.918	1	0.976	0.918	1	CLONAL	1	TRUE	1	0.649269663045625	2		582	849	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685330	86685330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	117	175	0	ENST00000274376.6:c.3046C>T	p.Arg1016Cys	p.R1016C	ENST00000274376	NM_002890.2	1016	Cgt/Tgt	24/25	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.649269663045625	2		175	273	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023591	31023594	+	frameshift_variant	Frame_Shift_Del	DEL	GGAT	GGAT	-	novel	NA	P-0024347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	220	602	0	ENST00000375687.4:c.3076_3079del	p.Gly1026LeufsTer20	p.G1026Lfs*20	ENST00000375687	NM_015338.5	1026	GGATct/ct	13/13	1	2	FACETS	0.968	0.905	1	0.968	0.905	1	CLONAL	1	TRUE	1	0.649269663045625	2		602	700	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713683	30713689	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGACG	CCTGACG	-	novel	NA	P-0024347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	171	482	0	ENST00000295754.5:c.1009_1015del	p.Leu337GlyfsTer49	p.L337Gfs*49	ENST00000295754	NM_003242.5	336	taCCTGACG/ta	4/7	1	2	FACETS	0.894	0.827	0.964	0.894	0.827	0.964	CLONAL	1	TRUE	1	0.649269663045625	2		482	589	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968664	55968669	+	inframe_deletion	In_Frame_Del	DEL	GTGCCA	GTGCCA	-	novel	NA	P-0024347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	466	555	0	ENST00000263923.4:c.1994_1999del	p.Val665_Pro667delinsAla	p.V665_P667delinsA	ENST00000263923	NM_002253.2	665	gTGGCACcc/gcc	14/30	0.151437250940877	6	FACETS	1	0.993	1			1	INDETERMINATE	3	TRUE	NA	0.649269663045625	6		555	963	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713602	30713605	+	protein_altering_variant	In_Frame_Del	DEL	GGCT	GGCT	C	novel	NA	P-0024347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	197	445	0	ENST00000295754.5:c.927_930delinsC	p.Ala310del	p.A310del	ENST00000295754	NM_003242.5	309	acGGCT/acC	4/7	1	2	FACETS	0.963	0.897	1	0.963	0.897	1	CLONAL	1	TRUE	1	0.649269663045625	2		445	630	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057520000	NA	P-0024349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	171	907	1	ENST00000269305.4:c.452C>A	p.Pro151His	p.P151H	ENST00000269305	NM_001126112.2	151	cCc/cAc	5/11	0.302387938846369	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.302387938846369	2		908	517	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913381	NA	P-0024349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	54	256	0	ENST00000304494.5:c.322G>T	p.Asp108Tyr	p.D108Y	ENST00000304494	NM_000077.4	108	Gat/Tat	2/3	0.302387938846369	1	FACETS	0.773	0.671	0.882	1	0.971	1	SUBCLONAL	2	TRUE	0	0.302387938846369	1		256	196	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0024349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	195	683	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	0.302387938846369	2	FACETS	0.879	0.816	0.943	0.879	0.816	0.943	CLONAL	2	TRUE	0	0.302387938846369	2		683	734	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468081	50468081	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	139	522	0	ENST00000331340.3:c.1316G>T	p.Arg439Leu	p.R439L	ENST00000331340	NM_006060.4	439	cGc/cTc	8/8	0.302387938846369	4	FACETS	1	0.939	1	1	0.939	1	CLONAL	3	TRUE	1	0.302387938846369	4		522	390	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023685	27023685	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	69	332	0	ENST00000324856.7:c.791C>A	p.Ser264Ter	p.S264*	ENST00000324856	NM_006015.4	264	tCg/tAg	1/20	0.247936657958535	3	FACETS	0.952	0.838	1	0.952	0.838	1	CLONAL	2	TRUE	1	0.302387938846369	3		332	276	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591641	38591641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	236	756	0	ENST00000299084.4:c.100C>T	p.Leu34Phe	p.L34F	ENST00000299084	NM_152594.2	34	Ctt/Ttt	2/7	0.29563496620783	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.302387938846369	2		756	715	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14016026	14016026	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	70	445	0	ENST00000311895.7:c.346G>T	p.Val116Phe	p.V116F	ENST00000311895	NM_005236.2	116	Gtt/Ttt	2/11	0.302387938846369	1	FACETS	0.891	0.78	1	0.891	0.78	1	CLONAL	1	TRUE	0	0.302387938846369	1		445	441	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468445	89468445	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	117	523	0	ENST00000336596.2:c.1979C>A	p.Thr660Lys	p.T660K	ENST00000336596	NM_005233.5	660	aCa/aAa	11/17	0.203895426914068	5	FACETS	0.955	0.864	1	0.637	0.576	0.701	CLONAL	2	TRUE	2	0.302387938846369	5		523	589	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956207	55956207	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	108	814	0	ENST00000263923.4:c.3108A>T	p.Leu1036Phe	p.L1036F	ENST00000263923	NM_002253.2	1036	ttA/ttT	23/30	0.247936657958535	3	FACETS	0.944	0.847	1	0.472	0.423	0.524	CLONAL	1	TRUE	1	0.302387938846369	3		814	871	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515196	106515196	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	81	661	0	ENST00000359195.3:c.2339C>A	p.Pro780His	p.P780H	ENST00000359195	NM_002649.2	780	cCc/cAc	5/11	0.302387938846369	3	FACETS	0.79	0.695	0.892	0.395	0.347	0.446	SUBCLONAL	1	TRUE	1	0.302387938846369	3		661	781	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372233	55372233	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	25	212	0	ENST00000297316.4:c.923G>T	p.Gly308Val	p.G308V	ENST00000297316	NM_022454.3	308	gGg/gTg	2/2	0.302387938846369	3	FACETS	1	0.884	1	0.588	0.467	0.723	CLONAL	1	TRUE	1	0.302387938846369	3		212	162	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0024352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	139	1169	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.23069885321464	1	FACETS	0.948	0.862	1	0.948	0.862	1	CLONAL	1	TRUE	0	0.23069885321464	1		1169	1124	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0024352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	110	1014	1	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	0.23069885321464	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.23069885321464	1		1015	745	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259089	153259089	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0024352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	31	431	0	ENST00000281708.4:c.727-1G>A		p.X243_splice	ENST00000281708	NM_033632.3	243			0.23069885321464	1	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	0	0.23069885321464	1		431	193	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443560	49443561	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	78	863	0	ENST00000301067.7:c.3810dup	p.Leu1271ThrfsTer15	p.L1271Tfs*15	ENST00000301067	NM_003482.3	1270	-/A	11/54	1	2	FACETS	0.832	0.73	0.942	0.832	0.73	0.942	CLONAL	1	TRUE	1	0.23069885321464	2		863	813	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958477	90958477	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	73	925	0	ENST00000265433.3:c.1961T>C	p.Leu654Pro	p.L654P	ENST00000265433	NM_002485.4	654	cTg/cCg	13/16	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.23069885321464	2		925	592	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072540	5072540	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	29	689	1	ENST00000381652.3:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000381652	NM_004972.3	564	Cga/Tga	13/25	0.23069885321464	1	FACETS	0.548	0.439	0.671	0.548	0.439	0.671	SUBCLONAL	1	TRUE	0	0.23069885321464	1		690	406	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309041	137309041	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs146295223	NA	P-0024352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	101	1146	0	ENST00000481739.1:c.648C>A	p.Asn216Lys	p.N216K	ENST00000481739	NM_002957.4	216	aaC/aaA	5/10	1	2	FACETS	0.882	0.787	0.983	0.882	0.787	0.983	CLONAL	1	TRUE	1	0.23069885321464	2		1146	993	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913233	NA	P-0024353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	186	944	0	ENST00000451590.1:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000451590	NM_001130442.1	61	cAg/cTg	3/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		944	489	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	184	629	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.205027411105209	3	FACETS	0.94	0.869	1	0.94	0.869	1	CLONAL	2	TRUE	1	0.269147368289873	3		629	825	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0024357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	101	884	2	ENST00000374080.3:c.3670C>T	p.Leu1224Phe	p.L1224F	ENST00000374080		1224	Ctc/Ttc	26/45	1	2	FACETS	0.946	0.846	1	0.946	0.846	1	CLONAL	1	TRUE	1	0.269147368289873	2		886	793	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0024357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	90	679	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.825	0.731	0.925	0.825	0.731	0.925	CLONAL	1	TRUE	1	0.269147368289873	2		679	811	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0024359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	110	683	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.374221282339959	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.374221282339959	1		683	383	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633320	8633320	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866980874	NA	P-0024359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	95	955	0	ENST00000356435.5:c.349C>T	p.Arg117Trp	p.R117W	ENST00000356435		117	Cgg/Tgg	3/35	0.285390080655273	2	FACETS	0.897	0.801	0.999	0.449	0.4	0.5	CLONAL	1	TRUE	0	0.374221282339959	2		955	566	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266516	115266516	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	42	971	0	ENST00000438362.2:c.1999A>T	p.Ile667Phe	p.I667F	ENST00000438362	NM_001242891.1	667	Att/Ttt	16/20	1	2	FACETS	0.407	0.339	0.482	0.407	0.339	0.482	SUBCLONAL	1	TRUE	1	0.374221282339959	2		971	552	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781450	3781450	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs770154926	NA	P-0024359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	48	626	0	ENST00000262367.5:c.4915G>T	p.Ala1639Ser	p.A1639S	ENST00000262367	NM_004380.2	1639	Gct/Tct	30/31	0.374221282339959	1	FACETS	0.961	0.822	1	0.961	0.822	1	CLONAL	1	TRUE	0	0.374221282339959	1		626	217	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828334	50828334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	21	700	0	ENST00000398568.2:c.2672G>T	p.Arg891Leu	p.R891L	ENST00000398568	NM_001042412.1	891	cGg/cTg	17/18	1	2	FACETS	0.283	0.217	0.359	0.283	0.217	0.359	SUBCLONAL	1	TRUE	1	0.374221282339959	2		700	397	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0024360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	52	249	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.7	0.599	0.81	0.7	0.599	0.81	SUBCLONAL	1	TRUE	1	0.435610901494763	2		249	341	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0024360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	87	238	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.902	0.802	1	0.902	0.802	1	CLONAL	1	TRUE	1	0.435610901494763	2		238	443	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692886	89692886	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121909223	NA	P-0024360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	290	273	0	ENST00000371953.3:c.370T>G	p.Cys124Gly	p.C124G	ENST00000371953	NM_000314.4	124	Tgt/Ggt	5/9	0.419664794637896	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	0	0.435610901494763	3		273	510	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445132	49445132	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	168	539	0	ENST00000301067.7:c.2334C>A	p.Cys778Ter	p.C778*	ENST00000301067	NM_003482.3	778	tgC/tgA	10/54	1	2	FACETS	0.865	0.795	0.937	0.865	0.795	0.937	CLONAL	1	TRUE	1	0.435610901494763	2		539	892	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38545389	38545389	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs1324903101	NA	P-0024360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	121	488	0	ENST00000299084.4:c.3G>A	p.Met1?	p.M1?	ENST00000299084	NM_152594.2	1	atG/atA	1/7	1	2	FACETS	0.792	0.717	0.872	0.792	0.717	0.872	SUBCLONAL	1	TRUE	1	0.435610901494763	2		488	701	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655489	67655490	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	116	306	0	ENST00000264010.4:c.1355dup	p.Leu452PhefsTer13	p.L452Ffs*13	ENST00000264010	NM_006565.3	451	gat/gaTt	7/12	1	2	FACETS	0.946	0.856	1	0.946	0.856	1	CLONAL	1	TRUE	1	0.435610901494763	2		306	563	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591272	67591318	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	GCAAAAGAAGTTGAACGAGTGGTTGGGCAATGAAAACACTGAAGAGT	GCAAAAGAAGTTGAACGAGTGGTTGGGCAATGAAAACACTGAAGAGT	-	novel	NA	P-0024360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	107	336	0	ENST00000274335.5:c.1770_1814+2del		p.X590_splice	ENST00000274335		590		13/15	0.435610901494763	3	FACETS	1	0.964	1	0.575	0.518	0.636	CLONAL	1	TRUE	1	0.435610901494763	3		336	520	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0024362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	48	966	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.999	0.844	1	0.999	0.844	1	CLONAL	1	TRUE	1	0.18	2		967	534	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828250	50828250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776677068	NA	P-0024362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	22	364	0	ENST00000398568.2:c.2588G>A	p.Cys863Tyr	p.C863Y	ENST00000398568	NM_001042412.1	863	tGc/tAc	17/18	1	2	FACETS	0.652	0.505	0.823	0.652	0.505	0.823	SUBCLONAL	1	TRUE	1	0.18	2		364	375	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267400	198267400	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	178	505	1	ENST00000335508.6:c.1957A>C	p.Lys653Gln	p.K653Q	ENST00000335508	NM_012433.2	653	Aaa/Caa	14/25	0.42190426030514	1	FACETS	0.359	0.332	0.388	0.359	0.332	0.388	INDETERMINATE	1	TRUE	0	0.835136836912113	1		506	691	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428973	47428973	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	262	669	0	ENST00000377045.4:c.1336G>C	p.Gly446Arg	p.G446R	ENST00000377045	NM_001654.4	446	Ggt/Cgt	13/16	NA	2	FACETS	0.578	0.541	0.615			1	INDETERMINATE	1	TRUE	NA	0.835136836912113	2		669	1086	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370709	55370709	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	25	476	0	ENST00000297316.4:c.11C>A	p.Pro4Gln	p.P4Q	ENST00000297316	NM_022454.3	4	cCg/cAg	1/2	1	2	FACETS	0.709	0.558	0.882	0.709	0.558	0.882	SUBCLONAL	1	TRUE	1	0.18	2		476	392	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94201029	94201029	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs781140391	NA	P-0024366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	10	387	0	ENST00000323929.3:c.1048G>T	p.Glu350Ter	p.E350*	ENST00000323929	NM_005591.3	350	Gaa/Taa	10/20	1	2	FACETS	0.703	0.477	0.986	0.703	0.477	0.986	CLONAL	1	TRUE	1	0.18	2		387	158	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240621	133240621	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	33	505	1	ENST00000320574.5:c.2675A>T	p.Tyr892Phe	p.Y892F	ENST00000320574	NM_006231.2	892	tAc/tTc	23/49	1	2	FACETS	0.952	0.776	1	0.952	0.776	1	CLONAL	1	TRUE	1	0.18	2		506	385	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379441	225379441	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	20	611	0	ENST00000264414.4:c.427G>C	p.Gly143Arg	p.G143R	ENST00000264414	NM_003590.4	143	Gga/Cga	4/16	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.18	2		611	176	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513532	41513532	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	31	494	0	ENST00000263253.7:c.436G>T	p.Gly146Cys	p.G146C	ENST00000263253	NM_001429.3	146	Ggt/Tgt	2/31	1	2	FACETS	0.923	0.747	1	0.923	0.747	1	CLONAL	1	TRUE	1	0.18	2		494	373	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295291	1295291	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0024366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	45	591	3				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.18	2		594	459	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041692	47041692	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	41	639	0	ENST00000377604.3:c.1917G>T	p.Lys639Asn	p.K639N	ENST00000377604	NM_001204468.1	639	aaG/aaT	17/24	0.161914808335285	1	FACETS	0.848	0.706	1	0.848	0.706	1	CLONAL	1	TRUE	0	0.18	1		639	489	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578496	7578496	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782197	NA	P-0024368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	170	685	2	ENST00000269305.4:c.434T>C	p.Leu145Pro	p.L145P	ENST00000269305	NM_001126112.2	145	cTg/cCg	5/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.28	2		687	1062	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981803	201981803	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	101	611	0	ENST00000359651.3:c.514G>T	p.Asp172Tyr	p.D172Y	ENST00000359651		172	Gac/Tac	4/8	1	2	FACETS	0.732	0.653	0.817	0.732	0.653	0.817	SUBCLONAL	1	TRUE	1	0.28	2		611	985	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653785	89653785	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	52	298	0	ENST00000371953.3:c.83T>G	p.Ile28Ser	p.I28S	ENST00000371953	NM_000314.4	28	aTt/aGt	2/9	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.28	2		298	351	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719561	61719561	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	32	439	0	ENST00000401558.2:c.1622C>A	p.Ala541Glu	p.A541E	ENST00000401558	NM_003400.3	541	gCa/gAa	15/25	0.288256150550797	1	FACETS	0.341	0.276	0.414	0.341	0.276	0.414	SUBCLONAL	1	TRUE	0	0.28	1		439	577	SUCCESS
APC	324	MSKCC	GRCh37	5	112173887	112173887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	80	294	0	ENST00000257430.4:c.2596G>A	p.Ala866Thr	p.A866T	ENST00000257430	NM_000038.5	866	Gca/Aca	16/16	0.28352560354047	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.28	1		294	435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578518	7578518	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934875	NA	P-0024369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	361	817	0	ENST00000269305.4:c.412G>C	p.Ala138Pro	p.A138P	ENST00000269305	NM_001126112.2	138	Gcc/Ccc	5/11	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.555405016173777	2		817	960	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644490	18644490	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs181773550	NA	P-0024369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	213	453	0	ENST00000266497.5:c.2668G>A	p.Asp890Asn	p.D890N	ENST00000266497		890	Gat/Aat	18/31	0.555405016173777	3	FACETS	1	0.99	1	0.671	0.626	0.718	CLONAL	1	TRUE	1	0.555405016173777	3		453	730	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0024369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	346	583	1	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	0.229155552633573	6	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.555405016173777	6		584	1087	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577330	64577333	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	rs587776841	NA	P-0024369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	194	570	0	ENST00000312049.6:c.249_252del	p.Ile85SerfsTer33	p.I85Sfs*33	ENST00000312049	NM_130799.2	83	ctGTCT/ct	2/10	0.555405016173777	1	FACETS	0.863	0.803	0.923	0.863	0.803	0.923	CLONAL	1	TRUE	0	0.555405016173777	1		570	585	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0024370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	153	617	0	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	0.335010457572295	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.335010457572295	1		617	717	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257570	19257570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368120349	NA	P-0024370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	105	626	1	ENST00000162023.5:c.656G>A	p.Arg219Gln	p.R219Q	ENST00000162023		219	cGa/cAa	10/13	1	2	FACETS	0.794	0.712	0.883	0.794	0.712	0.883	SUBCLONAL	1	TRUE	1	0.335010457572295	2		627	789	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245820	5245820	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746218785	NA	P-0024370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	147	759	2	ENST00000357368.4:c.955G>A	p.Val319Ile	p.V319I	ENST00000357368	NM_002850.3	319	Gtc/Atc	10/38	1	2	FACETS	0.916	0.836	1	0.916	0.836	1	CLONAL	1	TRUE	1	0.335010457572295	2		761	958	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524589	103524589	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	37	268	1	ENST00000355739.4:c.2720C>G	p.Pro907Arg	p.P907R	ENST00000355739	NM_000123.3	907	cCt/cGt	13/15	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.15	2		269	408	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0024373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	290	790	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.69727083811642	3	FACETS	0.974	0.926	1	0.974	0.926	1	CLONAL	2	TRUE	1	0.69727083811642	3		790	576	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0024373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	95	630	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	1	2	FACETS	0.868	0.782	0.957	0.868	0.782	0.957	CLONAL	1	TRUE	1	0.69727083811642	2		630	314	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0024381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	38	437	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	1	0.835	1	1	0.835	1	CLONAL	1	TRUE	1	0.16	2		437	470	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501356	140501356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	22	260	0	ENST00000288602.6:c.716G>A	p.Arg239Gln	p.R239Q	ENST00000288602	NM_004333.4	239	cGa/cAa	6/18	1	2	FACETS	0.902	0.699	1	0.902	0.699	1	CLONAL	1	TRUE	1	0.16	2		260	305	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953760	48953760	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913302	NA	P-0024382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	121	280	0	ENST00000267163.4:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000267163	NM_000321.2	455	Cga/Tga	14/27	0.336175248832373	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	0	0.336175248832373	2		280	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0024382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	323	917	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	2	TRUE	NA	0.336175248832373	2		918	915	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061602	38061602	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	47	239	0	ENST00000250448.2:c.387del	p.Tyr130ThrfsTer5	p.Y130Tfs*5	ENST00000250448	NM_004496.3	129	ccC/cc	2/2	1	2	FACETS	0.818	0.693	0.954	0.818	0.693	0.954	CLONAL	1	TRUE	1	0.336175248832373	2		239	342	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428429	72428430	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	148	622	0	ENST00000477973.2:c.572dup	p.Thr192AsnfsTer14	p.T192Nfs*14	ENST00000477973	NM_012234.5	192	acc/aAcc	2/4	0.277157601130043	1	FACETS	0.966	0.884	1	0.966	0.884	1	CLONAL	1	TRUE	0	0.336175248832373	1		622	758	SUCCESS
APC	324	MSKCC	GRCh37	5	112176748	112176748	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	44	294	0	ENST00000257430.4:c.5458del	p.Ser1820ProfsTer43	p.S1820Pfs*43	ENST00000257430	NM_000038.5	1819	aaT/aa	16/16	0.336175248832373	1	FACETS	0.781	0.659	0.914	0.781	0.659	0.914	CLONAL	1	TRUE	0	0.336175248832373	1		294	279	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0024383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	322	683	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.350922573308345	3	FACETS	0.962	0.917	1	0.962	0.917	1	CLONAL	3	TRUE	0	0.416898878942658	3		683	647	SUCCESS
APC	324	MSKCC	GRCh37	5	112174152	112174152	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0024383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	65	429	0	ENST00000257430.4:c.2861T>A	p.Leu954Ter	p.L954*	ENST00000257430	NM_000038.5	954	tTa/tAa	16/16	0.362727063663668	2	FACETS	0.791	0.698	0.888	0.791	0.698	0.888	SUBCLONAL	2	TRUE	0	0.416898878942658	2		429	197	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710994	114710994	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	51	386	0	ENST00000543371.1:c.220del	p.Ser74ValfsTer34	p.S74Vfs*34	ENST00000543371	NM_001198531.1	73	gAa/ga	2/14	0.390239738783619	3	FACETS	0.562	0.478	0.655	0.281	0.239	0.328	SUBCLONAL	1	TRUE	1	0.416898878942658	3		386	526	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0024384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	17	572	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.219	0.162	0.286	0.219	0.162	0.286	SUBCLONAL	1	TRUE	1	0.24	2		572	648	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0024384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	33	472	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.493	0.4	0.597	0.493	0.4	0.597	SUBCLONAL	1	TRUE	1	0.24	2		472	558	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279674	123279674	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs77543610	NA	P-0024384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	49	355	0	ENST00000358487.5:c.758C>G	p.Pro253Arg	p.P253R	ENST00000358487	NM_000141.4	253	cCt/cGt	7/18	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.24	2		355	369	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339328	70339328	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0024384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	28	446	0	ENST00000374080.3:c.204+1G>T		p.X68_splice	ENST00000374080		68			1	2	FACETS	0.479	0.382	0.59	0.479	0.382	0.59	SUBCLONAL	1	TRUE	1	0.24	2		446	487	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528930	157528930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1371496107	NA	P-0024384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	51	545	0	ENST00000346085.5:c.6655G>A	p.Glu2219Lys	p.E2219K	ENST00000346085	NM_020732.3	2219	Gag/Aag	20/20	1	2	FACETS	0.656	0.557	0.765	0.656	0.557	0.765	SUBCLONAL	1	TRUE	1	0.24	2		545	648	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188210	10188210	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs5030830	NA	P-0024385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	33	601	0	ENST00000256474.2:c.353T>C	p.Leu118Pro	p.L118P	ENST00000256474	NM_000551.3	118	cTc/cCc	2/3	0.398408185708606	1	FACETS	0.856	0.707	1	0.856	0.707	1	CLONAL	1	FALSE	0	0.398408185708606	1		601	155	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459776	149459776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765232439	NA	P-0024385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	68	624	1	ENST00000286301.3:c.431G>A	p.Arg144His	p.R144H	ENST00000286301	NM_005211.3	144	cGt/cAt	4/22	0.373725798535419	3	FACETS	1	0.949	1	0.585	0.512	0.663	CLONAL	1	FALSE	1	0.398408185708606	3		625	350	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50818285	50818286	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0024385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	34	460	0	ENST00000398568.2:c.1866dup	p.Glu623ArgfsTer9	p.E623Rfs*9	ENST00000398568	NM_001042412.1	621	-/A	11/18	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	1	0.398408185708606	2		460	125	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142980	47142980	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	38	607	0	ENST00000409792.3:c.4983G>C	p.Glu1661Asp	p.E1661D	ENST00000409792	NM_014159.6	1661	gaG/gaC	8/21	0.398408185708606	1	FACETS	0.937	0.786	1	0.937	0.786	1	CLONAL	1	FALSE	0	0.398408185708606	1		607	163	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643822	52643822	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	19	575	0	ENST00000394830.3:c.2074G>T	p.Glu692Ter	p.E692*	ENST00000394830	NM_018313.4	692	Gag/Tag	17/30	0.398408185708606	1	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	FALSE	0	0.398408185708606	1		575	62	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264587	1264587	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	35	663	0	ENST00000310581.5:c.2775C>G	p.His925Gln	p.H925Q	ENST00000310581	NM_198253.2	925	caC/caG	11/16	0.373725798535419	3	FACETS	0.804	0.663	0.961	0.402	0.331	0.481	CLONAL	1	FALSE	1	0.398408185708606	3		663	262	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0024386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	413	588	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.582732101598607	4	FACETS	1	0.971	1			1	CLONAL	3	TRUE	NA	0.774152520247051	4		588	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0024386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	235	696	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	1	2	FACETS	0.992	0.932	1	0.992	0.932	1	CLONAL	1	TRUE	1	0.774152520247051	2		696	612	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940211	71940211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201173863	NA	P-0024386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	285	844	1	ENST00000298229.2:c.596G>A	p.Gly199Asp	p.G199D	ENST00000298229	NM_001567.3	199	gGt/gAt	5/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.774152520247051	2		845	684	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967818	18967818	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	596	899	0	ENST00000262803.5:c.1957G>T	p.Gly653Trp	p.G653W	ENST00000262803	NM_002911.3	653	Ggg/Tgg	14/24	0.774152520247051	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.774152520247051	3		899	1032	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426737	212426737	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	262	607	0	ENST00000342788.4:c.2378A>T	p.Gln793Leu	p.Q793L	ENST00000342788	NM_005235.2	793	cAg/cTg	20/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.774152520247051	2		607	612	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661523	227661523	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	251	691	0	ENST00000305123.5:c.1932G>C	p.Gln644His	p.Q644H	ENST00000305123	NM_005544.2	644	caG/caC	1/2	1	2	FACETS	0.954	0.897	1	0.954	0.897	1	CLONAL	1	TRUE	1	0.774152520247051	2		691	680	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720831	176720831	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0024386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	291	442	0	ENST00000439151.2:c.6464-2A>T		p.X2155_splice	ENST00000439151	NM_022455.4	2155			NA	2	FACETS	0.919	0.884	0.953			1	INDETERMINATE	2	TRUE	NA	0.774152520247051	2		442	409	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275801	38275801	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	66	686	0	ENST00000425967.3:c.1468G>T	p.Gly490Trp	p.G490W	ENST00000425967	NM_001174067.1	490	Ggg/Tgg	11/19	0.774152520247051	4	FACETS	0.32	0.276	0.367	0.107	0.092	0.123	SUBCLONAL	1	TRUE	1	0.774152520247051	4		686	946	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0024387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	197	735	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.638459940036974	6	FACETS	1	0.97	1	0.538	0.5	0.577	CLONAL	2	TRUE	2	0.644867992722987	6		735	650	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876659675	NA	P-0024387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	426	807	0	ENST00000269305.4:c.764T>A	p.Ile255Asn	p.I255N	ENST00000269305	NM_001126112.2	255	aTc/aAc	7/11	0.644867992722987	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.644867992722987	2		807	552	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928078	178928080	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs587776933	NA	P-0024387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	155	661	0	ENST00000263967.3:c.1359_1361del	p.Glu453del	p.E453del	ENST00000263967	NM_006218.2	452	ttAGAa/tta	8/21	0.32989425902593	5	FACETS	0.981	0.905	1	0.654	0.603	0.706	INDETERMINATE	2	TRUE	2	0.644867992722987	5		661	482	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181765	56181765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1287268127	NA	P-0024387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	8	411	1	ENST00000399503.3:c.3989C>T	p.Ser1330Leu	p.S1330L	ENST00000399503	NM_005921.1	1330	tCg/tTg	17/20	0.328736339004447	6	FACETS	0.175	0.112	0.258	0.029	0.018	0.043	INDETERMINATE	1	TRUE	0	0.644867992722987	6		412	324	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422716	47422716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1413219188	NA	P-0024387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	119	599	0	ENST00000377045.4:c.188G>A	p.Arg63Gln	p.R63Q	ENST00000377045	NM_001654.4	63	cGa/cAa	3/16	0.644867992722987	3	FACETS	0.955	0.866	1			1	CLONAL	1	TRUE	NA	0.644867992722987	3		599	511	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880484	155880484	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1557962794	NA	P-0024387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	550	681	0	ENST00000368323.3:c.69A>C	p.Lys23Asn	p.K23N	ENST00000368323	NM_006912.5	23	aaA/aaC	2/6	0.644867992722987	7	FACETS	1	0.993	1			1	CLONAL	4	TRUE	NA	0.644867992722987	7		681	1003	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945972	17945972	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	98	961	0	ENST00000458235.1:c.1967C>G	p.Ala656Gly	p.A656G	ENST00000458235	NM_000215.3	656	gCt/gGt	15/24	0.644867992722987	8	FACETS	0.752	0.669	0.841			1	SUBCLONAL	1	TRUE	NA	0.644867992722987	8		961	1186	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0024389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	123	696	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.245073010521306	2	FACETS	0.913	0.829	1	0.913	0.829	1	CLONAL	2	TRUE	0	0.245073010521306	2		696	550	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	53	571	0				ENST00000310581	NM_198253.2	-/1132			0.108014949814912	0	FACETS	1	0.929	1			1	INDETERMINATE	1	TRUE	0	0.270936985581066	0		571	252	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0024396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	83	625	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.79	0.701	0.883	1	0.98	1	SUBCLONAL	2	TRUE	1	0.270936985581066	2		625	388	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268970	55268975	+	frameshift_variant	Frame_Shift_Del	DEL	TGCCGA	TGCCGA	CGTC	novel	NA	P-0024396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	124	484	6	ENST00000275493.2:c.3036_3041delinsCGTC	p.Ala1013ValfsTer38	p.A1013Vfs*38	ENST00000275493	NM_005228.3	1012	gaTGCCGAc/gaCGTCc	25/28	1	2	FACETS	0.835	0.759	0.915	1	0.988	1	CLONAL	2	TRUE	1	0.270936985581066	2		490	548	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593604	55593609	+	inframe_deletion	In_Frame_Del	DEL	GGAAGG	GGAAGG	-	novel	NA	P-0024398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	402	478	0	ENST00000288135.5:c.1670_1675del	p.Trp557_Val559delinsPhe	p.W557_V559delinsF	ENST00000288135	NM_000222.2	557	tGGAAGGtt/ttt	11/21	0.945848093799807	2	FACETS	0.991	0.975	1	0.991	0.975	1	CLONAL	2	TRUE	0	0.945848093799807	2		478	429	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594258	55594258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913523	NA	P-0024398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	595	512	0	ENST00000288135.5:c.1961T>C	p.Val654Ala	p.V654A	ENST00000288135	NM_000222.2	654	gTg/gCg	13/21	0.945848093799807	2	FACETS	0.999	0.986	1	0.999	0.986	1	CLONAL	2	TRUE	0	0.945848093799807	2		512	630	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593609	55593609	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	19	483	0	ENST00000288135.5:c.1675G>T	p.Val559Phe	p.V559F	ENST00000288135	NM_000222.2	559	Gtt/Ttt	11/21	0.945848093799807	2	FACETS	0.091	0.068	0.117	0.045	0.034	0.059	SUBCLONAL	1	TRUE	0	0.945848093799807	2		483	442	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653767	89653780	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	AACTAAAGTACTCA	AACTAAAGTACTCA	TAGTTAAG	novel	NA	P-0024398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	184	341	1	ENST00000371953.3:c.80-15_80-2delinsTAGTTAAG		p.X27_splice	ENST00000371953	NM_000314.4	27			0.945848093799807	2	FACETS	0.944	0.915	0.97	0.944	0.915	0.97	CLONAL	2	TRUE	0	0.945848093799807	2		342	206	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0024399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	388	683	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.731547735471922	2	FACETS	0.945	0.914	0.976	0.945	0.914	0.976	CLONAL	2	TRUE	0	0.747548788357666	2		683	549	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933290	49933290	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	122	639	1	ENST00000296474.3:c.2820T>A	p.His940Gln	p.H940Q	ENST00000296474	NM_002447.2	940	caT/caA	12/20	0.698367421696609	2	FACETS	0.476	0.431	0.524	0.238	0.215	0.262	SUBCLONAL	1	TRUE	0	0.747548788357666	2		640	685	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519893	NA	P-0024400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	123	519	0	ENST00000267101.3:c.310G>T	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ttg	3/28	0.326149441768941	3	FACETS	0.852	0.786	0.918	0.852	0.786	0.918	INDETERMINATE	2	TRUE	1	0.768942941813081	3		519	260	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs104886003	NA	P-0024400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	43	363	0	ENST00000263967.3:c.1633G>C	p.Glu545Gln	p.E545Q	ENST00000263967	NM_006218.2	545	Gag/Cag	10/21	0.320470535462465	3	FACETS	1	0.962	1	0.71	0.612	0.811	INDETERMINATE	1	TRUE	1	0.768942941813081	3		363	109	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115722	8115722	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	90	279	0	ENST00000346208.3:c.1068G>A	p.Met356Ile	p.M356I	ENST00000346208		356	atG/atA	6/6	0.345079744852737	1	FACETS	0.792	0.722	0.862	0.792	0.722	0.862	INDETERMINATE	1	TRUE	0	0.768942941813081	1		279	182	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143468	108143468	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1297911790	NA	P-0024400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	47	313	0	ENST00000278616.4:c.3173G>A	p.Trp1058Ter	p.W1058*	ENST00000278616	NM_000051.3	1058	tGg/tAg	22/63	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.768942941813081	2		313	100	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813612	50813612	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	60	407	0	ENST00000398568.2:c.1166C>G	p.Ser389Cys	p.S389C	ENST00000398568	NM_001042412.1	389	tCt/tGt	8/18	NA	2	FACETS	1	0.934	1			1	INDETERMINATE	1	TRUE	NA	0.768942941813081	2		407	144	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56801410	56801410	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	56	368	0	ENST00000337432.4:c.917del	p.Gly306AspfsTer8	p.G306Dfs*8	ENST00000337432	NM_058216.2	305	tGg/tg	7/9	0.378823917439809	6	FACETS	1	0.911	1			1	INDETERMINATE	2	TRUE	NA	0.768942941813081	6		368	175	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097155	178097155	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	70	232	0	ENST00000397062.3:c.559G>C	p.Val187Leu	p.V187L	ENST00000397062	NM_006164.4	187	Gtt/Ctt	4/5	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.768942941813081	2		232	175	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048806	180048806	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	60	552	0	ENST00000261937.6:c.1756G>C	p.Glu586Gln	p.E586Q	ENST00000261937	NM_182925.4	586	Gag/Cag	13/30	0.277882213929419	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.768942941813081	0		552	142	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513226	106513226	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	41	222	0	ENST00000359195.3:c.2130G>C	p.Gln710His	p.Q710H	ENST00000359195	NM_002649.2	710	caG/caC	4/11	0.768942941813081	3	FACETS	1	0.858	1	0.506	0.429	0.587	CLONAL	1	TRUE	1	0.768942941813081	3		222	146	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072490	5072490	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0024400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4	24	159	0	ENST00000381652.3:c.1642-2A>C		p.X548_splice	ENST00000381652	NM_004972.3	548			0.768942941813081	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.768942941813081	1		159	28	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80343519	80343519	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765491785	NA	P-0024400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	34	347	0	ENST00000286548.4:c.800C>T	p.Ser267Phe	p.S267F	ENST00000286548	NM_002072.3	267	tCc/tTc	6/7	0.166311147414098	2	FACETS	0.636	0.529	0.753	0.318	0.264	0.377	INDETERMINATE	1	TRUE	0	0.768942941813081	2		347	139	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858101	45858101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778075234	NA	P-0024401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	39	503	3	ENST00000391945.4:c.1552C>T	p.Arg518Trp	p.R518W	ENST00000391945	NM_000400.3	518	Cgg/Tgg	17/23	0.3	1	FACETS	0.676	0.561	0.804	0.676	0.561	0.804	SUBCLONAL	1	TRUE	0	0.25	1		506	404	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411853	116411877	+	intron_variant	Intron	DEL	GGCCCATGATAGCCGTCTTTAACAA	GGCCCATGATAGCCGTCTTTAACAA	-	novel	NA	P-0024401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	222	812	0	ENST00000397752.3:c.2888-49_2888-25del		p.*963*	ENST00000397752	NM_000245.2	-/1390			0.138832206959776	3	FACETS	0.833	0.774	0.893	0.555	0.516	0.596	INDETERMINATE	2	TRUE	0	0.25	3		812	1200	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	311	629	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.812	0.77	0.853	1	0.995	1	CLONAL	2	FALSE	1	0.525645108275484	2		629	729	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	301	511	0	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	1	2	FACETS	0.815	0.772	0.857	1	0.995	1	CLONAL	2	FALSE	1	0.525645108275484	2		511	703	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0024405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	536	458	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.33274667390545	6	FACETS	1	0.995	1			1	INDETERMINATE	6	FALSE	NA	0.556996287417233	6		458	641	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370173	40370173	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	198	673	1	ENST00000293328.3:c.1165C>T	p.Arg389Cys	p.R389C	ENST00000293328	NM_012448.3	389	Cgc/Tgc	9/19	0.556996287417233	7	FACETS	0.753	0.696	0.811			1	SUBCLONAL	2	FALSE	NA	0.556996287417233	7		674	1130	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812228	43812228	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	254	535	0	ENST00000372470.3:c.1093C>A	p.Leu365Ile	p.L365I	ENST00000372470	NM_005373.2	365	Ctt/Att	7/12	0.560155235546448	6	FACETS	1	0.957	1	0.513	0.481	0.547	CLONAL	2	FALSE	2	0.556996287417233	6		535	939	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241974	72241974	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	28	242	0	ENST00000357731.5:c.416C>T	p.Pro139Leu	p.P139L	ENST00000357731	NM_173808.2	139	cCt/cTt	3/7	0.467945127467151	4	FACETS	1	0.901	1	0.395	0.321	0.477	CLONAL	1	FALSE	1	0.556996287417233	4		242	132	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434539	110434539	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	366	420	0	ENST00000375856.3:c.3862C>G	p.Arg1288Gly	p.R1288G	ENST00000375856	NM_003749.2	1288	Cga/Gga	1/2	0.201691160315037	4	FACETS	1	0.994	1			1	INDETERMINATE	4	FALSE	NA	0.556996287417233	4		420	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577052	7577052	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	244	565	0	ENST00000269305.4:c.886C>G	p.His296Asp	p.H296D	ENST00000269305	NM_001126112.2	296	Cac/Gac	8/11	0.33274667390545	6	FACETS	0.961	0.898	1			1	INDETERMINATE	2	FALSE	NA	0.556996287417233	6		565	964	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618462	37618462	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	138	349	0	ENST00000447079.4:c.138G>C	p.Lys46Asn	p.K46N	ENST00000447079	NM_015083.1	46	aaG/aaC	1/14	0.556996287417233	7	FACETS	0.841	0.766	0.919			1	CLONAL	2	FALSE	NA	0.556996287417233	7		349	705	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41201161	41201161	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	173	632	0	ENST00000357654.3:c.5383C>G	p.Leu1795Val	p.L1795V	ENST00000357654	NM_007294.3	1795	Ctt/Gtt	21/23	0.556996287417233	7	FACETS	0.836	0.77	0.905			1	CLONAL	2	FALSE	NA	0.556996287417233	7		632	889	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39744962	39744962	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	101	388	0	ENST00000361337.2:c.1752G>C	p.Leu584Phe	p.L584F	ENST00000361337	NM_003286.2	584	ttG/ttC	17/21	0.436732515391884	4	FACETS	1	0.97	1	0.405	0.363	0.448	CLONAL	1	FALSE	1	0.556996287417233	4		388	465	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93629360	93629458	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTATTTGTTTTCTGAAACATTTACTGTTCCTCTTTGCCGTTGTGGTTTCTAGACTTGGTCAGCGGGTGGAATAATCTCAAGAATCAAATCATACTCCT	TGTATTTGTTTTCTGAAACATTTACTGTTCCTCTTTGCCGTTGTGGTTTCTAGACTTGGTCAGCGGGTGGAATAATCTCAAGAATCAAATCATACTCCT	-	novel	NA	P-0024405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	21	166	0	ENST00000375746.1:c.847-52_893del		p.X283_splice	ENST00000375746	NM_001174167.1	283		7/14	NA	2	FACETS	0.692	0.541	0.861			1	INDETERMINATE	1	FALSE	NA	0.556996287417233	2		166	109	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249753	110249753	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	128	452	0	ENST00000374672.4:c.922G>A	p.Gly308Arg	p.G308R	ENST00000374672	NM_004235.4	308	Ggg/Agg	3/5	0.539486692920443	3	FACETS	1	0.954	1			1	CLONAL	1	FALSE	NA	0.556996287417233	3		452	546	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657054	47657069	+	protein_altering_variant	In_Frame_Del	DEL	TTATACAGGCTCTGGA	TTATACAGGCTCTGGA	G	novel	NA	P-0024405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	31	216	0	ENST00000233146.2:c.1250_1265delinsG	p.Val417_Glu422delinsGly	p.V417_E422delinsG	ENST00000233146	NM_000251.2	417	gTTATACAGGCTCTGGAa/gGa	7/16	0.560155235546448	3	FACETS	0.734	0.598	0.884	0.367	0.299	0.442	SUBCLONAL	1	FALSE	1	0.556996287417233	3		216	194	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0024418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	254	966	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.524182987118036	2		967	930	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0024418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	203	372	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.524182987118036	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.524182987118036	1		372	528	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278106	41278106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	173	513	1	ENST00000349496.5:c.1982G>A	p.Arg661Gln	p.R661Q	ENST00000349496	NM_001904.3	661	cGa/cAa	13/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.524182987118036	2		514	593	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120258	70120259	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0024418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	289	724	0	ENST00000245479.2:c.1261dup	p.Ser421LysfsTer157	p.S421Kfs*157	ENST00000245479	NM_000346.3	420	-/A	3/3	0.378978320067204	1	FACETS	0.814	0.767	0.863	0.814	0.767	0.863	CLONAL	1	TRUE	0	0.524182987118036	1		724	999	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380352	14380352	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	73	290	2	ENST00000256196.4:c.65G>T	p.Gly22Val	p.G22V	ENST00000256196		22	gGg/gTg	1/6	0.378978320067204	1	FACETS	0.519	0.456	0.586	0.519	0.456	0.586	SUBCLONAL	1	TRUE	0	0.524182987118036	1		292	396	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123676	11123676	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	261	568	0	ENST00000358026.2:c.2326A>C	p.Ile776Leu	p.I776L	ENST00000358026	NM_001128849.1	776	Atc/Ctc	16/36	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.524182987118036	2		568	939	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589532	67589598	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTAGGATCAAGTTGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACAC	TCTAGGATCAAGTTGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACAC	-	novel	NA	P-0024418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	118	193	0	ENST00000274335.5:c.1300-3_1363del		p.X434_splice	ENST00000274335		434		10/15	0.524182987118036	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.524182987118036	1		193	227	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	35	855	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.187389367975119	3	FACETS	1	0.88	1	1	0.88	1	CLONAL	2	FALSE	1	0.187389367975119	3		855	189	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0024423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	11	234	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.788	0.546	1	0.788	0.546	1	CLONAL	1	FALSE	1	0.187389367975119	2		234	149	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0024423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	118	785	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.187389367975119	2	FACETS	0.985	0.891	1	0.985	0.891	1	CLONAL	2	FALSE	0	0.187389367975119	2		786	639	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0024423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	11	343	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.924	0.642	1	0.924	0.642	1	CLONAL	1	FALSE	1	0.187389367975119	2		343	127	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912188	114912188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	86	432	1	ENST00000543371.1:c.1258C>T	p.Arg420Trp	p.R420W	ENST00000543371	NM_001198531.1	420	Cgg/Tgg	11/14	0.187389367975119	3	FACETS	0.893	0.792	1	0.893	0.792	1	CLONAL	2	FALSE	1	0.187389367975119	3		433	562	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446329	29446329	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	113	491	0	ENST00000389048.3:c.3238C>G	p.Leu1080Val	p.L1080V	ENST00000389048	NM_004304.4	1080	Ctg/Gtg	20/29	1	2	FACETS	0.939	0.847	1	1	0.988	1	CLONAL	2	FALSE	1	0.187389367975119	2		491	642	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739910	145739910	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0024423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	32	350	0	ENST00000428558.2:c.1621-1G>T		p.X541_splice	ENST00000428558	NM_004260.3	541			0.187389367975119	6	FACETS	0.783	0.634	0.952	0.157	0.126	0.191	CLONAL	1	FALSE	1	0.187389367975119	6		350	600	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	67	571	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.959	0.835	1	0.959	0.835	1	CLONAL	1	TRUE	1	0.278333585754447	2		571	502	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0024424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	77	625	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.904	0.794	1	0.904	0.794	1	CLONAL	1	TRUE	1	0.278333585754447	2		625	612	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578446	7578446	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	142	606	0	ENST00000269305.4:c.484A>T	p.Ile162Phe	p.I162F	ENST00000269305	NM_001126112.2	162	Atc/Ttc	5/11	0.277385147092953	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.278333585754447	1		606	805	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928065	178928076	+	inframe_deletion	In_Frame_Del	DEL	TACCTCATGGAT	TACCTCATGGAT	-	novel	NA	P-0024424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	172	529	0	ENST00000263967.3:c.1345_1356del	p.Pro449_Leu452del	p.P449_L452del	ENST00000263967	NM_006218.2	448	gTACCTCATGGATta/gta	8/21	0.268378551035368	3	FACETS	0.833	0.767	0.902	0.833	0.767	0.902	CLONAL	2	TRUE	1	0.278333585754447	3		529	845	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326573	62326586	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTAGGGCACCTG	AGGTAGGGCACCTG	-	novel	NA	P-0024424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	104	617	0	ENST00000360203.5:c.3498_3499+12del		p.X1166_splice	ENST00000360203	NM_001283009.1	1166		33/35	1	2	FACETS	0.867	0.776	0.964	0.867	0.776	0.964	CLONAL	1	TRUE	1	0.278333585754447	2		617	862	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796331	42796331	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	359	983	1	ENST00000575354.2:c.2980C>T	p.Gln994Ter	p.Q994*	ENST00000575354	NM_015125.3	994	Cag/Tag	12/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.55	2		984	1300	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257338	16257338	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1167704638	NA	P-0024427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	241	587	0	ENST00000375759.3:c.4603A>G	p.Ile1535Val	p.I1535V	ENST00000375759	NM_015001.2	1535	Atc/Gtc	11/15	1	2	FACETS	0.986	0.922	1	0.986	0.922	1	CLONAL	1	TRUE	1	0.55	2		587	889	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0024428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	52	234	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.379004617699749	3	FACETS	1	0.926	1	0.565	0.484	0.652	CLONAL	1	TRUE	1	0.379004617699749	3		234	289	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579310	7579310	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1555526469	NA	P-0024428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	297	366	0	ENST00000269305.4:c.375+2T>C		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.379004617699749	2	FACETS	0.91	0.866	0.954	1	0.994	1	CLONAL	3	TRUE	0	0.379004617699749	2		366	574	SUCCESS
APC	324	MSKCC	GRCh37	5	112174266	112174267	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	119	268	0	ENST00000257430.4:c.2976dup	p.Lys993Ter	p.K993*	ENST00000257430	NM_000038.5	992	agt/agTt	16/16	0.379004617699749	3	FACETS	0.943	0.859	1	0.943	0.859	1	CLONAL	2	TRUE	1	0.379004617699749	3		268	396	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982956	201982956	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0024428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	312	451	0	ENST00000359651.3:c.806-1G>A		p.X269_splice	ENST00000359651		269			0.373243465294203	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.379004617699749	3		451	866	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99136563	99136563	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	251	510	0	ENST00000074304.5:c.52C>T	p.Gln18Ter	p.Q18*	ENST00000074304	NM_001134224.1	18	Cag/Tag	3/26	0.286634471406041	4	FACETS	0.846	0.792	0.903	0.846	0.792	0.903	CLONAL	2	TRUE	2	0.379004617699749	4		510	1079	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72897423	72897424	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0024428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	216	296	0	ENST00000325599.8:c.68dup	p.Tyr23Ter	p.Y23*	ENST00000325599	NM_018130.2	23	tac/taAc	1/11	0.379004617699749	5	FACETS	1	0.987	1			1	CLONAL	2	TRUE	NA	0.379004617699749	5		296	729	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372145	55372145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1242192356	NA	P-0024428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	179	435	0	ENST00000297316.4:c.835G>A	p.Ala279Thr	p.A279T	ENST00000297316	NM_022454.3	279	Gcg/Acg	2/2	0.358703806912255	3	FACETS	1	0.989	1	0.729	0.673	0.786	CLONAL	1	TRUE	1	0.379004617699749	3		435	771	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	75	661	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.225803946181287	2		661	627	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793433	18793433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202143029	NA	P-0024431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	61	446	0	ENST00000266497.5:c.4130G>A	p.Arg1377His	p.R1377H	ENST00000266497		1377	cGt/cAt	30/31	1	2	FACETS	0.973	0.84	1	0.973	0.84	1	CLONAL	1	TRUE	1	0.225803946181287	2		446	555	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	110	629	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.83	0.747	0.919	0.83	0.747	0.919	CLONAL	1	TRUE	1	0.37	2		629	716	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0024432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	85	399	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.872	0.773	0.977	0.872	0.773	0.977	CLONAL	1	TRUE	1	0.37	2		399	527	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100622	67100622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	80	459	0	ENST00000412916.2:c.320G>A	p.Cys107Tyr	p.C107Y	ENST00000412916		107	tGt/tAt	4/6	0.299178236715064	1	FACETS	0.658	0.58	0.74	0.658	0.58	0.74	SUBCLONAL	1	TRUE	0	0.37	1		459	536	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856142	151856142	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	78	347	1	ENST00000262189.6:c.11476C>T	p.Gln3826Ter	p.Q3826*	ENST00000262189	NM_170606.2	3826	Caa/Taa	44/59	0.299178236715064	3	FACETS	0.912	0.803	1	0.456	0.401	0.515	CLONAL	1	TRUE	1	0.37	3		348	548	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40476826	40476826	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	153	541	0	ENST00000264657.5:c.1503G>A	p.Trp501Ter	p.W501*	ENST00000264657	NM_139276.2	501	tgG/tgA	17/24	0.604607988514828	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.604607988514828	1		541	323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577598	7577608	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TCAGAGCCAAC	TCAGAGCCAAC	G	novel	NA	P-0024446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	110	562	0	ENST00000269305.4:c.673_683delinsC	p.Val225ProfsTer19	p.V225Pfs*19	ENST00000269305	NM_001126112.2	225	GTTGGCTCTGAc/Cc	7/11	0.604607988514828	1	FACETS	0.843	0.769	0.92	0.843	0.769	0.92	CLONAL	1	TRUE	0	0.604607988514828	1		562	301	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0024448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	249	754	1	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	0.462720263103756	2	FACETS	0.959	0.906	1	0.959	0.906	1	CLONAL	2	TRUE	0	0.462720263103756	2		755	561	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139286	108139286	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	32	795	1	ENST00000278616.4:c.2788T>G	p.Leu930Val	p.L930V	ENST00000278616	NM_000051.3	930	Tta/Gta	18/63	0.347444064951759	2	FACETS	0.314	0.255	0.382	0.157	0.127	0.191	SUBCLONAL	1	TRUE	0	0.462720263103756	2		796	440	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449920	29449920	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	174	1017	1	ENST00000389048.3:c.2935G>A	p.Val979Met	p.V979M	ENST00000389048	NM_004304.4	979	Gtg/Atg	18/29	0.218558835442252	3	FACETS	1	0.951	1	0.348	0.32	0.377	INDETERMINATE	1	TRUE	0	0.462720263103756	3		1018	887	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066617	94066617	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	115	600	0	ENST00000369303.4:c.1142C>A	p.Pro381His	p.P381H	ENST00000369303	NM_004440.3	381	cCc/cAc	5/17	0.183435056768568	5	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.462720263103756	5		600	571	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577595	7577598	+	frameshift_variant	Frame_Shift_Del	DEL	CAGT	CAGT	-	novel	NA	P-0024450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	197	586	0	ENST00000269305.4:c.683_686del	p.Asp228ValfsTer18	p.D228Vfs*18	ENST00000269305	NM_001126112.2	228	gACTGt/gt	7/11	0.547199589693514	2	FACETS	0.932	0.878	0.985	0.932	0.878	0.985	CLONAL	2	TRUE	0	0.574465055606096	2		586	368	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101597	27101597	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs151074395	NA	P-0024450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	30	784	0	ENST00000324856.7:c.4879C>G	p.Pro1627Ala	p.P1627A	ENST00000324856	NM_006015.4	1627	Cct/Gct	18/20	1	2	FACETS	0.193	0.155	0.236	0.193	0.155	0.236	SUBCLONAL	1	TRUE	1	0.574465055606096	2		784	542	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204499917	204499917	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200898280	NA	P-0024450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	78	516	2	ENST00000367182.3:c.259C>T	p.Arg87Cys	p.R87C	ENST00000367182	NM_001278516.1	87	Cgt/Tgt	4/11	1	2	FACETS	0.698	0.617	0.784	0.698	0.617	0.784	SUBCLONAL	1	TRUE	1	0.574465055606096	2		518	389	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565592	41565607	+	frameshift_variant	Frame_Shift_Del	DEL	GGATATTTAGAATATG	GGATATTTAGAATATG	-	novel	NA	P-0024450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	78	467	1	ENST00000263253.7:c.4258_4273del	p.Gly1420SerfsTer4	p.G1420Sfs*4	ENST00000263253	NM_001429.3	1420	GGATATTTAGAATATGtc/tc	26/31	0.547199589693514	2	FACETS	0.711	0.628	0.798	0.355	0.314	0.399	SUBCLONAL	1	TRUE	0	0.574465055606096	2		468	382	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842468	68842480	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGGTAGAGAAAG	CAGGTAGAGAAAG	-	novel	NA	P-0024451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	32	511	0	ENST00000261769.5:c.529_531+10del		p.X177_splice	ENST00000261769	NM_004360.3	177		4/16	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		511	624	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0024453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	175	684	0	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	0.224053102228781	2	FACETS	1	0.987	1	0.654	0.605	0.705	INDETERMINATE	1	TRUE	0	0.42	2		684	637	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0024453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	98	502	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.248513263584293	3	FACETS	0.917	0.828	1	0.611	0.552	0.673	INDETERMINATE	2	TRUE	0	0.42	3		502	308	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555525857	NA	P-0024453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	93	754	1	ENST00000269305.4:c.596G>A	p.Gly199Glu	p.G199E	ENST00000269305	NM_001126112.2	199	gGa/gAa	6/11	0.224053102228781	2	FACETS	0.712	0.634	0.795	0.356	0.317	0.398	INDETERMINATE	1	TRUE	0	0.42	2		755	622	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910883	114910883	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1477809102	NA	P-0024453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	113	454	4	ENST00000543371.1:c.1001+1G>A		p.X334_splice	ENST00000543371	NM_001198531.1	334			0.224053102228781	2	FACETS	1	0.978	1	0.638	0.578	0.7	INDETERMINATE	1	TRUE	0	0.42	2		458	422	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258310	16258310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542606165	NA	P-0024453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	62	525	2	ENST00000375759.3:c.5575C>T	p.Arg1859Trp	p.R1859W	ENST00000375759	NM_015001.2	1859	Cgg/Tgg	11/15	1	2	FACETS	0.594	0.514	0.681	0.594	0.514	0.681	SUBCLONAL	1	TRUE	1	0.42	2		527	497	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770125	56770125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879254131	NA	P-0024453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	57	416	0	ENST00000337432.4:c.121G>A	p.Val41Met	p.V41M	ENST00000337432	NM_058216.2	41	Gtg/Atg	1/9	0.289405350365751	3	FACETS	0.743	0.639	0.856	0.372	0.319	0.428	SUBCLONAL	1	TRUE	1	0.42	3		416	442	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30664727	30664727	+	intron_variant	Intron	SNP	G	G	T	novel	NA	P-0024453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	20	395	0	ENST00000295754.5:c.94+16258G>T		p.*32*	ENST00000295754	NM_003242.5	44/592			0.28126584911628	3	FACETS	0.352	0.269	0.45	0.117	0.089	0.15	SUBCLONAL	1	TRUE	0	0.42	3		395	327	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066702	94066702	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	55	531	0	ENST00000369303.4:c.1057C>A	p.Pro353Thr	p.P353T	ENST00000369303	NM_004440.3	353	Cct/Act	5/17	0.289405350365751	3	FACETS	0.593	0.508	0.687	0.297	0.254	0.344	SUBCLONAL	1	TRUE	1	0.42	3		531	534	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109322612	109322612	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	42	607	0	ENST00000436639.2:c.425A>G	p.Asn142Ser	p.N142S	ENST00000436639	NM_014454.2	142	aAc/aGc	3/10	0.289405350365751	3	FACETS	0.541	0.452	0.64	0.271	0.226	0.32	SUBCLONAL	1	TRUE	1	0.42	3		607	447	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38173530	38173530	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	35	541	0	ENST00000317025.8:c.1886C>T	p.Pro629Leu	p.P629L	ENST00000317025	NM_023034.1	629	cCt/cTt	10/24	0.3	3	FACETS	0.397	0.325	0.478	0.198	0.162	0.239	SUBCLONAL	1	TRUE	1	0.42	3		541	508	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969427	44969427	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	43	312	0	ENST00000377967.4:c.4109A>G	p.Glu1370Gly	p.E1370G	ENST00000377967	NM_021140.2	1370	gAa/gGa	28/29	0.3	2	FACETS	0.853	0.72	0.998			1	CLONAL	1	TRUE	NA	0.42	2		312	240	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0024461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	222	884	2	ENST00000374080.3:c.3670C>T	p.Leu1224Phe	p.L1224F	ENST00000374080		1224	Ctc/Ttc	26/45	1	1	FACETS	0.893	0.842	0.945	1	0.994	1	CLONAL	2	TRUE	0	0.423855798083568	1		886	462	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923738	72923738	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	197	792	2	ENST00000268489.5:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000268489	NM_006885.3	1114	Cga/Tga	4/10	0.423855798083568	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.423855798083568	1		794	515	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375049	31375049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779571584	NA	P-0024461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	145	737	0	ENST00000328111.2:c.446G>A	p.Arg149Gln	p.R149Q	ENST00000328111	NM_006892.3	149	cGg/cAg	6/23	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.423855798083568	2		737	614	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967757	90967757	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	206	345	0	ENST00000265433.3:c.1151T>A	p.Ile384Asn	p.I384N	ENST00000265433	NM_002485.4	384	aTc/aAc	10/16	0.423855798083568	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.423855798083568	3		345	554	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522598	157522598	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554236040	NA	P-0024465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	228	681	2	ENST00000346085.5:c.4870C>T	p.Arg1624Ter	p.R1624*	ENST00000346085	NM_020732.3	1624	Cga/Tga	18/20	1	2	FACETS	0.982	0.923	1	0.982	0.923	1	CLONAL	1	TRUE	1	0.856988662024782	2		683	542	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231783	36231783	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057519748	NA	P-0024465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	251	765	1	ENST00000300305.3:c.601C>T	p.Arg201Ter	p.R201*	ENST00000300305		201	Cga/Tga	5/8	1	2	FACETS	0.931	0.877	0.986	0.931	0.877	0.986	CLONAL	1	TRUE	1	0.856988662024782	2		766	629	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482425	56482425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	207	556	0	ENST00000267101.3:c.973G>A	p.Gly325Arg	p.G325R	ENST00000267101	NM_001982.3	325	Gga/Aga	8/28	1	2	FACETS	0.91	0.852	0.969	0.91	0.852	0.969	CLONAL	1	TRUE	1	0.856988662024782	2		556	531	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101273	27101273	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	220	640	1	ENST00000324856.7:c.4555C>T	p.Gln1519Ter	p.Q1519*	ENST00000324856	NM_006015.4	1519	Cag/Tag	18/20	1	2	FACETS	0.958	0.899	1	0.958	0.899	1	CLONAL	1	TRUE	1	0.856988662024782	2		641	536	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878530	151878530	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1396109953	NA	P-0024465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	229	707	0	ENST00000262189.6:c.6415C>T	p.Arg2139Ter	p.R2139*	ENST00000262189	NM_170606.2	2139	Cga/Tga	36/59	0.856988662024782	2	FACETS	0.954	0.897	1	0.477	0.448	0.506	CLONAL	1	TRUE	0	0.856988662024782	2		707	560	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106211	27106566	+	frameshift_variant	Frame_Shift_Del	DEL	TTGGCATTAGCCCAGCACAGAGCCACCGGAACATCAAGATCCTAGAGGACGAACCCCACAGTAAGGATGAGACCCCACTGTGTACCCTTCTGGACTGGCAGGATTCTCTTGCCAAGCGCTGCGTCTGTGTGTCCAATACCATTCGAAGCCTGTCATTTGTGCCAGGCAATGACTTTGAGATGTCCAAACACCCAGGGCTGCTGCTCATCCTGGGCAAGCTGATCCTGCTGCACCACAAGCACCCAGAACGGAAGCAGGCACCACTAACTTATGAAAAGGAGGAGGAACAGGACCAAGGGGTGAGCTGCAACAAAGTGGAGTGGTGGTGGGACTGCTTGGAGATGCTCCGGGAAAAC	TTGGCATTAGCCCAGCACAGAGCCACCGGAACATCAAGATCCTAGAGGACGAACCCCACAGTAAGGATGAGACCCCACTGTGTACCCTTCTGGACTGGCAGGATTCTCTTGCCAAGCGCTGCGTCTGTGTGTCCAATACCATTCGAAGCCTGTCATTTGTGCCAGGCAATGACTTTGAGATGTCCAAACACCCAGGGCTGCTGCTCATCCTGGGCAAGCTGATCCTGCTGCACCACAAGCACCCAGAACGGAAGCAGGCACCACTAACTTATGAAAAGGAGGAGGAACAGGACCAAGGGGTGAGCTGCAACAAAGTGGAGTGGTGGTGGGACTGCTTGGAGATGCTCCGGGAAAAC	-	novel	NA	P-0024465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	201	631	1	ENST00000324856.7:c.5822_6177del	p.Phe1941TyrfsTer39	p.F1941Yfs*39	ENST00000324856	NM_006015.4	1941	tTTGGCATTAGCCCAGCACAGAGCCACCGGAACATCAAGATCCTAGAGGACGAACCCCACAGTAAGGATGAGACCCCACTGTGTACCCTTCTGGACTGGCAGGATTCTCTTGCCAAGCGCTGCGTCTGTGTGTCCAATACCATTCGAAGCCTGTCATTTGTGCCAGGCAATGACTTTGAGATGTCCAAACACCCAGGGCTGCTGCTCATCCTGGGCAAGCTGATCCTGCTGCACCACAAGCACCCAGAACGGAAGCAGGCACCACTAACTTATGAAAAGGAGGAGGAACAGGACCAAGGGGTGAGCTGCAACAAAGTGGAGTGGTGGTGGGACTGCTTGGAGATGCTCCGGGAAAAC/t	20/20	1	2	FACETS	0.942	0.881	1	0.942	0.881	1	CLONAL	1	TRUE	1	0.856988662024782	2		632	498	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226769	2226769	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761386617	NA	P-0024465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	256	726	0	ENST00000398665.3:c.4249G>A	p.Glu1417Lys	p.E1417K	ENST00000398665	NM_032482.2	1417	Gag/Aag	27/28	0.856988662024782	1	FACETS	0.951	0.912	0.988	0.951	0.912	0.988	CLONAL	1	TRUE	0	0.856988662024782	1		726	359	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047034	128047034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1249110579	NA	P-0024465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	210	641	1	ENST00000285398.2:c.701G>A	p.Arg234Gln	p.R234Q	ENST00000285398	NM_000122.1	234	cGa/cAa	6/15	1	2	FACETS	0.978	0.918	1	0.978	0.918	1	CLONAL	1	TRUE	1	0.856988662024782	2		642	501	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247280	153247280	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	203	448	0	ENST00000281708.4:c.1522C>T	p.Gln508Ter	p.Q508*	ENST00000281708	NM_033632.3	508	Caa/Taa	10/12	1	2	FACETS	0.993	0.931	1	0.993	0.931	1	CLONAL	1	TRUE	1	0.856988662024782	2		448	477	SUCCESS
APC	324	MSKCC	GRCh37	5	112111372	112111373	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0024465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	83	307	0	ENST00000257430.4:c.469_470del	p.Trp157ValfsTer10	p.W157Vfs*10	ENST00000257430	NM_000038.5	157	TGg/g	5/16	1	2	FACETS	0.857	0.77	0.947	0.857	0.77	0.947	CLONAL	1	TRUE	1	0.856988662024782	2		307	226	SUCCESS
APC	324	MSKCC	GRCh37	5	112173685	112173685	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs879254110	NA	P-0024465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	150	391	0	ENST00000257430.4:c.2395del	p.Tyr799MetfsTer21	p.Y799Mfs*21	ENST00000257430	NM_000038.5	798	gaT/ga	16/16	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.856988662024782	2		391	347	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397827	116397827	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	151	577	0	ENST00000397752.3:c.2101A>G	p.Ser701Gly	p.S701G	ENST00000397752	NM_000245.2	701	Agt/Ggt	8/21	0.856988662024782	2	FACETS	0.987	0.915	1	0.494	0.457	0.53	CLONAL	1	TRUE	0	0.856988662024782	2		577	357	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0024466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	61	320	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.887	0.771	1	0.887	0.771	1	CLONAL	1	TRUE	1	0.428399713422531	2		320	321	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477873	140477873	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	86	573	0	ENST00000288602.6:c.1435G>A	p.Asp479Asn	p.D479N	ENST00000288602	NM_004333.4	479	Gat/Aat	12/18	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.428399713422531	2		573	378	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0024467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	155	802	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.343163389904837	5	FACETS	1	0.966	1			1	CLONAL	3	TRUE	NA	0.464606443942363	5		802	354	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005479	42005479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746445154	NA	P-0024467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	182	791	1	ENST00000219905.7:c.3215G>A	p.Arg1072His	p.R1072H	ENST00000219905	NM_001164273.1	1072	cGc/cAc	9/24	1	2	FACETS	0.758	0.699	0.82	0.758	0.699	0.82	SUBCLONAL	1	TRUE	1	0.464606443942363	2		792	1033	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313274	65313274	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs534249030	NA	P-0024467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	170	732	1	ENST00000342505.4:c.1840G>A	p.Glu614Lys	p.E614K	ENST00000342505	NM_002227.2	614	Gag/Aag	13/25	0.214179789520795	3	FACETS	0.982	0.903	1	0.491	0.451	0.533	INDETERMINATE	1	TRUE	1	0.464606443942363	3		733	918	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279949	18279949	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	634	913	0	ENST00000222254.8:c.2032G>T	p.Gly678Cys	p.G678C	ENST00000222254	NM_005027.3	678	Ggc/Tgc	16/16	0.464606443942363	3	FACETS	0.968	0.931	1	0.968	0.931	1	CLONAL	2	TRUE	1	0.464606443942363	3		913	1738	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259408	89259408	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	173	636	2	ENST00000336596.2:c.552A>T	p.Gln184His	p.Q184H	ENST00000336596	NM_005233.5	184	caA/caT	3/17	0.244402563190937	4	FACETS	1	0.946	1	1	0.946	1	INDETERMINATE	2	TRUE	2	0.464606443942363	4		638	532	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911529	101911529	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	90	517	0	ENST00000374994.4:c.1454del	p.Ala485AspfsTer62	p.A485Dfs*62	ENST00000374994	NM_004612.2	485	gCa/ga	9/9	0.44673869286614	2	FACETS	0.824	0.745	0.906	0.824	0.745	0.906	CLONAL	2	TRUE	0	0.464606443942363	2		517	235	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0024470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	115	726	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.239099281796969	1	FACETS	0.848	0.762	0.938	0.848	0.762	0.938	CLONAL	1	TRUE	0	0.239099281796969	1		726	999	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461057	120461057	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	45	732	0	ENST00000256646.2:c.5901A>C	p.Gln1967His	p.Q1967H	ENST00000256646	NM_024408.3	1967	caA/caC	32/34	0.239099281796969	1	FACETS	0.441	0.369	0.52	0.441	0.369	0.52	SUBCLONAL	1	TRUE	0	0.239099281796969	1		732	752	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844182	68844182	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555515446	NA	P-0024470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	269	989	0	ENST00000261769.5:c.770A>G	p.Asp257Gly	p.D257G	ENST00000261769	NM_004360.3	257	gAc/gGc	6/16	0.23570381219136	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.239099281796969	2		989	1044	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0024473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	460	651	0	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.95790605958676	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.965218107528006	1		651	465	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039385	49039385	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs794727372	NA	P-0024473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	592	752	0	ENST00000267163.4:c.2370C>A	p.Tyr790Ter	p.Y790*	ENST00000267163	NM_000321.2	790	taC/taA	23/27	0.95790605958676	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.965218107528006	1		752	606	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120019	70120031	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCCGCCGCCAC	GCGCCGCCGCCAC	-	novel	NA	P-0024473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	103	110	0	ENST00000245479.2:c.1021_1033del	p.Ala341ProfsTer38	p.A341Pfs*38	ENST00000245479	NM_000346.3	341	GCGCCGCCGCCACcc/cc	3/3	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.965218107528006	2		110	201	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86681152	86681152	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	168	459	0	ENST00000274376.6:c.2793A>G	p.Ile931Met	p.I931M	ENST00000274376	NM_002890.2	931	atA/atG	22/25	0.490007615813248	1	FACETS	0.34	0.315	0.367	0.34	0.315	0.367	INDETERMINATE	1	TRUE	0	0.965218107528006	1		459	529	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917682	151917682	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	290	319	0	ENST00000262189.6:c.3638G>C	p.Ser1213Thr	p.S1213T	ENST00000262189	NM_170606.2	1213	aGc/aCc	23/59	0.480264026047276	1	FACETS	0.721	0.692	0.75	0.721	0.692	0.75	INDETERMINATE	1	TRUE	0	0.965218107528006	1		319	431	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393422	139393425	+	frameshift_variant	Frame_Shift_Del	DEL	CGGC	CGGC	AGG	novel	NA	P-0024473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	229	756	4	ENST00000277541.6:c.6106_6109delinsCCT	p.Ala2036ProfsTer3	p.A2036Pfs*3	ENST00000277541	NM_017617.3	2036	GCCGcc/CCTcc	33/34	0.965218107528006	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.965218107528006	1		760	241	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	198	716	0	ENST00000263967.3:c.3012G>A	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atA	21/21	0.224728543831378	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	0	0.244145791580276	2		716	810	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281980	49281980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777806801	NA	P-0024474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	66	706	1	ENST00000282018.3:c.1027G>A	p.Glu343Lys	p.E343K	ENST00000282018	NM_020377.2	343	Gaa/Aaa	1/1	0.244145791580276	3	FACETS	0.553	0.478	0.634	0.276	0.239	0.317	SUBCLONAL	1	TRUE	1	0.244145791580276	3		707	1098	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215674233	215674233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs864622206	NA	P-0024474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	218	768	1	ENST00000260947.4:c.61C>T	p.Arg21Cys	p.R21C	ENST00000260947	NM_000465.2	21	Cgt/Tgt	1/11	0.108211735418519	4	FACETS	1	0.969	1	1	0.969	1	INDETERMINATE	2	TRUE	2	0.244145791580276	4		769	1036	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0024479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	173	391	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.978	0.908	1	0.978	0.908	1	CLONAL	1	TRUE	1	0.727783500684892	2		391	486	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154733	2154853	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCAGGACCCTCACCGGAAGCACGGTCGGAGGGGTCGACACGTCCCTCTCGGACTTGGCGGGGGTAGCACAGTACGTCTCCAGGAGGGCCAGGTCACAGCTGCGGAAACAGCACTCCTCAA	CCCAGGACCCTCACCGGAAGCACGGTCGGAGGGGTCGACACGTCCCTCTCGGACTTGGCGGGGGTAGCACAGTACGTCTCCAGGAGGGCCAGGTCACAGCTGCGGAAACAGCACTCCTCAA	-	novel	NA	P-0024479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	176	753	0	ENST00000434045.2:c.368_474+14del		p.X123_splice	ENST00000434045	NM_001127598.1	123		4/5	1		FACETS		0.688	0.802				SUBCLONAL	1	TRUE	1	0.727783500684892	2		753	650	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0024480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	784	472	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.696728579364883	5	FACETS	0.897	0.873	0.921	0.897	0.873	0.921	CLONAL	4	TRUE	1	0.696728579364883	5		472	1283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577146	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0024480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	146	607	1	ENST00000269305.4:c.792_794del	p.Leu265del	p.L265del	ENST00000269305	NM_001126112.2	264	ctACTg/ctg	8/11	0.19036256091105	4	FACETS	0.694	0.633	0.759			1	INDETERMINATE	1	TRUE	NA	0.696728579364883	4		608	1024	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988379	36988379	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	135	339	0	ENST00000354822.5:c.274G>T	p.Gly92Cys	p.G92C	ENST00000354822	NM_001079668.2	92	Ggc/Tgc	2/3	0.374902044738499	3	FACETS	0.93	0.849	1	0.31	0.283	0.338	INDETERMINATE	1	TRUE	0	0.696728579364883	3		339	562	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289844	15289844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	301	842	0	ENST00000263388.2:c.3710G>A	p.Gly1237Asp	p.G1237D	ENST00000263388	NM_000435.2	1237	gGc/gAc	22/33	0.189743987531205	1	FACETS	0.527	0.497	0.558	0.527	0.497	0.558	INDETERMINATE	1	TRUE	0	0.696728579364883	1		842	1068	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805979	32805979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293561966	NA	P-0024480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	269	833	0	ENST00000374899.4:c.32C>T	p.Ser11Phe	p.S11F	ENST00000374899	NM_018833.2	11	tCc/tTc	2/12	0.369588503286264	3	FACETS	0.761	0.712	0.811	0.38	0.356	0.406	INDETERMINATE	1	TRUE	1	0.696728579364883	3		833	1369	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	163148698	163148698	+	start_lost	Translation_Start_Site	SNP	C	C	G	novel	NA	P-0024480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	73	566	0	ENST00000366898.1:c.3G>C	p.Met1?	p.M1?	ENST00000366898	NM_004562.2	1	atG/atC	1/12	0.183631434693741	2	FACETS	0.293	0.255	0.333	0.146	0.127	0.167	INDETERMINATE	1	TRUE	0	0.696728579364883	2		566	716	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577551	+	protein_altering_variant	In_Frame_Del	DEL	TGCCGCC	TGCCGCC	A	novel	NA	P-0024480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	616	728	0	ENST00000269305.4:c.730_736delinsT	p.Gly244_Met246delinsLeu	p.G244_M246delinsL	ENST00000269305	NM_001126112.2	244	GGCGGCAtg/Ttg	7/11	0.19036256091105	4	FACETS	0.918	0.888	0.947			1	INDETERMINATE	3	TRUE	NA	0.696728579364883	4		728	1090	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0024481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	155	547	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.54	0.497	0.585	0.54	0.497	0.585	SUBCLONAL	1	TRUE	1	0.971144561225537	2		547	591	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098800	178098800	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	222	878	0	ENST00000397062.3:c.245A>G	p.Glu82Gly	p.E82G	ENST00000397062	NM_006164.4	82	gAa/gGa	2/5	1	2	FACETS	0.506	0.471	0.541	0.506	0.471	0.541	SUBCLONAL	1	TRUE	1	0.971144561225537	2		878	904	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142848	7142848	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	139	607	1	ENST00000302850.5:c.2521A>T	p.Ser841Cys	p.S841C	ENST00000302850	NM_000208.2	841	Agt/Tgt	12/22	1	2	FACETS	0.482	0.44	0.525	0.482	0.44	0.525	SUBCLONAL	1	TRUE	1	0.971144561225537	2		608	594	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0024482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	61	598	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.98	0.85	1	1	0.979	1	CLONAL	2	TRUE	1	0.17	2		598	366	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0024482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	17	782	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	1	2	FACETS	0.465	0.346	0.608	0.465	0.346	0.608	SUBCLONAL	1	TRUE	1	0.17	2		782	430	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031885	26031885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	12	245	0	ENST00000244661.2:c.404G>A	p.Arg135Lys	p.R135K	ENST00000244661	NM_003537.3	135	aGa/aAa	1/1	1	2	FACETS	0.666	0.468	0.909	0.666	0.468	0.909	SUBCLONAL	1	TRUE	1	0.17	2		245	212	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687287	117687287	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	29	479	0	ENST00000368508.3:c.2764A>G	p.Arg922Gly	p.R922G	ENST00000368508	NM_002944.2	922	Aga/Gga	18/43	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.17	2		479	314	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0024483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	149	436	1	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.373082491094427	3	FACETS	0.773	0.709	0.839	0.773	0.709	0.839	SUBCLONAL	2	TRUE	1	0.393765984067888	3		437	586	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527502	29527503	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0024483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	138	737	0	ENST00000356175.3:c.952_953del	p.Glu318LysfsTer11	p.E318Kfs*11	ENST00000356175	NM_000267.3	317	acAGaa/acaa	9/57	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.393765984067888	2		737	655	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522590	176522590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765924274	NA	P-0024483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	142	922	2	ENST00000292408.4:c.1687C>T	p.Arg563Trp	p.R563W	ENST00000292408	NM_213647.1	563	Cgg/Tgg	13/18	0.383282778233836	2	FACETS	1	0.946	1	0.524	0.479	0.572	CLONAL	1	TRUE	0	0.393765984067888	2		924	688	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740204	162740204	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749040833	NA	P-0024483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	327	729	1	ENST00000367921.3:c.1406C>T	p.Ser469Leu	p.S469L	ENST00000367921	NM_006182.2	469	tCg/tTg	12/18	0.263639516965861	5	FACETS	1	0.99	1	0.795	0.751	0.839	CLONAL	2	TRUE	2	0.393765984067888	5		730	1108	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	64	855	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.847	0.731	0.972	0.847	0.731	0.972	CLONAL	1	TRUE	1	0.18	2		855	840	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	61	915	1	ENST00000269305.4:c.880del	p.Glu294SerfsTer51	p.E294Sfs*51	ENST00000269305	NM_001126112.2	294	Gag/ag	8/11	1	2	FACETS	0.829	0.713	0.955	0.829	0.713	0.955	CLONAL	1	TRUE	1	0.18	2		916	818	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0024491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	28	361	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.792	0.633	0.973	0.792	0.633	0.973	CLONAL	1	TRUE	1	0.18	2		361	393	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911599	114911600	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0024491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	65	693	0	ENST00000543371.1:c.1118dup	p.Leu374ValfsTer49	p.L374Vfs*49	ENST00000543371	NM_001198531.1	373	acg/aCcg	10/14	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.18	2		693	619	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933971	39933971	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	57	844	0	ENST00000378444.4:c.628C>A	p.Pro210Thr	p.P210T	ENST00000378444	NM_001123385.1	210	Cca/Aca	4/15	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.18	2		844	616	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412196	63412196	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0024491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	69	1048	0	ENST00000330258.3:c.971C>G	p.Ser324Ter	p.S324*	ENST00000330258	NM_152424.3	324	tCa/tGa	2/2	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.18	2		1048	749	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913517	NA	P-0024492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	70	546	0	ENST00000288135.5:c.1676T>A	p.Val559Asp	p.V559D	ENST00000288135	NM_000222.2	559	gTt/gAt	11/21	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.862453481311916	2		546	159	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631817	90631817	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0024492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	147	656	0	ENST00000330062.3:c.534+2T>A		p.X178_splice	ENST00000330062	NM_002168.2	178			0.105384535161991	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.862453481311916	0		656	351	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0024493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	19	731	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.777	0.589	0.998	0.777	0.589	0.998	CLONAL	1	TRUE	1	0.15	2		732	326	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0024493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	39	870	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.15	2		870	457	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39074470	39074470	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1454741396	NA	P-0024493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	18	561	0	ENST00000357387.3:c.10A>G	p.Ile4Val	p.I4V	ENST00000357387	NM_152756.3	4	Atc/Gtc	1/38	1	2	FACETS	0.92	0.693	1	0.92	0.693	1	CLONAL	1	TRUE	1	0.15	2		561	261	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971098	21971099	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0024493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	18	568	0	ENST00000304494.5:c.259dup	p.Arg87ProfsTer33	p.R87Pfs*33	ENST00000304494	NM_000077.4	87	cgg/cCgg	2/3	1	2	FACETS	1	0.773	1	1	0.773	1	CLONAL	1	TRUE	1	0.15	2		568	234	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921447	39921451	+	frameshift_variant	Frame_Shift_Del	DEL	ACAAT	ACAAT	-	novel	NA	P-0024493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	23	357	0	ENST00000378444.4:c.4369_4373del	p.Ile1457GlnfsTer2	p.I1457Qfs*2	ENST00000378444	NM_001123385.1	1457	ATTGTc/c	10/15	1	1	FACETS	0.801	0.629	0.997	1	0.932	1	CLONAL	2	TRUE	0	0.15	1		357	177	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0024494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	91	683	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.891	0.792	0.996	0.891	0.792	0.996	CLONAL	1	TRUE	1	0.336011480728422	2		683	608	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0024494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	29	555	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	1	2	FACETS	0.361	0.289	0.443	0.361	0.289	0.443	SUBCLONAL	1	TRUE	1	0.336011480728422	2		555	478	SUCCESS
APC	324	MSKCC	GRCh37	5	112175273	112175273	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123121	NA	P-0024494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	27	336	0	ENST00000257430.4:c.3982C>T	p.Gln1328Ter	p.Q1328*	ENST00000257430	NM_000038.5	1328	Cag/Tag	16/16	1	2	FACETS	0.578	0.461	0.711	0.578	0.461	0.711	SUBCLONAL	1	TRUE	1	0.336011480728422	2		336	278	SUCCESS
APC	324	MSKCC	GRCh37	5	112174484	112174484	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	21	390	0	ENST00000257430.4:c.3193C>T	p.Gln1065Ter	p.Q1065*	ENST00000257430	NM_000038.5	1065	Caa/Taa	16/16	1	2	FACETS	0.358	0.275	0.455	0.358	0.275	0.455	SUBCLONAL	1	TRUE	1	0.336011480728422	2		390	349	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849819	156849819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765477124	NA	P-0024494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	28	700	1	ENST00000524377.1:c.2075G>A	p.Arg692His	p.R692H	ENST00000524377	NM_002529.3	692	cGc/cAc	16/17	1	2	FACETS	0.298	0.237	0.368	0.298	0.237	0.368	SUBCLONAL	1	TRUE	1	0.336011480728422	2		701	559	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400939	72400939	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	29	605	0	ENST00000357731.5:c.232A>G	p.Ile78Val	p.I78V	ENST00000357731	NM_173808.2	78	Att/Gtt	2/7	1	2	FACETS	0.341	0.273	0.419	0.341	0.273	0.419	SUBCLONAL	1	TRUE	1	0.336011480728422	2		605	506	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873719	35873720	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TAGA	novel	NA	P-0024494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	49	859	0	ENST00000216797.5:c.131_132insTCTA	p.Gln44HisfsTer43	p.Q44Hfs*43	ENST00000216797	NM_020529.2	44	cag/caTCTAg	1/6	1	2	FACETS	0.435	0.367	0.509	0.435	0.367	0.509	SUBCLONAL	1	TRUE	1	0.336011480728422	2		859	671	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477092	67477092	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	69	732	0	ENST00000327367.4:c.899G>T	p.Gly300Val	p.G300V	ENST00000327367	NM_005902.3	300	gGa/gTa	7/9	1	2	FACETS	0.729	0.636	0.831	0.729	0.636	0.831	SUBCLONAL	1	TRUE	1	0.336011480728422	2		732	563	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	183	855	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.30938208228378	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	1	0.322969833065379	4		855	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0024497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	30	780	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.322969833065379	2	FACETS	0.209	0.167	0.257	0.104	0.083	0.129	SUBCLONAL	1	TRUE	0	0.322969833065379	2		780	889	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0024497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	82	562	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.322969833065379	2		562	376	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332337	70332337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761821309	NA	P-0024497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	140	555	0	ENST00000373644.4:c.242G>A	p.Arg81His	p.R81H	ENST00000373644	NM_030625.2	81	cGc/cAc	2/12	1	2	FACETS	0.751	0.687	0.818	1	0.987	1	SUBCLONAL	2	TRUE	1	0.322969833065379	2		555	577	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250883	153250883	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	61	525	1	ENST00000281708.4:c.1177C>T	p.Arg393Ter	p.R393*	ENST00000281708	NM_033632.3	393	Cga/Tga	8/12	1	2	FACETS	0.832	0.727	0.943	1	0.976	1	CLONAL	2	TRUE	1	0.322969833065379	2		526	227	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115436	115115436	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	288	729	0	ENST00000257566.3:c.890A>G	p.Asn297Ser	p.N297S	ENST00000257566	NM_016569.3	297	aAc/aGc	5/8	0.30938208228378	4	FACETS	0.899	0.852	0.947	1	0.991	1	CLONAL	4	TRUE	1	0.322969833065379	4		729	656	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247373	153247373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	75	326	0	ENST00000281708.4:c.1429G>A	p.Gly477Ser	p.G477S	ENST00000281708	NM_033632.3	477	Ggt/Agt	10/12	1	2	FACETS	0.759	0.671	0.851	1	0.977	1	SUBCLONAL	2	TRUE	1	0.322969833065379	2		326	306	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579315	7579315	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1555526478	NA	P-0024497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	46	566	1	ENST00000269305.4:c.372C>A	p.Cys124Ter	p.C124*	ENST00000269305	NM_001126112.2	124	tgC/tgA	4/11	0.322969833065379	2	FACETS	0.459	0.386	0.541	0.23	0.193	0.271	SUBCLONAL	1	TRUE	0	0.322969833065379	2		567	620	SUCCESS
APC	324	MSKCC	GRCh37	5	112176030	112176030	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs886039682	NA	P-0024497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	103	363	0	ENST00000257430.4:c.4741del	p.Ser1581LeufsTer69	p.S1581Lfs*69	ENST00000257430	NM_000038.5	1580	aTt/at	16/16	1	2	FACETS	0.839	0.757	0.925	1	0.986	1	CLONAL	2	TRUE	1	0.322969833065379	2		363	380	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749442	41749442	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1476963248	NA	P-0024497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	147	533	1	ENST00000226382.2:c.353C>T	p.Ala118Val	p.A118V	ENST00000226382	NM_003924.3	118	gCg/gTg	2/3	1	2	FACETS	0.898	0.825	0.973	1	0.991	1	CLONAL	2	TRUE	1	0.322969833065379	2		534	507	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913647	32913647	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	26	449	0	ENST00000380152.3:c.5155A>G	p.Asn1719Asp	p.N1719D	ENST00000380152		1719	Aat/Gat	11/27	0.322969833065379	5	FACETS	0.595	0.47	0.737			1	SUBCLONAL	1	TRUE	NA	0.322969833065379	5		449	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578232	7578232	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0024497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	351	818	0	ENST00000269305.4:c.617T>A	p.Leu206Ter	p.L206*	ENST00000269305	NM_001126112.2	206	tTg/tAg	6/11	0.322969833065379	2	FACETS	0.875	0.833	0.917	1	0.994	1	CLONAL	3	TRUE	0	0.322969833065379	2		818	828	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248408	212248408	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	79	329	0	ENST00000342788.4:c.3859G>T	p.Glu1287Ter	p.E1287*	ENST00000342788	NM_005235.2	1287	Gag/Tag	28/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.322969833065379	2		329	350	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801503	1801503	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750990333	NA	P-0024497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	200	981	4	ENST00000260795.2:c.409G>A	p.Gly137Arg	p.G137R	ENST00000260795		137	Ggg/Agg	3/17	1	2	FACETS	0.819	0.761	0.879	1	0.992	1	CLONAL	2	TRUE	1	0.322969833065379	2		985	756	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467723	66467723	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	116	473	0	ENST00000273854.3:c.546C>A	p.Ser182Arg	p.S182R	ENST00000273854	NM_004439.5	182	agC/agA	3/18	1	2	FACETS	0.865	0.786	0.948	1	0.988	1	CLONAL	2	TRUE	1	0.322969833065379	2		473	415	SUCCESS
APC	324	MSKCC	GRCh37	5	112173639	112173645	+	frameshift_variant	Frame_Shift_Del	DEL	CATCTCA	CATCTCA	-	novel	NA	P-0024497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	89	427	0	ENST00000257430.4:c.2348_2354del	p.Ala783ValfsTer35	p.A783Vfs*35	ENST00000257430	NM_000038.5	783	gCATCTCAt/gt	16/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.322969833065379	2		427	368	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945318	151945318	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	42	108	0	ENST00000262189.6:c.2201C>T	p.Thr734Ile	p.T734I	ENST00000262189	NM_170606.2	734	aCt/aTt	14/59	0.322969833065379	4	FACETS	1	0.934	1	1	0.971	1	CLONAL	3	TRUE	2	0.322969833065379	4		108	100	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0024498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	144	386	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.907	0.834	0.982	0.907	0.834	0.982	CLONAL	1	TRUE	1	0.715147504315754	2		386	444	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462998	120462998	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	227	544	2	ENST00000256646.2:c.5333C>T	p.Ser1778Leu	p.S1778L	ENST00000256646	NM_024408.3	1778	tCa/tTa	30/34	1	2	FACETS	0.958	0.897	1	0.958	0.897	1	CLONAL	1	TRUE	1	0.715147504315754	2		546	663	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189447	94189447	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	191	749	0	ENST00000323929.3:c.1558C>G	p.Arg520Gly	p.R520G	ENST00000323929	NM_005591.3	520	Cgt/Ggt	14/20	1	2	FACETS	0.959	0.893	1	0.959	0.893	1	CLONAL	1	TRUE	1	0.715147504315754	2		749	557	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396232	396232	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	291	840	0	ENST00000262320.3:c.794del	p.Gly265GlufsTer149	p.G265Efs*149	ENST00000262320	NM_003502.3	265	gGa/ga	2/11	0.713415251738313	1	FACETS	0.867	0.824	0.911	0.867	0.824	0.911	CLONAL	1	TRUE	0	0.715147504315754	1		840	603	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508735	29508735	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1131691126	NA	P-0024498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	397	716	0	ENST00000356175.3:c.662G>A	p.Trp221Ter	p.W221*	ENST00000356175	NM_000267.3	221	tGg/tAg	7/57	0.710910389138191	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	0	0.715147504315754	3		716	502	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513276	44513276	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	341	839	0	ENST00000291552.4:c.659G>T	p.Gly220Val	p.G220V	ENST00000291552	NM_006758.2	220	gGt/gTt	8/8	1	2	FACETS	0.894	0.847	0.942	0.894	0.847	0.942	CLONAL	1	TRUE	1	0.715147504315754	2		839	1067	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495388	149495388	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	309	962	0	ENST00000261799.4:c.3259del	p.Glu1087AsnfsTer45	p.E1087Nfs*45	ENST00000261799	NM_002609.3	1087	Gaa/aa	23/23	1	2	FACETS	0.912	0.861	0.963	0.912	0.861	0.963	CLONAL	1	TRUE	1	0.715147504315754	2		962	948	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352756	70352756	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	364	429	0	ENST00000374080.3:c.4477G>T	p.Asp1493Tyr	p.D1493Y	ENST00000374080		1493	Gat/Tat	32/45	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.715147504315754	1		429	482	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909590	76909590	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0024498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	136	387	0	ENST00000373344.5:c.4315A>T	p.Lys1439Ter	p.K1439*	ENST00000373344	NM_000489.3	1439	Aag/Tag	14/35	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.715147504315754	1		387	200	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045559	47045560	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	T	novel	NA	P-0024498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	207	304	0	ENST00000377604.3:c.2526_2527delinsT	p.Thr843GlnfsTer4	p.T843Qfs*4	ENST00000377604	NM_001204468.1	842	tcCAca/tcTca	22/24	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.715147504315754	1		304	342	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024498-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	161	855	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.204597964139319	3	FACETS	0.896	0.825	0.968	0.896	0.825	0.968	CLONAL	3	TRUE	0	0.222312521588166	3		855	599	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319417	11319417	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024498-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	97	716	0	ENST00000361445.4:c.50del	p.Ser17ThrfsTer3	p.S17Tfs*3	ENST00000361445	NM_004958.3	17	aGc/ac	2/58	1	2	FACETS	0.964	0.858	1	0.964	0.858	1	CLONAL	1	TRUE	1	0.222312521588166	2		716	905	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092814	27092815	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0024498-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	65	722	0	ENST00000324856.7:c.2840dup	p.Tyr948IlefsTer59	p.Y948Ifs*59	ENST00000324856	NM_006015.4	945	-/C	9/20	1	2	FACETS	0.711	0.615	0.815	0.711	0.615	0.815	SUBCLONAL	1	TRUE	1	0.222312521588166	2		722	823	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986944	36986944	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852694	NA	P-0024498-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	236	783	2	ENST00000354822.5:c.745C>T	p.Gln249Ter	p.Q249*	ENST00000354822	NM_001079668.2	249	Cag/Tag	3/3	0.222312521588166	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.222312521588166	2		785	1010	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0024500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	125	588	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	0.544890223509721	2		588	416	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178342	56178343	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0024500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	126	324	0	ENST00000399503.3:c.3316dup	p.Ile1106AsnfsTer4	p.I1106Nfs*4	ENST00000399503	NM_005921.1	1105	-/A	14/20	0.214587093750971	3	FACETS	0.855	0.784	0.928	0.57	0.523	0.619	INDETERMINATE	2	TRUE	0	0.544890223509721	3		324	344	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179455	56179457	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	novel	NA	P-0024500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	56	448	0	ENST00000399503.3:c.3770_3772del	p.Cys1257del	p.C1257del	ENST00000399503	NM_005921.1	1256	tcTTGt/tct	15/20	0.214587093750971	3	FACETS	0.525	0.45	0.607	0.175	0.15	0.203	INDETERMINATE	1	TRUE	0	0.544890223509721	3		448	498	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	201	629	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.613238654037682	3	FACETS	1	0.986	1	0.618	0.575	0.662	CLONAL	1	TRUE	1	0.613238654037682	3		629	693	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0024507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	86	588	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.613238654037682	3	FACETS	0.762	0.676	0.853	0.381	0.338	0.427	SUBCLONAL	1	TRUE	1	0.613238654037682	3		588	481	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752411	57752412	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0024507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	76	235	0	ENST00000274289.3:c.1161_1162del	p.Arg387SerfsTer3	p.R387Sfs*3	ENST00000274289	NM_006622.3	387	agAGtg/agtg	9/14	0.608372219256822	4	FACETS	0.923	0.813	1	0.462	0.406	0.521	CLONAL	1	TRUE	2	0.613238654037682	4		235	433	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163315578	163315578	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	452	405	1	ENST00000271452.3:c.918T>A	p.Asn306Lys	p.N306K	ENST00000271452	NM_145697.2	306	aaT/aaA	11/14	0.613238654037682	6	FACETS	0.911	0.875	0.947	0.911	0.875	0.947	CLONAL	4	TRUE	2	0.613238654037682	6		406	901	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871602	35871602	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	61	284	0	ENST00000216797.5:c.904G>T	p.Glu302Ter	p.E302*	ENST00000216797	NM_020529.2	302	Gag/Tag	5/6	0.608372219256822	4	FACETS	0.964	0.837	1	0.482	0.418	0.55	CLONAL	1	TRUE	2	0.613238654037682	4		284	333	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250938	99250938	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	129	539	0	ENST00000268035.6:c.242T>C	p.Ile81Thr	p.I81T	ENST00000268035	NM_000875.3	81	aTt/aCt	2/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.613238654037682	2		539	388	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857333	68857333	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	254	415	2	ENST00000261769.5:c.1969del	p.Ala657ProfsTer2	p.A657Pfs*2	ENST00000261769	NM_004360.3	656	atG/at	13/16	0.613238654037682	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.613238654037682	2		417	414	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953237	81953237	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs963117904	NA	P-0024507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	168	366	0	ENST00000359376.3:c.2203G>A	p.Val735Met	p.V735M	ENST00000359376	NM_002661.3	735	Gtg/Atg	20/33	0.613238654037682	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.613238654037682	2		366	254	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016617	12016617	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	230	500	0	ENST00000353533.5:c.753T>G	p.Ser251Arg	p.S251R	ENST00000353533	NM_003010.3	251	agT/agG	7/11	0.613238654037682	2	FACETS	0.959	0.911	1	0.959	0.911	1	CLONAL	2	TRUE	0	0.613238654037682	2		500	391	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026826	71026826	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	103	361	0	ENST00000318789.4:c.1396C>A	p.Pro466Thr	p.P466T	ENST00000318789	NM_032682.5	466	Cca/Aca	16/21	0.613238654037682	3	FACETS	0.838	0.752	0.927	0.419	0.376	0.464	CLONAL	1	TRUE	1	0.613238654037682	3		361	524	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928226	178928226	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519872	NA	P-0024511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	84	427	1	ENST00000263967.3:c.1412C>T	p.Pro471Leu	p.P471L	ENST00000263967	NM_006218.2	471	cCa/cTa	9/21	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.400573948637886	2		428	394	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969978	81969978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755551138	NA	P-0024511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	86	366	0	ENST00000359376.3:c.3047C>T	p.Thr1016Met	p.T1016M	ENST00000359376	NM_002661.3	1016	aCg/aTg	27/33	1	2	FACETS	0.893	0.793	0.999	0.893	0.793	0.999	CLONAL	1	TRUE	1	0.400573948637886	2		366	481	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0024520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	183	589	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.342270164969411	2	FACETS	0.81	0.753	0.868	0.81	0.753	0.868	CLONAL	2	TRUE	0	0.426925872074706	2		589	529	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971000	21971000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	105	567	0	ENST00000304494.5:c.358G>T	p.Glu120Ter	p.E120*	ENST00000304494	NM_000077.4	120	Gag/Tag	2/3	0.426925872074706	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.426925872074706	1		567	346	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056210	26056210	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	65	506	0	ENST00000343677.2:c.447G>C	p.Lys149Asn	p.K149N	ENST00000343677	NM_005319.3	149	aaG/aaC	1/1	0.18272235155021	2	FACETS	0.576	0.499	0.658	0.288	0.249	0.329	INDETERMINATE	1	TRUE	0	0.426925872074706	2		506	529	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482854	67482854	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1206533102	NA	P-0024520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	62	497	0	ENST00000327367.4:c.1258C>T	p.Arg420Cys	p.R420C	ENST00000327367	NM_005902.3	420	Cgc/Tgc	9/9	1	2	FACETS	0.698	0.605	0.799	0.698	0.605	0.799	SUBCLONAL	1	TRUE	1	0.426925872074706	2		497	416	SUCCESS
APC	324	MSKCC	GRCh37	5	112137036	112137036	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	90	431	0	ENST00000257430.4:c.790C>T	p.Gln264Ter	p.Q264*	ENST00000257430	NM_000038.5	264	Caa/Taa	8/16	0.426925872074706	1	FACETS	0.926	0.829	1	0.926	0.829	1	CLONAL	1	TRUE	0	0.426925872074706	1		431	358	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891193	151891193	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	133	511	1	ENST00000262189.6:c.4561G>T	p.Glu1521Ter	p.E1521*	ENST00000262189	NM_170606.2	1521	Gaa/Taa	31/59	1	2	FACETS	0.951	0.866	1	0.951	0.866	1	CLONAL	1	TRUE	1	0.426925872074706	2		512	655	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56857686	56857686	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	81	503	0	ENST00000308159.5:c.722C>G	p.Ala241Gly	p.A241G	ENST00000308159	NM_014669.4	241	gCc/gGc	8/22	1	2	FACETS	0.694	0.612	0.781	0.694	0.612	0.781	SUBCLONAL	1	TRUE	1	0.426925872074706	2		503	547	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868304	56868304	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	52	274	0	ENST00000308159.5:c.1687G>C	p.Glu563Gln	p.E563Q	ENST00000308159	NM_014669.4	563	Gaa/Caa	15/22	1	2	FACETS	0.752	0.643	0.869	0.752	0.643	0.869	SUBCLONAL	1	TRUE	1	0.426925872074706	2		274	324	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18964084	18964084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	59	502	0	ENST00000262803.5:c.1081G>A	p.Glu361Lys	p.E361K	ENST00000262803	NM_002911.3	361	Gag/Aag	8/24	1	2	FACETS	0.655	0.565	0.752	0.655	0.565	0.752	SUBCLONAL	1	TRUE	1	0.426925872074706	2		502	422	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251647	212251647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	53	450	0	ENST00000342788.4:c.3412G>A	p.Glu1138Lys	p.E1138K	ENST00000342788	NM_005235.2	1138	Gaa/Aaa	27/28	1	2	FACETS	0.518	0.442	0.601	0.518	0.442	0.601	SUBCLONAL	1	TRUE	1	0.426925872074706	2		450	479	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41279562	41279562	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	115	421	0	ENST00000349496.5:c.2132A>T	p.Gln711Leu	p.Q711L	ENST00000349496	NM_001904.3	711	cAg/cTg	14/15	0.425875270803416	1	FACETS	0.979	0.888	1	0.979	0.888	1	CLONAL	1	TRUE	0	0.426925872074706	1		421	433	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164744	47164744	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0024520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	117	405	0	ENST00000409792.3:c.1382C>G	p.Ser461Ter	p.S461*	ENST00000409792	NM_014159.6	461	tCa/tGa	3/21	0.425875270803416	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.426925872074706	1		405	362	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048863	180048863	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	155	852	0	ENST00000261937.6:c.1699G>C	p.Glu567Gln	p.E567Q	ENST00000261937	NM_182925.4	567	Gag/Cag	13/30	0.426925872074706	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.426925872074706	1		852	488	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790752	89790752	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	65	710	0	ENST00000336032.3:c.139G>T	p.Asp47Tyr	p.D47Y	ENST00000336032	NM_006813.2	47	Gac/Tac	1/2	0.18272235155021	2	FACETS	0.527	0.457	0.603	0.263	0.228	0.302	INDETERMINATE	1	TRUE	0	0.426925872074706	2		710	578	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127911953	127911953	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	novel	NA	P-0024520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	104	385	0	ENST00000373547.4:c.917G>C	p.Ter306SerextTer7	p.*306Sext*7	ENST00000373547	NM_002721.4	306	tGa/tCa	7/7	0.426925872074706	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.426925872074706	1		385	363	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092983	27092984	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	T	novel	NA	P-0024520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	161	380	0	ENST00000324856.7:c.2914_2915delinsT	p.Asp972LeufsTer2	p.D972Lfs*2	ENST00000324856	NM_006015.4	972	GAt/Tt	10/20	0.342270164969411	2	FACETS	0.948	0.88	1	0.948	0.88	1	CLONAL	2	TRUE	0	0.426925872074706	2		380	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0024522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	181	873	3	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.213478771077472	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.213478771077472	2		876	755	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061833	38061850	+	inframe_deletion	In_Frame_Del	DEL	GGTGTTCATGGTCATGTA	GGTGTTCATGGTCATGTA	-	novel	NA	P-0024522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	135	994	1	ENST00000250448.2:c.139_156del	p.Tyr47_Thr52del	p.Y47_T52del	ENST00000250448	NM_004496.3	47	TACATGACCATGAACACC/-	2/2	0.213478771077472	5	FACETS	0.76	0.69	0.835	0.507	0.46	0.557	SUBCLONAL	2	TRUE	2	0.213478771077472	5		995	1098	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0024524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	244	419	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.530204221250904	4	FACETS	0.988	0.936	1	0.988	0.936	1	CLONAL	3	TRUE	1	0.530204221250904	4		419	475	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133772	41133772	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745385825	NA	P-0024524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	114	336	0	ENST00000379561.5:c.1856G>A	p.Arg619Gln	p.R619Q	ENST00000379561	NM_002015.3	619	cGg/cAg	2/3	0.530204221250904	3	FACETS	1	0.948	1	0.535	0.484	0.589	CLONAL	1	TRUE	1	0.530204221250904	3		336	508	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46738381	46738381	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	232	597	1	ENST00000371975.4:c.1282del	p.Leu428Ter	p.L428*	ENST00000371975	NM_003579.3	428	Ctg/tg	12/18	0.530204221250904	3	FACETS	1	0.967	1	0.53	0.494	0.567	CLONAL	1	TRUE	1	0.530204221250904	3		598	1045	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739096	46739096	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	287	633	0	ENST00000371975.4:c.1445C>G	p.Pro482Arg	p.P482R	ENST00000371975	NM_003579.3	482	cCt/cGt	13/18	0.530204221250904	3	FACETS	1	0.988	1	0.599	0.563	0.636	CLONAL	1	TRUE	1	0.530204221250904	3		633	1143	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739111	46739111	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372225086	NA	P-0024524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	247	615	0	ENST00000371975.4:c.1460C>T	p.Ser487Phe	p.S487F	ENST00000371975	NM_003579.3	487	tCt/tTt	13/18	0.530204221250904	3	FACETS	1	0.974	1	0.54	0.504	0.576	CLONAL	1	TRUE	1	0.530204221250904	3		615	1092	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739135	46739135	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1487464723	NA	P-0024524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	158	527	0	ENST00000371975.4:c.1484C>T	p.Ser495Leu	p.S495L	ENST00000371975	NM_003579.3	495	tCa/tTa	13/18	0.530204221250904	3	FACETS	0.853	0.782	0.927	0.426	0.391	0.464	CLONAL	1	TRUE	1	0.530204221250904	3		527	884	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860630	3860630	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	199	709	0	ENST00000262367.5:c.949A>G	p.Thr317Ala	p.T317A	ENST00000262367	NM_004380.2	317	Act/Gct	3/31	NA	2	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.530204221250904	2		709	730	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40490763	40490764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0024524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	183	613	0	ENST00000264657.5:c.535dup	p.Leu179ProfsTer42	p.L179Pfs*42	ENST00000264657	NM_139276.2	179	ctc/cCtc	6/24	0.530204221250904	2	FACETS	1	0.953	1	0.519	0.481	0.559	CLONAL	1	TRUE	0	0.530204221250904	2		613	665	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0024525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	62	698	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	NA	2	FACETS	0.657	0.567	0.756			1	INDETERMINATE	1	FALSE	NA	0.246249811457349	2		698	766	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0024525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	52	731	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.653	0.555	0.76	0.653	0.555	0.76	SUBCLONAL	1	FALSE	1	0.246249811457349	2		732	647	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916947	178916947	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	67	452	0	ENST00000263967.3:c.334A>T	p.Ile112Phe	p.I112F	ENST00000263967	NM_006218.2	112	Atc/Ttc	2/21	1	2	FACETS	0.875	0.76	0.999	0.875	0.76	0.999	CLONAL	1	FALSE	1	0.246249811457349	2		452	622	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353740	15353740	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768856782	NA	P-0024525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	69	973	1	ENST00000263377.2:c.3140G>A	p.Arg1047Gln	p.R1047Q	ENST00000263377	NM_058243.2	1047	cGg/cAg	14/20	NA	2	FACETS	0.555	0.482	0.634			1	INDETERMINATE	1	FALSE	NA	0.246249811457349	2		974	1010	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405942	49405942	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	40	762	0	ENST00000418115.1:c.196T>A	p.Tyr66Asn	p.Y66N	ENST00000418115	NM_001664.2	66	Tat/Aat	3/5	1	2	FACETS	0.413	0.342	0.492	0.413	0.342	0.492	SUBCLONAL	1	FALSE	1	0.246249811457349	2		762	787	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0024527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	15	811	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	NA	2	FACETS	0.305	0.222	0.404			1	INDETERMINATE	1	FALSE	NA	0.301096572152423	2		812	327	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992072	11992072	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0024527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	15	291	0	ENST00000396373.4:c.164-2A>T		p.X55_splice	ENST00000396373	NM_001987.4	55			0.301096572152423	5	FACETS	0.643	0.471	0.849			1	SUBCLONAL	1	FALSE	NA	0.301096572152423	5		291	225	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661856	29661856	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs906075234	NA	P-0024527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	25	528	0	ENST00000356175.3:c.5750G>A	p.Ser1917Asn	p.S1917N	ENST00000356175	NM_000267.3	1917	aGt/aAt	39/57	1	2	FACETS	0.439	0.346	0.547	0.439	0.346	0.547	SUBCLONAL	1	FALSE	1	0.301096572152423	2		528	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0024530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	239	665	1	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.166058145426907	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	TRUE	1	0.166058145426907	4		666	1045	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992930	72992930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1398839726	NA	P-0024530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	159	803	1	ENST00000268489.5:c.1115G>A	p.Arg372Gln	p.R372Q	ENST00000268489	NM_006885.3	372	cGa/cAa	2/10	0.12951306107905	2	FACETS	0.828	0.757	0.902	0.828	0.757	0.902	CLONAL	2	TRUE	0	0.166058145426907	2		804	1157	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105530	30105530	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	69	786	0	ENST00000331968.5:c.1156G>A	p.Asp386Asn	p.D386N	ENST00000331968	NM_002742.2	386	Gac/Aac	7/18	0.166058145426907	3	FACETS	0.858	0.745	0.981	0.429	0.372	0.491	CLONAL	1	TRUE	1	0.166058145426907	3		786	1049	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829170	72829170	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	76	701	1	ENST00000268489.5:c.7411C>T	p.Leu2471Phe	p.L2471F	ENST00000268489	NM_006885.3	2471	Ctc/Ttc	9/10	0.12951306107905	2	FACETS	1	0.911	1	0.525	0.459	0.596	CLONAL	1	TRUE	0	0.166058145426907	2		702	872	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11015680	11015680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1351621427	NA	P-0024530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	48	675	1	ENST00000327064.4:c.274C>T	p.Arg92Cys	p.R92C	ENST00000327064	NM_199141.1	92	Cgt/Tgt	2/16	1	2	FACETS	0.64	0.539	0.752	0.64	0.539	0.752	SUBCLONAL	1	TRUE	1	0.166058145426907	2		676	903	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17949175	17949175	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	63	789	2	ENST00000458235.1:c.1466A>T	p.Gln489Leu	p.Q489L	ENST00000458235	NM_000215.3	489	cAg/cTg	11/24	1	2	FACETS	0.694	0.598	0.799	0.694	0.598	0.799	SUBCLONAL	1	TRUE	1	0.166058145426907	2		791	1093	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932798	39932798	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1379881009	NA	P-0024530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	29	380	1	ENST00000378444.4:c.1801C>A	p.Pro601Thr	p.P601T	ENST00000378444	NM_001123385.1	601	Ccc/Acc	4/15	0.166058145426907	2	FACETS	0.602	0.482	0.74			1	SUBCLONAL	1	TRUE	NA	0.166058145426907	2		381	580	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519893	NA	P-0024531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1415	132	519	0	ENST00000267101.3:c.310G>T	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ttg	3/28	0.186039756122316	6	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.186039756122316	6		519	1547	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245033	46245033	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs139789595	NA	P-0024531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	94	725	1	ENST00000334344.6:c.3127C>T	p.Gln1043Ter	p.Q1043*	ENST00000334344	NM_152641.2	1043	Caa/Taa	15/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.186039756122316	2		726	840	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575149	48575149	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	64	442	0	ENST00000342988.3:c.343T>G	p.Cys115Gly	p.C115G	ENST00000342988	NM_005359.5	115	Tgt/Ggt	3/12	0.186039756122316	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.186039756122316	1		442	548	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	123	855	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.151816911706531	3	FACETS	1	0.971	1	0.597	0.539	0.658	CLONAL	1	TRUE	1	0.223551542881734	3		855	1025	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	149	760	0	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	0.223551542881734	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.223551542881734	1		760	967	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028638	12028638	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	54	513	1	ENST00000353533.5:c.841C>T	p.Arg281Ter	p.R281*	ENST00000353533	NM_003010.3	281	Cga/Tga	8/11	0.223551542881734	1	FACETS	0.694	0.592	0.806	0.694	0.592	0.806	SUBCLONAL	1	TRUE	0	0.223551542881734	1		514	618	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515211	103515211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759628522	NA	P-0024532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	45	441	1	ENST00000355739.4:c.1712C>T	p.Pro571Leu	p.P571L	ENST00000355739	NM_000123.3	571	cCg/cTg	8/15	1	2	FACETS	0.682	0.573	0.804	0.682	0.573	0.804	SUBCLONAL	1	TRUE	1	0.223551542881734	2		442	590	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259270	16259270	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs774668447	NA	P-0024532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	45	404	0	ENST00000375759.3:c.6535G>T	p.Ala2179Ser	p.A2179S	ENST00000375759	NM_015001.2	2179	Gca/Tca	11/15	1	2	FACETS	0.848	0.713	0.997	0.848	0.713	0.997	CLONAL	1	TRUE	1	0.223551542881734	2		404	475	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099123	27099123	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	75	644	0	ENST00000324856.7:c.3539+1del		p.S1180fs	ENST00000324856	NM_006015.4	1180	aGc/ac	13/20	1	2	FACETS	0.902	0.79	1	0.902	0.79	1	CLONAL	1	TRUE	1	0.223551542881734	2		644	744	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202830	133202830	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	123	840	0	ENST00000320574.5:c.6404T>C	p.Val2135Ala	p.V2135A	ENST00000320574	NM_006231.2	2135	gTc/gCc	46/49	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.223551542881734	2		840	891	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211685	36211685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1416954696	NA	P-0024532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	73	707	1	ENST00000222270.7:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000222270	NM_014727.1	479	cGg/cAg	3/37	1	2	FACETS	0.979	0.856	1	0.979	0.856	1	CLONAL	1	TRUE	1	0.223551542881734	2		708	667	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867493	101867493	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	10	65	0	ENST00000374994.4:c.7del	p.Ala3ArgfsTer47	p.A3Rfs*47	ENST00000374994	NM_004612.2	2	gaG/ga	1/9	0.223551542881734	1	FACETS	0.828	0.566	1	0.828	0.566	1	CLONAL	1	TRUE	0	0.223551542881734	1		65	96	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0024534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	407	653	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.822462357732332	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.822462357732332	2		653	478	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097738	8097738	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	205	660	0	ENST00000346208.3:c.120G>C	p.Gln40His	p.Q40H	ENST00000346208		40	caG/caC	2/6	0.822462357732332	3	FACETS	1	0.963	1	0.525	0.489	0.562	CLONAL	1	TRUE	1	0.822462357732332	3		660	670	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857926	9857926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	159	599	0	ENST00000330684.3:c.3475C>T	p.Arg1159Cys	p.R1159C	ENST00000330684	NM_001134407.1	1159	Cgc/Tgc	13/13	0.722345915993962	3	FACETS	0.759	0.697	0.823			1	SUBCLONAL	1	TRUE	NA	0.822462357732332	3		599	719	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78617593	78617593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	129	445	1	ENST00000306801.3:c.331G>A	p.Glu111Lys	p.E111K	ENST00000306801	NM_020761.2	111	Gag/Aag	3/34	0.782370843314253	4	FACETS	0.95	0.864	1	0.475	0.432	0.52	CLONAL	1	TRUE	2	0.822462357732332	4		446	602	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579315	7579316	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1267047192	NA	P-0024535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	127	613	0	ENST00000269305.4:c.371dup	p.Cys124TrpfsTer25	p.C124Wfs*25	ENST00000269305	NM_001126112.2	124	tgc/tgGc	4/11	0.460327129591667	1	FACETS	0.977	0.892	1	0.977	0.892	1	CLONAL	1	TRUE	0	0.460327129591667	1		613	435	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256943	16256943	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1308286819	NA	P-0024535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	193	771	1	ENST00000375759.3:c.4208G>A	p.Arg1403Gln	p.R1403Q	ENST00000375759	NM_015001.2	1403	cGa/cAa	11/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.460327129591667	2		772	775	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829722	72829722	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	351	970	0	ENST00000268489.5:c.6859G>C	p.Val2287Leu	p.V2287L	ENST00000268489	NM_006885.3	2287	Gtg/Ctg	9/10	1	2	FACETS	0.941	0.897	0.987	1	0.996	1	CLONAL	2	TRUE	1	0.460327129591667	2		970	810	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965217	81965217	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	145	672	0	ENST00000359376.3:c.2697G>T	p.Trp899Cys	p.W899C	ENST00000359376	NM_002661.3	899	tgG/tgT	25/33	1	2	FACETS	0.917	0.839	0.999	0.917	0.839	0.999	CLONAL	1	TRUE	1	0.460327129591667	2		672	687	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	42	855	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	0.250174707428795	2		855	283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253911	NA	P-0024537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	127	568	0	ENST00000269305.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000269305	NM_001126112.2	180	Gag/Aag	5/11	0.157610108422588	2	FACETS	0.765	0.694	0.839	0.765	0.694	0.839	SUBCLONAL	2	TRUE	0	0.250174707428795	2		568	664	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495620	56495621	+	missense_variant	Missense_Mutation	DNP	TG	TG	AT	novel	NA	P-0024537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	48	452	0	ENST00000267101.3:c.3810_3811delinsAT	p.Gly1271Cys	p.G1271C	ENST00000267101	NM_001982.3	1270	ggTGgt/ggATgt	28/28	1	2	FACETS	0.799	0.676	0.935	0.799	0.676	0.935	CLONAL	1	TRUE	1	0.250174707428795	2		452	480	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339981	70339981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	257	185	0	ENST00000374080.3:c.514G>A	p.Glu172Lys	p.E172K	ENST00000374080		172	Gag/Aag	4/45	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.948177051188463	1		185	264	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273231	18273231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1260910794	NA	P-0024538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	238	603	0	ENST00000222254.8:c.1024G>A	p.Glu342Lys	p.E342K	ENST00000222254	NM_005027.3	342	Gag/Aag	9/16	1	2	FACETS	0.901	0.849	0.954	0.901	0.849	0.954	CLONAL	1	TRUE	1	0.948177051188463	2		603	557	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261368	16261368	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781561009	NA	P-0024538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	292	524	0	ENST00000375759.3:c.8633C>T	p.Ala2878Val	p.A2878V	ENST00000375759	NM_015001.2	2878	gCg/gTg	11/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.948177051188463	2		524	558	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061132	38061145	+	protein_altering_variant	In_Frame_Del	DEL	CCGCTGCCCCCGCT	CCGCTGCCCCCGCT	GG	novel	NA	P-0024538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	117	237	3	ENST00000250448.2:c.844_857delinsCC	p.Ser282_Gly286delinsPro	p.S282_G286delinsP	ENST00000250448	NM_004496.3	282	AGCGGGGGCAGCGGc/CCc	2/2	1	2	FACETS	0.991	0.912	1	0.991	0.912	1	CLONAL	1	TRUE	1	0.948177051188463	2		240	249	SUCCESS
AR	367	MSKCC	GRCh37	X	66943551	66943551	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	224	219	0	ENST00000374690.3:c.2631C>A	p.Phe877Leu	p.F877L	ENST00000374690	NM_000044.3	877	ttC/ttA	8/8	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.948177051188463	1		219	237	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929386	44929386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1484235922	NA	P-0024538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	10	242	0	ENST00000377967.4:c.2486C>T	p.Ser829Phe	p.S829F	ENST00000377967	NM_021140.2	829	tCt/tTt	17/29	1	1	FACETS	0.347	0.246	0.459	0.347	0.246	0.459	SUBCLONAL	1	TRUE	0	0.948177051188463	1		242	32	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0024543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	450	780	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.709811691961338	2	FACETS	0.867	0.839	0.894	0.867	0.839	0.894	CLONAL	2	TRUE	0	0.779501032474881	2		780	666	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776541	9776541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779226622	NA	P-0024543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	386	1103	2	ENST00000377346.4:c.644C>T	p.Ala215Val	p.A215V	ENST00000377346	NM_005026.3	215	gCg/gTg	6/24	0.779501032474881	3	FACETS	0.797	0.761	0.833	0.797	0.761	0.833	SUBCLONAL	2	TRUE	1	0.779501032474881	3		1105	864	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249290	133249291	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs1255326788	NA	P-0024543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	114	1215	0	ENST00000320574.5:c.1608_1609del	p.Glu537AspfsTer24	p.E537Dfs*24	ENST00000320574	NM_006231.2	536	tcTGag/tcag	15/49	0.6481385514248	4	FACETS	0.408	0.366	0.453			1	SUBCLONAL	1	TRUE	NA	0.779501032474881	4		1215	1275	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300216	15300216	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	432	1150	1	ENST00000263388.2:c.1060G>A	p.Ala354Thr	p.A354T	ENST00000263388	NM_000435.2	354	Gcc/Acc	7/33	0.70160270434931	2	FACETS	0.866	0.837	0.894	0.866	0.837	0.894	CLONAL	2	TRUE	0	0.779501032474881	2		1151	640	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935005	49935005	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	162	1044	1	ENST00000296474.3:c.1994G>T	p.Gly665Val	p.G665V	ENST00000296474	NM_002447.2	665	gGc/gTc	6/20	0.68537431215265	4	FACETS	0.632	0.579	0.688	0.316	0.289	0.344	SUBCLONAL	1	TRUE	2	0.779501032474881	4		1045	1170	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158432	26158432	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	145	1125	0	ENST00000289316.2:c.35A>G	p.Lys12Arg	p.K12R	ENST00000289316	NM_138720.2	12	aAg/aGg	1/2	0.146582733672876	1	FACETS	0.343	0.314	0.374	0.343	0.314	0.374	INDETERMINATE	1	TRUE	0	0.779501032474881	1		1125	661	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859266	151859266	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1016393034	NA	P-0024543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	215	761	0	ENST00000262189.6:c.11396G>T	p.Cys3799Phe	p.C3799F	ENST00000262189	NM_170606.2	3799	tGt/tTt	43/59	0.779501032474881	3	FACETS	1	0.986	1	0.597	0.558	0.637	CLONAL	1	TRUE	1	0.779501032474881	3		761	642	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061184	38061187	+	frameshift_variant	Frame_Shift_Del	DEL	CGCA	CGCA	-	novel	NA	P-0024545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	92	753	2	ENST00000250448.2:c.802_805del	p.Cys268ArgfsTer52	p.C268Rfs*52	ENST00000250448	NM_004496.3	268	TGCGag/ag	2/2	0.437931071550246	14	FACETS	0.909	0.813	1			1	CLONAL	4	TRUE	NA	0.437931071550246	14		755	419	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058426	42058426	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs769929257	NA	P-0024551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	120	746	1	ENST00000219905.7:c.8146A>T	p.Thr2716Ser	p.T2716S	ENST00000219905	NM_001164273.1	2716	Acg/Tcg	24/24	1	2	FACETS	0.694	0.628	0.762	0.694	0.628	0.762	SUBCLONAL	1	TRUE	1	0.597455750891242	2		747	579	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058426	42058426	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs769929257	NA	P-0024551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	155	746	1	ENST00000219905.7:c.8146A>T	p.Thr2716Ser	p.T2716S	ENST00000219905	NM_001164273.1	2716	Acg/Tcg	24/24	1	2	FACETS	0.964	0.891	1	0.964	0.891	1	CLONAL	1	TRUE	1	0.736169072398352	2		747	437	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	469	855	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.47598166847246	2	FACETS	0.959	0.92	0.998	0.959	0.92	0.998	CLONAL	2	TRUE	0	0.476180908544884	2		855	1027	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs17849781	NA	P-0024552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	398	996	0	ENST00000269305.4:c.832C>G	p.Pro278Ala	p.P278A	ENST00000269305	NM_001126112.2	278	Cct/Gct	8/11	0.403164795648922	2	FACETS	0.861	0.821	0.9	0.861	0.821	0.9	CLONAL	2	TRUE	0	0.476180908544884	2		996	971	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484146	8484146	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	159	794	0	ENST00000356435.5:c.3386C>G	p.Pro1129Arg	p.P1129R	ENST00000356435		1129	cCt/cGt	19/35	0.476180908544884	1	FACETS	0.798	0.734	0.864	0.798	0.734	0.864	SUBCLONAL	1	TRUE	0	0.476180908544884	1		794	638	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0024553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	154	814	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	1	2	FACETS	0.918	0.841	0.998	0.918	0.841	0.998	CLONAL	1	TRUE	1	0.426008682132849	2		814	788	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690406	117690406	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs762367712	NA	P-0024553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	292	710	0	ENST00000369458.3:c.725-2A>G		p.X242_splice	ENST00000369458	NM_024626.3	242			0.426008682132849	1	FACETS	0.794	0.753	0.836	1	0.995	1	SUBCLONAL	2	TRUE	0	0.426008682132849	1		710	679	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150290	108150291	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0024553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	110	703	0	ENST00000278616.4:c.3359_3360del	p.Phe1120Ter	p.F1120*	ENST00000278616	NM_000051.3	1119	gcTTtt/gctt	23/63	0.426008682132849	1	FACETS	0.989	0.895	1	0.989	0.895	1	CLONAL	1	TRUE	0	0.426008682132849	1		703	411	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740458	58740458	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	183	905	2	ENST00000305921.3:c.1363del	p.Glu455ArgfsTer2	p.E455Rfs*2	ENST00000305921	NM_003620.3	455	Gag/ag	6/6	1	2	FACETS	0.993	0.917	1	0.993	0.917	1	CLONAL	1	TRUE	1	0.426008682132849	2		907	865	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132422	11132422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	224	944	0	ENST00000358026.2:c.2638G>A	p.Val880Met	p.V880M	ENST00000358026	NM_001128849.1	880	Gtg/Atg	19/36	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.426008682132849	2		944	1007	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495647	72495647	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	86	494	1	ENST00000477973.2:c.425G>A	p.Arg142Lys	p.R142K	ENST00000477973	NM_012234.5	142	aGa/aAa	1/4	0.426008682132849	1	FACETS	0.88	0.785	0.981	0.88	0.785	0.981	CLONAL	1	TRUE	0	0.426008682132849	1		495	361	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525131	157525131	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0024553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	67	339	1	ENST00000346085.5:c.5025+1G>T		p.X1675_splice	ENST00000346085	NM_020732.3	1675			1	2	FACETS	0.992	0.869	1	0.992	0.869	1	CLONAL	1	TRUE	1	0.426008682132849	2		340	317	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298142	123298142	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	413	823	2	ENST00000358487.5:c.712G>A	p.Gly238Arg	p.G238R	ENST00000358487	NM_000141.4	238	Ggg/Agg	6/18	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.765286070745501	2		825	954	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199878	108199878	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1555122149	NA	P-0024554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	174	393	0	ENST00000278616.4:c.7220C>A	p.Ser2407Ter	p.S2407*	ENST00000278616	NM_000051.3	2407	tCa/tAa	49/63	0.765286070745501	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.765286070745501	1		393	278	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92354938	92354938	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0024554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	98	355	0	ENST00000265734.4:c.537+2T>C		p.X179_splice	ENST00000265734	NM_001259.6	179			0.405511834546668	4	FACETS	0.821	0.734	0.912	0.205	0.183	0.228	INDETERMINATE	1	TRUE	0	0.765286070745501	4		355	551	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591104	67591115	+	inframe_deletion	In_Frame_Del	DEL	TTAAACCAGACC	TTAAACCAGACC	-	novel	NA	P-0024557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	41	331	0	ENST00000274335.5:c.1700_1711del	p.Lys567_Leu570del	p.K567_L570del	ENST00000274335		566	aTTAAACCAGACCtt/att	12/15	1	2	FACETS	1	0.84	1	1	0.84	1	CLONAL	1	TRUE	1	0.191869754544217	2		331	424	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692839	89692839	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	19	219	0	ENST00000371953.3:c.323T>G	p.Leu108Arg	p.L108R	ENST00000371953	NM_000314.4	108	cTt/cGt	5/9	1	2	FACETS	1	0.836	1	1	0.836	1	CLONAL	1	TRUE	1	0.191869754544217	2		219	176	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80021291	80021291	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs539295465	NA	P-0024557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	62	576	2	ENST00000265081.6:c.1360C>T	p.Arg454Ter	p.R454*	ENST00000265081	NM_002439.4	454	Cga/Tga	9/24	1	2	FACETS	0.856	0.738	0.984	0.856	0.738	0.984	CLONAL	1	TRUE	1	0.191869754544217	2		578	755	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189386	56189386	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	50	554	0	ENST00000399503.3:c.4418del	p.Ile1473ThrfsTer17	p.I1473Tfs*17	ENST00000399503	NM_005921.1	1473	aTc/ac	20/20	1	2	FACETS	0.905	0.767	1	0.905	0.767	1	CLONAL	1	TRUE	1	0.191869754544217	2		554	576	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900035	151900036	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0024557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	92	628	0	ENST00000262189.6:c.4075_4076del	p.Phe1359ProfsTer18	p.F1359Pfs*18	ENST00000262189	NM_170606.2	1359	TTc/c	26/59	0.167372048925631	3	FACETS	0.806	0.717	0.901			1	CLONAL	2	TRUE	NA	0.191869754544217	3		628	652	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577567	7577581	+	frameshift_variant	Frame_Shift_Del	DEL	ACACATGTAGTTGTA	ACACATGTAGTTGTA	T	novel	NA	P-0024557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	57	662	0	ENST00000269305.4:c.700_714delinsA	p.Tyr234LysfsTer25	p.Y234Kfs*25	ENST00000269305	NM_001126112.2	234	TACAACTACATGTGT/A	7/11	0.183851242898396	1	FACETS	0.941	0.807	1	0.941	0.807	1	CLONAL	1	TRUE	0	0.191869754544217	1		662	571	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794793	42794799	+	frameshift_variant	Frame_Shift_Del	DEL	GGAAACA	GGAAACA	TCC	novel	NA	P-0024560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	132	597	1	ENST00000575354.2:c.1873_1879delinsTCC	p.Gly625SerfsTer102	p.G625Sfs*102	ENST00000575354	NM_015125.3	625	GGAAACAtc/TCCtc	10/20	1	2	FACETS	0.935	0.855	1	0.935	0.855	1	CLONAL	1	TRUE	1	0.623420762363176	2		598	453	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188233	10188233	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	260	702	0	ENST00000256474.2:c.376del	p.Asp126MetfsTer33	p.D126Mfs*33	ENST00000256474	NM_000551.3	126	Gat/at	2/3	0.623420762363176	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.623420762363176	1		702	532	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846384	128846384	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	211	614	0	ENST00000249373.3:c.1220C>G	p.Pro407Arg	p.P407R	ENST00000249373	NM_005631.4	407	cCa/cGa	6/12	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.623420762363176	2		614	618	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181241	123181241	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	118	441	0	ENST00000218089.9:c.707del	p.Asn236IlefsTer20	p.N236Ifs*20	ENST00000218089	NM_001042749.1	235	ctA/ct	9/35	1	2	FACETS	0.912	0.83	0.998	0.912	0.83	0.998	CLONAL	1	TRUE	1	0.623420762363176	2		441	415	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0024561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	185	405	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.958	0.89	1	0.958	0.89	1	CLONAL	1	TRUE	1	0.653371776390831	2		405	591	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221226	1221227	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGGTCTG	novel	NA	P-0024561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	275	763	0	ENST00000326873.7:c.750_756dup	p.Tyr253GlyfsTer15	p.Y253Gfs*15	ENST00000326873	NM_000455.4	250	acg/acGGGTCTGg	6/10	0.652668695827139	1	FACETS	0.746	0.703	0.789	0.746	0.703	0.789	SUBCLONAL	1	TRUE	0	0.653371776390831	1		763	760	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578262	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs483352697	NA	P-0024562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	281	877	0	ENST00000269305.4:c.587G>C	p.Arg196Pro	p.R196P	ENST00000269305	NM_001126112.2	196	cGa/cCa	6/11	0.802601898995056	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.803908816536376	1		877	407	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467763	50467763	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1308	243	756	2	ENST00000331340.3:c.998C>T	p.Thr333Met	p.T333M	ENST00000331340	NM_006060.4	333	aCg/aTg	8/8	0.803908816536376	6	FACETS	1	0.945	1	0.254	0.236	0.273	CLONAL	1	TRUE	2	0.803908816536376	6		758	1551	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350976	89350994	+	frameshift_variant	Frame_Shift_Del	DEL	AGTAAAACTTTTCAACTTC	AGTAAAACTTTTCAACTTC	-	novel	NA	P-0024562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	251	1178	2	ENST00000301030.4:c.1956_1974del	p.Lys653ThrfsTer16	p.K653Tfs*16	ENST00000301030	NM_001256183.1	652	ctGAAGTTGAAAAGTTTTACT/ct	9/13	0.803908816536376	2	FACETS	0.821	0.771	0.871	0.41	0.385	0.436	CLONAL	1	TRUE	0	0.803908816536376	2		1180	761	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715721	30715721	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	165	618	1	ENST00000295754.5:c.1379G>C	p.Arg460Pro	p.R460P	ENST00000295754	NM_003242.5	460	cGc/cCc	5/7	0.802601898995056	1	FACETS	0.903	0.85	0.954	0.903	0.85	0.954	CLONAL	1	TRUE	0	0.803908816536376	1		619	272	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86682717	86682725	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGGGTATG	TGGGGTATG	-	novel	NA	P-0024562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	211	419	0	ENST00000274376.6:c.2923_2925+6del		p.X975_splice	ENST00000274376	NM_002890.2	975		23/25	0.803908816536376	2	FACETS	0.941	0.902	0.978	0.941	0.902	0.978	CLONAL	2	TRUE	0	0.803908816536376	2		419	279	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0024567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	220	802	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.3	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	0	0.24	3		802	618	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508064	106508064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	30	260	2	ENST00000359195.3:c.58C>T	p.Arg20Cys	p.R20C	ENST00000359195	NM_002649.2	20	Cgc/Tgc	2/11	0.3	4	FACETS	1	0.914	1	0.417	0.337	0.506	CLONAL	1	TRUE	1	0.24	4		262	248	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363628	40363628	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	98	697	0	ENST00000397332.2:c.601G>C	p.Asp201His	p.D201H	ENST00000397332	NM_001033082.2	201	Gat/Cat	3/3	0.231271546280605	3	FACETS	0.986	0.884	1	0.986	0.884	1	CLONAL	2	TRUE	1	0.24	3		697	464	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421620	49421620	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	257	913	0	ENST00000301067.7:c.14609A>G	p.Lys4870Arg	p.K4870R	ENST00000301067	NM_003482.3	4870	aAg/aGg	47/54	0.3	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	3	TRUE	0	0.24	3		913	778	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004248	29004248	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	92	645	1	ENST00000282397.4:c.1045G>T	p.Gly349Cys	p.G349C	ENST00000282397	NM_002019.4	349	Ggc/Tgc	8/30	0.235079527247838	2	FACETS	0.835	0.746	0.93	0.835	0.746	0.93	CLONAL	2	TRUE	0	0.24	2		646	459	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744461	41744462	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGGGTACCCTGTT	novel	NA	P-0024567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	100	985	0	ENST00000301178.4:c.1090_1102dup	p.Arg368ProfsTer123	p.R368Pfs*123	ENST00000301178	NM_021913.4	361	cag/cAGGGTACCCTGTTag	8/20	0.17196792803714	4	FACETS	1	0.979	1	0.705	0.63	0.785	CLONAL	1	TRUE	2	0.24	4		985	733	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160186	22160186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	36	512	0	ENST00000215832.6:c.445G>A	p.Asp149Asn	p.D149N	ENST00000215832	NM_002745.4	149	Gac/Aac	3/9	0.17196792803714	4	FACETS	0.937	0.771	1	0.469	0.385	0.562	CLONAL	1	TRUE	2	0.24	4		512	397	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259458	89259458	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	105	818	0	ENST00000336596.2:c.602A>T	p.Lys201Met	p.K201M	ENST00000336596	NM_005233.5	201	aAg/aTg	3/17	0.258022878158327	2	FACETS	0.957	0.863	1	0.957	0.863	1	CLONAL	2	TRUE	0	0.24	2		818	457	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518076	176518076	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	39	893	0	ENST00000292408.4:c.574C>G	p.His192Asp	p.H192D	ENST00000292408	NM_213647.1	192	Cat/Gat	5/18	1	2	FACETS	0.567	0.469	0.677	0.567	0.469	0.677	SUBCLONAL	1	TRUE	1	0.24	2		893	573	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066627	94066627	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs778960808	NA	P-0024567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	47	777	0	ENST00000369303.4:c.1132G>C	p.Glu378Gln	p.E378Q	ENST00000369303	NM_004440.3	378	Gaa/Caa	5/17	1	2	FACETS	0.88	0.744	1	0.88	0.744	1	CLONAL	1	TRUE	1	0.24	2		777	445	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729336	41729336	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	168	681	0	ENST00000242208.4:c.1193C>T	p.Pro398Leu	p.P398L	ENST00000242208	NM_002192.2	398	cCc/cTc	3/3	0.3	4	FACETS	0.963	0.889	1	0.963	0.889	1	CLONAL	3	TRUE	1	0.24	4		681	601	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967598	90967598	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	67	669	0	ENST00000265433.3:c.1310del	p.Pro437GlnfsTer3	p.P437Qfs*3	ENST00000265433	NM_002485.4	437	cCa/ca	10/16	0.208365496863922	4	FACETS	0.785	0.684	0.893	0.785	0.684	0.893	SUBCLONAL	2	TRUE	2	0.24	4		669	441	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967652	90967652	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	76	659	0	ENST00000265433.3:c.1256A>G	p.Asn419Ser	p.N419S	ENST00000265433	NM_002485.4	419	aAt/aGt	10/16	0.208365496863922	4	FACETS	0.882	0.777	0.995	0.882	0.777	0.995	CLONAL	2	TRUE	2	0.24	4		659	445	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127933411	127933411	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	33	865	3	ENST00000373547.4:c.124C>T	p.Gln42Ter	p.Q42*	ENST00000373547	NM_002721.4	42	Cag/Tag	2/7	1	2	FACETS	0.452	0.367	0.549	0.452	0.367	0.549	SUBCLONAL	1	TRUE	1	0.24	2		868	608	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0024568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	104	598	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.208004648568772	1	FACETS	0.836	0.753	0.923	0.836	0.753	0.923	INDETERMINATE	1	TRUE	0	0.425784813219726	1		598	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577595	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0024568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	257	809	0	ENST00000269305.4:c.686_687del	p.Cys229TyrfsTer10	p.C229Yfs*10	ENST00000269305	NM_001126112.2	229	tGT/t	7/11	0.31888779819201	3	FACETS	1	0.99	1	0.812	0.767	0.858	CLONAL	2	TRUE	0	0.425784813219726	3		809	601	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070639	67070639	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0024568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	60	340	0	ENST00000412916.2:c.263T>G	p.Leu88Ter	p.L88*	ENST00000412916		88	tTa/tGa	3/6	0.343758708397848	2	FACETS	1	0.928	1	0.55	0.479	0.626	CLONAL	1	TRUE	0	0.425784813219726	2		340	256	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931898	68931898	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	48	828	0	ENST00000288368.4:c.328C>G	p.Leu110Val	p.L110V	ENST00000288368	NM_024870.2	110	Ctt/Gtt	3/40	0.411118619121511	4	FACETS	0.387	0.326	0.454	0.129	0.108	0.152	SUBCLONAL	1	TRUE	1	0.425784813219726	4		828	831	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0024570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	38	625	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.905	0.75	1	0.905	0.75	1	CLONAL	1	TRUE	1	0.245520837934944	2		625	342	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs1202793339	NA	P-0024570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	76	699	1	ENST00000269305.4:c.560-1G>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.245520837934944	2		700	534	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944161	71944161	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755180843	NA	P-0024570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	87	784	0	ENST00000298229.2:c.1994G>A	p.Arg665Gln	p.R665Q	ENST00000298229	NM_001567.3	665	cGg/cAg	17/28	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.245520837934944	2		784	689	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46583304	46583304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370125133	NA	P-0024570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	46	455	0	ENST00000263734.3:c.232G>A	p.Glu78Lys	p.E78K	ENST00000263734	NM_001430.4	78	Gag/Aag	3/16	1	2	FACETS	0.786	0.662	0.922	0.786	0.662	0.922	CLONAL	1	TRUE	1	0.245520837934944	2		455	477	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924481	131924481	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150030986	NA	P-0024570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	28	628	1	ENST00000265335.6:c.1154G>A	p.Arg385His	p.R385H	ENST00000265335		385	cGt/cAt	8/25	1	2	FACETS	0.565	0.451	0.694	0.565	0.451	0.694	SUBCLONAL	1	TRUE	1	0.245520837934944	2		629	404	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5534888	5534888	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	54	642	2	ENST00000397747.3:c.199T>C	p.Ser67Pro	p.S67P	ENST00000397747	NM_025239.3	67	Tcc/Ccc	3/7	1	2	FACETS	0.844	0.721	0.979	0.844	0.721	0.979	CLONAL	1	TRUE	1	0.245520837934944	2		644	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577555	7577555	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs375874539	NA	P-0024571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	54	877	0	ENST00000269305.4:c.726C>G	p.Cys242Trp	p.C242W	ENST00000269305	NM_001126112.2	242	tgC/tgG	7/11	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.217288431841765	2		877	442	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306631	41306631	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	56	898	3	ENST00000373198.4:c.1028C>T	p.Pro343Leu	p.P343L	ENST00000373198	NM_133170.3	343	cCc/cTc	7/32	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.217288431841765	2		901	409	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466375	120466375	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	38	722	0	ENST00000256646.2:c.4744G>T	p.Asp1582Tyr	p.D1582Y	ENST00000256646	NM_024408.3	1582	Gac/Tac	26/34	1	2	FACETS	0.754	0.623	0.9	0.754	0.623	0.9	SUBCLONAL	1	TRUE	1	0.217288431841765	2		722	464	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056321	27056321	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	53	573	0	ENST00000324856.7:c.1317G>C	p.Gln439His	p.Q439H	ENST00000324856	NM_006015.4	439	caG/caC	2/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.217288431841765	2		573	370	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332972	70332972	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	36	897	3	ENST00000373644.4:c.877G>T	p.Glu293Ter	p.E293*	ENST00000373644	NM_030625.2	293	Gaa/Taa	2/12	1	2	FACETS	0.606	0.497	0.728	0.606	0.497	0.728	SUBCLONAL	1	TRUE	1	0.217288431841765	2		900	547	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609520	81609520	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs749925257	NA	P-0024571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	39	595	0	ENST00000298171.2:c.1118C>G	p.Pro373Arg	p.P373R	ENST00000298171	NM_000369.2	373	cCc/cGc	10/10	0.217288431841765	1	FACETS	0.808	0.671	0.961	0.808	0.671	0.961	CLONAL	1	TRUE	0	0.217288431841765	1		595	396	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690614	88690614	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	43	618	0	ENST00000360948.2:c.416T>A	p.Leu139His	p.L139H	ENST00000360948	NM_001012338.2	139	cTc/cAc	5/19	1	2	FACETS	0.883	0.74	1	0.883	0.74	1	CLONAL	1	TRUE	1	0.217288431841765	2		618	448	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78921118	78921118	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	40	760	0	ENST00000306801.3:c.3232G>T	p.Gly1078Cys	p.G1078C	ENST00000306801	NM_020761.2	1078	Ggc/Tgc	27/34	1	2	FACETS	0.8	0.665	0.951	0.8	0.665	0.951	CLONAL	1	TRUE	1	0.217288431841765	2		760	460	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207033	1207033	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	58	805	0	ENST00000326873.7:c.122del	p.Lys41SerfsTer10	p.K41Sfs*10	ENST00000326873	NM_000455.4	41	Aag/ag	1/10	0.217288431841765	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.217288431841765	1		805	440	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17389671	17389671	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	42	775	0	ENST00000359435.4:c.806del	p.Gly269AlafsTer100	p.G269Afs*100	ENST00000359435	NM_001033549.1	268	atG/at	9/9	0.217288431841765	1	FACETS	0.895	0.749	1	0.895	0.749	1	CLONAL	1	TRUE	0	0.217288431841765	1		775	385	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17941028	17941028	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0024571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	64	970	0	ENST00000458235.1:c.3097-1G>T		p.X1033_splice	ENST00000458235	NM_000215.3	1033			0.217288431841765	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.217288431841765	1		970	472	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910258	50910258	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	69	863	0	ENST00000440232.2:c.1513C>A	p.Arg505Ser	p.R505S	ENST00000440232	NM_002691.3	505	Cgc/Agc	13/27	NA	2	FACETS	1	0.967	1			1	INDETERMINATE	1	TRUE	NA	0.217288431841765	2		863	472	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370684	225370684	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	47	542	0	ENST00000264414.4:c.1195G>T	p.Gly399Ter	p.G399*	ENST00000264414	NM_003590.4	399	Gga/Tga	8/16	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.217288431841765	2		542	411	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259521	89259521	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	30	637	1	ENST00000336596.2:c.665C>A	p.Ser222Tyr	p.S222Y	ENST00000336596	NM_005233.5	222	tCc/tAc	3/17	1	2	FACETS	0.696	0.56	0.849	0.696	0.56	0.849	SUBCLONAL	1	TRUE	1	0.217288431841765	2		638	397	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534440	187534440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200812915	NA	P-0024571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	22	665	0	ENST00000441802.2:c.9286C>T	p.Leu3096Phe	p.L3096F	ENST00000441802	NM_005245.3	3096	Ctc/Ttc	13/27	0.205338016704995	1	FACETS	0.464	0.359	0.586	0.464	0.359	0.586	SUBCLONAL	1	TRUE	0	0.217288431841765	1		665	389	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751568	57751568	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	30	498	0	ENST00000274289.3:c.1423G>T	p.Val475Leu	p.V475L	ENST00000274289	NM_006622.3	475	Gtg/Ttg	11/14	0.217288431841765	1	FACETS	0.722	0.582	0.88	0.722	0.582	0.88	SUBCLONAL	1	TRUE	0	0.217288431841765	1		498	341	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149506143	149506143	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	29	778	0	ENST00000261799.4:c.1614C>G	p.Ile538Met	p.I538M	ENST00000261799	NM_002609.3	538	atC/atG	11/23	0.217288431841765	1	FACETS	0.641	0.515	0.785	0.641	0.515	0.785	SUBCLONAL	1	TRUE	0	0.217288431841765	1		778	371	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332918	152332918	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	56	489	0	ENST00000206249.3:c.1224G>C	p.Leu408Phe	p.L408F	ENST00000206249	NM_000125.3	408	ttG/ttC	5/8	0.217288431841765	1	FACETS	0.751	0.647	0.862	1	0.968	1	SUBCLONAL	2	TRUE	0	0.217288431841765	1		489	306	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205301	38205301	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	101	1213	0	ENST00000317025.8:c.389C>G	p.Pro130Arg	p.P130R	ENST00000317025	NM_023034.1	130	cCt/cGt	2/24	0.217288431841765	3	FACETS	1	0.972	1	0.632	0.564	0.703	CLONAL	1	TRUE	1	0.217288431841765	3		1213	816	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250445	110250445	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	25	755	0	ENST00000374672.4:c.230G>T	p.Gly77Val	p.G77V	ENST00000374672	NM_004235.4	77	gGc/gTc	3/5	0.0502188026596522	1	FACETS	0.553	0.435	0.688	0.553	0.435	0.688	INDETERMINATE	1	TRUE	0	0.217288431841765	1		755	371	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915943	127915943	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	42	767	1	ENST00000373547.4:c.538G>T	p.Glu180Ter	p.E180*	ENST00000373547	NM_002721.4	180	Gaa/Taa	6/7	0.0502188026596522	1	FACETS	0.648	0.54	0.767	0.648	0.54	0.767	INDETERMINATE	1	TRUE	0	0.217288431841765	1		768	532	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0024573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	97	790	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	0.214964998182732	2		790	864	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0024573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	74	696	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.214964998182732	1	FACETS	0.885	0.775	1	0.885	0.775	1	CLONAL	1	TRUE	0	0.214964998182732	1		696	694	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108765	2108765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755631210	NA	P-0024573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	73	806	2	ENST00000219476.3:c.866C>T	p.Ala289Val	p.A289V	ENST00000219476	NM_000548.3	289	gCg/gTg	10/42	1	2	FACETS	0.957	0.836	1	0.957	0.836	1	CLONAL	1	TRUE	1	0.214964998182732	2		808	710	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971087	21971087	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	65	598	0	ENST00000304494.5:c.271del	p.Leu91TrpfsTer55	p.L91Wfs*55	ENST00000304494	NM_000077.4	91	Ctg/tg	2/3	0.214964998182732	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.214964998182732	1		598	440	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581298	48581298	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0024573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	99	757	0	ENST00000342988.3:c.602T>A	p.Leu201Ter	p.L201*	ENST00000342988	NM_005359.5	201	tTa/tAa	5/12	0.160738524869975	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.214964998182732	1		757	754	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949155	44949155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	75	309	0	ENST00000377967.4:c.3716G>T	p.Trp1239Leu	p.W1239L	ENST00000377967	NM_021140.2	1239	tGg/tTg	25/29	1	1	FACETS	0.865	0.763	0.973	1	0.981	1	CLONAL	2	TRUE	0	0.214964998182732	1		309	360	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0024574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	35	547	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.155	0.126	0.187	0.155	0.126	0.187	SUBCLONAL	1	TRUE	1	0.709639643097777	2		547	637	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258670	16258670	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	33	654	0	ENST00000375759.3:c.5935G>C	p.Glu1979Gln	p.E1979Q	ENST00000375759	NM_015001.2	1979	Gag/Cag	11/15	1	2	FACETS	0.151	0.122	0.184	0.151	0.122	0.184	SUBCLONAL	1	TRUE	1	0.709639643097777	2		654	615	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032045	26032045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	32	521	0	ENST00000244661.2:c.244G>A	p.Asp82Asn	p.D82N	ENST00000244661	NM_003537.3	82	Gat/Aat	1/1	1	2	FACETS	0.158	0.128	0.193	0.158	0.128	0.193	SUBCLONAL	1	TRUE	1	0.709639643097777	2		521	570	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259936	16259936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	53	687	0	ENST00000375759.3:c.7201G>A	p.Asp2401Asn	p.D2401N	ENST00000375759	NM_015001.2	2401	Gac/Aac	11/15	1	2	FACETS	0.18	0.153	0.211	0.18	0.153	0.211	SUBCLONAL	1	TRUE	1	0.709639643097777	2		687	828	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259189	16259189	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	52	622	0	ENST00000375759.3:c.6454G>C	p.Asp2152His	p.D2152H	ENST00000375759	NM_015001.2	2152	Gac/Cac	11/15	1	2	FACETS	0.213	0.181	0.249	0.213	0.181	0.249	SUBCLONAL	1	TRUE	1	0.709639643097777	2		622	688	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259699	16259699	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	54	537	1	ENST00000375759.3:c.6964G>T	p.Glu2322Ter	p.E2322*	ENST00000375759	NM_015001.2	2322	Gaa/Taa	11/15	1	2	FACETS	0.212	0.18	0.247	0.212	0.18	0.247	SUBCLONAL	1	TRUE	1	0.709639643097777	2		538	718	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259830	16259830	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	42	595	0	ENST00000375759.3:c.7095G>C	p.Glu2365Asp	p.E2365D	ENST00000375759	NM_015001.2	2365	gaG/gaC	11/15	1	2	FACETS	0.159	0.132	0.189	0.159	0.132	0.189	SUBCLONAL	1	TRUE	1	0.709639643097777	2		595	743	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481375	56481375	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	142	776	1	ENST00000267101.3:c.562G>A	p.Glu188Lys	p.E188K	ENST00000267101	NM_001982.3	188	Gag/Aag	5/28	1	2	FACETS	0.432	0.393	0.472	0.432	0.393	0.472	SUBCLONAL	1	TRUE	1	0.709639643097777	2		777	927	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120750	115120750	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	215	638	0	ENST00000257566.3:c.256del	p.His86IlefsTer2	p.H86Ifs*2	ENST00000257566	NM_016569.3	86	Cat/at	1/8	1	2	FACETS	0.867	0.809	0.926	0.867	0.809	0.926	CLONAL	1	TRUE	1	0.709639643097777	2		638	699	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438345	110438345	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	96	230	0	ENST00000375856.3:c.56A>G	p.Asn19Ser	p.N19S	ENST00000375856	NM_003749.2	19	aAc/aGc	1/2	1	2	FACETS	0.771	0.693	0.852	0.771	0.693	0.852	SUBCLONAL	1	TRUE	1	0.709639643097777	2		230	351	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849650	68849650	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	197	524	0	ENST00000261769.5:c.1554del	p.Glu518AspfsTer4	p.E518Dfs*4	ENST00000261769	NM_004360.3	518	gAa/ga	10/16	0.709639643097777	1	FACETS	0.839	0.787	0.891	0.839	0.787	0.891	CLONAL	1	TRUE	0	0.709639643097777	1		524	427	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15960943	15960943	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	43	487	1	ENST00000268712.3:c.6277G>C	p.Val2093Leu	p.V2093L	ENST00000268712	NM_006311.3	2093	Gtg/Ctg	40/46	1	2	FACETS	0.185	0.154	0.219	0.185	0.154	0.219	SUBCLONAL	1	TRUE	1	0.709639643097777	2		488	656	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661936	29661936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	60	672	0	ENST00000356175.3:c.5830G>A	p.Asp1944Asn	p.D1944N	ENST00000356175	NM_000267.3	1944	Gat/Aat	39/57	1	2	FACETS	0.189	0.162	0.218	0.189	0.162	0.218	SUBCLONAL	1	TRUE	1	0.709639643097777	2		672	896	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627477	14627477	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	38	559	0	ENST00000254322.2:c.593G>C	p.Arg198Pro	p.R198P	ENST00000254322	NM_006145.1	198	cGa/cCa	2/3	1	2	FACETS	0.157	0.129	0.188	0.157	0.129	0.188	SUBCLONAL	1	TRUE	1	0.709639643097777	2		559	684	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295222	15295222	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142405648	NA	P-0024574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	145	889	0	ENST00000263388.2:c.2450C>T	p.Pro817Leu	p.P817L	ENST00000263388	NM_000435.2	817	cCc/cTc	16/33	1	2	FACETS	0.468	0.426	0.511	0.468	0.426	0.511	SUBCLONAL	1	TRUE	1	0.709639643097777	2		889	874	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574146	46574146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	222	692	0	ENST00000263734.3:c.161C>T	p.Ala54Val	p.A54V	ENST00000263734	NM_001430.4	54	gCc/gTc	2/16	1	2	FACETS	0.793	0.74	0.847	0.793	0.74	0.847	SUBCLONAL	1	TRUE	1	0.709639643097777	2		692	789	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37622819	37622819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	45	734	0	ENST00000249071.6:c.473C>T	p.Ser158Leu	p.S158L	ENST00000249071	NM_002872.4	158	tCa/tTa	6/7	0.709639643097777	1	FACETS	0.135	0.113	0.16	0.135	0.113	0.16	SUBCLONAL	1	TRUE	0	0.709639643097777	1		734	605	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0024578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	26	337	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.705	0.557	0.874	0.705	0.557	0.874	SUBCLONAL	1	TRUE	1	0.17	2		337	434	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710622	114710622	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1282664682	NA	P-0024578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	35	545	2	ENST00000543371.1:c.107C>T	p.Ser36Leu	p.S36L	ENST00000543371	NM_001198531.1	36	tCg/tTg	1/14	1	2	FACETS	0.999	0.82	1	0.999	0.82	1	CLONAL	1	TRUE	1	0.17	2		547	412	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835723	68835723	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1064795703	NA	P-0024578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	49	697	0	ENST00000261769.5:c.315del	p.Thr106ProfsTer11	p.T106Pfs*11	ENST00000261769	NM_004360.3	105	tCc/tc	3/16	0.203668101570172	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.17	1		697	460	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665755	29665756	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs876657715	NA	P-0024578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	40	423	0	ENST00000356175.3:c.6791dup	p.Tyr2264Ter	p.Y2264*	ENST00000356175	NM_000267.3	2264	tac/tAac	45/57	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.17	2		423	435	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696438	47696438	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	290	703	0	ENST00000347630.2:c.385A>G	p.Lys129Glu	p.K129E	ENST00000347630	NM_001007230.1	129	Aaa/Gaa	6/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.711447631992332	2		703	727	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776783	NA	P-0024584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	58	413	0	ENST00000267163.4:c.1215+1G>A		p.X405_splice	ENST00000267163	NM_000321.2	405			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		413	189	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0024585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	112	769	2	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	0.229458536964936	2	FACETS	1	0.978	1	0.649	0.585	0.716	CLONAL	1	TRUE	0	0.293477164367306	2		771	588	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712013	89712014	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1114167663	NA	P-0024585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	50	298	0	ENST00000371953.3:c.632dup	p.Cys211TrpfsTer32	p.C211Wfs*32	ENST00000371953	NM_000314.4	211	tgc/tGgc	6/9	0.24362007828823	2	FACETS	1	0.942	1	0.606	0.518	0.702	CLONAL	1	TRUE	0	0.293477164367306	2		298	281	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	48	629	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.49598445008999	3	FACETS	0.926	0.789	1	0.463	0.394	0.538	CLONAL	1	TRUE	1	0.497779549085955	3		629	260	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0024586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	240	804	0	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	0.468267870736533	2	FACETS	0.883	0.833	0.934	0.883	0.833	0.934	CLONAL	2	TRUE	0	0.497779549085955	2		804	546	SUCCESS
APC	324	MSKCC	GRCh37	5	112175240	112175240	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	44	391	0	ENST00000257430.4:c.3949G>T	p.Glu1317Ter	p.E1317*	ENST00000257430	NM_000038.5	1317	Gaa/Taa	16/16	0.49598445008999	3	FACETS	0.928	0.785	1	0.464	0.392	0.542	CLONAL	1	TRUE	1	0.497779549085955	3		391	238	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335697	81335697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779933934	NA	P-0024586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	50	646	1	ENST00000222390.5:c.1663G>A	p.Gly555Arg	p.G555R	ENST00000222390	NM_000601.4	555	Gga/Aga	15/18	0.49598445008999	3	FACETS	0.926	0.792	1	0.463	0.396	0.536	CLONAL	1	TRUE	1	0.497779549085955	3		647	271	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609757	81609757	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs781210779	NA	P-0024586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	30	512	0	ENST00000298171.2:c.1355T>C	p.Leu452Pro	p.L452P	ENST00000298171	NM_000369.2	452	cTc/cCc	10/10	1	2	FACETS	0.32	0.257	0.39	0.32	0.257	0.39	SUBCLONAL	1	TRUE	1	0.497779549085955	2		512	377	SUCCESS
APC	324	MSKCC	GRCh37	5	112174641	112174651	+	frameshift_variant	Frame_Shift_Del	DEL	CTAATCATGGA	CTAATCATGGA	-	novel	NA	P-0024586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	55	551	0	ENST00000257430.4:c.3350_3360del	p.Ser1117TyrfsTer2	p.S1117Yfs*2	ENST00000257430	NM_000038.5	1117	tCTAATCATGGA/t	16/16	0.49598445008999	3	FACETS	1	0.969	1	0.73	0.635	0.831	CLONAL	1	TRUE	1	0.497779549085955	3		551	189	SUCCESS
APC	324	MSKCC	GRCh37	5	112174668	112174668	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs767339739	NA	P-0024586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	53	522	1	ENST00000257430.4:c.3377G>T	p.Ser1126Ile	p.S1126I	ENST00000257430	NM_000038.5	1126	aGc/aTc	16/16	0.49598445008999	3	FACETS	0.773	0.671	0.88	0.773	0.671	0.88	SUBCLONAL	2	TRUE	1	0.497779549085955	3		523	172	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	174	855	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.175097160800197	3	FACETS	0.988	0.908	1	0.988	0.908	1	CLONAL	2	TRUE	1	0.175097160800197	3		855	1094	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0024587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	48	782	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.101366367276551	0	FACETS	0.641	0.54	0.752			1	INDETERMINATE	1	TRUE	0	0.175097160800197	0		782	706	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141793	108141793	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0024587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	56	573	0	ENST00000278616.4:c.2841T>A	p.Tyr947Ter	p.Y947*	ENST00000278616	NM_000051.3	947	taT/taA	19/63	0.175097160800197	3	FACETS	0.864	0.739	1	0.432	0.369	0.501	CLONAL	1	TRUE	1	0.175097160800197	3		573	805	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235428	235428	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768055345	NA	P-0024587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	39	718	0	ENST00000264932.6:c.1234G>A	p.Gly412Ser	p.G412S	ENST00000264932	NM_004168.2	412	Ggc/Agc	9/15	0.175097160800197	0	FACETS	0.625	0.517	0.746			1	SUBCLONAL	1	TRUE	0	0.175097160800197	0		718	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0024588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	222	778	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.498901462327336	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.498901462327336	1		778	663	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252873	36252873	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	169	577	0	ENST00000300305.3:c.489T>G	p.Phe163Leu	p.F163L	ENST00000300305		163	ttT/ttG	4/8	0.498901462327336	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.498901462327336	1		577	494	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	100	855	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.976	0.884	1	0.976	0.884	1	CLONAL	1	TRUE	1	0.719222084353983	2		855	285	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0024590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	275	683	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.685157243197379	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.719222084353983	1		683	484	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0024590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	140	602	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.318621981849226	3	FACETS	0.917	0.839	0.999	0.459	0.419	0.5	INDETERMINATE	1	TRUE	1	0.719222084353983	3		603	577	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0024590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	271	633	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.719222084353983	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.719222084353983	1		633	446	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245558	41245558	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	214	840	0	ENST00000357654.3:c.1990A>G	p.Arg664Gly	p.R664G	ENST00000357654	NM_007294.3	664	Aga/Gga	10/23	0.399912711339831	1	FACETS	0.899	0.847	0.95	0.899	0.847	0.95	INDETERMINATE	1	TRUE	0	0.719222084353983	1		840	424	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588896	52588896	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0024590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	173	472	0	ENST00000394830.3:c.4133-1G>A		p.X1378_splice	ENST00000394830	NM_018313.4	1378			0.719222084353983	1	FACETS	0.939	0.881	0.997	0.939	0.881	0.997	CLONAL	1	TRUE	0	0.719222084353983	1		472	328	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	306	855	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.247425011294113	5	FACETS	0.956	0.904	1			1	CLONAL	4	TRUE	NA	0.247425011294113	5		855	887	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0024591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	200	865	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.224530241773648	2	FACETS	0.838	0.776	0.901	0.838	0.776	0.901	CLONAL	2	TRUE	0	0.247425011294113	2		865	965	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528056	103528056	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	87	379	0	ENST00000355739.4:c.3364C>G	p.Pro1122Ala	p.P1122A	ENST00000355739	NM_000123.3	1122	Cca/Gca	15/15	0.228292307814164	4	FACETS	0.839	0.745	0.939	0.839	0.745	0.939	CLONAL	2	TRUE	2	0.247425011294113	4		379	523	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604739	48604739	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs786203930	NA	P-0024591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	60	429	0	ENST00000342988.3:c.1561A>C	p.Thr521Pro	p.T521P	ENST00000342988	NM_005359.5	521	Aca/Cca	12/12	0.247425011294113	1	FACETS	0.811	0.699	0.932	0.811	0.699	0.932	CLONAL	1	TRUE	0	0.247425011294113	1		429	524	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0024593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	35	572	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.446674684215809	3	FACETS	0.299	0.244	0.36	0.149	0.122	0.18	SUBCLONAL	1	TRUE	1	0.446674684215809	3		572	642	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188297	10188297	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs869025653	NA	P-0024593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	189	759	2	ENST00000256474.2:c.444del	p.Phe148LeufsTer11	p.F148Lfs*11	ENST00000256474	NM_000551.3	147	aTt/at	2/3	0.392296198183859	2	FACETS	1	0.991	1	0.744	0.692	0.797	CLONAL	1	TRUE	0	0.446674684215809	2		761	569	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884875	134884875	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368240835	NA	P-0024593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	152	637	2	ENST00000398015.3:c.1651G>A	p.Val551Met	p.V551M	ENST00000398015	NM_004441.4	551	Gtg/Atg	8/16	0.406605505412901	4	FACETS	0.84	0.772	0.911	0.84	0.772	0.911	CLONAL	2	TRUE	2	0.446674684215809	4		639	586	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442081	52442081	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	169	641	0	ENST00000460680.1:c.268T>C	p.Ser90Pro	p.S90P	ENST00000460680	NM_004656.3	90	Tct/Cct	5/17	0.392296198183859	2	FACETS	0.807	0.748	0.866	0.807	0.748	0.866	CLONAL	2	TRUE	0	0.446674684215809	2		641	469	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610624	52610624	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	186	742	0	ENST00000394830.3:c.3549A>C	p.Lys1183Asn	p.K1183N	ENST00000394830	NM_018313.4	1183	aaA/aaC	23/30	0.392296198183859	2	FACETS	0.859	0.8	0.918	0.859	0.8	0.918	CLONAL	2	TRUE	0	0.446674684215809	2		742	485	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191349	185191349	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	250	736	0	ENST00000265026.3:c.2230del	p.Asp744ThrfsTer80	p.D744Tfs*80	ENST00000265026	NM_004721.4	744	Gac/ac	11/14	0.446674684215809	7	FACETS	1	0.989	1	0.496	0.464	0.529	CLONAL	2	TRUE	2	0.446674684215809	7		736	955	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447088	187447089	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0024593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	203	782	0	ENST00000232014.4:c.1104_1105del	p.Asp369ProfsTer27	p.D369Pfs*27	ENST00000232014	NM_001130845.1	368	acTGac/acac	5/10	0.446674684215809	7	FACETS	0.989	0.917	1	0.395	0.366	0.426	CLONAL	2	TRUE	2	0.446674684215809	7		782	973	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436393	52436393	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1244342890	NA	P-0024594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	212	550	4	ENST00000460680.1:c.2101C>T	p.Arg701Cys	p.R701C	ENST00000460680	NM_004656.3	701	Cgc/Tgc	17/17	0.939557774205628	2	FACETS	0.695	0.649	0.742	0.348	0.324	0.371	SUBCLONAL	1	TRUE	0	0.947245825065368	2		554	644	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087346	27087346	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0024594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	16	396	0	ENST00000324856.7:c.1921-1G>A		p.X641_splice	ENST00000324856	NM_006015.4	641			0.947245825065368	1	FACETS	0.121	0.09	0.158	0.121	0.09	0.158	SUBCLONAL	1	TRUE	0	0.947245825065368	1		396	147	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103808	47103809	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0024594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	30	569	2	ENST00000409792.3:c.6137_6138delinsTT	p.Gly2046Val	p.G2046V	ENST00000409792	NM_014159.6	2046	gGC/gTT	14/21	0.939557774205628	2	FACETS	0.212	0.171	0.258	0.106	0.085	0.129	SUBCLONAL	1	TRUE	0	0.947245825065368	2		571	299	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840029	27840029	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	41	384	1	ENST00000328488.2:c.65C>A	p.Ala22Asp	p.A22D	ENST00000328488	NM_003533.2	22	gCc/gAc	1/1	1	2	FACETS	0.176	0.146	0.209	0.176	0.146	0.209	SUBCLONAL	1	TRUE	1	0.947245825065368	2		385	492	SUCCESS
BTK	695	MSKCC	GRCh37	X	100624994	100624994	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	16	535	0	ENST00000308731.7:c.383T>G	p.Leu128Arg	p.L128R	ENST00000308731	NM_000061.2	128	cTc/cGc	5/19	1	2	FACETS	0.109	0.08	0.144	0.109	0.08	0.144	SUBCLONAL	1	TRUE	1	0.947245825065368	2		535	310	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0024595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	450	690	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.759100542905804	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.747608018477527	3		690	747	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309787	65309787	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	200	726	0	ENST00000342505.4:c.2363A>G	p.Tyr788Cys	p.Y788C	ENST00000342505	NM_002227.2	788	tAc/tGc	17/25	0.759100542905804	3	FACETS	1	0.953	1	0.516	0.48	0.554	CLONAL	1	TRUE	1	0.747608018477527	3		726	712	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443695	29443695	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs863225281	NA	P-0121495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	182	592	0	ENST00000389048.3:c.3522C>A	p.Phe1174Leu	p.F1174L	ENST00000389048	NM_004304.4	1174	ttC/ttA	23/29	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	NA	1	0.93624410103789	2		592	353	SUCCESS
APC	324	MSKCC	GRCh37	5	112175358	112175358	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1554085480	NA	P-0024597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	78	275	0	ENST00000257430.4:c.4067C>G	p.Ser1356Ter	p.S1356*	ENST00000257430	NM_000038.5	1356	tCa/tGa	16/16	0.598019657042721	2	FACETS	0.758	0.685	0.831	0.758	0.685	0.831	SUBCLONAL	2	TRUE	0	0.635102264078644	2		275	162	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627224	37627224	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200075664	NA	P-0024597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	133	685	2	ENST00000447079.4:c.1139G>A	p.Arg380His	p.R380H	ENST00000447079	NM_015083.1	380	cGt/cAt	2/14	1	2	FACETS	0.929	0.85	1	0.929	0.85	1	CLONAL	1	TRUE	1	0.635102264078644	2		687	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577519	7577527	+	inframe_deletion	In_Frame_Del	DEL	GATGGTGAG	GATGGTGAG	-	novel	NA	P-0024597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	163	864	1	ENST00000269305.4:c.754_762del	p.Leu252_Ile254del	p.L252_I254del	ENST00000269305	NM_001126112.2	252	CTCACCATC/-	7/11	0.590475229031584	1	FACETS	0.934	0.869	1	0.934	0.869	1	CLONAL	1	TRUE	0	0.635102264078644	1		865	375	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589589	67589590	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0024597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	172	433	0	ENST00000274335.5:c.1356_1357dup	p.Asn453IlefsTer28	p.N453Ifs*28	ENST00000274335		451	gaa/gaATa	10/15	0.598019657042721	2	FACETS	0.865	0.812	0.918	0.865	0.812	0.918	CLONAL	2	TRUE	0	0.635102264078644	2		433	313	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104610	69104610	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	121	863	0	ENST00000288368.4:c.4454T>A	p.Leu1485Gln	p.L1485Q	ENST00000288368	NM_024870.2	1485	cTg/cAg	37/40	0.635102264078644	3	FACETS	0.611	0.552	0.674	0.306	0.276	0.337	SUBCLONAL	1	TRUE	1	0.635102264078644	3		863	821	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0024598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	215	750	3	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.704633056125906	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.704633056125906	1		753	381	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696644	47696644	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519964	NA	P-0024600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	85	453	0	ENST00000347630.2:c.304T>G	p.Phe102Val	p.F102V	ENST00000347630	NM_001007230.1	102	Ttc/Gtc	5/11	0.164345604438992	6	FACETS	0.962	0.862	1	0.962	0.862	1	INDETERMINATE	3	FALSE	3	0.369728481588691	6		453	277	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519996	NA	P-0024600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	147	765	0	ENST00000269305.4:c.395A>T	p.Lys132Met	p.K132M	ENST00000269305	NM_001126112.2	132	aAg/aTg	5/11	0.164345604438992	6	FACETS	1	0.981	1	0.825	0.757	0.895	INDETERMINATE	2	FALSE	3	0.369728481588691	6		765	559	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46736340	46736340	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs749669280	NA	P-0024600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	43	429	0	ENST00000371975.4:c.1052A>G	p.His351Arg	p.H351R	ENST00000371975	NM_003579.3	351	cAt/cGt	10/18	0.369728481588691	5	FACETS	0.776	0.655	0.907	0.776	0.655	0.907	CLONAL	2	FALSE	3	0.369728481588691	5		429	233	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093408	30093408	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	21	582	0	ENST00000331968.5:c.1855T>A	p.Phe619Ile	p.F619I	ENST00000331968	NM_002742.2	619	Ttt/Att	13/18	0.141592369556387	6	FACETS	0.633	0.488	0.803	0.211	0.162	0.268	INDETERMINATE	1	FALSE	3	0.369728481588691	6		582	312	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378335	225378335	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	48	293	0	ENST00000264414.4:c.560G>A	p.Cys187Tyr	p.C187Y	ENST00000264414	NM_003590.4	187	tGc/tAc	5/16	0.155970502140723	5	FACETS	1	0.948	1	0.82	0.706	0.941	INDETERMINATE	2	FALSE	2	0.369728481588691	5		293	164	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0024602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	359	750	3	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.837155012934292	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.837155012934292	2		753	410	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003746	45003746	+	start_lost	Translation_Start_Site	SNP	T	T	C	rs1057519879	NA	P-0024602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	124	537	0	ENST00000558401.1:c.2T>C	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	aTg/aCg	1/4	1	2	FACETS	0.876	0.827	0.923	1	0.992	1	CLONAL	2	TRUE	1	0.837155012934292	2		537	169	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287386	38287386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1162148796	NA	P-0024602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	129	667	1	ENST00000425967.3:c.271C>T	p.Arg91Trp	p.R91W	ENST00000425967	NM_001174067.1	91	Cgg/Tgg	4/19	0.837155012934292	3	FACETS	0.913	0.833	0.996	0.456	0.416	0.498	CLONAL	1	TRUE	1	0.837155012934292	3		668	479	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685269	89685269	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0024602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	164	347	1	ENST00000371953.3:c.165-1G>T		p.X55_splice	ENST00000371953	NM_000314.4	55			0.837155012934292	2	FACETS	0.928	0.886	0.968	0.928	0.886	0.968	CLONAL	2	TRUE	0	0.837155012934292	2		348	211	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951052	48951052	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0024602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	120	226	0	ENST00000267163.4:c.1216-2A>G		p.X406_splice	ENST00000267163	NM_000321.2	406			0.837155012934292	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.837155012934292	2		226	143	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448529	49448529	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	548	519	1	ENST00000301067.7:c.182del	p.Gly61ValfsTer69	p.G61Vfs*69	ENST00000301067	NM_003482.3	61	gGt/gt	3/54	0.8259863697103	5	FACETS	0.994	0.967	1			1	CLONAL	4	TRUE	NA	0.837155012934292	5		520	743	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939102	36939102	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	61	935	0	ENST00000361632.4:c.607G>T	p.Val203Leu	p.V203L	ENST00000361632		203	Gtg/Ttg	5/16	0.837155012934292	4	FACETS	0.308	0.265	0.355	0.154	0.132	0.178	SUBCLONAL	1	TRUE	2	0.837155012934292	4		935	869	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1022568	1022568	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	290	740	0	ENST00000358495.3:c.1246G>C	p.Asp416His	p.D416H	ENST00000358495	NM_134424.2	416	Gat/Cat	12/12	0.837155012934292	3	FACETS	1	0.992	1	0.646	0.61	0.682	CLONAL	1	TRUE	1	0.837155012934292	3		740	761	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658296	18658296	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	37	606	0	ENST00000266497.5:c.3101G>C	p.Arg1034Pro	p.R1034P	ENST00000266497		1034	cGt/cCt	22/31	0.837155012934292	3	FACETS	0.333	0.275	0.399	0.167	0.137	0.2	SUBCLONAL	1	TRUE	1	0.837155012934292	3		606	376	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281074	142281074	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	143	350	0	ENST00000350721.4:c.1170G>C	p.Glu390Asp	p.E390D	ENST00000350721	NM_001184.3	390	gaG/gaC	4/47	0.63649158999631	6	FACETS	0.991	0.911	1	0.661	0.607	0.716	CLONAL	2	TRUE	3	0.837155012934292	6		350	461	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127521	55127521	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	117	454	0	ENST00000257290.5:c.309C>A	p.Asn103Lys	p.N103K	ENST00000257290	NM_006206.4	103	aaC/aaA	3/23	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.837155012934292	2		454	272	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31435916	31435916	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	233	555	0	ENST00000344624.3:c.2998C>G	p.Arg1000Gly	p.R1000G	ENST00000344624		1000	Cgg/Ggg	22/33	0.837155012934292	6	FACETS	0.858	0.801	0.915			1	CLONAL	2	TRUE	NA	0.837155012934292	6		555	868	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31437371	31437371	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	629	854	1	ENST00000344624.3:c.2917G>T	p.Asp973Tyr	p.D973Y	ENST00000344624		973	Gat/Tat	21/33	0.837155012934292	6	FACETS	1	0.995	1			1	CLONAL	3	TRUE	NA	0.837155012934292	6		855	1185	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850913	128850913	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	140	765	0	ENST00000249373.3:c.1760T>C	p.Leu587Pro	p.L587P	ENST00000249373	NM_005631.4	587	cTg/cCg	10/12	1	2	FACETS	0.921	0.85	0.994	0.921	0.85	0.994	CLONAL	1	TRUE	1	0.837155012934292	2		765	363	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949144	151949144	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	111	594	0	ENST00000262189.6:c.1501G>T	p.Asp501Tyr	p.D501Y	ENST00000262189	NM_170606.2	501	Gat/Tat	11/59	1	2	FACETS	0.899	0.82	0.98	0.899	0.82	0.98	CLONAL	1	TRUE	1	0.837155012934292	2		594	295	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249458	110249458	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs757818947	NA	P-0024602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	490	1101	0	ENST00000374672.4:c.1115G>C	p.Gly372Ala	p.G372A	ENST00000374672	NM_004235.4	372	gGt/gCt	4/5	0.837155012934292	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.837155012934292	2		1101	576	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344188	70344188	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	92	506	0	ENST00000374080.3:c.1924G>C	p.Asp642His	p.D642H	ENST00000374080		642	Gat/Cat	13/45	0.837155012934292	3	FACETS	0.904	0.81	1	0.452	0.405	0.501	CLONAL	1	TRUE	1	0.837155012934292	3		506	345	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939537	76939537	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	273	687	0	ENST00000373344.5:c.1211A>G	p.Lys404Arg	p.K404R	ENST00000373344	NM_000489.3	404	aAg/aGg	9/35	0.733819494343619	4	FACETS	0.971	0.919	1			1	CLONAL	2	TRUE	NA	0.837155012934292	4		687	617	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0024603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	70	234	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.777	0.689	0.869	1	0.978	1	SUBCLONAL	2	TRUE	1	0.418794799489027	2		234	215	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578249	7578250	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	156	374	0	ENST00000269305.4:c.599dup	p.Asn200LysfsTer9	p.N200Kfs*9	ENST00000269305	NM_001126112.2	200	aat/aaAt	6/11	0.418794799489027	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.418794799489027	1		374	512	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981803	201981803	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748421327	NA	P-0024603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	78	419	0	ENST00000359651.3:c.514G>A	p.Asp172Asn	p.D172N	ENST00000359651		172	Gac/Aac	4/8	1	2	FACETS	0.619	0.544	0.699	0.619	0.544	0.699	SUBCLONAL	1	TRUE	1	0.418794799489027	2		419	602	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575551	64575551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1085307471	NA	P-0024603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	122	339	0	ENST00000312049.6:c.466G>A	p.Gly156Ser	p.G156S	ENST00000312049	NM_130799.2	156	Ggt/Agt	3/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.418794799489027	2		339	524	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672772	30672772	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	160	493	0	ENST00000376406.3:c.4188A>T	p.Lys1396Asn	p.K1396N	ENST00000376406	NM_014641.2	1396	aaA/aaT	10/15	1	2	FACETS	0.985	0.904	1	0.985	0.904	1	CLONAL	1	TRUE	1	0.418794799489027	2		493	776	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673782	30673782	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	37	321	0	ENST00000376406.3:c.3178C>A	p.His1060Asn	p.H1060N	ENST00000376406	NM_014641.2	1060	Cat/Aat	10/15	1	2	FACETS	0.364	0.3	0.436	0.364	0.3	0.436	SUBCLONAL	1	TRUE	1	0.418794799489027	2		321	485	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189104	38189104	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0024603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	53	270	0	ENST00000317025.8:c.911-1G>A		p.X304_splice	ENST00000317025	NM_023034.1	304			0.418794799489027	4	FACETS	0.468	0.398	0.545			1	SUBCLONAL	1	TRUE	NA	0.418794799489027	4		270	768	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087503	27087503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	93	709	2	ENST00000324856.7:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000324856	NM_006015.4	693	Cga/Tga	5/20	0.504938573586931	1	FACETS	0.286	0.255	0.32	0.286	0.255	0.32	SUBCLONAL	1	TRUE	0	0.740732858525553	1		711	552	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250827	26250827	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs936810302	NA	P-0024608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	88	283	0	ENST00000446824.2:c.7C>T	p.Arg3Cys	p.R3C	ENST00000446824	NM_021018.2	3	Cgc/Tgc	1/1	1	2	FACETS	0.764	0.684	0.847	0.764	0.684	0.847	SUBCLONAL	1	TRUE	1	0.740732858525553	2		283	311	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871040	12871047	+	frameshift_variant	Frame_Shift_Del	DEL	CAGACCCC	CAGACCCC	-	novel	NA	P-0024609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	30	284	0	ENST00000228872.4:c.268_275del	p.Arg90AlafsTer32	p.R90Afs*32	ENST00000228872	NM_004064.3	89	taCAGACCCCcg/tacg	1/3	0.27695672694754	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		284	343	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098981	178098981	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	34	239	0	ENST00000397062.3:c.64A>C	p.Ile22Leu	p.I22L	ENST00000397062	NM_006164.4	22	Ata/Cta	2/5	0.151587849897708	2	FACETS		NA	1			1	NA	NA	FALSE	0	NA	2		239	410	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8470994	8470994	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0024609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	33	331	1	ENST00000356435.5:c.3504+1G>A		p.X1168_splice	ENST00000356435		1168			0.120332818486296	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		332	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0024610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	67	539	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.248045629681431	2		539	450	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	157	571	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.963	0.892	1	0.963	0.892	1	CLONAL	1	TRUE	1	0.781847976845992	2		571	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0024611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	380	822	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.77516607209302	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.781847976845992	1		822	565	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593607	55593607	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	142	442	0	ENST00000288135.5:c.1673A>C	p.Lys558Thr	p.K558T	ENST00000288135	NM_000222.2	558	aAg/aCg	11/21	NA	2	FACETS	0.936	0.863	1			1	INDETERMINATE	1	TRUE	NA	0.781847976845992	2		442	388	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396176	396176	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0024611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	195	487	0	ENST00000262320.3:c.850A>T	p.Arg284Ter	p.R284*	ENST00000262320	NM_003502.3	284	Aga/Tga	2/11	0.77516607209302	1	FACETS	0.977	0.926	1	0.977	0.926	1	CLONAL	1	TRUE	0	0.781847976845992	1		487	311	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857467	9857467	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	169	460	0	ENST00000330684.3:c.3934del	p.Ser1312AlafsTer85	p.S1312Afs*85	ENST00000330684	NM_001134407.1	1312	Agc/gc	13/13	0.77516607209302	1	FACETS	0.944	0.889	0.997	0.944	0.889	0.997	CLONAL	1	TRUE	0	0.781847976845992	1		460	279	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965426	15965426	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567776756	NA	P-0024611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	169	346	0	ENST00000268712.3:c.5380C>T	p.Arg1794Ter	p.R1794*	ENST00000268712	NM_006311.3	1794	Cga/Tga	36/46	0.77516607209302	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.781847976845992	1		346	257	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467083	25467094	+	inframe_deletion	In_Frame_Del	DEL	GCCGCCGCAGCA	GCCGCCGCAGCA	-	novel	NA	P-0024611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	175	690	0	ENST00000264709.3:c.1781_1792del	p.Leu594_Arg597del	p.L594_R597del	ENST00000264709	NM_175629.2	594	cTGCTGCGGCGGCga/cga	15/23	0.781847976845992	1	FACETS	0.697	0.651	0.744	0.697	0.651	0.744	SUBCLONAL	1	TRUE	0	0.781847976845992	1		690	391	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211852	123211853	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAAGGCAG	novel	NA	P-0024611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	44	206	0	ENST00000218089.9:c.2720_2727dup	p.Ile910GlnfsTer4	p.I910Qfs*4	ENST00000218089	NM_001042749.1	907	aca/aCAAGGCAGca	27/35	1	1	FACETS	0.206	0.173	0.242	0.206	0.173	0.242	SUBCLONAL	1	TRUE	0	0.781847976845992	1		206	333	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0024613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	156	790	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.419539927041685	2		790	669	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979551	55979551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375035755	NA	P-0024613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	170	558	0	ENST00000263923.4:c.896G>A	p.Arg299Gln	p.R299Q	ENST00000263923	NM_002253.2	299	cGg/cAg	7/30	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.419539927041685	2		558	773	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0024613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	214	549	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.419539927041685	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.419539927041685	1		549	785	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175916343	175916343	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	82	399	0	ENST00000367669.3:c.2166G>C	p.Gln722His	p.Q722H	ENST00000367669	NM_022457.5	722	caG/caC	19/20	0.201582106328433	1	FACETS	0.713	0.632	0.8	0.713	0.632	0.8	INDETERMINATE	1	TRUE	0	0.419539927041685	1		399	433	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62008712	62008712	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	94	631	0	ENST00000392795.3:c.104G>T	p.Arg35Leu	p.R35L	ENST00000392795	NM_001039933.1	35	cGg/cTg	2/6	0.419539927041685	1	FACETS	0.454	0.403	0.508	0.454	0.403	0.508	SUBCLONAL	1	TRUE	0	0.419539927041685	1		631	780	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326183	62326183	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	186	628	1	ENST00000360203.5:c.3199G>A	p.Ala1067Thr	p.A1067T	ENST00000360203	NM_001283009.1	1067	Gcc/Acc	32/35	0.267122207338	3	FACETS	1	0.97	1			1	CLONAL	1	TRUE	NA	0.419539927041685	3		629	978	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0024615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	86	678	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.18	2		678	865	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47685288	47685288	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	52	428	0	ENST00000347630.2:c.662G>A	p.Arg221His	p.R221H	ENST00000347630	NM_001007230.1	221	cGt/cAt	8/11	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.18	2		428	563	SUCCESS
ATR	545	MSKCC	GRCh37	3	142241684	142241684	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0024615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	38	412	0	ENST00000350721.4:c.4153-1G>C		p.X1385_splice	ENST00000350721	NM_001184.3	1385			1	2	FACETS	0.782	0.646	0.935	0.782	0.646	0.935	CLONAL	1	TRUE	1	0.18	2		412	540	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651880	36651881	+	frameshift_variant,start_lost	Frame_Shift_Ins	INS	-	-	GTCAGAACCGGCTGGGGATGTCC	novel	NA	P-0024615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	101	550	0	ENST00000244741.5:c.12_34dup	p.Pro12?	p.P12?	ENST00000244741	NM_000389.4	1	atg/atGTCAGAACCGGCTGGGGATGTCCg	2/3	0.188809582999556	2	FACETS	1	0.969	1	0.619	0.553	0.69	CLONAL	1	TRUE	0	0.18	2		550	906	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415520	152415520	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	47	493	0	ENST00000206249.3:c.1370G>A	p.Gly457Glu	p.G457E	ENST00000206249	NM_000125.3	457	gGa/gAa	7/8	1	2	FACETS	0.821	0.692	0.964	0.821	0.692	0.964	CLONAL	1	TRUE	1	0.18	2		493	636	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	162	697	3	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	1	2	FACETS	0.926	0.849	1	0.926	0.849	1	CLONAL	1	TRUE	1	0.35	2		700	1000	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	131	537	0	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.35	2		537	745	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427721	72427721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1382885623	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	78	444	2	ENST00000477973.2:c.769G>A	p.Val257Ile	p.V257I	ENST00000477973	NM_012234.5	257	Gtc/Atc	4/4	1	2	FACETS	0.761	0.669	0.859	0.761	0.669	0.859	SUBCLONAL	1	TRUE	1	0.35	2		446	586	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	166	795	9	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.95	0.872	1	0.95	0.872	1	CLONAL	1	TRUE	1	0.35	2		804	999	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	150	797	1	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	0.691	0.63	0.755	0.691	0.63	0.755	SUBCLONAL	1	TRUE	1	0.35	2		798	1241	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278099	15278099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139983430	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	121	797	0	ENST00000263388.2:c.5323G>A	p.Ala1775Thr	p.A1775T	ENST00000263388	NM_000435.2	1775	Gca/Aca	29/33	1	2	FACETS	0.591	0.533	0.654	0.591	0.533	0.654	SUBCLONAL	1	TRUE	1	0.35	2		797	1169	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907421	32907421	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359306	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	89	399	2	ENST00000380152.3:c.1813del	p.Ile605TyrfsTer9	p.I605Yfs*9	ENST00000380152		602	ggA/gg	10/27	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.35	2		401	471	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567647	226567647	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	120	553	2	ENST00000366794.5:c.1519del	p.Ser507AlafsTer17	p.S507Afs*17	ENST00000366794	NM_001618.3	507	Agc/gc	10/23	1	2	FACETS	0.88	0.795	0.97	0.88	0.795	0.97	CLONAL	1	TRUE	1	0.35	2		555	779	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099579	157099579	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1562376341	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	33	179	0	ENST00000346085.5:c.521del	p.Pro174ArgfsTer6	p.P174Rfs*6	ENST00000346085	NM_020732.3	172	gaC/ga	1/20	1	2	FACETS	0.748	0.613	0.899	0.748	0.613	0.899	SUBCLONAL	1	TRUE	1	0.35	2		179	252	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405953	157405954	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1554294674	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	102	614	1	ENST00000346085.5:c.2201dup	p.Ser736IlefsTer27	p.S736Ifs*27	ENST00000346085	NM_020732.3	732	ccg/ccGg	6/20	1	2	FACETS	0.703	0.628	0.783	0.703	0.628	0.783	SUBCLONAL	1	TRUE	1	0.35	2		615	829	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755427	39755427	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	126	666	2	ENST00000288319.7:c.1338del	p.Phe446LeufsTer59	p.F446Lfs*59	ENST00000288319	NM_182918.3	446	ttT/tt	10/10	1	2	FACETS	0.866	0.784	0.953	0.866	0.784	0.953	CLONAL	1	TRUE	1	0.35	2		668	831	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732957	30732957	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504421	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	77	358	0	ENST00000295754.5:c.1570G>A	p.Asp524Asn	p.D524N	ENST00000295754	NM_003242.5	524	Gac/Aac	7/7	1	2	FACETS	0.832	0.732	0.939	0.832	0.732	0.939	CLONAL	1	TRUE	1	0.35	2		358	529	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240450	98240450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370354759	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	98	446	4	ENST00000331920.6:c.1234G>A	p.Ala412Thr	p.A412T	ENST00000331920	NM_000264.3	412	Gca/Aca	9/24	1	2	FACETS	0.862	0.769	0.959	0.862	0.769	0.959	CLONAL	1	TRUE	1	0.35	2		450	650	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435815	56435815	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755967475	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	115	500	0	ENST00000407977.2:c.1322del	p.Pro441LeufsTer61	p.P441Lfs*61	ENST00000407977		441	cCt/ct	9/10	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.35	2		500	632	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436128	56436128	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	146	705	4	ENST00000407977.2:c.1009C>T	p.Arg337Ter	p.R337*	ENST00000407977		337	Cga/Tga	9/10	1	2	FACETS	0.933	0.852	1	0.933	0.852	1	CLONAL	1	TRUE	1	0.35	2		709	894	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188297	32188297	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs753855314	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	159	875	2	ENST00000375023.3:c.1044del	p.Gly349AlafsTer49	p.G349Afs*49	ENST00000375023	NM_004557.3	348	ggC/gg	6/30	1	2	FACETS	0.724	0.662	0.789	0.724	0.662	0.789	SUBCLONAL	1	TRUE	1	0.35	2		877	1255	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105617	27105617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528936858	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	50	648	0	ENST00000324856.7:c.5228C>T	p.Thr1743Met	p.T1743M	ENST00000324856	NM_006015.4	1743	aCg/aTg	20/20	1	2	FACETS	0.353	0.298	0.413	0.353	0.298	0.413	SUBCLONAL	1	TRUE	1	0.35	2		648	810	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630235	100630235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868924845	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	111	561	1	ENST00000308731.7:c.38G>A	p.Arg13Gln	p.R13Q	ENST00000308731	NM_000061.2	13	cGa/cAa	2/19	1	2	FACETS	0.869	0.782	0.961	0.869	0.782	0.961	CLONAL	1	TRUE	1	0.35	2		562	730	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	144	1035	7	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.854	0.778	0.933	0.854	0.778	0.933	CLONAL	1	TRUE	1	0.35	2		1042	964	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998127	169998128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs753143066	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	129	807	6	ENST00000295797.4:c.826dup	p.Thr276AsnfsTer16	p.T276Nfs*16	ENST00000295797	NM_002740.5	273	tta/ttAa	9/18	1	2	FACETS	0.757	0.685	0.832	0.757	0.685	0.832	SUBCLONAL	1	TRUE	1	0.35	2		813	974	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966665	36966665	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	148	521	0	ENST00000358127.4:c.661C>T	p.Arg221Trp	p.R221W	ENST00000358127	NM_001280556.1	221	Cgg/Tgg	6/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.35	2		521	773	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223858	36223858	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	172	1022	6	ENST00000222270.7:c.6413del	p.Pro2138ArgfsTer15	p.P2138Rfs*15	ENST00000222270	NM_014727.1	2136	ctC/ct	28/37	1	2	FACETS	0.781	0.717	0.848	0.781	0.717	0.848	SUBCLONAL	1	TRUE	1	0.35	2		1028	1259	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288799	15288799	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764992581	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	71	216	0	ENST00000263388.2:c.3940G>A	p.Ala1314Thr	p.A1314T	ENST00000263388	NM_000435.2	1314	Gcc/Acc	24/33	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.35	2		216	397	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	176	669	0	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.35	2		669	987	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317100	11317100	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747458067	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	170	714	4	ENST00000361445.4:c.394C>T	p.Arg132Cys	p.R132C	ENST00000361445	NM_004958.3	132	Cgt/Tgt	4/58	1	2	FACETS	0.981	0.902	1	0.981	0.902	1	CLONAL	1	TRUE	1	0.35	2		718	990	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445149	49445149	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	190	832	1	ENST00000301067.7:c.2317del	p.Gln773SerfsTer157	p.Q773Sfs*157	ENST00000301067	NM_003482.3	773	Cag/ag	10/54	1	2	FACETS	0.926	0.855	1	0.926	0.855	1	CLONAL	1	TRUE	1	0.35	2		833	1172	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629975	187629975	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	137	685	0	ENST00000441802.2:c.1007T>C	p.Leu336Pro	p.L336P	ENST00000441802	NM_005245.3	336	cTa/cCa	2/27	1	2	FACETS	0.883	0.803	0.967	0.883	0.803	0.967	CLONAL	1	TRUE	1	0.35	2		685	887	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231462	46231462	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	68	421	0	ENST00000334344.6:c.1306del	p.Ile436LeufsTer4	p.I436Lfs*4	ENST00000334344	NM_152641.2	434	acA/ac	10/21	1	2	FACETS	0.875	0.764	0.995	0.875	0.764	0.995	CLONAL	1	TRUE	1	0.35	2		421	444	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627730	37627730	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	192	950	0	ENST00000447079.4:c.1649del	p.Pro550LeufsTer60	p.P550Lfs*60	ENST00000447079	NM_015083.1	549	Ccc/cc	2/14	1	2	FACETS	0.853	0.787	0.922	0.853	0.787	0.922	CLONAL	1	TRUE	1	0.35	2		950	1286	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527886	157527886	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	65	533	0	ENST00000346085.5:c.5614del	p.Ser1872AlafsTer3	p.S1872Afs*3	ENST00000346085	NM_020732.3	1871	Aaa/aa	20/20	1	2	FACETS	0.513	0.444	0.588	0.513	0.444	0.588	SUBCLONAL	1	TRUE	1	0.35	2		533	724	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294270	11294270	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	60	650	1	ENST00000361445.4:c.2261C>A	p.Ala754Asp	p.A754D	ENST00000361445	NM_004958.3	754	gCc/gAc	14/58	1	2	FACETS	0.381	0.327	0.44	0.381	0.327	0.44	SUBCLONAL	1	TRUE	1	0.35	2		651	900	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106137	27106138	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACTC	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	124	610	1	ENST00000324856.7:c.5749_5752dup	p.Arg1918HisfsTer4	p.R1918Hfs*4	ENST00000324856	NM_006015.4	1916	-/ACTC	20/20	1	2	FACETS	0.901	0.816	0.992	0.901	0.816	0.992	CLONAL	1	TRUE	1	0.35	2		611	786	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741736	17741736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	162	708	1	ENST00000250003.3:c.407C>T	p.Thr136Met	p.T136M	ENST00000250003	NM_002478.4	136	aCg/aTg	1/3	1	2	FACETS	0.906	0.83	0.985	0.906	0.83	0.985	CLONAL	1	TRUE	1	0.35	2		709	1022	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948455	71948455	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	196	1042	0	ENST00000298229.2:c.3167C>A	p.Pro1056Gln	p.P1056Q	ENST00000298229	NM_001567.3	1056	cCa/cAa	26/28	1	2	FACETS	0.849	0.784	0.917	0.849	0.784	0.917	CLONAL	1	TRUE	1	0.35	2		1042	1319	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641544	18641544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	85	485	2	ENST00000266497.5:c.2543C>T	p.Ala848Val	p.A848V	ENST00000266497		848	gCc/gTc	17/31	1	2	FACETS	0.896	0.794	1	0.896	0.794	1	CLONAL	1	TRUE	1	0.35	2		487	542	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244322	46244322	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1565622483	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	102	479	0	ENST00000334344.6:c.2416C>T	p.Gln806Ter	p.Q806*	ENST00000334344	NM_152641.2	806	Cag/Tag	15/21	1	2	FACETS	0.98	0.878	1	0.98	0.878	1	CLONAL	1	TRUE	1	0.35	2		479	595	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424755	49424755	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	128	773	0	ENST00000301067.7:c.13592G>T	p.Arg4531Met	p.R4531M	ENST00000301067	NM_003482.3	4531	aGg/aTg	40/54	1	2	FACETS	0.661	0.597	0.728	0.661	0.597	0.728	SUBCLONAL	1	TRUE	1	0.35	2		773	1107	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893651	28893651	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	110	499	0	ENST00000282397.4:c.3195G>T	p.Trp1065Cys	p.W1065C	ENST00000282397	NM_002019.4	1065	tgG/tgT	24/30	1	2	FACETS	0.967	0.87	1	0.967	0.87	1	CLONAL	1	TRUE	1	0.35	2		499	650	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005442	29005443	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	62	311	0	ENST00000282397.4:c.818dup	p.Asn273LysfsTer2	p.N273Kfs*2	ENST00000282397	NM_002019.4	273	aat/aaAt	7/30	1	2	FACETS	0.828	0.717	0.947	0.828	0.717	0.947	CLONAL	1	TRUE	1	0.35	2		311	428	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66737013	66737013	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	85	518	0	ENST00000307102.5:c.536A>G	p.Tyr179Cys	p.Y179C	ENST00000307102	NM_002755.3	179	tAt/tGt	5/11	1	2	FACETS	0.594	0.524	0.669	0.594	0.524	0.669	SUBCLONAL	1	TRUE	1	0.35	2		518	818	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640517	3640517	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	146	849	0	ENST00000294008.3:c.3122A>G	p.Gln1041Arg	p.Q1041R	ENST00000294008	NM_032444.2	1041	cAg/cGg	12/15	1	2	FACETS	0.748	0.682	0.818	0.748	0.682	0.818	SUBCLONAL	1	TRUE	1	0.35	2		849	1115	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771335	68771335	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746464544	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	99	400	0	ENST00000261769.5:c.17G>A	p.Arg6His	p.R6H	ENST00000261769	NM_004360.3	6	cGc/cAc	1/16	1	2	FACETS	0.998	0.893	1	0.998	0.893	1	CLONAL	1	TRUE	1	0.35	2		400	567	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827873	72827873	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479510222	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	170	736	0	ENST00000268489.5:c.8708G>A	p.Ser2903Asn	p.S2903N	ENST00000268489	NM_006885.3	2903	aGc/aAc	9/10	1	2	FACETS	0.964	0.886	1	0.964	0.886	1	CLONAL	1	TRUE	1	0.35	2		736	1008	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831221	72831221	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	93	469	0	ENST00000268489.5:c.5360T>A	p.Leu1787Gln	p.L1787Q	ENST00000268489	NM_006885.3	1787	cTg/cAg	9/10	1	2	FACETS	0.918	0.818	1	0.918	0.818	1	CLONAL	1	TRUE	1	0.35	2		469	579	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819605	81819605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199972098	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	135	474	2	ENST00000359376.3:c.11C>T	p.Thr4Met	p.T4M	ENST00000359376	NM_002661.3	4	aCg/aTg	2/33	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.35	2		476	691	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068445	16068445	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	11	128	0	ENST00000268712.3:c.466C>A	p.Pro156Thr	p.P156T	ENST00000268712	NM_006311.3	156	Cca/Aca	5/46	1	2	FACETS	0.355	0.245	0.491	0.355	0.245	0.491	SUBCLONAL	1	TRUE	1	0.35	2		128	177	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439948	56439948	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	163	807	3	ENST00000407977.2:c.644C>A	p.Ala215Asp	p.A215D	ENST00000407977		215	gCt/gAt	6/10	1	2	FACETS	0.838	0.768	0.912	0.838	0.768	0.912	CLONAL	1	TRUE	1	0.35	2		810	1111	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448293	56448293	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	121	749	0	ENST00000407977.2:c.354del	p.Cys119AlafsTer39	p.C119Afs*39	ENST00000407977		118	ccC/cc	3/10	1	2	FACETS	0.714	0.644	0.788	0.714	0.644	0.788	SUBCLONAL	1	TRUE	1	0.35	2		749	968	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007585	62007585	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs377108188	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	108	884	0	ENST00000392795.3:c.282G>T	p.Lys94Asn	p.K94N	ENST00000392795	NM_001039933.1	94	aaG/aaT	3/6	1	2	FACETS	0.577	0.517	0.642	0.577	0.517	0.642	SUBCLONAL	1	TRUE	1	0.35	2		884	1069	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119762	70119763	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	114	744	0	ENST00000245479.2:c.767_768dup	p.Arg257GlyfsTer23	p.R257Gfs*23	ENST00000245479	NM_000346.3	255	gag/gaGGg	3/3	1	2	FACETS	0.707	0.635	0.782	0.707	0.635	0.782	SUBCLONAL	1	TRUE	1	0.35	2		744	922	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249253	10249253	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	116	531	0	ENST00000340748.4:c.3929G>T	p.Arg1310Met	p.R1310M	ENST00000340748		1310	aGg/aTg	34/40	1	2	FACETS	0.902	0.813	0.995	0.902	0.813	0.995	CLONAL	1	TRUE	1	0.35	2		531	735	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223614	36223614	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	215	916	1	ENST00000222270.7:c.6169del	p.Arg2057AlafsTer34	p.R2057Afs*34	ENST00000222270	NM_014727.1	2055	gCc/gc	28/37	1	2	FACETS	0.961	0.891	1	0.961	0.891	1	CLONAL	1	TRUE	1	0.35	2		917	1279	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794950	42794950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141594034	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	185	720	0	ENST00000575354.2:c.2030G>A	p.Arg677Gln	p.R677Q	ENST00000575354	NM_015125.3	677	cGg/cAg	10/20	1	2	FACETS	0.997	0.92	1	0.997	0.92	1	CLONAL	1	TRUE	1	0.35	2		720	1060	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262550	39262550	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	108	583	0	ENST00000402219.2:c.956G>T	p.Gly319Val	p.G319V	ENST00000402219	NM_005633.3	319	gGg/gTg	7/23	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.35	2		583	564	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852527	42852527	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs748560513	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	131	717	1	ENST00000398585.3:c.559C>T	p.Arg187Cys	p.R187C	ENST00000398585	NM_001135099.1	187	Cgc/Tgc	6/14	1	2	FACETS	0.861	0.781	0.946	0.861	0.781	0.946	CLONAL	1	TRUE	1	0.35	2		718	869	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686325	30686325	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	98	517	0	ENST00000295754.5:c.181T>G	p.Cys61Gly	p.C61G	ENST00000295754	NM_003242.5	61	Tgt/Ggt	2/7	1	2	FACETS	0.801	0.715	0.893	0.801	0.715	0.893	CLONAL	1	TRUE	1	0.35	2		517	699	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49726033	49726033	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	18	203	0	ENST00000449682.2:c.92C>T	p.Pro31Leu	p.P31L	ENST00000449682	NM_020998.3	31	cCt/cTt	1/18	1	2	FACETS	0.378	0.285	0.489	0.378	0.285	0.489	SUBCLONAL	1	TRUE	1	0.35	2		203	272	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952079	178952079	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	12	438	0	ENST00000263967.3:c.3134A>G	p.Asp1045Gly	p.D1045G	ENST00000263967	NM_006218.2	1045	gAt/gGt	21/21	1	2	FACETS	0.146	0.101	0.2	0.146	0.101	0.2	SUBCLONAL	1	TRUE	1	0.35	2		438	471	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356281	66356282	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CA	CA	-	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	119	662	0	ENST00000273854.3:c.1215_1216del	p.Cys405Ter	p.C405*	ENST00000273854	NM_004439.5	405	tgTGag/tgag	5/18	1	2	FACETS	0.804	0.725	0.887	0.804	0.725	0.887	CLONAL	1	TRUE	1	0.35	2		662	846	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036924	180036924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375662657	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	146	756	1	ENST00000261937.6:c.3788C>T	p.Thr1263Met	p.T1263M	ENST00000261937	NM_182925.4	1263	aCg/aTg	28/30	1	2	FACETS	0.853	0.778	0.932	0.853	0.778	0.932	CLONAL	1	TRUE	1	0.35	2		757	978	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911213	29911213	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	46	216	0	ENST00000376809.5:c.514del	p.Glu172ArgfsTer9	p.E172Rfs*9	ENST00000376809	NM_002116.7	171	tGg/tg	3/8	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.35	2		216	252	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041251	112041251	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	91	387	0	ENST00000368678.4:c.4G>T	p.Gly2Cys	p.G2C	ENST00000368678		2	Ggc/Tgc	3/13	1	2	FACETS	0.927	0.825	1	0.927	0.825	1	CLONAL	1	TRUE	1	0.35	2		387	561	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5465594	5465594	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568608390	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	59	375	0	ENST00000381577.3:c.778C>T	p.Arg260Cys	p.R260C	ENST00000381577	NM_014143.3	260	Cgt/Tgt	5/7	1	2	FACETS	0.687	0.592	0.79	0.687	0.592	0.79	SUBCLONAL	1	TRUE	1	0.35	2		375	491	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396728	139396728	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	121	745	0	ENST00000277541.6:c.5380C>A	p.Leu1794Ile	p.L1794I	ENST00000277541	NM_017617.3	1794	Ctc/Atc	28/34	1	2	FACETS	0.765	0.69	0.844	0.765	0.69	0.844	SUBCLONAL	1	TRUE	1	0.35	2		745	904	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44920666	44920666	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	87	457	0	ENST00000377967.4:c.1425+2T>A		p.X475_splice	ENST00000377967	NM_021140.2	475			1	2	FACETS	0.894	0.793	1	0.894	0.793	1	CLONAL	1	TRUE	1	0.35	2		457	556	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428157	47428157	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	185	938	0	ENST00000377045.4:c.1117A>G	p.Met373Val	p.M373V	ENST00000377045	NM_001654.4	373	Atg/Gtg	11/16	1	2	FACETS	0.833	0.767	0.902	0.833	0.767	0.902	CLONAL	1	TRUE	1	0.35	2		938	1269	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	333	855	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.612615986847382	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.612615986847382	3		855	657	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913315	NA	P-0024635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	244	670	0	ENST00000326873.7:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000326873	NM_000455.4	194	Gac/Tac	4/10	0.55934118032763	2	FACETS	0.899	0.853	0.945	0.899	0.853	0.945	CLONAL	2	TRUE	0	0.612615986847382	2		670	443	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602488	10602488	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1397945617	NA	P-0024635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	265	536	1	ENST00000171111.5:c.1090G>T	p.Gly364Cys	p.G364C	ENST00000171111	NM_203500.1	364	Ggc/Tgc	3/6	0.55934118032763	2	FACETS	0.928	0.883	0.973	0.928	0.883	0.973	CLONAL	2	TRUE	0	0.612615986847382	2		537	466	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180050946	180050946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	194	872	0	ENST00000261937.6:c.1537G>A	p.Gly513Arg	p.G513R	ENST00000261937	NM_182925.4	513	Gga/Aga	11/30	1	2	FACETS	0.892	0.828	0.958	0.892	0.828	0.958	CLONAL	1	TRUE	1	0.612615986847382	2		872	710	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800965	243800965	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	489	609	0	ENST00000263826.5:c.509G>T	p.Ser170Ile	p.S170I	ENST00000263826	NM_005465.4	170	aGt/aTt	5/13	0.612615986847382	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.612615986847382	3		609	649	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717750	89717750	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	115	427	0	ENST00000371953.3:c.775C>T	p.His259Tyr	p.H259Y	ENST00000371953	NM_000314.4	259	Cac/Tac	7/9	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.612615986847382	2		427	369	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281813	49281813	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0024635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	174	610	0	ENST00000282018.3:c.860T>A	p.Leu287Ter	p.L287*	ENST00000282018	NM_020377.2	287	tTg/tAg	1/1	0.608529940878561	1	FACETS	0.998	0.931	1	0.998	0.931	1	CLONAL	1	TRUE	0	0.612615986847382	1		610	395	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657656	37657656	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	137	548	0	ENST00000447079.4:c.2573G>T	p.Arg858Leu	p.R858L	ENST00000447079	NM_015083.1	858	cGg/cTg	6/14	1	2	FACETS	0.862	0.788	0.938	0.862	0.788	0.938	CLONAL	1	TRUE	1	0.612615986847382	2		548	519	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905345	50905345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	330	787	0	ENST00000440232.2:c.553C>T	p.Pro185Ser	p.P185S	ENST00000440232	NM_002691.3	185	Ccg/Tcg	5/27	0.321167807465437	1	FACETS	1	0.989	1	1	0.989	1	INDETERMINATE	1	TRUE	0	0.612615986847382	1		787	666	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023837	31023837	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	134	552	0	ENST00000375687.4:c.3322G>C	p.Val1108Leu	p.V1108L	ENST00000375687	NM_015338.5	1108	Gtg/Ctg	13/13	1	2	FACETS	0.88	0.805	0.959	0.88	0.805	0.959	CLONAL	1	TRUE	1	0.612615986847382	2		552	497	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128848680	128848680	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	179	636	0	ENST00000249373.3:c.1345A>T	p.Met449Leu	p.M449L	ENST00000249373	NM_005631.4	449	Atg/Ttg	7/12	1	2	FACETS	0.982	0.91	1	0.982	0.91	1	CLONAL	1	TRUE	1	0.612615986847382	2		636	595	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0024636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	116	802	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.949	0.861	1	1	0.989	1	CLONAL	2	TRUE	1	0.272791883705824	2		802	448	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891030	112891030	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	30	383	0	ENST00000351677.2:c.364G>A	p.Ala122Thr	p.A122T	ENST00000351677	NM_002834.3	122	Gca/Aca	4/16	1	2	FACETS	0.576	0.464	0.703	0.576	0.464	0.703	SUBCLONAL	1	TRUE	1	0.272791883705824	2		383	382	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0024636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	87	625	1	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	NA	2	FACETS	1	0.893	1			1	INDETERMINATE	1	TRUE	NA	0.272791883705824	2		626	633	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652358	48652358	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	97	414	0	ENST00000376670.3:c.1029C>A	p.Ser343Arg	p.S343R	ENST00000376670	NM_002049.3	343	agC/agA	6/6	1	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.272791883705824	1		414	498	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034471	47034471	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	138	383	0	ENST00000377604.3:c.556C>T	p.Arg186Ter	p.R186*	ENST00000377604	NM_001204468.1	186	Cga/Tga	6/24	1	1	FACETS	0.888	0.813	0.965	1	0.99	1	CLONAL	2	TRUE	0	0.272791883705824	1		383	492	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625141	69625141	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	136	725	2	ENST00000334134.2:c.652G>T	p.Asp218Tyr	p.D218Y	ENST00000334134	NM_005247.2	218	Gat/Tat	3/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.272791883705824	2		727	785	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944908	31944908	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	43	311	0	ENST00000340398.3:c.193C>A	p.Leu65Met	p.L65M	ENST00000340398	NM_001013699.2	65	Ctg/Atg	1/1	1	2	FACETS	0.871	0.731	1	0.871	0.731	1	CLONAL	1	TRUE	1	0.272791883705824	2		311	362	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50488327	50488327	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	54	554	0	ENST00000394963.4:c.1241A>T	p.Gln414Leu	p.Q414L	ENST00000394963	NM_003076.4	414	cAa/cTa	10/13	1	2	FACETS	0.698	0.596	0.81	0.698	0.596	0.81	SUBCLONAL	1	TRUE	1	0.272791883705824	2		554	567	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41999982	41999982	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	82	811	1	ENST00000219905.7:c.2245G>T	p.Gly749Ter	p.G749*	ENST00000219905	NM_001164273.1	749	Gga/Tga	6/24	0.272791883705824	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.272791883705824	1		812	450	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118958	70118958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs794727246	NA	P-0024636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	88	755	0	ENST00000245479.2:c.530G>A	p.Arg177Gln	p.R177Q	ENST00000245479	NM_000346.3	177	cGg/cAg	2/3	1	2	FACETS	0.618	0.546	0.695	0.618	0.546	0.695	SUBCLONAL	1	TRUE	1	0.272791883705824	2		755	1044	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715976	52715976	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	107	552	0	ENST00000322088.6:c.541G>T	p.Val181Leu	p.V181L	ENST00000322088	NM_014225.5	181	Gtg/Ttg	5/15	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.272791883705824	2		552	719	SUCCESS
ATR	545	MSKCC	GRCh37	3	142177822	142177822	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	37	306	0	ENST00000350721.4:c.7481A>T	p.Asp2494Val	p.D2494V	ENST00000350721	NM_001184.3	2494	gAt/gTt	44/47	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.272791883705824	2		306	218	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127352	55127352	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	63	548	0	ENST00000257290.5:c.140T>A	p.Leu47Gln	p.L47Q	ENST00000257290	NM_006206.4	47	cTg/cAg	3/23	0.203012542266178	1	FACETS	0.672	0.581	0.77	0.672	0.581	0.77	SUBCLONAL	1	TRUE	0	0.272791883705824	1		548	594	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137528155	137528155	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	16	318	0	ENST00000367739.4:c.145G>T	p.Glu49Ter	p.E49*	ENST00000367739	NM_000416.2	49	Gag/Tag	2/7	0.272791883705824	1	FACETS	0.467	0.346	0.611	0.467	0.346	0.611	SUBCLONAL	1	TRUE	0	0.272791883705824	1		318	217	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128321967	128321967	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	113	629	1	ENST00000265960.3:c.793G>T	p.Val265Phe	p.V265F	ENST00000265960	NM_001006617.1	265	Gtt/Ttt	6/12	0.203012542266178	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.272791883705824	1		630	665	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798846	135798847	+	missense_variant	Missense_Mutation	DNP	CG	CG	AT	novel	NA	P-0024636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	18	264	0	ENST00000298552.3:c.396_397delinsAT	p.Val133Phe	p.V133F	ENST00000298552	NM_001162426.1	132	ggCGtc/ggATtc	6/23	0.215622180445169	3	FACETS	0.53	0.399	0.685	0.265	0.199	0.343	SUBCLONAL	1	TRUE	1	0.272791883705824	3		264	283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659675	NA	P-0024638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	35	690	0	ENST00000269305.4:c.764T>C	p.Ile255Thr	p.I255T	ENST00000269305	NM_001126112.2	255	aTc/aCc	7/11	1	2	FACETS	0.972	0.794	1	0.972	0.794	1	CLONAL	1	TRUE	1	0.11	2		690	655	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0024638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	30	714	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	0.738	0.593	0.905	0.738	0.593	0.905	CLONAL	1	TRUE	1	0.11	2		714	739	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	59	571	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.884358410180553	2		571	123	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074238	8074238	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	261	398	0	ENST00000377482.5:c.421C>T	p.Pro141Ser	p.P141S	ENST00000377482	NM_018948.3	141	Ccc/Tcc	4/4	0.631556970821185	3	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.884358410180553	3		398	350	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254692	16254692	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	70	512	0	ENST00000375759.3:c.1957C>T	p.Arg653Ter	p.R653*	ENST00000375759	NM_015001.2	653	Cga/Tga	11/15	0.631556970821185	3	FACETS	0.649	0.569	0.733			1	SUBCLONAL	1	TRUE	NA	0.884358410180553	3		512	352	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099361	27099361	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	62	581	0	ENST00000324856.7:c.3598C>T	p.Gln1200Ter	p.Q1200*	ENST00000324856	NM_006015.4	1200	Cag/Tag	14/20	0.59585843390033	3	FACETS	0.76	0.663	0.863	0.253	0.221	0.288	SUBCLONAL	1	TRUE	0	0.884358410180553	3		581	266	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932277	36932277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553151543	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	42	647	0	ENST00000361632.4:c.2192G>A	p.Gly731Glu	p.G731E	ENST00000361632		731	gGg/gAg	16/16	0.59585843390033	3	FACETS	0.552	0.464	0.648	0.184	0.154	0.216	SUBCLONAL	1	TRUE	0	0.884358410180553	3		647	248	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941175	36941175	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	229	635	0	ENST00000361632.4:c.164T>G	p.Leu55Arg	p.L55R	ENST00000361632		55	cTg/cGg	3/16	0.59585843390033	3	FACETS	1	0.993	1	0.803	0.77	0.835	CLONAL	2	TRUE	0	0.884358410180553	3		635	310	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65311270	65311270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	163	444	0	ENST00000342505.4:c.2041C>T	p.Arg681Trp	p.R681W	ENST00000342505	NM_002227.2	681	Cgg/Tgg	15/25	0.59585843390033	3	FACETS	1	0.991	1	0.82	0.781	0.857	CLONAL	2	TRUE	0	0.884358410180553	3		444	216	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273131	115273131	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	209	433	0	ENST00000438362.2:c.1327C>T	p.Pro443Ser	p.P443S	ENST00000438362	NM_001242891.1	443	Cct/Tct	11/20	0.59585843390033	3	FACETS	1	0.992	1	0.794	0.76	0.828	CLONAL	2	TRUE	0	0.884358410180553	3		433	286	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458306	120458306	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370648780	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	56	509	1	ENST00000256646.2:c.7039C>T	p.Arg2347Cys	p.R2347C	ENST00000256646	NM_024408.3	2347	Cgt/Tgt	34/34	0.59585843390033	3	FACETS	0.687	0.594	0.786	0.229	0.198	0.262	SUBCLONAL	1	TRUE	0	0.884358410180553	3		510	266	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120508139	120508139	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	144	379	0	ENST00000256646.2:c.1618C>T	p.Pro540Ser	p.P540S	ENST00000256646	NM_024408.3	540	Ccg/Tcg	10/34	0.59585843390033	3	FACETS	1	0.989	1	0.803	0.761	0.842	CLONAL	2	TRUE	0	0.884358410180553	3		379	195	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226549761	226549761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779988758	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	38	406	0	ENST00000366794.5:c.2872C>T	p.Pro958Ser	p.P958S	ENST00000366794	NM_001618.3	958	Cct/Tct	22/23	0.473259144677241	1	FACETS	0.375	0.316	0.437	0.375	0.316	0.437	INDETERMINATE	1	TRUE	0	0.884358410180553	1		406	128	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570806	226570806	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	117	523	0	ENST00000366794.5:c.1090T>A	p.Ser364Thr	p.S364T	ENST00000366794	NM_001618.3	364	Tcc/Acc	8/23	0.473259144677241	1	FACETS	0.789	0.736	0.841	0.789	0.736	0.841	INDETERMINATE	1	TRUE	0	0.884358410180553	1		523	187	SUCCESS
FH	2271	MSKCC	GRCh37	1	241665806	241665806	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	59	436	0	ENST00000366560.3:c.1173T>G	p.His391Gln	p.H391Q	ENST00000366560	NM_000143.3	391	caT/caG	8/10	0.473259144677241	1	FACETS	0.4	0.35	0.452	0.4	0.35	0.452	INDETERMINATE	1	TRUE	0	0.884358410180553	1		436	186	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406195	70406195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	89	556	0	ENST00000373644.4:c.3709C>T	p.Pro1237Ser	p.P1237S	ENST00000373644	NM_030625.2	1237	Cca/Tca	4/12	0.199188519035079	1	FACETS	0.54	0.489	0.592	0.54	0.489	0.592	INDETERMINATE	1	TRUE	0	0.884358410180553	1		556	208	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88672134	88672134	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	76	628	0	ENST00000372037.3:c.668C>T	p.Pro223Leu	p.P223L	ENST00000372037	NM_004329.2	223	cCt/cTt	8/13	0.199188519035079	1	FACETS	0.551	0.495	0.608	0.551	0.495	0.608	INDETERMINATE	1	TRUE	0	0.884358410180553	1		628	174	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518527	69518527	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	80	599	2	ENST00000294312.3:c.118G>A	p.Asp40Asn	p.D40N	ENST00000294312	NM_005117.2	40	Gac/Aac	1/3	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.884358410180553	2		601	156	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103408	77103408	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	75	377	0	ENST00000356341.3:c.158G>A	p.Arg53Gln	p.R53Q	ENST00000356341	NM_002576.4	53	cGa/cAa	2/15	1	2	FACETS	0.922	0.826	1	0.922	0.826	1	CLONAL	1	TRUE	1	0.884358410180553	2		377	184	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912815	100912815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1000609240	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	67	365	0	ENST00000325455.5:c.2507G>A	p.Arg836Gln	p.R836Q	ENST00000325455	NM_001202474.3	836	cGa/cAa	7/8	1	2	FACETS	0.953	0.849	1	0.953	0.849	1	CLONAL	1	TRUE	1	0.884358410180553	2		365	159	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362480	118362480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	80	318	0	ENST00000534358.1:c.4841C>T	p.Ser1614Phe	p.S1614F	ENST00000534358	NM_005933.3	1614	tCt/tTt	15/36	0.832249372314656	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.884358410180553	1		318	92	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466999	18466999	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs747404244	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	58	315	1	ENST00000266497.5:c.1137+1G>A		p.X379_splice	ENST00000266497		379			1	2	FACETS	0.979	0.866	1	0.979	0.866	1	CLONAL	1	TRUE	1	0.884358410180553	2		316	134	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573894	18573894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759658584	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	52	540	2	ENST00000266497.5:c.2212C>T	p.Arg738Cys	p.R738C	ENST00000266497		738	Cgt/Tgt	15/31	1	2	FACETS	0.941	0.825	1	0.941	0.825	1	CLONAL	1	TRUE	1	0.884358410180553	2		542	125	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715746	18715746	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1191317818	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	73	384	0	ENST00000266497.5:c.3577C>T	p.Pro1193Ser	p.P1193S	ENST00000266497		1193	Cct/Tct	25/31	1	2	FACETS	0.971	0.871	1	0.971	0.871	1	CLONAL	1	TRUE	1	0.884358410180553	2		384	170	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205281	46205285	+	frameshift_variant	Frame_Shift_Del	DEL	TTCCT	TTCCT	-	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	69	451	0	ENST00000334344.6:c.365_369del	p.Leu122HisfsTer30	p.L122Hfs*30	ENST00000334344	NM_152641.2	122	cTTCCT/c	4/21	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.884358410180553	2		451	154	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230571	46230571	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	105	430	1	ENST00000334344.6:c.820C>T	p.Arg274Ter	p.R274*	ENST00000334344	NM_152641.2	274	Cga/Tga	8/21	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.884358410180553	2		431	232	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231364	46231364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	98	435	0	ENST00000334344.6:c.1204G>A	p.Glu402Lys	p.E402K	ENST00000334344	NM_152641.2	402	Gag/Aag	10/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.884358410180553	2		435	197	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244859	46244859	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	129	636	0	ENST00000334344.6:c.2953C>T	p.Pro985Ser	p.P985S	ENST00000334344	NM_152641.2	985	Cct/Tct	15/21	1	2	FACETS	0.935	0.861	1	0.935	0.861	1	CLONAL	1	TRUE	1	0.884358410180553	2		636	312	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444789	49444789	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	135	754	0	ENST00000301067.7:c.2677C>T	p.Pro893Ser	p.P893S	ENST00000301067	NM_003482.3	893	Ccc/Tcc	10/54	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.884358410180553	2		754	286	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864354	57864354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368078339	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	92	611	0	ENST00000228682.2:c.1831C>T	p.Arg611Trp	p.R611W	ENST00000228682	NM_005269.2	611	Cgg/Tgg	12/12	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.884358410180553	2		611	205	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811603	102811603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	95	528	1	ENST00000307046.8:c.581G>A	p.Gly194Glu	p.G194E	ENST00000307046	NM_001111285.1	194	gGa/gAa	4/4	1	2	FACETS	0.951	0.864	1	0.951	0.864	1	CLONAL	1	TRUE	1	0.884358410180553	2		529	226	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557600	21557600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754974924	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	204	590	0	ENST00000382592.4:c.2245C>T	p.Pro749Ser	p.P749S	ENST00000382592	NM_014572.2	749	Cct/Tct	5/8	0.884358410180553	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.884358410180553	2		590	228	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923215	26923215	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs769996123	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	89	299	1	ENST00000381527.3:c.211C>T	p.Arg71Ter	p.R71*	ENST00000381527	NM_001260.1	71	Cga/Tga	3/13	0.884358410180553	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.884358410180553	2		300	97	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610099	28610099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	127	439	0	ENST00000241453.7:c.1391G>A	p.Trp464Ter	p.W464*	ENST00000241453	NM_004119.2	464	tGg/tAg	11/24	0.884358410180553	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.884358410180553	2		439	139	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919581	28919581	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	131	491	0	ENST00000282397.4:c.2355+1G>A		p.X785_splice	ENST00000282397	NM_002019.4	785			0.884358410180553	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.884358410180553	2		491	145	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954183	32954183	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	120	560	0	ENST00000380152.3:c.9157G>A	p.Glu3053Lys	p.E3053K	ENST00000380152		3053	Gag/Aag	24/27	0.884358410180553	2	FACETS	0.99	0.95	1	0.99	0.95	1	CLONAL	2	TRUE	0	0.884358410180553	2		560	137	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335890	73335890	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774993507	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	99	422	0	ENST00000377767.4:c.2405C>T	p.Pro802Leu	p.P802L	ENST00000377767	NM_014953.3	802	cCa/cTa	18/21	0.884358410180553	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.884358410180553	2		422	112	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873846	35873846	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	24	200	0	ENST00000216797.5:c.5T>C	p.Phe2Ser	p.F2S	ENST00000216797	NM_020529.2	2	tTc/tCc	1/6	0.223455703909045	3	FACETS	1	0.849	1	0.529	0.428	0.637	INDETERMINATE	1	TRUE	1	0.884358410180553	3		200	74	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562962	95562962	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747593690	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	133	392	0	ENST00000393063.1:c.4295C>T	p.Pro1432Leu	p.P1432L	ENST00000393063	NM_030621.3	1432	cCg/cTg	24/28	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.884358410180553	2		392	228	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582103	95582103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	106	337	0	ENST00000393063.1:c.1808C>T	p.Pro603Leu	p.P603L	ENST00000393063	NM_030621.3	603	cCt/cTt	12/28	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.884358410180553	2		337	187	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95592936	95592936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	106	489	0	ENST00000393063.1:c.884C>T	p.Ser295Phe	p.S295F	ENST00000393063	NM_030621.3	295	tCt/tTt	8/28	NA	2	FACETS	1	0.972	1			1	INDETERMINATE	1	TRUE	NA	0.884358410180553	2		489	211	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041623	42041623	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	107	537	0	ENST00000219905.7:c.5818C>T	p.Gln1940Ter	p.Q1940*	ENST00000219905	NM_001164273.1	1940	Cag/Tag	17/24	0.884358410180553	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.884358410180553	1		537	128	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707816	43707816	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1260186612	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	172	708	0	ENST00000382044.4:c.5065C>T	p.Arg1689Cys	p.R1689C	ENST00000382044	NM_001141980.1	1689	Cgc/Tgc	23/28	0.884358410180553	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.884358410180553	1		708	192	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748470	43748470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1400414596	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	104	621	0	ENST00000382044.4:c.2336C>T	p.Pro779Leu	p.P779L	ENST00000382044	NM_001141980.1	779	cCt/cTt	12/28	0.884358410180553	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.884358410180553	1		621	120	SUCCESS
BLM	641	MSKCC	GRCh37	15	91326155	91326155	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	56	295	0	ENST00000355112.3:c.2659C>T	p.Pro887Ser	p.P887S	ENST00000355112	NM_000057.2	887	Cca/Tca	13/22	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.884358410180553	2		295	118	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500580	99500580	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1330066958	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	89	422	0	ENST00000268035.6:c.4013C>T	p.Ala1338Val	p.A1338V	ENST00000268035	NM_000875.3	1338	gCc/gTc	21/21	1	2	FACETS	0.992	0.899	1	0.992	0.899	1	CLONAL	1	TRUE	1	0.884358410180553	2		422	203	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639164	3639164	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	154	708	0	ENST00000294008.3:c.4475C>T	p.Ser1492Phe	p.S1492F	ENST00000294008	NM_032444.2	1492	tCc/tTc	12/15	NA	2	FACETS	0.792	0.749	0.832			1	INDETERMINATE	2	TRUE	NA	0.884358410180553	2		708	220	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821455	72821455	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	54	719	1	ENST00000268489.5:c.10720C>T	p.His3574Tyr	p.H3574Y	ENST00000268489	NM_006885.3	3574	Cac/Tac	10/10	0.478582523375797	1	FACETS	0.376	0.327	0.429	0.376	0.327	0.429	INDETERMINATE	1	TRUE	0	0.884358410180553	1		720	181	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944273	81944273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	49	601	0	ENST00000359376.3:c.1882G>A	p.Glu628Lys	p.E628K	ENST00000359376	NM_002661.3	628	Gag/Aag	18/33	0.478582523375797	1	FACETS	0.355	0.306	0.408	0.355	0.306	0.408	INDETERMINATE	1	TRUE	0	0.884358410180553	1		601	174	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81973515	81973515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	51	465	1	ENST00000359376.3:c.3332C>T	p.Pro1111Leu	p.P1111L	ENST00000359376	NM_002661.3	1111	cCt/cTt	30/33	0.478582523375797	1	FACETS	0.432	0.375	0.491	0.432	0.375	0.491	INDETERMINATE	1	TRUE	0	0.884358410180553	1		466	149	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350510	89350510	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	785	784	0	ENST00000301030.4:c.2440T>A	p.Phe814Ile	p.F814I	ENST00000301030	NM_001256183.1	814	Ttt/Att	9/13	0.809332193618541	6	FACETS	0.996	0.976	1	0.996	0.976	1	CLONAL	5	TRUE	1	0.884358410180553	6		784	987	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352034	89352034	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774961018	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	608	666	1	ENST00000301030.4:c.916C>T	p.Pro306Ser	p.P306S	ENST00000301030	NM_001256183.1	306	Cca/Tca	9/13	0.809332193618541	6	FACETS	0.98	0.957	1	0.98	0.957	1	CLONAL	5	TRUE	1	0.884358410180553	6		667	777	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576898	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AT	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	118	573	1	ENST00000269305.4:c.948_949delinsAT	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	316	ccCCag/ccATag	9/11	0.884358410180553	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.884358410180553	1		574	140	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578278	7578278	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868590738	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	154	531	1	ENST00000269305.4:c.571C>T	p.Pro191Ser	p.P191S	ENST00000269305	NM_001126112.2	191	Cct/Tct	6/11	0.884358410180553	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.884358410180553	1		532	163	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110660	8110660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	135	520	0	ENST00000585124.1:c.232G>A	p.Glu78Lys	p.E78K	ENST00000585124	NM_004217.3	78	Gag/Aag	5/9	0.884358410180553	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.884358410180553	1		520	163	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546134	29546134	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	61	338	0	ENST00000356175.3:c.1639G>A	p.Glu547Lys	p.E547K	ENST00000356175	NM_000267.3	547	Gag/Aag	14/57	0.229578704742255	2	FACETS	0.683	0.599	0.771	0.341	0.299	0.386	INDETERMINATE	1	TRUE	0	0.884358410180553	2		338	202	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684368	29684368	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367858662	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	65	463	0	ENST00000356175.3:c.7888C>T	p.Pro2630Ser	p.P2630S	ENST00000356175	NM_000267.3	2630	Ccc/Tcc	53/57	0.229578704742255	2	FACETS	0.808	0.714	0.904	0.404	0.357	0.452	INDETERMINATE	1	TRUE	0	0.884358410180553	2		463	182	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37863342	37863342	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1298421770	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	145	680	1	ENST00000269571.5:c.173G>A	p.Gly58Glu	p.G58E	ENST00000269571		58	gGa/gAa	2/27	0.229578704742255	2	FACETS	1	0.988	1	0.648	0.606	0.69	INDETERMINATE	1	TRUE	0	0.884358410180553	2		681	253	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864748	37864749	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	97	493	1	ENST00000269571.5:c.400_401delinsTT	p.Pro134Leu	p.P134L	ENST00000269571		134	CCa/TTa	3/27	0.229578704742255	2	FACETS	1	0.984	1	0.669	0.617	0.72	INDETERMINATE	1	TRUE	0	0.884358410180553	2		494	164	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489466	40489466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	79	483	0	ENST00000264657.5:c.784C>T	p.Arg262Trp	p.R262W	ENST00000264657	NM_139276.2	262	Cgg/Tgg	8/24	0.229578704742255	2	FACETS	0.735	0.656	0.817	0.368	0.328	0.409	INDETERMINATE	1	TRUE	0	0.884358410180553	2		483	243	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436016	56436025	+	frameshift_variant	Frame_Shift_Del	DEL	GGACCAGGTC	GGACCAGGTC	-	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	85	341	0	ENST00000407977.2:c.1112_1121del	p.Arg371ProfsTer45	p.R371Pfs*45	ENST00000407977		371	cGACCTGGTCCc/cc	9/10	0.229578704742255	2	FACETS	1	0.979	1	0.632	0.578	0.686	INDETERMINATE	1	TRUE	0	0.884358410180553	2		341	152	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775164	73775164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867543814	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	133	576	0	ENST00000254810.4:c.92C>T	p.Pro31Leu	p.P31L	ENST00000254810	NM_005324.3	31	cCc/cTc	2/4	0.229578704742255	2	FACETS	1	0.988	1	0.657	0.613	0.7	INDETERMINATE	1	TRUE	0	0.884358410180553	2		576	229	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400676	56400676	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	92	332	0	ENST00000348428.3:c.1270T>C	p.Phe424Leu	p.F424L	ENST00000348428	NM_006785.3	424	Ttc/Ctc	11/17	0.884358410180553	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.884358410180553	2		332	99	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222259	2222259	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371443260	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	106	728	0	ENST00000398665.3:c.3091G>A	p.Asp1031Asn	p.D1031N	ENST00000398665	NM_032482.2	1031	Gat/Aat	24/28	1	2	FACETS	0.967	0.883	1	0.967	0.883	1	CLONAL	1	TRUE	1	0.884358410180553	2		728	248	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110197	3110197	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	92	706	1	ENST00000078429.4:c.187C>T	p.His63Tyr	p.H63Y	ENST00000078429	NM_002067.2	63	Cac/Tac	2/7	1	2	FACETS	0.933	0.846	1	0.933	0.846	1	CLONAL	1	TRUE	1	0.884358410180553	2		707	223	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122780	7122780	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	81	522	1	ENST00000302850.5:c.3374A>T	p.Asn1125Ile	p.N1125I	ENST00000302850	NM_000208.2	1125	aAt/aTt	19/22	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.884358410180553	2		523	170	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142914	7142914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	119	661	0	ENST00000302850.5:c.2455C>T	p.Arg819Cys	p.R819C	ENST00000302850	NM_000208.2	819	Cgc/Tgc	12/22	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.884358410180553	2		661	239	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7152846	7152846	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763692568	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	120	637	1	ENST00000302850.5:c.2122G>A	p.Glu708Lys	p.E708K	ENST00000302850	NM_000208.2	708	Gaa/Aaa	10/22	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.884358410180553	2		638	267	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166215	7166215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755906677	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	86	635	0	ENST00000302850.5:c.1811G>A	p.Arg604Gln	p.R604Q	ENST00000302850	NM_000208.2	604	cGg/cAg	8/22	1	2	FACETS	0.992	0.898	1	0.992	0.898	1	CLONAL	1	TRUE	1	0.884358410180553	2		635	196	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267533	7267533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	120	544	0	ENST00000302850.5:c.475G>A	p.Asp159Asn	p.D159N	ENST00000302850	NM_000208.2	159	Gac/Aac	2/22	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.884358410180553	2		544	255	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096985	11096985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747458180	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	95	702	1	ENST00000358026.2:c.476C>T	p.Pro159Leu	p.P159L	ENST00000358026	NM_001128849.1	159	cCc/cTc	4/36	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.884358410180553	2		703	202	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271983	15271984	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	63	599	1	ENST00000263388.2:c.6455_6456delinsTT	p.Pro2152Leu	p.P2152L	ENST00000263388	NM_000435.2	2152	cCC/cTT	33/33	1	2	FACETS	0.989	0.88	1	0.989	0.88	1	CLONAL	1	TRUE	1	0.884358410180553	2		600	144	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17940945	17940945	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	132	744	0	ENST00000458235.1:c.3179T>A	p.Leu1060Gln	p.L1060Q	ENST00000458235	NM_000215.3	1060	cTg/cAg	23/24	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.884358410180553	2		744	276	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968295	18968295	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	94	702	0	ENST00000262803.5:c.2135C>T	p.Pro712Leu	p.P712L	ENST00000262803	NM_002911.3	712	cCa/cTa	15/24	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.884358410180553	2		702	194	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215892	36215892	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	117	669	0	ENST00000222270.7:c.3432T>G	p.Asp1144Glu	p.D1144E	ENST00000222270	NM_014727.1	1144	gaT/gaG	10/37	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.884358410180553	2		669	228	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223545	36223545	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	116	770	0	ENST00000222270.7:c.6095C>A	p.Ser2032Tyr	p.S2032Y	ENST00000222270	NM_014727.1	2032	tCc/tAc	28/37	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.884358410180553	2		770	227	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40743950	40743951	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	107	616	1	ENST00000392038.2:c.756_757delinsTT	p.Arg253Trp	p.R253W	ENST00000392038	NM_001626.4	252	gcCCgg/gcTTgg	9/14	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.884358410180553	2		617	232	SUCCESS
AXL	558	MSKCC	GRCh37	19	41737103	41737103	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	90	711	0	ENST00000301178.4:c.683C>T	p.Pro228Leu	p.P228L	ENST00000301178	NM_021913.4	228	cCc/cTc	6/20	1	2	FACETS	0.929	0.841	1	0.929	0.841	1	CLONAL	1	TRUE	1	0.884358410180553	2		711	219	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432710	29432710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766988856	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	142	478	0	ENST00000389048.3:c.3778C>T	p.Pro1260Ser	p.P1260S	ENST00000389048	NM_004304.4	1260	Cca/Tca	25/29	0.443584173281623	3	FACETS	0.877	0.818	0.936	0.877	0.818	0.936	INDETERMINATE	2	TRUE	1	0.884358410180553	3		478	264	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519835	29519835	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1258283302	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	164	586	0	ENST00000389048.3:c.1736G>A	p.Arg579Lys	p.R579K	ENST00000389048	NM_004304.4	579	aGg/aAg	9/29	0.443584173281623	3	FACETS	0.86	0.805	0.915	0.86	0.805	0.915	INDETERMINATE	2	TRUE	1	0.884358410180553	3		586	311	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606708	29606708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768680011	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	95	490	0	ENST00000389048.3:c.1172G>A	p.Gly391Glu	p.G391E	ENST00000389048	NM_004304.4	391	gGa/gAa	5/29	0.443584173281623	3	FACETS	1	0.966	1	0.578	0.522	0.635	INDETERMINATE	1	TRUE	1	0.884358410180553	3		490	268	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754974	29754974	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	144	489	1	ENST00000389048.3:c.961C>T	p.Leu321Phe	p.L321F	ENST00000389048	NM_004304.4	321	Ctc/Ttc	4/29	0.443584173281623	3	FACETS	0.943	0.882	1	0.943	0.882	1	INDETERMINATE	2	TRUE	1	0.884358410180553	3		490	249	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607715	46607715	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	186	647	0	ENST00000263734.3:c.1904C>T	p.Ser635Phe	p.S635F	ENST00000263734	NM_001430.4	635	tCc/tTc	12/16	0.443584173281623	3	FACETS	0.945	0.891	0.998	0.945	0.891	0.998	INDETERMINATE	2	TRUE	1	0.884358410180553	3		647	321	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209108164	209108164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	56	390	0	ENST00000345146.2:c.685G>A	p.Glu229Lys	p.E229K	ENST00000345146	NM_005896.2	229	Gag/Aag	6/10	0.478582523375797	1	FACETS	0.728	0.653	0.802	0.728	0.653	0.802	INDETERMINATE	1	TRUE	0	0.884358410180553	1		390	97	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566827	212566827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202247795	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	42	292	0	ENST00000342788.4:c.1354G>A	p.Glu452Lys	p.E452K	ENST00000342788	NM_005235.2	452	Gaa/Aaa	12/28	0.478582523375797	1	FACETS	0.449	0.385	0.516	0.449	0.385	0.516	INDETERMINATE	1	TRUE	0	0.884358410180553	1		292	118	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660096	227660097	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	86	527	2	ENST00000305123.5:c.3358_3359delinsAA	p.Gly1120Lys	p.G1120K	ENST00000305123	NM_005544.2	1120	GGa/AAa	1/2	0.478582523375797	1	FACETS	0.723	0.662	0.783	0.723	0.662	0.783	INDETERMINATE	1	TRUE	0	0.884358410180553	1		529	150	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561263	9561263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769939031	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	105	456	0	ENST00000353224.5:c.519G>A	p.Met173Ile	p.M173I	ENST00000353224	NM_177990.2	173	atG/atA	4/10	0.832249372314656	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.884358410180553	1		456	122	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561547	9561547	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4	93	581	1	ENST00000353224.5:c.235G>A	p.Glu79Lys	p.E79K	ENST00000353224	NM_177990.2	79	Gaa/Aaa	4/10	0.832249372314656	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.884358410180553	1		582	97	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024321	31024321	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747065583	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	91	423	0	ENST00000375687.4:c.3806C>T	p.Ser1269Leu	p.S1269L	ENST00000375687	NM_015338.5	1269	tCg/tTg	13/13	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.884358410180553	2		423	201	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024707	31024707	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	102	491	0	ENST00000375687.4:c.4192C>T	p.His1398Tyr	p.H1398Y	ENST00000375687	NM_015338.5	1398	Cac/Tac	13/13	1	2	FACETS	0.957	0.873	1	0.957	0.873	1	CLONAL	1	TRUE	1	0.884358410180553	2		491	241	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030892	36030892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867805553	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	110	583	3	ENST00000358208.4:c.1171C>T	p.Arg391Cys	p.R391C	ENST00000358208		391	Cgt/Tgt	10/12	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.884358410180553	2		586	239	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39729953	39729953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	88	458	0	ENST00000361337.2:c.1268C>T	p.Ser423Phe	p.S423F	ENST00000361337	NM_003286.2	423	tCc/tTc	13/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.884358410180553	2		458	189	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827982	40827982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	90	450	0	ENST00000373198.4:c.2446G>A	p.Glu816Lys	p.E816K	ENST00000373198	NM_133170.3	816	Gag/Aag	17/32	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.884358410180553	2		450	181	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37628882	37628882	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555908409	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	351	726	1	ENST00000249071.6:c.184G>A	p.Glu62Lys	p.E62K	ENST00000249071	NM_002872.4	62	Gag/Aag	3/7	0.420392223007367	6	FACETS	1	0.992	1			1	INDETERMINATE	5	TRUE	NA	0.884358410180553	6		727	418	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543890	41543891	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	348	579	2	ENST00000263253.7:c.2181_2182delinsTT	p.Arg728Trp	p.R728W	ENST00000263253	NM_001429.3	727	ccCCgg/ccTTgg	12/31	0.420392223007367	6	FACETS	1	0.972	1			1	INDETERMINATE	5	TRUE	NA	0.884358410180553	6		581	435	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41554473	41554473	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745492786	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	250	498	0	ENST00000263253.7:c.3559C>T	p.Arg1187Cys	p.R1187C	ENST00000263253	NM_001429.3	1187	Cgt/Tgt	19/31	0.420392223007367	6	FACETS	0.963	0.927	0.997			1	INDETERMINATE	5	TRUE	NA	0.884358410180553	6		498	325	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163704	47163704	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	73	392	0	ENST00000409792.3:c.2422G>T	p.Glu808Ter	p.E808*	ENST00000409792	NM_014159.6	808	Gaa/Taa	3/21	1	2	FACETS	0.888	0.793	0.984	0.888	0.793	0.984	CLONAL	1	TRUE	1	0.884358410180553	2		392	186	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164001	47164001	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	56	305	0	ENST00000409792.3:c.2125C>T	p.Pro709Ser	p.P709S	ENST00000409792	NM_014159.6	709	Cct/Tct	3/21	1	2	FACETS	0.952	0.839	1	0.952	0.839	1	CLONAL	1	TRUE	1	0.884358410180553	2		305	133	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037222	71037222	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	63	330	0	ENST00000318789.4:c.1069A>G	p.Lys357Glu	p.K357E	ENST00000318789	NM_032682.5	357	Aaa/Gaa	14/21	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.884358410180553	2		330	125	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499393	89499393	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	120	446	1	ENST00000336596.2:c.2563C>T	p.Gln855Ter	p.Q855*	ENST00000336596	NM_005233.5	855	Cag/Tag	15/17	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.884358410180553	2		447	230	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199867	128199867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	60	315	0	ENST00000341105.2:c.1438G>A	p.Gly480Ser	p.G480S	ENST00000341105	NM_032638.4	480	Ggc/Agc	6/6	1	2	FACETS	0.998	0.885	1	0.998	0.885	1	CLONAL	1	TRUE	1	0.884358410180553	2		315	136	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664763	138664763	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	10	354	0	ENST00000330315.3:c.802C>G	p.Pro268Ala	p.P268A	ENST00000330315	NM_023067.3	268	Ccc/Gcc	1/1	1	2	FACETS	0.595	0.419	0.797	0.595	0.419	0.797	SUBCLONAL	1	TRUE	1	0.884358410180553	2		354	38	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952025	178952026	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	53	391	1	ENST00000263967.3:c.3080_3081delinsTT	p.Ala1027Val	p.A1027V	ENST00000263967	NM_006218.2	1027	gCC/gTT	21/21	1	2	FACETS	0.901	0.79	1	0.901	0.79	1	CLONAL	1	TRUE	1	0.884358410180553	2		392	133	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430393	181430393	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	82	647	0	ENST00000325404.1:c.245T>C	p.Leu82Ser	p.L82S	ENST00000325404	NM_003106.3	82	tTg/tCg	1/1	1	2	FACETS	0.961	0.867	1	0.961	0.867	1	CLONAL	1	TRUE	1	0.884358410180553	2		647	193	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505652	186505652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	64	311	0	ENST00000323963.5:c.1060C>T	p.Arg354Cys	p.R354C	ENST00000323963		354	Cgt/Tgt	10/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.884358410180553	2		311	129	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608604	189608604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	128	885	2	ENST00000264731.3:c.1679C>T	p.Ser560Leu	p.S560L	ENST00000264731	NM_003722.4	560	tCa/tTa	13/14	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.884358410180553	2		887	257	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612073	189612073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142762485	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	103	561	1	ENST00000264731.3:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000264731	NM_003722.4	609	Gaa/Aaa	14/14	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.884358410180553	2		562	210	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151594	55151594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1560488952	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	52	682	0	ENST00000257290.5:c.2380G>A	p.Asp794Asn	p.D794N	ENST00000257290	NM_006206.4	794	Gat/Aat	17/23	0.473259144677241	1	FACETS	0.36	0.312	0.412	0.36	0.312	0.412	INDETERMINATE	1	TRUE	0	0.884358410180553	1		682	182	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948196	55948196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	39	547	0	ENST00000263923.4:c.3775G>A	p.Asp1259Asn	p.D1259N	ENST00000263923	NM_002253.2	1259	Gac/Aac	29/30	0.473259144677241	1	FACETS	0.376	0.318	0.437	0.376	0.318	0.437	INDETERMINATE	1	TRUE	0	0.884358410180553	1		547	131	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958827	55958827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	53	498	0	ENST00000263923.4:c.3026G>A	p.Ser1009Asn	p.S1009N	ENST00000263923	NM_002253.2	1009	aGc/aAc	22/30	0.473259144677241	1	FACETS	0.369	0.32	0.421	0.369	0.32	0.421	INDETERMINATE	1	TRUE	0	0.884358410180553	1		498	181	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970987	55970987	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	86	511	1	ENST00000263923.4:c.1810A>T	p.Lys604Ter	p.K604*	ENST00000263923	NM_002253.2	604	Aag/Tag	13/30	0.473259144677241	1	FACETS	0.638	0.581	0.695	0.638	0.581	0.695	INDETERMINATE	1	TRUE	0	0.884358410180553	1		512	170	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286254	66286254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	64	387	1	ENST00000273854.3:c.1432G>A	p.Gly478Arg	p.G478R	ENST00000273854	NM_004439.5	478	Ggg/Agg	6/18	0.473259144677241	1	FACETS	0.776	0.704	0.846	0.776	0.704	0.846	INDETERMINATE	1	TRUE	0	0.884358410180553	1		388	104	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193980	106193981	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	45	223	0	ENST00000380013.4:c.4442_4443delinsTT	p.Ser1481Phe	p.S1481F	ENST00000380013	NM_001127208.2	1481	tCC/tTT	10/11	0.473259144677241	1	FACETS	0.631	0.552	0.709	0.631	0.552	0.709	INDETERMINATE	1	TRUE	0	0.884358410180553	1		223	90	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293635	1293635	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	102	772	0	ENST00000310581.5:c.1366A>C	p.Ser456Arg	p.S456R	ENST00000310581	NM_198253.2	456	Agc/Cgc	2/16	1	2	FACETS	0.949	0.865	1	0.949	0.865	1	CLONAL	1	TRUE	1	0.884358410180553	2		772	243	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294917	1294917	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1336720402	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	13	97	0	ENST00000310581.5:c.188G>A	p.Arg63Gln	p.R63Q	ENST00000310581	NM_198253.2	63	cGg/cAg	1/16	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.884358410180553	2		97	22	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876210	35876210	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	89	445	0	ENST00000303115.3:c.1002A>T	p.Glu334Asp	p.E334D	ENST00000303115	NM_002185.3	334	gaA/gaT	8/8	1	2	FACETS	0.968	0.877	1	0.968	0.877	1	CLONAL	1	TRUE	1	0.884358410180553	2		445	208	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950498	38950498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	86	402	0	ENST00000357387.3:c.3452C>T	p.Ser1151Phe	p.S1151F	ENST00000357387	NM_152756.3	1151	tCc/tTc	31/38	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.884358410180553	2		402	157	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111638	56111638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	11	359	2	ENST00000399503.3:c.238C>T	p.Leu80Phe	p.L80F	ENST00000399503	NM_005921.1	80	Ctt/Ttt	1/20	1	2	FACETS	0.541	0.386	0.719	0.541	0.386	0.719	SUBCLONAL	1	TRUE	1	0.884358410180553	2		361	46	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047254	180047254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1314469826	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	40	736	0	ENST00000261937.6:c.2461G>A	p.Glu821Lys	p.E821K	ENST00000261937	NM_182925.4	821	Gag/Aag	17/30	0.559279874468247	1	FACETS	0.341	0.288	0.397	0.341	0.288	0.397	SUBCLONAL	1	TRUE	0	0.884358410180553	1		736	148	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045756	26045756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	78	364	1	ENST00000540144.1:c.118C>T	p.His40Tyr	p.H40Y	ENST00000540144	NM_003531.2	40	Cat/Tat	1/1	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.884358410180553	2		365	162	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673656	30673656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867542960	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	126	632	0	ENST00000376406.3:c.3304C>T	p.His1102Tyr	p.H1102Y	ENST00000376406	NM_014641.2	1102	Cac/Tac	10/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.884358410180553	2		632	264	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169941	32169941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	144	741	0	ENST00000375023.3:c.3667C>T	p.Leu1223Phe	p.L1223F	ENST00000375023	NM_004557.3	1223	Ctc/Ttc	21/30	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.884358410180553	2		741	300	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188836	32188836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1046104152	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	108	592	1	ENST00000375023.3:c.718C>T	p.Pro240Ser	p.P240S	ENST00000375023	NM_004557.3	240	Cct/Tct	4/30	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.884358410180553	2		593	234	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289058	33289058	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	122	672	0	ENST00000374542.5:c.494C>T	p.Ser165Phe	p.S165F	ENST00000374542	NM_001141970.1	165	tCc/tTc	3/8	1	2	FACETS	0.958	0.881	1	0.958	0.881	1	CLONAL	1	TRUE	1	0.884358410180553	2		672	288	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41905131	41905131	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	67	313	0	ENST00000372991.4:c.416A>C	p.Asp139Ala	p.D139A	ENST00000372991	NM_001760.3	139	gAc/gCc	3/5	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.884358410180553	2		313	134	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748519	43748519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267601048	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	99	418	0	ENST00000523873.1:c.473C>T	p.Ser158Phe	p.S158F	ENST00000523873		158	tCc/tTc	6/8	1	2	FACETS	0.986	0.899	1	0.986	0.899	1	CLONAL	1	TRUE	1	0.884358410180553	2		418	227	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956681	93956681	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1287261842	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	83	374	0	ENST00000369303.4:c.2555G>A	p.Gly852Asp	p.G852D	ENST00000369303	NM_004440.3	852	gGt/gAt	15/17	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.884358410180553	2		374	180	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982137	93982137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	73	328	1	ENST00000369303.4:c.1328C>T	p.Pro443Leu	p.P443L	ENST00000369303	NM_004440.3	443	cCc/cTc	6/17	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.884358410180553	2		329	153	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041041	112041041	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	96	379	0	ENST00000368678.4:c.214C>T	p.His72Tyr	p.H72Y	ENST00000368678		72	Cat/Tat	3/13	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.884358410180553	2		379	205	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662320	117662320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	107	553	0	ENST00000368508.3:c.5057G>A	p.Arg1686Lys	p.R1686K	ENST00000368508	NM_002944.2	1686	aGa/aAa	30/43	NA	2	FACETS	0.949	0.867	1			1	INDETERMINATE	1	TRUE	NA	0.884358410180553	2		553	255	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674227	117674227	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	96	638	1	ENST00000368508.3:c.4247C>T	p.Ala1416Val	p.A1416V	ENST00000368508	NM_002944.2	1416	gCc/gTc	26/43	NA	2	FACETS	0.862	0.781	0.944			1	INDETERMINATE	1	TRUE	NA	0.884358410180553	2		639	252	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724419	117724419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	87	463	0	ENST00000368508.3:c.460G>A	p.Val154Met	p.V154M	ENST00000368508	NM_002944.2	154	Gtg/Atg	6/43	NA	2	FACETS	1	0.947	1			1	INDETERMINATE	1	TRUE	NA	0.884358410180553	2		463	185	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192564	138192564	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	76	362	0	ENST00000237289.4:c.200C>T	p.Ala67Val	p.A67V	ENST00000237289	NM_001270507.1	67	gCc/gTc	2/9	1	2	FACETS	0.877	0.785	0.971	0.877	0.785	0.971	CLONAL	1	TRUE	1	0.884358410180553	2		362	196	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997433	149997434	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	95	609	0	ENST00000253339.5:c.2845_2846delinsTT	p.Pro949Phe	p.P949F	ENST00000253339		949	CCt/TTt	6/7	1	2	FACETS	0.891	0.808	0.977	0.891	0.808	0.977	CLONAL	1	TRUE	1	0.884358410180553	2		609	241	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129244	152129244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	85	537	0	ENST00000206249.3:c.197C>T	p.Ala66Val	p.A66V	ENST00000206249	NM_000125.3	66	gCc/gTc	1/8	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.884358410180553	2		537	168	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522147	157522148	+	stop_gained	Nonsense_Mutation	DNP	TC	TC	AT	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	78	433	2	ENST00000346085.5:c.4419_4420delinsAT	p.Tyr1473_Pro1474delinsTer	p.Y1473_P1474delins*	ENST00000346085	NM_020732.3	1473	taTCcc/taATcc	18/20	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.884358410180553	2		435	176	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161990398	161990398	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	70	383	0	ENST00000366898.1:c.922G>A	p.Gly308Arg	p.G308R	ENST00000366898	NM_004562.2	308	Gga/Aga	8/12	1	2	FACETS	0.942	0.842	1	0.942	0.842	1	CLONAL	1	TRUE	1	0.884358410180553	2		383	168	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2969682	2969682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	135	664	0	ENST00000396946.4:c.1597G>A	p.Asp533Asn	p.D533N	ENST00000396946	NM_032415.4	533	Gac/Aac	12/25	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.884358410180553	2		664	282	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976739	2976739	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	154	659	0	ENST00000396946.4:c.1273G>A	p.Glu425Lys	p.E425K	ENST00000396946	NM_032415.4	425	Gag/Aag	9/25	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.884358410180553	2		659	302	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979457	2979457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769402864	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	125	638	0	ENST00000396946.4:c.790G>A	p.Glu264Lys	p.E264K	ENST00000396946	NM_032415.4	264	Gag/Aag	6/25	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.884358410180553	2		638	274	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739609	41739609	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	112	554	0	ENST00000242208.4:c.364G>C	p.Glu122Gln	p.E122Q	ENST00000242208	NM_002192.2	122	Gag/Cag	2/3	1	2	FACETS	0.989	0.907	1	0.989	0.907	1	CLONAL	1	TRUE	1	0.884358410180553	2		554	256	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467934	50467934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	60	348	0	ENST00000331340.3:c.1169C>T	p.Pro390Leu	p.P390L	ENST00000331340	NM_006060.4	390	cCg/cTg	8/8	1	2	FACETS	0.983	0.872	1	0.983	0.872	1	CLONAL	1	TRUE	1	0.884358410180553	2		348	138	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355289	81355289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	170	355	0	ENST00000222390.5:c.1085C>T	p.Ser362Leu	p.S362L	ENST00000222390	NM_000601.4	362	tCa/tTa	9/18	0.884358410180553	5	FACETS	1	0.963	1	1	0.963	1	CLONAL	3	TRUE	2	0.884358410180553	5		355	289	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845497	128845497	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	359	651	2	ENST00000249373.3:c.794T>C	p.Val265Ala	p.V265A	ENST00000249373	NM_005631.4	265	gTt/gCt	4/12	0.884358410180553	5	FACETS	1	0.968	1			1	CLONAL	3	TRUE	NA	0.884358410180553	5		653	623	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860169	151860169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769597625	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	102	419	0	ENST00000262189.6:c.10493C>T	p.Thr3498Ile	p.T3498I	ENST00000262189	NM_170606.2	3498	aCc/aTc	43/59	0.816357937858608	4	FACETS	1	0.955	1	0.369	0.332	0.407	CLONAL	1	TRUE	1	0.884358410180553	4		419	393	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878859	151878859	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754727782	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	289	533	0	ENST00000262189.6:c.6086C>T	p.Pro2029Leu	p.P2029L	ENST00000262189	NM_170606.2	2029	cCc/cTc	36/59	0.816357937858608	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	1	0.884358410180553	4		533	399	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38178630	38178630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	85	514	0	ENST00000317025.8:c.1769C>T	p.Ser590Phe	p.S590F	ENST00000317025	NM_023034.1	590	tCc/tTc	8/24	1	2	FACETS	0.938	0.847	1	0.938	0.847	1	CLONAL	1	TRUE	1	0.884358410180553	2		514	205	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271300	38271300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	127	715	0	ENST00000425967.3:c.2408C>T	p.Pro803Leu	p.P803L	ENST00000425967	NM_001174067.1	803	cCc/cTc	19/19	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.884358410180553	2		715	254	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69032459	69032459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	113	653	0	ENST00000288368.4:c.3533G>A	p.Gly1178Glu	p.G1178E	ENST00000288368	NM_024870.2	1178	gGg/gAg	29/40	1	2	FACETS	0.913	0.835	0.992	0.913	0.835	0.992	CLONAL	1	TRUE	1	0.884358410180553	2		653	280	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046342	69046342	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	83	421	0	ENST00000288368.4:c.3815T>C	p.Val1272Ala	p.V1272A	ENST00000288368	NM_024870.2	1272	gTg/gCg	32/40	1	2	FACETS	0.939	0.846	1	0.939	0.846	1	CLONAL	1	TRUE	1	0.884358410180553	2		421	200	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058575	69058575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	125	680	0	ENST00000288368.4:c.4219C>T	p.Leu1407Phe	p.L1407F	ENST00000288368	NM_024870.2	1407	Ctt/Ttt	34/40	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.884358410180553	2		680	251	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317921	8317921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150063446	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	84	391	1	ENST00000356435.5:c.5692C>T	p.Arg1898Cys	p.R1898C	ENST00000356435		1898	Cgt/Tgt	35/35	0.884358410180553	5	FACETS	1	0.948	1	0.279	0.248	0.312	CLONAL	1	TRUE	1	0.884358410180553	5		392	396	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341269	8341269	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	124	280	0	ENST00000356435.5:c.4948-1G>A		p.X1650_splice	ENST00000356435		1650			0.884358410180553	5	FACETS	1	0.98	1	0.85	0.795	0.902	CLONAL	3	TRUE	1	0.884358410180553	5		280	192	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341701	8341701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766088715	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	353	526	1	ENST00000356435.5:c.4939G>A	p.Glu1647Lys	p.E1647K	ENST00000356435		1647	Gaa/Aaa	29/35	0.884358410180553	5	FACETS	0.948	0.915	0.979	0.948	0.915	0.979	CLONAL	4	TRUE	1	0.884358410180553	5		527	490	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376071	8376071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	223	274	0	ENST00000356435.5:c.4526G>A	p.Arg1509Lys	p.R1509K	ENST00000356435		1509	aGa/aAa	28/35	0.884358410180553	5	FACETS	1	0.983	1	1	0.983	1	CLONAL	4	TRUE	1	0.884358410180553	5		274	282	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465632	8465632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	76	445	0	ENST00000356435.5:c.3548G>A	p.Gly1183Glu	p.G1183E	ENST00000356435		1183	gGg/gAg	21/35	0.884358410180553	5	FACETS	0.915	0.806	1	0.229	0.201	0.258	CLONAL	1	TRUE	1	0.884358410180553	5		445	437	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518175	8518175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1354824749	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	75	347	0	ENST00000356435.5:c.1216G>A	p.Glu406Lys	p.E406K	ENST00000356435		406	Gaa/Aaa	10/35	0.884358410180553	5	FACETS	1	0.891	1	0.253	0.223	0.285	CLONAL	1	TRUE	1	0.884358410180553	5		347	390	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528641	8528641	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	329	356	0	ENST00000356435.5:c.491T>A	p.Leu164Ter	p.L164*	ENST00000356435		164	tTa/tAa	4/35	0.884358410180553	5	FACETS	0.993	0.959	1	0.993	0.959	1	CLONAL	4	TRUE	1	0.884358410180553	5		356	436	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157993	27157993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	144	550	0	ENST00000380036.4:c.217G>A	p.Glu73Lys	p.E73K	ENST00000380036	NM_000459.3	73	Gaa/Aaa	2/23	0.884358410180553	5	FACETS	1	0.96	1	0.271	0.247	0.296	CLONAL	1	TRUE	1	0.884358410180553	5		550	699	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27183567	27183567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1296261695	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	310	448	0	ENST00000380036.4:c.1141G>A	p.Glu381Lys	p.E381K	ENST00000380036	NM_000459.3	381	Gaa/Aaa	8/23	0.884358410180553	5	FACETS	0.995	0.96	1	0.995	0.96	1	CLONAL	4	TRUE	1	0.884358410180553	5		448	410	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015115	37015115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	502	662	0	ENST00000358127.4:c.289G>A	p.Glu97Lys	p.E97K	ENST00000358127	NM_001280556.1	97	Gaa/Aaa	3/10	0.884358410180553	5	FACETS	1	0.993	1	1	0.993	1	CLONAL	4	TRUE	1	0.884358410180553	5		662	629	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93626932	93626932	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	76	544	0	ENST00000375746.1:c.779A>G	p.Gln260Arg	p.Q260R	ENST00000375746	NM_001174167.1	260	cAa/cGa	5/14	NA	2	FACETS	0.939	0.843	1			1	INDETERMINATE	1	TRUE	NA	0.884358410180553	2		544	183	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760621	133760621	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	174	915	0	ENST00000318560.5:c.2944C>T	p.Pro982Ser	p.P982S	ENST00000318560	NM_005157.4	982	Ccc/Tcc	11/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.884358410180553	2		915	353	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223740	53223740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	122	412	0	ENST00000375401.3:c.3619G>A	p.Asp1207Asn	p.D1207N	ENST00000375401	NM_004187.3	1207	Gac/Aac	23/26	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.884358410180553	1		412	130	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411246	63411246	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4	105	329	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	0.884358410180553	1		329	109	SUCCESS
AR	367	MSKCC	GRCh37	X	66941720	66941720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	115	346	0	ENST00000374690.3:c.2364G>A	p.Met788Ile	p.M788I	ENST00000374690	NM_000044.3	788	atG/atA	6/8	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.884358410180553	1		346	124	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148875	119148876	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GG	GG	A	novel	NA	P-0024639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	129	258	0	ENST00000264033.4:c.1096-1_1096delinsA		p.X366_splice	ENST00000264033	NM_005188.3	366		8/16	0.631556970821185	3	FACETS	0.948	0.909	0.981			1	CLONAL	3	TRUE	NA	0.884358410180553	3		258	148	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0024641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	348	887	3	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.676937290157019	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.676937290157019	1		890	636	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0024641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	218	756	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.676937290157019	2		756	607	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945129	32945129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80359104	NA	P-0024641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	37	368	2	ENST00000380152.3:c.8524C>T	p.Arg2842Cys	p.R2842C	ENST00000380152		2842	Cgc/Tgc	20/27	1	2	FACETS	0.248	0.204	0.297	0.248	0.204	0.297	SUBCLONAL	1	TRUE	1	0.676937290157019	2		370	441	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593491	48593494	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	rs80338965	NA	P-0024641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	11	425	0	ENST00000342988.3:c.1245_1248del	p.Asp415GlufsTer20	p.D415Efs*20	ENST00000342988	NM_005359.5	414	ttAGAC/tt	10/12	0.676937290157019	1	FACETS	0.118	0.081	0.164	0.118	0.081	0.164	SUBCLONAL	1	TRUE	0	0.676937290157019	1		425	182	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158713	26158713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	124	302	0	ENST00000289316.2:c.316G>A	p.Glu106Lys	p.E106K	ENST00000289316	NM_138720.2	106	Gag/Aag	1/2	1	2	FACETS	0.942	0.86	1	0.942	0.86	1	CLONAL	1	TRUE	1	0.676937290157019	2		302	389	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214618	5214618	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767215087	NA	P-0024641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	233	807	0	ENST00000357368.4:c.4448G>A	p.Arg1483Gln	p.R1483Q	ENST00000357368	NM_002850.3	1483	cGg/cAg	29/38	0.570960371032207	1	FACETS	0.819	0.771	0.868	0.819	0.771	0.868	CLONAL	1	TRUE	0	0.676937290157019	1		807	556	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971068	21971068	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	211	521	0	ENST00000304494.5:c.290T>C	p.Leu97Pro	p.L97P	ENST00000304494	NM_000077.4	97	cTg/cCg	2/3	0.676937290157019	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.676937290157019	1		521	383	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749509	41749509	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	133	589	0	ENST00000226382.2:c.286C>T	p.Arg96Cys	p.R96C	ENST00000226382	NM_003924.3	96	Cgc/Tgc	2/3	1	2	FACETS	0.675	0.615	0.737	0.675	0.615	0.737	SUBCLONAL	1	TRUE	1	0.676937290157019	2		589	582	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593515	48593521	+	frameshift_variant	Frame_Shift_Del	DEL	TGGAGAT	TGGAGAT	-	novel	NA	P-0024641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	15	312	0	ENST00000342988.3:c.1266_1272del	p.Gly423LeufsTer11	p.G423Lfs*11	ENST00000342988	NM_005359.5	422	ccTGGAGAT/cc	10/12	0.676937290157019	1	FACETS	0.183	0.134	0.241	0.183	0.134	0.241	SUBCLONAL	1	TRUE	0	0.676937290157019	1		312	160	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189909	66189909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	56	357	1	ENST00000273854.3:c.3037G>T	p.Val1013Phe	p.V1013F	ENST00000273854	NM_004439.5	1013	Gtc/Ttc	18/18	1	2	FACETS	0.402	0.345	0.463	0.402	0.345	0.463	SUBCLONAL	1	TRUE	1	0.676937290157019	2		358	412	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140454033	140454033	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	113	308	0	ENST00000288602.6:c.1695T>A	p.Asp565Glu	p.D565E	ENST00000288602	NM_004333.4	565	gaT/gaA	14/18	1	2	FACETS	0.915	0.831	1	0.915	0.831	1	CLONAL	1	TRUE	1	0.676937290157019	2		308	365	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0024642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	196	814	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	1	2	FACETS	0.995	0.923	1	0.995	0.923	1	CLONAL	1	TRUE	1	0.505890878318562	2		814	779	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860770	3860770	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	117	321	0	ENST00000262367.5:c.809C>G	p.Thr270Ser	p.T270S	ENST00000262367	NM_004380.2	270	aCt/aGt	3/31	1	2	FACETS	0.918	0.832	1	0.918	0.832	1	CLONAL	1	TRUE	1	0.505890878318562	2		321	504	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436023	56436023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201204271	NA	P-0024642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	150	324	0	ENST00000407977.2:c.1114C>T	p.Pro372Ser	p.P372S	ENST00000407977		372	Cct/Tct	9/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.505890878318562	2		324	542	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4097291	4097291	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	246	590	0	ENST00000262948.5:c.970T>C	p.Tyr324His	p.Y324H	ENST00000262948	NM_030662.3	324	Tat/Cat	8/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.505890878318562	2		590	924	SUCCESS
BTK	695	MSKCC	GRCh37	X	100629523	100629523	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0024642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	45	350	2	ENST00000308731.7:c.240+1G>A		p.X80_splice	ENST00000308731	NM_000061.2	80			1	1	FACETS	0.238	0.199	0.28	0.238	0.199	0.28	SUBCLONAL	1	TRUE	0	0.505890878318562	1		352	559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0024656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	289	683	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.532531153816703	1	FACETS	0.788	0.752	0.825	1	0.995	1	SUBCLONAL	2	TRUE	0	0.532531153816703	1		683	505	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445100	49445101	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0024656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	121	934	0	ENST00000301067.7:c.2365dup	p.Ser789PhefsTer5	p.S789Ffs*5	ENST00000301067	NM_003482.3	789	tcc/tTcc	10/54	0.200924431679504	1	FACETS	0.703	0.639	0.77	0.703	0.639	0.77	INDETERMINATE	1	TRUE	0	0.532531153816703	1		934	474	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780203	9780203	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	104	876	1	ENST00000377346.4:c.1373C>A	p.Thr458Asn	p.T458N	ENST00000377346	NM_005026.3	458	aCt/aAt	11/24	1	2	FACETS	0.299	0.268	0.333	0.299	0.268	0.333	SUBCLONAL	1	TRUE	1	0.88698672937607	2		877	783	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783259	9783259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	243	809	1	ENST00000377346.4:c.2503G>A	p.Ala835Thr	p.A835T	ENST00000377346	NM_005026.3	835	Gcc/Acc	20/24	1	2	FACETS	0.687	0.643	0.731	0.687	0.643	0.731	SUBCLONAL	1	TRUE	1	0.88698672937607	2		810	798	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17371301	17371301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854573	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	355	800	1	ENST00000375499.3:c.155C>T	p.Ala52Val	p.A52V	ENST00000375499	NM_003000.2	52	gCt/gTt	2/8	1	2	FACETS	0.917	0.873	0.962	0.917	0.873	0.962	CLONAL	1	TRUE	1	0.88698672937607	2		801	873	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094285	27094285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	227	441	0	ENST00000324856.7:c.2993C>T	p.Ser998Phe	p.S998F	ENST00000324856	NM_006015.4	998	tCc/tTc	11/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.88698672937607	2		441	492	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101611	27101612	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	128	947	2	ENST00000324856.7:c.4899dup	p.Met1634HisfsTer14	p.M1634Hfs*14	ENST00000324856	NM_006015.4	1631	-/C	18/20	1	2	FACETS	0.292	0.264	0.321	0.292	0.264	0.321	SUBCLONAL	1	TRUE	1	0.88698672937607	2		949	989	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46727017	46727017	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	323	641	1	ENST00000371975.4:c.851T>C	p.Val284Ala	p.V284A	ENST00000371975	NM_003579.3	284	gTc/gCc	8/18	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.88698672937607	2		642	716	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65323401	65323401	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs866286005	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	43	801	0	ENST00000342505.4:c.1396A>G	p.Arg466Gly	p.R466G	ENST00000342505	NM_002227.2	466	Agg/Ggg	10/25	1	2	FACETS	0.114	0.095	0.135	0.114	0.095	0.135	SUBCLONAL	1	TRUE	1	0.88698672937607	2		801	851	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339110	65339111	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	284	644	3	ENST00000342505.4:c.425dup	p.Ile143AspfsTer9	p.I143Dfs*9	ENST00000342505	NM_002227.2	142	aag/aaAg	5/25	1	2	FACETS	0.952	0.901	1	0.952	0.901	1	CLONAL	1	TRUE	1	0.88698672937607	2		647	673	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344828	65344828	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	141	270	0	ENST00000342505.4:c.209T>G	p.Ile70Ser	p.I70S	ENST00000342505	NM_002227.2	70	aTc/aGc	4/25	1	2	FACETS	0.919	0.849	0.99	0.919	0.849	0.99	CLONAL	1	TRUE	1	0.88698672937607	2		270	346	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430402	78430402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372081866	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	292	588	3	ENST00000370768.2:c.766C>T	p.Arg256Cys	p.R256C	ENST00000370768	NM_003902.3	256	Cgt/Tgt	10/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.88698672937607	2		591	615	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165744	118165744	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	214	454	0	ENST00000369448.3:c.254G>A	p.Gly85Asp	p.G85D	ENST00000369448	NM_017709.3	85	gGc/gAc	2/2	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.88698672937607	2		454	471	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649566	206649566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1464747771	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	280	662	0	ENST00000367120.3:c.401G>A	p.Arg134His	p.R134H	ENST00000367120	NM_014002.3	134	cGc/cAc	6/22	1	2	FACETS	0.979	0.927	1	0.979	0.927	1	CLONAL	1	TRUE	1	0.88698672937607	2		662	645	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612783	228612783	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1202634115	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	312	753	0	ENST00000366696.1:c.244G>A	p.Asp82Asn	p.D82N	ENST00000366696	NM_003493.2	82	Gac/Aac	1/1	1	2	FACETS	0.918	0.871	0.966	0.918	0.871	0.966	CLONAL	1	TRUE	1	0.88698672937607	2		753	766	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727126	243727126	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	293	568	0	ENST00000263826.5:c.844G>A	p.Asp282Asn	p.D282N	ENST00000263826	NM_005465.4	282	Gat/Aat	9/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.88698672937607	2		568	655	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851576	63851576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369904878	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	347	666	0	ENST00000279873.7:c.2354G>A	p.Arg785His	p.R785H	ENST00000279873	NM_032199.2	785	cGc/cAc	10/10	1	2	FACETS	0.985	0.938	1	0.985	0.938	1	CLONAL	1	TRUE	1	0.88698672937607	2		666	794	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332943	70332943	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	111	810	0	ENST00000373644.4:c.848C>A	p.Ser283Tyr	p.S283Y	ENST00000373644	NM_030625.2	283	tCt/tAt	2/12	1	2	FACETS	0.277	0.249	0.308	0.277	0.249	0.308	SUBCLONAL	1	TRUE	1	0.88698672937607	2		810	903	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333614	70333614	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	66	536	0	ENST00000373644.4:c.1519T>G	p.Phe507Val	p.F507V	ENST00000373644	NM_030625.2	507	Ttc/Gtc	2/12	1	2	FACETS	0.223	0.193	0.256	0.223	0.193	0.256	SUBCLONAL	1	TRUE	1	0.88698672937607	2		536	666	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533783	533783	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	321	841	0	ENST00000451590.1:c.273G>T	p.Glu91Asp	p.E91D	ENST00000451590	NM_001130442.1	91	gaG/gaT	3/5	1	2	FACETS	0.924	0.877	0.972	0.924	0.877	0.972	CLONAL	1	TRUE	1	0.88698672937607	2		841	783	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132937	64132937	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	150	614	2	ENST00000334205.4:c.1071G>T	p.Gln357His	p.Q357H	ENST00000334205	NM_003942.2	357	caG/caT	9/17	1	2	FACETS	0.653	0.6	0.707	0.653	0.6	0.707	SUBCLONAL	1	TRUE	1	0.88698672937607	2		616	518	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572629	64572629	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	117	876	2	ENST00000312049.6:c.1227C>A	p.Cys409Ter	p.C409*	ENST00000312049	NM_130799.2	409	tgC/tgA	9/10	1	2	FACETS	0.288	0.259	0.319	0.288	0.259	0.319	SUBCLONAL	1	TRUE	1	0.88698672937607	2		878	916	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457828	69457828	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	58	562	0	ENST00000227507.2:c.228G>T	p.Glu76Asp	p.E76D	ENST00000227507	NM_053056.2	76	gaG/gaT	2/5	1	2	FACETS	0.248	0.213	0.286	0.248	0.213	0.286	SUBCLONAL	1	TRUE	1	0.88698672937607	2		562	527	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941258	71941258	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	357	874	0	ENST00000298229.2:c.1033C>A	p.Leu345Met	p.L345M	ENST00000298229	NM_001567.3	345	Ctg/Atg	9/28	1	2	FACETS	0.936	0.891	0.981	0.936	0.891	0.981	CLONAL	1	TRUE	1	0.88698672937607	2		874	860	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941483	71941483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771324555	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	386	869	0	ENST00000298229.2:c.1168C>T	p.Arg390Cys	p.R390C	ENST00000298229	NM_001567.3	390	Cgc/Tgc	10/28	1	2	FACETS	0.978	0.934	1	0.978	0.934	1	CLONAL	1	TRUE	1	0.88698672937607	2		869	890	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946778	71946778	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs781674896	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	321	878	1	ENST00000298229.2:c.2719C>T	p.Arg907Ter	p.R907*	ENST00000298229	NM_001567.3	907	Cga/Tga	24/28	1	2	FACETS	0.939	0.891	0.987	0.939	0.891	0.987	CLONAL	1	TRUE	1	0.88698672937607	2		879	771	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197390	94197390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1013220083	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	265	635	0	ENST00000323929.3:c.1114G>A	p.Gly372Ser	p.G372S	ENST00000323929	NM_005591.3	372	Ggt/Agt	11/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.88698672937607	2		635	574	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102094453	102094453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	156	676	1	ENST00000282441.5:c.1133C>T	p.Thr378Met	p.T378M	ENST00000282441	NM_001130145.2	378	aCg/aTg	7/9	1	2	FACETS	0.509	0.467	0.553	0.509	0.467	0.553	SUBCLONAL	1	TRUE	1	0.88698672937607	2		677	691	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190734	108190734	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	243	671	2	ENST00000278616.4:c.6401C>A	p.Ser2134Tyr	p.S2134Y	ENST00000278616	NM_000051.3	2134	tCt/tAt	44/63	1	2	FACETS	0.91	0.857	0.964	0.91	0.857	0.964	CLONAL	1	TRUE	1	0.88698672937607	2		673	602	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199946	108199946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	131	261	0	ENST00000278616.4:c.7288C>T	p.His2430Tyr	p.H2430Y	ENST00000278616	NM_000051.3	2430	Cat/Tat	49/63	1	2	FACETS	0.962	0.887	1	0.962	0.887	1	CLONAL	1	TRUE	1	0.88698672937607	2		261	307	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343121	118343121	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	238	497	1	ENST00000534358.1:c.1247C>A	p.Ala416Asp	p.A416D	ENST00000534358	NM_005933.3	416	gCt/gAt	3/36	1	2	FACETS	0.829	0.779	0.881	0.829	0.779	0.881	CLONAL	1	TRUE	1	0.88698672937607	2		498	647	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376029	118376029	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	328	677	0	ENST00000534358.1:c.9422G>T	p.Ser3141Ile	p.S3141I	ENST00000534358	NM_005933.3	3141	aGc/aTc	27/36	1	2	FACETS	0.99	0.942	1	0.99	0.942	1	CLONAL	1	TRUE	1	0.88698672937607	2		677	747	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376266	118376266	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	298	611	0	ENST00000534358.1:c.9659G>A	p.Gly3220Glu	p.G3220E	ENST00000534358	NM_005933.3	3220	gGa/gAa	27/36	1	2	FACETS	0.985	0.935	1	0.985	0.935	1	CLONAL	1	TRUE	1	0.88698672937607	2		611	682	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376384	118376384	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	330	778	1	ENST00000534358.1:c.9777C>A	p.Asn3259Lys	p.N3259K	ENST00000534358	NM_005933.3	3259	aaC/aaA	27/36	1	2	FACETS	0.954	0.907	1	0.954	0.907	1	CLONAL	1	TRUE	1	0.88698672937607	2		779	780	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125523738	125523738	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	157	340	0	ENST00000428830.2:c.1331C>A	p.Ser444Tyr	p.S444Y	ENST00000428830	NM_001114121.2	444	tCt/tAt	12/14	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.88698672937607	2		340	348	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	464374	464374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1225548195	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	361	749	1	ENST00000399788.2:c.820G>A	p.Ala274Thr	p.A274T	ENST00000399788	NM_001042603.1	274	Gca/Aca	7/28	1	2	FACETS	0.966	0.92	1	0.966	0.92	1	CLONAL	1	TRUE	1	0.88698672937607	2		750	843	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022375	12022375	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	454	992	0	ENST00000396373.4:c.481A>G	p.Thr161Ala	p.T161A	ENST00000396373	NM_001987.4	161	Acc/Gcc	5/8	1	2	FACETS	0.991	0.95	1	0.991	0.95	1	CLONAL	1	TRUE	1	0.88698672937607	2		992	1033	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038876	12038876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	192	435	0	ENST00000396373.4:c.1169C>T	p.Thr390Ile	p.T390I	ENST00000396373	NM_001987.4	390	aCc/aTc	7/8	1	2	FACETS	0.876	0.818	0.936	0.876	0.818	0.936	CLONAL	1	TRUE	1	0.88698672937607	2		435	494	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398279	25398279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894365	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	271	747	2	ENST00000311936.3:c.40G>A	p.Val14Ile	p.V14I	ENST00000311936	NM_004985.3	14	Gta/Ata	2/5	1	2	FACETS	0.877	0.828	0.927	0.877	0.828	0.927	CLONAL	1	TRUE	1	0.88698672937607	2		749	697	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231103	46231103	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	68	535	0	ENST00000334344.6:c.1024-1G>T		p.X342_splice	ENST00000334344	NM_152641.2	342			1	2	FACETS	0.298	0.259	0.339	0.298	0.259	0.339	SUBCLONAL	1	TRUE	1	0.88698672937607	2		535	515	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245951	46245951	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	48	376	0	ENST00000334344.6:c.4045A>G	p.Ile1349Val	p.I1349V	ENST00000334344	NM_152641.2	1349	Atc/Gtc	15/21	1	2	FACETS	0.244	0.206	0.286	0.244	0.206	0.286	SUBCLONAL	1	TRUE	1	0.88698672937607	2		376	443	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448739	49448739	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	72	620	0	ENST00000301067.7:c.120G>T	p.Glu40Asp	p.E40D	ENST00000301067	NM_003482.3	40	gaG/gaT	2/54	1	2	FACETS	0.215	0.187	0.245	0.215	0.187	0.245	SUBCLONAL	1	TRUE	1	0.88698672937607	2		620	755	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484292	50484292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746406610	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	368	861	0	ENST00000394963.4:c.1052G>A	p.Arg351His	p.R351H	ENST00000394963	NM_003076.4	351	cGt/cAt	9/13	1	2	FACETS	0.928	0.884	0.973	0.928	0.884	0.973	CLONAL	1	TRUE	1	0.88698672937607	2		861	894	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494005	56494005	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	317	725	1	ENST00000267101.3:c.3177G>T	p.Gln1059His	p.Q1059H	ENST00000267101	NM_001982.3	1059	caG/caT	26/28	1	2	FACETS	0.916	0.869	0.964	0.916	0.869	0.964	CLONAL	1	TRUE	1	0.88698672937607	2		726	780	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145425	58145425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	295	572	1	ENST00000257904.6:c.76C>T	p.Pro26Ser	p.P26S	ENST00000257904	NM_000075.3	26	Ccc/Tcc	2/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.88698672937607	2		573	635	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145430	58145430	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894340	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	37	567	0	ENST00000257904.6:c.71G>T	p.Arg24Leu	p.R24L	ENST00000257904	NM_000075.3	24	cGt/cTt	2/8	1	2	FACETS	0.132	0.108	0.159	0.132	0.108	0.159	SUBCLONAL	1	TRUE	1	0.88698672937607	2		567	633	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891175	112891175	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	243	780	0	ENST00000351677.2:c.509T>C	p.Val170Ala	p.V170A	ENST00000351677	NM_002834.3	170	gTt/gCt	4/16	1	2	FACETS	0.561	0.524	0.599	0.561	0.524	0.599	SUBCLONAL	1	TRUE	1	0.88698672937607	2		780	977	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432068	121432068	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137853238	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	338	897	1	ENST00000257555.6:c.815G>A	p.Arg272His	p.R272H	ENST00000257555		272	cGc/cAc	4/10	1	2	FACETS	0.839	0.797	0.883	0.839	0.797	0.883	CLONAL	1	TRUE	1	0.88698672937607	2		898	908	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123889596	123889596	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	43	403	0	ENST00000330479.4:c.823T>G	p.Phe275Val	p.F275V	ENST00000330479	NM_020382.3	275	Ttt/Gtt	7/9	1	2	FACETS	0.241	0.202	0.285	0.241	0.202	0.285	SUBCLONAL	1	TRUE	1	0.88698672937607	2		403	402	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219908	133219908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs969429633	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	261	695	0	ENST00000320574.5:c.4453C>T	p.Arg1485Cys	p.R1485C	ENST00000320574	NM_006231.2	1485	Cgc/Tgc	35/49	1	2	FACETS	0.907	0.856	0.959	0.907	0.856	0.959	CLONAL	1	TRUE	1	0.88698672937607	2		695	649	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249842	133249842	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	249	559	0	ENST00000320574.5:c.1381T>C	p.Ser461Pro	p.S461P	ENST00000320574	NM_006231.2	461	Tca/Cca	14/49	1	2	FACETS	0.966	0.912	1	0.966	0.912	1	CLONAL	1	TRUE	1	0.88698672937607	2		559	581	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257789	133257789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143626223	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	361	770	2	ENST00000320574.5:c.139C>T	p.Arg47Trp	p.R47W	ENST00000320574	NM_006231.2	47	Cgg/Tgg	2/49	1	2	FACETS	0.962	0.917	1	0.962	0.917	1	CLONAL	1	TRUE	1	0.88698672937607	2		772	846	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549334	21549334	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	322	799	0	ENST00000382592.4:c.2942A>G	p.Asp981Gly	p.D981G	ENST00000382592	NM_014572.2	981	gAc/gGc	8/8	1	2	FACETS	0.894	0.848	0.94	0.894	0.848	0.94	CLONAL	1	TRUE	1	0.88698672937607	2		799	812	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563172	21563172	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs765750027	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	80	934	0	ENST00000382592.4:c.747G>T	p.Gln249His	p.Q249H	ENST00000382592	NM_014572.2	249	caG/caT	4/8	1	2	FACETS	0.237	0.208	0.268	0.237	0.208	0.268	SUBCLONAL	1	TRUE	1	0.88698672937607	2		934	761	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28883026	28883026	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	319	640	0	ENST00000282397.4:c.3674T>C	p.Ile1225Thr	p.I1225T	ENST00000282397	NM_002019.4	1225	aTc/aCc	28/30	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.88698672937607	2		640	695	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900706	32900706	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs80358818	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	277	815	1	ENST00000380152.3:c.587G>T	p.Ser196Ile	p.S196I	ENST00000380152		196	aGt/aTt	7/27	1	2	FACETS	0.903	0.853	0.953	0.903	0.853	0.953	CLONAL	1	TRUE	1	0.88698672937607	2		816	692	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527853	103527853	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	247	402	0	ENST00000355739.4:c.3161A>T	p.Lys1054Ile	p.K1054I	ENST00000355739	NM_000123.3	1054	aAa/aTa	15/15	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.88698672937607	2		402	528	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95599661	95599661	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	255	456	0	ENST00000393063.1:c.135A>C	p.Arg45Ser	p.R45S	ENST00000393063	NM_030621.3	45	agA/agC	3/28	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.88698672937607	2		456	567	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643228	38643228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479997969	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	191	412	1	ENST00000299084.4:c.698C>T	p.Ser233Leu	p.S233L	ENST00000299084	NM_152594.2	233	tCa/tTa	7/7	1	2	FACETS	0.916	0.856	0.977	0.916	0.856	0.977	CLONAL	1	TRUE	1	0.88698672937607	2		413	470	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989033	41989033	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs758606746	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	320	606	0	ENST00000219905.7:c.1825A>G	p.Asn609Asp	p.N609D	ENST00000219905	NM_001164273.1	609	Aat/Gat	3/24	1	2	FACETS	0.995	0.946	1	0.995	0.946	1	CLONAL	1	TRUE	1	0.88698672937607	2		606	725	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035203	42035203	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	411	896	0	ENST00000219905.7:c.5045C>A	p.Ser1682Tyr	p.S1682Y	ENST00000219905	NM_001164273.1	1682	tCt/tAt	15/24	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.88698672937607	2		896	920	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708452	43708452	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1353211209	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	88	747	0	ENST00000382044.4:c.4844C>T	p.Pro1615Leu	p.P1615L	ENST00000382044	NM_001141980.1	1615	cCt/cTt	22/28	1	2	FACETS	0.225	0.199	0.253	0.225	0.199	0.253	SUBCLONAL	1	TRUE	1	0.88698672937607	2		747	882	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713307	43713307	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	455	1091	1	ENST00000382044.4:c.4166G>T	p.Gly1389Val	p.G1389V	ENST00000382044	NM_001141980.1	1389	gGc/gTc	20/28	1	2	FACETS	0.937	0.897	0.977	0.937	0.897	0.977	CLONAL	1	TRUE	1	0.88698672937607	2		1092	1095	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99460049	99460049	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	61	586	1	ENST00000268035.6:c.2145G>T	p.Glu715Asp	p.E715D	ENST00000268035	NM_000875.3	715	gaG/gaT	10/21	1	2	FACETS	0.199	0.171	0.229	0.199	0.171	0.229	SUBCLONAL	1	TRUE	1	0.88698672937607	2		587	692	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2097769	2097769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	261	807	0	ENST00000219066.1:c.80C>T	p.Ala27Val	p.A27V	ENST00000219066	NM_002528.5	27	gCt/gTt	1/6	1	2	FACETS	0.962	0.908	1	0.962	0.908	1	CLONAL	1	TRUE	1	0.88698672937607	2		807	612	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641148	3641148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	617	1241	1	ENST00000294008.3:c.2491G>A	p.Glu831Lys	p.E831K	ENST00000294008	NM_032444.2	831	Gag/Aag	12/15	1	2	FACETS	0.994	0.958	1	0.994	0.958	1	CLONAL	1	TRUE	1	0.88698672937607	2		1242	1400	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777960	3777960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1266123570	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	519	1236	6	ENST00000262367.5:c.7088C>T	p.Pro2363Leu	p.P2363L	ENST00000262367	NM_004380.2	2363	cCg/cTg	31/31	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.88698672937607	2		1242	1114	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778385	3778385	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	342	820	1	ENST00000262367.5:c.6663G>T	p.Met2221Ile	p.M2221I	ENST00000262367	NM_004380.2	2221	atG/atT	31/31	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.88698672937607	2		821	724	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778500	3778500	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779996604	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	418	1061	1	ENST00000262367.5:c.6548C>T	p.Ala2183Val	p.A2183V	ENST00000262367	NM_004380.2	2183	gCg/gTg	31/31	1	2	FACETS	0.975	0.932	1	0.975	0.932	1	CLONAL	1	TRUE	1	0.88698672937607	2		1062	967	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786787	3786787	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	58	525	0	ENST00000262367.5:c.4424C>A	p.Pro1475His	p.P1475H	ENST00000262367	NM_004380.2	1475	cCt/cAt	27/31	1	2	FACETS	0.218	0.187	0.252	0.218	0.187	0.252	SUBCLONAL	1	TRUE	1	0.88698672937607	2		525	599	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128108	30128108	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	84	835	0	ENST00000263025.4:c.1021G>T	p.Val341Leu	p.V341L	ENST00000263025	NM_002746.2	341	Gtg/Ttg	8/9	1	2	FACETS	0.238	0.21	0.268	0.238	0.21	0.268	SUBCLONAL	1	TRUE	1	0.88698672937607	2		835	796	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783935	50783935	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	339	800	1	ENST00000398568.2:c.326G>T	p.Arg109Met	p.R109M	ENST00000398568	NM_001042412.1	109	aGg/aTg	3/18	1	2	FACETS	0.934	0.888	0.981	0.934	0.888	0.981	CLONAL	1	TRUE	1	0.88698672937607	2		801	818	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346682	89346682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	179	464	0	ENST00000301030.4:c.6268G>A	p.Ala2090Thr	p.A2090T	ENST00000301030	NM_001256183.1	2090	Gct/Act	9/13	1	2	FACETS	0.97	0.906	1	0.97	0.906	1	CLONAL	1	TRUE	1	0.88698672937607	2		464	416	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346781	89346781	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	190	441	0	ENST00000301030.4:c.6169G>A	p.Ala2057Thr	p.A2057T	ENST00000301030	NM_001256183.1	2057	Gcc/Acc	9/13	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.88698672937607	2		441	381	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348415	89348415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780686131	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	115	912	2	ENST00000301030.4:c.4535G>A	p.Arg1512His	p.R1512H	ENST00000301030	NM_001256183.1	1512	cGc/cAc	9/13	1	2	FACETS	0.266	0.239	0.295	0.266	0.239	0.295	SUBCLONAL	1	TRUE	1	0.88698672937607	2		914	974	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357099	89357099	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	371	858	0	ENST00000301030.4:c.535G>A	p.Gly179Arg	p.G179R	ENST00000301030	NM_001256183.1	179	Ggg/Agg	6/13	1	2	FACETS	0.956	0.911	1	0.956	0.911	1	CLONAL	1	TRUE	1	0.88698672937607	2		858	875	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831342	89831342	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	87	761	0	ENST00000389301.3:c.2734A>G	p.Thr912Ala	p.T912A	ENST00000389301	NM_000135.2	912	Aca/Gca	28/43	1	2	FACETS	0.254	0.224	0.286	0.254	0.224	0.286	SUBCLONAL	1	TRUE	1	0.88698672937607	2		761	772	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838111	89838111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148203537	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	360	712	0	ENST00000389301.3:c.2126C>T	p.Pro709Leu	p.P709L	ENST00000389301	NM_000135.2	709	cCg/cTg	23/43	1	2	FACETS	0.972	0.926	1	0.972	0.926	1	CLONAL	1	TRUE	1	0.88698672937607	2		712	835	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519999	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	316	726	1	ENST00000269305.4:c.716A>G	p.Asn239Ser	p.N239S	ENST00000269305	NM_001126112.2	239	aAc/aGc	7/11	1	2	FACETS	0.871	0.826	0.917	0.871	0.826	0.917	CLONAL	1	TRUE	1	0.88698672937607	2		727	818	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	310	632	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	1	2	FACETS	0.919	0.871	0.967	0.919	0.871	0.967	CLONAL	1	TRUE	1	0.88698672937607	2		632	761	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032581	12032581	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	289	666	0	ENST00000353533.5:c.1017T>A	p.Ser339Arg	p.S339R	ENST00000353533	NM_003010.3	339	agT/agA	9/11	1	2	FACETS	0.987	0.936	1	0.987	0.936	1	CLONAL	1	TRUE	1	0.88698672937607	2		666	660	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983784	15983784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150513105	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	296	614	2	ENST00000268712.3:c.3338G>A	p.Arg1113Gln	p.R1113Q	ENST00000268712	NM_006311.3	1113	cGa/cAa	25/46	1	2	FACETS	0.928	0.879	0.978	0.928	0.879	0.978	CLONAL	1	TRUE	1	0.88698672937607	2		616	719	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663417	29663417	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	69	679	0	ENST00000356175.3:c.6010T>G	p.Ser2004Ala	p.S2004A	ENST00000356175	NM_000267.3	2004	Tca/Gca	40/57	1	2	FACETS	0.215	0.187	0.246	0.215	0.187	0.246	SUBCLONAL	1	TRUE	1	0.88698672937607	2		679	724	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	206	471	1	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.88698672937607	2		472	439	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683557	29683558	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1060500295	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	165	498	0	ENST00000356175.3:c.7638dup	p.Lys2547GlnfsTer9	p.K2547Qfs*9	ENST00000356175	NM_000267.3	2544	-/C	51/57	1	2	FACETS	0.869	0.807	0.933	0.869	0.807	0.933	CLONAL	1	TRUE	1	0.88698672937607	2		498	428	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	681	839	1	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	0.886989505963813	3	FACETS	0.966	0.938	0.994	0.966	0.938	0.994	CLONAL	2	TRUE	1	0.88698672937607	3		840	1147	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510671	38510671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	312	745	0	ENST00000254066.5:c.925G>A	p.Val309Ile	p.V309I	ENST00000254066	NM_000964.3	309	Gtc/Atc	7/9	0.886989505963813	3	FACETS	0.974	0.919	1	0.487	0.459	0.515	CLONAL	1	TRUE	1	0.88698672937607	3		745	1043	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40447699	40447699	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	112	718	1	ENST00000345506.4:c.438G>T	p.Gln146His	p.Q146H	ENST00000345506	NM_003152.3	146	caG/caT	6/20	0.886989505963813	3	FACETS	0.29	0.26	0.323	0.145	0.13	0.162	SUBCLONAL	1	TRUE	1	0.88698672937607	3		719	1255	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40457701	40457701	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	290	732	0	ENST00000345506.4:c.1454A>G	p.Asp485Gly	p.D485G	ENST00000345506	NM_003152.3	485	gAc/gGc	13/20	0.886989505963813	3	FACETS	0.907	0.854	0.961	0.453	0.427	0.481	CLONAL	1	TRUE	1	0.88698672937607	3		732	1041	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40457719	40457719	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs370492942	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	256	618	0	ENST00000345506.4:c.1472C>T	p.Pro491Leu	p.P491L	ENST00000345506	NM_003152.3	491	cCg/cTg	13/20	0.886989505963813	3	FACETS	0.953	0.895	1	0.477	0.447	0.507	CLONAL	1	TRUE	1	0.88698672937607	3		618	874	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40500450	40500450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	337	629	0	ENST00000264657.5:c.85G>A	p.Glu29Lys	p.E29K	ENST00000264657	NM_139276.2	29	Gag/Aag	2/24	0.886989505963813	3	FACETS	1	0.976	1	0.526	0.498	0.555	CLONAL	1	TRUE	1	0.88698672937607	3		629	1042	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56811485	56811485	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	259	586	0	ENST00000337432.4:c.1033G>A	p.Gly345Arg	p.G345R	ENST00000337432	NM_058216.2	345	Gga/Aga	9/9	0.886989505963813	3	FACETS	0.992	0.931	1	0.496	0.465	0.527	CLONAL	1	TRUE	1	0.88698672937607	3		586	850	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885955	59885955	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758360637	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	111	692	2	ENST00000259008.2:c.791G>A	p.Arg264Gln	p.R264Q	ENST00000259008	NM_032043.2	264	cGg/cAg	7/20	0.886989505963813	3	FACETS	0.307	0.275	0.341	0.153	0.137	0.171	SUBCLONAL	1	TRUE	1	0.88698672937607	3		694	1177	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533556	63533556	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147716924	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	436	841	1	ENST00000307078.5:c.1598C>T	p.Ala533Val	p.A533V	ENST00000307078	NM_004655.3	533	gCg/gTg	6/11	0.886989505963813	3	FACETS	1	0.982	1	0.528	0.504	0.554	CLONAL	1	TRUE	1	0.88698672937607	3		842	1343	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756722	756722	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	301	654	0	ENST00000314574.4:c.106C>T	p.Pro36Ser	p.P36S	ENST00000314574	NM_005433.3	36	Ccc/Tcc	2/12	1	2	FACETS	0.931	0.882	0.98	0.931	0.882	0.98	CLONAL	1	TRUE	1	0.88698672937607	2		654	729	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191068	2191068	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757313197	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	298	527	0	ENST00000398665.3:c.322C>T	p.Arg108Cys	p.R108C	ENST00000398665	NM_032482.2	108	Cgc/Tgc	5/28	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.88698672937607	2		527	660	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2193747	2193747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767206745	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	76	779	1	ENST00000398665.3:c.553G>A	p.Val185Ile	p.V185I	ENST00000398665	NM_032482.2	185	Gtc/Atc	6/28	1	2	FACETS	0.191	0.167	0.217	0.191	0.167	0.217	SUBCLONAL	1	TRUE	1	0.88698672937607	2		780	898	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121031	3121031	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	102	787	0	ENST00000078429.4:c.934A>G	p.Met312Val	p.M312V	ENST00000078429	NM_002067.2	312	Atg/Gtg	7/7	1	2	FACETS	0.284	0.253	0.316	0.284	0.253	0.316	SUBCLONAL	1	TRUE	1	0.88698672937607	2		787	811	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215558	5215558	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs558948003	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	382	889	0	ENST00000357368.4:c.4145C>T	p.Thr1382Met	p.T1382M	ENST00000357368	NM_002850.3	1382	aCg/aTg	27/38	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.88698672937607	2		889	839	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229659	5229659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1273151991	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	13	46	1	ENST00000357368.4:c.2192C>T	p.Ala731Val	p.A731V	ENST00000357368	NM_002850.3	731	gCg/gTg	15/38	1	2	FACETS	0.497	0.364	0.65	0.497	0.364	0.65	SUBCLONAL	1	TRUE	1	0.88698672937607	2		47	59	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231432	5231432	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	89	1003	1	ENST00000357368.4:c.2044C>A	p.Leu682Met	p.L682M	ENST00000357368	NM_002850.3	682	Ctg/Atg	14/38	1	2	FACETS	0.225	0.199	0.253	0.225	0.199	0.253	SUBCLONAL	1	TRUE	1	0.88698672937607	2		1004	893	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244274	5244274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750721878	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	409	869	1	ENST00000357368.4:c.1208C>T	p.Ser403Leu	p.S403L	ENST00000357368	NM_002850.3	403	tCg/tTg	11/38	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.88698672937607	2		870	897	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260580	10260580	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	373	718	0	ENST00000340748.4:c.2282A>G	p.Asp761Gly	p.D761G	ENST00000340748		761	gAc/gGc	24/40	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.88698672937607	2		718	817	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031803	11031803	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	297	860	0	ENST00000327064.4:c.1615G>T	p.Ala539Ser	p.A539S	ENST00000327064	NM_199141.1	539	Gcc/Tcc	14/16	1	2	FACETS	0.883	0.836	0.931	0.883	0.836	0.931	CLONAL	1	TRUE	1	0.88698672937607	2		860	758	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288730	15288730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs998823130	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	44	110	0	ENST00000263388.2:c.4009G>A	p.Ala1337Thr	p.A1337T	ENST00000263388	NM_000435.2	1337	Gcc/Acc	24/33	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.88698672937607	2		110	88	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290248	15290248	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	415	972	0	ENST00000263388.2:c.3387G>T	p.Gln1129His	p.Q1129H	ENST00000263388	NM_000435.2	1129	caG/caT	21/33	1	2	FACETS	0.954	0.912	0.996	0.954	0.912	0.996	CLONAL	1	TRUE	1	0.88698672937607	2		972	981	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291889	15291889	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	352	998	0	ENST00000263388.2:c.2877C>A	p.Cys959Ter	p.C959*	ENST00000263388	NM_000435.2	959	tgC/tgA	18/33	1	2	FACETS	0.976	0.93	1	0.976	0.93	1	CLONAL	1	TRUE	1	0.88698672937607	2		998	813	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299904	15299904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	127	984	1	ENST00000263388.2:c.1274G>A	p.Gly425Glu	p.G425E	ENST00000263388	NM_000435.2	425	gGa/gAa	8/33	1	2	FACETS	0.325	0.294	0.357	0.325	0.294	0.357	SUBCLONAL	1	TRUE	1	0.88698672937607	2		985	882	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349220	15349220	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	73	702	0	ENST00000263377.2:c.4057C>A	p.Leu1353Ile	p.L1353I	ENST00000263377	NM_058243.2	1353	Cta/Ata	20/20	1	2	FACETS	0.239	0.208	0.271	0.239	0.208	0.271	SUBCLONAL	1	TRUE	1	0.88698672937607	2		702	690	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349937	15349937	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	289	689	0	ENST00000263377.2:c.3715A>G	p.Lys1239Glu	p.K1239E	ENST00000263377	NM_058243.2	1239	Aag/Gag	18/20	1	2	FACETS	0.935	0.885	0.985	0.935	0.885	0.985	CLONAL	1	TRUE	1	0.88698672937607	2		689	697	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937674	17937674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265005806	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	302	698	0	ENST00000458235.1:c.3253C>T	p.Arg1085Trp	p.R1085W	ENST00000458235	NM_000215.3	1085	Cgg/Tgg	24/24	1	2	FACETS	0.935	0.887	0.985	0.935	0.887	0.985	CLONAL	1	TRUE	1	0.88698672937607	2		698	728	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946819	17946819	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	374	892	0	ENST00000458235.1:c.1828A>C	p.Met610Leu	p.M610L	ENST00000458235	NM_000215.3	610	Atg/Ctg	14/24	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.88698672937607	2		892	840	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948863	17948863	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	87	664	0	ENST00000458235.1:c.1579C>A	p.Leu527Met	p.L527M	ENST00000458235	NM_000215.3	527	Ctg/Atg	12/24	1	2	FACETS	0.263	0.233	0.296	0.263	0.233	0.296	SUBCLONAL	1	TRUE	1	0.88698672937607	2		664	745	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966050	18966050	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	203	488	0	ENST00000262803.5:c.1543G>T	p.Gly515Trp	p.G515W	ENST00000262803	NM_002911.3	515	Ggg/Tgg	11/24	1	2	FACETS	0.997	0.935	1	0.997	0.935	1	CLONAL	1	TRUE	1	0.88698672937607	2		488	459	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210426	36210426	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750794495	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	344	657	0	ENST00000222270.7:c.419C>T	p.Ala140Val	p.A140V	ENST00000222270	NM_014727.1	140	gCg/gTg	2/37	1	2	FACETS	0.968	0.922	1	0.968	0.922	1	CLONAL	1	TRUE	1	0.88698672937607	2		657	801	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215621	36215621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1268488101	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	379	753	0	ENST00000222270.7:c.3418C>T	p.Arg1140Cys	p.R1140C	ENST00000222270	NM_014727.1	1140	Cgc/Tgc	9/37	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.88698672937607	2		753	806	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215951	36215951	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	428	1012	0	ENST00000222270.7:c.3491C>A	p.Ser1164Tyr	p.S1164Y	ENST00000222270	NM_014727.1	1164	tCt/tAt	10/37	1	2	FACETS	0.976	0.934	1	0.976	0.934	1	CLONAL	1	TRUE	1	0.88698672937607	2		1012	989	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220183	36220183	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1437697210	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	69	655	0	ENST00000222270.7:c.4903C>T	p.Arg1635Ter	p.R1635*	ENST00000222270	NM_014727.1	1635	Cga/Tga	22/37	1	2	FACETS	0.25	0.217	0.285	0.25	0.217	0.285	SUBCLONAL	1	TRUE	1	0.88698672937607	2		655	623	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745193	41745193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	45	679	0	ENST00000301178.4:c.1259C>T	p.Pro420Leu	p.P420L	ENST00000301178	NM_021913.4	420	cCa/cTa	9/20	1	2	FACETS	0.149	0.125	0.176	0.149	0.125	0.176	SUBCLONAL	1	TRUE	1	0.88698672937607	2		679	681	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752738	42752738	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	310	915	1	ENST00000222329.4:c.1526A>G	p.Glu509Gly	p.E509G	ENST00000222329	NM_006494.2	509	gAg/gGg	4/4	1	2	FACETS	0.923	0.876	0.972	0.923	0.876	0.972	CLONAL	1	TRUE	1	0.88698672937607	2		916	757	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905485	50905485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs914238978	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	384	974	1	ENST00000440232.2:c.613G>A	p.Gly205Ser	p.G205S	ENST00000440232	NM_002691.3	205	Ggc/Agc	6/27	1	2	FACETS	0.978	0.934	1	0.978	0.934	1	CLONAL	1	TRUE	1	0.88698672937607	2		975	885	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905731	50905731	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	402	1027	0	ENST00000440232.2:c.779T>C	p.Ile260Thr	p.I260T	ENST00000440232	NM_002691.3	260	aTc/aCc	7/27	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.88698672937607	2		1027	888	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086209	16086209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	272	523	1	ENST00000281043.3:c.1385G>A	p.Arg462Gln	p.R462Q	ENST00000281043	NM_005378.4	462	cGg/cAg	3/3	1	2	FACETS	0.989	0.936	1	0.989	0.936	1	CLONAL	1	TRUE	1	0.88698672937607	2		524	620	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457243	25457243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377577594	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	346	671	1	ENST00000264709.3:c.2644C>T	p.Arg882Cys	p.R882C	ENST00000264709	NM_175629.2	882	Cgc/Tgc	23/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.88698672937607	2		672	743	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966906	25966906	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	331	676	0	ENST00000435504.4:c.2300G>T	p.Ser767Ile	p.S767I	ENST00000435504		767	aGt/aTt	13/13	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.88698672937607	2		676	715	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972716	25972716	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	218	570	0	ENST00000435504.4:c.1709C>T	p.Ser570Phe	p.S570F	ENST00000435504		570	tCt/tTt	12/13	1	2	FACETS	0.858	0.804	0.913	0.858	0.804	0.913	CLONAL	1	TRUE	1	0.88698672937607	2		570	573	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39347559	39347559	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	149	458	0	ENST00000402219.2:c.5A>G	p.Gln2Arg	p.Q2R	ENST00000402219	NM_005633.3	2	cAg/cGg	1/23	1	2	FACETS	0.891	0.824	0.959	0.891	0.824	0.959	CLONAL	1	TRUE	1	0.88698672937607	2		458	377	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46588098	46588098	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	354	826	1	ENST00000263734.3:c.648G>T	p.Glu216Asp	p.E216D	ENST00000263734	NM_001430.4	216	gaG/gaT	6/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.88698672937607	2		827	780	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609677	46609677	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1265031766	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	398	928	0	ENST00000263734.3:c.2401C>A	p.Pro801Thr	p.P801T	ENST00000263734	NM_001430.4	801	Cca/Aca	15/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.88698672937607	2		928	856	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033643	48033643	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1553333453	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	251	616	0	ENST00000234420.5:c.3854T>C	p.Phe1285Ser	p.F1285S	ENST00000234420	NM_000179.2	1285	tTc/tCc	9/10	1	2	FACETS	0.953	0.899	1	0.953	0.899	1	CLONAL	1	TRUE	1	0.88698672937607	2		616	594	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719479	190719479	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752602525	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	157	328	0	ENST00000441310.2:c.1481C>T	p.Ser494Phe	p.S494F	ENST00000441310	NM_000534.4	494	tCt/tTt	9/13	1	2	FACETS	0.905	0.84	0.972	0.905	0.84	0.972	CLONAL	1	TRUE	1	0.88698672937607	2		328	391	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113283	209113283	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	260	576	0	ENST00000345146.2:c.224C>A	p.Thr75Asn	p.T75N	ENST00000345146	NM_005896.2	75	aCt/aAt	4/10	1	2	FACETS	0.923	0.871	0.976	0.923	0.871	0.976	CLONAL	1	TRUE	1	0.88698672937607	2		576	635	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113361	209113361	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765848107	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	232	439	0	ENST00000345146.2:c.146G>A	p.Arg49His	p.R49H	ENST00000345146	NM_005896.2	49	cGt/cAt	4/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.88698672937607	2		439	505	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212615395	212615395	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	70	617	0	ENST00000342788.4:c.591C>A	p.Cys197Ter	p.C197*	ENST00000342788	NM_005235.2	197	tgC/tgA	5/28	1	2	FACETS	0.209	0.182	0.239	0.209	0.182	0.239	SUBCLONAL	1	TRUE	1	0.88698672937607	2		617	754	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661537	227661537	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777987963	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	317	873	0	ENST00000305123.5:c.1918G>A	p.Val640Ile	p.V640I	ENST00000305123	NM_005544.2	640	Gta/Ata	1/2	1	2	FACETS	0.976	0.928	1	0.976	0.928	1	CLONAL	1	TRUE	1	0.88698672937607	2		873	732	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309952	30309952	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	326	645	0	ENST00000307677.4:c.70T>C	p.Trp24Arg	p.W24R	ENST00000307677	NM_138578.1	24	Tgg/Cgg	2/3	1	2	FACETS	0.953	0.906	1	0.953	0.906	1	CLONAL	1	TRUE	1	0.88698672937607	2		645	771	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023823	31023823	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	41	729	1	ENST00000375687.4:c.3308C>A	p.Ala1103Asp	p.A1103D	ENST00000375687	NM_015338.5	1103	gCc/gAc	13/13	1	2	FACETS	0.114	0.094	0.136	0.114	0.094	0.136	SUBCLONAL	1	TRUE	1	0.88698672937607	2		730	813	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420085	41420085	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1441265694	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	55	372	0	ENST00000373198.4:c.236G>T	p.Ser79Ile	p.S79I	ENST00000373198	NM_133170.3	79	aGc/aTc	3/32	1	2	FACETS	0.302	0.259	0.349	0.302	0.259	0.349	SUBCLONAL	1	TRUE	1	0.88698672937607	2		372	411	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62298865	62298865	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776356655	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	92	915	1	ENST00000360203.5:c.658G>A	p.Asp220Asn	p.D220N	ENST00000360203	NM_001283009.1	220	Gac/Aac	8/35	1	2	FACETS	0.226	0.2	0.254	0.226	0.2	0.254	SUBCLONAL	1	TRUE	1	0.88698672937607	2		916	917	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656999	45656999	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	54	853	0	ENST00000407780.3:c.157T>G	p.Tyr53Asp	p.Y53D	ENST00000407780	NM_001283052.1	53	Tat/Gat	3/7	NA	2	FACETS	0.135	0.115	0.158			1	INDETERMINATE	1	TRUE	NA	0.88698672937607	2		853	900	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288503	21288503	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	363	708	1	ENST00000354336.3:c.748G>A	p.Ala250Thr	p.A250T	ENST00000354336	NM_005207.3	250	Gct/Act	2/3	1	2	FACETS	0.964	0.919	1	0.964	0.919	1	CLONAL	1	TRUE	1	0.88698672937607	2		709	849	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095834	29095834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs864622371	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	315	727	1	ENST00000328354.6:c.1000G>A	p.Ala334Thr	p.A334T	ENST00000328354	NM_007194.3	334	Gct/Act	9/15	1	2	FACETS	0.933	0.886	0.981	0.933	0.886	0.981	CLONAL	1	TRUE	1	0.88698672937607	2		728	761	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29120965	29120965	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	248	530	0	ENST00000328354.6:c.592G>T	p.Val198Phe	p.V198F	ENST00000328354	NM_007194.3	198	Gtt/Ttt	4/15	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.88698672937607	2		530	559	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645760	12645760	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587777588	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	246	459	0	ENST00000251849.4:c.709G>A	p.Ala237Thr	p.A237T	ENST00000251849	NM_002880.3	237	Gcc/Acc	7/17	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.88698672937607	2		459	533	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691835	30691835	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	79	593	1	ENST00000295754.5:c.337C>A	p.Leu113Met	p.L113M	ENST00000295754	NM_003242.5	113	Ctg/Atg	3/7	1	2	FACETS	0.305	0.268	0.344	0.305	0.268	0.344	SUBCLONAL	1	TRUE	1	0.88698672937607	2		594	584	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182637	38182637	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs748659894	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	184	364	2	ENST00000396334.3:c.790C>T	p.Arg264Ter	p.R264*	ENST00000396334	NM_002468.4	264	Cga/Tga	5/5	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.88698672937607	2		366	405	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129617	47129617	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	263	614	0	ENST00000409792.3:c.5263C>A	p.Leu1755Met	p.L1755M	ENST00000409792	NM_014159.6	1755	Ctg/Atg	10/21	1	2	FACETS	0.897	0.846	0.948	0.897	0.846	0.948	CLONAL	1	TRUE	1	0.88698672937607	2		614	661	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164217	47164218	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	249	514	0	ENST00000409792.3:c.1908dup	p.Lys637Ter	p.K637*	ENST00000409792	NM_014159.6	636	-/T	3/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.88698672937607	2		514	556	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932758	49932758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	49	925	0	ENST00000296474.3:c.3113C>T	p.Ala1038Val	p.A1038V	ENST00000296474	NM_002447.2	1038	gCa/gTa	14/20	1	2	FACETS	0.116	0.097	0.136	0.116	0.097	0.136	SUBCLONAL	1	TRUE	1	0.88698672937607	2		925	955	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940393	49940393	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	360	793	0	ENST00000296474.3:c.650C>A	p.Ser217Tyr	p.S217Y	ENST00000296474	NM_002447.2	217	tCt/tAt	1/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.88698672937607	2		793	808	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440885	52440885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1323972421	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	359	805	0	ENST00000460680.1:c.619C>T	p.Arg207Trp	p.R207W	ENST00000460680	NM_004656.3	207	Cgg/Tgg	8/17	1	2	FACETS	0.994	0.948	1	0.994	0.948	1	CLONAL	1	TRUE	1	0.88698672937607	2		805	814	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72891538	72891538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs529764235	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	44	505	2	ENST00000325599.8:c.224G>A	p.Arg75His	p.R75H	ENST00000325599	NM_018130.2	75	cGc/cAc	3/11	1	2	FACETS	0.163	0.136	0.193	0.163	0.136	0.193	SUBCLONAL	1	TRUE	1	0.88698672937607	2		507	607	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468382	89468382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs570346631	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	196	282	0	ENST00000336596.2:c.1916G>A	p.Arg639His	p.R639H	ENST00000336596	NM_005233.5	639	cGc/cAc	11/17	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.88698672937607	2		282	382	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664654	138664654	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	10	73	0	ENST00000330315.3:c.911C>A	p.Ala304Glu	p.A304E	ENST00000330315	NM_023067.3	304	gCa/gAa	1/1	1	2	FACETS	0.305	0.209	0.421	0.305	0.209	0.421	SUBCLONAL	1	TRUE	1	0.88698672937607	2		73	74	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186799	142186799	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	61	507	0	ENST00000350721.4:c.6664C>A	p.Leu2222Ile	p.L2222I	ENST00000350721	NM_001184.3	2222	Ctt/Att	39/47	1	2	FACETS	0.277	0.239	0.319	0.277	0.239	0.319	SUBCLONAL	1	TRUE	1	0.88698672937607	2		507	496	SUCCESS
ATR	545	MSKCC	GRCh37	3	142212011	142212011	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	276	704	1	ENST00000350721.4:c.6041C>T	p.Ala2014Val	p.A2014V	ENST00000350721	NM_001184.3	2014	gCt/gTt	35/47	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.88698672937607	2		705	619	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268419	142268419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs980426116	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	210	507	0	ENST00000350721.4:c.3073C>T	p.Arg1025Cys	p.R1025C	ENST00000350721	NM_001184.3	1025	Cgt/Tgt	15/47	1	2	FACETS	0.997	0.936	1	0.997	0.936	1	CLONAL	1	TRUE	1	0.88698672937607	2		507	475	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281322	142281322	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	361	763	0	ENST00000350721.4:c.922G>T	p.Glu308Ter	p.E308*	ENST00000350721	NM_001184.3	308	Gaa/Taa	4/47	1	2	FACETS	0.945	0.9	0.991	0.945	0.9	0.991	CLONAL	1	TRUE	1	0.88698672937607	2		763	861	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191256	185191256	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	220	538	0	ENST00000265026.3:c.2137C>T	p.Pro713Ser	p.P713S	ENST00000265026	NM_004721.4	713	Cct/Tct	11/14	1	2	FACETS	0.915	0.859	0.972	0.915	0.859	0.972	CLONAL	1	TRUE	1	0.88698672937607	2		538	542	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504007	186504007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	157	409	0	ENST00000323963.5:c.572G>A	p.Arg191His	p.R191H	ENST00000323963		191	cGt/cAt	6/11	1	2	FACETS	0.894	0.829	0.96	0.894	0.829	0.96	CLONAL	1	TRUE	1	0.88698672937607	2		409	396	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590736	189590736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558374141	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	368	645	2	ENST00000264731.3:c.1301C>T	p.Thr434Met	p.T434M	ENST00000264731	NM_003722.4	434	aCg/aTg	10/14	1	2	FACETS	0.964	0.919	1	0.964	0.919	1	CLONAL	1	TRUE	1	0.88698672937607	2		647	861	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612017	189612017	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	253	553	0	ENST00000264731.3:c.1769C>A	p.Pro590His	p.P590H	ENST00000264731	NM_003722.4	590	cCt/cAt	14/14	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.88698672937607	2		553	563	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131116	55131116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	326	696	0	ENST00000257290.5:c.659C>T	p.Ala220Val	p.A220V	ENST00000257290	NM_006206.4	220	gCt/gTt	5/23	1	2	FACETS	0.984	0.936	1	0.984	0.936	1	CLONAL	1	TRUE	1	0.88698672937607	2		696	747	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589821	55589821	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	80	498	2	ENST00000288135.5:c.1303G>T	p.Glu435Ter	p.E435*	ENST00000288135	NM_000222.2	435	Gag/Tag	8/21	1	2	FACETS	0.285	0.25	0.321	0.285	0.25	0.321	SUBCLONAL	1	TRUE	1	0.88698672937607	2		500	634	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233141	66233141	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs146757388	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	249	627	2	ENST00000273854.3:c.1858C>T	p.Arg620Trp	p.R620W	ENST00000273854	NM_004439.5	620	Cgg/Tgg	10/18	1	2	FACETS	0.855	0.804	0.906	0.855	0.804	0.906	CLONAL	1	TRUE	1	0.88698672937607	2		629	657	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99823053	99823053	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	206	436	0	ENST00000280892.6:c.159C>A	p.His53Gln	p.H53Q	ENST00000280892	NM_001130678.1	53	caC/caA	2/7	1	2	FACETS	0.892	0.835	0.949	0.892	0.835	0.949	CLONAL	1	TRUE	1	0.88698672937607	2		436	521	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156139	106156139	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755979073	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	236	422	0	ENST00000380013.4:c.1040C>T	p.Ala347Val	p.A347V	ENST00000380013	NM_001127208.2	347	gCg/gTg	3/11	1	2	FACETS	0.954	0.898	1	0.954	0.898	1	CLONAL	1	TRUE	1	0.88698672937607	2		422	558	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157882	106157882	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	77	371	0	ENST00000380013.4:c.2783T>A	p.Phe928Tyr	p.F928Y	ENST00000380013	NM_001127208.2	928	tTt/tAt	3/11	1	2	FACETS	0.371	0.327	0.418	0.371	0.327	0.418	SUBCLONAL	1	TRUE	1	0.88698672937607	2		371	468	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519277	187519277	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	253	491	0	ENST00000441802.2:c.12106T>C	p.Tyr4036His	p.Y4036H	ENST00000441802	NM_005245.3	4036	Tat/Cat	23/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.88698672937607	2		491	532	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525533	187525533	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	62	487	0	ENST00000441802.2:c.10546A>G	p.Lys3516Glu	p.K3516E	ENST00000441802	NM_005245.3	3516	Aag/Gag	18/27	1	2	FACETS	0.252	0.218	0.29	0.252	0.218	0.29	SUBCLONAL	1	TRUE	1	0.88698672937607	2		487	554	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531148	187531148	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	35	434	0	ENST00000441802.2:c.9875A>G	p.Asn3292Ser	p.N3292S	ENST00000441802	NM_005245.3	3292	aAt/aGt	15/27	1	2	FACETS	0.141	0.115	0.17	0.141	0.115	0.17	SUBCLONAL	1	TRUE	1	0.88698672937607	2		434	561	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538318	187538318	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs762782942	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	258	680	0	ENST00000441802.2:c.8916A>G	p.Ile2972Met	p.I2972M	ENST00000441802	NM_005245.3	2972	atA/atG	11/27	1	2	FACETS	0.991	0.936	1	0.991	0.936	1	CLONAL	1	TRUE	1	0.88698672937607	2		680	587	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542153	187542153	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771682622	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	265	457	1	ENST00000441802.2:c.5587G>A	p.Ala1863Thr	p.A1863T	ENST00000441802	NM_005245.3	1863	Gcg/Acg	10/27	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.88698672937607	2		458	561	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629339	187629339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202126944	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	472	753	4	ENST00000441802.2:c.1643G>A	p.Arg548His	p.R548H	ENST00000441802	NM_005245.3	548	cGc/cAc	2/27	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.88698672937607	2		757	1006	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31424571	31424571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1186040397	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	368	871	0	ENST00000344624.3:c.3224G>A	p.Arg1075His	p.R1075H	ENST00000344624		1075	cGc/cAc	25/33	1	2	FACETS	0.924	0.88	0.968	0.924	0.88	0.968	CLONAL	1	TRUE	1	0.88698672937607	2		871	898	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161245	56161245	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	224	610	0	ENST00000399503.3:c.1114G>T	p.Asp372Tyr	p.D372Y	ENST00000399503	NM_005921.1	372	Gac/Tac	5/20	1	2	FACETS	0.934	0.877	0.991	0.934	0.877	0.991	CLONAL	1	TRUE	1	0.88698672937607	2		610	541	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178025	56178025	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	285	487	0	ENST00000399503.3:c.2998G>T	p.Asp1000Tyr	p.D1000Y	ENST00000399503	NM_005921.1	1000	Gat/Tat	14/20	1	2	FACETS	0.995	0.943	1	0.995	0.943	1	CLONAL	1	TRUE	1	0.88698672937607	2		487	646	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80063866	80063866	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750261457	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	281	727	1	ENST00000265081.6:c.2011G>A	p.Val671Ile	p.V671I	ENST00000265081	NM_002439.4	671	Gtt/Att	14/24	1	2	FACETS	0.978	0.926	1	0.978	0.926	1	CLONAL	1	TRUE	1	0.88698672937607	2		728	648	SUCCESS
APC	324	MSKCC	GRCh37	5	112102940	112102940	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	260	439	1	ENST00000257430.4:c.275C>T	p.Ser92Phe	p.S92F	ENST00000257430	NM_000038.5	92	tCc/tTc	4/16	1	2	FACETS	0.979	0.925	1	0.979	0.925	1	CLONAL	1	TRUE	1	0.88698672937607	2		440	599	SUCCESS
APC	324	MSKCC	GRCh37	5	112175463	112175463	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	217	388	1	ENST00000257430.4:c.4172G>T	p.Ser1391Ile	p.S1391I	ENST00000257430	NM_000038.5	1391	aGt/aTt	16/16	1	2	FACETS	0.986	0.927	1	0.986	0.927	1	CLONAL	1	TRUE	1	0.88698672937607	2		389	496	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449602	149449602	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	318	776	0	ENST00000286301.3:c.1344G>T	p.Gln448His	p.Q448H	ENST00000286301	NM_005211.3	448	caG/caT	10/22	1	2	FACETS	0.951	0.903	0.999	0.951	0.903	0.999	CLONAL	1	TRUE	1	0.88698672937607	2		776	754	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459795	149459795	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755093010	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	157	752	1	ENST00000286301.3:c.412G>A	p.Val138Ile	p.V138I	ENST00000286301	NM_005211.3	138	Gtc/Atc	4/22	1	2	FACETS	0.482	0.442	0.524	0.482	0.442	0.524	SUBCLONAL	1	TRUE	1	0.88698672937607	2		753	734	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170837564	170837564	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	14	113	0	ENST00000296930.5:c.880C>A	p.Leu294Ile	p.L294I	ENST00000296930	NM_002520.6	294	Ctt/Att	11/11	1	2	FACETS	0.234	0.17	0.31	0.234	0.17	0.31	SUBCLONAL	1	TRUE	1	0.88698672937607	2		113	135	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517526	176517526	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	122	1034	0	ENST00000292408.4:c.227C>A	p.Ala76Asp	p.A76D	ENST00000292408	NM_213647.1	76	gCt/gAt	3/18	1	2	FACETS	0.299	0.269	0.33	0.299	0.269	0.33	SUBCLONAL	1	TRUE	1	0.88698672937607	2		1034	921	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036049	180036049	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs765893009	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	288	676	0	ENST00000261937.6:c.3812A>G	p.Asn1271Ser	p.N1271S	ENST00000261937	NM_182925.4	1271	aAc/aGc	29/30	1	2	FACETS	0.962	0.911	1	0.962	0.911	1	CLONAL	1	TRUE	1	0.88698672937607	2		676	675	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673555	30673555	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	443	880	1	ENST00000376406.3:c.3405G>T	p.Gln1135His	p.Q1135H	ENST00000376406	NM_014641.2	1135	caG/caT	10/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.88698672937607	2		881	971	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679192	30679192	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	284	647	0	ENST00000376406.3:c.2218A>C	p.Thr740Pro	p.T740P	ENST00000376406	NM_014641.2	740	Aca/Cca	7/15	1	2	FACETS	0.993	0.941	1	0.993	0.941	1	CLONAL	1	TRUE	1	0.88698672937607	2		647	645	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948302	31948302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	353	839	1	ENST00000375333.2:c.890G>T	p.Arg297Ile	p.R297I	ENST00000375333	NM_032454.1	297	aGa/aTa	6/8	1	2	FACETS	0.973	0.927	1	0.973	0.927	1	CLONAL	1	TRUE	1	0.88698672937607	2		840	818	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287520	33287520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141395832	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	333	802	2	ENST00000374542.5:c.1577G>A	p.Arg526His	p.R526H	ENST00000374542	NM_001141970.1	526	cGc/cAc	6/8	1	2	FACETS	0.935	0.889	0.982	0.935	0.889	0.982	CLONAL	1	TRUE	1	0.88698672937607	2		804	803	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288764	33288764	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1429735040	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	224	442	0	ENST00000374542.5:c.788G>A	p.Arg263His	p.R263H	ENST00000374542	NM_001141970.1	263	cGc/cAc	3/8	1	2	FACETS	0.892	0.838	0.948	0.892	0.838	0.948	CLONAL	1	TRUE	1	0.88698672937607	2		442	566	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793712	89793712	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	27	446	0	ENST00000336032.3:c.781A>C	p.Asn261His	p.N261H	ENST00000336032	NM_006813.2	261	Aat/Cat	2/2	1	2	FACETS	0.115	0.091	0.143	0.115	0.091	0.143	SUBCLONAL	1	TRUE	1	0.88698672937607	2		446	530	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609665	117609665	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	24	442	0	ENST00000368508.3:c.7034G>T	p.Gly2345Val	p.G2345V	ENST00000368508	NM_002944.2	2345	gGg/gTg	43/43	1	2	FACETS	0.114	0.089	0.143	0.114	0.089	0.143	SUBCLONAL	1	TRUE	1	0.88698672937607	2		442	476	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638416	117638416	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	35	535	0	ENST00000368508.3:c.6025A>G	p.Ile2009Val	p.I2009V	ENST00000368508	NM_002944.2	2009	Att/Gtt	38/43	0.106988225985204	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.88698672937607	0		535	576	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658499	117658499	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	266	682	0	ENST00000368508.3:c.5084A>G	p.Lys1695Arg	p.K1695R	ENST00000368508	NM_002944.2	1695	aAa/aGa	31/43	0.106988225985204	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.88698672937607	0		682	627	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677856	117677856	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs760464623	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	39	413	0	ENST00000368508.3:c.4077G>T	p.Glu1359Asp	p.E1359D	ENST00000368508	NM_002944.2	1359	gaG/gaT	25/43	1	2	FACETS	0.189	0.156	0.226	0.189	0.156	0.226	SUBCLONAL	1	TRUE	1	0.88698672937607	2		413	465	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709017	117709017	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	320	652	1	ENST00000368508.3:c.1940T>A	p.Val647Asp	p.V647D	ENST00000368508	NM_002944.2	647	gTt/gAt	13/43	1	2	FACETS	0.992	0.943	1	0.992	0.943	1	CLONAL	1	TRUE	1	0.88698672937607	2		653	727	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710936	117710936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	236	449	0	ENST00000368508.3:c.1336G>A	p.Ala446Thr	p.A446T	ENST00000368508	NM_002944.2	446	Gct/Act	12/43	1	2	FACETS	0.985	0.929	1	0.985	0.929	1	CLONAL	1	TRUE	1	0.88698672937607	2		449	540	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519461	137519461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777316078	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	212	340	0	ENST00000367739.4:c.1177G>A	p.Ala393Thr	p.A393T	ENST00000367739	NM_000416.2	393	Gct/Act	7/7	1	2	FACETS	0.976	0.916	1	0.976	0.916	1	CLONAL	1	TRUE	1	0.88698672937607	2		340	490	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005704	150005704	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763594987	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	201	436	1	ENST00000253339.5:c.521G>A	p.Arg174His	p.R174H	ENST00000253339		174	cGc/cAc	3/7	1	2	FACETS	0.944	0.884	1	0.944	0.884	1	CLONAL	1	TRUE	1	0.88698672937607	2		437	480	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405986	157405986	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	347	677	1	ENST00000346085.5:c.2228C>T	p.Pro743Leu	p.P743L	ENST00000346085	NM_020732.3	743	cCt/cTt	6/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.88698672937607	2		678	759	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157406022	157406022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	289	556	0	ENST00000346085.5:c.2264C>T	p.Ser755Phe	p.S755F	ENST00000346085	NM_020732.3	755	tCt/tTt	6/20	1	2	FACETS	0.963	0.912	1	0.963	0.912	1	CLONAL	1	TRUE	1	0.88698672937607	2		556	677	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517412	157517412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138785718	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	357	665	0	ENST00000346085.5:c.3976C>T	p.Arg1326Cys	p.R1326C	ENST00000346085	NM_020732.3	1326	Cgc/Tgc	16/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.88698672937607	2		665	779	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268933	55268933	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	404	876	0	ENST00000275493.2:c.2999C>T	p.Ala1000Val	p.A1000V	ENST00000275493	NM_005228.3	1000	gCc/gTc	25/28	0.88698672937607	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.88698672937607	1		876	495	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508152	106508152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1446853033	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	104	230	0	ENST00000359195.3:c.146G>A	p.Arg49His	p.R49H	ENST00000359195	NM_002649.2	49	cGc/cAc	2/11	0.829575718849676	3	FACETS	0.859	0.775	0.946			1	CLONAL	1	TRUE	NA	0.88698672937607	3		230	394	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508635	106508635	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	259	657	1	ENST00000359195.3:c.629A>G	p.Tyr210Cys	p.Y210C	ENST00000359195	NM_002649.2	210	tAc/tGc	2/11	0.829575718849676	3	FACETS	0.884	0.829	0.94			1	CLONAL	1	TRUE	NA	0.88698672937607	3		658	954	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508746	106508746	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	318	577	1	ENST00000359195.3:c.740G>T	p.Ser247Ile	p.S247I	ENST00000359195	NM_002649.2	247	aGc/aTc	2/11	0.829575718849676	3	FACETS	1	0.972	1			1	CLONAL	1	TRUE	NA	0.88698672937607	3		578	993	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395494	116395494	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	87	575	0	ENST00000397752.3:c.1787T>G	p.Phe596Cys	p.F596C	ENST00000397752	NM_000245.2	596	tTt/tGt	6/21	0.829575718849676	3	FACETS	0.325	0.287	0.366			1	SUBCLONAL	1	TRUE	NA	0.88698672937607	3		575	870	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148507488	148507488	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	284	571	1	ENST00000320356.2:c.1966G>T	p.Ala656Ser	p.A656S	ENST00000320356	NM_004456.4	656	Gct/Tct	17/20	1	2	FACETS	0.985	0.933	1	0.985	0.933	1	CLONAL	1	TRUE	1	0.88698672937607	2		572	650	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878813	151878813	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	338	562	0	ENST00000262189.6:c.6132G>T	p.Lys2044Asn	p.K2044N	ENST00000262189	NM_170606.2	2044	aaG/aaT	36/59	1	2	FACETS	0.996	0.948	1	0.996	0.948	1	CLONAL	1	TRUE	1	0.88698672937607	2		562	765	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272353	38272353	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554548253	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	112	707	0	ENST00000425967.3:c.2014G>A	p.Asp672Asn	p.D672N	ENST00000425967	NM_001174067.1	672	Gac/Aac	15/19	1	2	FACETS	0.347	0.312	0.384	0.347	0.312	0.384	SUBCLONAL	1	TRUE	1	0.88698672937607	2		707	728	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864700	68864700	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	29	519	0	ENST00000288368.4:c.71G>A	p.Arg24His	p.R24H	ENST00000288368	NM_024870.2	24	cGc/cAc	1/40	1	2	FACETS	0.135	0.108	0.166	0.135	0.108	0.166	SUBCLONAL	1	TRUE	1	0.88698672937607	2		519	484	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993065	90993065	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	240	516	0	ENST00000265433.3:c.377C>T	p.Thr126Ile	p.T126I	ENST00000265433	NM_002485.4	126	aCt/aTt	4/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.88698672937607	2		516	538	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751226	128751226	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	210	430	0	ENST00000377970.2:c.763C>A	p.Leu255Ile	p.L255I	ENST00000377970	NM_002467.4	255	Ctc/Atc	2/3	1	2	FACETS	0.978	0.918	1	0.978	0.918	1	CLONAL	1	TRUE	1	0.88698672937607	2		430	484	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141545637	141545637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766748578	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	107	950	3	ENST00000220592.5:c.2201C>T	p.Thr734Met	p.T734M	ENST00000220592	NM_012154.3	734	aCg/aTg	17/19	1	2	FACETS	0.228	0.204	0.254	0.228	0.204	0.254	SUBCLONAL	1	TRUE	1	0.88698672937607	2		953	1059	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559375	141559375	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs777032894	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	329	771	0	ENST00000220592.5:c.1426A>C	p.Lys476Gln	p.K476Q	ENST00000220592	NM_012154.3	476	Aag/Cag	12/19	1	2	FACETS	0.943	0.896	0.99	0.943	0.896	0.99	CLONAL	1	TRUE	1	0.88698672937607	2		771	787	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8338977	8338977	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	287	610	1	ENST00000356435.5:c.5324C>T	p.Ala1775Val	p.A1775V	ENST00000356435		1775	gCt/gTt	32/35	1	2	FACETS	0.888	0.839	0.937	0.888	0.839	0.937	CLONAL	1	TRUE	1	0.88698672937607	2		611	729	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504333	8504333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754609275	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	391	694	2	ENST00000356435.5:c.1750C>T	p.Arg584Cys	p.R584C	ENST00000356435		584	Cgt/Tgt	12/35	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.88698672937607	2		696	836	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521451	8521451	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	75	804	1	ENST00000356435.5:c.787C>A	p.Pro263Thr	p.P263T	ENST00000356435		263	Cca/Aca	9/35	1	2	FACETS	0.196	0.171	0.222	0.196	0.171	0.222	SUBCLONAL	1	TRUE	1	0.88698672937607	2		805	865	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971137	21971137	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	53	505	0	ENST00000304494.5:c.221A>G	p.Asp74Gly	p.D74G	ENST00000304494	NM_000077.4	74	gAc/gGc	2/3	1	2	FACETS	0.272	0.232	0.315	0.272	0.232	0.315	SUBCLONAL	1	TRUE	1	0.88698672937607	2		505	440	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317126	87317126	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	288	570	1	ENST00000277120.3:c.265G>T	p.Ala89Ser	p.A89S	ENST00000277120		89	Gct/Tct	3/19	1	2	FACETS	0.975	0.924	1	0.975	0.924	1	CLONAL	1	TRUE	1	0.88698672937607	2		571	666	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97887460	97887460	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	87	602	0	ENST00000289081.3:c.904C>A	p.Leu302Ile	p.L302I	ENST00000289081	NM_000136.2	302	Ctc/Atc	10/15	1	2	FACETS	0.266	0.235	0.299	0.266	0.235	0.299	SUBCLONAL	1	TRUE	1	0.88698672937607	2		602	737	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209511	98209511	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200100952	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	96	671	1	ENST00000331920.6:c.4027G>A	p.Gly1343Arg	p.G1343R	ENST00000331920	NM_000264.3	1343	Ggg/Agg	23/24	1	2	FACETS	0.317	0.283	0.354	0.317	0.283	0.354	SUBCLONAL	1	TRUE	1	0.88698672937607	2		672	682	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391863	139391863	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs894965666	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	370	876	1	ENST00000277541.6:c.6328G>A	p.Val2110Met	p.V2110M	ENST00000277541	NM_017617.3	2110	Gtg/Atg	34/34	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.88698672937607	2		877	812	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412744	139412744	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	288	678	0	ENST00000277541.6:c.1100G>T	p.Gly367Val	p.G367V	ENST00000277541	NM_017617.3	367	gGt/gTt	7/34	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.88698672937607	2		678	623	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413259	139413259	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	313	908	0	ENST00000277541.6:c.883G>T	p.Asp295Tyr	p.D295Y	ENST00000277541	NM_017617.3	295	Gat/Tat	6/34	1	2	FACETS	0.913	0.866	0.961	0.913	0.866	0.961	CLONAL	1	TRUE	1	0.88698672937607	2		908	773	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413936	139413936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	361	938	3	ENST00000277541.6:c.824G>A	p.Gly275Asp	p.G275D	ENST00000277541	NM_017617.3	275	gGc/gAc	5/34	1	2	FACETS	0.967	0.921	1	0.967	0.921	1	CLONAL	1	TRUE	1	0.88698672937607	2		941	842	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913257	39913257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	390	341	0	ENST00000378444.4:c.4858C>T	p.Pro1620Ser	p.P1620S	ENST00000378444	NM_001123385.1	1620	Ccc/Tcc	14/15	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.88698672937607	1		341	438	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923604	39923604	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	287	408	0	ENST00000378444.4:c.3487C>T	p.Arg1163Ter	p.R1163*	ENST00000378444	NM_001123385.1	1163	Cga/Tga	7/15	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.88698672937607	1		408	319	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040672	47040672	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	352	482	0	ENST00000377604.3:c.1307G>T	p.Ser436Ile	p.S436I	ENST00000377604	NM_001204468.1	436	aGc/aTc	13/24	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.88698672937607	1		482	414	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246446	53246446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201805773	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	341	677	1	ENST00000375401.3:c.536G>A	p.Arg179His	p.R179H	ENST00000375401	NM_004187.3	179	cGt/cAt	5/26	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.88698672937607	1		678	369	SUCCESS
AR	367	MSKCC	GRCh37	X	66863204	66863204	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	83	353	0	ENST00000374690.3:c.1723C>A	p.Leu575Ile	p.L575I	ENST00000374690	NM_000044.3	575	Ctc/Atc	2/8	1	1	FACETS	0.283	0.251	0.317	0.283	0.251	0.317	SUBCLONAL	1	TRUE	0	0.88698672937607	1		353	368	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338644	70338644	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	107	401	0	ENST00000374080.3:c.40C>A	p.Leu14Met	p.L14M	ENST00000374080		14	Ctg/Atg	1/45	1	1	FACETS	0.335	0.302	0.369	0.335	0.302	0.369	SUBCLONAL	1	TRUE	0	0.88698672937607	1		401	401	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938974	76938974	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	113	430	0	ENST00000373344.5:c.1774C>A	p.Pro592Thr	p.P592T	ENST00000373344	NM_000489.3	592	Cct/Act	9/35	1	1	FACETS	0.321	0.29	0.353	0.321	0.29	0.353	SUBCLONAL	1	TRUE	0	0.88698672937607	1		430	442	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860070	152860070	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557026564	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	72	399	0	ENST00000406277.2:c.358G>A	p.Val120Met	p.V120M	ENST00000406277	NM_152274.4	120	Gtg/Atg	5/7	1		FACETS		0.188	0.244				SUBCLONAL	1	TRUE	0	0.88698672937607	1		399	420	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11301713	11301713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201601333	NA	P-0024668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	45	707	1	ENST00000361445.4:c.1438G>A	p.Ala480Thr	p.A480T	ENST00000361445	NM_004958.3	480	Gcc/Acc	10/58	1	2	FACETS	0.127	0.106	0.15	0.127	0.106	0.15	SUBCLONAL	1	TRUE	1	0.88698672937607	2		708	798	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0024670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	257	722	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.315160619154591	13	FACETS	1	0.955	1	1	0.955	1	CLONAL	9	TRUE	4	0.315160619154591	13		722	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0024670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	86	780	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.314746526134873	2	FACETS	1	0.961	1	1	0.986	1	CLONAL	3	TRUE	0	0.315160619154591	2		780	165	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120516	2120516	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	26	587	0	ENST00000219476.3:c.1776C>A	p.Ser592Arg	p.S592R	ENST00000219476	NM_000548.3	592	agC/agA	17/42	0.315160619154591	6	FACETS	0.791	0.627	0.979	0.264	0.209	0.327	CLONAL	1	TRUE	3	0.315160619154591	6		587	340	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786440	135786440	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	33	558	0	ENST00000298552.3:c.1090A>G	p.Asn364Asp	p.N364D	ENST00000298552	NM_001162426.1	364	Aat/Gat	11/23	0.167891416897397	2	FACETS	1	0.891	1	0.56	0.46	0.67	INDETERMINATE	1	TRUE	0	0.315160619154591	2		558	187	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0024671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	219	790	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.0647885845317699	3	FACETS	1	0.935	1	1	0.935	1	INDETERMINATE	2	TRUE	1	0.253886636418261	3		790	968	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519980	NA	P-0024671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	82	552	0	ENST00000269305.4:c.528C>G	p.Cys176Trp	p.C176W	ENST00000269305	NM_001126112.2	176	tgC/tgG	5/11	0.253886636418261	1	FACETS	0.998	0.882	1	0.998	0.882	1	CLONAL	1	TRUE	0	0.253886636418261	1		552	565	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457223	67457232	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	GTCCTGGCAG	GTCCTGGCAG	-	novel	NA	P-0024671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	78	442	0	ENST00000327367.4:c.207-6_210del		p.X69_splice	ENST00000327367	NM_005902.3	69			0.253886636418261	1	FACETS	0.922	0.811	1	0.922	0.811	1	CLONAL	1	TRUE	0	0.253886636418261	1		442	582	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199615	138199615	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs371548901	NA	P-0024672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	23	372	0	ENST00000237289.4:c.1033T>C	p.Tyr345His	p.Y345H	ENST00000237289	NM_001270507.1	345	Tac/Cac	7/9	0.28189678822096	5	FACETS	0.432	0.336	0.543	0.144	0.112	0.181	INDETERMINATE	1	TRUE	2	0.553718128393601	5		372	352	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100369	27100369	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs770710220	NA	P-0024672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	233	503	0	ENST00000324856.7:c.4081A>G	p.Met1361Val	p.M1361V	ENST00000324856	NM_006015.4	1361	Atg/Gtg	17/20	0.28189678822096	5	FACETS	1	0.985	1	0.77	0.722	0.819	INDETERMINATE	2	TRUE	2	0.553718128393601	5		503	667	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665213	138665213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	110	638	0	ENST00000330315.3:c.352G>A	p.Glu118Lys	p.E118K	ENST00000330315	NM_023067.3	118	Gag/Aag	1/1	0.235823106960967	2	FACETS	0.56	0.503	0.621	0.28	0.251	0.311	INDETERMINATE	1	TRUE	0	0.468983666745153	2		638	837	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456857	32456857	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	76	432	4	ENST00000332351.3:c.35C>T	p.Pro12Leu	p.P12L	ENST00000332351	NM_024426.4	12	cCg/cTg	1/10	0.245399032624062	1	FACETS	0.483	0.424	0.545	0.483	0.424	0.545	INDETERMINATE	1	TRUE	0	0.468983666745153	1		436	514	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564734	139564735	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0024674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	119	854	0	ENST00000308874.7:c.525_526del	p.Val177AlafsTer106	p.V177Afs*106	ENST00000308874		175	CTc/c	7/10	1	2	FACETS	0.514	0.463	0.568	0.514	0.463	0.568	SUBCLONAL	1	TRUE	1	0.468983666745153	2		854	987	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835651	68835651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	187	588	1	ENST00000261769.5:c.242G>A	p.Gly81Asp	p.G81D	ENST00000261769	NM_004360.3	81	gGt/gAt	3/16	1	2	FACETS	0.989	0.916	1	0.989	0.916	1	CLONAL	1	TRUE	1	0.468983666745153	2		589	806	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027436	48027436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750138	NA	P-0024674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	61	451	0	ENST00000234420.5:c.2314C>T	p.Arg772Trp	p.R772W	ENST00000234420	NM_000179.2	772	Cgg/Tgg	4/10	0.313951252336467	3	FACETS	0.484	0.417	0.557	0.242	0.208	0.279	SUBCLONAL	1	TRUE	1	0.468983666745153	3		451	664	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578552	7578556	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GTACT	GTACT	-	novel	NA	P-0024679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	191	732	0	ENST00000269305.4:c.376-2_378del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		732	839	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0024680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	1162	802	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.181244879994074	23	FACETS	1	0.988	1			1	CLONAL	22	TRUE	NA	0.181244879994074	23		802	1674	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186757	108186757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs864622251	NA	P-0024680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	68	505	1	ENST00000278616.4:c.6115G>A	p.Glu2039Lys	p.E2039K	ENST00000278616	NM_000051.3	2039	Gaa/Aaa	42/63	0.181244879994074	2	FACETS	0.825	0.719	0.938	0.825	0.719	0.938	CLONAL	2	TRUE	0	0.181244879994074	2		506	455	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867536	45867536	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767916267	NA	P-0024680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	44	697	3	ENST00000391945.4:c.772C>T	p.Arg258Trp	p.R258W	ENST00000391945	NM_000400.3	258	Cgg/Tgg	9/23	0.152910703239334	3	FACETS	1	0.842	1	0.502	0.421	0.593	CLONAL	1	TRUE	1	0.181244879994074	3		700	527	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317267	87317267	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1052977316	NA	P-0024680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	101	543	0	ENST00000277120.3:c.292A>G	p.Ile98Val	p.I98V	ENST00000277120		98	Att/Gtt	4/19	0.181244879994074	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.181244879994074	3		543	538	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849924	156849924	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	86	527	0	ENST00000524377.1:c.2180C>A	p.Pro727His	p.P727H	ENST00000524377	NM_002529.3	727	cCc/cAc	16/17	0.181244879994074	6	FACETS	1	0.945	1	0.555	0.492	0.623	CLONAL	2	TRUE	2	0.181244879994074	6		527	582	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877323	28877323	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	54	399	0	ENST00000282397.4:c.3998A>T	p.Tyr1333Phe	p.Y1333F	ENST00000282397	NM_002019.4	1333	tAc/tTc	30/30	0.181244879994074	2	FACETS	0.914	0.785	1	0.914	0.785	1	CLONAL	2	TRUE	0	0.181244879994074	2		399	326	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288854	15288854	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	13	118	0	ENST00000263388.2:c.3885G>C	p.Glu1295Asp	p.E1295D	ENST00000263388	NM_000435.2	1295	gaG/gaC	24/33	0.181244879994074	3	FACETS	1	0.87	1	0.724	0.522	0.966	CLONAL	1	TRUE	1	0.181244879994074	3		118	108	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022254	26022254	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	73	465	0	ENST00000435504.4:c.403G>T	p.Val135Leu	p.V135L	ENST00000435504		135	Gta/Tta	5/13	0.166766736934583	4	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	2	0.181244879994074	4		465	442	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319060	62319060	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	157	612	0	ENST00000360203.5:c.1418G>T	p.Arg473Leu	p.R473L	ENST00000360203	NM_001283009.1	473	cGc/cTc	17/35	0.181244879994074	5	FACETS	1	0.926	1	1	0.926	1	CLONAL	4	TRUE	1	0.181244879994074	5		612	548	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921365	178921365	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	78	603	0	ENST00000263967.3:c.847C>T	p.Pro283Ser	p.P283S	ENST00000263967	NM_006218.2	283	Ccc/Tcc	5/21	0.181244879994074	3	FACETS	0.844	0.743	0.953	0.844	0.743	0.953	CLONAL	2	TRUE	1	0.181244879994074	3		603	556	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193953	106193953	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	29	256	0	ENST00000380013.4:c.4415A>T	p.Lys1472Met	p.K1472M	ENST00000380013	NM_001127208.2	1472	aAg/aTg	10/11	0.166766736934583	4	FACETS	1	0.927	1	0.682	0.549	0.833	CLONAL	1	TRUE	2	0.181244879994074	4		256	277	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106974	11106975	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	320	587	0	ENST00000358026.2:c.1679_1680insT	p.Val561ArgfsTer3	p.V561Rfs*3	ENST00000358026	NM_001128849.1	560	tac/taTc	10/36	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.64	2		587	703	SUCCESS
ATR	545	MSKCC	GRCh37	3	142180921	142180921	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	62	363	0	ENST00000350721.4:c.7053A>T	p.Lys2351Asn	p.K2351N	ENST00000350721	NM_001184.3	2351	aaA/aaT	42/47	1	2	FACETS	0.282	0.243	0.324	0.282	0.243	0.324	SUBCLONAL	1	TRUE	1	0.64	2		363	688	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005301	150005302	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTT	novel	NA	P-0024681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	236	474	0	ENST00000253339.5:c.923_924insAAG	p.Ser308dup	p.S308dup	ENST00000253339		308	tcc/tcAAGc	3/7	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.64	2		474	726	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0024682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1653	2148	547	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.430717688453879	27	FACETS	0.985	0.968	1			1	CLONAL	17	TRUE	NA	0.430717688453879	27		547	3801	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942137	17942137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	71	630	0	ENST00000458235.1:c.2878G>A	p.Glu960Lys	p.E960K	ENST00000458235	NM_000215.3	960	Gag/Aag	21/24	0.430717688453879	3	FACETS	0.486	0.423	0.554	0.243	0.211	0.277	SUBCLONAL	1	TRUE	1	0.430717688453879	3		630	825	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201562	133201562	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	255	554	0	ENST00000320574.5:c.6676G>T	p.Gly2226Trp	p.G2226W	ENST00000320574	NM_006231.2	2226	Ggg/Tgg	48/49	0.430717688453879	3	FACETS	0.983	0.925	1	0.983	0.925	1	CLONAL	2	TRUE	1	0.430717688453879	3		554	732	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579329	7579329	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912658	NA	P-0024682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	264	532	0	ENST00000269305.4:c.358A>G	p.Lys120Glu	p.K120E	ENST00000269305	NM_001126112.2	120	Aag/Gag	4/11	0.305563645584999	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.430717688453879	2		532	577	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992301	72992301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	103	779	0	ENST00000268489.5:c.1744G>A	p.Ala582Thr	p.A582T	ENST00000268489	NM_006885.3	582	Gca/Aca	2/10	0.10105653794951	6	FACETS	0.735	0.656	0.82			1	INDETERMINATE	1	TRUE	NA	0.430717688453879	6		779	1211	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256623	19256623	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	76	223	0	ENST00000162023.5:c.1090G>T	p.Asp364Tyr	p.D364Y	ENST00000162023		364	Gac/Tac	13/13	0.430717688453879	3	FACETS	1	0.913	1	0.522	0.46	0.588	CLONAL	1	TRUE	1	0.430717688453879	3		223	411	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68993003	68993003	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs140494334	NA	P-0024682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	246	475	0	ENST00000288368.4:c.1808A>G	p.Tyr603Cys	p.Y603C	ENST00000288368	NM_024870.2	603	tAt/tGt	17/40	0.269911996103423	5	FACETS	1	0.989	1	0.826	0.775	0.878	CLONAL	2	TRUE	2	0.430717688453879	5		475	759	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169006	32169006	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1489506589	NA	P-0024684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	302	706	0	ENST00000375023.3:c.4027C>T	p.Pro1343Ser	p.P1343S	ENST00000375023	NM_004557.3	1343	Cct/Tct	22/30	0.49227244204333	3	FACETS	1	0.982	1	0.552	0.52	0.586	CLONAL	1	TRUE	1	0.579017520982436	3		706	1218	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221987	1221987	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	420	536	0	ENST00000326873.7:c.903del	p.Gln302ArgfsTer34	p.Q302Rfs*34	ENST00000326873	NM_000455.4	301	cGg/cg	7/10	0.579017520982436	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.579017520982436	2		536	710	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106126	27106126	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	165	496	0	ENST00000324856.7:c.5737G>A	p.Asp1913Asn	p.D1913N	ENST00000324856	NM_006015.4	1913	Gac/Aac	20/20	1	2	FACETS	0.831	0.765	0.899	0.831	0.765	0.899	CLONAL	1	TRUE	1	0.579017520982436	2		496	686	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196917	108196917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	238	426	1	ENST00000278616.4:c.6940C>T	p.Gln2314Ter	p.Q2314*	ENST00000278616	NM_000051.3	2314	Caa/Taa	47/63	0.579017520982436	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.579017520982436	2		427	403	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422729	49422729	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	177	502	0	ENST00000301067.7:c.14264C>G	p.Thr4755Ser	p.T4755S	ENST00000301067	NM_003482.3	4755	aCc/aGc	45/54	0.579017520982436	2	FACETS	1	0.943	1	0.51	0.472	0.549	CLONAL	1	TRUE	0	0.579017520982436	2		502	599	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42050038	42050038	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0024684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	81	348	0	ENST00000219905.7:c.7191+1G>T		p.X2397_splice	ENST00000219905	NM_001164273.1	2397			NA	2	FACETS	0.786	0.71	0.863			1	INDETERMINATE	2	TRUE	NA	0.579017520982436	2		348	178	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602335	10602342	+	frameshift_variant	Frame_Shift_Del	DEL	GGTTACGG	GGTTACGG	-	novel	NA	P-0024684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	517	685	2	ENST00000171111.5:c.1236_1243del	p.Arg413HisfsTer29	p.R413Hfs*29	ENST00000171111	NM_203500.1	412	ccCCGTAACCgc/ccgc	3/6	0.579017520982436	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.579017520982436	2		687	878	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461576	138461576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	317	543	1	ENST00000289153.2:c.445C>T	p.Arg149Ter	p.R149*	ENST00000289153	NM_006219.2	149	Cga/Tga	3/22	0.579017520982436	4	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.579017520982436	4		544	697	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553416	106553416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754668509	NA	P-0024684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	217	281	1	ENST00000369096.4:c.1381C>T	p.Leu461Phe	p.L461F	ENST00000369096	NM_001198.3	461	Ctc/Ttc	5/7	0.579017520982436	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.579017520982436	2		282	352	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0024685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	373	722	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.483575132475909	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.483575132475909	3		722	843	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0024685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	289	515	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.483575132475909	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.483575132475909	3		515	683	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375510	40375510	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768919211	NA	P-0024685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	52	761	1	ENST00000293328.3:c.440C>T	p.Thr147Met	p.T147M	ENST00000293328	NM_012448.3	147	aCg/aTg	5/19	1	2	FACETS	0.272	0.231	0.318	0.272	0.231	0.318	SUBCLONAL	1	TRUE	1	0.483575132475909	2		762	790	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482926	140482927	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs777474487	NA	P-0024685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	160	634	2	ENST00000288602.6:c.1208dup	p.Ala404CysfsTer9	p.A404Cfs*9	ENST00000288602	NM_004333.4	403	cct/ccCt	10/18	1	2	FACETS	0.92	0.846	0.998	0.92	0.846	0.998	CLONAL	1	TRUE	1	0.483575132475909	2		636	719	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716329	52716329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863225094	NA	P-0024685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	172	593	1	ENST00000322088.6:c.773G>A	p.Arg258His	p.R258H	ENST00000322088	NM_014225.5	258	cGc/cAc	6/15	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.483575132475909	2		594	685	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557739	21557739	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	173	698	0	ENST00000382592.4:c.2106G>T	p.Lys702Asn	p.K702N	ENST00000382592	NM_014572.2	702	aaG/aaT	5/8	1	2	FACETS	0.963	0.888	1	0.963	0.888	1	CLONAL	1	TRUE	1	0.483575132475909	2		698	743	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0024687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	143	547	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.604143475442268	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.633071043055989	2		547	216	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0024687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	191	885	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.604143475442268	2	FACETS	0.931	0.88	0.982	0.931	0.88	0.982	CLONAL	2	TRUE	0	0.633071043055989	2		885	324	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111499	8111500	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0024687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	182	899	0	ENST00000346208.3:c.987dup	p.Arg330GlufsTer22	p.R330Efs*22	ENST00000346208		329	agg/aGgg	5/6	0.633071043055989	4	FACETS	0.935	0.87	1	0.935	0.87	1	CLONAL	2	TRUE	2	0.633071043055989	4		899	502	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023601	27023602	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0024687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	76	210	0	ENST00000324856.7:c.708_709insCT	p.Gly237LeufsTer127	p.G237Lfs*127	ENST00000324856	NM_006015.4	236	ggt/ggTCt	1/20	0.633059590258816	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.633071043055989	2		210	110	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101985034	101985034	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	168	991	1	ENST00000282441.5:c.481C>T	p.Arg161Ter	p.R161*	ENST00000282441	NM_001130145.2	161	Cga/Tga	2/9	0.627320443550217	2	FACETS	0.951	0.896	1	0.951	0.896	1	CLONAL	2	TRUE	0	0.633071043055989	2		992	279	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774092	66774092	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0024687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	17	860	0	ENST00000307102.5:c.569-1G>A		p.X190_splice	ENST00000307102	NM_002755.3	190			0.604143475442268	2	FACETS	0.166	0.124	0.217	0.083	0.062	0.109	SUBCLONAL	1	TRUE	0	0.633071043055989	2		860	323	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448347	56448347	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1776	203	841	0	ENST00000407977.2:c.300G>C	p.Glu100Asp	p.E100D	ENST00000407977		100	gaG/gaC	3/10	0.633071043055989	10	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.633071043055989	10		841	1979	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285044	15285044	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	151	547	0	ENST00000263388.2:c.4571T>C	p.Leu1524Pro	p.L1524P	ENST00000263388	NM_000435.2	1524	cTa/cCa	25/33	0.359909279376879	5	FACETS	1	0.98	1	0.785	0.726	0.845	INDETERMINATE	2	TRUE	2	0.633071043055989	5		547	395	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121260	29121260	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs730881703	NA	P-0024687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	194	1086	0	ENST00000328354.6:c.415T>C	p.Tyr139His	p.Y139H	ENST00000328354	NM_007194.3	139	Tac/Cac	3/15	0.312212738357663	5	FACETS	1	0.985	1	0.792	0.739	0.845	INDETERMINATE	2	TRUE	2	0.633071043055989	5		1086	503	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717615	89717615	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909227	NA	P-0024688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	532	496	0	ENST00000371953.3:c.640C>T	p.Gln214Ter	p.Q214*	ENST00000371953	NM_000314.4	214	Cag/Tag	7/9	0.91133872486601	2	FACETS	0.988	0.971	1	0.988	0.971	1	CLONAL	2	TRUE	0	0.916209353333316	2		496	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519998	NA	P-0024688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	1027	579	3	ENST00000269305.4:c.581T>A	p.Leu194His	p.L194H	ENST00000269305	NM_001126112.2	194	cTt/cAt	6/11	0.916209353333316	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.916209353333316	2		582	1091	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878151	48878151	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778869	NA	P-0024688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	144	131	0	ENST00000267163.4:c.103C>T	p.Gln35Ter	p.Q35*	ENST00000267163	NM_000321.2	35	Cag/Tag	1/27	0.720131131699091	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.916209353333316	1		131	160	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976744	2976744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs577877958	NA	P-0024688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	204	816	4	ENST00000396946.4:c.1268G>A	p.Arg423Gln	p.R423Q	ENST00000396946	NM_032415.4	423	cGg/cAg	9/25	1	2	FACETS	0.334	0.308	0.36	0.334	0.308	0.36	SUBCLONAL	1	TRUE	1	0.916209353333316	2		820	1335	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885865	59885865	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	706	615	3	ENST00000259008.2:c.881G>C	p.Arg294Thr	p.R294T	ENST00000259008	NM_032043.2	294	aGa/aCa	7/20	0.916209353333316	2	FACETS	1	0.998	1	0.746	0.727	0.765	CLONAL	1	TRUE	0	0.916209353333316	2		618	1033	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180660	32180660	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	586	755	1	ENST00000375023.3:c.2467G>T	p.Asp823Tyr	p.D823Y	ENST00000375023	NM_004557.3	823	Gac/Tac	16/30	0.476665628417271	3	FACETS	1	0.995	1	0.623	0.599	0.648	INDETERMINATE	1	TRUE	1	0.916209353333316	3		756	1496	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222987	1222987	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	149	585	2	ENST00000326873.7:c.924G>T	p.Trp308Cys	p.W308C	ENST00000326873	NM_000455.4	308	tgG/tgT	8/10	0.516356282673124	1	FACETS	0.958	0.883	1	0.958	0.883	1	CLONAL	1	TRUE	0	0.516356282673124	1		587	447	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948747	71948748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760925109	NA	P-0024689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	134	791	10	ENST00000298229.2:c.3466dup	p.Arg1156ProfsTer59	p.R1156Pfs*59	ENST00000298229	NM_001567.3	1153	-/C	26/28	1	2	FACETS	0.797	0.726	0.872	0.797	0.726	0.872	SUBCLONAL	1	TRUE	1	0.516356282673124	2		801	651	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163295845	163295845	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	131	662	0	ENST00000271452.3:c.4G>A	p.Glu2Lys	p.E2K	ENST00000271452	NM_145697.2	2	Gaa/Aaa	2/14	0.516356282673124	3	FACETS	0.982	0.893	1	0.491	0.446	0.538	CLONAL	1	TRUE	1	0.516356282673124	3		662	650	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456272	32456272	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	191	953	1	ENST00000332351.3:c.620A>T	p.Glu207Val	p.E207V	ENST00000332351	NM_024426.4	207	gAg/gTg	1/10	0.474828426942838	1	FACETS	0.935	0.87	1	0.935	0.87	1	CLONAL	1	TRUE	0	0.516356282673124	1		954	587	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26978108	26978108	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	204	880	0	ENST00000381527.3:c.1285G>C	p.Ala429Pro	p.A429P	ENST00000381527	NM_001260.1	429	Gct/Cct	13/13	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.516356282673124	2		880	744	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582131	95582131	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	125	469	0	ENST00000393063.1:c.1780G>T	p.Val594Phe	p.V594F	ENST00000393063	NM_030621.3	594	Gtt/Ttt	12/28	NA	2	FACETS	1	0.935	1			1	INDETERMINATE	1	TRUE	NA	0.516356282673124	2		469	469	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602686	10602686	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	195	894	0	ENST00000171111.5:c.892A>G	p.Lys298Glu	p.K298E	ENST00000171111	NM_203500.1	298	Aag/Gag	3/6	0.516356282673124	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.516356282673124	1		894	526	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0024691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	208	405	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	0.80436021415833	2		405	515	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0024691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	219	372	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	0.143917859303818	3	FACETS	1	0.991	1	0.684	0.642	0.727	INDETERMINATE	1	TRUE	1	0.80436021415833	3		372	558	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593667	55593669	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	rs1060502543	NA	P-0024691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	1946	519	0	ENST00000288135.5:c.1735_1737del	p.Asp579del	p.D579del	ENST00000288135	NM_000222.2	578	tATGat/tat	11/21	0.80436021415833	10	FACETS	0.949	0.938	0.96			1	CLONAL	9	TRUE	NA	0.80436021415833	10		519	2389	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981130	201981130	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141663834	NA	P-0024691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	314	496	1	ENST00000359651.3:c.209C>T	p.Thr70Met	p.T70M	ENST00000359651		70	aCg/aTg	2/8	0.80436021415833	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.80436021415833	1		497	420	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782854	66782854	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs941943240	NA	P-0024691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	568	442	0	ENST00000307102.5:c.1083C>G	p.Ile361Met	p.I361M	ENST00000307102	NM_002755.3	361	atC/atG	11/11	0.714157302039287	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.80436021415833	3		442	963	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409993	63409994	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0024691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	162	391	0	ENST00000330258.3:c.3173_3174delinsAG	p.Pro1058Gln	p.P1058Q	ENST00000330258	NM_152424.3	1058	cCC/cAG	2/2	0.263224553888965	1	FACETS	0.533	0.493	0.573	0.533	0.493	0.573	INDETERMINATE	1	TRUE	0	0.80436021415833	1		391	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0024692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	407	802	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.319665738042809	3	FACETS	0.96	0.917	1	0.96	0.917	1	CLONAL	3	TRUE	0	0.319665738042809	3		802	1025	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0024692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	51	314	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	1	2	FACETS	0.881	0.752	1	0.881	0.752	1	CLONAL	1	TRUE	1	0.319665738042809	2		314	362	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352575	89352575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1301722354	NA	P-0024692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	168	457	1	ENST00000301030.4:c.764G>A	p.Arg255Gln	p.R255Q	ENST00000301030	NM_001256183.1	255	cGg/cAg	8/13	0.319665738042809	5	FACETS	1	0.971	1	0.739	0.681	0.8	CLONAL	2	TRUE	2	0.319665738042809	5		458	701	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884908	134884908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202034365	NA	P-0024692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	147	628	2	ENST00000398015.3:c.1684G>A	p.Val562Ile	p.V562I	ENST00000398015	NM_004441.4	562	Gtc/Atc	8/16	0.319665738042809	3	FACETS	0.828	0.758	0.901	0.828	0.758	0.901	CLONAL	2	TRUE	1	0.319665738042809	3		630	644	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120544	2120545	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0024692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	304	940	0	ENST00000219476.3:c.1807_1808dup	p.Leu604ProfsTer95	p.L604Pfs*95	ENST00000219476	NM_000548.3	602	tac/tACac	17/42	0.291641021385547	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.319665738042809	2		940	844	SUCCESS
APC	324	MSKCC	GRCh37	5	112176018	112176018	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	44	380	0	ENST00000257430.4:c.4728del	p.Glu1577AsnfsTer73	p.E1577Nfs*73	ENST00000257430	NM_000038.5	1576	gAa/ga	16/16	1	2	FACETS	0.842	0.709	0.988	0.842	0.709	0.988	CLONAL	1	TRUE	1	0.319665738042809	2		380	327	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	63	571	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.971	0.851	1	0.971	0.851	1	CLONAL	1	TRUE	1	0.549885709193213	2		571	236	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711891	89711891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	90	618	0	ENST00000371953.3:c.509G>A	p.Ser170Asn	p.S170N	ENST00000371953	NM_000314.4	170	aGt/aAt	6/9	0.549885709193213	1	FACETS	0.818	0.735	0.905	0.818	0.735	0.905	CLONAL	1	TRUE	0	0.549885709193213	1		618	290	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27190655	27190655	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334811	NA	P-0024694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	31	740	1	ENST00000380036.4:c.1456G>A	p.Val486Ile	p.V486I	ENST00000380036	NM_000459.3	486	Gtt/Att	10/23	0.525764785719292	0	FACETS	0.23	0.187	0.278			1	SUBCLONAL	1	TRUE	0	0.549885709193213	0		741	221	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593346	67593346	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	85	493	0	ENST00000274335.5:c.2092T>A	p.Tyr698Asn	p.Y698N	ENST00000274335		698	Tac/Aac	15/15	0.113614300920693	3	FACETS	1	0.962	1	0.59	0.526	0.657	INDETERMINATE	1	TRUE	1	0.549885709193213	3		493	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0024695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	92	683	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.175083057036191	2	FACETS	1	0.972	1	0.643	0.573	0.718	CLONAL	1	TRUE	0	0.26	2		683	550	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81957187	81957187	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	112	472	0	ENST00000359376.3:c.2405A>T	p.Glu802Val	p.E802V	ENST00000359376	NM_002661.3	802	gAg/gTg	22/33	0.175083057036191	2	FACETS	0.779	0.703	0.859	0.779	0.703	0.859	SUBCLONAL	2	TRUE	0	0.26	2		472	553	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038894	47038894	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	47	652	0	ENST00000377604.3:c.901A>T	p.Thr301Ser	p.T301S	ENST00000377604	NM_001204468.1	301	Acc/Tcc	9/24	0.114334225754186	4	FACETS	0.589	0.496	0.693	0.295	0.248	0.347	INDETERMINATE	1	TRUE	2	0.26	4		652	773	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0024722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	239	588	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.345363010936111	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.392763809390787	4		588	715	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78704456	78704469	+	frameshift_variant	Frame_Shift_Del	DEL	ATCGTCAAGTCCTT	ATCGTCAAGTCCTT	-	novel	NA	P-0024722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	88	465	0	ENST00000306801.3:c.604_617del	p.Ile202GlnfsTer55	p.I202Qfs*55	ENST00000306801	NM_020761.2	202	ATCGTCAAGTCCTTc/c	5/34	0.392763809390787	4	FACETS	0.777	0.688	0.873	0.389	0.344	0.437	SUBCLONAL	1	TRUE	2	0.392763809390787	4		465	803	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52729039	52729039	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	138	547	0	ENST00000322088.6:c.1731C>A	p.Tyr577Ter	p.Y577*	ENST00000322088	NM_014225.5	577	taC/taA	14/15	0.392763809390787	3	FACETS	1	0.957	1	0.542	0.494	0.593	CLONAL	1	TRUE	1	0.392763809390787	3		547	775	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161665	56161667	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	novel	NA	P-0024722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	259	492	0	ENST00000399503.3:c.1164_1166del	p.Leu388del	p.L388del	ENST00000399503	NM_005921.1	388	TTG/-	6/20	0.392763809390787	5	FACETS	1	0.97	1	0.704	0.66	0.75	CLONAL	2	TRUE	2	0.392763809390787	5		492	992	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179493	56179493	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	205	324	0	ENST00000399503.3:c.3806del	p.Met1269ArgfsTer6	p.M1269Rfs*6	ENST00000399503	NM_005921.1	1269	aTg/ag	15/20	0.392763809390787	5	FACETS	0.859	0.801	0.918	0.859	0.801	0.918	CLONAL	3	TRUE	2	0.392763809390787	5		324	644	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32814982	32814982	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0024722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	102	499	0	ENST00000354258.4:c.2084-1G>C		p.X695_splice	ENST00000354258	NM_000593.5	695			0.392763809390787	4	FACETS	0.931	0.832	1	0.466	0.416	0.518	CLONAL	1	TRUE	2	0.392763809390787	4		499	777	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0024725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	300	588	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.452531078402297	4	FACETS	0.921	0.876	0.966	1	0.994	1	CLONAL	3	FALSE	2	0.563129725101426	4		588	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0024725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	149	698	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.559688900872004	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	0	0.563129725101426	1		698	333	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372022	55372022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	18	492	2	ENST00000297316.4:c.712G>A	p.Ala238Thr	p.A238T	ENST00000297316	NM_022454.3	238	Gcc/Acc	2/2	0.444582783496648	3	FACETS	0.414	0.312	0.532	0.138	0.104	0.178	SUBCLONAL	1	FALSE	0	0.563129725101426	3		494	198	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0024735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	133	971	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.809	0.736	0.887	1	0.988	1	CLONAL	2	FALSE	1	0.21312422941063	2		973	771	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842633	68842633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	100	886	0	ENST00000261769.5:c.569A>G	p.Tyr190Cys	p.Y190C	ENST00000261769	NM_004360.3	190	tAc/tGc	5/16	0.109017288116901	3	FACETS	1	0.977	1	0.68	0.607	0.757	INDETERMINATE	1	FALSE	1	0.21312422941063	3		886	764	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861055	35861055	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	26	509	0	ENST00000303115.3:c.184C>A	p.Pro62Thr	p.P62T	ENST00000303115	NM_002185.3	62	Cca/Aca	2/8	1	2	FACETS	0.563	0.446	0.699	0.563	0.446	0.699	SUBCLONAL	1	FALSE	1	0.21312422941063	2		509	433	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844214	68844215	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGGGGTC	novel	NA	P-0024735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	43	808	0	ENST00000261769.5:c.803_809dup	p.Val271GlyfsTer24	p.V271Gfs*24	ENST00000261769	NM_004360.3	268	aag/aAGGGGTCag	6/16	0.109017288116901	3	FACETS	0.692	0.578	0.819	0.346	0.289	0.41	INDETERMINATE	1	FALSE	1	0.21312422941063	3		808	645	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286746	212286746	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	55	511	0	ENST00000342788.4:c.2950T>C	p.Tyr984His	p.Y984H	ENST00000342788	NM_005235.2	984	Tac/Cac	24/28	0.141843229555635	3	FACETS	1	0.908	1	0.541	0.463	0.626	CLONAL	1	FALSE	1	0.21312422941063	3		511	528	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0024737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	54	790	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.557	0.475	0.648	0.557	0.475	0.648	SUBCLONAL	1	TRUE	1	0.25	2		790	775	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0024737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	25	654	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	1	2	FACETS	0.418	0.329	0.522	0.418	0.329	0.522	SUBCLONAL	1	TRUE	1	0.25	2		654	478	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	175	855	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.244795940456419	5	FACETS	1	0.984	1	0.831	0.767	0.898	CLONAL	2	TRUE	2	0.244795940456419	5		855	784	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0024739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	112	971	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.184766523355132	2	FACETS	0.839	0.758	0.925	0.839	0.758	0.925	CLONAL	2	TRUE	0	0.244795940456419	2		973	545	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851697	134851697	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370730579	NA	P-0024739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	47	485	0	ENST00000398015.3:c.1103G>A	p.Arg368Gln	p.R368Q	ENST00000398015	NM_004441.4	368	cGg/cAg	5/16	0.244795940456419	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.244795940456419	1		485	287	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482649	56482649	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs200211366	NA	P-0024739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	167	631	0	ENST00000267101.3:c.1106A>G	p.Asn369Ser	p.N369S	ENST00000267101	NM_001982.3	369	aAt/aGt	9/28	0.244795940456419	5	FACETS	0.973	0.898	1	0.973	0.898	1	CLONAL	3	TRUE	2	0.244795940456419	5		631	639	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31379416	31379416	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	30	500	0	ENST00000328111.2:c.823G>T	p.Asp275Tyr	p.D275Y	ENST00000328111	NM_006892.3	275	Gac/Tac	8/23	1	2	FACETS	0.729	0.589	0.889	0.729	0.589	0.889	SUBCLONAL	1	TRUE	1	0.244795940456419	2		500	336	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	122	629	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.268578645092292	1	FACETS	0.444	0.401	0.489	0.444	0.401	0.489	INDETERMINATE	1	TRUE	0	0.538227641868267	1		629	746	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0024741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	343	617	0	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	0.538227641868267	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.538227641868267	1		617	779	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412110	63412110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852216	NA	P-0024742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	292	1050	1	ENST00000330258.3:c.1057C>T	p.Arg353Ter	p.R353*	ENST00000330258	NM_152424.3	353	Cga/Tga	2/2	0.199215384100804	1	FACETS	0.499	0.472	0.526	0.499	0.472	0.526	INDETERMINATE	1	TRUE	0	0.907747030927265	1		1051	704	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22123602	22123602	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	316	524	0	ENST00000215832.6:c.974C>A	p.Ala325Asp	p.A325D	ENST00000215832	NM_002745.4	325	gCc/gAc	8/9	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.907747030927265	2		524	670	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0024743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	85	555	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	1	2	FACETS	0.6	0.53	0.674	0.6	0.53	0.674	SUBCLONAL	1	TRUE	1	0.422961828641981	2		555	670	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591132	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	rs1057519842	NA	P-0024743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	61	257	0	ENST00000274335.5:c.1727_1729del	p.Thr576del	p.T576del	ENST00000274335		575	aaGACg/aag	12/15	1	2	FACETS	0.642	0.555	0.736	0.642	0.555	0.736	SUBCLONAL	1	TRUE	1	0.422961828641981	2		257	449	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0024743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	63	366	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	0.564	0.488	0.646	0.564	0.488	0.646	SUBCLONAL	1	TRUE	1	0.422961828641981	2		366	528	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052632	42052632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779811318	NA	P-0024743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	127	483	1	ENST00000219905.7:c.7303C>T	p.Arg2435Trp	p.R2435W	ENST00000219905	NM_001164273.1	2435	Cgg/Tgg	20/24	1	2	FACETS	0.686	0.621	0.754	0.686	0.621	0.754	SUBCLONAL	1	TRUE	1	0.422961828641981	2		484	876	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653820	89653820	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs869312778	NA	P-0024743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	225	473	0	ENST00000371953.3:c.118G>T	p.Glu40Ter	p.E40*	ENST00000371953	NM_000314.4	40	Gaa/Taa	2/9	0.267844506431524	3	FACETS	0.914	0.855	0.974	0.609	0.57	0.65	CLONAL	2	TRUE	0	0.422961828641981	3		473	705	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645982	67645982	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0024743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	166	548	1	ENST00000264010.4:c.910A>T	p.Arg304Ter	p.R304*	ENST00000264010	NM_006565.3	304	Aga/Tga	4/12	1	2	FACETS	0.793	0.728	0.861	0.793	0.728	0.861	SUBCLONAL	1	TRUE	1	0.422961828641981	2		549	990	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755406	39755406	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	99	603	0	ENST00000288319.7:c.1359G>A	p.Trp453Ter	p.W453*	ENST00000288319	NM_182918.3	453	tgG/tgA	10/10	1	2	FACETS	0.528	0.47	0.589	0.528	0.47	0.589	SUBCLONAL	1	TRUE	1	0.422961828641981	2		603	887	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987114	69987114	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145387068	NA	P-0024745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	93	474	0	ENST00000394351.3:c.175G>A	p.Asp59Asn	p.D59N	ENST00000394351	NM_000248.3	59	Gat/Aat	2/9	1	2	FACETS	0.946	0.844	1	0.946	0.844	1	CLONAL	1	FALSE	1	0.381938314843271	2		474	515	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596002	43596002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876658284	NA	P-0024745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	189	576	1	ENST00000355710.3:c.169C>T	p.Arg57Trp	p.R57W	ENST00000355710	NM_020975.4	57	Cgg/Tgg	2/20	0.381938314843271	3	FACETS	0.934	0.867	1	0.934	0.867	1	CLONAL	2	FALSE	1	0.381938314843271	3		577	631	SUCCESS
APC	324	MSKCC	GRCh37	5	112174094	112174095	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs863225332	NA	P-0024745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	43	340	1	ENST00000257430.4:c.2804dup	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	tac/tAac	16/16	1	2	FACETS	0.904	0.763	1	0.904	0.763	1	CLONAL	1	FALSE	1	0.381938314843271	2		341	249	SUCCESS
APC	324	MSKCC	GRCh37	5	112175770	112175770	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	46	251	0	ENST00000257430.4:c.4480del	p.Glu1494LysfsTer13	p.E1494Kfs*13	ENST00000257430	NM_000038.5	1493	acG/ac	16/16	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	FALSE	1	0.381938314843271	2		251	232	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119966	70120018	+	frameshift_variant	Frame_Shift_Del	DEL	GCACCGCGGCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAG	GCACCGCGGCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAG	-	novel	NA	P-0024745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	46	246	0	ENST00000245479.2:c.970_1022del	p.Thr324AlafsTer236	p.T324Afs*236	ENST00000245479	NM_000346.3	323	aGCACCGCGGCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAG/a	3/3	0.381938314843271	2	FACETS	1	0.93	1	0.582	0.496	0.675	CLONAL	1	FALSE	0	0.381938314843271	2		246	207	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549357	21549357	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	64	483	1	ENST00000382592.4:c.2919C>A	p.Phe973Leu	p.F973L	ENST00000382592	NM_014572.2	973	ttC/ttA	8/8	0.381938314843271	3	FACETS	0.7	0.607	0.802	0.35	0.303	0.401	SUBCLONAL	1	FALSE	1	0.381938314843271	3		484	570	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562128	21562128	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	194	1018	2	ENST00000382592.4:c.1791C>A	p.Tyr597Ter	p.Y597*	ENST00000382592	NM_014572.2	597	taC/taA	4/8	0.381938314843271	3	FACETS	1	0.965	1	0.538	0.497	0.581	CLONAL	1	FALSE	1	0.381938314843271	3		1020	1124	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350636	89350636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750596755	NA	P-0024745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	52	1084	2	ENST00000301030.4:c.2314C>T	p.Arg772Trp	p.R772W	ENST00000301030	NM_001256183.1	772	Cgg/Tgg	9/13	0.381938314843271	3	FACETS	0.377	0.319	0.44	0.188	0.159	0.22	SUBCLONAL	1	FALSE	1	0.381938314843271	3		1086	861	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618525	37618525	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	80	497	0	ENST00000447079.4:c.201C>G	p.Ile67Met	p.I67M	ENST00000447079	NM_015083.1	67	atC/atG	1/14	0.357700716470562	4	FACETS	0.858	0.755	0.968	0.286	0.251	0.323	CLONAL	1	FALSE	1	0.381938314843271	4		497	675	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577524	7577524	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	428	719	0	ENST00000269305.4:c.757A>G	p.Thr253Ala	p.T253A	ENST00000269305	NM_001126112.2	253	Acc/Gcc	7/11	0.892322937573169	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.892322937573169	2		719	463	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692800	89692800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204856	NA	P-0024746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	202	433	0	ENST00000371953.3:c.284C>T	p.Pro95Leu	p.P95L	ENST00000371953	NM_000314.4	95	cCa/cTa	5/9	0.892322937573169	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.892322937573169	1		433	239	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244377	46244377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	143	482	0	ENST00000334344.6:c.2471C>T	p.Thr824Ile	p.T824I	ENST00000334344	NM_152641.2	824	aCa/aTa	15/21	1	2	FACETS	0.672	0.617	0.729	0.672	0.617	0.729	SUBCLONAL	1	TRUE	1	0.892322937573169	2		482	477	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954187	48954187	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	rs1555286568	NA	P-0024746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	197	384	0	ENST00000267163.4:c.1390-2A>C		p.X464_splice	ENST00000267163	NM_000321.2	464			NA	2	FACETS	0.948	0.914	0.978			1	INDETERMINATE	2	TRUE	NA	0.892322937573169	2		384	233	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003122	42003122	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0024747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	487	734	0	ENST00000219905.7:c.2659A>T	p.Lys887Ter	p.K887*	ENST00000219905	NM_001164273.1	887	Aaa/Taa	8/24	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.623501536688807	2		734	1529	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317533	1317533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199794164	NA	P-0024747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	427	631	0	ENST00000400841.2:c.532G>A	p.Glu178Lys	p.E178K	ENST00000400841		178	Gag/Aag	5/6	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.623501536688807	2		631	1355	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0024750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	191	802	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.759	0.701	0.819	1	0.99	1	SUBCLONAL	2	TRUE	1	0.244443538304778	2		802	1030	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129430	64129430	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	96	696	1	ENST00000334205.4:c.862G>T	p.Gly288Trp	p.G288W	ENST00000334205	NM_003942.2	288	Ggg/Tgg	8/17	1	2	FACETS	0.715	0.636	0.801	0.715	0.636	0.801	SUBCLONAL	1	TRUE	1	0.244443538304778	2		697	1098	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0024750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	101	684	0	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	0.239076161501299	1	FACETS	0.768	0.685	0.856	0.768	0.685	0.856	SUBCLONAL	1	TRUE	0	0.244443538304778	1		684	945	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942053	71942053	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	72	679	4	ENST00000298229.2:c.1322del	p.Asn441ThrfsTer2	p.N441Tfs*2	ENST00000298229	NM_001567.3	439	ccA/cc	12/28	1	2	FACETS	0.591	0.515	0.674	0.591	0.515	0.674	SUBCLONAL	1	TRUE	1	0.244443538304778	2		683	997	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155394	47155394	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	75	477	0	ENST00000409792.3:c.4687G>T	p.Gly1563Cys	p.G1563C	ENST00000409792	NM_014159.6	1563	Ggc/Tgc	5/21	0.239076161501299	1	FACETS	0.772	0.676	0.875	0.772	0.676	0.875	SUBCLONAL	1	TRUE	0	0.244443538304778	1		477	698	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250223	133250223	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1190891892	NA	P-0024750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	125	642	0	ENST00000320574.5:c.1297G>T	p.Gly433Cys	p.G433C	ENST00000320574	NM_006231.2	433	Ggc/Tgc	13/49	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.244443538304778	2		642	1013	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38616968	38616968	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	72	364	0	ENST00000299084.4:c.384del	p.Glu129AsnfsTer23	p.E129Nfs*23	ENST00000299084	NM_152594.2	127	tgC/tg	4/7	1	2	FACETS	0.818	0.714	0.931	0.818	0.714	0.931	CLONAL	1	TRUE	1	0.244443538304778	2		364	720	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221279	1221279	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	113	717	0	ENST00000326873.7:c.804del	p.Lys269ArgfsTer18	p.K269Rfs*18	ENST00000326873	NM_000455.4	268	Ggg/gg	6/10	0.244443538304778	1	FACETS	0.907	0.815	1	0.907	0.815	1	CLONAL	1	TRUE	0	0.244443538304778	1		717	895	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170475	11170475	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	102	687	0	ENST00000358026.2:c.4778G>C	p.Arg1593Pro	p.R1593P	ENST00000358026	NM_001128849.1	1593	cGg/cCg	34/36	0.244443538304778	1	FACETS	0.81	0.724	0.903	0.81	0.724	0.903	CLONAL	1	TRUE	0	0.244443538304778	1		687	904	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874008	151874008	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	84	478	0	ENST00000262189.6:c.8530G>T	p.Glu2844Ter	p.E2844*	ENST00000262189	NM_170606.2	2844	Gag/Tag	38/59	1	2	FACETS	0.751	0.662	0.847	0.751	0.662	0.847	SUBCLONAL	1	TRUE	1	0.244443538304778	2		478	915	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29195903	29195903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180215862	NA	P-0024750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	132	691	1	ENST00000240100.2:c.695G>A	p.Cys232Tyr	p.C232Y	ENST00000240100	NM_001394.6	232	tGc/tAc	3/4	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.244443538304778	2		692	1069	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236104	108236104	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	62	508	1	ENST00000278616.4:c.9040C>T	p.Gln3014Ter	p.Q3014*	ENST00000278616	NM_000051.3	3014	Caa/Taa	63/63	0.621068132790214	1	FACETS	0.312	0.27	0.358	0.312	0.27	0.358	SUBCLONAL	1	TRUE	0	0.621068132790214	1		509	441	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549388	21549388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	264	389	0	ENST00000382592.4:c.2888G>A	p.Gly963Glu	p.G963E	ENST00000382592	NM_014572.2	963	gGg/gAg	8/8	1	2	FACETS	0.907	0.855	0.961	0.907	0.855	0.961	CLONAL	1	TRUE	1	0.78	2		389	746	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0024755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	84	555	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.294507361320309	5	FACETS	1	0.93	1	0.269	0.237	0.303	CLONAL	1	TRUE	1	0.294507361320309	5		555	764	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	308	915	1	ENST00000269305.4:c.880del	p.Glu294SerfsTer51	p.E294Sfs*51	ENST00000269305	NM_001126112.2	294	Gag/ag	8/11	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	2	TRUE	NA	0.294507361320309	2		916	936	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121909229	NA	P-0024755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	126	814	3	ENST00000371953.3:c.389G>T	p.Arg130Leu	p.R130L	ENST00000371953	NM_000314.4	130	cGa/cTa	5/9	0.270893420386624	2	FACETS	0.794	0.722	0.869	0.794	0.722	0.869	SUBCLONAL	2	TRUE	0	0.294507361320309	2		817	539	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625249	69625249	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781935233	NA	P-0024755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	143	738	0	ENST00000334134.2:c.544G>A	p.Val182Met	p.V182M	ENST00000334134	NM_005247.2	182	Gtg/Atg	3/3	0.294507361320309	2	FACETS	1	0.967	1	0.562	0.512	0.614	CLONAL	1	TRUE	0	0.294507361320309	2		738	864	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212248	5212248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776677741	NA	P-0024755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	81	491	1	ENST00000357368.4:c.4783C>T	p.Arg1595Cys	p.R1595C	ENST00000357368	NM_002850.3	1595	Cgc/Tgc	32/38	1	2	FACETS	0.809	0.713	0.912	0.809	0.713	0.912	CLONAL	1	TRUE	1	0.294507361320309	2		492	680	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307961	11307961	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	98	487	0	ENST00000361445.4:c.1031G>T	p.Gly344Val	p.G344V	ENST00000361445	NM_004958.3	344	gGa/gTa	7/58	0.231842905233817	3	FACETS	1	0.939	1	0.538	0.48	0.6	CLONAL	1	TRUE	1	0.294507361320309	3		487	709	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940731	71940731	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	234	655	0	ENST00000298229.2:c.778G>T	p.Glu260Ter	p.E260*	ENST00000298229	NM_001567.3	260	Gaa/Taa	7/28	0.294507361320309	2	FACETS	0.906	0.847	0.967	0.906	0.847	0.967	CLONAL	2	TRUE	0	0.294507361320309	2		655	877	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448161	49448161	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	134	567	2	ENST00000301067.7:c.439G>A	p.Ala147Thr	p.A147T	ENST00000301067	NM_003482.3	147	Gca/Aca	4/54	0.231242775884759	3	FACETS	1	0.961	1	0.555	0.503	0.609	CLONAL	1	TRUE	1	0.294507361320309	3		569	941	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127599	2127599	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	151	554	0	ENST00000219476.3:c.2838T>G	p.Ser946Arg	p.S946R	ENST00000219476	NM_000548.3	946	agT/agG	26/42	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.294507361320309	2		554	794	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245933	5245933	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	129	788	1	ENST00000357368.4:c.842G>T	p.Gly281Val	p.G281V	ENST00000357368	NM_002850.3	281	gGg/gTg	10/38	1	2	FACETS	0.853	0.772	0.938	0.853	0.772	0.938	CLONAL	1	TRUE	1	0.294507361320309	2		789	1027	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306605	41306605	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	227	653	1	ENST00000373198.4:c.1054C>A	p.Pro352Thr	p.P352T	ENST00000373198	NM_133170.3	352	Ccc/Acc	7/32	0.147438243365932	3	FACETS	0.921	0.859	0.985			1	INDETERMINATE	2	TRUE	NA	0.294507361320309	3		654	960	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246446	53246446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201805773	NA	P-0024756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	360	677	1	ENST00000375401.3:c.536G>A	p.Arg179His	p.R179H	ENST00000375401	NM_004187.3	179	cGt/cAt	5/26	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.715439863553911	2		678	959	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0024756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	209	588	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.939	0.877	1	0.939	0.877	1	CLONAL	1	TRUE	1	0.715439863553911	2		588	622	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692892	89692892	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554898129	NA	P-0024756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	425	370	1	ENST00000371953.3:c.376G>T	p.Ala126Ser	p.A126S	ENST00000371953	NM_000314.4	126	Gct/Tct	5/9	0.715439863553911	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.715439863553911	2		371	587	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0024756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	215	348	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.837	0.781	0.895	0.837	0.781	0.895	CLONAL	1	TRUE	1	0.715439863553911	2		348	718	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0024756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	264	586	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.842	0.792	0.895	0.842	0.792	0.895	CLONAL	1	TRUE	1	0.715439863553911	2		586	876	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0024756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	306	479	1	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	0.715439863553911	2		480	837	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429977	78429978	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1200882279	NA	P-0024756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	252	506	2	ENST00000370768.2:c.901dup	p.Ile301AsnfsTer4	p.I301Nfs*4	ENST00000370768	NM_003902.3	301	ata/aAta	11/20	1	2	FACETS	0.875	0.821	0.93	0.875	0.821	0.93	CLONAL	1	TRUE	1	0.715439863553911	2		508	805	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850705	63850705	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs201178069	NA	P-0024756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	214	361	1	ENST00000279873.7:c.1489del	p.Ile497Ter	p.I497*	ENST00000279873	NM_032199.2	495	Aaa/aa	10/10	0.715439863553911	2	FACETS	0.929	0.868	0.991	0.464	0.434	0.496	CLONAL	1	TRUE	0	0.715439863553911	2		362	644	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796883	42796883	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	424	885	4	ENST00000575354.2:c.3347del	p.Pro1116GlnfsTer45	p.P1116Qfs*45	ENST00000575354	NM_015125.3	1114	gCc/gc	14/20	1	2	FACETS	0.892	0.85	0.935	0.892	0.85	0.935	CLONAL	1	TRUE	1	0.715439863553911	2		889	1329	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625251	69625251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782147248	NA	P-0024756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	407	755	2	ENST00000334134.2:c.542G>A	p.Arg181His	p.R181H	ENST00000334134	NM_005247.2	181	cGc/cAc	3/3	1	2	FACETS	0.992	0.945	1	0.992	0.945	1	CLONAL	1	TRUE	1	0.715439863553911	2		757	1147	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794441	42794441	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	493	923	2	ENST00000575354.2:c.1526del	p.Pro509HisfsTer14	p.P509Hfs*14	ENST00000575354	NM_015125.3	507	cgC/cg	10/20	1	2	FACETS	0.948	0.907	0.989	0.948	0.907	0.989	CLONAL	1	TRUE	1	0.715439863553911	2		925	1454	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630626	158630626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912678	NA	P-0024756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	177	307	2	ENST00000263640.3:c.617G>A	p.Arg206His	p.R206H	ENST00000263640	NM_001105.4	206	cGc/cAc	6/11	1	2	FACETS	0.932	0.865	1	0.932	0.865	1	CLONAL	1	TRUE	1	0.715439863553911	2		309	531	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971080	21971080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	131	197	0	ENST00000304494.5:c.278C>T	p.Thr93Met	p.T93M	ENST00000304494	NM_000077.4	93	aCg/aTg	2/3	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.715439863553911	2		197	331	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106102	27106132	+	frameshift_variant	Frame_Shift_Del	DEL	AAACGGATCACAGCCACTATGGATGACATGT	AAACGGATCACAGCCACTATGGATGACATGT	-	novel	NA	P-0024756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	240	515	0	ENST00000324856.7:c.5713_5743del	p.Lys1905CysfsTer8	p.K1905Cfs*8	ENST00000324856	NM_006015.4	1905	AAACGGATCACAGCCACTATGGATGACATGTtg/tg	20/20	1	2	FACETS	0.849	0.796	0.904	0.849	0.796	0.904	CLONAL	1	TRUE	1	0.715439863553911	2		515	790	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622119	43622119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	303	547	2	ENST00000355710.3:c.3136G>A	p.Ala1046Thr	p.A1046T	ENST00000355710	NM_020975.4	1046	Gcc/Acc	19/20	1	2	FACETS	0.904	0.854	0.955	0.904	0.854	0.955	CLONAL	1	TRUE	1	0.715439863553911	2		549	937	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104356897	104356897	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs769755064	NA	P-0024756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	246	501	1	ENST00000369902.3:c.757G>A	p.Glu253Lys	p.E253K	ENST00000369902	NM_016169.3	253	Gag/Aag	7/12	0.715439863553911	2	FACETS	0.856	0.803	0.911	0.428	0.401	0.456	CLONAL	1	TRUE	0	0.715439863553911	2		502	803	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465969	69465969	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	349	595	0	ENST00000227507.2:c.807G>T	p.Lys269Asn	p.K269N	ENST00000227507	NM_053056.2	269	aaG/aaT	5/5	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.715439863553911	2		595	932	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219094	94219094	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	266	379	0	ENST00000323929.3:c.310A>G	p.Ser104Gly	p.S104G	ENST00000323929	NM_005591.3	104	Agt/Ggt	4/20	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.715439863553911	2		379	734	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727482	88727482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368510978	NA	P-0024756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	102	532	0	ENST00000360948.2:c.297G>A	p.Met99Ile	p.M99I	ENST00000360948	NM_001012338.2	99	atG/atA	3/19	1	2	FACETS	0.302	0.269	0.337	0.302	0.269	0.337	SUBCLONAL	1	TRUE	1	0.715439863553911	2		532	944	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636722	2636724	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0024756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	332	548	2	ENST00000342085.4:c.1179_1181del	p.Ser394del	p.S394del	ENST00000342085	NM_002613.4	391	TCC/-	11/14	1	2	FACETS	0.903	0.855	0.952	0.903	0.855	0.952	CLONAL	1	TRUE	1	0.715439863553911	2		550	1028	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989675	15989675	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	287	378	1	ENST00000268712.3:c.3098C>A	p.Pro1033Gln	p.P1033Q	ENST00000268712	NM_006311.3	1033	cCg/cAg	23/46	1	2	FACETS	0.956	0.902	1	0.956	0.902	1	CLONAL	1	TRUE	1	0.715439863553911	2		379	839	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679396	29679396	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	321	425	0	ENST00000356175.3:c.7516G>T	p.Gly2506Trp	p.G2506W	ENST00000356175	NM_000267.3	2506	Ggg/Tgg	50/57	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.715439863553911	2		425	839	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221080	5221080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	322	588	1	ENST00000357368.4:c.3386C>T	p.Ala1129Val	p.A1129V	ENST00000357368	NM_002850.3	1129	gCc/gTc	20/38	1	2	FACETS	0.943	0.892	0.994	0.943	0.892	0.994	CLONAL	1	TRUE	1	0.715439863553911	2		589	955	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244249	5244249	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	62	485	0	ENST00000357368.4:c.1233del	p.Ser414AlafsTer30	p.S414Afs*30	ENST00000357368	NM_002850.3	411	ggG/gg	11/38	1	2	FACETS	0.216	0.185	0.248	0.216	0.185	0.248	SUBCLONAL	1	TRUE	1	0.715439863553911	2		485	804	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285189	15285189	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886054255	NA	P-0024756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	400	620	0	ENST00000263388.2:c.4426G>A	p.Ala1476Thr	p.A1476T	ENST00000263388	NM_000435.2	1476	Gcc/Acc	25/33	1	2	FACETS	0.963	0.917	1	0.963	0.917	1	CLONAL	1	TRUE	1	0.715439863553911	2		620	1161	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919796	96919796	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866711036	NA	P-0024756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	314	531	2	ENST00000258439.3:c.467C>T	p.Ala156Val	p.A156V	ENST00000258439	NM_001193304.2	156	gCc/gTc	4/4	1	2	FACETS	0.96	0.909	1	0.96	0.909	1	CLONAL	1	TRUE	1	0.715439863553911	2		533	914	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936002	49936004	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0024756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	390	757	0	ENST00000296474.3:c.1666_1668del	p.Lys556del	p.K556del	ENST00000296474	NM_002447.2	556	AAG/-	4/20	1	2	FACETS	0.936	0.89	0.982	0.936	0.89	0.982	CLONAL	1	TRUE	1	0.715439863553911	2		757	1165	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204677	128204677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	122	691	3	ENST00000341105.2:c.764C>T	p.Ala255Val	p.A255V	ENST00000341105	NM_032638.4	255	gCg/gTg	3/6	1	2	FACETS	0.285	0.257	0.316	0.285	0.257	0.316	SUBCLONAL	1	TRUE	1	0.715439863553911	2		694	1195	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750390	41750390	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	60	409	1	ENST00000226382.2:c.238G>A	p.Ala80Thr	p.A80T	ENST00000226382	NM_003924.3	80	Gca/Aca	1/3	1	2	FACETS	0.283	0.243	0.326	0.283	0.243	0.326	SUBCLONAL	1	TRUE	1	0.715439863553911	2		410	593	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665434	176665434	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1554195885	NA	P-0024756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	244	381	0	ENST00000439151.2:c.4118T>C	p.Leu1373Ser	p.L1373S	ENST00000439151	NM_022455.4	1373	tTg/tCg	7/23	1	2	FACETS	0.928	0.871	0.986	0.928	0.871	0.986	CLONAL	1	TRUE	1	0.715439863553911	2		381	735	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522349	157522349	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554235882	NA	P-0024756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	435	739	1	ENST00000346085.5:c.4621C>T	p.Gln1541Ter	p.Q1541*	ENST00000346085	NM_020732.3	1541	Cag/Tag	18/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.715439863553911	2		740	1210	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527742	157527742	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	245	441	1	ENST00000346085.5:c.5471del	p.Gly1824ValfsTer27	p.G1824Vfs*27	ENST00000346085	NM_020732.3	1823	Ggg/gg	20/20	1	2	FACETS	0.82	0.769	0.873	0.82	0.769	0.873	CLONAL	1	TRUE	1	0.715439863553911	2		442	835	SUCCESS
MET	4233	MSKCC	GRCh37	7	116413865	116413865	+	intron_variant	Intron	SNP	C	C	A	rs1562931131	NA	P-0024756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1331	42	884	1	ENST00000397752.3:c.3029-1070C>A		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.086	0.071	0.102	0.086	0.071	0.102	SUBCLONAL	1	TRUE	1	0.715439863553911	2		885	1373	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738808	145738808	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367570292	NA	P-0024756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	106	810	2	ENST00000428558.2:c.2257C>T	p.Arg753Trp	p.R753W	ENST00000428558	NM_004260.3	753	Cgg/Tgg	14/22	1	2	FACETS	0.23	0.205	0.256	0.23	0.205	0.256	SUBCLONAL	1	TRUE	1	0.715439863553911	2		812	1289	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	85	629	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.408	0.36	0.46	0.408	0.36	0.46	SUBCLONAL	1	TRUE	1	0.465221801545438	2		629	895	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216379	7216380	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1216832021	NA	P-0024757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	78	622	0	ENST00000380728.2:c.868dup	p.Gln290ProfsTer?	p.Q290Pfs*?	ENST00000380728		290	cag/cCag	10/11	1	2	FACETS	0.348	0.305	0.395	0.348	0.305	0.395	SUBCLONAL	1	TRUE	1	0.465221801545438	2		622	963	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070608	67070608	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	35	275	0	ENST00000412916.2:c.232C>T	p.Arg78Ter	p.R78*	ENST00000412916		78	Cga/Tga	3/6	0.353041583985344	1	FACETS	0.25	0.205	0.302	0.25	0.205	0.302	SUBCLONAL	1	TRUE	0	0.465221801545438	1		275	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578518	7578518	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934875	NA	P-0024757-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	113	817	0	ENST00000269305.4:c.412G>C	p.Ala138Pro	p.A138P	ENST00000269305	NM_001126112.2	138	Gcc/Ccc	5/11	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.276880855842391	2		817	776	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0024757-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	78	563	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	1	2	FACETS	0.91	0.8	1	0.91	0.8	1	CLONAL	1	TRUE	1	0.276880855842391	2		563	619	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106534454	106534454	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024757-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	34	239	0	ENST00000369096.4:c.26G>C	p.Arg9Pro	p.R9P	ENST00000369096	NM_001198.3	9	cGt/cCt	1/7	0.275620726098515	3	FACETS	0.612	0.5	0.738	0.306	0.25	0.369	SUBCLONAL	1	TRUE	1	0.276880855842391	3		239	457	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	130	571	0				ENST00000310581	NM_198253.2	-/1132			0.32186549554988	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	1	0.36973961915928	3		571	398	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044699	47044699	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0024758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	223	477	0	ENST00000377604.3:c.2101-2A>T		p.X701_splice	ENST00000377604	NM_001204468.1	701			1	1	FACETS	0.805	0.754	0.856	1	0.993	1	CLONAL	2	TRUE	0	0.36973961915928	1		477	611	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143044500	143044500	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	107	488	0	ENST00000262992.4:c.1962G>C	p.Gln654His	p.Q654H	ENST00000262992	NM_001101669.1	654	caG/caC	18/24	1	2	FACETS	0.88	0.79	0.974	0.88	0.79	0.974	CLONAL	1	TRUE	1	0.36973961915928	2		488	658	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999317	100999317	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	70	929	0	ENST00000325455.5:c.485C>A	p.Ser162Tyr	p.S162Y	ENST00000325455	NM_001202474.3	162	tCc/tAc	1/8	1	2	FACETS	0.358	0.311	0.409	0.358	0.311	0.409	SUBCLONAL	1	TRUE	1	0.36973961915928	2		929	1057	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955527	48955527	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	39	485	0	ENST00000267163.4:c.1643A>T	p.Lys548Ile	p.K548I	ENST00000267163	NM_000321.2	548	aAa/aTa	17/27	1	2	FACETS	0.396	0.327	0.472	0.396	0.327	0.472	SUBCLONAL	1	TRUE	1	0.36973961915928	2		485	533	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509572	29509572	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	153	692	0	ENST00000356175.3:c.777del	p.Ser259ArgfsTer22	p.S259Rfs*22	ENST00000356175	NM_000267.3	259	agC/ag	8/57	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.36973961915928	2		692	819	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509681	29509681	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	A	A	T	rs1135402798	NA	P-0024758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	91	539	0	ENST00000356175.3:c.886A>T	p.Lys296Ter	p.K296*	ENST00000356175	NM_000267.3	296	Aag/Tag	8/57	1	2	FACETS	0.818	0.727	0.914	0.818	0.727	0.914	CLONAL	1	TRUE	1	0.36973961915928	2		539	602	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520155	9520155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	135	517	0	ENST00000353224.5:c.2114C>A	p.Pro705Gln	p.P705Q	ENST00000353224	NM_177990.2	705	cCa/cAa	10/10	1	2	FACETS	0.881	0.801	0.965	0.881	0.801	0.965	CLONAL	1	TRUE	1	0.36973961915928	2		517	829	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459687	149459687	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	205	807	0	ENST00000286301.3:c.520G>T	p.Asp174Tyr	p.D174Y	ENST00000286301	NM_005211.3	174	Gac/Tac	4/22	0.36973961915928	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.36973961915928	1		807	869	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288680	33288680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	116	471	0	ENST00000374542.5:c.872G>A	p.Arg291Gln	p.R291Q	ENST00000374542	NM_001141970.1	291	cGg/cAg	3/8	1	2	FACETS	0.895	0.808	0.987	0.895	0.808	0.987	CLONAL	1	TRUE	1	0.36973961915928	2		471	701	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0024760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	34	320	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.23	2		320	276	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257896	19257896	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	33	960	0	ENST00000162023.5:c.490C>A	p.Gln164Lys	p.Q164K	ENST00000162023		164	Cag/Aag	9/13	1	2	FACETS	0.506	0.411	0.614	0.506	0.411	0.614	SUBCLONAL	1	TRUE	1	0.23	2		960	567	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224232	36224232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755598760	NA	P-0024760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	27	388	1	ENST00000222270.7:c.6782C>T	p.Thr2261Met	p.T2261M	ENST00000222270	NM_014727.1	2261	aCg/aTg	28/37	1	2	FACETS	0.741	0.59	0.912	0.741	0.59	0.912	CLONAL	1	TRUE	1	0.23	2		389	317	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652032	36652032	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1019789691	NA	P-0024760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	43	790	0	ENST00000244741.5:c.154G>A	p.Asp52Asn	p.D52N	ENST00000244741	NM_000389.4	52	Gac/Aac	2/3	1	2	FACETS	0.827	0.693	0.976	0.827	0.693	0.976	CLONAL	1	TRUE	1	0.23	2		790	452	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652031	36652031	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	43	776	0	ENST00000244741.5:c.153del	p.Phe51LeufsTer97	p.F51Lfs*97	ENST00000244741	NM_000389.4	51	ttC/tt	2/3	1	2	FACETS	0.818	0.685	0.966	0.818	0.685	0.966	CLONAL	1	TRUE	1	0.23	2		776	457	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416557	49416557	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	228	629	2	ENST00000301067.7:c.16154C>A	p.Ser5385Ter	p.S5385*	ENST00000301067	NM_003482.3	5385	tCa/tAa	51/54	0.289084918853141	3	FACETS	0.964	0.9	1	0.964	0.9	1	CLONAL	2	TRUE	1	0.31462974919891	3		631	870	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576848	7576855	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTACCTG	AGTACCTG	-	novel	NA	P-0024762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	181	691	0	ENST00000269305.4:c.991_993+5del		p.X331_splice	ENST00000269305	NM_001126112.2	331		9/11	0.280674385279591	2	FACETS	0.787	0.728	0.848	0.787	0.728	0.848	SUBCLONAL	2	TRUE	0	0.31462974919891	2		691	731	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0024772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	141	732	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.19695019230645	2	FACETS	0.957	0.875	1	0.957	0.875	1	CLONAL	2	TRUE	0	0.231608830310764	2		732	636	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0024772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	28	580	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	0.703	0.562	0.863	0.703	0.562	0.863	SUBCLONAL	1	TRUE	1	0.231608830310764	2		580	344	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245432	153245432	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	36	681	0	ENST00000281708.4:c.1759A>G	p.Met587Val	p.M587V	ENST00000281708	NM_033632.3	587	Atg/Gtg	11/12	1	2	FACETS	0.558	0.458	0.671	0.558	0.458	0.671	SUBCLONAL	1	TRUE	1	0.231608830310764	2		681	557	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0024784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	46	533	1				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		534	99	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0024787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	67	598	0	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	0.33	2		598	330	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0024787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	95	625	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	0.33	2		625	444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	65	703	0	ENST00000269305.4:c.1045del	p.Glu349AsnfsTer21	p.E349Nfs*21	ENST00000269305	NM_001126112.2	349	Gaa/aa	10/11	0.270457576640057	1	FACETS	0.873	0.76	0.993	0.873	0.76	0.993	CLONAL	1	TRUE	0	0.33	1		703	377	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038233	30038233	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	26	664	0	ENST00000338641.4:c.406G>A	p.Glu136Lys	p.E136K	ENST00000338641	NM_000268.3	136	Gag/Aag	4/16	0.240925696290273	0	FACETS	0.271	0.214	0.336			1	SUBCLONAL	1	TRUE	0	0.33	0		664	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0024790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	817	651	0	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.886104888576298	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.886104888576298	2		651	901	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953760	48953760	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913302	NA	P-0024790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	249	280	0	ENST00000267163.4:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000267163	NM_000321.2	455	Cga/Tga	14/27	0.886104888576298	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.886104888576298	1		280	303	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100414	157100414	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1438676618	NA	P-0024790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	11	31	0	ENST00000346085.5:c.1351T>C	p.Ser451Pro	p.S451P	ENST00000346085	NM_020732.3	451	Tcg/Ccg	1/20	0.886104888576298	4	FACETS	0.323	0.224	0.445			1	SUBCLONAL	1	TRUE	NA	0.886104888576298	4		31	145	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46512220	46512222	+	splice_donor_variant,intron_variant	Splice_Site	DEL	TAC	TAC	-	novel	NA	P-0024790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	362	498	4	ENST00000262741.5:c.1016+1_1016+3del		p.X339_splice	ENST00000262741	NM_003629.3	339			1	2	FACETS	0.953	0.908	0.999	0.953	0.908	0.999	CLONAL	1	TRUE	1	0.886104888576298	2		502	857	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428538	78428538	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	404	610	1	ENST00000370768.2:c.1261G>T	p.Asp421Tyr	p.D421Y	ENST00000370768	NM_003902.3	421	Gat/Tat	14/20	1	2	FACETS	0.953	0.91	0.996	0.953	0.91	0.996	CLONAL	1	TRUE	1	0.886104888576298	2		611	957	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120457991	120457991	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	345	523	1	ENST00000256646.2:c.7354C>T	p.Gln2452Ter	p.Q2452*	ENST00000256646	NM_024408.3	2452	Cag/Tag	34/34	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.886104888576298	2		524	770	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332357	70332357	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	37	510	0	ENST00000373644.4:c.262G>T	p.Glu88Ter	p.E88*	ENST00000373644	NM_030625.2	88	Gag/Tag	2/12	0.886104888576298	1	FACETS	0.101	0.083	0.121	0.101	0.083	0.121	SUBCLONAL	1	TRUE	0	0.886104888576298	1		510	462	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114264	115114264	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	162	503	0	ENST00000257566.3:c.953C>A	p.Thr318Asn	p.T318N	ENST00000257566	NM_016569.3	318	aCc/aAc	6/8	0.853082852352051	3	FACETS	0.439	0.402	0.478	0.219	0.201	0.239	SUBCLONAL	1	TRUE	1	0.886104888576298	3		503	1202	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2224048	2224048	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	350	607	0	ENST00000326181.6:c.1262A>C	p.Lys421Thr	p.K421T	ENST00000326181	NM_032271.2	421	aAg/aCg	13/21	1	2	FACETS	0.934	0.889	0.979	0.934	0.889	0.979	CLONAL	1	TRUE	1	0.886104888576298	2		607	846	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556925	29556925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	150	145	0	ENST00000356175.3:c.2923C>T	p.His975Tyr	p.H975Y	ENST00000356175	NM_000267.3	975	Cat/Tat	22/57	0.886104888576298	3	FACETS	1	0.968	1	0.696	0.655	0.736	CLONAL	2	TRUE	0	0.886104888576298	3		145	234	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164022	106164022	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	249	411	1	ENST00000380013.4:c.3532G>T	p.Glu1178Ter	p.E1178*	ENST00000380013	NM_001127208.2	1178	Gaa/Taa	5/11	1	2	FACETS	0.878	0.827	0.93	0.878	0.827	0.93	CLONAL	1	TRUE	1	0.886104888576298	2		412	640	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523594	106523594	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	275	346	0	ENST00000359195.3:c.2746C>A	p.Pro916Thr	p.P916T	ENST00000359195	NM_002649.2	916	Cct/Act	8/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.886104888576298	2		346	606	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741443	145741443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs551940973	NA	P-0024790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	462	783	4	ENST00000428558.2:c.1060G>A	p.Val354Ile	p.V354I	ENST00000428558	NM_004260.3	354	Gta/Ata	5/22	0.886104888576298	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.886104888576298	1		787	568	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0024807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	170	533	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.935671811060808	2		534	353	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754531	42754531	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	319	377	0	ENST00000222329.4:c.209G>C	p.Arg70Pro	p.R70P	ENST00000222329	NM_006494.2	70	cGc/cCc	2/4	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.935671811060808	2		377	633	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714601	52714601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755649324	NA	P-0024807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	287	317	0	ENST00000322088.6:c.359C>T	p.Ser120Leu	p.S120L	ENST00000322088	NM_014225.5	120	tCg/tTg	4/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.935671811060808	2		317	575	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679595	86679595	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0024844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	139	488	0	ENST00000274376.6:c.2756C>G	p.Ser919Ter	p.S919*	ENST00000274376	NM_002890.2	919	tCa/tGa	21/25	0.422655584959708	2	FACETS	0.949	0.876	1	0.949	0.876	1	CLONAL	2	TRUE	0	0.430909211961218	2		488	340	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119660	108119660	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	56	129	0	ENST00000278616.4:c.1066G>A	p.Val356Ile	p.V356I	ENST00000278616	NM_000051.3	356	Gtt/Att	9/63	NA	2	FACETS	0.866	0.76	0.976			1	INDETERMINATE	2	TRUE	NA	0.430909211961218	2		129	150	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600393	10600393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	334	776	1	ENST00000171111.5:c.1462G>A	p.Glu488Lys	p.E488K	ENST00000171111	NM_203500.1	488	Gag/Aag	4/6	0.422655584959708	2	FACETS	0.956	0.908	1	0.956	0.908	1	CLONAL	2	TRUE	0	0.430909211961218	2		777	811	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863224683	NA	P-0024844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	404	720	0	ENST00000269305.4:c.388C>T	p.Leu130Phe	p.L130F	ENST00000269305	NM_001126112.2	130	Ctc/Ttc	5/11	0.431378013709734	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.430909211961218	2		720	912	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630977	187630977	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	99	404	0	ENST00000441802.2:c.5G>T	p.Gly2Val	p.G2V	ENST00000441802	NM_005245.3	2	gGg/gTg	2/27	0.431378013709734	3	FACETS	1	0.907	1	0.507	0.454	0.563	CLONAL	1	TRUE	1	0.430909211961218	3		404	551	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585361	29585361	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0024844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	177	625	1	ENST00000356175.3:c.4111-1G>T		p.X1371_splice	ENST00000356175	NM_000267.3	1371			0.431378013709734	2	FACETS	0.953	0.888	1	0.953	0.888	1	CLONAL	2	TRUE	0	0.430909211961218	2		626	431	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562490	95562490	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	164	343	0	ENST00000393063.1:c.4767G>T	p.Lys1589Asn	p.K1589N	ENST00000393063	NM_030621.3	1589	aaG/aaT	24/28	0.367273157779581	4	FACETS	0.88	0.811	0.951	0.88	0.811	0.951	CLONAL	2	TRUE	2	0.430909211961218	4		343	619	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129318	2129318	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	292	604	0	ENST00000219476.3:c.3173A>G	p.Lys1058Arg	p.K1058R	ENST00000219476	NM_000548.3	1058	aAa/aGa	28/42	0.431378013709734	2	FACETS	0.984	0.932	1	0.984	0.932	1	CLONAL	2	TRUE	0	0.430909211961218	2		604	689	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934347	81934347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	278	483	2	ENST00000359376.3:c.1324C>T	p.Pro442Ser	p.P442S	ENST00000359376	NM_002661.3	442	Ccc/Tcc	14/33	0.431378013709734	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.430909211961218	2		485	625	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511574	66511574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	65	307	0	ENST00000358598.2:c.34G>A	p.Ala12Thr	p.A12T	ENST00000358598	NM_212471.2	12	Gca/Aca	2/11	0.430909211961218	13	FACETS	0.859	0.742	0.987			1	CLONAL	1	TRUE	NA	0.430909211961218	13		307	1183	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221966	1221966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	270	690	0	ENST00000326873.7:c.881C>T	p.Pro294Leu	p.P294L	ENST00000326873	NM_000455.4	294	cCg/cTg	7/10	0.422655584959708	2	FACETS	0.924	0.873	0.976	0.924	0.873	0.976	CLONAL	2	TRUE	0	0.430909211961218	2		690	678	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170510	11170510	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	316	623	2	ENST00000358026.2:c.4813G>T	p.Glu1605Ter	p.E1605*	ENST00000358026	NM_001128849.1	1605	Gag/Tag	34/36	0.422655584959708	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.430909211961218	2		625	727	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138644	55138644	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	223	433	0	ENST00000257290.5:c.1321C>A	p.Pro441Thr	p.P441T	ENST00000257290	NM_006206.4	441	Ccg/Acg	9/23	0.431378013709734	4	FACETS	0.933	0.871	0.996			1	CLONAL	2	TRUE	NA	0.430909211961218	4		433	794	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139810	55139810	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	198	434	0	ENST00000257290.5:c.1471G>T	p.Ala491Ser	p.A491S	ENST00000257290	NM_006206.4	491	Gcc/Tcc	10/23	0.431378013709734	4	FACETS	0.918	0.853	0.985			1	CLONAL	2	TRUE	NA	0.430909211961218	4		434	716	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038374	180038384	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCGTCAGCC	CAGCGTCAGCC	-	novel	NA	P-0024844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	316	567	0	ENST00000261937.6:c.3633_3643del	p.Ala1212GlyfsTer30	p.A1212Gfs*30	ENST00000261937	NM_182925.4	1211	caGGCTGACGCTGag/caag	27/30	0.422655584959708	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.430909211961218	2		567	686	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818875	32818875	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	266	527	0	ENST00000354258.4:c.1076del	p.Leu359ArgfsTer5	p.L359Rfs*5	ENST00000354258	NM_000593.5	359	cTg/cg	4/11	0.430909211961218	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.430909211961218	2		527	614	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129295	152129295	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	256	437	3	ENST00000206249.3:c.248G>T	p.Gly83Val	p.G83V	ENST00000206249	NM_000125.3	83	gGg/gTg	1/8	0.430909211961218	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.430909211961218	2		440	555	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388023	81388023	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	80	523	0	ENST00000222390.5:c.352C>A	p.Leu118Ile	p.L118I	ENST00000222390	NM_000601.4	118	Ctc/Atc	3/18	0.431378013709734	3	FACETS	1	0.884	1	0.5	0.442	0.562	CLONAL	1	TRUE	1	0.430909211961218	3		523	451	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128322075	128322075	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	220	402	0	ENST00000265960.3:c.685G>T	p.Ala229Ser	p.A229S	ENST00000265960	NM_001006617.1	229	Gcc/Tcc	6/12	0.175971264941261	5	FACETS	0.882	0.826	0.94			1	INDETERMINATE	3	TRUE	NA	0.430909211961218	5		402	635	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781186	135781186	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	249	503	0	ENST00000298552.3:c.1779A>T	p.Arg593Ser	p.R593S	ENST00000298552	NM_001162426.1	593	agA/agT	15/23	0.431378013709734	4	FACETS	0.941	0.882	1	0.941	0.882	1	CLONAL	2	TRUE	2	0.430909211961218	4		503	879	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0024864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	70	790	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.746	0.65	0.85	0.746	0.65	0.85	SUBCLONAL	1	TRUE	1	0.267570433094519	2		790	701	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	31	571	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.692	0.56	0.84	0.692	0.56	0.84	SUBCLONAL	1	TRUE	1	0.267570433094519	2		571	335	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120103	70120103	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	16	67	0	ENST00000245479.2:c.1105C>T	p.Gln369Ter	p.Q369*	ENST00000245479	NM_000346.3	369	Cag/Tag	3/3	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.267570433094519	2		67	84	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267440	7267440	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1230564293	NA	P-0024864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	73	374	0	ENST00000302850.5:c.568G>A	p.Ala190Thr	p.A190T	ENST00000302850	NM_000208.2	190	Gcg/Acg	2/22	1	2	FACETS	0.916	0.801	1	0.916	0.801	1	CLONAL	1	TRUE	1	0.267570433094519	2		374	596	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088786	27088786	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	100	514	0	ENST00000324856.7:c.2395C>T	p.Gln799Ter	p.Q799*	ENST00000324856	NM_006015.4	799	Cag/Tag	7/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.267570433094519	2		514	660	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143303	108143303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	92	515	0	ENST00000278616.4:c.3122C>T	p.Ala1041Val	p.A1041V	ENST00000278616	NM_000051.3	1041	gCc/gTc	21/63	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.267570433094519	2		515	646	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254654	46254654	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	77	430	0	ENST00000334344.6:c.4844T>G	p.Phe1615Cys	p.F1615C	ENST00000334344	NM_152641.2	1615	tTc/tGc	16/21	0.228221930979675	2	FACETS	1	0.884	1	0.503	0.442	0.569	CLONAL	1	TRUE	0	0.267570433094519	2		430	572	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658470	3658470	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	98	583	2	ENST00000294008.3:c.496C>T	p.Gln166Ter	p.Q166*	ENST00000294008	NM_032444.2	166	Caa/Taa	2/15	1	2	FACETS	0.977	0.871	1	0.977	0.871	1	CLONAL	1	TRUE	1	0.267570433094519	2		585	750	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578374	7578375	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCTATCTG	novel	NA	P-0024864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	89	488	0	ENST00000269305.4:c.548_555dup	p.Asp186GlnfsTer64	p.D186Qfs*64	ENST00000269305	NM_001126112.2	185	-/CAGATAGC	5/11	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.267570433094519	2		488	661	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119856	70119856	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	93	501	1	ENST00000245479.2:c.858del	p.Ile286MetfsTer97	p.I286Mfs*97	ENST00000245479	NM_000346.3	286	atC/at	3/3	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.267570433094519	2		502	513	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713479	30713480	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGCAGTTTGAGACAGTGG	novel	NA	P-0024864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	41	445	0	ENST00000295754.5:c.805_823dup	p.Ala275GlyfsTer4	p.A275Gfs*4	ENST00000295754	NM_003242.5	268	-/GAGCAGTTTGAGACAGTGG	4/7	0.267570433094519	3	FACETS	0.55	0.457	0.653	0.183	0.152	0.218	SUBCLONAL	1	TRUE	0	0.267570433094519	3		445	632	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732949	30732949	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	73	267	0	ENST00000295754.5:c.1562G>A	p.Trp521Ter	p.W521*	ENST00000295754	NM_003242.5	521	tGg/tAg	7/7	0.267570433094519	3	FACETS	0.766	0.673	0.865	0.51	0.448	0.577	SUBCLONAL	2	TRUE	0	0.267570433094519	3		267	404	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266059	41266097	+	inframe_deletion	In_Frame_Del	DEL	AAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGG	AAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGG	-	novel	NA	P-0024864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	199	288	0	ENST00000349496.5:c.57_95del	p.Lys19_Asp32delinsAsn	p.K19_D32delinsN	ENST00000349496	NM_001904.3	19	aAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGac/aac	3/15	0.267570433094519	3	FACETS	1	0.951	1	1	0.991	1	CLONAL	4	TRUE	0	0.267570433094519	3		288	416	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030862	69030862	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	84	345	1	ENST00000288368.4:c.3404G>T	p.Ser1135Ile	p.S1135I	ENST00000288368	NM_024870.2	1135	aGt/aTt	27/40	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.267570433094519	2		346	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0024865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	96	808	3	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	FALSE	NA	0.258225135355832	2		811	555	SUCCESS
APC	324	MSKCC	GRCh37	5	112174466	112174466	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	19	278	1	ENST00000257430.4:c.3175G>T	p.Glu1059Ter	p.E1059*	ENST00000257430	NM_000038.5	1059	Gaa/Taa	16/16	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	FALSE	1	0.258225135355832	2		279	114	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021211	31021211	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs373145711	NA	P-0024865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	110	485	2	ENST00000375687.4:c.1210C>T	p.Arg404Ter	p.R404*	ENST00000375687	NM_015338.5	404	Cga/Tga	12/13	0.258225135355832	6	FACETS	1	0.982	1			1	CLONAL	1	FALSE	NA	0.258225135355832	6		487	878	SUCCESS
APC	324	MSKCC	GRCh37	5	112175271	112175271	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1554085429	NA	P-0024865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	36	204	0	ENST00000257430.4:c.3980C>G	p.Ser1327Ter	p.S1327*	ENST00000257430	NM_000038.5	1327	tCa/tGa	16/16	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	1	0.258225135355832	2		204	221	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114905790	114905790	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	98	560	0	ENST00000543371.1:c.809C>T	p.Pro270Leu	p.P270L	ENST00000543371	NM_001198531.1	270	cCa/cTa	8/14	0.252475064211539	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	0	0.258225135355832	1		560	524	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	94	571	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.91	0.816	1	0.91	0.816	1	CLONAL	1	TRUE	1	0.53087744410696	2		571	389	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	126	629	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.450114243502019	3	FACETS	0.838	0.76	0.92	0.419	0.38	0.46	CLONAL	1	TRUE	1	0.53087744410696	3		629	717	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	104	547	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.450114243502019	3	FACETS	0.793	0.712	0.88	0.397	0.356	0.44	SUBCLONAL	1	TRUE	1	0.53087744410696	3		547	625	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936103	178936103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519699	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	152	686	0	ENST00000263967.3:c.1645G>A	p.Asp549Asn	p.D549N	ENST00000263967	NM_006218.2	549	Gat/Aat	10/21	0.450114243502019	3	FACETS	0.852	0.779	0.927	0.426	0.389	0.464	CLONAL	1	TRUE	1	0.53087744410696	3		686	851	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915168	32915168	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	144	477	0	ENST00000380152.3:c.6676G>C	p.Glu2226Gln	p.E2226Q	ENST00000380152		2226	Gaa/Caa	11/27	1	2	FACETS	0.969	0.888	1	0.969	0.888	1	CLONAL	1	TRUE	1	0.53087744410696	2		477	560	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467485	25467485	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745721709	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	185	500	2	ENST00000264709.3:c.1591G>A	p.Asp531Asn	p.D531N	ENST00000264709	NM_175629.2	531	Gac/Aac	14/23	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.53087744410696	2		502	654	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166184	118166184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371434677	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	36	281	0	ENST00000369448.3:c.694G>A	p.Ala232Thr	p.A232T	ENST00000369448	NM_017709.3	232	Gcc/Acc	2/2	0.443777209807909	3	FACETS	0.314	0.258	0.378			1	SUBCLONAL	1	TRUE	NA	0.53087744410696	3		281	546	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189427	56189427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	194	524	1	ENST00000399503.3:c.4459C>T	p.Arg1487Cys	p.R1487C	ENST00000399503	NM_005921.1	1487	Cgt/Tgt	20/20	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.53087744410696	2		525	716	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120359	94120359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778087526	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	60	242	0	ENST00000369303.4:c.692G>A	p.Arg231Gln	p.R231Q	ENST00000369303	NM_004440.3	231	cGa/cAa	3/17	0.53087744410696	1	FACETS	0.843	0.738	0.953	0.843	0.738	0.953	CLONAL	1	TRUE	0	0.53087744410696	1		242	197	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038881	12038881	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	169	360	0	ENST00000396373.4:c.1174G>C	p.Glu392Gln	p.E392Q	ENST00000396373	NM_001987.4	392	Gag/Cag	7/8	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.53087744410696	2		360	605	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864769	68864769	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	103	331	0	ENST00000288368.4:c.140C>T	p.Ser47Leu	p.S47L	ENST00000288368	NM_024870.2	47	tCg/tTg	1/40	1	2	FACETS	0.92	0.828	1	0.92	0.828	1	CLONAL	1	TRUE	1	0.53087744410696	2		331	422	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778810	76778810	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	188	342	0	ENST00000373344.5:c.6769C>G	p.Leu2257Val	p.L2257V	ENST00000373344	NM_000489.3	2257	Ctt/Gtt	31/35	1	1	FACETS	0.752	0.708	0.796	1	0.993	1	SUBCLONAL	2	TRUE	0	0.53087744410696	1		342	346	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799159	45799159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	186	743	1	ENST00000450313.1:c.274G>A	p.Glu92Lys	p.E92K	ENST00000450313	NM_012222.2	92	Gaa/Aaa	3/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.53087744410696	2		744	662	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244590	41244590	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	195	606	0	ENST00000357654.3:c.2958C>G	p.Ile986Met	p.I986M	ENST00000357654	NM_007294.3	986	atC/atG	10/23	1	2	FACETS	0.98	0.909	1	0.98	0.909	1	CLONAL	1	TRUE	1	0.53087744410696	2		606	750	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798353	45798353	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	161	478	0	ENST00000450313.1:c.583G>C	p.Glu195Gln	p.E195Q	ENST00000450313	NM_012222.2	195	Gag/Cag	8/16	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.53087744410696	2		478	571	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798987	45798987	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	187	543	1	ENST00000450313.1:c.358G>A	p.Glu120Lys	p.E120K	ENST00000450313	NM_012222.2	120	Gag/Aag	4/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.53087744410696	2		544	661	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984428	201984428	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	178	489	0	ENST00000359651.3:c.1093G>C	p.Glu365Gln	p.E365Q	ENST00000359651		365	Gag/Cag	8/8	0.53087744410696	3	FACETS	0.99	0.913	1	0.33	0.304	0.357	CLONAL	1	TRUE	0	0.53087744410696	3		489	857	SUCCESS
FH	2271	MSKCC	GRCh37	1	241669450	241669450	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1131691239	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	105	347	0	ENST00000366560.3:c.757C>T	p.Gln253Ter	p.Q253*	ENST00000366560	NM_000143.3	253	Caa/Taa	6/10	0.487338668022367	4	FACETS	0.772	0.692	0.858	0.257	0.23	0.286	SUBCLONAL	1	TRUE	1	0.53087744410696	4		347	784	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850870	63850870	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	112	329	0	ENST00000279873.7:c.1648G>A	p.Glu550Lys	p.E550K	ENST00000279873	NM_032199.2	550	Gaa/Aaa	10/10	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.53087744410696	2		329	417	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404592	70404592	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	177	458	0	ENST00000373644.4:c.2106G>C	p.Met702Ile	p.M702I	ENST00000373644	NM_030625.2	702	atG/atC	4/12	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.53087744410696	2		458	644	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206798	102206798	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	224	549	0	ENST00000263464.3:c.1426G>C	p.Glu476Gln	p.E476Q	ENST00000263464	NM_001165.4	476	Gaa/Caa	7/9	0.53087744410696	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.53087744410696	1		549	605	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885279	111885279	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	148	467	0	ENST00000341259.2:c.1167C>A	p.Phe389Leu	p.F389L	ENST00000341259	NM_005475.2	389	ttC/ttA	6/8	1	2	FACETS	0.931	0.854	1	0.931	0.854	1	CLONAL	1	TRUE	1	0.53087744410696	2		467	599	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879672	123879673	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	20	118	0	ENST00000330479.4:c.368_369delinsTA	p.Pro123Leu	p.P123L	ENST00000330479	NM_020382.3	123	cCC/cTA	4/9	1	2	FACETS	0.516	0.398	0.651	0.516	0.398	0.651	SUBCLONAL	1	TRUE	1	0.53087744410696	2		118	146	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911530	32911530	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	132	437	0	ENST00000380152.3:c.3038C>T	p.Ser1013Leu	p.S1013L	ENST00000380152		1013	tCa/tTa	11/27	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.53087744410696	2		437	485	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923097	48923097	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	171	465	0	ENST00000267163.4:c.545C>A	p.Ser182Tyr	p.S182Y	ENST00000267163	NM_000321.2	182	tCt/tAt	6/27	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.53087744410696	2		465	583	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562918	95562918	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	88	354	0	ENST00000393063.1:c.4339C>G	p.Gln1447Glu	p.Q1447E	ENST00000393063	NM_030621.3	1447	Cag/Gag	24/28	1	2	FACETS	0.916	0.818	1	0.916	0.818	1	CLONAL	1	TRUE	1	0.53087744410696	2		354	362	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058201	42058201	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	51	175	0	ENST00000219905.7:c.7922-1G>C		p.X2641_splice	ENST00000219905	NM_001164273.1	2641			1	2	FACETS	0.873	0.751	1	0.873	0.751	1	CLONAL	1	TRUE	1	0.53087744410696	2		175	220	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058849	42058849	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	98	332	0	ENST00000219905.7:c.8569G>A	p.Gly2857Arg	p.G2857R	ENST00000219905	NM_001164273.1	2857	Ggg/Agg	24/24	1	2	FACETS	0.944	0.849	1	0.944	0.849	1	CLONAL	1	TRUE	1	0.53087744410696	2		332	391	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058936	42058936	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	104	336	0	ENST00000219905.7:c.8656G>C	p.Glu2886Gln	p.E2886Q	ENST00000219905	NM_001164273.1	2886	Gag/Cag	24/24	1	2	FACETS	0.977	0.882	1	0.977	0.882	1	CLONAL	1	TRUE	1	0.53087744410696	2		336	401	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762097	43762097	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	193	534	0	ENST00000382044.4:c.1348C>G	p.Pro450Ala	p.P450A	ENST00000382044	NM_001141980.1	450	Cct/Gct	11/28	1	2	FACETS	0.962	0.892	1	0.962	0.892	1	CLONAL	1	TRUE	1	0.53087744410696	2		534	756	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041572	14041572	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	135	423	0	ENST00000311895.7:c.2119G>A	p.Glu707Lys	p.E707K	ENST00000311895	NM_005236.2	707	Gaa/Aaa	11/11	1	2	FACETS	0.991	0.906	1	0.991	0.906	1	CLONAL	1	TRUE	1	0.53087744410696	2		423	513	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641643	23641643	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	118	495	0	ENST00000261584.4:c.1832A>T	p.Asp611Val	p.D611V	ENST00000261584	NM_024675.3	611	gAc/gTc	5/13	1	2	FACETS	0.694	0.627	0.764	0.694	0.627	0.764	SUBCLONAL	1	TRUE	1	0.53087744410696	2		495	641	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217837	7217837	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	231	712	0	ENST00000380728.2:c.174G>C	p.Glu58Asp	p.E58D	ENST00000380728		58	gaG/gaC	3/11	1	2	FACETS	0.937	0.874	1	0.937	0.874	1	CLONAL	1	TRUE	1	0.53087744410696	2		712	929	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223171	41223171	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs397509195	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	167	584	0	ENST00000357654.3:c.4760C>G	p.Ser1587Ter	p.S1587*	ENST00000357654	NM_007294.3	1587	tCa/tGa	15/23	1	2	FACETS	0.971	0.896	1	0.971	0.896	1	CLONAL	1	TRUE	1	0.53087744410696	2		584	648	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290990	15290990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	150	621	0	ENST00000263388.2:c.3220G>A	p.Glu1074Lys	p.E1074K	ENST00000263388	NM_000435.2	1074	Gag/Aag	20/33	0.450114243502019	3	FACETS	0.756	0.69	0.825	0.378	0.345	0.413	SUBCLONAL	1	TRUE	1	0.53087744410696	3		621	946	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917810	29917810	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	175	580	0	ENST00000389048.3:c.858G>C	p.Gln286His	p.Q286H	ENST00000389048	NM_004304.4	286	caG/caC	3/29	1	2	FACETS	0.904	0.835	0.976	0.904	0.835	0.976	CLONAL	1	TRUE	1	0.53087744410696	2		580	729	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142927	30142927	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	194	538	0	ENST00000389048.3:c.599G>C	p.Arg200Thr	p.R200T	ENST00000389048	NM_004304.4	200	aGa/aCa	1/29	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.53087744410696	2		538	670	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095698	178095698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	171	488	0	ENST00000397062.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000397062	NM_006164.4	545	Gaa/Aaa	5/5	1	2	FACETS	0.95	0.877	1	0.95	0.877	1	CLONAL	1	TRUE	1	0.53087744410696	2		488	678	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728473	190728473	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	84	290	0	ENST00000441310.2:c.1861G>A	p.Glu621Lys	p.E621K	ENST00000441310	NM_000534.4	621	Gaa/Aaa	10/13	1	2	FACETS	0.968	0.863	1	0.968	0.863	1	CLONAL	1	TRUE	1	0.53087744410696	2		290	327	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215595191	215595191	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	163	532	0	ENST00000260947.4:c.1945G>A	p.Glu649Lys	p.E649K	ENST00000260947	NM_000465.2	649	Gaa/Aaa	10/11	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.53087744410696	2		532	610	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62323156	62323156	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	104	325	0	ENST00000360203.5:c.2618G>T	p.Gly873Val	p.G873V	ENST00000360203	NM_001283009.1	873	gGa/gTa	28/35	1	2	FACETS	0.911	0.821	1	0.911	0.821	1	CLONAL	1	TRUE	1	0.53087744410696	2		325	430	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545177	41545177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	205	462	0	ENST00000263253.7:c.2377C>G	p.Gln793Glu	p.Q793E	ENST00000263253	NM_001429.3	793	Caa/Gaa	13/31	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.53087744410696	2		462	666	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568489	41568517	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCATGTTTTCACAGGATATTTTTAAACAA	GCATGTTTTCACAGGATATTTTTAAACAA	-	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	120	303	0	ENST00000263253.7:c.4453-12_4469del		p.X1485_splice	ENST00000263253	NM_001429.3	1485		28/31	1	2	FACETS	0.981	0.891	1	0.981	0.891	1	CLONAL	1	TRUE	1	0.53087744410696	2		303	461	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280627	41280627	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	157	529	0	ENST00000349496.5:c.2140C>G	p.Pro714Ala	p.P714A	ENST00000349496	NM_001904.3	714	Cct/Gct	15/15	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.53087744410696	2		529	579	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164255	47164255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	131	418	0	ENST00000409792.3:c.1871C>T	p.Ser624Leu	p.S624L	ENST00000409792	NM_014159.6	624	tCa/tTa	3/21	1	2	FACETS	0.962	0.878	1	0.962	0.878	1	CLONAL	1	TRUE	1	0.53087744410696	2		418	513	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441226	52441226	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	121	315	0	ENST00000460680.1:c.544G>C	p.Glu182Gln	p.E182Q	ENST00000460680	NM_004656.3	182	Gag/Cag	7/17	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.53087744410696	2		315	428	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643624	52643624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	152	504	0	ENST00000394830.3:c.2272G>A	p.Glu758Lys	p.E758K	ENST00000394830	NM_018313.4	758	Gaa/Aaa	17/30	1	2	FACETS	0.927	0.851	1	0.927	0.851	1	CLONAL	1	TRUE	1	0.53087744410696	2		504	618	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584506	189584506	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	117	363	0	ENST00000264731.3:c.802G>C	p.Glu268Gln	p.E268Q	ENST00000264731	NM_003722.4	268	Gag/Cag	6/14	0.450114243502019	3	FACETS	0.828	0.747	0.912	0.414	0.373	0.456	CLONAL	1	TRUE	1	0.53087744410696	3		363	674	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1940229	1940229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	35	279	0	ENST00000382891.5:c.1726G>A	p.Glu576Lys	p.E576K	ENST00000382891	NM_133335.3	576	Gag/Aag	8/22	1	2	FACETS	0.33	0.271	0.397	0.33	0.271	0.397	SUBCLONAL	1	TRUE	1	0.53087744410696	2		279	399	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153252020	153252020	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	154	453	0	ENST00000281708.4:c.986G>C	p.Gly329Ala	p.G329A	ENST00000281708	NM_033632.3	329	gGg/gCg	7/12	0.53087744410696	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.53087744410696	1		453	373	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332595	153332595	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	114	406	0	ENST00000281708.4:c.361G>T	p.Glu121Ter	p.E121*	ENST00000281708	NM_033632.3	121	Gag/Tag	2/12	0.53087744410696	1	FACETS	0.853	0.775	0.933	0.853	0.775	0.933	CLONAL	1	TRUE	0	0.53087744410696	1		406	370	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952406	38952406	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	129	316	0	ENST00000357387.3:c.3019G>C	p.Asp1007His	p.D1007H	ENST00000357387	NM_152756.3	1007	Gat/Cat	30/38	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.53087744410696	2		316	459	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819735	170819735	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	36	122	0	ENST00000296930.5:c.374C>G	p.Ser125Ter	p.S125*	ENST00000296930	NM_002520.6	125	tCa/tGa	5/11	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.53087744410696	2		122	132	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638911	176638911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367790484	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	43	495	0	ENST00000439151.2:c.3511C>T	p.Arg1171Cys	p.R1171C	ENST00000439151	NM_022455.4	1171	Cgt/Tgt	5/23	1	2	FACETS	0.234	0.195	0.277	0.234	0.195	0.277	SUBCLONAL	1	TRUE	1	0.53087744410696	2		495	693	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671570	30671570	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	164	559	0	ENST00000376406.3:c.5390C>G	p.Ser1797Cys	p.S1797C	ENST00000376406	NM_014641.2	1797	tCt/tGt	10/15	1	2	FACETS	0.892	0.821	0.965	0.892	0.821	0.965	CLONAL	1	TRUE	1	0.53087744410696	2		559	693	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680095	30680095	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	153	541	0	ENST00000376406.3:c.1624C>G	p.Gln542Glu	p.Q542E	ENST00000376406	NM_014641.2	542	Cag/Gag	5/15	1	2	FACETS	0.784	0.719	0.853	0.784	0.719	0.853	SUBCLONAL	1	TRUE	1	0.53087744410696	2		541	735	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324875	31324875	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1231905919	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	37	174	0	ENST00000412585.2:c.61G>T	p.Glu21Ter	p.E21*	ENST00000412585	NM_005514.6	21	Gag/Tag	1/8	1	2	FACETS	0.69	0.574	0.817	0.69	0.574	0.817	SUBCLONAL	1	TRUE	1	0.53087744410696	2		174	202	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163434	32163434	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752960355	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	36	506	0	ENST00000375023.3:c.5792G>A	p.Arg1931Gln	p.R1931Q	ENST00000375023	NM_004557.3	1931	cGa/cAa	30/30	1	2	FACETS	0.189	0.154	0.228	0.189	0.154	0.228	SUBCLONAL	1	TRUE	1	0.53087744410696	2		506	718	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120324	94120324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	53	241	0	ENST00000369303.4:c.727G>A	p.Glu243Lys	p.E243K	ENST00000369303	NM_004440.3	243	Gaa/Aaa	3/17	0.53087744410696	1	FACETS	0.806	0.699	0.919	0.806	0.699	0.919	CLONAL	1	TRUE	0	0.53087744410696	1		241	182	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92404114	92404114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	30	371	0	ENST00000265734.4:c.265G>A	p.Asp89Asn	p.D89N	ENST00000265734	NM_001259.6	89	Gac/Aac	3/8	1	2	FACETS	0.218	0.175	0.267	0.218	0.175	0.267	SUBCLONAL	1	TRUE	1	0.53087744410696	2		371	519	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534600	140534601	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	103	423	0	ENST00000288602.6:c.312dup	p.Asn105GlufsTer4	p.N105Efs*4	ENST00000288602	NM_004333.4	104	-/G	3/18	1	2	FACETS	0.77	0.692	0.852	0.77	0.692	0.852	SUBCLONAL	1	TRUE	1	0.53087744410696	2		423	504	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859732	151859732	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	91	325	0	ENST00000262189.6:c.10930C>G	p.Pro3644Ala	p.P3644A	ENST00000262189	NM_170606.2	3644	Cct/Gct	43/59	1	2	FACETS	0.875	0.782	0.972	0.875	0.782	0.972	CLONAL	1	TRUE	1	0.53087744410696	2		325	392	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859782	151859782	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	102	329	0	ENST00000262189.6:c.10880C>G	p.Ser3627Ter	p.S3627*	ENST00000262189	NM_170606.2	3627	tCa/tGa	43/59	1	2	FACETS	0.946	0.853	1	0.946	0.853	1	CLONAL	1	TRUE	1	0.53087744410696	2		329	406	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965489	90965489	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	22	313	1	ENST00000265433.3:c.1828G>A	p.Glu610Lys	p.E610K	ENST00000265433	NM_002485.4	610	Gaa/Aaa	11/16	1	2	FACETS	0.217	0.168	0.274	0.217	0.168	0.274	SUBCLONAL	1	TRUE	1	0.53087744410696	2		314	382	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760044	133760044	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	39	533	0	ENST00000318560.5:c.2367G>T	p.Lys789Asn	p.K789N	ENST00000318560	NM_005157.4	789	aaG/aaT	11/11	1	2	FACETS	0.238	0.196	0.284	0.238	0.196	0.284	SUBCLONAL	1	TRUE	1	0.53087744410696	2		533	618	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412639	139412639	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	141	476	0	ENST00000277541.6:c.1205C>A	p.Ser402Ter	p.S402*	ENST00000277541	NM_017617.3	402	tCg/tAg	7/34	1	2	FACETS	0.792	0.723	0.863	0.792	0.723	0.863	SUBCLONAL	1	TRUE	1	0.53087744410696	2		476	671	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793346	139793346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	147	497	0	ENST00000247668.2:c.154C>T	p.Arg52Trp	p.R52W	ENST00000247668	NM_021138.3	52	Cgg/Tgg	2/11	1	2	FACETS	0.943	0.865	1	0.943	0.865	1	CLONAL	1	TRUE	1	0.53087744410696	2		497	587	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412698	63412698	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	86	230	0	ENST00000330258.3:c.469G>C	p.Glu157Gln	p.E157Q	ENST00000330258	NM_152424.3	157	Gag/Cag	2/2	1	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.53087744410696	1		230	206	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0024871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	166	887	3	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.362525395919639	1	FACETS	0.968	0.891	1	0.968	0.891	1	CLONAL	1	TRUE	0	0.363968337025745	1		890	771	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0024871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	157	771	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.363968337025745	2		771	808	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048238	180048238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324497116	NA	P-0024871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	155	824	3	ENST00000261937.6:c.2035C>T	p.Arg679Trp	p.R679W	ENST00000261937	NM_182925.4	679	Cgg/Tgg	14/30	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.363968337025745	2		827	747	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359336	118359337	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTG	novel	NA	P-0024871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	84	303	0	ENST00000534358.1:c.4341_4343dup	p.Cys1448dup	p.C1448dup	ENST00000534358	NM_005933.3	1448	tat/taTTGt	11/36	0.362525395919639	1	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	0	0.363968337025745	1		303	377	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89809296	89809296	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	89	639	1	ENST00000389301.3:c.3677C>T	p.Ser1226Leu	p.S1226L	ENST00000389301	NM_000135.2	1226	tCa/tTa	37/43	1	2	FACETS	0.71	0.629	0.796	0.71	0.629	0.796	SUBCLONAL	1	TRUE	1	0.363968337025745	2		640	689	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7152816	7152816	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1365144382	NA	P-0024871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	131	675	0	ENST00000302850.5:c.2152C>T	p.Gln718Ter	p.Q718*	ENST00000302850	NM_000208.2	718	Cag/Tag	10/22	1	2	FACETS	0.951	0.864	1	0.951	0.864	1	CLONAL	1	TRUE	1	0.363968337025745	2		675	757	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53241070	53241070	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	110	520	0	ENST00000375401.3:c.1141G>A	p.Glu381Lys	p.E381K	ENST00000375401	NM_004187.3	381	Gaa/Aaa	9/26	1	2	FACETS	0.981	0.884	1	0.981	0.884	1	CLONAL	1	TRUE	1	0.363968337025745	2		520	616	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	95	855	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.162724099638007	3	FACETS	0.783	0.703	0.867	0.783	0.703	0.867	INDETERMINATE	2	TRUE	1	0.394595466246408	3		855	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579430	7579448	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGGGGCCGCCGGTGTAG	GCAGGGGCCGCCGGTGTAG	-	novel	NA	P-0024873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	324	548	0	ENST00000269305.4:c.239_257del	p.Pro80HisfsTer37	p.P80Hfs*37	ENST00000269305	NM_001126112.2	80	cCTACACCGGCGGCCCCTGCa/ca	4/11	0.370180270858681	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.394595466246408	1		548	1096	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578289	7578289	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	261	679	0	ENST00000269305.4:c.560del	p.Gly187ValfsTer60	p.G187Vfs*60	ENST00000269305	NM_001126112.2	187	gGt/gt	6/11	0.208171685400499	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	TRUE	1	0.208171685400499	4		679	953	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737135	145737135	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	174	764	0	ENST00000428558.2:c.3431del	p.Arg1144ProfsTer6	p.R1144Pfs*6	ENST00000428558	NM_004260.3	1144	cGc/cc	21/22	0.157643830712922	4	FACETS	0.816	0.749	0.885	0.816	0.749	0.885	CLONAL	2	TRUE	2	0.208171685400499	4		764	1238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0024877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	172	885	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.508420505442543	1	FACETS	0.85	0.786	0.915	0.85	0.786	0.915	CLONAL	1	TRUE	0	0.517446950459762	1		885	580	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439796	52439796	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	194	568	0	ENST00000460680.1:c.916G>T	p.Glu306Ter	p.E306*	ENST00000460680	NM_004656.3	306	Gag/Tag	10/17	0.493326185000847	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.517446950459762	1		568	526	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405044	70405044	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	54	604	1	ENST00000373644.4:c.2558G>T	p.Gly853Val	p.G853V	ENST00000373644	NM_030625.2	853	gGt/gTt	4/12	0.365659697000482	1	FACETS	0.418	0.358	0.483	0.418	0.358	0.483	SUBCLONAL	1	TRUE	0	0.517446950459762	1		605	370	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30060983	30060984	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0024877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	137	553	0	ENST00000338641.4:c.817_818dup	p.Lys274LeufsTer23	p.K274Lfs*23	ENST00000338641	NM_000268.3	272	act/acTAt	9/16	0.508420505442543	1	FACETS	0.986	0.907	1	0.986	0.907	1	CLONAL	1	TRUE	0	0.517446950459762	1		553	398	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164525	47164525	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	56	458	1	ENST00000409792.3:c.1601del	p.Pro534LeufsTer45	p.P534Lfs*45	ENST00000409792	NM_014159.6	534	cCt/ct	3/21	0.493326185000847	1	FACETS	0.79	0.687	0.899	0.79	0.687	0.899	SUBCLONAL	1	TRUE	0	0.517446950459762	1		459	203	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0024914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	348	853	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.220876046202057	3	FACETS	0.922	0.875	0.969	0.922	0.875	0.969	CLONAL	3	FALSE	0	0.307639453097858	3		853	944	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0024914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	280	659	0	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	0.126606507154236	4	FACETS	1	0.988	1			1	INDETERMINATE	3	FALSE	NA	0.307639453097858	4		659	686	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881392	37881392	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	577	885	0	ENST00000269571.5:c.2584A>G	p.Thr862Ala	p.T862A	ENST00000269571		862	Aca/Gca	21/27	0.126606507154236	4	FACETS	1	0.99	1			1	INDETERMINATE	4	FALSE	NA	0.307639453097858	4		885	1147	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424484	49424484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754146878	NA	P-0024914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	61	787	1	ENST00000301067.7:c.13739G>A	p.Gly4580Asp	p.G4580D	ENST00000301067	NM_003482.3	4580	gGc/gAc	41/54	0.174310720539101	3	FACETS	0.562	0.484	0.648	0.281	0.242	0.324	INDETERMINATE	1	FALSE	1	0.307639453097858	3		788	814	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724642	43724642	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	73	1009	0	ENST00000382044.4:c.3425A>G	p.Glu1142Gly	p.E1142G	ENST00000382044	NM_001141980.1	1142	gAa/gGa	17/28	1	2	FACETS	0.534	0.466	0.608	0.534	0.466	0.608	SUBCLONAL	1	FALSE	1	0.307639453097858	2		1009	888	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925146	81925146	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748440029	NA	P-0024914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	61	741	1	ENST00000359376.3:c.937G>A	p.Asp313Asn	p.D313N	ENST00000359376	NM_002661.3	313	Gac/Aac	11/33	0.307639453097858	3	FACETS	0.601	0.518	0.693	0.301	0.259	0.347	SUBCLONAL	1	FALSE	1	0.307639453097858	3		742	761	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101103	4101103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs727504382	NA	P-0024914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	64	538	2	ENST00000262948.5:c.619G>A	p.Glu207Lys	p.E207K	ENST00000262948	NM_030662.3	207	Gag/Aag	6/11	1	2	FACETS	0.872	0.757	0.997	0.872	0.757	0.997	CLONAL	1	FALSE	1	0.307639453097858	2		540	477	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626942	14626942	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	148	872	1	ENST00000254322.2:c.833G>T	p.Gly278Val	p.G278V	ENST00000254322	NM_006145.1	278	gGc/gTc	3/3	0.212564723544824	3	FACETS	1	0.976	1	0.599	0.546	0.654	CLONAL	1	FALSE	1	0.307639453097858	3		873	927	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953157	17953157	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	86	1051	0	ENST00000458235.1:c.829G>C	p.Gly277Arg	p.G277R	ENST00000458235	NM_000215.3	277	Ggc/Cgc	6/24	0.212564723544824	3	FACETS	0.652	0.576	0.735	0.326	0.288	0.368	SUBCLONAL	1	FALSE	1	0.307639453097858	3		1051	989	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0024915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	74	683	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.907	0.792	1	0.907	0.792	1	CLONAL	1	TRUE	1	0.17	2		683	960	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0024917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	202	657	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.752904331580883	2		657	516	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0024917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	268	678	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.752904331580883	2		678	636	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0024917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	139	432	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.752904331580883	2		432	337	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0024917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	180	591	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	0.974	0.906	1	0.974	0.906	1	CLONAL	1	TRUE	1	0.752904331580883	2		591	491	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934606	9934606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	159	546	0	ENST00000330684.3:c.1549G>A	p.Glu517Lys	p.E517K	ENST00000330684	NM_001134407.1	517	Gaa/Aaa	7/13	1	2	FACETS	0.924	0.855	0.995	0.924	0.855	0.995	CLONAL	1	TRUE	1	0.752904331580883	2		546	457	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134269	11134269	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	208	700	0	ENST00000358026.2:c.2935C>T	p.Arg979Ter	p.R979*	ENST00000358026	NM_001128849.1	979	Cga/Tga	20/36	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.752904331580883	2		700	513	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716134	243716134	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	214	801	0	ENST00000263826.5:c.1060C>T	p.Leu354Phe	p.L354F	ENST00000263826	NM_005465.4	354	Ctt/Ttt	10/13	0.752904331580883	3	FACETS	0.885	0.824	0.949	0.443	0.412	0.475	CLONAL	1	TRUE	1	0.752904331580883	3		801	884	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624256	89624256	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1564801689	NA	P-0024917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	114	362	0	ENST00000371953.3:c.30C>G	p.Ser10Arg	p.S10R	ENST00000371953	NM_000314.4	10	agC/agG	1/9	1	2	FACETS	0.971	0.886	1	0.971	0.886	1	CLONAL	1	TRUE	1	0.752904331580883	2		362	312	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717741	89717741	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	174	556	0	ENST00000371953.3:c.766del	p.Glu256SerfsTer10	p.E256Sfs*10	ENST00000371953	NM_000314.4	256	Gag/ag	7/9	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.752904331580883	2		556	459	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168977	11168977	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs758517117	NA	P-0024917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	194	800	2	ENST00000358026.2:c.4567C>T	p.Arg1523Ter	p.R1523*	ENST00000358026	NM_001128849.1	1523	Cga/Tga	32/36	1	2	FACETS	0.935	0.872	1	0.935	0.872	1	CLONAL	1	TRUE	1	0.752904331580883	2		802	551	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872810	136872811	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0024917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	135	465	0	ENST00000241393.3:c.687dup	p.Lys230GlnfsTer46	p.K230Qfs*46	ENST00000241393	NM_003467.2	229	-/C	2/2	1	2	FACETS	0.967	0.889	1	0.967	0.889	1	CLONAL	1	TRUE	1	0.752904331580883	2		465	371	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	332	855	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.267802428056126	3	FACETS	0.873	0.829	0.918	0.873	0.829	0.918	INDETERMINATE	2	TRUE	1	0.562549949996342	3		855	866	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342575	87342575	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	128	481	0	ENST00000277120.3:c.860C>A	p.Pro287Gln	p.P287Q	ENST00000277120		287	cCa/cAa	9/19	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.562549949996342	2		481	439	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615110	100615110	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	252	867	0	ENST00000308731.7:c.805G>A	p.Val269Ile	p.V269I	ENST00000308731	NM_000061.2	269	Gtc/Atc	9/19	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.562549949996342	2		867	807	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844747	156844747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771342578	NA	P-0024920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	190	867	0	ENST00000524377.1:c.1301C>T	p.Thr434Met	p.T434M	ENST00000524377	NM_002529.3	434	aCg/aTg	11/17	0.329972736731212	3	FACETS	0.644	0.594	0.696	0.215	0.198	0.232	INDETERMINATE	1	TRUE	0	0.656003443033738	3		867	1194	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986523	36986523	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1330324860	NA	P-0024920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	307	947	2	ENST00000354822.5:c.1166C>T	p.Thr389Ile	p.T389I	ENST00000354822	NM_001079668.2	389	aCc/aTc	3/3	1	2	FACETS	0.966	0.912	1	0.966	0.912	1	CLONAL	1	TRUE	1	0.656003443033738	2		949	969	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148922	119148922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768898787	NA	P-0024921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	104	489	0	ENST00000264033.4:c.1142G>A	p.Cys381Tyr	p.C381Y	ENST00000264033	NM_005188.3	381	tGt/tAt	8/16	0.438838013562128	1	FACETS	0.944	0.852	1	0.944	0.852	1	CLONAL	1	TRUE	0	0.438838013562128	1		489	392	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023108	31023108	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs147895689	NA	P-0024921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	174	593	0	ENST00000375687.4:c.2593G>T	p.Glu865Ter	p.E865*	ENST00000375687	NM_015338.5	865	Gaa/Taa	13/13	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.438838013562128	2		593	721	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844792	156844792	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	42	627	0	ENST00000524377.1:c.1346G>C	p.Gly449Ala	p.G449A	ENST00000524377	NM_002529.3	449	gGg/gCg	11/17	NA	2	FACETS	0.23	0.191	0.274			1	INDETERMINATE	1	TRUE	NA	0.438838013562128	2		627	832	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456423	32456424	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0024921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	195	718	2	ENST00000332351.3:c.468_469delinsAA	p.Cys156_Leu157delinsTer	p.C156_L157delins*	ENST00000332351	NM_024426.4	156	tgCCtg/tgAAtg	1/10	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.438838013562128	2		720	872	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857426	9857426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	121	562	0	ENST00000330684.3:c.3975C>A	p.Tyr1325Ter	p.Y1325*	ENST00000330684	NM_001134407.1	1325	taC/taA	13/13	0.438838013562128	1	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	0	0.438838013562128	1		562	430	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799517	72799517	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	158	752	1	ENST00000325599.8:c.1652A>G	p.Gln551Arg	p.Q551R	ENST00000325599	NM_018130.2	551	cAg/cGg	11/11	0.438838013562128	1	FACETS	0.806	0.741	0.875	0.806	0.741	0.875	CLONAL	1	TRUE	0	0.438838013562128	1		753	697	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919164	178919164	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	66	349	0	ENST00000263967.3:c.649C>G	p.Pro217Ala	p.P217A	ENST00000263967	NM_006218.2	217	Cca/Gca	4/21	0.270414893306781	3	FACETS	0.826	0.719	0.941	0.413	0.359	0.471	CLONAL	1	TRUE	1	0.438838013562128	3		349	444	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928053	178928053	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	160	678	0	ENST00000263967.3:c.1331A>T	p.Asn444Ile	p.N444I	ENST00000263967	NM_006218.2	444	aAt/aTt	8/21	0.270414893306781	3	FACETS	1	0.979	1	0.595	0.547	0.646	CLONAL	1	TRUE	1	0.438838013562128	3		678	747	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189937	66189937	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	67	298	1	ENST00000273854.3:c.3009G>T	p.Glu1003Asp	p.E1003D	ENST00000273854	NM_004439.5	1003	gaG/gaT	18/18	0.438838013562128	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.438838013562128	1		299	218	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401736	401736	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	107	625	0	ENST00000380956.4:c.1058A>T	p.Asp353Val	p.D353V	ENST00000380956	NM_001195286.1	353	gAc/gTc	7/9	1	2	FACETS	0.783	0.703	0.867	0.783	0.703	0.867	SUBCLONAL	1	TRUE	1	0.438838013562128	2		625	623	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050712	30050713	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0024923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	139	541	0	ENST00000338641.4:c.514_515del	p.Arg172GlyfsTer30	p.R172Gfs*30	ENST00000338641	NM_000268.3	172	AGg/g	5/16	0.724126898610589	1	FACETS	0.921	0.857	0.985	0.921	0.857	0.985	CLONAL	1	TRUE	0	0.724126898610589	1		541	266	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	133	629	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.427405440431607	3	FACETS	0.862	0.784	0.942			1	CLONAL	1	TRUE	NA	0.610581238065569	3		629	660	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584560	48584560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	121	551	0	ENST00000342988.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000342988	NM_005359.5	245	Cag/Tag	6/12	0.610581238065569	1	FACETS	0.987	0.907	1	0.987	0.907	1	CLONAL	1	TRUE	0	0.610581238065569	1		551	279	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0024924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	86	256	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.427405440431607	3	FACETS	1	0.937	1			1	CLONAL	1	TRUE	NA	0.610581238065569	3		256	343	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11177098	11177098	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	131	597	0	ENST00000361445.4:c.6979A>G	p.Met2327Val	p.M2327V	ENST00000361445	NM_004958.3	2327	Atg/Gtg	50/58	1	2	FACETS	0.881	0.805	0.96	0.881	0.805	0.96	CLONAL	1	TRUE	1	0.610581238065569	2		597	487	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0024924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	286	622	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.610581238065569	3	FACETS	0.907	0.859	0.956	0.907	0.859	0.956	CLONAL	2	TRUE	1	0.610581238065569	3		622	674	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521721	89521721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372594677	NA	P-0024924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	133	471	0	ENST00000336596.2:c.2798C>T	p.Thr933Met	p.T933M	ENST00000336596	NM_005233.5	933	aCg/aTg	16/17	0.610581238065569	3	FACETS	1	0.969	1	0.565	0.516	0.616	CLONAL	1	TRUE	1	0.610581238065569	3		471	503	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610043	43610043	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	82	841	2	ENST00000355710.3:c.1995C>A	p.His665Gln	p.H665Q	ENST00000355710	NM_020975.4	665	caC/caA	11/20	0.176433536632863	2	FACETS	0.633	0.561	0.71	0.317	0.28	0.355	INDETERMINATE	1	TRUE	0	0.610581238065569	2		843	424	SUCCESS
RET	5979	MSKCC	GRCh37	10	43613833	43613833	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1017108031	NA	P-0024924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	111	779	0	ENST00000355710.3:c.2297C>T	p.Pro766Leu	p.P766L	ENST00000355710	NM_020975.4	766	cCg/cTg	13/20	0.176433536632863	2	FACETS	0.797	0.721	0.877	0.399	0.36	0.439	INDETERMINATE	1	TRUE	0	0.610581238065569	2		779	456	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332772	70332772	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	118	551	0	ENST00000373644.4:c.677G>T	p.Gly226Val	p.G226V	ENST00000373644	NM_030625.2	226	gGa/gTa	2/12	0.610581238065569	3	FACETS	0.851	0.77	0.936	0.425	0.385	0.468	CLONAL	1	TRUE	1	0.610581238065569	3		551	593	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244702	41244702	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	198	778	0	ENST00000357654.3:c.2846G>C	p.Gly949Ala	p.G949A	ENST00000357654	NM_007294.3	949	gGc/gCc	10/23	0.610581238065569	3	FACETS	0.87	0.806	0.937	0.435	0.403	0.469	CLONAL	1	TRUE	1	0.610581238065569	3		778	973	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919537	78919538	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCCTTCACG	novel	NA	P-0024924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	119	552	0	ENST00000306801.3:c.3099_3107dup	p.Phe1034_Pro1036dup	p.F1034_P1036dup	ENST00000306801	NM_020761.2	1034	-/CCCTTCACG	26/34	0.610581238065569	3	FACETS	0.923	0.837	1	0.462	0.418	0.507	CLONAL	1	TRUE	1	0.610581238065569	3		552	551	SUCCESS
APC	324	MSKCC	GRCh37	5	112173879	112173879	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1561578213	NA	P-0024924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	76	416	0	ENST00000257430.4:c.2588A>G	p.Tyr863Cys	p.Y863C	ENST00000257430	NM_000038.5	863	tAc/tGc	16/16	0.427405440431607	3	FACETS	0.926	0.818	1			1	CLONAL	1	TRUE	NA	0.610581238065569	3		416	351	SUCCESS
APC	324	MSKCC	GRCh37	5	112174223	112174224	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0024924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	163	439	0	ENST00000257430.4:c.2935dup	p.Met979AsnfsTer6	p.M979Nfs*6	ENST00000257430	NM_000038.5	978	caa/cAaa	16/16	0.427405440431607	3	FACETS	0.761	0.705	0.818			1	SUBCLONAL	2	TRUE	NA	0.610581238065569	3		439	458	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381454	81381454	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	58	374	0	ENST00000222390.5:c.607A>G	p.Ile203Val	p.I203V	ENST00000222390	NM_000601.4	203	Att/Gtt	5/18	0.610581238065569	3	FACETS	0.758	0.655	0.869	0.379	0.327	0.435	SUBCLONAL	1	TRUE	1	0.610581238065569	3		374	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0024925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	213	683	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.202430679037409	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.202430679037409	2		683	842	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120987	115120987	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	40	675	0	ENST00000257566.3:c.19G>C	p.Asp7His	p.D7H	ENST00000257566	NM_016569.3	7	Gat/Cat	1/8	0.191778459463919	4	FACETS	0.678	0.562	0.808	0.226	0.187	0.27	SUBCLONAL	1	TRUE	1	0.202430679037409	4		675	701	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041353	42041353	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	84	752	0	ENST00000219905.7:c.5548G>C	p.Glu1850Gln	p.E1850Q	ENST00000219905	NM_001164273.1	1850	Gag/Cag	17/24	0.144565506967008	4	FACETS	1	0.882	1	0.5	0.441	0.565	CLONAL	1	TRUE	2	0.202430679037409	4		752	997	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346851	91346851	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	57	593	0	ENST00000355112.3:c.3459G>C	p.Lys1153Asn	p.K1153N	ENST00000355112	NM_000057.2	1153	aaG/aaC	18/22	0.144565506967008	4	FACETS	0.943	0.808	1	0.472	0.404	0.546	CLONAL	1	TRUE	2	0.202430679037409	4		593	718	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639021	3639021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769950582	NA	P-0024925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	78	755	1	ENST00000294008.3:c.4618G>A	p.Glu1540Lys	p.E1540K	ENST00000294008	NM_032444.2	1540	Gaa/Aaa	12/15	0.202430679037409	3	FACETS	1	0.94	1	0.558	0.49	0.632	CLONAL	1	TRUE	1	0.202430679037409	3		756	760	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900428	3900428	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	87	853	0	ENST00000262367.5:c.668G>C	p.Gly223Ala	p.G223A	ENST00000262367	NM_004380.2	223	gGa/gCa	2/31	0.202430679037409	3	FACETS	1	0.916	1	0.522	0.461	0.588	CLONAL	1	TRUE	1	0.202430679037409	3		853	906	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825479	50825479	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	44	459	0	ENST00000398568.2:c.2110C>G	p.Gln704Glu	p.Q704E	ENST00000398568	NM_001042412.1	704	Caa/Gaa	14/18	0.144565506967008	4	FACETS	1	0.862	1	0.515	0.432	0.608	CLONAL	1	TRUE	2	0.202430679037409	4		459	507	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968325	15968325	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	45	422	0	ENST00000268712.3:c.4960G>C	p.Asp1654His	p.D1654H	ENST00000268712	NM_006311.3	1654	Gac/Cac	34/46	0.202430679037409	2	FACETS	1	0.914	1	0.567	0.477	0.666	CLONAL	1	TRUE	0	0.202430679037409	2		422	392	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40880910	40880910	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	92	881	0	ENST00000428826.2:c.50G>C	p.Arg17Thr	p.R17T	ENST00000428826		17	aGa/aCa	3/21	0.202430679037409	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.202430679037409	1		881	783	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956522	93956522	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	46	545	0	ENST00000369303.4:c.2714G>C	p.Gly905Ala	p.G905A	ENST00000369303	NM_004440.3	905	gGa/gCa	15/17	0.202430679037409	2	FACETS	0.935	0.788	1	0.468	0.394	0.549	CLONAL	1	TRUE	0	0.202430679037409	2		545	486	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054879	5054879	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	33	505	0	ENST00000381652.3:c.931G>T	p.Glu311Ter	p.E311*	ENST00000381652	NM_004972.3	311	Gaa/Taa	7/25	0.202430679037409	1	FACETS	0.933	0.762	1	0.933	0.762	1	CLONAL	1	TRUE	0	0.202430679037409	1		505	314	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436624	52436624	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs387906848	NA	P-0000332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	146	698	0	ENST00000460680.1:c.2050C>T	p.Gln684Ter	p.Q684*	ENST00000460680	NM_004656.3	684	Cag/Tag	16/17	1	2	FACETS	0.918	0.839	1	0.918	0.839	1	CLONAL	1	TRUE	1	0.391572352278572	2		698	812	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263454	123263454	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	26	470	0	ENST00000358487.5:c.1289T>G	p.Val430Gly	p.V430G	ENST00000358487	NM_000141.4	430	gTt/gGt	10/18	1	2	FACETS	0.259	0.204	0.322	0.259	0.204	0.322	SUBCLONAL	1	TRUE	1	0.391572352278572	2		470	513	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519886	NA	P-0001244-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	136	524	0	ENST00000349496.5:c.97T>C	p.Ser33Pro	p.S33P	ENST00000349496	NM_001904.3	33	Tct/Cct	3/15	1	2	FACETS	0.968	0.885	1	0.968	0.885	1	CLONAL	1	TRUE	1	0.521238784413907	2		524	539	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288495	15288495	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001244-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	77	335	0	ENST00000263388.2:c.4244G>A	p.Gly1415Asp	p.G1415D	ENST00000263388	NM_000435.2	1415	gGc/gAc	24/33	1	2	FACETS	0.901	0.797	1	0.901	0.797	1	CLONAL	1	TRUE	1	0.521238784413907	2		335	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0002995-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	309	914	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.290585551094021	3	FACETS	0.916	0.867	0.967	0.916	0.867	0.967	CLONAL	3	TRUE	0	0.290929673712384	3		914	885	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567317	226567317	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002995-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	63	684	0	ENST00000366794.5:c.1569G>C	p.Met523Ile	p.M523I	ENST00000366794	NM_001618.3	523	atG/atC	11/23	0.195919599353158	5	FACETS	0.846	0.731	0.972	0.282	0.243	0.324	CLONAL	1	TRUE	2	0.290929673712384	5		684	735	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470950	25470950	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002995-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	95	858	1	ENST00000264709.3:c.811G>A	p.Asp271Asn	p.D271N	ENST00000264709	NM_175629.2	271	Gac/Aac	7/23	0.273078377131988	5	FACETS	0.97	0.862	1	0.323	0.287	0.362	CLONAL	1	TRUE	2	0.290929673712384	5		859	967	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965690	25965690	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002995-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	103	874	0	ENST00000435504.4:c.3516G>C	p.Glu1172Asp	p.E1172D	ENST00000435504		1172	gaG/gaC	13/13	0.273078377131988	5	FACETS	0.911	0.813	1	0.304	0.271	0.339	CLONAL	1	TRUE	2	0.290929673712384	5		874	1116	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702205	47702205	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002995-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	99	594	0	ENST00000233146.2:c.1801C>G	p.Gln601Glu	p.Q601E	ENST00000233146	NM_000251.2	601	Cag/Gag	12/16	0.273078377131988	5	FACETS	1	0.97	1	0.417	0.372	0.465	CLONAL	1	TRUE	2	0.290929673712384	5		594	781	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033771	48033771	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002995-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	40	368	0	ENST00000234420.5:c.3982C>A	p.Gln1328Lys	p.Q1328K	ENST00000234420	NM_000179.2	1328	Cag/Aag	9/10	0.273078377131988	5	FACETS	0.859	0.714	1	0.286	0.238	0.34	CLONAL	1	TRUE	2	0.290929673712384	5		368	460	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665015	138665015	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002995-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	38	220	0	ENST00000330315.3:c.550G>C	p.Asp184His	p.D184H	ENST00000330315	NM_023067.3	184	Gac/Cac	1/1	0.290929673712384	3	FACETS	1	0.947	1	0.689	0.575	0.815	CLONAL	1	TRUE	1	0.290929673712384	3		220	217	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645036	86645036	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002995-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	41	371	0	ENST00000274376.6:c.1108C>G	p.Gln370Glu	p.Q370E	ENST00000274376	NM_002890.2	370	Caa/Gaa	8/25	1	2	FACETS	0.74	0.617	0.875	0.74	0.617	0.875	SUBCLONAL	1	TRUE	1	0.290929673712384	2		371	381	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056399	180056399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002995-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	84	644	0	ENST00000261937.6:c.845G>A	p.Arg282Gln	p.R282Q	ENST00000261937	NM_182925.4	282	cGa/cAa	7/30	0.286111374920341	4	FACETS	1	0.928	1	0.357	0.315	0.401	CLONAL	1	TRUE	1	0.290929673712384	4		644	697	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158417	26158417	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs368384735	NA	P-0002995-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	110	974	0	ENST00000289316.2:c.20C>G	p.Ser7Cys	p.S7C	ENST00000289316	NM_138720.2	7	tCt/tGt	1/2	0.261201958601287	4	FACETS	0.892	0.799	0.99			1	CLONAL	1	TRUE	NA	0.290929673712384	4		974	1095	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277102	38277102	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002995-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1206	83	800	0	ENST00000425967.3:c.1326G>C	p.Gln442His	p.Q442H	ENST00000425967	NM_001174067.1	442	caG/caC	10/19	0.290929673712384	8	FACETS	0.829	0.729	0.937	0.118	0.104	0.134	CLONAL	1	TRUE	1	0.290929673712384	8		800	1289	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250386	110250386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752786911	NA	P-0002995-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	131	919	1	ENST00000374672.4:c.289G>A	p.Glu97Lys	p.E97K	ENST00000374672	NM_004235.4	97	Gag/Aag	3/5	0.259755314067774	2	FACETS	1	0.964	1	0.561	0.509	0.615	CLONAL	1	TRUE	0	0.290929673712384	2		920	803	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88672017	88672017	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1131691185	NA	P-0002995-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	75	705	0	ENST00000372037.3:c.551C>G	p.Ser184Ter	p.S184*	ENST00000372037	NM_004329.2	184	tCa/tGa	8/13	0.290929673712384	3	FACETS	0.855	0.749	0.969	0.427	0.374	0.485	CLONAL	1	TRUE	1	0.290929673712384	3		705	691	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795082	42795082	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002995-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	168	1001	0	ENST00000575354.2:c.2162C>G	p.Ser721Cys	p.S721C	ENST00000575354	NM_015125.3	721	tCc/tGc	10/20	0.290929673712384	5	FACETS	1	0.981	1	0.411	0.377	0.448	CLONAL	1	TRUE	2	0.290929673712384	5		1001	1344	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223756	53223756	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002995-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	107	1075	0	ENST00000375401.3:c.3603G>C	p.Gln1201His	p.Q1201H	ENST00000375401	NM_004187.3	1201	caG/caC	23/26	0.213154858186551	1	FACETS	0.677	0.607	0.753	0.677	0.607	0.753	SUBCLONAL	1	TRUE	0	0.290929673712384	1		1075	928	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117311	115117311	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002995-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	103	461	0	ENST00000257566.3:c.863del	p.Lys288ArgfsTer2	p.K288Rfs*2	ENST00000257566	NM_016569.3	288	aAg/ag	4/8	0.280476654378138	3	FACETS	0.836	0.752	0.925	0.836	0.752	0.925	CLONAL	2	TRUE	1	0.290929673712384	3		461	485	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855965	68856011	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCCCCATACCAGAACCTCGAACTATATTCTTCTGTGAGAGGAATC	CGCCCCCATACCAGAACCTCGAACTATATTCTTCTGTGAGAGGAATC	-	novel	NA	P-0002995-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	221	740	0	ENST00000261769.5:c.1774_1820del	p.Ala592LysfsTer9	p.A592Kfs*9	ENST00000261769	NM_004360.3	591	aaCGCCCCCATACCAGAACCTCGAACTATATTCTTCTGTGAGAGGAATCca/aaca	12/16	0.259755314067774	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.290929673712384	2		740	729	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12393128	12393128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002995-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	58	762	0	ENST00000287820.6:c.37G>A	p.Glu13Lys	p.E13K	ENST00000287820	NM_015869.4	13	Gaa/Aaa	1/7	1	2	FACETS	0.531	0.455	0.614	0.531	0.455	0.614	SUBCLONAL	1	TRUE	1	0.290929673712384	2		762	751	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128246731	128246731	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754789924	NA	P-0002995-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1474	88	673	0	ENST00000265960.3:c.1198G>A	p.Val400Ile	p.V400I	ENST00000265960	NM_001006617.1	400	Gta/Ata	9/12	0.290929673712384	11	FACETS	0.894	0.789	1			1	CLONAL	1	TRUE	NA	0.290929673712384	11		673	1562	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128321931	128321931	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002995-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1515	82	646	0	ENST00000265960.3:c.829G>C	p.Glu277Gln	p.E277Q	ENST00000265960	NM_001006617.1	277	Gag/Cag	6/12	0.290929673712384	11	FACETS	0.815	0.715	0.923			1	CLONAL	1	TRUE	NA	0.290929673712384	11		646	1597	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131215	55131215	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	rs1214333123	NA	P-0121460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	223	444	0	ENST00000257290.5:c.758T>A	p.Val253Glu	p.V253E	ENST00000257290	NM_006206.4	253	gTg/gAg	5/23	1	2	FACETS	0.905	0.85	0.96	0.905	0.85	0.96	CLONAL	1	NA	1	0.917978843853827	2		444	537	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982070	93982070	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0121460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	349	577	0	ENST00000369303.4:c.1395A>T	p.Glu465Asp	p.E465D	ENST00000369303	NM_004440.3	465	gaA/gaT	6/17	1	2	FACETS	0.984	0.937	1	0.984	0.937	1	CLONAL	1	NA	1	0.917978843853827	2		577	773	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937684	76937684	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0121460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	441	360	0	ENST00000373344.5:c.3064C>T	p.Arg1022Ter	p.R1022*	ENST00000373344	NM_000489.3	1022	Cga/Tga	9/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	NA	0	0.917978843853827	1		360	483	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817912	3817912	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0121460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	287	560	0	ENST00000262367.5:c.3061-2A>G		p.X1021_splice	ENST00000262367	NM_004380.2	1021			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	NA	1	0.917978843853827	2		560	599	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778455	3778455	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0121460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	427	763	0	ENST00000262367.5:c.6593del	p.Leu2198ArgfsTer104	p.L2198Rfs*104	ENST00000262367	NM_004380.2	2198	cTg/cg	31/31	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	NA	1	0.917978843853827	2		763	878	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89355037	89355037	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0121460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	367	720	0	ENST00000301030.4:c.643G>A	p.Asp215Asn	p.D215N	ENST00000301030	NM_001256183.1	215	Gac/Aac	7/13	0.917978843853827	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	NA	0	0.917978843853827	1		720	402	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353784	40353784	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1479	352	764	0	ENST00000293328.3:c.2336G>T	p.Ser779Ile	p.S779I	ENST00000293328	NM_012448.3	779	aGt/aTt	19/19	0.917978843853827	5	FACETS	0.996	0.94	1	0.249	0.235	0.264	CLONAL	1	NA	1	0.917978843853827	5		764	1831	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285891	39285891	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	391	614	0	ENST00000402219.2:c.268G>T	p.Ala90Ser	p.A90S	ENST00000402219	NM_005633.3	90	Gcc/Tcc	3/23	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	NA	1	0.917978843853827	2		614	849	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003274	143003274	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0121460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	469	688	0	ENST00000262992.4:c.2552T>C	p.Met851Thr	p.M851T	ENST00000262992	NM_001101669.1	851	aTg/aCg	23/24	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	NA	1	0.917978843853827	2		688	997	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628384	187628385	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0121460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	448	838	0	ENST00000441802.2:c.2597dup	p.Asp866GlufsTer6	p.D866Efs*6	ENST00000441802	NM_005245.3	866	gac/gaAc	2/27	0.917978843853827	3	FACETS	0.953	0.908	0.998	0.476	0.454	0.499	CLONAL	1	NA	1	0.917978843853827	3		838	1495	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003223-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	304	238	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.878124439353845	3	FACETS	1	0.968	1	0.518	0.489	0.548	CLONAL	1	TRUE	1	0.878124439353845	3		238	962	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912359	97912359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554302947	NA	P-0003223-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	240	547	0	ENST00000289081.3:c.532G>A	p.Glu178Lys	p.E178K	ENST00000289081	NM_000136.2	178	Gag/Aag	7/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.878124439353845	2		547	527	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857481	68857481	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003223-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	419	818	0	ENST00000261769.5:c.2116C>T	p.Gln706Ter	p.Q706*	ENST00000261769	NM_004360.3	706	Caa/Taa	13/16	0.878124439353845	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.878124439353845	1		818	513	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043412	6043412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1243546223	NA	P-0003223-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	10	65	0	ENST00000265849.7:c.262C>T	p.His88Tyr	p.H88Y	ENST00000265849	NM_000535.5	88	Cac/Tac	4/15	0.878124439353845	3	FACETS	0.345	0.236	0.479	0.173	0.118	0.24	SUBCLONAL	1	TRUE	1	0.878124439353845	3		65	95	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782329	NA	P-0003862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	216	288	0	ENST00000269305.4:c.746G>C	p.Arg249Thr	p.R249T	ENST00000269305	NM_001126112.2	249	aGg/aCg	7/11	0.449701150107585	2	FACETS	0.855	0.802	0.908	0.855	0.802	0.908	CLONAL	2	TRUE	0	0.479545482560064	2		288	527	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274854	142274854	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769252606	NA	P-0003862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	89	439	1	ENST00000350721.4:c.2206G>A	p.Gly736Arg	p.G736R	ENST00000350721	NM_001184.3	736	Gga/Aga	10/47	1	2	FACETS	0.423	0.374	0.476	0.423	0.374	0.476	SUBCLONAL	1	TRUE	1	0.479545482560064	2		440	877	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664899	29664899	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs1060500376	NA	P-0003862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	165	353	0	ENST00000356175.3:c.6641+1G>C		p.X2214_splice	ENST00000356175	NM_000267.3	2214			0.479545482560064	1	FACETS	0.911	0.842	0.983	0.911	0.842	0.983	CLONAL	1	TRUE	0	0.479545482560064	1		353	574	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483311	120483311	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0003862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	164	327	0	ENST00000256646.2:c.3050del	p.Phe1017SerfsTer19	p.F1017Sfs*19	ENST00000256646	NM_024408.3	1017	tTc/tc	19/34	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.479545482560064	2		327	649	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0004229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	16	230	0	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS	0.137	0.1	0.181	0.137	0.1	0.181	SUBCLONAL	1	TRUE	1	0.49	2		230	477	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964925	55964925	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	38	339	0	ENST00000263923.4:c.2312C>G	p.Thr771Arg	p.T771R	ENST00000263923	NM_002253.2	771	aCg/aGg	16/30	1	2	FACETS	0.26	0.214	0.311	0.26	0.214	0.311	SUBCLONAL	1	TRUE	1	0.49	2		339	597	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0004635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	65	214	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	1	2	FACETS	0.811	0.707	0.923	0.811	0.707	0.923	CLONAL	1	TRUE	1	0.425088907590717	2		214	377	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0004635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	34	336	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.737	0.607	0.881	0.737	0.607	0.881	SUBCLONAL	1	TRUE	1	0.425088907590717	2		336	217	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433650	49433650	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs794727549	NA	P-0004635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	80	181	0	ENST00000301067.7:c.7903C>T	p.Arg2635Ter	p.R2635*	ENST00000301067	NM_003482.3	2635	Cga/Tga	31/54	1	2	FACETS	0.774	0.692	0.86	1	0.981	1	SUBCLONAL	2	TRUE	1	0.425088907590717	2		181	243	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968473	55968610	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GATAACATCCCTGGGAAAGTTCTGCAACCCAAGAGTGATAGCCAAATTCTATTTACCTGAGTCTTCTACAAGGGTCTCATTATCTTTAAACCACATGATCTGTGGAGGGGGATTCCCAGATGCCGTGCATGAGACTTC	GATAACATCCCTGGGAAAGTTCTGCAACCCAAGAGTGATAGCCAAATTCTATTTACCTGAGTCTTCTACAAGGGTCTCATTATCTTTAAACCACATGATCTGTGGAGGGGGATTCCCAGATGCCGTGCATGAGACTTC	-	novel	NA	P-0004635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	102	122	0	ENST00000263923.4:c.2053_2134+56del		p.X685_splice	ENST00000263923	NM_002253.2	685		14/30	1	2	FACETS	1	0.929	1	1	0.989	1	CLONAL	2	TRUE	1	0.425088907590717	2		122	235	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0004722-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	267	830	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.806667240551958	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.814352610092936	2		832	316	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0005213-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	50	983	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.22	2		984	394	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696688	47696688	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519971	NA	P-0005213-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	37	370	0	ENST00000347630.2:c.260A>G	p.Tyr87Cys	p.Y87C	ENST00000347630	NM_001007230.1	87	tAc/tGc	5/11	1	2	FACETS	0.759	0.626	0.908	0.759	0.626	0.908	CLONAL	1	TRUE	1	0.22	2		370	443	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609314	39609314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766344105	NA	P-0005213-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	36	192	0	ENST00000262039.4:c.1616G>A	p.Arg539His	p.R539H	ENST00000262039	NM_002647.2	539	cGt/cAt	15/25	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.22	2		192	297	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740553	58740554	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0005213-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	25	369	0	ENST00000305921.3:c.1459dup	p.His487ProfsTer2	p.H487Pfs*2	ENST00000305921	NM_003620.3	486	-/C	6/6	1	2	FACETS	0.531	0.418	0.662	0.531	0.418	0.662	SUBCLONAL	1	TRUE	1	0.22	2		369	428	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0005423-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	181	238	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	NA	2	FACETS	1	0.96	1			1	INDETERMINATE	1	TRUE	NA	0.758691405424326	2		238	458	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115875	8115879	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCT	GCCCT	-	novel	NA	P-0005423-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	249	585	0	ENST00000346208.3:c.1221_1225del	p.Pro408GlnfsTer97	p.P408Qfs*97	ENST00000346208		407	tcGCCCTtc/tctc	6/6	1	2	FACETS	0.927	0.871	0.984	0.927	0.871	0.984	CLONAL	1	TRUE	1	0.758691405424326	2		585	708	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660603	190660603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005423-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	176	387	0	ENST00000441310.2:c.241C>T	p.His81Tyr	p.H81Y	ENST00000441310	NM_000534.4	81	Cat/Tat	3/13	1	2	FACETS	0.932	0.865	0.999	0.932	0.865	0.999	CLONAL	1	TRUE	1	0.758691405424326	2		387	498	SUCCESS
ATR	545	MSKCC	GRCh37	3	142168411	142168411	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005423-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	165	495	2	ENST00000350721.4:c.7795C>A	p.Leu2599Ile	p.L2599I	ENST00000350721	NM_001184.3	2599	Cta/Ata	47/47	NA	2	FACETS	0.946	0.876	1			1	INDETERMINATE	1	TRUE	NA	0.758691405424326	2		497	460	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982040	38982040	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005423-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	270	577	0	ENST00000357387.3:c.682A>T	p.Ile228Phe	p.I228F	ENST00000357387	NM_152756.3	228	Att/Ttt	8/38	0.719985636506816	3	FACETS	1	0.968	1	0.523	0.491	0.555	CLONAL	1	TRUE	1	0.758691405424326	3		577	939	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991118	41991118	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs761422551	NA	P-0005423-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	493	535	0	ENST00000219905.7:c.2071G>T	p.Ala691Ser	p.A691S	ENST00000219905	NM_001164273.1	691	Gca/Tca	4/24	1	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	1	0.758691405424326	2		535	899	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41276047	41276047	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	GG	novel	NA	P-0005423-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	220	578	0	ENST00000357654.3:c.67delinsCC	p.Glu23ProfsTer18	p.E23Pfs*18	ENST00000357654	NM_007294.3	23	Gag/CCag	2/23	1	2	FACETS	0.869	0.813	0.927	0.869	0.813	0.927	CLONAL	1	TRUE	1	0.758691405424326	2		578	667	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0005423-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	40	238	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.155704206701794	3	FACETS	0.761	0.634	0.903	0.381	0.317	0.452	INDETERMINATE	1	TRUE	1	0.32	3		238	381	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115875	8115879	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCT	GCCCT	-	novel	NA	P-0005423-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	45	585	0	ENST00000346208.3:c.1221_1225del	p.Pro408GlnfsTer97	p.P408Qfs*97	ENST00000346208		407	tcGCCCTtc/tctc	6/6	0.155704206701794	3	FACETS	0.891	0.751	1	0.446	0.375	0.523	INDETERMINATE	1	TRUE	1	0.32	3		585	366	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660603	190660603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005423-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	26	387	0	ENST00000441310.2:c.241C>T	p.His81Tyr	p.H81Y	ENST00000441310	NM_000534.4	81	Cat/Tat	3/13	0.155704206701794	3	FACETS	0.54	0.428	0.669	0.27	0.214	0.335	INDETERMINATE	1	TRUE	1	0.32	3		387	349	SUCCESS
ATR	545	MSKCC	GRCh37	3	142168411	142168411	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005423-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	42	495	2	ENST00000350721.4:c.7795C>A	p.Leu2599Ile	p.L2599I	ENST00000350721	NM_001184.3	2599	Cta/Ata	47/47	0.155704206701794	3	FACETS	0.767	0.641	0.906	0.384	0.32	0.453	INDETERMINATE	1	TRUE	1	0.32	3		497	397	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982040	38982040	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005423-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	40	577	0	ENST00000357387.3:c.682A>T	p.Ile228Phe	p.I228F	ENST00000357387	NM_152756.3	228	Att/Ttt	8/38	0.191428802480794	4	FACETS	0.71	0.59	0.843	0.355	0.295	0.422	INDETERMINATE	1	TRUE	2	0.32	4		577	465	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991118	41991118	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs761422551	NA	P-0005423-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	90	535	0	ENST00000219905.7:c.2071G>T	p.Ala691Ser	p.A691S	ENST00000219905	NM_001164273.1	691	Gca/Tca	4/24	0.155704206701794	3	FACETS	1	0.977	1	0.694	0.618	0.774	INDETERMINATE	1	TRUE	1	0.32	3		535	470	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41276047	41276047	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	GG	novel	NA	P-0005423-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	38	578	0	ENST00000357654.3:c.67delinsCC	p.Glu23ProfsTer18	p.E23Pfs*18	ENST00000357654	NM_007294.3	23	Gag/CCag	2/23	1	2	FACETS	0.543	0.449	0.649	0.543	0.449	0.649	SUBCLONAL	1	TRUE	1	0.32	2		578	437	SUCCESS
APC	324	MSKCC	GRCh37	5	112173626	112173626	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	243	561	0	ENST00000257430.4:c.2335T>G	p.Leu779Val	p.L779V	ENST00000257430	NM_000038.5	779	Tta/Gta	16/16	0.409450713182134	3	FACETS	1	0.975	1	0.54	0.506	0.574	INDETERMINATE	1	TRUE	1	0.791749073064792	3		561	794	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713534	30713534	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	203	398	0	ENST00000295754.5:c.859T>A	p.Trp287Arg	p.W287R	ENST00000295754	NM_003242.5	287	Tgg/Agg	4/7	1	2	FACETS	0.987	0.917	1	0.987	0.917	1	CLONAL	1	TRUE	1	0.513578529254117	2		398	801	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954033	32954033	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	185	496	0	ENST00000380152.3:c.9100C>A	p.Gln3034Lys	p.Q3034K	ENST00000380152		3034	Cag/Aag	23/27	1	2	FACETS	0.884	0.817	0.953	0.884	0.817	0.953	CLONAL	1	TRUE	1	0.513578529254117	2		496	815	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135246	2135246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1051502900	NA	P-0006145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	244	520	1	ENST00000219476.3:c.4585C>T	p.Arg1529Trp	p.R1529W	ENST00000219476	NM_000548.3	1529	Cgg/Tgg	36/42	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.513578529254117	2		521	920	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0006151-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	24	571	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.655	0.513	0.818	0.655	0.513	0.818	SUBCLONAL	1	TRUE	1	0.21	2		571	349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782620	NA	P-0006151-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	26	534	1	ENST00000269305.4:c.427G>A	p.Val143Met	p.V143M	ENST00000269305	NM_001126112.2	143	Gtg/Atg	5/11	1	2	FACETS	0.572	0.452	0.709	0.572	0.452	0.709	SUBCLONAL	1	TRUE	1	0.21	2		535	433	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0006335-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	295	722	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.7666964183196	2		722	762	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0006335-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	264	621	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	1	2	FACETS	0.884	0.832	0.937	0.884	0.832	0.937	CLONAL	1	TRUE	1	0.7666964183196	2		621	779	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741707	145741707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543009701	NA	P-0006335-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	403	955	2	ENST00000428558.2:c.796G>A	p.Glu266Lys	p.E266K	ENST00000428558	NM_004260.3	266	Gag/Aag	5/22	0.244514337445245	3	FACETS	1	0.996	1	0.732	0.699	0.766	INDETERMINATE	1	TRUE	1	0.7666964183196	3		957	993	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115111972	115111972	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006335-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	349	815	0	ENST00000257566.3:c.1768C>T	p.Gln590Ter	p.Q590*	ENST00000257566	NM_016569.3	590	Cag/Tag	7/8	1	2	FACETS	0.94	0.892	0.988	0.94	0.892	0.988	CLONAL	1	TRUE	1	0.7666964183196	2		815	969	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564677	86564677	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006335-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	395	810	0	ENST00000274376.6:c.409C>G	p.Leu137Val	p.L137V	ENST00000274376	NM_002890.2	137	Ctg/Gtg	1/25	0.244514337445245	3	FACETS	1	0.996	1	0.733	0.699	0.767	INDETERMINATE	1	TRUE	1	0.7666964183196	3		810	972	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865468	57865468	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752275003	NA	P-0006335-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	332	865	0	ENST00000228682.2:c.2945C>T	p.Ser982Leu	p.S982L	ENST00000228682	NM_005269.2	982	tCa/tTa	12/12	1	2	FACETS	0.91	0.862	0.958	0.91	0.862	0.958	CLONAL	1	TRUE	1	0.7666964183196	2		865	952	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913942	32913942	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs759741090	NA	P-0006335-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	95	706	0	ENST00000380152.3:c.5450C>G	p.Ser1817Cys	p.S1817C	ENST00000380152		1817	tCt/tGt	11/27	0.677617029177758	2	FACETS	0.32	0.285	0.358	0.16	0.142	0.179	SUBCLONAL	1	TRUE	0	0.7666964183196	2		706	774	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832769	3832769	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006335-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	338	758	2	ENST00000262367.5:c.1489C>T	p.Gln497Ter	p.Q497*	ENST00000262367	NM_004380.2	497	Cag/Tag	6/31	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.7666964183196	2		760	874	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40458263	40458263	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006335-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	381	1162	0	ENST00000345506.4:c.1478G>C	p.Arg493Thr	p.R493T	ENST00000345506	NM_003152.3	493	aGg/aCg	14/20	1	2	FACETS	0.836	0.794	0.878	0.836	0.794	0.878	CLONAL	1	TRUE	1	0.7666964183196	2		1162	1189	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862138	68862139	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0006335-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	353	826	0	ENST00000261769.5:c.2231dup	p.Glu745ArgfsTer3	p.E745Rfs*3	ENST00000261769	NM_004360.3	742	-/C	14/16	0.7666964183196	1	FACETS	0.932	0.894	0.971	0.932	0.894	0.971	CLONAL	1	TRUE	0	0.7666964183196	1		826	609	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584422	39584436	+	inframe_deletion	In_Frame_Del	DEL	TCCTTGGAGCTGTTA	TCCTTGGAGCTGTTA	-	novel	NA	P-0006335-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	240	611	0	ENST00000262039.4:c.1091_1105del	p.Leu364_Ser368del	p.L364_S368del	ENST00000262039	NM_002647.2	363	TCCTTGGAGCTGTTA/-	10/25	1	2	FACETS	0.947	0.89	1	0.947	0.89	1	CLONAL	1	TRUE	1	0.7666964183196	2		611	661	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112769019	112769019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006335-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	280	592	1	ENST00000369452.4:c.1298C>T	p.Ser433Leu	p.S433L	ENST00000369452	NM_007373.3	433	tCa/tTa	7/9	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.7666964183196	2		593	722	SUCCESS
AXL	558	MSKCC	GRCh37	19	41737159	41737159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006335-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	62	953	0	ENST00000301178.4:c.739C>T	p.Pro247Ser	p.P247S	ENST00000301178	NM_021913.4	247	Cca/Tca	6/20	1	2	FACETS	0.158	0.136	0.182	0.158	0.136	0.182	SUBCLONAL	1	TRUE	1	0.7666964183196	2		953	1024	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46583926	46583926	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006335-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	275	680	1	ENST00000263734.3:c.433G>T	p.Glu145Ter	p.E145*	ENST00000263734	NM_001430.4	145	Gag/Tag	4/16	1	2	FACETS	0.933	0.88	0.987	0.933	0.88	0.987	CLONAL	1	TRUE	1	0.7666964183196	2		681	769	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522526	67522526	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006335-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	43	312	0	ENST00000274335.5:c.23A>T	p.Tyr8Phe	p.Y8F	ENST00000274335		8	tAc/tTc	1/15	0.244514337445245	3	FACETS	0.368	0.308	0.434	0.184	0.154	0.217	INDETERMINATE	1	TRUE	1	0.7666964183196	3		312	422	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860485	151860485	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006335-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	365	805	1	ENST00000262189.6:c.10177G>T	p.Glu3393Ter	p.E3393*	ENST00000262189	NM_170606.2	3393	Gaa/Taa	43/59	1	2	FACETS	0.952	0.905	1	0.952	0.905	1	CLONAL	1	TRUE	1	0.7666964183196	2		806	1000	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089765	27089772	+	frameshift_variant	Frame_Shift_Del	DEL	TATCCAAA	TATCCAAA	G	novel	NA	P-0006335-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	553	683	0	ENST00000324856.7:c.2721_2728delinsG	p.Ile908ThrfsTer9	p.I908Tfs*9	ENST00000324856	NM_006015.4	907	tcTATCCAAAac/tcGac	8/20	0.677617029177758	2	FACETS	0.971	0.945	0.995	0.971	0.945	0.995	CLONAL	2	TRUE	0	0.7666964183196	2		683	743	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0006631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	146	515	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	0.687359568079817	2		515	391	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0006631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	208	612	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	0.998	0.934	0.871	0.998	CLONAL	1	TRUE	1	0.687359568079817	2		612	648	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0006631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	249	270	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.687359568079817	2		270	691	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144498	11144498	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746219091	NA	P-0006631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	264	776	0	ENST00000358026.2:c.3830C>T	p.Pro1277Leu	p.P1277L	ENST00000358026	NM_001128849.1	1277	cCg/cTg	27/36	1	2	FACETS	0.974	0.916	1	0.974	0.916	1	CLONAL	1	TRUE	1	0.687359568079817	2		776	789	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849442	68849442	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	226	728	1	ENST00000261769.5:c.1345C>T	p.Gln449Ter	p.Q449*	ENST00000261769	NM_004360.3	449	Cag/Tag	10/16	0.687359568079817	1	FACETS	0.988	0.933	1	0.988	0.933	1	CLONAL	1	TRUE	0	0.687359568079817	1		729	437	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197077	26197077	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs373554594	NA	P-0006631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	180	533	0	ENST00000356476.2:c.402G>C	p.Glu134Asp	p.E134D	ENST00000356476		134	gaG/gaC	1/1	0.687359568079817	3	FACETS	0.973	0.9	1	0.487	0.45	0.525	CLONAL	1	TRUE	1	0.687359568079817	3		533	723	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561232	9561232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	40	567	1	ENST00000353224.5:c.550G>A	p.Glu184Lys	p.E184K	ENST00000353224	NM_177990.2	184	Gag/Aag	4/10	0.687359568079817	3	FACETS	0.198	0.164	0.237	0.099	0.082	0.119	SUBCLONAL	1	TRUE	1	0.687359568079817	3		568	789	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041704	42041704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	178	530	1	ENST00000219905.7:c.5899C>T	p.Gln1967Ter	p.Q1967*	ENST00000219905	NM_001164273.1	1967	Cag/Tag	17/24	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.687359568079817	2		531	498	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042440	42042440	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	258	633	0	ENST00000219905.7:c.6635C>A	p.Ser2212Ter	p.S2212*	ENST00000219905	NM_001164273.1	2212	tCa/tAa	17/24	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.687359568079817	2		633	703	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748110	43748110	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	157	544	0	ENST00000382044.4:c.2696G>A	p.Ser899Asn	p.S899N	ENST00000382044	NM_001141980.1	899	aGc/aAc	12/28	1	2	FACETS	0.81	0.746	0.876	0.81	0.746	0.876	CLONAL	1	TRUE	1	0.687359568079817	2		544	564	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265598	152265598	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	191	568	0	ENST00000206249.3:c.1051G>A	p.Asp351Asn	p.D351N	ENST00000206249	NM_000125.3	351	Gac/Aac	4/8	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.687359568079817	2		568	556	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340024	116340024	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	174	367	0	ENST00000397752.3:c.886C>G	p.Leu296Val	p.L296V	ENST00000397752	NM_000245.2	296	Ctg/Gtg	2/21	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.687359568079817	2		367	439	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864624	56864624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	51	783	0	ENST00000519728.1:c.587C>T	p.Ser196Phe	p.S196F	ENST00000519728	NM_002350.3	196	tCt/tTt	7/13	1	2	FACETS	0.175	0.148	0.205	0.175	0.148	0.205	SUBCLONAL	1	TRUE	1	0.687359568079817	2		783	847	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0006862-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	363	628	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.324765800848841	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.324765800848841	2		628	1037	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0006862-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	659	595	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.324765800848841	5	FACETS	1	0.989	1			1	CLONAL	5	TRUE	NA	0.324765800848841	5		595	1157	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033640	48033640	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750836	NA	P-0006862-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	317	526	0	ENST00000234420.5:c.3851C>T	p.Thr1284Met	p.T1284M	ENST00000234420	NM_000179.2	1284	aCg/aTg	9/10	0.273784424758373	4	FACETS	0.953	0.902	1	0.953	0.902	1	CLONAL	3	TRUE	1	0.324765800848841	4		526	905	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103677	47103677	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006862-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	156	325	0	ENST00000409792.3:c.6269G>T	p.Arg2090Leu	p.R2090L	ENST00000409792	NM_014159.6	2090	cGg/cTg	14/21	0.324765800848841	3	FACETS	0.889	0.817	0.964	0.889	0.817	0.964	CLONAL	2	TRUE	1	0.324765800848841	3		325	628	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374745	118374745	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006862-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	87	344	0	ENST00000534358.1:c.8138A>G	p.Asp2713Gly	p.D2713G	ENST00000534358	NM_005933.3	2713	gAt/gGt	27/36	0.324765800848841	3	FACETS	0.998	0.885	1	0.499	0.442	0.56	CLONAL	1	TRUE	1	0.324765800848841	3		344	624	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929194	32929194	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006862-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	140	637	0	ENST00000380152.3:c.7204C>T	p.Pro2402Ser	p.P2402S	ENST00000380152		2402	Cca/Tca	14/27	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.324765800848841	2		637	777	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953274	17953274	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006862-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1256	181	752	0	ENST00000458235.1:c.712T>C	p.Tyr238His	p.Y238H	ENST00000458235	NM_000215.3	238	Tac/Cac	6/24	0.323440530028989	4	FACETS	1	0.941	1	0.514	0.472	0.557	CLONAL	1	TRUE	2	0.324765800848841	4		752	1437	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0007288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	141	612	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.836	0.763	0.912	1	0.989	1	CLONAL	2	TRUE	1	0.24	2		612	703	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0007288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	51	722	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.65	0.551	0.758	0.65	0.551	0.758	SUBCLONAL	1	TRUE	1	0.24	2		722	654	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645412	67645412	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	42	419	0	ENST00000264010.4:c.677A>G	p.Tyr226Cys	p.Y226C	ENST00000264010	NM_006565.3	226	tAc/tGc	3/12	0.18260152432426	1	FACETS	0.625	0.521	0.74	0.625	0.521	0.74	SUBCLONAL	1	TRUE	0	0.24	1		419	493	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160626	56160700	+	inframe_deletion	In_Frame_Del	DEL	CCCTGAGGAAACAAACCGCCGTGTTAACAAAGTGATGCGGGCCAGACTGTACTTACTGCAGCAGATAGGGCCTAA	CCCTGAGGAAACAAACCGCCGTGTTAACAAAGTGATGCGGGCCAGACTGTACTTACTGCAGCAGATAGGGCCTAA	-	novel	NA	P-0007288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	27	362	0	ENST00000399503.3:c.901_975del	p.Pro301_Asn325del	p.P301_N325del	ENST00000399503	NM_005921.1	300	agCCCTGAGGAAACAAACCGCCGTGTTAACAAAGTGATGCGGGCCAGACTGTACTTACTGCAGCAGATAGGGCCTAAc/agc	4/20	1	2	FACETS	0.485	0.385	0.599	0.485	0.385	0.599	SUBCLONAL	1	TRUE	1	0.24	2		362	464	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217872	7217875	+	frameshift_variant	Frame_Shift_Del	DEL	CTTC	CTTC	-	novel	NA	P-0007288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	92	641	1	ENST00000380728.2:c.136_139del	p.Glu46AsnfsTer16	p.E46Nfs*16	ENST00000380728		46	GAAGaa/aa	3/11	1	2	FACETS	0.969	0.861	1	0.969	0.861	1	CLONAL	1	TRUE	1	0.24	2		642	791	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180581	56180584	+	frameshift_variant	Frame_Shift_Del	DEL	CCAA	CCAA	-	novel	NA	P-0007288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	67	447	0	ENST00000399503.3:c.3910_3913del	p.Pro1304ThrfsTer31	p.P1304Tfs*31	ENST00000399503	NM_005921.1	1304	CCAAac/ac	16/20	1	2	FACETS	0.993	0.864	1	0.993	0.864	1	CLONAL	1	TRUE	1	0.24	2		447	562	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046281	180046281	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	104	286	1	ENST00000261937.6:c.2733C>A	p.Asn911Lys	p.N911K	ENST00000261937	NM_182925.4	911	aaC/aaA	19/30	0.272133818610491	3	FACETS	0.808	0.727	0.893	0.808	0.727	0.893	CLONAL	2	TRUE	1	0.310381717614548	3		287	479	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0008083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	219	756	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	0.301085292627647	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.851280178326956	0		756	712	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0008083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	456	941	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.850682946921677	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.851280178326956	1		941	561	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006194	22006194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	196	842	2	ENST00000276925.6:c.209C>T	p.Ala70Val	p.A70V	ENST00000276925	NM_004936.3	70	gCg/gTg	2/2	0.621271889195911	0	FACETS		NA	1			1	NA	1	TRUE	0	0.851280178326956	0		844	318	SUCCESS
APC	324	MSKCC	GRCh37	5	112164585	112164585	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398123116	NA	P-0008083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	347	286	0	ENST00000257430.4:c.1659G>A	p.Trp553Ter	p.W553*	ENST00000257430	NM_000038.5	553	tgG/tgA	14/16	0.848798093056468	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.851280178326956	1		286	463	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045946	26045946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	197	635	4	ENST00000540144.1:c.308G>T	p.Gly103Val	p.G103V	ENST00000540144	NM_003531.2	103	gGa/gTa	1/1	0.36347177710218	3	FACETS	0.701	0.649	0.755	0.234	0.216	0.252	INDETERMINATE	1	TRUE	0	0.851280178326956	3		639	941	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2952986	2952986	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747477589	NA	P-0008083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	556	891	0	ENST00000396946.4:c.2954C>G	p.Ala985Gly	p.A985G	ENST00000396946	NM_032415.4	985	gCc/gGc	22/25	0.485165228037987	3	FACETS	0.864	0.833	0.894	0.864	0.833	0.894	INDETERMINATE	2	TRUE	1	0.851280178326956	3		891	1078	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501331	140501331	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	397	463	0	ENST00000288602.6:c.741T>A	p.Phe247Leu	p.F247L	ENST00000288602	NM_004333.4	247	ttT/ttA	6/18	0.484901185626489	1	FACETS	0.819	0.788	0.85	0.819	0.788	0.85	INDETERMINATE	1	TRUE	0	0.851280178326956	1		463	654	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920396	114920396	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	234	702	0	ENST00000543371.1:c.1337A>C	p.Lys446Thr	p.K446T	ENST00000543371	NM_001198531.1	446	aAg/aCg	13/14	0.431406124803057	1	FACETS	0.359	0.335	0.384	0.359	0.335	0.384	INDETERMINATE	1	TRUE	0	0.851280178326956	1		702	879	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052630	42052630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372072518	NA	P-0008083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	432	741	0	ENST00000219905.7:c.7301G>A	p.Arg2434Gln	p.R2434Q	ENST00000219905	NM_001164273.1	2434	cGg/cAg	20/24	0.431406124803057	1	FACETS	0.716	0.688	0.744	0.716	0.688	0.744	INDETERMINATE	1	TRUE	0	0.851280178326956	1		741	814	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646234	23646234	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs180177103	NA	P-0008083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	687	837	0	ENST00000261584.4:c.1633G>T	p.Glu545Ter	p.E545*	ENST00000261584	NM_024675.3	545	Gaa/Taa	4/13	0.825378397651964	2	FACETS	0.957	0.938	0.976	0.957	0.938	0.976	CLONAL	2	TRUE	0	0.851280178326956	2		837	843	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581186	48581204	+	frameshift_variant	Frame_Shift_Del	DEL	CATGACTTTGAGGGACAGC	CATGACTTTGAGGGACAGC	-	novel	NA	P-0008083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	347	579	0	ENST00000342988.3:c.493_511del	p.Asp165ArgfsTer31	p.D165Rfs*31	ENST00000342988	NM_005359.5	164	CATGACTTTGAGGGACAGCca/ca	5/12	0.851280178326956	1	FACETS	0.992	0.959	1	0.992	0.959	1	CLONAL	1	TRUE	0	0.851280178326956	1		579	472	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221647	36221647	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	174	1035	2	ENST00000222270.7:c.5316G>T	p.Arg1772Ser	p.R1772S	ENST00000222270	NM_014727.1	1772	agG/agT	26/37	0.533198981101112	1	FACETS	0.313	0.289	0.339	0.313	0.289	0.339	SUBCLONAL	1	TRUE	0	0.851280178326956	1		1037	749	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930154	68930154	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0008083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	419	510	0	ENST00000288368.4:c.213+2T>C		p.X71_splice	ENST00000288368	NM_024870.2	71			0.485165228037987	3	FACETS	0.835	0.801	0.87	0.835	0.801	0.87	INDETERMINATE	2	TRUE	1	0.851280178326956	3		510	840	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128206802	128206802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	361	596	0	ENST00000265960.3:c.1421C>T	p.Thr474Ile	p.T474I	ENST00000265960	NM_001006617.1	474	aCc/aTc	11/12	0.851280178326956	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.851280178326956	1		596	464	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50482314	50482314	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	61	696	0	ENST00000394963.4:c.665C>A	p.Ser222Tyr	p.S222Y	ENST00000394963	NM_003076.4	222	tCc/tAc	6/13	0.301085292627647	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.851280178326956	0		696	637	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184941	32184941	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	90	694	1	ENST00000375023.3:c.1727A>G	p.Lys576Arg	p.K576R	ENST00000375023	NM_004557.3	576	aAg/aGg	10/30	0.440871374683751	2	FACETS	0.306	0.271	0.343	0.153	0.135	0.172	INDETERMINATE	1	TRUE	0	0.851280178326956	2		695	692	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136804	69136804	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	167	668	0	ENST00000288368.4:c.4718T>G	p.Val1573Gly	p.V1573G	ENST00000288368	NM_024870.2	1573	gTt/gGt	39/40	0.485165228037987	3	FACETS	0.546	0.501	0.593	0.273	0.25	0.297	INDETERMINATE	1	TRUE	1	0.851280178326956	3		668	1025	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0008083-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	147	756	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.591940650390456	2		756	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0008083-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	311	941	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.591940650390456	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.591940650390456	2		941	490	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006194	22006194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008083-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	217	842	2	ENST00000276925.6:c.209C>T	p.Ala70Val	p.A70V	ENST00000276925	NM_004936.3	70	gCg/gTg	2/2	0.591940650390456	2	FACETS	0.89	0.84	0.939	0.89	0.84	0.939	CLONAL	2	TRUE	0	0.591940650390456	2		844	412	SUCCESS
APC	324	MSKCC	GRCh37	5	112164585	112164585	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398123116	NA	P-0008083-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	152	286	0	ENST00000257430.4:c.1659G>A	p.Trp553Ter	p.W553*	ENST00000257430	NM_000038.5	553	tgG/tgA	14/16	0.591940650390456	2	FACETS	0.927	0.867	0.987	0.927	0.867	0.987	CLONAL	2	TRUE	0	0.591940650390456	2		286	277	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045946	26045946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008083-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	142	635	4	ENST00000540144.1:c.308G>T	p.Gly103Val	p.G103V	ENST00000540144	NM_003531.2	103	gGa/gTa	1/1	0.591940650390456	5	FACETS	1	0.976	1	0.298	0.272	0.326	CLONAL	1	TRUE	1	0.591940650390456	5		639	759	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2952986	2952986	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747477589	NA	P-0008083-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	369	891	0	ENST00000396946.4:c.2954C>G	p.Ala985Gly	p.A985G	ENST00000396946	NM_032415.4	985	gCc/gGc	22/25	0.591940650390456	5	FACETS	0.92	0.877	0.963	0.92	0.877	0.963	CLONAL	3	TRUE	2	0.591940650390456	5		891	853	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501331	140501331	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008083-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	164	463	0	ENST00000288602.6:c.741T>A	p.Phe247Leu	p.F247L	ENST00000288602	NM_004333.4	247	ttT/ttA	6/18	0.397190353494204	5	FACETS	1	0.98	1	0.773	0.717	0.831	CLONAL	2	TRUE	2	0.591940650390456	5		463	451	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920396	114920396	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008083-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	123	702	0	ENST00000543371.1:c.1337A>C	p.Lys446Thr	p.K446T	ENST00000543371	NM_001198531.1	446	aAg/aCg	13/14	0.591940650390456	3	FACETS	0.945	0.858	1	0.472	0.429	0.518	CLONAL	1	TRUE	1	0.591940650390456	3		702	570	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052630	42052630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372072518	NA	P-0008083-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	267	741	0	ENST00000219905.7:c.7301G>A	p.Arg2434Gln	p.R2434Q	ENST00000219905	NM_001164273.1	2434	cGg/cAg	20/24	0.591940650390456	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.591940650390456	3		741	538	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646234	23646234	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs180177103	NA	P-0008083-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	350	837	0	ENST00000261584.4:c.1633G>T	p.Glu545Ter	p.E545*	ENST00000261584	NM_024675.3	545	Gaa/Taa	4/13	0.591940650390456	3	FACETS	0.973	0.937	1	0.973	0.937	1	CLONAL	3	TRUE	0	0.591940650390456	3		837	525	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581186	48581204	+	frameshift_variant	Frame_Shift_Del	DEL	CATGACTTTGAGGGACAGC	CATGACTTTGAGGGACAGC	-	novel	NA	P-0008083-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	199	579	0	ENST00000342988.3:c.493_511del	p.Asp165ArgfsTer31	p.D165Rfs*31	ENST00000342988	NM_005359.5	164	CATGACTTTGAGGGACAGCca/ca	5/12	0.591940650390456	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.591940650390456	2		579	329	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221647	36221647	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008083-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	163	1035	2	ENST00000222270.7:c.5316G>T	p.Arg1772Ser	p.R1772S	ENST00000222270	NM_014727.1	1772	agG/agT	26/37	0.591940650390456	3	FACETS	0.975	0.897	1	0.488	0.448	0.528	CLONAL	1	TRUE	1	0.591940650390456	3		1037	732	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930154	68930154	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0008083-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	276	510	0	ENST00000288368.4:c.213+2T>C		p.X71_splice	ENST00000288368	NM_024870.2	71			0.530371203544169	5	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	TRUE	2	0.591940650390456	5		510	571	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128206802	128206802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008083-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	229	596	0	ENST00000265960.3:c.1421C>T	p.Thr474Ile	p.T474I	ENST00000265960	NM_001006617.1	474	aCc/aTc	11/12	0.591940650390456	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.591940650390456	2		596	379	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0008333-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	226	399	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.977	0.919	1	0.977	0.919	1	CLONAL	1	TRUE	1	0.881101683435084	2		399	525	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0008333-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	111	401	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.897	0.819	0.976	0.897	0.819	0.976	CLONAL	1	TRUE	1	0.881101683435084	2		401	281	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175857	24175859	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs875989800	NA	P-0008333-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	58	617	0	ENST00000263121.7:c.1091_1093del	p.Lys364del	p.K364del	ENST00000263121	NM_003073.3	362	gAGAag/gag	8/9	1	2	FACETS	0.223	0.191	0.258	0.223	0.191	0.258	SUBCLONAL	1	TRUE	1	0.881101683435084	2		617	590	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413070	139413072	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0008333-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	52	641	0	ENST00000277541.6:c.1070_1072del	p.Phe357del	p.F357del	ENST00000277541	NM_017617.3	357	tTCTac/tac	6/34	1	2	FACETS	0.166	0.14	0.193	0.166	0.14	0.193	SUBCLONAL	1	TRUE	1	0.881101683435084	2		641	713	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391997	139391998	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0008333-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	172	660	0	ENST00000277541.6:c.6193_6194del	p.Leu2065ValfsTer202	p.L2065Vfs*202	ENST00000277541	NM_017617.3	2065	CTg/g	34/34	1	2	FACETS	0.69	0.638	0.743	0.69	0.638	0.743	SUBCLONAL	1	TRUE	1	0.881101683435084	2		660	566	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251949	153251949	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008333-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	43	722	0	ENST00000281708.4:c.1057del	p.Ser353ValfsTer24	p.S353Vfs*24	ENST00000281708	NM_033632.3	353	Agt/gt	7/12	1	2	FACETS	0.145	0.121	0.172	0.145	0.121	0.172	SUBCLONAL	1	TRUE	1	0.881101683435084	2		722	674	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17947956	17947956	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1040476469	NA	P-0008333-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	231	722	2	ENST00000458235.1:c.1768G>A	p.Val590Met	p.V590M	ENST00000458235	NM_000215.3	590	Gtg/Atg	13/24	1	2	FACETS	0.697	0.652	0.743	0.697	0.652	0.743	SUBCLONAL	1	TRUE	1	0.881101683435084	2		724	752	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528266	157528267	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0008333-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	59	637	0	ENST00000346085.5:c.5991_5992insAT	p.Glu1998MetfsTer24	p.E1998Mfs*24	ENST00000346085	NM_020732.3	1997	-/AT	20/20	1	2	FACETS	0.245	0.211	0.283	0.245	0.211	0.283	SUBCLONAL	1	TRUE	1	0.881101683435084	2		637	546	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	227	692	4	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.901	0.848	0.955	0.901	0.848	0.955	CLONAL	1	TRUE	1	0.96	2		696	525	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210755	5210755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1157608522	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	181	1039	3	ENST00000357368.4:c.5296C>T	p.Arg1766Cys	p.R1766C	ENST00000357368	NM_002850.3	1766	Cgc/Tgc	34/38	1	2	FACETS	0.501	0.463	0.541	0.501	0.463	0.541	SUBCLONAL	1	TRUE	1	0.96	2		1042	752	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	307	641	2	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.976	0.928	1	0.976	0.928	1	CLONAL	1	TRUE	1	0.96	2		643	655	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	409	780	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.946	0.905	0.987	0.946	0.905	0.987	CLONAL	1	TRUE	1	0.96	2		780	901	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	454	795	1	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.96	2		796	926	SUCCESS
FH	2271	MSKCC	GRCh37	1	241661238	241661238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	40	916	0	ENST00000366560.3:c.1423G>A	p.Ala475Thr	p.A475T	ENST00000366560	NM_000143.3	475	Gca/Aca	10/10	0.3	1	FACETS	0.055	0.045	0.066	0.055	0.045	0.066	INDETERMINATE	1	TRUE	0	0.96	1		916	784	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023327	27023327	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	139	515	0	ENST00000324856.7:c.437del	p.Pro146GlnfsTer86	p.P146Qfs*86	ENST00000324856	NM_006015.4	145	Ccc/cc	1/20	1	2	FACETS	0.891	0.824	0.959	0.891	0.824	0.959	CLONAL	1	TRUE	1	0.96	2		515	325	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231437	46231437	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	343	637	1	ENST00000334344.6:c.1277C>T	p.Thr426Met	p.T426M	ENST00000334344	NM_152641.2	426	aCg/aTg	10/21	1	2	FACETS	0.95	0.905	0.995	0.95	0.905	0.995	CLONAL	1	TRUE	1	0.96	2		638	752	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405111	139405111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201620358	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	280	958	2	ENST00000277541.6:c.2734C>T	p.Arg912Trp	p.R912W	ENST00000277541	NM_017617.3	912	Cgg/Tgg	17/34	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.96	2		960	555	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	239	534	0	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.96	2		534	482	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	97	250	6	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	0.944	0.861	1	0.944	0.861	1	CLONAL	1	TRUE	1	0.96	2		256	214	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827732	72827732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241554729	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	80	728	1	ENST00000268489.5:c.8849G>A	p.Arg2950His	p.R2950H	ENST00000268489	NM_006885.3	2950	cGc/cAc	9/10	1	2	FACETS	0.306	0.269	0.345	0.306	0.269	0.345	SUBCLONAL	1	TRUE	1	0.96	2		729	545	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687472	37687472	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	56	464	2	ENST00000447079.4:c.4382del	p.Gly1461AlafsTer38	p.G1461Afs*38	ENST00000447079	NM_015083.1	1459	tGg/tg	14/14	0.121792467154397	3	FACETS	0.444	0.381	0.512	0.222	0.19	0.256	INDETERMINATE	1	TRUE	1	0.96	3		466	389	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161405	185161405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	361	707	0	ENST00000265026.3:c.832C>T	p.Arg278Cys	p.R278C	ENST00000265026	NM_004721.4	278	Cgt/Tgt	4/14	1	2	FACETS	0.959	0.915	1	0.959	0.915	1	CLONAL	1	TRUE	1	0.96	2		707	784	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9787030	9787030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397518423	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	79	844	1	ENST00000377346.4:c.3061G>A	p.Glu1021Lys	p.E1021K	ENST00000377346	NM_005026.3	1021	Gaa/Aaa	24/24	1	2	FACETS	0.243	0.213	0.275	0.243	0.213	0.275	SUBCLONAL	1	TRUE	1	0.96	2		845	677	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289908	15289908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257835251	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	353	960	1	ENST00000263388.2:c.3646G>A	p.Ala1216Thr	p.A1216T	ENST00000263388	NM_000435.2	1216	Gcg/Acg	22/33	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.96	2		961	730	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101057	27101057	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	110	1008	0	ENST00000324856.7:c.4339C>T	p.Pro1447Ser	p.P1447S	ENST00000324856	NM_006015.4	1447	Cca/Tca	18/20	1	2	FACETS	0.328	0.295	0.363	0.328	0.295	0.363	SUBCLONAL	1	TRUE	1	0.96	2		1008	699	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101294	27101294	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773815689	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	374	952	0	ENST00000324856.7:c.4576G>A	p.Val1526Met	p.V1526M	ENST00000324856	NM_006015.4	1526	Gtg/Atg	18/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.96	2		952	714	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416200	29416200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	310	787	1	ENST00000389048.3:c.4753G>A	p.Gly1585Ser	p.G1585S	ENST00000389048	NM_004304.4	1585	Ggc/Agc	29/29	0.0808932408601961	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.96	0		788	650	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189287	99189287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760873847	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	239	637	1	ENST00000074304.5:c.2543G>A	p.Arg848Gln	p.R848Q	ENST00000074304	NM_001134224.1	848	cGg/cAg	24/26	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.96	2		638	454	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630588	187630588	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	516	980	2	ENST00000441802.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000441802	NM_005245.3	132	Cga/Tga	2/27	0.121792467154397	3	FACETS	0.792	0.762	0.821	0.792	0.762	0.821	INDETERMINATE	2	TRUE	1	0.96	3		982	1005	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5073782	5073782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1168791735	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	347	729	0	ENST00000381652.3:c.1861G>A	p.Glu621Lys	p.E621K	ENST00000381652	NM_004972.3	621	Gag/Aag	14/25	0.3	2	FACETS	1	0.961	1			1	INDETERMINATE	1	TRUE	NA	0.96	2		729	717	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771903	135771903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	268	782	0	ENST00000298552.3:c.3214G>A	p.Ala1072Thr	p.A1072T	ENST00000298552	NM_001162426.1	1072	Gcc/Acc	23/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.96	2		782	539	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202552	67202552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373972783	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	287	924	1	ENST00000312629.5:c.1361C>T	p.Pro454Leu	p.P454L	ENST00000312629	NM_003952.2	454	cCg/cTg	15/15	1	2	FACETS	0.937	0.889	0.986	0.937	0.889	0.986	CLONAL	1	TRUE	1	0.96	2		925	638	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878064	48878064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886043138	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	201	537	0	ENST00000267163.4:c.16C>T	p.Pro6Ser	p.P6S	ENST00000267163	NM_000321.2	6	Ccc/Tcc	1/27	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.96	2		537	417	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341244	341244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773933232	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	49	907	2	ENST00000262320.3:c.2240C>T	p.Ala747Val	p.A747V	ENST00000262320	NM_003502.3	747	gCg/gTg	9/11	1	2	FACETS	0.162	0.136	0.19	0.162	0.136	0.19	SUBCLONAL	1	TRUE	1	0.96	2		909	631	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	360013	360013	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1439391940	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	352	857	0	ENST00000262320.3:c.1076G>A	p.Ser359Asn	p.S359N	ENST00000262320	NM_003502.3	359	aGc/aAc	4/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.96	2		857	716	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822346	72822346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747616488	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	361	1156	4	ENST00000268489.5:c.9829C>T	p.Pro3277Ser	p.P3277S	ENST00000268489	NM_006885.3	3277	Ccc/Tcc	10/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.96	2		1160	725	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220015	5220015	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866165812	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	366	1042	2	ENST00000357368.4:c.3700C>T	p.Arg1234Trp	p.R1234W	ENST00000357368	NM_002850.3	1234	Cgg/Tgg	22/38	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.96	2		1044	703	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292490	15292490	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	362	1013	1	ENST00000263388.2:c.2689G>A	p.Gly897Ser	p.G897S	ENST00000263388	NM_000435.2	897	Ggc/Agc	17/33	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.96	2		1014	741	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274078	18274078	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	284	756	3	ENST00000222254.8:c.1296G>T	p.Gln432His	p.Q432H	ENST00000222254	NM_005027.3	432	caG/caT	11/16	1	2	FACETS	0.959	0.909	1	0.959	0.909	1	CLONAL	1	TRUE	1	0.96	2		759	617	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912858	50912858	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1306540639	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	286	987	0	ENST00000440232.2:c.2089G>A	p.Ala697Thr	p.A697T	ENST00000440232	NM_002691.3	697	Gcc/Acc	17/27	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.96	2		987	573	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31381363	31381363	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138596278	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	427	796	0	ENST00000328111.2:c.1088G>A	p.Arg363His	p.R363H	ENST00000328111	NM_006892.3	363	cGt/cAt	10/23	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.96	2		796	846	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564512	41564512	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555911075	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	364	765	2	ENST00000263253.7:c.3934C>T	p.Arg1312Ter	p.R1312*	ENST00000263253	NM_001429.3	1312	Cga/Tga	24/31	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.96	2		767	734	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182928	123182928	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	335	301	2	ENST00000218089.9:c.893G>A	p.Arg298His	p.R298H	ENST00000218089	NM_001042749.1	298	cGt/cAt	10/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.96	1		303	344	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705459	47705459	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	275	603	0	ENST00000233146.2:c.2260del	p.Thr754LeufsTer9	p.T754Lfs*9	ENST00000233146	NM_000251.2	753	ggA/gg	14/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.96	2		603	557	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027087	71027087	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	300	779	3	ENST00000318789.4:c.1240del	p.Leu414Ter	p.L414*	ENST00000318789	NM_032682.5	414	Ctg/tg	15/21	1	2	FACETS	0.873	0.827	0.919	0.873	0.827	0.919	CLONAL	1	TRUE	1	0.96	2		782	716	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681752	78681752	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	312	893	0	ENST00000306801.3:c.463del	p.Val155CysfsTer47	p.V155Cfs*47	ENST00000306801	NM_020761.2	154	Ggg/gg	4/34	1	2	FACETS	0.917	0.871	0.963	0.917	0.871	0.963	CLONAL	1	TRUE	1	0.96	2		893	709	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651311	45651315	+	missense_variant	Missense_Mutation	ONP	CTCTC	CTCTC	TTTTT	novel	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	248	956	0	ENST00000407780.3:c.710_714delinsAAAAA	p.Gly237_Glu238delinsGluLys	p.G237_E238delinsEK	ENST00000407780	NM_001283052.1	237	gGAGAG/gAAAAA	5/7	0.3	2	FACETS	0.828	0.78	0.877			1	INDETERMINATE	1	TRUE	NA	0.96	2		956	624	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100947	41100947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372070542	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	185	876	1	ENST00000373198.4:c.1409G>A	p.Arg470Gln	p.R470Q	ENST00000373198	NM_133170.3	470	cGa/cAa	8/32	0.3	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.96	0		877	557	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425896	49425896	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783685	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	341	943	0	ENST00000301067.7:c.12592C>T	p.Arg4198Ter	p.R4198*	ENST00000301067	NM_003482.3	4198	Cga/Tga	39/54	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.96	2		943	688	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62294213	62294213	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750794827	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	185	916	2	ENST00000360203.5:c.509G>A	p.Arg170His	p.R170H	ENST00000360203	NM_001283009.1	170	cGc/cAc	6/35	1	2	FACETS	0.568	0.526	0.611	0.568	0.526	0.611	SUBCLONAL	1	TRUE	1	0.96	2		918	679	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610364	10610364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	249	1142	1	ENST00000171111.5:c.346C>T	p.Arg116Trp	p.R116W	ENST00000171111	NM_203500.1	116	Cgg/Tgg	2/6	1	2	FACETS	0.682	0.64	0.724	0.682	0.64	0.724	SUBCLONAL	1	TRUE	1	0.96	2		1143	761	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375276	118375276	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782765039	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	256	628	1	ENST00000534358.1:c.8669G>A	p.Arg2890His	p.R2890H	ENST00000534358	NM_005933.3	2890	cGt/cAt	27/36	1	2	FACETS	0.966	0.914	1	0.966	0.914	1	CLONAL	1	TRUE	1	0.96	2		629	552	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427010	49427013	+	frameshift_variant	Frame_Shift_Del	DEL	CTGT	CTGT	-	rs1057519067	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	191	784	0	ENST00000301067.7:c.11475_11478del	p.Gln3826CysfsTer3	p.Q3826Cfs*3	ENST00000301067	NM_003482.3	3825	agACAG/ag	39/54	1	2	FACETS	0.966	0.905	1	0.966	0.905	1	CLONAL	1	TRUE	1	0.96	2		784	412	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436102	49436102	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	37	438	0	ENST00000301067.7:c.5879del	p.Gly1960AlafsTer87	p.G1960Afs*87	ENST00000301067	NM_003482.3	1960	gGc/gc	28/54	1	2	FACETS	0.285	0.236	0.34	0.285	0.236	0.34	SUBCLONAL	1	TRUE	1	0.96	2		438	270	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772200	68772200	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	166	882	0	ENST00000261769.5:c.49G>A	p.Val17Ile	p.V17I	ENST00000261769	NM_004360.3	17	Gtc/Atc	2/16	1	2	FACETS	0.595	0.549	0.642	0.595	0.549	0.642	SUBCLONAL	1	TRUE	1	0.96	2		882	581	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40856671	40856671	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	149	703	1	ENST00000428826.2:c.1966G>A	p.Gly656Arg	p.G656R	ENST00000428826		656	Gga/Aga	18/21	1	2	FACETS	0.455	0.417	0.495	0.455	0.417	0.495	SUBCLONAL	1	TRUE	1	0.96	2		704	682	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40880869	40880869	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765876793	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	558	1066	1	ENST00000428826.2:c.91C>T	p.Arg31Trp	p.R31W	ENST00000428826		31	Cgg/Tgg	3/21	1	2	FACETS	0.958	0.922	0.993	0.958	0.922	0.993	CLONAL	1	TRUE	1	0.96	2		1067	1214	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213861	2213861	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1204733528	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	33	945	3	ENST00000398665.3:c.1673C>T	p.Ala558Val	p.A558V	ENST00000398665	NM_032482.2	558	gCg/gTg	18/28	1	2	FACETS	0.105	0.085	0.128	0.105	0.085	0.128	SUBCLONAL	1	TRUE	1	0.96	2		948	654	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231449	5231449	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	227	969	0	ENST00000357368.4:c.2027del	p.Pro676ArgfsTer134	p.P676Rfs*134	ENST00000357368	NM_002850.3	676	cCg/cg	14/38	1	2	FACETS	0.667	0.624	0.711	0.667	0.624	0.711	SUBCLONAL	1	TRUE	1	0.96	2		969	709	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754628	42754628	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568472872	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	233	933	0	ENST00000222329.4:c.112C>T	p.Arg38Trp	p.R38W	ENST00000222329	NM_006494.2	38	Cgg/Tgg	2/4	1	2	FACETS	0.901	0.848	0.954	0.901	0.848	0.954	CLONAL	1	TRUE	1	0.96	2		933	539	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799248	42799248	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	164	820	0	ENST00000575354.2:c.4736del	p.Pro1579GlnfsTer41	p.P1579Qfs*41	ENST00000575354	NM_015125.3	1578	Ccc/cc	20/20	1	2	FACETS	0.622	0.575	0.671	0.622	0.575	0.671	SUBCLONAL	1	TRUE	1	0.96	2		820	549	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326204	62326204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780364760	NA	P-0008345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	308	908	3	ENST00000360203.5:c.3220G>A	p.Ala1074Thr	p.A1074T	ENST00000360203	NM_001283009.1	1074	Gcg/Acg	32/35	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.96	2		911	625	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0008346-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	495	612	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.695223538653295	4	FACETS	0.996	0.973	1	0.996	0.973	1	CLONAL	4	TRUE	0	0.696600127003823	4		612	605	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884952	111884952	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1281832778	NA	P-0008346-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	246	707	0	ENST00000341259.2:c.950T>C	p.Met317Thr	p.M317T	ENST00000341259	NM_005475.2	317	aTg/aCg	5/8	0.624013031584386	4	FACETS	0.876	0.823	0.929	0.876	0.823	0.929	CLONAL	2	TRUE	2	0.696600127003823	4		707	684	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061137	38061161	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCCCGCTTCCGCTCCCGCCCCCG	GCCCCCGCTTCCGCTCCCGCCCCCG	-	novel	NA	P-0008346-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	153	374	0	ENST00000250448.2:c.828_852del	p.Gly277AlafsTer36	p.G277Afs*36	ENST00000250448	NM_004496.3	276	ggCGGGGGCGGGAGCGGAAGCGGGGGC/gg	2/2	0.624013031584386	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.696600127003823	4		374	309	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954334	48954335	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	rs587778832	NA	P-0008346-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	243	567	0	ENST00000267163.4:c.1456_1457del	p.Leu486IlefsTer6	p.L486Ifs*6	ENST00000267163	NM_000321.2	485	tcTTta/tcta	16/27	0.684265792056658	2	FACETS	0.892	0.85	0.934	0.892	0.85	0.934	CLONAL	2	TRUE	0	0.696600127003823	2		567	391	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004609	16004609	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008346-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	321	722	0	ENST00000268712.3:c.2645del	p.Thr882SerfsTer27	p.T882Sfs*27	ENST00000268712	NM_006311.3	882	aCg/ag	20/46	0.696600127003823	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.696600127003823	2		722	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579403	7579410	+	frameshift_variant	Frame_Shift_Del	DEL	GATGACAG	GATGACAG	-	novel	NA	P-0008346-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	361	836	0	ENST00000269305.4:c.277_284del	p.Leu93PhefsTer53	p.L93Ffs*53	ENST00000269305	NM_001126112.2	93	CTGTCATCt/t	4/11	0.696600127003823	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.696600127003823	2		836	493	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0008931-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	337	515	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.677174452716826	3	FACETS	0.978	0.933	1	0.978	0.933	1	CLONAL	2	TRUE	1	0.677174452716826	3		515	681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577507	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008931-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	312	893	0	ENST00000269305.4:c.774dup	p.Asp259ArgfsTer5	p.D259Rfs*5	ENST00000269305	NM_001126112.2	258	-/A	7/11	0.677174452716826	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.677174452716826	1		893	594	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522476	187522476	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008931-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	258	953	0	ENST00000441802.2:c.11587T>C	p.Ser3863Pro	p.S3863P	ENST00000441802	NM_005245.3	3863	Tcc/Ccc	21/27	1	2	FACETS	0.947	0.89	1	0.947	0.89	1	CLONAL	1	TRUE	1	0.677174452716826	2		953	805	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058738	42058738	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008931-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	15	345	0	ENST00000219905.7:c.8458G>T	p.Asp2820Tyr	p.D2820Y	ENST00000219905	NM_001164273.1	2820	Gat/Tat	24/24	1	2	FACETS	0.148	0.108	0.197	0.148	0.108	0.197	SUBCLONAL	1	TRUE	1	0.677174452716826	2		345	299	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945382	151945382	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008931-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	172	473	0	ENST00000262189.6:c.2137del	p.Glu713AsnfsTer5	p.E713Nfs*5	ENST00000262189	NM_170606.2	713	Gaa/aa	14/59	0.677174452716826	1	FACETS	0.991	0.928	1	0.991	0.928	1	CLONAL	1	TRUE	0	0.677174452716826	1		473	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	593	1170	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.376730899910041	5	FACETS	1	0.994	1			1	CLONAL	4	TRUE	NA	0.424782685943324	5		1170	1019	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531880	41531880	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	119	983	0	ENST00000263253.7:c.1592C>G	p.Ser531Ter	p.S531*	ENST00000263253	NM_001429.3	531	tCa/tGa	7/31	0.424782685943324	4	FACETS	0.927	0.836	1	0.309	0.278	0.341	CLONAL	1	TRUE	1	0.424782685943324	4		983	861	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520000	106520000	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs759433704	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	63	641	0	ENST00000359195.3:c.2428C>A	p.Pro810Thr	p.P810T	ENST00000359195	NM_002649.2	810	Cca/Aca	6/11	0.424782685943324	6	FACETS	0.803	0.694	0.922	0.201	0.173	0.231	CLONAL	1	TRUE	2	0.424782685943324	6		641	683	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741839	145741839	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758876038	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	286	1151	0	ENST00000428558.2:c.664C>T	p.Pro222Ser	p.P222S	ENST00000428558	NM_004260.3	222	Cct/Tct	5/22	0.424782685943324	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.424782685943324	3		1151	787	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522581	176522581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	388	1107	0	ENST00000292408.4:c.1678G>A	p.Glu560Lys	p.E560K	ENST00000292408	NM_213647.1	560	Gag/Aag	13/18	0.424782685943324	5	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	2	0.424782685943324	5		1107	913	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11314005	11314005	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	137	1232	1	ENST00000361445.4:c.731G>T	p.Gly244Val	p.G244V	ENST00000361445	NM_004958.3	244	gGa/gTa	6/58	0.424782685943324	3	FACETS	0.973	0.885	1	0.486	0.442	0.532	CLONAL	1	TRUE	1	0.424782685943324	3		1233	804	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39321570	39321570	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs758305071	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	190	665	0	ENST00000373001.3:c.451A>G	p.Met151Val	p.M151V	ENST00000373001	NM_022157.3	151	Atg/Gtg	3/7	0.424782685943324	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	1	0.424782685943324	3		665	528	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366622	40366622	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	194	916	1	ENST00000397332.2:c.575del	p.Pro192GlnfsTer12	p.P192Qfs*12	ENST00000397332	NM_001033082.2	192	cCa/ca	2/3	0.424782685943324	3	FACETS	0.918	0.855	0.983	0.918	0.855	0.983	CLONAL	2	TRUE	1	0.424782685943324	3		917	603	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430351	78430351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	111	971	0	ENST00000370768.2:c.817G>A	p.Gly273Arg	p.G273R	ENST00000370768	NM_003902.3	273	Gga/Aga	10/20	0.424782685943324	3	FACETS	0.901	0.811	0.997	0.451	0.405	0.499	CLONAL	1	TRUE	1	0.424782685943324	3		971	703	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166248	118166248	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	141	615	0	ENST00000369448.3:c.758G>C	p.Arg253Pro	p.R253P	ENST00000369448	NM_017709.3	253	cGg/cCg	2/2	0.424782685943324	3	FACETS	0.873	0.802	0.947	0.873	0.802	0.947	CLONAL	2	TRUE	1	0.424782685943324	3		615	461	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161326551	161326551	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	20	195	0	ENST00000367975.2:c.326G>T	p.Gly109Val	p.G109V	ENST00000367975	NM_003001.3	109	gGg/gTg	5/6	0.424782685943324	3	FACETS	0.968	0.75	1	0.484	0.375	0.607	CLONAL	1	TRUE	1	0.424782685943324	3		195	118	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332837	70332838	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	181	1072	2	ENST00000373644.4:c.747_748del	p.Ala250SerfsTer31	p.A250Sfs*31	ENST00000373644	NM_030625.2	248	GTg/g	2/12	0.344936679360785	4	FACETS	0.768	0.709	0.828	0.768	0.709	0.828	SUBCLONAL	2	TRUE	2	0.424782685943324	4		1074	791	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128998	64130020	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGTAGCAAGACGGGGCATGGCAAGGTAGGTTGGCAGGGAAGTGGGGCTGGGGGAGGTGGAAAGGTGGGGTGTGAGGCAGGGGAGATGCAGGCCCTCACCCCGGCTCCACCCGGCAGGCTGTGGACTGGTGGAGCCTGGGCATCTTGCTCTTCGAGCTGCTGACGGGGGCCTCGCCCTTCACCCTGGAGGGCGAGAGGAACACGCAGGCTGAGGTGTCTCGGTGAGTAGGGCTGGACGTGGAGGGCGGCCAGAGGGCTGCAGGGCCTGCCTGGGCAGGGCTGTGGGTGGGGGGCTTGCTGCCCCTGACACCCCCCCAATCCTCCCAGACGGATCCTGAAGTGCTCCCCTCCCTTCCCCCCTCGGATCGGGCCCGTGGCGCAGGACCTGCTGCAGCGGCTGCTTTGTAAGGATCCTAAGAAGCGATTGGGCGCGGGGCCCCAGGGGGCACAAGAAGTCCGGAACCATCCCTTCTTCCAGGTGAGGCTGACTCAGGGCCCCATACCTCCTGGTGCATACCCAGGTGGGGCTGCTGTTCCAGGTTGAGGTTGTGCCTGGCCAGTTTCACTTTATTTGGAAATCCCCCCAGAGAAAGAAAGCAAGTGTGTGTCAGCTAGGTTTCTCTTCACATCCATCCCCACTGAAACTTGGCAGATGTGTTCCTGAAAGAAAGGATTCTAGGTTCATTGGCTGTTGGGGCTGTCAGGGATTTGAGAATGGATTGGTCGGTCCTTTCACTGGACAGACCCAGAGAAGGCAGGTGACCTGCCCCCGACGGCACAGTAAATGGTGCCGAGTTGGGAATAGACCTTGGGTCTAGATAGATCTCCTGCTGGTCCAAATCAGTACGGAAACCCACACTTATGGCTTTTAGCACCCACCCAGGCATTTTGTTCTTTGTCCCCGTCCCTGTACAGTCTGTGTGCCTGTCATTCAGATGGACGGTTGATCAGCACACATGGGTGTTTGCTCACTTGTTAGGAGCACACACATGTTAGAGTGCAGTGCAGAGTGAATCTGGCCATG	CGTAGCAAGACGGGGCATGGCAAGGTAGGTTGGCAGGGAAGTGGGGCTGGGGGAGGTGGAAAGGTGGGGTGTGAGGCAGGGGAGATGCAGGCCCTCACCCCGGCTCCACCCGGCAGGCTGTGGACTGGTGGAGCCTGGGCATCTTGCTCTTCGAGCTGCTGACGGGGGCCTCGCCCTTCACCCTGGAGGGCGAGAGGAACACGCAGGCTGAGGTGTCTCGGTGAGTAGGGCTGGACGTGGAGGGCGGCCAGAGGGCTGCAGGGCCTGCCTGGGCAGGGCTGTGGGTGGGGGGCTTGCTGCCCCTGACACCCCCCCAATCCTCCCAGACGGATCCTGAAGTGCTCCCCTCCCTTCCCCCCTCGGATCGGGCCCGTGGCGCAGGACCTGCTGCAGCGGCTGCTTTGTAAGGATCCTAAGAAGCGATTGGGCGCGGGGCCCCAGGGGGCACAAGAAGTCCGGAACCATCCCTTCTTCCAGGTGAGGCTGACTCAGGGCCCCATACCTCCTGGTGCATACCCAGGTGGGGCTGCTGTTCCAGGTTGAGGTTGTGCCTGGCCAGTTTCACTTTATTTGGAAATCCCCCCAGAGAAAGAAAGCAAGTGTGTGTCAGCTAGGTTTCTCTTCACATCCATCCCCACTGAAACTTGGCAGATGTGTTCCTGAAAGAAAGGATTCTAGGTTCATTGGCTGTTGGGGCTGTCAGGGATTTGAGAATGGATTGGTCGGTCCTTTCACTGGACAGACCCAGAGAAGGCAGGTGACCTGCCCCCGACGGCACAGTAAATGGTGCCGAGTTGGGAATAGACCTTGGGTCTAGATAGATCTCCTGCTGGTCCAAATCAGTACGGAAACCCACACTTATGGCTTTTAGCACCCACCCAGGCATTTTGTTCTTTGTCCCCGTCCCTGTACAGTCTGTGTGCCTGTCATTCAGATGGACGGTTGATCAGCACACATGGGTGTTTGCTCACTTGTTAGGAGCACACACATGTTAGAGTGCAGTGCAGAGTGAATCTGGCCATG	-	novel	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	212	1131	0	ENST00000334205.4:c.630_906+548del		p.X210_splice	ENST00000334205	NM_003942.2	210		6-8/17	0.411476607403769	4	FACETS	0.815	0.759	0.874	0.815	0.759	0.874	CLONAL	2	TRUE	2	0.424782685943324	4		1131	872	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	464401	464401	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	190	898	0	ENST00000399788.2:c.793A>T	p.Arg265Ter	p.R265*	ENST00000399788	NM_001042603.1	265	Aga/Tga	7/28	0.424782685943324	4	FACETS	0.824	0.764	0.887	0.824	0.764	0.887	CLONAL	2	TRUE	2	0.424782685943324	4		898	773	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022526	12022526	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs111871763	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	206	968	1	ENST00000396373.4:c.632G>T	p.Arg211Leu	p.R211L	ENST00000396373	NM_001987.4	211	cGc/cTc	5/8	0.424782685943324	4	FACETS	0.889	0.827	0.953	0.889	0.827	0.953	CLONAL	2	TRUE	2	0.424782685943324	4		969	777	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859039	57859039	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	246	1161	0	ENST00000228682.2:c.534+1G>T		p.X178_splice	ENST00000228682	NM_005269.2	178			0.424782685943324	4	FACETS	0.963	0.902	1	0.481	0.451	0.513	CLONAL	2	TRUE	0	0.424782685943324	4		1161	857	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911809	32911809	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	236	1018	1	ENST00000380152.3:c.3317G>T	p.Ser1106Ile	p.S1106I	ENST00000380152		1106	aGc/aTc	11/27	0.422796185255302	2	FACETS	0.893	0.839	0.948	0.893	0.839	0.948	CLONAL	2	TRUE	0	0.424782685943324	2		1019	622	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336167	73336167	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs541536936	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	126	601	1	ENST00000377767.4:c.2236C>A	p.Arg746Ser	p.R746S	ENST00000377767	NM_014953.3	746	Cgc/Agc	17/21	0.422796185255302	2	FACETS	0.875	0.803	0.949	0.875	0.803	0.949	CLONAL	2	TRUE	0	0.424782685943324	2		602	339	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807840	3807840	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	198	845	2	ENST00000262367.5:c.3579G>T	p.Met1193Ile	p.M1193I	ENST00000262367	NM_004380.2	1193	atG/atT	18/31	0.424782685943324	4	FACETS	0.925	0.86	0.992	0.925	0.86	0.992	CLONAL	2	TRUE	2	0.424782685943324	4		847	718	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39576644	39576644	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	104	932	0	ENST00000262039.4:c.934G>C	p.Glu312Gln	p.E312Q	ENST00000262039	NM_002647.2	312	Gaa/Caa	9/25	0.397619364265604	1	FACETS	0.914	0.824	1	0.914	0.824	1	CLONAL	1	TRUE	0	0.424782685943324	1		932	422	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600335	10600335	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	233	1009	2	ENST00000171111.5:c.1520del	p.Arg507GlnfsTer25	p.R507Qfs*25	ENST00000171111	NM_203500.1	507	cGa/ca	4/6	0.406492822239521	2	FACETS	0.997	0.939	1	0.997	0.939	1	CLONAL	2	TRUE	0	0.424782685943324	2		1011	550	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519767	29519767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1165866210	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	204	1005	2	ENST00000389048.3:c.1804G>A	p.Asp602Asn	p.D602N	ENST00000389048	NM_004304.4	602	Gat/Aat	9/29	0.396068355150967	5	FACETS	0.975	0.907	1	0.65	0.604	0.698	CLONAL	2	TRUE	2	0.424782685943324	5		1007	806	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225449714	225449714	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	135	690	2	ENST00000264414.4:c.13A>T	p.Ser5Cys	p.S5C	ENST00000264414	NM_003590.4	5	Agc/Tgc	1/16	0.424782685943324	3	FACETS	0.944	0.867	1	0.944	0.867	1	CLONAL	2	TRUE	1	0.424782685943324	3		692	408	SUCCESS
ATR	545	MSKCC	GRCh37	3	142232476	142232476	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	154	717	0	ENST00000350721.4:c.4508G>T	p.Arg1503Leu	p.R1503L	ENST00000350721	NM_001184.3	1503	cGa/cTa	26/47	0.424782685943324	3	FACETS	0.895	0.825	0.967	0.895	0.825	0.967	CLONAL	2	TRUE	1	0.424782685943324	3		717	491	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808973	1808973	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	76	756	0	ENST00000260795.2:c.2405G>C	p.Gly802Ala	p.G802A	ENST00000260795		802	gGg/gCg	17/17	1	2	FACETS	0.877	0.773	0.988	0.877	0.773	0.988	CLONAL	1	TRUE	1	0.424782685943324	2		756	408	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573337	55573337	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs767936896	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	196	981	0	ENST00000288135.5:c.999G>C	p.Leu333Phe	p.L333F	ENST00000288135	NM_000222.2	333	ttG/ttC	6/21	0.424782685943324	3	FACETS	0.865	0.804	0.927	0.865	0.804	0.927	CLONAL	2	TRUE	1	0.424782685943324	3		981	647	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539027	187539027	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	256	1056	0	ENST00000441802.2:c.8713G>T	p.Asp2905Tyr	p.D2905Y	ENST00000441802	NM_005245.3	2905	Gat/Tat	10/27	0.411476607403769	4	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	2	0.424782685943324	4		1056	844	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539512	187539512	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	183	843	0	ENST00000441802.2:c.8228del	p.Pro2743GlnfsTer10	p.P2743Qfs*10	ENST00000441802	NM_005245.3	2743	cCa/ca	10/27	0.411476607403769	4	FACETS	0.872	0.807	0.939	0.872	0.807	0.939	CLONAL	2	TRUE	2	0.424782685943324	4		843	704	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540998	187540998	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	161	726	2	ENST00000441802.2:c.6742C>A	p.Pro2248Thr	p.P2248T	ENST00000441802	NM_005245.3	2248	Ccg/Acg	10/27	0.411476607403769	4	FACETS	0.961	0.886	1	0.961	0.886	1	CLONAL	2	TRUE	2	0.424782685943324	4		728	562	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505040	149505040	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs771835513	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	322	922	1	ENST00000261799.4:c.1775C>A	p.Thr592Lys	p.T592K	ENST00000261799	NM_002609.3	592	aCg/aAg	12/23	0.424782685943324	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	1	0.424782685943324	4		923	656	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287251	33287251	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	123	934	0	ENST00000374542.5:c.1846G>C	p.Gly616Arg	p.G616R	ENST00000374542	NM_001141970.1	616	Ggc/Cgc	6/8	0.424782685943324	3	FACETS	0.972	0.88	1	0.486	0.44	0.535	CLONAL	1	TRUE	1	0.424782685943324	3		934	722	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004729	150004729	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	274	869	0	ENST00000253339.5:c.1496A>C	p.Lys499Thr	p.K499T	ENST00000253339		499	aAa/aCa	3/7	0.422796185255302	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.424782685943324	2		869	610	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242454	55242454	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	201	990	0	ENST00000275493.2:c.2224G>T	p.Val742Phe	p.V742F	ENST00000275493	NM_005228.3	742	Gtc/Ttc	19/28	0.424782685943324	4	FACETS	0.901	0.838	0.967	0.901	0.838	0.967	CLONAL	2	TRUE	2	0.424782685943324	4		990	748	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572669	141572669	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	161	1045	0	ENST00000220592.5:c.401G>T	p.Trp134Leu	p.W134L	ENST00000220592	NM_012154.3	134	tGg/tTg	4/19	0.424782685943324	3	FACETS	1	0.984	1	0.642	0.59	0.696	CLONAL	1	TRUE	1	0.424782685943324	3		1045	716	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797217	135797217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	130	546	1	ENST00000298552.3:c.652G>A	p.Glu218Lys	p.E218K	ENST00000298552	NM_001162426.1	218	Gaa/Aaa	7/23	0.424782685943324	4	FACETS	0.922	0.842	1	0.922	0.842	1	CLONAL	2	TRUE	2	0.424782685943324	4		547	473	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404395	139404395	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	260	1237	0	ENST00000277541.6:c.2759del	p.Gly920AlafsTer259	p.G920Afs*259	ENST00000277541	NM_017617.3	920	gGc/gc	18/34	0.424782685943324	4	FACETS	0.98	0.92	1	0.98	0.92	1	CLONAL	2	TRUE	2	0.424782685943324	4		1237	890	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932338	39932338	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	130	732	0	ENST00000378444.4:c.2261G>T	p.Arg754Leu	p.R754L	ENST00000378444	NM_001123385.1	754	cGt/cTt	4/15	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.424782685943324	1		732	349	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456492	29456494	+	missense_variant	Missense_Mutation	TNP	CTG	CTG	TTT	novel	NA	P-0008938-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	378	1246	0	ENST00000389048.3:c.2424_2426delinsAAA	p.Asn808_Arg809delinsLysLys	p.N808_R809delinsKK	ENST00000389048	NM_004304.4	808	aaCAGa/aaAAAa	14/29	0.396068355150967	5	FACETS	0.855	0.813	0.898	0.855	0.813	0.898	CLONAL	3	TRUE	2	0.424782685943324	5		1246	1136	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009122-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	348	777	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.961	0.913	1	0.961	0.913	1	CLONAL	1	TRUE	1	0.791247801251964	2		777	915	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11999013	11999013	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0009122-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	184	346	0	ENST00000353533.5:c.513+2T>C		p.X171_splice	ENST00000353533	NM_003010.3	171			0.791247801251964	1	FACETS	0.969	0.917	1	0.969	0.917	1	CLONAL	1	TRUE	0	0.791247801251964	1		346	290	SUCCESS
ATR	545	MSKCC	GRCh37	3	142172040	142172040	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009122-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	436	743	0	ENST00000350721.4:c.7691A>G	p.Glu2564Gly	p.E2564G	ENST00000350721	NM_001184.3	2564	gAa/gGa	46/47	0.791247801251964	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.791247801251964	1		743	624	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1555525585	NA	P-0009122-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	313	660	0	ENST00000269305.4:c.673-2A>G		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.791247801251964	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.791247801251964	1		660	466	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346580	81346598	+	frameshift_variant	Frame_Shift_Del	DEL	AGTGGATTTCCCGTGTAGC	AGTGGATTTCCCGTGTAGC	-	novel	NA	P-0009122-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	99	504	0	ENST00000222390.5:c.1355_1373del	p.Cys452SerfsTer20	p.C452Sfs*20	ENST00000222390	NM_000601.4	452	tGCTACACGGGAAATCCACTc/tc	11/18	NA	2	FACETS	0.42	0.375	0.467			1	INDETERMINATE	1	TRUE	NA	0.791247801251964	2		504	596	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0009658-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	70	515	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.834	0.728	0.948	0.834	0.728	0.948	CLONAL	1	TRUE	1	0.304670263478848	2		515	551	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397217	397217	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753427028	NA	P-0009658-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	32	470	0	ENST00000380956.4:c.602G>A	p.Arg201His	p.R201H	ENST00000380956	NM_001195286.1	201	cGc/cAc	5/9	1	2	FACETS	0.452	0.366	0.549	0.452	0.366	0.549	SUBCLONAL	1	TRUE	1	0.304670263478848	2		470	465	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0009821-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	382	515	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.608401078528365	6	FACETS	0.89	0.851	0.929	1	0.993	1	CLONAL	4	TRUE	3	0.608401078528365	6		515	782	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009821-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	430	892	0	ENST00000206249.3:c.1610A>G	p.Tyr537Cys	p.Y537C	ENST00000206249	NM_000125.3	537	tAt/tGt	8/8	0.608401078528365	3	FACETS	1	0.969	1	0.675	0.647	0.704	CLONAL	2	TRUE	0	0.608401078528365	3		892	910	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900884	3900884	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009821-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1344	172	909	0	ENST00000262367.5:c.212C>T	p.Ser71Leu	p.S71L	ENST00000262367	NM_004380.2	71	tCg/tTg	2/31	0.608401078528365	6	FACETS	0.827	0.758	0.899			1	CLONAL	1	TRUE	NA	0.608401078528365	6		909	1516	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459212	120459212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009821-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	176	802	0	ENST00000256646.2:c.6133C>T	p.Leu2045Phe	p.L2045F	ENST00000256646	NM_024408.3	2045	Ctt/Ttt	34/34	0.570221808782994	4	FACETS	0.881	0.811	0.955	0.441	0.405	0.478	CLONAL	1	TRUE	2	0.608401078528365	4		802	1056	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74868226	74868226	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009821-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	84	425	0	ENST00000284811.8:c.68C>T	p.Ser23Leu	p.S23L	ENST00000284811		23	tCa/tTa	3/4	0.561475063322129	3	FACETS	0.781	0.693	0.875			1	SUBCLONAL	1	TRUE	NA	0.608401078528365	3		425	461	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754353	57754354	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	GACTAAG	novel	NA	P-0009821-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	208	558	0	ENST00000274289.3:c.496-5_497dup	p.Met167LeufsTer34	p.M167Lfs*34	ENST00000274289	NM_006622.3	166	tca/tcCTTAGTCa	4/14	0.608401078528365	2	FACETS	0.812	0.764	0.86	0.812	0.764	0.86	CLONAL	2	TRUE	0	0.608401078528365	2		558	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs587781702	NA	P-0009821-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	459	938	0	ENST00000269305.4:c.920-1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			NA	2	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.608401078528365	2		938	702	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731237	162731237	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009821-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	99	390	0	ENST00000367921.3:c.1092C>G	p.Phe364Leu	p.F364L	ENST00000367921	NM_006182.2	364	ttC/ttG	9/18	0.570221808782994	4	FACETS	1	0.92	1	0.515	0.461	0.572	CLONAL	1	TRUE	2	0.608401078528365	4		390	508	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519922	NA	P-0009935-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	126	839	1	ENST00000397062.3:c.235G>A	p.Glu79Lys	p.E79K	ENST00000397062	NM_006164.4	79	Gag/Aag	2/5	1	2	FACETS	0.592	0.535	0.652	0.592	0.535	0.652	SUBCLONAL	1	TRUE	1	0.413111785047224	2		840	1031	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144907	47144907	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009935-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	59	530	0	ENST00000409792.3:c.4846G>C	p.Asp1616His	p.D1616H	ENST00000409792	NM_014159.6	1616	Gat/Cat	7/21	1	2	FACETS	0.412	0.354	0.476	0.412	0.354	0.476	SUBCLONAL	1	TRUE	1	0.413111785047224	2		530	693	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578463	7578463	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371524413	NA	P-0009935-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	77	813	0	ENST00000269305.4:c.467G>C	p.Arg156Pro	p.R156P	ENST00000269305	NM_001126112.2	156	cGc/cCc	5/11	1	2	FACETS	0.444	0.389	0.503	0.444	0.389	0.503	SUBCLONAL	1	TRUE	1	0.413111785047224	2		813	840	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258428	16258428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009935-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	69	651	1	ENST00000375759.3:c.5693G>A	p.Arg1898Gln	p.R1898Q	ENST00000375759	NM_015001.2	1898	cGa/cAa	11/15	1	2	FACETS	0.395	0.343	0.452	0.395	0.343	0.452	SUBCLONAL	1	TRUE	1	0.413111785047224	2		652	845	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307472	118307472	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0009935-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	42	436	0	ENST00000534358.1:c.245C>G	p.Ser82Ter	p.S82*	ENST00000534358	NM_005933.3	82	tCa/tGa	1/36	1	2	FACETS	0.35	0.292	0.415	0.35	0.292	0.415	SUBCLONAL	1	TRUE	1	0.413111785047224	2		436	581	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134231	41134231	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009935-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	35	451	0	ENST00000379561.5:c.1397T>G	p.Leu466Arg	p.L466R	ENST00000379561	NM_002015.3	466	cTg/cGg	2/3	1	2	FACETS	0.298	0.244	0.36	0.298	0.244	0.36	SUBCLONAL	1	TRUE	1	0.413111785047224	2		451	568	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2093599	2093599	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009935-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	113	804	0	ENST00000219066.1:c.678G>T	p.Met226Ile	p.M226I	ENST00000219066	NM_002528.5	226	atG/atT	4/6	1	2	FACETS	0.523	0.469	0.579	0.523	0.469	0.579	SUBCLONAL	1	TRUE	1	0.413111785047224	2		804	1047	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772254	68772254	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009935-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	88	719	1	ENST00000261769.5:c.103G>T	p.Glu35Ter	p.E35*	ENST00000261769	NM_004360.3	35	Gag/Tag	2/16	1	2	FACETS	0.491	0.434	0.552	0.491	0.434	0.552	SUBCLONAL	1	TRUE	1	0.413111785047224	2		720	867	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748605	40748605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009935-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	51	522	0	ENST00000373198.4:c.2911C>T	p.His971Tyr	p.H971Y	ENST00000373198	NM_133170.3	971	Cat/Tat	21/32	1	2	FACETS	0.425	0.361	0.496	0.425	0.361	0.496	SUBCLONAL	1	TRUE	1	0.413111785047224	2		522	581	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141054	55141054	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009935-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	42	442	0	ENST00000257290.5:c.1700C>G	p.Pro567Arg	p.P567R	ENST00000257290	NM_006206.4	567	cCa/cGa	12/23	1	2	FACETS	0.348	0.29	0.412	0.348	0.29	0.412	SUBCLONAL	1	TRUE	1	0.413111785047224	2		442	585	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	211	482	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.929088590691214	2		482	451	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0010085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	227	401	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.995	0.938	1	0.995	0.938	1	CLONAL	1	TRUE	1	0.929088590691214	2		401	491	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799063	42799065	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs751580245	NA	P-0010085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	1001	1025	0	ENST00000575354.2:c.4550_4552del	p.Lys1517del	p.K1517del	ENST00000575354	NM_015125.3	1516	cAGAag/cag	20/20	NA	2	FACETS	0.968	0.956	0.98			1	INDETERMINATE	2	TRUE	NA	0.929088590691214	2		1025	1113	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400073	139400073	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	893	1040	0	ENST00000277541.6:c.4275C>G	p.Cys1425Trp	p.C1425W	ENST00000277541	NM_017617.3	1425	tgC/tgG	25/34	0.919286417489846	2	FACETS	0.976	0.963	0.988	0.976	0.963	0.988	CLONAL	2	TRUE	0	0.929088590691214	2		1040	985	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421684	49421684	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	364	775	0	ENST00000301067.7:c.14545A>G	p.Ser4849Gly	p.S4849G	ENST00000301067	NM_003482.3	4849	Agc/Ggc	47/54	1	2	FACETS	0.937	0.893	0.981	0.937	0.893	0.981	CLONAL	1	TRUE	1	0.929088590691214	2		775	836	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0010276-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	255	908	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.94	0.881	1	0.94	0.881	1	CLONAL	1	TRUE	1	0.576074081366362	2		908	942	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	166	786	2	ENST00000346208.3:c.1220_1221insA	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcAg	6/6	1	2	FACETS	0.931	0.856	1	0.931	0.856	1	CLONAL	1	TRUE	1	0.400633332369267	2		788	890	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0011038-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	439	571	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.275871386006482	7	FACETS	0.97	0.93	1	0.97	0.93	1	CLONAL	6	TRUE	1	0.275871386006482	7		571	924	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879961	44879961	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011038-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	66	252	0	ENST00000377967.4:c.550G>C	p.Glu184Gln	p.E184Q	ENST00000377967	NM_021140.2	184	Gag/Cag	6/29	0.259664285927312	2	FACETS	1	0.955	1			1	CLONAL	1	TRUE	NA	0.275871386006482	2		252	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578490	7578490	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1453167097	NA	P-0011038-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	215	689	0	ENST00000269305.4:c.440T>G	p.Val147Gly	p.V147G	ENST00000269305	NM_001126112.2	147	gTt/gGt	5/11	0.267380427135949	2	FACETS	0.955	0.89	1	0.955	0.89	1	CLONAL	2	TRUE	0	0.275871386006482	2		689	816	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950442	38950442	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011038-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	65	426	0	ENST00000357387.3:c.3508G>C	p.Glu1170Gln	p.E1170Q	ENST00000357387	NM_152756.3	1170	Gaa/Caa	31/38	0.275871386006482	11	FACETS	0.925	0.799	1	0.103	0.088	0.118	CLONAL	1	TRUE	2	0.275871386006482	11		426	1142	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69050687	69050687	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011038-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	82	531	0	ENST00000288368.4:c.4022C>A	p.Ala1341Glu	p.A1341E	ENST00000288368	NM_024870.2	1341	gCa/gAa	33/40	0.275871386006482	4	FACETS	1	0.887	1	0.336	0.296	0.379	CLONAL	1	TRUE	1	0.275871386006482	4		531	753	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981578	70981578	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011038-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	100	747	0	ENST00000276594.2:c.518C>T	p.Ser173Leu	p.S173L	ENST00000276594	NM_024504.3	173	tCa/tTa	2/8	0.275871386006482	4	FACETS	0.816	0.727	0.911	0.272	0.242	0.304	CLONAL	1	TRUE	1	0.275871386006482	4		747	1134	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048602	180048602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778453271	NA	P-0011247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	53	812	0	ENST00000261937.6:c.1960G>A	p.Glu654Lys	p.E654K	ENST00000261937	NM_182925.4	654	Gaa/Aaa	13/30	1	2	FACETS	0.395	0.336	0.461	0.395	0.336	0.461	SUBCLONAL	1	TRUE	1	0.29	2		812	925	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979201	93979201	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	31	392	0	ENST00000369303.4:c.1627T>G	p.Phe543Val	p.F543V	ENST00000369303	NM_004440.3	543	Ttt/Gtt	7/17	1	2	FACETS	0.433	0.349	0.528	0.433	0.349	0.528	SUBCLONAL	1	TRUE	1	0.29	2		392	494	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0012132-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	114	278	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.697115552850934	1	FACETS	0.982	0.907	1	0.982	0.907	1	CLONAL	1	TRUE	0	0.697115552850934	1		278	217	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248145	59248145	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012132-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	47	93	0	ENST00000371222.2:c.598C>G	p.Gln200Glu	p.Q200E	ENST00000371222	NM_002228.3	200	Caa/Gaa	1/1	0.667994229388784	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.697115552850934	1		93	73	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121588	2121596	+	frameshift_variant	Frame_Shift_Ins	INS	GTTCAGCCC	GTTCAGCCC	ACTACATGTACGCA	novel	NA	P-0012132-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	247	864	0	ENST00000219476.3:c.1917_1925delinsACTACATGTACGCA	p.Phe640LeufsTer60	p.F640Lfs*60	ENST00000219476	NM_000548.3	639	cgGTTCAGCCCc/cgACTACATGTACGCAc	18/42	1	2	FACETS	0.819	0.768	0.872	0.819	0.768	0.872	CLONAL	1	TRUE	1	0.697115552850934	2		864	865	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105645	27105645	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	123	617	0	ENST00000324856.7:c.5256G>C	p.Lys1752Asn	p.K1752N	ENST00000324856	NM_006015.4	1752	aaG/aaC	20/20	0.486114727080554	3	FACETS	0.876	0.793	0.964	0.438	0.396	0.482	CLONAL	1	TRUE	1	0.48591113437241	3		617	718	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307173	65307173	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs181919006	NA	P-0012214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	156	616	0	ENST00000342505.4:c.2515C>T	p.Arg839Ter	p.R839*	ENST00000342505	NM_002227.2	839	Cga/Tga	18/25	0.486114727080554	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.48591113437241	1		616	444	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437793	110437793	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	169	729	0	ENST00000375856.3:c.608A>G	p.Lys203Arg	p.K203R	ENST00000375856	NM_003749.2	203	aAg/aGg	1/2	0.459551195292965	5	FACETS	0.948	0.869	1	0.237	0.217	0.258	CLONAL	1	TRUE	1	0.48591113437241	5		729	1269	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576090	88576109	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GTGTCCGGCTTGTGGCAGTT	GTGTCCGGCTTGTGGCAGTT	-	novel	NA	P-0012214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	204	838	0	ENST00000360948.2:c.1564_1583del	p.Asn522ValfsTer6	p.N522Vfs*6	ENST00000360948	NM_001012338.2	522	AACTGCCACAAGCCGGACACg/g	13/19	0.486114727080554	3	FACETS	1	0.987	1	0.639	0.593	0.686	CLONAL	1	TRUE	1	0.48591113437241	3		838	817	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0012214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	461	803	2	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.46520685021219	3	FACETS	0.973	0.937	1	0.973	0.937	1	CLONAL	3	TRUE	0	0.48591113437241	3		805	808	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117243	7117243	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1701	226	1023	0	ENST00000302850.5:c.3973G>T	p.Glu1325Ter	p.E1325*	ENST00000302850	NM_000208.2	1325	Gag/Tag	22/22	0.48591113437241	7	FACETS	1	0.966	1			1	CLONAL	1	TRUE	NA	0.48591113437241	7		1023	1927	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252856	36252856	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	215	452	1	ENST00000300305.3:c.506G>A	p.Arg169Lys	p.R169K	ENST00000300305		169	aGa/aAa	4/8	0.486114727080554	3	FACETS	1	0.939	1			1	CLONAL	2	TRUE	NA	0.48591113437241	3		453	549	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252970	36252971	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	295	614	0	ENST00000300305.3:c.391dup	p.Thr131AsnfsTer7	p.T131Nfs*7	ENST00000300305		131	act/aAct	4/8	0.486114727080554	3	FACETS	1	0.964	1			1	CLONAL	2	TRUE	NA	0.48591113437241	3		614	738	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502386	186502386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs953593626	NA	P-0012214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	146	614	0	ENST00000323963.5:c.109G>A	p.Asp37Asn	p.D37N	ENST00000323963		37	Gat/Aat	3/11	0.486114727080554	3	FACETS	1	0.921	1	0.504	0.46	0.549	CLONAL	1	TRUE	1	0.48591113437241	3		614	741	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979242	93979242	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	124	540	0	ENST00000369303.4:c.1586G>C	p.Arg529Thr	p.R529T	ENST00000369303	NM_004440.3	529	aGa/aCa	7/17	0.486114727080554	4	FACETS	1	0.948	1			1	CLONAL	1	TRUE	NA	0.48591113437241	4		540	709	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001331	150001331	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	541	856	0	ENST00000253339.5:c.2273del	p.Ala758ValfsTer8	p.A758Vfs*8	ENST00000253339		758	gCt/gt	4/7	0.486114727080554	3	FACETS	0.971	0.938	1	0.971	0.938	1	CLONAL	3	TRUE	0	0.48591113437241	3		856	950	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221945	98221945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756465236	NA	P-0012214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	287	726	4	ENST00000331920.6:c.2824C>T	p.Arg942Trp	p.R942W	ENST00000331920	NM_000264.3	942	Cgg/Tgg	17/24	0.48123424064954	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.48591113437241	2		730	585	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0012520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	103	399	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.884	0.805	0.966	0.884	0.805	0.966	CLONAL	1	TRUE	1	0.882209055400734	2		399	264	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0012520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	218	908	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	0.974	1	CLONAL	1	TRUE	1	0.882209055400734	2		908	466	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299833	15299833	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	38	530	0	ENST00000263388.2:c.1345C>T	p.Arg449Cys	p.R449C	ENST00000263388	NM_000435.2	449	Cgc/Tgc	8/33	1	2	FACETS	0.159	0.131	0.191	0.159	0.131	0.191	SUBCLONAL	1	TRUE	1	0.882209055400734	2		530	541	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044941	47044941	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	282	630	0	ENST00000377604.3:c.2267G>A	p.Trp756Ter	p.W756*	ENST00000377604	NM_001204468.1	756	tGg/tAg	20/24	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.882209055400734	2		630	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0012646-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	320	644	1	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	0.87462133068512	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.87462133068512	1		645	382	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573899	41573899	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012646-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	371	924	0	ENST00000263253.7:c.6184A>T	p.Ser2062Cys	p.S2062C	ENST00000263253	NM_001429.3	2062	Agc/Tgc	31/31	NA	2	FACETS	0.999	0.953	1			1	INDETERMINATE	1	TRUE	NA	0.87462133068512	2		924	849	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0012819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	221	336	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.424671744096344	2	FACETS	0.975	0.915	1	0.975	0.915	1	CLONAL	2	TRUE	0	0.424671744096344	2		336	534	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913476	NA	P-0012819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	217	652	0	ENST00000358487.5:c.1647T>G	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaG	12/18	0.424671744096344	2	FACETS	0.878	0.815	0.943	0.439	0.407	0.472	CLONAL	1	TRUE	0	0.424671744096344	2		652	1164	SUCCESS
APC	324	MSKCC	GRCh37	5	112178805	112178805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147549623	NA	P-0012819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	203	580	2	ENST00000257430.4:c.7514G>A	p.Arg2505Gln	p.R2505Q	ENST00000257430	NM_000038.5	2505	cGa/cAa	16/16	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.424671744096344	2		582	943	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749415085	NA	P-0012819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	202	889	0	ENST00000263967.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000263967	NM_006218.2	38	Cgt/Tgt	2/21	1	2	FACETS	0.796	0.737	0.858	0.796	0.737	0.858	SUBCLONAL	1	TRUE	1	0.424671744096344	2		889	1195	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0012819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1230	158	722	1	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	1	2	FACETS	0.536	0.49	0.585	0.536	0.49	0.585	SUBCLONAL	1	TRUE	1	0.424671744096344	2		723	1388	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796883	42796883	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	223	624	0	ENST00000575354.2:c.3347del	p.Pro1116GlnfsTer45	p.P1116Qfs*45	ENST00000575354	NM_015125.3	1114	gCc/gc	14/20	1	2	FACETS	0.852	0.792	0.914	0.852	0.792	0.914	CLONAL	1	TRUE	1	0.424671744096344	2		624	1233	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	117	380	4	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	1	2	FACETS	0.772	0.696	0.851	0.772	0.696	0.851	SUBCLONAL	1	TRUE	1	0.424671744096344	2		384	714	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	244	723	0	ENST00000397062.3:c.246A>T	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaT	2/5	1	2	FACETS	0.862	0.804	0.922	0.862	0.804	0.922	CLONAL	1	TRUE	1	0.424671744096344	2		723	1333	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0012819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1173	289	750	7	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.931	0.874	0.99	0.931	0.874	0.99	CLONAL	1	TRUE	1	0.424671744096344	2		757	1462	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627774	187627774	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1183516785	NA	P-0012819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	240	675	3	ENST00000441802.2:c.3208C>T	p.Arg1070Ter	p.R1070*	ENST00000441802	NM_005245.3	1070	Cga/Tga	2/27	1	2	FACETS	0.903	0.842	0.966	0.903	0.842	0.966	CLONAL	1	TRUE	1	0.424671744096344	2		678	1252	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850704	63850705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	184	554	0	ENST00000279873.7:c.1489dup	p.Ile497AsnfsTer31	p.I497Nfs*31	ENST00000279873	NM_032199.2	494	-/A	10/10	0.424671744096344	2	FACETS	0.888	0.819	0.959	0.444	0.409	0.48	CLONAL	1	TRUE	0	0.424671744096344	2		554	976	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420253	49420253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758730277	NA	P-0012819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	59	569	2	ENST00000301067.7:c.15496G>A	p.Ala5166Thr	p.A5166T	ENST00000301067	NM_003482.3	5166	Gct/Act	48/54	1	2	FACETS	0.238	0.204	0.276	0.238	0.204	0.276	SUBCLONAL	1	TRUE	1	0.424671744096344	2		571	1168	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088659	27088659	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	209	657	0	ENST00000324856.7:c.2272del	p.Gln758ArgfsTer75	p.Q758Rfs*75	ENST00000324856	NM_006015.4	756	aaC/aa	7/20	1	2	FACETS	0.929	0.862	0.999	0.929	0.862	0.999	CLONAL	1	TRUE	1	0.424671744096344	2		657	1059	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780882	9780882	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	199	603	0	ENST00000377346.4:c.1604G>T	p.Arg535Leu	p.R535L	ENST00000377346	NM_005026.3	535	cGg/cTg	13/24	1	2	FACETS	0.87	0.805	0.938	0.87	0.805	0.938	CLONAL	1	TRUE	1	0.424671744096344	2		603	1077	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226595512	226595512	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	69	432	0	ENST00000366794.5:c.119A>G	p.Gln40Arg	p.Q40R	ENST00000366794	NM_001618.3	40	cAg/cGg	1/23	0.403004016975612	3	FACETS	0.47	0.408	0.536	0.235	0.204	0.268	SUBCLONAL	1	TRUE	1	0.424671744096344	3		432	839	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131330	202131330	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	135	423	0	ENST00000358485.4:c.298G>A	p.Ala100Thr	p.A100T	ENST00000358485	NM_001080125.1	100	Gcc/Acc	2/9	1	2	FACETS	0.814	0.74	0.891	0.814	0.74	0.891	CLONAL	1	TRUE	1	0.424671744096344	2		423	781	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938892	178938892	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	35	110	0	ENST00000263967.3:c.2134C>A	p.Leu712Ile	p.L712I	ENST00000263967	NM_006218.2	712	Ctc/Atc	14/21	1	2	FACETS	0.649	0.535	0.775	0.649	0.535	0.775	SUBCLONAL	1	TRUE	1	0.424671744096344	2		110	254	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979552	55979552	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368062574	NA	P-0012819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	205	683	0	ENST00000263923.4:c.895C>T	p.Arg299Trp	p.R299W	ENST00000263923	NM_002253.2	299	Cgg/Tgg	7/30	1	2	FACETS	0.767	0.71	0.827	0.767	0.71	0.827	SUBCLONAL	1	TRUE	1	0.424671744096344	2		683	1258	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629100	187629100	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs766787268	NA	P-0012819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	109	490	0	ENST00000441802.2:c.1882C>T	p.Arg628Ter	p.R628*	ENST00000441802	NM_005245.3	628	Cga/Tga	2/27	1	2	FACETS	0.581	0.521	0.644	0.581	0.521	0.644	SUBCLONAL	1	TRUE	1	0.424671744096344	2		490	884	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950304	38950304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs895560221	NA	P-0012819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	163	560	2	ENST00000357387.3:c.3646C>T	p.Arg1216Cys	p.R1216C	ENST00000357387	NM_152756.3	1216	Cgt/Tgt	31/38	1	2	FACETS	0.876	0.804	0.951	0.876	0.804	0.951	CLONAL	1	TRUE	1	0.424671744096344	2		562	876	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952420	38952420	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	140	490	0	ENST00000357387.3:c.3005C>A	p.Pro1002Gln	p.P1002Q	ENST00000357387	NM_152756.3	1002	cCa/cAa	30/38	1	2	FACETS	0.79	0.719	0.864	0.79	0.719	0.864	SUBCLONAL	1	TRUE	1	0.424671744096344	2		490	835	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877821	151877821	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	164	558	1	ENST00000262189.6:c.7124A>G	p.Gln2375Arg	p.Q2375R	ENST00000262189	NM_170606.2	2375	cAa/cGa	36/59	1	2	FACETS	0.844	0.775	0.916	0.844	0.775	0.916	CLONAL	1	TRUE	1	0.424671744096344	2		559	915	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465888	69465888	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	203	572	0	ENST00000227507.2:c.726C>A	p.Asp242Glu	p.D242E	ENST00000227507	NM_053056.2	242	gaC/gaA	5/5	1	2	FACETS	0.882	0.817	0.949	0.882	0.817	0.949	CLONAL	1	TRUE	1	0.424671744096344	2		572	1084	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249373	133249373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	219	523	1	ENST00000320574.5:c.1526C>T	p.Ala509Val	p.A509V	ENST00000320574	NM_006231.2	509	gCc/gTc	15/49	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.424671744096344	2		524	920	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30310083	30310083	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	16	25	0	ENST00000322652.5:c.983G>A	p.Ser328Asn	p.S328N	ENST00000322652	NM_015355.2	328	aGc/aAc	9/16	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.424671744096344	2		25	54	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117678	70117678	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1276737891	NA	P-0012819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	191	607	0	ENST00000245479.2:c.146A>G	p.Gln49Arg	p.Q49R	ENST00000245479	NM_000346.3	49	cAg/cGg	1/3	1	2	FACETS	0.894	0.826	0.965	0.894	0.826	0.965	CLONAL	1	TRUE	1	0.424671744096344	2		607	1006	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348462	70348463	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0012819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1342	122	743	0	ENST00000374080.3:c.3371_3372del	p.Phe1124SerfsTer2	p.F1124Sfs*2	ENST00000374080		1123	tcTTtt/tctt	24/45	1	2	FACETS	0.392	0.353	0.434	0.392	0.353	0.434	SUBCLONAL	1	TRUE	1	0.424671744096344	2		743	1464	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52692236	52692236	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	173	625	0	ENST00000394830.3:c.624del	p.Gln209ArgfsTer15	p.Q209Rfs*15	ENST00000394830	NM_018313.4	208	ttT/tt	6/30	1	2	FACETS	0.713	0.655	0.774	0.713	0.655	0.774	SUBCLONAL	1	TRUE	1	0.424671744096344	2		625	1142	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087513	27087513	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	276	615	0	ENST00000324856.7:c.2090del	p.Pro697ArgfsTer45	p.P697Rfs*45	ENST00000324856	NM_006015.4	696	tCc/tc	5/20	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.424671744096344	2		615	1283	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216734	7216739	+	inframe_deletion	In_Frame_Del	DEL	TAGGGC	TAGGGC	-	novel	NA	P-0012819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	255	821	0	ENST00000380728.2:c.684_689del	p.Gln228_Tyr230delinsHis	p.Q228_Y230delinsH	ENST00000380728		228	caGCCCTAt/cat	8/11	1	2	FACETS	0.89	0.832	0.951	0.89	0.832	0.951	CLONAL	1	TRUE	1	0.424671744096344	2		821	1349	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307280	65307283	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0012819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	105	286	1	ENST00000342505.4:c.2405_2408del	p.Lys802ArgfsTer11	p.K802Rfs*11	ENST00000342505	NM_002227.2	802	aAAGAg/ag	18/25	1	2	FACETS	0.907	0.816	1	0.907	0.816	1	CLONAL	1	TRUE	1	0.424671744096344	2		287	545	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191482	10191482	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs730882020	NA	P-0013027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	45	492	0	ENST00000256474.2:c.477del	p.Glu160SerfsTer10	p.E160Sfs*10	ENST00000256474	NM_000551.3	159	Aaa/aa	3/3	1	2	FACETS	0.977	0.82	1	0.977	0.82	1	CLONAL	1	TRUE	1	0.15	2		492	614	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0013059-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	614	515	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.843794872679219	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.843794872679219	3		515	1023	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519998	NA	P-0013059-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	407	668	0	ENST00000269305.4:c.581T>C	p.Leu194Pro	p.L194P	ENST00000269305	NM_001126112.2	194	cTt/cCt	6/11	0.830798220753986	1	FACETS	0.965	0.933	0.996	0.965	0.933	0.996	CLONAL	1	TRUE	0	0.843794872679219	1		668	578	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881001	37881002	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGCTCCCC	rs397516981	NA	P-0013172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	449	777	0	ENST00000269571.5:c.2331_2339dup	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	gtg/gtGGGCTCCCCg	20/27	0.595108589785792	2	FACETS	0.822	0.789	0.854	0.822	0.789	0.854	CLONAL	2	TRUE	0	0.632493934740337	2		777	864	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061191	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	136	409	0	ENST00000250448.2:c.798C>G	p.Phe266Leu	p.F266L	ENST00000250448	NM_004496.3	266	ttC/ttG	2/2	1	2	FACETS	0.832	0.761	0.906	0.832	0.761	0.906	CLONAL	1	TRUE	1	0.632493934740337	2		409	517	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118758	115118758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	283	657	0	ENST00000257566.3:c.583del	p.Glu195AsnfsTer13	p.E195Nfs*13	ENST00000257566	NM_016569.3	195	Gaa/aa	2/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.632493934740337	2		657	832	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190645	11190645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745409542	NA	P-0013172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	265	614	2	ENST00000361445.4:c.5554G>A	p.Glu1852Lys	p.E1852K	ENST00000361445	NM_004958.3	1852	Gag/Aag	39/58	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.632493934740337	2		616	772	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857530	68857531	+	splice_donor_variant	Splice_Site	DEL	GT	GT	-	novel	NA	P-0013172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	186	506	0	ENST00000261769.5:c.2164+1_2164+2del		p.X722_splice	ENST00000261769	NM_004360.3	722			0.632493934740337	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.632493934740337	1		506	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0013201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	144	806	0	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	0.709394428855406	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.777121031973113	1		806	207	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0013201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	172	675	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.458313514402902	3	FACETS	1	0.988	1	0.779	0.737	0.82	INDETERMINATE	2	TRUE	0	0.777121031973113	3		675	263	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11206806	11206806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760642166	NA	P-0013201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	143	472	0	ENST00000361445.4:c.4613G>A	p.Arg1538Gln	p.R1538Q	ENST00000361445	NM_004958.3	1538	cGg/cAg	32/58	0.465192478199031	2	FACETS	0.844	0.794	0.892	0.844	0.794	0.892	INDETERMINATE	2	TRUE	0	0.777121031973113	2		472	218	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020751	26020751	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	49	170	0	ENST00000357647.3:c.34A>G	p.Thr12Ala	p.T12A	ENST00000357647	NM_003529.2	12	Act/Gct	1/1	1	2	FACETS	0.92	0.799	1	0.92	0.799	1	CLONAL	1	TRUE	1	0.777121031973113	2		170	137	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410611	32410611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749266841	NA	P-0013201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	166	354	0	ENST00000332351.3:c.1547C>T	p.Ala516Val	p.A516V	ENST00000332351	NM_024426.4	516	gCg/gTg	10/10	0.765668287625207	2	FACETS	0.958	0.912	1	0.958	0.912	1	CLONAL	2	TRUE	0	0.777121031973113	2		354	223	SUCCESS
APC	324	MSKCC	GRCh37	5	112175667	112175682	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCTGAAAAGAGAGA	CTGCTGAAAAGAGAGA	AGAGT	novel	NA	P-0013201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	25	227	2	ENST00000257430.4:c.4376_4391delinsAGAGT	p.Thr1459LysfsTer6	p.T1459Kfs*6	ENST00000257430	NM_000038.5	1459	aCTGCTGAAAAGAGAGAg/aAGAGTg	16/16	0.374626318412206	1	FACETS	0.271	0.216	0.333	0.271	0.216	0.333	INDETERMINATE	1	TRUE	0	0.777121031973113	1		229	145	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416726	416726	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1021387076	NA	P-0014027-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	209	242	0	ENST00000399788.2:c.3824A>G	p.Lys1275Arg	p.K1275R	ENST00000399788	NM_001042603.1	1275	aAa/aGa	23/28	NA	2	FACETS	1	0.954	1			1	INDETERMINATE	1	TRUE	NA	0.852882546089503	2		242	481	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246550	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	TC	TC	CT	novel	NA	P-0014125-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	377	557	2	ENST00000349310.3:c.49_50delinsAG	p.Glu17Arg	p.E17R	ENST00000349310	NM_001014432.1	17	GAg/AGg	4/15	0.184163924139745	5	FACETS	1	0.963	1			1	INDETERMINATE	3	TRUE	NA	0.611820237032037	5		559	781	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90634871	90634871	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372928432	NA	P-0014125-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	211	562	0	ENST00000330062.3:c.121G>A	p.Asp41Asn	p.D41N	ENST00000330062	NM_002168.2	41	Gac/Aac	2/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.611820237032037	2		562	662	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577916	7578268	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GATCCGCCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACTGCGCCCAGCCAAGCAGGGGAGGCCCTTAGCCTCTGTAAGCTTCAGTTTTTTCAACTGTGCAATAGTTAAACCCATTTACTTTGCACATCTCATGGGGTTATAGGGAGGTCAAATAAGCAGCAGGAGAAAGCCCCCCTACTGCTCACCTGGAGGGCCACTGACAACCACCCTTAACCCCTCCTCCCAGAGACCCCAGTTGCAAACCAGACCTCAGGCGGCTCATAGGGCACCACCACACTATGTCGAAAAGTGTTTCTGTCATCCAAATACTCCACACGCAAATTTCCTTCCACTCGGATAA	GATCCGCCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACTGCGCCCAGCCAAGCAGGGGAGGCCCTTAGCCTCTGTAAGCTTCAGTTTTTTCAACTGTGCAATAGTTAAACCCATTTACTTTGCACATCTCATGGGGTTATAGGGAGGTCAAATAAGCAGCAGGAGAAAGCCCCCCTACTGCTCACCTGGAGGGCCACTGACAACCACCCTTAACCCCTCCTCCCAGAGACCCCAGTTGCAAACCAGACCTCAGGCGGCTCATAGGGCACCACCACACTATGTCGAAAAGTGTTTCTGTCATCCAAATACTCCACACGCAAATTTCCTTCCACTCGGATAA	-	novel	NA	P-0014125-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1	74	11	0	ENST00000269305.4:c.581_672+261del		p.X194_splice	ENST00000269305	NM_001126112.2	194		6/11	0.611820237032037	1	FACETS	1	0.989	1	1	0.99	1	CLONAL	2	TRUE	0	0.611820237032037	1		11	75	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011144	12011144	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014125-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	174	520	1	ENST00000353533.5:c.551C>A	p.Ser184Ter	p.S184*	ENST00000353533	NM_003010.3	184	tCg/tAg	5/11	0.611820237032037	1	FACETS	0.963	0.898	1	0.963	0.898	1	CLONAL	1	TRUE	0	0.611820237032037	1		521	410	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592359	29592359	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0014125-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	163	462	0	ENST00000356175.3:c.4772+2T>G		p.X1591_splice	ENST00000356175	NM_000267.3	1591			0.611820237032037	1	FACETS	0.92	0.855	0.986	0.92	0.855	0.986	CLONAL	1	TRUE	0	0.611820237032037	1		462	402	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158655953	158655953	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014125-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	168	541	0	ENST00000263640.3:c.53C>T	p.Ser18Phe	p.S18F	ENST00000263640	NM_001105.4	18	tCc/tTc	3/11	1	2	FACETS	0.883	0.815	0.953	0.883	0.815	0.953	CLONAL	1	TRUE	1	0.611820237032037	2		541	622	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878839	151878839	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014125-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	231	661	1	ENST00000262189.6:c.6106C>G	p.Leu2036Val	p.L2036V	ENST00000262189	NM_170606.2	2036	Ctt/Gtt	36/59	0.611820237032037	1	FACETS	0.991	0.933	1	0.991	0.933	1	CLONAL	1	TRUE	0	0.611820237032037	1		662	529	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543264	65543264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1176118785	NA	P-0014125-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	150	476	0	ENST00000358664.4:c.413C>T	p.Ser138Leu	p.S138L	ENST00000358664	NM_002382.4	138	tCg/tTg	5/5	1	2	FACETS	0.963	0.886	1	0.963	0.886	1	CLONAL	1	TRUE	1	0.611820237032037	2		476	509	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273179	55273179	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014125-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	240	630	0	ENST00000275493.2:c.3502G>C	p.Asp1168His	p.D1168H	ENST00000275493	NM_005228.3	1168	Gac/Cac	28/28	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.611820237032037	2		630	728	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879549	151879549	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0014125-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	176	443	0	ENST00000262189.6:c.5396C>G	p.Ser1799Ter	p.S1799*	ENST00000262189	NM_170606.2	1799	tCa/tGa	36/59	0.611820237032037	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.611820237032037	1		443	342	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272308	38272308	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs869320694	NA	P-0014433-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	425	973	0	ENST00000425967.3:c.2059A>G	p.Lys687Glu	p.K687E	ENST00000425967	NM_001174067.1	687	Aag/Gag	15/19	0.819590884801101	1	FACETS	0.997	0.966	1	0.997	0.966	1	CLONAL	1	TRUE	0	0.833131156464066	1		973	597	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543174	65543196	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	GCTGGCCTGCCCCGAGTGGCTTA	GCTGGCCTGCCCCGAGTGGCTTA	-	novel	NA	P-0014433-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	382	114	0	ENST00000358664.4:c.481_*20del		p.*161*	ENST00000358664	NM_002382.4	161		5/5	0.833131156464066	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.833131156464066	1		114	446	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147578	47147578	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014433-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	274	666	0	ENST00000409792.3:c.4748T>C	p.Val1583Ala	p.V1583A	ENST00000409792	NM_014159.6	1583	gTa/gCa	6/21	0.819590884801101	1	FACETS	0.981	0.942	1	0.981	0.942	1	CLONAL	1	TRUE	0	0.833131156464066	1		666	391	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0014645-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	249	921	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	0.353904768939349	3	FACETS	0.904	0.847	0.963	0.603	0.564	0.642	CLONAL	2	TRUE	0	0.353904768939349	3		921	916	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0014645-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	184	673	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	0.353904768939349	5	FACETS	0.937	0.866	1	0.625	0.577	0.674	CLONAL	2	TRUE	2	0.353904768939349	5		673	849	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578445	7578446	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014645-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	292	1016	0	ENST00000269305.4:c.484dup	p.Ile162AsnfsTer19	p.I162Nfs*19	ENST00000269305	NM_001126112.2	162	atc/aAtc	5/11	NA	2	FACETS	0.996	0.941	1			1	INDETERMINATE	2	TRUE	NA	0.353904768939349	2		1016	828	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291780	15291780	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014645-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	299	1021	1	ENST00000263388.2:c.2986C>T	p.Gln996Ter	p.Q996*	ENST00000263388	NM_000435.2	996	Cag/Tag	18/33	0.353904768939349	2	FACETS	0.964	0.911	1	0.964	0.911	1	CLONAL	2	TRUE	0	0.353904768939349	2		1022	876	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260600	1260600	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014645-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	131	812	0	ENST00000310581.5:c.2959C>G	p.Leu987Val	p.L987V	ENST00000310581	NM_198253.2	987	Ctg/Gtg	12/16	0.288944099515505	3	FACETS	1	0.911	1	0.502	0.455	0.551	CLONAL	1	TRUE	1	0.353904768939349	3		812	868	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109319929	109319929	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014645-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	97	800	0	ENST00000436639.2:c.759G>T	p.Trp253Cys	p.W253C	ENST00000436639	NM_014454.2	253	tgG/tgT	5/10	0.353904768939349	3	FACETS	0.758	0.675	0.847	0.379	0.337	0.424	SUBCLONAL	1	TRUE	1	0.353904768939349	3		800	851	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467718	50467718	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014645-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	376	854	0	ENST00000331340.3:c.953C>G	p.Ala318Gly	p.A318G	ENST00000331340	NM_006060.4	318	gCc/gGc	8/8	0.353904768939349	5	FACETS	0.929	0.883	0.976	0.929	0.883	0.976	CLONAL	3	TRUE	2	0.353904768939349	5		854	1167	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861020	35861020	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014645-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	64	566	0	ENST00000303115.3:c.149G>C	p.Gly50Ala	p.G50A	ENST00000303115	NM_002185.3	50	gGa/gCa	2/8	0.32593538417849	4	FACETS	0.725	0.628	0.832	0.363	0.314	0.416	SUBCLONAL	1	TRUE	2	0.353904768939349	4		566	675	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287461	33287461	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014645-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	96	742	0	ENST00000374542.5:c.1636G>T	p.Glu546Ter	p.E546*	ENST00000374542	NM_001141970.1	546	Gaa/Taa	6/8	0.32593538417849	4	FACETS	0.775	0.689	0.867	0.387	0.344	0.434	SUBCLONAL	1	TRUE	2	0.353904768939349	4		742	948	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0014729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	127	721	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.196683064705753	4	FACETS	0.764	0.693	0.839	0.764	0.693	0.839	SUBCLONAL	2	TRUE	2	0.29	4		721	739	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0014729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	87	625	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.196683064705753	4	FACETS	0.981	0.868	1	0.49	0.434	0.551	CLONAL	1	TRUE	2	0.29	4		625	789	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28929495	NA	P-0014729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	130	519	0	ENST00000275493.2:c.2155G>A	p.Gly719Ser	p.G719S	ENST00000275493	NM_005228.3	719	Ggc/Agc	18/28	0.196683064705753	4	FACETS	1	0.985	1	0.745	0.676	0.818	CLONAL	1	TRUE	2	0.29	4		519	776	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519985	NA	P-0014729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	113	721	0	ENST00000269305.4:c.857A>C	p.Glu286Ala	p.E286A	ENST00000269305	NM_001126112.2	286	gAa/gCa	8/11	0.192426561077844	2	FACETS	1	0.945	1	0.537	0.483	0.593	CLONAL	1	TRUE	0	0.29	2		721	726	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965377	25965377	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	148	637	0	ENST00000435504.4:c.3829G>T	p.Val1277Leu	p.V1277L	ENST00000435504		1277	Gtg/Ttg	13/13	0.192426561077844	2	FACETS	1	0.986	1	0.7	0.64	0.762	CLONAL	1	TRUE	0	0.29	2		637	729	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79960997	79960997	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	27	442	0	ENST00000265081.6:c.394A>G	p.Lys132Glu	p.K132E	ENST00000265081	NM_002439.4	132	Aag/Gag	3/24	1	2	FACETS	0.531	0.422	0.654	0.531	0.422	0.654	SUBCLONAL	1	TRUE	1	0.29	2		442	351	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014903-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	285	777	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.841	0.791	0.891	0.841	0.791	0.891	CLONAL	1	TRUE	1	0.688350744766811	2		777	985	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577017	7577017	+	splice_donor_variant	Splice_Site	SNP	A	A	C	rs1131691016	NA	P-0014903-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	382	680	0	ENST00000269305.4:c.919+2T>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.674260935937477	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.688350744766811	1		680	720	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249378	110249379	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CA	CA	-	novel	NA	P-0014903-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	494	971	0	ENST00000374672.4:c.1194_1195del	p.Cys398Ter	p.C398*	ENST00000374672	NM_004235.4	398	tgTGat/tgat	4/5	0.688350744766811	1	FACETS	0.938	0.902	0.973	0.938	0.902	0.973	CLONAL	1	TRUE	0	0.688350744766811	1		971	1004	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015116-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	132	657	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	0.277924403789469	5	FACETS	1	0.972	1	0.776	0.707	0.848	CLONAL	2	TRUE	2	0.277924403789469	5		657	578	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100189	27100189	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015116-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	42	461	0	ENST00000324856.7:c.3985C>T	p.Gln1329Ter	p.Q1329*	ENST00000324856	NM_006015.4	1329	Cag/Tag	16/20	0.277924403789469	3	FACETS	0.906	0.758	1	0.453	0.379	0.535	CLONAL	1	TRUE	1	0.277924403789469	3		461	380	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239876	41239876	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015116-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	55	421	0	ENST00000379561.5:c.474C>G	p.Asn158Lys	p.N158K	ENST00000379561	NM_002015.3	158	aaC/aaG	1/3	0.277924403789469	3	FACETS	1	0.934	1	0.385	0.33	0.445	CLONAL	1	TRUE	0	0.277924403789469	3		421	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0015116-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	130	553	0	ENST00000269305.4:c.673-2A>C		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.277924403789469	3	FACETS	1	0.978	1	0.807	0.738	0.879	CLONAL	2	TRUE	0	0.277924403789469	3		553	440	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164805	36164805	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015405-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	100	1066	1	ENST00000300305.3:c.1070del	p.Pro357ArgfsTer237	p.P357Rfs*237	ENST00000300305		357	cCg/cg	8/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.770937129739623	2		1067	208	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115842	8115843	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015405-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	117	866	0	ENST00000346208.3:c.1189dup	p.Ser397PhefsTer110	p.S397Ffs*110	ENST00000346208		396	-/T	6/6	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.770937129739623	2		866	281	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112992	2112992	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs796053486	NA	P-0015405-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	10	893	3	ENST00000219476.3:c.1381G>A	p.Val461Met	p.V461M	ENST00000219476	NM_000548.3	461	Gtg/Atg	14/42	1	2	FACETS	0.168	0.114	0.236	0.168	0.114	0.236	SUBCLONAL	1	FALSE	1	0.770937129739623	2		896	154	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223079	1223079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs567896256	NA	P-0015405-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	10	938	0	ENST00000326873.7:c.1016C>T	p.Pro339Leu	p.P339L	ENST00000326873	NM_000455.4	339	cCg/cTg	8/10	1	2	FACETS	0.142	0.096	0.199	0.142	0.096	0.199	SUBCLONAL	1	FALSE	1	0.770937129739623	2		938	183	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0015921-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	1144	609	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.569112768127722	7	FACETS	0.935	0.915	0.954			1	CLONAL	6	TRUE	NA	0.569112768127722	7		609	1737	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0015921-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2178	256	625	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.569112768127722	7	FACETS	0.895	0.834	0.96			1	CLONAL	1	TRUE	NA	0.569112768127722	7		625	2434	SUCCESS
ATR	545	MSKCC	GRCh37	3	142183989	142183989	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015921-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	155	441	0	ENST00000350721.4:c.6991G>T	p.Asp2331Tyr	p.D2331Y	ENST00000350721	NM_001184.3	2331	Gac/Tac	41/47	0.318469748699667	1	FACETS	0.473	0.433	0.515	0.473	0.433	0.515	INDETERMINATE	1	TRUE	0	0.569112768127722	1		441	824	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988204	36988204	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015921-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1637	268	445	0	ENST00000354822.5:c.449C>T	p.Pro150Leu	p.P150L	ENST00000354822	NM_001079668.2	150	cCg/cTg	2/3	0.569112768127722	6	FACETS	1	0.968	1	0.211	0.197	0.226	CLONAL	1	TRUE	1	0.569112768127722	6		445	1905	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579544	7579545	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	A	novel	NA	P-0015921-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	374	545	0	ENST00000269305.4:c.142_143delinsT	p.Asp48SerfsTer75	p.D48Sfs*75	ENST00000269305	NM_001126112.2	48	GAc/Tc	4/11	0.546939825350711	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.569112768127722	1		545	887	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696448	47696448	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015925-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	515	623	0	ENST00000347630.2:c.375T>G	p.Phe125Leu	p.F125L	ENST00000347630	NM_001007230.1	125	ttT/ttG	6/11	0.685653025759652	3	FACETS	0.985	0.948	1	0.985	0.948	1	CLONAL	2	TRUE	1	0.685653025759652	3		623	1024	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940490	31940490	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015925-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	273	709	0	ENST00000375333.2:c.523G>C	p.Val175Leu	p.V175L	ENST00000375333	NM_032454.1	175	Gtg/Ctg	3/8	1	2	FACETS	0.966	0.91	1	0.966	0.91	1	CLONAL	1	TRUE	1	0.685653025759652	2		709	824	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024546	31024546	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	119	566	0	ENST00000375687.4:c.4031C>T	p.Ser1344Phe	p.S1344F	ENST00000375687	NM_015338.5	1344	tCc/tTc	13/13	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.223526396026216	2		566	762	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829040	128829042	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	rs570242755	NA	P-0016221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	10	66	0	ENST00000249373.3:c.67_69del	p.Leu23del	p.L23del	ENST00000249373	NM_005631.4	16	ggGCTg/ggg	1/12	1	2	FACETS	0.549	0.372	0.77	0.549	0.372	0.77	SUBCLONAL	1	TRUE	1	0.223526396026216	2		66	163	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159048	143159048	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	36	494	0	ENST00000262992.4:c.805A>T	p.Ile269Phe	p.I269F	ENST00000262992	NM_001101669.1	269	Att/Ttt	10/24	1	2	FACETS	0.756	0.622	0.907	0.756	0.622	0.907	CLONAL	1	TRUE	1	0.223526396026216	2		494	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0017298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	169	687	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.264807734577246	5	FACETS	1	0.98	1			1	CLONAL	3	TRUE	NA	0.264807734577246	5		687	512	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110113	8110113	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	55	581	0	ENST00000585124.1:c.492G>T	p.Lys164Asn	p.K164N	ENST00000585124	NM_004217.3	164	aaG/aaT	6/9	0.264807734577246	5	FACETS	1	0.962	1			1	CLONAL	1	TRUE	NA	0.264807734577246	5		581	415	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031703	36031703	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2015	137	690	0	ENST00000358208.4:c.1532C>A	p.Thr511Asn	p.T511N	ENST00000358208		511	aCc/aAc	12/12	0.264807734577246	17	FACETS	1	0.984	1	0.12	0.108	0.132	CLONAL	1	TRUE	5	0.264807734577246	17		690	2152	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0017886-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	315	983	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.532859835260064	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	FALSE	0	0.532859835260064	2		984	582	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223979	36223979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017886-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	186	945	1	ENST00000222270.7:c.6529C>T	p.Leu2177Phe	p.L2177F	ENST00000222270	NM_014727.1	2177	Ctt/Ttt	28/37	0.527271109942516	3	FACETS	1	0.962	1	0.531	0.491	0.573	CLONAL	1	FALSE	1	0.532859835260064	3		946	832	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028031	48028031	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1054003194	NA	P-0017886-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	147	306	1	ENST00000234420.5:c.2913del	p.Ile972LeufsTer25	p.I972Lfs*25	ENST00000234420	NM_000179.2	970	tGg/tg	4/10	0.532859835260064	4	FACETS	0.972	0.896	1	0.972	0.896	1	CLONAL	2	FALSE	2	0.532859835260064	4		307	435	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215674235	215674235	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017886-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	285	800	0	ENST00000260947.4:c.59C>G	p.Pro20Arg	p.P20R	ENST00000260947	NM_000465.2	20	cCt/cGt	1/11	0.532859835260064	4	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	FALSE	2	0.532859835260064	4		800	818	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647510	117647510	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017886-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	129	593	0	ENST00000368508.3:c.5434A>T	p.Ser1812Cys	p.S1812C	ENST00000368508	NM_002944.2	1812	Agt/Tgt	33/43	0.377671758913117	4	FACETS	0.97	0.88	1	0.485	0.44	0.533	CLONAL	1	FALSE	2	0.532859835260064	4		593	765	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793310	139793310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1030517939	NA	P-0017886-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	177	803	1	ENST00000247668.2:c.118G>A	p.Val40Ile	p.V40I	ENST00000247668	NM_021138.3	40	Gtc/Atc	2/11	0.527271109942516	3	FACETS	1	0.957	1	0.527	0.486	0.57	CLONAL	1	FALSE	1	0.532859835260064	3		804	798	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273231	18273231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1260910794	NA	P-0017886-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	54	664	0	ENST00000222254.8:c.1024G>A	p.Glu342Lys	p.E342K	ENST00000222254	NM_005027.3	342	Gag/Aag	9/16	0.527271109942516	3	FACETS	0.373	0.318	0.434	0.187	0.159	0.217	SUBCLONAL	1	FALSE	1	0.532859835260064	3		664	688	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602923	10602923	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018187-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	368	862	0	ENST00000171111.5:c.655G>T	p.Glu219Ter	p.E219*	ENST00000171111	NM_203500.1	219	Gag/Tag	3/6	0.520824260056568	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.520824260056568	1		862	828	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221229	1221229	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881977	NA	P-0018187-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	334	719	0	ENST00000326873.7:c.752G>A	p.Gly251Asp	p.G251D	ENST00000326873	NM_000455.4	251	gGt/gAt	6/10	0.520824260056568	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.520824260056568	1		719	748	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962298	2962298	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769577430	NA	P-0018187-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	94	734	2	ENST00000396946.4:c.2239G>A	p.Val747Ile	p.V747I	ENST00000396946	NM_032415.4	747	Gtc/Atc	17/25	1	2	FACETS	0.428	0.38	0.479	0.428	0.38	0.479	SUBCLONAL	1	TRUE	1	0.520824260056568	2		736	843	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5077510	5077510	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018187-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	84	469	0	ENST00000381652.3:c.1922A>G	p.Asn641Ser	p.N641S	ENST00000381652	NM_004972.3	641	aAt/aGt	15/25	0.285412580910988	1	FACETS	0.477	0.422	0.535	0.477	0.422	0.535	INDETERMINATE	1	TRUE	0	0.520824260056568	1		469	500	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220703	1220703	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019252-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	229	774	0	ENST00000326873.7:c.721G>C	p.Ala241Pro	p.A241P	ENST00000326873	NM_000455.4	241	Gct/Cct	5/10	0.394649568923787	3	FACETS	0.894	0.842	0.947			1	CLONAL	3	TRUE	NA	0.396361780011318	3		774	516	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398286	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0019252-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	148	713	0	ENST00000311936.3:c.33_34delinsCT	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	11	gcTGgt/gcCTgt	2/5	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.396361780011318	2		713	523	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281634	15281634	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019252-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	135	904	2	ENST00000263388.2:c.4739C>T	p.Ser1580Leu	p.S1580L	ENST00000263388	NM_000435.2	1580	tCg/tTg	26/33	0.396361780011318	3	FACETS	1	0.953	1	0.358	0.325	0.392	CLONAL	1	TRUE	0	0.396361780011318	3		906	760	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787846	135787846	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	rs118203440	NA	P-0019252-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	59	360	0	ENST00000298552.3:c.738-2A>T		p.X246_splice	ENST00000298552	NM_001162426.1	246			1	2	FACETS	0.91	0.788	1	0.91	0.788	1	CLONAL	1	TRUE	1	0.396361780011318	2		360	327	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201851	152201851	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019252-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	79	520	0	ENST00000206249.3:c.705G>C	p.Lys235Asn	p.K235N	ENST00000206249	NM_000125.3	235	aaG/aaC	3/8	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.396361780011318	2		520	360	SUCCESS
BTK	695	MSKCC	GRCh37	X	100612503	100612503	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019252-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	189	566	0	ENST00000308731.7:c.1171G>T	p.Gly391Ter	p.G391*	ENST00000308731	NM_000061.2	391	Gga/Tga	13/19	0.396361780011318	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.396361780011318	3		566	505	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344287	118344287	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019252-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	59	437	0	ENST00000534358.1:c.2413C>G	p.Gln805Glu	p.Q805E	ENST00000534358	NM_005933.3	805	Cag/Gag	3/36	1	2	FACETS	0.805	0.695	0.922	0.805	0.695	0.922	CLONAL	1	TRUE	1	0.396361780011318	2		437	370	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194820	30194820	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019252-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	114	774	0	ENST00000331968.5:c.325A>G	p.Thr109Ala	p.T109A	ENST00000331968	NM_002742.2	109	Acc/Gcc	2/18	1	2	FACETS	0.937	0.846	1	0.937	0.846	1	CLONAL	1	TRUE	1	0.396361780011318	2		774	614	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610478	10610478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019252-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	116	803	0	ENST00000171111.5:c.232G>A	p.Asp78Asn	p.D78N	ENST00000171111	NM_203500.1	78	Gac/Aac	2/6	0.396361780011318	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.396361780011318	1		803	424	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158246	47158246	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0019252-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	73	426	0	ENST00000409792.3:c.4455-2A>T		p.X1485_splice	ENST00000409792	NM_014159.6	1485			1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.396361780011318	2		426	350	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73113215	73113215	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019252-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	44	133	0	ENST00000356692.5:c.556G>T	p.Ala186Ser	p.A186S	ENST00000356692		186	Gcc/Tcc	7/9	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.396361780011318	2		133	170	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604284	189604284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019252-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	107	545	0	ENST00000264731.3:c.1451C>T	p.Pro484Leu	p.P484L	ENST00000264731	NM_003722.4	484	cCt/cTt	11/14	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.396361780011318	2		545	540	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156727	106156727	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019252-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	76	416	2	ENST00000380013.4:c.1628G>T	p.Gly543Val	p.G543V	ENST00000380013	NM_001127208.2	543	gGt/gTt	3/11	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.396361780011318	2		418	367	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265395	152265395	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019252-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	94	495	0	ENST00000206249.3:c.848C>A	p.Ala283Asp	p.A283D	ENST00000206249	NM_000125.3	283	gCt/gAt	4/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.396361780011318	2		495	412	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146052	38146052	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019252-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	145	834	0	ENST00000317025.8:c.3454A>G	p.Thr1152Ala	p.T1152A	ENST00000317025	NM_023034.1	1152	Acg/Gcg	19/24	0.396361780011318	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.396361780011318	1		834	555	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	339	1170	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.736507512259153	3	FACETS	0.959	0.928	0.987	0.959	0.928	0.987	CLONAL	3	TRUE	0	0.736507512259153	3		1170	438	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162722894	162722894	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	233	879	0	ENST00000367921.3:c.92G>T	p.Arg31Leu	p.R31L	ENST00000367921	NM_006182.2	31	cGc/cTc	4/18	0.559047586817245	5	FACETS	1	0.986	1	0.775	0.728	0.821	CLONAL	2	TRUE	2	0.736507512259153	5		879	573	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46740279	46740279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150315374	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	145	641	0	ENST00000371975.4:c.1759C>T	p.Arg587Trp	p.R587W	ENST00000371975	NM_003579.3	587	Cgg/Tgg	16/18	0.392844085502808	4	FACETS	0.85	0.784	0.918	0.85	0.784	0.918	INDETERMINATE	2	TRUE	2	0.736507512259153	4		641	402	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	239	843	2	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.7327589801778	2	FACETS	0.938	0.897	0.977	0.938	0.897	0.977	CLONAL	2	TRUE	0	0.736507512259153	2		845	346	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670219	134670219	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	70	614	1	ENST00000398015.3:c.130G>T	p.Glu44Ter	p.E44*	ENST00000398015	NM_004441.4	44	Gaa/Taa	3/16	0.447546030460575	3	FACETS	0.786	0.69	0.887	0.262	0.23	0.296	SUBCLONAL	1	TRUE	0	0.736507512259153	3		615	331	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120460341	120460341	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	256	893	0	ENST00000256646.2:c.5974G>C	p.Ala1992Pro	p.A1992P	ENST00000256646	NM_024408.3	1992	Gca/Cca	33/34	0.392844085502808	4	FACETS	1	0.988	1	1	0.988	1	INDETERMINATE	2	TRUE	2	0.736507512259153	4		893	525	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471649	120471649	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	58	627	0	ENST00000256646.2:c.3842G>C	p.Cys1281Ser	p.C1281S	ENST00000256646	NM_024408.3	1281	tGt/tCt	23/34	0.392844085502808	4	FACETS	0.669	0.576	0.769	0.334	0.288	0.385	INDETERMINATE	1	TRUE	2	0.736507512259153	4		627	409	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512341	120512341	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	62	683	0	ENST00000256646.2:c.901G>A	p.Glu301Lys	p.E301K	ENST00000256646	NM_024408.3	301	Gaa/Aaa	6/34	0.392844085502808	4	FACETS	0.698	0.605	0.798	0.349	0.302	0.399	INDETERMINATE	1	TRUE	2	0.736507512259153	4		683	419	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741537	17741537	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	187	639	0	ENST00000250003.3:c.208C>G	p.His70Asp	p.H70D	ENST00000250003	NM_002478.4	70	Cac/Gac	1/3	0.447546030460575	3	FACETS	1	0.98	1	0.724	0.683	0.764	CLONAL	2	TRUE	0	0.736507512259153	3		639	320	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741742	17741742	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	62	766	0	ENST00000250003.3:c.413G>C	p.Ser138Thr	p.S138T	ENST00000250003	NM_002478.4	138	aGc/aCc	1/3	0.447546030460575	3	FACETS	0.635	0.551	0.725	0.212	0.183	0.242	SUBCLONAL	1	TRUE	0	0.736507512259153	3		766	363	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742477	17742477	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	60	866	0	ENST00000250003.3:c.659C>G	p.Ala220Gly	p.A220G	ENST00000250003	NM_002478.4	220	gCc/gGc	2/3	0.447546030460575	3	FACETS	0.708	0.614	0.808	0.236	0.204	0.27	SUBCLONAL	1	TRUE	0	0.736507512259153	3		866	315	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138852	64138852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	74	916	0	ENST00000334205.4:c.2219C>T	p.Ala740Val	p.A740V	ENST00000334205	NM_003942.2	740	gCc/gTc	17/17	0.447546030460575	3	FACETS	0.682	0.6	0.77	0.227	0.2	0.257	SUBCLONAL	1	TRUE	0	0.736507512259153	3		916	403	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625132	69625132	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	68	958	0	ENST00000334134.2:c.661G>T	p.Glu221Ter	p.E221*	ENST00000334134	NM_005247.2	221	Gag/Tag	3/3	0.447546030460575	3	FACETS	0.761	0.667	0.861	0.254	0.222	0.287	SUBCLONAL	1	TRUE	0	0.736507512259153	3		958	332	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180568	94180568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	65	618	0	ENST00000323929.3:c.1600G>A	p.Glu534Lys	p.E534K	ENST00000323929	NM_005591.3	534	Gag/Aag	15/20	0.447546030460575	3	FACETS	0.671	0.585	0.763	0.224	0.195	0.255	SUBCLONAL	1	TRUE	0	0.736507512259153	3		618	360	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489538	56489538	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	287	701	0	ENST00000267101.3:c.2003G>T	p.Gly668Val	p.G668V	ENST00000267101	NM_001982.3	668	gGg/gTg	17/28	0.447546030460575	3	FACETS	1	0.991	1	0.761	0.728	0.794	CLONAL	2	TRUE	0	0.736507512259153	3		701	467	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112910793	112910793	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397507527	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	345	743	1	ENST00000351677.2:c.802G>T	p.Gly268Cys	p.G268C	ENST00000351677	NM_002834.3	268	Ggt/Tgt	7/16	0.398482920311212	6	FACETS	0.895	0.856	0.934	1	0.993	1	INDETERMINATE	4	TRUE	3	0.736507512259153	6		744	647	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563091	21563091	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	170	1007	0	ENST00000382592.4:c.828G>T	p.Gln276His	p.Q276H	ENST00000382592	NM_014572.2	276	caG/caT	4/8	0.7327589801778	2	FACETS	0.836	0.789	0.883	0.836	0.789	0.883	CLONAL	2	TRUE	0	0.736507512259153	2		1007	276	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986631	36986731	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCCTGGCTGGTGGCCCGGGTGTGCGCCAAGGCCGGCGCCACCGCTGCCCACGGAGATGGCCGCTGCCGCCGCCTGCGCGGCCTGCGCCTGGTGCTGCGC	CTGCCTGGCTGGTGGCCCGGGTGTGCGCCAAGGCCGGCGCCACCGCTGCCCACGGAGATGGCCGCTGCCGCCGCCTGCGCGGCCTGCGCCTGGTGCTGCGC	-	novel	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3598	1575	388	0	ENST00000354822.5:c.958_1058del	p.Ala320ArgfsTer85	p.A320Rfs*85	ENST00000354822	NM_001079668.2	320	GCGCAGCACCAGGCGCAGGCCGCGCAGGCGGCGGCAGCGGCCATCTCCGTGGGCAGCGGTGGCGCCGGCCTTGGCGCACACCCGGGCCACCAGCCAGGCAGc/c	3/3	0.736507512259153	55	FACETS	0.998	0.973	1			1	CLONAL	17	TRUE	NA	0.736507512259153	55		388	5173	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992733	72992733	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	302	787	2	ENST00000268489.5:c.1312G>T	p.Ala438Ser	p.A438S	ENST00000268489	NM_006885.3	438	Gcg/Tcg	2/10	0.417605459894409	4	FACETS	0.946	0.904	0.986	0.709	0.678	0.74	INDETERMINATE	3	TRUE	0	0.736507512259153	4		789	502	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246290	41246290	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	104	952	0	ENST00000357654.3:c.1258G>C	p.Asp420His	p.D420H	ENST00000357654	NM_007294.3	420	Gat/Cat	10/23	0.417605459894409	4	FACETS	0.813	0.73	0.902	0.203	0.182	0.226	INDETERMINATE	1	TRUE	0	0.736507512259153	4		952	603	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805568	46805568	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	159	1109	0	ENST00000290295.7:c.388T>G	p.Tyr130Asp	p.Y130D	ENST00000290295	NM_006361.5	130	Tat/Gat	1/2	0.417605459894409	4	FACETS	0.753	0.695	0.812	0.376	0.347	0.406	INDETERMINATE	2	TRUE	0	0.736507512259153	4		1109	498	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117864	70117864	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	32	546	0	ENST00000245479.2:c.332C>G	p.Ala111Gly	p.A111G	ENST00000245479	NM_000346.3	111	gCc/gGc	1/3	0.417605459894409	4	FACETS	0.524	0.427	0.633	0.131	0.106	0.159	INDETERMINATE	1	TRUE	0	0.736507512259153	4		546	288	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600429	10600429	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	293	1104	0	ENST00000171111.5:c.1426G>T	p.Gly476Trp	p.G476W	ENST00000171111	NM_203500.1	476	Ggg/Tgg	4/6	0.7327589801778	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.736507512259153	2		1104	383	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966881	18966881	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	189	1075	0	ENST00000262803.5:c.1692G>C	p.Gln564His	p.Q564H	ENST00000262803	NM_002911.3	564	caG/caC	12/24	0.7327589801778	2	FACETS	1	0.99	1	0.66	0.619	0.701	CLONAL	1	TRUE	0	0.736507512259153	2		1075	389	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753170	42753170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753965187	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	208	865	3	ENST00000222329.4:c.1094C>T	p.Ser365Leu	p.S365L	ENST00000222329	NM_006494.2	365	tCg/tTg	4/4	0.581624567291474	3	FACETS	0.817	0.767	0.868	0.817	0.767	0.868	CLONAL	2	TRUE	1	0.736507512259153	3		868	473	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467177	25467177	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	275	711	0	ENST00000264709.3:c.1698G>C	p.Leu566Phe	p.L566F	ENST00000264709	NM_175629.2	566	ttG/ttC	15/23	0.736507512259153	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.736507512259153	3		711	332	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209108244	209108244	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	285	887	0	ENST00000345146.2:c.605C>G	p.Ser202Cys	p.S202C	ENST00000345146	NM_005896.2	202	tCt/tGt	6/10	0.398482920311212	6	FACETS	0.906	0.857	0.956	0.906	0.857	0.956	INDETERMINATE	3	TRUE	3	0.736507512259153	6		887	704	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205786	128205786	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	291	956	1	ENST00000341105.2:c.89C>A	p.Ala30Glu	p.A30E	ENST00000341105	NM_032638.4	30	gCg/gAg	2/6	0.447546030460575	3	FACETS	1	0.987	1	0.724	0.691	0.756	CLONAL	2	TRUE	0	0.736507512259153	3		957	498	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155059	55155059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	54	679	1	ENST00000257290.5:c.2768G>A	p.Ser923Asn	p.S923N	ENST00000257290	NM_006206.4	923	aGt/aAt	20/23	0.577054413868788	4	FACETS	0.788	0.677	0.909	0.263	0.225	0.303	CLONAL	1	TRUE	1	0.736507512259153	4		680	323	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280028	66280028	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1276862103	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	58	413	0	ENST00000273854.3:c.1661G>T	p.Arg554Ile	p.R554I	ENST00000273854	NM_004439.5	554	aGa/aTa	7/18	0.577054413868788	4	FACETS	0.855	0.739	0.979	0.285	0.246	0.327	CLONAL	1	TRUE	1	0.736507512259153	4		413	320	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138201315	138201315	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	254	775	0	ENST00000237289.4:c.2014G>C	p.Gly672Arg	p.G672R	ENST00000237289	NM_001270507.1	672	Gga/Cga	8/9	0.398482920311212	6	FACETS	1	0.947	1	1	0.947	1	INDETERMINATE	3	TRUE	3	0.736507512259153	6		775	567	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505469	157505469	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	268	646	0	ENST00000346085.5:c.3450T>A	p.Phe1150Leu	p.F1150L	ENST00000346085	NM_020732.3	1150	ttT/ttA	13/20	0.398482920311212	6	FACETS	0.954	0.902	1	0.954	0.902	1	INDETERMINATE	3	TRUE	3	0.736507512259153	6		646	629	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136798	69136798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	501	615	1	ENST00000288368.4:c.4712C>T	p.Ala1571Val	p.A1571V	ENST00000288368	NM_024870.2	1571	gCa/gTa	39/40	0.736507512259153	6	FACETS	1	0.981	1	1	0.981	1	CLONAL	4	TRUE	2	0.736507512259153	6		616	823	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317888	8317888	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	246	667	1	ENST00000356435.5:c.5725C>A	p.His1909Asn	p.H1909N	ENST00000356435		1909	Cac/Aac	35/35	0.736507512259153	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.736507512259153	2		668	319	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356384	70356384	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	180	744	0	ENST00000374080.3:c.5279A>T	p.Glu1760Val	p.E1760V	ENST00000374080		1760	gAg/gTg	37/45	0.7327589801778	2	FACETS	0.902	0.855	0.947	0.902	0.855	0.947	CLONAL	2	TRUE	0	0.736507512259153	2		744	271	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205861	128205861	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	124	542	0	ENST00000341105.2:c.14C>A	p.Pro5His	p.P5H	ENST00000341105	NM_032638.4	5	cCc/cAc	2/6	0.447546030460575	3	FACETS	0.964	0.893	1	0.643	0.595	0.69	CLONAL	2	TRUE	0	0.736507512259153	3		542	239	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36208951	36208951	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	12	45	0	ENST00000222270.7:c.31C>T	p.Pro11Ser	p.P11S	ENST00000222270	NM_014727.1	11	Ccc/Tcc	1/37	0.581624567291474	3	FACETS	0.929	0.708	1	0.929	0.708	1	CLONAL	2	TRUE	1	0.736507512259153	3		45	24	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967629	90967629	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554559171	NA	P-0019262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	80	643	0	ENST00000265433.3:c.1279C>A	p.Pro427Thr	p.P427T	ENST00000265433	NM_002485.4	427	Cca/Aca	10/16	0.736507512259153	6	FACETS	0.739	0.65	0.835	0.185	0.162	0.209	SUBCLONAL	1	TRUE	2	0.736507512259153	6		643	727	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	20	482	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		482	70	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020610-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	140	896	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.27425932374114	3	FACETS	1	0.983	1	0.66	0.603	0.72	CLONAL	1	TRUE	1	0.390712921660718	3		898	649	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0020610-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	74	835	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.75	0.658	0.849	0.75	0.658	0.849	SUBCLONAL	1	TRUE	1	0.390712921660718	2		835	505	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933575	39933575	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs151177114	NA	P-0020610-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	68	378	1	ENST00000378444.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000378444	NM_001123385.1	342	Cga/Tga	4/15	1	1	FACETS	0.949	0.834	1	0.949	0.834	1	CLONAL	1	TRUE	0	0.390712921660718	1		379	295	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486587	56486587	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020610-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	89	730	0	ENST00000267101.3:c.1166C>A	p.Thr389Lys	p.T389K	ENST00000267101	NM_001982.3	389	aCa/aAa	10/28	0.27425932374114	3	FACETS	0.712	0.631	0.799	0.356	0.315	0.4	SUBCLONAL	1	TRUE	1	0.390712921660718	3		730	765	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298048	11298048	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020610-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	94	876	0	ENST00000361445.4:c.2060T>C	p.Leu687Pro	p.L687P	ENST00000361445	NM_004958.3	687	cTg/cCg	13/58	1	2	FACETS	0.688	0.613	0.769	0.688	0.613	0.769	SUBCLONAL	1	TRUE	1	0.390712921660718	2		876	699	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464370	120464370	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs373166152	NA	P-0020610-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	74	766	0	ENST00000256646.2:c.5276T>C	p.Val1759Ala	p.V1759A	ENST00000256646	NM_024408.3	1759	gTc/gCc	29/34	1	2	FACETS	0.573	0.501	0.65	0.573	0.501	0.65	SUBCLONAL	1	TRUE	1	0.390712921660718	2		766	661	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422058	81422058	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020610-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	72	515	0	ENST00000298171.2:c.34C>A	p.Leu12Met	p.L12M	ENST00000298171	NM_000369.2	12	Ctg/Atg	1/10	1	2	FACETS	0.888	0.779	1	0.888	0.779	1	CLONAL	1	TRUE	1	0.390712921660718	2		515	415	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059347	42059347	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020610-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	34	447	0	ENST00000219905.7:c.9067T>C	p.Ser3023Pro	p.S3023P	ENST00000219905	NM_001164273.1	3023	Tca/Cca	24/24	1	2	FACETS	0.468	0.382	0.564	0.468	0.382	0.564	SUBCLONAL	1	TRUE	1	0.390712921660718	2		447	372	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43730613	43730614	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020610-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	65	515	0	ENST00000382044.4:c.3099dup	p.Pro1034SerfsTer13	p.P1034Sfs*13	ENST00000382044	NM_001141980.1	1033	-/T	16/28	1	2	FACETS	0.851	0.741	0.969	0.851	0.741	0.969	CLONAL	1	TRUE	1	0.390712921660718	2		515	391	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014088	14014088	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020610-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	72	788	0	ENST00000311895.7:c.67del	p.Val23CysfsTer10	p.V23Cfs*10	ENST00000311895	NM_005236.2	22	ctG/ct	1/11	1	2	FACETS	0.64	0.559	0.726	0.64	0.559	0.726	SUBCLONAL	1	TRUE	1	0.390712921660718	2		788	576	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131265	202131265	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1477942244	NA	P-0020610-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	59	569	0	ENST00000358485.4:c.233T>C	p.Leu78Pro	p.L78P	ENST00000358485	NM_001080125.1	78	cTg/cCg	2/9	1	2	FACETS	0.637	0.549	0.733	0.637	0.549	0.733	SUBCLONAL	1	TRUE	1	0.390712921660718	2		569	474	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566441	41566441	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020610-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	43	564	1	ENST00000263253.7:c.4318C>A	p.Pro1440Thr	p.P1440T	ENST00000263253	NM_001429.3	1440	Cca/Aca	27/31	1	2	FACETS	0.463	0.388	0.547	0.463	0.388	0.547	SUBCLONAL	1	TRUE	1	0.390712921660718	2		565	475	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977882	134977882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020610-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	50	596	0	ENST00000398015.3:c.2875G>A	p.Ala959Thr	p.A959T	ENST00000398015	NM_004441.4	959	Gca/Aca	16/16	1	2	FACETS	0.586	0.498	0.682	0.586	0.498	0.682	SUBCLONAL	1	TRUE	1	0.390712921660718	2		596	437	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217252	66217252	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020610-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	29	500	0	ENST00000273854.3:c.2363T>A	p.Met788Lys	p.M788K	ENST00000273854	NM_004439.5	788	aTg/aAg	14/18	1	2	FACETS	0.4	0.321	0.49	0.4	0.321	0.49	SUBCLONAL	1	TRUE	1	0.390712921660718	2		500	371	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670085	86670085	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020610-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	58	622	0	ENST00000274376.6:c.1882A>C	p.Thr628Pro	p.T628P	ENST00000274376	NM_002890.2	628	Act/Cct	14/25	1	2	FACETS	0.547	0.47	0.631	0.547	0.47	0.631	SUBCLONAL	1	TRUE	1	0.390712921660718	2		622	543	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710578	40710578	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021052-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	281	677	0	ENST00000373198.4:c.4273G>C	p.Val1425Leu	p.V1425L	ENST00000373198	NM_133170.3	1425	Gtg/Ctg	31/32	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.74	2		677	740	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	126	521	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	0.442498797360591	2		521	489	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913559	32913559	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359479	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	110	646	4	ENST00000380152.3:c.5073del	p.Lys1691AsnfsTer15	p.K1691Nfs*15	ENST00000380152		1689	gcA/gc	11/27	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.442498797360591	2		650	427	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	67	288	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.98	0.859	1	0.98	0.859	1	CLONAL	1	TRUE	1	0.442498797360591	2		288	309	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	58	417	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.776	0.67	0.889	0.776	0.67	0.889	SUBCLONAL	1	TRUE	1	0.442498797360591	2		417	338	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717769	89717770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	75	437	0	ENST00000371953.3:c.800dup	p.Asp268GlyfsTer30	p.D268Gfs*30	ENST00000371953	NM_000314.4	265	cta/ctAa	7/9	1	2	FACETS	0.997	0.88	1	0.997	0.88	1	CLONAL	1	TRUE	1	0.442498797360591	2		437	340	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743932	41743933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs778012871	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	156	816	2	ENST00000301178.4:c.874dup	p.His292ProfsTer47	p.H292Pfs*47	ENST00000301178	NM_021913.4	289	-/C	7/20	1	2	FACETS	0.884	0.81	0.96	0.884	0.81	0.96	CLONAL	1	TRUE	1	0.442498797360591	2		818	798	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797258	135797258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514834	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	54	369	0	ENST00000298552.3:c.611G>A	p.Arg204His	p.R204H	ENST00000298552	NM_001162426.1	204	cGt/cAt	7/23	1	2	FACETS	0.724	0.622	0.835	0.724	0.622	0.835	SUBCLONAL	1	TRUE	1	0.442498797360591	2		369	337	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524215	18524215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769408892	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	124	856	2	ENST00000266497.5:c.1727C>T	p.Ala576Val	p.A576V	ENST00000266497		576	gCg/gTg	11/31	1	2	FACETS	0.925	0.839	1	0.925	0.839	1	CLONAL	1	TRUE	1	0.442498797360591	2		858	606	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534473	187534473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	91	473	0	ENST00000441802.2:c.9253del	p.Asp3086IlefsTer30	p.D3086Ifs*30	ENST00000441802	NM_005245.3	3085	Ctt/tt	13/27	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.442498797360591	2		473	389	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	90	512	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.814	0.724	0.908	0.814	0.724	0.908	CLONAL	1	TRUE	1	0.442498797360591	2		512	500	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166916	32166916	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	187	1167	4	ENST00000375023.3:c.4322del	p.Pro1441LeufsTer17	p.P1441Lfs*17	ENST00000375023	NM_004557.3	1441	cCt/ct	24/30	0.442498797360591	2	FACETS	0.921	0.851	0.993	0.46	0.425	0.497	CLONAL	1	TRUE	0	0.442498797360591	2		1171	918	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257144	19257144	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	38	662	2	ENST00000162023.5:c.819del	p.Thr274ProfsTer?	p.T274Pfs*?	ENST00000162023		273	ccC/cc	12/13	1	2	FACETS	0.392	0.324	0.468	0.392	0.324	0.468	SUBCLONAL	1	TRUE	1	0.442498797360591	2		664	438	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074255	8074255	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	86	642	0	ENST00000377482.5:c.404del	p.Asn135ThrfsTer40	p.N135Tfs*40	ENST00000377482	NM_018948.3	135	aAc/ac	4/4	1	2	FACETS	0.877	0.78	0.981	0.877	0.78	0.981	CLONAL	1	TRUE	1	0.442498797360591	2		642	443	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588108	69588108	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	100	741	0	ENST00000168712.1:c.590T>C	p.Met197Thr	p.M197T	ENST00000168712	NM_002007.2	197	aTg/aCg	3/3	1	2	FACETS	0.922	0.828	1	0.922	0.828	1	CLONAL	1	TRUE	1	0.442498797360591	2		741	490	SUCCESS
APC	324	MSKCC	GRCh37	5	112175880	112175880	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	35	302	0	ENST00000257430.4:c.4592del	p.Asn1531MetfsTer34	p.N1531Mfs*34	ENST00000257430	NM_000038.5	1530	gAa/ga	16/16	1	2	FACETS	0.697	0.575	0.831	0.697	0.575	0.831	SUBCLONAL	1	TRUE	1	0.442498797360591	2		302	227	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905406	11905406	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	89	530	0	ENST00000396373.4:c.56C>A	p.Pro19His	p.P19H	ENST00000396373	NM_001987.4	19	cCt/cAt	2/8	0.123822060277619	4	FACETS	1	0.959	1	0.584	0.519	0.652	INDETERMINATE	1	TRUE	2	0.442498797360591	4		530	497	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249361	153249361	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	71	618	1	ENST00000281708.4:c.1417del	p.Arg473GlufsTer25	p.R473Efs*25	ENST00000281708	NM_033632.3	473	Aga/ga	9/12	1	2	FACETS	0.827	0.726	0.935	0.827	0.726	0.935	CLONAL	1	TRUE	1	0.442498797360591	2		619	388	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682810	190682810	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	143	578	4	ENST00000441310.2:c.492del	p.Lys164AsnfsTer6	p.K164Nfs*6	ENST00000441310	NM_000534.4	162	gcA/gc	5/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.442498797360591	2		582	494	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825519	50825519	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	102	674	0	ENST00000398568.2:c.2156del	p.Asn719MetfsTer13	p.N719Mfs*13	ENST00000398568	NM_001042412.1	717	gAa/ga	14/18	1	2	FACETS	0.949	0.852	1	0.949	0.852	1	CLONAL	1	TRUE	1	0.442498797360591	2		674	486	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129421	152129421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	138	588	0	ENST00000206249.3:c.374G>A	p.Gly125Asp	p.G125D	ENST00000206249	NM_000125.3	125	gGc/gAc	1/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.442498797360591	2		588	513	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176516607	176516607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs545721160	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	154	912	5	ENST00000292408.4:c.4C>T	p.Arg2Trp	p.R2W	ENST00000292408	NM_213647.1	2	Cgg/Tgg	2/18	1	2	FACETS	0.997	0.915	1	0.997	0.915	1	CLONAL	1	TRUE	1	0.442498797360591	2		917	698	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248285	59248285	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	22	192	0	ENST00000371222.2:c.458del	p.Gly153AlafsTer29	p.G153Afs*29	ENST00000371222	NM_002228.3	153	gGc/gc	1/1	1	2	FACETS	0.872	0.687	1	0.872	0.687	1	CLONAL	1	TRUE	1	0.442498797360591	2		192	114	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981614	101981614	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555075248	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	54	412	0	ENST00000282441.5:c.40del	p.Gln14ArgfsTer60	p.Q14Rfs*60	ENST00000282441	NM_001130145.2	12	gCc/gc	1/9	1	2	FACETS	0.744	0.639	0.858	0.744	0.639	0.858	SUBCLONAL	1	TRUE	1	0.442498797360591	2		412	328	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218894	133218894	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	145	1003	2	ENST00000320574.5:c.5042A>G	p.Asn1681Ser	p.N1681S	ENST00000320574	NM_006231.2	1681	aAc/aGc	38/49	1	2	FACETS	0.814	0.743	0.888	0.814	0.743	0.888	CLONAL	1	TRUE	1	0.442498797360591	2		1005	805	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133898	41133898	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	70	494	0	ENST00000379561.5:c.1730del	p.Gly577AlafsTer5	p.G577Afs*5	ENST00000379561	NM_002015.3	577	gGc/gc	2/3	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.442498797360591	2		494	289	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987036	36987036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	134	748	0	ENST00000354822.5:c.653C>T	p.Ala218Val	p.A218V	ENST00000354822	NM_001079668.2	218	gCg/gTg	3/3	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.442498797360591	2		748	592	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060881	38060881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs902772971	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	115	792	0	ENST00000250448.2:c.1108G>A	p.Val370Met	p.V370M	ENST00000250448	NM_004496.3	370	Gtg/Atg	2/2	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.442498797360591	2		792	476	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041897	42041898	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	92	670	0	ENST00000219905.7:c.6095dup	p.Leu2032PhefsTer3	p.L2032Ffs*3	ENST00000219905	NM_001164273.1	2031	cat/caTt	17/24	1	2	FACETS	0.954	0.852	1	0.954	0.852	1	CLONAL	1	TRUE	1	0.442498797360591	2		670	436	SUCCESS
BLM	641	MSKCC	GRCh37	15	91308643	91308643	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	51	465	0	ENST00000355112.3:c.2192A>G	p.Asp731Gly	p.D731G	ENST00000355112	NM_000057.2	731	gAt/gGt	9/22	1	2	FACETS	0.63	0.537	0.731	0.63	0.537	0.731	SUBCLONAL	1	TRUE	1	0.442498797360591	2		465	366	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778123	3778123	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	175	1164	1	ENST00000262367.5:c.6925G>T	p.Gly2309Cys	p.G2309C	ENST00000262367	NM_004380.2	2309	Ggc/Tgc	31/31	1	2	FACETS	0.961	0.886	1	0.961	0.886	1	CLONAL	1	TRUE	1	0.442498797360591	2		1165	823	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783668	50783668	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	111	828	2	ENST00000398568.2:c.64del	p.Tyr22ThrfsTer25	p.Y22Tfs*25	ENST00000398568	NM_001042412.1	20	aTt/at	3/18	1	2	FACETS	0.897	0.809	0.99	0.897	0.809	0.99	CLONAL	1	TRUE	1	0.442498797360591	2		830	559	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822604	72822604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	92	672	0	ENST00000268489.5:c.9571G>A	p.Gly3191Ser	p.G3191S	ENST00000268489	NM_006885.3	3191	Ggc/Agc	10/10	1	2	FACETS	0.96	0.858	1	0.96	0.858	1	CLONAL	1	TRUE	1	0.442498797360591	2		672	433	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8111109	8111109	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	123	963	0	ENST00000585124.1:c.98C>A	p.Pro33His	p.P33H	ENST00000585124	NM_004217.3	33	cCt/cAt	3/9	1	2	FACETS	0.73	0.66	0.803	0.73	0.66	0.803	SUBCLONAL	1	TRUE	1	0.442498797360591	2		963	762	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883579	37883579	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	49	812	0	ENST00000269571.5:c.3191A>G	p.Glu1064Gly	p.E1064G	ENST00000269571		1064	gAg/gGg	26/27	1	2	FACETS	0.306	0.258	0.359	0.306	0.258	0.359	SUBCLONAL	1	TRUE	1	0.442498797360591	2		812	724	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120114	70120115	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	28	177	0	ENST00000245479.2:c.1121dup	p.Gln375AlafsTer203	p.Q375Afs*203	ENST00000245479	NM_000346.3	372	-/C	3/3	1	2	FACETS	0.937	0.761	1	0.937	0.761	1	CLONAL	1	TRUE	1	0.442498797360591	2		177	135	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292565	15292565	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1394486464	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	169	1054	1	ENST00000263388.2:c.2614del	p.Ser872ProfsTer21	p.S872Pfs*21	ENST00000263388	NM_000435.2	872	Tcc/cc	17/33	1	2	FACETS	0.936	0.862	1	0.936	0.862	1	CLONAL	1	TRUE	1	0.442498797360591	2		1055	816	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353876	15353876	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1348028685	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	152	918	0	ENST00000263377.2:c.3004A>G	p.Met1002Val	p.M1002V	ENST00000263377	NM_058243.2	1002	Atg/Gtg	14/20	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.442498797360591	2		918	686	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961008	18961008	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	181	937	0	ENST00000262803.5:c.586T>C	p.Phe196Leu	p.F196L	ENST00000262803	NM_002911.3	196	Ttc/Ctc	4/24	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.442498797360591	2		937	816	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36208929	36208935	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCG	GGCGGCG	-	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	10	61	0	ENST00000222270.7:c.17_23del	p.Gly6AlafsTer38	p.G6Afs*38	ENST00000222270	NM_014727.1	3	gcGGCGGCG/gc	1/37	1	2	FACETS	0.822	0.57	1	0.822	0.57	1	CLONAL	1	TRUE	1	0.442498797360591	2		61	55	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224387	36224387	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1400709490	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	236	1170	0	ENST00000222270.7:c.6937G>A	p.Val2313Ile	p.V2313I	ENST00000222270	NM_014727.1	2313	Gtt/Att	28/37	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.442498797360591	2		1170	894	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794356	242794356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144217487	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	104	892	3	ENST00000334409.5:c.586G>A	p.Ala196Thr	p.A196T	ENST00000334409	NM_005018.2	196	Gca/Aca	3/5	1	2	FACETS	0.727	0.651	0.806	0.727	0.651	0.806	SUBCLONAL	1	TRUE	1	0.442498797360591	2		895	647	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30956834	30956834	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867857427	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	72	706	2	ENST00000375687.4:c.160G>A	p.Ala54Thr	p.A54T	ENST00000375687	NM_015338.5	54	Gca/Aca	4/13	1	2	FACETS	0.746	0.655	0.845	0.746	0.655	0.845	SUBCLONAL	1	TRUE	1	0.442498797360591	2		708	436	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566478	41566478	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	40	654	2	ENST00000263253.7:c.4355C>A	p.Pro1452His	p.P1452H	ENST00000263253	NM_001429.3	1452	cCt/cAt	27/31	1	2	FACETS	0.382	0.317	0.454	0.382	0.317	0.454	SUBCLONAL	1	TRUE	1	0.442498797360591	2		656	473	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648401	30648401	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	40	723	0	ENST00000295754.5:c.26T>C	p.Leu9Pro	p.L9P	ENST00000295754	NM_003242.5	9	cTg/cCg	1/7	1	2	FACETS	0.326	0.27	0.388	0.326	0.27	0.388	SUBCLONAL	1	TRUE	1	0.442498797360591	2		723	555	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277224	41277224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775666001	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	50	447	0	ENST00000349496.5:c.1693C>T	p.Arg565Cys	p.R565C	ENST00000349496	NM_001904.3	565	Cgc/Tgc	11/15	1	2	FACETS	0.799	0.682	0.924	0.799	0.682	0.924	CLONAL	1	TRUE	1	0.442498797360591	2		447	283	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72842190	72842190	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	G	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	71	379	0	ENST00000325599.8:c.1061-3T>C		p.X354_splice	ENST00000325599	NM_018130.2	354			1	2	FACETS	0.975	0.858	1	0.975	0.858	1	CLONAL	1	TRUE	1	0.442498797360591	2		379	329	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521091	187521091	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	96	570	0	ENST00000441802.2:c.12064T>C	p.Cys4022Arg	p.C4022R	ENST00000441802	NM_005245.3	4022	Tgc/Cgc	22/27	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.442498797360591	2		570	432	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324019	31324020	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	90	339	0	ENST00000412585.2:c.543_544del	p.Arg181SerfsTer26	p.R181Sfs*26	ENST00000412585	NM_005514.6	181	agAGcc/agcc	3/8	0.442498797360591	2	FACETS	0.823	0.743	0.906	0.823	0.743	0.906	CLONAL	2	TRUE	0	0.442498797360591	2		339	247	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265509	152265509	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	105	723	0	ENST00000206249.3:c.962A>G	p.Asp321Gly	p.D321G	ENST00000206249	NM_000125.3	321	gAt/gGt	4/8	1	2	FACETS	0.943	0.849	1	0.943	0.849	1	CLONAL	1	TRUE	1	0.442498797360591	2		723	503	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522089	157522089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	111	657	1	ENST00000346085.5:c.4361C>T	p.Ser1454Leu	p.S1454L	ENST00000346085	NM_020732.3	1454	tCg/tTg	18/20	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.442498797360591	2		658	472	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921610	39921610	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	136	363	0	ENST00000378444.4:c.4210A>G	p.Ser1404Gly	p.S1404G	ENST00000378444	NM_001123385.1	1404	Agt/Ggt	10/15	1	1	FACETS	0.78	0.721	0.839	1	0.989	1	SUBCLONAL	2	TRUE	0	0.442498797360591	1		363	307	SUCCESS
AR	367	MSKCC	GRCh37	X	66931394	66931394	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	130	438	0	ENST00000374690.3:c.2036A>G	p.Glu679Gly	p.E679G	ENST00000374690	NM_000044.3	679	gAa/gGa	4/8	1	1	FACETS	0.811	0.75	0.873	1	0.99	1	CLONAL	2	TRUE	0	0.442498797360591	1		438	282	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	96	521	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	0.37	2		521	349	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	206	620	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.783	0.729	0.838	1	0.992	1	SUBCLONAL	2	TRUE	1	0.37	2		620	711	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	51	288	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.37	2		288	268	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	151	585	2	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.37	2		587	559	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	27	419	2	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.493	0.393	0.607	0.493	0.393	0.607	SUBCLONAL	1	TRUE	1	0.37	2		421	296	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979987	7979987	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746723399	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	217	724	1	ENST00000319144.4:c.1350del	p.Leu451SerfsTer16	p.L451Sfs*16	ENST00000319144	NM_001139.2	450	ggG/gg	10/15	1	2	FACETS	0.784	0.731	0.838	1	0.992	1	SUBCLONAL	2	TRUE	1	0.37	2		725	748	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372184	55372184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs915105324	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	163	407	0	ENST00000297316.4:c.874G>A	p.Ala292Thr	p.A292T	ENST00000297316	NM_022454.3	292	Gcc/Acc	2/2	0.194005777954636	3	FACETS	1	0.968	1	1	0.968	1	INDETERMINATE	2	TRUE	1	0.37	3		407	481	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220116	5220116	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781371580	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	170	604	0	ENST00000357368.4:c.3599G>A	p.Arg1200His	p.R1200H	ENST00000357368	NM_002850.3	1200	cGt/cAt	22/38	1	2	FACETS	0.832	0.77	0.896	1	0.991	1	CLONAL	2	TRUE	1	0.37	2		604	552	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907683	111907683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146318804	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	127	448	1	ENST00000393256.3:c.457C>T	p.Arg153Trp	p.R153W	ENST00000393256	NM_006538.4	153	Cgg/Tgg	3/4	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.37	2		449	551	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116263	209116263	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	76	386	2	ENST00000345146.2:c.13del	p.Ile5SerfsTer7	p.I5Sfs*7	ENST00000345146	NM_005896.2	5	Atc/tc	3/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.37	2		388	323	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	213	843	4	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.37	2		847	859	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141587	202141587	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771150445	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	126	514	4	ENST00000358485.4:c.875G>A	p.Arg292Gln	p.R292Q	ENST00000358485	NM_001080125.1	292	cGg/cAg	7/9	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.37	2		518	518	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076740	102076740	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	43	585	2	ENST00000282441.5:c.919C>T	p.Arg307Ter	p.R307*	ENST00000282441	NM_001130145.2	307	Cga/Tga	5/9	1	2	FACETS	0.359	0.299	0.425	0.359	0.299	0.425	SUBCLONAL	1	TRUE	1	0.37	2		587	648	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413100	139413100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201236538	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	216	865	4	ENST00000277541.6:c.1042G>A	p.Ala348Thr	p.A348T	ENST00000277541	NM_017617.3	348	Gcc/Acc	6/34	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.37	2		869	848	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	90	863	2	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	0.702	0.623	0.786	0.702	0.623	0.786	SUBCLONAL	1	TRUE	1	0.37	2		865	693	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448297	56448298	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1567880599	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	175	684	1	ENST00000407977.2:c.349dup	p.Arg117ProfsTer8	p.R117Pfs*8	ENST00000407977		117	cgc/cCgc	3/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.37	2		685	745	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150512	157150512	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754042537	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	136	666	1	ENST00000346085.5:c.1694G>A	p.Arg565Gln	p.R565Q	ENST00000346085	NM_020732.3	565	cGg/cAg	2/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.37	2		667	501	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522741	67522741	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	72	234	0	ENST00000274335.5:c.244del	p.Ile82SerfsTer32	p.I82Sfs*32	ENST00000274335		80	Aaa/aa	1/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.37	2		234	276	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435201	18435202	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1565550462	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	17	292	0	ENST00000266497.5:c.192dup	p.Val65CysfsTer16	p.V65Cfs*16	ENST00000266497		62	-/T	1/31	1	2	FACETS	0.349	0.261	0.455	0.349	0.261	0.455	SUBCLONAL	1	TRUE	1	0.37	2		292	263	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	203	778	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.82	0.764	0.878	1	0.992	1	CLONAL	2	TRUE	1	0.37	2		783	669	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	135	823	8	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.37	2		831	580	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836386	89836386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746098172	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	32	634	0	ENST00000389301.3:c.2363C>T	p.Ala788Val	p.A788V	ENST00000389301	NM_000135.2	788	gCc/gTc	26/43	1	2	FACETS	0.275	0.223	0.335	0.275	0.223	0.335	SUBCLONAL	1	TRUE	1	0.37	2		634	628	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	207	730	3	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	1	2	FACETS	0.761	0.709	0.815	1	0.992	1	SUBCLONAL	2	TRUE	1	0.37	2		733	735	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	204	690	2	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.37	2		692	800	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	59	914	1	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.341	0.292	0.395	0.341	0.292	0.395	SUBCLONAL	1	TRUE	1	0.37	2		915	935	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294470	1294470	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	103	618	0	ENST00000310581.5:c.531G>C	p.Gln177His	p.Q177H	ENST00000310581	NM_198253.2	177	caG/caC	2/16	1	2	FACETS	0.801	0.717	0.89	0.801	0.717	0.89	CLONAL	1	TRUE	1	0.37	2		618	695	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519504	137519505	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	175	551	1	ENST00000367739.4:c.1132_1133dup	p.Ser378ArgfsTer6	p.S378Rfs*6	ENST00000367739	NM_000416.2	378	agt/agAGt	7/7	1	2	FACETS	1	0.987	1	1	0.994	1	CLONAL	2	TRUE	1	0.37	2		552	383	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309069	137309069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756234164	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	54	1055	2	ENST00000481739.1:c.676G>A	p.Ala226Thr	p.A226T	ENST00000481739	NM_002957.4	226	Gcc/Acc	5/10	1	2	FACETS	0.278	0.236	0.324	0.278	0.236	0.324	SUBCLONAL	1	TRUE	1	0.37	2		1057	1049	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2492062	2492062	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	167	739	0	ENST00000355716.4:c.461-1G>T		p.X154_splice	ENST00000355716	NM_003820.2	154			1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.37	2		739	669	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023819	27023819	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	180	452	0	ENST00000324856.7:c.925C>T	p.Gln309Ter	p.Q309*	ENST00000324856	NM_006015.4	309	Cag/Tag	1/20	1	2	FACETS	0.834	0.774	0.897	1	0.992	1	CLONAL	2	TRUE	1	0.37	2		452	583	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466317	120466317	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	39	579	0	ENST00000256646.2:c.4802A>C	p.Lys1601Thr	p.K1601T	ENST00000256646	NM_024408.3	1601	aAg/aCg	26/34	1	2	FACETS	0.416	0.344	0.496	0.416	0.344	0.496	SUBCLONAL	1	TRUE	1	0.37	2		579	507	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102098259	102098259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	69	621	0	ENST00000282441.5:c.1223G>A	p.Ser408Asn	p.S408N	ENST00000282441	NM_001130145.2	408	aGt/aAt	8/9	1	2	FACETS	0.608	0.53	0.693	0.608	0.53	0.693	SUBCLONAL	1	TRUE	1	0.37	2		621	613	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864125	57864125	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	216	702	0	ENST00000228682.2:c.1607del	p.Pro536GlnfsTer77	p.P536Qfs*77	ENST00000228682	NM_005269.2	534	ggC/gg	12/12	1	2	FACETS	0.802	0.748	0.857	1	0.993	1	CLONAL	2	TRUE	1	0.37	2		702	728	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591665	38591665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147204964	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	186	596	1	ENST00000299084.4:c.124G>A	p.Val42Ile	p.V42I	ENST00000299084	NM_152594.2	42	Gtc/Atc	2/7	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.37	2		597	708	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647662	2647662	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1389216086	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	175	614	1	ENST00000342085.4:c.1565C>T	p.Thr522Met	p.T522M	ENST00000342085	NM_002613.4	522	aCg/aTg	14/14	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.37	2		615	711	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807811	3807811	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	96	391	0	ENST00000262367.5:c.3608A>G	p.Lys1203Arg	p.K1203R	ENST00000262367	NM_004380.2	1203	aAg/aGg	18/31	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.37	2		391	381	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47700132	47700132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1412582124	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	170	526	1	ENST00000347630.2:c.41C>T	p.Ser14Leu	p.S14L	ENST00000347630	NM_001007230.1	14	tCg/tTg	3/11	1	2	FACETS	0.784	0.725	0.845	1	0.99	1	SUBCLONAL	2	TRUE	1	0.37	2		527	586	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435981	56435981	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777370175	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	92	363	1	ENST00000407977.2:c.1156C>T	p.Arg386Trp	p.R386W	ENST00000407977		386	Cgg/Tgg	9/10	1	2	FACETS	0.784	0.704	0.868	1	0.983	1	SUBCLONAL	2	TRUE	1	0.37	2		364	317	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120507	70120508	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	324	974	0	ENST00000245479.2:c.1510dup	p.Thr504AsnfsTer74	p.T504Nfs*74	ENST00000245479	NM_000346.3	503	-/A	3/3	1	2	FACETS	0.809	0.765	0.855	1	0.995	1	CLONAL	2	TRUE	1	0.37	2		974	1082	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612347	1612347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200962332	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	423	878	1	ENST00000344749.5:c.1672C>T	p.Arg558Cys	p.R558C	ENST00000344749	NM_001136139.2	558	Cgc/Tgc	18/19	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.37	2		879	953	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210490	5210490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	102	643	0	ENST00000357368.4:c.5477C>T	p.Thr1826Ile	p.T1826I	ENST00000357368	NM_002850.3	1826	aCa/aTa	35/38	1	2	FACETS	0.827	0.74	0.918	0.827	0.74	0.918	CLONAL	1	TRUE	1	0.37	2		643	667	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220916	36220916	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	87	375	0	ENST00000222270.7:c.4966del	p.Ser1656ProfsTer40	p.S1656Pfs*40	ENST00000222270	NM_014727.1	1656	Tcc/cc	23/37	1	2	FACETS	0.779	0.697	0.864	1	0.982	1	SUBCLONAL	2	TRUE	1	0.37	2		375	302	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753149	42753151	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs199960550	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	153	608	6	ENST00000222329.4:c.1113_1115del	p.Ser373del	p.S373del	ENST00000222329	NM_006494.2	371	tcTTCc/tcc	4/4	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.37	2		614	661	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860949	45860951	+	inframe_deletion	In_Frame_Del	DEL	TGG	TGG	-	rs778831415	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	216	804	0	ENST00000391945.4:c.1244_1246del	p.Thr415del	p.T415del	ENST00000391945	NM_000400.3	415	aCCAtc/atc	13/23	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.37	2		804	808	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222519	39222520	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	117	575	0	ENST00000402219.2:c.3090dup	p.Tyr1031IlefsTer2	p.Y1031Ifs*2	ENST00000402219	NM_005633.3	1030	-/A	20/23	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.37	2		575	491	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662935	227662935	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	205	785	0	ENST00000305123.5:c.520G>T	p.Gly174Cys	p.G174C	ENST00000305123	NM_005544.2	174	Ggt/Tgt	1/2	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.37	2		785	832	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321727	62321729	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs771771098	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	151	682	0	ENST00000360203.5:c.2351_2353del	p.Phe784del	p.F784del	ENST00000360203	NM_001283009.1	782	ccCTTc/ccc	26/35	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.37	2		682	723	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121088	29121088	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs748262921	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	160	820	0	ENST00000328354.6:c.469A>G	p.Ile157Val	p.I157V	ENST00000328354	NM_007194.3	157	Att/Gtt	4/15	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.37	2		820	602	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527461	41527461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs140538515	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	34	738	0	ENST00000263253.7:c.1352C>A	p.Pro451His	p.P451H	ENST00000263253	NM_001429.3	451	cCc/cAc	6/31	1	2	FACETS	0.285	0.232	0.345	0.285	0.232	0.345	SUBCLONAL	1	TRUE	1	0.37	2		738	644	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582176	52582176	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	140	422	0	ENST00000394830.3:c.4652C>G	p.Ala1551Gly	p.A1551G	ENST00000394830	NM_018313.4	1551	gCc/gGc	30/30	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.37	2		422	515	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1956908	1956908	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	253	940	0	ENST00000382891.5:c.2359C>T	p.Arg787Cys	p.R787C	ENST00000382891	NM_133335.3	787	Cgc/Tgc	13/22	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.37	2		940	992	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564725	55564725	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	124	482	0	ENST00000288135.5:c.613A>T	p.Arg205Trp	p.R205W	ENST00000288135	NM_000222.2	205	Agg/Tgg	3/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.37	2		482	494	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064779	80064780	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	70	543	0	ENST00000265081.6:c.2216dup	p.Asn739LysfsTer29	p.N739Kfs*29	ENST00000265081	NM_002439.4	737	cta/ctAa	15/24	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.37	2		543	323	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977952	131977952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201810	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	85	510	0	ENST00000265335.6:c.3835C>T	p.Arg1279Cys	p.R1279C	ENST00000265335		1279	Cgt/Tgt	25/25	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.37	2		510	450	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149440424	149440424	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	106	598	0	ENST00000286301.3:c.1969+1G>A		p.X657_splice	ENST00000286301	NM_005211.3	657			1	2	FACETS	0.957	0.86	1	0.957	0.86	1	CLONAL	1	TRUE	1	0.37	2		598	599	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911108	29911108	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199474502	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	153	956	0	ENST00000376809.5:c.407G>A	p.Gly136Glu	p.G136E	ENST00000376809	NM_002116.7	136	gGg/gAg	3/8	1	2	FACETS	0.882	0.806	0.961	0.882	0.806	0.961	CLONAL	1	TRUE	1	0.37	2		956	938	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420068	152420068	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	48	437	0	ENST00000206249.3:c.1759del	p.Glu587ArgfsTer20	p.E587Rfs*20	ENST00000206249	NM_000125.3	585	acG/ac	8/8	1	2	FACETS	0.565	0.478	0.661	0.565	0.478	0.661	SUBCLONAL	1	TRUE	1	0.37	2		437	459	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522556	157522556	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	147	769	1	ENST00000346085.5:c.4828C>A	p.Pro1610Thr	p.P1610T	ENST00000346085	NM_020732.3	1610	Cct/Act	18/20	1	2	FACETS	0.875	0.799	0.955	0.875	0.799	0.955	CLONAL	1	TRUE	1	0.37	2		770	908	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133227	38133227	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	257	793	2	ENST00000317025.8:c.4246C>T	p.Pro1416Ser	p.P1416S	ENST00000317025	NM_023034.1	1416	Cca/Tca	24/24	0.194005777954636	3	FACETS	1	0.948	1	1	0.948	1	INDETERMINATE	2	TRUE	1	0.37	3		795	815	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272115	38272115	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	45	753	0	ENST00000425967.3:c.2103G>T	p.Glu701Asp	p.E701D	ENST00000425967	NM_001174067.1	701	gaG/gaT	16/19	0.194005777954636	3	FACETS	0.326	0.273	0.386	0.163	0.136	0.193	INDETERMINATE	1	TRUE	1	0.37	3		753	883	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900296	101900296	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	79	504	1	ENST00000374994.4:c.730C>T	p.Arg244Cys	p.R244C	ENST00000374994	NM_004612.2	244	Cgt/Tgt	4/9	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.37	2		505	379	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934222	39934222	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1358504792	NA	P-0021292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	256	834	4	ENST00000378444.4:c.377C>T	p.Pro126Leu	p.P126L	ENST00000378444	NM_001123385.1	126	cCg/cTg	4/15	1	2	FACETS	0.805	0.755	0.855	1	0.994	1	CLONAL	2	TRUE	1	0.37	2		838	860	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	371	620	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.915	0.878	0.952	1	0.997	1	CLONAL	2	TRUE	1	0.631383040721128	2		620	642	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	44	512	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.279	0.233	0.329	0.279	0.233	0.329	SUBCLONAL	1	TRUE	1	0.631383040721128	2		512	500	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	131	778	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.631383040721128	2		783	393	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259681	11259681	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs939676380	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	174	834	2	ENST00000361445.4:c.4024G>A	p.Glu1342Lys	p.E1342K	ENST00000361445	NM_004958.3	1342	Gag/Aag	27/58	1	2	FACETS	0.895	0.828	0.964	0.895	0.828	0.964	CLONAL	1	TRUE	1	0.631383040721128	2		836	616	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257770	16257770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779103344	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	148	706	3	ENST00000375759.3:c.5035G>A	p.Val1679Ile	p.V1679I	ENST00000375759	NM_015001.2	1679	Gtc/Atc	11/15	1	2	FACETS	0.863	0.793	0.936	0.863	0.793	0.936	CLONAL	1	TRUE	1	0.631383040721128	2		709	543	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260837	16260837	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	236	740	0	ENST00000375759.3:c.8102C>T	p.Thr2701Met	p.T2701M	ENST00000375759	NM_015001.2	2701	aCg/aTg	11/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.631383040721128	2		740	703	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023021	27023021	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1329001050	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	39	133	0	ENST00000324856.7:c.127G>A	p.Ala43Thr	p.A43T	ENST00000324856	NM_006015.4	43	Gca/Aca	1/20	1	2	FACETS	0.922	0.78	1	0.922	0.78	1	CLONAL	1	TRUE	1	0.631383040721128	2		133	134	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097751	27097751	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	176	829	1	ENST00000324856.7:c.3344del	p.Pro1115GlnfsTer46	p.P1115Qfs*46	ENST00000324856	NM_006015.4	1114	Ccc/cc	12/20	1	2	FACETS	0.892	0.825	0.961	0.892	0.825	0.961	CLONAL	1	TRUE	1	0.631383040721128	2		830	625	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163297333	163297333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767890204	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	91	914	3	ENST00000271452.3:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000271452	NM_145697.2	60	cGa/cAa	3/14	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.631383040721128	2		917	277	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117069	193117069	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	59	681	4	ENST00000367435.3:c.802C>T	p.Arg268Ter	p.R268*	ENST00000367435	NM_024529.4	268	Cga/Tga	8/17	1	2	FACETS	0.644	0.559	0.736	0.644	0.559	0.736	SUBCLONAL	1	TRUE	1	0.631383040721128	2		685	290	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567719	226567719	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	35	725	1	ENST00000366794.5:c.1447del	p.Ala483GlnfsTer3	p.A483Qfs*3	ENST00000366794	NM_001618.3	483	Gca/ca	10/23	1	2	FACETS	0.193	0.157	0.233	0.193	0.157	0.233	SUBCLONAL	1	TRUE	1	0.631383040721128	2		726	575	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226568823	226568823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779381164	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	195	961	0	ENST00000366794.5:c.1246G>A	p.Gly416Arg	p.G416R	ENST00000366794	NM_001618.3	416	Ggg/Agg	9/23	1	2	FACETS	0.826	0.766	0.887	0.826	0.766	0.887	CLONAL	1	TRUE	1	0.631383040721128	2		961	748	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263973	104263974	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776579	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	79	472	0	ENST00000369902.3:c.71dup	p.Ala25GlyfsTer23	p.A25Gfs*23	ENST00000369902	NM_016169.3	22	gcc/gCcc	1/12	1	2	FACETS	0.613	0.542	0.689	0.613	0.542	0.689	SUBCLONAL	1	TRUE	1	0.631383040721128	2		472	408	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450167	32450167	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	147	718	0	ENST00000332351.3:c.647-2A>G		p.X216_splice	ENST00000332351	NM_024426.4	216			1	2	FACETS	0.815	0.748	0.885	0.815	0.748	0.885	CLONAL	1	TRUE	1	0.631383040721128	2		718	571	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195382	102195382	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	128	599	0	ENST00000263464.3:c.142A>G	p.Arg48Gly	p.R48G	ENST00000263464	NM_001165.4	48	Agg/Ggg	2/9	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.631383040721128	2		599	347	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514480	125514480	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	85	679	1	ENST00000428830.2:c.1175G>A	p.Cys392Tyr	p.C392Y	ENST00000428830	NM_001114121.2	392	tGc/tAc	11/14	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.631383040721128	2		680	267	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	139	616	10	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.631383040721128	2		626	418	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287469	46287469	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	88	874	1	ENST00000334344.6:c.5333del	p.Asn1778IlefsTer13	p.N1778Ifs*13	ENST00000334344	NM_152641.2	1776	ttA/tt	20/21	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.631383040721128	2		875	276	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418606	49418606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369156879	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	223	763	2	ENST00000301067.7:c.15908G>A	p.Arg5303His	p.R5303H	ENST00000301067	NM_003482.3	5303	cGc/cAc	49/54	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.631383040721128	2		765	694	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	212	969	2	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.886	0.826	0.948	0.886	0.826	0.948	CLONAL	1	TRUE	1	0.631383040721128	2		971	758	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489535	56489535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1403278713	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	176	839	0	ENST00000267101.3:c.2000G>A	p.Arg667His	p.R667H	ENST00000267101	NM_001982.3	667	cGt/cAt	17/28	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.631383040721128	2		839	525	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489582	56489582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56387488	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	134	736	0	ENST00000267101.3:c.2047C>T	p.Arg683Trp	p.R683W	ENST00000267101	NM_001982.3	683	Cgg/Tgg	17/28	1	2	FACETS	0.971	0.89	1	0.971	0.89	1	CLONAL	1	TRUE	1	0.631383040721128	2		736	437	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860150	57860150	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	46	868	3	ENST00000228682.2:c.890G>A	p.Gly297Asp	p.G297D	ENST00000228682	NM_005269.2	297	gGc/gAc	8/12	1	2	FACETS	0.182	0.152	0.214	0.182	0.152	0.214	SUBCLONAL	1	TRUE	1	0.631383040721128	2		871	802	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	200	717	12	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.83	0.771	0.891	0.83	0.771	0.891	CLONAL	1	TRUE	1	0.631383040721128	2		729	763	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562802	21562802	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1348445444	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	146	805	0	ENST00000382592.4:c.1117G>A	p.Ala373Thr	p.A373T	ENST00000382592	NM_014572.2	373	Gcc/Acc	4/8	1	2	FACETS	0.699	0.639	0.76	0.699	0.639	0.76	SUBCLONAL	1	TRUE	1	0.631383040721128	2		805	662	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891686	28891686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143726778	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	179	892	0	ENST00000282397.4:c.3335G>A	p.Arg1112His	p.R1112H	ENST00000282397	NM_002019.4	1112	cGc/cAc	25/30	1	2	FACETS	0.851	0.788	0.917	0.851	0.788	0.917	CLONAL	1	TRUE	1	0.631383040721128	2		892	666	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012359	29012359	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	93	703	0	ENST00000282397.4:c.512del	p.Lys171SerfsTer7	p.K171Sfs*7	ENST00000282397	NM_002019.4	171	aAg/ag	4/30	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.631383040721128	2		703	280	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986940	36986940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	44	801	3	ENST00000354822.5:c.749C>T	p.Ala250Val	p.A250V	ENST00000354822	NM_001079668.2	250	gCc/gTc	3/3	1	2	FACETS	0.207	0.173	0.245	0.207	0.173	0.245	SUBCLONAL	1	TRUE	1	0.631383040721128	2		804	673	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422161	81422161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	158	709	3	ENST00000298171.2:c.137G>A	p.Arg46His	p.R46H	ENST00000298171	NM_000369.2	46	cGc/cAc	1/10	1	2	FACETS	0.92	0.848	0.994	0.92	0.848	0.994	CLONAL	1	TRUE	1	0.631383040721128	2		712	544	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	335	720	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.784	0.747	0.82	1	0.996	1	SUBCLONAL	2	TRUE	1	0.631383040721128	2		720	677	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473780	67473780	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730880214	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	34	729	0	ENST00000327367.4:c.860G>A	p.Arg287Gln	p.R287Q	ENST00000327367	NM_005902.3	287	cGg/cAg	6/9	1	2	FACETS	0.165	0.134	0.2	0.165	0.134	0.2	SUBCLONAL	1	TRUE	1	0.631383040721128	2		729	654	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442709	99442709	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1567185393	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	45	740	0	ENST00000268035.6:c.1106A>G	p.Asn369Ser	p.N369S	ENST00000268035	NM_000875.3	369	aAc/aGc	5/21	1	2	FACETS	0.269	0.226	0.317	0.269	0.226	0.317	SUBCLONAL	1	TRUE	1	0.631383040721128	2		740	529	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347982	347983	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760961378	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	190	993	0	ENST00000262320.3:c.1523dup	p.Ala509CysfsTer82	p.A509Cfs*82	ENST00000262320	NM_003502.3	508	ggt/ggGt	6/11	1	2	FACETS	0.748	0.692	0.805	0.748	0.692	0.805	SUBCLONAL	1	TRUE	1	0.631383040721128	2		993	805	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396234	396234	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	161	901	0	ENST00000262320.3:c.792del	p.Gly265GlufsTer149	p.G265Efs*149	ENST00000262320	NM_003502.3	264	ccC/cc	2/11	1	2	FACETS	0.742	0.683	0.804	0.742	0.683	0.804	SUBCLONAL	1	TRUE	1	0.631383040721128	2		901	687	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640538	3640538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150453226	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	234	930	5	ENST00000294008.3:c.3101G>A	p.Arg1034His	p.R1034H	ENST00000294008	NM_032444.2	1034	cGc/cAc	12/15	1	2	FACETS	0.996	0.933	1	0.996	0.933	1	CLONAL	1	TRUE	1	0.631383040721128	2		935	744	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133311	30133311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200617125	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	227	764	0	ENST00000263025.4:c.187G>A	p.Val63Met	p.V63M	ENST00000263025	NM_002746.2	63	Gtg/Atg	2/9	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.631383040721128	2		764	715	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645104	67645105	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	156	1000	2	ENST00000264010.4:c.370_371del	p.Val124ThrfsTer15	p.V124Tfs*15	ENST00000264010	NM_006565.3	123	acTGta/acta	3/12	1	2	FACETS	0.939	0.866	1	0.939	0.866	1	CLONAL	1	TRUE	1	0.631383040721128	2		1002	526	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965144	81965144	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	171	831	0	ENST00000359376.3:c.2624T>C	p.Ile875Thr	p.I875T	ENST00000359376	NM_002661.3	875	aTc/aCc	25/33	1	2	FACETS	0.752	0.694	0.813	0.752	0.694	0.813	SUBCLONAL	1	TRUE	1	0.631383040721128	2		831	720	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805103	89805103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147406377	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	194	652	1	ENST00000389301.3:c.4274G>A	p.Arg1425His	p.R1425H	ENST00000389301	NM_000135.2	1425	cGt/cAt	43/43	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.631383040721128	2		653	601	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024480	16024480	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1432273966	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	188	610	0	ENST00000268712.3:c.1738C>T	p.Arg580Cys	p.R580C	ENST00000268712	NM_006311.3	580	Cgc/Tgc	16/46	1	2	FACETS	0.964	0.895	1	0.964	0.895	1	CLONAL	1	TRUE	1	0.631383040721128	2		610	618	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	214	891	7	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.882	0.822	0.943	0.882	0.822	0.943	CLONAL	1	TRUE	1	0.631383040721128	2		898	769	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879810	37879810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	143	582	2	ENST00000269571.5:c.2105C>T	p.Pro702Leu	p.P702L	ENST00000269571		702	cCt/cTt	18/27	1	2	FACETS	0.88	0.807	0.955	0.88	0.807	0.955	CLONAL	1	TRUE	1	0.631383040721128	2		584	515	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	149	630	2	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	1	2	FACETS	0.946	0.87	1	0.946	0.87	1	CLONAL	1	TRUE	1	0.631383040721128	2		632	499	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453399	40453399	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs759027671	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	278	885	7	ENST00000345506.4:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000345506	NM_003152.3	366	Ccc/cc	10/20	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.631383040721128	2		892	880	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007451	62007451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	164	703	0	ENST00000392795.3:c.416C>T	p.Thr139Ile	p.T139I	ENST00000392795	NM_001039933.1	139	aCa/aTa	3/6	1	2	FACETS	0.995	0.92	1	0.995	0.92	1	CLONAL	1	TRUE	1	0.631383040721128	2		703	522	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604782	48604782	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	280	696	1	ENST00000342988.3:c.1604T>C	p.Leu535Pro	p.L535P	ENST00000342988	NM_005359.5	535	cTc/cCc	12/12	0.631383040721128	2	FACETS	0.952	0.909	0.994	0.952	0.909	0.994	CLONAL	2	TRUE	0	0.631383040721128	2		697	466	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226617	1226617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754853898	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	188	642	4	ENST00000326873.7:c.1273C>T	p.Arg425Cys	p.R425C	ENST00000326873	NM_000455.4	425	Cgc/Tgc	9/10	0.120804433732269	3	FACETS	1	0.99	1	0.714	0.664	0.764	INDETERMINATE	1	TRUE	1	0.631383040721128	3		646	549	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226274	2226274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749003392	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	238	1009	5	ENST00000398665.3:c.3754G>A	p.Gly1252Ser	p.G1252S	ENST00000398665	NM_032482.2	1252	Ggc/Agc	27/28	0.120804433732269	3	FACETS	1	0.986	1	0.593	0.555	0.633	INDETERMINATE	1	TRUE	1	0.631383040721128	3		1014	836	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211674	5211674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1351895585	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	255	955	3	ENST00000357368.4:c.5161C>T	p.Arg1721Trp	p.R1721W	ENST00000357368	NM_002850.3	1721	Cgg/Tgg	33/38	0.120804433732269	3	FACETS	1	0.993	1	0.724	0.681	0.768	INDETERMINATE	1	TRUE	1	0.631383040721128	3		958	734	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247835	10247835	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	213	1005	1	ENST00000340748.4:c.4367G>T	p.Arg1456Leu	p.R1456L	ENST00000340748		1456	cGg/cTg	36/40	0.120804433732269	3	FACETS	0.965	0.897	1	0.482	0.448	0.518	INDETERMINATE	1	TRUE	1	0.631383040721128	3		1006	920	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262139	10262139	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	288	1073	9	ENST00000340748.4:c.2152del	p.Met718CysfsTer59	p.M718Cfs*59	ENST00000340748		718	Atg/tg	23/40	0.120804433732269	3	FACETS	0.765	0.722	0.808	0.765	0.722	0.808	INDETERMINATE	2	TRUE	1	0.631383040721128	3		1082	785	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599874	10599874	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1356624458	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	292	894	3	ENST00000171111.5:c.1702G>A	p.Val568Ile	p.V568I	ENST00000171111	NM_203500.1	568	Gtc/Atc	5/6	0.120804433732269	3	FACETS	1	0.993	1	0.701	0.662	0.741	INDETERMINATE	1	TRUE	1	0.631383040721128	3		897	868	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152139	11152139	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	239	870	4	ENST00000358026.2:c.4423C>T	p.Arg1475Cys	p.R1475C	ENST00000358026	NM_001128849.1	1475	Cgc/Tgc	31/36	0.120804433732269	3	FACETS	1	0.983	1	0.574	0.537	0.613	INDETERMINATE	1	TRUE	1	0.631383040721128	3		874	867	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276714	15276714	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376590511	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	206	866	3	ENST00000263388.2:c.5551C>T	p.Arg1851Cys	p.R1851C	ENST00000263388	NM_000435.2	1851	Cgt/Tgt	30/33	0.120804433732269	3	FACETS	1	0.976	1	0.552	0.514	0.592	INDETERMINATE	1	TRUE	1	0.631383040721128	3		869	777	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354232	15354232	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	347	1042	0	ENST00000263377.2:c.2648A>T	p.Lys883Met	p.K883M	ENST00000263377	NM_058243.2	883	aAg/aTg	14/20	0.120804433732269	3	FACETS	1	0.994	1	0.708	0.672	0.745	INDETERMINATE	1	TRUE	1	0.631383040721128	3		1042	1021	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214639	36214639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765234257	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	267	912	1	ENST00000222270.7:c.3065C>T	p.Thr1022Met	p.T1022M	ENST00000222270	NM_014727.1	1022	aCg/aTg	8/37	0.120804433732269	3	FACETS	0.773	0.728	0.818	0.773	0.728	0.818	INDETERMINATE	2	TRUE	1	0.631383040721128	3		913	720	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40743886	40743886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434593	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	259	810	0	ENST00000392038.2:c.821G>A	p.Arg274His	p.R274H	ENST00000392038	NM_001626.4	274	cGc/cAc	9/14	0.120804433732269	3	FACETS	0.763	0.719	0.809	0.763	0.719	0.809	INDETERMINATE	2	TRUE	1	0.631383040721128	3		810	707	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765712	41765712	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	271	836	7	ENST00000301178.4:c.2588C>T	p.Ala863Val	p.A863V	ENST00000301178	NM_021913.4	863	gCt/gTt	20/20	0.120804433732269	3	FACETS	1	0.993	1	0.733	0.691	0.776	INDETERMINATE	1	TRUE	1	0.631383040721128	3		843	770	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902191	50902191	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765097158	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	156	965	1	ENST00000440232.2:c.83C>T	p.Ala28Val	p.A28V	ENST00000440232	NM_002691.3	28	gCa/gTa	2/27	0.120804433732269	3	FACETS	0.969	0.89	1	0.484	0.445	0.526	INDETERMINATE	1	TRUE	1	0.631383040721128	3		966	671	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906786	50906786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778843530	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	64	1003	2	ENST00000440232.2:c.1174G>A	p.Val392Met	p.V392M	ENST00000440232	NM_002691.3	392	Gtg/Atg	10/27	0.120804433732269	3	FACETS	0.263	0.227	0.302	0.131	0.113	0.151	INDETERMINATE	1	TRUE	1	0.631383040721128	3		1005	1015	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462683	29462683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766541301	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	201	862	0	ENST00000389048.3:c.2218G>A	p.Gly740Arg	p.G740R	ENST00000389048	NM_004304.4	740	Gga/Aga	13/29	0.631383040721128	2	FACETS	0.894	0.832	0.959	0.447	0.416	0.48	CLONAL	1	TRUE	0	0.631383040721128	2		862	712	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702265	47702265	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750508	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	228	929	1	ENST00000233146.2:c.1861C>T	p.Arg621Ter	p.R621*	ENST00000233146	NM_000251.2	621	Cga/Tga	12/16	0.631383040721128	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.631383040721128	2		930	336	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030692	48030692	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs267608092	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	64	702	5	ENST00000234420.5:c.3312del	p.Phe1104LeufsTer11	p.F1104Lfs*11	ENST00000234420	NM_000179.2	1102	acT/ac	5/10	0.631383040721128	2	FACETS	0.683	0.596	0.775	0.341	0.298	0.388	SUBCLONAL	1	TRUE	0	0.631383040721128	2		707	297	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182192	99182192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763716402	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	201	805	0	ENST00000074304.5:c.2257G>A	p.Ala753Thr	p.A753T	ENST00000074304	NM_001134224.1	753	Gcc/Acc	21/26	1	2	FACETS	0.969	0.902	1	0.969	0.902	1	CLONAL	1	TRUE	1	0.631383040721128	2		805	657	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128017009	128017009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151216904	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	232	844	1	ENST00000285398.2:c.2080G>A	p.Ala694Thr	p.A694T	ENST00000285398	NM_000122.1	694	Gct/Act	14/15	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.631383040721128	2		845	646	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141631	202141631	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	86	705	0	ENST00000358485.4:c.919del	p.Arg307GlyfsTer23	p.R307Gfs*23	ENST00000358485	NM_001080125.1	307	Cgg/gg	7/9	1	2	FACETS	0.882	0.788	0.979	0.882	0.788	0.979	CLONAL	1	TRUE	1	0.631383040721128	2		705	309	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764347	39764347	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	209	802	1	ENST00000288319.7:c.765del	p.Arg256GlyfsTer35	p.R256Gfs*35	ENST00000288319	NM_182918.3	255	ccC/cc	7/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.631383040721128	2		803	645	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165615	47165615	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	149	755	2	ENST00000409792.3:c.511G>T	p.Ala171Ser	p.A171S	ENST00000409792	NM_014159.6	171	Gca/Tca	3/21	0.631383040721128	2	FACETS	0.849	0.78	0.921	0.424	0.39	0.461	CLONAL	1	TRUE	0	0.631383040721128	2		757	556	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722906	49722906	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	rs747477010	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	60	215	0	ENST00000449682.2:c.1421del	p.Pro474GlnfsTer52	p.P474Qfs*52	ENST00000449682	NM_020998.3	474	cCa/ca	12/18	0.631383040721128	2	FACETS	0.819	0.732	0.906	0.819	0.732	0.906	CLONAL	2	TRUE	0	0.631383040721128	2		215	116	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934243	49934243	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1407832113	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	230	933	9	ENST00000296474.3:c.2264del	p.Gly755ValfsTer19	p.G755Vfs*19	ENST00000296474	NM_002447.2	755	gGt/gt	8/20	0.631383040721128	2	FACETS	0.926	0.866	0.987	0.463	0.433	0.494	CLONAL	1	TRUE	0	0.631383040721128	2		942	787	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443613	52443613	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	358	621	0	ENST00000460680.1:c.79del	p.Val27CysfsTer45	p.V27Cfs*45	ENST00000460680	NM_004656.3	27	Gtg/tg	3/17	0.631383040721128	2	FACETS	0.979	0.941	1	0.979	0.941	1	CLONAL	2	TRUE	0	0.631383040721128	2		621	579	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920337	134920337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141607080	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	129	638	1	ENST00000398015.3:c.2152G>A	p.Val718Met	p.V718M	ENST00000398015	NM_004441.4	718	Gtg/Atg	12/16	0.631383040721128	2	FACETS	0.892	0.815	0.972	0.446	0.407	0.486	CLONAL	1	TRUE	0	0.631383040721128	2		639	458	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430201	181430202	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs398122803	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	59	396	0	ENST00000325404.1:c.59dup	p.Gly21ArgfsTer75	p.G21Rfs*75	ENST00000325404	NM_003106.3	18	tcg/tcGg	1/1	0.631383040721128	2	FACETS	0.525	0.454	0.602	0.262	0.227	0.301	SUBCLONAL	1	TRUE	0	0.631383040721128	2		396	356	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155411	185155411	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140970208	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	82	533	0	ENST00000265026.3:c.652G>A	p.Ala218Thr	p.A218T	ENST00000265026	NM_004721.4	218	Gca/Aca	3/14	0.631383040721128	2	FACETS	0.854	0.761	0.952	0.427	0.38	0.476	CLONAL	1	TRUE	0	0.631383040721128	2		533	304	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198259	185198259	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200441685	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	418	778	2	ENST00000265026.3:c.2741G>A	p.Arg914His	p.R914H	ENST00000265026	NM_004721.4	914	cGc/cAc	13/14	0.631383040721128	2	FACETS	0.993	0.957	1	0.993	0.957	1	CLONAL	2	TRUE	0	0.631383040721128	2		780	667	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968156	55968156	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	180	786	2	ENST00000263923.4:c.2174G>A	p.Arg725His	p.R725H	ENST00000263923	NM_002253.2	725	cGc/cAc	15/30	1	2	FACETS	0.965	0.895	1	0.965	0.895	1	CLONAL	1	TRUE	1	0.631383040721128	2		788	591	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	163	881	4	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	0.863	0.796	0.933	0.863	0.796	0.933	CLONAL	1	TRUE	1	0.631383040721128	2		885	598	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542693	187542694	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	76	761	1	ENST00000441802.2:c.5046dup	p.Gly1683TrpfsTer11	p.G1683Wfs*11	ENST00000441802	NM_005245.3	1682	-/T	10/27	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.631383040721128	2		762	239	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31493373	31493373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	18	730	1	ENST00000344624.3:c.1783G>A	p.Asp595Asn	p.D595N	ENST00000344624		595	Gat/Aat	10/33	1	2	FACETS	0.181	0.136	0.234	0.181	0.136	0.234	SUBCLONAL	1	TRUE	1	0.631383040721128	2		731	315	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526679	31526679	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	197	994	2	ENST00000344624.3:c.361C>T	p.Pro121Ser	p.P121S	ENST00000344624		121	Cca/Tca	2/33	1	2	FACETS	0.778	0.722	0.836	0.778	0.722	0.836	SUBCLONAL	1	TRUE	1	0.631383040721128	2		996	802	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	66	564	4	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.763	0.669	0.863	0.763	0.669	0.863	SUBCLONAL	1	TRUE	1	0.631383040721128	2		568	274	SUCCESS
APC	324	MSKCC	GRCh37	5	112179389	112179389	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	114	700	0	ENST00000257430.4:c.8098A>G	p.Asn2700Asp	p.N2700D	ENST00000257430	NM_000038.5	2700	Aat/Gat	16/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.631383040721128	2		700	325	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120318	94120318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41273629	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	109	433	0	ENST00000369303.4:c.733G>A	p.Ala245Thr	p.A245T	ENST00000369303	NM_004440.3	245	Gcc/Acc	3/17	0.120804433732269	3	FACETS	1	0.978	1	0.634	0.575	0.696	INDETERMINATE	1	TRUE	1	0.631383040721128	3		433	358	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017495	112017495	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	174	531	1	ENST00000368678.4:c.1018G>A	p.Glu340Lys	p.E340K	ENST00000368678		340	Gag/Aag	9/13	0.120804433732269	3	FACETS	0.817	0.76	0.874	0.817	0.76	0.874	INDETERMINATE	2	TRUE	1	0.631383040721128	3		532	444	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502151	157502151	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1248514225	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	200	577	5	ENST00000346085.5:c.3184G>A	p.Glu1062Lys	p.E1062K	ENST00000346085	NM_020732.3	1062	Gag/Aag	12/20	0.120804433732269	3	FACETS	1	0.991	1	0.706	0.659	0.755	INDETERMINATE	1	TRUE	1	0.631383040721128	3		582	590	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829282	128829282	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	252	849	0	ENST00000249373.3:c.290A>G	p.Asp97Gly	p.D97G	ENST00000249373	NM_005631.4	97	gAc/gGc	1/12	0.631383040721128	3	FACETS	1	0.982	1	0.562	0.526	0.598	CLONAL	1	TRUE	1	0.631383040721128	3		849	935	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515136	148515136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	158	661	1	ENST00000320356.2:c.1073G>A	p.Arg358His	p.R358H	ENST00000320356	NM_004456.4	358	cGc/cAc	10/20	0.631383040721128	3	FACETS	0.816	0.748	0.886	0.408	0.374	0.443	CLONAL	1	TRUE	1	0.631383040721128	3		662	807	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874147	151874148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs747256476	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	179	1009	15	ENST00000262189.6:c.8390dup	p.Glu2798GlyfsTer11	p.E2798Gfs*11	ENST00000262189	NM_170606.2	2797	aag/aaAg	38/59	0.631383040721128	3	FACETS	0.763	0.709	0.817	0.763	0.709	0.817	SUBCLONAL	2	TRUE	1	0.631383040721128	3		1024	489	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561429	141561430	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1391347693	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	486	656	2	ENST00000220592.5:c.1375dup	p.Gln459ProfsTer215	p.Q459Pfs*215	ENST00000220592	NM_012154.3	459	cag/cCag	11/19	0.631227248095253	3	FACETS	0.899	0.87	0.928	0.899	0.87	0.928	CLONAL	3	TRUE	0	0.631383040721128	3		658	751	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340407	8340407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201651279	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	142	819	1	ENST00000356435.5:c.5189G>A	p.Arg1730Gln	p.R1730Q	ENST00000356435		1730	cGg/cAg	31/35	1	2	FACETS	0.905	0.83	0.982	0.905	0.83	0.982	CLONAL	1	TRUE	1	0.631383040721128	2		820	497	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250478	110250478	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	126	672	3	ENST00000374672.4:c.197C>T	p.Ala66Val	p.A66V	ENST00000374672	NM_004235.4	66	gCg/gTg	3/5	1	2	FACETS	0.797	0.725	0.871	0.797	0.725	0.871	SUBCLONAL	1	TRUE	1	0.631383040721128	2		675	501	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309117	137309117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1383908613	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	295	1068	2	ENST00000481739.1:c.724G>A	p.Val242Met	p.V242M	ENST00000481739	NM_002957.4	242	Gtg/Atg	5/10	1	2	FACETS	0.997	0.941	1	0.997	0.941	1	CLONAL	1	TRUE	1	0.631383040721128	2		1070	937	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15838386	15838386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746675804	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	132	363	2	ENST00000307771.7:c.884G>A	p.Arg295Gln	p.R295Q	ENST00000307771	NM_005089.3	295	cGa/cAa	10/11	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.631383040721128	1		365	217	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949141	44949143	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	89	416	0	ENST00000377967.4:c.3707_3709del	p.Asn1236del	p.N1236del	ENST00000377967	NM_021140.2	1234	tgCAAc/tgc	25/29	1	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.631383040721128	1		416	166	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652397	48652397	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	190	478	0	ENST00000376670.3:c.1073del	p.Pro358GlnfsTer74	p.P358Qfs*74	ENST00000376670	NM_002049.3	356	ggC/gg	6/6	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.631383040721128	1		478	351	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411530	63411530	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	151	513	0	ENST00000330258.3:c.1637del	p.Leu546CysfsTer16	p.L546Cfs*16	ENST00000330258	NM_152424.3	546	tTg/tg	2/2	1	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.631383040721128	1		513	325	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279861	46279866	+	inframe_deletion	In_Frame_Del	DEL	CAGCAA	CAGCAA	-	rs748517056	NA	P-0021304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	50	414	0	ENST00000371998.3:c.3810_3815del	p.Gln1275_Gln1276del	p.Q1275_Q1276del	ENST00000371998		1263	CAGCAA/-	20/23	0.631383040721128	3	FACETS	0.324	0.274	0.379	0.162	0.137	0.19	SUBCLONAL	1	TRUE	1	0.631383040721128	3		414	643	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	68	515	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.873	0.763	0.991	0.873	0.763	0.991	CLONAL	1	TRUE	1	0.382816022802474	2		515	407	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	168	419	2	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	1	0.947	1	1	0.993	1	CLONAL	2	TRUE	1	0.382816022802474	2		421	429	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	95	460	3	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.382816022802474	2		463	470	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641389	18641389	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1229278001	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	58	386	0	ENST00000266497.5:c.2393del	p.Asn798MetfsTer16	p.N798Mfs*16	ENST00000266497		796	ctA/ct	17/31	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.382816022802474	2		386	290	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	100	751	0	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.382816022802474	2		751	522	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518437	204518437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201947927	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	109	581	0	ENST00000367182.3:c.1100C>T	p.Ser367Leu	p.S367L	ENST00000367182	NM_001278516.1	367	tCg/tTg	11/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.382816022802474	2		581	495	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	204	505	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.987	0.923	1	1	0.994	1	CLONAL	2	TRUE	1	0.382816022802474	2		511	540	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921764	111921764	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	115	732	0	ENST00000393256.3:c.553C>T	p.Arg185Ter	p.R185*	ENST00000393256	NM_006538.4	185	Cga/Tga	4/4	1	2	FACETS	0.982	0.887	1	0.982	0.887	1	CLONAL	1	TRUE	1	0.382816022802474	2		732	612	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057937	27057937	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	155	1065	1	ENST00000324856.7:c.1650del	p.Tyr551ThrfsTer68	p.Y551Tfs*68	ENST00000324856	NM_006015.4	549	Ccc/cc	3/20	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.382816022802474	2		1066	799	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257366	19257366	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	143	1006	2	ENST00000162023.5:c.767del	p.Pro256GlnfsTer?	p.P256Qfs*?	ENST00000162023		256	cCa/ca	11/13	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.382816022802474	2		1008	716	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806180	1806181	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760502257	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	175	1153	4	ENST00000260795.2:c.1206dup	p.Lys403GlnfsTer93	p.K403Qfs*93	ENST00000260795		400	agc/agCc	8/17	1	2	FACETS	0.981	0.903	1	0.981	0.903	1	CLONAL	1	TRUE	1	0.382816022802474	2		1157	932	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288323	33288323	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780262381	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	174	687	1	ENST00000374542.5:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000374542	NM_001141970.1	362	cGg/cAg	4/8	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.382816022802474	2		688	645	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294283	1294283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	122	1062	3	ENST00000310581.5:c.718C>T	p.Arg240Cys	p.R240C	ENST00000310581	NM_198253.2	240	Cgt/Tgt	2/16	1	2	FACETS	0.941	0.852	1	0.941	0.852	1	CLONAL	1	TRUE	1	0.382816022802474	2		1065	677	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780235	9780235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1397404017	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	193	1084	3	ENST00000377346.4:c.1405G>A	p.Ala469Thr	p.A469T	ENST00000377346	NM_005026.3	469	Gct/Act	11/24	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.382816022802474	2		1087	886	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221081	5221081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199805837	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	156	868	3	ENST00000357368.4:c.3385G>A	p.Ala1129Thr	p.A1129T	ENST00000357368	NM_002850.3	1129	Gcc/Acc	20/38	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.382816022802474	2		871	655	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	89	715	1	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	0.802	0.712	0.897	0.802	0.712	0.897	CLONAL	1	TRUE	1	0.382816022802474	2		716	580	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755553	39755554	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	63	667	0	ENST00000288319.7:c.1211dup	p.Glu405GlyfsTer61	p.E405Gfs*61	ENST00000288319	NM_182918.3	404	ccg/ccCg	10/10	1	2	FACETS	0.853	0.741	0.973	0.853	0.741	0.973	CLONAL	1	TRUE	1	0.382816022802474	2		667	386	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324917	31324917	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	208	931	0	ENST00000412585.2:c.19del	p.Arg7GlufsTer13	p.R7Efs*13	ENST00000412585	NM_005514.6	7	Cga/ga	1/8	1	2	FACETS	0.756	0.704	0.809	1	0.992	1	SUBCLONAL	2	TRUE	1	0.382816022802474	2		931	719	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438018	49438018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs111266743	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	167	1076	2	ENST00000301067.7:c.5153C>T	p.Ala1718Val	p.A1718V	ENST00000301067	NM_003482.3	1718	gCg/gTg	21/54	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.382816022802474	2		1078	812	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983029	201983029	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	219	1253	0	ENST00000359651.3:c.878T>G	p.Met293Arg	p.M293R	ENST00000359651		293	aTg/aGg	7/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.382816022802474	2		1253	999	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552719	226552719	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	91	549	0	ENST00000366794.5:c.2642C>T	p.Pro881Leu	p.P881L	ENST00000366794	NM_001618.3	881	cCg/cTg	19/23	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.382816022802474	2		549	413	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033923	49033923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	117	787	0	ENST00000267163.4:c.2060C>T	p.Thr687Ile	p.T687I	ENST00000267163	NM_000321.2	687	aCc/aTc	20/27	1	2	FACETS	0.946	0.855	1	0.946	0.855	1	CLONAL	1	TRUE	1	0.382816022802474	2		787	646	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281606	49281606	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	174	1115	1	ENST00000282018.3:c.653G>T	p.Ser218Ile	p.S218I	ENST00000282018	NM_020377.2	218	aGc/aTc	1/1	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.382816022802474	2		1116	824	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628580	90628580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	143	1145	5	ENST00000330062.3:c.1007G>A	p.Cys336Tyr	p.C336Y	ENST00000330062	NM_002168.2	336	tGc/tAc	8/11	1	2	FACETS	0.972	0.887	1	0.972	0.887	1	CLONAL	1	TRUE	1	0.382816022802474	2		1150	769	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826571	50826572	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	120	627	0	ENST00000398568.2:c.2301dup	p.Pro768SerfsTer12	p.P768Sfs*12	ENST00000398568	NM_001042412.1	766	att/aTtt	15/18	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.382816022802474	2		627	568	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346277	89346277	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	86	494	0	ENST00000301030.4:c.6673A>G	p.Thr2225Ala	p.T2225A	ENST00000301030	NM_001256183.1	2225	Acg/Gcg	9/13	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.382816022802474	2		494	430	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15975514	15975514	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	144	887	0	ENST00000268712.3:c.3840del	p.Ser1281ValfsTer16	p.S1281Vfs*16	ENST00000268712	NM_006311.3	1280	ggG/gg	29/46	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.382816022802474	2		887	659	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60795902	60795902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471182435	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	147	891	1	ENST00000333681.4:c.676G>A	p.Val226Met	p.V226M	ENST00000333681		226	Gtg/Atg	3/3	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.382816022802474	2		892	690	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211003	36211003	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	200	1390	0	ENST00000222270.7:c.758del	p.Pro253HisfsTer7	p.P253Hfs*7	ENST00000222270	NM_014727.1	252	Ccc/cc	3/37	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.382816022802474	2		1390	1013	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799146	42799146	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770823747	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	180	1147	5	ENST00000575354.2:c.4630G>A	p.Ala1544Thr	p.A1544T	ENST00000575354	NM_015125.3	1544	Gct/Act	20/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.382816022802474	2		1152	816	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919562	96919562	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	126	821	1	ENST00000258439.3:c.701del	p.Pro234LeufsTer73	p.P234Lfs*73	ENST00000258439	NM_001193304.2	234	cCt/ct	4/4	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.382816022802474	2		822	653	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738270	190738270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755396415	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	79	613	0	ENST00000441310.2:c.2522G>A	p.Cys841Tyr	p.C841Y	ENST00000441310	NM_000534.4	841	tGt/tAt	12/13	1	2	FACETS	0.834	0.735	0.939	0.834	0.735	0.939	CLONAL	1	TRUE	1	0.382816022802474	2		613	495	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131239	202131240	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	111	754	0	ENST00000358485.4:c.211dup	p.Glu71GlyfsTer6	p.E71Gfs*6	ENST00000358485	NM_001080125.1	69	-/G	2/9	1	2	FACETS	0.971	0.876	1	0.971	0.876	1	CLONAL	1	TRUE	1	0.382816022802474	2		754	597	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026133	71026133	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs775136381	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	122	765	0	ENST00000318789.4:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000318789	NM_032682.5	497	Cga/Tga	17/21	1	2	FACETS	0.893	0.808	0.982	0.893	0.808	0.982	CLONAL	1	TRUE	1	0.382816022802474	2		765	714	SUCCESS
APC	324	MSKCC	GRCh37	5	112174973	112174973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085227	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	46	394	0	ENST00000257430.4:c.3682C>T	p.Gln1228Ter	p.Q1228*	ENST00000257430	NM_000038.5	1228	Cag/Tag	16/16	1	2	FACETS	0.778	0.658	0.908	0.778	0.658	0.908	CLONAL	1	TRUE	1	0.382816022802474	2		394	309	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282076	38282076	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	182	1245	0	ENST00000425967.3:c.980A>G	p.Asn327Ser	p.N327S	ENST00000425967	NM_001174067.1	327	aAt/aGt	8/19	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.382816022802474	2		1245	931	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482251	87482251	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	135	1004	0	ENST00000277120.3:c.1538G>A	p.Gly513Asp	p.G513D	ENST00000277120		513	gGc/gAc	14/19	1	2	FACETS	0.966	0.879	1	0.966	0.879	1	CLONAL	1	TRUE	1	0.382816022802474	2		1004	730	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250280	110250282	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs1299866846	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	143	1092	0	ENST00000374672.4:c.393_395del	p.Ser135del	p.S135del	ENST00000374672	NM_004235.4	131	tcCTCt/tct	3/5	1	2	FACETS	0.942	0.86	1	0.942	0.86	1	CLONAL	1	TRUE	1	0.382816022802474	2		1092	793	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411798	63411799	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0021346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	110	620	0	ENST00000330258.3:c.1368_1369del	p.Gln457GlufsTer2	p.Q457Efs*2	ENST00000330258	NM_152424.3	456	ccTCag/ccag	2/2	1	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.382816022802474	1		620	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578539	7578539	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782160	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	251	965	0	ENST00000269305.4:c.391A>T	p.Asn131Tyr	p.N131Y	ENST00000269305	NM_001126112.2	131	Aac/Tac	5/11	0.273114587681094	3	FACETS	0.945	0.888	1	0.945	0.888	1	CLONAL	3	TRUE	0	0.273114587681094	3		965	737	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953837	55953837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	39	713	0	ENST00000263923.4:c.3599C>T	p.Ser1200Phe	p.S1200F	ENST00000263923	NM_002253.2	1200	tCc/tTc	27/30	1	2	FACETS	0.789	0.655	0.937	0.789	0.655	0.937	CLONAL	1	TRUE	1	0.273114587681094	2		713	362	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944914	31944914	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	43	346	0	ENST00000340398.3:c.187C>G	p.Arg63Gly	p.R63G	ENST00000340398	NM_001013699.2	63	Cgg/Ggg	1/1	0.273114587681094	3	FACETS	1	0.947	1	0.66	0.556	0.774	CLONAL	1	TRUE	1	0.273114587681094	3		346	271	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141507	11141507	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	89	673	1	ENST00000358026.2:c.3484G>T	p.Gly1162Cys	p.G1162C	ENST00000358026	NM_001128849.1	1162	Ggc/Tgc	25/36	0.273114587681094	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.273114587681094	1		674	410	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119624685	119624685	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	36	614	0	ENST00000316626.5:c.730G>T	p.Gly244Cys	p.G244C	ENST00000316626		244	Ggc/Tgc	7/12	0.273114587681094	3	FACETS	0.942	0.777	1	0.471	0.388	0.563	CLONAL	1	TRUE	1	0.273114587681094	3		614	318	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851274	156851274	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	55	694	0	ENST00000524377.1:c.2231G>C	p.Arg744Pro	p.R744P	ENST00000524377	NM_002529.3	744	cGt/cCt	17/17	0.273114587681094	3	FACETS	0.901	0.771	1	0.451	0.385	0.522	CLONAL	1	TRUE	1	0.273114587681094	3		694	508	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451477	70451477	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	61	759	0	ENST00000373644.4:c.6317C>G	p.Ser2106Cys	p.S2106C	ENST00000373644	NM_030625.2	2106	tCt/tGt	12/12	1	2	FACETS	0.948	0.82	1	0.948	0.82	1	CLONAL	1	TRUE	1	0.273114587681094	2		759	471	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137198	64137198	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	44	830	0	ENST00000334205.4:c.1630G>T	p.Gly544Trp	p.G544W	ENST00000334205	NM_003942.2	544	Ggg/Tgg	14/17	0.273114587681094	3	FACETS	0.638	0.534	0.753	0.319	0.267	0.377	SUBCLONAL	1	TRUE	1	0.273114587681094	3		830	574	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125496701	125496701	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	72	499	0	ENST00000428830.2:c.38A>T	p.Gln13Leu	p.Q13L	ENST00000428830	NM_001114121.2	13	cAa/cTa	2/14	0.273114587681094	3	FACETS	1	0.974	1	0.742	0.651	0.838	CLONAL	1	TRUE	1	0.273114587681094	3		499	404	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022766	12022766	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	56	572	1	ENST00000396373.4:c.872G>T	p.Arg291Met	p.R291M	ENST00000396373	NM_001987.4	291	aGg/aTg	5/8	0.273114587681094	3	FACETS	0.996	0.855	1	0.498	0.427	0.575	CLONAL	1	TRUE	1	0.273114587681094	3		573	468	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861995	57861996	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	45	446	0	ENST00000228682.2:c.1297dup	p.Glu433GlyfsTer19	p.E433Gfs*19	ENST00000228682	NM_005269.2	432	-/G	10/12	1	2	FACETS	0.99	0.835	1	0.99	0.835	1	CLONAL	1	TRUE	1	0.273114587681094	2		446	333	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109795	115109795	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	75	835	2	ENST00000257566.3:c.2083C>A	p.Arg695Ser	p.R695S	ENST00000257566	NM_016569.3	695	Cgc/Agc	8/8	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.273114587681094	2		837	501	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895693	28895693	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	54	767	0	ENST00000282397.4:c.3081C>A	p.Asn1027Lys	p.N1027K	ENST00000282397	NM_002019.4	1027	aaC/aaA	23/30	0.269647175290476	2	FACETS	0.869	0.744	1	0.435	0.372	0.503	CLONAL	1	TRUE	0	0.273114587681094	2		767	455	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574405	95574405	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	31	297	0	ENST00000393063.1:c.2462G>T	p.Arg821Leu	p.R821L	ENST00000393063	NM_030621.3	821	cGc/cTc	17/28	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.273114587681094	2		297	199	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420272	88420272	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	64	628	0	ENST00000360948.2:c.2414G>T	p.Gly805Val	p.G805V	ENST00000360948	NM_001012338.2	805	gGg/gTg	19/19	0.273114587681094	3	FACETS	1	0.935	1	0.564	0.49	0.645	CLONAL	1	TRUE	1	0.273114587681094	3		628	472	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483911	88483911	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	65	845	0	ENST00000360948.2:c.1659C>A	p.Phe553Leu	p.F553L	ENST00000360948	NM_001012338.2	553	ttC/ttA	14/19	0.273114587681094	3	FACETS	0.89	0.771	1	0.445	0.385	0.509	CLONAL	1	TRUE	1	0.273114587681094	3		845	608	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348175	348175	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	124	763	0	ENST00000262320.3:c.1331G>T	p.Trp444Leu	p.W444L	ENST00000262320	NM_003502.3	444	tGg/tTg	6/11	0.273114587681094	3	FACETS	0.905	0.822	0.992	0.905	0.822	0.992	CLONAL	2	TRUE	1	0.273114587681094	3		763	570	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213931	2213931	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	109	731	1	ENST00000326181.6:c.10G>T	p.Gly4Cys	p.G4C	ENST00000326181	NM_032271.2	4	Ggc/Tgc	2/21	0.273114587681094	3	FACETS	0.882	0.796	0.973	0.882	0.796	0.973	CLONAL	2	TRUE	1	0.273114587681094	3		732	514	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2221355	2221355	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	114	646	0	ENST00000326181.6:c.439G>T	p.Gly147Trp	p.G147W	ENST00000326181	NM_032271.2	147	Ggg/Tgg	6/21	0.273114587681094	3	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	1	0.273114587681094	3		646	452	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779157	3779157	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	84	594	1	ENST00000262367.5:c.5891G>T	p.Arg1964Leu	p.R1964L	ENST00000262367	NM_004380.2	1964	cGt/cTt	31/31	0.273114587681094	3	FACETS	0.853	0.757	0.953	0.853	0.757	0.953	CLONAL	2	TRUE	1	0.273114587681094	3		595	410	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991499	72991499	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	154	916	0	ENST00000268489.5:c.2546G>T	p.Gly849Val	p.G849V	ENST00000268489	NM_006885.3	849	gGc/gTc	2/10	0.273114587681094	3	FACETS	0.983	0.903	1	0.983	0.903	1	CLONAL	2	TRUE	1	0.273114587681094	3		916	652	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973761	15973761	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	104	572	1	ENST00000268712.3:c.4231A>T	p.Ser1411Cys	p.S1411C	ENST00000268712	NM_006311.3	1411	Agc/Tgc	31/46	0.273114587681094	3	FACETS	0.975	0.878	1	0.65	0.585	0.717	CLONAL	2	TRUE	0	0.273114587681094	3		573	444	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552227	29552227	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	37	600	0	ENST00000356175.3:c.1960C>A	p.Pro654Thr	p.P654T	ENST00000356175	NM_000267.3	654	Cct/Act	17/57	0.273114587681094	5	FACETS	0.987	0.815	1	0.329	0.271	0.393	CLONAL	1	TRUE	2	0.273114587681094	5		600	387	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435485	56435485	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	142	715	0	ENST00000407977.2:c.1652A>C	p.His551Pro	p.H551P	ENST00000407977		551	cAc/cCc	9/10	0.273114587681094	5	FACETS	1	0.98	1	0.824	0.754	0.897	CLONAL	2	TRUE	2	0.273114587681094	5		715	593	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39573238	39573238	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	509	37	0	ENST00000262039.4:c.719G>T	p.Gly240Val	p.G240V	ENST00000262039	NM_002647.2	240	gGt/gTt	7/25	0.253873871923344	4	FACETS	1	0.986	1	1	0.998	1	CLONAL	6	TRUE	2	0.273114587681094	4		37	767	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39573240	39573240	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	36	520	0	ENST00000262039.4:c.721G>T	p.Asp241Tyr	p.D241Y	ENST00000262039	NM_002647.2	241	Gat/Tat	7/25	0.253873871923344	4	FACETS	1	0.884	1	0.548	0.452	0.655	CLONAL	1	TRUE	2	0.273114587681094	4		520	306	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39576688	39576688	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	60	466	0	ENST00000262039.4:c.978A>T	p.Gln326His	p.Q326H	ENST00000262039	NM_002647.2	326	caA/caT	9/25	0.253873871923344	4	FACETS	0.877	0.76	1	0.877	0.76	1	CLONAL	2	TRUE	2	0.273114587681094	4		466	319	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641522	47641522	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	24	510	0	ENST00000233146.2:c.907G>T	p.Asp303Tyr	p.D303Y	ENST00000233146	NM_000251.2	303	Gat/Tat	5/16	0.199384014223388	2	FACETS	0.517	0.405	0.646	0.258	0.202	0.323	SUBCLONAL	1	TRUE	0	0.273114587681094	2		510	340	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257747	198257747	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	49	546	1	ENST00000335508.6:c.3705G>T	p.Glu1235Asp	p.E1235D	ENST00000335508	NM_012433.2	1235	gaG/gaT	24/25	0.273114587681094	3	FACETS	1	0.9	1	0.36	0.305	0.419	CLONAL	1	TRUE	0	0.273114587681094	3		547	378	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257748	198257748	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	21	543	0	ENST00000335508.6:c.3704A>T	p.Glu1235Val	p.E1235V	ENST00000335508	NM_012433.2	1235	gAg/gTg	24/25	0.273114587681094	3	FACETS	0.458	0.352	0.581	0.153	0.117	0.194	SUBCLONAL	1	TRUE	0	0.273114587681094	3		543	382	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403190	213403190	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1300045748	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	47	502	0	ENST00000342788.4:c.65C>T	p.Pro22Leu	p.P22L	ENST00000342788	NM_005235.2	22	cCc/cTc	1/28	0.273114587681094	3	FACETS	1	0.898	1	0.36	0.305	0.421	CLONAL	1	TRUE	0	0.273114587681094	3		502	362	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793436	242793436	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	41	711	0	ENST00000334409.5:c.641C>A	p.Ser214Ter	p.S214*	ENST00000334409	NM_005018.2	214	tCa/tAa	5/5	0.273114587681094	3	FACETS	0.75	0.625	0.889	0.25	0.208	0.297	SUBCLONAL	1	TRUE	0	0.273114587681094	3		711	455	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546651	9546651	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	154	565	0	ENST00000353224.5:c.1371A>T	p.Glu457Asp	p.E457D	ENST00000353224	NM_177990.2	457	gaA/gaT	5/10	0.273114587681094	3	FACETS	0.883	0.814	0.953	1	0.986	1	CLONAL	3	TRUE	1	0.273114587681094	3		565	484	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017234	31017234	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	20	331	0	ENST00000375687.4:c.565G>C	p.Gly189Arg	p.G189R	ENST00000375687	NM_015338.5	189	Ggg/Cgg	7/13	0.273114587681094	3	FACETS	0.564	0.432	0.72	0.282	0.216	0.36	SUBCLONAL	1	TRUE	1	0.273114587681094	3		331	295	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019162	31019162	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	45	733	3	ENST00000375687.4:c.757G>T	p.Glu253Ter	p.E253*	ENST00000375687	NM_015338.5	253	Gag/Tag	9/13	0.273114587681094	3	FACETS	0.713	0.599	0.84	0.357	0.299	0.42	SUBCLONAL	1	TRUE	1	0.273114587681094	3		736	525	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770556	40770556	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	34	630	2	ENST00000373198.4:c.2826del	p.Tyr943ThrfsTer6	p.Y943Tfs*6	ENST00000373198	NM_133170.3	942	tcC/tc	19/32	0.273114587681094	3	FACETS	0.692	0.565	0.834	0.346	0.282	0.417	SUBCLONAL	1	TRUE	1	0.273114587681094	3		632	409	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458454	12458454	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	52	766	0	ENST00000287820.6:c.1071G>T	p.Met357Ile	p.M357I	ENST00000287820	NM_015869.4	357	atG/atT	6/7	0.273114587681094	3	FACETS	0.746	0.635	0.868	0.373	0.317	0.434	SUBCLONAL	1	TRUE	1	0.273114587681094	3		766	580	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72842131	72842131	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	24	525	0	ENST00000325599.8:c.1117G>T	p.Asp373Tyr	p.D373Y	ENST00000325599	NM_018130.2	373	Gac/Tac	10/11	0.273114587681094	3	FACETS	0.552	0.432	0.69	0.276	0.216	0.345	SUBCLONAL	1	TRUE	1	0.273114587681094	3		525	362	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447681	187447681	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	35	653	0	ENST00000232014.4:c.512G>T	p.Ser171Ile	p.S171I	ENST00000232014	NM_001130845.1	171	aGc/aTc	5/10	0.199384014223388	2	FACETS	0.674	0.553	0.81	0.337	0.276	0.405	SUBCLONAL	1	TRUE	0	0.273114587681094	2		653	380	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627954	187627954	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	51	728	0	ENST00000441802.2:c.3028G>T	p.Val1010Phe	p.V1010F	ENST00000441802	NM_005245.3	1010	Gtt/Ttt	2/27	0.0870843784937541	1	FACETS	0.785	0.668	0.911	0.785	0.668	0.911	INDETERMINATE	1	TRUE	0	0.273114587681094	1		728	411	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679993	30679993	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	93	544	1	ENST00000376406.3:c.1726G>T	p.Asp576Tyr	p.D576Y	ENST00000376406	NM_014641.2	576	Gac/Tac	5/15	0.253873871923344	4	FACETS	0.968	0.865	1	0.968	0.865	1	CLONAL	2	TRUE	2	0.273114587681094	4		545	448	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117645554	117645554	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	46	600	0	ENST00000368508.3:c.5582G>T	p.Ser1861Ile	p.S1861I	ENST00000368508	NM_002944.2	1861	aGt/aTt	34/43	0.273114587681094	1	FACETS	0.989	0.838	1	0.989	0.838	1	CLONAL	1	TRUE	0	0.273114587681094	1		600	294	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200218	138200218	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	82	549	0	ENST00000237289.4:c.1636G>T	p.Glu546Ter	p.E546*	ENST00000237289	NM_001270507.1	546	Gag/Tag	7/9	0.273114587681094	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.273114587681094	1		549	434	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962930	2962930	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1349831751	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	231	919	0	ENST00000396946.4:c.1978C>G	p.Arg660Gly	p.R660G	ENST00000396946	NM_032415.4	660	Cgg/Ggg	16/25	0.273114587681094	5	FACETS	0.877	0.822	0.933	0.877	0.822	0.933	CLONAL	4	TRUE	1	0.273114587681094	5		919	680	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355212	81355213	+	stop_gained	Nonsense_Mutation	DNP	CA	CA	AT	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	25	357	1	ENST00000222390.5:c.1161_1162delinsAT	p.His387_Gly388delinsGlnTer	p.H387_G388delinsQ*	ENST00000222390	NM_000601.4	387	caTGga/caATga	9/18	0.273114587681094	3	FACETS	1	0.832	1	0.352	0.279	0.435	CLONAL	1	TRUE	0	0.273114587681094	3		358	197	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358944	81358944	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	31	583	0	ENST00000222390.5:c.1017G>T	p.Met339Ile	p.M339I	ENST00000222390	NM_000601.4	339	atG/atT	8/18	0.273114587681094	3	FACETS	0.614	0.497	0.748	0.205	0.165	0.25	SUBCLONAL	1	TRUE	0	0.273114587681094	3		583	420	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381579	81381579	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	13	232	0	ENST00000222390.5:c.483-1G>T		p.X161_splice	ENST00000222390	NM_000601.4	161			0.273114587681094	3	FACETS	0.442	0.315	0.597	0.147	0.105	0.199	SUBCLONAL	1	TRUE	0	0.273114587681094	3		232	245	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388037	81388037	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	37	719	2	ENST00000222390.5:c.338G>T	p.Gly113Val	p.G113V	ENST00000222390	NM_000601.4	113	gGc/gTc	3/18	0.273114587681094	3	FACETS	0.922	0.762	1	0.307	0.254	0.367	CLONAL	1	TRUE	0	0.273114587681094	3		721	334	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345971	152345971	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	119	641	0	ENST00000359321.1:c.599A>G	p.Gln200Arg	p.Q200R	ENST00000359321	NM_005431.1	200	cAg/cGg	3/3	0.273114587681094	3	FACETS	1	0.915	1	0.672	0.61	0.737	CLONAL	2	TRUE	0	0.273114587681094	3		641	491	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162829	38162829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773861449	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	30	706	0	ENST00000317025.8:c.2377C>T	p.Arg793Cys	p.R793C	ENST00000317025	NM_023034.1	793	Cgc/Tgc	13/24	1	2	FACETS	0.495	0.398	0.605	0.495	0.398	0.605	SUBCLONAL	1	TRUE	1	0.273114587681094	2		706	444	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021727	69021727	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	62	620	0	ENST00000288368.4:c.3015G>T	p.Gln1005His	p.Q1005H	ENST00000288368	NM_024870.2	1005	caG/caT	25/40	0.273114587681094	3	FACETS	1	0.94	1	0.385	0.333	0.441	CLONAL	1	TRUE	0	0.273114587681094	3		620	447	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376038	8376038	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	35	469	0	ENST00000356435.5:c.4559C>A	p.Pro1520His	p.P1520H	ENST00000356435		1520	cCt/cAt	28/35	0.273114587681094	1	FACETS	0.848	0.699	1	0.848	0.699	1	CLONAL	1	TRUE	0	0.273114587681094	1		469	261	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499645	8499645	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	58	443	0	ENST00000356435.5:c.2322+2T>A		p.X774_splice	ENST00000356435		774			0.273114587681094	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.273114587681094	1		443	292	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500843	8500843	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	49	600	0	ENST00000356435.5:c.2039G>T	p.Trp680Leu	p.W680L	ENST00000356435		680	tGg/tTg	13/35	0.273114587681094	1	FACETS	0.93	0.792	1	0.93	0.792	1	CLONAL	1	TRUE	0	0.273114587681094	1		600	333	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650170	93650170	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	33	577	0	ENST00000375746.1:c.1721G>T	p.Arg574Leu	p.R574L	ENST00000375746	NM_001174167.1	574	cGa/cTa	12/14	0.273114587681094	1	FACETS	0.65	0.531	0.784	0.65	0.531	0.784	SUBCLONAL	1	TRUE	0	0.273114587681094	1		577	321	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921559	39921559	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	87	739	1	ENST00000378444.4:c.4261C>A	p.Arg1421Ser	p.R1421S	ENST00000378444	NM_001123385.1	1421	Cgc/Agc	10/15	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.273114587681094	2		740	541	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933531	39933531	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	43	786	1	ENST00000378444.4:c.1068G>T	p.Glu356Asp	p.E356D	ENST00000378444	NM_001123385.1	356	gaG/gaT	4/15	1	2	FACETS	0.529	0.442	0.626	0.529	0.442	0.626	SUBCLONAL	1	TRUE	1	0.273114587681094	2		787	595	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038745	47038745	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	59	795	0	ENST00000377604.3:c.752C>A	p.Thr251Lys	p.T251K	ENST00000377604	NM_001204468.1	251	aCg/aAg	9/24	1	2	FACETS	0.828	0.713	0.953	0.828	0.713	0.953	CLONAL	1	TRUE	1	0.273114587681094	2		795	522	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245149	53245149	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1556851628	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	31	683	0	ENST00000375401.3:c.791G>T	p.Gly264Val	p.G264V	ENST00000375401	NM_004187.3	264	gGg/gTg	7/26	1	2	FACETS	0.51	0.412	0.621	0.51	0.412	0.621	SUBCLONAL	1	TRUE	1	0.273114587681094	2		683	445	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409862	63409862	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	42	479	1	ENST00000330258.3:c.3305A>T	p.Tyr1102Phe	p.Y1102F	ENST00000330258	NM_152424.3	1102	tAt/tTt	2/2	1	2	FACETS	0.739	0.618	0.874	0.739	0.618	0.874	SUBCLONAL	1	TRUE	1	0.273114587681094	2		480	416	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410239	63410239	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	34	719	0	ENST00000330258.3:c.2928C>A	p.Ser976Arg	p.S976R	ENST00000330258	NM_152424.3	976	agC/agA	2/2	1	2	FACETS	0.487	0.397	0.589	0.487	0.397	0.589	SUBCLONAL	1	TRUE	1	0.273114587681094	2		719	511	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411463	63411463	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	70	953	0	ENST00000330258.3:c.1704G>T	p.Leu568Phe	p.L568F	ENST00000330258	NM_152424.3	568	ttG/ttT	2/2	1	2	FACETS	0.823	0.717	0.937	0.823	0.717	0.937	CLONAL	1	TRUE	1	0.273114587681094	2		953	623	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412468	63412468	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	68	963	0	ENST00000330258.3:c.699T>A	p.Asp233Glu	p.D233E	ENST00000330258	NM_152424.3	233	gaT/gaA	2/2	1	2	FACETS	0.868	0.755	0.989	0.868	0.755	0.989	CLONAL	1	TRUE	1	0.273114587681094	2		963	574	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412988	63412988	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	82	986	0	ENST00000330258.3:c.179T>A	p.Phe60Tyr	p.F60Y	ENST00000330258	NM_152424.3	60	tTt/tAt	2/2	1	2	FACETS	0.89	0.784	1	0.89	0.784	1	CLONAL	1	TRUE	1	0.273114587681094	2		986	675	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344161	70344161	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	30	580	0	ENST00000374080.3:c.1897C>G	p.Pro633Ala	p.P633A	ENST00000374080		633	Cct/Gct	13/45	1	2	FACETS	0.511	0.411	0.624	0.511	0.411	0.624	SUBCLONAL	1	TRUE	1	0.273114587681094	2		580	430	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360708	70360708	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	14	156	0	ENST00000374080.3:c.6267+1G>T		p.X2089_splice	ENST00000374080		2089			1	2	FACETS	0.566	0.41	0.754	0.566	0.41	0.754	SUBCLONAL	1	TRUE	1	0.273114587681094	2		156	181	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76777865	76777865	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	28	590	1	ENST00000373344.5:c.6851G>T	p.Gly2284Val	p.G2284V	ENST00000373344	NM_000489.3	2284	gGa/gTa	32/35	1	2	FACETS	0.683	0.547	0.838	0.683	0.547	0.838	SUBCLONAL	1	TRUE	1	0.273114587681094	2		591	300	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891418	76891418	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	21	565	2	ENST00000373344.5:c.4687C>A	p.His1563Asn	p.H1563N	ENST00000373344	NM_000489.3	1563	Cat/Aat	16/35	1	2	FACETS	0.373	0.287	0.475	0.373	0.287	0.475	SUBCLONAL	1	TRUE	1	0.273114587681094	2		567	412	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019590	123019590	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	29	650	0	ENST00000355640.3:c.78G>T	p.Glu26Asp	p.E26D	ENST00000355640		26	gaG/gaT	2/7	1	2	FACETS	0.451	0.361	0.553	0.451	0.361	0.553	SUBCLONAL	1	TRUE	1	0.273114587681094	2		650	471	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627698	37627698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	1002	43	0	ENST00000447079.4:c.1613C>T	p.Pro538Leu	p.P538L	ENST00000447079	NM_015083.1	538	cCt/cTt	2/14	0.273114587681094	5	FACETS	1	0.982	1	1	0.999	1	CLONAL	6	TRUE	2	0.273114587681094	5		43	1710	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627694	37627694	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	44	950	0	ENST00000447079.4:c.1613del	p.Pro538LeufsTer72	p.P538Lfs*72	ENST00000447079	NM_015083.1	537	Ccc/cc	2/14	0.273114587681094	5	FACETS	0.631	0.528	0.746	0.21	0.176	0.249	SUBCLONAL	1	TRUE	2	0.273114587681094	5		950	720	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104377133	104377133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	850	36	0	ENST00000369902.3:c.1244G>A	p.Gly415Asp	p.G415D	ENST00000369902	NM_016169.3	415	gGc/gAc	10/12	1	2	FACETS	0.97	0.947	0.993			1	CLONAL	5	TRUE	1	0.273114587681094	2		36	1283	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112769491	112769491	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	25	640	0	ENST00000369452.4:c.1443C>A	p.Asn481Lys	p.N481K	ENST00000369452	NM_007373.3	481	aaC/aaA	8/9	1	2	FACETS	0.587	0.463	0.729	0.587	0.463	0.729	SUBCLONAL	1	TRUE	1	0.273114587681094	2		640	312	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828824	26828824	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	454	31	0	ENST00000381527.3:c.46G>T	p.Val16Phe	p.V16F	ENST00000381527	NM_001260.1	16	Gtc/Ttc	1/13	0.269647175290476	2	FACETS	0.927	0.896	0.959	1	0.998	1	CLONAL	5	TRUE	0	0.273114587681094	2		31	717	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872619	136872619	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	32	565	0	ENST00000241393.3:c.879C>G	p.Phe293Leu	p.F293L	ENST00000241393	NM_003467.2	293	ttC/ttG	2/2	0.273114587681094	3	FACETS	0.79	0.643	0.957	0.263	0.214	0.319	CLONAL	1	TRUE	0	0.273114587681094	3		565	337	SUCCESS
ATR	545	MSKCC	GRCh37	3	142224035	142224035	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	747	27	0	ENST00000350721.4:c.5142G>T	p.Leu1714Phe	p.L1714F	ENST00000350721	NM_001184.3	1714	ttG/ttT	29/47	0.273114587681094	3	FACETS	1	0.99	1	1	0.998	1	CLONAL	5	TRUE	1	0.273114587681094	3		27	1201	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509127	66509127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	480	15	0	ENST00000273854.3:c.200G>C	p.Arg67Pro	p.R67P	ENST00000273854	NM_004439.5	67	cGc/cCc	2/18	1	2	FACETS	1	0.979	1	1	0.998	1	CLONAL	5	TRUE	1	0.273114587681094	2		15	694	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90976731	90976731	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	17	536	0	ENST00000265433.3:c.901G>T	p.Gly301Cys	p.G301C	ENST00000265433	NM_002485.4	301	Ggt/Tgt	8/16	0.273114587681094	3	FACETS	0.452	0.337	0.589	0.151	0.112	0.197	SUBCLONAL	1	TRUE	0	0.273114587681094	3		536	313	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	485	620	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.938	0.906	0.968	1	0.997	1	CLONAL	2	TRUE	1	0.67	2		620	772	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	339	863	2	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	0.919	0.87	0.969	0.919	0.87	0.969	CLONAL	1	TRUE	1	0.67	2		865	1101	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	335	778	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.923	0.874	0.974	0.923	0.874	0.974	CLONAL	1	TRUE	1	0.67	2		783	1083	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	216	616	10	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	0.3	2	FACETS	0.965	0.902	1			1	INDETERMINATE	1	TRUE	NA	0.67	2		626	668	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795049	45795049	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs182537898	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	72	740	0	ENST00000450313.1:c.1579C>T	p.Gln527Ter	p.Q527*	ENST00000450313	NM_012222.2	527	Caa/Taa	16/16	1	2	FACETS	0.236	0.206	0.27	0.236	0.206	0.27	SUBCLONAL	1	TRUE	1	0.67	2		740	909	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550799	150550799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	287	603	0	ENST00000369026.2:c.857G>A	p.Cys286Tyr	p.C286Y	ENST00000369026	NM_021960.4	286	tGc/tAc	2/3	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.67	2		603	851	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253389	226253389	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	137	244	0	ENST00000366813.1:c.161G>A	p.Arg54His	p.R54H	ENST00000366813		54	cGt/cAt	2/3	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.67	2		244	398	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253418	226253418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	15	98	0	ENST00000366813.1:c.190C>T	p.Arg64Cys	p.R64C	ENST00000366813		64	Cgc/Tgc	2/3	1	2	FACETS	0.339	0.25	0.445	0.339	0.25	0.445	SUBCLONAL	1	TRUE	1	0.67	2		98	132	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	296	866	6	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.67	2		872	853	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998499	100998499	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs781055805	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	210	752	0	ENST00000325455.5:c.1303G>C	p.Gly435Arg	p.G435R	ENST00000325455	NM_001202474.3	435	Ggg/Cgg	1/8	1	2	FACETS	0.94	0.877	1	0.94	0.877	1	CLONAL	1	TRUE	1	0.67	2		752	667	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129749	108129749	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs780619951	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	230	701	0	ENST00000278616.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000278616	NM_000051.3	805	Cga/Tga	16/63	1	2	FACETS	0.83	0.776	0.886	0.83	0.776	0.886	CLONAL	1	TRUE	1	0.67	2		701	827	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022502	12022502	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1232497641	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	188	739	1	ENST00000396373.4:c.613del	p.Leu205TrpfsTer4	p.L205Wfs*4	ENST00000396373	NM_001987.4	203	tCc/tc	5/8	0.3	3	FACETS	0.89	0.823	0.959			1	INDETERMINATE	1	TRUE	NA	0.67	3		740	842	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628627	21628627	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	220	769	0	ENST00000421138.2:c.1081T>C	p.Ser361Pro	p.S361P	ENST00000421138		361	Tca/Cca	10/16	1	2	FACETS	0.964	0.902	1	0.964	0.902	1	CLONAL	1	TRUE	1	0.67	2		769	681	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420271	49420271	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	272	752	0	ENST00000301067.7:c.15478del	p.Asp5160ThrfsTer3	p.D5160Tfs*3	ENST00000301067	NM_003482.3	5160	Gac/ac	48/54	1	2	FACETS	0.882	0.829	0.936	0.882	0.829	0.936	CLONAL	1	TRUE	1	0.67	2		752	921	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439880	49439881	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	287	842	0	ENST00000301067.7:c.4660_4661del	p.Val1554LeufsTer48	p.V1554Lfs*48	ENST00000301067	NM_003482.3	1554	GTc/c	17/54	1	2	FACETS	0.944	0.889	0.999	0.944	0.889	0.999	CLONAL	1	TRUE	1	0.67	2		842	908	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434356	121434356	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	166	764	1	ENST00000257555.6:c.1124del	p.Gly375AlafsTer9	p.G375Afs*9	ENST00000257555		374	Ggg/gg	6/10	1	2	FACETS	0.609	0.56	0.66	0.609	0.56	0.66	SUBCLONAL	1	TRUE	1	0.67	2		765	814	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874028	123874028	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1296362061	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	53	77	1	ENST00000330479.4:c.59C>T	p.Ala20Val	p.A20V	ENST00000330479	NM_020382.3	20	gCg/gTg	2/9	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.67	2		78	126	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964077	28964077	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1565998842	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	53	586	0	ENST00000282397.4:c.1825del	p.Met609TrpfsTer16	p.M609Wfs*16	ENST00000282397	NM_002019.4	609	Atg/tg	13/30	1	2	FACETS	0.212	0.18	0.247	0.212	0.18	0.247	SUBCLONAL	1	TRUE	1	0.67	2		586	747	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134253	41134253	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	36	502	0	ENST00000379561.5:c.1375C>T	p.Pro459Ser	p.P459S	ENST00000379561	NM_002015.3	459	Cct/Tct	2/3	1	2	FACETS	0.189	0.155	0.227	0.189	0.155	0.227	SUBCLONAL	1	TRUE	1	0.67	2		502	569	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515285	103515285	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	204	433	0	ENST00000355739.4:c.1786G>A	p.Ala596Thr	p.A596T	ENST00000355739	NM_000123.3	596	Gca/Aca	8/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.67	2		433	547	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518071	103518071	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	117	375	0	ENST00000355739.4:c.2009T>C	p.Phe670Ser	p.F670S	ENST00000355739	NM_000123.3	670	tTc/tCc	9/15	1	2	FACETS	0.764	0.693	0.838	0.764	0.693	0.838	SUBCLONAL	1	TRUE	1	0.67	2		375	457	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872901	35872901	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	211	606	0	ENST00000216797.5:c.331C>T	p.Gln111Ter	p.Q111*	ENST00000216797	NM_020529.2	111	Cag/Tag	2/6	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.67	2		606	619	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707969	43707969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140309161	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	296	971	1	ENST00000382044.4:c.4912G>A	p.Val1638Ile	p.V1638I	ENST00000382044	NM_001141980.1	1638	Gtc/Atc	23/28	1	2	FACETS	0.803	0.756	0.851	0.803	0.756	0.851	CLONAL	1	TRUE	1	0.67	2		972	1101	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820594	3820594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376623633	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	51	847	0	ENST00000262367.5:c.2857C>T	p.His953Tyr	p.H953Y	ENST00000262367	NM_004380.2	953	Cac/Tac	14/31	1	2	FACETS	0.158	0.134	0.185	0.158	0.134	0.185	SUBCLONAL	1	TRUE	1	0.67	2		847	962	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646980	23646981	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	115	882	0	ENST00000261584.4:c.886dup	p.Met296AsnfsTer7	p.M296Nfs*7	ENST00000261584	NM_024675.3	296	atg/aAtg	4/13	1	2	FACETS	0.328	0.294	0.363	0.328	0.294	0.363	SUBCLONAL	1	TRUE	1	0.67	2		882	1047	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100669	67100669	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	289	766	0	ENST00000412916.2:c.367G>A	p.Gly123Ser	p.G123S	ENST00000412916		123	Ggc/Agc	4/6	1	2	FACETS	0.948	0.894	1	0.948	0.894	1	CLONAL	1	TRUE	1	0.67	2		766	910	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116168	67116168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1467426352	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	282	638	0	ENST00000412916.2:c.452G>A	p.Arg151His	p.R151H	ENST00000412916		151	cGc/cAc	5/6	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.67	2		638	819	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822174	72822174	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	261	757	1	ENST00000268489.5:c.10001C>A	p.Pro3334His	p.P3334H	ENST00000268489	NM_006885.3	3334	cCt/cAt	10/10	1	2	FACETS	0.968	0.91	1	0.968	0.91	1	CLONAL	1	TRUE	1	0.67	2		758	805	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822351	72822351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs62639993	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	375	1052	0	ENST00000268489.5:c.9824C>T	p.Pro3275Leu	p.P3275L	ENST00000268489	NM_006885.3	3275	cCg/cTg	10/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.67	2		1052	1022	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	304	862	0	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	1	2	FACETS	0.985	0.931	1	0.985	0.931	1	CLONAL	1	TRUE	1	0.67	2		862	921	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982805	7982805	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs989755310	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	213	983	2	ENST00000319144.4:c.980T>C	p.Val327Ala	p.V327A	ENST00000319144	NM_001139.2	327	gTg/gCg	8/15	1	2	FACETS	0.672	0.625	0.721	0.672	0.625	0.721	SUBCLONAL	1	TRUE	1	0.67	2		985	946	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687471	37687472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs760014508	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	104	350	2	ENST00000447079.4:c.4382dup	p.Thr1463AsnfsTer50	p.T1463Nfs*50	ENST00000447079	NM_015083.1	1459	tgg/tGgg	14/14	1	2	FACETS	0.815	0.736	0.897	0.815	0.736	0.897	CLONAL	1	TRUE	1	0.67	2		352	381	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727975	78727975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148973724	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	185	482	0	ENST00000306801.3:c.820G>A	p.Ala274Thr	p.A274T	ENST00000306801	NM_020761.2	274	Gcc/Acc	6/34	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.67	2		482	472	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617671	39617671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	100	494	0	ENST00000262039.4:c.1855G>A	p.Ala619Thr	p.A619T	ENST00000262039	NM_002647.2	619	Gca/Aca	17/25	1	2	FACETS	0.626	0.562	0.693	0.626	0.562	0.693	SUBCLONAL	1	TRUE	1	0.67	2		494	477	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210741	2210741	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	260	668	2	ENST00000398665.3:c.1238G>A	p.Arg413His	p.R413H	ENST00000398665	NM_032482.2	413	cGc/cAc	14/28	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.67	2		670	751	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210754	5210754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768674983	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	350	979	0	ENST00000357368.4:c.5297G>A	p.Arg1766His	p.R1766H	ENST00000357368	NM_002850.3	1766	cGc/cAc	34/38	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.67	2		979	1042	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	236	672	1	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	0.87	0.814	0.927	0.87	0.814	0.927	CLONAL	1	TRUE	1	0.67	2		673	810	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123700	11123700	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	281	845	2	ENST00000358026.2:c.2350G>A	p.Gly784Arg	p.G784R	ENST00000358026	NM_001128849.1	784	Ggg/Agg	16/36	1	2	FACETS	0.965	0.91	1	0.965	0.91	1	CLONAL	1	TRUE	1	0.67	2		847	869	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281251	15281251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1245716605	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	331	984	0	ENST00000263388.2:c.5005C>T	p.Arg1669Cys	p.R1669C	ENST00000263388	NM_000435.2	1669	Cgc/Tgc	27/33	1	2	FACETS	0.995	0.942	1	0.995	0.942	1	CLONAL	1	TRUE	1	0.67	2		984	993	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290908	15290908	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	327	1052	1	ENST00000263388.2:c.3302G>A	p.Gly1101Asp	p.G1101D	ENST00000263388	NM_000435.2	1101	gGc/gAc	20/33	1	2	FACETS	0.959	0.907	1	0.959	0.907	1	CLONAL	1	TRUE	1	0.67	2		1053	1018	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273883	18273883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149367522	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	245	835	0	ENST00000222254.8:c.1216C>T	p.Arg406Cys	p.R406C	ENST00000222254	NM_005027.3	406	Cgc/Tgc	10/16	1	2	FACETS	0.751	0.702	0.801	0.751	0.702	0.801	SUBCLONAL	1	TRUE	1	0.67	2		835	974	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976946	18976946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763281916	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	228	675	1	ENST00000262803.5:c.3331G>A	p.Gly1111Arg	p.G1111R	ENST00000262803	NM_002911.3	1111	Ggg/Agg	23/24	1	2	FACETS	0.994	0.93	1	0.994	0.93	1	CLONAL	1	TRUE	1	0.67	2		676	685	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	158	973	8	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	1	2	FACETS	0.431	0.394	0.469	0.431	0.394	0.469	SUBCLONAL	1	TRUE	1	0.67	2		981	1095	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223190	36223190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs949745356	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	242	1130	1	ENST00000222270.7:c.5740C>T	p.Arg1914Cys	p.R1914C	ENST00000222270	NM_014727.1	1914	Cgt/Tgt	28/37	1	2	FACETS	0.611	0.57	0.654	0.611	0.57	0.654	SUBCLONAL	1	TRUE	1	0.67	2		1131	1182	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	67	475	4	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	1	2	FACETS	0.503	0.438	0.571	0.503	0.438	0.571	SUBCLONAL	1	TRUE	1	0.67	2		479	398	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449824	29449824	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778021	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	82	1107	2	ENST00000389048.3:c.3031G>A	p.Gly1011Arg	p.G1011R	ENST00000389048	NM_004304.4	1011	Ggg/Agg	18/29	1	2	FACETS	0.223	0.196	0.253	0.223	0.196	0.253	SUBCLONAL	1	TRUE	1	0.67	2		1109	1097	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451783	29451784	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs772809305	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	142	858	2	ENST00000389048.3:c.2781dup	p.Cys928ValfsTer20	p.C928Vfs*20	ENST00000389048	NM_004304.4	927	-/G	16/29	1	2	FACETS	0.531	0.484	0.58	0.531	0.484	0.58	SUBCLONAL	1	TRUE	1	0.67	2		860	798	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213168	39213170	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs1272230145	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	83	984	0	ENST00000402219.2:c.3797_3799del	p.Pro1266del	p.P1266del	ENST00000402219	NM_005633.3	1266	cCTCac/cac	23/23	1	2	FACETS	0.239	0.21	0.27	0.239	0.21	0.27	SUBCLONAL	1	TRUE	1	0.67	2		984	1038	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151254	202151254	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	55	640	0	ENST00000358485.4:c.1557del	p.Lys520AsnfsTer10	p.K520Nfs*10	ENST00000358485	NM_001080125.1	518	atG/at	9/9	1	2	FACETS	0.204	0.174	0.237	0.204	0.174	0.237	SUBCLONAL	1	TRUE	1	0.67	2		640	804	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342934	225342934	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	265	637	0	ENST00000264414.4:c.2158A>G	p.Asn720Asp	p.N720D	ENST00000264414	NM_003590.4	720	Aat/Gat	15/16	1	2	FACETS	0.943	0.887	1	0.943	0.887	1	CLONAL	1	TRUE	1	0.67	2		637	839	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661664	227661664	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs761880048	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	151	575	11	ENST00000305123.5:c.1791del	p.His598ThrfsTer38	p.H598Tfs*38	ENST00000305123	NM_005544.2	597	ggG/gg	1/2	1	2	FACETS	0.912	0.84	0.987	0.912	0.84	0.987	CLONAL	1	TRUE	1	0.67	2		586	494	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092936	29092936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	306	715	1	ENST00000328354.6:c.1048C>T	p.Pro350Ser	p.P350S	ENST00000328354	NM_007194.3	350	Cca/Tca	10/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.67	2		716	888	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928945	49928945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	288	1030	1	ENST00000296474.3:c.3421C>T	p.Pro1141Ser	p.P1141S	ENST00000296474	NM_002447.2	1141	Ccg/Tcg	16/20	1	2	FACETS	0.914	0.861	0.967	0.914	0.861	0.967	CLONAL	1	TRUE	1	0.67	2		1031	941	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138409867	138409867	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	172	650	1	ENST00000289153.2:c.2011G>T	p.Gly671Trp	p.G671W	ENST00000289153	NM_006219.2	671	Ggg/Tgg	13/22	1	2	FACETS	0.695	0.641	0.751	0.695	0.641	0.751	SUBCLONAL	1	TRUE	1	0.67	2		651	739	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189349366	189349366	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs766583971	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	169	368	0	ENST00000264731.3:c.62G>A	p.Arg21His	p.R21H	ENST00000264731	NM_003722.4	21	cGt/cAt	1/14	1	2	FACETS	0.978	0.906	1	0.978	0.906	1	CLONAL	1	TRUE	1	0.67	2		368	516	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	204	567	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.841	0.783	0.901	0.841	0.783	0.901	CLONAL	1	TRUE	1	0.67	2		567	724	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31521250	31521250	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	318	832	0	ENST00000344624.3:c.927del	p.Glu310SerfsTer42	p.E310Sfs*42	ENST00000344624		309	aaA/aa	3/33	1	2	FACETS	0.933	0.882	0.985	0.933	0.882	0.985	CLONAL	1	TRUE	1	0.67	2		832	1017	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945141	38945141	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	111	371	0	ENST00000357387.3:c.4663T>C	p.Cys1555Arg	p.C1555R	ENST00000357387	NM_152756.3	1555	Tgt/Cgt	35/38	1	2	FACETS	0.81	0.734	0.889	0.81	0.734	0.889	CLONAL	1	TRUE	1	0.67	2		371	409	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38957755	38957755	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	211	543	0	ENST00000357387.3:c.2498G>A	p.Arg833Lys	p.R833K	ENST00000357387	NM_152756.3	833	aGg/aAg	25/38	1	2	FACETS	0.928	0.865	0.991	0.928	0.865	0.991	CLONAL	1	TRUE	1	0.67	2		543	679	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589576	67589576	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1289537429	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	142	362	0	ENST00000274335.5:c.1344del	p.Lys448AsnfsTer32	p.K448Nfs*32	ENST00000274335		447	Aaa/aa	10/15	1	2	FACETS	0.914	0.839	0.99	0.914	0.839	0.99	CLONAL	1	TRUE	1	0.67	2		362	464	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510113	149510113	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	274	765	0	ENST00000261799.4:c.1356A>C	p.Arg452Ser	p.R452S	ENST00000261799	NM_002609.3	452	agA/agC	9/23	1	2	FACETS	0.902	0.848	0.956	0.902	0.848	0.956	CLONAL	1	TRUE	1	0.67	2		765	907	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192645	138192645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776714084	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	32	465	0	ENST00000237289.4:c.281C>T	p.Ala94Val	p.A94V	ENST00000237289	NM_001270507.1	94	gCg/gTg	2/9	1	2	FACETS	0.151	0.122	0.184	0.151	0.122	0.184	SUBCLONAL	1	TRUE	1	0.67	2		465	633	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199889	138199889	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	168	479	0	ENST00000237289.4:c.1307G>A	p.Gly436Glu	p.G436E	ENST00000237289	NM_001270507.1	436	gGg/gAg	7/9	1	2	FACETS	0.979	0.907	1	0.979	0.907	1	CLONAL	1	TRUE	1	0.67	2		479	512	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	272	663	4	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.912	0.858	0.968	0.912	0.858	0.968	CLONAL	1	TRUE	1	0.67	2		667	890	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220281	55220281	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759106015	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	353	899	1	ENST00000275493.2:c.671G>A	p.Arg224His	p.R224H	ENST00000275493	NM_005228.3	224	cGt/cAt	6/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.67	2		900	1003	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38196074	38196074	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771088864	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	384	990	0	ENST00000317025.8:c.727G>A	p.Val243Ile	p.V243I	ENST00000317025	NM_023034.1	243	Gta/Ata	3/24	1	2	FACETS	0.968	0.92	1	0.968	0.92	1	CLONAL	1	TRUE	1	0.67	2		990	1184	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863054	56863054	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1266824391	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	312	481	0	ENST00000519728.1:c.327del	p.Glu110LysfsTer15	p.E110Kfs*15	ENST00000519728	NM_002350.3	107	acA/ac	5/13	1	2	FACETS	0.972	0.919	1	0.972	0.919	1	CLONAL	1	TRUE	1	0.67	2		481	958	SUCCESS
AR	367	MSKCC	GRCh37	X	66765149	66765151	+	inframe_deletion	In_Frame_Del	DEL	TGC	TGC	-	rs752055010	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	10	165	0	ENST00000374690.3:c.170_172del	p.Leu57del	p.L57del	ENST00000374690	NM_000044.3	54	tTGCtg/ttg	1/8	1	1	FACETS	0.16	0.109	0.224	0.16	0.109	0.224	SUBCLONAL	1	TRUE	0	0.67	1		165	124	SUCCESS
AR	367	MSKCC	GRCh37	X	66765158	66765158	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs78686797	NA	P-0021519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	32	134	2	ENST00000374690.3:c.170T>A	p.Leu57Gln	p.L57Q	ENST00000374690	NM_000044.3	57	cTg/cAg	1/8	1	1	FACETS	0.683	0.571	0.801	0.683	0.571	0.801	SUBCLONAL	1	TRUE	0	0.67	1		136	93	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021586-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	258	650	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.6	2		650	655	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820995	36820995	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749607113	NA	P-0021586-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	304	724	0	ENST00000373129.3:c.382C>T	p.Arg128Trp	p.R128W	ENST00000373129	NM_032017.1	128	Cgg/Tgg	6/12	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.6	2		724	763	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226169	53226179	+	frameshift_variant	Frame_Shift_Del	DEL	GTGAGGCCAGG	GTGAGGCCAGG	-	novel	NA	P-0021586-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	267	623	0	ENST00000375401.3:c.2670_2680del	p.Leu891AlafsTer23	p.L891Afs*23	ENST00000375401	NM_004187.3	890	gcCCTGGCCTCACtg/gctg	19/26	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.6	2		623	627	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	131	521	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.916	0.833	1	0.916	0.833	1	CLONAL	1	TRUE	1	0.469151442913583	2		521	610	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647657	3647657	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs774532876	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	235	878	3	ENST00000294008.3:c.1406del	p.Pro469HisfsTer4	p.P469Hfs*4	ENST00000294008	NM_032444.2	469	cCa/ca	7/15	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.469151442913583	2		881	1000	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	111	512	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.98	0.885	1	0.98	0.885	1	CLONAL	1	TRUE	1	0.469151442913583	2		512	483	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	199	778	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.89	0.825	0.958	0.89	0.825	0.958	CLONAL	1	TRUE	1	0.469151442913583	2		783	953	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	146	823	8	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.8	0.731	0.872	0.8	0.731	0.872	SUBCLONAL	1	TRUE	1	0.469151442913583	2		831	778	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	163	717	12	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.469151442913583	2		729	658	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9770533	9770534	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	176	741	0	ENST00000377346.4:c.24dup	p.Met9HisfsTer15	p.M9Hfs*15	ENST00000377346	NM_005026.3	7	tgc/tgCc	3/24	1	2	FACETS	0.972	0.897	1	0.972	0.897	1	CLONAL	1	TRUE	1	0.469151442913583	2		741	772	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247851	59247851	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	241	905	2	ENST00000371222.2:c.892G>A	p.Ala298Thr	p.A298T	ENST00000371222	NM_002228.3	298	Gcc/Acc	1/1	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.469151442913583	2		907	995	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100407	8100407	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	153	776	0	ENST00000346208.3:c.384del	p.Leu130SerfsTer65	p.L130Sfs*65	ENST00000346208		127	ccG/cc	3/6	1	2	FACETS	0.976	0.896	1	0.976	0.896	1	CLONAL	1	TRUE	1	0.469151442913583	2		776	668	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	62	315	1	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	1	2	FACETS	0.806	0.701	0.918	0.806	0.701	0.918	CLONAL	1	TRUE	1	0.469151442913583	2		316	328	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649974	88649974	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1554888142	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	166	779	0	ENST00000372037.3:c.223A>G	p.Thr75Ala	p.T75A	ENST00000372037	NM_004329.2	75	Aca/Gca	4/13	1	2	FACETS	0.941	0.866	1	0.941	0.866	1	CLONAL	1	TRUE	1	0.469151442913583	2		779	752	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136996	64136996	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	198	699	0	ENST00000334205.4:c.1507G>C	p.Glu503Gln	p.E503Q	ENST00000334205	NM_003942.2	503	Gag/Cag	13/17	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.469151442913583	2		699	784	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589830	69589830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	44	91	0	ENST00000168712.1:c.23C>T	p.Ala8Val	p.A8V	ENST00000168712	NM_002007.2	8	gCg/gTg	1/3	1	2	FACETS	0.816	0.704	0.931	1	0.969	1	CLONAL	2	TRUE	1	0.469151442913583	2		91	115	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139269	108139269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782298	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	200	794	5	ENST00000278616.4:c.2771G>A	p.Arg924Gln	p.R924Q	ENST00000278616	NM_000051.3	924	cGg/cAg	18/63	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.469151442913583	2		799	775	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216477	108216477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587782558	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	76	313	0	ENST00000278616.4:c.8432del	p.Lys2811SerfsTer46	p.K2811Sfs*46	ENST00000278616	NM_000051.3	2809	cAa/ca	58/63	1	2	FACETS	0.967	0.855	1	0.967	0.855	1	CLONAL	1	TRUE	1	0.469151442913583	2		313	335	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426046	49426046	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	157	720	0	ENST00000301067.7:c.12442A>G	p.Met4148Val	p.M4148V	ENST00000301067	NM_003482.3	4148	Atg/Gtg	39/54	1	2	FACETS	0.924	0.849	1	0.924	0.849	1	CLONAL	1	TRUE	1	0.469151442913583	2		720	724	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250163	133250163	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	134	609	0	ENST00000320574.5:c.1357del	p.Gln453ArgfsTer19	p.Q453Rfs*19	ENST00000320574	NM_006231.2	453	Cag/ag	13/49	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.469151442913583	2		609	545	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923249	26923249	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	108	488	0	ENST00000381527.3:c.248del	p.Lys83ArgfsTer25	p.K83Rfs*25	ENST00000381527	NM_001260.1	82	cAa/ca	3/13	1	2	FACETS	0.938	0.846	1	0.938	0.846	1	CLONAL	1	TRUE	1	0.469151442913583	2		488	491	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105560	30105560	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	196	870	1	ENST00000331968.5:c.1126C>T	p.Gln376Ter	p.Q376*	ENST00000331968	NM_002742.2	376	Cag/Tag	7/18	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.469151442913583	2		871	766	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986991	36986991	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	101	538	1	ENST00000354822.5:c.698C>T	p.Thr233Met	p.T233M	ENST00000354822	NM_001079668.2	233	aCg/aTg	3/3	1	2	FACETS	0.882	0.792	0.977	0.882	0.792	0.977	CLONAL	1	TRUE	1	0.469151442913583	2		539	488	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239313	105239313	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	172	797	0	ENST00000349310.3:c.1074del	p.Phe358LeufsTer89	p.F358Lfs*89	ENST00000349310	NM_001014432.1	358	ttT/tt	12/15	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.469151442913583	2		797	716	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304140	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	160	622	0	ENST00000355112.3:c.1543_1544del	p.Asn515Ter	p.N515*	ENST00000355112	NM_000057.2	512	ggAAaa/ggaa	7/22	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.469151442913583	2		622	681	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99192888	99192888	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	107	515	0	ENST00000268035.6:c.78G>A	p.Trp26Ter	p.W26*	ENST00000268035	NM_000875.3	26	tgG/tgA	1/21	1	2	FACETS	0.849	0.765	0.939	0.849	0.765	0.939	CLONAL	1	TRUE	1	0.469151442913583	2		515	537	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828111	3828111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	186	742	0	ENST00000262367.5:c.2014C>T	p.Arg672Cys	p.R672C	ENST00000262367	NM_004380.2	672	Cgt/Tgt	10/31	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.469151442913583	2		742	740	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943635	9943635	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555496111	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	129	749	0	ENST00000330684.3:c.1306T>C	p.Cys436Arg	p.C436R	ENST00000330684	NM_001134407.1	436	Tgt/Cgt	5/13	1	2	FACETS	0.808	0.733	0.885	0.808	0.733	0.885	CLONAL	1	TRUE	1	0.469151442913583	2		749	681	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348863	11348863	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	49	207	0	ENST00000332029.2:c.473C>G	p.Pro158Arg	p.P158R	ENST00000332029	NM_003745.1	158	cCg/cGg	2/2	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.469151442913583	2		207	196	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647027	23647028	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	195	786	0	ENST00000261584.4:c.839dup	p.Asn280LysfsTer3	p.N280Kfs*3	ENST00000261584	NM_024675.3	280	aac/aaAc	4/13	1	2	FACETS	0.925	0.856	0.995	0.925	0.856	0.995	CLONAL	1	TRUE	1	0.469151442913583	2		786	899	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835780	68835781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	120	634	0	ENST00000261769.5:c.377dup	p.Pro127AlafsTer41	p.P127Afs*41	ENST00000261769	NM_004360.3	124	cgc/cgCc	3/16	1	2	FACETS	0.685	0.619	0.755	0.685	0.619	0.755	SUBCLONAL	1	TRUE	1	0.469151442913583	2		634	747	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81962229	81962229	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs559219743	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	43	613	0	ENST00000359376.3:c.2581G>A	p.Val861Met	p.V861M	ENST00000359376	NM_002661.3	861	Gtg/Atg	24/33	1	2	FACETS	0.266	0.222	0.315	0.266	0.222	0.315	SUBCLONAL	1	TRUE	1	0.469151442913583	2		613	689	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346424	89346424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1228696930	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	152	711	2	ENST00000301030.4:c.6526G>A	p.Gly2176Ser	p.G2176S	ENST00000301030	NM_001256183.1	2176	Ggt/Agt	9/13	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.469151442913583	2		713	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	185	644	1	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.469151442913583	2		645	761	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	167	651	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.469151442913583	2		651	582	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032577	12032577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371746849	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	117	649	0	ENST00000353533.5:c.1013C>T	p.Pro338Leu	p.P338L	ENST00000353533	NM_003010.3	338	cCg/cTg	9/11	1	2	FACETS	0.863	0.781	0.949	0.863	0.781	0.949	CLONAL	1	TRUE	1	0.469151442913583	2		649	578	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435160	56435161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	104	664	0	ENST00000407977.2:c.1975_1976dup	p.Pro660ValfsTer41	p.P660Vfs*41	ENST00000407977		659	ggt/ggGGt	9/10	1	2	FACETS	0.621	0.556	0.69	0.621	0.556	0.69	SUBCLONAL	1	TRUE	1	0.469151442913583	2		664	714	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435815	56435815	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755967475	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	87	524	0	ENST00000407977.2:c.1322del	p.Pro441LeufsTer61	p.P441Lfs*61	ENST00000407977		441	cCt/ct	9/10	1	2	FACETS	0.787	0.7	0.88	0.787	0.7	0.88	SUBCLONAL	1	TRUE	1	0.469151442913583	2		524	471	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439936	56439936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377765604	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	209	564	3	ENST00000407977.2:c.656G>A	p.Arg219His	p.R219H	ENST00000407977		219	cGc/cAc	6/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.469151442913583	2		567	709	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821817	59821817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780235	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	188	706	1	ENST00000259008.2:c.2233G>A	p.Ala745Thr	p.A745T	ENST00000259008	NM_032043.2	745	Gca/Aca	15/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.469151442913583	2		707	713	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119084	70120018	+	splice_acceptor_variant,splice_donor_variant,frameshift_variant,stop_lost,intron_variant	Splice_Site	DEL	GCGAGGTGCACTCCCCCGGCGAGCACTCGGGTGAGTCGCCCCTCGACCCCACCGGACAAGCTATCTCCGTCCCGCCTGGCACACCCCCTGCCCTCCGCCTGGGAGATTCTTCGTGGGGACTTTATGCTTCCCGGGAGGGACACACTGCCCTTTGCGCCCGTCCCGCTCCCCTCTCTACCCAGAGCCTAAGAGGCATCCAAACAACACACACACAAACACACACACCCCAACTCAATCCCAGCATCCGAAGAGATTAACTTTTTTATTGGGAGGTAAAATGCCCTTAACAGCCTTACAAGACCTCTCCCTTCTTCTCTGCTCCCCCACCCCAAAAGCACACACAGGGCTCTTACACAAGTAGCAATTAGGTCTTCCGGACCCTCCGGGCCCCAGACCCTCCCCTGATAAAAGGGGGCTGTCCAGTGTGTACCGGCGGGTTAATCATTGGGCGACTTATCTCCGGTGCAGCGCGCCTCTTGCGCGGGTGCGGGCCCTTATTACACTTTAGCAGCGAGGGAGGGTCCCCGGAGGGTGCCTAAGACTAGGGCGTCTGCACAGCCCTTGTTGATTTTCTCGTGCTTGTTCTTTTATTGTCCACAGGGCAATCCCAGGGCCCACCGACCCCACCCACCACCCCCAAAACCGACGTGCAGCCGGGCAAGGCTGACCTGAAGCGAGAGGGGCGCCCCTTGCCAGAGGGGGGCAGACAGCCCCCTATCGACTTCCGCGACGTGGACATCGGCGAGCTGAGCAGCGACGTCATCTCCAACATCGAGACCTTCGATGTCAACGAGTTTGACCAGTACCTGCCGCCCAACGGCCACCCGGGGGTGCCGGCCACGCACGGCCAGGTCACCTACACGGGCAGCTACGGCATCAGCAGCACCGCGGCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAG	GCGAGGTGCACTCCCCCGGCGAGCACTCGGGTGAGTCGCCCCTCGACCCCACCGGACAAGCTATCTCCGTCCCGCCTGGCACACCCCCTGCCCTCCGCCTGGGAGATTCTTCGTGGGGACTTTATGCTTCCCGGGAGGGACACACTGCCCTTTGCGCCCGTCCCGCTCCCCTCTCTACCCAGAGCCTAAGAGGCATCCAAACAACACACACACAAACACACACACCCCAACTCAATCCCAGCATCCGAAGAGATTAACTTTTTTATTGGGAGGTAAAATGCCCTTAACAGCCTTACAAGACCTCTCCCTTCTTCTCTGCTCCCCCACCCCAAAAGCACACACAGGGCTCTTACACAAGTAGCAATTAGGTCTTCCGGACCCTCCGGGCCCCAGACCCTCCCCTGATAAAAGGGGGCTGTCCAGTGTGTACCGGCGGGTTAATCATTGGGCGACTTATCTCCGGTGCAGCGCGCCTCTTGCGCGGGTGCGGGCCCTTATTACACTTTAGCAGCGAGGGAGGGTCCCCGGAGGGTGCCTAAGACTAGGGCGTCTGCACAGCCCTTGTTGATTTTCTCGTGCTTGTTCTTTTATTGTCCACAGGGCAATCCCAGGGCCCACCGACCCCACCCACCACCCCCAAAACCGACGTGCAGCCGGGCAAGGCTGACCTGAAGCGAGAGGGGCGCCCCTTGCCAGAGGGGGGCAGACAGCCCCCTATCGACTTCCGCGACGTGGACATCGGCGAGCTGAGCAGCGACGTCATCTCCAACATCGAGACCTTCGATGTCAACGAGTTTGACCAGTACCTGCCGCCCAACGGCCACCCGGGGGTGCCGGCCACGCACGGCCAGGTCACCTACACGGGCAGCTACGGCATCAGCAGCACCGCGGCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAG	-	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	59	439	0	ENST00000245479.2:c.659_1023del		p.X220_splice	ENST00000245479	NM_000346.3	220	aGCGAGGTGCACTCCCCCGGCGAGCACTCGGGTGAGTCGCCCCTCGACCCCACCGGACAAGCTATCTCCGTCCCGCCTGGCACACCCCCTGCCCTCCGCCTGGGAGATTCTTCGTGGGGACTTTATGCTTCCCGGGAGGGACACACTGCCCTTTGCGCCCGTCCCGCTCCCCTCTCTACCCAGAGCCTAAGAGGCATCCAAACAACACACACACAAACACACACACCCCAACTCAATCCCAGCATCCGAAGAGATTAACTTTTTTATTGGGAGGTAAAATGCCCTTAACAGCCTTACAAGACCTCTCCCTTCTTCTCTGCTCCCCCACCCCAAAAGCACACACAGGGCTCTTACACAAGTAGCAATTAGGTCTTCCGGACCCTCCGGGCCCCAGACCCTCCCCTGATAAAAGGGGGCTGTCCAGTGTGTACCGGCGGGTTAATCATTGGGCGACTTATCTCCGGTGCAGCGCGCCTCTTGCGCGGGTGCGGGCCCTTATTACACTTTAGCAGCGAGGGAGGGTCCCCGGAGGGTGCCTAAGACTAGGGCGTCTGCACAGCCCTTGTTGATTTTCTCGTGCTTGTTCTTTTATTGTCCACAGGGCAATCCCAGGGCCCACCGACCCCACCCACCACCCCCAAAACCGACGTGCAGCCGGGCAAGGCTGACCTGAAGCGAGAGGGGCGCCCCTTGCCAGAGGGGGGCAGACAGCCCCCTATCGACTTCCGCGACGTGGACATCGGCGAGCTGAGCAGCGACGTCATCTCCAACATCGAGACCTTCGATGTCAACGAGTTTGACCAGTACCTGCCGCCCAACGGCCACCCGGGGGTGCCGGCCACGCACGGCCAGGTCACCTACACGGGCAGCTACGGCATCAGCAGCACCGCGGCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAG/a	2-3/3	1	2	FACETS	0.717	0.62	0.821	0.717	0.62	0.821	SUBCLONAL	1	TRUE	1	0.469151442913583	2		439	351	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274347	5274348	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	58	525	0	ENST00000357368.4:c.99dup	p.Arg34GlnfsTer26	p.R34Qfs*26	ENST00000357368	NM_002850.3	33	-/C	3/38	1	2	FACETS	0.528	0.455	0.608	0.528	0.455	0.608	SUBCLONAL	1	TRUE	1	0.469151442913583	2		525	468	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130337	11130337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs281875226	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	142	707	1	ENST00000358026.2:c.2576C>T	p.Thr859Met	p.T859M	ENST00000358026	NM_001128849.1	859	aCg/aTg	18/36	1	2	FACETS	0.864	0.789	0.942	0.864	0.789	0.942	CLONAL	1	TRUE	1	0.469151442913583	2		708	701	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288789	15288789	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	64	219	0	ENST00000263388.2:c.3950del	p.Pro1317GlnfsTer103	p.P1317Qfs*103	ENST00000263388	NM_000435.2	1317	cCa/ca	24/33	1	2	FACETS	0.971	0.849	1	0.971	0.849	1	CLONAL	1	TRUE	1	0.469151442913583	2		219	281	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349892	15349892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1427595023	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	159	534	2	ENST00000263377.2:c.3760C>T	p.Arg1254Trp	p.R1254W	ENST00000263377	NM_058243.2	1254	Cgg/Tgg	18/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.469151442913583	2		536	528	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18943041	18943041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	141	559	0	ENST00000262803.5:c.23C>T	p.Pro8Leu	p.P8L	ENST00000262803	NM_002911.3	8	cCc/cTc	1/24	1	2	FACETS	0.987	0.902	1	0.987	0.902	1	CLONAL	1	TRUE	1	0.469151442913583	2		559	609	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967091	18967092	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1384543747	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	134	755	0	ENST00000262803.5:c.1814_1815del	p.Glu605AlafsTer17	p.E605Afs*17	ENST00000262803	NM_002911.3	602	gcAGag/gcag	13/24	1	2	FACETS	0.74	0.673	0.811	0.74	0.673	0.811	SUBCLONAL	1	TRUE	1	0.469151442913583	2		755	772	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214899	36214899	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	177	738	0	ENST00000222270.7:c.3325C>T	p.Arg1109Ter	p.R1109*	ENST00000222270	NM_014727.1	1109	Cga/Tga	8/37	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.469151442913583	2		738	732	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793346	42793346	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	38	709	0	ENST00000575354.2:c.1148C>A	p.Pro383His	p.P383H	ENST00000575354	NM_015125.3	383	cCt/cAt	8/20	1	2	FACETS	0.251	0.207	0.301	0.251	0.207	0.301	SUBCLONAL	1	TRUE	1	0.469151442913583	2		709	645	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794819	42794820	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	115	559	0	ENST00000575354.2:c.1904dup	p.Asn636LysfsTer54	p.N636Kfs*54	ENST00000575354	NM_015125.3	633	-/C	10/20	1	2	FACETS	0.965	0.874	1	0.965	0.874	1	CLONAL	1	TRUE	1	0.469151442913583	2		559	508	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910394	50910394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	210	754	1	ENST00000440232.2:c.1649G>A	p.Gly550Asp	p.G550D	ENST00000440232	NM_002691.3	550	gGc/gAc	13/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.469151442913583	2		755	786	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607816	46607816	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	178	815	5	ENST00000263734.3:c.2009del	p.Pro670LeufsTer26	p.P670Lfs*26	ENST00000263734	NM_001430.4	669	Ccc/cc	12/16	1	2	FACETS	0.919	0.848	0.992	0.919	0.848	0.992	CLONAL	1	TRUE	1	0.469151442913583	2		820	826	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027807	48027807	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	132	530	0	ENST00000234420.5:c.2690del	p.Asn897IlefsTer9	p.N897Ifs*9	ENST00000234420	NM_000179.2	895	acA/ac	4/10	1	2	FACETS	0.902	0.821	0.986	0.902	0.821	0.986	CLONAL	1	TRUE	1	0.469151442913583	2		530	624	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587232	212587232	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	108	584	1	ENST00000342788.4:c.769G>T	p.Ala257Ser	p.A257S	ENST00000342788	NM_005235.2	257	Gca/Tca	7/28	1	2	FACETS	0.864	0.778	0.954	0.864	0.778	0.954	CLONAL	1	TRUE	1	0.469151442913583	2		585	533	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437223	220437223	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	195	871	1	ENST00000243786.2:c.132del	p.Ala45ArgfsTer2	p.A45Rfs*2	ENST00000243786	NM_002191.3	43	Ccc/cc	1/2	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.469151442913583	2		872	775	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	172	825	2	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.469151442913583	2		827	681	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017747	31017749	+	inframe_deletion	In_Frame_Del	DEL	CAG	CAG	-	rs745311249	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	129	645	7	ENST00000375687.4:c.619_621del	p.Ser207del	p.S207del	ENST00000375687	NM_015338.5	203	tcCAGc/tcc	8/13	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.469151442913583	2		652	483	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023045	31023046	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs750170870	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	179	701	0	ENST00000375687.4:c.2535dup	p.Ser846GlnfsTer5	p.S846Qfs*5	ENST00000375687	NM_015338.5	844	acc/aCcc	13/13	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.469151442913583	2		701	674	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395624	31395624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756972254	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	206	753	0	ENST00000328111.2:c.2477G>A	p.Arg826His	p.R826H	ENST00000328111	NM_006892.3	826	cGc/cAc	23/23	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.469151442913583	2		753	775	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281784	46281784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	192	837	0	ENST00000371998.3:c.4231C>T	p.Pro1411Ser	p.P1411S	ENST00000371998		1411	Ccc/Tcc	22/23	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.469151442913583	2		837	766	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961396	54961396	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	100	331	0	ENST00000312783.6:c.236T>G	p.Leu79Trp	p.L79W	ENST00000312783	NM_198436.1	79	tTg/tGg	4/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.469151442913583	2		331	361	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	117	463	2	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.823	0.744	0.906	0.823	0.744	0.906	CLONAL	1	TRUE	1	0.469151442913583	2		465	606	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62290766	62290766	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs758025445	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	23	261	0	ENST00000360203.5:c.11T>C	p.Ile4Thr	p.I4T	ENST00000360203	NM_001283009.1	4	aTa/aCa	2/35	1	2	FACETS	0.348	0.271	0.436	0.348	0.271	0.436	SUBCLONAL	1	TRUE	1	0.469151442913583	2		261	282	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292700	62292700	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	152	735	0	ENST00000360203.5:c.152G>A	p.Cys51Tyr	p.C51Y	ENST00000360203	NM_001283009.1	51	tGc/tAc	3/35	1	2	FACETS	0.97	0.89	1	0.97	0.89	1	CLONAL	1	TRUE	1	0.469151442913583	2		735	668	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091782	29091782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373073383	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	154	659	0	ENST00000328354.6:c.1175C>T	p.Ala392Val	p.A392V	ENST00000328354	NM_007194.3	392	gCg/gTg	11/15	1	2	FACETS	0.978	0.898	1	0.978	0.898	1	CLONAL	1	TRUE	1	0.469151442913583	2		659	671	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545897	41545897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1215000818	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	189	860	1	ENST00000263253.7:c.2512C>T	p.Arg838Cys	p.R838C	ENST00000263253	NM_001429.3	838	Cgt/Tgt	14/31	1	2	FACETS	0.928	0.859	1	0.928	0.859	1	CLONAL	1	TRUE	1	0.469151442913583	2		861	868	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713295	30713295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371209879	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	27	484	0	ENST00000295754.5:c.620G>A	p.Arg207Gln	p.R207Q	ENST00000295754	NM_003242.5	207	cGg/cAg	4/7	1	2	FACETS	0.234	0.186	0.29	0.234	0.186	0.29	SUBCLONAL	1	TRUE	1	0.469151442913583	2		484	491	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584478	52584478	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142726131	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	184	624	1	ENST00000394830.3:c.4535C>T	p.Ala1512Val	p.A1512V	ENST00000394830	NM_018313.4	1512	gCg/gTg	29/30	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.469151442913583	2		625	623	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	117	593	2	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	1	2	FACETS	0.881	0.797	0.969	0.881	0.797	0.969	CLONAL	1	TRUE	1	0.469151442913583	2		595	566	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998127	169998128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs753143066	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	242	823	9	ENST00000295797.4:c.826dup	p.Thr276AsnfsTer16	p.T276Nfs*16	ENST00000295797	NM_002740.5	273	tta/ttAa	9/18	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.469151442913583	2		832	1011	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156558	55156558	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	175	710	0	ENST00000257290.5:c.2959G>T	p.Ala987Ser	p.A987S	ENST00000257290	NM_006206.4	987	Gca/Tca	22/23	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.469151442913583	2		710	699	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242741	66242741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777294375	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	83	431	0	ENST00000273854.3:c.1831G>A	p.Ala611Thr	p.A611T	ENST00000273854	NM_004439.5	611	Gct/Act	9/18	1	2	FACETS	0.806	0.715	0.903	0.806	0.715	0.903	CLONAL	1	TRUE	1	0.469151442913583	2		431	439	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525698	187525698	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	139	481	0	ENST00000441802.2:c.10381C>T	p.Gln3461Ter	p.Q3461*	ENST00000441802	NM_005245.3	3461	Cag/Tag	18/27	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.469151442913583	2		481	521	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294408	1294408	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	186	656	2	ENST00000310581.5:c.593G>A	p.Gly198Glu	p.G198E	ENST00000310581	NM_198253.2	198	gGa/gAa	2/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.469151442913583	2		658	687	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876086	35876086	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	113	405	0	ENST00000303115.3:c.878A>G	p.Asn293Ser	p.N293S	ENST00000303115	NM_002185.3	293	aAt/aGt	8/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.469151442913583	2		405	383	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456907	149456907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	214	854	0	ENST00000286301.3:c.821G>A	p.Gly274Asp	p.G274D	ENST00000286301	NM_005211.3	274	gGc/gAc	6/22	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.469151442913583	2		854	731	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520545	176520545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770012793	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	182	732	0	ENST00000292408.4:c.1390C>T	p.Arg464Trp	p.R464W	ENST00000292408	NM_213647.1	464	Cgg/Tgg	10/18	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.469151442913583	2		732	713	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524552	176524552	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1163220407	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	189	867	0	ENST00000292408.4:c.2284G>A	p.Gly762Arg	p.G762R	ENST00000292408	NM_213647.1	762	Gga/Aga	18/18	1	2	FACETS	0.971	0.898	1	0.971	0.898	1	CLONAL	1	TRUE	1	0.469151442913583	2		867	830	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402833	20402833	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1216519626	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	16	54	0	ENST00000346618.3:c.370A>G	p.Ser124Gly	p.S124G	ENST00000346618	NM_001949.4	124	Agc/Ggc	1/7	0.469151442913583	1	FACETS	0.842	0.641	1	0.842	0.641	1	CLONAL	1	TRUE	0	0.469151442913583	1		54	62	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31947251	31947251	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	170	810	0	ENST00000375333.2:c.736G>A	p.Val246Ile	p.V246I	ENST00000375333	NM_032454.1	246	Gta/Ata	5/8	0.469151442913583	1	FACETS	0.965	0.892	1	0.965	0.892	1	CLONAL	1	TRUE	0	0.469151442913583	1		810	575	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818901	32818902	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	137	655	0	ENST00000354258.4:c.1049_1050del	p.Glu350GlyfsTer7	p.E350Gfs*7	ENST00000354258	NM_000593.5	350	gAG/g	4/11	0.469151442913583	1	FACETS	0.834	0.763	0.908	0.834	0.763	0.908	CLONAL	1	TRUE	0	0.469151442913583	1		655	536	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120753	94120754	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	150	613	0	ENST00000369303.4:c.297dup	p.Val100CysfsTer11	p.V100Cfs*11	ENST00000369303	NM_004440.3	99	-/T	3/17	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.469151442913583	2		613	629	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405954	157405954	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	132	631	3	ENST00000346085.5:c.2201del	p.Gly734AlafsTer11	p.G734Afs*11	ENST00000346085	NM_020732.3	732	ccG/cc	6/20	1	2	FACETS	0.962	0.877	1	0.962	0.877	1	CLONAL	1	TRUE	1	0.469151442913583	2		634	585	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6038876	6038876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	181	632	0	ENST00000265849.7:c.568G>A	p.Ala190Thr	p.A190T	ENST00000265849	NM_000535.5	190	Gca/Aca	6/15	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.469151442913583	2		632	759	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043349	6043349	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781716	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	58	247	2	ENST00000265849.7:c.325del	p.Glu109LysfsTer3	p.E109Kfs*3	ENST00000265849	NM_000535.5	109	Gaa/aa	4/15	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.469151442913583	2		249	218	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450279	50450279	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	117	646	0	ENST00000331340.3:c.463A>G	p.Thr155Ala	p.T155A	ENST00000331340	NM_006060.4	155	Acc/Gcc	5/8	1	2	FACETS	0.844	0.763	0.929	0.844	0.763	0.929	CLONAL	1	TRUE	1	0.469151442913583	2		646	591	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508235	106508235	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1448416221	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	81	358	1	ENST00000359195.3:c.229C>T	p.Arg77Ter	p.R77*	ENST00000359195	NM_002649.2	77	Cga/Tga	2/11	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.469151442913583	2		359	319	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508557	106508557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	44	284	0	ENST00000359195.3:c.551G>A	p.Arg184His	p.R184H	ENST00000359195	NM_002649.2	184	cGc/cAc	2/11	1	2	FACETS	0.856	0.726	0.998	0.856	0.726	0.998	CLONAL	1	TRUE	1	0.469151442913583	2		284	219	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992721	68992721	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs764112302	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	181	818	8	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	0.469151442913583	2		826	770	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965666	90965666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	113	542	0	ENST00000265433.3:c.1651del	p.Arg551GlyfsTer8	p.R551Gfs*8	ENST00000265433	NM_002485.4	551	Agg/gg	11/16	1	2	FACETS	0.886	0.8	0.975	0.886	0.8	0.975	CLONAL	1	TRUE	1	0.469151442913583	2		542	544	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862939	117862939	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	152	683	0	ENST00000297338.2:c.1538G>A	p.Cys513Tyr	p.C513Y	ENST00000297338	NM_006265.2	513	tGt/tAt	12/14	1	2	FACETS	0.888	0.813	0.965	0.888	0.813	0.965	CLONAL	1	TRUE	1	0.469151442913583	2		683	730	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971062	21971062	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754806883	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	62	508	2	ENST00000304494.5:c.296G>A	p.Arg99Gln	p.R99Q	ENST00000304494	NM_000077.4	99	cGg/cAg	2/3	1	2	FACETS	0.535	0.463	0.613	0.535	0.463	0.613	SUBCLONAL	1	TRUE	1	0.469151442913583	2		510	494	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020768	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs926053251	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	176	654	2	ENST00000358127.4:c.77T>G	p.Val26Gly	p.V26G	ENST00000358127	NM_001280556.1	26	gTt/gGt	2/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.469151442913583	2		656	668	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300039	137300040	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755912201	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	153	815	6	ENST00000481739.1:c.331dup	p.Leu111ProfsTer70	p.L111Pfs*70	ENST00000481739	NM_002957.4	108	-/C	3/10	1	2	FACETS	0.803	0.735	0.874	0.803	0.735	0.874	CLONAL	1	TRUE	1	0.469151442913583	2		821	812	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390697	139390697	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	199	898	2	ENST00000277541.6:c.7494del	p.Ser2499AlafsTer90	p.S2499Afs*90	ENST00000277541	NM_017617.3	2498	ccC/cc	34/34	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.469151442913583	2		900	839	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413229	139413229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	204	826	1	ENST00000277541.6:c.913G>A	p.Ala305Thr	p.A305T	ENST00000277541	NM_017617.3	305	Gcc/Acc	6/34	1	2	FACETS	0.976	0.906	1	0.976	0.906	1	CLONAL	1	TRUE	1	0.469151442913583	2		827	891	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564701	139564701	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	58	963	0	ENST00000308874.7:c.490T>C	p.Trp164Arg	p.W164R	ENST00000308874		164	Tgg/Cgg	7/10	1	2	FACETS	0.269	0.23	0.312	0.269	0.23	0.312	SUBCLONAL	1	TRUE	1	0.469151442913583	2		963	919	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325355	1325355	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	135	637	0	ENST00000400841.2:c.320del	p.Phe107SerfsTer11	p.F107Sfs*11	ENST00000400841		107	tTc/tc	3/6	1	2	FACETS	0.909	0.829	0.993	0.909	0.829	0.993	CLONAL	1	TRUE	1	0.469151442913583	2		637	633	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15821896	15821896	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	128	539	0	ENST00000307771.7:c.294del	p.Lys98AsnfsTer10	p.K98Nfs*10	ENST00000307771	NM_005089.3	97	Aaa/aa	4/11	1	2	FACETS	0.896	0.815	0.981	0.896	0.815	0.981	CLONAL	1	TRUE	1	0.469151442913583	2		539	609	SUCCESS
AR	367	MSKCC	GRCh37	X	66941772	66941772	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	116	773	0	ENST00000374690.3:c.2416C>A	p.Leu806Met	p.L806M	ENST00000374690	NM_000044.3	806	Ctg/Atg	6/8	1	2	FACETS	0.789	0.712	0.869	0.789	0.712	0.869	SUBCLONAL	1	TRUE	1	0.469151442913583	2		773	627	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70350054	70350054	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs966195679	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	93	496	0	ENST00000374080.3:c.4037G>A	p.Arg1346His	p.R1346H	ENST00000374080		1346	cGc/cAc	28/45	1	2	FACETS	0.935	0.836	1	0.935	0.836	1	CLONAL	1	TRUE	1	0.469151442913583	2		496	424	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857442	68857442	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs386833398	NA	P-0021744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	203	725	0	ENST00000261769.5:c.2077G>A	p.Gly693Ser	p.G693S	ENST00000261769	NM_004360.3	693	Ggc/Agc	13/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.469151442913583	2		725	763	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47607098	47607100	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs1424757619	NA	P-0021909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	71	609	0	ENST00000263735.4:c.852_854del	p.Val285del	p.V285del	ENST00000263735	NM_002354.2	283	aTTGtt/att	7/9	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.15	2		609	864	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	250	642	1	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	0.577597230341824	2	FACETS	1	0.976	1	0.538	0.505	0.572	CLONAL	1	TRUE	0	0.577597230341824	2		643	804	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578386	7578386	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	644	561	0	ENST00000269305.4:c.544del	p.Cys182AlafsTer65	p.C182Afs*65	ENST00000269305	NM_001126112.2	182	Tgc/gc	5/11	0.577597230341824	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.577597230341824	3		561	926	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18956915	18956915	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	171	445	0	ENST00000262803.5:c.358A>T	p.Ile120Leu	p.I120L	ENST00000262803	NM_002911.3	120	Ata/Tta	2/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.577597230341824	2		445	540	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564528	55564528	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	159	531	0	ENST00000288135.5:c.416C>A	p.Thr139Lys	p.T139K	ENST00000288135	NM_000222.2	139	aCa/aAa	3/21	0.577597230341824	3	FACETS	0.924	0.848	1	0.462	0.424	0.502	CLONAL	1	TRUE	1	0.577597230341824	3		531	768	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934103	39934103	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	57	574	0	ENST00000378444.4:c.496C>G	p.Leu166Val	p.L166V	ENST00000378444	NM_001123385.1	166	Ctg/Gtg	4/15	0.483789857701657	2	FACETS	0.231	0.197	0.268	0.115	0.098	0.134	SUBCLONAL	1	TRUE	0	0.577597230341824	2		574	855	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0022004-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	366	883	4	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.447288992868664	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.456929088869025	2		887	775	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432144	49432144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022004-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	149	806	0	ENST00000301067.7:c.8995G>A	p.Ala2999Thr	p.A2999T	ENST00000301067	NM_003482.3	2999	Gcc/Acc	34/54	1	2	FACETS	0.703	0.642	0.767	0.703	0.642	0.767	SUBCLONAL	1	TRUE	1	0.456929088869025	2		806	928	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563015	21563070	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCGGCGCCTGGCGGTCCTCCCTGGCCCTTCGTGGGCAGGCTGGCGTAACCCCCG	GGCCGGCGCCTGGCGGTCCTCCCTGGCCCTTCGTGGGCAGGCTGGCGTAACCCCCG	-	novel	NA	P-0022004-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	127	716	0	ENST00000382592.4:c.849_904del	p.Gly284ArgfsTer59	p.G284Rfs*59	ENST00000382592	NM_014572.2	283	acCGGGGGTTACGCCAGCCTGCCCACGAAGGGCCAGGGAGGACCGCCAGGCGCCGGCCtc/actc	4/8	0.264860559173784	1	FACETS	0.48	0.435	0.528	0.48	0.435	0.528	INDETERMINATE	1	TRUE	0	0.456929088869025	1		716	893	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796978	78796978	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022004-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	96	557	0	ENST00000306801.3:c.1091C>G	p.Pro364Arg	p.P364R	ENST00000306801	NM_020761.2	364	cCc/cGc	9/34	0.170581664573007	3	FACETS	0.579	0.515	0.648			1	INDETERMINATE	1	TRUE	NA	0.456929088869025	3		557	891	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397700	139397700	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	303	753	0	ENST00000277541.6:c.5101G>C	p.Ala1701Pro	p.A1701P	ENST00000277541	NM_017617.3	1701	Gca/Cca	27/34	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.915543486296146	2		753	641	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	345	866	2	ENST00000267101.3:c.310G>C	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ctg	3/28	0.915543486296146	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.915543486296146	1		868	373	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220632	1220632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782146	NA	P-0022062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	23	761	2	ENST00000326873.7:c.650C>T	p.Pro217Leu	p.P217L	ENST00000326873	NM_000455.4	217	cCg/cTg	5/10	0.915543486296146	1	FACETS	0.103	0.08	0.129	0.103	0.08	0.129	SUBCLONAL	1	TRUE	0	0.915543486296146	1		763	265	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944755	71944755	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	288	878	1	ENST00000298229.2:c.2179G>T	p.Val727Phe	p.V727F	ENST00000298229	NM_001567.3	727	Gtt/Ttt	19/28	0.872684750421488	3	FACETS	0.919	0.865	0.974			1	CLONAL	1	TRUE	NA	0.915543486296146	3		879	998	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579359	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGAAA	novel	NA	P-0022062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	336	785	0	ENST00000269305.4:c.324_328dup	p.Arg110LeufsTer15	p.R110Lfs*15	ENST00000269305	NM_001126112.2	110	cgt/cTTTCCgt	4/11	NA	2	FACETS	0.904	0.879	0.928			1	INDETERMINATE	2	TRUE	NA	0.915543486296146	2		785	406	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818216	43818218	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0022062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	256	660	0	ENST00000372470.3:c.1685_1687del	p.Glu562del	p.E562del	ENST00000372470	NM_005373.2	561	GAA/-	12/12	1	2	FACETS	0.954	0.901	1	0.954	0.901	1	CLONAL	1	TRUE	1	0.915543486296146	2		660	586	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736248	243736248	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	143	522	0	ENST00000263826.5:c.799A>T	p.Ile267Phe	p.I267F	ENST00000263826	NM_005465.4	267	Att/Ttt	8/13	0.674745632595605	4	FACETS	1	0.934	1	0.256	0.234	0.279	CLONAL	1	TRUE	0	0.915543486296146	4		522	585	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436450	110436450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6648	472	904	9	ENST00000375856.3:c.1951G>A	p.Asp651Asn	p.D651N	ENST00000375856	NM_003749.2	651	Gac/Aac	1/2	0.915543486296146	19	FACETS	1	0.993	1			1	CLONAL	1	TRUE	NA	0.915543486296146	19		913	7120	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199825	138199825	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	235	574	1	ENST00000237289.4:c.1243C>A	p.Gln415Lys	p.Q415K	ENST00000237289	NM_001270507.1	415	Caa/Aaa	7/9	0.873811133770042	4	FACETS	0.962	0.898	1			1	CLONAL	1	TRUE	NA	0.915543486296146	4		575	1022	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336651	81336664	+	frameshift_variant	Frame_Shift_Del	DEL	ATCAATGATCCTCC	ATCAATGATCCTCC	-	novel	NA	P-0022062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	39	523	0	ENST00000222390.5:c.1558_1571del	p.Gly520LysfsTer21	p.G520Kfs*21	ENST00000222390	NM_000601.4	520	GGAGGATCATTGATa/a	14/18	0.532544191282509	1	FACETS	0.151	0.125	0.179	0.151	0.125	0.179	INDETERMINATE	1	TRUE	0	0.915543486296146	1		523	306	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390843	139390844	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	GCTGGGGCCCAGTGGCTGCACGTCTGCCTGGCTCGGCTCTCCACTCAGGAAGCTCCGGCCCA	novel	NA	P-0022062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	81	807	0	ENST00000277541.6:c.7286_7347dup	p.Ser2450TrpfsTer6	p.S2450Wfs*6	ENST00000277541	NM_017617.3	2449	-/TGGGCCGGAGCTTCCTGAGTGGAGAGCCGAGCCAGGCAGACGTGCAGCCACTGGGCCCCAGC	34/34	1	2	FACETS	0.26	0.229	0.294	0.26	0.229	0.294	SUBCLONAL	1	TRUE	1	0.915543486296146	2		807	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578527	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	423	992	0	ENST00000269305.4:c.403dup	p.Cys135LeufsTer14	p.C135Lfs*14	ENST00000269305	NM_001126112.2	135	tgc/tTgc	5/11	0.56612324167021	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.56612324167021	1		992	970	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720854	89720872	+	frameshift_variant	Frame_Shift_Del	DEL	ATACTTTTCTCCAAATTTT	ATACTTTTCTCCAAATTTT	-	novel	NA	P-0022282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	58	474	0	ENST00000371953.3:c.1006_1024del	p.Tyr336ArgfsTer2	p.Y336Rfs*2	ENST00000371953	NM_000314.4	335	cgATACTTTTCTCCAAATTTT/cg	8/9	0.56612324167021	1	FACETS	0.451	0.389	0.517	0.451	0.389	0.517	SUBCLONAL	1	TRUE	0	0.56612324167021	1		474	326	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619344	1619344	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs565387667	NA	P-0022282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	310	781	0	ENST00000344749.5:c.1297A>G	p.Met433Val	p.M433V	ENST00000344749	NM_001136139.2	433	Atg/Gtg	15/19	0.56612324167021	1	FACETS	0.985	0.934	1	0.985	0.934	1	CLONAL	1	TRUE	0	0.56612324167021	1		781	797	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	397	896	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.29646496430741	4	FACETS	0.907	0.863	0.953			1	CLONAL	3	FALSE	NA	0.3	4		898	1264	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044965	47044966	+	missense_variant	Missense_Mutation	DNP	GC	GC	AT	novel	NA	P-0022290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	128	1093	2	ENST00000377604.3:c.2291_2292delinsAT	p.Cys764Tyr	p.C764Y	ENST00000377604	NM_001204468.1	764	tGC/tAT	20/24	1	2	FACETS	0.89	0.805	0.979	0.89	0.805	0.979	CLONAL	1	FALSE	1	0.3	2		1095	959	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662631	227662631	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs201110062	NA	P-0022290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	52	719	0	ENST00000305123.5:c.824A>C	p.Asn275Thr	p.N275T	ENST00000305123	NM_005544.2	275	aAc/aCc	1/2	0.124072629928535	3	FACETS	0.599	0.509	0.697	0.299	0.254	0.349	INDETERMINATE	1	FALSE	1	0.3	3		719	666	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118729	115118729	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1452419195	NA	P-0022335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	174	689	0	ENST00000257566.3:c.612C>G	p.Phe204Leu	p.F204L	ENST00000257566	NM_016569.3	204	ttC/ttG	2/8	1	2	FACETS	0.883	0.814	0.956	0.883	0.814	0.956	CLONAL	1	TRUE	1	0.455984767619243	2		689	864	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26928009	26928015	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AGAGATT	AGAGATT	-	novel	NA	P-0022335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	86	591	0	ENST00000381527.3:c.448_454del	p.Arg150Ter	p.R150*	ENST00000381527	NM_001260.1	150	AGAGATTtg/tg	4/13	1	2	FACETS	0.676	0.599	0.758	0.676	0.599	0.758	SUBCLONAL	1	TRUE	1	0.455984767619243	2		591	558	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845693	68845694	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	177	894	0	ENST00000261769.5:c.944dup	p.Asn315LysfsTer6	p.N315Kfs*6	ENST00000261769	NM_004360.3	313	-/A	7/16	0.383218279299649	1	FACETS	0.804	0.743	0.868	0.804	0.743	0.868	CLONAL	1	TRUE	0	0.455984767619243	1		894	745	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965878	25965878	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	152	737	0	ENST00000435504.4:c.3328T>C	p.Phe1110Leu	p.F1110L	ENST00000435504		1110	Ttt/Ctt	13/13	NA	2	FACETS	0.835	0.765	0.909			1	INDETERMINATE	1	TRUE	NA	0.455984767619243	2		737	798	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044479	128044480	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0022335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	156	735	0	ENST00000285398.2:c.1141_1142del	p.Trp381ValfsTer4	p.W381Vfs*4	ENST00000285398	NM_000122.1	381	TGg/g	8/15	1	2	FACETS	0.884	0.811	0.961	0.884	0.811	0.961	CLONAL	1	TRUE	1	0.455984767619243	2		735	774	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155650	56155650	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	127	516	1	ENST00000399503.3:c.742C>T	p.Arg248Ter	p.R248*	ENST00000399503	NM_005921.1	248	Cga/Tga	3/20	1	2	FACETS	0.879	0.798	0.963	0.879	0.798	0.963	CLONAL	1	TRUE	1	0.455984767619243	2		517	634	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860347	151860347	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	133	588	0	ENST00000262189.6:c.10315T>G	p.Ser3439Ala	p.S3439A	ENST00000262189	NM_170606.2	3439	Tct/Gct	43/59	0.455984767619243	3	FACETS	0.953	0.866	1			1	CLONAL	1	TRUE	NA	0.455984767619243	3		588	752	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0022341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	20	399	0				ENST00000310581	NM_198253.2	-/1132			0.3	0	FACETS	0.889	0.681	1			1	CLONAL	1	TRUE	0	0.15	0		399	255	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0022341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	34	804	1	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.2507258150258	3	FACETS	0.682	0.555	0.825	0.341	0.277	0.413	SUBCLONAL	1	TRUE	1	0.15	3		805	715	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262190	16262190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1367923445	NA	P-0022341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	10	299	0	ENST00000375759.3:c.9455C>T	p.Ser3152Phe	p.S3152F	ENST00000375759	NM_015001.2	3152	tCc/tTc	11/15	0.286811745282262	4	FACETS	0.958	0.651	1	0.479	0.325	0.672	CLONAL	1	TRUE	2	0.15	4		299	160	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984016	2984016	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	31	820	0	ENST00000396946.4:c.514G>C	p.Glu172Gln	p.E172Q	ENST00000396946	NM_032415.4	172	Gag/Cag	5/25	0.163706247792833	0	FACETS	0.605	0.488	0.738			1	SUBCLONAL	1	TRUE	0	0.15	0		820	581	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032069	26032069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1598	88	657	0	ENST00000244661.2:c.220G>A	p.Glu74Lys	p.E74K	ENST00000244661	NM_003537.3	74	Gaa/Aaa	1/1	0.3	19	FACETS	0.792	0.698	0.893			1	SUBCLONAL	2	TRUE	NA	0.15	19		657	1686	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631710	90631710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	39	839	0	ENST00000330062.3:c.559G>A	p.Asp187Asn	p.D187N	ENST00000330062	NM_002168.2	187	Gac/Aac	5/11	0.163706247792833	3	FACETS	0.785	0.649	0.938	0.393	0.324	0.469	CLONAL	1	TRUE	1	0.15	3		839	712	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226430	2226430	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1259812222	NA	P-0022341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	32	972	0	ENST00000398665.3:c.3910G>A	p.Asp1304Asn	p.D1304N	ENST00000398665	NM_032482.2	1304	Gac/Aac	27/28	0.163706247792833	1	FACETS	0.926	0.752	1	0.926	0.752	1	CLONAL	1	TRUE	0	0.15	1		972	426	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855848	45855848	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	22	905	0	ENST00000391945.4:c.1962C>G	p.Phe654Leu	p.F654L	ENST00000391945	NM_000400.3	654	ttC/ttG	21/23	0.3	1	FACETS	0.643	0.497	0.813	0.643	0.497	0.813	SUBCLONAL	1	TRUE	0	0.15	1		905	422	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39744053	39744053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	29	665	0	ENST00000361337.2:c.1681G>A	p.Glu561Lys	p.E561K	ENST00000361337	NM_003286.2	561	Gag/Aag	16/21	0.163706247792833	3	FACETS	0.775	0.621	0.952	0.388	0.31	0.476	CLONAL	1	TRUE	1	0.15	3		665	536	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541370	187541370	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	25	529	0	ENST00000441802.2:c.6370C>T	p.His2124Tyr	p.H2124Y	ENST00000441802	NM_005245.3	2124	Cat/Tat	10/27	1	2	FACETS	1	0.84	1	1	0.84	1	CLONAL	1	TRUE	1	0.15	2		529	309	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111605	56111605	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1339726940	NA	P-0022341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	53	406	0	ENST00000399503.3:c.205G>C	p.Glu69Gln	p.E69Q	ENST00000399503	NM_005921.1	69	Gag/Cag	1/20	0.377098674434973	5	FACETS	1	0.887	1	0.351	0.298	0.409	CLONAL	1	TRUE	2	0.15	5		406	823	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080261	5080261	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	12	364	0	ENST00000381652.3:c.2164G>A	p.Glu722Lys	p.E722K	ENST00000381652	NM_004972.3	722	Gaa/Aaa	17/25	1	2	FACETS	0.769	0.541	1	0.769	0.541	1	CLONAL	1	TRUE	1	0.15	2		364	208	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785984	135785984	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	45	814	0	ENST00000298552.3:c.1237C>T	p.Gln413Ter	p.Q413*	ENST00000298552	NM_001162426.1	413	Cag/Tag	12/23	1	2	FACETS	0.82	0.687	0.967	0.82	0.687	0.967	CLONAL	1	TRUE	1	0.15	2		814	732	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870266	44870266	+	splice_donor_variant	Splice_Site	SNP	T	T	A	rs1389828598	NA	P-0022341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	35	352	1	ENST00000377967.4:c.443+2T>A		p.X148_splice	ENST00000377967	NM_021140.2	148			0.3	2	FACETS	0.848	0.699	1	0.848	0.699	1	CLONAL	2	TRUE	0	0.15	2		353	275	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912664	NA	P-0022439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	24	792	1	ENST00000269305.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000269305	NM_001126112.2	337	cGc/cAc	10/11	0.202927028493014	0	FACETS	0.251	0.195	0.315			1	SUBCLONAL	1	FALSE	0	0.202927028493014	0		793	752	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964925	55964925	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	87	235	0	ENST00000263923.4:c.2312C>A	p.Thr771Lys	p.T771K	ENST00000263923	NM_002253.2	771	aCg/aAg	16/30	0.283872486692647	4	FACETS	1	0.964	1			1	CLONAL	2	TRUE	NA	0.283872486692647	4		235	331	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0022593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	19	926	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	0.421727703728138	4	FACETS	0.155	0.117	0.2	0.077	0.058	0.1	SUBCLONAL	1	FALSE	2	0.43231141371986	4		926	813	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	164	857	0	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	0.431328674162087	3	FACETS	1	0.986	1	0.673	0.619	0.728	CLONAL	1	FALSE	1	0.43231141371986	3		857	686	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101031	4101031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375843855	NA	P-0022593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	260	966	1	ENST00000262948.5:c.691C>T	p.Arg231Cys	p.R231C	ENST00000262948	NM_030662.3	231	Cgc/Tgc	6/11	0.351517957366841	3	FACETS	0.829	0.779	0.881	0.553	0.519	0.588	CLONAL	2	FALSE	0	0.43231141371986	3		967	882	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226550815	226550815	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0022593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	50	471	0	ENST00000366794.5:c.2833A>T	p.Lys945Ter	p.K945*	ENST00000366794	NM_001618.3	945	Aag/Tag	21/23	0.43231141371986	5	FACETS	0.628	0.532	0.734	0.209	0.177	0.245	SUBCLONAL	1	FALSE	2	0.43231141371986	5		471	607	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28624345	28624348	+	frameshift_variant	Frame_Shift_Del	DEL	CTTT	CTTT	-	novel	NA	P-0022593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	19	209	0	ENST00000241453.7:c.626_629del	p.Glu209ValfsTer20	p.E209Vfs*20	ENST00000241453	NM_004119.2	209	gAAAGt/gt	6/24	0.431328674162087	3	FACETS	0.486	0.37	0.622	0.243	0.185	0.311	SUBCLONAL	1	FALSE	1	0.43231141371986	3		209	220	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243482	41243482	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886040193	NA	P-0022593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	30	264	0	ENST00000357654.3:c.4066C>T	p.Gln1356Ter	p.Q1356*	ENST00000357654	NM_007294.3	1356	Caa/Taa	10/23	0.431328674162087	4	FACETS	0.908	0.736	1	0.303	0.245	0.367	CLONAL	1	FALSE	1	0.43231141371986	4		264	219	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27209173	27209173	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	39	323	0	ENST00000380036.4:c.2630G>A	p.Cys877Tyr	p.C877Y	ENST00000380036	NM_000459.3	877	tGt/tAt	16/23	0.431328674162087	4	FACETS	0.847	0.705	1	0.282	0.235	0.335	CLONAL	1	FALSE	1	0.43231141371986	4		323	305	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	104	521	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	0.351691271188294	2		521	456	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	215	778	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	TRUE	1	0.351691271188294	2		783	838	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	24	463	2	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.254	0.198	0.318	0.254	0.198	0.318	SUBCLONAL	1	TRUE	1	0.351691271188294	2		465	538	SUCCESS
RET	5979	MSKCC	GRCh37	10	43572750	43572755	+	inframe_deletion	In_Frame_Del	DEL	TGCTGC	TGCTGC	-	novel	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	54	229	0	ENST00000355710.3:c.53_58del	p.Leu18_Leu19del	p.L18_L19del	ENST00000355710	NM_020975.4	15	tTGCTGCtg/ttg	1/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.351691271188294	2		229	224	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246643	46246643	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	32	219	0	ENST00000334344.6:c.4737G>T	p.Gln1579His	p.Q1579H	ENST00000334344	NM_152641.2	1579	caG/caT	15/21	1	2	FACETS	0.994	0.815	1	0.994	0.815	1	CLONAL	1	TRUE	1	0.351691271188294	2		219	183	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285628	46285629	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	80	543	0	ENST00000334344.6:c.4989dup	p.Pro1664SerfsTer10	p.P1664Sfs*10	ENST00000334344	NM_152641.2	1663	tat/taTt	17/21	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.351691271188294	2		543	451	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	176	798	4	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.351691271188294	2		802	815	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109746	115109746	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	141	861	0	ENST00000257566.3:c.2132G>A	p.Cys711Tyr	p.C711Y	ENST00000257566	NM_016569.3	711	tGc/tAc	8/8	1	2	FACETS	0.899	0.819	0.983	0.899	0.819	0.983	CLONAL	1	TRUE	1	0.351691271188294	2		861	892	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434360	121434360	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	152	672	0	ENST00000257555.6:c.1124G>C	p.Gly375Ala	p.G375A	ENST00000257555		375	gGc/gCc	6/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.351691271188294	2		672	633	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930730	32930730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs74047012	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	157	591	0	ENST00000380152.3:c.7601C>T	p.Ala2534Val	p.A2534V	ENST00000380152		2534	gCg/gTg	15/27	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.351691271188294	2		591	606	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954198	48954198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123331	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	93	496	0	ENST00000267163.4:c.1399C>T	p.Arg467Ter	p.R467*	ENST00000267163	NM_000321.2	467	Cga/Tga	15/27	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.351691271188294	2		496	469	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032405	10032405	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	64	274	0	ENST00000330684.3:c.418C>A	p.Pro140Thr	p.P140T	ENST00000330684	NM_001134407.1	140	Ccg/Acg	3/13	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.351691271188294	2		274	266	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647028	23647028	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1555461597	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	46	797	0	ENST00000261584.4:c.839del	p.Asn280ThrfsTer8	p.N280Tfs*8	ENST00000261584	NM_024675.3	280	aAc/ac	4/13	1	2	FACETS	0.357	0.3	0.421	0.357	0.3	0.421	SUBCLONAL	1	TRUE	1	0.351691271188294	2		797	732	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856093	68856093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121964878	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	185	665	2	ENST00000261769.5:c.1901C>T	p.Ala634Val	p.A634V	ENST00000261769	NM_004360.3	634	gCg/gTg	12/16	1	2	FACETS	0.786	0.729	0.846	1	0.991	1	SUBCLONAL	2	TRUE	1	0.351691271188294	2		667	669	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829497	72829497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761486040	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	97	666	2	ENST00000268489.5:c.7084G>A	p.Asp2362Asn	p.D2362N	ENST00000268489	NM_006885.3	2362	Gac/Aac	9/10	1	2	FACETS	0.99	0.885	1	0.99	0.885	1	CLONAL	1	TRUE	1	0.351691271188294	2		668	557	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217705	7217707	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs757139280	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	125	529	1	ENST00000380728.2:c.220_222del	p.Glu74del	p.E74del	ENST00000380728		74	GAG/-	4/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.351691271188294	2		530	514	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118881	70118882	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	151	596	0	ENST00000245479.2:c.454dup	p.Arg152ProfsTer100	p.R152Pfs*100	ENST00000245479	NM_000346.3	151	-/C	2/3	1	2	FACETS	0.798	0.734	0.864	1	0.989	1	SUBCLONAL	2	TRUE	1	0.351691271188294	2		596	538	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40739787	40739787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769806554	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	226	905	2	ENST00000392038.2:c.1438C>T	p.Arg480Cys	p.R480C	ENST00000392038	NM_001626.4	480	Cgc/Tgc	14/14	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.351691271188294	2		907	885	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919007	50919007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1483458869	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	213	747	3	ENST00000440232.2:c.2744C>T	p.Ala915Val	p.A915V	ENST00000440232	NM_002691.3	915	gCg/gTg	22/27	1	2	FACETS	0.875	0.817	0.935	1	0.993	1	CLONAL	2	TRUE	1	0.351691271188294	2		750	692	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716301	52716301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	166	641	1	ENST00000322088.6:c.745C>T	p.Arg249Cys	p.R249C	ENST00000322088	NM_014225.5	249	Cgc/Tgc	6/15	1	2	FACETS	0.784	0.724	0.846	1	0.99	1	SUBCLONAL	2	TRUE	1	0.351691271188294	2		642	602	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920652	96920652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767739392	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	149	505	2	ENST00000258439.3:c.328G>A	p.Ala110Thr	p.A110T	ENST00000258439	NM_001193304.2	110	Gct/Act	3/4	1	2	FACETS	0.796	0.732	0.863	1	0.989	1	SUBCLONAL	2	TRUE	1	0.351691271188294	2		507	532	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172161	99172161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs571358585	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	119	641	1	ENST00000074304.5:c.1727C>T	p.Pro576Leu	p.P576L	ENST00000074304	NM_001134224.1	576	cCg/cTg	17/26	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.351691271188294	2		642	566	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215674206	215674206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	92	699	0	ENST00000260947.4:c.88G>A	p.Gly30Ser	p.G30S	ENST00000260947	NM_000465.2	30	Ggt/Agt	1/11	1	2	FACETS	0.985	0.878	1	0.985	0.878	1	CLONAL	1	TRUE	1	0.351691271188294	2		699	531	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39721125	39721125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	118	482	2	ENST00000361337.2:c.628C>T	p.Arg210Cys	p.R210C	ENST00000361337	NM_003286.2	210	Cgc/Tgc	9/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.351691271188294	2		484	540	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755786	39755786	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	104	407	0	ENST00000288319.7:c.979T>C	p.Ser327Pro	p.S327P	ENST00000288319	NM_182918.3	327	Tcc/Ccc	10/10	0.351691271188294	2	FACETS	0.812	0.734	0.894	0.812	0.734	0.894	CLONAL	2	TRUE	0	0.351691271188294	2		407	364	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747889	41747889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772358257	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	199	666	1	ENST00000226382.2:c.880G>A	p.Val294Ile	p.V294I	ENST00000226382	NM_003924.3	294	Gtc/Atc	3/3	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.351691271188294	2		667	776	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521384	187521384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375087606	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	120	500	0	ENST00000441802.2:c.11771G>A	p.Arg3924His	p.R3924H	ENST00000441802	NM_005245.3	3924	cGc/cAc	22/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.351691271188294	2		500	525	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629114	187629114	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	84	606	0	ENST00000441802.2:c.1868T>C	p.Val623Ala	p.V623A	ENST00000441802	NM_005245.3	623	gTa/gCa	2/27	1	2	FACETS	0.801	0.709	0.901	0.801	0.709	0.901	CLONAL	1	TRUE	1	0.351691271188294	2		606	596	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226016	226016	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	40	145	0	ENST00000264932.6:c.475C>T	p.Pro159Ser	p.P159S	ENST00000264932	NM_004168.2	159	Ccg/Tcg	5/15	1	2	FACETS	0.784	0.664	0.913	1	0.962	1	CLONAL	2	TRUE	1	0.351691271188294	2		145	145	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324132	31324132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41561215	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	85	553	0	ENST00000412585.2:c.431G>A	p.Gly144Asp	p.G144D	ENST00000412585	NM_005514.6	144	gGc/gAc	3/8	1	2	FACETS	0.961	0.852	1	0.961	0.852	1	CLONAL	1	TRUE	1	0.351691271188294	2		553	503	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268940	55268940	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	188	806	1	ENST00000275493.2:c.3006G>T	p.Met1002Ile	p.M1002I	ENST00000275493	NM_005228.3	1002	atG/atT	25/28	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.351691271188294	2		807	717	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513348	106513348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528601604	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	84	404	1	ENST00000359195.3:c.2252C>T	p.Ser751Leu	p.S751L	ENST00000359195	NM_002649.2	751	tCg/tTg	4/11	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.351691271188294	2		405	450	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169575	27169575	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	191	770	1	ENST00000380036.4:c.576G>T	p.Arg192Ser	p.R192S	ENST00000380036	NM_000459.3	192	agG/agT	4/23	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.351691271188294	2		771	774	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771932	135771932	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755396992	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	80	511	0	ENST00000298552.3:c.3185G>A	p.Arg1062Gln	p.R1062Q	ENST00000298552	NM_001162426.1	1062	cGg/cAg	23/23	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.351691271188294	2		511	413	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76812935	76812935	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	132	659	1	ENST00000373344.5:c.6686C>A	p.Pro2229His	p.P2229H	ENST00000373344	NM_000489.3	2229	cCc/cAc	30/35	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.351691271188294	2		660	580	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019795	123019795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745844064	NA	P-0022648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	125	585	0	ENST00000355640.3:c.283G>A	p.Gly95Ser	p.G95S	ENST00000355640		95	Ggc/Agc	2/7	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.351691271188294	2		585	600	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022762-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	184	515	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.358205831956908	4	FACETS	0.961	0.895	1	0.961	0.895	1	CLONAL	3	FALSE	1	0.358205831956908	4		515	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0022762-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	155	883	4	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.358205831956908	2	FACETS	0.962	0.888	1	0.962	0.888	1	CLONAL	2	FALSE	0	0.358205831956908	2		887	450	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061327	38061327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022762-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	287	639	1	ENST00000250448.2:c.662C>T	p.Ser221Leu	p.S221L	ENST00000250448	NM_004496.3	221	tCg/tTg	2/2	0.358205831956908	5	FACETS	0.992	0.936	1	0.992	0.936	1	CLONAL	3	FALSE	2	0.358205831956908	5		640	828	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660154	12660154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022762-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	80	598	1	ENST00000251849.4:c.67G>A	p.Asp23Asn	p.D23N	ENST00000251849	NM_002880.3	23	Gat/Aat	2/17	1	2	FACETS	0.792	0.698	0.892	0.792	0.698	0.892	SUBCLONAL	1	FALSE	1	0.358205831956908	2		599	564	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928074	178928074	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022762-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	277	557	1	ENST00000263967.3:c.1352G>T	p.Gly451Val	p.G451V	ENST00000263967	NM_006218.2	451	gGa/gTa	8/21	0.358205831956908	4	FACETS	0.946	0.893	1	0.946	0.893	1	CLONAL	3	FALSE	1	0.358205831956908	4		558	740	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442869	187442869	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	novel	NA	P-0022762-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	164	301	0	ENST00000232014.4:c.1840-3C>T		p.X614_splice	ENST00000232014	NM_001130845.1	614			0.358205831956908	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	FALSE	1	0.358205831956908	4		301	359	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578391	7578393	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	novel	NA	P-0022856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	170	561	1	ENST00000269305.4:c.537_539del	p.His179_Glu180delinsGln	p.H179_E180delinsQ	ENST00000269305	NM_001126112.2	179	caTGAg/cag	5/11	0.630813705140928	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.630813705140928	1		562	343	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931652	39931652	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	217	663	0	ENST00000378444.4:c.2947G>T	p.Glu983Ter	p.E983*	ENST00000378444	NM_001123385.1	983	Gaa/Taa	4/15	0.151951561636929	1	FACETS	0.802	0.751	0.854	0.802	0.751	0.854	INDETERMINATE	1	TRUE	0	0.630813705140928	1		663	587	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0022876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	73	461	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.881	0.771	1	0.881	0.771	1	CLONAL	1	TRUE	1	0.275201448988298	2		461	602	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216380	7216380	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	159	884	0	ENST00000380728.2:c.868C>T	p.Gln290Ter	p.Q290*	ENST00000380728		290	Cag/Tag	10/11	0.275201448988298	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.275201448988298	1		884	894	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	231	482	0				ENST00000310581	NM_198253.2	-/1132			0.352840147913655	3	FACETS	0.956	0.903	1	0.956	0.903	1	INDETERMINATE	2	TRUE	1	0.71682975058913	3		482	458	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104356980	104356981	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1477199832	NA	P-0022877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	213	712	0	ENST00000369902.3:c.846dup	p.Glu283ArgfsTer3	p.E283Rfs*3	ENST00000369902	NM_016169.3	280	-/C	7/12	0.71682975058913	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.71682975058913	1		712	368	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944178	71944178	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs748455961	NA	P-0022877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	204	847	2	ENST00000298229.2:c.2011T>C	p.Tyr671His	p.Y671H	ENST00000298229	NM_001567.3	671	Tat/Cat	17/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.71682975058913	2		849	528	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878067	48878067	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	108	539	1	ENST00000267163.4:c.19C>T	p.Arg7Ter	p.R7*	ENST00000267163	NM_000321.2	7	Cga/Tga	1/27	0.71682975058913	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.71682975058913	1		540	176	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094957	11094957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	253	1150	0	ENST00000358026.2:c.130G>A	p.Gly44Arg	p.G44R	ENST00000358026	NM_001128849.1	44	Ggg/Agg	2/36	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.71682975058913	2		1150	669	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552927	106552927	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776111636	NA	P-0022877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	251	1026	1	ENST00000369096.4:c.892G>A	p.Val298Ile	p.V298I	ENST00000369096	NM_001198.3	298	Gtt/Att	5/7	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.71682975058913	2		1027	685	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777894	NA	P-0022879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	235	942	0	ENST00000361445.4:c.6644C>T	p.Ser2215Phe	p.S2215F	ENST00000361445	NM_004958.3	2215	tCt/tTt	47/58	0.564313898029412	1	FACETS	0.855	0.802	0.91	0.855	0.802	0.91	CLONAL	1	TRUE	0	0.564313898029412	1		942	699	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0022879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	423	901	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	0.564313898029412	3	FACETS	0.92	0.879	0.961	0.92	0.879	0.961	CLONAL	2	TRUE	1	0.564313898029412	3		901	1045	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167577	NA	P-0022879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	256	404	0	ENST00000257430.4:c.4463del	p.Leu1488TyrfsTer19	p.L1488Yfs*19	ENST00000257430	NM_000038.5	1487	acT/ac	16/16	0.56184178984607	2	FACETS	0.98	0.931	1	0.98	0.931	1	CLONAL	2	TRUE	0	0.564313898029412	2		404	463	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056209	26056211	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs779842031	NA	P-0022879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	191	607	0	ENST00000343677.2:c.446_448del	p.Lys149del	p.K149del	ENST00000343677	NM_005319.3	149	aAGAgc/agc	1/1	1	2	FACETS	0.94	0.872	1	0.94	0.872	1	CLONAL	1	TRUE	1	0.564313898029412	2		607	720	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226397	133226397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	271	1029	0	ENST00000320574.5:c.3661C>T	p.Pro1221Ser	p.P1221S	ENST00000320574	NM_006231.2	1221	Cct/Tct	30/49	0.564313898029412	3	FACETS	0.98	0.918	1	0.49	0.459	0.522	CLONAL	1	TRUE	1	0.564313898029412	3		1029	1257	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358493	67358493	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0022879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	88	315	0	ENST00000327367.4:c.1A>G	p.Met1?	p.M1?	ENST00000327367	NM_005902.3	1	Atg/Gtg	1/9	0.564313898029412	1	FACETS	0.978	0.882	1	0.978	0.882	1	CLONAL	1	TRUE	0	0.564313898029412	1		315	229	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945945	17945945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	352	1423	2	ENST00000458235.1:c.1994C>T	p.Pro665Leu	p.P665L	ENST00000458235	NM_000215.3	665	cCc/cTc	15/24	1	2	FACETS	0.884	0.836	0.933	0.884	0.836	0.933	CLONAL	1	TRUE	1	0.564313898029412	2		1425	1412	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416658	29416658	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1374838786	NA	P-0022879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	165	529	0	ENST00000389048.3:c.4295G>A	p.Arg1432Gln	p.R1432Q	ENST00000389048	NM_004304.4	1432	cGg/cAg	29/29	1	2	FACETS	0.933	0.86	1	0.933	0.86	1	CLONAL	1	TRUE	1	0.564313898029412	2		529	627	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389269	8389269	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	60	925	0	ENST00000356435.5:c.4349C>G	p.Thr1450Arg	p.T1450R	ENST00000356435		1450	aCa/aGa	26/35	1	2	FACETS	0.27	0.232	0.312	0.27	0.232	0.312	SUBCLONAL	1	TRUE	1	0.566501959303603	2		925	785	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0022881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	117	830	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.272981063123779	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.272981063123779	1		832	703	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0022881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	210	676	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.272981063123779	5	FACETS	1	0.982	1	0.858	0.801	0.916	CLONAL	3	TRUE	1	0.272981063123779	5		676	632	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039147	49039147	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0022881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	75	499	0	ENST00000267163.4:c.2228del	p.Leu743Ter	p.L743*	ENST00000267163	NM_000321.2	742	gTt/gt	22/27	0.272981063123779	2	FACETS	1	0.975	1	0.727	0.641	0.818	CLONAL	1	TRUE	0	0.272981063123779	2		499	378	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692883	89692883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204931	NA	P-0022881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	39	575	2	ENST00000371953.3:c.367C>T	p.His123Tyr	p.H123Y	ENST00000371953	NM_000314.4	123	Cac/Tac	5/9	1	2	FACETS	0.907	0.755	1	0.907	0.755	1	CLONAL	1	TRUE	1	0.272981063123779	2		577	315	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637719	23637719	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0022881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	88	690	0	ENST00000261584.4:c.2587-1G>A		p.X863_splice	ENST00000261584	NM_024675.3	863			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.272981063123779	2		690	550	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66524004	66524004	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	41	406	0	ENST00000358598.2:c.732G>C	p.Lys244Asn	p.K244N	ENST00000358598	NM_212471.2	244	aaG/aaC	8/11	0.272981063123779	3	FACETS	0.933	0.779	1	0.466	0.389	0.552	CLONAL	1	TRUE	1	0.272981063123779	3		406	366	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637956	39637956	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	65	902	0	ENST00000262039.4:c.2373G>C	p.Gln791His	p.Q791H	ENST00000262039	NM_002647.2	791	caG/caC	22/25	0.191040106180819	2	FACETS	0.956	0.831	1	0.478	0.415	0.546	CLONAL	1	TRUE	0	0.272981063123779	2		902	498	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943410	17943410	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	123	1215	0	ENST00000458235.1:c.2598G>T	p.Arg866Ser	p.R866S	ENST00000458235	NM_000215.3	866	agG/agT	19/24	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.272981063123779	2		1215	835	SUCCESS
APC	324	MSKCC	GRCh37	5	112176344	112176344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	38	372	0	ENST00000257430.4:c.5053G>A	p.Glu1685Lys	p.E1685K	ENST00000257430	NM_000038.5	1685	Gaa/Aaa	16/16	1	2	FACETS	0.865	0.717	1	0.865	0.717	1	CLONAL	1	TRUE	1	0.272981063123779	2		372	322	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911302	29911302	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	33	530	0	ENST00000376809.5:c.601G>T	p.Glu201Ter	p.E201*	ENST00000376809	NM_002116.7	201	Gag/Tag	3/8	1	2	FACETS	0.657	0.536	0.794	0.657	0.536	0.794	SUBCLONAL	1	TRUE	1	0.272981063123779	2		530	368	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545590	106545590	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	68	678	0	ENST00000359195.3:c.3067C>A	p.His1023Asn	p.H1023N	ENST00000359195	NM_002649.2	1023	Cac/Aac	11/11	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.272981063123779	2		678	447	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360600	70360600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	109	619	1	ENST00000374080.3:c.6160C>T	p.Gln2054Ter	p.Q2054*	ENST00000374080		2054	Cag/Tag	42/45	1	1	FACETS	0.811	0.734	0.892	1	0.986	1	CLONAL	2	TRUE	0	0.272981063123779	1		620	425	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0022937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	1470	722	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.564892024374862	9	FACETS	0.978	0.962	0.994			1	CLONAL	8	TRUE	NA	0.564892024374862	9		722	1980	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200961	108200961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782310	NA	P-0022937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	175	480	0	ENST00000278616.4:c.7328G>A	p.Arg2443Gln	p.R2443Q	ENST00000278616	NM_000051.3	2443	cGa/cAa	50/63	0.559822450372119	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.564892024374862	1		480	423	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108831	2108831	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	125	912	1	ENST00000219476.3:c.932C>A	p.Ser311Tyr	p.S311Y	ENST00000219476	NM_000548.3	311	tCt/tAt	10/42	NA	2	FACETS	0.403	0.364	0.445			1	INDETERMINATE	1	TRUE	NA	0.564892024374862	2		913	1097	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913197	39913197	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	57	676	0	ENST00000378444.4:c.4918G>C	p.Glu1640Gln	p.E1640Q	ENST00000378444	NM_001123385.1	1640	Gaa/Caa	14/15	NA	2	FACETS	0.257	0.219	0.298			1	INDETERMINATE	1	TRUE	NA	0.564892024374862	2		676	786	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs760043106	NA	P-0022937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	227	712	0	ENST00000269305.4:c.584T>G	p.Ile195Ser	p.I195S	ENST00000269305	NM_001126112.2	195	aTc/aGc	6/11	0.559822450372119	1	FACETS	0.895	0.839	0.953	0.895	0.839	0.953	CLONAL	1	TRUE	0	0.564892024374862	1		712	644	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956723	68956723	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs750933833	NA	P-0022937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	93	650	2	ENST00000288368.4:c.841C>T	p.Arg281Trp	p.R281W	ENST00000288368	NM_024870.2	281	Cgg/Tgg	8/40	0.357184420580874	1	FACETS	0.434	0.387	0.484	0.434	0.387	0.484	SUBCLONAL	1	TRUE	0	0.564892024374862	1		652	544	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025542	1025542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1023065435	NA	P-0022937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	252	778	2	ENST00000358495.3:c.833G>A	p.Arg278Gln	p.R278Q	ENST00000358495	NM_134424.2	278	cGa/cAa	9/12	NA	2	FACETS	0.982	0.92	1			1	INDETERMINATE	1	TRUE	NA	0.564892024374862	2		780	909	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076731	72076731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	190	774	0	ENST00000357731.5:c.766G>A	p.Glu256Lys	p.E256K	ENST00000357731	NM_173808.2	256	Gaa/Aaa	5/7	0.542388645284934	1	FACETS	0.828	0.77	0.887	0.828	0.77	0.887	CLONAL	1	TRUE	0	0.564892024374862	1		774	583	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444873	49444873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	258	908	1	ENST00000301067.7:c.2593G>A	p.Glu865Lys	p.E865K	ENST00000301067	NM_003482.3	865	Gaa/Aaa	10/54	0.152531040042693	6	FACETS	0.793	0.742	0.846			1	INDETERMINATE	2	TRUE	NA	0.564892024374862	6		909	1226	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094722	2094722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746940807	NA	P-0022937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	131	854	0	ENST00000219066.1:c.458G>A	p.Arg153Gln	p.R153Q	ENST00000219066	NM_002528.5	153	cGa/cAa	3/6	NA	2	FACETS	0.438	0.396	0.481			1	INDETERMINATE	1	TRUE	NA	0.564892024374862	2		854	1060	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645399	67645399	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1386847711	NA	P-0022937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	61	468	0	ENST00000264010.4:c.664G>C	p.Asp222His	p.D222H	ENST00000264010	NM_006565.3	222	Gat/Cat	3/12	0.409331386742054	1	FACETS	0.354	0.306	0.406	0.354	0.306	0.406	SUBCLONAL	1	TRUE	0	0.564892024374862	1		468	438	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546128	29546128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	31	466	0	ENST00000356175.3:c.1633G>A	p.Ala545Thr	p.A545T	ENST00000356175	NM_000267.3	545	Gca/Aca	14/57	0.559822450372119	1	FACETS	0.201	0.163	0.245	0.201	0.163	0.245	SUBCLONAL	1	TRUE	0	0.564892024374862	1		466	391	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42384748	42384748	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	77	505	0	ENST00000221972.3:c.510G>C	p.Gln170His	p.Q170H	ENST00000221972	NM_021601.3	170	caG/caC	4/5	0.263456870253129	1	FACETS	0.385	0.339	0.435	0.385	0.339	0.435	INDETERMINATE	1	TRUE	0	0.564892024374862	1		505	508	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541636	187541636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	40	424	1	ENST00000441802.2:c.6104C>T	p.Thr2035Ile	p.T2035I	ENST00000441802	NM_005245.3	2035	aCt/aTt	10/27	0.357184420580874	1	FACETS	0.277	0.23	0.329	0.277	0.23	0.329	SUBCLONAL	1	TRUE	0	0.564892024374862	1		425	367	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31422943	31422943	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	138	857	0	ENST00000344624.3:c.3370C>G	p.Leu1124Val	p.L1124V	ENST00000344624		1124	Ctg/Gtg	26/33	0.289842736007399	1	FACETS	0.429	0.39	0.47	0.429	0.39	0.47	INDETERMINATE	1	TRUE	0	0.564892024374862	1		857	817	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045663	26045663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	15	303	0	ENST00000540144.1:c.25C>T	p.Arg9Cys	p.R9C	ENST00000540144	NM_003531.2	9	Cgc/Tgc	1/1	0.540009171928353	1	FACETS	0.152	0.111	0.201	0.152	0.111	0.201	SUBCLONAL	1	TRUE	0	0.564892024374862	1		303	251	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428952	47428952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	64	882	0	ENST00000377045.4:c.1315G>A	p.Glu439Lys	p.E439K	ENST00000377045	NM_001654.4	439	Gag/Aag	13/16	1	2	FACETS	0.267	0.231	0.307	0.267	0.231	0.307	SUBCLONAL	1	TRUE	1	0.564892024374862	2		882	848	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409875	63409875	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	57	517	2	ENST00000330258.3:c.3292C>T	p.Gln1098Ter	p.Q1098*	ENST00000330258	NM_152424.3	1098	Cag/Tag	2/2	1	2	FACETS	0.393	0.337	0.453	0.393	0.337	0.453	SUBCLONAL	1	TRUE	1	0.564892024374862	2		519	514	SUCCESS
AR	367	MSKCC	GRCh37	X	66905906	66905906	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137852573	NA	P-0022937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	193	694	1	ENST00000374690.3:c.1823G>A	p.Arg608Gln	p.R608Q	ENST00000374690	NM_000044.3	608	cGa/cAa	3/8	1	2	FACETS	0.935	0.867	1	0.935	0.867	1	CLONAL	1	TRUE	1	0.564892024374862	2		695	731	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104315	2104317	+	missense_variant	Missense_Mutation	TNP	CTC	CTC	TTT	novel	NA	P-0022937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	66	623	0	ENST00000219476.3:c.355_357delinsTTT	p.Leu119Phe	p.L119F	ENST00000219476	NM_000548.3	119	CTC/TTT	5/42	NA	2	FACETS	0.304	0.263	0.348			1	INDETERMINATE	1	TRUE	NA	0.564892024374862	2		623	769	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0022976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	344	919	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.756415128567681	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.756415128567681	1		920	537	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007330	143007330	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	247	537	0	ENST00000262992.4:c.2454A>C	p.Arg818Ser	p.R818S	ENST00000262992	NM_001101669.1	818	agA/agC	22/24	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.756415128567681	2		537	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0022996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	368	883	4	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.317855677923315	3	FACETS	0.894	0.854	0.934	0.894	0.854	0.934	CLONAL	3	FALSE	0	0.42897599248987	3		887	777	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508946	106508946	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	70	425	0	ENST00000359195.3:c.940G>A	p.Ala314Thr	p.A314T	ENST00000359195	NM_002649.2	314	Gcc/Acc	2/11	0.42897599248987	7	FACETS	0.848	0.738	0.967	0.212	0.184	0.242	CLONAL	1	FALSE	3	0.42897599248987	7		425	798	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541475	187541475	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs76613365	NA	P-0022996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	84	512	1	ENST00000441802.2:c.6265G>A	p.Val2089Ile	p.V2089I	ENST00000441802	NM_005245.3	2089	Gtt/Att	10/27	0.411874582946501	3	FACETS	0.846	0.749	0.95	0.282	0.249	0.317	CLONAL	1	FALSE	0	0.42897599248987	3		513	562	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372071	55372071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	188	539	0	ENST00000297316.4:c.761C>T	p.Ala254Val	p.A254V	ENST00000297316	NM_022454.3	254	gCg/gTg	2/2	0.42897599248987	7	FACETS	1	0.989	1	0.286	0.263	0.31	CLONAL	1	FALSE	2	0.42897599248987	7		539	1270	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981096	201981096	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	126	635	0	ENST00000359651.3:c.175T>A	p.Trp59Arg	p.W59R	ENST00000359651		59	Tgg/Agg	2/8	0.42897599248987	4	FACETS	1	0.942	1	0.264	0.238	0.29	CLONAL	1	FALSE	0	0.42897599248987	4		635	796	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774929	73774929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	173	597	0	ENST00000254810.4:c.244G>A	p.Asp82Asn	p.D82N	ENST00000254810	NM_005324.3	82	Gac/Aac	3/4	0.373617098469673	5	FACETS	1	0.95	1			1	CLONAL	1	FALSE	NA	0.42897599248987	5		597	1266	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090658	71090658	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	123	398	0	ENST00000318789.4:c.690G>T	p.Gln230His	p.Q230H	ENST00000318789	NM_032682.5	230	caG/caT	11/21	0.417711817296169	4	FACETS	0.818	0.744	0.895	0.409	0.372	0.448	CLONAL	2	FALSE	0	0.42897599248987	4		398	501	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339367	116339367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372320153	NA	P-0022996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	69	454	0	ENST00000397752.3:c.229G>A	p.Asp77Asn	p.D77N	ENST00000397752	NM_000245.2	77	Gac/Aac	2/21	0.42897599248987	7	FACETS	0.887	0.771	1	0.222	0.192	0.253	CLONAL	1	FALSE	3	0.42897599248987	7		454	752	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641164	93641167	+	frameshift_variant	Frame_Shift_Del	DEL	ACCC	ACCC	-	novel	NA	P-0022996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	106	621	0	ENST00000375746.1:c.1511_1514del	p.Thr504AsnfsTer57	p.T504Nfs*57	ENST00000375746	NM_001174167.1	504	ACCCaa/aa	11/14	0.42897599248987	6	FACETS	0.79	0.706	0.88			1	SUBCLONAL	1	FALSE	NA	0.42897599248987	6		621	1162	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0022997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	85	967	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.759	0.671	0.855	0.759	0.671	0.855	SUBCLONAL	1	TRUE	1	0.27875719202307	2		967	803	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0022997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	55	722	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.733	0.628	0.849	0.733	0.628	0.849	SUBCLONAL	1	TRUE	1	0.27875719202307	2		722	538	SUCCESS
APC	324	MSKCC	GRCh37	5	112174086	112174086	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs878853432	NA	P-0022997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	55	561	0	ENST00000257430.4:c.2795C>A	p.Ser932Ter	p.S932*	ENST00000257430	NM_000038.5	932	tCa/tAa	16/16	1	2	FACETS	0.716	0.613	0.829	0.716	0.613	0.829	SUBCLONAL	1	TRUE	1	0.27875719202307	2		561	551	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299983	15299983	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1390414547	NA	P-0022997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	114	805	0	ENST00000263388.2:c.1195G>A	p.Ala399Thr	p.A399T	ENST00000263388	NM_000435.2	399	Gcc/Acc	8/33	1	2	FACETS	0.966	0.869	1	0.966	0.869	1	CLONAL	1	TRUE	1	0.27875719202307	2		805	847	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	47	515	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.844	0.713	0.99	0.844	0.713	0.99	CLONAL	1	TRUE	1	0.22352597958643	2		515	498	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0022999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	65	806	0	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	0.22352597958643	1	FACETS	0.765	0.663	0.876	0.765	0.663	0.876	SUBCLONAL	1	TRUE	0	0.22352597958643	1		806	675	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631837	90631837	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	69	753	1	ENST00000330062.3:c.516G>T	p.Arg172Ser	p.R172S	ENST00000330062	NM_002168.2	172	agG/agT	4/11	1	2	FACETS	0.972	0.847	1	0.972	0.847	1	CLONAL	1	TRUE	1	0.22352597958643	2		754	635	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262193	10262193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	69	898	0	ENST00000340748.4:c.2098G>A	p.Asp700Asn	p.D700N	ENST00000340748		700	Gat/Aat	23/40	1	2	FACETS	0.748	0.65	0.855	0.748	0.65	0.855	SUBCLONAL	1	TRUE	1	0.22352597958643	2		898	825	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610468	10610468	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	129	819	0	ENST00000171111.5:c.242T>G	p.Leu81Arg	p.L81R	ENST00000171111	NM_203500.1	81	cTg/cGg	2/6	0.236795340055413	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.236795340055413	1		819	861	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	117	482	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.944	0.855	1	0.944	0.855	1	CLONAL	1	TRUE	1	0.5	2		482	496	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0023001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	99	336	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	0.5	2		336	393	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0023001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	274	534	0	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	1	0.981	1	1	0.996	1	CLONAL	2	TRUE	1	0.5	2		534	515	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982403	201982404	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0023001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	231	748	0	ENST00000359651.3:c.783dup	p.Glu262ArgfsTer39	p.E262Rfs*39	ENST00000359651		261	ctc/ctCc	6/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.5	2		748	878	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639936	3639936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	140	689	0	ENST00000294008.3:c.3703C>T	p.Pro1235Ser	p.P1235S	ENST00000294008	NM_032444.2	1235	Ccc/Tcc	12/15	1	2	FACETS	0.86	0.786	0.938	0.86	0.786	0.938	CLONAL	1	TRUE	1	0.5	2		689	651	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853089	151853089	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	160	532	0	ENST00000262189.6:c.11866G>C	p.Asp3956His	p.D3956H	ENST00000262189	NM_170606.2	3956	Gac/Cac	46/59	1	2	FACETS	0.971	0.893	1	0.971	0.893	1	CLONAL	1	TRUE	1	0.5	2		532	659	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969432	44969433	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0023001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	185	339	0	ENST00000377967.4:c.4115_4116del	p.Phe1372CysfsTer16	p.F1372Cfs*16	ENST00000377967	NM_021140.2	1372	TTt/t	28/29	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.5	1		339	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0023009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	77	649	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.486	0.426	0.55	0.486	0.426	0.55	SUBCLONAL	1	TRUE	1	0.49	2		649	647	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0023009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	102	566	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.553	0.494	0.615	0.553	0.494	0.615	SUBCLONAL	1	TRUE	1	0.49	2		566	753	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0023009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	36	433	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	1	2	FACETS	0.374	0.307	0.448	0.374	0.307	0.448	SUBCLONAL	1	TRUE	1	0.49	2		433	393	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573605	48573605	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	18	368	0	ENST00000342988.3:c.191del	p.Asn64MetfsTer30	p.N64Mfs*30	ENST00000342988	NM_005359.5	63	acA/ac	2/12	1	2	FACETS	0.209	0.157	0.27	0.209	0.157	0.27	SUBCLONAL	1	TRUE	1	0.49	2		368	352	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0023010-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	190	461	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.56	2		461	558	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115711	8115711	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023010-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	143	443	0	ENST00000346208.3:c.1060del	p.Leu354Ter	p.L354*	ENST00000346208		353	Ccc/cc	6/6	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.56	2		443	485	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247984	59247984	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023010-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	268	779	0	ENST00000371222.2:c.759C>G	p.Ile253Met	p.I253M	ENST00000371222	NM_002228.3	253	atC/atG	1/1	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.56	2		779	796	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063332	67063332	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023010-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	188	403	1	ENST00000412916.2:c.22C>T	p.Gln8Ter	p.Q8*	ENST00000412916		8	Cag/Tag	1/6	0.696725179002332	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.56	1		404	340	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0023012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	225	867	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.971	0.905	1	0.971	0.905	1	CLONAL	1	TRUE	1	0.493548981449768	2		868	939	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138521	11138521	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	226	1081	0	ENST00000358026.2:c.3277C>T	p.Arg1093Ter	p.R1093*	ENST00000358026	NM_001128849.1	1093	Cga/Tga	24/36	0.493548981449768	1	FACETS	0.741	0.691	0.793	0.741	0.691	0.793	SUBCLONAL	1	TRUE	0	0.493548981449768	1		1081	931	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615108	43615108	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	262	1049	0	ENST00000355710.3:c.2522C>A	p.Pro841Gln	p.P841Q	ENST00000355710	NM_020975.4	841	cCg/cAg	14/20	1	2	FACETS	0.984	0.922	1	0.984	0.922	1	CLONAL	1	TRUE	1	0.493548981449768	2		1049	1079	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918610	94918610	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	173	874	0	ENST00000536441.1:c.572T>C	p.Val191Ala	p.V191A	ENST00000536441	NM_144665.3	191	gTa/gCa	5/10	1	2	FACETS	0.795	0.732	0.86	0.795	0.732	0.86	SUBCLONAL	1	TRUE	1	0.493548981449768	2		874	882	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235833	108235833	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	108	674	0	ENST00000278616.4:c.8875G>A	p.Asp2959Asn	p.D2959N	ENST00000278616	NM_000051.3	2959	Gac/Aac	62/63	0.493548981449768	1	FACETS	0.596	0.537	0.659	0.596	0.537	0.659	SUBCLONAL	1	TRUE	0	0.493548981449768	1		674	553	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989407	7989407	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	130	1040	0	ENST00000319144.4:c.279C>A	p.Asn93Lys	p.N93K	ENST00000319144	NM_001139.2	93	aaC/aaA	2/15	0.271514284413096	1	FACETS	0.39	0.353	0.429	0.39	0.353	0.429	INDETERMINATE	1	TRUE	0	0.493548981449768	1		1040	1018	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221227	1221228	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0023012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	304	987	2	ENST00000326873.7:c.750_751delinsCT	p.Gly251Cys	p.G251C	ENST00000326873	NM_000455.4	250	acGGgt/acCTgt	6/10	0.493548981449768	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.493548981449768	1		989	896	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713354	30713355	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0023012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	33	645	0	ENST00000295754.5:c.679_680insC	p.Ile227ThrfsTer19	p.I227Tfs*19	ENST00000295754	NM_003242.5	227	atc/aCtc	4/7	0.271514284413096	1	FACETS	0.166	0.135	0.202	0.166	0.135	0.202	INDETERMINATE	1	TRUE	0	0.493548981449768	1		645	605	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891404	76891404	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0023012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	125	574	0	ENST00000373344.5:c.4699+2T>G		p.X1567_splice	ENST00000373344	NM_000489.3	1567			0.310706499637003	1	FACETS	0.707	0.642	0.774	0.707	0.642	0.774	SUBCLONAL	1	TRUE	0	0.493548981449768	1		574	540	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0023013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	128	724	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.962	0.872	1	1	0.989	1	CLONAL	2	TRUE	1	0.17	2		726	783	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0023013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	64	879	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.17	2		881	642	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593437	55593437	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55792975	NA	P-0023013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	66	628	2	ENST00000288135.5:c.1594G>A	p.Val532Ile	p.V532I	ENST00000288135	NM_000222.2	532	Gta/Ata	10/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.17	2		630	565	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209489	98209489	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs978722722	NA	P-0023013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	45	745	1	ENST00000331920.6:c.4049G>A	p.Arg1350Gln	p.R1350Q	ENST00000331920	NM_000264.3	1350	cGg/cAg	23/24	1	2	FACETS	0.991	0.833	1	0.991	0.833	1	CLONAL	1	TRUE	1	0.17	2		746	534	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0023014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	256	770	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.575628144830936	2		770	712	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525116	9525116	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	217	583	0	ENST00000353224.5:c.1769G>T	p.Cys590Phe	p.C590F	ENST00000353224	NM_177990.2	590	tGt/tTt	8/10	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.575628144830936	2		583	753	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14317322	14317322	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	111	675	0	ENST00000256196.4:c.188G>C	p.Arg63Pro	p.R63P	ENST00000256196		63	cGg/cCg	2/6	0.411484129414778	1	FACETS	0.379	0.341	0.42	0.379	0.341	0.42	SUBCLONAL	1	TRUE	0	0.575628144830936	1		675	724	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218431	1218436	+	inframe_deletion	In_Frame_Del	DEL	GAGGAG	GAGGAG	-	novel	NA	P-0023014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	353	821	0	ENST00000326873.7:c.307_312del	p.Arg103_Arg104del	p.R103_R104del	ENST00000326873	NM_000455.4	102	ctGAGGAGg/ctg	2/10	0.575628144830936	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.575628144830936	1		821	867	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599944	10599944	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	441	915	0	ENST00000171111.5:c.1632G>T	p.Trp544Cys	p.W544C	ENST00000171111	NM_203500.1	544	tgG/tgT	5/6	0.575628144830936	1	FACETS	0.955	0.913	0.997	0.955	0.913	0.997	CLONAL	1	TRUE	0	0.575628144830936	1		915	1143	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251857	212251857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	135	337	0	ENST00000342788.4:c.3202G>A	p.Asp1068Asn	p.D1068N	ENST00000342788	NM_005235.2	1068	Gat/Aat	27/28	1	2	FACETS	0.912	0.842	0.983	0.912	0.842	0.983	CLONAL	1	TRUE	1	0.936670198418623	2		337	316	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456886	32456886	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	413	663	0	ENST00000332351.3:c.6G>T	p.Gln2His	p.Q2H	ENST00000332351	NM_024426.4	2	caG/caT	1/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.936670198418623	2		663	810	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418394	49418394	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	411	832	0	ENST00000301067.7:c.16019G>C	p.Arg5340Pro	p.R5340P	ENST00000301067	NM_003482.3	5340	cGa/cCa	50/54	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.936670198418623	2		832	864	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955493	48955493	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0023039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	226	584	1	ENST00000267163.4:c.1609A>T	p.Lys537Ter	p.K537*	ENST00000267163	NM_000321.2	537	Aaa/Taa	17/27	0.936670198418623	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.936670198418623	1		585	245	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739097	40739097	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	493	802	0	ENST00000373198.4:c.3187C>T	p.Leu1063Phe	p.L1063F	ENST00000373198	NM_133170.3	1063	Ctc/Ttc	24/32	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.936670198418623	2		802	951	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31448684	31448684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1387790694	NA	P-0023039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	378	889	0	ENST00000344624.3:c.2852G>A	p.Arg951His	p.R951H	ENST00000344624		951	cGc/cAc	20/33	0.865907040760754	3	FACETS	0.945	0.897	0.994	0.473	0.448	0.497	CLONAL	1	TRUE	1	0.936670198418623	3		889	1254	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609893	117609893	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	381	986	0	ENST00000368508.3:c.6806G>C	p.Arg2269Pro	p.R2269P	ENST00000368508	NM_002944.2	2269	cGa/cCa	43/43	1	2	FACETS	0.963	0.919	1	0.963	0.919	1	CLONAL	1	TRUE	1	0.936670198418623	2		986	845	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	206	482	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.976	0.915	1	0.976	0.915	1	CLONAL	1	TRUE	1	0.85258902420974	2		482	495	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712018	89712018	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs727504114	NA	P-0023040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	145	294	0	ENST00000371953.3:c.634+2T>C		p.X212_splice	ENST00000371953	NM_000314.4	212			0.851275050810362	1	FACETS	0.952	0.9	1	0.952	0.9	1	CLONAL	1	TRUE	0	0.85258902420974	1		294	205	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41249295	41249295	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	359	604	0	ENST00000357654.3:c.559T>C	p.Ser187Pro	p.S187P	ENST00000357654	NM_007294.3	187	Tct/Cct	8/23	1	2	FACETS	0.987	0.94	1	0.987	0.94	1	CLONAL	1	TRUE	1	0.85258902420974	2		604	853	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0023042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	134	411	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.259148194663231	2	FACETS	0.825	0.757	0.896	0.825	0.757	0.896	CLONAL	2	TRUE	0	0.384752206421078	2		411	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578464	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1545	117	1260	0	ENST00000269305.4:c.466C>G	p.Arg156Gly	p.R156G	ENST00000269305	NM_001126112.2	156	Cgc/Ggc	5/11	0.176060327425672	3	FACETS	0.436	0.392	0.484	0.145	0.13	0.162	INDETERMINATE	1	TRUE	0	0.384752206421078	3		1260	1662	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0023042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	291	433	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	0.309114446318343	2	FACETS	0.915	0.864	0.966	0.915	0.864	0.966	CLONAL	2	TRUE	0	0.384752206421078	2		433	827	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0023042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	416	1014	0	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	0.176060327425672	3	FACETS	1	0.99	1	0.749	0.715	0.785	INDETERMINATE	2	TRUE	0	0.384752206421078	3		1014	1147	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056648	26056648	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs755438887	NA	P-0023042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	39	194	0	ENST00000343677.2:c.9G>C	p.Glu3Asp	p.E3D	ENST00000343677	NM_005319.3	3	gaG/gaC	1/1	0.384752206421078	6	FACETS	0.74	0.613	0.881	0.185	0.153	0.221	SUBCLONAL	1	TRUE	2	0.384752206421078	6		194	485	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998408	100998408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	129	397	0	ENST00000325455.5:c.1394C>T	p.Ala465Val	p.A465V	ENST00000325455	NM_001202474.3	465	gCg/gTg	1/8	0.384752206421078	2	FACETS	0.86	0.787	0.934	0.86	0.787	0.934	CLONAL	2	TRUE	0	0.384752206421078	2		397	390	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860126	57860126	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	329	1019	0	ENST00000228682.2:c.866T>G	p.Val289Gly	p.V289G	ENST00000228682	NM_005269.2	289	gTg/gGg	8/12	0.12752377710048	4	FACETS	0.799	0.753	0.846	0.799	0.753	0.846	INDETERMINATE	2	TRUE	2	0.384752206421078	4		1019	1482	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937056	48937056	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	93	422	0	ENST00000267163.4:c.824A>C	p.Glu275Ala	p.E275A	ENST00000267163	NM_000321.2	275	gAa/gCa	8/27	0.299788338699551	3	FACETS	1	0.972	1	0.801	0.725	0.878	CLONAL	2	TRUE	0	0.384752206421078	3		422	240	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031928	10031928	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	91	891	0	ENST00000330684.3:c.895C>A	p.Leu299Ile	p.L299I	ENST00000330684	NM_001134407.1	299	Cta/Ata	3/13	1	2	FACETS	0.555	0.492	0.622	0.555	0.492	0.622	SUBCLONAL	1	TRUE	1	0.384752206421078	2		891	853	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210497	2210498	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0023042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	219	1175	2	ENST00000398665.3:c.1104_1105del	p.Asp369ArgfsTer8	p.D369Rfs*8	ENST00000398665	NM_032482.2	368	gcCGac/gcac	13/28	0.309114446318343	2	FACETS	0.887	0.823	0.953	0.443	0.411	0.477	CLONAL	1	TRUE	0	0.384752206421078	2		1177	1284	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610172	10610172	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	410	999	0	ENST00000171111.5:c.538del	p.Asp180ThrfsTer50	p.D180Tfs*50	ENST00000171111	NM_203500.1	180	Gac/ac	2/6	0.309114446318343	2	FACETS	0.834	0.794	0.875	0.834	0.794	0.875	CLONAL	2	TRUE	0	0.384752206421078	2		999	1278	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628488	187628488	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	272	1204	0	ENST00000441802.2:c.2494A>C	p.Ser832Arg	p.S832R	ENST00000441802	NM_005245.3	832	Agt/Cgt	2/27	0.272169351082152	2	FACETS	1	0.993	1	0.726	0.682	0.771	CLONAL	1	TRUE	0	0.384752206421078	2		1204	974	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	198	482	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.742641299873972	2		482	477	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435100	110435100	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	320	965	0	ENST00000375856.3:c.3301C>G	p.Pro1101Ala	p.P1101A	ENST00000375856	NM_003749.2	1101	Ccg/Gcg	1/2	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.742641299873972	2		965	852	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900410	3900410	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	312	901	0	ENST00000262367.5:c.686del	p.Pro229GlnfsTer15	p.P229Qfs*15	ENST00000262367	NM_004380.2	229	cCa/ca	2/31	1	2	FACETS	0.951	0.899	1	0.951	0.899	1	CLONAL	1	TRUE	1	0.742641299873972	2		901	884	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443664	29443664	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs749016081	NA	P-0023043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	294	848	0	ENST00000389048.3:c.3553G>T	p.Val1185Leu	p.V1185L	ENST00000389048	NM_004304.4	1185	Gtg/Ttg	23/29	1	2	FACETS	0.933	0.881	0.985	0.933	0.881	0.985	CLONAL	1	TRUE	1	0.742641299873972	2		848	849	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413043	139413043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	193	550	0	ENST00000277541.6:c.1099G>C	p.Gly367Arg	p.G367R	ENST00000277541	NM_017617.3	367	Ggt/Cgt	6/34	1	2	FACETS	0.959	0.894	1	0.959	0.894	1	CLONAL	1	TRUE	1	0.742641299873972	2		550	542	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0023044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	19	919	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.229354595360569	1	FACETS	0.854	0.656	1	0.854	0.656	1	CLONAL	1	FALSE	0	0.312852630968982	1		920	120	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	41	896	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	FALSE	1	0.312852630968982	2		898	243	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480320	56480320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	36	485	0	ENST00000267101.3:c.427C>A	p.Leu143Met	p.L143M	ENST00000267101	NM_001982.3	143	Ctg/Atg	4/28	1	2	FACETS	0.778	0.65	0.916	1	0.956	1	CLONAL	2	FALSE	1	0.312852630968982	2		485	148	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267359	198267359	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs377023736	NA	P-0023044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	11	689	6	ENST00000335508.6:c.1998G>C	p.Lys666Asn	p.K666N	ENST00000335508	NM_012433.2	666	aaG/aaC	14/25	0.279000264368415	3	FACETS	0.336	0.232	0.466	0.168	0.116	0.233	SUBCLONAL	1	FALSE	1	0.312852630968982	3		695	242	SUCCESS
APC	324	MSKCC	GRCh37	5	112176926	112176926	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587779799	NA	P-0023044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	15	500	3	ENST00000257430.4:c.5635G>T	p.Ala1879Ser	p.A1879S	ENST00000257430	NM_000038.5	1879	Gct/Tct	16/16	0.312852630968982	3	FACETS	0.575	0.421	0.758	0.287	0.21	0.379	SUBCLONAL	1	FALSE	1	0.312852630968982	3		503	193	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108080	30108080	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1239799730	NA	P-0023044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	30	901	1	ENST00000331968.5:c.727C>T	p.Arg243Ter	p.R243*	ENST00000331968	NM_002742.2	243	Cga/Tga	5/18	0.279000264368415	3	FACETS	0.884	0.715	1	0.442	0.357	0.537	CLONAL	1	FALSE	1	0.312852630968982	3		902	251	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004864	16004864	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	11	771	0	ENST00000268712.3:c.2390A>T	p.Asp797Val	p.D797V	ENST00000268712	NM_006311.3	797	gAt/gTt	20/46	0.229354595360569	1	FACETS	0.378	0.262	0.521	0.378	0.262	0.521	SUBCLONAL	1	FALSE	0	0.312852630968982	1		771	157	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151195	202151195	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	26	366	0	ENST00000358485.4:c.1495C>G	p.Leu499Val	p.L499V	ENST00000358485	NM_001080125.1	499	Ctc/Gtc	9/9	0.279000264368415	3	FACETS	1	0.847	1	0.537	0.429	0.659	CLONAL	1	FALSE	1	0.312852630968982	3		366	179	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0023045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	234	722	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.51667728103387	2		722	828	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070577	67070578	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	109	326	0	ENST00000412916.2:c.207dup	p.Pro70SerfsTer13	p.P70Sfs*13	ENST00000412916		67	-/T	3/6	0.49737916935155	1	FACETS	0.945	0.859	1	0.945	0.859	1	CLONAL	1	TRUE	0	0.51667728103387	1		326	331	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0023046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	224	503	1	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		504	546	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063718	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0023046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	93	509	0	ENST00000412916.2:c.165+2dup		p.X55_splice	ENST00000412916		55			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		509	167	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374673	118374673	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	62	524	0	ENST00000534358.1:c.8066G>T	p.Arg2689Ile	p.R2689I	ENST00000534358	NM_005933.3	2689	aGa/aTa	27/36	0.327167490389686	3	FACETS	0.794	0.698	0.894	0.794	0.698	0.894	SUBCLONAL	2	TRUE	1	0.520836293146546	3		524	189	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0023049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	639	826	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	0.661454035827365	2	FACETS	0.879	0.856	0.902	0.879	0.856	0.902	CLONAL	2	TRUE	0	0.786417151763775	2		826	924	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100532	157100532	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	423	433	0	ENST00000346085.5:c.1469G>A	p.Trp490Ter	p.W490*	ENST00000346085	NM_020732.3	490	tGg/tAg	1/20	0.666427279298949	2	FACETS	0.861	0.832	0.889	0.861	0.832	0.889	CLONAL	2	TRUE	0	0.786417151763775	2		433	625	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030329	180030329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142322370	NA	P-0023049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	189	965	1	ENST00000261937.6:c.3955C>T	p.Arg1319Trp	p.R1319W	ENST00000261937	NM_182925.4	1319	Cgg/Tgg	30/30	0.661454035827365	2	FACETS	0.485	0.448	0.524	0.243	0.224	0.262	SUBCLONAL	1	TRUE	0	0.786417151763775	2		966	991	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117874164	117874164	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	54	561	0	ENST00000297338.2:c.290C>G	p.Pro97Arg	p.P97R	ENST00000297338	NM_006265.2	97	cCt/cGt	4/14	0.786417151763775	3	FACETS	0.52	0.446	0.6	0.26	0.223	0.3	SUBCLONAL	1	TRUE	1	0.786417151763775	3		561	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0023051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	57	983	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.573	0.491	0.663	0.573	0.491	0.663	SUBCLONAL	1	TRUE	1	0.29	2		984	686	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0023051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	46	609	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	1	2	FACETS	0.607	0.511	0.713	0.607	0.511	0.713	SUBCLONAL	1	TRUE	1	0.29	2		609	523	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194718	29194718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764669713	NA	P-0023051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	51	1125	0	ENST00000240100.2:c.1010C>T	p.Thr337Met	p.T337M	ENST00000240100	NM_001394.6	337	aCg/aTg	4/4	1	2	FACETS	0.454	0.385	0.531	0.454	0.385	0.531	SUBCLONAL	1	TRUE	1	0.29	2		1125	774	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0023052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	212	830	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.406060088862392	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.406060088862392	1		832	765	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716212	52716212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555791268	NA	P-0023052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	258	632	3	ENST00000322088.6:c.656C>T	p.Ser219Leu	p.S219L	ENST00000322088	NM_014225.5	219	tCg/tTg	6/15	0.406060088862392	1	FACETS	0.848	0.801	0.896	1	0.995	1	CLONAL	2	TRUE	0	0.406060088862392	1		635	597	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249510	153249510	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1157879635	NA	P-0023052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	167	618	1	ENST00000281708.4:c.1268G>T	p.Gly423Val	p.G423V	ENST00000281708	NM_033632.3	423	gGa/gTa	9/12	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.406060088862392	2		619	732	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	202	617	0	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.406060088862392	2		617	757	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476387	88476387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202056599	NA	P-0023052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	251	665	0	ENST00000360948.2:c.1745G>A	p.Arg582Gln	p.R582Q	ENST00000360948	NM_001012338.2	582	cGg/cAg	15/19	0.207795837464764	3	FACETS	0.907	0.851	0.964	0.907	0.851	0.964	INDETERMINATE	2	TRUE	1	0.406060088862392	3		665	820	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526498	66526498	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	68	566	0	ENST00000358598.2:c.1054C>T	p.Arg352Ter	p.R352*	ENST00000358598	NM_212471.2	352	Cga/Tga	11/11	0.406060088862392	4	FACETS	0.532	0.462	0.609	0.177	0.154	0.203	SUBCLONAL	1	TRUE	1	0.406060088862392	4		566	885	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106528	27106528	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	251	959	1	ENST00000324856.7:c.6139G>T	p.Glu2047Ter	p.E2047*	ENST00000324856	NM_006015.4	2047	Gag/Tag	20/20	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.406060088862392	2		960	1065	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285850	39285851	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAAGGGTTTCTTCGCTTCCTC	novel	NA	P-0023052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	133	723	0	ENST00000402219.2:c.288_308dup	p.Arg97_Leu103dup	p.R97_L103dup	ENST00000402219	NM_005633.3	97	tta/ttGAGGAAGCGAAGAAACCCTTTa	3/23	1	2	FACETS	0.895	0.814	0.98	0.895	0.814	0.98	CLONAL	1	TRUE	1	0.406060088862392	2		723	732	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141594	202141594	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0023052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	215	540	0	ENST00000358485.4:c.882C>G	p.Tyr294Ter	p.Y294*	ENST00000358485	NM_001080125.1	294	taC/taG	7/9	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.406060088862392	2		540	747	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916932	178916932	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	206	613	0	ENST00000263967.3:c.319A>C	p.Asn107His	p.N107H	ENST00000263967	NM_006218.2	107	Aac/Cac	2/21	1	2	FACETS	0.775	0.722	0.828	1	0.992	1	SUBCLONAL	2	TRUE	1	0.406060088862392	2		613	655	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	229	482	0				ENST00000310581	NM_198253.2	-/1132			0.278497220150221	5	FACETS	1	0.935	1	0.667	0.623	0.712	INDETERMINATE	2	TRUE	2	0.52908173737145	5		482	776	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100375	27100375	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	157	806	1	ENST00000324856.7:c.4087C>T	p.Gln1363Ter	p.Q1363*	ENST00000324856	NM_006015.4	1363	Caa/Taa	17/20	0.474870634915034	4	FACETS	0.982	0.899	1	0.327	0.299	0.357	CLONAL	1	TRUE	1	0.52908173737145	4		807	924	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265021	5265021	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0023053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	140	854	0	ENST00000357368.4:c.566C>G	p.Ser189Ter	p.S189*	ENST00000357368	NM_002850.3	189	tCa/tGa	5/38	0.457792641319469	3	FACETS	0.851	0.776	0.931	0.284	0.258	0.311	CLONAL	1	TRUE	0	0.52908173737145	3		854	786	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955578	48955578	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0023053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	515	417	0	ENST00000267163.4:c.1694C>G	p.Ser565Ter	p.S565*	ENST00000267163	NM_000321.2	565	tCa/tGa	17/27	0.52908173737145	5	FACETS	0.996	0.969	1			1	CLONAL	5	TRUE	NA	0.52908173737145	5		417	701	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646234	23646234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs180177103	NA	P-0023053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	186	809	0	ENST00000261584.4:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000261584	NM_024675.3	545	Gaa/Aaa	4/13	0.440515171977658	3	FACETS	1	0.961	1	0.53	0.49	0.572	CLONAL	1	TRUE	1	0.52908173737145	3		809	838	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81922876	81922876	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	122	614	1	ENST00000359376.3:c.865G>A	p.Glu289Lys	p.E289K	ENST00000359376	NM_002661.3	289	Gag/Aag	10/33	0.52908173737145	6	FACETS	0.882	0.796	0.974	0.221	0.199	0.244	CLONAL	1	TRUE	2	0.52908173737145	6		615	1076	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031997	26031997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	278	552	0	ENST00000244661.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000244661	NM_003537.3	98	Gag/Aag	1/1	0.362800444821063	6	FACETS	0.909	0.857	0.962	0.909	0.857	0.962	CLONAL	3	TRUE	3	0.52908173737145	6		552	793	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163315549	163315549	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	97	655	0	ENST00000271452.3:c.889C>G	p.Gln297Glu	p.Q297E	ENST00000271452	NM_145697.2	297	Caa/Gaa	11/14	0.52908173737145	5	FACETS	0.693	0.617	0.775	0.231	0.205	0.259	SUBCLONAL	1	TRUE	2	0.52908173737145	5		655	949	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861968	57861968	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	128	584	0	ENST00000228682.2:c.1269C>G	p.Ile423Met	p.I423M	ENST00000228682	NM_005269.2	423	atC/atG	10/12	0.470961486335817	3	FACETS	0.973	0.884	1	0.486	0.442	0.533	CLONAL	1	TRUE	1	0.52908173737145	3		584	629	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370212	40370212	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	436	1047	0	ENST00000293328.3:c.1126G>C	p.Glu376Gln	p.E376Q	ENST00000293328	NM_012448.3	376	Gag/Cag	9/19	0.52908173737145	6	FACETS	1	0.969	1	0.512	0.487	0.538	CLONAL	2	TRUE	2	0.52908173737145	6		1047	1655	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774771	73774771	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	671	851	0	ENST00000254810.4:c.316G>C	p.Glu106Gln	p.E106Q	ENST00000254810	NM_005324.3	106	Gaa/Caa	4/4	0.52908173737145	6	FACETS	0.992	0.96	1	0.992	0.96	1	CLONAL	4	TRUE	2	0.52908173737145	6		851	1315	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051153	13051153	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	124	692	0	ENST00000316448.5:c.589G>C	p.Glu197Gln	p.E197Q	ENST00000316448	NM_004343.3	197	Gaa/Caa	5/9	0.457792641319469	3	FACETS	0.835	0.756	0.918	0.278	0.252	0.306	CLONAL	1	TRUE	0	0.52908173737145	3		692	710	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42788864	42788864	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	136	800	0	ENST00000575354.2:c.8C>G	p.Ser3Trp	p.S3W	ENST00000575354	NM_015125.3	3	tCg/tGg	1/20	0.474870634915034	4	FACETS	0.85	0.772	0.932	0.283	0.257	0.311	CLONAL	1	TRUE	1	0.52908173737145	4		800	925	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793239	242793239	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	190	1139	0	ENST00000334409.5:c.838G>C	p.Glu280Gln	p.E280Q	ENST00000334409	NM_005018.2	280	Gag/Cag	5/5	1	2	FACETS	0.795	0.736	0.857	0.795	0.736	0.857	SUBCLONAL	1	TRUE	1	0.52908173737145	2		1139	903	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125716	47125716	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	117	535	0	ENST00000409792.3:c.5554C>A	p.His1852Asn	p.H1852N	ENST00000409792	NM_014159.6	1852	Cat/Aat	12/21	0.4661259542293	2	FACETS	0.914	0.829	1	0.457	0.414	0.502	CLONAL	1	TRUE	0	0.52908173737145	2		535	484	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935623	49935623	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	121	852	0	ENST00000296474.3:c.1741C>G	p.Leu581Val	p.L581V	ENST00000296474	NM_002447.2	581	Cta/Gta	5/20	0.4661259542293	2	FACETS	0.781	0.707	0.857	0.39	0.353	0.429	SUBCLONAL	1	TRUE	0	0.52908173737145	2		852	586	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081684	143081684	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	102	433	0	ENST00000262992.4:c.1390C>G	p.Gln464Glu	p.Q464E	ENST00000262992	NM_001101669.1	464	Caa/Gaa	15/24	0.52908173737145	4	FACETS	1	0.955	1	0.372	0.333	0.412	CLONAL	1	TRUE	1	0.52908173737145	4		433	529	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521451	187521451	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	371	599	1	ENST00000441802.2:c.11704C>T	p.Gln3902Ter	p.Q3902*	ENST00000441802	NM_005245.3	3902	Cag/Tag	22/27	0.52908173737145	4	FACETS	0.874	0.834	0.914	0.874	0.834	0.914	CLONAL	3	TRUE	1	0.52908173737145	4		600	818	SUCCESS
APC	324	MSKCC	GRCh37	5	112177701	112177701	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	58	453	0	ENST00000257430.4:c.6410C>A	p.Ser2137Tyr	p.S2137Y	ENST00000257430	NM_000038.5	2137	tCc/tAc	16/16	0.468369382561985	3	FACETS	0.632	0.544	0.727	0.316	0.272	0.364	SUBCLONAL	1	TRUE	1	0.52908173737145	3		453	439	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707668	176707668	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	112	630	0	ENST00000439151.2:c.5725T>G	p.Ser1909Ala	p.S1909A	ENST00000439151	NM_022455.4	1909	Tct/Gct	18/23	1	2	FACETS	0.837	0.756	0.921	0.837	0.756	0.921	CLONAL	1	TRUE	1	0.52908173737145	2		630	506	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528765	157528765	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	95	597	0	ENST00000346085.5:c.6490G>C	p.Glu2164Gln	p.E2164Q	ENST00000346085	NM_020732.3	2164	Gag/Cag	20/20	1	2	FACETS	0.851	0.762	0.944	0.851	0.762	0.944	CLONAL	1	TRUE	1	0.52908173737145	2		597	422	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335693	81335693	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	111	651	0	ENST00000222390.5:c.1667G>T	p.Arg556Ile	p.R556I	ENST00000222390	NM_000601.4	556	aGa/aTa	15/18	0.42801543140656	5	FACETS	0.743	0.667	0.824	0.248	0.222	0.275	SUBCLONAL	1	TRUE	2	0.52908173737145	5		651	1013	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38184335	38184335	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	357	814	0	ENST00000317025.8:c.1621G>C	p.Asp541His	p.D541H	ENST00000317025	NM_023034.1	541	Gac/Cac	7/24	0.468369382561985	3	FACETS	0.925	0.88	0.971	0.925	0.88	0.971	CLONAL	2	TRUE	1	0.52908173737145	3		814	922	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566418	139566418	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	302	924	0	ENST00000308874.7:c.677C>A	p.Ser226Ter	p.S226*	ENST00000308874		226	tCg/tAg	9/10	0.463991469560723	3	FACETS	0.894	0.846	0.943	0.596	0.564	0.629	CLONAL	2	TRUE	0	0.52908173737145	3		924	807	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475218	475218	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1404815403	NA	P-0023054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	66	1045	0	ENST00000399788.2:c.419C>G	p.Ser140Cys	p.S140C	ENST00000399788	NM_001042603.1	140	tCt/tGt	4/28	NA	2	FACETS	0.62	0.537	0.711			1	INDETERMINATE	1	TRUE	NA	0.219912103382077	2		1045	968	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822357	72822357	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0023054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	64	1134	0	ENST00000268489.5:c.9818C>G	p.Ser3273Ter	p.S3273*	ENST00000268489	NM_006885.3	3273	tCa/tGa	10/10	0.208291624161452	1	FACETS	0.668	0.578	0.767	0.668	0.578	0.767	SUBCLONAL	1	TRUE	0	0.219912103382077	1		1134	775	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917610	151917610	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	75	938	1	ENST00000262189.6:c.3710G>A	p.Arg1237Gln	p.R1237Q	ENST00000262189	NM_170606.2	1237	cGa/cAa	23/59	1	2	FACETS	0.768	0.672	0.872	0.768	0.672	0.872	SUBCLONAL	1	TRUE	1	0.219912103382077	2		939	888	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0023055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	437	521	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.79253537300299	4	FACETS	0.971	0.938	1	0.971	0.938	1	CLONAL	3	TRUE	1	0.793804173032709	4		521	678	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0023055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	240	728	1				ENST00000310581	NM_198253.2	-/1132			0.793804173032709	3	FACETS	0.989	0.939	1	0.989	0.939	1	CLONAL	2	TRUE	1	0.793804173032709	3		729	427	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0023056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	63	515	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.917	0.793	1	0.917	0.793	1	CLONAL	1	TRUE	1	0.240769145769411	2		515	571	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0023057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	125	453	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.443111269559169	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.443111269559169	1		453	400	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0023057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	465	977	1	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.443111269559169	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.443111269559169	2		978	965	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098533	108098533	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs55861249	NA	P-0023057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	209	461	2	ENST00000278616.4:c.103C>T	p.Arg35Ter	p.R35*	ENST00000278616	NM_000051.3	35	Cga/Tga	3/63	0.443111269559169	2	FACETS	0.902	0.845	0.96	0.902	0.845	0.96	CLONAL	2	TRUE	0	0.443111269559169	2		463	523	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926270	112926270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918457	NA	P-0023057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	257	687	2	ENST00000351677.2:c.1403C>T	p.Thr468Met	p.T468M	ENST00000351677	NM_002834.3	468	aCg/aTg	12/16	0.294276144360943	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.443111269559169	1		689	770	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572188	64572188	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1455443205	NA	P-0023057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	68	745	1	ENST00000312049.6:c.1451G>A	p.Arg484Gln	p.R484Q	ENST00000312049	NM_130799.2	484	cGg/cAg	10/10	0.443111269559169	2	FACETS	0.497	0.432	0.567	0.248	0.216	0.284	SUBCLONAL	1	TRUE	0	0.443111269559169	2		746	618	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170015175	170015175	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	51	737	0	ENST00000295797.4:c.1581G>A	p.Trp527Ter	p.W527*	ENST00000295797	NM_002740.5	527	tgG/tgA	16/18	0.121873802380083	4	FACETS	0.326	0.275	0.381	0.163	0.137	0.191	INDETERMINATE	1	TRUE	2	0.443111269559169	4		737	1020	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339193	116339193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	92	368	0	ENST00000397752.3:c.55G>A	p.Val19Met	p.V19M	ENST00000397752	NM_000245.2	19	Gtg/Atg	2/21	0.443111269559169	3	FACETS	1	0.892	1	0.5	0.446	0.558	CLONAL	1	TRUE	1	0.443111269559169	3		368	507	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750430	133750430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	159	737	1	ENST00000318560.5:c.1261G>A	p.Asp421Asn	p.D421N	ENST00000318560	NM_005157.4	421	Gac/Aac	7/11	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.443111269559169	2		738	701	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041391	47041391	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	168	647	0	ENST00000377604.3:c.1735G>A	p.Gly579Ser	p.G579S	ENST00000377604	NM_001204468.1	579	Ggc/Agc	16/24	0.368657330000376	2	FACETS	0.851	0.782	0.923			1	CLONAL	1	TRUE	NA	0.443111269559169	2		647	891	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612101	189612101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778606951	NA	P-0023060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	194	808	1	ENST00000264731.3:c.1853G>A	p.Arg618Gln	p.R618Q	ENST00000264731	NM_003722.4	618	cGg/cAg	14/14	0.367534049278368	3	FACETS	1	0.989	1	0.664	0.617	0.712	CLONAL	1	TRUE	1	0.586165212232377	3		809	645	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619281	37619281	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0023060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	147	512	0	ENST00000447079.4:c.957C>G	p.Tyr319Ter	p.Y319*	ENST00000447079	NM_015083.1	319	taC/taG	1/14	0.23433594671673	3	FACETS	1	0.978	1	0.594	0.545	0.645	INDETERMINATE	1	TRUE	1	0.586165212232377	3		512	546	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306556	163306556	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	64	683	1	ENST00000271452.3:c.353G>T	p.Ser118Ile	p.S118I	ENST00000271452	NM_145697.2	118	aGt/aTt	6/14	0.164006509441214	3	FACETS	0.807	0.703	0.918	0.403	0.351	0.459	INDETERMINATE	1	TRUE	1	0.586165212232377	3		684	350	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667825	37667825	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	84	590	1	ENST00000447079.4:c.2710C>T	p.Pro904Ser	p.P904S	ENST00000447079	NM_015083.1	904	Cca/Tca	8/14	0.23433594671673	3	FACETS	0.915	0.813	1	0.458	0.406	0.512	INDETERMINATE	1	TRUE	1	0.586165212232377	3		591	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579861	7579861	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs876658627	NA	P-0023064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	150	859	0	ENST00000269305.4:c.52del	p.Thr18HisfsTer26	p.T18Hfs*26	ENST00000269305	NM_001126112.2	18	Aca/ca	2/11	1	2	FACETS	0.797	0.727	0.871	1	0.988	1	SUBCLONAL	2	FALSE	1	0.169703237642489	2		859	1109	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187560908	187560908	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	38	513	0	ENST00000441802.2:c.3610G>A	p.Asp1204Asn	p.D1204N	ENST00000441802	NM_005245.3	1204	Gac/Aac	4/27	1	2	FACETS	0.965	0.798	1	0.965	0.798	1	CLONAL	1	FALSE	1	0.169703237642489	2		513	464	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061231	38061231	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	57	768	0	ENST00000250448.2:c.758T>C	p.Met253Thr	p.M253T	ENST00000250448	NM_004496.3	253	aTg/aCg	2/2	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		768	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934574	NA	P-0023066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	400	921	1	ENST00000269305.4:c.844C>G	p.Arg282Gly	p.R282G	ENST00000269305	NM_001126112.2	282	Cgg/Ggg	8/11	0.400380738918898	3	FACETS	0.914	0.874	0.954	0.914	0.874	0.954	CLONAL	3	FALSE	0	0.400380738918898	3		922	875	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560514	65560514	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	365	548	0	ENST00000358664.4:c.83A>G	p.His28Arg	p.H28R	ENST00000358664	NM_002382.4	28	cAt/cGt	3/5	0.400380738918898	5	FACETS	0.878	0.837	0.919	1	0.992	1	CLONAL	4	FALSE	2	0.400380738918898	5		548	831	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247367	153247367	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747241612	NA	P-0023066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	113	338	0	ENST00000281708.4:c.1435C>G	p.Arg479Gly	p.R479G	ENST00000281708	NM_033632.3	479	Cga/Gga	10/12	0.400380738918898	5	FACETS	0.959	0.875	1	0.959	0.875	1	CLONAL	3	FALSE	2	0.400380738918898	5		338	314	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028504	42028504	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751169367	NA	P-0023066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	87	596	1	ENST00000219905.7:c.4042C>T	p.Arg1348Trp	p.R1348W	ENST00000219905	NM_001164273.1	1348	Cgg/Tgg	13/24	0.400380738918898	3	FACETS	0.971	0.862	1			1	CLONAL	1	FALSE	NA	0.400380738918898	3		597	537	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573047	41573047	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	244	892	0	ENST00000263253.7:c.5334del	p.Cys1779AlafsTer29	p.C1779Afs*29	ENST00000263253	NM_001429.3	1778	Ggg/gg	31/31	0.21153679975076	4	FACETS	0.859	0.803	0.916			1	INDETERMINATE	2	FALSE	NA	0.400380738918898	4		892	994	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589583	67589596	+	protein_altering_variant	In_Frame_Del	DEL	TACATGAATATAAC	TACATGAATATAAC	GT	novel	NA	P-0023066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	82	345	2	ENST00000274335.5:c.1346_1359delinsGT	p.Leu449_Asn453delinsCys	p.L449_N453delinsC	ENST00000274335		449	tTACATGAATATAAC/tGT	10/15	0.372717461355425	3	FACETS	0.958	0.868	1	0.958	0.868	1	CLONAL	3	FALSE	0	0.400380738918898	3		347	171	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863054	56863054	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1266824391	NA	P-0023067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	18	481	0	ENST00000519728.1:c.327del	p.Glu110LysfsTer15	p.E110Kfs*15	ENST00000519728	NM_002350.3	107	acA/ac	5/13	1	2	FACETS	0.574	0.438	0.73	0.574	0.438	0.73	SUBCLONAL	1	TRUE	1	0.56	2		481	112	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0023067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	19	430	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.956	0.746	1	0.956	0.746	1	CLONAL	1	TRUE	1	0.56	2		431	71	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	23	349	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	0.148054820680826	3	FACETS	1	0.933	1	0.74	0.596	0.895	INDETERMINATE	1	TRUE	1	0.56	3		350	71	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339111	65339111	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	25	521	4	ENST00000342505.4:c.425del	p.Lys142ArgfsTer26	p.K142Rfs*26	ENST00000342505	NM_002227.2	142	aAg/ag	5/25	0.148054820680826	3	FACETS	0.853	0.681	1	0.426	0.34	0.522	INDETERMINATE	1	TRUE	1	0.56	3		525	134	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915673	131915673	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28903088	NA	P-0023067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	17	392	0	ENST00000265335.6:c.671G>A	p.Arg224His	p.R224H	ENST00000265335		224	cGt/cAt	5/25	0.148054820680826	3	FACETS	0.836	0.634	1	0.418	0.317	0.533	INDETERMINATE	1	TRUE	1	0.56	3		392	93	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1623969	1623969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147142249	NA	P-0023067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	81	595	0	ENST00000344749.5:c.530C>T	p.Pro177Leu	p.P177L	ENST00000344749	NM_001136139.2	177	cCg/cTg	8/19	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.56	2		595	272	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272201	15272201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113178142	NA	P-0023067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	43	624	0	ENST00000263388.2:c.6238C>T	p.Arg2080Trp	p.R2080W	ENST00000263388	NM_000435.2	2080	Cgg/Tgg	33/33	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.56	2		624	139	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348230	348230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748733363	NA	P-0023067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	27	825	0	ENST00000262320.3:c.1276G>A	p.Asp426Asn	p.D426N	ENST00000262320	NM_003502.3	426	Gat/Aat	6/11	1	2	FACETS	0.357	0.285	0.439	0.357	0.285	0.439	SUBCLONAL	1	TRUE	1	0.56	2		825	270	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149982885	149982885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139248642	NA	P-0023067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	10	411	0	ENST00000253339.5:c.3373C>T	p.Arg1125Cys	p.R1125C	ENST00000253339		1125	Cgc/Tgc	7/7	0.266041988679466	4	FACETS	0.655	0.449	0.908	0.328	0.224	0.454	INDETERMINATE	1	TRUE	2	0.56	4		411	85	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619849	1619849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758087547	NA	P-0023067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	25	742	0	ENST00000344749.5:c.1097C>T	p.Thr366Met	p.T366M	ENST00000344749	NM_001136139.2	366	aCg/aTg	14/19	1	2	FACETS	0.292	0.23	0.363	0.292	0.23	0.363	SUBCLONAL	1	TRUE	1	0.56	2		742	306	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944250	81944250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147396004	NA	P-0023067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	102	710	2	ENST00000359376.3:c.1859C>T	p.Thr620Met	p.T620M	ENST00000359376	NM_002661.3	620	aCg/aTg	18/33	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.56	2		712	331	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721099	61721099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1458439158	NA	P-0023067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	29	517	0	ENST00000401558.2:c.1175C>T	p.Pro392Leu	p.P392L	ENST00000401558	NM_003400.3	392	cCg/cTg	12/25	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.56	2		517	82	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992720	68992721	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs764112302	NA	P-0023067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	17	655	11	ENST00000288368.4:c.1693dup	p.Ser565PhefsTer3	p.S565Ffs*3	ENST00000288368	NM_024870.2	562	cgt/cgTt	16/40	1	2	FACETS	0.855	0.655	1	0.855	0.655	1	CLONAL	1	TRUE	1	0.56	2		666	71	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262433	16262433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	24	280	0	ENST00000375759.3:c.9698C>T	p.Ala3233Val	p.A3233V	ENST00000375759	NM_015001.2	3233	gCt/gTt	11/15	0.148054820680826	3	FACETS	0.751	0.596	0.926	0.376	0.298	0.463	INDETERMINATE	1	TRUE	1	0.56	3		280	146	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306549	163306549	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753469318	NA	P-0023067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	25	406	1	ENST00000271452.3:c.346C>T	p.Arg116Trp	p.R116W	ENST00000271452	NM_145697.2	116	Cgg/Tgg	6/14	0.148054820680826	3	FACETS	1	0.874	1	0.56	0.451	0.68	INDETERMINATE	1	TRUE	1	0.56	3		407	102	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63816910	63816910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756022924	NA	P-0023067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	19	170	0	ENST00000279873.7:c.881C>T	p.Pro294Leu	p.P294L	ENST00000279873	NM_032199.2	294	cCg/cTg	6/10	1	2	FACETS	0.771	0.597	0.966	0.771	0.597	0.966	CLONAL	1	TRUE	1	0.56	2		170	88	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465978	69465978	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	78	824	1	ENST00000227507.2:c.816G>T	p.Glu272Asp	p.E272D	ENST00000227507	NM_053056.2	272	gaG/gaT	5/5	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.56	2		825	246	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231383	46231383	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	17	399	0	ENST00000334344.6:c.1223C>A	p.Thr408Asn	p.T408N	ENST00000334344	NM_152641.2	408	aCt/aAt	10/21	0.266041988679466	4	FACETS	1	0.896	1	0.686	0.526	0.866	INDETERMINATE	1	TRUE	2	0.56	4		399	69	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669523	88669523	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750055690	NA	P-0023067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	17	458	0	ENST00000360948.2:c.1375C>T	p.Arg459Trp	p.R459W	ENST00000360948	NM_001012338.2	459	Cgg/Tgg	12/19	1	2	FACETS	0.843	0.645	1	0.843	0.645	1	CLONAL	1	TRUE	1	0.56	2		458	72	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779091	3779091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759638164	NA	P-0023067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	14	576	0	ENST00000262367.5:c.5957C>T	p.Thr1986Met	p.T1986M	ENST00000262367	NM_004380.2	1986	aCg/aTg	31/31	1	2	FACETS	0.307	0.222	0.408	0.307	0.222	0.408	SUBCLONAL	1	TRUE	1	0.56	2		576	163	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619412	1619412	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	40	929	1	ENST00000344749.5:c.1229G>A	p.Gly410Asp	p.G410D	ENST00000344749	NM_001136139.2	410	gGc/gAc	15/19	1	2	FACETS	0.364	0.303	0.433	0.364	0.303	0.433	SUBCLONAL	1	TRUE	1	0.56	2		930	392	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753795	42753795	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	110	924	0	ENST00000222329.4:c.469G>T	p.Glu157Ter	p.E157*	ENST00000222329	NM_006494.2	157	Gag/Tag	4/4	1	2	FACETS	0.817	0.738	0.9	0.817	0.738	0.9	CLONAL	1	TRUE	1	0.56	2		924	481	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082775	16082775	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	35	216	2	ENST00000281043.3:c.589G>A	p.Val197Met	p.V197M	ENST00000281043	NM_005378.4	197	Gtg/Atg	2/3	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.56	2		218	121	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469085	25469085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1468255229	NA	P-0023067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	85	805	0	ENST00000264709.3:c.1373G>A	p.Arg458Gln	p.R458Q	ENST00000264709	NM_175629.2	458	cGg/cAg	11/23	1	2	FACETS	0.97	0.866	1	0.97	0.866	1	CLONAL	1	TRUE	1	0.56	2		805	313	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940499	29940499	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	18	494	0	ENST00000389048.3:c.732T>A	p.Asn244Lys	p.N244K	ENST00000389048	NM_004304.4	244	aaT/aaA	2/29	1	2	FACETS	0.881	0.68	1	0.881	0.68	1	CLONAL	1	TRUE	1	0.56	2		494	73	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660633	190660633	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370300640	NA	P-0023067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	26	285	0	ENST00000441310.2:c.271G>A	p.Gly91Ser	p.G91S	ENST00000441310	NM_000534.4	91	Ggt/Agt	3/13	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.56	2		285	86	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162989	47162989	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	15	368	0	ENST00000409792.3:c.3137A>G	p.Asn1046Ser	p.N1046S	ENST00000409792	NM_014159.6	1046	aAt/aGt	3/21	0.148054820680826	3	FACETS	0.914	0.683	1	0.457	0.341	0.59	INDETERMINATE	1	TRUE	1	0.56	3		368	75	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427778	72427778	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	35	237	0	ENST00000477973.2:c.712A>G	p.Lys238Glu	p.K238E	ENST00000477973	NM_012234.5	238	Aaa/Gaa	4/4	0.148054820680826	3	FACETS	1	0.941	1	0.656	0.549	0.77	INDETERMINATE	1	TRUE	1	0.56	3		237	122	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628344	187628344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199836705	NA	P-0023067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	64	680	4	ENST00000441802.2:c.2638G>A	p.Ala880Thr	p.A880T	ENST00000441802	NM_005245.3	880	Gca/Aca	2/27	1	2	FACETS	0.998	0.876	1	0.998	0.876	1	CLONAL	1	TRUE	1	0.56	2		684	229	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858314	27858314	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	103	518	0	ENST00000359303.2:c.257A>G	p.Gln86Arg	p.Q86R	ENST00000359303	NM_003535.2	86	cAg/cGg	1/1	0.900108121789168	6	FACETS	0.94	0.847	1	0.626	0.564	0.691	CLONAL	2	TRUE	3	0.56	6		518	415	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168953	32168953	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	79	866	2	ENST00000375023.3:c.4080G>T	p.Gln1360His	p.Q1360H	ENST00000375023	NM_004557.3	1360	caG/caT	22/30	0.266041988679466	3	FACETS	1	0.954	1	0.573	0.509	0.641	INDETERMINATE	1	TRUE	1	0.56	3		868	315	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170102	32170102	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs748069011	NA	P-0023067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	80	769	0	ENST00000375023.3:c.3506G>T	p.Arg1169Leu	p.R1169L	ENST00000375023	NM_004557.3	1169	cGg/cTg	21/30	0.266041988679466	3	FACETS	1	0.93	1	0.533	0.473	0.597	INDETERMINATE	1	TRUE	1	0.56	3		769	343	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859589	151859589	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	24	439	0	ENST00000262189.6:c.11073A>C	p.Gln3691His	p.Q3691H	ENST00000262189	NM_170606.2	3691	caA/caC	43/59	1	2	FACETS	0.985	0.792	1	0.985	0.792	1	CLONAL	1	TRUE	1	0.56	2		439	87	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218678	98218679	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0023067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	39	373	0	ENST00000331920.6:c.3185_3186delinsCT	p.Leu1062Pro	p.L1062P	ENST00000331920	NM_000264.3	1062	cTG/cCT	19/24	1	2	FACETS	0.745	0.625	0.875	0.745	0.625	0.875	SUBCLONAL	1	TRUE	1	0.56	2		373	187	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309018	137309018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771883272	NA	P-0023067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	63	768	2	ENST00000481739.1:c.625C>T	p.Arg209Trp	p.R209W	ENST00000481739	NM_002957.4	209	Cgg/Tgg	5/10	1	2	FACETS	0.758	0.661	0.861	0.758	0.661	0.861	SUBCLONAL	1	TRUE	1	0.56	2		770	297	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0023070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	25	627	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	0.618	0.487	0.768	0.618	0.487	0.768	SUBCLONAL	1	TRUE	1	0.23	2		627	352	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0023087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	388	724	2	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	0.44	2		726	1194	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579582	7579583	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	123	669	0	ENST00000269305.4:c.104dup	p.Leu35PhefsTer8	p.L35Ffs*8	ENST00000269305	NM_001126112.2	35	ttg/ttTg	4/11	0.29656635398468	1	FACETS	0.576	0.521	0.634	0.576	0.521	0.634	SUBCLONAL	1	TRUE	0	0.44	1		669	757	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31939981	31939981	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573446910	NA	P-0023087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	142	572	1	ENST00000375333.2:c.208G>A	p.Gly70Arg	p.G70R	ENST00000375333	NM_032454.1	70	Gga/Aga	1/8	1	2	FACETS	0.833	0.76	0.909	0.833	0.76	0.909	CLONAL	1	TRUE	1	0.44	2		573	775	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593460	48593461	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0023087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	98	519	0	ENST00000342988.3:c.1213dup	p.His405ProfsTer24	p.H405Pfs*24	ENST00000342988	NM_005359.5	404	gac/gaCc	10/12	0.265919369533058	1	FACETS	0.577	0.516	0.642	0.577	0.516	0.642	SUBCLONAL	1	TRUE	0	0.44	1		519	602	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509624	106509624	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	91	586	0	ENST00000359195.3:c.1618G>A	p.Gly540Arg	p.G540R	ENST00000359195	NM_002649.2	540	Ggg/Agg	2/11	1	2	FACETS	0.58	0.515	0.65	0.58	0.515	0.65	SUBCLONAL	1	TRUE	1	0.44	2		586	713	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0023088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	100	567	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.564791039652277	1	FACETS	0.336	0.303	0.371	0.336	0.303	0.371	SUBCLONAL	1	TRUE	0	0.910466415234067	1		567	356	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0023088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	124	250	6	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.910466415234067	2		256	266	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	48	474	1	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	0.618337525394834	1	FACETS	0.169	0.143	0.197	0.169	0.143	0.197	SUBCLONAL	1	TRUE	0	0.910466415234067	1		475	340	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	211	566	1	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	0.422304396067373	1	FACETS	0.439	0.411	0.468	0.439	0.411	0.468	INDETERMINATE	1	TRUE	0	0.910466415234067	1		567	575	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158447	106158447	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	58	342	0	ENST00000380013.4:c.3353del	p.Asn1118IlefsTer19	p.N1118Ifs*19	ENST00000380013	NM_001127208.2	1116	atA/at	3/11	0.564791039652277	1	FACETS	0.329	0.286	0.374	0.329	0.286	0.374	SUBCLONAL	1	TRUE	0	0.910466415234067	1		342	211	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878061	48878062	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1131690852	NA	P-0023088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	343	289	0	ENST00000267163.4:c.19dup	p.Arg7ProfsTer24	p.R7Pfs*24	ENST00000267163	NM_000321.2	5	acc/aCcc	1/27	0.909036343426971	2	FACETS	0.899	0.874	0.923	0.899	0.874	0.923	CLONAL	2	TRUE	0	0.910466415234067	2		289	419	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0023088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	392	684	4	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	0.910466415234067	2	FACETS	1	0.985	1	0.531	0.508	0.554	CLONAL	1	TRUE	0	0.910466415234067	2		688	811	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691872	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs79375991	NA	P-0023088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	97	491	19	ENST00000295754.5:c.383del	p.Lys128SerfsTer35	p.K128Sfs*35	ENST00000295754	NM_003242.5	125	gAa/ga	3/7	0.910466415234067	1	FACETS	0.801	0.744	0.855	0.801	0.744	0.855	CLONAL	1	TRUE	0	0.910466415234067	1		510	145	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024636	31024637	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1555912897	NA	P-0023088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	266	613	0	ENST00000375687.4:c.4127dup	p.Pro1377SerfsTer3	p.P1377Sfs*3	ENST00000375687	NM_015338.5	1374	gtg/gtGg	13/13	1	2	FACETS	0.883	0.833	0.933	0.883	0.833	0.933	CLONAL	1	TRUE	1	0.910466415234067	2		613	662	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857867	89857867	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148473140	NA	P-0023088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	387	761	0	ENST00000389301.3:c.1303C>T	p.Arg435Cys	p.R435C	ENST00000389301	NM_000135.2	435	Cgc/Tgc	14/43	0.344192440052845	3	FACETS	1	0.992	1	0.597	0.568	0.626	INDETERMINATE	1	TRUE	1	0.910466415234067	3		761	1036	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0023088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	171	785	4	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	0.564791039652277	1	FACETS	0.36	0.333	0.388	0.36	0.333	0.388	SUBCLONAL	1	TRUE	0	0.910466415234067	1		789	568	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609331	81609331	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139286618	NA	P-0023088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	31	360	2	ENST00000298171.2:c.929G>A	p.Arg310His	p.R310H	ENST00000298171	NM_000369.2	310	cGc/cAc	10/10	0.564791039652277	1	FACETS	0.218	0.178	0.262	0.218	0.178	0.262	SUBCLONAL	1	TRUE	0	0.910466415234067	1		362	170	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564667	86564667	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	352	721	1	ENST00000274376.6:c.402del	p.Pro136LeufsTer38	p.P136Lfs*38	ENST00000274376	NM_002890.2	133	ggT/gg	1/25	0.910466415234067	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.910466415234067	1		722	411	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073803	8073804	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0023088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	76	335	0	ENST00000377482.5:c.855dup	p.Arg286GlnfsTer7	p.R286Qfs*7	ENST00000377482	NM_018948.3	285	-/C	4/4	0.422304396067373	1	FACETS	0.437	0.39	0.485	0.437	0.39	0.485	INDETERMINATE	1	TRUE	0	0.910466415234067	1		335	208	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518503	204518503	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	131	366	0	ENST00000367182.3:c.1166G>A	p.Cys389Tyr	p.C389Y	ENST00000367182	NM_001278516.1	389	tGc/tAc	11/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.910466415234067	2		366	260	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911882	94911882	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1412449950	NA	P-0023088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	233	709	0	ENST00000536441.1:c.1048C>T	p.Arg350Ter	p.R350*	ENST00000536441	NM_144665.3	350	Cga/Tga	7/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.910466415234067	2		709	495	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435156	49435156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	237	467	0	ENST00000301067.7:c.6397del	p.Ala2133ProfsTer11	p.A2133Pfs*11	ENST00000301067	NM_003482.3	2133	Gcc/cc	31/54	0.564791039652277	1	FACETS	0.727	0.692	0.762	0.727	0.692	0.762	SUBCLONAL	1	TRUE	0	0.910466415234067	1		467	390	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860152	57860152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374948623	NA	P-0023088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	166	668	0	ENST00000228682.2:c.892G>A	p.Glu298Lys	p.E298K	ENST00000228682	NM_005269.2	298	Gag/Aag	8/12	0.564791039652277	1	FACETS	0.338	0.312	0.366	0.338	0.312	0.366	SUBCLONAL	1	TRUE	0	0.910466415234067	1		668	587	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070578	67070578	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	61	381	0	ENST00000412916.2:c.207del	p.Pro70ArgfsTer19	p.P70Rfs*19	ENST00000412916		68	Ttt/tt	3/6	0.910466415234067	3	FACETS	0.269	0.231	0.31			1	SUBCLONAL	1	TRUE	NA	0.910466415234067	3		381	726	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830309	72830309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773210288	NA	P-0023088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	152	391	0	ENST00000268489.5:c.6272C>T	p.Pro2091Leu	p.P2091L	ENST00000268489	NM_006885.3	2091	cCg/cTg	9/10	0.910466415234067	3	FACETS	0.728	0.668	0.791			1	SUBCLONAL	1	TRUE	NA	0.910466415234067	3		391	667	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577143	7577144	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	294	585	0	ENST00000269305.4:c.794dup	p.Arg267ThrfsTer5	p.R267Tfs*5	ENST00000269305	NM_001126112.2	265	ctg/ctTg	8/11	0.910466415234067	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.910466415234067	1		585	332	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353896	15353896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1164538389	NA	P-0023088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	105	590	0	ENST00000263377.2:c.2984G>A	p.Arg995Gln	p.R995Q	ENST00000263377	NM_058243.2	995	cGg/cAg	14/20	0.564791039652277	1	FACETS	0.315	0.284	0.347	0.315	0.284	0.347	SUBCLONAL	1	TRUE	0	0.910466415234067	1		590	399	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308171	30308171	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	161	663	1	ENST00000262643.3:c.311del	p.Pro104ArgfsTer5	p.P104Rfs*5	ENST00000262643	NM_001238.2	103	tCc/tc	5/12	0.564791039652277	1	FACETS	0.362	0.334	0.391	0.362	0.334	0.391	SUBCLONAL	1	TRUE	0	0.910466415234067	1		664	532	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719795	190719796	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0023088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	61	467	0	ENST00000441310.2:c.1797_1798delinsAT	p.Asp600Tyr	p.D600Y	ENST00000441310	NM_000534.4	599	gaGGat/gaATat	9/13	0.564791039652277	1	FACETS	0.29	0.252	0.329	0.29	0.252	0.329	SUBCLONAL	1	TRUE	0	0.910466415234067	1		467	252	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067828	30067828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768053145	NA	P-0023088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	230	376	0	ENST00000338641.4:c.1013G>A	p.Arg338His	p.R338H	ENST00000338641	NM_000268.3	338	cGc/cAc	11/16	0.618337525394834	1	FACETS	0.742	0.706	0.777	0.742	0.706	0.777	SUBCLONAL	1	TRUE	0	0.910466415234067	1		376	371	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37045890	37045890	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs267607732	NA	P-0023088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	12	615	0	ENST00000231790.2:c.307-2A>G		p.X103_splice	ENST00000231790	NM_000249.3	103			0.910466415234067	1	FACETS	0.061	0.042	0.084	0.061	0.042	0.084	SUBCLONAL	1	TRUE	0	0.910466415234067	1		615	235	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37061799	37061799	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0023088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	193	519	0	ENST00000231790.2:c.885-2A>T		p.X295_splice	ENST00000231790	NM_000249.3	295			0.910466415234067	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.910466415234067	1		519	214	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247172	153247173	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0023088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	127	403	0	ENST00000281708.4:c.1629_1630del	p.Arg543SerfsTer7	p.R543Sfs*7	ENST00000281708	NM_033632.3	543	agAGtc/agtc	10/12	0.564791039652277	1	FACETS	0.691	0.643	0.738	0.691	0.643	0.738	SUBCLONAL	1	TRUE	0	0.910466415234067	1		403	220	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161786	56161786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	221	587	0	ENST00000399503.3:c.1283C>T	p.Thr428Met	p.T428M	ENST00000399503	NM_005921.1	428	aCg/aTg	6/20	0.895922456390513	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.910466415234067	1		587	254	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265545	152265545	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	219	582	0	ENST00000206249.3:c.998C>A	p.Pro333His	p.P333H	ENST00000206249	NM_000125.3	333	cCt/cAt	4/8	0.564791039652277	1	FACETS	0.652	0.616	0.687	0.652	0.616	0.687	SUBCLONAL	1	TRUE	0	0.910466415234067	1		582	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0023089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	72	883	4	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.721	0.629	0.821	0.721	0.629	0.821	SUBCLONAL	1	TRUE	1	0.261022501444947	2		887	765	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0023089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	68	859	1	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	0.66	0.573	0.755	0.66	0.573	0.755	SUBCLONAL	1	TRUE	1	0.261022501444947	2		860	789	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430245	181430245	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1360786606	NA	P-0023089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	53	483	0	ENST00000325404.1:c.97A>C	p.Asn33His	p.N33H	ENST00000325404	NM_003106.3	33	Aac/Cac	1/1	1	2	FACETS	0.599	0.51	0.697	0.599	0.51	0.697	SUBCLONAL	1	TRUE	1	0.261022501444947	2		483	678	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039904	47039904	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	63	420	0	ENST00000377604.3:c.1247A>T	p.Gln416Leu	p.Q416L	ENST00000377604	NM_001204468.1	416	cAg/cTg	12/24	1	1	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	0	0.261022501444947	1		420	409	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845234	151845234	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199858308	NA	P-0023089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	87	578	0	ENST00000262189.6:c.13778A>G	p.Asn4593Ser	p.N4593S	ENST00000262189	NM_170606.2	4593	aAt/aGt	52/59	0.261022501444947	3	FACETS	1	0.912	1	0.518	0.459	0.582	CLONAL	1	TRUE	1	0.261022501444947	3		578	727	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639647	3639647	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	136	1071	1	ENST00000294008.3:c.3992G>T	p.Gly1331Val	p.G1331V	ENST00000294008	NM_032444.2	1331	gGa/gTa	12/15	1	2	FACETS	0.967	0.877	1	0.967	0.877	1	CLONAL	1	TRUE	1	0.261022501444947	2		1072	1078	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552152	29552152	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	37	405	0	ENST00000356175.3:c.1885G>T	p.Gly629Trp	p.G629W	ENST00000356175	NM_000267.3	629	Ggg/Tgg	17/57	1	2	FACETS	0.923	0.764	1	0.923	0.764	1	CLONAL	1	TRUE	1	0.261022501444947	2		405	307	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546618	9546620	+	frameshift_variant	Frame_Shift_Del	DEL	CTC	CTC	TT	novel	NA	P-0023089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	70	711	1	ENST00000353224.5:c.1402_1404delinsAA	p.Glu468LysfsTer10	p.E468Kfs*10	ENST00000353224	NM_177990.2	468	GAG/AA	5/10	1	2	FACETS	0.725	0.631	0.826	0.725	0.631	0.826	SUBCLONAL	1	TRUE	1	0.261022501444947	2		712	740	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081681	143081681	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	66	422	0	ENST00000262992.4:c.1393C>A	p.Leu465Ile	p.L465I	ENST00000262992	NM_001101669.1	465	Ctt/Att	15/24	1	2	FACETS	0.913	0.793	1	0.913	0.793	1	CLONAL	1	TRUE	1	0.261022501444947	2		422	554	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430386	47430386	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	49	397	0	ENST00000377045.4:c.1661G>T	p.Arg554Leu	p.R554L	ENST00000377045	NM_001654.4	554	cGg/cTg	15/16	1	1	FACETS	0.829	0.704	0.965	0.829	0.704	0.965	CLONAL	1	TRUE	0	0.261022501444947	1		397	394	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405285	70405285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1273853414	NA	P-0023089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	46	653	0	ENST00000373644.4:c.2799C>G	p.Ile933Met	p.I933M	ENST00000373644	NM_030625.2	933	atC/atG	4/12	1	2	FACETS	0.582	0.489	0.684	0.582	0.489	0.684	SUBCLONAL	1	TRUE	1	0.261022501444947	2		653	606	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983481	90983481	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	26	555	0	ENST00000265433.3:c.622A>C	p.Lys208Gln	p.K208Q	ENST00000265433	NM_002485.4	208	Aaa/Caa	6/16	0.261022501444947	3	FACETS	0.459	0.362	0.57	0.229	0.181	0.285	SUBCLONAL	1	TRUE	1	0.261022501444947	3		555	491	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300086	137300086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199797293	NA	P-0023089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	70	914	0	ENST00000481739.1:c.371C>T	p.Ser124Leu	p.S124L	ENST00000481739	NM_002957.4	124	tCa/tTa	3/10	0.261022501444947	1	FACETS	0.445	0.387	0.509	0.445	0.387	0.509	SUBCLONAL	1	TRUE	0	0.261022501444947	1		914	1047	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0023089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	94	883	4	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.264606118753014	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.2	1		887	740	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0023089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	115	859	1	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.2	2		860	983	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430245	181430245	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1360786606	NA	P-0023089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	42	483	0	ENST00000325404.1:c.97A>C	p.Asn33His	p.N33H	ENST00000325404	NM_003106.3	33	Aac/Cac	1/1	1	2	FACETS	0.681	0.567	0.807	0.681	0.567	0.807	SUBCLONAL	1	TRUE	1	0.2	2		483	617	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039904	47039904	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	77	420	0	ENST00000377604.3:c.1247A>T	p.Gln416Leu	p.Q416L	ENST00000377604	NM_001204468.1	416	cAg/cTg	12/24	1	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.2	1		420	478	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845234	151845234	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199858308	NA	P-0023089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	43	578	0	ENST00000262189.6:c.13778A>G	p.Asn4593Ser	p.N4593S	ENST00000262189	NM_170606.2	4593	aAt/aGt	52/59	1	2	FACETS	0.63	0.526	0.747	0.63	0.526	0.747	SUBCLONAL	1	TRUE	1	0.2	2		578	682	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639647	3639647	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	83	1071	1	ENST00000294008.3:c.3992G>T	p.Gly1331Val	p.G1331V	ENST00000294008	NM_032444.2	1331	gGa/gTa	12/15	1	2	FACETS	0.767	0.675	0.866	0.767	0.675	0.866	SUBCLONAL	1	TRUE	1	0.2	2		1072	1082	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552152	29552152	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	41	405	0	ENST00000356175.3:c.1885G>T	p.Gly629Trp	p.G629W	ENST00000356175	NM_000267.3	629	Ggg/Tgg	17/57	1	2	FACETS	0.858	0.714	1	0.858	0.714	1	CLONAL	1	TRUE	1	0.2	2		405	478	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546618	9546620	+	frameshift_variant	Frame_Shift_Del	DEL	CTC	CTC	TT	novel	NA	P-0023089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	67	711	1	ENST00000353224.5:c.1402_1404delinsAA	p.Glu468LysfsTer10	p.E468Kfs*10	ENST00000353224	NM_177990.2	468	GAG/AA	5/10	1	2	FACETS	0.866	0.751	0.99	0.866	0.751	0.99	CLONAL	1	TRUE	1	0.2	2		712	774	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081681	143081681	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	38	422	0	ENST00000262992.4:c.1393C>A	p.Leu465Ile	p.L465I	ENST00000262992	NM_001101669.1	465	Ctt/Att	15/24	1	2	FACETS	0.739	0.611	0.883	0.739	0.611	0.883	SUBCLONAL	1	TRUE	1	0.2	2		422	514	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430386	47430386	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	79	397	0	ENST00000377045.4:c.1661G>T	p.Arg554Leu	p.R554L	ENST00000377045	NM_001654.4	554	cGg/cTg	15/16	1	1	FACETS	0.815	0.72	0.917	1	0.98	1	CLONAL	2	TRUE	0	0.2	1		397	436	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604785	48604786	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGACGA	novel	NA	P-0023090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	82	497	0	ENST00000342988.3:c.1610_1615dup	p.Asp537_Glu538dup	p.D537_E538dup	ENST00000342988	NM_005359.5	537	cta/ctAGACGAa	12/12	0.479850476197986	1	FACETS	0.658	0.583	0.736	0.658	0.583	0.736	SUBCLONAL	1	TRUE	0	0.479850476197986	1		497	395	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TC	novel	NA	P-0023090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	154	688	1	ENST00000311936.3:c.180_181inv	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggGAaa	3/5	0.142166264475323	0	FACETS	0.451	0.413	0.49			1	INDETERMINATE	1	TRUE	0	0.479850476197986	0		689	741	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578549	7578551	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0023090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	253	856	0	ENST00000269305.4:c.379_381del	p.Ser127del	p.S127del	ENST00000269305	NM_001126112.2	127	TCC/-	5/11	0.479850476197986	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.479850476197986	1		856	736	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0023093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	135	649	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.290470433419693	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.27	1		649	701	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855936	68855938	+	inframe_deletion	In_Frame_Del	DEL	CTG	CTG	-	rs1555516823	NA	P-0023093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	56	737	1	ENST00000261769.5:c.1747_1749del	p.Leu583del	p.L583del	ENST00000261769	NM_004360.3	582	CTG/-	12/16	0.3	1	FACETS	0.721	0.618	0.832	0.721	0.618	0.832	SUBCLONAL	1	TRUE	0	0.27	1		738	498	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847263	68847293	+	frameshift_variant	Frame_Shift_Del	DEL	ACTGAAAGTGACTGATGCTGATGCCCCCAAT	ACTGAAAGTGACTGATGCTGATGCCCCCAAT	-	novel	NA	P-0023093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	88	666	0	ENST00000261769.5:c.1187_1217del	p.Leu396ProfsTer11	p.L396Pfs*11	ENST00000261769	NM_004360.3	395	acACTGAAAGTGACTGATGCTGATGCCCCCAAT/ac	9/16	0.3	1	FACETS	0.943	0.837	1	0.943	0.837	1	CLONAL	1	TRUE	0	0.27	1		666	598	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	143	482	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.952	0.874	1	0.952	0.874	1	CLONAL	1	TRUE	1	0.633839936516627	2		482	474	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888210	112888210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121918464	NA	P-0023117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	36	556	0	ENST00000351677.2:c.226G>A	p.Glu76Lys	p.E76K	ENST00000351677	NM_002834.3	76	Gag/Aag	3/16	1	2	FACETS	0.138	0.113	0.166	0.138	0.113	0.166	SUBCLONAL	1	TRUE	1	0.633839936516627	2		556	824	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514495	NA	P-0023117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	44	503	2	ENST00000269305.4:c.542G>A	p.Arg181His	p.R181H	ENST00000269305	NM_001126112.2	181	cGc/cAc	5/11	1	2	FACETS	0.193	0.161	0.228	0.193	0.161	0.228	SUBCLONAL	1	TRUE	1	0.633839936516627	2		505	721	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0023117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	247	488	0	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.633839936516627	3	FACETS	0.965	0.902	1	0.482	0.451	0.515	CLONAL	1	TRUE	1	0.633839936516627	3		488	1064	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692794	89692794	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	156	362	0	ENST00000371953.3:c.278A>T	p.His93Leu	p.H93L	ENST00000371953	NM_000314.4	93	cAt/cTt	5/9	0.633839936516627	1	FACETS	0.95	0.883	1	0.95	0.883	1	CLONAL	1	TRUE	0	0.633839936516627	1		362	354	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713340	40713340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1272852268	NA	P-0023117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	236	602	2	ENST00000373198.4:c.4175G>A	p.Arg1392His	p.R1392H	ENST00000373198	NM_133170.3	1392	cGt/cAt	30/32	1	2	FACETS	0.914	0.855	0.974	0.914	0.855	0.974	CLONAL	1	TRUE	1	0.633839936516627	2		604	815	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225571	225571	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	34	75	0	ENST00000264932.6:c.350A>G	p.Asp117Gly	p.D117G	ENST00000264932	NM_004168.2	117	gAc/gGc	4/15	1	2	FACETS	1	0.84	1	1	0.84	1	CLONAL	1	TRUE	1	0.633839936516627	2		75	107	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522551	176522551	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774571806	NA	P-0023118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	8	793	2	ENST00000292408.4:c.1648G>A	p.Val550Met	p.V550M	ENST00000292408	NM_213647.1	550	Gtg/Atg	13/18	0.158843876366924	4	FACETS	0.311	0.199	0.458	0.156	0.099	0.229	SUBCLONAL	1	TRUE	2	0.158843876366924	4		795	375	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0023122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	26	623	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	1	2	FACETS	0.189	0.149	0.236	0.189	0.149	0.236	SUBCLONAL	1	TRUE	1	0.335412495452911	2		623	820	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115955	8115956	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	110	484	0	ENST00000346208.3:c.1301_1302insT	p.Ser436LeufsTer71	p.S436Lfs*71	ENST00000346208		434	cac/caTc	6/6	1	2	FACETS	0.818	0.741	0.898	1	0.986	1	CLONAL	2	TRUE	1	0.335412495452911	2		484	401	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0023125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	315	908	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		908	908	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085728	16085728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144939456	NA	P-0023125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	176	734	1	ENST00000281043.3:c.904C>T	p.Arg302Cys	p.R302C	ENST00000281043	NM_005378.4	302	Cgt/Tgt	3/3	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		735	544	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295799	15295800	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0023125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	182	959	3	ENST00000263388.2:c.2327_2328delinsAG	p.Thr776Lys	p.T776K	ENST00000263388	NM_000435.2	776	aCC/aAG	15/33	0.210184984932328	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		962	530	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0023126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	41	954	2	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.437921669907475	5	FACETS	0.774	0.646	0.916	0.258	0.215	0.306	CLONAL	1	FALSE	2	0.468428906347382	5		956	385	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842283	151842283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1162128184	NA	P-0023127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	43	658	0	ENST00000262189.6:c.14129G>A	p.Arg4710His	p.R4710H	ENST00000262189	NM_170606.2	4710	cGt/cAt	54/59	0.788769241297796	3	FACETS	0.249	0.208	0.295	0.125	0.104	0.148	SUBCLONAL	1	TRUE	1	0.788769241297796	3		658	610	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772225	68772226	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0023127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	259	1087	0	ENST00000261769.5:c.76dup	p.Glu26GlyfsTer8	p.E26Gfs*8	ENST00000261769	NM_004360.3	25	ccg/ccGg	2/16	0.788769241297796	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.788769241297796	1		1087	363	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178351	56178384	+	frameshift_variant	Frame_Shift_Del	DEL	TGACGAGACAGTGTTCACCCCAGTAGAGGAGAAA	TGACGAGACAGTGTTCACCCCAGTAGAGGAGAAA	-	novel	NA	P-0023127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	326	544	0	ENST00000399503.3:c.3326_3359del	p.Asp1109AlafsTer3	p.D1109Afs*3	ENST00000399503	NM_005921.1	1108	agTGACGAGACAGTGTTCACCCCAGTAGAGGAGAAA/ag	14/20	0.788769241297796	4	FACETS	0.909	0.871	0.947	0.909	0.871	0.947	CLONAL	3	TRUE	1	0.788769241297796	4		544	542	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012269	152012269	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	485	864	0	ENST00000262189.6:c.544G>T	p.Glu182Ter	p.E182*	ENST00000262189	NM_170606.2	182	Gag/Tag	4/59	0.788769241297796	3	FACETS	0.996	0.96	1	0.996	0.96	1	CLONAL	2	TRUE	1	0.788769241297796	3		864	861	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0023130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	205	583	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.535151117667296	1	FACETS	0.993	0.932	1	0.993	0.932	1	CLONAL	1	TRUE	0	0.626298611664018	1		583	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0023130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	298	793	0	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	0.626298611664018	2	FACETS	0.922	0.881	0.963	0.922	0.881	0.963	CLONAL	2	TRUE	0	0.626298611664018	2		793	516	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723068	52723068	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1486388431	NA	P-0023130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	141	605	2	ENST00000322088.6:c.1253G>A	p.Arg418Gln	p.R418Q	ENST00000322088	NM_014225.5	418	cGg/cAg	10/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.626298611664018	2		607	417	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188590	11188590	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	29	542	0	ENST00000361445.4:c.5831C>T	p.Ala1944Val	p.A1944V	ENST00000361445	NM_004958.3	1944	gCa/gTa	42/58	0.535151117667296	1	FACETS	0.195	0.156	0.239	0.195	0.156	0.239	SUBCLONAL	1	TRUE	0	0.626298611664018	1		542	326	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272559	142272559	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	238	792	0	ENST00000350721.4:c.2556A>T	p.Glu852Asp	p.E852D	ENST00000350721	NM_001184.3	852	gaA/gaT	12/47	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.626298611664018	2		792	632	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0023133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	144	730	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	0.398594720048095	1	FACETS	0.989	0.906	1	0.989	0.906	1	CLONAL	1	TRUE	0	0.398594720048095	1		730	585	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518184	103518184	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	70	398	0	ENST00000355739.4:c.2122G>T	p.Asp708Tyr	p.D708Y	ENST00000355739	NM_000123.3	708	Gac/Tac	9/15	1	2	FACETS	0.853	0.746	0.966	0.853	0.746	0.966	CLONAL	1	TRUE	1	0.398594720048095	2		398	412	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518732	103518732	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0023133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	30	445	0	ENST00000355739.4:c.2319+1G>T		p.X773_splice	ENST00000355739	NM_000123.3	773			1	2	FACETS	0.344	0.276	0.42	0.344	0.276	0.42	SUBCLONAL	1	TRUE	1	0.398594720048095	2		445	438	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599868	10599868	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	181	727	2	ENST00000171111.5:c.1708G>A	p.Gly570Arg	p.G570R	ENST00000171111	NM_203500.1	570	Gga/Aga	5/6	0.398594720048095	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.398594720048095	1		729	612	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416698	29416698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56181542	NA	P-0023133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	161	628	0	ENST00000389048.3:c.4255G>A	p.Glu1419Lys	p.E1419K	ENST00000389048	NM_004304.4	1419	Gag/Aag	29/29	0.231747914980261	1	FACETS	1	0.976	1	1	0.976	1	INDETERMINATE	1	TRUE	0	0.398594720048095	1		628	567	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643806	52643806	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	140	652	0	ENST00000394830.3:c.2090A>G	p.Tyr697Cys	p.Y697C	ENST00000394830	NM_018313.4	697	tAt/tGt	17/30	0.398594720048095	1	FACETS	0.933	0.853	1	0.933	0.853	1	CLONAL	1	TRUE	0	0.398594720048095	1		652	603	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808373	1808373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1430826425	NA	P-0023133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	405	1182	0	ENST00000260795.2:c.2131C>T	p.His711Tyr	p.H711Y	ENST00000260795		711	Cac/Tac	15/17	0.316323202795541	3	FACETS	0.974	0.927	1			1	CLONAL	2	TRUE	NA	0.398594720048095	3		1182	1251	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589599	67589616	+	inframe_deletion	In_Frame_Del	DEL	TCAGTTTCAAGAAAAAAG	TCAGTTTCAAGAAAAAAG	-	novel	NA	P-0023133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	78	529	0	ENST00000274335.5:c.1364_1381del	p.Gln455_Ser460del	p.Q455_S460del	ENST00000274335		454	acTCAGTTTCAAGAAAAAAGt/act	10/15	0.398594720048095	1	FACETS	0.791	0.699	0.889	0.791	0.699	0.889	SUBCLONAL	1	TRUE	0	0.398594720048095	1		529	396	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030493	47030493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	149	429	0	ENST00000377604.3:c.268C>T	p.Pro90Ser	p.P90S	ENST00000377604	NM_001204468.1	90	Ccc/Tcc	4/24	1	1	FACETS	0.777	0.719	0.837	1	0.99	1	SUBCLONAL	2	TRUE	0	0.398594720048095	1		429	385	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0023134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	183	867	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.931	0.861	1	0.931	0.861	1	CLONAL	1	TRUE	1	0.493870306929631	2		868	796	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0023134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	200	977	1	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.493870306929631	2		978	707	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662097	227662097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1014841546	NA	P-0023134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	134	861	1	ENST00000305123.5:c.1358C>T	p.Thr453Ile	p.T453I	ENST00000305123	NM_005544.2	453	aCc/aTc	1/2	1	2	FACETS	0.972	0.888	1	0.972	0.888	1	CLONAL	1	TRUE	1	0.493870306929631	2		862	558	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	135	560	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.493870306929631	2		560	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578206	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs886039484	NA	P-0023134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	163	1052	0	ENST00000269305.4:c.643A>G	p.Ser215Gly	p.S215G	ENST00000269305	NM_001126112.2	215	Agt/Ggt	6/11	1	2	FACETS	0.955	0.879	1	0.955	0.879	1	CLONAL	1	TRUE	1	0.493870306929631	2		1052	691	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926281	112926281	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	139	824	0	ENST00000351677.2:c.1414del	p.Ile472LeufsTer78	p.I472Lfs*78	ENST00000351677	NM_002834.3	472	Att/tt	12/16	1	2	FACETS	0.996	0.911	1	0.996	0.911	1	CLONAL	1	TRUE	1	0.493870306929631	2		824	565	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543355	65543355	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	150	771	1	ENST00000358664.4:c.322A>T	p.Ser108Cys	p.S108C	ENST00000358664	NM_002382.4	108	Agt/Tgt	5/5	1	2	FACETS	0.955	0.876	1	0.955	0.876	1	CLONAL	1	TRUE	1	0.493870306929631	2		772	636	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743909	41743909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	156	1020	0	ENST00000301178.4:c.844C>A	p.Pro282Thr	p.P282T	ENST00000301178	NM_021913.4	282	Ccc/Acc	7/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.493870306929631	2		1020	559	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118941	115118942	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	48	452	0	ENST00000257566.3:c.399dup	p.Pro134SerfsTer4	p.P134Sfs*4	ENST00000257566	NM_016569.3	133	-/T	2/8	0.110490438142174	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		452	355	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842746	68842747	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0023135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	35	654	1	ENST00000261769.5:c.683dup	p.Tyr228Ter	p.Y228*	ENST00000261769	NM_004360.3	228	tac/tAac	5/16	0.194972692767584	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		655	367	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944389	131944389	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	68	620	1	ENST00000265335.6:c.2801A>G	p.Asn934Ser	p.N934S	ENST00000265335		934	aAt/aGt	17/25	0.300778419386068	4	FACETS		NA	1			1	NA	NA	FALSE	2	NA	4		621	616	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0023136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	182	399	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.939	1			1	INDETERMINATE	1	TRUE	NA	0.69781512841108	2		399	516	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742679	39742679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	274	600	1	ENST00000361337.2:c.1522C>T	p.Arg508Cys	p.R508C	ENST00000361337	NM_003286.2	508	Cgt/Tgt	15/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.69781512841108	2		601	712	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619333	23619333	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	245	563	0	ENST00000261584.4:c.3202G>A	p.Gly1068Arg	p.G1068R	ENST00000261584	NM_024675.3	1068	Ggg/Agg	12/13	1	2	FACETS	0.971	0.912	1	0.971	0.912	1	CLONAL	1	TRUE	1	0.69781512841108	2		563	723	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983275	149983275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	675	794	1	ENST00000253339.5:c.2983C>T	p.Arg995Cys	p.R995C	ENST00000253339		995	Cgc/Tgc	7/7	0.69781512841108	2	FACETS	0.979	0.953	1	0.979	0.953	1	CLONAL	2	TRUE	0	0.69781512841108	2		795	988	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55603353	55603353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	213	609	0	ENST00000288135.5:c.2709G>A	p.Met903Ile	p.M903I	ENST00000288135	NM_000222.2	903	atG/atA	20/21	1	2	FACETS	0.914	0.853	0.976	0.914	0.853	0.976	CLONAL	1	TRUE	1	0.69781512841108	2		609	668	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765672	41765672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	262	782	0	ENST00000301178.4:c.2548G>A	p.Asp850Asn	p.D850N	ENST00000301178	NM_021913.4	850	Gat/Aat	20/20	1	2	FACETS	0.892	0.838	0.947	0.892	0.838	0.947	CLONAL	1	TRUE	1	0.69781512841108	2		782	842	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2220182	2220182	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	286	741	0	ENST00000398665.3:c.2767C>T	p.His923Tyr	p.H923Y	ENST00000398665	NM_032482.2	923	Cac/Tac	23/28	1	2	FACETS	0.941	0.887	0.996	0.941	0.887	0.996	CLONAL	1	TRUE	1	0.69781512841108	2		741	871	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913236	39913236	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774089771	NA	P-0023136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	351	861	0	ENST00000378444.4:c.4879G>A	p.Asp1627Asn	p.D1627N	ENST00000378444	NM_001123385.1	1627	Gat/Aat	14/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.69781512841108	2		861	913	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444311	50444311	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778251001	NA	P-0023136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	227	534	0	ENST00000331340.3:c.241G>A	p.Asp81Asn	p.D81N	ENST00000331340	NM_006060.4	81	Gat/Aat	4/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.69781512841108	2		534	606	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636826	8636826	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1353675904	NA	P-0023136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	483	711	0	ENST00000356435.5:c.83G>A	p.Arg28Gln	p.R28Q	ENST00000356435		28	cGa/cAa	2/35	0.668372929880884	3	FACETS	0.957	0.92	0.994	0.957	0.92	0.994	CLONAL	2	TRUE	1	0.69781512841108	3		711	976	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690374	117690374	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	289	779	0	ENST00000369458.3:c.755A>G	p.Gln252Arg	p.Q252R	ENST00000369458	NM_024626.3	252	cAg/cGg	5/6	1	2	FACETS	0.936	0.883	0.99	0.936	0.883	0.99	CLONAL	1	TRUE	1	0.69781512841108	2		779	885	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117027	193117027	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	294	650	1	ENST00000367435.3:c.760C>T	p.Gln254Ter	p.Q254*	ENST00000367435	NM_024529.4	254	Caa/Taa	8/17	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.69781512841108	2		651	830	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939439	71939444	+	inframe_deletion	In_Frame_Del	DEL	CATCGG	CATCGG	-	novel	NA	P-0023136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	332	851	1	ENST00000298229.2:c.295_300del	p.Ile99_Gly100del	p.I99_G100del	ENST00000298229	NM_001567.3	98	ctCATCGGc/ctc	3/28	1	2	FACETS	0.992	0.94	1	0.992	0.94	1	CLONAL	1	TRUE	1	0.69781512841108	2		852	959	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150268	108150268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064795850	NA	P-0023136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	284	688	0	ENST00000278616.4:c.3335C>T	p.Pro1112Leu	p.P1112L	ENST00000278616	NM_000051.3	1112	cCt/cTt	23/63	1	2	FACETS	0.996	0.94	1	0.996	0.94	1	CLONAL	1	TRUE	1	0.69781512841108	2		688	817	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487938	56487938	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	313	765	0	ENST00000267101.3:c.1669C>T	p.Gln557Ter	p.Q557*	ENST00000267101	NM_001982.3	557	Caa/Taa	14/28	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.69781512841108	2		765	864	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563350	21563351	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0023136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	318	916	2	ENST00000382592.4:c.568_569delinsTT	p.Pro190Phe	p.P190F	ENST00000382592	NM_014572.2	190	CCc/TTc	4/8	1	2	FACETS	0.941	0.89	0.992	0.941	0.89	0.992	CLONAL	1	TRUE	1	0.69781512841108	2		918	969	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420216	88420216	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	284	717	1	ENST00000360948.2:c.2470C>T	p.Leu824Phe	p.L824F	ENST00000360948	NM_001012338.2	824	Ctc/Ttc	19/19	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.69781512841108	2		718	796	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313035	30313035	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	229	639	0	ENST00000262643.3:c.838G>A	p.Glu280Lys	p.E280K	ENST00000262643	NM_001238.2	280	Gag/Aag	9/12	1	2	FACETS	0.948	0.888	1	0.948	0.888	1	CLONAL	1	TRUE	1	0.69781512841108	2		639	692	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172125	99172125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	287	736	0	ENST00000074304.5:c.1691C>T	p.Pro564Leu	p.P564L	ENST00000074304	NM_001134224.1	564	cCc/cTc	17/26	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.69781512841108	2		736	774	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566839	212566839	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	198	446	0	ENST00000342788.4:c.1342C>T	p.Gln448Ter	p.Q448*	ENST00000342788	NM_005235.2	448	Cag/Tag	12/28	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.69781512841108	2		446	553	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440115	220440115	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	274	839	0	ENST00000243786.2:c.968G>C	p.Gly323Ala	p.G323A	ENST00000243786	NM_002191.3	323	gGg/gCg	2/2	1	2	FACETS	0.904	0.851	0.958	0.904	0.851	0.958	CLONAL	1	TRUE	1	0.69781512841108	2		839	869	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31448661	31448661	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	338	816	1	ENST00000344624.3:c.2875C>T	p.Pro959Ser	p.P959S	ENST00000344624		959	Ccc/Tcc	20/33	1	2	FACETS	0.943	0.894	0.994	0.943	0.894	0.994	CLONAL	1	TRUE	1	0.69781512841108	2		817	1027	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845503	128845503	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	175	896	0	ENST00000249373.3:c.800T>A	p.Leu267His	p.L267H	ENST00000249373	NM_005631.4	267	cTc/cAc	4/12	1	2	FACETS	0.493	0.454	0.534	0.493	0.454	0.534	SUBCLONAL	1	TRUE	1	0.69781512841108	2		896	1017	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846411	128846411	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	113	613	6	ENST00000249373.3:c.1247G>A	p.Gly416Asp	p.G416D	ENST00000249373	NM_005631.4	416	gGc/gAc	6/12	1	2	FACETS	0.439	0.395	0.485	0.439	0.395	0.485	SUBCLONAL	1	TRUE	1	0.69781512841108	2		619	738	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8497265	8497266	+	stop_gained,splice_region_variant	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0023136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	385	626	0	ENST00000356435.5:c.2325_2326delinsAA	p.Trp775_Glu776delinsTer	p.W775_E776delins*	ENST00000356435		775	tgGGaa/tgAAaa	15/35	0.668372929880884	3	FACETS	0.869	0.83	0.909	0.869	0.83	0.909	CLONAL	2	TRUE	1	0.69781512841108	3		626	856	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239043	98239043	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	220	592	0	ENST00000331920.6:c.1600G>T	p.Glu534Ter	p.E534*	ENST00000331920	NM_000264.3	534	Gag/Tag	11/24	1	2	FACETS	0.948	0.887	1	0.948	0.887	1	CLONAL	1	TRUE	1	0.69781512841108	2		592	665	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240459	98240459	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	258	545	0	ENST00000331920.6:c.1225C>T	p.Gln409Ter	p.Q409*	ENST00000331920	NM_000264.3	409	Cag/Tag	9/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.69781512841108	2		545	662	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617503	158617503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1034717563	NA	P-0023140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	51	703	1	ENST00000263640.3:c.1153G>A	p.Glu385Lys	p.E385K	ENST00000263640	NM_001105.4	385	Gaa/Aaa	9/11	1	2	FACETS	0.186	0.157	0.217	0.186	0.157	0.217	SUBCLONAL	1	TRUE	1	0.752046142308556	2		704	730	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699360	117699360	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	356	800	0	ENST00000369458.3:c.281A>G	p.Asp94Gly	p.D94G	ENST00000369458	NM_024626.3	94	gAt/gGt	3/6	1	2	FACETS	0.987	0.938	1	0.987	0.938	1	CLONAL	1	TRUE	1	0.752046142308556	2		800	959	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440330	52440331	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	266	852	0	ENST00000460680.1:c.721dup	p.Tyr241LeufsTer2	p.Y241Lfs*2	ENST00000460680	NM_004656.3	241	tat/tTat	9/17	1	2	FACETS	0.871	0.82	0.924	0.871	0.82	0.924	CLONAL	1	TRUE	1	0.752046142308556	2		852	812	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063718	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0023160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	106	509	0	ENST00000412916.2:c.165+2dup		p.X55_splice	ENST00000412916		55			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		509	305	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115697	8115703	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTAGAT	TTTAGAT	-	novel	NA	P-0023160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	52	485	0	ENST00000346208.3:c.1048-4_1050del		p.X350_splice	ENST00000346208		350		6/6	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		485	367	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609993	81609993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139892516	NA	P-0023161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	109	325	0	ENST00000298171.2:c.1591C>T	p.Arg531Trp	p.R531W	ENST00000298171	NM_000369.2	531	Cgg/Tgg	10/10	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.533394645907417	2		325	400	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164417	47164419	+	frameshift_variant	Frame_Shift_Del	DEL	TTA	TTA	AT	novel	NA	P-0023161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	61	371	0	ENST00000409792.3:c.1707_1709delinsAT	p.Phe569LeufsTer2	p.F569Lfs*2	ENST00000409792	NM_014159.6	569	ttTAAa/ttATa	3/21	0.533394645907417	1	FACETS	0.769	0.673	0.871	0.769	0.673	0.871	SUBCLONAL	1	TRUE	0	0.533394645907417	1		371	218	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	113	896	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.231103534355206	2	FACETS	0.796	0.719	0.878	0.796	0.719	0.878	SUBCLONAL	2	TRUE	0	0.242552328556586	2		898	585	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271828	15271828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371738874	NA	P-0023165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	116	1069	0	ENST00000263388.2:c.6611C>T	p.Pro2204Leu	p.P2204L	ENST00000263388	NM_000435.2	2204	cCg/cTg	33/33	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.242552328556586	2		1069	922	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098407	108098407	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1064793029	NA	P-0023165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	57	663	0	ENST00000278616.4:c.56G>C	p.Arg19Thr	p.R19T	ENST00000278616	NM_000051.3	19	aGa/aCa	2/63	1	2	FACETS	0.994	0.854	1	0.994	0.854	1	CLONAL	1	TRUE	1	0.242552328556586	2		663	473	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	23	896	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.69	0.537	0.869	0.69	0.537	0.869	SUBCLONAL	1	TRUE	1	0.14	2		898	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0023166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	26	883	4	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.736	0.581	0.913	0.736	0.581	0.913	CLONAL	1	TRUE	1	0.14	2		887	505	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0023167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	79	967	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.997	0.88	1	0.997	0.88	1	CLONAL	1	TRUE	1	0.312462173611668	2		967	507	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182509	99182509	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	104	783	1	ENST00000074304.5:c.2312G>A	p.Arg771Gln	p.R771Q	ENST00000074304	NM_001134224.1	771	cGg/cAg	22/26	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.312462173611668	2		784	646	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553506	106553506	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	51	496	1	ENST00000369096.4:c.1471G>T	p.Ala491Ser	p.A491S	ENST00000369096	NM_001198.3	491	Gcg/Tcg	5/7	0.312462173611668	1	FACETS	0.894	0.765	1	0.894	0.765	1	CLONAL	1	TRUE	0	0.312462173611668	1		497	308	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0023168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	14	919	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.230556531131419	1	FACETS	0.161	0.115	0.217	0.161	0.115	0.217	SUBCLONAL	1	TRUE	0	0.24	1		920	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0023168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	32	1054	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	0.230556531131419	1	FACETS	0.348	0.281	0.424	0.348	0.281	0.424	SUBCLONAL	1	TRUE	0	0.24	1		1054	674	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398255	25398255	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913236	NA	P-0023168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	70	910	0	ENST00000311936.3:c.64C>A	p.Gln22Lys	p.Q22K	ENST00000311936	NM_004985.3	22	Cag/Aag	2/5	1	2	FACETS	0.864	0.753	0.984	0.864	0.753	0.984	CLONAL	1	TRUE	1	0.24	2		910	675	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038563	47038563	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0023168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	125	958	0	ENST00000377604.3:c.724+1G>T		p.X242_splice	ENST00000377604	NM_001204468.1	242			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.24	2		958	729	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729181	66729181	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121908595	NA	P-0023168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	75	977	0	ENST00000307102.5:c.389A>G	p.Tyr130Cys	p.Y130C	ENST00000307102	NM_002755.3	130	tAt/tGt	3/11	1	2	FACETS	0.795	0.696	0.902	0.795	0.696	0.902	CLONAL	1	TRUE	1	0.24	2		977	786	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627284	12627284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	60	582	0	ENST00000251849.4:c.1432G>A	p.Glu478Lys	p.E478K	ENST00000251849	NM_002880.3	478	Gaa/Aaa	14/17	1	2	FACETS	0.853	0.735	0.982	0.853	0.735	0.982	CLONAL	1	TRUE	1	0.24	2		582	586	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667422	241667422	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	70	748	0	ENST00000366560.3:c.1028G>T	p.Arg343Leu	p.R343L	ENST00000366560	NM_000143.3	343	cGa/cTa	7/10	0.290383802818658	3	FACETS	0.994	0.867	1	0.497	0.433	0.566	CLONAL	1	TRUE	1	0.24	3		748	657	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658283	18658283	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	47	719	0	ENST00000266497.5:c.3088G>T	p.Gly1030Ter	p.G1030*	ENST00000266497		1030	Gga/Tga	22/31	1	2	FACETS	0.715	0.603	0.838	0.715	0.603	0.838	SUBCLONAL	1	TRUE	1	0.24	2		719	548	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449779	149449779	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	91	799	0	ENST00000286301.3:c.1285G>T	p.Val429Leu	p.V429L	ENST00000286301	NM_005211.3	429	Gtg/Ttg	9/22	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.24	2		799	671	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553400	106553400	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	37	443	0	ENST00000369096.4:c.1365C>G	p.Ser455Arg	p.S455R	ENST00000369096	NM_001198.3	455	agC/agG	5/7	0.273589423160981	1	FACETS	0.983	0.815	1	0.983	0.815	1	CLONAL	1	TRUE	0	0.24	1		443	276	SUCCESS
AR	367	MSKCC	GRCh37	X	66765605	66765605	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	85	1173	0	ENST00000374690.3:c.617G>T	p.Ser206Ile	p.S206I	ENST00000374690	NM_000044.3	206	aGc/aTc	1/8	1	2	FACETS	0.866	0.764	0.975	0.866	0.764	0.975	CLONAL	1	TRUE	1	0.24	2		1173	818	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347783	70347783	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	107	667	0	ENST00000374080.3:c.3022G>T	p.Val1008Leu	p.V1008L	ENST00000374080		1008	Gtg/Ttg	22/45	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.24	2		667	649	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574369	95574369	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	26	366	0	ENST00000393063.1:c.2498A>G	p.Lys833Arg	p.K833R	ENST00000393063	NM_030621.3	833	aAg/aGg	17/28	1	2	FACETS	0.838	0.684	1	0.838	0.684	1	CLONAL	1	TRUE	1	0.756801826450993	2		366	82	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435188	56435188	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1348340748	NA	P-0023169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	174	737	2	ENST00000407977.2:c.1949G>A	p.Arg650Gln	p.R650Q	ENST00000407977		650	cGa/cAa	9/10	0.731372916538687	3	FACETS	0.933	0.862	1	0.467	0.431	0.504	CLONAL	1	TRUE	1	0.756801826450993	3		739	679	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	216	727	0	ENST00000347630.2:c.399C>A	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttA	6/11	1	2	FACETS	0.85	0.792	0.91	0.85	0.792	0.91	CLONAL	1	TRUE	1	0.602004412083612	2		727	844	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931464	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0023170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	141	452	0	ENST00000374690.3:c.2105_2106delinsAT	p.Leu702His	p.L702H	ENST00000374690	NM_000044.3	702	cTC/cAT	4/8	0.530171788623201	2	FACETS	0.669	0.611	0.73			1	SUBCLONAL	1	TRUE	NA	0.602004412083612	2		452	700	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0023171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	297	577	1	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.706378068376868	3	FACETS	1	0.991	1	0.771	0.737	0.804	CLONAL	2	TRUE	0	0.706278207913829	3		578	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0023171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	266	879	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.706278207913829	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.706278207913829	2		881	372	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562147	176562147	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	408	782	0	ENST00000439151.2:c.43C>G	p.Pro15Ala	p.P15A	ENST00000439151	NM_022455.4	15	Ccc/Gcc	2/23	0.602038519549955	4	FACETS	0.903	0.867	0.938	0.903	0.867	0.938	CLONAL	3	TRUE	1	0.706278207913829	4		782	728	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87338594	87338594	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	199	807	0	ENST00000277120.3:c.690G>A	p.Trp230Ter	p.W230*	ENST00000277120		230	tgG/tgA	7/19	0.423276507582028	4	FACETS	1	0.988	1	0.656	0.609	0.704	INDETERMINATE	1	TRUE	2	0.706278207913829	4		807	733	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870205	44870205	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0023171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	326	380	0	ENST00000377967.4:c.385-1G>A		p.X129_splice	ENST00000377967	NM_021140.2	129			0.704765672172448	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.706278207913829	2		380	400	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0023172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	42	883	4	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.975	0.812	1	0.975	0.812	1	CLONAL	1	TRUE	1	0.13	2		887	663	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918514	44918514	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	28	243	0	ENST00000377967.4:c.997C>T	p.Gln333Ter	p.Q333*	ENST00000377967	NM_021140.2	333	Cag/Tag	12/29	1	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.13	1		243	274	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0023173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	41	238	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.914	0.76	1	0.914	0.76	1	CLONAL	1	TRUE	1	0.17	2		238	528	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0023173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	53	270	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.112998170454293	3	FACETS	0.982	0.836	1	0.491	0.418	0.571	CLONAL	1	TRUE	1	0.17	3		270	689	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177433	56177434	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGT	novel	NA	P-0023173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	35	182	0	ENST00000399503.3:c.2408_2411dup	p.Ile805ValfsTer3	p.I805Vfs*3	ENST00000399503	NM_005921.1	802	-/CAGT	14/20	1	2	FACETS	0.863	0.707	1	0.863	0.707	1	CLONAL	1	TRUE	1	0.17	2		182	477	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	116	482	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.911	0.834	0.989	0.911	0.834	0.989	CLONAL	1	TRUE	1	0.884081729553014	2		482	288	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0023174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	519	641	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.884081729553014	3	FACETS	0.976	0.959	0.992			1	CLONAL	3	TRUE	NA	0.884081729553014	3		641	578	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350692	89350692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143279397	NA	P-0023174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	358	1148	1	ENST00000301030.4:c.2258C>T	p.Pro753Leu	p.P753L	ENST00000301030	NM_001256183.1	753	cCg/cTg	9/13	1	2	FACETS	0.955	0.91	1	0.955	0.91	1	CLONAL	1	TRUE	1	0.884081729553014	2		1149	848	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152093	55152093	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121908585	NA	P-0023175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	204	837	0	ENST00000257290.5:c.2525A>T	p.Asp842Val	p.D842V	ENST00000257290	NM_006206.4	842	gAc/gTc	18/23	1	2	FACETS	0.979	0.91	1	0.979	0.91	1	CLONAL	1	TRUE	1	0.558143440376189	2		837	747	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0023184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	89	521	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.933	0.839	1	1	0.99	1	CLONAL	4	TRUE	1	0.178666888617249	2		521	267	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	152	482	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.976	0.901	1	1	0.994	1	CLONAL	4	TRUE	1	0.178666888617249	2		482	436	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246445	105246445	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	239	941	0	ENST00000349310.3:c.155T>G	p.Leu52Arg	p.L52R	ENST00000349310	NM_001014432.1	52	cTc/cGc	4/15	1	2	FACETS	0.967	0.907	1	1	0.996	1	CLONAL	4	TRUE	1	0.178666888617249	2		941	692	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578371	7578371	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs776167460	NA	P-0023184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	12	701	0	ENST00000269305.4:c.559G>A	p.Gly187Ser	p.G187S	ENST00000269305	NM_001126112.2	187	Ggt/Agt	5/11	1	2	FACETS	0.246	0.172	0.338	0.246	0.172	0.338	SUBCLONAL	1	TRUE	1	0.178666888617249	2		701	546	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608246	100608246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	175	415	1	ENST00000308731.7:c.1844G>A	p.Arg615His	p.R615H	ENST00000308731	NM_000061.2	615	cGt/cAt	18/19	1	1	FACETS		NA	1			1	NA	NA	TRUE	0	NA	1		416	448	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921566	178921566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793349	NA	P-0023187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	57	397	0	ENST00000263967.3:c.1048G>A	p.Asp350Asn	p.D350N	ENST00000263967	NM_006218.2	350	Gac/Aac	5/21	1	2	FACETS	0.951	0.826	1	1	0.978	1	CLONAL	2	TRUE	1	0.262923547972947	2		397	228	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	78	597	0	ENST00000263967.3:c.333G>T	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaT	2/21	1	2	FACETS	0.831	0.735	0.932	1	0.981	1	CLONAL	2	TRUE	1	0.262923547972947	2		597	357	SUCCESS
APC	324	MSKCC	GRCh37	5	112175198	112175198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	46	280	0	ENST00000257430.4:c.3907C>T	p.Gln1303Ter	p.Q1303*	ENST00000257430	NM_000038.5	1303	Caa/Taa	16/16	0.254223994661643	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	0	0.262923547972947	2		280	149	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs863224499	NA	P-0023187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	169	935	1	ENST00000269305.4:c.672+1G>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.186970760154103	2	FACETS	0.962	0.888	1	0.962	0.888	1	CLONAL	2	TRUE	0	0.262923547972947	2		936	668	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944878	31944878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141415515	NA	P-0023187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	30	586	1	ENST00000340398.3:c.223G>A	p.Ala75Thr	p.A75T	ENST00000340398	NM_001013699.2	75	Gcg/Acg	1/1	0.186970760154103	2	FACETS	0.546	0.44	0.667	0.273	0.22	0.334	SUBCLONAL	1	TRUE	0	0.262923547972947	2		587	418	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228366	228366	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	47	599	0	ENST00000264932.6:c.688G>A	p.Glu230Lys	p.E230K	ENST00000264932	NM_004168.2	230	Gag/Aag	6/15	0.254223994661643	2	FACETS	0.841	0.711	0.984	0.421	0.355	0.492	CLONAL	1	TRUE	0	0.262923547972947	2		599	425	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375003	118375004	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0023188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	148	470	0	ENST00000534358.1:c.8396_8397del	p.Ser2799PhefsTer29	p.S2799Ffs*29	ENST00000534358	NM_005933.3	2799	tCC/t	27/36	0.532103726461931	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.532103726461931	1		470	366	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0023193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	53	515	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.3	3	FACETS	0.846	0.723	0.979	0.846	0.723	0.979	CLONAL	2	TRUE	1	0.17	3		515	400	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112182	115112182	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	27	814	0	ENST00000257566.3:c.1558del	p.Leu520CysfsTer112	p.L520Cfs*112	ENST00000257566	NM_016569.3	520	Ctg/tg	7/8	1	2	FACETS	0.739	0.587	0.912	0.739	0.587	0.912	CLONAL	1	TRUE	1	0.17	2		814	430	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134479	30134479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	52	558	0	ENST00000263025.4:c.52G>A	p.Glu18Lys	p.E18K	ENST00000263025	NM_002746.2	18	Gag/Aag	1/9	0.3	3	FACETS	0.756	0.645	0.877	0.756	0.645	0.877	SUBCLONAL	2	TRUE	1	0.17	3		558	439	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847244	68847245	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	58	690	0	ENST00000261769.5:c.1167dup	p.Asn390Ter	p.N390*	ENST00000261769	NM_004360.3	389	gct/gcTt	9/16	1	2	FACETS	0.762	0.656	0.876	1	0.969	1	SUBCLONAL	2	TRUE	1	0.17	2		690	448	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448338	49448338	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	97	859	0	ENST00000301067.7:c.373A>T	p.Thr125Ser	p.T125S	ENST00000301067	NM_003482.3	125	Aca/Tca	3/54	1	2	FACETS	0.992	0.882	1	0.992	0.882	1	CLONAL	1	TRUE	1	0.184412628378229	2		859	1061	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076905	41076905	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	93	783	0	ENST00000373198.4:c.1515G>C	p.Gln505His	p.Q505H	ENST00000373198	NM_133170.3	505	caG/caC	9/32	0.184412628378229	3	FACETS	1	0.967	1	0.618	0.549	0.693	CLONAL	1	TRUE	1	0.184412628378229	3		783	891	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955053	93955053	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	29	431	2	ENST00000369303.4:c.2845T>A	p.Tyr949Asn	p.Y949N	ENST00000369303	NM_004440.3	949	Tac/Aac	16/17	0.168263282451811	1	FACETS	0.609	0.488	0.747	0.609	0.488	0.747	SUBCLONAL	1	TRUE	0	0.184412628378229	1		433	469	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0023196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	27	621	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	1	2	FACETS	0.143	0.113	0.177	0.143	0.113	0.177	SUBCLONAL	1	TRUE	1	0.539607153755729	2		621	701	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057751	27057751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	371	1177	0	ENST00000324856.7:c.1459C>T	p.Gln487Ter	p.Q487*	ENST00000324856	NM_006015.4	487	Cag/Tag	3/20	1	2	FACETS	0.899	0.852	0.948	0.899	0.852	0.948	CLONAL	1	TRUE	1	0.539607153755729	2		1177	1529	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575082	64575083	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0023196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	224	825	0	ENST00000312049.6:c.724_725delinsTT	p.Ala242Phe	p.A242F	ENST00000312049	NM_130799.2	242	GCc/TTc	4/10	0.539607153755729	1	FACETS	0.875	0.818	0.933	0.875	0.818	0.933	CLONAL	1	TRUE	0	0.539607153755729	1		825	693	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532888	187532888	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	58	545	0	ENST00000441802.2:c.9505G>T	p.Asp3169Tyr	p.D3169Y	ENST00000441802	NM_005245.3	3169	Gat/Tat	14/27	1	2	FACETS	0.313	0.268	0.362	0.313	0.268	0.362	SUBCLONAL	1	TRUE	1	0.539607153755729	2		545	687	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	65	896	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.889	0.77	1	0.889	0.77	1	CLONAL	1	TRUE	1	0.200914559614952	2		898	728	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0023198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	104	921	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	0.0496274254144755	4	FACETS	1	0.963	1	0.584	0.523	0.65	INDETERMINATE	1	TRUE	2	0.257160667215689	4		921	870	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0023198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	69	722	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.0496274254144755	4	FACETS	0.938	0.816	1	0.469	0.408	0.535	INDETERMINATE	1	TRUE	2	0.257160667215689	4		722	719	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577075	7577075	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	181	950	0	ENST00000269305.4:c.863del	p.Asn288IlefsTer57	p.N288Ifs*57	ENST00000269305	NM_001126112.2	288	aAt/at	8/11	0.257160667215689	1	FACETS	0.762	0.704	0.822	1	0.99	1	SUBCLONAL	2	TRUE	0	0.257160667215689	1		950	805	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846275	156846275	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	34	918	1	ENST00000524377.1:c.1716C>G	p.Ile572Met	p.I572M	ENST00000524377	NM_002529.3	572	atC/atG	14/17	0.109112163917713	3	FACETS	0.441	0.359	0.534	0.221	0.179	0.267	INDETERMINATE	1	TRUE	1	0.257160667215689	3		919	676	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225656	133225656	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs780795309	NA	P-0023198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	33	667	0	ENST00000320574.5:c.4008C>G	p.Ile1336Met	p.I1336M	ENST00000320574	NM_006231.2	1336	atC/atG	32/49	0.0496274254144755	4	FACETS	0.556	0.452	0.674	0.278	0.226	0.337	INDETERMINATE	1	TRUE	2	0.257160667215689	4		667	580	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570407	95570407	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0023198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	36	400	0	ENST00000393063.1:c.3326C>G	p.Ser1109Ter	p.S1109*	ENST00000393063	NM_030621.3	1109	tCa/tGa	22/28	0.0496274254144755	4	FACETS	0.98	0.808	1	0.49	0.404	0.587	INDETERMINATE	1	TRUE	2	0.257160667215689	4		400	359	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708595	43708595	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	47	647	1	ENST00000382044.4:c.4701G>T	p.Arg1567Ser	p.R1567S	ENST00000382044	NM_001141980.1	1567	agG/agT	22/28	0.257160667215689	3	FACETS	0.883	0.746	1	0.442	0.373	0.518	CLONAL	1	TRUE	1	0.257160667215689	3		648	467	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326765	62326765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778286683	NA	P-0023198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	141	1058	2	ENST00000360203.5:c.3584C>T	p.Ala1195Val	p.A1195V	ENST00000360203	NM_001283009.1	1195	gCg/gTg	34/35	0.257160667215689	5	FACETS	0.842	0.767	0.921	0.562	0.511	0.614	CLONAL	2	TRUE	2	0.257160667215689	5		1060	902	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088734	27088735	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0023202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	68	723	0	ENST00000324856.7:c.2348_2349del	p.Thr783ArgfsTer33	p.T783Rfs*33	ENST00000324856	NM_006015.4	781	atACac/atac	7/20	0.408287406538761	4	FACETS	1	0.956	1	1	0.956	1	INDETERMINATE	2	TRUE	2	0.803853534828016	4		723	136	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65569039	65569039	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	220	525	0	ENST00000358664.4:c.19del	p.Ile7SerfsTer58	p.I7Sfs*58	ENST00000358664	NM_002382.4	7	Atc/tc	1/5	0.803853534828016	4	FACETS	0.924	0.892	0.955	0.924	0.892	0.955	CLONAL	4	TRUE	0	0.803853534828016	4		525	267	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545864	41545864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	85	823	0	ENST00000263253.7:c.2479C>T	p.Leu827Phe	p.L827F	ENST00000263253	NM_001429.3	827	Ctt/Ttt	14/31	1	2	FACETS	0.86	0.797	0.919	1	0.988	1	CLONAL	2	TRUE	1	0.803853534828016	2		823	123	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176176104	176176104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	371	669	2	ENST00000367669.3:c.11G>A	p.Ser4Asn	p.S4N	ENST00000367669	NM_022457.5	4	aGc/aAc	1/20	1	2	FACETS	0.956	0.911	1	0.956	0.911	1	CLONAL	1	TRUE	1	0.884316770408743	2		671	878	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798163	32798163	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	426	727	1	ENST00000374899.4:c.1516G>T	p.Gly506Trp	p.G506W	ENST00000374899	NM_018833.2	506	Ggg/Tgg	9/12	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.884316770408743	2		728	872	SUCCESS
FH	2271	MSKCC	GRCh37	1	241671911	241671911	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	29	518	0	ENST00000366560.3:c.730C>T	p.Leu244Phe	p.L244F	ENST00000366560	NM_000143.3	244	Ctt/Ttt	5/10	0.465406640268528	3	FACETS	0.318	0.254	0.39	0.106	0.084	0.13	SUBCLONAL	1	TRUE	0	0.466001980744447	3		518	483	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473636	67473636	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	127	677	0	ENST00000327367.4:c.716A>T	p.Glu239Val	p.E239V	ENST00000327367	NM_005902.3	239	gAg/gTg	6/9	0.157917848392462	1	FACETS	0.731	0.665	0.8	0.731	0.665	0.8	INDETERMINATE	1	TRUE	0	0.466001980744447	1		677	572	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900396	3900396	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1285192047	NA	P-0023206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	85	627	0	ENST00000262367.5:c.700G>A	p.Ala234Thr	p.A234T	ENST00000262367	NM_004380.2	234	Gcc/Acc	2/31	0.466001980744447	3	FACETS	0.583	0.515	0.657	0.292	0.257	0.329	SUBCLONAL	1	TRUE	1	0.466001980744447	3		627	771	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242485	+	protein_altering_variant	In_Frame_Del	DEL	ATTAAGAGAAGCAACATC	ATTAAGAGAAGCAACATC	GCAACA	novel	NA	P-0023206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	77	544	2	ENST00000275493.2:c.2238_2255delinsGCAACA	p.Leu747_Ser752delinsGlnHis	p.L747_S752delinsQH	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACATCt/gaGCAACAt	19/28	1	2	FACETS	0.703	0.619	0.793	0.703	0.619	0.793	SUBCLONAL	1	TRUE	1	0.466001980744447	2		546	470	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421519	32421519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	44	689	0	ENST00000332351.3:c.1073C>T	p.Thr358Met	p.T358M	ENST00000332351	NM_024426.4	358	aCg/aTg	6/10	0.183678639269498	4	FACETS	0.589	0.493	0.696	0.295	0.246	0.348	SUBCLONAL	1	TRUE	2	0.292291860312925	4		689	660	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961492	41961492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	52	678	1	ENST00000219905.7:c.400C>T	p.Arg134Cys	p.R134C	ENST00000219905	NM_001164273.1	134	Cgt/Tgt	2/24	0.150578763996354	3	FACETS	0.727	0.619	0.846	0.363	0.309	0.423	INDETERMINATE	1	TRUE	1	0.292291860312925	3		679	561	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740468	58740468	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371199697	NA	P-0023209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	43	644	0	ENST00000305921.3:c.1373G>A	p.Arg458Gln	p.R458Q	ENST00000305921	NM_003620.3	458	cGa/cAa	6/6	0.292291860312925	5	FACETS	0.526	0.438	0.623	0.175	0.146	0.208	SUBCLONAL	1	TRUE	2	0.292291860312925	5		644	805	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0023211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	42	566	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.829	0.694	0.978	0.829	0.694	0.978	CLONAL	1	TRUE	1	0.28	2		566	362	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796882	42796883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761345552	NA	P-0023211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	45	961	7	ENST00000575354.2:c.3347dup	p.Ser1117LysfsTer34	p.S1117Kfs*34	ENST00000575354	NM_015125.3	1114	gcc/gCcc	14/20	1	2	FACETS	0.748	0.629	0.878	0.748	0.629	0.878	SUBCLONAL	1	TRUE	1	0.28	2		968	430	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106626	27106626	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	49	700	1	ENST00000324856.7:c.6237del	p.Ser2079ArgfsTer56	p.S2079Rfs*56	ENST00000324856	NM_006015.4	2079	agC/ag	20/20	0.254292754834217	1	FACETS	0.912	0.776	1	0.912	0.776	1	CLONAL	1	TRUE	0	0.28	1		701	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579539	7579540	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0023211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	17	851	0	ENST00000269305.4:c.147_148insCA	p.Ile50GlnfsTer74	p.I50Qfs*74	ENST00000269305	NM_001126112.2	49	-/CA	4/11	0.3	1	FACETS	0.38	0.283	0.494	0.38	0.283	0.494	SUBCLONAL	1	TRUE	0	0.28	1		851	275	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591821	48591821	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	36	539	0	ENST00000342988.3:c.984C>A	p.Tyr328Ter	p.Y328*	ENST00000342988	NM_005359.5	328	taC/taA	9/12	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.28	2		539	205	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005681	150005681	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0023211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	24	357	0	ENST00000253339.5:c.544A>T	p.Lys182Ter	p.K182*	ENST00000253339		182	Aaa/Taa	3/7	1	2	FACETS	0.912	0.72	1	0.912	0.72	1	CLONAL	1	TRUE	1	0.28	2		357	188	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577101	7577102	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCAGGACAGGCACAAACACGCACCTCAAAGCTGTTCCGTCCCAGTAGATTACCA	novel	NA	P-0023212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	127	890	0	ENST00000269305.4:c.783_836dup	p.Gly262_Gly279dup	p.G262_G279dup	ENST00000269305	NM_001126112.2	262	ggg/ggTGGTAATCTACTGGGACGGAACAGCTTTGAGGTGCGTGTTTGTGCCTGTCCTGGg	8/11	0.596787760175249	1	FACETS	0.344	0.311	0.379	0.344	0.311	0.379	SUBCLONAL	1	TRUE	0	0.602496618102988	1		890	856	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350061	15350061	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	284	923	0	ENST00000263377.2:c.3591G>C	p.Lys1197Asn	p.K1197N	ENST00000263377	NM_058243.2	1197	aaG/aaC	18/20	1	2	FACETS	0.929	0.874	0.985	0.929	0.874	0.985	CLONAL	1	TRUE	1	0.602496618102988	2		923	1015	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111741	56111741	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	48	115	0	ENST00000399503.3:c.341A>T	p.His114Leu	p.H114L	ENST00000399503	NM_005921.1	114	cAc/cTc	1/20	0.596787760175249	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.602496618102988	1		115	90	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0023213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	156	919	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.186847725121017	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.231189768603316	2		920	585	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0023213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	34	303	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.984	0.807	1	0.984	0.807	1	CLONAL	1	TRUE	1	0.231189768603316	2		303	299	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875920	76875920	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	90	419	2	ENST00000373344.5:c.5215C>T	p.Arg1739Ter	p.R1739*	ENST00000373344	NM_000489.3	1739	Cga/Tga	20/35	1	1	FACETS	0.803	0.716	0.894	1	0.982	1	CLONAL	2	TRUE	0	0.231189768603316	1		421	429	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257290	16257290	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	103	731	0	ENST00000375759.3:c.4555G>C	p.Glu1519Gln	p.E1519Q	ENST00000375759	NM_015001.2	1519	Gag/Cag	11/15	0.249148469928926	4	FACETS	1	0.945	1			1	CLONAL	1	TRUE	NA	0.318031147697467	4		731	784	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190561	32190561	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	158	737	0	ENST00000375023.3:c.178G>C	p.Glu60Gln	p.E60Q	ENST00000375023	NM_004557.3	60	Gag/Cag	3/30	0.315250307587788	4	FACETS	0.904	0.831	0.981	0.452	0.415	0.491	CLONAL	2	TRUE	0	0.318031147697467	4		737	724	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39744994	39744994	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	111	608	0	ENST00000361337.2:c.1784C>G	p.Ser595Cys	p.S595C	ENST00000361337	NM_003286.2	595	tCc/tGc	17/21	0.318031147697467	5	FACETS	1	0.949	1	0.364	0.326	0.404	CLONAL	1	TRUE	2	0.318031147697467	5		608	945	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941711	48941711	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587778844	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	138	517	1	ENST00000267163.4:c.1024del	p.Thr342LeufsTer7	p.T342Lfs*7	ENST00000267163	NM_000321.2	341	Aaa/aa	10/27	0.318031147697467	2	FACETS	0.971	0.891	1	0.971	0.891	1	CLONAL	2	TRUE	0	0.318031147697467	2		518	447	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246518371	246518371	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	109	593	0	ENST00000388985.4:c.190C>T	p.Gln64Ter	p.Q64*	ENST00000388985		64	Cag/Tag	2/12	0.295711142467774	3	FACETS	1	0.93	1	0.348	0.313	0.386	CLONAL	1	TRUE	0	0.318031147697467	3		593	760	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712005	89712005	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	67	298	0	ENST00000371953.3:c.623G>A	p.Gly208Asp	p.G208D	ENST00000371953	NM_000314.4	208	gGc/gAc	6/9	0.318031147697467	3	FACETS	0.901	0.791	1	0.901	0.791	1	CLONAL	2	TRUE	1	0.318031147697467	3		298	271	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1555525429	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	322	728	2	ENST00000269305.4:c.782+1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.310127021914515	2	FACETS	0.9	0.855	0.945	1	0.994	1	CLONAL	3	TRUE	0	0.318031147697467	2		730	750	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256984	16256984	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	84	790	0	ENST00000375759.3:c.4249G>C	p.Glu1417Gln	p.E1417Q	ENST00000375759	NM_015001.2	1417	Gag/Cag	11/15	0.249148469928926	4	FACETS	0.842	0.743	0.949			1	CLONAL	1	TRUE	NA	0.318031147697467	4		790	827	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257272	16257272	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	99	692	0	ENST00000375759.3:c.4537G>C	p.Glu1513Gln	p.E1513Q	ENST00000375759	NM_015001.2	1513	Gag/Cag	11/15	0.249148469928926	4	FACETS	1	0.95	1			1	CLONAL	1	TRUE	NA	0.318031147697467	4		692	740	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310916	123310916	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	65	581	0	ENST00000358487.5:c.512C>G	p.Ala171Gly	p.A171G	ENST00000358487	NM_000141.4	171	gCg/gGg	5/18	0.318031147697467	3	FACETS	0.744	0.645	0.851	0.372	0.322	0.426	SUBCLONAL	1	TRUE	1	0.318031147697467	3		581	637	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456504	32456504	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	92	193	0	ENST00000332351.3:c.388C>A	p.Pro130Thr	p.P130T	ENST00000332351	NM_024426.4	130	Cca/Aca	1/10	0.318031147697467	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.318031147697467	2		193	234	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344042	118344042	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	43	441	0	ENST00000534358.1:c.2168C>T	p.Ser723Phe	p.S723F	ENST00000534358	NM_005933.3	723	tCt/tTt	3/36	0.318031147697467	2	FACETS	0.663	0.555	0.781	0.331	0.277	0.391	SUBCLONAL	1	TRUE	0	0.318031147697467	2		441	408	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552693	18552693	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	91	833	0	ENST00000266497.5:c.2104G>C	p.Asp702His	p.D702H	ENST00000266497		702	Gat/Cat	14/31	0.310127021914515	2	FACETS	0.868	0.772	0.972	0.434	0.386	0.486	CLONAL	1	TRUE	0	0.318031147697467	2		833	659	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865582	57865582	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	129	800	0	ENST00000228682.2:c.3059G>T	p.Gly1020Val	p.G1020V	ENST00000228682	NM_005269.2	1020	gGa/gTa	12/12	0.318031147697467	3	FACETS	1	0.972	1	0.59	0.535	0.648	CLONAL	1	TRUE	1	0.318031147697467	3		800	797	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865632	57865632	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	303	958	1	ENST00000228682.2:c.3109C>A	p.Leu1037Met	p.L1037M	ENST00000228682	NM_005269.2	1037	Ctg/Atg	12/12	0.318031147697467	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.318031147697467	3		959	1024	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225974	133225974	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	221	893	0	ENST00000320574.5:c.3923G>T	p.Arg1308Leu	p.R1308L	ENST00000320574	NM_006231.2	1308	cGg/cTg	31/49	0.151886288013662	4	FACETS	0.965	0.899	1	0.965	0.899	1	INDETERMINATE	2	TRUE	2	0.318031147697467	4		893	949	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281858	49281858	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1566111128	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	191	677	1	ENST00000282018.3:c.905C>T	p.Pro302Leu	p.P302L	ENST00000282018	NM_020377.2	302	cCt/cTt	1/1	0.318031147697467	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	0	0.318031147697467	2		678	588	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052659	42052659	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	95	578	0	ENST00000219905.7:c.7330G>C	p.Glu2444Gln	p.E2444Q	ENST00000219905	NM_001164273.1	2444	Gag/Cag	20/24	0.318031147697467	2	FACETS	1	0.894	1	0.501	0.447	0.559	CLONAL	1	TRUE	0	0.318031147697467	2		578	596	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058424	42058424	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	89	535	1	ENST00000219905.7:c.8144C>T	p.Pro2715Leu	p.P2715L	ENST00000219905	NM_001164273.1	2715	cCa/cTa	24/24	0.318031147697467	2	FACETS	1	0.954	1	0.569	0.506	0.635	CLONAL	1	TRUE	0	0.318031147697467	2		536	492	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66737044	66737044	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	204	629	0	ENST00000307102.5:c.567A>T	p.Arg189Ser	p.R189S	ENST00000307102	NM_002755.3	189	agA/agT	5/11	0.318031147697467	2	FACETS	0.915	0.852	0.98	0.915	0.852	0.98	CLONAL	2	TRUE	0	0.318031147697467	2		629	701	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509567	29509567	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	82	704	0	ENST00000356175.3:c.772G>C	p.Glu258Gln	p.E258Q	ENST00000356175	NM_000267.3	258	Gaa/Caa	8/57	0.318031147697467	3	FACETS	0.802	0.707	0.905	0.267	0.235	0.302	CLONAL	1	TRUE	0	0.318031147697467	3		704	745	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795270	42795270	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	101	756	0	ENST00000575354.2:c.2350G>C	p.Gly784Arg	p.G784R	ENST00000575354	NM_015125.3	784	Ggg/Cgg	10/20	0.318031147697467	6	FACETS	1	0.97	1	0.31	0.277	0.346	CLONAL	1	TRUE	2	0.318031147697467	6		756	837	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143438	30143438	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	189	490	0	ENST00000389048.3:c.88G>T	p.Gly30Cys	p.G30C	ENST00000389048	NM_004304.4	30	Ggc/Tgc	1/29	0.318031147697467	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	1	0.318031147697467	4		490	458	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032052	48032052	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	162	370	0	ENST00000234420.5:c.3442G>T	p.Gly1148Cys	p.G1148C	ENST00000234420	NM_000179.2	1148	Ggc/Tgc	6/10	0.318031147697467	4	FACETS	0.94	0.87	1	0.94	0.87	1	CLONAL	3	TRUE	1	0.318031147697467	4		370	476	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735444	204735444	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	53	410	0	ENST00000302823.3:c.245C>A	p.Thr82Asn	p.T82N	ENST00000302823	NM_005214.4	82	aCt/aAt	2/4	0.318031147697467	2	FACETS	0.911	0.78	1	0.455	0.39	0.527	CLONAL	1	TRUE	0	0.318031147697467	2		410	366	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439976	220439976	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	126	1061	1	ENST00000243786.2:c.829G>T	p.Glu277Ter	p.E277*	ENST00000243786	NM_002191.3	277	Gaa/Taa	2/2	0.318031147697467	2	FACETS	0.922	0.835	1	0.461	0.417	0.508	CLONAL	1	TRUE	0	0.318031147697467	2		1062	859	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662475	227662475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	92	559	2	ENST00000305123.5:c.980G>A	p.Arg327His	p.R327H	ENST00000305123	NM_005544.2	327	cGc/cAc	1/2	0.318031147697467	2	FACETS	1	0.96	1	0.583	0.52	0.65	CLONAL	1	TRUE	0	0.318031147697467	2		561	496	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794801	242794801	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	59	480	0	ENST00000334409.5:c.408G>T	p.Glu136Asp	p.E136D	ENST00000334409	NM_005018.2	136	gaG/gaT	2/5	0.318031147697467	2	FACETS	0.982	0.848	1	0.491	0.424	0.563	CLONAL	1	TRUE	0	0.318031147697467	2		480	378	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757429	40757429	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1175824163	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	207	774	2	ENST00000373198.4:c.2869C>A	p.Pro957Thr	p.P957T	ENST00000373198	NM_133170.3	957	Ccg/Acg	20/32	0.318031147697467	5	FACETS	0.998	0.927	1	0.666	0.618	0.715	CLONAL	2	TRUE	2	0.318031147697467	5		776	963	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62323105	62323105	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	168	586	0	ENST00000360203.5:c.2567G>T	p.Cys856Phe	p.C856F	ENST00000360203	NM_001283009.1	856	tGc/tTc	28/35	0.318031147697467	5	FACETS	1	0.94	1	0.684	0.629	0.74	CLONAL	2	TRUE	2	0.318031147697467	5		586	761	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527535	41527535	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	94	623	0	ENST00000263253.7:c.1426C>G	p.Gln476Glu	p.Q476E	ENST00000263253	NM_001429.3	476	Caa/Gaa	6/31	0.318031147697467	2	FACETS	1	0.942	1	0.542	0.484	0.604	CLONAL	1	TRUE	0	0.318031147697467	2		623	545	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573508	41573508	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	114	833	0	ENST00000263253.7:c.5793G>C	p.Gln1931His	p.Q1931H	ENST00000263253	NM_001429.3	1931	caG/caC	31/31	0.318031147697467	2	FACETS	1	0.973	1	0.61	0.55	0.672	CLONAL	1	TRUE	0	0.318031147697467	2		833	588	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163245	47163245	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	64	587	0	ENST00000409792.3:c.2881G>A	p.Glu961Lys	p.E961K	ENST00000409792	NM_014159.6	961	Gag/Aag	3/21	0.318031147697467	2	FACETS	0.775	0.672	0.887	0.388	0.336	0.444	SUBCLONAL	1	TRUE	0	0.318031147697467	2		587	519	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134885840	134885840	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	81	527	0	ENST00000398015.3:c.1751C>T	p.Thr584Ile	p.T584I	ENST00000398015	NM_004441.4	584	aCa/aTa	9/16	0.133994664122916	5	FACETS	1	0.961	1	0.406	0.358	0.458	INDETERMINATE	1	TRUE	2	0.318031147697467	5		527	617	SUCCESS
ATR	545	MSKCC	GRCh37	3	142232348	142232348	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	61	525	0	ENST00000350721.4:c.4636C>G	p.Gln1546Glu	p.Q1546E	ENST00000350721	NM_001184.3	1546	Cag/Gag	26/47	0.133994664122916	5	FACETS	1	0.891	1	0.346	0.298	0.398	INDETERMINATE	1	TRUE	2	0.318031147697467	5		525	546	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523321	176523321	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	355	915	3	ENST00000292408.4:c.1978G>T	p.Ala660Ser	p.A660S	ENST00000292408	NM_213647.1	660	Gcc/Tcc	15/18	0.318031147697467	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	TRUE	1	0.318031147697467	4		918	951	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048621	180048621	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	215	768	0	ENST00000261937.6:c.1941C>A	p.His647Gln	p.H647Q	ENST00000261937	NM_182925.4	647	caC/caA	13/30	1	2	FACETS	0.977	0.912	1	1	0.994	1	CLONAL	2	TRUE	1	0.318031147697467	2		768	692	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058714	180058714	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	103	897	0	ENST00000261937.6:c.123C>G	p.Ile41Met	p.I41M	ENST00000261937	NM_182925.4	41	atC/atG	2/30	1	2	FACETS	0.66	0.589	0.735	0.66	0.589	0.735	SUBCLONAL	1	TRUE	1	0.318031147697467	2		897	982	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681754	30681754	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	90	706	0	ENST00000376406.3:c.343C>G	p.Leu115Val	p.L115V	ENST00000376406	NM_014641.2	115	Ctg/Gtg	3/15	0.315250307587788	4	FACETS	1	0.919	1	0.261	0.231	0.293	CLONAL	1	TRUE	0	0.318031147697467	4		706	715	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978566	70978566	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	285	761	0	ENST00000276594.2:c.1087del	p.Val364CysfsTer15	p.V364Cfs*15	ENST00000276594	NM_024504.3	363	Ctt/tt	5/8	0.133850389852272	3	FACETS	0.851	0.803	0.899	0.851	0.803	0.899	INDETERMINATE	3	TRUE	0	0.318031147697467	3		761	814	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360661	70360661	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	51	171	0	ENST00000374080.3:c.6221del	p.Gln2074ArgfsTer145	p.Q2074Rfs*145	ENST00000374080		2074	cAg/cg	42/45	1	1	FACETS	0.843	0.731	0.961	1	0.973	1	CLONAL	2	TRUE	0	0.318031147697467	1		171	160	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985510	2985510	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	TTGGG	novel	NA	P-0023216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	77	727	0	ENST00000396946.4:c.301delinsCCCAA	p.Glu101ProfsTer63	p.E101Pfs*63	ENST00000396946	NM_032415.4	101	Gaa/CCCAAaa	4/25	0.318031147697467	3	FACETS	0.606	0.531	0.687	0.303	0.265	0.344	SUBCLONAL	1	TRUE	1	0.318031147697467	3		727	926	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0023218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	105	867	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.189907596470033	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	0	0.202124333990033	2		868	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0023218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	47	914	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	0.622	0.523	0.731	0.622	0.523	0.731	SUBCLONAL	1	TRUE	1	0.202124333990033	2		914	748	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0023218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	63	832	2	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	1	2	FACETS	0.866	0.748	0.994	0.866	0.748	0.994	CLONAL	1	TRUE	1	0.202124333990033	2		834	720	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916121	9916121	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	20	489	0	ENST00000330684.3:c.2168G>T	p.Gly723Val	p.G723V	ENST00000330684	NM_001134407.1	723	gGg/gTg	10/13	1	2	FACETS	0.495	0.377	0.633	0.495	0.377	0.633	SUBCLONAL	1	TRUE	1	0.202124333990033	2		489	400	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518419	69518419	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1345524461	NA	P-0023218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	19	169	1	ENST00000294312.3:c.226G>T	p.Ala76Ser	p.A76S	ENST00000294312	NM_005117.2	76	Gcg/Tcg	1/3	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.202124333990033	2		170	159	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394665	394665	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	40	733	0	ENST00000399788.2:c.5030T>G	p.Met1677Arg	p.M1677R	ENST00000399788	NM_001042603.1	1677	aTg/aGg	28/28	0.189907596470033	2	FACETS	0.61	0.506	0.727	0.305	0.253	0.364	SUBCLONAL	1	TRUE	0	0.202124333990033	2		733	649	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032133	10032133	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	46	714	1	ENST00000330684.3:c.690C>A	p.Tyr230Ter	p.Y230*	ENST00000330684	NM_001134407.1	230	taC/taA	3/13	1	2	FACETS	0.879	0.74	1	0.879	0.74	1	CLONAL	1	TRUE	1	0.202124333990033	2		715	518	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52621424	52621425	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0023218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	78	714	1	ENST00000394830.3:c.2992_2993insC	p.Tyr998SerfsTer7	p.Y998Sfs*7	ENST00000394830	NM_018313.4	998	tac/tCac	20/30	1	2	FACETS	0.761	0.67	0.858	1	0.977	1	SUBCLONAL	2	TRUE	1	0.202124333990033	2		715	507	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539950	187539950	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	40	496	0	ENST00000441802.2:c.7790G>T	p.Arg2597Leu	p.R2597L	ENST00000441802	NM_005245.3	2597	cGa/cTa	10/27	1	2	FACETS	0.929	0.773	1	0.929	0.773	1	CLONAL	1	TRUE	1	0.202124333990033	2		496	426	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864442	162864442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	49	601	0	ENST00000366898.1:c.71del	p.Phe24SerfsTer20	p.F24Sfs*20	ENST00000366898	NM_004562.2	24	tTc/tc	2/12	0.190715337583278	1	FACETS	0.841	0.713	0.983	0.841	0.713	0.983	CLONAL	1	TRUE	0	0.202124333990033	1		601	518	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0023219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	91	721	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.157629028624821	5	FACETS	0.79	0.701	0.887	0.527	0.467	0.591	SUBCLONAL	2	TRUE	2	0.157629028624821	5		721	903	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0023219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	114	725	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.157629028624821	5	FACETS	0.998	0.898	1	0.665	0.598	0.736	CLONAL	2	TRUE	2	0.157629028624821	5		725	896	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446207	29446207	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0023219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	43	446	0	ENST00000389048.3:c.3359+1G>T		p.X1120_splice	ENST00000389048	NM_004304.4	1120			0.102638042037788	3	FACETS	1	0.952	1	0.702	0.588	0.828	CLONAL	1	TRUE	1	0.157629028624821	3		446	419	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0023221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	1218	571	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.234271916226331	15	FACETS	1	0.991	1			1	CLONAL	15	TRUE	NA	0.234271916226331	15		571	1719	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0023221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	114	879	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.183464447319561	2	FACETS	1	0.976	1	0.639	0.576	0.707	CLONAL	1	TRUE	0	0.234271916226331	2		881	761	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484312	120484312	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	32	462	0	ENST00000256646.2:c.2818G>T	p.Gly940Cys	p.G940C	ENST00000256646	NM_024408.3	940	Ggt/Tgt	18/34	1	2	FACETS	0.629	0.511	0.764	0.629	0.511	0.764	SUBCLONAL	1	TRUE	1	0.234271916226331	2		462	434	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170817115	170817115	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	34	521	0	ENST00000296930.5:c.119A>G	p.His40Arg	p.H40R	ENST00000296930	NM_002520.6	40	cAc/cGc	2/11	0.160819288411147	5	FACETS	0.597	0.486	0.722	0.199	0.162	0.241	SUBCLONAL	1	TRUE	2	0.234271916226331	5		521	657	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0023222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	252	722	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.907	0.852	0.963	0.907	0.852	0.963	CLONAL	1	TRUE	1	0.737038078647596	2		722	754	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0023222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	288	721	3	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	0.954	0.901	1	0.954	0.901	1	CLONAL	1	TRUE	1	0.737038078647596	2		724	819	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772290	68772290	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	303	1093	2	ENST00000261769.5:c.139G>T	p.Glu47Ter	p.E47*	ENST00000261769	NM_004360.3	47	Gag/Tag	2/16	0.737038078647596	1	FACETS	0.929	0.886	0.972	0.929	0.886	0.972	CLONAL	1	TRUE	0	0.737038078647596	1		1095	559	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	41	777	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.511	0.425	0.607	0.511	0.425	0.607	SUBCLONAL	1	TRUE	1	0.284111725105934	2		777	565	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115962	8115978	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCATGGTCACCGCCA	CAGCATGGTCACCGCCA	-	novel	NA	P-0023224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	33	496	0	ENST00000346208.3:c.1308_1324del	p.Ser437GlyfsTer64	p.S437Gfs*64	ENST00000346208		436	tcCAGCATGGTCACCGCCAtg/tctg	6/6	1	2	FACETS	0.7	0.571	0.844	0.7	0.571	0.844	SUBCLONAL	1	TRUE	1	0.284111725105934	2		496	332	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0023249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	67	883	4	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.675212006783119	1	FACETS	0.993	0.901	1	0.993	0.901	1	CLONAL	1	FALSE	0	0.747509488857247	1		887	113	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0023250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	70	515	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	0.988	1	CLONAL	4	FALSE	1	0.19148851532504	2		515	165	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0023250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	112	620	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.191626639140518	3	FACETS	0.984	0.908	1	1	0.992	1	CLONAL	6	FALSE	1	0.19148851532504	3		620	217	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0023250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	67	409	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.921	0.816	1	1	0.987	1	CLONAL	4	FALSE	1	0.19148851532504	2		409	190	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487554	38487554	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	240	589	3	ENST00000254066.5:c.89del	p.Pro30LeufsTer12	p.P30Lfs*12	ENST00000254066	NM_000964.3	28	ttC/tt	2/9	0.191626639140518	3	FACETS	1	0.958	1	1	0.995	1	CLONAL	4	FALSE	1	0.19148851532504	3		592	670	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	117	624	0	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	0.19148851532504	6	FACETS	1	0.926	1	1	0.98	1	CLONAL	5	FALSE	2	0.19148851532504	6		624	333	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246445	105246445	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	62	657	0	ENST00000349310.3:c.155T>A	p.Leu52His	p.L52H	ENST00000349310	NM_001014432.1	52	cTc/cAc	4/15	1	2	FACETS	0.952	0.84	1	1	0.986	1	CLONAL	4	FALSE	1	0.19148851532504	2		657	170	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444659	78444659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs908264837	NA	P-0023250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	48	442	1	ENST00000370768.2:c.30del	p.Ser11LeufsTer43	p.S11Lfs*43	ENST00000370768	NM_003902.3	10	ccC/cc	1/20	1	2	FACETS	0.573	0.483	0.673	0.573	0.483	0.673	SUBCLONAL	1	FALSE	1	0.19148851532504	2		443	875	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913315	NA	P-0023250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	8	613	0	ENST00000326873.7:c.580G>A	p.Asp194Asn	p.D194N	ENST00000326873	NM_000455.4	194	Gac/Aac	4/10	1	2	FACETS	0.252	0.162	0.371	0.252	0.162	0.371	SUBCLONAL	1	FALSE	1	0.19148851532504	2		613	331	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188049	151188049	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519950	NA	P-0023250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	19	435	0	ENST00000262187.5:c.104A>G	p.Tyr35Cys	p.Y35C	ENST00000262187	NM_005614.3	35	tAc/tGc	2/8	1	2	FACETS	0.706	0.536	0.906	0.706	0.536	0.906	CLONAL	1	FALSE	1	0.19148851532504	2		435	281	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871029	12871029	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	159	364	0	ENST00000228872.4:c.256G>T	p.Glu86Ter	p.E86*	ENST00000228872	NM_004064.3	86	Gag/Tag	1/3	0.19148851532504	11	FACETS	0.947	0.878	1			1	CLONAL	8	FALSE	NA	0.19148851532504	11		364	408	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762439	41762439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371618406	NA	P-0023250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	61	559	0	ENST00000301178.4:c.2119C>T	p.Arg707Cys	p.R707C	ENST00000301178	NM_021913.4	707	Cgt/Tgt	18/20	0.19148851532504	1	FACETS	1	0.914	1	1	0.985	1	CLONAL	3	FALSE	0	0.19148851532504	1		559	183	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0023250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	19	762	0	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	0.19148851532504	1	FACETS	0.496	0.376	0.637	0.496	0.376	0.637	SUBCLONAL	1	FALSE	0	0.19148851532504	1		762	362	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	61	730	4	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	0.19148851532504	1	FACETS	1	0.91	1	1	0.985	1	CLONAL	3	FALSE	0	0.19148851532504	1		734	184	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214871	36214871	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	98	697	4	ENST00000222270.7:c.3302del	p.Pro1101LeufsTer81	p.P1101Lfs*81	ENST00000222270	NM_014727.1	1099	ggC/gg	8/37	0.19148851532504	1	FACETS	1	0.941	1	1	0.99	1	CLONAL	3	FALSE	0	0.19148851532504	1		701	292	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174386	11174386	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	47	625	0	ENST00000361445.4:c.7289G>T	p.Arg2430Met	p.R2430M	ENST00000361445	NM_004958.3	2430	aGg/aTg	53/58	NA	2	FACETS	0.886	0.753	1			1	INDETERMINATE	2	FALSE	NA	0.19148851532504	2		625	277	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465976	69465976	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	83	684	1	ENST00000227507.2:c.814G>T	p.Glu272Ter	p.E272*	ENST00000227507	NM_053056.2	272	Gag/Tag	5/5	1	2	FACETS	1	0.907	1	1	0.99	1	CLONAL	4	FALSE	1	0.19148851532504	2		685	215	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186802	11186802	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	73	481	0	ENST00000361445.4:c.6403G>T	p.Asp2135Tyr	p.D2135Y	ENST00000361445	NM_004958.3	2135	Gac/Tac	46/58	NA	2	FACETS	0.887	0.789	0.988			1	INDETERMINATE	4	FALSE	NA	0.19148851532504	2		481	215	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724496	112724496	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	11	533	0	ENST00000369452.4:c.380A>G	p.Glu127Gly	p.E127G	ENST00000369452	NM_007373.3	127	gAa/gGa	2/9	1	2	FACETS	0.544	0.376	0.754	0.544	0.376	0.754	SUBCLONAL	1	FALSE	1	0.19148851532504	2		533	211	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11032290	11032290	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0023250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	82	532	0	ENST00000327064.4:c.1685-1G>T		p.X562_splice	ENST00000327064	NM_199141.1	562			0.19148851532504	6	FACETS	0.949	0.854	1	1	0.986	1	CLONAL	6	FALSE	3	0.19148851532504	6		532	208	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868410	45868410	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs994071519	NA	P-0023250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	25	651	0	ENST00000391945.4:c.367C>A	p.Pro123Thr	p.P123T	ENST00000391945	NM_000400.3	123	Ccc/Acc	6/23	0.19148851532504	1	FACETS	0.811	0.641	1	0.811	0.641	1	CLONAL	1	FALSE	0	0.19148851532504	1		651	291	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439793	220439793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	84	637	0	ENST00000243786.2:c.646G>A	p.Val216Met	p.V216M	ENST00000243786	NM_002191.3	216	Gtg/Atg	2/2	1	2	FACETS	1	0.957	1	1	0.989	1	CLONAL	3	FALSE	1	0.19148851532504	2		637	258	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023151	31023152	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0023250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	78	592	0	ENST00000375687.4:c.2637_2638del	p.Thr880Ter	p.T880*	ENST00000375687	NM_015338.5	879	gAT/g	13/13	0.185530925602539	0	FACETS	0.93	0.838	1			1	CLONAL	4	FALSE	0	0.19148851532504	0		592	177	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306592	41306592	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	51	674	0	ENST00000373198.4:c.1067A>G	p.Tyr356Cys	p.Y356C	ENST00000373198	NM_133170.3	356	tAt/tGt	7/32	0.185530925602539	0	FACETS	0.903	0.783	1			1	CLONAL	3	FALSE	0	0.19148851532504	0		674	159	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775427	39775428	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CT	CT	-	novel	NA	P-0023250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	53	413	0	ENST00000288319.7:c.592_592+1del		p.X198_splice	ENST00000288319	NM_182918.3	198		4/10	0.19148851532504	1	FACETS	0.999	0.869	1	1	0.982	1	CLONAL	3	FALSE	0	0.19148851532504	1		413	167	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52663028	52663028	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	59	337	0	ENST00000394830.3:c.1325A>G	p.Tyr442Cys	p.Y442C	ENST00000394830	NM_018313.4	442	tAt/tGt	13/30	0.109490107596532	4	FACETS	1	0.888	1	1	0.983	1	INDETERMINATE	5	FALSE	2	0.19148851532504	4		337	146	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916861	178916861	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	108	653	0	ENST00000263967.3:c.248T>G	p.Phe83Cys	p.F83C	ENST00000263967	NM_006218.2	83	tTt/tGt	2/21	1	2	FACETS	1	0.961	1	1	0.991	1	CLONAL	3	FALSE	1	0.19148851532504	2		653	339	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430692	181430692	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	55	577	0	ENST00000325404.1:c.544C>T	p.Gln182Ter	p.Q182*	ENST00000325404	NM_003106.3	182	Cag/Tag	1/1	1	2	FACETS	1	0.887	1	1	0.985	1	CLONAL	4	FALSE	1	0.19148851532504	2		577	142	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924558	131924558	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	91	448	2	ENST00000265335.6:c.1231G>A	p.Ala411Thr	p.A411T	ENST00000265335		411	Gcc/Acc	8/25	0.120103215937727	3	FACETS	1	0.961	1			1	CLONAL	4	FALSE	NA	0.19148851532504	3		450	232	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903706	41903706	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	85	618	0	ENST00000372991.4:c.851C>A	p.Pro284His	p.P284H	ENST00000372991	NM_001760.3	284	cCt/cAt	5/5	1	2	FACETS	1	0.948	1	1	0.989	1	CLONAL	3	FALSE	1	0.19148851532504	2		618	270	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293604	137293604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1395477826	NA	P-0023250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	30	725	1	ENST00000481739.1:c.155G>A	p.Ser52Asn	p.S52N	ENST00000481739	NM_002957.4	52	aGc/aAc	2/10	1	2	FACETS	0.829	0.674	1	1	0.95	1	CLONAL	2	FALSE	1	0.19148851532504	2		726	189	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20152120	20152120	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	22	436	0	ENST00000379607.5:c.210G>C	p.Trp70Cys	p.W70C	ENST00000379607	NM_001412.3	70	tgG/tgC	4/7	0.19148851532504	1	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	FALSE	0	0.19148851532504	1		436	162	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123159767	123159767	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	15	372	0	ENST00000218089.9:c.122A>C	p.Lys41Thr	p.K41T	ENST00000218089	NM_001042749.1	41	aAa/aCa	4/35	0.191626639140518	0	FACETS	0.782	0.575	1			1	CLONAL	1	FALSE	0	0.19148851532504	0		372	162	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416482	29416482	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	12	672	0	ENST00000389048.3:c.4471A>G	p.Lys1491Glu	p.K1491E	ENST00000389048	NM_004304.4	1491	Aag/Gag	29/29	0.19148851532504	1	FACETS	0.584	0.411	0.797	0.584	0.411	0.797	SUBCLONAL	1	FALSE	0	0.19148851532504	1		672	194	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0023251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	171	238	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.666602458559161	3	FACETS	0.981	0.905	1	0.491	0.452	0.53	CLONAL	1	TRUE	1	0.687959178703886	3		238	681	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913255	NA	P-0023251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	250	813	0	ENST00000369535.4:c.183A>T	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caT	3/7	1	2	FACETS	0.969	0.91	1	0.969	0.91	1	CLONAL	1	TRUE	1	0.687959178703886	2		813	750	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0023251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	648	835	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.663751758672624	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.687959178703886	2		835	942	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729180	66729180	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs397516793	NA	P-0023251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	670	820	0	ENST00000307102.5:c.388T>C	p.Tyr130His	p.Y130H	ENST00000307102	NM_002755.3	130	Tat/Cat	3/11	0.666602458559161	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.687959178703886	3		820	1290	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358978	81358978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374484762	NA	P-0023251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	355	745	1	ENST00000222390.5:c.983G>A	p.Arg328His	p.R328H	ENST00000222390	NM_000601.4	328	cGt/cAt	8/18	0.666602458559161	3	FACETS	0.904	0.862	0.946	0.904	0.862	0.946	CLONAL	2	TRUE	1	0.687959178703886	3		746	767	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0023251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	310	413	1	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.663751758672624	2	FACETS	0.949	0.91	0.986	0.949	0.91	0.986	CLONAL	2	TRUE	0	0.687959178703886	2		414	475	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935409	36935409	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs756679232	NA	P-0023251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	271	804	2	ENST00000361632.4:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000361632		440	Cga/Tga	10/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.687959178703886	2		806	770	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356112	66356112	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	134	646	0	ENST00000273854.3:c.1385T>C	p.Val462Ala	p.V462A	ENST00000273854	NM_004439.5	462	gTa/gCa	5/18	0.663751758672624	2	FACETS	0.573	0.521	0.627	0.286	0.26	0.314	SUBCLONAL	1	TRUE	0	0.687959178703886	2		646	680	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056350	180056350	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	246	856	1	ENST00000261937.6:c.894C>A	p.His298Gln	p.H298Q	ENST00000261937	NM_182925.4	298	caC/caA	7/30	0.663751758672624	2	FACETS	0.877	0.823	0.934	0.439	0.411	0.467	CLONAL	1	TRUE	0	0.687959178703886	2		857	815	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64290041	64290041	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	238	728	0	ENST00000370651.3:c.484G>T	p.Asp162Tyr	p.D162Y	ENST00000370651	NM_003463.4	162	Gat/Tat	6/6	0.65372060530486	3	FACETS	0.98	0.916	1	0.49	0.458	0.523	CLONAL	1	TRUE	1	0.687959178703886	3		728	949	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0023253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	207	867	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.214050146038482	3	FACETS	0.922	0.857	0.989	0.615	0.571	0.66	CLONAL	2	TRUE	0	0.307970241715894	3		868	841	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207162	1207162	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs137853076	NA	P-0023253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	400	835	1	ENST00000326873.7:c.250A>T	p.Lys84Ter	p.K84*	ENST00000326873	NM_000455.4	84	Aag/Tag	1/10	0.285352949667511	3	FACETS	0.887	0.845	0.93	0.887	0.845	0.93	CLONAL	3	TRUE	0	0.307970241715894	3		836	1126	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040903	42040903	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	177	711	1	ENST00000219905.7:c.5281C>T	p.Arg1761Ter	p.R1761*	ENST00000219905	NM_001164273.1	1761	Cga/Tga	16/24	0.19712657505645	4	FACETS	0.838	0.772	0.906	0.838	0.772	0.906	CLONAL	2	TRUE	2	0.307970241715894	4		712	897	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245582	46245582	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	132	419	0	ENST00000334344.6:c.3676G>T	p.Gly1226Ter	p.G1226*	ENST00000334344	NM_152641.2	1226	Gga/Tga	15/21	0.214050146038482	3	FACETS	1	0.969	1	0.751	0.687	0.817	CLONAL	2	TRUE	0	0.307970241715894	3		419	439	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89335043	89335043	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	53	342	0	ENST00000301030.4:c.7835A>G	p.Glu2612Gly	p.E2612G	ENST00000301030	NM_001256183.1	2612	gAg/gGg	13/13	0.292567509079377	3	FACETS	0.988	0.845	1			1	CLONAL	1	TRUE	NA	0.307970241715894	3		342	402	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713574	30713574	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	110	537	0	ENST00000295754.5:c.899A>C	p.Lys300Thr	p.K300T	ENST00000295754	NM_003242.5	300	aAg/aCg	4/7	0.19712657505645	4	FACETS	1	0.978	1	0.67	0.603	0.742	CLONAL	1	TRUE	2	0.307970241715894	4		537	697	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523645	176523645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	119	838	0	ENST00000292408.4:c.2056G>T	p.Gly686Trp	p.G686W	ENST00000292408	NM_213647.1	686	Ggg/Tgg	16/18	0.111890905993289	3	FACETS	1	0.97	1	0.591	0.533	0.651	INDETERMINATE	1	TRUE	1	0.307970241715894	3		838	755	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127933445	127933445	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	146	641	0	ENST00000373547.4:c.90C>A	p.Tyr30Ter	p.Y30*	ENST00000373547	NM_002721.4	30	taC/taA	2/7	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.307970241715894	2		641	755	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426704	47426704	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	44	765	1	ENST00000377045.4:c.949G>T	p.Gly317Trp	p.G317W	ENST00000377045	NM_001654.4	317	Ggg/Tgg	10/16	0.294184407571995	1	FACETS	0.384	0.321	0.453	0.384	0.321	0.453	SUBCLONAL	1	TRUE	0	0.307970241715894	1		766	630	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426710	47426710	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1164055186	NA	P-0023253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	44	748	2	ENST00000377045.4:c.955G>T	p.Gly319Cys	p.G319C	ENST00000377045	NM_001654.4	319	Ggc/Tgc	10/16	0.294184407571995	1	FACETS	0.377	0.315	0.445	0.377	0.315	0.445	SUBCLONAL	1	TRUE	0	0.307970241715894	1		750	642	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0023254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	70	521	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		521	528	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038901	12038902	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0023257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	283	564	0	ENST00000396373.4:c.1196_1197del	p.Arg399ProfsTer26	p.R399Pfs*26	ENST00000396373	NM_001987.4	398	ctGCgc/ctgc	7/8	0.3	9	FACETS	1	0.962	1			1	CLONAL	6	TRUE	NA	0.21	9		564	761	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987040	36987045	+	inframe_deletion	In_Frame_Del	DEL	ACAGGT	ACAGGT	-	novel	NA	P-0023257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	32	600	0	ENST00000354822.5:c.644_649del	p.Tyr215_Leu216del	p.Y215_L216del	ENST00000354822	NM_001079668.2	215	tACCTGTcg/tcg	3/3	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.21	2		600	212	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0023259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	129	724	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.235517579508442	2		724	865	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103666	47103666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	85	512	0	ENST00000409792.3:c.6280del	p.Arg2094GlyfsTer53	p.R2094Gfs*53	ENST00000409792	NM_014159.6	2094	Agg/gg	14/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.235517579508442	2		512	568	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs770248150	NA	P-0023260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	93	528	1	ENST00000311936.3:c.351A>T	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaT	4/5	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.337678742328384	2		529	537	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207096	1207096	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0023260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	156	758	0	ENST00000326873.7:c.184A>T	p.Lys62Ter	p.K62*	ENST00000326873	NM_000455.4	62	Aag/Tag	1/10	0.337678742328384	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.337678742328384	1		758	584	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610288	10610288	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	166	802	0	ENST00000171111.5:c.422A>G	p.Tyr141Cys	p.Y141C	ENST00000171111	NM_203500.1	141	tAc/tGc	2/6	0.337678742328384	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.337678742328384	1		802	668	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355333	15355333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	91	426	0	ENST00000263377.2:c.2290C>T	p.Pro764Ser	p.P764S	ENST00000263377	NM_058243.2	764	Ccc/Tcc	13/20	0.337678742328384	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.337678742328384	1		426	350	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172059	32172059	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	148	744	0	ENST00000375023.3:c.2973C>G	p.His991Gln	p.H991Q	ENST00000375023	NM_004557.3	991	caC/caG	19/30	0.269989904084018	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.337678742328384	1		744	603	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140827	37140827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	119	599	0	ENST00000373509.5:c.663G>T	p.Arg221Ser	p.R221S	ENST00000373509	NM_002648.3	221	agG/agT	5/6	0.242263456490132	3	FACETS	1	0.969	1			1	CLONAL	1	TRUE	NA	0.337678742328384	3		599	700	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	152	482	0				ENST00000310581	NM_198253.2	-/1132			0.355869476922832	1	FACETS	0.737	0.681	0.795	0.737	0.681	0.795	INDETERMINATE	1	TRUE	0	0.644126616062215	1		482	434	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0023261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	41	722	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.345	0.288	0.408	0.345	0.288	0.408	SUBCLONAL	1	TRUE	1	0.644126616062215	2		722	369	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0023261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	343	794	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	1	TRUE	NA	0.644126616062215	2		795	770	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804322	46804322	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529100627	NA	P-0023261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	76	722	4	ENST00000290295.7:c.685C>T	p.Arg229Trp	p.R229W	ENST00000290295	NM_006361.5	229	Cgg/Tgg	2/2	0.189822627158229	2	FACETS	0.376	0.329	0.426	0.188	0.164	0.213	INDETERMINATE	1	TRUE	0	0.644126616062215	2		726	628	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257290	16257290	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	59	731	0	ENST00000375759.3:c.4555G>C	p.Glu1519Gln	p.E1519Q	ENST00000375759	NM_015001.2	1519	Gag/Cag	11/15	0.283219986251107	4	FACETS	0.384	0.33	0.444			1	INDETERMINATE	1	TRUE	NA	0.644126616062215	4		731	784	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257344	16257344	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	51	779	0	ENST00000375759.3:c.4609G>C	p.Glu1537Gln	p.E1537Q	ENST00000375759	NM_015001.2	1537	Gaa/Caa	11/15	0.283219986251107	4	FACETS	0.339	0.287	0.396			1	INDETERMINATE	1	TRUE	NA	0.644126616062215	4		779	768	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874166	155874166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777520196	NA	P-0023261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	82	769	1	ENST00000368323.3:c.365G>A	p.Arg122Gln	p.R122Q	ENST00000368323	NM_006912.5	122	cGa/cAa	5/6	0.189822627158229	2	FACETS	0.288	0.253	0.326	0.144	0.126	0.163	INDETERMINATE	1	TRUE	0	0.644126616062215	2		770	883	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682949	241682960	+	inframe_deletion	In_Frame_Del	DEL	GCCGAAGCTAAG	GCCGAAGCTAAG	-	novel	NA	P-0023261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	123	573	0	ENST00000366560.3:c.63_74del	p.Leu22_Ala25del	p.L22_A25del	ENST00000366560	NM_000143.3	21	gcCTTAGCTTCGGCt/gct	1/10	0.27789938057429	1	FACETS	0.594	0.541	0.649	0.594	0.541	0.649	INDETERMINATE	1	TRUE	0	0.644126616062215	1		573	436	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450706	70450706	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	56	637	0	ENST00000373644.4:c.5546C>A	p.Ser1849Tyr	p.S1849Y	ENST00000373644	NM_030625.2	1849	tCc/tAc	12/12	1	2	FACETS	0.276	0.236	0.32	0.276	0.236	0.32	SUBCLONAL	1	TRUE	1	0.644126616062215	2		637	629	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436647	49436647	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	200	642	0	ENST00000301067.7:c.5659G>T	p.Glu1887Ter	p.E1887*	ENST00000301067	NM_003482.3	1887	Gaa/Taa	26/54	NA	2	FACETS	0.948	0.883	1			1	INDETERMINATE	1	TRUE	NA	0.644126616062215	2		642	655	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495387	56495387	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	328	778	0	ENST00000267101.3:c.3577G>A	p.Glu1193Lys	p.E1193K	ENST00000267101	NM_001982.3	1193	Gaa/Aaa	28/28	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.644126616062215	2		778	748	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121438901	121438901	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0023261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1332	77	926	0	ENST00000257555.6:c.1802C>G	p.Ser601Ter	p.S601*	ENST00000257555		601	tCa/tGa	10/10	0.372591574182308	5	FACETS	0.334	0.291	0.379			1	INDETERMINATE	1	TRUE	NA	0.644126616062215	5		926	1409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577572	7577573	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0023261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	390	726	0	ENST00000269305.4:c.708_709insCC	p.Met237ProfsTer11	p.M237Pfs*11	ENST00000269305	NM_001126112.2	236	-/CC	7/11	0.590792310350681	2	FACETS	0.872	0.837	0.907	0.872	0.837	0.907	CLONAL	2	TRUE	0	0.644126616062215	2		726	694	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797300	42797300	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	70	858	0	ENST00000575354.2:c.3662C>G	p.Ser1221Cys	p.S1221C	ENST00000575354	NM_015125.3	1221	tCt/tGt	15/20	0.249645605469879	3	FACETS	0.382	0.332	0.435	0.191	0.166	0.218	INDETERMINATE	1	TRUE	1	0.644126616062215	3		858	753	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200774	128200774	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	58	648	0	ENST00000341105.2:c.1031G>C	p.Arg344Thr	p.R344T	ENST00000341105	NM_032638.4	344	aGa/aCa	5/6	1	2	FACETS	0.287	0.246	0.331	0.287	0.246	0.331	SUBCLONAL	1	TRUE	1	0.644126616062215	2		648	628	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541112	187541112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1480782466	NA	P-0023261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	46	487	0	ENST00000441802.2:c.6628G>A	p.Glu2210Lys	p.E2210K	ENST00000441802	NM_005245.3	2210	Gaa/Aaa	10/27	0.476325020676316	1	FACETS	0.3	0.253	0.351	0.3	0.253	0.351	SUBCLONAL	1	TRUE	0	0.644126616062215	1		487	323	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80024675	80024675	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	42	573	0	ENST00000265081.6:c.1459C>G	p.Gln487Glu	p.Q487E	ENST00000265081	NM_002439.4	487	Caa/Gaa	10/24	0.355869476922832	1	FACETS	0.233	0.194	0.275	0.233	0.194	0.275	INDETERMINATE	1	TRUE	0	0.644126616062215	1		573	380	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211125	55211125	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	51	626	0	ENST00000275493.2:c.368C>G	p.Ser123Cys	p.S123C	ENST00000275493	NM_005228.3	123	tCt/tGt	3/28	0.196537548585235	2	FACETS	0.298	0.253	0.347	0.149	0.126	0.174	INDETERMINATE	1	TRUE	0	0.644126616062215	2		626	532	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92355059	92355059	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs756963341	NA	P-0023261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	169	448	1	ENST00000265734.4:c.418C>T	p.Arg140Ter	p.R140*	ENST00000265734	NM_001259.6	140	Cga/Tga	4/8	0.384578101995843	3	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.644126616062215	3		449	485	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0023263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	82	472	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.958	0.85	1	0.958	0.85	1	CLONAL	1	TRUE	1	0.454166264752622	2		472	377	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870948	12870948	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	27	401	0	ENST00000228872.4:c.176del	p.Lys59SerfsTer12	p.K59Sfs*12	ENST00000228872	NM_004064.3	59	Aag/ag	1/3	1	2	FACETS	0.279	0.222	0.345	0.279	0.222	0.345	SUBCLONAL	1	TRUE	1	0.454166264752622	2		401	426	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029178	26029191	+	frameshift_variant	Frame_Shift_Del	DEL	CATTCAGGCATGCA	CATTCAGGCATGCA	-	novel	NA	P-0023263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	113	503	0	ENST00000435504.4:c.159_172del	p.Ala54AsnfsTer9	p.A54Nfs*9	ENST00000435504		53	ctTGCATGCCTGAATGca/ctca	4/13	1	2	FACETS	0.987	0.893	1	0.987	0.893	1	CLONAL	1	TRUE	1	0.454166264752622	2		503	504	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046400	69046400	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	136	634	0	ENST00000288368.4:c.3873C>A	p.Asp1291Glu	p.D1291E	ENST00000288368	NM_024870.2	1291	gaC/gaA	32/40	1	2	FACETS	0.98	0.894	1	0.98	0.894	1	CLONAL	1	TRUE	1	0.454166264752622	2		634	611	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501461	149501461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751904503	NA	P-0023264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	200	556	0	ENST00000261799.4:c.2326G>A	p.Asp776Asn	p.D776N	ENST00000261799	NM_002609.3	776	Gat/Aat	16/23	0.431729829925944	3	FACETS	1	0.978	1	0.56	0.521	0.6	CLONAL	1	TRUE	1	0.687562825559714	3		556	698	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856050	68856050	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	280	635	0	ENST00000261769.5:c.1859del	p.Pro620LeufsTer11	p.P620Lfs*11	ENST00000261769	NM_004360.3	620	Cct/ct	12/16	0.687562825559714	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.687562825559714	1		635	459	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984980	101984981	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0023264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	106	268	0	ENST00000282441.5:c.432dup	p.Thr145HisfsTer22	p.T145Hfs*22	ENST00000282441	NM_001130145.2	143	acc/aCcc	2/9	0.687562825559714	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.687562825559714	1		268	197	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658365	18658375	+	protein_altering_variant	In_Frame_Del	DEL	GTCATGCACAA	GTCATGCACAA	TC	novel	NA	P-0023264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	184	481	2	ENST00000266497.5:c.3170_3180delinsTC	p.Gly1057_Gln1060delinsVal	p.G1057_Q1060delinsV	ENST00000266497		1057	gGTCATGCACAA/gTC	22/31	1	2	FACETS	0.897	0.832	0.963	0.897	0.832	0.963	CLONAL	1	TRUE	1	0.687562825559714	2		483	597	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0023265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	34	238	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.354	0.289	0.428	0.354	0.289	0.428	SUBCLONAL	1	TRUE	1	0.405090761091298	2		238	474	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0023265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	45	411	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.473	0.397	0.556	0.473	0.397	0.556	SUBCLONAL	1	TRUE	1	0.405090761091298	2		411	470	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0023265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	24	722	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.218	0.17	0.273	0.218	0.17	0.273	SUBCLONAL	1	TRUE	1	0.405090761091298	2		722	544	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0023265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	47	431	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.247256639679651	3	FACETS	0.62	0.524	0.726	0.31	0.262	0.363	SUBCLONAL	1	TRUE	1	0.405090761091298	3		431	450	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0023265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	62	609	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	1	2	FACETS	0.469	0.405	0.54	0.469	0.405	0.54	SUBCLONAL	1	TRUE	1	0.405090761091298	2		609	652	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0023265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	33	467	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	0.318	0.258	0.385	0.318	0.258	0.385	SUBCLONAL	1	TRUE	1	0.405090761091298	2		467	513	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717661	89717661	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0023265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	55	627	0	ENST00000371953.3:c.686C>G	p.Ser229Ter	p.S229*	ENST00000371953	NM_000314.4	229	tCa/tGa	7/9	1	2	FACETS	0.381	0.325	0.443	0.381	0.325	0.443	SUBCLONAL	1	TRUE	1	0.405090761091298	2		627	712	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940000	76940000	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1311466929	NA	P-0023265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	84	599	1	ENST00000373344.5:c.748C>T	p.Arg250Ter	p.R250*	ENST00000373344	NM_000489.3	250	Cga/Tga	9/35	0.258313267596474	3	FACETS	0.629	0.555	0.709	0.314	0.277	0.355	SUBCLONAL	1	TRUE	1	0.405090761091298	3		600	793	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285326	212285326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1390491269	NA	P-0023265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	29	449	0	ENST00000342788.4:c.2975G>A	p.Arg992His	p.R992H	ENST00000342788	NM_005235.2	992	cGt/cAt	25/28	1	2	FACETS	0.315	0.253	0.387	0.315	0.253	0.387	SUBCLONAL	1	TRUE	1	0.405090761091298	2		449	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0023268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	8	792	2	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	1	2	FACETS	0.546	0.352	0.796	0.546	0.352	0.796	SUBCLONAL	1	TRUE	1	0.178787347670007	2		794	164	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0023269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	75	792	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.16	2		794	876	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519922	NA	P-0023269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	30	839	1	ENST00000397062.3:c.235G>A	p.Glu79Lys	p.E79K	ENST00000397062	NM_006164.4	79	Gag/Aag	2/5	1	2	FACETS	0.585	0.47	0.717	0.585	0.47	0.717	SUBCLONAL	1	TRUE	1	0.16	2		840	641	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424990	49424990	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	68	774	2	ENST00000301067.7:c.13498C>T	p.Gln4500Ter	p.Q4500*	ENST00000301067	NM_003482.3	4500	Cag/Tag	39/54	1	2	FACETS	0.965	0.838	1	0.965	0.838	1	CLONAL	1	TRUE	1	0.16	2		776	881	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346230	70346230	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	41	873	0	ENST00000374080.3:c.2581C>A	p.Leu861Ile	p.L861I	ENST00000374080		861	Ctt/Att	19/45	0.117838398892033	0	FACETS	0.533	0.443	0.635			1	SUBCLONAL	1	TRUE	0	0.16	0		873	807	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432011	49432011	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs746344900	NA	P-0023270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	43	898	0	ENST00000301067.7:c.9128A>G	p.Asn3043Ser	p.N3043S	ENST00000301067	NM_003482.3	3043	aAt/aGt	34/54	1	2	FACETS	0.754	0.629	0.892	0.754	0.629	0.892	SUBCLONAL	1	TRUE	1	0.18	2		898	634	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213616	2213616	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	92	830	0	ENST00000398665.3:c.1636C>G	p.Leu546Val	p.L546V	ENST00000398665	NM_032482.2	546	Ctg/Gtg	17/28	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.18	2		830	805	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	119	521	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	0.443951306370912	2		521	462	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	363	620	0	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	0.443951306370912	2		620	691	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150512	157150512	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754042537	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	138	666	1	ENST00000346085.5:c.1694G>A	p.Arg565Gln	p.R565Q	ENST00000346085	NM_020732.3	565	cGg/cAg	2/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.443951306370912	2		667	519	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	329	778	5	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	0.997	1	CLONAL	2	TRUE	1	0.443951306370912	2		783	670	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	131	823	8	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.934	0.85	1	0.934	0.85	1	CLONAL	1	TRUE	1	0.443951306370912	2		831	632	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263973	104263974	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776579	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	90	472	0	ENST00000369902.3:c.71dup	p.Ala25GlyfsTer23	p.A25Gfs*23	ENST00000369902	NM_016169.3	22	gcc/gCcc	1/12	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.443951306370912	2		472	339	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	137	616	10	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.443951306370912	2		626	611	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443613	52443613	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	32	621	0	ENST00000460680.1:c.79del	p.Val27CysfsTer45	p.V27Cfs*45	ENST00000460680	NM_004656.3	27	Gtg/tg	3/17	1	2	FACETS	0.244	0.197	0.297	0.244	0.197	0.297	SUBCLONAL	1	TRUE	1	0.443951306370912	2		621	591	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	248	505	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	0.995	1	CLONAL	2	TRUE	1	0.443951306370912	2		511	514	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	154	672	1	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.443951306370912	2		673	578	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	143	663	4	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.984	0.899	1	0.984	0.899	1	CLONAL	1	TRUE	1	0.443951306370912	2		667	655	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998127	169998128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs753143066	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	151	823	9	ENST00000295797.4:c.826dup	p.Thr276AsnfsTer16	p.T276Nfs*16	ENST00000295797	NM_002740.5	273	tta/ttAa	9/18	1	2	FACETS	0.968	0.887	1	0.968	0.887	1	CLONAL	1	TRUE	1	0.443951306370912	2		832	703	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	113	430	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.863	0.788	0.939	1	0.988	1	CLONAL	2	TRUE	1	0.443951306370912	2		431	295	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799299	42799300	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1158987717	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	60	448	0	ENST00000575354.2:c.4790dup	p.Pro1598ThrfsTer16	p.P1598Tfs*16	ENST00000575354	NM_015125.3	1595	tcc/tCcc	20/20	1	2	FACETS	0.952	0.827	1	0.952	0.827	1	CLONAL	1	TRUE	1	0.443951306370912	2		448	284	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143049	7143049	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777271464	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	131	672	0	ENST00000302850.5:c.2320G>A	p.Val774Met	p.V774M	ENST00000302850	NM_000208.2	774	Gtg/Atg	12/22	1	2	FACETS	0.823	0.748	0.902	0.823	0.748	0.902	CLONAL	1	TRUE	1	0.443951306370912	2		672	717	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779211	3779211	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783507	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	55	438	6	ENST00000262367.5:c.5837del	p.Pro1946HisfsTer30	p.P1946Hfs*30	ENST00000262367	NM_004380.2	1946	cCa/ca	31/31	1	2	FACETS	0.854	0.736	0.981	0.854	0.736	0.981	CLONAL	1	TRUE	1	0.443951306370912	2		444	290	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	129	409	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.443951306370912	2		409	510	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578496	7578496	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782197	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	30	888	0	ENST00000269305.4:c.434T>C	p.Leu145Pro	p.L145P	ENST00000269305	NM_001126112.2	145	cTg/cCg	5/11	1	2	FACETS	0.147	0.118	0.181	0.147	0.118	0.181	SUBCLONAL	1	TRUE	1	0.443951306370912	2		888	919	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538846	23538846	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746822077	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	90	521	0	ENST00000380871.4:c.593C>T	p.Pro198Leu	p.P198L	ENST00000380871	NM_006167.3	198	cCg/cTg	2/2	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.443951306370912	2		521	399	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	36	672	0	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	0.262	0.215	0.316	0.262	0.215	0.316	SUBCLONAL	1	TRUE	1	0.443951306370912	2		672	618	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944382	131944382	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs748536322	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	85	461	4	ENST00000265335.6:c.2801del	p.Asn934IlefsTer6	p.N934Ifs*6	ENST00000265335		932	Aaa/aa	17/25	1	2	FACETS	0.918	0.816	1	0.918	0.816	1	CLONAL	1	TRUE	1	0.443951306370912	2		465	417	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646981	23646981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	35	841	3	ENST00000261584.4:c.886del	p.Met296Ter	p.M296*	ENST00000261584	NM_024675.3	296	Atg/tg	4/13	1	2	FACETS	0.259	0.211	0.312	0.259	0.211	0.312	SUBCLONAL	1	TRUE	1	0.443951306370912	2		844	609	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660348	227660350	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	61	505	0	ENST00000305123.5:c.3105_3107del	p.Ser1038del	p.S1038del	ENST00000305123	NM_005544.2	1035	tcCTCa/tca	1/2	1	2	FACETS	0.861	0.748	0.983	0.861	0.748	0.983	CLONAL	1	TRUE	1	0.443951306370912	2		505	319	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	127	712	10	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.443951306370912	2		722	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577563	7577563	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1567549584	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	28	736	0	ENST00000269305.4:c.718A>G	p.Ser240Gly	p.S240G	ENST00000269305	NM_001126112.2	240	Agt/Ggt	7/11	1	2	FACETS	0.18	0.143	0.222	0.18	0.143	0.222	SUBCLONAL	1	TRUE	1	0.443951306370912	2		736	702	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099103	27099103	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	115	892	2	ENST00000324856.7:c.3524del	p.Pro1175HisfsTer5	p.P1175Hfs*5	ENST00000324856	NM_006015.4	1173	atC/at	13/20	1	2	FACETS	0.776	0.7	0.856	0.776	0.7	0.856	SUBCLONAL	1	TRUE	1	0.443951306370912	2		894	668	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151290	202151290	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	160	693	0	ENST00000358485.4:c.1596del	p.Lys532AsnfsTer73	p.K532Nfs*73	ENST00000358485	NM_001080125.1	530	agA/ag	9/9	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.443951306370912	2		693	663	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138172	64138172	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	175	732	2	ENST00000334205.4:c.2095C>T	p.Arg699Cys	p.R699C	ENST00000334205	NM_003942.2	699	Cgc/Tgc	16/17	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.443951306370912	2		734	640	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649561	48649561	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	175	447	0	ENST00000376670.3:c.49del	p.Gln17SerfsTer120	p.Q17Sfs*120	ENST00000376670	NM_002049.3	15	ctC/ct	2/6	1	1	FACETS	0.913	0.856	0.969	1	0.993	1	CLONAL	2	TRUE	0	0.443951306370912	1		447	336	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263394	123263394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773245022	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	179	597	1	ENST00000358487.5:c.1349G>A	p.Arg450His	p.R450H	ENST00000358487	NM_000141.4	450	cGc/cAc	10/18	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.443951306370912	2		598	603	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025857	48025857	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs267608041	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	70	439	0	ENST00000234420.5:c.741del	p.Lys247AsnfsTer32	p.K247Nfs*32	ENST00000234420	NM_000179.2	245	atA/at	4/10	1	2	FACETS	0.843	0.739	0.954	0.843	0.739	0.954	CLONAL	1	TRUE	1	0.443951306370912	2		439	374	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942053	71942053	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	166	789	1	ENST00000298229.2:c.1322del	p.Asn441ThrfsTer2	p.N441Tfs*2	ENST00000298229	NM_001567.3	439	ccA/cc	12/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.443951306370912	2		790	648	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	139	893	2	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	1	2	FACETS	0.846	0.771	0.925	0.846	0.771	0.925	CLONAL	1	TRUE	1	0.443951306370912	2		895	740	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984022	2984022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753614569	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	26	730	1	ENST00000396946.4:c.508C>T	p.Arg170Cys	p.R170C	ENST00000396946	NM_032415.4	170	Cgc/Tgc	5/25	1	2	FACETS	0.182	0.143	0.227	0.182	0.143	0.227	SUBCLONAL	1	TRUE	1	0.443951306370912	2		731	644	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421039	49421039	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398123721	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	151	642	0	ENST00000301067.7:c.14710C>T	p.Arg4904Ter	p.R4904*	ENST00000301067	NM_003482.3	4904	Cga/Tga	48/54	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.443951306370912	2		642	570	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942593	17942593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	107	593	5	ENST00000458235.1:c.2695C>T	p.Arg899Trp	p.R899W	ENST00000458235	NM_000215.3	899	Cgg/Tgg	20/24	1	2	FACETS	0.893	0.804	0.986	0.893	0.804	0.986	CLONAL	1	TRUE	1	0.443951306370912	2		598	540	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117872	70117872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	124	489	0	ENST00000245479.2:c.340G>A	p.Val114Met	p.V114M	ENST00000245479	NM_000346.3	114	Gtg/Atg	1/3	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.443951306370912	2		489	459	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007331	143007332	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs772784869	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	132	606	0	ENST00000262992.4:c.2452dup	p.Arg818LysfsTer26	p.R818Kfs*26	ENST00000262992	NM_001101669.1	818	aga/aAga	22/24	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.443951306370912	2		606	580	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942171	71942171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762627344	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	223	770	0	ENST00000298229.2:c.1435C>T	p.Arg479Cys	p.R479C	ENST00000298229	NM_001567.3	479	Cgc/Tgc	12/28	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.443951306370912	2		770	734	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11313900	11313900	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	166	621	1	ENST00000361445.4:c.836G>A	p.Gly279Glu	p.G279E	ENST00000361445	NM_004958.3	279	gGa/gAa	6/58	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.443951306370912	2		622	639	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36826845	36826846	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	155	733	0	ENST00000373129.3:c.88_89del	p.Lys30GlufsTer31	p.K30Efs*31	ENST00000373129	NM_032017.1	30	AAg/g	3/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.443951306370912	2		733	629	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366751	40366751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs976643781	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	83	556	1	ENST00000397332.2:c.446G>A	p.Arg149Gln	p.R149Q	ENST00000397332	NM_001033082.2	149	cGg/cAg	2/3	1	2	FACETS	0.864	0.766	0.967	0.864	0.766	0.967	CLONAL	1	TRUE	1	0.443951306370912	2		557	433	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534318	534318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1447218022	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	21	401	1	ENST00000451590.1:c.5C>T	p.Thr2Met	p.T2M	ENST00000451590	NM_001130442.1	2	aCg/aTg	2/5	1	2	FACETS	0.294	0.226	0.373	0.294	0.226	0.373	SUBCLONAL	1	TRUE	1	0.443951306370912	2		402	322	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945645	71945645	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	101	625	0	ENST00000298229.2:c.2401del	p.Arg801AlafsTer44	p.R801Afs*44	ENST00000298229	NM_001567.3	801	Cgc/gc	21/28	1	2	FACETS	0.835	0.749	0.926	0.835	0.749	0.926	CLONAL	1	TRUE	1	0.443951306370912	2		625	545	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962543	100962544	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	118	681	0	ENST00000325455.5:c.1853dup	p.Asn618LysfsTer8	p.N618Kfs*8	ENST00000325455	NM_001202474.3	618	aac/aaAc	3/8	1	2	FACETS	0.802	0.725	0.883	0.802	0.725	0.883	CLONAL	1	TRUE	1	0.443951306370912	2		681	663	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123593	108123593	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1057517300	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	137	625	0	ENST00000278616.4:c.1856del	p.Asn619ThrfsTer6	p.N619Tfs*6	ENST00000278616	NM_000051.3	618	Aaa/aa	12/63	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.443951306370912	2		625	511	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245541	46245541	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	52	436	0	ENST00000334344.6:c.3635T>G	p.Leu1212Arg	p.L1212R	ENST00000334344	NM_152641.2	1212	cTt/cGt	15/21	1	2	FACETS	0.625	0.534	0.724	0.625	0.534	0.724	SUBCLONAL	1	TRUE	1	0.443951306370912	2		436	375	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434054	49434054	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369604891	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	151	721	0	ENST00000301067.7:c.7499C>T	p.Ala2500Val	p.A2500V	ENST00000301067	NM_003482.3	2500	gCg/gTg	31/54	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.443951306370912	2		721	525	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864483	57864483	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	147	673	0	ENST00000228682.2:c.1960G>T	p.Val654Phe	p.V654F	ENST00000228682	NM_005269.2	654	Gtc/Ttc	12/12	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.443951306370912	2		673	523	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856434	111856434	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs776317487	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	90	406	4	ENST00000341259.2:c.489del	p.Thr165ProfsTer32	p.T165Pfs*32	ENST00000341259	NM_005475.2	162	gCc/gc	2/8	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.443951306370912	2		410	371	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426649	121426649	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774996577	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	33	666	3	ENST00000257555.6:c.340C>T	p.Arg114Cys	p.R114C	ENST00000257555		114	Cgt/Tgt	2/10	1	2	FACETS	0.228	0.185	0.277	0.228	0.185	0.277	SUBCLONAL	1	TRUE	1	0.443951306370912	2		669	651	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219168	133219168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753713315	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	191	811	0	ENST00000320574.5:c.4876C>T	p.Arg1626Cys	p.R1626C	ENST00000320574	NM_006231.2	1626	Cgc/Tgc	37/49	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.443951306370912	2		811	719	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610666	81610666	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	88	480	0	ENST00000298171.2:c.2264T>A	p.Ile755Asn	p.I755N	ENST00000298171	NM_000369.2	755	aTc/aAc	10/10	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.443951306370912	2		480	395	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562695	95562697	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	131	545	0	ENST00000393063.1:c.4560_4562del	p.Glu1520del	p.E1520del	ENST00000393063	NM_030621.3	1520	gaAGAt/gat	24/28	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.443951306370912	2		545	505	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988354	41988354	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	89	721	0	ENST00000219905.7:c.1146A>C	p.Lys382Asn	p.K382N	ENST00000219905	NM_001164273.1	382	aaA/aaC	3/24	1	2	FACETS	0.754	0.67	0.843	0.754	0.67	0.843	SUBCLONAL	1	TRUE	1	0.443951306370912	2		721	532	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900755	3900755	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	97	598	0	ENST00000262367.5:c.341G>C	p.Ser114Thr	p.S114T	ENST00000262367	NM_004380.2	114	aGc/aCc	2/31	1	2	FACETS	0.897	0.803	0.996	0.897	0.803	0.996	CLONAL	1	TRUE	1	0.443951306370912	2		598	487	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831834	72831834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139530177	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	225	906	1	ENST00000268489.5:c.4747G>A	p.Gly1583Ser	p.G1583S	ENST00000268489	NM_006885.3	1583	Ggt/Agt	9/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.443951306370912	2		907	914	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991701	72991715	+	inframe_deletion	In_Frame_Del	DEL	CCGCCGCCGCAGCCA	CCGCCGCCGCAGCCA	-	rs750272637	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	18	437	0	ENST00000268489.5:c.2330_2344del	p.Val777_Ala781del	p.V777_A781del	ENST00000268489	NM_006885.3	777	gTGGCTGCGGCGGCGGcg/gcg	2/10	1	2	FACETS	0.241	0.181	0.313	0.241	0.181	0.313	SUBCLONAL	1	TRUE	1	0.443951306370912	2		437	336	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953259	81953259	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756480279	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	78	420	0	ENST00000359376.3:c.2225G>A	p.Arg742His	p.R742H	ENST00000359376	NM_002661.3	742	cGc/cAc	20/33	1	2	FACETS	0.738	0.651	0.832	0.738	0.651	0.832	SUBCLONAL	1	TRUE	1	0.443951306370912	2		420	476	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972491	81972493	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	rs749338323	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	162	683	0	ENST00000359376.3:c.3291_3293del	p.Asn1097del	p.N1097del	ENST00000359376	NM_002661.3	1095	gACAac/gac	29/33	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.443951306370912	2		683	692	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351548	89351548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555075240	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	274	907	1	ENST00000301030.4:c.1402C>T	p.Arg468Cys	p.R468C	ENST00000301030	NM_001256183.1	468	Cgc/Tgc	9/13	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.443951306370912	2		908	919	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579440	7579440	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	39	777	0	ENST00000269305.4:c.247G>A	p.Ala83Thr	p.A83T	ENST00000269305	NM_001126112.2	83	Gcg/Acg	4/11	1	2	FACETS	0.259	0.214	0.309	0.259	0.214	0.309	SUBCLONAL	1	TRUE	1	0.443951306370912	2		777	679	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989469	7989469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1448682521	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	140	686	1	ENST00000319144.4:c.217C>T	p.Arg73Trp	p.R73W	ENST00000319144	NM_001139.2	73	Cgg/Tgg	2/15	1	2	FACETS	0.992	0.906	1	0.992	0.906	1	CLONAL	1	TRUE	1	0.443951306370912	2		687	636	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118505	17118505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	113	735	0	ENST00000285071.4:c.1426G>A	p.Asp476Asn	p.D476N	ENST00000285071	NM_144997.5	476	Gac/Aac	12/14	1	2	FACETS	0.82	0.739	0.904	0.82	0.739	0.904	CLONAL	1	TRUE	1	0.443951306370912	2		735	621	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677897	58677897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs552338842	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	118	474	0	ENST00000305921.3:c.122C>T	p.Pro41Leu	p.P41L	ENST00000305921	NM_003620.3	41	cCg/cTg	1/6	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.443951306370912	2		474	401	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207608	2207608	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	154	773	2	ENST00000398665.3:c.892C>T	p.Pro298Ser	p.P298S	ENST00000398665	NM_032482.2	298	Ccc/Tcc	11/28	1	2	FACETS	0.98	0.899	1	0.98	0.899	1	CLONAL	1	TRUE	1	0.443951306370912	2		775	708	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	107	803	0	ENST00000222270.7:c.520_521dup	p.Lys175GlnfsTer20	p.K175Qfs*20	ENST00000222270	NM_014727.1	172	acc/aCCcc	3/37	1	2	FACETS	0.669	0.6	0.741	0.669	0.6	0.741	SUBCLONAL	1	TRUE	1	0.443951306370912	2		803	721	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45864880	45864880	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752646404	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	188	903	1	ENST00000391945.4:c.1139G>A	p.Arg380Gln	p.R380Q	ENST00000391945	NM_000400.3	380	cGg/cAg	12/23	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.443951306370912	2		904	824	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241907	39241907	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	57	430	0	ENST00000402219.2:c.1939A>G	p.Arg647Gly	p.R647G	ENST00000402219	NM_005633.3	647	Agg/Ggg	11/23	1	2	FACETS	0.79	0.682	0.907	0.79	0.682	0.907	CLONAL	1	TRUE	1	0.443951306370912	2		430	325	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139630	202139630	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	31	512	2	ENST00000358485.4:c.791T>C	p.Val264Ala	p.V264A	ENST00000358485	NM_001080125.1	264	gTa/gCa	6/9	1	2	FACETS	0.267	0.215	0.325	0.267	0.215	0.325	SUBCLONAL	1	TRUE	1	0.443951306370912	2		514	524	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530142	212530143	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	72	568	0	ENST00000342788.4:c.1776dup	p.Cys593MetfsTer17	p.C593Mfs*17	ENST00000342788	NM_005235.2	592	-/A	15/28	1	2	FACETS	0.692	0.606	0.783	0.692	0.606	0.783	SUBCLONAL	1	TRUE	1	0.443951306370912	2		568	469	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41818310	41818310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	23	77	0	ENST00000373198.4:c.64G>A	p.Gly22Ser	p.G22S	ENST00000373198	NM_133170.3	22	Ggc/Agc	1/32	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.443951306370912	2		77	77	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121275	29121275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	111	933	1	ENST00000328354.6:c.400G>A	p.Asp134Asn	p.D134N	ENST00000328354	NM_007194.3	134	Gat/Aat	3/15	1	2	FACETS	0.787	0.709	0.87	0.787	0.709	0.87	SUBCLONAL	1	TRUE	1	0.443951306370912	2		934	635	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191621	10191621	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777130107	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	152	683	0	ENST00000256474.2:c.614G>A	p.Arg205His	p.R205H	ENST00000256474	NM_000551.3	205	cGc/cAc	3/3	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.443951306370912	2		683	667	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936539	49936539	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	178	812	0	ENST00000296474.3:c.1388A>G	p.His463Arg	p.H463R	ENST00000296474	NM_002447.2	463	cAc/cGc	2/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.443951306370912	2		812	676	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52621447	52621447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	175	698	0	ENST00000394830.3:c.2970del	p.Glu991LysfsTer17	p.E991Kfs*17	ENST00000394830	NM_018313.4	990	aaA/aa	20/30	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.443951306370912	2		698	643	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480428	89480428	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	142	467	0	ENST00000336596.2:c.2265C>A	p.Asn755Lys	p.N755K	ENST00000336596	NM_005233.5	755	aaC/aaA	13/17	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.443951306370912	2		467	517	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138382755	138382756	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1224981079	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	58	545	0	ENST00000289153.2:c.2788dup	p.Thr930AsnfsTer8	p.T930Nfs*8	ENST00000289153	NM_006219.2	930	act/aAct	19/22	1	2	FACETS	0.548	0.471	0.631	0.548	0.471	0.631	SUBCLONAL	1	TRUE	1	0.443951306370912	2		545	477	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664787	138664787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	106	305	0	ENST00000330315.3:c.778C>T	p.Arg260Cys	p.R260C	ENST00000330315	NM_023067.3	260	Cgc/Tgc	1/1	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.443951306370912	2		305	358	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1978227	1978227	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	208	864	0	ENST00000382891.5:c.3650del	p.Lys1217ArgfsTer112	p.K1217Rfs*112	ENST00000382891	NM_133335.3	1216	gAa/ga	21/22	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.443951306370912	2		864	863	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748146	41748146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	78	372	0	ENST00000226382.2:c.623G>A	p.Cys208Tyr	p.C208Y	ENST00000226382	NM_003924.3	208	tGc/tAc	3/3	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.443951306370912	2		372	318	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467372	66467373	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	45	276	0	ENST00000273854.3:c.896dup	p.Asn299LysfsTer32	p.N299Kfs*32	ENST00000273854	NM_004439.5	299	aat/aaAt	3/18	1	2	FACETS	0.814	0.69	0.949	0.814	0.69	0.949	CLONAL	1	TRUE	1	0.443951306370912	2		276	249	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520202	176520202	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763979974	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	116	731	0	ENST00000292408.4:c.1121C>T	p.Ala374Val	p.A374V	ENST00000292408	NM_213647.1	374	gCg/gTg	9/18	1	2	FACETS	0.848	0.766	0.934	0.848	0.766	0.934	CLONAL	1	TRUE	1	0.443951306370912	2		731	616	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158764	26158764	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	114	652	1	ENST00000289316.2:c.367A>G	p.Thr123Ala	p.T123A	ENST00000289316	NM_138720.2	123	Acc/Gcc	1/2	0.443951306370912	2	FACETS	0.744	0.671	0.822	0.372	0.335	0.411	SUBCLONAL	1	TRUE	0	0.443951306370912	2		653	690	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910696	29910697	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	386	1013	0	ENST00000376809.5:c.240dup	p.Pro81AlafsTer18	p.P81Afs*18	ENST00000376809	NM_002116.7	79	gag/gaGg	2/8	0.443951306370912	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.443951306370912	2		1013	799	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710740	117710740	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	94	475	0	ENST00000368508.3:c.1532T>C	p.Val511Ala	p.V511A	ENST00000368508	NM_002944.2	511	gTc/gCc	12/43	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.443951306370912	2		475	384	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023202	150023202	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1475297285	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	30	742	2	ENST00000253339.5:c.61A>G	p.Ser21Gly	p.S21G	ENST00000253339		21	Agt/Ggt	1/7	1	2	FACETS	0.241	0.193	0.295	0.241	0.193	0.295	SUBCLONAL	1	TRUE	1	0.443951306370912	2		744	561	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976790	2976790	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	236	1013	2	ENST00000396946.4:c.1222C>A	p.Arg408Ser	p.R408S	ENST00000396946	NM_032415.4	408	Cgc/Agc	9/25	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.443951306370912	2		1015	879	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964485	70964485	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	194	779	0	ENST00000276594.2:c.1543A>C	p.Lys515Gln	p.K515Q	ENST00000276594	NM_024504.3	515	Aag/Cag	8/8	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.443951306370912	2		779	723	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5462846	5462846	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	45	244	0	ENST00000381577.3:c.407A>C	p.Lys136Thr	p.K136T	ENST00000381577	NM_014143.3	136	aAa/aCa	4/7	1	2	FACETS	0.771	0.652	0.9	0.771	0.652	0.9	SUBCLONAL	1	TRUE	1	0.443951306370912	2		244	263	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802658	139802658	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1173498731	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	98	557	1	ENST00000247668.2:c.503C>T	p.Ala168Val	p.A168V	ENST00000247668	NM_021138.3	168	gCa/gTa	5/11	1	2	FACETS	0.99	0.888	1	0.99	0.888	1	CLONAL	1	TRUE	1	0.443951306370912	2		558	446	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424288	47424288	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs56197559	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	30	339	0	ENST00000377045.4:c.293T>C	p.Met98Thr	p.M98T	ENST00000377045	NM_001654.4	98	aTg/aCg	4/16	1	1	FACETS	0.299	0.241	0.364	0.299	0.241	0.364	SUBCLONAL	1	TRUE	0	0.443951306370912	1		339	352	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344915	70344915	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	176	382	0	ENST00000374080.3:c.2145G>T	p.Lys715Asn	p.K715N	ENST00000374080		715	aaG/aaT	15/45	1	1	FACETS	0.886	0.831	0.942	1	0.993	1	CLONAL	2	TRUE	0	0.443951306370912	1		382	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578528	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0023274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	674	870	0	ENST00000269305.4:c.402_403del	p.Phe134LeufsTer14	p.F134Lfs*14	ENST00000269305	NM_001126112.2	134	ttTTgc/ttgc	5/11	0.671688379470526	2	FACETS	0.969	0.943	0.995	0.969	0.943	0.995	CLONAL	2	TRUE	0	0.674460781909203	2		870	1031	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775612	9775612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772851443	NA	P-0023274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	239	576	2	ENST00000377346.4:c.155G>A	p.Arg52His	p.R52H	ENST00000377346	NM_005026.3	52	cGc/cAc	4/24	0.671688379470526	2	FACETS	0.959	0.899	1	0.48	0.449	0.51	CLONAL	1	TRUE	0	0.674460781909203	2		578	739	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807928	3807928	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	442	681	1	ENST00000262367.5:c.3491C>A	p.Ala1164Asp	p.A1164D	ENST00000262367	NM_004380.2	1164	gCc/gAc	18/31	0.67312968962215	3	FACETS	0.886	0.849	0.924	0.591	0.566	0.616	CLONAL	2	TRUE	0	0.674460781909203	3		682	989	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813099	76813107	+	inframe_deletion	In_Frame_Del	DEL	CTTATCTTC	CTTATCTTC	-	novel	NA	P-0023274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	236	642	0	ENST00000373344.5:c.6514_6522del	p.Glu2172_Lys2174del	p.E2172_K2174del	ENST00000373344	NM_000489.3	2172	GAAGATAAG/-	30/35	0.673961035442479	2	FACETS	0.877	0.833	0.92	0.877	0.833	0.92	CLONAL	2	TRUE	0	0.674460781909203	2		642	399	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0023275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	211	238	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.241500627312141	5	FACETS	1	0.941	1	1	0.941	1	CLONAL	4	TRUE	1	0.241500627312141	5		238	591	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	147	896	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.450247820816846	2		898	545	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0023278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	88	835	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.287702713344752	1	FACETS	0.759	0.677	0.846	0.759	0.677	0.846	SUBCLONAL	1	TRUE	0	0.450247820816846	1		835	399	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951852	2951852	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770667388	NA	P-0023278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	191	966	2	ENST00000396946.4:c.3098C>T	p.Ala1033Val	p.A1033V	ENST00000396946	NM_032415.4	1033	gCg/gTg	23/25	1	2	FACETS	0.967	0.895	1	0.967	0.895	1	CLONAL	1	TRUE	1	0.450247820816846	2		968	877	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435182	18435182	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	185	493	0	ENST00000266497.5:c.167G>T	p.Ser56Ile	p.S56I	ENST00000266497		56	aGt/aTt	1/31	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.555700199789011	2		493	579	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135373	30135373	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1168333527	NA	P-0023279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	201	617	1	ENST00000331968.5:c.445C>G	p.Leu149Val	p.L149V	ENST00000331968	NM_002742.2	149	Ctc/Gtc	3/18	1	2	FACETS	0.995	0.925	1	0.995	0.925	1	CLONAL	1	FALSE	1	0.555700199789011	2		618	727	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857257	9857257	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs777171195	NA	P-0023279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	183	649	0	ENST00000330684.3:c.4144T>C	p.Cys1382Arg	p.C1382R	ENST00000330684	NM_001134407.1	1382	Tgc/Cgc	13/13	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	1	0.555700199789011	2		649	643	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740583	58740617	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCCTTGTGCCTACTAATTCAACAAACACTGTCA	TGGCCTTGTGCCTACTAATTCAACAAACACTGTCA	-	novel	NA	P-0023279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	351	735	2	ENST00000305921.3:c.1491_1525del	p.Leu498ProfsTer18	p.L498Pfs*18	ENST00000305921	NM_003620.3	496	atTGGCCTTGTGCCTACTAATTCAACAAACACTGTCAtg/attg	6/6	0.555700199789011	3	FACETS	0.804	0.763	0.845	0.804	0.763	0.845	CLONAL	2	FALSE	1	0.555700199789011	3		737	1004	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971733	18971733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	219	849	2	ENST00000262803.5:c.2399G>A	p.Arg800His	p.R800H	ENST00000262803	NM_002911.3	800	cGc/cAc	17/24	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	1	0.555700199789011	2		851	773	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288290	21288290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1260646700	NA	P-0023279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	157	848	2	ENST00000354336.3:c.535G>A	p.Glu179Lys	p.E179K	ENST00000354336	NM_005207.3	179	Gaa/Aaa	2/3	1	2	FACETS	0.669	0.613	0.727	0.669	0.613	0.727	SUBCLONAL	1	FALSE	1	0.555700199789011	2		850	845	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133540	55134072	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTGAAAGACAGTGGAGATTACGAATGTGCTGCCCGCCAGGCTACCAGGGAGGTCAAAGAAATGAAGAAAGTCACTATTTCTGTCCATGGTACATTCCGCTTTCTAAAATGTCAGTTGTCCATGCTGCTCGGGATCCATATGTGGTAATCATTATTTAATGGAAACTCTTCCCTGTACAGAGAAAGGTTTCATTGAAATCAAACCCACCTTCAGCCAGTTGGAAGCTGTCAACCTGCATGAAGTCAAACATTTTGTTGTAGAGGTGCGGGCCTACCCACCTCCCAGGATATCCTGGCTGAAAAACAATCTGACTCTGATTGAAAATCTCACTGAGATCACCACTGATGTGGAAAAGATTCAGGAAATAAGGTAAAGAAACTCTCTGCCCAAGTATGCCTTTTTTTAGTGTGCATCAGAGGCGGACTGAGGTTTGTGTGTGTCTTACAACCCAGACCCAAAGTCAGTCTAGAAAATGTAACAATCTGAGTTAAGAGATGCTTGAAATCACATCCCTTTAATGATAACATTGCAAA	GTGAAAGACAGTGGAGATTACGAATGTGCTGCCCGCCAGGCTACCAGGGAGGTCAAAGAAATGAAGAAAGTCACTATTTCTGTCCATGGTACATTCCGCTTTCTAAAATGTCAGTTGTCCATGCTGCTCGGGATCCATATGTGGTAATCATTATTTAATGGAAACTCTTCCCTGTACAGAGAAAGGTTTCATTGAAATCAAACCCACCTTCAGCCAGTTGGAAGCTGTCAACCTGCATGAAGTCAAACATTTTGTTGTAGAGGTGCGGGCCTACCCACCTCCCAGGATATCCTGGCTGAAAAACAATCTGACTCTGATTGAAAATCTCACTGAGATCACCACTGATGTGGAAAAGATTCAGGAAATAAGGTAAAGAAACTCTCTGCCCAAGTATGCCTTTTTTTAGTGTGCATCAGAGGCGGACTGAGGTTTGTGTGTGTCTTACAACCCAGACCCAAAGTCAGTCTAGAAAATGTAACAATCTGAGTTAAGAGATGCTTGAAATCACATCCCTTTAATGATAACATTGCAAA	-	novel	NA	P-0023279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1277	4238	684	0	ENST00000257290.5:c.847_1121+167del		p.X283_splice	ENST00000257290	NM_006206.4	283		6-7/23	0.555700199789011	28	FACETS	0.989	0.98	0.998			1	CLONAL	23	FALSE	NA	0.555700199789011	28		684	5515	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525108	157525108	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	87	414	1	ENST00000346085.5:c.5003T>C	p.Val1668Ala	p.V1668A	ENST00000346085	NM_020732.3	1668	gTt/gCt	19/20	0.15833971524042	0	FACETS	0.366	0.326	0.408			1	INDETERMINATE	1	FALSE	0	0.555700199789011	0		415	380	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372451	55372451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	258	1069	0	ENST00000297316.4:c.1141G>A	p.Gly381Arg	p.G381R	ENST00000297316	NM_022454.3	381	Ggg/Agg	2/2	1	2	FACETS	0.994	0.932	1	0.994	0.932	1	CLONAL	1	FALSE	1	0.555700199789011	2		1069	934	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98222052	98222052	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764310195	NA	P-0023279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	165	548	0	ENST00000331920.6:c.2717G>A	p.Arg906His	p.R906H	ENST00000331920	NM_000264.3	906	cGt/cAt	17/24	0.555700199789011	3	FACETS	0.914	0.84	0.991	0.457	0.42	0.496	CLONAL	1	FALSE	1	0.555700199789011	3		548	830	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057520005	NA	P-0023281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	125	837	0	ENST00000269305.4:c.820G>C	p.Val274Leu	p.V274L	ENST00000269305	NM_001126112.2	274	Gtt/Ctt	8/11	0.310551113850349	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.310551113850349	1		837	663	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910884	114910896	+	splice_donor_variant,intron_variant	Splice_Site	DEL	TAAGTGTTGCTGT	TAAGTGTTGCTGT	-	novel	NA	P-0023281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	77	619	0	ENST00000543371.1:c.1001+3_1001+15del		p.X334_splice	ENST00000543371	NM_001198531.1	334			0.310551113850349	1	FACETS	0.956	0.843	1	0.956	0.843	1	CLONAL	1	TRUE	0	0.310551113850349	1		619	438	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862844	9862844	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs74458073	NA	P-0023281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	118	850	0	ENST00000330684.3:c.2459T>G	p.Val820Gly	p.V820G	ENST00000330684	NM_001134407.1	820	gTa/gGa	12/13	NA	2	FACETS	1	0.92	1			1	INDETERMINATE	1	TRUE	NA	0.310551113850349	2		850	744	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432691	29432691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	99	759	1	ENST00000389048.3:c.3797C>T	p.Ala1266Val	p.A1266V	ENST00000389048	NM_004304.4	1266	gCc/gTc	25/29	1	2	FACETS	0.97	0.867	1	0.97	0.867	1	CLONAL	1	TRUE	1	0.310551113850349	2		760	657	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665372	138665372	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	137	855	1	ENST00000330315.3:c.193A>T	p.Met65Leu	p.M65L	ENST00000330315	NM_023067.3	65	Atg/Ttg	1/1	0.268410602624422	3	FACETS	1	0.978	1	0.621	0.565	0.68	CLONAL	1	TRUE	1	0.310551113850349	3		856	821	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0023284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	15	238	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.092	0.067	0.123	0.092	0.067	0.123	SUBCLONAL	1	TRUE	1	0.7	2		238	464	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204737488	204737488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	150	707	0	ENST00000302823.3:c.625C>T	p.Pro209Ser	p.P209S	ENST00000302823	NM_005214.4	209	Cca/Tca	4/4	1	2	FACETS	0.726	0.667	0.788	0.726	0.667	0.788	SUBCLONAL	1	TRUE	1	0.7	2		707	590	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0023284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	44	95	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	0.137815216352376	3	FACETS	0.816	0.707	0.927	0.816	0.707	0.927	INDETERMINATE	2	TRUE	1	0.7	3		95	104	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740727	58740727	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	238	753	2	ENST00000305921.3:c.1636del	p.Leu546Ter	p.L546*	ENST00000305921	NM_003620.3	544	ggC/gg	6/6	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.7	2		755	669	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559859	29559862	+	frameshift_variant	Frame_Shift_Del	DEL	ACTC	ACTC	-	rs1321848637	NA	P-0023284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	135	473	0	ENST00000356175.3:c.3457_3460del	p.Leu1153MetfsTer4	p.L1153Mfs*4	ENST00000356175	NM_000267.3	1152	ttACTC/tt	26/57	1	2	FACETS	0.895	0.82	0.972	0.895	0.82	0.972	CLONAL	1	TRUE	1	0.7	2		473	431	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663825	29663825	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	294	931	1	ENST00000356175.3:c.6258del	p.Thr2087LeufsTer3	p.T2087Lfs*3	ENST00000356175	NM_000267.3	2086	gTt/gt	41/57	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.7	2		932	798	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161249	185161249	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	285	896	0	ENST00000265026.3:c.676G>A	p.Ala226Thr	p.A226T	ENST00000265026	NM_004721.4	226	Gcc/Acc	4/14	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.7	2		896	810	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98222016	98222016	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	172	645	0	ENST00000331920.6:c.2753C>T	p.Ala918Val	p.A918V	ENST00000331920	NM_000264.3	918	gCt/gTt	17/24	1	2	FACETS	0.846	0.783	0.911	0.846	0.783	0.911	CLONAL	1	TRUE	1	0.7	2		645	581	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0023285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	123	919	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.14734943985723	1	FACETS	0.919	0.831	1	1	0.988	1	CLONAL	2	TRUE	0	0.14734943985723	1		920	841	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468032	50468032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757907717	NA	P-0023285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	30	559	0	ENST00000331340.3:c.1267C>T	p.Arg423Cys	p.R423C	ENST00000331340	NM_006060.4	423	Cgc/Tgc	8/8	0.0864217592950016	3	FACETS	0.74	0.594	0.905	0.37	0.297	0.453	INDETERMINATE	1	TRUE	1	0.14734943985723	3		559	591	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678331	88678331	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0023285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	86	720	0	ENST00000360948.2:c.1204+1G>T		p.X402_splice	ENST00000360948	NM_001012338.2	402			1	2	FACETS	0.827	0.731	0.929	1	0.981	1	CLONAL	2	TRUE	1	0.14734943985723	2		720	706	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9928073	9928073	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	26	436	0	ENST00000330684.3:c.1666T>G	p.Ser556Ala	p.S556A	ENST00000330684	NM_001134407.1	556	Tct/Gct	8/13	0.14734943985723	1	FACETS	0.755	0.597	0.936	0.755	0.597	0.936	CLONAL	1	TRUE	0	0.14734943985723	1		436	433	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984714	11984714	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	38	345	0	ENST00000353533.5:c.260T>C	p.Leu87Pro	p.L87P	ENST00000353533	NM_003010.3	87	cTg/cCg	3/11	0.14734943985723	1	FACETS	0.804	0.668	0.956	1	0.957	1	CLONAL	2	TRUE	0	0.14734943985723	1		345	297	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573535	48573535	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	34	477	0	ENST00000342988.3:c.119T>A	p.Ile40Asn	p.I40N	ENST00000342988	NM_005359.5	40	aTt/aAt	2/12	0.14734943985723	1	FACETS	0.758	0.622	0.91	1	0.948	1	CLONAL	2	TRUE	0	0.14734943985723	1		477	282	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533686	63533686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1486551074	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	105	719	0	ENST00000307078.5:c.1468G>A	p.Ala490Thr	p.A490T	ENST00000307078	NM_004655.3	490	Gcg/Acg	6/11	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.287951766701862	2		719	691	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	103	748	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.918	0.822	1	0.918	0.822	1	CLONAL	1	TRUE	1	0.287951766701862	2		748	779	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133898	41133898	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	40	494	0	ENST00000379561.5:c.1730del	p.Gly577AlafsTer5	p.G577Afs*5	ENST00000379561	NM_002015.3	577	gGc/gc	2/3	1	2	FACETS	0.607	0.504	0.721	0.607	0.504	0.721	SUBCLONAL	1	TRUE	1	0.287951766701862	2		494	458	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519504	137519505	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	53	551	1	ENST00000367739.4:c.1132_1133dup	p.Ser378ArgfsTer6	p.S378Rfs*6	ENST00000367739	NM_000416.2	378	agt/agAGt	7/7	1	2	FACETS	0.77	0.657	0.893	0.77	0.657	0.893	SUBCLONAL	1	TRUE	1	0.287951766701862	2		552	478	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	40	409	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.47	0.39	0.56	0.47	0.39	0.56	SUBCLONAL	1	TRUE	1	0.287951766701862	2		409	591	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099103	27099103	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	85	892	2	ENST00000324856.7:c.3524del	p.Pro1175HisfsTer5	p.P1175Hfs*5	ENST00000324856	NM_006015.4	1173	atC/at	13/20	1	2	FACETS	0.742	0.655	0.835	0.742	0.655	0.835	SUBCLONAL	1	TRUE	1	0.287951766701862	2		894	796	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	83	726	1	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	0.776	0.684	0.874	0.776	0.684	0.874	SUBCLONAL	1	TRUE	1	0.287951766701862	2		727	743	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646085	215646085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	65	861	1	ENST00000260947.4:c.513del	p.Asp172MetfsTer40	p.D172Mfs*40	ENST00000260947	NM_000465.2	171	aaA/aa	4/11	1	2	FACETS	0.789	0.685	0.903	0.789	0.685	0.903	CLONAL	1	TRUE	1	0.287951766701862	2		862	572	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936518	49936518	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867261592	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	131	916	5	ENST00000296474.3:c.1409G>A	p.Arg470His	p.R470H	ENST00000296474	NM_002447.2	470	cGt/cAt	2/20	1	2	FACETS	0.932	0.845	1	0.932	0.845	1	CLONAL	1	TRUE	1	0.287951766701862	2		921	976	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088681	27088682	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	134	944	0	ENST00000324856.7:c.2296dup	p.Gln766ProfsTer51	p.Q766Pfs*51	ENST00000324856	NM_006015.4	764	tcc/tCcc	7/20	1	2	FACETS	0.904	0.82	0.992	0.904	0.82	0.992	CLONAL	1	TRUE	1	0.287951766701862	2		944	1030	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589618	67589618	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519838	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	34	490	0	ENST00000274335.5:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000274335		461	Cga/Tga	10/15	1	2	FACETS	0.747	0.612	0.898	0.747	0.612	0.898	SUBCLONAL	1	TRUE	1	0.287951766701862	2		490	316	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542584	141542584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1238499211	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	124	814	1	ENST00000220592.5:c.2402C>T	p.Ala801Val	p.A801V	ENST00000220592	NM_012154.3	801	gCg/gTg	18/19	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.287951766701862	2		815	830	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972512	81972512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1263457484	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	98	775	2	ENST00000359376.3:c.3305C>T	p.Thr1102Met	p.T1102M	ENST00000359376	NM_002661.3	1102	aCg/aTg	29/33	1	2	FACETS	0.82	0.731	0.915	0.82	0.731	0.915	CLONAL	1	TRUE	1	0.287951766701862	2		777	830	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096931	11096931	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060502073	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	110	1107	1	ENST00000358026.2:c.422C>T	p.Ser141Leu	p.S141L	ENST00000358026	NM_001128849.1	141	tCg/tTg	4/36	1	2	FACETS	0.793	0.711	0.879	0.793	0.711	0.879	SUBCLONAL	1	TRUE	1	0.287951766701862	2		1108	964	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261858	16261858	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	59	726	1	ENST00000375759.3:c.9126del	p.Ser3043AlafsTer48	p.S3043Afs*48	ENST00000375759	NM_015001.2	3041	caC/ca	11/15	1	2	FACETS	0.596	0.512	0.688	0.596	0.512	0.688	SUBCLONAL	1	TRUE	1	0.287951766701862	2		727	687	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137327	64137327	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	107	829	1	ENST00000334205.4:c.1759G>T	p.Asp587Tyr	p.D587Y	ENST00000334205	NM_003942.2	587	Gac/Tac	14/17	1	2	FACETS	0.878	0.787	0.975	0.878	0.787	0.975	CLONAL	1	TRUE	1	0.287951766701862	2		830	846	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102094425	102094425	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1433803164	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	48	762	1	ENST00000282441.5:c.1105G>A	p.Gly369Arg	p.G369R	ENST00000282441	NM_001130145.2	369	Ggg/Agg	7/9	1	2	FACETS	0.636	0.538	0.745	0.636	0.538	0.745	SUBCLONAL	1	TRUE	1	0.287951766701862	2		763	524	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431722	49431722	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555190550	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	111	896	1	ENST00000301067.7:c.9417del	p.Lys3140ArgfsTer2	p.K3140Rfs*2	ENST00000301067	NM_003482.3	3139	ccC/cc	34/54	1	2	FACETS	0.928	0.834	1	0.928	0.834	1	CLONAL	1	TRUE	1	0.287951766701862	2		897	831	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219446	133219446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	138	1021	0	ENST00000320574.5:c.4688C>T	p.Thr1563Ile	p.T1563I	ENST00000320574	NM_006231.2	1563	aCc/aTc	36/49	1	2	FACETS	0.934	0.849	1	0.934	0.849	1	CLONAL	1	TRUE	1	0.287951766701862	2		1021	1026	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562487	21562487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	20	158	0	ENST00000382592.4:c.1432G>A	p.Ala478Thr	p.A478T	ENST00000382592	NM_014572.2	478	Gcc/Acc	4/8	1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	1	0.287951766701862	2		158	123	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312714	91312714	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780514723	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	47	640	0	ENST00000355112.3:c.2453G>A	p.Arg818His	p.R818H	ENST00000355112	NM_000057.2	818	cGc/cAc	12/22	1	2	FACETS	0.553	0.466	0.65	0.553	0.466	0.65	SUBCLONAL	1	TRUE	1	0.287951766701862	2		640	590	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944286	81944286	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	56	807	0	ENST00000359376.3:c.1895C>A	p.Thr632Lys	p.T632K	ENST00000359376	NM_002661.3	632	aCg/aAg	18/33	1	2	FACETS	0.462	0.395	0.536	0.462	0.395	0.536	SUBCLONAL	1	TRUE	1	0.287951766701862	2		807	842	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346246	89346246	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1394383095	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	75	461	0	ENST00000301030.4:c.6704C>T	p.Pro2235Leu	p.P2235L	ENST00000301030	NM_001256183.1	2235	cCg/cTg	9/13	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.287951766701862	2		461	479	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989709	15989709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371483872	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	73	594	0	ENST00000268712.3:c.3064G>A	p.Val1022Ile	p.V1022I	ENST00000268712	NM_006311.3	1022	Gtt/Att	23/46	1	2	FACETS	0.756	0.661	0.858	0.756	0.661	0.858	SUBCLONAL	1	TRUE	1	0.287951766701862	2		594	671	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873631	37873631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758820578	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	148	978	0	ENST00000269571.5:c.1796G>A	p.Arg599His	p.R599H	ENST00000269571		599	cGc/cAc	15/27	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.287951766701862	2		978	1004	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489789	40489789	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	100	806	0	ENST00000264657.5:c.637A>G	p.Met213Val	p.M213V	ENST00000264657	NM_139276.2	213	Atg/Gtg	7/24	1	2	FACETS	0.902	0.806	1	0.902	0.806	1	CLONAL	1	TRUE	1	0.287951766701862	2		806	770	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031197	11031197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769775409	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	90	921	0	ENST00000327064.4:c.1282G>A	p.Ala428Thr	p.A428T	ENST00000327064	NM_199141.1	428	Gcc/Acc	11/16	1	2	FACETS	0.698	0.618	0.783	0.698	0.618	0.783	SUBCLONAL	1	TRUE	1	0.287951766701862	2		921	896	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470572	25470572	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	111	1017	0	ENST00000264709.3:c.902G>C	p.Arg301Pro	p.R301P	ENST00000264709	NM_175629.2	301	cGg/cCg	8/23	0.252830329500499	2	FACETS	0.76	0.681	0.843	0.38	0.34	0.422	SUBCLONAL	1	TRUE	0	0.287951766701862	2		1017	1015	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474101	29474101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373846404	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	116	709	1	ENST00000389048.3:c.2074G>A	p.Gly692Arg	p.G692R	ENST00000389048	NM_004304.4	692	Ggg/Agg	12/29	0.252830329500499	2	FACETS	1	0.956	1	0.553	0.498	0.61	CLONAL	1	TRUE	0	0.287951766701862	2		710	729	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728858	39728858	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756669367	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	71	501	1	ENST00000361337.2:c.1138G>A	p.Glu380Lys	p.E380K	ENST00000361337	NM_003286.2	380	Gag/Aag	12/21	1	2	FACETS	0.971	0.849	1	0.971	0.849	1	CLONAL	1	TRUE	1	0.287951766701862	2		502	508	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092947	29092947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881688	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	77	812	0	ENST00000328354.6:c.1037G>A	p.Arg346His	p.R346H	ENST00000328354	NM_007194.3	346	cGt/cAt	10/15	1	2	FACETS	0.978	0.86	1	0.978	0.86	1	CLONAL	1	TRUE	1	0.287951766701862	2		812	547	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31504712	31504712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369576938	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	97	897	3	ENST00000344624.3:c.1618G>A	p.Ala540Thr	p.A540T	ENST00000344624		540	Gca/Aca	8/33	1	2	FACETS	0.828	0.737	0.924	0.828	0.737	0.924	CLONAL	1	TRUE	1	0.287951766701862	2		900	814	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064793	80064793	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373556898	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	36	520	2	ENST00000265081.6:c.2224G>A	p.Ala742Thr	p.A742T	ENST00000265081	NM_002439.4	742	Gca/Aca	15/24	1	2	FACETS	0.7	0.577	0.838	0.7	0.577	0.838	SUBCLONAL	1	TRUE	1	0.287951766701862	2		522	357	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435804	149435804	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	115	919	0	ENST00000286301.3:c.2420C>T	p.Ser807Phe	p.S807F	ENST00000286301	NM_005211.3	807	tCc/tTc	18/22	1	2	FACETS	0.944	0.85	1	0.944	0.85	1	CLONAL	1	TRUE	1	0.287951766701862	2		919	846	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386587	81386587	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1032300573	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	36	728	1	ENST00000222390.5:c.400C>T	p.Arg134Cys	p.R134C	ENST00000222390	NM_000601.4	134	Cgc/Tgc	4/18	1	2	FACETS	0.561	0.461	0.673	0.561	0.461	0.673	SUBCLONAL	1	TRUE	1	0.287951766701862	2		729	446	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133748333	133748333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779478267	NA	P-0023287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	118	873	2	ENST00000318560.5:c.994C>T	p.Arg332Trp	p.R332W	ENST00000318560	NM_005157.4	332	Cgg/Tgg	6/11	1	2	FACETS	0.941	0.848	1	0.941	0.848	1	CLONAL	1	TRUE	1	0.287951766701862	2		875	871	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426121	47426121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519786	NA	P-0023297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	370	932	0	ENST00000377045.4:c.641C>T	p.Ser214Phe	p.S214F	ENST00000377045	NM_001654.4	214	tCc/tTc	7/16	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.562401319004861	2		932	1171	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0023298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	312	756	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	0.351469938895301	2	FACETS	0.912	0.862	0.963	0.912	0.862	0.963	CLONAL	2	TRUE	0	0.361519766867631	2		756	946	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119762	70119763	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0023298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	122	771	0	ENST00000245479.2:c.768dup	p.Arg257AlafsTer39	p.R257Afs*39	ENST00000245479	NM_000346.3	255	gag/gaGg	3/3	1	2	FACETS	0.869	0.785	0.956	0.869	0.785	0.956	CLONAL	1	TRUE	1	0.361519766867631	2		771	777	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46738475	46738475	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs762268075	NA	P-0023298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	151	619	3	ENST00000371975.4:c.1375+1G>A		p.X459_splice	ENST00000371975	NM_003579.3	459			1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.361519766867631	2		622	773	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683229	88683229	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs535109719	NA	P-0023298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	227	523	1	ENST00000372037.3:c.1439G>A	p.Arg480Gln	p.R480Q	ENST00000372037	NM_004329.2	480	cGg/cAg	12/13	0.351469938895301	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.361519766867631	2		524	609	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481898	56481898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	343	791	0	ENST00000267101.3:c.826C>T	p.Pro276Ser	p.P276S	ENST00000267101	NM_001982.3	276	Ccc/Tcc	7/28	0.351469938895301	2	FACETS	0.94	0.892	0.99	0.94	0.892	0.99	CLONAL	2	TRUE	0	0.361519766867631	2		791	1009	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349121	11349121	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs755668210	NA	P-0023298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	26	456	0	ENST00000332029.2:c.215C>A	p.Ala72Glu	p.A72E	ENST00000332029	NM_003745.1	72	gCg/gAg	2/2	0.26626113573662	2	FACETS	0.328	0.259	0.408	0.164	0.129	0.204	SUBCLONAL	1	TRUE	0	0.361519766867631	2		456	438	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879794	37879794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	93	537	0	ENST00000269571.5:c.2089G>A	p.Val697Met	p.V697M	ENST00000269571		697	Gtg/Atg	18/27	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.361519766867631	2		537	514	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118866	70118876	+	frameshift_variant	Frame_Shift_Del	DEL	GAACGAGAGCG	GAACGAGAGCG	-	novel	NA	P-0023298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	94	562	0	ENST00000245479.2:c.438_448del	p.Asn147GlufsTer101	p.N147Efs*101	ENST00000245479	NM_000346.3	146	ctGAACGAGAGCGag/ctag	2/3	1	2	FACETS	0.875	0.78	0.976	0.875	0.78	0.976	CLONAL	1	TRUE	1	0.361519766867631	2		562	594	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211138	36211138	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	215	977	2	ENST00000222270.7:c.889C>T	p.Arg297Ter	p.R297*	ENST00000222270	NM_014727.1	297	Cga/Tga	3/37	1	2	FACETS	0.936	0.868	1	0.936	0.868	1	CLONAL	1	TRUE	1	0.361519766867631	2		979	1271	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085659	16085659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs794727503	NA	P-0023298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	204	784	0	ENST00000281043.3:c.835G>A	p.Val279Met	p.V279M	ENST00000281043	NM_005378.4	279	Gtg/Atg	3/3	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.361519766867631	2		784	946	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713544	30713546	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0023298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	264	575	0	ENST00000295754.5:c.871_873del	p.Lys291del	p.K291del	ENST00000295754	NM_003242.5	290	gAGAag/gag	4/7	0.361519766867631	2	FACETS	0.985	0.928	1	0.985	0.928	1	CLONAL	2	TRUE	0	0.361519766867631	2		575	741	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156059	106156678	+	frameshift_variant	Frame_Shift_Del	DEL	ACAACTACAACAACAAAAATCAGTTTTTGAGATATGCCCATCTCCTGCAGAAAATAACATCCAGGGAACCACAAAGCTAGCGTCTGGTGAAGAATTCTGTTCAGGTTCCAGCAGCAATTTGCAAGCTCCTGGTGGCAGCTCTGAACGGTATTTAAAACAAAATGAAATGAATGGTGCTTACTTCAAGCAAAGCTCAGTGTTCACTAAGGATTCCTTTTCTGCCACTACCACACCACCACCACCATCACAATTGCTTCTTTCTCCCCCTCCTCCTCTTCCACAGGTTCCTCAGCTTCCTTCAGAAGGAAAAAGCACTCTGAATGGTGGAGTTTTAGAAGAACACCACCACTACCCCAACCAAAGTAACACAACACTTTTAAGGGAAGTGAAAATAGAGGGTAAACCTGAGGCACCACCTTCCCAGAGTCCTAATCCATCTACACATGTATGCAGCCCTTCTCCGATGCTTTCTGAAAGGCCTCAGAATAATTGTGTGAACAGGAATGACATACAGACTGCAGGGACAATGACTGTTCCATTGTGTTCTGAGAAAACAAGACCAATGTCAGAACACCTCAAGCATAACCCACCAATTTTTGGTAGCAGTGGAGAGCTACAGG	ACAACTACAACAACAAAAATCAGTTTTTGAGATATGCCCATCTCCTGCAGAAAATAACATCCAGGGAACCACAAAGCTAGCGTCTGGTGAAGAATTCTGTTCAGGTTCCAGCAGCAATTTGCAAGCTCCTGGTGGCAGCTCTGAACGGTATTTAAAACAAAATGAAATGAATGGTGCTTACTTCAAGCAAAGCTCAGTGTTCACTAAGGATTCCTTTTCTGCCACTACCACACCACCACCACCATCACAATTGCTTCTTTCTCCCCCTCCTCCTCTTCCACAGGTTCCTCAGCTTCCTTCAGAAGGAAAAAGCACTCTGAATGGTGGAGTTTTAGAAGAACACCACCACTACCCCAACCAAAGTAACACAACACTTTTAAGGGAAGTGAAAATAGAGGGTAAACCTGAGGCACCACCTTCCCAGAGTCCTAATCCATCTACACATGTATGCAGCCCTTCTCCGATGCTTTCTGAAAGGCCTCAGAATAATTGTGTGAACAGGAATGACATACAGACTGCAGGGACAATGACTGTTCCATTGTGTTCTGAGAAAACAAGACCAATGTCAGAACACCTCAAGCATAACCCACCAATTTTTGGTAGCAGTGGAGAGCTACAGG	-	novel	NA	P-0023298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	78	466	0	ENST00000380013.4:c.966_1585del	p.Gln323ProfsTer37	p.Q323Pfs*37	ENST00000380013	NM_001127208.2	320	gaACAACTACAACAACAAAAATCAGTTTTTGAGATATGCCCATCTCCTGCAGAAAATAACATCCAGGGAACCACAAAGCTAGCGTCTGGTGAAGAATTCTGTTCAGGTTCCAGCAGCAATTTGCAAGCTCCTGGTGGCAGCTCTGAACGGTATTTAAAACAAAATGAAATGAATGGTGCTTACTTCAAGCAAAGCTCAGTGTTCACTAAGGATTCCTTTTCTGCCACTACCACACCACCACCACCATCACAATTGCTTCTTTCTCCCCCTCCTCCTCTTCCACAGGTTCCTCAGCTTCCTTCAGAAGGAAAAAGCACTCTGAATGGTGGAGTTTTAGAAGAACACCACCACTACCCCAACCAAAGTAACACAACACTTTTAAGGGAAGTGAAAATAGAGGGTAAACCTGAGGCACCACCTTCCCAGAGTCCTAATCCATCTACACATGTATGCAGCCCTTCTCCGATGCTTTCTGAAAGGCCTCAGAATAATTGTGTGAACAGGAATGACATACAGACTGCAGGGACAATGACTGTTCCATTGTGTTCTGAGAAAACAAGACCAATGTCAGAACACCTCAAGCATAACCCACCAATTTTTGGTAGCAGTGGAGAGCTACAGGac/gaac	3/11	1	2	FACETS	0.687	0.604	0.776	0.687	0.604	0.776	SUBCLONAL	1	TRUE	1	0.361519766867631	2		466	628	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249456	153249456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	285	802	0	ENST00000281708.4:c.1322G>A	p.Arg441Gln	p.R441Q	ENST00000281708	NM_033632.3	441	cGg/cAg	9/12	0.361519766867631	2	FACETS	0.932	0.879	0.986	0.932	0.879	0.986	CLONAL	2	TRUE	0	0.361519766867631	2		802	846	SUCCESS
APC	324	MSKCC	GRCh37	5	112175351	112175352	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0023298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	133	360	0	ENST00000257430.4:c.4062_4063del	p.Ser1355PhefsTer19	p.S1355Ffs*19	ENST00000257430	NM_000038.5	1354	TTt/t	16/16	0.351469938895301	2	FACETS	0.827	0.757	0.899	0.827	0.757	0.899	CLONAL	2	TRUE	0	0.361519766867631	2		360	445	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323364	31323364	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs281864638	NA	P-0023298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	167	485	0	ENST00000412585.2:c.625C>T	p.Pro209Ser	p.P209S	ENST00000412585	NM_005514.6	209	Cca/Tca	4/8	0.351469938895301	2	FACETS	0.917	0.849	0.986	0.917	0.849	0.986	CLONAL	2	TRUE	0	0.361519766867631	2		485	504	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128201212	128201212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374025668	NA	P-0023298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	238	830	2	ENST00000265960.3:c.1523G>A	p.Arg508His	p.R508H	ENST00000265960	NM_001006617.1	508	cGt/cAt	12/12	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.361519766867631	2		832	1134	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041259	47041259	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	178	906	0	ENST00000377604.3:c.1687C>T	p.Gln563Ter	p.Q563*	ENST00000377604	NM_001204468.1	563	Cag/Tag	15/24	1	2	FACETS	0.984	0.906	1	0.984	0.906	1	CLONAL	1	TRUE	1	0.361519766867631	2		906	1001	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0023300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	77	472	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.179336389386611	3	FACETS	0.685	0.601	0.775	0.343	0.3	0.388	INDETERMINATE	1	TRUE	1	0.394691668333863	3		472	682	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115947	8115954	+	frameshift_variant	Frame_Shift_Del	DEL	ACCACACC	ACCACACC	-	novel	NA	P-0023300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	42	537	0	ENST00000346208.3:c.1296_1303del	p.His433LeufsTer71	p.H433Lfs*71	ENST00000346208		431	ggACCACACCac/ggac	6/6	1	2	FACETS	0.378	0.315	0.448	0.378	0.315	0.448	SUBCLONAL	1	TRUE	1	0.394691668333863	2		537	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691039	NA	P-0023302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	151	983	0	ENST00000269305.4:c.919+1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		983	743	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913409	NA	P-0023308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	30	496	0	ENST00000349496.5:c.134C>G	p.Ser45Cys	p.S45C	ENST00000349496	NM_001904.3	45	tCt/tGt	3/15	0.669527227816415	3	FACETS	0.307	0.247	0.375	0.153	0.123	0.188	SUBCLONAL	1	FALSE	1	0.669527227816415	3		496	390	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743275	743275	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	155	821	0	ENST00000314574.4:c.865G>C	p.Gly289Arg	p.G289R	ENST00000314574	NM_005433.3	289	Ggc/Cgc	7/12	0.461659156841389	4	FACETS	1	0.935	1			1	CLONAL	1	FALSE	NA	0.669527227816415	4		821	756	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069462	30069462	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	15	627	0	ENST00000338641.4:c.1327G>T	p.Glu443Ter	p.E443*	ENST00000338641	NM_000268.3	443	Gag/Tag	12/16	0.216565505876194	1	FACETS	0.262	0.191	0.346	0.262	0.191	0.346	SUBCLONAL	1	TRUE	0	0.353687001069778	1		627	267	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0023310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	436	676	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.504211492305549	3	FACETS	0.852	0.818	0.886			1	CLONAL	3	TRUE	NA	0.504211492305549	3		676	847	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204864	NA	P-0023310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	215	617	0	ENST00000371953.3:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000371953	NM_000314.4	171	Cag/Tag	6/9	0.504211492305549	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.504211492305549	1		617	549	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0023310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	345	561	0	ENST00000269305.4:c.375+1G>T		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.504211492305549	2	FACETS	0.987	0.943	1	0.987	0.943	1	CLONAL	2	TRUE	0	0.504211492305549	2		561	693	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27217701	27217701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772600804	NA	P-0023310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	165	735	0	ENST00000380036.4:c.3007C>T	p.Arg1003Cys	p.R1003C	ENST00000380036	NM_000459.3	1003	Cgc/Tgc	19/23	0.504211492305549	2	FACETS	0.992	0.914	1	0.496	0.457	0.536	CLONAL	1	TRUE	0	0.504211492305549	2		735	660	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570849	226570849	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	93	693	0	ENST00000366794.5:c.1047G>T	p.Lys349Asn	p.K349N	ENST00000366794	NM_001618.3	349	aaG/aaT	8/23	0.294424297789672	1	FACETS	0.409	0.364	0.456	0.409	0.364	0.456	INDETERMINATE	1	TRUE	0	0.582005076328911	1		693	554	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624424	21624424	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	156	879	2	ENST00000421138.2:c.1605del	p.Thr536HisfsTer15	p.T536Hfs*15	ENST00000421138		535	ccC/cc	14/16	1	2	FACETS	0.934	0.86	1	0.934	0.86	1	CLONAL	1	TRUE	1	0.582005076328911	2		881	574	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56872962	56872962	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	92	500	0	ENST00000308159.5:c.2117A>T	p.His706Leu	p.H706L	ENST00000308159	NM_014669.4	706	cAt/cTt	19/22	0.151138413807133	1	FACETS	0.617	0.553	0.685	0.617	0.553	0.685	INDETERMINATE	1	TRUE	0	0.582005076328911	1		500	363	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0023311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	226	766	2	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.582005076328911	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.582005076328911	1		768	514	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119749	70119749	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	249	818	1	ENST00000245479.2:c.751G>A	p.Asp251Asn	p.D251N	ENST00000245479	NM_000346.3	251	Gac/Aac	3/3	0.294424297789672	1	FACETS	0.923	0.869	0.979	0.923	0.869	0.979	INDETERMINATE	1	TRUE	0	0.582005076328911	1		819	657	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724456	724456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	246	810	0	ENST00000314574.4:c.1600G>A	p.Glu534Lys	p.E534K	ENST00000314574	NM_005433.3	534	Gag/Aag	12/12	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.582005076328911	2		810	697	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212076	5212076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377889959	NA	P-0023311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	298	820	1	ENST00000357368.4:c.4955G>A	p.Gly1652Asp	p.G1652D	ENST00000357368	NM_002850.3	1652	gGc/gAc	32/38	0.582005076328911	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.582005076328911	1		821	687	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867293	45867293	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	289	802	1	ENST00000391945.4:c.900G>T	p.Glu300Asp	p.E300D	ENST00000391945	NM_000400.3	300	gaG/gaT	10/23	0.582005076328911	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.582005076328911	1		803	595	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598148	52598148	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	230	815	0	ENST00000394830.3:c.3718G>C	p.Asp1240His	p.D1240H	ENST00000394830	NM_018313.4	1240	Gac/Cac	24/30	0.582005076328911	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.582005076328911	1		815	470	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598199	52598199	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	198	743	0	ENST00000394830.3:c.3667G>C	p.Glu1223Gln	p.E1223Q	ENST00000394830	NM_018313.4	1223	Gaa/Caa	24/30	0.582005076328911	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.582005076328911	1		743	416	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521316	187521316	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	60	817	0	ENST00000441802.2:c.11839G>C	p.Asp3947His	p.D3947H	ENST00000441802	NM_005245.3	3947	Gat/Cat	22/27	0.582005076328911	1	FACETS	0.306	0.264	0.352	0.306	0.264	0.352	SUBCLONAL	1	TRUE	0	0.582005076328911	1		817	477	SUCCESS
APC	324	MSKCC	GRCh37	5	112173354	112173354	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0023311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	113	465	0	ENST00000257430.4:c.2063C>G	p.Ser688Ter	p.S688*	ENST00000257430	NM_000038.5	688	tCa/tGa	16/16	0.582005076328911	1	FACETS	0.99	0.906	1	0.99	0.906	1	CLONAL	1	TRUE	0	0.582005076328911	1		465	278	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845102	128845102	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759466401	NA	P-0023311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	283	916	0	ENST00000249373.3:c.596G>A	p.Arg199Gln	p.R199Q	ENST00000249373	NM_005631.4	199	cGg/cAg	3/12	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.582005076328911	2		916	860	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956763	68956763	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	206	865	0	ENST00000288368.4:c.881A>T	p.Tyr294Phe	p.Y294F	ENST00000288368	NM_024870.2	294	tAc/tTc	8/40	0.582005076328911	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.582005076328911	1		865	478	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978732	70978732	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs751550241	NA	P-0023311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	144	564	0	ENST00000276594.2:c.921A>C	p.Glu307Asp	p.E307D	ENST00000276594	NM_024504.3	307	gaA/gaC	5/8	0.582005076328911	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.582005076328911	1		564	348	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484302	8484302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	159	741	0	ENST00000356435.5:c.3230C>A	p.Pro1077His	p.P1077H	ENST00000356435		1077	cCt/cAt	19/35	0.582005076328911	1	FACETS	0.931	0.863	1	0.931	0.863	1	CLONAL	1	TRUE	0	0.582005076328911	1		741	416	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652274	48652274	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	277	473	4	ENST00000376670.3:c.945G>T	p.Lys315Asn	p.K315N	ENST00000376670	NM_002049.3	315	aaG/aaT	6/6	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.582005076328911	1		477	455	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0023312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	44	724	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.888	0.743	1	0.888	0.743	1	CLONAL	1	TRUE	1	0.15	2		726	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691039	NA	P-0023312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	54	983	0	ENST00000269305.4:c.919+1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.15	2		983	649	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038958	12038958	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	24	553	1	ENST00000396373.4:c.1251C>A	p.Phe417Leu	p.F417L	ENST00000396373	NM_001987.4	417	ttC/ttA	7/8	0.171041098106061	3	FACETS	0.808	0.632	1	0.404	0.316	0.505	CLONAL	1	TRUE	1	0.15	3		554	426	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0023313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	149	401	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.955	1	1	0.993	1	CLONAL	2	TRUE	1	0.456178678404291	2		401	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0023313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	535	914	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.456178678404291	2	FACETS	1	0.994	1	1	0.998	1	CLONAL	4	TRUE	0	0.456178678404291	2		914	576	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829806	76829806	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	211	778	1	ENST00000373344.5:c.6235C>T	p.Arg2079Ter	p.R2079*	ENST00000373344	NM_000489.3	2079	Cga/Tga	28/35	1	2	FACETS	1	0.965	1	1	0.995	1	CLONAL	2	TRUE	1	0.456178678404291	2		779	446	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28886173	28886173	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	135	738	0	ENST00000282397.4:c.3449T>G	p.Leu1150Arg	p.L1150R	ENST00000282397	NM_002019.4	1150	cTt/cGt	26/30	1	2	FACETS	0.952	0.868	1	0.952	0.868	1	CLONAL	1	TRUE	1	0.456178678404291	2		738	622	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0023315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	33	813	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.205135402469609	1	FACETS	0.722	0.588	0.872	0.722	0.588	0.872	SUBCLONAL	1	TRUE	0	0.205135402469609	1		813	400	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0023316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	54	949	0	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	1	2	FACETS	0.501	0.427	0.582	0.501	0.427	0.582	SUBCLONAL	1	FALSE	1	0.284439319238734	2		949	758	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913250	NA	P-0023316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	33	634	0	ENST00000369535.4:c.34G>T	p.Gly12Cys	p.G12C	ENST00000369535	NM_002524.4	12	Ggt/Tgt	2/7	1	2	FACETS	0.346	0.281	0.42	0.346	0.281	0.42	SUBCLONAL	1	FALSE	1	0.284439319238734	2		634	671	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468082	120468082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1403190122	NA	P-0023316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	70	891	0	ENST00000256646.2:c.4357G>A	p.Gly1453Ser	p.G1453S	ENST00000256646	NM_024408.3	1453	Ggt/Agt	25/34	1	2	FACETS	0.651	0.567	0.742	0.651	0.567	0.742	SUBCLONAL	1	FALSE	1	0.284439319238734	2		891	756	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235926	133235926	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	34	749	1	ENST00000320574.5:c.3230G>T	p.Arg1077Leu	p.R1077L	ENST00000320574	NM_006231.2	1077	cGc/cTc	26/49	0.284439319238734	1	FACETS	0.358	0.292	0.433	0.358	0.292	0.433	SUBCLONAL	1	FALSE	0	0.284439319238734	1		750	573	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000369	42000370	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0023316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	22	646	2	ENST00000219905.7:c.2388_2389delinsTT	p.Arg796_Gly797delinsSerTer	p.R796_G797delinsS*	ENST00000219905	NM_001164273.1	796	agGGga/agTTga	7/24	1	2	FACETS	0.425	0.329	0.537	0.425	0.329	0.537	SUBCLONAL	1	FALSE	1	0.284439319238734	2		648	364	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217232	66217232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	42	695	0	ENST00000273854.3:c.2383G>A	p.Gly795Ser	p.G795S	ENST00000273854	NM_004439.5	795	Ggc/Agc	14/18	0.284439319238734	1	FACETS	0.538	0.449	0.636	0.538	0.449	0.636	SUBCLONAL	1	FALSE	0	0.284439319238734	1		695	471	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680017	30680017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	51	783	0	ENST00000376406.3:c.1702G>A	p.Glu568Lys	p.E568K	ENST00000376406	NM_014641.2	568	Gag/Aag	5/15	1	2	FACETS	0.56	0.475	0.654	0.56	0.475	0.654	SUBCLONAL	1	FALSE	1	0.284439319238734	2		783	640	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508772	106508772	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0023316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	38	720	1	ENST00000359195.3:c.766A>T	p.Lys256Ter	p.K256*	ENST00000359195	NM_002649.2	256	Aaa/Taa	2/11	1	2	FACETS	0.404	0.333	0.483	0.404	0.333	0.483	SUBCLONAL	1	FALSE	1	0.284439319238734	2		721	662	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38981977	38981977	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	24	441	0	ENST00000357387.3:c.745G>A	p.Glu249Lys	p.E249K	ENST00000357387	NM_152756.3	249	Gaa/Aaa	8/38	0.148168651471523	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		441	477	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635188	87635188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	39	568	0	ENST00000277120.3:c.2240C>T	p.Thr747Met	p.T747M	ENST00000277120		747	aCg/aTg	18/19	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		568	559	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057744	180057744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138831198	NA	P-0023318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	182	767	1	ENST00000261937.6:c.211G>A	p.Gly71Arg	p.G71R	ENST00000261937	NM_182925.4	71	Gga/Aga	3/30	0.444789707862743	3	FACETS	1	0.983	1	0.606	0.56	0.654	CLONAL	1	TRUE	1	0.444789707862743	3		768	825	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303755	65303755	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	137	704	0	ENST00000342505.4:c.3000del	p.His1001ThrfsTer17	p.H1001Tfs*17	ENST00000342505	NM_002227.2	1000	gtT/gt	22/25	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.444789707862743	2		704	575	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207682	102207682	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	94	524	0	ENST00000263464.3:c.1664G>T	p.Arg555Ile	p.R555I	ENST00000263464	NM_001165.4	555	aGa/aTa	9/9	0.444789707862743	3	FACETS	1	0.971	1	0.621	0.556	0.689	CLONAL	1	TRUE	1	0.444789707862743	3		524	416	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796979	78796980	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTCA	novel	NA	P-0023318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	128	756	0	ENST00000306801.3:c.1094_1097dup	p.Ser367GlnfsTer22	p.S367Qfs*22	ENST00000306801	NM_020761.2	364	-/GTCA	9/34	0.444789707862743	3	FACETS	0.938	0.851	1	0.469	0.425	0.515	CLONAL	1	TRUE	1	0.444789707862743	3		756	750	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495646	72495646	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0023318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	112	503	0	ENST00000477973.2:c.423+1del		p.X141_splice	ENST00000477973	NM_012234.5	141			0.444789707862743	4	FACETS	1	0.981	1	0.348	0.314	0.383	CLONAL	1	TRUE	0	0.444789707862743	4		503	523	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185061	123185061	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	9	393	0	ENST00000218089.9:c.1108C>G	p.Arg370Gly	p.R370G	ENST00000218089	NM_001042749.1	370	Cgg/Ggg	12/35	0.444789707862743	3	FACETS	0.122	0.08	0.177			1	SUBCLONAL	1	TRUE	NA	0.444789707862743	3		393	404	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0023319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	143	1087	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.242336203624906	3	FACETS	0.821	0.75	0.895	0.821	0.75	0.895	CLONAL	2	TRUE	1	0.28	3		1087	709	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416536	49416536	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	98	905	1	ENST00000301067.7:c.16175G>A	p.Arg5392His	p.R5392H	ENST00000301067	NM_003482.3	5392	cGc/cAc	51/54	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.28	2		906	621	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0023321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	510	985	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.62795847042842	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.624098322408955	2		985	788	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173715	108173716	+	missense_variant	Missense_Mutation	DNP	AC	AC	CA	novel	NA	P-0023321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	183	873	0	ENST00000278616.4:c.5455_5456delinsCA	p.Thr1819Gln	p.T1819Q	ENST00000278616	NM_000051.3	1819	ACa/CAa	36/63	0.62795847042842	2	FACETS	0.96	0.89	1	0.48	0.445	0.516	CLONAL	1	TRUE	0	0.624098322408955	2		873	611	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46215243	46215264	+	frameshift_variant	Frame_Shift_Del	DEL	AGAGAAGACTGATAGAGACTTC	AGAGAAGACTGATAGAGACTTC	-	novel	NA	P-0023321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	49	659	0	ENST00000334344.6:c.678_699del	p.Glu227LeufsTer58	p.E227Lfs*58	ENST00000334344	NM_152641.2	226	aaAGAGAAGACTGATAGAGACTTC/aa	6/21	0.62795847042842	2	FACETS	0.358	0.303	0.418	0.179	0.151	0.209	SUBCLONAL	1	TRUE	0	0.624098322408955	2		659	439	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061540	38061540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	162	472	0	ENST00000250448.2:c.449G>A	p.Arg150His	p.R150H	ENST00000250448	NM_004496.3	150	cGc/cAc	2/2	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.624098322408955	2		472	411	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096381	178096381	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	167	864	0	ENST00000397062.3:c.950T>G	p.Ile317Ser	p.I317S	ENST00000397062	NM_006164.4	317	aTt/aGt	5/5	0.40093824957767	6	FACETS	0.918	0.842	0.999			1	CLONAL	1	TRUE	NA	0.624098322408955	6		864	1310	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748554	43748554	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	227	782	0	ENST00000523873.1:c.508C>G	p.Arg170Gly	p.R170G	ENST00000523873		170	Cgc/Ggc	6/8	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.624098322408955	2		782	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0023321-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	188	985	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.720795157389674	2	FACETS	0.992	0.945	1	0.992	0.945	1	CLONAL	2	FALSE	0	0.723502611047345	2		985	262	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463191	25463191	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023321-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	96	732	1	ENST00000264709.3:c.2302G>A	p.Asp768Asn	p.D768N	ENST00000264709	NM_175629.2	768	Gac/Aac	19/23	0.720795157389674	3	FACETS	1	0.972	1	0.608	0.549	0.67	CLONAL	1	FALSE	1	0.723502611047345	3		733	297	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940013	49940013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023321-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	110	799	0	ENST00000296474.3:c.1030G>A	p.Glu344Lys	p.E344K	ENST00000296474	NM_002447.2	344	Gaa/Aaa	1/20	0.720795157389674	3	FACETS	1	0.949	1	0.357	0.323	0.392	CLONAL	1	FALSE	0	0.723502611047345	3		799	387	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173715	108173716	+	missense_variant	Missense_Mutation	DNP	AC	AC	CA	novel	NA	P-0023321-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	89	873	0	ENST00000278616.4:c.5455_5456delinsCA	p.Thr1819Gln	p.T1819Q	ENST00000278616	NM_000051.3	1819	ACa/CAa	36/63	0.720795157389674	2	FACETS	0.954	0.858	1	0.477	0.429	0.526	CLONAL	1	FALSE	0	0.723502611047345	2		873	258	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46215243	46215264	+	frameshift_variant	Frame_Shift_Del	DEL	AGAGAAGACTGATAGAGACTTC	AGAGAAGACTGATAGAGACTTC	-	novel	NA	P-0023321-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	32	659	0	ENST00000334344.6:c.678_699del	p.Glu227LeufsTer58	p.E227Lfs*58	ENST00000334344	NM_152641.2	226	aaAGAGAAGACTGATAGAGACTTC/aa	6/21	0.720795157389674	2	FACETS	0.447	0.366	0.537	0.223	0.183	0.269	SUBCLONAL	1	FALSE	0	0.723502611047345	2		659	198	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061540	38061540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023321-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	122	472	0	ENST00000250448.2:c.449G>A	p.Arg150His	p.R150H	ENST00000250448	NM_004496.3	150	cGc/cAc	2/2	0.577992764622587	4	FACETS	1	0.959	1			1	CLONAL	2	FALSE	NA	0.723502611047345	4		472	273	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38506159	38506160	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCA	novel	NA	P-0023321-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	69	685	0	ENST00000254066.5:c.452_453insCAT	p.Val151_Gly152insMet	p.V151_G152insM	ENST00000254066	NM_000964.3	151	gtg/gTCAtg	4/9	0.720795157389674	3	FACETS	0.863	0.758	0.974			1	CLONAL	1	FALSE	NA	0.723502611047345	3		685	301	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245302	41245310	+	inframe_deletion	In_Frame_Del	DEL	TCTTTGGGG	TCTTTGGGG	-	novel	NA	P-0023321-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	92	952	0	ENST00000357654.3:c.2238_2246del	p.Pro747_Asp749del	p.P747_D749del	ENST00000357654	NM_007294.3	746	gaCCCCAAAGAt/gat	10/23	0.720795157389674	3	FACETS	0.63	0.561	0.703			1	SUBCLONAL	1	FALSE	NA	0.723502611047345	3		952	550	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792467	33792467	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023321-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	70	708	0	ENST00000498907.2:c.854A>G	p.Tyr285Cys	p.Y285C	ENST00000498907	NM_004364.3	285	tAc/tGc	1/1	0.348838020512293	6	FACETS	1	0.967	1	0.441	0.387	0.499	INDETERMINATE	1	FALSE	3	0.723502611047345	6		708	358	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020855	112020855	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023321-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	71	523	1	ENST00000368678.4:c.716G>A	p.Cys239Tyr	p.C239Y	ENST00000368678		239	tGt/tAt	8/13	0.723502611047345	6	FACETS	1	0.941	1			1	CLONAL	1	FALSE	NA	0.723502611047345	6		524	426	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993681	90993681	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786202085	NA	P-0023321-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	89	568	0	ENST00000265433.3:c.242A>G	p.Glu81Gly	p.E81G	ENST00000265433	NM_002485.4	81	gAa/gGa	3/16	0.658559989235487	3	FACETS	0.918	0.82	1	0.459	0.41	0.51	CLONAL	1	FALSE	1	0.723502611047345	3		568	365	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974792	21974792	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs141798398	NA	P-0023322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	126	213	0	ENST00000304494.5:c.35C>A	p.Ser12Ter	p.S12*	ENST00000304494	NM_000077.4	12	tCg/tAg	1/3	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	2	TRUE	NA	0.435166411200528	2		213	253	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220691	1220691	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs878853247	NA	P-0023322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	548	1095	0	ENST00000326873.7:c.709G>C	p.Asp237His	p.D237H	ENST00000326873	NM_000455.4	237	Gac/Cac	5/10	0.435166411200528	3	FACETS	0.953	0.919	0.987	0.953	0.919	0.987	CLONAL	3	TRUE	0	0.435166411200528	3		1095	1073	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195668	102195668	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0023322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	311	805	2	ENST00000263464.3:c.428C>G	p.Ser143Ter	p.S143*	ENST00000263464	NM_001165.4	143	tCa/tGa	2/9	0.405353590088023	4	FACETS	0.935	0.882	0.989	0.935	0.882	0.989	CLONAL	2	TRUE	2	0.435166411200528	4		807	1097	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156170	119156170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1460460945	NA	P-0023322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	394	890	0	ENST00000264033.4:c.1835G>A	p.Arg612Lys	p.R612K	ENST00000264033	NM_005188.3	612	aGa/aAa	11/16	0.434289302283955	3	FACETS	0.907	0.863	0.952	0.907	0.863	0.952	CLONAL	2	TRUE	1	0.435166411200528	3		890	1215	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579553	7579577	+	frameshift_variant	Frame_Shift_Del	DEL	AGCATCAAATCATCCATTGCTTGGG	AGCATCAAATCATCCATTGCTTGGG	-	novel	NA	P-0023322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	291	1010	0	ENST00000269305.4:c.110_134del	p.Ser37CysfsTer78	p.S37Cfs*78	ENST00000269305	NM_001126112.2	37	tCCCAAGCAATGGATGATTTGATGCTg/tg	4/11	0.435166411200528	2	FACETS	0.8	0.755	0.845	0.8	0.755	0.845	SUBCLONAL	2	TRUE	0	0.435166411200528	2		1010	836	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554309	29554309	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	378	886	0	ENST00000356175.3:c.2325G>C	p.Glu775Asp	p.E775D	ENST00000356175	NM_000267.3	775	gaG/gaC	19/57	0.435166411200528	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.435166411200528	2		886	825	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937806	76937806	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	206	1052	2	ENST00000373344.5:c.2942A>T	p.Asp981Val	p.D981V	ENST00000373344	NM_000489.3	981	gAt/gTt	9/35	0.435166411200528	3	FACETS	1	0.93	1	0.502	0.465	0.54	CLONAL	1	TRUE	1	0.435166411200528	3		1054	1149	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0023341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	112	748	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.311493116771014	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.311493116771014	1		748	583	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	146	896	2	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	0.311493116771014	2		898	882	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971194	21971194	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	155	622	0	ENST00000304494.5:c.164del	p.Gly55AlafsTer91	p.G55Afs*91	ENST00000304494	NM_000077.4	55	gGc/gc	2/3	0.311493116771014	1	FACETS	0.813	0.749	0.878	1	0.99	1	CLONAL	2	TRUE	0	0.311493116771014	1		622	517	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974678	21974678	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs587778189	NA	P-0023341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	49	660	2	ENST00000304494.5:c.149A>C	p.Gln50Pro	p.Q50P	ENST00000304494	NM_000077.4	50	cAg/cCg	1/3	0.311493116771014				0.409	0.566				SUBCLONAL	1	TRUE	0	0.311493116771014	1		662	549	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0023342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	677	825	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	NA	2	FACETS	0.982	0.955	1			1	INDETERMINATE	2	TRUE	NA	0.685594956082644	2		825	1006	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	519	661	0	ENST00000206249.3:c.1607T>C	p.Leu536Pro	p.L536P	ENST00000206249	NM_000125.3	536	cTc/cCc	8/8	0.597052172017881	3	FACETS	0.86	0.833	0.886	0.86	0.833	0.886	CLONAL	3	TRUE	0	0.685594956082644	3		661	788	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149323	119149323	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	295	506	0	ENST00000264033.4:c.1331G>T	p.Arg444Met	p.R444M	ENST00000264033	NM_005188.3	444	aGg/aTg	9/16	0.26557949166569	2	FACETS	1	0.994	1	0.675	0.641	0.71	INDETERMINATE	1	TRUE	0	0.685594956082644	2		506	637	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385183	4385183	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	177	451	0	ENST00000261254.3:c.208C>G	p.Gln70Glu	p.Q70E	ENST00000261254	NM_001759.3	70	Cag/Gag	2/5	1	2	FACETS	0.903	0.837	0.97	0.903	0.837	0.97	CLONAL	1	TRUE	1	0.685594956082644	2		451	572	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112097	115112098	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0023342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	284	818	1	ENST00000257566.3:c.1642_1643delinsTT	p.Gly548Leu	p.G548L	ENST00000257566	NM_016569.3	548	GGg/TTg	7/8	1	2	FACETS	0.98	0.925	1	0.98	0.925	1	CLONAL	1	TRUE	1	0.685594956082644	2		819	845	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047507	49047507	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1131690906	NA	P-0023342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	109	482	0	ENST00000267163.4:c.2501C>A	p.Ser834Ter	p.S834*	ENST00000267163	NM_000321.2	834	tCa/tAa	24/27	0.655977522963418	1	FACETS	0.871	0.798	0.944	0.871	0.798	0.944	CLONAL	1	TRUE	0	0.685594956082644	1		482	240	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81914531	81914531	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	200	572	0	ENST00000359376.3:c.665A>C	p.Lys222Thr	p.K222T	ENST00000359376	NM_002661.3	222	aAa/aCa	8/33	1	2	FACETS	0.836	0.777	0.896	0.836	0.777	0.896	CLONAL	1	TRUE	1	0.685594956082644	2		572	698	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39708796	39708796	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	68	442	0	ENST00000361337.2:c.407T>C	p.Leu136Ser	p.L136S	ENST00000361337	NM_003286.2	136	tTa/tCa	6/21	0.244752999364405	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.685594956082644	0		442	290	SUCCESS
ATR	545	MSKCC	GRCh37	3	142180857	142180857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	128	663	0	ENST00000350721.4:c.7117G>A	p.Glu2373Lys	p.E2373K	ENST00000350721	NM_001184.3	2373	Gaa/Aaa	42/47	0.686093998483816	3	FACETS	0.974	0.887	1	0.487	0.443	0.532	CLONAL	1	TRUE	1	0.685594956082644	3		663	515	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169985715	169985715	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs567380681	NA	P-0023342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	231	518	0	ENST00000295797.4:c.377G>T	p.Arg126Leu	p.R126L	ENST00000295797	NM_002740.5	126	cGt/cTt	5/18	0.686093998483816	3	FACETS	1	0.974	1	0.54	0.504	0.576	CLONAL	1	TRUE	1	0.685594956082644	3		518	838	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139725	55139725	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	195	508	0	ENST00000257290.5:c.1386G>A	p.Trp462Ter	p.W462*	ENST00000257290	NM_006206.4	462	tgG/tgA	10/23	1	2	FACETS	0.937	0.872	1	0.937	0.872	1	CLONAL	1	TRUE	1	0.685594956082644	2		508	607	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972957	68972957	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	132	571	0	ENST00000288368.4:c.1282C>A	p.Pro428Thr	p.P428T	ENST00000288368	NM_024870.2	428	Cct/Act	11/40	1	2	FACETS	0.745	0.68	0.812	0.745	0.68	0.812	SUBCLONAL	1	TRUE	1	0.685594956082644	2		571	517	SUCCESS
AR	367	MSKCC	GRCh37	X	66765773	66765773	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	506	493	0	ENST00000374690.3:c.785A>G	p.Gln262Arg	p.Q262R	ENST00000374690	NM_000044.3	262	cAg/cGg	1/8	0.424224166962042	2	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.685594956082644	2		493	687	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019990	123019990	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	361	306	0	ENST00000355640.3:c.478A>G	p.Met160Val	p.M160V	ENST00000355640		160	Atg/Gtg	2/7	0.424224166962042	2	FACETS	1	0.983	1			1	CLONAL	2	TRUE	NA	0.685594956082644	2		306	512	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435185	49435186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	159	471	0	ENST00000301067.7:c.6367_6368insT	p.Thr2123IlefsTer32	p.T2123Ifs*32	ENST00000301067	NM_003482.3	2123	acc/aTcc	31/54	1	2	FACETS	0.874	0.806	0.943	0.874	0.806	0.943	CLONAL	1	TRUE	1	0.685594956082644	2		471	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201059	NA	P-0023344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	103	1008	0	ENST00000269305.4:c.856G>T	p.Glu286Ter	p.E286*	ENST00000269305	NM_001126112.2	286	Gaa/Taa	8/11	0.169275267634975	3	FACETS	0.869	0.778	0.966	0.29	0.259	0.322	INDETERMINATE	1	TRUE	0	0.374072061992958	3		1008	752	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893456	32893456	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	17	313	0	ENST00000380152.3:c.310G>A	p.Asp104Asn	p.D104N	ENST00000380152		104	Gac/Aac	3/27	0.114228966292778	4	FACETS	0.531	0.397	0.69	0.266	0.198	0.345	INDETERMINATE	1	TRUE	2	0.374072061992958	4		313	235	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519872	29519872	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	54	792	0	ENST00000389048.3:c.1699G>C	p.Val567Leu	p.V567L	ENST00000389048	NM_004304.4	567	Gtg/Ctg	9/29	0.374072061992958	1	FACETS	0.527	0.451	0.611	0.527	0.451	0.611	SUBCLONAL	1	TRUE	0	0.374072061992958	1		792	445	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371782	55371934	+	protein_altering_variant	In_Frame_Del	DEL	GGCCTGGCTGAGCCGCAGGCGGCCGCGCTGGGCCCCGAGGGCGGCCGCGTGGCCATGGACGGCCTGGGCCTCCAGTTCCCCGAGCAGGGCTTCCCCGCCGGCCCGCCGCTGCTGCCTCCGCACATGGGCGGCCACTACCGCGACTGCCAGAGT	GGCCTGGCTGAGCCGCAGGCGGCCGCGCTGGGCCCCGAGGGCGGCCGCGTGGCCATGGACGGCCTGGGCCTCCAGTTCCCCGAGCAGGGCTTCCCCGCCGGCCCGCCGCTGCTGCCTCCGCACATGGGCGGCCACTACCGCGACTGCCAGAGT	AGC	novel	NA	P-0023344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	169	637	5	ENST00000297316.4:c.472_624delinsAGC	p.Gly158_Gln207del	p.G158_Q207del	ENST00000297316	NM_022454.3	158	GGCCTGGCTGAGCCGCAGGCGGCCGCGCTGGGCCCCGAGGGCGGCCGCGTGGCCATGGACGGCCTGGGCCTCCAGTTCCCCGAGCAGGGCTTCCCCGCCGGCCCGCCGCTGCTGCCTCCGCACATGGGCGGCCACTACCGCGACTGCCAGAGT/AGC	2/2	0.374072061992958	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.374072061992958	3		642	482	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0023351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	27	621	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	1	2	FACETS	0.675	0.537	0.833	0.675	0.537	0.833	SUBCLONAL	1	TRUE	1	0.197577660310881	2		621	405	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372025	55372025	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	71	720	2	ENST00000297316.4:c.715G>A	p.Ala239Thr	p.A239T	ENST00000297316	NM_022454.3	239	Gcc/Acc	2/2	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.197577660310881	2		722	677	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021790	71021790	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	42	430	0	ENST00000318789.4:c.1568T>G	p.Phe523Cys	p.F523C	ENST00000318789	NM_032682.5	523	tTt/tGt	18/21	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.197577660310881	2		430	380	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858045	152858045	+	synonymous_variant	Silent	SNP	G	G	A	rs369691224	NA	P-0023351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	58	570	0	ENST00000406277.2:c.570C>T	p.Ala190=	p.A190=	ENST00000406277	NM_152274.4	190	gcC/gcT	6/7	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.197577660310881	2		570	521	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274803	123274803	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913477	NA	P-0023351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	118	666	0	ENST00000358487.5:c.1115C>G	p.Ser372Cys	p.S372C	ENST00000358487	NM_000141.4	372	tCc/tGc	9/18	0.176740783059539	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	2	TRUE	0	0.197577660310881	2		666	597	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937832	76937832	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	57	886	0	ENST00000373344.5:c.2916C>G	p.Asp972Glu	p.D972E	ENST00000373344	NM_000489.3	972	gaC/gaG	9/35	1	2	FACETS	0.84	0.72	0.971	0.84	0.72	0.971	CLONAL	1	TRUE	1	0.197577660310881	2		886	687	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953788	48953788	+	splice_donor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0023352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	104	298	0	ENST00000267163.4:c.1389+2del		p.X463_splice	ENST00000267163	NM_000321.2	463			NA	2	FACETS	0.974	0.905	1			1	INDETERMINATE	2	TRUE	NA	0.654837526462029	2		298	163	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430747	181430747	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	122	817	0	ENST00000325404.1:c.599A>C	p.Tyr200Ser	p.Y200S	ENST00000325404	NM_003106.3	200	tAc/tCc	1/1	0.654837526462029	8	FACETS	0.956	0.862	1	0.159	0.143	0.176	CLONAL	1	TRUE	2	0.654837526462029	8		817	1156	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0023353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	168	460	3	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.912	0.845	0.98	0.912	0.845	0.98	CLONAL	1	FALSE	1	0.759612016856697	2		463	485	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0023353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	242	954	2	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.874	0.82	0.929	0.874	0.82	0.929	CLONAL	1	FALSE	1	0.759612016856697	2		956	729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577544	7577544	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587780074	NA	P-0023353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	275	954	5	ENST00000269305.4:c.737T>A	p.Met246Lys	p.M246K	ENST00000269305	NM_001126112.2	246	aTg/aAg	7/11	0.612624667104472	1	FACETS	0.811	0.769	0.852	0.811	0.769	0.852	CLONAL	1	FALSE	0	0.759612016856697	1		959	554	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395664	45395664	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	198	678	0	ENST00000262160.6:c.470del	p.Lys157ArgfsTer6	p.K157Rfs*6	ENST00000262160	NM_005901.5	157	aAg/ag	4/11	0.678975726970812	1	FACETS	0.775	0.728	0.823	0.775	0.728	0.823	SUBCLONAL	1	FALSE	0	0.759612016856697	1		678	417	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771827	135771827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs118203750	NA	P-0023353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	230	888	9	ENST00000298552.3:c.3290G>A	p.Arg1097His	p.R1097H	ENST00000298552	NM_001162426.1	1097	cGt/cAt	23/23	0.74048165192645	3	FACETS	0.932	0.87	0.995	0.466	0.435	0.498	CLONAL	1	FALSE	1	0.759612016856697	3		897	897	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993695	72993695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	193	738	6	ENST00000268489.5:c.350G>A	p.Gly117Asp	p.G117D	ENST00000268489	NM_006885.3	117	gGt/gAt	2/10	1	2	FACETS	0.907	0.845	0.971	0.907	0.845	0.971	CLONAL	1	FALSE	1	0.759612016856697	2		744	560	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911633	114911633	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	180	628	5	ENST00000543371.1:c.1151T>G	p.Leu384Arg	p.L384R	ENST00000543371	NM_001198531.1	384	cTt/cGt	10/14	1	2	FACETS	0.884	0.821	0.949	0.884	0.821	0.949	CLONAL	1	FALSE	1	0.759612016856697	2		633	536	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457358	67457367	+	frameshift_variant	Frame_Shift_Del	DEL	TCGCCTTCAA	TCGCCTTCAA	-	novel	NA	P-0023353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	826	834	8	ENST00000327367.4:c.333_342del	p.Phe111LeufsTer2	p.F111Lfs*2	ENST00000327367	NM_005902.3	111	tTCGCCTTCAAt/tt	2/9	0.759612016856697	3	FACETS	0.906	0.887	0.925	0.906	0.887	0.925	CLONAL	3	FALSE	0	0.759612016856697	3		842	1104	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006063	22006063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	162	693	10	ENST00000276925.6:c.340C>T	p.Arg114Cys	p.R114C	ENST00000276925	NM_004936.3	114	Cgt/Tgt	2/2	0.74048165192645	3	FACETS	0.771	0.709	0.836	0.386	0.354	0.418	SUBCLONAL	1	FALSE	1	0.759612016856697	3		703	763	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717687	89717690	+	frameshift_variant	Frame_Shift_Del	DEL	TTCA	TTCA	-	novel	NA	P-0023355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	97	557	0	ENST00000371953.3:c.713_716del	p.Phe238CysfsTer17	p.F238Cfs*17	ENST00000371953	NM_000314.4	238	TTCAtg/tg	7/9	0.207163926975744	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.236641140858669	1		557	621	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576062	29576063	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTCT	novel	NA	P-0023355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	83	748	0	ENST00000356175.3:c.4037_4040dup	p.His1348LeufsTer27	p.H1348Lfs*27	ENST00000356175	NM_000267.3	1345	-/TTCT	30/57	0.236641140858669	1	FACETS	0.774	0.682	0.873	0.774	0.682	0.873	SUBCLONAL	1	TRUE	0	0.236641140858669	1		748	799	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0023358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	187	870	2	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.867446708565997	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.875213510014752	1		872	240	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276892	123276892	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121918487	NA	P-0023358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	89	631	0	ENST00000358487.5:c.1025G>T	p.Cys342Phe	p.C342F	ENST00000358487	NM_000141.4	342	tGc/tTc	8/18	1	2	FACETS	0.95	0.86	1	0.95	0.86	1	CLONAL	1	TRUE	1	0.875213510014752	2		631	214	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920713	100920718	+	inframe_deletion	In_Frame_Del	DEL	TGAAGC	TGAAGC	-	novel	NA	P-0023358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	134	775	0	ENST00000325455.5:c.2430_2435del	p.Leu811_Gln812del	p.L811_Q812del	ENST00000325455	NM_001202474.3	810	aaGCTTCAa/aaa	6/8	0.875213510014752	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.875213510014752	1		775	165	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663364	29663364	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	111	549	0	ENST00000356175.3:c.5957T>G	p.Leu1986Arg	p.L1986R	ENST00000356175	NM_000267.3	1986	cTt/cGt	40/57	0.617969599113991	3	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.875213510014752	3		549	262	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	45	896	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.381	0.32	0.449	0.381	0.32	0.449	SUBCLONAL	1	TRUE	1	0.464083863362782	2		898	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0023359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	70	941	2	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	1	2	FACETS	0.427	0.372	0.487	0.427	0.372	0.487	SUBCLONAL	1	TRUE	1	0.464083863362782	2		943	706	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593469	48593470	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0023359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	29	489	0	ENST00000342988.3:c.1221dup	p.Phe408LeufsTer21	p.F408Lfs*21	ENST00000342988	NM_005359.5	407	gtc/gtCc	10/12	1	2	FACETS	0.306	0.245	0.375	0.306	0.245	0.375	SUBCLONAL	1	TRUE	1	0.464083863362782	2		489	409	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402540	20402540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	51	600	1	ENST00000346618.3:c.77C>T	p.Ala26Val	p.A26V	ENST00000346618	NM_001949.4	26	gCc/gTc	1/7	0.18417581954813	3	FACETS	0.832	0.708	0.968	0.416	0.354	0.484	CLONAL	1	TRUE	1	0.293545660293869	3		601	479	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245546	46245546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334618271	NA	P-0023366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	48	331	0	ENST00000334344.6:c.3640G>A	p.Val1214Ile	p.V1214I	ENST00000334344	NM_152641.2	1214	Gta/Ata	15/21	0.221873927117902	2	FACETS	1	0.956	1	0.684	0.582	0.795	CLONAL	1	FALSE	0	0.237903809404853	2		331	295	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246092	46246092	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	80	404	0	ENST00000334344.6:c.4186C>T	p.Gln1396Ter	p.Q1396*	ENST00000334344	NM_152641.2	1396	Caa/Taa	15/21	0.221873927117902	2	FACETS	0.955	0.847	1	0.955	0.847	1	CLONAL	2	FALSE	0	0.237903809404853	2		404	352	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495415	56495415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373454755	NA	P-0023366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	140	679	0	ENST00000267101.3:c.3605G>A	p.Arg1202Gln	p.R1202Q	ENST00000267101	NM_001982.3	1202	cGg/cAg	28/28	0.221873927117902	2	FACETS	0.976	0.892	1	0.976	0.892	1	CLONAL	2	FALSE	0	0.237903809404853	2		679	603	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220529	133220529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs5744933	NA	P-0023366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	142	611	0	ENST00000320574.5:c.4184A>G	p.Tyr1395Cys	p.Y1395C	ENST00000320574	NM_006231.2	1395	tAc/tGc	33/49	0.221873927117902	2	FACETS	0.961	0.879	1	0.961	0.879	1	CLONAL	2	FALSE	0	0.237903809404853	2		611	621	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961500	41961500	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	54	598	2	ENST00000219905.7:c.408G>T	p.Lys136Asn	p.K136N	ENST00000219905	NM_001164273.1	136	aaG/aaT	2/24	1	2	FACETS	0.838	0.715	0.971	0.838	0.715	0.971	CLONAL	1	FALSE	1	0.237903809404853	2		600	542	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476342	88476342	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	85	746	0	ENST00000360948.2:c.1790A>G	p.His597Arg	p.H597R	ENST00000360948	NM_001012338.2	597	cAt/cGt	15/19	1	2	FACETS	0.976	0.863	1	0.976	0.863	1	CLONAL	1	FALSE	1	0.237903809404853	2		746	732	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478256	99478256	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	52	321	0	ENST00000268035.6:c.3160A>T	p.Met1054Leu	p.M1054L	ENST00000268035	NM_000875.3	1054	Atg/Ttg	16/21	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.237903809404853	2		321	321	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934599	9934599	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	77	509	0	ENST00000330684.3:c.1556C>A	p.Ser519Tyr	p.S519Y	ENST00000330684	NM_001134407.1	519	tCt/tAt	7/13	0.237903809404853	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	0	0.237903809404853	1		509	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0023366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	107	840	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.237903809404853	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	0	0.237903809404853	1		840	705	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004662	16004662	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	83	675	0	ENST00000268712.3:c.2592G>T	p.Gln864His	p.Q864H	ENST00000268712	NM_006311.3	864	caG/caT	20/46	0.237903809404853	1	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	FALSE	0	0.237903809404853	1		675	600	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428018	33428018	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	94	681	0	ENST00000345365.6:c.941G>T	p.Trp314Leu	p.W314L	ENST00000345365	NM_002878.3	314	tGg/tTg	10/10	0.144618923298907	3	FACETS	1	0.976	1	0.679	0.605	0.758	CLONAL	1	FALSE	1	0.237903809404853	3		681	651	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489787	40489787	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	96	608	0	ENST00000264657.5:c.639G>T	p.Met213Ile	p.M213I	ENST00000264657	NM_139276.2	213	atG/atT	7/24	0.144618923298907	3	FACETS	1	0.979	1	0.725	0.647	0.808	CLONAL	1	FALSE	1	0.237903809404853	3		608	623	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437533	56437533	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	93	667	0	ENST00000407977.2:c.929C>T	p.Pro310Leu	p.P310L	ENST00000407977		310	cCc/cTc	8/10	0.144618923298907	3	FACETS	1	0.963	1	0.599	0.533	0.67	CLONAL	1	FALSE	1	0.237903809404853	3		667	730	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451786	29451786	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	98	743	0	ENST00000389048.3:c.2779G>T	p.Gly927Trp	p.G927W	ENST00000389048	NM_004304.4	927	Ggg/Tgg	16/29	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.237903809404853	2		743	700	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149845	99149845	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	61	384	0	ENST00000074304.5:c.157A>G	p.Ser53Gly	p.S53G	ENST00000074304	NM_001134224.1	53	Agt/Ggt	5/26	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.237903809404853	2		384	353	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881716	111881716	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	35	534	0	ENST00000393256.3:c.394G>C	p.Ala132Pro	p.A132P	ENST00000393256	NM_006538.4	132	Gct/Cct	2/4	1	2	FACETS	0.445	0.364	0.537	0.445	0.364	0.537	SUBCLONAL	1	FALSE	1	0.237903809404853	2		534	661	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164804	36164805	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0023366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	69	828	0	ENST00000300305.3:c.1070dup	p.Thr358AspfsTer242	p.T358Dfs*242	ENST00000300305		357	ccg/ccCg	8/8	1	2	FACETS	0.759	0.66	0.867	0.759	0.66	0.867	SUBCLONAL	1	FALSE	1	0.237903809404853	2		828	764	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39772501	39772501	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	35	566	0	ENST00000288319.7:c.740G>T	p.Arg247Met	p.R247M	ENST00000288319	NM_182918.3	247	aGg/aTg	6/10	1	2	FACETS	0.613	0.502	0.738	0.613	0.502	0.738	SUBCLONAL	1	FALSE	1	0.237903809404853	2		566	480	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161166	56161166	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0023366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	25	388	0	ENST00000399503.3:c.1036-1G>A		p.X346_splice	ENST00000399503	NM_005921.1	346			0.221873927117902	2	FACETS	0.694	0.547	0.861	0.347	0.273	0.431	SUBCLONAL	1	FALSE	0	0.237903809404853	2		388	303	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188953	32188953	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	167	831	0	ENST00000375023.3:c.601G>T	p.Asp201Tyr	p.D201Y	ENST00000375023	NM_004557.3	201	Gac/Tac	4/30	0.221873927117902	2	FACETS	0.907	0.835	0.982	0.907	0.835	0.982	CLONAL	2	FALSE	0	0.237903809404853	2		831	774	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120431	94120431	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	42	390	2	ENST00000369303.4:c.620C>A	p.Ser207Tyr	p.S207Y	ENST00000369303	NM_004440.3	207	tCc/tAc	3/17	0.237903809404853	1	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	FALSE	0	0.237903809404853	1		392	285	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345929	152345929	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368445278	NA	P-0023366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	131	594	0	ENST00000359321.1:c.641G>A	p.Arg214Gln	p.R214Q	ENST00000359321	NM_005431.1	214	cGa/cAa	3/3	0.144618923298907	3	FACETS	0.922	0.839	1	0.922	0.839	1	CLONAL	2	FALSE	1	0.237903809404853	3		594	668	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964391	70964391	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	45	448	0	ENST00000276594.2:c.1637G>T	p.Cys546Phe	p.C546F	ENST00000276594	NM_024504.3	546	tGc/tTc	8/8	0.128454283155649	3	FACETS	0.824	0.692	0.969	0.275	0.23	0.323	INDETERMINATE	1	FALSE	0	0.237903809404853	3		448	514	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123066	5123066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	35	582	1	ENST00000381652.3:c.3122G>A	p.Gly1041Glu	p.G1041E	ENST00000381652	NM_004972.3	1041	gGa/gAa	23/25	0.237903809404853	1	FACETS	0.734	0.603	0.881	0.734	0.603	0.881	SUBCLONAL	1	FALSE	0	0.237903809404853	1		583	353	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518060	8518060	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	40	486	0	ENST00000356435.5:c.1331C>T	p.Pro444Leu	p.P444L	ENST00000356435		444	cCa/cTa	10/35	0.237903809404853	1	FACETS	0.728	0.606	0.864	0.728	0.606	0.864	SUBCLONAL	1	FALSE	0	0.237903809404853	1		486	407	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738312	133738312	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	78	534	0	ENST00000318560.5:c.712G>T	p.Glu238Ter	p.E238*	ENST00000318560	NM_005157.4	238	Gaa/Taa	4/11	0.237903809404853	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	0	0.237903809404853	1		534	445	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938427	76938427	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	45	362	0	ENST00000373344.5:c.2321A>G	p.Asp774Gly	p.D774G	ENST00000373344	NM_000489.3	774	gAt/gGt	9/35	1	1	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	FALSE	0	0.237903809404853	1		362	312	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039659	47039666	+	frameshift_variant	Frame_Shift_Del	DEL	ACTATCGA	ACTATCGA	-	novel	NA	P-0023368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	187	755	0	ENST00000377604.3:c.1111_1118del	p.Thr371ArgfsTer7	p.T371Rfs*7	ENST00000377604	NM_001204468.1	371	ACTATCGAc/c	11/24	1	2	FACETS	0.863	0.799	0.929	1	0.992	1	CLONAL	2	TRUE	1	0.284264195794437	2		755	762	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578196	7578197	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0023371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	283	671	0	ENST00000269305.4:c.652dup	p.Val218GlyfsTer4	p.V218Gfs*4	ENST00000269305	NM_001126112.2	218	gtg/gGtg	6/11	0.572454885845173	2	FACETS	0.947	0.902	0.992	0.947	0.902	0.992	CLONAL	2	TRUE	0	0.572454885845173	2		671	522	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0023373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	205	804	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.272879648772042	2	FACETS	0.887	0.831	0.945	0.887	0.831	0.945	CLONAL	2	TRUE	0	0.450379829061421	2		804	513	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974695	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691187	NA	P-0023373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	25	507	0	ENST00000304494.5:c.132del	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	taC/ta	1/3	0.412609872258949	0	FACETS	0.271	0.214	0.336			1	SUBCLONAL	1	TRUE	0	0.450379829061421	0		507	225	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92354975	92354975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1287192342	NA	P-0023373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	60	354	1	ENST00000265734.4:c.502C>T	p.Arg168Cys	p.R168C	ENST00000265734	NM_001259.6	168	Cgc/Tgc	4/8	0.257334874144117	4	FACETS	1	0.964	1	0.671	0.583	0.765	INDETERMINATE	1	TRUE	2	0.450379829061421	4		355	288	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0023379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	521	676	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.267950523768203	12	FACETS	0.972	0.938	1			1	CLONAL	10	TRUE	NA	0.267950523768203	12		676	936	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591837	48591837	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs867764109	NA	P-0023379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	79	480	1	ENST00000342988.3:c.1000C>T	p.Gln334Ter	p.Q334*	ENST00000342988	NM_005359.5	334	Cag/Tag	9/12	0.242594058853515	2	FACETS	1	0.97	1	0.661	0.584	0.743	CLONAL	1	TRUE	0	0.267950523768203	2		481	446	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587781525	NA	P-0023379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	102	716	0	ENST00000269305.4:c.842A>T	p.Asp281Val	p.D281V	ENST00000269305	NM_001126112.2	281	gAc/gTc	8/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.267950523768203	2		716	637	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175963	176175963	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	83	269	0	ENST00000367669.3:c.152G>T	p.Gly51Val	p.G51V	ENST00000367669	NM_022457.5	51	gGg/gTg	1/20	0.267950523768203	3	FACETS	0.915	0.819	1	1	0.977	1	CLONAL	3	TRUE	1	0.267950523768203	3		269	256	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39251213	39251213	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	36	794	0	ENST00000402219.2:c.1140G>T	p.Leu380Phe	p.L380F	ENST00000402219	NM_005633.3	380	ttG/ttT	9/23	0.267950523768203	3	FACETS	0.475	0.39	0.572	0.158	0.13	0.191	SUBCLONAL	1	TRUE	0	0.267950523768203	3		794	641	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285277	212285277	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	33	478	0	ENST00000342788.4:c.3024G>T	p.Leu1008Phe	p.L1008F	ENST00000342788	NM_005235.2	1008	ttG/ttT	25/28	1	2	FACETS	0.627	0.511	0.757	0.627	0.511	0.757	SUBCLONAL	1	TRUE	1	0.267950523768203	2		478	393	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55960981	55960981	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	144	507	0	ENST00000263923.4:c.2959G>T	p.Glu987Ter	p.E987*	ENST00000263923	NM_002253.2	987	Gaa/Taa	21/30	0.243908766939103	3	FACETS	1	0.933	1	1	0.933	1	CLONAL	3	TRUE	0	0.267950523768203	3		507	401	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969074	93969074	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	26	279	0	ENST00000369303.4:c.1922C>T	p.Ala641Val	p.A641V	ENST00000369303	NM_004440.3	641	gCa/gTa	10/17	0.267950523768203	3	FACETS	0.806	0.64	0.995			1	CLONAL	1	TRUE	NA	0.267950523768203	3		279	273	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6031690	6031690	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs587781339	NA	P-0023379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	38	574	0	ENST00000265849.7:c.904-2A>G		p.X302_splice	ENST00000265849	NM_000535.5	302			0.267950523768203	5	FACETS	0.541	0.446	0.648	0.135	0.111	0.162	SUBCLONAL	1	TRUE	1	0.267950523768203	5		574	735	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0023381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	2234	609	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.285202685474883	41	FACETS	0.999	0.987	1	0.949	0.938	0.959	CLONAL	38	TRUE	1	0.285202685474883	41		609	2709	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0023381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	203	1054	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	0.285202685474883	2	FACETS	0.98	0.912	1	0.98	0.912	1	CLONAL	2	TRUE	0	0.285202685474883	2		1054	726	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0023384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	475	830	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.772849351739064	2	FACETS	0.968	0.943	0.993	0.968	0.943	0.993	CLONAL	2	TRUE	0	0.808062468920069	2		832	607	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0023384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	70	401	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	0.808062468920069	2		401	163	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939813	76939814	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	163	429	0	ENST00000373344.5:c.934dup	p.Thr312AsnfsTer10	p.T312Nfs*10	ENST00000373344	NM_000489.3	312	aca/aAca	9/35	1	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.808062468920069	1		429	228	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0023386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	290	689	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.390734252917415	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.461632414741039	2		689	622	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717609	89717609	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs876661024	NA	P-0023386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	58	427	0	ENST00000371953.3:c.635-1G>A		p.X212_splice	ENST00000371953	NM_000314.4	212			0.461632414741039	1	FACETS	0.543	0.469	0.623	0.543	0.469	0.623	SUBCLONAL	1	TRUE	0	0.461632414741039	1		427	356	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544756	65544756	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0023386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	201	545	2	ENST00000358664.4:c.172-2A>T		p.X58_splice	ENST00000358664	NM_002382.4	58			0.401306333938089	2	FACETS	0.901	0.844	0.959	0.901	0.844	0.959	CLONAL	2	TRUE	0	0.461632414741039	2		547	483	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110807	2110847	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGCTCCAGGTGGGGTGGGGGCAGGAGCTCCGGGGAGCACCG	AGCTCCAGGTGGGGTGGGGGCAGGAGCTCCGGGGAGCACCG	-	novel	NA	P-0023386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	51	681	0	ENST00000219476.3:c.1112_1119+33del		p.X371_splice	ENST00000219476	NM_000548.3	371		11/42	0.461632414741039	1	FACETS	0.354	0.301	0.412	0.354	0.301	0.412	SUBCLONAL	1	TRUE	0	0.461632414741039	1		681	480	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985553	60985553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	130	433	0	ENST00000333681.4:c.347C>T	p.Ser116Phe	p.S116F	ENST00000333681		116	tCc/tTc	2/3	0.461632414741039	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.461632414741039	1		433	339	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096901	11096901	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555752952	NA	P-0023386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	45	885	0	ENST00000358026.2:c.392C>G	p.Ser131Cys	p.S131C	ENST00000358026	NM_001128849.1	131	tCt/tGt	4/36	0.461632414741039	1	FACETS	0.238	0.199	0.281	0.238	0.199	0.281	SUBCLONAL	1	TRUE	0	0.461632414741039	1		885	630	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971133	13971133	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	13	291	0	ENST00000405192.2:c.796G>T	p.Asp266Tyr	p.D266Y	ENST00000405192	NM_001163147.1	266	Gac/Tac	8/12	1	2	FACETS	0.869	0.622	1	0.869	0.622	1	CLONAL	1	TRUE	1	0.17	2		291	176	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298578	11298578	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	31	698	0	ENST00000361445.4:c.1883G>T	p.Arg628Leu	p.R628L	ENST00000361445	NM_004958.3	628	cGc/cTc	12/58	1	2	FACETS	0.95	0.769	1	0.95	0.769	1	CLONAL	1	TRUE	1	0.17	2		698	384	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444412	49444412	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	25	785	3	ENST00000301067.7:c.2959G>T	p.Glu987Ter	p.E987*	ENST00000301067	NM_003482.3	987	Gaa/Taa	11/54	1	2	FACETS	0.686	0.54	0.854	0.686	0.54	0.854	SUBCLONAL	1	TRUE	1	0.17	2		788	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579700	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0023387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	25	662	2	ENST00000269305.4:c.96_96+1delinsTT		p.X32_splice	ENST00000269305	NM_001126112.2	32		3/11	1	2	FACETS	0.819	0.646	1	0.819	0.646	1	CLONAL	1	TRUE	1	0.17	2		664	359	SUCCESS
ALK	238	MSKCC	GRCh37	2	29541271	29541271	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0023387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	22	420	1	ENST00000389048.3:c.1547-1G>T		p.X516_splice	ENST00000389048	NM_004304.4	516			1	2	FACETS	1	0.797	1	1	0.797	1	CLONAL	1	TRUE	1	0.17	2		421	252	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979543	55979543	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	23	654	0	ENST00000263923.4:c.904C>A	p.Gln302Lys	p.Q302K	ENST00000263923	NM_002253.2	302	Caa/Aaa	7/30	1	2	FACETS	0.601	0.468	0.757	0.601	0.468	0.757	SUBCLONAL	1	TRUE	1	0.17	2		654	450	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69143587	69143587	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	17	460	0	ENST00000288368.4:c.4795C>A	p.Pro1599Thr	p.P1599T	ENST00000288368	NM_024870.2	1599	Cca/Aca	40/40	1	2	FACETS	0.59	0.44	0.769	0.59	0.44	0.769	SUBCLONAL	1	TRUE	1	0.17	2		460	339	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930290	39930290	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	33	840	0	ENST00000378444.4:c.3174G>T	p.Gln1058His	p.Q1058H	ENST00000378444	NM_001123385.1	1058	caG/caT	6/15	1	2	FACETS	0.695	0.564	0.842	0.695	0.564	0.842	SUBCLONAL	1	TRUE	1	0.17	2		840	559	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028670	12028670	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	106	676	0	ENST00000353533.5:c.873G>T	p.Trp291Cys	p.W291C	ENST00000353533	NM_003010.3	291	tgG/tgT	8/11	0.524308088462404	1	FACETS	0.944	0.859	1	0.944	0.859	1	CLONAL	1	TRUE	0	0.559496836236119	1		676	289	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0023389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	294	399	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.997	0.943	1	0.997	0.943	1	CLONAL	1	TRUE	1	0.78	2		399	756	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0023389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	364	908	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.78	2		908	914	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748055	72748055	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	290	702	0	ENST00000357731.5:c.123del	p.Trp42GlyfsTer7	p.W42Gfs*7	ENST00000357731	NM_173808.2	41	ccC/cc	1/7	1	2	FACETS	0.976	0.923	1	0.976	0.923	1	CLONAL	1	TRUE	1	0.78	2		702	762	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267720	198267720	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	122	606	0	ENST00000335508.6:c.1759T>G	p.Tyr587Asp	p.Y587D	ENST00000335508	NM_012433.2	587	Tac/Gac	13/25	1	2	FACETS	0.468	0.424	0.515	0.468	0.424	0.515	SUBCLONAL	1	TRUE	1	0.78	2		606	668	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148726	20148726	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0023389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	212	299	1	ENST00000379607.5:c.338-1G>A		p.X113_splice	ENST00000379607	NM_001412.3	113			1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.78	1		300	286	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0023391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	232	724	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.93	0.868	0.993	0.93	0.868	0.993	CLONAL	1	TRUE	1	0.55092094459458	2		726	906	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28901685	28901685	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	146	500	0	ENST00000282397.4:c.2710C>T	p.Pro904Ser	p.P904S	ENST00000282397	NM_002019.4	904	Cct/Tct	20/30	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.55092094459458	2		500	514	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348729	118348729	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	192	399	0	ENST00000534358.1:c.3384del	p.Ile1129SerfsTer18	p.I1129Sfs*18	ENST00000534358	NM_005933.3	1128	Ccc/cc	5/36	0.521972150684311	2	FACETS	0.941	0.883	0.998	0.941	0.883	0.998	CLONAL	2	TRUE	0	0.521972150684311	2		399	391	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348756	118348756	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	208	432	1	ENST00000534358.1:c.3409A>G	p.Arg1137Gly	p.R1137G	ENST00000534358	NM_005933.3	1137	Aga/Gga	5/36	0.521972150684311	2	FACETS	0.94	0.885	0.995	0.94	0.885	0.995	CLONAL	2	TRUE	0	0.521972150684311	2		433	424	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522563	176522563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777277309	NA	P-0023392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	176	711	1	ENST00000292408.4:c.1660G>A	p.Ala554Thr	p.A554T	ENST00000292408	NM_213647.1	554	Gcc/Acc	13/18	0.426784368591691	4	FACETS	1	0.983	1	0.614	0.566	0.664	CLONAL	1	TRUE	2	0.521972150684311	4		712	836	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030367	49030368	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	83	501	0	ENST00000267163.4:c.1848dup	p.Gly617ArgfsTer36	p.G617Rfs*36	ENST00000267163	NM_000321.2	614	-/A	19/27	0.0609299373036225	3	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.354386363832712	3		501	391	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911143	40911143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370795038	NA	P-0023399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	119	560	0	ENST00000373198.4:c.2162G>A	p.Arg721His	p.R721H	ENST00000373198	NM_133170.3	721	cGt/cAt	13/32	0.335951077169253	2	FACETS	0.951	0.868	1	0.951	0.868	1	CLONAL	2	TRUE	0	0.354386363832712	2		560	353	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663199	227663199	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	111	764	0	ENST00000305123.5:c.256C>G	p.Leu86Val	p.L86V	ENST00000305123	NM_005544.2	86	Ctc/Gtc	1/2	0.309060372028006	4	FACETS	0.941	0.845	1	0.471	0.422	0.522	CLONAL	1	TRUE	2	0.309060372028006	4		764	999	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191501	10191501	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	170	606	0	ENST00000256474.2:c.494T>A	p.Val165Asp	p.V165D	ENST00000256474	NM_000551.3	165	gTt/gAt	3/3	0.309060372028006	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.309060372028006	2		606	521	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1953904	1953904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	62	1023	4	ENST00000382891.5:c.2083C>T	p.Leu695Phe	p.L695F	ENST00000382891	NM_133335.3	695	Ctt/Ttt	11/22	0.281783704290327	4	FACETS	0.452	0.389	0.521	0.226	0.194	0.261	SUBCLONAL	1	TRUE	2	0.309060372028006	4		1027	1162	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678426	88678426	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	198	754	0	ENST00000360948.2:c.1110C>G	p.His370Gln	p.H370Q	ENST00000360948	NM_001012338.2	370	caC/caG	9/19	1	2	FACETS	0.601	0.556	0.647	0.601	0.556	0.647	SUBCLONAL	1	TRUE	1	0.613227716442175	2		754	1075	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578189	7578189	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1567551150	NA	P-0023401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	265	652	1	ENST00000269305.4:c.660T>A	p.Tyr220Ter	p.Y220*	ENST00000269305	NM_001126112.2	220	taT/taA	6/11	0.613227716442175	1	FACETS	0.889	0.839	0.94	0.889	0.839	0.94	CLONAL	1	TRUE	0	0.613227716442175	1		653	674	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981495	55981495	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	121	588	0	ENST00000263923.4:c.442del	p.Ile148PhefsTer44	p.I148Ffs*44	ENST00000263923	NM_002253.2	148	Att/tt	4/30	0.308375265503395	1	FACETS	0.394	0.356	0.434	0.394	0.356	0.434	INDETERMINATE	1	TRUE	0	0.613227716442175	1		588	694	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0023403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	41	399	0				ENST00000310581	NM_198253.2	-/1132			0.3	0	FACETS	0.928	0.779	1			1	CLONAL	1	TRUE	0	0.27	0		399	239	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44896902	44896902	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	68	308	1	ENST00000377967.4:c.622C>T	p.Gln208Ter	p.Q208*	ENST00000377967	NM_021140.2	208	Caa/Taa	8/29	1	1	FACETS	0.97	0.847	1	0.97	0.847	1	CLONAL	1	TRUE	0	0.27	1		309	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0023403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	42	463	0	ENST00000269305.4:c.97-1G>A		p.X33_splice	ENST00000269305	NM_001126112.2	33			1	2	FACETS	0.804	0.672	0.949	0.804	0.672	0.949	CLONAL	1	TRUE	1	0.27	2		463	387	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230530	46230530	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	58	526	0	ENST00000334344.6:c.779del	p.Thr260AsnfsTer32	p.T260Nfs*32	ENST00000334344	NM_152641.2	260	aCa/aa	8/21	1	2	FACETS	0.791	0.683	0.907	1	0.972	1	CLONAL	2	TRUE	1	0.212493645765074	2		526	345	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578494	7578494	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs786203064	NA	P-0023406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	60	778	0	ENST00000269305.4:c.436T>G	p.Trp146Gly	p.W146G	ENST00000269305	NM_001126112.2	146	Tgg/Ggg	5/11	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	FALSE	1	0.196285423881052	2		778	588	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18496263	18496263	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	30	411	0	ENST00000266497.5:c.1402del	p.Tyr468IlefsTer11	p.Y468Ifs*11	ENST00000266497		466	aaT/aa	9/31	1	2	FACETS	0.704	0.567	0.86	0.704	0.567	0.86	SUBCLONAL	1	FALSE	1	0.196285423881052	2		411	434	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001930	29001930	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	29	636	1	ENST00000282397.4:c.1235C>A	p.Ser412Ter	p.S412*	ENST00000282397	NM_002019.4	412	tCa/tAa	9/30	1	2	FACETS	0.655	0.525	0.803	0.655	0.525	0.803	SUBCLONAL	1	FALSE	1	0.196285423881052	2		637	451	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144823	11144823	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	29	550	0	ENST00000358026.2:c.3898G>T	p.Glu1300Ter	p.E1300*	ENST00000358026	NM_001128849.1	1300	Gag/Tag	28/36	1	2	FACETS	0.712	0.571	0.872	0.712	0.571	0.872	SUBCLONAL	1	FALSE	1	0.196285423881052	2		550	415	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391052	89391052	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	23	651	0	ENST00000336596.2:c.1118G>T	p.Cys373Phe	p.C373F	ENST00000336596	NM_005233.5	373	tGt/tTt	5/17	1	2	FACETS	0.523	0.407	0.658	0.523	0.407	0.658	SUBCLONAL	1	FALSE	1	0.196285423881052	2		651	448	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31401629	31401629	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	44	592	0	ENST00000344624.3:c.4035A>C	p.Glu1345Asp	p.E1345D	ENST00000344624		1345	gaA/gaC	33/33	0.196285423881052	4	FACETS	0.993	0.832	1	0.497	0.416	0.586	CLONAL	1	FALSE	2	0.196285423881052	4		592	540	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638153	176638153	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	35	652	1	ENST00000439151.2:c.2753A>T	p.His918Leu	p.H918L	ENST00000439151	NM_022455.4	918	cAt/cTt	5/23	0.196285423881052	1	FACETS	0.617	0.505	0.744	0.617	0.505	0.744	SUBCLONAL	1	FALSE	0	0.196285423881052	1		653	521	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317915	8317915	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs748481193	NA	P-0023406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	16	476	0	ENST00000356435.5:c.5698G>T	p.Ala1900Ser	p.A1900S	ENST00000356435		1900	Gca/Tca	35/35	0.138433902862123	1	FACETS	0.459	0.339	0.604	0.459	0.339	0.604	SUBCLONAL	1	FALSE	0	0.196285423881052	1		476	320	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139438556	139438556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0023406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	48	630	1	ENST00000277541.6:c.62-2A>G		p.X21_splice	ENST00000277541	NM_017617.3	21			1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	FALSE	1	0.196285423881052	2		631	428	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874439	76874439	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	17	404	0	ENST00000373344.5:c.5283G>T	p.Met1761Ile	p.M1761I	ENST00000373344	NM_000489.3	1761	atG/atT	21/35	0.196285423881052	1	FACETS	0.562	0.419	0.731	0.562	0.419	0.731	SUBCLONAL	1	FALSE	0	0.196285423881052	1		404	278	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442735	99442735	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	27	616	0	ENST00000268035.6:c.1132A>T	p.Met378Leu	p.M378L	ENST00000268035	NM_000875.3	378	Atg/Ttg	5/21	1	2	FACETS	0.665	0.528	0.821	0.665	0.528	0.821	SUBCLONAL	1	FALSE	1	0.196285423881052	2		616	414	SUCCESS
ATR	545	MSKCC	GRCh37	3	142255021	142255021	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	21	373	0	ENST00000350721.4:c.3748C>T	p.His1250Tyr	p.H1250Y	ENST00000350721	NM_001184.3	1250	Cat/Tat	20/47	1	2	FACETS	0.581	0.447	0.738	0.581	0.447	0.738	SUBCLONAL	1	FALSE	1	0.196285423881052	2		373	368	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509979	187509979	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	26	452	0	ENST00000441802.2:c.13534T>G	p.Cys4512Gly	p.C4512G	ENST00000441802	NM_005245.3	4512	Tgt/Ggt	27/27	1	2	FACETS	0.666	0.527	0.825	0.666	0.527	0.825	SUBCLONAL	1	FALSE	1	0.196285423881052	2		452	398	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55260458	55260458	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0023406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	49	590	0	ENST00000275493.2:c.2626-1G>A		p.X876_splice	ENST00000275493	NM_005228.3	876			1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	FALSE	1	0.196285423881052	2		590	463	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921475	39921475	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs774520249	NA	P-0023406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	28	702	0	ENST00000378444.4:c.4345A>G	p.Met1449Val	p.M1449V	ENST00000378444	NM_001123385.1	1449	Atg/Gtg	10/15	NA	2	FACETS	0.66	0.527	0.813			1	INDETERMINATE	1	FALSE	NA	0.196285423881052	2		702	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578494	7578494	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs786203064	NA	P-0023406-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	74	778	0	ENST00000269305.4:c.436T>G	p.Trp146Gly	p.W146G	ENST00000269305	NM_001126112.2	146	Tgg/Ggg	5/11	1	2	FACETS	1	0.918	1	1	0.983	1	CLONAL	2	TRUE	1	0.131292620465203	2		778	531	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18496263	18496263	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023406-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	41	411	0	ENST00000266497.5:c.1402del	p.Tyr468IlefsTer11	p.Y468Ifs*11	ENST00000266497		466	aaT/aa	9/31	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.131292620465203	2		411	447	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001930	29001930	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023406-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	38	636	1	ENST00000282397.4:c.1235C>A	p.Ser412Ter	p.S412*	ENST00000282397	NM_002019.4	412	tCa/tAa	9/30	0.131292620465203	3	FACETS	1	0.938	1	0.662	0.547	0.79	CLONAL	1	TRUE	1	0.131292620465203	3		637	466	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144823	11144823	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023406-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	59	550	0	ENST00000358026.2:c.3898G>T	p.Glu1300Ter	p.E1300*	ENST00000358026	NM_001128849.1	1300	Gag/Tag	28/36	1	2	FACETS	1	0.927	1	1	0.98	1	CLONAL	2	TRUE	1	0.131292620465203	2		550	403	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391052	89391052	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023406-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	31	651	0	ENST00000336596.2:c.1118G>T	p.Cys373Phe	p.C373F	ENST00000336596	NM_005233.5	373	tGt/tTt	5/17	1	2	FACETS	0.996	0.805	1	0.996	0.805	1	CLONAL	1	TRUE	1	0.131292620465203	2		651	474	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31401629	31401629	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023406-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	35	592	0	ENST00000344624.3:c.4035A>C	p.Glu1345Asp	p.E1345D	ENST00000344624		1345	gaA/gaC	33/33	0.131292620465203	4	FACETS	1	0.926	1	0.638	0.522	0.767	CLONAL	1	TRUE	2	0.131292620465203	4		592	473	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638153	176638153	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023406-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	73	652	1	ENST00000439151.2:c.2753A>T	p.His918Leu	p.H918L	ENST00000439151	NM_022455.4	918	cAt/cTt	5/23	1	2	FACETS	1	0.924	1	1	0.983	1	CLONAL	2	TRUE	1	0.131292620465203	2		653	517	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317915	8317915	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs748481193	NA	P-0023406-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	34	476	0	ENST00000356435.5:c.5698G>T	p.Ala1900Ser	p.A1900S	ENST00000356435		1900	Gca/Tca	35/35	1	2	FACETS	0.827	0.678	0.994	1	0.954	1	CLONAL	2	TRUE	1	0.131292620465203	2		476	313	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139438556	139438556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0023406-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	44	630	1	ENST00000277541.6:c.62-2A>G		p.X21_splice	ENST00000277541	NM_017617.3	21			1	2	FACETS	0.974	0.82	1	1	0.97	1	CLONAL	2	TRUE	1	0.131292620465203	2		631	344	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874439	76874439	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023406-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	18	404	0	ENST00000373344.5:c.5283G>T	p.Met1761Ile	p.M1761I	ENST00000373344	NM_000489.3	1761	atG/atT	21/35	0.131292620465203	1	FACETS	0.783	0.589	1	0.783	0.589	1	CLONAL	1	TRUE	0	0.131292620465203	1		404	327	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14303226	14303226	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023406-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	22	802	0	ENST00000256196.4:c.449del	p.Lys150ArgfsTer2	p.K150Rfs*2	ENST00000256196		150	aAg/ag	5/6	1	2	FACETS	0.827	0.64	1	0.827	0.64	1	CLONAL	1	TRUE	1	0.131292620465203	2		802	405	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14303231	14303231	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023406-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	20	786	0	ENST00000256196.4:c.444G>C	p.Gln148His	p.Q148H	ENST00000256196		148	caG/caC	5/6	1	2	FACETS	0.765	0.584	0.978	0.765	0.584	0.978	CLONAL	1	TRUE	1	0.131292620465203	2		786	398	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715690	30715690	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023406-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	26	436	0	ENST00000295754.5:c.1348A>T	p.Met450Leu	p.M450L	ENST00000295754	NM_003242.5	450	Atg/Ttg	5/7	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.131292620465203	2		436	272	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390186	89390186	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023406-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	20	397	0	ENST00000336596.2:c.937del	p.Ala313GlnfsTer24	p.A313Qfs*24	ENST00000336596	NM_005233.5	312	cGg/cg	4/17	1	2	FACETS	0.856	0.654	1	0.856	0.654	1	CLONAL	1	TRUE	1	0.131292620465203	2		397	356	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293802	1293802	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023406-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	40	897	0	ENST00000310581.5:c.1199A>C	p.His400Pro	p.H400P	ENST00000310581	NM_198253.2	400	cAc/cCc	2/16	0.131292620465203	4	FACETS	1	0.939	1	0.655	0.544	0.779	CLONAL	1	TRUE	2	0.131292620465203	4		897	526	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683585	162683585	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023406-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	19	542	0	ENST00000366898.1:c.384G>T	p.Arg128Ser	p.R128S	ENST00000366898	NM_004562.2	128	agG/agT	3/12	1	2	FACETS	0.768	0.582	0.987	0.768	0.582	0.987	CLONAL	1	TRUE	1	0.131292620465203	2		542	377	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946123	13946123	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023406-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	38	608	3	ENST00000405192.2:c.973C>A	p.Pro325Thr	p.P325T	ENST00000405192	NM_001163147.1	325	Cct/Act	10/12	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.131292620465203	2		611	397	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729259	41729259	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs894989688	NA	P-0023406-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	21	415	0	ENST00000242208.4:c.1270G>T	p.Gly424Trp	p.G424W	ENST00000242208	NM_002192.2	424	Ggg/Tgg	3/3	1	2	FACETS	1	0.81	1	1	0.81	1	CLONAL	1	TRUE	1	0.131292620465203	2		415	302	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	334	545	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.93179116853142	2		545	717	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936093	178936093	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913275	NA	P-0023407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	270	637	1	ENST00000263967.3:c.1635G>T	p.Glu545Asp	p.E545D	ENST00000263967	NM_006218.2	545	gaG/gaT	10/21	0.515381762030461	4	FACETS	1	0.993	1	0.491	0.463	0.52	INDETERMINATE	1	TRUE	1	0.93179116853142	4		638	760	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215595164	215595164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3738888	NA	P-0023407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	98	620	0	ENST00000260947.4:c.1972C>T	p.Arg658Cys	p.R658C	ENST00000260947	NM_000465.2	658	Cgc/Tgc	10/11	1	2	FACETS	0.392	0.35	0.435	0.392	0.35	0.435	SUBCLONAL	1	TRUE	1	0.93179116853142	2		620	537	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039570	180039570	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1185976621	NA	P-0023407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	319	895	1	ENST00000261937.6:c.3473C>T	p.Ala1158Val	p.A1158V	ENST00000261937	NM_182925.4	1158	gCg/gTg	26/30	0.215325231736246	1	FACETS	0.469	0.445	0.493	0.469	0.445	0.493	INDETERMINATE	1	TRUE	0	0.93179116853142	1		896	780	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0023408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	246	645	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.549312401903362	4	FACETS	0.836	0.789	0.884	1	0.991	1	CLONAL	3	TRUE	2	0.549312401903362	4		645	553	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602340	10602340	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	230	807	0	ENST00000171111.5:c.1238G>T	p.Arg413Leu	p.R413L	ENST00000171111	NM_203500.1	413	cGt/cTt	3/6	0.549312401903362	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.549312401903362	2		807	356	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913343	28913343	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	213	762	2	ENST00000282397.4:c.2450C>A	p.Ala817Asp	p.A817D	ENST00000282397	NM_002019.4	817	gCc/gAc	17/30	0.530134058298042	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.549312401903362	3		764	435	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858691	9858691	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1555482933	NA	P-0023408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	76	518	0	ENST00000330684.3:c.2710A>T	p.Ile904Phe	p.I904F	ENST00000330684	NM_001134407.1	904	Att/Ttt	13/13	0.542279477112184	5	FACETS	0.99	0.87	1	0.247	0.217	0.28	CLONAL	1	TRUE	1	0.549312401903362	5		518	510	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1206992	1206993	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1568689930	NA	P-0023408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	201	628	0	ENST00000326873.7:c.82dup	p.Arg28ProfsTer135	p.R28Pfs*135	ENST00000326873	NM_000455.4	27	cac/caCc	1/10	0.549312401903362	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.549312401903362	2		628	336	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72897422	72897422	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1396485911	NA	P-0023408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	95	456	0	ENST00000325599.8:c.70G>T	p.Ala24Ser	p.A24S	ENST00000325599	NM_018130.2	24	Gcc/Tcc	1/11	0.549312401903362	3	FACETS	1	0.974	1	0.632	0.568	0.699	CLONAL	1	TRUE	1	0.549312401903362	3		456	349	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565934	55566106	+	splice_donor_variant,intron_variant	Splice_Site	DEL	TGAGTGAATCGCTTCATTCTTCTCATGTTCTGTCTCTGTGGGAGATGATAAGTTTTCTCTTTCAGAAGAGTCTGTCCTGAAACTGCCTCGACTAGTGCGTCTGTCAGAGGTGGATTGTCTGGGAGAGTGTTGGGATTGCATATTTCCCCCTTTCATACCTCCACATGGAGATA	TGAGTGAATCGCTTCATTCTTCTCATGTTCTGTCTCTGTGGGAGATGATAAGTTTTCTCTTTCAGAAGAGTCTGTCCTGAAACTGCCTCGACTAGTGCGTCTGTCAGAGGTGGATTGTCTGGGAGAGTGTTGGGATTGCATATTTCCCCCTTTCATACCTCCACATGGAGATA	-	novel	NA	P-0023408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	47	335	0	ENST00000288135.5:c.756+3_756+175del		p.X252_splice	ENST00000288135	NM_000222.2	252			0.508668621667507	3	FACETS	0.872	0.742	1	0.436	0.371	0.507	CLONAL	1	TRUE	1	0.549312401903362	3		335	250	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356416	66356416	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	75	407	0	ENST00000273854.3:c.1081C>A	p.Pro361Thr	p.P361T	ENST00000273854	NM_004439.5	361	Cct/Act	5/18	0.513382742954754	4	FACETS	1	0.94	1			1	CLONAL	1	TRUE	NA	0.549312401903362	4		407	382	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131895058	131895058	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	143	363	0	ENST00000265335.6:c.212A>T	p.Lys71Met	p.K71M	ENST00000265335		71	aAg/aTg	2/25	0.52003272734063	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.549312401903362	4		363	367	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700323	117700323	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0023408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	57	373	0	ENST00000368508.3:c.2497-1G>A		p.X833_splice	ENST00000368508	NM_002944.2	833			1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.549312401903362	2		373	204	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243968	53243968	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1556850832	NA	P-0023408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	153	913	0	ENST00000375401.3:c.1025G>T	p.Cys342Phe	p.C342F	ENST00000375401	NM_004187.3	342	tGt/tTt	8/26	0.333417740923987	3	FACETS	1	0.986	1	0.445	0.409	0.482	CLONAL	1	TRUE	0	0.549312401903362	3		913	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0023409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	484	879	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.684930522610286	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.685118757610994	2		881	645	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524464	187524464	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs74511500	NA	P-0023409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	63	721	0	ENST00000441802.2:c.11216C>T	p.Ala3739Val	p.A3739V	ENST00000441802	NM_005245.3	3739	gCg/gTg	19/27	0.679412221065924	2	FACETS	0.325	0.281	0.373	0.162	0.14	0.187	SUBCLONAL	1	TRUE	0	0.685118757610994	2		721	566	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143044	30143044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	212	963	1	ENST00000389048.3:c.482C>T	p.Ala161Val	p.A161V	ENST00000389048	NM_004304.4	161	gCg/gTg	1/29	0.685118757610994	3	FACETS	1	0.953	1	0.515	0.479	0.552	CLONAL	1	TRUE	1	0.685118757610994	3		964	807	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546105	41546105	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757344870	NA	P-0023409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	169	554	0	ENST00000263253.7:c.2720C>T	p.Ala907Val	p.A907V	ENST00000263253	NM_001429.3	907	gCt/gTt	14/31	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.685118757610994	2		554	479	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	495101	495101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201821956	NA	P-0023409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	175	627	1	ENST00000399788.2:c.205C>T	p.Arg69Cys	p.R69C	ENST00000399788	NM_001042603.1	69	Cgt/Tgt	2/28	0.232271079506472	3	FACETS	1	0.982	1	0.596	0.552	0.642	INDETERMINATE	1	TRUE	1	0.685118757610994	3		628	575	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38186914	38186914	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	209	744	0	ENST00000317025.8:c.1563A>T	p.Gln521His	p.Q521H	ENST00000317025	NM_023034.1	521	caA/caT	6/24	NA	2	FACETS	0.947	0.884	1			1	INDETERMINATE	1	TRUE	NA	0.685118757610994	2		744	644	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349901	70349901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556337063	NA	P-0023409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	223	479	0	ENST00000374080.3:c.3884G>A	p.Arg1295His	p.R1295H	ENST00000374080		1295	cGt/cAt	28/45	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.685118757610994	1		479	354	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89812996	89812996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	103	757	0	ENST00000389301.3:c.3509C>T	p.Ala1170Val	p.A1170V	ENST00000389301	NM_000135.2	1170	gCt/gTt	35/43	0.246501773764497	3	FACETS	0.548	0.489	0.611	0.274	0.244	0.306	SUBCLONAL	1	TRUE	1	0.37519413667407	3		757	1190	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224674	36224674	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	245	980	0	ENST00000222270.7:c.7060G>T	p.Glu2354Ter	p.E2354*	ENST00000222270	NM_014727.1	2354	Gaa/Taa	30/37	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.37519413667407	2		980	1302	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0023413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	31	757	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.831	1	1	0.831	1	CLONAL	1	TRUE	1	0.12	2		757	501	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121909229	NA	P-0023413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	27	588	1	ENST00000371953.3:c.389G>T	p.Arg130Leu	p.R130L	ENST00000371953	NM_000314.4	130	cGa/cTa	5/9	1	2	FACETS	0.771	0.614	0.948	1	0.937	1	CLONAL	2	TRUE	1	0.12	2		589	292	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879655	37879655	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	25	774	2	ENST00000269571.5:c.2030G>T	p.Arg677Leu	p.R677L	ENST00000269571		677	cGa/cTa	17/27	1	2	FACETS	0.854	0.672	1	0.854	0.672	1	CLONAL	1	TRUE	1	0.12	2		776	488	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527291	187527291	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	29	653	1	ENST00000441802.2:c.10283T>A	p.Ile3428Asn	p.I3428N	ENST00000441802	NM_005245.3	3428	aTc/aAc	17/27	1	2	FACETS	0.88	0.705	1	0.88	0.705	1	CLONAL	1	TRUE	1	0.12	2		654	549	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707585	176707585	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	19	622	0	ENST00000439151.2:c.5642G>A	p.Arg1881Lys	p.R1881K	ENST00000439151	NM_022455.4	1881	aGg/aAg	18/23	1	2	FACETS	0.868	0.658	1	0.868	0.658	1	CLONAL	1	TRUE	1	0.12	2		622	365	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188164	11188164	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587777893	NA	P-0023414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	55	554	0	ENST00000361445.4:c.5930C>A	p.Thr1977Lys	p.T1977K	ENST00000361445	NM_004958.3	1977	aCa/aAa	43/58	1	2	FACETS	0.671	0.574	0.778	0.671	0.574	0.778	SUBCLONAL	1	TRUE	1	0.27	2		554	607	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343540	343540	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	107	862	0	ENST00000262320.3:c.2134C>T	p.Arg712Ter	p.R712*	ENST00000262320	NM_003502.3	712	Cga/Tga	8/11	1	2	FACETS	0.998	0.895	1	0.998	0.895	1	CLONAL	1	TRUE	1	0.27	2		862	794	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163807	32163807	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751250725	NA	P-0023414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	80	677	1	ENST00000375023.3:c.5419G>A	p.Ala1807Thr	p.A1807T	ENST00000375023	NM_004557.3	1807	Gct/Act	30/30	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.27	2		678	573	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0023416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	602	722	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.71593330517501	6	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	3	0.71593330517501	6		722	1326	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0023416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	259	794	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.279380372418545	3	FACETS	0.86	0.805	0.917	0.287	0.268	0.306	INDETERMINATE	1	TRUE	0	0.71593330517501	3		795	1142	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913255	NA	P-0023416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	22	813	0	ENST00000369535.4:c.183A>T	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caT	3/7	0.165139376890222	4	FACETS	0.152	0.117	0.193	0.076	0.058	0.097	INDETERMINATE	1	TRUE	2	0.71593330517501	4		813	695	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1962801	1962801	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772470710	NA	P-0023416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	70	592	1	ENST00000382891.5:c.3295G>A	p.Glu1099Lys	p.E1099K	ENST00000382891	NM_133335.3	1099	Gag/Aag	18/22	0.317921974389854	1	FACETS	0.211	0.184	0.24	0.211	0.184	0.24	INDETERMINATE	1	TRUE	0	0.71593330517501	1		593	595	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808951	1808951	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	149	693	4	ENST00000260795.2:c.2387del	p.Pro796ArgfsTer24	p.P796Rfs*24	ENST00000260795		795	Ccc/cc	17/17	0.409230627554425	4	FACETS	0.846	0.773	0.923			1	INDETERMINATE	1	TRUE	NA	0.71593330517501	4		697	844	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973890	131973890	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373407069	NA	P-0023416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	51	354	0	ENST00000265335.6:c.3593G>A	p.Arg1198Gln	p.R1198Q	ENST00000265335		1198	cGa/cAa	23/25	1	2	FACETS	0.397	0.338	0.461	0.397	0.338	0.461	SUBCLONAL	1	TRUE	1	0.71593330517501	2		354	359	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045951	26045951	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	97	563	0	ENST00000540144.1:c.313T>C	p.Phe105Leu	p.F105L	ENST00000540144	NM_003531.2	105	Ttc/Ctc	1/1	0.602289658463068	6	FACETS	0.602	0.535	0.673	0.201	0.178	0.225	SUBCLONAL	1	TRUE	3	0.71593330517501	6		563	1095	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0023417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	221	983	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.442238206796473	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.433408604068023	2		984	449	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683228	88683228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876658515	NA	P-0023417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	197	508	0	ENST00000372037.3:c.1438C>T	p.Arg480Trp	p.R480W	ENST00000372037	NM_004329.2	480	Cgg/Tgg	12/13	0.442238206796473	2	FACETS	0.927	0.877	0.976	1	0.992	1	CLONAL	3	TRUE	0	0.433408604068023	2		508	327	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256206	16256206	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	112	609	0	ENST00000375759.3:c.3471A>C	p.Glu1157Asp	p.E1157D	ENST00000375759	NM_015001.2	1157	gaA/gaC	11/15	0.314917992880185	4	FACETS	0.793	0.717	0.872	0.793	0.717	0.872	SUBCLONAL	2	TRUE	2	0.433408604068023	4		609	467	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918616	94918616	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	145	658	0	ENST00000536441.1:c.566A>C	p.Glu189Ala	p.E189A	ENST00000536441	NM_144665.3	189	gAa/gCa	5/10	0.391757586931866	4	FACETS	0.985	0.905	1	0.985	0.905	1	CLONAL	2	TRUE	2	0.433408604068023	4		658	487	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240307	41240307	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	93	550	2	ENST00000379561.5:c.43G>A	p.Glu15Lys	p.E15K	ENST00000379561	NM_002015.3	15	Gag/Aag	1/3	0.279373876848711	5	FACETS	0.965	0.865	1	0.643	0.576	0.713	CLONAL	2	TRUE	2	0.433408604068023	5		552	367	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22123587	22123587	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	144	642	1	ENST00000215832.6:c.989A>C	p.Lys330Thr	p.K330T	ENST00000215832	NM_002745.4	330	aAg/aCg	8/9	0.276165736903092	4	FACETS	0.928	0.852	1			1	CLONAL	2	TRUE	NA	0.433408604068023	4		643	513	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630705	187630705	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	162	874	0	ENST00000441802.2:c.277T>G	p.Phe93Val	p.F93V	ENST00000441802	NM_005245.3	93	Ttt/Gtt	2/27	0.430259739252594	3	FACETS	1	0.988	1	0.728	0.67	0.787	CLONAL	1	TRUE	1	0.433408604068023	3		874	625	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250626	26250626	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	97	593	1	ENST00000446824.2:c.208C>T	p.Arg70Cys	p.R70C	ENST00000446824	NM_021018.2	70	Cgt/Tgt	1/1	0.279373876848711	5	FACETS	0.824	0.739	0.914	0.55	0.492	0.61	CLONAL	2	TRUE	2	0.433408604068023	5		594	448	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172984	38172984	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	192	797	0	ENST00000317025.8:c.2065A>C	p.Ser689Arg	p.S689R	ENST00000317025	NM_023034.1	689	Agt/Cgt	11/24	0.391757586931866	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	2	0.433408604068023	4		797	598	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203622	108203623	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0023419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	188	348	1	ENST00000278616.4:c.7925_7926del	p.Arg2642LysfsTer13	p.R2642Kfs*13	ENST00000278616	NM_000051.3	2641	cAG/c	53/63	0.811806573750325	2	FACETS	0.985	0.945	1	0.985	0.945	1	CLONAL	2	TRUE	0	0.812013253532995	2		349	235	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061222	38061230	+	inframe_deletion	In_Frame_Del	DEL	TTCTCGAAC	TTCTCGAAC	-	novel	NA	P-0023419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	1341	664	0	ENST00000250448.2:c.759_767del	p.Met253_Asn256delinsIle	p.M253_N256delinsI	ENST00000250448	NM_004496.3	253	atGTTCGAGAAc/atc	2/2	0.812013253532995	8	FACETS	1	0.991	1			1	CLONAL	6	TRUE	NA	0.812013253532995	8		664	1864	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0023420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	161	954	2	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.370433384041094	2		956	841	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0023420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	129	924	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.370433384041094	1	FACETS	0.876	0.796	0.959	0.876	0.796	0.959	CLONAL	1	TRUE	0	0.370433384041094	1		924	648	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713469	40713469	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528913627	NA	P-0023420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	92	834	5	ENST00000373198.4:c.4046G>A	p.Arg1349His	p.R1349H	ENST00000373198	NM_133170.3	1349	cGt/cAt	30/32	1	2	FACETS	0.768	0.683	0.858	0.768	0.683	0.858	SUBCLONAL	1	TRUE	1	0.370433384041094	2		839	647	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	166	773	0	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.370433384041094	2		773	840	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473779	67473779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906850	NA	P-0023420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	200	732	1	ENST00000327367.4:c.859C>T	p.Arg287Trp	p.R287W	ENST00000327367	NM_005902.3	287	Cgg/Tgg	6/9	0.370433384041094	2	FACETS	0.966	0.902	1	0.966	0.902	1	CLONAL	2	TRUE	0	0.370433384041094	2		733	559	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119762	70119763	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0023420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	83	771	0	ENST00000245479.2:c.768dup	p.Arg257AlafsTer39	p.R257Afs*39	ENST00000245479	NM_000346.3	255	gag/gaGg	3/3	1	2	FACETS	0.766	0.677	0.861	0.766	0.677	0.861	SUBCLONAL	1	TRUE	1	0.370433384041094	2		771	585	SUCCESS
APC	324	MSKCC	GRCh37	5	112173684	112173685	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs879254110	NA	P-0023420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	74	577	0	ENST00000257430.4:c.2395dup	p.Tyr799LeufsTer4	p.Y799Lfs*4	ENST00000257430	NM_000038.5	798	gat/gaTt	16/16	1	2	FACETS	0.791	0.694	0.895	0.791	0.694	0.895	SUBCLONAL	1	TRUE	1	0.370433384041094	2		577	505	SUCCESS
APC	324	MSKCC	GRCh37	5	112175625	112175625	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	60	470	0	ENST00000257430.4:c.4334del	p.Thr1445LysfsTer28	p.T1445Kfs*28	ENST00000257430	NM_000038.5	1445	aCa/aa	16/16	1	2	FACETS	0.769	0.665	0.882	0.769	0.665	0.882	SUBCLONAL	1	TRUE	1	0.370433384041094	2		470	421	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0023422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	378	609	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.454834389999522	6	FACETS	1	0.986	1			1	CLONAL	3	TRUE	NA	0.454834389999522	6		609	969	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66523985	66523985	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	119	309	0	ENST00000358598.2:c.713G>C	p.Ser238Thr	p.S238T	ENST00000358598	NM_212471.2	238	aGc/aCc	8/11	0.454834389999522	2	FACETS	0.928	0.852	1	0.928	0.852	1	CLONAL	2	TRUE	0	0.454834389999522	2		309	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0023422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	268	782	0	ENST00000269305.4:c.920-2A>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.454834389999522	2	FACETS	0.932	0.881	0.984	0.932	0.881	0.984	CLONAL	2	TRUE	0	0.454834389999522	2		782	632	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436504	110436504	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760629200	NA	P-0023422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	430	1177	1	ENST00000375856.3:c.1897G>A	p.Gly633Arg	p.G633R	ENST00000375856	NM_003749.2	633	Gga/Aga	1/2	0.454834389999522	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.454834389999522	3		1178	1035	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0023423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	123	521	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.465365022445642	2		521	382	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	51	482	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.465365022445642	2		482	162	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0023423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	133	629	1	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	NA	2	FACETS	0.91	0.84	0.982			1	INDETERMINATE	2	TRUE	NA	0.465365022445642	2		630	314	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28599058	28599058	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	23	862	1	ENST00000241453.7:c.2230C>T	p.Gln744Ter	p.Q744*	ENST00000241453	NM_004119.2	744	Cag/Tag	18/24	1	2	FACETS	0.24	0.186	0.302	0.24	0.186	0.302	SUBCLONAL	1	TRUE	1	0.465365022445642	2		863	412	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519496	137519496	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	25	527	0	ENST00000367739.4:c.1142C>T	p.Pro381Leu	p.P381L	ENST00000367739	NM_000416.2	381	cCt/cTt	7/7	1	2	FACETS	0.333	0.262	0.414	0.333	0.262	0.414	SUBCLONAL	1	TRUE	1	0.465365022445642	2		527	323	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132751	152132751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	71	677	0	ENST00000262189.6:c.121C>T	p.Arg41Cys	p.R41C	ENST00000262189	NM_170606.2	41	Cgc/Tgc	1/59	NA	2	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.465365022445642	2		677	265	SUCCESS
ATM	472	MSKCC	GRCh37	11	108214078	108214078	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	16	451	0	ENST00000278616.4:c.8398C>T	p.Gln2800Ter	p.Q2800*	ENST00000278616	NM_000051.3	2800	Cag/Tag	57/63	1	2	FACETS	0.247	0.182	0.325	0.247	0.182	0.325	SUBCLONAL	1	TRUE	1	0.465365022445642	2		451	278	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041821	14041821	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	17	686	0	ENST00000311895.7:c.2368C>G	p.Leu790Val	p.L790V	ENST00000311895	NM_005236.2	790	Ctt/Gtt	11/11	1	2	FACETS	0.216	0.16	0.281	0.216	0.16	0.281	SUBCLONAL	1	TRUE	1	0.465365022445642	2		686	339	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041975	14041975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1483270175	NA	P-0023423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	14	456	1	ENST00000311895.7:c.2522C>T	p.Ser841Leu	p.S841L	ENST00000311895	NM_005236.2	841	tCa/tTa	11/11	1	2	FACETS	0.225	0.162	0.302	0.225	0.162	0.302	SUBCLONAL	1	TRUE	1	0.465365022445642	2		457	267	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41489043	41489043	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758786824	NA	P-0023423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	19	687	1	ENST00000263253.7:c.35C>T	p.Ser12Leu	p.S12L	ENST00000263253	NM_001429.3	12	tCa/tTa	1/31	1	2	FACETS	0.245	0.186	0.315	0.245	0.186	0.315	SUBCLONAL	1	TRUE	1	0.465365022445642	2		688	333	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724314	117724314	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	24	713	0	ENST00000368508.3:c.565C>T	p.His189Tyr	p.H189Y	ENST00000368508	NM_002944.2	189	Cat/Tat	6/43	1	2	FACETS	0.285	0.223	0.356	0.285	0.223	0.356	SUBCLONAL	1	TRUE	1	0.465365022445642	2		713	362	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0023424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	119	399	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	0.948	0.865	1	0.948	0.865	1	CLONAL	1	TRUE	1	0.674567771622703	2		399	372	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0023424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	620	519	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	0.674567771622703	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.674567771622703	2		519	802	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33430296	33430296	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770250516	NA	P-0023424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	342	707	1	ENST00000345365.6:c.715C>T	p.Arg239Trp	p.R239W	ENST00000345365	NM_002878.3	239	Cgg/Tgg	8/10	1	2	FACETS	0.99	0.939	1	0.99	0.939	1	CLONAL	1	TRUE	1	0.674567771622703	2		708	1024	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24133981	24133981	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0023424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	301	467	0	ENST00000263121.7:c.132C>G	p.Tyr44Ter	p.Y44*	ENST00000263121	NM_003073.3	44	taC/taG	2/9	0.674567771622703	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.674567771622703	2		467	403	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0023425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	332	399	0				ENST00000310581	NM_198253.2	-/1132			0.626982747938498	4	FACETS	0.992	0.95	1	0.992	0.95	1	CLONAL	3	TRUE	1	0.626465555012721	4		399	579	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0023425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	50	722	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.626982747938498	3	FACETS	1	0.952	1	0.624	0.539	0.714	CLONAL	1	TRUE	1	0.626465555012721	3		722	168	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087944	27087944	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0023425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	267	823	0	ENST00000324856.7:c.2231C>G	p.Ser744Ter	p.S744*	ENST00000324856	NM_006015.4	744	tCa/tGa	6/20	0.486124696913032	3	FACETS	0.925	0.875	0.976			1	CLONAL	2	TRUE	NA	0.626465555012721	3		823	605	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0023425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	298	885	3	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.602481028616875	2	FACETS	0.935	0.893	0.976	0.935	0.893	0.976	CLONAL	2	TRUE	0	0.626465555012721	2		888	509	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248872	133248872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	156	913	0	ENST00000320574.5:c.1723G>A	p.Glu575Lys	p.E575K	ENST00000320574	NM_006231.2	575	Gag/Aag	16/49	NA	2	FACETS	0.98	0.904	1			1	INDETERMINATE	1	TRUE	NA	0.626465555012721	2		913	508	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120411	94120411	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs532369845	NA	P-0023425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	129	474	0	ENST00000369303.4:c.640A>G	p.Ile214Val	p.I214V	ENST00000369303	NM_004440.3	214	Atc/Gtc	3/17	0.626465555012721	2	FACETS	0.945	0.881	1	0.945	0.881	1	CLONAL	2	TRUE	0	0.626465555012721	2		474	218	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087473	27087473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	331	977	0	ENST00000324856.7:c.2047C>T	p.Pro683Ser	p.P683S	ENST00000324856	NM_006015.4	683	Cct/Tct	5/20	0.486124696913032	3	FACETS	0.998	0.951	1			1	CLONAL	2	TRUE	NA	0.626465555012721	3		977	695	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920781	100920781	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	31	609	0	ENST00000325455.5:c.2367G>A	p.Met789Ile	p.M789I	ENST00000325455	NM_001202474.3	789	atG/atA	6/8	0.543571617375976	4	FACETS	0.861	0.703	1	0.43	0.351	0.518	CLONAL	1	TRUE	2	0.626465555012721	4		609	187	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896954	28896954	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	133	698	0	ENST00000282397.4:c.2926del	p.Ser976ValfsTer2	p.S976Vfs*2	ENST00000282397	NM_002019.4	976	Agt/gt	21/30	0.626982747938498	2	FACETS	1	0.961	1	0.54	0.495	0.586	CLONAL	1	TRUE	0	0.626465555012721	2		698	393	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913428	28913428	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	168	573	0	ENST00000282397.4:c.2365G>C	p.Glu789Gln	p.E789Q	ENST00000282397	NM_002019.4	789	Gaa/Caa	17/30	0.626982747938498	2	FACETS	0.934	0.879	0.989	0.934	0.879	0.989	CLONAL	2	TRUE	0	0.626465555012721	2		573	287	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807978	3807978	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	449	827	0	ENST00000262367.5:c.3441C>A	p.Tyr1147Ter	p.Y1147*	ENST00000262367	NM_004380.2	1147	taC/taA	18/31	0.626982747938498	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	1	0.626465555012721	4		827	701	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936727	78936727	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0023425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	148	953	0	ENST00000306801.3:c.3810-1G>T		p.X1270_splice	ENST00000306801	NM_020761.2	1270			0.626982747938498	3	FACETS	1	0.957	1	0.533	0.489	0.579	CLONAL	1	TRUE	1	0.626465555012721	3		953	582	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702585	52702585	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	102	826	1	ENST00000394830.3:c.313G>C	p.Glu105Gln	p.E105Q	ENST00000394830	NM_018313.4	105	Gag/Cag	4/30	0.156155577901933	2	FACETS	0.99	0.895	1	0.495	0.447	0.544	INDETERMINATE	1	TRUE	0	0.626465555012721	2		827	329	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652057	36652058	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0023425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	384	944	0	ENST00000244741.5:c.182dup	p.Asp62Ter	p.D62*	ENST00000244741	NM_000389.4	60	gag/gaGg	2/3	0.626465555012721	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.626465555012721	2		944	608	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579575	7579575	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555526795	NA	P-0023427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	226	863	0	ENST00000269305.4:c.112del	p.Gln38LysfsTer6	p.Q38Kfs*6	ENST00000269305	NM_001126112.2	38	Caa/aa	4/11	0.857344209978811	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	0	0.857344209978811	1		863	294	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056320	27056321	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0023427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	156	507	0	ENST00000324856.7:c.1318_1319del	p.Ser440CysfsTer182	p.S440Cfs*182	ENST00000324856	NM_006015.4	439	cAG/c	2/20	1	2	FACETS	0.917	0.849	0.985	0.917	0.849	0.985	CLONAL	1	FALSE	1	0.857344209978811	2		507	397	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440351	52440351	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	219	811	0	ENST00000460680.1:c.701del	p.Val234GlyfsTer15	p.V234Gfs*15	ENST00000460680	NM_004656.3	234	gTg/gg	9/17	0.857344209978811	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	0	0.857344209978811	1		811	280	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390662	139390675	+	frameshift_variant	Frame_Shift_Del	DEL	AGGAAGGGGTGCTC	AGGAAGGGGTGCTC	-	novel	NA	P-0023427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	301	1106	0	ENST00000277541.6:c.7516_7529del	p.Glu2506HisfsTer5	p.E2506Hfs*5	ENST00000277541	NM_017617.3	2506	GAGCACCCCTTCCTc/c	34/34	0.195794711599188	4	FACETS	0.893	0.847	0.94	0.893	0.847	0.94	INDETERMINATE	2	FALSE	2	0.857344209978811	4		1106	730	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820568	44820568	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	214	1007	3	ENST00000377967.4:c.265G>T	p.Gly89Ter	p.G89*	ENST00000377967	NM_021140.2	89	Gga/Tga	3/29	0.59516494130527	1	FACETS	0.546	0.512	0.581	0.546	0.512	0.581	SUBCLONAL	1	FALSE	0	0.857344209978811	1		1010	522	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475061	40475063	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0023440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	39	727	0	ENST00000264657.5:c.1847_1849del	p.Glu616del	p.E616del	ENST00000264657	NM_139276.2	616	gAAGga/gga	20/24	0.325981592824357	1	FACETS	0.291	0.24	0.347	0.291	0.24	0.347	SUBCLONAL	1	TRUE	0	0.325981592824357	1		727	689	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0023440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	89	625	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.325981592824357	5	FACETS	0.836	0.74	0.94	0.279	0.246	0.314	CLONAL	1	TRUE	2	0.325981592824357	5		625	972	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0023440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	134	564	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.325981592824357	5	FACETS	0.797	0.725	0.873	0.531	0.483	0.582	SUBCLONAL	2	TRUE	2	0.325981592824357	5		564	768	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982004	38982004	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	75	600	0	ENST00000357387.3:c.718A>G	p.Thr240Ala	p.T240A	ENST00000357387	NM_152756.3	240	Act/Gct	8/38	0.325981592824357	3	FACETS	0.844	0.74	0.956	0.422	0.37	0.478	CLONAL	1	TRUE	1	0.325981592824357	3		600	634	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056108	26056108	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	29	464	0	ENST00000343677.2:c.549G>C	p.Lys183Asn	p.K183N	ENST00000343677	NM_005319.3	183	aaG/aaC	1/1	0.306905703065205	2	FACETS	0.333	0.267	0.409	0.167	0.133	0.205	SUBCLONAL	1	TRUE	0	0.325981592824357	2		464	534	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046372	69046372	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	39	521	0	ENST00000288368.4:c.3845T>A	p.Leu1282His	p.L1282H	ENST00000288368	NM_024870.2	1282	cTc/cAc	32/40	0.325981592824357	3	FACETS	0.396	0.327	0.473	0.198	0.163	0.237	SUBCLONAL	1	TRUE	1	0.325981592824357	3		521	703	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457102	5457102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	21	356	0	ENST00000381577.3:c.76G>A	p.Asp26Asn	p.D26N	ENST00000381577	NM_014143.3	26	Gac/Aac	3/7	0.162980115420924	2	FACETS	0.366	0.281	0.465	0.183	0.14	0.233	INDETERMINATE	1	TRUE	0	0.325981592824357	2		356	352	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938264	76938264	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	48	668	0	ENST00000373344.5:c.2484G>A	p.Met828Ile	p.M828I	ENST00000373344	NM_000489.3	828	atG/atA	9/35	0.202771466257083	5	FACETS	0.483	0.407	0.568	0.161	0.135	0.19	SUBCLONAL	1	TRUE	2	0.325981592824357	5		668	907	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0023442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	68	721	3	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	0.586	0.509	0.669	0.586	0.509	0.669	SUBCLONAL	1	TRUE	1	0.312920989612654	2		724	742	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0023442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	51	472	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.713	0.607	0.83	0.713	0.607	0.83	SUBCLONAL	1	TRUE	1	0.312920989612654	2		472	457	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070644	67070645	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0023442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	19	191	0	ENST00000412916.2:c.271_272del	p.Glu91SerfsTer24	p.E91Sfs*24	ENST00000412916		90	AGa/a	3/6	0.222370395918401	1	FACETS	0.427	0.324	0.547	0.427	0.324	0.547	SUBCLONAL	1	TRUE	0	0.312920989612654	1		191	240	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573176	41573176	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	64	615	1	ENST00000263253.7:c.5461C>T	p.Arg1821Ter	p.R1821*	ENST00000263253	NM_001429.3	1821	Cga/Tga	31/31	1	2	FACETS	0.531	0.459	0.61	0.531	0.459	0.61	SUBCLONAL	1	TRUE	1	0.312920989612654	2		616	770	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882019	NA	P-0023443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	465	782	0	ENST00000269305.4:c.455del	p.Pro152ArgfsTer18	p.P152Rfs*18	ENST00000269305	NM_001126112.2	152	cCg/cg	5/11	NA	2	FACETS	1	0.966	1			1	INDETERMINATE	2	TRUE	NA	0.554258547688716	2		782	836	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	98	218	0	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	0.554258547688716	3	FACETS	0.929	0.844	1	0.929	0.844	1	CLONAL	2	TRUE	1	0.554258547688716	3		218	243	SUCCESS
APC	324	MSKCC	GRCh37	5	112175096	112175097	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs786203760	NA	P-0023443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	43	191	0	ENST00000257430.4:c.3807_3808del	p.Ile1269MetfsTer6	p.I1269Mfs*6	ENST00000257430	NM_000038.5	1269	ATa/a	16/16	0.554258547688716	3	FACETS	0.865	0.731	1	0.433	0.365	0.506	CLONAL	1	TRUE	1	0.554258547688716	3		191	229	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176710894	176710894	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	53	432	0	ENST00000439151.2:c.6116G>A	p.Arg2039His	p.R2039H	ENST00000439151	NM_022455.4	2039	cGt/cAt	20/23	0.554258547688716	3	FACETS	0.421	0.359	0.49	0.211	0.179	0.245	SUBCLONAL	1	TRUE	1	0.554258547688716	3		432	580	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36208923	36208925	+	start_lost,inframe_deletion	Translation_Start_Site	DEL	GGC	GGC	-	rs898578503	NA	P-0023443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	10	26	0	ENST00000222270.7:c.14_16del	p.Ala5?	p.A5?	ENST00000222270	NM_014727.1	1	atGGCg/atg	1/37	0.554258547688716	4	FACETS	0.61	0.417	0.846	0.203	0.139	0.282	SUBCLONAL	1	TRUE	1	0.554258547688716	4		26	92	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436132	110436132	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1462	224	739	0	ENST00000375856.3:c.2269G>T	p.Asp757Tyr	p.D757Y	ENST00000375856	NM_003749.2	757	Gat/Tat	1/2	0.554258547688716	6	FACETS	1	0.937	1	0.253	0.234	0.272	CLONAL	1	TRUE	2	0.554258547688716	6		739	1686	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643531	38643531	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146702985	NA	P-0023443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	99	504	0	ENST00000299084.4:c.1001G>A	p.Arg334His	p.R334H	ENST00000299084	NM_152594.2	334	cGc/cAc	7/7	0.554258547688716	3	FACETS	0.877	0.786	0.974	0.439	0.393	0.487	CLONAL	1	TRUE	1	0.554258547688716	3		504	520	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117964	70117964	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0023443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	20	241	0	ENST00000245479.2:c.431+1G>T		p.X144_splice	ENST00000245479	NM_000346.3	144			0.554258547688716	2	FACETS	0.293	0.224	0.374	0.147	0.112	0.187	SUBCLONAL	1	TRUE	0	0.554258547688716	2		241	246	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752763	42752763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760204780	NA	P-0023443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1195	92	734	2	ENST00000222329.4:c.1501G>A	p.Ala501Thr	p.A501T	ENST00000222329	NM_006494.2	501	Gct/Act	4/4	0.554258547688716	4	FACETS	0.401	0.355	0.451	0.134	0.118	0.151	SUBCLONAL	1	TRUE	1	0.554258547688716	4		736	1287	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061240	38061240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023443-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	316	803	1	ENST00000250448.2:c.749C>T	p.Ser250Phe	p.S250F	ENST00000250448	NM_004496.3	250	tCc/tTc	2/2	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.751201280297746	2		804	839	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0023443-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	1541	721	3	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.751201280297746	8	FACETS	0.953	0.939	0.968			1	CLONAL	7	TRUE	NA	0.751201280297746	8		724	2000	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835781	68835781	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060501215	NA	P-0023443-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	290	636	2	ENST00000261769.5:c.377del	p.Pro126ArgfsTer89	p.P126Rfs*89	ENST00000261769	NM_004360.3	124	cgC/cg	3/16	0.751201280297746	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.751201280297746	1		638	460	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416404	49416404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023443-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	223	641	2	ENST00000301067.7:c.16307C>T	p.Ala5436Val	p.A5436V	ENST00000301067	NM_003482.3	5436	gCc/gTc	51/54	1	2	FACETS	0.945	0.886	1	0.945	0.886	1	CLONAL	1	TRUE	1	0.751201280297746	2		643	628	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120618	115120618	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023443-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	374	880	0	ENST00000257566.3:c.388A>G	p.Arg130Gly	p.R130G	ENST00000257566	NM_016569.3	130	Agg/Ggg	1/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.751201280297746	2		880	960	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676210	29676212	+	frameshift_variant	Frame_Shift_Ins	INS	ACA	ACA	GAAAAAAACT	novel	NA	P-0023443-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	239	552	0	ENST00000356175.3:c.7199_7201delinsGAAAAAAACT	p.Asn2400ArgfsTer9	p.N2400Rfs*9	ENST00000356175	NM_000267.3	2400	aACAaa/aGAAAAAAACTaa	48/57	0.751201280297746	1	FACETS	0.922	0.874	0.969	0.922	0.874	0.969	CLONAL	1	TRUE	0	0.751201280297746	1		552	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0023444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	213	919	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.793733134341934	1	FACETS	0.955	0.907	1	0.955	0.907	1	CLONAL	1	TRUE	0	0.793733134341934	1		920	339	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	196	896	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.863	0.805	0.923	0.863	0.805	0.923	CLONAL	1	TRUE	1	0.793733134341934	2		898	572	SUCCESS
APC	324	MSKCC	GRCh37	5	112164585	112164585	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398123116	NA	P-0023444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	135	286	0	ENST00000257430.4:c.1659G>A	p.Trp553Ter	p.W553*	ENST00000257430	NM_000038.5	553	tgG/tgA	14/16	0.392584464122843	1	FACETS	0.741	0.687	0.795	0.741	0.687	0.795	INDETERMINATE	1	TRUE	0	0.793733134341934	1		286	277	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	76	373	0	ENST00000257430.4:c.4199C>A	p.Ser1400Ter	p.S1400*	ENST00000257430	NM_000038.5	1400	tCg/tAg	16/16	0.392584464122843	1	FACETS	0.363	0.321	0.408	0.363	0.321	0.408	INDETERMINATE	1	TRUE	0	0.793733134341934	1		373	318	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562286	21562286	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755582869	NA	P-0023444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	530	854	0	ENST00000382592.4:c.1633C>T	p.Arg545Cys	p.R545C	ENST00000382592	NM_014572.2	545	Cgt/Tgt	4/8	0.793733134341934	3	FACETS	0.98	0.946	1	0.98	0.946	1	CLONAL	2	TRUE	1	0.793733134341934	3		854	952	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260312	16260312	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	83	555	1	ENST00000375759.3:c.7577A>T	p.Asp2526Val	p.D2526V	ENST00000375759	NM_015001.2	2526	gAt/gTt	11/15	0.484454216549963	1	FACETS	0.334	0.296	0.373	0.334	0.296	0.373	SUBCLONAL	1	TRUE	0	0.793733134341934	1		556	378	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843643	156843643	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	130	924	1	ENST00000524377.1:c.1069G>A	p.Gly357Ser	p.G357S	ENST00000524377	NM_002529.3	357	Ggc/Agc	8/17	0.421158027258243	1	FACETS	0.38	0.346	0.415	0.38	0.346	0.415	INDETERMINATE	1	TRUE	0	0.793733134341934	1		925	520	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920424	114920437	+	protein_altering_variant	In_Frame_Del	DEL	ACAGACTTTATGGT	ACAGACTTTATGGT	CG	novel	NA	P-0023444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	246	532	3	ENST00000543371.1:c.1365_1378delinsCG	p.Gln456_Cys460delinsGly	p.Q456_C460delinsG	ENST00000543371	NM_001198531.1	455	cgACAGACTTTATGGTgc/cgCGgc	13/14	0.484454216549963	1	FACETS	0.727	0.688	0.767	0.727	0.688	0.767	SUBCLONAL	1	TRUE	0	0.793733134341934	1		535	514	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729717	41729717	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	81	566	0	ENST00000242208.4:c.812A>C	p.Lys271Thr	p.K271T	ENST00000242208	NM_002192.2	271	aAg/aCg	3/3	1	2	FACETS	0.392	0.346	0.441	0.392	0.346	0.441	SUBCLONAL	1	TRUE	1	0.793733134341934	2		566	521	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69011974	69011974	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	463	824	1	ENST00000288368.4:c.2611A>G	p.Asn871Asp	p.N871D	ENST00000288368	NM_024870.2	871	Aat/Gat	23/40	0.763788147179965	2	FACETS	0.927	0.9	0.953	0.927	0.9	0.953	CLONAL	2	TRUE	0	0.793733134341934	2		825	629	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920436	114920436	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	246	515	0	ENST00000543371.1:c.1377G>C	p.Trp459Cys	p.W459C	ENST00000543371	NM_001198531.1	459	tgG/tgC	13/14	0.484454216549963	1	FACETS	0.751	0.71	0.791	0.751	0.71	0.791	SUBCLONAL	1	TRUE	0	0.793733134341934	1		515	498	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0023445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	174	722	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.409894595492859	3	FACETS	1	0.973	1	0.561	0.516	0.607	CLONAL	1	TRUE	1	0.434896589814549	3		722	869	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0023445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	298	877	1	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.434896589814549	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.434896589814549	1		878	1063	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341230	341230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756690670	NA	P-0023445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	511	796	0	ENST00000262320.3:c.2254G>A	p.Val752Met	p.V752M	ENST00000262320	NM_003502.3	752	Gtg/Atg	9/11	0.409894595492859	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.434896589814549	3		796	1409	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973694	15973694	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	144	501	0	ENST00000268712.3:c.4298del	p.Gly1433GlufsTer6	p.G1433Efs*6	ENST00000268712	NM_006311.3	1433	gGa/ga	31/46	0.434896589814549	1	FACETS	0.925	0.848	1	0.925	0.848	1	CLONAL	1	TRUE	0	0.434896589814549	1		501	560	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868686	37868686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758210687	NA	P-0023445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	181	643	0	ENST00000269571.5:c.1133C>T	p.Pro378Leu	p.P378L	ENST00000269571		378	cCg/cTg	9/27	0.426698869598054	3	FACETS	0.929	0.856	1			1	CLONAL	1	TRUE	NA	0.434896589814549	3		643	1091	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867546	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGC	GGCGGCGGC	-	rs11466445	NA	P-0023447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	27	72	3	ENST00000374994.4:c.70_78del	p.Ala24_Ala26del	p.A24_A26del	ENST00000374994	NM_004612.2	17	ctGGCGGCGGCg/ctg	1/9	0.442848947235246	3	FACETS	0.813	0.664	0.973	0.813	0.664	0.973	CLONAL	2	TRUE	1	0.452534252323468	3		75	90	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249468	153249468	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	207	536	1	ENST00000281708.4:c.1310G>T	p.Gly437Val	p.G437V	ENST00000281708	NM_033632.3	437	gGa/gTa	9/12	0.452534252323468	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.452534252323468	2		537	413	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111122	193111122	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	46	366	0	ENST00000367435.3:c.655G>C	p.Asp219His	p.D219H	ENST00000367435	NM_024529.4	219	Gat/Cat	7/17	0.402805289804182	4	FACETS	0.884	0.748	1	0.442	0.374	0.517	CLONAL	1	TRUE	2	0.452534252323468	4		366	334	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798342	42798342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	136	736	0	ENST00000575354.2:c.4213G>A	p.Glu1405Lys	p.E1405K	ENST00000575354	NM_015125.3	1405	Gag/Aag	18/20	0.402805289804182	4	FACETS	0.927	0.842	1	0.463	0.421	0.508	CLONAL	1	TRUE	2	0.452534252323468	4		736	942	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593585	55593593	+	inframe_deletion	In_Frame_Del	DEL	CCCATGTAT	CCCATGTAT	-	novel	NA	P-0023447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	103	330	0	ENST00000288135.5:c.1651_1659del	p.Pro551_Tyr553del	p.P551_Y553del	ENST00000288135	NM_000222.2	551	CCCATGTAT/-	11/21	0.452534252323468	2	FACETS	0.937	0.854	1	0.937	0.854	1	CLONAL	2	TRUE	0	0.452534252323468	2		330	243	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	51	482	0				ENST00000310581	NM_198253.2	-/1132			0.301224803016624	1	FACETS	0.931	0.834	1	0.931	0.834	1	INDETERMINATE	1	FALSE	0	0.8011163821379	1		482	82	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0023449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	71	401	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.8011163821379	2		401	154	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791260	42791261	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0023449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	89	774	0	ENST00000575354.2:c.320_321del	p.Gly107AlafsTer14	p.G107Afs*14	ENST00000575354	NM_015125.3	107	gGA/g	3/20	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	1	FALSE	NA	0.8011163821379	2		774	182	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417437	139417437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	41	895	1	ENST00000277541.6:c.607C>T	p.Arg203Cys	p.R203C	ENST00000277541	NM_017617.3	203	Cgc/Tgc	4/34	1	2	FACETS	0.228	0.19	0.271	0.228	0.19	0.271	SUBCLONAL	1	FALSE	1	0.8011163821379	2		896	448	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	31	482	0				ENST00000310581	NM_198253.2	-/1132			0.185911837906507	3	FACETS	0.562	0.454	0.685	0.281	0.227	0.343	SUBCLONAL	1	TRUE	1	0.25090412365724	3		482	495	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0023450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	310	724	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.25090412365724	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	0	0.25090412365724	3		726	859	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107180	27107180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1308037041	NA	P-0023450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	136	712	0	ENST00000324856.7:c.6791C>T	p.Ser2264Leu	p.S2264L	ENST00000324856	NM_006015.4	2264	tCa/tTa	20/20	0.187541526023879	2	FACETS	1	0.985	1	0.721	0.656	0.789	CLONAL	1	TRUE	0	0.25090412365724	2		712	752	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101195	27101195	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	141	762	1	ENST00000324856.7:c.4477C>T	p.Gln1493Ter	p.Q1493*	ENST00000324856	NM_006015.4	1493	Cag/Tag	18/20	0.187541526023879	2	FACETS	0.801	0.731	0.874	0.801	0.731	0.874	CLONAL	2	TRUE	0	0.25090412365724	2		763	702	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519874	NA	P-0023450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	49	659	2	ENST00000356142.4:c.85C>A	p.Pro29Thr	p.P29T	ENST00000356142	NM_018890.3	29	Cct/Act	2/7	0.185911837906507	3	FACETS	0.562	0.475	0.659	0.281	0.237	0.33	SUBCLONAL	1	TRUE	1	0.25090412365724	3		661	782	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828180	3828180	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	46	323	2	ENST00000262367.5:c.1945G>T	p.Glu649Ter	p.E649*	ENST00000262367	NM_004380.2	649	Gaa/Taa	10/31	0.185911837906507	3	FACETS	1	0.864	1	0.513	0.433	0.602	CLONAL	1	TRUE	1	0.25090412365724	3		325	402	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434235	49434235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375114492	NA	P-0023450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	100	1067	0	ENST00000301067.7:c.7318G>A	p.Val2440Ile	p.V2440I	ENST00000301067	NM_003482.3	2440	Gtt/Att	31/54	0.185002569575648	3	FACETS	0.827	0.737	0.923	0.276	0.245	0.308	CLONAL	1	TRUE	0	0.25090412365724	3		1067	1085	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101360	27101360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	161	675	0	ENST00000324856.7:c.4642C>T	p.His1548Tyr	p.H1548Y	ENST00000324856	NM_006015.4	1548	Cat/Tat	18/20	0.187541526023879	2	FACETS	0.873	0.802	0.947	0.873	0.802	0.947	CLONAL	2	TRUE	0	0.25090412365724	2		675	735	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981809	201981809	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	58	748	1	ENST00000359651.3:c.520C>T	p.Gln174Ter	p.Q174*	ENST00000359651		174	Cag/Tag	4/8	0.135428503001357	4	FACETS	0.653	0.559	0.755	0.326	0.279	0.378	INDETERMINATE	1	TRUE	2	0.25090412365724	4		749	886	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983105	201983105	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	67	751	0	ENST00000359651.3:c.954G>C	p.Lys318Asn	p.K318N	ENST00000359651		318	aaG/aaC	7/8	0.135428503001357	4	FACETS	0.702	0.609	0.805	0.351	0.304	0.403	INDETERMINATE	1	TRUE	2	0.25090412365724	4		751	951	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274824	123274824	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	256	570	0	ENST00000358487.5:c.1094G>C	p.Arg365Thr	p.R365T	ENST00000358487	NM_000141.4	365	aGa/aCa	9/18	0.25090412365724	4	FACETS	0.886	0.834	0.94	0.886	0.834	0.94	CLONAL	4	TRUE	0	0.25090412365724	4		570	720	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118350916	118350916	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	100	668	0	ENST00000534358.1:c.3597G>C	p.Trp1199Cys	p.W1199C	ENST00000534358	NM_005933.3	1199	tgG/tgC	6/36	0.207378019429491	4	FACETS	1	0.975	1	0.665	0.594	0.74	CLONAL	1	TRUE	2	0.25090412365724	4		668	750	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373813	118373814	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	59	386	0	ENST00000534358.1:c.7210dup	p.Thr2404AsnfsTer21	p.T2404Nfs*21	ENST00000534358	NM_005933.3	2402	-/A	27/36	0.207378019429491	4	FACETS	1	0.921	1	0.552	0.475	0.635	CLONAL	1	TRUE	2	0.25090412365724	4		386	533	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869472	102869472	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	139	568	0	ENST00000307046.8:c.169G>A	p.Glu57Lys	p.E57K	ENST00000307046	NM_001111285.1	57	Gag/Aag	2/4	0.185002569575648	3	FACETS	1	0.953	1	0.709	0.648	0.773	CLONAL	2	TRUE	0	0.25090412365724	3		568	586	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061334	38061334	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	79	774	0	ENST00000250448.2:c.655del	p.Arg219AlafsTer102	p.R219Afs*102	ENST00000250448	NM_004496.3	219	Cgc/gc	2/2	0.185911837906507	3	FACETS	0.854	0.75	0.966	0.427	0.375	0.483	CLONAL	1	TRUE	1	0.25090412365724	3		774	830	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124285	2124285	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	70	829	0	ENST00000219476.3:c.2440G>C	p.Glu814Gln	p.E814Q	ENST00000219476	NM_000548.3	814	Gag/Cag	22/42	0.185911837906507	3	FACETS	0.688	0.598	0.785	0.344	0.299	0.393	SUBCLONAL	1	TRUE	1	0.25090412365724	3		829	913	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804406	46804406	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0023450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	35	481	0	ENST00000290295.7:c.602-1G>C		p.X201_splice	ENST00000290295	NM_006361.5	201			0.135428503001357	4	FACETS	0.699	0.573	0.842	0.35	0.286	0.421	INDETERMINATE	1	TRUE	2	0.25090412365724	4		481	499	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017232	31017232	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0023450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	81	385	0	ENST00000375687.4:c.563C>G	p.Ser188Ter	p.S188*	ENST00000375687	NM_015338.5	188	tCa/tGa	7/13	0.207378019429491	4	FACETS	0.859	0.76	0.965	0.859	0.76	0.965	CLONAL	2	TRUE	2	0.25090412365724	4		385	470	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022987	31022987	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	143	667	0	ENST00000375687.4:c.2472G>C	p.Glu824Asp	p.E824D	ENST00000375687	NM_015338.5	824	gaG/gaC	13/13	0.207378019429491	4	FACETS	0.922	0.842	1	0.922	0.842	1	CLONAL	2	TRUE	2	0.25090412365724	4		667	773	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39713173	39713173	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	106	438	0	ENST00000361337.2:c.579G>C	p.Lys193Asn	p.K193N	ENST00000361337	NM_003286.2	193	aaG/aaC	8/21	0.207378019429491	4	FACETS	0.971	0.874	1	0.971	0.874	1	CLONAL	2	TRUE	2	0.25090412365724	4		438	544	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237701	133237701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	85	881	0	ENST00000320574.5:c.2914G>A	p.Glu972Lys	p.E972K	ENST00000320574	NM_006231.2	972	Gag/Aag	25/49	1	2	FACETS	0.661	0.585	0.741	0.661	0.585	0.741	SUBCLONAL	1	TRUE	1	0.476436053816904	2		881	540	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692790	89692790	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	190	577	0	ENST00000371953.3:c.274G>C	p.Asp92His	p.D92H	ENST00000371953	NM_000314.4	92	Gac/Cac	5/9	0.45279922473871	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.476436053816904	2		577	367	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057519990	NA	P-0023451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	249	796	0	ENST00000269305.4:c.796G>T	p.Gly266Ter	p.G266*	ENST00000269305	NM_001126112.2	266	Gga/Tga	8/11	0.45279922473871	2	FACETS	0.986	0.932	1	0.986	0.932	1	CLONAL	2	TRUE	0	0.476436053816904	2		796	530	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651336	52651336	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	48	896	1	ENST00000394830.3:c.1760T>C	p.Ile587Thr	p.I587T	ENST00000394830	NM_018313.4	587	aTa/aCa	15/30	0.476436053816904	1	FACETS	0.298	0.252	0.349	0.298	0.252	0.349	SUBCLONAL	1	TRUE	0	0.476436053816904	1		897	515	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860097	152860097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201043377	NA	P-0023451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	341	457	0	ENST00000406277.2:c.331C>T	p.Arg111Cys	p.R111C	ENST00000406277	NM_152274.4	111	Cgc/Tgc	5/7	0.443172691378851		FACETS		0.879	0.949				CLONAL	3	TRUE	NA	0.476436053816904	2		457	522	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432432	78432432	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	95	599	0	ENST00000370768.2:c.419G>T	p.Ser140Ile	p.S140I	ENST00000370768	NM_003902.3	140	aGt/aTt	7/20	0.15124324340119	2	FACETS	0.836	0.748	0.929	0.418	0.374	0.465	INDETERMINATE	1	TRUE	0	0.476436053816904	2		599	477	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725095	89725095	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	54	171	0	ENST00000371953.3:c.1078A>T	p.Ser360Cys	p.S360C	ENST00000371953	NM_000314.4	360	Agc/Tgc	9/9	0.45279922473871	2	FACETS	0.986	0.871	1	0.986	0.871	1	CLONAL	2	TRUE	0	0.476436053816904	2		171	115	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441836	49441836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064794026	NA	P-0023451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	152	762	0	ENST00000301067.7:c.4148G>A	p.Cys1383Tyr	p.C1383Y	ENST00000301067	NM_003482.3	1383	tGt/tAt	14/54	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.476436053816904	2		762	519	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443512	49443512	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	68	732	0	ENST00000301067.7:c.3859G>T	p.Glu1287Ter	p.E1287*	ENST00000301067	NM_003482.3	1287	Gag/Tag	11/54	1	2	FACETS	0.593	0.517	0.675	0.593	0.517	0.675	SUBCLONAL	1	TRUE	1	0.476436053816904	2		732	481	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345073	73345073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765260071	NA	P-0023451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	83	669	0	ENST00000377767.4:c.1724C>T	p.Thr575Met	p.T575M	ENST00000377767	NM_014953.3	575	aCg/aTg	13/21	0.47112130664786	2	FACETS	0.673	0.595	0.755	0.336	0.297	0.378	SUBCLONAL	1	TRUE	0	0.476436053816904	2		669	518	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562749	95562749	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	79	595	0	ENST00000393063.1:c.4508A>G	p.Tyr1503Cys	p.Y1503C	ENST00000393063	NM_030621.3	1503	tAc/tGc	24/28	1	2	FACETS	0.825	0.729	0.926	0.825	0.729	0.926	CLONAL	1	TRUE	1	0.476436053816904	2		595	402	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943765	9943765	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	207	670	0	ENST00000330684.3:c.1176G>T	p.Arg392Ser	p.R392S	ENST00000330684	NM_001134407.1	392	agG/agT	5/13	0.476436053816904	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.476436053816904	3		670	525	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308401	30308401	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1244	275	916	0	ENST00000262643.3:c.415C>G	p.Leu139Val	p.L139V	ENST00000262643	NM_001238.2	139	Ctt/Gtt	6/12	0.476436053816904	7	FACETS	0.833	0.779	0.887			1	CLONAL	2	TRUE	NA	0.476436053816904	7		916	1519	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082895	16082895	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	36	308	0	ENST00000281043.3:c.709C>A	p.Pro237Thr	p.P237T	ENST00000281043	NM_005378.4	237	Ccg/Acg	2/3	0.160855098011966	2	FACETS	0.771	0.64	0.914	0.386	0.32	0.457	INDETERMINATE	1	TRUE	0	0.476436053816904	2		308	196	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719573	61719575	+	inframe_deletion	In_Frame_Del	DEL	TTA	TTA	-	novel	NA	P-0023451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	94	872	0	ENST00000401558.2:c.1608_1610del	p.Asn536del	p.N536del	ENST00000401558	NM_003400.3	536	aaTAAa/aaa	15/25	0.160855098011966	2	FACETS	0.629	0.561	0.702	0.315	0.28	0.351	INDETERMINATE	1	TRUE	0	0.476436053816904	2		872	627	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99160436	99160436	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0023451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	75	749	0	ENST00000074304.5:c.915C>G	p.Tyr305Ter	p.Y305*	ENST00000074304	NM_001134224.1	305	taC/taG	11/26	0.160855098011966	2	FACETS	0.627	0.551	0.709	0.314	0.275	0.355	INDETERMINATE	1	TRUE	0	0.476436053816904	2		749	502	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461552	138461552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs530305907	NA	P-0023451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	177	792	1	ENST00000289153.2:c.469G>A	p.Glu157Lys	p.E157K	ENST00000289153	NM_006219.2	157	Gag/Aag	3/22	0.476436053816904	5	FACETS	0.827	0.764	0.893	0.552	0.509	0.596	CLONAL	2	TRUE	2	0.476436053816904	5		793	770	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374921	149374921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	315	917	4	ENST00000360632.3:c.173C>T	p.Ser58Leu	p.S58L	ENST00000360632	NM_015472.4	58	tCg/tTg	2/7	0.476436053816904	5	FACETS	0.891	0.844	0.939	0.891	0.844	0.939	CLONAL	3	TRUE	2	0.476436053816904	5		921	848	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958804	55958804	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	61	884	0	ENST00000263923.4:c.3049G>T	p.Glu1017Ter	p.E1017*	ENST00000263923	NM_002253.2	1017	Gag/Tag	22/30	1	2	FACETS	0.488	0.421	0.56	0.488	0.421	0.56	SUBCLONAL	1	TRUE	1	0.476436053816904	2		884	525	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295245	1295245	+	upstream_gene_variant	5'Flank	SNP	C	C	T	rs937365057	NA	P-0023451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	46	667	0				ENST00000310581	NM_198253.2	-/1132			0.314926131717055	5	FACETS	0.814	0.686	0.953	0.271	0.228	0.318	CLONAL	1	TRUE	2	0.476436053816904	5		667	407	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2949746	2949746	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	90	986	0	ENST00000396946.4:c.3198G>C	p.Lys1066Asn	p.K1066N	ENST00000396946	NM_032415.4	1066	aaG/aaC	24/25	0.476436053816904	3	FACETS	0.637	0.565	0.714	0.319	0.282	0.357	SUBCLONAL	1	TRUE	1	0.476436053816904	3		986	734	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266446	55266446	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	68	778	0	ENST00000275493.2:c.2738A>T	p.Lys913Met	p.K913M	ENST00000275493	NM_005228.3	913	aAg/aTg	23/28	0.476436053816904	3	FACETS	0.614	0.534	0.7	0.307	0.267	0.35	SUBCLONAL	1	TRUE	1	0.476436053816904	3		778	576	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900061	151900061	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	99	848	0	ENST00000262189.6:c.4050A>C	p.Lys1350Asn	p.K1350N	ENST00000262189	NM_170606.2	1350	aaA/aaC	26/59	0.476436053816904	3	FACETS	0.793	0.709	0.882	0.396	0.354	0.441	SUBCLONAL	1	TRUE	1	0.476436053816904	3		848	649	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0023455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	115	976	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.823	0.74	0.911	0.823	0.74	0.911	CLONAL	1	FALSE	1	0.294506874665629	2		976	949	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	94	993	1	ENST00000269305.4:c.503A>T	p.His168Leu	p.H168L	ENST00000269305	NM_001126112.2	168	cAc/cTc	5/11	0.241071730976652	1	FACETS	0.626	0.556	0.701	0.626	0.556	0.701	SUBCLONAL	1	FALSE	0	0.294506874665629	1		994	869	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526145	189526145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	214	877	1	ENST00000264731.3:c.409G>A	p.Asp137Asn	p.D137N	ENST00000264731	NM_003722.4	137	Gac/Aac	4/14	0.199309385882524	2	FACETS	0.832	0.775	0.892	0.832	0.775	0.892	CLONAL	2	FALSE	0	0.294506874665629	2		878	873	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519237	187519237	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	271	895	0	ENST00000441802.2:c.12146G>C	p.Cys4049Ser	p.C4049S	ENST00000441802	NM_005245.3	4049	tGt/tCt	23/27	1	2	FACETS	0.994	0.938	1	0.994	0.938	1	CLONAL	1	TRUE	1	0.758294106958856	2		895	719	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346960	70346960	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	179	716	0	ENST00000374080.3:c.2827C>A	p.Gln943Lys	p.Q943K	ENST00000374080		943	Cag/Aag	20/45	0.758294106958856	3	FACETS	0.867	0.801	0.935	0.433	0.4	0.468	CLONAL	1	TRUE	1	0.758294106958856	3		716	751	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936955	48936955	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	666	510	0	ENST00000267163.4:c.723del	p.Ala242LeufsTer22	p.A242Lfs*22	ENST00000267163	NM_000321.2	241	acA/ac	8/27	0.758294106958856	4	FACETS	0.984	0.965	1	0.984	0.965	1	CLONAL	4	TRUE	0	0.758294106958856	4		510	785	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0023457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	662	882	0	ENST00000269305.4:c.919+1del		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.729825373792145	3	FACETS	0.945	0.924	0.966	0.945	0.924	0.966	CLONAL	3	TRUE	0	0.758294106958856	3		882	849	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395765	45395765	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	235	586	0	ENST00000262160.6:c.369G>C	p.Leu123Phe	p.L123F	ENST00000262160	NM_005901.5	123	ttG/ttC	4/11	0.427180785651469	6	FACETS	0.886	0.828	0.946	0.443	0.414	0.473	INDETERMINATE	2	TRUE	2	0.758294106958856	6		586	880	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233625	233625	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	123	450	0	ENST00000264932.6:c.929G>T	p.Gly310Val	p.G310V	ENST00000264932	NM_004168.2	310	gGa/gTa	8/15	0.736291798039349	5	FACETS	1	0.908	1	0.334	0.302	0.367	CLONAL	1	TRUE	2	0.758294106958856	5		450	692	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637112	176637112	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	281	814	0	ENST00000439151.2:c.1712C>G	p.Ser571Cys	p.S571C	ENST00000439151	NM_022455.4	571	tCt/tGt	5/23	0.758294106958856	2	FACETS	1	0.979	1	0.536	0.506	0.565	CLONAL	1	TRUE	0	0.758294106958856	2		814	692	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046488	69046488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	197	872	1	ENST00000288368.4:c.3961C>T	p.Gln1321Ter	p.Q1321*	ENST00000288368	NM_024870.2	1321	Cag/Tag	32/40	0.758294106958856	3	FACETS	0.777	0.72	0.837	0.389	0.36	0.419	SUBCLONAL	1	TRUE	1	0.758294106958856	3		873	922	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636218	87636218	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	486	711	0	ENST00000277120.3:c.2383C>G	p.Pro795Ala	p.P795A	ENST00000277120		795	Ccc/Gcc	19/19	0.758294106958856	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.758294106958856	2		711	624	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933070	39933071	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0023457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	316	1139	0	ENST00000378444.4:c.1528dup	p.Val510GlyfsTer8	p.V510Gfs*8	ENST00000378444	NM_001123385.1	510	gtg/gGtg	4/15	0.758294106958856	3	FACETS	0.901	0.849	0.954	0.45	0.424	0.477	CLONAL	1	TRUE	1	0.758294106958856	3		1139	1276	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236676	236676	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	199	574	0	ENST00000264932.6:c.1394G>C	p.Arg465Pro	p.R465P	ENST00000264932	NM_004168.2	465	cGg/cCg	10/15	1	2	FACETS	0.991	0.929	1	0.991	0.929	1	CLONAL	1	TRUE	1	0.902542649423506	2		574	445	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149452934	149452999	+	inframe_deletion	In_Frame_Del	DEL	AGGTCCAGTTAAAACCTTGCAGGCCTGGGTAGGCCTCCACCATGACTTTGAGGTTGAGCCCCTCCC	AGGTCCAGTTAAAACCTTGCAGGCCTGGGTAGGCCTCCACCATGACTTTGAGGTTGAGCCCCTCCC	-	novel	NA	P-0023459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	438	1028	0	ENST00000286301.3:c.947_1012del	p.Gly316_Tyr338delinsAsp	p.G316_Y338delinsD	ENST00000286301	NM_005211.3	316	gGGGAGGGGCTCAACCTCAAAGTCATGGTGGAGGCCTACCCAGGCCTGCAAGGTTTTAACTGGACCTac/gac	7/22	0.130004665255872	4	FACETS	0.856	0.819	0.894	0.856	0.819	0.894	INDETERMINATE	2	TRUE	2	0.902542649423506	4		1028	1078	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0023461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	269	724	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.37031743183955	3	FACETS	0.926	0.871	0.982	0.926	0.871	0.982	CLONAL	2	TRUE	1	0.409104998312557	3		726	855	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0023461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	202	722	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.409104998312557	3	FACETS	0.916	0.854	0.981	0.916	0.854	0.981	CLONAL	2	TRUE	1	0.409104998312557	3		722	649	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0023461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	229	761	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	0.409104998312557	3	FACETS	0.938	0.878	0.999	0.938	0.878	0.999	CLONAL	2	TRUE	1	0.409104998312557	3		761	719	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806228	1806228	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868356240	NA	P-0023461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	299	935	1	ENST00000260795.2:c.1247G>A	p.Arg416His	p.R416H	ENST00000260795		416	cGc/cAc	8/17	0.37031743183955	3	FACETS	0.916	0.864	0.969	0.916	0.864	0.969	CLONAL	2	TRUE	1	0.409104998312557	3		936	961	SUCCESS
APC	324	MSKCC	GRCh37	5	112175148	112175148	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	197	369	0	ENST00000257430.4:c.3859del	p.Ile1287Ter	p.I1287*	ENST00000257430	NM_000038.5	1286	gAa/ga	16/16	0.409104998312557	3	FACETS	0.927	0.87	0.984	0.927	0.87	0.984	CLONAL	3	TRUE	0	0.409104998312557	3		369	417	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052633	42052633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	231	730	0	ENST00000219905.7:c.7304G>A	p.Arg2435Gln	p.R2435Q	ENST00000219905	NM_001164273.1	2435	cGg/cAg	20/24	0.37031743183955	3	FACETS	0.81	0.757	0.864	0.81	0.757	0.864	CLONAL	2	TRUE	1	0.409104998312557	3		730	840	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087892	27087907	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCCACCCAGTGGCC	CGGCCACCCAGTGGCC	-	novel	NA	P-0023461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	134	874	3	ENST00000324856.7:c.2179_2194del	p.Arg727SerfsTer10	p.R727Sfs*10	ENST00000324856	NM_006015.4	727	CGGCCACCCAGTGGCCag/ag	6/20	1	2	FACETS	0.791	0.719	0.867	0.791	0.719	0.867	SUBCLONAL	1	TRUE	1	0.409104998312557	2		877	828	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120229	70120230	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGCA	novel	NA	P-0023461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	156	1028	0	ENST00000245479.2:c.1232_1235dup	p.His413AlafsTer166	p.H413Afs*166	ENST00000245479	NM_000346.3	411	cag/cAGCAag	3/3	0.37031743183955	3	FACETS	0.828	0.757	0.903	0.414	0.378	0.452	CLONAL	1	TRUE	1	0.409104998312557	3		1028	1109	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220579	1220579	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0023461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	286	835	0	ENST00000326873.7:c.598del		p.X200_splice	ENST00000326873	NM_000455.4	200			0.304786040582667	4	FACETS	0.92	0.865	0.976	0.92	0.865	0.976	CLONAL	2	TRUE	2	0.409104998312557	4		835	1071	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578277	212578277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	96	936	0	ENST00000342788.4:c.980C>T	p.Thr327Ile	p.T327I	ENST00000342788	NM_005235.2	327	aCt/aTt	8/28	0.397160167579235	4	FACETS	0.788	0.702	0.881	0.263	0.234	0.294	SUBCLONAL	1	TRUE	1	0.409104998312557	4		936	839	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215674254	215674268	+	inframe_deletion	In_Frame_Del	DEL	TCCTCGGCTGCCGGT	TCCTCGGCTGCCGGT	-	rs587781979	NA	P-0023461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	93	834	0	ENST00000260947.4:c.26_40del	p.Asn9_Arg13del	p.N9_R13del	ENST00000260947	NM_000465.2	9	aACCGGCAGCCGAGGAtc/atc	1/11	0.397160167579235	4	FACETS	0.69	0.613	0.774	0.23	0.204	0.258	SUBCLONAL	1	TRUE	1	0.409104998312557	4		834	928	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259664	89259664	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	48	356	0	ENST00000336596.2:c.808T>C	p.Cys270Arg	p.C270R	ENST00000336596	NM_005233.5	270	Tgc/Cgc	3/17	0.409104998312557	3	FACETS	0.738	0.626	0.861	0.369	0.313	0.431	SUBCLONAL	1	TRUE	1	0.409104998312557	3		356	383	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98011444	98011444	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	265	853	0	ENST00000289081.3:c.130T>A	p.Phe44Ile	p.F44I	ENST00000289081	NM_000136.2	44	Ttc/Atc	2/15	0.304786040582667	4	FACETS	0.932	0.875	0.991	0.932	0.875	0.991	CLONAL	2	TRUE	2	0.409104998312557	4		853	979	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624581	21624581	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	88	615	0	ENST00000421138.2:c.1448C>T	p.Ala483Val	p.A483V	ENST00000421138		483	gCa/gTa	14/16	0.490799038710225	1	FACETS	0.754	0.674	0.838	0.754	0.674	0.838	SUBCLONAL	1	TRUE	0	0.51109174779711	1		615	340	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730019	41730019	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	190	794	0	ENST00000242208.4:c.510del	p.Val171SerfsTer27	p.V171Sfs*27	ENST00000242208	NM_002192.2	170	aaA/aa	3/3	1	2	FACETS	0.839	0.776	0.904	0.839	0.776	0.904	CLONAL	1	TRUE	1	0.51109174779711	2		794	886	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971167	21971167	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	163	640	0	ENST00000304494.5:c.191T>G	p.Leu64Arg	p.L64R	ENST00000304494	NM_000077.4	64	cTg/cGg	2/3	1	2	FACETS	0.945	0.87	1	0.945	0.87	1	CLONAL	1	TRUE	1	0.51109174779711	2		640	675	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	93	482	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.872	0.775	0.975	0.872	0.775	0.975	CLONAL	1	TRUE	1	0.287886046787599	2		482	741	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954198	48954198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123331	NA	P-0023463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	47	496	0	ENST00000267163.4:c.1399C>T	p.Arg467Ter	p.R467*	ENST00000267163	NM_000321.2	467	Cga/Tga	15/27	0.232813194127576	2	FACETS	1	0.926	1	0.577	0.49	0.672	CLONAL	1	TRUE	0	0.287886046787599	2		496	283	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533378	29533378	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs878853865	NA	P-0023463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	52	427	0	ENST00000356175.3:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000356175	NM_000267.3	461	Cga/Tga	12/57	0.27775432125915	2	FACETS	0.832	0.717	0.955	0.832	0.717	0.955	CLONAL	2	TRUE	0	0.287886046787599	2		427	217	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs786201057	NA	P-0023463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	242	847	0	ENST00000269305.4:c.374C>G	p.Thr125Arg	p.T125R	ENST00000269305	NM_001126112.2	125	aCg/aGg	4/11	0.27775432125915	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.287886046787599	2		847	813	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961086	55961086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs13129474	NA	P-0023463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	157	1121	0	ENST00000263923.4:c.2854G>A	p.Val952Ile	p.V952I	ENST00000263923	NM_002253.2	952	Gtt/Att	21/30	1	2	FACETS	0.924	0.845	1	0.924	0.845	1	CLONAL	1	TRUE	1	0.287886046787599	2		1121	1180	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105554	30105554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757417278	NA	P-0023463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	199	1194	0	ENST00000331968.5:c.1132G>A	p.Asp378Asn	p.D378N	ENST00000331968	NM_002742.2	378	Gac/Aac	7/18	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.287886046787599	2		1194	1365	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612641	228612641	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1431559822	NA	P-0023463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	180	989	1	ENST00000366696.1:c.386G>A	p.Arg129His	p.R129H	ENST00000366696	NM_003493.2	129	cGc/cAc	1/1	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.287886046787599	2		990	962	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725053	89725058	+	inframe_deletion	In_Frame_Del	DEL	TACTTC	TACTTC	-	novel	NA	P-0023465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	37	360	0	ENST00000371953.3:c.1036_1041del	p.Tyr346_Phe347del	p.Y346_F347del	ENST00000371953	NM_000314.4	346	TACTTC/-	9/9	1	2	FACETS	0.643	0.532	0.766	0.643	0.532	0.766	SUBCLONAL	1	TRUE	1	0.37	2		360	311	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0023466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	26	944	4	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.832	0.657	1	0.832	0.657	1	CLONAL	1	TRUE	1	0.11	2		948	568	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0023466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	41	645	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.11	2		645	688	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0023468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	140	867	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	1	0.311464426827815	2		868	886	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612754	228612754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	106	927	1	ENST00000366696.1:c.273G>A	p.Met91Ile	p.M91I	ENST00000366696	NM_003493.2	91	atG/atA	1/1	0.280866361573897	1	FACETS	0.927	0.833	1	0.927	0.833	1	CLONAL	1	FALSE	0	0.311464426827815	1		928	620	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344809	118344809	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs782226053	NA	P-0023468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	75	564	0	ENST00000534358.1:c.2935A>G	p.Thr979Ala	p.T979A	ENST00000534358	NM_005933.3	979	Act/Gct	3/36	1	2	FACETS	0.917	0.805	1	0.917	0.805	1	CLONAL	1	FALSE	1	0.311464426827815	2		564	525	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17120387	17120387	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	82	700	0	ENST00000285071.4:c.1172T>C	p.Leu391Pro	p.L391P	ENST00000285071	NM_144997.5	391	cTt/cCt	10/14	0.311464426827815	1	FACETS	0.936	0.828	1	0.936	0.828	1	CLONAL	1	FALSE	0	0.311464426827815	1		700	475	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589774	55589774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1368874379	NA	P-0023468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	38	539	0	ENST00000288135.5:c.1256A>G	p.Asp419Gly	p.D419G	ENST00000288135	NM_000222.2	419	gAc/gGc	8/21	0.280866361573897	1	FACETS	0.449	0.371	0.536	0.449	0.371	0.536	SUBCLONAL	1	FALSE	0	0.311464426827815	1		539	459	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974751	21974751	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	67	408	0	ENST00000304494.5:c.76G>T	p.Glu26Ter	p.E26*	ENST00000304494	NM_000077.4	26	Gag/Tag	1/3	0.376380226438478	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.376380226438478	1		408	223	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2220221	2220221	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	78	693	2	ENST00000398665.3:c.2806G>T	p.Gly936Cys	p.G936C	ENST00000398665	NM_032482.2	936	Ggc/Tgc	23/28	0.198773874149411	2	FACETS	1	0.909	1	0.517	0.456	0.581	INDETERMINATE	1	TRUE	0	0.376380226438478	2		695	401	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523275	9523275	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	78	728	3	ENST00000353224.5:c.1962G>T	p.Arg654Ser	p.R654S	ENST00000353224	NM_177990.2	654	agG/agT	9/10	1	2	FACETS	0.968	0.855	1	0.968	0.855	1	CLONAL	1	TRUE	1	0.376380226438478	2		731	428	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1555525367	NA	P-0023469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	73	688	0	ENST00000269305.4:c.783-1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.216965361380082	3	FACETS	0.993	0.872	1	0.497	0.436	0.562	INDETERMINATE	1	TRUE	1	0.376380226438478	3		688	464	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733453	85733453	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	102	699	0	ENST00000370580.1:c.559T>G	p.Phe187Val	p.F187V	ENST00000370580	NM_003921.4	187	Ttc/Gtc	3/3	0.187381096339532	2	FACETS	1	0.947	1	0.543	0.488	0.601	INDETERMINATE	1	TRUE	0	0.376380226438478	2		699	499	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220509	133220509	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs767191767	NA	P-0023469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	51	817	0	ENST00000320574.5:c.4204G>T	p.Val1402Leu	p.V1402L	ENST00000320574	NM_006231.2	1402	Gtg/Ttg	33/49	0.277640415723861	1	FACETS	0.539	0.459	0.627	0.539	0.459	0.627	SUBCLONAL	1	TRUE	0	0.376380226438478	1		817	408	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576101	88576101	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs759925027	NA	P-0023469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	29	832	0	ENST00000360948.2:c.1572C>G	p.His524Gln	p.H524Q	ENST00000360948	NM_001012338.2	524	caC/caG	13/19	0.337071625295426	0	FACETS	0.265	0.212	0.324			1	SUBCLONAL	1	TRUE	0	0.376380226438478	0		832	363	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969983	81969983	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	14	422	0	ENST00000359376.3:c.3052G>T	p.Asp1018Tyr	p.D1018Y	ENST00000359376	NM_002661.3	1018	Gat/Tat	27/33	0.276392444472261	0	FACETS	0.205	0.148	0.274			1	SUBCLONAL	1	TRUE	0	0.376380226438478	0		422	226	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40880928	40880928	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	38	858	3	ENST00000428826.2:c.32G>T	p.Cys11Phe	p.C11F	ENST00000428826		11	tGt/tTt	3/21	0.216965361380082	3	FACETS	0.322	0.265	0.386	0.161	0.132	0.193	INDETERMINATE	1	TRUE	1	0.376380226438478	3		861	745	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219910	36219910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	57	883	1	ENST00000222270.7:c.4712C>T	p.Ala1571Val	p.A1571V	ENST00000222270	NM_014727.1	1571	gCc/gTc	21/37	0.244853448533559	3	FACETS	0.529	0.453	0.612			1	SUBCLONAL	1	TRUE	NA	0.376380226438478	3		884	680	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221012	36221012	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	43	760	0	ENST00000222270.7:c.5062C>G	p.Leu1688Val	p.L1688V	ENST00000222270	NM_014727.1	1688	Ctc/Gtc	23/37	0.244853448533559	3	FACETS	0.426	0.356	0.505			1	SUBCLONAL	1	TRUE	NA	0.376380226438478	3		760	637	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432688	29432688	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	664	35	0	ENST00000389048.3:c.3800A>C	p.Lys1267Thr	p.K1267T	ENST00000389048	NM_004304.4	1267	aAg/aCg	25/29	0.376380226438478	1	FACETS	0.908	0.882	0.933	1	0.998	1	CLONAL	3	TRUE	0	0.376380226438478	1		35	1052	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100937	41100937	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	680	78	0	ENST00000373198.4:c.1419C>A	p.Ser473Arg	p.S473R	ENST00000373198	NM_133170.3	473	agC/agA	8/32	0.337071625295426	0	FACETS	0.806	0.786	0.825			1	CLONAL	3	TRUE	0	0.376380226438478	0		78	932	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130475	29130475	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	74	870	0	ENST00000328354.6:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000328354	NM_007194.3	79	Gaa/Caa	2/15	0.170458293154935	4	FACETS	0.873	0.764	0.99	0.436	0.382	0.495	INDETERMINATE	1	TRUE	2	0.376380226438478	4		870	620	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007302	143007302	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	33	706	0	ENST00000262992.4:c.2482G>C	p.Ala828Pro	p.A828P	ENST00000262992	NM_001101669.1	828	Gca/Cca	22/24	0.339707805158472	1	FACETS	0.373	0.303	0.45	0.373	0.303	0.45	SUBCLONAL	1	TRUE	0	0.376380226438478	1		706	382	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953019	2953019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750407488	NA	P-0023469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	108	851	3	ENST00000396946.4:c.2921G>A	p.Arg974His	p.R974H	ENST00000396946	NM_032415.4	974	cGc/cAc	22/25	0.236387771109505	1	FACETS	0.955	0.861	1	0.955	0.861	1	CLONAL	1	TRUE	0	0.376380226438478	1		854	488	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522611	106522611	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	56	747	0	ENST00000359195.3:c.2588G>T	p.Cys863Phe	p.C863F	ENST00000359195	NM_002649.2	863	tGc/tTc	7/11	1	2	FACETS	0.585	0.501	0.676	0.585	0.501	0.676	SUBCLONAL	1	TRUE	1	0.376380226438478	2		747	509	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499651	8499651	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	503	16	0	ENST00000356435.5:c.2318C>A	p.Ala773Glu	p.A773E	ENST00000356435		773	gCa/gAa	14/35	0.376380226438478	1	FACETS	0.903	0.873	0.932	1	0.998	1	CLONAL	3	TRUE	0	0.376380226438478	1		16	801	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250074	110250074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	43	755	2	ENST00000374672.4:c.601G>A	p.Ala201Thr	p.A201T	ENST00000374672	NM_004235.4	201	Gcc/Acc	3/5	0.198773874149411	2	FACETS	0.621	0.521	0.731	0.31	0.26	0.366	INDETERMINATE	1	TRUE	0	0.376380226438478	2		757	368	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545740	106545740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	200	916	2	ENST00000359195.3:c.3217G>A	p.Glu1073Lys	p.E1073K	ENST00000359195	NM_002649.2	1073	Gaa/Aaa	11/11	0.492234772515669	2	FACETS	0.958	0.9	1	0.958	0.9	1	CLONAL	2	TRUE	0	0.492234772515669	2		918	424	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499649	149499747	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATGCTCTCCGGAGCCATCCACTTTAAAGGCAAAAAGGTCTGTAGGGAGGTCAGGACAGGTGCTGAGTGCAAGGAAGGACCTCAGCCCCACTCTGCACCT	ATGCTCTCCGGAGCCATCCACTTTAAAGGCAAAAAGGTCTGTAGGGAGGTCAGGACAGGTGCTGAGTGCAAGGAAGGACCTCAGCCCCACTCTGCACCT	-	novel	NA	P-0023470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	130	746	0	ENST00000261799.4:c.2587-61_2624del		p.X863_splice	ENST00000261799	NM_002609.3	863		19/23	0.492234772515669	3	FACETS	1	0.986	1	0.735	0.671	0.8	CLONAL	1	TRUE	1	0.492234772515669	3		746	448	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937302	76937387	+	frameshift_variant	Frame_Shift_Del	DEL	ATTTCCTTAGTATTTCTCTTTGAACTTAAATTTCTTCTTTCCCTCAATTCTATTCTTTTCAGTCTCTTATCAGAAGAGTTACAACC	ATTTCCTTAGTATTTCTCTTTGAACTTAAATTTCTTCTTTCCCTCAATTCTATTCTTTTCAGTCTCTTATCAGAAGAGTTACAACC	-	novel	NA	P-0023470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	213	414	0	ENST00000373344.5:c.3361_3446del	p.Gly1121ThrfsTer8	p.G1121Tfs*8	ENST00000373344	NM_000489.3	1121	GGTTGTAACTCTTCTGATAAGAGACTGAAAAGAATAGAATTGAGGGAAAGAAGAAATTTAAGTTCAAAGAGAAATACTAAGGAAATa/a	9/35	0.478429728868197	2	FACETS	0.848	0.806	0.89			1	CLONAL	3	TRUE	NA	0.492234772515669	2		414	340	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0023471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	149	770	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.158634187827649	2	FACETS	0.97	0.886	1	0.97	0.886	1	CLONAL	2	FALSE	0	0.158634187827649	2		770	968	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579314	7579314	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs1057520003	NA	P-0023471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	55	730	0	ENST00000269305.4:c.373A>C	p.Thr125Pro	p.T125P	ENST00000269305	NM_001126112.2	125	Acg/Ccg	4/11	1	2	FACETS	0.993	0.849	1	0.993	0.849	1	CLONAL	1	FALSE	1	0.158634187827649	2		730	698	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220394	1220395	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0023471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	47	895	2	ENST00000326873.7:c.487_488delinsTT	p.Gly163Phe	p.G163F	ENST00000326873	NM_000455.4	163	GGc/TTc	4/10	1	2	FACETS	0.742	0.624	0.872	0.742	0.624	0.872	SUBCLONAL	1	FALSE	1	0.158634187827649	2		897	799	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272213	15272213	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	68	809	2	ENST00000263388.2:c.6226G>T	p.Gly2076Trp	p.G2076W	ENST00000263388	NM_000435.2	2076	Ggg/Tgg	33/33	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.158634187827649	2		811	660	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584776	48584779	+	frameshift_variant	Frame_Shift_Del	DEL	ACGG	ACGG	CCT	novel	NA	P-0023471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	70	746	1	ENST00000342988.3:c.854_857delinsCCT	p.Asn285ThrfsTer51	p.N285Tfs*51	ENST00000342988	NM_005359.5	285	aACGGc/aCCTc	7/12	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.158634187827649	2		747	711	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1650225	1650225	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	84	1004	0	ENST00000344749.5:c.23C>G	p.Ala8Gly	p.A8G	ENST00000344749	NM_001136139.2	8	gCg/gGg	2/19	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	1	0.158634187827649	2		1004	979	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860941	45860941	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	74	1006	0	ENST00000391945.4:c.1254C>G	p.Ile418Met	p.I418M	ENST00000391945	NM_000400.3	418	atC/atG	13/23	1	2	FACETS	0.996	0.87	1	0.996	0.87	1	CLONAL	1	FALSE	1	0.158634187827649	2		1006	937	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391057	89391057	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	887	75	0	ENST00000336596.2:c.1123C>G	p.Pro375Ala	p.P375A	ENST00000336596	NM_005233.5	375	Cca/Gca	5/17	1	2	FACETS	0.946	0.92	0.972			1	CLONAL	7	FALSE	1	0.158634187827649	2		75	1689	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825409	134825409	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	55	849	1	ENST00000398015.3:c.925C>T	p.Arg309Ter	p.R309*	ENST00000398015	NM_004441.4	309	Cga/Tga	4/16	1	2	FACETS	0.843	0.719	0.978	0.843	0.719	0.978	CLONAL	1	FALSE	1	0.158634187827649	2		850	823	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356169	66356169	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	70	813	0	ENST00000273854.3:c.1328C>G	p.Ala443Gly	p.A443G	ENST00000273854	NM_004439.5	443	gCa/gGa	5/18	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.158634187827649	2		813	722	SUCCESS
APC	324	MSKCC	GRCh37	5	112170702	112170702	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	39	810	0	ENST00000257430.4:c.1798A>T	p.Thr600Ser	p.T600S	ENST00000257430	NM_000038.5	600	Act/Tct	15/16	1	2	FACETS	0.632	0.522	0.755	0.632	0.522	0.755	SUBCLONAL	1	FALSE	1	0.158634187827649	2		810	778	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501544	149501544	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	66	809	0	ENST00000261799.4:c.2243C>G	p.Ser748Trp	p.S748W	ENST00000261799	NM_002609.3	748	tCg/tGg	16/23	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	FALSE	1	0.158634187827649	2		809	790	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911075	29911075	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	54	955	3	ENST00000376809.5:c.374G>T	p.Cys125Phe	p.C125F	ENST00000376809	NM_002116.7	125	tGc/tTc	3/8	1	2	FACETS	0.839	0.715	0.976	0.839	0.715	0.976	CLONAL	1	FALSE	1	0.158634187827649	2		958	811	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346547	81346547	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0023471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	44	468	0	ENST00000222390.5:c.1405+1G>T		p.X469_splice	ENST00000222390	NM_000601.4	469			1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	FALSE	1	0.158634187827649	2		468	417	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90976658	90976659	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0023471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	45	820	2	ENST00000265433.3:c.973_974delinsAT	p.Pro325Ile	p.P325I	ENST00000265433	NM_002485.4	325	CCt/ATt	8/16	1	2	FACETS	0.692	0.58	0.817	0.692	0.58	0.817	SUBCLONAL	1	FALSE	1	0.158634187827649	2		822	820	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0023473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	56	515	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	0.529790090313539	2		515	174	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867234	68867234	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0023473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	115	535	0	ENST00000261769.5:c.2481T>A	p.Tyr827Ter	p.Y827*	ENST00000261769	NM_004360.3	827	taT/taA	16/16	0.529790090313539	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.529790090313539	1		535	277	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166710	32166710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	100	719	1	ENST00000375023.3:c.4528G>A	p.Gly1510Ser	p.G1510S	ENST00000375023	NM_004557.3	1510	Ggt/Agt	24/30	1	2	FACETS	0.791	0.71	0.877	0.791	0.71	0.877	SUBCLONAL	1	TRUE	1	0.529790090313539	2		720	477	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249441	110249441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	153	797	0	ENST00000374672.4:c.1132G>A	p.Glu378Lys	p.E378K	ENST00000374672	NM_004235.4	378	Gag/Aag	4/5	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.529790090313539	2		797	570	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984157	2984157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	35	431	0	ENST00000396946.4:c.373G>A	p.Glu125Lys	p.E125K	ENST00000396946	NM_032415.4	125	Gag/Aag	5/25	0.233296165749527	3	FACETS	0.855	0.701	1	0.427	0.35	0.514	CLONAL	1	TRUE	1	0.233296165749527	3		431	392	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103508448	103508451	+	frameshift_variant	Frame_Shift_Del	DEL	AAAC	AAAC	-	novel	NA	P-0023482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	34	572	0	ENST00000355739.4:c.516_519del	p.Gln173HisfsTer13	p.Q173Hfs*13	ENST00000355739	NM_000123.3	172	AAACaa/aa	5/15	0.159995359377181	2	FACETS	0.504	0.411	0.61	0.252	0.205	0.305	SUBCLONAL	1	TRUE	0	0.233296165749527	2		572	578	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640710	3640710	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	46	819	0	ENST00000294008.3:c.2929T>G	p.Ser977Ala	p.S977A	ENST00000294008	NM_032444.2	977	Tca/Gca	12/15	0.233296165749527	3	FACETS	0.598	0.502	0.705	0.299	0.251	0.353	SUBCLONAL	1	TRUE	1	0.233296165749527	3		819	736	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066675	94066675	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	63	762	1	ENST00000369303.4:c.1084G>T	p.Asp362Tyr	p.D362Y	ENST00000369303	NM_004440.3	362	Gat/Tat	5/17	1	2	FACETS	0.705	0.609	0.81	0.705	0.609	0.81	SUBCLONAL	1	TRUE	1	0.233296165749527	2		763	766	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878287	151878287	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	140	892	0	ENST00000262189.6:c.6658C>T	p.Gln2220Ter	p.Q2220*	ENST00000262189	NM_170606.2	2220	Cag/Tag	36/59	0.233296165749527	3	FACETS	0.809	0.737	0.885	0.809	0.737	0.885	CLONAL	2	TRUE	1	0.233296165749527	3		892	828	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226568887	226568887	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	49	464	0	ENST00000366794.5:c.1182G>C	p.Lys394Asn	p.K394N	ENST00000366794	NM_001618.3	394	aaG/aaC	9/23	1	2	FACETS	0.584	0.495	0.682	0.584	0.495	0.682	SUBCLONAL	1	TRUE	1	0.356771434129029	2		464	470	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727510	66727510	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	25	518	0	ENST00000307102.5:c.226G>T	p.Ala76Ser	p.A76S	ENST00000307102	NM_002755.3	76	Gct/Tct	2/11	0.211836701111348	0	FACETS	0.213	0.167	0.266			1	INDETERMINATE	1	TRUE	0	0.356771434129029	0		518	423	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411872	116411900	+	splice_region_variant,intron_variant	Splice_Region	DEL	TAACAAGCTCTTTCTTTCTCTCTGTTTTA	TAACAAGCTCTTTCTTTCTCTCTGTTTTA	-	novel	NA	P-0023504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	237	989	1	ENST00000397752.3:c.2888-31_2888-3del		p.X963_splice	ENST00000397752	NM_000245.2	963			0.325226647233865	2	FACETS	0.817	0.765	0.871	0.817	0.765	0.871	CLONAL	2	TRUE	0	0.356771434129029	2		990	813	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748914	41748914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751855310	NA	P-0023505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	33	454	0	ENST00000301178.4:c.1439G>A	p.Arg480His	p.R480H	ENST00000301178	NM_021913.4	480	cGt/cAt	11/20	0.518735281878301	3	FACETS	0.439	0.359	0.528	0.146	0.119	0.176	SUBCLONAL	1	TRUE	0	0.76793973773934	3		454	271	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519996	NA	P-0023505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	569	618	0	ENST00000269305.4:c.395A>C	p.Lys132Thr	p.K132T	ENST00000269305	NM_001126112.2	132	aAg/aCg	5/11	0.486932849224669	6	FACETS	0.997	0.981	1			1	CLONAL	6	TRUE	NA	0.76793973773934	6		618	628	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916779	48916779	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	274	455	0	ENST00000267163.4:c.309del	p.Phe104LeufsTer7	p.F104Lfs*7	ENST00000267163	NM_000321.2	103	atC/at	3/27	0.721867015245961	3	FACETS	0.925	0.892	0.956	0.925	0.892	0.956	CLONAL	3	TRUE	0	0.76793973773934	3		455	356	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56402456	56402456	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	385	348	0	ENST00000348428.3:c.1498G>T	p.Glu500Ter	p.E500*	ENST00000348428	NM_006785.3	500	Gaa/Taa	13/17	0.76793973773934	5	FACETS	1	0.98	1			1	CLONAL	5	TRUE	NA	0.76793973773934	5		348	431	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480495	57480495	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	21	353	0	ENST00000371085.3:c.490G>C	p.Glu164Gln	p.E164Q	ENST00000371085	NM_000516.4	164	Gaa/Caa	6/13	0.677189125880082	4	FACETS	0.263	0.202	0.335	0.132	0.101	0.168	SUBCLONAL	1	TRUE	2	0.76793973773934	4		353	367	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938552	76938552	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	24	529	0	ENST00000373344.5:c.2196T>G	p.Asp732Glu	p.D732E	ENST00000373344	NM_000489.3	732	gaT/gaG	9/35	0.72397132454083	2	FACETS	0.311	0.245	0.386	0.155	0.122	0.193	SUBCLONAL	1	TRUE	0	0.76793973773934	2		529	201	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940450	76940451	+	stop_gained	Nonsense_Mutation	DNP	CA	CA	AT	novel	NA	P-0023505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	16	542	0	ENST00000373344.5:c.642_643delinsAT	p.Asp214_Gly215delinsGluTer	p.D214_G215delinsE*	ENST00000373344	NM_000489.3	214	gaTGga/gaATga	8/35	0.72397132454083	2	FACETS	0.132	0.097	0.174	0.066	0.048	0.087	SUBCLONAL	1	TRUE	0	0.76793973773934	2		542	316	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0023506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	658	515	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.616132397604682	10	FACETS	0.976	0.945	1	0.837	0.81	0.864	CLONAL	6	TRUE	3	0.616132397604682	10		515	1263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0023506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	410	914	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.590740637890473	2	FACETS	0.979	0.942	1	0.979	0.942	1	CLONAL	2	TRUE	0	0.616132397604682	2		914	680	SUCCESS
APC	324	MSKCC	GRCh37	5	112170676	112170676	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	114	449	0	ENST00000257430.4:c.1772C>A	p.Ala591Asp	p.A591D	ENST00000257430	NM_000038.5	591	gCc/gAc	15/16	0.616132397604682	3	FACETS	0.864	0.781	0.952	0.432	0.39	0.476	CLONAL	1	TRUE	1	0.616132397604682	3		449	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0023507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	519	983	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.108015556321626	5	FACETS	0.958	0.942	0.974			1	INDETERMINATE	5	TRUE	NA	0.866360092960973	5		984	575	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150289	108150314	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTTGAAAATGCATACTTGAAAGCT	CTTTTGAAAATGCATACTTGAAAGCT	-	novel	NA	P-0023507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	26	360	0	ENST00000278616.4:c.3357_3382del	p.Phe1120GlyfsTer9	p.F1120Gfs*9	ENST00000278616	NM_000051.3	1119	gCTTTTGAAAATGCATACTTGAAAGCT/g	23/63	1	2	FACETS	0.159	0.126	0.198	0.159	0.126	0.198	SUBCLONAL	1	TRUE	1	0.866360092960973	2		360	377	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864270	57864270	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	403	395	0	ENST00000228682.2:c.1747C>G	p.Pro583Ala	p.P583A	ENST00000228682	NM_005269.2	583	Cct/Gct	12/12	0.710236750889509	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.866360092960973	4		395	857	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81558901	81558901	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	210	425	0	ENST00000298171.2:c.494C>G	p.Thr165Arg	p.T165R	ENST00000298171	NM_000369.2	165	aCg/aGg	6/10	0.339174466897643	5	FACETS	1	0.985	1	0.304	0.282	0.327	INDETERMINATE	1	TRUE	1	0.866360092960973	5		425	916	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40376849	40376849	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	567	544	0	ENST00000293328.3:c.323G>T	p.Cys108Phe	p.C108F	ENST00000293328	NM_012448.3	108	tGc/tTc	4/19	0.866360092960973	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.866360092960973	2		544	641	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922307	39922307	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	133	208	0	ENST00000378444.4:c.3865G>T	p.Gly1289Cys	p.G1289C	ENST00000378444	NM_001123385.1	1289	Ggc/Tgc	9/15	0.866360092960973	2	FACETS	1	0.973	1	0.554	0.513	0.596	CLONAL	1	TRUE	0	0.866360092960973	2		208	277	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0023511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	176	724	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.274914411950225	3	FACETS	1	0.958	1	0.353	0.325	0.381	INDETERMINATE	1	TRUE	0	0.527857366541201	3		726	797	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	472142	472142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1309760726	NA	P-0023511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	166	568	0	ENST00000399788.2:c.659G>A	p.Arg220His	p.R220H	ENST00000399788	NM_001042603.1	220	cGt/cAt	5/28	0.274914411950225	3	FACETS	1	0.963	1	0.359	0.33	0.389	INDETERMINATE	1	TRUE	0	0.527857366541201	3		568	738	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211707	5211707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145108936	NA	P-0023511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	180	819	1	ENST00000357368.4:c.5128C>T	p.Arg1710Cys	p.R1710C	ENST00000357368	NM_002850.3	1710	Cgc/Tgc	33/38	1	2	FACETS	0.877	0.81	0.946	0.877	0.81	0.946	CLONAL	1	TRUE	1	0.527857366541201	2		820	778	SUCCESS
APC	324	MSKCC	GRCh37	5	112175577	112175577	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	200	401	0	ENST00000257430.4:c.4288del	p.Thr1430ProfsTer43	p.T1430Pfs*43	ENST00000257430	NM_000038.5	1429	cAa/ca	16/16	0.527857366541201	2	FACETS	0.913	0.858	0.968	0.913	0.858	0.968	CLONAL	2	TRUE	0	0.527857366541201	2		401	415	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0023513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	231	954	2	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.96	0.896	1	0.96	0.896	1	CLONAL	1	TRUE	1	0.527022139617501	2		956	913	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0023513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	475	883	4	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.527022139617501	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.527022139617501	2		887	875	SUCCESS
APC	324	MSKCC	GRCh37	5	112174379	112174379	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs587779786	NA	P-0023513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	106	336	0	ENST00000257430.4:c.3088A>T	p.Lys1030Ter	p.K1030*	ENST00000257430	NM_000038.5	1030	Aaa/Taa	16/16	1	2	FACETS	0.96	0.867	1	0.96	0.867	1	CLONAL	1	TRUE	1	0.527022139617501	2		336	419	SUCCESS
APC	324	MSKCC	GRCh37	5	112175541	112175542	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0023513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	126	430	0	ENST00000257430.4:c.4253_4254dup	p.Ser1419Ter	p.S1419*	ENST00000257430	NM_000038.5	1417	att/atTAt	16/16	1	2	FACETS	0.881	0.801	0.964	0.881	0.801	0.964	CLONAL	1	TRUE	1	0.527022139617501	2		430	543	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16097778	16097778	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	224	694	0	ENST00000268712.3:c.106C>T	p.Gln36Ter	p.Q36*	ENST00000268712	NM_006311.3	36	Cag/Tag	2/46	1	2	FACETS	0.887	0.827	0.95	0.887	0.827	0.95	CLONAL	1	TRUE	1	0.527022139617501	2		694	958	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399237	139399242	+	inframe_deletion	In_Frame_Del	DEL	CGGCGG	CGGCGG	-	novel	NA	P-0023515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	171	780	0	ENST00000277541.6:c.4901_4906del	p.Ala1634_Ala1635del	p.A1634_A1635del	ENST00000277541	NM_017617.3	1634	gCCGCCGag/gag	26/34	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		780	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0023516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	468	835	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.836771026508851	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.836771026508851	1		835	602	SUCCESS
APC	324	MSKCC	GRCh37	5	112175288	112175288	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0023516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	149	291	0	ENST00000257430.4:c.3997A>T	p.Lys1333Ter	p.K1333*	ENST00000257430	NM_000038.5	1333	Aaa/Taa	16/16	0.347703472386516	1	FACETS	0.69	0.643	0.738	0.69	0.643	0.738	INDETERMINATE	1	TRUE	0	0.836771026508851	1		291	300	SUCCESS
APC	324	MSKCC	GRCh37	5	112174670	112174670	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	138	503	0	ENST00000257430.4:c.3379C>T	p.Gln1127Ter	p.Q1127*	ENST00000257430	NM_000038.5	1127	Cag/Tag	16/16	0.347703472386516	1	FACETS	0.551	0.508	0.595	0.551	0.508	0.595	INDETERMINATE	1	TRUE	0	0.836771026508851	1		503	348	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872145	37872145	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142456637	NA	P-0023516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7580	1886	837	1	ENST00000269571.5:c.1466C>T	p.Pro489Leu	p.P489L	ENST00000269571		489	cCg/cTg	12/27	0.836771026508851	20	FACETS	1	0.986	1			1	CLONAL	4	TRUE	NA	0.836771026508851	20		838	9466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577062	7577062	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	20	884	1	ENST00000269305.4:c.876A>T	p.Lys292Asn	p.K292N	ENST00000269305	NM_001126112.2	292	aaA/aaT	8/11	0.836771026508851	1	FACETS	0.046	0.034	0.059	0.046	0.034	0.059	SUBCLONAL	1	TRUE	0	0.836771026508851	1		885	608	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37875531	37876056	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAAAAAGAATATGGGTCCAGATCCATATGGATCCTAGATCCAGATCACGGTGTTAGAACATGGAAAAACATTGCAAGATTCTGCTAAGTGAAAAAAGCATTTGCAAACAGTATGTACAGTCTATATTCAGAGGAGGAACTGCTGGGTCATAGATGATATTTCATAGGTATTGCCAAACCGTTCTCTGGAGAAGTGGTATGGGTTTACCCTGGGATTCTTCTATGGAGGGAATAGTTGAGCTCCCGGGCTTGCTCTTCTGGGTGCCCCTCCCCGCTTCCTATCCACCACAAGGAGCTGCAGGGGAGCGGGGCATGCCGGTTCCTTGGCTGGAGAAGGAGTCTCCTTGTGAGGTGGTAGAAGGAGCACTGACGGCCTTGAGCCCAGTTTCTGCCTTTGTCAAATGGGGATAATGACCCAGCCACACCCCTCCCAGGGTTGTTGTGAGGCTGGAAAGGTGGTTCCCAAGAGGGTGGTTCCCAGAATTGTTGATGAGACTGTTTCTCCTGCAGCTGTGTGGACCTGGATG	AAAAAAGAATATGGGTCCAGATCCATATGGATCCTAGATCCAGATCACGGTGTTAGAACATGGAAAAACATTGCAAGATTCTGCTAAGTGAAAAAAGCATTTGCAAACAGTATGTACAGTCTATATTCAGAGGAGGAACTGCTGGGTCATAGATGATATTTCATAGGTATTGCCAAACCGTTCTCTGGAGAAGTGGTATGGGTTTACCCTGGGATTCTTCTATGGAGGGAATAGTTGAGCTCCCGGGCTTGCTCTTCTGGGTGCCCCTCCCCGCTTCCTATCCACCACAAGGAGCTGCAGGGGAGCGGGGCATGCCGGTTCCTTGGCTGGAGAAGGAGTCTCCTTGTGAGGTGGTAGAAGGAGCACTGACGGCCTTGAGCCCAGTTTCTGCCTTTGTCAAATGGGGATAATGACCCAGCCACACCCCTCCCAGGGTTGTTGTGAGGCTGGAAAGGTGGTTCCCAAGAGGGTGGTTCCCAGAATTGTTGATGAGACTGTTTCTCCTGCAGCTGTGTGGACCTGGATG	-	novel	NA	P-0023516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4891	2754	0	0	ENST00000269571.5:c.1899-508_1916del		p.X633_splice	ENST00000269571		633		16/27	0.836771026508851	20	FACETS	1	0.996	1			1	CLONAL	7	TRUE	NA	0.836771026508851	20		0	7645	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309657	30309657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1578	206	776	0	ENST00000307677.4:c.365G>A	p.Ser122Asn	p.S122N	ENST00000307677	NM_138578.1	122	aGc/aAc	2/3	0.480654806630319	5	FACETS	0.622	0.575	0.672	0.207	0.191	0.224	INDETERMINATE	1	TRUE	2	0.836771026508851	5		776	1784	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0023520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	66	372	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.37	2		372	311	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181378	185181378	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	102	506	0	ENST00000265026.3:c.1319T>A	p.Ile440Asn	p.I440N	ENST00000265026	NM_004721.4	440	aTc/aAc	8/14	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.37	2		506	529	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230747	66230747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	48	446	0	ENST00000273854.3:c.2224G>A	p.Val742Met	p.V742M	ENST00000273854	NM_004439.5	742	Gtg/Atg	12/18	1	2	FACETS	0.573	0.485	0.67	0.573	0.485	0.67	SUBCLONAL	1	TRUE	1	0.37	2		446	453	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0023521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	25	675	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.539	0.423	0.674	0.539	0.423	0.674	SUBCLONAL	1	TRUE	1	0.14	2		675	662	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	40	585	2	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.794	0.658	0.946	0.794	0.658	0.946	CLONAL	1	TRUE	1	0.14	2		587	720	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332709	65332710	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0023521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	41	552	0	ENST00000342505.4:c.829_830del	p.Leu277AspfsTer7	p.L277Dfs*7	ENST00000342505	NM_002227.2	277	TTg/g	7/25	1	2	FACETS	0.826	0.686	0.982	0.826	0.686	0.982	CLONAL	1	TRUE	1	0.14	2		552	709	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1040397	1040397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35008685	NA	P-0023521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	45	558	0	ENST00000358495.3:c.175G>A	p.Gly59Arg	p.G59R	ENST00000358495	NM_134424.2	59	Gga/Aga	3/12	1	2	FACETS	0.796	0.667	0.939	0.796	0.667	0.939	CLONAL	1	TRUE	1	0.14	2		558	808	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99491870	99491870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1185222113	NA	P-0023521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	46	609	0	ENST00000268035.6:c.3655G>A	p.Glu1219Lys	p.E1219K	ENST00000268035	NM_000875.3	1219	Gag/Aag	20/21	1	2	FACETS	0.755	0.634	0.89	0.755	0.634	0.89	SUBCLONAL	1	TRUE	1	0.14	2		609	870	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119710	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0023521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	36	502	0	ENST00000285071.4:c.1284_1285del	p.His429ArgfsTer26	p.H429Rfs*26	ENST00000285071	NM_144997.5	428	ccCCac/ccac	11/14	1	2	FACETS	0.79	0.648	0.95	0.79	0.648	0.95	CLONAL	1	TRUE	1	0.14	2		502	651	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110332	3110332	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0023521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	50	662	1	ENST00000078429.4:c.321+1G>A		p.X107_splice	ENST00000078429	NM_002067.2	107			1	2	FACETS	0.804	0.68	0.942	0.804	0.68	0.942	CLONAL	1	TRUE	1	0.14	2		663	888	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10244345	10244345	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	novel	NA	P-0023521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	63	675	0	ENST00000340748.4:c.4849T>C	p.Ter1617GlnextTer23	p.*1617Qext*23	ENST00000340748		1617	Tag/Cag	40/40	1	2	FACETS	0.947	0.817	1	0.947	0.817	1	CLONAL	1	TRUE	1	0.14	2		675	950	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144482	11144482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776672640	NA	P-0023521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	53	730	0	ENST00000358026.2:c.3814G>A	p.Ala1272Thr	p.A1272T	ENST00000358026	NM_001128849.1	1272	Gcc/Acc	27/36	1	2	FACETS	0.749	0.636	0.873	0.749	0.636	0.873	SUBCLONAL	1	TRUE	1	0.14	2		730	1011	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216184	36216184	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	59	690	3	ENST00000222270.7:c.3596del	p.Gly1199AlafsTer156	p.G1199Afs*156	ENST00000222270	NM_014727.1	1198	Ggg/gg	11/37	1	2	FACETS	0.974	0.836	1	0.974	0.836	1	CLONAL	1	TRUE	1	0.14	2		693	865	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753181	42753181	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	68	699	0	ENST00000222329.4:c.1083del	p.Ser362ProfsTer35	p.S362Pfs*35	ENST00000222329	NM_006494.2	361	ccC/cc	4/4	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.14	2		699	926	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61753592	61753592	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	46	714	0	ENST00000401558.2:c.191A>G	p.Asp64Gly	p.D64G	ENST00000401558	NM_003400.3	64	gAc/gGc	3/25	1	2	FACETS	0.999	0.84	1	0.999	0.84	1	CLONAL	1	TRUE	1	0.14	2		714	658	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880956	134880956	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	55	609	0	ENST00000398015.3:c.1519C>T	p.Arg507Cys	p.R507C	ENST00000398015	NM_004441.4	507	Cgt/Tgt	7/16	1	2	FACETS	0.938	0.8	1	0.938	0.8	1	CLONAL	1	TRUE	1	0.14	2		609	838	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	8	420	0	ENST00000263967.3:c.1034A>G	p.Asn345Ser	p.N345S	ENST00000263967	NM_006218.2	345	aAt/aGt	5/21	1	2	FACETS	0.308	0.197	0.453	0.308	0.197	0.453	SUBCLONAL	1	TRUE	1	0.14	2		420	371	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807328	1807328	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	68	805	0	ENST00000260795.2:c.1577T>C	p.Met526Thr	p.M526T	ENST00000260795		526	aTg/aCg	11/17	1	2	FACETS	0.966	0.838	1	0.966	0.838	1	CLONAL	1	TRUE	1	0.14	2		805	1006	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876586	35876586	+	stop_lost	Nonstop_Mutation	SNP	T	T	C	novel	NA	P-0023521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	40	475	0	ENST00000303115.3:c.1378T>C	p.Ter460ArgextTer7	p.*460Rext*7	ENST00000303115	NM_002185.3	460	Tga/Cga	8/8	1	2	FACETS	0.994	0.825	1	0.994	0.825	1	CLONAL	1	TRUE	1	0.14	2		475	575	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459795	149459795	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755093010	NA	P-0023521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	59	709	1	ENST00000286301.3:c.412G>A	p.Val138Ile	p.V138I	ENST00000286301	NM_005211.3	138	Gtc/Atc	4/22	1	2	FACETS	0.95	0.815	1	0.95	0.815	1	CLONAL	1	TRUE	1	0.14	2		710	887	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051023	180051023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749803588	NA	P-0023521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	57	803	0	ENST00000261937.6:c.1460G>A	p.Arg487His	p.R487H	ENST00000261937	NM_182925.4	487	cGt/cAt	11/30	1	2	FACETS	0.799	0.683	0.926	0.799	0.683	0.926	CLONAL	1	TRUE	1	0.14	2		803	1019	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055919	180055919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1368679940	NA	P-0023521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	44	595	2	ENST00000261937.6:c.1066G>A	p.Val356Met	p.V356M	ENST00000261937	NM_182925.4	356	Gtg/Atg	8/30	1	2	FACETS	0.733	0.612	0.867	0.733	0.612	0.867	SUBCLONAL	1	TRUE	1	0.14	2		597	858	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911172	29911172	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	34	350	0	ENST00000376809.5:c.471G>T	p.Trp157Cys	p.W157C	ENST00000376809	NM_002116.7	157	tgG/tgT	3/8	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.14	2		350	423	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900288	101900288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111854391	NA	P-0023521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	42	518	1	ENST00000374994.4:c.722C>T	p.Ser241Leu	p.S241L	ENST00000374994	NM_004612.2	241	tCg/tTg	4/9	1	2	FACETS	0.901	0.751	1	0.901	0.751	1	CLONAL	1	TRUE	1	0.14	2		519	666	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250133	110250133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs554677478	NA	P-0023521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	46	639	1	ENST00000374672.4:c.542C>T	p.Pro181Leu	p.P181L	ENST00000374672	NM_004235.4	181	cCg/cTg	3/5	1	2	FACETS	0.812	0.682	0.957	0.812	0.682	0.957	CLONAL	1	TRUE	1	0.14	2		640	809	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738211	133738211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370646520	NA	P-0023521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	41	576	0	ENST00000318560.5:c.611C>T	p.Thr204Met	p.T204M	ENST00000318560	NM_005157.4	204	aCg/aTg	4/11	1	2	FACETS	0.748	0.621	0.89	0.748	0.621	0.89	SUBCLONAL	1	TRUE	1	0.14	2		576	783	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	47	326	0	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	1	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.14	1		326	475	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324886	31324887	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760037174	NA	P-0023521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	28	301	0	ENST00000412585.2:c.49_50insG	p.Leu17ArgfsTer82	p.L17Rfs*82	ENST00000412585	NM_005514.6	17	ctg/cGtg	1/8	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.14	2		301	346	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066712	77066712	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1482673833	NA	P-0023524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	57	501	0	ENST00000356341.3:c.772+1G>A		p.X258_splice	ENST00000356341	NM_002576.4	258			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		501	295	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	298	896	2	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	0.74	2		898	783	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0023525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	172	522	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.74	2		522	449	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174489	11174499	+	frameshift_variant	Frame_Shift_Del	DEL	AGTTGCCATCC	AGTTGCCATCC	-	novel	NA	P-0023525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	174	864	0	ENST00000361445.4:c.7176_7186del	p.Asp2393GlnfsTer28	p.D2393Qfs*28	ENST00000361445	NM_004958.3	2392	ctGGATGGCAACTac/ctac	53/58	1	2	FACETS	0.828	0.767	0.891	0.828	0.767	0.891	CLONAL	1	TRUE	1	0.74	2		864	568	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023420	27023421	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	247	814	0	ENST00000324856.7:c.528dup	p.Gln177ThrfsTer223	p.Q177Tfs*223	ENST00000324856	NM_006015.4	176	caa/cAaa	1/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.74	2		814	651	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056234	27056235	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0023525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	192	729	0	ENST00000324856.7:c.1232dup	p.Gln412AlafsTer211	p.Q412Afs*211	ENST00000324856	NM_006015.4	410	-/C	2/20	1	2	FACETS	0.943	0.879	1	0.943	0.879	1	CLONAL	1	TRUE	1	0.74	2		729	550	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653809	89653809	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554893792	NA	P-0023525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	232	696	0	ENST00000371953.3:c.107G>A	p.Gly36Glu	p.G36E	ENST00000371953	NM_000314.4	36	gGa/gAa	2/9	1	2	FACETS	0.978	0.918	1	0.978	0.918	1	CLONAL	1	TRUE	1	0.74	2		696	641	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720858	89720858	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1564568660	NA	P-0023525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	246	501	0	ENST00000371953.3:c.1012del	p.Ser338LeufsTer6	p.S338Lfs*6	ENST00000371953	NM_000314.4	337	Ttt/tt	8/9	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.74	2		501	562	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250822	153250822	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0023525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	184	572	0	ENST00000281708.4:c.1236+2T>G		p.X412_splice	ENST00000281708	NM_033632.3	412			1	2	FACETS	0.995	0.926	1	0.995	0.926	1	CLONAL	1	TRUE	1	0.74	2		572	500	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528930	157528930	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1371496107	NA	P-0023525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	190	717	0	ENST00000346085.5:c.6655G>T	p.Glu2219Ter	p.E2219*	ENST00000346085	NM_020732.3	2219	Gag/Tag	20/20	1	2	FACETS	0.893	0.831	0.957	0.893	0.831	0.957	CLONAL	1	TRUE	1	0.74	2		717	575	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55229252	55229252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	187	733	0	ENST00000275493.2:c.1559C>T	p.Pro520Leu	p.P520L	ENST00000275493	NM_005228.3	520	cCc/cTc	13/28	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.74	2		733	501	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0023526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	111	725	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	0.408852896017016	3	FACETS	0.843	0.764	0.924	0.843	0.764	0.924	CLONAL	2	TRUE	1	0.408852896017016	3		725	388	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913338	NA	P-0023526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	109	598	0	ENST00000288602.6:c.1781A>C	p.Asp594Ala	p.D594A	ENST00000288602	NM_004333.4	594	gAt/gCt	15/18	0.408852896017016	4	FACETS	0.797	0.72	0.879	0.797	0.72	0.879	SUBCLONAL	2	TRUE	2	0.408852896017016	4		598	471	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0023526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	82	384	1	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.408852896017016	2		385	329	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0023526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	81	488	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	1	2	FACETS	0.881	0.779	0.988	0.881	0.779	0.988	CLONAL	1	TRUE	1	0.408852896017016	2		488	450	SUCCESS
APC	324	MSKCC	GRCh37	5	112137024	112137024	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	90	560	0	ENST00000257430.4:c.778C>T	p.Gln260Ter	p.Q260*	ENST00000257430	NM_000038.5	260	Cag/Tag	8/16	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.408852896017016	2		560	420	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464961	120464961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764895571	NA	P-0023526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	153	771	0	ENST00000256646.2:c.5111G>A	p.Arg1704His	p.R1704H	ENST00000256646	NM_024408.3	1704	cGt/cAt	28/34	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.408852896017016	2		771	662	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106335	27106359	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTGTGTCCAATACCATTCGAAGC	CTGTGTGTCCAATACCATTCGAAGC	-	novel	NA	P-0023526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	151	741	0	ENST00000324856.7:c.5950_5974del	p.Val1984HisfsTer23	p.V1984Hfs*23	ENST00000324856	NM_006015.4	1982	gtCTGTGTGTCCAATACCATTCGAAGC/gt	20/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.408852896017016	2		741	696	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115722	108115722	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	48	380	0	ENST00000278616.4:c.870T>G	p.His290Gln	p.H290Q	ENST00000278616	NM_000051.3	290	caT/caG	7/63	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.408852896017016	2		380	208	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052635	42052635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	142	680	3	ENST00000219905.7:c.7306C>T	p.Arg2436Cys	p.R2436C	ENST00000219905	NM_001164273.1	2436	Cgt/Tgt	20/24	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.408852896017016	2		683	647	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014170	70014170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769488988	NA	P-0023526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	164	841	0	ENST00000394351.3:c.1031C>T	p.Thr344Met	p.T344M	ENST00000394351	NM_000248.3	344	aCg/aTg	9/9	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.408852896017016	2		841	793	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0023527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	115	399	0				ENST00000310581	NM_198253.2	-/1132			0.63401443343762	3	FACETS	1	0.947	1	0.531	0.482	0.582	CLONAL	1	TRUE	1	0.719590310436673	3		399	409	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0023527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	60	472	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.489	0.424	0.559	0.489	0.424	0.559	SUBCLONAL	1	TRUE	1	0.719590310436673	2		472	341	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220274	55220274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19429	1641	885	0	ENST00000275493.2:c.664C>T	p.Arg222Cys	p.R222C	ENST00000275493	NM_005228.3	222	Cgc/Tgc	6/28	0.719590310436673	33	FACETS	0.877	0.852	0.902	0.08	0.077	0.082	CLONAL	3	TRUE	0	0.719590310436673	33		885	21070	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947585	48947585	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	308	686	0	ENST00000267163.4:c.1172C>A	p.Ser391Ter	p.S391*	ENST00000267163	NM_000321.2	391	tCa/tAa	12/27	0.710360492824972	2	FACETS	0.984	0.947	1	0.984	0.947	1	CLONAL	2	TRUE	0	0.719590310436673	2		686	435	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344958	70344958	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	115	414	0	ENST00000374080.3:c.2188C>T	p.Arg730Ter	p.R730*	ENST00000374080		730	Cga/Tga	15/45	1	1	FACETS	0.758	0.695	0.822	0.758	0.695	0.822	SUBCLONAL	1	TRUE	0	0.719590310436673	1		414	270	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	109	482	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.309338457610453	2		482	570	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612642	228612642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	63	815	0	ENST00000366696.1:c.385C>T	p.Arg129Cys	p.R129C	ENST00000366696	NM_003493.2	129	Cgc/Tgc	1/1	NA	2	FACETS	0.458	0.395	0.526			1	INDETERMINATE	1	TRUE	NA	0.309338457610453	2		815	890	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720744	89720745	+	stop_gained	Nonsense_Mutation	DNP	GA	GA	TG	novel	NA	P-0023531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	13	232	0	ENST00000371953.3:c.895_896delinsTG	p.Glu299Ter	p.E299*	ENST00000371953	NM_000314.4	299	GAa/TGa	8/9	0.309338457610453	2	FACETS	0.564	0.404	0.757	0.282	0.202	0.379	SUBCLONAL	1	TRUE	0	0.309338457610453	2		232	149	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942134	17942134	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	206	940	2	ENST00000458235.1:c.2881G>A	p.Ala961Thr	p.A961T	ENST00000458235	NM_000215.3	961	Gca/Aca	21/24	0.309338457610453	3	FACETS	1	0.98	1	0.583	0.539	0.628	CLONAL	1	TRUE	1	0.309338457610453	3		942	1320	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55232991	55232992	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGTGTGCCCACTACATTGACGGCCCCCACTGCGTCAAGACCTGCCCGGCAGGAGTCATGGGAG	novel	NA	P-0023531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	79	523	0	ENST00000275493.2:c.1743_1805dup	p.Cys582_Glu602dup	p.C582_E602dup	ENST00000275493	NM_005228.3	582	cag/cAGTGTGCCCACTACATTGACGGCCCCCACTGCGTCAAGACCTGCCCGGCAGGAGTCATGGGAGag	15/28	0.309338457610453	3	FACETS	0.664	0.583	0.752	0.332	0.291	0.376	SUBCLONAL	1	TRUE	1	0.309338457610453	3		523	888	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0023532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	617	689	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.70306209171008	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.70306209171008	2		689	874	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981767	201981767	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0023532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	307	946	0	ENST00000359651.3:c.479-1G>C		p.X160_splice	ENST00000359651		160			0.70020492744192	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.70306209171008	1		946	480	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274777	123274777	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs387906678	NA	P-0023532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	266	934	0	ENST00000358487.5:c.1141T>C	p.Tyr381His	p.Y381H	ENST00000358487	NM_000141.4	381	Tac/Cac	9/18	0.70020492744192	1	FACETS	0.981	0.932	1	0.981	0.932	1	CLONAL	1	TRUE	0	0.70306209171008	1		934	500	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992188	11992188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	522	773	0	ENST00000396373.4:c.278C>T	p.Ala93Val	p.A93V	ENST00000396373	NM_001987.4	93	gCt/gTt	3/8	0.685588277514289	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.70306209171008	2		773	741	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882091	36882091	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	251	997	0	ENST00000358127.4:c.922G>T	p.Ala308Ser	p.A308S	ENST00000358127	NM_001280556.1	308	Gcg/Tcg	8/10	1	2	FACETS	0.983	0.924	1	0.983	0.924	1	CLONAL	1	TRUE	1	0.70306209171008	2		997	726	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87356827	87356827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	143	790	0	ENST00000277120.3:c.1180G>T	p.Asp394Tyr	p.D394Y	ENST00000277120		394	Gat/Tat	10/19	0.70306209171008	1	FACETS	0.735	0.679	0.792	0.735	0.679	0.792	SUBCLONAL	1	TRUE	0	0.70306209171008	1		790	359	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128321993	128321993	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	314	958	2	ENST00000265960.3:c.767A>G	p.Lys256Arg	p.K256R	ENST00000265960	NM_001006617.1	256	aAg/aGg	6/12	0.70306209171008	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.70306209171008	1		960	571	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412228	139412228	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	378	1111	0	ENST00000277541.6:c.1417G>T	p.Glu473Ter	p.E473*	ENST00000277541	NM_017617.3	473	Gag/Tag	8/34	0.70306209171008	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.70306209171008	1		1111	646	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342400	70342401	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0023532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	318	523	0	ENST00000374080.3:c.1295dup	p.Gln433ThrfsTer4	p.Q433Tfs*4	ENST00000374080		431	cgg/cGgg	9/45	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.70306209171008	1		523	487	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	73	482	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.233315469731257	2		482	533	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0023533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	56	501	2	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.976	0.837	1	0.976	0.837	1	CLONAL	1	TRUE	1	0.233315469731257	2		503	492	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974748	21974748	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1554656411	NA	P-0023533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	57	389	0	ENST00000304494.5:c.79G>T	p.Glu27Ter	p.E27*	ENST00000304494	NM_000077.4	27	Gag/Tag	1/3	0.233315469731257	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.233315469731257	1		389	312	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850619	63850619	+	splice_acceptor_variant	Splice_Site	DEL	A	A	-	novel	NA	P-0023533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	37	300	0	ENST00000279873.7:c.1399-2del		p.X467_splice	ENST00000279873	NM_032199.2	467			1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.233315469731257	2		300	287	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73352462	73352462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768054707	NA	P-0023533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	103	840	2	ENST00000377767.4:c.443C>T	p.Ala148Val	p.A148V	ENST00000377767	NM_014953.3	148	gCg/gTg	3/21	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.233315469731257	2		842	851	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220957	36220962	+	inframe_deletion	In_Frame_Del	DEL	CAGCTA	CAGCTA	-	novel	NA	P-0023533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	74	662	0	ENST00000222270.7:c.5008_5013del	p.Ser1670_Tyr1671del	p.S1670_Y1671del	ENST00000222270	NM_014727.1	1669	gcCAGCTAc/gcc	23/37	0.124370359742667	3	FACETS	1	0.963	1	0.632	0.554	0.716	INDETERMINATE	1	TRUE	1	0.233315469731257	3		662	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	412	944	4	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.52241153908298	3	FACETS	0.926	0.893	0.958	0.926	0.893	0.958	CLONAL	3	TRUE	0	0.602158801478659	3		948	641	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519922	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1249	85	839	1	ENST00000397062.3:c.235G>A	p.Glu79Lys	p.E79K	ENST00000397062	NM_006164.4	79	Gag/Aag	2/5	0.602158801478659	7	FACETS	0.53	0.467	0.599	0.106	0.093	0.12	SUBCLONAL	1	TRUE	2	0.602158801478659	7		840	1334	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	369	724	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	0.602158801478659	7	FACETS	1	0.989	1	0.46	0.436	0.485	CLONAL	2	TRUE	2	0.602158801478659	7		724	1334	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681129	37681129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	142	601	1	ENST00000447079.4:c.3298G>A	p.Asp1100Asn	p.D1100N	ENST00000447079	NM_015083.1	1100	Gat/Aat	12/14	0.536887378448298	4	FACETS	1	0.983	1	0.656	0.6	0.714	CLONAL	1	TRUE	2	0.602158801478659	4		602	576	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119666165	119666165	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	151	535	0	ENST00000316626.5:c.316C>G	p.His106Asp	p.H106D	ENST00000316626		106	Cac/Gac	3/12	0.555707158264491	2	FACETS	1	0.981	1	0.6	0.554	0.647	CLONAL	1	TRUE	0	0.602158801478659	2		535	418	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602840	10602840	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	213	986	0	ENST00000171111.5:c.738C>G	p.Phe246Leu	p.F246L	ENST00000171111	NM_203500.1	246	ttC/ttG	3/6	0.1974845793958	6	FACETS	0.807	0.75	0.866	0.538	0.5	0.578	INDETERMINATE	2	TRUE	3	0.602158801478659	6		986	966	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974762	21974762	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	108	267	0	ENST00000304494.5:c.65G>C	p.Arg22Pro	p.R22P	ENST00000304494	NM_000077.4	22	cGg/cCg	1/3	0.586178830755477	2	FACETS	0.925	0.854	0.994	0.925	0.854	0.994	CLONAL	2	TRUE	0	0.602158801478659	2		267	194	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256799	16256800	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	53	724	0	ENST00000375759.3:c.4067dup	p.Asn1357LysfsTer5	p.N1357Kfs*5	ENST00000375759	NM_015001.2	1355	ttc/ttCc	11/15	0.555707158264491	2	FACETS	0.347	0.295	0.402	0.173	0.147	0.201	SUBCLONAL	1	TRUE	0	0.602158801478659	2		724	508	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107041	27107041	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760749276	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	229	507	0	ENST00000324856.7:c.6652A>G	p.Met2218Val	p.M2218V	ENST00000324856	NM_006015.4	2218	Atg/Gtg	20/20	0.555707158264491	2	FACETS	0.99	0.941	1	0.99	0.941	1	CLONAL	2	TRUE	0	0.602158801478659	2		507	384	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797175	45797175	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs766420907	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	346	806	0	ENST00000450313.1:c.1240C>T	p.Gln414Ter	p.Q414*	ENST00000450313	NM_012222.2	414	Cag/Tag	13/16	0.44026706900596	5	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.602158801478659	5		806	885	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589379	28589379	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	136	507	0	ENST00000241453.7:c.2668C>A	p.Pro890Thr	p.P890T	ENST00000241453	NM_004119.2	890	Cct/Act	22/24	0.602158801478659	3	FACETS	1	0.985	1	0.687	0.63	0.745	CLONAL	1	TRUE	1	0.602158801478659	3		507	428	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134933	41134933	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	60	403	0	ENST00000379561.5:c.695G>C	p.Gly232Ala	p.G232A	ENST00000379561	NM_002015.3	232	gGa/gCa	2/3	0.602158801478659	3	FACETS	0.737	0.638	0.843	0.368	0.319	0.422	SUBCLONAL	1	TRUE	1	0.602158801478659	3		403	352	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103498676	103498676	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	139	572	0	ENST00000355739.4:c.60A>C	p.Glu20Asp	p.E20D	ENST00000355739	NM_000123.3	20	gaA/gaC	1/15	0.469775410581142	3	FACETS	1	0.987	1	0.722	0.663	0.782	CLONAL	1	TRUE	1	0.602158801478659	3		572	416	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506163	103506163	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	76	386	0	ENST00000355739.4:c.321G>C	p.Glu107Asp	p.E107D	ENST00000355739	NM_000123.3	107	gaG/gaC	3/15	0.469775410581142	3	FACETS	1	0.886	1	0.501	0.443	0.562	CLONAL	1	TRUE	1	0.602158801478659	3		386	328	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514694	103514694	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	71	437	0	ENST00000355739.4:c.1195G>T	p.Glu399Ter	p.E399*	ENST00000355739	NM_000123.3	399	Gaa/Taa	8/15	0.469775410581142	3	FACETS	1	0.897	1	0.51	0.449	0.574	CLONAL	1	TRUE	1	0.602158801478659	3		437	301	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103520519	103520519	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778950664	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	22	384	0	ENST00000355739.4:c.2590G>A	p.Glu864Lys	p.E864K	ENST00000355739	NM_000123.3	864	Gaa/Aaa	12/15	0.469775410581142	3	FACETS	0.252	0.194	0.318	0.126	0.097	0.159	SUBCLONAL	1	TRUE	1	0.602158801478659	3		384	378	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828071	72828071	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	230	876	0	ENST00000268489.5:c.8510C>G	p.Ser2837Cys	p.S2837C	ENST00000268489	NM_006885.3	2837	tCt/tGt	9/10	0.1974845793958	6	FACETS	0.966	0.902	1	0.644	0.601	0.688	INDETERMINATE	2	TRUE	3	0.602158801478659	6		876	872	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831462	89831462	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	50	611	0	ENST00000389301.3:c.2614A>G	p.Met872Val	p.M872V	ENST00000389301	NM_000135.2	872	Atg/Gtg	28/43	0.1974845793958	6	FACETS	0.589	0.499	0.689	0.196	0.166	0.23	INDETERMINATE	1	TRUE	3	0.602158801478659	6		611	621	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586073	29586073	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1391955681	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	187	496	0	ENST00000356175.3:c.4293T>A	p.His1431Gln	p.H1431Q	ENST00000356175	NM_000267.3	1431	caT/caA	32/57	0.536887378448298	4	FACETS	0.893	0.831	0.957	0.893	0.831	0.957	CLONAL	2	TRUE	2	0.602158801478659	4		496	557	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40864469	40864469	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	60	799	0	ENST00000428826.2:c.1239del	p.Lys414ArgfsTer11	p.K414Rfs*11	ENST00000428826		413	caG/ca	12/21	0.536887378448298	4	FACETS	0.333	0.285	0.384	0.166	0.142	0.192	SUBCLONAL	1	TRUE	2	0.602158801478659	4		799	960	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760989	59760989	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	201	738	0	ENST00000259008.2:c.3418G>C	p.Glu1140Gln	p.E1140Q	ENST00000259008	NM_032043.2	1140	Gaa/Caa	20/20	0.536887378448298	4	FACETS	1	0.987	1	0.636	0.59	0.683	CLONAL	1	TRUE	2	0.602158801478659	4		738	841	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007645	62007652	+	frameshift_variant	Frame_Shift_Del	DEL	ATTGCCGG	ATTGCCGG	-	novel	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	37	696	0	ENST00000392795.3:c.215_222del	p.Ser72CysfsTer42	p.S72Cfs*42	ENST00000392795	NM_001039933.1	72	tCCGGCAAT/t	3/6	0.536887378448298	4	FACETS	0.292	0.24	0.35	0.146	0.12	0.175	SUBCLONAL	1	TRUE	2	0.602158801478659	4		696	675	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210420	36210420	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	233	679	0	ENST00000222270.7:c.413G>T	p.Arg138Leu	p.R138L	ENST00000222270	NM_014727.1	138	cGc/cTc	2/37	0.1974845793958	6	FACETS	1	0.985	1	0.781	0.731	0.832	INDETERMINATE	2	TRUE	3	0.602158801478659	6		679	728	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595786	52595786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	53	519	0	ENST00000394830.3:c.4129G>A	p.Glu1377Lys	p.E1377K	ENST00000394830	NM_018313.4	1377	Gaa/Aaa	26/30	0.555707158264491	2	FACETS	0.438	0.374	0.507	0.219	0.187	0.254	SUBCLONAL	1	TRUE	0	0.602158801478659	2		519	402	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643604	52643604	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	194	607	0	ENST00000394830.3:c.2292G>C	p.Glu764Asp	p.E764D	ENST00000394830	NM_018313.4	764	gaG/gaC	17/30	0.555707158264491	2	FACETS	0.905	0.853	0.957	0.905	0.853	0.957	CLONAL	2	TRUE	0	0.602158801478659	2		607	356	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1976637	1976637	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1586	106	772	0	ENST00000382891.5:c.3420G>C	p.Met1140Ile	p.M1140I	ENST00000382891	NM_133335.3	1140	atG/atC	19/22	0.602158801478659	9	FACETS	0.647	0.577	0.721			1	SUBCLONAL	1	TRUE	NA	0.602158801478659	9		772	1692	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535436	66535455	+	frameshift_variant	Frame_Shift_Del	DEL	CACCCCGGGGCCCCGAGCCC	CACCCCGGGGCCCCGAGCCC	-	novel	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	225	525	0	ENST00000273854.3:c.6_25del	p.Ser4ThrfsTer78	p.S4Tfs*78	ENST00000273854	NM_004439.5	2	cgGGGCTCGGGGCCCCGGGGTGcg/cgcg	1/18	0.475920985708847	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.602158801478659	4		525	517	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111648	56111648	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	133	407	0	ENST00000399503.3:c.248C>G	p.Ser83Ter	p.S83*	ENST00000399503	NM_005921.1	83	tCa/tGa	1/20	0.555707158264491	2	FACETS	1	0.987	1	0.701	0.647	0.756	CLONAL	1	TRUE	0	0.602158801478659	2		407	315	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31947317	31947317	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	181	603	0	ENST00000375333.2:c.802G>C	p.Asp268His	p.D268H	ENST00000375333	NM_032454.1	268	Gac/Cac	5/8	0.300178727464645	3	FACETS	0.793	0.738	0.85	0.529	0.492	0.567	INDETERMINATE	2	TRUE	0	0.602158801478659	3		603	493	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190354	32190354	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	50	720	0	ENST00000375023.3:c.385A>G	p.Lys129Glu	p.K129E	ENST00000375023	NM_004557.3	129	Aaa/Gaa	3/30	0.300178727464645	3	FACETS	0.386	0.327	0.451	0.129	0.109	0.151	INDETERMINATE	1	TRUE	0	0.602158801478659	3		720	560	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622245	117622245	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	44	681	0	ENST00000368508.3:c.6625C>A	p.His2209Asn	p.H2209N	ENST00000368508	NM_002944.2	2209	Cat/Aat	42/43	0.461301732323223	4	FACETS	0.339	0.283	0.401	0.169	0.141	0.201	SUBCLONAL	1	TRUE	2	0.602158801478659	4		681	691	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355206	81355206	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs962122628	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	50	299	0	ENST00000222390.5:c.1168G>A	p.Asp390Asn	p.D390N	ENST00000222390	NM_000601.4	390	Gat/Aat	9/18	0.602158801478659	3	FACETS	0.847	0.725	0.979	0.424	0.362	0.49	CLONAL	1	TRUE	1	0.602158801478659	3		299	255	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523725	148523725	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	66	296	0	ENST00000320356.2:c.729-1G>A		p.X243_splice	ENST00000320356	NM_004456.4	243			0.536887378448298	4	FACETS	1	0.917	1	0.532	0.465	0.604	CLONAL	1	TRUE	2	0.602158801478659	4		296	330	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978648	70978648	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	292	832	0	ENST00000276594.2:c.1005G>C	p.Lys335Asn	p.K335N	ENST00000276594	NM_024504.3	335	aaG/aaC	5/8	0.192383576300103	3	FACETS	0.944	0.895	0.994	0.63	0.597	0.663	INDETERMINATE	2	TRUE	0	0.602158801478659	3		832	668	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317909	8317909	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs139384612	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	142	603	2	ENST00000356435.5:c.5704G>C	p.Glu1902Gln	p.E1902Q	ENST00000356435		1902	Gag/Cag	35/35	0.586178830755477	2	FACETS	1	0.981	1	0.606	0.559	0.655	CLONAL	1	TRUE	0	0.602158801478659	2		605	389	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22008869	22008869	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	251	709	0	ENST00000276925.6:c.84G>C	p.Glu28Asp	p.E28D	ENST00000276925	NM_004936.3	28	gaG/gaC	1/2	0.586178830755477	2	FACETS	1	0.994	1	0.736	0.695	0.778	CLONAL	1	TRUE	0	0.602158801478659	2		709	566	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641083	93641083	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	210	628	0	ENST00000375746.1:c.1429C>G	p.Gln477Glu	p.Q477E	ENST00000375746	NM_001174167.1	477	Cag/Gag	11/14	0.602158801478659	3	FACETS	0.763	0.713	0.813	0.508	0.475	0.542	SUBCLONAL	2	TRUE	0	0.602158801478659	3		628	595	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0023538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	160	722	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.932	0.858	1	0.932	0.858	1	CLONAL	1	TRUE	1	0.582225222146747	2		722	590	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724317	112724317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	189	592	0	ENST00000369452.4:c.201del	p.Val68LeufsTer23	p.V68Lfs*23	ENST00000369452	NM_007373.3	67	tcA/tc	2/9	1	2	FACETS	0.959	0.89	1	0.959	0.89	1	CLONAL	1	TRUE	1	0.582225222146747	2		592	677	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194137	94194137	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	209	692	0	ENST00000323929.3:c.1291del	p.Asp431IlefsTer3	p.D431Ifs*3	ENST00000323929	NM_005591.3	431	Gat/at	12/20	0.39734005785508	1	FACETS	0.837	0.782	0.893	0.837	0.782	0.893	CLONAL	1	TRUE	0	0.582225222146747	1		692	608	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426763	121426763	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	215	730	0	ENST00000257555.6:c.454A>G	p.Thr152Ala	p.T152A	ENST00000257555		152	Act/Gct	2/10	0.367885476970871	1	FACETS	0.919	0.86	0.978	0.919	0.86	0.978	CLONAL	1	TRUE	0	0.582225222146747	1		730	570	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389320	8389320	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	39	750	0	ENST00000356435.5:c.4298C>T	p.Pro1433Leu	p.P1433L	ENST00000356435		1433	cCc/cTc	26/35	0.34910288757666	1	FACETS	0.14	0.115	0.168	0.14	0.115	0.168	INDETERMINATE	1	TRUE	0	0.582225222146747	1		750	678	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0023539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	189	399	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.652730548585678	2		399	569	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0023539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	234	859	1	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	0.965	0.904	1	0.965	0.904	1	CLONAL	1	TRUE	1	0.652730548585678	2		860	743	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381466	81381466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	143	372	2	ENST00000222390.5:c.595G>A	p.Glu199Lys	p.E199K	ENST00000222390	NM_000601.4	199	Gaa/Aaa	5/18	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.652730548585678	2		374	401	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672423	30672423	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370120921	NA	P-0023539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	233	630	0	ENST00000376406.3:c.4537C>T	p.Arg1513Trp	p.R1513W	ENST00000376406	NM_014641.2	1513	Cgg/Tgg	10/15	0.645070644168725	3	FACETS	1	0.938	1	0.503	0.469	0.537	CLONAL	1	TRUE	1	0.652730548585678	3		630	942	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254692	16254692	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	214	533	0	ENST00000375759.3:c.1957C>T	p.Arg653Ter	p.R653*	ENST00000375759	NM_015001.2	653	Cga/Tga	11/15	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.652730548585678	2		533	641	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163313656	163313656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	243	232	0	ENST00000271452.3:c.803C>T	p.Ala268Val	p.A268V	ENST00000271452	NM_145697.2	268	gCc/gTc	10/14	0.562235471703641	5	FACETS	0.914	0.87	0.958	0.914	0.87	0.958	CLONAL	4	TRUE	1	0.652730548585678	5		232	403	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123260439	123260439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	251	640	0	ENST00000358487.5:c.1462G>A	p.Gly488Arg	p.G488R	ENST00000358487	NM_000141.4	488	Gga/Aga	11/18	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.652730548585678	2		640	633	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32971081	32971081	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs755201475	NA	P-0023539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	195	497	0	ENST00000380152.3:c.9548T>C	p.Ile3183Thr	p.I3183T	ENST00000380152		3183	aTa/aCa	26/27	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.652730548585678	2		497	568	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508400	29508442	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTATTCTAGAGTTAATTTTTAAAAATTGTGTTTTTTCCAGAAA	TTATTCTAGAGTTAATTTTTAAAAATTGTGTTTTTTCCAGAAA	-	novel	NA	P-0023539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	133	181	0	ENST00000356175.3:c.587-40_589del		p.X196_splice	ENST00000356175	NM_000267.3	196		6/57	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.652730548585678	2		181	280	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682429	52682429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	190	499	0	ENST00000394830.3:c.744G>A	p.Met248Ile	p.M248I	ENST00000394830	NM_018313.4	248	atG/atA	8/30	1	2	FACETS	0.975	0.907	1	0.975	0.907	1	CLONAL	1	TRUE	1	0.652730548585678	2		499	597	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522420	176522420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	246	709	0	ENST00000292408.4:c.1609C>T	p.Leu537Phe	p.L537F	ENST00000292408	NM_213647.1	537	Ctt/Ttt	12/18	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.652730548585678	2		709	747	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339609	116339610	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0023539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	112	331	0	ENST00000397752.3:c.471_472delinsAA	p.Val158Ile	p.V158I	ENST00000397752	NM_000245.2	157	gaGGtt/gaAAtt	2/21	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.652730548585678	2		331	329	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180271	27180271	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	224	583	0	ENST00000380036.4:c.935A>G	p.Lys312Arg	p.K312R	ENST00000380036	NM_000459.3	312	aAg/aGg	7/23	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.652730548585678	2		583	666	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626595	100626620	+	splice_donor_variant,intron_variant	Splice_Site	DEL	AGATTTGGTGAGAGAAAATAACTCAC	AGATTTGGTGAGAGAAAATAACTCAC	-	novel	NA	P-0023539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	155	164	0	ENST00000308731.7:c.309+1_309+26del		p.X103_splice	ENST00000308731	NM_000061.2	103			0.369978945202856	2	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.652730548585678	2		164	204	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0023540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	53	867	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.832	0.709	0.967	0.832	0.709	0.967	CLONAL	1	TRUE	1	0.22	2		868	579	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948160	178948160	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	20	225	0	ENST00000263967.3:c.2932G>C	p.Glu978Gln	p.E978Q	ENST00000263967	NM_006218.2	978	Gag/Cag	20/21	1	2	FACETS	0.676	0.517	0.861	0.676	0.517	0.861	SUBCLONAL	1	TRUE	1	0.22	2		225	269	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647926	3647927	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCTTCCGCCTCTTCCGTGGCT	novel	NA	P-0023540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	53	814	0	ENST00000294008.3:c.1217_1237dup	p.Glu406_Lys412dup	p.E406_K412dup	ENST00000294008	NM_032444.2	406	gtg/gAGCCACGGAAGAGGCGGAAGGtg	6/15	0.177173709198458	3	FACETS	0.642	0.546	0.748	0.321	0.273	0.374	SUBCLONAL	1	TRUE	1	0.22	3		814	833	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858024	9858024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	43	593	0	ENST00000330684.3:c.3377C>T	p.Pro1126Leu	p.P1126L	ENST00000330684	NM_001134407.1	1126	cCt/cTt	13/13	0.177173709198458	3	FACETS	0.817	0.683	0.966	0.409	0.341	0.483	CLONAL	1	TRUE	1	0.22	3		593	531	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942080	17942080	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	46	694	0	ENST00000458235.1:c.2935G>C	p.Asp979His	p.D979H	ENST00000458235	NM_000215.3	979	Gac/Cac	21/24	1	2	FACETS	0.726	0.611	0.854	0.726	0.611	0.854	SUBCLONAL	1	TRUE	1	0.22	2		694	576	SUCCESS
ATR	545	MSKCC	GRCh37	3	142185188	142185188	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	62	496	0	ENST00000350721.4:c.6875A>G	p.Tyr2292Cys	p.Y2292C	ENST00000350721	NM_001184.3	2292	tAt/tGt	40/47	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.22	2		496	446	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170312	32170312	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	66	832	0	ENST00000375023.3:c.3296G>T	p.Gly1099Val	p.G1099V	ENST00000375023	NM_004557.3	1099	gGa/gTa	21/30	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.22	2		832	525	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845618	128845618	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	16	354	0	ENST00000249373.3:c.915del	p.Glu305AspfsTer21	p.E305Dfs*21	ENST00000249373	NM_005631.4	305	gaG/ga	4/12	1	2	FACETS	0.483	0.357	0.635	0.483	0.357	0.635	SUBCLONAL	1	TRUE	1	0.22	2		354	301	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209256	98209256	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	66	703	0	ENST00000331920.6:c.4282del	p.Glu1428LysfsTer24	p.E1428Kfs*24	ENST00000331920	NM_000264.3	1428	Gaa/aa	23/24	1	2	FACETS	0.977	0.848	1	0.977	0.848	1	CLONAL	1	TRUE	1	0.22	2		703	614	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939615	76939615	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	62	620	0	ENST00000373344.5:c.1133C>A	p.Thr378Lys	p.T378K	ENST00000373344	NM_000489.3	378	aCa/aAa	9/35	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.22	2		620	561	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0023541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	259	724	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.583596128264901	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.583596128264901	1		726	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579348	7579348	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	303	666	0	ENST00000269305.4:c.339del	p.Leu114CysfsTer9	p.L114Cfs*9	ENST00000269305	NM_001126112.2	113	ttC/tt	4/11	0.583596128264901	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.583596128264901	1		666	675	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346154	89346154	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1040188778	NA	P-0023541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	77	236	1	ENST00000301030.4:c.6796G>A	p.Ala2266Thr	p.A2266T	ENST00000301030	NM_001256183.1	2266	Gcg/Acg	9/13	1	2	FACETS	0.86	0.762	0.962	0.86	0.762	0.962	CLONAL	1	TRUE	1	0.583596128264901	2		237	307	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954200	48954201	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	313	416	0	ENST00000267163.4:c.1403dup	p.Leu468PhefsTer7	p.L468Ffs*7	ENST00000267163	NM_000321.2	467	-/T	15/27	0.583596128264901	2	FACETS	0.904	0.863	0.946	0.904	0.863	0.946	CLONAL	2	TRUE	0	0.583596128264901	2		416	593	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950442	38950442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	207	461	0	ENST00000357387.3:c.3508G>A	p.Glu1170Lys	p.E1170K	ENST00000357387	NM_152756.3	1170	Gaa/Aaa	31/38	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.583596128264901	2		461	695	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211449	98211449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779844193	NA	P-0023541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	214	577	0	ENST00000331920.6:c.3706G>A	p.Glu1236Lys	p.E1236K	ENST00000331920	NM_000264.3	1236	Gag/Aag	22/24	0.229684424618785	1	FACETS	0.85	0.795	0.906	0.85	0.795	0.906	INDETERMINATE	1	TRUE	0	0.583596128264901	1		577	611	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509421	149509421	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	331	681	0	ENST00000261799.4:c.1478G>T	p.Ser493Ile	p.S493I	ENST00000261799	NM_002609.3	493	aGc/aTc	10/23	0.415690650039894	5	FACETS	1	0.974	1	0.699	0.661	0.738	CLONAL	2	TRUE	2	0.464656424888045	5		681	1153	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226125	226125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762956849	NA	P-0023542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	330	686	0	ENST00000264932.6:c.584G>A	p.Arg195Gln	p.R195Q	ENST00000264932	NM_004168.2	195	cGg/cAg	5/15	0.415690650039894	5	FACETS	1	0.957	1	0.676	0.639	0.714	CLONAL	2	TRUE	2	0.464656424888045	5		686	1188	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0023543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	138	884	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	1	2	FACETS	0.768	0.699	0.839	1	0.987	1	SUBCLONAL	2	TRUE	1	0.24	2		884	749	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849276	76849276	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	43	606	0	ENST00000373344.5:c.6000del	p.Trp2001GlyfsTer14	p.W2001Gfs*14	ENST00000373344	NM_000489.3	2000	gaC/ga	26/35	1	2	FACETS	0.95	0.797	1	0.95	0.797	1	CLONAL	1	TRUE	1	0.24	2		606	377	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77069963	77069963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370942329	NA	P-0023544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	135	626	1	ENST00000356341.3:c.577C>T	p.Arg193Cys	p.R193C	ENST00000356341	NM_002576.4	193	Cgc/Tgc	6/15	0.322923269158785	3	FACETS	0.792	0.727	0.86	0.792	0.727	0.86	SUBCLONAL	2	FALSE	1	0.521354136935195	3		627	412	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653781	89653781	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0023544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	117	424	0	ENST00000371953.3:c.80-1del		p.X27_splice	ENST00000371953	NM_000314.4	27			0.47649873070398	2	FACETS	0.853	0.784	0.923	0.853	0.784	0.923	CLONAL	2	FALSE	0	0.521354136935195	2		424	263	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223857	36223858	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs754806477	NA	P-0023544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	201	942	0	ENST00000222270.7:c.6413dup	p.Ala2139GlyfsTer6	p.A2139Gfs*6	ENST00000222270	NM_014727.1	2136	ctc/ctCc	28/37	0.215546671182012	5	FACETS	1	0.979	1	0.747	0.696	0.799	INDETERMINATE	2	FALSE	2	0.521354136935195	5		942	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0023546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	360	628	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.835504014026014	3	FACETS	0.933	0.908	0.955	0.933	0.908	0.955	CLONAL	3	TRUE	0	0.865627647901116	3		628	426	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913396	NA	P-0023546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	95	390	0	ENST00000349496.5:c.95A>C	p.Asp32Ala	p.D32A	ENST00000349496	NM_001904.3	32	gAc/gCc	3/15	0.363945489080159	6	FACETS	0.828	0.744	0.916	0.552	0.496	0.611	INDETERMINATE	2	TRUE	3	0.865627647901116	6		390	362	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106519962	106519962	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0023546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	54	243	1	ENST00000359195.3:c.2392-2A>T		p.X798_splice	ENST00000359195	NM_002649.2	798			0.760160242522575	3	FACETS	0.926	0.803	1	0.463	0.401	0.528	CLONAL	1	TRUE	1	0.865627647901116	3		244	193	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856079	151856079	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	118	579	0	ENST00000262189.6:c.11539A>G	p.Lys3847Glu	p.K3847E	ENST00000262189	NM_170606.2	3847	Aag/Gag	44/59	0.625043340832666	3	FACETS	1	0.939	1	0.519	0.473	0.567	CLONAL	1	TRUE	1	0.865627647901116	3		579	376	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433706	149433706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	238	659	2	ENST00000286301.3:c.2845G>A	p.Glu949Lys	p.E949K	ENST00000286301	NM_005211.3	949	Gag/Aag	22/22	1	2	FACETS	0.959	0.903	1	0.959	0.903	1	CLONAL	1	TRUE	1	0.914543709142873	2		661	543	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121912666	NA	P-0023547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	524	738	0	ENST00000269305.4:c.659A>C	p.Tyr220Ser	p.Y220S	ENST00000269305	NM_001126112.2	220	tAt/tCt	6/11	NA	2	FACETS	0.979	0.962	0.996			1	INDETERMINATE	2	TRUE	NA	0.914543709142873	2		738	585	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569644	41569644	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	72	246	0	ENST00000263253.7:c.4635C>G	p.Ser1545Arg	p.S1545R	ENST00000263253	NM_001429.3	1545	agC/agG	29/31	NA	2	FACETS	0.932	0.834	1			1	INDETERMINATE	1	TRUE	NA	0.914543709142873	2		246	169	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574577	41574577	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	283	829	0	ENST00000263253.7:c.6862C>G	p.Gln2288Glu	p.Q2288E	ENST00000263253	NM_001429.3	2288	Cag/Gag	31/31	NA	2	FACETS	1	0.958	1			1	INDETERMINATE	1	TRUE	NA	0.914543709142873	2		829	612	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	76	482	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.943	0.841	1	0.943	0.841	1	CLONAL	1	TRUE	1	0.725961267557952	2		482	222	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0023548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	81	401	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	0.725961267557952	2		401	210	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795608	42795609	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1555770200	NA	P-0023548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	68	836	0	ENST00000575354.2:c.2694dup	p.Lys899GlnfsTer32	p.K899Qfs*32	ENST00000575354	NM_015125.3	896	-/C	10/20	0.725961267557952	1	FACETS	0.422	0.37	0.476	0.422	0.37	0.476	SUBCLONAL	1	TRUE	0	0.725961267557952	1		836	283	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11313960	11313960	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	44	791	0	ENST00000361445.4:c.776A>G	p.Asp259Gly	p.D259G	ENST00000361445	NM_004958.3	259	gAt/gGt	6/58	0.725961267557952	1	FACETS	0.276	0.232	0.323	0.276	0.232	0.323	SUBCLONAL	1	TRUE	0	0.725961267557952	1		791	280	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091458	193091458	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	30	443	0	ENST00000367435.3:c.128G>C	p.Trp43Ser	p.W43S	ENST00000367435	NM_024529.4	43	tGg/tCg	1/17	1	2	FACETS	0.352	0.285	0.427	0.352	0.285	0.427	SUBCLONAL	1	TRUE	1	0.725961267557952	2		443	235	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25368488	25368488	+	intron_variant	Intron	SNP	C	C	G	novel	NA	P-0023548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	86	604	0	ENST00000311936.3:c.451-5643G>C		p.*151*	ENST00000311936	NM_004985.3	153/189			1	2	FACETS	0.5	0.444	0.559	0.5	0.444	0.559	SUBCLONAL	1	TRUE	1	0.725961267557952	2		604	474	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	155	795	1	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.350346028583479	2		796	735	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101117	27101117	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	86	740	0	ENST00000324856.7:c.4403del	p.Pro1468LeufsTer13	p.P1468Lfs*13	ENST00000324856	NM_006015.4	1467	Ccc/cc	18/20	1	2	FACETS	0.742	0.656	0.833	0.742	0.656	0.833	SUBCLONAL	1	TRUE	1	0.350346028583479	2		740	662	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	53	288	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.350346028583479	2		288	249	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	170	540	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	1	2	FACETS	1	0.97	1	1	0.993	1	CLONAL	2	TRUE	1	0.350346028583479	2		540	449	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	84	692	4	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.350346028583479	2		696	478	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	78	603	2	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	1	2	FACETS	0.878	0.774	0.99	0.878	0.774	0.99	CLONAL	1	TRUE	1	0.350346028583479	2		605	507	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111402	56111403	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGC	rs779149827	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	76	385	0	ENST00000399503.3:c.14_16dup	p.Ala5dup	p.A5dup	ENST00000399503	NM_005921.1	5	atg/atGGCg	1/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.350346028583479	2		385	378	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	152	393	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.350346028583479	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.350346028583479	2		393	385	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33446586	33446586	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs797044943	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	32	627	0	ENST00000345365.6:c.47T>C	p.Met16Thr	p.M16T	ENST00000345365	NM_002878.3	16	aTg/aCg	1/10	1	2	FACETS	0.287	0.232	0.349	0.287	0.232	0.349	SUBCLONAL	1	TRUE	1	0.350346028583479	2		627	637	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391986	139391986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs567909904	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	147	709	2	ENST00000277541.6:c.6205G>A	p.Ala2069Thr	p.A2069T	ENST00000277541	NM_017617.3	2069	Gcc/Acc	34/34	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.350346028583479	2		711	665	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648416	30648416	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	102	543	0	ENST00000295754.5:c.41T>C	p.Ile14Thr	p.I14T	ENST00000295754	NM_003242.5	14	aTc/aCc	1/7	0.350346028583479	2	FACETS	1	0.909	1	0.507	0.455	0.563	CLONAL	1	TRUE	0	0.350346028583479	2		543	574	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572649	64572649	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746135199	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	146	730	0	ENST00000312049.6:c.1207G>A	p.Ala403Thr	p.A403T	ENST00000312049	NM_130799.2	403	Gcc/Acc	9/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.350346028583479	2		730	705	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	141	747	4	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.350346028583479	2		751	735	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711960	89711960	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1554900620	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	71	547	0	ENST00000371953.3:c.578T>C	p.Leu193Pro	p.L193P	ENST00000371953	NM_000314.4	193	cTg/cCg	6/9	1	2	FACETS	0.843	0.737	0.956	0.843	0.737	0.956	CLONAL	1	TRUE	1	0.350346028583479	2		547	481	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272337	15272337	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs771517374	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	163	896	9	ENST00000263388.2:c.6102del	p.Gly2035ValfsTer50	p.G2035Vfs*50	ENST00000263388	NM_000435.2	2034	ccC/cc	33/33	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.350346028583479	2		905	789	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513282	44513287	+	inframe_deletion	In_Frame_Del	DEL	CCACCG	CCACCG	-	rs745888281	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	93	794	1	ENST00000291552.4:c.648_653del	p.Gly222_Gly223del	p.G222_G223del	ENST00000291552	NM_006758.2	216	ggCGGTGGt/ggt	8/8	1	2	FACETS	0.605	0.537	0.677	0.605	0.537	0.677	SUBCLONAL	1	TRUE	1	0.350346028583479	2		795	878	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591131	67591148	+	inframe_deletion	In_Frame_Del	DEL	AGACGAGAGACCAATACT	AGACGAGAGACCAATACT	-	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	53	363	0	ENST00000274335.5:c.1724_1741del	p.Lys575_Leu581delinsMet	p.K575_L581delinsM	ENST00000274335		575	aAGACGAGAGACCAATACTtg/atg	12/15	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.350346028583479	2		363	297	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656840	45656840	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	143	616	7	ENST00000407780.3:c.316del	p.Gln106ArgfsTer11	p.Q106Rfs*11	ENST00000407780	NM_001283052.1	106	Cag/ag	3/7	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.350346028583479	2		623	638	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	144	764	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	0.350346028583479	2		767	620	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800902	120800903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs748469666	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	183	827	7	ENST00000257552.2:c.345dup	p.Leu116AlafsTer15	p.L116Afs*15	ENST00000257552	NM_002442.3	115	-/G	6/15	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.350346028583479	2		834	985	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913836	32913837	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359507	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	81	571	1	ENST00000380152.3:c.5351dup	p.Asn1784LysfsTer3	p.N1784Kfs*3	ENST00000380152		1782	caa/cAaa	11/27	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.350346028583479	2		572	377	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204992	128204992	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	121	702	1	ENST00000341105.2:c.449del	p.Gly150GlufsTer68	p.G150Efs*68	ENST00000341105	NM_032638.4	150	gGa/ga	3/6	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.350346028583479	2		703	562	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085954	16085954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1558536330	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	99	571	0	ENST00000281043.3:c.1130C>T	p.Ser377Leu	p.S377L	ENST00000281043	NM_005378.4	377	tCg/tTg	3/3	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.350346028583479	2		571	524	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138845	64138845	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761843231	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	159	735	0	ENST00000334205.4:c.2212G>A	p.Ala738Thr	p.A738T	ENST00000334205	NM_003942.2	738	Gcc/Acc	17/17	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.350346028583479	2		735	668	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788609	3788609	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs945398646	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	124	491	0	ENST00000262367.5:c.4345G>A	p.Val1449Ile	p.V1449I	ENST00000262367	NM_004380.2	1449	Gtt/Att	26/31	0.350346028583479	2	FACETS	1	0.979	1	0.641	0.582	0.703	CLONAL	1	TRUE	0	0.350346028583479	2		491	552	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142991	30142991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs62129830	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	217	898	2	ENST00000389048.3:c.535C>T	p.Arg179Cys	p.R179C	ENST00000389048	NM_004304.4	179	Cgc/Tgc	1/29	1	2	FACETS	0.76	0.708	0.813	1	0.992	1	SUBCLONAL	2	TRUE	1	0.350346028583479	2		900	815	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554345	141554345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748399150	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	190	929	6	ENST00000220592.5:c.1806del	p.Ala603ProfsTer92	p.A603Pfs*92	ENST00000220592	NM_012154.3	602	ccC/cc	14/19	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.350346028583479	2		935	901	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115446	115115446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	127	672	0	ENST00000257566.3:c.880del	p.Ile294Ter	p.I294*	ENST00000257566	NM_016569.3	294	Ata/ta	5/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.350346028583479	2		672	609	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946453	2946453	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368574818	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	140	673	3	ENST00000396946.4:c.3284C>T	p.Thr1095Met	p.T1095M	ENST00000396946	NM_032415.4	1095	aCg/aTg	25/25	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.350346028583479	2		676	697	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780039	9780039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	118	753	2	ENST00000377346.4:c.1303G>A	p.Gly435Arg	p.G435R	ENST00000377346	NM_005026.3	435	Ggg/Agg	10/24	1	2	FACETS	0.923	0.833	1	0.923	0.833	1	CLONAL	1	TRUE	1	0.350346028583479	2		755	730	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2966388	2966388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145836432	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	152	674	0	ENST00000396946.4:c.1792G>A	p.Ala598Thr	p.A598T	ENST00000396946	NM_032415.4	598	Gcc/Acc	14/25	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.350346028583479	2		674	698	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11193154	11193154	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471906651	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	120	606	1	ENST00000361445.4:c.5347G>A	p.Asp1783Asn	p.D1783N	ENST00000361445	NM_004958.3	1783	Gac/Aac	38/58	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.350346028583479	2		607	580	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101369	27101369	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141670393	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	122	709	2	ENST00000324856.7:c.4651C>T	p.Arg1551Cys	p.R1551C	ENST00000324856	NM_006015.4	1551	Cgc/Tgc	18/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.350346028583479	2		711	557	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743794	46743794	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1317322008	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	151	753	0	ENST00000371975.4:c.2084A>G	p.Asp695Gly	p.D695G	ENST00000371975	NM_003579.3	695	gAt/gGt	18/18	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.350346028583479	2		753	720	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248126	59248126	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs763958620	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	37	174	0	ENST00000371222.2:c.617A>C	p.Gln206Pro	p.Q206P	ENST00000371222	NM_002228.3	206	cAg/cCg	1/1	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.350346028583479	2		174	143	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491737	120491737	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	24	438	0	ENST00000256646.2:c.2492A>G	p.Gln831Arg	p.Q831R	ENST00000256646	NM_024408.3	831	cAg/cGg	16/34	1	2	FACETS	0.29	0.227	0.364	0.29	0.227	0.364	SUBCLONAL	1	TRUE	1	0.350346028583479	2		438	472	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570787	226570787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1397522095	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	134	575	0	ENST00000366794.5:c.1109C>T	p.Pro370Leu	p.P370L	ENST00000366794	NM_001618.3	370	cCg/cTg	8/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.350346028583479	2		575	629	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263999	104264000	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	87	512	1	ENST00000369902.3:c.95dup	p.Leu34ThrfsTer14	p.L34Tfs*14	ENST00000369902	NM_016169.3	30	-/C	1/12	1	2	FACETS	0.887	0.787	0.993	0.887	0.787	0.993	CLONAL	1	TRUE	1	0.350346028583479	2		513	560	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710557	114710558	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	94	540	0	ENST00000543371.1:c.44dup	p.Asn15LysfsTer29	p.N15Kfs*29	ENST00000543371	NM_001198531.1	14	-/A	1/14	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.350346028583479	2		540	489	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936081	71936081	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	16	122	0	ENST00000298229.2:c.57del	p.Ser20ProfsTer7	p.S20Pfs*7	ENST00000298229	NM_001567.3	18	gCc/gc	1/28	1	2	FACETS	0.564	0.419	0.735	0.564	0.419	0.735	SUBCLONAL	1	TRUE	1	0.350346028583479	2		122	162	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197308	94197308	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	86	539	4	ENST00000323929.3:c.1196del	p.Phe399SerfsTer29	p.F399Sfs*29	ENST00000323929	NM_005591.3	399	tTc/tc	11/20	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.350346028583479	2		543	445	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431638	431638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	107	639	0	ENST00000399788.2:c.2371G>A	p.Ala791Thr	p.A791T	ENST00000399788	NM_001042603.1	791	Gct/Act	17/28	1	2	FACETS	0.974	0.876	1	0.974	0.876	1	CLONAL	1	TRUE	1	0.350346028583479	2		639	627	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025533	1025533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1489679789	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	149	759	0	ENST00000358495.3:c.842C>T	p.Thr281Met	p.T281M	ENST00000358495	NM_134424.2	281	aCg/aTg	9/12	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.350346028583479	2		759	765	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715671	18715671	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	70	402	0	ENST00000266497.5:c.3502A>G	p.Lys1168Glu	p.K1168E	ENST00000266497		1168	Aaa/Gaa	25/31	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.350346028583479	2		402	297	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426679	49426696	+	inframe_deletion	In_Frame_Del	DEL	GCTGTTGCTGCTGTTGAA	GCTGTTGCTGCTGTTGAA	-	rs752843878	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	47	444	0	ENST00000301067.7:c.11792_11809del	p.Leu3931_Gln3936del	p.L3931_Q3936del	ENST00000301067	NM_003482.3	3931	cTTCAACAGCAGCAACAGCag/cag	39/54	1	2	FACETS	0.625	0.528	0.732	0.625	0.528	0.732	SUBCLONAL	1	TRUE	1	0.350346028583479	2		444	429	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112000	115112000	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	178	773	0	ENST00000257566.3:c.1740C>A	p.Phe580Leu	p.F580L	ENST00000257566	NM_016569.3	580	ttC/ttA	7/8	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.350346028583479	2		773	757	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800917	120800919	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	170	751	1	ENST00000257552.2:c.329_331del	p.Lys110del	p.K110del	ENST00000257552	NM_002442.3	110	aAGAtc/atc	6/15	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.350346028583479	2		752	851	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609704	28609704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	136	778	0	ENST00000241453.7:c.1525G>A	p.Gly509Arg	p.G509R	ENST00000241453	NM_004119.2	509	Ggg/Agg	12/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.350346028583479	2		778	684	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41020908	41020908	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	80	607	4	ENST00000267868.3:c.531-1G>T		p.X177_splice	ENST00000267868	NM_002875.4	177			1	2	FACETS	0.817	0.72	0.92	0.817	0.72	0.92	CLONAL	1	TRUE	1	0.350346028583479	2		611	559	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923696	72923696	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	94	685	0	ENST00000268489.5:c.3382C>A	p.Leu1128Ile	p.L1128I	ENST00000268489	NM_006885.3	1128	Ctt/Att	4/10	1	2	FACETS	0.801	0.713	0.894	0.801	0.713	0.894	CLONAL	1	TRUE	1	0.350346028583479	2		685	670	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349770	89349770	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	181	917	1	ENST00000301030.4:c.3180del	p.Asp1061IlefsTer257	p.D1061Ifs*257	ENST00000301030	NM_001256183.1	1060	aaA/aa	9/13	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.350346028583479	2		918	900	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7218328	7218328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	125	713	1	ENST00000380728.2:c.44C>T	p.Ala15Val	p.A15V	ENST00000380728		15	gCc/gTc	2/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.350346028583479	2		714	611	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979584	7979584	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	122	702	1	ENST00000319144.4:c.1441C>A	p.Leu481Ile	p.L481I	ENST00000319144	NM_001139.2	481	Ctc/Atc	11/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.350346028583479	2		703	595	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618494	37618494	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	126	601	0	ENST00000447079.4:c.174del	p.Glu59LysfsTer33	p.E59Kfs*33	ENST00000447079	NM_015083.1	57	aCc/ac	1/14	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.350346028583479	2		601	573	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	97	904	0	ENST00000293328.3:c.1101_1102dup	p.Gln368ProfsTer3	p.Q368Pfs*3	ENST00000293328	NM_012448.3	368	cag/cCCag	9/19	1	2	FACETS	0.654	0.582	0.73	0.654	0.582	0.73	SUBCLONAL	1	TRUE	1	0.350346028583479	2		904	847	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530102	63530102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555576374	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	164	706	1	ENST00000307078.5:c.2333G>A	p.Arg778Gln	p.R778Q	ENST00000307078	NM_004655.3	778	cGg/cAg	10/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.350346028583479	2		707	705	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532555	63532556	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	118	764	0	ENST00000307078.5:c.2023dup	p.Arg675ProfsTer32	p.R675Pfs*32	ENST00000307078	NM_004655.3	675	cgt/cCgt	8/11	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.350346028583479	2		764	673	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622384	1622384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775205212	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	159	875	0	ENST00000344749.5:c.580G>A	p.Gly194Ser	p.G194S	ENST00000344749	NM_001136139.2	194	Ggc/Agc	9/19	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.350346028583479	2		875	814	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7119536	7119536	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	147	665	1	ENST00000302850.5:c.3718C>A	p.Leu1240Met	p.L1240M	ENST00000302850	NM_000208.2	1240	Ctg/Atg	21/22	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.350346028583479	2		666	712	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752802	42752802	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	134	820	0	ENST00000222329.4:c.1462T>G	p.Trp488Gly	p.W488G	ENST00000222329	NM_006494.2	488	Tgg/Ggg	4/4	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.350346028583479	2		820	750	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213243	39213243	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	160	898	3	ENST00000402219.2:c.3724del	p.Ser1242ValfsTer37	p.S1242Vfs*37	ENST00000402219	NM_005633.3	1242	Agt/gt	23/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.350346028583479	2		901	781	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661635	227661635	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	98	617	0	ENST00000305123.5:c.1820A>G	p.His607Arg	p.H607R	ENST00000305123	NM_005544.2	607	cAc/cGc	1/2	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.350346028583479	2		617	450	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024822	31024822	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	144	657	0	ENST00000375687.4:c.4307T>C	p.Ile1436Thr	p.I1436T	ENST00000375687	NM_015338.5	1436	aTc/aCc	13/13	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.350346028583479	2		657	736	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089053	37089053	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	176	462	0	ENST00000231790.2:c.1775del	p.Ser592IlefsTer24	p.S592Ifs*24	ENST00000231790	NM_000249.3	592	aGt/at	16/19	0.350346028583479	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.350346028583479	2		462	493	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584655	52584655	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	109	622	0	ENST00000394830.3:c.4360-2A>G		p.X1454_splice	ENST00000394830	NM_018313.4	1454			0.350346028583479	2	FACETS	1	0.96	1	0.564	0.508	0.622	CLONAL	1	TRUE	0	0.350346028583479	2		622	552	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662972	52662972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779427834	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	126	550	3	ENST00000394830.3:c.1381C>T	p.Arg461Cys	p.R461C	ENST00000394830	NM_018313.4	461	Cgc/Tgc	13/30	0.350346028583479	2	FACETS	1	0.98	1	0.641	0.583	0.702	CLONAL	1	TRUE	0	0.350346028583479	2		553	561	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928437	69928437	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs756658674	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	125	683	0	ENST00000352241.4:c.257T>C	p.Met86Thr	p.M86T	ENST00000352241	NM_198159.2	86	aTg/aCg	2/10	0.350346028583479	2	FACETS	1	0.95	1	0.537	0.486	0.589	CLONAL	1	TRUE	0	0.350346028583479	2		683	665	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279286	142279286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1289739042	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	19	500	0	ENST00000350721.4:c.1360G>A	p.Val454Met	p.V454M	ENST00000350721	NM_001184.3	454	Gtg/Atg	6/47	1	2	FACETS	0.302	0.229	0.389	0.302	0.229	0.389	SUBCLONAL	1	TRUE	1	0.350346028583479	2		500	359	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916894	178916894	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	35	754	0	ENST00000263967.3:c.285del	p.Gln96AsnfsTer4	p.Q96Nfs*4	ENST00000263967	NM_006218.2	94	cTt/ct	2/21	1	2	FACETS	0.331	0.27	0.399	0.331	0.27	0.399	SUBCLONAL	1	TRUE	1	0.350346028583479	2		754	604	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430482	181430482	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	129	711	0	ENST00000325404.1:c.337del	p.Arg113GlyfsTer8	p.R113Gfs*8	ENST00000325404	NM_003106.3	112	Ccc/cc	1/1	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.350346028583479	2		711	700	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182679041	182679042	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	85	586	0	ENST00000292782.4:c.492dup	p.Ala165CysfsTer23	p.A165Cfs*23	ENST00000292782	NM_020640.2	164	-/T	4/7	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.350346028583479	2		586	445	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185169182	185169182	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	85	478	0	ENST00000265026.3:c.1277A>G	p.Gln426Arg	p.Q426R	ENST00000265026	NM_004721.4	426	cAg/cGg	7/14	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.350346028583479	2		478	445	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201845	66201845	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	71	465	0	ENST00000273854.3:c.2659-2A>G		p.X887_splice	ENST00000273854	NM_004439.5	887			1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.350346028583479	2		465	363	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522545	187522545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767796174	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	117	609	1	ENST00000441802.2:c.11518G>A	p.Val3840Met	p.V3840M	ENST00000441802	NM_005245.3	3840	Gtg/Atg	21/27	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.350346028583479	2		610	585	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539855	187539855	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	110	461	1	ENST00000441802.2:c.7885G>A	p.Ala2629Thr	p.A2629T	ENST00000441802	NM_005245.3	2629	Gcc/Acc	10/27	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.350346028583479	2		462	485	SUCCESS
APC	324	MSKCC	GRCh37	5	112173818	112173818	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs536223189	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	55	431	0	ENST00000257430.4:c.2527A>G	p.Ser843Gly	p.S843G	ENST00000257430	NM_000038.5	843	Agt/Ggt	16/16	1	2	FACETS	0.94	0.809	1	0.94	0.809	1	CLONAL	1	TRUE	1	0.350346028583479	2		431	334	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131976379	131976379	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1554101170	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	143	613	0	ENST00000265335.6:c.3634A>G	p.Ile1212Val	p.I1212V	ENST00000265335		1212	Atc/Gtc	24/25	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.350346028583479	2		613	660	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777973	27777973	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs576862710	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	85	529	2	ENST00000369163.2:c.122G>A	p.Arg41His	p.R41H	ENST00000369163	NM_003536.2	41	cGc/cAc	1/1	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.350346028583479	2		531	403	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322976	31322976	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	211	1123	0	ENST00000412585.2:c.920C>A	p.Pro307His	p.P307H	ENST00000412585	NM_005514.6	307	cCc/cAc	5/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.350346028583479	2		1123	1020	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286806	33286806	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	85	554	1	ENST00000374542.5:c.2131C>A	p.His711Asn	p.H711N	ENST00000374542	NM_001141970.1	711	Cat/Aat	7/8	1	2	FACETS	0.998	0.886	1	0.998	0.886	1	CLONAL	1	TRUE	1	0.350346028583479	2		555	486	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106543584	106543584	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	50	323	0	ENST00000369096.4:c.386A>G	p.Asn129Ser	p.N129S	ENST00000369096	NM_001198.3	129	aAc/aGc	3/7	1	2	FACETS	0.991	0.847	1	0.991	0.847	1	CLONAL	1	TRUE	1	0.350346028583479	2		323	288	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527329	137527329	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	126	715	0	ENST00000367739.4:c.317T>C	p.Val106Ala	p.V106A	ENST00000367739	NM_000416.2	106	gTt/gCt	3/7	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.350346028583479	2		715	625	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13949301	13949301	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	66	349	0	ENST00000405192.2:c.827G>T	p.Arg276Met	p.R276M	ENST00000405192	NM_001163147.1	276	aGg/aTg	9/12	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.350346028583479	2		349	310	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374358	81374358	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	82	459	0	ENST00000222390.5:c.704G>T	p.Trp235Leu	p.W235L	ENST00000222390	NM_000601.4	235	tGg/tTg	6/18	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.350346028583479	2		459	407	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845684	151845684	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	93	651	1	ENST00000262189.6:c.13328A>G	p.Gln4443Arg	p.Q4443R	ENST00000262189	NM_170606.2	4443	cAg/cGg	52/59	1	2	FACETS	0.951	0.848	1	0.951	0.848	1	CLONAL	1	TRUE	1	0.350346028583479	2		652	558	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194702	29194702	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	164	778	0	ENST00000240100.2:c.1026G>T	p.Glu342Asp	p.E342D	ENST00000240100	NM_001394.6	342	gaG/gaT	4/4	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.350346028583479	2		778	738	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006077	22006077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377723228	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	126	606	0	ENST00000276925.6:c.326G>A	p.Arg109His	p.R109H	ENST00000276925	NM_004936.3	109	cGc/cAc	2/2	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.350346028583479	2		606	536	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137299993	137299993	+	splice_acceptor_variant	Splice_Site	DEL	A	A	-	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	110	557	0	ENST00000481739.1:c.280-2del		p.X94_splice	ENST00000481739	NM_002957.4	94			1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.350346028583479	2		557	598	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793278	139793278	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	147	743	0	ENST00000247668.2:c.86A>G	p.Glu29Gly	p.E29G	ENST00000247668	NM_021138.3	29	gAa/gGa	2/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.350346028583479	2		743	747	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139811047	139811047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559816825	NA	P-0023551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	144	631	3	ENST00000247668.2:c.658G>A	p.Ala220Thr	p.A220T	ENST00000247668	NM_021138.3	220	Gcc/Acc	7/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.350346028583479	2		634	697	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0023552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	43	238	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.658	0.551	0.777	0.658	0.551	0.777	SUBCLONAL	1	TRUE	1	0.287690506171802	2		238	454	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0023552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	173	1087	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.287690506171802	3	FACETS	0.841	0.775	0.909	0.561	0.516	0.606	CLONAL	2	TRUE	0	0.287690506171802	3		1087	818	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0023553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	287	879	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.36554465108776	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.507145133657831	2		881	507	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528105	157528105	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1028186690	NA	P-0023553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	162	504	1	ENST00000346085.5:c.5830C>T	p.Arg1944Ter	p.R1944*	ENST00000346085	NM_020732.3	1944	Cga/Tga	20/20	0.507145133657831	3	FACETS	1	0.989	1	0.75	0.692	0.809	CLONAL	1	TRUE	1	0.507145133657831	3		505	534	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955187	17955187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs896064879	NA	P-0023553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	341	979	1	ENST00000458235.1:c.40C>T	p.Arg14Cys	p.R14C	ENST00000458235	NM_000215.3	14	Cgt/Tgt	2/24	0.507145133657831	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.507145133657831	3		980	754	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627190	37627190	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	26	670	1	ENST00000447079.4:c.1105C>T	p.His369Tyr	p.H369Y	ENST00000447079	NM_015083.1	369	Cat/Tat	2/14	0.243913290275558	5	FACETS	0.366	0.289	0.455	0.122	0.096	0.152	INDETERMINATE	1	TRUE	2	0.507145133657831	5		671	493	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384818	17384818	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	79	737	0	ENST00000359435.4:c.450C>A	p.Asn150Lys	p.N150K	ENST00000359435	NM_001033549.1	150	aaC/aaA	4/9	0.507145133657831	3	FACETS	0.503	0.441	0.569	0.251	0.22	0.285	SUBCLONAL	1	TRUE	1	0.507145133657831	3		737	777	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530116	212530116	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	66	522	1	ENST00000342788.4:c.1803C>A	p.Asn601Lys	p.N601K	ENST00000342788	NM_005235.2	601	aaC/aaA	15/28	0.507145133657831	3	FACETS	0.85	0.741	0.966	0.425	0.37	0.483	CLONAL	1	TRUE	1	0.507145133657831	3		523	384	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439590	220439590	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	98	663	0	ENST00000243786.2:c.443C>G	p.Ser148Cys	p.S148C	ENST00000243786	NM_002191.3	148	tCt/tGt	2/2	0.507145133657831	3	FACETS	0.873	0.781	0.97	0.436	0.39	0.485	CLONAL	1	TRUE	1	0.507145133657831	3		663	555	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555305	106555305	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	64	635	0	ENST00000369096.4:c.2422C>A	p.Leu808Ile	p.L808I	ENST00000369096	NM_001198.3	808	Cta/Ata	7/7	0.507145133657831	3	FACETS	0.732	0.636	0.836	0.366	0.318	0.418	SUBCLONAL	1	TRUE	1	0.507145133657831	3		635	432	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663587	117663587	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	89	864	1	ENST00000368508.3:c.4645A>T	p.Ile1549Phe	p.I1549F	ENST00000368508	NM_002944.2	1549	Att/Ttt	28/43	0.121219318515156	3	FACETS	0.946	0.843	1			1	INDETERMINATE	1	TRUE	NA	0.507145133657831	3		865	465	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227986	55227986	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769434273	NA	P-0023553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	71	366	0	ENST00000275493.2:c.1453G>A	p.Gly485Ser	p.G485S	ENST00000275493	NM_005228.3	485	Ggt/Agt	12/28	0.507145133657831	3	FACETS	1	0.969	1	0.655	0.578	0.736	CLONAL	1	TRUE	1	0.507145133657831	3		366	268	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136839	69136839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780008732	NA	P-0023553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	176	527	1	ENST00000288368.4:c.4753C>T	p.Arg1585Trp	p.R1585W	ENST00000288368	NM_024870.2	1585	Cgg/Tgg	39/40	0.43734055264687	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	2	0.507145133657831	4		528	499	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098957	178098957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	75	455	0	ENST00000397062.3:c.88C>T	p.Leu30Phe	p.L30F	ENST00000397062	NM_006164.4	30	Ctt/Ttt	2/5	1	2	FACETS	0.761	0.67	0.858	1	0.977	1	SUBCLONAL	2	TRUE	1	0.239280237099085	2		455	412	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0023554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	54	428	1	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	1	2	FACETS	0.979	0.838	1	0.979	0.838	1	CLONAL	1	TRUE	1	0.239280237099085	2		429	461	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310503	65310503	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	70	697	0	ENST00000342505.4:c.2185A>T	p.Ser729Cys	p.S729C	ENST00000342505	NM_002227.2	729	Agt/Tgt	16/25	1	2	FACETS	0.906	0.79	1	0.906	0.79	1	CLONAL	1	TRUE	1	0.239280237099085	2		697	646	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877881	151877881	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	59	525	0	ENST00000262189.6:c.7064T>G	p.Leu2355Arg	p.L2355R	ENST00000262189	NM_170606.2	2355	cTt/cGt	36/59	1	2	FACETS	0.975	0.84	1	0.975	0.84	1	CLONAL	1	TRUE	1	0.239280237099085	2		525	506	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0023556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	62	515	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.244678903419707	2		515	494	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0023556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	69	399	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.879	0.765	1	0.879	0.765	1	CLONAL	1	TRUE	1	0.244678903419707	2		399	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0023556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	124	1030	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.244678903419707	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.244678903419707	1		1030	858	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0023556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	408	1010	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.244671794371866	4	FACETS	0.886	0.844	0.929			1	CLONAL	4	TRUE	NA	0.244678903419707	4		1010	1171	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0023556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	82	689	3	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	0.921	0.811	1	0.921	0.811	1	CLONAL	1	TRUE	1	0.244678903419707	2		692	728	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216714	7216714	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	61	647	0	ENST00000380728.2:c.709C>T	p.Gln237Ter	p.Q237*	ENST00000380728		237	Cag/Tag	8/11	0.244678903419707	1	FACETS	0.882	0.762	1	0.882	0.762	1	CLONAL	1	TRUE	0	0.244678903419707	1		647	496	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216947	7216947	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	36	703	0	ENST00000380728.2:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000380728		192	Cag/Tag	7/11	0.244678903419707	1	FACETS	0.5	0.41	0.6	0.5	0.41	0.6	SUBCLONAL	1	TRUE	0	0.244678903419707	1		703	517	SUCCESS
BLM	641	MSKCC	GRCh37	15	91328178	91328178	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	80	622	0	ENST00000355112.3:c.2690C>T	p.Ser897Phe	p.S897F	ENST00000355112	NM_000057.2	897	tCc/tTc	14/22	0.244678903419707	1	FACETS	0.936	0.825	1	0.936	0.825	1	CLONAL	1	TRUE	0	0.244678903419707	1		622	613	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849565	68849565	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	99	880	2	ENST00000261769.5:c.1468G>T	p.Glu490Ter	p.E490*	ENST00000261769	NM_004360.3	490	Gaa/Taa	10/16	0.244678903419707	1	FACETS	0.972	0.868	1	0.972	0.868	1	CLONAL	1	TRUE	0	0.244678903419707	1		882	731	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599995	28599995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	97	966	0	ENST00000253063.3:c.877G>A	p.Glu293Lys	p.E293K	ENST00000253063	NM_031459.4	293	Gag/Aag	6/10	1	2	FACETS	0.917	0.816	1	0.917	0.816	1	CLONAL	1	TRUE	1	0.244678903419707	2		966	865	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729743	162729743	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	200	809	0	ENST00000367921.3:c.829C>A	p.Arg277Ser	p.R277S	ENST00000367921	NM_006182.2	277	Cgc/Agc	8/18	0.244678903419707	4	FACETS	1	0.965	1	0.711	0.659	0.765	CLONAL	2	TRUE	1	0.244678903419707	4		809	954	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32439151	32439151	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs865829249	NA	P-0023556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	104	911	2	ENST00000332351.3:c.922C>T	p.Gln308Ter	p.Q308*	ENST00000332351	NM_024426.4	308	Cag/Tag	4/10	1	2	FACETS	0.982	0.878	1	0.982	0.878	1	CLONAL	1	TRUE	1	0.244678903419707	2		913	866	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772207	68772207	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1221633501	NA	P-0023556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	97	976	0	ENST00000261769.5:c.56C>G	p.Ser19Cys	p.S19C	ENST00000261769	NM_004360.3	19	tCt/tGt	2/16	0.244678903419707	1	FACETS	0.88	0.784	0.982	0.88	0.784	0.982	CLONAL	1	TRUE	0	0.244678903419707	1		976	791	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923828	72923828	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	63	776	0	ENST00000268489.5:c.3250G>C	p.Glu1084Gln	p.E1084Q	ENST00000268489	NM_006885.3	1084	Gag/Cag	4/10	0.244678903419707	1	FACETS	0.797	0.69	0.914	0.797	0.69	0.914	CLONAL	1	TRUE	0	0.244678903419707	1		776	567	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351364	89351364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	130	1108	0	ENST00000301030.4:c.1586C>T	p.Ser529Phe	p.S529F	ENST00000301030	NM_001256183.1	529	tCt/tTt	9/13	0.244678903419707	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.244678903419707	1		1108	867	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216439	7216439	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs772570395	NA	P-0023556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	105	867	0	ENST00000380728.2:c.809C>G	p.Ser270Cys	p.S270C	ENST00000380728		270	tCt/tGt	10/11	0.244678903419707	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.244678903419707	1		867	737	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17947996	17947996	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	123	1064	0	ENST00000458235.1:c.1728G>T	p.Met576Ile	p.M576I	ENST00000458235	NM_000215.3	576	atG/atT	13/24	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.244678903419707	2		1064	1002	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791385	42791385	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	117	893	0	ENST00000575354.2:c.445G>C	p.Asp149His	p.D149H	ENST00000575354	NM_015125.3	149	Gat/Cat	3/20	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.244678903419707	2		893	886	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719694	190719694	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs140854388	NA	P-0023556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	54	437	0	ENST00000441310.2:c.1696C>G	p.Leu566Val	p.L566V	ENST00000441310	NM_000534.4	566	Ctt/Gtt	9/13	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.244678903419707	2		437	415	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114806	73114806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1440424261	NA	P-0023556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	15	11	0	ENST00000356692.5:c.1187C>T	p.Ser396Leu	p.S396L	ENST00000356692		396	tCa/tTa	9/9	1	2	FACETS	0.929	0.761	1	1	0.951	1	CLONAL	6	TRUE	1	0.244678903419707	2		11	22	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542840	187542840	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	54	714	0	ENST00000441802.2:c.4900G>A	p.Asp1634Asn	p.D1634N	ENST00000441802	NM_005245.3	1634	Gat/Aat	10/27	1	2	FACETS	0.676	0.577	0.785	0.676	0.577	0.785	SUBCLONAL	1	TRUE	1	0.244678903419707	2		714	653	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339418	116339418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs899151863	NA	P-0023556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	76	540	0	ENST00000397752.3:c.280G>A	p.Asp94Asn	p.D94N	ENST00000397752	NM_000245.2	94	Gat/Aat	2/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.244678903419707	2		540	485	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248153	110248153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	62	663	0	ENST00000374672.4:c.1319C>T	p.Ser440Leu	p.S440L	ENST00000374672	NM_004235.4	440	tCa/tTa	5/5	1	2	FACETS	0.863	0.746	0.991	0.863	0.746	0.991	CLONAL	1	TRUE	1	0.244678903419707	2		663	587	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841195	15841206	+	inframe_deletion	In_Frame_Del	DEL	AGGGACCGCAGC	AGGGACCGCAGC	-	rs754928493	NA	P-0023556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	32	718	0	ENST00000307771.7:c.1291_1302del	p.Asp432_Arg435del	p.D432_R435del	ENST00000307771	NM_005089.3	427	AGGGACCGCAGC/-	11/11	0.244678903419707	1	FACETS	0.408	0.331	0.497	0.408	0.331	0.497	SUBCLONAL	1	TRUE	0	0.244678903419707	1		718	562	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227935	123227935	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	72	676	0	ENST00000218089.9:c.3646G>A	p.Glu1216Lys	p.E1216K	ENST00000218089	NM_001042749.1	1216	Gaa/Aaa	33/35	0.244678903419707	1	FACETS	0.908	0.794	1	0.908	0.794	1	CLONAL	1	TRUE	0	0.244678903419707	1		676	569	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0023557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	121	399	0				ENST00000310581	NM_198253.2	-/1132			0.34277869864394	3	FACETS	0.8	0.727	0.876	0.8	0.727	0.876	SUBCLONAL	2	TRUE	1	0.367579172805959	3		399	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579536	7579536	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567556930	NA	P-0023557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	246	855	0	ENST00000269305.4:c.151G>T	p.Glu51Ter	p.E51*	ENST00000269305	NM_001126112.2	51	Gaa/Taa	4/11	0.363579980339655	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.367579172805959	2		855	648	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952100	178952100	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	61	468	0	ENST00000263967.3:c.3155C>A	p.Thr1052Lys	p.T1052K	ENST00000263967	NM_006218.2	1052	aCa/aAa	21/21	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.367579172805959	2		468	332	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579864	7579864	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	222	725	1	ENST00000269305.4:c.49G>T	p.Glu17Ter	p.E17*	ENST00000269305	NM_001126112.2	17	Gaa/Taa	2/11	0.363579980339655	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	0	0.367579172805959	2		726	600	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603090	48603090	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	100	571	0	ENST00000342988.3:c.1391C>G	p.Ala464Gly	p.A464G	ENST00000342988	NM_005359.5	464	gCc/gGc	11/12	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.367579172805959	2		571	510	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022242	31022242	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	63	344	0	ENST00000375687.4:c.1729del	p.Ser577HisfsTer126	p.S577Hfs*126	ENST00000375687	NM_015338.5	576	cTt/ct	13/13	1	2	FACETS	0.979	0.852	1	0.979	0.852	1	CLONAL	1	TRUE	1	0.367579172805959	2		344	350	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713707	30713707	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	71	418	0	ENST00000295754.5:c.1032G>A	p.Trp344Ter	p.W344*	ENST00000295754	NM_003242.5	344	tgG/tgA	4/7	0.367579172805959	1	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	0	0.367579172805959	1		418	308	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591247	67591247	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0023558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	59	512	0	ENST00000274335.5:c.1746-1G>C		p.X582_splice	ENST00000274335		582			0.468812595202459	3	FACETS	0.909	0.787	1	0.455	0.393	0.52	CLONAL	1	TRUE	1	0.514935405897118	3		512	317	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577529	7577529	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs730882027	NA	P-0023558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	218	830	0	ENST00000269305.4:c.752T>A	p.Ile251Asn	p.I251N	ENST00000269305	NM_001126112.2	251	aTc/aAc	7/11	0.451266035195414	2	FACETS	0.877	0.824	0.929	0.877	0.824	0.929	CLONAL	2	TRUE	0	0.514935405897118	2		830	483	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076761	72076761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	130	814	0	ENST00000357731.5:c.736G>A	p.Glu246Lys	p.E246K	ENST00000357731	NM_173808.2	246	Gaa/Aaa	5/7	0.468812595202459	3	FACETS	1	0.911	1	0.501	0.455	0.548	CLONAL	1	TRUE	1	0.514935405897118	3		814	634	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971068	21971068	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	214	668	2	ENST00000304494.5:c.290T>C	p.Leu97Pro	p.L97P	ENST00000304494	NM_000077.4	97	cTg/cCg	2/3	0.456036997808921	2	FACETS	0.969	0.913	1	0.969	0.913	1	CLONAL	2	TRUE	0	0.514935405897118	2		670	429	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396701	396701	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	160	639	0	ENST00000262320.3:c.325G>C	p.Glu109Gln	p.E109Q	ENST00000262320	NM_003502.3	109	Gag/Cag	2/11	0.336012363077684	4	FACETS	0.778	0.717	0.842	0.778	0.717	0.842	SUBCLONAL	2	TRUE	2	0.514935405897118	4		639	605	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15280897	15280897	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	225	751	0	ENST00000263388.2:c.5199G>T	p.Lys1733Asn	p.K1733N	ENST00000263388	NM_000435.2	1733	aaG/aaT	28/33	0.225161775869668	4	FACETS	0.936	0.876	0.998	0.936	0.876	0.998	INDETERMINATE	2	TRUE	2	0.514935405897118	4		751	707	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160731	56160731	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	55	549	0	ENST00000399503.3:c.1005C>A	p.Asp335Glu	p.D335E	ENST00000399503	NM_005921.1	335	gaC/gaA	4/20	0.468812595202459	3	FACETS	0.694	0.596	0.801	0.347	0.298	0.401	SUBCLONAL	1	TRUE	1	0.514935405897118	3		549	387	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140500195	140500195	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0023558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	427	785	0	ENST00000288602.6:c.947C>G	p.Ser316Ter	p.S316*	ENST00000288602	NM_004333.4	316	tCa/tGa	7/18	0.514935405897118	3	FACETS	0.972	0.936	1	0.972	0.936	1	CLONAL	3	TRUE	0	0.514935405897118	3		785	715	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229650	98229651	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0023558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	190	465	0	ENST00000331920.6:c.2307_2308del	p.Arg770SerfsTer19	p.R770Sfs*19	ENST00000331920	NM_000264.3	769	acCCga/acga	15/24	0.45432143269986	3	FACETS	1	0.988	1	0.814	0.764	0.864	CLONAL	2	TRUE	0	0.514935405897118	3		465	380	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	72	896	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.606988884977981	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.606988884977981	2		898	108	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593464	55593464	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs3822214	NA	P-0023561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	9	549	0	ENST00000288135.5:c.1621A>C	p.Met541Leu	p.M541L	ENST00000288135	NM_000222.2	541	Atg/Ctg	10/21	0.29411305442278	5	FACETS	0.177	0.116	0.254	0.059	0.038	0.085	SUBCLONAL	1	FALSE	2	0.414180245570171	5		549	399	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176176063	176176064	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0023561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	61	897	0	ENST00000367669.3:c.51dup	p.Ser18ValfsTer60	p.S18Vfs*60	ENST00000367669	NM_022457.5	17	-/G	1/20	0.414180245570171	6	FACETS	0.613	0.528	0.707	0.204	0.176	0.236	SUBCLONAL	1	FALSE	3	0.414180245570171	6		897	878	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900099	151900099	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	52	787	0	ENST00000262189.6:c.4012del	p.Thr1338LeufsTer7	p.T1338Lfs*7	ENST00000262189	NM_170606.2	1338	Act/ct	26/59	NA	2	FACETS	0.756	0.647	0.875			1	INDETERMINATE	1	FALSE	NA	0.414180245570171	2		787	332	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538923	23538923	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	31	791	1	ENST00000380871.4:c.516C>A	p.Phe172Leu	p.F172L	ENST00000380871	NM_006167.3	172	ttC/ttA	2/2	0.414180245570171	3	FACETS	0.423	0.342	0.515	0.141	0.114	0.172	SUBCLONAL	1	FALSE	0	0.414180245570171	3		792	427	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	135	482	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.986	0.907	1	0.986	0.907	1	CLONAL	1	TRUE	1	0.720264996473599	2		482	380	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0023566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	21	722	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.114	0.087	0.146	0.114	0.087	0.146	SUBCLONAL	1	TRUE	1	0.720264996473599	2		722	510	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919236	48919236	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0023566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	120	253	0	ENST00000267163.4:c.401T>A	p.Leu134Ter	p.L134*	ENST00000267163	NM_000321.2	134	tTa/tAa	4/27	0.716637733031328	1	FACETS	0.931	0.861	1	0.931	0.861	1	CLONAL	1	TRUE	0	0.720264996473599	1		253	229	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43767797	43767797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	179	564	1	ENST00000382044.4:c.1051G>A	p.Gly351Ser	p.G351S	ENST00000382044	NM_001141980.1	351	Ggt/Agt	9/28	1	2	FACETS	0.815	0.755	0.876	0.815	0.755	0.876	CLONAL	1	TRUE	1	0.720264996473599	2		565	610	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	267	811	1	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.720264996473599	2		812	710	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589149	67589151	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	novel	NA	P-0023566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	60	303	0	ENST00000274335.5:c.1138_1140del	p.Leu380del	p.L380del	ENST00000274335		379	aaATTa/aaa	9/15	1	2	FACETS	0.387	0.334	0.445	0.387	0.334	0.445	SUBCLONAL	1	TRUE	1	0.720264996473599	2		303	430	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691025	NA	P-0023567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	630	593	3	ENST00000269305.4:c.785G>T	p.Gly262Val	p.G262V	ENST00000269305	NM_001126112.2	262	gGt/gTt	8/11	0.743185808432926	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.743185808432926	2		596	820	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244226	46244226	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	242	473	0	ENST00000334344.6:c.2320C>G	p.Pro774Ala	p.P774A	ENST00000334344	NM_152641.2	774	Cca/Gca	15/21	0.743185808432926	2	FACETS	1	0.983	1	0.558	0.525	0.591	CLONAL	1	TRUE	0	0.743185808432926	2		473	584	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602379	10602379	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	484	908	2	ENST00000171111.5:c.1199C>G	p.Thr400Ser	p.T400S	ENST00000171111	NM_203500.1	400	aCc/aGc	3/6	0.743185808432926	2	FACETS	1	0.991	1	0.554	0.531	0.577	CLONAL	1	TRUE	0	0.743185808432926	2		910	1176	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0023569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	113	967	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.201184653978017	3	FACETS	1	0.965	1	0.743	0.677	0.811	INDETERMINATE	2	TRUE	0	0.376404111470727	3		967	320	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0023569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	27	431	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.332187814485597	3	FACETS	1	0.837	1			1	CLONAL	1	TRUE	NA	0.376404111470727	3		431	163	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850887	63850887	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	20	595	0	ENST00000279873.7:c.1665G>T	p.Leu555Phe	p.L555F	ENST00000279873	NM_032199.2	555	ttG/ttT	10/10	0.194560811811621	3	FACETS	0.908	0.702	1	0.454	0.351	0.573	INDETERMINATE	1	TRUE	1	0.376404111470727	3		595	139	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446144	70446144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	16	720	0	ENST00000373644.4:c.5084C>T	p.Ser1695Phe	p.S1695F	ENST00000373644	NM_030625.2	1695	tCt/tTt	11/12	0.194560811811621	3	FACETS	0.765	0.571	0.993	0.383	0.285	0.497	INDETERMINATE	1	TRUE	1	0.376404111470727	3		720	132	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424999	49424999	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	13	955	1	ENST00000301067.7:c.13489G>T	p.Gly4497Trp	p.G4497W	ENST00000301067	NM_003482.3	4497	Ggg/Tgg	39/54	0.201184653978017	3	FACETS	0.5	0.358	0.673	0.167	0.119	0.225	INDETERMINATE	1	TRUE	0	0.376404111470727	3		956	164	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915229	32915229	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782038	NA	P-0023569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	41	820	0	ENST00000380152.3:c.6737C>G	p.Pro2246Arg	p.P2246R	ENST00000380152		2246	cCa/cGa	11/27	0.215628882340206	4	FACETS	1	0.943	1	0.649	0.545	0.762	INDETERMINATE	1	TRUE	2	0.376404111470727	4		820	231	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59820448	59820448	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	27	818	0	ENST00000259008.2:c.2305C>A	p.Leu769Met	p.L769M	ENST00000259008	NM_032043.2	769	Ctg/Atg	16/20	0.156177302058982	4	FACETS	1	0.873	1	0.561	0.45	0.685	INDETERMINATE	1	TRUE	2	0.376404111470727	4		818	176	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980602	1980602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1280034307	NA	P-0023569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	24	666	1	ENST00000382891.5:c.4064G>A	p.Arg1355Gln	p.R1355Q	ENST00000382891	NM_133335.3	1355	cGg/cAg	22/22	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.376404111470727	2		667	98	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846380	128846380	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757620819	NA	P-0023569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	39	860	1	ENST00000249373.3:c.1216G>A	p.Ala406Thr	p.A406T	ENST00000249373	NM_005631.4	406	Gcc/Acc	6/12	0.194560811811621	3	FACETS	0.855	0.722	0.997	0.855	0.722	0.997	INDETERMINATE	2	TRUE	1	0.376404111470727	3		861	144	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964500	70964500	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	20	897	0	ENST00000276594.2:c.1528C>A	p.Gln510Lys	p.Q510K	ENST00000276594	NM_024504.3	510	Cag/Aag	8/8	1	2	FACETS	0.793	0.613	0.999	0.793	0.613	0.999	CLONAL	1	TRUE	1	0.376404111470727	2		897	134	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0023570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	420	735	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	NA	2	FACETS	0.981	0.939	1			1	INDETERMINATE	2	TRUE	NA	0.454807296812426	2		735	941	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710553	40710553	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778726076	NA	P-0023570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	298	677	0	ENST00000373198.4:c.4298G>A	p.Arg1433His	p.R1433H	ENST00000373198	NM_133170.3	1433	cGt/cAt	31/32	0.454807296812426	5	FACETS	0.842	0.792	0.894	0.561	0.528	0.596	CLONAL	2	TRUE	2	0.454807296812426	5		677	1309	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155654	56155654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746479827	NA	P-0023570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1315	237	434	0	ENST00000399503.3:c.746G>A	p.Arg249His	p.R249H	ENST00000399503	NM_005921.1	249	cGc/cAc	3/20	0.454807296812426	12	FACETS	1	0.975	1			1	CLONAL	2	TRUE	NA	0.454807296812426	12		434	1552	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106064	27106064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	134	439	1	ENST00000324856.7:c.5675C>T	p.Thr1892Ile	p.T1892I	ENST00000324856	NM_006015.4	1892	aCa/aTa	20/20	0.454807296812426	5	FACETS	1	0.924	1	0.255	0.231	0.28	CLONAL	1	TRUE	1	0.454807296812426	5		440	972	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450053	32450053	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	166	476	0	ENST00000332351.3:c.759G>T	p.Gln253His	p.Q253H	ENST00000332351	NM_024426.4	253	caG/caT	2/10	0.454807296812426	3	FACETS	1	0.982	1	0.618	0.569	0.669	CLONAL	1	TRUE	1	0.454807296812426	3		476	725	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456701	32456701	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	257	567	2	ENST00000332351.3:c.191C>A	p.Ser64Tyr	p.S64Y	ENST00000332351	NM_024426.4	64	tCt/tAt	1/10	0.454807296812426	3	FACETS	0.907	0.852	0.962	0.907	0.852	0.962	CLONAL	2	TRUE	1	0.454807296812426	3		569	765	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200852	67200852	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	306	599	0	ENST00000312629.5:c.840G>C	p.Lys280Asn	p.K280N	ENST00000312629	NM_003952.2	280	aaG/aaC	10/15	0.454807296812426	3	FACETS	0.895	0.845	0.945	0.895	0.845	0.945	CLONAL	2	TRUE	1	0.454807296812426	3		599	923	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344318	118344318	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	91	317	0	ENST00000534358.1:c.2444G>C	p.Arg815Thr	p.R815T	ENST00000534358	NM_005933.3	815	aGa/aCa	3/36	0.454807296812426	4	FACETS	0.941	0.836	1	0.314	0.278	0.351	CLONAL	1	TRUE	1	0.454807296812426	4		317	619	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589772	28589772	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	288	661	0	ENST00000241453.7:c.2608G>T	p.Asp870Tyr	p.D870Y	ENST00000241453	NM_004119.2	870	Gat/Tat	21/24	NA	2	FACETS	0.843	0.797	0.89			1	INDETERMINATE	2	TRUE	NA	0.454807296812426	2		661	751	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807337	3807337	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	255	453	0	ENST00000262367.5:c.3650A>G	p.Gln1217Arg	p.Q1217R	ENST00000262367	NM_004380.2	1217	cAg/cGg	19/31	0.454807296812426	3	FACETS	0.936	0.881	0.993	0.936	0.881	0.993	CLONAL	2	TRUE	1	0.454807296812426	3		453	735	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348870	11348870	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1322228094	NA	P-0023570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	61	245	0	ENST00000332029.2:c.466G>T	p.Ala156Ser	p.A156S	ENST00000332029	NM_003745.1	156	Gcg/Tcg	2/2	0.454807296812426	3	FACETS	1	0.874	1	0.503	0.437	0.575	CLONAL	1	TRUE	1	0.454807296812426	3		245	327	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347163	89347163	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	379	518	0	ENST00000301030.4:c.5787C>A	p.Ser1929Arg	p.S1929R	ENST00000301030	NM_001256183.1	1929	agC/agA	9/13	0.454807296812426	3	FACETS	0.958	0.918	0.998	0.958	0.918	0.998	CLONAL	3	TRUE	0	0.454807296812426	3		518	712	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664591	29664591	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	124	474	1	ENST00000356175.3:c.6570G>T	p.Glu2190Asp	p.E2190D	ENST00000356175	NM_000267.3	2190	gaG/gaT	42/57	0.454807296812426	3	FACETS	0.926	0.838	1	0.463	0.419	0.509	CLONAL	1	TRUE	1	0.454807296812426	3		475	723	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919736	96919736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	260	525	2	ENST00000258439.3:c.527G>A	p.Ser176Asn	p.S176N	ENST00000258439	NM_001193304.2	176	aGc/aAc	4/4	0.454807296812426	3	FACETS	0.898	0.845	0.953	0.898	0.845	0.953	CLONAL	2	TRUE	1	0.454807296812426	3		527	781	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730847	40730847	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755992110	NA	P-0023570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	434	731	0	ENST00000373198.4:c.3688G>A	p.Val1230Met	p.V1230M	ENST00000373198	NM_133170.3	1230	Gtg/Atg	27/32	0.454807296812426	5	FACETS	0.847	0.808	0.886	0.847	0.808	0.886	CLONAL	3	TRUE	2	0.454807296812426	5		731	1264	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827946	40827946	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	363	576	0	ENST00000373198.4:c.2482A>T	p.Thr828Ser	p.T828S	ENST00000373198	NM_133170.3	828	Acc/Tcc	17/32	0.454807296812426	5	FACETS	0.964	0.917	1	0.964	0.917	1	CLONAL	3	TRUE	2	0.454807296812426	5		576	929	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670713	134670713	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	277	602	0	ENST00000398015.3:c.624G>T	p.Glu208Asp	p.E208D	ENST00000398015	NM_004441.4	208	gaG/gaT	3/16	0.454807296812426	4	FACETS	0.939	0.883	0.996	0.939	0.883	0.996	CLONAL	2	TRUE	2	0.454807296812426	4		602	944	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977960	134977960	+	stop_lost	Nonstop_Mutation	SNP	T	T	A	novel	NA	P-0023570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	273	550	0	ENST00000398015.3:c.2953T>A	p.Ter985ArgextTer22	p.*985Rext*22	ENST00000398015	NM_004441.4	985	Tga/Aga	16/16	0.454807296812426	4	FACETS	0.905	0.851	0.961	0.905	0.851	0.961	CLONAL	2	TRUE	2	0.454807296812426	4		550	965	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197519	106197519	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs958792109	NA	P-0023570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	188	358	0	ENST00000380013.4:c.5852G>A	p.Arg1951Gln	p.R1951Q	ENST00000380013	NM_001127208.2	1951	cGg/cAg	11/11	0.454807296812426	3	FACETS	0.895	0.832	0.959	0.895	0.832	0.959	CLONAL	2	TRUE	1	0.454807296812426	3		358	567	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542174	187542174	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs576312211	NA	P-0023570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	226	465	1	ENST00000441802.2:c.5566C>T	p.Arg1856Cys	p.R1856C	ENST00000441802	NM_005245.3	1856	Cgt/Tgt	10/27	0.454807296812426	4	FACETS	0.905	0.845	0.966			1	CLONAL	2	TRUE	NA	0.454807296812426	4		466	799	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542653	187542653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	234	522	0	ENST00000441802.2:c.5087C>T	p.Ser1696Leu	p.S1696L	ENST00000441802	NM_005245.3	1696	tCa/tTa	10/27	0.454807296812426	4	FACETS	0.821	0.767	0.876			1	CLONAL	2	TRUE	NA	0.454807296812426	4		522	912	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526193	31526193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs970773905	NA	P-0023570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2227	154	649	2	ENST00000344624.3:c.847C>T	p.Arg283Trp	p.R283W	ENST00000344624		283	Cgg/Tgg	2/33	0.454807296812426	10	FACETS	0.802	0.73	0.878	0.115	0.104	0.126	CLONAL	1	TRUE	3	0.454807296812426	10		651	2381	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86642543	86642543	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0023570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	332	559	0	ENST00000274376.6:c.1102+2T>A		p.X368_splice	ENST00000274376	NM_002890.2	368			0.454807296812426	3	FACETS	0.894	0.853	0.936	0.894	0.853	0.936	CLONAL	3	TRUE	0	0.454807296812426	3		559	668	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374315	81374315	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0023570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	67	318	0	ENST00000222390.5:c.746+1del		p.X249_splice	ENST00000222390	NM_000601.4	249			0.454807296812426	5	FACETS	0.827	0.719	0.945	0.207	0.179	0.237	CLONAL	1	TRUE	1	0.454807296812426	5		318	599	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282059	38282059	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	579	885	0	ENST00000425967.3:c.997C>G	p.Pro333Ala	p.P333A	ENST00000425967	NM_001174067.1	333	Cca/Gca	8/19	0.242341838408209	5	FACETS	0.932	0.899	0.965			1	INDETERMINATE	4	TRUE	NA	0.454807296812426	5		885	1149	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101910062	101910062	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	130	258	0	ENST00000374994.4:c.1382G>T	p.Cys461Phe	p.C461F	ENST00000374994	NM_004612.2	461	tGt/tTt	8/9	0.454807296812426	4	FACETS	0.832	0.759	0.907	0.832	0.759	0.907	CLONAL	2	TRUE	2	0.454807296812426	4		258	500	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422655	47422655	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	154	605	0	ENST00000377045.4:c.127G>T	p.Asp43Tyr	p.D43Y	ENST00000377045	NM_001654.4	43	Gac/Tac	3/16	1	2	FACETS	0.933	0.855	1	0.933	0.855	1	CLONAL	1	TRUE	1	0.454807296812426	2		605	726	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230889	53230889	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	153	666	0	ENST00000375401.3:c.1904G>T	p.Arg635Leu	p.R635L	ENST00000375401	NM_004187.3	635	cGg/cTg	14/26	1	2	FACETS	0.915	0.839	0.995	0.915	0.839	0.995	CLONAL	1	TRUE	1	0.454807296812426	2		666	735	SUCCESS
AR	367	MSKCC	GRCh37	X	66863181	66863181	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	126	577	1	ENST00000374690.3:c.1700C>A	p.Ala567Asp	p.A567D	ENST00000374690	NM_000044.3	567	gCt/gAt	2/8	1	2	FACETS	0.856	0.777	0.939	0.856	0.777	0.939	CLONAL	1	TRUE	1	0.454807296812426	2		578	647	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361144	70361144	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	137	705	0	ENST00000374080.3:c.6332A>C	p.Gln2111Pro	p.Q2111P	ENST00000374080		2111	cAg/cCg	43/45	1	2	FACETS	0.723	0.658	0.792	0.723	0.658	0.792	SUBCLONAL	1	TRUE	1	0.454807296812426	2		705	833	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197025	123197025	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	111	605	0	ENST00000218089.9:c.1791G>T	p.Leu597Phe	p.L597F	ENST00000218089	NM_001042749.1	597	ttG/ttT	19/35	0.454807296812426	4	FACETS	0.745	0.669	0.826	0.248	0.223	0.276	SUBCLONAL	1	TRUE	1	0.454807296812426	4		605	953	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519920	NA	P-0023572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	16	486	0	ENST00000397062.3:c.85G>C	p.Asp29His	p.D29H	ENST00000397062	NM_006164.4	29	Gat/Cat	2/5	1	2	FACETS	0.344	0.253	0.454	0.344	0.253	0.454	SUBCLONAL	1	TRUE	1	0.17	2		486	547	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579541	7579541	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	114	910	3	ENST00000269305.4:c.146A>T	p.Asp49Val	p.D49V	ENST00000269305	NM_001126112.2	49	gAt/gTt	4/11	1	2	FACETS	0.98	0.884	1	1	0.988	1	CLONAL	2	TRUE	1	0.17	2		913	684	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347142	89347142	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	29	613	4	ENST00000301030.4:c.5808G>T	p.Glu1936Asp	p.E1936D	ENST00000301030	NM_001256183.1	1936	gaG/gaT	9/13	1	2	FACETS	0.945	0.759	1	0.945	0.759	1	CLONAL	1	TRUE	1	0.17	2		617	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579542	7579543	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0023572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	110	898	0	ENST00000269305.4:c.144dup	p.Asp49ArgfsTer3	p.D49Rfs*3	ENST00000269305	NM_001126112.2	48	-/C	4/11	1	2	FACETS	0.963	0.866	1	1	0.988	1	CLONAL	2	TRUE	1	0.17	2		898	672	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618392	37618392	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs761257011	NA	P-0023572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	23	454	0	ENST00000447079.4:c.68C>A	p.Pro23Gln	p.P23Q	ENST00000447079	NM_015083.1	23	cCg/cAg	1/14	1	2	FACETS	0.833	0.649	1	0.833	0.649	1	CLONAL	1	TRUE	1	0.17	2		454	325	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630524	187630524	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0023572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	44	933	0	ENST00000441802.2:c.458C>G	p.Ser153Ter	p.S153*	ENST00000441802	NM_005245.3	153	tCa/tGa	2/27	1	2	FACETS	0.61	0.51	0.722	0.61	0.51	0.722	SUBCLONAL	1	TRUE	1	0.17	2		933	848	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628396	86628396	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	54	473	0	ENST00000274376.6:c.766del	p.Tyr256ThrfsTer23	p.Y256Tfs*23	ENST00000274376	NM_002890.2	255	taT/ta	3/25	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.17	2		473	621	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888847	76888847	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	76	376	0	ENST00000373344.5:c.4982G>T	p.Arg1661Leu	p.R1661L	ENST00000373344	NM_000489.3	1661	cGt/cTt	19/35	1	1	FACETS	0.88	0.774	0.992	1	0.981	1	CLONAL	2	TRUE	0	0.17	1		376	465	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0023574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	530	609	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.620700782487052	7	FACETS	1	0.993	1	0.904	0.88	0.926	CLONAL	6	TRUE	0	0.620700782487052	7		609	689	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779103	135779103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1564478519	NA	P-0023574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	97	524	0	ENST00000298552.3:c.2143C>T	p.Arg715Trp	p.R715W	ENST00000298552	NM_001162426.1	715	Cgg/Tgg	17/23	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.620700782487052	2		524	290	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797198	45797198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559963863	NA	P-0023574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	99	738	0	ENST00000450313.1:c.1217C>T	p.Ser406Phe	p.S406F	ENST00000450313	NM_012222.2	406	tCc/tTc	13/16	0.544176737255889	4	FACETS	1	0.929	1	0.523	0.469	0.581	CLONAL	1	TRUE	2	0.620700782487052	4		738	494	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923347	9923347	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	86	670	1	ENST00000330684.3:c.1940C>A	p.Ala647Asp	p.A647D	ENST00000330684	NM_001134407.1	647	gCc/gAc	9/13	0.620700782487052	5	FACETS	0.91	0.806	1	0.303	0.268	0.341	CLONAL	1	TRUE	2	0.620700782487052	5		671	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577554	7577559	+	inframe_deletion	In_Frame_Del	DEL	TGCAGG	TGCAGG	-	novel	NA	P-0023574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	220	700	1	ENST00000269305.4:c.722_727del	p.Ser241_Met243delinsLeu	p.S241_M243delinsL	ENST00000269305	NM_001126112.2	241	tCCTGCAtg/ttg	7/11	0.541424462967454	2	FACETS	0.921	0.872	0.969	0.921	0.872	0.969	CLONAL	2	TRUE	0	0.620700782487052	2		701	385	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197079	26197079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	89	509	1	ENST00000356476.2:c.400G>A	p.Glu134Lys	p.E134K	ENST00000356476		134	Gag/Aag	1/1	0.544176737255889	4	FACETS	0.919	0.817	1	0.459	0.408	0.513	CLONAL	1	TRUE	2	0.620700782487052	4		510	506	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500900	8500900	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	82	646	0	ENST00000356435.5:c.1982A>T	p.Glu661Val	p.E661V	ENST00000356435		661	gAg/gTg	13/35	1	2	FACETS	0.718	0.637	0.803	0.718	0.637	0.803	SUBCLONAL	1	TRUE	1	0.620700782487052	2		646	368	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344212	70344212	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	41	394	0	ENST00000374080.3:c.1948G>T	p.Glu650Ter	p.E650*	ENST00000374080		650	Gaa/Taa	13/45	0.508130964822458	6	FACETS	0.775	0.647	0.917			1	CLONAL	1	TRUE	NA	0.620700782487052	6		394	382	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0023575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	29	737	0	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	0.21835869631275	6	FACETS	0.798	0.644	0.972	0.399	0.322	0.486	CLONAL	2	TRUE	2	0.21835869631275	6		737	239	SUCCESS
APC	324	MSKCC	GRCh37	5	112170683	112170683	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554083132	NA	P-0023575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	19	584	1	ENST00000257430.4:c.1779G>A	p.Trp593Ter	p.W593*	ENST00000257430	NM_000038.5	593	tgG/tgA	15/16	0.21835869631275	6	FACETS	1	0.842	1	0.382	0.291	0.489	CLONAL	1	TRUE	3	0.21835869631275	6		585	218	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023459	27023459	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	27	796	0	ENST00000324856.7:c.565G>T	p.Gly189Cys	p.G189C	ENST00000324856	NM_006015.4	189	Ggc/Tgc	1/20	0.21835869631275	5	FACETS	0.904	0.72	1	0.452	0.36	0.558	CLONAL	1	TRUE	3	0.21835869631275	5		796	363	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402162	402162	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	32	920	1	ENST00000399788.2:c.4629C>A	p.Asp1543Glu	p.D1543E	ENST00000399788	NM_001042603.1	1543	gaC/gaA	27/28	0.170798664235457	4	FACETS	0.838	0.68	1	0.419	0.34	0.509	CLONAL	1	TRUE	2	0.21835869631275	4		921	426	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231337	46231337	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	28	655	0	ENST00000334344.6:c.1177G>T	p.Glu393Ter	p.E393*	ENST00000334344	NM_152641.2	393	Gaa/Taa	10/21	0.21835869631275	6	FACETS	1	0.927	1	0.348	0.278	0.426	CLONAL	1	TRUE	2	0.21835869631275	6		655	265	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651404	52651404	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	43	811	0	ENST00000394830.3:c.1692G>T	p.Glu564Asp	p.E564D	ENST00000394830	NM_018313.4	564	gaG/gaT	15/30	0.21835869631275	5	FACETS	0.827	0.695	0.972	0.552	0.463	0.648	CLONAL	2	TRUE	2	0.21835869631275	5		811	316	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564101	139564101	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	18	1001	1	ENST00000308874.7:c.241C>T	p.Pro81Ser	p.P81S	ENST00000308874		81	Cct/Tct	5/10	0.173521332779001	3	FACETS	0.835	0.63	1	0.418	0.315	0.538	CLONAL	1	TRUE	1	0.21835869631275	3		1002	219	SUCCESS
AR	367	MSKCC	GRCh37	X	66765907	66765908	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0023575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	11	508	0	ENST00000374690.3:c.919_920delinsAA	p.Ala307Asn	p.A307N	ENST00000374690	NM_000044.3	307	GCt/AAt	1/8	0.21835869631275	2	FACETS	0.908	0.632	1			1	CLONAL	1	TRUE	NA	0.21835869631275	2		508	111	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0023576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	59	673	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	0.117663562739308	3	FACETS	1	0.92	1	0.55	0.474	0.633	INDETERMINATE	1	TRUE	1	0.249832622020624	3		673	483	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106466	108106466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771166271	NA	P-0023576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	30	339	0	ENST00000278616.4:c.401G>A	p.Gly134Asp	p.G134D	ENST00000278616	NM_000051.3	134	gGt/gAt	5/63	1	2	FACETS	0.876	0.709	1	0.876	0.709	1	CLONAL	1	TRUE	1	0.249832622020624	2		339	274	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510674	38510674	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	48	649	0	ENST00000254066.5:c.928T>G	p.Phe310Val	p.F310V	ENST00000254066	NM_000964.3	310	Ttt/Gtt	7/9	1	2	FACETS	0.689	0.582	0.806	0.689	0.582	0.806	SUBCLONAL	1	TRUE	1	0.249832622020624	2		649	558	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038200	30038200	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	62	618	1	ENST00000338641.4:c.373C>T	p.Gln125Ter	p.Q125*	ENST00000338641	NM_000268.3	125	Cag/Tag	4/16	0.249832622020624	1	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	0	0.249832622020624	1		619	428	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0023577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	208	521	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.459401461500712	2		521	721	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	158	482	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.459401461500712	2		482	553	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361809	70361809	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	235	642	0	ENST00000374080.3:c.6485T>C	p.Leu2162Pro	p.L2162P	ENST00000374080		2162	cTc/cCc	44/45	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.459401461500712	2		642	915	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0023583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	135	1170	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.0560037733404579	4	FACETS	1	0.985	1	0.726	0.658	0.797	INDETERMINATE	1	FALSE	2	0.200304823302943	4		1170	1115	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0023583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	91	705	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.0560037733404579	4	FACETS	1	0.972	1	0.655	0.58	0.734	INDETERMINATE	1	FALSE	2	0.200304823302943	4		705	833	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218486	1218486	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	123	751	0	ENST00000326873.7:c.361G>T	p.Glu121Ter	p.E121*	ENST00000326873	NM_000455.4	121	Gag/Tag	2/10	0.132788020135751	3	FACETS	0.961	0.87	1	0.641	0.58	0.704	CLONAL	2	FALSE	0	0.200304823302943	3		751	703	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380412	14380412	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	82	264	0	ENST00000256196.4:c.5C>T	p.Ala2Val	p.A2V	ENST00000256196		2	gCc/gTc	1/6	0.13092846512781	3	FACETS	0.858	0.762	0.958	1	0.97	1	CLONAL	3	FALSE	1	0.200304823302943	3		264	350	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050880	49050880	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1204453868	NA	P-0023583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	36	603	1	ENST00000267163.4:c.2564G>A	p.Ser855Asn	p.S855N	ENST00000267163	NM_000321.2	855	aGc/aAc	25/27	0.199396495958667	2	FACETS	1	0.939	1	0.671	0.554	0.8	CLONAL	1	FALSE	0	0.200304823302943	2		604	268	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637570	23637570	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	80	701	0	ENST00000261584.4:c.2735G>T	p.Trp912Leu	p.W912L	ENST00000261584	NM_024675.3	912	tGg/tTg	7/13	0.132788020135751	3	FACETS	1	0.973	1	0.466	0.41	0.525	CLONAL	1	FALSE	0	0.200304823302943	3		701	629	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117568	70117568	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	133	652	0	ENST00000245479.2:c.36C>A	p.Asp12Glu	p.D12E	ENST00000245479	NM_000346.3	12	gaC/gaA	1/3	0.0560037733404579	4	FACETS	1	0.923	1	1	0.923	1	INDETERMINATE	2	FALSE	2	0.200304823302943	4		652	783	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602745	10602745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1040740503	NA	P-0023583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	194	844	0	ENST00000171111.5:c.833C>T	p.Pro278Leu	p.P278L	ENST00000171111	NM_203500.1	278	cCg/cTg	3/6	0.132788020135751	3	FACETS	1	0.943	1	0.682	0.631	0.736	CLONAL	2	FALSE	0	0.200304823302943	3		844	1041	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015081	27015081	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	81	541	0	ENST00000335756.4:c.183G>T	p.Leu61Phe	p.L61F	ENST00000335756	NM_001809.3	61	ttG/ttT	2/5	0.150682817739036	3	FACETS	1	0.963	1	0.62	0.546	0.7	CLONAL	1	FALSE	1	0.200304823302943	3		541	717	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530186	212530186	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	34	498	1	ENST00000342788.4:c.1733C>T	p.Thr578Ile	p.T578I	ENST00000342788	NM_005235.2	578	aCa/aTa	15/28	0.200304823302943	5	FACETS	1	0.917	1	0.615	0.503	0.74	CLONAL	1	FALSE	3	0.200304823302943	5		499	359	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46255889	46255889	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	35	438	2	ENST00000371998.3:c.501G>T	p.Lys167Asn	p.K167N	ENST00000371998		167	aaG/aaT	6/23	0.0560037733404579	4	FACETS	1	0.895	1	1	0.895	1	INDETERMINATE	2	FALSE	2	0.200304823302943	4		440	188	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169024	32169024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	94	898	0	ENST00000375023.3:c.4009G>A	p.Asp1337Asn	p.D1337N	ENST00000375023	NM_004557.3	1337	Gac/Aac	22/30	0.13092846512781	3	FACETS	1	0.928	1	0.53	0.47	0.593	CLONAL	1	FALSE	1	0.200304823302943	3		898	975	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0023601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	44	722	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.889	0.744	1	0.889	0.744	1	CLONAL	1	TRUE	1	0.16	2		722	619	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61197647	61197647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	41	518	0	ENST00000301761.2:c.29C>T	p.Ser10Leu	p.S10L	ENST00000301761	NM_017841.2	10	tCg/tTg	1/4	1	2	FACETS	0.963	0.802	1	0.963	0.802	1	CLONAL	1	TRUE	1	0.16	2		518	532	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179502	56179502	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	50	300	0	ENST00000399503.3:c.3815A>C	p.Lys1272Thr	p.K1272T	ENST00000399503	NM_005921.1	1272	aAa/aCa	15/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.16	2		300	463	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658883	3658883	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	56	630	0	ENST00000294008.3:c.83del	p.Pro28LeufsTer16	p.P28Lfs*16	ENST00000294008	NM_032444.2	28	cCt/ct	2/15	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.16	2		630	676	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835700	68835701	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0023601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	46	623	0	ENST00000261769.5:c.292_293del	p.Phe98LeufsTer69	p.F98Lfs*69	ENST00000261769	NM_004360.3	97	caTTtc/catc	3/16	1	2	FACETS	0.906	0.761	1	0.906	0.761	1	CLONAL	1	TRUE	1	0.16	2		623	635	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923045	44923046	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	58	708	0	ENST00000377967.4:c.1907dup	p.Ser637IlefsTer2	p.S637Ifs*2	ENST00000377967	NM_021140.2	636	cta/cTta	16/29	1	2	FACETS	0.915	0.785	1	0.915	0.785	1	CLONAL	1	TRUE	1	0.16	2		708	792	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178080	56178082	+	frameshift_variant	Frame_Shift_Del	DEL	CTC	CTC	T	novel	NA	P-0023601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	22	344	0	ENST00000399503.3:c.3053_3055delinsT	p.Ser1018PhefsTer17	p.S1018Ffs*17	ENST00000399503	NM_005921.1	1018	tCTCct/tTct	14/20	1	2	FACETS	0.644	0.498	0.814	0.644	0.498	0.814	SUBCLONAL	1	TRUE	1	0.16	2		344	427	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0023602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	149	724	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.95	0.869	1	0.95	0.869	1	CLONAL	1	TRUE	1	0.421753971134965	2		726	744	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165077	47165078	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0023602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	115	377	0	ENST00000409792.3:c.1048_1049del	p.Asp350PhefsTer2	p.D350Ffs*2	ENST00000409792	NM_014159.6	350	GAt/t	3/21	1	2	FACETS	0.995	0.9	1	0.995	0.9	1	CLONAL	1	TRUE	1	0.421753971134965	2		377	548	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260596	16260596	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	36	688	1	ENST00000375759.3:c.7861G>T	p.Val2621Phe	p.V2621F	ENST00000375759	NM_015001.2	2621	Gtt/Ttt	11/15	1	2	FACETS	0.323	0.265	0.389	0.323	0.265	0.389	SUBCLONAL	1	TRUE	1	0.421753971134965	2		689	528	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981136	201981143	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTGGAC	TTCTGGAC	-	novel	NA	P-0023602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	318	627	0	ENST00000359651.3:c.216_223del	p.Leu73AspfsTer16	p.L73Dfs*16	ENST00000359651		72	gTTCTGGAC/g	2/8	0.421753971134965	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	1	0.421753971134965	4		627	683	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281275	49281275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200289548	NA	P-0023602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	117	726	0	ENST00000282018.3:c.322G>A	p.Asp108Asn	p.D108N	ENST00000282018	NM_020377.2	108	Gac/Aac	1/1	1	2	FACETS	0.902	0.816	0.993	0.902	0.816	0.993	CLONAL	1	TRUE	1	0.421753971134965	2		726	615	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560488	65560488	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	114	579	1	ENST00000358664.4:c.109del	p.Asp37ThrfsTer28	p.D37Tfs*28	ENST00000358664	NM_002382.4	37	Gac/ac	3/5	0.421753971134965	1	FACETS	0.957	0.867	1	0.957	0.867	1	CLONAL	1	TRUE	0	0.421753971134965	1		580	446	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757458	40757458	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	101	682	1	ENST00000373198.4:c.2840G>A	p.Arg947Gln	p.R947Q	ENST00000373198	NM_133170.3	947	cGg/cAg	20/32	1	2	FACETS	0.911	0.817	1	0.911	0.817	1	CLONAL	1	TRUE	1	0.421753971134965	2		683	526	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252877	36252877	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	19	478	1	ENST00000300305.3:c.485G>T	p.Arg162Met	p.R162M	ENST00000300305		162	aGg/aTg	4/8	1	2	FACETS	0.165	0.125	0.213	0.165	0.125	0.213	SUBCLONAL	1	TRUE	1	0.421753971134965	2		479	545	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602977	55602977	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	106	382	0	ENST00000288135.5:c.2687C>G	p.Pro896Arg	p.P896R	ENST00000288135	NM_000222.2	896	cCt/cGt	19/21	1	2	FACETS	0.97	0.873	1	0.97	0.873	1	CLONAL	1	TRUE	1	0.421753971134965	2		382	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0023604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	209	649	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.296664756345954	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.29	2		649	695	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494609	2494609	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	87	745	0	ENST00000355716.4:c.749G>T	p.Gly250Val	p.G250V	ENST00000355716	NM_003820.2	250	gGt/gTt	8/8	0.283830513739925	3	FACETS	1	0.913	1	0.518	0.459	0.582	CLONAL	1	TRUE	1	0.29	3		745	663	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98011422	98011422	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	79	614	0	ENST00000289081.3:c.152C>A	p.Ala51Asp	p.A51D	ENST00000289081	NM_000136.2	51	gCc/gAc	2/15	0.296664756345954	2	FACETS	0.948	0.835	1	0.474	0.417	0.535	CLONAL	1	TRUE	0	0.29	2		614	575	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99440132	99440132	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	57	361	0	ENST00000268035.6:c.1100G>A	p.Gly367Glu	p.G367E	ENST00000268035	NM_000875.3	367	gGg/gAg	4/21	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.21	2		361	543	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40743901	40743901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761347839	NA	P-0023605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	78	563	0	ENST00000392038.2:c.806G>A	p.Arg269Gln	p.R269Q	ENST00000392038	NM_001626.4	269	cGg/cAg	9/14	1	2	FACETS	0.916	0.804	1	0.916	0.804	1	CLONAL	1	TRUE	1	0.21	2		563	811	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156848975	156849006	+	frameshift_variant	Frame_Shift_Del	DEL	GGTCTGGGGCAGCTGCTGGCCGTGGCTAGCCA	GGTCTGGGGCAGCTGCTGGCCGTGGCTAGCCA	-	novel	NA	P-0023605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	90	583	0	ENST00000524377.1:c.1871_1902del	p.Leu624ArgfsTer34	p.L624Rfs*34	ENST00000524377	NM_002529.3	623	GGTCTGGGGCAGCTGCTGGCCGTGGCTAGCCAg/g	15/17	1	2	FACETS	0.959	0.849	1	0.959	0.849	1	CLONAL	1	TRUE	1	0.21	2		583	894	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497383	149497383	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	69	455	0	ENST00000261799.4:c.2935A>T	p.Arg979Trp	p.R979W	ENST00000261799	NM_002609.3	979	Agg/Tgg	22/23	1	2	FACETS	0.946	0.823	1	0.946	0.823	1	CLONAL	1	TRUE	1	0.21	2		455	695	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0023606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	203	399	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.930264498018987	2		399	419	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0023606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	302	641	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.985	1	1	0.997	1	CLONAL	2	TRUE	1	0.930264498018987	2		641	323	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556727	41556727	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0023606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	190	453	1	ENST00000263253.7:c.3671+1G>A		p.X1224_splice	ENST00000263253	NM_001429.3	1224			1	2	FACETS	0.948	0.887	1	0.948	0.887	1	CLONAL	1	TRUE	1	0.930264498018987	2		454	431	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833933	44833933	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0023606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	301	354	0	ENST00000377967.4:c.357C>G	p.Tyr119Ter	p.Y119*	ENST00000377967	NM_021140.2	119	taC/taG	4/29	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.930264498018987	1		354	336	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0023608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	113	521	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.137666988251501	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		521	399	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0023609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	156	515	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.942	0.87	1	0.942	0.87	1	CLONAL	1	TRUE	1	0.724747903516344	2		515	457	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0023609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	1967	669	1	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	0.724747903516344	9	FACETS	0.97	0.958	0.982			1	CLONAL	8	TRUE	NA	0.724747903516344	9		670	2473	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720711	89720712	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	35	120	0	ENST00000371953.3:c.867dup	p.Val290SerfsTer8	p.V290Sfs*8	ENST00000371953	NM_000314.4	288	gaa/gAaa	8/9	0.724747903516344	1	FACETS	0.684	0.58	0.793	0.684	0.58	0.793	SUBCLONAL	1	TRUE	0	0.724747903516344	1		120	90	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842439	68842439	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs864622655	NA	P-0023609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	247	718	2	ENST00000261769.5:c.504del	p.Gly169AlafsTer46	p.G169Afs*46	ENST00000261769	NM_004360.3	167	gAa/ga	4/16	0.724747903516344	1	FACETS	0.992	0.942	1	0.992	0.942	1	CLONAL	1	TRUE	0	0.724747903516344	1		720	438	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6439769	6439788	+	frameshift_variant	Frame_Shift_Del	DEL	ATTTGCTTTTCCCTTGTGAG	ATTTGCTTTTCCCTTGTGAG	-	novel	NA	P-0023609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	245	594	0	ENST00000356142.4:c.295_314del	p.Ile99SerfsTer5	p.I99Sfs*5	ENST00000356142	NM_018890.3	99	ATTTGCTTTTCCCTTGTGAGt/t	5/7	1	2	FACETS	0.994	0.934	1	0.994	0.934	1	CLONAL	1	TRUE	1	0.724747903516344	2		594	680	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	107	482	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.797809214214103	2		482	263	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0023611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	138	401	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	0.797809214214103	2		401	328	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795712	42795715	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CAGT	CAGT	-	novel	NA	P-0023611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	223	914	0	ENST00000575354.2:c.2705_2708del	p.Ser902PhefsTer21	p.S902Ffs*21	ENST00000575354	NM_015125.3	901	CAGTca/ca	11/20	0.797809214214103	1	FACETS	0.936	0.89	0.981	0.936	0.89	0.981	CLONAL	1	TRUE	0	0.797809214214103	1		914	359	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438481	52438482	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCGGA	novel	NA	P-0023612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	216	497	0	ENST00000460680.1:c.1237_1238insTCCGA	p.Asn413IlefsTer19	p.N413Ifs*19	ENST00000460680	NM_004656.3	413	aac/aTCCGAac	12/17	0.48822300384922	2	FACETS	0.948	0.893	1	0.948	0.893	1	CLONAL	2	TRUE	0	0.500606047117906	2		497	455	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449820	149449820	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	62	700	0	ENST00000286301.3:c.1244G>C	p.Gly415Ala	p.G415A	ENST00000286301	NM_005211.3	415	gGc/gCc	9/22	0.500606047117906	3	FACETS	0.399	0.344	0.459	0.133	0.114	0.153	SUBCLONAL	1	TRUE	0	0.500606047117906	3		700	776	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0023613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	219	472	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.532534607073312	4	FACETS	0.916	0.861	0.971	0.916	0.861	0.971	INDETERMINATE	2	TRUE	2	0.919550689638082	4		472	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0023613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	351	836	2	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.919550689638082	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.919550689638082	1		838	384	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938141	36938141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759587248	NA	P-0023613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	468	922	1	ENST00000361632.4:c.820C>T	p.Arg274Cys	p.R274C	ENST00000361632		274	Cgt/Tgt	6/16	NA	2	FACETS	0.996	0.956	1			1	INDETERMINATE	1	TRUE	NA	0.919550689638082	2		923	1022	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725086	89725086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	18	196	0	ENST00000371953.3:c.1069C>T	p.Pro357Ser	p.P357S	ENST00000371953	NM_000314.4	357	Cca/Tca	9/9	0.787932639395931	1	FACETS	0.207	0.158	0.263	0.207	0.158	0.263	SUBCLONAL	1	TRUE	0	0.919550689638082	1		196	102	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950854	32950854	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	227	727	0	ENST00000380152.3:c.8680C>G	p.Gln2894Glu	p.Q2894E	ENST00000380152		2894	Caa/Gaa	21/27	0.283508237025397	1	FACETS	0.415	0.388	0.442	0.415	0.388	0.442	INDETERMINATE	1	TRUE	0	0.919550689638082	1		727	643	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350600	15350626	+	protein_altering_variant	In_Frame_Del	DEL	CTGGGGCTGGACCACGGAGGCAGCACG	CTGGGGCTGGACCACGGAGGCAGCACG	ATGGCA	novel	NA	P-0023613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	64	1010	5	ENST00000263377.2:c.3289_3315delinsTGCCAT	p.Arg1097_Gln1105delinsCysHis	p.R1097_Q1105delinsCH	ENST00000263377	NM_058243.2	1097	CGTGCTGCCTCCGTGGTCCAGCCCCAG/TGCCAT	16/20	1	2	FACETS	0.154	0.133	0.177	0.154	0.133	0.177	SUBCLONAL	1	TRUE	1	0.919550689638082	2		1015	904	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557280	187557280	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs373079568	NA	P-0023613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	19	707	0	ENST00000441802.2:c.4082C>A	p.Ser1361Ter	p.S1361*	ENST00000441802	NM_005245.3	1361	tCa/tAa	6/27	0.909510147626174	1	FACETS	0.062	0.046	0.08	0.062	0.046	0.08	SUBCLONAL	1	TRUE	0	0.919550689638082	1		707	362	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028893	47028893	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	47	626	0	ENST00000377604.3:c.197C>G	p.Ala66Gly	p.A66G	ENST00000377604	NM_001204468.1	66	gCg/gGg	3/24	0.283508237025397	1	FACETS	0.108	0.091	0.127	0.108	0.091	0.127	INDETERMINATE	1	TRUE	0	0.919550689638082	1		626	510	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0023617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	118	577	1	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.350950059012441	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.350950059012441	1		578	488	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0023619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	174	238	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.871	0.806	0.938	0.871	0.806	0.938	CLONAL	1	TRUE	1	0.649654152579899	2		238	615	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115435	115115437	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	rs1319662056	NA	P-0023619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	205	858	0	ENST00000257566.3:c.889_891del	p.Asn297del	p.N297del	ENST00000257566	NM_016569.3	297	AAC/-	5/8	1	2	FACETS	0.685	0.636	0.736	0.685	0.636	0.736	SUBCLONAL	1	TRUE	1	0.649654152579899	2		858	921	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431404	121431404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780357	NA	P-0023619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	127	809	0	ENST00000257555.6:c.608G>A	p.Arg203His	p.R203H	ENST00000257555		203	cGt/cAt	3/10	1	2	FACETS	0.777	0.708	0.849	0.777	0.708	0.849	SUBCLONAL	1	TRUE	1	0.649654152579899	2		809	503	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574406	41574406	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs780235974	NA	P-0023619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	159	663	0	ENST00000263253.7:c.6691A>G	p.Met2231Val	p.M2231V	ENST00000263253	NM_001429.3	2231	Atg/Gtg	31/31	1	2	FACETS	0.918	0.847	0.992	0.918	0.847	0.992	CLONAL	1	TRUE	1	0.649654152579899	2		663	533	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177996	56177996	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1272333048	NA	P-0023619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	133	562	0	ENST00000399503.3:c.2972del	p.Pro991HisfsTer91	p.P991Hfs*91	ENST00000399503	NM_005921.1	990	aCc/ac	14/20	0.464361270439583	1	FACETS	0.733	0.673	0.795	0.733	0.673	0.795	SUBCLONAL	1	TRUE	0	0.649654152579899	1		562	377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0023620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	84	883	4	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.297102755310678	3	FACETS	1	0.965	1	0.772	0.697	0.849	CLONAL	2	FALSE	0	0.440158813615626	3		887	201	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912763	32912763	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	17	473	1	ENST00000380152.3:c.4271C>T	p.Ser1424Phe	p.S1424F	ENST00000380152		1424	tCt/tTt	11/27	0.436464778099571	2	FACETS	1	0.913	1	0.743	0.576	0.923	CLONAL	1	FALSE	0	0.440158813615626	2		474	52	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942190	17942190	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	46	586	0	ENST00000458235.1:c.2825C>G	p.Ser942Cys	p.S942C	ENST00000458235	NM_000215.3	942	tCc/tGc	21/24	0.342670504156064	3	FACETS	0.839	0.71	0.979	0.419	0.355	0.49	CLONAL	1	FALSE	1	0.440158813615626	3		586	304	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160570	56160570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	13	342	0	ENST00000399503.3:c.844G>A	p.Gly282Ser	p.G282S	ENST00000399503	NM_005921.1	282	Ggc/Agc	4/20	0.440158813615626	6	FACETS	0.926	0.69	1	0.555	0.414	0.71	CLONAL	3	FALSE	1	0.440158813615626	6		342	40	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90970983	90970983	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	15	508	0	ENST00000265433.3:c.1094C>G	p.Ala365Gly	p.A365G	ENST00000265433	NM_002485.4	365	gCt/gGt	9/16	0.440158813615626	11	FACETS	1	0.774	1	0.299	0.222	0.389	CLONAL	2	FALSE	4	0.440158813615626	11		508	97	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0023621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	177	792	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.343096078010472	1	FACETS	0.942	0.869	1	0.942	0.869	1	CLONAL	1	TRUE	0	0.352517056655032	1		792	878	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489543	40489543	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs371541785	NA	P-0023621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	174	777	0	ENST00000264657.5:c.707C>G	p.Thr236Arg	p.T236R	ENST00000264657	NM_139276.2	236	aCg/aGg	8/24	0.352517056655032	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.352517056655032	1		777	800	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28901656	28901656	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	119	578	0	ENST00000282397.4:c.2739A>C	p.Lys913Asn	p.K913N	ENST00000282397	NM_002019.4	913	aaA/aaC	20/30	1	2	FACETS	0.933	0.842	1	0.933	0.842	1	CLONAL	1	TRUE	1	0.352517056655032	2		578	724	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489529	40489529	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	170	770	0	ENST00000264657.5:c.721del	p.Ala241LeufsTer20	p.A241Lfs*20	ENST00000264657	NM_139276.2	241	Gct/ct	8/24	0.352517056655032	1	FACETS	0.967	0.89	1	0.967	0.89	1	CLONAL	1	TRUE	0	0.352517056655032	1		770	822	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0023622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	126	867	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.279726717941605	3	FACETS	0.913	0.827	1	0.913	0.827	1	CLONAL	2	TRUE	1	0.19	3		868	795	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778353	3778353	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	52	743	0	ENST00000262367.5:c.6695A>T	p.Gln2232Leu	p.Q2232L	ENST00000262367	NM_004380.2	2232	cAg/cTg	31/31	1	2	FACETS	0.76	0.646	0.886	0.76	0.646	0.886	SUBCLONAL	1	TRUE	1	0.19	2		743	720	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243863	41243863	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	96	746	0	ENST00000357654.3:c.3685T>A	p.Leu1229Met	p.L1229M	ENST00000357654	NM_007294.3	1229	Ttg/Atg	10/23	0.150379236118612	3	FACETS	1	0.976	1	0.686	0.61	0.766	CLONAL	1	TRUE	1	0.19	3		746	807	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944615	40944615	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	31	482	0	ENST00000373198.4:c.1887G>T	p.Lys629Asn	p.K629N	ENST00000373198	NM_133170.3	629	aaG/aaT	12/32	1	2	FACETS	0.788	0.637	0.959	0.788	0.637	0.959	CLONAL	1	TRUE	1	0.19	2		482	414	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80169088	80169088	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	35	520	0	ENST00000265081.6:c.3284G>T	p.Gly1095Val	p.G1095V	ENST00000265081	NM_002439.4	1095	gGa/gTa	23/24	1	2	FACETS	0.737	0.603	0.887	0.737	0.603	0.887	SUBCLONAL	1	TRUE	1	0.19	2		520	500	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685340	86685340	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	11	172	0	ENST00000274376.6:c.3056A>T	p.Gln1019Leu	p.Q1019L	ENST00000274376	NM_002890.2	1019	cAg/cTg	24/25	1	2	FACETS	0.557	0.384	0.771	0.557	0.384	0.771	SUBCLONAL	1	TRUE	1	0.19	2		172	208	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028840	47028840	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0023622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	69	501	0	ENST00000377604.3:c.144T>A	p.Tyr48Ter	p.Y48*	ENST00000377604	NM_001204468.1	48	taT/taA	3/24	1	1	FACETS	0.8	0.699	0.907	1	0.976	1	CLONAL	2	TRUE	0	0.19	1		501	411	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	188	896	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.166668714591043	1	FACETS	0.772	0.715	0.83	0.772	0.715	0.83	INDETERMINATE	1	TRUE	0	0.498422340974692	1		898	734	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0023623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	240	879	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.498422340974692	1	FACETS	0.956	0.897	1	0.956	0.897	1	CLONAL	1	TRUE	0	0.498422340974692	1		881	756	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729271	41729271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749989847	NA	P-0023623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	136	503	1	ENST00000242208.4:c.1258G>A	p.Val420Met	p.V420M	ENST00000242208	NM_002192.2	420	Gtg/Atg	3/3	1	2	FACETS	0.893	0.815	0.975	0.893	0.815	0.975	CLONAL	1	TRUE	1	0.498422340974692	2		504	611	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99440126	99440126	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	239	512	1	ENST00000268035.6:c.1094G>T	p.Arg365Leu	p.R365L	ENST00000268035	NM_000875.3	365	cGa/cTa	4/21	0.457484685918393	2	FACETS	0.828	0.78	0.877	0.828	0.78	0.877	CLONAL	2	TRUE	0	0.498422340974692	2		513	579	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32439146	32439146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	214	838	1	ENST00000332351.3:c.927G>A	p.Met309Ile	p.M309I	ENST00000332351	NM_024426.4	309	atG/atA	4/10	1	2	FACETS	0.904	0.84	0.969	0.904	0.84	0.969	CLONAL	1	TRUE	1	0.498422340974692	2		839	950	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295774	15295774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1289281166	NA	P-0023623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	424	1073	1	ENST00000263388.2:c.2353C>T	p.Arg785Cys	p.R785C	ENST00000263388	NM_000435.2	785	Cgc/Tgc	15/33	0.191290214754034	4	FACETS	0.858	0.817	0.901	0.858	0.817	0.901	INDETERMINATE	2	TRUE	2	0.498422340974692	4		1074	1485	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-0023623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	124	461	0	ENST00000349496.5:c.63_455del		p.X21_splice	ENST00000349496	NM_001904.3	21	GCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCAAGATGATGCAGAACTTGCCACACGT/-	3-4/15	1	2	FACETS	0.95	0.863	1	0.95	0.863	1	CLONAL	1	TRUE	1	0.498422340974692	2		461	524	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0023624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	87	721	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	1	2	FACETS	0.746	0.659	0.839	0.746	0.659	0.839	SUBCLONAL	1	TRUE	1	0.24	2		721	972	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882025	NA	P-0023624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	107	943	1	ENST00000269305.4:c.646G>T	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ttg	6/11	1	2	FACETS	0.792	0.708	0.881	0.792	0.708	0.881	SUBCLONAL	1	TRUE	1	0.24	2		944	1126	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31495463	31495463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	237	680	1	ENST00000344624.3:c.1685G>A	p.Arg562His	p.R562H	ENST00000344624		562	cGt/cAt	9/33	0.237655069498991	4	FACETS	1	0.977	1			1	CLONAL	2	TRUE	NA	0.24	4		681	1107	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611875	100611875	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1179	110	997	0	ENST00000308731.7:c.1246G>T	p.Val416Leu	p.V416L	ENST00000308731	NM_000061.2	416	Gtg/Ttg	14/19	1	2	FACETS	0.711	0.637	0.79	0.711	0.637	0.79	SUBCLONAL	1	TRUE	1	0.24	2		997	1289	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692920	89692921	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs398123323	NA	P-0023625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	22	572	0	ENST00000371953.3:c.405dup	p.Cys136MetfsTer44	p.C136Mfs*44	ENST00000371953	NM_000314.4	135	ata/atAa	5/9	1	2	FACETS	0.539	0.418	0.679	0.539	0.418	0.679	SUBCLONAL	1	TRUE	1	0.3	2		572	272	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859427	57859427	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151317566	NA	P-0023625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	85	664	0	ENST00000228682.2:c.572G>A	p.Arg191Gln	p.R191Q	ENST00000228682	NM_005269.2	191	cGg/cAg	6/12	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.3	2		664	557	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670711	134670711	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	83	673	0	ENST00000398015.3:c.622G>T	p.Glu208Ter	p.E208*	ENST00000398015	NM_004441.4	208	Gag/Tag	3/16	1	2	FACETS	0.992	0.877	1	0.992	0.877	1	CLONAL	1	TRUE	1	0.3	2		673	558	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0023628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	18	461	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.131629751738768	4	FACETS	0.872	0.658	1	0.436	0.329	0.563	CLONAL	1	TRUE	2	0.195845228716267	4		461	252	SUCCESS
AR	367	MSKCC	GRCh37	X	66943588	66943588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886041133	NA	P-0023628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	26	757	0	ENST00000374690.3:c.2668G>A	p.Val890Met	p.V890M	ENST00000374690	NM_000044.3	890	Gtg/Atg	8/8	1	2	FACETS	0.75	0.594	0.929	0.75	0.594	0.929	CLONAL	1	TRUE	1	0.195845228716267	2		757	354	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442012	52442043	+	frameshift_variant	Frame_Shift_Del	DEL	TCAGGGTGGGTCCCAGGTCCACGCTGCTGCAG	TCAGGGTGGGTCCCAGGTCCACGCTGCTGCAG	-	novel	NA	P-0023628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	48	645	0	ENST00000460680.1:c.306_337del	p.Asn102LysfsTer13	p.N102Kfs*13	ENST00000460680	NM_004656.3	102	aaCTGCAGCAGCGTGGACCTGGGACCCACCCTGAgt/aagt	5/17	0.195845228716267	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.195845228716267	1		645	303	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216477	108216477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587782558	NA	P-0023630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	76	313	0	ENST00000278616.4:c.8432del	p.Lys2811SerfsTer46	p.K2811Sfs*46	ENST00000278616	NM_000051.3	2809	cAa/ca	58/63	1	2	FACETS	0.593	0.521	0.67	0.593	0.521	0.67	SUBCLONAL	1	TRUE	1	0.51149764558508	2		313	501	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0023630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	268	770	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.983	0.922	1	0.983	0.922	1	CLONAL	1	TRUE	1	0.51149764558508	2		770	1066	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164447	47164447	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0023630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	170	452	0	ENST00000409792.3:c.1679C>G	p.Ser560Ter	p.S560*	ENST00000409792	NM_014159.6	560	tCa/tGa	3/21	1	2	FACETS	0.885	0.816	0.957	0.885	0.816	0.957	CLONAL	1	TRUE	1	0.51149764558508	2		452	751	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579398	7579398	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882023	NA	P-0023630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	253	721	1	ENST00000269305.4:c.289G>T	p.Val97Phe	p.V97F	ENST00000269305	NM_001126112.2	97	Gtc/Ttc	4/11	1	2	FACETS	0.974	0.912	1	0.974	0.912	1	CLONAL	1	TRUE	1	0.51149764558508	2		722	1016	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213552	2213561	+	frameshift_variant	Frame_Shift_Del	DEL	GCTCCTGGGT	GCTCCTGGGT	-	novel	NA	P-0023630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	224	692	0	ENST00000398665.3:c.1574_1583del	p.Leu525ArgfsTer29	p.L525Rfs*29	ENST00000398665	NM_032482.2	524	caGCTCCTGGGT/ca	17/28	0.51149764558508	1	FACETS	0.995	0.932	1	0.995	0.932	1	CLONAL	1	TRUE	0	0.51149764558508	1		692	655	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610576	10610576	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	244	688	0	ENST00000171111.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000171111	NM_203500.1	45	tCc/tTc	2/6	0.51149764558508	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.51149764558508	1		688	689	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659802	227659802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	126	362	0	ENST00000305123.5:c.3653C>T	p.Ser1218Phe	p.S1218F	ENST00000305123	NM_005544.2	1218	tCc/tTc	1/2	1	2	FACETS	0.864	0.786	0.947	0.864	0.786	0.947	CLONAL	1	TRUE	1	0.51149764558508	2		362	570	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259390	36259390	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	202	575	0	ENST00000300305.3:c.101C>G	p.Ala34Gly	p.A34G	ENST00000300305		34	gCc/gGc	3/8	1	2	FACETS	0.889	0.825	0.956	0.889	0.825	0.956	CLONAL	1	TRUE	1	0.51149764558508	2		575	888	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636842	8636842	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	161	439	1	ENST00000356435.5:c.67C>T	p.Pro23Ser	p.P23S	ENST00000356435		23	Cct/Tct	2/35	1	2	FACETS	0.981	0.903	1	0.981	0.903	1	CLONAL	1	TRUE	1	0.51149764558508	2		440	642	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0023631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	172	566	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.227570817184019	2	FACETS	0.802	0.739	0.867	0.802	0.739	0.867	CLONAL	2	TRUE	0	0.271604922609091	2		566	790	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983093	111983093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771152377	NA	P-0023631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	161	701	0	ENST00000368678.4:c.1454C>T	p.Pro485Leu	p.P485L	ENST00000368678		485	cCg/cTg	13/13	0.227570817184019	2	FACETS	0.75	0.689	0.814	0.75	0.689	0.814	SUBCLONAL	2	TRUE	0	0.271604922609091	2		701	790	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577530	7577530	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	150	791	0	ENST00000269305.4:c.751A>T	p.Ile251Phe	p.I251F	ENST00000269305	NM_001126112.2	251	Atc/Ttc	7/11	0.271604922609091	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.271604922609091	1		791	778	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729888	41729888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1043609570	NA	P-0023631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	164	528	0	ENST00000242208.4:c.641G>A	p.Arg214Gln	p.R214Q	ENST00000242208	NM_002192.2	214	cGg/cAg	3/3	0.271604922609091	5	FACETS	0.849	0.779	0.922	0.566	0.519	0.615	CLONAL	2	TRUE	2	0.271604922609091	5		528	1001	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149516600	149516600	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs144923639	NA	P-0023631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	153	730	0	ENST00000261799.4:c.11C>A	p.Pro4Gln	p.P4Q	ENST00000261799	NM_002609.3	4	cCg/cAg	2/23	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.271604922609091	2		730	859	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964483	93964483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	148	675	1	ENST00000369303.4:c.2414C>T	p.Pro805Leu	p.P805L	ENST00000369303	NM_004440.3	805	cCc/cTc	14/17	0.227570817184019	2	FACETS	0.791	0.724	0.861	0.791	0.724	0.861	SUBCLONAL	2	TRUE	0	0.271604922609091	2		676	689	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514211	69514211	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	140	745	2	ENST00000294312.3:c.470G>A	p.Arg157Lys	p.R157K	ENST00000294312	NM_005117.2	157	aGa/aAa	3/3	0.197751285505213	3	FACETS	1	0.981	1	0.65	0.591	0.711	CLONAL	1	TRUE	1	0.271604922609091	3		747	901	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28886150	28886150	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	36	587	1	ENST00000282397.4:c.3472C>A	p.Leu1158Ile	p.L1158I	ENST00000282397	NM_002019.4	1158	Ctt/Att	26/30	0.227570817184019	2	FACETS	0.393	0.322	0.473	0.196	0.161	0.237	SUBCLONAL	1	TRUE	0	0.271604922609091	2		588	675	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42057123	42057133	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTTGTGATG	ACCTTGTGATG	-	novel	NA	P-0023631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	42	780	0	ENST00000219905.7:c.7786_7796del	p.Leu2596SerfsTer23	p.L2596Sfs*23	ENST00000219905	NM_001164273.1	2595	aACCTTGTGATG/a	23/24	0.271604922609091	1	FACETS	0.32	0.266	0.381	0.32	0.266	0.381	SUBCLONAL	1	TRUE	0	0.271604922609091	1		780	834	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106644	2106644	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs794727906	NA	P-0023631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	48	677	0	ENST00000219476.3:c.649-1G>A		p.X217_splice	ENST00000219476	NM_000548.3	217			1	2	FACETS	0.473	0.398	0.555	0.473	0.398	0.555	SUBCLONAL	1	TRUE	1	0.271604922609091	2		677	748	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741932	40741932	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202125073	NA	P-0023631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	100	817	2	ENST00000392038.2:c.1040G>A	p.Arg347His	p.R347H	ENST00000392038	NM_001626.4	347	cGc/cAc	11/14	0.197751285505213	3	FACETS	0.842	0.751	0.94	0.421	0.375	0.47	CLONAL	1	TRUE	1	0.271604922609091	3		819	993	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143461	30143461	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	51	454	0	ENST00000389048.3:c.65G>T	p.Gly22Val	p.G22V	ENST00000389048	NM_004304.4	22	gGg/gTg	1/29	1	2	FACETS	0.629	0.534	0.733	0.629	0.534	0.733	SUBCLONAL	1	TRUE	1	0.271604922609091	2		454	597	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448570	89448570	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	252	642	0	ENST00000336596.2:c.1534C>G	p.Arg512Gly	p.R512G	ENST00000336596	NM_005233.5	512	Cga/Gga	7/17	0.213193765271728	3	FACETS	0.847	0.795	0.901	0.847	0.795	0.901	CLONAL	3	TRUE	0	0.271604922609091	3		642	829	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99823121	99823121	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	61	450	0	ENST00000280892.6:c.91A>T	p.Thr31Ser	p.T31S	ENST00000280892	NM_001130678.1	31	Act/Tct	2/7	0.16959141143816	4	FACETS	1	0.941	1	0.389	0.335	0.446	CLONAL	1	TRUE	1	0.271604922609091	4		450	490	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513542	149513542	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	53	644	0	ENST00000261799.4:c.661G>T	p.Val221Leu	p.V221L	ENST00000261799	NM_002609.3	221	Gtg/Ttg	5/23	1	2	FACETS	0.495	0.421	0.577	0.495	0.421	0.577	SUBCLONAL	1	TRUE	1	0.271604922609091	2		644	788	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273091	55273091	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0023631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	84	650	0	ENST00000275493.2:c.3414T>G	p.Tyr1138Ter	p.Y1138*	ENST00000275493	NM_005228.3	1138	taT/taG	28/28	0.271604922609091	5	FACETS	0.904	0.797	1	0.301	0.265	0.34	CLONAL	1	TRUE	2	0.271604922609091	5		650	963	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339792	116339792	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs35284565	NA	P-0023631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	162	501	2	ENST00000397752.3:c.654G>T	p.Arg218Ser	p.R218S	ENST00000397752	NM_000245.2	218	agG/agT	2/21	0.271604922609091	5	FACETS	0.967	0.888	1	0.645	0.592	0.7	CLONAL	2	TRUE	2	0.271604922609091	5		503	868	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180363	27180363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	105	422	1	ENST00000380036.4:c.1027G>A	p.Glu343Lys	p.E343K	ENST00000380036	NM_000459.3	343	Gaa/Aaa	7/23	0.227570817184019	2	FACETS	0.802	0.722	0.886	0.802	0.722	0.886	CLONAL	2	TRUE	0	0.271604922609091	2		423	482	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404296	139404296	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	85	787	0	ENST00000277541.6:c.2858C>T	p.Pro953Leu	p.P953L	ENST00000277541	NM_017617.3	953	cCc/cTc	18/34	0.227570817184019	2	FACETS	0.703	0.62	0.792	0.352	0.31	0.396	SUBCLONAL	1	TRUE	0	0.271604922609091	2		787	890	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922978	39922978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	63	736	0	ENST00000378444.4:c.3730G>A	p.Glu1244Lys	p.E1244K	ENST00000378444	NM_001123385.1	1244	Gag/Aag	8/15	1	2	FACETS	0.538	0.464	0.618	0.538	0.464	0.618	SUBCLONAL	1	TRUE	1	0.271604922609091	2		736	863	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0023633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	82	724	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.239280378343384	3	FACETS	1	0.977	1	0.729	0.647	0.817	CLONAL	1	TRUE	1	0.328986098191722	3		726	398	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742144	145742144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779891153	NA	P-0023633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	80	605	0	ENST00000428558.2:c.359G>A	p.Gly120Glu	p.G120E	ENST00000428558	NM_004260.3	120	gGa/gAa	5/22	0.312499398775234	4	FACETS	1	0.96	1	0.604	0.533	0.68	CLONAL	1	TRUE	2	0.328986098191722	4		605	535	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828133	243828134	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0023633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	52	689	1	ENST00000263826.5:c.224_225delinsTT	p.Arg75Ile	p.R75I	ENST00000263826	NM_005465.4	75	aGA/aTT	3/13	0.328986098191722	4	FACETS	0.628	0.534	0.732	0.209	0.178	0.244	SUBCLONAL	1	TRUE	1	0.328986098191722	4		690	669	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226276	133226276	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	162	752	0	ENST00000320574.5:c.3782T>G	p.Leu1261Arg	p.L1261R	ENST00000320574	NM_006231.2	1261	cTg/cGg	30/49	0.239280378343384	3	FACETS	0.928	0.855	1	0.928	0.855	1	CLONAL	2	TRUE	1	0.328986098191722	3		752	618	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226387	41226387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28897691	NA	P-0023633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	90	758	2	ENST00000357654.3:c.4636G>A	p.Asp1546Asn	p.D1546N	ENST00000357654	NM_007294.3	1546	Gat/Aat	14/23	0.251359241663811	4	FACETS	1	0.944	1	0.367	0.326	0.411	CLONAL	1	TRUE	1	0.328986098191722	4		760	660	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441991	52442005	+	inframe_deletion	In_Frame_Del	DEL	TGGTGAAGTCCTTCA	TGGTGAAGTCCTTCA	-	novel	NA	P-0023633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	110	566	0	ENST00000460680.1:c.344_358del	p.Met115_Thr119del	p.M115_T119del	ENST00000460680	NM_004656.3	115	aTGAAGGACTTCACCAag/aag	5/17	0.270425419025542	2	FACETS	0.838	0.759	0.92	0.838	0.759	0.92	CLONAL	2	TRUE	0	0.328986098191722	2		566	399	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0023634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	155	770	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.362781397645443	1	FACETS	0.623	0.572	0.676	0.623	0.572	0.676	SUBCLONAL	1	TRUE	0	0.566260689319064	1		770	630	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916836	178916836	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1551	152	649	0	ENST00000263967.3:c.223C>G	p.Gln75Glu	p.Q75E	ENST00000263967	NM_006218.2	75	Caa/Gaa	2/21	0.566260689319064	9	FACETS	0.94	0.856	1	0.118	0.107	0.129	CLONAL	1	TRUE	1	0.566260689319064	9		649	1703	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841301	15841301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1195011512	NA	P-0023634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	114	563	0	ENST00000307771.7:c.1385G>A	p.Arg462Gln	p.R462Q	ENST00000307771	NM_005089.3	462	cGa/cAa	11/11	0.474102148155456	1	FACETS	0.557	0.504	0.613	0.557	0.504	0.613	SUBCLONAL	1	TRUE	0	0.566260689319064	1		563	518	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874031	123874031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1447464550	NA	P-0023634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	10	54	2	ENST00000330479.4:c.62C>T	p.Ala21Val	p.A21V	ENST00000330479	NM_020382.3	21	gCg/gTg	2/9	NA	2	FACETS	0.631	0.437	0.862			1	INDETERMINATE	1	TRUE	NA	0.566260689319064	2		56	56	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434307	49434307	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	32	787	0	ENST00000301067.7:c.7246C>T	p.Gln2416Ter	p.Q2416*	ENST00000301067	NM_003482.3	2416	Cag/Tag	31/54	0.104850832329612	4	FACETS	0.283	0.229	0.345	0.142	0.114	0.173	INDETERMINATE	1	TRUE	2	0.566260689319064	4		787	625	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41276091	41276091	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	209	544	2	ENST00000357654.3:c.23T>A	p.Val8Asp	p.V8D	ENST00000357654	NM_007294.3	8	gTt/gAt	2/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.566260689319064	2		546	683	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4090673	4090673	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	129	684	0	ENST00000262948.5:c.1126G>A	p.Glu376Lys	p.E376K	ENST00000262948	NM_030662.3	376	Gaa/Aaa	11/11	1	2	FACETS	0.842	0.767	0.92	0.842	0.767	0.92	CLONAL	1	TRUE	1	0.566260689319064	2		684	541	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719241	61719241	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	126	528	0	ENST00000401558.2:c.1816G>C	p.Glu606Gln	p.E606Q	ENST00000401558	NM_003400.3	606	Gaa/Caa	16/25	0.172966085022757	5	FACETS	0.779	0.709	0.853			1	INDETERMINATE	2	TRUE	NA	0.566260689319064	5		528	528	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150003	202150003	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	131	563	1	ENST00000358485.4:c.1444C>T	p.Gln482Ter	p.Q482*	ENST00000358485	NM_001080125.1	482	Cag/Tag	8/9	1	2	FACETS	0.866	0.79	0.946	0.866	0.79	0.946	CLONAL	1	TRUE	1	0.566260689319064	2		564	534	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285227	212285227	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	30	538	0	ENST00000342788.4:c.3074C>T	p.Pro1025Leu	p.P1025L	ENST00000342788	NM_005235.2	1025	cCt/cTt	25/28	0.566260689319064	1	FACETS	0.216	0.174	0.263	0.216	0.174	0.263	SUBCLONAL	1	TRUE	0	0.566260689319064	1		538	352	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648378	30648378	+	start_lost	Translation_Start_Site	SNP	G	G	C	novel	NA	P-0023634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	68	354	0	ENST00000295754.5:c.3G>C	p.Met1?	p.M1?	ENST00000295754	NM_003242.5	1	atG/atC	1/7	0.550088376199166	1	FACETS	0.73	0.643	0.82	0.73	0.643	0.82	SUBCLONAL	1	TRUE	0	0.566260689319064	1		354	236	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383885	84383885	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	138	594	0	ENST00000321945.7:c.967C>G	p.Leu323Val	p.L323V	ENST00000321945	NM_139076.2	323	Ctg/Gtg	9/9	0.246453854963228	3	FACETS	0.891	0.812	0.973	0.297	0.27	0.325	INDETERMINATE	1	TRUE	0	0.566260689319064	3		594	702	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348217	70348217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	144	660	0	ENST00000374080.3:c.3281G>A	p.Gly1094Glu	p.G1094E	ENST00000374080		1094	gGa/gAa	23/45	0.431738091736032	1	FACETS	0.848	0.781	0.917	0.848	0.781	0.917	CLONAL	1	TRUE	0	0.566260689319064	1		660	430	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	173	482	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.969	0.901	1	0.969	0.901	1	CLONAL	1	TRUE	1	0.805978358474741	2		482	443	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813361	102813361	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1280732914	NA	P-0023638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	255	520	0	ENST00000307046.8:c.328G>A	p.Ala110Thr	p.A110T	ENST00000307046	NM_001111285.1	110	Gca/Aca	3/4	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.805978358474741	2		520	633	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63817050	63817050	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	87	322	0	ENST00000279873.7:c.1021C>T	p.Arg341Ter	p.R341*	ENST00000279873	NM_032199.2	341	Cga/Tga	6/10	0.800031587228396	1	FACETS	0.895	0.823	0.965	0.895	0.823	0.965	CLONAL	1	TRUE	0	0.805978358474741	1		322	144	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390435	56390435	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757096789	NA	P-0023638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	168	460	0	ENST00000348428.3:c.1174C>T	p.Arg392Cys	p.R392C	ENST00000348428	NM_006785.3	392	Cgt/Tgt	10/17	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.805978358474741	2		460	371	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723045	49723046	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0023638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	256	109	0	ENST00000449682.2:c.1370dup	p.Cys457TrpfsTer8	p.C457Wfs*8	ENST00000449682	NM_020998.3	457	tgt/tgGt	11/18	1	2	FACETS	0.758	0.722	0.793	1	0.995	1	SUBCLONAL	2	TRUE	1	0.805978358474741	2		109	419	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874319	76874319	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	769	189	1	ENST00000373344.5:c.5403A>T	p.Lys1801Asn	p.K1801N	ENST00000373344	NM_000489.3	1801	aaA/aaT	21/35	1	2	FACETS	0.91	0.89	0.931	1	0.998	1	CLONAL	2	TRUE	1	0.805978358474741	2		190	1048	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	101	521	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.816	0.731	0.906	0.816	0.731	0.906	CLONAL	1	TRUE	1	0.41	2		521	604	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	70	417	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.727	0.635	0.825	0.727	0.635	0.825	SUBCLONAL	1	TRUE	1	0.41	2		417	470	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743932	41743933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs778012871	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	188	816	2	ENST00000301178.4:c.874dup	p.His292ProfsTer47	p.H292Pfs*47	ENST00000301178	NM_021913.4	289	-/C	7/20	1	2	FACETS	0.909	0.839	0.981	0.909	0.839	0.981	CLONAL	1	TRUE	1	0.41	2		818	1009	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	65	419	2	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.764	0.665	0.871	0.764	0.665	0.871	SUBCLONAL	1	TRUE	1	0.41	2		421	415	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453399	40453399	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs759027671	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	232	885	7	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	0.41	2		892	1099	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	271	505	6	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	0.996	1	CLONAL	2	TRUE	1	0.41	2		511	651	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944382	131944382	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs748536322	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	98	461	4	ENST00000265335.6:c.2801del	p.Asn934IlefsTer6	p.N934Ifs*6	ENST00000265335		932	Aaa/aa	17/25	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.41	2		465	452	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769886672	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	66	389	1	ENST00000405192.2:c.414dup	p.Thr139HisfsTer24	p.T139Hfs*24	ENST00000405192	NM_001163147.1	138	-/C	7/12	1	2	FACETS	0.638	0.554	0.727	0.638	0.554	0.727	SUBCLONAL	1	TRUE	1	0.41	2		390	505	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	85	517	2	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.715	0.633	0.802	0.715	0.633	0.802	SUBCLONAL	1	TRUE	1	0.41	2		519	580	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	85	501	1	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.911	0.809	1	0.911	0.809	1	CLONAL	1	TRUE	1	0.41	2		502	455	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720857	89720857	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs786201816	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	76	357	0	ENST00000371953.3:c.1008C>G	p.Tyr336Ter	p.Y336*	ENST00000371953	NM_000314.4	336	taC/taG	8/9	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.41	2		357	341	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210755	5210755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1157608522	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	224	1039	3	ENST00000357368.4:c.5296C>T	p.Arg1766Cys	p.R1766C	ENST00000357368	NM_002850.3	1766	Cgc/Tgc	34/38	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.41	2		1042	1038	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346884	73346884	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	64	368	1	ENST00000377767.4:c.1333del	p.Ser445HisfsTer20	p.S445Hfs*20	ENST00000377767	NM_014953.3	445	Tca/ca	9/21	1	2	FACETS	0.809	0.704	0.922	0.809	0.704	0.922	CLONAL	1	TRUE	1	0.41	2		369	386	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446269	187446270	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770320988	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	150	635	0	ENST00000232014.4:c.1418dup	p.Lys474GlufsTer26	p.K474Efs*26	ENST00000232014	NM_001130845.1	473	ccg/ccCg	6/10	1	2	FACETS	0.812	0.742	0.886	0.812	0.742	0.886	CLONAL	1	TRUE	1	0.41	2		635	901	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1627375	1627375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368163858	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	99	672	0	ENST00000344749.5:c.349G>A	p.Val117Met	p.V117M	ENST00000344749	NM_001136139.2	117	Gtg/Atg	6/19	1	2	FACETS	0.568	0.506	0.634	0.568	0.506	0.634	SUBCLONAL	1	TRUE	1	0.41	2		672	850	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	122	496	7	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.41	2		503	580	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270530	98270530	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs751977093	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	100	354	1	ENST00000331920.6:c.114del	p.Leu39CysfsTer41	p.L39Cfs*41	ENST00000331920	NM_000264.3	38	ggG/gg	1/24	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.41	2		355	455	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132896	64132896	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	75	677	0	ENST00000334205.4:c.1034del	p.Pro345LeufsTer30	p.P345Lfs*30	ENST00000334205	NM_003942.2	344	Ccc/cc	9/17	1	2	FACETS	0.416	0.363	0.472	0.416	0.363	0.472	SUBCLONAL	1	TRUE	1	0.41	2		677	880	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911311	29911311	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs199474579	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	70	558	3	ENST00000376809.5:c.610C>T	p.Gln204Ter	p.Q204*	ENST00000376809	NM_002116.7	204	Cag/Tag	3/8	1	2	FACETS	0.523	0.456	0.596	0.523	0.456	0.596	SUBCLONAL	1	TRUE	1	0.41	2		561	653	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604665	48604665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660045	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	105	461	2	ENST00000342988.3:c.1487G>A	p.Arg496His	p.R496H	ENST00000342988	NM_005359.5	496	cGt/cAt	12/12	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.41	2		463	486	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5239002	5239002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775100072	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	54	674	1	ENST00000357368.4:c.1777C>T	p.Arg593Cys	p.R593C	ENST00000357368	NM_002850.3	593	Cgc/Tgc	13/38	1	2	FACETS	0.313	0.266	0.364	0.313	0.266	0.364	SUBCLONAL	1	TRUE	1	0.41	2		675	842	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038451	180038451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370304760	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	152	685	1	ENST00000261937.6:c.3566G>A	p.Arg1189His	p.R1189H	ENST00000261937	NM_182925.4	1189	cGc/cAc	27/30	1	2	FACETS	0.859	0.786	0.936	0.859	0.786	0.936	CLONAL	1	TRUE	1	0.41	2		686	863	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831386	72831388	+	inframe_deletion	In_Frame_Del	DEL	TGC	TGC	-	novel	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	47	392	2	ENST00000268489.5:c.5193_5195del	p.Gln1741del	p.Q1741del	ENST00000268489	NM_006885.3	1731	caGCAa/caa	9/10	1	2	FACETS	0.548	0.463	0.642	0.548	0.463	0.642	SUBCLONAL	1	TRUE	1	0.41	2		394	418	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726051	61726052	+	splice_region_variant,intron_variant	Splice_Region	DEL	AA	AA	-	rs372688892	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	80	410	2	ENST00000401558.2:c.591-4_591-3del		p.X197_splice	ENST00000401558	NM_003400.3	197			1	2	FACETS	0.823	0.727	0.926	0.823	0.727	0.926	CLONAL	1	TRUE	1	0.41	2		412	474	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11019828	11019828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	170	601	0	ENST00000327064.4:c.503G>A	p.Arg168Gln	p.R168Q	ENST00000327064	NM_199141.1	168	cGg/cAg	4/16	1	2	FACETS	0.961	0.884	1	0.961	0.884	1	CLONAL	1	TRUE	1	0.41	2		601	863	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998128	169998128	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs753143066	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	122	727	4	ENST00000295797.4:c.826del	p.Thr276GlnfsTer7	p.T276Qfs*7	ENST00000295797	NM_002740.5	273	ttA/tt	9/18	1	2	FACETS	0.687	0.621	0.757	0.687	0.621	0.757	SUBCLONAL	1	TRUE	1	0.41	2		731	866	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230692	46230692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs916056847	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	90	579	3	ENST00000334344.6:c.941G>A	p.Arg314His	p.R314H	ENST00000334344	NM_152641.2	314	cGt/cAt	8/21	1	2	FACETS	0.761	0.676	0.851	0.761	0.676	0.851	SUBCLONAL	1	TRUE	1	0.41	2		582	577	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447565	187447565	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151194132	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	133	527	0	ENST00000232014.4:c.628G>A	p.Asp210Asn	p.D210N	ENST00000232014	NM_001130845.1	210	Gat/Aat	5/10	1	2	FACETS	0.919	0.836	1	0.919	0.836	1	CLONAL	1	TRUE	1	0.41	2		527	706	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420204	49420204	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	64	714	0	ENST00000301067.7:c.15545del	p.Gly5182AlafsTer61	p.G5182Afs*61	ENST00000301067	NM_003482.3	5182	gGc/gc	48/54	1	2	FACETS	0.348	0.3	0.4	0.348	0.3	0.4	SUBCLONAL	1	TRUE	1	0.41	2		714	897	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504375	186504375	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	36	431	0	ENST00000323963.5:c.716del	p.Lys239ArgfsTer4	p.K239Rfs*4	ENST00000323963		238	Aaa/aa	7/11	1	2	FACETS	0.353	0.29	0.425	0.353	0.29	0.425	SUBCLONAL	1	TRUE	1	0.41	2		431	497	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256768	19256769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	42	581	0	ENST00000162023.5:c.943_944dup	p.Val316GlnfsTer?	p.V316Qfs*?	ENST00000162023		315	cca/ccCCa	13/13	1	2	FACETS	0.281	0.234	0.334	0.281	0.234	0.334	SUBCLONAL	1	TRUE	1	0.41	2		581	729	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436297	110436302	+	inframe_deletion	In_Frame_Del	DEL	CGGCGG	CGGCGG	-	rs34412495	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	69	384	0	ENST00000375856.3:c.2099_2104del	p.Ala700_Ala701del	p.A700_A701del	ENST00000375856	NM_003749.2	700	gCCGCCGtg/gtg	1/2	1	2	FACETS	0.813	0.711	0.922	0.813	0.711	0.922	CLONAL	1	TRUE	1	0.41	2		384	414	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778282	3778282	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	66	669	1	ENST00000262367.5:c.6766del	p.Leu2256SerfsTer46	p.L2256Sfs*46	ENST00000262367	NM_004380.2	2256	Ctc/tc	31/31	1	2	FACETS	0.423	0.366	0.485	0.423	0.366	0.485	SUBCLONAL	1	TRUE	1	0.41	2		670	761	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256831	16256831	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	731	148	0	ENST00000375759.3:c.4096C>T	p.Arg1366Ter	p.R1366*	ENST00000375759	NM_015001.2	1366	Cga/Tga	11/15	1	2	FACETS	1	0.997	1	1	0.998	1	CLONAL	2	TRUE	1	0.41	2		148	1451	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716356	18716356	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	105	562	0	ENST00000266497.5:c.3703A>G	p.Thr1235Ala	p.T1235A	ENST00000266497		1235	Aca/Gca	26/31	1	2	FACETS	0.802	0.719	0.889	0.802	0.719	0.889	CLONAL	1	TRUE	1	0.41	2		562	639	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438262	49438262	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	165	672	0	ENST00000301067.7:c.5007del	p.Val1670SerfsTer52	p.V1670Sfs*52	ENST00000301067	NM_003482.3	1669	ccC/cc	20/54	1	2	FACETS	0.846	0.777	0.919	0.846	0.777	0.919	CLONAL	1	TRUE	1	0.41	2		672	951	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112940021	112940021	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	83	715	0	ENST00000351677.2:c.1673G>A	p.Ser558Asn	p.S558N	ENST00000351677	NM_002834.3	558	aGc/aAc	14/16	1	2	FACETS	0.395	0.348	0.447	0.395	0.348	0.447	SUBCLONAL	1	TRUE	1	0.41	2		715	1024	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478167	99478167	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs768997684	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	99	503	0	ENST00000268035.6:c.3071A>G	p.Asp1024Gly	p.D1024G	ENST00000268035	NM_000875.3	1024	gAt/gGt	16/21	1	2	FACETS	0.711	0.635	0.792	0.711	0.635	0.792	SUBCLONAL	1	TRUE	1	0.41	2		503	679	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134574	2134574	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369553241	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	194	777	1	ENST00000219476.3:c.4351C>T	p.Arg1451Cys	p.R1451C	ENST00000219476	NM_000548.3	1451	Cgc/Tgc	34/42	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.41	2		778	930	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634450	23634450	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs878855113	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	115	462	0	ENST00000261584.4:c.2836G>A	p.Ala946Thr	p.A946T	ENST00000261584	NM_024675.3	946	Gca/Aca	9/13	1	2	FACETS	0.979	0.885	1	0.979	0.885	1	CLONAL	1	TRUE	1	0.41	2		462	573	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836279	89836279	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	130	822	0	ENST00000389301.3:c.2470T>C	p.Cys824Arg	p.C824R	ENST00000389301	NM_000135.2	824	Tgt/Cgt	26/43	1	2	FACETS	0.647	0.586	0.711	0.647	0.586	0.711	SUBCLONAL	1	TRUE	1	0.41	2		822	980	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984840	11984840	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	84	403	0	ENST00000353533.5:c.386C>T	p.Ala129Val	p.A129V	ENST00000353533	NM_003010.3	129	gCa/gTa	3/11	1	2	FACETS	0.838	0.743	0.939	0.838	0.743	0.939	CLONAL	1	TRUE	1	0.41	2		403	489	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029396	16029396	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	115	689	0	ENST00000268712.3:c.1634A>C	p.Lys545Thr	p.K545T	ENST00000268712	NM_006311.3	545	aAa/aCa	15/46	1	2	FACETS	0.804	0.725	0.887	0.804	0.725	0.887	CLONAL	1	TRUE	1	0.41	2		689	698	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440951	56440951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777370273	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	139	569	2	ENST00000407977.2:c.386C>T	p.Ala129Val	p.A129V	ENST00000407977		129	gCg/gTg	4/10	1	2	FACETS	0.821	0.747	0.898	0.821	0.747	0.898	CLONAL	1	TRUE	1	0.41	2		571	826	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231398	5231398	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	56	726	3	ENST00000357368.4:c.2078G>A	p.Arg693His	p.R693H	ENST00000357368	NM_002850.3	693	cGc/cAc	14/38	1	2	FACETS	0.263	0.224	0.306	0.263	0.224	0.306	SUBCLONAL	1	TRUE	1	0.41	2		729	1039	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143094	7143094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752552480	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	85	507	0	ENST00000302850.5:c.2275C>T	p.Arg759Trp	p.R759W	ENST00000302850	NM_000208.2	759	Cgg/Tgg	12/22	1	2	FACETS	0.654	0.578	0.735	0.654	0.578	0.735	SUBCLONAL	1	TRUE	1	0.41	2		507	634	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7174701	7174701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1413147628	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	107	689	0	ENST00000302850.5:c.1016G>A	p.Cys339Tyr	p.C339Y	ENST00000302850	NM_000208.2	339	tGc/tAc	4/22	1	2	FACETS	0.648	0.581	0.719	0.648	0.581	0.719	SUBCLONAL	1	TRUE	1	0.41	2		689	806	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096051	11096051	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	141	740	1	ENST00000358026.2:c.325C>A	p.Pro109Thr	p.P109T	ENST00000358026	NM_001128849.1	109	Ccg/Acg	3/36	1	2	FACETS	0.765	0.697	0.837	0.765	0.697	0.837	SUBCLONAL	1	TRUE	1	0.41	2		741	899	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11114058	11114060	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	639	85	0	ENST00000358026.2:c.1992_1994del	p.Glu672del	p.E672del	ENST00000358026	NM_001128849.1	662	tcAGAa/tca	13/36	1	2	FACETS	1	0.995	1	1	0.998	1	CLONAL	2	TRUE	1	0.41	2		85	1340	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273793	18273793	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs886041591	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	659	151	0	ENST00000222254.8:c.1126A>G	p.Lys376Glu	p.K376E	ENST00000222254	NM_005027.3	376	Aag/Gag	10/16	1	2	FACETS	1	0.995	1	1	0.998	1	CLONAL	2	TRUE	1	0.41	2		151	1385	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312915	30312915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1411284279	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	109	613	1	ENST00000262643.3:c.718C>T	p.Arg240Cys	p.R240C	ENST00000262643	NM_001238.2	240	Cgt/Tgt	9/12	1	2	FACETS	0.735	0.661	0.815	0.735	0.661	0.815	SUBCLONAL	1	TRUE	1	0.41	2		614	723	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210725	36210725	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	690	113	2	ENST00000222270.7:c.481del	p.Leu161PhefsTer6	p.L161Ffs*6	ENST00000222270	NM_014727.1	159	aCc/ac	3/37	1	2	FACETS	1	0.991	1	1	0.998	1	CLONAL	2	TRUE	1	0.41	2		115	1569	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211939	36211939	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519283	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	847	235	3	ENST00000222270.7:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000222270	NM_014727.1	564	Cga/Tga	3/37	1	2	FACETS	1	0.996	1	1	0.998	1	CLONAL	2	TRUE	1	0.41	2		238	1764	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41521966	41521966	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	43	709	0	ENST00000263253.7:c.832del	p.Thr278LeufsTer39	p.T278Lfs*39	ENST00000263253	NM_001429.3	276	acA/ac	3/31	1	2	FACETS	0.264	0.22	0.313	0.264	0.22	0.313	SUBCLONAL	1	TRUE	1	0.41	2		709	795	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572820	41572820	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	745	179	1	ENST00000263253.7:c.5105A>G	p.Asp1702Gly	p.D1702G	ENST00000263253	NM_001429.3	1702	gAc/gGc	31/31	1	2	FACETS	1	0.997	1	1	0.998	1	CLONAL	2	TRUE	1	0.41	2		180	1469	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665504	138665504	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	80	597	0	ENST00000330315.3:c.61G>A	p.Gly21Ser	p.G21S	ENST00000330315	NM_023067.3	21	Ggt/Agt	1/1	1	2	FACETS	0.593	0.522	0.669	0.593	0.522	0.669	SUBCLONAL	1	TRUE	1	0.41	2		597	658	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156703	55156703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	443	95	1	ENST00000257290.5:c.3104G>A	p.Gly1035Asp	p.G1035D	ENST00000257290	NM_006206.4	1035	gGc/gAc	22/23	1	2	FACETS	0.862	0.828	0.895	1	0.997	1	CLONAL	3	TRUE	1	0.41	2		96	836	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950111	38950112	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	645	132	0	ENST00000357387.3:c.3838_3839del	p.Ser1280GlnfsTer18	p.S1280Qfs*18	ENST00000357387	NM_152756.3	1280	TCc/c	31/38	1	2	FACETS	0.834	0.806	0.861	1	0.998	1	CLONAL	3	TRUE	1	0.41	2		132	1258	SUCCESS
APC	324	MSKCC	GRCh37	5	112173375	112173375	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	410	31	0	ENST00000257430.4:c.2084A>G	p.Gln695Arg	p.Q695R	ENST00000257430	NM_000038.5	695	cAg/cGg	16/16	1	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	1	0.41	2		31	873	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197223	26197223	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	111	606	0	ENST00000356476.2:c.256C>T	p.Gln86Ter	p.Q86*	ENST00000356476		86	Cag/Tag	1/1	1	2	FACETS	0.806	0.725	0.891	0.806	0.725	0.891	CLONAL	1	TRUE	1	0.41	2		606	672	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323148	31323148	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	760	202	1	ENST00000412585.2:c.841T>G	p.Tyr281Asp	p.Y281D	ENST00000412585	NM_005514.6	281	Tac/Gac	4/8	1	2	FACETS	0.842	0.816	0.867	1	0.998	1	CLONAL	3	TRUE	1	0.41	2		203	1468	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829014	128829014	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	41	89	0	ENST00000249373.3:c.22C>T	p.Arg8Trp	p.R8W	ENST00000249373	NM_005631.4	8	Cgg/Tgg	1/12	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.41	2		89	190	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884798	151884798	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	443	37	0	ENST00000262189.6:c.4793+2T>C		p.X1598_splice	ENST00000262189	NM_170606.2	1598			1	2	FACETS	0.844	0.811	0.878	1	0.997	1	CLONAL	3	TRUE	1	0.41	2		37	853	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375991	8375991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200669619	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	93	445	0	ENST00000356435.5:c.4606C>T	p.Arg1536Cys	p.R1536C	ENST00000356435		1536	Cgt/Tgt	28/35	1	2	FACETS	0.856	0.763	0.954	0.856	0.763	0.954	CLONAL	1	TRUE	1	0.41	2		445	530	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27203105	27203105	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	603	135	0	ENST00000380036.4:c.2197C>A	p.Pro733Thr	p.P733T	ENST00000380036	NM_000459.3	733	Cca/Aca	13/23	1	2	FACETS	1	0.996	1	1	0.998	1	CLONAL	2	TRUE	1	0.41	2		135	1188	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916498	39916498	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	190	784	0	ENST00000378444.4:c.4505A>G	p.His1502Arg	p.H1502R	ENST00000378444	NM_001123385.1	1502	cAt/cGt	11/15	1	2	FACETS	0.88	0.813	0.95	0.88	0.813	0.95	CLONAL	1	TRUE	1	0.41	2		784	1053	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932963	39932963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	648	155	0	ENST00000378444.4:c.1636C>T	p.Arg546Cys	p.R546C	ENST00000378444	NM_001123385.1	546	Cgc/Tgc	4/15	1	2	FACETS	1	0.996	1	1	0.998	1	CLONAL	2	TRUE	1	0.41	2		155	1319	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040765	47040765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782379006	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	137	775	1	ENST00000377604.3:c.1400G>A	p.Gly467Asp	p.G467D	ENST00000377604	NM_001204468.1	467	gGc/gAc	13/24	1	2	FACETS	0.813	0.74	0.89	0.813	0.74	0.89	CLONAL	1	TRUE	1	0.41	2		776	822	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939136	76939136	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	627	111	1	ENST00000373344.5:c.1612G>T	p.Val538Phe	p.V538F	ENST00000373344	NM_000489.3	538	Gtt/Ttt	9/35	1	2	FACETS	0.871	0.842	0.899	1	0.998	1	CLONAL	3	TRUE	1	0.41	2		112	1171	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0023640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	146	521	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.936	0.855	1	0.936	0.855	1	CLONAL	1	TRUE	1	0.427516150879574	2		521	730	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	156	482	0				ENST00000310581	NM_198253.2	-/1132			0.281558210019328	1	FACETS	0.981	0.903	1	0.981	0.903	1	CLONAL	1	TRUE	0	0.427516150879574	1		482	585	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098551	178098878	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAGGTTGGGTACTGAACTCAGGTTAGGTACTGAACTCATCAGGAGGCTGAGGTTGGAAAGTAGATTTGACAAGGTTAAGTAAAAGAAAGGCAAAGCTGGAACTCAAATCCAGATATTTTAATTCCTTGCTCAGTGTTTCCTTAAACCTGCCATAACTTTCCCAAGAACTGAGTACTCTGTACCTGGGAGTAGTTGGCAGATCCACTGGTTTCTGACTGGATGTGCTGGGCTGGCTGAATTGGGAGAAATTCACCTGTCTCTTCATCTAGTTGTAACTGAGCGAAAAAGGCTTTCTCTTGCTCCTTTTGGAGTTGTTCTTGTCTTTCCT	TAGGTTGGGTACTGAACTCAGGTTAGGTACTGAACTCATCAGGAGGCTGAGGTTGGAAAGTAGATTTGACAAGGTTAAGTAAAAGAAAGGCAAAGCTGGAACTCAAATCCAGATATTTTAATTCCTTGCTCAGTGTTTCCTTAAACCTGCCATAACTTTCCCAAGAACTGAGTACTCTGTACCTGGGAGTAGTTGGCAGATCCACTGGTTTCTGACTGGATGTGCTGGGCTGGCTGAATTGGGAGAAATTCACCTGTCTCTTCATCTAGTTGTAACTGAGCGAAAAAGGCTTTCTCTTGCTCCTTTTGGAGTTGTTCTTGTCTTTCCT	-	novel	NA	P-0023640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	30	29	0	ENST00000397062.3:c.167_312+182del		p.X56_splice	ENST00000397062	NM_006164.4	56		2/5	1	2	FACETS	1	0.865	1	1	0.965	1	CLONAL	2	TRUE	1	0.427516150879574	2		29	68	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348566	89348568	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs753054998	NA	P-0023641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	73	1060	2	ENST00000301030.4:c.4382_4384del	p.Lys1461del	p.K1461del	ENST00000301030	NM_001256183.1	1461	aAGAga/aga	9/13	0.32735664944734	2	FACETS	0.592	0.517	0.673	0.296	0.258	0.337	SUBCLONAL	1	TRUE	0	0.32735664944734	2		1062	753	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927985	+	inframe_deletion	In_Frame_Del	DEL	TGTCCA	TGTCCA	-	novel	NA	P-0023641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	106	335	0	ENST00000263967.3:c.1259_1264del	p.Cys420_Pro421del	p.C420_P421del	ENST00000263967	NM_006218.2	420	TGTCCA/-	8/21	0.32735664944734	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.32735664944734	3		335	343	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2193750	2193750	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	189	691	0	ENST00000398665.3:c.556G>C	p.Glu186Gln	p.E186Q	ENST00000398665	NM_032482.2	186	Gag/Cag	6/28	0.32735664944734	2	FACETS	0.881	0.824	0.938	1	0.99	1	CLONAL	3	TRUE	0	0.32735664944734	2		691	437	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428494	72428496	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0023641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	608	82	0	ENST00000477973.2:c.506_508del	p.Lys170del	p.K170del	ENST00000477973	NM_012234.5	170	AAG/-	2/4	0.32735664944734	3	FACETS	0.882	0.852	0.913	1	0.998	1	CLONAL	4	TRUE	1	0.32735664944734	3		82	1225	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106989	27107026	+	frameshift_variant	Frame_Shift_Del	DEL	GGACAGCCTTGCCGCCACACAGTTCCAGCAGAGCCAGG	GGACAGCCTTGCCGCCACACAGTTCCAGCAGAGCCAGG	-	novel	NA	P-0023644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	65	591	0	ENST00000324856.7:c.6600_6637del	p.Glu2200AspfsTer12	p.E2200Dfs*12	ENST00000324856	NM_006015.4	2200	gaGGACAGCCTTGCCGCCACACAGTTCCAGCAGAGCCAGGcc/gacc	20/20	0.365477675000472	1	FACETS	0.821	0.718	0.931	0.821	0.718	0.931	CLONAL	1	TRUE	0	0.41874276371442	1		591	299	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715672	18715672	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	448	133	1	ENST00000266497.5:c.3503A>T	p.Lys1168Ile	p.K1168I	ENST00000266497		1168	aAa/aTa	25/31	0.41874276371442	3	FACETS	1	0.994	1	1	0.997	1	CLONAL	3	TRUE	1	0.41874276371442	3		134	754	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937630	32937630	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	79	627	4	ENST00000380152.3:c.8292del	p.Cys2765ValfsTer12	p.C2765Vfs*12	ENST00000380152		2764	gCc/gc	18/27	0.41874276371442	3	FACETS	0.764	0.673	0.862	0.255	0.224	0.288	SUBCLONAL	1	TRUE	0	0.41874276371442	3		631	597	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40876429	40876429	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	718	47	2	ENST00000428826.2:c.260G>C	p.Ser87Thr	p.S87T	ENST00000428826		87	aGc/aCc	5/21	0.394546760287077	3	FACETS	1	0.996	1	1	0.998	1	CLONAL	3	TRUE	1	0.41874276371442	3		49	1219	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796478	42796517	+	frameshift_variant	Frame_Shift_Del	DEL	GGCACGCGCTGCCCCTGGGTACCAGCCCTGCGTCCAGCCA	GGCACGCGCTGCCCCTGGGTACCAGCCCTGCGTCCAGCCA	-	novel	NA	P-0023644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	836	126	4	ENST00000575354.2:c.3038_3077del	p.His1013LeufsTer13	p.H1013Lfs*13	ENST00000575354	NM_015125.3	1012	gGGCACGCGCTGCCCCTGGGTACCAGCCCTGCGTCCAGCCAg/gg	13/20	0.41874276371442	3	FACETS	0.875	0.852	0.898	1	0.998	1	CLONAL	4	TRUE	1	0.41874276371442	3		130	1379	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39708772	39708772	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1242408105	NA	P-0023644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	229	552	1	ENST00000361337.2:c.383C>T	p.Pro128Leu	p.P128L	ENST00000361337	NM_003286.2	128	cCt/cTt	6/21	0.41874276371442	5	FACETS	0.895	0.834	0.957	0.447	0.417	0.479	CLONAL	2	TRUE	1	0.41874276371442	5		553	995	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670656	86670656	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0023644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	392	70	1	ENST00000274376.6:c.1935-1G>T		p.X645_splice	ENST00000274376	NM_002890.2	645			0.297553025720357	1	FACETS	1	0.99	1	1	0.997	1	CLONAL	2	TRUE	0	0.41874276371442	1		71	677	SUCCESS
APC	324	MSKCC	GRCh37	5	112164609	112164609	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	24	519	0	ENST00000257430.4:c.1683del	p.Thr562ArgfsTer8	p.T562Rfs*8	ENST00000257430	NM_000038.5	561	aaG/aa	14/16	0.297553025720357	1	FACETS	0.245	0.192	0.306	0.245	0.192	0.306	SUBCLONAL	1	TRUE	0	0.41874276371442	1		519	370	SUCCESS
APC	324	MSKCC	GRCh37	5	112177025	112177030	+	inframe_deletion	In_Frame_Del	DEL	GCTATT	GCTATT	-	novel	NA	P-0023644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	36	614	1	ENST00000257430.4:c.5736_5741del	p.Ile1913_Ala1914del	p.I1913_A1914del	ENST00000257430	NM_000038.5	1912	GCTATT/-	16/16	0.297553025720357	1	FACETS	0.323	0.265	0.387	0.323	0.265	0.387	SUBCLONAL	1	TRUE	0	0.41874276371442	1		615	421	SUCCESS
APC	324	MSKCC	GRCh37	5	112177633	112177633	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	19	442	0	ENST00000257430.4:c.6344del	p.Leu2115TyrfsTer24	p.L2115Yfs*24	ENST00000257430	NM_000038.5	2114	agT/ag	16/16	0.297553025720357	1	FACETS	0.256	0.194	0.329	0.256	0.194	0.329	SUBCLONAL	1	TRUE	0	0.41874276371442	1		442	280	SUCCESS
APC	324	MSKCC	GRCh37	5	112177863	112177864	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAAA	novel	NA	P-0023644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	24	407	0	ENST00000257430.4:c.6576_6579dup	p.Val2194LysfsTer4	p.V2194Kfs*4	ENST00000257430	NM_000038.5	2191	gga/ggAAAAa	16/16	0.297553025720357	1	FACETS	0.282	0.221	0.353	0.282	0.221	0.353	SUBCLONAL	1	TRUE	0	0.41874276371442	1		407	321	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686369	117686369	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs775466876	NA	P-0023644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	69	338	0	ENST00000368508.3:c.2974-2A>G		p.X992_splice	ENST00000368508	NM_002944.2	992			0.41874276371442	5	FACETS	0.896	0.78	1			1	CLONAL	1	TRUE	NA	0.41874276371442	5		338	599	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978662	70978662	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	115	741	4	ENST00000276594.2:c.991G>A	p.Ala331Thr	p.A331T	ENST00000276594	NM_024504.3	331	Gcc/Acc	5/8	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.41874276371442	2		745	501	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740618	145740618	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	84	704	2	ENST00000428558.2:c.1399del	p.Ala467LeufsTer91	p.A467Lfs*91	ENST00000428558	NM_004260.3	467	Gct/ct	8/22	0.41874276371442	5	FACETS	0.822	0.725	0.926			1	CLONAL	1	TRUE	NA	0.41874276371442	5		706	795	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0023645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	160	521	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.29178560357268	3	FACETS	0.978	0.902	1	0.978	0.902	1	CLONAL	2	TRUE	1	0.3465476043137	3		521	554	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	79	482	0				ENST00000310581	NM_198253.2	-/1132			0.170128378881811	3	FACETS	1	0.939	1	0.551	0.486	0.621	INDETERMINATE	1	TRUE	1	0.3465476043137	3		482	485	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692896	89692896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123322	NA	P-0023645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	77	379	0	ENST00000371953.3:c.380G>A	p.Gly127Glu	p.G127E	ENST00000371953	NM_000314.4	127	gGa/gAa	5/9	0.281008246210509	2	FACETS	1	0.973	1	0.682	0.603	0.764	CLONAL	1	TRUE	0	0.3465476043137	2		379	326	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016609	12016609	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	82	540	0	ENST00000353533.5:c.745G>T	p.Gly249Cys	p.G249C	ENST00000353533	NM_003010.3	249	Ggc/Tgc	7/11	1	2	FACETS	0.952	0.842	1	0.952	0.842	1	CLONAL	1	TRUE	1	0.3465476043137	2		540	497	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0023645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	128	711	0	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	1	2	FACETS	0.928	0.841	1	0.928	0.841	1	CLONAL	1	TRUE	1	0.3465476043137	2		711	796	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202178	108202178	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	39	437	0	ENST00000278616.4:c.7523G>A	p.Gly2508Glu	p.G2508E	ENST00000278616	NM_000051.3	2508	gGa/gAa	51/63	1	2	FACETS	0.787	0.655	0.932	0.787	0.655	0.932	CLONAL	1	TRUE	1	0.3465476043137	2		437	286	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262217	10262217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	84	604	0	ENST00000340748.4:c.2074C>T	p.Pro692Ser	p.P692S	ENST00000340748		692	Ccc/Tcc	23/40	1	2	FACETS	0.832	0.735	0.934	0.832	0.735	0.934	CLONAL	1	TRUE	1	0.3465476043137	2		604	583	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009100	27009101	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0023645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	58	237	0	ENST00000335756.4:c.36_37delinsTT	p.Pro13Ser	p.P13S	ENST00000335756	NM_001809.3	12	gcCCcg/gcTTcg	1/5	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.3465476043137	2		237	287	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395464	116395464	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	114	496	0	ENST00000397752.3:c.1757G>C	p.Trp586Ser	p.W586S	ENST00000397752	NM_000245.2	586	tGg/tCg	6/21	0.29178560357268	3	FACETS	1	0.961	1	0.564	0.509	0.623	CLONAL	1	TRUE	1	0.3465476043137	3		496	684	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540374	23540374	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	86	395	0	ENST00000380871.4:c.29G>A	p.Gly10Glu	p.G10E	ENST00000380871	NM_006167.3	10	gGg/gAg	1/2	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.3465476043137	2		395	412	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981881	70981881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	471	630	1	ENST00000276594.2:c.215G>A	p.Arg72Gln	p.R72Q	ENST00000276594	NM_024504.3	72	cGg/cAg	2/8	0.3465476043137	5	FACETS	1	0.991	1	1	0.991	1	CLONAL	4	TRUE	1	0.3465476043137	5		631	934	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410414	63410414	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	97	624	0	ENST00000330258.3:c.2753C>T	p.Ser918Phe	p.S918F	ENST00000330258	NM_152424.3	918	tCt/tTt	2/2	1	2	FACETS	0.9	0.804	1	0.9	0.804	1	CLONAL	1	TRUE	1	0.3465476043137	2		624	622	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104359295	104359295	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	41	484	2	ENST00000369902.3:c.1018del	p.Ala340ProfsTer21	p.A340Pfs*21	ENST00000369902	NM_016169.3	339	cGg/cg	8/12	0.714090583626535	1	FACETS	0.195	0.163	0.231	0.195	0.163	0.231	SUBCLONAL	1	TRUE	0	0.714090583626535	1		486	378	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100390	8100390	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	198	669	0	ENST00000346208.3:c.364A>G	p.Ile122Val	p.I122V	ENST00000346208		122	Atc/Gtc	3/6	0.686627711159224	1	FACETS	0.925	0.871	0.979	0.925	0.871	0.979	CLONAL	1	TRUE	0	0.724176314140465	1		669	377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577561	+	frameshift_variant	Frame_Shift_Del	DEL	CCATGCAGGAA	CCATGCAGGAA	-	novel	NA	P-0023662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	251	620	0	ENST00000269305.4:c.720_730del	p.Ser240ArgfsTer20	p.S240Rfs*20	ENST00000269305	NM_001126112.2	240	agTTCCTGCATGGgc/aggc	7/11	0.724176314140465	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.724176314140465	1		620	397	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490255	29490255	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	169	327	0	ENST00000356175.3:c.340del	p.Leu114CysfsTer51	p.L114Cfs*51	ENST00000356175	NM_000267.3	114	Ctg/tg	4/57	0.724176314140465	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.724176314140465	1		327	285	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720737	89720737	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0023663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	12	124	0	ENST00000371953.3:c.888T>A	p.Cys296Ter	p.C296*	ENST00000371953	NM_000314.4	296	tgT/tgA	8/9	0.327859758126021	1	FACETS	0.766	0.572	0.971	0.766	0.572	0.971	INDETERMINATE	1	TRUE	0	0.686308257250734	1		124	30	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772239	68772239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	275	721	1	ENST00000261769.5:c.88C>T	p.Pro30Ser	p.P30S	ENST00000261769	NM_004360.3	30	Cct/Tct	2/16	0.640042610312146	4	FACETS	0.965	0.912	1	0.965	0.912	1	CLONAL	2	TRUE	2	0.686308257250734	4		722	700	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	93	752	0	ENST00000397752.3:c.3028G>C	p.Asp1010His	p.D1010H	ENST00000397752	NM_000245.2	1010	Gat/Cat	14/21	1	2	FACETS	0.809	0.721	0.901	0.809	0.721	0.901	CLONAL	1	TRUE	1	0.43	2		752	535	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480092	50480092	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	20	482	0	ENST00000394963.4:c.326A>C	p.Gln109Pro	p.Q109P	ENST00000394963	NM_003076.4	109	cAg/cCg	2/13	1	2	FACETS	0.358	0.274	0.456	0.358	0.274	0.456	SUBCLONAL	1	TRUE	1	0.43	2		482	260	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968148	18968148	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	26	525	0	ENST00000262803.5:c.1988A>C	p.His663Pro	p.H663P	ENST00000262803	NM_002911.3	663	cAc/cCc	15/24	1	2	FACETS	0.42	0.333	0.519	0.42	0.333	0.519	SUBCLONAL	1	TRUE	1	0.43	2		525	288	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267781	46267781	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs755361920	NA	P-0023664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	21	502	0	ENST00000371998.3:c.2542A>G	p.Ile848Val	p.I848V	ENST00000371998		848	Att/Gtt	14/23	1	2	FACETS	0.254	0.195	0.323	0.254	0.195	0.323	SUBCLONAL	1	TRUE	1	0.43	2		502	385	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	209	657	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	0.239984118228151	7	FACETS	0.971	0.908	1	1	0.987	1	CLONAL	5	FALSE	3	0.239984118228151	7		657	574	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143999	11143999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1171822727	NA	P-0023665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	122	468	1	ENST00000358026.2:c.3580G>A	p.Gly1194Arg	p.G1194R	ENST00000358026	NM_001128849.1	1194	Ggg/Agg	26/36	0.239984118228151	5	FACETS	1	0.965	1	1	0.965	1	CLONAL	3	FALSE	2	0.239984118228151	5		469	413	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982440	25982440	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	113	424	0	ENST00000435504.4:c.850C>T	p.Arg284Ter	p.R284*	ENST00000435504		284	Cga/Tga	9/13	0.586659473511581	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.62172812462603	1		424	229	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43730535	43730536	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0023666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	107	453	0	ENST00000382044.4:c.3177dup	p.Thr1060HisfsTer26	p.T1060Hfs*26	ENST00000382044	NM_001141980.1	1059	-/C	16/28	0.62172812462603	1	FACETS	0.773	0.702	0.845	0.773	0.702	0.845	SUBCLONAL	1	TRUE	0	0.62172812462603	1		453	307	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37871776	37871776	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	174	727	0	ENST00000269571.5:c.1300C>T	p.Arg434Ter	p.R434*	ENST00000269571		434	Cga/Tga	11/27	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.62172812462603	2		727	558	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089016	37089016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs864622530	NA	P-0023666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	69	285	0	ENST00000231790.2:c.1738G>A	p.Ala580Thr	p.A580T	ENST00000231790	NM_000249.3	580	Gca/Aca	16/19	1	2	FACETS	0.76	0.668	0.857	0.76	0.668	0.857	SUBCLONAL	1	TRUE	1	0.62172812462603	2		285	292	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328441	137328441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1306245171	NA	P-0023666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	199	721	1	ENST00000481739.1:c.1370C>T	p.Ala457Val	p.A457V	ENST00000481739	NM_002957.4	457	gCg/gTg	10/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.62172812462603	2		722	554	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0023667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	83	336	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.559116972243139	2		336	274	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0023667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	95	368	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.559116972243139	2		368	276	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022913	27022938	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGCCGCCGCCAGCAGCCTGGGCAA	CCCGCCGCCGCCAGCAGCCTGGGCAA	-	rs797045262	NA	P-0023667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	11	26	0	ENST00000324856.7:c.31_56del	p.Ser11AlafsTer91	p.S11Afs*91	ENST00000324856	NM_006015.4	7	CCCGCCGCCGCCAGCAGCCTGGGCAAc/c	1/20	1	2	FACETS	0.715	0.507	0.96	0.715	0.507	0.96	CLONAL	1	TRUE	1	0.559116972243139	2		26	55	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916946	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0023667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	73	405	0	ENST00000263967.3:c.332_334del	p.Lys111del	p.K111del	ENST00000263967	NM_006218.2	111	AAG/-	2/21	1	2	FACETS	0.989	0.876	1	0.989	0.876	1	CLONAL	1	TRUE	1	0.559116972243139	2		405	264	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0023667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	109	440	0	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.559116972243139	2		440	376	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654643	67654643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs968244943	NA	P-0023667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	170	509	1	ENST00000264010.4:c.1130G>A	p.Arg377His	p.R377H	ENST00000264010	NM_006565.3	377	cGt/cAt	6/12	0.559116972243139	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.559116972243139	1		510	359	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692792	89692792	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs779530981	NA	P-0023667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	65	364	0	ENST00000371953.3:c.276C>A	p.Asp92Glu	p.D92E	ENST00000371953	NM_000314.4	92	gaC/gaA	5/9	1	2	FACETS	0.957	0.84	1	0.957	0.84	1	CLONAL	1	TRUE	1	0.559116972243139	2		364	243	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044470	12044470	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	76	267	0	ENST00000353533.5:c.1093C>T	p.Pro365Ser	p.P365S	ENST00000353533	NM_003010.3	365	Ccc/Tcc	11/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.559116972243139	2		267	205	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839984	27839984	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	169	525	0	ENST00000328488.2:c.110A>T	p.Lys37Met	p.K37M	ENST00000328488	NM_003533.2	37	aAg/aTg	1/1	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.559116972243139	2		525	498	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170537	11170537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768899897	NA	P-0023667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	228	607	0	ENST00000358026.2:c.4840G>A	p.Glu1614Lys	p.E1614K	ENST00000358026	NM_001128849.1	1614	Gag/Aag	34/36	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.559116972243139	2		607	745	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929302	44929302	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1196875808	NA	P-0023667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	172	669	0	ENST00000377967.4:c.2402A>G	p.Asn801Ser	p.N801S	ENST00000377967	NM_021140.2	801	aAt/aGt	17/29	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.559116972243139	2		669	534	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47004903	47004903	+	intron_variant	Intron	SNP	C	C	T	novel	NA	P-0023667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	149	445	0	ENST00000377604.3:c.-126+19C>T		p.*42*	ENST00000377604	NM_001204468.1	-/163			1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.559116972243139	2		445	513	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0023668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	83	461	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.251690081643512	3	FACETS	0.907	0.81	1	0.907	0.81	1	CLONAL	3	TRUE	0	0.251690081643512	3		461	273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0023668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	93	489	2	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.184095520755119	2	FACETS	0.899	0.804	0.998	0.899	0.804	0.998	CLONAL	2	TRUE	0	0.251690081643512	2		491	411	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951156	48951156	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	26	428	0	ENST00000267163.4:c.1318G>T	p.Glu440Ter	p.E440*	ENST00000267163	NM_000321.2	440	Gaa/Taa	13/27	0.225365319489193	2	FACETS	0.854	0.679	1	0.427	0.339	0.526	CLONAL	1	TRUE	0	0.251690081643512	2		428	242	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427606	427606	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	26	353	0	ENST00000399788.2:c.2563G>C	p.Glu855Gln	p.E855Q	ENST00000399788	NM_001042603.1	855	Gag/Cag	19/28	1	2	FACETS	0.82	0.652	1	0.82	0.652	1	CLONAL	1	TRUE	1	0.251690081643512	2		353	252	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512266	38512266	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	43	489	0	ENST00000254066.5:c.1177G>A	p.Glu393Lys	p.E393K	ENST00000254066	NM_000964.3	393	Gag/Aag	9/9	0.251690081643512	8	FACETS	0.883	0.737	1			1	CLONAL	1	TRUE	NA	0.251690081643512	8		489	679	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133746	55133746	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	35	422	0	ENST00000257290.5:c.960del	p.Phe321SerfsTer17	p.F321Sfs*17	ENST00000257290	NM_006206.4	320	aCc/ac	7/23	0.251690081643512	3	FACETS	0.756	0.62	0.909	0.378	0.31	0.455	CLONAL	1	TRUE	1	0.251690081643512	3		422	414	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518193	103518193	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs760008264	NA	P-0023670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	63	264	0	ENST00000355739.4:c.2131G>T	p.Asp711Tyr	p.D711Y	ENST00000355739	NM_000123.3	711	Gat/Tat	9/15	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.464136331252977	2		264	260	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187300	38187301	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	117	578	0	ENST00000317025.8:c.1176dup	p.Ile393TyrfsTer4	p.I393Yfs*4	ENST00000317025	NM_023034.1	392	-/T	6/24	1	2	FACETS	0.846	0.765	0.931	0.846	0.765	0.931	CLONAL	1	TRUE	1	0.464136331252977	2		578	596	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0023671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	135	724	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.18533424961012	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	3	TRUE	1	0.18533424961012	4		726	515	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0023671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	63	883	4	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.18533424961012	2		887	613	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291504	15291504	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767672719	NA	P-0023671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	42	665	3	ENST00000263388.2:c.3130G>A	p.Ala1044Thr	p.A1044T	ENST00000263388	NM_000435.2	1044	Gca/Aca	19/33	1	2	FACETS	0.812	0.677	0.962	0.812	0.677	0.962	CLONAL	1	TRUE	1	0.18533424961012	2		668	558	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860499	151860499	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs200302468	NA	P-0023671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	59	843	1	ENST00000262189.6:c.10163A>G	p.Asn3388Ser	p.N3388S	ENST00000262189	NM_170606.2	3388	aAc/aGc	43/59	1	2	FACETS	0.996	0.857	1	0.996	0.857	1	CLONAL	1	TRUE	1	0.18533424961012	2		844	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0023673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	56	705	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.16	2		705	513	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306741	41306741	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	33	633	2	ENST00000373198.4:c.918G>T	p.Trp306Cys	p.W306C	ENST00000373198	NM_133170.3	306	tgG/tgT	7/32	0.135749730293359	3	FACETS	0.964	0.785	1	0.482	0.392	0.584	CLONAL	1	TRUE	1	0.16	3		635	462	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266714	142266714	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	48	687	0	ENST00000350721.4:c.3210A>T	p.Gln1070His	p.Q1070H	ENST00000350721	NM_001184.3	1070	caA/caT	16/47	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.16	2		687	537	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674306	86674306	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	34	555	0	ENST00000274376.6:c.2438C>A	p.Ala813Asp	p.A813D	ENST00000274376	NM_002890.2	813	gCt/gAt	18/25	1	2	FACETS	0.926	0.756	1	0.926	0.756	1	CLONAL	1	TRUE	1	0.16	2		555	459	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0023675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	292	724	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.433707491755479	3	FACETS	0.975	0.921	1	0.975	0.921	1	CLONAL	2	TRUE	1	0.433707491755479	3		726	840	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0023675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	113	326	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.418345877154108	2	FACETS	0.965	0.884	1	0.965	0.884	1	CLONAL	2	TRUE	0	0.433707491755479	2		326	270	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374881	45374881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	173	785	0	ENST00000262160.6:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000262160	NM_005901.5	321	cGa/cAa	8/11	1	2	FACETS	0.931	0.857	1	0.931	0.857	1	CLONAL	1	TRUE	1	0.433707491755479	2		785	857	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739819	41739819	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	127	719	0	ENST00000242208.4:c.154C>A	p.Pro52Thr	p.P52T	ENST00000242208	NM_002192.2	52	Cca/Aca	2/3	0.433707491755479	3	FACETS	0.844	0.765	0.928	0.422	0.382	0.464	CLONAL	1	TRUE	1	0.433707491755479	3		719	844	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252940	36252940	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	298	622	0	ENST00000300305.3:c.422C>A	p.Ser141Ter	p.S141*	ENST00000300305		141	tCg/tAg	4/8	0.433707491755479	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.433707491755479	2		622	685	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518442	204518442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140091735	NA	P-0023675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	128	547	0	ENST00000367182.3:c.1105C>T	p.Pro369Ser	p.P369S	ENST00000367182	NM_001278516.1	369	Cct/Tct	11/11	0.433707491755479	2	FACETS	1	0.919	1	0.505	0.459	0.553	CLONAL	1	TRUE	0	0.433707491755479	2		547	584	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427372	427372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	183	769	0	ENST00000399788.2:c.2797G>A	p.Ala933Thr	p.A933T	ENST00000399788	NM_001042603.1	933	Gca/Aca	19/28	0.0106420453648493	4	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.433707491755479	4		769	990	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713483	30713483	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	166	639	0	ENST00000295754.5:c.808C>T	p.Gln270Ter	p.Q270*	ENST00000295754	NM_003242.5	270	Cag/Tag	4/7	0.418345877154108	2	FACETS	1	0.977	1	0.578	0.533	0.625	CLONAL	1	TRUE	0	0.433707491755479	2		639	662	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713811	30713811	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	144	822	0	ENST00000295754.5:c.1136A>G	p.Asp379Gly	p.D379G	ENST00000295754	NM_003242.5	379	gAc/gGc	4/7	0.418345877154108	2	FACETS	0.841	0.767	0.917	0.42	0.383	0.459	CLONAL	1	TRUE	0	0.433707491755479	2		822	790	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265619	41266368	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTGCCATTAAGCCAGTCTGGCTGAGATCCCCCTGCTTTCCTCTCTCCCTGCTTACTTGTCAGGCTACCTTTTGCTCCATTTTCTGCTCACTCCTCCTAATGGCTTGGTGAAATAGCAAACAAGCCACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCAC	TTGCCATTAAGCCAGTCTGGCTGAGATCCCCCTGCTTTCCTCTCTCCCTGCTTACTTGTCAGGCTACCTTTTGCTCCATTTTCTGCTCACTCCTCCTAATGGCTTGGTGAAATAGCAAACAAGCCACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCAC	-	novel	NA	P-0023675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	208	484	0	ENST00000349496.5:c.13+49_242-75del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.418345877154108	2	FACETS	0.893	0.836	0.951	0.893	0.836	0.951	CLONAL	2	TRUE	0	0.433707491755479	2		484	537	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591095	67591148	+	inframe_deletion	In_Frame_Del	DEL	TGAACAGCATTAAACCAGACCTTATCCAGCTGAGAAAGACGAGAGACCAATACT	TGAACAGCATTAAACCAGACCTTATCCAGCTGAGAAAGACGAGAGACCAATACT	-	novel	NA	P-0023675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	51	447	0	ENST00000274335.5:c.1691_1744del	p.Asn564_Leu581del	p.N564_L581del	ENST00000274335		563	aTGAACAGCATTAAACCAGACCTTATCCAGCTGAGAAAGACGAGAGACCAATACTtg/atg	12/15	0.433707491755479	3	FACETS	0.666	0.567	0.774	0.333	0.283	0.387	SUBCLONAL	1	TRUE	1	0.433707491755479	3		447	430	SUCCESS
APC	324	MSKCC	GRCh37	5	112179746	112179746	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	114	463	0	ENST00000257430.4:c.8455A>G	p.Lys2819Glu	p.K2819E	ENST00000257430	NM_000038.5	2819	Aaa/Gaa	16/16	0.433707491755479	3	FACETS	1	0.914	1	0.507	0.457	0.559	CLONAL	1	TRUE	1	0.433707491755479	3		463	631	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508589	106508589	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1257245065	NA	P-0023675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	84	489	0	ENST00000359195.3:c.583C>A	p.Leu195Ile	p.L195I	ENST00000359195	NM_002649.2	195	Ctc/Atc	2/11	0.433707491755479	3	FACETS	0.912	0.807	1	0.456	0.403	0.512	CLONAL	1	TRUE	1	0.433707491755479	3		489	517	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521466	8521466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	186	839	0	ENST00000356435.5:c.772G>A	p.Val258Met	p.V258M	ENST00000356435		258	Gtg/Atg	9/35	1	2	FACETS	0.948	0.876	1	0.948	0.876	1	CLONAL	1	TRUE	1	0.433707491755479	2		839	905	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911616	39911616	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1223567941	NA	P-0023675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	181	405	0	ENST00000378444.4:c.5014A>G	p.Lys1672Glu	p.K1672E	ENST00000378444	NM_001123385.1	1672	Aaa/Gaa	15/15	0.168092896141848	3	FACETS	0.844	0.782	0.907			1	INDETERMINATE	2	TRUE	NA	0.433707491755479	3		405	602	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0023678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	112	571	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.775	0.695	0.86	1	0.984	1	SUBCLONAL	2	TRUE	1	0.128535411444573	2		571	1124	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519938	NA	P-0023678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	14	463	0	ENST00000263967.3:c.1034A>T	p.Asn345Ile	p.N345I	ENST00000263967	NM_006218.2	345	aAt/aTt	5/21	1	2	FACETS	0.543	0.391	0.729	0.543	0.391	0.729	SUBCLONAL	1	TRUE	1	0.128535411444573	2		463	401	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27192600	27192600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs539332352	NA	P-0023678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	45	685	3	ENST00000380036.4:c.1603C>T	p.Arg535Cys	p.R535C	ENST00000380036	NM_000459.3	535	Cgc/Tgc	11/23	0.128349881178788	1	FACETS	0.787	0.66	0.93	0.787	0.66	0.93	CLONAL	1	TRUE	0	0.128535411444573	1		688	832	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465283	120465283	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	47	522	0	ENST00000256646.2:c.4978T>A	p.Ser1660Thr	p.S1660T	ENST00000256646	NM_024408.3	1660	Tca/Aca	27/34	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.128535411444573	2		522	711	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0023680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	120	593	2	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	1	2	FACETS	0.665	0.602	0.731	0.665	0.602	0.731	SUBCLONAL	1	TRUE	1	0.600230937190321	2		595	601	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0023680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	351	725	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	NA	2	FACETS	0.893	0.854	0.931			1	INDETERMINATE	2	TRUE	NA	0.600230937190321	2		725	655	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115747	108115747	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	64	295	0	ENST00000278616.4:c.895G>T	p.Glu299Ter	p.E299*	ENST00000278616	NM_000051.3	299	Gaa/Taa	7/63	1	2	FACETS	0.827	0.724	0.935	0.827	0.724	0.935	CLONAL	1	TRUE	1	0.600230937190321	2		295	258	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430353	47430353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773486607	NA	P-0023680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	247	521	0	ENST00000377045.4:c.1628G>A	p.Arg543Gln	p.R543Q	ENST00000377045	NM_001654.4	543	cGg/cAg	15/16	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.600230937190321	1		521	505	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998426	100998426	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	145	488	0	ENST00000325455.5:c.1376A>C	p.Glu459Ala	p.E459A	ENST00000325455	NM_001202474.3	459	gAg/gCg	1/8	1	2	FACETS	0.962	0.884	1	0.962	0.884	1	CLONAL	1	TRUE	1	0.600230937190321	2		488	502	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604703	48604703	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	135	584	0	ENST00000342988.3:c.1525T>C	p.Trp509Arg	p.W509R	ENST00000342988	NM_005359.5	509	Tgg/Cgg	12/12	0.496153130252301	1	FACETS	0.664	0.608	0.723	0.664	0.608	0.723	SUBCLONAL	1	TRUE	0	0.600230937190321	1		584	474	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754718	42754718	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0023680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	45	257	0	ENST00000222329.4:c.23-1G>C		p.X8_splice	ENST00000222329	NM_006494.2	8			1	2	FACETS	0.773	0.658	0.896	0.773	0.658	0.896	SUBCLONAL	1	TRUE	1	0.600230937190321	2		257	194	SUCCESS
APC	324	MSKCC	GRCh37	5	112164552	112164552	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0023680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	44	326	1	ENST00000257430.4:c.1627-1G>T		p.X543_splice	ENST00000257430	NM_000038.5	543			1	2	FACETS	0.399	0.336	0.47	0.399	0.336	0.47	SUBCLONAL	1	TRUE	1	0.600230937190321	2		327	367	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647465	117647465	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	170	736	1	ENST00000368508.3:c.5479C>A	p.Gln1827Lys	p.Q1827K	ENST00000368508	NM_002944.2	1827	Cag/Aag	33/43	1	2	FACETS	0.79	0.728	0.854	0.79	0.728	0.854	SUBCLONAL	1	TRUE	1	0.600230937190321	2		737	717	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911573	39911573	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	206	398	0	ENST00000378444.4:c.5057A>T	p.Asn1686Ile	p.N1686I	ENST00000378444	NM_001123385.1	1686	aAc/aTc	15/15	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.600230937190321	1		398	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0023700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	214	792	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.523998431623512	1	FACETS	0.945	0.884	1	0.945	0.884	1	CLONAL	1	TRUE	0	0.545967016018082	1		794	603	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0023700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	514	867	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.994	1	1	0.998	1	CLONAL	2	TRUE	1	0.545967016018082	2		868	843	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0023700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	116	345	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	0.545967016018082	2		345	379	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0023700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	101	442	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	1	2	FACETS	0.854	0.768	0.945	0.854	0.768	0.945	CLONAL	1	TRUE	1	0.545967016018082	2		442	433	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812466	43812466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1298113648	NA	P-0023700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	56	448	0	ENST00000372470.3:c.1169G>A	p.Arg390His	p.R390H	ENST00000372470	NM_005373.2	390	cGc/cAc	8/12	0.274943389011764	1	FACETS	0.36	0.309	0.416	0.36	0.309	0.416	INDETERMINATE	1	TRUE	0	0.545967016018082	1		448	414	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800928	120800928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1337094477	NA	P-0023700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	169	625	0	ENST00000257552.2:c.320G>A	p.Arg107Gln	p.R107Q	ENST00000257552	NM_002442.3	107	cGa/cAa	6/15	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.545967016018082	2		625	614	SUCCESS
EED	8726	MSKCC	GRCh37	11	85979530	85979530	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	163	558	0	ENST00000263360.6:c.893A>G	p.Asp298Gly	p.D298G	ENST00000263360	NM_003797.3	298	gAt/gGt	9/12	1	2	FACETS	0.885	0.814	0.957	0.885	0.814	0.957	CLONAL	1	TRUE	1	0.545967016018082	2		558	675	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177576	56177576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	134	434	1	ENST00000399503.3:c.2549C>T	p.Thr850Ile	p.T850I	ENST00000399503	NM_005921.1	850	aCc/aTc	14/20	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.545967016018082	2		435	490	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729443	41729443	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	197	686	0	ENST00000242208.4:c.1086del	p.Ser364ProfsTer33	p.S364Pfs*33	ENST00000242208	NM_002192.2	362	tcC/tc	3/3	0.244329471255467	2	FACETS	1	0.985	1	0.606	0.565	0.649	INDETERMINATE	1	TRUE	0	0.545967016018082	2		686	595	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860112	152860112	+	synonymous_variant	Silent	SNP	G	G	A	novel	NA	P-0023700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	223	355	1	ENST00000406277.2:c.316C>T	p.Leu106=	p.L106=	ENST00000406277	NM_152274.4	106	Ctg/Ttg	5/7	1		FACETS		0.753	0.834				SUBCLONAL	2	TRUE	0	0.545967016018082	1		356	374	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207631	2207631	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	116	734	0	ENST00000398665.3:c.915G>T	p.Trp305Cys	p.W305C	ENST00000398665	NM_032482.2	305	tgG/tgT	11/28	0.585974447005504	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.606820047490596	1		734	199	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913381	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	135	423	0	ENST00000304494.5:c.322G>A	p.Asp108Asn	p.D108N	ENST00000304494	NM_000077.4	108	Gat/Aat	2/3	0.506095681413681	2	FACETS	0.989	0.924	1	0.989	0.924	1	CLONAL	2	TRUE	0	0.606820047490596	2		423	225	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587780070	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	255	699	0	ENST00000269305.4:c.535C>G	p.His179Asp	p.H179D	ENST00000269305	NM_001126112.2	179	Cat/Gat	5/11	0.606820047490596	3	FACETS	0.982	0.94	1	0.982	0.94	1	CLONAL	3	TRUE	0	0.606820047490596	3		699	372	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972913	55972913	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	141	770	0	ENST00000263923.4:c.1477G>T	p.Gly493Ter	p.G493*	ENST00000263923	NM_002253.2	493	Gga/Tga	11/30	NA	2	FACETS	0.956	0.877	1			1	INDETERMINATE	1	TRUE	NA	0.606820047490596	2		770	486	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602328	10602328	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	168	836	0	ENST00000171111.5:c.1250G>T	p.Gly417Val	p.G417V	ENST00000171111	NM_203500.1	417	gGg/gTg	3/6	0.514744701504234	2	FACETS	0.899	0.843	0.954	0.899	0.843	0.954	CLONAL	2	TRUE	0	0.606820047490596	2		836	308	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898765	134898765	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	145	478	0	ENST00000398015.3:c.1823G>T	p.Arg608Leu	p.R608L	ENST00000398015	NM_004441.4	608	cGg/cTg	10/16	NA	2	FACETS	0.791	0.735	0.848			1	INDETERMINATE	2	TRUE	NA	0.606820047490596	2		478	302	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944290	206944290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	65	625	0	ENST00000423557.1:c.340G>A	p.Glu114Lys	p.E114K	ENST00000423557	NM_000572.2	114	Gag/Aag	3/5	0.557209701464024	4	FACETS	0.88	0.767	1	0.293	0.255	0.334	CLONAL	1	TRUE	1	0.606820047490596	4		625	391	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485897	8485897	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	107	515	0	ENST00000356435.5:c.2920C>A	p.Pro974Thr	p.P974T	ENST00000356435		974	Cca/Aca	17/35	0.506095681413681	2	FACETS	0.816	0.75	0.883	0.816	0.75	0.883	CLONAL	2	TRUE	0	0.606820047490596	2		515	216	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237701	133237701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	73	881	0	ENST00000320574.5:c.2914G>A	p.Glu972Lys	p.E972K	ENST00000320574	NM_006231.2	972	Gag/Aag	25/49	NA	2	FACETS	0.901	0.797	1			1	INDETERMINATE	1	TRUE	NA	0.606820047490596	2		881	267	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106795	27106795	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	145	641	0	ENST00000324856.7:c.6406C>G	p.Leu2136Val	p.L2136V	ENST00000324856	NM_006015.4	2136	Ctg/Gtg	20/20	0.513399650249314	2	FACETS	0.821	0.764	0.878	0.821	0.764	0.878	CLONAL	2	TRUE	0	0.606820047490596	2		641	291	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107111	27107111	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	154	542	0	ENST00000324856.7:c.6722T>G	p.Leu2241Trp	p.L2241W	ENST00000324856	NM_006015.4	2241	tTg/tGg	20/20	0.513399650249314	2	FACETS	0.906	0.848	0.964	0.906	0.848	0.964	CLONAL	2	TRUE	0	0.606820047490596	2		542	280	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206943219	206943219	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	33	480	1	ENST00000423557.1:c.399A>T	p.Glu133Asp	p.E133D	ENST00000423557	NM_000572.2	133	gaA/gaT	4/5	0.557209701464024	4	FACETS	0.541	0.442	0.653	0.18	0.147	0.218	SUBCLONAL	1	TRUE	1	0.606820047490596	4		481	323	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606876	43606876	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	164	936	0	ENST00000355710.3:c.1485G>T	p.Gln495His	p.Q495H	ENST00000355710	NM_020975.4	495	caG/caT	7/20	0.483776325691533	2	FACETS	0.855	0.8	0.91	0.855	0.8	0.91	CLONAL	2	TRUE	0	0.606820047490596	2		936	316	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405407	70405407	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	119	823	0	ENST00000373644.4:c.2921C>G	p.Thr974Ser	p.T974S	ENST00000373644	NM_030625.2	974	aCt/aGt	4/12	0.499762939428781	3	FACETS	1	0.94	1	0.349	0.317	0.383	CLONAL	1	TRUE	0	0.606820047490596	3		823	488	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742818	17742818	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	138	805	0	ENST00000250003.3:c.726G>C	p.Lys242Asn	p.K242N	ENST00000250003	NM_002478.4	242	aaG/aaC	3/3	0.483776325691533	2	FACETS	0.836	0.777	0.895	0.836	0.777	0.895	CLONAL	2	TRUE	0	0.606820047490596	2		805	272	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138797	64138797	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	50	667	2	ENST00000334205.4:c.2164G>T	p.Val722Leu	p.V722L	ENST00000334205	NM_003942.2	722	Gtg/Ttg	17/17	0.350576601221952	3	FACETS	0.693	0.591	0.803			1	INDETERMINATE	1	TRUE	NA	0.606820047490596	3		669	310	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245732	46245732	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs534804460	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	74	463	0	ENST00000334344.6:c.3826A>G	p.Thr1276Ala	p.T1276A	ENST00000334344	NM_152641.2	1276	Aca/Gca	15/21	0.252209112548049	3	FACETS	0.859	0.757	0.968	0.43	0.378	0.484	INDETERMINATE	1	TRUE	1	0.606820047490596	3		463	370	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298726	46298726	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	122	456	0	ENST00000334344.6:c.5373G>T	p.Lys1791Asn	p.K1791N	ENST00000334344	NM_152641.2	1791	aaG/aaT	21/21	0.252209112548049	3	FACETS	0.794	0.727	0.863	0.794	0.727	0.863	INDETERMINATE	2	TRUE	1	0.606820047490596	3		456	330	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448479	49448479	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	120	651	0	ENST00000301067.7:c.232G>T	p.Gly78Trp	p.G78W	ENST00000301067	NM_003482.3	78	Ggg/Tgg	3/54	0.252209112548049	3	FACETS	0.811	0.742	0.88	0.811	0.742	0.88	INDETERMINATE	2	TRUE	1	0.606820047490596	3		651	318	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858585	57858585	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	104	809	0	ENST00000228682.2:c.323C>A	p.Ala108Asp	p.A108D	ENST00000228682	NM_005269.2	108	gCt/gAt	4/12	0.252209112548049	3	FACETS	1	0.984	1	0.75	0.68	0.821	INDETERMINATE	1	TRUE	1	0.606820047490596	3		809	298	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28880860	28880860	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	118	654	0	ENST00000282397.4:c.3770G>T	p.Arg1257Leu	p.R1257L	ENST00000282397	NM_002019.4	1257	cGc/cTc	29/30	0.606820047490596	4	FACETS	1	0.971	1	0.591	0.535	0.649	CLONAL	1	TRUE	2	0.606820047490596	4		654	529	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893605	28893605	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	221	525	0	ENST00000282397.4:c.3241G>C	p.Asp1081His	p.D1081H	ENST00000282397	NM_002019.4	1081	Gac/Cac	24/30	0.606820047490596	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	2	0.606820047490596	4		525	553	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914173	32914173	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	219	619	0	ENST00000380152.3:c.5681A>T	p.Tyr1894Phe	p.Y1894F	ENST00000380152		1894	tAc/tTc	11/27	0.606820047490596	4	FACETS	0.792	0.74	0.846	0.792	0.74	0.846	SUBCLONAL	2	TRUE	2	0.606820047490596	4		619	732	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473727	67473727	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	137	688	0	ENST00000327367.4:c.807C>A	p.Phe269Leu	p.F269L	ENST00000327367	NM_005902.3	269	ttC/ttA	6/9	0.506095681413681	2	FACETS	0.941	0.878	1	0.941	0.878	1	CLONAL	2	TRUE	0	0.606820047490596	2		688	240	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576184	88576184	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	114	616	0	ENST00000360948.2:c.1489G>C	p.Gly497Arg	p.G497R	ENST00000360948	NM_001012338.2	497	Ggg/Cgg	13/19	0.506095681413681	2	FACETS	0.767	0.705	0.829	0.767	0.705	0.829	SUBCLONAL	2	TRUE	0	0.606820047490596	2		616	245	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3824629	3824629	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	123	568	1	ENST00000262367.5:c.2224C>A	p.Arg742Ser	p.R742S	ENST00000262367	NM_004380.2	742	Cgt/Agt	12/31	0.582855094656253	3	FACETS	0.823	0.755	0.893	0.823	0.755	0.893	CLONAL	2	TRUE	1	0.606820047490596	3		569	321	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858304	9858304	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	50	495	1	ENST00000330684.3:c.3097C>T	p.Gln1033Ter	p.Q1033*	ENST00000330684	NM_001134407.1	1033	Cag/Tag	13/13	0.582855094656253	3	FACETS	0.829	0.71	0.958	0.415	0.355	0.479	CLONAL	1	TRUE	1	0.606820047490596	3		496	259	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858950	89858950	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	102	527	0	ENST00000389301.3:c.1012G>T	p.Asp338Tyr	p.D338Y	ENST00000389301	NM_000135.2	338	Gat/Tat	12/43	0.506095681413681	2	FACETS	0.793	0.726	0.86	0.793	0.726	0.86	SUBCLONAL	2	TRUE	0	0.606820047490596	2		527	212	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552222	29552222	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	81	624	1	ENST00000356175.3:c.1955G>C	p.Arg652Pro	p.R652P	ENST00000356175	NM_000267.3	652	cGt/cCt	17/57	0.496191622520749	3	FACETS	0.832	0.737	0.934	0.416	0.368	0.467	CLONAL	1	TRUE	1	0.606820047490596	3		625	418	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097194	11097194	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	110	809	0	ENST00000358026.2:c.685G>T	p.Gly229Ter	p.G229*	ENST00000358026	NM_001128849.1	229	Gga/Tga	4/36	0.514744701504234	2	FACETS	0.855	0.788	0.922	0.855	0.788	0.922	CLONAL	2	TRUE	0	0.606820047490596	2		809	212	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937660	17937660	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	136	661	0	ENST00000458235.1:c.3267C>G	p.Ser1089Arg	p.S1089R	ENST00000458235	NM_000215.3	1089	agC/agG	24/24	0.514744701504234	2	FACETS	0.962	0.898	1	0.962	0.898	1	CLONAL	2	TRUE	0	0.606820047490596	2		661	233	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955161	17955161	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	168	812	0	ENST00000458235.1:c.66G>T	p.Glu22Asp	p.E22D	ENST00000458235	NM_000215.3	22	gaG/gaT	2/24	0.514744701504234	2	FACETS	0.935	0.879	0.991	0.935	0.879	0.991	CLONAL	2	TRUE	0	0.606820047490596	2		812	296	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794640	42794640	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	215	731	1	ENST00000575354.2:c.1720C>T	p.Pro574Ser	p.P574S	ENST00000575354	NM_015125.3	574	Cca/Tca	10/20	0.499762939428781	3	FACETS	0.965	0.92	1	0.965	0.92	1	CLONAL	3	TRUE	0	0.606820047490596	3		732	319	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46603793	46603793	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1396288218	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	105	771	0	ENST00000263734.3:c.1150G>C	p.Glu384Gln	p.E384Q	ENST00000263734	NM_001430.4	384	Gag/Cag	9/16	0.606820047490596	3	FACETS	1	0.911	1	0.506	0.456	0.558	CLONAL	1	TRUE	1	0.606820047490596	3		771	446	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483901	212483901	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	101	604	0	ENST00000342788.4:c.2301+1G>C		p.X767_splice	ENST00000342788	NM_005235.2	767			0.496191622520749	3	FACETS	1	0.936	1	0.527	0.474	0.582	CLONAL	1	TRUE	1	0.606820047490596	3		604	412	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525035	9525035	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	100	493	0	ENST00000353224.5:c.1850G>T	p.Arg617Met	p.R617M	ENST00000353224	NM_177990.2	617	aGg/aTg	8/10	0.279413105371005	3	FACETS	0.804	0.73	0.881	0.536	0.487	0.587	INDETERMINATE	2	TRUE	0	0.606820047490596	3		493	267	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024521	31024521	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	49	656	1	ENST00000375687.4:c.4008del	p.Lys1337SerfsTer113	p.K1337Sfs*113	ENST00000375687	NM_015338.5	1336	Ggg/gg	13/13	0.279413105371005	3	FACETS	0.652	0.555	0.757	0.217	0.185	0.253	INDETERMINATE	1	TRUE	0	0.606820047490596	3		657	323	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306620	41306620	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	135	727	1	ENST00000373198.4:c.1039C>A	p.Leu347Met	p.L347M	ENST00000373198	NM_133170.3	347	Ctg/Atg	7/32	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.606820047490596	2		728	322	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419852	41419852	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	57	530	0	ENST00000373198.4:c.469T>C	p.Trp157Arg	p.W157R	ENST00000373198	NM_133170.3	157	Tgg/Cgg	3/32	NA	2	FACETS	0.676	0.585	0.773			1	INDETERMINATE	1	TRUE	NA	0.606820047490596	2		530	278	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46251025	46251025	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	182	591	0	ENST00000371998.3:c.34G>T	p.Ala12Ser	p.A12S	ENST00000371998		12	Gcc/Tcc	3/23	0.582855094656253	3	FACETS	0.863	0.805	0.922	0.863	0.805	0.922	CLONAL	2	TRUE	1	0.606820047490596	3		591	453	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713433	30713433	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	86	602	0	ENST00000295754.5:c.758G>T	p.Gly253Val	p.G253V	ENST00000295754	NM_003242.5	253	gGt/gTt	4/7	1	2	FACETS	0.9	0.804	1	0.9	0.804	1	CLONAL	1	TRUE	1	0.606820047490596	2		602	315	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259060	89259060	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	43	322	0	ENST00000336596.2:c.204C>A	p.Tyr68Ter	p.Y68*	ENST00000336596	NM_005233.5	68	taC/taA	3/17	1	2	FACETS	0.796	0.676	0.925	0.796	0.676	0.925	CLONAL	1	TRUE	1	0.606820047490596	2		322	178	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390219	89390219	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	53	359	0	ENST00000336596.2:c.970del	p.Arg324AspfsTer13	p.R324Dfs*13	ENST00000336596	NM_005233.5	323	aCc/ac	4/17	1	2	FACETS	0.812	0.702	0.93	0.812	0.702	0.93	CLONAL	1	TRUE	1	0.606820047490596	2		359	215	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664859	138665217	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCCGCGGCTGCAGCCGCAGCTGCTGCAGCCGCTGCGGCTGCCGCCATCTGGCAGGAGGCATAGGGCATGGGTGAGGGAGGCTGCGGTAGCGGCCACGAGTTGTTGAGGAAGCCAGACTGCAGGTACTTGGGGGGCGCCAGGTAGCCGTAGCCGTCGGCCCCGGCGCCCGCCACGCCGCACCCGCCTGCGGCGCCTCCGGCCCCGAAGAGCCCCTTGCCGGGCTGGAAGTGCGCGGGCGGCGGCCGGAAGGGCCTCTTCATGCGGCGGCGGCGCCGGTAGTTGCCCTTCTCGAACATGTCTTCGCAGGCCGGGTCCAGCGTCCAGTAGTTGCCCTTGCGCTCGCCGCCGCCCTCGCGC	GGCCCGCGGCTGCAGCCGCAGCTGCTGCAGCCGCTGCGGCTGCCGCCATCTGGCAGGAGGCATAGGGCATGGGTGAGGGAGGCTGCGGTAGCGGCCACGAGTTGTTGAGGAAGCCAGACTGCAGGTACTTGGGGGGCGCCAGGTAGCCGTAGCCGTCGGCCCCGGCGCCCGCCACGCCGCACCCGCCTGCGGCGCCTCCGGCCCCGAAGAGCCCCTTGCCGGGCTGGAAGTGCGCGGGCGGCGGCCGGAAGGGCCTCTTCATGCGGCGGCGGCGCCGGTAGTTGCCCTTCTCGAACATGTCTTCGCAGGCCGGGTCCAGCGTCCAGTAGTTGCCCTTGCGCTCGCCGCCGCCCTCGCGC	-	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	54	124	0	ENST00000330315.3:c.348_706del	p.Glu118Ter	p.E118*	ENST00000330315	NM_023067.3	116	ccGCGCGAGGGCGGCGGCGAGCGCAAGGGCAACTACTGGACGCTGGACCCGGCCTGCGAAGACATGTTCGAGAAGGGCAACTACCGGCGCCGCCGCCGCATGAAGAGGCCCTTCCGGCCGCCGCCCGCGCACTTCCAGCCCGGCAAGGGGCTCTTCGGGGCCGGAGGCGCCGCAGGCGGGTGCGGCGTGGCGGGCGCCGGGGCCGACGGCTACGGCTACCTGGCGCCCCCCAAGTACCTGCAGTCTGGCTTCCTCAACAACTCGTGGCCGCTACCGCAGCCTCCCTCACCCATGCCCTATGCCTCCTGCCAGATGGCGGCAGCCGCAGCGGCTGCAGCAGCTGCGGCTGCAGCCGCGGGCCcc/cccc	1/1	0.306268568978425	4	FACETS	0.851	0.753	0.95			1	INDETERMINATE	3	TRUE	NA	0.606820047490596	4		124	112	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665419	138665419	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	151	714	0	ENST00000330315.3:c.146C>A	p.Pro49Gln	p.P49Q	ENST00000330315	NM_023067.3	49	cCg/cAg	1/1	0.306268568978425	4	FACETS	1	0.983	1			1	INDETERMINATE	2	TRUE	NA	0.606820047490596	4		714	335	SUCCESS
ATR	545	MSKCC	GRCh37	3	142286956	142286956	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	110	709	0	ENST00000350721.4:c.100A>T	p.Arg34Ter	p.R34*	ENST00000350721	NM_001184.3	34	Aga/Tga	2/47	0.524898095998332	4	FACETS	0.858	0.772	0.949	0.286	0.257	0.317	CLONAL	1	TRUE	1	0.606820047490596	4		709	679	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612248	189612248	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	46	494	0	ENST00000264731.3:c.2000C>T	p.Ala667Val	p.A667V	ENST00000264731	NM_003722.4	667	gCt/gTt	14/14	0.524898095998332	4	FACETS	0.778	0.659	0.909	0.259	0.219	0.303	CLONAL	1	TRUE	1	0.606820047490596	4		494	313	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157191	106157191	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	99	524	0	ENST00000380013.4:c.2092G>T	p.Val698Leu	p.V698L	ENST00000380013	NM_001127208.2	698	Gtg/Ttg	3/11	1	2	FACETS	0.859	0.773	0.948	0.859	0.773	0.948	CLONAL	1	TRUE	1	0.606820047490596	2		524	380	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114307	143114307	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	79	501	0	ENST00000262992.4:c.1114C>A	p.His372Asn	p.H372N	ENST00000262992	NM_001101669.1	372	Cat/Aat	13/24	1	2	FACETS	0.851	0.756	0.951	0.851	0.756	0.951	CLONAL	1	TRUE	1	0.606820047490596	2		501	306	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80040323	80040323	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	80	463	0	ENST00000265081.6:c.1654-2A>T		p.X552_splice	ENST00000265081	NM_002439.4	552			1	2	FACETS	0.718	0.637	0.805	0.718	0.637	0.805	SUBCLONAL	1	TRUE	1	0.606820047490596	2		463	367	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86668002	86668002	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	80	370	0	ENST00000274376.6:c.1766G>T	p.Arg589Leu	p.R589L	ENST00000274376	NM_002890.2	589	cGc/cTc	13/25	0.30121769224734	1	FACETS	0.778	0.696	0.863	0.778	0.696	0.863	INDETERMINATE	1	TRUE	0	0.606820047490596	1		370	236	SUCCESS
APC	324	MSKCC	GRCh37	5	112178282	112178282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	76	486	1	ENST00000257430.4:c.6991C>T	p.Pro2331Ser	p.P2331S	ENST00000257430	NM_000038.5	2331	Cct/Tct	16/16	NA	2	FACETS	0.832	0.737	0.932			1	INDETERMINATE	1	TRUE	NA	0.606820047490596	2		487	301	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696690	176696691	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	59	432	0	ENST00000439151.2:c.5397dup	p.Gly1800TrpfsTer3	p.G1800Wfs*3	ENST00000439151	NM_022455.4	1797	-/T	16/23	1	2	FACETS	0.757	0.658	0.862	0.757	0.658	0.862	SUBCLONAL	1	TRUE	1	0.606820047490596	2		432	257	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057649	180057649	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	73	883	0	ENST00000261937.6:c.306T>A	p.His102Gln	p.H102Q	ENST00000261937	NM_182925.4	102	caT/caA	3/30	1	2	FACETS	0.905	0.801	1	0.905	0.801	1	CLONAL	1	TRUE	1	0.606820047490596	2		883	266	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109415059	109415059	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	118	870	0	ENST00000436639.2:c.218C>G	p.Ser73Cys	p.S73C	ENST00000436639	NM_014454.2	73	tCt/tGt	1/10	1	2	FACETS	0.864	0.785	0.947	0.864	0.785	0.947	CLONAL	1	TRUE	1	0.606820047490596	2		870	450	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001594	150001594	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	78	434	0	ENST00000253339.5:c.2011-1G>T		p.X671_splice	ENST00000253339		671			NA	2	FACETS	0.843	0.748	0.943			1	INDETERMINATE	1	TRUE	NA	0.606820047490596	2		434	305	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382204	152382204	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	75	625	0	ENST00000206249.3:c.1314G>A	p.Met438Ile	p.M438I	ENST00000206249	NM_000125.3	438	atG/atA	6/8	NA	2	FACETS	0.725	0.64	0.815			1	INDETERMINATE	1	TRUE	NA	0.606820047490596	2		625	341	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350112	81350112	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	70	565	0	ENST00000222390.5:c.1220G>T	p.Arg407Ile	p.R407I	ENST00000222390	NM_000601.4	407	aGa/aTa	10/18	0.582855094656253	3	FACETS	0.688	0.602	0.78	0.344	0.301	0.39	SUBCLONAL	1	TRUE	1	0.606820047490596	3		565	437	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350126	81350129	+	frameshift_variant	Frame_Shift_Del	DEL	GTTG	GTTG	TTT	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	141	556	2	ENST00000222390.5:c.1203_1206delinsAAA	p.Leu403TyrfsTer8	p.L403Yfs*8	ENST00000222390	NM_000601.4	401	ggCAAC/ggAAA	10/18	0.582855094656253	3	FACETS	1	0.987	1	0.719	0.662	0.779	CLONAL	1	TRUE	1	0.606820047490596	3		558	421	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146180	38146180	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	87	784	0	ENST00000317025.8:c.3326G>T	p.Gly1109Val	p.G1109V	ENST00000317025	NM_023034.1	1109	gGc/gTc	19/24	0.606820047490596	3	FACETS	0.637	0.564	0.714	0.318	0.282	0.357	SUBCLONAL	1	TRUE	1	0.606820047490596	3		784	587	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028037	69028037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	89	704	1	ENST00000288368.4:c.3196G>A	p.Glu1066Lys	p.E1066K	ENST00000288368	NM_024870.2	1066	Gag/Aag	26/40	0.190162077393986	1	FACETS	0.505	0.45	0.562	0.505	0.45	0.562	INDETERMINATE	1	TRUE	0	0.606820047490596	1		705	405	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928823	44928823	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	33	346	0	ENST00000377967.4:c.1924-1G>A		p.X642_splice	ENST00000377967	NM_021140.2	642			1	2	FACETS	0.566	0.466	0.678	0.566	0.466	0.678	SUBCLONAL	1	TRUE	1	0.606820047490596	2		346	192	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422725	47422725	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	40	555	0	ENST00000377045.4:c.197A>T	p.Lys66Met	p.K66M	ENST00000377045	NM_001654.4	66	aAg/aTg	3/16	NA	2	FACETS	0.649	0.545	0.763			1	INDETERMINATE	1	TRUE	NA	0.606820047490596	2		555	203	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371735	55371735	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	51	637	0	ENST00000297316.4:c.425G>A	p.Arg142His	p.R142H	ENST00000297316	NM_022454.3	142	cGc/cAc	2/2	0.276535174422819	3	FACETS	0.758	0.644	0.883	0.379	0.322	0.442	SUBCLONAL	1	TRUE	1	0.276535174422819	3		637	554	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0023704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	203	571	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.407921280774557	2		571	824	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0023704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	127	214	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.407921280774557	2		214	466	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971192	21971192	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	25	518	0	ENST00000304494.5:c.166A>G	p.Ser56Gly	p.S56G	ENST00000304494	NM_000077.4	56	Agc/Ggc	2/3	0.407921280774557	1	FACETS	0.249	0.196	0.31	0.249	0.196	0.31	SUBCLONAL	1	TRUE	0	0.407921280774557	1		518	392	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	207	777	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.907	0.843	0.972	0.907	0.843	0.972	CLONAL	1	TRUE	1	0.569320133207865	2		777	802	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252949	36252951	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	novel	NA	P-0023705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	183	512	0	ENST00000300305.3:c.411_413del	p.Asp137del	p.D137del	ENST00000300305		137	gaTGAa/gaa	4/8	1	2	FACETS	0.968	0.897	1	0.968	0.897	1	CLONAL	1	TRUE	1	0.569320133207865	2		512	664	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0023706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	291	830	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.255593245088299	3	FACETS	0.985	0.93	1	0.985	0.93	1	CLONAL	3	TRUE	0	0.255593245088299	3		832	869	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743319	162743319	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	181	588	4	ENST00000367921.3:c.1789G>T	p.Val597Phe	p.V597F	ENST00000367921	NM_006182.2	597	Gtc/Ttc	14/18	0.255593245088299	6	FACETS	0.929	0.859	1	0.929	0.859	1	CLONAL	3	TRUE	3	0.255593245088299	6		592	768	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852007	63852007	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	63	610	1	ENST00000279873.7:c.2785A>G	p.Thr929Ala	p.T929A	ENST00000279873	NM_032199.2	929	Aca/Gca	10/10	0.245479179612007	3	FACETS	0.939	0.812	1	0.47	0.406	0.539	CLONAL	1	TRUE	1	0.255593245088299	3		611	592	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881469	48881469	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0023706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	146	501	3	ENST00000267163.4:c.191T>A	p.Leu64Ter	p.L64*	ENST00000267163	NM_000321.2	64	tTa/tAa	2/27	0.255593245088299	3	FACETS	0.862	0.792	0.935	0.862	0.792	0.935	CLONAL	3	TRUE	0	0.255593245088299	3		504	498	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244017	41244018	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0023706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	286	850	9	ENST00000357654.3:c.3530_3531del	p.Phe1177Ter	p.F1177*	ENST00000357654	NM_007294.3	1177	tTT/t	10/23	0.255593245088299	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.255593245088299	3		859	759	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0023708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	513	752	2	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.906080782510012	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.906080782510012	1		754	583	SUCCESS
ATM	472	MSKCC	GRCh37	11	108225597	108225597	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	294	552	0	ENST00000278616.4:c.8846T>C	p.Val2949Ala	p.V2949A	ENST00000278616	NM_000051.3	2949	gTa/gCa	61/63	0.906080782510012	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.906080782510012	1		552	343	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236072	108236072	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	369	585	0	ENST00000278616.4:c.9008A>C	p.Asn3003Thr	p.N3003T	ENST00000278616	NM_000051.3	3003	aAc/aCc	63/63	0.906080782510012	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.906080782510012	1		585	423	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231429	46231429	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0023708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	246	550	0	ENST00000334344.6:c.1269C>G	p.Tyr423Ter	p.Y423*	ENST00000334344	NM_152641.2	423	taC/taG	10/21	1	2	FACETS	0.905	0.853	0.958	0.905	0.853	0.958	CLONAL	1	TRUE	1	0.906080782510012	2		550	600	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562220	21562220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	543	1021	1	ENST00000382592.4:c.1699G>A	p.Gly567Arg	p.G567R	ENST00000382592	NM_014572.2	567	Gga/Aga	4/8	0.906080782510012	1	FACETS	0.963	0.94	0.985	0.963	0.94	0.985	CLONAL	1	TRUE	0	0.906080782510012	1		1022	681	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609930	81609930	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	19	412	0	ENST00000298171.2:c.1528T>C	p.Tyr510His	p.Y510H	ENST00000298171	NM_000369.2	510	Tat/Cat	10/10	0.906080782510012	1	FACETS	0.077	0.058	0.099	0.077	0.058	0.099	SUBCLONAL	1	TRUE	0	0.906080782510012	1		412	298	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828426	72828426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	355	668	0	ENST00000268489.5:c.8155C>T	p.Leu2719Phe	p.L2719F	ENST00000268489	NM_006885.3	2719	Ctc/Ttc	9/10	1	2	FACETS	0.987	0.941	1	0.987	0.941	1	CLONAL	1	TRUE	1	0.906080782510012	2		668	794	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880988	37880988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772054394	NA	P-0023708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	100	873	0	ENST00000269571.5:c.2317G>A	p.Val773Met	p.V773M	ENST00000269571		773	Gtg/Atg	20/27	0.906080782510012	1	FACETS	0.201	0.179	0.224	0.201	0.179	0.224	SUBCLONAL	1	TRUE	0	0.906080782510012	1		873	601	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435386	56435386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372159496	NA	P-0023708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	494	872	0	ENST00000407977.2:c.1751G>A	p.Arg584Gln	p.R584Q	ENST00000407977		584	cGg/cAg	9/10	0.906080782510012	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.906080782510012	1		872	587	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732335	74732335	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149695427	NA	P-0023708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	254	466	0	ENST00000359995.5:c.574C>T	p.Pro192Ser	p.P192S	ENST00000359995	NM_001195427.1	192	Cct/Tct	2/3	0.906080782510012	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.906080782510012	1		466	302	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132428	11132428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	71	856	0	ENST00000358026.2:c.2644G>A	p.Glu882Lys	p.E882K	ENST00000358026	NM_001128849.1	882	Gaa/Aaa	19/36	0.906080782510012	1	FACETS	0.156	0.136	0.178	0.156	0.136	0.178	SUBCLONAL	1	TRUE	0	0.906080782510012	1		856	548	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919914	50919914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs550922227	NA	P-0023708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	30	817	1	ENST00000440232.2:c.3001G>A	p.Gly1001Ser	p.G1001S	ENST00000440232	NM_002691.3	1001	Ggc/Agc	24/27	0.906080782510012	1	FACETS	0.07	0.055	0.085	0.07	0.055	0.085	SUBCLONAL	1	TRUE	0	0.906080782510012	1		818	521	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026678	48026694	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGTACACAGACTTAC	AGGGTACACAGACTTAC	-	novel	NA	P-0023708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	310	581	0	ENST00000234420.5:c.1558_1574del	p.Gly520CysfsTer5	p.G520Cfs*5	ENST00000234420	NM_000179.2	519	aAGGGTACACAGACTTAC/a	4/10	0.906080782510012	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.906080782510012	1		581	373	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99180102	99180102	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0023708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	312	535	0	ENST00000074304.5:c.2043+2T>C		p.X681_splice	ENST00000074304	NM_001134224.1	681			0.906080782510012	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.906080782510012	1		535	376	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623218	52623218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1402934247	NA	P-0023708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	291	545	0	ENST00000394830.3:c.2833C>T	p.Arg945Cys	p.R945C	ENST00000394830	NM_018313.4	945	Cgc/Tgc	19/30	0.906080782510012	1	FACETS	0.845	0.812	0.876	0.845	0.812	0.876	CLONAL	1	TRUE	0	0.906080782510012	1		545	416	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950154	38950154	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	416	647	0	ENST00000357387.3:c.3796A>T	p.Thr1266Ser	p.T1266S	ENST00000357387	NM_152756.3	1266	Aca/Tca	31/38	1	2	FACETS	0.987	0.945	1	0.987	0.945	1	CLONAL	1	TRUE	1	0.906080782510012	2		647	930	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753951	57753951	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751097714	NA	P-0023708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	73	573	1	ENST00000274289.3:c.673G>A	p.Gly225Ser	p.G225S	ENST00000274289	NM_006622.3	225	Ggt/Agt	5/14	1	2	FACETS	0.218	0.19	0.248	0.218	0.19	0.248	SUBCLONAL	1	TRUE	1	0.906080782510012	2		574	739	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267600319	NA	P-0023708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	275	414	0	ENST00000257430.4:c.4199C>T	p.Ser1400Leu	p.S1400L	ENST00000257430	NM_000038.5	1400	tCg/tTg	16/16	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.906080782510012	2		414	605	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911581	39911581	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	70	746	0	ENST00000378444.4:c.5049T>A	p.Asn1683Lys	p.N1683K	ENST00000378444	NM_001123385.1	1683	aaT/aaA	15/15	0.906080782510012	1	FACETS	0.156	0.135	0.177	0.156	0.135	0.177	SUBCLONAL	1	TRUE	0	0.906080782510012	1		746	543	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650778	48650778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104894809	NA	P-0023708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	485	905	1	ENST00000376670.3:c.647G>A	p.Arg216Gln	p.R216Q	ENST00000376670	NM_002049.3	216	cGg/cAg	4/6	0.906080782510012	1	FACETS	0.952	0.928	0.975	0.952	0.928	0.975	CLONAL	1	TRUE	0	0.906080782510012	1		906	615	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50816263	50816263	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	85	375	0	ENST00000398568.2:c.1703T>C	p.Val568Ala	p.V568A	ENST00000398568	NM_001042412.1	568	gTa/gCa	10/18	0.533284984770466	1	FACETS	0.97	0.872	1	0.97	0.872	1	CLONAL	1	TRUE	0	0.533284984770466	1		375	241	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0023711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	149	612	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.481285727569389	1	FACETS	0.944	0.869	1	0.944	0.869	1	CLONAL	1	TRUE	0	0.481285727569389	1		612	498	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397800	49397800	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	94	838	0	ENST00000418115.1:c.424G>A	p.Glu142Lys	p.E142K	ENST00000418115	NM_001664.2	142	Gaa/Aaa	5/5	1	2	FACETS	0.451	0.4	0.504	0.451	0.4	0.504	SUBCLONAL	1	TRUE	1	0.481285727569389	2		838	867	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835596	68835596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587783047	NA	P-0023711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	167	755	0	ENST00000261769.5:c.187C>T	p.Arg63Ter	p.R63*	ENST00000261769	NM_004360.3	63	Cga/Tga	3/16	0.481285727569389	1	FACETS	0.978	0.904	1	0.978	0.904	1	CLONAL	1	TRUE	0	0.481285727569389	1		755	539	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112312	115112313	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0023711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	41	220	0	ENST00000257566.3:c.1426_1427dup	p.Glu477ArgfsTer156	p.E477Rfs*156	ENST00000257566	NM_016569.3	476	aag/aaAAg	7/8	1	2	FACETS	0.86	0.725	1	0.86	0.725	1	CLONAL	1	TRUE	1	0.481285727569389	2		220	198	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354353	354353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142097791	NA	P-0023712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	133	775	3	ENST00000262320.3:c.1205C>T	p.Thr402Met	p.T402M	ENST00000262320	NM_003502.3	402	aCg/aTg	5/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.592977169909124	2		778	419	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188257	10188257	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	167	1011	0	ENST00000256474.2:c.400del	p.Glu134AsnfsTer25	p.E134Nfs*25	ENST00000256474	NM_000551.3	134	Gaa/aa	2/3	0.592977169909124	1	FACETS	0.922	0.856	0.988	0.922	0.856	0.988	CLONAL	1	TRUE	0	0.592977169909124	1		1011	430	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436410	52436410	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	83	593	0	ENST00000460680.1:c.2084del	p.Asn695ThrfsTer41	p.N695Tfs*41	ENST00000460680	NM_004656.3	695	aAc/ac	17/17	0.592977169909124	1	FACETS	0.895	0.805	0.988	0.895	0.805	0.988	CLONAL	1	TRUE	0	0.592977169909124	1		593	220	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023715-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	72	482	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.708	0.619	0.802	0.708	0.619	0.802	SUBCLONAL	1	TRUE	1	0.395121352967548	2		482	515	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196994	106196994	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023715-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	37	355	0	ENST00000380013.4:c.5327C>T	p.Ser1776Phe	p.S1776F	ENST00000380013	NM_001127208.2	1776	tCt/tTt	11/11	1	2	FACETS	0.517	0.427	0.618	0.517	0.427	0.618	SUBCLONAL	1	TRUE	1	0.395121352967548	2		355	362	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991961	72991961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1262542686	NA	P-0023715-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	31	617	0	ENST00000268489.5:c.2084C>T	p.Pro695Leu	p.P695L	ENST00000268489	NM_006885.3	695	cCg/cTg	2/10	1	2	FACETS	0.254	0.205	0.311	0.254	0.205	0.311	SUBCLONAL	1	TRUE	1	0.395121352967548	2		617	617	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855029	76855029	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1557085898	NA	P-0023715-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	10	293	0	ENST00000373344.5:c.5807A>G	p.Lys1936Arg	p.K1936R	ENST00000373344	NM_000489.3	1936	aAg/aGg	25/35	0.131730368864095	2	FACETS	0.104	0.07	0.147			1	INDETERMINATE	1	TRUE	NA	0.395121352967548	2		293	487	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946237	81946237	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023715-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	74	671	0	ENST00000359376.3:c.1970A>T	p.Glu657Val	p.E657V	ENST00000359376	NM_002661.3	657	gAg/gTg	19/33	1	2	FACETS	0.525	0.459	0.597	0.525	0.459	0.597	SUBCLONAL	1	TRUE	1	0.395121352967548	2		671	713	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213443	39213443	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023715-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	184	538	0	ENST00000402219.2:c.3524A>G	p.His1175Arg	p.H1175R	ENST00000402219	NM_005633.3	1175	cAt/cGt	23/23	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.395121352967548	2		538	742	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156791	106156791	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023715-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	64	566	0	ENST00000380013.4:c.1692G>A	p.Trp564Ter	p.W564*	ENST00000380013	NM_001127208.2	564	tgG/tgA	3/11	1	2	FACETS	0.466	0.403	0.535	0.466	0.403	0.535	SUBCLONAL	1	TRUE	1	0.395121352967548	2		566	695	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658497	117658497	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023715-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	57	714	0	ENST00000368508.3:c.5086T>A	p.Tyr1696Asn	p.Y1696N	ENST00000368508	NM_002944.2	1696	Tac/Aac	31/43	0.129325968233972	3	FACETS	0.4	0.342	0.464	0.2	0.171	0.232	INDETERMINATE	1	TRUE	1	0.395121352967548	3		714	863	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	106	482	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.905782498880453	2		482	182	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420183	49420183	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	246	898	0	ENST00000301067.7:c.15566G>C	p.Gly5189Ala	p.G5189A	ENST00000301067	NM_003482.3	5189	gGa/gCa	48/54	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.905782498880453	2		898	516	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420515	49420515	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	233	865	1	ENST00000301067.7:c.15234G>T	p.Met5078Ile	p.M5078I	ENST00000301067	NM_003482.3	5078	atG/atT	48/54	1	2	FACETS	0.974	0.918	1	0.974	0.918	1	CLONAL	1	TRUE	1	0.905782498880453	2		866	528	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420619	49420619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	227	877	0	ENST00000301067.7:c.15130G>A	p.Asp5044Asn	p.D5044N	ENST00000301067	NM_003482.3	5044	Gat/Aat	48/54	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.905782498880453	2		877	486	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431661	49431662	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0023716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	195	985	0	ENST00000301067.7:c.9477dup	p.Met3160HisfsTer16	p.M3160Hfs*16	ENST00000301067	NM_003482.3	3159	-/C	34/54	1	2	FACETS	0.97	0.908	1	0.97	0.908	1	CLONAL	1	TRUE	1	0.905782498880453	2		985	444	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988400	41988400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1403178526	NA	P-0023716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	214	734	0	ENST00000219905.7:c.1192G>A	p.Glu398Lys	p.E398K	ENST00000219905	NM_001164273.1	398	Gaa/Aaa	3/24	1	2	FACETS	0.939	0.882	0.997	0.939	0.882	0.997	CLONAL	1	TRUE	1	0.905782498880453	2		734	503	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988910	41988910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1422434612	NA	P-0023716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	199	783	0	ENST00000219905.7:c.1702G>A	p.Asp568Asn	p.D568N	ENST00000219905	NM_001164273.1	568	Gat/Aat	3/24	1	2	FACETS	0.906	0.848	0.965	0.906	0.848	0.965	CLONAL	1	TRUE	1	0.905782498880453	2		783	485	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059120	42059120	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	20	481	0	ENST00000219905.7:c.8840G>T	p.Gly2947Val	p.G2947V	ENST00000219905	NM_001164273.1	2947	gGa/gTa	24/24	1	2	FACETS	0.123	0.094	0.158	0.123	0.094	0.158	SUBCLONAL	1	TRUE	1	0.905782498880453	2		481	359	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059298	42059298	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	22	548	1	ENST00000219905.7:c.9018G>C	p.Gln3006His	p.Q3006H	ENST00000219905	NM_001164273.1	3006	caG/caC	24/24	1	2	FACETS	0.142	0.11	0.18	0.142	0.11	0.18	SUBCLONAL	1	TRUE	1	0.905782498880453	2		549	342	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0023716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	187	629	1	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.905782498880453	2		630	383	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740498	58740498	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs375975790	NA	P-0023716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	243	1019	0	ENST00000305921.3:c.1403C>G	p.Ser468Ter	p.S468*	ENST00000305921	NM_003620.3	468	tCa/tGa	6/6	1	2	FACETS	0.976	0.92	1	0.976	0.92	1	CLONAL	1	TRUE	1	0.905782498880453	2		1019	550	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134277	11134277	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	192	825	0	ENST00000358026.2:c.2943G>C	p.Lys981Asn	p.K981N	ENST00000358026	NM_001128849.1	981	aaG/aaC	20/36	1	2	FACETS	0.998	0.935	1	0.998	0.935	1	CLONAL	1	TRUE	1	0.905782498880453	2		825	425	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366951	15366951	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	276	1270	0	ENST00000263377.2:c.1675G>C	p.Glu559Gln	p.E559Q	ENST00000263377	NM_058243.2	559	Gag/Cag	9/20	1	2	FACETS	0.993	0.94	1	0.993	0.94	1	CLONAL	1	TRUE	1	0.905782498880453	2		1270	614	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260220	19260234	+	inframe_deletion	In_Frame_Del	DEL	TCCGCTTGGTGAACG	TCCGCTTGGTGAACG	-	novel	NA	P-0023716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	228	1008	1	ENST00000162023.5:c.59_73del	p.Thr20_Arg24del	p.T20_R24del	ENST00000162023		20	aCGTTCACCAAGCGGAag/aag	7/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.905782498880453	2		1009	495	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010526	48010526	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167719	NA	P-0023716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	23	493	0	ENST00000234420.5:c.154G>T	p.Glu52Ter	p.E52*	ENST00000234420	NM_000179.2	52	Gag/Tag	1/10	1	2	FACETS	0.206	0.161	0.259	0.206	0.161	0.259	SUBCLONAL	1	TRUE	1	0.905782498880453	2		493	246	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556696	41556696	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	248	803	0	ENST00000263253.7:c.3641C>T	p.Ser1214Phe	p.S1214F	ENST00000263253	NM_001429.3	1214	tCt/tTt	20/31	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.905782498880453	2		803	505	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0023716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	218	641	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	TRUE	1	0.905782498880453	2		641	374	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518251	187518251	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	114	425	0	ENST00000441802.2:c.12443C>G	p.Ser4148Cys	p.S4148C	ENST00000441802	NM_005245.3	4148	tCc/tGc	25/27	1	2	FACETS	0.953	0.874	1	0.953	0.874	1	CLONAL	1	TRUE	1	0.905782498880453	2		425	264	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753342	57753342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	209	779	0	ENST00000274289.3:c.782C>T	p.Ser261Leu	p.S261L	ENST00000274289	NM_006622.3	261	tCa/tTa	6/14	1	2	FACETS	0.923	0.865	0.981	0.923	0.865	0.981	CLONAL	1	TRUE	1	0.905782498880453	2		779	500	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797301	135797301	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	30	460	0	ENST00000298552.3:c.568del	p.Arg190AlafsTer20	p.R190Afs*20	ENST00000298552	NM_001162426.1	190	Cgc/gc	7/23	0.905782498880453	1	FACETS	0.188	0.152	0.227	0.188	0.152	0.227	SUBCLONAL	1	TRUE	0	0.905782498880453	1		460	193	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0023718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	514	628	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.661412843877891	2	FACETS	0.928	0.898	0.958	0.928	0.898	0.958	CLONAL	2	TRUE	0	0.678777014567128	2		628	816	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325894	65325894	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	202	568	0	ENST00000342505.4:c.1228G>C	p.Asp410His	p.D410H	ENST00000342505	NM_002227.2	410	Gat/Cat	9/25	0.678777014567128	1	FACETS	0.898	0.843	0.953	0.898	0.843	0.953	CLONAL	1	TRUE	0	0.678777014567128	1		568	438	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41201203	41201203	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	79	823	0	ENST00000357654.3:c.5341G>C	p.Glu1781Gln	p.E1781Q	ENST00000357654	NM_007294.3	1781	Gaa/Caa	21/23	0.661412843877891	2	FACETS	0.278	0.244	0.315	0.139	0.122	0.158	SUBCLONAL	1	TRUE	0	0.678777014567128	2		823	837	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5065009	5065009	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	79	500	0	ENST00000381652.3:c.1183A>G	p.Asn395Asp	p.N395D	ENST00000381652	NM_004972.3	395	Aat/Gat	9/25	0.623774325196044	5	FACETS	0.632	0.556	0.715	0.126	0.111	0.143	SUBCLONAL	1	TRUE	0	0.678777014567128	5		500	743	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	57	896	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.327413873758519	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		898	595	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303491	91303491	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	42	584	0	ENST00000355112.3:c.1202T>A	p.Leu401His	p.L401H	ENST00000355112	NM_000057.2	401	cTt/cAt	6/22	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		584	552	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266835	+	missense_variant	Missense_Mutation	DNP	TC	TC	CA	novel	NA	P-0023719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	30	658	1	ENST00000335508.6:c.2097_2098delinsTG	p.Gln699_Lys700delinsHisGlu	p.Q699_K700delinsHE	ENST00000335508	NM_012433.2	699	caGAaa/caTGaa	15/25	0.180811516879194	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		659	527	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443403	187443403	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755666072	NA	P-0023719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	30	434	0	ENST00000232014.4:c.1723C>T	p.Arg575Cys	p.R575C	ENST00000232014	NM_001130845.1	575	Cgt/Tgt	8/10	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		434	290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0023720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	228	853	1	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	0.423036397668834	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	0	0.423036397668834	3		854	407	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984819	11984824	+	frameshift_variant	Frame_Shift_Del	DEL	AACCAA	AACCAA	TATG	novel	NA	P-0023720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	75	587	1	ENST00000353533.5:c.365_370delinsTATG	p.Lys122IlefsTer9	p.K122Ifs*9	ENST00000353533	NM_003010.3	122	aAACCAAgt/aTATGgt	3/11	0.423036397668834	1	FACETS	0.768	0.688	0.849	1	0.981	1	SUBCLONAL	2	TRUE	0	0.423036397668834	1		588	182	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	70	896	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.773	0.673	0.883	0.773	0.673	0.883	SUBCLONAL	1	TRUE	1	0.201136702650977	2		898	900	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577119	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	115	910	0	ENST00000269305.4:c.819dup	p.Val274CysfsTer32	p.V274Cfs*32	ENST00000269305	NM_001126112.2	273	-/T	8/11	0.201136702650977	1	FACETS	0.974	0.876	1	0.974	0.876	1	CLONAL	1	TRUE	0	0.201136702650977	1		910	1056	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	155	899	1	ENST00000267101.3:c.273G>T	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atT	3/28	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.201136702650977	2		900	1090	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137348	64137348	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	65	909	0	ENST00000334205.4:c.1780A>C	p.Ser594Arg	p.S594R	ENST00000334205	NM_003942.2	594	Agc/Cgc	14/17	0.123229205960147	1	FACETS	0.602	0.521	0.692	0.602	0.521	0.692	SUBCLONAL	1	TRUE	0	0.201136702650977	1		909	965	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100088	11100095	+	frameshift_variant	Frame_Shift_Del	DEL	AGGCCCTC	AGGCCCTC	-	novel	NA	P-0023721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	103	801	0	ENST00000358026.2:c.1218_1225del	p.Leu407AlafsTer28	p.L407Afs*28	ENST00000358026	NM_001128849.1	405	aAGGCCCTC/a	7/36	0.201136702650977	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.201136702650977	1		801	808	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401176	139401176	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	52	797	3	ENST00000277541.6:c.3893G>T	p.Gly1298Val	p.G1298V	ENST00000277541	NM_017617.3	1298	gGt/gTt	23/34	0.201136702650977	1	FACETS	0.516	0.438	0.603	0.516	0.438	0.603	SUBCLONAL	1	TRUE	0	0.201136702650977	1		800	901	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867546	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGC	GGCGGCGGC	-	rs11466445	NA	P-0023722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	17	72	3	ENST00000374994.4:c.70_78del	p.Ala24_Ala26del	p.A24_A26del	ENST00000374994	NM_004612.2	17	ctGGCGGCGGCg/ctg	1/9	0.28324904015376	1	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	0	0.403441721330162	1		75	52	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0023722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	139	712	0	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	0.403441721330162	2		712	602	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100096	27100096	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	68	749	0	ENST00000324856.7:c.3892G>T	p.Gly1298Ter	p.G1298*	ENST00000324856	NM_006015.4	1298	Gga/Tga	16/20	0.403441721330162	1	FACETS	0.457	0.397	0.521	0.457	0.397	0.521	SUBCLONAL	1	TRUE	0	0.403441721330162	1		749	589	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349814	89349814	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	212	1177	0	ENST00000301030.4:c.3136T>G	p.Cys1046Gly	p.C1046G	ENST00000301030	NM_001256183.1	1046	Tgt/Ggt	9/13	1	2	FACETS	0.831	0.77	0.894	0.831	0.77	0.894	CLONAL	1	TRUE	1	0.403441721330162	2		1177	1265	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	350	896	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.808319150729002	3	FACETS	0.909	0.869	0.949	0.909	0.869	0.949	CLONAL	2	TRUE	1	0.808319150729002	3		898	669	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0023731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	205	921	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	0.903	0.843	0.963	0.903	0.843	0.963	CLONAL	1	TRUE	1	0.808319150729002	2		921	562	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0023731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	282	583	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.808319150729002	3	FACETS	0.972	0.926	1	0.972	0.926	1	CLONAL	2	TRUE	1	0.808319150729002	3		583	504	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0023731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	102	288	0	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	0.808319150729002	3	FACETS	1	0.907	1	0.502	0.453	0.553	CLONAL	1	TRUE	1	0.808319150729002	3		288	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577522	7577522	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567549129	NA	P-0023731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	210	746	0	ENST00000269305.4:c.759del	p.Ile254SerfsTer91	p.I254Sfs*91	ENST00000269305	NM_001126112.2	253	acC/ac	7/11	0.808319150729002	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.808319150729002	1		746	280	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102198862	102198862	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0023731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	102	490	0	ENST00000263464.3:c.1032+1G>T		p.X344_splice	ENST00000263464	NM_001165.4	344			0.808319150729002	2	FACETS	0.673	0.607	0.742	0.337	0.303	0.371	SUBCLONAL	1	TRUE	0	0.808319150729002	2		490	375	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53244025	53244025	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	106	681	0	ENST00000375401.3:c.968A>C	p.Glu323Ala	p.E323A	ENST00000375401	NM_004187.3	323	gAg/gCg	8/26	0.808319150729002	4	FACETS	0.581	0.52	0.645	0.194	0.173	0.215	SUBCLONAL	1	TRUE	1	0.808319150729002	4		681	817	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289234	33289234	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	251	475	0	ENST00000374542.5:c.318C>A	p.Cys106Ter	p.C106*	ENST00000374542	NM_001141970.1	106	tgC/tgA	3/8	0.803506565707848	1	FACETS	0.953	0.91	0.996	0.953	0.91	0.996	CLONAL	1	TRUE	0	0.803506565707848	1		475	392	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572290	64572290	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0023732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	313	608	0	ENST00000312049.6:c.1351-2A>T		p.X451_splice	ENST00000312049	NM_130799.2	451			0.803506565707848	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.803506565707848	1		608	449	SUCCESS
MET	4233	MSKCC	GRCh37	7	116399446	116399446	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	236	603	1	ENST00000397752.3:c.2266G>T	p.Gly756Cys	p.G756C	ENST00000397752	NM_000245.2	756	Ggt/Tgt	10/21	0.803506565707848	1	FACETS	0.976	0.931	1	0.976	0.931	1	CLONAL	1	TRUE	0	0.803506565707848	1		604	360	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	71	482	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.924	0.824	1	0.924	0.824	1	CLONAL	1	TRUE	1	0.830661274091717	2		482	185	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0023735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	224	623	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.830661274091717	1	FACETS	0.985	0.942	1	0.985	0.942	1	CLONAL	1	TRUE	0	0.830661274091717	1		623	320	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522568	106522568	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs754441790	NA	P-0023735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	185	520	0	ENST00000359195.3:c.2545C>T	p.Arg849Ter	p.R849*	ENST00000359195	NM_002649.2	849	Cga/Tga	7/11	0.465747180451876	3	FACETS	1	0.981	1	0.575	0.535	0.617	INDETERMINATE	1	TRUE	1	0.830661274091717	3		520	548	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0023736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	38	1087	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	1	2	FACETS	0.48	0.396	0.575	0.48	0.396	0.575	SUBCLONAL	1	FALSE	1	0.252361222473106	2		1087	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579572	7579572	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	43	546	0	ENST00000269305.4:c.115del	p.Ala39GlnfsTer5	p.A39Qfs*5	ENST00000269305	NM_001126112.2	39	Gca/ca	4/11	1	2	FACETS	0.582	0.486	0.688	0.582	0.486	0.688	SUBCLONAL	1	FALSE	1	0.252361222473106	2		546	586	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995527	68995531	+	frameshift_variant	Frame_Shift_Del	DEL	TTTTT	TTTTT	-	novel	NA	P-0023736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	51	609	0	ENST00000288368.4:c.1931_1935del	p.Val644AspfsTer6	p.V644Dfs*6	ENST00000288368	NM_024870.2	644	gTTTTT/g	18/40	1	2	FACETS	0.637	0.54	0.742	0.637	0.54	0.742	SUBCLONAL	1	FALSE	1	0.252361222473106	2		609	635	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0023737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	419	701	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.655740879527548	3	FACETS	0.869	0.838	0.899	0.869	0.838	0.899	CLONAL	3	TRUE	0	0.655740879527548	3		701	651	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512269	120512269	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	70	586	0	ENST00000256646.2:c.973G>C	p.Val325Leu	p.V325L	ENST00000256646	NM_024408.3	325	Gta/Cta	6/34	0.250048416039374	4	FACETS	0.844	0.739	0.956	0.281	0.246	0.319	INDETERMINATE	1	TRUE	1	0.655740879527548	4		586	419	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62311283	62311283	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	75	371	0	ENST00000360203.5:c.1119C>G	p.Ile373Met	p.I373M	ENST00000360203	NM_001283009.1	373	atC/atG	13/35	0.502709937164432	5	FACETS	0.93	0.817	1	0.232	0.204	0.263	CLONAL	1	TRUE	1	0.655740879527548	5		371	488	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864407	162864407	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	52	575	0	ENST00000366898.1:c.106G>T	p.Val36Phe	p.V36F	ENST00000366898	NM_004562.2	36	Gtt/Ttt	2/12	0.229273556417001	4	FACETS	0.931	0.799	1	0.466	0.399	0.537	INDETERMINATE	1	TRUE	2	0.655740879527548	4		575	282	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	21	896	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.144	0.11	0.184	0.144	0.11	0.184	SUBCLONAL	1	TRUE	1	0.421253346500932	2		898	692	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0023738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	82	466	1	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.123252795145659	0	FACETS	0.651	0.579	0.728			1	INDETERMINATE	1	TRUE	0	0.421253346500932	0		467	346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0023738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	138	752	2	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.403074069402806	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.421253346500932	1		754	433	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11554273	NA	P-0023738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	148	472	0	ENST00000371085.3:c.601C>A	p.Arg201Ser	p.R201S	ENST00000371085	NM_000516.4	201	Cgt/Agt	8/13	NA	2	FACETS	0.8	0.738	0.865			1	INDETERMINATE	2	TRUE	NA	0.421253346500932	2		472	439	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351487	89351487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	56	583	0	ENST00000301030.4:c.1463G>A	p.Ser488Asn	p.S488N	ENST00000301030	NM_001256183.1	488	aGt/aAt	9/13	NA	2	FACETS	0.623	0.535	0.718			1	INDETERMINATE	1	TRUE	NA	0.421253346500932	2		583	427	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170737	99170737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747795003	NA	P-0023738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	47	360	0	ENST00000074304.5:c.1366C>T	p.Arg456Trp	p.R456W	ENST00000074304	NM_001134224.1	456	Cgg/Tgg	16/26	0.123252795145659	0	FACETS	0.503	0.427	0.584			1	INDETERMINATE	1	TRUE	0	0.421253346500932	0		360	257	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55219026	55219026	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	133	471	1	ENST00000275493.2:c.599G>T	p.Trp200Leu	p.W200L	ENST00000275493	NM_005228.3	200	tGg/tTg	5/28	0.421253346500932	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.421253346500932	1		472	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs28934577	NA	P-0023739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	149	596	0	ENST00000269305.4:c.770T>G	p.Leu257Arg	p.L257R	ENST00000269305	NM_001126112.2	257	cTg/cGg	7/11	0.307108402525263	1	FACETS	0.973	0.889	1	0.973	0.889	1	CLONAL	1	TRUE	0	0.307108402525263	1		596	844	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855936	68855938	+	inframe_deletion	In_Frame_Del	DEL	CTG	CTG	-	rs1555516823	NA	P-0023739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	93	737	1	ENST00000261769.5:c.1747_1749del	p.Leu583del	p.L583del	ENST00000261769	NM_004360.3	582	CTG/-	12/16	0.307108402525263	1	FACETS	0.857	0.764	0.957	0.857	0.764	0.957	CLONAL	1	TRUE	0	0.307108402525263	1		738	598	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148516654	148516694	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTACCCTCTGCAATAATTAGGCACTAAGTCTTACCAAATGC	GTACCCTCTGCAATAATTAGGCACTAAGTCTTACCAAATGC	TT	novel	NA	P-0023739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	67	455	2	ENST00000320356.2:c.993_999+34delinsAA		p.X331_splice	ENST00000320356	NM_004456.4	331		9/20	1	2	FACETS	0.724	0.629	0.826	0.724	0.629	0.826	SUBCLONAL	1	TRUE	1	0.307108402525263	2		457	603	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944256	206944256	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374619208	NA	P-0023741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	87	383	4	ENST00000423557.1:c.374G>A	p.Arg125His	p.R125H	ENST00000423557	NM_000572.2	125	cGc/cAc	3/5	0.538400748992202	3	FACETS	0.794	0.705	0.888	0.397	0.352	0.444	SUBCLONAL	1	TRUE	1	0.550091109532776	3		387	508	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931463	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622007	NA	P-0023741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1317	159	295	0	ENST00000374690.3:c.2105T>A	p.Leu702His	p.L702H	ENST00000374690	NM_000044.3	702	cTc/cAc	4/8	0.550091109532776	8	FACETS	1	0.941	1			1	CLONAL	1	TRUE	NA	0.550091109532776	8		295	1476	SUCCESS
AR	367	MSKCC	GRCh37	X	66943543	66943543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852581	NA	P-0023741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	873	234	0	ENST00000374690.3:c.2623C>T	p.His875Tyr	p.H875Y	ENST00000374690	NM_000044.3	875	Cat/Tat	8/8	0.550091109532776	8	FACETS	0.966	0.949	0.984			1	CLONAL	8	TRUE	NA	0.550091109532776	8		234	1088	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554278	29554278	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199474777	NA	P-0023741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	137	530	0	ENST00000356175.3:c.2294G>A	p.Arg765His	p.R765H	ENST00000356175	NM_000267.3	765	cGc/cAc	19/57	0.538400748992202	3	FACETS	1	0.917	1	0.502	0.458	0.549	CLONAL	1	TRUE	1	0.550091109532776	3		530	632	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0023741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	181	668	0	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.550091109532776	2		668	652	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949157	151949157	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0023741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	145	565	0	ENST00000262189.6:c.1488T>A	p.Cys496Ter	p.C496*	ENST00000262189	NM_170606.2	496	tgT/tgA	11/59	0.550091109532776	4	FACETS	1	0.927	1	0.508	0.464	0.555	CLONAL	1	TRUE	2	0.550091109532776	4		565	804	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484285	8484286	+	missense_variant	Missense_Mutation	DNP	AT	AT	TC	novel	NA	P-0023741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	148	520	0	ENST00000356435.5:c.3246_3247delinsGA	p.Phe1083Ile	p.F1083I	ENST00000356435		1082	tcATtt/tcGAtt	19/35	0.471657846901763	4	FACETS	0.96	0.877	1	0.48	0.438	0.524	CLONAL	1	TRUE	2	0.550091109532776	4		520	869	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143968	11143968	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	161	494	0	ENST00000358026.2:c.3550del	p.Leu1184CysfsTer32	p.L1184Cfs*32	ENST00000358026	NM_001128849.1	1183	gaC/ga	26/36	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		494	350	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0023744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	23	675	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.099	0.077	0.126	0.099	0.077	0.126	SUBCLONAL	1	TRUE	1	0.605912312364665	2		675	764	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0023744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	162	567	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.847	0.781	0.917	0.847	0.781	0.917	CLONAL	1	TRUE	1	0.605912312364665	2		567	631	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821373	72821373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775404633	NA	P-0023744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	61	421	1	ENST00000268489.5:c.10802C>T	p.Ser3601Leu	p.S3601L	ENST00000268489	NM_006885.3	3601	tCg/tTg	10/10	0.605912312364665	4	FACETS	0.627	0.541	0.719	0.209	0.18	0.24	SUBCLONAL	1	TRUE	1	0.605912312364665	4		422	516	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248409	59248409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184098204	NA	P-0023744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	75	451	1	ENST00000371222.2:c.334G>A	p.Glu112Lys	p.E112K	ENST00000371222	NM_002228.3	112	Gag/Aag	1/1	0.605912312364665	3	FACETS	0.575	0.504	0.651	0.287	0.252	0.326	SUBCLONAL	1	TRUE	1	0.605912312364665	3		452	561	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241878	72241878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	132	422	0	ENST00000357731.5:c.512C>T	p.Ser171Phe	p.S171F	ENST00000357731	NM_173808.2	171	tCt/tTt	3/7	0.605912312364665	3	FACETS	0.987	0.9	1	0.494	0.45	0.539	CLONAL	1	TRUE	1	0.605912312364665	3		422	575	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658826	3658826	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	206	662	1	ENST00000294008.3:c.140C>T	p.Ser47Phe	p.S47F	ENST00000294008	NM_032444.2	47	tCt/tTt	2/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.605912312364665	2		663	657	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936282	78936282	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	201	631	0	ENST00000306801.3:c.3714C>G	p.Ile1238Met	p.I1238M	ENST00000306801	NM_020761.2	1238	atC/atG	32/34	0.176330904528258	3	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.605912312364665	3		631	759	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	199	652	0	ENST00000326873.7:c.647C>A	p.Ser216Tyr	p.S216Y	ENST00000326873	NM_000455.4	216	tCc/tAc	5/10	0.605912312364665	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.605912312364665	1		652	442	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135028	11135028	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555779989	NA	P-0023744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	189	606	0	ENST00000358026.2:c.2995G>A	p.Asp999Asn	p.D999N	ENST00000358026	NM_001128849.1	999	Gac/Aac	21/36	0.605912312364665	3	FACETS	0.97	0.898	1	0.485	0.449	0.523	CLONAL	1	TRUE	1	0.605912312364665	3		606	838	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158594129	158594129	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	165	507	0	ENST00000263640.3:c.1444C>G	p.Pro482Ala	p.P482A	ENST00000263640	NM_001105.4	482	Cca/Gca	11/11	1	2	FACETS	0.983	0.908	1	0.983	0.908	1	CLONAL	1	TRUE	1	0.605912312364665	2		507	554	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572932	41572932	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	122	670	0	ENST00000263253.7:c.5217C>G	p.Ile1739Met	p.I1739M	ENST00000263253	NM_001429.3	1739	atC/atG	31/31	1	2	FACETS	0.606	0.549	0.667	0.606	0.549	0.667	SUBCLONAL	1	TRUE	1	0.605912312364665	2		670	664	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573596	41573596	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751120457	NA	P-0023744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	101	678	0	ENST00000263253.7:c.5881C>T	p.Pro1961Ser	p.P1961S	ENST00000263253	NM_001429.3	1961	Ccc/Tcc	31/31	1	2	FACETS	0.544	0.487	0.604	0.544	0.487	0.604	SUBCLONAL	1	TRUE	1	0.605912312364665	2		678	613	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574511	41574511	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	88	699	1	ENST00000263253.7:c.6796C>A	p.Gln2266Lys	p.Q2266K	ENST00000263253	NM_001429.3	2266	Cag/Aag	31/31	1	2	FACETS	0.478	0.424	0.535	0.478	0.424	0.535	SUBCLONAL	1	TRUE	1	0.605912312364665	2		700	608	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502437	186502437	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	103	206	0	ENST00000323963.5:c.160G>C	p.Glu54Gln	p.E54Q	ENST00000323963		54	Gag/Cag	3/11	0.547028918293113	4	FACETS	0.592	0.529	0.659	0.296	0.264	0.33	SUBCLONAL	1	TRUE	2	0.605912312364665	4		206	922	SUCCESS
APC	324	MSKCC	GRCh37	5	112170717	112170717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060503278	NA	P-0023744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	174	576	0	ENST00000257430.4:c.1813G>A	p.Asp605Asn	p.D605N	ENST00000257430	NM_000038.5	605	Gat/Aat	15/16	1	2	FACETS	0.907	0.839	0.978	0.907	0.839	0.978	CLONAL	1	TRUE	1	0.605912312364665	2		576	633	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324471	31324471	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs41559613	NA	P-0023744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	339	507	0	ENST00000412585.2:c.337G>T	p.Glu113Ter	p.E113*	ENST00000412585	NM_005514.6	113	Gag/Tag	2/8	0.605912312364665	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.605912312364665	2		507	498	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324627	31324627	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs41561613	NA	P-0023744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	314	309	0	ENST00000412585.2:c.181G>C	p.Asp61His	p.D61H	ENST00000412585	NM_005514.6	61	Gac/Cac	2/8	0.605912312364665	2	FACETS	0.855	0.827	0.882	1	0.996	1	CLONAL	3	TRUE	0	0.605912312364665	2		309	404	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98241404	98241404	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs267606984	NA	P-0023744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	168	545	0	ENST00000331920.6:c.1093C>T	p.Gln365Ter	p.Q365*	ENST00000331920	NM_000264.3	365	Cag/Tag	8/24	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.605912312364665	2		545	534	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0023745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	28	571	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.776	0.619	0.956	0.776	0.619	0.956	CLONAL	1	TRUE	1	0.15	2		571	481	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211008	55211008	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	41	521	1	ENST00000275493.2:c.251A>T	p.Glu84Val	p.E84V	ENST00000275493	NM_005228.3	84	gAg/gTg	3/28	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.15	2		522	470	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243777031	243777031	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	35	561	0	ENST00000263826.5:c.638A>G	p.Tyr213Cys	p.Y213C	ENST00000263826	NM_005465.4	213	tAt/tGt	7/13	1	2	FACETS	0.805	0.658	0.97	0.805	0.658	0.97	CLONAL	1	TRUE	1	0.15	2		561	580	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	29	482	0				ENST00000310581	NM_198253.2	-/1132			0.122659122267897	0	FACETS	0.901	0.727	1			1	CLONAL	2	TRUE	0	0.12	0		482	236	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0023746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	57	610	1	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.209629945489645	4	FACETS	0.817	0.7	0.945	0.817	0.7	0.945	CLONAL	2	TRUE	2	0.12	4		611	651	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982329	201982330	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0023746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	70	706	0	ENST00000359651.3:c.709_710dup	p.Gly238ArgfsTer17	p.G238Rfs*17	ENST00000359651		236	-/AA	6/8	1	2	FACETS	0.889	0.775	1	1	0.979	1	CLONAL	2	TRUE	1	0.12	2		706	656	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426279	49426279	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	95	758	1	ENST00000301067.7:c.12209C>T	p.Ser4070Phe	p.S4070F	ENST00000301067	NM_003482.3	4070	tCt/tTt	39/54	0.209629945489645	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.12	4		759	751	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426355	49426355	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	81	842	1	ENST00000301067.7:c.12133C>T	p.Gln4045Ter	p.Q4045*	ENST00000301067	NM_003482.3	4045	Cag/Tag	39/54	0.209629945489645	4	FACETS	0.963	0.848	1	0.963	0.848	1	CLONAL	2	TRUE	2	0.12	4		843	785	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426526	49426526	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	81	736	1	ENST00000301067.7:c.11962C>T	p.Gln3988Ter	p.Q3988*	ENST00000301067	NM_003482.3	3988	Cag/Tag	39/54	0.209629945489645	4	FACETS	0.853	0.75	0.964	0.853	0.75	0.964	CLONAL	2	TRUE	2	0.12	4		737	886	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426531	49426531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	79	731	0	ENST00000301067.7:c.11957C>T	p.Ser3986Phe	p.S3986F	ENST00000301067	NM_003482.3	3986	tCt/tTt	39/54	0.209629945489645	4	FACETS	0.834	0.732	0.944	0.834	0.732	0.944	CLONAL	2	TRUE	2	0.12	4		731	884	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426595	49426595	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	69	530	2	ENST00000301067.7:c.11893C>T	p.Gln3965Ter	p.Q3965*	ENST00000301067	NM_003482.3	3965	Cag/Tag	39/54	0.209629945489645	4	FACETS	0.954	0.831	1	0.954	0.831	1	CLONAL	2	TRUE	2	0.12	4		532	675	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426751	49426751	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	34	258	0	ENST00000301067.7:c.11737C>T	p.Gln3913Ter	p.Q3913*	ENST00000301067	NM_003482.3	3913	Cag/Tag	39/54	0.209629945489645	4	FACETS	1	0.908	1	1	0.908	1	CLONAL	2	TRUE	2	0.12	4		258	269	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116176	67116176	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	40	538	0	ENST00000412916.2:c.460G>C	p.Glu154Gln	p.E154Q	ENST00000412916		154	Gaa/Caa	5/6	1	2	FACETS	0.956	0.793	1	0.956	0.793	1	CLONAL	1	TRUE	1	0.12	2		538	697	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14628969	14628969	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	39	503	0	ENST00000254322.2:c.193G>C	p.Asp65His	p.D65H	ENST00000254322	NM_006145.1	65	Gac/Cac	1/3	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.12	2		503	585	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541890	187541891	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	35	591	0	ENST00000441802.2:c.5849dup	p.Thr1951AsnfsTer3	p.T1951Nfs*3	ENST00000441802	NM_005245.3	1950	cta/ctTa	10/27	1	2	FACETS	0.964	0.789	1	0.964	0.789	1	CLONAL	1	TRUE	1	0.12	2		591	605	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778143	27778143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	48	648	2	ENST00000369163.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000369163	NM_003536.2	98	Gag/Aag	1/1	0.3	3	FACETS	1	0.958	1			1	CLONAL	1	TRUE	NA	0.12	3		650	590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577595	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0023747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	300	558	0	ENST00000269305.4:c.686_687del	p.Cys229TyrfsTer10	p.C229Yfs*10	ENST00000269305	NM_001126112.2	229	tGT/t	7/11	0.787488868035524	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.787488868035524	1		558	434	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440124	49440124	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	237	586	0	ENST00000301067.7:c.4502G>T	p.Cys1501Phe	p.C1501F	ENST00000301067	NM_003482.3	1501	tGt/tTt	16/54	0.217694424325103	4	FACETS	1	0.992	1	0.718	0.673	0.765	INDETERMINATE	1	TRUE	2	0.787488868035524	4		586	749	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950325	15950325	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	99	723	0	ENST00000268712.3:c.6619T>C	p.Ser2207Pro	p.S2207P	ENST00000268712	NM_006311.3	2207	Tca/Cca	42/46	0.787488868035524	1	FACETS	0.334	0.299	0.37	0.334	0.299	0.37	SUBCLONAL	1	TRUE	0	0.787488868035524	1		723	457	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730008	41730008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537531066	NA	P-0023747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	79	542	0	ENST00000242208.4:c.521G>A	p.Arg174His	p.R174H	ENST00000242208	NM_002192.2	174	cGc/cAc	3/3	0.597732679967959	1	FACETS	0.286	0.252	0.321	0.286	0.252	0.321	SUBCLONAL	1	TRUE	0	0.787488868035524	1		542	426	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763928	76763928	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0023747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	73	577	2	ENST00000373344.5:c.7380T>A	p.Tyr2460Ter	p.Y2460*	ENST00000373344	NM_000489.3	2460	taT/taA	35/35	0.397612928541749	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.787488868035524	0		579	294	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0023748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	38	515	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.301722469239306	5	FACETS	0.985	0.845	1	1	0.962	1	CLONAL	6	TRUE	1	0.19	5		515	87	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182641	38182641	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs387907272	NA	P-0023748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	10	399	0	ENST00000396334.3:c.794T>C	p.Leu265Pro	p.L265P	ENST00000396334	NM_002468.4	265	cTg/cCg	5/5	1	2	FACETS	0.452	0.305	0.636	0.452	0.305	0.636	SUBCLONAL	1	TRUE	1	0.19	2		399	233	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0023748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	16	722	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.301722469239306	5	FACETS	1	0.823	1	0.564	0.423	0.726	CLONAL	2	TRUE	1	0.19	5		722	96	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832398	72832398	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	39	563	1	ENST00000268489.5:c.4183G>C	p.Asp1395His	p.D1395H	ENST00000268489	NM_006885.3	1395	Gat/Cat	9/10	0.202794555653422	3	FACETS	0.875	0.73	1	0.583	0.486	0.69	CLONAL	2	TRUE	0	0.19	3		564	257	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577596	7577597	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0023748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	32	703	0	ENST00000269305.4:c.683_684dup	p.Cys229ThrfsTer19	p.C229Tfs*19	ENST00000269305	NM_001126112.2	228	-/AC	7/11	0.231780186912884	3	FACETS	1	0.893	1	0.575	0.467	0.695	CLONAL	1	TRUE	1	0.19	3		703	321	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526700	106526700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	23	598	1	ENST00000359195.3:c.2993C>T	p.Ser998Phe	p.S998F	ENST00000359195	NM_002649.2	998	tCt/tTt	10/11	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.19	2		599	164	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444784	49444784	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	211	945	0	ENST00000301067.7:c.2682G>T	p.Leu894Phe	p.L894F	ENST00000301067	NM_003482.3	894	ttG/ttT	10/54	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.614054122096254	2		945	679	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858340	89858342	+	inframe_deletion	In_Frame_Del	DEL	AGC	AGC	-	novel	NA	P-0023749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	135	531	1	ENST00000389301.3:c.1218_1220del	p.Leu407del	p.L407del	ENST00000389301	NM_000135.2	406	ctGCTt/ctt	13/43	0.614054122096254	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.614054122096254	1		532	293	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713559	30713559	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1365040421	NA	P-0023749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	147	587	0	ENST00000295754.5:c.884C>T	p.Ser295Leu	p.S295L	ENST00000295754	NM_003242.5	295	tCa/tTa	4/7	0.614054122096254	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.614054122096254	1		587	322	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356412	66356412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763166233	NA	P-0023749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	127	537	0	ENST00000273854.3:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000273854	NM_004439.5	362	cGg/cAg	5/18	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.614054122096254	2		537	401	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530378	187530378	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	154	509	0	ENST00000441802.2:c.10165A>T	p.Arg3389Trp	p.R3389W	ENST00000441802	NM_005245.3	3389	Agg/Tgg	16/27	1	2	FACETS	0.983	0.906	1	0.983	0.906	1	CLONAL	1	TRUE	1	0.614054122096254	2		509	510	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628270	187628270	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	193	755	1	ENST00000441802.2:c.2712G>T	p.Glu904Asp	p.E904D	ENST00000441802	NM_005245.3	904	gaG/gaT	2/27	1	2	FACETS	0.942	0.876	1	0.942	0.876	1	CLONAL	1	TRUE	1	0.614054122096254	2		756	667	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192565	138192567	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-	novel	NA	P-0023749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	174	589	0	ENST00000237289.4:c.202_204del	p.Leu68del	p.L68del	ENST00000237289	NM_001270507.1	67	gcCCTc/gcc	2/9	0.202514795049729	3	FACETS	1	0.98	1	0.585	0.541	0.631	INDETERMINATE	1	TRUE	1	0.614054122096254	3		589	633	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920191	76920191	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	241	407	1	ENST00000373344.5:c.3886C>T	p.Pro1296Ser	p.P1296S	ENST00000373344	NM_000489.3	1296	Cca/Tca	11/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.614054122096254	1		408	389	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0023751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	136	521	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.76146831740094	2		521	337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0023751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	205	860	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	0.76146831740094	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.76146831740094	1		860	311	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636818	8636818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146973770	NA	P-0023751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	131	582	3	ENST00000356435.5:c.91G>A	p.Val31Ile	p.V31I	ENST00000356435		31	Gtt/Att	2/35	1	2	FACETS	0.829	0.759	0.901	0.829	0.759	0.901	CLONAL	1	TRUE	1	0.76146831740094	2		585	415	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032159	10032159	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	137	733	0	ENST00000330684.3:c.664A>T	p.Ile222Phe	p.I222F	ENST00000330684	NM_001134407.1	222	Atc/Ttc	3/13	1	2	FACETS	0.81	0.743	0.88	0.81	0.743	0.88	CLONAL	1	TRUE	1	0.76146831740094	2		733	444	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435418	56435418	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	212	700	0	ENST00000407977.2:c.1719del	p.Gly574GlufsTer126	p.G574Efs*126	ENST00000407977		573	acC/ac	9/10	0.76146831740094	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.76146831740094	1		700	315	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331724	8331724	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs763525789	NA	P-0023751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	94	448	0	ENST00000356435.5:c.5392C>T	p.Arg1798Ter	p.R1798*	ENST00000356435		1798	Cga/Tga	33/35	1	2	FACETS	0.809	0.729	0.893	0.809	0.729	0.893	CLONAL	1	TRUE	1	0.76146831740094	2		448	305	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123691	11123691	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	303	700	0	ENST00000358026.2:c.2341A>T	p.Met781Leu	p.M781L	ENST00000358026	NM_001128849.1	781	Atg/Ttg	16/36	1	2	FACETS	0.977	0.926	1	0.977	0.926	1	CLONAL	1	FALSE	1	0.824958512108696	2		700	752	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934027	39934027	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	366	338	0	ENST00000378444.4:c.572G>A	p.Trp191Ter	p.W191*	ENST00000378444	NM_001123385.1	191	tGg/tAg	4/15	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	FALSE	0	0.824958512108696	1		338	455	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031915	10031915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	78	847	0	ENST00000330684.3:c.908C>T	p.Ala303Val	p.A303V	ENST00000330684	NM_001134407.1	303	gCa/gTa	3/13	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		847	576	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72833975	72833975	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	83	711	0	ENST00000268489.5:c.3918del	p.Pro1307GlnfsTer38	p.P1307Qfs*38	ENST00000268489	NM_006885.3	1306	gtT/gt	8/10	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		711	614	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	53	487	0	ENST00000263967.3:c.3012G>A	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atA	21/21	1	2	FACETS	0.969	0.827	1	0.969	0.827	1	CLONAL	1	TRUE	1	0.24	2		487	456	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115852	8115853	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs1085307641	NA	P-0023754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	43	650	0	ENST00000346208.3:c.1198_1199del	p.Met400ValfsTer106	p.M400Vfs*106	ENST00000346208		400	ATg/g	6/6	1	2	FACETS	0.74	0.62	0.874	0.74	0.62	0.874	SUBCLONAL	1	TRUE	1	0.24	2		650	484	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0023756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	19	238	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.181892449517605	3	FACETS	1	0.823	1	0.551	0.419	0.706	CLONAL	1	TRUE	1	0.15	3		238	247	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0023756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	20	976	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.785	1	1	0.785	1	CLONAL	1	TRUE	1	0.15	2		976	260	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578496	7578496	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587782197	NA	P-0023756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	26	577	1	ENST00000269305.4:c.434T>A	p.Leu145Gln	p.L145Q	ENST00000269305	NM_001126112.2	145	cTg/cAg	5/11	1	2	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	TRUE	1	0.15	2		578	320	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479774	67479774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906856	NA	P-0023756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	20	462	0	ENST00000327367.4:c.1081G>A	p.Glu361Lys	p.E361K	ENST00000327367	NM_005902.3	361	Gag/Aag	8/9	1	2	FACETS	0.977	0.748	1	0.977	0.748	1	CLONAL	1	TRUE	1	0.15	2		462	273	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631613	90631613	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	37	440	0	ENST00000330062.3:c.656T>C	p.Met219Thr	p.M219T	ENST00000330062	NM_002168.2	219	aTg/aCg	5/11	0.181892449517605	3	FACETS	0.858	0.71	1	0.858	0.71	1	CLONAL	2	TRUE	1	0.15	3		440	309	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934542	9934542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	20	379	0	ENST00000330684.3:c.1613C>T	p.Ser538Leu	p.S538L	ENST00000330684	NM_001134407.1	538	tCa/tTa	7/13	1	2	FACETS	1	0.798	1	1	0.798	1	CLONAL	1	TRUE	1	0.15	2		379	255	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575085	48575085	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	15	326	1	ENST00000342988.3:c.279del	p.Ile94SerfsTer16	p.I94Sfs*16	ENST00000342988	NM_005359.5	93	gtG/gt	3/12	1	2	FACETS	0.858	0.628	1	0.858	0.628	1	CLONAL	1	TRUE	1	0.15	2		327	233	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943433	17943433	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	25	497	0	ENST00000458235.1:c.2575C>G	p.His859Asp	p.H859D	ENST00000458235	NM_000215.3	859	Cac/Gac	19/24	1	2	FACETS	0.978	0.771	1	0.978	0.771	1	CLONAL	1	TRUE	1	0.15	2		497	341	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527778	157527778	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	15	357	0	ENST00000346085.5:c.5503G>A	p.Glu1835Lys	p.E1835K	ENST00000346085	NM_020732.3	1835	Gag/Aag	20/20	1	2	FACETS	0.709	0.518	0.939	0.709	0.518	0.939	CLONAL	1	TRUE	1	0.15	2		357	282	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443467	49443467	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	287	255	0	ENST00000301067.7:c.3904C>T	p.Gln1302Ter	p.Q1302*	ENST00000301067	NM_003482.3	1302	Cag/Tag	11/54	0.892013123670257	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.892013123670257	3		255	432	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696637	47696637	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	27	383	0	ENST00000347630.2:c.311T>G	p.Phe104Cys	p.F104C	ENST00000347630	NM_001007230.1	104	tTc/tGc	5/11	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	FALSE	1	0.3	2		383	167	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426940	49426941	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCCC	novel	NA	P-0023760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	11	329	0	ENST00000301067.7:c.11544_11547dup	p.His3850GlyfsTer163	p.H3850Gfs*163	ENST00000301067	NM_003482.3	3849	-/GGGA	39/54	0.111508998282907	4	FACETS	0.611	0.423	0.843	0.306	0.211	0.422	INDETERMINATE	1	FALSE	2	0.3	4		329	156	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330613	65330613	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0023761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	102	403	0	ENST00000342505.4:c.1033A>T	p.Lys345Ter	p.K345*	ENST00000342505	NM_002227.2	345	Aaa/Taa	8/25	0.595939502555264	1	FACETS	0.973	0.886	1	0.973	0.886	1	CLONAL	1	TRUE	0	0.595939502555264	1		403	247	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575427	64575427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	133	519	0	ENST00000312049.6:c.590C>T	p.Thr197Ile	p.T197I	ENST00000312049	NM_130799.2	197	aCc/aTc	3/10	0.595939502555264	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.595939502555264	1		519	308	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863697	68863701	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TGAAG	TGAAG	-	novel	NA	P-0023761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	62	217	1	ENST00000261769.5:c.2437_2439+2del		p.X813_splice	ENST00000261769	NM_004360.3	813		15/16	0.595939502555264	1	FACETS	0.885	0.782	0.992	0.885	0.782	0.992	CLONAL	1	TRUE	0	0.595939502555264	1		218	165	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0023764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	59	792	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.549157346488215	1	FACETS	0.561	0.487	0.64	0.561	0.487	0.64	SUBCLONAL	1	TRUE	0	0.549157346488215	1		794	278	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0023764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	32	461	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.932	0.771	1	0.932	0.771	1	CLONAL	1	TRUE	1	0.549157346488215	2		461	125	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166282	7166282	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	32	391	0	ENST00000302850.5:c.1744G>T	p.Gly582Cys	p.G582C	ENST00000302850	NM_000208.2	582	Ggt/Tgt	8/22	1	2	FACETS	0.292	0.237	0.354	0.292	0.237	0.354	SUBCLONAL	1	TRUE	1	0.549157346488215	2		391	399	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831467	72831467	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0023764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	103	358	0	ENST00000268489.5:c.5114C>G	p.Ser1705Ter	p.S1705*	ENST00000268489	NM_006885.3	1705	tCa/tGa	9/10	0.259666999626396	4	FACETS	0.914	0.828	1	0.914	0.828	1	INDETERMINATE	2	TRUE	2	0.549157346488215	4		358	318	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599278	55599278	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1334674972	NA	P-0023766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	219	371	0	ENST00000288135.5:c.2404C>T	p.His802Tyr	p.H802Y	ENST00000288135	NM_000222.2	802	Cat/Tat	17/21	0.280665791626857	5	FACETS	1	0.981	1			1	CLONAL	3	TRUE	NA	0.280665791626857	5		371	658	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999570	100999570	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	47	593	1	ENST00000325455.5:c.232C>T	p.Gln78Ter	p.Q78*	ENST00000325455	NM_001202474.3	78	Cag/Tag	1/8	1	2	FACETS	0.502	0.423	0.59	0.502	0.423	0.59	SUBCLONAL	1	TRUE	1	0.280665791626857	2		594	667	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900239	32900239	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	rs886040519	NA	P-0023766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	29	259	0	ENST00000380152.3:c.428del	p.Pro143LeufsTer9	p.P143Lfs*9	ENST00000380152		143	Cct/ct	5/27	1	2	FACETS	0.499	0.4	0.612	0.499	0.4	0.612	SUBCLONAL	1	TRUE	1	0.280665791626857	2		259	414	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023307	27023307	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	73	118	0	ENST00000324856.7:c.413C>A	p.Ser138Ter	p.S138*	ENST00000324856	NM_006015.4	138	tCa/tAa	1/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.545558691603468	2		118	218	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295774	212295774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754127388	NA	P-0023768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	172	365	0	ENST00000342788.4:c.2539C>T	p.Arg847Cys	p.R847C	ENST00000342788	NM_005235.2	847	Cgt/Tgt	21/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.545558691603468	2		365	552	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727096	243727096	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	140	392	0	ENST00000263826.5:c.874C>G	p.Leu292Val	p.L292V	ENST00000263826	NM_005465.4	292	Ctt/Gtt	9/13	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.545558691603468	2		392	501	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0023769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	99	387	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	1	2	FACETS	0.692	0.623	0.765	0.692	0.623	0.765	SUBCLONAL	1	TRUE	1	0.729641342137683	2		387	392	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874781	151874781	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs762665429	NA	P-0023769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	11	215	0	ENST00000262189.6:c.7757C>G	p.Ser2586Cys	p.S2586C	ENST00000262189	NM_170606.2	2586	tCt/tGt	38/59	NA	2	FACETS	0.14	0.096	0.195			1	INDETERMINATE	1	TRUE	NA	0.729641342137683	2		215	215	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257129	19257129	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	22	235	0	ENST00000162023.5:c.834G>A	p.Trp278Ter	p.W278*	ENST00000162023		278	tgG/tgA	12/13	1	2	FACETS	0.359	0.28	0.449	0.359	0.28	0.449	SUBCLONAL	1	TRUE	1	0.729641342137683	2		235	168	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954196	48954198	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	novel	NA	P-0023771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	50	238	0	ENST00000267163.4:c.1397_1399del	p.Glu466_Arg467delinsGly	p.E466_R467delinsG	ENST00000267163	NM_000321.2	466	gAACga/gga	15/27	0.584360065745071	1	FACETS	0.638	0.549	0.732	0.638	0.549	0.732	SUBCLONAL	1	TRUE	0	0.584360065745071	1		238	190	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577052	7577053	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0023771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	255	478	0	ENST00000269305.4:c.885_886del	p.His296ProfsTer9	p.H296Pfs*9	ENST00000269305	NM_001126112.2	295	ccTCac/ccac	8/11	0.527328095056205	2	FACETS	0.873	0.827	0.918	0.873	0.827	0.918	CLONAL	2	TRUE	0	0.584360065745071	2		478	500	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372094	55372094	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1041891434	NA	P-0023771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	239	281	0	ENST00000297316.4:c.784C>T	p.Pro262Ser	p.P262S	ENST00000297316	NM_022454.3	262	Ccc/Tcc	2/2	0.584360065745071	4	FACETS	1	0.989	1	0.799	0.753	0.845	CLONAL	2	TRUE	1	0.584360065745071	4		281	541	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182641	38182641	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs387907272	NA	P-0023772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	9	399	0	ENST00000396334.3:c.794T>C	p.Leu265Pro	p.L265P	ENST00000396334	NM_002468.4	265	cTg/cCg	5/5	1	2	FACETS	0.208	0.137	0.297	0.208	0.137	0.297	SUBCLONAL	1	TRUE	1	0.559183145350196	2		399	155	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646851	23646852	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	69	642	0	ENST00000261584.4:c.1015_1016insA	p.Ala339AspfsTer3	p.A339Dfs*3	ENST00000261584	NM_024675.3	339	gca/gAca	4/13	0.559183145350196	3	FACETS	1	0.948	1	0.572	0.503	0.645	CLONAL	1	TRUE	1	0.559183145350196	3		642	276	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4102423	4102441	+	frameshift_variant	Frame_Shift_Del	DEL	TTCAGCACCTGGTCCAGGG	TTCAGCACCTGGTCCAGGG	-	novel	NA	P-0023774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	26	479	0	ENST00000262948.5:c.461_479del	p.Ser154Ter	p.S154*	ENST00000262948	NM_030662.3	154	tCCCTGGACCAGGTGCTGAAa/ta	4/11	0.0864948892887035	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		479	384	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266102	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0023774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	109	248	0	ENST00000349496.5:c.97_99del	p.Ser33del	p.S33del	ENST00000349496	NM_001904.3	33	TCT/-	3/15	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		248	331	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0023776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	33	460	3	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.403725649129291	3	FACETS	1	0.911	1	0.59	0.486	0.703	CLONAL	1	TRUE	1	0.414592283557369	3		463	163	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176330	24176330	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1057517825	NA	P-0023776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	74	440	0	ENST00000263121.7:c.1121G>A	p.Arg374Gln	p.R374Q	ENST00000263121	NM_003073.3	374	cGg/cAg	9/9	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.414592283557369	2		440	255	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791393	42791393	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0023776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	125	508	0	ENST00000575354.2:c.452+1G>A		p.X151_splice	ENST00000575354	NM_015125.3	151			0.338464170897089	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.414592283557369	4		508	366	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874713	151874713	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	77	357	1	ENST00000262189.6:c.7825C>T	p.Arg2609Ter	p.R2609*	ENST00000262189	NM_170606.2	2609	Cga/Tga	38/59	0.338464170897089	4	FACETS	0.984	0.875	1	0.984	0.875	1	CLONAL	2	TRUE	2	0.414592283557369	4		358	267	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578448	7578455	+	frameshift_variant	Frame_Shift_Del	DEL	GCCATGGC	GCCATGGC	-	novel	NA	P-0023776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	83	453	0	ENST00000269305.4:c.475_482del	p.Ala159HisfsTer19	p.A159Hfs*19	ENST00000269305	NM_001126112.2	159	GCCATGGCc/c	5/11	0.414592283557369	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.414592283557369	1		453	222	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798357	42798357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	46	452	0	ENST00000575354.2:c.4228C>T	p.Pro1410Ser	p.P1410S	ENST00000575354	NM_015125.3	1410	Ccc/Tcc	18/20	0.338464170897089	4	FACETS	0.993	0.841	1	0.497	0.42	0.58	CLONAL	1	TRUE	2	0.414592283557369	4		452	316	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661632	227661632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893642	NA	P-0023776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	107	408	0	ENST00000305123.5:c.1823C>T	p.Thr608Met	p.T608M	ENST00000305123	NM_005544.2	608	aCg/aTg	1/2	0.364271310415454	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.414592283557369	4		408	306	SUCCESS
APC	324	MSKCC	GRCh37	5	112111374	112111374	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1060503328	NA	P-0023776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	31	242	0	ENST00000257430.4:c.471G>A	p.Trp157Ter	p.W157*	ENST00000257430	NM_000038.5	157	tgG/tgA	5/16	0.403725649129291	3	FACETS	1	0.888	1	0.561	0.459	0.673	CLONAL	1	TRUE	1	0.414592283557369	3		242	161	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0023778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	92	461	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.886	0.795	0.981	1	0.985	1	CLONAL	2	TRUE	1	0.308174260006179	2		461	337	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0023778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	126	498	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.308174260006179	2		498	659	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609291	81609291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	11	167	0	ENST00000298171.2:c.889G>A	p.Glu297Lys	p.E297K	ENST00000298171	NM_000369.2	297	Gag/Aag	10/10	1	2	FACETS	0.342	0.236	0.473	0.342	0.236	0.473	SUBCLONAL	1	TRUE	1	0.308174260006179	2		167	209	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40864438	40864438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139326526	NA	P-0023778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	45	617	2	ENST00000428826.2:c.1270G>A	p.Val424Ile	p.V424I	ENST00000428826		424	Gta/Ata	12/21	0.190144216000234	2	FACETS	0.437	0.366	0.516	0.219	0.183	0.258	SUBCLONAL	1	TRUE	0	0.308174260006179	2		619	668	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223419	36223426	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTGGAC	ACCTGGAC	-	novel	NA	P-0023778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	32	637	0	ENST00000222270.7:c.5969_5976del	p.Asp1990ValfsTer9	p.D1990Vfs*9	ENST00000222270	NM_014727.1	1990	gACCTGGAC/g	28/37	1	2	FACETS	0.337	0.272	0.41	0.337	0.272	0.41	SUBCLONAL	1	TRUE	1	0.308174260006179	2		637	617	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920307	50920307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501858	NA	P-0023778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	86	485	0	ENST00000440232.2:c.3073G>A	p.Val1025Met	p.V1025M	ENST00000440232	NM_002691.3	1025	Gtg/Atg	25/27	1	2	FACETS	0.93	0.824	1	0.93	0.824	1	CLONAL	1	TRUE	1	0.308174260006179	2		485	600	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288958	212288958	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	36	461	0	ENST00000342788.4:c.2788C>G	p.Pro930Ala	p.P930A	ENST00000342788	NM_005235.2	930	Cct/Gct	23/28	1	2	FACETS	0.566	0.465	0.678	0.566	0.465	0.678	SUBCLONAL	1	TRUE	1	0.308174260006179	2		461	413	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091172	29091172	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587780176	NA	P-0023778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	53	290	0	ENST00000328354.6:c.1318A>T	p.Ile440Phe	p.I440F	ENST00000328354	NM_007194.3	440	Atc/Ttc	12/15	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.308174260006179	2		290	333	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958821	38958821	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	27	323	0	ENST00000357387.3:c.2291A>C	p.Lys764Thr	p.K764T	ENST00000357387	NM_152756.3	764	aAa/aCa	23/38	0.298957429667814	4	FACETS	0.449	0.356	0.555			1	SUBCLONAL	1	TRUE	NA	0.308174260006179	4		323	511	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14027791	14027791	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	30	308	0	ENST00000405192.2:c.53G>T	p.Arg18Leu	p.R18L	ENST00000405192	NM_001163147.1	18	cGt/cTt	3/12	1	2	FACETS	0.477	0.384	0.583	0.477	0.384	0.583	SUBCLONAL	1	TRUE	1	0.308174260006179	2		308	408	SUCCESS
AR	367	MSKCC	GRCh37	X	66942777	66942777	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	56	525	2	ENST00000374690.3:c.2558G>T	p.Cys853Phe	p.C853F	ENST00000374690	NM_000044.3	853	tGc/tTc	7/8	1	2	FACETS	0.605	0.518	0.7	0.605	0.518	0.7	SUBCLONAL	1	TRUE	1	0.308174260006179	2		527	601	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0023779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	180	967	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.477146941889883	2		967	593	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136162	11136162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	152	411	2	ENST00000358026.2:c.3146C>T	p.Pro1049Leu	p.P1049L	ENST00000358026	NM_001128849.1	1049	cCc/cTc	22/36	0.477146941889883	1	FACETS	0.938	0.864	1	0.938	0.864	1	CLONAL	1	TRUE	0	0.477146941889883	1		413	517	SUCCESS
APC	324	MSKCC	GRCh37	5	112155011	112155011	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	196	401	0	ENST00000257430.4:c.1282G>T	p.Glu428Ter	p.E428*	ENST00000257430	NM_000038.5	428	Gaa/Taa	10/16	0.439419447587224	2	FACETS	0.887	0.83	0.945	0.887	0.83	0.945	CLONAL	2	TRUE	0	0.477146941889883	2		401	463	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207042	1207042	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0023779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	191	407	1	ENST00000326873.7:c.130A>T	p.Lys44Ter	p.K44*	ENST00000326873	NM_000455.4	44	Aag/Tag	1/10	0.477146941889883	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.477146941889883	1		408	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579336	7579372	+	frameshift_variant	Frame_Shift_Del	DEL	CCCAGAATGCAAGAAGCCCAGACGGAAACCGTAGCTG	CCCAGAATGCAAGAAGCCCAGACGGAAACCGTAGCTG	-	novel	NA	P-0023779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	121	398	0	ENST00000269305.4:c.315_351del	p.Ser106GlnfsTer5	p.S106Qfs*5	ENST00000269305	NM_001126112.2	105	ggCAGCTACGGTTTCCGTCTGGGCTTCTTGCATTCTGGG/gg	4/11	0.477146941889883	1	FACETS	0.922	0.84	1	0.922	0.84	1	CLONAL	1	TRUE	0	0.477146941889883	1		398	419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579449	7579449	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	164	478	0	ENST00000269305.4:c.238C>G	p.Pro80Ala	p.P80A	ENST00000269305	NM_001126112.2	80	Cct/Gct	4/11	0.477146941889883	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.477146941889883	1		478	474	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600490	10600502	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGGCCACCAAG	TGGGGCCACCAAG	-	novel	NA	P-0023779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	134	381	0	ENST00000171111.5:c.1353_1365del	p.His451GlnfsTer3	p.H451Qfs*3	ENST00000171111	NM_203500.1	451	caCTTGGTGGCCCCA/ca	4/6	0.477146941889883	1	FACETS	0.93	0.851	1	0.93	0.851	1	CLONAL	1	TRUE	0	0.477146941889883	1		381	460	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211116	55211116	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	154	350	0	ENST00000275493.2:c.359C>G	p.Ala120Gly	p.A120G	ENST00000275493	NM_005228.3	120	gCa/gGa	3/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.477146941889883	2		350	503	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841849	151841849	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	109	237	0	ENST00000262189.6:c.14292G>C	p.Lys4764Asn	p.K4764N	ENST00000262189	NM_170606.2	4764	aaG/aaC	55/59	0.348192996915165	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.477146941889883	1		237	324	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68984772	68984772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	111	341	1	ENST00000288368.4:c.1536G>A	p.Met512Ile	p.M512I	ENST00000288368	NM_024870.2	512	atG/atA	14/40	1	2	FACETS	0.99	0.895	1	0.99	0.895	1	CLONAL	1	TRUE	1	0.477146941889883	2		342	470	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	48	896	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.712	0.603	0.833	0.712	0.603	0.833	SUBCLONAL	1	TRUE	1	0.289138120037568	2		898	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578219	7578220	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	110	354	0	ENST00000269305.4:c.629dup	p.Asn210LysfsTer6	p.N210Kfs*6	ENST00000269305	NM_001126112.2	210	aac/aaAc	6/11	0.289138120037568	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.289138120037568	1		354	493	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981300	201981300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	99	308	1	ENST00000359651.3:c.379G>A	p.Asp127Asn	p.D127N	ENST00000359651		127	Gac/Aac	2/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.289138120037568	2		309	472	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895619	28895619	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1175540976	NA	P-0023786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	81	273	0	ENST00000282397.4:c.3155A>G	p.Asp1052Gly	p.D1052G	ENST00000282397	NM_002019.4	1052	gAt/gGt	23/30	0.141599488122078	3	FACETS	0.754	0.668	0.846			1	INDETERMINATE	2	TRUE	NA	0.289138120037568	3		273	425	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955499	48955499	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	31	245	0	ENST00000267163.4:c.1615G>T	p.Glu539Ter	p.E539*	ENST00000267163	NM_000321.2	539	Gaa/Taa	17/27	0.289138120037568	1	FACETS	0.62	0.503	0.751	0.62	0.503	0.751	SUBCLONAL	1	TRUE	0	0.289138120037568	1		245	296	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0023787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	235	748	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.444104958014905	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.444104958014905	2		748	505	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416516	49416516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	284	349	1	ENST00000301067.7:c.16195G>A	p.Val5399Met	p.V5399M	ENST00000301067	NM_003482.3	5399	Gtg/Atg	51/54	0.419971052032505	3	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.444104958014905	3		350	673	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125499138	125499138	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	171	240	0	ENST00000428830.2:c.302del	p.Gly101AlafsTer26	p.G101Afs*26	ENST00000428830	NM_001114121.2	101	Ggc/gc	4/14	0.398528339476132	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	2	0.444104958014905	4		240	519	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896412	28896412	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	60	231	0	ENST00000282397.4:c.3038T>A	p.Leu1013Gln	p.L1013Q	ENST00000282397	NM_002019.4	1013	cTg/cAg	22/30	0.444104958014905	2	FACETS	0.799	0.693	0.914	0.4	0.346	0.457	CLONAL	1	TRUE	0	0.444104958014905	2		231	338	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858410	89858410	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs751071791	NA	P-0023787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	140	420	2	ENST00000389301.3:c.1150G>T	p.Val384Phe	p.V384F	ENST00000389301	NM_000135.2	384	Gtt/Ttt	13/43	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.444104958014905	2		422	608	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211784	2211795	+	protein_altering_variant	In_Frame_Del	DEL	ATACACAAAGAC	ATACACAAAGAC	CTGGAA	novel	NA	P-0023787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	144	376	2	ENST00000398665.3:c.1500_1511delinsCTGGAA	p.Tyr501_Thr504delinsTrpAsn	p.Y501_T504delinsWN	ENST00000398665	NM_032482.2	500	gcATACACAAAGACc/gcCTGGAAc	16/28	0.444104958014905	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.444104958014905	1		378	426	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752756	42752756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	48	388	0	ENST00000222329.4:c.1508G>A	p.Gly503Asp	p.G503D	ENST00000222329	NM_006494.2	503	gGc/gAc	4/4	0.235911992775479	3	FACETS	0.383	0.323	0.45	0.192	0.161	0.225	INDETERMINATE	1	TRUE	1	0.444104958014905	3		388	689	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873311	151873311	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	17	173	0	ENST00000262189.6:c.9227T>A	p.Ile3076Asn	p.I3076N	ENST00000262189	NM_170606.2	3076	aTt/aAt	38/59	0.444104958014905	2	FACETS	0.288	0.215	0.375	0.144	0.107	0.188	SUBCLONAL	1	TRUE	0	0.444104958014905	2		173	266	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003768	45003797	+	inframe_deletion	In_Frame_Del	DEL	TGTGCTCGCGCTACTCTCTCTTTCTGGCCT	TGTGCTCGCGCTACTCTCTCTTTCTGGCCT	-	novel	NA	P-0023787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	68	273	0	ENST00000558401.1:c.24_53del	p.Val9_Leu18del	p.V9_L18del	ENST00000558401	NM_004048.2	8	gcTGTGCTCGCGCTACTCTCTCTTTCTGGCCTg/gcg	1/4	1	2	FACETS	0.917	0.803	1	0.917	0.803	1	CLONAL	1	TRUE	1	0.444104958014905	2		273	334	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641091	23641092	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	A	novel	NA	P-0023787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	140	349	1	ENST00000261584.4:c.2383_2384delinsT	p.Gln795Ter	p.Q795*	ENST00000261584	NM_024675.3	795	CAa/Ta	5/13	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.444104958014905	2		350	602	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	240	896	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.397035479749762	3	FACETS	1	0.986	1	0.762	0.719	0.805	CLONAL	2	TRUE	0	0.497888036923852	3		898	527	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577518	7577518	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519995	NA	P-0023790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	147	426	0	ENST00000269305.4:c.763A>T	p.Ile255Phe	p.I255F	ENST00000269305	NM_001126112.2	255	Atc/Ttc	7/11	0.497888036923852	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.497888036923852	1		426	391	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211355	36211357	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs201152143	NA	P-0023790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	93	315	5	ENST00000222270.7:c.1117_1119del	p.Glu373del	p.E373del	ENST00000222270	NM_014727.1	369	aAAGaa/aaa	3/37	0.135122938995452	4	FACETS	0.973	0.867	1	0.243	0.216	0.272	INDETERMINATE	1	TRUE	0	0.497888036923852	4		320	575	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880287	155880287	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748634085	NA	P-0023790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	63	278	0	ENST00000368323.3:c.117G>A	p.Met39Ile	p.M39I	ENST00000368323	NM_006912.5	39	atG/atA	3/6	0.251255711069319	3	FACETS	0.742	0.644	0.848	0.371	0.322	0.424	INDETERMINATE	1	TRUE	1	0.497888036923852	3		278	426	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527419	137527420	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAT	novel	NA	P-0023790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	29	184	0	ENST00000367739.4:c.224_226dup	p.Asp75dup	p.D75dup	ENST00000367739	NM_000416.2	75	gcc/gATGcc	3/7	0.497888036923852	1	FACETS	0.409	0.33	0.497	0.409	0.33	0.497	SUBCLONAL	1	TRUE	0	0.497888036923852	1		184	214	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502437	186502437	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	57	206	0	ENST00000323963.5:c.160G>C	p.Glu54Gln	p.E54Q	ENST00000323963		54	Gag/Cag	3/11	0.523891403588975	3	FACETS	0.915	0.791	1	0.458	0.395	0.525	CLONAL	1	TRUE	1	0.523891403588975	3		206	300	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0023791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	117	954	2	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.523891403588975	3	FACETS	0.805	0.734	0.878	0.805	0.734	0.878	CLONAL	2	TRUE	1	0.523891403588975	3		956	350	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805730	46805730	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1390422355	NA	P-0023791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	113	325	2	ENST00000290295.7:c.226G>T	p.Ala76Ser	p.A76S	ENST00000290295	NM_006361.5	76	Gct/Tct	1/2	0.487496527634078	3	FACETS	0.983	0.899	1	0.983	0.899	1	CLONAL	2	TRUE	1	0.523891403588975	3		327	277	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65348960	65348960	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs762318572	NA	P-0023791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	61	126	0	ENST00000342505.4:c.205C>T	p.Arg69Cys	p.R69C	ENST00000342505	NM_002227.2	69	Cgt/Tgt	3/25	0.523891403588975	3	FACETS	0.936	0.827	1	0.936	0.827	1	CLONAL	2	TRUE	1	0.523891403588975	3		126	157	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398228	25398228	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	59	341	0	ENST00000311936.3:c.91G>T	p.Glu31Ter	p.E31*	ENST00000311936	NM_004985.3	31	Gaa/Taa	2/5	0.523891403588975	3	FACETS	0.841	0.728	0.963	0.42	0.364	0.482	CLONAL	1	TRUE	1	0.523891403588975	3		341	338	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073487	8073487	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0023791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	26	321	0	ENST00000377482.5:c.1172C>G	p.Ser391Ter	p.S391*	ENST00000377482	NM_018948.3	391	tCa/tGa	4/4	0.438429365702331	1	FACETS	0.374	0.298	0.459	0.374	0.298	0.459	SUBCLONAL	1	TRUE	0	0.523891403588975	1		321	196	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436536	110436536	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	43	427	0	ENST00000375856.3:c.1865A>T	p.Lys622Met	p.K622M	ENST00000375856	NM_003749.2	622	aAg/aTg	1/2	0.491222849935208	3	FACETS	0.571	0.479	0.672			1	SUBCLONAL	1	TRUE	NA	0.523891403588975	3		427	363	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602268	10602268	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	122	359	0	ENST00000171111.5:c.1310A>G	p.His437Arg	p.H437R	ENST00000171111	NM_203500.1	437	cAc/cGc	3/6	0.479887375982103	2	FACETS	0.931	0.86	1	0.931	0.86	1	CLONAL	2	TRUE	0	0.523891403588975	2		359	250	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169491	11169510	+	frameshift_variant	Frame_Shift_Del	DEL	AGCCTCAACGACCTAGAGAA	AGCCTCAACGACCTAGAGAA	-	novel	NA	P-0023791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	116	379	0	ENST00000358026.2:c.4657_4676del	p.Ser1553GlyfsTer21	p.S1553Gfs*21	ENST00000358026	NM_001128849.1	1553	AGCCTCAACGACCTAGAGAAg/g	33/36	0.479887375982103	2	FACETS	0.852	0.782	0.922	0.852	0.782	0.922	CLONAL	2	TRUE	0	0.523891403588975	2		379	260	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39725906	39725906	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	17	252	0	ENST00000361337.2:c.777C>G	p.Phe259Leu	p.F259L	ENST00000361337	NM_003286.2	259	ttC/ttG	10/21	0.479887375982103	2	FACETS	0.252	0.188	0.327	0.126	0.094	0.164	SUBCLONAL	1	TRUE	0	0.523891403588975	2		252	258	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050691	30050691	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	117	277	0	ENST00000338641.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000338641	NM_000268.3	165	Caa/Taa	5/16	0.364211991639914	3	FACETS	0.908	0.842	0.973	0.908	0.842	0.973	CLONAL	3	TRUE	0	0.523891403588975	3		277	207	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526312	31526312	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	160	469	0	ENST00000344624.3:c.728G>C	p.Arg243Thr	p.R243T	ENST00000344624		243	aGg/aCg	2/33	0.523891403588975	3	FACETS	0.862	0.798	0.928	0.862	0.798	0.928	CLONAL	2	TRUE	1	0.523891403588975	3		469	447	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517812	176517812	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	100	341	1	ENST00000292408.4:c.422G>T	p.Ser141Ile	p.S141I	ENST00000292408	NM_213647.1	141	aGt/aTt	4/18	0.523891403588975	5	FACETS	1	0.98	1	0.47	0.421	0.521	CLONAL	1	TRUE	2	0.523891403588975	5		342	484	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170367	32170367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	110	302	0	ENST00000375023.3:c.3241G>A	p.Gly1081Ser	p.G1081S	ENST00000375023	NM_004557.3	1081	Ggc/Agc	21/30	0.523891403588975	4	FACETS	0.967	0.879	1	0.967	0.879	1	CLONAL	2	TRUE	2	0.523891403588975	4		302	331	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923372	36923372	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	129	333	0	ENST00000358127.4:c.890A>G	p.Gln297Arg	p.Q297R	ENST00000358127	NM_001280556.1	297	cAg/cGg	7/10	0.523891403588975	3	FACETS	0.919	0.845	0.995	0.919	0.845	0.995	CLONAL	2	TRUE	1	0.523891403588975	3		333	338	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042245	42042245	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	36	281	0	ENST00000219905.7:c.6441del	p.Met2148TrpfsTer31	p.M2148Wfs*31	ENST00000219905	NM_001164273.1	2147	gTt/gt	17/24	0.375756258059496	1	FACETS	0.884	0.736	1	0.884	0.736	1	CLONAL	1	TRUE	0	0.375756258059496	1		281	176	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578404	+	missense_variant	Missense_Mutation	DNP	CA	CA	AC	novel	NA	P-0023792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	27	375	0	ENST00000269305.4:c.526_527delinsGT	p.Cys176Val	p.C176V	ENST00000269305	NM_001126112.2	176	TGc/GTc	5/11	0.171052848260521	1	FACETS	0.456	0.364	0.56	0.456	0.364	0.56	INDETERMINATE	1	TRUE	0	0.375756258059496	1		375	256	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431019	181431019	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0023792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	21	383	1	ENST00000325404.1:c.871A>T	p.Arg291Ter	p.R291*	ENST00000325404	NM_003106.3	291	Aga/Tga	1/1	0.375756258059496	2	FACETS	0.406	0.313	0.515	0.203	0.156	0.258	SUBCLONAL	1	TRUE	0	0.375756258059496	2		384	275	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0023795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	22	976	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.858	0.665	1	0.858	0.665	1	CLONAL	1	TRUE	1	0.15	2		976	342	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0023795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	24	577	1	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.15	2		578	284	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581201	48581201	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	16	256	1	ENST00000342988.3:c.505C>T	p.Gln169Ter	p.Q169*	ENST00000342988	NM_005359.5	169	Cag/Tag	5/12	1	2	FACETS	0.84	0.621	1	0.84	0.621	1	CLONAL	1	TRUE	1	0.15	2		257	254	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115973	8115974	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0023797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	12	242	0	ENST00000346208.3:c.1319_1320del	p.Thr440SerfsTer66	p.T440Sfs*66	ENST00000346208		440	aCC/a	6/6	1	2	FACETS	0.212	0.149	0.289	0.212	0.149	0.289	SUBCLONAL	1	TRUE	1	0.59	2		242	192	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336157	73336157	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	12	225	0	ENST00000377767.4:c.2246T>C	p.Met749Thr	p.M749T	ENST00000377767	NM_014953.3	749	aTg/aCg	17/21	1	2	FACETS	0.176	0.123	0.241	0.176	0.123	0.241	SUBCLONAL	1	TRUE	1	0.59	2		225	231	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570416	95570416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	17	234	0	ENST00000393063.1:c.3317C>T	p.Ser1106Phe	p.S1106F	ENST00000393063	NM_030621.3	1106	tCt/tTt	22/28	1	2	FACETS	0.232	0.173	0.302	0.232	0.173	0.302	SUBCLONAL	1	TRUE	1	0.59	2		234	248	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0023798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	41	724	2	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	0.215122730796807	2		726	317	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916861	178916861	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1560137208	NA	P-0023798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	24	364	0	ENST00000263967.3:c.248T>C	p.Phe83Ser	p.F83S	ENST00000263967	NM_006218.2	83	tTt/tCt	2/21	1	2	FACETS	0.689	0.54	0.86	0.689	0.54	0.86	SUBCLONAL	1	TRUE	1	0.215122730796807	2		364	324	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523600	106523600	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	21	175	0	ENST00000359195.3:c.2752G>A	p.Glu918Lys	p.E918K	ENST00000359195	NM_002649.2	918	Gaa/Aaa	8/11	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.215122730796807	2		175	166	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519895	NA	P-0023798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	34	298	0	ENST00000281708.4:c.1394G>T	p.Arg465Leu	p.R465L	ENST00000281708	NM_033632.3	465	cGt/cTt	9/12	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.215122730796807	2		298	260	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542576	187542576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	25	288	1	ENST00000441802.2:c.5164C>T	p.Gln1722Ter	p.Q1722*	ENST00000441802	NM_005245.3	1722	Cag/Tag	10/27	1	2	FACETS	0.904	0.715	1	0.904	0.715	1	CLONAL	1	TRUE	1	0.215122730796807	2		289	257	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007833	45007834	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	20	276	0	ENST00000558401.1:c.285dup	p.Asp96ArgfsTer2	p.D96Rfs*2	ENST00000558401	NM_004048.2	94	gaa/gAaa	2/4	0.215122730796807	1	FACETS	0.817	0.628	1	0.817	0.628	1	CLONAL	1	TRUE	0	0.215122730796807	1		276	203	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40367020	40367020	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	25	367	0	ENST00000397332.2:c.177C>G	p.Ile59Met	p.I59M	ENST00000397332	NM_001033082.2	59	atC/atG	2/3	0.215122730796807	1	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	0	0.215122730796807	1		367	174	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058732	42058732	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	14	150	0	ENST00000219905.7:c.8452G>T	p.Asp2818Tyr	p.D2818Y	ENST00000219905	NM_001164273.1	2818	Gat/Tat	24/24	0.215122730796807	1	FACETS	1	0.804	1	1	0.804	1	CLONAL	1	TRUE	0	0.215122730796807	1		150	103	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035909	47035909	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1227774964	NA	P-0023798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	35	343	0	ENST00000377604.3:c.587A>G	p.Asn196Ser	p.N196S	ENST00000377604	NM_001204468.1	196	aAc/aGc	7/24	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.215122730796807	2		343	259	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0023799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	13	399	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.376	0.268	0.506	0.376	0.268	0.506	SUBCLONAL	1	TRUE	1	0.378154524557038	2		399	183	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582117	189582117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	16	283	0	ENST00000264731.3:c.676C>T	p.Arg226Cys	p.R226C	ENST00000264731	NM_003722.4	226	Cgc/Tgc	5/14	1	2	FACETS	0.354	0.262	0.464	0.354	0.262	0.464	SUBCLONAL	1	TRUE	1	0.378154524557038	2		283	239	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0023814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	121	515	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.689796220114838	3	FACETS	0.959	0.885	1	0.959	0.885	1	CLONAL	2	TRUE	1	0.689796220114838	3		515	246	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160677	56160678	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	159	262	0	ENST00000399503.3:c.953dup	p.Leu318PhefsTer8	p.L318Ffs*8	ENST00000399503	NM_005921.1	317	-/T	4/20	0.667965438525513	4	FACETS	0.969	0.899	1	0.969	0.899	1	CLONAL	2	TRUE	2	0.689796220114838	4		262	402	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168719	56168720	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	146	207	0	ENST00000399503.3:c.1574dup	p.Gln526AlafsTer15	p.Q526Afs*15	ENST00000399503	NM_005921.1	525	cag/cAag	9/20	0.667965438525513	4	FACETS	0.964	0.891	1	0.964	0.891	1	CLONAL	2	TRUE	2	0.689796220114838	4		207	371	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56912105	56912105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	102	324	0	ENST00000519728.1:c.1333C>T	p.Pro445Ser	p.P445S	ENST00000519728	NM_002350.3	445	Cca/Tca	12/13	0.689796220114838	3	FACETS	1	0.941	1	0.53	0.478	0.585	CLONAL	1	TRUE	1	0.689796220114838	3		324	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0023815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	40	649	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.202421966187425	1	FACETS	0.914	0.761	1	0.914	0.761	1	CLONAL	1	TRUE	0	0.21681925713285	1		649	360	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322774	30322774	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	23	214	0	ENST00000322652.5:c.1787C>A	p.Thr596Asn	p.T596N	ENST00000322652	NM_015355.2	596	aCc/aAc	14/16	1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	1	0.21681925713285	2		214	200	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801727	3801727	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs777015995	NA	P-0023815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	50	274	0	ENST00000262367.5:c.3779C>T	p.Thr1260Met	p.T1260M	ENST00000262367	NM_004380.2	1260	aCg/aTg	20/31	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.21681925713285	2		274	353	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0023819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	135	612	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.87	0.801	0.939	0.87	0.801	0.939	CLONAL	1	TRUE	1	0.902637223578952	2		612	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0023819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	293	394	1	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.902637223578952	2		395	602	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039133	49039133	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0023819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	41	129	1	ENST00000267163.4:c.2212-1G>C		p.X738_splice	ENST00000267163	NM_000321.2	738			0.902637223578952	1	FACETS	0.959	0.871	1	0.959	0.871	1	CLONAL	1	TRUE	0	0.902637223578952	1		130	52	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579329	7579329	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs121912658	NA	P-0023819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	261	388	0	ENST00000269305.4:c.358A>T	p.Lys120Ter	p.K120*	ENST00000269305	NM_001126112.2	120	Aag/Tag	4/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.902637223578952	2		388	534	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789597	3789597	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	149	250	0	ENST00000262367.5:c.4262G>T	p.Cys1421Phe	p.C1421F	ENST00000262367	NM_004380.2	1421	tGc/tTc	25/31	0.49574952146914	1	FACETS	0.686	0.642	0.73	0.686	0.642	0.73	INDETERMINATE	1	TRUE	0	0.902637223578952	1		250	264	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440919	56440919	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	256	383	0	ENST00000407977.2:c.418G>C	p.Asp140His	p.D140H	ENST00000407977		140	Gac/Cac	4/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.902637223578952	2		383	547	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533686	63533686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1486551074	NA	P-0023819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	152	719	0	ENST00000307078.5:c.1468G>A	p.Ala490Thr	p.A490T	ENST00000307078	NM_004655.3	490	Gcg/Acg	6/11	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.902637223578952	2		719	334	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206943225	206943225	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	197	267	0	ENST00000423557.1:c.393del	p.Cys132ValfsTer11	p.C132Vfs*11	ENST00000423557	NM_000572.2	131	ccC/cc	4/5	0.499151388438238	2	FACETS	1	0.994	1	0.735	0.698	0.771	INDETERMINATE	1	TRUE	0	0.902637223578952	2		267	297	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573220	64573220	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	259	525	0	ENST00000312049.6:c.1072G>T	p.Glu358Ter	p.E358*	ENST00000312049	NM_130799.2	358	Gag/Tag	8/10	1	2	FACETS	0.908	0.857	0.96	0.908	0.857	0.96	CLONAL	1	TRUE	1	0.902637223578952	2		525	632	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041600	42041600	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	156	413	1	ENST00000219905.7:c.5795G>T	p.Gly1932Val	p.G1932V	ENST00000219905	NM_001164273.1	1932	gGt/gTt	17/24	0.902637223578952	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.902637223578952	1		414	186	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36014504	36014504	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	189	386	0	ENST00000358208.4:c.277T>C	p.Tyr93His	p.Y93H	ENST00000358208		93	Tat/Cat	3/12	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.902637223578952	2		386	407	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160243	22160243	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	93	220	0	ENST00000215832.6:c.388C>G	p.Leu130Val	p.L130V	ENST00000215832	NM_002745.4	130	Ctc/Gtc	3/9	0.556211670055741	1	FACETS	0.595	0.543	0.647	0.595	0.543	0.647	SUBCLONAL	1	TRUE	0	0.902637223578952	1		220	190	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151576	55151576	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	107	369	0	ENST00000257290.5:c.2362G>C	p.Glu788Gln	p.E788Q	ENST00000257290	NM_006206.4	788	Gaa/Caa	17/23	1	2	FACETS	0.856	0.78	0.933	0.856	0.78	0.933	CLONAL	1	TRUE	1	0.902637223578952	2		369	277	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534425	187534425	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	159	254	0	ENST00000441802.2:c.9301G>C	p.Asp3101His	p.D3101H	ENST00000441802	NM_005245.3	3101	Gat/Cat	13/27	0.902637223578952	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.902637223578952	1		254	172	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790641	89790641	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1056804363	NA	P-0023819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	390	450	1	ENST00000336032.3:c.28G>C	p.Glu10Gln	p.E10Q	ENST00000336032	NM_006813.2	10	Gag/Cag	1/2	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.902637223578952	2		451	752	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681075	117681075	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	91	388	0	ENST00000368508.3:c.3545G>C	p.Arg1182Thr	p.R1182T	ENST00000368508	NM_002944.2	1182	aGa/aCa	23/43	1	2	FACETS	0.947	0.859	1	0.947	0.859	1	CLONAL	1	TRUE	1	0.902637223578952	2		388	213	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163845	152163845	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs748649052	NA	P-0023819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	137	325	0	ENST00000206249.3:c.566A>G	p.Asn189Ser	p.N189S	ENST00000206249	NM_000125.3	189	aAt/aGt	2/8	1	2	FACETS	0.949	0.876	1	0.949	0.876	1	CLONAL	1	TRUE	1	0.902637223578952	2		325	320	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851602	128851602	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	211	425	1	ENST00000249373.3:c.1927G>T	p.Ala643Ser	p.A643S	ENST00000249373	NM_005631.4	643	Gca/Tca	11/12	1	2	FACETS	0.917	0.86	0.974	0.917	0.86	0.974	CLONAL	1	TRUE	1	0.902637223578952	2		426	510	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0023822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	31	328	0	ENST00000311936.3:c.180_181delinsAA	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggAAaa	3/5	1	2	FACETS	0.922	0.755	1	0.922	0.755	1	CLONAL	1	TRUE	1	0.41	2		328	164	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654721	67654721	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0023822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	47	303	0	ENST00000264010.4:c.1207+1G>T		p.X403_splice	ENST00000264010	NM_006565.3	403			1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.41	2		303	189	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0023823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	106	399	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.56626507301884	2		399	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0023823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	105	919	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.804	0.725	0.888	0.804	0.725	0.888	CLONAL	1	TRUE	1	0.56626507301884	2		920	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579366	7579369	+	frameshift_variant	Frame_Shift_Del	DEL	GTAG	GTAG	-	novel	NA	P-0023823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	31	475	0	ENST00000269305.4:c.318_321del	p.Ser106ArgfsTer16	p.S106Rfs*16	ENST00000269305	NM_001126112.2	106	agCTAC/ag	4/11	1	2	FACETS	0.205	0.165	0.251	0.205	0.165	0.251	SUBCLONAL	1	TRUE	1	0.56626507301884	2		475	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519989	NA	P-0023823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	152	449	0	ENST00000269305.4:c.730G>C	p.Gly244Arg	p.G244R	ENST00000269305	NM_001126112.2	244	Ggc/Cgc	7/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.56626507301884	2		449	452	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653844	89653844	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	21	330	0	ENST00000371953.3:c.142A>T	p.Asn48Tyr	p.N48Y	ENST00000371953	NM_000314.4	48	Aac/Tac	2/9	0.56626507301884	1	FACETS	0.673	0.532	0.828	0.673	0.532	0.828	SUBCLONAL	1	TRUE	0	0.56626507301884	1		330	79	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591271	67591271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771674865	NA	P-0023823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	34	273	0	ENST00000274335.5:c.1769G>A	p.Arg590Gln	p.R590Q	ENST00000274335		590	cGg/cAg	13/15	1	2	FACETS	0.834	0.693	0.987	0.834	0.693	0.987	CLONAL	1	TRUE	1	0.56626507301884	2		273	144	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953984	131953984	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	30	220	1	ENST00000265335.6:c.3387C>A	p.Asp1129Glu	p.D1129E	ENST00000265335		1129	gaC/gaA	21/25	1	2	FACETS	0.913	0.751	1	0.913	0.751	1	CLONAL	1	TRUE	1	0.56626507301884	2		221	116	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27228210	27228210	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	37	333	0	ENST00000380036.4:c.3207T>G	p.Asp1069Glu	p.D1069E	ENST00000380036	NM_000459.3	1069	gaT/gaG	22/23	1	2	FACETS	0.706	0.589	0.834	0.706	0.589	0.834	SUBCLONAL	1	TRUE	1	0.56626507301884	2		333	185	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0023824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	184	395	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.674620297817428	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.674620297817428	1		395	311	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267440	7267440	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1230564293	NA	P-0023824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	104	279	2	ENST00000302850.5:c.568G>A	p.Ala190Thr	p.A190T	ENST00000302850	NM_000208.2	190	Gcg/Acg	2/22	0.674620297817428	3	FACETS	0.922	0.831	1	0.461	0.415	0.509	CLONAL	1	TRUE	1	0.674620297817428	3		281	447	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444575	187444575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761133130	NA	P-0023824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	191	377	0	ENST00000232014.4:c.1652G>A	p.Cys551Tyr	p.C551Y	ENST00000232014	NM_001130845.1	551	tGc/tAc	7/10	0.674620297817428	3	FACETS	1	0.979	1	0.57	0.529	0.612	CLONAL	1	TRUE	1	0.674620297817428	3		377	664	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15838368	15838368	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	101	162	0	ENST00000307771.7:c.866G>T	p.Gly289Val	p.G289V	ENST00000307771	NM_005089.3	289	gGa/gTa	10/11	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.674620297817428	1		162	135	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786706	3786706	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	82	469	0	ENST00000262367.5:c.4505G>T	p.Trp1502Leu	p.W1502L	ENST00000262367	NM_004380.2	1502	tGg/tTg	27/31	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.500498930290848	2		469	314	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0023825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	19	366	1	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.360672992243292	1	FACETS	0.401	0.307	0.509	0.401	0.307	0.509	SUBCLONAL	1	TRUE	0	0.500498930290848	1		367	142	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0023825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	82	345	0	ENST00000269305.4:c.560-1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.493573216519464	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.500498930290848	1		345	192	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70967599	70967599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	54	364	0	ENST00000276594.2:c.1424G>A	p.Ser475Asn	p.S475N	ENST00000276594	NM_024504.3	475	aGc/aAc	7/8	0.432417348673976	3	FACETS	0.911	0.784	1	0.456	0.392	0.525	CLONAL	1	TRUE	1	0.500498930290848	3		364	296	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862709	9862709	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	43	204	0	ENST00000330684.3:c.2594G>T	p.Arg865Met	p.R865M	ENST00000330684	NM_001134407.1	865	aGg/aTg	12/13	1	2	FACETS	0.982	0.834	1	0.982	0.834	1	CLONAL	1	TRUE	1	0.500498930290848	2		204	175	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248434	212248434	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	43	201	0	ENST00000342788.4:c.3833T>G	p.Val1278Gly	p.V1278G	ENST00000342788	NM_005235.2	1278	gTg/gGg	28/28	0.500498930290848	1	FACETS	0.901	0.769	1	0.901	0.769	1	CLONAL	1	TRUE	0	0.500498930290848	1		201	143	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1953881	1953881	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	17	518	0	ENST00000382891.5:c.2060G>T	p.Cys687Phe	p.C687F	ENST00000382891	NM_133335.3	687	tGc/tTc	11/22	NA	2	FACETS	0.218	0.163	0.285			1	INDETERMINATE	1	TRUE	NA	0.500498930290848	2		518	311	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955557	55955557	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	21	394	0	ENST00000263923.4:c.3388T>C	p.Tyr1130His	p.Y1130H	ENST00000263923	NM_002253.2	1130	Tat/Cat	25/30	0.19389553618518	1	FACETS	0.368	0.285	0.463	0.368	0.285	0.463	INDETERMINATE	1	TRUE	0	0.500498930290848	1		394	171	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270149	66270149	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	46	239	0	ENST00000273854.3:c.1733C>G	p.Ser578Cys	p.S578C	ENST00000273854	NM_004439.5	578	tCt/tGt	8/18	0.19389553618518	1	FACETS	0.774	0.662	0.894	0.774	0.662	0.894	INDETERMINATE	1	TRUE	0	0.500498930290848	1		239	178	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176618982	176618982	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	41	349	0	ENST00000439151.2:c.1025G>T	p.Cys342Phe	p.C342F	ENST00000439151	NM_022455.4	342	tGt/tTt	3/23	1	2	FACETS	0.625	0.524	0.736	0.625	0.524	0.736	SUBCLONAL	1	TRUE	1	0.500498930290848	2		349	262	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371000	55371000	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	64	355	0	ENST00000297316.4:c.302T>C	p.Met101Thr	p.M101T	ENST00000297316	NM_022454.3	101	aTg/aCg	1/2	0.432417348673976	3	FACETS	1	0.887	1	0.509	0.444	0.579	CLONAL	1	TRUE	1	0.500498930290848	3		355	314	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094798	2094798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370228590	NA	P-0023827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	65	330	0	ENST00000219066.1:c.382C>T	p.Arg128Cys	p.R128C	ENST00000219066	NM_002528.5	128	Cgc/Tgc	3/6	0.493642540553447	4	FACETS	0.89	0.774	1	0.297	0.258	0.339	CLONAL	1	TRUE	1	0.493642540553447	4		330	442	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348115	89348115	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	104	467	0	ENST00000301030.4:c.4835G>T	p.Arg1612Met	p.R1612M	ENST00000301030	NM_001256183.1	1612	aGg/aTg	9/13	0.474795867054201	2	FACETS	0.88	0.792	0.972	0.44	0.396	0.486	CLONAL	1	TRUE	0	0.493642540553447	2		467	479	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793085	42793086	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	88	371	1	ENST00000575354.2:c.978dup	p.Asp327ArgfsTer80	p.D327Rfs*80	ENST00000575354	NM_015125.3	326	tca/tcAa	7/20	0.493642540553447	1	FACETS	0.973	0.874	1	0.973	0.874	1	CLONAL	1	TRUE	0	0.493642540553447	1		372	276	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206641	27206641	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs778454536	NA	P-0023827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	110	320	0	ENST00000380036.4:c.2426A>G	p.Asn809Ser	p.N809S	ENST00000380036	NM_000459.3	809	aAc/aGc	15/23	0.493642540553447	4	FACETS	1	0.984	1	0.492	0.445	0.542	CLONAL	1	TRUE	1	0.493642540553447	4		320	451	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97863991	97863991	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	rs750866823	NA	P-0023827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	131	265	0	ENST00000289081.3:c.1675T>C	p.Ter559GlnextTer11	p.*559Qext*11	ENST00000289081	NM_000136.2	559	Tag/Cag	15/15	0.447350682494083	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	1	0.493642540553447	3		265	320	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0023832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	54	515	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.281280742534805	4	FACETS	1	0.907	1	0.755	0.681	0.826	INDETERMINATE	3	TRUE	0	0.741413532680808	4		515	84	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0023832-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	23	515	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.248677874194777	2	FACETS	0.979	0.793	1	1	0.935	1	CLONAL	3	TRUE	0	0.248677874194777	2		515	63	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160759	56160759	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023832-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	22	236	0	ENST00000399503.3:c.1033C>T	p.Gln345Ter	p.Q345*	ENST00000399503	NM_005921.1	345	Cag/Tag	4/20	0.248677874194777	3	FACETS	0.861	0.686	1	1	0.909	1	CLONAL	3	TRUE	1	0.248677874194777	3		236	77	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161199	56161201	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	novel	NA	P-0023832-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	32	333	0	ENST00000399503.3:c.1070_1072del	p.His357del	p.H357del	ENST00000399503	NM_005921.1	356	atTCAt/att	5/20	0.248677874194777	3	FACETS	1	0.864	1	1	0.864	1	CLONAL	2	TRUE	1	0.248677874194777	3		333	137	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0023835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	142	515	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	0.763407148927309	2		515	344	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	148	282	1	ENST00000206249.3:c.1607T>A	p.Leu536His	p.L536H	ENST00000206249	NM_000125.3	536	cTc/cAc	8/8	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.763407148927309	2		283	376	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061191	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs879499034	NA	P-0023835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	135	239	0	ENST00000250448.2:c.798C>A	p.Phe266Leu	p.F266L	ENST00000250448	NM_004496.3	266	ttC/ttA	2/2	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.763407148927309	2		239	331	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938922	178938922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	109	291	0	ENST00000263967.3:c.2164G>A	p.Glu722Lys	p.E722K	ENST00000263967	NM_006218.2	722	Gag/Aag	14/21	1	2	FACETS	0.818	0.743	0.896	0.818	0.743	0.896	CLONAL	1	TRUE	1	0.763407148927309	2		291	349	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317627	163317627	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	134	332	0	ENST00000271452.3:c.1023C>G	p.Phe341Leu	p.F341L	ENST00000271452	NM_145697.2	341	ttC/ttG	12/14	1	2	FACETS	0.917	0.842	0.993	0.917	0.842	0.993	CLONAL	1	TRUE	1	0.763407148927309	2		332	383	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849649	68849649	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	133	287	0	ENST00000261769.5:c.1552G>T	p.Glu518Ter	p.E518*	ENST00000261769	NM_004360.3	518	Gaa/Taa	10/16	1	2	FACETS	0.955	0.877	1	0.955	0.877	1	CLONAL	1	TRUE	1	0.763407148927309	2		287	365	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125593	47125593	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	94	211	0	ENST00000409792.3:c.5677del	p.Ile1893SerfsTer8	p.I1893Sfs*8	ENST00000409792	NM_014159.6	1893	Atc/tc	12/21	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.763407148927309	2		211	246	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857311	68857312	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	52	209	1	ENST00000261769.5:c.1947dup	p.Ile650TyrfsTer13	p.I650Yfs*13	ENST00000261769	NM_004360.3	649	tct/tcTt	13/16	0.582924310470183	1	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	0	0.582924310470183	1		210	121	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246078851	246078851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61762672	NA	P-0023836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	155	387	0	ENST00000388985.4:c.794G>A	p.Arg265His	p.R265H	ENST00000388985		265	cGt/cAt	8/12	0.328404972740755	6	FACETS	0.897	0.824	0.973	0.449	0.412	0.487	INDETERMINATE	2	TRUE	2	0.582924310470183	6		387	642	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685309	89685310	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0023836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	113	296	0	ENST00000371953.3:c.205_206dup	p.Asn69LysfsTer31	p.N69Kfs*31	ENST00000371953	NM_000314.4	68	-/AA	3/9	0.582223078532143	2	FACETS	0.877	0.809	0.945	0.877	0.809	0.945	CLONAL	2	TRUE	0	0.582924310470183	2		296	221	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0023838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	113	748	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.221365815288023	1	FACETS	1	0.977	1	1	0.977	1	INDETERMINATE	1	TRUE	0	0.490321453564806	1		748	288	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325126	123325126	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374996878	NA	P-0023838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	53	471	0	ENST00000358487.5:c.202G>A	p.Ala68Thr	p.A68T	ENST00000358487	NM_000141.4	68	Gcc/Acc	3/18	0.238573365848109	3	FACETS	0.541	0.461	0.627	0.27	0.23	0.314	INDETERMINATE	1	TRUE	1	0.490321453564806	3		471	498	SUCCESS
ATR	545	MSKCC	GRCh37	3	142297488	142297488	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	42	312	0	ENST00000350721.4:c.59G>A	p.Ser20Asn	p.S20N	ENST00000350721	NM_001184.3	20	aGt/aAt	1/47	1	2	FACETS	0.51	0.427	0.601	0.51	0.427	0.601	SUBCLONAL	1	TRUE	1	0.490321453564806	2		312	336	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518044	8518044	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	37	332	0	ENST00000356435.5:c.1347A>T	p.Gln449His	p.Q449H	ENST00000356435		449	caA/caT	10/35	1	2	FACETS	0.423	0.352	0.501	0.423	0.352	0.501	SUBCLONAL	1	TRUE	1	0.853467427353452	2		332	205	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115911	8115912	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	133	448	0	ENST00000346208.3:c.1258dup	p.Thr420AsnfsTer87	p.T420Nfs*87	ENST00000346208		419	-/A	6/6	0.278800146273835	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.853467427353452	0		448	382	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575476	64575476	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	125	493	0	ENST00000312049.6:c.541C>G	p.His181Asp	p.H181D	ENST00000312049	NM_130799.2	181	Cat/Gat	3/10	0.832830010475888	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.853467427353452	1		493	163	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962595	100962595	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	28	401	0	ENST00000325455.5:c.1802A>G	p.Tyr601Cys	p.Y601C	ENST00000325455	NM_001202474.3	601	tAc/tGc	3/8	0.853467427353452	1	FACETS	0.164	0.131	0.2	0.164	0.131	0.2	SUBCLONAL	1	TRUE	0	0.853467427353452	1		401	230	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0023843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	95	521	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.29293620131208	2	FACETS	0.907	0.815	1	0.907	0.815	1	CLONAL	2	TRUE	0	0.29	2		521	361	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	49	482	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.782	0.664	0.912	0.782	0.664	0.912	CLONAL	1	TRUE	1	0.29	2		482	432	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266792	198266792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	62	333	0	ENST00000335508.6:c.2140G>A	p.Glu714Lys	p.E714K	ENST00000335508	NM_012433.2	714	Gaa/Aaa	15/25	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.29	2		333	424	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591132	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	rs1057519842	NA	P-0023844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	32	185	0	ENST00000274335.5:c.1727_1729del	p.Thr576del	p.T576del	ENST00000274335		575	aaGACg/aag	12/15	0.222863272841597	4	FACETS	0.896	0.734	1	0.896	0.734	1	CLONAL	2	TRUE	2	0.222863272841597	4		185	196	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0023846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	112	967	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	0.989	1	CLONAL	2	TRUE	1	0.224856339483582	2		967	459	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0023846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	14	303	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.75	0.544	0.997	0.75	0.544	0.997	CLONAL	1	TRUE	1	0.224856339483582	2		303	166	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670847	134670847	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	12	192	0	ENST00000398015.3:c.758G>T	p.Cys253Phe	p.C253F	ENST00000398015	NM_004441.4	253	tGc/tTc	3/16	1	2	FACETS	0.721	0.509	0.98	0.721	0.509	0.98	CLONAL	1	TRUE	1	0.224856339483582	2		192	148	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375966	8375966	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	22	182	0	ENST00000356435.5:c.4631C>T	p.Pro1544Leu	p.P1544L	ENST00000356435		1544	cCc/cTc	28/35	0.181413972381859	3	FACETS	0.864	0.671	1	0.432	0.335	0.543	CLONAL	1	TRUE	1	0.224856339483582	3		182	252	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030477	49030477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	24	256	0	ENST00000267163.4:c.1952del	p.Tyr651LeufsTer7	p.Y651Lfs*7	ENST00000267163	NM_000321.2	651	tAt/tt	19/27	1	2	FACETS	0.649	0.509	0.81	0.649	0.509	0.81	SUBCLONAL	1	TRUE	1	0.224856339483582	2		256	329	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610059	81610059	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	25	230	0	ENST00000298171.2:c.1657G>C	p.Ala553Pro	p.A553P	ENST00000298171	NM_000369.2	553	Gcc/Ccc	10/10	1	2	FACETS	0.967	0.765	1	0.967	0.765	1	CLONAL	1	TRUE	1	0.224856339483582	2		230	230	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222917	36222917	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0023846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	48	459	0	ENST00000222270.7:c.5546C>G	p.Ser1849Ter	p.S1849*	ENST00000222270	NM_014727.1	1849	tCa/tGa	27/37	1	2	FACETS	0.995	0.843	1	0.995	0.843	1	CLONAL	1	TRUE	1	0.224856339483582	2		459	429	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528636	89528636	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	17	103	0	ENST00000336596.2:c.2936G>T	p.Gly979Val	p.G979V	ENST00000336596	NM_005233.5	979	gGc/gTc	17/17	1	2	FACETS	0.951	0.714	1	0.951	0.714	1	CLONAL	1	TRUE	1	0.224856339483582	2		103	159	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	89	482	0				ENST00000310581	NM_198253.2	-/1132			0.48696373360416	4	FACETS	0.885	0.802	0.969	1	0.979	1	CLONAL	3	TRUE	2	0.486264054285393	4		482	205	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934573	NA	P-0023853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	268	451	0	ENST00000269305.4:c.722C>A	p.Ser241Tyr	p.S241Y	ENST00000269305	NM_001126112.2	241	tCc/tAc	7/11	0.411445883024061	6	FACETS	0.988	0.943	1	0.824	0.786	0.861	CLONAL	5	TRUE	0	0.486264054285393	6		451	440	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0023853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	140	610	1	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.361865598545223	5	FACETS	0.836	0.77	0.904	0.836	0.77	0.904	CLONAL	3	TRUE	2	0.486264054285393	5		611	397	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486068	29486068	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	76	407	0	ENST00000356175.3:c.245C>G	p.Ser82Cys	p.S82C	ENST00000356175	NM_000267.3	82	tCt/tGt	3/57	0.361865598545223	5	FACETS	1	0.904	1	0.68	0.604	0.76	CLONAL	2	TRUE	2	0.486264054285393	5		407	265	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878177	48878300	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTCGTCAGGTGAGCGAGCAGAGCCGCCGTCGCCTCACGCGGGAAGGGCGCCCCGGGTGTGCGTAGGGCGGGCGCCAAGGCGGCTCGGCGGGGATCCGTCCTCGCCAGGGGCCGGGTCCCGGCG	TCTCGTCAGGTGAGCGAGCAGAGCCGCCGTCGCCTCACGCGGGAAGGGCGCCCCGGGTGTGCGTAGGGCGGGCGCCAAGGCGGCTCGGCGGGGATCCGTCCTCGCCAGGGGCCGGGTCCCGGCG	-	novel	NA	P-0023853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	31	152	0	ENST00000267163.4:c.129_137+115del		p.X43_splice	ENST00000267163	NM_000321.2	43		1/27	0.48696373360416	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	2	TRUE	0	0.486264054285393	2		152	60	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90627550	90627550	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	20	419	0	ENST00000330062.3:c.1307A>G	p.Asp436Gly	p.D436G	ENST00000330062	NM_002168.2	436	gAc/gGc	11/11	1	2	FACETS	0.399	0.306	0.507	0.399	0.306	0.507	SUBCLONAL	1	TRUE	1	0.486264054285393	2		419	206	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856077	68856077	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	165	435	0	ENST00000261769.5:c.1885G>T	p.Glu629Ter	p.E629*	ENST00000261769	NM_004360.3	629	Gaa/Taa	12/16	0.436536259600524	3	FACETS	0.976	0.917	1	0.976	0.917	1	CLONAL	3	TRUE	0	0.486264054285393	3		435	288	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009081	27009081	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1445559127	NA	P-0023853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	43	151	0	ENST00000335756.4:c.17G>A	p.Arg6Gln	p.R6Q	ENST00000335756	NM_001809.3	6	cGg/cAg	1/5	0.271868903017551	3	FACETS	0.894	0.767	1	0.596	0.511	0.684	INDETERMINATE	2	TRUE	0	0.486264054285393	3		151	123	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339045	225339045	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0023853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	147	354	0	ENST00000264414.4:c.2224A>T	p.Lys742Ter	p.K742*	ENST00000264414	NM_003590.4	742	Aag/Tag	16/16	0.48696373360416	3	FACETS	0.928	0.866	0.989	1	0.989	1	CLONAL	3	TRUE	1	0.486264054285393	3		354	270	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815328	32815328	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	75	567	0	ENST00000354258.4:c.2045A>G	p.His682Arg	p.H682R	ENST00000354258	NM_000593.5	682	cAt/cGt	9/11	0.320392258995774	3	FACETS	0.938	0.826	1	0.469	0.413	0.529	CLONAL	1	TRUE	1	0.486264054285393	3		567	409	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0023856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	102	748	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	0.157862439309577	1	FACETS	1	0.93	1	1	0.991	1	CLONAL	4	FALSE	0	0.18812466973247	1		748	240	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	72	316	0	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	0.18812466973247	6	FACETS	0.908	0.801	1			1	CLONAL	4	FALSE	NA	0.18812466973247	6		316	290	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023351	27023351	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	56	266	0	ENST00000324856.7:c.459del	p.Tyr154ThrfsTer78	p.Y154Tfs*78	ENST00000324856	NM_006015.4	153	Ccc/cc	1/20	NA	2	FACETS	1	0.936	1			1	INDETERMINATE	3	FALSE	NA	0.18812466973247	2		266	177	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025534	1025534	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	152	593	0	ENST00000358495.3:c.841A>C	p.Thr281Pro	p.T281P	ENST00000358495	NM_134424.2	281	Acg/Ccg	9/12	1	2	FACETS	0.94	0.872	1	1	0.994	1	CLONAL	5	FALSE	1	0.18812466973247	2		593	344	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39234309	39234309	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397517159	NA	P-0023856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	115	424	0	ENST00000402219.2:c.2536G>A	p.Glu846Lys	p.E846K	ENST00000402219	NM_005633.3	846	Gaa/Aaa	16/23	1	2	FACETS	0.93	0.853	1	1	0.993	1	CLONAL	5	FALSE	1	0.18812466973247	2		424	263	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	41	515	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.653	0.546	0.77	0.653	0.546	0.77	SUBCLONAL	1	TRUE	1	0.424389723658983	2		515	296	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	159	366	1	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.421471552975163	2	FACETS	0.886	0.821	0.952	0.886	0.821	0.952	CLONAL	2	TRUE	0	0.424389723658983	2		367	423	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	37	420	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	0.421471552975163	2	FACETS	0.314	0.258	0.377	0.157	0.129	0.189	SUBCLONAL	1	TRUE	0	0.424389723658983	2		420	555	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	23	484	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	1	2	FACETS	0.2	0.155	0.253	0.2	0.155	0.253	SUBCLONAL	1	TRUE	1	0.424389723658983	2		484	541	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	139	620	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.424389723658983	2		620	504	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	45	211	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.791	0.67	0.924	0.791	0.67	0.924	CLONAL	1	TRUE	1	0.424389723658983	2		211	268	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	47	411	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.719	0.61	0.838	0.719	0.61	0.838	SUBCLONAL	1	TRUE	1	0.424389723658983	2		411	308	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17743002	17743002	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	100	460	0	ENST00000250003.3:c.910G>A	p.Ala304Thr	p.A304T	ENST00000250003	NM_002478.4	304	Gcc/Acc	3/3	1	2	FACETS	0.964	0.865	1	0.964	0.865	1	CLONAL	1	TRUE	1	0.424389723658983	2		460	489	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	70	401	5	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.725	0.634	0.823	0.725	0.634	0.823	SUBCLONAL	1	TRUE	1	0.424389723658983	2		406	455	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	111	757	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.882	0.795	0.974	0.882	0.795	0.974	CLONAL	1	TRUE	1	0.424389723658983	2		757	593	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807543	1807543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	109	571	0	ENST00000260795.2:c.1712G>A	p.Arg571Gln	p.R571Q	ENST00000260795		571	cGg/cAg	12/17	1	2	FACETS	0.838	0.754	0.926	0.838	0.754	0.926	CLONAL	1	TRUE	1	0.424389723658983	2		571	613	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	31	795	1	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.25	0.201	0.305	0.25	0.201	0.305	SUBCLONAL	1	TRUE	1	0.424389723658983	2		796	585	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821890	72821890	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	58	345	0	ENST00000268489.5:c.10285del	p.Arg3429ValfsTer56	p.R3429Vfs*56	ENST00000268489	NM_006885.3	3429	Cgt/gt	10/10	1	2	FACETS	0.729	0.629	0.837	0.729	0.629	0.837	SUBCLONAL	1	TRUE	1	0.424389723658983	2		345	375	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	46	556	2	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.304	0.255	0.358	0.304	0.255	0.358	SUBCLONAL	1	TRUE	1	0.424389723658983	2		558	714	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150030	202150030	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs931648756	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	83	397	0	ENST00000358485.4:c.1471C>T	p.Arg491Ter	p.R491*	ENST00000358485	NM_001080125.1	491	Cga/Tga	8/9	1	2	FACETS	0.749	0.663	0.841	0.749	0.663	0.841	SUBCLONAL	1	TRUE	1	0.424389723658983	2		397	522	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	21	313	0	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.24	0.184	0.306	0.24	0.184	0.306	SUBCLONAL	1	TRUE	1	0.424389723658983	2		313	412	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540532	187540532	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	19	289	0	ENST00000441802.2:c.7208C>T	p.Ala2403Val	p.A2403V	ENST00000441802	NM_005245.3	2403	gCc/gTc	10/27	1	2	FACETS	0.266	0.201	0.342	0.266	0.201	0.342	SUBCLONAL	1	TRUE	1	0.424389723658983	2		289	337	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101117	27101117	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	106	740	0	ENST00000324856.7:c.4403del	p.Pro1468LeufsTer13	p.P1468Lfs*13	ENST00000324856	NM_006015.4	1467	Ccc/cc	18/20	1	2	FACETS	0.851	0.765	0.942	0.851	0.765	0.942	CLONAL	1	TRUE	1	0.424389723658983	2		740	587	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267899	7267899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748177213	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	34	209	0	ENST00000302850.5:c.109G>A	p.Gly37Ser	p.G37S	ENST00000302850	NM_000208.2	37	Ggc/Agc	2/22	1	2	FACETS	0.668	0.549	0.799	0.668	0.549	0.799	SUBCLONAL	1	TRUE	1	0.424389723658983	2		209	240	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259729	16259729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758740337	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	57	334	0	ENST00000375759.3:c.6994C>T	p.Arg2332Cys	p.R2332C	ENST00000375759	NM_015001.2	2332	Cgc/Tgc	11/15	1	2	FACETS	0.655	0.564	0.754	0.655	0.564	0.754	SUBCLONAL	1	TRUE	1	0.424389723658983	2		334	410	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774746	73774746	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	15	185	0	ENST00000254810.4:c.341A>C	p.His114Pro	p.H114P	ENST00000254810	NM_005324.3	114	cAc/cCc	4/4	1	2	FACETS	0.275	0.201	0.364	0.275	0.201	0.364	SUBCLONAL	1	TRUE	1	0.424389723658983	2		185	257	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	42	669	2	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.254	0.211	0.302	0.254	0.211	0.302	SUBCLONAL	1	TRUE	1	0.424389723658983	2		671	780	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647657	3647657	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs774532876	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	97	878	3	ENST00000294008.3:c.1406del	p.Pro469HisfsTer4	p.P469Hfs*4	ENST00000294008	NM_032444.2	469	cCa/ca	7/15	1	2	FACETS	0.623	0.555	0.695	0.623	0.555	0.695	SUBCLONAL	1	TRUE	1	0.424389723658983	2		881	734	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799401	88799402	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	A	novel	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	31	172	0	ENST00000360948.2:c.-15-3dup		p.X5_splice	ENST00000360948	NM_001012338.2	5			1	2	FACETS	0.734	0.599	0.885	0.734	0.599	0.885	SUBCLONAL	1	TRUE	1	0.424389723658983	2		172	199	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163608	32163608	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	65	397	0	ENST00000375023.3:c.5618del	p.Gly1873AlafsTer12	p.G1873Afs*12	ENST00000375023	NM_004557.3	1873	gGc/gc	30/30	1	2	FACETS	0.8	0.697	0.91	0.8	0.697	0.91	CLONAL	1	TRUE	1	0.424389723658983	2		397	383	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435550	110435550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746157298	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	104	389	0	ENST00000375856.3:c.2851G>A	p.Ala951Thr	p.A951T	ENST00000375856	NM_003749.2	951	Gcc/Acc	1/2	1	2	FACETS	0.894	0.803	0.99	0.894	0.803	0.99	CLONAL	1	TRUE	1	0.424389723658983	2		389	548	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933694	36933694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777148168	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	103	660	0	ENST00000361632.4:c.1705G>A	p.Ala569Thr	p.A569T	ENST00000361632		569	Gct/Act	12/16	1	2	FACETS	0.719	0.644	0.799	0.719	0.644	0.799	SUBCLONAL	1	TRUE	1	0.424389723658983	2		660	675	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175463	108175463	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	53	345	0	ENST00000278616.4:c.5558A>G	p.Asp1853Gly	p.D1853G	ENST00000278616	NM_000051.3	1853	gAt/gGt	37/63	1	2	FACETS	0.631	0.539	0.73	0.631	0.539	0.73	SUBCLONAL	1	TRUE	1	0.424389723658983	2		345	396	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885187	111885187	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	75	430	0	ENST00000341259.2:c.1075C>A	p.Leu359Met	p.L359M	ENST00000341259	NM_005475.2	359	Ctg/Atg	6/8	1	2	FACETS	0.754	0.662	0.851	0.754	0.662	0.851	SUBCLONAL	1	TRUE	1	0.424389723658983	2		430	469	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906523	32906523	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs867323565	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	47	355	1	ENST00000380152.3:c.908C>A	p.Ser303Tyr	p.S303Y	ENST00000380152		303	tCt/tAt	10/27	1	2	FACETS	0.557	0.47	0.651	0.557	0.47	0.651	SUBCLONAL	1	TRUE	1	0.424389723658983	2		356	398	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436101	110436101	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	38	687	0	ENST00000375856.3:c.2300T>C	p.Leu767Pro	p.L767P	ENST00000375856	NM_003749.2	767	cTc/cCc	1/2	1	2	FACETS	0.243	0.2	0.291	0.243	0.2	0.291	SUBCLONAL	1	TRUE	1	0.424389723658983	2		687	737	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104304	2104305	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	74	402	0	ENST00000219476.3:c.347dup	p.Leu116PhefsTer10	p.L116Ffs*10	ENST00000219476	NM_000548.3	115	cgt/cgTt	5/42	1	2	FACETS	0.719	0.631	0.813	0.719	0.631	0.813	SUBCLONAL	1	TRUE	1	0.424389723658983	2		402	485	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2132505	2132505	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	25	478	0	ENST00000219476.3:c.3883G>T	p.Asp1295Tyr	p.D1295Y	ENST00000219476	NM_000548.3	1295	Gac/Tac	32/42	1	2	FACETS	0.236	0.185	0.294	0.236	0.185	0.294	SUBCLONAL	1	TRUE	1	0.424389723658983	2		478	500	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653035	29653035	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555533347	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	66	326	0	ENST00000356175.3:c.4970A>G	p.Tyr1657Cys	p.Y1657C	ENST00000356175	NM_000267.3	1657	tAt/tGt	36/57	1	2	FACETS	0.804	0.701	0.914	0.804	0.701	0.914	CLONAL	1	TRUE	1	0.424389723658983	2		326	387	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685515	29685515	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786202579	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	66	288	0	ENST00000356175.3:c.7925C>G	p.Ser2642Cys	p.S2642C	ENST00000356175	NM_000267.3	2642	tCt/tGt	54/57	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.424389723658983	2		288	306	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627218	37627218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375280392	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	60	413	2	ENST00000447079.4:c.1133G>A	p.Arg378His	p.R378H	ENST00000447079	NM_015083.1	378	cGc/cAc	2/14	1	2	FACETS	0.523	0.45	0.601	0.523	0.45	0.601	SUBCLONAL	1	TRUE	1	0.424389723658983	2		415	541	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858232	59858232	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	30	459	1	ENST00000259008.2:c.1763T>C	p.Val588Ala	p.V588A	ENST00000259008	NM_032043.2	588	gTg/gCg	12/20	1	2	FACETS	0.257	0.206	0.315	0.257	0.206	0.315	SUBCLONAL	1	TRUE	1	0.424389723658983	2		460	550	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223506	36223506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561976569	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	106	564	0	ENST00000222270.7:c.6056G>A	p.Gly2019Asp	p.G2019D	ENST00000222270	NM_014727.1	2019	gGc/gAc	28/37	1	2	FACETS	0.79	0.71	0.876	0.79	0.71	0.876	SUBCLONAL	1	TRUE	1	0.424389723658983	2		564	632	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140172	50140172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774218911	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	30	415	0	ENST00000246792.3:c.253G>A	p.Ala85Thr	p.A85T	ENST00000246792	NM_006270.3	85	Gcg/Acg	3/6	1	2	FACETS	0.313	0.252	0.383	0.313	0.252	0.383	SUBCLONAL	1	TRUE	1	0.424389723658983	2		415	451	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99137164	99137164	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	23	342	0	ENST00000074304.5:c.121C>A	p.Pro41Thr	p.P41T	ENST00000074304	NM_001134224.1	41	Cca/Aca	4/26	1	2	FACETS	0.238	0.185	0.299	0.238	0.185	0.299	SUBCLONAL	1	TRUE	1	0.424389723658983	2		342	456	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264650	46264650	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	11	210	0	ENST00000371998.3:c.1520T>C	p.Met507Thr	p.M507T	ENST00000371998		507	aTg/aCg	12/23	1	2	FACETS	0.236	0.162	0.327	0.236	0.162	0.327	SUBCLONAL	1	TRUE	1	0.424389723658983	2		210	220	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546161	41546162	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	59	270	0	ENST00000263253.7:c.2780dup	p.Thr928AsnfsTer21	p.T928Nfs*21	ENST00000263253	NM_001429.3	926	acc/aCcc	14/31	1	2	FACETS	0.797	0.689	0.913	0.797	0.689	0.913	CLONAL	1	TRUE	1	0.424389723658983	2		270	349	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160671	56160671	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	80	346	0	ENST00000399503.3:c.945A>T	p.Arg315Ser	p.R315S	ENST00000399503	NM_005921.1	315	agA/agT	4/20	1	2	FACETS	0.938	0.83	1	0.938	0.83	1	CLONAL	1	TRUE	1	0.424389723658983	2		346	402	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910774	29910774	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs9260139	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	70	558	0	ENST00000376809.5:c.314T>C	p.Leu105Pro	p.L105P	ENST00000376809	NM_002116.7	105	cTg/cCg	2/8	1	2	FACETS	0.589	0.514	0.67	0.589	0.514	0.67	SUBCLONAL	1	TRUE	1	0.424389723658983	2		558	560	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227955	53227955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	81	480	0	ENST00000375401.3:c.2359C>T	p.Arg787Trp	p.R787W	ENST00000375401	NM_004187.3	787	Cgg/Tgg	16/26	1	2	FACETS	0.603	0.531	0.68	0.603	0.531	0.68	SUBCLONAL	1	TRUE	1	0.424389723658983	2		480	633	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349214	70349214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	105	494	0	ENST00000374080.3:c.3626C>T	p.Ala1209Val	p.A1209V	ENST00000374080		1209	gCt/gTt	26/45	1	2	FACETS	0.777	0.697	0.861	0.777	0.697	0.861	SUBCLONAL	1	TRUE	1	0.424389723658983	2		494	637	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727454	66727454	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519909	NA	P-0023859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	31	496	0	ENST00000307102.5:c.170A>C	p.Lys57Thr	p.K57T	ENST00000307102	NM_002755.3	57	aAg/aCg	2/11	0.114072957448785	1	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	0	0.114072957448785	1		496	458	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974161	2974161	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	36	685	1	ENST00000396946.4:c.1444G>A	p.Glu482Lys	p.E482K	ENST00000396946	NM_032415.4	482	Gag/Aag	10/25	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.114072957448785	2		686	539	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820898	36820898	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	41	670	0	ENST00000373129.3:c.479A>T	p.Gln160Leu	p.Q160L	ENST00000373129	NM_032017.1	160	cAg/cTg	6/12	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.114072957448785	2		670	654	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606858	43606858	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs372648203	NA	P-0023859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	42	784	0	ENST00000355710.3:c.1467C>A	p.Asp489Glu	p.D489E	ENST00000355710	NM_020975.4	489	gaC/gaA	7/20	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.114072957448785	2		784	609	SUCCESS
ATM	472	MSKCC	GRCh37	11	108183181	108183181	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	40	472	0	ENST00000278616.4:c.5962A>T	p.Ser1988Cys	p.S1988C	ENST00000278616	NM_000051.3	1988	Agc/Tgc	40/63	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.114072957448785	2		472	531	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23635355	23635355	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	51	696	0	ENST00000261584.4:c.2809G>T	p.Gly937Ter	p.G937*	ENST00000261584	NM_024675.3	937	Gga/Tga	8/13	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.114072957448785	2		696	810	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955186	17955186	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	46	759	2	ENST00000458235.1:c.41G>T	p.Arg14Leu	p.R14L	ENST00000458235	NM_000215.3	14	cGt/cTt	2/24	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.114072957448785	2		761	588	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215634037	215634037	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0023859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	31	484	1	ENST00000260947.4:c.1315-1G>T		p.X439_splice	ENST00000260947	NM_000465.2	439			1	2	FACETS	0.972	0.785	1	0.972	0.785	1	CLONAL	1	TRUE	1	0.114072957448785	2		485	559	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100911	41100911	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	35	614	0	ENST00000373198.4:c.1445A>T	p.Glu482Val	p.E482V	ENST00000373198	NM_133170.3	482	gAa/gTa	8/32	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.114072957448785	2		614	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578191	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs530941076	NA	P-0023860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	95	894	0	ENST00000269305.4:c.658T>C	p.Tyr220His	p.Y220H	ENST00000269305	NM_001126112.2	220	Tat/Cat	6/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.15	2		894	965	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0023860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	110	731	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	1	2	FACETS	0.892	0.801	0.989	1	0.986	1	CLONAL	2	TRUE	1	0.15	2		731	822	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073851	8073852	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0023860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	38	421	0	ENST00000377482.5:c.806_807dup	p.His270TyrfsTer26	p.H270Yfs*26	ENST00000377482	NM_018948.3	269	-/TA	4/4	1	2	FACETS	0.978	0.808	1	0.978	0.808	1	CLONAL	1	TRUE	1	0.15	2		421	518	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696658	47696658	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	60	810	0	ENST00000347630.2:c.290A>C	p.Glu97Ala	p.E97A	ENST00000347630	NM_001007230.1	97	gAa/gCa	5/11	1	2	FACETS	0.899	0.772	1	0.899	0.772	1	CLONAL	1	TRUE	1	0.15	2		810	890	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910371	29910371	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs2230954	NA	P-0023860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	73	996	2	ENST00000376809.5:c.41C>A	p.Ser14Ter	p.S14*	ENST00000376809	NM_002116.7	14	tCg/tAg	1/8	1	2	FACETS	0.899	0.784	1	0.899	0.784	1	CLONAL	1	TRUE	1	0.15	2		998	1083	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035159	30035159	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	197	809	0	ENST00000338641.4:c.322del	p.Glu108SerfsTer15	p.E108Sfs*15	ENST00000338641	NM_000268.3	107	gaG/ga	3/16	0.425291746586009	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.427825181519586	2		809	442	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933998	39933998	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	95	379	0	ENST00000378444.4:c.601C>G	p.Pro201Ala	p.P201A	ENST00000378444	NM_001123385.1	201	Cca/Gca	4/15	1	1	FACETS	0.823	0.75	0.898	1	0.986	1	CLONAL	2	TRUE	0	0.427825181519586	1		379	212	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442589	52442589	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	154	498	0	ENST00000460680.1:c.156G>A	p.Trp52Ter	p.W52*	ENST00000460680	NM_004656.3	52	tgG/tgA	4/17	0.216142238338974	3	FACETS	0.759	0.699	0.821	0.759	0.699	0.821	INDETERMINATE	2	TRUE	1	0.472136221714766	3		498	531	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441466	52441528	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TATCCTTTGCTCTACGGGGAAGAAAATAAGGCCGTATCAGAATAATTTCTCCTCAGGTAGGAC	TATCCTTTGCTCTACGGGGAAGAAAATAAGGCCGTATCAGAATAATTTCTCCTCAGGTAGGAC	-	novel	NA	P-0023863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	82	657	0	ENST00000460680.1:c.376-52_386del		p.X126_splice	ENST00000460680	NM_004656.3	126		6/17	0.216142238338974	3	FACETS	0.74	0.654	0.833	0.37	0.327	0.417	INDETERMINATE	1	TRUE	1	0.472136221714766	3		657	580	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38186995	38186995	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	158	908	0	ENST00000317025.8:c.1482G>C	p.Lys494Asn	p.K494N	ENST00000317025	NM_023034.1	494	aaG/aaC	6/24	1	2	FACETS	0.786	0.72	0.854	0.786	0.72	0.854	SUBCLONAL	1	TRUE	1	0.472136221714766	2		908	852	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033844	49033844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853294	NA	P-0023865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	102	625	4	ENST00000267163.4:c.1981C>T	p.Arg661Trp	p.R661W	ENST00000267163	NM_000321.2	661	Cgg/Tgg	20/27	0.509041617811054	1	FACETS	0.849	0.767	0.934	0.849	0.767	0.934	CLONAL	1	TRUE	0	0.509041617811054	1		629	352	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861162	57861162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564027387	NA	P-0023865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	167	683	1	ENST00000228682.2:c.959C>T	p.Thr320Met	p.T320M	ENST00000228682	NM_005269.2	320	aCg/aTg	9/12	0.484185900536706	1	FACETS	0.86	0.794	0.927	0.86	0.794	0.927	CLONAL	1	TRUE	0	0.509041617811054	1		684	569	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702406	47702428	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTGGTAAAAAACCTGGTTTTTG	ACTGGTAAAAAACCTGGTTTTTG	-	novel	NA	P-0023865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	17	347	0	ENST00000233146.2:c.2002_2005+19del		p.X668_splice	ENST00000233146	NM_000251.2	668		12/16	0.485615038569567	1	FACETS	0.38	0.286	0.489	0.38	0.286	0.489	SUBCLONAL	1	TRUE	0	0.509041617811054	1		347	131	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0023866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	10	411	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.34549199707756	1	FACETS	0.026	0.017	0.037	0.026	0.017	0.037	INDETERMINATE	1	TRUE	0	0.917009317439352	1		411	463	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28931588	NA	P-0023866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	16	410	0	ENST00000349496.5:c.94G>C	p.Asp32His	p.D32H	ENST00000349496	NM_001904.3	32	Gac/Cac	3/15	0.34549199707756	1	FACETS	0.041	0.03	0.055	0.041	0.03	0.055	INDETERMINATE	1	TRUE	0	0.917009317439352	1		410	457	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178942554	178942554	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	148	521	0	ENST00000263967.3:c.2361C>G	p.Asp787Glu	p.D787E	ENST00000263967	NM_006218.2	787	gaC/gaG	16/21	1	2	FACETS	0.485	0.444	0.527	0.485	0.444	0.527	SUBCLONAL	1	TRUE	1	0.917009317439352	2		521	666	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1906093	1906093	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	490	730	0	ENST00000382891.5:c.748A>G	p.Thr250Ala	p.T250A	ENST00000382891	NM_133335.3	250	Acc/Gcc	3/22	1	2	FACETS	0.997	0.957	1	0.997	0.957	1	CLONAL	1	TRUE	1	0.917009317439352	2		730	1072	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	17	896	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.397	0.295	0.517	0.397	0.295	0.517	SUBCLONAL	1	FALSE	1	0.266238826613184	2		898	322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0023872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	25	792	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	NA	2	FACETS	0.622	0.491	0.772			1	INDETERMINATE	1	FALSE	NA	0.266238826613184	2		794	302	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481915	56481915	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	58	426	0	ENST00000267101.3:c.843G>C	p.Gln281His	p.Q281H	ENST00000267101	NM_001982.3	281	caG/caC	7/28	0.196886387681736	4	FACETS	1	0.957	1	0.433	0.373	0.498	CLONAL	1	FALSE	1	0.266238826613184	4		426	425	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597855	43597855	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	12	553	0	ENST00000355710.3:c.403G>A	p.Gly135Ser	p.G135S	ENST00000355710	NM_020975.4	135	Ggc/Agc	3/20	0.270168492688816	0	FACETS	0.389	0.274	0.53			1	SUBCLONAL	1	FALSE	0	0.266238826613184	0		553	170	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913676	32913677	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	23	316	0	ENST00000380152.3:c.5189dup	p.Asn1730LysfsTer13	p.N1730Kfs*13	ENST00000380152		1728	-/A	11/27	NA	2	FACETS	0.86	0.674	1			1	INDETERMINATE	1	FALSE	NA	0.266238826613184	2		316	201	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225563	2225563	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	14	447	0	ENST00000326181.6:c.1566G>C	p.Trp522Cys	p.W522C	ENST00000326181	NM_032271.2	522	tgG/tgC	17/21	1	2	FACETS	0.521	0.377	0.694	0.521	0.377	0.694	SUBCLONAL	1	FALSE	1	0.266238826613184	2		447	202	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857640	78857673	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCTTGCTGCGCCAGTGGGTGGCCATCTGCCTC	CCCCTTGCTGCGCCAGTGGGTGGCCATCTGCCTC	-	novel	NA	P-0023872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	14	458	0	ENST00000306801.3:c.1710_1743del	p.His570GlnfsTer16	p.H570Qfs*16	ENST00000306801	NM_020761.2	570	caCCCCTTGCTGCGCCAGTGGGTGGCCATCTGCCTC/ca	16/34	NA	2	FACETS	0.476	0.344	0.635			1	INDETERMINATE	1	FALSE	NA	0.266238826613184	2		458	221	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1955153	1955153	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	14	475	0	ENST00000382891.5:c.2240A>C	p.Tyr747Ser	p.Y747S	ENST00000382891	NM_133335.3	747	tAc/tCc	12/22	0.270168492688816	1	FACETS	0.402	0.29	0.536	0.402	0.29	0.536	SUBCLONAL	1	FALSE	0	0.266238826613184	1		475	227	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107136	27107137	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0023875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	62	322	0	ENST00000324856.7:c.6749_6750del	p.Glu2250ValfsTer27	p.E2250Vfs*27	ENST00000324856	NM_006015.4	2249	tcAGag/tcag	20/20	1	2	FACETS	0.75	0.654	0.851	0.75	0.654	0.851	SUBCLONAL	1	FALSE	1	0.621848694276444	2		322	266	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939086	36939086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372288734	NA	P-0023875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	109	460	3	ENST00000361632.4:c.623C>T	p.Ala208Val	p.A208V	ENST00000361632		208	gCg/gTg	5/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.621848694276444	2		463	319	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462900	120462902	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0023875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	51	243	0	ENST00000256646.2:c.5429_5431del	p.Pro1810del	p.P1810del	ENST00000256646	NM_024408.3	1810	cCTCag/cag	30/34	1	2	FACETS	0.901	0.778	1	0.901	0.778	1	CLONAL	1	FALSE	1	0.621848694276444	2		243	182	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244135	46244137	+	missense_variant	Missense_Mutation	TNP	TGT	TGT	GTG	novel	NA	P-0023875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	77	313	0	ENST00000334344.6:c.2229_2231delinsGTG	p.Val744Cys	p.V744C	ENST00000334344	NM_152641.2	743	gtTGTt/gtGTGt	15/21	1	2	FACETS	0.931	0.828	1	0.931	0.828	1	CLONAL	1	FALSE	1	0.621848694276444	2		313	266	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856515	111856515	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1195675821	NA	P-0023875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	79	317	0	ENST00000341259.2:c.566G>A	p.Arg189Gln	p.R189Q	ENST00000341259	NM_005475.2	189	cGg/cAg	2/8	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.621848694276444	2		317	187	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975713	26975715	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0023875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	96	297	0	ENST00000381527.3:c.1225_1227del	p.Pro409del	p.P409del	ENST00000381527	NM_001260.1	407	gtTCCt/gtt	12/13	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	FALSE	1	0.621848694276444	2		297	300	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781324	3781326	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs587783502	NA	P-0023875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	103	543	0	ENST00000262367.5:c.5039_5041del	p.Ser1680del	p.S1680del	ENST00000262367	NM_004380.2	1680	tCCTtg/ttg	30/31	1	2	FACETS	0.854	0.77	0.941	0.854	0.77	0.941	CLONAL	1	FALSE	1	0.621848694276444	2		543	388	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0023875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	48	401	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.540278402178551	3	FACETS	1	0.889	1	0.522	0.447	0.601	CLONAL	1	FALSE	1	0.621848694276444	3		401	194	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721132	176721132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	34	275	0	ENST00000439151.2:c.6763C>T	p.Pro2255Ser	p.P2255S	ENST00000439151	NM_022455.4	2255	Cct/Tct	23/23	1	2	FACETS	0.688	0.57	0.817	0.688	0.57	0.817	SUBCLONAL	1	FALSE	1	0.621848694276444	2		275	159	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974745	21974747	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-	novel	NA	P-0023875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	19	183	0	ENST00000304494.5:c.80_82del	p.Glu27del	p.E27del	ENST00000304494	NM_000077.4	27	gAGGtg/gtg	1/3	0.621848694276444	1	FACETS	0.54	0.42	0.673	0.54	0.42	0.673	SUBCLONAL	1	FALSE	0	0.621848694276444	1		183	78	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209346	98209347	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0023875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	59	372	0	ENST00000331920.6:c.4191_4192del	p.Cys1398ProfsTer5	p.C1398Pfs*5	ENST00000331920	NM_000264.3	1397	ctCTgc/ctgc	23/24	0.111606511824801	0	FACETS	0.27	0.234	0.308			1	INDETERMINATE	1	FALSE	0	0.621848694276444	0		372	266	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918921	76918921	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	153	293	0	ENST00000373344.5:c.4070del	p.Lys1357ArgfsTer18	p.K1357Rfs*18	ENST00000373344	NM_000489.3	1357	aAg/ag	12/35	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	0	0.621848694276444	1		293	245	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	69	416	0	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	1	2	FACETS	0.884	0.777	0.998	0.884	0.777	0.998	CLONAL	1	TRUE	1	0.516913648781996	2		416	302	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846046	68846047	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACGTATACCCTGGTGGTTCAAGCTGCTG	novel	NA	P-0023876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	45	465	0	ENST00000261769.5:c.1020_1047dup	p.Leu350ValfsTer9	p.L350Vfs*9	ENST00000261769	NM_004360.3	339	-/ACGTATACCCTGGTGGTTCAAGCTGCTG	8/16	0.516913648781996	1	FACETS	0.41	0.346	0.48	0.41	0.346	0.48	SUBCLONAL	1	TRUE	0	0.516913648781996	1		465	315	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860361	151860371	+	frameshift_variant	Frame_Shift_Del	DEL	TGCTGCTCCAT	TGCTGCTCCAT	-	novel	NA	P-0023876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	72	361	0	ENST00000262189.6:c.10291_10301del	p.Met3431TrpfsTer6	p.M3431Wfs*6	ENST00000262189	NM_170606.2	3431	ATGGAGCAGCAt/t	43/59	1	2	FACETS	0.805	0.708	0.908	0.805	0.708	0.908	CLONAL	1	TRUE	1	0.516913648781996	2		361	346	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	85	399	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.945	0.844	1			1	INDETERMINATE	1	TRUE	NA	0.599773222672177	2		399	300	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9770520	9770520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750425882	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	141	406	1	ENST00000377346.4:c.7C>T	p.Pro3Ser	p.P3S	ENST00000377346	NM_005026.3	3	Cct/Tct	3/24	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.599773222672177	2		407	398	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11291109	11291110	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	85	388	1	ENST00000361445.4:c.2651_2652delinsTT	p.Ala884Val	p.A884V	ENST00000361445	NM_004958.3	884	gCC/gTT	18/58	1	2	FACETS	0.948	0.847	1	0.948	0.847	1	CLONAL	1	TRUE	1	0.599773222672177	2		389	299	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057926	27057926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775882868	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	127	539	0	ENST00000324856.7:c.1634C>T	p.Pro545Leu	p.P545L	ENST00000324856	NM_006015.4	545	cCc/cTc	3/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.599773222672177	2		539	393	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058632	72058632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	101	259	0	ENST00000357731.5:c.808G>A	p.Gly270Arg	p.G270R	ENST00000357731	NM_173808.2	270	Gga/Aga	6/7	1	2	FACETS	0.938	0.846	1	0.938	0.846	1	CLONAL	1	TRUE	1	0.599773222672177	2		259	359	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275358	115275358	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	162	444	1	ENST00000438362.2:c.1055C>T	p.Ser352Phe	p.S352F	ENST00000438362	NM_001242891.1	352	tCc/tTc	10/20	1	2	FACETS	0.989	0.913	1	0.989	0.913	1	CLONAL	1	TRUE	1	0.599773222672177	2		445	546	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690298	117690299	+	missense_variant	Missense_Mutation	DNP	AG	AG	GA	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	89	271	1	ENST00000369458.3:c.830_831delinsTC	p.Pro277Leu	p.P277L	ENST00000369458	NM_024626.3	277	cCT/cTC	5/6	1	2	FACETS	0.925	0.828	1	0.925	0.828	1	CLONAL	1	TRUE	1	0.599773222672177	2		272	321	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510783	120510783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	127	404	0	ENST00000256646.2:c.1181C>T	p.Pro394Leu	p.P394L	ENST00000256646	NM_024408.3	394	cCc/cTc	7/34	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.599773222672177	2		404	418	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745580	162745580	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	122	415	0	ENST00000367921.3:c.1995T>A	p.Phe665Leu	p.F665L	ENST00000367921	NM_006182.2	665	ttT/ttA	15/18	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.599773222672177	2		415	398	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649527	206649527	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	71	290	0	ENST00000367120.3:c.362C>T	p.Ala121Val	p.A121V	ENST00000367120	NM_014002.3	121	gCc/gTc	6/22	1	2	FACETS	0.893	0.789	1	0.893	0.789	1	CLONAL	1	TRUE	1	0.599773222672177	2		290	265	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567730	226567730	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	111	407	0	ENST00000366794.5:c.1436C>T	p.Ser479Phe	p.S479F	ENST00000366794	NM_001618.3	479	tCc/tTc	10/23	1	2	FACETS	0.944	0.856	1	0.944	0.856	1	CLONAL	1	TRUE	1	0.599773222672177	2		407	392	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226590001	226590001	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	127	396	0	ENST00000366794.5:c.200C>T	p.Pro67Leu	p.P67L	ENST00000366794	NM_001618.3	67	cCt/cTt	2/23	1	2	FACETS	0.945	0.863	1	0.945	0.863	1	CLONAL	1	TRUE	1	0.599773222672177	2		396	448	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692781	89692781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587783059	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	105	291	0	ENST00000371953.3:c.265C>T	p.Pro89Ser	p.P89S	ENST00000371953	NM_000314.4	89	Cct/Tct	5/9	1	2	FACETS	0.921	0.833	1	0.921	0.833	1	CLONAL	1	TRUE	1	0.599773222672177	2		291	380	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104353812	104353812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	103	423	0	ENST00000369902.3:c.746C>T	p.Pro249Leu	p.P249L	ENST00000369902	NM_016169.3	249	cCa/cTa	6/12	1	2	FACETS	0.946	0.855	1	0.946	0.855	1	CLONAL	1	TRUE	1	0.599773222672177	2		423	363	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742960	17742960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1241501765	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	110	460	0	ENST00000250003.3:c.868G>A	p.Glu290Lys	p.E290K	ENST00000250003	NM_002478.4	290	Gag/Aag	3/3	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.599773222672177	2		460	358	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949322	71949323	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	113	456	0	ENST00000298229.2:c.3702_3703delinsAA	p.Asp1235Asn	p.D1235N	ENST00000298229	NM_001567.3	1234	gaGGac/gaAAac	28/28	1	2	FACETS	0.984	0.894	1	0.984	0.894	1	CLONAL	1	TRUE	1	0.599773222672177	2		456	383	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205756	108205756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531980488	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	102	278	0	ENST00000278616.4:c.8071C>T	p.Arg2691Cys	p.R2691C	ENST00000278616	NM_000051.3	2691	Cgc/Tgc	55/63	0.589601960578434	1	FACETS	0.956	0.871	1	0.956	0.871	1	CLONAL	1	TRUE	0	0.599773222672177	1		278	249	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420167	420167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	104	356	0	ENST00000399788.2:c.3100C>T	p.Pro1034Ser	p.P1034S	ENST00000399788	NM_001042603.1	1034	Cct/Tct	21/28	NA	2	FACETS	0.925	0.835	1			1	INDETERMINATE	1	TRUE	NA	0.599773222672177	2		356	375	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800885	18800885	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	120	353	0	ENST00000266497.5:c.4261G>A	p.Gly1421Arg	p.G1421R	ENST00000266497		1421	Gga/Aga	31/31	1	2	FACETS	0.928	0.845	1	0.928	0.845	1	CLONAL	1	TRUE	1	0.599773222672177	2		353	431	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416115	49416116	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	74	308	0	ENST00000301067.7:c.16359_16360delinsTT	p.Arg5454Ter	p.R5454*	ENST00000301067	NM_003482.3	5453	ttCCga/ttTTga	52/54	1	2	FACETS	0.842	0.745	0.945	0.842	0.745	0.945	CLONAL	1	TRUE	1	0.599773222672177	2		308	293	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421045	49421046	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	75	375	1	ENST00000301067.7:c.14703_14704delinsAA	p.Asp4902Asn	p.D4902N	ENST00000301067	NM_003482.3	4901	ctGGat/ctAAat	48/54	1	2	FACETS	0.874	0.775	0.98	0.874	0.775	0.98	CLONAL	1	TRUE	1	0.599773222672177	2		376	286	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422937	49422937	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	105	465	0	ENST00000301067.7:c.14158C>T	p.Pro4720Ser	p.P4720S	ENST00000301067	NM_003482.3	4720	Cct/Tct	44/54	1	2	FACETS	0.902	0.815	0.993	0.902	0.815	0.993	CLONAL	1	TRUE	1	0.599773222672177	2		465	388	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426978	49426978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	100	383	0	ENST00000301067.7:c.11510C>T	p.Ser3837Phe	p.S3837F	ENST00000301067	NM_003482.3	3837	tCc/tTc	39/54	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.599773222672177	2		383	315	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864432	57864432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200606293	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	114	352	0	ENST00000228682.2:c.1909C>T	p.Arg637Trp	p.R637W	ENST00000228682	NM_005269.2	637	Cgg/Tgg	12/12	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.599773222672177	2		352	313	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620099	21620099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	137	451	0	ENST00000382592.4:c.67C>T	p.Arg23Cys	p.R23C	ENST00000382592	NM_014572.2	23	Cgt/Tgt	2/8	0.587030850531275	2	FACETS	0.932	0.854	1	0.466	0.427	0.507	CLONAL	1	TRUE	0	0.599773222672177	2		451	490	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895604	28895604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	110	345	0	ENST00000282397.4:c.3170G>A	p.Gly1057Glu	p.G1057E	ENST00000282397	NM_002019.4	1057	gGa/gAa	23/30	0.587030850531275	2	FACETS	0.906	0.82	0.995	0.453	0.41	0.498	CLONAL	1	TRUE	0	0.599773222672177	2		345	405	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913374	28913375	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	133	521	1	ENST00000282397.4:c.2418_2419delinsAA	p.Asp807Asn	p.D807N	ENST00000282397	NM_002019.4	806	ttGGat/ttAAat	17/30	0.587030850531275	2	FACETS	0.868	0.793	0.946	0.434	0.396	0.473	CLONAL	1	TRUE	0	0.599773222672177	2		522	511	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514524	103514524	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	50	198	0	ENST00000355739.4:c.1025C>T	p.Pro342Leu	p.P342L	ENST00000355739	NM_000123.3	342	cCa/cTa	8/15	0.593726056973509	2	FACETS	0.751	0.644	0.865	0.376	0.322	0.433	SUBCLONAL	1	TRUE	0	0.599773222672177	2		198	222	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436194	110436194	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs918898281	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	140	407	0	ENST00000375856.3:c.2207C>T	p.Ser736Phe	p.S736F	ENST00000375856	NM_003749.2	736	tCc/tTc	1/2	0.593726056973509	2	FACETS	1	0.956	1	0.531	0.487	0.575	CLONAL	1	TRUE	0	0.599773222672177	2		407	440	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052693	42052693	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	136	388	1	ENST00000219905.7:c.7364C>T	p.Ser2455Phe	p.S2455F	ENST00000219905	NM_001164273.1	2455	tCt/tTt	20/24	1	2	FACETS	0.984	0.901	1	0.984	0.901	1	CLONAL	1	TRUE	1	0.599773222672177	2		389	461	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467191	99467191	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773555066	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	87	282	0	ENST00000268035.6:c.2572C>T	p.Pro858Ser	p.P858S	ENST00000268035	NM_000875.3	858	Ccc/Tcc	12/21	1	2	FACETS	0.851	0.76	0.946	0.851	0.76	0.946	CLONAL	1	TRUE	1	0.599773222672177	2		282	341	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343558	343558	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	92	580	0	ENST00000262320.3:c.2116C>T	p.Gln706Ter	p.Q706*	ENST00000262320	NM_003502.3	706	Cag/Tag	8/11	NA	2	FACETS	0.779	0.697	0.865			1	INDETERMINATE	1	TRUE	NA	0.599773222672177	2		580	394	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220646	2220646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	121	543	1	ENST00000326181.6:c.263C>T	p.Ser88Phe	p.S88F	ENST00000326181	NM_032271.2	88	tCc/tTc	5/21	NA	2	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.599773222672177	2		544	372	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639063	3639063	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs111866205	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	123	443	0	ENST00000294008.3:c.4576C>T	p.Pro1526Ser	p.P1526S	ENST00000294008	NM_032444.2	1526	Cct/Tct	12/15	NA	2	FACETS	0.977	0.89	1			1	INDETERMINATE	1	TRUE	NA	0.599773222672177	2		443	420	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274085	10274085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	98	499	0	ENST00000330684.3:c.184G>A	p.Gly62Arg	p.G62R	ENST00000330684	NM_001134407.1	62	Ggg/Agg	2/13	1	2	FACETS	0.961	0.866	1	0.961	0.866	1	CLONAL	1	TRUE	1	0.599773222672177	2		499	340	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782267	56782268	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	102	315	1	ENST00000308159.5:c.108_109delinsTT	p.Gln37Ter	p.Q37*	ENST00000308159	NM_014669.4	36	atCCag/atTTag	2/22	NA	2	FACETS	0.977	0.883	1			1	INDETERMINATE	1	TRUE	NA	0.599773222672177	2		316	348	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868064	56868064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	96	281	1	ENST00000308159.5:c.1562C>T	p.Pro521Leu	p.P521L	ENST00000308159	NM_014669.4	521	cCt/cTt	14/22	NA	2	FACETS	0.92	0.827	1			1	INDETERMINATE	1	TRUE	NA	0.599773222672177	2		282	348	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67132676	67132676	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536749790	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	105	381	1	ENST00000412916.2:c.559C>T	p.Arg187Cys	p.R187C	ENST00000412916		187	Cgt/Tgt	6/6	0.599773222672177	1	FACETS	0.632	0.571	0.696	0.632	0.571	0.696	SUBCLONAL	1	TRUE	0	0.599773222672177	1		382	388	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972436	81972437	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	134	404	2	ENST00000359376.3:c.3229_3230delinsAA	p.Gly1077Lys	p.G1077K	ENST00000359376	NM_002661.3	1077	GGa/AAa	29/33	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.599773222672177	2		406	415	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216995	7216995	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	89	326	0	ENST00000380728.2:c.526G>A	p.Glu176Lys	p.E176K	ENST00000380728		176	Gag/Aag	7/11	1	2	FACETS	0.848	0.758	0.942	0.848	0.758	0.942	CLONAL	1	TRUE	1	0.599773222672177	2		326	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574004	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	116	475	2	ENST00000269305.4:c.1023_1024delinsTT	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	341	ttCCga/ttTTga	10/11	1	2	FACETS	0.839	0.761	0.921	0.839	0.761	0.921	CLONAL	1	TRUE	1	0.599773222672177	2		477	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579415	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	86	491	1	ENST00000269305.4:c.272_273delinsAA	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tGG/tAA	4/11	1	2	FACETS	0.735	0.655	0.82	0.735	0.655	0.82	SUBCLONAL	1	TRUE	1	0.599773222672177	2		492	390	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049694	16049694	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	134	341	0	ENST00000268712.3:c.1078C>T	p.Gln360Ter	p.Q360*	ENST00000268712	NM_006311.3	360	Cag/Tag	10/46	1	2	FACETS	0.901	0.824	0.981	0.901	0.824	0.981	CLONAL	1	TRUE	1	0.599773222672177	2		341	496	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687532	29687532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	138	382	0	ENST00000356175.3:c.8125C>T	p.Leu2709Phe	p.L2709F	ENST00000356175	NM_000267.3	2709	Ctt/Ttt	56/57	1	2	FACETS	0.992	0.909	1	0.992	0.909	1	CLONAL	1	TRUE	1	0.599773222672177	2		382	464	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474493	40474494	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	87	291	2	ENST00000264657.5:c.1907_1908delinsTT	p.Ser636Phe	p.S636F	ENST00000264657	NM_139276.2	636	tCC/tTT	21/24	1	2	FACETS	0.909	0.813	1	0.909	0.813	1	CLONAL	1	TRUE	1	0.599773222672177	2		293	319	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243586	41243586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	150	434	0	ENST00000357654.3:c.3962C>T	p.Ser1321Phe	p.S1321F	ENST00000357654	NM_007294.3	1321	tCc/tTc	10/23	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.599773222672177	2		434	491	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55334132	55334132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	92	319	0	ENST00000284073.2:c.29C>T	p.Ser10Leu	p.S10L	ENST00000284073	NM_138962.2	10	tCg/tTg	1/14	1	2	FACETS	0.935	0.84	1	0.935	0.84	1	CLONAL	1	TRUE	1	0.599773222672177	2		319	328	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533916	63533916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1399215718	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	97	348	0	ENST00000307078.5:c.1238C>T	p.Ser413Leu	p.S413L	ENST00000307078	NM_004655.3	413	tCg/tTg	6/11	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.599773222672177	2		348	319	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348563	56348563	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	72	201	0	ENST00000348428.3:c.371C>T	p.Pro124Leu	p.P124L	ENST00000348428	NM_006785.3	124	cCc/cTc	2/17	1	2	FACETS	0.903	0.798	1	0.903	0.798	1	CLONAL	1	TRUE	1	0.599773222672177	2		201	266	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2208950	2208950	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	110	421	0	ENST00000398665.3:c.980C>T	p.Ser327Phe	p.S327F	ENST00000398665	NM_032482.2	327	tCt/tTt	12/28	0.139764724273874	0	FACETS	0.377	0.342	0.414			1	INDETERMINATE	1	TRUE	0	0.599773222672177	0		421	389	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223272	5223272	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	109	547	1	ENST00000357368.4:c.2531C>T	p.Pro844Leu	p.P844L	ENST00000357368	NM_002850.3	844	cCc/cTc	18/38	0.139764724273874	0	FACETS	0.387	0.35	0.425			1	INDETERMINATE	1	TRUE	0	0.599773222672177	0		548	376	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143080	7143081	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	86	427	0	ENST00000302850.5:c.2288_2289delinsTT	p.Ser763Phe	p.S763F	ENST00000302850	NM_000208.2	763	tCC/tTT	12/22	0.139764724273874	0	FACETS	0.34	0.303	0.378			1	INDETERMINATE	1	TRUE	0	0.599773222672177	0		427	338	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097649	11097649	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767947665	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	124	545	0	ENST00000358026.2:c.829C>T	p.Pro277Ser	p.P277S	ENST00000358026	NM_001128849.1	277	Cct/Tct	5/36	1	2	FACETS	0.955	0.871	1	0.955	0.871	1	CLONAL	1	TRUE	1	0.599773222672177	2		545	433	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113793	11113793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	119	417	0	ENST00000358026.2:c.1901C>T	p.Pro634Leu	p.P634L	ENST00000358026	NM_001128849.1	634	cCc/cTc	12/36	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.599773222672177	2		417	367	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123784	11123784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	90	359	0	ENST00000358026.2:c.2434C>T	p.Leu812Phe	p.L812F	ENST00000358026	NM_001128849.1	812	Ctc/Ttc	16/36	1	2	FACETS	0.941	0.844	1	0.941	0.844	1	CLONAL	1	TRUE	1	0.599773222672177	2		359	319	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290262	15290262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767385674	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	111	581	0	ENST00000263388.2:c.3373G>A	p.Glu1125Lys	p.E1125K	ENST00000263388	NM_000435.2	1125	Gag/Aag	21/33	1	2	FACETS	0.805	0.728	0.885	0.805	0.728	0.885	CLONAL	1	TRUE	1	0.599773222672177	2		581	460	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300161	15300161	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	129	504	0	ENST00000263388.2:c.1115A>G	p.Asn372Ser	p.N372S	ENST00000263388	NM_000435.2	372	aAc/aGc	7/33	1	2	FACETS	0.958	0.875	1	0.958	0.875	1	CLONAL	1	TRUE	1	0.599773222672177	2		504	449	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266735	18266735	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs80233027	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	138	473	0	ENST00000222254.8:c.46C>A	p.Arg16Ser	p.R16S	ENST00000222254	NM_005027.3	16	Cgc/Agc	2/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.599773222672177	2		473	377	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976936	18976937	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	76	408	1	ENST00000262803.5:c.3321_3322delinsTT	p.Gln1108Ter	p.Q1108*	ENST00000262803	NM_002911.3	1107	taCCag/taTTag	23/24	1	2	FACETS	0.922	0.818	1	0.922	0.818	1	CLONAL	1	TRUE	1	0.599773222672177	2		409	275	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258559	19258559	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141688102	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	132	561	0	ENST00000162023.5:c.341G>A	p.Arg114Gln	p.R114Q	ENST00000162023		114	cGg/cAg	8/13	1	2	FACETS	0.987	0.903	1	0.987	0.903	1	CLONAL	1	TRUE	1	0.599773222672177	2		561	446	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210709	36210709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780868475	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	135	508	1	ENST00000222270.7:c.460C>T	p.Arg154Cys	p.R154C	ENST00000222270	NM_014727.1	154	Cgc/Tgc	3/37	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.599773222672177	2		509	402	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213582	36213583	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	135	685	2	ENST00000222270.7:c.2684_2685delinsTT	p.Ala895Val	p.A895V	ENST00000222270	NM_014727.1	895	gCC/gTT	5/37	1	2	FACETS	0.94	0.86	1	0.94	0.86	1	CLONAL	1	TRUE	1	0.599773222672177	2		687	479	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42790980	42790980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	122	473	0	ENST00000575354.2:c.125C>T	p.Pro42Leu	p.P42L	ENST00000575354	NM_015125.3	42	cCc/cTc	2/20	1	2	FACETS	0.983	0.896	1	0.983	0.896	1	CLONAL	1	TRUE	1	0.599773222672177	2		473	414	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909727	50909727	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	136	513	1	ENST00000440232.2:c.1447G>A	p.Gly483Ser	p.G483S	ENST00000440232	NM_002691.3	483	Ggc/Agc	12/27	NA	2	FACETS	1	0.921	1			1	INDETERMINATE	1	TRUE	NA	0.599773222672177	2		514	451	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082318	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	169	591	1	ENST00000281043.3:c.131_132delinsTT	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCC/cTT	2/3	NA	2	FACETS	0.984	0.909	1			1	INDETERMINATE	1	TRUE	NA	0.599773222672177	2		592	573	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451794	29451794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs75861155	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	160	403	0	ENST00000389048.3:c.2771G>A	p.Gly924Asp	p.G924D	ENST00000389048	NM_004304.4	924	gGt/gAt	16/29	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.599773222672177	2		403	426	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715885	61715885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777247294	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	116	333	0	ENST00000401558.2:c.2044C>T	p.Pro682Ser	p.P682S	ENST00000401558	NM_003400.3	682	Cct/Tct	18/25	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.599773222672177	2		333	383	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047347	128047347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	102	312	0	ENST00000285398.2:c.575C>T	p.Pro192Leu	p.P192L	ENST00000285398	NM_000122.1	192	cCc/cTc	5/15	1	2	FACETS	0.953	0.86	1	0.953	0.86	1	CLONAL	1	TRUE	1	0.599773222672177	2		312	357	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158636923	158636923	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773459224	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	137	323	0	ENST00000263640.3:c.257C>T	p.Ser86Phe	p.S86F	ENST00000263640	NM_001105.4	86	tCc/tTc	4/11	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.599773222672177	2		323	437	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274541	198274541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	114	366	0	ENST00000335508.6:c.857C>T	p.Ser286Phe	p.S286F	ENST00000335508	NM_012433.2	286	tCc/tTc	7/25	0.593726056973509	2	FACETS	0.909	0.825	0.997	0.455	0.412	0.499	CLONAL	1	TRUE	0	0.599773222672177	2		366	418	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149893	202149893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770193825	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	114	441	0	ENST00000358485.4:c.1334C>T	p.Ser445Leu	p.S445L	ENST00000358485	NM_001080125.1	445	tCa/tTa	8/9	0.593726056973509	2	FACETS	0.894	0.811	0.981	0.447	0.405	0.491	CLONAL	1	TRUE	0	0.599773222672177	2		441	425	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645426	215645426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	283	433	0	ENST00000260947.4:c.1172C>T	p.Ser391Leu	p.S391L	ENST00000260947	NM_000465.2	391	tCa/tTa	4/11	0.593726056973509	2	FACETS	0.963	0.918	1	0.963	0.918	1	CLONAL	2	TRUE	0	0.599773222672177	2		433	490	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024503	31024503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1470476757	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	120	393	0	ENST00000375687.4:c.3988C>T	p.Pro1330Ser	p.P1330S	ENST00000375687	NM_015338.5	1330	Cct/Tct	13/13	1	2	FACETS	0.988	0.9	1	0.988	0.9	1	CLONAL	1	TRUE	1	0.599773222672177	2		393	405	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031687	36031687	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1159129326	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	135	537	2	ENST00000358208.4:c.1516C>T	p.Pro506Ser	p.P506S	ENST00000358208		506	Cct/Tct	12/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.599773222672177	2		539	360	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264955	46264955	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	94	266	0	ENST00000371998.3:c.1825C>T	p.Gln609Ter	p.Q609*	ENST00000371998		609	Caa/Taa	12/23	1	2	FACETS	0.956	0.859	1	0.956	0.859	1	CLONAL	1	TRUE	1	0.599773222672177	2		266	328	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46276050	46276051	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	98	410	2	ENST00000371998.3:c.3486_3487delinsTT	p.Arg1163Trp	p.R1163W	ENST00000371998		1162	ccCCgg/ccTTgg	18/23	1	2	FACETS	0.803	0.721	0.889	0.803	0.721	0.889	CLONAL	1	TRUE	1	0.599773222672177	2		412	407	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319675	62319676	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	76	414	1	ENST00000360203.5:c.1658_1659delinsTT	p.Pro553Leu	p.P553L	ENST00000360203	NM_001283009.1	553	cCC/cTT	20/35	1	2	FACETS	0.78	0.69	0.875	0.78	0.69	0.875	SUBCLONAL	1	TRUE	1	0.599773222672177	2		415	325	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447416	12447416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	116	349	0	ENST00000287820.6:c.655G>A	p.Glu219Lys	p.E219K	ENST00000287820	NM_015869.4	219	Gag/Aag	5/7	1	2	FACETS	0.946	0.859	1	0.946	0.859	1	CLONAL	1	TRUE	1	0.599773222672177	2		349	409	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940970	49940970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	93	357	0	ENST00000296474.3:c.73G>A	p.Glu25Lys	p.E25K	ENST00000296474	NM_002447.2	25	Gag/Aag	1/20	NA	2	FACETS	0.975	0.877	1			1	INDETERMINATE	1	TRUE	NA	0.599773222672177	2		357	318	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443589	52443590	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	122	379	0	ENST00000460680.1:c.102_103delinsTT	p.Leu35Phe	p.L35F	ENST00000460680	NM_004656.3	34	gaCCtt/gaTTtt	3/17	1	2	FACETS	0.978	0.891	1	0.978	0.891	1	CLONAL	1	TRUE	1	0.599773222672177	2		379	416	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71019906	71019906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	63	212	0	ENST00000318789.4:c.1703C>T	p.Pro568Leu	p.P568L	ENST00000318789	NM_032682.5	568	cCt/cTt	19/21	1	2	FACETS	0.894	0.783	1	0.894	0.783	1	CLONAL	1	TRUE	1	0.599773222672177	2		212	235	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114148	73114148	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	112	339	0	ENST00000356692.5:c.784C>T	p.Gln262Ter	p.Q262*	ENST00000356692		262	Caa/Taa	8/9	1	2	FACETS	0.906	0.822	0.995	0.906	0.822	0.995	CLONAL	1	TRUE	1	0.599773222672177	2		339	412	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468357	89468357	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs867931903	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	64	215	0	ENST00000336596.2:c.1891G>A	p.Glu631Lys	p.E631K	ENST00000336596	NM_005233.5	631	Gaa/Aaa	11/17	1	2	FACETS	0.979	0.86	1	0.979	0.86	1	CLONAL	1	TRUE	1	0.599773222672177	2		215	218	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521768	89521768	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	87	178	0	ENST00000336596.2:c.2845G>A	p.Asp949Asn	p.D949N	ENST00000336596	NM_005233.5	949	Gat/Aat	16/17	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.599773222672177	2		178	265	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199974	128199974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781161922	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	116	469	1	ENST00000341105.2:c.1331C>T	p.Pro444Leu	p.P444L	ENST00000341105	NM_032638.4	444	cCg/cTg	6/6	NA	2	FACETS	1	0.947	1			1	INDETERMINATE	1	TRUE	NA	0.599773222672177	2		470	366	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205766	128205767	+	missense_variant	Missense_Mutation	DNP	CG	CG	TT	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	147	508	1	ENST00000341105.2:c.108_109delinsAA	p.Ala37Thr	p.A37T	ENST00000341105	NM_032638.4	36	ccCGcg/ccAAcg	2/6	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.599773222672177	2		509	428	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442794	187442794	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1176821201	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	124	354	0	ENST00000232014.4:c.1912C>T	p.Arg638Cys	p.R638C	ENST00000232014	NM_001130845.1	638	Cgt/Tgt	9/10	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.599773222672177	2		354	398	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146538	55146538	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	103	304	0	ENST00000257290.5:c.2212G>A	p.Asp738Asn	p.D738N	ENST00000257290	NM_006206.4	738	Gat/Aat	16/23	1	2	FACETS	0.981	0.887	1	0.981	0.887	1	CLONAL	1	TRUE	1	0.599773222672177	2		304	350	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564581	55564581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1276125047	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	118	400	0	ENST00000288135.5:c.469C>T	p.Pro157Ser	p.P157S	ENST00000288135	NM_000222.2	157	Ccc/Tcc	3/21	1	2	FACETS	0.89	0.809	0.975	0.89	0.809	0.975	CLONAL	1	TRUE	1	0.599773222672177	2		400	442	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361168	66361168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1212449572	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	101	299	0	ENST00000273854.3:c.1004C>T	p.Ser335Phe	p.S335F	ENST00000273854	NM_004439.5	335	tCt/tTt	4/18	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.599773222672177	2		299	332	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045845	143045845	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	144	399	0	ENST00000262992.4:c.1789C>T	p.Arg597Ter	p.R597*	ENST00000262992	NM_001101669.1	597	Cga/Tga	17/24	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.599773222672177	2		399	424	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114298	143114298	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	133	334	0	ENST00000262992.4:c.1123G>A	p.Gly375Arg	p.G375R	ENST00000262992	NM_001101669.1	375	Gga/Aga	13/24	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.599773222672177	2		334	395	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517747	187517747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	49	152	0	ENST00000441802.2:c.12947C>T	p.Ser4316Phe	p.S4316F	ENST00000441802	NM_005245.3	4316	tCc/tTc	25/27	1	2	FACETS	0.913	0.786	1	0.913	0.786	1	CLONAL	1	TRUE	1	0.599773222672177	2		152	179	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524908	187524908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1345646956	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	153	427	0	ENST00000441802.2:c.10772C>T	p.Ser3591Phe	p.S3591F	ENST00000441802	NM_005245.3	3591	tCt/tTt	19/27	1	2	FACETS	0.959	0.883	1	0.959	0.883	1	CLONAL	1	TRUE	1	0.599773222672177	2		427	532	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534359	187534359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372404115	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	148	441	1	ENST00000441802.2:c.9367C>T	p.Pro3123Ser	p.P3123S	ENST00000441802	NM_005245.3	3123	Ccc/Tcc	13/27	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.599773222672177	2		442	437	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539998	187539998	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	101	310	0	ENST00000441802.2:c.7742C>T	p.Thr2581Ile	p.T2581I	ENST00000441802	NM_005245.3	2581	aCc/aTc	10/27	1	2	FACETS	0.957	0.864	1	0.957	0.864	1	CLONAL	1	TRUE	1	0.599773222672177	2		310	352	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1268717	1268718	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	124	558	0	ENST00000310581.5:c.2499_2500delinsAA	p.Gly834Ser	p.G834S	ENST00000310581	NM_198253.2	833	caGGgc/caAAgc	9/16	NA	2	FACETS	0.927	0.845	1			1	INDETERMINATE	1	TRUE	NA	0.599773222672177	2		558	446	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959389	38959389	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	108	310	0	ENST00000357387.3:c.2086C>T	p.His696Tyr	p.H696Y	ENST00000357387	NM_152756.3	696	Cac/Tac	22/38	1	2	FACETS	0.966	0.875	1	0.966	0.875	1	CLONAL	1	TRUE	1	0.599773222672177	2		310	373	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959413	38959413	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	88	246	1	ENST00000357387.3:c.2062C>T	p.Leu688Phe	p.L688F	ENST00000357387	NM_152756.3	688	Ctt/Ttt	22/38	1	2	FACETS	0.981	0.88	1	0.981	0.88	1	CLONAL	1	TRUE	1	0.599773222672177	2		247	299	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963067	38963067	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	106	258	0	ENST00000357387.3:c.1477C>T	p.His493Tyr	p.H493Y	ENST00000357387	NM_152756.3	493	Cat/Tat	17/38	1	2	FACETS	0.974	0.881	1	0.974	0.881	1	CLONAL	1	TRUE	1	0.599773222672177	2		258	363	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564701	86564702	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	142	434	0	ENST00000274376.6:c.433_434delinsTT	p.Pro145Phe	p.P145F	ENST00000274376	NM_002890.2	145	CCt/TTt	1/25	1	2	FACETS	0.989	0.907	1	0.989	0.907	1	CLONAL	1	TRUE	1	0.599773222672177	2		434	479	SUCCESS
APC	324	MSKCC	GRCh37	5	112103020	112103020	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	140	314	0	ENST00000257430.4:c.355C>T	p.Pro119Ser	p.P119S	ENST00000257430	NM_000038.5	119	Cca/Tca	4/16	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.599773222672177	2		314	441	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499687	149499687	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	62	308	0	ENST00000261799.4:c.2587-1G>A		p.X863_splice	ENST00000261799	NM_002609.3	863			1	2	FACETS	0.774	0.676	0.879	0.774	0.676	0.879	SUBCLONAL	1	TRUE	1	0.599773222672177	2		308	267	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519330	176519331	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	94	376	1	ENST00000292408.4:c.736_737delinsTT	p.Pro246Leu	p.P246L	ENST00000292408	NM_213647.1	246	CCg/TTg	7/18	1	2	FACETS	0.964	0.867	1	0.964	0.867	1	CLONAL	1	TRUE	1	0.599773222672177	2		377	325	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665245	176665245	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	65	198	0	ENST00000439151.2:c.3929C>G	p.Ser1310Cys	p.S1310C	ENST00000439151	NM_022455.4	1310	tCc/tGc	7/23	1	2	FACETS	0.934	0.821	1	0.934	0.821	1	CLONAL	1	TRUE	1	0.599773222672177	2		198	232	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722197	176722197	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	82	291	0	ENST00000439151.2:c.7828C>T	p.Leu2610Phe	p.L2610F	ENST00000439151	NM_022455.4	2610	Ctc/Ttc	23/23	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.599773222672177	2		291	259	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840029	27840029	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	79	351	0	ENST00000328488.2:c.65C>T	p.Ala22Val	p.A22V	ENST00000328488	NM_003533.2	22	gCc/gTc	1/1	0.599773222672177	3	FACETS	0.846	0.748	0.949	0.423	0.374	0.475	CLONAL	1	TRUE	1	0.599773222672177	3		351	405	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323303	31323303	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	90	157	1	ENST00000412585.2:c.686C>T	p.Ala229Val	p.A229V	ENST00000412585	NM_005514.6	229	gCc/gTc	4/8	0.599773222672177	3	FACETS	1	0.977	1	0.673	0.604	0.744	CLONAL	1	TRUE	1	0.599773222672177	3		158	290	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170093	32170093	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	144	578	0	ENST00000375023.3:c.3515A>T	p.Lys1172Ile	p.K1172I	ENST00000375023	NM_004557.3	1172	aAa/aTa	21/30	0.599773222672177	3	FACETS	1	0.921	1	0.503	0.46	0.548	CLONAL	1	TRUE	1	0.599773222672177	3		578	620	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967910	93967910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	218	426	0	ENST00000369303.4:c.2017G>A	p.Glu673Lys	p.E673K	ENST00000369303	NM_004440.3	673	Gaa/Aaa	11/17	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.599773222672177	2		426	583	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124486	94124486	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	128	288	0	ENST00000369303.4:c.98-1G>A		p.X33_splice	ENST00000369303	NM_004440.3	33			1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.599773222672177	2		288	414	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382185	152382185	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	140	404	0	ENST00000206249.3:c.1295C>T	p.Ser432Leu	p.S432L	ENST00000206249	NM_000125.3	432	tCa/tTa	6/8	1	2	FACETS	0.995	0.913	1	0.995	0.913	1	CLONAL	1	TRUE	1	0.599773222672177	2		404	469	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157256639	157256639	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	97	265	0	ENST00000346085.5:c.1966C>T	p.Pro656Ser	p.P656S	ENST00000346085	NM_020732.3	656	Cct/Tct	5/20	1	2	FACETS	0.86	0.773	0.951	0.86	0.773	0.951	CLONAL	1	TRUE	1	0.599773222672177	2		265	376	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521981	157521981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	105	313	0	ENST00000346085.5:c.4253C>T	p.Pro1418Leu	p.P1418L	ENST00000346085	NM_020732.3	1418	cCc/cTc	18/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.599773222672177	2		313	298	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962882	2962882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1466824771	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	117	590	1	ENST00000396946.4:c.2026C>T	p.Leu676Phe	p.L676F	ENST00000396946	NM_032415.4	676	Ctc/Ttc	16/25	1	2	FACETS	0.916	0.832	1	0.916	0.832	1	CLONAL	1	TRUE	1	0.599773222672177	2		591	426	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935537	13935538	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	99	277	0	ENST00000405192.2:c.1318_1319delinsAA	p.Gly440Lys	p.G440K	ENST00000405192	NM_001163147.1	440	GGg/AAg	12/12	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.599773222672177	2		277	305	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335690	81335690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	121	381	1	ENST00000222390.5:c.1670G>A	p.Gly557Glu	p.G557E	ENST00000222390	NM_000601.4	557	gGa/gAa	15/18	1	2	FACETS	0.956	0.871	1	0.956	0.871	1	CLONAL	1	TRUE	1	0.599773222672177	2		382	422	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336636	81336636	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1186981920	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	130	305	0	ENST00000222390.5:c.1586T>C	p.Val529Ala	p.V529A	ENST00000222390	NM_000601.4	529	gTt/gCt	14/18	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.599773222672177	2		305	422	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845099	128845099	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	155	475	0	ENST00000249373.3:c.593T>C	p.Val198Ala	p.V198A	ENST00000249373	NM_005631.4	198	gTt/gCt	3/12	1	2	FACETS	0.99	0.912	1	0.99	0.912	1	CLONAL	1	TRUE	1	0.599773222672177	2		475	522	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140487360	140487360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507472	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	206	461	0	ENST00000288602.6:c.1165C>T	p.Arg389Cys	p.R389C	ENST00000288602	NM_004333.4	389	Cgt/Tgt	9/18	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.599773222672177	2		461	673	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874697	151874698	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	75	334	0	ENST00000262189.6:c.7840_7841delinsAA	p.Gly2614Asn	p.G2614N	ENST00000262189	NM_170606.2	2614	GGt/AAt	38/59	1	2	FACETS	0.77	0.68	0.864	0.77	0.68	0.864	SUBCLONAL	1	TRUE	1	0.599773222672177	2		334	325	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945396	151945396	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	147	400	0	ENST00000262189.6:c.2123C>T	p.Ser708Leu	p.S708L	ENST00000262189	NM_170606.2	708	tCa/tTa	14/59	1	2	FACETS	0.959	0.881	1	0.959	0.881	1	CLONAL	1	TRUE	1	0.599773222672177	2		400	511	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205518	38205518	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	169	581	1	ENST00000317025.8:c.172C>T	p.Gln58Ter	p.Q58*	ENST00000317025	NM_023034.1	58	Cag/Tag	2/24	1	2	FACETS	0.89	0.822	0.961	0.89	0.822	0.961	CLONAL	1	TRUE	1	0.599773222672177	2		582	633	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372430	55372430	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775790177	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	197	604	0	ENST00000297316.4:c.1120G>A	p.Glu374Lys	p.E374K	ENST00000297316	NM_022454.3	374	Gag/Aag	2/2	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.599773222672177	2		604	559	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965340	68965340	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	155	405	0	ENST00000288368.4:c.952C>A	p.His318Asn	p.H318N	ENST00000288368	NM_024870.2	318	Cat/Aat	9/40	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.599773222672177	2		405	516	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68984773	68984773	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1323273757	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	101	339	0	ENST00000288368.4:c.1537G>A	p.Ala513Thr	p.A513T	ENST00000288368	NM_024870.2	513	Gcc/Acc	14/40	1	2	FACETS	0.819	0.738	0.905	0.819	0.738	0.905	CLONAL	1	TRUE	1	0.599773222672177	2		339	411	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68993059	68993059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	122	269	0	ENST00000288368.4:c.1864G>A	p.Gly622Arg	p.G622R	ENST00000288368	NM_024870.2	622	Gga/Aga	17/40	1	2	FACETS	0.973	0.887	1	0.973	0.887	1	CLONAL	1	TRUE	1	0.599773222672177	2		269	418	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970945	70970945	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1242917883	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	165	434	1	ENST00000276594.2:c.1316G>A	p.Arg439Gln	p.R439Q	ENST00000276594	NM_024504.3	439	cGa/cAa	6/8	1	2	FACETS	0.969	0.895	1	0.969	0.895	1	CLONAL	1	TRUE	1	0.599773222672177	2		435	568	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868963	117868963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	123	290	0	ENST00000297338.2:c.736C>T	p.Pro246Ser	p.P246S	ENST00000297338	NM_006265.2	246	Cct/Tct	7/14	1	2	FACETS	0.932	0.849	1	0.932	0.849	1	CLONAL	1	TRUE	1	0.599773222672177	2		290	440	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486280	8486280	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	61	226	0	ENST00000356435.5:c.2537C>T	p.Pro846Leu	p.P846L	ENST00000356435		846	cCg/cTg	17/35	1	2	FACETS	0.904	0.79	1	0.904	0.79	1	CLONAL	1	TRUE	1	0.599773222672177	2		226	225	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500886	8500886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	129	365	0	ENST00000356435.5:c.1996C>T	p.Pro666Ser	p.P666S	ENST00000356435		666	Cct/Tct	13/35	1	2	FACETS	0.896	0.818	0.978	0.896	0.818	0.978	CLONAL	1	TRUE	1	0.599773222672177	2		365	480	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504333	8504333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754609275	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	140	424	0	ENST00000356435.5:c.1750C>T	p.Arg584Cys	p.R584C	ENST00000356435		584	Cgt/Tgt	12/35	1	2	FACETS	0.953	0.874	1	0.953	0.874	1	CLONAL	1	TRUE	1	0.599773222672177	2		424	490	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633355	8633355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	131	384	0	ENST00000356435.5:c.314G>A	p.Gly105Glu	p.G105E	ENST00000356435		105	gGa/gAa	3/35	1	2	FACETS	0.988	0.904	1	0.988	0.904	1	CLONAL	1	TRUE	1	0.599773222672177	2		384	442	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242250	98242251	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	200	358	0	ENST00000331920.6:c.1067_1067+1delinsAA		p.X356_splice	ENST00000331920	NM_000264.3	356		7/24	0.593726056973509	2	FACETS	0.942	0.89	0.994	0.942	0.89	0.994	CLONAL	2	TRUE	0	0.599773222672177	2		358	354	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923172	39923172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	113	438	0	ENST00000378444.4:c.3536C>T	p.Ser1179Phe	p.S1179F	ENST00000378444	NM_001123385.1	1179	tCc/tTc	8/15	1	2	FACETS	0.885	0.802	0.971	0.885	0.802	0.971	CLONAL	1	TRUE	1	0.599773222672177	2		438	426	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922814	44922814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761667415	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	91	267	0	ENST00000377967.4:c.1675C>T	p.Arg559Cys	p.R559C	ENST00000377967	NM_021140.2	559	Cgt/Tgt	16/29	1	2	FACETS	0.939	0.843	1	0.939	0.843	1	CLONAL	1	TRUE	1	0.599773222672177	2		267	323	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649557	48649557	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1478971085	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	127	536	0	ENST00000376670.3:c.41C>T	p.Pro14Leu	p.P14L	ENST00000376670	NM_002049.3	14	cCc/cTc	2/6	1	2	FACETS	0.983	0.897	1	0.983	0.897	1	CLONAL	1	TRUE	1	0.599773222672177	2		536	431	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649605	48649605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	157	554	0	ENST00000376670.3:c.89C>T	p.Ser30Leu	p.S30L	ENST00000376670	NM_002049.3	30	tCa/tTa	2/6	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.599773222672177	2		554	520	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223673	53223673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	172	533	0	ENST00000375401.3:c.3686C>T	p.Ser1229Leu	p.S1229L	ENST00000375401	NM_004187.3	1229	tCa/tTa	23/26	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.599773222672177	2		533	533	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411550	63411550	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	172	520	0	ENST00000330258.3:c.1617C>G	p.Phe539Leu	p.F539L	ENST00000330258	NM_152424.3	539	ttC/ttG	2/2	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.599773222672177	2		520	565	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412589	63412589	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1569192378	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	84	400	0	ENST00000330258.3:c.578G>A	p.Gly193Glu	p.G193E	ENST00000330258	NM_152424.3	193	gGg/gAg	2/2	1	2	FACETS	0.841	0.75	0.937	0.841	0.75	0.937	CLONAL	1	TRUE	1	0.599773222672177	2		400	333	SUCCESS
AR	367	MSKCC	GRCh37	X	66765782	66765782	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	187	650	1	ENST00000374690.3:c.794G>A	p.Gly265Glu	p.G265E	ENST00000374690	NM_000044.3	265	gGg/gAg	1/8	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.599773222672177	2		651	589	SUCCESS
AR	367	MSKCC	GRCh37	X	66766097	66766097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	132	534	0	ENST00000374690.3:c.1109C>T	p.Ala370Val	p.A370V	ENST00000374690	NM_000044.3	370	gCt/gTt	1/8	1	2	FACETS	0.915	0.836	0.997	0.915	0.836	0.997	CLONAL	1	TRUE	1	0.599773222672177	2		534	481	SUCCESS
AR	367	MSKCC	GRCh37	X	66766135	66766135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	91	395	0	ENST00000374690.3:c.1147C>T	p.Pro383Ser	p.P383S	ENST00000374690	NM_000044.3	383	Ccc/Tcc	1/8	1	2	FACETS	0.874	0.783	0.97	0.874	0.783	0.97	CLONAL	1	TRUE	1	0.599773222672177	2		395	347	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344933	70344934	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	107	510	1	ENST00000374080.3:c.2163_2164delinsTT	p.Leu722Phe	p.L722F	ENST00000374080		721	acCCtt/acTTtt	15/45	1	2	FACETS	0.777	0.701	0.857	0.777	0.701	0.857	SUBCLONAL	1	TRUE	1	0.599773222672177	2		511	459	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70350026	70350026	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057520129	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	82	344	0	ENST00000374080.3:c.4009G>A	p.Glu1337Lys	p.E1337K	ENST00000374080		1337	Gaa/Aaa	28/45	1	2	FACETS	0.779	0.692	0.87	0.779	0.692	0.87	SUBCLONAL	1	TRUE	1	0.599773222672177	2		344	351	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361204	70361204	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1212501146	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	126	540	0	ENST00000374080.3:c.6392C>T	p.Pro2131Leu	p.P2131L	ENST00000374080		2131	cCc/cTc	43/45	1	2	FACETS	0.845	0.77	0.924	0.845	0.77	0.924	CLONAL	1	TRUE	1	0.599773222672177	2		540	497	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776325	76776325	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557041077	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	146	530	0	ENST00000373344.5:c.7141G>A	p.Glu2381Lys	p.E2381K	ENST00000373344	NM_000489.3	2381	Gag/Aag	34/35	1	2	FACETS	0.892	0.818	0.968	0.892	0.818	0.968	CLONAL	1	TRUE	1	0.599773222672177	2		530	546	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888754	76888754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	150	452	0	ENST00000373344.5:c.5075G>A	p.Gly1692Glu	p.G1692E	ENST00000373344	NM_000489.3	1692	gGa/gAa	19/35	1	2	FACETS	0.933	0.858	1	0.933	0.858	1	CLONAL	1	TRUE	1	0.599773222672177	2		452	536	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918942	76918942	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	179	481	0	ENST00000373344.5:c.4049G>A	p.Gly1350Glu	p.G1350E	ENST00000373344	NM_000489.3	1350	gGa/gAa	12/35	1	2	FACETS	0.92	0.851	0.99	0.92	0.851	0.99	CLONAL	1	TRUE	1	0.599773222672177	2		481	649	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76919048	76919048	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	78	182	0	ENST00000373344.5:c.3944-1G>A		p.X1315_splice	ENST00000373344	NM_000489.3	1315			1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.599773222672177	2		182	240	SUCCESS
BTK	695	MSKCC	GRCh37	X	100614283	100614283	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	134	388	0	ENST00000308731.7:c.892G>A	p.Glu298Lys	p.E298K	ENST00000308731	NM_000061.2	298	Gag/Aag	10/19	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.599773222672177	2		388	415	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034411	123034411	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	136	352	0	ENST00000355640.3:c.1168A>T	p.Lys390Ter	p.K390*	ENST00000355640		390	Aag/Tag	6/7	1	2	FACETS	0.939	0.86	1	0.939	0.86	1	CLONAL	1	TRUE	1	0.599773222672177	2		352	483	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200028	123200029	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	62	239	2	ENST00000218089.9:c.2100_2101delinsTT	p.His701Tyr	p.H701Y	ENST00000218089	NM_001042749.1	700	gcCCat/gcTTat	22/35	1	2	FACETS	0.774	0.676	0.879	0.774	0.676	0.879	SUBCLONAL	1	TRUE	1	0.599773222672177	2		241	267	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143081	7143081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	86	423	0	ENST00000302850.5:c.2288C>T	p.Ser763Phe	p.S763F	ENST00000302850	NM_000208.2	763	tCc/tTc	12/22	0.139764724273874	0	FACETS	0.34	0.303	0.378			1	INDETERMINATE	1	TRUE	0	0.599773222672177	0		423	338	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649606	48649607	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0023879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	142	557	0	ENST00000376670.3:c.90_91del	p.Val32PhefsTer7	p.V32Ffs*7	ENST00000376670	NM_002049.3	30	tcAGgg/tcgg	2/6	1	2	FACETS	0.914	0.838	0.993	0.914	0.838	0.993	CLONAL	1	TRUE	1	0.599773222672177	2		557	518	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0023881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	58	436	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.26643221370673	3	FACETS	0.848	0.74	0.961	1	0.96	1	CLONAL	3	TRUE	1	0.26643221370673	3		436	194	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934571	NA	P-0023881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	62	466	0	ENST00000269305.4:c.747G>C	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agC	7/11	0.26643221370673	2	FACETS	0.999	0.874	1	0.999	0.874	1	CLONAL	2	TRUE	0	0.26643221370673	2		466	233	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104607	69104607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs563106453	NA	P-0023881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	75	411	0	ENST00000288368.4:c.4451G>A	p.Arg1484Gln	p.R1484Q	ENST00000288368	NM_024870.2	1484	cGa/cAa	37/40	0.26643221370673	3	FACETS	0.985	0.87	1	0.985	0.87	1	CLONAL	2	TRUE	1	0.26643221370673	3		411	324	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646194	3646194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	79	459	0	ENST00000294008.3:c.1884G>A	p.Trp628Ter	p.W628*	ENST00000294008	NM_032444.2	628	tgG/tgA	8/15	0.169296519844604	5	FACETS	0.957	0.851	1	0.957	0.851	1	CLONAL	3	TRUE	2	0.26643221370673	5		459	289	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0023895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	27	454	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	0.177142399638446	2		454	241	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023546	27023546	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	48	442	0	ENST00000324856.7:c.653del	p.Asn218ThrfsTer14	p.N218Tfs*14	ENST00000324856	NM_006015.4	218	Aac/ac	1/20	0.177142399638446	2	FACETS	1	0.888	1	1	0.968	1	CLONAL	3	TRUE	0	0.177142399638446	2		442	174	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226590011	226590011	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs750007700	NA	P-0023895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	27	464	0	ENST00000366794.5:c.190A>G	p.Ile64Val	p.I64V	ENST00000366794	NM_001618.3	64	Atc/Gtc	2/23	0.177142399638446	5	FACETS	1	0.85	1	0.271	0.215	0.334	CLONAL	1	TRUE	1	0.177142399638446	5		464	356	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720846	89720847	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCAA	novel	NA	P-0023895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	15	255	0	ENST00000371953.3:c.1000_1003dup	p.Arg335GlnfsTer9	p.R335Qfs*9	ENST00000371953	NM_000314.4	333	gcc/gCCAAcc	8/9	0.177142399638446	2	FACETS	0.799	0.591	1	0.799	0.591	1	CLONAL	2	TRUE	0	0.177142399638446	2		255	106	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445535	49445535	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	66	648	0	ENST00000301067.7:c.1931del	p.Met644SerfsTer286	p.M644Sfs*286	ENST00000301067	NM_003482.3	644	aTg/ag	10/54	0.177142399638446	3	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	1	0.177142399638446	3		648	369	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639963	3639963	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	36	579	0	ENST00000294008.3:c.3676C>G	p.Arg1226Gly	p.R1226G	ENST00000294008	NM_032444.2	1226	Cgg/Ggg	12/15	1	2	FACETS	0.755	0.624	0.901	1	0.951	1	CLONAL	2	TRUE	1	0.177142399638446	2		579	269	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778596	3778596	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749783719	NA	P-0023895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	41	546	0	ENST00000262367.5:c.6452G>A	p.Arg2151Gln	p.R2151Q	ENST00000262367	NM_004380.2	2151	cGg/cAg	31/31	1	2	FACETS	0.836	0.7	0.984	1	0.963	1	CLONAL	2	TRUE	1	0.177142399638446	2		546	277	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589605	67589607	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	novel	NA	P-0023895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	12	265	0	ENST00000274335.5:c.1368_1370del	p.Phe456_Gln457delinsLeu	p.F456_Q457delinsL	ENST00000274335		456	ttTCAa/tta	10/15	1	2	FACETS	0.941	0.664	1	0.941	0.664	1	CLONAL	1	TRUE	1	0.177142399638446	2		265	144	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157431611	157431611	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554298188	NA	P-0023895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	79	402	1	ENST00000346085.5:c.2287C>T	p.Gln763Ter	p.Q763*	ENST00000346085	NM_020732.3	763	Cag/Tag	7/20	0.177142399638446	3	FACETS	1	0.945	1	1	0.981	1	CLONAL	3	TRUE	1	0.177142399638446	3		403	293	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900080	151900081	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	20	397	0	ENST00000262189.6:c.4030dup	p.Ile1344AsnfsTer11	p.I1344Nfs*11	ENST00000262189	NM_170606.2	1344	ata/aAta	26/59	1	2	FACETS	1	0.816	1	1	0.816	1	CLONAL	1	TRUE	1	0.177142399638446	2		397	210	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120164	70120164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	20	319	0	ENST00000245479.2:c.1166C>T	p.Pro389Leu	p.P389L	ENST00000245479	NM_000346.3	389	cCg/cTg	3/3	1	2	FACETS	0.332	0.255	0.422	0.332	0.255	0.422	SUBCLONAL	1	FALSE	1	0.59937819124948	2		319	201	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851765	134851765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	61	545	0	ENST00000398015.3:c.1171G>A	p.Val391Ile	p.V391I	ENST00000398015	NM_004441.4	391	Gtc/Atc	5/16	1	2	FACETS	0.613	0.532	0.7	0.613	0.532	0.7	SUBCLONAL	1	FALSE	1	0.59937819124948	2		545	332	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs149680468	NA	P-0023896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	27	288	0	ENST00000281708.4:c.1513C>A	p.Arg505Ser	p.R505S	ENST00000281708	NM_033632.3	505	Cgc/Agc	10/12	1	2	FACETS	0.382	0.305	0.469	0.382	0.305	0.469	SUBCLONAL	1	FALSE	1	0.59937819124948	2		288	236	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118568	17118568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759637055	NA	P-0023896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	49	529	1	ENST00000285071.4:c.1363G>A	p.Glu455Lys	p.E455K	ENST00000285071	NM_144997.5	455	Gag/Aag	12/14	1	2	FACETS	0.448	0.38	0.522	0.448	0.38	0.522	SUBCLONAL	1	FALSE	1	0.59937819124948	2		530	365	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0023898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	80	976	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.915	0.813	1	0.915	0.813	1	CLONAL	1	TRUE	1	0.533032785010451	2		976	328	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435160	56435161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755128667	NA	P-0023898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	28	440	2	ENST00000407977.2:c.1976dup	p.Pro660SerfsTer87	p.P660Sfs*87	ENST00000407977		659	ggt/ggGt	9/10	0.533032785010451	1	FACETS	0.213	0.17	0.263	0.213	0.17	0.263	SUBCLONAL	1	TRUE	0	0.533032785010451	1		442	361	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591925	48591925	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	12	302	2	ENST00000342988.3:c.1088G>T	p.Cys363Phe	p.C363F	ENST00000342988	NM_005359.5	363	tGt/tTt	9/12	0.443342576005447	1	FACETS	0.141	0.099	0.193	0.141	0.099	0.193	SUBCLONAL	1	TRUE	0	0.533032785010451	1		304	234	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578539	7578539	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782160	NA	P-0023898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	133	965	0	ENST00000269305.4:c.391A>T	p.Asn131Tyr	p.N131Y	ENST00000269305	NM_001126112.2	131	Aac/Tac	5/11	0.443342576005447	1	FACETS	0.963	0.885	1	0.963	0.885	1	CLONAL	1	TRUE	0	0.533032785010451	1		965	380	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971015	21971049	+	frameshift_variant	Frame_Shift_Del	DEL	CGGGCAGACGGCCCCAGGCATCGCGCACGTCCAGC	CGGGCAGACGGCCCCAGGCATCGCGCACGTCCAGC	-	novel	NA	P-0023898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	54	374	0	ENST00000304494.5:c.309_343del	p.Leu104GlyfsTer4	p.L104Gfs*4	ENST00000304494	NM_000077.4	103	cgGCTGGACGTGCGCGATGCCTGGGGCCGTCTGCCCGtg/cgtg	2/3	0.268321783511307	1	FACETS	0.448	0.384	0.516	0.448	0.384	0.516	INDETERMINATE	1	TRUE	0	0.533032785010451	1		374	332	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974758	21974788	+	frameshift_variant	Frame_Shift_Del	DEL	ACCCCGGGCCGCGGCCGTGGCCAGCCAGTCA	ACCCCGGGCCGCGGCCGTGGCCAGCCAGTCA	-	novel	NA	P-0023898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	31	212	0	ENST00000304494.5:c.39_69del	p.Asp14GlyfsTer2	p.D14Gfs*2	ENST00000304494	NM_000077.4	13	gcTGACTGGCTGGCCACGGCCGCGGCCCGGGGT/gc	1/3	0.268321783511307				0.381	0.561				INDETERMINATE	1	TRUE	0	0.533032785010451	1		212	183	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0023899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	127	983	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.439269139771105	2	FACETS	0.97	0.894	1	0.97	0.894	1	CLONAL	2	TRUE	0	0.439269139771105	2		984	298	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389095	31389095	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756558325	NA	P-0023899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	39	360	0	ENST00000328111.2:c.2008C>T	p.Arg670Trp	p.R670W	ENST00000328111	NM_006892.3	670	Cgg/Tgg	19/23	0.357649036254108	3	FACETS	1	0.882	1	0.533	0.447	0.628	CLONAL	1	TRUE	1	0.439269139771105	3		360	203	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508490	106508490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	24	189	0	ENST00000359195.3:c.484G>A	p.Val162Ile	p.V162I	ENST00000359195	NM_002649.2	162	Gtc/Atc	2/11	1	2	FACETS	0.928	0.742	1	0.928	0.742	1	CLONAL	1	TRUE	1	0.50736142722402	2		189	102	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515375	103515375	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	25	279	0	ENST00000355739.4:c.1876T>C	p.Ser626Pro	p.S626P	ENST00000355739	NM_000123.3	626	Tct/Cct	8/15	0.470422984835382	1	FACETS	0.497	0.396	0.61	0.497	0.396	0.61	SUBCLONAL	1	TRUE	0	0.50736142722402	1		279	148	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125232	47125232	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	47	390	0	ENST00000409792.3:c.6038T>G	p.Leu2013Arg	p.L2013R	ENST00000409792	NM_014159.6	2013	cTg/cGg	12/21	1	2	FACETS	0.702	0.597	0.816	0.702	0.597	0.816	SUBCLONAL	1	TRUE	1	0.50736142722402	2		390	264	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0023901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	129	436	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.91	0.835	0.987	0.91	0.835	0.987	CLONAL	1	TRUE	1	0.796169200487728	2		436	356	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0023901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	267	724	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.283928171006673	3	FACETS	1	0.993	1	0.705	0.666	0.745	INDETERMINATE	1	TRUE	1	0.796169200487728	3		726	665	SUCCESS
APC	324	MSKCC	GRCh37	5	112175162	112175162	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561588104	NA	P-0023901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	63	191	0	ENST00000257430.4:c.3871C>T	p.Gln1291Ter	p.Q1291*	ENST00000257430	NM_000038.5	1291	Cag/Tag	16/16	1	2	FACETS	0.807	0.711	0.909	0.807	0.711	0.909	CLONAL	1	TRUE	1	0.796169200487728	2		191	196	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245496	46245496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	49	277	0	ENST00000334344.6:c.3590C>T	p.Ala1197Val	p.A1197V	ENST00000334344	NM_152641.2	1197	gCt/gTt	15/21	0.330726207272814	1	FACETS	0.273	0.233	0.317	0.273	0.233	0.317	INDETERMINATE	1	TRUE	0	0.796169200487728	1		277	271	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578538	7578538	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	360	709	0	ENST00000269305.4:c.392del	p.Asn131ThrfsTer39	p.N131Tfs*39	ENST00000269305	NM_001126112.2	131	aAc/ac	5/11	0.796169200487728	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.796169200487728	1		709	530	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721489	49721489	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	197	458	1	ENST00000449682.2:c.2150G>A	p.Trp717Ter	p.W717*	ENST00000449682	NM_020998.3	717	tGg/tAg	18/18	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.796169200487728	2		459	469	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0023906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	123	724	2	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.360755074555407	2	FACETS	0.895	0.82	0.972	0.895	0.82	0.972	CLONAL	2	TRUE	0	0.411427685082072	2		726	334	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141492	11141492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	57	404	0	ENST00000358026.2:c.3469C>T	p.Arg1157Trp	p.R1157W	ENST00000358026	NM_001128849.1	1157	Cgg/Tgg	25/36	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.411427685082072	2		404	246	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577024	7577045	+	frameshift_variant	Frame_Shift_Del	DEL	TTAGTGCTCCCTGGGGGCAGCT	TTAGTGCTCCCTGGGGGCAGCT	-	novel	NA	P-0023906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	106	390	0	ENST00000269305.4:c.893_914del	p.Glu298GlyfsTer40	p.E298Gfs*40	ENST00000269305	NM_001126112.2	298	gAGCTGCCCCCAGGGAGCACTAAg/gg	8/11	0.360755074555407	2	FACETS	0.901	0.82	0.984	0.901	0.82	0.984	CLONAL	2	TRUE	0	0.411427685082072	2		390	286	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604704	48604704	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	50	282	1	ENST00000342988.3:c.1526G>A	p.Trp509Ter	p.W509*	ENST00000342988	NM_005359.5	509	tGg/tAg	12/12	0.411427685082072	1	FACETS	0.818	0.701	0.944	0.818	0.701	0.944	CLONAL	1	TRUE	0	0.411427685082072	1		283	236	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73110202	73110204	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs778949580	NA	P-0023906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	37	288	0	ENST00000356692.5:c.414_416del	p.Ser139del	p.S139del	ENST00000356692		137	cCTTct/cct	5/9	1	2	FACETS	0.705	0.585	0.838	0.705	0.585	0.838	SUBCLONAL	1	TRUE	1	0.411427685082072	2		288	255	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266134	41266136	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs587776850	NA	P-0023909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	45	209	0	ENST00000349496.5:c.133_135del	p.Ser45del	p.S45del	ENST00000349496	NM_001904.3	44	cCTTct/cct	3/15	0.179274239350274	3	FACETS	0.84	0.712	0.978	0.42	0.356	0.489	INDETERMINATE	1	TRUE	1	0.575133680534401	3		209	240	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226279	2226281	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0023909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	92	414	0	ENST00000326181.6:c.1895_1897del	p.Asn632del	p.N632del	ENST00000326181	NM_032271.2	631	gACAac/gac	20/21	0.287401021323003	1	FACETS	0.653	0.585	0.724	0.653	0.585	0.724	INDETERMINATE	1	TRUE	0	0.575133680534401	1		414	349	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0023910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	124	571	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.298471461335151	2	FACETS	1	0.953	1	1	0.99	1	CLONAL	3	TRUE	0	0.38	2		571	211	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445007	89445007	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	35	420	0	ENST00000336596.2:c.1327A>G	p.Ile443Val	p.I443V	ENST00000336596	NM_005233.5	443	Att/Gtt	6/17	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.38	2		420	169	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280314	1280314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561203868	NA	P-0023910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	65	600	0	ENST00000310581.5:c.1909G>A	p.Asp637Asn	p.D637N	ENST00000310581	NM_198253.2	637	Gac/Aac	4/16	0.241747830892059	5	FACETS	1	0.961	1	0.43	0.374	0.491	CLONAL	1	TRUE	2	0.38	5		600	416	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259442	55259442	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397517127	NA	P-0023910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	34	283	0	ENST00000275493.2:c.2500G>C	p.Val834Leu	p.V834L	ENST00000275493	NM_005228.3	834	Gtg/Ctg	21/28	0.298471461335151	2	FACETS	0.957	0.79	1	0.478	0.395	0.57	CLONAL	1	TRUE	0	0.38	2		283	187	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039380	47039380	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0023910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	87	495	1	ENST00000377604.3:c.1003A>T	p.Lys335Ter	p.K335*	ENST00000377604	NM_001204468.1	335	Aag/Tag	10/24	0.226026700721954	2	FACETS	1	0.937	1	1	0.937	1	INDETERMINATE	2	TRUE	0	0.38	2		496	218	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100566	8100567	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0023911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	47	511	0	ENST00000346208.3:c.542_543dup	p.Glu182LysfsTer14	p.E182Kfs*14	ENST00000346208		180	-/AA	3/6	0.644417945643754	3	FACETS	0.856	0.73	0.99	0.428	0.365	0.495	CLONAL	1	TRUE	1	0.703903048898245	3		511	211	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772314	68772314	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	78	358	0	ENST00000261769.5:c.163G>A	p.Val55Met	p.V55M	ENST00000261769	NM_004360.3	55	Gtg/Atg	2/16	0.703903048898245	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.703903048898245	2		358	101	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519989	NA	P-0023917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	440	449	0	ENST00000269305.4:c.730G>C	p.Gly244Arg	p.G244R	ENST00000269305	NM_001126112.2	244	Ggc/Cgc	7/11	0.797734291245748	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.797734291245748	3		449	496	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940056	76940057	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	384	261	0	ENST00000373344.5:c.691dup	p.Cys231LeufsTer3	p.C231Lfs*3	ENST00000373344	NM_000489.3	231	tgt/tTgt	9/35	0.797734291245748	3	FACETS	1	0.993	1			1	CLONAL	3	TRUE	NA	0.797734291245748	3		261	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0023919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	160	689	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.650498912612118	2	FACETS	0.971	0.919	1	0.971	0.919	1	CLONAL	2	TRUE	0	0.713435027227952	2		689	231	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0023919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	147	466	1	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.650498912612118	2	FACETS	0.945	0.891	0.997	0.945	0.891	0.997	CLONAL	2	TRUE	0	0.713435027227952	2		467	218	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113234	209113234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs887664727	NA	P-0023919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	92	382	0	ENST00000345146.2:c.273G>A	p.Met91Ile	p.M91I	ENST00000345146	NM_005896.2	91	atG/atA	4/10	0.713435027227952	4	FACETS	1	0.951	1	0.278	0.248	0.309	CLONAL	1	TRUE	0	0.713435027227952	4		382	398	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307989	11307989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	79	336	0	ENST00000361445.4:c.1003G>A	p.Gly335Arg	p.G335R	ENST00000361445	NM_004958.3	335	Ggg/Agg	7/58	0.402631955493039	4	FACETS	1	0.947	1			1	INDETERMINATE	1	TRUE	NA	0.713435027227952	4		336	339	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461937	120461937	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	131	219	0	ENST00000256646.2:c.5779del	p.Gln1927ArgfsTer3	p.Q1927Rfs*3	ENST00000256646	NM_024408.3	1927	Cag/ag	31/34	0.713435027227952	4	FACETS	0.965	0.889	1			1	CLONAL	2	TRUE	NA	0.713435027227952	4		219	326	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865285	57865285	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	518	523	3	ENST00000228682.2:c.2762A>T	p.Gln921Leu	p.Q921L	ENST00000228682	NM_005269.2	921	cAg/cTg	12/12	0.713435027227952	4	FACETS	0.947	0.915	0.978	1	0.997	1	CLONAL	3	TRUE	2	0.713435027227952	4		526	876	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121877	2121877	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs756536921	NA	P-0023919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	141	605	0	ENST00000219476.3:c.2039G>C	p.Arg680Pro	p.R680P	ENST00000219476	NM_000548.3	680	cGg/cCg	19/42	0.561135317481924	4	FACETS	1	0.986	1	0.7	0.642	0.759	CLONAL	1	TRUE	2	0.713435027227952	4		605	484	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41199660	41199660	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs80357212	NA	P-0023919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	188	517	0	ENST00000357654.3:c.5467G>A	p.Ala1823Thr	p.A1823T	ENST00000357654	NM_007294.3	1823	Gca/Aca	22/23	0.483776060015776	4	FACETS	0.873	0.814	0.934	0.873	0.814	0.934	CLONAL	2	TRUE	2	0.713435027227952	4		517	517	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281209	15281209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	39	616	0	ENST00000263388.2:c.5047C>T	p.His1683Tyr	p.H1683Y	ENST00000263388	NM_000435.2	1683	Cac/Tac	27/33	0.584626914695161	3	FACETS	0.317	0.262	0.378	0.158	0.131	0.189	SUBCLONAL	1	TRUE	1	0.713435027227952	3		616	468	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867354	45867354	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	91	513	0	ENST00000391945.4:c.839G>T	p.Arg280Leu	p.R280L	ENST00000391945	NM_000400.3	280	cGc/cTc	10/23	0.713435027227952	3	FACETS	0.801	0.715	0.892	0.401	0.357	0.446	CLONAL	1	TRUE	1	0.713435027227952	3		513	432	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281470	198281470	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	280	300	0	ENST00000335508.6:c.661G>T	p.Ala221Ser	p.A221S	ENST00000335508	NM_012433.2	221	Gca/Tca	6/25	0.713435027227952	4	FACETS	0.961	0.929	0.99	0.961	0.929	0.99	CLONAL	4	TRUE	0	0.713435027227952	4		300	350	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374428	31374428	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	172	317	0	ENST00000328111.2:c.427A>T	p.Thr143Ser	p.T143S	ENST00000328111	NM_006892.3	143	Acc/Tcc	5/23	NA	2	FACETS	1	0.951	1			1	INDETERMINATE	2	TRUE	NA	0.713435027227952	2		317	241	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015158	71015158	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	85	186	2	ENST00000318789.4:c.1772del	p.Gly591GlufsTer8	p.G591Efs*8	ENST00000318789	NM_032682.5	591	gGa/ga	20/21	0.650498912612118	2	FACETS	0.961	0.89	1	0.961	0.89	1	CLONAL	2	TRUE	0	0.713435027227952	2		188	124	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31422954	31422954	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	77	527	0	ENST00000344624.3:c.3359A>G	p.His1120Arg	p.H1120R	ENST00000344624		1120	cAt/cGt	26/33	0.713435027227952	3	FACETS	0.559	0.492	0.631	0.279	0.246	0.316	SUBCLONAL	1	TRUE	1	0.713435027227952	3		527	524	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047947	180047947	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	207	509	2	ENST00000261937.6:c.2228C>T	p.Ala743Val	p.A743V	ENST00000261937	NM_182925.4	743	gCg/gTg	15/30	0.650498912612118	2	FACETS	0.904	0.859	0.948	0.904	0.859	0.948	CLONAL	2	TRUE	0	0.713435027227952	2		511	321	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484238	8484238	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	159	386	0	ENST00000356435.5:c.3294G>T	p.Arg1098Ser	p.R1098S	ENST00000356435		1098	agG/agT	19/35	0.650498912612118	2	FACETS	0.864	0.813	0.914	0.864	0.813	0.914	CLONAL	2	TRUE	0	0.713435027227952	2		386	258	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801044	135801050	+	frameshift_variant	Frame_Shift_Del	DEL	CTTATGA	CTTATGA	-	novel	NA	P-0023919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	188	373	0	ENST00000298552.3:c.287_293del	p.Val96AspfsTer20	p.V96Dfs*20	ENST00000298552	NM_001162426.1	96	gTCATAAGa/ga	5/23	0.713435027227952	3	FACETS	0.87	0.827	0.911	0.87	0.827	0.911	CLONAL	3	TRUE	0	0.713435027227952	3		373	274	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608247	100608247	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	48	544	0	ENST00000308731.7:c.1843C>A	p.Arg615Ser	p.R615S	ENST00000308731	NM_000061.2	615	Cgt/Agt	18/19	0.384252069881658	1	FACETS	0.383	0.327	0.443	0.383	0.327	0.443	INDETERMINATE	1	TRUE	0	0.713435027227952	1		544	226	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184148	123184148	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	22	264	1	ENST00000218089.9:c.1006A>T	p.Met336Leu	p.M336L	ENST00000218089	NM_001042749.1	336	Atg/Ttg	11/35	0.384252069881658	1	FACETS	0.256	0.2	0.32	0.256	0.2	0.32	INDETERMINATE	1	TRUE	0	0.713435027227952	1		265	155	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594210	55594212	+	missense_variant	Missense_Mutation	TNP	TGT	TGT	AGC	novel	NA	P-0023919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	79	317	0	ENST00000288135.5:c.1913_1915delinsAGC	p.Met638_Ser639delinsLysPro	p.M638_S639delinsKP	ENST00000288135	NM_000222.2	638	aTGTct/aAGCct	13/21	1	2	FACETS	0.893	0.797	0.993	0.893	0.797	0.993	CLONAL	1	TRUE	1	0.713435027227952	2		317	248	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0023986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	200	238	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.340894026883064	8	FACETS	0.949	0.878	1	0.271	0.25	0.293	CLONAL	2	TRUE	1	0.340894026883064	8		238	1250	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098957	178098957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	110	455	0	ENST00000397062.3:c.88C>T	p.Leu30Phe	p.L30F	ENST00000397062	NM_006164.4	30	Ctt/Ttt	2/5	1	2	FACETS	0.877	0.788	0.971	0.877	0.788	0.971	CLONAL	1	TRUE	1	0.340894026883064	2		455	736	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882319	89882319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	98	98	0	ENST00000389301.3:c.155G>A	p.Arg52Gln	p.R52Q	ENST00000389301	NM_000135.2	52	cGa/cAa	2/43	1	2	FACETS	0.783	0.699	0.873	0.783	0.699	0.873	SUBCLONAL	1	TRUE	1	0.340894026883064	2		98	734	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439859	49439874	+	frameshift_variant	Frame_Shift_Del	DEL	ACCACGTAGGGCTGGC	ACCACGTAGGGCTGGC	-	novel	NA	P-0023986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	86	99	0	ENST00000301067.7:c.4667_4682del	p.Cys1556Ter	p.C1556*	ENST00000301067	NM_003482.3	1556	tGCCAGCCCTACGTGGTa/ta	17/54	0.186922907748177	3	FACETS	0.692	0.611	0.779			1	INDETERMINATE	1	TRUE	NA	0.340894026883064	3		99	853	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446061	49446062	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	200	116	0	ENST00000301067.7:c.1404dup	p.Pro469ThrfsTer4	p.P469Tfs*4	ENST00000301067	NM_003482.3	468	-/A	10/54	0.186922907748177	3	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.340894026883064	3		116	1163	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383125	42383125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1383009914	NA	P-0023986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	106	115	0	ENST00000221972.3:c.145G>A	p.Asp49Asn	p.D49N	ENST00000221972	NM_021601.3	49	Gac/Aac	2/5	1	2	FACETS	0.762	0.683	0.846	0.762	0.683	0.846	SUBCLONAL	1	TRUE	1	0.340894026883064	2		115	816	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358946	81358946	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	81	170	0	ENST00000222390.5:c.1015A>G	p.Met339Val	p.M339V	ENST00000222390	NM_000601.4	339	Atg/Gtg	8/18	1	2	FACETS	0.622	0.547	0.702	0.622	0.547	0.702	SUBCLONAL	1	TRUE	1	0.340894026883064	2		170	764	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971153	21971153	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913383	NA	P-0023994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	57	623	0	ENST00000304494.5:c.205G>T	p.Glu69Ter	p.E69*	ENST00000304494	NM_000077.4	69	Gag/Tag	2/3	1	2	FACETS	0.568	0.488	0.655	0.568	0.488	0.655	SUBCLONAL	1	TRUE	1	0.42	2		623	478	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0023994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	54	515	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.532	0.455	0.617	0.532	0.455	0.617	SUBCLONAL	1	TRUE	1	0.42	2		515	483	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115928	8115929	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	57	602	0	ENST00000346208.3:c.1275dup	p.Ser426IlefsTer81	p.S426Ifs*81	ENST00000346208		425	cca/ccAa	6/6	1	2	FACETS	0.431	0.369	0.498	0.431	0.369	0.498	SUBCLONAL	1	TRUE	1	0.42	2		602	630	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405968	49405968	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	73	645	0	ENST00000418115.1:c.170T>C	p.Leu57Ser	p.L57S	ENST00000418115	NM_001664.2	57	tTg/tCg	3/5	1	2	FACETS	0.493	0.431	0.56	0.493	0.431	0.56	SUBCLONAL	1	TRUE	1	0.42	2		645	705	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873687	151873688	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATGA	novel	NA	P-0023994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	108	712	0	ENST00000262189.6:c.8847_8850dup	p.Val2951SerfsTer18	p.V2951Sfs*18	ENST00000262189	NM_170606.2	2950	-/TCAT	38/59	0.230554591490749	3	FACETS	0.953	0.857	1	0.476	0.428	0.528	INDETERMINATE	1	TRUE	1	0.42	3		712	653	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878867	151878868	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0023994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	69	783	0	ENST00000262189.6:c.6077dup	p.Tyr2026Ter	p.Y2026*	ENST00000262189	NM_170606.2	2026	tat/taAt	36/59	0.230554591490749	3	FACETS	0.483	0.42	0.552	0.242	0.21	0.276	INDETERMINATE	1	TRUE	1	0.42	3		783	823	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111462	8111463	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGT	novel	NA	P-0023994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	71	721	0	ENST00000346208.3:c.949_951dup	p.Cys317dup	p.C317dup	ENST00000346208		317	-/TGT	5/6	1	2	FACETS	0.424	0.369	0.483	0.424	0.369	0.483	SUBCLONAL	1	TRUE	1	0.42	2		721	798	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971153	21971153	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913383	NA	P-0023994-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	73	623	0	ENST00000304494.5:c.205G>T	p.Glu69Ter	p.E69*	ENST00000304494	NM_000077.4	69	Gag/Tag	2/3	0.3	1	FACETS	0.837	0.734	0.947	0.837	0.734	0.947	CLONAL	1	TRUE	0	0.32	1		623	458	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0023994-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	74	515	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	NA	3	FACETS	1	0.947	1	0.572	0.502	0.647	INDETERMINATE	1	TRUE	1	0.32	3		515	469	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115928	8115929	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023994-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	74	602	0	ENST00000346208.3:c.1275dup	p.Ser426IlefsTer81	p.S426Ifs*81	ENST00000346208		425	cca/ccAa	6/6	1	2	FACETS	0.884	0.776	1	0.884	0.776	1	CLONAL	1	TRUE	1	0.32	2		602	523	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405968	49405968	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023994-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	72	645	0	ENST00000418115.1:c.170T>C	p.Leu57Ser	p.L57S	ENST00000418115	NM_001664.2	57	tTg/tCg	3/5	NA	3	FACETS	0.822	0.718	0.934	0.411	0.359	0.467	INDETERMINATE	1	TRUE	1	0.32	3		645	635	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873687	151873688	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATGA	novel	NA	P-0023994-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	170	712	0	ENST00000262189.6:c.8847_8850dup	p.Val2951SerfsTer18	p.V2951Sfs*18	ENST00000262189	NM_170606.2	2950	-/TCAT	38/59	0.274476888831266	5	FACETS	1	0.944	1	0.687	0.633	0.743	CLONAL	2	TRUE	2	0.32	5		712	763	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878867	151878868	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0023994-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	61	783	0	ENST00000262189.6:c.6077dup	p.Tyr2026Ter	p.Y2026*	ENST00000262189	NM_170606.2	2026	tat/taAt	36/59	0.274476888831266	5	FACETS	0.698	0.601	0.805	0.233	0.2	0.269	SUBCLONAL	1	TRUE	2	0.32	5		783	808	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579369	7579369	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555526581	NA	P-0023996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	225	715	0	ENST00000269305.4:c.318C>G	p.Ser106Arg	p.S106R	ENST00000269305	NM_001126112.2	106	agC/agG	4/11	0.459950966564297	2	FACETS	0.952	0.895	1	0.952	0.895	1	CLONAL	2	TRUE	0	0.459950966564297	2		715	514	SUCCESS
AR	367	MSKCC	GRCh37	X	66765263	66765263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	173	501	0	ENST00000374690.3:c.275G>A	p.Gly92Asp	p.G92D	ENST00000374690	NM_000044.3	92	gGt/gAt	1/8	0.459950966564297	6	FACETS	1	0.977	1	0.571	0.528	0.616	CLONAL	2	TRUE	2	0.459950966564297	6		501	632	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30103654	30103654	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	46	667	0	ENST00000331968.5:c.1284G>C	p.Trp428Cys	p.W428C	ENST00000331968	NM_002742.2	428	tgG/tgC	8/18	0.458250816301607	4	FACETS	0.41	0.344	0.482	0.205	0.172	0.241	SUBCLONAL	1	TRUE	2	0.459950966564297	4		667	713	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135313	2135313	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	192	606	0	ENST00000219476.3:c.4652G>C	p.Gly1551Ala	p.G1551A	ENST00000219476	NM_000548.3	1551	gGa/gCa	36/42	0.459950966564297	2	FACETS	0.953	0.892	1	0.953	0.892	1	CLONAL	2	TRUE	0	0.459950966564297	2		606	438	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663317	67663317	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	151	484	0	ENST00000264010.4:c.1718A>G	p.His573Arg	p.H573R	ENST00000264010	NM_006565.3	573	cAt/cGt	10/12	0.459950966564297	2	FACETS	0.827	0.765	0.89	0.827	0.765	0.89	CLONAL	2	TRUE	0	0.459950966564297	2		484	397	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665410	182665410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	99	428	0	ENST00000292782.4:c.531G>A	p.Met177Ile	p.M177I	ENST00000292782	NM_020640.2	177	atG/atA	5/7	0.459950966564297	7	FACETS	0.863	0.773	0.959	0.345	0.309	0.384	CLONAL	2	TRUE	2	0.459950966564297	7		428	536	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001281-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	85	445	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.932	1			1	INDETERMINATE	1	TRUE	NA	0.31	2		445	511	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0001281-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3316	3056	715	0	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.304055607840107	31	FACETS	1	0.984	1	0.548	0.54	0.557	CLONAL	17	TRUE	0	0.31	31		715	6372	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168468	56168468	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001281-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	73	232	0	ENST00000399503.3:c.1424G>C	p.Trp475Ser	p.W475S	ENST00000399503	NM_005921.1	475	tGg/tCg	8/20	1	2	FACETS	0.987	0.866	1	0.987	0.866	1	CLONAL	1	TRUE	1	0.31	2		232	477	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956964	2956964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1395288944	NA	P-0001281-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	128	578	1	ENST00000396946.4:c.2663G>A	p.Arg888His	p.R888H	ENST00000396946	NM_032415.4	888	cGt/cAt	20/25	0.106095433682641	3	FACETS	1	0.97	1	0.389	0.352	0.428	INDETERMINATE	1	TRUE	0	0.31	3		579	817	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692995	89692995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554898225	NA	P-0001281-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	123	380	0	ENST00000371953.3:c.479C>T	p.Thr160Ile	p.T160I	ENST00000371953	NM_000314.4	160	aCc/aTc	5/9	0.304055607840107	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.31	1		380	508	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046560	30046560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs541601115	NA	P-0001281-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	150	594	1	ENST00000331968.5:c.2623G>A	p.Glu875Lys	p.E875K	ENST00000331968	NM_002742.2	875	Gag/Aag	18/18	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.31	2		595	967	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223604	55223604	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001281-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	2901	422	0	ENST00000275493.2:c.971G>T	p.Arg324Leu	p.R324L	ENST00000275493	NM_005228.3	324	cGc/cTc	8/28	0.304055607840107	31	FACETS	1	0.996	1	0.885	0.875	0.895	CLONAL	27	TRUE	0	0.31	31		422	3748	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001971-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	82	445	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.906	0.803	1	0.906	0.803	1	CLONAL	1	TRUE	1	0.429090586082992	2		445	422	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459525	50459525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778820674	NA	P-0001971-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	83	517	0	ENST00000331340.3:c.814G>A	p.Ala272Thr	p.A272T	ENST00000331340	NM_006060.4	272	Gcc/Acc	7/8	0.408421197188933	3	FACETS	0.731	0.645	0.822	0.365	0.322	0.411	SUBCLONAL	1	TRUE	1	0.429090586082992	3		517	643	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913444	NA	P-0001971-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	22	969	0	ENST00000275493.2:c.2582T>G	p.Leu861Arg	p.L861R	ENST00000275493	NM_005228.3	861	cTg/cGg	21/28	0.408421197188933	3	FACETS	0.15	0.115	0.19	0.075	0.057	0.095	SUBCLONAL	1	TRUE	1	0.429090586082992	3		969	833	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655248	45655248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs533193731	NA	P-0001971-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	125	1079	0	ENST00000407780.3:c.604G>A	p.Val202Met	p.V202M	ENST00000407780	NM_001283052.1	202	Gtg/Atg	4/7	0.332005574268534	3	FACETS	0.898	0.813	0.987	0.449	0.406	0.494	CLONAL	1	TRUE	1	0.429090586082992	3		1079	788	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092852	27092852	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001971-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	81	787	0	ENST00000324856.7:c.2873C>A	p.Ser958Tyr	p.S958Y	ENST00000324856	NM_006015.4	958	tCt/tAt	9/20	0.122074064061519	0	FACETS	0.394	0.348	0.444			1	INDETERMINATE	1	TRUE	0	0.429090586082992	0		787	547	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457231	25457231	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs752280049	NA	P-0001971-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	26	820	7	ENST00000264709.3:c.2656C>T	p.Gln886Ter	p.Q886*	ENST00000264709	NM_175629.2	886	Cag/Tag	23/23	0.429090586082992	1	FACETS	0.191	0.151	0.238	0.191	0.151	0.238	SUBCLONAL	1	TRUE	0	0.429090586082992	1		827	498	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233077	55233077	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001971-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	138	805	0	ENST00000275493.2:c.1827G>T	p.Lys609Asn	p.K609N	ENST00000275493	NM_005228.3	609	aaG/aaT	15/28	0.408421197188933	3	FACETS	0.981	0.894	1	0.491	0.447	0.537	CLONAL	1	TRUE	1	0.429090586082992	3		805	796	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0002506-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	35	550	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.118051923294117	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		552	254	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0002506-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	375	501	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.3	8	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	8		501	788	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0002506-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	53	285	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	0.3	3	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	3		285	408	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098328	47098328	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs771957568	NA	P-0002506-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	35	321	0	ENST00000409792.3:c.6946A>G	p.Thr2316Ala	p.T2316A	ENST00000409792	NM_014159.6	2316	Act/Gct	15/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		321	444	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670519	134670519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002506-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	36	419	0	ENST00000398015.3:c.430G>A	p.Glu144Lys	p.E144K	ENST00000398015	NM_004441.4	144	Gag/Aag	3/16	0.118051923294117	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		419	588	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0002841-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	52	549	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.886	0.754	1	0.886	0.754	1	CLONAL	1	FALSE	1	0.197508525809766	2		549	594	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002841-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	71	783	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.986	0.86	1	0.986	0.86	1	CLONAL	1	FALSE	1	0.197508525809766	2		783	729	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002841-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	68	532	0	ENST00000263967.3:c.333G>T	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaT	2/21	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	FALSE	1	0.197508525809766	2		532	649	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458591	120458591	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002841-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	75	719	0	ENST00000256646.2:c.6754G>A	p.Asp2252Asn	p.D2252N	ENST00000256646	NM_024408.3	2252	Gat/Aat	34/34	0.197508525809766	3	FACETS	1	0.902	1	0.518	0.453	0.588	CLONAL	1	FALSE	1	0.197508525809766	3		719	805	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463227	25463227	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002841-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	61	738	0	ENST00000264709.3:c.2266G>C	p.Glu756Gln	p.E756Q	ENST00000264709	NM_175629.2	756	Gag/Cag	19/23	1	2	FACETS	0.826	0.711	0.951	0.826	0.711	0.951	CLONAL	1	FALSE	1	0.197508525809766	2		738	748	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88651921	88651921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002841-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	70	666	1	ENST00000372037.3:c.268G>A	p.Asp90Asn	p.D90N	ENST00000372037	NM_004329.2	90	Gac/Aac	5/13	0.113825385383844	1	FACETS	0.852	0.742	0.971	0.852	0.742	0.971	INDETERMINATE	1	FALSE	0	0.197508525809766	1		667	750	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534316	534316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002841-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	34	510	0	ENST00000451590.1:c.7G>A	p.Glu3Lys	p.E3K	ENST00000451590	NM_001130442.1	3	Gaa/Aaa	2/5	NA	2	FACETS	0.803	0.656	0.968			1	INDETERMINATE	1	FALSE	NA	0.197508525809766	2		510	429	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213538	2213538	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002841-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	63	702	0	ENST00000398665.3:c.1558G>A	p.Glu520Lys	p.E520K	ENST00000398665	NM_032482.2	520	Gag/Aag	17/28	0.113825385383844	1	FACETS	0.842	0.727	0.966	0.842	0.727	0.966	INDETERMINATE	1	FALSE	0	0.197508525809766	1		702	683	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533763	533763	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0002841-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	76	692	2	ENST00000451590.1:c.290+3G>A		p.X97_splice	ENST00000451590	NM_001130442.1	97			NA	2	FACETS	1	0.902	1			1	INDETERMINATE	1	FALSE	NA	0.197508525809766	2		694	744	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213003	39213003	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002841-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	94	974	0	ENST00000402219.2:c.3964G>C	p.Asp1322His	p.D1322H	ENST00000402219	NM_005633.3	1322	Gat/Cat	23/23	1	2	FACETS	0.89	0.79	0.997	0.89	0.79	0.997	CLONAL	1	FALSE	1	0.197508525809766	2		974	1070	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55945935	55946136	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	CCTCTTCCAGGATATGCCTAGAAGACTGGCTCCCTGCAGTCCGAGGTCCTTTTTCTGTTGTCGAAATGAAAATCAAATGCGGCTACTTCCTGCTGGTGGAAAGAACAACACTTGAAAATCTGAGCAGCACCTCTCATGTGATGTCCAGGAGTTGGGGGTGTGGATGCTTCCTTTTAAACAGGAGGAGAGCTCAGTGTGGTCC	CCTCTTCCAGGATATGCCTAGAAGACTGGCTCCCTGCAGTCCGAGGTCCTTTTTCTGTTGTCGAAATGAAAATCAAATGCGGCTACTTCCTGCTGGTGGAAAGAACAACACTTGAAAATCTGAGCAGCACCTCTCATGTGATGTCCAGGAGTTGGGGGTGTGGATGCTTCCTTTTAAACAGGAGGAGAGCTCAGTGTGGTCC	-	novel	NA	P-0002841-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	33	29	0	ENST00000263923.4:c.4043_*173del		p.*1348*	ENST00000263923	NM_002253.2	1348		30/30	0.197508525809766	3	FACETS	1	0.911	1			1	CLONAL	6	FALSE	NA	0.197508525809766	3		29	57	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946319	55946336	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCACCATTCCACTGCAG	GGCACCATTCCACTGCAG	AT	novel	NA	P-0002841-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	31	327	1	ENST00000263923.4:c.3849-6_3860delinsAT		p.X1283_splice	ENST00000263923	NM_002253.2	1283		30/30	0.197508525809766	3	FACETS	0.887	0.717	1			1	CLONAL	1	FALSE	NA	0.197508525809766	3		328	389	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412046	116412046	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	G	novel	NA	P-0004703-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	52	961	0	ENST00000397752.3:c.3028+3A>G		p.X1010_splice	ENST00000397752	NM_000245.2	1010			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		961	931	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0005264-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1821	211	680	2	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.259861344914257	12	FACETS	0.919	0.849	0.991			1	CLONAL	2	TRUE	NA	0.259861344914257	12		682	2032	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0005264-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	962	644	1	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.259861344914257	12	FACETS	0.959	0.933	0.984			1	CLONAL	10	TRUE	NA	0.259861344914257	12		645	1776	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300206	15300206	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005264-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	60	837	2	ENST00000263388.2:c.1070G>T	p.Ser357Ile	p.S357I	ENST00000263388	NM_000435.2	357	aGc/aTc	7/33	1	2	FACETS	0.588	0.506	0.679	0.588	0.506	0.679	SUBCLONAL	1	TRUE	1	0.259861344914257	2		839	785	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006890	47006891	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005264-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	155	400	0	ENST00000377604.3:c.13dup	p.Arg5LysfsTer7	p.R5Kfs*7	ENST00000377604	NM_001204468.1	4	gaa/gAaa	2/24	1	1	FACETS	0.965	0.888	1	1	0.992	1	CLONAL	2	TRUE	0	0.259861344914257	1		400	538	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281344	49281344	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202077345	NA	P-0005264-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	98	851	1	ENST00000282018.3:c.391G>A	p.Val131Met	p.V131M	ENST00000282018	NM_020377.2	131	Gtg/Atg	1/1	0.259861344914257	1	FACETS	0.624	0.555	0.697	0.624	0.555	0.697	SUBCLONAL	1	TRUE	0	0.259861344914257	1		852	1052	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740620	145740620	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005344-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	323	794	0	ENST00000428558.2:c.1397C>G	p.Pro466Arg	p.P466R	ENST00000428558	NM_004260.3	466	cCg/cGg	8/22	0.783475879780306	4	FACETS	0.981	0.924	1	0.327	0.308	0.347	CLONAL	1	TRUE	1	0.783475879780306	4		794	1499	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4097290	4097290	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730880512	NA	P-0005344-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	332	756	0	ENST00000262948.5:c.971A>G	p.Tyr324Cys	p.Y324C	ENST00000262948	NM_030662.3	324	tAt/tGt	8/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.783475879780306	2		756	825	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40498723	40498723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868859792	NA	P-0005344-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	133	610	0	ENST00000264657.5:c.137C>T	p.Ala46Val	p.A46V	ENST00000264657	NM_139276.2	46	gCg/gTg	3/24	1	2	FACETS	0.456	0.414	0.499	0.456	0.414	0.499	SUBCLONAL	1	TRUE	1	0.783475879780306	2		610	745	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647636	3647636	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005693-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	273	1184	0	ENST00000294008.3:c.1427C>G	p.Ser476Cys	p.S476C	ENST00000294008	NM_032444.2	476	tCt/tGt	7/15	0.119422154931074	1	FACETS	0.718	0.677	0.759	0.718	0.677	0.759	INDETERMINATE	1	TRUE	0	0.69	1		1184	722	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878082	151878082	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005693-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	166	557	0	ENST00000262189.6:c.6863G>C	p.Ser2288Thr	p.S2288T	ENST00000262189	NM_170606.2	2288	aGc/aCc	36/59	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.69	2		557	457	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0006010-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	163	736	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.494857095322394	2		736	652	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0006010-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	95	779	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	1	2	FACETS	0.936	0.839	1	0.936	0.839	1	CLONAL	1	TRUE	1	0.494857095322394	2		779	410	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584629	52584629	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006010-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	199	777	1	ENST00000394830.3:c.4384C>T	p.Gln1462Ter	p.Q1462*	ENST00000394830	NM_018313.4	1462	Cag/Tag	29/30	0.121009543454914	3	FACETS	1	0.986	1	0.63	0.585	0.677	INDETERMINATE	1	TRUE	1	0.494857095322394	3		778	796	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006010-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	74	549	0	ENST00000263967.3:c.1034A>G	p.Asn345Ser	p.N345S	ENST00000263967	NM_006218.2	345	aAt/aGt	5/21	1	2	FACETS	0.952	0.841	1	0.952	0.841	1	CLONAL	1	TRUE	1	0.494857095322394	2		549	314	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197359	26197359	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006010-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	142	610	0	ENST00000356476.2:c.120C>G	p.His40Gln	p.H40Q	ENST00000356476		40	caC/caG	1/1	0.428875690536657	3	FACETS	1	0.975	1	0.39	0.356	0.425	CLONAL	1	TRUE	0	0.494857095322394	3		610	612	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904885	101904885	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0006010-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	142	646	0	ENST00000374994.4:c.873C>G	p.Tyr291Ter	p.Y291*	ENST00000374994	NM_004612.2	291	taC/taG	5/9	0.494857095322394	1	FACETS	0.951	0.874	1	0.951	0.874	1	CLONAL	1	TRUE	0	0.494857095322394	1		646	454	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123022514	123022514	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006010-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	222	437	0	ENST00000355640.3:c.923C>G	p.Thr308Ser	p.T308S	ENST00000355640		308	aCt/aGt	3/7	1	1	FACETS	0.848	0.803	0.893	1	0.994	1	CLONAL	2	TRUE	0	0.494857095322394	1		437	398	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106879	27106895	+	frameshift_variant	Frame_Shift_Del	DEL	CGGGAGATGGCTGTGGT	CGGGAGATGGCTGTGGT	-	novel	NA	P-0006010-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	179	757	0	ENST00000324856.7:c.6490_6506del	p.Arg2164ThrfsTer55	p.R2164Tfs*55	ENST00000324856	NM_006015.4	2164	CGGGAGATGGCTGTGGTa/a	20/20	0.42611865339262	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.494857095322394	1		757	505	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202773	16202773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140309172	NA	P-0006010-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	32	772	1	ENST00000375759.3:c.481C>T	p.Arg161Trp	p.R161W	ENST00000375759	NM_015001.2	161	Cgg/Tgg	3/15	0.42611865339262	1	FACETS	0.17	0.138	0.208	0.17	0.138	0.208	SUBCLONAL	1	TRUE	0	0.494857095322394	1		773	571	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784068	120784068	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006010-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	53	1035	0	ENST00000257552.2:c.917G>C	p.Gly306Ala	p.G306A	ENST00000257552	NM_002442.3	306	gGc/gCc	13/15	1	2	FACETS	0.215	0.182	0.251	0.215	0.182	0.251	SUBCLONAL	1	TRUE	1	0.494857095322394	2		1035	998	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602352	10602352	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006117-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	84	1009	0	ENST00000171111.5:c.1226T>C	p.Met409Thr	p.M409T	ENST00000171111	NM_203500.1	409	aTg/aCg	3/6	0.184384193240312	0	FACETS	0.384	0.341	0.43			1	INDETERMINATE	1	TRUE	0	0.531696674415586	0		1009	385	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188248	10188248	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006117-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	141	924	0	ENST00000256474.2:c.392del	p.Asn131ThrfsTer28	p.N131Tfs*28	ENST00000256474	NM_000551.3	131	Aac/ac	2/3	0.488284318955191	1	FACETS	0.897	0.825	0.972	0.897	0.825	0.972	CLONAL	1	TRUE	0	0.531696674415586	1		924	434	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023864	27023880	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGCCGGCAAGGGCCC	GGCGCCGGCAAGGGCCC	-	novel	NA	P-0006117-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	43	292	0	ENST00000324856.7:c.974_990del	p.Ala325GlyfsTer69	p.A325Gfs*69	ENST00000324856	NM_006015.4	324	GGCGCCGGCAAGGGCCCg/g	1/20	1	2	FACETS	0.829	0.703	0.966	0.829	0.703	0.966	CLONAL	1	TRUE	1	0.531696674415586	2		292	195	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61709537	61709537	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006117-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	107	554	0	ENST00000401558.2:c.2950T>C	p.Ser984Pro	p.S984P	ENST00000401558	NM_003400.3	984	Tcg/Ccg	23/25	1	2	FACETS	0.725	0.652	0.802	0.725	0.652	0.802	SUBCLONAL	1	TRUE	1	0.531696674415586	2		554	555	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268421	46268421	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006117-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	183	605	0	ENST00000371998.3:c.2808C>G	p.Asn936Lys	p.N936K	ENST00000371998		936	aaC/aaG	15/23	0.474033246480418	3	FACETS	0.979	0.914	1	0.979	0.914	1	CLONAL	2	TRUE	1	0.531696674415586	3		605	445	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47079269	47079269	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0006117-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	115	594	0	ENST00000409792.3:c.7239-2A>G		p.X2413_splice	ENST00000409792	NM_014159.6	2413			0.531696674415586	1	FACETS	0.974	0.889	1	0.974	0.889	1	CLONAL	1	TRUE	0	0.531696674415586	1		594	326	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651382	52651383	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006117-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	139	820	0	ENST00000394830.3:c.1713dup	p.Glu572Ter	p.E572*	ENST00000394830	NM_018313.4	571	-/T	15/30	0.531696674415586	1	FACETS	0.775	0.71	0.843	0.775	0.71	0.843	SUBCLONAL	1	TRUE	0	0.531696674415586	1		820	495	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631837	90631837	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	230	809	0	ENST00000330062.3:c.516G>T	p.Arg172Ser	p.R172S	ENST00000330062	NM_002168.2	172	agG/agT	4/11	1	2	FACETS	0.994	0.93	1	0.994	0.93	1	CLONAL	1	TRUE	1	0.600135898796536	2		809	771	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626925	14626925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374296355	NA	P-0006242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	223	918	1	ENST00000254322.2:c.850G>A	p.Val284Ile	p.V284I	ENST00000254322	NM_006145.1	284	Gta/Ata	3/3	1	2	FACETS	0.838	0.781	0.896	0.838	0.781	0.896	CLONAL	1	TRUE	1	0.600135898796536	2		919	887	SUCCESS
AR	367	MSKCC	GRCh37	X	66765159	66765194	+	inframe_deletion	In_Frame_Del	DEL	GCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA	GCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA	-	rs3032358	NA	P-0006242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	60	347	0	ENST00000374690.3:c.204_239del	p.Gln69_Gln80del	p.Q69_Q80del	ENST00000374690	NM_000044.3	57	ctGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAg/ctg	1/8	1	2	FACETS	0.549	0.475	0.629	0.549	0.475	0.629	SUBCLONAL	1	TRUE	1	0.600135898796536	2		347	364	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005688	42005689	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	AATA	novel	NA	P-0006242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	44	225	1	ENST00000219905.7:c.3425_3428dup	p.Tyr1143Ter	p.Y1143*	ENST00000219905	NM_001164273.1	1142	gaa/gAATAaa	9/24	1	2	FACETS	0.603	0.51	0.705	0.603	0.51	0.705	SUBCLONAL	1	TRUE	1	0.600135898796536	2		226	243	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879337	151879337	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	205	633	1	ENST00000262189.6:c.5608C>T	p.Gln1870Ter	p.Q1870*	ENST00000262189	NM_170606.2	1870	Cag/Tag	36/59	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.600135898796536	2		634	644	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193988	106193988	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0121456-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	222	427	0	ENST00000380013.4:c.4450A>C	p.Asn1484His	p.N1484H	ENST00000380013	NM_001127208.2	1484	Aac/Cac	10/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	NA	1	0.890920978149158	2		427	486	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246179	41246180	+	stop_gained	Nonsense_Mutation	DNP	CA	CA	AT	novel	NA	P-0121456-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	363	831	3	ENST00000357654.3:c.1368_1369delinsAT	p.Glu457Ter	p.E457*	ENST00000357654	NM_007294.3	456	atTGaa/atATaa	10/23	1	2	FACETS	0.982	0.936	1	0.982	0.936	1	CLONAL	1	NA	1	0.890920978149158	2		834	830	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573682	41573682	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121456-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	62	901	1	ENST00000263253.7:c.5967G>T	p.Met1989Ile	p.M1989I	ENST00000263253	NM_001429.3	1989	atG/atT	31/31	1	2	FACETS	0.159	0.137	0.184	0.159	0.137	0.184	SUBCLONAL	1	NA	1	0.890920978149158	2		902	874	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412958	49412958	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006424-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	149	813	0	ENST00000418115.1:c.65T>G	p.Leu22Arg	p.L22R	ENST00000418115	NM_001664.2	22	cTc/cGc	2/5	1	2	FACETS	0.897	0.819	0.978	0.897	0.819	0.978	CLONAL	1	TRUE	1	0.375815708943501	2		813	884	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100584	67100584	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0006424-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	112	564	0	ENST00000412916.2:c.283-1G>A		p.X95_splice	ENST00000412916		95			0.375815708943501	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.375815708943501	1		564	477	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862203	68862204	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0006424-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	113	578	0	ENST00000261769.5:c.2293dup	p.Gln765ProfsTer4	p.Q765Pfs*4	ENST00000261769	NM_004360.3	764	gac/gaCc	14/16	0.375815708943501	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.375815708943501	1		578	454	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273093	18273093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006424-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	150	756	1	ENST00000222254.8:c.983C>T	p.Ala328Val	p.A328V	ENST00000222254	NM_005027.3	328	gCt/gTt	8/16	1	2	FACETS	0.923	0.844	1	0.923	0.844	1	CLONAL	1	TRUE	1	0.375815708943501	2		757	865	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198262794	198262794	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006424-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	36	596	0	ENST00000335508.6:c.3181G>C	p.Glu1061Gln	p.E1061Q	ENST00000335508	NM_012433.2	1061	Gag/Cag	22/25	1	2	FACETS	0.3	0.246	0.361	0.3	0.246	0.361	SUBCLONAL	1	TRUE	1	0.375815708943501	2		596	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0006767-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	361	826	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.841498543972808	2		828	417	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941715	48941716	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0006767-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	102	509	0	ENST00000267163.4:c.1027_1028del	p.Leu343SerfsTer3	p.L343Sfs*3	ENST00000267163	NM_000321.2	342	aCT/a	10/27	0.836047381924759	1	FACETS	0.975	0.912	1	0.975	0.912	1	CLONAL	1	TRUE	0	0.841498543972808	1		509	144	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138376590	138376590	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006767-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	316	731	0	ENST00000289153.2:c.2884T>A	p.Tyr962Asn	p.Y962N	ENST00000289153	NM_006219.2	962	Tat/Aat	20/22	0.841498543972808	4	FACETS	1	0.986	1			1	CLONAL	2	TRUE	NA	0.841498543972808	4		731	634	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223310	36223310	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006767-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	437	1194	1	ENST00000222270.7:c.5860A>G	p.Thr1954Ala	p.T1954A	ENST00000222270	NM_014727.1	1954	Acc/Gcc	28/37	0.811407423681196	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.841498543972808	4		1195	947	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110046	115110046	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867049310	NA	P-0007550-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	135	1089	0	ENST00000257566.3:c.1832C>T	p.Ala611Val	p.A611V	ENST00000257566	NM_016569.3	611	gCg/gTg	8/8	0.460161157999376	3	FACETS	1	0.976	1	0.599	0.547	0.655	CLONAL	1	TRUE	1	0.460161157999376	3		1089	602	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667784	37667784	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007550-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2355	1289	489	0	ENST00000447079.4:c.2669G>A	p.Arg890His	p.R890H	ENST00000447079	NM_015083.1	890	cGc/cAc	8/14	0.460161157999376	47	FACETS	1	0.988	1			1	CLONAL	17	TRUE	NA	0.460161157999376	47		489	3644	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412059	63412059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007550-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	114	1086	0	ENST00000330258.3:c.1108G>A	p.Glu370Lys	p.E370K	ENST00000330258	NM_152424.3	370	Gag/Aag	2/2	0.413086642295213	5	FACETS	0.997	0.897	1			1	CLONAL	1	TRUE	NA	0.460161157999376	5		1086	840	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579372	7579373	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0007550-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	202	873	0	ENST00000269305.4:c.314dup	p.Ser106GlnfsTer43	p.S106Qfs*43	ENST00000269305	NM_001126112.2	105	ggc/ggGc	4/11	0.460161157999376	2	FACETS	0.984	0.924	1	0.984	0.924	1	CLONAL	2	TRUE	0	0.460161157999376	2		873	446	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007704-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	165	445	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.81235766927576	2		445	346	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76764069	76764069	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007704-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	142	715	0	ENST00000373344.5:c.7239G>T	p.Arg2413Ser	p.R2413S	ENST00000373344	NM_000489.3	2413	agG/agT	35/35	0.481555270690881	1	FACETS	0.354	0.324	0.386	0.354	0.324	0.386	INDETERMINATE	1	TRUE	0	0.81235766927576	1		715	586	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0008205-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	454	930	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.477075818174573	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.512672875058092	2		931	839	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039459	49039459	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008205-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	194	429	1	ENST00000267163.4:c.2446del	p.Ser816GlnfsTer10	p.S816Qfs*10	ENST00000267163	NM_000321.2	815	aTt/at	23/27	0.512672875058092	1	FACETS	0.996	0.928	1	0.996	0.928	1	CLONAL	1	TRUE	0	0.512672875058092	1		430	565	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185173	123185174	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0008205-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	150	202	0	ENST00000218089.9:c.1128_1129del	p.Ser377TyrfsTer4	p.S377Yfs*4	ENST00000218089	NM_001042749.1	375	atTGtg/attg	13/35	0.337277964052491	2	FACETS	0.887	0.823	0.95			1	CLONAL	2	TRUE	NA	0.512672875058092	2		202	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0008422-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	400	641	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	NA	2	FACETS	0.965	0.933	0.997			1	INDETERMINATE	2	TRUE	NA	0.720611380895662	2		641	575	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216631	2216631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769937964	NA	P-0008422-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	140	564	1	ENST00000398665.3:c.2275C>T	p.Arg759Cys	p.R759C	ENST00000398665	NM_032482.2	759	Cgc/Tgc	20/28	0.720611380895662	3	FACETS	0.649	0.591	0.71	0.325	0.295	0.355	SUBCLONAL	1	TRUE	1	0.720611380895662	3		565	814	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917845	29917845	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008422-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	352	613	2	ENST00000389048.3:c.823G>T	p.Glu275Ter	p.E275*	ENST00000389048	NM_004304.4	275	Gag/Tag	3/29	0.633440479270562	4	FACETS	0.804	0.763	0.846	0.536	0.509	0.564	CLONAL	2	TRUE	1	0.720611380895662	4		615	1045	SUCCESS
ATR	545	MSKCC	GRCh37	3	142184044	142184044	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008422-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	264	508	0	ENST00000350721.4:c.6936T>G	p.Ile2312Met	p.I2312M	ENST00000350721	NM_001184.3	2312	atT/atG	41/47	0.720611380895662	7	FACETS	0.785	0.735	0.837	0.262	0.245	0.279	SUBCLONAL	2	TRUE	1	0.720611380895662	7		508	1307	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022344	26022344	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008422-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	110	509	0	ENST00000435504.4:c.313C>T	p.Gln105Ter	p.Q105*	ENST00000435504		105	Cag/Tag	5/13	0.633440479270562	4	FACETS	0.534	0.479	0.593	0.178	0.159	0.198	SUBCLONAL	1	TRUE	1	0.720611380895662	4		509	983	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400086	41400086	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008422-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	28	445	2	ENST00000373198.4:c.673C>A	p.Leu225Ile	p.L225I	ENST00000373198	NM_133170.3	225	Ctt/Att	5/32	0.35520196411404	3	FACETS	0.213	0.17	0.263	0.071	0.056	0.088	INDETERMINATE	1	TRUE	0	0.720611380895662	3		447	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0008789-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	541	887	1	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.642354812481584	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.642354812481584	3		888	716	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881462	48881462	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008789-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	231	583	1	ENST00000267163.4:c.184C>T	p.Gln62Ter	p.Q62*	ENST00000267163	NM_000321.2	62	Cag/Tag	2/27	0.642354812481584	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.642354812481584	2		584	353	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56411587	56411587	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs763591328	NA	P-0008789-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	283	724	0	ENST00000348428.3:c.1771T>C	p.Cys591Arg	p.C591R	ENST00000348428	NM_006785.3	591	Tgt/Cgt	15/17	0.642354812481584	4	FACETS	0.991	0.937	1	0.991	0.937	1	CLONAL	2	TRUE	2	0.642354812481584	4		724	730	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273252	18273252	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008789-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	596	760	2	ENST00000222254.8:c.1045G>T	p.Asp349Tyr	p.D349Y	ENST00000222254	NM_005027.3	349	Gat/Tat	9/16	0.642354812481584	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.642354812481584	3		762	751	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212522529	212522529	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008789-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	312	661	0	ENST00000342788.4:c.1896C>A	p.Asp632Glu	p.D632E	ENST00000342788	NM_005235.2	632	gaC/gaA	16/28	0.642354812481584	3	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	1	0.642354812481584	3		661	642	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967234	134967234	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008789-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	384	747	0	ENST00000398015.3:c.2573T>A	p.Leu858Gln	p.L858Q	ENST00000398015	NM_004441.4	858	cTg/cAg	14/16	0.642354812481584	6	FACETS	1	0.986	1	0.551	0.523	0.579	CLONAL	2	TRUE	2	0.642354812481584	6		747	1240	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235304	235304	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008789-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	122	581	0	ENST00000264932.6:c.1110C>G	p.His370Gln	p.H370Q	ENST00000264932	NM_004168.2	370	caC/caG	9/15	0.642354812481584	8	FACETS	0.959	0.865	1	0.192	0.173	0.212	CLONAL	1	TRUE	3	0.642354812481584	8		581	1159	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38942477	38942477	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008789-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	419	719	0	ENST00000357387.3:c.5056C>A	p.His1686Asn	p.H1686N	ENST00000357387	NM_152756.3	1686	Cat/Aat	38/38	0.642354812481584	6	FACETS	0.976	0.933	1	0.976	0.933	1	CLONAL	3	TRUE	3	0.642354812481584	6		719	1018	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010000-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	277	693	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.233522599595487	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.23688344772241	2		693	1112	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0010000-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	283	737	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.233522599595487	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.23688344772241	2		739	1173	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100175	27100176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0010000-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	82	598	0	ENST00000324856.7:c.3977dup	p.Gln1327AlafsTer11	p.Q1327Afs*11	ENST00000324856	NM_006015.4	1324	tac/taCc	16/20	1	2	FACETS	0.845	0.744	0.954	0.845	0.744	0.954	CLONAL	1	TRUE	1	0.23688344772241	2		598	819	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003763	45003763	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010000-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	111	694	0	ENST00000558401.1:c.19T>G	p.Leu7Val	p.L7V	ENST00000558401	NM_004048.2	7	Tta/Gta	1/4	1	2	FACETS	0.997	0.895	1	0.997	0.895	1	CLONAL	1	TRUE	1	0.23688344772241	2		694	940	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572289	64572289	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs794728629	NA	P-0010652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	710	651	1	ENST00000312049.6:c.1351-1G>A		p.X451_splice	ENST00000312049	NM_130799.2	451			0.866551995265055	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.866551995265055	1		652	912	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945515	17945515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	330	325	0	ENST00000458235.1:c.2215G>A	p.Glu739Lys	p.E739K	ENST00000458235	NM_000215.3	739	Gag/Aag	17/24	1	2	FACETS	0.932	0.885	0.98	0.932	0.885	0.98	CLONAL	1	TRUE	1	0.866551995265055	2		325	817	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287842	33287843	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	AT	novel	NA	P-0010652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	697	767	2	ENST00000374542.5:c.1410_1411delinsAT	p.Met470_Gln471delinsIleTer	p.M470_Q471delinsI*	ENST00000374542	NM_001141970.1	470	atGCag/atATag	5/8	0.866551995265055	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.866551995265055	1		769	901	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880219	37880220	+	missense_variant	Missense_Mutation	DNP	TT	TT	CC	rs121913469	NA	P-0010927-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	239	442	0	ENST00000269571.5:c.2263_2264delinsCC	p.Leu755Pro	p.L755P	ENST00000269571		755	TTg/CCg	19/27	0.322320028997278	3	FACETS	0.858	0.801	0.916	0.858	0.801	0.916	CLONAL	2	TRUE	1	0.322320028997278	3		442	1004	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527973	157527973	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010927-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	110	391	0	ENST00000346085.5:c.5698A>G	p.Ser1900Gly	p.S1900G	ENST00000346085	NM_020732.3	1900	Agc/Ggc	20/20	0.188124015843401	3	FACETS	0.988	0.888	1	0.494	0.444	0.548	INDETERMINATE	1	TRUE	1	0.322320028997278	3		391	802	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574032	7574032	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010927-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	118	465	0	ENST00000269305.4:c.995T>G	p.Ile332Ser	p.I332S	ENST00000269305	NM_001126112.2	332	aTc/aGc	10/11	0.322320028997278	1	FACETS	0.865	0.781	0.953	0.865	0.781	0.953	CLONAL	1	TRUE	0	0.322320028997278	1		465	710	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225531	26225531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010927-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	35	283	0	ENST00000360408.1:c.149G>A	p.Arg50His	p.R50H	ENST00000360408	NM_003532.2	50	cGc/cAc	1/1	1	2	FACETS	0.388	0.317	0.468	0.388	0.317	0.468	SUBCLONAL	1	TRUE	1	0.322320028997278	2		283	560	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136843	69136874	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCCACAGTCTGCACCAAGGTAAGTGCATCCC	CTCCACAGTCTGCACCAAGGTAAGTGCATCCC	-	novel	NA	P-0010927-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	41	299	0	ENST00000288368.4:c.4759_4775+15del		p.X1587_splice	ENST00000288368	NM_024870.2	1587		39/40	1	2	FACETS	0.468	0.389	0.555	0.468	0.389	0.555	SUBCLONAL	1	TRUE	1	0.322320028997278	2		299	544	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78938077	78938077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011466-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	159	1184	0	ENST00000306801.3:c.3955G>A	p.Gly1319Arg	p.G1319R	ENST00000306801	NM_020761.2	1319	Gga/Aga	34/34	1	2	FACETS	0.848	0.78	0.918	0.848	0.78	0.918	CLONAL	1	TRUE	1	0.605037515322535	2		1184	620	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426003	138426003	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011466-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	154	787	0	ENST00000289153.2:c.1528A>C	p.Lys510Gln	p.K510Q	ENST00000289153	NM_006219.2	510	Aag/Cag	9/22	1	2	FACETS	0.901	0.829	0.976	0.901	0.829	0.976	CLONAL	1	TRUE	1	0.605037515322535	2		787	565	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857339	9857339	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	50	432	0	ENST00000330684.3:c.4062C>A	p.Ser1354Arg	p.S1354R	ENST00000330684	NM_001134407.1	1354	agC/agA	13/13	0.369872128972889	3	FACETS	0.507	0.429	0.592	0.253	0.214	0.296	SUBCLONAL	1	TRUE	1	0.369872128972889	3		432	632	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56867193	56867193	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	54	514	0	ENST00000308159.5:c.1412A>T	p.Gln471Leu	p.Q471L	ENST00000308159	NM_014669.4	471	cAg/cTg	13/22	0.369872128972889	3	FACETS	0.392	0.334	0.457	0.196	0.167	0.229	SUBCLONAL	1	TRUE	1	0.369872128972889	3		514	882	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934574	NA	P-0012056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	169	656	0	ENST00000269305.4:c.844C>G	p.Arg282Gly	p.R282G	ENST00000269305	NM_001126112.2	282	Cgg/Ggg	8/11	0.369872128972889	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.369872128972889	1		656	641	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108259	8108259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	159	618	3	ENST00000585124.1:c.965C>T	p.Ser322Leu	p.S322L	ENST00000585124	NM_004217.3	322	tCa/tTa	9/9	0.369872128972889	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.369872128972889	1		621	613	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673793	37673793	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1724	297	597	0	ENST00000447079.4:c.2947C>G	p.Arg983Gly	p.R983G	ENST00000447079	NM_015083.1	983	Cga/Gga	10/14	0.369872128972889	12	FACETS	1	0.983	1			1	CLONAL	2	TRUE	NA	0.369872128972889	12		597	2021	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141512	11141513	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0012056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	249	611	3	ENST00000358026.2:c.3489_3490delinsTT	p.Asn1164Tyr	p.N1164Y	ENST00000358026	NM_001128849.1	1163	ctGAac/ctTTac	25/36	0.369872128972889	2	FACETS	0.946	0.889	1	0.946	0.889	1	CLONAL	2	TRUE	0	0.369872128972889	2		614	712	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180222	38180222	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768025686	NA	P-0012056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	140	445	1	ENST00000396334.3:c.70G>A	p.Ala24Thr	p.A24T	ENST00000396334	NM_002468.4	24	Gcg/Acg	1/5	0.332362661738556	3	FACETS	1	0.987	1	0.49	0.448	0.534	CLONAL	1	TRUE	0	0.369872128972889	3		446	610	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059223	47059223	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	153	378	0	ENST00000409792.3:c.7438C>G	p.Gln2480Glu	p.Q2480E	ENST00000409792	NM_014159.6	2480	Cag/Gag	20/21	0.332362661738556	3	FACETS	1	0.979	1	0.774	0.716	0.834	CLONAL	2	TRUE	0	0.369872128972889	3		378	422	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670711	134670711	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	55	501	0	ENST00000398015.3:c.622G>C	p.Glu208Gln	p.E208Q	ENST00000398015	NM_004441.4	208	Gag/Cag	3/16	0.369872128972889	6	FACETS	0.497	0.423	0.578	0.166	0.141	0.193	SUBCLONAL	1	TRUE	3	0.369872128972889	6		501	1042	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111499	56111609	+	inframe_deletion	In_Frame_Del	DEL	GAGCAGCGCGCCCGCGGCTGCCGCGGGACTGCTGCGGGAGGCGGGCAGCGGGGGCCGCGAGCGGGCGGACTGGCGGCGGCGGCAGCTGCGCAAAGTGCGGAGTGTGGAGCT	GAGCAGCGCGCCCGCGGCTGCCGCGGGACTGCTGCGGGAGGCGGGCAGCGGGGGCCGCGAGCGGGCGGACTGGCGGCGGCGGCAGCTGCGCAAAGTGCGGAGTGTGGAGCT	-	novel	NA	P-0012056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	10	121	0	ENST00000399503.3:c.100_210del	p.Ser34_Leu70del	p.S34_L70del	ENST00000399503	NM_005921.1	33	gcGAGCAGCGCGCCCGCGGCTGCCGCGGGACTGCTGCGGGAGGCGGGCAGCGGGGGCCGCGAGCGGGCGGACTGGCGGCGGCGGCAGCTGCGCAAAGTGCGGAGTGTGGAGCTg/gcg	1/20	0.326777946366975	4	FACETS	0.431	0.292	0.604			1	SUBCLONAL	1	TRUE	NA	0.369872128972889	4		121	172	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273230	55273230	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	215	538	2	ENST00000275493.2:c.3553G>A	p.Gly1185Ser	p.G1185S	ENST00000275493	NM_005228.3	1185	Ggc/Agc	28/28	0.338145561658966	3	FACETS	0.937	0.874	1	0.937	0.874	1	CLONAL	2	TRUE	1	0.369872128972889	3		540	735	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978551	70978551	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	141	556	0	ENST00000276594.2:c.1102G>T	p.Asp368Tyr	p.D368Y	ENST00000276594	NM_024504.3	368	Gac/Tac	5/8	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.369872128972889	2		556	688	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231707	66231707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1211795184	NA	P-0012128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	93	595	0	ENST00000273854.3:c.1993G>A	p.Glu665Lys	p.E665K	ENST00000273854	NM_004439.5	665	Gaa/Aaa	11/18	1	2	FACETS	0.842	0.748	0.942	0.842	0.748	0.942	CLONAL	1	TRUE	1	0.28	2		595	789	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637690	52637690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239654517	NA	P-0012128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	53	567	0	ENST00000394830.3:c.2626C>T	p.Arg876Cys	p.R876C	ENST00000394830	NM_018313.4	876	Cgt/Tgt	18/30	1	2	FACETS	0.419	0.356	0.489	0.419	0.356	0.489	SUBCLONAL	1	TRUE	1	0.28	2		567	903	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968275	134968275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1242081780	NA	P-0012128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	43	644	0	ENST00000398015.3:c.2788G>A	p.Asp930Asn	p.D930N	ENST00000398015	NM_004441.4	930	Gac/Aac	15/16	0.3	1	FACETS	0.391	0.326	0.463	0.391	0.326	0.463	SUBCLONAL	1	TRUE	0	0.28	1		644	676	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935426	36935426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	99	692	1	ENST00000361632.4:c.1301G>A	p.Arg434Lys	p.R434K	ENST00000361632		434	aGa/aAa	10/16	1	2	FACETS	0.886	0.791	0.988	0.886	0.791	0.988	CLONAL	1	TRUE	1	0.28	2		693	798	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440882	52440882	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	79	645	0	ENST00000460680.1:c.622C>G	p.Arg208Gly	p.R208G	ENST00000460680	NM_004656.3	208	Cgg/Ggg	8/17	1	2	FACETS	0.732	0.643	0.828	0.732	0.643	0.828	SUBCLONAL	1	TRUE	1	0.28	2		645	771	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523654	176523654	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	89	769	0	ENST00000292408.4:c.2065C>T	p.Pro689Ser	p.P689S	ENST00000292408	NM_213647.1	689	Ccg/Tcg	16/18	1	2	FACETS	0.715	0.633	0.803	0.715	0.633	0.803	SUBCLONAL	1	TRUE	1	0.28	2		769	889	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672972	30672972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	84	713	0	ENST00000376406.3:c.3988C>T	p.Pro1330Ser	p.P1330S	ENST00000376406	NM_014641.2	1330	Cct/Tct	10/15	1	2	FACETS	0.716	0.631	0.807	0.716	0.631	0.807	SUBCLONAL	1	TRUE	1	0.28	2		713	838	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673742	30673742	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	57	586	0	ENST00000376406.3:c.3218C>T	p.Ser1073Phe	p.S1073F	ENST00000376406	NM_014641.2	1073	tCt/tTt	10/15	1	2	FACETS	0.63	0.54	0.729	0.63	0.54	0.729	SUBCLONAL	1	TRUE	1	0.28	2		586	646	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984943	9984943	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	71	551	0	ENST00000330684.3:c.1022T>C	p.Val341Ala	p.V341A	ENST00000330684	NM_001134407.1	341	gTt/gCt	4/13	1	2	FACETS	0.646	0.563	0.736	0.646	0.563	0.736	SUBCLONAL	1	TRUE	1	0.28	2		551	785	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775629	39775629	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	57	344	0	ENST00000288319.7:c.391C>T	p.Pro131Ser	p.P131S	ENST00000288319	NM_182918.3	131	Cct/Tct	4/10	1	2	FACETS	0.942	0.811	1	0.942	0.811	1	CLONAL	1	TRUE	1	0.28	2		344	432	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262570	16262570	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	33	521	1	ENST00000375759.3:c.9835C>T	p.Gln3279Ter	p.Q3279*	ENST00000375759	NM_015001.2	3279	Cag/Tag	11/15	1	2	FACETS	0.433	0.351	0.524	0.433	0.351	0.524	SUBCLONAL	1	TRUE	1	0.28	2		522	545	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021480	42021480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs71472500	NA	P-0012128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	78	697	1	ENST00000219905.7:c.3776C>T	p.Ser1259Phe	p.S1259F	ENST00000219905	NM_001164273.1	1259	tCc/tTc	11/24	1	2	FACETS	0.6	0.526	0.68	0.6	0.526	0.68	SUBCLONAL	1	TRUE	1	0.28	2		698	928	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640578	3640578	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138344471	NA	P-0012128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	84	707	1	ENST00000294008.3:c.3061C>T	p.Arg1021Cys	p.R1021C	ENST00000294008	NM_032444.2	1021	Cgc/Tgc	12/15	1	2	FACETS	0.729	0.643	0.821	0.729	0.643	0.821	SUBCLONAL	1	TRUE	1	0.28	2		708	823	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1255522	1255522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	62	474	0	ENST00000310581.5:c.3037C>T	p.His1013Tyr	p.H1013Y	ENST00000310581	NM_198253.2	1013	Cac/Tac	14/16	1	2	FACETS	0.863	0.747	0.99	0.863	0.747	0.99	CLONAL	1	TRUE	1	0.28	2		474	513	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169928	32169928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1281810767	NA	P-0012128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	44	651	0	ENST00000375023.3:c.3680G>A	p.Gly1227Glu	p.G1227E	ENST00000375023	NM_004557.3	1227	gGg/gAg	21/30	1	2	FACETS	0.395	0.33	0.468	0.395	0.33	0.468	SUBCLONAL	1	TRUE	1	0.28	2		651	795	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933770	39933770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	32	564	0	ENST00000378444.4:c.829C>T	p.Pro277Ser	p.P277S	ENST00000378444	NM_001123385.1	277	Ccg/Tcg	4/15	1	2	FACETS	0.392	0.317	0.477	0.392	0.317	0.477	SUBCLONAL	1	TRUE	1	0.28	2		564	583	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	172	701	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.450881374437465	2		701	695	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1555525367	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	163	665	0	ENST00000269305.4:c.783-1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	0.965	0.888	1	0.965	0.888	1	CLONAL	1	TRUE	1	0.450881374437465	2		665	749	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962804	2962804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772900135	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	232	915	1	ENST00000396946.4:c.2104G>A	p.Glu702Lys	p.E702K	ENST00000396946	NM_032415.4	702	Gag/Aag	16/25	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.450881374437465	2		916	1023	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913286	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	143	808	0	ENST00000263967.3:c.1636C>G	p.Gln546Glu	p.Q546E	ENST00000263967	NM_006218.2	546	Cag/Gag	10/21	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.450881374437465	2		808	600	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781371	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	244	967	3	ENST00000269305.4:c.328C>T	p.Arg110Cys	p.R110C	ENST00000269305	NM_001126112.2	110	Cgt/Tgt	4/11	1	2	FACETS	0.964	0.9	1	0.964	0.9	1	CLONAL	1	TRUE	1	0.450881374437465	2		970	1123	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983275	149983275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	183	888	0	ENST00000253339.5:c.2983C>T	p.Arg995Cys	p.R995C	ENST00000253339		995	Cgc/Tgc	7/7	1	2	FACETS	0.864	0.797	0.933	0.864	0.797	0.933	CLONAL	1	TRUE	1	0.450881374437465	2		888	940	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141026	55141026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765680542	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	129	583	0	ENST00000257290.5:c.1672C>T	p.Arg558Cys	p.R558C	ENST00000257290	NM_006206.4	558	Cgc/Tgc	12/23	1	2	FACETS	0.938	0.853	1	0.938	0.853	1	CLONAL	1	TRUE	1	0.450881374437465	2		583	610	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846031	128846031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1307431013	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	230	950	0	ENST00000249373.3:c.961G>A	p.Val321Met	p.V321M	ENST00000249373	NM_005631.4	321	Gtg/Atg	5/12	1	2	FACETS	0.962	0.896	1	0.962	0.896	1	CLONAL	1	TRUE	1	0.450881374437465	2		950	1061	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445067	89445067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	126	693	0	ENST00000336596.2:c.1387C>T	p.Pro463Ser	p.P463S	ENST00000336596	NM_005233.5	463	Cct/Tct	6/17	1	2	FACETS	0.752	0.682	0.826	0.752	0.682	0.826	SUBCLONAL	1	TRUE	1	0.450881374437465	2		693	743	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178638	32178638	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140125037	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	250	956	0	ENST00000375023.3:c.2756C>T	p.Pro919Leu	p.P919L	ENST00000375023	NM_004557.3	919	cCc/cTc	18/30	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.450881374437465	2		956	1001	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11273604	11273604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	136	588	0	ENST00000361445.4:c.3137C>T	p.Thr1046Ile	p.T1046I	ENST00000361445	NM_004958.3	1046	aCc/aTc	21/58	1	2	FACETS	0.845	0.769	0.924	0.845	0.769	0.924	CLONAL	1	TRUE	1	0.450881374437465	2		588	714	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363460	40363460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	259	895	0	ENST00000397332.2:c.769G>A	p.Glu257Lys	p.E257K	ENST00000397332	NM_001033082.2	257	Gag/Aag	3/3	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.450881374437465	2		895	995	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675413	241675413	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	137	544	0	ENST00000366560.3:c.409C>T	p.Pro137Ser	p.P137S	ENST00000366560	NM_000143.3	137	Cct/Tct	4/10	1	2	FACETS	0.915	0.835	1	0.915	0.835	1	CLONAL	1	TRUE	1	0.450881374437465	2		544	664	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966091	25966091	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	220	914	0	ENST00000435504.4:c.3115T>A	p.Phe1039Ile	p.F1039I	ENST00000435504		1039	Ttt/Att	13/13	1	2	FACETS	0.99	0.921	1	0.99	0.921	1	CLONAL	1	TRUE	1	0.450881374437465	2		914	986	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735473	204735473	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	140	673	0	ENST00000302823.3:c.274G>A	p.Gly92Arg	p.G92R	ENST00000302823	NM_005214.4	92	Ggg/Agg	2/4	1	2	FACETS	0.875	0.798	0.955	0.875	0.798	0.955	CLONAL	1	TRUE	1	0.450881374437465	2		673	710	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480418	89480418	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	150	569	0	ENST00000336596.2:c.2255T>A	p.Ile752Asn	p.I752N	ENST00000336596	NM_005233.5	752	aTc/aAc	13/17	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.450881374437465	2		569	617	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467791	66467791	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774667775	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	134	582	1	ENST00000273854.3:c.478G>A	p.Asp160Asn	p.D160N	ENST00000273854	NM_004439.5	160	Gat/Aat	3/18	1	2	FACETS	0.96	0.875	1	0.96	0.875	1	CLONAL	1	TRUE	1	0.450881374437465	2		583	619	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048754	180048754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	255	1062	0	ENST00000261937.6:c.1808G>A	p.Gly603Glu	p.G603E	ENST00000261937	NM_182925.4	603	gGg/gAg	13/30	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.450881374437465	2		1062	1122	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066570	94066570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	136	676	1	ENST00000369303.4:c.1189G>A	p.Asp397Asn	p.D397N	ENST00000369303	NM_004440.3	397	Gat/Aat	5/17	1	2	FACETS	0.892	0.813	0.975	0.892	0.813	0.975	CLONAL	1	TRUE	1	0.450881374437465	2		677	676	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715509	117715509	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	117	541	0	ENST00000368508.3:c.980G>A	p.Gly327Glu	p.G327E	ENST00000368508	NM_002944.2	327	gGa/gAa	10/43	1	2	FACETS	0.893	0.808	0.983	0.893	0.808	0.983	CLONAL	1	TRUE	1	0.450881374437465	2		541	581	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005147	150005147	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	181	730	0	ENST00000253339.5:c.1078C>T	p.Gln360Ter	p.Q360*	ENST00000253339		360	Caa/Taa	3/7	1	2	FACETS	0.957	0.884	1	0.957	0.884	1	CLONAL	1	TRUE	1	0.450881374437465	2		730	839	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98009731	98009731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	318	679	0	ENST00000289081.3:c.233C>T	p.Pro78Leu	p.P78L	ENST00000289081	NM_000136.2	78	cCt/cTt	3/15	0.450881374437465	2	FACETS	0.967	0.919	1	0.967	0.919	1	CLONAL	2	TRUE	0	0.450881374437465	2		679	729	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220478	98220478	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	479	953	0	ENST00000331920.6:c.2985G>T	p.Arg995Ser	p.R995S	ENST00000331920	NM_000264.3	995	agG/agT	18/24	0.450881374437465	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.450881374437465	2		953	971	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245544	46245544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	98	472	2	ENST00000334344.6:c.3638C>T	p.Pro1213Leu	p.P1213L	ENST00000334344	NM_152641.2	1213	cCa/cTa	15/21	1	2	FACETS	0.786	0.703	0.874	0.786	0.703	0.874	SUBCLONAL	1	TRUE	1	0.450881374437465	2		474	553	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248853	133248853	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753890723	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	189	952	2	ENST00000320574.5:c.1742C>T	p.Ala581Val	p.A581V	ENST00000320574	NM_006231.2	581	gCc/gTc	16/49	1	2	FACETS	0.876	0.81	0.945	0.876	0.81	0.945	CLONAL	1	TRUE	1	0.450881374437465	2		954	957	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557509	21557509	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	205	948	0	ENST00000382592.4:c.2336T>A	p.Ile779Asn	p.I779N	ENST00000382592	NM_014572.2	779	aTt/aAt	5/8	1	2	FACETS	0.956	0.887	1	0.956	0.887	1	CLONAL	1	TRUE	1	0.450881374437465	2		948	951	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059276	42059276	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	128	601	0	ENST00000219905.7:c.8996C>T	p.Pro2999Leu	p.P2999L	ENST00000219905	NM_001164273.1	2999	cCt/cTt	24/24	1	2	FACETS	0.907	0.824	0.994	0.907	0.824	0.994	CLONAL	1	TRUE	1	0.450881374437465	2		601	626	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996003	73996003	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1320456567	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	192	867	1	ENST00000318443.5:c.737C>T	p.Ala246Val	p.A246V	ENST00000318443	NM_001024736.1	246	gCc/gTc	5/10	1	2	FACETS	0.919	0.85	0.99	0.919	0.85	0.99	CLONAL	1	TRUE	1	0.450881374437465	2		868	927	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801795	3801795	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	175	860	0	ENST00000262367.5:c.3711T>G	p.Cys1237Trp	p.C1237W	ENST00000262367	NM_004380.2	1237	tgT/tgG	20/31	1	2	FACETS	0.866	0.798	0.937	0.866	0.798	0.937	CLONAL	1	TRUE	1	0.450881374437465	2		860	896	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979029	7979029	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	203	831	0	ENST00000319144.4:c.1538T>G	p.Val513Gly	p.V513G	ENST00000319144	NM_001139.2	513	gTg/gGg	12/15	1	2	FACETS	0.898	0.832	0.966	0.898	0.832	0.966	CLONAL	1	TRUE	1	0.450881374437465	2		831	1003	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686943	37686943	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	194	764	0	ENST00000447079.4:c.3847G>A	p.Glu1283Lys	p.E1283K	ENST00000447079	NM_015083.1	1283	Gaa/Aaa	14/14	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.450881374437465	2		764	836	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512312	38512312	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	218	1002	0	ENST00000254066.5:c.1223C>T	p.Pro408Leu	p.P408L	ENST00000254066	NM_000964.3	408	cCt/cTt	9/9	1	2	FACETS	0.986	0.917	1	0.986	0.917	1	CLONAL	1	TRUE	1	0.450881374437465	2		1002	981	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7120670	7120670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	240	997	0	ENST00000302850.5:c.3620C>T	p.Ser1207Phe	p.S1207F	ENST00000302850	NM_000208.2	1207	tCc/tTc	20/22	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.450881374437465	2		997	1058	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514883	44514883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	157	604	0	ENST00000291552.4:c.364G>A	p.Asp122Asn	p.D122N	ENST00000291552	NM_006758.2	122	Gat/Aat	6/8	1	2	FACETS	0.984	0.903	1	0.984	0.903	1	CLONAL	1	TRUE	1	0.450881374437465	2		604	708	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933653	39933653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200052076	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	225	366	0	ENST00000378444.4:c.946C>T	p.Pro316Ser	p.P316S	ENST00000378444	NM_001123385.1	316	Ccc/Tcc	4/15	1	1	FACETS	0.792	0.746	0.838	1	0.994	1	SUBCLONAL	2	TRUE	0	0.450881374437465	1		366	488	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	276	1085	2	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	1	2	FACETS	0.969	0.908	1	0.969	0.908	1	CLONAL	1	TRUE	1	0.450881374437465	2		1087	1264	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	264	1019	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.450881374437465	2		1019	1166	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112745510	112745511	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	132	627	0	ENST00000369452.4:c.828_829delinsTT	p.Pro277Ser	p.P277S	ENST00000369452	NM_007373.3	276	ctCCca/ctTTca	3/9	1	2	FACETS	0.874	0.795	0.956	0.874	0.795	0.956	CLONAL	1	TRUE	1	0.450881374437465	2		627	670	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211269	36211270	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	301	1323	4	ENST00000222270.7:c.1020_1021delinsTT	p.Gln341Ter	p.Q341*	ENST00000222270	NM_014727.1	340	ccCCaa/ccTTaa	3/37	1	2	FACETS	0.917	0.862	0.974	0.917	0.862	0.974	CLONAL	1	TRUE	1	0.450881374437465	2		1327	1456	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223350	36223350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	269	1171	1	ENST00000222270.7:c.5900C>T	p.Pro1967Leu	p.P1967L	ENST00000222270	NM_014727.1	1967	cCa/cTa	28/37	1	2	FACETS	0.955	0.894	1	0.955	0.894	1	CLONAL	1	TRUE	1	0.450881374437465	2		1172	1250	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851726	134851726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1434477593	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	180	754	0	ENST00000398015.3:c.1132G>A	p.Glu378Lys	p.E378K	ENST00000398015	NM_004441.4	378	Gag/Aag	5/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.450881374437465	2		754	732	SUCCESS
ATR	545	MSKCC	GRCh37	3	142184066	142184066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757887087	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	110	587	0	ENST00000350721.4:c.6914C>T	p.Ser2305Phe	p.S2305F	ENST00000350721	NM_001184.3	2305	tCt/tTt	41/47	1	2	FACETS	0.951	0.858	1	0.951	0.858	1	CLONAL	1	TRUE	1	0.450881374437465	2		587	513	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281667	142281667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	223	777	1	ENST00000350721.4:c.577C>T	p.Pro193Ser	p.P193S	ENST00000350721	NM_001184.3	193	Cct/Tct	4/47	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.450881374437465	2		778	850	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878652	151878652	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867645492	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	181	770	0	ENST00000262189.6:c.6293C>T	p.Pro2098Leu	p.P2098L	ENST00000262189	NM_170606.2	2098	cCc/cTc	36/59	1	2	FACETS	0.996	0.92	1	0.996	0.92	1	CLONAL	1	TRUE	1	0.450881374437465	2		770	806	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128322087	128322087	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	173	713	0	ENST00000265960.3:c.673G>A	p.Asp225Asn	p.D225N	ENST00000265960	NM_001006617.1	225	Gac/Aac	6/12	0.450881374437465	2	FACETS	0.947	0.873	1	0.474	0.436	0.513	CLONAL	1	TRUE	0	0.450881374437465	2		713	810	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138615	37138615	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778032371	NA	P-0013530-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	399	735	1	ENST00000373509.5:c.149G>A	p.Gly50Asp	p.G50D	ENST00000373509	NM_002648.3	50	gGc/gAc	2/6	1	2	FACETS	0.938	0.894	0.982	0.938	0.894	0.982	CLONAL	1	TRUE	1	0.825992901322192	2		736	1030	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097689	8097689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1485724723	NA	P-0013530-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	286	496	0	ENST00000346208.3:c.71C>T	p.Pro24Leu	p.P24L	ENST00000346208		24	cCg/cTg	2/6	0.825992901322192	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.825992901322192	1		496	396	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170618	7170618	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013530-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	391	737	0	ENST00000302850.5:c.1413A>T	p.Glu471Asp	p.E471D	ENST00000302850	NM_000208.2	471	gaA/gaT	6/22	1	2	FACETS	0.949	0.904	0.993	0.949	0.904	0.993	CLONAL	1	TRUE	1	0.825992901322192	2		737	998	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0013706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	110	763	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.444435359521687	1	FACETS	0.958	0.867	1	0.958	0.867	1	CLONAL	1	TRUE	0	0.444435359521687	1		763	402	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242647	16242647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777234386	NA	P-0013706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	86	563	0	ENST00000375759.3:c.1268G>A	p.Arg423His	p.R423H	ENST00000375759	NM_015001.2	423	cGc/cAc	6/15	1	2	FACETS	0.849	0.754	0.949	0.849	0.754	0.949	CLONAL	1	TRUE	1	0.444435359521687	2		563	456	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0013706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	75	487	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	0.395923091528041	5	FACETS	1	0.949	1	0.384	0.337	0.434	CLONAL	1	TRUE	2	0.444435359521687	5		487	488	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	102	513	0	ENST00000304494.5:c.172del	p.Arg58GlufsTer88	p.R58Efs*88	ENST00000304494	NM_000077.4	58	Cga/ga	2/3	0.444435359521687	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.444435359521687	1		513	290	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	87	255	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	1	1	FACETS	0.777	0.704	0.851	1	0.984	1	SUBCLONAL	2	TRUE	0	0.444435359521687	1		255	196	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098975	178098975	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1328994103	NA	P-0013706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	44	364	0	ENST00000397062.3:c.70T>C	p.Trp24Arg	p.W24R	ENST00000397062	NM_006164.4	24	Tgg/Cgg	2/5	1	2	FACETS	0.715	0.603	0.837	0.715	0.603	0.837	SUBCLONAL	1	TRUE	1	0.444435359521687	2		364	277	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780684	56780684	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	89	566	0	ENST00000337432.4:c.699C>G	p.His233Gln	p.H233Q	ENST00000337432	NM_058216.2	233	caC/caG	4/9	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.444435359521687	2		566	386	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157443	106157443	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	70	405	0	ENST00000380013.4:c.2344G>T	p.Glu782Ter	p.E782*	ENST00000380013	NM_001127208.2	782	Gaa/Taa	3/11	0.444435359521687	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.444435359521687	1		405	230	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126682	5126682	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0013706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	59	478	0	ENST00000381652.3:c.3292-2A>G		p.X1098_splice	ENST00000381652	NM_004972.3	1098			0.444435359521687	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.444435359521687	1		478	190	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874620	151874620	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	146	493	0	ENST00000262189.6:c.7918C>A	p.His2640Asn	p.H2640N	ENST00000262189	NM_170606.2	2640	Cat/Aat	38/59	0.444435359521687	3	FACETS	0.902	0.831	0.976	0.902	0.831	0.976	CLONAL	2	TRUE	1	0.444435359521687	3		493	445	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0013895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	89	640	0	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	0.531456041150794	2		640	259	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0013895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	141	814	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.523942059178835	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.531456041150794	1		815	367	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0013895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	74	520	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.991	0.877	1	0.991	0.877	1	CLONAL	1	TRUE	1	0.531456041150794	2		520	281	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650748	67650748	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	139	624	0	ENST00000264010.4:c.1053C>G	p.Phe351Leu	p.F351L	ENST00000264010	NM_006565.3	351	ttC/ttG	5/12	0.531456041150794	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.531456041150794	1		624	367	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0013895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	78	452	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	0.531456041150794	1	FACETS	0.869	0.775	0.967	0.869	0.775	0.967	CLONAL	1	TRUE	0	0.531456041150794	1		452	248	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061191	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	91	496	0	ENST00000250448.2:c.798C>G	p.Phe266Leu	p.F266L	ENST00000250448	NM_004496.3	266	ttC/ttG	2/2	1	2	FACETS	0.954	0.854	1	0.954	0.854	1	CLONAL	1	TRUE	1	0.531456041150794	2		496	359	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549134	21549134	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	115	630	0	ENST00000382592.4:c.3142G>A	p.Asp1048Asn	p.D1048N	ENST00000382592	NM_014572.2	1048	Gac/Aac	8/8	0.531456041150794	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.531456041150794	1		630	295	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772269	68772290	+	frameshift_variant	Frame_Shift_Del	DEL	ACGGTGCCCCGGCGCCACCTGG	ACGGTGCCCCGGCGCCACCTGG	-	novel	NA	P-0013895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	131	865	0	ENST00000261769.5:c.119_140del	p.Thr40ArgfsTer9	p.T40Rfs*9	ENST00000261769	NM_004360.3	40	ACGGTGCCCCGGCGCCACCTGGag/ag	2/16	0.531456041150794	1	FACETS	0.903	0.827	0.98	0.903	0.827	0.98	CLONAL	1	TRUE	0	0.531456041150794	1		865	401	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216899	7216899	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	100	472	0	ENST00000380728.2:c.622C>T	p.Gln208Ter	p.Q208*	ENST00000380728		208	Cag/Tag	7/11	0.523942059178835	1	FACETS	0.903	0.817	0.992	0.903	0.817	0.992	CLONAL	1	TRUE	0	0.531456041150794	1		472	306	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528086	29528086	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs864622107	NA	P-0013895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	66	350	0	ENST00000356175.3:c.1094C>G	p.Ser365Ter	p.S365*	ENST00000356175	NM_000267.3	365	tCa/tGa	10/57	0.531456041150794	1	FACETS	0.981	0.868	1	0.981	0.868	1	CLONAL	1	TRUE	0	0.531456041150794	1		350	186	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524466	44524466	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	80	297	0	ENST00000291552.4:c.91G>C	p.Asp31His	p.D31H	ENST00000291552	NM_006758.2	31	Gac/Cac	2/8	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.531456041150794	2		297	292	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259011	153259011	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	59	368	0	ENST00000281708.4:c.804G>C	p.Met268Ile	p.M268I	ENST00000281708	NM_033632.3	268	atG/atC	5/12	1	2	FACETS	0.945	0.823	1	0.945	0.823	1	CLONAL	1	TRUE	1	0.531456041150794	2		368	235	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26046026	26046026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	64	332	0	ENST00000540144.1:c.388C>T	p.Arg130Cys	p.R130C	ENST00000540144	NM_003531.2	130	Cgc/Tgc	1/1	1	2	FACETS	0.934	0.817	1	0.934	0.817	1	CLONAL	1	TRUE	1	0.531456041150794	2		332	258	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993741	90993742	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs768378152	NA	P-0013895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	62	370	0	ENST00000265433.3:c.181_182del	p.Asp61Ter	p.D61*	ENST00000265433	NM_002485.4	61	GAt/t	3/16	0.531456041150794	3	FACETS	0.781	0.678	0.892	0.391	0.339	0.446	SUBCLONAL	1	TRUE	1	0.531456041150794	3		370	378	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5081808	5081808	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013895-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	47	393	0	ENST00000381652.3:c.2518G>C	p.Asp840His	p.D840H	ENST00000381652	NM_004972.3	840	Gat/Cat	19/25	1	2	FACETS	0.743	0.633	0.862	0.743	0.633	0.862	SUBCLONAL	1	TRUE	1	0.531456041150794	2		393	238	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0014003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	366	649	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.85980474017418	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.85980474017418	3		649	605	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0014003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	460	654	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.85980474017418	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.85980474017418	2		654	525	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056314	26056314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1355795147	NA	P-0014003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	152	560	0	ENST00000343677.2:c.343G>A	p.Glu115Lys	p.E115K	ENST00000343677	NM_005319.3	115	Gaa/Aaa	1/1	0.645093876671234	5	FACETS	1	0.966	1	0.369	0.337	0.401	CLONAL	1	TRUE	2	0.85980474017418	5		560	732	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606672	43606672	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	454	708	4	ENST00000355710.3:c.1282del	p.Glu428LysfsTer25	p.E428Kfs*25	ENST00000355710	NM_020975.4	427	gtG/gt	7/20	0.793609249615802	2	FACETS	0.95	0.926	0.972	0.95	0.926	0.972	CLONAL	2	TRUE	0	0.85980474017418	2		712	556	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63545771	63545771	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0014003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	365	454	0	ENST00000307078.5:c.823A>T	p.Lys275Ter	p.K275*	ENST00000307078	NM_004655.3	275	Aag/Tag	3/11	0.85980474017418	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.85980474017418	3		454	399	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467199	25467199	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1313738991	NA	P-0014003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	147	612	0	ENST00000264709.3:c.1676G>T	p.Cys559Phe	p.C559F	ENST00000264709	NM_175629.2	559	tGc/tTc	15/23	0.814756845822467	4	FACETS	0.972	0.89	1	0.486	0.445	0.529	CLONAL	1	TRUE	2	0.85980474017418	4		612	654	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39708706	39708725	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAATTTTTTTTCTCTTTAGT	CAATTTTTTTTCTCTTTAGT	-	novel	NA	P-0014003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	130	621	0	ENST00000361337.2:c.336-18_337del		p.X112_splice	ENST00000361337	NM_003286.2	112		6/21	0.412275427975259	5	FACETS	1	0.975	1			1	INDETERMINATE	1	TRUE	NA	0.85980474017418	5		621	579	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518056	187518056	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	390	714	0	ENST00000441802.2:c.12638A>T	p.Gln4213Leu	p.Q4213L	ENST00000441802	NM_005245.3	4213	cAg/cTg	25/27	0.814756845822467	4	FACETS	0.959	0.916	1	0.959	0.916	1	CLONAL	2	TRUE	2	0.85980474017418	4		714	880	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053126	180053126	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	182	775	0	ENST00000261937.6:c.1243G>T	p.Glu415Ter	p.E415*	ENST00000261937	NM_182925.4	415	Gag/Tag	9/30	0.85980474017418	3	FACETS	0.961	0.891	1	0.48	0.445	0.517	CLONAL	1	TRUE	1	0.85980474017418	3		775	630	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305262	39305262	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759007028	NA	P-0014003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1434	230	718	3	ENST00000373001.3:c.1163C>T	p.Ala388Val	p.A388V	ENST00000373001	NM_022157.3	388	gCg/gTg	7/7	0.802586538730684	4	FACETS	0.598	0.555	0.642			1	SUBCLONAL	1	TRUE	NA	0.85980474017418	4		721	1664	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14026065	14026065	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	32	626	0	ENST00000311895.7:c.1025G>T	p.Arg342Met	p.R342M	ENST00000311895	NM_005236.2	342	aGg/aTg	6/11	0.85980474017418	3	FACETS	0.197	0.159	0.239	0.098	0.079	0.12	SUBCLONAL	1	TRUE	1	0.85980474017418	3		626	541	SUCCESS
APC	324	MSKCC	GRCh37	5	112137021	112137021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762117133	NA	P-0014003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	49	666	2	ENST00000257430.4:c.775C>T	p.Arg259Trp	p.R259W	ENST00000257430	NM_000038.5	259	Cgg/Tgg	8/16	0.85980474017418	3	FACETS	0.333	0.282	0.389	0.167	0.141	0.195	SUBCLONAL	1	TRUE	1	0.85980474017418	3		668	489	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670452	88670452	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143617169	NA	P-0014075-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	23	470	0	ENST00000360948.2:c.1234G>A	p.Glu412Lys	p.E412K	ENST00000360948	NM_001012338.2	412	Gaa/Aaa	11/19	0.16902424014528	1	FACETS	0.369	0.287	0.464	0.369	0.287	0.464	SUBCLONAL	1	TRUE	0	0.255973045492981	1		470	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578456	7578467	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGACGCGGGT	GCGGACGCGGGT	CC	novel	NA	P-0014075-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	146	806	5	ENST00000269305.4:c.463_474delinsGG	p.Thr155GlyfsTer12	p.T155Gfs*12	ENST00000269305	NM_001126112.2	155	ACCCGCGTCCGC/GG	5/11	0.255973045492981	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.255973045492981	1		811	739	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411879	116411918	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCTTTCTTTCTCTCTGTTTTAAGATCTGGGCAGTGAATT	CTCTTTCTTTCTCTCTGTTTTAAGATCTGGGCAGTGAATT	-	novel	NA	P-0014075-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	500	1073	0	ENST00000397752.3:c.2888-24_2903del		p.X963_splice	ENST00000397752	NM_000245.2	963		14/21	0.243663168566937	4	FACETS	0.958	0.919	0.998			1	CLONAL	4	TRUE	NA	0.255973045492981	4		1073	1280	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349892	70349892	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014075-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	114	360	0	ENST00000374080.3:c.3875T>A	p.Val1292Glu	p.V1292E	ENST00000374080		1292	gTa/gAa	28/45	0.156995407826725	2	FACETS	1	0.943	1			1	CLONAL	2	TRUE	NA	0.255973045492981	2		360	422	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144898	47144898	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014075-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	34	569	0	ENST00000409792.3:c.4855C>G	p.Gln1619Glu	p.Q1619E	ENST00000409792	NM_014159.6	1619	Caa/Gaa	7/21	0.16902424014528	1	FACETS	0.398	0.324	0.481	0.398	0.324	0.481	SUBCLONAL	1	TRUE	0	0.255973045492981	1		569	582	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31422997	31422997	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014075-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	107	812	0	ENST00000344624.3:c.3316A>C	p.Lys1106Gln	p.K1106Q	ENST00000344624		1106	Aaa/Caa	26/33	0.255973045492981	3	FACETS	0.904	0.809	1	0.452	0.404	0.503	CLONAL	1	TRUE	1	0.255973045492981	3		812	1043	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412046	116412046	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	G	novel	NA	P-0014524-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	126	961	0	ENST00000397752.3:c.3028+3A>G		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.206764954762956	2	FACETS	0.897	0.814	0.985	0.897	0.814	0.985	CLONAL	2	TRUE	0	0.206764954762956	2		961	679	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202197	108202197	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0014524-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	35	516	1	ENST00000278616.4:c.7542T>A	p.Tyr2514Ter	p.Y2514*	ENST00000278616	NM_000051.3	2514	taT/taA	51/63	0.158036898668316	2	FACETS	1	0.919	1	0.609	0.501	0.729	CLONAL	1	TRUE	0	0.206764954762956	2		517	278	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645681	12645681	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs397516830	NA	P-0014524-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	21	255	0	ENST00000251849.4:c.788T>A	p.Val263Asp	p.V263D	ENST00000251849	NM_002880.3	263	gTc/gAc	7/17	0.206764954762956	3	FACETS	0.958	0.74	1	0.479	0.37	0.605	CLONAL	1	TRUE	1	0.206764954762956	3		255	234	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46714238	46714243	+	inframe_deletion	In_Frame_Del	DEL	TGTGAT	TGTGAT	-	novel	NA	P-0014524-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	65	575	0	ENST00000371975.4:c.58_63del	p.Cys20_Asp21del	p.C20_D21del	ENST00000371975	NM_003579.3	20	TGTGAT/-	2/18	0.202861781347813	4	FACETS	1	0.968	1	0.708	0.614	0.809	CLONAL	1	TRUE	2	0.206764954762956	4		575	536	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146610	185146610	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014524-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	34	619	2	ENST00000265026.3:c.241G>C	p.Glu81Gln	p.E81Q	ENST00000265026	NM_004721.4	81	Gag/Cag	2/14	0.204391648461019	3	FACETS	0.703	0.574	0.849	0.234	0.191	0.283	SUBCLONAL	1	TRUE	0	0.206764954762956	3		621	516	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412046	116412046	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	G	novel	NA	P-0014524-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	131	961	0	ENST00000397752.3:c.3028+3A>G		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.24498183343677	5	FACETS	0.889	0.806	0.977	0.593	0.537	0.651	CLONAL	2	TRUE	2	0.2	5		961	958	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202197	108202197	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0014524-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	46	516	1	ENST00000278616.4:c.7542T>A	p.Tyr2514Ter	p.Y2514*	ENST00000278616	NM_000051.3	2514	taT/taA	51/63	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.2	2		517	449	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645681	12645681	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs397516830	NA	P-0014524-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	27	255	0	ENST00000251849.4:c.788T>A	p.Val263Asp	p.V263D	ENST00000251849	NM_002880.3	263	gTc/gAc	7/17	1	2	FACETS	1	0.807	1	1	0.807	1	CLONAL	1	TRUE	1	0.2	2		255	267	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099124	27099124	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0014968-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	43	523	0	ENST00000324856.7:c.3539+1G>T		p.X1180_splice	ENST00000324856	NM_006015.4	1180			0.271239307368177	1	FACETS	0.425	0.355	0.503	0.425	0.355	0.503	SUBCLONAL	1	TRUE	0	0.320978687098422	1		523	529	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784400	9784400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014968-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	87	858	1	ENST00000377346.4:c.2785C>T	p.Arg929Cys	p.R929C	ENST00000377346	NM_005026.3	929	Cgt/Tgt	22/24	0.271239307368177	1	FACETS	0.486	0.429	0.547	0.486	0.429	0.547	SUBCLONAL	1	TRUE	0	0.320978687098422	1		859	936	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015194-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	226	445	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.835	0.783	0.888	0.835	0.783	0.888	CLONAL	1	TRUE	1	0.887150885946382	2		445	610	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519938	NA	P-0015194-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	238	479	0	ENST00000263967.3:c.1034A>C	p.Asn345Thr	p.N345T	ENST00000263967	NM_006218.2	345	aAt/aCt	5/21	1	2	FACETS	0.906	0.853	0.961	0.906	0.853	0.961	CLONAL	1	TRUE	1	0.887150885946382	2		479	592	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41219623	41219623	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0015194-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	123	569	0	ENST00000357654.3:c.5074+2T>G		p.X1692_splice	ENST00000357654	NM_007294.3	1692			1	2	FACETS	0.343	0.31	0.378	0.343	0.31	0.378	SUBCLONAL	1	TRUE	1	0.887150885946382	2		569	809	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97934357	97934357	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015194-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	65	586	0	ENST00000289081.3:c.418T>C	p.Tyr140His	p.Y140H	ENST00000289081	NM_000136.2	140	Tat/Cat	5/15	1	2	FACETS	0.173	0.149	0.199	0.173	0.149	0.199	SUBCLONAL	1	TRUE	1	0.887150885946382	2		586	847	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899050	40899050	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016055-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1498	156	667	0	ENST00000373198.4:c.2220C>G	p.Cys740Trp	p.C740W	ENST00000373198	NM_133170.3	740	tgC/tgG	14/32	0.503913705198652	6	FACETS	0.752	0.685	0.821	0.15	0.137	0.165	SUBCLONAL	1	TRUE	1	0.503913705198652	6		667	1654	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243668580	243668580	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016055-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	145	522	0	ENST00000263826.5:c.1411T>C	p.Phe471Leu	p.F471L	ENST00000263826	NM_005465.4	471	Ttt/Ctt	13/13	0.169207132106157	5	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.503913705198652	5		522	799	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060868	38060868	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016055-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1344	365	757	0	ENST00000250448.2:c.1121A>T	p.His374Leu	p.H374L	ENST00000250448	NM_004496.3	374	cAc/cTc	2/2	0.402251831150157	5	FACETS	1	0.995	1	0.496	0.469	0.524	CLONAL	1	TRUE	2	0.503913705198652	5		757	1709	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56792543	56792543	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016055-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	132	536	0	ENST00000308159.5:c.273G>C	p.Glu91Asp	p.E91D	ENST00000308159	NM_014669.4	91	gaG/gaC	3/22	0.422354633838307	4	FACETS	0.833	0.755	0.915	0.416	0.377	0.458	CLONAL	1	TRUE	2	0.503913705198652	4		536	946	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0016903-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	30	170	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	0.218945141950876	3	FACETS	0.74	0.6	0.896	0.247	0.2	0.299	INDETERMINATE	1	FALSE	0	0.462008619712318	3		170	216	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118930	115118930	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016903-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	10	121	0	ENST00000257566.3:c.411A>T	p.Lys137Asn	p.K137N	ENST00000257566	NM_016569.3	137	aaA/aaT	2/8	0.357303182010707	4	FACETS	0.541	0.368	0.755	0.27	0.184	0.378	SUBCLONAL	1	FALSE	2	0.462008619712318	4		121	117	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0016969-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	119	930	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.339169386068729	1	FACETS	0.968	0.877	1	0.968	0.877	1	CLONAL	1	TRUE	0	0.355894914190018	1		931	568	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661621	227661621	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016969-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	35	809	0	ENST00000305123.5:c.1834T>C	p.Tyr612His	p.Y612H	ENST00000305123	NM_005544.2	612	Tac/Cac	1/2	0.127081454240392	1	FACETS	0.378	0.309	0.454	0.378	0.309	0.454	INDETERMINATE	1	TRUE	0	0.355894914190018	1		809	428	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928071	178928098	+	protein_altering_variant	In_Frame_Del	DEL	ATGGATTAGAAGATTTGCTGAACCCTAT	ATGGATTAGAAGATTTGCTGAACCCTAT	G	novel	NA	P-0016969-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	124	775	0	ENST00000263967.3:c.1349_1376delinsG	p.His450_Ile459delinsArg	p.H450_I459delinsR	ENST00000263967	NM_006218.2	450	cATGGATTAGAAGATTTGCTGAACCCTATt/cGt	8/21	0.335779638217581	2	FACETS	1	0.98	1	0.651	0.592	0.713	CLONAL	1	TRUE	0	0.355894914190018	2		775	535	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	384	701	0				ENST00000310581	NM_198253.2	-/1132			0.140627235567895	0	FACETS	0.635	0.605	0.666			1	INDETERMINATE	1	TRUE	0	0.549556259563565	0		701	991	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	282	845	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.342595804346165	3	FACETS	1	0.968	1	0.349	0.327	0.371	CLONAL	1	TRUE	0	0.549556259563565	3		845	1250	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579346	7579348	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs764486868	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	1051	879	0	ENST00000269305.4:c.339_341del	p.Phe113del	p.F113del	ENST00000269305	NM_001126112.2	113	ttCTTg/ttg	4/11	0.541277326702038	3	FACETS	0.947	0.925	0.969			1	CLONAL	3	TRUE	NA	0.549556259563565	3		879	1716	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287398	38287398	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778531708	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	312	649	1	ENST00000425967.3:c.259C>T	p.Arg87Cys	p.R87C	ENST00000425967	NM_001174067.1	87	Cgc/Tgc	4/19	0.517731622923585	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.549556259563565	1		650	785	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115252327	115252327	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	344	522	0	ENST00000369535.4:c.313G>C	p.Asp105His	p.D105H	ENST00000369535	NM_002524.4	105	Gac/Cac	4/7	0.529100891978645	3	FACETS	0.974	0.927	1	0.974	0.927	1	CLONAL	2	TRUE	1	0.549556259563565	3		522	819	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95598909	95598909	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	115	716	0	ENST00000393063.1:c.250C>G	p.Gln84Glu	p.Q84E	ENST00000393063	NM_030621.3	84	Cag/Gag	4/28	0.529100891978645	3	FACETS	0.739	0.666	0.816	0.369	0.333	0.408	SUBCLONAL	1	TRUE	1	0.549556259563565	3		716	722	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817799	3817799	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1357	106	924	0	ENST00000262367.5:c.3172G>C	p.Glu1058Gln	p.E1058Q	ENST00000262367	NM_004380.2	1058	Gaa/Caa	16/31	0.549556259563565	3	FACETS	0.336	0.3	0.375	0.112	0.1	0.125	SUBCLONAL	1	TRUE	0	0.549556259563565	3		924	1463	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817871	3817871	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	123	747	1	ENST00000262367.5:c.3100G>T	p.Glu1034Ter	p.E1034*	ENST00000262367	NM_004380.2	1034	Gaa/Taa	16/31	0.549556259563565	3	FACETS	0.482	0.434	0.532	0.161	0.144	0.178	SUBCLONAL	1	TRUE	0	0.549556259563565	3		748	1184	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041572	14041572	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	688	641	0	ENST00000311895.7:c.2119G>C	p.Glu707Gln	p.E707Q	ENST00000311895	NM_005236.2	707	Gaa/Caa	11/11	0.549556259563565	3	FACETS	1	0.993	1	0.734	0.71	0.759	CLONAL	2	TRUE	0	0.549556259563565	3		641	1449	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346511	89346511	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1387	275	820	1	ENST00000301030.4:c.6439G>T	p.Asp2147Tyr	p.D2147Y	ENST00000301030	NM_001256183.1	2147	Gat/Tat	9/13	0.541277326702038	3	FACETS	0.768	0.718	0.819			1	SUBCLONAL	1	TRUE	NA	0.549556259563565	3		821	1662	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37865697	37865697	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	217	678	0	ENST00000269571.5:c.566C>G	p.Ser189Cys	p.S189C	ENST00000269571		189	tCt/tGt	4/27	0.342595804346165	3	FACETS	1	0.936	1	0.336	0.312	0.36	CLONAL	1	TRUE	0	0.549556259563565	3		678	1000	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375565	40375565	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	250	557	0	ENST00000293328.3:c.385C>G	p.Pro129Ala	p.P129A	ENST00000293328	NM_012448.3	129	Cca/Gca	5/19	0.342595804346165	3	FACETS	1	0.965	1	0.35	0.327	0.373	CLONAL	1	TRUE	0	0.549556259563565	3		557	1106	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41242986	41242986	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	148	707	0	ENST00000357654.3:c.4160C>T	p.Ser1387Phe	p.S1387F	ENST00000357654	NM_007294.3	1387	tCt/tTt	11/23	0.342595804346165	3	FACETS	0.608	0.554	0.664	0.203	0.184	0.222	SUBCLONAL	1	TRUE	0	0.549556259563565	3		707	1130	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677936	58677936	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	342	407	1	ENST00000305921.3:c.161C>A	p.Ser54Ter	p.S54*	ENST00000305921	NM_003620.3	54	tCg/tAg	1/6	0.342595804346165	3	FACETS	1	0.993	1	0.435	0.411	0.459	CLONAL	1	TRUE	0	0.549556259563565	3		408	1216	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774737	73774737	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	185	267	0	ENST00000254810.4:c.350G>C	p.Arg117Thr	p.R117T	ENST00000254810	NM_005324.3	117	aGa/aCa	4/4	0.342595804346165	3	FACETS	1	0.99	1	0.471	0.437	0.505	CLONAL	1	TRUE	0	0.549556259563565	3		267	608	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39620667	39620667	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	106	570	0	ENST00000262039.4:c.2065C>G	p.Pro689Ala	p.P689A	ENST00000262039	NM_002647.2	689	Cct/Gct	19/25	0.34937196537558	2	FACETS	0.962	0.869	1	0.481	0.434	0.53	CLONAL	1	TRUE	0	0.549556259563565	2		570	401	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130320	11130320	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	322	842	0	ENST00000358026.2:c.2559C>G	p.Phe853Leu	p.F853L	ENST00000358026	NM_001128849.1	853	ttC/ttG	18/36	NA	2	FACETS	1	0.955	1			1	INDETERMINATE	1	TRUE	NA	0.549556259563565	2		842	1157	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637445	47637445	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	241	591	0	ENST00000233146.2:c.579G>C	p.Gln193His	p.Q193H	ENST00000233146	NM_000251.2	193	caG/caC	3/16	0.549556259563565	1	FACETS	0.917	0.86	0.974	0.917	0.86	0.974	CLONAL	1	TRUE	0	0.549556259563565	1		591	694	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736181	204736181	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	155	527	0	ENST00000302823.3:c.538C>G	p.Leu180Val	p.L180V	ENST00000302823	NM_005214.4	180	Ctc/Gtc	3/4	1	2	FACETS	0.746	0.684	0.811	0.746	0.684	0.811	SUBCLONAL	1	TRUE	1	0.549556259563565	2		527	756	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225360637	225360637	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	146	580	0	ENST00000264414.4:c.1754C>G	p.Ser585Cys	p.S585C	ENST00000264414	NM_003590.4	585	tCt/tGt	13/16	1	2	FACETS	0.803	0.735	0.874	0.803	0.735	0.874	CLONAL	1	TRUE	1	0.549556259563565	2		580	662	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44515836	44515836	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1213	259	795	0	ENST00000291552.4:c.217G>C	p.Glu73Gln	p.E73Q	ENST00000291552	NM_006758.2	73	Gag/Cag	4/8	0.549556259563565	3	FACETS	0.816	0.763	0.872	0.408	0.381	0.436	CLONAL	1	TRUE	1	0.549556259563565	3		795	1472	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556686	41556686	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	127	717	0	ENST00000263253.7:c.3631G>A	p.Glu1211Lys	p.E1211K	ENST00000263253	NM_001429.3	1211	Gag/Aag	20/31	0.297750914944516	1	FACETS	0.388	0.351	0.427	0.388	0.351	0.427	INDETERMINATE	1	TRUE	0	0.549556259563565	1		717	864	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52621413	52621413	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	189	782	1	ENST00000394830.3:c.3004C>T	p.Pro1002Ser	p.P1002S	ENST00000394830	NM_018313.4	1002	Cca/Tca	20/30	0.259255878649785	3	FACETS	1	0.964	1	0.534	0.494	0.575	INDETERMINATE	1	TRUE	1	0.549556259563565	3		783	821	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72897378	72897378	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs768322266	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	171	667	0	ENST00000325599.8:c.114C>G	p.Phe38Leu	p.F38L	ENST00000325599	NM_018130.2	38	ttC/ttG	1/11	1	2	FACETS	0.619	0.568	0.671	0.619	0.568	0.671	SUBCLONAL	1	TRUE	1	0.549556259563565	2		667	1006	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260177	149260177	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	145	690	0	ENST00000360632.3:c.716G>C	p.Arg239Thr	p.R239T	ENST00000360632	NM_015472.4	239	aGa/aCa	4/7	0.448762268162427	1	FACETS	0.518	0.473	0.565	0.518	0.473	0.565	SUBCLONAL	1	TRUE	0	0.549556259563565	1		690	739	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182679095	182679095	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	103	760	0	ENST00000292782.4:c.439G>C	p.Glu147Gln	p.E147Q	ENST00000292782	NM_020640.2	147	Gaa/Caa	4/7	0.432348945236567	3	FACETS	1	0.899	1	0.5	0.449	0.553	CLONAL	1	TRUE	1	0.549556259563565	3		760	478	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31483667	31483667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	105	438	0	ENST00000344624.3:c.2065C>T	p.Leu689Phe	p.L689F	ENST00000344624		689	Ctt/Ttt	13/33	0.140627235567895	0	FACETS	0.344	0.309	0.381			1	INDETERMINATE	1	TRUE	0	0.549556259563565	0		438	500	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958917	38958917	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	45	369	1	ENST00000357387.3:c.2195C>T	p.Ala732Val	p.A732V	ENST00000357387	NM_152756.3	732	gCa/gTa	23/38	0.140627235567895	0	FACETS	0.304	0.257	0.354			1	INDETERMINATE	1	TRUE	0	0.549556259563565	0		370	243	SUCCESS
APC	324	MSKCC	GRCh37	5	112174893	112174893	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	97	435	2	ENST00000257430.4:c.3602C>T	p.Ser1201Leu	p.S1201L	ENST00000257430	NM_000038.5	1201	tCa/tTa	16/16	0.448762268162427	1	FACETS	0.552	0.494	0.612	0.552	0.494	0.612	SUBCLONAL	1	TRUE	0	0.549556259563565	1		437	464	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	132	386	0	ENST00000257430.4:c.4099C>G	p.Gln1367Glu	p.Q1367E	ENST00000257430	NM_000038.5	1367	Cag/Gag	16/16	0.448762268162427	1	FACETS	0.7	0.639	0.763	0.7	0.639	0.763	SUBCLONAL	1	TRUE	0	0.549556259563565	1		386	498	SUCCESS
APC	324	MSKCC	GRCh37	5	112176641	112176641	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1561599480	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	87	382	0	ENST00000257430.4:c.5350G>A	p.Glu1784Lys	p.E1784K	ENST00000257430	NM_000038.5	1784	Gaa/Aaa	16/16	0.448762268162427	1	FACETS	0.574	0.511	0.64	0.574	0.511	0.64	SUBCLONAL	1	TRUE	0	0.549556259563565	1		382	400	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973778	131973778	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	106	343	0	ENST00000265335.6:c.3481G>C	p.Glu1161Gln	p.E1161Q	ENST00000265335		1161	Gaa/Caa	23/25	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.549556259563565	NA		343	478	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407554	407554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	125	741	0	ENST00000380956.4:c.1312G>A	p.Glu438Lys	p.E438K	ENST00000380956	NM_001195286.1	438	Gaa/Aaa	9/9	0.549556259563565	1	FACETS	0.525	0.477	0.576	0.525	0.477	0.576	SUBCLONAL	1	TRUE	0	0.549556259563565	1		741	628	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675735	30675735	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1389	428	1177	0	ENST00000376406.3:c.2621C>G	p.Ser874Cys	p.S874C	ENST00000376406	NM_014641.2	874	tCt/tGt	8/15	0.168012565155283	5	FACETS	0.782	0.743	0.822			1	INDETERMINATE	2	TRUE	NA	0.549556259563565	5		1177	1817	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026915	6026915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782602	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	67	133	0	ENST00000265849.7:c.1481C>T	p.Ser494Leu	p.S494L	ENST00000265849	NM_000535.5	494	tCg/tTg	11/15	0.386092547985686	4	FACETS	1	0.954	1	0.299	0.261	0.339	CLONAL	1	TRUE	0	0.549556259563565	4		133	316	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92247469	92247469	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	156	470	0	ENST00000265734.4:c.751A>T	p.Arg251Trp	p.R251W	ENST00000265734	NM_001259.6	251	Agg/Tgg	7/8	0.343774265438247	2	FACETS	0.739	0.678	0.803	0.37	0.339	0.402	SUBCLONAL	1	TRUE	0	0.549556259563565	2		470	768	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050746	5050746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	72	643	0	ENST00000381652.3:c.529G>A	p.Glu177Lys	p.E177K	ENST00000381652	NM_004972.3	177	Gaa/Aaa	6/25	0.549556259563565	1	FACETS	0.367	0.321	0.416	0.367	0.321	0.416	SUBCLONAL	1	TRUE	0	0.549556259563565	1		643	518	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27220139	27220139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762495403	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	112	703	1	ENST00000380036.4:c.3196G>A	p.Glu1066Lys	p.E1066K	ENST00000380036	NM_000459.3	1066	Gag/Aag	21/23	0.549556259563565	1	FACETS	0.402	0.361	0.444	0.402	0.361	0.444	SUBCLONAL	1	TRUE	0	0.549556259563565	1		704	736	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399318	139399318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	310	961	1	ENST00000277541.6:c.4825G>A	p.Asp1609Asn	p.D1609N	ENST00000277541	NM_017617.3	1609	Gac/Aac	26/34	0.515826257429924	2	FACETS	0.783	0.737	0.83	0.391	0.368	0.415	SUBCLONAL	1	TRUE	0	0.549556259563565	2		962	1441	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184398	7184398	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	151	843	0	ENST00000302850.5:c.903C>A	p.Cys301Ter	p.C301*	ENST00000302850	NM_000208.2	301	tgC/tgA	3/22	0.280191350830909	1	FACETS	0.353	0.322	0.385	0.353	0.322	0.385	INDETERMINATE	1	TRUE	0	0.549556259563565	1		843	1130	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564557	41564557	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	193	764	0	ENST00000263253.7:c.3979C>T	p.His1327Tyr	p.H1327Y	ENST00000263253	NM_001429.3	1327	Cat/Tat	24/31	0.297750914944516	1	FACETS	0.48	0.444	0.518	0.48	0.444	0.518	INDETERMINATE	1	TRUE	0	0.549556259563565	1		764	1061	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026586	6026586	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1064793426	NA	P-0018186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1664	358	1206	0	ENST00000265849.7:c.1810C>G	p.Gln604Glu	p.Q604E	ENST00000265849	NM_000535.5	604	Cag/Gag	11/15	0.386092547985686	4	FACETS	0.998	0.942	1	0.25	0.235	0.264	CLONAL	1	TRUE	0	0.549556259563565	4		1206	2022	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	181	778	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.528903103778784	2		778	626	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99440116	99440116	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019942-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	225	591	1	ENST00000268035.6:c.1084A>T	p.Ile362Phe	p.I362F	ENST00000268035	NM_000875.3	362	Att/Ttt	4/21	0.312054437086536	3	FACETS	1	0.936	1	0.501	0.468	0.536	INDETERMINATE	1	TRUE	1	0.748904498047217	3		592	824	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119235	3119235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529942770	NA	P-0020168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	22	846	2	ENST00000078429.4:c.767G>A	p.Arg256Gln	p.R256Q	ENST00000078429	NM_002067.2	256	cGg/cAg	6/7	0.45447311746986	3	FACETS	0.13	0.1	0.165	0.065	0.05	0.083	SUBCLONAL	1	TRUE	1	0.513271978227206	3		848	831	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574022	+	frameshift_variant	Frame_Shift_Del	DEL	CGAAGCGCTCA	CGAAGCGCTCA	-	novel	NA	P-0020168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	305	847	1	ENST00000269305.4:c.1005_1015del	p.Glu336AspfsTer7	p.E336Dfs*7	ENST00000269305	NM_001126112.2	335	cgTGAGCGCTTCGag/cgag	10/11	0.501815470569969	2	FACETS	0.869	0.825	0.913	0.869	0.825	0.913	CLONAL	2	TRUE	0	0.513271978227206	2		848	684	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324302	62324302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781430438	NA	P-0020168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	100	902	1	ENST00000360203.5:c.2797G>A	p.Ala933Thr	p.A933T	ENST00000360203	NM_001283009.1	933	Gcc/Acc	29/35	0.436808003777419	4	FACETS	0.585	0.521	0.653	0.292	0.26	0.327	SUBCLONAL	1	TRUE	2	0.513271978227206	4		903	1008	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627224	37627224	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200075664	NA	P-0020942-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	56	651	0	ENST00000447079.4:c.1139G>A	p.Arg380His	p.R380H	ENST00000447079	NM_015083.1	380	cGt/cAt	2/14	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	FALSE	1	0.169544613346731	2		651	594	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	148	445	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.871	0.802	0.943	0.871	0.802	0.943	CLONAL	1	TRUE	1	0.703349606035401	2		445	483	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0021317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	224	640	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.865	0.809	0.923	0.865	0.809	0.923	CLONAL	1	TRUE	1	0.703349606035401	2		640	736	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577362	64577371	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCAGGCGG	CGCCAGGCGG	-	novel	NA	P-0021317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	283	521	0	ENST00000312049.6:c.211_220del	p.Pro71AlafsTer45	p.P71Afs*45	ENST00000312049	NM_130799.2	71	CCGCCTGGCGgc/gc	2/10	0.633416299927775	2	FACETS	0.818	0.78	0.855	0.818	0.78	0.855	CLONAL	2	TRUE	0	0.703349606035401	2		521	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021454-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	564	1097	0	ENST00000269305.4:c.403del	p.Cys135AlafsTer35	p.C135Afs*35	ENST00000269305	NM_001126112.2	135	Tgc/gc	5/11	NA	2	FACETS	0.97	0.933	1			1	INDETERMINATE	2	TRUE	NA	0.453999089163268	2		1097	1281	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467800	66467800	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021454-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	82	432	0	ENST00000273854.3:c.469G>C	p.Glu157Gln	p.E157Q	ENST00000273854	NM_004439.5	157	Gag/Cag	3/18	1	2	FACETS	0.654	0.578	0.736	0.654	0.578	0.736	SUBCLONAL	1	TRUE	1	0.453999089163268	2		432	552	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16247477	16247477	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021454-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	118	243	0	ENST00000375759.3:c.1748A>C	p.Lys583Thr	p.K583T	ENST00000375759	NM_015001.2	583	aAg/aCg	9/15	0.383210578981595	2	FACETS	0.795	0.726	0.865	0.795	0.726	0.865	SUBCLONAL	2	TRUE	0	0.453999089163268	2		243	327	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513595	41513595	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs776659580	NA	P-0021454-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	228	719	0	ENST00000263253.7:c.499A>G	p.Thr167Ala	p.T167A	ENST00000263253	NM_001429.3	167	Aca/Gca	2/31	0.167889836446581	2	FACETS	1	0.99	1	0.661	0.618	0.705	INDETERMINATE	1	TRUE	0	0.453999089163268	2		719	760	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41521995	41521995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764980716	NA	P-0021454-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	106	700	0	ENST00000263253.7:c.857C>T	p.Pro286Leu	p.P286L	ENST00000263253	NM_001429.3	286	cCa/cTa	3/31	0.167889836446581	2	FACETS	0.522	0.467	0.581	0.261	0.233	0.291	INDETERMINATE	1	TRUE	0	0.453999089163268	2		700	894	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89176385	89176385	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs760801471	NA	P-0021454-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	57	552	0	ENST00000336596.2:c.115C>G	p.Gln39Glu	p.Q39E	ENST00000336596	NM_005233.5	39	Caa/Gaa	2/17	0.453999089163268	1	FACETS	0.491	0.423	0.566	0.491	0.423	0.566	SUBCLONAL	1	TRUE	0	0.453999089163268	1		552	395	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201668	66201668	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021454-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	115	704	0	ENST00000273854.3:c.2834T>A	p.Leu945Gln	p.L945Q	ENST00000273854	NM_004439.5	945	cTg/cAg	16/18	1	2	FACETS	0.725	0.654	0.8	0.725	0.654	0.8	SUBCLONAL	1	TRUE	1	0.453999089163268	2		704	699	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978595	70978595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750600524	NA	P-0021454-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	366	857	0	ENST00000276594.2:c.1058G>A	p.Cys353Tyr	p.C353Y	ENST00000276594	NM_024504.3	353	tGc/tAc	5/8	0.438781228931485	3	FACETS	0.836	0.793	0.88	0.557	0.529	0.587	CLONAL	2	TRUE	0	0.453999089163268	3		857	1183	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063717	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0021555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	25	352	0	ENST00000412916.2:c.165+1G>T		p.X55_splice	ENST00000412916		55			0.159345634083575	1	FACETS	0.616	0.487	0.765	0.616	0.487	0.765	SUBCLONAL	1	TRUE	0	0.258697801606551	1		352	273	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115712	8115715	+	frameshift_variant	Frame_Shift_Del	DEL	CCCT	CCCT	-	novel	NA	P-0021555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	38	472	0	ENST00000346208.3:c.1058_1061del	p.Pro353ArgfsTer3	p.P353Rfs*3	ENST00000346208		353	cCCCTg/cg	6/6	1	2	FACETS	0.64	0.529	0.764	0.64	0.529	0.764	SUBCLONAL	1	TRUE	1	0.258697801606551	2		472	459	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151164299	151164299	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0021555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	57	767	0	ENST00000262187.5:c.463-2A>G		p.X155_splice	ENST00000262187	NM_005614.3	155			1	2	FACETS	0.578	0.494	0.669	0.578	0.494	0.669	SUBCLONAL	1	TRUE	1	0.258697801606551	2		767	763	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0021630-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	72	597	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.241207541390454	1	FACETS	0.816	0.714	0.926	0.816	0.714	0.926	CLONAL	1	TRUE	0	0.278103401777697	1		597	546	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0021630-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	46	501	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	1	2	FACETS	0.48	0.403	0.565	0.48	0.403	0.565	SUBCLONAL	1	TRUE	1	0.278103401777697	2		501	689	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519996	NA	P-0021630-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	133	887	1	ENST00000269305.4:c.395A>T	p.Lys132Met	p.K132M	ENST00000269305	NM_001126112.2	132	aAg/aTg	5/11	0.241207541390454	1	FACETS	0.982	0.891	1	0.982	0.891	1	CLONAL	1	TRUE	0	0.278103401777697	1		888	839	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805584	46805584	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021630-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	114	863	0	ENST00000290295.7:c.372del	p.Thr125LeufsTer154	p.T125Lfs*154	ENST00000290295	NM_006361.5	124	ccC/cc	1/2	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.278103401777697	2		863	787	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007442	62007442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777737578	NA	P-0021630-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	43	509	0	ENST00000392795.3:c.425G>A	p.Arg142Gln	p.R142Q	ENST00000392795	NM_001039933.1	142	cGa/cAa	3/6	1	2	FACETS	0.689	0.577	0.813	0.689	0.577	0.813	SUBCLONAL	1	TRUE	1	0.278103401777697	2		509	449	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881384	111881384	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021630-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	33	630	1	ENST00000393256.3:c.62C>T	p.Pro21Leu	p.P21L	ENST00000393256	NM_006538.4	21	cCt/cTt	2/4	1	2	FACETS	0.418	0.339	0.507	0.418	0.339	0.507	SUBCLONAL	1	TRUE	1	0.278103401777697	2		631	568	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0021665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	39	628	1	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.399	0.329	0.477	0.399	0.329	0.477	SUBCLONAL	1	TRUE	1	0.25	2		629	782	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0021665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	81	913	2	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.25	2		915	601	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0021665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	91	862	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	0.971	0.862	1	0.971	0.862	1	CLONAL	1	TRUE	1	0.25	2		862	750	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	86	579	0	ENST00000397062.3:c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	NM_006164.4	34	Cga/Gga	2/5	0.215817003097796	2	FACETS	1	0.978	1	0.738	0.656	0.826	CLONAL	1	TRUE	0	0.25	2		579	466	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960136	134960136	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	37	924	0	ENST00000398015.3:c.2493A>C	p.Gln831His	p.Q831H	ENST00000398015	NM_004441.4	831	caA/caC	13/16	1	2	FACETS	0.433	0.356	0.52	0.433	0.356	0.52	SUBCLONAL	1	TRUE	1	0.25	2		924	683	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916726	178916726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772110575	NA	P-0021665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	45	657	1	ENST00000263967.3:c.113G>A	p.Arg38His	p.R38H	ENST00000263967	NM_006218.2	38	cGt/cAt	2/21	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.25	2		658	346	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849297	89849297	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	64	949	0	ENST00000389301.3:c.1596G>C	p.Glu532Asp	p.E532D	ENST00000389301	NM_000135.2	532	gaG/gaC	17/43	1	2	FACETS	0.682	0.589	0.782	0.682	0.589	0.782	SUBCLONAL	1	TRUE	1	0.25	2		949	751	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474404	40474404	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	43	903	0	ENST00000264657.5:c.1997T>C	p.Leu666Pro	p.L666P	ENST00000264657	NM_139276.2	666	cTg/cCg	21/24	1	2	FACETS	0.536	0.447	0.634	0.536	0.447	0.634	SUBCLONAL	1	TRUE	1	0.25	2		903	642	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021761-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	326	445	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.775994880300454	2		445	788	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0021761-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	492	569	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.384093379427804	1	FACETS	0.77	0.74	0.8	0.77	0.74	0.8	INDETERMINATE	1	TRUE	0	0.775994880300454	1		569	1008	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0021761-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	514	748	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	1	2	FACETS	0.906	0.868	0.945	0.906	0.868	0.945	CLONAL	1	TRUE	1	0.775994880300454	2		748	1462	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339243	70339278	+	inframe_deletion	In_Frame_Del	DEL	TGTAAAACAAGGTTTCAATAACCAGCCTGCTGTCTC	TGTAAAACAAGGTTTCAATAACCAGCCTGCTGTCTC	-	novel	NA	P-0021761-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	334	758	0	ENST00000374080.3:c.122_157del	p.Val41_Ser52del	p.V41_S52del	ENST00000374080		40	aaTGTAAAACAAGGTTTCAATAACCAGCCTGCTGTCTCt/aat	2/45	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.775994880300454	2		758	815	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496924	29496927	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs786201874	NA	P-0021761-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	252	401	0	ENST00000356175.3:c.499_502del	p.Cys167GlnfsTer10	p.C167Qfs*10	ENST00000356175	NM_000267.3	165	acTGTT/ac	5/57	1	2	FACETS	0.851	0.8	0.904	0.851	0.8	0.904	CLONAL	1	TRUE	1	0.775994880300454	2		401	763	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818206	43818207	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0021761-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	193	603	0	ENST00000372470.3:c.1672_1673del	p.Asp558TyrfsTer3	p.D558Yfs*3	ENST00000372470	NM_005373.2	557	tcAGat/tcat	12/12	1	2	FACETS	0.484	0.448	0.523	0.484	0.448	0.523	SUBCLONAL	1	TRUE	1	0.775994880300454	2		603	1027	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310938	123310938	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0021761-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	150	538	0	ENST00000358487.5:c.490A>T	p.Lys164Ter	p.K164*	ENST00000358487	NM_000141.4	164	Aag/Tag	5/18	NA	2	FACETS	0.473	0.433	0.516			1	INDETERMINATE	1	TRUE	NA	0.775994880300454	2		538	817	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129189	64129190	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0021761-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	488	835	0	ENST00000334205.4:c.730_731del	p.Arg244GlufsTer5	p.R244Efs*5	ENST00000334205	NM_003942.2	243	GAg/g	7/17	0.775994880300454	1	FACETS	0.961	0.928	0.993	0.961	0.928	0.993	CLONAL	1	TRUE	0	0.775994880300454	1		835	801	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885173	111885173	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021761-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	216	692	0	ENST00000341259.2:c.1061A>C	p.Lys354Thr	p.K354T	ENST00000341259	NM_005475.2	354	aAg/aCg	6/8	1	2	FACETS	0.485	0.45	0.522	0.485	0.45	0.522	SUBCLONAL	1	TRUE	1	0.775994880300454	2		692	1147	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003042	42003043	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0021761-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	320	857	0	ENST00000219905.7:c.2581_2582del	p.Ser861TyrfsTer8	p.S861Yfs*8	ENST00000219905	NM_001164273.1	860	aAG/a	8/24	0.33641051484062	2	FACETS	0.574	0.54	0.608	0.287	0.27	0.304	INDETERMINATE	1	TRUE	0	0.775994880300454	2		857	1438	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860625	45860626	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0021761-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	240	857	0	ENST00000391945.4:c.1381_1382del	p.Leu461ValfsTer39	p.L461Vfs*39	ENST00000391945	NM_000400.3	461	CTg/g	15/23	0.51766690761731	1	FACETS	0.335	0.313	0.359	0.335	0.313	0.359	SUBCLONAL	1	TRUE	0	0.775994880300454	1		857	1129	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206827	36206827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021761-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	423	542	1	ENST00000300305.3:c.685G>A	p.Glu229Lys	p.E229K	ENST00000300305		229	Gag/Aag	6/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.775994880300454	2		543	1062	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	209	445	0				ENST00000310581	NM_198253.2	-/1132			0.574351160905915	1	FACETS	0.997	0.934	1	0.997	0.934	1	CLONAL	1	TRUE	0	0.574703480327514	1		445	520	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	197	743	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	1	2	FACETS	0.698	0.646	0.752	0.698	0.646	0.752	SUBCLONAL	1	TRUE	1	0.574703480327514	2		743	982	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	381	1019	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	1	2	FACETS	0.998	0.947	1	0.998	0.947	1	CLONAL	1	TRUE	1	0.574703480327514	2		1019	1329	SUCCESS
BLM	641	MSKCC	GRCh37	15	91290720	91290720	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs139282091	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	167	489	0	ENST00000355112.3:c.98C>T	p.Ser33Leu	p.S33L	ENST00000355112	NM_000057.2	33	tCa/tTa	2/22	1	2	FACETS	0.889	0.82	0.96	0.889	0.82	0.96	CLONAL	1	TRUE	1	0.574703480327514	2		489	654	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	270	850	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	0.832	0.78	0.886	0.832	0.78	0.886	CLONAL	1	TRUE	1	0.574703480327514	2		850	1129	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	404	980	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.505288850355241	1	FACETS	0.899	0.856	0.941	0.899	0.856	0.941	CLONAL	1	TRUE	0	0.574703480327514	1		980	1115	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561263	9561263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769939031	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	280	676	0	ENST00000353224.5:c.519G>A	p.Met173Ile	p.M173I	ENST00000353224	NM_177990.2	173	atG/atA	4/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.574703480327514	2		676	949	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	331	585	0	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	0.574703480327514	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.574703480327514	1		585	691	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857197	9857197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866121846	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	262	617	0	ENST00000330684.3:c.4204C>T	p.Arg1402Trp	p.R1402W	ENST00000330684	NM_001134407.1	1402	Cgg/Tgg	13/13	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.574703480327514	2		617	887	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958208	2958208	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1162658658	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	217	771	0	ENST00000396946.4:c.2524C>T	p.Leu842Phe	p.L842F	ENST00000396946	NM_032415.4	842	Ctc/Ttc	19/25	1	2	FACETS	0.737	0.685	0.79	0.737	0.685	0.79	SUBCLONAL	1	TRUE	1	0.574703480327514	2		771	1025	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	208	436	0	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.574703480327514	2		436	600	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912815	100912815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1000609240	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	159	575	2	ENST00000325455.5:c.2507G>A	p.Arg836Gln	p.R836Q	ENST00000325455	NM_001202474.3	836	cGa/cAa	7/8	1	2	FACETS	0.867	0.798	0.939	0.867	0.798	0.939	CLONAL	1	TRUE	1	0.574703480327514	2		577	638	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805719	43805719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528834914	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	274	849	0	ENST00000372470.3:c.775G>A	p.Glu259Lys	p.E259K	ENST00000372470	NM_005373.2	259	Gaa/Aaa	5/12	NA	2	FACETS	0.874	0.82	0.929			1	INDETERMINATE	1	TRUE	NA	0.574703480327514	2		849	1091	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226926	2226926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375062102	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	219	497	3	ENST00000398665.3:c.4406C>T	p.Pro1469Leu	p.P1469L	ENST00000398665	NM_032482.2	1469	cCg/cTg	27/28	1	2	FACETS	0.977	0.912	1	0.977	0.912	1	CLONAL	1	TRUE	1	0.574703480327514	2		500	780	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188847	32188847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	411	862	0	ENST00000375023.3:c.707G>A	p.Gly236Glu	p.G236E	ENST00000375023	NM_004557.3	236	gGa/gAa	4/30	0.574703480327514	3	FACETS	1	0.991	1	0.594	0.565	0.625	CLONAL	1	TRUE	1	0.574703480327514	3		862	1549	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65304233	65304233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1163790865	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	250	657	1	ENST00000342505.4:c.2882C>T	p.Ser961Leu	p.S961L	ENST00000342505	NM_002227.2	961	tCg/tTg	21/25	1	2	FACETS	0.943	0.883	1	0.943	0.883	1	CLONAL	1	TRUE	1	0.574703480327514	2		658	923	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066482	94066482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542602078	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	187	513	3	ENST00000369303.4:c.1277G>A	p.Arg426Gln	p.R426Q	ENST00000369303	NM_004440.3	426	cGa/cAa	5/17	0.574703480327514	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.574703480327514	1		516	453	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462410	89462410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	240	752	0	ENST00000336596.2:c.1882G>A	p.Gly628Arg	p.G628R	ENST00000336596	NM_005233.5	628	Gga/Aga	10/17	1	2	FACETS	0.896	0.838	0.956	0.896	0.838	0.956	CLONAL	1	TRUE	1	0.574703480327514	2		752	932	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031971	10031971	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555455618	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	353	906	0	ENST00000330684.3:c.852G>A	p.Trp284Ter	p.W284*	ENST00000330684	NM_001134407.1	284	tgG/tgA	3/13	1	2	FACETS	0.974	0.922	1	0.974	0.922	1	CLONAL	1	TRUE	1	0.574703480327514	2		906	1261	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790158	40790158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781621750	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	220	620	1	ENST00000373198.4:c.2573C>T	p.Ser858Phe	p.S858F	ENST00000373198	NM_133170.3	858	tCc/tTc	18/32	1	2	FACETS	0.885	0.825	0.947	0.885	0.825	0.947	CLONAL	1	TRUE	1	0.574703480327514	2		621	865	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858687	9858687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	230	628	0	ENST00000330684.3:c.2714C>T	p.Ser905Phe	p.S905F	ENST00000330684	NM_001134407.1	905	tCc/tTc	13/13	1	2	FACETS	0.934	0.872	0.997	0.934	0.872	0.997	CLONAL	1	TRUE	1	0.574703480327514	2		628	857	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939506	68939506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1309816810	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	192	653	0	ENST00000288368.4:c.491G>A	p.Gly164Glu	p.G164E	ENST00000288368	NM_024870.2	164	gGa/gAa	5/40	1	2	FACETS	0.94	0.872	1	0.94	0.872	1	CLONAL	1	TRUE	1	0.574703480327514	2		653	711	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968619	55968619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775179342	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	251	755	0	ENST00000263923.4:c.2044G>A	p.Glu682Lys	p.E682K	ENST00000263923	NM_002253.2	682	Gaa/Aaa	14/30	1	2	FACETS	0.805	0.753	0.859	0.805	0.753	0.859	CLONAL	1	TRUE	1	0.574703480327514	2		755	1085	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781830	9781830	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	365	1039	0	ENST00000377346.4:c.1967A>G	p.His656Arg	p.H656R	ENST00000377346	NM_005026.3	656	cAc/cGc	16/24	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.574703480327514	2		1039	1248	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256667	16256667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1387045955	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	205	672	0	ENST00000375759.3:c.3932C>T	p.Pro1311Leu	p.P1311L	ENST00000375759	NM_015001.2	1311	cCt/cTt	11/15	1	2	FACETS	0.764	0.709	0.821	0.764	0.709	0.821	SUBCLONAL	1	TRUE	1	0.574703480327514	2		672	934	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259715	16259715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765733962	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	258	633	0	ENST00000375759.3:c.6980G>A	p.Arg2327Gln	p.R2327Q	ENST00000375759	NM_015001.2	2327	cGg/cAg	11/15	1	2	FACETS	0.901	0.844	0.959	0.901	0.844	0.959	CLONAL	1	TRUE	1	0.574703480327514	2		633	997	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262237	16262237	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs576149674	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	113	289	0	ENST00000375759.3:c.9502C>G	p.Arg3168Gly	p.R3168G	ENST00000375759	NM_015001.2	3168	Cga/Gga	11/15	1	2	FACETS	0.888	0.804	0.975	0.888	0.804	0.975	CLONAL	1	TRUE	1	0.574703480327514	2		289	443	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458089	120458089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	319	783	0	ENST00000256646.2:c.7256C>T	p.Pro2419Leu	p.P2419L	ENST00000256646	NM_024408.3	2419	cCa/cTa	34/34	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.574703480327514	2		783	1042	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834189	156834189	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1315	818	1086	0	ENST00000524377.1:c.256G>A	p.Asp86Asn	p.D86N	ENST00000524377	NM_002529.3	86	Gat/Aat	2/17	0.574703480327514	3	FACETS	0.859	0.831	0.887	0.859	0.831	0.887	CLONAL	2	TRUE	1	0.574703480327514	3		1086	2133	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118353205	118353205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	201	384	0	ENST00000534358.1:c.4081G>A	p.Glu1361Lys	p.E1361K	ENST00000534358	NM_005933.3	1361	Gaa/Aaa	8/36	0.546762168145463	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.574703480327514	1		384	470	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120807	115120807	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	242	653	0	ENST00000257566.3:c.199C>T	p.Gln67Ter	p.Q67*	ENST00000257566	NM_016569.3	67	Caa/Taa	1/8	1	2	FACETS	0.987	0.924	1	0.987	0.924	1	CLONAL	1	TRUE	1	0.574703480327514	2		653	853	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431385	121431385	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	273	667	0	ENST00000257555.6:c.589A>T	p.Lys197Ter	p.K197*	ENST00000257555		197	Aag/Tag	3/10	1	2	FACETS	0.943	0.885	1	0.943	0.885	1	CLONAL	1	TRUE	1	0.574703480327514	2		667	1008	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218393	133218393	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	386	977	0	ENST00000320574.5:c.5218C>T	p.Leu1740Phe	p.L1740F	ENST00000320574	NM_006231.2	1740	Ctc/Ttc	39/49	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.574703480327514	2		977	1327	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32903613	32903613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555281352	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	110	616	0	ENST00000380152.3:c.665C>T	p.Pro222Leu	p.P222L	ENST00000380152		222	cCt/cTt	8/27	0.152801057310478	1	FACETS	0.476	0.429	0.526	0.476	0.429	0.526	INDETERMINATE	1	TRUE	0	0.574703480327514	1		616	573	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762085	43762085	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	256	758	0	ENST00000382044.4:c.1360C>T	p.Pro454Ser	p.P454S	ENST00000382044	NM_001141980.1	454	Cct/Tct	11/28	1	2	FACETS	0.872	0.816	0.929	0.872	0.816	0.929	CLONAL	1	TRUE	1	0.574703480327514	2		758	1022	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777965	3777966	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1532	507	1375	4	ENST00000262367.5:c.7082_7083delinsTT	p.Ser2361Phe	p.S2361F	ENST00000262367	NM_004380.2	2361	tCC/tTT	31/31	1	2	FACETS	0.865	0.826	0.905	0.865	0.826	0.905	CLONAL	1	TRUE	1	0.574703480327514	2		1379	2039	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646654	23646654	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	256	658	0	ENST00000261584.4:c.1213C>T	p.Pro405Ser	p.P405S	ENST00000261584	NM_024675.3	405	Cct/Tct	4/13	1	2	FACETS	0.925	0.867	0.985	0.925	0.867	0.985	CLONAL	1	TRUE	1	0.574703480327514	2		658	963	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644985	67644985	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	281	710	0	ENST00000264010.4:c.250C>T	p.Pro84Ser	p.P84S	ENST00000264010	NM_006565.3	84	Cca/Tca	3/12	1	2	FACETS	0.977	0.919	1	0.977	0.919	1	CLONAL	1	TRUE	1	0.574703480327514	2		710	1001	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992910	72992910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147445846	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	390	953	0	ENST00000268489.5:c.1135C>T	p.Leu379Phe	p.L379F	ENST00000268489	NM_006885.3	379	Ctc/Ttc	2/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.574703480327514	2		953	1332	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676264	29676264	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	146	532	1	ENST00000356175.3:c.7253T>A	p.Leu2418Ter	p.L2418*	ENST00000356175	NM_000267.3	2418	tTa/tAa	48/57	1	2	FACETS	0.893	0.819	0.97	0.893	0.819	0.97	CLONAL	1	TRUE	1	0.574703480327514	2		533	569	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218426	36218426	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746495710	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	351	874	4	ENST00000222270.7:c.4205G>A	p.Arg1402Gln	p.R1402Q	ENST00000222270	NM_014727.1	1402	cGa/cAa	16/37	0.152801057310478	1	FACETS	0.778	0.737	0.819	0.778	0.737	0.819	INDETERMINATE	1	TRUE	0	0.574703480327514	1		878	1119	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224527	36224527	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	392	1221	1	ENST00000222270.7:c.6989C>T	p.Thr2330Ile	p.T2330I	ENST00000222270	NM_014727.1	2330	aCa/aTa	29/37	0.152801057310478	1	FACETS	0.608	0.576	0.64	0.608	0.576	0.64	INDETERMINATE	1	TRUE	0	0.574703480327514	1		1222	1599	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085863	16085863	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	245	673	1	ENST00000281043.3:c.1039C>A	p.Gln347Lys	p.Q347K	ENST00000281043	NM_005378.4	347	Cag/Aag	3/3	0.152801057310478	1	FACETS	0.767	0.719	0.816	0.767	0.719	0.816	INDETERMINATE	1	TRUE	0	0.574703480327514	1		674	792	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467462	25467463	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	336	957	1	ENST00000264709.3:c.1613_1614delinsTT	p.Thr538Ile	p.T538I	ENST00000264709	NM_175629.2	538	aCC/aTT	14/23	0.152801057310478	1	FACETS	0.688	0.65	0.726	0.688	0.65	0.726	INDETERMINATE	1	TRUE	0	0.574703480327514	1		958	1212	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497836	25497836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	197	827	0	ENST00000264709.3:c.613G>A	p.Glu205Lys	p.E205K	ENST00000264709	NM_175629.2	205	Gag/Aag	6/23	0.152801057310478	1	FACETS	0.499	0.461	0.537	0.499	0.461	0.537	INDETERMINATE	1	TRUE	0	0.574703480327514	1		827	980	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917787	29917787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	256	893	0	ENST00000389048.3:c.881C>T	p.Pro294Leu	p.P294L	ENST00000389048	NM_004304.4	294	cCc/cTc	3/29	0.152801057310478	1	FACETS	0.542	0.507	0.578	0.542	0.507	0.578	INDETERMINATE	1	TRUE	0	0.574703480327514	1		893	1172	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718720	190718720	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	160	733	1	ENST00000441310.2:c.878C>T	p.Pro293Leu	p.P293L	ENST00000441310	NM_000534.4	293	cCt/cTt	8/13	0.152801057310478	1	FACETS	0.479	0.44	0.521	0.479	0.44	0.521	INDETERMINATE	1	TRUE	0	0.574703480327514	1		734	828	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248504	212248504	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	332	614	0	ENST00000342788.4:c.3763C>A	p.His1255Asn	p.H1255N	ENST00000342788	NM_005235.2	1255	Cac/Aac	28/28	0.152801057310478	1	FACETS	0.888	0.842	0.935	0.888	0.842	0.935	INDETERMINATE	1	TRUE	0	0.574703480327514	1		614	927	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293205	212293205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747975697	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	172	448	0	ENST00000342788.4:c.2647C>T	p.Pro883Ser	p.P883S	ENST00000342788	NM_005235.2	883	Cca/Tca	22/28	0.152801057310478	1	FACETS	0.744	0.689	0.802	0.744	0.689	0.802	INDETERMINATE	1	TRUE	0	0.574703480327514	1		448	573	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561201	9561201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	278	644	0	ENST00000353224.5:c.581G>A	p.Arg194Lys	p.R194K	ENST00000353224	NM_177990.2	194	aGa/aAa	4/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.574703480327514	2		644	899	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42851187	42851187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	184	656	0	ENST00000398585.3:c.706G>A	p.Gly236Arg	p.G236R	ENST00000398585	NM_001135099.1	236	Gga/Aga	7/14	0.152801057310478	1	FACETS	0.484	0.447	0.523	0.484	0.447	0.523	INDETERMINATE	1	TRUE	0	0.574703480327514	1		656	942	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545057	41545057	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	616	754	1	ENST00000263253.7:c.2257C>T	p.Pro753Ser	p.P753S	ENST00000263253	NM_001429.3	753	Cct/Tct	13/31	0.468711690207344	4	FACETS	0.882	0.851	0.912	0.882	0.851	0.912	CLONAL	3	TRUE	1	0.574703480327514	4		755	1276	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637740	52637740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	220	580	0	ENST00000394830.3:c.2576C>T	p.Ser859Leu	p.S859L	ENST00000394830	NM_018313.4	859	tCa/tTa	18/30	1	2	FACETS	0.938	0.875	1	0.938	0.875	1	CLONAL	1	TRUE	1	0.574703480327514	2		580	816	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920326	134920326	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	225	539	0	ENST00000398015.3:c.2141G>A	p.Gly714Glu	p.G714E	ENST00000398015	NM_004441.4	714	gGg/gAg	12/16	1	2	FACETS	0.962	0.898	1	0.962	0.898	1	CLONAL	1	TRUE	1	0.574703480327514	2		539	814	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582157	189582157	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	275	688	0	ENST00000264731.3:c.716A>T	p.Glu239Val	p.E239V	ENST00000264731	NM_003722.4	239	gAg/gTg	5/14	1	2	FACETS	0.991	0.931	1	0.991	0.931	1	CLONAL	1	TRUE	1	0.574703480327514	2		688	966	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526934	31526934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	385	964	0	ENST00000344624.3:c.106C>T	p.Pro36Ser	p.P36S	ENST00000344624		36	Ccc/Tcc	2/33	1	2	FACETS	0.952	0.903	1	0.952	0.903	1	CLONAL	1	TRUE	1	0.574703480327514	2		964	1408	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80057385	80057385	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	243	535	0	ENST00000265081.6:c.1784A>G	p.Asp595Gly	p.D595G	ENST00000265081	NM_002439.4	595	gAt/gGt	13/24	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.574703480327514	2		535	822	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672362	30672364	+	frameshift_variant	Frame_Shift_Del	DEL	GCG	GCG	CA	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1154	382	836	2	ENST00000376406.3:c.4596_4598delinsTG	p.Ala1533GlufsTer42	p.A1533Efs*42	ENST00000376406	NM_014641.2	1532	ccCGCa/ccTGa	10/15	0.574703480327514	3	FACETS	1	0.987	1	0.557	0.528	0.587	CLONAL	1	TRUE	1	0.574703480327514	3		838	1536	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188196	32188196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	299	796	0	ENST00000375023.3:c.1145C>T	p.Pro382Leu	p.P382L	ENST00000375023	NM_004557.3	382	cCa/cTa	6/30	0.574703480327514	3	FACETS	0.963	0.905	1	0.482	0.452	0.511	CLONAL	1	TRUE	1	0.574703480327514	3		796	1391	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242451	55242451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	203	648	0	ENST00000275493.2:c.2221C>T	p.Pro741Ser	p.P741S	ENST00000275493	NM_005228.3	741	Ccc/Tcc	19/28	0.152801057310478	1	FACETS	0.539	0.5	0.58	0.539	0.5	0.58	INDETERMINATE	1	TRUE	0	0.574703480327514	1		648	934	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509537	106509537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774366285	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	330	778	1	ENST00000359195.3:c.1531G>A	p.Glu511Lys	p.E511K	ENST00000359195	NM_002649.2	511	Gag/Aag	2/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.574703480327514	2		779	1048	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020471	69020471	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	332	901	0	ENST00000288368.4:c.2843C>T	p.Pro948Leu	p.P948L	ENST00000288368	NM_024870.2	948	cCc/cTc	24/40	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.574703480327514	2		901	1137	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058471	69058471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	169	611	0	ENST00000288368.4:c.4115G>A	p.Gly1372Glu	p.G1372E	ENST00000288368	NM_024870.2	1372	gGa/gAa	34/40	1	2	FACETS	0.887	0.818	0.958	0.887	0.818	0.958	CLONAL	1	TRUE	1	0.574703480327514	2		611	663	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058549	69058549	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	236	939	0	ENST00000288368.4:c.4193G>A	p.Gly1398Glu	p.G1398E	ENST00000288368	NM_024870.2	1398	gGa/gAa	34/40	1	2	FACETS	0.959	0.897	1	0.959	0.897	1	CLONAL	1	TRUE	1	0.574703480327514	2		939	856	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340396	8340397	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	292	683	1	ENST00000356435.5:c.5199_5200delinsAA	p.Trp1733_Glu1734delinsTer	p.W1733_E1734delins*	ENST00000356435		1733	tgGGaa/tgAAaa	31/35	0.574703480327514	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.574703480327514	1		684	693	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404555	8404555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	144	373	0	ENST00000356435.5:c.4192C>T	p.Leu1398Phe	p.L1398F	ENST00000356435		1398	Ctc/Ttc	25/35	0.574703480327514	1	FACETS	0.989	0.914	1	0.989	0.914	1	CLONAL	1	TRUE	0	0.574703480327514	1		373	361	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482167	87482167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	380	890	0	ENST00000277120.3:c.1454C>T	p.Ser485Phe	p.S485F	ENST00000277120		485	tCc/tTc	14/19	0.574703480327514	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.574703480327514	1		890	938	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340396	8340396	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	292	671	1	ENST00000356435.5:c.5200G>A	p.Glu1734Lys	p.E1734K	ENST00000356435		1734	Gaa/Aaa	31/35	0.574703480327514	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.574703480327514	1		672	693	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16235914	16235914	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	415	752	0	ENST00000375759.3:c.980A>G	p.Glu327Gly	p.E327G	ENST00000375759	NM_015001.2	327	gAa/gGa	4/15	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.574703480327514	2		752	1102	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957447	175957447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	170	623	1	ENST00000367669.3:c.1949C>T	p.Ser650Phe	p.S650F	ENST00000367669	NM_022457.5	650	tCc/tTc	17/20	0.574703480327514	3	FACETS	0.738	0.678	0.801	0.369	0.339	0.401	SUBCLONAL	1	TRUE	1	0.574703480327514	3		624	1032	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149241	119149242	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	272	741	0	ENST00000264033.4:c.1249_1250delinsTT	p.Pro417Phe	p.P417F	ENST00000264033	NM_005188.3	417	CCt/TTt	9/16	0.546762168145463	1	FACETS	0.971	0.916	1	0.971	0.916	1	CLONAL	1	TRUE	0	0.574703480327514	1		741	695	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476254	88476254	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	316	807	1	ENST00000360948.2:c.1878T>A	p.Asn626Lys	p.N626K	ENST00000360948	NM_001012338.2	626	aaT/aaA	15/19	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.574703480327514	2		808	1053	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129029	30129030	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	360	881	3	ENST00000263025.4:c.736_737delinsTT	p.Pro246Phe	p.P246F	ENST00000263025	NM_002746.2	246	CCt/TTt	5/9	1	2	FACETS	0.962	0.912	1	0.962	0.912	1	CLONAL	1	TRUE	1	0.574703480327514	2		884	1302	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615802	1615802	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113960238	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	323	736	1	ENST00000344749.5:c.1469C>T	p.Ala490Val	p.A490V	ENST00000344749	NM_001136139.2	490	gCc/gTc	17/19	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.574703480327514	2		737	1110	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257883	19257883	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746375406	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	547	1141	0	ENST00000162023.5:c.503C>T	p.Ser168Phe	p.S168F	ENST00000162023		168	tCt/tTt	9/13	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.574703480327514	2		1141	1663	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793406	242793406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	264	969	1	ENST00000334409.5:c.671G>A	p.Gly224Glu	p.G224E	ENST00000334409	NM_005018.2	224	gGg/gAg	5/5	0.152801057310478	1	FACETS	0.497	0.465	0.53	0.497	0.465	0.53	INDETERMINATE	1	TRUE	0	0.574703480327514	1		970	1317	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458560	12458560	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	361	955	1	ENST00000287820.6:c.1177G>A	p.Glu393Lys	p.E393K	ENST00000287820	NM_015869.4	393	Gag/Aag	6/7	1	2	FACETS	0.924	0.875	0.974	0.924	0.875	0.974	CLONAL	1	TRUE	1	0.574703480327514	2		956	1360	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467462	66467462	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	139	437	0	ENST00000273854.3:c.807T>A	p.Asp269Glu	p.D269E	ENST00000273854	NM_004439.5	269	gaT/gaA	3/18	1	2	FACETS	0.855	0.781	0.931	0.855	0.781	0.931	CLONAL	1	TRUE	1	0.574703480327514	2		437	566	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196512	106196512	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866252212	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	176	567	0	ENST00000380013.4:c.4845G>A	p.Met1615Ile	p.M1615I	ENST00000380013	NM_001127208.2	1615	atG/atA	11/11	1	2	FACETS	0.777	0.717	0.84	0.777	0.717	0.84	SUBCLONAL	1	TRUE	1	0.574703480327514	2		567	788	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509527	149509527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	243	660	0	ENST00000261799.4:c.1372C>T	p.Pro458Ser	p.P458S	ENST00000261799	NM_002609.3	458	Cca/Tca	10/23	1	2	FACETS	0.966	0.905	1	0.966	0.905	1	CLONAL	1	TRUE	1	0.574703480327514	2		660	875	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055937	180055937	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766452541	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	403	1048	2	ENST00000261937.6:c.1048G>A	p.Glu350Lys	p.E350K	ENST00000261937	NM_182925.4	350	Gag/Aag	8/30	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.574703480327514	2		1050	1320	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401627	401627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	269	661	0	ENST00000380956.4:c.949C>T	p.Leu317Phe	p.L317F	ENST00000380956	NM_001195286.1	317	Ctc/Ttc	7/9	0.574703480327514	3	FACETS	1	0.974	1	0.536	0.503	0.571	CLONAL	1	TRUE	1	0.574703480327514	3		661	1124	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26021057	26021057	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	239	662	0	ENST00000357647.3:c.340C>T	p.His114Tyr	p.H114Y	ENST00000357647	NM_003529.2	114	Cac/Tac	1/1	0.574703480327514	3	FACETS	0.875	0.816	0.937	0.438	0.408	0.469	CLONAL	1	TRUE	1	0.574703480327514	3		662	1223	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995622	68995622	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	194	672	2	ENST00000288368.4:c.2026G>A	p.Glu676Lys	p.E676K	ENST00000288368	NM_024870.2	676	Gag/Aag	18/40	1	2	FACETS	0.967	0.898	1	0.967	0.898	1	CLONAL	1	TRUE	1	0.574703480327514	2		674	698	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518073	8518073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1480778931	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	277	642	1	ENST00000356435.5:c.1318G>A	p.Glu440Lys	p.E440K	ENST00000356435		440	Gaa/Aaa	10/35	0.574703480327514	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.574703480327514	1		643	602	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760817	133760817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	377	851	0	ENST00000318560.5:c.3140C>T	p.Ser1047Phe	p.S1047F	ENST00000318560	NM_005157.4	1047	tCc/tTc	11/11	0.574703480327514	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.574703480327514	1		851	874	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0021835-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	67	550	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.227464179745181	4	FACETS	0.771	0.672	0.878	0.771	0.672	0.878	SUBCLONAL	2	TRUE	2	0.227464179745181	4		552	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0021835-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	187	935	2	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.223369523162685	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.227464179745181	2		937	695	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0021835-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	86	721	1	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	0.205558896838745	3	FACETS	0.888	0.789	0.994	0.888	0.789	0.994	CLONAL	2	TRUE	1	0.227464179745181	3		722	474	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443857	49443857	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021835-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	205	1169	0	ENST00000301067.7:c.3514T>C	p.Cys1172Arg	p.C1172R	ENST00000301067	NM_003482.3	1172	Tgc/Cgc	11/54	0.205558896838745	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.227464179745181	3		1169	877	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143001	30143001	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021835-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	218	1202	0	ENST00000389048.3:c.525T>G	p.Ser175Arg	p.S175R	ENST00000389048	NM_004304.4	175	agT/agG	1/29	0.216194314530669	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.227464179745181	4		1202	1005	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644594	3644594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777279668	NA	P-0021835-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	66	963	1	ENST00000294008.3:c.2020C>T	p.Leu674Phe	p.L674F	ENST00000294008	NM_032444.2	674	Ctc/Ttc	10/15	0.227464179745181	4	FACETS	0.895	0.775	1	0.447	0.387	0.513	CLONAL	1	TRUE	2	0.227464179745181	4		964	796	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0021878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	76	693	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.742332853604738	4	FACETS	1	0.964	1	1	0.964	1	CLONAL	4	TRUE	0	0.742332853604738	4		693	87	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220371	1220371	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0021878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	426	600	1	ENST00000326873.7:c.465-1G>T		p.X155_splice	ENST00000326873	NM_000455.4	155			0.6121565225027	3	FACETS	0.864	0.836	0.891	0.864	0.836	0.891	CLONAL	3	TRUE	0	0.742332853604738	3		601	607	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610499	10610500	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0021878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	477	734	0	ENST00000171111.5:c.210dup	p.Arg71AlafsTer8	p.R71Afs*8	ENST00000171111	NM_203500.1	70	-/G	2/6	0.6121565225027	3	FACETS	1	0.995	1	0.771	0.745	0.797	CLONAL	2	TRUE	0	0.742332853604738	3		734	762	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129631	11129631	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0021878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	411	588	0	ENST00000358026.2:c.2439-2A>G		p.X813_splice	ENST00000358026	NM_001128849.1	813			0.6121565225027	3	FACETS	0.842	0.814	0.87	0.842	0.814	0.87	CLONAL	3	TRUE	0	0.742332853604738	3		588	601	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541297	187541297	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	99	377	0	ENST00000441802.2:c.6443A>G	p.Lys2148Arg	p.K2148R	ENST00000441802	NM_005245.3	2148	aAa/aGa	10/27	0.685699669190341	2	FACETS	0.959	0.896	1	0.959	0.896	1	CLONAL	2	TRUE	0	0.742332853604738	2		377	139	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413042	63413042	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0021878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	458	439	0	ENST00000330258.3:c.125C>G	p.Ser42Ter	p.S42*	ENST00000330258	NM_152424.3	42	tCa/tGa	2/2	0.742332853604738	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.742332853604738	2		439	555	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229652	5229652	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	10	87	0	ENST00000357368.4:c.2199C>A	p.Asn733Lys	p.N733K	ENST00000357368	NM_002850.3	733	aaC/aaA	15/38	0.6121565225027	3	FACETS	0.298	0.203	0.416	0.099	0.067	0.139	SUBCLONAL	1	TRUE	0	0.742332853604738	3		87	124	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0021890-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	244	804	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.660474791573861	1	FACETS	0.839	0.791	0.888	0.839	0.791	0.888	CLONAL	1	TRUE	0	0.675508150943872	1		804	570	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58701089	58701089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021890-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	557	703	0	ENST00000305921.3:c.680G>A	p.Arg227Gln	p.R227Q	ENST00000305921	NM_003620.3	227	cGa/cAa	2/6	NA	2	FACETS	0.911	0.882	0.94			1	INDETERMINATE	2	TRUE	NA	0.675508150943872	2		703	905	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11293499	11293499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021890-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	125	678	0	ENST00000361445.4:c.2377G>A	p.Gly793Ser	p.G793S	ENST00000361445	NM_004958.3	793	Ggt/Agt	15/58	1	2	FACETS	0.48	0.434	0.528	0.48	0.434	0.528	SUBCLONAL	1	TRUE	1	0.675508150943872	2		678	771	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258093	123258093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867786977	NA	P-0021890-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	215	653	0	ENST00000358487.5:c.1588G>A	p.Asp530Asn	p.D530N	ENST00000358487	NM_000141.4	530	Gat/Aat	12/18	1	2	FACETS	0.913	0.853	0.975	0.913	0.853	0.975	CLONAL	1	TRUE	1	0.675508150943872	2		653	697	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109807	115109807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021890-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	149	770	2	ENST00000257566.3:c.2071G>A	p.Glu691Lys	p.E691K	ENST00000257566	NM_016569.3	691	Gaa/Aaa	8/8	1	2	FACETS	0.374	0.341	0.41	0.374	0.341	0.41	SUBCLONAL	1	TRUE	1	0.675508150943872	2		772	1178	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198079	185198079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021890-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	56	468	0	ENST00000265026.3:c.2561C>T	p.Ser854Phe	p.S854F	ENST00000265026	NM_004721.4	854	tCt/tTt	13/14	1	2	FACETS	0.236	0.201	0.273	0.236	0.201	0.273	SUBCLONAL	1	TRUE	1	0.675508150943872	2		468	704	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138575	55138575	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021890-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	243	625	0	ENST00000257290.5:c.1252C>G	p.Leu418Val	p.L418V	ENST00000257290	NM_006206.4	418	Ctg/Gtg	9/23	0.675508150943872	1	FACETS	0.869	0.82	0.919	0.869	0.82	0.919	CLONAL	1	TRUE	0	0.675508150943872	1		625	548	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0021902-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	341	862	1	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	0.8912446041547	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.8912446041547	1		863	406	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543573	148543574	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0021902-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	65	523	0	ENST00000320356.2:c.234_235del	p.Gly79AspfsTer2	p.G79Dfs*2	ENST00000320356	NM_004456.4	78	cgCGgg/cggg	3/20	NA	2	FACETS	0.226	0.196	0.26			1	INDETERMINATE	1	TRUE	NA	0.8912446041547	2		523	644	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411096	63411096	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021902-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	225	707	0	ENST00000330258.3:c.2071A>T	p.Ser691Cys	p.S691C	ENST00000330258	NM_152424.3	691	Agc/Tgc	2/2	1	2	FACETS	0.894	0.839	0.949	0.894	0.839	0.949	CLONAL	1	TRUE	1	0.8912446041547	2		707	565	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920147	76920147	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021902-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	377	791	2	ENST00000373344.5:c.3930C>A	p.Asn1310Lys	p.N1310K	ENST00000373344	NM_000489.3	1310	aaC/aaA	11/35	1	2	FACETS	0.893	0.851	0.936	0.893	0.851	0.936	CLONAL	1	TRUE	1	0.8912446041547	2		793	947	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0021969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	64	598	1	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	1	2	FACETS	0.383	0.331	0.441	0.383	0.331	0.441	SUBCLONAL	1	TRUE	1	0.34	2		599	982	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	122	745	1	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.182278439384738	2		746	1222	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0021971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1221	82	845	1	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	1	2	FACETS	0.691	0.606	0.781	0.691	0.606	0.781	SUBCLONAL	1	TRUE	1	0.182278439384738	2		846	1303	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278073	18278073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1294	170	867	5	ENST00000222254.8:c.1693C>T	p.Pro565Ser	p.P565S	ENST00000222254	NM_005027.3	565	Ccg/Tcg	13/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.182278439384738	2		872	1464	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245345	46245345	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	128	608	0	ENST00000334344.6:c.3439A>T	p.Asn1147Tyr	p.N1147Y	ENST00000334344	NM_152641.2	1147	Aac/Tac	15/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.182278439384738	2		608	1009	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873005	35873005	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0021971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	45	551	0	ENST00000216797.5:c.228-1G>A		p.X76_splice	ENST00000216797	NM_020529.2	76			1	2	FACETS	0.573	0.48	0.676	0.573	0.48	0.676	SUBCLONAL	1	TRUE	1	0.182278439384738	2		551	862	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251518	10251518	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1225	146	870	0	ENST00000340748.4:c.3414G>T	p.Lys1138Asn	p.K1138N	ENST00000340748		1138	aaG/aaT	31/40	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.182278439384738	2		870	1371	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591092	67591092	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	31	332	0	ENST00000274335.5:c.1685G>C	p.Arg562Pro	p.R562P	ENST00000274335		562	cGt/cCt	12/15	1	2	FACETS	0.737	0.596	0.897	0.737	0.596	0.897	SUBCLONAL	1	TRUE	1	0.198413595641166	2		332	424	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591140	67591145	+	inframe_deletion	In_Frame_Del	DEL	ACCAAT	ACCAAT	-	rs751582616	NA	P-0021974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	29	347	0	ENST00000274335.5:c.1735_1740del	p.Gln579_Tyr580del	p.Q579_Y580del	ENST00000274335		578	gACCAATac/gac	12/15	1	2	FACETS	0.67	0.538	0.822	0.67	0.538	0.822	SUBCLONAL	1	TRUE	1	0.198413595641166	2		347	436	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023071	27023074	+	frameshift_variant	Frame_Shift_Del	DEL	GGGC	GGGC	-	novel	NA	P-0021974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	11	131	0	ENST00000324856.7:c.177_180del	p.Glu59AspfsTer41	p.E59Dfs*41	ENST00000324856	NM_006015.4	59	gaGGGC/ga	1/20	1	2	FACETS	0.84	0.583	1	0.84	0.583	1	CLONAL	1	TRUE	1	0.198413595641166	2		131	132	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097784	27097785	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	T	novel	NA	P-0021974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	62	501	0	ENST00000324856.7:c.3373_3374delinsT	p.Lys1125CysfsTer36	p.K1125Cfs*36	ENST00000324856	NM_006015.4	1125	AAg/Tg	12/20	1	2	FACETS	0.94	0.811	1	0.94	0.811	1	CLONAL	1	TRUE	1	0.198413595641166	2		501	665	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672323	86672323	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554049422	NA	P-0021979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	188	446	0	ENST00000274376.6:c.2125C>T	p.Arg709Ter	p.R709*	ENST00000274376	NM_002890.2	709	Cga/Tga	16/25	0.354449965186173	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.354449965186173	2		446	499	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143984	11143984	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs267607070	NA	P-0021979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	126	561	0	ENST00000358026.2:c.3565C>T	p.Arg1189Ter	p.R1189*	ENST00000358026	NM_001128849.1	1189	Cga/Tga	26/36	0.354449965186173	2	FACETS	0.987	0.905	1	0.987	0.905	1	CLONAL	2	TRUE	0	0.354449965186173	2		561	360	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332702	65332702	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	79	527	0	ENST00000342505.4:c.837A>C	p.Lys279Asn	p.K279N	ENST00000342505	NM_002227.2	279	aaA/aaC	7/25	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.354449965186173	2		527	441	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14303192	14303192	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	66	577	1	ENST00000256196.4:c.483del	p.Met162Ter	p.M162*	ENST00000256196		161	agG/ag	5/6	1	2	FACETS	0.826	0.719	0.941	0.826	0.719	0.941	CLONAL	1	TRUE	1	0.354449965186173	2		578	451	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251156	99251156	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	87	649	0	ENST00000268035.6:c.460A>T	p.Thr154Ser	p.T154S	ENST00000268035	NM_000875.3	154	Act/Tct	2/21	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.354449965186173	2		649	427	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900453	3900453	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	185	782	0	ENST00000262367.5:c.643del	p.Ala215LeufsTer29	p.A215Lfs*29	ENST00000262367	NM_004380.2	215	Gct/ct	2/31	0.354449965186173	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.354449965186173	2		782	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577113	7577115	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0021979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	155	679	0	ENST00000269305.4:c.823_825del	p.Cys275del	p.C275del	ENST00000269305	NM_001126112.2	275	TGT/-	8/11	0.354449965186173	2	FACETS	0.976	0.902	1	0.976	0.902	1	CLONAL	2	TRUE	0	0.354449965186173	2		679	448	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976145	7976145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	147	700	2	ENST00000319144.4:c.2050C>T	p.Pro684Ser	p.P684S	ENST00000319144	NM_001139.2	684	Ccc/Tcc	15/15	0.354449965186173	2	FACETS	0.985	0.908	1	0.985	0.908	1	CLONAL	2	TRUE	0	0.354449965186173	2		702	421	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610394	10610394	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	181	850	1	ENST00000171111.5:c.316G>T	p.Val106Phe	p.V106F	ENST00000171111	NM_203500.1	106	Gtc/Ttc	2/6	0.354449965186173	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.354449965186173	2		851	473	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917000	50917000	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	45	532	0	ENST00000440232.2:c.2252T>C	p.Val751Ala	p.V751A	ENST00000440232	NM_002691.3	751	gTg/gCg	19/27	0.354449965186173	4	FACETS	0.86	0.724	1	0.215	0.181	0.253	CLONAL	1	TRUE	0	0.354449965186173	4		532	400	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274526	198274526	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	73	605	0	ENST00000335508.6:c.872A>G	p.Asn291Ser	p.N291S	ENST00000335508	NM_012433.2	291	aAc/aGc	7/25	0.354449965186173	3	FACETS	0.883	0.774	1	0.442	0.387	0.501	CLONAL	1	TRUE	1	0.354449965186173	3		605	549	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39709863	39709863	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	48	308	1	ENST00000361337.2:c.490A>G	p.Lys164Glu	p.K164E	ENST00000361337	NM_003286.2	164	Aaa/Gaa	7/21	NA	2	FACETS	0.96	0.817	1			1	INDETERMINATE	1	TRUE	NA	0.354449965186173	2		309	282	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164498	36164498	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	47	513	0	ENST00000300305.3:c.1377C>G	p.His459Gln	p.H459Q	ENST00000300305		459	caC/caG	8/8	0.224151437417313	3	FACETS	0.853	0.722	0.996	0.284	0.24	0.332	CLONAL	1	TRUE	0	0.354449965186173	3		513	366	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390975	89390975	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	149	542	2	ENST00000336596.2:c.1041G>T	p.Trp347Cys	p.W347C	ENST00000336596	NM_005233.5	347	tgG/tgT	5/17	0.254582245326864	5	FACETS	0.871	0.801	0.942	0.871	0.801	0.942	CLONAL	3	TRUE	2	0.354449965186173	5		544	493	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156640	55156640	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	640	612	4	ENST00000257290.5:c.3041C>T	p.Ala1014Val	p.A1014V	ENST00000257290	NM_006206.4	1014	gCt/gTt	22/23	0.354449965186173	9	FACETS	1	0.981	1	1	0.981	1	CLONAL	8	TRUE	1	0.354449965186173	9		616	999	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534382	187534382	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs756909611	NA	P-0021979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	70	631	0	ENST00000441802.2:c.9344T>A	p.Leu3115Gln	p.L3115Q	ENST00000441802	NM_005245.3	3115	cTa/cAa	13/27	1	2	FACETS	0.866	0.758	0.983	0.866	0.758	0.983	CLONAL	1	TRUE	1	0.354449965186173	2		631	456	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852101	128852101	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	112	829	1	ENST00000249373.3:c.2173T>G	p.Cys725Gly	p.C725G	ENST00000249373	NM_005631.4	725	Tgc/Ggc	12/12	0.354449965186173	3	FACETS	1	0.974	1	0.623	0.562	0.688	CLONAL	1	TRUE	1	0.354449965186173	3		830	597	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874413	151874413	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	145	475	0	ENST00000262189.6:c.8125G>T	p.Val2709Phe	p.V2709F	ENST00000262189	NM_170606.2	2709	Gtc/Ttc	38/59	0.354449965186173	3	FACETS	0.877	0.804	0.953	0.877	0.804	0.953	CLONAL	2	TRUE	1	0.354449965186173	3		475	549	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877175	151877176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTGCTGCTGGAGAA	novel	NA	P-0021979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	88	473	0	ENST00000262189.6:c.7172_7185dup	p.Gln2396PhefsTer61	p.Q2396Ffs*61	ENST00000262189	NM_170606.2	2395	-/TTCTCCAGCAGCAA	37/59	0.354449965186173	3	FACETS	1	0.973	1	0.66	0.587	0.736	CLONAL	1	TRUE	1	0.354449965186173	3		473	443	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27192496	27192496	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	86	565	0	ENST00000380036.4:c.1499A>C	p.Glu500Ala	p.E500A	ENST00000380036	NM_000459.3	500	gAg/gCg	11/23	0.354449965186173	3	FACETS	1	0.9	1	0.339	0.3	0.38	CLONAL	1	TRUE	0	0.354449965186173	3		565	562	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413052	139413052	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	109	429	0	ENST00000277541.6:c.1090G>T	p.Gly364Cys	p.G364C	ENST00000277541	NM_017617.3	364	Ggc/Tgc	6/34	0.354449965186173	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.354449965186173	2		429	276	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123245021	123245021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	62	536	0	ENST00000358487.5:c.2083G>A	p.Glu695Lys	p.E695K	ENST00000358487	NM_000141.4	695	Gag/Aag	16/18	1	2	FACETS	0.761	0.66	0.87	0.761	0.66	0.87	SUBCLONAL	1	TRUE	1	0.413549148626568	2		536	394	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332478	70332478	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	97	622	0	ENST00000373644.4:c.384del	p.Pro129HisfsTer6	p.P129Hfs*6	ENST00000373644	NM_030625.2	128	gTt/gt	2/12	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.413549148626568	2		622	462	SUCCESS
EED	8726	MSKCC	GRCh37	11	85975146	85975238	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTCACAAGATGTTGAAAGTTCACAGTAAATAAAAAACATTCGCCTAATTTTTGTATGTTTATACTAGATCATGCTTTACGATTATGGAATAT	TTTCACAAGATGTTGAAAGTTCACAGTAAATAAAAAACATTCGCCTAATTTTTGTATGTTTATACTAGATCATGCTTTACGATTATGGAATAT	-	novel	NA	P-0021980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	13	74	0	ENST00000263360.6:c.635-68_659del		p.X212_splice	ENST00000263360	NM_003797.3	212		7/12	1	2	FACETS	0.898	0.675	1	1	0.912	1	CLONAL	2	TRUE	1	0.413549148626568	2		74	35	SUCCESS
AR	367	MSKCC	GRCh37	X	66943609	66943609	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	96	681	1	ENST00000374690.3:c.2689G>T	p.Ala897Ser	p.A897S	ENST00000374690	NM_000044.3	897	Gca/Tca	8/8	0.140081162495703	4	FACETS	1	0.957	1			1	INDETERMINATE	1	TRUE	NA	0.413549148626568	4		682	576	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021984-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	28	855	0	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	1	2	FACETS	0.552	0.44	0.679	0.552	0.44	0.679	SUBCLONAL	1	TRUE	1	0.24	2		855	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578386	7578386	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021984-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	50	828	0	ENST00000269305.4:c.544del	p.Cys182AlafsTer65	p.C182Afs*65	ENST00000269305	NM_001126112.2	182	Tgc/gc	5/11	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.24	2		828	361	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18956915	18956915	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021984-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	19	607	2	ENST00000262803.5:c.358A>T	p.Ile120Leu	p.I120L	ENST00000262803	NM_002911.3	120	Ata/Tta	2/24	0.11198444473922	0	FACETS	0.386	0.292	0.495			1	INDETERMINATE	1	TRUE	0	0.24	0		609	312	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279130	142279133	+	frameshift_variant	Frame_Shift_Del	DEL	GAAC	GAAC	-	novel	NA	P-0021984-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	18	629	0	ENST00000350721.4:c.1513_1516del	p.Val505IlefsTer7	p.V505Ifs*7	ENST00000350721	NM_001184.3	505	GTTCat/at	6/47	0.240099716052232	3	FACETS	0.669	0.504	0.864			1	SUBCLONAL	1	TRUE	NA	0.24	3		629	251	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101300	27101300	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	40	672	0	ENST00000324856.7:c.4582C>T	p.Arg1528Ter	p.R1528*	ENST00000324856	NM_006015.4	1528	Cga/Tga	18/20	1	2	FACETS	0.608	0.504	0.724	0.608	0.504	0.724	SUBCLONAL	1	TRUE	1	0.21	2		672	627	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127399	55127399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	34	701	0	ENST00000257290.5:c.187G>A	p.Glu63Lys	p.E63K	ENST00000257290	NM_006206.4	63	Gaa/Aaa	3/23	0.3	1	FACETS	0.44	0.359	0.533	0.44	0.359	0.533	SUBCLONAL	1	TRUE	0	0.21	1		701	658	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0021992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	213	652	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.413917673508781	3	FACETS	1	0.967	1	0.535	0.497	0.575	CLONAL	1	TRUE	1	0.476437514880958	3		652	1034	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0021992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	325	714	1	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	0.476437514880958	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.476437514880958	1		715	791	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099093	27099093	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	195	670	0	ENST00000324856.7:c.3509A>C	p.His1170Pro	p.H1170P	ENST00000324856	NM_006015.4	1170	cAc/cCc	13/20	1	2	FACETS	0.911	0.843	0.98	0.911	0.843	0.98	CLONAL	1	TRUE	1	0.476437514880958	2		670	899	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453148	140453148	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs397507483	NA	P-0021992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	112	496	0	ENST00000288602.6:c.1787G>T	p.Gly596Val	p.G596V	ENST00000288602	NM_004333.4	596	gGt/gTt	15/18	1	2	FACETS	0.756	0.681	0.834	0.756	0.681	0.834	SUBCLONAL	1	TRUE	1	0.476437514880958	2		496	622	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067050	143067050	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1188846860	NA	P-0021992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	134	614	0	ENST00000262992.4:c.1663A>C	p.Asn555His	p.N555H	ENST00000262992	NM_001101669.1	555	Aac/Cac	16/24	0.380068279906355	1	FACETS	0.743	0.677	0.811	0.743	0.677	0.811	SUBCLONAL	1	TRUE	0	0.476437514880958	1		614	577	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31435899	31435899	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	38	506	0	ENST00000344624.3:c.3015G>T	p.Gln1005His	p.Q1005H	ENST00000344624		1005	caG/caT	22/33	0.449639280419969	3	FACETS	0.266	0.219	0.319	0.133	0.109	0.16	SUBCLONAL	1	TRUE	1	0.476437514880958	3		506	742	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514290	69514290	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	353	729	2	ENST00000294312.3:c.391T>A	p.Tyr131Asn	p.Y131N	ENST00000294312	NM_005117.2	131	Tac/Aac	3/3	0.383817745474891	3	FACETS	0.9	0.855	0.947	0.9	0.855	0.947	CLONAL	2	TRUE	1	0.476437514880958	3		731	1019	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352490	118352490	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	159	583	0	ENST00000534358.1:c.3695G>T	p.Ser1232Ile	p.S1232I	ENST00000534358	NM_005933.3	1232	aGt/aTt	7/36	1	2	FACETS	0.913	0.839	0.99	0.913	0.839	0.99	CLONAL	1	TRUE	1	0.476437514880958	2		583	731	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944913	31944913	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	134	258	0	ENST00000340398.3:c.188G>C	p.Arg63Pro	p.R63P	ENST00000340398	NM_001013699.2	63	cGg/cCg	1/1	0.413917673508781	3	FACETS	1	0.981	1	0.639	0.583	0.697	CLONAL	1	TRUE	1	0.476437514880958	3		258	545	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281237	49281237	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	161	781	1	ENST00000282018.3:c.284C>A	p.Ala95Asp	p.A95D	ENST00000282018	NM_020377.2	95	gCt/gAt	1/1	0.297032993250265	1	FACETS	0.716	0.658	0.776	0.716	0.658	0.776	SUBCLONAL	1	TRUE	0	0.476437514880958	1		782	719	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560425	65560425	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0021992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	65	348	0	ENST00000358664.4:c.171+1G>T		p.X57_splice	ENST00000358664	NM_002382.4	57			0.292770138932601	2	FACETS	0.506	0.439	0.579	0.253	0.219	0.29	SUBCLONAL	1	TRUE	0	0.476437514880958	2		348	539	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943819	9943819	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0021992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	112	354	0	ENST00000330684.3:c.1123-1G>C		p.X375_splice	ENST00000330684	NM_001134407.1	375			1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.476437514880958	2		354	450	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991761	72991761	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	127	417	0	ENST00000268489.5:c.2284G>T	p.Gly762Trp	p.G762W	ENST00000268489	NM_006885.3	762	Ggg/Tgg	2/10	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.476437514880958	2		417	532	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33430338	33430338	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	220	634	0	ENST00000345365.6:c.673G>T	p.Ala225Ser	p.A225S	ENST00000345365	NM_002878.3	225	Gcc/Tcc	8/10	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.476437514880958	2		634	700	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804336	46804336	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	203	600	0	ENST00000290295.7:c.671G>T	p.Ser224Ile	p.S224I	ENST00000290295	NM_006361.5	224	aGc/aTc	2/2	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.476437514880958	2		600	744	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756628	756628	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	126	582	0	ENST00000314574.4:c.200G>T	p.Gly67Val	p.G67V	ENST00000314574	NM_005433.3	67	gGg/gTg	2/12	0.383817745474891	3	FACETS	0.845	0.766	0.929	0.423	0.383	0.465	CLONAL	1	TRUE	1	0.476437514880958	3		582	775	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955123	17955123	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	267	706	0	ENST00000458235.1:c.104C>G	p.Pro35Arg	p.P35R	ENST00000458235	NM_000215.3	35	cCc/cGc	2/24	0.476437514880958	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.476437514880958	1		706	693	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738269	190738270	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0021992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	152	398	0	ENST00000441310.2:c.2521_2522insA	p.Cys841Ter	p.C841*	ENST00000441310	NM_000534.4	841	tgt/tAgt	12/13	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.476437514880958	2		398	550	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660217	227660217	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	218	767	0	ENST00000305123.5:c.3238A>C	p.Asn1080His	p.N1080H	ENST00000305123	NM_005544.2	1080	Aac/Cac	1/2	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.476437514880958	2		767	905	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727174	40727175	+	missense_variant	Missense_Mutation	DNP	CG	CG	AC	novel	NA	P-0021992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	200	567	1	ENST00000373198.4:c.3789_3790delinsGT	p.Ala1264Ser	p.A1264S	ENST00000373198	NM_133170.3	1263	gcCGcc/gcGTcc	28/32	0.252583433200651	3	FACETS	1	0.981	1	0.585	0.543	0.629	INDETERMINATE	1	TRUE	1	0.476437514880958	3		568	888	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528582	89528582	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	23	399	0	ENST00000336596.2:c.2882C>A	p.Pro961Gln	p.P961Q	ENST00000336596	NM_005233.5	961	cCa/cAa	17/17	0.476437514880958	1	FACETS	0.179	0.139	0.225	0.179	0.139	0.225	SUBCLONAL	1	TRUE	0	0.476437514880958	1		399	411	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094963	143094963	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0021992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	46	437	2	ENST00000262992.4:c.1182-1G>T		p.X394_splice	ENST00000262992	NM_001101669.1	394			0.380068279906355	1	FACETS	0.333	0.28	0.391	0.333	0.28	0.391	SUBCLONAL	1	TRUE	0	0.476437514880958	1		439	442	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521269	187521269	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	175	663	1	ENST00000441802.2:c.11886G>T	p.Arg3962Ser	p.R3962S	ENST00000441802	NM_005245.3	3962	agG/agT	22/27	0.380068279906355	1	FACETS	0.755	0.697	0.815	0.755	0.697	0.815	SUBCLONAL	1	TRUE	0	0.476437514880958	1		664	741	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052955	180052955	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	222	802	0	ENST00000261937.6:c.1335del	p.Cys445Ter	p.C445*	ENST00000261937	NM_182925.4	445	tgC/tg	10/30	0.476437514880958	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.476437514880958	1		802	700	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962826	2962827	+	missense_variant	Missense_Mutation	DNP	CG	CG	GA	novel	NA	P-0021992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	213	639	2	ENST00000396946.4:c.2081_2082delinsTC	p.Ser694Phe	p.S694F	ENST00000396946	NM_032415.4	694	tCG/tTC	16/25	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.476437514880958	2		641	817	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521418	8521418	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	273	736	0	ENST00000356435.5:c.820G>C	p.Glu274Gln	p.E274Q	ENST00000356435		274	Gaa/Caa	9/35	0.476437514880958	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.476437514880958	1		736	766	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020693	37020693	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	216	549	0	ENST00000358127.4:c.152C>A	p.Pro51His	p.P51H	ENST00000358127	NM_001280556.1	51	cCc/cAc	2/10	0.232646895036876	1	FACETS	0.955	0.892	1	0.955	0.892	1	INDETERMINATE	1	TRUE	0	0.476437514880958	1		549	723	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938389	76938389	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	31	383	2	ENST00000373344.5:c.2359G>T	p.Gly787Cys	p.G787C	ENST00000373344	NM_000489.3	787	Ggc/Tgc	9/35	1	1	FACETS	0.194	0.157	0.237	0.194	0.157	0.237	SUBCLONAL	1	TRUE	0	0.476437514880958	1		385	510	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579378	7579378	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	506	681	0	ENST00000269305.4:c.309C>A	p.Tyr103Ter	p.Y103*	ENST00000269305	NM_001126112.2	103	taC/taA	4/11	0.603581743654459	2	FACETS	0.976	0.943	1	0.976	0.943	1	CLONAL	2	TRUE	0	0.603581743654459	2		681	859	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999581	100999581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	285	838	2	ENST00000325455.5:c.221C>T	p.Thr74Met	p.T74M	ENST00000325455	NM_001202474.3	74	aCg/aTg	1/8	0.603581743654459	3	FACETS	0.97	0.91	1	0.485	0.455	0.515	CLONAL	1	TRUE	1	0.603581743654459	3		840	1268	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186756	108186756	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs774993357	NA	P-0021997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	235	456	0	ENST00000278616.4:c.6114C>A	p.His2038Gln	p.H2038Q	ENST00000278616	NM_000051.3	2038	caC/caA	42/63	0.603581743654459	3	FACETS	0.913	0.86	0.967	0.913	0.86	0.967	CLONAL	2	TRUE	1	0.603581743654459	3		456	555	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870984	12870984	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	272	370	1	ENST00000228872.4:c.211G>T	p.Glu71Ter	p.E71*	ENST00000228872	NM_004064.3	71	Gag/Tag	1/3	0.603581743654459	3	FACETS	0.897	0.848	0.947	0.897	0.848	0.947	CLONAL	2	TRUE	1	0.603581743654459	3		371	654	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455533	189455533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144315591	NA	P-0021997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	115	510	0	ENST00000264731.3:c.67G>A	p.Val23Ile	p.V23I	ENST00000264731	NM_003722.4	23	Gta/Ata	2/14	0.603581743654459	3	FACETS	0.986	0.893	1	0.493	0.446	0.542	CLONAL	1	TRUE	1	0.603581743654459	3		510	503	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0021998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	82	636	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.818	0.724	0.918	0.818	0.724	0.918	CLONAL	1	TRUE	1	0.419406524975583	2		638	478	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0021998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	93	550	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.419406524975583	2		552	428	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777894	NA	P-0021998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	125	805	0	ENST00000361445.4:c.6644C>T	p.Ser2215Phe	p.S2215F	ENST00000361445	NM_004958.3	2215	tCt/tTt	47/58	1	2	FACETS	0.939	0.852	1	0.939	0.852	1	CLONAL	1	TRUE	1	0.419406524975583	2		805	635	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0021998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	186	548	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.419406524975583	2	FACETS	0.882	0.821	0.943	0.882	0.821	0.943	CLONAL	2	TRUE	0	0.419406524975583	2		548	503	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	62	525	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	0.83	0.721	0.948	0.83	0.721	0.948	CLONAL	1	TRUE	1	0.419406524975583	2		525	356	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	95	796	2	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	1	2	FACETS	0.926	0.828	1	0.926	0.828	1	CLONAL	1	TRUE	1	0.419406524975583	2		798	489	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044850	47044850	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	336	419	1	ENST00000377604.3:c.2176C>T	p.Arg726Ter	p.R726*	ENST00000377604	NM_001204468.1	726	Cga/Tga	20/24	0.318279299829369	2	FACETS	1	0.978	1			1	CLONAL	3	TRUE	NA	0.419406524975583	2		420	520	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910617	29910617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199474377	NA	P-0021998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	97	842	0	ENST00000376809.5:c.157G>A	p.Asp53Asn	p.D53N	ENST00000376809	NM_002116.7	53	Gac/Aac	2/8	1	2	FACETS	0.693	0.619	0.773	0.693	0.619	0.773	SUBCLONAL	1	TRUE	1	0.419406524975583	2		842	667	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347680	118347680	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	102	545	0	ENST00000534358.1:c.3317C>G	p.Ser1106Cys	p.S1106C	ENST00000534358	NM_005933.3	1106	tCt/tGt	4/36	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.419406524975583	2		545	468	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991387	72991387	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs781071051	NA	P-0021998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	140	811	0	ENST00000268489.5:c.2658C>G	p.Phe886Leu	p.F886L	ENST00000268489	NM_006885.3	886	ttC/ttG	2/10	1	2	FACETS	0.858	0.782	0.938	0.858	0.782	0.938	CLONAL	1	TRUE	1	0.419406524975583	2		811	778	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934576	NA	P-0022003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	336	720	1	ENST00000269305.4:c.818G>C	p.Arg273Pro	p.R273P	ENST00000269305	NM_001126112.2	273	cGt/cCt	8/11	0.586540421600877	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.582960547813066	2		721	549	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056437	26056437	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	180	313	0	ENST00000343677.2:c.220G>C	p.Glu74Gln	p.E74Q	ENST00000343677	NM_005319.3	74	Gag/Cag	1/1	0.582960547813066	7	FACETS	1	0.983	1			1	CLONAL	2	TRUE	NA	0.582960547813066	7		313	628	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	472205	472205	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2753	169	663	0	ENST00000399788.2:c.596C>G	p.Thr199Ser	p.T199S	ENST00000399788	NM_001042603.1	199	aCt/aGt	5/28	0.582960547813066	16	FACETS	1	0.921	1	0.092	0.083	0.1	CLONAL	1	TRUE	5	0.582960547813066	16		663	2922	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940930	49940930	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	103	658	2	ENST00000296474.3:c.113G>A	p.Arg38His	p.R38H	ENST00000296474	NM_002447.2	38	cGc/cAc	1/20	0.586540421600877	2	FACETS	0.976	0.882	1	0.488	0.441	0.537	CLONAL	1	TRUE	0	0.582960547813066	2		660	362	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119624607	119624607	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	262	583	0	ENST00000316626.5:c.808A>G	p.Ile270Val	p.I270V	ENST00000316626		270	Atc/Gtc	7/12	0.586540421600877	4	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	2	0.582960547813066	4		583	707	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911534	134911534	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	132	663	0	ENST00000398015.3:c.1999A>T	p.Ser667Cys	p.S667C	ENST00000398015	NM_004441.4	667	Agt/Tgt	11/16	0.586540421600877	4	FACETS	0.895	0.813	0.981	0.447	0.406	0.491	CLONAL	1	TRUE	2	0.582960547813066	4		663	801	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250727	26250727	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	134	510	0	ENST00000446824.2:c.107T>G	p.Val36Gly	p.V36G	ENST00000446824	NM_021018.2	36	gTg/gGg	1/1	0.582960547813066	7	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.582960547813066	7		510	816	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971057	21971118	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCCCGGTGCAGCACCACCAGCGTGTCCAGGAAGCCCTCCCGGGCAGCGTCGTGCACGGGT	CGGCCCGGTGCAGCACCACCAGCGTGTCCAGGAAGCCCTCCCGGGCAGCGTCGTGCACGGGT	-	novel	NA	P-0022003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	84	435	0	ENST00000304494.5:c.240_301del	p.Pro81GlyfsTer18	p.P81Gfs*18	ENST00000304494	NM_000077.4	80	cgACCCGTGCACGACGCTGCCCGGGAGGGCTTCCTGGACACGCTGGTGGTGCTGCACCGGGCCGgg/cggg	2/3	0.572079980855507	1	FACETS	0.798	0.715	0.883	0.798	0.715	0.883	SUBCLONAL	1	TRUE	0	0.582960547813066	1		435	256	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249941	110249941	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167152871	NA	P-0022003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	101	494	0	ENST00000374672.4:c.734C>T	p.Pro245Leu	p.P245L	ENST00000374672	NM_004235.4	245	cCg/cTg	3/5	0.188699055740225	6	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.582960547813066	6		494	605	SUCCESS
AR	367	MSKCC	GRCh37	X	66941704	66941704	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	163	724	0	ENST00000374690.3:c.2348G>T	p.Ser783Ile	p.S783I	ENST00000374690	NM_000044.3	783	aGc/aTc	6/8	0.586540421600877	3	FACETS	0.975	0.896	1	0.325	0.298	0.352	CLONAL	1	TRUE	0	0.582960547813066	3		724	741	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0022004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	33	737	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.343	0.278	0.416	0.343	0.278	0.416	SUBCLONAL	1	TRUE	1	0.29	2		739	664	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374401	81374401	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	43	589	0	ENST00000222390.5:c.661G>A	p.Gly221Ser	p.G221S	ENST00000222390	NM_000601.4	221	Ggt/Agt	6/18	1	2	FACETS	0.498	0.416	0.589	0.498	0.416	0.589	SUBCLONAL	1	TRUE	1	0.29	2		589	596	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577575	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587782289	NA	P-0022006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	112	582	0	ENST00000269305.4:c.706T>G	p.Tyr236Asp	p.Y236D	ENST00000269305	NM_001126112.2	236	Tac/Gac	7/11	0.505444756862046	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.505444756862046	1		582	251	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279165	142279165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	27	470	0	ENST00000350721.4:c.1481C>T	p.Ala494Val	p.A494V	ENST00000350721	NM_001184.3	494	gCt/gTt	6/47	0.109110311146022	4	FACETS	0.298	0.236	0.369	0.149	0.118	0.185	INDETERMINATE	1	TRUE	2	0.505444756862046	4		470	540	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0022009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	133	693	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.249826749926857	2	FACETS	1	0.986	1	0.746	0.681	0.814	CLONAL	1	TRUE	0	0.318875071488367	2		693	559	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0022009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	70	382	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.318875071488367	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.318875071488367	1		382	293	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0022009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	24	308	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.161177645558511	1	FACETS	0.36	0.282	0.451	0.36	0.282	0.451	INDETERMINATE	1	TRUE	0	0.318875071488367	1		308	351	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099338	193099338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	70	620	0	ENST00000367435.3:c.272G>A	p.Arg91Gln	p.R91Q	ENST00000367435	NM_024529.4	91	cGa/cAa	3/17	0.318875071488367	4	FACETS	0.922	0.804	1	0.307	0.268	0.35	CLONAL	1	TRUE	1	0.318875071488367	4		620	628	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576010	29576010	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	27	548	1	ENST00000356175.3:c.3983C>T	p.Pro1328Leu	p.P1328L	ENST00000356175	NM_000267.3	1328	cCa/cTa	30/57	0.166550287052945	2	FACETS	0.379	0.301	0.468	0.189	0.15	0.234	INDETERMINATE	1	TRUE	0	0.318875071488367	2		549	447	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028076	69028076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	76	844	1	ENST00000288368.4:c.3235G>A	p.Glu1079Lys	p.E1079K	ENST00000288368	NM_024870.2	1079	Gaa/Aaa	26/40	0.120098508730833	5	FACETS	1	0.942	1	0.281	0.247	0.319	INDETERMINATE	1	TRUE	1	0.318875071488367	5		845	626	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624625	93624625	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	57	533	0	ENST00000375746.1:c.716A>G	p.Gln239Arg	p.Q239R	ENST00000375746	NM_001174167.1	239	cAg/cGg	4/14	0.282984118901607	3	FACETS	1	0.942	1	0.59	0.509	0.678	CLONAL	1	TRUE	1	0.318875071488367	3		533	351	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	66	445	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.436633211444157	2		445	272	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690811	89690811	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	136	508	0	ENST00000371953.3:c.220del	p.Arg74AspfsTer25	p.R74Dfs*25	ENST00000371953	NM_000314.4	73	gAa/ga	4/9	0.436633211444157	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.436633211444157	1		508	422	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934254	48934254	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1131690904	NA	P-0022012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	49	697	0	ENST00000267163.4:c.709G>T	p.Glu237Ter	p.E237*	ENST00000267163	NM_000321.2	237	Gaa/Taa	7/27	0.436633211444157	1	FACETS	0.392	0.332	0.457	0.392	0.332	0.457	SUBCLONAL	1	TRUE	0	0.436633211444157	1		697	448	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134629	2134629	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs45517342	NA	P-0022012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	145	892	1	ENST00000219476.3:c.4406C>A	p.Ser1469Ter	p.S1469*	ENST00000219476	NM_000548.3	1469	tCa/tAa	34/42	0.436633211444157	1	FACETS	0.887	0.813	0.965	0.887	0.813	0.965	CLONAL	1	TRUE	0	0.436633211444157	1		893	585	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652774	212652774	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	27	542	0	ENST00000342788.4:c.532G>A	p.Val178Met	p.V178M	ENST00000342788	NM_005235.2	178	Gtg/Atg	4/28	1	2	FACETS	0.312	0.248	0.386	0.312	0.248	0.386	SUBCLONAL	1	TRUE	1	0.436633211444157	2		542	396	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825394	134825394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757739384	NA	P-0022012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	150	716	5	ENST00000398015.3:c.910C>T	p.Arg304Trp	p.R304W	ENST00000398015	NM_004441.4	304	Cgg/Tgg	4/16	1	2	FACETS	0.999	0.915	1	0.999	0.915	1	CLONAL	1	TRUE	1	0.436633211444157	2		721	688	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812162	212812162	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	137	531	1	ENST00000342788.4:c.414C>A	p.Asn138Lys	p.N138K	ENST00000342788	NM_005235.2	138	aaC/aaA	3/28	0.583520674389675	4	FACETS	0.925	0.853	0.998	0.925	0.853	0.998	CLONAL	2	TRUE	2	0.760614748175614	4		532	343	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0022015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	60	484	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.198130870623326	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.200421275662914	1		484	430	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413568	32413568	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	51	680	1	ENST00000332351.3:c.1382C>A	p.Ser461Tyr	p.S461Y	ENST00000332351	NM_024426.4	461	tCc/tAc	9/10	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.200421275662914	2		681	430	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740529	58740529	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs146477590	NA	P-0022015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	109	707	0	ENST00000305921.3:c.1434C>A	p.Cys478Ter	p.C478*	ENST00000305921	NM_003620.3	478	tgC/tgA	6/6	0.200421275662914	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.200421275662914	2		707	451	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136166	11136166	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	80	894	0	ENST00000358026.2:c.3150C>A	p.Tyr1050Ter	p.Y1050*	ENST00000358026	NM_001128849.1	1050	taC/taA	22/36	0.198130870623326	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.200421275662914	1		894	533	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334791	81334791	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	30	674	0	ENST00000222390.5:c.1925G>A	p.Cys642Tyr	p.C642Y	ENST00000222390	NM_000601.4	642	tGc/tAc	17/18	1	2	FACETS	0.725	0.584	0.885	0.725	0.584	0.885	SUBCLONAL	1	TRUE	1	0.200421275662914	2		674	413	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508239	106508239	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	30	425	0	ENST00000359195.3:c.233C>A	p.Ala78Glu	p.A78E	ENST00000359195	NM_002649.2	78	gCg/gAg	2/11	1	2	FACETS	0.985	0.795	1	0.985	0.795	1	CLONAL	1	TRUE	1	0.200421275662914	2		425	304	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738271	145738271	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	57	1121	0	ENST00000428558.2:c.2714C>G	p.Pro905Arg	p.P905R	ENST00000428558	NM_004260.3	905	cCa/cGa	16/22	0.200421275662914	3	FACETS	0.927	0.795	1	0.464	0.397	0.536	CLONAL	1	TRUE	1	0.200421275662914	3		1121	675	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0022016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	334	870	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.404054022784858	5	FACETS	0.973	0.946	0.999			1	INDETERMINATE	5	TRUE	NA	0.696737320872212	5		871	403	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676268	37676268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	843	875	0	ENST00000447079.4:c.3023G>A	p.Arg1008Gln	p.R1008Q	ENST00000447079	NM_015083.1	1008	cGg/cAg	11/14	0.696737320872212	11	FACETS	1	0.995	1			1	CLONAL	11	TRUE	NA	0.696737320872212	11		875	899	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524325	148524325	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	83	718	0	ENST00000320356.2:c.659C>G	p.Ser220Cys	p.S220C	ENST00000320356	NM_004456.4	220	tCt/tGt	7/20	0.438855751602507	5	FACETS	1	0.974	1	0.452	0.402	0.505	CLONAL	1	TRUE	2	0.696737320872212	5		718	359	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752848	128752848	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	35	509	2	ENST00000377970.2:c.1009G>A	p.Ala337Thr	p.A337T	ENST00000377970	NM_002467.4	337	Gcc/Acc	3/3	0.476757768744683	1	FACETS	0.201	0.165	0.241	0.201	0.165	0.241	SUBCLONAL	1	TRUE	0	0.696737320872212	1		511	326	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0022023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	57	569	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.911	0.781	1	0.911	0.781	1	CLONAL	1	TRUE	1	0.22	2		569	569	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0022023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	33	487	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	1	2	FACETS	0.802	0.654	0.969	0.802	0.654	0.969	CLONAL	1	TRUE	1	0.22	2		487	374	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591889	48591889	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	15	658	0	ENST00000342988.3:c.1052A>C	p.Asp351Ala	p.D351A	ENST00000342988	NM_005359.5	351	gAt/gCt	9/12	1	2	FACETS	0.297	0.216	0.395	0.297	0.216	0.395	SUBCLONAL	1	TRUE	1	0.22	2		658	459	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0022025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	494	693	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.494370578885812	3	FACETS	0.884	0.853	0.915	0.884	0.853	0.915	CLONAL	3	TRUE	0	0.543891465024176	3		693	871	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612740	228612740	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747322437	NA	P-0022025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	172	646	1	ENST00000366696.1:c.287C>T	p.Ala96Val	p.A96V	ENST00000366696	NM_003493.2	96	gCg/gTg	1/1	0.461359816790583	4	FACETS	0.996	0.916	1	0.498	0.458	0.54	CLONAL	1	TRUE	2	0.543891465024176	4		647	980	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578187	7578188	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CATA	novel	NA	P-0022025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	428	859	0	ENST00000269305.4:c.658_661dup	p.Glu221ValfsTer2	p.E221Vfs*2	ENST00000269305	NM_001126112.2	221	gag/gTATGag	6/11	0.533028230538341	2	FACETS	0.963	0.925	1	0.963	0.925	1	CLONAL	2	TRUE	0	0.543891465024176	2		859	817	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573941	41573941	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766166888	NA	P-0022025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	175	751	2	ENST00000263253.7:c.6226G>A	p.Ala2076Thr	p.A2076T	ENST00000263253	NM_001429.3	2076	Gcc/Acc	31/31	0.445121837532204	4	FACETS	0.952	0.876	1			1	CLONAL	1	TRUE	NA	0.543891465024176	4		753	1044	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	88	636	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.996	0.884	1	0.996	0.884	1	CLONAL	1	TRUE	1	0.300135687056277	2		638	589	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056420	180056420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372030421	NA	P-0022028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	69	564	0	ENST00000261937.6:c.824G>A	p.Arg275Gln	p.R275Q	ENST00000261937	NM_182925.4	275	cGg/cAg	7/30	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.300135687056277	2		564	437	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	43	445	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.87	0.733	1	0.87	0.733	1	CLONAL	1	TRUE	1	0.371580436478573	2		445	266	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556079	29556079	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886041347	NA	P-0022029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	49	292	0	ENST00000356175.3:c.2446C>T	p.Arg816Ter	p.R816*	ENST00000356175	NM_000267.3	816	Cga/Tga	21/57	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.371580436478573	2		292	260	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999484	100999484	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	141	852	0	ENST00000325455.5:c.318G>T	p.Lys106Asn	p.K106N	ENST00000325455	NM_001202474.3	106	aaG/aaT	1/8	1	2	FACETS	0.997	0.91	1	0.997	0.91	1	CLONAL	1	TRUE	1	0.371580436478573	2		852	761	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43766967	43766967	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0022029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	51	288	0	ENST00000382044.4:c.1086-2A>G		p.X362_splice	ENST00000382044	NM_001141980.1	362			1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.371580436478573	2		288	255	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654751	29654751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	97	507	0	ENST00000356175.3:c.5440C>T	p.Gln1814Ter	p.Q1814*	ENST00000356175	NM_000267.3	1814	Cag/Tag	37/57	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.371580436478573	2		507	496	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415705	152415705	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0022029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	76	507	0	ENST00000206249.3:c.1553+2T>C		p.X518_splice	ENST00000206249	NM_000125.3	518			1	2	FACETS	0.882	0.776	0.995	0.882	0.776	0.995	CLONAL	1	TRUE	1	0.371580436478573	2		507	464	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	154	445	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.874286667469906	2		445	294	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0022032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12906	1311	680	2	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.874286667469906	26	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.874286667469906	26		682	14217	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0022032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14090	553	653	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.874286667469906	26	FACETS	0.993	0.944	1			1	CLONAL	1	TRUE	NA	0.874286667469906	26		653	14643	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs149840192	NA	P-0022032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	15033	785	3	ENST00000275493.2:c.866C>A	p.Ala289Asp	p.A289D	ENST00000275493	NM_005228.3	289	gCc/gAc	7/28	0.874286667469906	26	FACETS	0.994	0.992	0.997			1	CLONAL	25	TRUE	NA	0.874286667469906	26		788	15898	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913428	NA	P-0022032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12928	1715	652	1	ENST00000275493.2:c.2156G>A	p.Gly719Asp	p.G719D	ENST00000275493	NM_005228.3	719	gGc/gAc	18/28	0.874286667469906	26	FACETS	1	0.988	1			1	CLONAL	3	TRUE	NA	0.874286667469906	26		653	14643	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0022041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	159	693	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.276652427817948	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	2	0.276652427817948	4		693	682	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0022041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	208	826	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.273876819698775	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.276652427817948	2		828	714	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0022041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	64	560	1	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.276652427817948	1	FACETS	0.97	0.843	1	0.97	0.843	1	CLONAL	1	TRUE	0	0.276652427817948	1		561	411	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508173	106508173	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1315748037	NA	P-0022041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	46	340	1	ENST00000359195.3:c.167C>T	p.Thr56Met	p.T56M	ENST00000359195	NM_002649.2	56	aCg/aTg	2/11	0.23035045454755	4	FACETS	1	0.959	1	0.722	0.611	0.843	CLONAL	1	TRUE	2	0.276652427817948	4		341	294	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971109	+	missense_variant	Missense_Mutation	DNP	CG	CG	GT	novel	NA	P-0022041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	61	583	1	ENST00000304494.5:c.249_250delinsAC	p.His83_Asp84delinsGlnHis	p.H83_D84delinsQH	ENST00000304494	NM_000077.4	83	caCGac/caACac	2/3	0.276652427817948	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.276652427817948	1		584	336	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0022043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	47	272	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.476480947387823	1	FACETS	0.707	0.604	0.817	0.707	0.604	0.817	SUBCLONAL	1	TRUE	0	0.502869451059581	1		272	198	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0022043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	177	484	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.476480947387823	1	FACETS	0.924	0.857	0.994	0.924	0.857	0.994	CLONAL	1	TRUE	0	0.502869451059581	1		484	570	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0022043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	218	408	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.201448577703049	4	FACETS	0.886	0.833	0.94	0.665	0.625	0.705	INDETERMINATE	3	TRUE	0	0.502869451059581	4		408	490	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250883	153250883	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	87	343	1	ENST00000281708.4:c.1177C>T	p.Arg393Ter	p.R393*	ENST00000281708	NM_033632.3	393	Cga/Tga	8/12	0.467813434904404	1	FACETS	0.935	0.839	1	0.935	0.839	1	CLONAL	1	TRUE	0	0.502869451059581	1		344	277	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169182	32169182	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	222	516	0	ENST00000375023.3:c.3851G>C	p.Cys1284Ser	p.C1284S	ENST00000375023	NM_004557.3	1284	tGc/tCc	22/30	1	2	FACETS	0.923	0.859	0.988	0.923	0.859	0.988	CLONAL	1	TRUE	1	0.502869451059581	2		516	957	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0022046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	346	693	0	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.838782608790797	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.839332596330272	1		693	474	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256021	16256021	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	94	585	0	ENST00000375759.3:c.3286G>C	p.Val1096Leu	p.V1096L	ENST00000375759	NM_015001.2	1096	Gtg/Ctg	11/15	NA	2	FACETS	0.262	0.232	0.293			1	INDETERMINATE	1	TRUE	NA	0.839332596330272	2		585	855	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43772092	43772093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	268	731	0	ENST00000382044.4:c.622_623insA	p.Gly208GlufsTer7	p.G208Efs*7	ENST00000382044	NM_001141980.1	208	ggt/gAgt	6/28	0.839332596330272	1	FACETS	0.752	0.715	0.789	0.752	0.715	0.789	SUBCLONAL	1	TRUE	0	0.839332596330272	1		731	493	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678022	58678022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	157	200	0	ENST00000305921.3:c.247G>A	p.Gly83Arg	p.G83R	ENST00000305921	NM_003620.3	83	Ggg/Agg	1/6	0.830419188123128	2	FACETS	0.99	0.949	1	0.99	0.949	1	CLONAL	2	TRUE	0	0.839332596330272	2		200	189	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313395	30313395	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1404	95	625	0	ENST00000262643.3:c.995T>G	p.Val332Gly	p.V332G	ENST00000262643	NM_001238.2	332	gTt/gGt	11/12	0.839332596330272	4	FACETS	0.278	0.246	0.312			1	SUBCLONAL	1	TRUE	NA	0.839332596330272	4		625	1499	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259236	36259236	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	76	524	0	ENST00000300305.3:c.255C>A	p.His85Gln	p.H85Q	ENST00000300305		85	caC/caA	3/8	0.220825360965992	2	FACETS	0.335	0.294	0.379	0.167	0.147	0.19	INDETERMINATE	1	TRUE	0	0.839332596330272	2		524	541	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750437	133750437	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	239	554	2	ENST00000318560.5:c.1268G>T	p.Trp423Leu	p.W423L	ENST00000318560	NM_005157.4	423	tGg/tTg	7/11	1	2	FACETS	0.701	0.657	0.747	0.701	0.657	0.747	SUBCLONAL	1	TRUE	1	0.839332596330272	2		556	812	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944633	40944634	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AA	AA	C	novel	NA	P-0022046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	179	302	0	ENST00000373198.4:c.1868_1869delinsG	p.Val623GlyfsTer28	p.V623Gfs*28	ENST00000373198	NM_133170.3	623	gTT/gG	12/32	0.530297150756855	3	FACETS	1	0.968	1	0.539	0.5	0.579	CLONAL	1	TRUE	1	0.839332596330272	3		302	562	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0022047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	110	712	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	NA	2	FACETS	1	0.942	1			1	INDETERMINATE	1	TRUE	NA	0.273767341634257	2		712	752	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350279	89350279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	211	921	1	ENST00000301030.4:c.2671G>A	p.Asp891Asn	p.D891N	ENST00000301030	NM_001256183.1	891	Gac/Aac	9/13	0.2544215056149	2	FACETS	0.976	0.908	1	0.976	0.908	1	CLONAL	2	TRUE	0	0.273767341634257	2		922	790	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220691	1220691	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs878853247	NA	P-0022047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	172	740	0	ENST00000326873.7:c.709G>T	p.Asp237Tyr	p.D237Y	ENST00000326873	NM_000455.4	237	Gac/Tac	5/10	0.2544215056149	2	FACETS	0.928	0.857	1	0.928	0.857	1	CLONAL	2	TRUE	0	0.273767341634257	2		740	677	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156046	119156046	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs483352825	NA	P-0022047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	147	750	1	ENST00000264033.4:c.1711G>A	p.Asp571Asn	p.D571N	ENST00000264033	NM_005188.3	571	Gac/Aac	11/16	0.2544215056149	2	FACETS	0.856	0.785	0.931	0.856	0.785	0.931	CLONAL	2	TRUE	0	0.273767341634257	2		751	627	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259631	89259631	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	77	423	0	ENST00000336596.2:c.775T>A	p.Cys259Ser	p.C259S	ENST00000336596	NM_005233.5	259	Tgc/Agc	3/17	0.2544215056149	2	FACETS	1	0.977	1	0.744	0.657	0.836	CLONAL	1	TRUE	0	0.273767341634257	2		423	378	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120854	115120854	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	56	448	1	ENST00000257566.3:c.152C>T	p.Ala51Val	p.A51V	ENST00000257566	NM_016569.3	51	gCg/gTg	1/8	0.244596933417175	3	FACETS	0.975	0.837	1	0.488	0.418	0.563	CLONAL	1	TRUE	1	0.273767341634257	3		449	477	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907073	32907073	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	52	569	0	ENST00000380152.3:c.1458G>T	p.Gln486His	p.Q486H	ENST00000380152		486	caG/caT	10/27	0.244596933417175	3	FACETS	0.742	0.631	0.864	0.371	0.315	0.432	SUBCLONAL	1	TRUE	1	0.273767341634257	3		569	582	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003764	45003765	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0022047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	75	603	0	ENST00000558401.1:c.20_21insC	p.Leu7PhefsTer50	p.L7Ffs*50	ENST00000558401	NM_004048.2	7	tta/ttCa	1/4	0.273767341634257	1	FACETS	0.969	0.852	1	0.969	0.852	1	CLONAL	1	TRUE	0	0.273767341634257	1		603	488	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533704	63533704	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	113	561	0	ENST00000307078.5:c.1450G>T	p.Gly484Cys	p.G484C	ENST00000307078	NM_004655.3	484	Ggt/Tgt	6/11	0.244596933417175	3	FACETS	0.976	0.883	1	0.976	0.883	1	CLONAL	2	TRUE	1	0.273767341634257	3		561	481	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597407	10597409	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	novel	NA	P-0022047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	217	829	0	ENST00000171111.5:c.1794_1796del	p.Ser599del	p.S599del	ENST00000171111	NM_203500.1	598	acATCg/acg	6/6	0.2544215056149	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.273767341634257	2		829	769	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99137153	99137153	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	52	447	0	ENST00000074304.5:c.110A>T	p.Asn37Ile	p.N37I	ENST00000074304	NM_001134224.1	37	aAt/aTt	4/26	0.215595915872445	4	FACETS	0.853	0.726	0.993	0.427	0.363	0.497	CLONAL	1	TRUE	2	0.273767341634257	4		447	567	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858234	27858234	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	75	577	0	ENST00000359303.2:c.337A>G	p.Ile113Val	p.I113V	ENST00000359303	NM_003535.2	113	Att/Gtt	1/1	0.244596933417175	3	FACETS	1	0.878	1	0.501	0.439	0.567	CLONAL	1	TRUE	1	0.273767341634257	3		577	622	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188055	32188055	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	145	695	0	ENST00000375023.3:c.1166T>A	p.Leu389Gln	p.L389Q	ENST00000375023	NM_004557.3	389	cTg/cAg	7/30	0.210013118795621	5	FACETS	0.826	0.754	0.903	0.551	0.502	0.602	CLONAL	2	TRUE	2	0.273767341634257	5		695	904	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797515	45797515	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs765808018	NA	P-0022049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1268	138	755	0	ENST00000450313.1:c.1004A>G	p.Asn335Ser	p.N335S	ENST00000450313	NM_012222.2	335	aAc/aGc	12/16	0.472344883761915	6	FACETS	0.808	0.733	0.888			1	CLONAL	1	TRUE	NA	0.472344883761915	6		755	1406	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577101	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0022049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	354	706	0	ENST00000269305.4:c.837_839del	p.Arg280del	p.R280del	ENST00000269305	NM_001126112.2	279	ggGAGa/gga	8/11	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.472344883761915	2		706	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0022058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	473	649	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.324181710292059	5	FACETS	0.974	0.942	1			1	CLONAL	5	TRUE	NA	0.428918559706831	5		649	744	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003808	45003808	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	160	431	0	ENST00000558401.1:c.64C>T	p.Gln22Ter	p.Q22*	ENST00000558401	NM_004048.2	22	Cag/Tag	1/4	0.428918559706831	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	0	0.428918559706831	2		431	372	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412453	63412453	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	100	714	0	ENST00000330258.3:c.714A>C	p.Lys238Asn	p.K238N	ENST00000330258	NM_152424.3	238	aaA/aaC	2/2	0.428918559706831	5	FACETS	1	0.915	1	0.343	0.306	0.382	CLONAL	1	TRUE	2	0.428918559706831	5		714	745	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864705	57864705	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	85	648	0	ENST00000228682.2:c.2182G>A	p.Asp728Asn	p.D728N	ENST00000228682	NM_005269.2	728	Gat/Aat	12/12	0.428918559706831	6	FACETS	0.854	0.754	0.962			1	CLONAL	1	TRUE	NA	0.428918559706831	6		648	862	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610580	52610580	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	64	468	0	ENST00000394830.3:c.3593C>G	p.Thr1198Ser	p.T1198S	ENST00000394830	NM_018313.4	1198	aCc/aGc	23/30	0.428918559706831	4	FACETS	0.662	0.573	0.759	0.331	0.286	0.38	SUBCLONAL	1	TRUE	2	0.428918559706831	4		468	644	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808661	1808661	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs747369218	NA	P-0022058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	93	667	0	ENST00000260795.2:c.2274C>G	p.Asp758Glu	p.D758E	ENST00000260795		758	gaC/gaG	16/17	0.428918559706831	7	FACETS	0.979	0.869	1			1	CLONAL	1	TRUE	NA	0.428918559706831	7		667	918	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517962	187517962	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	337	510	0	ENST00000441802.2:c.12732C>A	p.Asp4244Glu	p.D4244E	ENST00000441802	NM_005245.3	4244	gaC/gaA	25/27	0.428918559706831	5	FACETS	0.917	0.874	0.96			1	CLONAL	4	TRUE	NA	0.428918559706831	5		510	704	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181354	123181378	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTAAACTTTTATATTGAATATTT	AGGTAAACTTTTATATTGAATATTT	-	novel	NA	P-0022058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	62	216	0	ENST00000218089.9:c.819+2_819+26del		p.X273_splice	ENST00000218089	NM_001042749.1	273		9/35	0.42234331515791	5	FACETS	1	0.964	1			1	CLONAL	1	TRUE	NA	0.428918559706831	5		216	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0022064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	19	713	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.097	0.073	0.126	0.097	0.073	0.126	SUBCLONAL	1	TRUE	1	0.532680764650286	2		715	732	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873806	35873807	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0022064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	175	516	0	ENST00000216797.5:c.44dup	p.Arg17ProfsTer69	p.R17Pfs*69	ENST00000216797	NM_020529.2	15	ggc/ggGc	1/6	0.532680764650286	1	FACETS	0.966	0.897	1	0.966	0.897	1	CLONAL	1	TRUE	0	0.532680764650286	1		516	499	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591888	48591888	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	128	648	0	ENST00000342988.3:c.1051G>T	p.Asp351Tyr	p.D351Y	ENST00000342988	NM_005359.5	351	Gat/Tat	9/12	0.595924423260639	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.595924423260639	1		648	289	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0022065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	453	878	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.595924423260639	2	FACETS	0.965	0.929	1	0.965	0.929	1	CLONAL	2	TRUE	0	0.595924423260639	2		878	788	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177933	56177933	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750940532	NA	P-0022065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	290	653	0	ENST00000399503.3:c.2906C>T	p.Ser969Phe	p.S969F	ENST00000399503	NM_005921.1	969	tCc/tTc	14/20	0.595924423260639	2	FACETS	0.941	0.897	0.985	0.941	0.897	0.985	CLONAL	2	TRUE	0	0.595924423260639	2		653	517	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920401	114920401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1422891742	NA	P-0022065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	384	619	0	ENST00000543371.1:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000543371	NM_001198531.1	448	Cgg/Tgg	13/14	0.595924423260639	2	FACETS	0.976	0.938	1	0.976	0.938	1	CLONAL	2	TRUE	0	0.595924423260639	2		619	660	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572164	64572164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1025851127	NA	P-0022065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	36	585	0	ENST00000312049.6:c.1475C>T	p.Pro492Leu	p.P492L	ENST00000312049	NM_130799.2	492	cCc/cTc	10/10	0.595924423260639	3	FACETS	0.251	0.206	0.303	0.126	0.103	0.152	SUBCLONAL	1	TRUE	1	0.595924423260639	3		585	624	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77051789	77051789	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	167	656	0	ENST00000356341.3:c.1018C>G	p.Leu340Val	p.L340V	ENST00000356341	NM_002576.4	340	Ctg/Gtg	11/15	0.595924423260639	3	FACETS	0.973	0.895	1	0.486	0.447	0.527	CLONAL	1	TRUE	1	0.595924423260639	3		656	748	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939492	76939492	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374958282	NA	P-0022065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	21	819	0	ENST00000373344.5:c.1256C>T	p.Ala419Val	p.A419V	ENST00000373344	NM_000489.3	419	gCg/gTg	9/35	0.595924423260639	1	FACETS	0.181	0.139	0.23	0.181	0.139	0.23	SUBCLONAL	1	TRUE	0	0.595924423260639	1		819	273	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930388	39930388	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	186	488	0	ENST00000378444.4:c.3076T>G	p.Leu1026Val	p.L1026V	ENST00000378444	NM_001123385.1	1026	Ttg/Gtg	6/15	NA	2	FACETS	1	0.953	1			1	INDETERMINATE	1	TRUE	NA	0.72444445809243	2		488	499	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	205	778	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.2600773848991	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.2600773848991	3		778	784	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0022073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	251	928	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	0.184980593486438	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	2	0.2600773848991	4		928	1141	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952075	+	missense_variant	Missense_Mutation	DNP	GA	GA	TC	novel	NA	P-0022073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	1784	569	1	ENST00000263967.3:c.3129_3130inv	p.Met1043_Asn1044delinsIleHis	p.M1043_N1044delinsIH	ENST00000263967	NM_006218.2	1043	atGAat/atTCat	21/21	0.2600773848991	46	FACETS	1	0.991	1			1	CLONAL	44	TRUE	NA	0.2600773848991	46		570	2090	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999801	100999801	+	start_lost	Translation_Start_Site	SNP	T	T	G	rs1267126541	NA	P-0022073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	40	699	0	ENST00000325455.5:c.1A>C	p.Met1?	p.M1?	ENST00000325455	NM_001202474.3	1	Atg/Ctg	1/8	0.2600773848991	5	FACETS	0.619	0.513	0.737	0.155	0.128	0.185	SUBCLONAL	1	TRUE	1	0.2600773848991	5		699	691	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863687	68863688	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	45	434	0	ENST00000261769.5:c.2430dup	p.Ile811TyrfsTer2	p.I811Yfs*2	ENST00000261769	NM_004360.3	809	aat/aaTt	15/16	0.250137663445775	4	FACETS	0.776	0.651	0.914	0.259	0.217	0.305	CLONAL	1	TRUE	1	0.2600773848991	4		434	562	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579556	7579565	+	frameshift_variant	Frame_Shift_Del	DEL	ATCAAATCAT	ATCAAATCAT	-	novel	NA	P-0022073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	193	908	0	ENST00000269305.4:c.122_131del	p.Asp41GlyfsTer79	p.D41Gfs*79	ENST00000269305	NM_001126112.2	41	gATGATTTGATg/gg	4/11	0.2600773848991	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.2600773848991	2		908	710	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375320	15375320	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	57	868	0	ENST00000263377.2:c.1107C>G	p.His369Gln	p.H369Q	ENST00000263377	NM_058243.2	369	caC/caG	6/20	0.2600773848991	3	FACETS	0.56	0.479	0.649			1	SUBCLONAL	1	TRUE	NA	0.2600773848991	3		868	885	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898785	134898785	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	75	685	0	ENST00000398015.3:c.1843G>C	p.Asp615His	p.D615H	ENST00000398015	NM_004441.4	615	Gat/Cat	10/16	0.226548687690887	3	FACETS	1	0.92	1	0.532	0.467	0.603	CLONAL	1	TRUE	1	0.2600773848991	3		685	612	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958124	2958124	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0022073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	84	843	0	ENST00000396946.4:c.2607+1G>A		p.X869_splice	ENST00000396946	NM_032415.4	869			0.2600773848991	4	FACETS	0.967	0.853	1	0.322	0.284	0.363	CLONAL	1	TRUE	1	0.2600773848991	4		843	842	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160672	56160679	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTACTT	CTGTACTT	A	novel	NA	P-0022073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	121	575	0	ENST00000399503.3:c.946_953delinsA	p.Leu316AsnfsTer5	p.L316Nfs*5	ENST00000399503	NM_005921.1	316	CTGTACTTa/Aa	4/20	0.2600773848991	3	FACETS	0.942	0.855	1	0.942	0.855	1	CLONAL	2	TRUE	1	0.2600773848991	3		575	558	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916947	178916947	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	105	501	0	ENST00000263967.3:c.334A>T	p.Ile112Phe	p.I112F	ENST00000263967	NM_006218.2	112	Atc/Ttc	2/21	0.154359448798254	3	FACETS	0.847	0.761	0.937	1	0.974	1	CLONAL	3	TRUE	1	0.154359448798254	3		501	577	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961036	18961036	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	34	653	0	ENST00000262803.5:c.614T>A	p.Val205Glu	p.V205E	ENST00000262803	NM_002911.3	205	gTg/gAg	4/24	0.154359448798254	3	FACETS	0.768	0.626	0.928	0.384	0.313	0.464	CLONAL	1	TRUE	1	0.154359448798254	3		653	618	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980413	1980413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	67	1056	2	ENST00000382891.5:c.3875C>T	p.Ser1292Leu	p.S1292L	ENST00000382891	NM_133335.3	1292	tCg/tTg	22/22	0.143386418315342	4	FACETS	0.989	0.857	1	0.495	0.428	0.567	CLONAL	1	TRUE	2	0.154359448798254	4		1058	1013	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1023835002	NA	P-0022082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	87	523	0	ENST00000558401.1:c.1A>G	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Gtg	1/4	0.450469740441804	1	FACETS	0.968	0.867	1	0.968	0.867	1	CLONAL	1	TRUE	0	0.450469740441804	1		523	309	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873716	35873732	+	frameshift_variant	Frame_Shift_Del	DEL	CATCTGCTCGTACTCCT	CATCTGCTCGTACTCCT	-	novel	NA	P-0022082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	120	657	0	ENST00000216797.5:c.119_135del	p.Glu40GlyfsTer40	p.E40Gfs*40	ENST00000216797	NM_020529.2	40	gAGGAGTACGAGCAGATG/g	1/6	0.256095919374777	3	FACETS	0.885	0.807	0.964	0.59	0.538	0.643	INDETERMINATE	2	TRUE	0	0.450469740441804	3		657	369	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0022083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	312	630	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	0.971	0.918	1	0.971	0.918	1	CLONAL	1	TRUE	1	0.661005527633402	2		630	972	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	140	636	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.25	2		638	881	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0022085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	95	737	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.3	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.25	1		739	603	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477089	67477103	+	inframe_deletion	In_Frame_Del	DEL	TCGGAGGGGAGGTCT	TCGGAGGGGAGGTCT	-	novel	NA	P-0022085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	182	496	0	ENST00000327367.4:c.899_913del	p.Gly300_Phe304del	p.G300_F304del	ENST00000327367	NM_005902.3	299	aTCGGAGGGGAGGTCTtc/atc	7/9	1	2	FACETS	1	0.97	1	1	0.993	1	CLONAL	2	TRUE	1	0.25	2		496	668	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753597	42753597	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	139	790	1	ENST00000222329.4:c.667G>T	p.Ala223Ser	p.A223S	ENST00000222329	NM_006494.2	223	Gcc/Tcc	4/4	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.25	2		791	814	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200670	128200670	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	99	677	0	ENST00000341105.2:c.1135C>G	p.Leu379Val	p.L379V	ENST00000341105	NM_032638.4	379	Ctg/Gtg	5/6	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.25	2		677	682	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268984	142268984	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558627427	NA	P-0022085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	94	422	0	ENST00000350721.4:c.2966G>A	p.Arg989His	p.R989H	ENST00000350721	NM_001184.3	989	cGt/cAt	14/47	0.249752805264602	3	FACETS	1	0.978	1	0.701	0.625	0.783	CLONAL	1	TRUE	1	0.25	3		422	603	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	20	549	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.609116688255741	4	FACETS	0.207	0.158	0.266	0.069	0.052	0.089	SUBCLONAL	1	TRUE	1	0.746676603933415	4		549	451	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0022088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	88	550	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.609116688255741	4	FACETS	0.55	0.487	0.617	0.183	0.162	0.206	SUBCLONAL	1	TRUE	1	0.746676603933415	4		552	749	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463286	25463286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139293773	NA	P-0022088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	178	446	0	ENST00000264709.3:c.2207G>A	p.Arg736His	p.R736H	ENST00000264709	NM_175629.2	736	cGc/cAc	19/23	0.472246264000566	4	FACETS	0.919	0.856	0.983	0.919	0.856	0.983	CLONAL	2	TRUE	2	0.746676603933415	4		446	453	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111542	8111543	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0022088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	199	596	0	ENST00000346208.3:c.1029dup	p.Tyr344LeufsTer8	p.Y344Lfs*8	ENST00000346208		343	ctc/ctCc	5/6	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.746676603933415	2		596	491	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178037	56178037	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	17	314	0	ENST00000399503.3:c.3010C>A	p.His1004Asn	p.H1004N	ENST00000399503	NM_005921.1	1004	Cat/Aat	14/20	0.746676603933415	8	FACETS	0.533	0.397	0.693			1	SUBCLONAL	1	TRUE	NA	0.746676603933415	8		314	277	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712017	89712017	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0022091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	117	265	0	ENST00000371953.3:c.634+1G>T		p.X212_splice	ENST00000371953	NM_000314.4	212			0.626686193755859	2	FACETS	0.768	0.708	0.829	0.768	0.708	0.829	SUBCLONAL	2	TRUE	0	0.626686193755859	2		265	243	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11032379	11032379	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1427308204	NA	P-0022091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	148	774	0	ENST00000327064.4:c.1773C>G	p.Ile591Met	p.I591M	ENST00000327064	NM_199141.1	591	atC/atG	16/16	0.626686193755859	3	FACETS	0.784	0.717	0.855	0.261	0.239	0.285	SUBCLONAL	1	TRUE	0	0.626686193755859	3		774	791	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484336	8484336	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	91	527	0	ENST00000356435.5:c.3196C>T	p.Arg1066Ter	p.R1066*	ENST00000356435		1066	Cga/Tga	19/35	0.379027916186871	3	FACETS	0.558	0.495	0.624	0.186	0.165	0.208	SUBCLONAL	1	TRUE	0	0.626686193755859	3		527	684	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399998	139400009	+	inframe_deletion	In_Frame_Del	DEL	CTCGCACGCCTC	CTCGCACGCCTC	-	novel	NA	P-0022091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	432	847	2	ENST00000277541.6:c.4339_4350del	p.Glu1447_Glu1450del	p.E1447_E1450del	ENST00000277541	NM_017617.3	1447	GAGGCGTGCGAG/-	25/34	0.379027916186871	3	FACETS	1	0.993	1	0.762	0.732	0.792	CLONAL	2	TRUE	0	0.626686193755859	3		849	792	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6442013	6442013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	52	261	0	ENST00000356142.4:c.572C>T	p.Ala191Val	p.A191V	ENST00000356142	NM_018890.3	191	gCg/gTg	7/7	1	2	FACETS	0.781	0.667	0.904	0.781	0.667	0.904	CLONAL	1	FALSE	1	0.372169725495365	2		261	358	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852568	63852568	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	101	429	0	ENST00000279873.7:c.3346A>T	p.Met1116Leu	p.M1116L	ENST00000279873	NM_032199.2	1116	Atg/Ttg	10/10	0.372169725495365	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	0	0.372169725495365	1		429	411	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111517	8111518	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	275	912	0	ENST00000346208.3:c.1004dup	p.Asp335GlufsTer17	p.D335Efs*17	ENST00000346208		335	gac/gAac	5/6	0.498836408597721	3	FACETS	1	0.972	1	0.532	0.498	0.566	CLONAL	1	TRUE	1	0.498836408597721	3		912	1295	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533605	63533605	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	1655	1228	0	ENST00000307078.5:c.1549C>G	p.His517Asp	p.H517D	ENST00000307078	NM_004655.3	517	Cac/Gac	6/11	0.498836408597721	6	FACETS	0.996	0.98	1			1	CLONAL	6	TRUE	NA	0.498836408597721	6		1228	2219	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719497	190719497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	28	357	0	ENST00000441310.2:c.1499G>A	p.Arg500Lys	p.R500K	ENST00000441310	NM_000534.4	500	aGg/aAg	9/13	1	2	FACETS	0.51	0.41	0.623	0.51	0.41	0.623	SUBCLONAL	1	TRUE	1	0.498836408597721	2		357	220	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0022100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	342	713	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.538006296320069	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.538006296320069	1		715	927	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519893	NA	P-0022100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	355	982	0	ENST00000267101.3:c.310G>T	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ttg	3/28	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.538006296320069	2		982	1309	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215634023	215634023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	48	565	0	ENST00000260947.4:c.1328C>T	p.Ser443Phe	p.S443F	ENST00000260947	NM_000465.2	443	tCt/tTt	5/11	1	2	FACETS	0.249	0.209	0.292	0.249	0.209	0.292	SUBCLONAL	1	TRUE	1	0.538006296320069	2		565	718	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277892	41277892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	201	573	1	ENST00000349496.5:c.1856G>A	p.Cys619Tyr	p.C619Y	ENST00000349496	NM_001904.3	619	tGt/tAt	12/15	0.52668376534342	1	FACETS	0.977	0.912	1	0.977	0.912	1	CLONAL	1	TRUE	0	0.538006296320069	1		574	559	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0022103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	240	623	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.240683452421222	4	FACETS	0.948	0.887	1	0.948	0.887	1	CLONAL	3	TRUE	1	0.240683452421222	4		623	870	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024001	27024002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0022103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	20	135	0	ENST00000324856.7:c.1113dup	p.Gln372AlafsTer28	p.Q372Afs*28	ENST00000324856	NM_006015.4	369	-/G	1/20	0.179916404854917	3	FACETS	0.99	0.761	1			1	CLONAL	1	TRUE	NA	0.240683452421222	3		135	188	SUCCESS
APC	324	MSKCC	GRCh37	5	112174691	112174691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	44	363	0	ENST00000257430.4:c.3400G>A	p.Asp1134Asn	p.D1134N	ENST00000257430	NM_000038.5	1134	Gac/Aac	16/16	0.240683452421222	6	FACETS	0.894	0.748	1	0.223	0.187	0.264	CLONAL	1	TRUE	2	0.240683452421222	6		363	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577505	7577505	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs745425759	NA	P-0022103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	281	698	0	ENST00000269305.4:c.776A>T	p.Asp259Val	p.D259V	ENST00000269305	NM_001126112.2	259	gAc/gTc	7/11	0.240683452421222	3	FACETS	0.974	0.918	1	0.974	0.918	1	CLONAL	3	TRUE	0	0.240683452421222	3		698	895	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873630	35873630	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	80	341	0	ENST00000303115.3:c.586C>T	p.Gln196Ter	p.Q196*	ENST00000303115	NM_002185.3	196	Caa/Taa	5/8	0.240683452421222	7	FACETS	0.815	0.718	0.92	0.326	0.287	0.368	CLONAL	2	TRUE	2	0.240683452421222	7		341	653	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0022109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	343	693	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.539951796638077	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	3	TRUE	0	0.539951796638077	3		693	536	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0022109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	140	289	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.539951796638077	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.539951796638077	2		289	224	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0022109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	519	713	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.539951796638077	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	0	0.539951796638077	3		715	788	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	85	596	0	ENST00000342988.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000342988	NM_005359.5	356	cCt/cTt	9/12	0.539951796638077	1	FACETS	0.824	0.737	0.914	0.824	0.737	0.914	CLONAL	1	TRUE	0	0.539951796638077	1		596	279	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124713	108124713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	196	564	0	ENST00000278616.4:c.2071G>A	p.Asp691Asn	p.D691N	ENST00000278616	NM_000051.3	691	Gat/Aat	13/63	0.539951796638077	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	1	0.539951796638077	3		564	456	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590951	95590951	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1461043339	NA	P-0022109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	21	359	0	ENST00000393063.1:c.958A>G	p.Lys320Glu	p.K320E	ENST00000393063	NM_030621.3	320	Aaa/Gaa	9/28	0.363067563686065	4	FACETS	0.337	0.259	0.429	0.169	0.129	0.215	SUBCLONAL	1	TRUE	2	0.539951796638077	4		359	355	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577111	7577111	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786202082	NA	P-0022110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	214	872	7	ENST00000269305.4:c.827C>A	p.Ala276Asp	p.A276D	ENST00000269305	NM_001126112.2	276	gCc/gAc	8/11	1	2	FACETS	0.782	0.727	0.839	1	0.992	1	SUBCLONAL	2	TRUE	1	0.288894047902967	2		879	947	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752627	42752627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs936669722	NA	P-0022110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	55	672	0	ENST00000222329.4:c.1637G>A	p.Arg546Gln	p.R546Q	ENST00000222329	NM_006494.2	546	cGa/cAa	4/4	1	2	FACETS	0.616	0.527	0.714	0.616	0.527	0.714	SUBCLONAL	1	TRUE	1	0.288894047902967	2		672	618	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489095	56489095	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1427383787	NA	P-0022110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	107	635	1	ENST00000267101.3:c.1913+1G>A		p.X638_splice	ENST00000267101	NM_001982.3	638			1	2	FACETS	0.926	0.83	1	0.926	0.83	1	CLONAL	1	TRUE	1	0.288894047902967	2		636	800	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435744	56435744	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	26	618	0	ENST00000407977.2:c.1393G>A	p.Asp465Asn	p.D465N	ENST00000407977		465	Gac/Aac	9/10	0.222429319645399	2	FACETS	0.359	0.284	0.446	0.18	0.142	0.223	SUBCLONAL	1	TRUE	0	0.288894047902967	2		618	501	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942689	48942695	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGTAA	AAAGTAA	GTT	novel	NA	P-0022113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	42	420	1	ENST00000267163.4:c.1076_1082delinsGTT	p.Lys359SerfsTer7	p.K359Sfs*7	ENST00000267163	NM_000321.2	359	aAAAGTAAc/aGTTc	11/27	1	2	FACETS	0.915	0.765	1	0.915	0.765	1	CLONAL	1	FALSE	1	0.202582380301078	2		421	453	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961859	15961859	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	100	542	0	ENST00000268712.3:c.5936C>T	p.Ala1979Val	p.A1979V	ENST00000268712	NM_006311.3	1979	gCc/gTc	38/46	1	2	FACETS	0.858	0.769	0.953	1	0.985	1	CLONAL	2	FALSE	1	0.202582380301078	2		542	575	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24129377	24129377	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	74	500	0	ENST00000263121.7:c.21C>A	p.Ser7Arg	p.S7R	ENST00000263121	NM_003073.3	7	agC/agA	1/9	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	FALSE	1	0.202582380301078	2		500	675	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31401596	31401596	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	75	730	0	ENST00000344624.3:c.4068G>C	p.Arg1356Ser	p.R1356S	ENST00000344624		1356	agG/agC	33/33	1	2	FACETS	0.87	0.761	0.988	0.87	0.761	0.988	CLONAL	1	FALSE	1	0.202582380301078	2		730	851	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858284	27858284	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	97	663	1	ENST00000359303.2:c.287C>T	p.Ala96Val	p.A96V	ENST00000359303	NM_003535.2	96	gCg/gTg	1/1	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.202582380301078	2		664	747	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518409	8518409	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	38	254	0	ENST00000356435.5:c.982A>C	p.Thr328Pro	p.T328P	ENST00000356435		328	Act/Cct	10/35	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	1	0.202582380301078	2		254	300	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0022118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	248	569	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.49174659685357	4	FACETS	0.99	0.93	1	0.99	0.93	1	CLONAL	2	TRUE	2	0.511851731821169	4		569	740	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0022118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	492	713	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.511851731821169	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.511851731821169	3		715	768	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971053	21971054	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0022118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	162	509	0	ENST00000304494.5:c.304dup	p.Ala102GlyfsTer18	p.A102Gfs*18	ENST00000304494	NM_000077.4	102	gcg/gGcg	2/3	NA	2	FACETS	0.842	0.783	0.901			1	INDETERMINATE	2	TRUE	NA	0.511851731821169	2		509	376	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0022124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	300	524	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.933	0.902	0.963	1	0.997	1	CLONAL	2	TRUE	1	0.824248062585389	2		524	390	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012280	152012280	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs780827585	NA	P-0022124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	255	733	0	ENST00000262189.6:c.533A>G	p.Asn178Ser	p.N178S	ENST00000262189	NM_170606.2	178	aAt/aGt	4/59	1	2	FACETS	0.958	0.903	1	0.958	0.903	1	CLONAL	1	TRUE	1	0.824248062585389	2		733	646	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798773	135798773	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	139	424	0	ENST00000298552.3:c.470T>A	p.Ile157Asn	p.I157N	ENST00000298552	NM_001162426.1	157	aTt/aAt	6/23	0.824248062585389	1	FACETS	0.982	0.925	1	0.982	0.925	1	CLONAL	1	TRUE	0	0.824248062585389	1		424	202	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0022127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2608	78	644	1	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.945369467821583	8	FACETS		NA	1			1	NA	NA	FALSE	1	NA	8		645	2686	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040904	47040904	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0022127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	109	867	0	ENST00000377604.3:c.1436-2A>T		p.X479_splice	ENST00000377604	NM_001204468.1	479			1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		867	804	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359039	81359039	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	46	673	1	ENST00000222390.5:c.922G>T	p.Gly308Cys	p.G308C	ENST00000222390	NM_000601.4	308	Ggt/Tgt	8/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		674	721	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429754	78429754	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	24	408	0	ENST00000370768.2:c.1034del	p.Ser345MetfsTer46	p.S345Mfs*46	ENST00000370768	NM_003902.3	345	aGt/at	12/20	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		408	410	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	47	1074	1	ENST00000397752.3:c.3028G>A	p.Asp1010Asn	p.D1010N	ENST00000397752	NM_000245.2	1010	Gat/Aat	14/21	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.14	2		1075	661	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560494	65560494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	30	683	1	ENST00000358664.4:c.103C>T	p.Arg35Cys	p.R35C	ENST00000358664	NM_002382.4	35	Cgt/Tgt	3/5	1	2	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	TRUE	1	0.14	2		684	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0022130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	318	929	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.582747142725849	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.583706932962091	2		930	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0022136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	125	929	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.257421205907184	1	FACETS	0.937	0.847	1	0.937	0.847	1	CLONAL	1	TRUE	0	0.257421205907184	1		930	903	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121831	2121831	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	42	1035	0	ENST00000219476.3:c.1993C>T	p.Pro665Ser	p.P665S	ENST00000219476	NM_000548.3	665	Cct/Tct	19/42	1	2	FACETS	0.391	0.325	0.465	0.391	0.325	0.465	SUBCLONAL	1	TRUE	1	0.257421205907184	2		1035	834	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0022136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	90	1039	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	0.257421205907184	2		1039	664	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	195	445	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.86192792295261	2		445	419	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339176	87339176	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	147	619	0	ENST00000277120.3:c.758C>T	p.Thr253Ile	p.T253I	ENST00000277120		253	aCt/aTt	8/19	1	2	FACETS	0.403	0.367	0.44	0.403	0.367	0.44	SUBCLONAL	1	TRUE	1	0.86192792295261	2		619	847	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649544	206649544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370426628	NA	P-0022142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	366	497	0	ENST00000367120.3:c.379C>T	p.Arg127Trp	p.R127W	ENST00000367120	NM_014002.3	127	Cgg/Tgg	6/22	0.86192792295261	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.86192792295261	1		497	474	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574693	64574693	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0022142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	426	614	0	ENST00000312049.6:c.784-2A>C		p.X262_splice	ENST00000312049	NM_130799.2	262			0.86192792295261	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.86192792295261	1		614	541	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464495	25464498	+	frameshift_variant	Frame_Shift_Del	DEL	CCCA	CCCA	-	novel	NA	P-0022142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	693	767	0	ENST00000264709.3:c.2015_2018del	p.Val672AlafsTer32	p.V672Afs*32	ENST00000264709	NM_175629.2	672	gTGGGc/gc	17/23	0.831111778632944	2	FACETS	0.925	0.906	0.944	0.925	0.906	0.944	CLONAL	2	TRUE	0	0.86192792295261	2		767	869	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043668	6043668	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	105	566	0	ENST00000265849.7:c.185G>T	p.Gly62Val	p.G62V	ENST00000265849	NM_000535.5	62	gGa/gTa	3/15	1	2	FACETS	0.381	0.342	0.423	0.381	0.342	0.423	SUBCLONAL	1	TRUE	1	0.86192792295261	2		566	639	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0022143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	17	314	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.350731479048766	1	FACETS	0.32	0.239	0.416	0.32	0.239	0.416	SUBCLONAL	1	FALSE	0	0.39456047941767	1		314	216	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577524	7577524	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	234	730	0	ENST00000269305.4:c.757A>C	p.Thr253Pro	p.T253P	ENST00000269305	NM_001126112.2	253	Acc/Ccc	7/11	NA	2	FACETS	0.792	0.741	0.843			1	INDETERMINATE	2	FALSE	NA	0.39456047941767	2		730	749	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138917	64138917	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs950765689	NA	P-0022143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	82	340	1	ENST00000334205.4:c.2284C>T	p.Pro762Ser	p.P762S	ENST00000334205	NM_003942.2	762	Ccc/Tcc	17/17	0.259460802549436	3	FACETS	1	0.958	1			1	CLONAL	1	FALSE	NA	0.39456047941767	3		341	424	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788633	3788633	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1271038944	NA	P-0022143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	72	548	2	ENST00000262367.5:c.4321C>T	p.Arg1441Trp	p.R1441W	ENST00000262367	NM_004380.2	1441	Cgg/Tgg	26/31	1	2	FACETS	0.673	0.589	0.764	0.673	0.589	0.764	SUBCLONAL	1	FALSE	1	0.39456047941767	2		550	542	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335690	81335690	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	93	670	0	ENST00000222390.5:c.1670G>T	p.Gly557Val	p.G557V	ENST00000222390	NM_000601.4	557	gGa/gTa	15/18	0.259460802549436	3	FACETS	0.511	0.453	0.574			1	SUBCLONAL	1	FALSE	NA	0.39456047941767	3		670	1104	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0022144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	190	737	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.261163874469667	2	FACETS	0.929	0.864	0.994	0.929	0.864	0.994	CLONAL	2	TRUE	0	0.364685933308432	2		739	561	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971029	21971029	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519852	NA	P-0022144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	70	385	0	ENST00000304494.5:c.329G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tGg/tAg	2/3	0.182358749838595	3	FACETS	1	0.956	1	0.602	0.528	0.681	INDETERMINATE	1	TRUE	1	0.364685933308432	3		385	377	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252994	36252995	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0022144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	145	638	0	ENST00000300305.3:c.366_367dup	p.Asp123GlyfsTer11	p.D123Gfs*11	ENST00000300305		123	gat/gGGat	4/8	0.298642813883468	2	FACETS	1	0.988	1	0.749	0.687	0.813	CLONAL	1	TRUE	0	0.364685933308432	2		638	531	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489852	2489852	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	186	913	0	ENST00000355716.4:c.249C>A	p.Tyr83Ter	p.Y83*	ENST00000355716	NM_003820.2	83	taC/taA	3/8	NA	2	FACETS	0.86	0.799	0.923			1	INDETERMINATE	2	TRUE	NA	0.364685933308432	2		913	593	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	443419	443419	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs780378301	NA	P-0022144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	169	478	0	ENST00000399788.2:c.1478A>G	p.Asn493Ser	p.N493S	ENST00000399788	NM_001042603.1	493	aAc/aGc	11/28	0.364685933308432	4	FACETS	0.965	0.896	1	0.965	0.896	1	CLONAL	3	TRUE	1	0.364685933308432	4		478	437	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644882	67644882	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	32	551	0	ENST00000264010.4:c.147G>T	p.Glu49Asp	p.E49D	ENST00000264010	NM_006565.3	49	gaG/gaT	3/12	1	2	FACETS	0.33	0.267	0.401	0.33	0.267	0.401	SUBCLONAL	1	TRUE	1	0.364685933308432	2		551	532	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346565	89346565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	66	644	0	ENST00000301030.4:c.6385G>A	p.Asp2129Asn	p.D2129N	ENST00000301030	NM_001256183.1	2129	Gac/Aac	9/13	1	2	FACETS	0.81	0.705	0.923	0.81	0.705	0.923	CLONAL	1	TRUE	1	0.364685933308432	2		644	447	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357487	89357487	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	83	851	0	ENST00000301030.4:c.331C>G	p.Leu111Val	p.L111V	ENST00000301030	NM_001256183.1	111	Ctc/Gtc	5/13	1	2	FACETS	0.672	0.593	0.757	0.672	0.593	0.757	SUBCLONAL	1	TRUE	1	0.364685933308432	2		851	677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0022150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	368	794	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.333105038277949	3	FACETS	0.9	0.858	0.943	0.9	0.858	0.943	CLONAL	3	TRUE	0	0.359646018470874	3		794	894	SUCCESS
APC	324	MSKCC	GRCh37	5	112175163	112175170	+	frameshift_variant	Frame_Shift_Del	DEL	AGACGACA	AGACGACA	-	novel	NA	P-0022150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	73	309	0	ENST00000257430.4:c.3872_3879del	p.Gln1291ProfsTer7	p.Q1291Pfs*7	ENST00000257430	NM_000038.5	1291	cAGACGACA/c	16/16	0.359646018470874	2	FACETS	0.805	0.714	0.902	0.805	0.714	0.902	CLONAL	2	TRUE	0	0.359646018470874	2		309	252	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426498	47426498	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372763934	NA	P-0022150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	27	430	0	ENST00000377045.4:c.841C>T	p.Arg281Trp	p.R281W	ENST00000377045	NM_001654.4	281	Cgg/Tgg	9/16	0.359646018470874	2	FACETS	0.289	0.229	0.357			1	SUBCLONAL	1	TRUE	NA	0.359646018470874	2		430	520	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181348	123181348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	40	148	1	ENST00000218089.9:c.812G>A	p.Arg271Gln	p.R271Q	ENST00000218089	NM_001042749.1	271	cGg/cAg	9/35	0.359646018470874	2	FACETS	1	0.955	1			1	CLONAL	1	TRUE	NA	0.359646018470874	2		149	156	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0022152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	155	693	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.297706013462063	3	FACETS	0.812	0.744	0.883	0.812	0.744	0.883	CLONAL	2	TRUE	1	0.28	3		693	777	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0022152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	45	386	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.81	0.682	0.95	0.81	0.682	0.95	CLONAL	1	TRUE	1	0.28	2		386	397	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	44	447	0	ENST00000263967.3:c.3129G>C	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atC	21/21	1	2	FACETS	0.731	0.614	0.86	0.731	0.614	0.86	SUBCLONAL	1	TRUE	1	0.28	2		447	430	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368208	45368208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	71	450	0	ENST00000262160.6:c.1394G>A	p.Ser465Asn	p.S465N	ENST00000262160	NM_005901.5	465	aGc/aAc	11/11	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.28	2		450	460	SUCCESS
APC	324	MSKCC	GRCh37	5	112176027	112176027	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0022152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	40	344	0	ENST00000257430.4:c.4737del	p.Ile1580PhefsTer70	p.I1580Ffs*70	ENST00000257430	NM_000038.5	1579	aTt/at	16/16	1	2	FACETS	0.697	0.58	0.827	0.697	0.58	0.827	SUBCLONAL	1	TRUE	1	0.28	2		344	410	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374882	45374882	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs776149698	NA	P-0022152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	59	752	0	ENST00000262160.6:c.961C>T	p.Arg321Ter	p.R321*	ENST00000262160	NM_005901.5	321	Cga/Tga	8/11	1	2	FACETS	0.594	0.51	0.685	0.594	0.51	0.685	SUBCLONAL	1	TRUE	1	0.28	2		752	710	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710561	114710581	+	inframe_deletion	In_Frame_Del	DEL	GACGAACTGATTTCCTTCAAA	GACGAACTGATTTCCTTCAAA	-	novel	NA	P-0022152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	64	481	0	ENST00000543371.1:c.51_71del	p.Leu18_Glu24del	p.L18_E24del	ENST00000543371	NM_001198531.1	16	GACGAACTGATTTCCTTCAAA/-	1/14	1	2	FACETS	0.757	0.655	0.867	0.757	0.655	0.867	SUBCLONAL	1	TRUE	1	0.28	2		481	604	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416362	49416371	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CCAGCTCATA	CCAGCTCATA	-	novel	NA	P-0022152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	138	477	6	ENST00000301067.7:c.16338+2_16338+11del		p.X5446_splice	ENST00000301067	NM_003482.3	5446			0.297706013462063	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.28	3		483	498	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473735	67473735	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	172	703	2	ENST00000327367.4:c.815G>A	p.Gly272Glu	p.G272E	ENST00000327367	NM_005902.3	272	gGg/gAg	6/9	0.181772197176184	2	FACETS	0.934	0.862	1	0.934	0.862	1	CLONAL	2	TRUE	0	0.28	2		705	658	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209106766	209106766	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	86	708	0	ENST00000345146.2:c.802G>T	p.Ala268Ser	p.A268S	ENST00000345146	NM_005896.2	268	Gcc/Tcc	7/10	1	2	FACETS	0.818	0.723	0.92	0.818	0.723	0.92	CLONAL	1	TRUE	1	0.28	2		708	751	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161750	56161750	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	88	622	0	ENST00000399503.3:c.1247C>A	p.Ser416Ter	p.S416*	ENST00000399503	NM_005921.1	416	tCa/tAa	6/20	1	2	FACETS	0.847	0.75	0.951	0.847	0.75	0.951	CLONAL	1	TRUE	1	0.28	2		622	742	SUCCESS
APC	324	MSKCC	GRCh37	5	112174228	112174229	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAAC	novel	NA	P-0022152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	47	533	0	ENST00000257430.4:c.2938_2941dup	p.Pro981GlnfsTer5	p.P981Qfs*5	ENST00000257430	NM_000038.5	979	-/AAAC	16/16	1	2	FACETS	0.681	0.575	0.798	0.681	0.575	0.798	SUBCLONAL	1	TRUE	1	0.28	2		533	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0022154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	161	721	1	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.514142258201987	2		722	266	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265285	16265285	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	54	847	2	ENST00000375759.3:c.10777G>A	p.Glu3593Lys	p.E3593K	ENST00000375759	NM_015001.2	3593	Gag/Aag	14/15	1	2	FACETS	0.84	0.725	0.964	0.84	0.725	0.964	CLONAL	1	TRUE	1	0.514142258201987	2		849	250	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998925	100998925	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs770624085	NA	P-0022154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	41	618	0	ENST00000325455.5:c.877C>A	p.Arg293Ser	p.R293S	ENST00000325455	NM_001202474.3	293	Cgc/Agc	1/8	0.516482585774713	2	FACETS	0.867	0.731	1	0.433	0.365	0.507	CLONAL	1	TRUE	0	0.514142258201987	2		618	184	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591247	67591247	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0022166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	296	465	1	ENST00000274335.5:c.1746-1G>T		p.X582_splice	ENST00000274335		582			0.780863552806389	4	FACETS	0.865	0.819	0.913	0.865	0.819	0.913	CLONAL	2	TRUE	2	0.790010206087942	4		466	775	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128482	30128482	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	216	644	0	ENST00000263025.4:c.900C>G	p.Asp300Glu	p.D300E	ENST00000263025	NM_002746.2	300	gaC/gaG	6/9	0.727832655792025	4	FACETS	1	0.931	1			1	CLONAL	1	TRUE	NA	0.790010206087942	4		644	978	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245586	41245587	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs80357522	NA	P-0022166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	438	827	5	ENST00000357654.3:c.1961dup	p.Tyr655ValfsTer18	p.Y655Vfs*18	ENST00000357654	NM_007294.3	654	aag/aaAg	10/23	0.730944677214416	5	FACETS	0.792	0.754	0.83	0.528	0.503	0.554	SUBCLONAL	2	TRUE	2	0.790010206087942	5		832	1530	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216703	7216704	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	311	547	0	ENST00000380728.2:c.719dup	p.Thr241AspfsTer20	p.T241Dfs*20	ENST00000380728		240	cag/caAg	8/11	NA	2	FACETS	0.916	0.882	0.948			1	INDETERMINATE	2	TRUE	NA	0.790010206087942	2		547	430	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798830	42798830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	243	858	0	ENST00000575354.2:c.4402G>A	p.Asp1468Asn	p.D1468N	ENST00000575354	NM_015125.3	1468	Gac/Aac	19/20	0.740359458230737	3	FACETS	0.914	0.855	0.975	0.457	0.427	0.488	CLONAL	1	TRUE	1	0.790010206087942	3		858	939	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389324	8389324	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	260	854	0	ENST00000356435.5:c.4294C>G	p.Leu1432Val	p.L1432V	ENST00000356435		1432	Ctc/Gtc	26/35	0.773550115651989	2	FACETS	0.94	0.886	0.996	0.47	0.443	0.498	CLONAL	1	TRUE	0	0.790010206087942	2		854	700	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793663	NA	P-0022167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	54	822	0	ENST00000263967.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000263967	NM_006218.2	93	cGg/cAg	2/21	0.571879003535786	5	FACETS	0.442	0.376	0.514	0.088	0.075	0.103	SUBCLONAL	1	FALSE	0	0.571879003535786	5		822	794	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0022167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	301	497	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.571879003535786	5	FACETS	0.954	0.919	0.987	0.954	0.919	0.987	CLONAL	5	FALSE	0	0.571879003535786	5		497	410	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0022167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	361	550	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	0.571879003535786	5	FACETS	1	0.982	1	1	0.982	1	CLONAL	5	FALSE	0	0.571879003535786	5		550	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0022170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	115	737	2	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	0.280809507883098	2		739	586	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359410	118359410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	34	486	0	ENST00000534358.1:c.4414G>A	p.Glu1472Lys	p.E1472K	ENST00000534358	NM_005933.3	1472	Gaa/Aaa	11/36	1	2	FACETS	0.398	0.324	0.482	0.398	0.324	0.482	SUBCLONAL	1	TRUE	1	0.280809507883098	2		486	608	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3795345	3795345	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	22	491	0	ENST00000262367.5:c.3847T>C	p.Cys1283Arg	p.C1283R	ENST00000262367	NM_004380.2	1283	Tgc/Cgc	22/31	0.150186685293872	0	FACETS	0.261	0.202	0.331			1	INDETERMINATE	1	TRUE	0	0.280809507883098	0		491	431	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22008806	22008807	+	missense_variant	Missense_Mutation	DNP	GC	GC	AG	novel	NA	P-0022170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	28	387	1	ENST00000276925.6:c.146_147delinsCT	p.Arg49Pro	p.R49P	ENST00000276925	NM_004936.3	49	cGC/cCT	1/2	0.280809507883098	3	FACETS	0.457	0.364	0.563			1	SUBCLONAL	1	TRUE	NA	0.280809507883098	3		388	498	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912664	NA	P-0022173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	422	749	1	ENST00000269305.4:c.1010G>C	p.Arg337Pro	p.R337P	ENST00000269305	NM_001126112.2	337	cGc/cCc	10/11	0.873763151626499	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.873763151626499	1		750	536	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941720	48941720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	122	441	0	ENST00000267163.4:c.1030C>T	p.Gln344Ter	p.Q344*	ENST00000267163	NM_000321.2	344	Cag/Tag	10/27	0.873763151626499	1	FACETS	0.983	0.929	1	0.983	0.929	1	CLONAL	1	TRUE	0	0.873763151626499	1		441	160	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641487	23641487	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1462734899	NA	P-0022173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	345	774	0	ENST00000261584.4:c.1988G>A	p.Arg663His	p.R663H	ENST00000261584	NM_024675.3	663	cGc/cAc	5/13	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.873763151626499	2		774	722	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937905	36937905	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	544	901	1	ENST00000361632.4:c.931C>A	p.Arg311Ser	p.R311S	ENST00000361632		311	Cgc/Agc	7/16	1	2	FACETS	0.953	0.916	0.99	0.953	0.916	0.99	CLONAL	1	TRUE	1	0.873763151626499	2		902	1307	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650671	18650671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	107	458	0	ENST00000266497.5:c.2882G>T	p.Gly961Val	p.G961V	ENST00000266497		961	gGa/gTa	20/31	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.873763151626499	2		458	238	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779355	3779355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1383477288	NA	P-0022173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	439	767	0	ENST00000262367.5:c.5693G>A	p.Ser1898Asn	p.S1898N	ENST00000262367	NM_004380.2	1898	aGc/aAc	31/31	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.873763151626499	2		767	979	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788656	3788656	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	49	431	0	ENST00000262367.5:c.4298A>T	p.Tyr1433Phe	p.Y1433F	ENST00000262367	NM_004380.2	1433	tAt/tTt	26/31	NA	2	FACETS	0.18	0.152	0.211			1	INDETERMINATE	1	TRUE	NA	0.873763151626499	2		431	623	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783617	50783617	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0022173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	75	485	0	ENST00000398568.2:c.8C>G	p.Ser3Ter	p.S3*	ENST00000398568	NM_001042412.1	3	tCa/tGa	3/18	0.873763151626499	1	FACETS	0.488	0.436	0.542	0.488	0.436	0.542	SUBCLONAL	1	TRUE	0	0.873763151626499	1		485	198	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78931452	78931452	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	457	719	1	ENST00000306801.3:c.3399G>T	p.Gln1133His	p.Q1133H	ENST00000306801	NM_020761.2	1133	caG/caT	29/34	1	2	FACETS	0.992	0.95	1	0.992	0.95	1	CLONAL	1	TRUE	1	0.873763151626499	2		720	1055	SUCCESS
ALK	238	MSKCC	GRCh37	2	29436902	29436902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771475772	NA	P-0022173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	64	617	3	ENST00000389048.3:c.3691C>T	p.Arg1231Trp	p.R1231W	ENST00000389048	NM_004304.4	1231	Cgg/Tgg	24/29	1	2	FACETS	0.144	0.124	0.166	0.144	0.124	0.166	SUBCLONAL	1	TRUE	1	0.873763151626499	2		620	1017	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445228	29445228	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	499	767	0	ENST00000389048.3:c.3497T>A	p.Met1166Lys	p.M1166K	ENST00000389048	NM_004304.4	1166	aTg/aAg	22/29	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.873763151626499	2		767	1096	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212615430	212615430	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0022173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	244	504	0	ENST00000342788.4:c.557-1G>T		p.X186_splice	ENST00000342788	NM_005235.2	186			1	2	FACETS	0.975	0.919	1	0.975	0.919	1	CLONAL	1	TRUE	1	0.873763151626499	2		504	573	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217400	123217400	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0022173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	193	249	0	ENST00000218089.9:c.3053+1G>A		p.X1018_splice	ENST00000218089	NM_001042749.1	1018			1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.873763151626499	1		249	216	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0022176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	133	435	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	0.854871317383565	2		436	303	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578179	7578179	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	615	866	0	ENST00000269305.4:c.670G>T	p.Glu224Ter	p.E224*	ENST00000269305	NM_001126112.2	224	Gag/Tag	6/11	0.827079800696652	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.854871317383565	2		866	691	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937602	76937602	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	157	269	0	ENST00000373344.5:c.3146del	p.Ile1049LysfsTer69	p.I1049Kfs*69	ENST00000373344	NM_000489.3	1049	aTa/aa	9/35	1	1	FACETS	0.96	0.911	1	0.96	0.911	1	CLONAL	1	TRUE	0	0.854871317383565	1		269	219	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643360	52643360	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	32	753	0	ENST00000394830.3:c.2536G>T	p.Glu846Ter	p.E846*	ENST00000394830	NM_018313.4	846	Gaa/Taa	17/30	0.620073560649405	1	FACETS	0.102	0.082	0.124	0.102	0.082	0.124	SUBCLONAL	1	TRUE	0	0.854871317383565	1		753	420	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0022176-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	131	435	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.225694647035706	1	FACETS	0.992	0.912	1	1	0.993	1	CLONAL	3	FALSE	0	0.225656885438088	1		436	346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578179	7578179	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022176-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	757	866	0	ENST00000269305.4:c.670G>T	p.Glu224Ter	p.E224*	ENST00000269305	NM_001126112.2	224	Gag/Tag	6/11	0.225694647035706	2	FACETS	1	0.985	1	1	0.999	1	CLONAL	7	FALSE	0	0.225656885438088	2		866	953	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937602	76937602	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022176-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	136	269	0	ENST00000373344.5:c.3146del	p.Ile1049LysfsTer69	p.I1049Kfs*69	ENST00000373344	NM_000489.3	1049	aTa/aa	9/35	1	1	FACETS	1	0.977	1	1	0.994	1	CLONAL	5	FALSE	0	0.225656885438088	1		269	198	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613069	52613069	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0022176-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	19	442	1	ENST00000394830.3:c.3458+1G>A		p.X1153_splice	ENST00000394830	NM_018313.4	1153			0.225694647035706	0	FACETS	0.425	0.322	0.545			1	SUBCLONAL	1	FALSE	0	0.225656885438088	0		443	307	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643801	52644823	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCAGATAGTAGTCAGGCAACTCAGATCTAGAGGGAAGCCTCAGAAATATGGCACTGAGGCGGCGACCCCTCTTATCAGTATAGTTCTTTACAGCTTCATAGACCTCATTTAGTTTCTGCTGCATTGGAGTCATGTATTTTGATTTTTTAGGAGAAATGCCACTCTTCCTACCTAAAGAGAGATATTTAATGTTAAATGAATAAAATAAATGAACCTAAATTTGTATACAGATGGTAGCATAACCACAAGGGACGATTCCAAGTAATTTGTAAAATCTAGCAATTAGCATGTCTATAGTGAAATATAACCTGCAGACAAAAAAGTACTAAAAATTTTTTTTAACTGTTTTCAGTAATTATATTTTTGATGGGAGACTACTGTAAGGTTGAGAAAGCTGTGAATAAGAAGGAATAAAGCAAATGAGTAGCTATGTGACATTCTATCACCTCTGGTATCCTGGAGAACTGAGATTTTCATCATGGGATAAAAAGAGATAACGGATGTTAAAACGTAGGACATTAATAATTACCTTGAGGCCTTTAATCTCAATTGAAAGTATCACTATGAACTTATGATGTAATTTATCTTTAAATATAAACATACAAACAAACACACAAATTTCCTAGCTCTGTCCACTGAAAATCGTACAAACAATGACTACCTCAGTAGCAGTATAGCCCACATTAGAGTTTTAAAATACTAATTCCAAATAGTAATGTTGAGGAGCCCTCACCTTTCAGCAGAAACATGAAAAAGGTAGGGCTCCTTGGTAAATGGCTGATTCCCAGTCTGGTATATCTTCAAACACTAGACAGTAAAGAATCTATCAATGACTTCTTACCATGACTTCATGTCAATAGAATATAGGAACCGGCTGGGCGTGGTGGCTCATGCCTGTAATCCCAACACTTTGGGAGGCCAAGGTGGGTGGATCACCTGAGGTCAGGAGTTCAAGATCAACCTGGCCAACATGGCGAAACCCTGTGTCCATTAAAAATACAAAAAATTAGCCGAGTGTGGTGG	TCAGATAGTAGTCAGGCAACTCAGATCTAGAGGGAAGCCTCAGAAATATGGCACTGAGGCGGCGACCCCTCTTATCAGTATAGTTCTTTACAGCTTCATAGACCTCATTTAGTTTCTGCTGCATTGGAGTCATGTATTTTGATTTTTTAGGAGAAATGCCACTCTTCCTACCTAAAGAGAGATATTTAATGTTAAATGAATAAAATAAATGAACCTAAATTTGTATACAGATGGTAGCATAACCACAAGGGACGATTCCAAGTAATTTGTAAAATCTAGCAATTAGCATGTCTATAGTGAAATATAACCTGCAGACAAAAAAGTACTAAAAATTTTTTTTAACTGTTTTCAGTAATTATATTTTTGATGGGAGACTACTGTAAGGTTGAGAAAGCTGTGAATAAGAAGGAATAAAGCAAATGAGTAGCTATGTGACATTCTATCACCTCTGGTATCCTGGAGAACTGAGATTTTCATCATGGGATAAAAAGAGATAACGGATGTTAAAACGTAGGACATTAATAATTACCTTGAGGCCTTTAATCTCAATTGAAAGTATCACTATGAACTTATGATGTAATTTATCTTTAAATATAAACATACAAACAAACACACAAATTTCCTAGCTCTGTCCACTGAAAATCGTACAAACAATGACTACCTCAGTAGCAGTATAGCCCACATTAGAGTTTTAAAATACTAATTCCAAATAGTAATGTTGAGGAGCCCTCACCTTTCAGCAGAAACATGAAAAAGGTAGGGCTCCTTGGTAAATGGCTGATTCCCAGTCTGGTATATCTTCAAACACTAGACAGTAAAGAATCTATCAATGACTTCTTACCATGACTTCATGTCAATAGAATATAGGAACCGGCTGGGCGTGGTGGCTCATGCCTGTAATCCCAACACTTTGGGAGGCCAAGGTGGGTGGATCACCTGAGGTCAGGAGTTCAAGATCAACCTGGCCAACATGGCGAAACCCTGTGTCCATTAAAAATACAAAAAATTAGCCGAGTGTGGTGG	-	novel	NA	P-0022176-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	66	855	0	ENST00000394830.3:c.1925-851_2096del		p.X642_splice	ENST00000394830	NM_018313.4	642		17/30	0.225694647035706	0	FACETS	1	0.904	1			1	CLONAL	1	FALSE	0	0.225656885438088	0		855	433	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712614	52712614	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0022176-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	52	567	0	ENST00000394830.3:c.139-1G>C		p.X47_splice	ENST00000394830	NM_018313.4	47			0.225694647035706	0	FACETS	1	0.931	1			1	CLONAL	1	FALSE	0	0.225656885438088	0		567	310	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0022177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	312	640	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.371032136147604	4	FACETS	1	0.975	1	1	0.995	1	CLONAL	3	FALSE	2	0.371032136147604	4		640	737	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0022182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	548	748	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.045843566109808	3	FACETS	0.872	0.847	0.895			1	INDETERMINATE	3	TRUE	NA	0.747730147548208	3		748	770	SUCCESS
BLM	641	MSKCC	GRCh37	15	91290720	91290720	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs139282091	NA	P-0022182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	84	489	0	ENST00000355112.3:c.98C>T	p.Ser33Leu	p.S33L	ENST00000355112	NM_000057.2	33	tCa/tTa	2/22	0.747730147548208	4	FACETS	0.708	0.626	0.794			1	SUBCLONAL	1	TRUE	NA	0.747730147548208	4		489	555	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161326601	161326601	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	179	511	0	ENST00000367975.2:c.376T>C	p.Tyr126His	p.Y126H	ENST00000367975	NM_003001.3	126	Tat/Cat	5/6	0.747730147548208	6	FACETS	1	0.952	1	0.262	0.241	0.284	CLONAL	1	TRUE	2	0.747730147548208	6		511	1141	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633221	3633221	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1595	153	990	0	ENST00000294008.3:c.5030C>G	p.Pro1677Arg	p.P1677R	ENST00000294008	NM_032444.2	1677	cCc/cGc	14/15	0.747730147548208	4	FACETS	0.409	0.372	0.448	0.205	0.186	0.224	SUBCLONAL	1	TRUE	2	0.747730147548208	4		990	1748	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78704358	78704358	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0022182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	147	359	0	ENST00000306801.3:c.508-2A>G		p.X170_splice	ENST00000306801	NM_020761.2	170			0.642566811892731	4	FACETS	0.82	0.749	0.895	0.41	0.374	0.448	CLONAL	1	TRUE	2	0.747730147548208	4		359	838	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874448	76874448	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0022182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	153	336	0	ENST00000373344.5:c.5274T>A	p.Tyr1758Ter	p.Y1758*	ENST00000373344	NM_000489.3	1758	taT/taA	21/35	0.612398533724775	4	FACETS	0.832	0.768	0.896	0.832	0.768	0.896	CLONAL	2	TRUE	2	0.747730147548208	4		336	430	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47088064	47088065	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	143	770	0	ENST00000409792.3:c.7010dup	p.Thr2338HisfsTer31	p.T2338Hfs*31	ENST00000409792	NM_014159.6	2337	ttc/ttTc	16/21	0.410394664267257	1	FACETS	0.825	0.757	0.896	0.825	0.757	0.896	CLONAL	1	TRUE	0	0.501946194634293	1		770	517	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711928	89711928	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554900593	NA	P-0022183-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	85	946	0	ENST00000371953.3:c.548del	p.Lys183ArgfsTer16	p.K183Rfs*16	ENST00000371953	NM_000314.4	182	ttA/tt	6/9	0.29597964773815	1	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	0	0.29597964773815	1		946	474	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47088064	47088065	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022183-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	108	770	0	ENST00000409792.3:c.7010dup	p.Thr2338HisfsTer31	p.T2338Hfs*31	ENST00000409792	NM_014159.6	2337	ttc/ttTc	16/21	0.29597964773815	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.29597964773815	1		770	529	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222508	157222508	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0022183-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	74	761	0	ENST00000346085.5:c.1777-2A>T		p.X593_splice	ENST00000346085	NM_020732.3	593			1	2	FACETS	0.899	0.788	1	0.899	0.788	1	CLONAL	1	TRUE	1	0.29597964773815	2		761	556	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894228	NA	P-0022188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	409	724	0	ENST00000451590.1:c.37G>C	p.Gly13Arg	p.G13R	ENST00000451590	NM_001130442.1	13	Ggt/Cgt	2/5	1	2	FACETS	0.897	0.855	0.94	0.897	0.855	0.94	CLONAL	1	TRUE	1	0.814013868919808	2		724	1120	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419989	41419989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	369	710	0	ENST00000373198.4:c.332G>A	p.Ser111Asn	p.S111N	ENST00000373198	NM_133170.3	111	aGc/aAc	3/32	1	2	FACETS	0.954	0.908	1	0.954	0.908	1	CLONAL	1	TRUE	1	0.814013868919808	2		710	950	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259516	+	missense_variant	Missense_Mutation	DNP	TG	TG	GT	rs1057519848	NA	P-0022193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	164	699	1	ENST00000275493.2:c.2573_2574delinsGT	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTG/cGT	21/28	0.214778694827967	4	FACETS	0.932	0.856	1	0.932	0.856	1	CLONAL	2	TRUE	2	0.25	4		700	880	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	31	445	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.505	0.407	0.616	0.505	0.407	0.616	SUBCLONAL	1	TRUE	1	0.23	2		445	534	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0022194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	54	520	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.779	0.665	0.904	0.779	0.665	0.904	CLONAL	1	TRUE	1	0.23	2		520	603	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450885	70450885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	42	680	0	ENST00000373644.4:c.5725C>T	p.Pro1909Ser	p.P1909S	ENST00000373644	NM_030625.2	1909	Cct/Tct	12/12	1	2	FACETS	0.507	0.422	0.601	0.507	0.422	0.601	SUBCLONAL	1	TRUE	1	0.23	2		680	721	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450901	70450901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	57	686	0	ENST00000373644.4:c.5741C>T	p.Ser1914Phe	p.S1914F	ENST00000373644	NM_030625.2	1914	tCt/tTt	12/12	1	2	FACETS	0.619	0.53	0.717	0.619	0.53	0.717	SUBCLONAL	1	TRUE	1	0.23	2		686	801	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451522	70451522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	112	997	1	ENST00000373644.4:c.6362C>T	p.Ser2121Phe	p.S2121F	ENST00000373644	NM_030625.2	2121	tCc/tTc	12/12	1	2	FACETS	0.86	0.771	0.954	0.86	0.771	0.954	CLONAL	1	TRUE	1	0.23	2		998	1133	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427746	49427746	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	113	882	2	ENST00000301067.7:c.10742T>G	p.Val3581Gly	p.V3581G	ENST00000301067	NM_003482.3	3581	gTc/gGc	39/54	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.23	2		884	938	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81927337	81927337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1164040767	NA	P-0022194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	51	939	0	ENST00000359376.3:c.1010G>A	p.Arg337Gln	p.R337Q	ENST00000359376	NM_002661.3	337	cGg/cAg	12/33	1	2	FACETS	0.445	0.376	0.52	0.445	0.376	0.52	SUBCLONAL	1	TRUE	1	0.23	2		939	997	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879598	37879599	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCG	novel	NA	P-0022194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	81	887	0	ENST00000269571.5:c.1973_1974insCCG	p.Val658_Val659insArg	p.V658_V659insR	ENST00000269571		658	gtg/gtCCGg	17/27	1	2	FACETS	0.641	0.563	0.725	0.641	0.563	0.725	SUBCLONAL	1	TRUE	1	0.23	2		887	1099	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211899	36211899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	101	1128	3	ENST00000222270.7:c.1656del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	550	gaC/ga	3/37	1	2	FACETS	0.671	0.598	0.75	0.671	0.598	0.75	SUBCLONAL	1	TRUE	1	0.23	2		1131	1308	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843243	128843243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173715127	NA	P-0022194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	74	964	1	ENST00000249373.3:c.350G>A	p.Arg117His	p.R117H	ENST00000249373	NM_005631.4	117	cGc/cAc	2/12	1	2	FACETS	0.688	0.601	0.783	0.688	0.601	0.783	SUBCLONAL	1	TRUE	1	0.23	2		965	935	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798755	135798755	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0022194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	46	451	0	ENST00000298552.3:c.488C>G	p.Ser163Ter	p.S163*	ENST00000298552	NM_001162426.1	163	tCa/tGa	6/23	1	2	FACETS	0.808	0.681	0.949	0.808	0.681	0.949	CLONAL	1	TRUE	1	0.23	2		451	495	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256670	16256670	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	134	553	1	ENST00000375759.3:c.3935A>T	p.Tyr1312Phe	p.Y1312F	ENST00000375759	NM_015001.2	1312	tAt/tTt	11/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.472256275789284	2		554	457	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827928	72827929	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	188	756	0	ENST00000268489.5:c.8652dup	p.Glu2885Ter	p.E2885*	ENST00000268489	NM_006885.3	2884	-/T	9/10	0.204573939134688	3	FACETS	1	0.986	1	0.633	0.586	0.681	INDETERMINATE	1	TRUE	1	0.472256275789284	3		756	778	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832341	72832341	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375134893	NA	P-0022197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	48	529	0	ENST00000268489.5:c.4240G>A	p.Glu1414Lys	p.E1414K	ENST00000268489	NM_006885.3	1414	Gaa/Aaa	9/10	0.204573939134688	3	FACETS	0.442	0.373	0.517	0.221	0.186	0.259	INDETERMINATE	1	TRUE	1	0.472256275789284	3		529	569	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	112	445	0				ENST00000310581	NM_198253.2	-/1132			0.208367352977012	1	FACETS	1	0.963	1	1	0.992	1	CLONAL	3	TRUE	0	0.209721623959826	1		445	289	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557629	95557629	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	389	792	0	ENST00000393063.1:c.5438A>G	p.Glu1813Gly	p.E1813G	ENST00000393063	NM_030621.3	1813	gAg/gGg	26/28	1	2	FACETS	1	0.985	1	1	0.997	1	CLONAL	4	TRUE	1	0.209721623959826	2		792	867	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190742	108190742	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1389038955	NA	P-0022199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	229	677	0	ENST00000278616.4:c.6409G>C	p.Asp2137His	p.D2137H	ENST00000278616	NM_000051.3	2137	Gac/Cac	44/63	1	2	FACETS	0.991	0.932	1	1	0.996	1	CLONAL	4	TRUE	1	0.209721623959826	2		677	551	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560495	95560495	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0022199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	265	556	0	ENST00000393063.1:c.5096-2A>G		p.X1699_splice	ENST00000393063	NM_030621.3	1699			1	2	FACETS	1	0.985	1	1	0.996	1	CLONAL	4	TRUE	1	0.209721623959826	2		556	568	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	201	549	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.307177104775755	4	FACETS	0.957	0.898	1	1	0.989	1	CLONAL	4	TRUE	1	0.307177104775754	4		549	447	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0022230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	80	422	1	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.201565190878233	3	FACETS	0.772	0.684	0.866	0.772	0.684	0.866	SUBCLONAL	2	TRUE	1	0.307177104775754	3		423	389	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0022230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	239	651	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.307177104775755	4	FACETS	0.994	0.933	1	0.994	0.933	1	CLONAL	3	TRUE	1	0.307177104775754	4		651	682	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0022230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	26	391	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	0.307177104775755	3	FACETS	0.552	0.437	0.683	0.276	0.218	0.342	SUBCLONAL	1	TRUE	1	0.307177104775754	3		391	354	SUCCESS
APC	324	MSKCC	GRCh37	5	112163696	112163697	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1131691555	NA	P-0022230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	67	453	0	ENST00000257430.4:c.1620dup	p.Gln541ThrfsTer19	p.Q541Tfs*19	ENST00000257430	NM_000038.5	540	tta/ttAa	13/16	0.201565190878233	3	FACETS	1	0.96	1	0.629	0.549	0.715	CLONAL	1	TRUE	1	0.307177104775754	3		453	400	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347217	70347217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338758	NA	P-0022230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	255	351	0	ENST00000374080.3:c.2881C>T	p.Arg961Trp	p.R961W	ENST00000374080		961	Cgg/Tgg	21/45	0.307177104775754	3	FACETS	1	0.972	1			1	CLONAL	4	TRUE	NA	0.307177104775754	3		351	463	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473704	67473704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1201995588	NA	P-0022230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	171	674	0	ENST00000327367.4:c.784G>A	p.Asp262Asn	p.D262N	ENST00000327367	NM_005902.3	262	Gac/Aac	6/9	0.280405615675037	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	1	0.307177104775754	3		674	615	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246078897	246078897	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145023938	NA	P-0022230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	193	698	2	ENST00000388985.4:c.748C>T	p.Arg250Trp	p.R250W	ENST00000388985		250	Cgg/Tgg	8/12	0.260377999087573	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	2	0.307177104775754	4		700	781	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375464	40375464	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs759250756	NA	P-0022230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	138	832	0	ENST00000293328.3:c.486A>T	p.Leu162Phe	p.L162F	ENST00000293328	NM_012448.3	162	ttA/ttT	5/19	0.280405615675037	3	FACETS	1	0.966	1	0.563	0.512	0.617	CLONAL	1	TRUE	1	0.307177104775754	3		832	920	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212611	36212611	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	231	959	0	ENST00000222270.7:c.2362G>T	p.Val788Leu	p.V788L	ENST00000222270	NM_014727.1	788	Gta/Tta	3/37	0.307177104775755	4	FACETS	0.979	0.913	1	0.653	0.609	0.698	CLONAL	2	TRUE	1	0.307177104775754	4		959	1004	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220868	36220868	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	22	181	0	ENST00000222270.7:c.4918C>T	p.Arg1640Cys	p.R1640C	ENST00000222270	NM_014727.1	1640	Cgc/Tgc	23/37	0.307177104775755	4	FACETS	0.896	0.698	1	0.299	0.232	0.375	CLONAL	1	TRUE	1	0.307177104775754	4		181	209	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0022233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	495	654	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.884491948952804	2		654	1081	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0022236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	79	654	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.221292668244125	2		654	650	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0022236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	37	548	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.548	0.451	0.658	0.548	0.451	0.658	SUBCLONAL	1	TRUE	1	0.221292668244125	2		548	610	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928425	69928425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781567478	NA	P-0022236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	38	561	3	ENST00000352241.4:c.245C>T	p.Ala82Val	p.A82V	ENST00000352241	NM_198159.2	82	gCg/gTg	2/10	1	2	FACETS	0.543	0.447	0.649	0.543	0.447	0.649	SUBCLONAL	1	TRUE	1	0.221292668244125	2		564	633	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945061	31945061	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	63	694	1	ENST00000340398.3:c.40G>T	p.Gly14Trp	p.G14W	ENST00000340398	NM_001013699.2	14	Ggg/Tgg	1/1	0.128526857271915	3	FACETS	0.748	0.646	0.86	0.374	0.323	0.43	INDETERMINATE	1	TRUE	1	0.221292668244125	3		695	845	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557771	21557771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs575902148	NA	P-0022236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	87	719	2	ENST00000382592.4:c.2074G>A	p.Ala692Thr	p.A692T	ENST00000382592	NM_014572.2	692	Gcc/Acc	5/8	1	2	FACETS	0.951	0.841	1	0.951	0.841	1	CLONAL	1	TRUE	1	0.221292668244125	2		721	827	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354506	91354506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779179608	NA	P-0022236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	54	441	2	ENST00000355112.3:c.3946G>A	p.Asp1316Asn	p.D1316N	ENST00000355112	NM_000057.2	1316	Gac/Aac	21/22	0.128526857271915	3	FACETS	0.93	0.794	1	0.465	0.397	0.54	INDETERMINATE	1	TRUE	1	0.221292668244125	3		443	583	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359689	40359689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	46	709	0	ENST00000293328.3:c.1964C>T	p.Ser655Phe	p.S655F	ENST00000293328	NM_012448.3	655	tCc/tTc	16/19	0.128526857271915	3	FACETS	0.533	0.447	0.629	0.267	0.223	0.315	INDETERMINATE	1	TRUE	1	0.221292668244125	3		709	866	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0022243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	145	652	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.803	0.732	0.876	0.803	0.732	0.876	CLONAL	1	TRUE	1	0.415301566923101	2		652	870	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0022243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	126	550	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.995	0.903	1	0.995	0.903	1	CLONAL	1	TRUE	1	0.415301566923101	2		552	610	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479811	67479811	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500766	NA	P-0022243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	149	632	0	ENST00000327367.4:c.1118G>A	p.Arg373His	p.R373H	ENST00000327367	NM_005902.3	373	cGc/cAc	8/9	1	2	FACETS	0.809	0.739	0.882	0.809	0.739	0.882	CLONAL	1	TRUE	1	0.415301566923101	2		632	887	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0022243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	136	629	1	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.862	0.784	0.943	0.862	0.784	0.943	CLONAL	1	TRUE	1	0.415301566923101	2		630	760	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348280	89348280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371945379	NA	P-0022243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	266	1008	1	ENST00000301030.4:c.4670C>T	p.Pro1557Leu	p.P1557L	ENST00000301030	NM_001256183.1	1557	cCa/cTa	9/13	1	2	FACETS	0.917	0.858	0.978	0.917	0.858	0.978	CLONAL	1	TRUE	1	0.415301566923101	2		1009	1397	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174497	11174497	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	173	714	0	ENST00000361445.4:c.7178A>G	p.Asp2393Gly	p.D2393G	ENST00000361445	NM_004958.3	2393	gAt/gGt	53/58	1	2	FACETS	0.883	0.813	0.957	0.883	0.813	0.957	CLONAL	1	TRUE	1	0.415301566923101	2		714	943	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701201	43701202	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0022243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	143	721	0	ENST00000382044.4:c.5493_5494del	p.His1833CysfsTer5	p.H1833Cfs*5	ENST00000382044	NM_001141980.1	1831	gtGTct/gtct	26/28	1	2	FACETS	0.781	0.712	0.853	0.781	0.712	0.853	SUBCLONAL	1	TRUE	1	0.415301566923101	2		721	882	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647845	3647845	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761726340	NA	P-0022243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	248	786	0	ENST00000294008.3:c.1319C>T	p.Ala440Val	p.A440V	ENST00000294008	NM_032444.2	440	gCg/gTg	6/15	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.415301566923101	2		786	1102	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119955	70119955	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	104	432	1	ENST00000245479.2:c.957del	p.Tyr319Ter	p.Y319*	ENST00000245479	NM_000346.3	319	taC/ta	3/3	1	2	FACETS	0.886	0.796	0.982	0.886	0.796	0.982	CLONAL	1	TRUE	1	0.415301566923101	2		433	565	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375001	45375001	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	283	587	0	ENST00000262160.6:c.842A>T	p.Glu281Val	p.E281V	ENST00000262160	NM_005901.5	281	gAa/gTa	8/11	0.328854852683312	2	FACETS	0.972	0.919	1	0.972	0.919	1	CLONAL	2	TRUE	0	0.415301566923101	2		587	701	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858047	45858047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142568756	NA	P-0022243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	221	802	0	ENST00000391945.4:c.1606G>A	p.Val536Met	p.V536M	ENST00000391945	NM_000400.3	536	Gtg/Atg	17/23	1	2	FACETS	0.988	0.919	1	0.988	0.919	1	CLONAL	1	TRUE	1	0.415301566923101	2		802	1077	SUCCESS
APC	324	MSKCC	GRCh37	5	112175537	112175541	+	frameshift_variant	Frame_Shift_Del	DEL	GGCAT	GGCAT	ATTA	novel	NA	P-0022243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	96	414	3	ENST00000257430.4:c.4246_4250delinsATTA	p.Gly1416IlefsTer3	p.G1416Ifs*3	ENST00000257430	NM_000038.5	1416	GGCATt/ATTAt	16/16	0.390334975026961	1	FACETS	0.812	0.727	0.902	0.812	0.727	0.902	CLONAL	1	TRUE	0	0.415301566923101	1		417	451	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0022247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	161	693	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.198596730889057	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.18	3		693	802	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155357	99155357	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	40	443	2	ENST00000074304.5:c.583G>T	p.Val195Phe	p.V195F	ENST00000074304	NM_001134224.1	195	Gtt/Ttt	9/26	1	2	FACETS	0.86	0.714	1	0.86	0.714	1	CLONAL	1	TRUE	1	0.18	2		445	517	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520152	9520152	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	39	504	0	ENST00000353224.5:c.2117C>A	p.Pro706Gln	p.P706Q	ENST00000353224	NM_177990.2	706	cCg/cAg	10/10	1	2	FACETS	0.745	0.616	0.888	0.745	0.616	0.888	SUBCLONAL	1	TRUE	1	0.18	2		504	582	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041800	42041800	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	41	502	2	ENST00000219905.7:c.5995G>T	p.Glu1999Ter	p.E1999*	ENST00000219905	NM_001164273.1	1999	Gag/Tag	17/24	1	2	FACETS	0.781	0.65	0.928	0.781	0.65	0.928	CLONAL	1	TRUE	1	0.18	2		504	583	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741681	17741681	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	66	601	0	ENST00000250003.3:c.352G>T	p.Glu118Ter	p.E118*	ENST00000250003	NM_002478.4	118	Gag/Tag	1/3	1	2	FACETS	0.762	0.663	0.869	1	0.973	1	SUBCLONAL	2	TRUE	1	0.18	2		601	481	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141986	108141986	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660628	NA	P-0022247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	60	501	2	ENST00000278616.4:c.2930G>T	p.Cys977Phe	p.C977F	ENST00000278616	NM_000051.3	977	tGt/tTt	20/63	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.18	2		503	534	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831923	72831923	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	87	913	0	ENST00000268489.5:c.4658C>T	p.Ser1553Phe	p.S1553F	ENST00000268489	NM_006885.3	1553	tCt/tTt	9/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.18	2		913	870	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244877	41244877	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	58	686	0	ENST00000357654.3:c.2671T>A	p.Ser891Thr	p.S891T	ENST00000357654	NM_007294.3	891	Tcc/Acc	10/23	1	2	FACETS	0.847	0.726	0.979	0.847	0.726	0.979	CLONAL	1	TRUE	1	0.18	2		686	761	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247857	10247857	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	57	873	0	ENST00000340748.4:c.4345G>T	p.Gly1449Cys	p.G1449C	ENST00000340748		1449	Ggc/Tgc	36/40	0.136847506870606	1	FACETS	0.869	0.745	1	0.869	0.745	1	CLONAL	1	TRUE	0	0.18	1		873	663	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213999	36213999	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	71	850	1	ENST00000222270.7:c.2825G>T	p.Gly942Val	p.G942V	ENST00000222270	NM_014727.1	942	gGa/gTa	6/37	0.136847506870606	1	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	0	0.18	1		851	705	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713353	40713353	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	66	764	0	ENST00000373198.4:c.4162G>C	p.Gly1388Arg	p.G1388R	ENST00000373198	NM_133170.3	1388	Ggg/Cgg	30/32	1	2	FACETS	0.999	0.866	1	0.999	0.866	1	CLONAL	1	TRUE	1	0.18	2		764	734	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164234	47164234	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	49	474	0	ENST00000409792.3:c.1892A>T	p.Asp631Val	p.D631V	ENST00000409792	NM_014159.6	631	gAt/gTt	3/21	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.18	2		474	530	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409357	31409357	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	110	595	0	ENST00000344624.3:c.3750A>T	p.Lys1250Asn	p.K1250N	ENST00000344624		1250	aaA/aaT	29/33	0.198596730889057	3	FACETS	0.98	0.881	1	0.98	0.881	1	CLONAL	2	TRUE	1	0.18	3		595	680	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501467	149501467	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	65	826	2	ENST00000261799.4:c.2320C>A	p.Pro774Thr	p.P774T	ENST00000261799	NM_002609.3	774	Cct/Act	16/23	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.18	2		828	717	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339827	116339827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780740	NA	P-0022247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	40	588	1	ENST00000397752.3:c.689C>T	p.Thr230Met	p.T230M	ENST00000397752	NM_000245.2	230	aCg/aTg	2/21	1	2	FACETS	0.636	0.527	0.758	0.636	0.527	0.758	SUBCLONAL	1	TRUE	1	0.18	2		589	699	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760450	133760450	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	45	676	1	ENST00000318560.5:c.2773G>T	p.Glu925Ter	p.E925*	ENST00000318560	NM_005157.4	925	Gag/Tag	11/11	1	2	FACETS	0.998	0.839	1	0.998	0.839	1	CLONAL	1	TRUE	1	0.18	2		677	501	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955465	48955465	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0022248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	259	558	0	ENST00000267163.4:c.1585del	p.Tyr529ThrfsTer3	p.Y529Tfs*3	ENST00000267163	NM_000321.2	527	gaT/ga	17/27	0.901598523593466	1	FACETS	0.894	0.859	0.927	0.894	0.859	0.927	CLONAL	1	TRUE	0	0.901598523593466	1		558	353	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918600	94918604	+	frameshift_variant	Frame_Shift_Del	DEL	CACAG	CACAG	-	novel	NA	P-0022248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	315	693	0	ENST00000536441.1:c.578_582del	p.Ala193GlyfsTer16	p.A193Gfs*16	ENST00000536441	NM_144665.3	193	gCTGTG/g	5/10	1	2	FACETS	0.959	0.91	1	0.959	0.91	1	CLONAL	1	TRUE	1	0.901598523593466	2		693	729	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2114282	2114292	+	frameshift_variant	Frame_Shift_Del	DEL	ATTAACTCAGT	ATTAACTCAGT	-	novel	NA	P-0022248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	395	748	0	ENST00000219476.3:c.1453_1463del	p.Ile485GlyfsTer12	p.I485Gfs*12	ENST00000219476	NM_000548.3	485	ATTAACTCAGTg/g	15/42	0.901598523593466	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.901598523593466	1		748	477	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651692	48651692	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	491	756	0	ENST00000376670.3:c.858C>A	p.Tyr286Ter	p.Y286*	ENST00000376670	NM_002049.3	286	taC/taA	5/6	1	2	FACETS	0.988	0.949	1	0.988	0.949	1	CLONAL	1	TRUE	1	0.901598523593466	2		756	1102	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0022251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	58	649	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.213943511796194	3	FACETS	1	0.93	1	0.567	0.488	0.654	CLONAL	1	TRUE	1	0.213943511796194	3		649	529	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357575	70357575	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0022251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	77	672	1	ENST00000374080.3:c.5827-1G>T		p.X1943_splice	ENST00000374080		1943			0.213641505281755	1	FACETS	0.765	0.675	0.861	1	0.977	1	SUBCLONAL	2	TRUE	0	0.213943511796194	1		673	420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577107	7577107	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1057523347	NA	P-0022251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	91	672	0	ENST00000269305.4:c.831T>A	p.Cys277Ter	p.C277*	ENST00000269305	NM_001126112.2	277	tgT/tgA	8/11	0.213641505281755	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.213943511796194	1		672	566	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289116	33289116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	76	647	0	ENST00000374542.5:c.436G>A	p.Ala146Thr	p.A146T	ENST00000374542	NM_001141970.1	146	Gcc/Acc	3/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.213943511796194	2		647	552	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111080	193111080	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	41	366	0	ENST00000367435.3:c.613A>G	p.Ile205Val	p.I205V	ENST00000367435	NM_024529.4	205	Ata/Gta	7/17	0.162739131179285	3	FACETS	0.76	0.637	0.896	0.507	0.424	0.597	SUBCLONAL	2	TRUE	0	0.213943511796194	3		366	279	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983123	201983129	+	frameshift_variant	Frame_Shift_Del	DEL	GACCTAC	GACCTAC	-	novel	NA	P-0022251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	62	589	0	ENST00000359651.3:c.974_980del	p.Thr325ArgfsTer3	p.T325Rfs*3	ENST00000359651		324	atGACCTAC/at	7/8	0.162739131179285	3	FACETS	1	0.962	1	0.445	0.385	0.51	CLONAL	1	TRUE	0	0.213943511796194	3		589	481	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316109	14316109	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	21	341	0	ENST00000256196.4:c.316A>G	p.Lys106Glu	p.K106E	ENST00000256196		106	Aag/Gag	4/6	1	2	FACETS	0.654	0.504	0.829	0.654	0.504	0.829	SUBCLONAL	1	TRUE	1	0.213943511796194	2		341	300	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946469	71946469	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	71	687	2	ENST00000298229.2:c.2633G>T	p.Arg878Leu	p.R878L	ENST00000298229	NM_001567.3	878	cGc/cTc	23/28	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.213943511796194	2		689	491	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426489	49426489	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	60	858	1	ENST00000301067.7:c.11999G>T	p.Gly4000Val	p.G4000V	ENST00000301067	NM_003482.3	4000	gGc/gTc	39/54	0.213943511796194	3	FACETS	0.92	0.792	1	0.46	0.396	0.53	CLONAL	1	TRUE	1	0.213943511796194	3		859	675	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784012	120784012	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	64	713	0	ENST00000257552.2:c.973C>A	p.Gln325Lys	p.Q325K	ENST00000257552	NM_002442.3	325	Cag/Aag	13/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.213943511796194	2		713	458	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989179	41989179	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	62	695	0	ENST00000219905.7:c.1972del	p.Glu658LysfsTer17	p.E658Kfs*17	ENST00000219905	NM_001164273.1	657	ctG/ct	3/24	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.213943511796194	2		695	531	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233671	233671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	22	264	0	ENST00000264932.6:c.975G>T	p.Arg325Ser	p.R325S	ENST00000264932	NM_004168.2	325	agG/agT	8/15	0.213943511796194	3	FACETS	0.889	0.691	1	0.445	0.345	0.56	CLONAL	1	TRUE	1	0.213943511796194	3		264	256	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293894	1293894	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	42	879	0	ENST00000310581.5:c.1107G>T	p.Arg369Ser	p.R369S	ENST00000310581	NM_198253.2	369	agG/agT	2/16	0.213943511796194	3	FACETS	0.799	0.666	0.946	0.399	0.333	0.473	CLONAL	1	TRUE	1	0.213943511796194	3		879	544	SUCCESS
APC	324	MSKCC	GRCh37	5	112177569	112177569	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs876660816	NA	P-0022251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	26	407	0	ENST00000257430.4:c.6281del	p.Pro2094LeufsTer18	p.P2094Lfs*18	ENST00000257430	NM_000038.5	2093	tCc/tc	16/16	0.187777061653915	3	FACETS	0.706	0.559	0.875	0.353	0.279	0.438	SUBCLONAL	1	TRUE	1	0.213943511796194	3		407	381	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515423	149515423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	67	474	0	ENST00000261799.4:c.59C>T	p.Ser20Phe	p.S20F	ENST00000261799	NM_002609.3	20	tCt/tTt	3/23	0.187777061653915	3	FACETS	0.869	0.758	0.987	0.869	0.758	0.987	CLONAL	2	TRUE	1	0.213943511796194	3		474	399	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372431	55372431	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	51	778	0	ENST00000297316.4:c.1121A>T	p.Glu374Val	p.E374V	ENST00000297316	NM_022454.3	374	gAg/gTg	2/2	1	2	FACETS	0.9	0.765	1	0.9	0.765	1	CLONAL	1	TRUE	1	0.213943511796194	2		778	530	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56879407	56879410	+	missense_variant	Missense_Mutation	ONP	GGTC	GGTC	TTGT	novel	NA	P-0022251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	34	643	3	ENST00000519728.1:c.924_927delinsTTGT	p.Val309Cys	p.V309C	ENST00000519728	NM_002350.3	308	gtGGTC/gtTTGT	9/13	1	2	FACETS	0.545	0.444	0.659	0.545	0.444	0.659	SUBCLONAL	1	TRUE	1	0.213943511796194	2		646	583	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0022254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	68	649	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.218030844433744	1	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	0	0.246767677339538	1		649	476	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915115	131915115	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501980	NA	P-0022254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	76	615	0	ENST00000265335.6:c.472C>T	p.His158Tyr	p.H158Y	ENST00000265335		158	Cat/Tat	4/25	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.246767677339538	2		615	578	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981857	201981858	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0022254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	67	759	0	ENST00000359651.3:c.572dup	p.Gly192TrpfsTer4	p.G192Wfs*4	ENST00000359651		190	tcc/tCcc	4/8	1	2	FACETS	0.856	0.744	0.978	0.856	0.744	0.978	CLONAL	1	TRUE	1	0.246767677339538	2		759	634	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	218	445	0				ENST00000310581	NM_198253.2	-/1132			0.770356703227	3	FACETS	0.945	0.892	0.997	0.945	0.892	0.997	CLONAL	2	TRUE	1	0.770356703227	3		445	415	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0022256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	127	524	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.918	0.842	0.997	0.918	0.842	0.997	CLONAL	1	TRUE	1	0.770356703227	2		524	359	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644754	67644754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779609208	NA	P-0022256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	196	531	1	ENST00000264010.4:c.19G>A	p.Glu7Lys	p.E7K	ENST00000264010	NM_006565.3	7	Gaa/Aaa	3/12	0.439182424770868	1	FACETS	0.646	0.604	0.689	0.646	0.604	0.689	INDETERMINATE	1	TRUE	0	0.770356703227	1		532	484	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117319	115117319	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	163	447	0	ENST00000257566.3:c.855G>C	p.Gln285His	p.Q285H	ENST00000257566	NM_016569.3	285	caG/caC	4/8	1	2	FACETS	0.827	0.764	0.891	0.827	0.764	0.891	CLONAL	1	TRUE	1	0.770356703227	2		447	512	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446160	49446160	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776768333	NA	P-0022256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	238	685	1	ENST00000301067.7:c.1306G>A	p.Glu436Lys	p.E436K	ENST00000301067	NM_003482.3	436	Gag/Aag	10/54	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.770356703227	2		686	577	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052574	42052574	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	217	500	0	ENST00000219905.7:c.7245G>C	p.Gln2415His	p.Q2415H	ENST00000219905	NM_001164273.1	2415	caG/caC	20/24	0.439182424770868	1	FACETS	0.705	0.663	0.748	0.705	0.663	0.748	INDETERMINATE	1	TRUE	0	0.770356703227	1		500	491	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546098	29546098	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	123	521	0	ENST00000356175.3:c.1603C>G	p.Gln535Glu	p.Q535E	ENST00000356175	NM_000267.3	535	Cag/Gag	14/57	0.439182424770868	1	FACETS	0.41	0.373	0.449	0.41	0.373	0.449	INDETERMINATE	1	TRUE	0	0.770356703227	1		521	479	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540680	187540680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768285583	NA	P-0022256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	38	462	1	ENST00000441802.2:c.7060C>T	p.Arg2354Trp	p.R2354W	ENST00000441802	NM_005245.3	2354	Cgg/Tgg	10/27	1	2	FACETS	0.208	0.171	0.248	0.208	0.171	0.248	SUBCLONAL	1	TRUE	1	0.770356703227	2		463	475	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658409	117658409	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	255	656	0	ENST00000368508.3:c.5174A>G	p.Tyr1725Cys	p.Y1725C	ENST00000368508	NM_002944.2	1725	tAt/tGt	31/43	0.439182424770868	1	FACETS	0.754	0.713	0.795	0.754	0.713	0.795	INDETERMINATE	1	TRUE	0	0.770356703227	1		656	540	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738032	145738032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	41	746	0	ENST00000428558.2:c.2878G>A	p.Ala960Thr	p.A960T	ENST00000428558	NM_004260.3	960	Gcc/Acc	17/22	1	2	FACETS	0.184	0.153	0.219	0.184	0.153	0.219	SUBCLONAL	1	TRUE	1	0.770356703227	2		746	577	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781140	135781140	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs118203587	NA	P-0022256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	229	608	1	ENST00000298552.3:c.1825G>T	p.Glu609Ter	p.E609*	ENST00000298552	NM_001162426.1	609	Gag/Tag	15/23	0.770356703227	1	FACETS	0.887	0.841	0.933	0.887	0.841	0.933	CLONAL	1	TRUE	0	0.770356703227	1		609	412	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928846	44928846	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0022256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	148	198	0	ENST00000377967.4:c.1946C>G	p.Ser649Ter	p.S649*	ENST00000377967	NM_021140.2	649	tCa/tGa	17/29	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.770356703227	1		198	195	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473650	67473650	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	238	601	0	ENST00000327367.4:c.730del	p.Val244SerfsTer12	p.V244Sfs*12	ENST00000327367	NM_005902.3	244	Gtc/tc	6/9	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.628897920262533	2		601	695	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349958	15349958	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	207	497	0	ENST00000263377.2:c.3694C>T	p.Arg1232Trp	p.R1232W	ENST00000263377	NM_058243.2	1232	Cgg/Tgg	18/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.628897920262533	2		497	631	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38137066	38137066	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	192	495	0	ENST00000317025.8:c.3752T>G	p.Ile1251Ser	p.I1251S	ENST00000317025	NM_023034.1	1251	aTt/aGt	21/24	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.628897920262533	2		495	540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0022284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	309	742	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.552660206405584	1	FACETS	0.941	0.89	0.992	0.941	0.89	0.992	CLONAL	1	TRUE	0	0.552660206405584	1		742	860	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0022284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	293	841	1	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	0.295846607840097	1	FACETS	0.821	0.774	0.868	0.821	0.774	0.868	INDETERMINATE	1	TRUE	0	0.552660206405584	1		842	935	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0022284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	237	795	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.295846607840097	1	FACETS	0.824	0.772	0.878	0.824	0.772	0.878	INDETERMINATE	1	TRUE	0	0.552660206405584	1		795	753	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247168	153247168	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1560758208	NA	P-0022284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	88	325	0	ENST00000281708.4:c.1634A>G	p.Tyr545Cys	p.Y545C	ENST00000281708	NM_033632.3	545	tAt/tGt	10/12	0.116837471754568	0	FACETS	0.454	0.406	0.504			1	INDETERMINATE	1	TRUE	0	0.552660206405584	0		325	314	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106467	27106467	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	228	600	0	ENST00000324856.7:c.6079del	p.Ala2027HisfsTer3	p.A2027Hfs*3	ENST00000324856	NM_006015.4	2026	caG/ca	20/20	0.295846607840097	1	FACETS	0.824	0.771	0.878	0.824	0.771	0.878	INDETERMINATE	1	TRUE	0	0.552660206405584	1		600	725	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457283	89457283	+	splice_donor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0022284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	85	458	0	ENST00000336596.2:c.1762+2del		p.X588_splice	ENST00000336596	NM_005233.5	588			0.295846607840097	1	FACETS	0.88	0.789	0.973	0.88	0.789	0.973	INDETERMINATE	1	TRUE	0	0.552660206405584	1		458	253	SUCCESS
APC	324	MSKCC	GRCh37	5	112155044	112155044	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	T	novel	NA	P-0022284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	185	437	0	ENST00000257430.4:c.1312+3A>T		p.X438_splice	ENST00000257430	NM_000038.5	438			0.384783201644512	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.552660206405584	1		437	440	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413565	32413565	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121907903	NA	P-0022285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	9	529	1	ENST00000332351.3:c.1385G>A	p.Arg462Gln	p.R462Q	ENST00000332351	NM_024426.4	462	cGg/cAg	9/10	1	2	FACETS	0.416	0.274	0.598	0.416	0.274	0.598	SUBCLONAL	1	TRUE	1	0.13	2		530	333	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0022287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	36	701	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.995	0.82	1	0.995	0.82	1	CLONAL	1	TRUE	1	0.22	2		701	329	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913355	NA	P-0022287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	18	559	0	ENST00000288602.6:c.1406G>T	p.Gly469Val	p.G469V	ENST00000288602	NM_004333.4	469	gGa/gTa	11/18	0.27108288172973	3	FACETS	0.993	0.751	1	0.496	0.375	0.638	CLONAL	1	TRUE	1	0.22	3		559	183	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031697	36031697	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	59	958	1	ENST00000358208.4:c.1526G>A	p.Arg509Gln	p.R509Q	ENST00000358208		509	cGg/cAg	12/12	1	2	FACETS	0.941	0.81	1	0.941	0.81	1	CLONAL	1	TRUE	1	0.22	2		959	570	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653032	29653037	+	inframe_deletion	In_Frame_Del	DEL	TCTATA	TCTATA	-	rs1135402868	NA	P-0022287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	23	506	0	ENST00000356175.3:c.4973_4978del	p.Ile1658_Tyr1659del	p.I1658_Y1659del	ENST00000356175	NM_000267.3	1656	gTCTATAtc/gtc	36/57	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.22	2		506	184	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975675	26975675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	18	540	0	ENST00000381527.3:c.1183C>T	p.His395Tyr	p.H395Y	ENST00000381527	NM_001260.1	395	Cac/Tac	12/13	1	2	FACETS	0.599	0.451	0.774	0.599	0.451	0.774	SUBCLONAL	1	TRUE	1	0.22	2		540	273	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56875732	56875732	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	55	632	0	ENST00000308159.5:c.2336A>T	p.Glu779Val	p.E779V	ENST00000308159	NM_014669.4	779	gAg/gTg	21/22	0.135518217803496	3	FACETS	1	0.959	1	0.675	0.579	0.78	CLONAL	1	TRUE	1	0.22	3		632	411	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0022288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	135	382	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.192191974457938	4	FACETS	0.968	0.886	1	0.968	0.886	1	CLONAL	3	FALSE	1	0.240181487110969	4		382	480	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0022288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	124	591	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.240181487110969	2		591	784	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999656	100999656	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	64	1050	0	ENST00000325455.5:c.146C>G	p.Ser49Trp	p.S49W	ENST00000325455	NM_001202474.3	49	tCg/tGg	1/8	1	2	FACETS	0.465	0.401	0.535	0.465	0.401	0.535	SUBCLONAL	1	FALSE	1	0.240181487110969	2		1050	1146	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307526	118307526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	58	768	0	ENST00000534358.1:c.299C>T	p.Ser100Phe	p.S100F	ENST00000534358	NM_005933.3	100	tCt/tTt	1/36	1	2	FACETS	0.543	0.465	0.629	0.543	0.465	0.629	SUBCLONAL	1	FALSE	1	0.240181487110969	2		768	889	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112608	115112608	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	57	843	0	ENST00000257566.3:c.1132G>T	p.Glu378Ter	p.E378*	ENST00000257566	NM_016569.3	378	Gag/Tag	7/8	1	2	FACETS	0.464	0.396	0.538	0.464	0.396	0.538	SUBCLONAL	1	FALSE	1	0.240181487110969	2		843	1023	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577126	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-	novel	NA	P-0022288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	216	724	1	ENST00000269305.4:c.812_814del	p.Glu271del	p.E271del	ENST00000269305	NM_001126112.2	271	gAGGtg/gtg	8/11	0.231335268092851	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	FALSE	0	0.240181487110969	2		725	864	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068079	94068079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375147203	NA	P-0022288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	33	435	0	ENST00000369303.4:c.883C>T	p.Arg295Cys	p.R295C	ENST00000369303	NM_004440.3	295	Cgt/Tgt	4/17	1	2	FACETS	0.553	0.45	0.67	0.553	0.45	0.67	SUBCLONAL	1	FALSE	1	0.240181487110969	2		435	497	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0022291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	165	435	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.472716204350888	3	FACETS	1	0.988	1	0.832	0.781	0.883	CLONAL	2	TRUE	0	0.584969364879219	3		435	292	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220578	1220578	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0022291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	261	696	1	ENST00000326873.7:c.598-2A>T		p.X200_splice	ENST00000326873	NM_000455.4	200			0.521813954068358	2	FACETS	0.813	0.769	0.856	0.813	0.769	0.856	CLONAL	2	TRUE	0	0.584969364879219	2		697	549	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781380	135781380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751125011	NA	P-0022291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	149	568	1	ENST00000298552.3:c.1585G>A	p.Ala529Thr	p.A529T	ENST00000298552	NM_001162426.1	529	Gcc/Acc	15/23	0.509205552094588	2	FACETS	0.925	0.849	1	0.462	0.424	0.502	CLONAL	1	TRUE	0	0.584969364879219	2		569	551	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36826887	36826887	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	326	754	0	ENST00000373129.3:c.47G>T	p.Arg16Met	p.R16M	ENST00000373129	NM_032017.1	16	aGg/aTg	3/12	0.302988183942754	3	FACETS	1	0.966	1	0.679	0.646	0.712	INDETERMINATE	2	TRUE	0	0.584969364879219	3		754	707	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651643	206651643	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	176	801	0	ENST00000367120.3:c.953A>T	p.Gln318Leu	p.Q318L	ENST00000367120	NM_014002.3	318	cAg/cTg	9/22	0.322912800002536	5	FACETS	1	0.969	1	0.368	0.338	0.399	INDETERMINATE	1	TRUE	2	0.584969364879219	5		801	1024	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186757	108186757	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs864622251	NA	P-0022291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	42	468	0	ENST00000278616.4:c.6115G>T	p.Glu2039Ter	p.E2039*	ENST00000278616	NM_000051.3	2039	Gaa/Taa	42/63	0.421897110730101	4	FACETS	0.389	0.324	0.461	0.097	0.081	0.116	SUBCLONAL	1	TRUE	0	0.584969364879219	4		468	585	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218027	108218027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555139531	NA	P-0022291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	116	375	0	ENST00000278616.4:c.8606G>A	p.Gly2869Asp	p.G2869D	ENST00000278616	NM_000051.3	2869	gGt/gAt	59/63	0.421897110730101	4	FACETS	1	0.948	1	0.77	0.714	0.826	CLONAL	3	TRUE	0	0.584969364879219	4		375	204	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302935	15302936	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0022291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	358	879	1	ENST00000263388.2:c.514_515delinsTT	p.Gly172Phe	p.G172F	ENST00000263388	NM_000435.2	172	GGc/TTc	4/33	0.521813954068358	2	FACETS	0.893	0.854	0.932	0.893	0.854	0.932	CLONAL	2	TRUE	0	0.584969364879219	2		880	685	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388732	31388732	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0022291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	119	528	0	ENST00000328111.2:c.1996+1G>A		p.X666_splice	ENST00000328111	NM_006892.3	666			0.559765932956454	3	FACETS	0.947	0.858	1	0.474	0.429	0.521	CLONAL	1	TRUE	1	0.584969364879219	3		528	555	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0022292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	17	693	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.262918257483986	4	FACETS	0.133	0.099	0.175	0.067	0.049	0.088	INDETERMINATE	1	TRUE	2	0.52	4		693	745	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523109	25523109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781524740	NA	P-0022305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	88	599	0	ENST00000264709.3:c.76G>A	p.Gly26Arg	p.G26R	ENST00000264709	NM_175629.2	26	Gga/Aga	3/23	1	2	FACETS	0.997	0.886	1	0.997	0.886	1	CLONAL	1	TRUE	1	0.341288964622208	2		599	517	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627721	14627722	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1239666815	NA	P-0022305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	112	619	0	ENST00000254322.2:c.348dup	p.Gly117TrpfsTer12	p.G117Wfs*12	ENST00000254322	NM_006145.1	116	-/T	2/3	1	2	FACETS	0.985	0.888	1	0.985	0.888	1	CLONAL	1	TRUE	1	0.341288964622208	2		619	666	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277963	41277966	+	frameshift_variant	Frame_Shift_Del	DEL	TTAC	TTAC	-	novel	NA	P-0022305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	66	367	0	ENST00000349496.5:c.1929_1932del	p.Leu643PhefsTer35	p.L643Ffs*35	ENST00000349496	NM_001904.3	643	TTACtt/tt	12/15	1	2	FACETS	0.962	0.839	1	0.962	0.839	1	CLONAL	1	TRUE	1	0.341288964622208	2		367	402	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591085	67591085	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519839	NA	P-0022306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	41	284	0	ENST00000274335.5:c.1678G>T	p.Asp560Tyr	p.D560Y	ENST00000274335		560	Gac/Tac	12/15	0.646620605391538	1	FACETS	0.913	0.788	1	0.913	0.788	1	CLONAL	1	TRUE	0	0.646620605391538	1		284	94	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244157	41244157	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	96	642	0	ENST00000357654.3:c.3391G>C	p.Asp1131His	p.D1131H	ENST00000357654	NM_007294.3	1131	Gat/Cat	10/23	0.516574501119102	4	FACETS	0.992	0.887	1	0.248	0.221	0.276	CLONAL	1	TRUE	0	0.646620605391538	4		642	493	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533893	533893	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	190	771	0	ENST00000451590.1:c.163A>G	p.Ile55Val	p.I55V	ENST00000451590	NM_001130442.1	55	Atc/Gtc	3/5	0.311281246832616	3	FACETS	0.918	0.85	0.989	0.306	0.283	0.33	INDETERMINATE	1	TRUE	0	0.646620605391538	3		771	847	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503201	125503201	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	162	349	0	ENST00000428830.2:c.568G>C	p.Asp190His	p.D190H	ENST00000428830	NM_001114121.2	190	Gat/Cat	6/14	0.500133241238297	5	FACETS	1	0.982	1			1	CLONAL	2	TRUE	NA	0.646620605391538	5		349	416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579353	7579363	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGACGGAAA	CCAGACGGAAA	GTTT	novel	NA	P-0022306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	624	784	2	ENST00000269305.4:c.324_334delinsAAAC	p.Phe109AsnfsTer12	p.F109Nfs*12	ENST00000269305	NM_001126112.2	108	ggTTTCCGTCTGGgc/ggAAACgc	4/11	0.516574501119102	4	FACETS	1	0.99	1	0.784	0.76	0.807	CLONAL	3	TRUE	0	0.646620605391538	4		786	1014	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215926	142215926	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	107	545	0	ENST00000350721.4:c.5667G>T	p.Met1889Ile	p.M1889I	ENST00000350721	NM_001184.3	1889	atG/atT	33/47	0.524645497889001	6	FACETS	1	0.976	1	0.215	0.193	0.238	CLONAL	1	TRUE	0	0.646620605391538	6		545	588	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471015	8471015	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	60	527	0	ENST00000356435.5:c.3484G>T	p.Asp1162Tyr	p.D1162Y	ENST00000356435		1162	Gat/Tat	20/35	0.309295867231729	5	FACETS	0.862	0.745	0.989	0.287	0.248	0.33	INDETERMINATE	1	TRUE	2	0.646620605391538	5		527	424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577519	7577527	+	inframe_deletion	In_Frame_Del	DEL	GATGGTGAG	GATGGTGAG	-	novel	NA	P-0022321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	381	769	1	ENST00000269305.4:c.754_762del	p.Leu252_Ile254del	p.L252_I254del	ENST00000269305	NM_001126112.2	252	CTCACCATC/-	7/11	0.691603879196025	2	FACETS	0.92	0.885	0.953	0.92	0.885	0.953	CLONAL	2	TRUE	0	0.691603879196025	2		770	599	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475641	40475641	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs769706649	NA	P-0022326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	96	481	0	ENST00000264657.5:c.1603C>T	p.Pro535Ser	p.P535S	ENST00000264657	NM_139276.2	535	Cct/Tct	18/24	0.529449131310178	3	FACETS	0.8	0.715	0.891	0.4	0.357	0.446	SUBCLONAL	1	TRUE	1	0.552666365598387	3		481	554	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349750	15349750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	147	719	0	ENST00000263377.2:c.3824C>T	p.Ala1275Val	p.A1275V	ENST00000263377	NM_058243.2	1275	gCc/gTc	19/20	0.141832817164426	3	FACETS	0.877	0.802	0.956	0.292	0.267	0.319	INDETERMINATE	1	TRUE	0	0.552666365598387	3		719	774	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023092	150023092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	128	688	1	ENST00000253339.5:c.171G>A	p.Met57Ile	p.M57I	ENST00000253339		57	atG/atA	1/7	0.496231934435178	3	FACETS	0.728	0.66	0.8	0.364	0.33	0.4	SUBCLONAL	1	TRUE	1	0.552666365598387	3		689	812	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215352	123215353	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0022326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	131	304	0	ENST00000218089.9:c.2898_2899del	p.Glu968SerfsTer15	p.E968Sfs*15	ENST00000218089	NM_001042749.1	966	acAAga/acga	28/35	0.483275159070421	2	FACETS	1	0.936	1			1	CLONAL	1	TRUE	NA	0.552666365598387	2		304	461	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888873	76888873	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0022327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	431	339	0	ENST00000373344.5:c.4957-1G>A		p.X1653_splice	ENST00000373344	NM_000489.3	1653			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		339	502	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015094	37015094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	25	812	1	ENST00000358127.4:c.310C>T	p.Arg104Cys	p.R104C	ENST00000358127	NM_001280556.1	104	Cgc/Tgc	3/10	1	2	FACETS	0.509	0.4	0.635	0.509	0.4	0.635	SUBCLONAL	1	TRUE	1	0.2	2		813	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0022330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	48	749	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.2	2		749	466	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879646	151879646	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0022330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	25	254	0	ENST00000262189.6:c.5299del	p.Ile1767LeufsTer10	p.I1767Lfs*10	ENST00000262189	NM_170606.2	1767	Att/tt	36/59	1	2	FACETS	0.988	0.781	1	0.988	0.781	1	CLONAL	1	TRUE	1	0.2	2		254	253	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	268	549	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.588436507220663	3	FACETS	0.945	0.894	0.996	0.945	0.894	0.996	CLONAL	2	TRUE	1	0.624320482960905	3		549	596	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1131691023	NA	P-0022337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	50	895	0	ENST00000269305.4:c.470T>C	p.Val157Ala	p.V157A	ENST00000269305	NM_001126112.2	157	gTc/gCc	5/11	0.624320482960905	1	FACETS	0.24	0.203	0.279	0.24	0.203	0.279	SUBCLONAL	1	TRUE	0	0.624320482960905	1		895	460	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984825	72984825	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	141	663	0	ENST00000268489.5:c.2759G>A	p.Gly920Glu	p.G920E	ENST00000268489	NM_006885.3	920	gGg/gAg	3/10	1	2	FACETS	0.859	0.787	0.933	0.859	0.787	0.933	CLONAL	1	TRUE	1	0.624320482960905	2		663	526	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894230	NA	P-0022338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	2397	724	0	ENST00000451590.1:c.35G>A	p.Gly12Asp	p.G12D	ENST00000451590	NM_001130442.1	12	gGc/gAc	2/5	0.561610173694	10	FACETS	0.966	0.954	0.978			1	CLONAL	9	TRUE	NA	0.561610173694	10		724	3186	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38631980	38631981	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	240	830	0	ENST00000299084.4:c.471dup	p.Gln158SerfsTer9	p.Q158Sfs*9	ENST00000299084	NM_152594.2	156	ctt/cTtt	5/7	1	2	FACETS	0.884	0.826	0.943	0.884	0.826	0.943	CLONAL	1	TRUE	1	0.561610173694	2		830	967	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0022339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	75	649	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.945	0.827	1	0.945	0.827	1	CLONAL	1	TRUE	1	0.202620276976875	2		649	783	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0022339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	50	550	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.709	0.6	0.829	0.709	0.6	0.829	SUBCLONAL	1	TRUE	1	0.202620276976875	2		552	696	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0022339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	38	314	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.967	0.8	1	0.967	0.8	1	CLONAL	1	TRUE	1	0.202620276976875	2		314	388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578266	7578266	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs942158624	NA	P-0022342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	125	801	0	ENST00000269305.4:c.583A>T	p.Ile195Phe	p.I195F	ENST00000269305	NM_001126112.2	195	Atc/Ttc	6/11	0.229148924041648	1	FACETS	0.999	0.904	1	0.999	0.904	1	CLONAL	1	TRUE	0	0.28	1		801	769	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0022342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	32	643	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	0.365	0.295	0.444	0.365	0.295	0.444	SUBCLONAL	1	TRUE	1	0.28	2		643	626	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354069	15354069	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	41	629	0	ENST00000263377.2:c.2811G>C	p.Lys937Asn	p.K937N	ENST00000263377	NM_058243.2	937	aaG/aaC	14/20	0.244429258171733	1	FACETS	0.482	0.401	0.573	0.482	0.401	0.573	SUBCLONAL	1	TRUE	0	0.28	1		629	522	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578538	7578538	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	65	861	0	ENST00000269305.4:c.392A>G	p.Asn131Ser	p.N131S	ENST00000269305	NM_001126112.2	131	aAc/aGc	5/11	1	2	FACETS	0.591	0.511	0.679	0.591	0.511	0.679	SUBCLONAL	1	TRUE	1	0.228801115396792	2		861	961	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495726	72495726	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	47	600	0	ENST00000477973.2:c.346T>G	p.Cys116Gly	p.C116G	ENST00000477973	NM_012234.5	116	Tgt/Ggt	1/4	1	2	FACETS	0.573	0.482	0.674	0.573	0.482	0.674	SUBCLONAL	1	TRUE	1	0.228801115396792	2		600	717	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545631	106545631	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	50	580	0	ENST00000359195.3:c.3108G>T	p.Met1036Ile	p.M1036I	ENST00000359195	NM_002649.2	1036	atG/atT	11/11	0.0974478574345063	3	FACETS	0.625	0.529	0.732	0.313	0.264	0.366	INDETERMINATE	1	TRUE	1	0.228801115396792	3		580	779	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760513	133760513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	67	758	1	ENST00000318560.5:c.2836G>A	p.Ala946Thr	p.A946T	ENST00000318560	NM_005157.4	946	Gcc/Acc	11/11	1	2	FACETS	0.704	0.61	0.806	0.704	0.61	0.806	SUBCLONAL	1	TRUE	1	0.228801115396792	2		759	832	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858005	152858005	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	38	308	0	ENST00000406277.2:c.610G>C	p.Glu204Gln	p.E204Q	ENST00000406277	NM_152274.4	204	Gag/Cag	6/7	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.228801115396792	2		308	290	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99454670	99454670	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs780247189	NA	P-0022348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	134	598	0	ENST00000268035.6:c.1589C>T	p.Ala530Val	p.A530V	ENST00000268035	NM_000875.3	530	gCa/gTa	7/21	0.330856722200251	4	FACETS	0.783	0.713	0.855	0.783	0.713	0.855	SUBCLONAL	2	TRUE	2	0.390219512447743	4		598	610	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436839	52436839	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	195	849	0	ENST00000460680.1:c.1939G>T	p.Glu647Ter	p.E647*	ENST00000460680	NM_004656.3	647	Gag/Tag	15/17	0.283729560562569	3	FACETS	0.927	0.862	0.994	0.618	0.575	0.663	CLONAL	2	TRUE	0	0.390219512447743	3		849	644	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	266	636	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.698314551950949	3	FACETS	0.895	0.847	0.943	0.895	0.847	0.943	CLONAL	2	TRUE	1	0.710466806254721	3		638	567	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0022349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	382	826	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.684777789686666	2	FACETS	0.992	0.959	1	0.992	0.959	1	CLONAL	2	TRUE	0	0.710466806254721	2		828	542	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913143	32913143	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876661062	NA	P-0022349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	145	624	1	ENST00000380152.3:c.4651C>T	p.Gln1551Ter	p.Q1551*	ENST00000380152		1551	Caa/Taa	11/27	0.684777789686666	2	FACETS	0.858	0.788	0.929	0.429	0.394	0.465	CLONAL	1	TRUE	0	0.710466806254721	2		625	476	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604688	48604688	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	111	540	0	ENST00000342988.3:c.1510A>C	p.Ser504Arg	p.S504R	ENST00000342988	NM_005359.5	504	Agt/Cgt	12/12	0.703694592596311	1	FACETS	0.933	0.86	1	0.933	0.86	1	CLONAL	1	TRUE	0	0.710466806254721	1		540	216	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348980	89348980	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	98	941	0	ENST00000301030.4:c.3970T>C	p.Ser1324Pro	p.S1324P	ENST00000301030	NM_001256183.1	1324	Tct/Cct	9/13	0.710466806254721	3	FACETS	0.412	0.367	0.461	0.206	0.183	0.231	SUBCLONAL	1	TRUE	1	0.710466806254721	3		941	907	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260061	19260061	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	78	1126	0	ENST00000162023.5:c.232A>G	p.Ser78Gly	p.S78G	ENST00000162023		78	Agc/Ggc	7/13	0.684777789686666	2	FACETS	0.31	0.272	0.351	0.155	0.136	0.176	SUBCLONAL	1	TRUE	0	0.710466806254721	2		1126	708	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2952926	2952926	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	90	900	0	ENST00000396946.4:c.3014A>G	p.Lys1005Arg	p.K1005R	ENST00000396946	NM_032415.4	1005	aAg/aGg	22/25	0.67236206963863	4	FACETS	0.473	0.418	0.531	0.158	0.139	0.177	SUBCLONAL	1	TRUE	1	0.710466806254721	4		900	917	SUCCESS
AR	367	MSKCC	GRCh37	X	66863202	66863202	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769546220	NA	P-0022349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	164	379	0	ENST00000374690.3:c.1721C>T	p.Ala574Val	p.A574V	ENST00000374690	NM_000044.3	574	gCt/gTt	2/8	0.661204483722891	2	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.710466806254721	2		379	399	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0022350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	44	469	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.36	0.302	0.424	0.36	0.302	0.424	SUBCLONAL	1	TRUE	1	0.560969014871917	2		469	436	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0022350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	104	693	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.300066435575046	3	FACETS	0.602	0.539	0.669			1	INDETERMINATE	1	TRUE	NA	0.560969014871917	3		693	789	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772209	68772231	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCTCTGCCAGGAGCCGGAGCC	TGGCTCTGCCAGGAGCCGGAGCC	-	novel	NA	P-0022350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	78	908	0	ENST00000261769.5:c.58_80del	p.Trp20LeufsTer6	p.W20Lfs*6	ENST00000261769	NM_004360.3	20	TGGCTCTGCCAGGAGCCGGAGCCc/c	2/16	1	2	FACETS	0.322	0.282	0.365	0.322	0.282	0.365	SUBCLONAL	1	TRUE	1	0.560969014871917	2		908	863	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904831	101904831	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	290	478	1	ENST00000374994.4:c.819G>A	p.Trp273Ter	p.W273*	ENST00000374994	NM_004612.2	273	tgG/tgA	5/9	0.587027092977722	3	FACETS	0.833	0.798	0.868	0.833	0.798	0.868	CLONAL	3	TRUE	0	0.688407010560439	3		479	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201059	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	809	897	0	ENST00000269305.4:c.856G>T	p.Glu286Ter	p.E286*	ENST00000269305	NM_001126112.2	286	Gaa/Taa	8/11	0.586558492480403	4	FACETS	0.911	0.891	0.93	0.911	0.891	0.93	CLONAL	4	TRUE	0	0.688407010560439	4		897	1089	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057835	27057835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	357	1071	2	ENST00000324856.7:c.1543C>T	p.Gln515Ter	p.Q515*	ENST00000324856	NM_006015.4	515	Cag/Tag	3/20	0.481212718397459	3	FACETS	0.788	0.749	0.826	0.788	0.749	0.826	SUBCLONAL	2	TRUE	1	0.688407010560439	3		1073	885	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056024	26056024	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs750505144	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	50	366	0	ENST00000343677.2:c.633G>C	p.Lys211Asn	p.K211N	ENST00000343677	NM_005319.3	211	aaG/aaC	1/1	0.614072392411537	4	FACETS	0.545	0.463	0.635	0.136	0.115	0.159	SUBCLONAL	1	TRUE	0	0.688407010560439	4		366	450	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436088	49436088	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	229	475	1	ENST00000301067.7:c.5893G>T	p.Glu1965Ter	p.E1965*	ENST00000301067	NM_003482.3	1965	Gaa/Taa	28/54	0.268176886882596	5	FACETS	1	0.987	1	0.678	0.643	0.713	INDETERMINATE	3	TRUE	0	0.688407010560439	5		476	399	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561756	55561756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376469897	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	54	465	0	ENST00000288135.5:c.146G>A	p.Arg49His	p.R49H	ENST00000288135	NM_000222.2	49	cGc/cAc	2/21	0.626612416913991	3	FACETS	0.444	0.379	0.514	0.222	0.189	0.257	SUBCLONAL	1	TRUE	1	0.688407010560439	3		465	475	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491373	2491373	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	179	938	0	ENST00000355716.4:c.416G>T	p.Arg139Leu	p.R139L	ENST00000355716	NM_003820.2	139	cGc/cTc	4/8	NA	2	FACETS	0.644	0.595	0.696			1	INDETERMINATE	1	TRUE	NA	0.688407010560439	2		938	807	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780699	9780699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs999028906	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	78	724	2	ENST00000377346.4:c.1501G>A	p.Val501Met	p.V501M	ENST00000377346	NM_005026.3	501	Gtg/Atg	12/24	NA	2	FACETS	0.371	0.326	0.42			1	INDETERMINATE	1	TRUE	NA	0.688407010560439	2		726	610	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057841	27057841	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	354	1055	1	ENST00000324856.7:c.1549C>A	p.Pro517Thr	p.P517T	ENST00000324856	NM_006015.4	517	Cca/Aca	3/20	0.481212718397459	3	FACETS	0.793	0.754	0.832	0.793	0.754	0.832	SUBCLONAL	2	TRUE	1	0.688407010560439	3		1056	872	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161310405	161310405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	290	674	0	ENST00000367975.2:c.201G>A	p.Met67Ile	p.M67I	ENST00000367975	NM_003001.3	67	atG/atA	4/6	0.642067351521446	4	FACETS	1	0.992	1	0.44	0.414	0.467	CLONAL	1	TRUE	1	0.688407010560439	4		674	1077	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195806	102195806	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	116	525	0	ENST00000263464.3:c.566T>C	p.Leu189Pro	p.L189P	ENST00000263464	NM_001165.4	189	cTg/cCg	2/9	1	2	FACETS	0.828	0.752	0.906	0.828	0.752	0.906	CLONAL	1	TRUE	1	0.688407010560439	2		525	407	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491359	18491359	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	73	405	0	ENST00000266497.5:c.1273del		p.X425_splice	ENST00000266497		425			0.255855658655122	3	FACETS	0.75	0.66	0.847	0.25	0.22	0.283	INDETERMINATE	1	TRUE	0	0.688407010560439	3		405	380	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109646	115109646	+	stop_lost	Nonstop_Mutation	SNP	C	C	A	novel	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	163	967	0	ENST00000257566.3:c.2232G>T	p.Ter744TyrextTer22	p.*744Yext*22	ENST00000257566	NM_016569.3	744	taG/taT	8/8	1	2	FACETS	0.599	0.55	0.649	0.599	0.55	0.649	SUBCLONAL	1	TRUE	1	0.688407010560439	2		967	791	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437361	121437361	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751368921	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	330	891	1	ENST00000257555.6:c.1699G>A	p.Val567Ile	p.V567I	ENST00000257555		567	Gtc/Atc	9/10	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.688407010560439	2		892	665	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037896	49037896	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	285	670	0	ENST00000267163.4:c.2136C>A	p.Cys712Ter	p.C712*	ENST00000267163	NM_000321.2	712	tgC/tgA	21/27	0.62319378542156	2	FACETS	0.904	0.864	0.943	0.904	0.864	0.943	CLONAL	2	TRUE	0	0.688407010560439	2		670	458	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032306	42032306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747008860	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	443	797	0	ENST00000219905.7:c.4490C>T	p.Ser1497Leu	p.S1497L	ENST00000219905	NM_001164273.1	1497	tCa/tTa	14/24	0.587027092977722	3	FACETS	0.865	0.836	0.893	0.865	0.836	0.893	CLONAL	3	TRUE	0	0.688407010560439	3		797	667	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343541	343542	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	332	931	0	ENST00000262320.3:c.2132_2133del	p.Arg711ProfsTer70	p.R711Pfs*70	ENST00000262320	NM_003502.3	711	cGC/c	8/11	0.626612416913991	3	FACETS	0.795	0.756	0.836	0.795	0.756	0.836	SUBCLONAL	2	TRUE	1	0.688407010560439	3		931	815	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89851273	89851273	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143083764	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	310	676	0	ENST00000389301.3:c.1459C>T	p.Arg487Trp	p.R487W	ENST00000389301	NM_000135.2	487	Cgg/Tgg	15/43	0.636001923149706	2	FACETS	0.979	0.941	1	0.979	0.941	1	CLONAL	2	TRUE	0	0.688407010560439	2		676	460	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597384	10597384	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	837	1071	0	ENST00000171111.5:c.1819G>C	p.Ala607Pro	p.A607P	ENST00000171111	NM_203500.1	607	Gct/Cct	6/6	0.642000934489983	3	FACETS	0.968	0.947	0.988	0.968	0.947	0.988	CLONAL	3	TRUE	0	0.688407010560439	3		1071	1126	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792557	33792557	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	95	120	2	ENST00000498907.2:c.764G>T	p.Gly255Val	p.G255V	ENST00000498907	NM_004364.3	255	gGg/gTg	1/1	0.393063366933979	5	FACETS	0.882	0.813	0.949	1	0.977	1	INDETERMINATE	4	TRUE	2	0.688407010560439	5		122	159	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794949	242794949	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	373	1038	0	ENST00000334409.5:c.260G>T	p.Ser87Ile	p.S87I	ENST00000334409	NM_005018.2	87	aGc/aTc	2/5	NA	2	FACETS	0.873	0.838	0.906			1	INDETERMINATE	2	TRUE	NA	0.688407010560439	2		1038	621	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017139	31017139	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	204	362	0	ENST00000375687.4:c.472-2A>T		p.X158_splice	ENST00000375687	NM_015338.5	158			0.372478883474302	5	FACETS	0.854	0.801	0.908	0.854	0.801	0.908	INDETERMINATE	3	TRUE	2	0.688407010560439	5		362	470	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498424	89498424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	271	422	0	ENST00000336596.2:c.2396G>T	p.Arg799Leu	p.R799L	ENST00000336596	NM_005233.5	799	cGc/cTc	14/17	0.688407010560439	3	FACETS	0.875	0.839	0.911			1	CLONAL	3	TRUE	NA	0.688407010560439	3		422	403	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139826	55139826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	252	585	0	ENST00000257290.5:c.1487C>T	p.Thr496Ile	p.T496I	ENST00000257290	NM_006206.4	496	aCc/aTc	10/23	0.626612416913991	3	FACETS	0.869	0.821	0.918	0.869	0.821	0.918	CLONAL	2	TRUE	1	0.688407010560439	3		585	566	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196964	106196964	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	108	365	0	ENST00000380013.4:c.5297A>T	p.Tyr1766Phe	p.Y1766F	ENST00000380013	NM_001127208.2	1766	tAc/tTc	11/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.688407010560439	2		365	285	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143191856	143191857	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	148	694	2	ENST00000262992.4:c.574_575delinsTT	p.Gly192Leu	p.G192L	ENST00000262992	NM_001101669.1	192	GGg/TTg	8/24	1	2	FACETS	0.796	0.731	0.864	0.796	0.731	0.864	SUBCLONAL	1	TRUE	1	0.688407010560439	2		696	540	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1266634	1266634	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs201159197	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	135	664	0	ENST00000310581.5:c.2599G>T	p.Val867Leu	p.V867L	ENST00000310581	NM_198253.2	867	Gtg/Ttg	10/16	0.0704397157183019	3	FACETS	0.84	0.765	0.917			1	INDETERMINATE	1	TRUE	NA	0.688407010560439	3		664	628	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180040023	180040023	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	765	1015	0	ENST00000261937.6:c.3419C>A	p.Ala1140Asp	p.A1140D	ENST00000261937	NM_182925.4	1140	gCc/gAc	25/30	0.558419548503403	3	FACETS	1	0.995	1			1	CLONAL	3	TRUE	NA	0.688407010560439	3		1015	947	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120885	94120885	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	616	524	0	ENST00000369303.4:c.166del	p.Glu56LysfsTer45	p.E56Kfs*45	ENST00000369303	NM_004440.3	56	Gaa/aa	3/17	0.688407010560439	5	FACETS	0.921	0.9	0.942	0.921	0.9	0.942	CLONAL	5	TRUE	0	0.688407010560439	5		524	790	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729259	41729259	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	197	472	0	ENST00000242208.4:c.1270G>C	p.Gly424Arg	p.G424R	ENST00000242208	NM_002192.2	424	Ggg/Cgg	3/3	0.393063366933979	5	FACETS	0.984	0.917	1	0.656	0.611	0.702	INDETERMINATE	2	TRUE	2	0.688407010560439	5		472	591	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151216590	151216590	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	58	262	0	ENST00000262187.5:c.8A>T	p.Gln3Leu	p.Q3L	ENST00000262187	NM_005614.3	3	cAg/cTg	1/8	0.634813452159815	3	FACETS	1	0.937	1	0.563	0.491	0.639	CLONAL	1	TRUE	1	0.688407010560439	3		262	201	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993117	90993117	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587780096	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	113	418	0	ENST00000265433.3:c.325G>T	p.Glu109Ter	p.E109*	ENST00000265433	NM_002485.4	109	Gag/Tag	4/16	0.497200245713071	4	FACETS	1	0.949	1	0.359	0.324	0.395	CLONAL	1	TRUE	1	0.688407010560439	4		418	515	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742150	145742150	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	316	579	0	ENST00000428558.2:c.355-2A>T		p.X119_splice	ENST00000428558	NM_004260.3	119			0.497200245713071	4	FACETS	0.835	0.796	0.874	0.835	0.796	0.874	CLONAL	3	TRUE	1	0.688407010560439	4		579	619	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396918	139396918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	224	527	0	ENST00000277541.6:c.5190del	p.Pro1731ArgfsTer67	p.P1731Rfs*67	ENST00000277541	NM_017617.3	1730	ccG/cc	28/34	0.659747476602886	2	FACETS	0.863	0.819	0.906	0.863	0.819	0.906	CLONAL	2	TRUE	0	0.688407010560439	2		527	377	SUCCESS
AR	367	MSKCC	GRCh37	X	66931251	66931251	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	215	253	0	ENST00000374690.3:c.1893G>C	p.Lys631Asn	p.K631N	ENST00000374690	NM_000044.3	631	aaG/aaC	4/8	0.58666962123637	2	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.688407010560439	2		253	285	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937785	76937786	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0022354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	398	374	1	ENST00000373344.5:c.2962_2963delinsTT	p.Gly988Leu	p.G988L	ENST00000373344	NM_000489.3	988	GGa/TTa	9/35	0.58666962123637	2	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.688407010560439	2		375	551	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0022356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	106	412	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.904	0.813	1	0.904	0.813	1	CLONAL	1	TRUE	1	0.43265405981001	2		413	542	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0022356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	162	831	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.432238455760478	1	FACETS	0.916	0.843	0.991	0.916	0.843	0.991	CLONAL	1	TRUE	0	0.43265405981001	1		832	641	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983863	2983863	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	126	709	1	ENST00000396946.4:c.667C>T	p.Arg223Ter	p.R223*	ENST00000396946	NM_032415.4	223	Cga/Tga	5/25	1	2	FACETS	0.857	0.777	0.94	0.857	0.777	0.94	CLONAL	1	TRUE	1	0.43265405981001	2		710	680	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741891	17741891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	37	146	0	ENST00000250003.3:c.562C>T	p.Arg188Cys	p.R188C	ENST00000250003	NM_002478.4	188	Cgc/Tgc	1/3	NA	2	FACETS	1	0.957	1			1	INDETERMINATE	1	TRUE	NA	0.43265405981001	2		146	115	SUCCESS
APC	324	MSKCC	GRCh37	5	112175241	112175241	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	57	276	0	ENST00000257430.4:c.3951del	p.Asp1318IlefsTer3	p.D1318Ifs*3	ENST00000257430	NM_000038.5	1317	gAa/ga	16/16	1	2	FACETS	0.78	0.672	0.895	0.78	0.672	0.895	SUBCLONAL	1	TRUE	1	0.43265405981001	2		276	338	SUCCESS
MET	4233	MSKCC	GRCh37	7	116381018	116381018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761951444	NA	P-0022356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	176	754	0	ENST00000397752.3:c.1640G>A	p.Arg547Gln	p.R547Q	ENST00000397752	NM_000245.2	547	cGa/cAa	5/21	1	2	FACETS	0.953	0.878	1	0.953	0.878	1	CLONAL	1	TRUE	1	0.43265405981001	2		754	854	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152098	55152107	+	protein_altering_variant	In_Frame_Del	DEL	ATGCATGATT	ATGCATGATT	C	novel	NA	P-0022357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	572	861	0	ENST00000257290.5:c.2530_2539delinsC	p.Met844_Ser847delinsPro	p.M844_S847delinsP	ENST00000257290	NM_006206.4	844	ATGCATGATTcg/Ccg	18/23	0.488775748473978	6	FACETS	0.938	0.902	0.975			1	CLONAL	3	TRUE	NA	0.637991621158003	6		861	1450	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	205	445	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.989	0.926	1	0.989	0.926	1	CLONAL	1	TRUE	1	0.81	2		445	512	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0022360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	410	840	2	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	0.81	2		842	999	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453130	140453138	+	inframe_deletion	In_Frame_Del	DEL	GATTTCACT	GATTTCACT	-	novel	NA	P-0022360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	208	568	0	ENST00000288602.6:c.1797_1805del	p.Val600_Ser602del	p.V600_S602del	ENST00000288602	NM_004333.4	599	acAGTGAAATCt/act	15/18	1	2	FACETS	0.879	0.822	0.938	0.879	0.822	0.938	CLONAL	1	TRUE	1	0.81	2		568	584	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187726	11187726	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	436	829	0	ENST00000361445.4:c.6171G>C	p.Met2057Ile	p.M2057I	ENST00000361445	NM_004958.3	2057	atG/atC	44/58	0.249041927639759	1	FACETS	0.573	0.548	0.597	0.573	0.548	0.597	INDETERMINATE	1	TRUE	0	0.863064256800138	1		829	1003	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344928	118344928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	39	335	0	ENST00000534358.1:c.3054G>A	p.Met1018Ile	p.M1018I	ENST00000534358	NM_005933.3	1018	atG/atA	3/36	1	2	FACETS	0.167	0.138	0.2	0.167	0.138	0.2	SUBCLONAL	1	TRUE	1	0.863064256800138	2		335	540	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134885785	134885785	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	118	685	0	ENST00000398015.3:c.1696A>G	p.Lys566Glu	p.K566E	ENST00000398015	NM_004441.4	566	Aaa/Gaa	9/16	0.495911652128099	1	FACETS	0.235	0.212	0.259	0.235	0.212	0.259	INDETERMINATE	1	TRUE	0	0.863064256800138	1		685	661	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593602	55593610	+	inframe_deletion	In_Frame_Del	DEL	GTGGAAGGT	GTGGAAGGT	-	novel	NA	P-0022363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	583	613	0	ENST00000288135.5:c.1668_1676del	p.Gln556_Val559delinsHis	p.Q556_V559delinsH	ENST00000288135	NM_000222.2	556	caGTGGAAGGTt/cat	11/21	0.711836228027865	4	FACETS	0.847	0.82	0.873			1	CLONAL	3	TRUE	NA	0.863064256800138	4		613	991	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287970	33287970	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	63	576	0	ENST00000374542.5:c.1283C>T	p.Pro428Leu	p.P428L	ENST00000374542	NM_001141970.1	428	cCt/cTt	5/8	0.293433576599149	1	FACETS	0.11	0.094	0.127	0.11	0.094	0.127	INDETERMINATE	1	TRUE	0	0.863064256800138	1		576	756	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0022366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	31	640	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.693	0.558	0.846	0.693	0.558	0.846	SUBCLONAL	1	TRUE	1	0.12	2		640	746	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346770	89346771	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0022366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	14	537	1	ENST00000301030.4:c.6179_6180delinsTT	p.Ser2060Phe	p.S2060F	ENST00000301030	NM_001256183.1	2060	tCC/tTT	9/13	0.127564840820143	0	FACETS	0.755	0.545	1			1	CLONAL	1	TRUE	0	0.12	0		538	272	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518553	69518554	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0022366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	19	696	3	ENST00000294312.3:c.91_92delinsAA	p.Gly31Lys	p.G31K	ENST00000294312	NM_005117.2	31	GGg/AAg	1/3	0.3	0	FACETS	0.753	0.571	0.968			1	CLONAL	1	TRUE	0	0.12	0		699	370	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425470	49425471	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0022366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	36	968	0	ENST00000301067.7:c.13017_13018delinsTT	p.His4340Tyr	p.H4340Y	ENST00000301067	NM_003482.3	4339	acCCat/acTTat	39/54	1	2	FACETS	0.966	0.793	1	0.966	0.793	1	CLONAL	1	TRUE	1	0.12	2		968	621	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410150	63410150	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1473629829	NA	P-0022366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	19	455	0	ENST00000330258.3:c.3017C>T	p.Ser1006Leu	p.S1006L	ENST00000330258	NM_152424.3	1006	tCa/tTa	2/2	1	1	FACETS	1	0.812	1	1	0.812	1	CLONAL	1	TRUE	0	0.12	1		455	275	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0022368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	146	792	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.17056171780603	3	FACETS	0.766	0.7	0.835	0.766	0.7	0.835	INDETERMINATE	2	TRUE	1	0.285315484027832	3		792	763	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424197	47424197	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	46	752	1	ENST00000377045.4:c.202C>T	p.Arg68Ter	p.R68*	ENST00000377045	NM_001654.4	68	Cga/Tga	4/16	1	2	FACETS	0.415	0.348	0.489	0.415	0.348	0.489	SUBCLONAL	1	TRUE	1	0.285315484027832	2		753	777	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161950	47161951	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	48	471	0	ENST00000409792.3:c.4175dup	p.Asn1392LysfsTer6	p.N1392Kfs*6	ENST00000409792	NM_014159.6	1392	aac/aaAc	3/21	1	2	FACETS	0.643	0.544	0.753	0.643	0.544	0.753	SUBCLONAL	1	TRUE	1	0.285315484027832	2		471	523	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734069	58734069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61739281	NA	P-0022368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	45	823	0	ENST00000305921.3:c.1127C>T	p.Ser376Phe	p.S376F	ENST00000305921	NM_003620.3	376	tCt/tTt	5/6	1	2	FACETS	0.385	0.322	0.455	0.385	0.322	0.455	SUBCLONAL	1	TRUE	1	0.285315484027832	2		823	819	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612923	228612923	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1201973529	NA	P-0022372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	145	730	2	ENST00000366696.1:c.104G>A	p.Gly35Asp	p.G35D	ENST00000366696	NM_003493.2	35	gGc/gAc	1/1	0.240657280583729	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	2	0.240657280583729	4		732	702	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056279	27056279	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	125	621	0	ENST00000324856.7:c.1275G>T	p.Gln425His	p.Q425H	ENST00000324856	NM_006015.4	425	caG/caT	2/20	0.240657280583729	4	FACETS	1	0.915	1	1	0.915	1	CLONAL	2	TRUE	2	0.240657280583729	4		621	639	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946465	71946465	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	80	999	0	ENST00000298229.2:c.2629G>A	p.Glu877Lys	p.E877K	ENST00000298229	NM_001567.3	877	Gag/Aag	23/28	0.240657280583729	4	FACETS	0.968	0.851	1	0.484	0.425	0.547	CLONAL	1	TRUE	2	0.240657280583729	4		999	852	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949125	71949125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745724027	NA	P-0022372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	83	905	1	ENST00000298229.2:c.3592G>A	p.Glu1198Lys	p.E1198K	ENST00000298229	NM_001567.3	1198	Gag/Aag	27/28	0.240657280583729	4	FACETS	1	0.884	1	0.502	0.442	0.566	CLONAL	1	TRUE	2	0.240657280583729	4		906	853	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609656	28609656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	57	739	1	ENST00000241453.7:c.1573G>A	p.Glu525Lys	p.E525K	ENST00000241453	NM_004119.2	525	Gag/Aag	12/24	0.238329517213322	2	FACETS	0.909	0.781	1	0.455	0.39	0.525	CLONAL	1	TRUE	0	0.240657280583729	2		740	521	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652842	29652842	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	49	268	0	ENST00000356175.3:c.4780del	p.Thr1594LeufsTer9	p.T1594Lfs*9	ENST00000356175	NM_000267.3	1593	Aaa/aa	36/57	0.240657280583729	4	FACETS	0.957	0.817	1	0.957	0.817	1	CLONAL	2	TRUE	2	0.240657280583729	4		268	264	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40477038	40477038	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	76	737	0	ENST00000264657.5:c.1407G>C	p.Gln469His	p.Q469H	ENST00000264657	NM_139276.2	469	caG/caC	16/24	0.240657280583729	4	FACETS	0.998	0.874	1	0.499	0.437	0.566	CLONAL	1	TRUE	2	0.240657280583729	4		737	785	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40478175	40478175	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	80	863	0	ENST00000264657.5:c.1324G>C	p.Glu442Gln	p.E442Q	ENST00000264657	NM_139276.2	442	Gag/Cag	15/24	0.240657280583729	4	FACETS	0.913	0.802	1	0.457	0.401	0.517	CLONAL	1	TRUE	2	0.240657280583729	4		863	903	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359074	81359074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1410083247	NA	P-0022372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	89	522	0	ENST00000222390.5:c.887C>T	p.Thr296Ile	p.T296I	ENST00000222390	NM_000601.4	296	aCt/aTt	8/18	0.240657280583729	5	FACETS	1	0.924	1	0.699	0.622	0.781	CLONAL	2	TRUE	2	0.240657280583729	5		522	480	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	697	636	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.556128531525886	3	FACETS	0.948	0.917	0.979	0.948	0.917	0.979	CLONAL	2	TRUE	1	0.671425222768578	3		638	1463	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0022375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	191	308	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	NA	2	FACETS	0.993	0.924	1			1	INDETERMINATE	1	TRUE	NA	0.671425222768578	2		308	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0022375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	243	631	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.671425222768578	1	FACETS	0.884	0.834	0.934	0.884	0.834	0.934	CLONAL	1	TRUE	0	0.671425222768578	1		631	544	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225923	2225923	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1421625187	NA	P-0022375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	295	761	0	ENST00000326181.6:c.1715T>C	p.Ile572Thr	p.I572T	ENST00000326181	NM_032271.2	572	aTt/aCt	18/21	NA	2	FACETS	0.965	0.91	1			1	INDETERMINATE	1	TRUE	NA	0.671425222768578	2		761	911	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196522	106196522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	222	392	0	ENST00000380013.4:c.4855C>T	p.Pro1619Ser	p.P1619S	ENST00000380013	NM_001127208.2	1619	Cct/Tct	11/11	0.300656202478688	2	FACETS	1	0.945	1	0.506	0.473	0.539	INDETERMINATE	1	TRUE	0	0.671425222768578	2		392	654	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949630	151949630	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0022375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	254	417	0	ENST00000262189.6:c.1469+1G>A		p.X490_splice	ENST00000262189	NM_170606.2	490			NA	2	FACETS	0.947	0.889	1			1	INDETERMINATE	1	TRUE	NA	0.671425222768578	2		417	799	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0022377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	438	681	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.432255117033976	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.432255117033976	2		681	984	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851424	151851436	+	frameshift_variant	Frame_Shift_Del	DEL	ATGACAGATCTGG	ATGACAGATCTGG	-	novel	NA	P-0022377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	77	694	0	ENST00000262189.6:c.12055_12067del	p.Pro4019TrpfsTer60	p.P4019Wfs*60	ENST00000262189	NM_170606.2	4019	CCAGATCTGTCATtg/tg	47/59	0.238029330805203	3	FACETS	0.45	0.394	0.511	0.225	0.197	0.256	INDETERMINATE	1	TRUE	1	0.432255117033976	3		694	963	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0022383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	161	435	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.172320653820083	3	FACETS	1	0.982	1	1	0.982	1	INDETERMINATE	2	FALSE	1	0.3	3		435	512	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624467	21624467	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	295	946	3	ENST00000421138.2:c.1562G>C	p.Gly521Ala	p.G521A	ENST00000421138		521	gGa/gCa	14/16	0.172320653820083	3	FACETS	1	0.991	1	1	0.991	1	INDETERMINATE	2	FALSE	1	0.3	3		949	914	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618691	37618697	+	frameshift_variant	Frame_Shift_Del	DEL	CTAAAAG	CTAAAAG	-	novel	NA	P-0022383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	169	721	0	ENST00000447079.4:c.372_378del	p.Lys124AsnfsTer18	p.K124Nfs*18	ENST00000447079	NM_015083.1	123	CTAAAAGct/ct	1/14	0.3	0	FACETS	0.943	0.877	1			1	CLONAL	2	FALSE	0	0.3	0		721	418	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594078	55594078	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	191	540	0	ENST00000288135.5:c.1864G>A	p.Val622Ile	p.V622I	ENST00000288135	NM_000222.2	622	Gta/Ata	12/21	1	2	FACETS	1	0.942	1	1	0.993	1	CLONAL	2	FALSE	1	0.3	2		540	627	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469874	157469874	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	167	806	1	ENST00000346085.5:c.2668C>A	p.Pro890Thr	p.P890T	ENST00000346085	NM_020732.3	890	Cca/Aca	9/20	0.172320653820083	3	FACETS	0.955	0.881	1	0.955	0.881	1	INDETERMINATE	2	FALSE	1	0.3	3		807	670	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226024	53226024	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	55	527	0	ENST00000375401.3:c.2825C>G	p.Ala942Gly	p.A942G	ENST00000375401	NM_004187.3	942	gCc/gGc	19/26	0.3	4	FACETS	0.789	0.675	0.915			1	CLONAL	1	FALSE	NA	0.3	4		527	604	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226022	53226022	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	56	526	0	ENST00000375401.3:c.2827del	p.Arg943GlufsTer18	p.R943Efs*18	ENST00000375401	NM_004187.3	943	Cga/ga	19/26	0.3	4	FACETS	0.81	0.694	0.938			1	CLONAL	1	FALSE	NA	0.3	4		526	599	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584560	48584560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	403	554	0	ENST00000342988.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000342988	NM_005359.5	245	Cag/Tag	6/12	0.639081267460632	2	FACETS	0.999	0.963	1	0.999	0.963	1	CLONAL	2	TRUE	0	0.639081267460632	2		554	631	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256365	46256365	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773838233	NA	P-0022385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	333	593	1	ENST00000371998.3:c.593G>A	p.Arg198His	p.R198H	ENST00000371998		198	cGt/cAt	7/23	0.387044032468724	6	FACETS	0.941	0.889	0.995	0.471	0.444	0.498	CLONAL	2	TRUE	2	0.639081267460632	6		594	1261	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	rs886039483	NA	P-0022385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	651	924	0	ENST00000269305.4:c.376T>G	p.Tyr126Asp	p.Y126D	ENST00000269305	NM_001126112.2	126	Tac/Gac	5/11	0.639081267460632	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.639081267460632	2		924	979	SUCCESS
AR	367	MSKCC	GRCh37	X	66765159	66765200	+	inframe_deletion	In_Frame_Del	DEL	GCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA	GCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA	-	rs3032358	NA	P-0022385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	125	307	0	ENST00000374690.3:c.198_239del	p.Gln67_Gln80del	p.Q67_Q80del	ENST00000374690	NM_000044.3	57	ctGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAg/ctg	1/8	0.543002921889818	4	FACETS	0.782	0.714	0.852	0.782	0.714	0.852	SUBCLONAL	2	TRUE	2	0.639081267460632	4		307	410	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17120399	17120399	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	237	543	0	ENST00000285071.4:c.1160C>G	p.Ala387Gly	p.A387G	ENST00000285071	NM_144997.5	387	gCt/gGt	10/14	0.639081267460632	2	FACETS	1	0.986	1	0.585	0.549	0.621	CLONAL	1	TRUE	0	0.639081267460632	2		543	634	SUCCESS
APC	324	MSKCC	GRCh37	5	112175039	112175039	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0022385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	85	258	0	ENST00000257430.4:c.3748A>T	p.Lys1250Ter	p.K1250*	ENST00000257430	NM_000038.5	1250	Aaa/Taa	16/16	0.639081267460632	3	FACETS	0.926	0.824	1	0.463	0.412	0.517	CLONAL	1	TRUE	1	0.639081267460632	3		258	379	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683819	117683819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1191924885	NA	P-0022385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	215	647	2	ENST00000368508.3:c.3328G>A	p.Val1110Met	p.V1110M	ENST00000368508	NM_002944.2	1110	Gtg/Atg	21/43	0.639081267460632	3	FACETS	1	0.983	1	0.582	0.542	0.622	CLONAL	1	TRUE	1	0.639081267460632	3		649	763	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0022388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	190	929	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.337386555180331	2	FACETS	0.926	0.864	0.99	0.926	0.864	0.99	CLONAL	2	TRUE	0	0.411832169448129	2		930	498	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	360001	360001	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs771361430	NA	P-0022388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	161	1178	0	ENST00000262320.3:c.1088A>G	p.Asn363Ser	p.N363S	ENST00000262320	NM_003502.3	363	aAt/aGt	4/11	0.411832169448129	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.411832169448129	1		1178	433	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266846	198266846	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	135	932	0	ENST00000335508.6:c.2086G>A	p.Asp696Asn	p.D696N	ENST00000335508	NM_012433.2	696	Gat/Aat	15/25	0.0890068392271324	4	FACETS	0.829	0.757	0.905	0.829	0.757	0.905	INDETERMINATE	2	TRUE	2	0.411832169448129	4		932	558	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347020	89347020	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	98	686	1	ENST00000301030.4:c.5930C>A	p.Ser1977Ter	p.S1977*	ENST00000301030	NM_001256183.1	1977	tCg/tAg	9/13	0.498359702421877	1	FACETS	0.411	0.367	0.459	0.411	0.367	0.459	SUBCLONAL	1	TRUE	0	0.498359702421877	1		687	718	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115827	8115828	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	115	810	0	ENST00000346208.3:c.1175dup	p.Asn392LysfsTer115	p.N392Kfs*115	ENST00000346208		391	-/A	6/6	1	2	FACETS	0.373	0.335	0.413	0.373	0.335	0.413	SUBCLONAL	1	TRUE	1	0.707183699092719	2		810	872	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0022395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	100	308	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.225186939213592	3	FACETS	0.817	0.731	0.907	0.817	0.731	0.907	CLONAL	2	TRUE	1	0.225186939213592	3		308	605	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248998	55248999	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCCAGCG	rs727504263	NA	P-0022395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	167	672	0	ENST00000275493.2:c.2300_2308dup	p.Ala767_Val769dup	p.A767_V769dup	ENST00000275493	NM_005228.3	767	atg/aTGGCCAGCGtg	20/28	0.225186939213592	4	FACETS	0.933	0.857	1	0.933	0.857	1	CLONAL	2	TRUE	2	0.225186939213592	4		672	974	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409089	4409089	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777848359	NA	P-0022395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	63	456	0	ENST00000261254.3:c.784C>T	p.Arg262Cys	p.R262C	ENST00000261254	NM_001759.3	262	Cgt/Tgt	5/5	0.225186939213592	1	FACETS	0.901	0.78	1	0.901	0.78	1	CLONAL	1	TRUE	0	0.225186939213592	1		456	551	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627676	14627676	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	194	724	0	ENST00000254322.2:c.394T>C	p.Ser132Pro	p.S132P	ENST00000254322	NM_006145.1	132	Tct/Cct	2/3	0.225186939213592	3	FACETS	0.933	0.863	1	0.933	0.863	1	CLONAL	2	TRUE	1	0.225186939213592	3		724	1027	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003319	42003319	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0022398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	182	668	0	ENST00000219905.7:c.2856del	p.Asn952LysfsTer42	p.N952Kfs*42	ENST00000219905	NM_001164273.1	952	aaT/aa	8/24	0.398063564609433	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.398063564609433	1		668	724	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748396	43748396	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	220	844	2	ENST00000382044.4:c.2410G>A	p.Glu804Lys	p.E804K	ENST00000382044	NM_001141980.1	804	Gag/Aag	12/28	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.398063564609433	2		846	1105	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40458452	40458452	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	212	905	0	ENST00000345506.4:c.1667C>G	p.Ser556Cys	p.S556C	ENST00000345506	NM_003152.3	556	tCc/tGc	14/20	1	2	FACETS	0.925	0.859	0.995	0.925	0.859	0.995	CLONAL	1	TRUE	1	0.398063564609433	2		905	1151	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466782	25466782	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	170	687	0	ENST00000264709.3:c.1921G>C	p.Asp641His	p.D641H	ENST00000264709	NM_175629.2	641	Gat/Cat	16/23	0.398063564609433	1	FACETS	0.977	0.901	1	0.977	0.901	1	CLONAL	1	TRUE	0	0.398063564609433	1		687	700	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972753	25972753	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs369128452	NA	P-0022398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	135	503	0	ENST00000435504.4:c.1672C>G	p.Leu558Val	p.L558V	ENST00000435504		558	Ctt/Gtt	12/13	NA	2	FACETS	0.957	0.871	1			1	INDETERMINATE	1	TRUE	NA	0.398063564609433	2		503	709	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443695	29443695	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs863225281	NA	P-0022398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	197	729	1	ENST00000389048.3:c.3522C>G	p.Phe1174Leu	p.F1174L	ENST00000389048	NM_004304.4	1174	ttC/ttG	23/29	NA	2	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.398063564609433	2		730	957	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121018	29121018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853009	NA	P-0022398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	236	823	2	ENST00000328354.6:c.539G>A	p.Arg180His	p.R180H	ENST00000328354	NM_007194.3	180	cGc/cAc	4/15	0.398063564609433	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.398063564609433	1		825	856	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197612	106197612	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	114	439	0	ENST00000380013.4:c.5945C>G	p.Ser1982Cys	p.S1982C	ENST00000380013	NM_001127208.2	1982	tCc/tGc	11/11	1	2	FACETS	0.919	0.83	1	0.919	0.83	1	CLONAL	1	TRUE	1	0.398063564609433	2		439	623	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185011	32185011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769158159	NA	P-0022398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	197	857	0	ENST00000375023.3:c.1657G>A	p.Asp553Asn	p.D553N	ENST00000375023	NM_004557.3	553	Gat/Aat	10/30	0.391304722652841	2	FACETS	1	0.96	1	0.526	0.487	0.567	CLONAL	1	TRUE	0	0.398063564609433	2		857	940	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148645	20148645	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	183	527	0	ENST00000379607.5:c.418G>C	p.Asp140His	p.D140H	ENST00000379607	NM_001412.3	140	Gat/Cat	6/7	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.398063564609433	2		527	795	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0022399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	39	623	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.102368308002211	3	FACETS	0.878	0.726	1	0.439	0.363	0.524	CLONAL	1	TRUE	1	0.15	3		623	637	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	67	1297	4	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.892	0.772	1	0.892	0.772	1	CLONAL	1	TRUE	1	0.15	2		1301	1002	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0022399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	31	572	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.863	0.697	1	0.863	0.697	1	CLONAL	1	TRUE	1	0.15	2		573	479	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101099	27101099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	51	960	2	ENST00000324856.7:c.4381C>T	p.Arg1461Ter	p.R1461*	ENST00000324856	NM_006015.4	1461	Cga/Tga	18/20	1	2	FACETS	0.896	0.76	1	0.896	0.76	1	CLONAL	1	TRUE	1	0.15	2		962	759	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0022399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	41	676	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.813	0.676	0.967	0.813	0.676	0.967	CLONAL	1	TRUE	1	0.15	2		676	672	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466022	+	missense_variant	Missense_Mutation	DNP	CC	CC	GA	novel	NA	P-0022399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	60	1166	2	ENST00000227507.2:c.859_860delinsGA	p.Pro287Asp	p.P287D	ENST00000227507	NM_053056.2	287	CCc/GAc	5/5	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.15	2		1168	792	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0022399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	52	937	4	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.993	0.844	1	0.993	0.844	1	CLONAL	1	TRUE	1	0.15	2		941	698	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246296	46246296	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760589011	NA	P-0022399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	33	474	0	ENST00000334344.6:c.4390C>T	p.Arg1464Cys	p.R1464C	ENST00000334344	NM_152641.2	1464	Cgc/Tgc	15/21	0.102368308002211	3	FACETS	0.851	0.692	1	0.425	0.346	0.516	CLONAL	1	TRUE	1	0.15	3		474	556	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644943	67644944	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	33	680	0	ENST00000264010.4:c.210dup	p.Leu71SerfsTer6	p.L71Sfs*6	ENST00000264010	NM_006565.3	70	ctt/cTtt	3/12	1	2	FACETS	0.756	0.614	0.916	0.756	0.614	0.916	CLONAL	1	TRUE	1	0.15	2		680	582	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29579995	29579996	+	intron_variant	Intron	INS	-	-	A	novel	NA	P-0022399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	32	680	3	ENST00000356175.3:c.4110+3865dup		p.*1370*	ENST00000356175	NM_000267.3	1384/2839			1	2	FACETS	0.934	0.757	1	0.934	0.757	1	CLONAL	1	TRUE	1	0.15	2		683	457	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0022399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	80	933	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.764	0.672	0.863	1	0.977	1	SUBCLONAL	2	TRUE	1	0.15	2		937	698	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0022399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	44	819	0	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	1	2	FACETS	0.973	0.815	1	0.973	0.815	1	CLONAL	1	TRUE	1	0.15	2		819	603	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198306	185198306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528512189	NA	P-0022399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	44	695	1	ENST00000265026.3:c.2788C>T	p.Arg930Cys	p.R930C	ENST00000265026	NM_004721.4	930	Cgt/Tgt	13/14	1	2	FACETS	0.886	0.742	1	0.886	0.742	1	CLONAL	1	TRUE	1	0.15	2		696	662	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576487	67576487	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	36	770	0	ENST00000274335.5:c.770del	p.Asn257IlefsTer3	p.N257Ifs*3	ENST00000274335		256	Aaa/aa	5/15	1	2	FACETS	0.734	0.602	0.883	0.734	0.602	0.883	SUBCLONAL	1	TRUE	1	0.15	2		770	654	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591288	67591288	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	32	569	0	ENST00000274335.5:c.1786G>T	p.Glu596Ter	p.E596*	ENST00000274335		596	Gag/Tag	13/15	1	2	FACETS	0.758	0.614	0.921	0.758	0.614	0.921	CLONAL	1	TRUE	1	0.15	2		569	563	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0022401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	271	640	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.245098730931594	6	FACETS	1	0.979	1	0.89	0.842	0.938	CLONAL	5	TRUE	0	0.245098730931594	6		640	617	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209274	133209274	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs181570274	NA	P-0022401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	76	832	0	ENST00000320574.5:c.6112G>A	p.Glu2038Lys	p.E2038K	ENST00000320574	NM_006231.2	2038	Gag/Aag	44/49	1	2	FACETS	0.559	0.488	0.635	0.559	0.488	0.635	SUBCLONAL	1	TRUE	1	0.245098730931594	2		832	1110	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371409680	NA	P-0022401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	337	911	0	ENST00000269305.4:c.848G>C	p.Arg283Pro	p.R283P	ENST00000269305	NM_001126112.2	283	cGc/cCc	8/11	0.245098730931594	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.245098730931594	3		911	1312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576910	7576910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	80	883	0	ENST00000269305.4:c.936del	p.Ser313AlafsTer32	p.S313Afs*32	ENST00000269305	NM_001126112.2	312	acC/ac	9/11	0.245098730931594	3	FACETS	0.643	0.564	0.729	0.322	0.282	0.365	SUBCLONAL	1	TRUE	1	0.245098730931594	3		883	1139	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336116	73336116	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	21	297	0	ENST00000377767.4:c.2287C>T	p.His763Tyr	p.H763Y	ENST00000377767	NM_014953.3	763	Cat/Tat	17/21	1	2	FACETS	0.527	0.406	0.669	0.527	0.406	0.669	SUBCLONAL	1	TRUE	1	0.245098730931594	2		297	325	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716326	52716326	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	275	705	0	ENST00000322088.6:c.770G>T	p.Trp257Leu	p.W257L	ENST00000322088	NM_014225.5	257	tGg/tTg	6/15	0.229357948080734	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.245098730931594	3		705	1187	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11291023	11291023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	46	569	0	ENST00000361445.4:c.2738C>T	p.Ser913Phe	p.S913F	ENST00000361445	NM_004958.3	913	tCt/tTt	18/58	0.245098730931594	3	FACETS	0.478	0.401	0.564	0.239	0.2	0.282	SUBCLONAL	1	TRUE	1	0.245098730931594	3		569	881	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728705	39728705	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	41	417	0	ENST00000361337.2:c.985G>T	p.Glu329Ter	p.E329*	ENST00000361337	NM_003286.2	329	Gag/Tag	12/21	0.114240828432767	5	FACETS	0.82	0.682	0.974	0.273	0.227	0.325	INDETERMINATE	1	TRUE	2	0.245098730931594	5		417	558	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399459	139399460	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0022403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	763	1110	0	ENST00000277541.6:c.4683_4684del	p.Ala1562GlyfsTer47	p.A1562Gfs*47	ENST00000277541	NM_017617.3	1561	tgTGcg/tgcg	26/34	0.909654940423419	3	FACETS	0.984	0.971	0.995	0.984	0.971	0.995	CLONAL	3	TRUE	0	0.909654940423419	3		1110	827	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937065	76937065	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	53	423	0	ENST00000373344.5:c.3683C>T	p.Pro1228Leu	p.P1228L	ENST00000373344	NM_000489.3	1228	cCt/cTt	9/35	0.898325728937154	2	FACETS	0.267	0.227	0.309			1	SUBCLONAL	1	TRUE	NA	0.909654940423419	2		423	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0022405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	560	737	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.606012635821888	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.606012635821888	2		739	858	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0022405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	488	629	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	NA	2	FACETS	1	0.967	1			1	INDETERMINATE	2	TRUE	NA	0.606012635821888	2		629	804	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057988	27057988	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	111	852	1	ENST00000324856.7:c.1696C>T	p.Gln566Ter	p.Q566*	ENST00000324856	NM_006015.4	566	Cag/Tag	3/20	0.606012635821888	3	FACETS	0.391	0.35	0.435	0.196	0.175	0.218	SUBCLONAL	1	TRUE	1	0.606012635821888	3		853	1220	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572056	95572056	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	506	836	0	ENST00000393063.1:c.3052G>A	p.Glu1018Lys	p.E1018K	ENST00000393063	NM_030621.3	1018	Gag/Aag	20/28	0.309548746408584	4	FACETS	0.987	0.946	1	0.987	0.946	1	INDETERMINATE	2	TRUE	2	0.606012635821888	4		836	1358	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462112	120462112	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	138	838	0	ENST00000256646.2:c.5604C>G	p.Ser1868Arg	p.S1868R	ENST00000256646	NM_024408.3	1868	agC/agG	31/34	0.606012635821888	3	FACETS	0.497	0.451	0.546	0.249	0.225	0.273	SUBCLONAL	1	TRUE	1	0.606012635821888	3		838	1194	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843604	156843604	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	700	966	0	ENST00000524377.1:c.1030G>C	p.Gly344Arg	p.G344R	ENST00000524377	NM_002529.3	344	Ggg/Cgg	8/17	0.594786604176773	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	2	0.606012635821888	4		966	1724	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286764	212286764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	111	643	4	ENST00000342788.4:c.2932G>A	p.Ala978Thr	p.A978T	ENST00000342788	NM_005235.2	978	Gct/Act	24/28	0.606012635821888	3	FACETS	0.49	0.439	0.543	0.245	0.219	0.272	SUBCLONAL	1	TRUE	1	0.606012635821888	3		647	975	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880915	134880915	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	57	695	1	ENST00000398015.3:c.1478T>A	p.Ile493Asn	p.I493N	ENST00000398015	NM_004441.4	493	aTt/aAt	7/16	0.426285454981801	4	FACETS	0.271	0.232	0.315	0.136	0.116	0.158	SUBCLONAL	1	TRUE	2	0.606012635821888	4		696	1113	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526291	189526291	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	63	559	0	ENST00000264731.3:c.555C>A	p.Ser185Arg	p.S185R	ENST00000264731	NM_003722.4	185	agC/agA	4/14	0.426285454981801	4	FACETS	0.364	0.313	0.419	0.182	0.156	0.21	SUBCLONAL	1	TRUE	2	0.606012635821888	4		559	918	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161750	56161750	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0022405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	579	728	0	ENST00000399503.3:c.1247C>G	p.Ser416Ter	p.S416*	ENST00000399503	NM_005921.1	416	tCa/tGa	6/20	0.606012635821888	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.606012635821888	2		728	925	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935699	13935699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	440	596	0	ENST00000405192.2:c.1157G>A	p.Arg386Lys	p.R386K	ENST00000405192	NM_001163147.1	386	aGa/aAa	12/12	0.366236527982776	6	FACETS	0.859	0.82	0.898	0.859	0.82	0.898	CLONAL	3	TRUE	3	0.606012635821888	6		596	1247	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970877	70970877	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs764236708	NA	P-0022405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	68	560	0	ENST00000276594.2:c.1384A>G	p.Lys462Glu	p.K462E	ENST00000276594	NM_024504.3	462	Aag/Gag	6/8	0.594786604176773	4	FACETS	0.319	0.276	0.366	0.16	0.138	0.183	SUBCLONAL	1	TRUE	2	0.606012635821888	4		560	1129	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367325	50367326	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	A	novel	NA	P-0022405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	100	524	0	ENST00000331340.3:c.132_133delinsA	p.Gln45LysfsTer15	p.Q45Kfs*15	ENST00000331340	NM_006060.4	44	caGCaa/caAaa	3/8	0.366236527982776	6	FACETS	0.658	0.586	0.735	0.219	0.195	0.245	SUBCLONAL	1	TRUE	3	0.606012635821888	6		524	1110	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0022407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	200	649	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.203650910897641	3	FACETS	1	0.953	1	0.679	0.637	0.72	INDETERMINATE	2	TRUE	0	0.60123604530547	3		649	425	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0022407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	188	289	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.60123604530547	3	FACETS	0.935	0.886	0.982	0.935	0.886	0.982	CLONAL	3	TRUE	0	0.60123604530547	3		289	290	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561495	9561495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559966028	NA	P-0022407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	347	815	1	ENST00000353224.5:c.287G>A	p.Arg96His	p.R96H	ENST00000353224	NM_177990.2	96	cGc/cAc	4/10	0.60123604530547	6	FACETS	0.912	0.862	0.963	0.456	0.431	0.482	CLONAL	2	TRUE	2	0.60123604530547	6		816	1394	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117750	70117750	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	451	888	4	ENST00000245479.2:c.218T>A	p.Ile73Asn	p.I73N	ENST00000245479	NM_000346.3	73	aTc/aAc	1/3	0.60123604530547	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.60123604530547	2		892	749	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0022407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	514	860	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.60123604530547	2	FACETS	0.999	0.965	1	0.999	0.965	1	CLONAL	2	TRUE	0	0.60123604530547	2		860	856	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606671	43606671	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	354	765	0	ENST00000355710.3:c.1280T>C	p.Val427Ala	p.V427A	ENST00000355710	NM_020975.4	427	gTg/gCg	7/20	0.232612565489243	4	FACETS	1	0.989	1	1	0.989	1	INDETERMINATE	2	TRUE	2	0.60123604530547	4		765	841	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214791	36214791	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768140943	NA	P-0022407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	397	820	1	ENST00000222270.7:c.3217C>T	p.Arg1073Cys	p.R1073C	ENST00000222270	NM_014727.1	1073	Cgc/Tgc	8/37	0.517125156486939	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.60123604530547	4		821	985	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765543	41765543	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	455	810	3	ENST00000301178.4:c.2419C>A	p.Leu807Met	p.L807M	ENST00000301178	NM_021913.4	807	Ctg/Atg	20/20	0.517125156486939	4	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	2	0.60123604530547	4		813	1209	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502390	186502390	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	43	620	0	ENST00000323963.5:c.113T>G	p.Met38Arg	p.M38R	ENST00000323963		38	aTg/aGg	3/11	0.466111350388835	4	FACETS	0.388	0.324	0.459	0.194	0.162	0.23	SUBCLONAL	1	TRUE	2	0.60123604530547	4		620	591	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467928	50467946	+	frameshift_variant	Frame_Shift_Del	DEL	CGTCCCCGAGCAACAGCTG	CGTCCCCGAGCAACAGCTG	AGTCC	novel	NA	P-0022407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	190	584	3	ENST00000331340.3:c.1163_1181delinsAGTCC	p.Ala388GlufsTer96	p.A388Efs*96	ENST00000331340	NM_006060.4	388	gCGTCCCCGAGCAACAGCTGc/gAGTCCc	8/8	0.60123604530547	3	FACETS	1	0.988	1	0.658	0.611	0.706	CLONAL	1	TRUE	1	0.60123604530547	3		587	625	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443695	29443695	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs863225281	NA	P-0121444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	426	729	1	ENST00000389048.3:c.3522C>G	p.Phe1174Leu	p.F1174L	ENST00000389048	NM_004304.4	1174	ttC/ttG	23/29	0.749854811569414	3	FACETS	1	0.978	1	0.683	0.657	0.71	CLONAL	2	NA	0	0.749854811569414	3		730	762	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914127	32914127	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs55996097	NA	P-0121444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	120	627	0	ENST00000380152.3:c.5635G>T	p.Glu1879Ter	p.E1879*	ENST00000380152		1879	Gag/Tag	11/27	0.697426743522284	3	FACETS	0.915	0.831	1	0.457	0.415	0.501	CLONAL	1	NA	1	0.749854811569414	3		627	481	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0022409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	214	948	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.500360376612758	1	FACETS	0.774	0.722	0.828	0.774	0.722	0.828	SUBCLONAL	1	TRUE	0	0.53338309940388	1		948	760	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0022409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	88	550	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.49062889684456	1	FACETS	0.676	0.604	0.752	0.676	0.604	0.752	SUBCLONAL	1	TRUE	0	0.53338309940388	1		550	358	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469898	157469898	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs794727977	NA	P-0022409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	402	743	0	ENST00000346085.5:c.2692C>T	p.Arg898Ter	p.R898*	ENST00000346085	NM_020732.3	898	Cga/Tga	9/20	0.53338309940388	3	FACETS	0.932	0.889	0.976	0.932	0.889	0.976	CLONAL	2	TRUE	1	0.53338309940388	3		743	1024	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11923761	11924268	+	coding_sequence_variant,5_prime_UTR_variant	Frame_Shift_Del	DEL	TGTGTTAGCGACTGGAGGAGAAAGGGATCCCTGGGATCCTTTTCAGCTTTACTATTCTGATTTGGGGTTCTGAGATTCCAACAAAGTGGACTTTTGGGAGTCACAGACCTCCATGGGAATGATGAAAGCTGCGTACCTTCTTTCCGCACAAATGCAGGCCCACCTTTAATTCTGCAAACCACTTTAGGCCCCGCGGGCCCGCAGCCCTGGTCCAAGACAGCTGTCTGCTTCACAGGTCGCGCACCCAGAGCCGGGCGGTTCTGCAGCTCAGCATCTGGCCCGGGCTGCGCGTCGGGCTCTGGCGGGGGCGTGTCAGGAGGCGTGTCCGGGGCGTGTCGGAGGCGGGGCCAAGGCGGGGGTAAGCCTCGCCCCTCGGCCGTGCGAGAGGCCGAGCTTGCTGCATTGCAGCCGCCGCGGCGCCGCTCGGCTCTTCACTCCCAACAATGGCGGCTCCGAGCCCGAGCGGCGGCGGCGGCTCCGGGGGCGGCAGCGGCAGCGGCACCCCCGG	TGTGTTAGCGACTGGAGGAGAAAGGGATCCCTGGGATCCTTTTCAGCTTTACTATTCTGATTTGGGGTTCTGAGATTCCAACAAAGTGGACTTTTGGGAGTCACAGACCTCCATGGGAATGATGAAAGCTGCGTACCTTCTTTCCGCACAAATGCAGGCCCACCTTTAATTCTGCAAACCACTTTAGGCCCCGCGGGCCCGCAGCCCTGGTCCAAGACAGCTGTCTGCTTCACAGGTCGCGCACCCAGAGCCGGGCGGTTCTGCAGCTCAGCATCTGGCCCGGGCTGCGCGTCGGGCTCTGGCGGGGGCGTGTCAGGAGGCGTGTCCGGGGCGTGTCGGAGGCGGGGCCAAGGCGGGGGTAAGCCTCGCCCCTCGGCCGTGCGAGAGGCCGAGCTTGCTGCATTGCAGCCGCCGCGGCGCCGCTCGGCTCTTCACTCCCAACAATGGCGGCTCCGAGCCCGAGCGGCGGCGGCGGCTCCGGGGGCGGCAGCGGCAGCGGCACCCCCGG	-	novel	NA	P-0022409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1	117	0	0				ENST00000353533	NM_003010.3	?-22/399		1/11	0.500360376612758	1	FACETS		NA	1	1	0.994	1	NA	3	TRUE	0	0.53338309940388	1		0	118	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554626	29554626	+	splice_donor_variant	Splice_Site	SNP	T	T	G	rs876660826	NA	P-0022409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	108	418	0	ENST00000356175.3:c.2409+2T>G		p.X803_splice	ENST00000356175	NM_000267.3	803			0.500360376612758	1	FACETS	0.977	0.889	1	0.977	0.889	1	CLONAL	1	TRUE	0	0.53338309940388	1		418	304	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599871	10599871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1433112931	NA	P-0022409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	265	1000	0	ENST00000171111.5:c.1705C>T	p.Leu569Phe	p.L569F	ENST00000171111	NM_203500.1	569	Ctt/Ttt	5/6	1	2	FACETS	0.879	0.823	0.935	0.879	0.823	0.935	CLONAL	1	TRUE	1	0.53338309940388	2		1000	1131	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950433	17950433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768522857	NA	P-0022409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	227	841	1	ENST00000458235.1:c.1294C>T	p.Arg432Cys	p.R432C	ENST00000458235	NM_000215.3	432	Cgc/Tgc	10/24	1	2	FACETS	0.843	0.785	0.902	0.843	0.785	0.902	CLONAL	1	TRUE	1	0.53338309940388	2		842	1010	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955112	93955112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	91	715	0	ENST00000369303.4:c.2786G>A	p.Gly929Glu	p.G929E	ENST00000369303	NM_004440.3	929	gGa/gAa	16/17	0.53338309940388	3	FACETS	0.819	0.729	0.914	0.409	0.364	0.457	CLONAL	1	TRUE	1	0.53338309940388	3		715	528	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0022411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	166	520	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.700754054526474	5	FACETS	1	0.979	1	0.298	0.274	0.323	CLONAL	1	TRUE	1	0.73996259222122	5		520	794	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279927	18279927	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	110	808	0	ENST00000222254.8:c.2010C>G	p.Ile670Met	p.I670M	ENST00000222254	NM_005027.3	670	atC/atG	16/16	0.73996259222122	3	FACETS	0.358	0.32	0.398	0.179	0.16	0.199	SUBCLONAL	1	TRUE	1	0.73996259222122	3		808	1138	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38954896	38954896	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	67	390	0	ENST00000357387.3:c.2677T>A	p.Cys893Ser	p.C893S	ENST00000357387	NM_152756.3	893	Tgc/Agc	27/38	0.73996259222122	4	FACETS	0.812	0.709	0.922			1	CLONAL	1	TRUE	NA	0.73996259222122	4		390	388	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187086	38187086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1376200162	NA	P-0022411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	207	795	0	ENST00000317025.8:c.1391C>T	p.Pro464Leu	p.P464L	ENST00000317025	NM_023034.1	464	cCg/cTg	6/24	0.696534643477065	3	FACETS	0.62	0.574	0.668			1	SUBCLONAL	1	TRUE	NA	0.73996259222122	3		795	1236	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863224683	NA	P-0022420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	183	1222	2	ENST00000269305.4:c.388C>T	p.Leu130Phe	p.L130F	ENST00000269305	NM_001126112.2	130	Ctc/Ttc	5/11	0.915462258794264	1	FACETS	0.885	0.845	0.923	0.885	0.845	0.923	CLONAL	1	TRUE	0	0.915462258794264	1		1224	245	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814532	43814532	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs895171793	NA	P-0022420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	67	642	0	ENST00000372470.3:c.1327G>C	p.Gly443Arg	p.G443R	ENST00000372470	NM_005373.2	443	Ggg/Cgg	9/12	1	2	FACETS	0.486	0.426	0.55	0.486	0.426	0.55	SUBCLONAL	1	TRUE	1	0.915462258794264	2		642	301	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390460	56390692	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCTTTTAGACAAGGGAGTATATGGTAAGATATTTATAATGTTTGTTTTTACAATTATCCATTATTCTTTTCATTATACAAGTTAGGTTAAGAATTGAAAATCAGATAAAGATAAGGTAAACATGTTGTTGAATGGAAGAGTTTTATTTTTCTTATTAAGATGATACATTTGATCTTCATTCCATCTGAATAACTAATTAGCTTCATGTCTTTACTTTTATGTTTCCTGTTTT	TCCTTTTAGACAAGGGAGTATATGGTAAGATATTTATAATGTTTGTTTTTACAATTATCCATTATTCTTTTCATTATACAAGTTAGGTTAAGAATTGAAAATCAGATAAAGATAAGGTAAACATGTTGTTGAATGGAAGAGTTTTATTTTTCTTATTAAGATGATACATTTGATCTTCATTCCATCTGAATAACTAATTAGCTTCATGTCTTTACTTTTATGTTTCCTGTTTT	-	novel	NA	P-0022420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	152	549	0	ENST00000348428.3:c.1199_1222+209del		p.X400_splice	ENST00000348428	NM_006785.3	400		10/17	1	2	FACETS	0.905	0.839	0.972	0.905	0.839	0.972	CLONAL	1	TRUE	1	0.915462258794264	2		549	367	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212673	36212673	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1342415250	NA	P-0022420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	32	1139	2	ENST00000222270.7:c.2424G>T	p.Gln808His	p.Q808H	ENST00000222270	NM_014727.1	808	caG/caT	3/37	0.456253585492655	1	FACETS	0.07	0.056	0.086	0.07	0.056	0.086	INDETERMINATE	1	TRUE	0	0.915462258794264	1		1141	541	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0022421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	370	826	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.565451551927179	1	FACETS	0.938	0.892	0.984	0.938	0.892	0.984	CLONAL	1	TRUE	0	0.565451551927179	1		828	1001	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	624	833	2	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.498674584548546	3	FACETS	0.947	0.912	0.982	0.947	0.912	0.982	CLONAL	2	TRUE	1	0.565451551927179	3		835	1495	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28601351	28601351	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	317	796	0	ENST00000253063.3:c.1036G>C	p.Asp346His	p.D346H	ENST00000253063	NM_031459.4	346	Gac/Cac	8/10	1	2	FACETS	0.947	0.894	1	0.947	0.894	1	CLONAL	1	TRUE	1	0.565451551927179	2		796	1184	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721228	176721228	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	211	529	0	ENST00000439151.2:c.6859G>C	p.Asp2287His	p.D2287H	ENST00000439151	NM_022455.4	2287	Gac/Cac	23/23	1	2	FACETS	0.912	0.849	0.978	0.912	0.849	0.978	CLONAL	1	TRUE	1	0.565451551927179	2		529	818	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105554	30105554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757417278	NA	P-0022425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	587	863	0	ENST00000331968.5:c.1132G>A	p.Asp378Asn	p.D378N	ENST00000331968	NM_002742.2	378	Gac/Aac	7/18	1	2	FACETS	0.969	0.933	1	0.969	0.933	1	CLONAL	1	TRUE	1	0.865208977253274	2		863	1400	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0022426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	133	970	1	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	0.201347474419848	3	FACETS	1	0.971	1	0.587	0.531	0.645	CLONAL	1	TRUE	1	0.221662733653516	3		971	1136	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1555525367	NA	P-0022426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	148	665	0	ENST00000269305.4:c.783-1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.204693900247941	2	FACETS	0.86	0.787	0.937	0.86	0.787	0.937	CLONAL	2	TRUE	0	0.221662733653516	2		665	776	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491295	2491295	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	209	1084	0	ENST00000355716.4:c.338G>C	p.Arg113Thr	p.R113T	ENST00000355716	NM_003820.2	113	aGg/aCg	4/8	0.117406739645304	4	FACETS	1	0.942	1	1	0.942	1	INDETERMINATE	2	TRUE	2	0.221662733653516	4		1084	1131	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004217	150004217	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1431439182	NA	P-0022428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	22	524	1	ENST00000253339.5:c.2008C>T	p.Arg670Trp	p.R670W	ENST00000253339		670	Cgg/Tgg	3/7	0.21467359294197	1	FACETS	0.43	0.333	0.544	0.43	0.333	0.544	SUBCLONAL	1	TRUE	0	0.21467359294197	1		525	425	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806089	1806089	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913479	NA	P-0022428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	18	910	1	ENST00000260795.2:c.1108G>T	p.Gly370Cys	p.G370C	ENST00000260795		370	Ggc/Tgc	8/17	1	2	FACETS	0.23	0.172	0.299	0.23	0.172	0.299	SUBCLONAL	1	TRUE	1	0.21467359294197	2		911	730	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591247	67591247	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0022428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	41	465	1	ENST00000274335.5:c.1746-1G>T		p.X582_splice	ENST00000274335		582			1	2	FACETS	0.862	0.719	1	0.862	0.719	1	CLONAL	1	TRUE	1	0.21467359294197	2		466	443	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431121	49431121	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	74	836	1	ENST00000301067.7:c.10018C>T	p.Gln3340Ter	p.Q3340*	ENST00000301067	NM_003482.3	3340	Cag/Tag	34/54	1	2	FACETS	0.986	0.863	1	0.986	0.863	1	CLONAL	1	TRUE	1	0.21467359294197	2		837	699	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902506	1902506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1560591705	NA	P-0022428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	79	737	2	ENST00000382891.5:c.125G>A	p.Arg42His	p.R42H	ENST00000382891	NM_133335.3	42	cGc/cAc	2/22	1	2	FACETS	0.905	0.795	1	0.905	0.795	1	CLONAL	1	TRUE	1	0.21467359294197	2		739	813	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968251	134968251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373797543	NA	P-0022430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	306	767	2	ENST00000398015.3:c.2764G>A	p.Ala922Thr	p.A922T	ENST00000398015	NM_004441.4	922	Gcc/Acc	15/16	NA	2	FACETS	0.697	0.657	0.738			1	INDETERMINATE	1	TRUE	NA	0.782714774331695	2		769	1122	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578441	7578441	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1567553246	NA	P-0022430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	468	850	0	ENST00000269305.4:c.489C>G	p.Tyr163Ter	p.Y163*	ENST00000269305	NM_001126112.2	163	taC/taG	5/11	0.729815495485316	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.782714774331695	1		850	686	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427543	49427543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	329	590	0	ENST00000301067.7:c.10945G>A	p.Gly3649Ser	p.G3649S	ENST00000301067	NM_003482.3	3649	Ggt/Agt	39/54	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.782714774331695	2		590	715	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068253	30068253	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	307	687	0	ENST00000331968.5:c.2146T>G	p.Ser716Ala	p.S716A	ENST00000331968	NM_002742.2	716	Tca/Gca	15/18	NA	2	FACETS	0.981	0.929	1			1	INDETERMINATE	1	TRUE	NA	0.782714774331695	2		687	800	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832556	72832556	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	253	545	0	ENST00000268489.5:c.4025G>T	p.Gly1342Val	p.G1342V	ENST00000268489	NM_006885.3	1342	gGa/gTa	9/10	NA	2	FACETS	0.899	0.846	0.954			1	INDETERMINATE	1	TRUE	NA	0.782714774331695	2		545	719	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723103	52723106	+	frameshift_variant	Frame_Shift_Del	DEL	CTGG	CTGG	-	novel	NA	P-0022430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	136	548	1	ENST00000322088.6:c.1292_1295del	p.Ala431AspfsTer35	p.A431Dfs*35	ENST00000322088	NM_014225.5	430	CTGGct/ct	10/15	0.273701691194364	3	FACETS	0.434	0.394	0.477			1	INDETERMINATE	1	TRUE	NA	0.782714774331695	3		549	1114	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976929	55976929	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs767143286	NA	P-0022430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	209	485	0	ENST00000263923.4:c.983C>A	p.Pro328His	p.P328H	ENST00000263923	NM_002253.2	328	cCt/cAt	8/30	0.76435770356718	3	FACETS	0.955	0.889	1	0.478	0.444	0.512	CLONAL	1	TRUE	1	0.782714774331695	3		485	778	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394945	394945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	293	674	0	ENST00000380956.4:c.341G>A	p.Ser114Asn	p.S114N	ENST00000380956	NM_001195286.1	114	aGc/aAc	3/9	NA	2	FACETS	0.989	0.936	1			1	INDETERMINATE	1	TRUE	NA	0.782714774331695	2		674	757	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490284	29490309	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTCGTGAAGGAAACCAGCATGCAG	CTGTCGTGAAGGAAACCAGCATGCAG	-	novel	NA	P-0022431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	478	607	0	ENST00000356175.3:c.372_397del	p.Cys124Ter	p.C124*	ENST00000356175	NM_000267.3	123	acCTGTCGTGAAGGAAACCAGCATGCAGct/acct	4/57	0.552167986238406	2	FACETS	0.997	0.961	1	0.997	0.961	1	CLONAL	2	TRUE	0	0.552167986238406	2		607	868	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	146	445	0				ENST00000310581	NM_198253.2	-/1132			0.149845939402904	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		445	591	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0022432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	129	640	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		640	385	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0022433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	303	649	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.258692418424402	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	3	TRUE	0	0.258692418424402	3		649	858	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200072	138200072	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	170	580	0	ENST00000237289.4:c.1490G>T	p.Arg497Leu	p.R497L	ENST00000237289	NM_001270507.1	497	cGt/cTt	7/9	0.258692418424402	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.258692418424402	2		580	621	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793016	33793016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1358539228	NA	P-0022433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	26	151	0	ENST00000498907.2:c.305G>A	p.Gly102Asp	p.G102D	ENST00000498907	NM_004364.3	102	gGc/gAc	1/1	0.258692418424402	3	FACETS	1	0.887	1	0.588	0.469	0.722	CLONAL	1	TRUE	1	0.258692418424402	3		151	193	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636763	8636763	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	168	708	0	ENST00000356435.5:c.146del	p.Gly49GlufsTer23	p.G49Efs*23	ENST00000356435		49	gGa/ga	2/35	0.258692418424402	3	FACETS	0.931	0.857	1	0.931	0.857	1	CLONAL	2	TRUE	1	0.258692418424402	3		708	788	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939111	76939111	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	108	708	2	ENST00000373344.5:c.1637G>T	p.Gly546Val	p.G546V	ENST00000373344	NM_000489.3	546	gGg/gTg	9/35	0.258692418424402	3	FACETS	1	0.902	1			1	CLONAL	1	TRUE	NA	0.258692418424402	3		710	937	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280121	115280121	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	179	764	1	ENST00000438362.2:c.511A>T	p.Thr171Ser	p.T171S	ENST00000438362	NM_001242891.1	171	Aca/Tca	5/20	0.258692418424402	4	FACETS	0.945	0.871	1	0.945	0.871	1	CLONAL	2	TRUE	2	0.258692418424402	4		765	922	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115284194	115284194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	191	716	0	ENST00000438362.2:c.92C>T	p.Ser31Leu	p.S31L	ENST00000438362	NM_001242891.1	31	tCa/tTa	2/20	0.258692418424402	4	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	2	0.258692418424402	4		716	923	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615108	43615108	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	245	987	0	ENST00000355710.3:c.2522C>A	p.Pro841Gln	p.P841Q	ENST00000355710	NM_020975.4	841	cCg/cAg	14/20	0.249682954381066	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.258692418424402	4		987	1111	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121427	108121427	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs1408719214	NA	P-0022433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	90	308	0	ENST00000278616.4:c.1236-1G>T		p.X412_splice	ENST00000278616	NM_000051.3	412			0.258692418424402	3	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	1	0.258692418424402	3		308	377	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199908	108199908	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	45	398	0	ENST00000278616.4:c.7250T>C	p.Leu2417Pro	p.L2417P	ENST00000278616	NM_000051.3	2417	cTg/cCg	49/63	0.258692418424402	3	FACETS	0.879	0.739	1	0.439	0.369	0.517	CLONAL	1	TRUE	1	0.258692418424402	3		398	447	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133725	41133725	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	61	540	0	ENST00000379561.5:c.1903G>T	p.Val635Leu	p.V635L	ENST00000379561	NM_002015.3	635	Gtg/Ttg	2/3	1	2	FACETS	0.782	0.675	0.899	0.782	0.675	0.899	SUBCLONAL	1	TRUE	1	0.258692418424402	2		540	603	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226351	2226351	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	279	904	1	ENST00000326181.6:c.1964G>T	p.Arg655Leu	p.R655L	ENST00000326181	NM_032271.2	655	cGa/cTa	20/21	0.258692418424402	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.258692418424402	3		905	1114	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868190	45868190	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	116	915	1	ENST00000391945.4:c.500A>T	p.Glu167Val	p.E167V	ENST00000391945	NM_000400.3	167	gAg/gTg	7/23	0.258692418424402	3	FACETS	0.934	0.84	1	0.467	0.42	0.517	CLONAL	1	TRUE	1	0.258692418424402	3		916	1084	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474002	29474002	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	218	908	0	ENST00000389048.3:c.2173A>G	p.Ile725Val	p.I725V	ENST00000389048	NM_004304.4	725	Atc/Gtc	12/29	0.258692418424402	4	FACETS	0.938	0.871	1	0.938	0.871	1	CLONAL	2	TRUE	2	0.258692418424402	4		908	1131	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189855	66189855	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	104	716	0	ENST00000273854.3:c.3091G>T	p.Val1031Leu	p.V1031L	ENST00000273854	NM_004439.5	1031	Gta/Tta	18/18	0.258692418424402	3	FACETS	1	0.965	1	0.59	0.528	0.655	CLONAL	1	TRUE	1	0.258692418424402	3		716	770	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538934	187538934	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	89	647	0	ENST00000441802.2:c.8806del	p.Val2936Ter	p.V2936*	ENST00000441802	NM_005245.3	2936	Gtg/tg	10/27	0.258692418424402	3	FACETS	1	0.945	1	0.554	0.491	0.622	CLONAL	1	TRUE	1	0.258692418424402	3		647	701	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358944	81358944	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1249789201	NA	P-0022433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	327	688	1	ENST00000222390.5:c.1017G>A	p.Met339Ile	p.M339I	ENST00000222390	NM_000601.4	339	atG/atA	8/18	0.258692418424402	6	FACETS	0.937	0.886	0.988	0.937	0.886	0.988	CLONAL	4	TRUE	2	0.258692418424402	6		689	1024	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507426	8507426	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	40	382	0	ENST00000356435.5:c.1552C>A	p.Gln518Lys	p.Q518K	ENST00000356435		518	Cag/Aag	11/35	0.258692418424402	3	FACETS	0.794	0.66	0.943	0.397	0.33	0.472	CLONAL	1	TRUE	1	0.258692418424402	3		382	440	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528622	8528622	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	73	615	0	ENST00000356435.5:c.510C>A	p.Asn170Lys	p.N170K	ENST00000356435		170	aaC/aaA	4/35	0.258692418424402	3	FACETS	0.909	0.795	1	0.455	0.397	0.517	CLONAL	1	TRUE	1	0.258692418424402	3		615	701	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231037	53231037	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	103	701	0	ENST00000375401.3:c.1865G>T	p.Trp622Leu	p.W622L	ENST00000375401	NM_004187.3	622	tGg/tTg	13/26	0.258612743899651	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.258692418424402	1		701	666	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412376	63412376	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	119	929	1	ENST00000330258.3:c.791C>A	p.Ala264Asp	p.A264D	ENST00000330258	NM_152424.3	264	gCc/gAc	2/2	0.258692418424402	3	FACETS	1	0.921	1			1	CLONAL	1	TRUE	NA	0.258692418424402	3		930	1014	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625652	1625652	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs533848977	NA	P-0022436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	282	1035	0	ENST00000344749.5:c.422C>T	p.Ser141Leu	p.S141L	ENST00000344749	NM_001136139.2	141	tCg/tTg	7/19	0.250741109446323	5	FACETS	0.837	0.787	0.889	0.558	0.525	0.593	INDETERMINATE	2	TRUE	2	0.611534788521444	5		1035	1056	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210417	2210417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	420	894	3	ENST00000398665.3:c.1024C>T	p.Arg342Trp	p.R342W	ENST00000398665	NM_032482.2	342	Cgg/Tgg	13/28	0.250741109446323	5	FACETS	1	0.967	1	1	0.967	1	INDETERMINATE	3	TRUE	2	0.611534788521444	5		897	869	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061244	38061244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	332	948	1	ENST00000250448.2:c.745G>A	p.Asp249Asn	p.D249N	ENST00000250448	NM_004496.3	249	Gac/Aac	2/2	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.611534788521444	2		949	848	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041623	14041623	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1204895453	NA	P-0022436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	148	679	1	ENST00000311895.7:c.2170G>A	p.Val724Met	p.V724M	ENST00000311895	NM_005236.2	724	Gtg/Atg	11/11	0.543076686598222	4	FACETS	1	0.947	1			1	CLONAL	1	TRUE	NA	0.611534788521444	4		680	744	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753330	42753330	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755455023	NA	P-0022436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1253	287	1218	1	ENST00000222329.4:c.934C>T	p.Arg312Trp	p.R312W	ENST00000222329	NM_006494.2	312	Cgg/Tgg	4/4	0.448113269920816	4	FACETS	0.982	0.921	1	0.491	0.46	0.523	CLONAL	1	TRUE	2	0.611534788521444	4		1219	1540	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267696	198267696	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	174	717	0	ENST00000335508.6:c.1783G>C	p.Glu595Gln	p.E595Q	ENST00000335508	NM_012433.2	595	Gag/Cag	13/25	0.618370153327043	4	FACETS	1	0.961	1	0.356	0.328	0.385	CLONAL	1	TRUE	1	0.611534788521444	4		717	859	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131197	55131197	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	58	635	0	ENST00000257290.5:c.740G>T	p.Trp247Leu	p.W247L	ENST00000257290	NM_006206.4	247	tGg/tTg	5/23	0.382712715860829	5	FACETS	0.493	0.423	0.571	0.164	0.141	0.191	SUBCLONAL	1	TRUE	2	0.611534788521444	5		635	737	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459476	50459476	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	116	465	0	ENST00000331340.3:c.765G>C	p.Lys255Asn	p.K255N	ENST00000331340	NM_006060.4	255	aaG/aaC	7/8	0.202961369644944	2	FACETS	1	0.943	1	0.524	0.477	0.572	INDETERMINATE	1	TRUE	0	0.611534788521444	2		465	362	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185627	27185627	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	78	783	0	ENST00000380036.4:c.1327G>C	p.Val443Leu	p.V443L	ENST00000380036	NM_000459.3	443	Gtt/Ctt	9/23	0.618370153327043	3	FACETS	0.381	0.334	0.431	0.19	0.167	0.216	SUBCLONAL	1	TRUE	1	0.611534788521444	3		783	875	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922669	44922670	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	245	197	0	ENST00000377967.4:c.1531dup	p.Arg511LysfsTer15	p.R511Kfs*15	ENST00000377967	NM_021140.2	510	-/A	16/29	0.569599582773733	2	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.792931107290051	2		197	288	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	483	729	2	ENST00000269305.4:c.542G>C	p.Arg181Pro	p.R181P	ENST00000269305	NM_001126112.2	181	cGc/cCc	5/11	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	2	TRUE	NA	0.792931107290051	2		731	572	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590816	95590816	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	543	560	3	ENST00000393063.1:c.1093C>T	p.Pro365Ser	p.P365S	ENST00000393063	NM_030621.3	365	Cct/Tct	9/28	0.792931107290051	5	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	2	0.792931107290051	5		563	989	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050667	30050667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	135	600	1	ENST00000338641.4:c.469G>A	p.Val157Ile	p.V157I	ENST00000338641	NM_000268.3	157	Gtt/Att	5/16	0.792931107290051	2	FACETS	0.774	0.709	0.841	0.387	0.354	0.421	SUBCLONAL	1	TRUE	0	0.792931107290051	2		601	440	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0022438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	37	649	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.659	0.542	0.79	0.659	0.542	0.79	SUBCLONAL	1	TRUE	1	0.19	2		649	591	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0022438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	28	559	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.659	0.526	0.811	0.659	0.526	0.811	SUBCLONAL	1	TRUE	1	0.19	2		559	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0022438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	78	484	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.19	2		484	673	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354226	70354226	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1423751717	NA	P-0022438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	97	820	4	ENST00000374080.3:c.4637C>T	p.Thr1546Met	p.T1546M	ENST00000374080		1546	aCg/aTg	34/45	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.19	2		824	816	SUCCESS
APC	324	MSKCC	GRCh37	5	112155043	112155043	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1114167579	NA	P-0022438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	62	482	0	ENST00000257430.4:c.1312+2T>C		p.X438_splice	ENST00000257430	NM_000038.5	438			1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.19	2		482	547	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107004	27107005	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0022438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	46	671	0	ENST00000324856.7:c.6619_6620del	p.Gln2207ValfsTer17	p.Q2207Vfs*17	ENST00000324856	NM_006015.4	2205	gcCAca/gcca	20/20	1	2	FACETS	0.895	0.753	1	0.895	0.753	1	CLONAL	1	TRUE	1	0.19	2		671	541	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920405	114920405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	64	707	1	ENST00000543371.1:c.1346C>T	p.Ala449Val	p.A449V	ENST00000543371	NM_001198531.1	449	gCa/gTa	13/14	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.19	2		708	669	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832683	3832683	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0022438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	38	470	0	ENST00000262367.5:c.1573+2T>C		p.X525_splice	ENST00000262367	NM_004380.2	525			1	2	FACETS	0.828	0.684	0.989	0.828	0.684	0.989	CLONAL	1	TRUE	1	0.19	2		470	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912664	NA	P-0022439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	110	736	0	ENST00000269305.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000269305	NM_001126112.2	337	cGc/cAc	10/11	0.411439248185599	1	FACETS	0.533	0.478	0.59	0.533	0.478	0.59	SUBCLONAL	1	TRUE	0	0.422115240305604	1		736	772	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	161	549	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.238981260954536	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.260113960303366	4		549	666	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732996	30732996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893809	NA	P-0022441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	64	479	1	ENST00000295754.5:c.1609C>T	p.Arg537Cys	p.R537C	ENST00000295754	NM_003242.5	537	Cgc/Tgc	7/7	0.171798759976035	1	FACETS	0.767	0.665	0.878	0.767	0.665	0.878	SUBCLONAL	1	TRUE	0	0.260113960303366	1		480	558	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984447	201984457	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	ACTGAGGGTTG	ACTGAGGGTTG	-	novel	NA	P-0022441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	557	46	0	ENST00000359651.3:c.1112_*6del		p.*371*	ENST00000359651		371		8/8	1	2	FACETS	1	0.991	1	1	0.998	1	CLONAL	3	TRUE	1	0.260113960303366	2		46	1307	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349363	73349363	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	71	506	0	ENST00000377767.4:c.973G>C	p.Glu325Gln	p.E325Q	ENST00000377767	NM_014953.3	325	Gag/Cag	6/21	0.171798759976035	1	FACETS	0.667	0.582	0.759	0.667	0.582	0.759	SUBCLONAL	1	TRUE	0	0.260113960303366	1		506	712	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821746	72821746	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145105101	NA	P-0022441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	62	536	0	ENST00000268489.5:c.10429G>A	p.Glu3477Lys	p.E3477K	ENST00000268489	NM_006885.3	3477	Gag/Aag	10/10	1	2	FACETS	0.614	0.53	0.707	0.614	0.53	0.707	SUBCLONAL	1	TRUE	1	0.260113960303366	2		536	776	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577595	+	inframe_deletion	In_Frame_Del	DEL	AGTTGTAGTGGATGGTGGTAC	AGTTGTAGTGGATGGTGGTAC	-	novel	NA	P-0022441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	96	731	0	ENST00000269305.4:c.686_706del	p.Cys229_Asn235del	p.C229_N235del	ENST00000269305	NM_001126112.2	229	tGTACCACCATCCACTACAACTac/tac	7/11	0.154852466100291	2	FACETS	0.739	0.657	0.827	0.369	0.328	0.414	INDETERMINATE	1	TRUE	0	0.260113960303366	2		731	999	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16062085	16062085	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1391940374	NA	P-0022441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	46	485	0	ENST00000268712.3:c.721G>C	p.Asp241His	p.D241H	ENST00000268712	NM_006311.3	241	Gat/Cat	6/46	0.154852466100291	2	FACETS	0.462	0.388	0.544	0.231	0.194	0.272	INDETERMINATE	1	TRUE	0	0.260113960303366	2		485	766	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656948	47656948	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs752373431	NA	P-0022441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	40	446	0	ENST00000233146.2:c.1144C>G	p.Arg382Gly	p.R382G	ENST00000233146	NM_000251.2	382	Cgt/Ggt	7/16	0.154852466100291	2	FACETS	0.521	0.432	0.621	0.261	0.216	0.311	INDETERMINATE	1	TRUE	0	0.260113960303366	2		446	590	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557888	187557892	+	frameshift_variant	Frame_Shift_Del	DEL	TGACG	TGACG	-	novel	NA	P-0022441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	65	672	0	ENST00000441802.2:c.3819_3823del	p.Val1274SerfsTer6	p.V1274Sfs*6	ENST00000441802	NM_005245.3	1273	caCGTCAta/cata	5/27	0.260113960303366	1	FACETS	0.544	0.471	0.624	0.544	0.471	0.624	SUBCLONAL	1	TRUE	0	0.260113960303366	1		672	799	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589166	67589166	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	47	364	0	ENST00000274335.5:c.1154A>G	p.His385Arg	p.H385R	ENST00000274335		385	cAt/cGt	9/15	0.171798759976035	1	FACETS	0.696	0.587	0.814	0.696	0.587	0.814	SUBCLONAL	1	TRUE	0	0.260113960303366	1		364	452	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323232	31323232	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	71	552	0	ENST00000412585.2:c.757G>T	p.Glu253Ter	p.E253*	ENST00000412585	NM_005514.6	253	Gag/Tag	4/8	1	2	FACETS	0.548	0.477	0.625	0.548	0.477	0.625	SUBCLONAL	1	TRUE	1	0.260113960303366	2		552	996	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686868	117686868	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	42	470	0	ENST00000368508.3:c.2849C>G	p.Ser950Cys	p.S950C	ENST00000368508	NM_002944.2	950	tCt/tGt	19/43	1	2	FACETS	0.595	0.496	0.705	0.595	0.496	0.705	SUBCLONAL	1	TRUE	1	0.260113960303366	2		470	543	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069076	5069076	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	48	430	0	ENST00000381652.3:c.1381G>T	p.Glu461Ter	p.E461*	ENST00000381652	NM_004972.3	461	Gag/Tag	11/25	0.260113960303366	1	FACETS	0.709	0.6	0.828	0.709	0.6	0.828	SUBCLONAL	1	TRUE	0	0.260113960303366	1		430	453	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	181	549	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.255461350636691	2	FACETS	0.837	0.776	0.9	0.837	0.776	0.9	CLONAL	2	TRUE	0	0.356871867791075	2		549	606	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539018	187539018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374444088	NA	P-0022444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	41	766	1	ENST00000441802.2:c.8722G>A	p.Val2908Ile	p.V2908I	ENST00000441802	NM_005245.3	2908	Gtc/Atc	10/27	0.172702270037931	1	FACETS	0.24	0.199	0.285	0.24	0.199	0.285	INDETERMINATE	1	TRUE	0	0.356871867791075	1		767	788	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961321	54961321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs2230743	NA	P-0022444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	100	886	1	ENST00000312783.6:c.311C>T	p.Ser104Leu	p.S104L	ENST00000312783	NM_198436.1	104	tCg/tTg	4/10	0.162374113658164	4	FACETS	0.8	0.713	0.892	0.4	0.356	0.446	INDETERMINATE	1	TRUE	2	0.356871867791075	4		887	951	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219962	5219962	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	242	942	0	ENST00000357368.4:c.3753G>C	p.Gln1251His	p.Q1251H	ENST00000357368	NM_002850.3	1251	caG/caC	22/38	0.356871867791075	2	FACETS	1	0.992	1	0.732	0.685	0.781	CLONAL	1	TRUE	0	0.356871867791075	2		942	926	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141549464	141549464	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	80	701	0	ENST00000220592.5:c.2124G>C	p.Gln708His	p.Q708H	ENST00000220592	NM_012154.3	708	caG/caC	16/19	0.356871867791075	4	FACETS	0.684	0.6	0.773	0.228	0.2	0.258	SUBCLONAL	1	TRUE	1	0.356871867791075	4		701	890	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874229	155874229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	182	861	3	ENST00000368323.3:c.302C>T	p.Ser101Phe	p.S101F	ENST00000368323	NM_006912.5	101	tCt/tTt	5/6	1	2	FACETS	0.947	0.873	1	0.947	0.873	1	CLONAL	1	TRUE	1	0.356871867791075	2		864	1077	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054989	176054989	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0022444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	42	775	0	ENST00000367669.3:c.1064C>G	p.Ser355Ter	p.S355*	ENST00000367669	NM_022457.5	355	tCa/tGa	10/20	1	2	FACETS	0.318	0.265	0.378	0.318	0.265	0.378	SUBCLONAL	1	TRUE	1	0.356871867791075	2		775	740	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233255	46233255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	61	623	0	ENST00000334344.6:c.1474C>A	p.Gln492Lys	p.Q492K	ENST00000334344	NM_152641.2	492	Cag/Aag	11/21	0.312857507442328	4	FACETS	0.574	0.494	0.661			1	SUBCLONAL	1	TRUE	NA	0.356871867791075	4		623	808	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233276	46233276	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	55	560	0	ENST00000334344.6:c.1495C>A	p.Pro499Thr	p.P499T	ENST00000334344	NM_152641.2	499	Cca/Aca	11/21	0.312857507442328	4	FACETS	0.564	0.482	0.655			1	SUBCLONAL	1	TRUE	NA	0.356871867791075	4		560	741	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424446	49424461	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTCAGCTGGCTCTG	CCCTCAGCTGGCTCTG	-	novel	NA	P-0022444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	69	937	0	ENST00000301067.7:c.13762_13777del	p.Gln4588GlyfsTer24	p.Q4588Gfs*24	ENST00000301067	NM_003482.3	4588	CAGAGCCAGCTGAGGGgg/gg	41/54	0.312857507442328	4	FACETS	0.479	0.416	0.548			1	SUBCLONAL	1	TRUE	NA	0.356871867791075	4		937	1095	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427104	49427104	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	75	779	0	ENST00000301067.7:c.11384C>A	p.Pro3795His	p.P3795H	ENST00000301067	NM_003482.3	3795	cCc/cAc	39/54	0.312857507442328	4	FACETS	0.566	0.494	0.643			1	SUBCLONAL	1	TRUE	NA	0.356871867791075	4		779	1008	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054438	42054438	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	45	667	0	ENST00000219905.7:c.7622C>G	p.Ser2541Cys	p.S2541C	ENST00000219905	NM_001164273.1	2541	tCt/tGt	22/24	0.172702270037931	1	FACETS	0.296	0.248	0.35	0.296	0.248	0.35	INDETERMINATE	1	TRUE	0	0.356871867791075	1		667	699	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579359	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	290	948	0	ENST00000269305.4:c.328C>G	p.Arg110Gly	p.R110G	ENST00000269305	NM_001126112.2	110	Cgt/Ggt	4/11	0.255461350636691	2	FACETS	0.927	0.874	0.98	0.927	0.874	0.98	CLONAL	2	TRUE	0	0.356871867791075	2		948	877	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602449	10602449	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	132	838	0	ENST00000171111.5:c.1129G>A	p.Val377Met	p.V377M	ENST00000171111	NM_203500.1	377	Gtg/Atg	3/6	0.356871867791075	1	FACETS	0.756	0.686	0.829	0.756	0.686	0.829	SUBCLONAL	1	TRUE	0	0.356871867791075	1		838	804	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626737	12626737	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	46	708	3	ENST00000251849.4:c.1552C>T	p.Arg518Ter	p.R518*	ENST00000251849	NM_002880.3	518	Cga/Tga	15/17	0.214322303871557	3	FACETS	0.369	0.31	0.435	0.123	0.103	0.145	SUBCLONAL	1	TRUE	0	0.356871867791075	3		711	823	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288999	33288999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766610163	NA	P-0022444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	44	724	0	ENST00000374542.5:c.553C>T	p.Arg185Trp	p.R185W	ENST00000374542	NM_001141970.1	185	Cgg/Tgg	3/8	1	2	FACETS	0.284	0.237	0.336	0.284	0.237	0.336	SUBCLONAL	1	TRUE	1	0.356871867791075	2		724	869	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395524	116395524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	55	755	0	ENST00000397752.3:c.1817G>A	p.Gly606Glu	p.G606E	ENST00000397752	NM_000245.2	606	gGa/gAa	6/21	1	2	FACETS	0.406	0.346	0.471	0.406	0.346	0.471	SUBCLONAL	1	TRUE	1	0.356871867791075	2		755	760	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878659	151878659	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	105	703	1	ENST00000262189.6:c.6286C>T	p.Gln2096Ter	p.Q2096*	ENST00000262189	NM_170606.2	2096	Cag/Tag	36/59	0.315453845902124	3	FACETS	0.88	0.788	0.977			1	CLONAL	1	TRUE	NA	0.356871867791075	3		704	788	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233219	46233219	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	AA	novel	NA	P-0022444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	72	637	0	ENST00000334344.6:c.1438delinsAA	p.Glu480LysfsTer3	p.E480Kfs*3	ENST00000334344	NM_152641.2	480	Gaa/AAaa	11/21	0.312857507442328	4	FACETS	0.64	0.558	0.728			1	SUBCLONAL	1	TRUE	NA	0.356871867791075	4		637	856	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0022445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	775	930	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	1	0.993	1	1	0.998	1	CLONAL	2	FALSE	1	0.596773987441534	2		931	1234	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252994	36252995	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0022445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	264	608	0	ENST00000300305.3:c.367dup	p.Asp123GlyfsTer15	p.D123Gfs*15	ENST00000300305		123	gat/gGat	4/8	1	2	FACETS	0.999	0.938	1	0.999	0.938	1	CLONAL	1	FALSE	1	0.596773987441534	2		608	886	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242741	66242741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777294375	NA	P-0022445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	142	471	2	ENST00000273854.3:c.1831G>A	p.Ala611Thr	p.A611T	ENST00000273854	NM_004439.5	611	Gct/Act	9/18	NA	2	FACETS	0.912	0.836	0.99			1	INDETERMINATE	1	FALSE	NA	0.596773987441534	2		473	522	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453355	40453355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	422	1055	0	ENST00000345506.4:c.1052C>T	p.Thr351Ile	p.T351I	ENST00000345506	NM_003152.3	351	aCc/aTc	10/20	1	2	FACETS	0.982	0.935	1	0.982	0.935	1	CLONAL	1	FALSE	1	0.596773987441534	2		1055	1440	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259204	36259204	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	351	801	0	ENST00000300305.3:c.287A>T	p.Asn96Ile	p.N96I	ENST00000300305		96	aAc/aTc	3/8	1	2	FACETS	0.983	0.931	1	0.983	0.931	1	CLONAL	1	FALSE	1	0.596773987441534	2		801	1197	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168491	56168491	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	180	505	0	ENST00000399503.3:c.1447del	p.Arg483GlufsTer4	p.R483Efs*4	ENST00000399503	NM_005921.1	483	Aga/ga	8/20	1	2	FACETS	0.946	0.876	1	0.946	0.876	1	CLONAL	1	FALSE	1	0.596773987441534	2		505	638	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168668	56168668	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	221	604	0	ENST00000399503.3:c.1523del	p.Pro508LeufsTer49	p.P508Lfs*49	ENST00000399503	NM_005921.1	508	Cct/ct	9/20	1	2	FACETS	0.883	0.823	0.944	0.883	0.823	0.944	CLONAL	1	FALSE	1	0.596773987441534	2		604	839	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370898	55370898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1392	505	797	0	ENST00000297316.4:c.200G>A	p.Arg67His	p.R67H	ENST00000297316	NM_022454.3	67	cGt/cAt	1/2	0.596773987441534	6	FACETS	0.979	0.935	1	0.391	0.373	0.41	CLONAL	2	FALSE	1	0.596773987441534	6		797	1897	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0022447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	64	701	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.912	0.797	1	0.912	0.797	1	CLONAL	1	TRUE	1	0.488839701305838	2		701	287	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916957	178916957	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200018596	NA	P-0022447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	36	525	0	ENST00000263967.3:c.344G>T	p.Arg115Leu	p.R115L	ENST00000263967	NM_006218.2	115	cGa/cTa	2/21	1	2	FACETS	0.33	0.271	0.396	0.33	0.271	0.396	SUBCLONAL	1	TRUE	1	0.488839701305838	2		525	446	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527534	29527535	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	204	826	0	ENST00000356175.3:c.984dup	p.Lys329Ter	p.K329*	ENST00000356175	NM_000267.3	328	tgt/tgTt	9/57	0.439854542462199	3	FACETS	0.944	0.883	1	0.629	0.588	0.671	CLONAL	2	TRUE	0	0.488839701305838	3		826	550	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645701	12645701	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs397516826	NA	P-0022447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	84	434	0	ENST00000251849.4:c.768G>T	p.Arg256Ser	p.R256S	ENST00000251849	NM_002880.3	256	agG/agT	7/17	1	2	FACETS	0.985	0.877	1	0.985	0.877	1	CLONAL	1	TRUE	1	0.488839701305838	2		434	349	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404312	139404321	+	frameshift_variant	Frame_Shift_Del	DEL	CGTTGATGTC	CGTTGATGTC	-	novel	NA	P-0022447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	66	970	0	ENST00000277541.6:c.2833_2842del	p.Asp945SerfsTer231	p.D945Sfs*231	ENST00000277541	NM_017617.3	945	GACATCAACGag/ag	18/34	1	2	FACETS	0.393	0.341	0.45	0.393	0.341	0.45	SUBCLONAL	1	TRUE	1	0.488839701305838	2		970	687	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0022448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	398	846	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.33697753423221	3	FACETS	0.931	0.889	0.973	0.931	0.889	0.973	CLONAL	3	TRUE	0	0.363814202501737	3		846	926	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916774	48916775	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs587778825	NA	P-0022448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	75	702	1	ENST00000267163.4:c.305_306del	p.Cys102TyrfsTer7	p.C102Yfs*7	ENST00000267163	NM_000321.2	102	TGt/t	3/27	NA	2	FACETS	0.931	0.819	1			1	INDETERMINATE	1	TRUE	NA	0.363814202501737	2		703	443	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657420	29657421	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0022448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	429	838	0	ENST00000356175.3:c.5655_5656del	p.Phe1886TyrfsTer5	p.F1886Yfs*5	ENST00000356175	NM_000267.3	1885	CTc/c	38/57	0.33697753423221	3	FACETS	0.917	0.877	0.957	0.917	0.877	0.957	CLONAL	3	TRUE	0	0.363814202501737	3		838	1013	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572929	41572937	+	inframe_deletion	In_Frame_Del	DEL	CATCCAGTC	CATCCAGTC	-	novel	NA	P-0022448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	136	826	0	ENST00000263253.7:c.5214_5222del	p.Ile1739_Ser1741del	p.I1739_S1741del	ENST00000263253	NM_001429.3	1738	tgCATCCAGTCt/tgt	31/31	0.35536413298181	3	FACETS	0.972	0.883	1	0.486	0.441	0.533	CLONAL	1	TRUE	1	0.363814202501737	3		826	909	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589618	67589619	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAGAATATGATA	novel	NA	P-0022448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	54	483	0	ENST00000274335.5:c.1384_1395dup	p.Glu462_Arg465dup	p.E462_R465dup	ENST00000274335		462	cga/cGAGAATATGATAga	10/15	1	2	FACETS	0.655	0.561	0.759	0.655	0.561	0.759	SUBCLONAL	1	TRUE	1	0.363814202501737	2		483	453	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164805	32164806	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0022448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	114	775	0	ENST00000375023.3:c.5096_5097del	p.Glu1699GlyfsTer19	p.E1699Gfs*19	ENST00000375023	NM_004557.3	1699	gAG/g	28/30	0.35536413298181	3	FACETS	0.859	0.773	0.951	0.43	0.386	0.476	CLONAL	1	TRUE	1	0.363814202501737	3		775	862	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0022449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	223	693	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.224344736909197	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.224344736909197	1		693	1197	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579361	7579361	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1064796722	NA	P-0022449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	120	972	0	ENST00000269305.4:c.326T>G	p.Phe109Cys	p.F109C	ENST00000269305	NM_001126112.2	109	tTc/tGc	4/11	1	2	FACETS	0.97	0.874	1	0.97	0.874	1	CLONAL	1	TRUE	1	0.224344736909197	2		972	1103	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245720	46245720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	92	618	0	ENST00000334344.6:c.3814C>T	p.Arg1272Ter	p.R1272*	ENST00000334344	NM_152641.2	1272	Cga/Tga	15/21	0.224344736909197	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.224344736909197	1		618	695	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31393154	31393154	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770423841	NA	P-0022451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	46	596	0	ENST00000328111.2:c.2242G>A	p.Ala748Thr	p.A748T	ENST00000328111	NM_006892.3	748	Gca/Aca	21/23	1	2	FACETS	0.152	0.127	0.179	0.152	0.127	0.179	SUBCLONAL	1	TRUE	1	0.9540637897153	2		596	636	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593576	55593604	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCACAGAAACCCATGTATGAAGTACAGTG	CCACAGAAACCCATGTATGAAGTACAGTG	-	novel	NA	P-0022451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	261	522	0	ENST00000288135.5:c.1648-6_1670del		p.X550_splice	ENST00000288135	NM_000222.2	550		11/21	1	2	FACETS	0.935	0.884	0.987	0.935	0.884	0.987	CLONAL	1	TRUE	1	0.9540637897153	2		522	585	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151947014	151947014	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	299	719	0	ENST00000262189.6:c.1760A>C	p.Gln587Pro	p.Q587P	ENST00000262189	NM_170606.2	587	cAa/cCa	13/59	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.9540637897153	2		719	610	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0022453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	132	644	1	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.271622865366626	5	FACETS	0.877	0.797	0.961			1	CLONAL	2	TRUE	NA	0.271622865366626	5		645	780	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0022453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	155	935	2	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	NA	2	FACETS	1	0.937	1			1	INDETERMINATE	2	TRUE	NA	0.271622865366626	2		937	559	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100952	41100952	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	87	845	0	ENST00000373198.4:c.1404G>T	p.Glu468Asp	p.E468D	ENST00000373198	NM_133170.3	468	gaG/gaT	8/32	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.271622865366626	2		845	593	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257756	133257756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316755014	NA	P-0022453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	75	969	0	ENST00000320574.5:c.172G>A	p.Glu58Lys	p.E58K	ENST00000320574	NM_006231.2	58	Gag/Aag	2/49	1	2	FACETS	0.85	0.744	0.963	0.85	0.744	0.963	CLONAL	1	TRUE	1	0.271622865366626	2		969	650	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639376	3639376	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	62	995	0	ENST00000294008.3:c.4263T>G	p.Ile1421Met	p.I1421M	ENST00000294008	NM_032444.2	1421	atT/atG	12/15	0.271622865366626	3	FACETS	0.748	0.646	0.86	0.374	0.323	0.43	SUBCLONAL	1	TRUE	1	0.271622865366626	3		995	693	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777729	3777729	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	87	1138	0	ENST00000262367.5:c.7319A>T	p.Glu2440Val	p.E2440V	ENST00000262367	NM_004380.2	2440	gAg/gTg	31/31	0.271622865366626	3	FACETS	0.793	0.701	0.893	0.397	0.35	0.447	SUBCLONAL	1	TRUE	1	0.271622865366626	3		1138	917	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164773	106164773	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	66	708	0	ENST00000380013.4:c.3641G>T	p.Arg1214Leu	p.R1214L	ENST00000380013	NM_001127208.2	1214	cGg/cTg	6/11	1	2	FACETS	0.998	0.868	1	0.998	0.868	1	CLONAL	1	TRUE	1	0.271622865366626	2		708	487	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295305	1295305	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0022453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	85	778	0				ENST00000310581	NM_198253.2	-/1132			0.271622865366626	4	FACETS	0.973	0.865	1	0.973	0.865	1	CLONAL	2	TRUE	2	0.271622865366626	4		778	409	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79974749	79974749	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	129	725	1	ENST00000265081.6:c.1177G>T	p.Val393Leu	p.V393L	ENST00000265081	NM_002439.4	393	Gtg/Ttg	8/24	0.271622865366626	3	FACETS	0.844	0.767	0.925	0.844	0.767	0.925	CLONAL	2	TRUE	1	0.271622865366626	3		726	639	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187966	32187967	+	missense_variant	Missense_Mutation	DNP	GG	GG	TC	novel	NA	P-0022453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	132	1014	3	ENST00000375023.3:c.1254_1255delinsGA	p.Cys418_Leu419delinsTrpMet	p.C418_L419delinsWM	ENST00000375023	NM_004557.3	418	tgCCtg/tgGAtg	7/30	0.271622865366626	4	FACETS	0.841	0.764	0.921	0.841	0.764	0.921	CLONAL	2	TRUE	2	0.271622865366626	4		1017	735	SUCCESS
AR	367	MSKCC	GRCh37	X	66943526	66943526	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0022453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	93	632	0	ENST00000374690.3:c.2608-2A>T		p.X870_splice	ENST00000374690	NM_000044.3	870			0.271622865366626	3	FACETS	0.836	0.747	0.931	0.836	0.747	0.931	CLONAL	2	TRUE	1	0.271622865366626	3		632	465	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348452	70348452	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	154	740	0	ENST00000374080.3:c.3359G>T	p.Ser1120Ile	p.S1120I	ENST00000374080		1120	aGt/aTt	24/45	0.271622865366626	3	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	1	0.271622865366626	3		740	631	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691022	NA	P-0022454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	386	863	16	ENST00000269305.4:c.1024del	p.Arg342GlufsTer3	p.R342Efs*3	ENST00000269305	NM_001126112.2	342	Cga/ga	10/11	0.701552526798621	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.701552526798621	1		879	692	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242647	16242647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777234386	NA	P-0022454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	296	563	0	ENST00000375759.3:c.1268G>A	p.Arg423His	p.R423H	ENST00000375759	NM_015001.2	423	cGc/cAc	6/15	0.668931198717434	1	FACETS	0.951	0.905	0.997	0.951	0.905	0.997	CLONAL	1	TRUE	0	0.701552526798621	1		563	576	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772211	68772211	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786203576	NA	P-0022454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	426	770	2	ENST00000261769.5:c.60G>A	p.Trp20Ter	p.W20*	ENST00000261769	NM_004360.3	20	tgG/tgA	2/16	0.701552526798621	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.701552526798621	1		772	728	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772215	68772215	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	441	818	0	ENST00000261769.5:c.64T>A	p.Cys22Ser	p.C22S	ENST00000261769	NM_004360.3	22	Tgc/Agc	2/16	0.701552526798621	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.701552526798621	1		818	745	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439125	52439125	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0022454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	325	667	5	ENST00000460680.1:c.1116+1G>A		p.X372_splice	ENST00000460680	NM_004656.3	372			0.701552526798621	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.701552526798621	1		672	567	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293771	1293771	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	429	914	7	ENST00000310581.5:c.1230G>C	p.Lys410Asn	p.K410N	ENST00000310581	NM_198253.2	410	aaG/aaC	2/16	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.701552526798621	2		921	1133	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358928	81358928	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0022454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	278	588	2	ENST00000222390.5:c.1033A>T	p.Lys345Ter	p.K345*	ENST00000222390	NM_000601.4	345	Aag/Tag	8/18	1	2	FACETS	0.962	0.907	1	0.962	0.907	1	CLONAL	1	TRUE	1	0.701552526798621	2		590	824	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971020	21971020	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	257	575	3	ENST00000304494.5:c.338T>C	p.Leu113Pro	p.L113P	ENST00000304494	NM_000077.4	113	cTg/cCg	2/3	0.701552526798621	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.701552526798621	1		578	474	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618878	37618878	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	107	802	0	ENST00000447079.4:c.555del	p.Glu187AsnfsTer4	p.E187Nfs*4	ENST00000447079	NM_015083.1	185	aGg/ag	1/14	1	2	FACETS	0.785	0.705	0.87	0.785	0.705	0.87	SUBCLONAL	1	TRUE	1	0.388266319240427	2		802	702	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627388	37627388	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	122	859	0	ENST00000447079.4:c.1303del	p.Val435Ter	p.V435*	ENST00000447079	NM_015083.1	435	Gta/ta	2/14	1	2	FACETS	0.798	0.721	0.878	0.798	0.721	0.878	SUBCLONAL	1	TRUE	1	0.388266319240427	2		859	788	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273215	198273215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749887399	NA	P-0022455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	71	800	3	ENST00000335508.6:c.995G>A	p.Ser332Asn	p.S332N	ENST00000335508	NM_012433.2	332	aGt/aAt	8/25	1	2	FACETS	0.576	0.503	0.655	0.576	0.503	0.655	SUBCLONAL	1	TRUE	1	0.388266319240427	2		803	635	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	83	318	0	ENST00000257430.4:c.3919dup	p.Ile1307AsnfsTer8	p.I1307Nfs*8	ENST00000257430	NM_000038.5	1306	gaa/gAaa	16/16	1	2	FACETS	0.877	0.783	0.976	0.877	0.783	0.976	CLONAL	1	TRUE	1	0.654662865996083	2		318	289	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0022456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	163	467	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.654662865996083	2		467	485	SUCCESS
RET	5979	MSKCC	GRCh37	10	43595926	43595926	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2342	263	791	0	ENST00000355710.3:c.93C>G	p.Phe31Leu	p.F31L	ENST00000355710	NM_020975.4	31	ttC/ttG	2/20	0.654662865996083	8	FACETS	0.914	0.852	0.979	0.152	0.142	0.164	CLONAL	1	TRUE	2	0.654662865996083	8		791	2605	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562493	21562493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1417916199	NA	P-0022456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	12	99	1	ENST00000382592.4:c.1426G>A	p.Ala476Thr	p.A476T	ENST00000382592	NM_014572.2	476	Gcc/Acc	4/8	0.654662865996083	5	FACETS	0.367	0.258	0.501	0.122	0.086	0.167	SUBCLONAL	1	TRUE	2	0.654662865996083	5		100	198	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041546	42041546	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	221	745	0	ENST00000219905.7:c.5741G>T	p.Ser1914Ile	p.S1914I	ENST00000219905	NM_001164273.1	1914	aGt/aTt	17/24	0.654662865996083	3	FACETS	1	0.972	1	0.539	0.503	0.577	CLONAL	1	TRUE	1	0.654662865996083	3		745	831	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	895	886	0	ENST00000269305.4:c.159del	p.Trp53CysfsTer70	p.W53Cfs*70	ENST00000269305	NM_001126112.2	53	tgG/tg	4/11	0.654662865996083	3	FACETS	0.98	0.959	1	0.98	0.959	1	CLONAL	3	TRUE	0	0.654662865996083	3		886	1235	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240320	5240320	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1456886552	NA	P-0022456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	331	796	1	ENST00000357368.4:c.1594C>T	p.Arg532Trp	p.R532W	ENST00000357368	NM_002850.3	532	Cgg/Tgg	12/38	0.654662865996083	3	FACETS	1	0.963	1	0.512	0.483	0.542	CLONAL	1	TRUE	1	0.654662865996083	3		797	1310	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379420	225379420	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	133	861	1	ENST00000264414.4:c.448C>A	p.Gln150Lys	p.Q150K	ENST00000264414	NM_003590.4	150	Caa/Aaa	4/16	0.550112227288423	3	FACETS	0.961	0.877	1	0.481	0.438	0.525	CLONAL	1	TRUE	1	0.654662865996083	3		862	561	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466808	57466822	+	inframe_deletion	In_Frame_Del	DEL	CGAGGACCAGCGCAA	CGAGGACCAGCGCAA	-	novel	NA	P-0022456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1333	117	369	1	ENST00000371085.3:c.33_47del	p.Asp11_Glu15del	p.D11_E15del	ENST00000371085	NM_000516.4	9	acCGAGGACCAGCGCAAc/acc	1/13	0.654662865996083	10	FACETS	0.892	0.801	0.989	0.112	0.1	0.124	CLONAL	1	TRUE	2	0.654662865996083	10		370	1450	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753960	57753960	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	149	547	0	ENST00000274289.3:c.664G>T	p.Gly222Trp	p.G222W	ENST00000274289	NM_006622.3	222	Ggg/Tgg	5/14	1	2	FACETS	0.886	0.814	0.959	0.886	0.814	0.959	CLONAL	1	TRUE	1	0.654662865996083	2		547	514	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16001751	16001755	+	frameshift_variant	Frame_Shift_Del	DEL	GAGAC	GAGAC	-	novel	NA	P-0022466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	97	533	1	ENST00000268712.3:c.2746_2750del	p.Val916IlefsTer30	p.V916Ifs*30	ENST00000268712	NM_006311.3	916	GTCTCa/a	21/46	0.284775955312771	1	FACETS	0.669	0.596	0.746	0.669	0.596	0.746	SUBCLONAL	1	TRUE	0	0.33	1		534	734	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115873	8115874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0022468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	101	595	0	ENST00000346208.3:c.1220dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tCcg	6/6	1	2	FACETS	0.943	0.843	1	0.943	0.843	1	CLONAL	1	FALSE	1	0.286125560802514	2		595	749	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120795696	120795696	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	34	422	0	ENST00000257552.2:c.457G>A	p.Gly153Arg	p.G153R	ENST00000257552	NM_002442.3	153	Ggg/Agg	8/15	1	2	FACETS	0.367	0.299	0.444	0.367	0.299	0.444	SUBCLONAL	1	FALSE	1	0.286125560802514	2		422	648	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66525130	66525130	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	127	267	0	ENST00000358598.2:c.889G>C	p.Glu297Gln	p.E297Q	ENST00000358598	NM_212471.2	297	Gag/Cag	9/11	0.286125560802514	6	FACETS	1	0.984	1			1	CLONAL	1	FALSE	NA	0.286125560802514	6		267	950	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288753	15288753	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1484088604	NA	P-0022468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	35	148	0	ENST00000263388.2:c.3986G>T	p.Gly1329Val	p.G1329V	ENST00000263388	NM_000435.2	1329	gGg/gTg	24/33	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	FALSE	1	0.286125560802514	2		148	226	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965821	90965821	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	34	322	0	ENST00000265433.3:c.1496C>A	p.Ser499Ter	p.S499*	ENST00000265433	NM_002485.4	499	tCa/tAa	11/16	1	2	FACETS	0.452	0.368	0.546	0.452	0.368	0.546	SUBCLONAL	1	FALSE	1	0.286125560802514	2		322	526	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	169	445	0				ENST00000310581	NM_198253.2	-/1132			0.194491248243526	3	FACETS	1	0.981	1	0.595	0.549	0.642	INDETERMINATE	1	TRUE	1	0.628635213805729	3		445	594	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0022471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	622	654	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.331336700570005	3	FACETS	1	0.989	1	1	0.998	1	INDETERMINATE	3	TRUE	1	0.628635213805729	3		654	844	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456932	149456932	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148357861	NA	P-0022471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	271	552	0	ENST00000286301.3:c.796G>A	p.Asp266Asn	p.D266N	ENST00000286301	NM_005211.3	266	Gat/Aat	6/22	0.194491248243526	3	FACETS	1	0.987	1	0.587	0.551	0.624	INDETERMINATE	1	TRUE	1	0.628635213805729	3		552	965	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612073	189612073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142762485	NA	P-0022471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	362	557	1	ENST00000264731.3:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000264731	NM_003722.4	609	Gaa/Aaa	14/14	0.139269711929883	6	FACETS	0.911	0.867	0.956	0.911	0.867	0.956	INDETERMINATE	3	TRUE	3	0.628635213805729	6		558	951	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548939	29548939	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs863224489	NA	P-0022471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	92	297	0	ENST00000356175.3:c.1713G>A	p.Trp571Ter	p.W571*	ENST00000356175	NM_000267.3	571	tgG/tgA	15/57	0.331336700570005	3	FACETS	1	0.955	1	0.561	0.503	0.621	INDETERMINATE	1	TRUE	1	0.628635213805729	3		297	343	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619154	43619154	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs794728687	NA	P-0022471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	222	538	1	ENST00000355710.3:c.2837C>T	p.Thr946Ile	p.T946I	ENST00000355710	NM_020975.4	946	aCc/aTc	17/20	1	2	FACETS	0.989	0.925	1	0.989	0.925	1	CLONAL	1	TRUE	1	0.628635213805729	2		539	714	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202290	133202290	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752113614	NA	P-0022471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	267	651	0	ENST00000320574.5:c.6598G>A	p.Glu2200Lys	p.E2200K	ENST00000320574	NM_006231.2	2200	Gag/Aag	47/49	0.448903711600956	3	FACETS	1	0.975	1	0.536	0.503	0.571	CLONAL	1	TRUE	1	0.628635213805729	3		651	1041	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740809	145740809	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	312	652	0	ENST00000428558.2:c.1291G>T	p.Glu431Ter	p.E431*	ENST00000428558	NM_004260.3	431	Gag/Tag	7/22	0.194491248243526	3	FACETS	1	0.992	1	0.656	0.619	0.693	INDETERMINATE	1	TRUE	1	0.628635213805729	3		652	995	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915524	112915524	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121918455	NA	P-0022471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	309	480	0	ENST00000351677.2:c.923A>C	p.Asn308Thr	p.N308T	ENST00000351677	NM_002834.3	308	aAt/aCt	8/16	0.448903711600956	3	FACETS	0.84	0.796	0.884	0.84	0.796	0.884	CLONAL	2	TRUE	1	0.628635213805729	3		480	769	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120493418	120493418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	688	487	0	ENST00000256646.2:c.2408C>T	p.Pro803Leu	p.P803L	ENST00000256646	NM_024408.3	803	cCa/cTa	15/34	0.628635213805729	7	FACETS	1	0.995	1			1	CLONAL	3	TRUE	NA	0.628635213805729	7		487	1622	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998614	100998615	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0022471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	211	632	2	ENST00000325455.5:c.1187_1188delinsTT	p.Ala396Val	p.A396V	ENST00000325455	NM_001202474.3	396	gCC/gTT	1/8	0.331336700570005	3	FACETS	1	0.979	1	0.562	0.523	0.602	INDETERMINATE	1	TRUE	1	0.628635213805729	3		634	785	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371833	118371833	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1447733910	NA	P-0022471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	333	454	0	ENST00000534358.1:c.6290C>T	p.Thr2097Ile	p.T2097I	ENST00000534358	NM_005933.3	2097	aCc/aTc	25/36	0.331336700570005	3	FACETS	0.834	0.792	0.876	0.834	0.792	0.876	INDETERMINATE	2	TRUE	1	0.628635213805729	3		454	835	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466999	18466999	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs747404244	NA	P-0022471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	203	289	0	ENST00000266497.5:c.1137+1G>A		p.X379_splice	ENST00000266497		379			0.448903711600956	3	FACETS	0.901	0.845	0.958	0.901	0.845	0.958	CLONAL	2	TRUE	1	0.628635213805729	3		289	471	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491475	18491475	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1358085326	NA	P-0022471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	146	364	0	ENST00000266497.5:c.1388A>C	p.Lys463Thr	p.K463T	ENST00000266497		463	aAa/aCa	8/31	0.448903711600956	3	FACETS	1	0.966	1	0.55	0.504	0.597	CLONAL	1	TRUE	1	0.628635213805729	3		364	555	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427530	49427531	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0022471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	270	449	1	ENST00000301067.7:c.10957_10958delinsAA	p.Gly3653Lys	p.G3653K	ENST00000301067	NM_003482.3	3653	GGa/AAa	39/54	0.448903711600956	3	FACETS	0.983	0.932	1	0.983	0.932	1	CLONAL	2	TRUE	1	0.628635213805729	3		450	574	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233316	69233316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	187	268	0	ENST00000462284.1:c.1181C>T	p.Ser394Leu	p.S394L	ENST00000462284	NM_002392.5	394	tCa/tTa	11/11	0.448903711600956	3	FACETS	0.899	0.84	0.958	0.899	0.84	0.958	CLONAL	2	TRUE	1	0.628635213805729	3		268	435	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896437	28896437	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	272	412	0	ENST00000282397.4:c.3013C>A	p.Gln1005Lys	p.Q1005K	ENST00000282397	NM_002019.4	1005	Caa/Aaa	22/30	0.331336700570005	3	FACETS	0.794	0.749	0.84	0.794	0.749	0.84	INDETERMINATE	2	TRUE	1	0.628635213805729	3		412	716	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40681712	40681712	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	133	315	0	ENST00000249776.8:c.491A>G	p.Lys164Arg	p.K164R	ENST00000249776	NM_033286.3	164	aAa/aGa	5/9	0.331336700570005	3	FACETS	1	0.964	1	0.553	0.505	0.603	INDETERMINATE	1	TRUE	1	0.628635213805729	3		315	503	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059173	42059173	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771172244	NA	P-0022471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	195	351	0	ENST00000219905.7:c.8893C>T	p.Pro2965Ser	p.P2965S	ENST00000219905	NM_001164273.1	2965	Ccc/Tcc	24/24	0.331336700570005	3	FACETS	0.799	0.746	0.853	0.799	0.746	0.853	INDETERMINATE	2	TRUE	1	0.628635213805729	3		351	510	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89383382	89383382	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	336	717	1	ENST00000301030.4:c.46C>T	p.Pro16Ser	p.P16S	ENST00000301030	NM_001256183.1	16	Ccc/Tcc	3/13	0.194491248243526	3	FACETS	1	0.994	1	0.682	0.646	0.719	INDETERMINATE	1	TRUE	1	0.628635213805729	3		718	1030	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683999	29683999	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	237	542	1	ENST00000356175.3:c.7697C>A	p.Ser2566Ter	p.S2566*	ENST00000356175	NM_000267.3	2566	tCa/tAa	52/57	0.331336700570005	3	FACETS	1	0.982	1	0.566	0.529	0.604	INDETERMINATE	1	TRUE	1	0.628635213805729	3		543	876	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256349	46256349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	190	423	0	ENST00000371998.3:c.577C>T	p.His193Tyr	p.H193Y	ENST00000371998		193	Cat/Tat	7/23	0.194491248243526	3	FACETS	1	0.968	1	0.539	0.499	0.58	INDETERMINATE	1	TRUE	1	0.628635213805729	3		423	737	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138376634	138376634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774495137	NA	P-0022471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	332	455	0	ENST00000289153.2:c.2840C>T	p.Ser947Phe	p.S947F	ENST00000289153	NM_006219.2	947	tCt/tTt	20/22	0.139269711929883	6	FACETS	0.893	0.847	0.939	0.893	0.847	0.939	INDETERMINATE	3	TRUE	3	0.628635213805729	6		455	890	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754575	57754575	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751788063	NA	P-0022471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	253	396	1	ENST00000274289.3:c.472C>T	p.Leu158Phe	p.L158F	ENST00000274289	NM_006622.3	158	Ctc/Ttc	3/14	0.331336700570005	3	FACETS	0.864	0.815	0.914	0.864	0.815	0.914	INDETERMINATE	2	TRUE	1	0.628635213805729	3		397	612	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322982	31322982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	451	770	0	ENST00000412585.2:c.914C>T	p.Thr305Ile	p.T305I	ENST00000412585	NM_005514.6	305	aCc/aTc	5/8	0.331336700570005	3	FACETS	0.774	0.739	0.808	0.774	0.739	0.808	INDETERMINATE	2	TRUE	1	0.628635213805729	3		770	1219	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27204970	27204970	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	347	493	0	ENST00000380036.4:c.2271G>A	p.Met757Ile	p.M757I	ENST00000380036	NM_000459.3	757	atG/atA	14/23	0.628635213805729	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.628635213805729	1		493	524	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321335	1321350	+	frameshift_variant	Frame_Shift_Del	DEL	GTCAGAACACGTCACC	GTCAGAACACGTCACC	-	novel	NA	P-0022471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	288	563	0	ENST00000400841.2:c.405_420del	p.Val136CysfsTer32	p.V136Cfs*32	ENST00000400841		135	acGGTGACGTGTTCTGAC/ac	4/6	0.564571882557214	2	FACETS	0.905	0.863	0.947			1	CLONAL	2	TRUE	NA	0.628635213805729	2		563	506	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508805	106508805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762805000	NA	P-0022473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	108	444	0	ENST00000359195.3:c.799G>A	p.Glu267Lys	p.E267K	ENST00000359195	NM_002649.2	267	Gaa/Aaa	2/11	0.708453386396074	3	FACETS	0.869	0.784	0.958	0.435	0.392	0.479	CLONAL	1	TRUE	1	0.708453386396074	3		444	475	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409043	4409043	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	95	316	0	ENST00000261254.3:c.738C>A	p.Cys246Ter	p.C246*	ENST00000261254	NM_001759.3	246	tgC/tgA	5/5	0.12347762038103	5	FACETS	0.842	0.766	0.919			1	INDETERMINATE	3	TRUE	NA	0.708453386396074	5		316	219	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462891	69462891	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	144	685	0	ENST00000227507.2:c.704G>C	p.Arg235Thr	p.R235T	ENST00000227507	NM_053056.2	235	aGa/aCa	4/5	1	2	FACETS	0.88	0.809	0.953	0.88	0.809	0.953	CLONAL	1	TRUE	1	0.708453386396074	2		685	462	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716359	18716360	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	118	361	0	ENST00000266497.5:c.3711dup	p.Ser1238IlefsTer3	p.S1238Ifs*3	ENST00000266497		1236	gaa/gAaa	26/31	0.708453386396074	3	FACETS	1	0.963	1	0.557	0.507	0.609	CLONAL	1	TRUE	1	0.708453386396074	3		361	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579400	7579401	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0022473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	116	721	0	ENST00000269305.4:c.286_287insTC	p.Ser96PhefsTer28	p.S96Ffs*28	ENST00000269305	NM_001126112.2	96	tct/tTCct	4/11	0.645146866991012	1	FACETS	0.786	0.721	0.852	0.786	0.721	0.852	SUBCLONAL	1	TRUE	0	0.708453386396074	1		721	269	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606500	93606500	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	112	735	1	ENST00000375746.1:c.320T>C	p.Phe107Ser	p.F107S	ENST00000375746	NM_001174167.1	107	tTc/tCc	2/14	1	2	FACETS	0.764	0.692	0.838	0.764	0.692	0.838	SUBCLONAL	1	TRUE	1	0.708453386396074	2		736	414	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916947	178916947	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	89	501	0	ENST00000263967.3:c.334A>T	p.Ile112Phe	p.I112F	ENST00000263967	NM_006218.2	112	Atc/Ttc	2/21	0.377557329530519	5	FACETS	1	0.906	1			1	CLONAL	1	TRUE	NA	0.377557329530519	5		501	721	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589623	67589634	+	inframe_deletion	In_Frame_Del	DEL	ATATGATAGATT	ATATGATAGATT	-	novel	NA	P-0022475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	73	269	0	ENST00000274335.5:c.1392_1403del	p.Asp464_Tyr467del	p.D464_Y467del	ENST00000274335		462	gaATATGATAGATTa/gaa	10/15	0.381628565806716	3	FACETS	1	0.954	1	0.591	0.519	0.667	CLONAL	1	TRUE	1	0.377557329530519	3		269	389	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005553	42005553	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	110	464	1	ENST00000219905.7:c.3289A>G	p.Lys1097Glu	p.K1097E	ENST00000219905	NM_001164273.1	1097	Aag/Gag	9/24	0.332255846082123	1	FACETS	0.877	0.791	0.967	0.877	0.791	0.967	CLONAL	1	TRUE	0	0.377557329530519	1		465	539	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341251	341251	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	102	652	0	ENST00000262320.3:c.2233G>C	p.Ala745Pro	p.A745P	ENST00000262320	NM_003502.3	745	Gcg/Ccg	9/11	1	2	FACETS	0.945	0.847	1	0.945	0.847	1	CLONAL	1	TRUE	1	0.377557329530519	2		652	572	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615802	1615802	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	84	491	2	ENST00000344749.5:c.1469C>A	p.Ala490Asp	p.A490D	ENST00000344749	NM_001136139.2	490	gCc/gAc	17/19	0.16177017903854	0	FACETS	0.54	0.478	0.606			1	INDETERMINATE	1	TRUE	0	0.377557329530519	0		493	513	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641857	12641906	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTGTTGGCTAAATGACTATGGAAAAGTACCTGATTCGCTGTGACTTCGA	ATTGTTGGCTAAATGACTATGGAAAAGTACCTGATTCGCTGTGACTTCGA	-	novel	NA	P-0022475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	94	213	0	ENST00000251849.4:c.843_862+30del		p.X281_splice	ENST00000251849	NM_002880.3	281		8/17	NA	2	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.377557329530519	2		213	435	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149453016	149453016	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	59	349	0	ENST00000286301.3:c.930C>G	p.Ile310Met	p.I310M	ENST00000286301	NM_005211.3	310	atC/atG	7/22	0.381628565806716	1	FACETS	0.653	0.564	0.75	0.653	0.564	0.75	SUBCLONAL	1	TRUE	0	0.377557329530519	1		349	388	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74868231	74868231	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	59	281	0	ENST00000284811.8:c.63G>C	p.Leu21Phe	p.L21F	ENST00000284811		21	ttG/ttC	3/4	0.314312953899176	4	FACETS	1	0.906	1			1	CLONAL	1	TRUE	NA	0.377557329530519	4		281	405	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871092	12871115	+	inframe_deletion	In_Frame_Del	DEL	CAGGATGTCAGCGGGAGCCGCCCG	CAGGATGTCAGCGGGAGCCGCCCG	-	novel	NA	P-0022475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	82	219	0	ENST00000228872.4:c.319_342del	p.Gln107_Pro114del	p.Q107_P114del	ENST00000228872	NM_004064.3	107	CAGGATGTCAGCGGGAGCCGCCCG/-	1/3	0.240279278863292	2	FACETS	1	0.946	1	0.555	0.493	0.622	CLONAL	1	TRUE	0	0.377557329530519	2		219	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0022476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	35	930	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	0.655	0.534	0.791	0.655	0.534	0.791	SUBCLONAL	1	TRUE	1	0.12	2		931	891	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0022476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	17	278	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	1	2	FACETS	0.494	0.367	0.646	0.494	0.367	0.646	SUBCLONAL	1	TRUE	1	0.12	2		278	574	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0022479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	133	701	0				ENST00000310581	NM_198253.2	-/1132			0.282913543004822	1	FACETS	1	0.972	1	1	0.972	1	INDETERMINATE	1	TRUE	0	0.490938125258583	1		701	361	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0022479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	326	708	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.390172362558162	2	FACETS	0.954	0.908	1	0.954	0.908	1	CLONAL	2	TRUE	0	0.490938125258583	2		709	696	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0022479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	278	814	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.175928130604948	3	FACETS	0.822	0.774	0.871	0.548	0.516	0.581	INDETERMINATE	2	TRUE	0	0.490938125258583	3		815	858	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710622	114710622	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	108	530	0	ENST00000543371.1:c.107C>A	p.Ser36Ter	p.S36*	ENST00000543371	NM_001198531.1	36	tCg/tAg	1/14	0.252868998028772	2	FACETS	0.856	0.771	0.945	0.428	0.385	0.473	INDETERMINATE	1	TRUE	0	0.490938125258583	2		530	514	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436047	51436047	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	168	345	0	ENST00000262662.1:c.7G>A	p.Glu3Lys	p.E3K	ENST00000262662		3	Gag/Aag	3/4	0.486601371446707	3	FACETS	1	0.987	1	0.675	0.623	0.729	CLONAL	1	TRUE	1	0.490938125258583	3		345	631	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426814	49426814	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	113	431	0	ENST00000301067.7:c.11674C>T	p.Gln3892Ter	p.Q3892*	ENST00000301067	NM_003482.3	3892	Cag/Tag	39/54	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.490938125258583	2		431	342	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341206	341206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764346231	NA	P-0022479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	255	931	0	ENST00000262320.3:c.2278G>A	p.Glu760Lys	p.E760K	ENST00000262320	NM_003502.3	760	Gag/Aag	9/11	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.490938125258583	2		931	726	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343517	343517	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	260	952	0	ENST00000262320.3:c.2157G>C	p.Lys719Asn	p.K719N	ENST00000262320	NM_003502.3	719	aaG/aaC	8/11	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.490938125258583	2		952	749	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23635337	23635337	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	194	662	0	ENST00000261584.4:c.2827G>C	p.Glu943Gln	p.E943Q	ENST00000261584	NM_024675.3	943	Gag/Cag	8/13	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.490938125258583	2		662	561	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89842194	89842194	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	130	726	0	ENST00000389301.3:c.1856C>G	p.Ser619Cys	p.S619C	ENST00000389301	NM_000135.2	619	tCc/tGc	21/43	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.490938125258583	NA		726	878	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627804	14627804	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	157	725	0	ENST00000254322.2:c.266C>G	p.Ser89Cys	p.S89C	ENST00000254322	NM_006145.1	89	tCt/tGt	2/3	1	2	FACETS	0.745	0.683	0.811	0.745	0.683	0.811	SUBCLONAL	1	TRUE	1	0.490938125258583	2		725	858	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964935	55964935	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	41	463	0	ENST00000263923.4:c.2302C>G	p.Leu768Val	p.L768V	ENST00000263923	NM_002253.2	768	Cta/Gta	16/30	0.431143958146496	1	FACETS	0.5	0.419	0.588	0.5	0.419	0.588	SUBCLONAL	1	TRUE	0	0.490938125258583	1		463	252	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143191840	143191840	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	122	567	0	ENST00000262992.4:c.591C>G	p.Ile197Met	p.I197M	ENST00000262992	NM_001101669.1	197	atC/atG	8/24	1	2	FACETS	0.866	0.785	0.95	0.866	0.785	0.95	CLONAL	1	TRUE	1	0.490938125258583	2		567	574	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673499	30673499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	291	705	0	ENST00000376406.3:c.3461C>T	p.Ser1154Phe	p.S1154F	ENST00000376406	NM_014641.2	1154	tCt/tTt	10/15	0.490938125258583	5	FACETS	0.856	0.808	0.904	0.856	0.808	0.904	CLONAL	3	TRUE	2	0.490938125258583	5		705	802	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32802933	32802933	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	203	372	0	ENST00000374899.4:c.943C>G	p.Gln315Glu	p.Q315E	ENST00000374899	NM_018833.2	315	Cag/Gag	5/12	0.490938125258583	5	FACETS	0.901	0.843	0.961	0.901	0.843	0.961	CLONAL	3	TRUE	2	0.490938125258583	5		372	531	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938390	44938390	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0022479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	61	396	0	ENST00000377967.4:c.2939-1G>A		p.X980_splice	ENST00000377967	NM_021140.2	980			0.490938125258583	1	FACETS	0.665	0.579	0.757	0.665	0.579	0.757	SUBCLONAL	1	TRUE	0	0.490938125258583	1		396	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0022480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2015	125	1075	2	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.11	2		1077	2140	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973671	15973671	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	61	530	0	ENST00000268712.3:c.4321G>C	p.Gly1441Arg	p.G1441R	ENST00000268712	NM_006311.3	1441	Ggc/Cgc	31/46	1	2	FACETS	0.999	0.859	1	0.999	0.859	1	CLONAL	1	TRUE	1	0.11	2		530	1110	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711876	89711876	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	94	524	0	ENST00000371953.3:c.494G>A	p.Gly165Glu	p.G165E	ENST00000371953	NM_000314.4	165	gGa/gAa	6/9	0.485221921676077	2	FACETS	0.888	0.808	0.97	0.888	0.808	0.97	CLONAL	2	TRUE	0	0.489840355183224	2		524	216	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220339	98220339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772406487	NA	P-0022482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	147	452	0	ENST00000331920.6:c.3124G>A	p.Val1042Met	p.V1042M	ENST00000331920	NM_000264.3	1042	Gtg/Atg	18/24	0.228147536701138	3	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.32	3		452	837	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262240	115262240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	231	565	0	ENST00000438362.2:c.2314C>T	p.Arg772Cys	p.R772C	ENST00000438362	NM_001242891.1	772	Cgc/Tgc	18/20	0.201707673647406	3	FACETS	1	0.989	1	0.666	0.619	0.714	CLONAL	1	TRUE	1	0.32	3		565	1258	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22008901	22008901	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1588	318	876	0	ENST00000276925.6:c.52C>G	p.Leu18Val	p.L18V	ENST00000276925	NM_004936.3	18	Ctg/Gtg	1/2	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.32	2		876	1906	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0022483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	143	831	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.375022985624978	3	FACETS	1	0.97	1	0.729	0.674	0.785	CLONAL	2	FALSE	0	0.47605338025658	3		832	340	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431634	6431634	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	45	497	0	ENST00000356142.4:c.187G>C	p.Asp63His	p.D63H	ENST00000356142	NM_018890.3	63	Gat/Cat	3/7	0.47605338025658	3	FACETS	1	0.926	1	0.576	0.49	0.669	CLONAL	1	FALSE	1	0.47605338025658	3		497	203	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913381	NA	P-0022483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	120	600	0	ENST00000304494.5:c.322G>T	p.Asp108Tyr	p.D108Y	ENST00000304494	NM_000077.4	108	Gat/Tat	2/3	0.425228056171036	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	FALSE	0	0.47605338025658	2		600	232	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867546	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGC	GGCGGCGGC	-	rs11466445	NA	P-0022483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	14	55	2	ENST00000374994.4:c.70_78del	p.Ala24_Ala26del	p.A24_A26del	ENST00000374994	NM_004612.2	17	ctGGCGGCGGCg/ctg	1/9	0.425228056171036	2	FACETS	0.828	0.612	1	0.414	0.306	0.539	CLONAL	1	FALSE	0	0.47605338025658	2		57	71	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001999	29001999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1004788109	NA	P-0022483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	19	537	0	ENST00000282397.4:c.1166C>T	p.Ser389Leu	p.S389L	ENST00000282397	NM_002019.4	389	tCg/tTg	9/30	1	2	FACETS	0.525	0.402	0.668	0.525	0.402	0.668	SUBCLONAL	1	FALSE	1	0.47605338025658	2		537	152	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833924	44833924	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0022483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	123	271	0	ENST00000377967.4:c.348C>G	p.Tyr116Ter	p.Y116*	ENST00000377967	NM_021140.2	116	taC/taG	4/29	0.441083864006062	2	FACETS	1	0.978	1			1	CLONAL	3	FALSE	NA	0.47605338025658	2		271	161	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982403	201982404	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0022483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	246	815	0	ENST00000359651.3:c.783dup	p.Glu262ArgfsTer39	p.E262Rfs*39	ENST00000359651		261	ctc/ctCc	6/8	0.240111896030339	5	FACETS	1	0.976	1	1	0.976	1	INDETERMINATE	3	FALSE	2	0.47605338025658	5		815	556	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786740	3786740	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	41	705	0	ENST00000262367.5:c.4471C>G	p.Gln1491Glu	p.Q1491E	ENST00000262367	NM_004380.2	1491	Caa/Gaa	27/31	1	2	FACETS	0.816	0.687	0.957	0.816	0.687	0.957	CLONAL	1	FALSE	1	0.47605338025658	2		705	211	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163315571	163315571	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0022483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	22	384	0	ENST00000271452.3:c.911C>G	p.Ser304Ter	p.S304*	ENST00000271452	NM_145697.2	304	tCa/tGa	11/14	0.240111896030339	5	FACETS	1	0.855	1	0.375	0.293	0.467	INDETERMINATE	1	FALSE	2	0.47605338025658	5		384	141	SUCCESS
RET	5979	MSKCC	GRCh37	10	43598002	43598002	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	33	765	0	ENST00000355710.3:c.550A>T	p.Thr184Ser	p.T184S	ENST00000355710	NM_020975.4	184	Acc/Tcc	3/20	0.400209137551723	5	FACETS	0.614	0.5	0.742	0.205	0.166	0.248	SUBCLONAL	1	FALSE	2	0.47605338025658	5		765	387	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494891	56494891	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	140	590	0	ENST00000267101.3:c.3248C>G	p.Ser1083Cys	p.S1083C	ENST00000267101	NM_001982.3	1083	tCt/tGt	27/28	0.47605338025658	5	FACETS	1	0.953	1	0.705	0.646	0.765	CLONAL	2	FALSE	2	0.47605338025658	5		590	477	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991137	41991137	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	17	612	1	ENST00000219905.7:c.2090C>A	p.Ser697Ter	p.S697*	ENST00000219905	NM_001164273.1	697	tCa/tAa	4/24	1	2	FACETS	0.444	0.333	0.573	0.444	0.333	0.573	SUBCLONAL	1	FALSE	1	0.47605338025658	2		613	161	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30946599	30946599	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	169	467	0	ENST00000375687.4:c.21G>T	p.Lys7Asn	p.K7N	ENST00000375687	NM_015338.5	7	aaG/aaT	1/13	0.240111896030339	5	FACETS	0.843	0.777	0.911	0.562	0.518	0.608	INDETERMINATE	2	FALSE	2	0.47605338025658	5		467	722	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164515	36164515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	38	604	0	ENST00000300305.3:c.1360G>A	p.Glu454Lys	p.E454K	ENST00000300305		454	Gag/Aag	8/8	1	2	FACETS	0.682	0.568	0.807	0.682	0.568	0.807	SUBCLONAL	1	FALSE	1	0.47605338025658	2		604	234	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566071	141566071	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	93	721	0	ENST00000220592.5:c.1193G>C	p.Gly398Ala	p.G398A	ENST00000220592	NM_012154.3	398	gGa/gCa	10/19	0.47605338025658	4	FACETS	0.874	0.785	0.967	0.874	0.785	0.967	CLONAL	2	FALSE	2	0.47605338025658	4		721	330	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195112	123195112	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	60	253	0	ENST00000218089.9:c.1455G>A	p.Trp485Ter	p.W485*	ENST00000218089	NM_001042749.1	485	tgG/tgA	16/35	0.441083864006062	2	FACETS	1	0.939	1			1	CLONAL	2	FALSE	NA	0.47605338025658	2		253	117	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0022484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	15	693	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		693	603	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732976	30732976	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	23	456	0	ENST00000295754.5:c.1589C>T	p.Thr530Ile	p.T530I	ENST00000295754	NM_003242.5	530	aCa/aTa	7/7	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		456	445	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602664	55602664	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs1057519713	NA	P-0022487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	174	304	1	ENST00000288135.5:c.2485G>C	p.Ala829Pro	p.A829P	ENST00000288135	NM_000222.2	829	Gct/Cct	18/21	0.738473666898639	8	FACETS	0.979	0.914	1			1	CLONAL	4	TRUE	NA	0.738473666898639	8		305	387	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593590	55593607	+	inframe_deletion	In_Frame_Del	DEL	GTATGAAGTACAGTGGAA	GTATGAAGTACAGTGGAA	-	novel	NA	P-0022487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	149	387	0	ENST00000288135.5:c.1657_1674del	p.Tyr553_Lys558del	p.Y553_K558del	ENST00000288135	NM_000222.2	552	atGTATGAAGTACAGTGGAAg/atg	11/21	0.738473666898639	8	FACETS	1	0.926	1			1	CLONAL	3	TRUE	NA	0.738473666898639	8		387	431	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005499	42005521	+	frameshift_variant	Frame_Shift_Del	DEL	GGTTGTACTTGTTTGAAAAGAAA	GGTTGTACTTGTTTGAAAAGAAA	-	novel	NA	P-0022487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	218	692	0	ENST00000219905.7:c.3235_3257del	p.Gly1079SerfsTer5	p.G1079Sfs*5	ENST00000219905	NM_001164273.1	1079	GGTTGTACTTGTTTGAAAAGAAAa/a	9/24	NA	2	FACETS	0.834	0.792	0.875			1	INDETERMINATE	2	TRUE	NA	0.738473666898639	2		692	354	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982461	10982461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	13	147	1	ENST00000327064.4:c.83C>T	p.Thr28Ile	p.T28I	ENST00000327064	NM_199141.1	28	aCc/aTc	1/16	1	2	FACETS	0.154	0.109	0.208	0.154	0.109	0.208	SUBCLONAL	1	TRUE	1	0.738473666898639	2		148	229	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161376	185161376	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	41	597	0	ENST00000265026.3:c.803A>C	p.Asn268Thr	p.N268T	ENST00000265026	NM_004721.4	268	aAt/aCt	4/14	1	2	FACETS	0.463	0.388	0.544	0.463	0.388	0.544	SUBCLONAL	1	TRUE	1	0.738473666898639	2		597	240	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672432	30672432	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	89	632	0	ENST00000376406.3:c.4528C>G	p.Pro1510Ala	p.P1510A	ENST00000376406	NM_014641.2	1510	Ccc/Gcc	10/15	0.232800383187537	5	FACETS	1	0.979	1	0.477	0.426	0.53	INDETERMINATE	1	TRUE	2	0.738473666898639	5		632	355	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644667	134644667	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	46	469	0	ENST00000398015.3:c.68T>C	p.Met23Thr	p.M23T	ENST00000398015	NM_004441.4	23	aTg/aCg	2/16	1	2	FACETS	0.823	0.692	0.969	0.823	0.692	0.969	CLONAL	1	TRUE	1	0.15	2		469	745	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0022489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	193	412	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	0.764532790184391	4	FACETS	0.859	0.801	0.917	0.859	0.801	0.917	CLONAL	2	TRUE	2	0.76668839334368	4		412	518	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544682	65544682	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	421	875	1	ENST00000358664.4:c.244C>T	p.Gln82Ter	p.Q82*	ENST00000358664	NM_002382.4	82	Cag/Tag	4/5	0.76668839334368	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.76668839334368	2		876	501	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0022490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	187	734	3	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.414474056991851	3	FACETS	1	0.973	1	1	0.993	1	CLONAL	3	FALSE	1	0.405788517447425	3		737	349	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243777010	243777010	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200428825	NA	P-0022490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	48	595	1	ENST00000263826.5:c.659G>A	p.Arg220His	p.R220H	ENST00000263826	NM_005465.4	220	cGt/cAt	7/13	0.185576690084594	3	FACETS	1	0.96	1			1	INDETERMINATE	1	FALSE	NA	0.405788517447425	3		596	203	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180252	38180252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	110	578	0	ENST00000396334.3:c.100C>T	p.Pro34Ser	p.P34S	ENST00000396334	NM_002468.4	34	Ccc/Tcc	1/5	0.405788517447425	5	FACETS	1	0.934	1	0.694	0.628	0.763	CLONAL	2	FALSE	2	0.405788517447425	5		578	419	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710518	114710518	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0022490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	67	271	0	ENST00000543371.1:c.3G>A	p.Met1?	p.M1?	ENST00000543371	NM_001198531.1	1	atG/atA	1/14	0.414474056991851	3	FACETS	1	0.944	1	0.572	0.5	0.649	CLONAL	1	FALSE	1	0.405788517447425	3		271	347	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346811	89346811	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748373867	NA	P-0022490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	10	264	0	ENST00000301030.4:c.6139G>A	p.Ala2047Thr	p.A2047T	ENST00000301030	NM_001256183.1	2047	Gcc/Acc	9/13	0.372321863216562	5	FACETS	0.515	0.349	0.721	0.172	0.116	0.241	SUBCLONAL	1	FALSE	2	0.405788517447425	5		264	154	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719828	190719828	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	27	264	0	ENST00000441310.2:c.1830G>T	p.Lys610Asn	p.K610N	ENST00000441310	NM_000534.4	610	aaG/aaT	9/13	0.263178282183774	5	FACETS	0.759	0.612	0.922	0.506	0.408	0.615	CLONAL	2	FALSE	2	0.405788517447425	5		264	141	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0022491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	184	501	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.143687293966831	3	FACETS	1	0.989	1	0.703	0.65	0.759	INDETERMINATE	1	TRUE	1	0.349220926111421	3		501	880	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553588	106553588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753673199	NA	P-0022491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	44	336	1	ENST00000369096.4:c.1553C>T	p.Thr518Met	p.T518M	ENST00000369096	NM_001198.3	518	aCg/aTg	5/7	0.318629995936332	1	FACETS	0.407	0.341	0.48	0.407	0.341	0.48	SUBCLONAL	1	TRUE	0	0.349220926111421	1		337	511	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379883	17379883	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1229	117	970	0	ENST00000359435.4:c.268A>C	p.Asn90His	p.N90H	ENST00000359435	NM_001033549.1	90	Aac/Cac	2/9	0.318629995936332	1	FACETS	0.411	0.369	0.455	0.411	0.369	0.455	SUBCLONAL	1	TRUE	0	0.349220926111421	1		970	1346	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158036	27158036	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0022500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	204	1018	0	ENST00000380036.4:c.262del	p.Trp88GlyfsTer29	p.W88Gfs*29	ENST00000380036	NM_000459.3	87	gTt/gt	2/23	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.53193347265664	2		1018	756	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0022501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	386	713	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.506220327921493	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.506220327921493	1		715	899	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913471	NA	P-0022501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	2630	1494	2	ENST00000269571.5:c.2329G>C	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ctg	20/27	0.506220327921493	12	FACETS	0.965	0.955	0.974			1	CLONAL	12	TRUE	NA	0.506220327921493	12		1496	3169	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859426	57859426	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756656703	NA	P-0022501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	47	1058	0	ENST00000228682.2:c.571C>T	p.Arg191Trp	p.R191W	ENST00000228682	NM_005269.2	191	Cgg/Tgg	6/12	0.170755702888668	4	FACETS	0.339	0.285	0.4	0.17	0.142	0.2	INDETERMINATE	1	TRUE	2	0.506220327921493	4		1058	824	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023737	27023737	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	309	1258	0	ENST00000324856.7:c.844del	p.Ala282ProfsTer81	p.A282Pfs*81	ENST00000324856	NM_006015.4	281	gcG/gc	1/20	0.170755702888668	4	FACETS	0.907	0.856	0.958	0.907	0.856	0.958	INDETERMINATE	2	TRUE	2	0.506220327921493	4		1258	1014	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106490	27106490	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	116	1236	0	ENST00000324856.7:c.6101A>G	p.Glu2034Gly	p.E2034G	ENST00000324856	NM_006015.4	2034	gAg/gGg	20/20	0.170755702888668	4	FACETS	0.656	0.589	0.726	0.328	0.294	0.363	INDETERMINATE	1	TRUE	2	0.506220327921493	4		1236	1053	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973695	15973695	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	237	947	1	ENST00000268712.3:c.4297G>T	p.Gly1433Ter	p.G1433*	ENST00000268712	NM_006311.3	1433	Gga/Tga	31/46	0.506220327921493	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.506220327921493	1		948	632	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191051	2191051	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	225	889	1	ENST00000398665.3:c.305C>T	p.Pro102Leu	p.P102L	ENST00000398665	NM_032482.2	102	cCg/cTg	5/28	0.506220327921493	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.506220327921493	1		890	574	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279175	142279175	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	125	1085	0	ENST00000350721.4:c.1471G>A	p.Glu491Lys	p.E491K	ENST00000350721	NM_001184.3	491	Gaa/Aaa	6/47	0.304914921852885	4	FACETS	1	0.97	1	0.582	0.528	0.639	CLONAL	1	TRUE	2	0.506220327921493	4		1085	639	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158549	26158549	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	139	1229	2	ENST00000289316.2:c.152C>T	p.Pro51Leu	p.P51L	ENST00000289316	NM_138720.2	51	cCc/cTc	1/2	1	2	FACETS	0.792	0.723	0.865	0.792	0.723	0.865	SUBCLONAL	1	TRUE	1	0.506220327921493	2		1231	693	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602314	10602314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	538	1053	0	ENST00000171111.5:c.1264G>A	p.Asp422Asn	p.D422N	ENST00000171111	NM_203500.1	422	Gat/Aat	3/6	0.669127216319315	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.669127216319315	1		1053	1007	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944157	81944157	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761094228	NA	P-0022502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	389	715	0	ENST00000359376.3:c.1766G>A	p.Arg589His	p.R589H	ENST00000359376	NM_002661.3	589	cGc/cAc	18/33	1	2	FACETS	0.97	0.922	1	0.97	0.922	1	CLONAL	1	TRUE	1	0.669127216319315	2		715	1199	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045839	180045839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140041761	NA	P-0022502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	491	850	3	ENST00000261937.6:c.2932G>A	p.Asp978Asn	p.D978N	ENST00000261937	NM_182925.4	978	Gac/Aac	21/30	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.669127216319315	2		853	1390	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221981	1221981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	469	854	1	ENST00000326873.7:c.896C>T	p.Ser299Phe	p.S299F	ENST00000326873	NM_000455.4	299	tCc/tTc	7/10	0.669127216319315	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.669127216319315	1		855	924	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416417	49416417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565753611	NA	P-0022502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	345	703	1	ENST00000301067.7:c.16294C>T	p.Arg5432Trp	p.R5432W	ENST00000301067	NM_003482.3	5432	Cgg/Tgg	51/54	1	2	FACETS	0.955	0.905	1	0.955	0.905	1	CLONAL	1	TRUE	1	0.669127216319315	2		704	1080	SUCCESS
EED	8726	MSKCC	GRCh37	11	85966317	85966317	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	113	512	0	ENST00000263360.6:c.414C>A	p.Tyr138Ter	p.Y138*	ENST00000263360	NM_003797.3	138	taC/taA	4/12	0.669127216319315	1	FACETS	0.973	0.896	1	0.973	0.896	1	CLONAL	1	TRUE	0	0.669127216319315	1		512	231	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658881	3658881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144832924	NA	P-0022502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	329	694	0	ENST00000294008.3:c.85C>T	p.Arg29Cys	p.R29C	ENST00000294008	NM_032444.2	29	Cgc/Tgc	2/15	1	2	FACETS	0.953	0.902	1	0.953	0.902	1	CLONAL	1	TRUE	1	0.669127216319315	2		694	1032	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785817	50785817	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	110	439	0	ENST00000398568.2:c.807G>C	p.Met269Ile	p.M269I	ENST00000398568	NM_001042412.1	269	atG/atC	4/18	1	2	FACETS	0.85	0.77	0.932	0.85	0.77	0.932	CLONAL	1	TRUE	1	0.669127216319315	2		439	387	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932666	49932666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	437	962	0	ENST00000296474.3:c.3205G>A	p.Glu1069Lys	p.E1069K	ENST00000296474	NM_002447.2	1069	Gag/Aag	14/20	0.666501136945278	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.669127216319315	1		962	822	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201726	66201726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	293	725	1	ENST00000273854.3:c.2776G>A	p.Asp926Asn	p.D926N	ENST00000273854	NM_004439.5	926	Gat/Aat	16/18	1	2	FACETS	0.936	0.882	0.99	0.936	0.882	0.99	CLONAL	1	TRUE	1	0.669127216319315	2		726	936	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176678849	176678849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1316313643	NA	P-0022502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	199	465	0	ENST00000439151.2:c.4760G>A	p.Arg1587His	p.R1587H	ENST00000439151	NM_022455.4	1587	cGc/cAc	12/23	1	2	FACETS	0.986	0.919	1	0.986	0.919	1	CLONAL	1	TRUE	1	0.669127216319315	2		465	603	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271269	26271269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755274030	NA	P-0022502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	314	737	0	ENST00000305910.3:c.344C>T	p.Ala115Val	p.A115V	ENST00000305910	NM_003534.2	115	gCt/gTt	1/1	0.669127216319315	2	FACETS	1	0.959	1	0.508	0.48	0.536	CLONAL	1	TRUE	0	0.669127216319315	2		737	924	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5073735	5073735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	154	597	0	ENST00000381652.3:c.1814C>T	p.Ser605Phe	p.S605F	ENST00000381652	NM_004972.3	605	tCt/tTt	14/25	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.669127216319315	2		597	444	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5077458	5077458	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs776937429	NA	P-0022502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	87	488	0	ENST00000381652.3:c.1870C>G	p.Leu624Val	p.L624V	ENST00000381652	NM_004972.3	624	Ctg/Gtg	15/25	1	2	FACETS	0.818	0.731	0.908	0.818	0.731	0.908	CLONAL	1	TRUE	1	0.669127216319315	2		488	318	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0022503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	30	845	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	1	2	FACETS	0.483	0.388	0.593	0.483	0.388	0.593	SUBCLONAL	1	TRUE	1	0.17	2		845	730	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436099	51436125	+	inframe_deletion	In_Frame_Del	DEL	AACTTACTAGTTTGTTGCAAAATAATG	AACTTACTAGTTTGTTGCAAAATAATG	-	novel	NA	P-0022503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	40	525	0	ENST00000262662.1:c.59_85del	p.Gln20_Val29delinsLeu	p.Q20_V29delinsL	ENST00000262662		20	cAACTTACTAGTTTGTTGCAAAATAATGta/cta	3/4	1	2	FACETS	0.989	0.821	1	0.989	0.821	1	CLONAL	1	TRUE	1	0.17	2		525	476	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196079	108196079	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555119041	NA	P-0022503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	24	718	2	ENST00000278616.4:c.6615G>A	p.Trp2205Ter	p.W2205*	ENST00000278616	NM_000051.3	2205	tgG/tgA	46/63	1	2	FACETS	0.713	0.558	0.892	0.713	0.558	0.892	SUBCLONAL	1	TRUE	1	0.17	2		720	396	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433904	49433904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	43	1058	1	ENST00000301067.7:c.7649del	p.Pro2550LeufsTer33	p.P2550Lfs*33	ENST00000301067	NM_003482.3	2550	cCt/ct	31/54	1	2	FACETS	0.701	0.585	0.83	0.701	0.585	0.83	SUBCLONAL	1	TRUE	1	0.17	2		1059	722	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669525	88669525	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1361454724	NA	P-0022503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	32	762	2	ENST00000360948.2:c.1373G>A	p.Arg458Gln	p.R458Q	ENST00000360948	NM_001012338.2	458	cGa/cAa	12/19	1	2	FACETS	0.686	0.555	0.834	0.686	0.555	0.834	SUBCLONAL	1	TRUE	1	0.17	2		764	549	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829847	72829847	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750842718	NA	P-0022503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	39	1063	0	ENST00000268489.5:c.6734C>T	p.Ser2245Leu	p.S2245L	ENST00000268489	NM_006885.3	2245	tCa/tTa	9/10	1	2	FACETS	0.613	0.507	0.733	0.613	0.507	0.733	SUBCLONAL	1	TRUE	1	0.17	2		1063	748	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843770	151843770	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	42	632	1	ENST00000262189.6:c.13945G>T	p.Glu4649Ter	p.E4649*	ENST00000262189	NM_170606.2	4649	Gaa/Taa	53/59	1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	1	0.17	2		633	486	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0022506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	109	281	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.737322886758461	2	FACETS	0.88	0.82	0.938	0.88	0.82	0.938	CLONAL	2	TRUE	0	0.737322886758461	2		281	168	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0022506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	299	484	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.737322886758461	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.737322886758461	1		484	473	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0022506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	337	724	2	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.737322886758461	2		726	868	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0022506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	347	560	1	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.737322886758461	2	FACETS	0.919	0.885	0.952	0.919	0.885	0.952	CLONAL	2	TRUE	0	0.737322886758461	2		561	512	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736254	243736254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772090769	NA	P-0022506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	136	544	0	ENST00000263826.5:c.793G>A	p.Gly265Arg	p.G265R	ENST00000263826	NM_005465.4	265	Gga/Aga	8/13	1	2	FACETS	0.883	0.81	0.957	0.883	0.81	0.957	CLONAL	1	TRUE	1	0.737322886758461	2		544	418	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39774503	39774503	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	268	768	0	ENST00000288319.7:c.649C>T	p.Arg217Trp	p.R217W	ENST00000288319	NM_182918.3	217	Cgg/Tgg	5/10	1	2	FACETS	0.902	0.849	0.956	0.902	0.849	0.956	CLONAL	1	TRUE	1	0.737322886758461	2		768	806	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535414	187535414	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs375045636	NA	P-0022506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	24	707	0	ENST00000441802.2:c.9160T>C	p.Ser3054Pro	p.S3054P	ENST00000441802	NM_005245.3	3054	Tct/Cct	12/27	0.737322886758461	1	FACETS	0.137	0.107	0.171	0.137	0.107	0.171	SUBCLONAL	1	TRUE	0	0.737322886758461	1		707	300	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914562	32914562	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	108	849	0	ENST00000380152.3:c.6070C>A	p.Gln2024Lys	p.Q2024K	ENST00000380152		2024	Cag/Aag	11/27	0.3	3	FACETS	1	0.98	1	0.69	0.621	0.763	CLONAL	1	FALSE	1	0.3	3		849	600	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0022510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	210	929	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.963	0.894	1	0.963	0.894	1	CLONAL	1	TRUE	1	0.404941925655265	2		930	1077	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0022510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	250	953	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.404941925655265	2		955	1089	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056283	26056283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1459637809	NA	P-0022510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	112	651	0	ENST00000343677.2:c.374G>A	p.Gly125Glu	p.G125E	ENST00000343677	NM_005319.3	125	gGa/gAa	1/1	0.376344267947005	3	FACETS	0.755	0.678	0.836	0.378	0.339	0.418	SUBCLONAL	1	TRUE	1	0.404941925655265	3		651	881	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999634	100999634	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	57	1319	1	ENST00000325455.5:c.168C>A	p.Asp56Glu	p.D56E	ENST00000325455	NM_001202474.3	56	gaC/gaA	1/8	0.404941925655265	1	FACETS	0.214	0.183	0.249	0.214	0.183	0.249	SUBCLONAL	1	TRUE	0	0.404941925655265	1		1320	1048	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715741	61715741	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	114	537	0	ENST00000401558.2:c.2188G>A	p.Ala730Thr	p.A730T	ENST00000401558	NM_003400.3	730	Gca/Aca	18/25	1	2	FACETS	0.773	0.697	0.854	0.773	0.697	0.854	SUBCLONAL	1	TRUE	1	0.404941925655265	2		537	728	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981914	70981914	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	78	1036	0	ENST00000276594.2:c.182C>G	p.Ser61Cys	p.S61C	ENST00000276594	NM_024504.3	61	tCt/tGt	2/8	1	2	FACETS	0.447	0.392	0.506	0.447	0.392	0.506	SUBCLONAL	1	TRUE	1	0.404941925655265	2		1036	862	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527568	29527569	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555610903	NA	P-0022511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	31	906	0	ENST00000356175.3:c.1019_1020del	p.Ser340CysfsTer12	p.S340Cfs*12	ENST00000356175	NM_000267.3	339	aaCTct/aact	9/57	0.310299654777765	2	FACETS	0.829	0.675	1	0.415	0.337	0.501	CLONAL	1	TRUE	0	0.339814456730887	2		906	220	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578466	7578466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	266	1044	0	ENST00000269305.4:c.464C>T	p.Thr155Ile	p.T155I	ENST00000269305	NM_001126112.2	155	aCc/aTc	5/11	0.310299654777765	2	FACETS	0.985	0.927	1	0.985	0.927	1	CLONAL	2	TRUE	0	0.339814456730887	2		1044	795	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828126	243828126	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	31	831	4	ENST00000263826.5:c.232C>A	p.Gln78Lys	p.Q78K	ENST00000263826	NM_005465.4	78	Cag/Aag	3/13	1	2	FACETS	0.221	0.179	0.268	0.221	0.179	0.268	SUBCLONAL	1	TRUE	1	0.899879658916352	2		835	312	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101054	27101054	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	548	1085	3	ENST00000324856.7:c.4336C>T	p.Arg1446Ter	p.R1446*	ENST00000324856	NM_006015.4	1446	Cga/Tga	18/20	0.888725684980969	2	FACETS	1	0.97	1	0.505	0.485	0.524	CLONAL	1	TRUE	0	0.899879658916352	2		1088	1207	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0022519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	367	714	1	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.880511529948152	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.899879658916352	1		715	419	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447772	49447773	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0022519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	374	736	0	ENST00000301067.7:c.661dup	p.Ala221GlyfsTer13	p.A221Gfs*13	ENST00000301067	NM_003482.3	221	gct/gGct	5/54	NA	2	FACETS	0.904	0.861	0.947			1	INDETERMINATE	1	TRUE	NA	0.899879658916352	2		736	920	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456804	32456804	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	504	906	0	ENST00000332351.3:c.88C>A	p.Gln30Lys	p.Q30K	ENST00000332351	NM_024426.4	30	Cag/Aag	1/10	0.237472579278492	1	FACETS	0.595	0.572	0.618	0.595	0.572	0.618	INDETERMINATE	1	TRUE	0	0.899879658916352	1		906	1036	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135712	64135712	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	536	933	1	ENST00000334205.4:c.1180G>T	p.Ala394Ser	p.A394S	ENST00000334205	NM_003942.2	394	Gcc/Tcc	10/17	0.237472579278492	1	FACETS	0.53	0.509	0.551	0.53	0.509	0.551	INDETERMINATE	1	TRUE	0	0.899879658916352	1		934	1237	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219167	133219167	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs766252708	NA	P-0022519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	519	1023	1	ENST00000320574.5:c.4877G>T	p.Arg1626Leu	p.R1626L	ENST00000320574	NM_006231.2	1626	cGc/cTc	37/49	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.899879658916352	2		1024	1128	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245650	41245650	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80357851	NA	P-0022519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	173	871	0	ENST00000357654.3:c.1898del	p.Pro633HisfsTer18	p.P633Hfs*18	ENST00000357654	NM_007294.3	633	cCa/ca	10/23	1	2	FACETS	0.961	0.896	1	0.961	0.896	1	CLONAL	1	TRUE	1	0.899879658916352	2		871	400	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212138	36212138	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1258696516	NA	P-0022519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1210	307	567	0	ENST00000222270.7:c.1893del	p.Ser632ProfsTer28	p.S632Pfs*28	ENST00000222270	NM_014727.1	630	gCc/gc	3/37	0.86751965093805	5	FACETS	1	0.972	1			1	CLONAL	1	TRUE	NA	0.899879658916352	5		567	1517	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651543	52651543	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	145	638	0	ENST00000394830.3:c.1553T>A	p.Ile518Lys	p.I518K	ENST00000394830	NM_018313.4	518	aTa/aAa	15/30	0.899879658916352	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.899879658916352	1		638	177	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80021321	80021321	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	139	846	0	ENST00000265081.6:c.1390del	p.Glu464AsnfsTer32	p.E464Nfs*32	ENST00000265081	NM_002439.4	464	Gaa/aa	9/24	0.237472579278492	1	FACETS	0.494	0.456	0.533	0.494	0.456	0.533	INDETERMINATE	1	TRUE	0	0.899879658916352	1		846	344	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694619	176694619	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	238	631	0	ENST00000439151.2:c.5203A>G	p.Asn1735Asp	p.N1735D	ENST00000439151	NM_022455.4	1735	Aac/Gac	15/23	0.237472579278492	1	FACETS	0.553	0.522	0.585	0.553	0.522	0.585	INDETERMINATE	1	TRUE	0	0.899879658916352	1		631	526	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265548	152265548	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	361	727	0	ENST00000206249.3:c.1001C>G	p.Thr334Ser	p.T334S	ENST00000206249	NM_000125.3	334	aCc/aGc	4/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.899879658916352	2		727	765	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729640	41729640	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	279	774	0	ENST00000242208.4:c.889G>A	p.Ala297Thr	p.A297T	ENST00000242208	NM_002192.2	297	Gcc/Acc	3/3	1	2	FACETS	0.92	0.87	0.97	0.92	0.87	0.97	CLONAL	1	TRUE	1	0.899879658916352	2		774	674	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900145	151900145	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	52	503	0	ENST00000262189.6:c.3966G>T	p.Trp1322Cys	p.W1322C	ENST00000262189	NM_170606.2	1322	tgG/tgT	26/59	1	2	FACETS	0.947	0.831	1	0.947	0.831	1	CLONAL	1	TRUE	1	0.899879658916352	2		503	122	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447778	49447778	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	424	740	0	ENST00000301067.7:c.656A>T	p.Glu219Val	p.E219V	ENST00000301067	NM_003482.3	219	gAg/gTg	5/54	NA	2	FACETS	0.97	0.928	1			1	INDETERMINATE	1	TRUE	NA	0.899879658916352	2		740	971	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156713	20156713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	81	693	0	ENST00000379607.5:c.44G>A	p.Gly15Asp	p.G15D	ENST00000379607	NM_001412.3	15	gGt/gAt	2/7	0.41004251315648	4	FACETS	1	0.94	1			1	CLONAL	1	TRUE	NA	0.531197175904182	4		693	425	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179198	123179198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	40	499	0	ENST00000218089.9:c.647G>A	p.Arg216Gln	p.R216Q	ENST00000218089	NM_001042749.1	216	cGa/cAa	8/35	NA	2	FACETS	0.772	0.649	0.906			1	INDETERMINATE	1	TRUE	NA	0.531197175904182	2		499	195	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437605	56437605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329721997	NA	P-0022522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	102	581	0	ENST00000407977.2:c.857G>A	p.Arg286Gln	p.R286Q	ENST00000407977		286	cGg/cAg	8/10	0.518909837430918	3	FACETS	1	0.961	1	0.379	0.34	0.418	CLONAL	1	TRUE	0	0.531197175904182	3		581	428	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799281	42799281	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	69	692	0	ENST00000575354.2:c.4765G>C	p.Glu1589Gln	p.E1589Q	ENST00000575354	NM_015125.3	1589	Gag/Cag	20/20	0.531197175904182	3	FACETS	0.847	0.742	0.96	0.424	0.371	0.48	CLONAL	1	TRUE	1	0.531197175904182	3		692	388	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504048	123504048	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	36	505	0	ENST00000371139.4:c.224G>T	p.Arg75Ile	p.R75I	ENST00000371139	NM_001114937.2	75	aGa/aTa	3/4	NA	2	FACETS	0.706	0.586	0.837			1	INDETERMINATE	1	TRUE	NA	0.531197175904182	2		505	192	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs878854073	NA	P-0022522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	226	739	0	ENST00000269305.4:c.673-1G>A		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.524109128013126	2	FACETS	0.999	0.945	1	0.999	0.945	1	CLONAL	2	TRUE	0	0.531197175904182	2		739	426	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374265	118374266	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1057520177	NA	P-0022522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	226	573	0	ENST00000534358.1:c.7659dup	p.Glu2554ArgfsTer13	p.E2554Rfs*13	ENST00000534358	NM_005933.3	2553	ata/atAa	27/36	0.531197175904182	5	FACETS	1	0.987	1	0.804	0.753	0.855	CLONAL	2	TRUE	2	0.531197175904182	5		573	634	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10305557	10305557	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	67	712	0	ENST00000340748.4:c.19C>G	p.Pro7Ala	p.P7A	ENST00000340748		7	Cca/Gca	1/40	0.531197175904182	3	FACETS	0.751	0.655	0.854	0.25	0.218	0.285	SUBCLONAL	1	TRUE	0	0.531197175904182	3		712	425	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36217202	36217202	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	142	1033	2	ENST00000222270.7:c.3951G>T	p.Glu1317Asp	p.E1317D	ENST00000222270	NM_014727.1	1317	gaG/gaT	14/37	0.531197175904182	4	FACETS	0.816	0.743	0.893	0.272	0.247	0.298	CLONAL	1	TRUE	1	0.531197175904182	4		1035	1003	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163749	32163749	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	144	826	0	ENST00000375023.3:c.5477A>G	p.Glu1826Gly	p.E1826G	ENST00000375023	NM_004557.3	1826	gAg/gGg	30/30	0.531197175904182	5	FACETS	0.864	0.791	0.939	0.432	0.395	0.47	CLONAL	2	TRUE	1	0.531197175904182	5		826	564	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971156	21971156	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	183	648	1	ENST00000304494.5:c.202G>A	p.Ala68Thr	p.A68T	ENST00000304494	NM_000077.4	68	Gcg/Acg	2/3	1	2	FACETS	0.885	0.82	0.953	0.885	0.82	0.953	CLONAL	1	TRUE	1	0.593204471512083	2		649	697	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652339	206652339	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1553386246	NA	P-0022524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1677	293	1049	1	ENST00000367120.3:c.1046A>T	p.His349Leu	p.H349L	ENST00000367120	NM_014002.3	349	cAc/cTc	10/22	0.593204471512083	5	FACETS	0.948	0.888	1	0.237	0.222	0.253	CLONAL	1	TRUE	1	0.593204471512083	5		1050	1970	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572929	7572929	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	novel	NA	P-0022524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	167	755	0	ENST00000269305.4:c.1180T>C	p.Ter394ArgextTer9	p.*394Rext*9	ENST00000269305	NM_001126112.2	394	Tga/Cga	11/11	1	2	FACETS	0.779	0.717	0.843	0.779	0.717	0.843	SUBCLONAL	1	TRUE	1	0.593204471512083	2		755	723	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467370	66467370	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs778192399	NA	P-0022524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	69	259	0	ENST00000273854.3:c.899G>C	p.Gly300Ala	p.G300A	ENST00000273854	NM_004439.5	300	gGc/gCc	3/18	0.582276698322813	3	FACETS	0.792	0.693	0.897	0.396	0.346	0.449	SUBCLONAL	1	TRUE	1	0.593204471512083	3		259	381	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151933019	151933019	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0022524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	38	183	0	ENST00000262189.6:c.2653-1G>A		p.X885_splice	ENST00000262189	NM_170606.2	885			0.582276698322813	3	FACETS	0.664	0.553	0.787	0.332	0.276	0.394	SUBCLONAL	1	TRUE	1	0.593204471512083	3		183	250	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457127	5457127	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	161	513	0	ENST00000381577.3:c.101G>A	p.Ser34Asn	p.S34N	ENST00000381577	NM_014143.3	34	aGc/aAc	3/7	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.593204471512083	2		513	538	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216560	2216560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777525091	NA	P-0022526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	409	1113	4	ENST00000398665.3:c.2204C>T	p.Thr735Met	p.T735M	ENST00000398665	NM_032482.2	735	aCg/aTg	20/28	0.363788252545605	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.363700569366872	3		1117	1185	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294577	1294577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	157	761	1	ENST00000310581.5:c.424C>T	p.Arg142Cys	p.R142C	ENST00000310581	NM_198253.2	142	Cgc/Tgc	2/16	0.300059832419998	3	FACETS	1	0.981	1	0.616	0.565	0.67	CLONAL	1	TRUE	1	0.363700569366872	3		762	828	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440748	56440748	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	115	692	1	ENST00000407977.2:c.470T>C	p.Leu157Pro	p.L157P	ENST00000407977		157	cTg/cCg	5/10	0.363788252545605	3	FACETS	0.817	0.735	0.904	0.408	0.367	0.452	CLONAL	1	TRUE	1	0.363700569366872	3		693	915	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732286	74732286	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	61	358	0	ENST00000359995.5:c.623G>T	p.Ser208Ile	p.S208I	ENST00000359995	NM_001195427.1	208	aGt/aTt	2/3	0.363788252545605	3	FACETS	0.843	0.729	0.967	0.422	0.364	0.484	CLONAL	1	TRUE	1	0.363700569366872	3		358	470	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953298	17953298	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	186	1142	1	ENST00000458235.1:c.688G>C	p.Asp230His	p.D230H	ENST00000458235	NM_000215.3	230	Gac/Cac	6/24	0.363788252545605	3	FACETS	0.997	0.919	1	0.499	0.459	0.54	CLONAL	1	TRUE	1	0.363700569366872	3		1143	1212	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22123594	22123594	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	90	715	0	ENST00000215832.6:c.982C>A	p.Pro328Thr	p.P328T	ENST00000215832	NM_002745.4	328	Cca/Aca	8/9	0.363788252545605	3	FACETS	0.767	0.68	0.859	0.383	0.34	0.43	SUBCLONAL	1	TRUE	1	0.363700569366872	3		715	763	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643705	52643715	+	frameshift_variant	Frame_Shift_Del	DEL	TCATGACAAAG	TCATGACAAAG	-	novel	NA	P-0022526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	134	748	0	ENST00000394830.3:c.2181_2191del	p.Phe728ValfsTer2	p.F728Vfs*2	ENST00000394830	NM_018313.4	727	gaCTTTGTCATGAtg/gatg	17/30	0.363788252545605	3	FACETS	0.94	0.854	1	0.47	0.427	0.516	CLONAL	1	TRUE	1	0.363700569366872	3		748	926	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52663004	52663004	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	80	550	0	ENST00000394830.3:c.1349G>C	p.Cys450Ser	p.C450S	ENST00000394830	NM_018313.4	450	tGt/tCt	13/30	0.363788252545605	3	FACETS	0.816	0.719	0.921	0.408	0.359	0.461	CLONAL	1	TRUE	1	0.363700569366872	3		550	637	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231667	66231667	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	57	741	0	ENST00000273854.3:c.2033A>G	p.Glu678Gly	p.E678G	ENST00000273854	NM_004439.5	678	gAg/gGg	11/18	1	2	FACETS	0.868	0.748	0.998	0.868	0.748	0.998	CLONAL	1	TRUE	1	0.363700569366872	2		741	361	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405684	139405684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747068023	NA	P-0022526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1241	174	1212	0	ENST00000277541.6:c.2507G>A	p.Ser836Asn	p.S836N	ENST00000277541	NM_017617.3	836	aGc/aAc	16/34	0.363788252545605	3	FACETS	0.799	0.733	0.868	0.4	0.366	0.434	SUBCLONAL	1	TRUE	1	0.363700569366872	3		1212	1415	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645695	12645699	+	protein_altering_variant	In_Frame_Del	DEL	TGTCG	TGTCG	GA	novel	NA	P-0022527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	61	337	0	ENST00000251849.4:c.770_774delinsTC	p.Ser257_Thr258delinsPhe	p.S257_T258delinsF	ENST00000251849	NM_002880.3	257	tCGACA/tTC	7/17	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.290755704749105	2		337	350	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101048	27101048	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	74	954	1	ENST00000324856.7:c.4330G>T	p.Glu1444Ter	p.E1444*	ENST00000324856	NM_006015.4	1444	Gag/Tag	18/20	1	2	FACETS	0.363	0.317	0.413	0.363	0.317	0.413	SUBCLONAL	1	TRUE	1	0.373646183970288	2		955	1091	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006644	62006644	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	62	852	0	ENST00000392795.3:c.635T>C	p.Val212Ala	p.V212A	ENST00000392795	NM_001039933.1	212	gTg/gCg	6/6	1	2	FACETS	0.335	0.288	0.386	0.335	0.288	0.386	SUBCLONAL	1	TRUE	1	0.373646183970288	2		852	991	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252994	36252995	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0022530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	170	608	0	ENST00000300305.3:c.367dup	p.Asp123GlyfsTer15	p.D123Gfs*15	ENST00000300305		123	gat/gGat	4/8	1	2	FACETS	0.992	0.913	1	1	0.992	1	CLONAL	2	FALSE	1	0.20544458101255	2		608	834	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	193	749	3	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	0.20544458101255	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	FALSE	1	0.20544458101255	3		752	992	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	256	909	0	ENST00000267101.3:c.850G>C	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Cga	7/28	0.20544458101255	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	FALSE	1	0.20544458101255	3		909	1148	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577148	7577148	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1060501194	NA	P-0022530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	80	747	2	ENST00000269305.4:c.790del	p.Leu264TyrfsTer81	p.L264Yfs*81	ENST00000269305	NM_001126112.2	264	Cta/ta	8/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	1	0.20544458101255	2		749	637	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948172	55948172	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	41	833	0	ENST00000263923.4:c.3799G>A	p.Glu1267Lys	p.E1267K	ENST00000263923	NM_002253.2	1267	Gaa/Aaa	29/30	0.20544458101255	1	FACETS	0.48	0.399	0.571	0.48	0.399	0.571	SUBCLONAL	1	FALSE	0	0.20544458101255	1		833	746	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38135877	38135877	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs780032475	NA	P-0022530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	50	795	0	ENST00000317025.8:c.3814G>C	p.Glu1272Gln	p.E1272Q	ENST00000317025	NM_023034.1	1272	Gag/Cag	22/24	0.19076742656412	1	FACETS	0.494	0.417	0.578	0.494	0.417	0.578	SUBCLONAL	1	FALSE	0	0.20544458101255	1		795	885	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950030	44950031	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	63	859	0	ENST00000377967.4:c.3800dup	p.Val1268SerfsTer23	p.V1268Sfs*23	ENST00000377967	NM_021140.2	1267	ata/aTta	26/29	0.19076742656412	1	FACETS	0.761	0.657	0.874	0.761	0.657	0.874	SUBCLONAL	1	FALSE	0	0.20544458101255	1		859	723	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	197	445	0				ENST00000310581	NM_198253.2	-/1132			0.54305984132735	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.577580066020191	4		445	501	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953730	48953730	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs3092891	NA	P-0022532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	171	246	2	ENST00000267163.4:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000267163	NM_000321.2	445	Cga/Tga	14/27	0.575545854666744	3	FACETS	0.886	0.835	0.937			1	CLONAL	3	TRUE	NA	0.577580066020191	3		248	287	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573983	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0022532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	419	823	1	ENST00000269305.4:c.1044_1045delinsTT	p.Leu348_Glu349delinsPheTer	p.L348_E349delinsF*	ENST00000269305	NM_001126112.2	348	ttGGaa/ttTTaa	10/11	0.558199430513132	2	FACETS	0.956	0.918	0.993	0.956	0.918	0.993	CLONAL	2	TRUE	0	0.577580066020191	2		824	759	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651944	36651945	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0022532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	161	663	0	ENST00000244741.5:c.68dup	p.Val25SerfsTer11	p.V25Sfs*11	ENST00000244741	NM_000389.4	22	-/G	2/3	0.576900015611124	3	FACETS	0.932	0.856	1	0.466	0.428	0.506	CLONAL	1	TRUE	1	0.577580066020191	3		663	771	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0022535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	252	636	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.434193481769936	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.434193481769936	2		636	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0022537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	311	737	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.342179152029784	2	FACETS	0.848	0.801	0.895	0.848	0.801	0.895	CLONAL	2	TRUE	0	0.379360801777891	2		739	967	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0022537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	100	289	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.265558293928824	2	FACETS	0.766	0.691	0.844	0.766	0.691	0.844	SUBCLONAL	2	TRUE	0	0.379360801777891	2		289	344	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239938	41239938	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs934983863	NA	P-0022537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	59	52	0	ENST00000379561.5:c.412C>T	p.Pro138Ser	p.P138S	ENST00000379561	NM_002015.3	138	Ccc/Tcc	1/3	0.379360801777891	9	FACETS	1	0.906	1	0.525	0.457	0.596	CLONAL	3	TRUE	3	0.379360801777891	9		52	230	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2111887	2111887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	187	610	1	ENST00000219476.3:c.1135G>A	p.Glu379Lys	p.E379K	ENST00000219476	NM_000548.3	379	Gag/Aag	12/42	0.254690717115896	3	FACETS	1	0.985	1	0.423	0.391	0.457	CLONAL	1	TRUE	0	0.379360801777891	3		611	924	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	39	636	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.488	0.403	0.582	0.488	0.403	0.582	SUBCLONAL	1	TRUE	1	0.258818375052466	2		638	618	SUCCESS
APC	324	MSKCC	GRCh37	5	112175175	112175175	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	45	232	0	ENST00000257430.4:c.3885del	p.Ala1296GlnfsTer9	p.A1296Qfs*9	ENST00000257430	NM_000038.5	1295	gAa/ga	16/16	0.249365795311428	2	FACETS	1	0.944	1	0.635	0.537	0.741	CLONAL	1	TRUE	0	0.258818375052466	2		232	274	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0022539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	111	607	1	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.258818375052466	2		608	784	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111497	8111497	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	138	700	1	ENST00000346208.3:c.983G>T	p.Trp328Leu	p.W328L	ENST00000346208		328	tGg/tTg	5/6	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.258818375052466	2		701	915	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	45	445	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	FALSE	1	0.199820510441723	2		445	419	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148919	119148919	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1377506801	NA	P-0022540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	21	452	1	ENST00000264033.4:c.1139T>C	p.Leu380Pro	p.L380P	ENST00000264033	NM_005188.3	380	cTa/cCa	8/16	1	2	FACETS	0.322	0.247	0.411	0.322	0.247	0.411	SUBCLONAL	1	FALSE	1	0.199820510441723	2		453	652	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226084	133226084	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	72	784	0	ENST00000320574.5:c.3813G>T	p.Trp1271Cys	p.W1271C	ENST00000320574	NM_006231.2	1271	tgG/tgT	31/49	1	2	FACETS	0.867	0.756	0.987	0.867	0.756	0.987	CLONAL	1	FALSE	1	0.199820510441723	2		784	831	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665522	138665522	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	69	672	0	ENST00000330315.3:c.43C>A	p.Leu15Met	p.L15M	ENST00000330315	NM_023067.3	15	Ctg/Atg	1/1	0.199820510441723	3	FACETS	1	0.936	1	0.563	0.49	0.642	CLONAL	1	FALSE	1	0.199820510441723	3		672	675	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0022549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	50	293	1	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.825934250714783	1	FACETS	0.646	0.567	0.726	0.646	0.567	0.726	SUBCLONAL	1	TRUE	0	0.825934250714783	1		294	110	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	332	921	0	ENST00000269305.4:c.455C>G	p.Pro152Arg	p.P152R	ENST00000269305	NM_001126112.2	152	cCg/cGg	5/11	0.825934250714783	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.825934250714783	1		921	450	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	229	636	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.439641742141656	3	FACETS	0.985	0.932	1	0.985	0.932	1	CLONAL	3	TRUE	0	0.439641742141656	3		638	430	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0022550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	493	952	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.439641742141656	4	FACETS	0.941	0.908	0.974	0.941	0.908	0.974	CLONAL	4	TRUE	0	0.439641742141656	4		952	858	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775689	9775689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	314	969	0	ENST00000377346.4:c.232G>A	p.Glu78Lys	p.E78K	ENST00000377346	NM_005026.3	78	Gag/Aag	4/24	0.431891337159252	4	FACETS	1	0.964	1	1	0.964	1	CLONAL	3	TRUE	1	0.439641742141656	4		969	674	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449854	149449854	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	227	954	0	ENST00000286301.3:c.1210del	p.Val404Ter	p.V404*	ENST00000286301	NM_005211.3	404	Gta/ta	9/22	0.386465964402176	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.439641742141656	4		954	720	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950042	44950042	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	75	849	0	ENST00000377967.4:c.3811G>C	p.Val1271Leu	p.V1271L	ENST00000377967	NM_021140.2	1271	Gtt/Ctt	26/29	0.386465964402176	4	FACETS	0.975	0.856	1	0.487	0.428	0.551	CLONAL	1	TRUE	2	0.439641742141656	4		849	504	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152864447	152864447	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	40	208	0	ENST00000406277.2:c.79C>T	p.Arg27Ter	p.R27*	ENST00000406277	NM_152274.4	27	Cga/Tga	3/7	0.386465964402176		FACETS		0.894	1				CLONAL	2	TRUE	2	0.439641742141656	4		208	123	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500488	149500488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1060499540	NA	P-0022553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	142	679	0	ENST00000261799.4:c.2549A>T	p.Asp850Val	p.D850V	ENST00000261799	NM_002609.3	850	gAc/gTc	18/23	0.377501438136469	2	FACETS	0.85	0.775	0.929	0.425	0.387	0.465	CLONAL	1	TRUE	0	0.377501438136469	2		679	885	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428059	49428059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	267	625	0	ENST00000301067.7:c.10531G>A	p.Glu3511Lys	p.E3511K	ENST00000301067	NM_003482.3	3511	Gag/Aag	38/54	0.377501438136469	3	FACETS	0.974	0.916	1	0.974	0.916	1	CLONAL	2	TRUE	1	0.377501438136469	3		625	863	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0022554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	304	795	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.986	0.936	1	0.986	0.936	1	CLONAL	1	TRUE	1	0.870641685519567	2		795	708	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522551	176522551	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	311	855	0	ENST00000292408.4:c.1648G>C	p.Val550Leu	p.V550L	ENST00000292408	NM_213647.1	550	Gtg/Ctg	13/18	0.403680162558325	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	1	0.403680162558325	3		855	919	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926248	112926248	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs121918468	NA	P-0022556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	137	696	1	ENST00000351677.2:c.1381G>A	p.Ala461Thr	p.A461T	ENST00000351677	NM_002834.3	461	Gct/Act	12/16	1	2	FACETS	0.891	0.811	0.974	0.891	0.811	0.974	CLONAL	1	TRUE	1	0.403680162558325	2		697	762	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257289	16257289	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	175	844	0	ENST00000375759.3:c.4554A>T	p.Glu1518Asp	p.E1518D	ENST00000375759	NM_015001.2	1518	gaA/gaT	11/15	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.403680162558325	2		844	853	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740516	58740516	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0022556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	161	806	0	ENST00000305921.3:c.1422del	p.Glu475LysfsTer8	p.E475Kfs*8	ENST00000305921	NM_003620.3	474	cTt/ct	6/6	0.368170287613495	4	FACETS	1	0.918	1	0.334	0.306	0.364	CLONAL	1	TRUE	1	0.403680162558325	4		806	1117	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950690	38950690	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	110	482	0	ENST00000357387.3:c.3260T>C	p.Phe1087Ser	p.F1087S	ENST00000357387	NM_152756.3	1087	tTc/tCc	31/38	0.403680162558325	3	FACETS	1	0.936	1	0.527	0.474	0.582	CLONAL	1	TRUE	1	0.403680162558325	3		482	622	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250535	26250535	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	43	704	0	ENST00000446824.2:c.299A>G	p.Tyr100Cys	p.Y100C	ENST00000446824	NM_021018.2	100	tAc/tGc	1/1	0.403680162558325	2	FACETS	0.304	0.254	0.361	0.152	0.127	0.181	SUBCLONAL	1	TRUE	0	0.403680162558325	2		704	700	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864843	117864871	+	frameshift_variant	Frame_Shift_Del	DEL	ATTTTCAAATTCTTTGAGGAATTCATCCA	ATTTTCAAATTCTTTGAGGAATTCATCCA	-	novel	NA	P-0022556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	125	635	0	ENST00000297338.2:c.1238_1266del	p.Leu413SerfsTer5	p.L413Sfs*5	ENST00000297338	NM_006265.2	413	tTGGATGAATTCCTCAAAGAATTTGAAAAT/t	10/14	0.368170287613495	4	FACETS	0.923	0.834	1	0.308	0.278	0.339	CLONAL	1	TRUE	1	0.403680162558325	4		635	942	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577546	7577547	+	missense_variant	Missense_Mutation	DNP	GC	GC	TG	novel	NA	P-0022557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	397	859	3	ENST00000269305.4:c.734_735delinsCA	p.Gly245Ala	p.G245A	ENST00000269305	NM_001126112.2	245	gGC/gCA	7/11	0.586071001070184	2	FACETS	0.995	0.958	1	0.995	0.958	1	CLONAL	2	TRUE	0	0.615629445733491	2		862	648	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277070	38277070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	1544	796	0	ENST00000425967.3:c.1358C>T	p.Pro453Leu	p.P453L	ENST00000425967	NM_001174067.1	453	cCt/cTt	10/19	0.615629445733491	12	FACETS	1	0.996	1			1	CLONAL	9	TRUE	NA	0.615629445733491	12		796	2168	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711974	89711974	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	35	564	0	ENST00000371953.3:c.592del	p.Met198Ter	p.M198*	ENST00000371953	NM_000314.4	198	Atg/tg	6/9	1	2	FACETS	0.758	0.621	0.911	0.758	0.621	0.911	CLONAL	1	TRUE	1	0.21	2		564	440	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059127	47059127	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0022559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	55	662	1	ENST00000409792.3:c.7533+1G>A		p.X2511_splice	ENST00000409792	NM_014159.6	2511			1	2	FACETS	0.956	0.818	1	0.956	0.818	1	CLONAL	1	TRUE	1	0.21	2		663	548	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220370	1220370	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0022560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	118	744	2	ENST00000326873.7:c.465-2A>T		p.X155_splice	ENST00000326873	NM_000455.4	155			0.180664807364895	2	FACETS	0.991	0.897	1	0.991	0.897	1	CLONAL	2	TRUE	0	0.204300754693622	2		746	583	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675664	30675664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	295	1081	0	ENST00000376406.3:c.2692G>A	p.Glu898Lys	p.E898K	ENST00000376406	NM_014641.2	898	Gag/Aag	8/15	0.204300754693622	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	0	0.204300754693622	3		1081	989	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884145	37884145	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	85	953	1	ENST00000269571.5:c.3616C>G	p.Gln1206Glu	p.Q1206E	ENST00000269571		1206	Cag/Gag	27/27	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.204300754693622	2		954	673	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109720	115109720	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	120	1073	0	ENST00000257566.3:c.2158G>A	p.Glu720Lys	p.E720K	ENST00000257566	NM_016569.3	720	Gaa/Aaa	8/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.204300754693622	2		1073	809	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216988	2216988	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	175	1033	1	ENST00000398665.3:c.2443C>T	p.Gln815Ter	p.Q815*	ENST00000398665	NM_032482.2	815	Cag/Tag	21/28	0.180664807364895	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.204300754693622	2		1034	722	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597328	10597329	+	frameshift_variant,stop_lost	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0022560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	120	926	0	ENST00000171111.5:c.1874dup	p.Ter625TrpfsTer26	p.*625Wfs*26	ENST00000171111	NM_203500.1	625	tga/tgGa	6/6	0.180664807364895	2	FACETS	0.877	0.793	0.965	0.877	0.793	0.965	CLONAL	2	TRUE	0	0.204300754693622	2		926	670	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141551	11141551	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	107	820	0	ENST00000358026.2:c.3528C>A	p.Ser1176Arg	p.S1176R	ENST00000358026	NM_001128849.1	1176	agC/agA	25/36	0.180664807364895	2	FACETS	0.877	0.789	0.971	0.877	0.789	0.971	CLONAL	2	TRUE	0	0.204300754693622	2		820	597	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965375	68965375	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	43	810	0	ENST00000288368.4:c.987G>C	p.Lys329Asn	p.K329N	ENST00000288368	NM_024870.2	329	aaG/aaC	9/40	1	2	FACETS	0.946	0.792	1	0.946	0.792	1	CLONAL	1	TRUE	1	0.204300754693622	2		810	445	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95579470	95579470	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	48	566	0	ENST00000393063.1:c.1999C>G	p.Leu667Val	p.L667V	ENST00000393063	NM_030621.3	667	Ctt/Gtt	13/28	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.204300754693622	2		566	335	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028418	42028418	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	21	433	0	ENST00000219905.7:c.3956C>G	p.Ser1319Cys	p.S1319C	ENST00000219905	NM_001164273.1	1319	tCt/tGt	13/24	1	2	FACETS	0.667	0.514	0.846	0.667	0.514	0.846	SUBCLONAL	1	TRUE	1	0.204300754693622	2		433	308	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552239	29552239	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	30	655	0	ENST00000356175.3:c.1972C>G	p.Leu658Val	p.L658V	ENST00000356175	NM_000267.3	658	Ctc/Gtc	17/57	1	2	FACETS	0.837	0.675	1	0.837	0.675	1	CLONAL	1	TRUE	1	0.204300754693622	2		655	351	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978922	25978922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1217311360	NA	P-0022560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	58	552	1	ENST00000435504.4:c.1001C>T	p.Ser334Leu	p.S334L	ENST00000435504		334	tCa/tTa	10/13	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.204300754693622	2		553	461	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027263	48027263	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730881796	NA	P-0022560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	33	511	0	ENST00000234420.5:c.2141C>G	p.Ser714Cys	p.S714C	ENST00000234420	NM_000179.2	714	tCt/tGt	4/10	1	2	FACETS	0.915	0.747	1	0.915	0.747	1	CLONAL	1	TRUE	1	0.204300754693622	2		511	353	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1941447	1941447	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	39	795	0	ENST00000382891.5:c.1823C>G	p.Ser608Cys	p.S608C	ENST00000382891	NM_133335.3	608	tCt/tGt	9/22	1	2	FACETS	0.605	0.5	0.722	0.605	0.5	0.722	SUBCLONAL	1	TRUE	1	0.204300754693622	2		795	631	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938505	76938505	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	26	579	0	ENST00000373344.5:c.2243C>G	p.Ser748Cys	p.S748C	ENST00000373344	NM_000489.3	748	tCt/tGt	9/35	1	2	FACETS	0.672	0.532	0.832	0.672	0.532	0.832	SUBCLONAL	1	TRUE	1	0.204300754693622	2		579	379	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220370	1220370	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0022560-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	46	744	2	ENST00000326873.7:c.465-2A>T		p.X155_splice	ENST00000326873	NM_000455.4	155			1	2	FACETS	0.405	0.34	0.476	0.405	0.34	0.476	SUBCLONAL	1	FALSE	1	0.399630753165254	2		746	569	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675664	30675664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022560-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	30	1081	0	ENST00000376406.3:c.2692G>A	p.Glu898Lys	p.E898K	ENST00000376406	NM_014641.2	898	Gag/Aag	8/15	0.399630753165254	0	FACETS	0.249	0.2	0.304			1	SUBCLONAL	1	FALSE	0	0.399630753165254	0		1081	362	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884145	37884145	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022560-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	39	953	1	ENST00000269571.5:c.3616C>G	p.Gln1206Glu	p.Q1206E	ENST00000269571		1206	Cag/Gag	27/27	NA	2	FACETS	0.278	0.23	0.333			1	INDETERMINATE	1	FALSE	NA	0.399630753165254	2		954	701	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109720	115109720	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022560-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	110	1073	0	ENST00000257566.3:c.2158G>A	p.Glu720Lys	p.E720K	ENST00000257566	NM_016569.3	720	Gaa/Aaa	8/8	0.221946753969593	3	FACETS	0.515	0.461	0.573	0.258	0.23	0.287	INDETERMINATE	1	FALSE	1	0.399630753165254	3		1073	1282	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216988	2216988	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022560-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	74	1033	1	ENST00000398665.3:c.2443C>T	p.Gln815Ter	p.Q815*	ENST00000398665	NM_032482.2	815	Cag/Tag	21/28	1	2	FACETS	0.357	0.311	0.407	0.357	0.311	0.407	SUBCLONAL	1	FALSE	1	0.399630753165254	2		1034	1037	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597328	10597329	+	frameshift_variant,stop_lost	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0022560-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	37	926	0	ENST00000171111.5:c.1874dup	p.Ter625TrpfsTer26	p.*625Wfs*26	ENST00000171111	NM_203500.1	625	tga/tgGa	6/6	0.221946753969593	3	FACETS	0.351	0.288	0.421	0.175	0.144	0.211	INDETERMINATE	1	FALSE	1	0.399630753165254	3		926	633	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141551	11141551	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022560-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	28	820	0	ENST00000358026.2:c.3528C>A	p.Ser1176Arg	p.S1176R	ENST00000358026	NM_001128849.1	1176	agC/agA	25/36	0.221946753969593	3	FACETS	0.306	0.244	0.378	0.153	0.122	0.189	INDETERMINATE	1	FALSE	1	0.399630753165254	3		820	549	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965375	68965375	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022560-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	10	810	0	ENST00000288368.4:c.987G>C	p.Lys329Asn	p.K329N	ENST00000288368	NM_024870.2	329	aaG/aaC	9/40	1	2	FACETS	0.305	0.207	0.428	0.305	0.207	0.428	SUBCLONAL	1	FALSE	1	0.399630753165254	2		810	164	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	185	636	2	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	0.55752737092665	2		638	561	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0022561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	117	568	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.95	0.862	1	0.95	0.862	1	CLONAL	1	TRUE	1	0.55752737092665	2		568	442	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs121913292	NA	P-0022561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	154	568	0	ENST00000371953.3:c.389del	p.Arg130GlnfsTer4	p.R130Qfs*4	ENST00000371953	NM_000314.4	130	cGa/ca	5/9	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.55752737092665	2		568	442	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188049	151188049	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519950	NA	P-0022561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	126	437	0	ENST00000262187.5:c.104A>G	p.Tyr35Cys	p.Y35C	ENST00000262187	NM_005614.3	35	tAc/tGc	2/8	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.55752737092665	2		437	410	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355769	73355769	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs915976842	NA	P-0022561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	241	584	0	ENST00000377767.4:c.202C>T	p.Pro68Ser	p.P68S	ENST00000377767	NM_014953.3	68	Ccc/Tcc	1/21	0.554757141487923	1	FACETS	0.938	0.881	0.995	0.938	0.881	0.995	CLONAL	1	TRUE	0	0.55752737092665	1		584	665	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046743	42046744	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0022561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	38	633	0	ENST00000219905.7:c.7123_7124del	p.Gln2375ValfsTer14	p.Q2375Vfs*14	ENST00000219905	NM_001164273.1	2373	CAc/c	18/24	0.55752737092665	1	FACETS	0.213	0.176	0.254	0.213	0.176	0.254	SUBCLONAL	1	TRUE	0	0.55752737092665	1		633	462	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022332	31022332	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	30	378	0	ENST00000375687.4:c.1820del	p.Gly607ValfsTer96	p.G607Vfs*96	ENST00000375687	NM_015338.5	606	cGg/cg	13/13	1	2	FACETS	0.231	0.186	0.283	0.231	0.186	0.283	SUBCLONAL	1	TRUE	1	0.55752737092665	2		378	465	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486019	8486019	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	177	569	0	ENST00000356435.5:c.2798C>G	p.Thr933Ser	p.T933S	ENST00000356435		933	aCc/aGc	17/35	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.55752737092665	2		569	606	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776286	76776286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	117	781	0	ENST00000373344.5:c.7180G>A	p.Val2394Ile	p.V2394I	ENST00000373344	NM_000489.3	2394	Gta/Ata	34/35	0.307021083071015	1	FACETS	0.659	0.598	0.723	0.659	0.598	0.723	INDETERMINATE	1	TRUE	0	0.55752737092665	1		781	459	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169173	119169173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	157	598	0	ENST00000264033.4:c.2357C>T	p.Ala786Val	p.A786V	ENST00000264033	NM_005188.3	786	gCc/gTc	15/16	1	2	FACETS	0.695	0.638	0.754	0.695	0.638	0.754	SUBCLONAL	1	TRUE	1	0.641866128811943	2		598	704	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750498	128750498	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	56	602	0	ENST00000377970.2:c.35C>T	p.Pro12Leu	p.P12L	ENST00000377970	NM_002467.4	12	cCt/cTt	2/3	0.641866128811943	3	FACETS	0.311	0.265	0.36	0.155	0.132	0.18	SUBCLONAL	1	TRUE	1	0.641866128811943	3		602	742	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430637	80430637	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	115	452	0	ENST00000286548.4:c.371T>C	p.Phe124Ser	p.F124S	ENST00000286548	NM_002072.3	124	tTt/tCt	3/7	0.641866128811943	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.641866128811943	1		452	235	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0022563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	93	628	1	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.851	0.757	0.952	0.851	0.757	0.952	CLONAL	1	TRUE	1	0.31128578482076	2		629	702	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101195	27101195	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	121	703	1	ENST00000324856.7:c.4477C>T	p.Gln1493Ter	p.Q1493*	ENST00000324856	NM_006015.4	1493	Cag/Tag	18/20	0.31128578482076	1	FACETS	0.972	0.88	1	0.972	0.88	1	CLONAL	1	TRUE	0	0.31128578482076	1		704	675	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980299	201980300	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAACTACTTCAGTGCGATGTACAGCT	novel	NA	P-0022563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1185	242	804	0	ENST00000359651.3:c.37_62dup	p.Glu22ThrfsTer30	p.E22Tfs*30	ENST00000359651		12	agc/agCAACTACTTCAGTGCGATGTACAGCTc	1/8	0.309718144550024	4	FACETS	1	0.991	1	0.476	0.444	0.51	CLONAL	1	TRUE	1	0.31128578482076	4		804	1427	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16052778	16052778	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	102	620	1	ENST00000268712.3:c.896C>T	p.Ala299Val	p.A299V	ENST00000268712	NM_006311.3	299	gCa/gTa	9/46	1	2	FACETS	0.955	0.855	1	0.955	0.855	1	CLONAL	1	TRUE	1	0.31128578482076	2		621	686	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591822	48591822	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0022563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	89	530	0	ENST00000342988.3:c.987del	p.Phe329LeufsTer7	p.F329Lfs*7	ENST00000342988	NM_005359.5	329	Ttt/tt	9/12	0.31128578482076	1	FACETS	0.888	0.789	0.992	0.888	0.789	0.992	CLONAL	1	TRUE	0	0.31128578482076	1		530	544	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938526	44938527	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0022563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	144	628	0	ENST00000377967.4:c.3075_3076dup	p.Asn1026IlefsTer23	p.N1026Ifs*23	ENST00000377967	NM_021140.2	1025	agt/agTAt	20/29	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.31128578482076	2		628	882	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398287	+	missense_variant	Missense_Mutation	TNP	CAG	CAG	AAC	novel	NA	P-0022563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	80	697	0	ENST00000311936.3:c.32_34delinsGTT	p.Ala11_Gly12delinsGlyCys	p.A11_G12delinsGC	ENST00000311936	NM_004985.3	11	gCTGgt/gGTTgt	2/5	1	2	FACETS	0.613	0.538	0.693	0.613	0.538	0.693	SUBCLONAL	1	TRUE	1	0.31128578482076	2		697	839	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0022566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	300	798	0	ENST00000269305.4:c.838del	p.Arg280GlufsTer65	p.R280Efs*65	ENST00000269305	NM_001126112.2	280	Aga/ga	8/11	0.491500328395009	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.511284891339607	2		798	564	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937723	44937723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	54	643	0	ENST00000377967.4:c.2911C>T	p.Arg971Cys	p.R971C	ENST00000377967	NM_021140.2	971	Cgt/Tgt	19/29	0.517291536944266	2	FACETS	0.556	0.476	0.642	0.278	0.238	0.321	SUBCLONAL	1	TRUE	0	0.511284891339607	2		643	380	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110046	115110046	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867049310	NA	P-0022566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	119	1089	0	ENST00000257566.3:c.1832C>T	p.Ala611Val	p.A611V	ENST00000257566	NM_016569.3	611	gCg/gTg	8/8	0.173385526099285	2	FACETS	1	0.962	1	0.554	0.504	0.606	INDETERMINATE	1	TRUE	0	0.511284891339607	2		1089	420	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385308	4385308	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	20	417	0	ENST00000261254.3:c.333A>C	p.Lys111Asn	p.K111N	ENST00000261254	NM_001759.3	111	aaA/aaC	2/5	0.139332063985231	3	FACETS	0.261	0.199	0.333	0.13	0.099	0.167	INDETERMINATE	1	TRUE	1	0.511284891339607	3		417	377	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027730	48027730	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0022566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	71	435	0	ENST00000234420.5:c.2608A>T	p.Lys870Ter	p.K870*	ENST00000234420	NM_000179.2	870	Aaa/Taa	4/10	0.517291536944266	4	FACETS	0.99	0.868	1	0.247	0.217	0.281	CLONAL	1	TRUE	0	0.511284891339607	4		435	424	SUCCESS
APC	324	MSKCC	GRCh37	5	112175600	112175600	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	118	377	0	ENST00000257430.4:c.4312del	p.Thr1438HisfsTer35	p.T1438Hfs*35	ENST00000257430	NM_000038.5	1437	Aaa/aa	16/16	0.216702653120977	3	FACETS	0.924	0.835	1	0.924	0.835	1	CLONAL	2	TRUE	1	0.216702653120977	3		377	653	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0022567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	66	529	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.216702653120977	3	FACETS	0.871	0.755	0.997	0.436	0.377	0.499	CLONAL	1	TRUE	1	0.216702653120977	3		529	775	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577563	7577565	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0022567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	224	756	1	ENST00000269305.4:c.716_718del	p.Asn239del	p.N239del	ENST00000269305	NM_001126112.2	239	aACAgt/agt	7/11	0.196748498201893	2	FACETS	0.93	0.865	0.997	0.93	0.865	0.997	CLONAL	2	TRUE	0	0.216702653120977	2		757	1112	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965476	68965476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751712561	NA	P-0022567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1381	118	733	2	ENST00000288368.4:c.1088G>A	p.Arg363Gln	p.R363Q	ENST00000288368	NM_024870.2	363	cGg/cAg	9/40	0.216702653120977	6	FACETS	1	0.929	1	0.208	0.187	0.231	CLONAL	1	TRUE	1	0.216702653120977	6		735	1499	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118379891	118379891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	53	390	1	ENST00000534358.1:c.10876C>T	p.Pro3626Ser	p.P3626S	ENST00000534358	NM_005933.3	3626	Cca/Tca	29/36	0.216702653120977	5	FACETS	0.895	0.762	1	0.298	0.254	0.348	CLONAL	1	TRUE	2	0.216702653120977	5		391	724	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656235	18656235	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	93	565	0	ENST00000266497.5:c.2914G>C	p.Asp972His	p.D972H	ENST00000266497		972	Gat/Cat	21/31	0.216702653120977	3	FACETS	1	0.907	1			1	CLONAL	1	TRUE	NA	0.216702653120977	3		565	929	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419965	41419965	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	444	645	0	ENST00000373198.4:c.356C>G	p.Ala119Gly	p.A119G	ENST00000373198	NM_133170.3	119	gCc/gGc	3/32	0.216702653120977	8	FACETS	1	0.988	1	0.908	0.867	0.95	CLONAL	5	TRUE	2	0.216702653120977	8		645	1241	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539034	23539034	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	97	614	1	ENST00000380871.4:c.405G>T	p.Gln135His	p.Q135H	ENST00000380871	NM_006167.3	135	caG/caT	2/2	0.216702653120977	1	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	0	0.216702653120977	1		615	795	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	133	549	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	0.436941363256798	2		549	554	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248633	59248634	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0022568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	69	920	0	ENST00000371222.2:c.109_110del	p.Ser37HisfsTer69	p.S37Hfs*69	ENST00000371222	NM_002228.3	37	AGc/c	1/1	1	2	FACETS	0.294	0.254	0.336	0.294	0.254	0.336	SUBCLONAL	1	TRUE	1	0.436941363256798	2		920	1076	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	DEL	C	C	-	rs1567550969	NA	P-0022568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	286	851	0	ENST00000269305.4:c.672+1del		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.436941363256798	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.436941363256798	1		851	925	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343017	118343017	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	57	313	0	ENST00000534358.1:c.1147del	p.Ala383LeufsTer17	p.A383Lfs*17	ENST00000534358	NM_005933.3	381	aaG/aa	3/36	1	2	FACETS	0.567	0.487	0.654	0.567	0.487	0.654	SUBCLONAL	1	TRUE	1	0.436941363256798	2		313	460	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434990	49434990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs541122919	NA	P-0022568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	83	561	1	ENST00000301067.7:c.6563G>A	p.Arg2188His	p.R2188H	ENST00000301067	NM_003482.3	2188	cGc/cAc	31/54	1	2	FACETS	0.533	0.47	0.6	0.533	0.47	0.6	SUBCLONAL	1	TRUE	1	0.436941363256798	2		562	713	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168684	56168687	+	frameshift_variant	Frame_Shift_Del	DEL	CTTC	CTTC	-	novel	NA	P-0022568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	87	578	0	ENST00000399503.3:c.1539_1542del	p.Leu515GlufsTer41	p.L515Efs*41	ENST00000399503	NM_005921.1	513	tCTTCc/tc	9/20	1	2	FACETS	0.602	0.533	0.676	0.602	0.533	0.676	SUBCLONAL	1	TRUE	1	0.436941363256798	2		578	661	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230655	46230949	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AATGTTAAGCTCTTGGCAGCTAATCGTACCTGTCTTCGTTTCCTATTACTTTCTGCACATAGTCATTTTATTTCTTTAAGGCAATTAGGCCTTGACACATTAGGAAATATTGCAGCTGAGGTAAGCATGTGACTGTACCTTAAACTAGTTTTTATAGTTAGCAACATTTATGTTACAATTTTAGGATGTGGCATTTTATAGTTGCCATATTTATAGACTATTAAATGCTTACATGTATTAGTTGCTAAAAATGGTGATGTAGAAGTATCACATACTTTTATGGAAAAAAGTATTT	AATGTTAAGCTCTTGGCAGCTAATCGTACCTGTCTTCGTTTCCTATTACTTTCTGCACATAGTCATTTTATTTCTTTAAGGCAATTAGGCCTTGACACATTAGGAAATATTGCAGCTGAGGTAAGCATGTGACTGTACCTTAAACTAGTTTTTATAGTTAGCAACATTTATGTTACAATTTTAGGATGTGGCATTTTATAGTTGCCATATTTATAGACTATTAAATGCTTACATGTATTAGTTGCTAAAAATGGTGATGTAGAAGTATCACATACTTTTATGGAAAAAAGTATTT	-	novel	NA	P-0022569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	68	637	0	ENST00000334344.6:c.904_1024-155del		p.X302_splice	ENST00000334344	NM_152641.2	302		8/21	0.370642740670565	4	FACETS	0.706	0.613	0.806	0.353	0.306	0.403	SUBCLONAL	1	TRUE	2	0.359910444338616	4		637	728	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023329	33023337	+	inframe_deletion	In_Frame_Del	DEL	CAAGAAATT	CAAGAAATT	-	novel	NA	P-0022569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	73	979	0	ENST00000300177.4:c.440_448del	p.Lys147_Phe149del	p.K147_F149del	ENST00000300177	NM_001191322.1	146	ccCAAGAAATTc/ccc	2/2	0.284808257466118	0	FACETS	0.339	0.295	0.385			1	SUBCLONAL	1	TRUE	0	0.359910444338616	0		979	767	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56870591	56870591	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	148	644	0	ENST00000308159.5:c.1861C>A	p.Leu621Met	p.L621M	ENST00000308159	NM_014669.4	621	Ctg/Atg	17/22	0.121244383070243	6	FACETS	0.787	0.718	0.858	0.524	0.479	0.572	INDETERMINATE	2	TRUE	3	0.359910444338616	6		644	899	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578510	7578515	+	inframe_deletion	In_Frame_Del	DEL	GGTCTT	GGTCTT	-	novel	NA	P-0022569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	532	1055	0	ENST00000269305.4:c.415_420del	p.Lys139_Thr140del	p.K139_T140del	ENST00000269305	NM_001126112.2	139	AAGACC/-	5/11	0.252680110258468	4	FACETS	0.92	0.883	0.959	0.69	0.662	0.719	CLONAL	3	TRUE	0	0.359910444338616	4		1055	1456	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200161	128200161	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1559984811	NA	P-0022569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	188	740	1	ENST00000341105.2:c.1144G>T	p.Val382Phe	p.V382F	ENST00000341105	NM_032638.4	382	Gtt/Ttt	6/6	0.190707036255956	2	FACETS	1	0.99	1	0.744	0.69	0.8	INDETERMINATE	1	TRUE	0	0.359910444338616	2		741	702	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0022571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	179	895	0	ENST00000269305.4:c.838A>T	p.Arg280Ter	p.R280*	ENST00000269305	NM_001126112.2	280	Aga/Tga	8/11	0.720850441960638	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.724854450022482	1		895	303	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950869	32950869	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397507411	NA	P-0022571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	149	617	0	ENST00000380152.3:c.8695C>T	p.Gln2899Ter	p.Q2899*	ENST00000380152		2899	Caa/Taa	21/27	0.724854450022482	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.724854450022482	1		617	249	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828387	72828387	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	243	619	0	ENST00000268489.5:c.8194T>C	p.Ser2732Pro	p.S2732P	ENST00000268489	NM_006885.3	2732	Tcc/Ccc	9/10	0.290739235230138	4	FACETS	0.822	0.77	0.876	0.822	0.77	0.876	INDETERMINATE	2	TRUE	2	0.531893220694055	4		619	851	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578202	7578202	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057520004	NA	P-0022572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	467	879	1	ENST00000269305.4:c.647T>A	p.Val216Glu	p.V216E	ENST00000269305	NM_001126112.2	216	gTg/gAg	6/11	0.498404679012083	2	FACETS	0.922	0.886	0.959	0.922	0.886	0.959	CLONAL	2	TRUE	0	0.531893220694055	2		880	952	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220590	1220591	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0022572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	638	682	1	ENST00000326873.7:c.609_610dup	p.Phe204CysfsTer84	p.F204Cfs*84	ENST00000326873	NM_000455.4	203	ccg/ccGTg	5/10	0.516044727884958	3	FACETS	0.984	0.955	1	0.984	0.955	1	CLONAL	3	TRUE	0	0.531893220694055	3		683	1029	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696220	52696220	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	428	866	3	ENST00000394830.3:c.457C>T	p.Gln153Ter	p.Q153*	ENST00000394830	NM_018313.4	153	Cag/Tag	5/30	0.498404679012083	2	FACETS	0.948	0.909	0.986	0.948	0.909	0.986	CLONAL	2	TRUE	0	0.531893220694055	2		869	849	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665219	138665219	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	546	948	2	ENST00000330315.3:c.346C>A	p.Pro116Thr	p.P116T	ENST00000330315	NM_023067.3	116	Ccg/Acg	1/1	0.532048763380887	3	FACETS	0.958	0.921	0.996	0.958	0.921	0.996	CLONAL	2	TRUE	1	0.531893220694055	3		950	1356	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157961	106157961	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	88	349	2	ENST00000380013.4:c.2862G>A	p.Trp954Ter	p.W954*	ENST00000380013	NM_001127208.2	954	tgG/tgA	3/11	0.532048763380887	3	FACETS	0.891	0.793	0.995	0.446	0.396	0.498	CLONAL	1	TRUE	1	0.531893220694055	3		351	470	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910617	29910617	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199474377	NA	P-0022572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	146	827	1	ENST00000376809.5:c.157G>T	p.Asp53Tyr	p.D53Y	ENST00000376809	NM_002116.7	53	Gac/Tac	2/8	0.50108448839816	4	FACETS	0.633	0.576	0.693	0.211	0.192	0.231	SUBCLONAL	1	TRUE	1	0.531893220694055	4		828	1329	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910685	29910685	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs199474408	NA	P-0022572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1569	232	1134	0	ENST00000376809.5:c.225G>A	p.Trp75Ter	p.W75*	ENST00000376809	NM_002116.7	75	tgG/tgA	2/8	0.50108448839816	4	FACETS	0.742	0.689	0.797	0.247	0.229	0.266	SUBCLONAL	1	TRUE	1	0.531893220694055	4		1134	1801	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910689	29910689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1584	248	1145	0	ENST00000376809.5:c.229G>A	p.Glu77Lys	p.E77K	ENST00000376809	NM_002116.7	77	Gag/Aag	2/8	0.50108448839816	4	FACETS	0.78	0.726	0.836	0.26	0.242	0.279	SUBCLONAL	1	TRUE	1	0.531893220694055	4		1145	1832	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910704	29910704	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs199474415	NA	P-0022572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1631	251	1180	0	ENST00000376809.5:c.244G>C	p.Glu82Gln	p.E82Q	ENST00000376809	NM_002116.7	82	Gag/Cag	2/8	0.50108448839816	4	FACETS	0.768	0.716	0.823	0.256	0.238	0.275	SUBCLONAL	1	TRUE	1	0.531893220694055	4		1180	1882	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912346	29912346	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	156	405	0	ENST00000376809.5:c.965T>A	p.Ile322Asn	p.I322N	ENST00000376809	NM_002116.7	322	aTc/aAc	5/8	0.50108448839816	4	FACETS	1	0.964	1	0.364	0.333	0.396	CLONAL	1	TRUE	1	0.531893220694055	4		405	823	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864365	162864365	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	135	559	3	ENST00000366898.1:c.148C>A	p.Leu50Met	p.L50M	ENST00000366898	NM_004562.2	50	Ctg/Atg	2/12	1	2	FACETS	0.92	0.84	1	0.92	0.84	1	CLONAL	1	TRUE	1	0.531893220694055	2		562	552	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	32	636	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.805	0.652	0.978	0.805	0.652	0.978	CLONAL	1	TRUE	1	0.14	2		638	568	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0022573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	36	554	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	1	0.822	1	1	0.822	1	CLONAL	1	TRUE	1	0.14	2		554	514	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086032	16086032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777508469	NA	P-0022577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	239	660	2	ENST00000281043.3:c.1208C>T	p.Thr403Met	p.T403M	ENST00000281043	NM_005378.4	403	aCg/aTg	3/3	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.865995027145242	2		662	499	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708542	43708542	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	259	860	2	ENST00000382044.4:c.4754G>A	p.Trp1585Ter	p.W1585*	ENST00000382044	NM_001141980.1	1585	tGg/tAg	22/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.865995027145242	2		862	570	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348413	89348413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1289430140	NA	P-0022577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	255	854	1	ENST00000301030.4:c.4537G>A	p.Val1513Met	p.V1513M	ENST00000301030	NM_001256183.1	1513	Gtg/Atg	9/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.865995027145242	2		855	560	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591246	67591246	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0022578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	52	527	1	ENST00000274335.5:c.1746-2A>T		p.X582_splice	ENST00000274335		582			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		528	316	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578471	7578480	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCGGGGGT	GGGCGGGGGT	-	rs137852791	NA	P-0022579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	149	372	0	ENST00000269305.4:c.450_459del	p.Pro151AlafsTer16	p.P151Afs*16	ENST00000269305	NM_001126112.2	150	acACCCCCGCCC/ac	5/11	0.218067352289792	3	FACETS	0.987	0.903	1	0.658	0.602	0.716	CLONAL	2	TRUE	0	0.218067352289792	3		372	768	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259517	+	missense_variant	Missense_Mutation	TNP	TGG	TGG	GCT	novel	NA	P-0022579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	231	362	0	ENST00000275493.2:c.2573_2575delinsGCT	p.Leu858_Ala859delinsArgSer	p.L858_A859delinsRS	ENST00000275493	NM_005228.3	858	cTGGcc/cGCTcc	21/28	0.218067352289792	5	FACETS	0.903	0.845	0.963			1	CLONAL	4	TRUE	NA	0.218067352289792	5		362	778	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206594	108206594	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	118	473	0	ENST00000278616.4:c.8174A>T	p.Asp2725Val	p.D2725V	ENST00000278616	NM_000051.3	2725	gAt/gTt	56/63	0.297283725319832	2	FACETS	0.864	0.784	0.947	0.864	0.784	0.947	CLONAL	2	TRUE	0	0.29	2		473	471	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159754	20159754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	155	459	0	ENST00000379607.5:c.5C>T	p.Pro2Leu	p.P2L	ENST00000379607	NM_001412.3	2	cCc/cTc	1/7	NA	2	FACETS	1	0.978	1			1	INDETERMINATE	2	TRUE	NA	0.29	2		459	460	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211666	36211666	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	142	567	1	ENST00000222270.7:c.1417C>G	p.Pro473Ala	p.P473A	ENST00000222270	NM_014727.1	473	Ccc/Gcc	3/37	0.211928741190325	4	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	2	0.29	4		568	618	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206594	108206594	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	58	473	0	ENST00000278616.4:c.8174A>T	p.Asp2725Val	p.D2725V	ENST00000278616	NM_000051.3	2725	gAt/gTt	56/63	0.812230402222898	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.812230402222898	1		473	74	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159754	20159754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	82	459	0	ENST00000379607.5:c.5C>T	p.Pro2Leu	p.P2L	ENST00000379607	NM_001412.3	2	cCc/cTc	1/7	0.812230402222898	1	FACETS	0.959	0.884	1	0.959	0.884	1	CLONAL	1	TRUE	0	0.812230402222898	1		459	125	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5535014	5535014	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200938803	NA	P-0022582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	73	375	1	ENST00000397747.3:c.325G>A	p.Ala109Thr	p.A109T	ENST00000397747	NM_025239.3	109	Gcc/Acc	3/7	1	2	FACETS	0.936	0.836	1	0.936	0.836	1	CLONAL	1	TRUE	1	0.812230402222898	2		376	192	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578451	7578451	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	88	782	0	ENST00000269305.4:c.479T>A	p.Met160Lys	p.M160K	ENST00000269305	NM_001126112.2	160	aTg/aAg	5/11	0.358578970259921	0	FACETS	0.944	0.853	1			1	CLONAL	1	TRUE	0	0.455322653635491	0		782	223	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658679	3658682	+	frameshift_variant	Frame_Shift_Del	DEL	GTTT	GTTT	-	novel	NA	P-0022585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	102	1003	0	ENST00000294008.3:c.284_287del	p.Gln95LeufsTer30	p.Q95Lfs*30	ENST00000294008	NM_032444.2	95	cAAACt/ct	2/15	0.102297671651762	3	FACETS	1	0.957	1			1	INDETERMINATE	1	TRUE	NA	0.455322653635491	3		1003	490	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805501	1805501	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs768739746	NA	P-0022585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	15	744	0	ENST00000260795.2:c.1013C>G	p.Thr338Ser	p.T338S	ENST00000260795		338	aCc/aGc	7/17	NA	2	FACETS	0.226	0.165	0.3			1	INDETERMINATE	1	TRUE	NA	0.455322653635491	2		744	291	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64286830	64286830	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	96	537	0	ENST00000370651.3:c.45G>C	p.Lys15Asn	p.K15N	ENST00000370651	NM_003463.4	15	aaG/aaC	2/6	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.455322653635491	2		537	331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0022590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1380	176	763	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	1	2	FACETS	0.754	0.692	0.819	1	0.989	1	SUBCLONAL	2	TRUE	1	0.15	2		763	1556	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748455	162748455	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	24	184	0	ENST00000367921.3:c.2369C>A	p.Ser790Tyr	p.S790Y	ENST00000367921	NM_006182.2	790	tCc/tAc	17/18	0.192553281329129	3	FACETS	1	0.882	1	0.599	0.471	0.747	CLONAL	1	TRUE	1	0.15	3		184	287	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938173	76938174	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	61	117	0	ENST00000373344.5:c.2574dup	p.Gly859ArgfsTer4	p.G859Rfs*4	ENST00000373344	NM_000489.3	858	-/A	9/35	1	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.699838833385092	1		117	105	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788638	3788638	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	93	192	0	ENST00000262367.5:c.4316del	p.Phe1439SerfsTer20	p.F1439Sfs*20	ENST00000262367	NM_004380.2	1439	tTc/tc	26/31	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.699838833385092	2		192	229	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787825	135787825	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	15	366	0	ENST00000298552.3:c.757C>A	p.His253Asn	p.H253N	ENST00000298552	NM_001162426.1	253	Cat/Aat	9/23	0.699838833385092	1	FACETS	0.116	0.084	0.153	0.116	0.084	0.153	SUBCLONAL	1	TRUE	0	0.699838833385092	1		366	241	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0022592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	188	826	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.314834306567338	2	FACETS	0.82	0.76	0.882	0.82	0.76	0.882	CLONAL	2	TRUE	0	0.330301255145402	2		828	694	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044971	47044971	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	127	1761	0	ENST00000377604.3:c.2297G>C	p.Arg766Pro	p.R766P	ENST00000377604	NM_001204468.1	766	cGc/cCc	20/24	1	2	FACETS	0.669	0.604	0.737	0.669	0.604	0.737	SUBCLONAL	1	TRUE	1	0.330301255145402	2		1761	1150	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874166	155874166	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs777520196	NA	P-0022592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	52	321	0	ENST00000368323.3:c.365G>T	p.Arg122Leu	p.R122L	ENST00000368323	NM_006912.5	122	cGa/cTa	5/6	0.330301255145402	1	FACETS	0.804	0.688	0.93	0.804	0.688	0.93	CLONAL	1	TRUE	0	0.330301255145402	1		321	327	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222982	1222982	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0022592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	129	827	0	ENST00000326873.7:c.921-2A>G		p.X307_splice	ENST00000326873	NM_000455.4	307			0.212415282738641	2	FACETS	1	0.974	1	0.6	0.545	0.657	CLONAL	1	TRUE	0	0.330301255145402	2		827	651	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096081	11096081	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	159	1143	0	ENST00000358026.2:c.355G>A	p.Gly119Ser	p.G119S	ENST00000358026	NM_001128849.1	119	Ggt/Agt	3/36	0.212415282738641	2	FACETS	1	0.982	1	0.621	0.57	0.674	CLONAL	1	TRUE	0	0.330301255145402	2		1143	775	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209101853	209101853	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	13	131	0	ENST00000345146.2:c.1195G>T	p.Asp399Tyr	p.D399Y	ENST00000345146	NM_005896.2	399	Gat/Tat	10/10	1	2	FACETS	0.601	0.431	0.805	0.601	0.431	0.805	SUBCLONAL	1	TRUE	1	0.330301255145402	2		131	131	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157520003	157520003	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	57	902	0	ENST00000346085.5:c.4072T>A	p.Tyr1358Asn	p.Y1358N	ENST00000346085	NM_020732.3	1358	Tat/Aat	17/20	0.212415282738641	2	FACETS	0.569	0.487	0.657	0.284	0.243	0.329	SUBCLONAL	1	TRUE	0	0.330301255145402	2		902	607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0022598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	40	826	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.698	0.578	0.832	0.698	0.578	0.832	SUBCLONAL	1	TRUE	1	0.14	2		828	819	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419884	152419884	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	119	726	0	ENST00000206249.3:c.1571A>T	p.His524Leu	p.H524L	ENST00000206249	NM_000125.3	524	cAt/cTt	8/8	0.481450444469822	1	FACETS	0.863	0.785	0.943	0.863	0.785	0.943	CLONAL	1	TRUE	0	0.502489184877573	1		726	411	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56860187	56860187	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	135	717	0	ENST00000519728.1:c.189A>C	p.Glu63Asp	p.E63D	ENST00000519728	NM_002350.3	63	gaA/gaC	4/13	0.399821106988724	4	FACETS	0.938	0.852	1			1	CLONAL	1	TRUE	NA	0.502489184877573	4		717	861	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870974	12870975	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	37	441	0	ENST00000228872.4:c.204dup	p.Pro69ThrfsTer56	p.P69Tfs*56	ENST00000228872	NM_004064.3	67	-/A	1/3	1	2	FACETS	0.528	0.435	0.632	0.528	0.435	0.632	SUBCLONAL	1	TRUE	1	0.275435828598979	2		441	509	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772208	68772226	+	frameshift_variant	Frame_Shift_Del	DEL	TTGGCTCTGCCAGGAGCCG	TTGGCTCTGCCAGGAGCCG	CAGAGCCAA	novel	NA	P-0022603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	75	1017	0	ENST00000261769.5:c.57_75delinsCAGAGCCAA	p.Trp20ArgfsTer33	p.W20Rfs*33	ENST00000261769	NM_004360.3	19	tcTTGGCTCTGCCAGGAGCCG/tcCAGAGCCAA	2/16	0.275435828598979	1	FACETS	0.708	0.62	0.803	0.708	0.62	0.803	SUBCLONAL	1	TRUE	0	0.275435828598979	1		1017	663	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041720	47041720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	74	656	0	ENST00000377604.3:c.1945C>T	p.Gln649Ter	p.Q649*	ENST00000377604	NM_001204468.1	649	Caa/Taa	17/24	NA	2	FACETS	0.758	0.665	0.858			1	INDETERMINATE	1	TRUE	NA	0.369714576142604	2		656	528	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0022604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	452	653	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.369714576142604	5	FACETS	0.942	0.903	0.981			1	CLONAL	4	TRUE	NA	0.369714576142604	5		653	1009	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0022604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	375	602	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.369714576142604	5	FACETS	0.989	0.945	1			1	CLONAL	4	TRUE	NA	0.369714576142604	5		602	797	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717695	89717696	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1060500115	NA	P-0022604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	59	623	0	ENST00000371953.3:c.723dup	p.Glu242Ter	p.E242*	ENST00000371953	NM_000314.4	240	-/T	7/9	0.278973232164053	1	FACETS	0.5	0.431	0.576	0.5	0.431	0.576	SUBCLONAL	1	TRUE	0	0.369714576142604	1		623	520	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494677	2494677	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	76	943	0	ENST00000355716.4:c.817A>G	p.Ile273Val	p.I273V	ENST00000355716	NM_003820.2	273	Ata/Gta	8/8	1	2	FACETS	0.665	0.584	0.753	0.665	0.584	0.753	SUBCLONAL	1	TRUE	1	0.369714576142604	2		943	618	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57569913	57569914	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0022604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	49	371	0	ENST00000316660.6:c.95_96dup	p.Gly33LeufsTer5	p.G33Lfs*5	ENST00000316660	NM_021127.2	31	-/TT	2/2	1	2	FACETS	0.659	0.56	0.768	0.659	0.56	0.768	SUBCLONAL	1	TRUE	1	0.369714576142604	2		371	402	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483999	212483999	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs868485519	NA	P-0022604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	76	471	0	ENST00000342788.4:c.2204G>T	p.Gly735Val	p.G735V	ENST00000342788	NM_005235.2	735	gGt/gTt	19/28	1	2	FACETS	0.822	0.723	0.928	0.822	0.723	0.928	CLONAL	1	TRUE	1	0.369714576142604	2		471	500	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357096	70357096	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	112	995	0	ENST00000374080.3:c.5611C>T	p.Arg1871Ter	p.R1871*	ENST00000374080		1871	Cga/Tga	39/45	NA	2	FACETS	0.75	0.674	0.83			1	INDETERMINATE	1	TRUE	NA	0.369714576142604	2		995	808	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	310	636	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.369255728144894	4	FACETS	1	0.944	1			1	CLONAL	2	TRUE	NA	0.412081443132033	4		638	1062	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974765	21974765	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1329324238	NA	P-0022606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	140	373	0	ENST00000304494.5:c.62C>A	p.Ala21Asp	p.A21D	ENST00000304494	NM_000077.4	21	gCc/gAc	1/3	0.412081443132033	2	FACETS	0.962	0.888	1	0.962	0.888	1	CLONAL	2	TRUE	0	0.412081443132033	2		373	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs760043106	NA	P-0022606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	345	896	0	ENST00000269305.4:c.584T>G	p.Ile195Ser	p.I195S	ENST00000269305	NM_001126112.2	195	aTc/aGc	6/11	0.334903745331611	3	FACETS	1	0.991	1	0.783	0.744	0.822	CLONAL	2	TRUE	0	0.412081443132033	3		896	860	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524346	148524346	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs377467108	NA	P-0022606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	152	544	0	ENST00000320356.2:c.638G>T	p.Arg213Leu	p.R213L	ENST00000320356	NM_004456.4	213	cGc/cTc	7/20	0.412081443132033	3	FACETS	0.879	0.81	0.951	0.879	0.81	0.951	CLONAL	2	TRUE	1	0.412081443132033	3		544	506	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0022607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	78	619	1				ENST00000310581	NM_198253.2	-/1132			0.238018485032702	5	FACETS	0.953	0.85	1	0.635	0.567	0.706	INDETERMINATE	2	TRUE	2	0.73	5		620	235	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028820	47028823	+	frameshift_variant	Frame_Shift_Del	DEL	CGTT	CGTT	-	novel	NA	P-0022607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	112	879	0	ENST00000377604.3:c.125_128del	p.Arg42HisfsTer91	p.R42Hfs*91	ENST00000377604	NM_001204468.1	42	CGTTca/ca	3/24	0.445336753783875	1	FACETS	0.658	0.601	0.717	0.658	0.601	0.717	SUBCLONAL	1	TRUE	0	0.73	1		879	296	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111407	8111435	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TTCACCCTCTCCTCTCTCCCCACTCTCAG	TTCACCCTCTCCTCTCTCCCCACTCTCAG	-	novel	NA	P-0022607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	26	348	0	ENST00000346208.3:c.922-28_922del		p.X308_splice	ENST00000346208		308			1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.73	2		348	61	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022615	31022615	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0022608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	156	892	0	ENST00000375687.4:c.2100T>G	p.Tyr700Ter	p.Y700*	ENST00000375687	NM_015338.5	700	taT/taG	13/13	1	2	FACETS	0.89	0.828	0.953	1	0.994	1	CLONAL	3	TRUE	1	0.344574613429171	2		892	339	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671050	30671050	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	143	944	0	ENST00000376406.3:c.5696G>C	p.Gly1899Ala	p.G1899A	ENST00000376406	NM_014641.2	1899	gGa/gCa	12/15	1	2	FACETS	1	0.982	1	1	0.993	1	CLONAL	2	TRUE	1	0.344574613429171	2		944	345	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0022610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	447	804	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.716947278936334	3	FACETS	1	0.997	1			1	CLONAL	3	FALSE	NA	0.711801281550321	3		804	492	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435370	121435370	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	163	1151	1	ENST00000257555.6:c.1403T>A	p.Leu468Gln	p.L468Q	ENST00000257555		468	cTg/cAg	7/10	0.686010417409207	4	FACETS	1	0.985	1	0.435	0.401	0.47	CLONAL	1	FALSE	1	0.711801281550321	4		1152	601	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8111058	8111058	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	91	998	0	ENST00000585124.1:c.149C>T	p.Thr50Ile	p.T50I	ENST00000585124	NM_004217.3	50	aCa/aTa	3/9	0.716947278936334	3	FACETS	0.663	0.59	0.74			1	SUBCLONAL	1	FALSE	NA	0.711801281550321	3		998	523	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45377672	45377672	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	69	409	0	ENST00000262160.6:c.757A>T	p.Thr253Ser	p.T253S	ENST00000262160	NM_005901.5	253	Act/Tct	7/11	0.705137946070176	3	FACETS	1	0.938	1	0.55	0.485	0.618	CLONAL	1	FALSE	1	0.711801281550321	3		409	239	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855951	76855951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	92	911	1	ENST00000373344.5:c.5649G>A	p.Trp1883Ter	p.W1883*	ENST00000373344	NM_000489.3	1883	tgG/tgA	23/35	0.170842673844228	4	FACETS	1	0.963	1			1	INDETERMINATE	1	FALSE	NA	0.711801281550321	4		912	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578504	7578540	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTG	AGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTG	-	novel	NA	P-0022611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	310	1248	0	ENST00000269305.4:c.390_426del	p.Asn131CysfsTer27	p.N131Cfs*27	ENST00000269305	NM_001126112.2	130	ctCAACAAGATGTTTTGCCAACTGGCCAAGACCTGCCCT/ct	5/11	0.651680516566923	1	FACETS	0.861	0.817	0.906	0.861	0.817	0.906	CLONAL	1	TRUE	0	0.651680516566923	1		1248	745	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368233	45368233	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	248	575	0	ENST00000262160.6:c.1369G>A	p.Gly457Arg	p.G457R	ENST00000262160	NM_005901.5	457	Gga/Aga	11/11	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.651680516566923	2		575	624	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358659	67358659	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	269	810	0	ENST00000327367.4:c.167C>G	p.Thr56Ser	p.T56S	ENST00000327367	NM_005902.3	56	aCc/aGc	1/9	1	2	FACETS	0.966	0.908	1	0.966	0.908	1	CLONAL	1	TRUE	1	0.651680516566923	2		810	855	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021248	31021273	+	frameshift_variant	Frame_Shift_Del	DEL	TCCGAACCAGAGCCAGAAGGAATCTG	TCCGAACCAGAGCCAGAAGGAATCTG	-	novel	NA	P-0022611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	197	650	0	ENST00000375687.4:c.1248_1273del	p.Arg417GlnfsTer12	p.R417Qfs*12	ENST00000375687	NM_015338.5	416	cTCCGAACCAGAGCCAGAAGGAATCTG/c	12/13	1	2	FACETS	0.872	0.811	0.936	0.872	0.811	0.936	CLONAL	1	TRUE	1	0.651680516566923	2		650	693	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864336	117864787	+	splice_acceptor_variant,splice_donor_variant,intron_variant	Splice_Site	DEL	CTGCAATTGGTCATATGAAGAGAAAACATAGGTCATACAGTTTTGAACAGTATTATAGAACCATTTATTTTTTAAACTAGTACACTAAGACATACATAATGCTTTCTTTAATGAAGAAGGCCAGATAAAATTTTAGCTCCATAAAGATTTACTCAATTTTTAGCAATATACGTAAAGGGGAAAGGGGATCTTAAAAGGACAAGTCCTACCCTCAGTACAATGTAGGACAATTCTTTAGCAGACTATCTACCCTGCCAGTTCTGAACCTTAAAACTCTGGAAAGACAGGAGGCTTCATACTTAAATAAGGCAATCAGATCCAATGCATTTCCCTGCCCAAACATTTGAGTATATCTTTGATTCCTCATTTCTTTCACTCTGACAGTATAAAGGTAAATTTTAAGCCAAATACTCATGTGAACTTCATCAAGGAACTATTCCAACAGAACAAAC	CTGCAATTGGTCATATGAAGAGAAAACATAGGTCATACAGTTTTGAACAGTATTATAGAACCATTTATTTTTTAAACTAGTACACTAAGACATACATAATGCTTTCTTTAATGAAGAAGGCCAGATAAAATTTTAGCTCCATAAAGATTTACTCAATTTTTAGCAATATACGTAAAGGGGAAAGGGGATCTTAAAAGGACAAGTCCTACCCTCAGTACAATGTAGGACAATTCTTTAGCAGACTATCTACCCTGCCAGTTCTGAACCTTAAAACTCTGGAAAGACAGGAGGCTTCATACTTAAATAAGGCAATCAGATCCAATGCATTTCCCTGCCCAAACATTTGAGTATATCTTTGATTCCTCATTTCTTTCACTCTGACAGTATAAAGGTAAATTTTAAGCCAAATACTCATGTGAACTTCATCAAGGAACTATTCCAACAGAACAAAC	-	novel	NA	P-0022611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	236	434	0	ENST00000297338.2:c.1321+1_1322-1del		p.X441_splice	ENST00000297338	NM_006265.2	441			1	2	FACETS	0.939	0.88	1	0.939	0.88	1	CLONAL	1	TRUE	1	0.651680516566923	2		434	771	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864802	117864802	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	292	504	0	ENST00000297338.2:c.1307A>T	p.Gln436Leu	p.Q436L	ENST00000297338	NM_006265.2	436	cAg/cTg	10/14	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.651680516566923	2		504	854	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869711	117870588	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACCTAAACAAATTTTAATTTGTCATTAGTTTAGAAAGATTAGAAATAGCACTGTGATAAAAGAAAACTGCTAATGATTTATTCTAATTATGTCACATTTGCTTACTGAAGTCTTACTTCAAATGTTAAAATATCTAGTTTAAACTTTAATTCTTTAGCATCTGAATTTTTTAAAATGACTCAATTACACACAGTTACAACACTGGGGCATGACTAGCAAATTCAAACTTAGATCTAGATTTAAATGATCCTAAAATATGTTTGATAAACTCTAAATATGTATGTATGTTAAGTTACATTAACAGTCACAGCTGAAACTTTCCCGTTATAATGTGTTTCATCAAGAAAAGAATCTGGTTCTGGGCACAGTGGCATGTGCCTGTAGTCCCAGCTACTTGAGGCTGAAGTGGGAGGATCACTTGAATCCAAGAGTTCGAGGCTGTAGTGTGCTATAATCCAGCCTGTGAAGAGCCACGGCACTCCAGCATGGATAACACAGCAGAGACCCCGCCTCTTAAAAAACAATATGCCTTGCTAACTAGTTTTGAATACCTGTTTTTGAATAGCAAGTATAACAGGGAAACTAACTGTTCCAAAATGGTTGGTTTAAACGTGATCACCACTTCAATGTTGGGACTCCTCGCAGAAATCAATATATAGGTTCTATGATTGCATATAGGGAGAGAAGTAGGTAAACAATTAGCTCCAAGTATGAAAATAATGCTTAATCTACTGGTAGAAAGCCAAATTCTTTTCTTGATGAAAATGCATTACATGAAATTTTAAGTCTTTCTGTCTATAGTCTGGTTTTCTTTTGAAATTGCTATTAGCAACACAATATAACATTATAATTAATGGCTAATAATTTGTTTCTCTTTT	ACCTAAACAAATTTTAATTTGTCATTAGTTTAGAAAGATTAGAAATAGCACTGTGATAAAAGAAAACTGCTAATGATTTATTCTAATTATGTCACATTTGCTTACTGAAGTCTTACTTCAAATGTTAAAATATCTAGTTTAAACTTTAATTCTTTAGCATCTGAATTTTTTAAAATGACTCAATTACACACAGTTACAACACTGGGGCATGACTAGCAAATTCAAACTTAGATCTAGATTTAAATGATCCTAAAATATGTTTGATAAACTCTAAATATGTATGTATGTTAAGTTACATTAACAGTCACAGCTGAAACTTTCCCGTTATAATGTGTTTCATCAAGAAAAGAATCTGGTTCTGGGCACAGTGGCATGTGCCTGTAGTCCCAGCTACTTGAGGCTGAAGTGGGAGGATCACTTGAATCCAAGAGTTCGAGGCTGTAGTGTGCTATAATCCAGCCTGTGAAGAGCCACGGCACTCCAGCATGGATAACACAGCAGAGACCCCGCCTCTTAAAAAACAATATGCCTTGCTAACTAGTTTTGAATACCTGTTTTTGAATAGCAAGTATAACAGGGAAACTAACTGTTCCAAAATGGTTGGTTTAAACGTGATCACCACTTCAATGTTGGGACTCCTCGCAGAAATCAATATATAGGTTCTATGATTGCATATAGGGAGAGAAGTAGGTAAACAATTAGCTCCAAGTATGAAAATAATGCTTAATCTACTGGTAGAAAGCCAAATTCTTTTCTTGATGAAAATGCATTACATGAAATTTTAAGTCTTTCTGTCTATAGTCTGGTTTTCTTTTGAAATTGCTATTAGCAACACAATATAACATTATAATTAATGGCTAATAATTTGTTTCTCTTTT	-	novel	NA	P-0022611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	224	405	0	ENST00000297338.2:c.481+3_483del		p.X161_splice	ENST00000297338	NM_006265.2	161		6/14	1	2	FACETS	0.893	0.834	0.953	0.893	0.834	0.953	CLONAL	1	TRUE	1	0.651680516566923	2		405	770	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117874178	117875200	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACCTAGAAAAGAAATGCTAAGCTTAAATATCTAGCTACCCATAAATTATCTAGGGATCAGAGGGAGATAAGTAGGTATAACTTCCTAAGTTTATATTCTCATAGAAAGGTTGATAACATATGCAAAATACCTTGAAGCACAAGTACTTCTCTTTTTCCATGCTCATAAATTGTATTCCTTGCTTTAGGAAAAAGTCAAAGCACTAATTATGCATTAAGCTCATAAATGTTTAAACGGACATATCAACAAATAACTAGTAATAGTTTCCTAATTAAACATGATATTTATGAGGGGGAAAAAGAATAACTGCAGAAGAGTACCTTAAATGTTAAAAGGAGCTGGTTATTTTGGAGAAAGAATTACACAATTTTAATTTTCTTTATCTTTTTCCTATATTTTTCAAGTTGTCTATAATAAATATGCCTTACTTTGAAAGACAAAAAAAAGCATGTTATTTAGATAAAATGTGCTTATTGGTCACATGTTAATTTAAGTATTGTAGTCTTTTTCTAAATATTTTACTTTTAAATAAAATCTTAGATCTCAGACATTTTACTGTTCACATACTGACATAAACTGAAGTACTAGAATGTATCCTCAGTAGAAACTGTTTAAGGCATTTCTTAATAAAATACACATTATTTTAATTAGAATAAAAATTTCATCAATGCTTTTAAAAATTATAGAAAGATATGTGAATTTAAATATTAATTATCTTCTTAGATGGTGGTGTGGTTGGCAGACTCCAGTTTTATAACCAATCATTACCTAAAACAAAATAACAAAAAACTACGAAGAATATTTACTTAGGAAAAAAAGTTTAAAATCCTAAAATTGTCTTTTCTGAGCTATATTTTAAAAAATCATCACATAACAATTAGTTTCCAACATTTTAACCTCTTGATGACTCAAGTCTATGTAAGCTGCTGAAAAAAGTATTAAAAAGGCAGCTCCAAAGGAAGAACAAATGGGGGTGAGCTCCATTACTTCACAGGGAGAACAGACGCAAGTAGGTTTCCTCCC	ACCTAGAAAAGAAATGCTAAGCTTAAATATCTAGCTACCCATAAATTATCTAGGGATCAGAGGGAGATAAGTAGGTATAACTTCCTAAGTTTATATTCTCATAGAAAGGTTGATAACATATGCAAAATACCTTGAAGCACAAGTACTTCTCTTTTTCCATGCTCATAAATTGTATTCCTTGCTTTAGGAAAAAGTCAAAGCACTAATTATGCATTAAGCTCATAAATGTTTAAACGGACATATCAACAAATAACTAGTAATAGTTTCCTAATTAAACATGATATTTATGAGGGGGAAAAAGAATAACTGCAGAAGAGTACCTTAAATGTTAAAAGGAGCTGGTTATTTTGGAGAAAGAATTACACAATTTTAATTTTCTTTATCTTTTTCCTATATTTTTCAAGTTGTCTATAATAAATATGCCTTACTTTGAAAGACAAAAAAAAGCATGTTATTTAGATAAAATGTGCTTATTGGTCACATGTTAATTTAAGTATTGTAGTCTTTTTCTAAATATTTTACTTTTAAATAAAATCTTAGATCTCAGACATTTTACTGTTCACATACTGACATAAACTGAAGTACTAGAATGTATCCTCAGTAGAAACTGTTTAAGGCATTTCTTAATAAAATACACATTATTTTAATTAGAATAAAAATTTCATCAATGCTTTTAAAAATTATAGAAAGATATGTGAATTTAAATATTAATTATCTTCTTAGATGGTGGTGTGGTTGGCAGACTCCAGTTTTATAACCAATCATTACCTAAAACAAAATAACAAAAAACTACGAAGAATATTTACTTAGGAAAAAAAGTTTAAAATCCTAAAATTGTCTTTTCTGAGCTATATTTTAAAAAATCATCACATAACAATTAGTTTCCAACATTTTAACCTCTTGATGACTCAAGTCTATGTAAGCTGCTGAAAAAAGTATTAAAAAGGCAGCTCCAAAGGAAGAACAAATGGGGGTGAGCTCCATTACTTCACAGGGAGAACAGACGCAAGTAGGTTTCCTCCC	-	novel	NA	P-0022611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	125	443	0	ENST00000297338.2:c.274+170_277del		p.X92_splice	ENST00000297338	NM_006265.2	92		4/14	1	2	FACETS	0.539	0.488	0.592	0.539	0.488	0.592	SUBCLONAL	1	TRUE	1	0.651680516566923	2		443	712	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696399	47696399	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	89	689	0	ENST00000347630.2:c.424C>A	p.Leu142Ile	p.L142I	ENST00000347630	NM_001007230.1	142	Ctt/Att	6/11	1	2	FACETS	0.97	0.881	1	0.97	0.881	1	CLONAL	1	TRUE	1	0.921757767961412	2		689	199	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593607	+	protein_altering_variant	In_Frame_Del	DEL	AGTGGAA	AGTGGAA	G	novel	NA	P-0022613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	158	551	0	ENST00000288135.5:c.1667_1673delinsG	p.Gln556_Lys558delinsArg	p.Q556_K558delinsR	ENST00000288135	NM_000222.2	556	cAGTGGAAg/cGg	11/21	0.921757767961412	5	FACETS	0.928	0.88	0.974	0.928	0.88	0.974	CLONAL	4	TRUE	1	0.921757767961412	5		551	220	SUCCESS
APC	324	MSKCC	GRCh37	5	112174577	112174577	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587783029	NA	P-0022638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	75	518	0	ENST00000257430.4:c.3286C>T	p.Gln1096Ter	p.Q1096*	ENST00000257430	NM_000038.5	1096	Cag/Tag	16/16	0.30179852923819	1	FACETS	0.938	0.824	1	0.938	0.824	1	CLONAL	1	TRUE	0	0.26	1		518	535	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32905124	32905127	+	frameshift_variant	Frame_Shift_Del	DEL	GACA	GACA	-	rs80359659	NA	P-0022638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	98	533	0	ENST00000380152.3:c.755_758del	p.Asp252ValfsTer24	p.D252Vfs*24	ENST00000380152		250	gtGACA/gt	9/27	1	2	FACETS	0.935	0.834	1	0.935	0.834	1	CLONAL	1	TRUE	1	0.26	2		533	806	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112760179	112760179	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	93	568	0	ENST00000369452.4:c.848T>A	p.Leu283Gln	p.L283Q	ENST00000369452	NM_007373.3	283	cTg/cAg	4/9	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.26	2		568	707	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967284	134967284	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	87	695	0	ENST00000398015.3:c.2623G>T	p.Val875Phe	p.V875F	ENST00000398015	NM_004441.4	875	Gtc/Ttc	14/16	0.30179852923819	1	FACETS	0.755	0.668	0.849	0.755	0.668	0.849	SUBCLONAL	1	TRUE	0	0.26	1		695	771	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1932445	1932463	+	frameshift_variant	Frame_Shift_Del	DEL	CTACAACACCAAGTTTGCC	CTACAACACCAAGTTTGCC	-	novel	NA	P-0022638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	72	807	0	ENST00000382891.5:c.1505_1523del	p.Tyr502TrpfsTer14	p.Y502Wfs*14	ENST00000382891	NM_133335.3	501	cgCTACAACACCAAGTTTGCC/cg	6/22	1	2	FACETS	0.664	0.579	0.756	0.664	0.579	0.756	SUBCLONAL	1	TRUE	1	0.26	2		807	834	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410944	31410965	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCGCTACCTTGGCCTGAGTT	CTCCGCTACCTTGGCCTGAGTT	-	novel	NA	P-0022638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	87	795	0	ENST00000344624.3:c.3555_3576del	p.Thr1186SerfsTer9	p.T1186Sfs*9	ENST00000344624		1185	agAACTCAGGCCAAGGTAGCGGAG/ag	28/33	0.222636756864334	3	FACETS	0.69	0.609	0.777	0.345	0.304	0.389	SUBCLONAL	1	TRUE	1	0.26	3		795	1096	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141569508	141569531	+	inframe_deletion	In_Frame_Del	DEL	GTAAACTTTACCCTTTGGGAATCT	GTAAACTTTACCCTTTGGGAATCT	-	novel	NA	P-0022638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	64	679	0	ENST00000220592.5:c.753_776del	p.Asp252_Thr259del	p.D252_T259del	ENST00000220592	NM_012154.3	251	acAGATTCCCAAAGGGTAAAGTTTACc/acc	6/19	0.222636756864334	3	FACETS	0.645	0.557	0.74	0.322	0.278	0.37	SUBCLONAL	1	TRUE	1	0.26	3		679	863	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0022640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	295	925	0	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	0.778835030199219	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.778835030199219	1		925	438	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20483047	20483047	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	407	415	0	ENST00000346618.3:c.783del	p.Glu262LysfsTer2	p.E262Kfs*2	ENST00000346618	NM_001949.4	260	tcA/tc	4/7	0.298478922055727	5	FACETS	0.93	0.898	0.962			1	INDETERMINATE	4	TRUE	NA	0.778835030199219	5		415	609	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118370100	118370100	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs782113867	NA	P-0022641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	52	392	0	ENST00000534358.1:c.6044A>G	p.Asn2015Ser	p.N2015S	ENST00000534358	NM_005933.3	2015	aAt/aGt	23/36	1	2	FACETS	0.976	0.834	1	0.976	0.834	1	CLONAL	1	TRUE	1	0.275374237180724	2		392	387	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164064	47164064	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs761377537	NA	P-0022641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	44	430	0	ENST00000409792.3:c.2062A>C	p.Thr688Pro	p.T688P	ENST00000409792	NM_014159.6	688	Act/Cct	3/21	1	2	FACETS	0.795	0.668	0.935	0.795	0.668	0.935	CLONAL	1	TRUE	1	0.275374237180724	2		430	402	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495684	72495684	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	53	511	0	ENST00000477973.2:c.388T>G	p.Cys130Gly	p.C130G	ENST00000477973	NM_012234.5	130	Tgc/Ggc	1/4	1	2	FACETS	0.79	0.675	0.917	0.79	0.675	0.917	CLONAL	1	TRUE	1	0.275374237180724	2		511	487	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	154	445	0				ENST00000310581	NM_198253.2	-/1132			0.586652337523347	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.6342615759995	3		445	286	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572506	41572506	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	128	924	0	ENST00000263253.7:c.5035A>G	p.Thr1679Ala	p.T1679A	ENST00000263253	NM_001429.3	1679	Aca/Gca	30/31	0.6342615759995	1	FACETS	0.804	0.738	0.871	0.804	0.738	0.871	CLONAL	1	TRUE	0	0.6342615759995	1		924	343	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0022643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	604	935	2	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.904041152847962	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.912106729889574	2		937	658	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916734	48916734	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0022643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	288	520	7	ENST00000267163.4:c.265-1G>A		p.X89_splice	ENST00000267163	NM_000321.2	89			0.912106729889574	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.912106729889574	2		527	305	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429281	78429281	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	425	676	2	ENST00000370768.2:c.1161A>T	p.Lys387Asn	p.K387N	ENST00000370768	NM_003902.3	387	aaA/aaT	13/20	0.27656559453516	3	FACETS	1	0.993	1	0.737	0.713	0.76	INDETERMINATE	2	TRUE	0	0.912106729889574	3		678	614	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422891	49422891	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	488	597	4	ENST00000301067.7:c.14204G>T	p.Arg4735Leu	p.R4735L	ENST00000301067	NM_003482.3	4735	cGg/cTg	44/54	0.188480110875265	5	FACETS	1	0.995	1	0.685	0.663	0.706	INDETERMINATE	3	TRUE	0	0.912106729889574	5		601	740	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478852	56478852	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	326	918	6	ENST00000267101.3:c.308G>T	p.Arg103Leu	p.R103L	ENST00000267101	NM_001982.3	103	cGc/cTc	3/28	0.188480110875265	5	FACETS	0.833	0.788	0.879	0.333	0.315	0.352	INDETERMINATE	2	TRUE	0	0.912106729889574	5		924	1016	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508467	29508467	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555608659	NA	P-0022643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	90	504	3	ENST00000356175.3:c.614A>G	p.Lys205Arg	p.K205R	ENST00000356175	NM_000267.3	205	aAg/aGg	6/57	0.361912726266987	3	FACETS	0.655	0.584	0.729	0.218	0.194	0.243	INDETERMINATE	1	TRUE	0	0.912106729889574	3		507	439	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514590	44514590	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	136	447	3	ENST00000291552.4:c.566G>A	p.Arg189His	p.R189H	ENST00000291552	NM_006758.2	189	cGt/cAt	7/8	0.418449057051651	1	FACETS	0.4	0.367	0.433	0.4	0.367	0.433	INDETERMINATE	1	TRUE	0	0.912106729889574	1		450	406	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109415168	109415168	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	406	1056	6	ENST00000436639.2:c.109G>T	p.Glu37Ter	p.E37*	ENST00000436639	NM_014454.2	37	Gag/Tag	1/10	0.316151211661444	4	FACETS	1	0.994	1	0.331	0.315	0.348	INDETERMINATE	1	TRUE	0	0.912106729889574	4		1062	1286	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020471	69020471	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	379	774	6	ENST00000288368.4:c.2843C>A	p.Pro948His	p.P948H	ENST00000288368	NM_024870.2	948	cCc/cAc	24/40	0.301018302391233	3	FACETS	0.827	0.791	0.862	0.827	0.791	0.862	INDETERMINATE	2	TRUE	1	0.912106729889574	3		780	732	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969478	44969478	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs924520918	NA	P-0022643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	121	582	2	ENST00000377967.4:c.4160A>G	p.Tyr1387Cys	p.Y1387C	ENST00000377967	NM_021140.2	1387	tAt/tGt	28/29	0.34180349345597	1	FACETS	0.519	0.477	0.562	0.519	0.477	0.562	INDETERMINATE	1	TRUE	0	0.912106729889574	1		584	278	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0022644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	62	792	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	0.506	0.436	0.583	0.506	0.436	0.583	SUBCLONAL	1	TRUE	1	0.294723134944513	2		792	831	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0022644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	316	708	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.281218070852776	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.294723134944513	2		708	1044	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692968	89692968	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	17	577	1	ENST00000371953.3:c.452C>A	p.Ala151Asp	p.A151D	ENST00000371953	NM_000314.4	151	gCc/gAc	5/9	0.294723134944513	1	FACETS	0.199	0.148	0.261	0.199	0.148	0.261	SUBCLONAL	1	TRUE	0	0.294723134944513	1		578	494	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165659	118165659	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	28	375	0	ENST00000369448.3:c.169A>T	p.Ser57Cys	p.S57C	ENST00000369448	NM_017709.3	57	Agt/Tgt	2/2	1	2	FACETS	0.443	0.353	0.545	0.443	0.353	0.545	SUBCLONAL	1	TRUE	1	0.294723134944513	2		375	429	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691933	30691934	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	65	446	0	ENST00000295754.5:c.435_436insT	p.Asn146Ter	p.N146*	ENST00000295754	NM_003242.5	145	-/T	3/7	0.294723134944513	1	FACETS	0.66	0.572	0.755	0.66	0.572	0.755	SUBCLONAL	1	TRUE	0	0.294723134944513	1		446	570	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	96	549	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.206706365025996	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.206706365025996	3		549	414	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0022646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	145	701	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.97	1	1	0.992	1	CLONAL	2	TRUE	1	0.206706365025996	2		701	623	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022441	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	27	218	0	ENST00000375687.4:c.1926del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	642	ggA/gg	13/13	0.206706365025996	3	FACETS	1	0.912	1	0.641	0.512	0.785	CLONAL	1	TRUE	1	0.206706365025996	3		218	225	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850820	63850820	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746755575	NA	P-0022646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	86	392	0	ENST00000279873.7:c.1598C>T	p.Ala533Val	p.A533V	ENST00000279873	NM_032199.2	533	gCg/gTg	10/10	0.206706365025996	7	FACETS	0.903	0.802	1			1	CLONAL	3	TRUE	NA	0.206706365025996	7		392	466	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437462	49437462	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs794727379	NA	P-0022646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	215	678	1	ENST00000301067.7:c.5423del	p.Gly1808GlufsTer44	p.G1808Efs*44	ENST00000301067	NM_003482.3	1808	gGa/ga	23/54	0.206706365025996	3	FACETS	1	0.936	1	1	0.992	1	CLONAL	3	TRUE	1	0.206706365025996	3		679	762	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245525	133245525	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	104	365	0	ENST00000320574.5:c.1795G>T	p.Val599Leu	p.V599L	ENST00000320574	NM_006231.2	599	Gtg/Ttg	17/49	0.206706365025996	3	FACETS	1	0.926	1	1	0.984	1	CLONAL	3	TRUE	1	0.206706365025996	3		365	360	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350360	89350360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	85	778	0	ENST00000301030.4:c.2590G>A	p.Asp864Asn	p.D864N	ENST00000301030	NM_001256183.1	864	Gac/Aac	9/13	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.206706365025996	2		778	722	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577572	7577573	+	stop_gained	Nonsense_Mutation	DNP	TG	TG	AC	novel	NA	P-0022646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	125	639	1	ENST00000269305.4:c.708_709delinsGT	p.Tyr236_Met237delinsTer	p.Y236_M237delins*	ENST00000269305	NM_001126112.2	236	taCAtg/taGTtg	7/11	1	2	FACETS	1	0.909	1	1	0.99	1	CLONAL	2	TRUE	1	0.206706365025996	2		640	604	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546050	41546050	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	182	752	0	ENST00000263253.7:c.2665C>A	p.Pro889Thr	p.P889T	ENST00000263253	NM_001429.3	889	Cca/Aca	14/31	0.206706365025996	1	FACETS	1	0.976	1	1	0.993	1	CLONAL	2	TRUE	0	0.206706365025996	1		752	699	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178020	56178020	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	28	441	0	ENST00000399503.3:c.2993C>G	p.Ala998Gly	p.A998G	ENST00000399503	NM_005921.1	998	gCa/gGa	14/20	1	2	FACETS	0.797	0.637	0.978	0.797	0.637	0.978	CLONAL	1	TRUE	1	0.206706365025996	2		441	340	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099508	157099508	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	55	416	0	ENST00000346085.5:c.445C>G	p.Gln149Glu	p.Q149E	ENST00000346085	NM_020732.3	149	Cag/Gag	1/20	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.206706365025996	2		416	525	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965795	90965795	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	28	346	0	ENST00000265433.3:c.1522C>G	p.Leu508Val	p.L508V	ENST00000265433	NM_002485.4	508	Cta/Gta	11/16	0.206706365025996	5	FACETS	0.803	0.641	0.988	0.201	0.16	0.247	CLONAL	1	TRUE	1	0.206706365025996	5		346	442	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226309	2226309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	175	879	1	ENST00000326181.6:c.1922G>A	p.Arg641His	p.R641H	ENST00000326181	NM_032271.2	641	cGt/cAt	20/21	0.36293745743999	1	FACETS	0.961	0.894	1	0.961	0.894	1	CLONAL	1	TRUE	0	0.569050834946405	1		880	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0022651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	373	740	0	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	0.382100729271649	4	FACETS	1	0.992	1	0.839	0.806	0.871	CLONAL	3	TRUE	0	0.570924407321336	4		740	612	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166763	32166763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761314959	NA	P-0022651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	284	775	0	ENST00000375023.3:c.4475G>A	p.Arg1492Gln	p.R1492Q	ENST00000375023	NM_004557.3	1492	cGg/cAg	24/30	0.570924407321336	5	FACETS	0.897	0.843	0.951	0.598	0.562	0.634	CLONAL	2	TRUE	2	0.570924407321336	5		775	1030	SUCCESS
AR	367	MSKCC	GRCh37	X	66765533	66765533	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	101	794	0	ENST00000374690.3:c.545A>G	p.Lys182Arg	p.K182R	ENST00000374690	NM_000044.3	182	aAa/aGa	1/8	0.356312571507167	5	FACETS	1	0.938	1	0.355	0.318	0.395	CLONAL	1	TRUE	2	0.570924407321336	5		794	616	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575035	64575035	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886039416	NA	P-0022652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	206	582	0	ENST00000312049.6:c.772C>T	p.Gln258Ter	p.Q258*	ENST00000312049	NM_130799.2	258	Cag/Tag	4/10	0.58580602789378	1	FACETS	0.993	0.93	1	0.993	0.93	1	CLONAL	1	TRUE	0	0.58580602789378	1		582	501	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939291	76939291	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0022652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	150	979	0	ENST00000373344.5:c.1457del	p.Asn486IlefsTer28	p.N486Ifs*28	ENST00000373344	NM_000489.3	486	aAt/at	9/35	0.58580602789378	1	FACETS	0.808	0.745	0.873	0.808	0.745	0.873	CLONAL	1	TRUE	0	0.58580602789378	1		979	448	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0022653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	144	517	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			0.579766598745727	4	FACETS	1	0.962	1			1	CLONAL	1	TRUE	NA	0.579766598745727	4		517	717	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096313	2096313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774831009	NA	P-0022653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	203	872	0	ENST00000219066.1:c.194G>A	p.Arg65His	p.R65H	ENST00000219066	NM_002528.5	65	cGt/cAt	2/6	0.43312289564595	4	FACETS	0.948	0.878	1			1	CLONAL	1	TRUE	NA	0.579766598745727	4		872	1167	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037210	71037210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748393867	NA	P-0022653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	97	463	0	ENST00000318789.4:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000318789	NM_032682.5	361	Cgc/Tgc	14/21	1	2	FACETS	0.865	0.777	0.957	0.865	0.777	0.957	CLONAL	1	TRUE	1	0.579766598745727	2		463	387	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527273	187527273	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	153	626	0	ENST00000441802.2:c.10301A>G	p.Asn3434Ser	p.N3434S	ENST00000441802	NM_005245.3	3434	aAt/aGt	17/27	0.579766598745727	3	FACETS	0.944	0.866	1	0.472	0.433	0.513	CLONAL	1	TRUE	1	0.579766598745727	3		626	721	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393283	393283	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	356	804	0	ENST00000380956.4:c.131A>G	p.Asn44Ser	p.N44S	ENST00000380956	NM_001195286.1	44	aAc/aGc	2/9	0.573195794982045	3	FACETS	0.942	0.897	0.987			1	CLONAL	2	TRUE	NA	0.579766598745727	3		804	841	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913315	NA	P-0022654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	37	775	0	ENST00000326873.7:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000326873	NM_000455.4	194	Gac/Tac	4/10	1	2	FACETS	0.832	0.686	0.996	0.832	0.686	0.996	CLONAL	1	TRUE	1	0.18	2		775	494	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0022654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	42	706	1	ENST00000311936.3:c.34_35delinsTT	p.Gly12Phe	p.G12F	ENST00000311936	NM_004985.3	12	GGt/TTt	2/5	1	2	FACETS	0.832	0.694	0.985	0.832	0.694	0.985	CLONAL	1	TRUE	1	0.18	2		707	561	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515248	103515248	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	25	470	0	ENST00000355739.4:c.1749G>T	p.Leu583Phe	p.L583F	ENST00000355739	NM_000123.3	583	ttG/ttT	8/15	1	2	FACETS	0.612	0.481	0.763	0.612	0.481	0.763	SUBCLONAL	1	TRUE	1	0.18	2		470	454	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660731	227660731	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0022654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	45	791	0	ENST00000305123.5:c.2724C>G	p.Tyr908Ter	p.Y908*	ENST00000305123	NM_005544.2	908	taC/taG	1/2	1	2	FACETS	0.942	0.791	1	0.942	0.791	1	CLONAL	1	TRUE	1	0.18	2		791	531	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0022656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	240	817	3	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.984	0.918	1	0.984	0.918	1	CLONAL	1	TRUE	1	0.400089225178718	2		820	1219	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121912580	NA	P-0022656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	110	427	1	ENST00000342988.3:c.1157G>T	p.Gly386Val	p.G386V	ENST00000342988	NM_005359.5	386	gGt/gTt	10/12	0.400089225178718	1	FACETS	0.838	0.756	0.924	0.838	0.756	0.924	CLONAL	1	TRUE	0	0.400089225178718	1		428	525	SUCCESS
APC	324	MSKCC	GRCh37	5	112175684	112175685	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0022656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	52	377	0	ENST00000257430.4:c.4394_4395insGG	p.Ser1465ArgfsTer9	p.S1465Rfs*9	ENST00000257430	NM_000038.5	1465	agt/aGGgt	16/16	0.400089225178718	1	FACETS	0.489	0.417	0.568	0.489	0.417	0.568	SUBCLONAL	1	TRUE	0	0.400089225178718	1		377	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0022657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	610	953	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.894506580146426	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	FALSE	0	0.894506580146426	1		955	701	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916850	48916850	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1131690843	NA	P-0022657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	228	426	0	ENST00000267163.4:c.380G>A	p.Ser127Asn	p.S127N	ENST00000267163	NM_000321.2	127	aGt/aAt	3/27	0.894506580146426	1	FACETS	0.939	0.902	0.975	0.939	0.902	0.975	CLONAL	1	FALSE	0	0.894506580146426	1		426	300	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437427	110437427	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	376	488	0	ENST00000375856.3:c.974A>G	p.His325Arg	p.H325R	ENST00000375856	NM_003749.2	325	cAc/cGc	1/2	NA	2	FACETS	0.913	0.87	0.956			1	INDETERMINATE	1	FALSE	NA	0.894506580146426	2		488	921	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433142	49433142	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0022657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	297	551	0	ENST00000301067.7:c.8230-1G>T		p.X2744_splice	ENST00000301067	NM_003482.3	2744			1	2	FACETS	0.93	0.881	0.979	0.93	0.881	0.979	CLONAL	1	FALSE	1	0.894506580146426	2		551	714	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133865	41133865	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	225	285	0	ENST00000379561.5:c.1763G>T	p.Gly588Val	p.G588V	ENST00000379561	NM_002015.3	588	gGc/gTc	2/3	0.894506580146426	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	0	0.894506580146426	1		285	277	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40379656	40379656	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	376	694	0	ENST00000293328.3:c.176A>T	p.Gln59Leu	p.Q59L	ENST00000293328	NM_012448.3	59	cAg/cTg	3/19	0.112586304383676	3	FACETS	1	0.987	1	0.368	0.35	0.387	INDETERMINATE	1	FALSE	0	0.894506580146426	3		694	1102	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231554	5231554	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	147	442	0	ENST00000357368.4:c.1922C>A	p.Pro641Gln	p.P641Q	ENST00000357368	NM_002850.3	641	cCg/cAg	14/38	0.590107216832601	1	FACETS	0.295	0.27	0.321	0.295	0.27	0.321	SUBCLONAL	1	FALSE	0	0.894506580146426	1		442	616	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96931038	96931038	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs776127077	NA	P-0022657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	119	316	0	ENST00000258439.3:c.82G>T	p.Glu28Ter	p.E28*	ENST00000258439	NM_001193304.2	28	Gag/Tag	2/4	0.497374095350739	1	FACETS	0.421	0.385	0.459	0.421	0.385	0.459	INDETERMINATE	1	FALSE	0	0.894506580146426	1		316	349	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266810	198266810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	52	603	0	ENST00000335508.6:c.2122G>A	p.Ala708Thr	p.A708T	ENST00000335508	NM_012433.2	708	Gcc/Acc	15/25	0.398967968953577	1	FACETS	0.08	0.068	0.094	0.08	0.068	0.094	INDETERMINATE	1	FALSE	0	0.894506580146426	1		603	801	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024372	31024372	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	193	600	0	ENST00000375687.4:c.3857A>T	p.Gln1286Leu	p.Q1286L	ENST00000375687	NM_015338.5	1286	cAg/cTg	13/13	0.571911075173507	1	FACETS	0.33	0.306	0.355	0.33	0.306	0.355	SUBCLONAL	1	FALSE	0	0.894506580146426	1		600	723	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582140	52582140	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	259	437	1	ENST00000394830.3:c.4688G>T	p.Arg1563Leu	p.R1563L	ENST00000394830	NM_018313.4	1563	cGa/cTa	30/30	0.894506580146426	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	0	0.894506580146426	1		438	309	SUCCESS
APC	324	MSKCC	GRCh37	5	112175549	112175549	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	233	318	0	ENST00000257430.4:c.4258C>G	p.Pro1420Ala	p.P1420A	ENST00000257430	NM_000038.5	1420	Ccc/Gcc	16/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.894506580146426	2		318	497	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515256	149515256	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	353	549	0	ENST00000261799.4:c.226G>T	p.Ala76Ser	p.A76S	ENST00000261799	NM_002609.3	76	Gcc/Tcc	3/23	0.113895679243689	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.894506580146426	0		549	775	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517775	176517775	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	407	758	1	ENST00000292408.4:c.385G>T	p.Asp129Tyr	p.D129Y	ENST00000292408	NM_213647.1	129	Gac/Tac	4/18	0.113895679243689	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.894506580146426	0		759	902	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0022660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	310	550	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.63292132469296	3	FACETS	1	0.942	1	0.5	0.471	0.53	CLONAL	1	TRUE	1	0.63844724914188	3		552	1281	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	250	713	1	ENST00000269305.4:c.859G>T	p.Glu287Ter	p.E287*	ENST00000269305	NM_001126112.2	287	Gag/Tag	8/11	0.63844724914188	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.63844724914188	1		714	516	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402119	402119	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	137	771	0	ENST00000399788.2:c.4672G>C	p.Glu1558Gln	p.E1558Q	ENST00000399788	NM_001042603.1	1558	Gaa/Caa	27/28	1	2	FACETS	0.38	0.345	0.418	0.38	0.345	0.418	SUBCLONAL	1	TRUE	1	0.63844724914188	2		771	1128	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434505	110434535	+	frameshift_variant	Frame_Shift_Del	DEL	ACGCCCACAGCGCTGATGAGACCCCCGAGGC	ACGCCCACAGCGCTGATGAGACCCCCGAGGC	-	novel	NA	P-0022660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	204	679	0	ENST00000375856.3:c.3866_3896del	p.Ser1289ThrfsTer32	p.S1289Tfs*32	ENST00000375856	NM_003749.2	1289	aGCCTCGGGGGTCTCATCAGCGCTGTGGGCGTc/ac	1/2	1	2	FACETS	0.834	0.776	0.895	0.834	0.776	0.895	CLONAL	1	TRUE	1	0.63844724914188	2		679	766	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628575	90628575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	146	716	0	ENST00000330062.3:c.1012G>A	p.Asp338Asn	p.D338N	ENST00000330062	NM_002168.2	338	Gat/Aat	8/11	1	2	FACETS	0.606	0.553	0.66	0.606	0.553	0.66	SUBCLONAL	1	TRUE	1	0.63844724914188	2		716	755	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2193759	2193759	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	199	675	0	ENST00000398665.3:c.565G>A	p.Asp189Asn	p.D189N	ENST00000398665	NM_032482.2	189	Gac/Aac	6/28	0.172460668703828	0	FACETS	0.399	0.372	0.426			1	INDETERMINATE	1	TRUE	0	0.63844724914188	0		675	565	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321681	62321681	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	95	630	0	ENST00000360203.5:c.2300G>A	p.Ser767Asn	p.S767N	ENST00000360203	NM_001283009.1	767	aGt/aAt	26/35	1	2	FACETS	0.498	0.444	0.555	0.498	0.444	0.555	SUBCLONAL	1	TRUE	1	0.63844724914188	2		630	598	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729943	41729944	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0022660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	232	585	1	ENST00000242208.4:c.585_586delinsTA	p.Gly196Ser	p.G196S	ENST00000242208	NM_002192.2	195	gtGGgc/gtTAgc	3/3	1	2	FACETS	0.838	0.783	0.895	0.838	0.783	0.895	CLONAL	1	TRUE	1	0.63844724914188	2		586	867	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534572	140534572	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	150	498	0	ENST00000288602.6:c.341C>T	p.Ser114Phe	p.S114F	ENST00000288602	NM_004333.4	114	tCt/tTt	3/18	1	2	FACETS	0.544	0.498	0.594	0.544	0.498	0.594	SUBCLONAL	1	TRUE	1	0.63844724914188	2		498	863	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227021	53227021	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	140	315	0	ENST00000375401.3:c.2554G>C	p.Glu852Gln	p.E852Q	ENST00000375401	NM_004187.3	852	Gag/Cag	18/26	1	1	FACETS	0.788	0.726	0.851	0.788	0.726	0.851	SUBCLONAL	1	TRUE	0	0.63844724914188	1		315	379	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521087	187521094	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCAAGG	TGGCAAGG	A	novel	NA	P-0022660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	181	400	0	ENST00000441802.2:c.12061_12068delinsT	p.Pro4021Ter	p.P4021*	ENST00000441802	NM_005245.3	4021	CCTTGCCAg/Tg	22/27	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.63844724914188	2		400	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0022661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	490	717	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.698095617824103	2		717	685	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197506	106197506	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	23	380	1	ENST00000380013.4:c.5844del	p.Val1949Ter	p.V1949*	ENST00000380013	NM_001127208.2	1947	Aaa/aa	11/11	1	2	FACETS	0.179	0.139	0.225	0.179	0.139	0.225	SUBCLONAL	1	TRUE	1	0.698095617824103	2		381	369	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288785	33288785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765273333	NA	P-0022661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	37	413	0	ENST00000374542.5:c.767G>A	p.Arg256His	p.R256H	ENST00000374542	NM_001141970.1	256	cGc/cAc	3/8	0.691428192130598	4	FACETS	0.275	0.226	0.33	0.092	0.075	0.11	SUBCLONAL	1	TRUE	1	0.698095617824103	4		413	655	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0022661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	242	771	0	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	0.698095617824103	3	FACETS	1	0.951	1	0.51	0.477	0.544	CLONAL	1	TRUE	1	0.698095617824103	3		771	917	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120460308	120460308	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs312262801	NA	P-0022661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	43	566	1	ENST00000256646.2:c.6007C>T	p.Arg2003Ter	p.R2003*	ENST00000256646	NM_024408.3	2003	Cga/Tga	33/34	0.698095617824103	3	FACETS	0.222	0.185	0.264	0.111	0.092	0.132	SUBCLONAL	1	TRUE	1	0.698095617824103	3		567	747	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934189	48934189	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs768305224	NA	P-0022661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	76	508	0	ENST00000267163.4:c.644C>A	p.Ser215Ter	p.S215*	ENST00000267163	NM_000321.2	215	tCa/tAa	7/27	0.606556489233449	1	FACETS	0.886	0.799	0.973	0.886	0.799	0.973	CLONAL	1	TRUE	0	0.698095617824103	1		508	160	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223817	2223817	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	211	843	2	ENST00000326181.6:c.1115T>C	p.Leu372Pro	p.L372P	ENST00000326181	NM_032271.2	372	cTg/cCg	12/21	NA	2	FACETS	0.95	0.888	1			1	INDETERMINATE	1	TRUE	NA	0.698095617824103	2		845	636	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579379	7579379	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	148	810	2	ENST00000269305.4:c.308A>G	p.Tyr103Cys	p.Y103C	ENST00000269305	NM_001126112.2	103	tAc/tGc	4/11	NA	2	FACETS	0.615	0.562	0.669			1	INDETERMINATE	1	TRUE	NA	0.698095617824103	2		812	690	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976261	7976261	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	199	422	0	ENST00000319144.4:c.1934T>G	p.Leu645Arg	p.L645R	ENST00000319144	NM_001139.2	645	cTg/cGg	15/15	NA	2	FACETS	1	0.972	1			1	INDETERMINATE	2	TRUE	NA	0.698095617824103	2		422	278	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756677	756677	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	138	598	2	ENST00000314574.4:c.151G>A	p.Ala51Thr	p.A51T	ENST00000314574	NM_005433.3	51	Gca/Aca	2/12	0.698095617824103	3	FACETS	0.942	0.861	1	0.314	0.287	0.343	CLONAL	1	TRUE	0	0.698095617824103	3		600	566	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610610	10610610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372654184	NA	P-0022661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	47	697	0	ENST00000171111.5:c.100G>A	p.Ala34Thr	p.A34T	ENST00000171111	NM_203500.1	34	Gcc/Acc	2/6	0.698095617824103	3	FACETS	0.221	0.186	0.26	0.11	0.093	0.13	SUBCLONAL	1	TRUE	1	0.698095617824103	3		697	822	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99163122	99163123	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	34	537	0	ENST00000074304.5:c.1133dup	p.Leu379AlafsTer5	p.L379Afs*5	ENST00000074304	NM_001134224.1	376	-/A	13/26	0.686664089009241	3	FACETS	0.194	0.158	0.236	0.097	0.079	0.118	SUBCLONAL	1	TRUE	1	0.698095617824103	3		537	676	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144835	47144836	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	22	626	0	ENST00000409792.3:c.4917dup	p.Trp1640MetfsTer26	p.W1640Mfs*26	ENST00000409792	NM_014159.6	1639	-/A		0.670409186686818	2	FACETS	0.182	0.14	0.23	0.091	0.07	0.115	SUBCLONAL	1	TRUE	0	0.698095617824103	2		626	347	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158446	106158447	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs748419340	NA	P-0022661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	60	297	0	ENST00000380013.4:c.3353dup	p.Asn1118LysfsTer12	p.N1118Kfs*12	ENST00000380013	NM_001127208.2	1116	ata/atAa	3/11	1	2	FACETS	0.819	0.716	0.927	0.819	0.716	0.927	CLONAL	1	TRUE	1	0.698095617824103	2		297	210	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1272316	1272316	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	64	681	0	ENST00000310581.5:c.2366C>T	p.Ala789Val	p.A789V	ENST00000310581	NM_198253.2	789	gCc/gTc	7/16	0.651226903072469	5	FACETS	0.318	0.274	0.366	0.079	0.068	0.092	SUBCLONAL	1	TRUE	1	0.698095617824103	5		681	1182	SUCCESS
APC	324	MSKCC	GRCh37	5	112176193	112176193	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	118	435	0	ENST00000257430.4:c.4906del	p.Asp1636MetfsTer14	p.D1636Mfs*14	ENST00000257430	NM_000038.5	1634	ccG/cc	16/16	0.682966250664013	1	FACETS	0.78	0.716	0.846	0.78	0.716	0.846	SUBCLONAL	1	TRUE	0	0.698095617824103	1		435	282	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490627	20490627	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	182	563	0	ENST00000346618.3:c.1364A>G	p.Lys455Arg	p.K455R	ENST00000346618	NM_001949.4	455	aAg/aGg	7/7	0.691428192130598	4	FACETS	1	0.954	1	0.348	0.322	0.376	CLONAL	1	TRUE	1	0.698095617824103	4		563	847	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225632	26225632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	200	678	2	ENST00000360408.1:c.250C>T	p.Arg84Cys	p.R84C	ENST00000360408	NM_003532.2	84	Cgc/Tgc	1/1	0.691428192130598	4	FACETS	0.921	0.853	0.992	0.307	0.284	0.331	CLONAL	1	TRUE	1	0.698095617824103	4		680	1056	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391698	139391699	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	190	866	0	ENST00000277541.6:c.6492dup	p.Gly2165ArgfsTer103	p.G2165Rfs*103	ENST00000277541	NM_017617.3	2164	-/A	34/34	0.698095617824103	3	FACETS	0.855	0.791	0.921	0.427	0.395	0.461	CLONAL	1	TRUE	1	0.698095617824103	3		866	859	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15840961	15840961	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	22	220	0	ENST00000307771.7:c.1045T>C	p.Ser349Pro	p.S349P	ENST00000307771	NM_005089.3	349	Tct/Cct	11/11	0.61757094736898	2	FACETS	0.19	0.147	0.241			1	SUBCLONAL	1	TRUE	NA	0.698095617824103	2		220	331	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	32	549	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.571736901885015	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	0	0.571736901885015	2		549	48	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443683	49443683	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	89	583	0	ENST00000301067.7:c.3688C>G	p.Pro1230Ala	p.P1230A	ENST00000301067	NM_003482.3	1230	Cca/Gca	11/54	0.571736901885015	3	FACETS	1	0.895	1	0.502	0.447	0.559	CLONAL	1	TRUE	1	0.571736901885015	3		583	399	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134724	41134724	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	30	364	0	ENST00000379561.5:c.904C>A	p.His302Asn	p.H302N	ENST00000379561	NM_002015.3	302	Cac/Aac	2/3	0.571736901885015	2	FACETS	0.772	0.632	0.925	0.386	0.316	0.463	CLONAL	1	TRUE	0	0.571736901885015	2		364	136	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980356	7980356	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	116	536	0	ENST00000319144.4:c.1227C>G	p.Phe409Leu	p.F409L	ENST00000319144	NM_001139.2	409	ttC/ttG	9/15	0.571736901885015	2	FACETS	1	0.964	1	0.557	0.507	0.609	CLONAL	1	TRUE	0	0.571736901885015	2		536	364	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799734	72799734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	41	597	0	ENST00000325599.8:c.1435G>A	p.Glu479Lys	p.E479K	ENST00000325599	NM_018130.2	479	Gaa/Aaa	11/11	0.571736901885015	2	FACETS	0.976	0.828	1	0.488	0.414	0.567	CLONAL	1	TRUE	0	0.571736901885015	2		597	147	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520088	106520088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1484305297	NA	P-0022664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	12	402	0	ENST00000359195.3:c.2516G>A	p.Arg839His	p.R839H	ENST00000359195	NM_002649.2	839	cGc/cAc	6/11	0.571736901885015	1	FACETS	0.697	0.509	0.909	0.697	0.509	0.909	SUBCLONAL	1	TRUE	0	0.571736901885015	1		402	43	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554371	141554371	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	305	765	0	ENST00000220592.5:c.1780C>G	p.Leu594Val	p.L594V	ENST00000220592	NM_012154.3	594	Ctg/Gtg	14/19	0.571736901885015	5	FACETS	1	0.985	1	0.74	0.699	0.781	CLONAL	2	TRUE	2	0.571736901885015	5		765	893	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	160	445	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.951	0.879	1	0.951	0.879	1	CLONAL	1	TRUE	1	0.682626353634724	2		445	493	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0022666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	122	435	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.917	0.836	0.999	0.917	0.836	0.999	CLONAL	1	TRUE	1	0.682626353634724	2		436	390	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76812945	76812947	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs1557059596	NA	P-0022666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	270	325	6	ENST00000373344.5:c.6674_6676del	p.Lys2225del	p.K2225del	ENST00000373344	NM_000489.3	2225	aAGAgg/agg	30/35	1	1	FACETS	0.979	0.93	1	0.979	0.93	1	CLONAL	1	TRUE	0	0.682626353634724	1		331	532	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78425915	78425915	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	202	420	0	ENST00000370768.2:c.1530G>A	p.Trp510Ter	p.W510*	ENST00000370768	NM_003902.3	510	tgG/tgA	16/20	0.682626353634724	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.682626353634724	1		420	386	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795176	42795177	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0022666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	253	848	0	ENST00000575354.2:c.2258_2259del	p.Val753GlyfsTer9	p.V753Gfs*9	ENST00000575354	NM_015125.3	752	acTGtg/actg	10/20	0.682626353634724	1	FACETS	0.899	0.85	0.948	0.899	0.85	0.948	CLONAL	1	TRUE	0	0.682626353634724	1		848	543	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721401	176721403	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0022666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	154	484	0	ENST00000439151.2:c.7032_7034del	p.Val2345del	p.V2345del	ENST00000439151	NM_022455.4	2344	tcAGTc/tcc	23/23	1	2	FACETS	0.681	0.625	0.739	0.681	0.625	0.739	SUBCLONAL	1	TRUE	1	0.682626353634724	2		484	663	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0022667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	157	412	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.473478266929222	2	FACETS	0.929	0.864	0.993	0.929	0.864	0.993	CLONAL	2	TRUE	0	0.500249141599828	2		413	338	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0022667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	264	713	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.473478266929222	2	FACETS	0.848	0.802	0.896	0.848	0.802	0.896	CLONAL	2	TRUE	0	0.500249141599828	2		715	622	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0022667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	238	408	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.423198050758371	4	FACETS	1	0.982	1	0.813	0.77	0.855	CLONAL	3	TRUE	0	0.500249141599828	4		408	439	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925634	114925641	+	frameshift_variant	Frame_Shift_Del	DEL	CAATTGCA	CAATTGCA	-	novel	NA	P-0022667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	114	777	0	ENST00000543371.1:c.1714_1721del	p.Ile572AlafsTer34	p.I572Afs*34	ENST00000543371	NM_001198531.1	571	tCAATTGCA/t	14/14	1	2	FACETS	0.704	0.635	0.777	0.704	0.635	0.777	SUBCLONAL	1	TRUE	1	0.500249141599828	2		777	647	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066509	94066509	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	100	346	0	ENST00000369303.4:c.1250C>T	p.Ala417Val	p.A417V	ENST00000369303	NM_004440.3	417	gCt/gTt	5/17	0.445953636770195	3	FACETS	1	0.933	1	0.526	0.472	0.583	CLONAL	1	TRUE	1	0.500249141599828	3		346	475	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764146326	NA	P-0022672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	282	782	0	ENST00000269305.4:c.841G>T	p.Asp281Tyr	p.D281Y	ENST00000269305	NM_001126112.2	281	Gac/Tac	8/11	0.3	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.31	2		782	848	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949342	71949342	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	141	756	0	ENST00000298229.2:c.3722T>A	p.Val1241Glu	p.V1241E	ENST00000298229	NM_001567.3	1241	gTg/gAg	28/28	0.3	3	FACETS	1	0.968	1	0.567	0.516	0.621	CLONAL	1	TRUE	1	0.31	3		756	926	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831860	72831860	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0022672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	327	950	0	ENST00000268489.5:c.4721del	p.Lys1574ArgfsTer42	p.K1574Rfs*42	ENST00000268489	NM_006885.3	1574	aAg/ag	9/10	0.3	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.31	2		950	944	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0022673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	255	609	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.41343858433751	3	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	1	0.430150346101937	3		609	719	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063628	67063628	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0022673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	307	692	2	ENST00000412916.2:c.79-2A>G		p.X27_splice	ENST00000412916		27			0.430150346101937	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.430150346101937	2		694	711	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845627	151845627	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	574	737	0	ENST00000262189.6:c.13385G>T	p.Cys4462Phe	p.C4462F	ENST00000262189	NM_170606.2	4462	tGt/tTt	52/59	0.430150346101937	4	FACETS	0.951	0.92	0.982	0.951	0.92	0.982	CLONAL	4	TRUE	0	0.430150346101937	4		737	1003	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0022674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	32	794	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.640312562783933	1	FACETS	0.232	0.189	0.281	0.232	0.189	0.281	SUBCLONAL	1	TRUE	0	0.640832227052096	1		794	292	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881414	37881414	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1131692237	NA	P-0022674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	174	716	0	ENST00000269571.5:c.2606T>G	p.Leu869Arg	p.L869R	ENST00000269571		869	cTg/cGg	21/27	1	2	FACETS	0.938	0.868	1	0.938	0.868	1	CLONAL	1	TRUE	1	0.640832227052096	2		716	579	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231773	36231773	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1569061762	NA	P-0022674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	9	677	5	ENST00000300305.3:c.611G>A	p.Arg204Gln	p.R204Q	ENST00000300305		204	cGa/cAa	5/8	0.305237870409868	0	FACETS	0.025	0.016	0.037			1	INDETERMINATE	1	TRUE	0	0.640832227052096	0		682	396	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983984	2983984	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	38	832	0	ENST00000396946.4:c.546G>C	p.Lys182Asn	p.K182N	ENST00000396946	NM_032415.4	182	aaG/aaC	5/25	0.395430513912521	0	FACETS	0.108	0.089	0.129			1	SUBCLONAL	1	TRUE	0	0.640832227052096	0		832	395	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577260	64577260	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs794728647	NA	P-0022674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	24	679	0	ENST00000312049.6:c.322C>G	p.Arg108Gly	p.R108G	ENST00000312049	NM_130799.2	108	Cga/Gga	2/10	0.28508172229223	4	FACETS	0.274	0.214	0.343			1	INDETERMINATE	1	TRUE	NA	0.640832227052096	4		679	449	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625360	69625360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs577116996	NA	P-0022674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	27	717	1	ENST00000334134.2:c.433C>T	p.Arg145Trp	p.R145W	ENST00000334134	NM_005247.2	145	Cgg/Tgg	3/3	0.476346834220454	0	FACETS	0.125	0.099	0.153			1	SUBCLONAL	1	TRUE	0	0.640832227052096	0		718	243	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434141	49434141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770491652	NA	P-0022674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	26	699	2	ENST00000301067.7:c.7412G>A	p.Arg2471Gln	p.R2471Q	ENST00000301067	NM_003482.3	2471	cGa/cAa	31/54	0.186014136797646	3	FACETS	0.272	0.215	0.337	0.136	0.107	0.169	INDETERMINATE	1	TRUE	1	0.640832227052096	3		701	394	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515078	103515078	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	13	291	0	ENST00000355739.4:c.1579C>G	p.Pro527Ala	p.P527A	ENST00000355739	NM_000123.3	527	Cca/Gca	8/15	1	2	FACETS	0.163	0.116	0.22	0.163	0.116	0.22	SUBCLONAL	1	TRUE	1	0.640832227052096	2		291	249	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842359	68842360	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	118	577	0	ENST00000261769.5:c.421dup	p.Thr141AsnfsTer27	p.T141Nfs*27	ENST00000261769	NM_004360.3	140	-/A	4/16	0.640832227052096	1	FACETS	0.93	0.855	1	0.93	0.855	1	CLONAL	1	TRUE	0	0.640832227052096	1		577	269	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244517	41244517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876659974	NA	P-0022674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	34	696	1	ENST00000357654.3:c.3031G>A	p.Glu1011Lys	p.E1011K	ENST00000357654	NM_007294.3	1011	Gaa/Aaa	10/23	1	2	FACETS	0.225	0.183	0.272	0.225	0.183	0.272	SUBCLONAL	1	TRUE	1	0.640832227052096	2		697	472	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10259621	10259621	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	22	679	0	ENST00000340748.4:c.2611C>G	p.Gln871Glu	p.Q871E	ENST00000340748		871	Caa/Gaa	26/40	0.311041409679916	1	FACETS	0.116	0.089	0.147	0.116	0.089	0.147	INDETERMINATE	1	TRUE	0	0.640832227052096	1		679	402	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973247	25973247	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	19	438	0	ENST00000435504.4:c.1178C>A	p.Thr393Lys	p.T393K	ENST00000435504		393	aCa/aAa	12/13	1	2	FACETS	0.181	0.137	0.233	0.181	0.137	0.233	SUBCLONAL	1	TRUE	1	0.640832227052096	2		438	327	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815761	32815761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755212442	NA	P-0022674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	109	783	0	ENST00000354258.4:c.1855G>A	p.Gly619Arg	p.G619R	ENST00000354258	NM_000593.5	619	Ggg/Agg	8/11	0.44896534106532	4	FACETS	0.809	0.727	0.895			1	CLONAL	1	TRUE	NA	0.640832227052096	4		783	690	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874290	151874292	+	frameshift_variant	Frame_Shift_Ins	INS	TTA	TTA	ATCCAGG	novel	NA	P-0022674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	93	484	1	ENST00000262189.6:c.8246_8248delinsCCTGGAT	p.Leu2749SerfsTer8	p.L2749Sfs*8	ENST00000262189	NM_170606.2	2749	tTAAgg/tCCTGGATgg	38/59	1	2	FACETS	0.851	0.764	0.942	0.851	0.764	0.942	CLONAL	1	TRUE	1	0.640832227052096	2		485	341	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430635	80430635	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	25	346	0	ENST00000286548.4:c.373G>C	p.Glu125Gln	p.E125Q	ENST00000286548	NM_002072.3	125	Gag/Cag	3/7	1	2	FACETS	0.328	0.259	0.406	0.328	0.259	0.406	SUBCLONAL	1	TRUE	1	0.640832227052096	2		346	238	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650302	48650302	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs937198370	NA	P-0022674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	29	701	0	ENST00000376670.3:c.272C>T	p.Ser91Leu	p.S91L	ENST00000376670	NM_002049.3	91	tCa/tTa	3/6	0.237550734723632	0	FACETS	0.104	0.083	0.127			1	INDETERMINATE	1	TRUE	0	0.640832227052096	0		701	314	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907768	76907768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	31	571	0	ENST00000373344.5:c.4393G>A	p.Asp1465Asn	p.D1465N	ENST00000373344	NM_000489.3	1465	Gat/Aat	15/35	0.237550734723632	0	FACETS	0.09	0.073	0.11			1	INDETERMINATE	1	TRUE	0	0.640832227052096	0		571	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0022676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	618	763	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	2	TRUE	NA	0.70739371056299	2		763	798	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0022676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	71	292	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.205675992627643	1	FACETS	0.449	0.395	0.505	0.449	0.395	0.505	INDETERMINATE	1	TRUE	0	0.70739371056299	1		292	289	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051652	30051652	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555993336	NA	P-0022676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	242	392	0	ENST00000338641.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000338641	NM_000268.3	196	Cga/Tga	6/16	0.70739371056299	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.70739371056299	1		392	404	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16001692	16001692	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	161	423	2	ENST00000268712.3:c.2809A>C	p.Ile937Leu	p.I937L	ENST00000268712	NM_006311.3	937	Atc/Ctc	21/46	0.70739371056299	4	FACETS	0.963	0.884	1			1	CLONAL	1	TRUE	NA	0.70739371056299	4		425	807	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004850	16004850	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	195	647	1	ENST00000268712.3:c.2404G>C	p.Glu802Gln	p.E802Q	ENST00000268712	NM_006311.3	802	Gag/Cag	20/46	0.70739371056299	4	FACETS	0.765	0.707	0.826			1	SUBCLONAL	1	TRUE	NA	0.70739371056299	4		648	1230	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004869	16004869	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	189	648	1	ENST00000268712.3:c.2385G>C	p.Gln795His	p.Q795H	ENST00000268712	NM_006311.3	795	caG/caC	20/46	0.70739371056299	4	FACETS	0.732	0.675	0.792			1	SUBCLONAL	1	TRUE	NA	0.70739371056299	4		649	1246	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582117	52582117	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	87	427	0	ENST00000394830.3:c.4711del	p.Leu1571SerfsTer9	p.L1571Sfs*9	ENST00000394830	NM_018313.4	1571	Ctc/tc	30/30	0.341337681698612	1	FACETS	0.353	0.314	0.395	0.353	0.314	0.395	INDETERMINATE	1	TRUE	0	0.70739371056299	1		427	450	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49724798	49724798	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs138710044	NA	P-0022677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	10	103	0	ENST00000449682.2:c.469A>C	p.Lys157Gln	p.K157Q	ENST00000449682	NM_020998.3	157	Aag/Cag	4/18	0.830744734129291	1	FACETS	0.293	0.204	0.398	0.293	0.204	0.398	SUBCLONAL	1	TRUE	0	0.830744734129291	1		103	48	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951081	48951081	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	205	362	0	ENST00000267163.4:c.1243del	p.Ile415TyrfsTer2	p.I415Yfs*2	ENST00000267163	NM_000321.2	415	Ata/ta	13/27	0.781998172415464	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.830744734129291	1		362	288	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578467	7578480	+	frameshift_variant	Frame_Shift_Del	DEL	TGCCGGGCGGGGGT	TGCCGGGCGGGGGT	GCGGGGGGC	novel	NA	P-0022677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	354	1011	6	ENST00000269305.4:c.450_463delinsGCCCCCCGC	p.Pro153AlafsTer26	p.P153Afs*26	ENST00000269305	NM_001126112.2	150	acACCCCCGCCCGGCAcc/acGCCCCCCGCcc	5/11	0.830744734129291	1	FACETS	0.947	0.912	0.981	0.947	0.912	0.981	CLONAL	1	TRUE	0	0.830744734129291	1		1017	526	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38173510	38173510	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	327	699	0	ENST00000317025.8:c.1906G>T	p.Ala636Ser	p.A636S	ENST00000317025	NM_023034.1	636	Gcc/Tcc	10/24	1	2	FACETS	0.933	0.885	0.981	0.933	0.885	0.981	CLONAL	1	TRUE	1	0.830744734129291	2		699	844	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	79	701	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.883	0.78	0.993	1	0.982	1	CLONAL	2	TRUE	1	0.201520188824523	2		701	444	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	27	743	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.201520188824523	0	FACETS	0.91	0.728	1			1	CLONAL	1	TRUE	0	0.201520188824523	0		743	235	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609612	81609612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	40	640	1	ENST00000298171.2:c.1210G>A	p.Glu404Lys	p.E404K	ENST00000298171	NM_000369.2	404	Gag/Aag	10/10	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.201520188824523	2		641	348	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230691	46230691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424958105	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	22	545	0	ENST00000334344.6:c.940C>T	p.Arg314Cys	p.R314C	ENST00000334344	NM_152641.2	314	Cgt/Tgt	8/21	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.201520188824523	2		545	176	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976476	25976476	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	13	656	2	ENST00000435504.4:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000435504		357	Cga/Tga	11/13	1	2	FACETS	0.787	0.563	1	0.787	0.563	1	CLONAL	1	TRUE	1	0.201520188824523	2		658	164	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	41	580	1	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.179335244664329	4	FACETS	0.994	0.841	1	0.994	0.841	1	CLONAL	3	TRUE	1	0.201520188824523	4		581	164	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566827	212566827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202247795	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	18	332	0	ENST00000342788.4:c.1354G>A	p.Glu452Lys	p.E452K	ENST00000342788	NM_005235.2	452	Gaa/Aaa	12/28	1	2	FACETS	1	0.76	1	1	0.76	1	CLONAL	1	TRUE	1	0.201520188824523	2		332	178	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6031649	6031649	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs200640585	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	37	656	0	ENST00000265849.7:c.943C>T	p.Arg315Ter	p.R315*	ENST00000265849	NM_000535.5	315	Cga/Tga	9/15	0.201520188824523	0	FACETS	1	0.929	1			1	CLONAL	1	TRUE	0	0.201520188824523	0		656	236	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754827	29754827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373120394	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	63	523	1	ENST00000389048.3:c.1108G>A	p.Glu370Lys	p.E370K	ENST00000389048	NM_004304.4	370	Gag/Aag	4/29	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.201520188824523	2		524	419	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499706	8499706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	38	618	0	ENST00000356435.5:c.2263G>A	p.Glu755Lys	p.E755K	ENST00000356435		755	Gaa/Aaa	14/35	0.201520188824523	1	FACETS	0.785	0.649	0.937	0.785	0.649	0.937	CLONAL	1	TRUE	0	0.201520188824523	1		618	432	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70005680	70005680	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	13	495	0	ENST00000394351.3:c.709C>T	p.Pro237Ser	p.P237S	ENST00000394351	NM_000248.3	237	Cca/Tca	7/9	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.201520188824523	2		495	94	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051208	128051208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	109	759	0	ENST00000285398.2:c.115C>T	p.Pro39Ser	p.P39S	ENST00000285398	NM_000122.1	39	Ccc/Tcc	2/15	1	2	FACETS	0.894	0.805	0.988	1	0.987	1	CLONAL	2	TRUE	1	0.201520188824523	2		759	605	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430866	78430866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	31	664	1	ENST00000370768.2:c.523C>T	p.Pro175Ser	p.P175S	ENST00000370768	NM_003902.3	175	Cct/Tct	8/20	0.167544924329981	3	FACETS	1	0.87	1	0.548	0.444	0.665	CLONAL	1	TRUE	1	0.201520188824523	3		665	309	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851411	63851411	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	59	661	1	ENST00000279873.7:c.2189C>T	p.Ser730Phe	p.S730F	ENST00000279873	NM_032199.2	730	tCc/tTc	10/10	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.201520188824523	2		662	524	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332813	70332813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767959452	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	42	705	0	ENST00000373644.4:c.718C>T	p.Pro240Ser	p.P240S	ENST00000373644	NM_030625.2	240	Cca/Tca	2/12	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.201520188824523	2		705	339	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344714	118344714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1473233037	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	24	507	0	ENST00000534358.1:c.2840C>T	p.Ser947Phe	p.S947F	ENST00000534358	NM_005933.3	947	tCt/tTt	3/36	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.201520188824523	2		507	213	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118361912	118361955	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AAACTTCTGCCCTCTCTGTGACAAATGTTATGATGATGATGACT	AAACTTCTGCCCTCTCTGTGACAAATGTTATGATGATGATGACT	-	novel	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	28	252	0	ENST00000534358.1:c.4699_4742del	p.Asn1567Ter	p.N1567*	ENST00000534358	NM_005933.3	1566	ggAAACTTCTGCCCTCTCTGTGACAAATGTTATGATGATGATGACTat/ggat	14/36	1	2	FACETS	0.952	0.771	1	1	0.955	1	CLONAL	2	TRUE	1	0.201520188824523	2		252	146	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793420	18793420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267603404	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	17	619	0	ENST00000266497.5:c.4117C>T	p.Pro1373Ser	p.P1373S	ENST00000266497		1373	Ccc/Tcc	30/31	1	2	FACETS	0.888	0.674	1	1	0.922	1	CLONAL	2	TRUE	1	0.201520188824523	2		619	95	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420991	49420992	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	58	540	1	ENST00000301067.7:c.14757_14758delinsTT	p.Pro4920Ser	p.P4920S	ENST00000301067	NM_003482.3	4919	tcCCcc/tcTTcc	48/54	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.201520188824523	2		541	420	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434113	121434113	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	70	761	1	ENST00000257555.6:c.1004C>T	p.Ser335Leu	p.S335L	ENST00000257555		335	tCa/tTa	5/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.201520188824523	2		762	577	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929302	32929302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776936973	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	13	610	0	ENST00000380152.3:c.7312G>A	p.Asp2438Asn	p.D2438N	ENST00000380152		2438	Gat/Aat	14/27	0.184073695192307	0	FACETS	0.954	0.687	1			1	CLONAL	1	TRUE	0	0.201520188824523	0		610	108	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868589	37868589	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	68	641	0	ENST00000269571.5:c.1036G>C	p.Gly346Arg	p.G346R	ENST00000269571		346	Ggc/Cgc	9/27	0.167544924329981	3	FACETS	1	0.964	1	0.662	0.576	0.755	CLONAL	1	TRUE	1	0.201520188824523	3		641	561	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945732	17945732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs961989934	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	87	753	0	ENST00000458235.1:c.2128G>A	p.Gly710Ser	p.G710S	ENST00000458235	NM_000215.3	710	Ggc/Agc	16/24	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.201520188824523	2		753	580	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210905	36210907	+	frameshift_variant	Frame_Shift_Del	DEL	CTC	CTC	AT	novel	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	98	842	5	ENST00000222270.7:c.656_658delinsAT	p.Ser219TyrfsTer20	p.S219Yfs*20	ENST00000222270	NM_014727.1	219	tCTCgg/tATgg	3/37	1	2	FACETS	0.809	0.723	0.9	1	0.983	1	CLONAL	2	TRUE	1	0.201520188824523	2		847	601	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222961	36222961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	104	1027	0	ENST00000222270.7:c.5590C>T	p.Arg1864Ter	p.R1864*	ENST00000222270	NM_014727.1	1864	Cga/Tga	27/37	1	2	FACETS	0.814	0.73	0.903	1	0.984	1	CLONAL	2	TRUE	1	0.201520188824523	2		1027	634	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762859	40762859	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	85	681	0	ENST00000392038.2:c.149C>T	p.Pro50Leu	p.P50L	ENST00000392038	NM_001626.4	50	cCc/cTc	3/14	1	2	FACETS	0.881	0.781	0.986	1	0.983	1	CLONAL	2	TRUE	1	0.201520188824523	2		681	479	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530166	212530166	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	16	483	0	ENST00000342788.4:c.1753G>A	p.Asp585Asn	p.D585N	ENST00000342788	NM_005235.2	585	Gat/Aat	15/28	1	2	FACETS	0.827	0.613	1	0.827	0.613	1	CLONAL	1	TRUE	1	0.201520188824523	2		483	192	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525058	9525058	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	28	643	1	ENST00000353224.5:c.1827G>A	p.Trp609Ter	p.W609*	ENST00000353224	NM_177990.2	609	tgG/tgA	8/10	1	2	FACETS	0.982	0.787	1	0.982	0.787	1	CLONAL	1	TRUE	1	0.201520188824523	2		644	283	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070415	37070415	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	29	316	0	ENST00000231790.2:c.1550G>A	p.Gly517Glu	p.G517E	ENST00000231790	NM_000249.3	517	gGa/gAa	13/19	1	2	FACETS	1	0.813	1	1	0.813	1	CLONAL	1	TRUE	1	0.201520188824523	2		316	285	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71008496	71008496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756987886	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	34	420	1	ENST00000318789.4:c.1936G>A	p.Glu646Lys	p.E646K	ENST00000318789	NM_032682.5	646	Gaa/Aaa	21/21	1	2	FACETS	1	0.839	1	1	0.839	1	CLONAL	1	TRUE	1	0.201520188824523	2		421	329	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916788	178916788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1266632047	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	16	649	0	ENST00000263967.3:c.175C>T	p.His59Tyr	p.H59Y	ENST00000263967	NM_006218.2	59	Cat/Tat	2/21	1	2	FACETS	1	0.761	1	1	0.761	1	CLONAL	1	TRUE	1	0.201520188824523	2		649	155	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748119	41748119	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	17	259	2	ENST00000226382.2:c.650G>A	p.Gly217Glu	p.G217E	ENST00000226382	NM_003924.3	217	gGg/gAg	3/3	1	2	FACETS	0.922	0.691	1	0.922	0.691	1	CLONAL	1	TRUE	1	0.201520188824523	2		261	183	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278899	1278899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	46	669	2	ENST00000310581.5:c.2143G>A	p.Gly715Ser	p.G715S	ENST00000310581	NM_198253.2	715	Ggc/Agc	6/16	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.201520188824523	2		671	452	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409229	31409229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	26	610	2	ENST00000344624.3:c.3788C>T	p.Ser1263Phe	p.S1263F	ENST00000344624		1263	tCc/tTc	30/33	1	2	FACETS	0.902	0.716	1	0.902	0.716	1	CLONAL	1	TRUE	1	0.201520188824523	2		612	286	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31468104	31468104	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	23	726	0	ENST00000344624.3:c.2308C>T	p.Pro770Ser	p.P770S	ENST00000344624		770	Ccg/Tcg	15/33	1	2	FACETS	0.871	0.681	1	0.871	0.681	1	CLONAL	1	TRUE	1	0.201520188824523	2		726	262	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001518	150001518	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	11	720	0	ENST00000253339.5:c.2086A>G	p.Lys696Glu	p.K696E	ENST00000253339		696	Aaa/Gaa	4/7	0.179335244664329	4	FACETS	1	0.731	1	0.353	0.245	0.485	CLONAL	1	TRUE	1	0.201520188824523	4		720	124	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405960	157405960	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	52	708	0	ENST00000346085.5:c.2204del	p.Pro735HisfsTer10	p.P735Hfs*10	ENST00000346085	NM_020732.3	734	ggC/gg	6/20	0.179335244664329	4	FACETS	1	0.943	1	0.411	0.35	0.478	CLONAL	1	TRUE	1	0.201520188824523	4		708	503	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683691	162683691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	56	672	0	ENST00000366898.1:c.278G>A	p.Gly93Glu	p.G93E	ENST00000366898	NM_004562.2	93	gGa/gAa	3/12	0.179335244664329	4	FACETS	1	0.966	1	0.489	0.42	0.565	CLONAL	1	TRUE	1	0.201520188824523	4		672	455	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221711	55221711	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	8	450	0	ENST00000275493.2:c.755G>T	p.Arg252Leu	p.R252L	ENST00000275493	NM_005228.3	252	cGc/cTc	7/28	0.095580182902139	1	FACETS	0.22	0.141	0.324	0.22	0.141	0.324	INDETERMINATE	1	TRUE	0	0.201520188824523	1		450	324	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371824	55371824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	43	360	1	ENST00000297316.4:c.514G>A	p.Gly172Ser	p.G172S	ENST00000297316	NM_022454.3	172	Ggc/Agc	2/2	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.201520188824523	2		361	299	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054594	5054594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	11	405	0	ENST00000381652.3:c.646G>A	p.Ala216Thr	p.A216T	ENST00000381652	NM_004972.3	216	Gca/Aca	7/25	0.201520188824523	1	FACETS	1	0.808	1	1	0.808	1	CLONAL	1	TRUE	0	0.201520188824523	1		405	80	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169591	27169591	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	58	878	1	ENST00000380036.4:c.592C>T	p.Leu198Phe	p.L198F	ENST00000380036	NM_000459.3	198	Ctc/Ttc	4/23	0.201520188824523	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.201520188824523	1		879	444	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117835	70117836	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	75	628	1	ENST00000245479.2:c.305dup	p.Pro103AlafsTer149	p.P103Afs*149	ENST00000245479	NM_000346.3	101	-/A	1/3	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.2	2		629	606	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966792	25966792	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	98	785	0	ENST00000435504.4:c.2414A>G	p.Lys805Arg	p.K805R	ENST00000435504		805	aAa/aGa	13/13	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.2	2		785	909	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500900	8500900	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	38	725	0	ENST00000356435.5:c.1982A>C	p.Glu661Ala	p.E661A	ENST00000356435		661	gAg/gCg	13/35	1	2	FACETS	0.503	0.415	0.603	0.503	0.415	0.603	SUBCLONAL	1	TRUE	1	0.2	2		725	755	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0022684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	95	853	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.95	0.846	1	1	0.985	1	CLONAL	2	TRUE	1	0.15	2		853	667	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120296	70120296	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	68	1297	1	ENST00000245479.2:c.1298C>A	p.Pro433Gln	p.P433Q	ENST00000245479	NM_000346.3	433	cCg/cAg	3/3	1	2	FACETS	0.691	0.598	0.791	0.691	0.598	0.791	SUBCLONAL	1	TRUE	1	0.15	2		1298	1313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0022684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	53	833	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			1	2	FACETS	0.908	0.773	1	0.908	0.773	1	CLONAL	1	TRUE	1	0.15	2		833	778	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056255	27056255	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	68	631	0	ENST00000324856.7:c.1251C>A	p.Tyr417Ter	p.Y417*	ENST00000324856	NM_006015.4	417	taC/taA	2/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.15	2		631	676	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458452	120458452	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	39	643	0	ENST00000256646.2:c.6893G>T	p.Arg2298Leu	p.R2298L	ENST00000256646	NM_024408.3	2298	cGg/cTg	34/34	1	2	FACETS	0.793	0.655	0.946	0.793	0.655	0.946	CLONAL	1	TRUE	1	0.15	2		643	656	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466375	120466375	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	37	668	0	ENST00000256646.2:c.4744G>T	p.Asp1582Tyr	p.D1582Y	ENST00000256646	NM_024408.3	1582	Gac/Tac	26/34	1	2	FACETS	0.733	0.603	0.88	0.733	0.603	0.88	SUBCLONAL	1	TRUE	1	0.15	2		668	673	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649674	48649674	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	63	932	0	ENST00000376670.3:c.158C>G	p.Ala53Gly	p.A53G	ENST00000376670	NM_002049.3	53	gCc/gGc	2/6	1	2	FACETS	0.818	0.705	0.941	0.818	0.705	0.941	CLONAL	1	TRUE	1	0.15	2		932	1027	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971124	21971125	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0022685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	144	811	0	ENST00000304494.5:c.233_234del	p.Leu78HisfsTer41	p.L78Hfs*41	ENST00000304494	NM_000077.4	78	cTC/c	2/3	0.207340676469269	2	FACETS	0.885	0.809	0.965	0.885	0.809	0.965	CLONAL	2	TRUE	0	0.228235845890163	2		811	713	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402690	139402690	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs41309764	NA	P-0022685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	196	1013	0	ENST00000277541.6:c.3319C>T	p.Arg1107Ter	p.R1107*	ENST00000277541	NM_017617.3	1107	Cga/Tga	20/34	0.207340676469269	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.228235845890163	2		1013	836	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0022685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	333	649	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.215602625901806	4	FACETS	1	0.988	1	0.86	0.814	0.907	CLONAL	3	TRUE	0	0.228235845890163	4		649	1042	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107180	27107180	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0022685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	225	798	0	ENST00000324856.7:c.6791C>G	p.Ser2264Ter	p.S2264*	ENST00000324856	NM_006015.4	2264	tCa/tGa	20/20	0.228235845890163	3	FACETS	0.879	0.82	0.939	0.879	0.82	0.939	CLONAL	3	TRUE	0	0.228235845890163	3		798	833	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198299701	198299701	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	68	579	0	ENST00000335508.6:c.23A>G	p.His8Arg	p.H8R	ENST00000335508	NM_012433.2	8	cAc/cGc	1/25	0.228235845890163	3	FACETS	1	0.964	1	0.656	0.572	0.747	CLONAL	1	TRUE	1	0.228235845890163	3		579	506	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711931	89711931	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876659227	NA	P-0022685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	82	757	0	ENST00000371953.3:c.549G>T	p.Lys183Asn	p.K183N	ENST00000371953	NM_000314.4	183	aaG/aaT	6/9	0.207340676469269	2	FACETS	0.843	0.747	0.945	0.843	0.747	0.945	CLONAL	2	TRUE	0	0.228235845890163	2		757	426	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608284	28608284	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520024	NA	P-0022685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	84	934	0	ENST00000241453.7:c.1772A>G	p.Tyr591Cys	p.Y591C	ENST00000241453	NM_004119.2	591	tAc/tGc	14/24	0.228235845890163	3	FACETS	1	0.97	1	0.655	0.579	0.736	CLONAL	1	TRUE	1	0.228235845890163	3		934	626	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244548	46244548	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	115	754	0	ENST00000334344.6:c.2642C>G	p.Ala881Gly	p.A881G	ENST00000334344	NM_152641.2	881	gCt/gGt	15/21	0.201498264248023	4	FACETS	0.976	0.881	1	0.976	0.881	1	CLONAL	2	TRUE	2	0.228235845890163	4		754	634	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007842	45007842	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	74	677	0	ENST00000558401.1:c.289G>T	p.Glu97Ter	p.E97*	ENST00000558401	NM_004048.2	97	Gag/Tag	2/4	0.207340676469269	2	FACETS	1	0.968	1	0.669	0.587	0.756	CLONAL	1	TRUE	0	0.228235845890163	2		677	485	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750470	41750470	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1488529123	NA	P-0022685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	116	689	1	ENST00000226382.2:c.158C>A	p.Ala53Asp	p.A53D	ENST00000226382	NM_003924.3	53	gCc/gAc	1/3	0.169449892103433	4	FACETS	0.795	0.717	0.878	0.795	0.717	0.878	SUBCLONAL	2	TRUE	2	0.228235845890163	4		690	785	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248733	59248733	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1527	257	767	0	ENST00000371222.2:c.10A>G	p.Lys4Glu	p.K4E	ENST00000371222	NM_002228.3	4	Aag/Gag	1/1	0.352478309324129	5	FACETS	1	0.964	1	0.263	0.245	0.281	CLONAL	1	TRUE	1	0.465828115770504	5		767	1784	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211140	2211140	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1188	326	892	1	ENST00000398665.3:c.1394C>A	p.Pro465Gln	p.P465Q	ENST00000398665	NM_032482.2	465	cCg/cAg	15/28	0.269546828018713	4	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.465828115770504	4		893	1514	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210299	123210300	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	126	450	0	ENST00000218089.9:c.2652dup	p.Ile885TyrfsTer10	p.I885Yfs*10	ENST00000218089	NM_001042749.1	884	gat/gaTt	26/35	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.465828115770504	2		450	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0022687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	35	681	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	0.227	0.185	0.275	0.227	0.185	0.275	SUBCLONAL	1	TRUE	1	0.291866464467266	2		681	1057	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0022687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	23	623	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.207354056064997	4	FACETS	0.194	0.15	0.246	0.065	0.05	0.082	SUBCLONAL	1	TRUE	1	0.291866464467266	4		623	1048	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201930	102201931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGGAGAG	novel	NA	P-0022687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	33	423	0	ENST00000263464.3:c.1286_1287insGAGGGGA	p.Glu430ArgfsTer10	p.E430Rfs*10	ENST00000263464	NM_001165.4	428	agg/aGGGAGAGgg	6/9	1	2	FACETS	0.56	0.456	0.677	0.56	0.456	0.677	SUBCLONAL	1	TRUE	1	0.291866464467266	2		423	404	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903707	41903707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1405358214	NA	P-0022687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	155	958	5	ENST00000372991.4:c.850C>T	p.Pro284Ser	p.P284S	ENST00000372991	NM_001760.3	284	Cct/Tct	5/5	1	2	FACETS	0.888	0.811	0.969	0.888	0.811	0.969	CLONAL	1	TRUE	1	0.291866464467266	2		963	1196	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677896	117677896	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	178	697	27	ENST00000368508.3:c.4037A>T	p.Asn1346Ile	p.N1346I	ENST00000368508	NM_002944.2	1346	aAc/aTc	25/43	1	2	FACETS	0.822	0.759	0.887	1	0.991	1	CLONAL	2	TRUE	1	0.291866464467266	2		724	742	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224163	98224163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138154222	NA	P-0022688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	143	366	2	ENST00000331920.6:c.2678G>A	p.Arg893His	p.R893H	ENST00000331920	NM_000264.3	893	cGc/cAc	16/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.487205194306951	2		368	521	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122722	108122722	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0022688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	465	675	4	ENST00000278616.4:c.1766T>A	p.Leu589Ter	p.L589*	ENST00000278616	NM_000051.3	589	tTa/tAa	11/63	0.481661072441933	2	FACETS	0.906	0.868	0.943	0.906	0.868	0.943	CLONAL	2	TRUE	0	0.487205194306951	2		679	1054	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577044	7577044	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	427	947	1	ENST00000269305.4:c.894del	p.Glu298AspfsTer47	p.E298Dfs*47	ENST00000269305	NM_001126112.2	298	gaG/ga	8/11	0.460539415283511	2	FACETS	0.832	0.795	0.87	0.832	0.795	0.87	CLONAL	2	TRUE	0	0.487205194306951	2		948	1053	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260219	19260219	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	313	889	0	ENST00000162023.5:c.74A>C	p.Lys25Thr	p.K25T	ENST00000162023		25	aAg/aCg	7/13	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.487205194306951	2		889	1132	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0022690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	143	930	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.305806759650385	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.305806759650385	3		931	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0022691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	65	831	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.17866487198072	1	FACETS	0.758	0.659	0.865	1	0.972	1	SUBCLONAL	2	TRUE	0	0.17866487198072	1		832	437	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0022691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	60	422	1	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.17866487198072	3	FACETS	0.843	0.728	0.967	0.843	0.728	0.967	CLONAL	2	TRUE	1	0.17866487198072	3		423	434	SUCCESS
APC	324	MSKCC	GRCh37	5	112154942	112154942	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779780	NA	P-0022691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	137	812	0	ENST00000257430.4:c.1213C>T	p.Arg405Ter	p.R405*	ENST00000257430	NM_000038.5	405	Cga/Tga	10/16	0.17866487198072	3	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	1	0.17866487198072	3		812	805	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920435	114920435	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	59	617	0	ENST00000543371.1:c.1376G>T	p.Trp459Leu	p.W459L	ENST00000543371	NM_001198531.1	459	tGg/tTg	13/14	0.17866487198072	2	FACETS	1	0.884	1	0.516	0.443	0.595	CLONAL	1	TRUE	0	0.17866487198072	2		617	640	SUCCESS
ATR	545	MSKCC	GRCh37	3	142285059	142285059	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	51	615	0	ENST00000350721.4:c.196G>C	p.Val66Leu	p.V66L	ENST00000350721	NM_001184.3	66	Gtg/Ctg	3/47	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.17866487198072	2		615	565	SUCCESS
APC	324	MSKCC	GRCh37	5	112177149	112177149	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	91	465	0	ENST00000257430.4:c.5858A>G	p.Asn1953Ser	p.N1953S	ENST00000257430	NM_000038.5	1953	aAt/aGt	16/16	0.17866487198072	3	FACETS	0.982	0.874	1	0.982	0.874	1	CLONAL	2	TRUE	1	0.17866487198072	3		465	565	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394436	162394436	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	50	526	0	ENST00000366898.1:c.632A>C	p.Lys211Thr	p.K211T	ENST00000366898	NM_004562.2	211	aAa/aCa	6/12	0.17866487198072	2	FACETS	0.814	0.693	0.945	0.814	0.693	0.945	CLONAL	2	TRUE	0	0.17866487198072	2		526	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0022691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	100	831	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.154408170875463	2		832	930	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0022691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	28	422	1	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.882	0.705	1	0.882	0.705	1	CLONAL	1	TRUE	1	0.154408170875463	2		423	411	SUCCESS
APC	324	MSKCC	GRCh37	5	112154942	112154942	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779780	NA	P-0022691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	96	812	0	ENST00000257430.4:c.1213C>T	p.Arg405Ter	p.R405*	ENST00000257430	NM_000038.5	405	Cga/Tga	10/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.154408170875463	2		812	940	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920435	114920435	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	44	617	0	ENST00000543371.1:c.1376G>T	p.Trp459Leu	p.W459L	ENST00000543371	NM_001198531.1	459	tGg/tTg	13/14	1	2	FACETS	0.788	0.659	0.932	0.788	0.659	0.932	CLONAL	1	TRUE	1	0.154408170875463	2		617	723	SUCCESS
ATR	545	MSKCC	GRCh37	3	142285059	142285059	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	36	615	0	ENST00000350721.4:c.196G>C	p.Val66Leu	p.V66L	ENST00000350721	NM_001184.3	66	Gtg/Ctg	3/47	1	2	FACETS	0.689	0.565	0.829	0.689	0.565	0.829	SUBCLONAL	1	TRUE	1	0.154408170875463	2		615	677	SUCCESS
APC	324	MSKCC	GRCh37	5	112177149	112177149	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	52	465	0	ENST00000257430.4:c.5858A>G	p.Asn1953Ser	p.N1953S	ENST00000257430	NM_000038.5	1953	aAt/aGt	16/16	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.154408170875463	2		465	500	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394436	162394436	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	51	526	0	ENST00000366898.1:c.632A>C	p.Lys211Thr	p.K211T	ENST00000366898	NM_004562.2	211	aAa/aCa	6/12	0.154408170875463	2	FACETS	1	0.94	1	0.609	0.518	0.71	CLONAL	1	TRUE	0	0.154408170875463	2		526	542	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	109	636	2	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	0.18	2		638	966	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0022692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	63	654	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.214010223570497	1	FACETS	0.87	0.752	0.999	0.87	0.752	0.999	CLONAL	1	TRUE	0	0.18	1		654	732	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063717	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0022693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	123	354	0	ENST00000412916.2:c.165+1G>C		p.X55_splice	ENST00000412916		55			0.498653330196232	1	FACETS	0.942	0.86	1	0.942	0.86	1	CLONAL	1	TRUE	0	0.498653330196232	1		354	393	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350973	89350974	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0022693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	269	1174	1	ENST00000301030.4:c.1976dup	p.Tyr659Ter	p.Y659*	ENST00000301030	NM_001256183.1	659	tac/taAc	9/13	0.498653330196232	1	FACETS	0.688	0.644	0.732	0.688	0.644	0.732	SUBCLONAL	1	TRUE	0	0.498653330196232	1		1175	1178	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40761127	40761128	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATGACAAAGGTGTTGGGTCGCGGCCTCTCGGTCTTC	novel	NA	P-0022693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	134	919	0	ENST00000392038.2:c.189_224dup	p.Met63_Val74dup	p.M63_V74dup	ENST00000392038	NM_001626.4	63	ata/atGAAGACCGAGAGGCCGCGACCCAACACCTTTGTCATa	4/14	1	2	FACETS	0.454	0.411	0.499	0.454	0.411	0.499	SUBCLONAL	1	TRUE	1	0.498653330196232	2		919	1185	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0022694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	123	314	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.65397145496784	1	FACETS	0.941	0.867	1	0.941	0.867	1	CLONAL	1	TRUE	0	0.65397145496784	1		314	269	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246482	105246482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	233	984	1	ENST00000349310.3:c.118G>A	p.Glu40Lys	p.E40K	ENST00000349310	NM_001014432.1	40	Gag/Aag	4/15	0.400315946001306	1	FACETS	0.462	0.431	0.494	0.462	0.431	0.494	SUBCLONAL	1	TRUE	0	0.65397145496784	1		985	1038	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145744	11145744	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	422	1066	0	ENST00000358026.2:c.4106G>C	p.Arg1369Pro	p.R1369P	ENST00000358026	NM_001128849.1	1369	cGt/cCt	29/36	0.65397145496784	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.65397145496784	1		1066	806	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645075	86645075	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs774867968	NA	P-0022694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	123	495	0	ENST00000274376.6:c.1148del	p.Pro383LeufsTer28	p.P383Lfs*28	ENST00000274376	NM_002890.2	383	Cct/ct	8/25	0.65397145496784	1	FACETS	0.858	0.789	0.929	0.858	0.789	0.929	CLONAL	1	TRUE	0	0.65397145496784	1		495	295	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851324	156851324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759637817	NA	P-0022696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	27	888	3	ENST00000524377.1:c.2281C>T	p.Arg761Trp	p.R761W	ENST00000524377	NM_002529.3	761	Cgg/Tgg	17/17	1	2	FACETS	0.271	0.216	0.334	0.271	0.216	0.334	SUBCLONAL	1	TRUE	1	0.66	2		891	302	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398266	25398266	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	213	824	0	ENST00000311936.3:c.53C>A	p.Ala18Asp	p.A18D	ENST00000311936	NM_004985.3	18	gCc/gAc	2/5	0.0880491925176984	3	FACETS	1	0.981	1	0.569	0.53	0.608	INDETERMINATE	1	TRUE	1	0.66	3		824	755	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128321915	128321915	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	130	592	3	ENST00000265960.3:c.845G>T	p.Arg282Leu	p.R282L	ENST00000265960	NM_001006617.1	282	cGa/cTa	6/12	1	2	FACETS	0.899	0.822	0.979	0.899	0.822	0.979	CLONAL	1	TRUE	1	0.66	2		595	438	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939738	76939738	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	42	926	1	ENST00000373344.5:c.1010G>T	p.Gly337Val	p.G337V	ENST00000373344	NM_000489.3	337	gGc/gTc	9/35	0.182796778703729	1	FACETS	0.116	0.097	0.139	0.116	0.097	0.139	INDETERMINATE	1	TRUE	0	0.66	1		927	732	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	114	445	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.958	1			1	INDETERMINATE	1	TRUE	NA	0.822776353537084	2		445	259	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577567	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1567549651	NA	P-0022697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	248	913	1	ENST00000269305.4:c.714dup	p.Asn239Ter	p.N239*	ENST00000269305	NM_001126112.2	238	-/T	7/11	0.822776353537084	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.822776353537084	1		914	315	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127650	2127651	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0022697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	166	961	1	ENST00000219476.3:c.2889_2890del	p.Lys964ArgfsTer20	p.K964Rfs*20	ENST00000219476	NM_000548.3	963	gtGAaa/gtaa	26/42	NA	2	FACETS	0.936	0.869	1			1	INDETERMINATE	1	TRUE	NA	0.822776353537084	2		962	431	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518244	8518244	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	78	523	0	ENST00000356435.5:c.1147C>G	p.Leu383Val	p.L383V	ENST00000356435		383	Cta/Gta	10/35	0.822776353537084	4	FACETS	0.484	0.425	0.548	0.161	0.141	0.183	SUBCLONAL	1	TRUE	1	0.822776353537084	4		523	714	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0022699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	444	953	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.466066343474217	2		955	889	SUCCESS
APC	324	MSKCC	GRCh37	5	112175328	112175328	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	70	313	1	ENST00000257430.4:c.4037C>A	p.Ser1346Ter	p.S1346*	ENST00000257430	NM_000038.5	1346	tCa/tAa	16/16	0.466066343474217	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.466066343474217	1		314	186	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916929	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	17	788	1	ENST00000263967.3:c.316G>T	p.Gly106Cys	p.G106C	ENST00000263967	NM_006218.2	106	Ggc/Tgc	2/21	1	2	FACETS	0.185	0.137	0.241	0.185	0.137	0.241	SUBCLONAL	1	TRUE	1	0.466066343474217	2		789	395	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505312	25505312	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs767055283	NA	P-0022699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	318	878	0	ENST00000264709.3:c.446C>T	p.Ala149Val	p.A149V	ENST00000264709	NM_175629.2	149	gCg/gTg	4/23	0.466066343474217	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.466066343474217	3		878	797	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239859	105239859	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	135	902	0	ENST00000349310.3:c.761G>A	p.Gly254Asp	p.G254D	ENST00000349310	NM_001014432.1	254	gGc/gAc	10/15	1	2	FACETS	0.921	0.84	1	0.921	0.84	1	CLONAL	1	TRUE	1	0.466066343474217	2		902	629	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578241	7578241	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	349	930	0	ENST00000269305.4:c.608T>A	p.Val203Glu	p.V203E	ENST00000269305	NM_001126112.2	203	gTg/gAg	6/11	0.638409133646445	1	FACETS	0.97	0.925	1	0.97	0.925	1	CLONAL	1	TRUE	0	0.638409133646445	1		930	767	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0022702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	68	701	0				ENST00000310581	NM_198253.2	-/1132			0.415897106053485	0	FACETS	0.402	0.355	0.452			1	SUBCLONAL	1	TRUE	0	0.592971600140559	0		701	232	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0022702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	252	862	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.592971600140559	2		862	667	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168916	32168916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs919103129	NA	P-0022702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	255	984	0	ENST00000375023.3:c.4117G>A	p.Glu1373Lys	p.E1373K	ENST00000375023	NM_004557.3	1373	Gag/Aag	22/30	0.592971600140559	3	FACETS	1	0.989	1	0.629	0.589	0.669	CLONAL	1	TRUE	1	0.592971600140559	3		984	887	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467675	50467675	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759124417	NA	P-0022702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	136	677	0	ENST00000331340.3:c.910G>A	p.Glu304Lys	p.E304K	ENST00000331340	NM_006060.4	304	Gaa/Aaa	8/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.592971600140559	2		677	373	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699323	18699323	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199904184	NA	P-0022702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	156	559	0	ENST00000266497.5:c.3424C>T	p.Arg1142Cys	p.R1142C	ENST00000266497		1142	Cgt/Tgt	24/31	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.592971600140559	2		559	391	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488718	212488718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267599191	NA	P-0022702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	175	698	0	ENST00000342788.4:c.2131C>T	p.Arg711Cys	p.R711C	ENST00000342788	NM_005235.2	711	Cgt/Tgt	18/28	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.592971600140559	2		698	550	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925412	114925412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs573425555	NA	P-0022702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	226	819	1	ENST00000543371.1:c.1490C>T	p.Pro497Leu	p.P497L	ENST00000543371	NM_001198531.1	497	cCg/cTg	14/14	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.592971600140559	2		820	584	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122880	2122880	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45517222	NA	P-0022702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	186	826	4	ENST00000219476.3:c.2251C>T	p.Arg751Ter	p.R751*	ENST00000219476	NM_000548.3	751	Cga/Tga	21/42	0.210331280790633	0	FACETS	0.535	0.499	0.572			1	INDETERMINATE	1	TRUE	0	0.592971600140559	0		830	477	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481408	140481408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867748453	NA	P-0022702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	148	575	1	ENST00000288602.6:c.1400C>T	p.Ser467Leu	p.S467L	ENST00000288602	NM_004333.4	467	tCa/tTa	11/18	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.592971600140559	2		576	421	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518175	8518175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1354824749	NA	P-0022702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	53	479	1	ENST00000356435.5:c.1216G>A	p.Glu406Lys	p.E406K	ENST00000356435		406	Gaa/Aaa	10/35	0.592971600140559	1	FACETS	0.379	0.324	0.438	0.379	0.324	0.438	SUBCLONAL	1	TRUE	0	0.592971600140559	1		480	332	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211154	36211154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	223	1214	0	ENST00000222270.7:c.905C>T	p.Pro302Leu	p.P302L	ENST00000222270	NM_014727.1	302	cCc/cTc	3/37	0.230078500504281	0	FACETS	0.494	0.462	0.526			1	INDETERMINATE	1	TRUE	0	0.592971600140559	0		1214	620	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965985	18965985	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	177	748	0	ENST00000262803.5:c.1478C>T	p.Pro493Leu	p.P493L	ENST00000262803	NM_002911.3	493	cCg/cTg	11/24	0.230078500504281	0	FACETS	0.577	0.538	0.617			1	INDETERMINATE	1	TRUE	0	0.592971600140559	0		748	421	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254692	16254692	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	191	704	0	ENST00000375759.3:c.1957C>T	p.Arg653Ter	p.R653*	ENST00000375759	NM_015001.2	653	Cga/Tga	11/15	0.225700712866341	1	FACETS	0.919	0.858	0.982	0.919	0.858	0.982	INDETERMINATE	1	TRUE	0	0.592971600140559	1		704	493	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307265	65307265	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	158	537	0	ENST00000342505.4:c.2423G>A	p.Ser808Asn	p.S808N	ENST00000342505	NM_002227.2	808	aGc/aAc	18/25	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.592971600140559	2		537	420	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18762554	18762554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	113	475	0	ENST00000266497.5:c.4050G>A	p.Met1350Ile	p.M1350I	ENST00000266497		1350	atG/atA	29/31	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.592971600140559	2		475	334	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861263	57861263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1447419974	NA	P-0022702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	197	602	0	ENST00000228682.2:c.1060C>T	p.Arg354Trp	p.R354W	ENST00000228682	NM_005269.2	354	Cgg/Tgg	9/12	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.592971600140559	2		602	504	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926513	59926513	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs747604569	NA	P-0022702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	275	889	0	ENST00000259008.2:c.484C>T	p.Arg162Ter	p.R162*	ENST00000259008	NM_032043.2	162	Cga/Tga	5/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.592971600140559	2		889	749	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374975	45374975	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	141	744	0	ENST00000262160.6:c.868T>C	p.Phe290Leu	p.F290L	ENST00000262160	NM_005901.5	290	Ttc/Ctc	8/11	1	2	FACETS	0.889	0.814	0.966	0.889	0.814	0.966	CLONAL	1	TRUE	1	0.592971600140559	2		744	535	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332697	153332698	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0022702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	194	664	0	ENST00000281708.4:c.258_259delinsAA	p.Val87Ile	p.V87I	ENST00000281708	NM_033632.3	86	tcGGta/tcAAta	2/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.592971600140559	2		664	581	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120702	94120702	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	174	571	0	ENST00000369303.4:c.349G>A	p.Gly117Arg	p.G117R	ENST00000369303	NM_004440.3	117	Gga/Aga	3/17	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.592971600140559	2		571	506	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566719	139566719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	299	922	0	ENST00000308874.7:c.803C>T	p.Ser268Phe	p.S268F	ENST00000308874		268	tCc/tTc	10/10	0.592971600140559	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.592971600140559	2		922	453	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231079	53231079	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	159	383	0	ENST00000375401.3:c.1823G>C	p.Gly608Ala	p.G608A	ENST00000375401	NM_004187.3	608	gGc/gCc	13/26	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.592971600140559	1		383	291	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0022704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	47	623	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.485	0.409	0.569	0.485	0.409	0.569	SUBCLONAL	1	TRUE	1	0.3623799970073	2		623	535	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699369	47699369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	39	675	0	ENST00000347630.2:c.139G>A	p.Glu47Lys	p.E47K	ENST00000347630	NM_001007230.1	47	Gaa/Aaa	4/11	1	2	FACETS	0.345	0.285	0.412	0.345	0.285	0.412	SUBCLONAL	1	TRUE	1	0.3623799970073	2		675	624	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941968	44941968	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	44	634	0	ENST00000377967.4:c.3218G>C	p.Arg1073Thr	p.R1073T	ENST00000377967	NM_021140.2	1073	aGg/aCg	22/29	1	2	FACETS	0.377	0.315	0.446	0.377	0.315	0.446	SUBCLONAL	1	TRUE	1	0.3623799970073	2		634	644	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961970	41961970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749795351	NA	P-0022706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	125	513	0	ENST00000219905.7:c.878G>A	p.Arg293His	p.R293H	ENST00000219905	NM_001164273.1	293	cGt/cAt	2/24	0.789359808506248	5	FACETS	0.9	0.815	0.989	0.3	0.271	0.33	CLONAL	1	TRUE	2	0.795706015703279	5		513	766	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0022707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	312	630	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	0.974	0.921	1	0.974	0.921	1	CLONAL	1	TRUE	1	0.725093235442254	2		630	884	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913836	32913837	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359507	NA	P-0022707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	191	592	0	ENST00000380152.3:c.5351dup	p.Asn1784LysfsTer3	p.N1784Kfs*3	ENST00000380152		1782	caa/cAaa	11/27	0.725093235442254	1	FACETS	0.807	0.756	0.858	0.807	0.756	0.858	CLONAL	1	TRUE	0	0.725093235442254	1		592	416	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858549	9858549	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs139795367	NA	P-0022707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	267	581	0	ENST00000330684.3:c.2852G>T	p.Gly951Val	p.G951V	ENST00000330684	NM_001134407.1	951	gGg/gTg	13/13	0.674953100476292	3	FACETS	0.945	0.886	1	0.472	0.443	0.503	CLONAL	1	TRUE	1	0.725093235442254	3		581	1062	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421277	12421277	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	318	762	0	ENST00000287820.6:c.157A>G	p.Met53Val	p.M53V	ENST00000287820	NM_015869.4	53	Atg/Gtg	2/7	1	2	FACETS	0.905	0.856	0.955	0.905	0.856	0.955	CLONAL	1	TRUE	1	0.725093235442254	2		762	969	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421286	12421286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	333	782	1	ENST00000287820.6:c.166C>T	p.His56Tyr	p.H56Y	ENST00000287820	NM_015869.4	56	Cac/Tac	2/7	1	2	FACETS	0.916	0.867	0.965	0.916	0.867	0.965	CLONAL	1	TRUE	1	0.725093235442254	2		783	1003	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270129	66270129	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	68	389	0	ENST00000273854.3:c.1753T>A	p.Leu585Met	p.L585M	ENST00000273854	NM_004439.5	585	Ttg/Atg	8/18	0.3	3	FACETS	0.964	0.839	1	0.482	0.419	0.55	CLONAL	1	TRUE	1	0.26	3		389	613	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813047	76813047	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	95	287	0	ENST00000373344.5:c.6574C>T	p.Gln2192Ter	p.Q2192*	ENST00000373344	NM_000489.3	2192	Cag/Tag	30/35	1	1	FACETS	1	0.938	1	1	0.988	1	CLONAL	2	TRUE	0	0.26	1		287	301	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106697	27106697	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1292	341	743	2	ENST00000324856.7:c.6308T>G	p.Phe2103Cys	p.F2103C	ENST00000324856	NM_006015.4	2103	tTt/tGt	20/20	0.445088828585301	4	FACETS	1	0.99	1	0.406	0.383	0.43	CLONAL	1	TRUE	1	0.521804742117571	4		745	1633	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740256	162740256	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	532	479	0	ENST00000367921.3:c.1458G>C	p.Arg486Ser	p.R486S	ENST00000367921	NM_006182.2	486	agG/agC	12/18	0.445088828585301	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	1	0.521804742117571	4		479	942	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176153800	176153800	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	92	561	0	ENST00000367669.3:c.436G>T	p.Ala146Ser	p.A146S	ENST00000367669	NM_022457.5	146	Gca/Tca	2/20	0.521804742117571	3	FACETS	1	0.954	1	0.56	0.501	0.622	CLONAL	1	TRUE	1	0.521804742117571	3		561	397	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720762	89720767	+	frameshift_variant	Frame_Shift_Del	DEL	AGTATA	AGTATA	TT	novel	NA	P-0022715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	22	213	0	ENST00000371953.3:c.913_918delinsTT	p.Ser305LeufsTer11	p.S305Lfs*11	ENST00000371953	NM_000314.4	305	AGTATA/TT	8/9	0.521804742117571	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	0	0.521804742117571	2		213	34	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878176	48878185	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CTCTCGTCAG	CTCTCGTCAG	-	novel	NA	P-0022715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	327	404	0	ENST00000267163.4:c.128_137del	p.Pro43ArgfsTer19	p.P43Rfs*19	ENST00000267163	NM_000321.2	43	cCTCTCGTCAGg/cg	1/27	0.506313511376529	4	FACETS	0.936	0.886	0.987	0.936	0.886	0.987	CLONAL	2	TRUE	2	0.521804742117571	4		404	1019	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953745	48953746	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	260	370	0	ENST00000267163.4:c.1350dup	p.Arg451SerfsTer12	p.R451Sfs*12	ENST00000267163	NM_000321.2	450	gtt/gTtt	14/27	0.506313511376529	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.521804742117571	4		370	649	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669508	88669508	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	290	687	1	ENST00000360948.2:c.1390A>C	p.Met464Leu	p.M464L	ENST00000360948	NM_001012338.2	464	Atg/Ctg	12/19	1	2	FACETS	0.768	0.726	0.809	1	0.994	1	SUBCLONAL	2	TRUE	1	0.521804742117571	2		688	724	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467119	99467119	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	247	477	0	ENST00000268035.6:c.2500A>T	p.Ile834Phe	p.I834F	ENST00000268035	NM_000875.3	834	Att/Ttt	12/21	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.521804742117571	2		477	636	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	1249	990	2	ENST00000269305.4:c.470T>G	p.Val157Gly	p.V157G	ENST00000269305	NM_001126112.2	157	gTc/gGc	5/11	0.521804742117571	2	FACETS	1	0.996	1	1	0.999	1	CLONAL	3	TRUE	0	0.521804742117571	2		992	1542	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866610	37866610	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	342	696	0	ENST00000269571.5:c.777C>G	p.Asn259Lys	p.N259K	ENST00000269571		259	aaC/aaG	7/27	0.479835710857407	4	FACETS	1	0.993	1	0.442	0.417	0.467	CLONAL	1	TRUE	1	0.521804742117571	4		696	1505	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795061	42795061	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1157	792	1185	3	ENST00000575354.2:c.2141G>T	p.Gly714Val	p.G714V	ENST00000575354	NM_015125.3	714	gGg/gTg	10/20	1	2	FACETS	0.779	0.753	0.804	1	0.998	1	SUBCLONAL	2	TRUE	1	0.521804742117571	2		1188	1949	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143179	30143179	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	515	795	0	ENST00000389048.3:c.347C>A	p.Ala116Asp	p.A116D	ENST00000389048	NM_004304.4	116	gCc/gAc	1/29	1	2	FACETS	0.805	0.773	0.837	1	0.997	1	CLONAL	2	TRUE	1	0.521804742117571	2		795	1226	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129833	55129833	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0022715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	178	541	0	ENST00000257290.5:c.368-1G>C		p.X123_splice	ENST00000257290	NM_006206.4	123			1	2	FACETS	0.788	0.734	0.842	1	0.992	1	SUBCLONAL	2	TRUE	1	0.521804742117571	2		541	433	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197163	26197163	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	494	633	0	ENST00000356476.2:c.316G>C	p.Glu106Gln	p.E106Q	ENST00000356476		106	Gag/Cag	1/1	0.462560514551193	3	FACETS	1	0.965	1			1	CLONAL	2	TRUE	NA	0.521804742117571	3		633	1186	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997741	149997741	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	266	559	0	ENST00000253339.5:c.2726C>G	p.Ser909Cys	p.S909C	ENST00000253339		909	tCt/tGt	5/7	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.521804742117571	2		559	708	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335628	81335628	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	85	563	0	ENST00000222390.5:c.1732G>T	p.Asp578Tyr	p.D578Y	ENST00000222390	NM_000601.4	578	Gat/Tat	15/18	1	2	FACETS	0.814	0.718	0.917	0.814	0.718	0.917	CLONAL	1	TRUE	1	0.234402020090588	2		563	891	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820303	139820303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774782158	NA	P-0022716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	115	787	0	ENST00000247668.2:c.1456C>T	p.Arg486Trp	p.R486W	ENST00000247668	NM_021138.3	486	Cgg/Tgg	11/11	1	2	FACETS	0.963	0.866	1	0.963	0.866	1	CLONAL	1	TRUE	1	0.234402020090588	2		787	1019	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937117	39937117	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs947946150	NA	P-0022716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	64	926	0	ENST00000378444.4:c.66G>T	p.Met22Ile	p.M22I	ENST00000378444	NM_001123385.1	22	atG/atT	2/15	NA	2	FACETS	0.468	0.404	0.539			1	INDETERMINATE	1	TRUE	NA	0.234402020090588	2		926	1166	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112164	115112164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	58	875	1	ENST00000257566.3:c.1576G>A	p.Ala526Thr	p.A526T	ENST00000257566	NM_016569.3	526	Gcc/Acc	7/8	1	2	FACETS	0.477	0.408	0.553	0.477	0.408	0.553	SUBCLONAL	1	TRUE	1	0.234402020090588	2		876	1037	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566172	95566172	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	48	670	0	ENST00000393063.1:c.4151del	p.Gly1384ValfsTer3	p.G1384Vfs*3	ENST00000393063	NM_030621.3	1384	gGt/gt	23/28	1	2	FACETS	0.439	0.37	0.516	0.439	0.37	0.516	SUBCLONAL	1	TRUE	1	0.234402020090588	2		670	933	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577101	7577102	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0022716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	108	880	0	ENST00000269305.4:c.836_837delinsAT	p.Gly279Asp	p.G279D	ENST00000269305	NM_001126112.2	279	gGG/gAT	8/11	1	2	FACETS	0.859	0.769	0.955	0.859	0.769	0.955	CLONAL	1	TRUE	1	0.234402020090588	2		880	1073	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600471	10600471	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	156	822	0	ENST00000171111.5:c.1384G>C	p.Gly462Arg	p.G462R	ENST00000171111	NM_203500.1	462	Ggg/Cgg	4/6	0.234402020090588	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.234402020090588	1		822	987	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721190	61721190	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	90	559	0	ENST00000401558.2:c.1084G>A	p.Glu362Lys	p.E362K	ENST00000401558	NM_003400.3	362	Gaa/Aaa	12/25	1	2	FACETS	0.861	0.763	0.966	0.861	0.763	0.966	CLONAL	1	TRUE	1	0.234402020090588	2		559	892	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546073	41546073	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	206	734	0	ENST00000263253.7:c.2688A>C	p.Gln896His	p.Q896H	ENST00000263253	NM_001429.3	896	caA/caC	14/31	NA	2	FACETS	0.753	0.698	0.811			1	INDETERMINATE	2	TRUE	NA	0.234402020090588	2		734	1167	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0022717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	358	737	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.581915068641777	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.581915068641777	1		739	791	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0022717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	90	731	2	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.350430886744176	1	FACETS	0.772	0.694	0.853	0.772	0.694	0.853	SUBCLONAL	1	TRUE	0	0.581915068641777	1		733	284	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	469	899	1	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.312930185167474	3	FACETS	1	0.988	1	0.722	0.692	0.753	CLONAL	2	TRUE	0	0.466272251724166	3		900	1145	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600475	43600475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756216318	NA	P-0022718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1462	84	789	0	ENST00000355710.3:c.701G>A	p.Arg234Gln	p.R234Q	ENST00000355710	NM_020975.4	234	cGg/cAg	4/20	0.440903861125994	4	FACETS	0.342	0.3	0.387	0.171	0.15	0.194	SUBCLONAL	1	TRUE	2	0.466272251724166	4		789	1546	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336073	73336073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	11	317	0	ENST00000377767.4:c.2330C>T	p.Ser777Leu	p.S777L	ENST00000377767	NM_014953.3	777	tCa/tTa	17/21	0.466272251724166	3	FACETS	0.268	0.185	0.372	0.134	0.092	0.186	SUBCLONAL	1	TRUE	1	0.466272251724166	3		317	217	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114102	115114156	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTGACATGGTTTACCTTTGAGGTTCGATGTCCCTACAGTGGAGGCGGCTGGAG	AGGTGACATGGTTTACCTTTGAGGTTCGATGTCCCTACAGTGGAGGCGGCTGGAG	-	novel	NA	P-0022718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	323	458	0	ENST00000257566.3:c.1061_1099+16del		p.X354_splice	ENST00000257566	NM_016569.3	354		6/8	0.220053368417464	5	FACETS	0.935	0.887	0.984	0.935	0.887	0.984	INDETERMINATE	3	TRUE	2	0.466272251724166	5		458	839	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839759	27839759	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	510	684	0	ENST00000328488.2:c.335C>T	p.Ala112Val	p.A112V	ENST00000328488	NM_003533.2	112	gCc/gTc	1/1	0.466272251724166	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.466272251724166	3		684	1315	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873843	151873843	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	330	603	0	ENST00000262189.6:c.8695C>T	p.Gln2899Ter	p.Q2899*	ENST00000262189	NM_170606.2	2899	Caa/Taa	38/59	0.415878657514534	5	FACETS	1	0.991	1	0.803	0.76	0.846	CLONAL	2	TRUE	2	0.466272251724166	5		603	999	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039481	49039481	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	351	741	0	ENST00000267163.4:c.2467del	p.Thr823GlnfsTer3	p.T823Qfs*3	ENST00000267163	NM_000321.2	822	ccA/cc	23/27	0.74707673028131	2	FACETS	0.971	0.939	1	0.971	0.939	1	CLONAL	2	TRUE	0	0.759515699542588	2		741	476	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0022723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	375	649	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.124675962300646	6	FACETS	0.96	0.912	1			1	CLONAL	5	TRUE	NA	0.19	6		649	1135	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	148	713	1	ENST00000269305.4:c.859G>T	p.Glu287Ter	p.E287*	ENST00000269305	NM_001126112.2	287	Gag/Tag	8/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.19	2		714	1314	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140508735	140508735	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	78	710	1	ENST00000288602.6:c.565G>T	p.Gly189Cys	p.G189C	ENST00000288602	NM_004333.4	189	Ggt/Tgt	4/18	0.0768190076759478	3	FACETS	1	0.897	1	0.513	0.449	0.581	INDETERMINATE	1	TRUE	1	0.19	3		711	877	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724995	162724995	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	44	567	0	ENST00000367921.3:c.467A>G	p.Glu156Gly	p.E156G	ENST00000367921	NM_006182.2	156	gAg/gGg	6/18	1	2	FACETS	0.564	0.471	0.667	0.564	0.471	0.667	SUBCLONAL	1	TRUE	1	0.19	2		567	821	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052680	42052680	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	69	694	0	ENST00000219905.7:c.7351G>T	p.Gly2451Ter	p.G2451*	ENST00000219905	NM_001164273.1	2451	Gga/Tga	20/24	1	2	FACETS	0.8	0.695	0.914	0.8	0.695	0.914	CLONAL	1	TRUE	1	0.19	2		694	908	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349170	11349170	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	30	329	0	ENST00000332029.2:c.166C>T	p.Arg56Cys	p.R56C	ENST00000332029	NM_003745.1	56	Cgc/Tgc	2/2	1	2	FACETS	0.693	0.557	0.846	0.693	0.557	0.846	SUBCLONAL	1	TRUE	1	0.19	2		329	456	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8111083	8111083	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753945703	NA	P-0022723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	145	891	0	ENST00000585124.1:c.124A>G	p.Met42Val	p.M42V	ENST00000585124	NM_004217.3	42	Atg/Gtg	3/9	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.19	2		891	1146	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217801	2217801	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	82	928	0	ENST00000398665.3:c.2575G>T	p.Gly859Trp	p.G859W	ENST00000398665	NM_032482.2	859	Ggg/Tgg	22/28	1	2	FACETS	0.778	0.684	0.879	0.778	0.684	0.879	SUBCLONAL	1	TRUE	1	0.19	2		928	1110	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792867	33792867	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	51	443	0	ENST00000498907.2:c.454G>C	p.Ala152Pro	p.A152P	ENST00000498907	NM_004364.3	152	Gcg/Ccg	1/1	0.0768190076759478	3	FACETS	0.881	0.748	1	0.441	0.374	0.514	INDETERMINATE	1	TRUE	1	0.19	3		443	667	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733328	40733328	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	57	501	0	ENST00000373198.4:c.3478C>G	p.Leu1160Val	p.L1160V	ENST00000373198	NM_133170.3	1160	Ctg/Gtg	26/32	1	2	FACETS	0.801	0.686	0.927	0.801	0.686	0.927	CLONAL	1	TRUE	1	0.19	2		501	749	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326835	62326835	+	synonymous_variant	Silent	SNP	T	T	A	novel	NA	P-0022723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	117	1020	0	ENST00000360203.5:c.3654T>A	p.Gly1218=	p.G1218=	ENST00000360203	NM_001283009.1	1218	ggT/ggA	34/35	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.19	2		1020	1227	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526658	106526658	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	85	604	0	ENST00000359195.3:c.2951C>T	p.Pro984Leu	p.P984L	ENST00000359195	NM_002649.2	984	cCa/cTa	10/11	0.0768190076759478	3	FACETS	1	0.944	1	0.559	0.493	0.629	INDETERMINATE	1	TRUE	1	0.19	3		604	877	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851936	128851936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	91	860	0	ENST00000249373.3:c.2008G>A	p.Gly670Ser	p.G670S	ENST00000249373	NM_005631.4	670	Ggc/Agc	12/12	0.0768190076759478	3	FACETS	1	0.891	1	0.503	0.446	0.565	INDETERMINATE	1	TRUE	1	0.19	3		860	1042	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139818370	139818370	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	125	844	0	ENST00000247668.2:c.1205G>T	p.Gly402Val	p.G402V	ENST00000247668	NM_021138.3	402	gGg/gTg	10/11	0.297187769493651	1	FACETS	0.976	0.881	1	0.976	0.881	1	CLONAL	1	TRUE	0	0.19	1		844	1220	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	162	445	0				ENST00000310581	NM_198253.2	-/1132			0.323053049654681	1	FACETS	0.609	0.564	0.655	0.609	0.564	0.655	INDETERMINATE	1	TRUE	0	0.752411600632787	1		445	441	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947827	178947827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	161	351	0	ENST00000263967.3:c.2702G>T	p.Cys901Phe	p.C901F	ENST00000263967	NM_006218.2	901	tGt/tTt	19/21	1	2	FACETS	0.875	0.809	0.943	0.875	0.809	0.943	CLONAL	1	TRUE	1	0.752411600632787	2		351	489	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117799	108117799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202160435	NA	P-0022724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	11	526	0	ENST00000278616.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000278616	NM_000051.3	337	cGt/cAt	8/63	0.752411600632787	1	FACETS	0.04	0.027	0.056	0.04	0.027	0.056	SUBCLONAL	1	TRUE	0	0.752411600632787	1		526	459	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309613	30309613	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	388	803	0	ENST00000307677.4:c.409T>A	p.Trp137Arg	p.W137R	ENST00000307677	NM_138578.1	137	Tgg/Agg	2/3	0.252734049858578	1	FACETS	0.635	0.605	0.666	0.635	0.605	0.666	INDETERMINATE	1	TRUE	0	0.752411600632787	1		803	1013	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	260	445	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.98	0.92	1	0.98	0.92	1	CLONAL	1	TRUE	1	0.574092851735346	2		445	924	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148991	119148991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs192712314	NA	P-0022725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	24	568	2	ENST00000264033.4:c.1211G>A	p.Cys404Tyr	p.C404Y	ENST00000264033	NM_005188.3	404	tGt/tAt	8/16	1	2	FACETS	0.115	0.089	0.144	0.115	0.089	0.144	SUBCLONAL	1	TRUE	1	0.574092851735346	2		570	729	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720818	89720818	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0022725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	142	346	0	ENST00000371953.3:c.969del	p.Asn323LysfsTer21	p.N323Kfs*21	ENST00000371953	NM_000314.4	323	aaT/aa	8/9	0.574092851735346	2	FACETS	1	0.989	1	0.747	0.691	0.804	CLONAL	1	TRUE	0	0.574092851735346	2		346	331	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707887	43707887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	381	974	0	ENST00000382044.4:c.4994C>T	p.Ser1665Phe	p.S1665F	ENST00000382044	NM_001141980.1	1665	tCc/tTc	23/28	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.574092851735346	2		974	1317	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533264	29533264	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0022725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	145	344	0	ENST00000356175.3:c.1268del	p.Leu423TrpfsTer50	p.L423Wfs*50	ENST00000356175	NM_000267.3	423	Ttg/tg	12/57	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.574092851735346	2		344	467	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489538	40489538	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	57	748	3	ENST00000264657.5:c.712G>T	p.Glu238Ter	p.E238*	ENST00000264657	NM_139276.2	238	Gag/Tag	8/24	0.574092851735346	1	FACETS	0.191	0.163	0.221	0.191	0.163	0.221	SUBCLONAL	1	TRUE	0	0.574092851735346	1		751	742	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152092	55152092	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913265	NA	P-0022727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	296	732	2	ENST00000257290.5:c.2524G>T	p.Asp842Tyr	p.D842Y	ENST00000257290	NM_006206.4	842	Gac/Tac	18/23	1	2	FACETS	0.916	0.863	0.97	0.916	0.863	0.97	CLONAL	1	TRUE	1	0.627290586366049	2		734	1030	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0022728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	130	559	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.972	0.889	1	0.972	0.889	1	CLONAL	1	TRUE	1	0.640219469416953	2		559	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0022728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	341	925	0	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	0.631590807275582	1	FACETS	0.98	0.934	1	0.98	0.934	1	CLONAL	1	TRUE	0	0.640219469416953	1		925	739	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214879	36214879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	341	1015	0	ENST00000222270.7:c.3305C>T	p.Ala1102Val	p.A1102V	ENST00000222270	NM_014727.1	1102	gCt/gTt	8/37	0.631590807275582	1	FACETS	0.963	0.917	1	0.963	0.917	1	CLONAL	1	TRUE	0	0.640219469416953	1		1015	752	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0022728-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	197	559	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.993	0.93	1	0.993	0.93	1	CLONAL	1	TRUE	1	0.85320202928954	2		559	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0022728-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	450	925	0	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	0.85320202928954	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.85320202928954	1		925	593	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214879	36214879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022728-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	461	1015	0	ENST00000222270.7:c.3305C>T	p.Ala1102Val	p.A1102V	ENST00000222270	NM_014727.1	1102	gCt/gTt	8/37	0.846939365313265	1	FACETS	0.914	0.885	0.942	0.914	0.885	0.942	CLONAL	1	TRUE	0	0.85320202928954	1		1015	678	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0022729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	510	705	1	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.636216845975736	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.636216845975736	1		706	952	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0022732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	88	840	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	1	2	FACETS	1	0.924	1	1	0.986	1	CLONAL	2	TRUE	1	0.11	2		840	757	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219367	5219367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763007823	NA	P-0022732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	55	875	1	ENST00000357368.4:c.3877G>A	p.Val1293Met	p.V1293M	ENST00000357368	NM_002850.3	1293	Gtg/Atg	23/38	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.11	2		876	844	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982989	201982990	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0022732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	154	886	0	ENST00000359651.3:c.841dup	p.Asp281GlyfsTer20	p.D281Gfs*20	ENST00000359651		280	cgg/cGgg	7/8	0.173571295443337	3	FACETS	1	0.953	1	1	0.989	1	CLONAL	3	TRUE	1	0.11	3		886	928	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0022734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	201	737	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.445634951693508	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.445634951693508	1		739	659	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249503	153249503	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	122	534	0	ENST00000281708.4:c.1275G>C	p.Trp425Cys	p.W425C	ENST00000281708	NM_033632.3	425	tgG/tgC	9/12	0.445634951693508	1	FACETS	0.778	0.706	0.853	0.778	0.706	0.853	SUBCLONAL	1	TRUE	0	0.445634951693508	1		534	547	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119966	70120018	+	frameshift_variant	Frame_Shift_Del	DEL	GCACCGCGGCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAG	GCACCGCGGCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAG	-	novel	NA	P-0022734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	57	301	0	ENST00000245479.2:c.970_1022del	p.Thr324AlafsTer236	p.T324Afs*236	ENST00000245479	NM_000346.3	323	aGCACCGCGGCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAG/a	3/3	0.445634951693508	1	FACETS	0.495	0.426	0.569	0.495	0.426	0.569	SUBCLONAL	1	TRUE	0	0.445634951693508	1		301	402	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965809	25965809	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1285225904	NA	P-0022734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	212	601	0	ENST00000435504.4:c.3397C>T	p.Arg1133Trp	p.R1133W	ENST00000435504		1133	Cgg/Tgg	13/13	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.445634951693508	2		601	918	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55603417	55603417	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	42	337	0	ENST00000288135.5:c.2773G>T	p.Glu925Ter	p.E925*	ENST00000288135	NM_000222.2	925	Gag/Tag	20/21	0.445634951693508	1	FACETS	0.383	0.321	0.453	0.383	0.321	0.453	SUBCLONAL	1	TRUE	0	0.445634951693508	1		337	382	SUCCESS
APC	324	MSKCC	GRCh37	5	112175394	112175395	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	65	242	0	ENST00000257430.4:c.4103_4104insT	p.Pro1369ThrfsTer6	p.P1369Tfs*6	ENST00000257430	NM_000038.5	1368	aca/acTa	16/16	0.445634951693508	1	FACETS	0.83	0.727	0.94	0.83	0.727	0.94	CLONAL	1	TRUE	0	0.445634951693508	1		242	273	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048896	180048896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	242	635	0	ENST00000261937.6:c.1666G>A	p.Asp556Asn	p.D556N	ENST00000261937	NM_182925.4	556	Gac/Aac	13/30	0.445634951693508	1	FACETS	0.91	0.851	0.97	0.91	0.851	0.97	CLONAL	1	TRUE	0	0.445634951693508	1		635	928	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	122	445	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.360377625102092	2		445	547	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0022735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	183	521	0	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	0.360377625102092	4	FACETS	0.876	0.809	0.944	0.876	0.809	0.944	CLONAL	2	TRUE	2	0.360377625102092	4		521	789	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0022735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	216	815	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.360377625102092	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.360377625102092	1		815	817	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339981	70339981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	120	530	1	ENST00000374080.3:c.514G>A	p.Glu172Lys	p.E172K	ENST00000374080		172	Gag/Aag	4/45	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.360377625102092	2		531	613	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165273	32165273	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs755664291	NA	P-0022735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	123	843	0	ENST00000375023.3:c.4855C>G	p.Leu1619Val	p.L1619V	ENST00000375023	NM_004557.3	1619	Ctg/Gtg	27/30	1	2	FACETS	0.643	0.581	0.71	0.643	0.581	0.71	SUBCLONAL	1	TRUE	1	0.360377625102092	2		843	1061	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922271	100922271	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	88	482	0	ENST00000325455.5:c.2241G>C	p.Gln747His	p.Q747H	ENST00000325455	NM_001202474.3	747	caG/caC	5/8	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.360377625102092	2		482	457	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66518924	66518924	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	163	369	1	ENST00000358598.2:c.205C>A	p.Gln69Lys	p.Q69K	ENST00000358598	NM_212471.2	69	Cag/Aag	3/11	0.360377625102092	4	FACETS	0.884	0.814	0.957	0.884	0.814	0.957	CLONAL	2	TRUE	2	0.360377625102092	4		370	696	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117614	70117614	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	154	715	0	ENST00000245479.2:c.82G>C	p.Glu28Gln	p.E28Q	ENST00000245479	NM_000346.3	28	Gag/Cag	1/3	0.360377625102092	4	FACETS	1	0.963	1	0.549	0.502	0.599	CLONAL	1	TRUE	2	0.360377625102092	4		715	1058	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278351	39278352	+	missense_variant	Missense_Mutation	DNP	TG	TG	CT	novel	NA	P-0022735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	75	823	2	ENST00000402219.2:c.797_798delinsAG	p.Thr266Lys	p.T266K	ENST00000402219	NM_005633.3	266	aCA/aAG	6/23	1	2	FACETS	0.627	0.549	0.711	0.627	0.549	0.711	SUBCLONAL	1	TRUE	1	0.360377625102092	2		825	664	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698199	47698199	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	78	322	0	ENST00000233146.2:c.1757C>T	p.Ser586Leu	p.S586L	ENST00000233146	NM_000251.2	586	tCa/tTa	11/16	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.360377625102092	2		322	410	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932800	49932800	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	154	852	1	ENST00000296474.3:c.3071C>T	p.Pro1024Leu	p.P1024L	ENST00000296474	NM_002447.2	1024	cCt/cTt	14/20	1	2	FACETS	0.783	0.716	0.854	0.783	0.716	0.854	SUBCLONAL	1	TRUE	1	0.360377625102092	2		853	1091	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538966	187538966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	130	529	0	ENST00000441802.2:c.8774G>A	p.Gly2925Glu	p.G2925E	ENST00000441802	NM_005245.3	2925	gGg/gAg	10/27	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.360377625102092	2		529	712	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591128	67591128	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	54	332	0	ENST00000274335.5:c.1721G>C	p.Arg574Thr	p.R574T	ENST00000274335		574	aGa/aCa	12/15	1	2	FACETS	0.707	0.605	0.818	0.707	0.605	0.818	SUBCLONAL	1	TRUE	1	0.360377625102092	2		332	424	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843753	151843754	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0022735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	124	543	0	ENST00000262189.6:c.13960_13961dup	p.Pro4655SerfsTer5	p.P4655Sfs*5	ENST00000262189	NM_170606.2	4654	ttc/ttTTc	53/59	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.360377625102092	2		543	687	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518403	8518403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	22	233	0	ENST00000356435.5:c.988G>A	p.Val330Ile	p.V330I	ENST00000356435		330	Gta/Ata	10/35	0.329456030966707	2	FACETS	0.377	0.292	0.476	0.188	0.146	0.238	SUBCLONAL	1	TRUE	0	0.360377625102092	2		233	324	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032526	47032526	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0022735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	209	649	0	ENST00000377604.3:c.433-1G>A		p.X145_splice	ENST00000377604	NM_001204468.1	145			1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.360377625102092	2		649	847	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245159	53245159	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0022735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	170	575	0	ENST00000375401.3:c.782-1G>C		p.X261_splice	ENST00000375401	NM_004187.3	261			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.360377625102092	2		575	799	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	67	549	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.139021701814695	3	FACETS	0.979	0.856	1	0.979	0.856	1	CLONAL	2	TRUE	1	0.21	3		549	360	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555526097	NA	P-0022739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	101	771	0	ENST00000269305.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000269305	NM_001126112.2	167	Cag/Tag	5/11	0.3	1	FACETS	0.821	0.737	0.911	1	0.984	1	CLONAL	2	TRUE	0	0.21	1		771	524	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71008398	71008398	+	stop_lost	Nonstop_Mutation	SNP	T	T	C	novel	NA	P-0022739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	73	424	0	ENST00000318789.4:c.2034A>G	p.Ter678TrpextTer51	p.*678Wext*51	ENST00000318789	NM_032682.5	678	tgA/tgG	21/21	0.3	1	FACETS	0.832	0.732	0.938	1	0.979	1	CLONAL	2	TRUE	0	0.21	1		424	374	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0022745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	214	653	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	0.946	0.882	1	0.946	0.882	1	CLONAL	1	TRUE	1	0.58	2		653	780	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156729	20156729	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs757280897	NA	P-0022745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	283	226	0	ENST00000379607.5:c.28A>G	p.Lys10Glu	p.K10E	ENST00000379607	NM_001412.3	10	Aaa/Gaa	2/7	1	1	FACETS	0.778	0.745	0.812	1	0.995	1	SUBCLONAL	2	TRUE	0	0.58	1		226	445	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098779	47098779	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	624	833	0	ENST00000409792.3:c.6495del	p.Gly2166ValfsTer82	p.G2166Vfs*82	ENST00000409792	NM_014159.6	2165	gcT/gc	15/21	0.609050757430324	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.58	2		833	1036	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442555	52442556	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0022745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	563	775	0	ENST00000460680.1:c.188_189dup	p.Thr64LeufsTer9	p.T64Lfs*9	ENST00000460680	NM_004656.3	63	-/CT	4/17	0.609050757430324	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.58	2		775	955	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0022747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	173	559	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.490550462682714	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.491763490767389	2		559	318	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118704	115118706	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0022747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	138	610	0	ENST00000257566.3:c.635_637del	p.Asn212del	p.N212del	ENST00000257566	NM_016569.3	212	aACAtt/att	2/8	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.491763490767389	2		610	544	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198382	108198382	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	78	504	0	ENST00000278616.4:c.6986G>T	p.Ser2329Ile	p.S2329I	ENST00000278616	NM_000051.3	2329	aGc/aTc	48/63	0.46861933482212	1	FACETS	0.79	0.701	0.883	0.79	0.701	0.883	SUBCLONAL	1	TRUE	0	0.491763490767389	1		504	303	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771355	68771381	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGCTGCTGCAGGTACCCCGGATCCCC	CTGCTGCTGCAGGTACCCCGGATCCCC	-	novel	NA	P-0022747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	93	505	0	ENST00000261769.5:c.37_48+15del		p.X13_splice	ENST00000261769	NM_004360.3	13		1/16	0.491763490767389	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.491763490767389	1		505	238	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923368	131923368	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	50	226	0	ENST00000265335.6:c.871G>C	p.Glu291Gln	p.E291Q	ENST00000265335		291	Gag/Cag	6/25	1	2	FACETS	0.916	0.786	1	0.916	0.786	1	CLONAL	1	TRUE	1	0.491763490767389	2		226	222	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6038756	6038756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1562677528	NA	P-0022747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	185	709	1	ENST00000265849.7:c.688G>A	p.Val230Met	p.V230M	ENST00000265849	NM_000535.5	230	Gtg/Atg	6/15	1	2	FACETS	0.949	0.878	1	0.949	0.878	1	CLONAL	1	TRUE	1	0.491763490767389	2		710	793	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821794	72821794	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	170	711	0	ENST00000268489.5:c.10381del	p.Val3461CysfsTer24	p.V3461Cfs*24	ENST00000268489	NM_006885.3	3461	Gtg/tg	10/10	0.285652467280006	3	FACETS	0.948	0.874	1	0.474	0.437	0.512	INDETERMINATE	1	TRUE	1	0.685289280807728	3		711	703	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352802	70352802	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	160	419	0	ENST00000374080.3:c.4523A>T	p.His1508Leu	p.H1508L	ENST00000374080		1508	cAc/cTc	32/45	1	1	FACETS	0.905	0.844	0.967	0.905	0.844	0.967	CLONAL	1	TRUE	0	0.685289280807728	1		419	339	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298757	46298757	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	190	597	0	ENST00000334344.6:c.5404A>G	p.Ile1802Val	p.I1802V	ENST00000334344	NM_152641.2	1802	Att/Gtt	21/21	0.519108747546336	4	FACETS	0.995	0.919	1	0.498	0.459	0.537	CLONAL	1	TRUE	2	0.57148022878076	4		597	1050	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024193	112024193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	209	591	1	ENST00000368678.4:c.592G>A	p.Asp198Asn	p.D198N	ENST00000368678		198	Gac/Aac	7/13	0.569755251127198	3	FACETS	1	0.961	1	0.525	0.488	0.563	CLONAL	1	TRUE	1	0.57148022878076	3		592	896	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0022750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	37	640	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.97	0.799	1	0.97	0.799	1	CLONAL	1	TRUE	1	0.14	2		640	545	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	35	549	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	0.14	2		549	462	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	197	445	0				ENST00000310581	NM_198253.2	-/1132			0.13482466115673	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.879855748137038	0		445	488	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0022752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34137	1660	715	0	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.879855748137038	27	FACETS	1	0.998	1	0.047	0.045	0.049	CLONAL	1	TRUE	0	0.879855748137038	27		715	35797	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934370	68934370	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	401	582	0	ENST00000288368.4:c.436C>G	p.Leu146Val	p.L146V	ENST00000288368	NM_024870.2	146	Ctt/Gtt	4/40	1	2	FACETS	0.919	0.877	0.961	0.919	0.877	0.961	CLONAL	1	TRUE	1	0.879855748137038	2		582	992	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0022755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	619	826	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.676198976713017	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.676465429959146	3		828	793	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0022755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	96	435	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.676465429959146	3	FACETS	0.929	0.833	1	0.464	0.416	0.515	CLONAL	1	TRUE	1	0.676465429959146	3		436	409	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133901	55133901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	4164	379	0	ENST00000257290.5:c.1114G>A	p.Glu372Lys	p.E372K	ENST00000257290	NM_006206.4	372	Gaa/Aaa	7/23	0.676465429959146	35	FACETS	0.996	0.99	1			1	CLONAL	33	TRUE	NA	0.676465429959146	35		379	4555	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662714	117662714	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	138	537	0	ENST00000368508.3:c.4751C>G	p.Pro1584Arg	p.P1584R	ENST00000368508	NM_002944.2	1584	cCa/cGa	29/43	0.676465429959146	3	FACETS	0.968	0.885	1	0.484	0.442	0.528	CLONAL	1	TRUE	1	0.676465429959146	3		537	564	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539108	23539108	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	145	634	1	ENST00000380871.4:c.331G>A	p.Gly111Ser	p.G111S	ENST00000380871	NM_006167.3	111	Ggc/Agc	2/2	0.316246736188323	5	FACETS	1	0.967	1	0.373	0.34	0.407	INDETERMINATE	1	TRUE	2	0.676465429959146	5		635	772	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321318	1321318	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	76	663	0	ENST00000400841.2:c.437T>A	p.Leu146His	p.L146H	ENST00000400841		146	cTc/cAc	4/6	1	1	FACETS	0.284	0.249	0.321	0.284	0.249	0.321	SUBCLONAL	1	TRUE	0	0.676465429959146	1		663	524	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889105	76889106	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	ATCCAATTCAAAGCAGTATTAAGAGGACAAACCACTAACGCCGTGCTGAA	novel	NA	P-0022755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	67	324	0	ENST00000373344.5:c.4855_4904dup	p.Met1635IlefsTer6	p.M1635Ifs*6	ENST00000373344	NM_000489.3	1635	atg/atTTCAGCACGGCGTTAGTGGTTTGTCCTCTTAATACTGCTTTGAATTGGATg	18/35	0.153367992619488	3	FACETS	0.628	0.548	0.714			1	INDETERMINATE	1	TRUE	NA	0.676465429959146	3		324	422	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102196	27102196	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	105	491	0	ENST00000324856.7:c.5122C>T	p.Gln1708Ter	p.Q1708*	ENST00000324856	NM_006015.4	1708	Cag/Tag	19/20	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.550953331142806	2		491	370	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851661	63851662	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	190	609	0	ENST00000279873.7:c.2441dup	p.Leu814PhefsTer13	p.L814Ffs*13	ENST00000279873	NM_032199.2	813	-/T	10/10	0.537766666726108	3	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.550953331142806	3		609	771	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183769	10183771	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0022757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	172	537	0	ENST00000256474.2:c.238_240del	p.Ser80del	p.S80del	ENST00000256474	NM_000551.3	80	AGT/-	1/3	0.550953331142806	1	FACETS	0.931	0.864	0.999	0.931	0.864	0.999	CLONAL	1	TRUE	0	0.550953331142806	1		537	486	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125739	47125739	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	136	467	0	ENST00000409792.3:c.5531del	p.Ser1844LeufsTer21	p.S1844Lfs*21	ENST00000409792	NM_014159.6	1844	tCt/tt	12/21	0.550953331142806	1	FACETS	0.877	0.805	0.95	0.877	0.805	0.95	CLONAL	1	TRUE	0	0.550953331142806	1		467	408	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554937	106554937	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	179	519	0	ENST00000369096.4:c.2054G>C	p.Arg685Pro	p.R685P	ENST00000369096	NM_001198.3	685	cGg/cCg	7/7	1	2	FACETS	0.977	0.904	1	0.977	0.904	1	CLONAL	1	TRUE	1	0.550953331142806	2		519	665	SUCCESS
APC	324	MSKCC	GRCh37	5	112174577	112174577	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587783029	NA	P-0022758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	90	518	0	ENST00000257430.4:c.3286C>T	p.Gln1096Ter	p.Q1096*	ENST00000257430	NM_000038.5	1096	Cag/Tag	16/16	0.390957381222654	1	FACETS	0.969	0.866	1	0.969	0.866	1	CLONAL	1	TRUE	0	0.398018196031417	1		518	374	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645693	12645693	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397516827	NA	P-0022758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	48	432	0	ENST00000251849.4:c.776C>G	p.Ser259Cys	p.S259C	ENST00000251849	NM_002880.3	259	tCc/tGc	7/17	0.216004739906995	0	FACETS	0.471	0.4	0.549			1	INDETERMINATE	1	TRUE	0	0.398018196031417	0		432	308	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031691	69031691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748595305	NA	P-0022758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	213	770	3	ENST00000288368.4:c.3446G>A	p.Arg1149His	p.R1149H	ENST00000288368	NM_024870.2	1149	cGc/cAc	28/40	0.398018196031417	3	FACETS	0.811	0.756	0.868	0.811	0.756	0.868	CLONAL	2	TRUE	1	0.398018196031417	3		773	791	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151890	108151890	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	68	548	0	ENST00000278616.4:c.3571A>G	p.Lys1191Glu	p.K1191E	ENST00000278616	NM_000051.3	1191	Aaa/Gaa	24/63	1	2	FACETS	0.885	0.774	1	0.885	0.774	1	CLONAL	1	TRUE	1	0.398018196031417	2		548	386	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161968	47161968	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	33	581	0	ENST00000409792.3:c.4158del	p.Asp1388IlefsTer6	p.D1388Ifs*6	ENST00000409792	NM_014159.6	1386	aaG/aa	3/21	0.216004739906995	0	FACETS	0.238	0.194	0.288			1	INDETERMINATE	1	TRUE	0	0.398018196031417	0		581	419	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026184	71026184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	76	601	0	ENST00000318789.4:c.1438G>A	p.Glu480Lys	p.E480K	ENST00000318789	NM_032682.5	480	Gaa/Aaa	17/21	1	2	FACETS	0.636	0.559	0.72	0.636	0.559	0.72	SUBCLONAL	1	TRUE	1	0.398018196031417	2		601	600	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840014	27840014	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	79	575	0	ENST00000328488.2:c.80G>T	p.Arg27Leu	p.R27L	ENST00000328488	NM_003533.2	27	cGc/cTc	1/1	0.297621609893481	3	FACETS	1	0.972	1	0.444	0.393	0.498	CLONAL	1	TRUE	0	0.398018196031417	3		575	357	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860673	151860673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	100	758	0	ENST00000262189.6:c.9989C>T	p.Pro3330Leu	p.P3330L	ENST00000262189	NM_170606.2	3330	cCc/cTc	43/59	1	2	FACETS	0.924	0.828	1	0.924	0.828	1	CLONAL	1	TRUE	1	0.398018196031417	2		758	544	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104673	69104673	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	285	816	0	ENST00000288368.4:c.4517C>T	p.Ser1506Phe	p.S1506F	ENST00000288368	NM_024870.2	1506	tCt/tTt	37/40	0.398018196031417	3	FACETS	0.92	0.867	0.975	0.92	0.867	0.975	CLONAL	2	TRUE	1	0.398018196031417	3		816	933	SUCCESS
AR	367	MSKCC	GRCh37	X	66765974	66765974	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	145	519	0	ENST00000374690.3:c.986G>C	p.Gly329Ala	p.G329A	ENST00000374690	NM_000044.3	329	gGc/gCc	1/8	0.103841428671572	2	FACETS	1	0.983	1			1	INDETERMINATE	2	TRUE	NA	0.398018196031417	2		519	302	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	127	636	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.186094893187667	3	FACETS	1	0.981	1	0.443	0.402	0.485	INDETERMINATE	1	FALSE	0	0.353323101267349	3		638	637	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0022760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	108	929	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.171330284892585	2	FACETS	1	0.976	1	0.637	0.574	0.702	INDETERMINATE	1	FALSE	0	0.353323101267349	2		930	480	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0022760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	61	560	1	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.23025306101207	2	FACETS	0.861	0.746	0.986	0.431	0.373	0.493	CLONAL	1	FALSE	0	0.353323101267349	2		561	401	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058705	47058706	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	57	655	0	ENST00000409792.3:c.7572dup	p.Lys2525Ter	p.K2525*	ENST00000409792	NM_014159.6	2524	-/T	21/21	0.225254892415964	3	FACETS	0.719	0.617	0.83	0.36	0.308	0.415	SUBCLONAL	1	FALSE	1	0.353323101267349	3		655	528	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951168	48951168	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	105	506	0	ENST00000267163.4:c.1330C>T	p.Gln444Ter	p.Q444*	ENST00000267163	NM_000321.2	444	Cag/Tag	13/27	0.353323101267349	3	FACETS	1	0.978	1	0.666	0.599	0.737	CLONAL	1	FALSE	1	0.353323101267349	3		506	525	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245511	41245511	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	69	859	0	ENST00000357654.3:c.2037G>T	p.Lys679Asn	p.K679N	ENST00000357654	NM_007294.3	679	aaG/aaT	10/23	0.345788741612729	3	FACETS	0.602	0.523	0.687	0.301	0.261	0.344	SUBCLONAL	1	FALSE	1	0.353323101267349	3		859	764	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212522485	212522485	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	27	522	0	ENST00000342788.4:c.1940A>G	p.His647Arg	p.H647R	ENST00000342788	NM_005235.2	647	cAt/cGt	16/28	0.345788741612729	3	FACETS	0.36	0.286	0.446	0.18	0.143	0.223	SUBCLONAL	1	FALSE	1	0.353323101267349	3		522	499	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435833	149435833	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	61	767	0	ENST00000286301.3:c.2391C>G	p.Phe797Leu	p.F797L	ENST00000286301	NM_005211.3	797	ttC/ttG	18/22	NA	2	FACETS	0.705	0.609	0.809			1	INDETERMINATE	1	FALSE	NA	0.353323101267349	2		767	490	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0022761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	734	550	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.641336773165102	3	FACETS	0.925	0.902	0.949	0.925	0.902	0.949	CLONAL	3	TRUE	0	0.641336773165102	3		552	1089	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138729528	NA	P-0022761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	414	899	0	ENST00000269305.4:c.523C>G	p.Arg175Gly	p.R175G	ENST00000269305	NM_001126112.2	175	Cgc/Ggc	5/11	0.574181319460322	1	FACETS	0.894	0.854	0.934	0.894	0.854	0.934	CLONAL	1	TRUE	0	0.641336773165102	1		899	981	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702657	52702657	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	225	469	1	ENST00000394830.3:c.241C>T	p.Gln81Ter	p.Q81*	ENST00000394830	NM_018313.4	81	Caa/Taa	4/30	0.574181319460322	1	FACETS	0.857	0.805	0.91	0.857	0.805	0.91	CLONAL	1	TRUE	0	0.641336773165102	1		470	556	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256138	123256138	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	230	884	0	ENST00000358487.5:c.1771A>C	p.Asn591His	p.N591H	ENST00000358487	NM_000141.4	591	Aac/Cac	13/18	0.301907517100956	1	FACETS	0.396	0.369	0.425	0.396	0.369	0.425	INDETERMINATE	1	TRUE	0	0.641336773165102	1		884	1229	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15960892	15960892	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	141	469	0	ENST00000268712.3:c.6328G>C	p.Val2110Leu	p.V2110L	ENST00000268712	NM_006311.3	2110	Gtc/Ctc	40/46	0.574181319460322	1	FACETS	0.482	0.44	0.525	0.482	0.44	0.525	SUBCLONAL	1	TRUE	0	0.641336773165102	1		469	620	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922658	56922658	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	311	818	0	ENST00000519728.1:c.1528C>G	p.Gln510Glu	p.Q510E	ENST00000519728	NM_002350.3	510	Cag/Gag	13/13	0.397521993168932	1	FACETS	0.629	0.593	0.665	0.629	0.593	0.665	SUBCLONAL	1	TRUE	0	0.641336773165102	1		818	1048	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	168	549	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.214894496061225	5	FACETS	1	0.946	1	0.774	0.714	0.836	CLONAL	3	TRUE	1	0.214894496061225	5		549	668	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0022762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	197	737	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.214894496061225	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.214894496061225	3		739	974	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061327	38061327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	215	920	2	ENST00000250448.2:c.662C>T	p.Ser221Leu	p.S221L	ENST00000250448	NM_004496.3	221	tCg/tTg	2/2	0.214894496061225	3	FACETS	0.942	0.875	1	0.942	0.875	1	CLONAL	2	TRUE	1	0.214894496061225	3		922	1176	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660154	12660154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	121	856	0	ENST00000251849.4:c.67G>A	p.Asp23Asn	p.D23N	ENST00000251849	NM_002880.3	23	Gat/Aat	2/17	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.214894496061225	2		856	930	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928074	178928074	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	265	761	0	ENST00000263967.3:c.1352G>T	p.Gly451Val	p.G451V	ENST00000263967	NM_006218.2	451	gGa/gTa	8/21	0.214894496061225	5	FACETS	0.975	0.914	1	0.731	0.685	0.779	CLONAL	3	TRUE	1	0.214894496061225	5		761	1115	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0022763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	356	792	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.457387076650853	3	FACETS	1	0.995	1	0.747	0.708	0.787	CLONAL	1	TRUE	1	0.494766771001706	3		792	1201	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782369	9782369	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	129	890	1	ENST00000377346.4:c.2302G>A	p.Ala768Thr	p.A768T	ENST00000377346	NM_005026.3	768	Gca/Aca	18/24	0.399590312724928	1	FACETS	0.342	0.309	0.377	0.342	0.309	0.377	SUBCLONAL	1	TRUE	0	0.494766771001706	1		891	1146	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992043	72992043	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	53	842	0	ENST00000268489.5:c.2002T>C	p.Cys668Arg	p.C668R	ENST00000268489	NM_006885.3	668	Tgt/Cgt	2/10	0.494766771001706	1	FACETS	0.166	0.14	0.193	0.166	0.14	0.193	SUBCLONAL	1	TRUE	0	0.494766771001706	1		842	974	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348743	89348743	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542863039	NA	P-0022763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1238	194	1131	0	ENST00000301030.4:c.4207G>A	p.Gly1403Arg	p.G1403R	ENST00000301030	NM_001256183.1	1403	Gga/Aga	9/13	0.494766771001706	1	FACETS	0.412	0.38	0.446	0.412	0.38	0.446	SUBCLONAL	1	TRUE	0	0.494766771001706	1		1131	1432	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	186	549	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.913	0.848	0.979	0.913	0.848	0.979	CLONAL	1	TRUE	1	0.701569752891451	2		549	581	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427086	49427133	+	inframe_deletion	In_Frame_Del	DEL	ATGCCCTGGGGCCCCTGGGGTGGTTGAGGGGACAGCTGCTGGACCAGG	ATGCCCTGGGGCCCCTGGGGTGGTTGAGGGGACAGCTGCTGGACCAGG	-	novel	NA	P-0022765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	26	663	0	ENST00000301067.7:c.11355_11402del	p.Val3787_Leu3802del	p.V3787_L3802del	ENST00000301067	NM_003482.3	3785	ctCCTGGTCCAGCAGCTGTCCCCTCAACCACCCCAGGGGCCCCAGGGCATg/ctg	39/54	1	2	FACETS	0.304	0.24	0.377	0.304	0.24	0.377	SUBCLONAL	1	FALSE	1	0.402928295106109	2		663	425	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	487	636	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.608875912785433	3	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.728265024731231	3		638	798	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0022766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	117	308	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.728265024731231	3	FACETS	0.981	0.89	1	0.49	0.445	0.538	CLONAL	1	TRUE	1	0.728265024731231	3		308	447	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45423058	45423058	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	118	448	0	ENST00000262160.6:c.70G>T	p.Gly24Trp	p.G24W	ENST00000262160	NM_005901.5	24	Ggg/Tgg	2/11	0.431108132840023	4	FACETS	0.898	0.812	0.988			1	INDETERMINATE	1	TRUE	NA	0.728265024731231	4		448	624	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730801	40730801	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	291	791	0	ENST00000373198.4:c.3734G>T	p.Gly1245Val	p.G1245V	ENST00000373198	NM_133170.3	1245	gGa/gTa	27/32	NA	2	FACETS	0.758	0.723	0.794			1	INDETERMINATE	2	TRUE	NA	0.728265024731231	2		791	527	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44527604	44527604	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0022766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	118	724	0	ENST00000291552.4:c.1A>G	p.Met1?	p.M1?	ENST00000291552	NM_006758.2	1	Atg/Gtg	1/8	0.728265024731231	3	FACETS	0.875	0.794	0.961	0.438	0.397	0.481	CLONAL	1	TRUE	1	0.728265024731231	3		724	505	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159022	143159022	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	137	430	0	ENST00000262992.4:c.831G>T	p.Leu277Phe	p.L277F	ENST00000262992	NM_001101669.1	277	ttG/ttT	10/24	0.728265024731231	3	FACETS	1	0.942	1	0.518	0.474	0.564	CLONAL	1	TRUE	1	0.728265024731231	3		430	495	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751131	128751131	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	151	847	0	ENST00000377970.2:c.668G>T	p.Cys223Phe	p.C223F	ENST00000377970	NM_002467.4	223	tGc/tTc	2/3	0.665290139461271	5	FACETS	0.976	0.892	1	0.325	0.297	0.355	CLONAL	1	TRUE	2	0.728265024731231	5		847	889	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0022767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	143	759	1	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.329489534309437	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.331825505856739	1		760	710	SUCCESS
H3C13	653604	MSKCC	GRCh37	1	149784833	149784833	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1285610295	NA	P-0022767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	33	270	0	ENST00000331491.1:c.404G>A	p.Arg135Gln	p.R135Q	ENST00000331491	NM_001123375.2	135	cGg/cAg	1/1	0.331825505856739	3	FACETS	0.574	0.467	0.694	0.287	0.233	0.347	SUBCLONAL	1	TRUE	1	0.331825505856739	3		270	404	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114116	115114117	+	splice_donor_variant	Splice_Site	INS	-	-	C	novel	NA	P-0022767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	97	544	0	ENST00000257566.3:c.1099+1dup		p.X367_splice	ENST00000257566	NM_016569.3	367			0.329489534309437	1	FACETS	0.874	0.781	0.972	0.874	0.781	0.972	CLONAL	1	TRUE	0	0.331825505856739	1		544	558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0022777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	144	826	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.398416433075473	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.398416433075473	1		828	574	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0022777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	345	501	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.398416433075473	4	FACETS	0.889	0.845	0.934	0.889	0.845	0.934	CLONAL	3	TRUE	1	0.398416433075473	4		501	908	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909921	100909921	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	207	753	0	ENST00000325455.5:c.2728T>C	p.Ser910Pro	p.S910P	ENST00000325455	NM_001202474.3	910	Tct/Cct	8/8	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.631473152341149	2		753	504	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945343	151945343	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	64	286	0	ENST00000262189.6:c.2176C>T	p.Gln726Ter	p.Q726*	ENST00000262189	NM_170606.2	726	Cag/Tag	14/59	0.208348957845469	4	FACETS	0.914	0.807	1	0.609	0.538	0.683	INDETERMINATE	2	FALSE	1	0.631473152341149	4		286	181	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	344	636	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.331540795754739	3	FACETS	0.875	0.83	0.92	0.875	0.83	0.92	CLONAL	2	TRUE	1	0.495110205284614	3		638	991	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0022783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	387	711	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.495110205284614	2	FACETS	0.882	0.842	0.922	0.882	0.842	0.922	CLONAL	2	TRUE	0	0.495110205284614	2		711	886	SUCCESS
APC	324	MSKCC	GRCh37	5	112170862	112170862	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1060503318	NA	P-0022783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	237	505	0	ENST00000257430.4:c.1958G>A	p.Arg653Lys	p.R653K	ENST00000257430	NM_000038.5	653	aGg/aAg	15/16	0.495110205284614	3	FACETS	0.84	0.788	0.893	0.84	0.788	0.893	CLONAL	2	TRUE	1	0.495110205284614	3		505	711	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725021	162725021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542584476	NA	P-0022783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	176	529	0	ENST00000367921.3:c.493C>T	p.Arg165Trp	p.R165W	ENST00000367921	NM_006182.2	165	Cgg/Tgg	6/18	0.495110205284614	3	FACETS	0.916	0.844	0.992	0.458	0.422	0.496	CLONAL	1	TRUE	1	0.495110205284614	3		529	968	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955094	55955094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	162	618	0	ENST00000263923.4:c.3451C>T	p.Pro1151Ser	p.P1151S	ENST00000263923	NM_002253.2	1151	Ccc/Tcc	26/30	1	2	FACETS	0.957	0.88	1	0.957	0.88	1	CLONAL	1	TRUE	1	0.495110205284614	2		618	684	SUCCESS
APC	324	MSKCC	GRCh37	5	112175546	112175547	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0022783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	97	392	0	ENST00000257430.4:c.4255_4256del	p.Ser1419ProfsTer3	p.S1419Pfs*3	ENST00000257430	NM_000038.5	1419	AGc/c	16/16	0.495110205284614	3	FACETS	0.873	0.78	0.971	0.436	0.39	0.486	CLONAL	1	TRUE	1	0.495110205284614	3		392	560	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611149	100611149	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	98	725	1	ENST00000308731.7:c.1457T>A	p.Leu486Gln	p.L486Q	ENST00000308731	NM_000061.2	486	cTg/cAg	15/19	1	2	FACETS	0.347	0.309	0.388	0.347	0.309	0.388	SUBCLONAL	1	TRUE	1	0.679545185547249	2		726	831	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611159	100611159	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	85	713	0	ENST00000308731.7:c.1447C>A	p.Leu483Met	p.L483M	ENST00000308731	NM_000061.2	483	Ctg/Atg	15/19	1	2	FACETS	0.315	0.278	0.355	0.315	0.278	0.355	SUBCLONAL	1	TRUE	1	0.679545185547249	2		713	794	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023501	27023502	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	60	637	0	ENST00000324856.7:c.608dup	p.His203GlnfsTer197	p.H203Qfs*197	ENST00000324856	NM_006015.4	203	cac/cAac	1/20	1	2	FACETS	0.189	0.163	0.219	0.189	0.163	0.219	SUBCLONAL	1	TRUE	1	0.838851637676711	2		637	755	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633647	69633647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	53	40	0	ENST00000334134.2:c.55G>A	p.Ala19Thr	p.A19T	ENST00000334134	NM_005247.2	19	Gcg/Acg	1/3	1	2	FACETS	0.79	0.713	0.862	1	0.979	1	SUBCLONAL	2	TRUE	1	0.838851637676711	2		40	80	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32182013	32182013	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141422504	NA	P-0022785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	428	873	3	ENST00000375023.3:c.2041G>A	p.Val681Met	p.V681M	ENST00000375023	NM_004557.3	681	Gtg/Atg	13/30	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.838851637676711	2		876	950	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	156	636	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.157779519643977	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.18	2		638	749	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0022786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	103	953	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.18	2		955	1074	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366802	40366802	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	66	643	0	ENST00000397332.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000397332	NM_001033082.2	132	cGg/cTg	2/3	1	2	FACETS	0.987	0.856	1	0.987	0.856	1	CLONAL	1	TRUE	1	0.18	2		643	743	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971011	21971012	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCA	novel	NA	P-0022786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	66	665	0	ENST00000304494.5:c.344_346dup	p.Val115dup	p.V115dup	ENST00000304494	NM_000077.4	115	gac/gTGGac	2/3	0.3	1	FACETS	0.88	0.763	1	0.88	0.763	1	CLONAL	1	TRUE	0	0.18	1		665	758	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0022787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	220	1009	6	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	0.373576050829495	2	FACETS	0.836	0.783	0.89	0.836	0.783	0.89	CLONAL	2	TRUE	0	0.433412105524127	2		1015	607	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871758	12871758	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0022787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	80	266	0	ENST00000228872.4:c.476-1G>T		p.X159_splice	ENST00000228872	NM_004064.3	159			0.433412105524127	3	FACETS	1	0.976	1	0.706	0.627	0.789	CLONAL	1	TRUE	1	0.433412105524127	3		266	318	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873711	35873711	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	164	695	3	ENST00000303115.3:c.667A>G	p.Ser223Gly	p.S223G	ENST00000303115	NM_002185.3	223	Agt/Ggt	5/8	0.337216841360571	4	FACETS	0.868	0.8	0.938			1	CLONAL	2	TRUE	NA	0.433412105524127	4		698	625	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170834762	170834762	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777550167	NA	P-0022787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	65	689	2	ENST00000296930.5:c.830G>A	p.Arg277Gln	p.R277Q	ENST00000296930	NM_002520.6	277	cGg/cAg	10/11	0.119530478140521	3	FACETS	0.672	0.583	0.768	0.224	0.194	0.256	INDETERMINATE	1	TRUE	0	0.433412105524127	3		691	543	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637890	176637890	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	221	863	2	ENST00000439151.2:c.2490T>G	p.Ser830Arg	p.S830R	ENST00000439151	NM_022455.4	830	agT/agG	5/23	0.119530478140521	3	FACETS	0.863	0.806	0.921	0.575	0.537	0.614	INDETERMINATE	2	TRUE	0	0.433412105524127	3		865	719	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069621	69069622	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0022787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	90	960	2	ENST00000288368.4:c.4296_4297delinsAT	p.Ile1433Leu	p.I1433L	ENST00000288368	NM_024870.2	1432	caGAta/caATta	35/40	0.433412105524127	3	FACETS	0.589	0.522	0.661	0.294	0.261	0.331	SUBCLONAL	1	TRUE	1	0.433412105524127	3		962	858	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044416	5044416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147483622	NA	P-0022787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	188	859	1	ENST00000381652.3:c.364C>T	p.Arg122Cys	p.R122C	ENST00000381652	NM_004972.3	122	Cgt/Tgt	5/25	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.433412105524127	2		860	708	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412718	139412718	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	29	978	1	ENST00000277541.6:c.1126T>C	p.Cys376Arg	p.C376R	ENST00000277541	NM_017617.3	376	Tgc/Cgc	7/34	0.292725003007027	1	FACETS	0.182	0.146	0.224	0.182	0.146	0.224	SUBCLONAL	1	TRUE	0	0.433412105524127	1		979	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0022788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	373	826	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.583147961585575	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.644546455291556	1		828	642	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481417	140481417	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913348	NA	P-0022788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	41	670	2	ENST00000288602.6:c.1391G>T	p.Gly464Val	p.G464V	ENST00000288602	NM_004333.4	464	gGa/gTa	11/18	0.168747676224225	2	FACETS	0.358	0.299	0.424	0.179	0.149	0.212	INDETERMINATE	1	TRUE	0	0.644546455291556	2		672	355	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142990	30142990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316424431	NA	P-0022788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1379	173	1072	1	ENST00000389048.3:c.536G>A	p.Arg179His	p.R179H	ENST00000389048	NM_004304.4	179	cGc/cAc	1/29	0.514130948739592	4	FACETS	0.569	0.522	0.618			1	SUBCLONAL	1	TRUE	NA	0.644546455291556	4		1073	1552	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809789	36809789	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	113	978	0	ENST00000373129.3:c.816C>G	p.Phe272Leu	p.F272L	ENST00000373129	NM_032017.1	272	ttC/ttG	9/12	0.289038955545519	4	FACETS	0.458	0.41	0.508			1	INDETERMINATE	1	TRUE	NA	0.644546455291556	4		978	1260	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204670	108204684	+	inframe_deletion	In_Frame_Del	DEL	TTGTTGTCCCTACTA	TTGTTGTCCCTACTA	-	novel	NA	P-0022788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	57	463	0	ENST00000278616.4:c.7986_8000del	p.Val2663_Met2667del	p.V2663_M2667del	ENST00000278616	NM_000051.3	2662	gTTGTTGTCCCTACTAtg/gtg	54/63	0.19354425066328	2	FACETS	0.779	0.677	0.888	0.39	0.338	0.444	INDETERMINATE	1	TRUE	0	0.644546455291556	2		463	227	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56474100	56474100	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	155	844	0	ENST00000267101.3:c.16G>T	p.Ala6Ser	p.A6S	ENST00000267101	NM_001982.3	6	Gct/Tct	1/28	0.38574106155816	3	FACETS	0.765	0.701	0.832	0.383	0.35	0.416	INDETERMINATE	1	TRUE	1	0.644546455291556	3		844	831	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332739	153332739	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	159	756	0	ENST00000281708.4:c.217C>T	p.Gln73Ter	p.Q73*	ENST00000281708	NM_033632.3	73	Cag/Tag	2/12	0.498165041876488	2	FACETS	1	0.991	1	0.741	0.69	0.791	CLONAL	1	TRUE	0	0.644546455291556	2		756	333	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168816	56168816	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	51	600	3	ENST00000399503.3:c.1670C>T	p.Ala557Val	p.A557V	ENST00000399503	NM_005921.1	557	gCt/gTt	9/20	0.491749337628295	2	FACETS	0.528	0.451	0.61	0.264	0.225	0.305	SUBCLONAL	1	TRUE	0	0.644546455291556	2		603	300	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120567	94120567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	133	662	0	ENST00000369303.4:c.484G>A	p.Glu162Lys	p.E162K	ENST00000369303	NM_004440.3	162	Gaa/Aaa	3/17	0.198101757367945	5	FACETS	0.902	0.825	0.981	0.601	0.55	0.654	INDETERMINATE	2	TRUE	2	0.644546455291556	5		662	450	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341821	8341821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1250220732	NA	P-0022788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	92	948	2	ENST00000356435.5:c.4819G>A	p.Asp1607Asn	p.D1607N	ENST00000356435		1607	Gat/Aat	29/35	0.563023356507779	1	FACETS	0.508	0.454	0.564	0.508	0.454	0.564	SUBCLONAL	1	TRUE	0	0.644546455291556	1		950	381	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748308	41748308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	66	913	0	ENST00000226382.2:c.461G>A	p.Arg154His	p.R154H	ENST00000226382	NM_003924.3	154	cGc/cAc	3/3	0.562852291230495	3	FACETS	0.462	0.401	0.528	0.231	0.2	0.264	SUBCLONAL	1	TRUE	1	0.606528474368203	3		913	614	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0022790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	264	859	2	ENST00000269305.4:c.809_810dup	p.Glu271LeufsTer75	p.E271Lfs*75	ENST00000269305	NM_001126112.2	270	-/TT	8/11	0.490817695711396	2	FACETS	0.793	0.751	0.835	0.793	0.751	0.835	SUBCLONAL	2	TRUE	0	0.606528474368203	2		861	549	SUCCESS
APC	324	MSKCC	GRCh37	5	112175349	112175350	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0022790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	225	426	0	ENST00000257430.4:c.4058_4059del	p.Glu1353ValfsTer21	p.E1353Vfs*21	ENST00000257430	NM_000038.5	1353	gAA/g	16/16	0.606528474368203	3	FACETS	0.878	0.834	0.921	0.878	0.834	0.921	CLONAL	3	TRUE	0	0.606528474368203	3		426	367	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636723	8636723	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	90	478	0	ENST00000356435.5:c.186G>C	p.Lys62Asn	p.K62N	ENST00000356435		62	aaG/aaC	2/35	0.430979359431558	3	FACETS	1	0.921	1	0.518	0.463	0.576	CLONAL	1	TRUE	1	0.606528474368203	3		478	373	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	8	549	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.96	0.621	1	0.96	0.621	1	CLONAL	1	TRUE	1	0.14	2		549	119	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0022792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	10	731	2	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.835	0.567	1	0.835	0.567	1	CLONAL	1	TRUE	1	0.14	2		733	171	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0022792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	12	554	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	1	0.727	1	1	0.727	1	CLONAL	1	TRUE	1	0.14	2		554	166	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309565	30309565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	16	752	2	ENST00000307677.4:c.457G>A	p.Glu153Lys	p.E153K	ENST00000307677	NM_138578.1	153	Gaa/Aaa	2/3	1	2	FACETS	0.721	0.532	0.947	0.721	0.532	0.947	CLONAL	1	TRUE	1	0.14	2		754	317	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	23	636	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.13282354363682	1	FACETS	0.354	0.275	0.446	0.354	0.275	0.446	SUBCLONAL	1	TRUE	0	0.2	1		638	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579357	7579358	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTTT	novel	NA	P-0022793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	28	780	0	ENST00000269305.4:c.329_330insAAAG	p.Leu111LysfsTer39	p.L111Kfs*39	ENST00000269305	NM_001126112.2	110	cgt/cgAAAGt	4/11	1	2	FACETS	0.507	0.404	0.625	0.507	0.404	0.625	SUBCLONAL	1	TRUE	1	0.2	2		780	552	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126409	5126409	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs371455894	NA	P-0022793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	27	503	0	ENST00000381652.3:c.3254A>G	p.Asn1085Ser	p.N1085S	ENST00000381652	NM_004972.3	1085	aAt/aGt	24/25	1	2	FACETS	0.523	0.415	0.647	0.523	0.415	0.647	SUBCLONAL	1	TRUE	1	0.2	2		503	516	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	39	490	0	ENST00000304494.5:c.341C>G	p.Pro114Arg	p.P114R	ENST00000304494	NM_000077.4	114	cCc/cGc	2/3	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.2	2		490	349	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0022797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	88	652	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.793	0.704	0.889	0.793	0.704	0.889	SUBCLONAL	1	TRUE	1	0.372886073159708	2		652	595	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0022797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	129	289	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.323157960329377	2	FACETS	0.994	0.913	1	0.994	0.913	1	CLONAL	2	TRUE	0	0.372886073159708	2		289	348	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37092047	37092047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs566928243	NA	P-0022797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	39	713	0	ENST00000231790.2:c.2174G>A	p.Arg725His	p.R725H	ENST00000231790	NM_000249.3	725	cGc/cAc	19/19	1	2	FACETS	0.337	0.279	0.403	0.337	0.279	0.403	SUBCLONAL	1	TRUE	1	0.372886073159708	2		713	620	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577144	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs879253942	NA	P-0022797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	251	721	0	ENST00000269305.4:c.794T>C	p.Leu265Pro	p.L265P	ENST00000269305	NM_001126112.2	265	cTg/cCg	8/11	0.363005128664224	2	FACETS	0.943	0.886	1	0.943	0.886	1	CLONAL	2	TRUE	0	0.372886073159708	2		721	714	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385182	41385182	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367872006	NA	P-0022797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	240	814	0	ENST00000373198.4:c.779G>A	p.Arg260Gln	p.R260Q	ENST00000373198	NM_133170.3	260	cGg/cAg	6/32	0.372886073159708	5	FACETS	0.905	0.845	0.967	0.603	0.563	0.645	CLONAL	2	TRUE	2	0.372886073159708	5		814	1109	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972009	55972009	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	53	581	3	ENST00000263923.4:c.1635C>A	p.Phe545Leu	p.F545L	ENST00000263923	NM_002253.2	545	ttC/ttA	12/30	0.323157960329377	2	FACETS	0.496	0.423	0.577	0.248	0.211	0.289	SUBCLONAL	1	TRUE	0	0.372886073159708	2		584	573	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658563	206658563	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	233	647	0	ENST00000367120.3:c.1536T>G	p.Asn512Lys	p.N512K	ENST00000367120	NM_014002.3	512	aaT/aaG	15/22	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.543393853599652	2		647	677	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061214	38061214	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	100	598	0	ENST00000250448.2:c.775T>A	p.Tyr259Asn	p.Y259N	ENST00000250448	NM_004496.3	259	Tac/Aac	2/2	0.25716018834051	6	FACETS	0.86	0.767	0.959			1	INDETERMINATE	1	TRUE	NA	0.543393853599652	6		598	893	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618626	37618627	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	303	784	0	ENST00000447079.4:c.302_303insT	p.Ser102IlefsTer25	p.S102Ifs*25	ENST00000447079	NM_015083.1	101	gga/ggTa	1/14	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.543393853599652	2		784	852	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657501	37657501	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0022798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	232	579	0	ENST00000447079.4:c.2420-2A>G		p.X807_splice	ENST00000447079	NM_015083.1	807			1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.543393853599652	2		579	721	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	80	636	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.938	0.83	1	0.938	0.83	1	CLONAL	1	TRUE	1	0.386695759506308	2		638	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0022801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	170	737	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.386695759506308	1	FACETS	0.986	0.91	1	0.986	0.91	1	CLONAL	1	TRUE	0	0.386695759506308	1		739	719	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324674	31324674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11546719	NA	P-0022801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	31	465	3	ENST00000412585.2:c.134G>A	p.Arg45His	p.R45H	ENST00000412585	NM_005514.6	45	cGc/cAc	2/8	1	2	FACETS	0.301	0.243	0.368	0.301	0.243	0.368	SUBCLONAL	1	TRUE	1	0.386695759506308	2		468	532	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447333	49447333	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	219	833	2	ENST00000301067.7:c.765C>A	p.Cys255Ter	p.C255*	ENST00000301067	NM_003482.3	255	tgC/tgA	6/54	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.386695759506308	2		835	1005	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	47	549	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.766	0.646	0.899	0.766	0.646	0.899	SUBCLONAL	1	TRUE	1	0.211610267518002	2		549	580	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405960	157405960	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	58	708	0	ENST00000346085.5:c.2204del	p.Pro735HisfsTer10	p.P735Hfs*10	ENST00000346085	NM_020732.3	734	ggC/gg	6/20	1	2	FACETS	0.702	0.602	0.812	0.702	0.602	0.812	SUBCLONAL	1	TRUE	1	0.211610267518002	2		708	781	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	25	355	1	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.498	0.392	0.622	0.498	0.392	0.622	SUBCLONAL	1	TRUE	1	0.211610267518002	2		356	474	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	88	482	1	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.211610267518002	2		483	595	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913559	32913559	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359479	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	76	710	3	ENST00000380152.3:c.5073del	p.Lys1691AsnfsTer15	p.K1691Nfs*15	ENST00000380152		1689	gcA/gc	11/27	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.211610267518002	2		713	551	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	30	514	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.569	0.458	0.696	0.569	0.458	0.696	SUBCLONAL	1	TRUE	1	0.211610267518002	2		515	498	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	78	654	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.211610267518002	2		655	566	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979987	7979987	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746723399	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	51	774	2	ENST00000319144.4:c.1350del	p.Leu451SerfsTer16	p.L451Sfs*16	ENST00000319144	NM_001139.2	450	ggG/gg	10/15	1	2	FACETS	0.503	0.426	0.588	0.503	0.426	0.588	SUBCLONAL	1	TRUE	1	0.211610267518002	2		776	959	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	35	572	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.519	0.424	0.626	0.519	0.424	0.626	SUBCLONAL	1	TRUE	1	0.211610267518002	2		573	637	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356326	70356326	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	74	751	1	ENST00000374080.3:c.5221C>T	p.Pro1741Ser	p.P1741S	ENST00000374080		1741	Cca/Tca	37/45	1	2	FACETS	0.769	0.671	0.874	0.769	0.671	0.874	SUBCLONAL	1	TRUE	1	0.211610267518002	2		752	910	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	39	451	0	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	0.554	0.458	0.662	0.554	0.458	0.662	SUBCLONAL	1	TRUE	1	0.211610267518002	2		451	665	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874314	76874314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	70	980	1	ENST00000373344.5:c.5408G>A	p.Arg1803His	p.R1803H	ENST00000373344	NM_000489.3	1803	cGt/cAt	21/35	1	2	FACETS	0.817	0.711	0.932	0.817	0.711	0.932	CLONAL	1	TRUE	1	0.211610267518002	2		981	810	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204842	128204842	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs768767517	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	81	1000	1	ENST00000341105.2:c.599del	p.Gly200ValfsTer18	p.G200Vfs*18	ENST00000341105	NM_032638.4	200	gGt/gt	3/6	1	2	FACETS	0.63	0.553	0.713	0.63	0.553	0.713	SUBCLONAL	1	TRUE	1	0.211610267518002	2		1001	1216	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	87	588	0	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	0.211610267518002	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.211610267518002	1		588	632	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445005	89445005	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112239794	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	104	730	2	ENST00000336596.2:c.1325C>T	p.Thr442Met	p.T442M	ENST00000336596	NM_005233.5	442	aCg/aTg	6/17	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.211610267518002	2		732	824	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074255	8074255	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	35	597	0	ENST00000377482.5:c.404del	p.Asn135ThrfsTer40	p.N135Tfs*40	ENST00000377482	NM_018948.3	135	aAc/ac	4/4	0.211610267518002	1	FACETS	0.424	0.347	0.512	0.424	0.347	0.512	SUBCLONAL	1	TRUE	0	0.211610267518002	1		597	697	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588798	52588798	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1559827261	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	52	646	0	ENST00000394830.3:c.4230del	p.Pro1411LeufsTer21	p.P1411Lfs*21	ENST00000394830	NM_018313.4	1410	ggG/gg	27/30	0.211610267518002	1	FACETS	0.573	0.487	0.668	0.573	0.487	0.668	SUBCLONAL	1	TRUE	0	0.211610267518002	1		646	767	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682400	52682400	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	54	773	0	ENST00000394830.3:c.773del	p.Asn258MetfsTer25	p.N258Mfs*25	ENST00000394830	NM_018313.4	258	aAt/at	8/30	0.211610267518002	1	FACETS	0.694	0.592	0.806	0.694	0.592	0.806	SUBCLONAL	1	TRUE	0	0.211610267518002	1		773	658	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202351	138202351	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	104	681	0	ENST00000237289.4:c.2274del	p.Lys759SerfsTer57	p.K759Sfs*57	ENST00000237289	NM_001270507.1	756	gaC/ga	9/9	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.211610267518002	2		681	823	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821614	72821614	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1462530890	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	12	39	0	ENST00000268489.5:c.10561G>A	p.Gly3521Ser	p.G3521S	ENST00000268489	NM_006885.3	3521	Ggc/Agc	10/10	1	2	FACETS	1	0.82	1	1	0.82	1	CLONAL	1	TRUE	1	0.211610267518002	2		39	92	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372238	55372238	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	53	478	0	ENST00000297316.4:c.928G>A	p.Gly310Ser	p.G310S	ENST00000297316	NM_022454.3	310	Ggc/Agc	2/2	0.211610267518002	3	FACETS	0.92	0.784	1	0.46	0.392	0.535	CLONAL	1	TRUE	1	0.211610267518002	3		478	602	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	75	783	4	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	0.211610267518002	3	FACETS	0.782	0.683	0.888	0.391	0.341	0.444	SUBCLONAL	1	TRUE	1	0.211610267518002	3		787	1003	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46602913	46602913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766854881	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	62	817	1	ENST00000263734.3:c.971C>T	p.Thr324Met	p.T324M	ENST00000263734	NM_001430.4	324	aCg/aTg	8/16	1	2	FACETS	0.6	0.517	0.692	0.6	0.517	0.692	SUBCLONAL	1	TRUE	1	0.211610267518002	2		818	976	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201815	66201815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764665078	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	49	673	2	ENST00000273854.3:c.2687G>A	p.Arg896His	p.R896H	ENST00000273854	NM_004439.5	896	cGt/cAt	16/18	1	2	FACETS	0.549	0.463	0.643	0.549	0.463	0.643	SUBCLONAL	1	TRUE	1	0.211610267518002	2		675	844	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431746	49431748	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs748239185	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	61	746	0	ENST00000301067.7:c.9391_9393del	p.Pro3131del	p.P3131del	ENST00000301067	NM_003482.3	3131	CCT/-	34/54	0.211610267518002	3	FACETS	0.673	0.578	0.776	0.336	0.289	0.388	SUBCLONAL	1	TRUE	1	0.211610267518002	3		746	948	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233751	233751	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199844384	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	68	744	3	ENST00000264932.6:c.1055G>A	p.Arg352Gln	p.R352Q	ENST00000264932	NM_004168.2	352	cGa/cAa	8/15	1	2	FACETS	0.799	0.694	0.914	0.799	0.694	0.914	CLONAL	1	TRUE	1	0.211610267518002	2		747	804	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17349144	17349144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786203251	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	59	763	1	ENST00000375499.3:c.724C>T	p.Arg242Cys	p.R242C	ENST00000375499	NM_003000.2	242	Cgc/Tgc	7/8	0.211610267518002	1	FACETS	0.58	0.498	0.671	0.58	0.498	0.671	SUBCLONAL	1	TRUE	0	0.211610267518002	1		764	859	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803535	43803535	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	53	765	0	ENST00000372470.3:c.16C>A	p.Leu6Ile	p.L6I	ENST00000372470	NM_005373.2	6	Ctc/Atc	1/12	0.0927637564437358	3	FACETS	0.586	0.498	0.683			1	INDETERMINATE	1	TRUE	NA	0.211610267518002	3		765	946	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531777	46531779	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	65	859	0	ENST00000262741.5:c.568_570del	p.Glu190del	p.E190del	ENST00000262741	NM_003629.3	190	GAG/-	5/10	0.0927637564437358	3	FACETS	0.834	0.721	0.956			1	INDETERMINATE	1	TRUE	NA	0.211610267518002	3		859	815	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280096	115280096	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	77	814	0	ENST00000438362.2:c.536A>T	p.Asn179Ile	p.N179I	ENST00000438362	NM_001242891.1	179	aAt/aTt	5/20	1	2	FACETS	0.759	0.665	0.861	0.759	0.665	0.861	SUBCLONAL	1	TRUE	1	0.211610267518002	2		814	959	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102198790	102198790	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	52	622	0	ENST00000263464.3:c.961T>C	p.Tyr321His	p.Y321H	ENST00000263464	NM_001165.4	321	Tac/Cac	4/9	1	2	FACETS	0.858	0.73	0.998	0.858	0.73	0.998	CLONAL	1	TRUE	1	0.211610267518002	2		622	573	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115544	108115544	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	55	726	0	ENST00000278616.4:c.692A>T	p.His231Leu	p.H231L	ENST00000278616	NM_000051.3	231	cAt/cTt	7/63	1	2	FACETS	0.909	0.777	1	0.909	0.777	1	CLONAL	1	TRUE	1	0.211610267518002	2		726	572	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864655	57864655	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	91	944	0	ENST00000228682.2:c.2132C>T	p.Thr711Ile	p.T711I	ENST00000228682	NM_005269.2	711	aCc/aTc	12/12	0.211610267518002	3	FACETS	0.763	0.675	0.858	0.382	0.337	0.429	SUBCLONAL	1	TRUE	1	0.211610267518002	3		944	1246	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856056	111856056	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs574829930	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	58	612	0	ENST00000341259.2:c.107C>T	p.Ala36Val	p.A36V	ENST00000341259	NM_005475.2	36	gCg/gTg	2/8	0.210496522793312	2	FACETS	0.735	0.63	0.849	0.367	0.315	0.425	SUBCLONAL	1	TRUE	0	0.211610267518002	2		612	746	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95596469	95596469	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	39	710	0	ENST00000393063.1:c.499T>G	p.Ser167Ala	p.S167A	ENST00000393063	NM_030621.3	167	Tca/Gca	6/28	1	2	FACETS	0.627	0.519	0.748	0.627	0.519	0.748	SUBCLONAL	1	TRUE	1	0.211610267518002	2		710	588	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239591	105239591	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	49	534	0	ENST00000349310.3:c.954del	p.Glu319ArgfsTer24	p.E319Rfs*24	ENST00000349310	NM_001014432.1	318	ccC/cc	11/15	1	2	FACETS	0.661	0.558	0.774	0.661	0.558	0.774	SUBCLONAL	1	TRUE	1	0.211610267518002	2		534	701	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729187	66729187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	76	896	3	ENST00000307102.5:c.395C>T	p.Ala132Val	p.A132V	ENST00000307102	NM_002755.3	132	gCg/gTg	3/11	1	2	FACETS	0.665	0.581	0.756	0.665	0.581	0.756	SUBCLONAL	1	TRUE	1	0.211610267518002	2		899	1080	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639237	3639237	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760497928	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	64	887	0	ENST00000294008.3:c.4402C>T	p.Arg1468Cys	p.R1468C	ENST00000294008	NM_032444.2	1468	Cgc/Tgc	12/15	1	2	FACETS	0.507	0.438	0.584	0.507	0.438	0.584	SUBCLONAL	1	TRUE	1	0.211610267518002	2		887	1192	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781210	3781210	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	59	783	0	ENST00000262367.5:c.5155C>T	p.His1719Tyr	p.H1719Y	ENST00000262367	NM_004380.2	1719	Cac/Tac	30/31	1	2	FACETS	0.531	0.455	0.614	0.531	0.455	0.614	SUBCLONAL	1	TRUE	1	0.211610267518002	2		783	1051	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807815	3807815	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	100	558	0	ENST00000262367.5:c.3604C>T	p.Arg1202Cys	p.R1202C	ENST00000262367	NM_004380.2	1202	Cgc/Tgc	18/31	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.211610267518002	2		558	677	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817765	3817765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746263232	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	65	905	3	ENST00000262367.5:c.3206G>A	p.Gly1069Asp	p.G1069D	ENST00000262367	NM_004380.2	1069	gGc/gAc	16/31	1	2	FACETS	0.589	0.509	0.676	0.589	0.509	0.676	SUBCLONAL	1	TRUE	1	0.211610267518002	2		908	1043	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032303	10032303	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	52	733	0	ENST00000330684.3:c.520A>T	p.Thr174Ser	p.T174S	ENST00000330684	NM_001134407.1	174	Acc/Tcc	3/13	1	2	FACETS	0.549	0.465	0.64	0.549	0.465	0.64	SUBCLONAL	1	TRUE	1	0.211610267518002	2		733	896	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846083	68846083	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	96	960	1	ENST00000261769.5:c.1054G>A	p.Gly352Ser	p.G352S	ENST00000261769	NM_004360.3	352	Ggt/Agt	8/16	1	2	FACETS	0.747	0.664	0.837	0.747	0.664	0.837	SUBCLONAL	1	TRUE	1	0.211610267518002	2		961	1214	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853283	68853283	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	76	810	0	ENST00000261769.5:c.1666del	p.Val556Ter	p.V556*	ENST00000261769	NM_004360.3	556	Gtg/tg	11/16	1	2	FACETS	0.728	0.637	0.826	0.728	0.637	0.826	SUBCLONAL	1	TRUE	1	0.211610267518002	2		810	987	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054628	13054628	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1159150142	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	49	512	0	ENST00000316448.5:c.1155G>T	p.Lys385Asn	p.K385N	ENST00000316448	NM_004343.3	385	aaG/aaT	9/9	1	2	FACETS	0.673	0.569	0.788	0.673	0.569	0.788	SUBCLONAL	1	TRUE	1	0.211610267518002	2		512	688	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211109	36211109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756303519	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	87	998	1	ENST00000222270.7:c.860G>A	p.Arg287His	p.R287H	ENST00000222270	NM_014727.1	287	cGt/cAt	3/37	1	2	FACETS	0.635	0.56	0.716	0.635	0.56	0.716	SUBCLONAL	1	TRUE	1	0.211610267518002	2		999	1295	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641411	47641411	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1114167887	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	94	628	0	ENST00000233146.2:c.796G>A	p.Ala266Thr	p.A266T	ENST00000233146	NM_000251.2	266	Gca/Aca	5/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.211610267518002	2		628	665	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022791	31022791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	65	650	1	ENST00000375687.4:c.2276G>A	p.Cys759Tyr	p.C759Y	ENST00000375687	NM_015338.5	759	tGc/tAc	13/13	1	2	FACETS	0.733	0.634	0.841	0.733	0.634	0.841	SUBCLONAL	1	TRUE	1	0.211610267518002	2		651	838	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877351	40877351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	67	615	0	ENST00000373198.4:c.2345G>A	p.Gly782Asp	p.G782D	ENST00000373198	NM_133170.3	782	gGc/gAc	15/32	1	2	FACETS	0.799	0.693	0.914	0.799	0.693	0.914	CLONAL	1	TRUE	1	0.211610267518002	2		615	793	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637581	52637581	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	55	868	0	ENST00000394830.3:c.2735A>C	p.Lys912Thr	p.K912T	ENST00000394830	NM_018313.4	912	aAa/aCa	18/30	0.211610267518002	1	FACETS	0.62	0.529	0.719	0.62	0.529	0.719	SUBCLONAL	1	TRUE	0	0.211610267518002	1		868	750	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593392	55593392	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	50	560	0	ENST00000288135.5:c.1549C>A	p.His517Asn	p.H517N	ENST00000288135	NM_000222.2	517	Cat/Aat	10/21	1	2	FACETS	0.845	0.717	0.987	0.845	0.717	0.987	CLONAL	1	TRUE	1	0.211610267518002	2		560	559	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201788	66201788	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	57	723	0	ENST00000273854.3:c.2714C>A	p.Ala905Asp	p.A905D	ENST00000273854	NM_004439.5	905	gCt/gAt	16/18	1	2	FACETS	0.586	0.501	0.679	0.586	0.501	0.679	SUBCLONAL	1	TRUE	1	0.211610267518002	2		723	920	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441611	6441611	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	62	656	0	ENST00000356142.4:c.458T>C	p.Leu153Pro	p.L153P	ENST00000356142	NM_018890.3	153	cTg/cCg	6/7	0.211610267518002	3	FACETS	0.784	0.676	0.903	0.392	0.338	0.452	CLONAL	1	TRUE	1	0.211610267518002	3		656	826	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90996774	90996774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881859	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	69	629	1	ENST00000265433.3:c.16C>T	p.Pro6Ser	p.P6S	ENST00000265433	NM_002485.4	6	Ccc/Tcc	1/16	0.211610267518002	3	FACETS	0.705	0.612	0.806	0.352	0.306	0.403	SUBCLONAL	1	TRUE	1	0.211610267518002	3		630	1023	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738997	145738997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	71	758	0	ENST00000428558.2:c.2158C>T	p.Leu720Phe	p.L720F	ENST00000428558	NM_004260.3	720	Ctc/Ttc	13/22	0.211610267518002	3	FACETS	0.771	0.671	0.879	0.385	0.335	0.44	SUBCLONAL	1	TRUE	1	0.211610267518002	3		758	963	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405688	139405688	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	64	837	0	ENST00000277541.6:c.2503C>A	p.Pro835Thr	p.P835T	ENST00000277541	NM_017617.3	835	Ccc/Acc	16/34	1	2	FACETS	0.512	0.441	0.589	0.512	0.441	0.589	SUBCLONAL	1	TRUE	1	0.211610267518002	2		837	1182	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44733169	44733169	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	62	638	1	ENST00000377967.4:c.162-1G>A		p.X54_splice	ENST00000377967	NM_021140.2	54			1	2	FACETS	0.58	0.499	0.669	0.58	0.499	0.669	SUBCLONAL	1	TRUE	1	0.211610267518002	2		639	1010	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424387	47424387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1275641708	NA	P-0022803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	59	665	4	ENST00000377045.4:c.307C>T	p.Arg103Trp	p.R103W	ENST00000377045	NM_001654.4	103	Cgg/Tgg	5/16	1	2	FACETS	0.589	0.505	0.681	0.589	0.505	0.681	SUBCLONAL	1	TRUE	1	0.211610267518002	2		669	947	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0022806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	74	649	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.9	0.787	1	0.9	0.787	1	CLONAL	1	FALSE	1	0.188316016193245	2		649	873	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106710	27106710	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	66	725	1	ENST00000324856.7:c.6324del	p.Asn2109MetfsTer26	p.N2109Mfs*26	ENST00000324856	NM_006015.4	2107	ggC/gg	20/20	1	2	FACETS	0.881	0.763	1	0.881	0.763	1	CLONAL	1	FALSE	1	0.188316016193245	2		726	796	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047232	77047232	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs747098916	NA	P-0022806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	80	681	1	ENST00000356341.3:c.1312C>T	p.Arg438Ter	p.R438*	ENST00000356341	NM_002576.4	438	Cga/Tga	13/15	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	FALSE	1	0.188316016193245	2		682	828	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896455	28896455	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	72	574	1	ENST00000282397.4:c.2995C>A	p.Leu999Met	p.L999M	ENST00000282397	NM_002019.4	999	Ctg/Atg	22/30	0.188316016193245	1	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	FALSE	0	0.188316016193245	1		575	659	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28971157	28971157	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	54	627	0	ENST00000282397.4:c.1600A>T	p.Ile534Phe	p.I534F	ENST00000282397	NM_002019.4	534	Att/Ttt	12/30	0.188316016193245	1	FACETS	0.833	0.71	0.966	0.833	0.71	0.966	CLONAL	1	FALSE	0	0.188316016193245	1		627	624	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641155	23641155	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs757892044	NA	P-0022806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	96	790	0	ENST00000261584.4:c.2320A>G	p.Lys774Glu	p.K774E	ENST00000261584	NM_024675.3	774	Aaa/Gaa	5/13	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	1	0.188316016193245	2		790	936	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219391	1219391	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	76	769	0	ENST00000326873.7:c.443T>C	p.Phe148Ser	p.F148S	ENST00000326873	NM_000455.4	148	tTc/tCc	3/10	0.188316016193245	1	FACETS	0.934	0.818	1	0.934	0.818	1	CLONAL	1	FALSE	0	0.188316016193245	1		769	783	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2206758	2206758	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	87	673	0	ENST00000398665.3:c.818C>A	p.Ala273Glu	p.A273E	ENST00000398665	NM_032482.2	273	gCa/gAa	10/28	0.188316016193245	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	0	0.188316016193245	1		673	780	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226504	2226504	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	99	943	0	ENST00000398665.3:c.3984A>T	p.Leu1328Phe	p.L1328F	ENST00000398665	NM_032482.2	1328	ttA/ttT	27/28	0.188316016193245	1	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	FALSE	0	0.188316016193245	1		943	950	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298005	15298005	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	83	929	2	ENST00000263388.2:c.1751A>G	p.Asp584Gly	p.D584G	ENST00000263388	NM_000435.2	584	gAc/gGc	11/33	0.188316016193245	1	FACETS	0.919	0.81	1	0.919	0.81	1	CLONAL	1	FALSE	0	0.188316016193245	1		931	869	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752648	42752648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	124	743	0	ENST00000222329.4:c.1616C>T	p.Ala539Val	p.A539V	ENST00000222329	NM_006494.2	539	gCc/gTc	4/4	0.188316016193245	3	FACETS	0.867	0.784	0.954	0.867	0.784	0.954	CLONAL	2	FALSE	1	0.188316016193245	3		743	831	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156038	99156038	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	90	750	0	ENST00000074304.5:c.718G>A	p.Gly240Ser	p.G240S	ENST00000074304	NM_001134224.1	240	Ggt/Agt	10/26	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	1	0.188316016193245	2		750	862	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55524211	55524211	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	70	737	0	ENST00000288135.5:c.30T>A	p.Phe10Leu	p.F10L	ENST00000288135	NM_000222.2	10	ttT/ttA	1/21	1	2	FACETS	0.948	0.826	1	0.948	0.826	1	CLONAL	1	FALSE	1	0.188316016193245	2		737	784	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964343	55964343	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	71	663	0	ENST00000263923.4:c.2470G>T	p.Ala824Ser	p.A824S	ENST00000263923	NM_002253.2	824	Gcc/Tcc	17/30	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	FALSE	1	0.188316016193245	2		663	739	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	190	636	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.384452460751336	2	FACETS	0.89	0.829	0.953	0.89	0.829	0.953	CLONAL	2	TRUE	0	0.384452460751336	2		638	555	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89815074	89815074	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	42	645	0	ENST00000389301.3:c.3341C>G	p.Ser1114Cys	p.S1114C	ENST00000389301	NM_000135.2	1114	tCt/tGt	33/43	0.0622022326922056	3	FACETS	0.448	0.373	0.531			1	INDETERMINATE	1	TRUE	NA	0.384452460751336	3		645	582	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652822	212652822	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780954188	NA	P-0022808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	96	647	0	ENST00000342788.4:c.484C>T	p.His162Tyr	p.H162Y	ENST00000342788	NM_005235.2	162	Cat/Tat	4/28	0.274137444089503	4	FACETS	1	0.925	1	0.524	0.467	0.584	CLONAL	1	TRUE	2	0.384452460751336	4		647	660	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948071	178948071	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	60	502	0	ENST00000263967.3:c.2843A>C	p.Lys948Thr	p.K948T	ENST00000263967	NM_006218.2	948	aAa/aCa	20/21	0.384452460751336	3	FACETS	0.919	0.794	1	0.459	0.397	0.527	CLONAL	1	TRUE	1	0.384452460751336	3		502	405	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980503	70980503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	119	865	1	ENST00000276594.2:c.874G>A	p.Glu292Lys	p.E292K	ENST00000276594	NM_024504.3	292	Gaa/Aaa	4/8	0.352503633420006	5	FACETS	0.979	0.882	1	0.326	0.294	0.361	CLONAL	1	TRUE	2	0.384452460751336	5		866	997	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577131	7577140	+	protein_altering_variant	In_Frame_Del	DEL	GCTGTTCCGT	GCTGTTCCGT	A	novel	NA	P-0022808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	102	753	0	ENST00000269305.4:c.798_807delinsT	p.Arg267_Ser269del	p.R267_S269del	ENST00000269305	NM_001126112.2	266	ggACGGAACAGC/ggT	8/11	0.384452460751336	1	FACETS	0.904	0.813	1	0.904	0.813	1	CLONAL	1	TRUE	0	0.384452460751336	1		753	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0022809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	197	887	1	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.410101698682163	1	FACETS	0.998	0.927	1	0.998	0.927	1	CLONAL	1	TRUE	0	0.439113462361458	1		888	702	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0022809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	676	644	1	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.313804291190628	5	FACETS	0.935	0.905	0.966			1	CLONAL	4	TRUE	NA	0.439113462361458	5		645	1365	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259554	55259554	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs397517134	NA	P-0022809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	643	777	0	ENST00000275493.2:c.2612C>G	p.Ala871Gly	p.A871G	ENST00000275493	NM_005228.3	871	gCa/gGa	21/28	0.313804291190628	5	FACETS	0.927	0.896	0.958			1	CLONAL	4	TRUE	NA	0.439113462361458	5		777	1310	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129574	2129574	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	187	961	0	ENST00000219476.3:c.3301C>A	p.His1101Asn	p.H1101N	ENST00000219476	NM_000548.3	1101	Cat/Aat	29/42	1	2	FACETS	0.968	0.895	1	0.968	0.895	1	CLONAL	1	TRUE	1	0.439113462361458	2		961	880	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918125	50918127	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs763850764	NA	P-0022809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	164	976	0	ENST00000440232.2:c.2446_2448del	p.Ser816del	p.S816del	ENST00000440232	NM_002691.3	814	ttCTCc/ttc	20/27	0.439113462361458	1	FACETS	0.814	0.749	0.882	0.814	0.749	0.882	CLONAL	1	TRUE	0	0.439113462361458	1		976	716	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673635	30673635	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	190	925	0	ENST00000376406.3:c.3325A>T	p.Thr1109Ser	p.T1109S	ENST00000376406	NM_014641.2	1109	Act/Tct	10/15	0.385454537998428	3	FACETS	0.963	0.889	1	0.481	0.444	0.52	CLONAL	1	TRUE	1	0.439113462361458	3		925	1096	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020657	37020657	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	129	626	0	ENST00000358127.4:c.188G>C	p.Gly63Ala	p.G63A	ENST00000358127	NM_001280556.1	63	gGt/gCt	2/10	1	2	FACETS	0.942	0.856	1	0.942	0.856	1	CLONAL	1	TRUE	1	0.439113462361458	2		626	624	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050682	30050682	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0022812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	28	602	2	ENST00000338641.4:c.488del	p.Leu163TrpfsTer11	p.L163Wfs*11	ENST00000338641	NM_000268.3	162	Ttt/tt	5/16	0.445958737147935	1	FACETS	0.258	0.206	0.318	0.258	0.206	0.318	SUBCLONAL	1	TRUE	0	0.463934514394553	1		604	359	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111435	56111435	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	75	500	0	ENST00000399503.3:c.35C>T	p.Ser12Leu	p.S12L	ENST00000399503	NM_005921.1	12	tCg/tTg	1/20	1	2	FACETS	0.806	0.71	0.909	0.806	0.71	0.909	CLONAL	1	TRUE	1	0.463934514394553	2		500	401	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106648	27106648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553153748	NA	P-0022813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	134	826	3	ENST00000324856.7:c.6259G>A	p.Gly2087Arg	p.G2087R	ENST00000324856	NM_006015.4	2087	Gga/Aga	20/20	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.322047119095888	2		829	807	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0022813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	100	557	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	0.892	0.798	0.993	0.892	0.798	0.993	CLONAL	1	TRUE	1	0.322047119095888	2		557	696	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928071	178928097	+	inframe_deletion	In_Frame_Del	DEL	ATGGATTAGAAGATTTGCTGAACCCTA	ATGGATTAGAAGATTTGCTGAACCCTA	-	novel	NA	P-0022813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	56	755	0	ENST00000263967.3:c.1349_1375del	p.His450_Ile459delinsLeu	p.H450_I459delinsL	ENST00000263967	NM_006218.2	450	cATGGATTAGAAGATTTGCTGAACCCTAtt/ctt	8/21	1	2	FACETS	0.422	0.36	0.489	0.422	0.36	0.489	SUBCLONAL	1	TRUE	1	0.322047119095888	2		755	825	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579722	7579722	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0022813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	315	766	0	ENST00000269305.4:c.75-1G>C		p.X25_splice	ENST00000269305	NM_001126112.2	25			NA	2	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.322047119095888	2		766	850	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068438	16068438	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	17	137	0	ENST00000268712.3:c.473C>T	p.Ser158Phe	p.S158F	ENST00000268712	NM_006311.3	158	tCt/tTt	5/46	0.322047119095888	1	FACETS	0.709	0.534	0.911	0.709	0.534	0.911	CLONAL	1	TRUE	0	0.322047119095888	1		137	125	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227019	2227019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	505	962	1	ENST00000398665.3:c.4499C>T	p.Ser1500Phe	p.S1500F	ENST00000398665	NM_032482.2	1500	tCt/tTt	27/28	0.255683953930719	3	FACETS	1	0.99	1			1	CLONAL	3	TRUE	NA	0.322047119095888	3		963	1120	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513503	149513503	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0022813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	53	810	0	ENST00000261799.4:c.700del	p.Met234CysfsTer4	p.M234Cfs*4	ENST00000261799	NM_002609.3	234	Atg/tg	5/23	1	2	FACETS	0.386	0.328	0.45	0.386	0.328	0.45	SUBCLONAL	1	TRUE	1	0.322047119095888	2		810	853	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752968	128752969	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGAGCGCCAGAGGAGGAACGAGC	novel	NA	P-0022813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	215	624	0	ENST00000377970.2:c.1131_1154dup	p.Glu378_Leu385dup	p.E378_L385dup	ENST00000377970	NM_002467.4	378	ttg/tTGGAGCGCCAGAGGAGGAACGAGCtg	3/3	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.322047119095888	2		624	972	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0022814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	328	840	2	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.612103809156569	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.612103809156569	2		842	525	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114905788	114905788	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0022814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	167	683	0	ENST00000543371.1:c.807C>G	p.Tyr269Ter	p.Y269*	ENST00000543371	NM_001198531.1	269	taC/taG	8/14	0.612103809156569	3	FACETS	1	0.947	1	0.518	0.477	0.56	CLONAL	1	TRUE	1	0.612103809156569	3		683	688	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858985	57858985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142957882	NA	P-0022814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	189	850	6	ENST00000228682.2:c.481C>T	p.Arg161Trp	p.R161W	ENST00000228682	NM_005269.2	161	Cgg/Tgg	5/12	0.612103809156569	3	FACETS	1	0.96	1	0.351	0.325	0.378	CLONAL	1	TRUE	0	0.612103809156569	3		856	766	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0022814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	418	898	2	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.612103809156569	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.612103809156569	2		900	676	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257633	19257633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	196	942	5	ENST00000162023.5:c.593C>T	p.Pro198Leu	p.P198L	ENST00000162023		198	cCc/cTc	10/13	0.612103809156569	3	FACETS	0.932	0.864	1	0.466	0.432	0.502	CLONAL	1	TRUE	1	0.612103809156569	3		947	897	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228778	36228778	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	172	786	1	ENST00000222270.7:c.7677G>T	p.Glu2559Asp	p.E2559D	ENST00000222270	NM_014727.1	2559	gaG/gaT	35/37	0.612103809156569	3	FACETS	0.977	0.901	1	0.489	0.45	0.528	CLONAL	1	TRUE	1	0.612103809156569	3		787	751	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100975	41100975	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	297	690	2	ENST00000373198.4:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000373198	NM_133170.3	461	Cga/Tga	8/32	0.612103809156569	6	FACETS	1	0.969	1	0.52	0.49	0.551	CLONAL	2	TRUE	2	0.612103809156569	6		692	1037	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958788	55958788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780764266	NA	P-0022814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	131	695	0	ENST00000263923.4:c.3065G>A	p.Arg1022Gln	p.R1022Q	ENST00000263923	NM_002253.2	1022	cGa/cAa	22/30	0.612103809156569	2	FACETS	1	0.956	1	0.534	0.489	0.58	CLONAL	1	TRUE	0	0.612103809156569	2		695	401	SUCCESS
APC	324	MSKCC	GRCh37	5	112174241	112174241	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1254176854	NA	P-0022814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	101	518	2	ENST00000257430.4:c.2950G>T	p.Glu984Ter	p.E984*	ENST00000257430	NM_000038.5	984	Gaa/Taa	16/16	0.559664068438589	3	FACETS	1	0.936	1	0.527	0.474	0.582	CLONAL	1	TRUE	1	0.612103809156569	3		520	409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0022818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	186	484	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.308764683089747	3	FACETS	0.984	0.911	1	0.656	0.607	0.706	CLONAL	2	TRUE	0	0.308764683089747	3		484	707	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440943	56440943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786205215	NA	P-0022818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	218	751	3	ENST00000407977.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000407977		132	Cga/Tga	4/10	0.308764683089747	3	FACETS	0.874	0.818	0.931	0.874	0.818	0.931	CLONAL	3	TRUE	0	0.308764683089747	3		754	622	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535450	66535450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	93	709	0	ENST00000273854.3:c.11C>T	p.Ser4Leu	p.S4L	ENST00000273854	NM_004439.5	4	tCg/tTg	1/18	0.272140332487434	4	FACETS	1	0.98	1	0.744	0.663	0.829	CLONAL	1	TRUE	2	0.308764683089747	4		709	530	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261631	16261631	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	152	730	0	ENST00000375759.3:c.8896C>G	p.Leu2966Val	p.L2966V	ENST00000375759	NM_015001.2	2966	Ctt/Gtt	11/15	0.308764683089747	4	FACETS	0.841	0.77	0.915	0.841	0.77	0.915	CLONAL	2	TRUE	2	0.308764683089747	4		730	766	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999104	100999104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779926918	NA	P-0022818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	58	877	1	ENST00000325455.5:c.698C>T	p.Ala233Val	p.A233V	ENST00000325455	NM_001202474.3	233	gCg/gTg	1/8	0.272140332487434	4	FACETS	0.732	0.628	0.845	0.366	0.314	0.423	SUBCLONAL	1	TRUE	2	0.308764683089747	4		878	672	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602746	10602746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1250	237	1156	0	ENST00000171111.5:c.832C>T	p.Pro278Ser	p.P278S	ENST00000171111	NM_203500.1	278	Ccg/Tcg	3/6	0.175396835815003	2	FACETS	1	0.991	1	0.715	0.665	0.766	CLONAL	1	TRUE	0	0.222989921613519	2		1156	1487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579485	7579485	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs869312782	NA	P-0022819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	198	1099	2	ENST00000269305.4:c.202G>T	p.Glu68Ter	p.E68*	ENST00000269305	NM_001126112.2	68	Gag/Tag	4/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.222989921613519	2		1101	1305	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023577	27023592	+	frameshift_variant	Frame_Shift_Del	DEL	CCTACGCGCTGAGCTC	CCTACGCGCTGAGCTC	-	novel	NA	P-0022819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1405	119	1093	0	ENST00000324856.7:c.685_700del	p.Tyr229ArgfsTer129	p.Y229Rfs*129	ENST00000324856	NM_006015.4	228	gCCTACGCGCTGAGCTCc/gc	1/20	1	2	FACETS	0.7	0.63	0.776	0.7	0.63	0.776	SUBCLONAL	1	TRUE	1	0.222989921613519	2		1093	1524	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124762	108124762	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	18	440	0	ENST00000278616.4:c.2120C>G	p.Ser707Cys	p.S707C	ENST00000278616	NM_000051.3	707	tCt/tGt	13/63	0.222989921613519	1	FACETS	0.49	0.368	0.633	0.49	0.368	0.633	SUBCLONAL	1	TRUE	0	0.222989921613519	1		440	293	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982474	25982474	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	105	611	0	ENST00000435504.4:c.816G>T	p.Glu272Asp	p.E272D	ENST00000435504		272	gaG/gaT	9/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.222989921613519	2		611	799	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52676042	52676042	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	99	755	1	ENST00000394830.3:c.1015G>T	p.Gly339Ter	p.G339*	ENST00000394830	NM_018313.4	339	Gga/Tga	11/30	0.175396835815003	2	FACETS	1	0.978	1	0.693	0.619	0.771	CLONAL	1	TRUE	0	0.222989921613519	2		756	641	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045869	143045870	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0022819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	73	733	0	ENST00000262992.4:c.1764_1765delinsAT	p.Asp589Tyr	p.D589Y	ENST00000262992	NM_001101669.1	588	aaGGac/aaATac	17/24	1	2	FACETS	0.81	0.708	0.922	0.81	0.708	0.922	CLONAL	1	TRUE	1	0.222989921613519	2		733	808	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151947021	151947021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	24	727	0	ENST00000262189.6:c.1753G>A	p.Glu585Lys	p.E585K	ENST00000262189	NM_170606.2	585	Gaa/Aaa	13/59	0.159909898319339	3	FACETS	0.522	0.409	0.654	0.174	0.136	0.218	SUBCLONAL	1	TRUE	0	0.222989921613519	3		727	458	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	137	636	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.9	0.819	0.986	0.9	0.819	0.986	CLONAL	1	TRUE	1	0.350574858892283	2		638	868	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0022820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	170	755	2	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.320329848461823	1	FACETS	0.911	0.838	0.987	0.911	0.838	0.987	CLONAL	1	TRUE	0	0.350574858892283	1		757	878	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941694	48941694	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0022820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	205	588	0	ENST00000267163.4:c.1004T>A	p.Leu335Ter	p.L335*	ENST00000267163	NM_000321.2	335	tTa/tAa	10/27	0.326426796162344	2	FACETS	0.973	0.908	1	0.973	0.908	1	CLONAL	2	TRUE	0	0.350574858892283	2		588	601	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211811	2211817	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCCTG	CAGCCTG	-	novel	NA	P-0022820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	169	923	0	ENST00000398665.3:c.1530_1536del	p.Ser510ArgfsTer45	p.S510Rfs*45	ENST00000398665	NM_032482.2	509	gcCAGCCTG/gc	16/28	1	2	FACETS	0.921	0.846	0.999	0.921	0.846	0.999	CLONAL	1	TRUE	1	0.350574858892283	2		923	1047	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921510	39921510	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0022820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	184	439	0	ENST00000378444.4:c.4310C>G	p.Ser1437Ter	p.S1437*	ENST00000378444	NM_001123385.1	1437	tCa/tGa	10/15	1	1	FACETS	0.772	0.717	0.828	1	0.991	1	SUBCLONAL	2	TRUE	0	0.350574858892283	1		439	561	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209274	133209274	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs181570274	NA	P-0022821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	144	832	0	ENST00000320574.5:c.6112G>A	p.Glu2038Lys	p.E2038K	ENST00000320574	NM_006231.2	2038	Gag/Aag	44/49	0.410386703359527	2	FACETS	0.943	0.862	1	0.472	0.431	0.514	CLONAL	1	TRUE	0	0.4258883957647	2		832	717	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857524	57857524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	136	793	4	ENST00000228682.2:c.50G>A	p.Cys17Tyr	p.C17Y	ENST00000228682	NM_005269.2	17	tGc/tAc	2/12	0.410386703359527	2	FACETS	0.868	0.79	0.949	0.434	0.395	0.475	CLONAL	1	TRUE	0	0.4258883957647	2		797	736	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579561	7579565	+	frameshift_variant	Frame_Shift_Del	DEL	ATCAT	ATCAT	-	novel	NA	P-0022821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	270	800	0	ENST00000269305.4:c.122_126del	p.Asp41ValfsTer9	p.D41Vfs*9	ENST00000269305	NM_001126112.2	41	gATGAT/g	4/11	0.310886369805015	2	FACETS	0.816	0.769	0.864	0.816	0.769	0.864	CLONAL	2	TRUE	0	0.4258883957647	2		800	777	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243457	41243457	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	185	879	1	ENST00000357654.3:c.4091A>T	p.Asn1364Ile	p.N1364I	ENST00000357654	NM_007294.3	1364	aAc/aTc	10/23	0.404130408009266	3	FACETS	1	0.954	1	0.349	0.322	0.377	CLONAL	1	TRUE	0	0.4258883957647	3		880	1007	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023964	31023964	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	279	806	0	ENST00000375687.4:c.3449G>C	p.Gly1150Ala	p.G1150A	ENST00000375687	NM_015338.5	1150	gGa/gCa	13/13	0.300743846308225	4	FACETS	0.981	0.923	1	0.981	0.923	1	CLONAL	2	TRUE	2	0.4258883957647	4		806	952	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119624589	119624622	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCAACCTTCTCACCTTGATTATTTCTACCAACTG	TCAACCTTCTCACCTTGATTATTTCTACCAACTG	-	novel	NA	P-0022821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	55	610	0	ENST00000316626.5:c.793_813+13del		p.X265_splice	ENST00000316626		265		7/12	0.386318552665172	3	FACETS	0.612	0.524	0.708	0.306	0.262	0.354	SUBCLONAL	1	TRUE	1	0.4258883957647	3		610	512	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864351	151864680	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTCTTAGATTTTCTGTGAGCACCAATTTGTTCTTCAAGATACTTCTGCTGCATTTGAAGCAGCTGTTGGGTCTCCTGGAGCCACTCTTCATACTGCTTACGCTGTGAATCATCTGAGGAAAAATTAAAATTCAGTTGTGTTAATTTTCTAAAGAGTCCAACATTATAAGTTACACAAATCTATTTTGTAAGGAAGTAGTTTCACCATGACCACATAATAGGAAATTTGAAAACACAATACTAAATATTAGACGATTATGTAATGATAAAATATCAGATTTTAGAAAAATATTTAATTGAGAAAGCCAGAGAATGCACATTCTTGAGATA	CTTCTTAGATTTTCTGTGAGCACCAATTTGTTCTTCAAGATACTTCTGCTGCATTTGAAGCAGCTGTTGGGTCTCCTGGAGCCACTCTTCATACTGCTTACGCTGTGAATCATCTGAGGAAAAATTAAAATTCAGTTGTGTTAATTTTCTAAAGAGTCCAACATTATAAGTTACACAAATCTATTTTGTAAGGAAGTAGTTTCACCATGACCACATAATAGGAAATTTGAAAACACAATACTAAATATTAGACGATTATGTAATGATAAAATATCAGATTTTAGAAAAATATTTAATTGAGAAAGCCAGAGAATGCACATTCTTGAGATA	-	novel	NA	P-0022821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	64	683	0	ENST00000262189.6:c.9518-217_9630del		p.X3173_splice	ENST00000262189	NM_170606.2	3173		42/59	0.4258883957647	4	FACETS	0.434	0.374	0.499			1	SUBCLONAL	1	TRUE	NA	0.4258883957647	4		683	988	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0022822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	228	929	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.29098972541891	3	FACETS	0.933	0.875	0.993	0.933	0.875	0.993	CLONAL	3	TRUE	0	0.29098972541891	3		930	641	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94209542	94209542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746932208	NA	P-0022822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	112	607	1	ENST00000323929.3:c.572G>A	p.Arg191Gln	p.R191Q	ENST00000323929	NM_005591.3	191	cGa/cAa	7/20	0.213456203208279	4	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	2	0.29098972541891	4		608	460	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30102148	30102148	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	90	652	0	ENST00000331968.5:c.1319A>C	p.Lys440Thr	p.K440T	ENST00000331968	NM_002742.2	440	aAa/aCa	9/18	0.252854514025672	3	FACETS	0.777	0.693	0.866	0.777	0.693	0.866	SUBCLONAL	2	TRUE	1	0.29098972541891	3		652	456	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165700	47166476	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AATTTTGCCCAATTCCACCCTTGACTTTGGTGGGGAAGATTCTTCTGCAGTAGATAAGGTATCACCAATTTCCATTTTCATTTTAGGAGTCGAGTCTACCTGAAGAGGTACAGCTGGAGGGTTTGGAGTATCACTTTGCTTTTCATTGCCAAGTGCAGTGAGAAACCTATTCTGCAAAGTTTTCTTTGTAAGGCTGAAGCTGAATGACACCTTCTGTCGTCCCTGTTCTTCCAAATTAACTTTTGTTTTGGTGCCTTTGGGCAAAAATCGACTAGAAGCAACACCTTTGAACATTGGTCCTTTGATGAAACCTGTTTTCTGCACATTTTCAATCTTTGCCTACAAATGAACAAAATAAGCAATTACTACTACAATAAATAGTTACTTTCAAATGGACTGCACAGTTTAAAATGTTTACTGGAGAAATGAAAAGCCCTTTTTAATAACAAATAGTATGAATTTCACTAAGCTATATATATCTTTATTATGAAAATTTTCAAACACAGTCAAAAGTATAGAAAATGGTATAATAAATCCCTAAGTATCCACTCCAAGCTTCAACAATTACCTATTTTCCCCATTCTTACTTTCTCGTACATAAATAACTTTTTTCAGTTTTATAACTATTTTCCAGGTAGCATTTTTTAAAAAGAATTTTTTAAAAACCTGACATATGTTTGAAAGACATTTGTATAAAGGGCAATATCTAACATCTCAGTACTCAATATGGTTTGTTCTTGTGTTCTATCAGAGATGAAAAATCAGAGGTCATCAAGA	AATTTTGCCCAATTCCACCCTTGACTTTGGTGGGGAAGATTCTTCTGCAGTAGATAAGGTATCACCAATTTCCATTTTCATTTTAGGAGTCGAGTCTACCTGAAGAGGTACAGCTGGAGGGTTTGGAGTATCACTTTGCTTTTCATTGCCAAGTGCAGTGAGAAACCTATTCTGCAAAGTTTTCTTTGTAAGGCTGAAGCTGAATGACACCTTCTGTCGTCCCTGTTCTTCCAAATTAACTTTTGTTTTGGTGCCTTTGGGCAAAAATCGACTAGAAGCAACACCTTTGAACATTGGTCCTTTGATGAAACCTGTTTTCTGCACATTTTCAATCTTTGCCTACAAATGAACAAAATAAGCAATTACTACTACAATAAATAGTTACTTTCAAATGGACTGCACAGTTTAAAATGTTTACTGGAGAAATGAAAAGCCCTTTTTAATAACAAATAGTATGAATTTCACTAAGCTATATATATCTTTATTATGAAAATTTTCAAACACAGTCAAAAGTATAGAAAATGGTATAATAAATCCCTAAGTATCCACTCCAAGCTTCAACAATTACCTATTTTCCCCATTCTTACTTTCTCGTACATAAATAACTTTTTTCAGTTTTATAACTATTTTCCAGGTAGCATTTTTTAAAAAGAATTTTTTAAAAACCTGACATATGTTTGAAAGACATTTGTATAAAGGGCAATATCTAACATCTCAGTACTCAATATGGTTTGTTCTTGTGTTCTATCAGAGATGAAAAATCAGAGGTCATCAAGA	-	novel	NA	P-0022822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	43	585	0	ENST00000409792.3:c.88-438_426del		p.X30_splice	ENST00000409792	NM_014159.6	30		3/21	0.229318168688373	2	FACETS	0.792	0.665	0.933	0.396	0.332	0.467	CLONAL	1	TRUE	0	0.29098972541891	2		585	373	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137540464	137540464	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0022822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	67	448	0	ENST00000367739.4:c.1A>G	p.Met1?	p.M1?	ENST00000367739	NM_000416.2	1	Atg/Gtg	1/7	0.252854514025672	3	FACETS	0.966	0.848	1	0.966	0.848	1	CLONAL	2	TRUE	1	0.29098972541891	3		448	273	SUCCESS
AR	367	MSKCC	GRCh37	X	66931282	66931282	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs111468555	NA	P-0022822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	41	293	0	ENST00000374690.3:c.1924G>A	p.Glu642Lys	p.E642K	ENST00000374690	NM_000044.3	642	Gag/Aag	4/8	0.29098972541891	2	FACETS	1	0.931	1			1	CLONAL	1	TRUE	NA	0.29098972541891	2		293	232	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882025	NA	P-0022825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	424	892	4	ENST00000269305.4:c.646G>T	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ttg	6/11	0.545664534424192	3	FACETS	0.96	0.925	0.994	0.96	0.925	0.994	CLONAL	3	TRUE	0	0.545664534424192	3		896	687	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267359	198267359	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs377023736	NA	P-0022825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	160	765	1	ENST00000335508.6:c.1998G>T	p.Lys666Asn	p.K666N	ENST00000335508	NM_012433.2	666	aaG/aaT	14/25	0.545664534424192	3	FACETS	1	0.971	1	0.56	0.515	0.607	CLONAL	1	TRUE	1	0.545664534424192	3		766	666	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417920	32417920	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	123	705	0	ENST00000332351.3:c.1132C>G	p.Leu378Val	p.L378V	ENST00000332351	NM_024426.4	378	Ctt/Gtt	7/10	0.542567494529381	4	FACETS	0.99	0.896	1	0.495	0.448	0.544	CLONAL	1	TRUE	2	0.545664534424192	4		705	704	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	74	549	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.791	0.694	0.895	0.791	0.694	0.895	SUBCLONAL	1	TRUE	1	0.387315504107652	2		549	483	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070567	67070567	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	70	432	0	ENST00000412916.2:c.191T>G	p.Leu64Arg	p.L64R	ENST00000412916		64	cTg/cGg	3/6	0.387315504107652	1	FACETS	0.828	0.727	0.936	0.828	0.727	0.936	CLONAL	1	TRUE	0	0.387315504107652	1		432	352	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860235	151860236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0022829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	197	710	0	ENST00000262189.6:c.10426dup	p.Gln3476ProfsTer19	p.Q3476Pfs*19	ENST00000262189	NM_170606.2	3476	caa/cCaa	43/59	0.353012557178142	3	FACETS	0.832	0.772	0.893	0.832	0.772	0.893	CLONAL	2	TRUE	1	0.387315504107652	3		710	730	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593613	55593613	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913521	NA	P-0022831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	274	620	0	ENST00000288135.5:c.1679T>G	p.Val560Gly	p.V560G	ENST00000288135	NM_000222.2	560	gTt/gGt	11/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.886812537807147	2		620	580	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0022832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	177	640	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		640	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0022833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	373	826	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.392978670682602	3	FACETS	0.857	0.817	0.898	0.857	0.817	0.898	CLONAL	3	TRUE	0	0.392978670682602	3		828	883	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940161	71940163	+	inframe_deletion	In_Frame_Del	DEL	GCA	GCA	-	novel	NA	P-0022833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	59	731	0	ENST00000298229.2:c.546_548del	p.His183del	p.H183del	ENST00000298229	NM_001567.3	182	tcGCAc/tcc	5/28	0.392978670682602	3	FACETS	0.393	0.337	0.454	0.196	0.168	0.227	SUBCLONAL	1	TRUE	1	0.392978670682602	3		731	915	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279907	18279907	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	153	685	4	ENST00000222254.8:c.1990G>T	p.Asp664Tyr	p.D664Y	ENST00000222254	NM_005027.3	664	Gac/Tac	16/16	0.392978670682602	3	FACETS	1	0.98	1	0.61	0.558	0.663	CLONAL	1	TRUE	1	0.392978670682602	3		689	764	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	83	445	0				ENST00000310581	NM_198253.2	-/1132			0.251551174547998	3	FACETS	0.866	0.773	0.963	1	0.973	1	CLONAL	3	TRUE	1	0.251551174547998	3		445	286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064794618	NA	P-0022834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	225	980	0	ENST00000269305.4:c.159G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgG/tgA	4/11	0.251551174547998	2	FACETS	0.893	0.836	0.951	1	0.991	1	CLONAL	3	TRUE	0	0.251551174547998	2		980	668	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923060	44923060	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	745	415	0	ENST00000377967.4:c.1921C>T	p.Gln641Ter	p.Q641*	ENST00000377967	NM_021140.2	641	Cag/Tag	16/29	0.251551174547998	10	FACETS	0.965	0.945	0.985			1	CLONAL	13	TRUE	NA	0.251551174547998	10		415	947	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732494	74732494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	41	278	0	ENST00000359995.5:c.415C>T	p.Arg139Cys	p.R139C	ENST00000359995	NM_001195427.1	139	Cgc/Tgc	2/3	0.251551174547998	3	FACETS	1	0.948	1	0.682	0.572	0.803	CLONAL	1	TRUE	1	0.251551174547998	3		278	269	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183814	10183814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1376530057	NA	P-0022834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	292	873	2	ENST00000256474.2:c.283C>T	p.Pro95Ser	p.P95S	ENST00000256474	NM_000551.3	95	Ccg/Tcg	1/3	0.251551174547998	5	FACETS	0.908	0.857	0.961	1	0.99	1	CLONAL	4	TRUE	2	0.251551174547998	5		875	880	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797258	135797258	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	141	467	0	ENST00000298552.3:c.611del	p.Arg204LeufsTer6	p.R204Lfs*6	ENST00000298552	NM_001162426.1	204	cGt/ct	7/23	0.251551174547998	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	TRUE	0	0.251551174547998	3		467	368	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0022835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	123	693	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		693	967	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0022838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	123	569	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.142160304690876	3	FACETS	1	0.958	1	0.557	0.503	0.615	CLONAL	1	TRUE	1	0.221636118819744	3		569	1106	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218052	108218052	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1064794840	NA	P-0022838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	123	534	0	ENST00000278616.4:c.8631G>C	p.Leu2877Phe	p.L2877F	ENST00000278616	NM_000051.3	2877	ttG/ttC	59/63	0.173475780318237	2	FACETS	0.807	0.731	0.887	0.807	0.731	0.887	CLONAL	2	TRUE	0	0.221636118819744	2		534	688	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874011	123874013	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs780061449	NA	P-0022838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	13	78	1	ENST00000330479.4:c.62_64del	p.Ala21del	p.A21del	ENST00000330479	NM_020382.3	14	gaGGCg/gag	2/9	1	2	FACETS	0.793	0.568	1	0.793	0.568	1	CLONAL	1	TRUE	1	0.221636118819744	2		79	148	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027380	48027380	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs876660934	NA	P-0022838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	57	401	0	ENST00000234420.5:c.2258C>G	p.Ser753Cys	p.S753C	ENST00000234420	NM_000179.2	753	tCt/tGt	4/10	1	2	FACETS	0.777	0.666	0.899	0.777	0.666	0.899	SUBCLONAL	1	TRUE	1	0.221636118819744	2		401	662	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371596	225371596	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	43	599	0	ENST00000264414.4:c.1008G>C	p.Lys336Asn	p.K336N	ENST00000264414	NM_003590.4	336	aaG/aaC	7/16	1	2	FACETS	0.572	0.478	0.678	0.572	0.478	0.678	SUBCLONAL	1	TRUE	1	0.221636118819744	2		599	678	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799499	72799499	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	96	805	0	ENST00000325599.8:c.1670del	p.Gly557AlafsTer5	p.G557Afs*5	ENST00000325599	NM_018130.2	557	gGc/gc	11/11	1	2	FACETS	0.699	0.621	0.783	0.699	0.621	0.783	SUBCLONAL	1	TRUE	1	0.221636118819744	2		805	1239	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	256518	256518	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	86	377	0	ENST00000264932.6:c.1978G>T	p.Ala660Ser	p.A660S	ENST00000264932	NM_004168.2	660	Gcc/Tcc	15/15	0.221636118819744	3	FACETS	1	0.944	1	0.558	0.493	0.627	CLONAL	1	TRUE	1	0.221636118819744	3		377	773	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0022843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	205	640	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	TRUE	1	0.718697440733604	2		640	500	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707894	47707894	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	47	478	0	ENST00000233146.2:c.2518G>C	p.Val840Leu	p.V840L	ENST00000233146	NM_000251.2	840	Gta/Cta	15/16	1	2	FACETS	0.271	0.228	0.318	0.271	0.228	0.318	SUBCLONAL	1	TRUE	1	0.718697440733604	2		478	483	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858119	152858119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370810560	NA	P-0022843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	130	727	3	ENST00000406277.2:c.496G>A	p.Val166Ile	p.V166I	ENST00000406277	NM_152274.4	166	Gtc/Atc	6/7	NA	2	FACETS	0.765	0.698	0.834			1	INDETERMINATE	1	TRUE	NA	0.718697440733604	2		730	473	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0022844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	42	550	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.333	0.277	0.397	0.333	0.277	0.397	SUBCLONAL	1	TRUE	1	0.275594261678826	2		552	914	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032069	26032069	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	21	450	0	ENST00000244661.2:c.220G>C	p.Glu74Gln	p.E74Q	ENST00000244661	NM_003537.3	74	Gaa/Caa	1/1	1	2	FACETS	0.243	0.186	0.31	0.243	0.186	0.31	SUBCLONAL	1	TRUE	1	0.275594261678826	2		450	626	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523321	9523321	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	43	511	0	ENST00000353224.5:c.1916G>T	p.Gly639Val	p.G639V	ENST00000353224	NM_177990.2	639	gGc/gTc	9/10	1	2	FACETS	0.507	0.423	0.599	0.507	0.423	0.599	SUBCLONAL	1	TRUE	1	0.275594261678826	2		511	616	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420299	88420299	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	70	465	0	ENST00000360948.2:c.2387C>A	p.Pro796His	p.P796H	ENST00000360948	NM_001012338.2	796	cCc/cAc	19/19	1	2	FACETS	0.893	0.779	1	0.893	0.779	1	CLONAL	1	TRUE	1	0.275594261678826	2		465	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578453	7578453	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	103	689	0	ENST00000269305.4:c.477del	p.Met160TrpfsTer10	p.M160Wfs*10	ENST00000269305	NM_001126112.2	159	gcC/gc	5/11	0.249500898672041	1	FACETS	0.833	0.745	0.926	0.833	0.745	0.926	CLONAL	1	TRUE	0	0.275594261678826	1		689	774	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400957	72400957	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	58	388	0	ENST00000357731.5:c.214C>A	p.Leu72Met	p.L72M	ENST00000357731	NM_173808.2	72	Ctg/Atg	2/7	1	2	FACETS	0.757	0.651	0.873	0.757	0.651	0.873	SUBCLONAL	1	TRUE	1	0.275594261678826	2		388	556	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276469	115276469	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	78	541	0	ENST00000438362.2:c.859G>A	p.Val287Ile	p.V287I	ENST00000438362	NM_001242891.1	287	Gtt/Att	9/20	1	2	FACETS	0.664	0.582	0.752	0.664	0.582	0.752	SUBCLONAL	1	TRUE	1	0.275594261678826	2		541	853	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451032	70451032	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	75	494	2	ENST00000373644.4:c.5872G>T	p.Glu1958Ter	p.E1958*	ENST00000373644	NM_030625.2	1958	Gaa/Taa	12/12	NA	2	FACETS	0.864	0.757	0.979			1	INDETERMINATE	1	TRUE	NA	0.275594261678826	2		496	630	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230597	46230598	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0022844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	90	454	0	ENST00000334344.6:c.848dup	p.Gln284ThrfsTer16	p.Q284Tfs*16	ENST00000334344	NM_152641.2	282	-/G	8/21	1	2	FACETS	0.886	0.786	0.993	0.886	0.786	0.993	CLONAL	1	TRUE	1	0.275594261678826	2		454	737	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420191	88420191	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	67	510	0	ENST00000360948.2:c.2495C>A	p.Pro832Gln	p.P832Q	ENST00000360948	NM_001012338.2	832	cCa/cAa	19/19	1	2	FACETS	0.835	0.726	0.953	0.835	0.726	0.953	CLONAL	1	TRUE	1	0.275594261678826	2		510	582	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312699	91312699	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	59	371	1	ENST00000355112.3:c.2438G>T	p.Arg813Ile	p.R813I	ENST00000355112	NM_000057.2	813	aGa/aTa	12/22	1	2	FACETS	0.814	0.701	0.937	0.814	0.701	0.937	CLONAL	1	TRUE	1	0.275594261678826	2		372	526	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858892	89858892	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	80	622	0	ENST00000389301.3:c.1070C>A	p.Ser357Ter	p.S357*	ENST00000389301	NM_000135.2	357	tCa/tAa	12/43	1	2	FACETS	0.791	0.696	0.893	0.791	0.696	0.893	SUBCLONAL	1	TRUE	1	0.275594261678826	2		622	734	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602859	10602859	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	156	885	2	ENST00000171111.5:c.719G>T	p.Arg240Leu	p.R240L	ENST00000171111	NM_203500.1	240	cGc/cTc	3/6	0.275594261678826	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.275594261678826	1		887	898	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943474	17943474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	91	660	0	ENST00000458235.1:c.2534G>A	p.Gly845Asp	p.G845D	ENST00000458235	NM_000215.3	845	gGc/gAc	19/24	0.275594261678826	1	FACETS	0.915	0.814	1	0.915	0.814	1	CLONAL	1	TRUE	0	0.275594261678826	1		660	622	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964958	25964958	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	78	394	0	ENST00000435504.4:c.4248C>G	p.Phe1416Leu	p.F1416L	ENST00000435504		1416	ttC/ttG	13/13	1	2	FACETS	0.936	0.823	1	0.936	0.823	1	CLONAL	1	TRUE	1	0.275594261678826	2		394	605	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525048	9525048	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	58	478	0	ENST00000353224.5:c.1837G>T	p.Glu613Ter	p.E613*	ENST00000353224	NM_177990.2	613	Gag/Tag	8/10	1	2	FACETS	0.678	0.582	0.782	0.678	0.582	0.782	SUBCLONAL	1	TRUE	1	0.275594261678826	2		478	621	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069436	30069436	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	66	526	1	ENST00000338641.4:c.1301A>T	p.Glu434Val	p.E434V	ENST00000338641	NM_000268.3	434	gAg/gTg	12/16	0.249500898672041	1	FACETS	0.807	0.701	0.92	0.807	0.701	0.92	CLONAL	1	TRUE	0	0.275594261678826	1		527	512	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286215	66286215	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	102	478	0	ENST00000273854.3:c.1471G>T	p.Glu491Ter	p.E491*	ENST00000273854	NM_004439.5	491	Gaa/Taa	6/18	0.249500898672041	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.275594261678826	1		478	591	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356428	66356428	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	41	317	0	ENST00000273854.3:c.1069C>T	p.Pro357Ser	p.P357S	ENST00000273854	NM_004439.5	357	Ccc/Tcc	5/18	0.249500898672041	1	FACETS	0.651	0.543	0.771	0.651	0.543	0.771	SUBCLONAL	1	TRUE	0	0.275594261678826	1		317	394	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056813	180056813	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	176	739	0	ENST00000261937.6:c.699G>C	p.Gln233His	p.Q233H	ENST00000261937	NM_182925.4	233	caG/caC	6/30	1	2	FACETS	0.827	0.763	0.893	1	0.991	1	CLONAL	2	TRUE	1	0.275594261678826	2		739	772	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323253	31323253	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs45445194	NA	P-0022844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	85	425	0	ENST00000412585.2:c.736G>T	p.Glu246Ter	p.E246*	ENST00000412585	NM_005514.6	246	Gag/Tag	4/8	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.275594261678826	2		425	575	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129891	69129891	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs773214113	NA	P-0022844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	58	351	0	ENST00000288368.4:c.4645G>T	p.Ala1549Ser	p.A1549S	ENST00000288368	NM_024870.2	1549	Gcc/Tcc	38/40	0.260891677144175	3	FACETS	0.884	0.76	1	0.442	0.38	0.51	CLONAL	1	TRUE	1	0.275594261678826	3		351	542	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939769	76939769	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	145	321	0	ENST00000373344.5:c.979G>A	p.Glu327Lys	p.E327K	ENST00000373344	NM_000489.3	327	Gaa/Aaa	9/35	1	1	FACETS	0.812	0.744	0.882	1	0.989	1	CLONAL	2	TRUE	0	0.275594261678826	1		321	559	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	237	619	3	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.84	0.787	0.893	1	0.995	1	CLONAL	3	TRUE	1	0.27	2		622	697	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	384	911	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	0.997	1	CLONAL	3	TRUE	1	0.27	2		911	890	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	292	514	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	0.807	0.903	1	0.996	1	CLONAL	3	TRUE	1	0.27	2		514	844	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717715	89717716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587782341	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	212	537	0	ENST00000371953.3:c.741dup	p.Pro248ThrfsTer5	p.P248Tfs*5	ENST00000371953	NM_000314.4	247	tta/ttAa	7/9	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.27	2		537	666	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25468901	25468901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	49	816	1	ENST00000264709.3:c.1462C>T	p.Arg488Trp	p.R488W	ENST00000264709	NM_175629.2	488	Cgg/Tgg	12/23	1	2	FACETS	0.503	0.425	0.59	0.503	0.425	0.59	SUBCLONAL	1	TRUE	1	0.27	2		817	721	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952086	178952086	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519932	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	164	421	0	ENST00000263967.3:c.3141T>G	p.His1047Gln	p.H1047Q	ENST00000263967	NM_006218.2	1047	caT/caG	21/21	1	2	FACETS	0.871	0.807	0.936	1	0.994	1	CLONAL	3	TRUE	1	0.27	2		421	465	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	131	355	1	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.898	0.825	0.974	1	0.992	1	CLONAL	3	TRUE	1	0.27	2		356	360	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540230	23540235	+	inframe_deletion	In_Frame_Del	DEL	GGCTCC	GGCTCC	-	rs753037741	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	145	524	0	ENST00000380871.4:c.168_173del	p.Pro62_Glu63del	p.P62_E63del	ENST00000380871	NM_006167.3	56	ccGGAGCCa/cca	1/2	1	2	FACETS	1	0.936	1	1	0.991	1	CLONAL	2	TRUE	1	0.27	2		524	525	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	167	371	7	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	1	2	FACETS	0.927	0.86	0.994	1	0.994	1	CLONAL	3	TRUE	1	0.27	2		378	445	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007824	45007825	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	250	516	0	ENST00000558401.1:c.276dup	p.Thr93HisfsTer2	p.T93Hfs*2	ENST00000558401	NM_004048.2	91	acc/aCcc	2/4	1	2	FACETS	1	0.985	1	1	0.995	1	CLONAL	2	TRUE	1	0.27	2		516	799	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931589	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	184	372	0	ENST00000349496.5:c.101G>A	p.Gly34Glu	p.G34E	ENST00000349496	NM_001904.3	34	gGa/gAa	3/15	1	2	FACETS	0.937	0.873	1	1	0.994	1	CLONAL	3	TRUE	1	0.27	2		372	485	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775720	9775720	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769029561	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	233	729	3	ENST00000377346.4:c.263G>A	p.Arg88His	p.R88H	ENST00000377346	NM_005026.3	88	cGt/cAt	4/24	0.3	1	FACETS	0.835	0.785	0.886	1	0.995	1	CLONAL	3	TRUE	0	0.27	1		732	596	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	126	482	1	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	0.166071648612241	0	FACETS	0.993	0.911	1			1	CLONAL	2	TRUE	0	0.27	0		483	343	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	336	588	1	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	0.919	0.872	0.966	1	0.997	1	CLONAL	3	TRUE	1	0.27	2		589	903	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423598	88423598	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	40	615	0	ENST00000360948.2:c.2237A>C	p.Lys746Thr	p.K746T	ENST00000360948	NM_001012338.2	746	aAg/aCg	18/19	0.3	0	FACETS	0.421	0.349	0.501			1	SUBCLONAL	1	TRUE	0	0.27	0		615	514	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023831	27023831	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1415214478	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	233	490	0	ENST00000324856.7:c.941del	p.Gly314AlafsTer49	p.G314Afs*49	ENST00000324856	NM_006015.4	313	Ggg/gg	1/20	1	2	FACETS	1	0.979	1	1	0.996	1	CLONAL	3	TRUE	1	0.27	2		490	532	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052626	42052626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	284	513	0	ENST00000219905.7:c.7297C>T	p.Arg2433Trp	p.R2433W	ENST00000219905	NM_001164273.1	2433	Cgg/Tgg	20/24	1	2	FACETS	0.935	0.883	0.987	1	0.996	1	CLONAL	3	TRUE	1	0.27	2		513	750	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435160	56435161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	199	646	0	ENST00000407977.2:c.1975_1976dup	p.Pro660ValfsTer41	p.P660Vfs*41	ENST00000407977		659	ggt/ggGGt	9/10	0.0819194955859546	3	FACETS	1	0.979	1	1	0.979	1	INDETERMINATE	2	TRUE	1	0.27	3		646	739	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	361	1297	4	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	1	0.975	1	1	0.997	1	CLONAL	3	TRUE	1	0.27	2		1301	860	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7120689	7120689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568426700	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	210	823	2	ENST00000302850.5:c.3601C>T	p.Arg1201Trp	p.R1201W	ENST00000302850	NM_000208.2	1201	Cgg/Tgg	20/22	0.3	1	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	TRUE	0	0.27	1		825	539	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100283	8100283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	212	730	1	ENST00000346208.3:c.257G>A	p.Arg86His	p.R86H	ENST00000346208		86	cGc/cAc	3/6	0.232746037932957	0	FACETS	0.709	0.664	0.754			1	SUBCLONAL	3	TRUE	0	0.27	0		731	539	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431874	49431874	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	262	731	1	ENST00000301067.7:c.9265del	p.Val3089TrpfsTer30	p.V3089Wfs*30	ENST00000301067	NM_003482.3	3089	Gtg/tg	34/54	1	2	FACETS	0.935	0.881	0.989	1	0.996	1	CLONAL	3	TRUE	1	0.27	2		732	692	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863054	56863054	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1266824391	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	210	648	2	ENST00000519728.1:c.327del	p.Glu110LysfsTer15	p.E110Kfs*15	ENST00000519728	NM_002350.3	107	acA/ac	5/13	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	1	0.27	2		650	648	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31369177	31369177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17123590	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	210	594	0	ENST00000328111.2:c.161G>A	p.Arg54Gln	p.R54Q	ENST00000328111	NM_006892.3	54	cGa/cAa	3/23	1	2	FACETS	1	0.94	1	1	0.995	1	CLONAL	3	TRUE	1	0.27	2		594	517	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436297	110436302	+	inframe_deletion	In_Frame_Del	DEL	CGGCGG	CGGCGG	-	rs34412495	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	122	246	1	ENST00000375856.3:c.2099_2104del	p.Ala700_Ala701del	p.A700_A701del	ENST00000375856	NM_003749.2	700	gCCGCCGtg/gtg	1/2	1	2	FACETS	0.981	0.9	1	1	0.992	1	CLONAL	3	TRUE	1	0.27	2		247	307	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216184	36216184	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	229	710	2	ENST00000222270.7:c.3596del	p.Gly1199AlafsTer156	p.G1199Afs*156	ENST00000222270	NM_014727.1	1198	Ggg/gg	11/37	0.166071648612241	0	FACETS	1	0.961	1			1	CLONAL	2	TRUE	0	0.27	0		712	600	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272966	11272966	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	159	337	0	ENST00000361445.4:c.3286-1G>T		p.X1096_splice	ENST00000361445	NM_004958.3	1096			0.3	1	FACETS	1	0.985	1	1	0.993	1	CLONAL	2	TRUE	0	0.27	1		337	410	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803823	43803823	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs775885799	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	213	814	0	ENST00000372470.3:c.133T>C	p.Phe45Leu	p.F45L	ENST00000372470	NM_005373.2	45	Ttt/Ctt	2/12	1	2	FACETS	0.882	0.825	0.941	1	0.995	1	CLONAL	3	TRUE	1	0.27	2		814	596	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430393	78430393	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	266	639	0	ENST00000370768.2:c.775G>T	p.Gly259Cys	p.G259C	ENST00000370768	NM_003902.3	259	Ggc/Tgc	10/20	1	2	FACETS	0.93	0.877	0.984	1	0.996	1	CLONAL	3	TRUE	1	0.27	2		639	706	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610131	43610131	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	39	795	0	ENST00000355710.3:c.2083C>T	p.Pro695Ser	p.P695S	ENST00000355710	NM_020975.4	695	Ccc/Tcc	11/20	0.232746037932957	0	FACETS	0.419	0.347	0.5			1	SUBCLONAL	1	TRUE	0	0.27	0		795	503	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852571	63852571	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	33	474	1	ENST00000279873.7:c.3349C>T	p.Gln1117Ter	p.Q1117*	ENST00000279873	NM_032199.2	1117	Cag/Tag	10/10	0.284645480783373	5	FACETS	0.623	0.507	0.755			1	SUBCLONAL	1	TRUE	NA	0.27	5		475	551	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717659	89717659	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	325	631	0	ENST00000371953.3:c.685del	p.Ser229GlnfsTer27	p.S229Qfs*27	ENST00000371953	NM_000314.4	228	aaT/aa	7/9	1	2	FACETS	0.992	0.942	1	1	0.997	1	CLONAL	3	TRUE	1	0.27	2		631	809	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114901028	114901028	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	313	585	0	ENST00000543371.1:c.638C>A	p.Pro213Gln	p.P213Q	ENST00000543371	NM_001198531.1	213	cCg/cAg	6/14	1	2	FACETS	1	0.961	1	1	0.997	1	CLONAL	3	TRUE	1	0.27	2		585	761	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279595	123279595	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	233	720	0	ENST00000358487.5:c.837G>T	p.Lys279Asn	p.K279N	ENST00000358487	NM_000141.4	279	aaG/aaT	7/18	0.166071648612241	0	FACETS	0.932	0.874	0.991			1	CLONAL	2	TRUE	0	0.27	0		720	676	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236180	108236180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	243	731	3	ENST00000278616.4:c.9116C>T	p.Ala3039Val	p.A3039V	ENST00000278616	NM_000051.3	3039	gCc/gTc	63/63	1	2	FACETS	0.871	0.818	0.925	1	0.996	1	CLONAL	3	TRUE	1	0.27	2		734	689	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246491	46246491	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	34	280	0	ENST00000334344.6:c.4585G>T	p.Gly1529Ter	p.G1529*	ENST00000334344	NM_152641.2	1529	Gga/Tga	15/21	1	2	FACETS	0.739	0.605	0.889	0.739	0.605	0.889	SUBCLONAL	1	TRUE	1	0.27	2		280	341	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961094	41961094	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	99	238	0	ENST00000219905.7:c.2T>C	p.Met1?	p.M1?	ENST00000219905	NM_001164273.1	1	aTg/aCg	2/24	1	2	FACETS	0.886	0.803	0.971	1	0.99	1	CLONAL	3	TRUE	1	0.27	2		238	276	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994850	73994850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141119771	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	28	116	1	ENST00000318443.5:c.334G>A	p.Val112Met	p.V112M	ENST00000318443	NM_001024736.1	112	Gtg/Atg	3/10	0.3	1	FACETS	1	0.908	1	1	0.964	1	CLONAL	2	TRUE	0	0.27	1		117	77	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16046994	16046994	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	197	486	0	ENST00000268712.3:c.1099G>T	p.Ala367Ser	p.A367S	ENST00000268712	NM_006311.3	367	Gct/Tct	11/46	1	2	FACETS	0.899	0.839	0.96	1	0.995	1	CLONAL	3	TRUE	1	0.27	2		486	541	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63545671	63545671	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779083840	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	255	557	1	ENST00000307078.5:c.923C>T	p.Thr308Met	p.T308M	ENST00000307078	NM_004655.3	308	aCg/aTg	3/11	0.0819194955859546	3	FACETS	1	0.96	1	1	0.994	1	INDETERMINATE	3	TRUE	1	0.27	3		558	697	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350301	15350301	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	208	596	0	ENST00000263377.2:c.3478C>A	p.Pro1160Thr	p.P1160T	ENST00000263377	NM_058243.2	1160	Cct/Act	17/20	0.3	1	FACETS	0.907	0.85	0.964	1	0.995	1	CLONAL	3	TRUE	0	0.27	1		596	490	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350722	15350722	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	241	954	2	ENST00000263377.2:c.3281A>G	p.Gln1094Arg	p.Q1094R	ENST00000263377	NM_058243.2	1094	cAg/cGg	15/20	0.3	1	FACETS	0.841	0.791	0.892	1	0.995	1	CLONAL	3	TRUE	0	0.27	1		956	612	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218450	36218451	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	206	541	1	ENST00000222270.7:c.4235dup	p.Leu1413ProfsTer265	p.L1413Pfs*265	ENST00000222270	NM_014727.1	1410	cag/caGg	16/37	0.166071648612241	0	FACETS	0.71	0.664	0.756			1	SUBCLONAL	3	TRUE	0	0.27	0		542	523	SUCCESS
ALK	238	MSKCC	GRCh37	2	29419653	29419653	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	51	573	1	ENST00000389048.3:c.4147A>G	p.Ile1383Val	p.I1383V	ENST00000389048	NM_004304.4	1383	Att/Gtt	28/29	1	2	FACETS	0.667	0.567	0.778	0.667	0.567	0.778	SUBCLONAL	1	TRUE	1	0.27	2		574	566	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535343	66535343	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	314	775	1	ENST00000273854.3:c.118C>A	p.Leu40Ile	p.L40I	ENST00000273854	NM_004439.5	40	Ctc/Atc	1/18	1	2	FACETS	0.999	0.948	1	1	0.997	1	CLONAL	3	TRUE	1	0.27	2		776	776	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170147	32170147	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	68	819	1	ENST00000375023.3:c.3461del	p.Gly1154AlafsTer150	p.G1154Afs*150	ENST00000375023	NM_004557.3	1154	gGc/gc	21/30	0.3	1	FACETS	0.73	0.635	0.832	0.73	0.635	0.832	SUBCLONAL	1	TRUE	0	0.27	1		820	597	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547230	106547230	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	221	315	1	ENST00000369096.4:c.467G>A	p.Ser156Asn	p.S156N	ENST00000369096	NM_001198.3	156	aGc/aAc	4/7	1	2	FACETS	0.952	0.893	1	1	0.995	1	CLONAL	3	TRUE	1	0.27	2		316	573	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100487	157100487	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	60	88	0	ENST00000346085.5:c.1424T>C	p.Leu475Ser	p.L475S	ENST00000346085	NM_020732.3	475	tTg/tCg	1/20	1	2	FACETS	1	0.916	1	1	0.985	1	CLONAL	3	TRUE	1	0.27	2		88	142	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846106	128846106	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	271	857	0	ENST00000249373.3:c.1036C>A	p.Leu346Met	p.L346M	ENST00000249373	NM_005631.4	346	Ctg/Atg	5/12	1	2	FACETS	1	0.953	1	1	0.996	1	CLONAL	3	TRUE	1	0.27	2		857	663	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981626	70981626	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	249	971	4	ENST00000276594.2:c.470C>T	p.Ala157Val	p.A157V	ENST00000276594	NM_024504.3	157	gCt/gTt	2/8	0.27204211126777	0	FACETS	0.748	0.705	0.791			1	SUBCLONAL	3	TRUE	0	0.27	0		975	600	SUCCESS
AR	367	MSKCC	GRCh37	X	66766529	66766529	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	230	789	0	ENST00000374690.3:c.1541A>G	p.Tyr514Cys	p.Y514C	ENST00000374690	NM_000044.3	514	tAt/tGt	1/8	0.232746037932957	0	FACETS	1	0.97	1			1	CLONAL	2	TRUE	0	0.27	0		789	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0022847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	294	714	1	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	0.316498039055528	2	FACETS	0.919	0.868	0.971	0.919	0.868	0.971	CLONAL	2	TRUE	0	0.376442009820127	2		715	850	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415856	49415858	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	rs587783704	NA	P-0022847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	284	462	0	ENST00000301067.7:c.16489_16491del	p.Ile5497del	p.I5497del	ENST00000301067	NM_003482.3	5497	ATC/-	53/54	0.376442009820127	3	FACETS	0.918	0.87	0.967	0.918	0.87	0.967	CLONAL	3	TRUE	0	0.376442009820127	3		462	651	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50784001	50784001	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	83	707	0	ENST00000398568.2:c.392T>A	p.Val131Glu	p.V131E	ENST00000398568	NM_001042412.1	131	gTg/gAg	3/18	1	2	FACETS	0.652	0.576	0.735	0.652	0.576	0.735	SUBCLONAL	1	TRUE	1	0.376442009820127	2		707	676	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984673	72984673	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	136	754	0	ENST00000268489.5:c.2911C>G	p.Leu971Val	p.L971V	ENST00000268489	NM_006885.3	971	Ctg/Gtg	3/10	1	2	FACETS	0.958	0.872	1	0.958	0.872	1	CLONAL	1	TRUE	1	0.376442009820127	2		754	754	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221322	1221322	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	194	674	0	ENST00000326873.7:c.845T>G	p.Leu282Arg	p.L282R	ENST00000326873	NM_000455.4	282	cTc/cGc	6/10	0.23192376417647	2	FACETS	0.775	0.72	0.831	0.775	0.72	0.831	SUBCLONAL	2	TRUE	0	0.376442009820127	2		674	665	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163429	47163429	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	53	391	0	ENST00000409792.3:c.2697A>C	p.Lys899Asn	p.K899N	ENST00000409792	NM_014159.6	899	aaA/aaC	3/21	1	2	FACETS	0.771	0.66	0.892	0.771	0.66	0.892	SUBCLONAL	1	TRUE	1	0.376442009820127	2		391	365	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0022848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	324	644	1	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.201009872149486	6	FACETS	1	0.985	1	1	0.985	1	CLONAL	4	FALSE	2	0.201009872149486	6		645	1015	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0022848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	158	713	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.201009872149486	3	FACETS	0.932	0.854	1	0.932	0.854	1	CLONAL	2	FALSE	1	0.201009872149486	3		715	928	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321369	65321369	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764468267	NA	P-0022848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	58	677	0	ENST00000342505.4:c.1471G>A	p.Ala491Thr	p.A491T	ENST00000342505	NM_002227.2	491	Gcc/Acc	11/25	0.201009872149486	3	FACETS	0.907	0.778	1	0.454	0.389	0.524	CLONAL	1	FALSE	1	0.201009872149486	3		677	700	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321371	65321371	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	57	664	0	ENST00000342505.4:c.1469G>T	p.Gly490Val	p.G490V	ENST00000342505	NM_002227.2	490	gGt/gTt	11/25	0.201009872149486	3	FACETS	0.899	0.771	1	0.45	0.385	0.52	CLONAL	1	FALSE	1	0.201009872149486	3		664	694	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321375	65321375	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	57	654	0	ENST00000342505.4:c.1465C>A	p.Gln489Lys	p.Q489K	ENST00000342505	NM_002227.2	489	Cag/Aag	11/25	0.201009872149486	3	FACETS	0.922	0.79	1	0.461	0.395	0.533	CLONAL	1	FALSE	1	0.201009872149486	3		654	677	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3827631	3827631	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs141098117	NA	P-0022848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	39	682	0	ENST00000262367.5:c.2141G>T	p.Arg714Leu	p.R714L	ENST00000262367	NM_004380.2	714	cGc/cTc	11/31	0.191525186333386	3	FACETS	0.578	0.477	0.691	0.289	0.238	0.346	SUBCLONAL	1	FALSE	1	0.201009872149486	3		682	739	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579380	7579396	+	frameshift_variant	Frame_Shift_Del	DEL	AGGTTTTCTGGGAAGGG	AGGTTTTCTGGGAAGGG	-	novel	NA	P-0022848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	56	866	1	ENST00000269305.4:c.291_307del	p.Ser99GlyfsTer44	p.S99Gfs*44	ENST00000269305	NM_001126112.2	97	gtCCCTTCCCAGAAAACCTac/gtac	4/11	0.201009872149486	3	FACETS	0.678	0.579	0.787	0.339	0.289	0.394	SUBCLONAL	1	FALSE	1	0.201009872149486	3		867	904	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0022862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	173	550	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.868	0.8	0.939	0.868	0.8	0.939	CLONAL	1	TRUE	1	0.489114471859289	2		552	815	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0022862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	180	537	2	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.410725991250337	1	FACETS	0.9	0.834	0.968	0.9	0.834	0.968	CLONAL	1	TRUE	0	0.489114471859289	1		539	618	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0022862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	134	404	4	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.973	0.888	1	0.973	0.888	1	CLONAL	1	TRUE	1	0.489114471859289	2		408	563	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0022863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	28	550	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.350288882228046	5	FACETS	0.166	0.132	0.206	0.055	0.044	0.069	INDETERMINATE	1	TRUE	2	0.678915545448374	5		552	1002	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11027430	11027430	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	153	852	0	ENST00000327064.4:c.997G>C	p.Glu333Gln	p.E333Q	ENST00000327064	NM_199141.1	333	Gag/Cag	8/16	0.192126431703427	3	FACETS	0.511	0.466	0.558	0.17	0.155	0.186	INDETERMINATE	1	TRUE	0	0.678915545448374	3		852	1181	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0022864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	99	640	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.37491710464503	3	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.468207763219273	3		640	391	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164709	36164709	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1350744261	NA	P-0022864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	140	772	0	ENST00000300305.3:c.1166C>T	p.Ser389Leu	p.S389L	ENST00000300305		389	tCg/tTg	8/8	0.336783805214169	5	FACETS	1	0.951	1	0.701	0.643	0.761	CLONAL	2	TRUE	2	0.468207763219273	5		772	484	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405927	49405927	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	93	771	0	ENST00000418115.1:c.211C>A	p.Pro71Thr	p.P71T	ENST00000418115	NM_001664.2	71	Ccc/Acc	3/5	0.468207763219273	1	FACETS	0.988	0.889	1	0.988	0.889	1	CLONAL	1	TRUE	0	0.468207763219273	1		771	308	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713591	52713591	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	53	561	0	ENST00000394830.3:c.137del	p.Pro46LeufsTer49	p.P46Lfs*49	ENST00000394830	NM_018313.4	46	cCt/ct	2/30	0.468207763219273	1	FACETS	0.735	0.633	0.843	0.735	0.633	0.843	SUBCLONAL	1	TRUE	0	0.468207763219273	1		561	236	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781129	161781129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	75	689	1	ENST00000366898.1:c.1276G>A	p.Glu426Lys	p.E426K	ENST00000366898	NM_004562.2	426	Gaa/Aaa	11/12	1	2	FACETS	0.971	0.858	1	0.971	0.858	1	CLONAL	1	TRUE	1	0.468207763219273	2		690	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579463	7579463	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	122	884	0	ENST00000269305.4:c.224del	p.Pro75LeufsTer48	p.P75Lfs*48	ENST00000269305	NM_001126112.2	75	cCt/ct	4/11	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.438711611599362	2		884	374	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061459	38061459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1349901575	NA	P-0022865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	106	751	1	ENST00000250448.2:c.530C>T	p.Ser177Leu	p.S177L	ENST00000250448	NM_004496.3	177	tCg/tTg	2/2	0.304895560069762	4	FACETS	0.88	0.795	0.968	0.88	0.795	0.968	CLONAL	2	TRUE	2	0.438711611599362	4		752	395	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347949	73347949	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	49	382	0	ENST00000377767.4:c.1112A>T	p.His371Leu	p.H371L	ENST00000377767	NM_014953.3	371	cAt/cTt	8/21	0.438711611599362	3	FACETS	1	0.957	1	0.668	0.573	0.769	CLONAL	1	TRUE	1	0.438711611599362	3		382	204	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143181714	143181714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	30	601	0	ENST00000262992.4:c.619G>A	p.Ala207Thr	p.A207T	ENST00000262992	NM_001101669.1	207	Gcc/Acc	9/24	0.308861729925784	3	FACETS	0.575	0.465	0.7	0.288	0.232	0.35	SUBCLONAL	1	TRUE	1	0.438711611599362	3		601	290	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950593	79950593	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs944680882	NA	P-0022865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	96	751	0	ENST00000265081.6:c.47C>G	p.Ser16Ter	p.S16*	ENST00000265081	NM_002439.4	16	tCa/tGa	1/24	0.244600671837237	4	FACETS	0.799	0.717	0.885	0.799	0.717	0.885	INDETERMINATE	2	TRUE	2	0.438711611599362	4		751	394	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779503	3779504	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0022866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	168	688	0	ENST00000262367.5:c.5544_5545del	p.His1848GlnfsTer117	p.H1848Qfs*117	ENST00000262367	NM_004380.2	1848	caCAag/caag	31/31	1	2	FACETS	0.811	0.746	0.878	0.811	0.746	0.878	CLONAL	1	TRUE	1	0.516041474555156	2		688	803	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098380	47098393	+	frameshift_variant	Frame_Shift_Del	DEL	TTGATAATATATGG	TTGATAATATATGG	-	novel	NA	P-0022866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	260	478	0	ENST00000409792.3:c.6881_6894del	p.Thr2294ArgfsTer70	p.T2294Rfs*70	ENST00000409792	NM_014159.6	2294	aCCATATATTATCAA/a	15/21	0.514868336648783	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.516041474555156	2		478	466	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604655	55604655	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502568	NA	P-0022866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	183	422	2	ENST00000288135.5:c.2863G>A	p.Val955Met	p.V955M	ENST00000288135	NM_000222.2	955	Gtg/Atg	21/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.516041474555156	2		424	667	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346338	73346338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	9	599	0	ENST00000377767.4:c.1462G>A	p.Asp488Asn	p.D488N	ENST00000377767	NM_014953.3	488	Gat/Aat	10/21	0.437502038948981	2	FACETS	0.269	0.178	0.383	0.134	0.089	0.192	SUBCLONAL	1	FALSE	0	0.536033051784649	2		599	125	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856167	111856167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs905084632	NA	P-0022869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	33	486	2	ENST00000341259.2:c.218G>A	p.Arg73His	p.R73H	ENST00000341259	NM_005475.2	73	cGc/cAc	2/8	0.503714606346236	5	FACETS	0.663	0.541	0.8	0.221	0.18	0.267	SUBCLONAL	1	FALSE	2	0.536033051784649	5		488	335	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189387	56189387	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	93	688	0	ENST00000399503.3:c.4421del	p.Pro1474LeufsTer16	p.P1474Lfs*16	ENST00000399503	NM_005921.1	1473	atC/at	20/20	0.52150507286257	2	FACETS	0.908	0.829	0.988	0.908	0.829	0.988	CLONAL	2	FALSE	0	0.536033051784649	2		688	191	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197700	123197700	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	13	478	0	ENST00000218089.9:c.1824T>A	p.His608Gln	p.H608Q	ENST00000218089	NM_001042749.1	608	caT/caA	20/35	0.170630190909014	2	FACETS	0.404	0.29	0.54	0.202	0.145	0.27	INDETERMINATE	1	FALSE	0	0.536033051784649	2		478	120	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579406	7579406	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0022870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	633	809	0	ENST00000269305.4:c.281C>G	p.Ser94Ter	p.S94*	ENST00000269305	NM_001126112.2	94	tCa/tGa	4/11	0.592785014824028	4	FACETS	0.892	0.871	0.914	0.892	0.871	0.914	CLONAL	4	FALSE	0	0.717351654320678	4		809	849	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720676	89720677	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0022870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	162	263	0	ENST00000371953.3:c.828_829del	p.Thr277IlefsTer20	p.T277Ifs*20	ENST00000371953	NM_000314.4	276	aAT/a	8/9	0.607980172816581	3	FACETS	0.926	0.88	0.969	0.926	0.88	0.969	CLONAL	3	FALSE	0	0.717351654320678	3		263	221	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141621	202141621	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	374	490	1	ENST00000358485.4:c.909T>A	p.Phe303Leu	p.F303L	ENST00000358485	NM_001080125.1	303	ttT/ttA	7/9	0.644932302041042	3	FACETS	0.886	0.856	0.916	0.886	0.856	0.916	CLONAL	3	FALSE	0	0.717351654320678	3		491	533	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856113	68856113	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782750	NA	P-0022872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	75	751	0	ENST00000261769.5:c.1921C>T	p.Gln641Ter	p.Q641*	ENST00000261769	NM_004360.3	641	Cag/Tag	12/16	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.2	2		751	749	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	461372	461372	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	42	482	0	ENST00000399788.2:c.1148A>C	p.His383Pro	p.H383P	ENST00000399788	NM_001042603.1	383	cAt/cCt	9/28	1	2	FACETS	0.764	0.637	0.905	0.764	0.637	0.905	CLONAL	1	TRUE	1	0.2	2		482	550	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28624361	28624361	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0022872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	39	543	0	ENST00000241453.7:c.615-2A>G		p.X205_splice	ENST00000241453	NM_004119.2	205			1	2	FACETS	0.677	0.56	0.808	0.677	0.56	0.808	SUBCLONAL	1	TRUE	1	0.2	2		543	576	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180543	56180543	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	47	489	0	ENST00000399503.3:c.3872T>C	p.Leu1291Pro	p.L1291P	ENST00000399503	NM_005921.1	1291	cTa/cCa	16/20	1	2	FACETS	0.948	0.8	1	0.948	0.8	1	CLONAL	1	TRUE	1	0.2	2		489	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0022873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	259	742	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.492750414531509	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.492750414531509	3		742	628	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0022873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	87	281	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.492750414531509	3	FACETS	1	0.969	1	0.78	0.708	0.853	CLONAL	2	TRUE	0	0.492750414531509	3		281	188	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256141	133256141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1250780418	NA	P-0022873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	98	657	1	ENST00000320574.5:c.520G>A	p.Val174Met	p.V174M	ENST00000320574	NM_006231.2	174	Gtg/Atg	6/49	0.181675881253003	2	FACETS	0.829	0.743	0.919	0.414	0.371	0.46	INDETERMINATE	1	TRUE	0	0.492750414531509	2		658	480	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138382756	138382756	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0022873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	86	577	2	ENST00000289153.2:c.2788del	p.Thr930LeufsTer62	p.T930Lfs*62	ENST00000289153	NM_006219.2	930	Act/ct	19/22	0.492750414531509	3	FACETS	1	0.921	1	0.522	0.464	0.583	CLONAL	1	TRUE	1	0.492750414531509	3		579	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578408	7578434	+	inframe_deletion	In_Frame_Del	DEL	CCTCACAACCTCCGTCATGTGCTGTGA	CCTCACAACCTCCGTCATGTGCTGTGA	-	novel	NA	P-0022873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	72	759	0	ENST00000269305.4:c.496_522del	p.Ser166_Arg174del	p.S166_R174del	ENST00000269305	NM_001126112.2	166	TCACAGCACATGACGGAGGTTGTGAGG/-	5/11	0.492750414531509	3	FACETS	0.753	0.659	0.853	0.376	0.329	0.427	SUBCLONAL	1	TRUE	1	0.492750414531509	3		759	484	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10284577	10284577	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1474694064	NA	P-0022873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	72	574	0	ENST00000340748.4:c.605A>G	p.Glu202Gly	p.E202G	ENST00000340748		202	gAg/gGg	7/40	0.25926449958147	3	FACETS	0.904	0.793	1	0.301	0.264	0.341	INDETERMINATE	1	TRUE	0	0.492750414531509	3		574	403	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385230	41385230	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	73	706	0	ENST00000373198.4:c.731A>C	p.Asn244Thr	p.N244T	ENST00000373198	NM_133170.3	244	aAc/aCc	6/32	0.492750414531509	5	FACETS	0.441	0.384	0.503	0.147	0.128	0.168	SUBCLONAL	1	TRUE	2	0.492750414531509	5		706	1169	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446156	187446156	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	73	829	0	ENST00000232014.4:c.1532C>G	p.Ser511Cys	p.S511C	ENST00000232014	NM_001130845.1	511	tCt/tGt	6/10	0.492750414531509	3	FACETS	0.6	0.524	0.68	0.3	0.262	0.34	SUBCLONAL	1	TRUE	1	0.492750414531509	3		829	616	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31451736	31451736	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	48	404	0	ENST00000344624.3:c.2586G>T	p.Met862Ile	p.M862I	ENST00000344624		862	atG/atT	18/33	0.480672991229576	3	FACETS	0.999	0.853	1	0.333	0.284	0.386	CLONAL	1	TRUE	0	0.492750414531509	3		404	243	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992762	68992762	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	169	792	0	ENST00000288368.4:c.1727A>T	p.His576Leu	p.H576L	ENST00000288368	NM_024870.2	576	cAt/cTt	16/40	0.492750414531509	4	FACETS	0.806	0.744	0.87	0.538	0.496	0.58	CLONAL	2	TRUE	1	0.492750414531509	4		792	635	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249857	110249857	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	179	734	4	ENST00000374672.4:c.818C>T	p.Thr273Met	p.T273M	ENST00000374672	NM_004235.4	273	aCg/aTg	3/5	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.492750414531509	2		738	565	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759590	133759590	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	35	850	1	ENST00000318560.5:c.1913G>A	p.Gly638Asp	p.G638D	ENST00000318560	NM_005157.4	638	gGc/gAc	11/11	1	2	FACETS	0.308	0.252	0.371	0.308	0.252	0.371	SUBCLONAL	1	TRUE	1	0.492750414531509	2		851	461	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0022874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	36	272	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.752	0.62	0.9	0.752	0.62	0.9	SUBCLONAL	1	TRUE	1	0.29	2		272	330	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0022874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	82	569	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.854	0.753	0.962	0.854	0.753	0.962	CLONAL	1	TRUE	1	0.29	2		569	662	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0022874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	119	628	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	0.29	2		629	653	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	100	855	0	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	1	2	FACETS	0.839	0.749	0.935	0.839	0.749	0.935	CLONAL	1	TRUE	1	0.29	2		855	822	SUCCESS
APC	324	MSKCC	GRCh37	5	112175630	112175630	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	29	382	1	ENST00000257430.4:c.4339C>T	p.Gln1447Ter	p.Q1447*	ENST00000257430	NM_000038.5	1447	Caa/Taa	16/16	1	2	FACETS	0.557	0.447	0.682	0.557	0.447	0.682	SUBCLONAL	1	TRUE	1	0.29	2		383	359	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636204	87636204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs532184896	NA	P-0022874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	56	547	0	ENST00000277120.3:c.2369G>A	p.Arg790Gln	p.R790Q	ENST00000277120		790	cGa/cAa	19/19	1	2	FACETS	0.707	0.606	0.818	0.707	0.606	0.818	SUBCLONAL	1	TRUE	1	0.29	2		547	546	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0022874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	82	443	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	1	2	FACETS	0.827	0.735	0.923	1	0.982	1	CLONAL	2	TRUE	1	0.29	2		443	342	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031883	26031884	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs758780418	NA	P-0022874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	55	251	0	ENST00000244661.2:c.405_406del	p.Arg135SerfsTer12	p.R135Sfs*12	ENST00000244661	NM_003537.3	135	agAGcg/agcg	1/1	1	2	FACETS	0.998	0.857	1	0.998	0.857	1	CLONAL	1	TRUE	1	0.29	2		251	380	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984743	72984743	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	146	801	0	ENST00000268489.5:c.2841C>G	p.Cys947Trp	p.C947W	ENST00000268489	NM_006885.3	947	tgC/tgG	3/10	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.29	2		801	959	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375332	15375332	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	104	753	0	ENST00000263377.2:c.1095T>G	p.Phe365Leu	p.F365L	ENST00000263377	NM_058243.2	365	ttT/ttG	6/20	1	2	FACETS	0.889	0.795	0.988	0.889	0.795	0.988	CLONAL	1	TRUE	1	0.29	2		753	807	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592075	67592075	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs761888083	NA	P-0022874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	63	328	0	ENST00000274335.5:c.1891C>T	p.Arg631Ter	p.R631*	ENST00000274335		631	Cga/Tga	14/15	1	2	FACETS	0.932	0.808	1	0.932	0.808	1	CLONAL	1	TRUE	1	0.29	2		328	466	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592139	67592140	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	61	298	0	ENST00000274335.5:c.1956dup	p.Lys653Ter	p.K653*	ENST00000274335		652	agt/agTt	14/15	1	2	FACETS	0.999	0.865	1	0.999	0.865	1	CLONAL	1	TRUE	1	0.29	2		298	421	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998971	11998972	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0022875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	13	401	0	ENST00000353533.5:c.476dup	p.Tyr160IlefsTer14	p.Y160Ifs*14	ENST00000353533	NM_003010.3	158	tgc/tgCc	4/11	0.480909489253246	1	FACETS	0.244	0.175	0.329	0.244	0.175	0.329	SUBCLONAL	1	TRUE	0	0.480909489253246	1		401	168	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922364	178922364	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397514565	NA	P-0022875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	31	424	1	ENST00000263967.3:c.1133G>A	p.Cys378Tyr	p.C378Y	ENST00000263967	NM_006218.2	378	tGt/tAt	6/21	1	2	FACETS	0.737	0.602	0.885	0.737	0.602	0.885	SUBCLONAL	1	TRUE	1	0.480909489253246	2		425	175	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637813	176637813	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	65	622	1	ENST00000439151.2:c.2413G>A	p.Val805Ile	p.V805I	ENST00000439151	NM_022455.4	805	Gtt/Att	5/23	1	2	FACETS	0.99	0.867	1	0.99	0.867	1	CLONAL	1	TRUE	1	0.480909489253246	2		623	273	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521543	8521543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868728165	NA	P-0022882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	57	563	0	ENST00000356435.5:c.695G>A	p.Arg232His	p.R232H	ENST00000356435		232	cGc/cAc	9/35	0.158477024301603	4	FACETS	0.939	0.807	1	0.47	0.403	0.542	INDETERMINATE	1	TRUE	2	0.313086548130691	4		563	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0022882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	255	954	1	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.313086548130691	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.313086548130691	2		955	758	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510648	38510648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	2751	1140	0	ENST00000254066.5:c.902G>A	p.Gly301Asp	p.G301D	ENST00000254066	NM_000964.3	301	gGc/gAc	7/9	0.313086548130691	20	FACETS	0.981	0.969	0.992			1	CLONAL	19	TRUE	NA	0.313086548130691	20		1140	3601	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29197761	29197762	+	splice_acceptor_variant	Splice_Site	INS	-	-	TGTA	novel	NA	P-0022882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	158	1215	0	ENST00000240100.2:c.434-5_434-2dup		p.X145_splice	ENST00000240100	NM_001394.6	145			0.313086548130691	3	FACETS	1	0.931	1	0.51	0.466	0.556	CLONAL	1	TRUE	1	0.313086548130691	3		1215	1144	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	568	445	0				ENST00000310581	NM_198253.2	-/1132			0.564855246570399	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	1	0.564855246570399	4		445	937	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0022887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	349	640	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.556547851041939	3	FACETS	0.957	0.911	1	0.957	0.911	1	CLONAL	2	TRUE	1	0.564855246570399	3		640	828	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253448	226253448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	40	187	0	ENST00000366813.1:c.220G>A	p.Glu74Lys	p.E74K	ENST00000366813		74	Gaa/Aaa	2/3	0.558702586368757	4	FACETS	0.951	0.797	1	0.317	0.265	0.374	CLONAL	1	TRUE	1	0.564855246570399	4		187	233	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245118	46245118	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0022887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	134	745	0	ENST00000334344.6:c.3212C>G	p.Ser1071Ter	p.S1071*	ENST00000334344	NM_152641.2	1071	tCa/tGa	15/21	1	2	FACETS	0.86	0.785	0.938	0.86	0.785	0.938	CLONAL	1	TRUE	1	0.564855246570399	2		745	552	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245192	46245192	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	140	683	0	ENST00000334344.6:c.3286C>G	p.Gln1096Glu	p.Q1096E	ENST00000334344	NM_152641.2	1096	Cag/Gag	15/21	1	2	FACETS	0.925	0.847	1	0.925	0.847	1	CLONAL	1	TRUE	1	0.564855246570399	2		683	536	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640117	3640117	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	379	1497	0	ENST00000294008.3:c.3522T>G	p.Asp1174Glu	p.D1174E	ENST00000294008	NM_032444.2	1174	gaT/gaG	12/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.564855246570399	2		1497	1284	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945726	17945726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1178958564	NA	P-0022887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	212	1082	1	ENST00000458235.1:c.2134G>A	p.Gly712Ser	p.G712S	ENST00000458235	NM_000215.3	712	Ggc/Agc	16/24	1	2	FACETS	0.929	0.865	0.995	0.929	0.865	0.995	CLONAL	1	TRUE	1	0.564855246570399	2		1083	808	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096244	71096244	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	226	260	0	ENST00000318789.4:c.513A>C	p.Gln171His	p.Q171H	ENST00000318789	NM_032682.5	171	caA/caC	10/21	0.558702586368757	4	FACETS	0.93	0.878	0.981	0.93	0.878	0.981	CLONAL	3	TRUE	1	0.564855246570399	4		260	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0022892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	104	953	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.991	0.891	1	0.991	0.891	1	CLONAL	1	FALSE	1	0.394571367069482	2		955	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	107	1171	0	ENST00000269305.4:c.472C>A	p.Arg158Ser	p.R158S	ENST00000269305	NM_001126112.2	158	Cgc/Agc	5/11	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	1	0.394571367069482	2		1171	521	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538909	23538909	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs373263457	NA	P-0022892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	98	734	0	ENST00000380871.4:c.530A>G	p.Tyr177Cys	p.Y177C	ENST00000380871	NM_006167.3	177	tAt/tGt	2/2	0.331287934485803	3	FACETS	0.778	0.7	0.861	0.778	0.7	0.861	SUBCLONAL	2	FALSE	1	0.394571367069482	3		734	382	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141493	11141493	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	161	910	1	ENST00000358026.2:c.3470G>A	p.Arg1157Gln	p.R1157Q	ENST00000358026	NM_001128849.1	1157	cGg/cAg	25/36	0.337398532364347	2	FACETS	1	0.961	1	0.54	0.496	0.587	CLONAL	1	TRUE	0	0.337398532364347	2		911	883	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249331	133249331	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	337	1194	0	ENST00000320574.5:c.1568A>G	p.Glu523Gly	p.E523G	ENST00000320574	NM_006231.2	523	gAg/gGg	15/49	0.330236560273061	4	FACETS	0.962	0.908	1	0.962	0.908	1	CLONAL	2	TRUE	2	0.337398532364347	4		1194	1389	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748284	43748284	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	576	1227	0	ENST00000382044.4:c.2522del	p.Pro841LeufsTer2	p.P841Lfs*2	ENST00000382044	NM_001141980.1	841	cCt/ct	12/28	0.329881739330737	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.337398532364347	3		1227	1258	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652844	29652844	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	123	277	0	ENST00000356175.3:c.4779A>C	p.Lys1593Asn	p.K1593N	ENST00000356175	NM_000267.3	1593	aaA/aaC	36/57	0.330236560273061	4	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	2	0.337398532364347	4		277	470	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508188	38508188	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	216	546	0	ENST00000254066.5:c.496A>G	p.Lys166Glu	p.K166E	ENST00000254066	NM_000964.3	166	Aag/Gag	5/9	0.330236560273061	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.337398532364347	4		546	793	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0022904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	38	550	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.244231552493688	3	FACETS	0.538	0.444	0.644	0.269	0.222	0.322	SUBCLONAL	1	TRUE	1	0.24423103756344	3		552	649	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830751	72830751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761415382	NA	P-0022904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	79	899	1	ENST00000268489.5:c.5830G>A	p.Ala1944Thr	p.A1944T	ENST00000268489	NM_006885.3	1944	Gcc/Acc	9/10	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.24423103756344	2		900	599	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427480	427480	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs566852836	NA	P-0022904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	86	999	0	ENST00000399788.2:c.2689G>C	p.Glu897Gln	p.E897Q	ENST00000399788	NM_001042603.1	897	Gag/Cag	19/28	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.24423103756344	2		999	649	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061131	38061202	+	inframe_deletion	In_Frame_Del	DEL	GCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTG	GCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTG	-	novel	NA	P-0022904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	115	337	0	ENST00000250448.2:c.787_858del	p.Gln263_Gly286del	p.Q263_G286del	ENST00000250448	NM_004496.3	263	CAGAAGCGCTTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGCGGC/-	2/2	1	2	FACETS	0.892	0.818	0.966	1	0.992	1	CLONAL	4	TRUE	1	0.24423103756344	2		337	264	SUCCESS
APC	324	MSKCC	GRCh37	5	112157630	112157631	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	46	905	0	ENST00000257430.4:c.1351dup	p.Cys451LeufsTer9	p.C451Lfs*9	ENST00000257430	NM_000038.5	450	-/T	11/16	1	2	FACETS	0.923	0.779	1	0.923	0.779	1	CLONAL	1	TRUE	1	0.24423103756344	2		905	408	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0022906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	161	840	2	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.181079695087713	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.181079695087713	3		842	866	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0022906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	67	412	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.178717939591601	2	FACETS	0.971	0.848	1	0.971	0.848	1	CLONAL	2	TRUE	0	0.181079695087713	2		413	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578476	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTGCCGGGCGG	GGGTGCCGGGCGG	-	rs876659215	NA	P-0022906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	357	1256	0	ENST00000269305.4:c.454_466del	p.Pro152AlafsTer14	p.P152Afs*14	ENST00000269305	NM_001126112.2	152	CCGCCCGGCACCCgc/gc	5/11	0.181079695087713	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.181079695087713	3		1256	1283	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10244964	10244964	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1248265917	NA	P-0022906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	88	882	1	ENST00000340748.4:c.4745C>T	p.Pro1582Leu	p.P1582L	ENST00000340748		1582	cCg/cTg	39/40	0.181079695087713	3	FACETS	1	0.967	1	0.632	0.559	0.711	CLONAL	1	TRUE	1	0.181079695087713	3		883	838	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120106	70120106	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	30	154	0	ENST00000245479.2:c.1109del	p.Pro370ArgfsTer13	p.P370Rfs*13	ENST00000245479	NM_000346.3	370	Ccg/cg	3/3	0.181079695087713	3	FACETS	1	0.894	1	1	0.894	1	CLONAL	3	TRUE	0	0.181079695087713	3		154	107	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2966388	2966388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145836432	NA	P-0022906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	171	955	0	ENST00000396946.4:c.1792G>A	p.Ala598Thr	p.A598T	ENST00000396946	NM_032415.4	598	Gcc/Acc	14/25	0.103326015127433	4	FACETS	0.983	0.903	1	0.983	0.903	1	INDETERMINATE	2	TRUE	2	0.181079695087713	4		955	1135	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432664	29432664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113994087	NA	P-0121428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	131	706	0	ENST00000389048.3:c.3824G>A	p.Arg1275Gln	p.R1275Q	ENST00000389048	NM_004304.4	1275	cGa/cAa	25/29	0.63792993744528	3	FACETS	0.944	0.86	1	0.472	0.43	0.516	CLONAL	1	NA	1	0.63792993744528	3		706	574	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999351	100999351	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	151	1188	0	ENST00000325455.5:c.451C>A	p.Pro151Thr	p.P151T	ENST00000325455	NM_001202474.3	151	Cca/Aca	1/8	0.63792993744528	3	FACETS	0.793	0.726	0.864	0.397	0.363	0.432	SUBCLONAL	1	NA	1	0.63792993744528	3		1188	787	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	83	445	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.758	0.672	0.849	0.758	0.672	0.849	SUBCLONAL	1	TRUE	1	0.520206593805605	2		445	421	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0022912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	169	815	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	0.520206593805605	2		816	590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934576	NA	P-0022913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	716	720	1	ENST00000269305.4:c.818G>C	p.Arg273Pro	p.R273P	ENST00000269305	NM_001126112.2	273	cGt/cCt	8/11	0.928806049517281	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.928806049517281	1		721	776	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919252	48919253	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	109	341	0	ENST00000267163.4:c.418dup	p.Thr140AsnfsTer6	p.T140Nfs*6	ENST00000267163	NM_000321.2	139	-/A	4/27	0.928806049517281	1	FACETS	0.892	0.841	0.938	0.892	0.841	0.938	CLONAL	1	TRUE	0	0.928806049517281	1		341	141	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944310	206944310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755490123	NA	P-0022913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	476	789	0	ENST00000423557.1:c.320C>T	p.Ala107Val	p.A107V	ENST00000423557	NM_000572.2	107	gCg/gTg	3/5	1	2	FACETS	0.946	0.907	0.984	0.946	0.907	0.984	CLONAL	1	TRUE	1	0.928806049517281	2		789	1084	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891647	28891647	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	569	876	1	ENST00000282397.4:c.3374C>A	p.Ser1125Tyr	p.S1125Y	ENST00000282397	NM_002019.4	1125	tCt/tAt	25/30	0.928806049517281	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.928806049517281	1		877	625	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863630	68863630	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	689	1000	0	ENST00000261769.5:c.2369C>A	p.Thr790Asn	p.T790N	ENST00000261769	NM_004360.3	790	aCc/aAc	15/16	1	2	FACETS	0.974	0.941	1	0.974	0.941	1	CLONAL	1	TRUE	1	0.928806049517281	2		1000	1523	SUCCESS
APC	324	MSKCC	GRCh37	5	112176227	112176227	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	286	580	0	ENST00000257430.4:c.4936G>T	p.Gly1646Trp	p.G1646W	ENST00000257430	NM_000038.5	1646	Ggg/Tgg	16/16	1	2	FACETS	0.995	0.944	1	0.995	0.944	1	CLONAL	1	TRUE	1	0.928806049517281	2		580	619	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924564	131924564	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs373428259	NA	P-0022913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	204	533	0	ENST00000265335.6:c.1237C>G	p.Gln413Glu	p.Q413E	ENST00000265335		413	Caa/Gaa	8/25	1	2	FACETS	0.902	0.845	0.959	0.902	0.845	0.959	CLONAL	1	TRUE	1	0.928806049517281	2		533	487	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729695	41729696	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0022913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	434	726	3	ENST00000242208.4:c.833_834delinsTT	p.Gly278Val	p.G278V	ENST00000242208	NM_002192.2	278	gGG/gTT	3/3	1	2	FACETS	0.956	0.915	0.996	0.956	0.915	0.996	CLONAL	1	TRUE	1	0.928806049517281	2		729	978	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455127	50455127	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	232	402	0	ENST00000331340.3:c.674A>T	p.Asn225Ile	p.N225I	ENST00000331340	NM_006060.4	225	aAc/aTc	6/8	1	2	FACETS	0.953	0.898	1	0.953	0.898	1	CLONAL	1	TRUE	1	0.928806049517281	2		402	524	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521291	8521291	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	207	320	0	ENST00000356435.5:c.947A>C	p.Gln316Pro	p.Q316P	ENST00000356435		316	cAg/cCg	9/35	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.928806049517281	2		320	413	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137320967	137320968	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0022913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	824	1379	1	ENST00000481739.1:c.924_925delinsTT	p.Leu309Phe	p.L309F	ENST00000481739	NM_002957.4	308	ctGCtc/ctTTtc	7/10	1	2	FACETS	0.945	0.915	0.974	0.945	0.915	0.974	CLONAL	1	TRUE	1	0.928806049517281	2		1380	1878	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933445	39933445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1177018779	NA	P-0022913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	571	834	1	ENST00000378444.4:c.1154C>T	p.Ala385Val	p.A385V	ENST00000378444	NM_001123385.1	385	gCg/gTg	4/15	1	2	FACETS	0.957	0.921	0.993	0.957	0.921	0.993	CLONAL	1	TRUE	1	0.928806049517281	2		835	1285	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	45	445	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.812	0.687	0.947	0.812	0.687	0.947	CLONAL	1	TRUE	1	0.429654680213494	2		445	258	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	244	602	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	0.429654680213494	2	FACETS	0.959	0.904	1	0.959	0.904	1	CLONAL	2	TRUE	0	0.429654680213494	2		602	592	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696462	47696462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	212	639	3	ENST00000347630.2:c.361C>T	p.Arg121Trp	p.R121W	ENST00000347630	NM_001007230.1	121	Cgg/Tgg	6/11	0.429654680213494	2	FACETS	0.905	0.848	0.963	0.905	0.848	0.963	CLONAL	2	TRUE	0	0.429654680213494	2		642	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576955	7577033	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGTGAATCTGAGGCATAACTGCACCCTTGGTCTCCTCCACCGCTTCTTGTCCTGCTTGCTTACCTCGCTTAGTGCTCC	AAGTGAATCTGAGGCATAACTGCACCCTTGGTCTCCTCCACCGCTTCTTGTCCTGCTTGCTTACCTCGCTTAGTGCTCC	-	novel	NA	P-0022914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	173	757	0	ENST00000269305.4:c.905_920-29del		p.X302_splice	ENST00000269305	NM_001126112.2	302		8/11	0.429654680213494	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.429654680213494	1		757	563	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25458586	25458586	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	91	549	0	ENST00000264709.3:c.2587G>T	p.Glu863Ter	p.E863*	ENST00000264709	NM_175629.2	863	Gaa/Taa	22/23	1	2	FACETS	0.931	0.831	1	0.931	0.831	1	CLONAL	1	TRUE	1	0.429654680213494	2		549	455	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848657	151848657	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	73	321	0	ENST00000262189.6:c.12536G>C	p.Gly4179Ala	p.G4179A	ENST00000262189	NM_170606.2	4179	gGa/gCa	50/59	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.429654680213494	2		321	325	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650326	48650326	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	154	854	1	ENST00000376670.3:c.296G>A	p.Gly99Asp	p.G99D	ENST00000376670	NM_002049.3	99	gGc/gAc	3/6	1	2	FACETS	0.986	0.904	1	0.986	0.904	1	CLONAL	1	TRUE	1	0.429654680213494	2		855	727	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0022916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	386	737	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.503537132794384	2	FACETS	0.921	0.881	0.961	0.921	0.881	0.961	CLONAL	2	TRUE	0	0.527780616795143	2		739	794	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210451	2210451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138206172	NA	P-0022916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	150	756	3	ENST00000398665.3:c.1058C>T	p.Ala353Val	p.A353V	ENST00000398665	NM_032482.2	353	gCg/gTg	13/28	0.527780616795143	1	FACETS	0.655	0.6	0.711	0.655	0.6	0.711	SUBCLONAL	1	TRUE	0	0.527780616795143	1		759	639	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500637	99500637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200539075	NA	P-0022916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	186	465	1	ENST00000268035.6:c.4070G>A	p.Arg1357Gln	p.R1357Q	ENST00000268035	NM_000875.3	1357	cGg/cAg	21/21	0.527780616795143	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.527780616795143	1		466	447	SUCCESS
BLM	641	MSKCC	GRCh37	15	91306247	91306247	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs377563699	NA	P-0022916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	79	626	0	ENST00000355112.3:c.1934A>G	p.Gln645Arg	p.Q645R	ENST00000355112	NM_000057.2	645	cAa/cGa	8/22	0.527780616795143	1	FACETS	0.346	0.304	0.391	0.346	0.304	0.391	SUBCLONAL	1	TRUE	0	0.527780616795143	1		626	637	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40486041	40486041	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	276	646	0	ENST00000264657.5:c.824T>C	p.Leu275Pro	p.L275P	ENST00000264657	NM_139276.2	275	cTt/cCt	9/24	0.18569780563567	2	FACETS	1	0.988	1	0.596	0.561	0.631	INDETERMINATE	1	TRUE	0	0.527780616795143	2		646	878	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804385	46804386	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	102	481	0	ENST00000290295.7:c.621dup	p.Pro208SerfsTer2	p.P208Sfs*2	ENST00000290295	NM_006361.5	207	-/T	2/2	0.18569780563567	2	FACETS	0.683	0.612	0.757	0.341	0.306	0.379	INDETERMINATE	1	TRUE	0	0.527780616795143	2		481	566	SUCCESS
APC	324	MSKCC	GRCh37	5	112155043	112155043	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0022916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	205	474	0	ENST00000257430.4:c.1312+2T>G		p.X438_splice	ENST00000257430	NM_000038.5	438			0.527780616795143	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.527780616795143	1		474	541	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711033	114711034	+	splice_donor_variant	Splice_Site	DNP	GT	GT	CA	novel	NA	P-0022916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	85	311	0	ENST00000543371.1:c.256+1_256+2delinsCA		p.X86_splice	ENST00000543371	NM_001198531.1	86			0.159554606938905	2	FACETS	0.997	0.89	1	0.499	0.445	0.555	INDETERMINATE	1	TRUE	0	0.527780616795143	2		311	323	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0022917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	34	652	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.609	0.497	0.736	0.609	0.497	0.736	SUBCLONAL	1	TRUE	1	0.2	2		652	558	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268525	46268525	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199688314	NA	P-0022917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	39	417	0	ENST00000371998.3:c.2912C>T	p.Ala971Val	p.A971V	ENST00000371998		971	gCg/gTg	15/23	1	2	FACETS	0.97	0.805	1	0.97	0.805	1	CLONAL	1	TRUE	1	0.2	2		417	402	SUCCESS
APC	324	MSKCC	GRCh37	5	112111420	112111420	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	19	361	0	ENST00000257430.4:c.518del	p.Pro173LeufsTer2	p.P173Lfs*2	ENST00000257430	NM_000038.5	173	Cct/ct	5/16	1	2	FACETS	0.995	0.759	1	0.995	0.759	1	CLONAL	1	TRUE	1	0.2	2		361	191	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0022919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	2603	708	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.301234054763394	25	FACETS	1	0.997	1			1	CLONAL	23	FALSE	NA	0.301234054763394	25		709	3285	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0022919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	249	893	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.300451951327336	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	FALSE	0	0.301234054763394	2		893	797	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289639	15289639	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	117	969	0	ENST00000263388.2:c.3832G>A	p.Ala1278Thr	p.A1278T	ENST00000263388	NM_000435.2	1278	Gcc/Acc	23/33	0.301234054763394	3	FACETS	0.859	0.773	0.951	0.43	0.386	0.476	CLONAL	1	FALSE	1	0.301234054763394	3		969	1040	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518695	176518695	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	439	769	0	ENST00000292408.4:c.613C>T	p.Gln205Ter	p.Q205*	ENST00000292408	NM_213647.1	205	Cag/Tag	6/18	0.301234054763394	10	FACETS	0.935	0.891	0.979			1	CLONAL	5	FALSE	NA	0.301234054763394	10		769	1375	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435114	110435114	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763264747	NA	P-0022920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	187	1085	1	ENST00000375856.3:c.3287C>T	p.Ala1096Val	p.A1096V	ENST00000375856	NM_003749.2	1096	gCc/gTc	1/2	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.507319759217917	2		1086	690	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992187	11992187	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	151	733	0	ENST00000396373.4:c.277G>C	p.Ala93Pro	p.A93P	ENST00000396373	NM_001987.4	93	Gct/Cct	3/8	0.123917710758986	4	FACETS	1	0.985	1	0.678	0.621	0.736	INDETERMINATE	1	TRUE	2	0.507319759217917	4		733	662	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873684	35873684	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	218	827	0	ENST00000216797.5:c.167C>G	p.Pro56Arg	p.P56R	ENST00000216797	NM_020529.2	56	cCg/cGg	1/6	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.507319759217917	2		827	809	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847298	68847369	+	inframe_deletion	In_Frame_Del	DEL	CAGCGTGGGAGGCTGTATACACCATATTGAATGATGATGGTGGACAATTTGTCGTCACCACAAATCCAGTGA	CAGCGTGGGAGGCTGTATACACCATATTGAATGATGATGGTGGACAATTTGTCGTCACCACAAATCCAGTGA	-	novel	NA	P-0022920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	59	891	0	ENST00000261769.5:c.1220_1291del	p.Pro407_Asn431delinsHis	p.P407_N431delinsH	ENST00000261769	NM_004360.3	407	cCAGCGTGGGAGGCTGTATACACCATATTGAATGATGATGGTGGACAATTTGTCGTCACCACAAATCCAGTGAac/cac	9/16	0.507319759217917	1	FACETS	0.334	0.288	0.385	0.334	0.288	0.385	SUBCLONAL	1	TRUE	0	0.507319759217917	1		891	519	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0022923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	42	943	1	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.225036451385599	5	FACETS	0.832	0.694	0.986	0.277	0.231	0.329	CLONAL	1	FALSE	2	0.225036451385599	5		944	600	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341817	8341817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	19	957	1	ENST00000356435.5:c.4823C>T	p.Ala1608Val	p.A1608V	ENST00000356435		1608	gCa/gTa	29/35	0.225036451385599	1	FACETS	0.442	0.335	0.568	0.442	0.335	0.568	SUBCLONAL	1	FALSE	0	0.225036451385599	1		958	339	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600332	10600332	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	53	875	1	ENST00000171111.5:c.1523G>A	p.Ser508Asn	p.S508N	ENST00000171111	NM_203500.1	508	aGc/aAc	4/6	0.170749017706084	3	FACETS	0.788	0.671	0.917	0.394	0.335	0.459	CLONAL	1	FALSE	1	0.225036451385599	3		876	665	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979620	7979620	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559401066	NA	P-0022926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	51	697	1	ENST00000319144.4:c.1405C>T	p.Arg469Trp	p.R469W	ENST00000319144	NM_001139.2	469	Cgg/Tgg	11/15	1	2	FACETS	0.983	0.833	1	0.983	0.833	1	CLONAL	1	TRUE	1	0.12	2		698	865	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435065	56435065	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	52	724	0	ENST00000407977.2:c.2072C>G	p.Pro691Arg	p.P691R	ENST00000407977		691	cCt/cGt	9/10	1	2	FACETS	0.875	0.743	1	0.875	0.743	1	CLONAL	1	TRUE	1	0.12	2		724	990	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0022930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	492	734	3	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.445470714749834	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.445470714749834	2		737	1103	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610382	10610382	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	453	884	0	ENST00000171111.5:c.328A>G	p.Met110Val	p.M110V	ENST00000171111	NM_203500.1	110	Atg/Gtg	2/6	0.445470714749834	2	FACETS	0.932	0.892	0.972	0.932	0.892	0.972	CLONAL	2	TRUE	0	0.445470714749834	2		884	1091	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219321	1219321	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0022930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	391	708	0	ENST00000326873.7:c.375-2A>T		p.X125_splice	ENST00000326873	NM_000455.4	125			0.445470714749834	2	FACETS	0.947	0.904	0.99	0.947	0.904	0.99	CLONAL	2	TRUE	0	0.445470714749834	2		708	927	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243777010	243777010	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	489	710	0	ENST00000263826.5:c.659G>C	p.Arg220Pro	p.R220P	ENST00000263826	NM_005465.4	220	cGt/cCt	7/13	0.445470714749834	3	FACETS	0.914	0.879	0.949	0.914	0.879	0.949	CLONAL	3	TRUE	0	0.445470714749834	3		710	979	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628853	187628853	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs370215067	NA	P-0022930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	200	730	0	ENST00000441802.2:c.2129A>G	p.Asn710Ser	p.N710S	ENST00000441802	NM_005245.3	710	aAt/aGt	2/27	1	2	FACETS	0.921	0.853	0.991	0.921	0.853	0.991	CLONAL	1	TRUE	1	0.445470714749834	2		730	975	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0022934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	242	649	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.221946485912824	3	FACETS	0.866	0.81	0.924	1	0.99	1	CLONAL	3	TRUE	1	0.221946485912824	3		649	932	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0022934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	37	706	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.221946485912824	1	FACETS	0.665	0.548	0.795	0.665	0.548	0.795	SUBCLONAL	1	TRUE	0	0.221946485912824	1		706	446	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943652	17943652	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	133	1212	2	ENST00000458235.1:c.2437G>T	p.Asp813Tyr	p.D813Y	ENST00000458235	NM_000215.3	813	Gac/Tac	18/24	0.125221756794973	3	FACETS	1	0.974	1	0.604	0.547	0.664	INDETERMINATE	1	TRUE	1	0.221946485912824	3		1214	1102	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579582	7579583	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	88	939	1	ENST00000269305.4:c.104dup	p.Leu35PhefsTer8	p.L35Ffs*8	ENST00000269305	NM_001126112.2	35	ttg/ttTg	4/11	0.221946485912824	1	FACETS	0.981	0.869	1	0.981	0.869	1	CLONAL	1	TRUE	0	0.221946485912824	1		940	719	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797406	45797406	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	52	963	0	ENST00000450313.1:c.1113C>G	p.Ser371Arg	p.S371R	ENST00000450313	NM_012222.2	371	agC/agG	12/16	1	2	FACETS	0.632	0.537	0.737	0.632	0.537	0.737	SUBCLONAL	1	TRUE	1	0.221946485912824	2		963	741	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851186	63851186	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	101	805	0	ENST00000279873.7:c.1964A>G	p.Asp655Gly	p.D655G	ENST00000279873	NM_032199.2	655	gAc/gGc	10/10	0.125221756794973	3	FACETS	1	0.959	1	0.575	0.513	0.641	INDETERMINATE	1	TRUE	1	0.221946485912824	3		805	879	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456797	32456797	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	92	972	0	ENST00000332351.3:c.95G>T	p.Gly32Val	p.G32V	ENST00000332351	NM_024426.4	32	gGa/gTa	1/10	1	2	FACETS	0.982	0.872	1	0.982	0.872	1	CLONAL	1	TRUE	1	0.221946485912824	2		972	844	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022675	12022675	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	81	776	1	ENST00000396373.4:c.781G>T	p.Glu261Ter	p.E261*	ENST00000396373	NM_001987.4	261	Gag/Tag	5/8	0.109762739047241	4	FACETS	1	0.972	1	0.685	0.604	0.772	INDETERMINATE	1	TRUE	2	0.221946485912824	4		777	651	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984395	72984395	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	31	776	0	ENST00000268489.5:c.3189G>T	p.Arg1063Ser	p.R1063S	ENST00000268489	NM_006885.3	1063	agG/agT	3/10	0.216533924373713	1	FACETS	0.408	0.329	0.498	0.408	0.329	0.498	SUBCLONAL	1	TRUE	0	0.221946485912824	1		776	609	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89871737	89871737	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555571174	NA	P-0022934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	47	946	0	ENST00000389301.3:c.660G>C	p.Gln220His	p.Q220H	ENST00000389301	NM_000135.2	220	caG/caC	7/43	0.216533924373713	1	FACETS	0.472	0.397	0.556	0.472	0.397	0.556	SUBCLONAL	1	TRUE	0	0.221946485912824	1		946	797	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369273	40369273	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	141	757	0	ENST00000293328.3:c.1285C>A	p.Arg429Ser	p.R429S	ENST00000293328	NM_012448.3	429	Cgt/Agt	11/19	0.125221756794973	3	FACETS	0.774	0.705	0.847	0.774	0.705	0.847	INDETERMINATE	2	TRUE	1	0.221946485912824	3		757	912	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155362	185155362	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	47	669	0	ENST00000265026.3:c.603T>G	p.Asn201Lys	p.N201K	ENST00000265026	NM_004721.4	201	aaT/aaG	3/14	0.120096855527097	3	FACETS	0.679	0.572	0.798	0.226	0.19	0.266	INDETERMINATE	1	TRUE	0	0.221946485912824	3		669	693	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133552	55133552	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	94	771	0	ENST00000257290.5:c.856G>T	p.Gly286Ter	p.G286*	ENST00000257290	NM_006206.4	286	Gga/Tga	6/23	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.221946485912824	2		771	640	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081585	143081585	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	40	827	1	ENST00000262992.4:c.1489C>A	p.Pro497Thr	p.P497T	ENST00000262992	NM_001101669.1	497	Ccc/Acc	15/24	1	2	FACETS	0.599	0.497	0.713	0.599	0.497	0.713	SUBCLONAL	1	TRUE	1	0.221946485912824	2		828	602	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891335	101891336	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	119	805	0	ENST00000374994.4:c.298dup	p.Cys100LeufsTer9	p.C100Lfs*9	ENST00000374994	NM_004612.2	99	tat/taTt	2/9	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.221946485912824	2		805	781	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328329	137328329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	127	1021	0	ENST00000481739.1:c.1258C>T	p.Leu420Phe	p.L420F	ENST00000481739	NM_002957.4	420	Ctc/Ttc	10/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.221946485912824	2		1021	943	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038717	47038717	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0022934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	60	1029	0	ENST00000377604.3:c.725-1G>T		p.X242_splice	ENST00000377604	NM_001204468.1	242			0.216533924373713	1	FACETS	0.72	0.619	0.829	0.72	0.619	0.829	SUBCLONAL	1	TRUE	0	0.221946485912824	1		1029	668	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453135	140453136	+	missense_variant	Missense_Mutation	DNP	CA	CA	TT	rs121913377	NA	P-0022935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	60	645	0	ENST00000288602.6:c.1799_1800delinsAA	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTG/gAA	15/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		645	404	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	112	445	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.955	0.869	1	0.955	0.869	1	CLONAL	1	FALSE	1	0.691819698160705	2		445	339	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489787	2489787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139725610	NA	P-0022938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	152	732	4	ENST00000355716.4:c.184C>T	p.Arg62Cys	p.R62C	ENST00000355716	NM_003820.2	62	Cgt/Tgt	3/8	1	2	FACETS	0.951	0.877	1	0.951	0.877	1	CLONAL	1	FALSE	1	0.691819698160705	2		736	462	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	217	605	0	ENST00000371953.3:c.517C>G	p.Arg173Gly	p.R173G	ENST00000371953	NM_000314.4	173	Cgc/Ggc	6/9	0.691819698160705	1	FACETS	0.933	0.879	0.986	0.933	0.879	0.986	CLONAL	1	FALSE	0	0.691819698160705	1		605	440	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748872	43748872	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	329	903	0	ENST00000382044.4:c.1934G>T	p.Ser645Ile	p.S645I	ENST00000382044	NM_001141980.1	645	aGt/aTt	12/28	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.691819698160705	2		903	852	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0022939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	20	841	1	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	0.231718702339943	4	FACETS	0.221	0.168	0.283	0.111	0.084	0.142	INDETERMINATE	1	TRUE	2	0.817952129018057	4		842	402	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475550	12475550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479145908	NA	P-0022939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	80	647	1	ENST00000287820.6:c.1424C>T	p.Thr475Met	p.T475M	ENST00000287820	NM_015869.4	475	aCg/aTg	7/7	0.268332540122459	5	FACETS	1	0.942	1	0.368	0.325	0.413	INDETERMINATE	1	TRUE	2	0.817952129018057	5		648	395	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222293	2222293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763973302	NA	P-0022939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	15	811	0	ENST00000326181.6:c.577C>T	p.Arg193Trp	p.R193W	ENST00000326181	NM_032271.2	193	Cgg/Tgg	8/21	0.211560336053773	3	FACETS	0.217	0.159	0.287	0.072	0.053	0.096	INDETERMINATE	1	TRUE	0	0.817952129018057	3		811	238	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849417	68849417	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0022939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	77	631	0	ENST00000261769.5:c.1321-1G>C		p.X441_splice	ENST00000261769	NM_004360.3	441			0.211560336053773	3	FACETS	0.99	0.88	1	0.33	0.293	0.369	INDETERMINATE	1	TRUE	0	0.817952129018057	3		631	268	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0022945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	186	826	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.271864965006668	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.271864965006668	1		828	865	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491645	56491645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	120	699	1	ENST00000267101.3:c.2537G>T	p.Ser846Ile	p.S846I	ENST00000267101	NM_001982.3	846	aGt/aTt	21/28	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.271864965006668	2		700	785	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248408	59248409	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CG	novel	NA	P-0022945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	138	421	5	ENST00000371222.2:c.333_334dup	p.Glu112AlafsTer37	p.E112Afs*37	ENST00000371222	NM_002228.3	112	gag/gCGag	1/1	0.265336068243361	2	FACETS	0.839	0.766	0.915	0.839	0.766	0.915	CLONAL	2	TRUE	0	0.271864965006668	2		426	605	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346492	89346493	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTTCAC	novel	NA	P-0022945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	270	756	2	ENST00000301030.4:c.6452_6457dup	p.Gly2151_Glu2152dup	p.G2151_E2152dup	ENST00000301030	NM_001256183.1	2151	gcg/gGTGAAGcg	9/13	0.271864965006668	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.271864965006668	3		758	1087	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265933	41266400	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTA	AATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTA	-	novel	NA	P-0022945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	79	55	2	ENST00000349496.5:c.14-80_242-41del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.271864965006668	2	FACETS	1	0.964	1	1	0.988	1	CLONAL	4	TRUE	0	0.271864965006668	2		57	131	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0022946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	82	693	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.696	0.615	0.782	0.696	0.615	0.782	SUBCLONAL	1	TRUE	1	0.451501409588633	2		693	522	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0022946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	165	737	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.451501409588633	1	FACETS	0.673	0.618	0.73	0.673	0.618	0.73	SUBCLONAL	1	TRUE	0	0.451501409588633	1		739	841	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0022946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	175	631	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.451501409588633	1	FACETS	0.926	0.856	0.998	0.926	0.856	0.998	CLONAL	1	TRUE	0	0.451501409588633	1		631	648	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30098287	30098287	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	93	741	0	ENST00000331968.5:c.1685T>A	p.Val562Glu	p.V562E	ENST00000331968	NM_002742.2	562	gTg/gAg	11/18	1	2	FACETS	0.892	0.797	0.992	0.892	0.797	0.992	CLONAL	1	TRUE	1	0.451501409588633	2		741	462	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259216	89259216	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	49	517	0	ENST00000336596.2:c.360C>A	p.Phe120Leu	p.F120L	ENST00000336596	NM_005233.5	120	ttC/ttA	3/17	1	2	FACETS	0.77	0.656	0.893	0.77	0.656	0.893	SUBCLONAL	1	TRUE	1	0.451501409588633	2		517	282	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937752	44937752	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0022946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	91	855	0	ENST00000377967.4:c.2938+2T>G		p.X980_splice	ENST00000377967	NM_021140.2	980			0.451501409588633	1	FACETS	0.767	0.685	0.853	0.767	0.685	0.853	SUBCLONAL	1	TRUE	0	0.451501409588633	1		855	407	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0022947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	173	759	1	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.0644527519912099	3	FACETS	0.891	0.821	0.963			1	INDETERMINATE	2	TRUE	NA	0.274797948919794	3		760	804	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15827390	15827390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770397614	NA	P-0022947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	133	301	0	ENST00000307771.7:c.506G>A	p.Arg169Gln	p.R169Q	ENST00000307771	NM_005089.3	169	cGa/cAa	7/11	0.241241724368129	2	FACETS	1	0.956	1			1	CLONAL	3	TRUE	NA	0.274797948919794	2		301	307	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0022949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	138	917	1	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.183266109722597	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.194846939391101	3		918	670	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145430	58145430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894340	NA	P-0022949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	74	567	0	ENST00000257904.6:c.71G>A	p.Arg24His	p.R24H	ENST00000257904	NM_000075.3	24	cGt/cAt	2/8	1	2	FACETS	0.785	0.689	0.887	1	0.977	1	SUBCLONAL	2	TRUE	1	0.194846939391101	2		567	484	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054182	30054182	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	53	459	0	ENST00000338641.4:c.604G>T	p.Glu202Ter	p.E202*	ENST00000338641	NM_000268.3	202	Gaa/Taa	7/16	0.194846939391101	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.194846939391101	1		459	380	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253238	133253238	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	54	634	0	ENST00000320574.5:c.803A>C	p.Asp268Ala	p.D268A	ENST00000320574	NM_006231.2	268	gAc/gCc	9/49	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.194846939391101	2		634	450	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984250	7984250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1376422554	NA	P-0022949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	27	692	0	ENST00000319144.4:c.479C>T	p.Pro160Leu	p.P160L	ENST00000319144	NM_001139.2	160	cCc/cTc	4/15	0.183266109722597	3	FACETS	0.589	0.468	0.729	0.295	0.234	0.365	SUBCLONAL	1	TRUE	1	0.194846939391101	3		692	516	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29563013	29563014	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	43	566	1	ENST00000356175.3:c.3948_3949insA	p.Val1317SerfsTer2	p.V1317Sfs*2	ENST00000356175	NM_000267.3	1316	-/A	29/57	0.183266109722597	3	FACETS	1	0.955	1	0.719	0.603	0.845	CLONAL	1	TRUE	1	0.194846939391101	3		567	337	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602939	10602939	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0022949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	78	831	1	ENST00000171111.5:c.640-1G>T		p.X214_splice	ENST00000171111	NM_203500.1	214			0.194846939391101	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.194846939391101	1		832	526	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039429	47039429	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	40	319	0	ENST00000377604.3:c.1052C>G	p.Ser351Cys	p.S351C	ENST00000377604	NM_001204468.1	351	tCc/tGc	10/24	1	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.194846939391101	1		319	283	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210275	123210275	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	24	333	0	ENST00000218089.9:c.2627T>G	p.Val876Gly	p.V876G	ENST00000218089	NM_001042749.1	876	gTg/gGg	26/35	1	1	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	0	0.194846939391101	1		333	190	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210277	123210277	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	23	329	1	ENST00000218089.9:c.2629G>T	p.Val877Leu	p.V877L	ENST00000218089	NM_001042749.1	877	Gtg/Ttg	26/35	1	1	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	0	0.194846939391101	1		330	190	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426790	121426790	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201095611	NA	P-0022952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	81	577	5	ENST00000257555.6:c.481G>A	p.Ala161Thr	p.A161T	ENST00000257555		161	Gcc/Acc	2/10	0.188709167375661	5	FACETS	0.998	0.876	1	0.249	0.219	0.283	CLONAL	1	FALSE	1	0.188709167375661	5		582	1104	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579317	7579317	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	163	622	0	ENST00000269305.4:c.370T>C	p.Cys124Arg	p.C124R	ENST00000269305	NM_001126112.2	124	Tgc/Cgc	4/11	0.188709167375661	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	FALSE	0	0.188709167375661	2		622	707	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971115	21971115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060504185	NA	P-0022952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	120	466	0	ENST00000579755.1:c.286C>T	p.Arg96Cys	p.R96C	ENST00000579755		96	Cgt/Tgt	2/3	0.177613060093364	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	FALSE	1	0.188709167375661	3		466	623	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003043	42003043	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	178	900	0	ENST00000219905.7:c.2580G>C	p.Lys860Asn	p.K860N	ENST00000219905	NM_001164273.1	860	aaG/aaC	8/24	0.188709167375661	3	FACETS	0.998	0.919	1	0.998	0.919	1	CLONAL	2	FALSE	1	0.188709167375661	3		900	1034	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911655	134911655	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	98	408	1	ENST00000398015.3:c.2120C>A	p.Ser707Tyr	p.S707Y	ENST00000398015	NM_004441.4	707	tCt/tAt	11/16	0.127826133129266	4	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	FALSE	2	0.188709167375661	4		409	576	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430467	181430467	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	187	557	0	ENST00000325404.1:c.319G>T	p.Asp107Tyr	p.D107Y	ENST00000325404	NM_003106.3	107	Gat/Tat	1/1	0.127826133129266	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	FALSE	2	0.188709167375661	4		557	1073	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509083	66509083	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	36	459	0	ENST00000273854.3:c.244G>C	p.Gly82Arg	p.G82R	ENST00000273854	NM_004439.5	82	Ggg/Cgg	2/18	1	2	FACETS	0.819	0.673	0.982	0.819	0.673	0.982	CLONAL	1	FALSE	1	0.188709167375661	2		459	466	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509352	106509352	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	49	624	0	ENST00000359195.3:c.1346C>A	p.Ser449Tyr	p.S449Y	ENST00000359195	NM_002649.2	449	tCc/tAc	2/11	0.177613060093364	3	FACETS	0.708	0.598	0.829	0.354	0.299	0.415	SUBCLONAL	1	FALSE	1	0.188709167375661	3		624	803	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772071	135772071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1020905743	NA	P-0022952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	59	503	1	ENST00000298552.3:c.3046G>A	p.Gly1016Ser	p.G1016S	ENST00000298552	NM_001162426.1	1016	Ggt/Agt	23/23	0.177613060093364	3	FACETS	0.983	0.845	1	0.492	0.422	0.567	CLONAL	1	FALSE	1	0.188709167375661	3		504	696	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143174	24143174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	88	647	0	ENST00000263121.7:c.406C>T	p.Pro136Ser	p.P136S	ENST00000263121	NM_003073.3	136	Ccc/Tcc	4/9	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.429184058893946	2		647	320	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129903	69129903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752113779	NA	P-0022953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	20	420	1	ENST00000288368.4:c.4657G>A	p.Gly1553Arg	p.G1553R	ENST00000288368	NM_024870.2	1553	Gga/Aga	38/40	0.429184058893946	1	FACETS	0.266	0.203	0.339	0.266	0.203	0.339	SUBCLONAL	1	FALSE	0	0.429184058893946	1		421	275	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241924	72241924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs552625764	NA	P-0022953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	19	591	1	ENST00000357731.5:c.466G>A	p.Val156Ile	p.V156I	ENST00000357731	NM_173808.2	156	Gtc/Atc	3/7	1	2	FACETS	0.459	0.35	0.586	0.459	0.35	0.586	SUBCLONAL	1	FALSE	1	0.429184058893946	2		592	193	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439704	49439704	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0022953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	43	628	0	ENST00000301067.7:c.4740del	p.Glu1581SerfsTer12	p.E1581Sfs*12	ENST00000301067	NM_003482.3	1580	ccA/cc	18/54	0.245646552890771	4	FACETS	0.725	0.608	0.854	0.363	0.304	0.427	INDETERMINATE	1	FALSE	2	0.429184058893946	4		628	395	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874710	151874710	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	51	491	1	ENST00000262189.6:c.7828C>T	p.Arg2610Ter	p.R2610*	ENST00000262189	NM_170606.2	2610	Cga/Tga	38/59	0.238878172991775	3	FACETS	1	0.877	1	0.514	0.44	0.594	INDETERMINATE	1	FALSE	1	0.429184058893946	3		492	281	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0022957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	61	693	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.135325521843995	2		693	831	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0022957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	92	717	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.135325521843995	2		717	924	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729829	47729829	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	73	988	0	ENST00000449228.1:c.560G>T	p.Arg187Leu	p.R187L	ENST00000449228	NM_001127240.2	187	cGa/cTa	3/4	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.135325521843995	2		988	750	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294052	1294052	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	89	1253	1	ENST00000310581.5:c.949T>A	p.Trp317Arg	p.W317R	ENST00000310581	NM_198253.2	317	Tgg/Agg	2/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.135325521843995	2		1254	1016	SUCCESS
APC	324	MSKCC	GRCh37	5	112175689	112175693	+	stop_gained,protein_altering_variant	Nonsense_Mutation	DEL	ACCTA	ACCTA	CT	novel	NA	P-0022957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	70	406	1	ENST00000257430.4:c.4398_4402delinsCT	p.Pro1467_Lys1468delinsTer	p.P1467_K1468delins*	ENST00000257430	NM_000038.5	1466	ggACCTAag/ggCTag	16/16	0.135325521843995	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	0	0.135325521843995	2		407	479	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256493	46256493	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs770319259	NA	P-0022968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	62	429	0	ENST00000371998.3:c.721G>A	p.Asp241Asn	p.D241N	ENST00000371998		241	Gat/Aat	7/23	1	2	FACETS	0.758	0.657	0.867	0.758	0.657	0.867	SUBCLONAL	1	TRUE	1	0.4	2		429	409	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953191	17953191	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs778908329	NA	P-0121419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	148	706	1	ENST00000458235.1:c.795C>A	p.His265Gln	p.H265Q	ENST00000458235	NM_000215.3	265	caC/caA	6/24	1	2	FACETS	0.92	0.843	1	0.92	0.843	1	CLONAL	1	NA	1	0.46477453335052	2		707	692	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0022972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	39	550	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.153516679469997	1	FACETS	0.48	0.398	0.572	0.48	0.398	0.572	INDETERMINATE	1	TRUE	0	0.308544756617832	1		552	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577026	7577026	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	133	783	2	ENST00000269305.4:c.912del	p.Lys305SerfsTer40	p.K305Sfs*40	ENST00000269305	NM_001126112.2	304	acT/ac	8/11	0.308544756617832	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.308544756617832	1		785	657	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56376638	56376638	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	74	510	0	ENST00000348428.3:c.678G>C	p.Lys226Asn	p.K226N	ENST00000348428	NM_006785.3	226	aaG/aaC	5/17	0.291852743455022	1	FACETS	0.838	0.736	0.948	0.838	0.736	0.948	CLONAL	1	TRUE	0	0.308544756617832	1		510	484	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0022973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	154	693	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.979	0.904	1	0.979	0.904	1	CLONAL	1	TRUE	1	0.68408629588697	2		693	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0022973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	233	742	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.655809538292035	1	FACETS	0.842	0.794	0.892	0.842	0.794	0.892	CLONAL	1	TRUE	0	0.68408629588697	1		742	532	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	175	420	2	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	0.649069103355963	2	FACETS	0.785	0.737	0.833	0.785	0.737	0.833	SUBCLONAL	2	TRUE	0	0.68408629588697	2		422	326	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273548	5273548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1475010322	NA	P-0022973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	274	690	2	ENST00000357368.4:c.284C>T	p.Pro95Leu	p.P95L	ENST00000357368	NM_002850.3	95	cCg/cTg	4/38	1	2	FACETS	0.994	0.937	1	0.994	0.937	1	CLONAL	1	TRUE	1	0.68408629588697	2		692	806	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938089	76938092	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	novel	NA	P-0022975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	184	694	0	ENST00000373344.5:c.2656_2659del	p.Glu886LeufsTer18	p.E886Lfs*18	ENST00000373344	NM_000489.3	886	GAGAct/ct	9/35	0.402648682214714	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	2	0.596931473180854	4		694	461	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63816982	63816982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	90	314	1	ENST00000279873.7:c.953G>A	p.Arg318Lys	p.R318K	ENST00000279873	NM_032199.2	318	aGg/aAg	6/10	0.334650839313815	5	FACETS	1	0.965	1	0.771	0.696	0.849	INDETERMINATE	2	TRUE	2	0.596931473180854	5		315	247	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409039	139409039	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	25	988	0	ENST00000277541.6:c.2130C>G	p.Asp710Glu	p.D710E	ENST00000277541	NM_017617.3	710	gaC/gaG	13/34	0.479610813737692	3	FACETS	0.218	0.171	0.272	0.109	0.085	0.136	SUBCLONAL	1	TRUE	1	0.596931473180854	3		988	499	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0022977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	14	370	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	0.405	0.291	0.544	0.405	0.291	0.544	SUBCLONAL	1	TRUE	1	0.15	2		370	461	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855029	76855029	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1557085898	NA	P-0022977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	16	559	4	ENST00000373344.5:c.5807A>G	p.Lys1936Arg	p.K1936R	ENST00000373344	NM_000489.3	1936	aAg/aGg	25/35	1	2	FACETS	0.466	0.343	0.614	0.466	0.343	0.614	SUBCLONAL	1	TRUE	1	0.15	2		563	458	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37045935	37045935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750781	NA	P-0022977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	32	503	0	ENST00000231790.2:c.350C>T	p.Thr117Met	p.T117M	ENST00000231790	NM_000249.3	117	aCg/aTg	4/19	1	2	FACETS	0.703	0.569	0.855	0.703	0.569	0.855	SUBCLONAL	1	TRUE	1	0.15	2		503	607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0022979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	553	982	1	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	NA	2	FACETS	0.927	0.893	0.961			1	INDETERMINATE	3	TRUE	NA	0.336450235410599	2		983	1182	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143985	11143985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	325	616	2	ENST00000358026.2:c.3566G>A	p.Arg1189Gln	p.R1189Q	ENST00000358026	NM_001128849.1	1189	cGa/cAa	26/36	0.336450235410599	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.336450235410599	3		618	906	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974783	21974783	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658556	NA	P-0022979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	169	246	0	ENST00000304494.5:c.44G>A	p.Trp15Ter	p.W15*	ENST00000304494	NM_000077.4	15	tGg/tAg	1/3	0.336450235410599	2	FACETS	0.856	0.798	0.916	1	0.988	1	CLONAL	3	TRUE	0	0.336450235410599	2		246	391	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106196	2106196	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs45517117	NA	P-0022979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	391	917	0	ENST00000219476.3:c.600-1G>A		p.X200_splice	ENST00000219476	NM_000548.3	200			0.336450235410599	2	FACETS	0.856	0.817	0.895	1	0.994	1	CLONAL	3	TRUE	0	0.336450235410599	2		917	905	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11022948	11022948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	246	843	2	ENST00000327064.4:c.647G>A	p.Ser216Asn	p.S216N	ENST00000327064	NM_199141.1	216	aGc/aAc	5/16	0.336450235410599	3	FACETS	1	0.989	1	0.655	0.611	0.7	CLONAL	1	TRUE	1	0.336450235410599	3		845	1305	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72897368	72897368	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	243	511	4	ENST00000325599.8:c.124G>A	p.Ala42Thr	p.A42T	ENST00000325599	NM_018130.2	42	Gcc/Acc	1/11	0.322696604618004	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.336450235410599	4		515	817	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0022980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	34	609	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.704	0.573	0.852	0.704	0.573	0.852	SUBCLONAL	1	TRUE	1	0.14	2		609	690	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0022980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	52	569	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.984	0.836	1	0.984	0.836	1	CLONAL	1	TRUE	1	0.14	2		569	755	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0022980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	54	677	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.997	0.849	1	0.997	0.849	1	CLONAL	1	TRUE	1	0.14	2		677	774	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935499	13935499	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767552829	NA	P-0022980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	33	354	0	ENST00000405192.2:c.1357G>A	p.Val453Met	p.V453M	ENST00000405192	NM_001163147.1	453	Gtg/Atg	12/12	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.14	2		354	418	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864719	68864719	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	41	614	0	ENST00000288368.4:c.90G>T	p.Glu30Asp	p.E30D	ENST00000288368	NM_024870.2	30	gaG/gaT	1/40	1	2	FACETS	0.919	0.764	1	0.919	0.764	1	CLONAL	1	TRUE	1	0.14	2		614	637	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	18	549	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.293	0.219	0.38	0.293	0.219	0.38	SUBCLONAL	1	TRUE	1	0.24	2		549	512	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0022982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	113	799	0	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	1	2	FACETS	0.769	0.694	0.849	1	0.984	1	SUBCLONAL	2	TRUE	1	0.24	2		799	612	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663366	29663366	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	32	613	0	ENST00000356175.3:c.5959G>C	p.Asp1987His	p.D1987H	ENST00000356175	NM_000267.3	1987	Gat/Cat	40/57	1	2	FACETS	0.435	0.352	0.529	0.435	0.352	0.529	SUBCLONAL	1	TRUE	1	0.24	2		613	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0022990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	76	737	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.241647798562377	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.241647798562377	1		739	512	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0022990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	62	731	2	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.943	0.815	1	0.943	0.815	1	CLONAL	1	TRUE	1	0.241647798562377	2		733	544	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120812	94120812	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs200883289	NA	P-0022990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	33	666	0	ENST00000369303.4:c.239A>G	p.Asn80Ser	p.N80S	ENST00000369303	NM_004440.3	80	aAc/aGc	3/17	1	2	FACETS	0.515	0.419	0.624	0.515	0.419	0.624	SUBCLONAL	1	TRUE	1	0.241647798562377	2		666	530	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210302	123210302	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	60	266	0	ENST00000218089.9:c.2654T>C	p.Ile885Thr	p.I885T	ENST00000218089	NM_001042749.1	885	aTc/aCc	26/35	1	1	FACETS	1	0.9	1	1	0.981	1	CLONAL	2	TRUE	0	0.241647798562377	1		266	211	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0023004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	70	469	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.996	0.872	1	0.996	0.872	1	CLONAL	1	TRUE	1	0.333986621653902	2		469	421	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111502	8111503	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0023004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	158	854	0	ENST00000346208.3:c.990dup	p.Asn331GlufsTer21	p.N331Efs*21	ENST00000346208		330	agg/aGgg	5/6	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.333986621653902	2		854	811	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946178	71946178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1450585135	NA	P-0023004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	96	900	0	ENST00000298229.2:c.2434G>A	p.Asp812Asn	p.D812N	ENST00000298229	NM_001567.3	812	Gat/Aat	22/28	1	2	FACETS	0.745	0.663	0.832	0.745	0.663	0.832	SUBCLONAL	1	TRUE	1	0.333986621653902	2		900	772	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577122	7577122	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	164	856	2	ENST00000269305.4:c.816del	p.Arg273ValfsTer72	p.R273Vfs*72	ENST00000269305	NM_001126112.2	272	gtG/gt	8/11	0.333986621653902	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.333986621653902	1		858	670	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0023004-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	74	469	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.895	0.785	1	0.895	0.785	1	CLONAL	1	TRUE	1	0.313855624493887	2		469	527	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111502	8111503	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0023004-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	143	854	0	ENST00000346208.3:c.990dup	p.Asn331GlufsTer21	p.N331Efs*21	ENST00000346208		330	agg/aGgg	5/6	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.313855624493887	2		854	911	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946178	71946178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1450585135	NA	P-0023004-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	104	900	0	ENST00000298229.2:c.2434G>A	p.Asp812Asn	p.D812N	ENST00000298229	NM_001567.3	812	Gat/Aat	22/28	1	2	FACETS	0.65	0.581	0.724	0.65	0.581	0.724	SUBCLONAL	1	TRUE	1	0.313855624493887	2		900	1019	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577122	7577122	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023004-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	188	856	2	ENST00000269305.4:c.816del	p.Arg273ValfsTer72	p.R273Vfs*72	ENST00000269305	NM_001126112.2	272	gtG/gt	8/11	0.313855624493887	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.313855624493887	1		858	923	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0023006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	389	550	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.771101084266699	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	1	0.771101084266699	3		552	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577567	7577568	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs1555525539	NA	P-0023006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	443	869	0	ENST00000269305.4:c.713_714del	p.Cys238Ter	p.C238*	ENST00000269305	NM_001126112.2	238	tGT/t	7/11	0.771101084266699	2	FACETS	0.909	0.88	0.937	0.909	0.88	0.937	CLONAL	2	TRUE	0	0.771101084266699	2		869	632	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727981	78727981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1481790013	NA	P-0023006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	148	489	0	ENST00000306801.3:c.826C>T	p.Arg276Cys	p.R276C	ENST00000306801	NM_020761.2	276	Cgc/Tgc	6/34	0.771101084266699	4	FACETS	1	0.937	1	0.257	0.235	0.28	CLONAL	1	TRUE	0	0.771101084266699	4		489	662	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	57	445	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.49	0.419	0.567	0.49	0.419	0.567	SUBCLONAL	1	FALSE	1	0.335057590109351	2		445	695	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579566	7579584	+	frameshift_variant	Frame_Shift_Del	DEL	CCATTGCTTGGGACGGCAA	CCATTGCTTGGGACGGCAA	-	novel	NA	P-0023007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	58	834	0	ENST00000269305.4:c.103_121del	p.Leu35MetfsTer3	p.L35Mfs*3	ENST00000269305	NM_001126112.2	35	TTGCCGTCCCAAGCAATGGat/at	4/11	1	2	FACETS	0.332	0.284	0.385	0.332	0.284	0.385	SUBCLONAL	1	FALSE	1	0.335057590109351	2		834	1043	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289104	33289104	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	133	786	0	ENST00000374542.5:c.448A>G	p.Thr150Ala	p.T150A	ENST00000374542	NM_001141970.1	150	Acc/Gcc	3/8	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.524901351706509	2		786	469	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0023017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	510	609	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.357879780791497	6	FACETS	0.957	0.924	0.989			1	CLONAL	6	TRUE	NA	0.357879780791497	6		609	852	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0023017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	270	931	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.348579248378886	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.357879780791497	2		931	750	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	62	445	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.898	0.781	1	0.898	0.781	1	CLONAL	1	TRUE	1	0.434404072818823	2		445	318	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148758	119149302	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTGACATTTTTATATAAGCAAAATTTGTATAGGAAACAAGTCTTCACTTTTTCTGTTAACATTTATAATTGCAGTTATTTATTCAACTAATAGTCTTTTAATTTTTTTTAATCAAAGGAACAATATGAATTATACTGTGAGATGGGCTCCACATTCCAACTATGTAAAATATGTGCTGAAAATGATAAGGATGTAAAGATTGAGCCCTGTGGACACCTCATGTGCACATCCTGTCTTACATCCTGGCAGGTACGGATCTAAACAGCGACTTTTTTCAGCTATGTAATAACCTTGGAAAATTCGGTATTATATAGCCTTTACTGATACAAGGGGTGGCCTGGCTTTTGGGGTTAGGTTTAAACTTTTACTTTTTTTTGATCTCTAGGAAATGTATTTTCTAGTAGATTAATATTTTAAGTATTTTCAGATGCATCTGTTACTATCTTTTGCTTCTTCTGCAGGAATCAGAAGGTCAGGGCTGTCCTTTCTGCCGATGTGAAATTAAAGGTACTGAACCCATCGTGGTAGATCCGTTTGATCCTAG	TGTGACATTTTTATATAAGCAAAATTTGTATAGGAAACAAGTCTTCACTTTTTCTGTTAACATTTATAATTGCAGTTATTTATTCAACTAATAGTCTTTTAATTTTTTTTAATCAAAGGAACAATATGAATTATACTGTGAGATGGGCTCCACATTCCAACTATGTAAAATATGTGCTGAAAATGATAAGGATGTAAAGATTGAGCCCTGTGGACACCTCATGTGCACATCCTGTCTTACATCCTGGCAGGTACGGATCTAAACAGCGACTTTTTTCAGCTATGTAATAACCTTGGAAAATTCGGTATTATATAGCCTTTACTGATACAAGGGGTGGCCTGGCTTTTGGGGTTAGGTTTAAACTTTTACTTTTTTTTGATCTCTAGGAAATGTATTTTCTAGTAGATTAATATTTTAAGTATTTTCAGATGCATCTGTTACTATCTTTTGCTTCTTCTGCAGGAATCAGAAGGTCAGGGCTGTCCTTTCTGCCGATGTGAAATTAAAGGTACTGAACCCATCGTGGTAGATCCGTTTGATCCTAG	-	novel	NA	P-0023019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	16	73	0	ENST00000264033.4:c.1096-118_1310del		p.X366_splice	ENST00000264033	NM_005188.3	366		8-9/16	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.434404072818823	2		73	52	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110191	3110191	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	121	771	0	ENST00000078429.4:c.181A>C	p.Ile61Leu	p.I61L	ENST00000078429	NM_002067.2	61	Atc/Ctc	2/7	0.393588156018433	3	FACETS	1	0.958	1	0.55	0.498	0.605	CLONAL	1	TRUE	1	0.434404072818823	3		771	616	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589588	67589593	+	protein_altering_variant	In_Frame_Del	DEL	GAATAT	GAATAT	ATC	novel	NA	P-0023019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	98	386	1	ENST00000274335.5:c.1351_1356delinsATC	p.Glu451_Tyr452delinsIle	p.E451_Y452delinsI	ENST00000274335		451	GAATAT/ATC	10/15	1	2	FACETS	0.904	0.81	1	0.904	0.81	1	CLONAL	1	TRUE	1	0.434404072818823	2		387	499	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	262	805	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	0.222809800467255	4	FACETS	0.934	0.875	0.994	0.934	0.875	0.994	CLONAL	2	FALSE	2	0.344060493738295	4		805	1096	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627436	14627436	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	58	848	0	ENST00000254322.2:c.634T>C	p.Trp212Arg	p.W212R	ENST00000254322	NM_006145.1	212	Tgg/Cgg	2/3	0.197938397681491	2	FACETS	0.897	0.774	1	0.448	0.387	0.515	INDETERMINATE	1	FALSE	0	0.344060493738295	2		848	376	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738222	133738222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	128	647	1	ENST00000318560.5:c.622G>A	p.Gly208Arg	p.G208R	ENST00000318560	NM_005157.4	208	Ggg/Agg	4/11	1	2	FACETS	0.885	0.802	0.972	0.885	0.802	0.972	CLONAL	1	FALSE	1	0.344060493738295	2		648	841	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0023022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	234	649	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.515567856606503	2		649	760	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578277	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs1555525902	NA	P-0023022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	182	741	3	ENST00000269305.4:c.572_574del	p.Pro191del	p.P191del	ENST00000269305	NM_001126112.2	191	cCTCag/cag	6/11	0.456635319232769	1	FACETS	0.845	0.784	0.909	0.845	0.784	0.909	CLONAL	1	TRUE	0	0.515567856606503	1		744	620	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0023022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	72	826	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.456635319232769	1	FACETS	0.259	0.226	0.296	0.259	0.226	0.296	SUBCLONAL	1	TRUE	0	0.515567856606503	1		828	799	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0023022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	113	272	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.515567856606503	2		272	391	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0023022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	81	280	1	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.515567856606503	2		281	242	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577146	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0023022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	86	728	5	ENST00000269305.4:c.792_794del	p.Leu265del	p.L265del	ENST00000269305	NM_001126112.2	264	ctACTg/ctg	8/11	0.456635319232769	1	FACETS	0.376	0.332	0.422	0.376	0.332	0.422	SUBCLONAL	1	TRUE	0	0.515567856606503	1		733	659	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117739	70117739	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	325	862	1	ENST00000245479.2:c.210del	p.Val71CysfsTer39	p.V71Cfs*39	ENST00000245479	NM_000346.3	69	ttC/tt	1/3	0.456635319232769	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.515567856606503	1		863	780	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919110	178919110	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	113	402	0	ENST00000263967.3:c.595T>C	p.Ser199Pro	p.S199P	ENST00000263967	NM_006218.2	199	Tct/Cct	4/21	1	2	FACETS	0.99	0.896	1	0.99	0.896	1	CLONAL	1	TRUE	1	0.515567856606503	2		402	443	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295271	1295271	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0023022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	42	605	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.243	0.202	0.289	0.243	0.202	0.289	SUBCLONAL	1	TRUE	1	0.515567856606503	2		605	670	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80150077	80150077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761465174	NA	P-0023022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	208	786	5	ENST00000265081.6:c.2942C>T	p.Thr981Met	p.T981M	ENST00000265081	NM_002439.4	981	aCg/aTg	21/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.515567856606503	2		791	672	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38173545	38173545	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	141	524	0	ENST00000317025.8:c.1871C>A	p.Ser624Ter	p.S624*	ENST00000317025	NM_023034.1	624	tCa/tAa	10/24	0.19332674598491	3	FACETS	0.981	0.896	1	0.327	0.298	0.357	INDETERMINATE	1	TRUE	0	0.515567856606503	3		524	701	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	745	1100	0	ENST00000397752.3:c.3028G>T	p.Asp1010Tyr	p.D1010Y	ENST00000397752	NM_000245.2	1010	Gat/Tat	14/21	0.244190908212182	5	FACETS	0.964	0.935	0.994			1	CLONAL	6	TRUE	NA	0.244190908212182	5		1100	1441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578483	7578483	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	148	1060	1	ENST00000269305.4:c.447del	p.Thr150HisfsTer20	p.T150Hfs*20	ENST00000269305	NM_001126112.2	149	tcC/tc	5/11	0.244190908212182	1	FACETS	0.993	0.905	1	0.993	0.905	1	CLONAL	1	TRUE	0	0.244190908212182	1		1061	1072	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850879	128850879	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767688088	NA	P-0023023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	52	920	0	ENST00000249373.3:c.1726C>T	p.Arg576Trp	p.R576W	ENST00000249373	NM_005631.4	576	Cgg/Tgg	10/12	0.244190908212182	3	FACETS	0.492	0.417	0.574			1	SUBCLONAL	1	TRUE	NA	0.244190908212182	3		920	972	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120951	115120951	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	81	749	0	ENST00000257566.3:c.55C>T	p.Pro19Ser	p.P19S	ENST00000257566	NM_016569.3	19	Ccg/Tcg	1/8	1	2	FACETS	0.95	0.837	1	0.95	0.837	1	CLONAL	1	TRUE	1	0.244190908212182	2		749	698	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39567832	39567832	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	31	486	0	ENST00000262039.4:c.588G>T	p.Leu196Phe	p.L196F	ENST00000262039	NM_002647.2	196	ttG/ttT	5/25	1	2	FACETS	0.512	0.413	0.624	0.512	0.413	0.624	SUBCLONAL	1	TRUE	1	0.244190908212182	2		486	496	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279235	142279235	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	144	838	0	ENST00000350721.4:c.1411G>A	p.Glu471Lys	p.E471K	ENST00000350721	NM_001184.3	471	Gaa/Aaa	6/47	0.244190908212182	3	FACETS	0.858	0.784	0.936			1	CLONAL	2	TRUE	NA	0.244190908212182	3		838	771	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183016	32183016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs8192566	NA	P-0023023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	37	861	4	ENST00000375023.3:c.2008G>A	p.Gly670Arg	p.G670R	ENST00000375023	NM_004557.3	670	Ggg/Agg	12/30	NA	2	FACETS	0.453	0.372	0.544			1	INDETERMINATE	1	TRUE	NA	0.244190908212182	2		865	669	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293660	137293660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	51	1147	0	ENST00000481739.1:c.211C>T	p.Pro71Ser	p.P71S	ENST00000481739	NM_002957.4	71	Ccc/Tcc	2/10	0.244190908212182	1	FACETS	0.4	0.339	0.468	0.4	0.339	0.468	SUBCLONAL	1	TRUE	0	0.244190908212182	1		1147	916	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325345	1325345	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	50	666	1	ENST00000400841.2:c.330T>A	p.Ser110Arg	p.S110R	ENST00000400841		110	agT/agA	3/6	1	1	FACETS	0.589	0.499	0.688	0.589	0.499	0.688	SUBCLONAL	1	TRUE	0	0.244190908212182	1		667	610	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0023025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	118	693	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.368372348550303	3	FACETS	0.873	0.794	0.956	0.873	0.794	0.956	CLONAL	2	TRUE	1	0.380081214500266	3		693	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519996	NA	P-0023025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	81	1183	0	ENST00000269305.4:c.395A>C	p.Lys132Thr	p.K132T	ENST00000269305	NM_001126112.2	132	aAg/aCg	5/11	0.380081214500266	1	FACETS	0.894	0.793	1	0.894	0.793	1	CLONAL	1	TRUE	0	0.380081214500266	1		1183	386	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286761	212286761	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	14	627	0	ENST00000342788.4:c.2935C>T	p.Arg979Ter	p.R979*	ENST00000342788	NM_005235.2	979	Cga/Tga	24/28	1	2	FACETS	0.951	0.697	1	0.951	0.697	1	CLONAL	1	TRUE	1	0.32	2		627	92	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118365081	118365081	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	255	622	1	ENST00000534358.1:c.5257del	p.Ala1753ProfsTer70	p.A1753Pfs*70	ENST00000534358	NM_005933.3	1753	Gcc/cc	17/36	0.708274984372883	3	FACETS	0.892	0.835	0.951	0.446	0.417	0.476	CLONAL	1	TRUE	1	0.708274984372883	3		623	1093	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919693	50919693	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374016016	NA	P-0023028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	412	1106	2	ENST00000440232.2:c.2861C>T	p.Thr954Met	p.T954M	ENST00000440232	NM_002691.3	954	aCg/aTg	23/27	0.708274984372883	2	FACETS	0.887	0.845	0.931	0.444	0.422	0.466	CLONAL	1	TRUE	0	0.708274984372883	2		1108	1311	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858327	27858327	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	46	707	1	ENST00000359303.2:c.244G>A	p.Asp82Asn	p.D82N	ENST00000359303	NM_003535.2	82	Gac/Aac	1/1	1	2	FACETS	0.18	0.151	0.213	0.18	0.151	0.213	SUBCLONAL	1	TRUE	1	0.593135910697087	2		708	860	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256198	16256198	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	211	553	0	ENST00000375759.3:c.3463A>T	p.Thr1155Ser	p.T1155S	ENST00000375759	NM_015001.2	1155	Act/Tct	11/15	1	2	FACETS	0.973	0.907	1	0.973	0.907	1	CLONAL	1	TRUE	1	0.593135910697087	2		553	731	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259474	16259474	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs772223605	NA	P-0023029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	214	504	0	ENST00000375759.3:c.6739C>A	p.Leu2247Met	p.L2247M	ENST00000375759	NM_015001.2	2247	Ctg/Atg	11/15	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.593135910697087	2		504	624	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17359604	17359611	+	frameshift_variant	Frame_Shift_Del	DEL	AATCTTGA	AATCTTGA	-	novel	NA	P-0023029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	180	664	0	ENST00000375499.3:c.230_237del	p.Ile77LysfsTer3	p.I77Kfs*3	ENST00000375499	NM_003000.2	77	aTCAAGATT/a	3/8	1	2	FACETS	0.88	0.814	0.948	0.88	0.814	0.948	CLONAL	1	TRUE	1	0.593135910697087	2		664	690	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267402	198267402	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	207	601	0	ENST00000335508.6:c.1955G>A	p.Cys652Tyr	p.C652Y	ENST00000335508	NM_012433.2	652	tGc/tAc	14/25	1	2	FACETS	0.947	0.882	1	0.947	0.882	1	CLONAL	1	TRUE	1	0.593135910697087	2		601	737	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188248	10188255	+	frameshift_variant	Frame_Shift_Del	DEL	AACCAAAC	AACCAAAC	-	novel	NA	P-0023029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	294	900	0	ENST00000256474.2:c.391_398del	p.Asn131Ter	p.N131*	ENST00000256474	NM_000551.3	131	AACCAAACt/t	2/3	0.593135910697087	1	FACETS	0.953	0.902	1	0.953	0.902	1	CLONAL	1	TRUE	0	0.593135910697087	1		900	732	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978404	2978405	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGTCGTGTTCCAAGATGTCCAGGATGGCCTTGTCTGAGTCTGGGAA	novel	NA	P-0023029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1162	176	1108	0	ENST00000396946.4:c.925_926insTTCCCAGACTCAGACAAGGCCATCCTGGACATCTTGGAACACGACC	p.Arg309LeufsTer66	p.R309Lfs*66	ENST00000396946	NM_032415.4	309	cgc/cTTCCCAGACTCAGACAAGGCCATCCTGGACATCTTGGAACACGACCgc	7/25	1	2	FACETS	0.444	0.407	0.482	0.444	0.407	0.482	SUBCLONAL	1	TRUE	1	0.593135910697087	2		1108	1338	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331618	8331618	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	199	576	0	ENST00000356435.5:c.5498A>C	p.Gln1833Pro	p.Q1833P	ENST00000356435		1833	cAg/cCg	33/35	0.451142257133113	1	FACETS	0.903	0.843	0.963	0.903	0.843	0.963	CLONAL	1	TRUE	0	0.593135910697087	1		576	523	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225127	53225127	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	286	441	0	ENST00000375401.3:c.3091del	p.Ala1031ProfsTer24	p.A1031Pfs*24	ENST00000375401	NM_004187.3	1031	Gcc/cc	20/26	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.593135910697087	1		441	509	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0023031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	149	497	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.561823640949381	1	FACETS	0.915	0.85	0.981	0.915	0.85	0.981	CLONAL	1	TRUE	0	0.666144377791119	1		497	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0023031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	396	712	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.666144377791119	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.666144377791119	1		712	699	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137620	202137620	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0023031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	527	655	0	ENST00000358485.4:c.728-1G>C		p.X243_splice	ENST00000358485	NM_001080125.1	243			0.220642927109046	6	FACETS	1	0.973	1			1	INDETERMINATE	4	TRUE	NA	0.666144377791119	6		655	915	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426638	47426638	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	62	747	0	ENST00000377045.4:c.883G>T	p.Gly295Trp	p.G295W	ENST00000377045	NM_001654.4	295	Ggg/Tgg	10/16	NA	2	FACETS	0.307	0.265	0.353			1	INDETERMINATE	1	TRUE	NA	0.666144377791119	2		747	606	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912113	32912113	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0023031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	333	856	0	ENST00000380152.3:c.3621T>A	p.Tyr1207Ter	p.Y1207*	ENST00000380152		1207	taT/taA	11/27	0.666144377791119	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.666144377791119	1		856	623	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0023032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	251	701	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.681795401004595	2		701	685	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0023032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	257	840	2	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.841	0.789	0.895	0.841	0.789	0.895	CLONAL	1	TRUE	1	0.681795401004595	2		842	896	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857500	9857500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	132	446	0	ENST00000330684.3:c.3901G>A	p.Glu1301Lys	p.E1301K	ENST00000330684	NM_001134407.1	1301	Gag/Aag	13/13	1	2	FACETS	0.9	0.824	0.979	0.9	0.824	0.979	CLONAL	1	TRUE	1	0.681795401004595	2		446	430	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024758	31024758	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs754129466	NA	P-0023032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	228	670	0	ENST00000375687.4:c.4243C>T	p.Arg1415Ter	p.R1415*	ENST00000375687	NM_015338.5	1415	Cga/Tga	13/13	1	2	FACETS	0.985	0.923	1	0.985	0.923	1	CLONAL	1	TRUE	1	0.681795401004595	2		670	679	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285048	15285048	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	288	900	0	ENST00000263388.2:c.4567G>A	p.Glu1523Lys	p.E1523K	ENST00000263388	NM_000435.2	1523	Gag/Aag	25/33	1	2	FACETS	0.896	0.844	0.949	0.896	0.844	0.949	CLONAL	1	TRUE	1	0.681795401004595	2		900	943	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058566	69058566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866534903	NA	P-0023032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2175	302	825	1	ENST00000288368.4:c.4210C>T	p.His1404Tyr	p.H1404Y	ENST00000288368	NM_024870.2	1404	Cat/Tat	34/40	0.654054380417815	5	FACETS	0.723	0.678	0.771	0.181	0.169	0.193	SUBCLONAL	1	TRUE	1	0.681795401004595	5		826	2477	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041468	42041468	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	227	663	0	ENST00000219905.7:c.5663C>T	p.Ser1888Phe	p.S1888F	ENST00000219905	NM_001164273.1	1888	tCc/tTc	17/24	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.681795401004595	2		663	658	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727442	66727442	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	188	491	0	ENST00000307102.5:c.158T>A	p.Phe53Tyr	p.F53Y	ENST00000307102	NM_002755.3	53	tTt/tAt	2/11	1	2	FACETS	0.826	0.766	0.887	0.826	0.766	0.887	CLONAL	1	TRUE	1	0.681795401004595	2		491	668	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943670	9943670	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs375260513	NA	P-0023032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	269	701	0	ENST00000330684.3:c.1271C>A	p.Pro424His	p.P424H	ENST00000330684	NM_001134407.1	424	cCc/cAc	5/13	1	2	FACETS	0.942	0.886	0.998	0.942	0.886	0.998	CLONAL	1	TRUE	1	0.681795401004595	2		701	838	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010571	48010571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878853712	NA	P-0023032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	261	699	0	ENST00000234420.5:c.199C>T	p.Pro67Ser	p.P67S	ENST00000234420	NM_000179.2	67	Ccc/Tcc	1/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.681795401004595	2		699	653	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266976	41266976	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	160	441	0	ENST00000349496.5:c.647G>A	p.Gly216Glu	p.G216E	ENST00000349496	NM_001904.3	216	gGg/gAg	5/15	1	2	FACETS	0.868	0.8	0.937	0.868	0.8	0.937	CLONAL	1	TRUE	1	0.681795401004595	2		441	541	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114856	73114856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	54	58	0	ENST00000356692.5:c.1237C>T	p.Pro413Ser	p.P413S	ENST00000356692		413	Cca/Tca	9/9	1	2	FACETS	0.87	0.78	0.958	1	0.98	1	CLONAL	2	TRUE	1	0.681795401004595	2		58	91	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146671	185146671	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	261	577	0	ENST00000265026.3:c.302A>G	p.Asn101Ser	p.N101S	ENST00000265026	NM_004721.4	101	aAc/aGc	2/14	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.681795401004595	2		577	721	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628151	187628151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	270	860	1	ENST00000441802.2:c.2831C>T	p.Thr944Ile	p.T944I	ENST00000441802	NM_005245.3	944	aCc/aTc	2/27	1	2	FACETS	0.96	0.904	1	0.96	0.904	1	CLONAL	1	TRUE	1	0.681795401004595	2		861	825	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979318	93979318	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	305	524	0	ENST00000369303.4:c.1510A>G	p.Asn504Asp	p.N504D	ENST00000369303	NM_004440.3	504	Aat/Gat	7/17	0.330318687068461	3	FACETS	0.842	0.799	0.886	0.842	0.799	0.886	INDETERMINATE	2	TRUE	1	0.681795401004595	3		524	712	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519344	137519344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	125	348	0	ENST00000367739.4:c.1294C>T	p.Pro432Ser	p.P432S	ENST00000367739	NM_000416.2	432	Cca/Tca	7/7	0.681795401004595	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.681795401004595	1		348	237	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956979	2956979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1562480062	NA	P-0023032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	299	675	1	ENST00000396946.4:c.2648C>T	p.Pro883Leu	p.P883L	ENST00000396946	NM_032415.4	883	cCc/cTc	20/25	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.681795401004595	2		676	800	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729525	41729525	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	226	662	1	ENST00000242208.4:c.1004G>A	p.Trp335Ter	p.W335*	ENST00000242208	NM_002192.2	335	tGg/tAg	3/3	1	2	FACETS	0.954	0.893	1	0.954	0.893	1	CLONAL	1	TRUE	1	0.681795401004595	2		663	695	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74868149	74868149	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	166	226	0	ENST00000284811.8:c.145C>A	p.Pro49Thr	p.P49T	ENST00000284811		49	Cca/Aca	3/4	0.681795401004595	9	FACETS	0.951	0.874	1			1	CLONAL	2	TRUE	NA	0.681795401004595	9		226	867	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410253	63410253	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	225	375	0	ENST00000330258.3:c.2914C>T	p.Pro972Ser	p.P972S	ENST00000330258	NM_152424.3	972	Cct/Tct	2/2	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.681795401004595	1		375	318	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480595	123480595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	235	304	0	ENST00000371139.4:c.103G>A	p.Glu35Lys	p.E35K	ENST00000371139	NM_001114937.2	35	Gag/Aag	1/4	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.681795401004595	1		304	346	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0023033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	21	414	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	1	2	FACETS	0.516	0.396	0.656	0.516	0.396	0.656	SUBCLONAL	1	TRUE	1	0.17	2		414	479	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665372	117665372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	33	367	0	ENST00000368508.3:c.4375G>A	p.Ala1459Thr	p.A1459T	ENST00000368508	NM_002944.2	1459	Gcc/Acc	27/43	1	2	FACETS	0.666	0.541	0.807	0.666	0.541	0.807	SUBCLONAL	1	TRUE	1	0.17	2		367	583	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150039	202150039	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1368296717	NA	P-0023033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	72	663	0	ENST00000358485.4:c.1480C>T	p.Arg494Ter	p.R494*	ENST00000358485	NM_001080125.1	494	Cga/Tga	8/9	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.17	2		663	800	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655479	67655479	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs769948988	NA	P-0023033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	40	501	0	ENST00000264010.4:c.1342C>T	p.Arg448Ter	p.R448*	ENST00000264010	NM_006565.3	448	Cga/Tga	7/12	1	2	FACETS	0.613	0.507	0.731	0.613	0.507	0.731	SUBCLONAL	1	TRUE	1	0.17	2		501	768	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818294	43818294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	54	762	1	ENST00000372470.3:c.1759G>A	p.Ala587Thr	p.A587T	ENST00000372470	NM_005373.2	587	Gcc/Acc	12/12	1	2	FACETS	0.724	0.616	0.842	0.724	0.616	0.842	SUBCLONAL	1	TRUE	1	0.17	2		763	878	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713811	30713811	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs886038847	NA	P-0023033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	44	709	1	ENST00000295754.5:c.1136A>T	p.Asp379Val	p.D379V	ENST00000295754	NM_003242.5	379	gAc/gTc	4/7	1	2	FACETS	0.658	0.55	0.778	0.658	0.55	0.778	SUBCLONAL	1	TRUE	1	0.17	2		710	787	SUCCESS
AR	367	MSKCC	GRCh37	X	66765699	66765699	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1223	84	1346	0	ENST00000374690.3:c.711G>T	p.Lys237Asn	p.K237N	ENST00000374690	NM_000044.3	237	aaG/aaT	1/8	1	2	FACETS	0.756	0.665	0.854	0.756	0.665	0.854	SUBCLONAL	1	TRUE	1	0.17	2		1346	1307	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189847	11189847	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	75	784	0	ENST00000361445.4:c.5662T>C	p.Phe1888Leu	p.F1888L	ENST00000361445	NM_004958.3	1888	Ttc/Ctc	40/58	0.334437735436021	0	FACETS	0.591	0.519	0.668			1	SUBCLONAL	1	TRUE	0	0.334437735436021	0		784	505	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136934	64136934	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	80	837	0	ENST00000334205.4:c.1445T>A	p.Val482Asp	p.V482D	ENST00000334205	NM_003942.2	482	gTc/gAc	13/17	1	2	FACETS	0.986	0.871	1	0.986	0.871	1	CLONAL	1	TRUE	1	0.334437735436021	2		837	485	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406310	406310	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	173	935	0	ENST00000399788.2:c.4131A>T	p.Glu1377Asp	p.E1377D	ENST00000399788	NM_001042603.1	1377	gaA/gaT	25/28	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.334437735436021	2		935	841	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243997	46243997	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	159	807	0	ENST00000334344.6:c.2091T>G	p.Asn697Lys	p.N697K	ENST00000334344	NM_152641.2	697	aaT/aaG	15/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.334437735436021	2		807	873	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457267	67457267	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	108	986	0	ENST00000327367.4:c.241A>G	p.Lys81Glu	p.K81E	ENST00000327367	NM_005902.3	81	Aag/Gag	2/9	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.334437735436021	2		986	601	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610637	52610637	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	122	950	0	ENST00000394830.3:c.3536A>G	p.His1179Arg	p.H1179R	ENST00000394830	NM_018313.4	1179	cAt/cGt	23/30	0.334437735436021	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.334437735436021	1		950	587	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967266	134967266	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	84	808	1	ENST00000398015.3:c.2608del	p.Arg870GlyfsTer9	p.R870Gfs*9	ENST00000398015	NM_004441.4	869	Ccc/cc	14/16	1	2	FACETS	0.754	0.666	0.848	0.754	0.666	0.848	SUBCLONAL	1	TRUE	1	0.334437735436021	2		809	666	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0023035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1491	301	957	2	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.178391815201414	2	FACETS	0.793	0.744	0.844	0.793	0.744	0.844	SUBCLONAL	2	TRUE	0	0.211766653447642	2		959	1792	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633564	69633574	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGCGCCGGG	GCGGCGCCGGG	-	novel	NA	P-0023035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2635	154	587	1	ENST00000334134.2:c.128_138del	p.Pro43GlnfsTer81	p.P43Qfs*81	ENST00000334134	NM_005247.2	43	cCCCGGCGCCGC/c	1/3	0.211766653447642	17	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.211766653447642	17		588	2789	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405920	49405920	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	267	927	0	ENST00000418115.1:c.218C>A	p.Ser73Tyr	p.S73Y	ENST00000418115	NM_001664.2	73	tCc/tAc	3/5	0.194494828223172	2	FACETS	0.871	0.815	0.929	0.871	0.815	0.929	CLONAL	2	TRUE	0	0.211766653447642	2		927	1447	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936023	44936023	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	34	429	2	ENST00000377967.4:c.2784C>A	p.Tyr928Ter	p.Y928*	ENST00000377967	NM_021140.2	928	taC/taA	18/29	0.139308023915711	2	FACETS	0.917	0.759	1			1	CLONAL	2	TRUE	NA	0.211766653447642	2		431	175	SUCCESS
APC	324	MSKCC	GRCh37	5	112175600	112175600	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	112	377	0	ENST00000257430.4:c.4312del	p.Thr1438HisfsTer35	p.T1438Hfs*35	ENST00000257430	NM_000038.5	1437	Aaa/aa	16/16	1	2	FACETS	0.751	0.678	0.828	0.751	0.678	0.828	SUBCLONAL	1	TRUE	1	0.541501628493015	2		377	551	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0023063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	123	529	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.76	0.689	0.834	0.76	0.689	0.834	SUBCLONAL	1	TRUE	1	0.541501628493015	2		529	598	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0023063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	234	652	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.93	0.869	0.994	0.93	0.869	0.994	CLONAL	1	TRUE	1	0.541501628493015	2		652	929	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs985033810	NA	P-0023063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	306	888	0	ENST00000269305.4:c.731G>T	p.Gly244Val	p.G244V	ENST00000269305	NM_001126112.2	244	gGc/gTc	7/11	0.541501628493015	1	FACETS	0.941	0.89	0.993	0.941	0.89	0.993	CLONAL	1	TRUE	0	0.541501628493015	1		888	876	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20483132	20483132	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	139	409	0	ENST00000346618.3:c.865G>A	p.Glu289Lys	p.E289K	ENST00000346618	NM_001949.4	289	Gag/Aag	4/7	0.541501628493015	1	FACETS	0.877	0.805	0.95	0.877	0.805	0.95	CLONAL	1	TRUE	0	0.541501628493015	1		409	427	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759935	63759935	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	137	408	0	ENST00000279873.7:c.588T>G	p.Asp196Glu	p.D196E	ENST00000279873	NM_032199.2	196	gaT/gaG	4/10	1	2	FACETS	0.922	0.842	1	0.922	0.842	1	CLONAL	1	TRUE	1	0.541501628493015	2		408	549	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823891	3823891	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	308	882	0	ENST00000262367.5:c.2324T>A	p.Met775Lys	p.M775K	ENST00000262367	NM_004380.2	775	aTg/aAg	13/31	1	2	FACETS	0.88	0.828	0.932	0.88	0.828	0.932	CLONAL	1	TRUE	1	0.541501628493015	2		882	1293	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271204	153271204	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	196	378	0	ENST00000281708.4:c.574G>T	p.Glu192Ter	p.E192*	ENST00000281708	NM_033632.3	192	Gaa/Taa	3/12	0.541501628493015	2	FACETS	0.994	0.937	1	0.994	0.937	1	CLONAL	2	TRUE	0	0.541501628493015	2		378	364	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851940	128851940	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573599556	NA	P-0023063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1212	317	780	0	ENST00000249373.3:c.2012G>A	p.Arg671Gln	p.R671Q	ENST00000249373	NM_005631.4	671	cGg/cAg	12/12	0.539150595441346	3	FACETS	0.973	0.916	1	0.487	0.458	0.516	CLONAL	1	TRUE	1	0.541501628493015	3		780	1529	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	54	636	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.179999360006487	1	FACETS	0.879	0.75	1	0.879	0.75	1	CLONAL	1	TRUE	0	0.179999360006487	1		638	621	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0023068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	80	840	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.179999360006487	1	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	0	0.179999360006487	1		840	775	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575194	48575194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555685186	NA	P-0023068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	37	304	0	ENST00000342988.3:c.388C>T	p.Pro130Ser	p.P130S	ENST00000342988	NM_005359.5	130	Cca/Tca	3/12	0.179999360006487	1	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	0	0.179999360006487	1		304	358	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016621	12016621	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	29	518	0	ENST00000353533.5:c.757C>T	p.Gln253Ter	p.Q253*	ENST00000353533	NM_003010.3	253	Cag/Tag	7/11	0.179999360006487	1	FACETS	0.695	0.557	0.852	0.695	0.557	0.852	SUBCLONAL	1	TRUE	0	0.179999360006487	1		518	422	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974717	21974718	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0023068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	30	412	0	ENST00000304494.5:c.108_109dup	p.Leu37ArgfsTer17	p.L37Rfs*17	ENST00000304494	NM_000077.4	37	ctg/cGCtg	1/3	0.179999360006487	1	FACETS	0.794	0.64	0.969	0.794	0.64	0.969	CLONAL	1	TRUE	0	0.179999360006487	1		412	382	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0023069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	353	804	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.611383995977252	2	FACETS	0.918	0.881	0.953	0.918	0.881	0.953	CLONAL	2	TRUE	0	0.671429313796555	2		804	573	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373865	118373865	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	50	301	0	ENST00000534358.1:c.7258C>A	p.His2420Asn	p.H2420N	ENST00000534358	NM_005933.3	2420	Cat/Aat	27/36	0.673346297091282	3	FACETS	0.873	0.748	1			1	CLONAL	1	TRUE	NA	0.671429313796555	3		301	228	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94201031	94201031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs864622683	NA	P-0023072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	84	404	0	ENST00000323929.3:c.1046G>A	p.Arg349Gln	p.R349Q	ENST00000323929	NM_005591.3	349	cGg/cAg	10/20	0.529828140850683	1	FACETS	0.821	0.734	0.911	0.821	0.734	0.911	CLONAL	1	TRUE	0	0.529828140850683	1		404	284	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727455	66727455	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs869025608	NA	P-0023096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	261	651	0	ENST00000307102.5:c.171G>T	p.Lys57Asn	p.K57N	ENST00000307102	NM_002755.3	57	aaG/aaT	2/11	0.622278736138063	3	FACETS	0.891	0.842	0.941	0.891	0.842	0.941	CLONAL	2	TRUE	1	0.622278736138063	3		651	617	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600470	10600470	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	589	769	0	ENST00000171111.5:c.1385G>T	p.Gly462Val	p.G462V	ENST00000171111	NM_203500.1	462	gGg/gTg	4/6	0.622278736138063	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.622278736138063	3		769	773	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245336	41245336	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	239	912	0	ENST00000357654.3:c.2212G>T	p.Val738Phe	p.V738F	ENST00000357654	NM_007294.3	738	Gtt/Ttt	10/23	0.622278736138063	3	FACETS	1	0.965	1	0.525	0.49	0.561	CLONAL	1	TRUE	1	0.622278736138063	3		912	959	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220449	1220450	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCTGCT	novel	NA	P-0023096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	585	982	0	ENST00000326873.7:c.543_548dup	p.Leu183_Leu184dup	p.L183_L184dup	ENST00000326873	NM_000455.4	183	aac/aaCCTGCTc	4/10	0.622278736138063	3	FACETS	0.922	0.895	0.949	0.922	0.895	0.949	CLONAL	3	TRUE	0	0.622278736138063	3		982	891	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670544	134670544	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	420	930	1	ENST00000398015.3:c.455G>T	p.Gly152Val	p.G152V	ENST00000398015	NM_004441.4	152	gGg/gTg	3/16	0.622278736138063	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.622278736138063	2		931	669	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0023097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	177	689	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		689	461	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412692	63412692	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	198	752	0	ENST00000330258.3:c.475T>A	p.Phe159Ile	p.F159I	ENST00000330258	NM_152424.3	159	Ttt/Att	2/2	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		752	576	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	70	445	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.933	0.825	1	0.933	0.825	1	CLONAL	1	TRUE	1	0.649801484931513	2		445	231	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0023099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	168	524	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.813	0.762	0.864	1	0.992	1	CLONAL	2	TRUE	1	0.649801484931513	2		524	318	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0023099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	196	829	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.649801484931513	2		829	477	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	194	886	0	ENST00000267101.3:c.310G>C	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ctg	3/28	1	2	FACETS	0.91	0.846	0.976	0.91	0.846	0.976	CLONAL	1	TRUE	1	0.649801484931513	2		886	656	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718999	190718999	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147084726	NA	P-0023099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	105	400	0	ENST00000441310.2:c.1001C>T	p.Thr334Met	p.T334M	ENST00000441310	NM_000534.4	334	aCg/aTg	9/13	0.121592510331035	4	FACETS	1	0.979	1	0.663	0.599	0.73	INDETERMINATE	1	TRUE	2	0.649801484931513	4		400	402	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981220	201981220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	206	887	1	ENST00000359651.3:c.299C>A	p.Ala100Asp	p.A100D	ENST00000359651		100	gCc/gAc	2/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.649801484931513	2		888	569	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842331	68842331	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	117	568	0	ENST00000261769.5:c.392C>A	p.Ser131Tyr	p.S131Y	ENST00000261769	NM_004360.3	131	tCc/tAc	4/16	1	2	FACETS	0.945	0.861	1	0.945	0.861	1	CLONAL	1	TRUE	1	0.649801484931513	2		568	381	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813299	89813299	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0023099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	107	633	0	ENST00000389301.3:c.3349-1G>C		p.X1117_splice	ENST00000389301	NM_000135.2	1117			1	2	FACETS	0.883	0.799	0.97	0.883	0.799	0.97	CLONAL	1	TRUE	1	0.649801484931513	2		633	373	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55674306	55674306	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	139	654	0	ENST00000284073.2:c.532A>G	p.Lys178Glu	p.K178E	ENST00000284073	NM_138962.2	178	Aaa/Gaa	8/14	1	2	FACETS	0.988	0.907	1	0.988	0.907	1	CLONAL	1	TRUE	1	0.649801484931513	2		654	433	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949996	44949997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0023099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	131	665	0	ENST00000377967.4:c.3766_3767dup	p.Glu1257ThrfsTer9	p.E1257Tfs*9	ENST00000377967	NM_021140.2	1255	-/TA	26/29	0.572506514784025	3	FACETS	0.87	0.792	0.952	0.435	0.396	0.476	CLONAL	1	TRUE	1	0.649801484931513	3		665	614	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399409	139399411	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	rs761020817	NA	P-0023101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	207	859	5	ENST00000277541.6:c.4732_4734del	p.Val1578del	p.V1578del	ENST00000277541	NM_017617.3	1578	GTG/-	26/34	0.439944721177238	3	FACETS	0.785	0.733	0.837	0.785	0.733	0.837	SUBCLONAL	2	TRUE	1	0.58586130817074	3		864	582	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692783	89692827	+	inframe_deletion	In_Frame_Del	DEL	TTTTGAAGACCATAACCCACCACAGCTAGAACTTATCAAACCCTT	TTTTGAAGACCATAACCCACCACAGCTAGAACTTATCAAACCCTT	-	novel	NA	P-0023101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	18	601	0	ENST00000371953.3:c.269_313del	p.Phe90_Phe104del	p.F90_F104del	ENST00000371953	NM_000314.4	89	ccTTTTGAAGACCATAACCCACCACAGCTAGAACTTATCAAACCCTTt/cct	5/9	0.268872727176814	3	FACETS	0.285	0.214	0.368	0.142	0.107	0.184	INDETERMINATE	1	TRUE	1	0.58586130817074	3		601	279	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911484	32911484	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	86	688	0	ENST00000380152.3:c.2993del	p.Gly998ValfsTer45	p.G998Vfs*45	ENST00000380152		998	Ggt/gt	11/27	1	2	FACETS	0.926	0.828	1	0.926	0.828	1	CLONAL	1	TRUE	1	0.58586130817074	2		688	317	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361184	66361184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56205382	NA	P-0023101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	81	541	1	ENST00000273854.3:c.988G>A	p.Glu330Lys	p.E330K	ENST00000273854	NM_004439.5	330	Gag/Aag	4/18	1	2	FACETS	0.797	0.708	0.891	0.797	0.708	0.891	SUBCLONAL	1	TRUE	1	0.58586130817074	2		542	347	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994261	21994261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1406669428	NA	P-0023101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	116	657	0	ENST00000579755.1:c.70G>A	p.Val24Met	p.V24M	ENST00000579755		24	Gtg/Atg	1/3	1		FACETS		0.854	1				CLONAL	1	TRUE	1	0.58586130817074	2		657	421	SUCCESS
AR	367	MSKCC	GRCh37	X	66931471	66931471	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	183	857	0	ENST00000374690.3:c.2113C>A	p.Leu705Ile	p.L705I	ENST00000374690	NM_000044.3	705	Ctc/Atc	4/8	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.58586130817074	2		857	620	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801020	1801020	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	255	991	0	ENST00000260795.2:c.149T>A	p.Val50Asp	p.V50D	ENST00000260795		50	gTc/gAc	2/17	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.529882779381813	2		991	900	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0023104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	67	693	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.906	0.789	1	0.906	0.789	1	CLONAL	1	TRUE	1	0.30071153208946	2		693	492	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0023104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	136	550	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	0.28129423646603	1	FACETS	0.818	0.743	0.896	0.818	0.743	0.896	CLONAL	1	TRUE	0	0.30071153208946	1		550	940	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579400	7579400	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	213	829	0	ENST00000269305.4:c.287del	p.Ser96LeufsTer27	p.S96Lfs*27	ENST00000269305	NM_001126112.2	96	tCt/tt	4/11	0.28129423646603	1	FACETS	0.991	0.919	1	0.991	0.919	1	CLONAL	1	TRUE	0	0.30071153208946	1		829	1215	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604707	48604707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	109	577	1	ENST00000342988.3:c.1529G>A	p.Gly510Glu	p.G510E	ENST00000342988	NM_005359.5	510	gGa/gAa	12/12	0.279093928532653	2	FACETS	1	0.92	1	0.513	0.461	0.569	CLONAL	1	TRUE	0	0.30071153208946	2		578	706	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858957	243858958	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATGA	novel	NA	P-0023104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	28	641	1	ENST00000263826.5:c.104_107dup	p.Gly37HisfsTer4	p.G37Hfs*4	ENST00000263826	NM_005465.4	36	ata/atTCATa	2/13	1	2	FACETS	0.537	0.429	0.659	0.537	0.429	0.659	SUBCLONAL	1	TRUE	1	0.30071153208946	2		642	347	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744482	41744482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752081844	NA	P-0023105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	35	962	2	ENST00000301178.4:c.1102C>T	p.Arg368Trp	p.R368W	ENST00000301178	NM_021913.4	368	Cgg/Tgg	8/20	0.180404374843263	1	FACETS	0.414	0.338	0.5	0.414	0.338	0.5	SUBCLONAL	1	TRUE	0	0.236872591960062	1		964	629	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410441	139410441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	68	836	1	ENST00000277541.6:c.1661G>A	p.Cys554Tyr	p.C554Y	ENST00000277541	NM_017617.3	554	tGc/tAc	10/34	0.180404374843263	1	FACETS	0.854	0.743	0.973	0.854	0.743	0.973	CLONAL	1	TRUE	0	0.236872591960062	1		837	593	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913517	NA	P-0023107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	232	650	0	ENST00000288135.5:c.1676T>C	p.Val559Ala	p.V559A	ENST00000288135	NM_000222.2	559	gTt/gCt	11/21	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.806470551629331	2		650	561	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0023128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	224	693	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.807	0.753	0.863	1	0.993	1	CLONAL	2	TRUE	1	0.33551924692002	2		693	827	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0023128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	217	850	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.33551924692002	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.33551924692002	1		851	728	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133523	55133523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142492533	NA	P-0023128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	66	685	1	ENST00000257290.5:c.827C>T	p.Thr276Met	p.T276M	ENST00000257290	NM_006206.4	276	aCg/aTg	6/23	0.33551924692002	1	FACETS	0.484	0.419	0.553	0.484	0.419	0.553	SUBCLONAL	1	TRUE	0	0.33551924692002	1		686	677	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212841	94212841	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	103	529	0	ENST00000323929.3:c.401G>A	p.Gly134Glu	p.G134E	ENST00000323929	NM_005591.3	134	gGg/gAg	5/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.33551924692002	2		529	532	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910458	32910458	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	211	626	0	ENST00000380152.3:c.1966A>C	p.Thr656Pro	p.T656P	ENST00000380152		656	Act/Cct	11/27	0.245977549047819	4	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	2	0.33551924692002	4		626	808	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40854917	40854917	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1260794915	NA	P-0023128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	170	763	1	ENST00000428826.2:c.2161G>A	p.Glu721Lys	p.E721K	ENST00000428826		721	Gaa/Aaa	20/21	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.33551924692002	2		764	739	SUCCESS
YES1	7525	MSKCC	GRCh37	18	742921	742921	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	75	653	0	ENST00000314574.4:c.1057A>C	p.Lys353Gln	p.K353Q	ENST00000314574	NM_005433.3	353	Aaa/Caa	8/12	0.161449009340118	0	FACETS	0.49	0.43	0.555			1	INDETERMINATE	1	TRUE	0	0.33551924692002	0		653	606	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409377	31409377	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	66	676	0	ENST00000344624.3:c.3730T>C	p.Cys1244Arg	p.C1244R	ENST00000344624		1244	Tgc/Cgc	29/33	0.173682309309535	2	FACETS	0.497	0.43	0.569	0.248	0.215	0.285	INDETERMINATE	1	TRUE	0	0.33551924692002	2		676	792	SUCCESS
APC	324	MSKCC	GRCh37	5	112174268	112174268	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	48	546	0	ENST00000257430.4:c.2978del	p.Lys993SerfsTer12	p.K993Sfs*12	ENST00000257430	NM_000038.5	993	Aag/ag	16/16	1	2	FACETS	0.475	0.4	0.556	0.475	0.4	0.556	SUBCLONAL	1	TRUE	1	0.33551924692002	2		546	603	SUCCESS
APC	324	MSKCC	GRCh37	5	112175788	112175789	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0023128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	105	440	0	ENST00000257430.4:c.4500_4501dup	p.Ser1501PhefsTer7	p.S1501Ffs*7	ENST00000257430	NM_000038.5	1499	-/TT	16/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.33551924692002	2		440	497	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622198	162622198	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	42	557	0	ENST00000366898.1:c.499A>G	p.Ser167Gly	p.S167G	ENST00000366898	NM_004562.2	167	Agc/Ggc	4/12	0.1068891368306	3	FACETS	0.554	0.462	0.656	0.277	0.231	0.328	INDETERMINATE	1	TRUE	1	0.33551924692002	3		557	528	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046299	69046299	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	48	485	0	ENST00000288368.4:c.3772G>T	p.Glu1258Ter	p.E1258*	ENST00000288368	NM_024870.2	1258	Gag/Tag	32/40	1	2	FACETS	0.583	0.493	0.682	0.583	0.493	0.682	SUBCLONAL	1	TRUE	1	0.33551924692002	2		485	491	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242804	98242804	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	51	757	0	ENST00000331920.6:c.813A>G	p.Ile271Met	p.I271M	ENST00000331920	NM_000264.3	271	atA/atG	6/24	0.238711532081403	1	FACETS	0.343	0.29	0.401	0.343	0.29	0.401	SUBCLONAL	1	TRUE	0	0.33551924692002	1		757	738	SUCCESS
AR	367	MSKCC	GRCh37	X	66765635	66765635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	26	434	0	ENST00000374690.3:c.647G>A	p.Gly216Glu	p.G216E	ENST00000374690	NM_000044.3	216	gGg/gAg	1/8	0.22415499391603	2	FACETS	0.362	0.286	0.449			1	SUBCLONAL	1	TRUE	NA	0.33551924692002	2		434	428	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0023131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	72	549	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	0.263600669422286	2		549	488	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0023131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	12	382	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.186	0.13	0.256	0.186	0.13	0.256	SUBCLONAL	1	TRUE	1	0.263600669422286	2		382	489	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063717	+	splice_donor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0023131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	19	322	0	ENST00000412916.2:c.165+1del		p.X55_splice	ENST00000412916		55			0.263600669422286	1	FACETS	0.629	0.479	0.803	0.629	0.479	0.803	SUBCLONAL	1	TRUE	0	0.263600669422286	1		322	199	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0023132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	245	549	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.210766465815089	3	FACETS	0.957	0.9	1	0.957	0.9	1	INDETERMINATE	2	TRUE	1	0.489466858381078	3		549	651	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372080	55372080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	67	506	0	ENST00000297316.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000297316	NM_022454.3	257	tCg/tTg	2/2	0.211091953194821	3	FACETS	0.63	0.548	0.718	0.315	0.274	0.359	INDETERMINATE	1	TRUE	1	0.489466858381078	3		506	541	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934576	NA	P-0023132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	273	720	1	ENST00000269305.4:c.818G>C	p.Arg273Pro	p.R273P	ENST00000269305	NM_001126112.2	273	cGt/cCt	8/11	0.489466858381078	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.489466858381078	1		721	571	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857349	68857349	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	107	745	1	ENST00000261769.5:c.1984G>A	p.Asp662Asn	p.D662N	ENST00000261769	NM_004360.3	662	Gac/Aac	13/16	0.23764081332366	2	FACETS	0.513	0.46	0.57	0.257	0.23	0.285	INDETERMINATE	1	TRUE	0	0.489466858381078	2		746	852	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822672	72822672	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs375370132	NA	P-0023132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1173	352	876	0	ENST00000268489.5:c.9503G>T	p.Gly3168Val	p.G3168V	ENST00000268489	NM_006885.3	3168	gGa/gTa	10/10	0.489466858381078	6	FACETS	0.933	0.882	0.986			1	CLONAL	2	TRUE	NA	0.489466858381078	6		876	1525	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11015623	11015638	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTAGATGAAGATGTGT	GTAGATGAAGATGTGT	-	novel	NA	P-0023132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	154	634	0	ENST00000327064.4:c.221-2_234del		p.X74_splice	ENST00000327064	NM_199141.1	74		2/16	0.489466858381078	3	FACETS	0.961	0.88	1	0.481	0.44	0.523	CLONAL	1	TRUE	1	0.489466858381078	3		634	815	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299917	15299917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555729068	NA	P-0023132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	116	794	3	ENST00000263388.2:c.1261C>T	p.Arg421Cys	p.R421C	ENST00000263388	NM_000435.2	421	Cgt/Tgt	8/33	0.489466858381078	3	FACETS	0.592	0.533	0.656	0.296	0.266	0.328	SUBCLONAL	1	TRUE	1	0.489466858381078	3		797	996	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793663	NA	P-0023137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	220	822	0	ENST00000263967.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000263967	NM_006218.2	93	cGg/cAg	2/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.427888779357042	2		822	872	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0023137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	154	552	0	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.427888779357042	2		552	536	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850704	63850705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	149	597	2	ENST00000279873.7:c.1489dup	p.Ile497AsnfsTer31	p.I497Nfs*31	ENST00000279873	NM_032199.2	494	-/A	10/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.427888779357042	2		599	626	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466040	69466040	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	195	845	0	ENST00000227507.2:c.878T>A	p.Val293Glu	p.V293E	ENST00000227507	NM_053056.2	293	gTg/gAg	5/5	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.427888779357042	2		845	808	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105997	27105998	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0023137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	195	679	0	ENST00000324856.7:c.5610_5611dup	p.His1871LeufsTer13	p.H1871Lfs*13	ENST00000324856	NM_006015.4	1870	cct/cCTct	20/20	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.427888779357042	2		679	630	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645454	67645454	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	152	661	0	ENST00000264010.4:c.720del	p.Asn241MetfsTer9	p.N241Mfs*9	ENST00000264010	NM_006565.3	240	gTt/gt	3/12	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.427888779357042	2		661	677	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755560	57755560	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	231	775	0	ENST00000274289.3:c.227C>G	p.Pro76Arg	p.P76R	ENST00000274289	NM_006622.3	76	cCc/cGc	1/14	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.427888779357042	2		775	917	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589578	67589579	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAATTACATGAATAT	novel	NA	P-0023137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	107	558	0	ENST00000274335.5:c.1344_1358dup	p.Lys448_Tyr452dup	p.K448_Y452dup	ENST00000274335		448	-/AAATTACATGAATAT	10/15	1	2	FACETS	0.842	0.757	0.932	0.842	0.757	0.932	CLONAL	1	TRUE	1	0.427888779357042	2		558	594	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720851	176720851	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	229	680	0	ENST00000439151.2:c.6482G>A	p.Trp2161Ter	p.W2161*	ENST00000439151	NM_022455.4	2161	tGg/tAg	23/23	1	2	FACETS	0.755	0.707	0.804	1	0.993	1	SUBCLONAL	2	TRUE	1	0.427888779357042	2		680	709	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	85	445	0				ENST00000310581	NM_198253.2	-/1132			0.294022231346802	5	FACETS	1	0.949	1	0.738	0.659	0.822	CLONAL	2	TRUE	2	0.370930961342996	5		445	322	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0023138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	138	640	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.370930961342996	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.370930961342996	4		640	474	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63531801	63531801	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200460573	NA	P-0023138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	87	788	2	ENST00000307078.5:c.2180C>T	p.Ser727Leu	p.S727L	ENST00000307078	NM_004655.3	727	tCg/tTg	9/11	0.370930961342996	5	FACETS	0.851	0.752	0.957	0.284	0.25	0.319	CLONAL	1	TRUE	2	0.370930961342996	5		790	858	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981110	201981111	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0023138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	86	793	0	ENST00000359651.3:c.193dup	p.Gln65ProfsTer27	p.Q65Pfs*27	ENST00000359651		63	-/C	2/8	0.332311132122596	4	FACETS	1	0.933	1	0.538	0.476	0.603	CLONAL	1	TRUE	2	0.370930961342996	4		793	591	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127791	64127791	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	59	710	2	ENST00000334205.4:c.284C>T	p.Ala95Val	p.A95V	ENST00000334205	NM_003942.2	95	gCg/gTg	3/17	0.274368282262786	3	FACETS	0.695	0.598	0.8	0.347	0.299	0.4	SUBCLONAL	1	TRUE	1	0.370930961342996	3		712	543	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197398	94197398	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs746283923	NA	P-0023138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	319	633	0	ENST00000323929.3:c.1106A>G	p.Tyr369Cys	p.Y369C	ENST00000323929	NM_005591.3	369	tAt/tGt	11/20	0.370930961342996	6	FACETS	0.995	0.945	1	0.995	0.945	1	CLONAL	4	TRUE	2	0.370930961342996	6		633	753	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922264	100922264	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	70	694	0	ENST00000325455.5:c.2248C>G	p.Leu750Val	p.L750V	ENST00000325455	NM_001202474.3	750	Ctc/Gtc	5/8	0.370930961342996	6	FACETS	1	0.88	1	0.252	0.22	0.288	CLONAL	1	TRUE	2	0.370930961342996	6		694	651	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156101	119156101	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0023138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	66	868	0	ENST00000264033.4:c.1766C>G	p.Ser589Ter	p.S589*	ENST00000264033	NM_005188.3	589	tCa/tGa	11/16	0.370930961342996	6	FACETS	0.705	0.611	0.808	0.176	0.152	0.202	SUBCLONAL	1	TRUE	2	0.370930961342996	6		868	879	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156203	119156203	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	56	777	1	ENST00000264033.4:c.1868C>A	p.Ser623Ter	p.S623*	ENST00000264033	NM_005188.3	623	tCa/tAa	11/16	0.370930961342996	6	FACETS	0.616	0.526	0.714	0.154	0.131	0.179	SUBCLONAL	1	TRUE	2	0.370930961342996	6		778	854	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50830296	50830296	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	97	749	0	ENST00000398568.2:c.2739G>C	p.Leu913Phe	p.L913F	ENST00000398568	NM_001042412.1	913	ttG/ttC	18/18	0.332311132122596	4	FACETS	1	0.975	1	0.658	0.588	0.732	CLONAL	1	TRUE	2	0.370930961342996	4		749	545	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467362	66467362	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	15	284	0	ENST00000273854.3:c.907C>G	p.Gln303Glu	p.Q303E	ENST00000273854	NM_004439.5	303	Caa/Gaa	3/18	0.370930961342996	4	FACETS	0.462	0.338	0.611	0.154	0.112	0.204	SUBCLONAL	1	TRUE	1	0.370930961342996	4		284	240	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638590	176638590	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	76	946	0	ENST00000439151.2:c.3190C>G	p.Leu1064Val	p.L1064V	ENST00000439151	NM_022455.4	1064	Ctt/Gtt	5/23	0.370930961342996	3	FACETS	0.649	0.568	0.735	0.324	0.284	0.368	SUBCLONAL	1	TRUE	1	0.370930961342996	3		946	749	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913186	39913186	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	41	374	0	ENST00000378444.4:c.4929G>C	p.Glu1643Asp	p.E1643D	ENST00000378444	NM_001123385.1	1643	gaG/gaC	14/15	0.370930961342996	2	FACETS	0.689	0.576	0.813			1	SUBCLONAL	1	TRUE	NA	0.370930961342996	2		374	321	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0023153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	111	640	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	0.372154787434455	2		640	502	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0023153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	86	520	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.912	0.809	1	0.912	0.809	1	CLONAL	1	TRUE	1	0.372154787434455	2		520	507	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209652	98209652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372828014	NA	P-0023153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	165	770	6	ENST00000331920.6:c.3886G>A	p.Gly1296Arg	p.G1296R	ENST00000331920	NM_000264.3	1296	Gga/Aga	23/24	1	2	FACETS	0.942	0.865	1	0.942	0.865	1	CLONAL	1	TRUE	1	0.372154787434455	2		776	941	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922945	39922945	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	225	820	1	ENST00000378444.4:c.3763G>T	p.Glu1255Ter	p.E1255*	ENST00000378444	NM_001123385.1	1255	Gag/Tag	8/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.372154787434455	2		821	1038	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303196	11303196	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	145	687	0	ENST00000361445.4:c.1387C>G	p.Leu463Val	p.L463V	ENST00000361445	NM_004958.3	463	Ctg/Gtg	9/58	1	2	FACETS	0.858	0.783	0.937	0.858	0.783	0.937	CLONAL	1	TRUE	1	0.372154787434455	2		687	908	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480623	120480623	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	87	465	0	ENST00000256646.2:c.3194A>G	p.Asn1065Ser	p.N1065S	ENST00000256646	NM_024408.3	1065	aAt/aGt	20/34	1	2	FACETS	0.823	0.73	0.922	0.823	0.73	0.922	CLONAL	1	TRUE	1	0.372154787434455	2		465	568	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0023157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	252	680	2	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.33582310723235	5	FACETS	0.966	0.903	1	0.483	0.451	0.516	CLONAL	2	TRUE	1	0.33582310723235	5		682	1168	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0023157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	301	792	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.33582310723235	5	FACETS	0.995	0.94	1	0.746	0.705	0.789	CLONAL	3	TRUE	1	0.33582310723235	5		792	903	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851074	63851074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143074852	NA	P-0023157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	127	649	0	ENST00000279873.7:c.1852G>A	p.Ala618Thr	p.A618T	ENST00000279873	NM_032199.2	618	Gcc/Acc	10/10	0.33582310723235	3	FACETS	1	0.962	1	0.559	0.506	0.614	CLONAL	1	TRUE	1	0.33582310723235	3		649	790	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0023157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	254	790	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	0.325841163580267	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.33582310723235	2		790	713	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938407	76938407	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	102	974	1	ENST00000373344.5:c.2341C>T	p.Arg781Ter	p.R781*	ENST00000373344	NM_000489.3	781	Cga/Tga	9/35	0.105672262894909	3	FACETS	0.759	0.677	0.845			1	INDETERMINATE	1	TRUE	NA	0.33582310723235	3		975	935	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267276	41267299	+	inframe_deletion	In_Frame_Del	DEL	ACAAAACAAATGTTAAATTCTTGG	ACAAAACAAATGTTAAATTCTTGG	-	novel	NA	P-0023157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	96	646	0	ENST00000349496.5:c.860_883del	p.Asn287_Ala295delinsThr	p.N287_A295delinsT	ENST00000349496	NM_001904.3	287	aACAAAACAAATGTTAAATTCTTGGct/act	6/15	0.270005237341217	3	FACETS	1	0.94	1	0.36	0.321	0.401	CLONAL	1	TRUE	0	0.33582310723235	3		646	619	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449639	187449639	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	49	686	0	ENST00000232014.4:c.241G>A	p.Glu81Lys	p.E81K	ENST00000232014	NM_001130845.1	81	Gag/Aag	4/10	0.270005237341217	3	FACETS	0.448	0.379	0.526	0.149	0.126	0.176	SUBCLONAL	1	TRUE	0	0.33582310723235	3		686	760	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443979	49443979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201623566	NA	P-0023159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	52	1005	1	ENST00000301067.7:c.3392C>T	p.Pro1131Leu	p.P1131L	ENST00000301067	NM_003482.3	1131	cCg/cTg	11/54	1	2	FACETS	0.679	0.577	0.793	0.679	0.577	0.793	SUBCLONAL	1	TRUE	1	0.171982089231042	2		1006	890	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497958	25497958	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0023159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	52	540	0	ENST00000264709.3:c.493-2A>C		p.X165_splice	ENST00000264709	NM_175629.2	165			1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.171982089231042	2		540	539	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872533	136872533	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	27	370	0	ENST00000241393.3:c.965G>C	p.Arg322Thr	p.R322T	ENST00000241393	NM_003467.2	322	aGa/aCa	2/2	0.171982089231042	3	FACETS	0.842	0.67	1	0.421	0.335	0.52	CLONAL	1	TRUE	1	0.171982089231042	3		370	405	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752883	57752883	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	70	577	0	ENST00000274289.3:c.1045C>G	p.His349Asp	p.H349D	ENST00000274289	NM_006622.3	349	Cat/Gat	8/14	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.171982089231042	2		577	662	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0001766-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	557	782	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.514936732538107	4	FACETS	1	0.994	1	0.773	0.744	0.803	CLONAL	2	TRUE	1	0.609421108625494	4		782	1268	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178129298	178129298	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001766-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	137	629	0	ENST00000397062.3:c.7G>A	p.Asp3Asn	p.D3N	ENST00000397062	NM_006164.4	3	Gac/Aac	1/5	0.312001026426794	1	FACETS	0.403	0.366	0.441	0.403	0.366	0.441	INDETERMINATE	1	TRUE	0	0.609421108625494	1		629	776	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0001767-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	171	832	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.283993206567367	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.28	2		832	523	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288967	212288967	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs537458255	NA	P-0001767-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	103	805	0	ENST00000342788.4:c.2779C>T	p.Arg927Ter	p.R927*	ENST00000342788	NM_005235.2	927	Cga/Tga	23/28	0.295929235033923	3	FACETS	0.819	0.736	0.907	0.819	0.736	0.907	CLONAL	2	TRUE	1	0.28	3		805	512	SUCCESS
APC	324	MSKCC	GRCh37	5	112155042	112155042	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs863225310	NA	P-0001767-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	35	598	0	ENST00000257430.4:c.1312+1G>A		p.X438_splice	ENST00000257430	NM_000038.5	438			0.196495250876513	3	FACETS	0.764	0.627	0.917	0.382	0.313	0.459	CLONAL	1	TRUE	1	0.28	3		598	373	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001767-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	54	516	0	ENST00000257430.4:c.4199C>A	p.Ser1400Ter	p.S1400*	ENST00000257430	NM_000038.5	1400	tCg/tAg	16/16	0.196495250876513	3	FACETS	1	0.887	1	0.521	0.446	0.603	CLONAL	1	TRUE	1	0.28	3		516	422	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163405	108163405	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001767-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	50	833	1	ENST00000278616.4:c.4496G>T	p.Ser1499Ile	p.S1499I	ENST00000278616	NM_000051.3	1499	aGt/aTt	30/63	1	2	FACETS	0.68	0.577	0.794	0.68	0.577	0.794	SUBCLONAL	1	TRUE	1	0.28	2		834	525	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937769	76937770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0001767-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	34	920	0	ENST00000373344.5:c.2978dup	p.Lys994GlufsTer6	p.K994Efs*6	ENST00000373344	NM_000489.3	993	aag/aaAg	9/35	0.235785383753977	3	FACETS	0.414	0.337	0.502			1	SUBCLONAL	1	TRUE	NA	0.28	3		920	668	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394820	394820	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	149	511	0	ENST00000399788.2:c.4875G>A	p.Trp1625Ter	p.W1625*	ENST00000399788	NM_001042603.1	1625	tgG/tgA	28/28	0.416896908998752	6	FACETS	0.838	0.767	0.913			1	CLONAL	2	TRUE	NA	0.416896908998752	6		511	782	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578415	7578415	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	264	658	1	ENST00000269305.4:c.515T>A	p.Val172Asp	p.V172D	ENST00000269305	NM_001126112.2	172	gTt/gAt	5/11	0.283822018901602	2	FACETS	0.834	0.785	0.884	0.834	0.785	0.884	CLONAL	2	TRUE	0	0.416896908998752	2		659	759	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282496	115282496	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs376185926	NA	P-0003100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	127	471	0	ENST00000438362.2:c.154A>G	p.Asn52Asp	p.N52D	ENST00000438362	NM_001242891.1	52	Aac/Gac	3/20	0.392708688406544	3	FACETS	0.923	0.844	1	0.923	0.844	1	CLONAL	2	TRUE	1	0.416896908998752	3		471	399	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18649088	18649088	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	78	448	0	ENST00000266497.5:c.2763+1del		p.K921fs	ENST00000266497		921	aaG/aa	19/31	0.26985344116927	6	FACETS	1	0.951	1	0.566	0.502	0.633	CLONAL	2	TRUE	2	0.416896908998752	6		448	303	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62322217	62322217	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	599	899	2	ENST00000360203.5:c.2473G>T	p.Val825Phe	p.V825F	ENST00000360203	NM_001283009.1	825	Gtt/Ttt	27/35	0.310905580065547	5	FACETS	1	0.987	1			1	CLONAL	3	TRUE	NA	0.416896908998752	5		901	1476	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324729	31324743	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGAGCCTGGGGGTG	GGGAGCCTGGGGGTG	-	novel	NA	P-0003100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	105	534	0	ENST00000412585.2:c.74-9_79del		p.X25_splice	ENST00000412585	NM_005514.6	25		2/8	0.390466700027613	3	FACETS	0.731	0.654	0.812	0.244	0.218	0.271	SUBCLONAL	1	TRUE	0	0.416896908998752	3		534	833	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50811826	50811826	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs886040872	NA	P-0003757-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	429	644	0	ENST00000398568.2:c.1103C>A	p.Ser368Ter	p.S368*	ENST00000398568	NM_001042412.1	368	tCa/tAa	7/18	0.779055618942076	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.779055618942076	1		644	646	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510155	120510155	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003757-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	369	602	2	ENST00000256646.2:c.1354C>T	p.Arg452Cys	p.R452C	ENST00000256646	NM_024408.3	452	Cgt/Tgt	8/34	1	2	FACETS	0.99	0.942	1	0.99	0.942	1	CLONAL	1	TRUE	1	0.779055618942076	2		604	957	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872061	35872068	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTGGCCTG	GTGGCCTG	-	novel	NA	P-0003757-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	150	415	0	ENST00000216797.5:c.548-3_552del		p.X183_splice	ENST00000216797	NM_020529.2	183		4/6	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.779055618942076	2		415	379	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0003825-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	175	851	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	1	0.966	1	1	0.995	1	CLONAL	5	TRUE	1	0.15	2		851	440	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778017	27778017	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003825-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	113	602	1	ENST00000369163.2:c.166C>T	p.Gln56Ter	p.Q56*	ENST00000369163	NM_003536.2	56	Cag/Tag	1/1	0.15335674834671	3	FACETS	1	0.958	1	1	0.99	1	CLONAL	4	TRUE	1	0.15	3		603	370	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057749	27057749	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003825-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	224	956	0	ENST00000324856.7:c.1459del	p.Gln487SerfsTer132	p.Q487Sfs*132	ENST00000324856	NM_006015.4	486	tCc/tc	3/20	1	2	FACETS	1	0.95	1	1	0.996	1	CLONAL	4	TRUE	1	0.15	2		956	733	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226002	133226002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753514393	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	67	902	1	ENST00000320574.5:c.3895G>A	p.Glu1299Lys	p.E1299K	ENST00000320574	NM_006231.2	1299	Gag/Aag	31/49	1	2	FACETS	0.169	0.146	0.194	0.169	0.146	0.194	SUBCLONAL	1	TRUE	1	0.747380463198909	2		903	1063	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	41	658	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	1	2	FACETS	0.091	0.075	0.109	0.091	0.075	0.109	SUBCLONAL	1	TRUE	1	0.747380463198909	2		658	1207	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984767	11984767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773665341	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	30	509	1	ENST00000353533.5:c.313C>T	p.Leu105Phe	p.L105F	ENST00000353533	NM_003010.3	105	Ctt/Ttt	3/11	1	2	FACETS	0.156	0.125	0.191	0.156	0.125	0.191	SUBCLONAL	1	TRUE	1	0.747380463198909	2		510	516	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131505	202131505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	28	590	0	ENST00000358485.4:c.473C>T	p.Ser158Phe	p.S158F	ENST00000358485	NM_001080125.1	158	tCt/tTt	2/9	0.747380463198909	1	FACETS	0.104	0.082	0.128	0.104	0.082	0.128	SUBCLONAL	1	TRUE	0	0.747380463198909	1		590	453	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129420	2129420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781774	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	41	639	3	ENST00000219476.3:c.3275C>T	p.Pro1092Leu	p.P1092L	ENST00000219476	NM_000548.3	1092	cCg/cTg	28/42	0.747380463198909	1	FACETS	0.119	0.098	0.142	0.119	0.098	0.142	SUBCLONAL	1	TRUE	0	0.747380463198909	1		642	578	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557687	95557687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	296	789	0	ENST00000393063.1:c.5380G>A	p.Glu1794Lys	p.E1794K	ENST00000393063	NM_030621.3	1794	Gag/Aag	26/28	1	2	FACETS	0.899	0.849	0.95	0.899	0.849	0.95	CLONAL	1	TRUE	1	0.747380463198909	2		789	881	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149546	61149546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	23	709	0	ENST00000295025.8:c.1736G>A	p.Gly579Glu	p.G579E	ENST00000295025	NM_002908.2	579	gGa/gAa	11/11	0.747380463198909	1	FACETS	0.095	0.074	0.12	0.095	0.074	0.12	SUBCLONAL	1	TRUE	0	0.747380463198909	1		709	404	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190503	32190503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	37	930	2	ENST00000375023.3:c.236G>A	p.Ser79Asn	p.S79N	ENST00000375023	NM_004557.3	79	aGc/aAc	3/30	0.747380463198909	1	FACETS	0.087	0.071	0.105	0.087	0.071	0.105	SUBCLONAL	1	TRUE	0	0.747380463198909	1		932	714	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250436	26250436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	39	639	1	ENST00000446824.2:c.398G>A	p.Gly133Glu	p.G133E	ENST00000446824	NM_021018.2	133	gGa/gAa	1/1	0.589436179130851	2	FACETS	0.178	0.147	0.213	0.089	0.073	0.107	SUBCLONAL	1	TRUE	0	0.747380463198909	2		640	587	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226677	2226677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763271310	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	24	962	0	ENST00000398665.3:c.4157G>A	p.Gly1386Asp	p.G1386D	ENST00000398665	NM_032482.2	1386	gGc/gAc	27/28	1	2	FACETS	0.059	0.046	0.075	0.059	0.046	0.075	SUBCLONAL	1	TRUE	1	0.747380463198909	2		962	1083	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288749	33288749	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	276	594	0	ENST00000374542.5:c.803A>G	p.Asn268Ser	p.N268S	ENST00000374542	NM_001141970.1	268	aAc/aGc	3/8	0.747380463198909	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.747380463198909	1		594	452	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778800	76778800	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	314	491	0	ENST00000373344.5:c.6779A>G	p.His2260Arg	p.H2260R	ENST00000373344	NM_000489.3	2260	cAc/cGc	31/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.747380463198909	1		491	434	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573786	64573786	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1114167541	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	482	907	0	ENST00000312049.6:c.967del	p.Tyr323ThrfsTer45	p.Y323Tfs*45	ENST00000312049	NM_130799.2	323	Tac/ac	7/10	0.747380463198909	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.747380463198909	1		907	728	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008242	29008242	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	31	662	1	ENST00000282397.4:c.629C>T	p.Thr210Ile	p.T210I	ENST00000282397	NM_002019.4	210	aCa/aTa	5/30	1	2	FACETS	0.135	0.109	0.165	0.135	0.109	0.165	SUBCLONAL	1	TRUE	1	0.747380463198909	2		663	614	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969939	161969939	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	43	761	2	ENST00000366898.1:c.1030G>A	p.Glu344Lys	p.E344K	ENST00000366898	NM_004562.2	344	Gag/Aag	9/12	0.747380463198909	1	FACETS	0.115	0.096	0.137	0.115	0.096	0.137	SUBCLONAL	1	TRUE	0	0.747380463198909	1		763	625	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259047	89259047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	34	391	0	ENST00000336596.2:c.191C>T	p.Pro64Leu	p.P64L	ENST00000336596	NM_005233.5	64	cCc/cTc	3/17	0.747380463198909	1	FACETS	0.2	0.164	0.24	0.2	0.164	0.24	SUBCLONAL	1	TRUE	0	0.747380463198909	1		391	285	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332436	70332436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772124361	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	61	851	2	ENST00000373644.4:c.341G>A	p.Arg114Gln	p.R114Q	ENST00000373644	NM_030625.2	114	cGa/cAa	2/12	0.747380463198909	1	FACETS	0.141	0.121	0.163	0.141	0.121	0.163	SUBCLONAL	1	TRUE	0	0.747380463198909	1		853	724	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526232	189526232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267599729	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	54	933	0	ENST00000264731.3:c.496C>T	p.Pro166Ser	p.P166S	ENST00000264731	NM_003722.4	166	Ccc/Tcc	4/14	0.747380463198909	1	FACETS	0.112	0.095	0.131	0.112	0.095	0.131	SUBCLONAL	1	TRUE	0	0.747380463198909	1		933	805	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250169	110250169	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	78	768	0	ENST00000374672.4:c.506G>A	p.Gly169Glu	p.G169E	ENST00000374672	NM_004235.4	169	gGa/gAa	3/5	1	2	FACETS	0.222	0.195	0.252	0.222	0.195	0.252	SUBCLONAL	1	TRUE	1	0.747380463198909	2		768	939	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874719	151874719	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	62	671	0	ENST00000262189.6:c.7819C>T	p.Pro2607Ser	p.P2607S	ENST00000262189	NM_170606.2	2607	Ccc/Tcc	38/59	1	2	FACETS	0.193	0.166	0.223	0.193	0.166	0.223	SUBCLONAL	1	TRUE	1	0.747380463198909	2		671	858	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578184	7578184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146340390	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1228	78	904	0	ENST00000269305.4:c.665C>T	p.Pro222Leu	p.P222L	ENST00000269305	NM_001126112.2	222	cCg/cTg	6/11	1	2	FACETS	0.16	0.139	0.182	0.16	0.139	0.182	SUBCLONAL	1	TRUE	1	0.747380463198909	2		904	1306	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108877	2108877	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	C	rs1131692179	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	370	756	0	ENST00000219476.3:c.975+3A>C		p.X325_splice	ENST00000219476	NM_000548.3	325			0.747380463198909	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.747380463198909	1		756	600	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961013	55961013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	391	849	0	ENST00000263923.4:c.2927G>A	p.Gly976Glu	p.G976E	ENST00000263923	NM_002253.2	976	gGa/gAa	21/30	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.747380463198909	2		849	1007	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657122	215657122	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659356	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	40	743	0	ENST00000260947.4:c.263C>T	p.Thr88Ile	p.T88I	ENST00000260947	NM_000465.2	88	aCc/aTc	3/11	0.747380463198909	1	FACETS	0.152	0.126	0.181	0.152	0.126	0.181	SUBCLONAL	1	TRUE	0	0.747380463198909	1		743	440	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397538	116397538	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	43	813	0	ENST00000397752.3:c.1910C>T	p.Ser637Phe	p.S637F	ENST00000397752	NM_000245.2	637	tCc/tTc	7/21	1	2	FACETS	0.151	0.126	0.179	0.151	0.126	0.179	SUBCLONAL	1	TRUE	1	0.747380463198909	2		813	762	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143500	108143500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751714261	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	31	788	0	ENST00000278616.4:c.3205C>T	p.Pro1069Ser	p.P1069S	ENST00000278616	NM_000051.3	1069	Cct/Tct	22/63	0.747380463198909	1	FACETS	0.109	0.087	0.133	0.109	0.087	0.133	SUBCLONAL	1	TRUE	0	0.747380463198909	1		788	478	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131357	202131357	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	44	697	0	ENST00000358485.4:c.325G>A	p.Glu109Lys	p.E109K	ENST00000358485	NM_001080125.1	109	Gaa/Aaa	2/9	0.747380463198909	1	FACETS	0.156	0.13	0.184	0.156	0.13	0.184	SUBCLONAL	1	TRUE	0	0.747380463198909	1		697	473	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881389	111881389	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	31	703	0	ENST00000393256.3:c.67G>A	p.Glu23Lys	p.E23K	ENST00000393256	NM_006538.4	23	Gag/Aag	2/4	0.747380463198909	1	FACETS	0.093	0.075	0.114	0.093	0.075	0.114	SUBCLONAL	1	TRUE	0	0.747380463198909	1		703	557	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491280	2491280	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	100	785	0	ENST00000355716.4:c.323G>A	p.Ser108Asn	p.S108N	ENST00000355716	NM_003820.2	108	aGc/aAc	4/8	0.747380463198909	1	FACETS	0.254	0.226	0.282	0.254	0.226	0.282	SUBCLONAL	1	TRUE	0	0.747380463198909	1		785	661	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074045	8074045	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768654470	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	40	587	0	ENST00000377482.5:c.614G>A	p.Gly205Glu	p.G205E	ENST00000377482	NM_018948.3	205	gGa/gAa	4/4	0.747380463198909	1	FACETS	0.162	0.134	0.192	0.162	0.134	0.192	SUBCLONAL	1	TRUE	0	0.747380463198909	1		587	415	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11206831	11206831	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	36	853	0	ENST00000361445.4:c.4588G>A	p.Glu1530Lys	p.E1530K	ENST00000361445	NM_004958.3	1530	Gaa/Aaa	32/58	0.747380463198909	1	FACETS	0.109	0.089	0.132	0.109	0.089	0.132	SUBCLONAL	1	TRUE	0	0.747380463198909	1		853	552	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16203164	16203164	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	27	595	0	ENST00000375759.3:c.872G>A	p.Ser291Asn	p.S291N	ENST00000375759	NM_015001.2	291	aGc/aAc	3/15	0.747380463198909	1	FACETS	0.088	0.069	0.109	0.088	0.069	0.109	SUBCLONAL	1	TRUE	0	0.747380463198909	1		595	514	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088718	27088718	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	80	935	0	ENST00000324856.7:c.2327C>T	p.Pro776Leu	p.P776L	ENST00000324856	NM_006015.4	776	cCt/cTt	7/20	0.747380463198909	1	FACETS	0.172	0.151	0.195	0.172	0.151	0.195	SUBCLONAL	1	TRUE	0	0.747380463198909	1		935	778	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100917	27100917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	62	692	0	ENST00000324856.7:c.4199C>T	p.Pro1400Leu	p.P1400L	ENST00000324856	NM_006015.4	1400	cCt/cTt	18/20	0.747380463198909	1	FACETS	0.191	0.165	0.22	0.191	0.165	0.22	SUBCLONAL	1	TRUE	0	0.747380463198909	1		692	543	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106349	27106349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	399	788	0	ENST00000324856.7:c.5960C>T	p.Thr1987Ile	p.T1987I	ENST00000324856	NM_006015.4	1987	aCc/aTc	20/20	0.747380463198909	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.747380463198909	1		788	645	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938260	36938260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	37	915	0	ENST00000361632.4:c.701C>T	p.Thr234Ile	p.T234I	ENST00000361632		234	aCc/aTc	6/16	0.747380463198909	1	FACETS	0.087	0.071	0.105	0.087	0.071	0.105	SUBCLONAL	1	TRUE	0	0.747380463198909	1		915	709	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305263	39305263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	72	845	0	ENST00000373001.3:c.1162G>A	p.Ala388Thr	p.A388T	ENST00000373001	NM_022157.3	388	Gcg/Acg	7/7	0.747380463198909	1	FACETS	0.176	0.153	0.2	0.176	0.153	0.2	SUBCLONAL	1	TRUE	0	0.747380463198909	1		845	686	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363420	40363420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	45	873	0	ENST00000397332.2:c.809G>A	p.Arg270Lys	p.R270K	ENST00000397332	NM_001033082.2	270	aGa/aAa	3/3	0.747380463198909	1	FACETS	0.106	0.089	0.126	0.106	0.089	0.126	SUBCLONAL	1	TRUE	0	0.747380463198909	1		873	710	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428606	78428606	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	25	594	0	ENST00000370768.2:c.1193C>T	p.Thr398Ile	p.T398I	ENST00000370768	NM_003902.3	398	aCc/aTc	14/20	0.747380463198909	1	FACETS	0.103	0.08	0.128	0.103	0.08	0.128	SUBCLONAL	1	TRUE	0	0.747380463198909	1		594	408	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166364	118166364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	32	517	0	ENST00000369448.3:c.874C>T	p.Leu292Phe	p.L292F	ENST00000369448	NM_017709.3	292	Ctt/Ttt	2/2	0.747380463198909	1	FACETS	0.124	0.101	0.151	0.124	0.101	0.151	SUBCLONAL	1	TRUE	0	0.747380463198909	1		517	431	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746116	162746116	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	33	550	2	ENST00000367921.3:c.2239G>A	p.Ala747Thr	p.A747T	ENST00000367921	NM_006182.2	747	Gca/Aca	16/18	0.747380463198909	1	FACETS	0.136	0.11	0.164	0.136	0.11	0.164	SUBCLONAL	1	TRUE	0	0.747380463198909	1		552	408	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226580009	226580009	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	37	652	0	ENST00000366794.5:c.293G>A	p.Gly98Asp	p.G98D	ENST00000366794	NM_001618.3	98	gGc/gAc	3/23	0.747380463198909	1	FACETS	0.106	0.087	0.128	0.106	0.087	0.128	SUBCLONAL	1	TRUE	0	0.747380463198909	1		652	583	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927411	245927411	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	55	799	0	ENST00000388985.4:c.1117G>A	p.Val373Met	p.V373M	ENST00000388985		373	Gtg/Atg	11/12	0.747380463198909	1	FACETS	0.134	0.114	0.156	0.134	0.114	0.156	SUBCLONAL	1	TRUE	0	0.747380463198909	1		799	686	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606854	43606854	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1218693745	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	49	886	3	ENST00000355710.3:c.1463C>T	p.Thr488Ile	p.T488I	ENST00000355710	NM_020975.4	488	aCc/aTc	7/20	0.747380463198909	1	FACETS	0.113	0.095	0.132	0.113	0.095	0.132	SUBCLONAL	1	TRUE	0	0.747380463198909	1		889	730	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63810748	63810748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	37	663	0	ENST00000279873.7:c.835G>A	p.Ala279Thr	p.A279T	ENST00000279873	NM_032199.2	279	Gcc/Acc	5/10	0.747380463198909	1	FACETS	0.114	0.094	0.138	0.114	0.094	0.138	SUBCLONAL	1	TRUE	0	0.747380463198909	1		663	542	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70432764	70432764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	33	874	0	ENST00000373644.4:c.4786C>T	p.Pro1596Ser	p.P1596S	ENST00000373644	NM_030625.2	1596	Ccc/Tcc	8/12	0.747380463198909	1	FACETS	0.107	0.087	0.13	0.107	0.087	0.13	SUBCLONAL	1	TRUE	0	0.747380463198909	1		874	516	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161405	2161405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	40	823	1	ENST00000434045.2:c.122G>A	p.Gly41Asp	p.G41D	ENST00000434045	NM_001127598.1	41	gGc/gAc	2/5	0.747380463198909	1	FACETS	0.094	0.077	0.112	0.094	0.077	0.112	SUBCLONAL	1	TRUE	0	0.747380463198909	1		824	716	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414272	32414272	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	29	775	0	ENST00000332351.3:c.1279G>A	p.Asp427Asn	p.D427N	ENST00000332351	NM_024426.4	427	Gac/Aac	8/10	0.747380463198909	1	FACETS	0.086	0.068	0.106	0.086	0.068	0.106	SUBCLONAL	1	TRUE	0	0.747380463198909	1		775	568	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136957	64136957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	27	722	0	ENST00000334205.4:c.1468G>A	p.Glu490Lys	p.E490K	ENST00000334205	NM_003942.2	490	Gag/Aag	13/17	0.747380463198909	1	FACETS	0.084	0.066	0.104	0.084	0.066	0.104	SUBCLONAL	1	TRUE	0	0.747380463198909	1		722	539	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137755	64137755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	63	1015	1	ENST00000334205.4:c.1856G>A	p.Ser619Asn	p.S619N	ENST00000334205	NM_003942.2	619	aGc/aAc	15/17	0.747380463198909	1	FACETS	0.142	0.122	0.164	0.142	0.122	0.164	SUBCLONAL	1	TRUE	0	0.747380463198909	1		1016	743	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940216	71940216	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	471	887	1	ENST00000298229.2:c.601G>A	p.Ala201Thr	p.A201T	ENST00000298229	NM_001567.3	201	Gcc/Acc	5/28	0.747380463198909	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.747380463198909	1		888	756	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103525	77103525	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	53	657	0	ENST00000356341.3:c.41C>T	p.Ala14Val	p.A14V	ENST00000356341	NM_002576.4	14	gCc/gTc	2/15	0.747380463198909	1	FACETS	0.179	0.153	0.209	0.179	0.153	0.209	SUBCLONAL	1	TRUE	0	0.747380463198909	1		657	495	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203636	94203636	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	20	463	0	ENST00000323929.3:c.1017+1G>A		p.X339_splice	ENST00000323929	NM_005591.3	339			0.747380463198909	1	FACETS	0.136	0.104	0.173	0.136	0.104	0.173	SUBCLONAL	1	TRUE	0	0.747380463198909	1		463	247	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999428	100999428	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780204100	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	109	1117	1	ENST00000325455.5:c.374G>A	p.Gly125Glu	p.G125E	ENST00000325455	NM_001202474.3	125	gGg/gAg	1/8	0.747380463198909	1	FACETS	0.244	0.219	0.271	0.244	0.219	0.271	SUBCLONAL	1	TRUE	0	0.747380463198909	1		1118	749	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139331	108139331	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	20	754	0	ENST00000278616.4:c.2833C>T	p.His945Tyr	p.H945Y	ENST00000278616	NM_000051.3	945	Cat/Tat	18/63	0.747380463198909	1	FACETS	0.085	0.065	0.109	0.085	0.065	0.109	SUBCLONAL	1	TRUE	0	0.747380463198909	1		754	393	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173752	108173752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555106575	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	15	524	1	ENST00000278616.4:c.5492G>A	p.Cys1831Tyr	p.C1831Y	ENST00000278616	NM_000051.3	1831	tGt/tAt	36/63	0.747380463198909	1	FACETS	0.084	0.061	0.111	0.084	0.061	0.111	SUBCLONAL	1	TRUE	0	0.747380463198909	1		525	300	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111958611	111958611	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	49	556	0	ENST00000375549.3:c.83C>T	p.Pro28Leu	p.P28L	ENST00000375549	NM_003002.3	28	cCt/cTt	2/4	0.747380463198909	1	FACETS	0.196	0.166	0.229	0.196	0.166	0.229	SUBCLONAL	1	TRUE	0	0.747380463198909	1		556	419	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420122	420122	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	78	859	0	ENST00000399788.2:c.3145G>A	p.Ala1049Thr	p.A1049T	ENST00000399788	NM_001042603.1	1049	Gca/Aca	21/28	1	2	FACETS	0.175	0.153	0.199	0.175	0.153	0.199	SUBCLONAL	1	TRUE	1	0.747380463198909	2		859	1192	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245654	46245654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1300029603	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	35	572	0	ENST00000334344.6:c.3748G>A	p.Ala1250Thr	p.A1250T	ENST00000334344	NM_152641.2	1250	Gca/Aca	15/21	1	2	FACETS	0.141	0.115	0.171	0.141	0.115	0.171	SUBCLONAL	1	TRUE	1	0.747380463198909	2		572	662	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427332	49427332	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	65	653	0	ENST00000301067.7:c.11156G>A	p.Arg3719Lys	p.R3719K	ENST00000301067	NM_003482.3	3719	aGg/aAg	39/54	1	2	FACETS	0.19	0.164	0.218	0.19	0.164	0.218	SUBCLONAL	1	TRUE	1	0.747380463198909	2		653	916	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433799	49433799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	531	1073	1	ENST00000301067.7:c.7754G>A	p.Gly2585Glu	p.G2585E	ENST00000301067	NM_003482.3	2585	gGg/gAg	31/54	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.747380463198909	2		1074	1332	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434963	49434963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750565501	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	387	589	0	ENST00000301067.7:c.6590C>T	p.Pro2197Leu	p.P2197L	ENST00000301067	NM_003482.3	2197	cCc/cTc	31/54	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.747380463198909	2		589	872	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440438	49440438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1250	67	971	1	ENST00000301067.7:c.4372G>A	p.Asp1458Asn	p.D1458N	ENST00000301067	NM_003482.3	1458	Gac/Aac	15/54	1	2	FACETS	0.136	0.117	0.157	0.136	0.117	0.157	SUBCLONAL	1	TRUE	1	0.747380463198909	2		972	1317	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447848	49447848	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	395	830	0	ENST00000301067.7:c.586C>T	p.Pro196Ser	p.P196S	ENST00000301067	NM_003482.3	196	Ccc/Tcc	5/54	1	2	FACETS	0.941	0.896	0.987	0.941	0.896	0.987	CLONAL	1	TRUE	1	0.747380463198909	2		830	1123	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885927	111885927	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	365	737	2	ENST00000341259.2:c.1549G>A	p.Gly517Arg	p.G517R	ENST00000341259	NM_005475.2	517	Ggg/Agg	8/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.747380463198909	2		739	905	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120805894	120805894	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	72	865	1	ENST00000257552.2:c.184G>A	p.Gly62Ser	p.G62S	ENST00000257552	NM_002442.3	62	Ggt/Agt	4/15	1	2	FACETS	0.183	0.159	0.209	0.183	0.159	0.209	SUBCLONAL	1	TRUE	1	0.747380463198909	2		866	1054	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008300	29008300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	38	620	0	ENST00000282397.4:c.571G>A	p.Gly191Ser	p.G191S	ENST00000282397	NM_002019.4	191	Ggc/Agc	5/30	1	2	FACETS	0.165	0.136	0.198	0.165	0.136	0.198	SUBCLONAL	1	TRUE	1	0.747380463198909	2		620	616	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134733	41134733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	38	587	1	ENST00000379561.5:c.895C>T	p.Pro299Ser	p.P299S	ENST00000379561	NM_002015.3	299	Cct/Tct	2/3	1	2	FACETS	0.163	0.134	0.196	0.163	0.134	0.196	SUBCLONAL	1	TRUE	1	0.747380463198909	2		588	622	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872936	35872936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184836139	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	63	692	0	ENST00000216797.5:c.296G>A	p.Gly99Glu	p.G99E	ENST00000216797	NM_020529.2	99	gGa/gAa	2/6	1	2	FACETS	0.17	0.146	0.196	0.17	0.146	0.196	SUBCLONAL	1	TRUE	1	0.747380463198909	2		692	992	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061039	38061039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	40	432	0	ENST00000250448.2:c.950C>T	p.Thr317Ile	p.T317I	ENST00000250448	NM_004496.3	317	aCc/aTc	2/2	1	2	FACETS	0.209	0.174	0.249	0.209	0.174	0.249	SUBCLONAL	1	TRUE	1	0.747380463198909	2		432	511	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590657	95590657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	48	703	1	ENST00000393063.1:c.1252G>A	p.Asp418Asn	p.D418N	ENST00000393063	NM_030621.3	418	Gat/Aat	9/28	1	2	FACETS	0.18	0.152	0.212	0.18	0.152	0.212	SUBCLONAL	1	TRUE	1	0.747380463198909	2		704	712	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701849	43701849	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	40	580	1	ENST00000382044.4:c.5396C>T	p.Ala1799Val	p.A1799V	ENST00000382044	NM_001141980.1	1799	gCc/gTc	25/28	1	2	FACETS	0.162	0.134	0.194	0.162	0.134	0.194	SUBCLONAL	1	TRUE	1	0.747380463198909	2		581	660	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724433	43724433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	87	1112	1	ENST00000382044.4:c.3634G>A	p.Val1212Ile	p.V1212I	ENST00000382044	NM_001141980.1	1212	Gtc/Atc	17/28	1	2	FACETS	0.188	0.166	0.212	0.188	0.166	0.212	SUBCLONAL	1	TRUE	1	0.747380463198909	2		1113	1237	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465411	99465411	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	69	617	0	ENST00000268035.6:c.2236G>A	p.Ala746Thr	p.A746T	ENST00000268035	NM_000875.3	746	Gcc/Acc	11/21	1	2	FACETS	0.212	0.184	0.243	0.212	0.184	0.243	SUBCLONAL	1	TRUE	1	0.747380463198909	2		617	871	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121835	2121835	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	63	866	0	ENST00000219476.3:c.1997C>T	p.Pro666Leu	p.P666L	ENST00000219476	NM_000548.3	666	cCc/cTc	19/42	0.747380463198909	1	FACETS	0.166	0.143	0.191	0.166	0.143	0.191	SUBCLONAL	1	TRUE	0	0.747380463198909	1		866	637	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126137	2126137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	45	971	0	ENST00000219476.3:c.2708C>T	p.Pro903Leu	p.P903L	ENST00000219476	NM_000548.3	903	cCc/cTc	24/42	0.747380463198909	1	FACETS	0.093	0.077	0.11	0.093	0.077	0.11	SUBCLONAL	1	TRUE	0	0.747380463198909	1		971	814	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226271	2226271	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	30	805	0	ENST00000326181.6:c.1884G>A	p.Trp628Ter	p.W628*	ENST00000326181	NM_032271.2	628	tgG/tgA	20/21	0.747380463198909	1	FACETS	0.085	0.067	0.104	0.085	0.067	0.104	SUBCLONAL	1	TRUE	0	0.747380463198909	1		805	595	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779787	3779787	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	43	857	0	ENST00000262367.5:c.5261G>A	p.Ser1754Asn	p.S1754N	ENST00000262367	NM_004380.2	1754	aGc/aAc	31/31	0.747380463198909	1	FACETS	0.107	0.089	0.128	0.107	0.089	0.128	SUBCLONAL	1	TRUE	0	0.747380463198909	1		857	671	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50827525	50827525	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	33	825	1	ENST00000398568.2:c.2410G>T	p.Asp804Tyr	p.D804Y	ENST00000398568	NM_001042412.1	804	Gac/Tac	16/18	0.747380463198909	1	FACETS	0.084	0.068	0.103	0.084	0.068	0.103	SUBCLONAL	1	TRUE	0	0.747380463198909	1		826	657	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828171	50828171	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	40	670	0	ENST00000398568.2:c.2509C>T	p.Leu837Phe	p.L837F	ENST00000398568	NM_001042412.1	837	Ctt/Ttt	17/18	0.747380463198909	1	FACETS	0.126	0.104	0.15	0.126	0.104	0.15	SUBCLONAL	1	TRUE	0	0.747380463198909	1		670	533	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782278	56782278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	71	804	1	ENST00000308159.5:c.119G>A	p.Gly40Glu	p.G40E	ENST00000308159	NM_014669.4	40	gGa/gAa	2/22	0.747380463198909	1	FACETS	0.18	0.157	0.206	0.18	0.157	0.206	SUBCLONAL	1	TRUE	0	0.747380463198909	1		805	660	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868658	56868658	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	26	635	0	ENST00000308159.5:c.1750C>T	p.Leu584Phe	p.L584F	ENST00000308159	NM_014669.4	584	Ctt/Ttt	16/22	0.747380463198909	1	FACETS	0.095	0.074	0.118	0.095	0.074	0.118	SUBCLONAL	1	TRUE	0	0.747380463198909	1		635	460	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830255	72830255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	22	402	1	ENST00000268489.5:c.6326C>T	p.Thr2109Ile	p.T2109I	ENST00000268489	NM_006885.3	2109	aCc/aTc	9/10	0.747380463198909	1	FACETS	0.12	0.093	0.152	0.12	0.093	0.152	SUBCLONAL	1	TRUE	0	0.747380463198909	1		403	307	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991722	72991722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	21	419	1	ENST00000268489.5:c.2323G>A	p.Ala775Thr	p.A775T	ENST00000268489	NM_006885.3	775	Gcg/Acg	2/10	0.747380463198909	1	FACETS	0.111	0.085	0.141	0.111	0.085	0.141	SUBCLONAL	1	TRUE	0	0.747380463198909	1		420	318	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992766	72992766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	73	783	1	ENST00000268489.5:c.1279C>T	p.Pro427Ser	p.P427S	ENST00000268489	NM_006885.3	427	Cct/Tct	2/10	0.747380463198909	1	FACETS	0.22	0.192	0.25	0.22	0.192	0.25	SUBCLONAL	1	TRUE	0	0.747380463198909	1		784	556	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934321	81934321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	88	839	1	ENST00000359376.3:c.1298C>T	p.Pro433Leu	p.P433L	ENST00000359376	NM_002661.3	433	cCc/cTc	14/33	0.747380463198909	1	FACETS	0.205	0.182	0.231	0.205	0.182	0.231	SUBCLONAL	1	TRUE	0	0.747380463198909	1		840	718	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347614	89347614	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	47	799	1	ENST00000301030.4:c.5336C>T	p.Pro1779Leu	p.P1779L	ENST00000301030	NM_001256183.1	1779	cCt/cTt	9/13	0.747380463198909	1	FACETS	0.112	0.094	0.132	0.112	0.094	0.132	SUBCLONAL	1	TRUE	0	0.747380463198909	1		800	703	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350747	89350747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	74	1093	0	ENST00000301030.4:c.2203G>A	p.Glu735Lys	p.E735K	ENST00000301030	NM_001256183.1	735	Gag/Aag	9/13	0.747380463198909	1	FACETS	0.155	0.135	0.177	0.155	0.135	0.177	SUBCLONAL	1	TRUE	0	0.747380463198909	1		1093	798	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849510	89849510	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	32	702	0	ENST00000389301.3:c.1471G>A	p.Val491Met	p.V491M	ENST00000389301	NM_000135.2	491	Gtg/Atg	16/43	0.747380463198909	1	FACETS	0.103	0.083	0.126	0.103	0.083	0.126	SUBCLONAL	1	TRUE	0	0.747380463198909	1		702	519	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579503	7579503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	78	977	0	ENST00000269305.4:c.184G>A	p.Glu62Lys	p.E62K	ENST00000269305	NM_001126112.2	62	Gaa/Aaa	4/11	1	2	FACETS	0.172	0.15	0.195	0.172	0.15	0.195	SUBCLONAL	1	TRUE	1	0.747380463198909	2		977	1214	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110686	8110686	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1220103779	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	58	548	0	ENST00000585124.1:c.207-1G>A		p.X69_splice	ENST00000585124	NM_004217.3	69			1	2	FACETS	0.204	0.174	0.236	0.204	0.174	0.236	SUBCLONAL	1	TRUE	1	0.747380463198909	2		548	762	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974856	15974856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	44	705	2	ENST00000268712.3:c.4019G>A	p.Gly1340Asp	p.G1340D	ENST00000268712	NM_006311.3	1340	gGc/gAc	30/46	1	2	FACETS	0.156	0.13	0.185	0.156	0.13	0.185	SUBCLONAL	1	TRUE	1	0.747380463198909	2		707	756	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37865669	37865669	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	76	821	0	ENST00000269571.5:c.538G>A	p.Ala180Thr	p.A180T	ENST00000269571		180	Gct/Act	4/27	1	2	FACETS	0.174	0.152	0.198	0.174	0.152	0.198	SUBCLONAL	1	TRUE	1	0.747380463198909	2		821	1168	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40460280	40460280	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	67	803	0	ENST00000345506.4:c.1991G>A	p.Ser664Asn	p.S664N	ENST00000345506	NM_003152.3	664	aGc/aAc	17/20	1	2	FACETS	0.177	0.153	0.203	0.177	0.153	0.203	SUBCLONAL	1	TRUE	1	0.747380463198909	2		803	1015	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226371	41226371	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	53	925	0	ENST00000357654.3:c.4652C>T	p.Ser1551Phe	p.S1551F	ENST00000357654	NM_007294.3	1551	tCt/tTt	14/23	1	2	FACETS	0.134	0.113	0.157	0.134	0.113	0.157	SUBCLONAL	1	TRUE	1	0.747380463198909	2		925	1058	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805861	46805861	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	283	695	0	ENST00000290295.7:c.95C>T	p.Pro32Leu	p.P32L	ENST00000290295	NM_006361.5	32	cCt/cTt	1/2	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.747380463198909	2		695	729	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440712	56440712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	441	803	0	ENST00000407977.2:c.506C>T	p.Ala169Val	p.A169V	ENST00000407977		169	gCt/gTt	5/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.747380463198909	2		803	1073	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677986	58677986	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	27	343	3	ENST00000305921.3:c.211G>A	p.Ala71Thr	p.A71T	ENST00000305921	NM_003620.3	71	Gca/Aca	1/6	1	2	FACETS	0.161	0.127	0.199	0.161	0.127	0.199	SUBCLONAL	1	TRUE	1	0.747380463198909	2		346	449	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678106	58678106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	85	673	0	ENST00000305921.3:c.331G>A	p.Glu111Lys	p.E111K	ENST00000305921	NM_003620.3	111	Gag/Aag	1/6	1	2	FACETS	0.222	0.195	0.25	0.222	0.195	0.25	SUBCLONAL	1	TRUE	1	0.747380463198909	2		673	1026	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120377	70120377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1454	135	1157	0	ENST00000245479.2:c.1379C>T	p.Thr460Ile	p.T460I	ENST00000245479	NM_000346.3	460	aCc/aTc	3/3	1	2	FACETS	0.227	0.205	0.251	0.227	0.205	0.251	SUBCLONAL	1	TRUE	1	0.747380463198909	2		1157	1589	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56338909	56338909	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1478045882	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	11	79	0	ENST00000348428.3:c.34C>T	p.Pro12Ser	p.P12S	ENST00000348428	NM_006785.3	12	Ccg/Tcg	1/17	1	2	FACETS	0.241	0.167	0.332	0.241	0.167	0.332	SUBCLONAL	1	TRUE	1	0.747380463198909	2		79	122	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622189	1622189	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	83	728	0	ENST00000344749.5:c.686G>A	p.Ser229Asn	p.S229N	ENST00000344749	NM_001136139.2	229	aGt/aAt	10/19	1	2	FACETS	0.235	0.206	0.265	0.235	0.206	0.265	SUBCLONAL	1	TRUE	1	0.747380463198909	2		728	946	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219399	5219399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035903725	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	74	908	1	ENST00000357368.4:c.3845G>A	p.Gly1282Glu	p.G1282E	ENST00000357368	NM_002850.3	1282	gGg/gAg	23/38	1	2	FACETS	0.166	0.145	0.19	0.166	0.145	0.19	SUBCLONAL	1	TRUE	1	0.747380463198909	2		909	1191	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223252	5223252	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763535247	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	64	867	0	ENST00000357368.4:c.2551C>T	p.Arg851Cys	p.R851C	ENST00000357368	NM_002850.3	851	Cgc/Tgc	18/38	1	2	FACETS	0.156	0.134	0.179	0.156	0.134	0.179	SUBCLONAL	1	TRUE	1	0.747380463198909	2		867	1101	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353891	15353891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747935780	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	72	699	2	ENST00000263377.2:c.2989G>A	p.Val997Met	p.V997M	ENST00000263377	NM_058243.2	997	Gtg/Atg	14/20	1	2	FACETS	0.21	0.183	0.24	0.21	0.183	0.24	SUBCLONAL	1	TRUE	1	0.747380463198909	2		701	917	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366263	15366263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	78	895	0	ENST00000263377.2:c.1892G>A	p.Gly631Asp	p.G631D	ENST00000263377	NM_058243.2	631	gGc/gAc	10/20	1	2	FACETS	0.181	0.158	0.205	0.181	0.158	0.205	SUBCLONAL	1	TRUE	1	0.747380463198909	2		895	1156	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950285	17950285	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	79	825	1	ENST00000458235.1:c.1441+1G>A		p.X481_splice	ENST00000458235	NM_000215.3	481			1	2	FACETS	0.193	0.168	0.219	0.193	0.168	0.219	SUBCLONAL	1	TRUE	1	0.747380463198909	2		826	1098	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256751	19256751	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	360	725	0	ENST00000162023.5:c.962A>T	p.Glu321Val	p.E321V	ENST00000162023		321	gAg/gTg	13/13	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.747380463198909	2		725	957	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257372	19257372	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1338729674	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	76	798	1	ENST00000162023.5:c.761G>A	p.Gly254Asp	p.G254D	ENST00000162023		254	gGc/gAc	11/13	1	2	FACETS	0.214	0.187	0.243	0.214	0.187	0.243	SUBCLONAL	1	TRUE	1	0.747380463198909	2		799	952	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793034	33793034	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	195	285	1	ENST00000498907.2:c.287G>A	p.Gly96Asp	p.G96D	ENST00000498907	NM_004364.3	96	gGc/gAc	1/1	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.747380463198909	2		286	464	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213986	36213986	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	93	953	1	ENST00000222270.7:c.2812C>T	p.Pro938Ser	p.P938S	ENST00000222270	NM_014727.1	938	Ccc/Tcc	6/37	1	2	FACETS	0.194	0.172	0.219	0.194	0.172	0.219	SUBCLONAL	1	TRUE	1	0.747380463198909	2		954	1280	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218431	36218431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	381	738	1	ENST00000222270.7:c.4210G>A	p.Ala1404Thr	p.A1404T	ENST00000222270	NM_014727.1	1404	Gcc/Acc	16/37	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.747380463198909	2		739	978	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218632	36218632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	92	888	1	ENST00000222270.7:c.4336C>T	p.Pro1446Ser	p.P1446S	ENST00000222270	NM_014727.1	1446	Ccc/Tcc	17/37	1	2	FACETS	0.213	0.188	0.239	0.213	0.188	0.239	SUBCLONAL	1	TRUE	1	0.747380463198909	2		889	1156	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223359	36223359	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1257	96	967	0	ENST00000222270.7:c.5909C>T	p.Pro1970Leu	p.P1970L	ENST00000222270	NM_014727.1	1970	cCt/cTt	28/37	1	2	FACETS	0.19	0.168	0.213	0.19	0.168	0.213	SUBCLONAL	1	TRUE	1	0.747380463198909	2		967	1353	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753230	42753230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265977248	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	81	928	0	ENST00000222329.4:c.1034C>T	p.Pro345Leu	p.P345L	ENST00000222329	NM_006494.2	345	cCt/cTt	4/4	1	2	FACETS	0.178	0.156	0.202	0.178	0.156	0.202	SUBCLONAL	1	TRUE	1	0.747380463198909	2		928	1216	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966007	25966007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	44	995	0	ENST00000435504.4:c.3199C>T	p.Leu1067Phe	p.L1067F	ENST00000435504		1067	Ctt/Ttt	13/13	0.747380463198909	1	FACETS	0.095	0.079	0.113	0.095	0.079	0.113	SUBCLONAL	1	TRUE	0	0.747380463198909	1		995	773	SUCCESS
ALK	238	MSKCC	GRCh37	2	29420414	29420414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	40	791	1	ENST00000389048.3:c.4067G>A	p.Gly1356Glu	p.G1356E	ENST00000389048	NM_004304.4	1356	gGg/gAg	27/29	0.747380463198909	1	FACETS	0.111	0.091	0.132	0.111	0.091	0.132	SUBCLONAL	1	TRUE	0	0.747380463198909	1		792	606	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449875	29449875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150344432	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	50	1111	3	ENST00000389048.3:c.2980G>A	p.Glu994Lys	p.E994K	ENST00000389048	NM_004304.4	994	Gaa/Aaa	18/29	0.747380463198909	1	FACETS	0.099	0.084	0.117	0.099	0.084	0.117	SUBCLONAL	1	TRUE	0	0.747380463198909	1		1114	843	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032840	48032840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1114167744	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	273	698	2	ENST00000234420.5:c.3640G>A	p.Glu1214Lys	p.E1214K	ENST00000234420	NM_000179.2	1214	Gaa/Aaa	7/10	0.747380463198909	1	FACETS	0.951	0.906	0.996	0.951	0.906	0.996	CLONAL	1	TRUE	0	0.747380463198909	1		700	481	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182201	99182201	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	38	779	1	ENST00000074304.5:c.2266G>A	p.Asp756Asn	p.D756N	ENST00000074304	NM_001134224.1	756	Gac/Aac	21/26	0.747380463198909	1	FACETS	0.087	0.071	0.104	0.087	0.071	0.104	SUBCLONAL	1	TRUE	0	0.747380463198909	1		780	734	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198269804	198269804	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	71	895	0	ENST00000335508.6:c.1535G>A	p.Arg512Lys	p.R512K	ENST00000335508	NM_012433.2	512	aGa/aAa	11/25	0.747380463198909	1	FACETS	0.161	0.14	0.184	0.161	0.14	0.184	SUBCLONAL	1	TRUE	0	0.747380463198909	1		895	737	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661134	227661134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745446733	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	416	905	3	ENST00000305123.5:c.2321C>T	p.Thr774Ile	p.T774I	ENST00000305123	NM_005544.2	774	aCc/aTc	1/2	0.747380463198909	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.747380463198909	1		908	657	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662373	227662373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746340033	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	29	775	0	ENST00000305123.5:c.1082G>A	p.Gly361Asp	p.G361D	ENST00000305123	NM_005544.2	361	gGc/gAc	1/2	0.747380463198909	1	FACETS	0.088	0.07	0.109	0.088	0.07	0.109	SUBCLONAL	1	TRUE	0	0.747380463198909	1		775	552	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031636	36031636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	72	858	0	ENST00000358208.4:c.1465G>A	p.Glu489Lys	p.E489K	ENST00000358208		489	Gag/Aag	12/12	1	2	FACETS	0.178	0.155	0.203	0.178	0.155	0.203	SUBCLONAL	1	TRUE	1	0.747380463198909	2		858	1082	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256415	46256415	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	50	772	1	ENST00000371998.3:c.643C>T	p.Pro215Ser	p.P215S	ENST00000371998		215	Cct/Tct	7/23	1	2	FACETS	0.17	0.143	0.199	0.17	0.143	0.199	SUBCLONAL	1	TRUE	1	0.747380463198909	2		773	789	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324612	62324612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751124641	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	95	704	6	ENST00000360203.5:c.2968G>A	p.Ala990Thr	p.A990T	ENST00000360203	NM_001283009.1	990	Gca/Aca	30/35	1	2	FACETS	0.26	0.231	0.292	0.26	0.231	0.292	SUBCLONAL	1	TRUE	1	0.747380463198909	2		710	976	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121024	29121024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs864622691	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	46	998	1	ENST00000328354.6:c.533G>A	p.Gly178Glu	p.G178E	ENST00000328354	NM_007194.3	178	gGa/gAa	4/15	0.747380463198909	1	FACETS	0.109	0.091	0.129	0.109	0.091	0.129	SUBCLONAL	1	TRUE	0	0.747380463198909	1		999	708	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556722	41556722	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	58	665	0	ENST00000263253.7:c.3667C>T	p.Gln1223Ter	p.Q1223*	ENST00000263253	NM_001429.3	1223	Caa/Taa	20/31	0.747380463198909	1	FACETS	0.198	0.17	0.228	0.198	0.17	0.228	SUBCLONAL	1	TRUE	0	0.747380463198909	1		665	491	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660202	12660202	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	45	827	1	ENST00000251849.4:c.19G>A	p.Ala7Thr	p.A7T	ENST00000251849	NM_002880.3	7	Gct/Act	2/17	0.747380463198909	1	FACETS	0.129	0.108	0.152	0.129	0.108	0.152	SUBCLONAL	1	TRUE	0	0.747380463198909	1		828	585	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713603	30713603	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553630181	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	288	655	3	ENST00000295754.5:c.928G>A	p.Ala310Thr	p.A310T	ENST00000295754	NM_003242.5	310	Gct/Act	4/7	0.747380463198909	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.747380463198909	1		658	467	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103803	47103803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	39	782	1	ENST00000409792.3:c.6143G>A	p.Arg2048Lys	p.R2048K	ENST00000409792	NM_014159.6	2048	aGa/aAa	14/21	0.747380463198909	1	FACETS	0.113	0.093	0.135	0.113	0.093	0.135	SUBCLONAL	1	TRUE	0	0.747380463198909	1		783	579	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397760	49397760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	52	997	0	ENST00000418115.1:c.464G>A	p.Gly155Glu	p.G155E	ENST00000418115	NM_001664.2	155	gGg/gAg	5/5	0.747380463198909	1	FACETS	0.095	0.08	0.111	0.095	0.08	0.111	SUBCLONAL	1	TRUE	0	0.747380463198909	1		997	919	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928652	49928652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372151789	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	41	845	0	ENST00000296474.3:c.3622G>A	p.Asp1208Asn	p.D1208N	ENST00000296474	NM_002447.2	1208	Gac/Aac	17/20	0.747380463198909	1	FACETS	0.091	0.075	0.108	0.091	0.075	0.108	SUBCLONAL	1	TRUE	0	0.747380463198909	1		845	757	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932879	49932879	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	38	955	0	ENST00000296474.3:c.3064+1G>A		p.X1022_splice	ENST00000296474	NM_002447.2	1022			0.747380463198909	1	FACETS	0.092	0.075	0.11	0.092	0.075	0.11	SUBCLONAL	1	TRUE	0	0.747380463198909	1		955	695	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934241	49934241	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375227799	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	38	801	0	ENST00000296474.3:c.2266G>A	p.Ala756Thr	p.A756T	ENST00000296474	NM_002447.2	756	Gcc/Acc	8/20	0.747380463198909	1	FACETS	0.1	0.082	0.12	0.1	0.082	0.12	SUBCLONAL	1	TRUE	0	0.747380463198909	1		801	640	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940565	49940565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	33	768	3	ENST00000296474.3:c.478C>T	p.Pro160Ser	p.P160S	ENST00000296474	NM_002447.2	160	Cca/Tca	1/20	0.747380463198909	1	FACETS	0.089	0.072	0.108	0.089	0.072	0.108	SUBCLONAL	1	TRUE	0	0.747380463198909	1		771	622	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014310	70014310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	78	871	0	ENST00000394351.3:c.1171C>T	p.Pro391Ser	p.P391S	ENST00000394351	NM_000248.3	391	Cca/Tca	9/9	0.747380463198909	1	FACETS	0.201	0.176	0.227	0.201	0.176	0.227	SUBCLONAL	1	TRUE	0	0.747380463198909	1		871	651	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670822	134670822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	41	654	1	ENST00000398015.3:c.733G>A	p.Glu245Lys	p.E245K	ENST00000398015	NM_004441.4	245	Gaa/Aaa	3/16	0.747380463198909	1	FACETS	0.139	0.115	0.165	0.139	0.115	0.165	SUBCLONAL	1	TRUE	0	0.747380463198909	1		655	496	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664852	138664852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760287518	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	24	265	0	ENST00000330315.3:c.713G>A	p.Ser238Asn	p.S238N	ENST00000330315	NM_023067.3	238	aGc/aAc	1/1	0.747380463198909	1	FACETS	0.187	0.147	0.233	0.187	0.147	0.233	SUBCLONAL	1	TRUE	0	0.747380463198909	1		265	215	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149238663	149238663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	37	857	1	ENST00000360632.3:c.1132G>A	p.Asp378Asn	p.D378N	ENST00000360632	NM_015472.4	378	Gac/Aac	7/7	0.747380463198909	1	FACETS	0.115	0.094	0.138	0.115	0.094	0.138	SUBCLONAL	1	TRUE	0	0.747380463198909	1		858	541	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1932369	1932369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	76	676	0	ENST00000382891.5:c.1427C>T	p.Pro476Leu	p.P476L	ENST00000382891	NM_133335.3	476	cCa/cTa	6/22	1	2	FACETS	0.223	0.195	0.253	0.223	0.195	0.253	SUBCLONAL	1	TRUE	1	0.747380463198909	2		676	913	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127306	55127306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	62	831	0	ENST00000257290.5:c.94C>T	p.Pro32Ser	p.P32S	ENST00000257290	NM_006206.4	32	Cca/Tca	3/23	1	2	FACETS	0.174	0.15	0.201	0.174	0.15	0.201	SUBCLONAL	1	TRUE	1	0.747380463198909	2		831	953	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55569983	55569983	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	37	747	0	ENST00000288135.5:c.850G>A	p.Asp284Asn	p.D284N	ENST00000288135	NM_000222.2	284	Gat/Aat	5/21	1	2	FACETS	0.144	0.118	0.173	0.144	0.118	0.173	SUBCLONAL	1	TRUE	1	0.747380463198909	2		747	689	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598105	55598105	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	56	832	2	ENST00000288135.5:c.2302G>A	p.Asp768Asn	p.D768N	ENST00000288135	NM_000222.2	768	Gac/Aac	16/21	1	2	FACETS	0.152	0.129	0.176	0.152	0.129	0.176	SUBCLONAL	1	TRUE	1	0.747380463198909	2		834	988	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946328	55946328	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	28	350	0	ENST00000263923.4:c.3851G>A	p.Gly1284Glu	p.G1284E	ENST00000263923	NM_002253.2	1284	gGa/gAa	30/30	1	2	FACETS	0.169	0.134	0.208	0.169	0.134	0.208	SUBCLONAL	1	TRUE	1	0.747380463198909	2		350	444	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156666	106156666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	48	510	1	ENST00000380013.4:c.1567G>A	p.Gly523Arg	p.G523R	ENST00000380013	NM_001127208.2	523	Gga/Aga	3/11	1	2	FACETS	0.176	0.148	0.207	0.176	0.148	0.207	SUBCLONAL	1	TRUE	1	0.747380463198909	2		511	728	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157812	106157812	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	33	427	0	ENST00000380013.4:c.2713G>A	p.Asp905Asn	p.D905N	ENST00000380013	NM_001127208.2	905	Gat/Aat	3/11	1	2	FACETS	0.173	0.141	0.211	0.173	0.141	0.211	SUBCLONAL	1	TRUE	1	0.747380463198909	2		427	509	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143350338	143350338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	28	503	1	ENST00000262992.4:c.124G>A	p.Glu42Lys	p.E42K	ENST00000262992	NM_001101669.1	42	Gaa/Aaa	3/24	1	2	FACETS	0.151	0.12	0.187	0.151	0.12	0.187	SUBCLONAL	1	TRUE	1	0.747380463198909	2		504	495	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332531	153332531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	33	717	0	ENST00000281708.4:c.425G>A	p.Ser142Asn	p.S142N	ENST00000281708	NM_033632.3	142	aGt/aAt	2/12	1	2	FACETS	0.136	0.11	0.165	0.136	0.11	0.165	SUBCLONAL	1	TRUE	1	0.747380463198909	2		717	651	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332894	153332894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs548137658	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	296	800	0	ENST00000281708.4:c.62G>A	p.Gly21Asp	p.G21D	ENST00000281708	NM_033632.3	21	gGt/gAt	2/12	1	2	FACETS	0.998	0.943	1	0.998	0.943	1	CLONAL	1	TRUE	1	0.747380463198909	2		800	794	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517940	187517940	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759440990	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	128	714	0	ENST00000441802.2:c.12754C>T	p.Arg4252Trp	p.R4252W	ENST00000441802	NM_005245.3	4252	Cgg/Tgg	25/27	1	2	FACETS	0.358	0.324	0.394	0.358	0.324	0.394	SUBCLONAL	1	TRUE	1	0.747380463198909	2		714	957	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278898	1278898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	51	718	0	ENST00000310581.5:c.2144G>A	p.Gly715Asp	p.G715D	ENST00000310581	NM_198253.2	715	gGc/gAc	6/16	1	2	FACETS	0.143	0.121	0.168	0.143	0.121	0.168	SUBCLONAL	1	TRUE	1	0.747380463198909	2		718	954	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31483733	31483733	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs769977886	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	20	337	0	ENST00000344624.3:c.1999C>T	p.Pro667Ser	p.P667S	ENST00000344624		667	Cct/Tct	13/33	1	2	FACETS	0.148	0.113	0.189	0.148	0.113	0.189	SUBCLONAL	1	TRUE	1	0.747380463198909	2		337	362	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970900	79970900	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	68	955	2	ENST00000265081.6:c.1126G>A	p.Glu376Lys	p.E376K	ENST00000265081	NM_002439.4	376	Gaa/Aaa	7/24	0.747380463198909	1	FACETS	0.164	0.142	0.187	0.164	0.142	0.187	SUBCLONAL	1	TRUE	0	0.747380463198909	1		957	696	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512352	149512352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	48	801	3	ENST00000261799.4:c.1088G>A	p.Gly363Asp	p.G363D	ENST00000261799	NM_002609.3	363	gGc/gAc	7/23	0.747380463198909	1	FACETS	0.116	0.097	0.136	0.116	0.097	0.136	SUBCLONAL	1	TRUE	0	0.747380463198909	1		804	694	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045769	180045769	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs996955454	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	71	825	0	ENST00000261937.6:c.3001+1G>A		p.X1001_splice	ENST00000261937	NM_182925.4	1001			0.747380463198909	1	FACETS	0.195	0.17	0.222	0.195	0.17	0.222	SUBCLONAL	1	TRUE	0	0.747380463198909	1		825	611	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057226	180057226	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs56258152	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	37	702	0	ENST00000261937.6:c.512C>T	p.Ser171Leu	p.S171L	ENST00000261937	NM_182925.4	171	tCg/tTg	4/30	0.747380463198909	1	FACETS	0.117	0.096	0.141	0.117	0.096	0.141	SUBCLONAL	1	TRUE	0	0.747380463198909	1		702	529	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402783	20402783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	27	361	0	ENST00000346618.3:c.320C>T	p.Ser107Phe	p.S107F	ENST00000346618	NM_001949.4	107	tCc/tTc	1/7	0.747380463198909	1	FACETS	0.135	0.107	0.167	0.135	0.107	0.167	SUBCLONAL	1	TRUE	0	0.747380463198909	1		361	334	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032286	26032286	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	20	311	0	ENST00000244661.2:c.3G>A	p.Met1?	p.M1?	ENST00000244661	NM_003537.3	1	atG/atA	1/1	0.589436179130851	2	FACETS	0.165	0.126	0.211	0.083	0.063	0.106	SUBCLONAL	1	TRUE	0	0.747380463198909	2		311	324	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169092	32169092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs189264181	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	44	815	2	ENST00000375023.3:c.3941C>T	p.Ala1314Val	p.A1314V	ENST00000375023	NM_004557.3	1314	gCc/gTc	22/30	0.747380463198909	1	FACETS	0.115	0.096	0.136	0.115	0.096	0.136	SUBCLONAL	1	TRUE	0	0.747380463198909	1		817	642	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184953	32184953	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755035712	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	44	839	1	ENST00000375023.3:c.1715C>T	p.Ala572Val	p.A572V	ENST00000375023	NM_004557.3	572	gCc/gTc	10/30	0.747380463198909	1	FACETS	0.123	0.102	0.145	0.123	0.102	0.145	SUBCLONAL	1	TRUE	0	0.747380463198909	1		840	601	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43749825	43749825	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	28	510	1	ENST00000523873.1:c.677+1G>A		p.X226_splice	ENST00000523873		226			0.747380463198909	1	FACETS	0.101	0.08	0.125	0.101	0.08	0.125	SUBCLONAL	1	TRUE	0	0.747380463198909	1		511	464	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89791128	89791128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	21	242	0	ENST00000336032.3:c.515C>T	p.Pro172Leu	p.P172L	ENST00000336032	NM_006813.2	172	cCc/cTc	1/2	0.747380463198909	1	FACETS	0.158	0.122	0.2	0.158	0.122	0.2	SUBCLONAL	1	TRUE	0	0.747380463198909	1		242	223	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109313998	109313998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199611315	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	28	626	0	ENST00000436639.2:c.1225C>T	p.Arg409Cys	p.R409C	ENST00000436639	NM_014454.2	409	Cgt/Tgt	7/10	0.747380463198909	1	FACETS	0.119	0.094	0.146	0.119	0.094	0.146	SUBCLONAL	1	TRUE	0	0.747380463198909	1		626	395	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111995811	111995811	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	67	656	0	ENST00000368678.4:c.1287G>A	p.Trp429Ter	p.W429*	ENST00000368678		429	tgG/tgA	12/13	0.747380463198909	1	FACETS	0.192	0.166	0.219	0.192	0.166	0.219	SUBCLONAL	1	TRUE	0	0.747380463198909	1		656	586	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265553	152265553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	33	802	0	ENST00000206249.3:c.1006C>T	p.Pro336Ser	p.P336S	ENST00000206249	NM_000125.3	336	Ccc/Tcc	4/8	0.612757004222304	1	FACETS	0.09	0.072	0.109	0.09	0.072	0.109	SUBCLONAL	1	TRUE	0	0.747380463198909	1		802	617	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510898	157510898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	53	695	0	ENST00000346085.5:c.3673C>T	p.Pro1225Ser	p.P1225S	ENST00000346085	NM_020732.3	1225	Cca/Tca	14/20	0.612757004222304	1	FACETS	0.163	0.138	0.189	0.163	0.138	0.189	SUBCLONAL	1	TRUE	0	0.747380463198909	1		695	546	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962378	2962378	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1275601330	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	60	845	0	ENST00000396946.4:c.2159G>A	p.Arg720Gln	p.R720Q	ENST00000396946	NM_032415.4	720	cGa/cAa	17/25	1	2	FACETS	0.168	0.144	0.195	0.168	0.144	0.195	SUBCLONAL	1	TRUE	1	0.747380463198909	2		845	954	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423386	116423386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	35	570	3	ENST00000397752.3:c.3661G>A	p.Ala1221Thr	p.A1221T	ENST00000397752	NM_000245.2	1221	Gct/Act	19/21	1	2	FACETS	0.168	0.137	0.202	0.168	0.137	0.202	SUBCLONAL	1	TRUE	1	0.747380463198909	2		573	559	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207671	29207671	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	59	785	2	ENST00000240100.2:c.125G>A	p.Gly42Asp	p.G42D	ENST00000240100	NM_001394.6	42	gGc/gAc	1/4	0.747380463198909	1	FACETS	0.168	0.144	0.194	0.168	0.144	0.194	SUBCLONAL	1	TRUE	0	0.747380463198909	1		787	589	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370735	55370735	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	30	890	1	ENST00000297316.4:c.37C>T	p.Gln13Ter	p.Q13*	ENST00000297316	NM_022454.3	13	Cag/Tag	1/2	0.747380463198909	1	FACETS	0.097	0.077	0.119	0.097	0.077	0.119	SUBCLONAL	1	TRUE	0	0.747380463198909	1		891	520	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104702	69104702	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	42	788	0	ENST00000288368.4:c.4546G>A	p.Glu1516Lys	p.E1516K	ENST00000288368	NM_024870.2	1516	Gag/Aag	37/40	0.747380463198909	1	FACETS	0.107	0.089	0.128	0.107	0.089	0.128	SUBCLONAL	1	TRUE	0	0.747380463198909	1		788	656	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982071	70982071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	74	679	0	ENST00000276594.2:c.25G>A	p.Ala9Thr	p.A9T	ENST00000276594	NM_024504.3	9	Gcc/Acc	2/8	0.747380463198909	1	FACETS	0.208	0.182	0.237	0.208	0.182	0.237	SUBCLONAL	1	TRUE	0	0.747380463198909	1		679	595	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551451	141551451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	38	606	0	ENST00000220592.5:c.1846G>A	p.Gly616Ser	p.G616S	ENST00000220592	NM_012154.3	616	Ggc/Agc	15/19	0.747380463198909	1	FACETS	0.123	0.101	0.147	0.123	0.101	0.147	SUBCLONAL	1	TRUE	0	0.747380463198909	1		606	518	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090514	5090514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	34	663	2	ENST00000381652.3:c.2830C>T	p.His944Tyr	p.H944Y	ENST00000381652	NM_004972.3	944	Cat/Tat	21/25	0.747380463198909	1	FACETS	0.145	0.118	0.175	0.145	0.118	0.175	SUBCLONAL	1	TRUE	0	0.747380463198909	1		665	393	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5462915	5462915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	27	440	1	ENST00000381577.3:c.476G>A	p.Gly159Asp	p.G159D	ENST00000381577	NM_014143.3	159	gGc/gAc	4/7	0.747380463198909	1	FACETS	0.129	0.103	0.16	0.129	0.103	0.16	SUBCLONAL	1	TRUE	0	0.747380463198909	1		441	350	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518118	8518118	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	57	674	0	ENST00000356435.5:c.1273C>T	p.Gln425Ter	p.Q425*	ENST00000356435		425	Cag/Tag	10/35	0.747380463198909	1	FACETS	0.159	0.136	0.184	0.159	0.136	0.184	SUBCLONAL	1	TRUE	0	0.747380463198909	1		674	600	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27183540	27183540	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs527402232	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	26	793	2	ENST00000380036.4:c.1114G>A	p.Ala372Thr	p.A372T	ENST00000380036	NM_000459.3	372	Gct/Act	8/23	0.747380463198909	1	FACETS	0.09	0.071	0.113	0.09	0.071	0.113	SUBCLONAL	1	TRUE	0	0.747380463198909	1		795	482	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27217711	27217711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	44	856	1	ENST00000380036.4:c.3017C>T	p.Ala1006Val	p.A1006V	ENST00000380036	NM_000459.3	1006	gCc/gTc	19/23	0.747380463198909	1	FACETS	0.109	0.091	0.13	0.109	0.091	0.13	SUBCLONAL	1	TRUE	0	0.747380463198909	1		857	675	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002746	37002746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	56	640	0	ENST00000358127.4:c.503C>T	p.Ser168Phe	p.S168F	ENST00000358127	NM_001280556.1	168	tCc/tTc	5/10	0.747380463198909	1	FACETS	0.201	0.172	0.233	0.201	0.172	0.233	SUBCLONAL	1	TRUE	0	0.747380463198909	1		640	466	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391434	139391434	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	89	864	0	ENST00000277541.6:c.6757C>T	p.Pro2253Ser	p.P2253S	ENST00000277541	NM_017617.3	2253	Ccc/Tcc	34/34	1	2	FACETS	0.22	0.194	0.247	0.22	0.194	0.247	SUBCLONAL	1	TRUE	1	0.747380463198909	2		864	1085	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922811	44922811	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	62	315	0	ENST00000377967.4:c.1672G>A	p.Val558Ile	p.V558I	ENST00000377967	NM_021140.2	558	Gtc/Atc	16/29	1	1	FACETS	0.243	0.211	0.279	0.243	0.211	0.279	SUBCLONAL	1	TRUE	0	0.747380463198909	1		315	427	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239618	53239618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	38	431	0	ENST00000375401.3:c.1724C>T	p.Thr575Ile	p.T575I	ENST00000375401	NM_004187.3	575	aCc/aTc	12/26	1	1	FACETS	0.103	0.085	0.124	0.103	0.085	0.124	SUBCLONAL	1	TRUE	0	0.747380463198909	1		431	616	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409931	63409931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	22	291	0	ENST00000330258.3:c.3236G>A	p.Gly1079Asp	p.G1079D	ENST00000330258	NM_152424.3	1079	gGc/gAc	2/2	1	1	FACETS	0.107	0.082	0.135	0.107	0.082	0.135	SUBCLONAL	1	TRUE	0	0.747380463198909	1		291	345	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339941	70339941	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	40	357	0	ENST00000374080.3:c.474G>A	p.Trp158Ter	p.W158*	ENST00000374080		158	tgG/tgA	4/45	1	1	FACETS	0.137	0.114	0.164	0.137	0.114	0.164	SUBCLONAL	1	TRUE	0	0.747380463198909	1		357	488	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349234	70349234	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	40	498	0	ENST00000374080.3:c.3646G>A	p.Val1216Met	p.V1216M	ENST00000374080		1216	Gtg/Atg	26/45	1	1	FACETS	0.107	0.088	0.128	0.107	0.088	0.128	SUBCLONAL	1	TRUE	0	0.747380463198909	1		498	627	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354657	70354657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	96	461	0	ENST00000374080.3:c.4822G>A	p.Glu1608Lys	p.E1608K	ENST00000374080		1608	Gaa/Aaa	35/45	1	1	FACETS	0.257	0.229	0.287	0.257	0.229	0.287	SUBCLONAL	1	TRUE	0	0.747380463198909	1		461	625	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76812968	76812968	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	37	433	0	ENST00000373344.5:c.6653C>T	p.Pro2218Leu	p.P2218L	ENST00000373344	NM_000489.3	2218	cCt/cTt	30/35	1	1	FACETS	0.176	0.145	0.21	0.176	0.145	0.21	SUBCLONAL	1	TRUE	0	0.747380463198909	1		433	353	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855911	76855911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	21	361	0	ENST00000373344.5:c.5689G>A	p.Glu1897Lys	p.E1897K	ENST00000373344	NM_000489.3	1897	Gaa/Aaa	23/35	1	1	FACETS	0.111	0.085	0.141	0.111	0.085	0.141	SUBCLONAL	1	TRUE	0	0.747380463198909	1		361	317	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891522	76891522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	39	360	1	ENST00000373344.5:c.4583C>T	p.Pro1528Leu	p.P1528L	ENST00000373344	NM_000489.3	1528	cCc/cTc	16/35	1	1	FACETS	0.134	0.111	0.16	0.134	0.111	0.16	SUBCLONAL	1	TRUE	0	0.747380463198909	1		361	487	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938278	76938278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	22	409	0	ENST00000373344.5:c.2470G>A	p.Glu824Lys	p.E824K	ENST00000373344	NM_000489.3	824	Gag/Aag	9/35	1	1	FACETS	0.086	0.066	0.109	0.086	0.066	0.109	SUBCLONAL	1	TRUE	0	0.747380463198909	1		409	430	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611913	100611913	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1169941199	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	59	534	1	ENST00000308731.7:c.1208C>T	p.Thr403Ile	p.T403I	ENST00000308731	NM_000061.2	403	aCc/aTc	14/19	1	1	FACETS	0.185	0.159	0.213	0.185	0.159	0.213	SUBCLONAL	1	TRUE	0	0.747380463198909	1		535	535	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613626	100613626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555978197	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	43	482	0	ENST00000308731.7:c.953C>T	p.Ser318Phe	p.S318F	ENST00000308731	NM_000061.2	318	tCt/tTt	11/19	1	1	FACETS	0.121	0.101	0.143	0.121	0.101	0.143	SUBCLONAL	1	TRUE	0	0.747380463198909	1		482	596	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019731	123019731	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	38	406	0	ENST00000355640.3:c.219G>A	p.Trp73Ter	p.W73*	ENST00000355640		73	tgG/tgA	2/7	1	1	FACETS	0.154	0.127	0.184	0.154	0.127	0.184	SUBCLONAL	1	TRUE	0	0.747380463198909	1		406	413	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123040837	123040837	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	50	439	0	ENST00000355640.3:c.1301-1G>A		p.X434_splice	ENST00000355640		434			1	1	FACETS	0.159	0.134	0.186	0.159	0.134	0.186	SUBCLONAL	1	TRUE	0	0.747380463198909	1		439	528	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181227	123181227	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	17	314	0	ENST00000218089.9:c.691G>A	p.Val231Met	p.V231M	ENST00000218089	NM_001042749.1	231	Gtg/Atg	9/35	1	1	FACETS	0.107	0.08	0.14	0.107	0.08	0.14	SUBCLONAL	1	TRUE	0	0.747380463198909	1		314	266	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0005303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	144	662	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.913	0.835	0.994	0.913	0.835	0.994	CLONAL	1	TRUE	1	0.479534982042966	2		663	658	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984241	7984241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	184	690	2	ENST00000319144.4:c.488G>A	p.Arg163His	p.R163H	ENST00000319144	NM_001139.2	163	cGc/cAc	4/15	1	2	FACETS	0.945	0.874	1	0.945	0.874	1	CLONAL	1	TRUE	1	0.479534982042966	2		692	812	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562738	29562739	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555615472	NA	P-0005303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	169	624	0	ENST00000356175.3:c.3822_3823del	p.Phe1275ProfsTer8	p.F1275Pfs*8	ENST00000356175	NM_000267.3	1273	aCT/a	28/57	1	2	FACETS	0.854	0.786	0.925	0.854	0.786	0.925	CLONAL	1	TRUE	1	0.479534982042966	2		624	825	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720679	89720679	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs398123329	NA	P-0005303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	49	172	0	ENST00000371953.3:c.830C>A	p.Thr277Lys	p.T277K	ENST00000371953	NM_000314.4	277	aCa/aAa	8/9	0.479534982042966	1	FACETS	0.983	0.849	1	0.983	0.849	1	CLONAL	1	TRUE	0	0.479534982042966	1		172	158	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720679	89720680	+	missense_variant	Missense_Mutation	DNP	CA	CA	AT	novel	NA	P-0005303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	71	172	0	ENST00000371953.3:c.830_831delinsAT	p.Thr277Asn	p.T277N	ENST00000371953	NM_000314.4	277	aCA/aAT	8/9	0.479534982042966	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.479534982042966	1		172	164	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541468	29541468	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs1131691131	NA	P-0005303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	63	176	0	ENST00000356175.3:c.1393-1G>C		p.X465_splice	ENST00000356175	NM_000267.3	465			1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.479534982042966	2		176	227	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162252	47162252	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	151	470	1	ENST00000409792.3:c.3874C>T	p.Gln1292Ter	p.Q1292*	ENST00000409792	NM_014159.6	1292	Cag/Tag	3/21	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.479534982042966	2		471	603	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117630048	117630048	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005832-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	131	694	1	ENST00000368508.3:c.6478C>T	p.Gln2160Ter	p.Q2160*	ENST00000368508	NM_002944.2	2160	Cag/Tag	41/43	0.768344344246791	3	FACETS	0.948	0.865	1	0.474	0.432	0.517	CLONAL	1	FALSE	1	0.781552720871244	3		695	492	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344788	65344788	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005832-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	159	596	0	ENST00000342505.4:c.249G>C	p.Glu83Asp	p.E83D	ENST00000342505	NM_002227.2	83	gaG/gaC	4/25	0.220546058799051	6	FACETS	0.825	0.759	0.893			1	INDETERMINATE	2	FALSE	NA	0.781552720871244	6		596	632	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520253	176520253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375466821	NA	P-0005832-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	328	822	2	ENST00000292408.4:c.1172G>A	p.Arg391Gln	p.R391Q	ENST00000292408	NM_213647.1	391	cGa/cAa	9/18	0.609132422134456	3	FACETS	0.971	0.928	1	0.971	0.928	1	CLONAL	2	FALSE	1	0.781552720871244	3		824	601	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544706	65544706	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005832-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	238	998	0	ENST00000358664.4:c.220A>G	p.Met74Val	p.M74V	ENST00000358664	NM_002382.4	74	Atg/Gtg	4/5	0.781552720871244	3	FACETS	0.968	0.905	1	0.484	0.452	0.516	CLONAL	1	FALSE	1	0.781552720871244	3		998	875	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988919	41988919	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005832-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	164	749	0	ENST00000219905.7:c.1711G>C	p.Asp571His	p.D571H	ENST00000219905	NM_001164273.1	571	Gat/Cat	3/24	0.569913662094778	3	FACETS	1	0.962	1	0.533	0.492	0.575	CLONAL	1	FALSE	1	0.781552720871244	3		749	548	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857925	9857925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs534440095	NA	P-0005832-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	196	781	3	ENST00000330684.3:c.3476G>A	p.Arg1159His	p.R1159H	ENST00000330684	NM_001134407.1	1159	cGc/cAc	13/13	0.768344344246791	3	FACETS	1	0.98	1	0.57	0.53	0.61	CLONAL	1	FALSE	1	0.781552720871244	3		784	612	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993389	72993389	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0005832-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	195	901	0	ENST00000268489.5:c.656C>G	p.Ser219Ter	p.S219*	ENST00000268489	NM_006885.3	219	tCa/tGa	2/10	0.729081818233959	4	FACETS	0.898	0.831	0.968	0.449	0.415	0.484	CLONAL	1	FALSE	2	0.781552720871244	4		901	990	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383106	42383106	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005832-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	114	716	0	ENST00000221972.3:c.126G>C	p.Leu42Phe	p.L42F	ENST00000221972	NM_021601.3	42	ttG/ttC	2/5	0.643780943423384	4	FACETS	0.806	0.727	0.889	0.403	0.363	0.445	CLONAL	1	FALSE	2	0.781552720871244	4		716	645	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931616	39931616	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005832-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	138	650	0	ENST00000378444.4:c.2983C>A	p.Gln995Lys	p.Q995K	ENST00000378444	NM_001123385.1	995	Caa/Aaa	4/15	0.637839565931591	5	FACETS	0.932	0.848	1			1	CLONAL	1	FALSE	NA	0.781552720871244	5		650	823	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22412959	22412959	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005832-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	47	277	1	ENST00000344548.3:c.206C>A	p.Pro69Gln	p.P69Q	ENST00000344548	NM_001039802.1	69	cCg/cAg	5/7	1	2	FACETS	0.695	0.596	0.801	0.695	0.596	0.801	SUBCLONAL	1	FALSE	1	0.781552720871244	2		278	173	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362561	118362561	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005832-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	163	786	0	ENST00000534358.1:c.4922A>C	p.Lys1641Thr	p.K1641T	ENST00000534358	NM_005933.3	1641	aAa/aCa	15/36	0.781552720871244	4	FACETS	0.858	0.788	0.931	0.286	0.262	0.311	CLONAL	1	FALSE	1	0.781552720871244	4		786	866	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912437	50912437	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005832-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	148	911	0	ENST00000440232.2:c.1951G>C	p.Val651Leu	p.V651L	ENST00000440232	NM_002691.3	651	Gtg/Ctg	16/27	0.643780943423384	4	FACETS	0.839	0.767	0.915	0.42	0.383	0.458	CLONAL	1	FALSE	2	0.781552720871244	4		911	804	SUCCESS
APC	324	MSKCC	GRCh37	5	112175941	112175941	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005832-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	70	378	0	ENST00000257430.4:c.4650G>C	p.Glu1550Asp	p.E1550D	ENST00000257430	NM_000038.5	1550	gaG/gaC	16/16	0.609132422134456	3	FACETS	0.806	0.709	0.909	0.403	0.354	0.455	CLONAL	1	FALSE	1	0.781552720871244	3		378	309	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638086	176638086	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005832-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	196	840	0	ENST00000439151.2:c.2686C>G	p.Gln896Glu	p.Q896E	ENST00000439151	NM_022455.4	896	Cag/Gag	5/23	0.609132422134456	3	FACETS	0.981	0.911	1	0.491	0.455	0.527	CLONAL	1	FALSE	1	0.781552720871244	3		840	711	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328377	137328377	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005832-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	170	1054	0	ENST00000481739.1:c.1306C>G	p.Leu436Val	p.L436V	ENST00000481739	NM_002957.4	436	Ctc/Gtc	10/10	0.729081818233959	4	FACETS	0.893	0.822	0.967	0.446	0.411	0.484	CLONAL	1	FALSE	2	0.781552720871244	4		1054	868	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328388	137328388	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005832-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	182	1065	0	ENST00000481739.1:c.1317C>G	p.Phe439Leu	p.F439L	ENST00000481739	NM_002957.4	439	ttC/ttG	10/10	0.729081818233959	4	FACETS	0.928	0.857	1	0.464	0.428	0.501	CLONAL	1	FALSE	2	0.781552720871244	4		1065	894	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0005927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	276	779	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.336967322690602	4	FACETS	0.997	0.941	1	0.997	0.941	1	CLONAL	3	TRUE	1	0.336967322690602	4		779	732	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0005927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	274	1488	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.315498328779506	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.336967322690602	2		1488	687	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164150	108164150	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	133	687	0	ENST00000278616.4:c.4722G>C	p.Leu1574Phe	p.L1574F	ENST00000278616	NM_000051.3	1574	ttG/ttC	31/63	0.336967322690602	4	FACETS	0.879	0.802	0.961	0.879	0.802	0.961	CLONAL	2	TRUE	2	0.336967322690602	4		687	600	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336064	73336064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	64	338	2	ENST00000377767.4:c.2339G>A	p.Arg780Lys	p.R780K	ENST00000377767	NM_014953.3	780	aGa/aAa	17/21	0.336967322690602	4	FACETS	0.907	0.793	1	0.605	0.528	0.686	CLONAL	2	TRUE	1	0.336967322690602	4		340	280	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634420	23634420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1219715328	NA	P-0005927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	75	908	0	ENST00000261584.4:c.2866G>A	p.Glu956Lys	p.E956K	ENST00000261584	NM_024675.3	956	Gaa/Aaa	9/13	0.161837713988823	5	FACETS	1	0.934	1	0.367	0.321	0.416	INDETERMINATE	1	TRUE	2	0.336967322690602	5		908	609	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992798	72992798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1201946037	NA	P-0005927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	68	892	0	ENST00000268489.5:c.1247C>T	p.Thr416Ile	p.T416I	ENST00000268489	NM_006885.3	416	aCc/aTc	2/10	0.161837713988823	5	FACETS	1	0.94	1	0.379	0.33	0.432	INDETERMINATE	1	TRUE	2	0.336967322690602	5		892	534	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89828385	89828385	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	86	896	0	ENST00000389301.3:c.2824G>C	p.Glu942Gln	p.E942Q	ENST00000389301	NM_000135.2	942	Gaa/Caa	29/43	0.161837713988823	5	FACETS	1	0.963	1	0.406	0.359	0.456	INDETERMINATE	1	TRUE	2	0.336967322690602	5		896	631	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216502	2216502	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	194	1247	0	ENST00000398665.3:c.2146C>T	p.Gln716Ter	p.Q716*	ENST00000398665	NM_032482.2	716	Cag/Tag	20/28	0.336967322690602	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.336967322690602	2		1247	532	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3113328	3113328	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	107	863	1	ENST00000078429.4:c.322G>T	p.Ala108Ser	p.A108S	ENST00000078429	NM_002067.2	108	Gcc/Tcc	3/7	0.336967322690602	2	FACETS	0.821	0.742	0.902	0.821	0.742	0.902	CLONAL	2	TRUE	0	0.336967322690602	2		864	387	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416702	29416702	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	119	762	1	ENST00000389048.3:c.4251C>A	p.Asp1417Glu	p.D1417E	ENST00000389048	NM_004304.4	1417	gaC/gaA	29/29	0.335913566948246	2	FACETS	0.949	0.866	1	0.949	0.866	1	CLONAL	2	TRUE	0	0.336967322690602	2		763	372	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672170	30672170	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	105	1193	0	ENST00000376406.3:c.4790C>G	p.Thr1597Ser	p.T1597S	ENST00000376406	NM_014641.2	1597	aCt/aGt	10/15	0.336967322690602	5	FACETS	1	0.947	1	0.364	0.326	0.405	CLONAL	1	TRUE	2	0.336967322690602	5		1193	858	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672546	30672546	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	73	1021	0	ENST00000376406.3:c.4414C>G	p.Gln1472Glu	p.Q1472E	ENST00000376406	NM_014641.2	1472	Cag/Gag	10/15	0.336967322690602	5	FACETS	0.834	0.728	0.948	0.278	0.242	0.316	CLONAL	1	TRUE	2	0.336967322690602	5		1021	782	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41905028	41905028	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	34	884	0	ENST00000372991.4:c.519C>A	p.Asp173Glu	p.D173E	ENST00000372991	NM_001760.3	173	gaC/gaA	3/5	0.336967322690602	5	FACETS	0.453	0.369	0.549	0.151	0.123	0.183	SUBCLONAL	1	TRUE	2	0.336967322690602	5		884	670	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372731	81372731	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	176	737	0	ENST00000222390.5:c.803G>T	p.Arg268Met	p.R268M	ENST00000222390	NM_000601.4	268	aGg/aTg	7/18	0.279277344935099	4	FACETS	1	0.984	1	0.817	0.757	0.878	CLONAL	2	TRUE	1	0.336967322690602	4		737	570	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162844	38162844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	85	1131	1	ENST00000317025.8:c.2362G>A	p.Glu788Lys	p.E788K	ENST00000317025	NM_023034.1	788	Gaa/Aaa	13/24	0.336967322690602	3	FACETS	0.766	0.676	0.862			1	SUBCLONAL	1	TRUE	NA	0.336967322690602	3		1132	770	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738351	133738351	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	132	759	0	ENST00000318560.5:c.751G>T	p.Gly251Cys	p.G251C	ENST00000318560	NM_005157.4	251	Ggc/Tgc	4/11	0.336967322690602	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.336967322690602	3		759	397	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782690	135782690	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	rs118203512	NA	P-0005927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	79	950	0	ENST00000298552.3:c.1331C>G	p.Ser444Ter	p.S444*	ENST00000298552	NM_001162426.1	444	tCa/tGa	13/23	0.336967322690602	3	FACETS	1	0.881	1	0.5	0.44	0.564	CLONAL	1	TRUE	1	0.336967322690602	3		950	548	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007973-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	739	779	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.710932717511681	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	1	0.710932717511681	3		779	1178	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007973-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	158	669	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.710932717511681	2		669	406	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0007973-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	164	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.710932717511681	3	FACETS	1	0.969	1	0.548	0.505	0.591	CLONAL	1	TRUE	1	0.710932717511681	3		434	571	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0007973-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	143	472	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.710932717511681	2		472	389	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007973-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	214	871	1	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.710932717511681	2		872	582	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482854	67482854	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1206533102	NA	P-0007973-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	220	710	2	ENST00000327367.4:c.1258C>T	p.Arg420Cys	p.R420C	ENST00000327367	NM_005902.3	420	Cgc/Tgc	9/9	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.710932717511681	2		712	544	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562409	21562409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs538663790	NA	P-0007973-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	222	864	0	ENST00000382592.4:c.1510G>A	p.Val504Met	p.V504M	ENST00000382592	NM_014572.2	504	Gtg/Atg	4/8	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.710932717511681	2		864	611	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845757	68845757	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587780784	NA	P-0008398-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	225	478	0	ENST00000261769.5:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000261769	NM_004360.3	335	Cga/Tga	7/16	0.642641361813002	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.642641361813002	1		478	447	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259368	89259368	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008398-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	292	642	0	ENST00000336596.2:c.512T>C	p.Val171Ala	p.V171A	ENST00000336596	NM_005233.5	171	gTa/gCa	3/17	1	2	FACETS	0.952	0.897	1	0.952	0.897	1	CLONAL	1	TRUE	1	0.642641361813002	2		642	955	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132751	152132751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008398-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	78	668	0	ENST00000262189.6:c.121C>T	p.Arg41Cys	p.R41C	ENST00000262189	NM_170606.2	41	Cgc/Tgc	1/59	1	2	FACETS	0.281	0.246	0.318	0.281	0.246	0.318	SUBCLONAL	1	TRUE	1	0.642641361813002	2		668	865	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367825	15367825	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008398-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1289	125	1041	0	ENST00000263377.2:c.1501G>C	p.Asp501His	p.D501H	ENST00000263377	NM_058243.2	501	Gat/Cat	8/20	1	2	FACETS	0.275	0.248	0.304	0.275	0.248	0.304	SUBCLONAL	1	TRUE	1	0.642641361813002	2		1041	1414	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845413	156845413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772559075	NA	P-0008398-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1933	470	1084	0	ENST00000524377.1:c.1456C>T	p.Leu486Phe	p.L486F	ENST00000524377	NM_002529.3	486	Ctc/Ttc	12/17	0.642641361813002	4	FACETS	1	0.951	1	0.5	0.475	0.525	CLONAL	1	TRUE	2	0.642641361813002	4		1084	2403	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628626	21628626	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008398-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	301	846	0	ENST00000421138.2:c.1082C>T	p.Ser361Leu	p.S361L	ENST00000421138		361	tCa/tTa	10/16	1	2	FACETS	0.98	0.925	1	0.98	0.925	1	CLONAL	1	TRUE	1	0.642641361813002	2		846	956	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58142368	58142368	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008398-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	255	667	0	ENST00000257904.6:c.852C>G	p.Ile284Met	p.I284M	ENST00000257904	NM_000075.3	284	atC/atG	8/8	1	2	FACETS	0.926	0.869	0.984	0.926	0.869	0.984	CLONAL	1	TRUE	1	0.642641361813002	2		667	857	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873518	151873518	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008398-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	352	733	0	ENST00000262189.6:c.9020del	p.Gly3007GlufsTer25	p.G3007Efs*25	ENST00000262189	NM_170606.2	3007	gGa/ga	38/59	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.642641361813002	2		733	1088	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0009423-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	78	795	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.274746776642595	4	FACETS	1	0.957	1	0.603	0.529	0.683	CLONAL	1	TRUE	2	0.2	4		795	776	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140716	55140716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs904415979	NA	P-0009423-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	102	951	3	ENST00000257290.5:c.1577C>T	p.Thr526Met	p.T526M	ENST00000257290	NM_006206.4	526	aCg/aTg	11/23	0.199294631822198	3	FACETS	0.974	0.869	1	0.487	0.434	0.543	CLONAL	1	TRUE	1	0.2	3		954	1152	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs786203436	NA	P-0009423-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	424	1077	0	ENST00000269305.4:c.487T>G	p.Tyr163Asp	p.Y163D	ENST00000269305	NM_001126112.2	163	Tac/Gac	5/11	0.227508257969021	4	FACETS	0.961	0.916	1			1	CLONAL	4	TRUE	NA	0.2	4		1077	1323	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256250	41256251	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs80357604	NA	P-0009423-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	51	608	3	ENST00000357654.3:c.329dup	p.Glu111GlyfsTer3	p.E111Gfs*3	ENST00000357654	NM_007294.3	110	aag/aaAg	6/23	0.142989642334984	3	FACETS	0.892	0.757	1	0.297	0.252	0.347	CLONAL	1	TRUE	0	0.2	3		611	629	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963935	2963935	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs551716345	NA	P-0009423-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1265	101	1179	0	ENST00000396946.4:c.1872A>T	p.Gln624His	p.Q624H	ENST00000396946	NM_032415.4	624	caA/caT	15/25	0.274746776642595	4	FACETS	0.887	0.79	0.991	0.444	0.395	0.496	CLONAL	1	TRUE	2	0.2	4		1179	1366	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0009955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	351	658	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.655940787180155	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.655940787180155	2		658	481	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602493	10602493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	215	732	1	ENST00000171111.5:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000171111	NM_203500.1	362	cGg/cAg	3/6	0.655940787180155	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.655940787180155	2		733	318	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954648	17954648	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	384	1198	0	ENST00000458235.1:c.246C>A	p.Phe82Leu	p.F82L	ENST00000458235	NM_000215.3	82	ttC/ttA	3/24	0.655940787180155	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.655940787180155	2		1198	562	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170545	108170545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	289	702	0	ENST00000278616.4:c.5110G>A	p.Glu1704Lys	p.E1704K	ENST00000278616	NM_000051.3	1704	Gaa/Aaa	34/63	0.638590770144182	2	FACETS	0.924	0.883	0.964	0.924	0.883	0.964	CLONAL	2	TRUE	0	0.655940787180155	2		702	477	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335596	73335596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	156	545	0	ENST00000377767.4:c.2575G>A	p.Ala859Thr	p.A859T	ENST00000377767	NM_014953.3	859	Gcc/Acc	19/21	0.564287244007794	3	FACETS	1	0.984	1	0.419	0.386	0.452	CLONAL	1	TRUE	0	0.655940787180155	3		545	503	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030344	11030344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	238	799	0	ENST00000327064.4:c.1094G>A	p.Gly365Glu	p.G365E	ENST00000327064	NM_199141.1	365	gGa/gAa	9/16	0.655940787180155	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.655940787180155	2		799	335	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954681	17954681	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	340	1121	0	ENST00000458235.1:c.213T>A	p.Phe71Leu	p.F71L	ENST00000458235	NM_000215.3	71	ttT/ttA	3/24	0.655940787180155	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.655940787180155	2		1121	507	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451908	29451908	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1452092742	NA	P-0009955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	177	1016	1	ENST00000389048.3:c.2657A>T	p.Asn886Ile	p.N886I	ENST00000389048	NM_004304.4	886	aAc/aTc	16/29	0.655940787180155	3	FACETS	1	0.94	1	0.51	0.471	0.55	CLONAL	1	TRUE	1	0.655940787180155	3		1017	703	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719194	190719194	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	238	540	0	ENST00000441310.2:c.1196C>G	p.Ser399Cys	p.S399C	ENST00000441310	NM_000534.4	399	tCt/tGt	9/13	0.655940787180155	3	FACETS	0.969	0.916	1	0.969	0.916	1	CLONAL	2	TRUE	1	0.655940787180155	3		540	497	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920434	134920434	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	47	914	0	ENST00000398015.3:c.2249T>C	p.Ile750Thr	p.I750T	ENST00000398015	NM_004441.4	750	aTt/aCt	12/16	0.638590770144182	2	FACETS	0.273	0.23	0.321	0.137	0.115	0.161	SUBCLONAL	1	TRUE	0	0.655940787180155	2		914	524	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928219	178928219	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	239	535	0	ENST00000263967.3:c.1405G>A	p.Glu469Lys	p.E469K	ENST00000263967	NM_006218.2	469	Gaa/Aaa	9/21	0.638590770144182	2	FACETS	0.985	0.939	1	0.985	0.939	1	CLONAL	2	TRUE	0	0.655940787180155	2		535	370	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031997	26031997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	273	541	0	ENST00000244661.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000244661	NM_003537.3	98	Gag/Aag	1/1	0.553495423021684	3	FACETS	0.894	0.856	0.931	0.894	0.856	0.931	CLONAL	3	TRUE	0	0.655940787180155	3		541	412	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015609	112015609	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	314	689	0	ENST00000368678.4:c.1233G>C	p.Leu411Phe	p.L411F	ENST00000368678		411	ttG/ttC	11/13	0.530845496625484	3	FACETS	0.89	0.855	0.925	0.89	0.855	0.925	CLONAL	3	TRUE	0	0.655940787180155	3		689	476	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225109	53225109	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	132	441	0	ENST00000375401.3:c.3109G>C	p.Asp1037His	p.D1037H	ENST00000375401	NM_004187.3	1037	Gat/Cat	20/26	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.655940787180155	1		441	184	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225237	53225237	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0009955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	106	360	0	ENST00000375401.3:c.2982-1G>T		p.X994_splice	ENST00000375401	NM_004187.3	994			1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.655940787180155	1		360	162	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0009972-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	201	784	4	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.363099610459262	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.383233800405228	1		788	820	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920430	114920430	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009972-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	266	592	0	ENST00000543371.1:c.1373del	p.Leu458TyrfsTer33	p.L458Yfs*33	ENST00000543371	NM_001198531.1	457	acT/ac	13/14	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.383233800405228	2		592	1064	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045755	143045755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781219504	NA	P-0009972-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	73	247	0	ENST00000262992.4:c.1879G>A	p.Val627Ile	p.V627I	ENST00000262992	NM_001101669.1	627	Gtc/Atc	17/24	0.307608769156664	1	FACETS	0.73	0.641	0.825	0.73	0.641	0.825	SUBCLONAL	1	TRUE	0	0.383233800405228	1		247	422	SUCCESS
APC	324	MSKCC	GRCh37	5	112175306	112175314	+	frameshift_variant	Frame_Shift_Del	DEL	GGTTCTAGT	GGTTCTAGT	A	novel	NA	P-0009972-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	141	301	0	ENST00000257430.4:c.4015_4023delinsA	p.Gly1339IlefsTer12	p.G1339Ifs*12	ENST00000257430	NM_000038.5	1339	GGTTCTAGT/A	16/16	0.383233800405228	2	FACETS	1	0.988	1	0.749	0.687	0.814	CLONAL	1	TRUE	0	0.383233800405228	2		301	491	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118683	115118683	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0010178-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	318	672	0	ENST00000257566.3:c.657+1G>T		p.X219_splice	ENST00000257566	NM_016569.3	219			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		672	690	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0010458-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	76	573	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.931	0.818	1	0.931	0.818	1	CLONAL	1	TRUE	1	0.29257637639738	2		573	558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0010458-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	118	1043	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.218616879812632	1	FACETS	0.971	0.877	1	0.971	0.877	1	CLONAL	1	TRUE	0	0.29257637639738	1		1044	709	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958311	11958311	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	T	novel	NA	P-0010458-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	65	464	1	ENST00000353533.5:c.218+3G>T		p.X73_splice	ENST00000353533	NM_003010.3	73			0.218616879812632	1	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	0	0.29257637639738	1		465	363	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864400	151864427	+	frameshift_variant	Frame_Shift_Del	DEL	TGCATTTGAAGCAGCTGTTGGGTCTCCT	TGCATTTGAAGCAGCTGTTGGGTCTCCT	-	novel	NA	P-0010458-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	67	547	0	ENST00000262189.6:c.9554_9581del	p.Gln3185ArgfsTer55	p.Q3185Rfs*55	ENST00000262189	NM_170606.2	3185	cAGGAGACCCAACAGCTGCTTCAAATGCAg/cg	42/59	1	2	FACETS	0.948	0.826	1	0.948	0.826	1	CLONAL	1	TRUE	1	0.29257637639738	2		547	483	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0010524-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	176	1033	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.0984219755449088	6	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.619356478003121	6		1033	991	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102080248	102080248	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010524-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	120	751	3	ENST00000282441.5:c.985G>T	p.Ala329Ser	p.A329S	ENST00000282441	NM_001130145.2	329	Gca/Tca	6/9	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.619356478003121	2		754	344	SUCCESS
AR	367	MSKCC	GRCh37	X	66943552	66943552	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137852578	NA	P-0012104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	130	391	0	ENST00000374690.3:c.2632A>G	p.Thr878Ala	p.T878A	ENST00000374690	NM_000044.3	878	Act/Gct	8/8	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.458062225814484	1		391	342	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779440	3779440	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	184	1029	0	ENST00000262367.5:c.5608G>C	p.Ala1870Pro	p.A1870P	ENST00000262367	NM_004380.2	1870	Gcc/Ccc	31/31	1	2	FACETS	0.9	0.831	0.971	0.9	0.831	0.971	CLONAL	1	TRUE	1	0.458062225814484	2		1029	893	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942622	71942623	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACGTCCAGTGTGAAG	novel	NA	P-0012104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	245	931	0	ENST00000298229.2:c.1581_1595dup	p.Ser528_Thr532dup	p.S528_T532dup	ENST00000298229	NM_001567.3	528	-/ACGTCCAGTGTGAAG	13/28	0.458062225814484	2	FACETS	1	0.989	1	0.635	0.595	0.676	CLONAL	1	TRUE	0	0.458062225814484	2		931	842	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390321	56390321	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	99	613	0	ENST00000348428.3:c.1060C>G	p.Arg354Gly	p.R354G	ENST00000348428	NM_006785.3	354	Cgg/Ggg	10/17	1	2	FACETS	0.816	0.73	0.905	0.816	0.73	0.905	CLONAL	1	TRUE	1	0.458062225814484	2		613	530	SUCCESS
AR	367	MSKCC	GRCh37	X	66941725	66941725	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	190	490	0	ENST00000374690.3:c.2369A>G	p.His790Arg	p.H790R	ENST00000374690	NM_000044.3	790	cAc/cGc	6/8	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.458062225814484	1		490	438	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	125	772	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.91	0.83	0.992	0.91	0.83	0.992	CLONAL	1	TRUE	1	0.648210674889982	2		772	424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	698	795	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.929	0.915	0.942	1	0.998	1	CLONAL	3	TRUE	1	0.648210674889982	2		796	773	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412252	139412252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057523819	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	184	1083	5	ENST00000277541.6:c.1393G>A	p.Ala465Thr	p.A465T	ENST00000277541	NM_017617.3	465	Gcc/Acc	8/34	0.235600034888891	3	FACETS	0.784	0.723	0.847	0.392	0.361	0.424	INDETERMINATE	1	TRUE	1	0.648210674889982	3		1088	959	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	87	418	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.648210674889982	2		418	258	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316074	11316074	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	55	689	1	ENST00000361445.4:c.680A>G	p.Glu227Gly	p.E227G	ENST00000361445	NM_004958.3	227	gAg/gGg	5/58	1	2	FACETS	0.298	0.254	0.345	0.298	0.254	0.345	SUBCLONAL	1	TRUE	1	0.648210674889982	2		690	570	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263913	16263913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1486750640	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	149	1086	0	ENST00000375759.3:c.10282C>T	p.Pro3428Ser	p.P3428S	ENST00000375759	NM_015001.2	3428	Ccg/Tcg	12/15	1	2	FACETS	0.48	0.438	0.524	0.48	0.438	0.524	SUBCLONAL	1	TRUE	1	0.648210674889982	2		1086	958	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17371266	17371266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	96	796	0	ENST00000375499.3:c.190G>A	p.Asp64Asn	p.D64N	ENST00000375499	NM_003000.2	64	Gac/Aac	2/8	1	2	FACETS	0.516	0.461	0.575	0.516	0.461	0.575	SUBCLONAL	1	TRUE	1	0.648210674889982	2		796	574	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056146	27056146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	53	496	0	ENST00000324856.7:c.1142C>T	p.Ser381Phe	p.S381F	ENST00000324856	NM_006015.4	381	tCc/tTc	2/20	1	2	FACETS	0.411	0.351	0.476	0.411	0.351	0.476	SUBCLONAL	1	TRUE	1	0.648210674889982	2		496	398	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28605739	28605739	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150802897	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	133	734	1	ENST00000253063.3:c.1343G>A	p.Arg448His	p.R448H	ENST00000253063	NM_031459.4	448	cGc/cAc	9/10	1	2	FACETS	0.729	0.665	0.796	0.729	0.665	0.796	SUBCLONAL	1	TRUE	1	0.648210674889982	2		735	563	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797944	45797944	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557471507	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	52	962	2	ENST00000450313.1:c.827G>A	p.Gly276Glu	p.G276E	ENST00000450313	NM_012222.2	276	gGa/gAa	10/16	1	2	FACETS	0.209	0.177	0.244	0.209	0.177	0.244	SUBCLONAL	1	TRUE	1	0.648210674889982	2		964	769	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176176069	176176069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs930088523	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	146	972	0	ENST00000367669.3:c.46C>T	p.Pro16Ser	p.P16S	ENST00000367669	NM_022457.5	16	Ccc/Tcc	1/20	1	2	FACETS	0.59	0.539	0.643	0.59	0.539	0.643	SUBCLONAL	1	TRUE	1	0.648210674889982	2		972	764	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206646650	206646650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553384304	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	64	967	3	ENST00000367120.3:c.80G>A	p.Arg27His	p.R27H	ENST00000367120	NM_014002.3	27	cGc/cAc	3/22	1	2	FACETS	0.257	0.222	0.295	0.257	0.222	0.295	SUBCLONAL	1	TRUE	1	0.648210674889982	2		970	769	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648207	206648207	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	108	382	0	ENST00000367120.3:c.229-1G>A		p.X77_splice	ENST00000367120	NM_014002.3	77			1	2	FACETS	0.992	0.9	1	0.992	0.9	1	CLONAL	1	TRUE	1	0.648210674889982	2		382	336	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450579	70450579	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1015969210	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	44	598	0	ENST00000373644.4:c.5419A>G	p.Thr1807Ala	p.T1807A	ENST00000373644	NM_030625.2	1807	Acc/Gcc	12/12	1	2	FACETS	0.278	0.233	0.328	0.278	0.233	0.328	SUBCLONAL	1	TRUE	1	0.648210674889982	2		598	488	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925591	114925591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	74	873	0	ENST00000543371.1:c.1669G>A	p.Asp557Asn	p.D557N	ENST00000543371	NM_001198531.1	557	Gac/Aac	14/14	0.276477455541294	1	FACETS	0.222	0.194	0.252	0.222	0.194	0.252	INDETERMINATE	1	TRUE	0	0.648210674889982	1		873	696	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988149	85988149	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	59	639	0	ENST00000263360.6:c.1094A>G	p.Tyr365Cys	p.Y365C	ENST00000263360	NM_003797.3	365	tAc/tGc	10/12	0.235600034888891	3	FACETS	0.733	0.634	0.838	0.366	0.317	0.419	INDETERMINATE	1	TRUE	1	0.648210674889982	3		639	329	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988167	85988167	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	93	601	0	ENST00000263360.6:c.1112A>G	p.Asp371Gly	p.D371G	ENST00000263360	NM_003797.3	371	gAt/gGt	10/12	0.235600034888891	3	FACETS	1	0.974	1	0.629	0.566	0.695	INDETERMINATE	1	TRUE	1	0.648210674889982	3		601	302	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121656	108121656	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs377597949	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	98	605	0	ENST00000278616.4:c.1464G>A	p.Trp488Ter	p.W488*	ENST00000278616	NM_000051.3	488	tgG/tgA	10/63	0.235600034888891	3	FACETS	0.767	0.687	0.852	0.383	0.343	0.426	INDETERMINATE	1	TRUE	1	0.648210674889982	3		605	522	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347629	118347629	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	50	688	0	ENST00000534358.1:c.3266A>G	p.Asp1089Gly	p.D1089G	ENST00000534358	NM_005933.3	1089	gAc/gGc	4/36	0.235600034888891	3	FACETS	0.292	0.247	0.342	0.146	0.123	0.171	INDETERMINATE	1	TRUE	1	0.648210674889982	3		688	699	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376139	118376139	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	168	630	0	ENST00000534358.1:c.9532C>T	p.Pro3178Ser	p.P3178S	ENST00000534358	NM_005933.3	3178	Cca/Tca	27/36	0.235600034888891	3	FACETS	1	0.969	1	0.547	0.505	0.591	INDETERMINATE	1	TRUE	1	0.648210674889982	3		630	627	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376379	118376379	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	137	736	0	ENST00000534358.1:c.9772A>T	p.Ile3258Phe	p.I3258F	ENST00000534358	NM_005933.3	3258	Att/Ttt	27/36	0.235600034888891	3	FACETS	0.783	0.713	0.856	0.391	0.356	0.428	INDETERMINATE	1	TRUE	1	0.648210674889982	3		736	715	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	472178	472178	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372866054	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	227	791	0	ENST00000399788.2:c.623G>A	p.Gly208Asp	p.G208D	ENST00000399788	NM_001042603.1	208	gGc/gAc	5/28	NA	2	FACETS	0.953	0.891	1			1	INDETERMINATE	1	TRUE	NA	0.648210674889982	2		791	735	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480386	56480386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	119	764	0	ENST00000267101.3:c.493G>A	p.Asp165Asn	p.D165N	ENST00000267101	NM_001982.3	165	Gac/Aac	4/28	1	2	FACETS	0.556	0.503	0.613	0.556	0.503	0.613	SUBCLONAL	1	TRUE	1	0.648210674889982	2		764	660	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885876	111885876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	222	926	2	ENST00000341259.2:c.1498C>T	p.His500Tyr	p.H500Y	ENST00000341259	NM_005475.2	500	Cac/Tac	8/8	1	2	FACETS	0.899	0.839	0.96	0.899	0.839	0.96	CLONAL	1	TRUE	1	0.648210674889982	2		928	762	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235926	133235926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768950975	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	110	718	0	ENST00000320574.5:c.3230G>A	p.Arg1077His	p.R1077H	ENST00000320574	NM_006231.2	1077	cGc/cAc	26/49	NA	2	FACETS	0.735	0.664	0.809			1	INDETERMINATE	1	TRUE	NA	0.648210674889982	2		718	462	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240615	133240615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	160	619	0	ENST00000320574.5:c.2681G>A	p.Gly894Asp	p.G894D	ENST00000320574	NM_006231.2	894	gGc/gAc	23/49	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.648210674889982	2		619	427	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563051	21563051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	242	889	0	ENST00000382592.4:c.868C>T	p.Pro290Ser	p.P290S	ENST00000382592	NM_014572.2	290	Ccc/Tcc	4/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.648210674889982	2		889	703	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001963	29001963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	114	682	0	ENST00000282397.4:c.1202G>A	p.Gly401Glu	p.G401E	ENST00000282397	NM_002019.4	401	gGg/gAg	9/30	1	2	FACETS	0.654	0.591	0.72	0.654	0.591	0.72	SUBCLONAL	1	TRUE	1	0.648210674889982	2		682	538	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910830	32910830	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	29	537	0	ENST00000380152.3:c.2338T>C	p.Ser780Pro	p.S780P	ENST00000380152		780	Tca/Cca	11/27	1	2	FACETS	0.241	0.193	0.295	0.241	0.193	0.295	SUBCLONAL	1	TRUE	1	0.648210674889982	2		537	372	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937606	32937606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	129	653	2	ENST00000380152.3:c.8267C>T	p.Ala2756Val	p.A2756V	ENST00000380152		2756	gCa/gTa	18/27	1	2	FACETS	0.738	0.673	0.807	0.738	0.673	0.807	SUBCLONAL	1	TRUE	1	0.648210674889982	2		655	539	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134561	41134561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780271950	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	87	506	1	ENST00000379561.5:c.1067C>T	p.Ala356Val	p.A356V	ENST00000379561	NM_002015.3	356	gCc/gTc	2/3	1	2	FACETS	0.609	0.541	0.68	0.609	0.541	0.68	SUBCLONAL	1	TRUE	1	0.648210674889982	2		507	441	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435115	110435115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	75	948	2	ENST00000375856.3:c.3286G>A	p.Ala1096Thr	p.A1096T	ENST00000375856	NM_003749.2	1096	Gcc/Acc	1/2	1	2	FACETS	0.312	0.273	0.354	0.312	0.273	0.354	SUBCLONAL	1	TRUE	1	0.648210674889982	2		950	742	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246463	105246463	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	100	871	0	ENST00000349310.3:c.137A>T	p.Asp46Val	p.D46V	ENST00000349310	NM_001014432.1	46	gAc/gTc	4/15	0.459031051386028	1	FACETS	0.385	0.345	0.428	0.385	0.345	0.428	SUBCLONAL	1	TRUE	0	0.648210674889982	1		871	541	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058423	42058423	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781780633	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	97	582	0	ENST00000219905.7:c.8143C>T	p.Pro2715Ser	p.P2715S	ENST00000219905	NM_001164273.1	2715	Cca/Tca	24/24	1	2	FACETS	0.652	0.584	0.724	0.652	0.584	0.724	SUBCLONAL	1	TRUE	1	0.648210674889982	2		582	459	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727367	66727367	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	48	399	0	ENST00000307102.5:c.83C>T	p.Thr28Ile	p.T28I	ENST00000307102	NM_002755.3	28	aCc/aTc	2/11	1	2	FACETS	0.478	0.406	0.556	0.478	0.406	0.556	SUBCLONAL	1	TRUE	1	0.648210674889982	2		399	310	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678343	88678343	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	256	839	0	ENST00000360948.2:c.1193A>T	p.Glu398Val	p.E398V	ENST00000360948	NM_001012338.2	398	gAg/gTg	9/19	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.648210674889982	2		839	610	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347132	347132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	204	1161	0	ENST00000262320.3:c.1879G>A	p.Glu627Lys	p.E627K	ENST00000262320	NM_003502.3	627	Gag/Aag	7/11	1	2	FACETS	0.66	0.612	0.709	0.66	0.612	0.709	SUBCLONAL	1	TRUE	1	0.648210674889982	2		1161	954	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646217	3646217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	65	981	0	ENST00000294008.3:c.1861G>A	p.Glu621Lys	p.E621K	ENST00000294008	NM_032444.2	621	Gag/Aag	8/15	1	2	FACETS	0.279	0.242	0.32	0.279	0.242	0.32	SUBCLONAL	1	TRUE	1	0.648210674889982	2		981	718	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658877	3658877	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373743309	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	95	694	1	ENST00000294008.3:c.89C>T	p.Ser30Phe	p.S30F	ENST00000294008	NM_032444.2	30	tCc/tTc	2/15	1	2	FACETS	0.484	0.431	0.539	0.484	0.431	0.539	SUBCLONAL	1	TRUE	1	0.648210674889982	2		695	606	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779578	3779578	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	207	1277	4	ENST00000262367.5:c.5470G>A	p.Ala1824Thr	p.A1824T	ENST00000262367	NM_004380.2	1824	Gcc/Acc	31/31	1	2	FACETS	0.572	0.53	0.616	0.572	0.53	0.616	SUBCLONAL	1	TRUE	1	0.648210674889982	2		1281	1116	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786077	3786077	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	88	1085	0	ENST00000262367.5:c.4688G>T	p.Arg1563Met	p.R1563M	ENST00000262367	NM_004380.2	1563	aGg/aTg	28/31	1	2	FACETS	0.311	0.275	0.35	0.311	0.275	0.35	SUBCLONAL	1	TRUE	1	0.648210674889982	2		1085	872	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789590	3789591	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	47	543	0	ENST00000262367.5:c.4268dup	p.Pro1424SerfsTer13	p.P1424Sfs*13	ENST00000262367	NM_004380.2	1423	cct/ccCt	25/31	1	2	FACETS	0.283	0.239	0.332	0.283	0.239	0.332	SUBCLONAL	1	TRUE	1	0.648210674889982	2		543	512	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3929902	3929902	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	52	683	2	ENST00000262367.5:c.16C>A	p.Leu6Met	p.L6M	ENST00000262367	NM_004380.2	6	Ctg/Atg	1/31	1	2	FACETS	0.257	0.218	0.299	0.257	0.218	0.299	SUBCLONAL	1	TRUE	1	0.648210674889982	2		685	625	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024607	14024607	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	115	543	0	ENST00000311895.7:c.833G>A	p.Gly278Glu	p.G278E	ENST00000311895	NM_005236.2	278	gGa/gAa	5/11	1	2	FACETS	0.954	0.868	1	0.954	0.868	1	CLONAL	1	TRUE	1	0.648210674889982	2		543	372	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619279	23619279	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587776527	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	229	784	3	ENST00000261584.4:c.3256C>T	p.Arg1086Ter	p.R1086*	ENST00000261584	NM_024675.3	1086	Cga/Tga	12/13	1	2	FACETS	0.98	0.917	1	0.98	0.917	1	CLONAL	1	TRUE	1	0.648210674889982	2		787	721	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56872878	56872878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	66	610	0	ENST00000308159.5:c.2033G>A	p.Gly678Glu	p.G678E	ENST00000308159	NM_014669.4	678	gGa/gAa	19/22	NA	2	FACETS	0.447	0.388	0.509			1	INDETERMINATE	1	TRUE	NA	0.648210674889982	2		610	456	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845641	68845641	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	102	936	0	ENST00000261769.5:c.887A>G	p.Tyr296Cys	p.Y296C	ENST00000261769	NM_004360.3	296	tAc/tGc	7/16	NA	2	FACETS	0.507	0.454	0.563			1	INDETERMINATE	1	TRUE	NA	0.648210674889982	2		936	621	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829644	72829644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769074546	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	53	812	1	ENST00000268489.5:c.6937C>T	p.Arg2313Cys	p.R2313C	ENST00000268489	NM_006885.3	2313	Cgt/Tgt	9/10	NA	2	FACETS	0.254	0.216	0.296			1	INDETERMINATE	1	TRUE	NA	0.648210674889982	2		813	643	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992507	72992507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	34	1011	1	ENST00000268489.5:c.1538C>T	p.Ala513Val	p.A513V	ENST00000268489	NM_006885.3	513	gCc/gTc	2/10	NA	2	FACETS	0.155	0.126	0.188			1	INDETERMINATE	1	TRUE	NA	0.648210674889982	2		1012	678	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819715	81819715	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	86	690	0	ENST00000359376.3:c.121A>G	p.Arg41Gly	p.R41G	ENST00000359376	NM_002661.3	41	Aga/Gga	2/33	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.648210674889982	NA		690	514	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805669	89805669	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751928369	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	99	739	2	ENST00000389301.3:c.4039G>A	p.Ala1347Thr	p.A1347T	ENST00000389301	NM_000135.2	1347	Gcc/Acc	41/43	1	2	FACETS	0.55	0.493	0.612	0.55	0.493	0.612	SUBCLONAL	1	TRUE	1	0.648210674889982	2		741	555	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980453	7980453	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	91	879	1	ENST00000319144.4:c.1130A>G	p.Asp377Gly	p.D377G	ENST00000319144	NM_001139.2	377	gAc/gGc	9/15	1	2	FACETS	0.359	0.318	0.403	0.359	0.318	0.403	SUBCLONAL	1	TRUE	1	0.648210674889982	2		880	782	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968798	15968798	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	58	424	2	ENST00000268712.3:c.4951+1G>A		p.X1651_splice	ENST00000268712	NM_006311.3	1651			0.313743560605726	3	FACETS	0.57	0.491	0.655	0.285	0.245	0.328	INDETERMINATE	1	TRUE	1	0.648210674889982	3		426	416	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16001746	16001746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	77	757	1	ENST00000268712.3:c.2755C>T	p.Pro919Ser	p.P919S	ENST00000268712	NM_006311.3	919	Ccg/Tcg	21/46	0.313743560605726	3	FACETS	0.477	0.418	0.539	0.238	0.209	0.27	INDETERMINATE	1	TRUE	1	0.648210674889982	3		758	660	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024540	16024540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	91	766	0	ENST00000268712.3:c.1678G>A	p.Glu560Lys	p.E560K	ENST00000268712	NM_006311.3	560	Gaa/Aaa	16/46	0.313743560605726	3	FACETS	0.482	0.428	0.54	0.241	0.214	0.27	INDETERMINATE	1	TRUE	1	0.648210674889982	3		766	771	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131300	17131300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	84	982	0	ENST00000285071.4:c.152G>A	p.Gly51Asp	p.G51D	ENST00000285071	NM_144997.5	51	gGc/gAc	4/14	0.313743560605726	3	FACETS	0.348	0.307	0.393	0.174	0.153	0.197	INDETERMINATE	1	TRUE	1	0.648210674889982	3		982	985	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667875	37667875	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	58	492	0	ENST00000447079.4:c.2760G>A	p.Trp920Ter	p.W920*	ENST00000447079	NM_015083.1	920	tgG/tgA	8/14	0.645505290910733	3	FACETS	0.387	0.332	0.447	0.194	0.166	0.224	SUBCLONAL	1	TRUE	1	0.648210674889982	3		492	612	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677929	58677929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	38	346	0	ENST00000305921.3:c.154C>T	p.Arg52Trp	p.R52W	ENST00000305921	NM_003620.3	52	Cgg/Tgg	1/6	0.645505290910733	3	FACETS	0.447	0.371	0.533	0.224	0.185	0.267	SUBCLONAL	1	TRUE	1	0.648210674889982	3		346	347	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625683	1625683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	141	1073	0	ENST00000344749.5:c.391G>A	p.Ala131Thr	p.A131T	ENST00000344749	NM_001136139.2	131	Gcc/Acc	7/19	1	2	FACETS	0.535	0.488	0.585	0.535	0.488	0.585	SUBCLONAL	1	TRUE	1	0.648210674889982	2		1073	813	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216439	2216439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	229	855	0	ENST00000398665.3:c.2083G>A	p.Asp695Asn	p.D695N	ENST00000398665	NM_032482.2	695	Gac/Aac	20/28	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.648210674889982	2		855	690	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217891	2217891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	144	1065	1	ENST00000398665.3:c.2665G>A	p.Val889Met	p.V889M	ENST00000398665	NM_032482.2	889	Gtg/Atg	22/28	1	2	FACETS	0.542	0.495	0.592	0.542	0.495	0.592	SUBCLONAL	1	TRUE	1	0.648210674889982	2		1066	819	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2225394	2225394	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	191	707	0	ENST00000398665.3:c.3604A>G	p.Arg1202Gly	p.R1202G	ENST00000398665	NM_032482.2	1202	Aga/Gga	26/28	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.648210674889982	2		707	580	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208037	5208037	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	114	782	0	ENST00000357368.4:c.5674A>G	p.Thr1892Ala	p.T1892A	ENST00000357368	NM_002850.3	1892	Acg/Gcg	37/38	1	2	FACETS	0.541	0.488	0.597	0.541	0.488	0.597	SUBCLONAL	1	TRUE	1	0.648210674889982	2		782	650	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291058	10291058	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	48	697	0	ENST00000340748.4:c.413C>T	p.Pro138Leu	p.P138L	ENST00000340748		138	cCc/cTc	4/40	1	2	FACETS	0.254	0.215	0.298	0.254	0.215	0.298	SUBCLONAL	1	TRUE	1	0.648210674889982	2		697	582	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976372	18976372	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	136	943	1	ENST00000262803.5:c.3022C>T	p.Arg1008Ter	p.R1008*	ENST00000262803	NM_002911.3	1008	Cga/Tga	22/24	1	2	FACETS	0.584	0.531	0.638	0.584	0.531	0.638	SUBCLONAL	1	TRUE	1	0.648210674889982	2		944	719	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220181	36220181	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	107	666	0	ENST00000222270.7:c.4901C>A	p.Ala1634Asp	p.A1634D	ENST00000222270	NM_014727.1	1634	gCc/gAc	22/37	1	2	FACETS	0.532	0.478	0.589	0.532	0.478	0.589	SUBCLONAL	1	TRUE	1	0.648210674889982	2		666	621	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753276	42753276	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756887571	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	94	1050	0	ENST00000222329.4:c.988G>A	p.Ala330Thr	p.A330T	ENST00000222329	NM_006494.2	330	Gcc/Acc	4/4	0.648210674889982	1	FACETS	0.314	0.28	0.351	0.314	0.28	0.351	SUBCLONAL	1	TRUE	0	0.648210674889982	1		1050	624	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796882	42796883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761345552	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	162	1243	6	ENST00000575354.2:c.3347dup	p.Ser1117LysfsTer34	p.S1117Kfs*34	ENST00000575354	NM_015125.3	1114	gcc/gCcc	14/20	0.648210674889982	1	FACETS	0.494	0.454	0.535	0.494	0.454	0.535	SUBCLONAL	1	TRUE	0	0.648210674889982	1		1249	684	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139890	50139890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	313	1091	0	ENST00000246792.3:c.439G>A	p.Glu147Lys	p.E147K	ENST00000246792	NM_006270.3	147	Gag/Aag	4/6	0.648210674889982	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.648210674889982	1		1091	623	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082895	16082895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1412185126	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	25	170	0	ENST00000281043.3:c.709C>T	p.Pro237Ser	p.P237S	ENST00000281043	NM_005378.4	237	Ccg/Tcg	2/3	1	2	FACETS	0.525	0.418	0.644	0.525	0.418	0.644	SUBCLONAL	1	TRUE	1	0.648210674889982	2		170	147	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966345	25966345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	144	861	0	ENST00000435504.4:c.2861C>T	p.Thr954Ile	p.T954I	ENST00000435504		954	aCt/aTt	13/13	1	2	FACETS	0.591	0.539	0.645	0.591	0.539	0.645	SUBCLONAL	1	TRUE	1	0.648210674889982	2		861	752	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143428	30143428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	118	368	0	ENST00000389048.3:c.98C>T	p.Ala33Val	p.A33V	ENST00000389048	NM_004304.4	33	gCt/gTt	1/29	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.648210674889982	2		368	329	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222380	39222380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	139	941	1	ENST00000402219.2:c.3230C>T	p.Ala1077Val	p.A1077V	ENST00000402219	NM_005633.3	1077	gCa/gTa	20/23	1	2	FACETS	0.573	0.522	0.627	0.573	0.522	0.627	SUBCLONAL	1	TRUE	1	0.648210674889982	2		942	748	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99181170	99181170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759905070	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	60	671	2	ENST00000074304.5:c.2111G>A	p.Arg704His	p.R704H	ENST00000074304	NM_001134224.1	704	cGc/cAc	20/26	1	2	FACETS	0.312	0.268	0.359	0.312	0.268	0.359	SUBCLONAL	1	TRUE	1	0.648210674889982	2		673	594	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728681	190728681	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1352098988	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	89	532	0	ENST00000441310.2:c.2069G>A	p.Arg690Lys	p.R690K	ENST00000441310	NM_000534.4	690	aGg/aAg	10/13	1	2	FACETS	0.665	0.593	0.741	0.665	0.593	0.741	SUBCLONAL	1	TRUE	1	0.648210674889982	2		532	413	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281474	198281474	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	97	511	0	ENST00000335508.6:c.657T>A	p.Asp219Glu	p.D219E	ENST00000335508	NM_012433.2	219	gaT/gaA	6/25	1	2	FACETS	0.617	0.552	0.685	0.617	0.552	0.685	SUBCLONAL	1	TRUE	1	0.648210674889982	2		511	485	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149583	202149583	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	165	620	1	ENST00000358485.4:c.1024C>T	p.Pro342Ser	p.P342S	ENST00000358485	NM_001080125.1	342	Ccc/Tcc	8/9	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.648210674889982	2		621	482	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566856	212566856	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	23	394	0	ENST00000342788.4:c.1325T>C	p.Ile442Thr	p.I442T	ENST00000342788	NM_005235.2	442	aTc/aCc	12/28	1	2	FACETS	0.228	0.178	0.287	0.228	0.178	0.287	SUBCLONAL	1	TRUE	1	0.648210674889982	2		394	311	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661663	227661664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761880048	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	113	571	21	ENST00000305123.5:c.1791dup	p.His598AlafsTer13	p.H598Afs*13	ENST00000305123	NM_005544.2	597	-/G	1/2	1	2	FACETS	0.8	0.725	0.878	0.8	0.725	0.878	SUBCLONAL	1	TRUE	1	0.648210674889982	2		592	436	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793398	242793398	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	113	1064	1	ENST00000334409.5:c.679G>A	p.Asp227Asn	p.D227N	ENST00000334409	NM_005018.2	227	Gat/Aat	5/5	0.607130343847381	1	FACETS	0.383	0.345	0.422	0.383	0.345	0.422	SUBCLONAL	1	TRUE	0	0.648210674889982	1		1065	616	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024575	31024575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	42	655	0	ENST00000375687.4:c.4060G>A	p.Glu1354Lys	p.E1354K	ENST00000375687	NM_015338.5	1354	Gaa/Aaa	13/13	1	2	FACETS	0.24	0.2	0.285	0.24	0.2	0.285	SUBCLONAL	1	TRUE	1	0.648210674889982	2		655	539	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39721148	39721148	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	78	741	1	ENST00000361337.2:c.651G>A	p.Trp217Ter	p.W217*	ENST00000361337	NM_003286.2	217	tgG/tgA	9/21	1	2	FACETS	0.448	0.394	0.506	0.448	0.394	0.506	SUBCLONAL	1	TRUE	1	0.648210674889982	2		742	537	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319939	62319939	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	215	872	2	ENST00000360203.5:c.1781G>A	p.Ser594Asn	p.S594N	ENST00000360203	NM_001283009.1	594	aGc/aAc	21/35	1	2	FACETS	0.957	0.894	1	0.957	0.894	1	CLONAL	1	TRUE	1	0.648210674889982	2		874	693	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321717	62321717	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761805038	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	230	807	1	ENST00000360203.5:c.2336C>T	p.Ser779Leu	p.S779L	ENST00000360203	NM_001283009.1	779	tCg/tTg	26/35	1	2	FACETS	0.991	0.928	1	0.991	0.928	1	CLONAL	1	TRUE	1	0.648210674889982	2		808	716	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775475	39775475	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	67	738	0	ENST00000288319.7:c.545G>T	p.Ser182Ile	p.S182I	ENST00000288319	NM_182918.3	182	aGc/aTc	4/10	1	2	FACETS	0.381	0.331	0.434	0.381	0.331	0.434	SUBCLONAL	1	TRUE	1	0.648210674889982	2		738	543	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845379	42845379	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1350930206	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	90	832	0	ENST00000398585.3:c.883G>A	p.Gly295Ser	p.G295S	ENST00000398585	NM_001135099.1	295	Ggc/Agc	9/14	1	2	FACETS	0.396	0.351	0.443	0.396	0.351	0.443	SUBCLONAL	1	TRUE	1	0.648210674889982	2		832	702	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162041	22162041	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1035981670	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	60	813	0	ENST00000215832.6:c.214A>G	p.Ile72Val	p.I72V	ENST00000215832	NM_002745.4	72	Ata/Gta	2/9	1	2	FACETS	0.283	0.243	0.326	0.283	0.243	0.326	SUBCLONAL	1	TRUE	1	0.648210674889982	2		813	654	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143232	24143232	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	146	901	4	ENST00000263121.7:c.464G>A	p.Arg155His	p.R155H	ENST00000263121	NM_003073.3	155	cGc/cAc	4/9	1	2	FACETS	0.582	0.532	0.635	0.582	0.532	0.635	SUBCLONAL	1	TRUE	1	0.648210674889982	2		905	774	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52621388	52621388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	109	751	0	ENST00000394830.3:c.3029G>A	p.Cys1010Tyr	p.C1010Y	ENST00000394830	NM_018313.4	1010	tGt/tAt	20/30	1	2	FACETS	0.513	0.461	0.567	0.513	0.461	0.567	SUBCLONAL	1	TRUE	1	0.648210674889982	2		751	656	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149245714	149245714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	98	797	0	ENST00000360632.3:c.814C>T	p.Leu272Phe	p.L272F	ENST00000360632	NM_015472.4	272	Ctt/Ttt	5/7	1	2	FACETS	0.465	0.415	0.518	0.465	0.415	0.518	SUBCLONAL	1	TRUE	1	0.648210674889982	2		797	650	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260295	149260295	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1168613130	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	188	1146	3	ENST00000360632.3:c.598G>A	p.Ala200Thr	p.A200T	ENST00000360632	NM_015472.4	200	Gcc/Acc	4/7	1	2	FACETS	0.574	0.53	0.62	0.574	0.53	0.62	SUBCLONAL	1	TRUE	1	0.648210674889982	2		1149	1010	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921416	178921416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	53	814	0	ENST00000263967.3:c.898G>A	p.Asp300Asn	p.D300N	ENST00000263967	NM_006218.2	300	Gac/Aac	5/21	1	2	FACETS	0.27	0.23	0.314	0.27	0.23	0.314	SUBCLONAL	1	TRUE	1	0.648210674889982	2		814	605	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183578	185183578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465764941	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	44	555	2	ENST00000265026.3:c.1432C>T	p.Arg478Trp	p.R478W	ENST00000265026	NM_004721.4	478	Cgg/Tgg	9/14	1	2	FACETS	0.296	0.248	0.349	0.296	0.248	0.349	SUBCLONAL	1	TRUE	1	0.648210674889982	2		557	459	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526295	189526295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	36	511	0	ENST00000264731.3:c.559G>A	p.Ala187Thr	p.A187T	ENST00000264731	NM_003722.4	187	Gcc/Acc	4/14	1	2	FACETS	0.3	0.247	0.36	0.3	0.247	0.36	SUBCLONAL	1	TRUE	1	0.648210674889982	2		511	370	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1919991	1919991	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	85	931	0	ENST00000382891.5:c.1051G>A	p.Asp351Asn	p.D351N	ENST00000382891	NM_133335.3	351	Gac/Aac	5/22	1	2	FACETS	0.378	0.334	0.426	0.378	0.334	0.426	SUBCLONAL	1	TRUE	1	0.648210674889982	2		931	693	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749509	41749509	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	53	703	0	ENST00000226382.2:c.286C>T	p.Arg96Cys	p.R96C	ENST00000226382	NM_003924.3	96	Cgc/Tgc	2/3	1	2	FACETS	0.246	0.209	0.286	0.246	0.209	0.286	SUBCLONAL	1	TRUE	1	0.648210674889982	2		703	666	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750534	41750534	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	139	683	1	ENST00000226382.2:c.94G>A	p.Asp32Asn	p.D32N	ENST00000226382	NM_003924.3	32	Gac/Aac	1/3	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.648210674889982	2		684	425	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270180	66270180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763063348	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	73	408	0	ENST00000273854.3:c.1702G>A	p.Asp568Asn	p.D568N	ENST00000273854	NM_004439.5	568	Gat/Aat	8/18	1	2	FACETS	0.647	0.57	0.729	0.647	0.57	0.729	SUBCLONAL	1	TRUE	1	0.648210674889982	2		408	348	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467743	66467743	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	29	441	0	ENST00000273854.3:c.526A>G	p.Thr176Ala	p.T176A	ENST00000273854	NM_004439.5	176	Acc/Gcc	3/18	1	2	FACETS	0.207	0.166	0.254	0.207	0.166	0.254	SUBCLONAL	1	TRUE	1	0.648210674889982	2		441	432	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106194051	106194051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765803723	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	92	366	0	ENST00000380013.4:c.4513G>A	p.Ala1505Thr	p.A1505T	ENST00000380013	NM_001127208.2	1505	Gca/Aca	10/11	1	2	FACETS	0.782	0.701	0.867	0.782	0.701	0.867	SUBCLONAL	1	TRUE	1	0.648210674889982	2		366	363	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094955	143094955	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	101	534	0	ENST00000262992.4:c.1189T>C	p.Tyr397His	p.Y397H	ENST00000262992	NM_001101669.1	397	Tac/Cac	14/24	0.648210674889982	1	FACETS	0.904	0.824	0.985	0.904	0.824	0.985	CLONAL	1	TRUE	0	0.648210674889982	1		534	233	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517781	187517781	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	12	297	1	ENST00000441802.2:c.12913G>A	p.Ala4305Thr	p.A4305T	ENST00000441802	NM_005245.3	4305	Gcg/Acg	25/27	0.648210674889982	1	FACETS	0.139	0.097	0.19	0.139	0.097	0.19	SUBCLONAL	1	TRUE	0	0.648210674889982	1		298	180	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271247	1271247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746621306	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	79	355	0	ENST00000310581.5:c.2455C>T	p.Arg819Cys	p.R819C	ENST00000310581	NM_198253.2	819	Cgc/Tgc	8/16	0.276477455541294	1	FACETS	0.792	0.71	0.876	0.792	0.71	0.876	INDETERMINATE	1	TRUE	0	0.648210674889982	1		355	208	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31511216	31511216	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	227	1079	0	ENST00000344624.3:c.1358G>A	p.Gly453Glu	p.G453E	ENST00000344624		453	gGg/gAg	6/33	0.276477455541294	1	FACETS	0.633	0.592	0.675	0.633	0.592	0.675	INDETERMINATE	1	TRUE	0	0.648210674889982	1		1079	748	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876328	35876328	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1223538431	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	76	636	0	ENST00000303115.3:c.1120G>A	p.Val374Ile	p.V374I	ENST00000303115	NM_002185.3	374	Gtc/Atc	8/8	0.276477455541294	1	FACETS	0.379	0.334	0.427	0.379	0.334	0.427	INDETERMINATE	1	TRUE	0	0.648210674889982	1		636	418	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79968560	79968560	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	80	541	0	ENST00000265081.6:c.910G>A	p.Val304Met	p.V304M	ENST00000265081	NM_002439.4	304	Gtg/Atg	6/24	1	2	FACETS	0.539	0.476	0.606	0.539	0.476	0.606	SUBCLONAL	1	TRUE	1	0.648210674889982	2		541	458	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180040084	180040084	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	88	989	0	ENST00000261937.6:c.3358A>T	p.Ile1120Phe	p.I1120F	ENST00000261937	NM_182925.4	1120	Atc/Ttc	25/30	0.648210674889982	1	FACETS	0.366	0.325	0.409	0.366	0.325	0.409	SUBCLONAL	1	TRUE	0	0.648210674889982	1		989	502	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048670	180048670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1362559080	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	118	835	2	ENST00000261937.6:c.1892C>T	p.Ala631Val	p.A631V	ENST00000261937	NM_182925.4	631	gCg/gTg	13/30	0.648210674889982	1	FACETS	0.612	0.557	0.669	0.612	0.557	0.669	SUBCLONAL	1	TRUE	0	0.648210674889982	1		837	402	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056191	26056191	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1311035166	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	56	575	0	ENST00000343677.2:c.466A>G	p.Lys156Glu	p.K156E	ENST00000343677	NM_005319.3	156	Aag/Gag	1/1	1	2	FACETS	0.319	0.273	0.369	0.319	0.273	0.369	SUBCLONAL	1	TRUE	1	0.648210674889982	2		575	542	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117707015	117707015	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	168	671	1	ENST00000368508.3:c.2135G>A	p.Trp712Ter	p.W712*	ENST00000368508	NM_002944.2	712	tGg/tAg	15/43	1	2	FACETS	0.871	0.805	0.94	0.871	0.805	0.94	CLONAL	1	TRUE	1	0.648210674889982	2		672	595	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971291	13971291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748182764	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	98	554	0	ENST00000405192.2:c.638G>A	p.Arg213His	p.R213H	ENST00000405192	NM_001163147.1	213	cGc/cAc	8/12	NA	2	FACETS	0.679	0.609	0.753			1	INDETERMINATE	1	TRUE	NA	0.648210674889982	2		554	445	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455144	50455144	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	76	375	0	ENST00000331340.3:c.691G>A	p.Gly231Ser	p.G231S	ENST00000331340	NM_006060.4	231	Ggc/Agc	6/8	1	2	FACETS	0.733	0.648	0.822	0.733	0.648	0.822	SUBCLONAL	1	TRUE	1	0.648210674889982	2		375	320	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273108	55273108	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	181	706	0	ENST00000275493.2:c.3431C>T	p.Pro1144Leu	p.P1144L	ENST00000275493	NM_005228.3	1144	cCc/cTc	28/28	1	2	FACETS	0.875	0.811	0.942	0.875	0.811	0.942	CLONAL	1	TRUE	1	0.648210674889982	2		706	638	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340094	116340094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	51	275	0	ENST00000397752.3:c.956C>T	p.Ala319Val	p.A319V	ENST00000397752	NM_000245.2	319	gCt/gTt	2/21	1	2	FACETS	0.664	0.57	0.765	0.664	0.57	0.765	SUBCLONAL	1	TRUE	1	0.648210674889982	2		275	237	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423423	116423423	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	28	428	0	ENST00000397752.3:c.3698A>G	p.Glu1233Gly	p.E1233G	ENST00000397752	NM_000245.2	1233	gAa/gGa	19/21	1	2	FACETS	0.302	0.242	0.37	0.302	0.242	0.37	SUBCLONAL	1	TRUE	1	0.648210674889982	2		428	286	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845569	128845569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	191	688	2	ENST00000249373.3:c.866C>T	p.Ala289Val	p.A289V	ENST00000249373	NM_005631.4	289	gCc/gTc	4/12	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.648210674889982	2		690	529	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434413	140434413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775889922	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	52	622	1	ENST00000288602.6:c.2285C>T	p.Ala762Val	p.A762V	ENST00000288602	NM_004333.4	762	gCg/gTg	18/18	1	2	FACETS	0.342	0.291	0.398	0.342	0.291	0.398	SUBCLONAL	1	TRUE	1	0.648210674889982	2		623	469	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849874	151849874	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	73	385	0	ENST00000262189.6:c.12442C>T	p.Pro4148Ser	p.P4148S	ENST00000262189	NM_170606.2	4148	Ccg/Tcg	49/59	1	2	FACETS	0.555	0.487	0.627	0.555	0.487	0.627	SUBCLONAL	1	TRUE	1	0.648210674889982	2		385	406	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853127	151853127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	56	583	1	ENST00000262189.6:c.11828G>A	p.Gly3943Glu	p.G3943E	ENST00000262189	NM_170606.2	3943	gGa/gAa	46/59	1	2	FACETS	0.373	0.32	0.431	0.373	0.32	0.431	SUBCLONAL	1	TRUE	1	0.648210674889982	2		584	463	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859984	151859984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	33	337	0	ENST00000262189.6:c.10678G>A	p.Ala3560Thr	p.A3560T	ENST00000262189	NM_170606.2	3560	Gca/Aca	43/59	1	2	FACETS	0.309	0.252	0.374	0.309	0.252	0.374	SUBCLONAL	1	TRUE	1	0.648210674889982	2		337	329	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007101	152007101	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	31	621	0	ENST00000262189.6:c.799G>A	p.Glu267Lys	p.E267K	ENST00000262189	NM_170606.2	267	Gaa/Aaa	6/59	1	2	FACETS	0.169	0.136	0.206	0.169	0.136	0.206	SUBCLONAL	1	TRUE	1	0.648210674889982	2		621	567	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146944	38146945	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	107	1001	2	ENST00000317025.8:c.3197dup	p.Asn1066LysfsTer14	p.N1066Kfs*14	ENST00000317025	NM_023034.1	1066	aac/aaAc	18/24	1	2	FACETS	0.399	0.357	0.443	0.399	0.357	0.443	SUBCLONAL	1	TRUE	1	0.648210674889982	2		1003	828	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287325	38287325	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754968374	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	142	900	0	ENST00000425967.3:c.332G>A	p.Arg111His	p.R111H	ENST00000425967	NM_001174067.1	111	cGc/cAc	4/19	1	2	FACETS	0.627	0.572	0.684	0.627	0.572	0.684	SUBCLONAL	1	TRUE	1	0.648210674889982	2		900	699	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372361	55372361	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	219	929	5	ENST00000297316.4:c.1051C>T	p.Pro351Ser	p.P351S	ENST00000297316	NM_022454.3	351	Ccc/Tcc	2/2	0.382786864824427	1	FACETS	0.702	0.656	0.748	0.702	0.656	0.748	INDETERMINATE	1	TRUE	0	0.648210674889982	1		934	651	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868965	117868965	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	46	513	0	ENST00000297338.2:c.734C>T	p.Pro245Leu	p.P245L	ENST00000297338	NM_006265.2	245	cCc/cTc	7/14	0.235600034888891	3	FACETS	0.38	0.32	0.447	0.19	0.16	0.224	INDETERMINATE	1	TRUE	1	0.648210674889982	3		513	494	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971050	21971054	+	missense_variant	Missense_Mutation	ONP	CGCGC	CGCGC	GCGCG	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	39	470	3	ENST00000304494.5:c.304_308inv	p.Ala102_Arg103delinsArgAla	p.A102_R103delinsRA	ENST00000304494	NM_000077.4	102	GCGCGg/CGCGCg	2/3	0.648210674889982	1	FACETS	0.278	0.231	0.329	0.278	0.231	0.329	SUBCLONAL	1	TRUE	0	0.648210674889982	1		473	293	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212731	27212731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	60	972	1	ENST00000380036.4:c.2713G>A	p.Ala905Thr	p.A905T	ENST00000380036	NM_000459.3	905	Gcg/Acg	17/23	1	2	FACETS	0.218	0.187	0.252	0.218	0.187	0.252	SUBCLONAL	1	TRUE	1	0.648210674889982	2		973	848	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760843	133760843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	308	844	0	ENST00000318560.5:c.3166G>A	p.Val1056Met	p.V1056M	ENST00000318560	NM_005157.4	1056	Gtg/Atg	11/11	0.235600034888891	3	FACETS	0.793	0.752	0.836	0.793	0.752	0.836	INDETERMINATE	2	TRUE	1	0.648210674889982	3		844	793	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772605	135772605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	121	719	0	ENST00000298552.3:c.2941G>A	p.Glu981Lys	p.E981K	ENST00000298552	NM_001162426.1	981	Gaa/Aaa	22/23	0.235600034888891	3	FACETS	0.688	0.623	0.758	0.344	0.311	0.379	INDETERMINATE	1	TRUE	1	0.648210674889982	3		719	718	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781286	135781286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1395737285	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	104	670	0	ENST00000298552.3:c.1679G>A	p.Gly560Asp	p.G560D	ENST00000298552	NM_001162426.1	560	gGc/gAc	15/23	0.235600034888891	3	FACETS	0.695	0.624	0.771	0.348	0.312	0.386	INDETERMINATE	1	TRUE	1	0.648210674889982	3		670	611	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300076	137300076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373515948	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	194	1105	0	ENST00000481739.1:c.361G>A	p.Ala121Thr	p.A121T	ENST00000481739	NM_002957.4	121	Gcc/Acc	3/10	0.235600034888891	3	FACETS	0.794	0.735	0.856	0.397	0.367	0.428	INDETERMINATE	1	TRUE	1	0.648210674889982	3		1105	998	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413100	139413100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201236538	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	238	918	3	ENST00000277541.6:c.1042G>A	p.Ala348Thr	p.A348T	ENST00000277541	NM_017617.3	348	Gcc/Acc	6/34	0.235600034888891	3	FACETS	1	0.985	1	0.583	0.545	0.622	INDETERMINATE	1	TRUE	1	0.648210674889982	3		921	834	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916574	39916574	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	17	309	0	ENST00000378444.4:c.4429G>A	p.Glu1477Lys	p.E1477K	ENST00000378444	NM_001123385.1	1477	Gaa/Aaa	11/15	1	1	FACETS	0.135	0.1	0.176	0.135	0.1	0.176	SUBCLONAL	1	TRUE	0	0.648210674889982	1		309	263	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922297	39922297	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	39	241	0	ENST00000378444.4:c.3875C>T	p.Pro1292Leu	p.P1292L	ENST00000378444	NM_001123385.1	1292	cCc/cTc	9/15	1	1	FACETS	0.521	0.439	0.61	0.521	0.439	0.61	SUBCLONAL	1	TRUE	0	0.648210674889982	1		241	156	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933731	39933731	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	104	329	0	ENST00000378444.4:c.868A>T	p.Lys290Ter	p.K290*	ENST00000378444	NM_001123385.1	290	Aag/Tag	4/15	1	1	FACETS	0.841	0.766	0.917	0.841	0.766	0.917	CLONAL	1	TRUE	0	0.648210674889982	1		329	258	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045695	47045695	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	32	508	0	ENST00000377604.3:c.2576A>G	p.Asp859Gly	p.D859G	ENST00000377604	NM_001204468.1	859	gAc/gGc	23/24	1	1	FACETS	0.154	0.125	0.187	0.154	0.125	0.187	SUBCLONAL	1	TRUE	0	0.648210674889982	1		508	433	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430729	47430729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	24	455	1	ENST00000377045.4:c.1694C>T	p.Ala565Val	p.A565V	ENST00000377045	NM_001654.4	565	gCc/gTc	16/16	1	1	FACETS	0.139	0.108	0.174	0.139	0.108	0.174	SUBCLONAL	1	TRUE	0	0.648210674889982	1		456	361	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222385	53222385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	109	624	2	ENST00000375401.3:c.4447C>T	p.Arg1483Trp	p.R1483W	ENST00000375401	NM_004187.3	1483	Cgg/Tgg	26/26	1	1	FACETS	0.498	0.45	0.549	0.498	0.45	0.549	SUBCLONAL	1	TRUE	0	0.648210674889982	1		626	456	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412541	63412541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	104	313	0	ENST00000330258.3:c.626G>A	p.Ser209Asn	p.S209N	ENST00000330258	NM_152424.3	209	aGc/aAc	2/2	1	1	FACETS	0.923	0.843	1	0.923	0.843	1	CLONAL	1	TRUE	0	0.648210674889982	1		313	235	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874295	76874296	+	stop_gained,inframe_insertion	Nonsense_Mutation	INS	-	-	TAT	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	210	376	0	ENST00000373344.5:c.5426_5427insATA	p.Glu1809_Met1810insTer	p.E1809_M1810ins*	ENST00000373344	NM_000489.3	1809	gag/gaATAg	21/35	1	1	FACETS	0.859	0.828	0.887	1	0.995	1	CLONAL	2	TRUE	0	0.648210674889982	1		376	255	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889087	76889087	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	110	289	3	ENST00000373344.5:c.4923G>A	p.Trp1641Ter	p.W1641*	ENST00000373344	NM_000489.3	1641	tgG/tgA	18/35	1	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.648210674889982	1		292	183	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164833	123164833	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	47	160	0	ENST00000218089.9:c.146G>A	p.Gly49Asp	p.G49D	ENST00000218089	NM_001042749.1	49	gGc/gAc	5/35	1	1	FACETS	0.754	0.652	0.86	0.754	0.652	0.86	SUBCLONAL	1	TRUE	0	0.648210674889982	1		160	130	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014275-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	298	779	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.27974610946513	1	FACETS	0.719	0.677	0.762	0.719	0.677	0.762	INDETERMINATE	1	TRUE	0	0.525725615276648	1		779	1162	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0014275-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	324	824	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.503579519096369	1	FACETS	0.959	0.908	1	0.959	0.908	1	CLONAL	1	TRUE	0	0.525725615276648	1		825	947	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0014275-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	287	726	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.91	0.855	0.966	0.91	0.855	0.966	CLONAL	1	TRUE	1	0.525725615276648	2		726	1200	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591933	48591933	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	GT	novel	NA	P-0014275-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	217	499	0	ENST00000342988.3:c.1096delinsGT	p.Gln366ValfsTer12	p.Q366Vfs*12	ENST00000342988	NM_005359.5	366	Caa/GTaa	9/12	0.525725615276648	1	FACETS	0.926	0.866	0.988	0.926	0.866	0.988	CLONAL	1	TRUE	0	0.525725615276648	1		499	657	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482861	67482861	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014275-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	454	508	0	ENST00000327367.4:c.1265C>T	p.Ser422Phe	p.S422F	ENST00000327367	NM_005902.3	422	tCc/tTc	9/9	0.525196085914892	2	FACETS	0.947	0.909	0.984	0.947	0.909	0.984	CLONAL	2	TRUE	0	0.525725615276648	2		508	912	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772062	135772062	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1317622700	NA	P-0014275-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	262	508	0	ENST00000298552.3:c.3055A>G	p.Lys1019Glu	p.K1019E	ENST00000298552	NM_001162426.1	1019	Aag/Gag	23/23	1	2	FACETS	0.971	0.911	1	0.971	0.911	1	CLONAL	1	TRUE	1	0.525725615276648	2		508	1026	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014487-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	229	779	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.379151329542874	4	FACETS	0.998	0.935	1	0.998	0.935	1	CLONAL	2	FALSE	2	0.536757769540508	4		779	657	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939182	131939182	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0014487-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	206	610	0	ENST00000265335.6:c.2397+1G>T		p.X799_splice	ENST00000265335		799			0.536757769540508	4	FACETS	0.936	0.881	0.991	0.936	0.881	0.991	CLONAL	3	FALSE	1	0.536757769540508	4		610	420	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251917	8251917	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1441070721	NA	P-0014487-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	165	709	0	ENST00000335790.3:c.160T>C	p.Cys54Arg	p.C54R	ENST00000335790	NM_002315.2	54	Tgt/Cgt	2/4	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	FALSE	1	0.536757769540508	2		709	606	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014501-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	44	669	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.757	0.642	0.882	0.757	0.642	0.882	SUBCLONAL	1	TRUE	1	0.540549883735748	2		669	215	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435402	121435475	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTGTGCAGAGCCATGTGACCCAGAGCCCCTTCATGGCCACCATGGCTCAGCTGCAGAGCCCCCACGGTGAGCG	CCTGTGCAGAGCCATGTGACCCAGAGCCCCTTCATGGCCACCATGGCTCAGCTGCAGAGCCCCCACGGTGAGCG	-	novel	NA	P-0014501-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	39	962	0	ENST00000257555.6:c.1437_1501+9del		p.X479_splice	ENST00000257555		479		7/10	1	2	FACETS	0.517	0.431	0.612	0.517	0.431	0.612	SUBCLONAL	1	TRUE	1	0.540549883735748	2		962	279	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231688	66231688	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014501-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	34	887	0	ENST00000273854.3:c.2012A>G	p.Glu671Gly	p.E671G	ENST00000273854	NM_004439.5	671	gAa/gGa	11/18	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.540549883735748	2		887	116	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0015348-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	630	916	3	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.652242044363268	6	FACETS	0.879	0.85	0.908	0.879	0.85	0.908	CLONAL	4	TRUE	2	0.702142249318009	6		919	1227	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544630	65544630	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0015348-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	320	624	0	ENST00000358664.4:c.295+1G>T		p.X99_splice	ENST00000358664	NM_002382.4	99			0.561067941824565	2	FACETS	0.849	0.812	0.884	0.849	0.812	0.884	CLONAL	2	TRUE	0	0.702142249318009	2		624	537	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731136	162731136	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015348-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	277	706	2	ENST00000367921.3:c.991G>T	p.Ala331Ser	p.A331S	ENST00000367921	NM_006182.2	331	Gct/Tct	9/18	0.632752889278297	3	FACETS	0.8	0.757	0.844	0.8	0.757	0.844	SUBCLONAL	2	TRUE	1	0.702142249318009	3		708	666	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163309268	163309268	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0015348-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	90	673	0	ENST00000271452.3:c.606+1G>T		p.X202_splice	ENST00000271452	NM_145697.2	202			0.632752889278297	3	FACETS	0.827	0.738	0.92	0.413	0.369	0.46	CLONAL	1	TRUE	1	0.702142249318009	3		673	419	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675391	241675391	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057521425	NA	P-0015348-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	259	720	1	ENST00000366560.3:c.431G>T	p.Gly144Val	p.G144V	ENST00000366560	NM_000143.3	144	gGa/gTa	4/10	0.632752889278297	3	FACETS	0.821	0.775	0.867	0.821	0.775	0.867	CLONAL	2	TRUE	1	0.702142249318009	3		721	607	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250217	133250217	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015348-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	166	922	0	ENST00000320574.5:c.1303G>T	p.Asp435Tyr	p.D435Y	ENST00000320574	NM_006231.2	435	Gat/Tat	13/49	NA	2	FACETS	0.793	0.732	0.856			1	INDETERMINATE	1	TRUE	NA	0.702142249318009	2		922	596	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0015348-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	302	735	0	ENST00000269305.4:c.673-2A>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			NA	2	FACETS	0.804	0.767	0.84			1	INDETERMINATE	2	TRUE	NA	0.702142249318009	2		735	535	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166845	32166845	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015348-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	317	817	1	ENST00000375023.3:c.4393C>A	p.Leu1465Ile	p.L1465I	ENST00000375023	NM_004557.3	1465	Ctt/Att	24/30	0.556910096996603	3	FACETS	0.823	0.782	0.865	0.823	0.782	0.865	CLONAL	2	TRUE	1	0.702142249318009	3		818	741	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987294	2987294	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015348-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	378	782	0	ENST00000396946.4:c.135C>A	p.Tyr45Ter	p.Y45*	ENST00000396946	NM_032415.4	45	taC/taA	3/25	0.406278524381782	5	FACETS	1	0.992	1	0.797	0.759	0.834	INDETERMINATE	2	TRUE	2	0.702142249318009	5		782	925	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069040	5069040	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015348-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	103	534	0	ENST00000381652.3:c.1345T>C	p.Tyr449His	p.Y449H	ENST00000381652	NM_004972.3	449	Tat/Cat	11/25	0.550609913232353	2	FACETS	0.782	0.706	0.862	0.391	0.353	0.431	SUBCLONAL	1	TRUE	0	0.702142249318009	2		534	375	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805589	46805589	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015348-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	287	872	0	ENST00000290295.7:c.367C>G	p.Arg123Gly	p.R123G	ENST00000290295	NM_006361.5	123	Cgc/Ggc	1/2	0.522618766606162	4	FACETS	0.77	0.726	0.816	0.77	0.726	0.816	SUBCLONAL	2	TRUE	2	0.702142249318009	4		872	903	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257839	133257839	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs997586826	NA	P-0015348-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	147	605	0	ENST00000320574.5:c.89C>T	p.Ser30Leu	p.S30L	ENST00000320574	NM_006231.2	30	tCg/tTg	2/49	NA	2	FACETS	0.899	0.827	0.972			1	INDETERMINATE	1	TRUE	NA	0.702142249318009	2		605	466	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30098301	30098301	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0015348-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	114	752	0	ENST00000331968.5:c.1673-2A>T		p.X558_splice	ENST00000331968	NM_002742.2	558			NA	2	FACETS	0.717	0.649	0.787			1	INDETERMINATE	1	TRUE	NA	0.702142249318009	2		752	453	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266963	41266963	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770795614	NA	P-0015348-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	152	644	0	ENST00000349496.5:c.634C>T	p.Arg212Cys	p.R212C	ENST00000349496	NM_001904.3	212	Cgt/Tgt	5/15	0.264822810696246	3	FACETS	1	0.972	1	0.562	0.518	0.609	INDETERMINATE	1	TRUE	1	0.702142249318009	3		644	520	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415082	116415082	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015348-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	40	833	0	ENST00000397752.3:c.3176A>T	p.Asn1059Ile	p.N1059I	ENST00000397752	NM_000245.2	1059	aAt/aTt	15/21	1	2	FACETS	0.185	0.153	0.221	0.185	0.153	0.221	SUBCLONAL	1	TRUE	1	0.702142249318009	2		833	615	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015918-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	31	779	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.998	0.807	1	0.998	0.807	1	CLONAL	1	TRUE	1	0.15	2		779	414	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278343	39278343	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015918-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	25	978	0	ENST00000402219.2:c.806T>A	p.Met269Lys	p.M269K	ENST00000402219	NM_005633.3	269	aTg/aAg	6/23	1	2	FACETS	0.711	0.559	0.886	0.711	0.559	0.886	SUBCLONAL	1	TRUE	1	0.15	2		978	469	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575152	48575152	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015918-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	22	458	1	ENST00000342988.3:c.346C>G	p.Gln116Glu	p.Q116E	ENST00000342988	NM_005359.5	116	Cag/Gag	3/12	1	2	FACETS	0.978	0.758	1	0.978	0.758	1	CLONAL	1	TRUE	1	0.15	2		459	300	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476264	88476264	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016507-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	314	756	0	ENST00000360948.2:c.1868G>A	p.Gly623Glu	p.G623E	ENST00000360948	NM_001012338.2	623	gGa/gAa	15/19	0.430042212271624	3	FACETS	0.761	0.718	0.805	0.761	0.718	0.805	SUBCLONAL	2	TRUE	1	0.430042212271624	3		756	1166	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751095	57751141	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAAGCCACAGTACTTACATCCATGAGGTTCTCCTCCATGTAATGAGA	AAAGCCACAGTACTTACATCCATGAGGTTCTCCTCCATGTAATGAGA	-	novel	NA	P-0016507-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	45	329	0	ENST00000274289.3:c.1726_1755+17del		p.X576_splice	ENST00000274289	NM_006622.3	576		12/14	1	2	FACETS	0.513	0.432	0.602	0.513	0.432	0.602	SUBCLONAL	1	TRUE	1	0.430042212271624	2		329	408	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971155	21971164	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCCGTGGA	GCGCCGTGGA	-	novel	NA	P-0016507-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	294	493	0	ENST00000304494.5:c.194_203del	p.Leu65ArgfsTer78	p.L65Rfs*78	ENST00000304494	NM_000077.4	65	cTCCACGGCGCg/cg	2/3	0.430042212271624	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.430042212271624	2		493	560	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017517-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	92	669	0				ENST00000310581	NM_198253.2	-/1132			0.189293939856247	0	FACETS	1	0.936	1			1	CLONAL	1	TRUE	0	0.31529668410177	0		669	376	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950066	44950066	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs863224886	NA	P-0017517-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	45	742	0	ENST00000377967.4:c.3835C>T	p.Arg1279Ter	p.R1279*	ENST00000377967	NM_021140.2	1279	Cga/Tga	26/29	0.314643481594533	1	FACETS	0.402	0.337	0.474	0.402	0.337	0.474	SUBCLONAL	1	TRUE	0	0.31529668410177	1		742	598	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817729	3817729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780618828	NA	P-0017517-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	81	598	0	ENST00000262367.5:c.3242G>A	p.Arg1081His	p.R1081H	ENST00000262367	NM_004380.2	1081	cGc/cAc	16/31	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.31529668410177	2		598	479	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692980	89692980	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1060500126	NA	P-0017517-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	26	483	0	ENST00000371953.3:c.464A>G	p.Tyr155Cys	p.Y155C	ENST00000371953	NM_000314.4	155	tAt/tGt	5/9	0.31529668410177	1	FACETS	0.344	0.272	0.427	0.344	0.272	0.427	SUBCLONAL	1	TRUE	0	0.31529668410177	1		483	404	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390873	139390874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0017517-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	83	886	0	ENST00000277541.6:c.7316_7317dup	p.Gln2440AlafsTer38	p.Q2440Afs*38	ENST00000277541	NM_017617.3	2439	-/GC	34/34	1	2	FACETS	0.666	0.587	0.75	0.666	0.587	0.75	SUBCLONAL	1	TRUE	1	0.31529668410177	2		886	791	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949128	44949129	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017517-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	39	615	0	ENST00000377967.4:c.3690dup	p.Ile1231TyrfsTer20	p.I1231Yfs*20	ENST00000377967	NM_021140.2	1230	gct/gcTt	25/29	0.314643481594533	1	FACETS	0.357	0.295	0.427	0.357	0.295	0.427	SUBCLONAL	1	TRUE	0	0.31529668410177	1		615	583	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247908	59247908	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017517-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	152	991	1	ENST00000371222.2:c.835del	p.Arg279GlyfsTer6	p.R279Gfs*6	ENST00000371222	NM_002228.3	279	Cgg/gg	1/1	1	2	FACETS	0.783	0.715	0.856	0.783	0.715	0.856	SUBCLONAL	1	TRUE	1	0.31529668410177	2		992	1231	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164665	47164665	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017517-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	57	398	0	ENST00000409792.3:c.1461del	p.Tyr488IlefsTer15	p.Y488Ifs*15	ENST00000409792	NM_014159.6	487	tcC/tc	3/21	1	2	FACETS	0.886	0.763	1	0.886	0.763	1	CLONAL	1	TRUE	1	0.31529668410177	2		398	408	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150505	157150505	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1203546101	NA	P-0017517-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	37	591	1	ENST00000346085.5:c.1687C>T	p.Gln563Ter	p.Q563*	ENST00000346085	NM_020732.3	563	Cag/Tag	2/20	0.155969052540412	3	FACETS	0.371	0.304	0.445	0.185	0.152	0.223	INDETERMINATE	1	TRUE	1	0.31529668410177	3		592	733	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0017882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	234	735	0	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	0.19767445189775	0	FACETS	0.768	0.723	0.813			1	INDETERMINATE	2	TRUE	0	0.36	0		735	542	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341730	8341730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41281783	NA	P-0017882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	102	788	1	ENST00000356435.5:c.4910C>T	p.Thr1637Met	p.T1637M	ENST00000356435		1637	aCg/aTg	29/35	0.258871457176273	2	FACETS	0.73	0.653	0.813	0.365	0.326	0.407	SUBCLONAL	1	TRUE	0	0.36	2		789	776	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953041	2953041	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149857605	NA	P-0017882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	108	823	4	ENST00000396946.4:c.2899C>T	p.Arg967Cys	p.R967C	ENST00000396946	NM_032415.4	967	Cgc/Tgc	22/25	0.255591639237761	2	FACETS	0.748	0.671	0.83	0.374	0.335	0.415	SUBCLONAL	1	TRUE	0	0.36	2		827	802	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0017920-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	492	772	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.614220997842147	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.614220997842147	3		772	987	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0017920-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	240	726	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.918	0.859	0.979	0.918	0.859	0.979	CLONAL	1	TRUE	1	0.614220997842147	2		726	851	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070577	67070578	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017920-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	134	313	0	ENST00000412916.2:c.207dup	p.Pro70SerfsTer13	p.P70Sfs*13	ENST00000412916		67	-/T	3/6	0.614220997842147	1	FACETS	0.945	0.872	1	0.945	0.872	1	CLONAL	1	TRUE	0	0.614220997842147	1		313	320	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593401	48593409	+	inframe_deletion	In_Frame_Del	DEL	CAAAGGTGT	CAAAGGTGT	-	novel	NA	P-0018476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	48	520	0	ENST00000342988.3:c.1152_1160del	p.Lys385_Val387del	p.K385_V387del	ENST00000342988	NM_005359.5	384	ggCAAAGGTGTg/ggg	10/12	0.315227500735544	1	FACETS	0.665	0.563	0.776	0.665	0.563	0.776	SUBCLONAL	1	TRUE	0	0.315227500735544	1		520	386	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802625	139802625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149585522	NA	P-0019393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	251	750	1	ENST00000247668.2:c.470C>T	p.Pro157Leu	p.P157L	ENST00000247668	NM_021138.3	157	cCg/cTg	5/11	0.337017112266648	2	FACETS	0.779	0.732	0.827	0.779	0.732	0.827	SUBCLONAL	2	TRUE	0	0.449279685916934	2		751	717	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874263	155874263	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1557960039	NA	P-0019393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	520	802	1	ENST00000368323.3:c.268A>G	p.Met90Val	p.M90V	ENST00000368323	NM_006912.5	90	Atg/Gtg	5/6	0.449279685916934	4	FACETS	0.91	0.874	0.946	0.91	0.874	0.946	CLONAL	3	TRUE	1	0.449279685916934	4		803	1229	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194747	30194747	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	228	828	0	ENST00000331968.5:c.398T>G	p.Leu133Trp	p.L133W	ENST00000331968	NM_002742.2	133	tTg/tGg	2/18	0.375305697811513	2	FACETS	1	0.992	1	0.733	0.687	0.781	CLONAL	1	TRUE	0	0.449279685916934	2		828	692	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934644	9934644	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	154	466	1	ENST00000330684.3:c.1511G>T	p.Arg504Leu	p.R504L	ENST00000330684	NM_001134407.1	504	cGg/cTg	7/13	0.32060054819301	3	FACETS	1	0.988	1	0.724	0.665	0.784	CLONAL	1	TRUE	1	0.449279685916934	3		467	580	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984852	9984852	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	233	738	0	ENST00000330684.3:c.1113A>C	p.Glu371Asp	p.E371D	ENST00000330684	NM_001134407.1	371	gaA/gaC	4/13	0.32060054819301	3	FACETS	1	0.991	1	0.711	0.664	0.76	CLONAL	1	TRUE	1	0.449279685916934	3		738	893	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519272	187519272	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0019393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	124	702	0	ENST00000441802.2:c.12111C>G	p.Tyr4037Ter	p.Y4037*	ENST00000441802	NM_005245.3	4037	taC/taG	23/27	0.392623319174895	1	FACETS	0.766	0.695	0.839	0.766	0.695	0.839	SUBCLONAL	1	TRUE	0	0.449279685916934	1		702	559	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200413	138200413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756591879	NA	P-0019393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	246	706	2	ENST00000237289.4:c.1831G>A	p.Gly611Ser	p.G611S	ENST00000237289	NM_001270507.1	611	Ggc/Agc	7/9	0.326947708317419	2	FACETS	1	0.991	1	0.658	0.617	0.701	CLONAL	1	TRUE	0	0.449279685916934	2		708	832	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032573	47032573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	126	764	2	ENST00000377604.3:c.479G>A	p.Arg160Gln	p.R160Q	ENST00000377604	NM_001204468.1	160	cGg/cAg	5/24	0.449279685916934	1	FACETS	0.682	0.619	0.748	0.682	0.619	0.748	SUBCLONAL	1	TRUE	0	0.449279685916934	1		766	638	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732511	74732511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019401-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	66	242	0	ENST00000359995.5:c.398G>A	p.Arg133Gln	p.R133Q	ENST00000359995	NM_001195427.1	133	cGg/cAg	2/3	0.446091999037975	3	FACETS	0.913	0.809	1	0.913	0.809	1	CLONAL	2	TRUE	1	0.492336326891133	3		242	183	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821638	72821638	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs200561133	NA	P-0019502-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	17	91	0	ENST00000268489.5:c.10537A>G	p.Ser3513Gly	p.S3513G	ENST00000268489	NM_006885.3	3513	Agt/Ggt	10/10	0.467433864317151	3	FACETS	0.794	0.6	1	0.397	0.3	0.509	CLONAL	1	TRUE	1	0.467433864317151	3		91	113	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784903	9784903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761274254	NA	P-0019502-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	142	769	1	ENST00000377346.4:c.2906G>A	p.Arg969His	p.R969H	ENST00000377346	NM_005026.3	969	cGc/cAc	23/24	1	2	FACETS	0.935	0.854	1	0.935	0.854	1	CLONAL	1	TRUE	1	0.467433864317151	2		770	650	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955420	48955420	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019502-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	57	463	0	ENST00000267163.4:c.1536G>C	p.Leu512Phe	p.L512F	ENST00000267163	NM_000321.2	512	ttG/ttC	17/27	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.467433864317151	2		463	222	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070865	30070865	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019502-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	248	639	0	ENST00000338641.4:c.1381del	p.Ala461HisfsTer24	p.A461Hfs*24	ENST00000338641	NM_000268.3	461	Gca/ca	13/16	0.467433864317151	2	FACETS	0.965	0.911	1	0.965	0.911	1	CLONAL	2	TRUE	0	0.467433864317151	2		639	550	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935502	49935502	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019502-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	129	820	0	ENST00000296474.3:c.1862A>G	p.Lys621Arg	p.K621R	ENST00000296474	NM_002447.2	621	aAg/aGg	5/20	1	2	FACETS	0.96	0.874	1	0.96	0.874	1	CLONAL	1	TRUE	1	0.467433864317151	2		820	575	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019804-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	279	779	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.277601792681476	2	FACETS	0.957	0.9	1	0.957	0.9	1	CLONAL	2	TRUE	0	0.277601792681476	2		779	1050	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793131	33793131	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019804-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	100	636	0	ENST00000498907.2:c.190A>G	p.Ile64Val	p.I64V	ENST00000498907	NM_004364.3	64	Atc/Gtc	1/1	1	2	FACETS	0.882	0.787	0.983	0.882	0.787	0.983	CLONAL	1	TRUE	1	0.277601792681476	2		636	817	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435918	110435918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774519000	NA	P-0019804-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	117	815	3	ENST00000375856.3:c.2483C>T	p.Ser828Phe	p.S828F	ENST00000375856	NM_003749.2	828	tCc/tTc	1/2	1	2	FACETS	0.902	0.812	0.996	0.902	0.812	0.996	CLONAL	1	TRUE	1	0.277601792681476	2		818	935	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226308	2226308	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019804-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	108	840	0	ENST00000326181.6:c.1921C>G	p.Arg641Gly	p.R641G	ENST00000326181	NM_032271.2	641	Cgt/Ggt	20/21	1	2	FACETS	0.877	0.786	0.974	0.877	0.786	0.974	CLONAL	1	TRUE	1	0.277601792681476	2		840	887	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259079	89259079	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019804-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	62	351	0	ENST00000336596.2:c.223G>T	p.Asp75Tyr	p.D75Y	ENST00000336596	NM_005233.5	75	Gac/Tac	3/17	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.277601792681476	2		351	406	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670870	134670870	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs752301410	NA	P-0019804-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	46	342	0	ENST00000398015.3:c.781C>G	p.Pro261Ala	p.P261A	ENST00000398015	NM_004441.4	261	Cct/Gct	3/16	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.277601792681476	2		342	326	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250607	26250607	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019804-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	108	672	0	ENST00000446824.2:c.227C>A	p.Ala76Glu	p.A76E	ENST00000446824	NM_021018.2	76	gCg/gAg	1/1	0.277601792681476	9	FACETS	0.94	0.843	1	0.376	0.337	0.417	CLONAL	2	TRUE	4	0.277601792681476	9		672	816	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940102	31940102	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019804-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	164	847	0	ENST00000375333.2:c.244C>G	p.Arg82Gly	p.R82G	ENST00000375333	NM_032454.1	82	Cgt/Ggt	2/8	0.277601792681476	8	FACETS	0.857	0.784	0.932	0.428	0.392	0.466	CLONAL	2	TRUE	4	0.277601792681476	8		847	1264	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220691	1220691	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs878853247	NA	P-0019979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	453	945	1	ENST00000326873.7:c.709G>T	p.Asp237Tyr	p.D237Y	ENST00000326873	NM_000455.4	237	Gac/Tac	5/10	0.730266953328679	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.730266953328679	1		946	772	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395260	139395260	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	562	767	0	ENST00000277541.6:c.5678del	p.Gly1893AlafsTer88	p.G1893Afs*88	ENST00000277541	NM_017617.3	1893	gGc/gc	31/34	0.68335406129188	2	FACETS	0.82	0.793	0.846	0.82	0.793	0.846	CLONAL	2	TRUE	0	0.730266953328679	2		767	939	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109813	115109813	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	432	759	0	ENST00000257566.3:c.2065G>T	p.Gly689Cys	p.G689C	ENST00000257566	NM_016569.3	689	Ggc/Tgc	8/8	0.730266953328679	3	FACETS	1	0.969	1	0.512	0.487	0.537	CLONAL	1	TRUE	1	0.730266953328679	3		759	1578	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36931998	36931998	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	386	707	1	ENST00000361632.4:c.2471G>T	p.Gly824Val	p.G824V	ENST00000361632		824	gGg/gTg	16/16	0.730266953328679	1	FACETS	0.993	0.953	1	0.993	0.953	1	CLONAL	1	TRUE	0	0.730266953328679	1		708	676	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741817	162741817	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	173	382	1	ENST00000367921.3:c.1508G>T	p.Cys503Phe	p.C503F	ENST00000367921	NM_006182.2	503	tGc/tTc	13/18	0.456296122726204	3	FACETS	1	0.925	1	0.501	0.462	0.54	CLONAL	1	TRUE	1	0.730266953328679	3		383	646	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206719	102206719	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	195	566	0	ENST00000263464.3:c.1347G>T	p.Lys449Asn	p.K449N	ENST00000263464	NM_001165.4	449	aaG/aaT	7/9	1	2	FACETS	0.857	0.798	0.918	0.857	0.798	0.918	CLONAL	1	TRUE	1	0.730266953328679	2		566	623	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514113	125514113	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	258	709	0	ENST00000428830.2:c.1051G>T	p.Asp351Tyr	p.D351Y	ENST00000428830	NM_001114121.2	351	Gat/Tat	10/14	1	2	FACETS	0.872	0.82	0.926	0.872	0.82	0.926	CLONAL	1	TRUE	1	0.730266953328679	2		709	810	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120811	115120811	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	491	527	1	ENST00000257566.3:c.195G>T	p.Met65Ile	p.M65I	ENST00000257566	NM_016569.3	65	atG/atT	1/8	0.730266953328679	3	FACETS	0.984	0.947	1	0.984	0.947	1	CLONAL	2	TRUE	1	0.730266953328679	3		528	933	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762071	43762071	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	147	640	0	ENST00000382044.4:c.1374G>T	p.Gln458His	p.Q458H	ENST00000382044	NM_001141980.1	458	caG/caT	11/28	0.398991247146137	1	FACETS	0.396	0.362	0.431	0.396	0.362	0.431	INDETERMINATE	1	TRUE	0	0.730266953328679	1		640	646	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	DEL	C	C	-	rs1131691033	NA	P-0019979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	540	636	0	ENST00000269305.4:c.993+1del		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.40320770027069	1	FACETS	1	0.996	1	1	0.996	1	INDETERMINATE	1	TRUE	0	0.730266953328679	1		636	781	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37876071	37876071	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	416	735	1	ENST00000269571.5:c.1930G>T	p.Ala644Ser	p.A644S	ENST00000269571		644	Gcc/Tcc	16/27	0.39776016632294	1	FACETS	0.797	0.763	0.832	0.797	0.763	0.832	INDETERMINATE	1	TRUE	0	0.730266953328679	1		736	907	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37882896	37882896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1377136060	NA	P-0019979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	397	781	1	ENST00000269571.5:c.2954G>A	p.Arg985His	p.R985H	ENST00000269571		985	cGc/cAc	24/27	0.39776016632294	1	FACETS	0.774	0.739	0.809	0.774	0.739	0.809	INDETERMINATE	1	TRUE	0	0.730266953328679	1		782	892	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629017	14629017	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	382	745	0	ENST00000254322.2:c.145G>C	p.Ala49Pro	p.A49P	ENST00000254322	NM_006145.1	49	Gct/Cct	1/3	0.730266953328679	1	FACETS	0.993	0.953	1	0.993	0.953	1	CLONAL	1	TRUE	0	0.730266953328679	1		745	669	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934713	49934713	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	190	699	0	ENST00000296474.3:c.2183G>T	p.Arg728Leu	p.R728L	ENST00000296474	NM_002447.2	728	cGg/cTg	7/20	0.39776016632294	1	FACETS	0.394	0.365	0.425	0.394	0.365	0.425	INDETERMINATE	1	TRUE	0	0.730266953328679	1		699	838	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215258	142215258	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	387	657	0	ENST00000350721.4:c.5843G>T	p.Gly1948Val	p.G1948V	ENST00000350721	NM_001184.3	1948	gGg/gTg	34/47	0.730266953328679	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.730266953328679	1		657	631	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155914	106155914	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs771918929	NA	P-0019979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	219	415	0	ENST00000380013.4:c.815G>T	p.Gly272Val	p.G272V	ENST00000380013	NM_001127208.2	272	gGg/gTg	3/11	0.398991247146137	1	FACETS	0.797	0.75	0.844	0.797	0.75	0.844	INDETERMINATE	1	TRUE	0	0.730266953328679	1		415	478	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30676116	30676116	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	220	466	0	ENST00000376406.3:c.2240G>A	p.Trp747Ter	p.W747*	ENST00000376406	NM_014641.2	747	tGg/tAg	8/15	0.730266953328679	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.730266953328679	1		466	366	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525548	137525548	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	268	742	1	ENST00000367739.4:c.467A>T	p.Glu156Val	p.E156V	ENST00000367739	NM_000416.2	156	gAg/gTg	4/7	0.730266953328679	1	FACETS	0.938	0.891	0.984	0.938	0.891	0.984	CLONAL	1	TRUE	0	0.730266953328679	1		743	497	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864489	162864490	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	210	510	0	ENST00000366898.1:c.23dup	p.Asn8LysfsTer13	p.N8Kfs*13	ENST00000366898	NM_004562.2	8	aac/aaAc	2/12	0.730266953328679	1	FACETS	0.961	0.908	1	0.961	0.908	1	CLONAL	1	TRUE	0	0.730266953328679	1		510	380	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968190	68968190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769155626	NA	P-0019979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	256	726	0	ENST00000288368.4:c.1219C>T	p.Pro407Ser	p.P407S	ENST00000288368	NM_024870.2	407	Cct/Tct	10/40	0.730266953328679	3	FACETS	0.822	0.769	0.877	0.411	0.384	0.439	CLONAL	1	TRUE	1	0.730266953328679	3		726	1164	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028112	69028112	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	633	887	1	ENST00000288368.4:c.3271G>A	p.Gly1091Arg	p.G1091R	ENST00000288368	NM_024870.2	1091	Gga/Aga	26/40	0.730266953328679	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.730266953328679	3		888	1155	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090449	5090449	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	85	333	1	ENST00000381652.3:c.2765G>T	p.Arg922Leu	p.R922L	ENST00000381652	NM_004972.3	922	cGg/cTg	21/25	0.730266953328679	1	FACETS	0.817	0.74	0.893	0.817	0.74	0.893	CLONAL	1	TRUE	0	0.730266953328679	1		334	181	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126366	5126366	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	151	484	0	ENST00000381652.3:c.3211G>C	p.Gly1071Arg	p.G1071R	ENST00000381652	NM_004972.3	1071	Gga/Cga	24/25	0.730266953328679	1	FACETS	0.931	0.87	0.992	0.931	0.87	0.992	CLONAL	1	TRUE	0	0.730266953328679	1		484	282	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1331521	1331521	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374874204	NA	P-0019979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	694	710	2	ENST00000400841.2:c.7C>T	p.Arg3Trp	p.R3W	ENST00000400841		3	Cgg/Tgg	1/6	0.730266953328679	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.730266953328679	3		712	1274	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933293	39933293	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs960778355	NA	P-0019979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	857	998	1	ENST00000378444.4:c.1306G>T	p.Val436Phe	p.V436F	ENST00000378444	NM_001123385.1	436	Gtc/Ttc	4/15	0.730266953328679	3	FACETS	0.924	0.898	0.951	0.924	0.898	0.951	CLONAL	2	TRUE	1	0.730266953328679	3		999	1733	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045923	47045923	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	765	752	0	ENST00000377604.3:c.2718C>A	p.Tyr906Ter	p.Y906*	ENST00000377604	NM_001204468.1	906	taC/taA	24/24	0.730266953328679	3	FACETS	0.99	0.961	1	0.99	0.961	1	CLONAL	2	TRUE	1	0.730266953328679	3		752	1444	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349594	70349594	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	354	811	1	ENST00000374080.3:c.3756G>T	p.Glu1252Asp	p.E1252D	ENST00000374080		1252	gaG/gaT	27/45	1	2	FACETS	0.902	0.856	0.949	0.902	0.856	0.949	CLONAL	1	TRUE	1	0.730266953328679	2		812	1075	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0020008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	234	875	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.385711887990153	3	FACETS	0.885	0.827	0.943	0.885	0.827	0.943	CLONAL	2	TRUE	1	0.385711887990153	3		877	818	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0020008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	113	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.270468608744846	3	FACETS	1	0.974	1	0.784	0.716	0.854	CLONAL	2	TRUE	0	0.385711887990153	3		434	297	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587118	189587118	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761885185	NA	P-0020008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	8	648	1	ENST00000264731.3:c.1135C>T	p.Arg379Cys	p.R379C	ENST00000264731	NM_003722.4	379	Cgt/Tgt	9/14	0.270468608744846	3	FACETS	0.152	0.097	0.224	0.051	0.032	0.075	SUBCLONAL	1	TRUE	0	0.385711887990153	3		649	325	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255280	16255280	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	32	733	0	ENST00000375759.3:c.2545G>A	p.Glu849Lys	p.E849K	ENST00000375759	NM_015001.2	849	Gaa/Aaa	11/15	1	2	FACETS	0.337	0.273	0.409	0.337	0.273	0.409	SUBCLONAL	1	TRUE	1	0.385711887990153	2		733	493	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256177	16256177	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	29	786	0	ENST00000375759.3:c.3442G>C	p.Glu1148Gln	p.E1148Q	ENST00000375759	NM_015001.2	1148	Gag/Cag	11/15	1	2	FACETS	0.31	0.248	0.381	0.31	0.248	0.381	SUBCLONAL	1	TRUE	1	0.385711887990153	2		786	485	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256303	16256303	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	25	791	0	ENST00000375759.3:c.3568G>A	p.Glu1190Lys	p.E1190K	ENST00000375759	NM_015001.2	1190	Gag/Aag	11/15	1	2	FACETS	0.261	0.205	0.326	0.261	0.205	0.326	SUBCLONAL	1	TRUE	1	0.385711887990153	2		791	496	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257344	16257344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	32	905	1	ENST00000375759.3:c.4609G>A	p.Glu1537Lys	p.E1537K	ENST00000375759	NM_015001.2	1537	Gaa/Aaa	11/15	1	2	FACETS	0.329	0.267	0.4	0.329	0.267	0.4	SUBCLONAL	1	TRUE	1	0.385711887990153	2		906	504	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257779	16257779	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1336582924	NA	P-0020008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	53	642	2	ENST00000375759.3:c.5044G>A	p.Glu1682Lys	p.E1682K	ENST00000375759	NM_015001.2	1682	Gaa/Aaa	11/15	1	2	FACETS	0.512	0.436	0.594	0.512	0.436	0.594	SUBCLONAL	1	TRUE	1	0.385711887990153	2		644	537	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249241	133249241	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145370369	NA	P-0020008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	49	796	3	ENST00000320574.5:c.1658G>A	p.Arg553His	p.R553H	ENST00000320574	NM_006231.2	553	cGc/cAc	15/49	0.23581742319197	3	FACETS	0.428	0.362	0.502			1	SUBCLONAL	1	TRUE	NA	0.385711887990153	3		799	708	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0020540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	353	692	2	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.498177766227942	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.498177766227942	3		694	829	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0020540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	169	726	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.945	0.871	1	0.945	0.871	1	CLONAL	1	TRUE	1	0.498177766227942	2		726	718	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857311	68857312	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	99	501	0	ENST00000261769.5:c.1947dup	p.Ile650TyrfsTer13	p.I650Yfs*13	ENST00000261769	NM_004360.3	649	tct/tcTt	13/16	0.461416842146138	1	FACETS	0.957	0.864	1	0.957	0.864	1	CLONAL	1	TRUE	0	0.498177766227942	1		501	312	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160659	56160660	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATGCGGGCCAGACT	novel	NA	P-0020540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	88	463	0	ENST00000399503.3:c.934_947dup	p.Tyr317CysfsTer11	p.Y317Cfs*11	ENST00000399503	NM_005921.1	311	-/ATGCGGGCCAGACT	4/20	1	2	FACETS	0.711	0.632	0.795	0.711	0.632	0.795	SUBCLONAL	1	TRUE	1	0.498177766227942	2		463	497	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0020731-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	110	710	1	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	0.923	1	CLONAL	1	TRUE	1	0.635902746140144	2		711	340	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0020731-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	201	548	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.635902746140144	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.635902746140144	2		548	277	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859788	117859788	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020731-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	108	661	0	ENST00000297338.2:c.1847C>T	p.Pro616Leu	p.P616L	ENST00000297338	NM_006265.2	616	cCg/cTg	14/14	0.59594390116871	3	FACETS	0.988	0.892	1	0.494	0.446	0.545	CLONAL	1	TRUE	1	0.635902746140144	3		661	453	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256988	16256988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs938826668	NA	P-0020731-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	128	1040	2	ENST00000375759.3:c.4253G>A	p.Arg1418Gln	p.R1418Q	ENST00000375759	NM_015001.2	1418	cGa/cAa	11/15	1	2	FACETS	0.999	0.914	1	0.999	0.914	1	CLONAL	1	TRUE	1	0.635902746140144	2		1042	403	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332632	65332632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020731-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	133	787	1	ENST00000342505.4:c.907C>T	p.His303Tyr	p.H303Y	ENST00000342505	NM_002227.2	303	Cat/Tat	7/25	0.197519737532547	4	FACETS	0.893	0.82	0.968	0.893	0.82	0.968	INDETERMINATE	2	TRUE	2	0.635902746140144	4		788	383	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293191	212293191	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754748646	NA	P-0020731-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	117	827	0	ENST00000342788.4:c.2661G>A	p.Met887Ile	p.M887I	ENST00000342788	NM_005235.2	887	atG/atA	22/28	1	2	FACETS	0.893	0.812	0.977	0.893	0.812	0.977	CLONAL	1	TRUE	1	0.635902746140144	2		827	412	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660027	227660027	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020731-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	123	795	1	ENST00000305123.5:c.3428C>T	p.Ser1143Phe	p.S1143F	ENST00000305123	NM_005544.2	1143	tCt/tTt	1/2	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.635902746140144	2		796	385	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067312	37067313	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0020731-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	109	812	0	ENST00000231790.2:c.1223_1224delinsTT	p.Pro408Leu	p.P408L	ENST00000231790	NM_000249.3	408	cCC/cTT	12/19	1	2	FACETS	0.939	0.852	1	0.939	0.852	1	CLONAL	1	TRUE	1	0.635902746140144	2		812	365	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467840	50467841	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0020731-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	97	753	3	ENST00000331340.3:c.1075_1076delinsTT	p.Pro359Leu	p.P359L	ENST00000331340	NM_006060.4	359	CCg/TTg	8/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.635902746140144	2		756	253	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874755	151874755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020731-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	123	635	4	ENST00000262189.6:c.7783C>T	p.Pro2595Ser	p.P2595S	ENST00000262189	NM_170606.2	2595	Ccc/Tcc	38/59	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.635902746140144	2		639	358	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971164	21971178	+	frameshift_variant	Frame_Shift_Del	DEL	AGCAGCAGCAGCTCC	AGCAGCAGCAGCTCC	TGCT	novel	NA	P-0020731-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	206	882	2	ENST00000304494.5:c.180_194delinsAGCA	p.Glu61AlafsTer55	p.E61Afs*55	ENST00000304494	NM_000077.4	60	gcGGAGCTGCTGCTGCTc/gcAGCAc	2/3	0.635902746140144	2	FACETS	0.831	0.783	0.878	0.831	0.783	0.878	CLONAL	2	TRUE	0	0.635902746140144	2		884	390	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323312	31323312	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020731-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	24	177	0	ENST00000412585.2:c.677G>A	p.Arg226Lys	p.R226K	ENST00000412585	NM_005514.6	226	aGg/aAg	4/8	1	2	FACETS	0.839	0.674	1	0.839	0.674	1	CLONAL	1	TRUE	1	0.635902746140144	2		177	90	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0020747-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	91	916	3	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.995	0.883	1	0.995	0.883	1	CLONAL	1	TRUE	1	0.24	2		919	762	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391234	89391234	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1317883302	NA	P-0020747-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	61	398	0	ENST00000336596.2:c.1300C>T	p.Gln434Ter	p.Q434*	ENST00000336596	NM_005233.5	434	Cag/Tag	5/17	1	2	FACETS	0.993	0.858	1	0.993	0.858	1	CLONAL	1	TRUE	1	0.24	2		398	512	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62008701	62008701	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020747-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	62	679	1	ENST00000392795.3:c.115C>A	p.Pro39Thr	p.P39T	ENST00000392795	NM_001039933.1	39	Ccc/Acc	2/6	0.3	3	FACETS	0.774	0.667	0.89	0.387	0.333	0.445	SUBCLONAL	1	TRUE	1	0.24	3		680	748	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602727	10602727	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020747-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	95	745	0	ENST00000171111.5:c.851A>T	p.Gln284Leu	p.Q284L	ENST00000171111	NM_203500.1	284	cAg/cTg	3/6	0.174946019044839	3	FACETS	0.922	0.819	1	0.461	0.409	0.516	CLONAL	1	TRUE	1	0.24	3		745	962	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214908	36214908	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020747-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	55	660	0	ENST00000222270.7:c.3334G>T	p.Glu1112Ter	p.E1112*	ENST00000222270	NM_014727.1	1112	Gag/Tag	8/37	1	2	FACETS	0.632	0.54	0.734	0.632	0.54	0.734	SUBCLONAL	1	TRUE	1	0.24	2		660	725	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966341	25966341	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020747-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	80	684	0	ENST00000435504.4:c.2865G>T	p.Gln955His	p.Q955H	ENST00000435504		955	caG/caT	13/13	NA	2	FACETS	0.734	0.645	0.83			1	INDETERMINATE	1	TRUE	NA	0.24	2		684	908	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944403	40944403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs747700602	NA	P-0020747-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	89	706	1	ENST00000373198.4:c.2099G>T	p.Ser700Ile	p.S700I	ENST00000373198	NM_133170.3	700	aGc/aTc	12/32	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.24	2		707	715	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259565	89259565	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020747-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	58	420	0	ENST00000336596.2:c.709G>T	p.Glu237Ter	p.E237*	ENST00000336596	NM_005233.5	237	Gaa/Taa	3/17	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.24	2		420	460	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522460	157522460	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs139214813	NA	P-0020747-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	96	762	0	ENST00000346085.5:c.4732A>G	p.Met1578Val	p.M1578V	ENST00000346085	NM_020732.3	1578	Atg/Gtg	18/20	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.24	2		762	774	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50358673	50358673	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020747-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	71	394	0	ENST00000331340.3:c.16G>T	p.Gly6Cys	p.G6C	ENST00000331340	NM_006060.4	6	Ggt/Tgt	2/8	0.174946019044839	3	FACETS	1	0.973	1	0.73	0.639	0.827	CLONAL	1	TRUE	1	0.24	3		394	454	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633364	8633364	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020747-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	68	590	0	ENST00000356435.5:c.305A>C	p.Asn102Thr	p.N102T	ENST00000356435		102	aAt/aCt	3/35	1	2	FACETS	0.803	0.698	0.916	0.803	0.698	0.916	CLONAL	1	TRUE	1	0.24	2		590	706	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039861	47039861	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020747-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	87	831	2	ENST00000377604.3:c.1204G>A	p.Val402Met	p.V402M	ENST00000377604	NM_001204468.1	402	Gtg/Atg	12/24	1	2	FACETS	0.818	0.723	0.92	0.818	0.723	0.92	CLONAL	1	TRUE	1	0.24	2		833	886	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340021	70340021	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0020747-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	56	419	0	ENST00000374080.3:c.553+1G>T		p.X185_splice	ENST00000374080		185			1	2	FACETS	0.892	0.765	1	0.892	0.765	1	CLONAL	1	TRUE	1	0.24	2		419	523	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939289	76939289	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0020747-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	99	772	0	ENST00000373344.5:c.1459A>T	p.Lys487Ter	p.K487*	ENST00000373344	NM_000489.3	487	Aaa/Taa	9/35	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.24	2		772	818	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972626	76972626	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs868945321	NA	P-0020747-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	111	600	0	ENST00000373344.5:c.115G>T	p.Ala39Ser	p.A39S	ENST00000373344	NM_000489.3	39	Gca/Tca	2/35	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.24	2		600	911	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161308	55161308	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020747-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	31	507	0	ENST00000257290.5:c.3139G>T	p.Glu1047Ter	p.E1047*	ENST00000257290	NM_006206.4	1047	Gag/Tag	23/23	1	2	FACETS	0.484	0.39	0.59	0.484	0.39	0.59	SUBCLONAL	1	TRUE	1	0.24	2		507	534	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184113	123184113	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020747-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	58	532	0	ENST00000218089.9:c.971T>G	p.Leu324Arg	p.L324R	ENST00000218089	NM_001042749.1	324	cTt/cGt	11/35	1	2	FACETS	0.822	0.706	0.948	0.822	0.706	0.948	CLONAL	1	TRUE	1	0.24	2		532	588	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197747	123197747	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020747-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	65	638	1	ENST00000218089.9:c.1871C>A	p.Thr624Lys	p.T624K	ENST00000218089	NM_001042749.1	624	aCa/aAa	20/35	1	2	FACETS	0.785	0.68	0.899	0.785	0.68	0.899	SUBCLONAL	1	TRUE	1	0.24	2		639	690	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227957	123227957	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020747-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	44	572	0	ENST00000218089.9:c.3668A>G	p.Asn1223Ser	p.N1223S	ENST00000218089	NM_001042749.1	1223	aAt/aGt	33/35	1	2	FACETS	0.526	0.44	0.622	0.526	0.44	0.622	SUBCLONAL	1	TRUE	1	0.24	2		572	697	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930314	39930316	+	missense_variant	Missense_Mutation	TNP	GTC	GTC	TTT	novel	NA	P-0020747-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	63	679	0	ENST00000378444.4:c.3148_3150delinsAAA	p.Asp1050Lys	p.D1050K	ENST00000378444	NM_001123385.1	1050	GAC/AAA	6/15	1	2	FACETS	0.598	0.516	0.688	0.598	0.516	0.688	SUBCLONAL	1	TRUE	1	0.24	2		679	878	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0020803-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	79	618	0	ENST00000269305.4:c.97-1G>T		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.172660575923724	2	FACETS	1	0.976	1	0.746	0.657	0.84	CLONAL	1	TRUE	0	0.200657369263548	2		618	528	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911491	114911491	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020803-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	29	304	0	ENST00000543371.1:c.1009C>G	p.Gln337Glu	p.Q337E	ENST00000543371	NM_001198531.1	337	Cag/Gag	10/14	0.148558158112808	2	FACETS	1	0.931	1	0.695	0.561	0.844	CLONAL	1	TRUE	0	0.200657369263548	2		304	208	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665346	138665346	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020803-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	95	958	0	ENST00000330315.3:c.219G>C	p.Lys73Asn	p.K73N	ENST00000330315	NM_023067.3	73	aaG/aaC	1/1	0.200657369263548	2	FACETS	0.989	0.879	1	0.495	0.439	0.554	CLONAL	1	TRUE	0	0.200657369263548	2		958	957	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481452	20481452	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0020803-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	30	456	0	ENST00000346618.3:c.521C>G	p.Ser174Ter	p.S174*	ENST00000346618	NM_001949.4	174	tCa/tGa	3/7	0.200657369263548	3	FACETS	0.771	0.62	0.941	0.385	0.31	0.471	CLONAL	1	TRUE	1	0.200657369263548	3		456	427	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242481	+	protein_altering_variant	In_Frame_Del	DEL	GAATTAAGAGAAGCAA	GAATTAAGAGAAGCAA	ATTC	novel	NA	P-0020803-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	57	725	2	ENST00000275493.2:c.2236_2251delinsATTC	p.Glu746_Thr751delinsIlePro	p.E746_T751delinsIP	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCAAca/ATTCca	19/28	0.129908684571694	3	FACETS	0.968	0.83	1	0.484	0.415	0.56	CLONAL	1	TRUE	1	0.200657369263548	3		727	646	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152357789	152357789	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020803-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	37	638	1	ENST00000359321.1:c.118C>T	p.His40Tyr	p.H40Y	ENST00000359321	NM_005431.1	40	Cat/Tat	2/3	0.129908684571694	3	FACETS	0.799	0.658	0.957	0.399	0.329	0.479	CLONAL	1	TRUE	1	0.200657369263548	3		639	508	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352389	70352389	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0020803-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	102	563	0	ENST00000374080.3:c.4415+1G>C		p.X1472_splice	ENST00000374080		1472			0.129908684571694	3	FACETS	0.943	0.846	1	0.943	0.846	1	CLONAL	2	TRUE	1	0.200657369263548	3		563	593	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867546	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGC	GGCGGCGGC	-	rs11466445	NA	P-0020812-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	14	46	2	ENST00000374994.4:c.70_78del	p.Ala24_Ala26del	p.A24_A26del	ENST00000374994	NM_004612.2	17	ctGGCGGCGGCg/ctg	1/9	1	2	FACETS	0.672	0.5	0.867	0.672	0.5	0.867	SUBCLONAL	1	TRUE	1	0.718391585642763	2		48	58	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577054	7577054	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020812-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	184	949	0	ENST00000269305.4:c.884del	p.Pro295LeufsTer50	p.P295Lfs*50	ENST00000269305	NM_001126112.2	295	cCt/ct	8/11	0.647495197490467	1	FACETS	0.853	0.799	0.907	0.853	0.799	0.907	CLONAL	1	TRUE	0	0.718391585642763	1		949	385	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101170	41101170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41279256	NA	P-0020812-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	27	879	0	ENST00000373198.4:c.1186G>A	p.Val396Ile	p.V396I	ENST00000373198	NM_133170.3	396	Gta/Ata	8/32	1	2	FACETS	0.144	0.114	0.178	0.144	0.114	0.178	SUBCLONAL	1	TRUE	1	0.718391585642763	2		879	522	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420464	49420464	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020812-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	158	796	0	ENST00000301067.7:c.15285C>G	p.Cys5095Trp	p.C5095W	ENST00000301067	NM_003482.3	5095	tgC/tgG	48/54	1	2	FACETS	0.838	0.773	0.905	0.838	0.773	0.905	CLONAL	1	TRUE	1	0.718391585642763	2		796	525	SUCCESS
APC	324	MSKCC	GRCh37	5	112175921	112175922	+	stop_gained	Nonsense_Mutation	DNP	GA	GA	TG	novel	NA	P-0020812-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	105	333	0	ENST00000257430.4:c.4630_4631delinsTG	p.Glu1544Ter	p.E1544*	ENST00000257430	NM_000038.5	1544	GAa/TGa	16/16	0.678051219048235	2	FACETS	0.799	0.738	0.858	0.799	0.738	0.858	SUBCLONAL	2	TRUE	0	0.718391585642763	2		333	183	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108003	8108479	+	splice_acceptor_variant,coding_sequence_variant,3_prime_UTR_variant,intron_variant	Splice_Site	DEL	GAACAGCTTCCTCCACAGCAAAGCCTCCACCTAGAAACATCTACACTCATGAGTACAAAAAGCTTCAGCCTTTATTAAACAAAGGAGGAGGTAGAAAACAGATAAGGGAACAGTTAGGGATCCCTTCTTTCCCCTATACATACACAGACATACAAACACACGCACCCGAGTGAATGACAGGGACCATCAGGCGACAGATTGAAGGGCAGAGGGAGGCAGCACCCTCCGAGAGTTGGCCCGGACCCAAGGGTGGGCTGAGACCTGGGCCAGGGGCAGCCGTTCCGAGGGGTTATGCCTGAGCAGTTTGGAGATGAGGTCCTGGGCTCCCATGGGCACGGAAGCGGGGAACTTTAGGTCCACCTGCAGGTGTGAAGAGATGGAAGGGCTGCATTAGTTTCACCCTGGCTACATCTTCCTTGACTACCCATTCTGTTTGGAGTTACTTAGGGCCATGCAAATACACTCTGCCCACCCCCA	GAACAGCTTCCTCCACAGCAAAGCCTCCACCTAGAAACATCTACACTCATGAGTACAAAAAGCTTCAGCCTTTATTAAACAAAGGAGGAGGTAGAAAACAGATAAGGGAACAGTTAGGGATCCCTTCTTTCCCCTATACATACACAGACATACAAACACACGCACCCGAGTGAATGACAGGGACCATCAGGCGACAGATTGAAGGGCAGAGGGAGGCAGCACCCTCCGAGAGTTGGCCCGGACCCAAGGGTGGGCTGAGACCTGGGCCAGGGGCAGCCGTTCCGAGGGGTTATGCCTGAGCAGTTTGGAGATGAGGTCCTGGGCTCCCATGGGCACGGAAGCGGGGAACTTTAGGTCCACCTGCAGGTGTGAAGAGATGGAAGGGCTGCATTAGTTTCACCCTGGCTACATCTTCCTTGACTACCCATTCTGTTTGGAGTTACTTAGGGCCATGCAAATACACTCTGCCCACCCCCA	-	novel	NA	P-0020812-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	17	30	0				ENST00000585124	NM_004217.3	-/344		9/9	1	2	FACETS	0.845	0.69	0.99	1	0.939	1	CLONAL	2	TRUE	1	0.718391585642763	2		30	28	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743940	46743940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372007047	NA	P-0020953-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	191	724	2	ENST00000371975.4:c.2230C>T	p.Arg744Trp	p.R744W	ENST00000371975	NM_003579.3	744	Cgg/Tgg	18/18	0.808207227494042	3	FACETS	0.897	0.831	0.964	0.448	0.415	0.482	CLONAL	1	TRUE	1	0.819445373029131	3		726	733	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729997	41729997	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	97	682	0	ENST00000242208.4:c.532C>T	p.Gln178Ter	p.Q178*	ENST00000242208	NM_002192.2	178	Cag/Tag	3/3	0.190418248450005	3	FACETS	1	0.895	1	0.502	0.447	0.561	CLONAL	1	TRUE	1	0.268453647406634	3		682	816	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254813	16254813	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	40	595	0	ENST00000375759.3:c.2078G>T	p.Arg693Met	p.R693M	ENST00000375759	NM_015001.2	693	aGg/aTg	11/15	0.190418248450005	3	FACETS	0.453	0.375	0.54	0.227	0.187	0.27	SUBCLONAL	1	TRUE	1	0.268453647406634	3		595	746	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847340	68847341	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0020997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	121	656	0	ENST00000261769.5:c.1262_1263del	p.Gly421AlafsTer24	p.G421Afs*24	ENST00000261769	NM_004360.3	421	gGA/g	9/16	0.268453647406634	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.268453647406634	1		656	673	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011118	12011118	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	84	520	0	ENST00000353533.5:c.525G>A	p.Trp175Ter	p.W175*	ENST00000353533	NM_003010.3	175	tgG/tgA	5/11	0.268453647406634	1	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	0	0.268453647406634	1		520	542	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475126	40475126	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	33	663	0	ENST00000264657.5:c.1784G>C	p.Arg595Pro	p.R595P	ENST00000264657	NM_139276.2	595	cGg/cCg	20/24	0.268453647406634	1	FACETS	0.331	0.269	0.402	0.331	0.269	0.402	SUBCLONAL	1	TRUE	0	0.268453647406634	1		663	643	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632778	23632778	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	TA	novel	NA	P-0020997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	47	573	0	ENST00000261584.4:c.3018delinsTA	p.Leu1006PhefsTer5	p.L1006Ffs*5	ENST00000261584	NM_024675.3	1006	ttG/ttTA	10/13	1	2	FACETS	0.451	0.379	0.53	0.451	0.379	0.53	SUBCLONAL	1	TRUE	1	0.268453647406634	2		573	777	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249237	133249237	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs752219944	NA	P-0020997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	47	642	1	ENST00000320574.5:c.1662C>A	p.Ser554Arg	p.S554R	ENST00000320574	NM_006231.2	554	agC/agA	15/49	NA	2	FACETS	0.556	0.468	0.653			1	INDETERMINATE	1	TRUE	NA	0.268453647406634	2		643	630	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0020998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	91	916	3	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.33182996995081	2		919	511	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219939	36219939	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	69	811	0	ENST00000222270.7:c.4741T>C	p.Cys1581Arg	p.C1581R	ENST00000222270	NM_014727.1	1581	Tgt/Cgt	21/37	1	2	FACETS	0.607	0.528	0.692	0.607	0.528	0.692	SUBCLONAL	1	TRUE	1	0.33182996995081	2		811	685	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871306	35871306	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs149833809	NA	P-0020998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	24	443	0	ENST00000303115.3:c.528C>A	p.Asn176Lys	p.N176K	ENST00000303115	NM_002185.3	176	aaC/aaA	4/8	1	2	FACETS	0.552	0.434	0.688	0.552	0.434	0.688	SUBCLONAL	1	TRUE	1	0.33182996995081	2		443	262	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882025	NA	P-0020998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	196	704	0	ENST00000269305.4:c.646G>T	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ttg	6/11	0.245413686676972	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.25	2		704	735	SUCCESS
AR	367	MSKCC	GRCh37	X	66765851	66765851	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	227	831	0	ENST00000374690.3:c.863C>A	p.Ala288Asp	p.A288D	ENST00000374690	NM_000044.3	288	gCc/gAc	1/8	0.0928220443093892	4	FACETS	1	0.967	1	1	0.967	1	INDETERMINATE	2	TRUE	2	0.25	4		831	1069	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72833967	72833967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	151	584	0	ENST00000268489.5:c.3926G>A	p.Arg1309Gln	p.R1309Q	ENST00000268489	NM_006885.3	1309	cGa/cAa	8/10	0.233423359334607	4	FACETS	0.978	0.895	1	0.978	0.895	1	CLONAL	2	TRUE	2	0.25	4		584	772	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163772	72163772	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	125	694	1	ENST00000357731.5:c.586G>T	p.Asp196Tyr	p.D196Y	ENST00000357731	NM_173808.2	196	Gac/Tac	4/7	0.150350643782126	4	FACETS	0.857	0.777	0.942	0.857	0.777	0.942	CLONAL	2	TRUE	2	0.25	4		695	729	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459310	120459310	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	77	498	0	ENST00000256646.2:c.6035C>A	p.Thr2012Lys	p.T2012K	ENST00000256646	NM_024408.3	2012	aCa/aAa	34/34	0.150350643782126	4	FACETS	1	0.975	1	0.739	0.65	0.834	CLONAL	1	TRUE	2	0.25	4		498	521	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421617	49421617	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	194	716	0	ENST00000301067.7:c.14612G>T	p.Ser4871Ile	p.S4871I	ENST00000301067	NM_003482.3	4871	aGc/aTc	47/54	0.18380579604821	4	FACETS	0.979	0.906	1	0.979	0.906	1	CLONAL	2	TRUE	2	0.25	4		716	991	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2097811	2097833	+	frameshift_variant	Frame_Shift_Del	DEL	CTCAAGGCGGTCATGCCGGACTC	CTCAAGGCGGTCATGCCGGACTC	-	novel	NA	P-0020998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	64	622	0	ENST00000219066.1:c.16_38del	p.Glu6ArgfsTer20	p.E6Rfs*20	ENST00000219066	NM_002528.5	6	GAGTCCGGCATGACCGCCTTGAGc/c	1/6	0.18380579604821	4	FACETS	0.726	0.627	0.833	0.363	0.313	0.417	SUBCLONAL	1	TRUE	2	0.25	4		622	882	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41209097	41209097	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	49	806	0	ENST00000357654.3:c.5249A>C	p.Lys1750Thr	p.K1750T	ENST00000357654	NM_007294.3	1750	aAg/aCg	19/23	0.245413686676972	2	FACETS	0.483	0.408	0.566	0.241	0.204	0.283	SUBCLONAL	1	TRUE	0	0.25	2		806	812	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972074	55972074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	148	534	0	ENST00000263923.4:c.1570G>A	p.Val524Met	p.V524M	ENST00000263923	NM_002253.2	524	Gtg/Atg	12/30	0.150350643782126	4	FACETS	0.944	0.863	1	0.944	0.863	1	CLONAL	2	TRUE	2	0.25	4		534	784	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631338	117631338	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	135	598	0	ENST00000368508.3:c.6340T>A	p.Tyr2114Asn	p.Y2114N	ENST00000368508	NM_002944.2	2114	Tac/Aac	40/43	0.145012802888424	3	FACETS	0.92	0.839	1			1	INDETERMINATE	2	TRUE	NA	0.25	3		598	660	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878539	151878539	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	377	715	0	ENST00000262189.6:c.6406G>T	p.Gly2136Ter	p.G2136*	ENST00000262189	NM_170606.2	2136	Gga/Tga	36/59	0.3	5	FACETS	0.931	0.885	0.977			1	CLONAL	4	TRUE	NA	0.25	5		715	1114	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0021001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	127	662	1				ENST00000310581	NM_198253.2	-/1132			0.348308370544722	0	FACETS	0.591	0.542	0.641			1	SUBCLONAL	2	FALSE	0	0.384347663368413	0		663	344	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610285	10610285	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	334	834	2	ENST00000171111.5:c.425C>T	p.Thr142Met	p.T142M	ENST00000171111	NM_203500.1	142	aCg/aTg	2/6	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	2	FALSE	NA	0.384347663368413	2		836	839	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430573	78430580	+	frameshift_variant	Frame_Shift_Del	DEL	TCCTGTAA	TCCTGTAA	-	novel	NA	P-0021001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	224	548	0	ENST00000370768.2:c.710_717del	p.Ile237ArgfsTer4	p.I237Rfs*4	ENST00000370768	NM_003902.3	237	aTTACAGGA/a	9/20	0.302568642975255	3	FACETS	0.973	0.91	1	0.973	0.91	1	CLONAL	2	FALSE	1	0.384347663368413	3		548	714	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602390	10602390	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	195	870	1	ENST00000171111.5:c.1188C>A	p.Tyr396Ter	p.Y396*	ENST00000171111	NM_203500.1	396	taC/taA	3/6	NA	2	FACETS	0.829	0.772	0.888			1	INDETERMINATE	2	FALSE	NA	0.384347663368413	2		871	612	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858384	27858384	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	246	628	0	ENST00000359303.2:c.187A>C	p.Ile63Leu	p.I63L	ENST00000359303	NM_003535.2	63	Atc/Ctc	1/1	0.386345266426825	4	FACETS	0.866	0.814	0.919			1	CLONAL	3	FALSE	NA	0.384347663368413	4		628	682	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0021002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	189	1047	2	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	0.335708605324605	2		1049	1033	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0021002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	233	695	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.335708605324605	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.335708605324605	1		695	894	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482874	67482874	+	stop_lost	Nonstop_Mutation	SNP	G	G	T	novel	NA	P-0021002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	198	410	0	ENST00000327367.4:c.1278G>T	p.Ter426TyrextTer6	p.*426Yext*6	ENST00000327367	NM_005902.3	426	taG/taT	9/9	0.263022215819452	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	0	0.335708605324605	2		410	585	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811753	102811753	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369105057	NA	P-0021002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	182	745	1	ENST00000307046.8:c.431C>T	p.Thr144Met	p.T144M	ENST00000307046	NM_001111285.1	144	aCg/aTg	4/4	0.274986432954166	1	FACETS	0.99	0.914	1	0.99	0.914	1	CLONAL	1	TRUE	0	0.335708605324605	1		746	911	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502183	157502183	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	72	482	0	ENST00000346085.5:c.3216G>T	p.Trp1072Cys	p.W1072C	ENST00000346085	NM_020732.3	1072	tgG/tgT	12/20	0.222256852253775	1	FACETS	0.489	0.427	0.556	0.489	0.427	0.556	SUBCLONAL	1	TRUE	0	0.335708605324605	1		482	730	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971177	21971178	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0021002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	372	523	2	ENST00000304494.5:c.180_181delinsTT	p.Glu61Ter	p.E61*	ENST00000304494	NM_000077.4	60	gcGGag/gcTTag	2/3	0.335708605324605	2	FACETS	0.886	0.845	0.927	1	0.995	1	CLONAL	3	TRUE	0	0.335708605324605	2		525	834	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120881	115120881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	28	457	0	ENST00000257566.3:c.125C>T	p.Pro42Leu	p.P42L	ENST00000257566	NM_016569.3	42	cCc/cTc	1/8	0.274986432954166	1	FACETS	0.26	0.207	0.321	0.26	0.207	0.321	SUBCLONAL	1	TRUE	0	0.335708605324605	1		457	533	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0021003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	5262	782	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.669601820861047	23	FACETS	0.979	0.973	0.984			1	CLONAL	22	TRUE	NA	0.669601820861047	23		782	5862	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0021003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	634	822	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.669601820861047	2		822	923	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916766	48916766	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	269	668	0	ENST00000267163.4:c.299del	p.Gly100GlufsTer11	p.G100Efs*11	ENST00000267163	NM_000321.2	99	tGg/tg	3/27	0.669601820861047	2	FACETS	0.959	0.917	1	0.959	0.917	1	CLONAL	2	TRUE	0	0.669601820861047	2		668	419	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346352	73346352	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	257	581	1	ENST00000377767.4:c.1448G>T	p.Cys483Phe	p.C483F	ENST00000377767	NM_014953.3	483	tGt/tTt	10/21	0.545698003416434	4	FACETS	0.951	0.896	1	0.951	0.896	1	CLONAL	2	TRUE	2	0.669601820861047	4		582	674	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075190	16075190	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	394	491	1	ENST00000268712.3:c.362G>T	p.Arg121Leu	p.R121L	ENST00000268712	NM_006311.3	121	cGt/cTt	4/46	0.623420998227235	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.669601820861047	3		492	778	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350082	81350082	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	289	524	0	ENST00000222390.5:c.1250A>G	p.Lys417Arg	p.K417R	ENST00000222390	NM_000601.4	417	aAg/aGg	10/18	0.545698003416434	4	FACETS	0.983	0.93	1	0.983	0.93	1	CLONAL	2	TRUE	2	0.669601820861047	4		524	733	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780071	NA	P-0021004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	287	799	2	ENST00000269305.4:c.580C>T	p.Leu194Phe	p.L194F	ENST00000269305	NM_001126112.2	194	Ctt/Ttt	6/11	0.560839129792435	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.624150580931097	2		801	444	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416417	49416417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565753611	NA	P-0021004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	265	731	1	ENST00000301067.7:c.16294C>T	p.Arg5432Trp	p.R5432W	ENST00000301067	NM_003482.3	5432	Cgg/Tgg	51/54	0.492337349347681	5	FACETS	1	0.971	1	0.701	0.66	0.743	CLONAL	2	TRUE	2	0.624150580931097	5		732	782	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544125	18544125	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	127	581	0	ENST00000266497.5:c.1942G>C	p.Glu648Gln	p.E648Q	ENST00000266497		648	Gag/Cag	13/31	0.205640271888546	5	FACETS	0.802	0.731	0.876	0.535	0.487	0.584	INDETERMINATE	2	TRUE	2	0.624150580931097	5		581	491	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416115	49416115	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs267607239	NA	P-0021004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	212	539	1	ENST00000301067.7:c.16360C>T	p.Arg5454Ter	p.R5454*	ENST00000301067	NM_003482.3	5454	Cga/Tga	52/54	0.492337349347681	5	FACETS	0.99	0.925	1	0.66	0.616	0.705	CLONAL	2	TRUE	2	0.624150580931097	5		540	664	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240334	41240334	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	185	565	0	ENST00000379561.5:c.16C>T	p.Gln6Ter	p.Q6*	ENST00000379561	NM_002015.3	6	Cag/Tag	1/3	0.508263886133502	3	FACETS	1	0.983	1	0.754	0.709	0.798	CLONAL	2	TRUE	0	0.624150580931097	3		565	344	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209526	98209547	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCCCTATTGCTAGGGCCAGA	GGGCCCTATTGCTAGGGCCAGA	-	novel	NA	P-0021004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	18	639	0	ENST00000331920.6:c.3991_4012del	p.Ser1331AlafsTer34	p.S1331Afs*34	ENST00000331920	NM_000264.3	1331	TCTGGCCCTAGCAATAGGGCCCgc/gc	23/24	0.576433745653492	2	FACETS	0.198	0.149	0.256	0.099	0.074	0.128	SUBCLONAL	1	TRUE	0	0.624150580931097	2		639	291	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0021005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	227	662	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.521520242910711	2		663	828	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0021005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	247	842	1	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	1	2	FACETS	0.976	0.913	1	0.976	0.913	1	CLONAL	1	TRUE	1	0.521520242910711	2		843	971	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0021005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	146	546	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.832	0.761	0.906	0.832	0.761	0.906	CLONAL	1	TRUE	1	0.521520242910711	2		546	673	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833925	44833925	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	171	717	0	ENST00000377967.4:c.349C>T	p.Gln117Ter	p.Q117*	ENST00000377967	NM_021140.2	117	Cag/Tag	4/29	0.521520242910711	1	FACETS	0.949	0.879	1	0.949	0.879	1	CLONAL	1	TRUE	0	0.521520242910711	1		717	511	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044473	5044473	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	200	788	0	ENST00000381652.3:c.421G>A	p.Glu141Lys	p.E141K	ENST00000381652	NM_004972.3	141	Gaa/Aaa	5/25	0.521520242910711	1	FACETS	0.928	0.865	0.993	0.928	0.865	0.993	CLONAL	1	TRUE	0	0.521520242910711	1		788	611	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092990	27092999	+	frameshift_variant	Frame_Shift_Del	DEL	AGTTAACTCC	AGTTAACTCC	-	novel	NA	P-0021005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	123	504	0	ENST00000324856.7:c.2923_2932del	p.Leu975ProfsTer4	p.L975Pfs*4	ENST00000324856	NM_006015.4	974	aAGTTAACTCCa/aa	10/20	1	2	FACETS	0.877	0.796	0.961	0.877	0.796	0.961	CLONAL	1	TRUE	1	0.521520242910711	2		504	538	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2224282	2224282	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	281	1004	0	ENST00000326181.6:c.1294C>G	p.Gln432Glu	p.Q432E	ENST00000326181	NM_032271.2	432	Cag/Gag	14/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.521520242910711	2		1004	1001	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523655	41523656	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	240	882	0	ENST00000263253.7:c.1073dup	p.Asn358LysfsTer53	p.N358Kfs*53	ENST00000263253	NM_001429.3	357	-/A	4/31	1	2	FACETS	0.961	0.898	1	0.961	0.898	1	CLONAL	1	TRUE	1	0.521520242910711	2		882	958	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778095	27778095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	242	818	0	ENST00000369163.2:c.244G>A	p.Asp82Asn	p.D82N	ENST00000369163	NM_003536.2	82	Gac/Aac	1/1	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.521520242910711	2		818	890	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	164	669	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.84033619859099	2		669	351	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0021006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	572	546	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.84033619859099	5	FACETS	0.959	0.933	0.985			1	CLONAL	4	TRUE	NA	0.84033619859099	5		546	802	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553582	29553582	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	39	265	0	ENST00000356175.3:c.2131C>A	p.Arg711Ser	p.R711S	ENST00000356175	NM_000267.3	711	Cgc/Agc	18/57	1	2	FACETS	0.619	0.522	0.723	0.619	0.522	0.723	SUBCLONAL	1	TRUE	1	0.84033619859099	2		265	150	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096052	178096052	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	141	417	0	ENST00000397062.3:c.1279G>C	p.Glu427Gln	p.E427Q	ENST00000397062	NM_006164.4	427	Gag/Cag	5/5	1	2	FACETS	0.996	0.921	1	0.996	0.921	1	CLONAL	1	TRUE	1	0.84033619859099	2		417	337	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923055	44923055	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	209	593	0	ENST00000377967.4:c.1917del	p.Thr640LeufsTer51	p.T640Lfs*51	ENST00000377967	NM_021140.2	639	tCc/tc	16/29	0.84033619859099	1	FACETS	0.991	0.947	1	0.991	0.947	1	CLONAL	1	TRUE	0	0.84033619859099	1		593	291	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0021018-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	268	795	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.332660064720116	2	FACETS	0.964	0.907	1	0.964	0.907	1	CLONAL	2	TRUE	0	0.332771726137082	2		796	835	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984024	2984024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021018-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	243	225	3	ENST00000396946.4:c.506C>T	p.Thr169Met	p.T169M	ENST00000396946	NM_032415.4	169	aCg/aTg	5/25	0.222433405769453	5	FACETS	1	0.987	1	0.807	0.755	0.861	CLONAL	2	TRUE	2	0.332771726137082	5		228	904	SUCCESS
APC	324	MSKCC	GRCh37	5	112175232	112175232	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021018-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	69	172	0	ENST00000257430.4:c.3942del	p.Arg1314SerfsTer7	p.R1314Sfs*7	ENST00000257430	NM_000038.5	1314	aGg/ag	16/16	0.332771726137082	2	FACETS	0.917	0.811	1	0.917	0.811	1	CLONAL	2	TRUE	0	0.332771726137082	2		172	226	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18762491	18762491	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021018-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	37	286	0	ENST00000266497.5:c.3987G>T	p.Lys1329Asn	p.K1329N	ENST00000266497		1329	aaG/aaT	29/31	0.332771726137082	3	FACETS	0.754	0.623	0.9	0.377	0.311	0.45	SUBCLONAL	1	TRUE	1	0.332771726137082	3		286	344	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675070	40675070	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021018-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	56	314	0	ENST00000249776.8:c.34G>T	p.Val12Phe	p.V12F	ENST00000249776	NM_033286.3	12	Gtt/Ttt	1/9	0.19858218393559	3	FACETS	0.431	0.368	0.5	0.144	0.122	0.167	INDETERMINATE	1	TRUE	0	0.332771726137082	3		314	911	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0021022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	260	733	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.26275879408233	3	FACETS	0.86	0.809	0.912	0.86	0.809	0.912	CLONAL	3	TRUE	0	0.301082830846554	3		733	770	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566250	95566250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780488568	NA	P-0021022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	95	554	0	ENST00000393063.1:c.4073G>A	p.Arg1358His	p.R1358H	ENST00000393063	NM_030621.3	1358	cGc/cAc	23/28	0.259312974925362	4	FACETS	1	0.968	1	0.617	0.55	0.689	CLONAL	1	TRUE	2	0.301082830846554	4		554	665	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220370	1220370	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0021022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	212	733	1	ENST00000326873.7:c.465-2A>T		p.X155_splice	ENST00000326873	NM_000455.4	155			0.26275879408233	3	FACETS	0.928	0.868	0.989	0.928	0.868	0.989	CLONAL	3	TRUE	0	0.301082830846554	3		734	582	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106434	108106434	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0021022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	78	289	0	ENST00000278616.4:c.369T>G	p.Tyr123Ter	p.Y123*	ENST00000278616	NM_000051.3	123	taT/taG	5/63	0.301082830846554	2	FACETS	0.878	0.78	0.981	0.878	0.78	0.981	CLONAL	2	TRUE	0	0.301082830846554	2		289	295	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913987	32913987	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs138489917	NA	P-0021022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	49	543	0	ENST00000380152.3:c.5495C>G	p.Ser1832Cys	p.S1832C	ENST00000380152		1832	tCt/tGt	11/27	0.301082830846554	3	FACETS	0.57	0.482	0.667	0.285	0.241	0.334	SUBCLONAL	1	TRUE	1	0.301082830846554	3		543	657	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573992	7573992	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	281	817	0	ENST00000269305.4:c.1035del	p.Asn345LysfsTer25	p.N345Kfs*25	ENST00000269305	NM_001126112.2	345	aaT/aa	10/11	0.125484560209256	3	FACETS	0.888	0.838	0.939			1	INDETERMINATE	3	TRUE	NA	0.301082830846554	3		817	806	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058724	47058727	+	frameshift_variant	Frame_Shift_Del	DEL	ATTC	ATTC	-	novel	NA	P-0021022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	95	572	0	ENST00000409792.3:c.7551_7554del	p.Met2517IlefsTer4	p.M2517Ifs*4	ENST00000409792	NM_014159.6	2517	atGAAT/at	21/21	0.133057625396368	3	FACETS	1	0.969	1	0.622	0.554	0.693	INDETERMINATE	1	TRUE	1	0.301082830846554	3		572	584	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963978	2963978	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1273116310	NA	P-0021022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	327	753	0	ENST00000396946.4:c.1829C>A	p.Ser610Tyr	p.S610Y	ENST00000396946	NM_032415.4	610	tCc/tAc	15/25	0.301082830846554	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	1	0.301082830846554	4		753	914	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041002	47041002	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0021022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	234	775	0	ENST00000377604.3:c.1532C>G	p.Ser511Ter	p.S511*	ENST00000377604	NM_001204468.1	511	tCa/tGa	14/24	0.294963016542217	3	FACETS	1	0.985	1			1	CLONAL	2	TRUE	NA	0.301082830846554	3		775	764	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275290	142275293	+	protein_altering_variant	In_Frame_Del	DEL	ACAA	ACAA	T	novel	NA	P-0021022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	168	649	0	ENST00000350721.4:c.2010_2013delinsA	p.Ser670_Cys671delinsArg	p.S670_C671delinsR	ENST00000350721	NM_001184.3	670	agTTGT/agA	9/47	0.301082830846554	3	FACETS	0.816	0.751	0.883	0.816	0.751	0.883	CLONAL	2	TRUE	1	0.301082830846554	3		649	787	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs17849781	NA	P-0021033-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	487	916	0	ENST00000269305.4:c.832C>A	p.Pro278Thr	p.P278T	ENST00000269305	NM_001126112.2	278	Cct/Act	8/11	0.818081428606177	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.839722179275575	2		916	576	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0021033-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	154	767	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.776408744992333	3	FACETS	1	0.934	1	0.508	0.467	0.549	CLONAL	1	TRUE	1	0.839722179275575	3		767	513	SUCCESS
APC	324	MSKCC	GRCh37	5	112174885	112174886	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs864622106	NA	P-0021033-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	205	490	0	ENST00000257430.4:c.3595_3596del	p.Lys1199GlufsTer8	p.K1199Efs*8	ENST00000257430	NM_000038.5	1198	tcAAag/tcag	16/16	0.776408744992333	3	FACETS	0.873	0.823	0.923	0.873	0.823	0.923	CLONAL	2	TRUE	1	0.839722179275575	3		490	397	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995569	68995569	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021033-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	226	893	1	ENST00000288368.4:c.1973C>A	p.Ser658Ter	p.S658*	ENST00000288368	NM_024870.2	658	tCg/tAg	18/40	0.776408744992333	3	FACETS	0.986	0.922	1	0.493	0.461	0.526	CLONAL	1	TRUE	1	0.839722179275575	3		894	775	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10305575	10305575	+	start_lost	Translation_Start_Site	SNP	T	T	A	novel	NA	P-0021033-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	28	737	0	ENST00000340748.4:c.1A>T	p.Met1?	p.M1?	ENST00000340748		1	Atg/Ttg	1/40	0.836991648957634	4	FACETS	0.23	0.183	0.283	0.077	0.061	0.095	SUBCLONAL	1	TRUE	1	0.839722179275575	4		737	534	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0021060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	80	710	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.301431720819402	4	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	FALSE	2	0.301431720819402	4		711	316	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870854	12870854	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	14	288	0	ENST00000228872.4:c.82del	p.Ala28ProfsTer14	p.A28Pfs*14	ENST00000228872	NM_004064.3	27	tcG/tc	1/3	1	2	FACETS	0.615	0.447	0.816	0.615	0.447	0.816	SUBCLONAL	1	FALSE	1	0.301431720819402	2		288	151	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943725	9943725	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	37	781	0	ENST00000330684.3:c.1216C>T	p.Leu406Phe	p.L406F	ENST00000330684	NM_001134407.1	406	Ctc/Ttc	5/13	0.17959175778259	5	FACETS	0.812	0.67	0.971	0.271	0.223	0.324	INDETERMINATE	1	FALSE	2	0.301431720819402	5		781	439	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574032	7574032	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	81	785	0	ENST00000269305.4:c.995T>A	p.Ile332Asn	p.I332N	ENST00000269305	NM_001126112.2	332	aTc/aAc	10/11	0.226589920287034	3	FACETS	0.795	0.705	0.891			1	SUBCLONAL	2	FALSE	NA	0.301431720819402	3		785	389	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949162	151949162	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	77	730	1	ENST00000262189.6:c.1483G>T	p.Glu495Ter	p.E495*	ENST00000262189	NM_170606.2	495	Gag/Tag	11/59	0.301431720819402	4	FACETS	0.884	0.781	0.994	0.884	0.781	0.994	CLONAL	2	FALSE	2	0.301431720819402	4		731	376	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419840	41419840	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	34	571	1	ENST00000373198.4:c.481T>C	p.Tyr161His	p.Y161H	ENST00000373198	NM_133170.3	161	Tat/Cat	3/32	0.342085844646503	2	FACETS	0.351	0.286	0.425	0.176	0.143	0.213	SUBCLONAL	1	TRUE	0	0.342085844646503	2		572	566	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876269	35876269	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	161	719	0	ENST00000303115.3:c.1061T>C	p.Val354Ala	p.V354A	ENST00000303115	NM_002185.3	354	gTa/gCa	8/8	0.342085844646503	3	FACETS	1	0.987	1	0.711	0.653	0.772	CLONAL	1	TRUE	1	0.342085844646503	3		719	775	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938161	76938161	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	123	529	0	ENST00000373344.5:c.2587C>T	p.Gln863Ter	p.Q863*	ENST00000373344	NM_000489.3	863	Caa/Taa	9/35	1	1	FACETS	0.852	0.779	0.926	1	0.989	1	CLONAL	2	TRUE	0	0.342085844646503	1		529	350	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0021062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	47	857	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.12	2		857	748	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0021062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	35	736	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	1	2	FACETS	0.971	0.794	1	0.971	0.794	1	CLONAL	1	TRUE	1	0.12	2		736	601	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40865275	40865277	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0021062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	42	862	0	ENST00000428826.2:c.1154_1156del	p.Glu385del	p.E385del	ENST00000428826		385	gAAGga/gga	11/21	1	2	FACETS	0.87	0.724	1	0.87	0.724	1	CLONAL	1	TRUE	1	0.12	2		862	805	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	224	690	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	1	2	FACETS	0.984	0.925	1	0.984	0.925	1	CLONAL	1	TRUE	1	0.831939527871595	2		690	547	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0021064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	192	563	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.825884260180114	6	FACETS	0.801	0.742	0.861	0.4	0.371	0.431	CLONAL	2	TRUE	2	0.831939527871595	6		563	768	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050415	176050415	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	58	349	0	ENST00000367669.3:c.1150C>G	p.Arg384Gly	p.R384G	ENST00000367669	NM_022457.5	384	Cga/Gga	11/20	0.395928977074602	3	FACETS	0.433	0.373	0.499	0.144	0.124	0.167	INDETERMINATE	1	TRUE	0	0.831939527871595	3		349	456	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175540	108175540	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	93	559	0	ENST00000278616.4:c.5635C>G	p.Gln1879Glu	p.Q1879E	ENST00000278616	NM_000051.3	1879	Caa/Gaa	37/63	1	2	FACETS	0.343	0.305	0.384	0.343	0.305	0.384	SUBCLONAL	1	TRUE	1	0.831939527871595	2		559	651	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376372	118376372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	93	726	1	ENST00000534358.1:c.9765G>A	p.Met3255Ile	p.M3255I	ENST00000534358	NM_005933.3	3255	atG/atA	27/36	1	2	FACETS	0.378	0.337	0.422	0.378	0.337	0.422	SUBCLONAL	1	TRUE	1	0.831939527871595	2		727	591	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003111	42003111	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	665	718	0	ENST00000219905.7:c.2648C>G	p.Ser883Cys	p.S883C	ENST00000219905	NM_001164273.1	883	tCt/tGt	8/24	NA	2	FACETS	0.949	0.929	0.969			1	INDETERMINATE	2	TRUE	NA	0.831939527871595	2		718	842	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	rs786202799	NA	P-0021064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	364	723	0	ENST00000269305.4:c.376-2A>C		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.782272071965324	1	FACETS	0.928	0.893	0.961	0.928	0.893	0.961	CLONAL	1	TRUE	0	0.831939527871595	1		723	551	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024584	11024584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757525257	NA	P-0021064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	80	653	2	ENST00000327064.4:c.701G>A	p.Arg234His	p.R234H	ENST00000327064	NM_199141.1	234	cGc/cAc	6/16	0.832734023857458	3	FACETS	0.344	0.302	0.389			1	SUBCLONAL	1	TRUE	NA	0.831939527871595	3		655	791	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607799	46607799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371608362	NA	P-0021064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	465	748	0	ENST00000263734.3:c.1988G>A	p.Gly663Glu	p.G663E	ENST00000263734	NM_001430.4	663	gGa/gAa	12/16	0.40439155302419	4	FACETS	1	0.982	1	1	0.982	1	INDETERMINATE	2	TRUE	2	0.831939527871595	4		748	985	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0021066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	123	487	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	0.421372106003764	2	FACETS	0.783	0.717	0.85	0.783	0.717	0.85	SUBCLONAL	2	TRUE	0	0.466345540965579	2		487	337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0021066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	253	899	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.421372106003764	2	FACETS	0.892	0.842	0.944	0.892	0.842	0.944	CLONAL	2	TRUE	0	0.466345540965579	2		900	608	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904887	101904888	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	181	626	0	ENST00000374994.4:c.878dup	p.Asn293LysfsTer40	p.N293Kfs*40	ENST00000374994	NM_004612.2	292	tta/ttAa	5/9	0.421372106003764	2	FACETS	0.763	0.709	0.817	0.763	0.709	0.817	SUBCLONAL	2	TRUE	0	0.466345540965579	2		626	509	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803470	1803470	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	186	865	0	ENST00000260795.2:c.739G>C	p.Glu247Gln	p.E247Q	ENST00000260795		247	Gag/Cag	5/17	0.421372106003764	2	FACETS	0.777	0.724	0.832	0.777	0.724	0.832	SUBCLONAL	2	TRUE	0	0.466345540965579	2		865	513	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044713	47044713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs887995752	NA	P-0021066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	239	486	2	ENST00000377604.3:c.2113G>A	p.Glu705Lys	p.E705K	ENST00000377604	NM_001204468.1	705	Gag/Aag	19/24	0.367849086442477	2	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.466345540965579	2		488	420	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0021067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	38	107	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.785341191362448	2		107	92	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740546	58740546	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs766524048	NA	P-0021067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	350	864	0	ENST00000305921.3:c.1451T>G	p.Leu484Ter	p.L484*	ENST00000305921	NM_003620.3	484	tTa/tGa	6/6	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.785341191362448	2		864	840	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891456	76891456	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	363	473	1	ENST00000373344.5:c.4649T>A	p.Val1550Glu	p.V1550E	ENST00000373344	NM_000489.3	1550	gTg/gAg	16/35	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.785341191362448	1		474	423	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	110	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.3	5	FACETS	1	0.915	1	0.407	0.366	0.449	CLONAL	2	TRUE	0	0.27	5		434	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0021069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	85	658	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.258546631741504	1	FACETS	0.906	0.802	1	0.906	0.802	1	CLONAL	1	TRUE	0	0.27	1		658	601	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933400	39933400	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	53	558	0	ENST00000378444.4:c.1199del	p.Gly400AlafsTer42	p.G400Afs*42	ENST00000378444	NM_001123385.1	400	gGc/gc	4/15	1	2	FACETS	0.627	0.534	0.729	0.627	0.534	0.729	SUBCLONAL	1	TRUE	1	0.27	2		558	626	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56857716	56857716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370111038	NA	P-0021069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	42	585	0	ENST00000308159.5:c.752G>A	p.Arg251His	p.R251H	ENST00000308159	NM_014669.4	251	cGc/cAc	8/22	1	2	FACETS	0.526	0.439	0.624	0.526	0.439	0.624	SUBCLONAL	1	TRUE	1	0.27	2		585	591	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719463	190719463	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	22	331	0	ENST00000441310.2:c.1465A>T	p.Asn489Tyr	p.N489Y	ENST00000441310	NM_000534.4	489	Aac/Tac	9/13	0.193480983454643	3	FACETS	0.638	0.495	0.804	0.319	0.247	0.402	SUBCLONAL	1	TRUE	1	0.27	3		331	290	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419977	41419977	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	60	532	0	ENST00000373198.4:c.344C>A	p.Ser115Tyr	p.S115Y	ENST00000373198	NM_133170.3	115	tCc/tAc	3/32	1	2	FACETS	0.88	0.759	1	0.88	0.759	1	CLONAL	1	TRUE	1	0.27	2		532	505	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164883	47164883	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	28	316	0	ENST00000409792.3:c.1243A>G	p.Thr415Ala	p.T415A	ENST00000409792	NM_014159.6	415	Act/Gct	3/21	0.3	1	FACETS	0.682	0.547	0.835	0.682	0.547	0.835	SUBCLONAL	1	TRUE	0	0.27	1		316	263	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971153	21971153	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	61	524	0	ENST00000304494.5:c.205del	p.Glu69SerfsTer77	p.E69Sfs*77	ENST00000304494	NM_000077.4	69	Gag/ag	2/3	0.3	1	FACETS	0.985	0.853	1	0.985	0.853	1	CLONAL	1	TRUE	0	0.27	1		524	397	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652222	48652222	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	72	594	0	ENST00000376670.3:c.893G>T	p.Arg298Leu	p.R298L	ENST00000376670	NM_002049.3	298	cGg/cTg	6/6	1	2	FACETS	0.895	0.782	1	0.895	0.782	1	CLONAL	1	TRUE	1	0.27	2		594	596	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357421	70357421	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	72	769	0	ENST00000374080.3:c.5762T>A	p.Met1921Lys	p.M1921K	ENST00000374080		1921	aTg/aAg	40/45	1	2	FACETS	0.764	0.667	0.869	0.764	0.667	0.869	SUBCLONAL	1	TRUE	1	0.27	2		769	698	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0021073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	263	534	1	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.651855976626398	3	FACETS	0.974	0.923	1	0.974	0.923	1	CLONAL	2	TRUE	1	0.651855976626398	3		535	549	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0021073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	279	1047	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.337285495215468	2	FACETS	1	0.994	1	0.713	0.676	0.751	INDETERMINATE	1	TRUE	0	0.651855976626398	2		1049	600	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0021073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	155	713	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.651855976626398	3	FACETS	0.987	0.907	1	0.493	0.453	0.535	CLONAL	1	TRUE	1	0.651855976626398	3		714	639	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775128	73775128	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	201	766	1	ENST00000254810.4:c.128G>A	p.Arg43Lys	p.R43K	ENST00000254810	NM_005324.3	43	aGg/aAg	2/4	1	2	FACETS	0.831	0.773	0.891	0.831	0.773	0.891	CLONAL	1	TRUE	1	0.651855976626398	2		767	742	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797817	32797817	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1283438032	NA	P-0021073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	236	869	0	ENST00000374899.4:c.1685del	p.Asn562ThrfsTer15	p.N562Tfs*15	ENST00000374899	NM_018833.2	562	aAc/ac	10/12	1	2	FACETS	0.978	0.917	1	0.978	0.917	1	CLONAL	1	TRUE	1	0.651855976626398	2		869	740	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	291	669	0				ENST00000310581	NM_198253.2	-/1132			0.605104995730293	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.605104995730293	3		669	583	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	179	666	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.954	0.884	1	0.954	0.884	1	CLONAL	1	TRUE	1	0.605104995730293	2		667	620	SUCCESS
APC	324	MSKCC	GRCh37	5	112175876	112175876	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085992	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	99	318	0	ENST00000257430.4:c.4585C>T	p.Gln1529Ter	p.Q1529*	ENST00000257430	NM_000038.5	1529	Cag/Tag	16/16	0.605104995730293	1	FACETS	0.992	0.904	1	0.992	0.904	1	CLONAL	1	TRUE	0	0.605104995730293	1		318	230	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28901639	28901639	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	215	741	0	ENST00000282397.4:c.2756A>G	p.Asn919Ser	p.N919S	ENST00000282397	NM_002019.4	919	aAc/aGc	20/30	1	2	FACETS	0.889	0.829	0.952	0.889	0.829	0.952	CLONAL	1	TRUE	1	0.605104995730293	2		741	799	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456447	189456447	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	137	538	1	ENST00000264731.3:c.208C>T	p.Gln70Ter	p.Q70*	ENST00000264731	NM_003722.4	70	Cag/Tag	3/14	0.605104995730293	3	FACETS	0.869	0.792	0.949	0.434	0.396	0.475	CLONAL	1	TRUE	1	0.605104995730293	3		539	679	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272140	15272140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	217	702	2	ENST00000263388.2:c.6299C>T	p.Ser2100Leu	p.S2100L	ENST00000263388	NM_000435.2	2100	tCg/tTg	33/33	1	2	FACETS	0.971	0.906	1	0.971	0.906	1	CLONAL	1	TRUE	1	0.605104995730293	2		704	739	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	247	664	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.605104995730293	3	FACETS	0.812	0.764	0.861	0.812	0.764	0.861	CLONAL	2	TRUE	1	0.605104995730293	3		664	655	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871053	12871053	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	132	421	1	ENST00000228872.4:c.285del	p.Gly97ValfsTer22	p.G97Vfs*22	ENST00000228872	NM_004064.3	94	Ccc/cc	1/3	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.605104995730293	2		422	425	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453185	140453185	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	101	495	1	ENST00000288602.6:c.1750C>T	p.Leu584Phe	p.L584F	ENST00000288602	NM_004333.4	584	Ctt/Ttt	15/18	0.605104995730293	3	FACETS	0.849	0.762	0.941	0.425	0.381	0.471	CLONAL	1	TRUE	1	0.605104995730293	3		496	512	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678351	88678351	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	234	828	1	ENST00000360948.2:c.1185C>A	p.Phe395Leu	p.F395L	ENST00000360948	NM_001012338.2	395	ttC/ttA	9/19	0.605104995730293	3	FACETS	0.999	0.933	1	0.5	0.466	0.534	CLONAL	1	TRUE	1	0.605104995730293	3		829	1008	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169586	27169586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	270	970	0	ENST00000380036.4:c.587G>A	p.Gly196Glu	p.G196E	ENST00000380036	NM_000459.3	196	gGa/gAa	4/23	0.605104995730293	1	FACETS	0.965	0.912	1	0.965	0.912	1	CLONAL	1	TRUE	0	0.605104995730293	1		970	645	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940079	31940079	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	451	796	0	ENST00000375333.2:c.221G>A	p.Gly74Glu	p.G74E	ENST00000375333	NM_032454.1	74	gGa/gAa	2/8	0.605104995730293	3	FACETS	0.933	0.893	0.972	0.933	0.893	0.972	CLONAL	2	TRUE	1	0.605104995730293	3		796	1041	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747138	40747138	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	207	706	1	ENST00000373198.4:c.2944C>T	p.Pro982Ser	p.P982S	ENST00000373198	NM_133170.3	982	Ccg/Tcg	22/32	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.605104995730293	2		707	627	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073905	8073905	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	163	555	0	ENST00000377482.5:c.754G>A	p.Gly252Arg	p.G252R	ENST00000377482	NM_018948.3	252	Gga/Aga	4/4	1	2	FACETS	0.987	0.911	1	0.987	0.911	1	CLONAL	1	TRUE	1	0.605104995730293	2		555	546	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599252	28599252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	260	815	2	ENST00000253063.3:c.698C>T	p.Pro233Leu	p.P233L	ENST00000253063	NM_031459.4	233	cCc/cTc	5/10	1	2	FACETS	0.962	0.903	1	0.962	0.903	1	CLONAL	1	TRUE	1	0.605104995730293	2		817	893	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28600656	28600656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	206	806	0	ENST00000253063.3:c.1007C>T	p.Thr336Ile	p.T336I	ENST00000253063	NM_031459.4	336	aCc/aTc	7/10	1	2	FACETS	0.871	0.81	0.933	0.871	0.81	0.933	CLONAL	1	TRUE	1	0.605104995730293	2		806	782	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804352	43804352	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	221	715	0	ENST00000372470.3:c.352C>T	p.Gln118Ter	p.Q118*	ENST00000372470	NM_005373.2	118	Cag/Tag	3/12	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.605104995730293	2		715	680	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156702	2156702	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	267	808	0	ENST00000434045.2:c.220T>G	p.Phe74Val	p.F74V	ENST00000434045	NM_001127598.1	74	Ttc/Gtc	3/5	0.605104995730293	1	FACETS	0.996	0.942	1	0.996	0.942	1	CLONAL	1	TRUE	0	0.605104995730293	1		808	618	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344458	118344458	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	108	348	1	ENST00000534358.1:c.2584C>T	p.Arg862Ter	p.R862*	ENST00000534358	NM_005933.3	862	Cga/Tga	3/36	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.605104995730293	2		349	353	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156149	119156149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	232	801	0	ENST00000264033.4:c.1814C>T	p.Ser605Phe	p.S605F	ENST00000264033	NM_005188.3	605	tCc/tTc	11/16	1	2	FACETS	0.937	0.876	1	0.937	0.876	1	CLONAL	1	TRUE	1	0.605104995730293	2		801	818	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385234	4385234	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	215	725	1	ENST00000261254.3:c.259T>A	p.Phe87Ile	p.F87I	ENST00000261254	NM_001759.3	87	Ttc/Atc	2/5	1	2	FACETS	0.984	0.918	1	0.984	0.918	1	CLONAL	1	TRUE	1	0.605104995730293	2		726	722	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218855	133218855	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	252	841	0	ENST00000320574.5:c.5081T>A	p.Leu1694Gln	p.L1694Q	ENST00000320574	NM_006231.2	1694	cTg/cAg	38/49	1	2	FACETS	0.995	0.934	1	0.995	0.934	1	CLONAL	1	TRUE	1	0.605104995730293	2		841	837	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636700	2636700	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	253	713	0	ENST00000342085.4:c.1149T>G	p.Phe383Leu	p.F383L	ENST00000342085	NM_002613.4	383	ttT/ttG	11/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.605104995730293	2		713	762	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984477	72984477	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	275	884	0	ENST00000268489.5:c.3107A>G	p.Asn1036Ser	p.N1036S	ENST00000268489	NM_006885.3	1036	aAc/aGc	3/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.605104995730293	2		884	836	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144107	11144107	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	279	908	0	ENST00000358026.2:c.3688C>T	p.Gln1230Ter	p.Q1230*	ENST00000358026	NM_001128849.1	1230	Cag/Tag	26/36	1	2	FACETS	0.984	0.926	1	0.984	0.926	1	CLONAL	1	TRUE	1	0.605104995730293	2		908	937	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657037	47657037	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	186	550	0	ENST00000233146.2:c.1233A>G	p.Ile411Met	p.I411M	ENST00000233146	NM_000251.2	411	atA/atG	7/16	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.605104995730293	2		550	610	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989590	212989590	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	146	532	0	ENST00000342788.4:c.121G>A	p.Asp41Asn	p.D41N	ENST00000342788	NM_005235.2	41	Gac/Aac	2/28	1	2	FACETS	0.983	0.903	1	0.983	0.903	1	CLONAL	1	TRUE	1	0.605104995730293	2		532	491	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101026	41101039	+	frameshift_variant	Frame_Shift_Del	DEL	AGGTCTGGATGACC	AGGTCTGGATGACC	-	novel	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	228	763	0	ENST00000373198.4:c.1317_1330del	p.Glu439AspfsTer23	p.E439Dfs*23	ENST00000373198	NM_133170.3	439	gaGGTCATCCAGACCTcc/gacc	8/32	1	2	FACETS	0.913	0.853	0.975	0.913	0.853	0.975	CLONAL	1	TRUE	1	0.605104995730293	2		763	825	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967267	134967267	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1340747830	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	190	803	0	ENST00000398015.3:c.2606C>T	p.Pro869Leu	p.P869L	ENST00000398015	NM_004441.4	869	cCc/cTc	14/16	1	2	FACETS	0.878	0.815	0.944	0.878	0.815	0.944	CLONAL	1	TRUE	1	0.605104995730293	2		803	715	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607208	189607209	+	missense_variant	Missense_Mutation	DNP	CT	CT	TA	novel	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	255	1047	3	ENST00000264731.3:c.1587_1588delinsTA	p.Ser530Thr	p.S530T	ENST00000264731	NM_003722.4	529	ctCTcc/ctTAcc	12/14	0.605104995730293	3	FACETS	0.935	0.875	0.998	0.468	0.437	0.499	CLONAL	1	TRUE	1	0.605104995730293	3		1050	1174	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1941489	1941489	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	155	562	0	ENST00000382891.5:c.1865C>T	p.Ser622Phe	p.S622F	ENST00000382891	NM_133335.3	622	tCc/tTc	9/22	1	2	FACETS	0.864	0.794	0.936	0.864	0.794	0.936	CLONAL	1	TRUE	1	0.605104995730293	2		562	593	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972011	55972011	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	178	672	0	ENST00000263923.4:c.1633T>G	p.Phe545Val	p.F545V	ENST00000263923	NM_002253.2	545	Ttc/Gtc	12/30	1	2	FACETS	0.875	0.81	0.943	0.875	0.81	0.943	CLONAL	1	TRUE	1	0.605104995730293	2		672	672	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662371	117662371	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	213	717	0	ENST00000368508.3:c.5006A>G	p.Asn1669Ser	p.N1669S	ENST00000368508	NM_002944.2	1669	aAc/aGc	30/43	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.605104995730293	2		717	677	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706938	117706938	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	240	813	0	ENST00000368508.3:c.2212G>A	p.Glu738Lys	p.E738K	ENST00000368508	NM_002944.2	738	Gag/Aag	15/43	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.605104995730293	2		813	785	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963963	2963963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267601476	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	254	925	0	ENST00000396946.4:c.1844C>T	p.Ser615Phe	p.S615F	ENST00000396946	NM_032415.4	615	tCc/tTc	15/25	1	2	FACETS	0.919	0.861	0.977	0.919	0.861	0.977	CLONAL	1	TRUE	1	0.605104995730293	2		925	914	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240696	55240696	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	313	997	2	ENST00000275493.2:c.1940C>T	p.Ala647Val	p.A647V	ENST00000275493	NM_005228.3	647	gCc/gTc	17/28	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.605104995730293	2		999	992	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106519997	106519997	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	118	506	0	ENST00000359195.3:c.2425A>G	p.Lys809Glu	p.K809E	ENST00000359195	NM_002649.2	809	Aaa/Gaa	6/11	0.605104995730293	3	FACETS	0.836	0.756	0.919	0.418	0.378	0.46	CLONAL	1	TRUE	1	0.605104995730293	3		506	608	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104594	69104594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	256	852	0	ENST00000288368.4:c.4438G>A	p.Asp1480Asn	p.D1480N	ENST00000288368	NM_024870.2	1480	Gat/Aat	37/40	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.605104995730293	2		852	838	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169552	27169552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	264	973	1	ENST00000380036.4:c.553G>A	p.Asp185Asn	p.D185N	ENST00000380036	NM_000459.3	185	Gat/Aat	4/23	0.605104995730293	1	FACETS	0.969	0.915	1	0.969	0.915	1	CLONAL	1	TRUE	0	0.605104995730293	1		974	628	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27209136	27209136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	227	763	0	ENST00000380036.4:c.2593G>A	p.Asp865Asn	p.D865N	ENST00000380036	NM_000459.3	865	Gat/Aat	16/23	0.605104995730293	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.605104995730293	1		763	493	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0021077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	42	541	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.653	0.544	0.775	0.653	0.544	0.775	SUBCLONAL	1	TRUE	1	0.19	2		541	677	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0021077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	168	844	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.895	0.822	0.971	1	0.991	1	CLONAL	2	TRUE	1	0.19	2		846	988	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939797	71939797	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	163	943	0	ENST00000298229.2:c.428del	p.Pro143ArgfsTer36	p.P143Rfs*36	ENST00000298229	NM_001567.3	142	Ccc/cc	4/28	1	2	FACETS	0.8	0.733	0.87	1	0.989	1	SUBCLONAL	2	TRUE	1	0.19	2		943	1072	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0021077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	47	440	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.974	0.822	1	0.974	0.822	1	CLONAL	1	TRUE	1	0.19	2		440	508	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0021077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	55	735	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.19	2		735	540	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795016	42795016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150818299	NA	P-0021077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	95	904	2	ENST00000575354.2:c.2096C>T	p.Ala699Val	p.A699V	ENST00000575354	NM_015125.3	699	gCg/gTg	10/20	1	2	FACETS	0.903	0.802	1	0.903	0.802	1	CLONAL	1	TRUE	1	0.19	2		906	1107	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528825	157528825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	39	673	0	ENST00000346085.5:c.6554del	p.Pro2185ArgfsTer8	p.P2185Rfs*8	ENST00000346085	NM_020732.3	2184	Ccc/cc	20/20	1	2	FACETS	0.526	0.435	0.629	0.526	0.435	0.629	SUBCLONAL	1	TRUE	1	0.19	2		673	780	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933617	39933617	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	52	746	0	ENST00000378444.4:c.982del	p.Asp328ThrfsTer50	p.D328Tfs*50	ENST00000378444	NM_001123385.1	328	Gac/ac	4/15	1	2	FACETS	0.67	0.569	0.782	0.67	0.569	0.782	SUBCLONAL	1	TRUE	1	0.19	2		746	817	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197518	106197518	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1043057789	NA	P-0021077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	52	609	2	ENST00000380013.4:c.5851C>T	p.Arg1951Trp	p.R1951W	ENST00000380013	NM_001127208.2	1951	Cgg/Tgg	11/11	1	2	FACETS	0.876	0.745	1	0.876	0.745	1	CLONAL	1	TRUE	1	0.19	2		611	625	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101346	27101347	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0021077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	74	865	0	ENST00000324856.7:c.4630_4631dup	p.Trp1545ArgfsTer21	p.W1545Rfs*21	ENST00000324856	NM_006015.4	1543	ggc/ggCTc	18/20	1	2	FACETS	0.752	0.656	0.856	0.752	0.656	0.856	SUBCLONAL	1	TRUE	1	0.19	2		865	1036	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120493457	120493457	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs782522898	NA	P-0021077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	48	619	0	ENST00000256646.2:c.2369A>G	p.Tyr790Cys	p.Y790C	ENST00000256646	NM_024408.3	790	tAt/tGt	15/34	1	2	FACETS	0.718	0.605	0.842	0.718	0.605	0.842	SUBCLONAL	1	TRUE	1	0.19	2		619	704	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514277	69514277	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	176	919	0	ENST00000294312.3:c.404G>C	p.Arg135Pro	p.R135P	ENST00000294312	NM_005117.2	135	cGa/cCa	3/3	1	2	FACETS	0.915	0.843	0.991	1	0.992	1	CLONAL	2	TRUE	1	0.19	2		919	1012	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981613	101981613	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs927540361	NA	P-0021077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	37	291	0	ENST00000282441.5:c.34G>C	p.Ala12Pro	p.A12P	ENST00000282441	NM_001130145.2	12	Gcc/Ccc	1/9	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.19	2		291	316	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427984	49427984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	95	792	2	ENST00000301067.7:c.10606C>T	p.Arg3536Cys	p.R3536C	ENST00000301067	NM_003482.3	3536	Cgc/Tgc	38/54	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.19	2		794	989	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622555	28622556	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	39	584	0	ENST00000241453.7:c.1061dup	p.Asn354LysfsTer4	p.N354Kfs*4	ENST00000241453	NM_004119.2	354	aat/aaAt	9/24	1	2	FACETS	0.788	0.652	0.939	0.788	0.652	0.939	CLONAL	1	TRUE	1	0.19	2		584	521	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274013	10274013	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758742694	NA	P-0021077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	92	882	2	ENST00000330684.3:c.256G>A	p.Val86Met	p.V86M	ENST00000330684	NM_001134407.1	86	Gtg/Atg	2/13	1	2	FACETS	0.873	0.774	0.98	0.873	0.774	0.98	CLONAL	1	TRUE	1	0.19	2		884	1109	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845582	72845582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370933867	NA	P-0021077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	78	885	3	ENST00000268489.5:c.3758G>A	p.Arg1253His	p.R1253H	ENST00000268489	NM_006885.3	1253	cGc/cAc	7/10	1	2	FACETS	0.84	0.736	0.952	0.84	0.736	0.952	CLONAL	1	TRUE	1	0.19	2		888	978	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964848	15964848	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	68	946	0	ENST00000268712.3:c.5748G>T	p.Glu1916Asp	p.E1916D	ENST00000268712	NM_006311.3	1916	gaG/gaT	37/46	1	2	FACETS	0.829	0.72	0.948	0.829	0.72	0.948	CLONAL	1	TRUE	1	0.19	2		946	863	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919758	50919758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750457028	NA	P-0021077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	83	806	1	ENST00000440232.2:c.2926G>A	p.Glu976Lys	p.E976K	ENST00000440232	NM_002691.3	976	Gag/Aag	23/27	1	2	FACETS	0.862	0.759	0.974	0.862	0.759	0.974	CLONAL	1	TRUE	1	0.19	2		807	1013	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52709282	52709282	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	59	786	0	ENST00000322088.6:c.236T>G	p.Leu79Arg	p.L79R	ENST00000322088	NM_014225.5	79	cTg/cGg	3/15	1	2	FACETS	0.718	0.616	0.83	0.718	0.616	0.83	SUBCLONAL	1	TRUE	1	0.19	2		786	865	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100975	41100975	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	74	770	0	ENST00000373198.4:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000373198	NM_133170.3	461	Cga/Tga	8/32	1	2	FACETS	0.897	0.784	1	0.897	0.784	1	CLONAL	1	TRUE	1	0.19	2		770	868	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101187	41101187	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	126	781	1	ENST00000373198.4:c.1169C>T	p.Pro390Leu	p.P390L	ENST00000373198	NM_133170.3	390	cCa/cTa	8/32	1	2	FACETS	0.796	0.721	0.876	1	0.986	1	SUBCLONAL	2	TRUE	1	0.19	2		782	833	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230764	66230764	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	25	600	0	ENST00000273854.3:c.2207T>C	p.Ile736Thr	p.I736T	ENST00000273854	NM_004439.5	736	aTc/aCc	12/18	1	2	FACETS	0.797	0.629	0.991	0.797	0.629	0.991	CLONAL	1	TRUE	1	0.19	2		600	330	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521354	187521354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1268188397	NA	P-0021077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	78	766	1	ENST00000441802.2:c.11801C>T	p.Ser3934Leu	p.S3934L	ENST00000441802	NM_005245.3	3934	tCg/tTg	22/27	1	2	FACETS	0.906	0.795	1	0.906	0.795	1	CLONAL	1	TRUE	1	0.19	2		767	906	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637892	176637892	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs765630779	NA	P-0021077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	69	860	1	ENST00000439151.2:c.2492G>T	p.Gly831Val	p.G831V	ENST00000439151	NM_022455.4	831	gGg/gTg	5/23	1	2	FACETS	0.779	0.677	0.891	0.779	0.677	0.891	SUBCLONAL	1	TRUE	1	0.19	2		861	932	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860172	151860172	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1315673360	NA	P-0021077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	46	717	0	ENST00000262189.6:c.10490C>G	p.Ser3497Cys	p.S3497C	ENST00000262189	NM_170606.2	3497	tCc/tGc	43/59	1	2	FACETS	0.595	0.499	0.701	0.595	0.499	0.701	SUBCLONAL	1	TRUE	1	0.19	2		717	814	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146945	38146945	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	57	1056	0	ENST00000317025.8:c.3197del	p.Asn1066ThrfsTer16	p.N1066Tfs*16	ENST00000317025	NM_023034.1	1066	aAc/ac	18/24	1	2	FACETS	0.579	0.495	0.672	0.579	0.495	0.672	SUBCLONAL	1	TRUE	1	0.19	2		1056	1036	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371798	55371812	+	frameshift_variant	Frame_Shift_Del	DEL	AGGCGGCCGCGCTGG	AGGCGGCCGCGCTGG	C	novel	NA	P-0021077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	29	186	0	ENST00000297316.4:c.488_502delinsC	p.Gln163ProfsTer197	p.Q163Pfs*197	ENST00000297316	NM_022454.3	163	cAGGCGGCCGCGCTGGgc/cCgc	2/2	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.19	2		186	206	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0021102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	198	857	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.222022281513752	4	FACETS	0.899	0.832	0.969	0.899	0.832	0.969	CLONAL	2	TRUE	2	0.242377700414291	4		857	1129	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0021102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	118	1091	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.242377700414291	2		1091	848	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557647	21557647	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	77	1134	0	ENST00000382592.4:c.2198A>G	p.Tyr733Cys	p.Y733C	ENST00000382592	NM_014572.2	733	tAc/tGc	5/8	1	2	FACETS	0.792	0.695	0.898	0.792	0.695	0.898	SUBCLONAL	1	TRUE	1	0.242377700414291	2		1134	802	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224545	123224545	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	77	516	0	ENST00000218089.9:c.3398G>T	p.Arg1133Leu	p.R1133L	ENST00000218089	NM_001042749.1	1133	cGg/cTg	31/35	1	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.242377700414291	1		516	446	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	229	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.648605626792611	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	1	0.656424348502364	3		434	455	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012359	152012359	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	123	667	0	ENST00000262189.6:c.454C>T	p.Gln152Ter	p.Q152*	ENST00000262189	NM_170606.2	152	Caa/Taa	4/59	1	2	FACETS	0.854	0.778	0.932	0.854	0.778	0.932	CLONAL	1	TRUE	1	0.656424348502364	2		667	439	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399444	139399444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1333725995	NA	P-0021103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	312	1060	4	ENST00000277541.6:c.4699G>A	p.Glu1567Lys	p.E1567K	ENST00000277541	NM_017617.3	1567	Gag/Aag	26/34	1	2	FACETS	0.922	0.871	0.974	0.922	0.871	0.974	CLONAL	1	TRUE	1	0.656424348502364	2		1064	1031	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39074231	39074231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs980024517	NA	P-0021104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	110	714	1	ENST00000357387.3:c.79C>T	p.Pro27Ser	p.P27S	ENST00000357387	NM_152756.3	27	Ccg/Tcg	2/38	1	2	FACETS	0.974	0.879	1	0.974	0.879	1	CLONAL	1	TRUE	1	0.45450292816106	2		715	497	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437578	56437578	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs746762909	NA	P-0021104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	132	819	0	ENST00000407977.2:c.884A>G	p.His295Arg	p.H295R	ENST00000407977		295	cAt/cGt	8/10	0.45450292816106	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.45450292816106	1		819	446	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0021105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	94	857	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	0.20938361519016	2		857	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0021105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	115	1078	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.20938361519016	2		1078	851	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29107994	29107994	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779322187	NA	P-0021105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	125	763	0	ENST00000328354.6:c.695G>A	p.Gly232Glu	p.G232E	ENST00000328354	NM_007194.3	232	gGa/gAa	6/15	0.151204329881427	1	FACETS	0.915	0.831	1	1	0.989	1	CLONAL	2	TRUE	0	0.20938361519016	1		763	584	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183813	10183813	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	81	992	0	ENST00000256474.2:c.282G>T	p.Glu94Asp	p.E94D	ENST00000256474	NM_000551.3	94	gaG/gaT	1/3	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.20938361519016	2		992	745	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041425	47041425	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	97	957	0	ENST00000377604.3:c.1769del	p.Tyr590LeufsTer114	p.Y590Lfs*114	ENST00000377604	NM_001204468.1	590	tAt/tt	16/24	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.20938361519016	2		957	802	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	180	669	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.907	0.844	0.971	0.907	0.844	0.971	CLONAL	1	TRUE	1	0.840917395707411	2		669	472	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0021106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	65	418	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.375140369261958	2	FACETS	0.528	0.461	0.598	0.264	0.23	0.299	INDETERMINATE	1	TRUE	0	0.840917395707411	2		418	293	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791797	42791797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	328	892	1	ENST00000575354.2:c.683G>A	p.Arg228Gln	p.R228Q	ENST00000575354	NM_015125.3	228	cGg/cAg	5/20	0.840917395707411	1	FACETS	0.987	0.952	1	0.987	0.952	1	CLONAL	1	TRUE	0	0.840917395707411	1		893	458	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294577	1294577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	40	797	1	ENST00000310581.5:c.424C>T	p.Arg142Cys	p.R142C	ENST00000310581	NM_198253.2	142	Cgc/Tgc	2/16	1	2	FACETS	0.133	0.11	0.159	0.133	0.11	0.159	SUBCLONAL	1	TRUE	1	0.840917395707411	2		798	714	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264033	16264033	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	55	1209	0	ENST00000375759.3:c.10402C>T	p.Pro3468Ser	p.P3468S	ENST00000375759	NM_015001.2	3468	Cca/Tca	12/15	0.840917395707411	1	FACETS	0.116	0.099	0.135	0.116	0.099	0.135	SUBCLONAL	1	TRUE	0	0.840917395707411	1		1209	652	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46727001	46727001	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766711957	NA	P-0021106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	234	738	1	ENST00000371975.4:c.835C>T	p.Arg279Cys	p.R279C	ENST00000371975	NM_003579.3	279	Cgc/Tgc	8/18	0.840917395707411	1	FACETS	0.874	0.832	0.915	0.874	0.832	0.915	CLONAL	1	TRUE	0	0.840917395707411	1		739	369	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95596451	95596451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	15	756	0	ENST00000393063.1:c.517G>A	p.Val173Met	p.V173M	ENST00000393063	NM_030621.3	173	Gtg/Atg	6/28	0.840917395707411	1	FACETS	0.09	0.065	0.119	0.09	0.065	0.119	SUBCLONAL	1	TRUE	0	0.840917395707411	1		756	230	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120635	94120635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	27	664	1	ENST00000369303.4:c.416G>A	p.Arg139Lys	p.R139K	ENST00000369303	NM_004440.3	139	aGa/aAa	3/17	1	2	FACETS	0.123	0.097	0.153	0.123	0.097	0.153	SUBCLONAL	1	TRUE	1	0.840917395707411	2		665	522	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755795	133755891	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTTACCTTACAAAGAAAGAGAACCACCACACCAAGCCAACACCAGTACTGATGGCTGCTGGATTTTTGTTTCTGTCCCTGTATGATTCTTAGAAGTG	GTTACCTTACAAAGAAAGAGAACCACCACACCAAGCCAACACCAGTACTGATGGCTGCTGGATTTTTGTTTCTGTCCCTGTATGATTCTTAGAAGTG	-	novel	NA	P-0021106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	23	188	0	ENST00000318560.5:c.1514-91_1519del		p.X505_splice	ENST00000318560	NM_005157.4	505		10/11	1	2	FACETS	0.37	0.291	0.458	0.37	0.291	0.458	SUBCLONAL	1	TRUE	1	0.840917395707411	2		188	148	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226004	53226004	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782457267	NA	P-0021106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	55	1193	2	ENST00000375401.3:c.2845G>A	p.Val949Ile	p.V949I	ENST00000375401	NM_004187.3	949	Gtc/Atc	19/26	1	2	FACETS	0.139	0.118	0.162	0.139	0.118	0.162	SUBCLONAL	1	TRUE	1	0.840917395707411	2		1195	940	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410837	63410837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	38	962	0	ENST00000330258.3:c.2330C>T	p.Thr777Ile	p.T777I	ENST00000330258	NM_152424.3	777	aCc/aTc	2/2	1	2	FACETS	0.125	0.103	0.151	0.125	0.103	0.151	SUBCLONAL	1	TRUE	1	0.840917395707411	2		962	721	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70355063	70355063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	58	1132	0	ENST00000374080.3:c.4985G>A	p.Gly1662Asp	p.G1662D	ENST00000374080		1662	gGc/gAc	36/45	1	2	FACETS	0.14	0.12	0.163	0.14	0.12	0.163	SUBCLONAL	1	TRUE	1	0.840917395707411	2		1132	984	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371409680	NA	P-0021107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	44	1121	0	ENST00000269305.4:c.848G>C	p.Arg283Pro	p.R283P	ENST00000269305	NM_001126112.2	283	cGc/cCc	8/11	1	2	FACETS	0.638	0.534	0.754	0.638	0.534	0.754	SUBCLONAL	1	FALSE	1	0.210260795032379	2		1121	656	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272198	15272198	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774932838	NA	P-0021107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	41	885	0	ENST00000263388.2:c.6241G>A	p.Gly2081Ser	p.G2081S	ENST00000263388	NM_000435.2	2081	Ggc/Agc	33/33	1	2	FACETS	0.771	0.646	0.907	1	0.959	1	CLONAL	2	FALSE	1	0.210260795032379	2		885	253	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923582	39923603	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCTCACCTTTAGAGACTCGTC	GGCTCACCTTTAGAGACTCGTC	-	novel	NA	P-0021107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	20	998	0	ENST00000378444.4:c.3488_3502+7del		p.X1163_splice	ENST00000378444	NM_001123385.1	1163		7/15	0.210260795032379	1	FACETS	0.539	0.412	0.687	0.539	0.412	0.687	SUBCLONAL	1	FALSE	0	0.210260795032379	1		998	316	SUCCESS
AR	367	MSKCC	GRCh37	X	66766484	66766484	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	43	1029	0	ENST00000374690.3:c.1496C>A	p.Ala499Glu	p.A499E	ENST00000374690	NM_000044.3	499	gCa/gAa	1/8	0.210260795032379	1	FACETS	0.882	0.739	1	0.882	0.739	1	CLONAL	1	FALSE	0	0.210260795032379	1		1029	415	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879925	44879925	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs189751539	NA	P-0021109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	501	1065	0	ENST00000377967.4:c.514C>T	p.Arg172Ter	p.R172*	ENST00000377967	NM_021140.2	172	Cga/Tga	6/29	0.93394350762707	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.93394350762707	1		1065	521	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105916	27105916	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	234	759	0	ENST00000324856.7:c.5527C>A	p.His1843Asn	p.H1843N	ENST00000324856	NM_006015.4	1843	Cac/Aac	20/20	1	2	FACETS	0.923	0.869	0.977	0.923	0.869	0.977	CLONAL	1	TRUE	1	0.93394350762707	2		759	543	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	418989	418989	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs865840614	NA	P-0021109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	554	1343	0	ENST00000399788.2:c.3358A>G	p.Thr1120Ala	p.T1120A	ENST00000399788	NM_001042603.1	1120	Acc/Gcc	22/28	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.93394350762707	2		1343	1167	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973785	15973785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	378	833	0	ENST00000268712.3:c.4207G>A	p.Val1403Ile	p.V1403I	ENST00000268712	NM_006311.3	1403	Gtc/Atc	31/46	0.93394350762707	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.93394350762707	1		833	404	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106931	11106931	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	462	1307	0	ENST00000358026.2:c.1636A>G	p.Lys546Glu	p.K546E	ENST00000358026	NM_001128849.1	546	Aag/Gag	10/36	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.93394350762707	2		1307	938	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721766	49721766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572214141	NA	P-0021109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	22	38	0	ENST00000449682.2:c.1997C>T	p.Ala666Val	p.A666V	ENST00000449682	NM_020998.3	666	gCc/gTc	17/18	1	2	FACETS	0.857	0.694	1	0.857	0.694	1	CLONAL	1	TRUE	1	0.93394350762707	2		38	55	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848525	151848525	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0021109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	164	558	0	ENST00000262189.6:c.12666+2T>C		p.X4222_splice	ENST00000262189	NM_170606.2	4222			1	2	FACETS	0.867	0.806	0.93	0.867	0.806	0.93	CLONAL	1	TRUE	1	0.93394350762707	2		558	405	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0021111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	298	1047	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.993	0.942	1	0.993	0.942	1	CLONAL	1	TRUE	1	0.870955614543034	2		1047	689	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73342984	73342989	+	inframe_deletion	In_Frame_Del	DEL	TGGTAA	TGGTAA	-	novel	NA	P-0021111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	239	641	0	ENST00000377767.4:c.1817_1822del	p.Ile606_Thr607del	p.I606_T607del	ENST00000377767	NM_014953.3	606	aTTACCAct/act	14/21	0.870955614543034	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.870955614543034	1		641	295	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0021114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	434	815	1	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.816811957461746	3	FACETS	0.922	0.898	0.945	0.922	0.898	0.945	CLONAL	3	TRUE	0	0.816811957461746	3		816	541	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021135-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	18	669	0				ENST00000310581	NM_198253.2	-/1132			0.124725671608465	0	FACETS	0.946	0.746	1			1	CLONAL	5	FALSE	0	0.139373441175408	0		669	47	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0021135-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	69	851	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	0.139373441175408	0	FACETS	0.926	0.842	1			1	CLONAL	8	FALSE	0	0.139373441175408	0		851	115	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021135-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	41	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.139373441175408	7	FACETS	1	0.887	1	1	0.96	1	CLONAL	8	FALSE	1	0.139373441175408	7		434	96	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0021135-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	12	748	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	FALSE	1	0.139373441175408	2		748	116	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0021135-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	8	487	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	0.139373441175408	7	FACETS	1	0.681	1	0.212	0.136	0.309	CLONAL	1	FALSE	2	0.139373441175408	7		487	146	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913273	NA	P-0021135-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	52	609	0	ENST00000263967.3:c.1624G>C	p.Glu542Gln	p.E542Q	ENST00000263967	NM_006218.2	542	Gaa/Caa	10/21	0.139373441175408	7	FACETS	1	0.915	1	1	0.975	1	CLONAL	9	FALSE	1	0.139373441175408	7		609	107	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578237	7578238	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0021135-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	51	773	0	ENST00000269305.4:c.611_612del	p.Glu204ValfsTer4	p.E204Vfs*4	ENST00000269305	NM_001126112.2	204	gAG/g	6/11	1	2	FACETS	0.888	0.765	1	1	0.982	1	CLONAL	4	FALSE	1	0.139373441175408	2		773	206	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0021150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	79	769	1	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	1	2	FACETS	0.786	0.69	0.889	0.786	0.69	0.889	SUBCLONAL	1	TRUE	1	0.235220515837586	2		770	855	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457327	67457327	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	42	717	0	ENST00000327367.4:c.301C>G	p.His101Asp	p.H101D	ENST00000327367	NM_005902.3	101	Cac/Gac	2/9	1	2	FACETS	0.472	0.393	0.561	0.472	0.393	0.561	SUBCLONAL	1	TRUE	1	0.235220515837586	2		717	756	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56409172	56409172	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	19	500	0	ENST00000348428.3:c.1679T>C	p.Leu560Pro	p.L560P	ENST00000348428	NM_006785.3	560	cTt/cCt	14/17	1	2	FACETS	0.478	0.362	0.614	0.478	0.362	0.614	SUBCLONAL	1	TRUE	1	0.235220515837586	2		500	338	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172103	99172103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1193458054	NA	P-0021150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	46	596	1	ENST00000074304.5:c.1669G>A	p.Glu557Lys	p.E557K	ENST00000074304	NM_001134224.1	557	Gag/Aag	17/26	1	2	FACETS	0.502	0.421	0.592	0.502	0.421	0.592	SUBCLONAL	1	TRUE	1	0.235220515837586	2		597	779	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180558	56180564	+	frameshift_variant	Frame_Shift_Del	DEL	GAATGAT	GAATGAT	-	novel	NA	P-0021150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	23	425	0	ENST00000399503.3:c.3889_3895del	p.Met1297AlafsTer3	p.M1297Afs*3	ENST00000399503	NM_005921.1	1296	aGAATGATg/ag	16/20	0.231906433681487	3	FACETS	0.741	0.578	0.929	0.37	0.289	0.465	CLONAL	1	TRUE	1	0.235220515837586	3		425	295	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279873	46279873	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	54	861	1	ENST00000371998.3:c.3799C>T	p.Gln1267Ter	p.Q1267*	ENST00000371998		1267	Cag/Tag	20/23	0.422937581986128	3	FACETS	0.317	0.27	0.37	0.159	0.135	0.185	SUBCLONAL	1	TRUE	1	0.422937581986128	3		862	975	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184140	56184140	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	136	672	0	ENST00000399503.3:c.4345T>A	p.Trp1449Arg	p.W1449R	ENST00000399503	NM_005921.1	1449	Tgg/Agg	19/20	1	2	FACETS	0.94	0.857	1	0.94	0.857	1	CLONAL	1	TRUE	1	0.422937581986128	2		672	684	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691039	NA	P-0021155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	365	818	0	ENST00000269305.4:c.919+1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.822427693673784	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.822427693673784	2		818	433	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115277091	115277091	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	183	838	0	ENST00000438362.2:c.692G>T	p.Arg231Leu	p.R231L	ENST00000438362	NM_001242891.1	231	cGc/cTc	7/20	0.812405624832814	3	FACETS	1	0.972	1	0.547	0.508	0.587	CLONAL	1	TRUE	1	0.822427693673784	3		838	574	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742897	17742897	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	323	893	0	ENST00000250003.3:c.805C>A	p.Leu269Ile	p.L269I	ENST00000250003	NM_002478.4	269	Ctc/Atc	3/3	0.730171603533973	4	FACETS	0.922	0.876	0.969	0.922	0.876	0.969	CLONAL	2	TRUE	2	0.822427693673784	4		893	776	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94224028	94224028	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	375	836	2	ENST00000323929.3:c.124G>A	p.Glu42Lys	p.E42K	ENST00000323929	NM_005591.3	42	Gaa/Aaa	3/20	0.730171603533973	4	FACETS	0.953	0.909	0.997	0.953	0.909	0.997	CLONAL	2	TRUE	2	0.822427693673784	4		838	872	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112201	115112201	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	339	795	0	ENST00000257566.3:c.1539C>A	p.Phe513Leu	p.F513L	ENST00000257566	NM_016569.3	513	ttC/ttA	7/8	0.730171603533973	4	FACETS	0.99	0.942	1	0.99	0.942	1	CLONAL	2	TRUE	2	0.822427693673784	4		795	759	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959385	26959385	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	255	583	0	ENST00000381527.3:c.552G>C	p.Leu184Phe	p.L184F	ENST00000381527	NM_001260.1	184	ttG/ttC	6/13	0.815812944837422	5	FACETS	1	0.991	1	0.45	0.422	0.48	CLONAL	1	TRUE	2	0.822427693673784	5		583	1025	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771155	161771155	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs757263675	NA	P-0021155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	350	813	0	ENST00000366898.1:c.1374G>T	p.Met458Ile	p.M458I	ENST00000366898	NM_004562.2	458	atG/atT	12/12	0.673256464260499	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	2	0.822427693673784	4		813	775	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355246	81355246	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	110	464	0	ENST00000222390.5:c.1128C>A	p.Tyr376Ter	p.Y376*	ENST00000222390	NM_000601.4	376	taC/taA	9/18	0.812405624832814	3	FACETS	0.963	0.873	1	0.482	0.436	0.529	CLONAL	1	TRUE	1	0.822427693673784	3		464	392	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90995038	90995038	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	121	601	0	ENST00000265433.3:c.83G>C	p.Arg28Thr	p.R28T	ENST00000265433	NM_002485.4	28	aGg/aCg	2/16	0.812405624832814	3	FACETS	0.878	0.798	0.961	0.439	0.399	0.481	CLONAL	1	TRUE	1	0.822427693673784	3		601	473	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546721	9546721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	116	353	0	ENST00000353224.5:c.1301C>T	p.Ala434Val	p.A434V	ENST00000353224	NM_177990.2	434	gCg/gTg	5/10	1	2	FACETS	0.94	0.855	1	0.94	0.855	1	CLONAL	1	TRUE	1	0.621764852933036	2		353	397	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	173	379	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.882	0.815	0.951	0.882	0.815	0.951	CLONAL	1	TRUE	1	0.621764852933036	2		379	631	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0021157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	178	600	10	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	0.621764852933036	1	FACETS	0.832	0.774	0.891	0.832	0.774	0.891	CLONAL	1	TRUE	0	0.621764852933036	1		610	474	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	172	471	1	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	0.823	0.76	0.889	0.823	0.76	0.889	CLONAL	1	TRUE	1	0.621764852933036	2		472	672	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0021157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	375	571	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.615931130551755	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.621764852933036	2		571	586	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119910	70119910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1297203260	NA	P-0021157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	57	710	1	ENST00000245479.2:c.916del	p.Val306CysfsTer77	p.V306Cfs*77	ENST00000245479	NM_000346.3	304	ccG/cc	3/3	1	2	FACETS	0.221	0.188	0.256	0.221	0.188	0.256	SUBCLONAL	1	TRUE	1	0.621764852933036	2		711	831	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527278	137527278	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146914620	NA	P-0021157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	105	664	2	ENST00000367739.4:c.368G>A	p.Arg123Gln	p.R123Q	ENST00000367739	NM_000416.2	123	cGa/cAa	3/7	1	2	FACETS	0.422	0.377	0.469	0.422	0.377	0.469	SUBCLONAL	1	TRUE	1	0.621764852933036	2		666	801	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106490	27106490	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	283	775	0	ENST00000324856.7:c.6101del	p.Glu2034GlyfsTer8	p.E2034Gfs*8	ENST00000324856	NM_006015.4	2034	gAg/gg	20/20	1	2	FACETS	0.944	0.889	1	0.944	0.889	1	CLONAL	1	TRUE	1	0.621764852933036	2		775	964	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922258	100922259	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	194	537	0	ENST00000325455.5:c.2253dup	p.Gln752SerfsTer30	p.Q752Sfs*30	ENST00000325455	NM_001202474.3	751	-/T	5/8	1	2	FACETS	0.902	0.838	0.968	0.902	0.838	0.968	CLONAL	1	TRUE	1	0.621764852933036	2		537	692	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220100	133220100	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	337	871	0	ENST00000320574.5:c.4337T>C	p.Val1446Ala	p.V1446A	ENST00000320574	NM_006231.2	1446	gTg/gCg	34/49	1	2	FACETS	0.948	0.897	1	0.948	0.897	1	CLONAL	1	TRUE	1	0.621764852933036	2		871	1143	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240657	133240657	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1337524033	NA	P-0021157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	241	743	1	ENST00000320574.5:c.2639C>T	p.Thr880Met	p.T880M	ENST00000320574	NM_006231.2	880	aCg/aTg	23/49	1	2	FACETS	0.902	0.845	0.962	0.902	0.845	0.962	CLONAL	1	TRUE	1	0.621764852933036	2		744	859	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912256	32912256	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	235	607	0	ENST00000380152.3:c.3764T>C	p.Val1255Ala	p.V1255A	ENST00000380152		1255	gTa/gCa	11/27	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.621764852933036	2		607	736	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061011	38061011	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	114	388	6	ENST00000250448.2:c.978del	p.Ala329ProfsTer21	p.A329Pfs*21	ENST00000250448	NM_004496.3	326	ccC/cc	2/2	1	2	FACETS	0.738	0.668	0.811	0.738	0.668	0.811	SUBCLONAL	1	TRUE	1	0.621764852933036	2		394	497	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061726	38061726	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	184	640	1	ENST00000250448.2:c.263del	p.Gly88AlafsTer6	p.G88Afs*6	ENST00000250448	NM_004496.3	88	gGc/gc	2/2	1	2	FACETS	0.958	0.889	1	0.958	0.889	1	CLONAL	1	TRUE	1	0.621764852933036	2		641	618	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133752	2133752	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	407	976	0	ENST00000219476.3:c.3944del	p.Pro1315GlnfsTer10	p.P1315Qfs*10	ENST00000219476	NM_000548.3	1314	Ccc/cc	33/42	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.621764852933036	2		976	1148	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831309	72831309	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	167	372	1	ENST00000268489.5:c.5272C>T	p.Gln1758Ter	p.Q1758*	ENST00000268489	NM_006885.3	1758	Cag/Tag	9/10	NA	2	FACETS	1	0.937	1			1	INDETERMINATE	1	TRUE	NA	0.621764852933036	2		373	530	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118671	11118671	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	337	877	0	ENST00000358026.2:c.2095T>G	p.Ser699Ala	p.S699A	ENST00000358026	NM_001128849.1	699	Tct/Gct	14/36	1	2	FACETS	0.916	0.866	0.966	0.916	0.866	0.966	CLONAL	1	TRUE	1	0.621764852933036	2		877	1184	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574901	41574901	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs764376096	NA	P-0021157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	330	792	0	ENST00000263253.7:c.7186A>G	p.Ser2396Gly	p.S2396G	ENST00000263253	NM_001429.3	2396	Agc/Ggc	31/31	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.621764852933036	2		792	1033	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165665	47165665	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	210	576	0	ENST00000409792.3:c.461G>T	p.Arg154Met	p.R154M	ENST00000409792	NM_014159.6	154	aGg/aTg	3/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.621764852933036	2		576	654	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149238768	149238768	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs188215356	NA	P-0021157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	300	921	0	ENST00000360632.3:c.1027G>A	p.Ala343Thr	p.A343T	ENST00000360632	NM_015472.4	343	Gca/Aca	7/7	1	2	FACETS	0.969	0.914	1	0.969	0.914	1	CLONAL	1	TRUE	1	0.621764852933036	2		921	996	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591107	67591145	+	inframe_deletion	In_Frame_Del	DEL	AACCAGACCTTATCCAGCTGAGAAAGACGAGAGACCAAT	AACCAGACCTTATCCAGCTGAGAAAGACGAGAGACCAAT	-	novel	NA	P-0021157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	70	339	0	ENST00000274335.5:c.1701_1739del	p.Lys567_Tyr580delinsAsn	p.K567_Y580delinsN	ENST00000274335		567	aAACCAGACCTTATCCAGCTGAGAAAGACGAGAGACCAATac/aac	12/15	1	2	FACETS	0.617	0.541	0.698	0.617	0.541	0.698	SUBCLONAL	1	TRUE	1	0.621764852933036	2		339	365	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038367	180038367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746879565	NA	P-0021157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	267	842	1	ENST00000261937.6:c.3650G>A	p.Ser1217Asn	p.S1217N	ENST00000261937	NM_182925.4	1217	aGc/aAc	27/30	1	2	FACETS	0.928	0.872	0.986	0.928	0.872	0.986	CLONAL	1	TRUE	1	0.621764852933036	2		843	925	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056160	26056161	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs970660865	NA	P-0021157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	182	598	0	ENST00000343677.2:c.496_497del	p.Val166AsnfsTer6	p.V166Nfs*6	ENST00000343677	NM_005319.3	166	GTa/a	1/1	1	2	FACETS	0.764	0.707	0.824	0.764	0.707	0.824	SUBCLONAL	1	TRUE	1	0.621764852933036	2		598	766	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314877	1314877	+	downstream_gene_variant	3'Flank	SNP	G	G	A	rs768027040	NA	P-0021157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	122	287	0				ENST00000400841		-/233			0.621764852933036	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.621764852933036	1		287	264	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0021158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	128	314	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.130094822188327	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		314	408	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578181	7578181	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138983188	NA	P-0021158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	328	801	1	ENST00000269305.4:c.668C>T	p.Pro223Leu	p.P223L	ENST00000269305	NM_001126112.2	223	cCt/cTt	6/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		802	946	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576881	7576941	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTTTCTTCTTTGGCTGGGGAGAGGAGCTGGTGTTGTTGGGCAGTGCTAGGAAAGAGGCAA	GGTTTCTTCTTTGGCTGGGGAGAGGAGCTGGTGTTGTTGGGCAGTGCTAGGAAAGAGGCAA	-	novel	NA	P-0021158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	171	777	0	ENST00000269305.4:c.920-15_965del		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		777	762	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795046	42795046	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	411	978	1	ENST00000575354.2:c.2126C>T	p.Thr709Ile	p.T709I	ENST00000575354	NM_015125.3	709	aCt/aTt	10/20	0.3	3	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	3		979	1182	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939878	76939879	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	324	360	0	ENST00000373344.5:c.869dup	p.Leu290PhefsTer6	p.L290Ffs*6	ENST00000373344	NM_000489.3	290	ttg/ttTg	9/35	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		360	498	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs17849781	NA	P-0021165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	729	916	0	ENST00000269305.4:c.832C>A	p.Pro278Thr	p.P278T	ENST00000269305	NM_001126112.2	278	Cct/Act	8/11	0.698496253150556	3	FACETS	1	0.984	1			1	CLONAL	3	TRUE	NA	0.698496253150556	3		916	933	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565564	41565564	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	395	654	13	ENST00000263253.7:c.4230G>T	p.Arg1410Ser	p.R1410S	ENST00000263253	NM_001429.3	1410	agG/agT	26/31	0.698496253150556	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.698496253150556	3		667	746	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556080	29556080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762709897	NA	P-0021165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	93	315	2	ENST00000356175.3:c.2447G>A	p.Arg816Gln	p.R816Q	ENST00000356175	NM_000267.3	816	cGa/cAa	21/57	0.698496253150556	3	FACETS	1	0.948	1	0.363	0.326	0.402	CLONAL	1	TRUE	0	0.698496253150556	3		317	330	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858394	9858394	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	158	511	12	ENST00000330684.3:c.3007G>A	p.Glu1003Lys	p.E1003K	ENST00000330684	NM_001134407.1	1003	Gaa/Aaa	13/13	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.698496253150556	2		523	413	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435536	56435536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs752167360	NA	P-0021165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	639	758	27	ENST00000407977.2:c.1601A>G	p.Asp534Gly	p.D534G	ENST00000407977		534	gAc/gGc	9/10	0.659911521578255	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	0	0.698496253150556	3		785	815	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117339	7117339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs959800826	NA	P-0021165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	341	973	19	ENST00000302850.5:c.3877G>A	p.Asp1293Asn	p.D1293N	ENST00000302850	NM_000208.2	1293	Gac/Aac	22/22	0.549023676159106	5	FACETS	0.901	0.853	0.949	0.6	0.568	0.633	CLONAL	2	TRUE	2	0.698496253150556	5		992	1110	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095902	178095902	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	118	523	7	ENST00000397062.3:c.1429C>T	p.Pro477Ser	p.P477S	ENST00000397062	NM_006164.4	477	Cct/Tct	5/5	0.698496253150556	3	FACETS	0.767	0.694	0.844	0.384	0.347	0.422	SUBCLONAL	1	TRUE	1	0.698496253150556	3		530	594	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97934327	97934327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	72	353	2	ENST00000289081.3:c.448C>T	p.Leu150Phe	p.L150F	ENST00000289081	NM_000136.2	150	Ctt/Ttt	5/15	0.698496253150556	3	FACETS	0.726	0.638	0.82	0.242	0.212	0.274	SUBCLONAL	1	TRUE	0	0.698496253150556	3		355	383	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	30	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.662975842783653	4	FACETS	0.201	0.161	0.246			1	SUBCLONAL	1	FALSE	NA	0.662975842783653	4		434	750	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0021166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	647	818	1	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.453161837942294	4	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	FALSE	2	0.662975842783653	4		819	1367	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265627	152265627	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	265	377	0	ENST00000206249.3:c.1080G>T	p.Trp360Cys	p.W360C	ENST00000206249	NM_000125.3	360	tgG/tgT	4/8	0.64305241191661	2	FACETS	0.956	0.913	0.998	0.956	0.913	0.998	CLONAL	2	FALSE	0	0.662975842783653	2		377	418	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144684	119144684	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	222	584	0	ENST00000264033.4:c.697A>C	p.Asn233His	p.N233H	ENST00000264033	NM_005188.3	233	Aat/Cat	4/16	0.64305241191661	2	FACETS	0.95	0.888	1	0.475	0.444	0.507	CLONAL	1	FALSE	0	0.662975842783653	2		584	705	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346331	73346331	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	145	542	0	ENST00000377767.4:c.1469T>G	p.Leu490Arg	p.L490R	ENST00000377767	NM_014953.3	490	cTa/cGa	10/21	0.66290040671382	4	FACETS	0.786	0.716	0.858	0.196	0.179	0.215	SUBCLONAL	1	FALSE	0	0.662975842783653	4		542	926	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060916	38060916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	445	570	2	ENST00000250448.2:c.1073C>T	p.Pro358Leu	p.P358L	ENST00000250448	NM_004496.3	358	cCc/cTc	2/2	0.662975842783653	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	FALSE	2	0.662975842783653	4		572	974	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993573	72993573	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	246	577	0	ENST00000268489.5:c.472G>T	p.Gly158Trp	p.G158W	ENST00000268489	NM_006885.3	158	Ggg/Tgg	2/10	0.598415541705897	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	0	0.662975842783653	1		577	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577137	+	inframe_deletion	In_Frame_Del	DEL	ACACGCACCTCAAAGCTGTTC	ACACGCACCTCAAAGCTGTTC	-	novel	NA	P-0021166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	257	788	0	ENST00000269305.4:c.801_821del	p.Asn268_Val274del	p.N268_V274del	ENST00000269305	NM_001126112.2	267	cgGAACAGCTTTGAGGTGCGTGTt/cgt	8/11	0.453161837942294	4	FACETS	1	0.945	1	0.506	0.473	0.54	CLONAL	1	FALSE	2	0.662975842783653	4		788	1274	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610396	10610397	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	590	851	3	ENST00000171111.5:c.313_314delinsTT	p.Pro105Phe	p.P105F	ENST00000171111	NM_203500.1	105	CCt/TTt	2/6	0.64305241191661	2	FACETS	0.984	0.956	1	0.984	0.956	1	CLONAL	2	FALSE	0	0.662975842783653	2		854	904	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713520	30713520	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	379	521	0	ENST00000295754.5:c.845A>G	p.Glu282Gly	p.E282G	ENST00000295754	NM_003242.5	282	gAg/gGg	4/7	0.587604182222866	3	FACETS	0.866	0.834	0.897	0.866	0.834	0.897	CLONAL	3	FALSE	0	0.662975842783653	3		521	586	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84393419	84393419	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	220	451	0	ENST00000321945.7:c.238G>C	p.Val80Leu	p.V80L	ENST00000321945	NM_139076.2	80	Gta/Cta	4/9	0.635682830848221	2	FACETS	0.84	0.795	0.885	0.84	0.795	0.885	CLONAL	2	FALSE	0	0.662975842783653	2		451	395	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696730	176696730	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	371	483	0	ENST00000439151.2:c.5431C>G	p.Arg1811Gly	p.R1811G	ENST00000439151	NM_022455.4	1811	Cga/Gga	16/23	0.662975842783653	2	FACETS	0.966	0.93	1	0.966	0.93	1	CLONAL	2	FALSE	0	0.662975842783653	2		483	579	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32191704	32191704	+	start_lost	Translation_Start_Site	SNP	A	A	C	novel	NA	P-0021166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	471	829	0	ENST00000375023.3:c.2T>G	p.Met1?	p.M1?	ENST00000375023	NM_004557.3	1	aTg/aGg	1/30	0.64305241191661	2	FACETS	0.858	0.827	0.889	0.858	0.827	0.889	CLONAL	2	FALSE	0	0.662975842783653	2		829	828	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499774	8499774	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	279	634	0	ENST00000356435.5:c.2195G>A	p.Trp732Ter	p.W732*	ENST00000356435		732	tGg/tAg	14/35	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.662975842783653	2		634	834	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0021168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	284	779	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.391802365912529	4	FACETS	0.895	0.842	0.95			1	CLONAL	2	TRUE	NA	0.420138279834566	4		779	1072	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0021168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	328	784	4	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.390466522431369	2	FACETS	0.943	0.895	0.991	0.943	0.895	0.991	CLONAL	2	TRUE	0	0.420138279834566	2		788	828	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971138	21971164	+	inframe_deletion	In_Frame_Del	DEL	CGGCGCAGTTGGGCTCCGCGCCGTGGA	CGGCGCAGTTGGGCTCCGCGCCGTGGA	-	novel	NA	P-0021168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	187	698	0	ENST00000304494.5:c.194_220del	p.Leu65_Asp74delinsHis	p.L65_D74delinsH	ENST00000304494	NM_000077.4	65	cTCCACGGCGCGGAGCCCAACTGCGCCGac/cac	2/3	0.390466522431369	2	FACETS	0.869	0.81	0.93	0.869	0.81	0.93	CLONAL	2	TRUE	0	0.420138279834566	2		698	512	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846342	156846342	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746049437	NA	P-0021170-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	123	882	0	ENST00000524377.1:c.1783G>A	p.Gly595Arg	p.G595R	ENST00000524377	NM_002529.3	595	Ggg/Agg	14/17	NA	2	FACETS	0.802	0.73	0.877			1	INDETERMINATE	1	TRUE	NA	0.672694578981425	2		882	456	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293481	1293481	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021170-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	94	1029	1	ENST00000310581.5:c.1520A>G	p.Glu507Gly	p.E507G	ENST00000310581	NM_198253.2	507	gAg/gGg	2/16	0.547088253420471	5	FACETS	0.76	0.676	0.849			1	SUBCLONAL	1	TRUE	NA	0.672694578981425	5		1030	739	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0021173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	1328	993	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.322439298798678	13	FACETS	1	0.995	1			1	CLONAL	11	TRUE	NA	0.322439298798678	13		993	2003	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578529	7578529	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs780442292	NA	P-0021173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	208	1458	0	ENST00000269305.4:c.401T>G	p.Phe134Cys	p.F134C	ENST00000269305	NM_001126112.2	134	tTt/tGt	5/11	0.322439298798678	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.322439298798678	1		1458	885	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279766	46279766	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	54	943	0	ENST00000371998.3:c.3692G>C	p.Arg1231Thr	p.R1231T	ENST00000371998		1231	aGa/aCa	20/23	0.322439298798678	3	FACETS	0.441	0.376	0.514	0.221	0.188	0.257	SUBCLONAL	1	TRUE	1	0.322439298798678	3		943	881	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64126717	64126717	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	32	709	0	ENST00000334205.4:c.10G>C	p.Glu4Gln	p.E4Q	ENST00000334205	NM_003942.2	4	Gag/Cag	1/17	1	2	FACETS	0.378	0.306	0.46	0.378	0.306	0.46	SUBCLONAL	1	TRUE	1	0.322439298798678	2		709	525	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387115	31387115	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	50	1046	0	ENST00000328111.2:c.1740G>C	p.Leu580Phe	p.L580F	ENST00000328111	NM_006892.3	580	ttG/ttC	16/23	0.322439298798678	3	FACETS	0.404	0.341	0.473	0.202	0.17	0.237	SUBCLONAL	1	TRUE	1	0.322439298798678	3		1046	892	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680989	30680989	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	64	984	0	ENST00000376406.3:c.730G>C	p.Glu244Gln	p.E244Q	ENST00000376406	NM_014641.2	244	Gag/Cag	5/15	0.322439298798678	3	FACETS	0.529	0.457	0.608	0.265	0.228	0.304	SUBCLONAL	1	TRUE	1	0.322439298798678	3		984	871	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683572	162683572	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	37	729	0	ENST00000366898.1:c.397C>G	p.Pro133Ala	p.P133A	ENST00000366898	NM_004562.2	133	Cca/Gca	3/12	1	2	FACETS	0.384	0.316	0.46	0.384	0.316	0.46	SUBCLONAL	1	TRUE	1	0.322439298798678	2		729	598	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842368	151842368	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	84	286	0	ENST00000262189.6:c.14044G>T	p.Glu4682Ter	p.E4682*	ENST00000262189	NM_170606.2	4682	Gag/Tag	54/59	0.269571938127484	4	FACETS	0.976	0.869	1	0.976	0.869	1	CLONAL	2	TRUE	2	0.322439298798678	4		286	353	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274925	38274929	+	frameshift_variant	Frame_Shift_Del	DEL	GTTGC	GTTGC	-	novel	NA	P-0021173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	254	1351	0	ENST00000425967.3:c.1651_1655del	p.Ala551ArgfsTer21	p.A551Rfs*21	ENST00000425967	NM_001174067.1	551	GCAACa/a	13/19	0.212604474738284	4	FACETS	1	0.966	1	0.698	0.654	0.744	CLONAL	2	TRUE	1	0.322439298798678	4		1351	995	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197363	27197363	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1283376594	NA	P-0021173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	51	1042	0	ENST00000380036.4:c.1675C>G	p.Leu559Val	p.L559V	ENST00000380036	NM_000459.3	559	Cta/Gta	12/23	NA	2	FACETS	0.364	0.308	0.426			1	INDETERMINATE	1	TRUE	NA	0.322439298798678	2		1042	869	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650448	48650448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781904528	NA	P-0021173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	63	1419	5	ENST00000376670.3:c.418C>T	p.Arg140Trp	p.R140W	ENST00000376670	NM_002049.3	140	Cgg/Tgg	3/6	0.289414748178871	3	FACETS	0.416	0.358	0.479	0.208	0.179	0.24	SUBCLONAL	1	TRUE	1	0.322439298798678	3		1424	1091	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0021176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	166	662	1				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.826702428539592	2		663	377	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	224	1052	0	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	1	2	FACETS	0.951	0.892	1	0.951	0.892	1	CLONAL	1	TRUE	1	0.826702428539592	2		1052	570	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913136	44913136	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	317	481	0	ENST00000377967.4:c.811C>T	p.Gln271Ter	p.Q271*	ENST00000377967	NM_021140.2	271	Cag/Tag	10/29	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.826702428539592	1		481	387	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403413	139403413	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	293	1107	0	ENST00000277541.6:c.3080C>T	p.Ser1027Leu	p.S1027L	ENST00000277541	NM_017617.3	1027	tCa/tTa	19/34	1	2	FACETS	0.987	0.935	1	0.987	0.935	1	CLONAL	1	TRUE	1	0.826702428539592	2		1107	718	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22405068	22405068	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	161	461	0	ENST00000344548.3:c.97G>T	p.Val33Leu	p.V33L	ENST00000344548	NM_001039802.1	33	Gta/Tta	3/7	1	2	FACETS	0.798	0.738	0.86	0.798	0.738	0.86	SUBCLONAL	1	TRUE	1	0.826702428539592	2		461	488	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248735	59248735	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs865974199	NA	P-0021176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	366	1063	1	ENST00000371222.2:c.8C>T	p.Ala3Val	p.A3V	ENST00000371222	NM_002228.3	3	gCa/gTa	1/1	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.826702428539592	2		1064	831	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8105989	8105989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	253	561	0	ENST00000346208.3:c.809C>T	p.Ser270Leu	p.S270L	ENST00000346208		270	tCg/tTg	4/6	0.826702428539592	3	FACETS	1	0.988	1	0.593	0.558	0.63	CLONAL	1	TRUE	1	0.826702428539592	3		561	729	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298779	46298779	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	261	702	0	ENST00000334344.6:c.5426C>A	p.Ser1809Tyr	p.S1809Y	ENST00000334344	NM_152641.2	1809	tCc/tAc	21/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.826702428539592	2		702	622	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954353	48954353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060503084	NA	P-0021176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	272	646	0	ENST00000267163.4:c.1474G>A	p.Glu492Lys	p.E492K	ENST00000267163	NM_000321.2	492	Gag/Aag	16/27	0.765122117181118	1	FACETS	0.965	0.925	1	0.965	0.925	1	CLONAL	1	TRUE	0	0.826702428539592	1		646	400	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42026774	42026774	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	232	653	1	ENST00000219905.7:c.3898G>A	p.Asp1300Asn	p.D1300N	ENST00000219905	NM_001164273.1	1300	Gat/Aat	12/24	1	2	FACETS	0.899	0.844	0.956	0.899	0.844	0.956	CLONAL	1	TRUE	1	0.826702428539592	2		654	624	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467863	99467863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	148	496	0	ENST00000268035.6:c.2732C>T	p.Ser911Phe	p.S911F	ENST00000268035	NM_000875.3	911	tCt/tTt	13/21	1	2	FACETS	0.84	0.775	0.907	0.84	0.775	0.907	CLONAL	1	TRUE	1	0.826702428539592	2		496	426	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3794879	3795568	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTTCCCGAAACTTACTCTTAGCACTGAATTTGTTTTCTTTTCGAGGTCTGCCAGTTTTCTTCAAGCAGTTGTCGCACACAAAACTGCAAAATAATAGTGGTATGATGAGACTGTATATAATGATGTAAATTGTCAAACCAACAAAATGCAGCATTCAGATAGTTTGTTGGCAGTTTAAATCACATTATTATAAAATTAAAGAGTGAAGAGGCAGACTGCTTTGATTCCACAATTCCTAAAGCGGACAAACGCTTAGAACTTAAATTTAGAACCAACTGCCATCTCTCTTAATCGCTGAATTCTTGCTGACAACAATGAATGAGATGCAGTAGCCACTGCAACTGCCCCGCCACTGGCTCTGTGCAGAACTGCCCTCCAGGCCAGGGGAAACAACTCACCCTGAAGGCCAAATGATGTCATAGTGCAGAACGCAAATCTGATGCATCTTCCGGCCACACTCCTTGCAATCAACGAAACTAGGAGGCAAAGAAGGCGCACTGTTAAAGCACACGGAACCACAAGACCAGAGTCACTTGTAGAAGTCTGTGTGTGCGTCCACACCTTGTTCTCTGGGTTACTTTGAGTAGTGCTGACATTAATGCGTGTGTTGGCTGATTCAGCTATATTTTACAATGCATCCGTATGATATCTTCTACAGGAAAAAGCTTTCTTCTTTTGTTTGTACAAGC	GCTTCCCGAAACTTACTCTTAGCACTGAATTTGTTTTCTTTTCGAGGTCTGCCAGTTTTCTTCAAGCAGTTGTCGCACACAAAACTGCAAAATAATAGTGGTATGATGAGACTGTATATAATGATGTAAATTGTCAAACCAACAAAATGCAGCATTCAGATAGTTTGTTGGCAGTTTAAATCACATTATTATAAAATTAAAGAGTGAAGAGGCAGACTGCTTTGATTCCACAATTCCTAAAGCGGACAAACGCTTAGAACTTAAATTTAGAACCAACTGCCATCTCTCTTAATCGCTGAATTCTTGCTGACAACAATGAATGAGATGCAGTAGCCACTGCAACTGCCCCGCCACTGGCTCTGTGCAGAACTGCCCTCCAGGCCAGGGGAAACAACTCACCCTGAAGGCCAAATGATGTCATAGTGCAGAACGCAAATCTGATGCATCTTCCGGCCACACTCCTTGCAATCAACGAAACTAGGAGGCAAAGAAGGCGCACTGTTAAAGCACACGGAACCACAAGACCAGAGTCACTTGTAGAAGTCTGTGTGTGCGTCCACACCTTGTTCTCTGGGTTACTTTGAGTAGTGCTGACATTAATGCGTGTGTTGGCTGATTCAGCTATATTTTACAATGCATCCGTATGATATCTTCTACAGGAAAAAGCTTTCTTCTTTTGTTTGTACAAGC	-	novel	NA	P-0021176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	47	780	0	ENST00000262367.5:c.3837-213_3982+16del		p.X1279_splice	ENST00000262367	NM_004380.2	1279		22-23/31	1	2	FACETS	0.265	0.224	0.311	0.265	0.224	0.311	SUBCLONAL	1	TRUE	1	0.826702428539592	2		780	429	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3824616	3824616	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	185	595	1	ENST00000262367.5:c.2237C>T	p.Pro746Leu	p.P746L	ENST00000262367	NM_004380.2	746	cCa/cTa	12/31	1	2	FACETS	0.904	0.842	0.967	0.904	0.842	0.967	CLONAL	1	TRUE	1	0.826702428539592	2		596	495	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774070	56774070	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780837	NA	P-0021176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	517	823	0	ENST00000337432.4:c.421G>A	p.Asp141Asn	p.D141N	ENST00000337432	NM_058216.2	141	Gat/Aat	3/9	0.826702428539592	3	FACETS	0.943	0.91	0.976	0.943	0.91	0.976	CLONAL	2	TRUE	1	0.826702428539592	3		823	937	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985407	60985407	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	305	1024	0	ENST00000333681.4:c.493G>A	p.Glu165Lys	p.E165K	ENST00000333681		165	Gag/Aag	2/3	1	2	FACETS	0.945	0.895	0.995	0.945	0.895	0.995	CLONAL	1	TRUE	1	0.826702428539592	2		1024	781	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184382	7184382	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	290	929	0	ENST00000302850.5:c.919C>T	p.His307Tyr	p.H307Y	ENST00000302850	NM_000208.2	307	Cac/Tac	3/22	1	2	FACETS	0.908	0.858	0.958	0.908	0.858	0.958	CLONAL	1	TRUE	1	0.826702428539592	2		929	773	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082748	16082748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	80	220	0	ENST00000281043.3:c.562G>A	p.Asp188Asn	p.D188N	ENST00000281043	NM_005378.4	188	Gat/Aat	2/3	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.826702428539592	2		220	163	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551332	29551332	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	220	826	1	ENST00000389048.3:c.1298C>A	p.Ser433Tyr	p.S433Y	ENST00000389048	NM_004304.4	433	tCc/tAc	6/29	NA	2	FACETS	0.956	0.896	1			1	INDETERMINATE	1	TRUE	NA	0.826702428539592	2		827	557	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46603793	46603793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	245	903	0	ENST00000263734.3:c.1150G>A	p.Glu384Lys	p.E384K	ENST00000263734	NM_001430.4	384	Gag/Aag	9/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.826702428539592	2		903	582	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033363	48033368	+	inframe_deletion	In_Frame_Del	DEL	GATGGG	GATGGG	-	novel	NA	P-0021176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	234	728	0	ENST00000234420.5:c.3667_3672del	p.Asp1223_Gly1224del	p.D1223_G1224del	ENST00000234420	NM_000179.2	1223	GATGGG/-	8/10	1	2	FACETS	0.841	0.789	0.894	0.841	0.789	0.894	CLONAL	1	TRUE	1	0.826702428539592	2		728	673	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198262794	198262794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	317	629	0	ENST00000335508.6:c.3181G>A	p.Glu1061Lys	p.E1061K	ENST00000335508	NM_012433.2	1061	Gag/Aag	22/25	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.826702428539592	2		629	701	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39658087	39658087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761127035	NA	P-0021176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	175	591	0	ENST00000361337.2:c.50G>A	p.Arg17Gln	p.R17Q	ENST00000361337	NM_003286.2	17	cGa/cAa	2/21	1	2	FACETS	0.893	0.83	0.957	0.893	0.83	0.957	CLONAL	1	TRUE	1	0.826702428539592	2		591	474	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127167	22127167	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	240	618	0	ENST00000215832.6:c.961G>T	p.Asp321Tyr	p.D321Y	ENST00000215832	NM_002745.4	321	Gac/Tac	7/9	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.826702428539592	2		618	542	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537180	41537180	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	343	873	0	ENST00000263253.7:c.2007G>A	p.Met669Ile	p.M669I	ENST00000263253	NM_001429.3	669	atG/atA	10/31	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.826702428539592	2		873	812	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873113	134873113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	228	734	2	ENST00000398015.3:c.1417G>A	p.Glu473Lys	p.E473K	ENST00000398015	NM_004441.4	473	Gag/Aag	6/16	NA	2	FACETS	1	0.958	1			1	INDETERMINATE	1	TRUE	NA	0.826702428539592	2		736	539	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279226	142279226	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	367	779	0	ENST00000350721.4:c.1420C>T	p.Gln474Ter	p.Q474*	ENST00000350721	NM_001184.3	474	Cag/Tag	6/47	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.826702428539592	2		779	873	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247247	153247247	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	305	607	0	ENST00000281708.4:c.1555T>G	p.Tyr519Asp	p.Y519D	ENST00000281708	NM_033632.3	519	Tat/Gat	10/12	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.826702428539592	2		607	715	SUCCESS
APC	324	MSKCC	GRCh37	5	112163655	112163655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	223	515	0	ENST00000257430.4:c.1578G>A	p.Met526Ile	p.M526I	ENST00000257430	NM_000038.5	526	atG/atA	13/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.826702428539592	2		515	507	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393267	393267	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	251	908	0	ENST00000380956.4:c.117del	p.Leu40TrpfsTer62	p.L40Wfs*62	ENST00000380956	NM_001195286.1	39	Ggg/gg	2/9	NA	2	FACETS	0.901	0.848	0.955			1	INDETERMINATE	1	TRUE	NA	0.826702428539592	2		908	674	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056141	26056141	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	286	656	0	ENST00000343677.2:c.516G>C	p.Lys172Asn	p.K172N	ENST00000343677	NM_005319.3	172	aaG/aaC	1/1	0.564142644323548	3	FACETS	1	0.994	1			1	CLONAL	1	TRUE	NA	0.826702428539592	3		656	654	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43738985	43738985	+	start_lost	Translation_Start_Site	SNP	T	T	G	novel	NA	P-0021176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	262	629	0	ENST00000523873.1:c.2T>G	p.Met1?	p.M1?	ENST00000523873		1	aTg/aGg	1/8	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.826702428539592	2		629	618	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120428	94120428	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	78	466	0	ENST00000369303.4:c.623T>A	p.Ile208Asn	p.I208N	ENST00000369303	NM_004440.3	208	aTt/aAt	3/17	0.408006981007293	1	FACETS	0.404	0.359	0.451	0.404	0.359	0.451	INDETERMINATE	1	TRUE	0	0.826702428539592	1		466	274	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527337	137527337	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	198	936	0	ENST00000367739.4:c.309A>C	p.Lys103Asn	p.K103N	ENST00000367739	NM_000416.2	103	aaA/aaC	3/7	0.394302533232532	1	FACETS	0.373	0.346	0.4	0.373	0.346	0.4	INDETERMINATE	1	TRUE	0	0.826702428539592	1		936	754	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270585	98270585	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	31	93	0	ENST00000331920.6:c.59G>A	p.Cys20Tyr	p.C20Y	ENST00000331920	NM_000264.3	20	tGt/tAt	1/24	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.826702428539592	2		93	62	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	266	1076	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.633607656034875	1	FACETS	0.979	0.926	1	0.979	0.926	1	CLONAL	1	TRUE	0	0.634374971879959	1		1076	585	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115947	8115948	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0021178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	118	645	0	ENST00000346208.3:c.1295dup	p.His433ThrfsTer74	p.H433Tfs*74	ENST00000346208		431	-/C	6/6	1	2	FACETS	0.744	0.675	0.817	0.744	0.675	0.817	SUBCLONAL	1	TRUE	1	0.634374971879959	2		645	500	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968189	134968189	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	200	879	0	ENST00000398015.3:c.2702C>A	p.Pro901His	p.P901H	ENST00000398015	NM_004441.4	901	cCc/cAc	15/16	1	2	FACETS	0.976	0.909	1	0.976	0.909	1	CLONAL	1	TRUE	1	0.634374971879959	2		879	646	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133480	55133480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	117	812	0	ENST00000257290.5:c.784G>T	p.Glu262Ter	p.E262*	ENST00000257290	NM_006206.4	262	Gaa/Taa	6/23	0.634374971879959	1	FACETS	0.768	0.701	0.836	0.768	0.701	0.836	SUBCLONAL	1	TRUE	0	0.634374971879959	1		812	328	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480483	57480483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	116	616	1	ENST00000371085.3:c.478C>T	p.Arg160Cys	p.R160C	ENST00000371085	NM_000516.4	160	Cgt/Tgt	6/13	0.162077949703698	3	FACETS	0.849	0.773	0.927	0.566	0.515	0.618	INDETERMINATE	2	FALSE	0	0.454710374997705	3		617	369	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42843761	42843761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	37	1039	1	ENST00000398585.3:c.1158G>A	p.Met386Ile	p.M386I	ENST00000398585	NM_001135099.1	386	atG/atA	10/14	0.454710374997705	6	FACETS	0.501	0.412	0.601			1	SUBCLONAL	1	FALSE	NA	0.454710374997705	6		1040	620	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220649	1220649	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	53	964	2	ENST00000326873.7:c.667G>T	p.Glu223Ter	p.E223*	ENST00000326873	NM_000455.4	223	Gag/Tag	5/10	0.3	2	FACETS	1	0.918	1			1	CLONAL	1	TRUE	NA	0.13	2		966	727	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602799	10602799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	55	1004	1	ENST00000171111.5:c.779G>T	p.Arg260Leu	p.R260L	ENST00000171111	NM_203500.1	260	cGa/cTa	3/6	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.13	2		1005	763	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680562	241680562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	57	1076	1	ENST00000366560.3:c.187C>T	p.Pro63Ser	p.P63S	ENST00000366560	NM_000143.3	63	Cca/Tca	2/10	1	2	FACETS	0.883	0.755	1	0.883	0.755	1	CLONAL	1	TRUE	1	0.13	2		1077	993	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506963	186506964	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCTTC	novel	NA	P-0021191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	29	491	0	ENST00000323963.5:c.1130_1131insCTTCT	p.Thr378PhefsTer26	p.T378Ffs*26	ENST00000323963		377	gtt/gTCTTCtt	11/11	1	2	FACETS	0.861	0.69	1	0.861	0.69	1	CLONAL	1	TRUE	1	0.13	2		491	518	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913492	NA	P-0021192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	198	752	0	ENST00000286548.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000286548	NM_002072.3	209	cAa/cTa	5/7	1	2	FACETS	0.978	0.912	1	0.978	0.912	1	CLONAL	1	TRUE	1	0.736378480954269	2		752	550	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0021194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	10	814	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.276207979551121	1	FACETS	0.16	0.108	0.226	0.16	0.108	0.226	SUBCLONAL	1	TRUE	0	0.276207979551121	1		814	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0021194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	113	1014	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.276207979551121	2		1014	597	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16062187	16062187	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	106	812	1	ENST00000268712.3:c.619C>T	p.Gln207Ter	p.Q207*	ENST00000268712	NM_006311.3	207	Caa/Taa	6/46	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.276207979551121	2		813	514	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	352	772	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.772600483843377	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.772600483843377	3		772	608	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78519547	78519547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	256	771	3	ENST00000306801.3:c.118G>A	p.Glu40Lys	p.E40K	ENST00000306801	NM_020761.2	40	Gaa/Aaa	1/34	0.772600483843377	4	FACETS	1	0.955	1	0.256	0.239	0.274	CLONAL	1	TRUE	0	0.772600483843377	4		774	1146	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	265	846	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.772600483843377	3	FACETS	0.981	0.921	1	0.327	0.307	0.348	CLONAL	1	TRUE	0	0.772600483843377	3		846	969	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581157	48581157	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1555685624	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	156	561	0	ENST00000342988.3:c.461C>G	p.Ser154Ter	p.S154*	ENST00000342988	NM_005359.5	154	tCa/tGa	5/12	0.772600483843377	2	FACETS	1	0.981	1	0.58	0.539	0.621	CLONAL	1	TRUE	0	0.772600483843377	2		561	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577599	7577599	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	39	806	0	ENST00000269305.4:c.682G>C	p.Asp228His	p.D228H	ENST00000269305	NM_001126112.2	228	Gac/Cac	7/11	0.772600483843377	2	FACETS	0.139	0.115	0.167	0.07	0.057	0.084	SUBCLONAL	1	TRUE	0	0.772600483843377	2		806	726	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6048643	6048643	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs375507981	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1310	270	732	0	ENST00000265849.7:c.8G>C	p.Arg3Pro	p.R3P	ENST00000265849	NM_000535.5	3	cGa/cCa	1/15	0.772600483843377	5	FACETS	0.955	0.893	1	0.318	0.297	0.34	CLONAL	1	TRUE	2	0.772600483843377	5		732	1580	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242909	142242909	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	300	944	0	ENST00000350721.4:c.4078G>C	p.Glu1360Gln	p.E1360Q	ENST00000350721	NM_001184.3	1360	Gaa/Caa	22/47	0.772600483843377	3	FACETS	1	0.982	1	0.547	0.516	0.579	CLONAL	1	TRUE	1	0.772600483843377	3		944	984	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556049	29556049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	169	456	0	ENST00000356175.3:c.2416G>A	p.Glu806Lys	p.E806K	ENST00000356175	NM_000267.3	806	Gaa/Aaa	21/57	0.772600483843377	2	FACETS	1	0.985	1	0.603	0.562	0.643	CLONAL	1	TRUE	0	0.772600483843377	2		456	363	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247951	59247951	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	360	993	0	ENST00000371222.2:c.792C>G	p.Ile264Met	p.I264M	ENST00000371222	NM_002228.3	264	atC/atG	1/1	0.712966799531195	3	FACETS	1	0.977	1	0.527	0.5	0.556	CLONAL	1	TRUE	1	0.772600483843377	3		993	1225	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411558	63411558	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	282	992	0	ENST00000330258.3:c.1609G>C	p.Asp537His	p.D537H	ENST00000330258	NM_152424.3	537	Gac/Cac	2/2	0.659923264454235	4	FACETS	0.951	0.892	1	0.475	0.446	0.506	CLONAL	1	TRUE	2	0.772600483843377	4		992	1361	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180493	94180493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1444076984	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	245	848	2	ENST00000323929.3:c.1675G>A	p.Asp559Asn	p.D559N	ENST00000323929	NM_005591.3	559	Gat/Aat	15/20	0.772600483843377	3	FACETS	1	0.971	1	0.53	0.497	0.565	CLONAL	1	TRUE	1	0.772600483843377	3		850	829	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445077	49445077	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057518680	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	266	815	0	ENST00000301067.7:c.2389C>G	p.Leu797Val	p.L797V	ENST00000301067	NM_003482.3	797	Ctg/Gtg	10/54	0.772600483843377	3	FACETS	1	0.976	1	0.537	0.504	0.57	CLONAL	1	TRUE	1	0.772600483843377	3		815	889	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885825	111885825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1247081124	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	281	1066	1	ENST00000341259.2:c.1447C>T	p.His483Tyr	p.H483Y	ENST00000341259	NM_005475.2	483	Cac/Tac	8/8	0.772600483843377	3	FACETS	0.878	0.825	0.933	0.439	0.412	0.467	CLONAL	1	TRUE	1	0.772600483843377	3		1067	1148	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601358	28601358	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	178	797	0	ENST00000241453.7:c.2074G>C	p.Glu692Gln	p.E692Q	ENST00000241453	NM_004119.2	692	Gaa/Caa	17/24	0.659923264454235	4	FACETS	0.848	0.781	0.918	0.424	0.39	0.459	CLONAL	1	TRUE	2	0.772600483843377	4		797	963	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913391	32913391	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1028371302	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	208	785	1	ENST00000380152.3:c.4899C>G	p.Ile1633Met	p.I1633M	ENST00000380152		1633	atC/atG	11/27	0.659923264454235	4	FACETS	1	0.935	1	0.503	0.467	0.541	CLONAL	1	TRUE	2	0.772600483843377	4		786	948	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042337	42042337	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1158518906	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	266	882	0	ENST00000219905.7:c.6532C>A	p.Leu2178Met	p.L2178M	ENST00000219905	NM_001164273.1	2178	Ctg/Atg	17/24	0.712966799531195	3	FACETS	1	0.986	1	0.575	0.541	0.61	CLONAL	1	TRUE	1	0.772600483843377	3		882	830	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748549	43748549	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	345	1092	3	ENST00000382044.4:c.2257G>A	p.Glu753Lys	p.E753K	ENST00000382044	NM_001141980.1	753	Gaa/Aaa	12/28	0.712966799531195	3	FACETS	1	0.978	1	0.531	0.502	0.56	CLONAL	1	TRUE	1	0.772600483843377	3		1095	1166	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749104	43749104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	328	1186	3	ENST00000382044.4:c.1702G>A	p.Glu568Lys	p.E568K	ENST00000382044	NM_001141980.1	568	Gaa/Aaa	12/28	0.712966799531195	3	FACETS	1	0.963	1	0.512	0.484	0.541	CLONAL	1	TRUE	1	0.772600483843377	3		1189	1149	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670100	29670100	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	268	831	0	ENST00000356175.3:c.7073G>C	p.Gly2358Ala	p.G2358A	ENST00000356175	NM_000267.3	2358	gGa/gCa	47/57	0.772600483843377	2	FACETS	0.886	0.834	0.939	0.443	0.417	0.47	CLONAL	1	TRUE	0	0.772600483843377	2		831	783	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485720	40485720	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	266	786	0	ENST00000264657.5:c.1020G>C	p.Lys340Asn	p.K340N	ENST00000264657	NM_139276.2	340	aaG/aaC	10/24	0.772600483843377	2	FACETS	1	0.953	1	0.506	0.477	0.535	CLONAL	1	TRUE	0	0.772600483843377	2		786	681	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966640	25966640	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1262466888	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	255	827	1	ENST00000435504.4:c.2566G>A	p.Glu856Lys	p.E856K	ENST00000435504		856	Gag/Aag	13/13	0.756262863771444	4	FACETS	1	0.939	1	0.502	0.469	0.535	CLONAL	1	TRUE	2	0.772600483843377	4		828	1166	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163474	47163474	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs369914066	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	169	605	0	ENST00000409792.3:c.2652G>C	p.Gln884His	p.Q884H	ENST00000409792	NM_014159.6	884	caG/caC	3/21	0.772600483843377	3	FACETS	1	0.963	1	0.533	0.493	0.574	CLONAL	1	TRUE	1	0.772600483843377	3		605	569	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71050137	71050137	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	413	652	1	ENST00000318789.4:c.1048C>T	p.Gln350Ter	p.Q350*	ENST00000318789	NM_032682.5	350	Cag/Tag	13/21	0.772600483843377	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.772600483843377	3		653	740	SUCCESS
ATR	545	MSKCC	GRCh37	3	142212003	142212003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	255	926	0	ENST00000350721.4:c.6049G>A	p.Glu2017Lys	p.E2017K	ENST00000350721	NM_001184.3	2017	Gaa/Aaa	35/47	0.772600483843377	3	FACETS	1	0.963	1	0.518	0.486	0.551	CLONAL	1	TRUE	1	0.772600483843377	3		926	883	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242864	142242864	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	271	909	0	ENST00000350721.4:c.4123G>T	p.Glu1375Ter	p.E1375*	ENST00000350721	NM_001184.3	1375	Gaa/Taa	22/47	0.772600483843377	3	FACETS	1	0.96	1	0.514	0.483	0.546	CLONAL	1	TRUE	1	0.772600483843377	3		909	946	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186501413	186501413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779490566	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	161	508	0	ENST00000323963.5:c.14C>T	p.Ser5Phe	p.S5F	ENST00000323963		5	tCc/tTc	1/11	0.772600483843377	3	FACETS	0.879	0.809	0.952	0.44	0.404	0.476	CLONAL	1	TRUE	1	0.772600483843377	3		508	657	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952412	38952412	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	156	655	1	ENST00000357387.3:c.3013C>G	p.Pro1005Ala	p.P1005A	ENST00000357387	NM_152756.3	1005	Cca/Gca	30/38	0.756262863771444	4	FACETS	0.843	0.772	0.917	0.422	0.386	0.459	CLONAL	1	TRUE	2	0.772600483843377	4		656	849	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79952348	79952348	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	197	649	2	ENST00000265081.6:c.356C>G	p.Ser119Cys	p.S119C	ENST00000265081	NM_002439.4	119	tCt/tGt	2/24	0.756262863771444	4	FACETS	0.998	0.925	1	0.499	0.462	0.537	CLONAL	1	TRUE	2	0.772600483843377	4		651	906	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80149998	80149998	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	189	831	0	ENST00000265081.6:c.2863G>C	p.Glu955Gln	p.E955Q	ENST00000265081	NM_002439.4	955	Gaa/Caa	21/24	0.756262863771444	4	FACETS	0.926	0.856	0.998	0.463	0.428	0.499	CLONAL	1	TRUE	2	0.772600483843377	4		831	937	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940523	31940523	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1184	282	755	0	ENST00000375333.2:c.556G>C	p.Asp186His	p.D186H	ENST00000375333	NM_032454.1	186	Gac/Cac	3/8	0.772600483843377	5	FACETS	1	0.975	1	0.358	0.336	0.382	CLONAL	1	TRUE	2	0.772600483843377	5		755	1466	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332804	152332804	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	272	871	0	ENST00000206249.3:c.1110G>C	p.Leu370Phe	p.L370F	ENST00000206249	NM_000125.3	370	ttG/ttC	5/8	0.772600483843377	3	FACETS	0.997	0.937	1	0.332	0.312	0.353	CLONAL	1	TRUE	0	0.772600483843377	3		871	979	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859749	151859749	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1487587482	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	192	632	0	ENST00000262189.6:c.10913C>G	p.Ser3638Ter	p.S3638*	ENST00000262189	NM_170606.2	3638	tCa/tGa	43/59	0.772600483843377	5	FACETS	1	0.97	1	0.365	0.337	0.393	CLONAL	1	TRUE	2	0.772600483843377	5		632	981	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69143608	69143608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	154	524	0	ENST00000288368.4:c.4816G>A	p.Glu1606Lys	p.E1606K	ENST00000288368	NM_024870.2	1606	Gaa/Aaa	40/40	0.772600483843377	3	FACETS	0.886	0.814	0.96	0.443	0.407	0.48	CLONAL	1	TRUE	1	0.772600483843377	3		524	624	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396743	139396743	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1198855127	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	210	817	0	ENST00000277541.6:c.5365G>A	p.Glu1789Lys	p.E1789K	ENST00000277541	NM_017617.3	1789	Gag/Aag	28/34	1	2	FACETS	0.769	0.717	0.822	0.769	0.717	0.822	SUBCLONAL	1	TRUE	1	0.772600483843377	2		817	707	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410643	63410643	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	334	1045	2	ENST00000330258.3:c.2524G>C	p.Glu842Gln	p.E842Q	ENST00000330258	NM_152424.3	842	Gag/Cag	2/2	0.659923264454235	4	FACETS	1	0.982	1	0.546	0.515	0.577	CLONAL	1	TRUE	2	0.772600483843377	4		1047	1404	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347265	70347265	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	276	830	0	ENST00000374080.3:c.2929G>C	p.Asp977His	p.D977H	ENST00000374080		977	Gat/Cat	21/45	0.690650573984848	3	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.772600483843377	3		830	891	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861531	152861531	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	222	840	1	ENST00000406277.2:c.221C>A	p.Ser74Ter	p.S74*	ENST00000406277	NM_152274.4	74	tCa/tAa	4/7	0.646712247099338		FACETS		0.868	1				CLONAL	1	TRUE	NA	0.772600483843377	4		841	1092	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0021196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	8	509	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.102	0.065	0.15	0.102	0.065	0.15	SUBCLONAL	1	FALSE	1	0.429819182407556	2		509	366	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0021196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	145	818	1	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.429819182407556	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	0	0.429819182407556	1		819	477	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498465	89498465	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	51	595	1	ENST00000336596.2:c.2437G>T	p.Val813Phe	p.V813F	ENST00000336596	NM_005233.5	813	Gtt/Ttt	14/17	1	2	FACETS	0.595	0.507	0.691	0.595	0.507	0.691	SUBCLONAL	1	FALSE	1	0.429819182407556	2		596	399	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249007	+	missense_variant	Missense_Mutation	TNP	GCG	GCG	TCC	novel	NA	P-0021196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	327	690	1	ENST00000275493.2:c.2303_2305delinsTCC	p.Ser768_Val769delinsIleLeu	p.S768_V769delinsIL	ENST00000275493	NM_005228.3	768	aGCGtg/aTCCtg	20/28	0.429819182407556	4	FACETS	0.968	0.921	1	0.968	0.921	1	CLONAL	3	FALSE	1	0.429819182407556	4		691	749	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355961	73355961	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	165	923	0	ENST00000377767.4:c.10T>G	p.Ser4Ala	p.S4A	ENST00000377767	NM_014953.3	4	Tcc/Gcc	1/21	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.429819182407556	2		923	540	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279352	18279352	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	68	744	1	ENST00000222254.8:c.1804G>A	p.Glu602Lys	p.E602K	ENST00000222254	NM_005027.3	602	Gag/Aag	14/16	1	2	FACETS	0.709	0.619	0.807	0.709	0.619	0.807	SUBCLONAL	1	FALSE	1	0.429819182407556	2		745	446	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0021199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	137	772	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.971	0.889	1	0.971	0.889	1	CLONAL	1	TRUE	1	0.584404927406222	2		772	483	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0021199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	157	692	2	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.928	0.854	1	0.928	0.854	1	CLONAL	1	TRUE	1	0.584404927406222	2		694	579	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846106	151846106	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	128	622	0	ENST00000262189.6:c.12906del	p.Ala4303ProfsTer23	p.A4303Pfs*23	ENST00000262189	NM_170606.2	4302	ccT/cc	52/59	1	2	FACETS	0.842	0.767	0.921	0.842	0.767	0.921	CLONAL	1	TRUE	1	0.584404927406222	2		622	520	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0021200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	32	1047	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.188559330750968	2	FACETS	0.77	0.646	0.899	0.77	0.646	0.899	INDETERMINATE	2	TRUE	0	0.488898646995697	2		1049	85	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0021200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	11	583	1	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	0.488898646995697	1	FACETS	0.391	0.273	0.533	0.391	0.273	0.533	SUBCLONAL	1	TRUE	0	0.488898646995697	1		584	87	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577146	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0021200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	134	804	0	ENST00000269305.4:c.792_794del	p.Leu265del	p.L265del	ENST00000269305	NM_001126112.2	264	ctACTg/ctg	8/11	0.314426566478107	3	FACETS	1	0.977	1	0.763	0.705	0.821	CLONAL	2	TRUE	0	0.488898646995697	3		804	298	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468309	50468309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1159541845	NA	P-0021200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	59	761	5	ENST00000331340.3:c.1544G>A	p.Arg515His	p.R515H	ENST00000331340	NM_006060.4	515	cGc/cAc	8/8	0.488898646995697	4	FACETS	0.82	0.708	0.943	0.273	0.236	0.315	CLONAL	1	TRUE	1	0.488898646995697	4		766	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0021201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	246	520	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.565530375625681	1	FACETS	0.997	0.938	1	0.997	0.938	1	CLONAL	1	TRUE	0	0.565530375625681	1		520	626	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692922	89692922	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201044	NA	P-0021201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	165	595	0	ENST00000371953.3:c.406T>C	p.Cys136Arg	p.C136R	ENST00000371953	NM_000314.4	136	Tgt/Cgt	5/9	0.565530375625681	1	FACETS	0.851	0.787	0.915	0.851	0.787	0.915	CLONAL	1	TRUE	0	0.565530375625681	1		595	492	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519938	NA	P-0021201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	107	394	1	ENST00000263967.3:c.1034A>T	p.Asn345Ile	p.N345I	ENST00000263967	NM_006218.2	345	aAt/aTt	5/21	1	2	FACETS	0.623	0.56	0.69	0.623	0.56	0.69	SUBCLONAL	1	TRUE	1	0.565530375625681	2		395	607	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952052	178952052	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	104	492	0	ENST00000263967.3:c.3107T>C	p.Leu1036Ser	p.L1036S	ENST00000263967	NM_006218.2	1036	tTg/tCg	21/21	1	2	FACETS	0.55	0.493	0.61	0.55	0.493	0.61	SUBCLONAL	1	TRUE	1	0.565530375625681	2		492	669	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945331	71945331	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0021201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	58	802	0	ENST00000298229.2:c.2219C>G	p.Ser740Ter	p.S740*	ENST00000298229	NM_001567.3	740	tCa/tGa	20/28	1	2	FACETS	0.199	0.17	0.231	0.199	0.17	0.231	SUBCLONAL	1	TRUE	1	0.565530375625681	2		802	1029	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984734	11984735	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	130	303	1	ENST00000353533.5:c.281dup	p.His94GlnfsTer38	p.H94Qfs*38	ENST00000353533	NM_003010.3	94	cac/cAac	3/11	0.565530375625681	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.565530375625681	1		304	317	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952064	178952064	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	95	465	0	ENST00000263967.3:c.3119T>C	p.Met1040Thr	p.M1040T	ENST00000263967	NM_006218.2	1040	aTg/aCg	21/21	1	2	FACETS	0.532	0.474	0.593	0.532	0.474	0.593	SUBCLONAL	1	TRUE	1	0.565530375625681	2		465	632	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115012	3115012	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555702147	NA	P-0021203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	29	1239	4	ENST00000078429.4:c.547C>T	p.Arg183Cys	p.R183C	ENST00000078429	NM_002067.2	183	Cgc/Tgc	4/7	1	2	FACETS	0.085	0.067	0.105	0.085	0.067	0.105	SUBCLONAL	1	TRUE	1	0.683869147255827	2		1243	1002	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995482	68995482	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	26	721	0	ENST00000288368.4:c.1886G>T	p.Gly629Val	p.G629V	ENST00000288368	NM_024870.2	629	gGc/gTc	18/40	0.415500038602198	3	FACETS	0.483	0.383	0.597	0.161	0.127	0.199	SUBCLONAL	1	TRUE	0	0.415500038602198	3		721	313	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0021207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	26	710	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.811837072741991	3	FACETS	0.097	0.076	0.121	0.048	0.038	0.061	SUBCLONAL	1	FALSE	1	0.811837072741991	3		711	929	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711955	89711956	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0021207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	249	667	0	ENST00000371953.3:c.574_575dup	p.Leu193HisfsTer7	p.L193Hfs*7	ENST00000371953	NM_000314.4	191	-/GC	6/9	0.811837072741991	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	0	0.811837072741991	1		667	350	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138664	55138664	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11966	2400	635	0	ENST00000257290.5:c.1341G>C	p.Trp447Cys	p.W447C	ENST00000257290	NM_006206.4	447	tgG/tgC	9/23	0.811837072741991	34	FACETS	0.96	0.938	0.981			1	CLONAL	6	FALSE	NA	0.811837072741991	34		635	14366	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513012	106513012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758968659	NA	P-0021207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	166	528	1	ENST00000359195.3:c.2026G>A	p.Ala676Thr	p.A676T	ENST00000359195	NM_002649.2	676	Gcc/Acc	3/11	0.811837072741991	3	FACETS	0.862	0.794	0.932	0.431	0.397	0.466	CLONAL	1	FALSE	1	0.811837072741991	3		529	667	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341262	8341262	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	159	474	0	ENST00000356435.5:c.4954G>A	p.Ala1652Thr	p.A1652T	ENST00000356435		1652	Gcc/Acc	30/35	1	2	FACETS	0.979	0.908	1	0.979	0.908	1	CLONAL	1	FALSE	1	0.811837072741991	2		474	400	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339576	70339576	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	240	782	0	ENST00000374080.3:c.245G>A	p.Arg82His	p.R82H	ENST00000374080		82	cGt/cAt	3/45	1	2	FACETS	0.968	0.91	1	0.968	0.91	1	CLONAL	1	FALSE	1	0.811837072741991	2		782	611	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0021210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	222	662	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.968	0.909	1	0.968	0.909	1	CLONAL	1	TRUE	1	0.852759579213222	2		663	538	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0021210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	592	706	2	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.852759579213222	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.852759579213222	2		708	677	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953760	48953760	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913302	NA	P-0021210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	207	525	1	ENST00000267163.4:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000267163	NM_000321.2	455	Cga/Tga	14/27	0.852759579213222	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.852759579213222	1		526	276	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007818	45007818	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	94	845	0	ENST00000558401.1:c.265G>T	p.Glu89Ter	p.E89*	ENST00000558401	NM_004048.2	89	Gaa/Taa	2/4	0.350264624639465	1	FACETS	0.681	0.607	0.76	0.681	0.607	0.76	SUBCLONAL	1	TRUE	0	0.372988635120119	1		845	602	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000078	30000084	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGAGA	GCCGAGA	-	novel	NA	P-0021212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	208	918	0	ENST00000338641.4:c.91_97del	p.Ala31TrpfsTer7	p.A31Wfs*7	ENST00000338641	NM_000268.3	31	GCCGAGAtg/tg	1/16	0.278732562796723	2	FACETS	1	0.991	1	0.717	0.667	0.768	CLONAL	1	TRUE	0	0.372988635120119	2		918	778	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437316	52437316	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0021212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	174	749	0	ENST00000460680.1:c.1730-2A>T		p.X577_splice	ENST00000460680	NM_004656.3	577			NA	2	FACETS	0.792	0.733	0.853			1	INDETERMINATE	2	TRUE	NA	0.372988635120119	2		749	589	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860737	151860737	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	89	750	0	ENST00000262189.6:c.9925C>T	p.Gln3309Ter	p.Q3309*	ENST00000262189	NM_170606.2	3309	Cag/Tag	43/59	0.300855656234997	3	FACETS	0.774	0.686	0.868	0.387	0.343	0.434	SUBCLONAL	1	TRUE	1	0.372988635120119	3		750	732	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	131	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.261179346541814	1	FACETS	1	0.971	1	1	0.992	1	CLONAL	2	TRUE	0	0.261179346541814	1		434	385	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0021218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	31	488	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	0.261179346541814	1	FACETS	0.631	0.511	0.766	0.631	0.511	0.766	SUBCLONAL	1	TRUE	0	0.261179346541814	1		488	327	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286830	33286830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775787032	NA	P-0021218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	166	648	0	ENST00000374542.5:c.2107C>T	p.Pro703Ser	p.P703S	ENST00000374542	NM_001141970.1	703	Cca/Tca	7/8	1	2	FACETS	0.842	0.78	0.907	1	0.994	1	CLONAL	3	TRUE	1	0.261179346541814	2		648	503	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877199	151877200	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	179	572	0	ENST00000262189.6:c.7161dup	p.Arg2388ThrfsTer2	p.R2388Tfs*2	ENST00000262189	NM_170606.2	2387	-/A	37/59	0.218934541686142	3	FACETS	0.967	0.898	1	1	0.99	1	CLONAL	3	TRUE	1	0.261179346541814	3		572	534	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0021219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	553	795	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.612775215085977	3	FACETS	1	0.997	1			1	CLONAL	3	TRUE	NA	0.649735623734322	3		796	666	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0021219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	210	418	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.649735623734322	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.649735623734322	3		418	389	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11297916	11297916	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	159	655	2	ENST00000361445.4:c.2192G>A	p.Arg731His	p.R731H	ENST00000361445	NM_004958.3	731	cGc/cAc	13/58	0.579200868296718	3	FACETS	1	0.977	1	0.577	0.532	0.624	CLONAL	1	TRUE	1	0.649735623734322	3		657	562	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514472	103514473	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	33	379	3	ENST00000355739.4:c.973_974delinsTT	p.Pro325Leu	p.P325L	ENST00000355739	NM_000123.3	325	CCa/TTa	8/15	0.358298111149109	3	FACETS	0.45	0.368	0.542	0.15	0.122	0.181	INDETERMINATE	1	TRUE	0	0.649735623734322	3		382	299	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114133	73114133	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	114	663	0	ENST00000356692.5:c.769A>G	p.Arg257Gly	p.R257G	ENST00000356692		257	Aga/Gga	8/9	0.649735623734322	4	FACETS	0.823	0.742	0.909	0.412	0.371	0.455	CLONAL	1	TRUE	2	0.649735623734322	4		663	703	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224201	53224201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782064942	NA	P-0021219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	176	490	2	ENST00000375401.3:c.3350G>A	p.Arg1117Gln	p.R1117Q	ENST00000375401	NM_004187.3	1117	cGg/cAg	22/26	0.348912484737891	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.649735623734322	2		492	434	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288616	33288621	+	inframe_deletion	In_Frame_Del	DEL	CATGAG	CATGAG	-	novel	NA	P-0021222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	405	642	0	ENST00000374542.5:c.931_936del	p.Leu311_Met312del	p.L311_M312del	ENST00000374542	NM_001141970.1	311	CTCATG/-	3/8	0.919450537277968	1	FACETS	0.958	0.932	0.982	0.958	0.932	0.982	CLONAL	1	TRUE	0	0.919450537277968	1		642	497	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0021224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	105	916	3	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.533336103098968	5	FACETS	0.99	0.896	1			1	CLONAL	2	FALSE	NA	0.533336103098968	5		919	358	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207076	1207077	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs121913319	NA	P-0021224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	351	944	0	ENST00000326873.7:c.169dup	p.Glu57GlyfsTer106	p.E57Gfs*106	ENST00000326873	NM_000455.4	55	ctg/ctGg	1/10	0.533336103098968	5	FACETS	1	0.972	1	0.813	0.78	0.845	CLONAL	4	FALSE	0	0.533336103098968	5		944	583	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226424	2226424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	666	941	0	ENST00000398665.3:c.3904G>T	p.Gly1302Trp	p.G1302W	ENST00000398665	NM_032482.2	1302	Ggg/Tgg	27/28	0.533336103098968	5	FACETS	1	0.995	1	0.887	0.862	0.911	CLONAL	4	FALSE	0	0.533336103098968	5		941	1014	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058697	47058709	+	frameshift_variant	Frame_Shift_Del	DEL	AGGATTCTTACAG	AGGATTCTTACAG	-	novel	NA	P-0021224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	48	852	0	ENST00000409792.3:c.7569_7581del	p.Tyr2523Ter	p.Y2523*	ENST00000409792	NM_014159.6	2523	taCTGTAAGAATCCT/ta	21/21	0.4305379660646	3	FACETS	0.844	0.731	0.962	0.844	0.731	0.962	CLONAL	2	FALSE	1	0.533336103098968	3		852	135	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968622	55968622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	46	1035	0	ENST00000263923.4:c.2041G>A	p.Gly681Arg	p.G681R	ENST00000263923	NM_002253.2	681	Ggg/Agg	14/30	0.239579798290955	3	FACETS	0.918	0.795	1	0.612	0.53	0.697	INDETERMINATE	2	FALSE	0	0.533336103098968	3		1035	119	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048793	180048793	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	172	989	1	ENST00000261937.6:c.1769G>A	p.Trp590Ter	p.W590*	ENST00000261937	NM_182925.4	590	tGg/tAg	13/30	0.513840192064351	3	FACETS	0.859	0.79	0.931	0.43	0.395	0.466	CLONAL	1	FALSE	1	0.533336103098968	3		990	951	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	82	669	0				ENST00000310581	NM_198253.2	-/1132			0.18217993869528	3	FACETS	1	0.935	1	0.545	0.481	0.614	CLONAL	1	TRUE	1	0.249502905721305	3		669	678	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0021226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	62	1047	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.477	0.41	0.55	0.477	0.41	0.55	SUBCLONAL	1	TRUE	1	0.249502905721305	2		1047	1042	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0021226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	85	990	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	1	2	FACETS	0.641	0.565	0.723	0.641	0.565	0.723	SUBCLONAL	1	TRUE	1	0.249502905721305	2		990	1063	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47205368	47205368	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	59	678	0	ENST00000409792.3:c.47A>G	p.Tyr16Cys	p.Y16C	ENST00000409792	NM_014159.6	16	tAc/tGc	1/21	1	2	FACETS	0.558	0.479	0.645	0.558	0.479	0.645	SUBCLONAL	1	TRUE	1	0.249502905721305	2		678	847	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0021227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	150	931	1	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	1	2	FACETS	1	0.942	1	1	0.991	1	CLONAL	2	FALSE	1	0.161850562684347	2		932	891	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031973	26031973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	35	621	0	ENST00000244661.2:c.316G>C	p.Glu106Gln	p.E106Q	ENST00000244661	NM_003537.3	106	Gag/Cag	1/1	1	2	FACETS	0.782	0.64	0.942	0.782	0.64	0.942	CLONAL	1	FALSE	1	0.161850562684347	2		621	553	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248768	212248768	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	38	410	0	ENST00000342788.4:c.3499G>T	p.Glu1167Ter	p.E1167*	ENST00000342788	NM_005235.2	1167	Gag/Tag	28/28	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	1	0.161850562684347	2		410	373	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115595	108115595	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs769166447	NA	P-0021227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	112	911	0	ENST00000278616.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000278616	NM_000051.3	248	cGa/cTa	7/63	0.158194597844042	2	FACETS	0.896	0.806	0.992	0.896	0.806	0.992	CLONAL	2	FALSE	0	0.161850562684347	2		911	772	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988819	41988820	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0021227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	97	888	0	ENST00000219905.7:c.1611_1612del	p.Arg538SerfsTer17	p.R538Sfs*17	ENST00000219905	NM_001164273.1	537	ctCAga/ctga	3/24	1	2	FACETS	0.771	0.687	0.861	1	0.981	1	SUBCLONAL	2	FALSE	1	0.161850562684347	2		888	777	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463286	25463286	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	58	684	0	ENST00000264709.3:c.2207G>T	p.Arg736Leu	p.R736L	ENST00000264709	NM_175629.2	736	cGc/cTc	19/23	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.161850562684347	2		684	544	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593408	215593408	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	18	375	0	ENST00000260947.4:c.2326G>C	p.Asp776His	p.D776H	ENST00000260947	NM_000465.2	776	Gac/Cac	11/11	1	2	FACETS	0.749	0.564	0.968	0.749	0.564	0.968	CLONAL	1	FALSE	1	0.161850562684347	2		375	297	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594016	55594016	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	49	694	2	ENST00000288135.5:c.1802G>T	p.Gly601Val	p.G601V	ENST00000288135	NM_000222.2	601	gGg/gTg	12/21	1	2	FACETS	0.966	0.817	1	0.966	0.817	1	CLONAL	1	FALSE	1	0.161850562684347	2		696	627	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038844	47038844	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	92	968	0	ENST00000377604.3:c.853del	p.Gln285LysfsTer23	p.Q285Kfs*23	ENST00000377604	NM_001204468.1	284	tCc/tc	9/24	1	2	FACETS	0.758	0.673	0.848	1	0.98	1	SUBCLONAL	2	FALSE	1	0.161850562684347	2		968	750	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256174	123256174	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1564875549	NA	P-0021228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	24	858	7	ENST00000358487.5:c.1735C>T	p.Arg579Trp	p.R579W	ENST00000358487	NM_000141.4	579	Cgg/Tgg	13/18	0.405276602092701	1	FACETS	0.249	0.195	0.312	0.249	0.195	0.312	SUBCLONAL	1	FALSE	0	0.43729467501961	1		865	344	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603007	48603007	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0021228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	20	514	0	ENST00000342988.3:c.1309-1G>T		p.X437_splice	ENST00000342988	NM_005359.5	437			0.43729467501961	1	FACETS	0.3	0.23	0.382	0.3	0.23	0.382	SUBCLONAL	1	FALSE	0	0.43729467501961	1		514	238	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753432	42753432	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	63	856	0	ENST00000222329.4:c.832A>G	p.Thr278Ala	p.T278A	ENST00000222329	NM_006494.2	278	Act/Gct	4/4	0.121351593332441	0	FACETS	0.466	0.405	0.531			1	INDETERMINATE	1	FALSE	0	0.43729467501961	0		856	348	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022629	31022629	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	77	953	1	ENST00000375687.4:c.2114A>G	p.Glu705Gly	p.E705G	ENST00000375687	NM_015338.5	705	gAg/gGg	13/13	0.43729467501961	1	FACETS	0.99	0.879	1	0.99	0.879	1	CLONAL	1	FALSE	0	0.43729467501961	1		954	278	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958606	38958606	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1358737956	NA	P-0021228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	15	414	0	ENST00000357387.3:c.2359C>G	p.Leu787Val	p.L787V	ENST00000357387	NM_152756.3	787	Ctc/Gtc	24/38	0.335080049251561	3	FACETS	0.325	0.238	0.431	0.163	0.119	0.216	SUBCLONAL	1	FALSE	1	0.43729467501961	3		414	257	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139818376	139818376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	14	1021	2	ENST00000247668.2:c.1211G>A	p.Gly404Glu	p.G404E	ENST00000247668	NM_021138.3	404	gGa/gAa	10/11	0.43729467501961	1	FACETS	0.187	0.134	0.25	0.187	0.134	0.25	SUBCLONAL	1	FALSE	0	0.43729467501961	1		1023	268	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922293	100922293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149186732	NA	P-0021229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	113	469	0	ENST00000325455.5:c.2219G>A	p.Arg740Gln	p.R740Q	ENST00000325455	NM_001202474.3	740	cGa/cAa	5/8	0.702729154038772	1	FACETS	0.957	0.883	1	0.957	0.883	1	CLONAL	1	TRUE	0	0.702729154038772	1		469	218	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0021230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	127	857	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.257664425362514	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.257664425362514	1		859	762	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0021232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	276	733	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.483545009617873	3	FACETS	0.824	0.778	0.871	0.824	0.778	0.871	CLONAL	2	TRUE	1	0.61496965221736	3		733	712	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0021232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	123	772	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.741	0.673	0.812	0.741	0.673	0.812	SUBCLONAL	1	TRUE	1	0.61496965221736	2		772	540	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0021232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	182	465	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.61496965221736	2	FACETS	0.873	0.821	0.925	0.873	0.821	0.925	CLONAL	2	TRUE	0	0.61496965221736	2		465	339	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0021232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	74	753	2	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.349462400444934	3	FACETS	0.413	0.361	0.469	0.206	0.18	0.235	INDETERMINATE	1	TRUE	1	0.61496965221736	3		755	762	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351412	89351412	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	141	838	0	ENST00000301030.4:c.1538C>A	p.Ser513Tyr	p.S513Y	ENST00000301030	NM_001256183.1	513	tCc/tAc	9/13	1	2	FACETS	0.655	0.598	0.715	0.655	0.598	0.715	SUBCLONAL	1	TRUE	1	0.61496965221736	2		838	700	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38991161	38991161	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1346388651	NA	P-0021232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	94	748	0	ENST00000357387.3:c.473C>T	p.Ala158Val	p.A158V	ENST00000357387	NM_152756.3	158	gCt/gTt	7/38	1	2	FACETS	0.59	0.527	0.657	0.59	0.527	0.657	SUBCLONAL	1	TRUE	1	0.61496965221736	2		748	518	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950518	68950518	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	78	590	1	ENST00000288368.4:c.830G>T	p.Arg277Ile	p.R277I	ENST00000288368	NM_024870.2	277	aGa/aTa	7/40	0.6053599120116	4	FACETS	0.55	0.483	0.622	0.183	0.161	0.208	SUBCLONAL	1	TRUE	1	0.61496965221736	4		591	745	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631839	90631839	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519906	NA	P-0021233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	28	822	0	ENST00000330062.3:c.514A>G	p.Arg172Gly	p.R172G	ENST00000330062	NM_002168.2	172	Agg/Ggg	4/11	1	2	FACETS	0.588	0.468	0.726	0.588	0.468	0.726	SUBCLONAL	1	TRUE	1	0.14	2		822	680	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417887	32417887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1564972874	NA	P-0021233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	60	869	0	ENST00000332351.3:c.1165C>T	p.Arg389Cys	p.R389C	ENST00000332351	NM_024426.4	389	Cgc/Tgc	7/10	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.14	2		869	840	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637684	52637684	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	37	977	0	ENST00000394830.3:c.2632G>T	p.Glu878Ter	p.E878*	ENST00000394830	NM_018313.4	878	Gaa/Taa	18/30	1	2	FACETS	0.981	0.807	1	0.981	0.807	1	CLONAL	1	TRUE	1	0.14	2		977	539	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0021235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	194	784	4	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.291171926427975	3	FACETS	0.98	0.909	1	0.98	0.909	1	CLONAL	2	TRUE	1	0.291171926427975	3		788	779	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974727	21974744	+	inframe_deletion	In_Frame_Del	DEL	CCTCCAGCAGCGCCCGCA	CCTCCAGCAGCGCCCGCA	-	novel	NA	P-0021235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	107	438	0	ENST00000304494.5:c.83_100del	p.Val28_Glu33del	p.V28_E33del	ENST00000304494	NM_000077.4	28	gTGCGGGCGCTGCTGGAGGcg/gcg	1/3	0.291171926427975	1	FACETS	0.771	0.697	0.849	1	0.985	1	SUBCLONAL	2	TRUE	0	0.291171926427975	1		438	407	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573882	41573882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758996869	NA	P-0021235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	213	915	1	ENST00000263253.7:c.6167G>A	p.Arg2056Gln	p.R2056Q	ENST00000263253	NM_001429.3	2056	cGg/cAg	31/31	0.291171926427975	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	0	0.291171926427975	2		916	727	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0021236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	150	916	3	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.26	2		919	1134	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159748	20159748	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	57	648	0	ENST00000379607.5:c.11A>G	p.Asn4Ser	p.N4S	ENST00000379607	NM_001412.3	4	aAt/aGt	1/7	1	2	FACETS	0.937	0.805	1	0.937	0.805	1	CLONAL	1	TRUE	1	0.26	2		648	468	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281768	49281768	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148425155	NA	P-0021236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	105	902	1	ENST00000282018.3:c.815C>T	p.Thr272Met	p.T272M	ENST00000282018	NM_020377.2	272	aCg/aTg	1/1	1	2	FACETS	0.857	0.766	0.953	0.857	0.766	0.953	CLONAL	1	TRUE	1	0.26	2		903	943	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021451	31021451	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	44	799	0	ENST00000375687.4:c.1450G>T	p.Glu484Ter	p.E484*	ENST00000375687	NM_015338.5	484	Gag/Tag	12/13	1	2	FACETS	0.542	0.454	0.641	0.542	0.454	0.641	SUBCLONAL	1	TRUE	1	0.26	2		799	624	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739657	41739657	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	128	1105	0	ENST00000242208.4:c.316G>T	p.Asp106Tyr	p.D106Y	ENST00000242208	NM_002192.2	106	Gac/Tac	2/3	1	2	FACETS	0.98	0.887	1	0.98	0.887	1	CLONAL	1	TRUE	1	0.26	2		1105	1005	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628437	86628437	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	62	504	0	ENST00000274376.6:c.808del	p.Tyr270ThrfsTer9	p.Y270Tfs*9	ENST00000274376	NM_002890.2	269	cTt/ct	3/25	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.40818338239508	2		504	301	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685322	86685326	+	frameshift_variant	Frame_Shift_Del	DEL	GTAAT	GTAAT	-	novel	NA	P-0021237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	42	248	0	ENST00000274376.6:c.3039_3043del	p.Ser1013ArgfsTer31	p.S1013Rfs*31	ENST00000274376	NM_002890.2	1013	aGTAAT/a	24/25	1	2	FACETS	0.817	0.687	0.958	0.817	0.687	0.958	CLONAL	1	TRUE	1	0.40818338239508	2		248	252	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797769	32797769	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs78328107	NA	P-0021238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	47	1009	3	ENST00000374899.4:c.1733C>T	p.Ala578Val	p.A578V	ENST00000374899	NM_018833.2	578	gCg/gTg	10/12	1	2	FACETS	0.144	0.121	0.17	0.144	0.121	0.17	SUBCLONAL	1	TRUE	1	0.765117658638715	2		1012	854	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216588	108216592	+	protein_altering_variant	In_Frame_Del	DEL	TTGAG	TTGAG	AT	novel	NA	P-0021239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	101	601	2	ENST00000278616.4:c.8537_8541delinsAT	p.Phe2846_Glu2847delinsTyr	p.F2846_E2847delinsY	ENST00000278616	NM_000051.3	2846	tTTGAG/tAT	58/63	0.234184392134973	2	FACETS	1	0.98	1	0.715	0.64	0.794	CLONAL	1	TRUE	0	0.234184392134973	2		603	603	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021492	42021492	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	106	933	0	ENST00000219905.7:c.3788C>A	p.Ser1263Ter	p.S1263*	ENST00000219905	NM_001164273.1	1263	tCa/tAa	11/24	0.234184392134973	1	FACETS	0.908	0.813	1	0.908	0.813	1	CLONAL	1	TRUE	0	0.234184392134973	1		933	880	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846086	68846086	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	101	903	2	ENST00000261769.5:c.1057G>T	p.Glu353Ter	p.E353*	ENST00000261769	NM_004360.3	353	Gag/Tag	8/16	0.231324260948429	1	FACETS	0.91	0.813	1	0.91	0.813	1	CLONAL	1	TRUE	0	0.234184392134973	1		905	837	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151168677	151168751	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTAATCACTTCAAAACTATAAAACAAAAAGTATAAATTAGACATCCATTTTAATGTTGAAGTTTTTAAATGTATG	TTAATCACTTCAAAACTATAAAACAAAAAGTATAAATTAGACATCCATTTTAATGTTGAAGTTTTTAAATGTATG	-	novel	NA	P-0021239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	71	589	0	ENST00000262187.5:c.276-60_290del		p.X92_splice	ENST00000262187	NM_005614.3	92		5/8	1	2	FACETS	0.76	0.662	0.866	0.76	0.662	0.866	SUBCLONAL	1	TRUE	1	0.234184392134973	2		589	798	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004254	29004254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143093353	NA	P-0021240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	108	763	3	ENST00000282397.4:c.1039G>A	p.Val347Ile	p.V347I	ENST00000282397	NM_002019.4	347	Gta/Ata	8/30	0.800886925990135	3	FACETS	0.882	0.798	0.97	0.441	0.399	0.485	CLONAL	1	TRUE	1	0.839763254556893	3		766	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578434	+	stop_gained	Nonsense_Mutation	INS	-	-	ACTGCT	novel	NA	P-0021240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	379	1010	0	ENST00000269305.4:c.491_496dup	p.Gln165_Ser166insTer	p.Q165_S166ins*	ENST00000269305	NM_001126112.2	166	tca/tAGCAGTca	5/11	0.787158643985693	2	FACETS	0.875	0.846	0.902	0.875	0.846	0.902	CLONAL	2	TRUE	0	0.839763254556893	2		1010	516	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383862	84383863	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0021240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	117	1043	0	ENST00000321945.7:c.989_990del	p.Thr330ArgfsTer4	p.T330Rfs*4	ENST00000321945	NM_139076.2	330	aCT/a	9/9	0.818449800277858	3	FACETS	0.931	0.846	1	0.465	0.423	0.51	CLONAL	1	TRUE	1	0.839763254556893	3		1043	425	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862980	117862981	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0021240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	153	863	0	ENST00000297338.2:c.1496_1497del	p.Ile499ThrfsTer37	p.I499Tfs*37	ENST00000297338	NM_006265.2	499	aTA/a	12/14	0.743424848255967	4	FACETS	0.816	0.754	0.878	0.816	0.754	0.878	CLONAL	2	TRUE	2	0.839763254556893	4		863	411	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115947	8115951	+	frameshift_variant	Frame_Shift_Del	DEL	ACCAC	ACCAC	-	novel	NA	P-0021242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	88	636	0	ENST00000346208.3:c.1298_1302del	p.His433ProfsTer72	p.H433Pfs*72	ENST00000346208		431	ggACCACac/ggac	6/6	1	2	FACETS	0.701	0.623	0.784	0.701	0.623	0.784	SUBCLONAL	1	TRUE	1	0.490557626623507	2		636	512	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984779	11984783	+	frameshift_variant	Frame_Shift_Del	DEL	GGACG	GGACG	-	novel	NA	P-0021242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	73	625	0	ENST00000353533.5:c.325_329del	p.Gly109ArgfsTer21	p.G109Rfs*21	ENST00000353533	NM_003010.3	109	GGACGa/a	3/11	0.490557626623507	1	FACETS	0.564	0.496	0.637	0.564	0.496	0.637	SUBCLONAL	1	TRUE	0	0.490557626623507	1		625	398	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933889	39933889	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	213	906	0	ENST00000378444.4:c.710T>A	p.Val237Asp	p.V237D	ENST00000378444	NM_001123385.1	237	gTc/gAc	4/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.490557626623507	2		906	763	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs864622237	NA	P-0021243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	332	976	0	ENST00000269305.4:c.700T>G	p.Tyr234Asp	p.Y234D	ENST00000269305	NM_001126112.2	234	Tac/Gac	7/11	0.580006807213417	2	FACETS	0.996	0.953	1	0.996	0.953	1	CLONAL	2	TRUE	0	0.581846908321938	2		976	573	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0021249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	143	860	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.839	0.767	0.913	0.839	0.767	0.913	CLONAL	1	TRUE	1	0.565642816900787	2		860	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0021249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	247	784	4	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.565642816900787	1	FACETS	0.974	0.917	1	0.974	0.917	1	CLONAL	1	TRUE	0	0.565642816900787	1		788	643	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573584	48573584	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	112	552	0	ENST00000342988.3:c.170del	p.Leu57Ter	p.L57*	ENST00000342988	NM_005359.5	56	tcT/tc	2/12	0.565642816900787	1	FACETS	0.91	0.83	0.993	0.91	0.83	0.993	CLONAL	1	TRUE	0	0.565642816900787	1		552	312	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971032	21971038	+	frameshift_variant	Frame_Shift_Del	DEL	GCATCGC	GCATCGC	-	novel	NA	P-0021249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	150	636	0	ENST00000304494.5:c.320_326del	p.Arg107ProfsTer37	p.R107Pfs*37	ENST00000304494	NM_000077.4	107	cGCGATGCc/cc	2/3	0.565642816900787	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.565642816900787	1		636	363	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	170	669	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.945	0.878	1	0.945	0.878	1	CLONAL	1	TRUE	1	0.780118158410027	2		669	461	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs149840192	NA	P-0021250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	15801	913	0	ENST00000275493.2:c.866C>A	p.Ala289Asp	p.A289D	ENST00000275493	NM_005228.3	289	gCc/gAc	7/28	0.780118158410027	23	FACETS	0.981	0.978	0.983			1	CLONAL	23	TRUE	NA	0.780118158410027	23		913	16508	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41542772	41542772	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200624197	NA	P-0021250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	368	782	2	ENST00000263253.7:c.2083C>T	p.Arg695Cys	p.R695C	ENST00000263253	NM_001429.3	695	Cgt/Tgt	11/31	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.780118158410027	2		784	943	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872672	136872672	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs751975722	NA	P-0021250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	72	693	1	ENST00000241393.3:c.826T>A	p.Phe276Ile	p.F276I	ENST00000241393	NM_003467.2	276	Ttt/Att	2/2	1	2	FACETS	0.247	0.216	0.282	0.247	0.216	0.282	SUBCLONAL	1	TRUE	1	0.780118158410027	2		694	746	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0021253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	70	720	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.21	2		720	479	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004254	29004254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143093353	NA	P-0021254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	94	763	3	ENST00000282397.4:c.1039G>A	p.Val347Ile	p.V347I	ENST00000282397	NM_002019.4	347	Gta/Ata	8/30	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.371692591556186	2		766	408	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202233	108202233	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	75	755	0	ENST00000278616.4:c.7578A>T	p.Arg2526Ser	p.R2526S	ENST00000278616	NM_000051.3	2526	agA/agT	51/63	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.371692591556186	2		755	363	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206669	108206669	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0021254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	96	613	0	ENST00000278616.4:c.8249T>A	p.Leu2750Ter	p.L2750*	ENST00000278616	NM_000051.3	2750	tTa/tAa	56/63	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.371692591556186	2		613	483	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912436	32912437	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	33	471	0	ENST00000380152.3:c.3947dup	p.Asn1316LysfsTer3	p.N1316Kfs*3	ENST00000380152		1315	aga/agAa	11/27	1	2	FACETS	0.756	0.619	0.907	0.756	0.619	0.907	CLONAL	1	TRUE	1	0.371692591556186	2		471	235	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	620	669	0				ENST00000310581	NM_198253.2	-/1132			0.568268218546754	4	FACETS	1	0.992	1	1	0.998	1	CLONAL	4	FALSE	2	0.568268218546754	4		669	823	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0021255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	801	785	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.567270815916415	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	4	FALSE	0	0.568268218546754	4		786	1103	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105667	27105667	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	274	342	0	ENST00000324856.7:c.5278G>T	p.Glu1760Ter	p.E1760*	ENST00000324856	NM_006015.4	1760	Gag/Tag	20/20	NA	2	FACETS	0.915	0.869	0.96			1	INDETERMINATE	2	FALSE	NA	0.568268218546754	2		342	527	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444289	50444289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	257	425	0	ENST00000331340.3:c.219G>A	p.Met73Ile	p.M73I	ENST00000331340	NM_006060.4	73	atG/atA	4/8	0.493039925178925	4	FACETS	0.84	0.794	0.886	0.84	0.794	0.886	CLONAL	3	FALSE	1	0.568268218546754	4		425	563	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784896	9784896	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	402	703	0	ENST00000377346.4:c.2899C>A	p.Leu967Met	p.L967M	ENST00000377346	NM_005026.3	967	Ctg/Atg	23/24	0.331075964950655	5	FACETS	0.971	0.928	1	0.971	0.928	1	INDETERMINATE	3	FALSE	2	0.568268218546754	5		703	900	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105736	27105736	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	216	241	0	ENST00000324856.7:c.5347G>A	p.Glu1783Lys	p.E1783K	ENST00000324856	NM_006015.4	1783	Gaa/Aaa	20/20	NA	2	FACETS	0.886	0.836	0.936			1	INDETERMINATE	2	FALSE	NA	0.568268218546754	2		241	429	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608374	43608374	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1221	134	846	0	ENST00000355710.3:c.1722G>C	p.Glu574Asp	p.E574D	ENST00000355710	NM_020975.4	574	gaG/gaC	9/20	0.383003636293913	5	FACETS	0.645	0.584	0.709			1	SUBCLONAL	1	FALSE	NA	0.568268218546754	5		846	1355	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129725	108129725	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	315	470	0	ENST00000278616.4:c.2390del	p.Lys797ArgfsTer11	p.K797Rfs*11	ENST00000278616	NM_000051.3	797	Aag/ag	16/63	0.382709850075429	3	FACETS	0.819	0.776	0.863	0.819	0.776	0.863	CLONAL	2	FALSE	1	0.568268218546754	3		470	869	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342550	118342550	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	135	224	1	ENST00000534358.1:c.678del	p.Thr227ProfsTer5	p.T227Pfs*5	ENST00000534358	NM_005933.3	226	Ccc/cc	3/36	0.382709850075429	3	FACETS	1	0.987	1	0.725	0.665	0.786	CLONAL	1	FALSE	1	0.568268218546754	3		225	421	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431734	49431734	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	279	639	0	ENST00000301067.7:c.9405del	p.Ile3136LeufsTer6	p.I3136Lfs*6	ENST00000301067	NM_003482.3	3135	acC/ac	34/54	0.382709850075429	3	FACETS	0.866	0.818	0.915	0.866	0.818	0.915	CLONAL	2	FALSE	1	0.568268218546754	3		639	728	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433995	49433995	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759516070	NA	P-0021255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	104	696	0	ENST00000301067.7:c.7558C>T	p.Arg2520Trp	p.R2520W	ENST00000301067	NM_003482.3	2520	Cgg/Tgg	31/54	0.382709850075429	3	FACETS	0.593	0.531	0.66	0.297	0.265	0.33	SUBCLONAL	1	FALSE	1	0.568268218546754	3		696	792	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349046	11349046	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	187	471	1	ENST00000332029.2:c.290C>T	p.Pro97Leu	p.P97L	ENST00000332029	NM_003745.1	97	cCc/cTc	2/2	0.2750789681894	1	FACETS	1	0.985	1	1	0.985	1	INDETERMINATE	1	FALSE	0	0.568268218546754	1		472	403	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573505	48573505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	87	319	0	ENST00000342988.3:c.89G>A	p.Gly30Glu	p.G30E	ENST00000342988	NM_005359.5	30	gGa/gAa	2/12	0.30797101976747	5	FACETS	1	0.958	1			1	INDETERMINATE	1	FALSE	NA	0.568268218546754	5		319	486	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143273	30143273	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1043811061	NA	P-0021255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	354	653	0	ENST00000389048.3:c.253C>T	p.Pro85Ser	p.P85S	ENST00000389048	NM_004304.4	85	Ccc/Tcc	1/29	0.421037395127266	5	FACETS	1	0.99	1	0.779	0.74	0.819	CLONAL	2	FALSE	2	0.568268218546754	5		653	987	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47601108	47601108	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	74	505	0	ENST00000263735.4:c.346T>C	p.Cys116Arg	p.C116R	ENST00000263735	NM_002354.2	116	Tgc/Cgc	3/9	0.421037395127266	5	FACETS	0.522	0.455	0.593	0.174	0.151	0.198	SUBCLONAL	1	FALSE	2	0.568268218546754	5		505	925	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138407812	138407812	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	281	327	0	ENST00000289153.2:c.2041G>C	p.Glu681Gln	p.E681Q	ENST00000289153	NM_006219.2	681	Gaa/Caa	14/22	0.331075964950655	5	FACETS	1	0.989	1	0.795	0.751	0.84	INDETERMINATE	2	FALSE	2	0.568268218546754	5		327	768	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261533	142261533	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs149008479	NA	P-0021255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	260	413	0	ENST00000350721.4:c.3424A>G	p.Ser1142Gly	p.S1142G	ENST00000350721	NM_001184.3	1142	Agt/Ggt	17/47	0.331075964950655	5	FACETS	0.928	0.871	0.987	0.619	0.581	0.658	INDETERMINATE	2	FALSE	2	0.568268218546754	5		413	913	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44919378	44919382	+	frameshift_variant	Frame_Shift_Del	DEL	GGTGC	GGTGC	-	novel	NA	P-0021255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	229	182	0	ENST00000377967.4:c.1306_1310del	p.Gly436HisfsTer10	p.G436Hfs*10	ENST00000377967	NM_021140.2	436	GGTGCc/c	13/29	0.383003636293913	2	FACETS	0.893	0.857	0.926			1	CLONAL	3	FALSE	NA	0.568268218546754	2		182	301	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207021	1207021	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913324	NA	P-0021259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	230	823	0	ENST00000326873.7:c.109C>T	p.Gln37Ter	p.Q37*	ENST00000326873	NM_000455.4	37	Cag/Tag	1/10	0.429315185692169	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.429315185692169	1		823	803	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148875	119148875	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs397517076	NA	P-0021259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	141	388	0	ENST00000264033.4:c.1096-1G>T		p.X366_splice	ENST00000264033	NM_005188.3	366			0.429315185692169	2	FACETS	0.876	0.807	0.946	0.876	0.807	0.946	CLONAL	2	TRUE	0	0.429315185692169	2		388	375	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777677	9777677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145191685	NA	P-0021259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	179	728	2	ENST00000377346.4:c.1013G>A	p.Arg338Gln	p.R338Q	ENST00000377346	NM_005026.3	338	cGg/cAg	8/24	0.230478748703868	1	FACETS	0.866	0.8	0.935	0.866	0.8	0.935	INDETERMINATE	1	TRUE	0	0.429315185692169	1		730	756	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0021260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	109	552	0	ENST00000374080.3:c.3670C>T	p.Leu1224Phe	p.L1224F	ENST00000374080		1224	Ctc/Ttc	26/45	1	1	FACETS	0.882	0.798	0.97	1	0.987	1	CLONAL	2	FALSE	0	0.260162182813891	1		552	413	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450105	32450105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1190263054	NA	P-0021262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	52	829	0	ENST00000332351.3:c.707C>T	p.Ala236Val	p.A236V	ENST00000332351	NM_024426.4	236	gCg/gTg	2/10	0.183082790200582	3	FACETS	0.512	0.434	0.597	0.256	0.217	0.299	SUBCLONAL	1	FALSE	1	0.291020920125257	3		829	800	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	35	669	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.856	0.704	1	0.856	0.704	1	CLONAL	1	TRUE	1	0.27	2		669	303	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774776	73774776	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	93	757	0	ENST00000254810.4:c.311T>C	p.Leu104Pro	p.L104P	ENST00000254810	NM_005324.3	104	cTg/cCg	4/4	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.27	2		757	610	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218415	1218415	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs112675807	NA	P-0021265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	157	666	1	ENST00000326873.7:c.291-1G>T		p.X97_splice	ENST00000326873	NM_000455.4	97			1	2	FACETS	0.932	0.856	1	0.932	0.856	1	CLONAL	1	TRUE	1	0.47855131059911	2		667	704	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245464	133245464	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	119	739	0	ENST00000320574.5:c.1856G>C	p.Cys619Ser	p.C619S	ENST00000320574	NM_006231.2	619	tGt/tCt	17/49	NA	2	FACETS	0.693	0.626	0.763			1	INDETERMINATE	1	TRUE	NA	0.47855131059911	2		739	718	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52692227	52692228	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	128	427	0	ENST00000394830.3:c.632dup	p.Pro212AlafsTer3	p.P212Afs*3	ENST00000394830	NM_018313.4	211	ctg/ctTg	6/30	0.47855131059911	1	FACETS	0.99	0.906	1	0.99	0.906	1	CLONAL	1	TRUE	0	0.47855131059911	1		427	411	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808050	1808067	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GACGTGTACGTGTCCTGC	GACGTGTACGTGTCCTGC	-	novel	NA	P-0021265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	123	1032	0	ENST00000260795.2:c.2026_2030+13del		p.X676_splice	ENST00000260795		676		14/17	NA	2	FACETS	0.451	0.407	0.498			1	INDETERMINATE	1	TRUE	NA	0.47855131059911	2		1032	1139	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	115	669	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.745596299987974	2		669	296	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0021267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	162	458	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.745596299987974	2		459	404	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868193	37868193	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	287	732	0	ENST00000269571.5:c.914C>G	p.Ser305Cys	p.S305C	ENST00000269571		305	tCt/tGt	8/27	0.21294456999798	4	FACETS	0.761	0.717	0.805	0.761	0.717	0.805	INDETERMINATE	2	TRUE	2	0.745596299987974	4		732	883	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507340	8507340	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	117	565	1	ENST00000356435.5:c.1638C>A	p.Asn546Lys	p.N546K	ENST00000356435		546	aaC/aaA	11/35	1	2	FACETS	0.907	0.827	0.989	0.907	0.827	0.989	CLONAL	1	TRUE	1	0.745596299987974	2		566	346	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088653	27088653	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	55	885	0	ENST00000324856.7:c.2262G>C	p.Gln754His	p.Q754H	ENST00000324856	NM_006015.4	754	caG/caC	7/20	1	2	FACETS	0.184	0.156	0.214	0.184	0.156	0.214	SUBCLONAL	1	TRUE	1	0.745596299987974	2		885	803	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088728	27088729	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0021267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	60	807	0	ENST00000324856.7:c.2338_2339del	p.Gln780AspfsTer36	p.Q780Dfs*36	ENST00000324856	NM_006015.4	779	ggACag/ggag	7/20	1	2	FACETS	0.224	0.193	0.259	0.224	0.193	0.259	SUBCLONAL	1	TRUE	1	0.745596299987974	2		807	717	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625117	69625117	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	212	867	0	ENST00000334134.2:c.676C>T	p.Gln226Ter	p.Q226*	ENST00000334134	NM_005247.2	226	Cag/Tag	3/3	1	2	FACETS	0.938	0.877	1	0.938	0.877	1	CLONAL	1	TRUE	1	0.745596299987974	2		867	606	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716425	18716425	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs775783280	NA	P-0021267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	122	461	0	ENST00000266497.5:c.3772C>G	p.Leu1258Val	p.L1258V	ENST00000266497		1258	Ctc/Gtc	26/31	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.745596299987974	2		461	314	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81922789	81922789	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	144	425	1	ENST00000359376.3:c.778C>T	p.Gln260Ter	p.Q260*	ENST00000359376	NM_002661.3	260	Cag/Tag	10/33	0.745596299987974	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.745596299987974	1		426	239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	119	910	1	ENST00000269305.4:c.166G>A	p.Glu56Lys	p.E56K	ENST00000269305	NM_001126112.2	56	Gaa/Aaa	4/11	0.21294456999798	4	FACETS	0.595	0.537	0.658	0.298	0.268	0.329	INDETERMINATE	1	TRUE	2	0.745596299987974	4		911	936	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579545	7579545	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	105	860	1	ENST00000269305.4:c.142G>A	p.Asp48Asn	p.D48N	ENST00000269305	NM_001126112.2	48	Gac/Aac	4/11	0.21294456999798	4	FACETS	0.547	0.49	0.609	0.274	0.245	0.305	INDETERMINATE	1	TRUE	2	0.745596299987974	4		861	898	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004574	16004574	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	228	420	0	ENST00000268712.3:c.2680G>A	p.Glu894Lys	p.E894K	ENST00000268712	NM_006311.3	894	Gag/Aag	20/46	0.21294456999798	4	FACETS	0.971	0.913	1	0.971	0.913	1	INDETERMINATE	2	TRUE	2	0.745596299987974	4		420	550	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213965	2213965	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200802307	NA	P-0021267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	216	775	0	ENST00000398665.3:c.1777C>T	p.Arg593Cys	p.R593C	ENST00000398665	NM_032482.2	593	Cgc/Tgc	18/28	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.745596299987974	2		775	573	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222026	2222026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754105540	NA	P-0021267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	59	934	2	ENST00000398665.3:c.2858C>T	p.Pro953Leu	p.P953L	ENST00000398665	NM_032482.2	953	cCg/cTg	24/28	1	2	FACETS	0.224	0.192	0.259	0.224	0.192	0.259	SUBCLONAL	1	TRUE	1	0.745596299987974	2		936	707	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281566	15281566	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	64	1015	1	ENST00000263388.2:c.4807G>T	p.Asp1603Tyr	p.D1603Y	ENST00000263388	NM_000435.2	1603	Gat/Tat	26/33	1	2	FACETS	0.192	0.165	0.22	0.192	0.165	0.22	SUBCLONAL	1	TRUE	1	0.745596299987974	2		1016	896	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495208	212495208	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	130	724	0	ENST00000342788.4:c.2058G>C	p.Leu686Phe	p.L686F	ENST00000342788	NM_005235.2	686	ttG/ttC	17/28	1	2	FACETS	0.811	0.742	0.882	0.811	0.742	0.882	CLONAL	1	TRUE	1	0.745596299987974	2		724	430	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656866	45656866	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	209	670	0	ENST00000407780.3:c.290C>G	p.Ser97Cys	p.S97C	ENST00000407780	NM_001283052.1	97	tCc/tGc	3/7	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.745596299987974	2		670	549	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244167	153244167	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	239	694	0	ENST00000281708.4:c.1990G>T	p.Glu664Ter	p.E664*	ENST00000281708	NM_033632.3	664	Gag/Tag	12/12	1	2	FACETS	0.921	0.864	0.979	0.921	0.864	0.979	CLONAL	1	TRUE	1	0.745596299987974	2		694	696	SUCCESS
APC	324	MSKCC	GRCh37	5	112178268	112178268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs531178000	NA	P-0021267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	129	472	1	ENST00000257430.4:c.6977G>A	p.Arg2326Gln	p.R2326Q	ENST00000257430	NM_000038.5	2326	cGa/cAa	16/16	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.745596299987974	2		473	339	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748574	43748574	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	159	488	0	ENST00000523873.1:c.528G>C	p.Trp176Cys	p.W176C	ENST00000523873		176	tgG/tgC	6/8	1	2	FACETS	0.867	0.801	0.935	0.867	0.801	0.935	CLONAL	1	TRUE	1	0.745596299987974	2		488	492	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525095	157525095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	110	328	0	ENST00000346085.5:c.4990G>A	p.Asp1664Asn	p.D1664N	ENST00000346085	NM_020732.3	1664	Gat/Aat	19/20	0.745596299987974	1	FACETS	0.964	0.892	1	0.964	0.892	1	CLONAL	1	TRUE	0	0.745596299987974	1		328	192	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484129	8484129	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	157	513	0	ENST00000356435.5:c.3403G>C	p.Glu1135Gln	p.E1135Q	ENST00000356435		1135	Gag/Cag	19/35	1	2	FACETS	0.904	0.835	0.974	0.904	0.835	0.974	CLONAL	1	TRUE	1	0.745596299987974	2		513	466	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608969	100608969	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	196	315	0	ENST00000308731.7:c.1639C>A	p.Leu547Met	p.L547M	ENST00000308731	NM_000061.2	547	Ctg/Atg	17/19	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.745596299987974	1		315	254	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0021270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	979	857	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.577041717650931	7	FACETS	1	0.984	1			1	CLONAL	7	TRUE	NA	0.577041717650931	7		857	1183	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303790	65303790	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	novel	NA	P-0021270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	85	386	1	ENST00000342505.4:c.2968-3C>T		p.X990_splice	ENST00000342505	NM_002227.2	990			0.481991341519001	1	FACETS	0.927	0.835	1	0.927	0.835	1	CLONAL	1	TRUE	0	0.577041717650931	1		387	226	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864118	57864118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200306754	NA	P-0021270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	192	691	0	ENST00000228682.2:c.1595G>A	p.Arg532His	p.R532H	ENST00000228682	NM_005269.2	532	cGc/cAc	12/12	0.348914039923111	4	FACETS	0.956	0.891	1	0.956	0.891	1	CLONAL	2	TRUE	2	0.577041717650931	4		691	549	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0021270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	640	762	1	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.350615420854542	5	FACETS	0.938	0.915	0.961			1	CLONAL	5	TRUE	NA	0.577041717650931	5		763	882	SUCCESS
YES1	7525	MSKCC	GRCh37	18	732902	732902	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	271	747	1	ENST00000314574.4:c.1355del	p.Lys452SerfsTer14	p.K452Sfs*14	ENST00000314574	NM_005433.3	452	aAg/ag	11/12	0.494163710042222	3	FACETS	0.86	0.811	0.909	0.573	0.541	0.606	CLONAL	2	TRUE	0	0.577041717650931	3		748	704	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31504729	31504729	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	709	684	2	ENST00000344624.3:c.1601C>T	p.Pro534Leu	p.P534L	ENST00000344624		534	cCa/cTa	8/33	0.577041717650931	9	FACETS	0.961	0.929	0.992			1	CLONAL	5	TRUE	NA	0.577041717650931	9		686	1545	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497196	149497196	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	110	571	1	ENST00000261799.4:c.3122C>A	p.Ser1041Tyr	p.S1041Y	ENST00000261799	NM_002609.3	1041	tCc/tAc	22/23	0.577041717650931	5	FACETS	1	0.907	1	0.336	0.302	0.372	CLONAL	1	TRUE	2	0.577041717650931	5		572	705	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921606	39921606	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	136	362	0	ENST00000378444.4:c.4214C>T	p.Ser1405Leu	p.S1405L	ENST00000378444	NM_001123385.1	1405	tCg/tTg	10/15	0.577041717650931	2	FACETS	0.758	0.7	0.816			1	SUBCLONAL	2	TRUE	NA	0.577041717650931	2		362	311	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227950	123227950	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1192437434	NA	P-0021270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	125	310	0	ENST00000218089.9:c.3661G>T	p.Asp1221Tyr	p.D1221Y	ENST00000218089	NM_001042749.1	1221	Gat/Tat	33/35	0.577041717650931	2	FACETS	0.814	0.752	0.877			1	CLONAL	2	TRUE	NA	0.577041717650931	2		310	266	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0021271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	127	502	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.596266591713172	2		502	396	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249338	133249338	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	205	932	0	ENST00000320574.5:c.1561G>T	p.Glu521Ter	p.E521*	ENST00000320574	NM_006231.2	521	Gag/Tag	15/49	1	2	FACETS	0.934	0.869	1	0.934	0.869	1	CLONAL	1	TRUE	1	0.596266591713172	2		932	736	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066937	30066937	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771413120	NA	P-0021271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	114	489	0	ENST00000331968.5:c.2194C>T	p.Arg732Trp	p.R732W	ENST00000331968	NM_002742.2	732	Cgg/Tgg	16/18	1	2	FACETS	0.954	0.866	1	0.954	0.866	1	CLONAL	1	TRUE	1	0.596266591713172	2		489	401	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0021273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	228	1047	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.259765511235917	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.377195022725783	3		1049	682	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0021273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	228	795	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.321181441231571	2	FACETS	0.822	0.769	0.877	0.822	0.769	0.877	CLONAL	2	TRUE	0	0.377195022725783	2		796	735	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575671	48575671	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0021273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	162	679	0	ENST00000342988.3:c.431C>G	p.Ser144Ter	p.S144*	ENST00000342988	NM_005359.5	144	tCa/tGa	4/12	0.321181441231571	2	FACETS	0.922	0.853	0.992	0.922	0.853	0.992	CLONAL	2	TRUE	0	0.377195022725783	2		679	466	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37671997	37671997	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267604832	NA	P-0021274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	221	703	1	ENST00000447079.4:c.2782G>A	p.Glu928Lys	p.E928K	ENST00000447079	NM_015083.1	928	Gaa/Aaa	9/14	0.261542520010668	5	FACETS	1	0.973	1			1	CLONAL	4	TRUE	NA	0.261542520010668	5		704	553	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0021282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	63	552	0	ENST00000374080.3:c.3670C>T	p.Leu1224Phe	p.L1224F	ENST00000374080		1224	Ctc/Ttc	26/45	1	1	FACETS	0.786	0.683	0.895	0.786	0.683	0.895	SUBCLONAL	1	TRUE	0	0.377212997383664	1		552	345	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961332	41961332	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	16	526	0	ENST00000219905.7:c.240del	p.Asp80GlufsTer16	p.D80Efs*16	ENST00000219905	NM_001164273.1	80	gaT/ga	2/24	1	2	FACETS	0.293	0.216	0.384	0.293	0.216	0.384	SUBCLONAL	1	TRUE	1	0.377212997383664	2		526	290	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281193	15281193	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	68	1183	0	ENST00000263388.2:c.5063C>G	p.Ser1688Cys	p.S1688C	ENST00000263388	NM_000435.2	1688	tCt/tGt	27/33	1	2	FACETS	0.398	0.345	0.455	0.398	0.345	0.455	SUBCLONAL	1	TRUE	1	0.377212997383664	2		1183	907	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0021285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	22	715	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.211	0.162	0.267	0.211	0.162	0.267	SUBCLONAL	1	TRUE	1	0.35	2		716	597	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0021285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	150	528	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.35235436138537	4	FACETS	0.897	0.822	0.974			1	CLONAL	2	TRUE	NA	0.35	4		528	645	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579589	7579675	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GACTGTAGATGGGTGAAAAGAGCAGTCAGAGGACCAGGTCCTCAGCCCCCCAGCCCCCCAGCCCTCCAGGTCCCCAGCCCTCCAGGT	GACTGTAGATGGGTGAAAAGAGCAGTCAGAGGACCAGGTCCTCAGCCCCCCAGCCCCCCAGCCCTCCAGGTCCCCAGCCCTCCAGGT	-	novel	NA	P-0021286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	365	646	0	ENST00000269305.4:c.96+25_98del		p.X32_splice	ENST00000269305	NM_001126112.2	32		4/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		646	434	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0021288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	26	358	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.159	0.125	0.197	0.159	0.125	0.197	SUBCLONAL	1	TRUE	1	0.83	2		358	395	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566442	41566442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	193	515	0	ENST00000263253.7:c.4319C>T	p.Pro1440Leu	p.P1440L	ENST00000263253	NM_001429.3	1440	cCa/cTa	27/31	1	2	FACETS	0.896	0.836	0.957	0.896	0.836	0.957	CLONAL	1	TRUE	1	0.83	2		515	519	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0021289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	353	772	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.285417860358741	4	FACETS	0.921	0.878	0.965	0.921	0.878	0.965	CLONAL	4	TRUE	0	0.321208180255795	4		772	788	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149917	202149917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	86	749	0	ENST00000358485.4:c.1358C>T	p.Pro453Leu	p.P453L	ENST00000358485	NM_001080125.1	453	cCg/cTg	8/9	1	2	FACETS	0.897	0.795	1	0.897	0.795	1	CLONAL	1	TRUE	1	0.321208180255795	2		749	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0021289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	237	1043	2	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.321208180255795	2	FACETS	0.944	0.884	1	0.944	0.884	1	CLONAL	2	TRUE	0	0.321208180255795	2		1045	782	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346338	73346338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	77	632	1	ENST00000377767.4:c.1462G>A	p.Asp488Asn	p.D488N	ENST00000377767	NM_014953.3	488	Gat/Aat	10/21	1	2	FACETS	0.955	0.841	1	0.955	0.841	1	CLONAL	1	TRUE	1	0.321208180255795	2		633	502	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625120	69625120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782246758	NA	P-0021289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	89	826	4	ENST00000334134.2:c.673G>A	p.Val225Ile	p.V225I	ENST00000334134	NM_005247.2	225	Gtt/Att	3/3	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.321208180255795	2		830	544	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020769	37020769	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	57	704	0	ENST00000358127.4:c.76G>T	p.Val26Phe	p.V26F	ENST00000358127	NM_001280556.1	26	Gtt/Ttt	2/10	0.315047680668983	2	FACETS	0.718	0.617	0.829	0.359	0.308	0.415	SUBCLONAL	1	TRUE	0	0.321208180255795	2		704	494	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107180	27107180	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	172	701	0	ENST00000324856.7:c.6791C>A	p.Ser2264Ter	p.S2264*	ENST00000324856	NM_006015.4	2264	tCa/tAa	20/20	0.284381482866745	2	FACETS	0.887	0.82	0.955	0.887	0.82	0.955	CLONAL	2	TRUE	0	0.321208180255795	2		701	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573999	7574008	+	frameshift_variant	Frame_Shift_Del	DEL	TCTCGGAACA	TCTCGGAACA	-	novel	NA	P-0021289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	71	983	0	ENST00000269305.4:c.1019_1028del	p.Met340SerfsTer2	p.M340Sfs*2	ENST00000269305	NM_001126112.2	340	aTGTTCCGAGAg/ag	10/11	0.321208180255795	2	FACETS	0.623	0.543	0.709	0.311	0.271	0.355	SUBCLONAL	1	TRUE	0	0.321208180255795	2		983	710	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39251221	39251221	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	369	958	0	ENST00000402219.2:c.1132A>T	p.Thr378Ser	p.T378S	ENST00000402219	NM_005633.3	378	Aca/Tca	9/23	0.300608871743444	3	FACETS	0.857	0.815	0.9	0.857	0.815	0.9	CLONAL	3	TRUE	0	0.321208180255795	3		958	1037	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844792	156844792	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	72	793	0	ENST00000524377.1:c.1346G>A	p.Gly449Glu	p.G449E	ENST00000524377	NM_002529.3	449	gGg/gAg	11/17	0.289281995879129	3	FACETS	0.885	0.774	1	0.442	0.387	0.503	CLONAL	1	TRUE	1	0.321208180255795	3		793	588	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822682	72822682	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	77	806	0	ENST00000268489.5:c.9493C>T	p.Pro3165Ser	p.P3165S	ENST00000268489	NM_006885.3	3165	Ccc/Tcc	10/10	1	2	FACETS	0.765	0.672	0.865	0.765	0.672	0.865	SUBCLONAL	1	TRUE	1	0.321208180255795	2		806	627	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051370	13051370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1019627616	NA	P-0021289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	54	312	0	ENST00000316448.5:c.718G>A	p.Glu240Lys	p.E240K	ENST00000316448	NM_004343.3	240	Gag/Aag	6/9	0.292545365101176	3	FACETS	0.837	0.723	0.959	0.558	0.482	0.64	CLONAL	2	TRUE	0	0.321208180255795	3		312	233	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186501400	186501400	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs571299759	NA	P-0021289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	156	419	0	ENST00000323963.5:c.1A>G	p.Met1?	p.M1?	ENST00000323963		1	Atg/Gtg	1/11	0.321208180255795	5	FACETS	0.956	0.882	1	0.956	0.882	1	CLONAL	3	TRUE	2	0.321208180255795	5		419	502	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981942	70981942	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	91	1076	4	ENST00000276594.2:c.154C>A	p.Pro52Thr	p.P52T	ENST00000276594	NM_024504.3	52	Cct/Act	2/8	0.321208180255795	4	FACETS	0.802	0.711	0.9	0.267	0.237	0.3	CLONAL	1	TRUE	1	0.321208180255795	4		1080	933	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0021290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	154	710	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.917	0.847	0.99	0.917	0.847	0.99	CLONAL	1	TRUE	1	0.729809794275566	2		711	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576900	7576901	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0021290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	635	833	0	ENST00000269305.4:c.945_946del	p.Gln317AlafsTer19	p.Q317Afs*19	ENST00000269305	NM_001126112.2	315	tcTCcc/tccc	9/11	0.729809794275566	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.729809794275566	2		833	851	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs80338963	NA	P-0021290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	179	515	1	ENST00000342988.3:c.1081C>A	p.Arg361Ser	p.R361S	ENST00000342988	NM_005359.5	361	Cgc/Agc	9/12	0.729809794275566	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.729809794275566	1		516	286	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438183	438183	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	135	406	0	ENST00000399788.2:c.1786C>T	p.Arg596Cys	p.R596C	ENST00000399788	NM_001042603.1	596	Cgt/Tgt	14/28	1	2	FACETS	0.875	0.802	0.949	0.875	0.802	0.949	CLONAL	1	TRUE	1	0.729809794275566	2		406	423	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170608	108170608	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1555104799	NA	P-0021290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	100	433	0	ENST00000278616.4:c.5173G>T	p.Asp1725Tyr	p.D1725Y	ENST00000278616	NM_000051.3	1725	Gat/Tat	34/63	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.729809794275566	2		433	258	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636390	21636390	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	235	937	1	ENST00000421138.2:c.620C>A	p.Ala207Asp	p.A207D	ENST00000421138		207	gCc/gAc	7/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.729809794275566	2		938	637	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996231	73996231	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1186699933	NA	P-0021290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	147	393	1	ENST00000318443.5:c.965A>G	p.Asn322Ser	p.N322S	ENST00000318443	NM_001024736.1	322	aAt/aGt	5/10	1	2	FACETS	0.941	0.868	1	0.941	0.868	1	CLONAL	1	TRUE	1	0.729809794275566	2		394	428	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99440093	99440093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	423	690	0	ENST00000268035.6:c.1061C>T	p.Thr354Ile	p.T354I	ENST00000268035	NM_000875.3	354	aCc/aTc	4/21	0.729809794275566	3	FACETS	0.965	0.926	1	0.965	0.926	1	CLONAL	2	TRUE	1	0.729809794275566	3		690	820	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99486150	99486150	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0021290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	181	488	0	ENST00000268035.6:c.3458-2A>G		p.X1153_splice	ENST00000268035	NM_000875.3	1153			0.729809794275566	3	FACETS	0.966	0.894	1	0.483	0.447	0.52	CLONAL	1	TRUE	1	0.729809794275566	3		488	701	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979992	7979992	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1342884275	NA	P-0021290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	338	777	0	ENST00000319144.4:c.1345G>C	p.Gly449Arg	p.G449R	ENST00000319144	NM_001139.2	449	Ggg/Cgg	10/15	0.729809794275566	2	FACETS	1	0.968	1	0.513	0.487	0.54	CLONAL	1	TRUE	0	0.729809794275566	2		777	902	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448315	56448426	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCTCCAGCTTGACGATGCTGATGAATCCAGGCTCCAGATTGTCGTCATCACTGGCATTGCACAGGTACAGCGGGTGGGACTGCAGAGAGAGACAGACTTGGGTTAGGGAGG	CTCTCCAGCTTGACGATGCTGATGAATCCAGGCTCCAGATTGTCGTCATCACTGGCATTGCACAGGTACAGCGGGTGGGACTGCAGAGAGAGACAGACTTGGGTTAGGGAGG	-	novel	NA	P-0021290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	143	888	0	ENST00000407977.2:c.253-32_332del		p.X85_splice	ENST00000407977		85		3/10	0.729809794275566	1	FACETS	0.6	0.552	0.649	0.6	0.552	0.649	SUBCLONAL	1	TRUE	0	0.729809794275566	1		888	415	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212439	5212439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150241840	NA	P-0021290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	416	931	3	ENST00000357368.4:c.4678G>A	p.Val1560Met	p.V1560M	ENST00000357368	NM_002850.3	1560	Gtg/Atg	31/38	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.729809794275566	2		934	1061	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202123022	202123022	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781595738	NA	P-0021290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	148	607	0	ENST00000358485.4:c.68C>T	p.Pro23Leu	p.P23L	ENST00000358485	NM_001080125.1	23	cCc/cTc	1/9	1	2	FACETS	0.882	0.812	0.953	0.882	0.812	0.953	CLONAL	1	TRUE	1	0.729809794275566	2		607	460	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657031	45657031	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	270	638	0	ENST00000407780.3:c.125G>A	p.Gly42Glu	p.G42E	ENST00000407780	NM_001283052.1	42	gGa/gAa	3/7	1	2	FACETS	0.985	0.929	1	0.985	0.929	1	CLONAL	1	TRUE	1	0.729809794275566	2		638	751	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505404	157505406	+	frameshift_variant	Frame_Shift_Del	DEL	CTA	CTA	TT	novel	NA	P-0021290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	179	556	1	ENST00000346085.5:c.3385_3387delinsTT	p.Asn1130ThrfsTer12	p.N1130Tfs*12	ENST00000346085	NM_020732.3	1129	CTA/TT	13/20	1	2	FACETS	0.885	0.822	0.951	0.885	0.822	0.951	CLONAL	1	TRUE	1	0.729809794275566	2		557	554	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370889	55370917	+	frameshift_variant	Frame_Shift_Del	DEL	GCGAGTCCCGTATCCGGCGGCCGATGAAC	GCGAGTCCCGTATCCGGCGGCCGATGAAC	-	novel	NA	P-0021290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	309	768	0	ENST00000297316.4:c.193_221del	p.Glu65PhefsTer6	p.E65Ffs*6	ENST00000297316	NM_022454.3	64	gGCGAGTCCCGTATCCGGCGGCCGATGAAC/g	1/2	NA	2	FACETS	1	0.961	1			1	INDETERMINATE	1	TRUE	NA	0.729809794275566	2		768	832	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371656	55372034	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTTCGTGGAGGAGGCAGAGCGGCTGCGCGTGCAGCACATGCAGGACCACCCCAACTACAAGTACCGGCCGCGGCGGCGCAAGCAGGTGAAGCGGCTGAAGCGGGTGGAGGGCGGCTTCCTGCACGGCCTGGCTGAGCCGCAGGCGGCCGCGCTGGGCCCCGAGGGCGGCCGCGTGGCCATGGACGGCCTGGGCCTCCAGTTCCCCGAGCAGGGCTTCCCCGCCGGCCCGCCGCTGCTGCCTCCGCACATGGGCGGCCACTACCGCGACTGCCAGAGTCTGGGCGCGCCTCCGCTCGACGGCTACCCGTTGCCCACGCCCGACACGTCCCCGCTGGACGGCGTGGACCCCGACCCGGCTTTCTTCGCCGCCCCGATGC	CCCTTCGTGGAGGAGGCAGAGCGGCTGCGCGTGCAGCACATGCAGGACCACCCCAACTACAAGTACCGGCCGCGGCGGCGCAAGCAGGTGAAGCGGCTGAAGCGGGTGGAGGGCGGCTTCCTGCACGGCCTGGCTGAGCCGCAGGCGGCCGCGCTGGGCCCCGAGGGCGGCCGCGTGGCCATGGACGGCCTGGGCCTCCAGTTCCCCGAGCAGGGCTTCCCCGCCGGCCCGCCGCTGCTGCCTCCGCACATGGGCGGCCACTACCGCGACTGCCAGAGTCTGGGCGCGCCTCCGCTCGACGGCTACCCGTTGCCCACGCCCGACACGTCCCCGCTGGACGGCGTGGACCCCGACCCGGCTTTCTTCGCCGCCCCGATGC	-	novel	NA	P-0021290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	286	903	0	ENST00000297316.4:c.348_726del	p.Phe117GlyfsTer144	p.F117Gfs*144	ENST00000297316	NM_022454.3	116	CCCTTCGTGGAGGAGGCAGAGCGGCTGCGCGTGCAGCACATGCAGGACCACCCCAACTACAAGTACCGGCCGCGGCGGCGCAAGCAGGTGAAGCGGCTGAAGCGGGTGGAGGGCGGCTTCCTGCACGGCCTGGCTGAGCCGCAGGCGGCCGCGCTGGGCCCCGAGGGCGGCCGCGTGGCCATGGACGGCCTGGGCCTCCAGTTCCCCGAGCAGGGCTTCCCCGCCGGCCCGCCGCTGCTGCCTCCGCACATGGGCGGCCACTACCGCGACTGCCAGAGTCTGGGCGCGCCTCCGCTCGACGGCTACCCGTTGCCCACGCCCGACACGTCCCCGCTGGACGGCGTGGACCCCGACCCGGCTTTCTTCGCCGCCCCGATGCcc/cc	2/2	NA	2	FACETS	0.861	0.812	0.912			1	INDETERMINATE	1	TRUE	NA	0.729809794275566	2		903	910	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0021293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	177	662	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.953	0.888	1	0.953	0.888	1	CLONAL	1	TRUE	1	0.827233931787992	2		663	449	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0021293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	13	563	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.072	0.05	0.098	0.072	0.05	0.098	SUBCLONAL	1	TRUE	1	0.827233931787992	2		563	439	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0021293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	181	418	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	0.827233931787992	2		418	397	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444577	78444578	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0021293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	193	573	0	ENST00000370768.2:c.111_112del	p.Arg37SerfsTer11	p.R37Sfs*11	ENST00000370768	NM_003902.3	37	agAGcc/agcc	1/20	0.827233931787992	1	FACETS	0.891	0.844	0.937	0.891	0.844	0.937	CLONAL	1	TRUE	0	0.827233931787992	1		573	307	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794062	42794063	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0021293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	263	699	0	ENST00000575354.2:c.1426_1427del	p.Ser476TrpfsTer37	p.S476Wfs*37	ENST00000575354	NM_015125.3	475	GAg/g	9/20	0.827233931787992	1	FACETS	0.966	0.925	1	0.966	0.925	1	CLONAL	1	TRUE	0	0.827233931787992	1		699	386	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413067	139413069	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0021293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	354	712	0	ENST00000277541.6:c.1073_1075del	p.Tyr358del	p.Y358del	ENST00000277541	NM_017617.3	358	tACTgc/tgc	6/34	NA	2	FACETS	0.809	0.779	0.838			1	INDETERMINATE	2	TRUE	NA	0.827233931787992	2		712	529	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0021295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	3013	878	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.525301910655402	27	FACETS	0.983	0.974	0.993	0.944	0.935	0.953	CLONAL	24	TRUE	2	0.525301910655402	27		878	3678	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0021295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	2507	782	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.525301910655402	27	FACETS	0.996	0.986	1	0.956	0.946	0.966	CLONAL	24	TRUE	2	0.525301910655402	27		782	3021	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576853	7576853	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs11575996	NA	P-0021295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	360	821	0	ENST00000269305.4:c.993G>T	p.Gln331His	p.Q331H	ENST00000269305	NM_001126112.2	331	caG/caT	9/11	0.435485407938556	3	FACETS	0.889	0.851	0.926	0.889	0.851	0.926	CLONAL	3	TRUE	0	0.525301910655402	3		821	649	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120460296	120460296	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	64	765	1	ENST00000256646.2:c.6019G>A	p.Asp2007Asn	p.D2007N	ENST00000256646	NM_024408.3	2007	Gac/Aac	33/34	0.299204601789963	3	FACETS	0.574	0.497	0.657	0.191	0.165	0.219	INDETERMINATE	1	TRUE	0	0.525301910655402	3		766	536	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104375118	104375118	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	39	853	0	ENST00000369902.3:c.1116A>T	p.Lys372Asn	p.K372N	ENST00000369902	NM_016169.3	372	aaA/aaT	9/12	0.478412599728963	2	FACETS	0.3	0.248	0.358	0.15	0.124	0.179	SUBCLONAL	1	TRUE	0	0.525301910655402	2		853	495	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543330	65543330	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	62	723	1	ENST00000358664.4:c.347C>T	p.Pro116Leu	p.P116L	ENST00000358664	NM_002382.4	116	cCc/cTc	5/5	0.394925507897953	5	FACETS	0.608	0.525	0.699	0.203	0.175	0.233	SUBCLONAL	1	TRUE	2	0.525301910655402	5		724	694	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523142	176523142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778323767	NA	P-0021295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	31	959	1	ENST00000292408.4:c.1906G>A	p.Gly636Ser	p.G636S	ENST00000292408	NM_213647.1	636	Ggc/Agc	14/18	0.147538937458124	4	FACETS	0.305	0.245	0.372	0.152	0.122	0.186	INDETERMINATE	1	TRUE	2	0.525301910655402	4		960	591	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249092	55249092	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3478	304	904	0	ENST00000275493.2:c.2390G>C	p.Cys797Ser	p.C797S	ENST00000275493	NM_005228.3	797	tGc/tCc	20/28	0.525301910655402	27	FACETS	1	0.985	1	0.093	0.086	0.099	CLONAL	2	TRUE	2	0.525301910655402	27		904	3782	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151882692	151882692	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	31	554	0	ENST00000262189.6:c.5033T>C	p.Ile1678Thr	p.I1678T	ENST00000262189	NM_170606.2	1678	aTt/aCt	34/59	0.524487872170561	4	FACETS	0.344	0.278	0.42	0.172	0.139	0.21	SUBCLONAL	1	TRUE	2	0.525301910655402	4		554	523	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593613	55593614	+	missense_variant	Missense_Mutation	DNP	TT	TT	AG	novel	NA	P-0021296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	395	760	1	ENST00000288135.5:c.1679_1680delinsAG	p.Val560Glu	p.V560E	ENST00000288135	NM_000222.2	560	gTT/gAG	11/21	0.408465551739151	5	FACETS	1	0.987	1			1	CLONAL	2	TRUE	NA	0.408465551739151	5		761	1409	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099403	157099426	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAGCAGCAA	CAGCAGCAGCAGCAGCAGCAGCAA	-	rs770869529	NA	P-0021299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	56	354	0	ENST00000346085.5:c.369_392del	p.Gln124_Gln131del	p.Q124_Q131del	ENST00000346085	NM_020732.3	114	CAGCAGCAGCAGCAGCAGCAGCAA/-	1/20	1	2	FACETS	0.61	0.525	0.701	0.61	0.525	0.701	SUBCLONAL	1	TRUE	1	0.538716778350073	2		354	341	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805599	89805599	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	189	864	1	ENST00000389301.3:c.4109C>A	p.Ala1370Asp	p.A1370D	ENST00000389301	NM_000135.2	1370	gCt/gAt	41/43	1	2	FACETS	0.949	0.88	1	0.949	0.88	1	CLONAL	1	TRUE	1	0.538716778350073	2		865	739	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845959	151845959	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	172	841	3	ENST00000262189.6:c.13053del	p.Lys4351AsnfsTer5	p.K4351Nfs*5	ENST00000262189	NM_170606.2	4351	aaA/aa	52/59	1	2	FACETS	0.802	0.739	0.868	0.802	0.739	0.868	CLONAL	1	TRUE	1	0.538716778350073	2		844	796	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856070	151856070	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	211	719	2	ENST00000262189.6:c.11548C>T	p.Arg3850Ter	p.R3850*	ENST00000262189	NM_170606.2	3850	Cga/Tga	44/59	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.538716778350073	2		721	778	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	124	669	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.389631298602024	2		669	464	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0021302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	77	710	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.389631298602024	2		711	370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0021303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	397	919	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.606381837905596	2	FACETS	0.995	0.957	1	0.995	0.957	1	CLONAL	2	TRUE	0	0.606381837905596	2		919	658	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298470	11298470	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	73	627	0	ENST00000361445.4:c.1991T>A	p.Ile664Lys	p.I664K	ENST00000361445	NM_004958.3	664	aTa/aAa	12/58	0.606381837905596	4	FACETS	0.561	0.491	0.638	0.14	0.122	0.16	SUBCLONAL	1	TRUE	0	0.606381837905596	4		627	689	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17355187	17355187	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	57	873	0	ENST00000375499.3:c.331C>G	p.Leu111Val	p.L111V	ENST00000375499	NM_003000.2	111	Cta/Gta	4/8	0.606381837905596	4	FACETS	0.343	0.293	0.397	0.086	0.073	0.1	SUBCLONAL	1	TRUE	0	0.606381837905596	4		873	881	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204651	108204651	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	68	645	0	ENST00000278616.4:c.7966C>A	p.Leu2656Ile	p.L2656I	ENST00000278616	NM_000051.3	2656	Ctt/Att	54/63	NA	2	FACETS	0.626	0.548	0.71			1	INDETERMINATE	1	TRUE	NA	0.606381837905596	2		645	358	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435421	121435422	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0021303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	138	900	3	ENST00000257555.6:c.1454_1455delinsAG	p.Thr485Lys	p.T485K	ENST00000257555		485	aCC/aAG	7/10	0.606381837905596	2	FACETS	0.985	0.903	1	0.493	0.451	0.535	CLONAL	1	TRUE	0	0.606381837905596	2		903	462	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141101	55141101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745983139	NA	P-0021303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	112	726	1	ENST00000257290.5:c.1747G>A	p.Asp583Asn	p.D583N	ENST00000257290	NM_006206.4	583	Gac/Aac	12/23	0.528247228038328	5	FACETS	1	0.983	1	0.477	0.431	0.525	CLONAL	1	TRUE	2	0.606381837905596	5		727	493	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526508	31526508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1235	256	1147	1	ENST00000344624.3:c.532C>T	p.Pro178Ser	p.P178S	ENST00000344624		178	Cca/Tca	2/33	0.398022860176528	6	FACETS	1	0.988	1	0.313	0.292	0.335	CLONAL	1	TRUE	2	0.606381837905596	6		1148	1491	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389296	8389296	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	42	1013	1	ENST00000356435.5:c.4322G>T	p.Arg1441Ile	p.R1441I	ENST00000356435		1441	aGa/aTa	26/35	0.138834792846361	3	FACETS	0.321	0.267	0.38	0.107	0.089	0.127	INDETERMINATE	1	TRUE	0	0.606381837905596	3		1014	563	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760304	133760304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	38	663	0	ENST00000318560.5:c.2627G>A	p.Arg876Lys	p.R876K	ENST00000318560	NM_005157.4	876	aGg/aAg	11/11	0.606381837905596	2	FACETS	0.387	0.321	0.46	0.193	0.16	0.23	SUBCLONAL	1	TRUE	0	0.606381837905596	2		663	324	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430338	47430338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	85	931	1	ENST00000377045.4:c.1613G>A	p.Cys538Tyr	p.C538Y	ENST00000377045	NM_001654.4	538	tGc/tAc	15/16	0.40484619305897	3	FACETS	0.548	0.484	0.616	0.274	0.242	0.308	SUBCLONAL	1	TRUE	1	0.606381837905596	3		932	667	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650434	48650434	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	76	1026	1	ENST00000376670.3:c.404C>A	p.Thr135Asn	p.T135N	ENST00000376670	NM_002049.3	135	aCt/aAt	3/6	0.40484619305897	3	FACETS	0.511	0.448	0.579	0.256	0.224	0.29	SUBCLONAL	1	TRUE	1	0.606381837905596	3		1027	639	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0021311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	36	662	1				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	1	0.83	1	1	0.83	1	CLONAL	1	TRUE	0	0.16	1		663	410	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131505	202131505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	29	590	0	ENST00000358485.4:c.473C>T	p.Ser158Phe	p.S158F	ENST00000358485	NM_001080125.1	158	tCt/tTt	2/9	0.275367873433374	3	FACETS	0.804	0.644	0.986	0.402	0.322	0.493	CLONAL	1	TRUE	1	0.16	3		590	487	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843614	156843614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs797045060	NA	P-0021311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	78	1030	1	ENST00000524377.1:c.1040G>A	p.Arg347His	p.R347H	ENST00000524377	NM_002529.3	347	cGc/cAc	8/17	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.16	2		1031	876	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686299	30686299	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs767191783	NA	P-0021311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	99	703	0	ENST00000295754.5:c.155A>C	p.Lys52Thr	p.K52T	ENST00000295754	NM_003242.5	52	aAa/aCa	2/7	1	2	FACETS	0.864	0.772	0.962	1	0.984	1	CLONAL	2	TRUE	1	0.16	2		703	716	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307897	11307897	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	55	828	0	ENST00000361445.4:c.1095G>C	p.Leu365Phe	p.L365F	ENST00000361445	NM_004958.3	365	ttG/ttC	7/58	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.16	2		828	654	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258339	16258339	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	45	780	0	ENST00000375759.3:c.5604G>C	p.Leu1868Phe	p.L1868F	ENST00000375759	NM_015001.2	1868	ttG/ttC	11/15	1	2	FACETS	0.802	0.673	0.946	0.802	0.673	0.946	CLONAL	1	TRUE	1	0.16	2		780	701	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426318	49426318	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0021311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	67	1202	0	ENST00000301067.7:c.12170C>G	p.Ser4057Ter	p.S4057*	ENST00000301067	NM_003482.3	4057	tCa/tGa	39/54	0.275367873433374	3	FACETS	0.903	0.782	1	0.451	0.391	0.517	CLONAL	1	TRUE	1	0.16	3		1202	1002	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647397	23647397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749078410	NA	P-0021311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	53	883	2	ENST00000261584.4:c.470C>T	p.Ser157Leu	p.S157L	ENST00000261584	NM_024675.3	157	tCa/tTa	4/13	0.3	1	FACETS	0.988	0.842	1	0.988	0.842	1	CLONAL	1	TRUE	0	0.16	1		885	617	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475623	40475623	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	52	732	0	ENST00000264657.5:c.1621G>C	p.Gly541Arg	p.G541R	ENST00000264657	NM_139276.2	541	Ggg/Cgg	18/24	1	2	FACETS	0.925	0.786	1	0.925	0.786	1	CLONAL	1	TRUE	1	0.16	2		732	703	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306611	41306611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	38	967	0	ENST00000373198.4:c.1048del	p.Leu350TrpfsTer47	p.L350Wfs*47	ENST00000373198	NM_133170.3	350	Ctg/tg	7/32	0.3	0	FACETS	0.681	0.562	0.814			1	SUBCLONAL	1	TRUE	0	0.16	0		967	586	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391023	89391023	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	41	833	0	ENST00000336596.2:c.1089T>G	p.Cys363Trp	p.C363W	ENST00000336596	NM_005233.5	363	tgT/tgG	5/17	1	2	FACETS	0.714	0.593	0.849	0.714	0.593	0.849	SUBCLONAL	1	TRUE	1	0.16	2		833	718	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522538	67522538	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs963171218	NA	P-0021311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	22	302	0	ENST00000274335.5:c.35A>G	p.Tyr12Cys	p.Y12C	ENST00000274335		12	tAt/tGt	1/15	1	2	FACETS	0.879	0.681	1	0.879	0.681	1	CLONAL	1	TRUE	1	0.16	2		302	313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0021314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	418	886	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.660430314338269	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.660430314338269	2		886	614	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184646	185184646	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	150	555	1	ENST00000265026.3:c.1538G>T	p.Gly513Val	p.G513V	ENST00000265026	NM_004721.4	513	gGg/gTg	10/14	0.660430314338269	2	FACETS	1	0.962	1	0.534	0.493	0.577	CLONAL	1	TRUE	0	0.660430314338269	2		556	425	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307696	11307696	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	159	709	0	ENST00000361445.4:c.1211C>G	p.Pro404Arg	p.P404R	ENST00000361445	NM_004958.3	404	cCt/cGt	8/58	0.2358031427678	5	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.660430314338269	5		709	739	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830059	72830059	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	219	841	0	ENST00000268489.5:c.6522A>C	p.Gln2174His	p.Q2174H	ENST00000268489	NM_006885.3	2174	caA/caC	9/10	0.333272147515437	3	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.660430314338269	3		841	688	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101947	11101947	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	269	963	0	ENST00000358026.2:c.1367T>C	p.Leu456Pro	p.L456P	ENST00000358026	NM_001128849.1	456	cTg/cCg	8/36	0.660430314338269	3	FACETS	1	0.989	1	0.608	0.572	0.645	CLONAL	1	TRUE	1	0.660430314338269	3		963	891	SUCCESS
ATR	545	MSKCC	GRCh37	3	142185225	142185225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	306	776	1	ENST00000350721.4:c.6838C>T	p.His2280Tyr	p.H2280Y	ENST00000350721	NM_001184.3	2280	Cat/Tat	40/47	0.660430314338269	5	FACETS	0.869	0.82	0.92	0.58	0.547	0.613	CLONAL	2	TRUE	2	0.660430314338269	5		777	1061	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683451	182683451	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	381	691	0	ENST00000292782.4:c.94C>G	p.Gln32Glu	p.Q32E	ENST00000292782	NM_020640.2	32	Caa/Gaa	2/7	0.565587938467544	3	FACETS	1	0.984	1			1	CLONAL	2	TRUE	NA	0.660430314338269	3		691	726	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178553	32178575	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCATGCAGGTGGCCCCGTTCT	GGCCATGCAGGTGGCCCCGTTCT	-	novel	NA	P-0021314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	155	721	0	ENST00000375023.3:c.2819_2841del	p.Gln940ProfsTer57	p.Q940Pfs*57	ENST00000375023	NM_004557.3	940	cAGAACGGGGCCACCTGCATGGCC/c	18/30	0.660430314338269	3	FACETS	1	0.957	1	0.53	0.487	0.574	CLONAL	1	TRUE	1	0.660430314338269	3		721	589	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	74	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.234632815075122	2		434	529	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281778	39281778	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519963	NA	P-0021316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	87	633	0	ENST00000402219.2:c.697A>T	p.Asn233Tyr	p.N233Y	ENST00000402219	NM_005633.3	233	Aat/Tat	5/23	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.234632815075122	2		633	638	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0021316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	131	1071	2	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.234632815075122	2		1073	1050	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058036	27058036	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	98	723	0	ENST00000324856.7:c.1747del	p.Gln583SerfsTer36	p.Q583Sfs*36	ENST00000324856	NM_006015.4	582	Ccc/cc	3/20	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.234632815075122	2		723	803	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106532	27106532	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	151	1030	0	ENST00000324856.7:c.6143G>A	p.Trp2048Ter	p.W2048*	ENST00000324856	NM_006015.4	2048	tGg/tAg	20/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.234632815075122	2		1030	1181	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624268	89624277	+	frameshift_variant	Frame_Shift_Del	DEL	GAGATATCAA	GAGATATCAA	-	novel	NA	P-0021316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	175	524	0	ENST00000371953.3:c.45_54del	p.Tyr16MetfsTer5	p.Y16Mfs*5	ENST00000371953	NM_000314.4	14	agGAGATATCAA/ag	1/9	0.234632815075122	2	FACETS	0.834	0.772	0.898	1	0.985	1	CLONAL	3	TRUE	0	0.234632815075122	2		524	596	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696725	47696725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	196	601	1	ENST00000347630.2:c.223G>A	p.Gly75Arg	p.G75R	ENST00000347630	NM_001007230.1	75	Ggg/Agg	5/11	0.234632815075122	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.234632815075122	2		602	675	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11032314	11032314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765509075	NA	P-0021316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	76	821	1	ENST00000327064.4:c.1708G>A	p.Gly570Ser	p.G570S	ENST00000327064	NM_199141.1	570	Ggt/Agt	16/16	1	2	FACETS	0.797	0.698	0.904	0.797	0.698	0.904	CLONAL	1	TRUE	1	0.234632815075122	2		822	813	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210426	36210426	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750794495	NA	P-0021316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	100	789	0	ENST00000222270.7:c.419C>T	p.Ala140Val	p.A140V	ENST00000222270	NM_014727.1	140	gCg/gTg	2/37	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.234632815075122	2		789	837	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	92	669	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.958	0.87	1	1	0.991	1	CLONAL	7	TRUE	1	0.13	2		669	211	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0021317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	145	710	1	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	0.994	1	CLONAL	7	TRUE	1	0.13	2		711	318	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577362	64577371	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCAGGCGG	CGCCAGGCGG	-	novel	NA	P-0021317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	164	710	0	ENST00000312049.6:c.211_220del	p.Pro71AlafsTer45	p.P71Afs*45	ENST00000312049	NM_130799.2	71	CCGCCTGGCGgc/gc	2/10	0.3	2	FACETS	0.978	0.932	1	1	0.995	1	CLONAL	12	TRUE	0	0.13	2		710	215	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78933972	78933972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	18	948	1	ENST00000306801.3:c.3572G>A	p.Arg1191His	p.R1191H	ENST00000306801	NM_020761.2	1191	cGc/cAc	30/34	1	2	FACETS	0.849	0.639	1	0.849	0.639	1	CLONAL	1	TRUE	1	0.13	2		949	326	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0021319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	282	1047	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.902	0.85	0.955	0.902	0.85	0.955	CLONAL	1	TRUE	1	0.70648741872053	2		1049	885	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0021319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	232	710	1	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	0.70648741872053	2		711	657	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141875	108141875	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0021319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	207	444	0	ENST00000278616.4:c.2921+2T>G		p.X974_splice	ENST00000278616	NM_000051.3	974			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.70648741872053	2		444	553	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193519	99193519	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	280	817	0	ENST00000074304.5:c.2714C>G	p.Ser905Trp	p.S905W	ENST00000074304	NM_001134224.1	905	tCg/tGg	25/26	1	2	FACETS	0.92	0.866	0.974	0.92	0.866	0.974	CLONAL	1	TRUE	1	0.70648741872053	2		817	862	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056332	26056333	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0021319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	207	520	0	ENST00000343677.2:c.324dup	p.Lys109GlnfsTer13	p.K109Qfs*13	ENST00000343677	NM_005319.3	108	-/C	1/1	1	2	FACETS	0.929	0.867	0.992	0.929	0.867	0.992	CLONAL	1	TRUE	1	0.70648741872053	2		520	631	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727455	66727455	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs869025608	NA	P-0021324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	39	685	0	ENST00000307102.5:c.171G>T	p.Lys57Asn	p.K57N	ENST00000307102	NM_002755.3	57	aaG/aaT	2/11	1	2	FACETS	0.621	0.514	0.741	0.621	0.514	0.741	SUBCLONAL	1	TRUE	1	0.23	2		685	546	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619923	21619923	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	49	940	0	ENST00000382592.4:c.243A>C	p.Arg81Ser	p.R81S	ENST00000382592	NM_014572.2	81	agA/agC	2/8	1	2	FACETS	0.783	0.663	0.915	0.783	0.663	0.915	CLONAL	1	TRUE	1	0.23	2		940	544	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435403	110435403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	54	1147	3	ENST00000375856.3:c.2998G>A	p.Gly1000Ser	p.G1000S	ENST00000375856	NM_003749.2	1000	Ggc/Agc	1/2	NA	2	FACETS	0.77	0.657	0.893			1	INDETERMINATE	1	TRUE	NA	0.23	2		1150	610	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221334	1221334	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	41	919	0	ENST00000326873.7:c.857T>C	p.Leu286Pro	p.L286P	ENST00000326873	NM_000455.4	286	cTg/cCg	6/10	0.3	1	FACETS	0.725	0.605	0.859	0.725	0.605	0.859	SUBCLONAL	1	TRUE	0	0.23	1		919	435	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645684	12645684	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	26	339	0	ENST00000251849.4:c.785A>G	p.Asn262Ser	p.N262S	ENST00000251849	NM_002880.3	262	aAt/aGt	7/17	1	2	FACETS	0.713	0.565	0.882	0.713	0.565	0.882	SUBCLONAL	1	TRUE	1	0.23	2		339	317	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0021328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	385	1034	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.916	0.871	0.961	1	0.997	1	CLONAL	3	TRUE	1	0.251386794146549	2		1037	1115	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0021328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	192	725	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.251386794146549	2		725	1068	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0021328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	31	406	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.801	0.656	0.959	1	0.951	1	CLONAL	2	TRUE	1	0.251386794146549	2		406	154	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120802531	120802531	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	152	829	0	ENST00000257552.2:c.295C>G	p.Arg99Gly	p.R99G	ENST00000257552	NM_002442.3	99	Cga/Gga	5/15	1	2	FACETS	0.791	0.725	0.861	1	0.989	1	SUBCLONAL	2	TRUE	1	0.251386794146549	2		829	764	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519187	103519187	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	54	612	0	ENST00000355739.4:c.2525A>G	p.Asn842Ser	p.N842S	ENST00000355739	NM_000123.3	842	aAt/aGt	11/15	0.163236652911382	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.251386794146549	1		612	286	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	85	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.323194076754873	2		434	451	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845616	68845616	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	146	896	1	ENST00000261769.5:c.862G>A	p.Asp288Asn	p.D288N	ENST00000261769	NM_004360.3	288	Gac/Aac	7/16	0.323194076754873	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.323194076754873	1		897	637	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760678	133760678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753104701	NA	P-0021330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	193	1445	2	ENST00000318560.5:c.3001G>A	p.Ala1001Thr	p.A1001T	ENST00000318560	NM_005157.4	1001	Gcc/Acc	11/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.323194076754873	2		1447	1097	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0021331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	42	662	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.601	0.5	0.712	0.601	0.5	0.712	SUBCLONAL	1	TRUE	1	0.216843929586511	2		663	645	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0021331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	42	710	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.185919193259255	4	FACETS	0.763	0.636	0.904	0.381	0.318	0.452	CLONAL	1	TRUE	2	0.216843929586511	4		711	618	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248715	59248715	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	76	1346	0	ENST00000371222.2:c.28T>C	p.Tyr10His	p.Y10H	ENST00000371222	NM_002228.3	10	Tat/Cat	1/1	1	2	FACETS	0.65	0.568	0.739	0.65	0.568	0.739	SUBCLONAL	1	TRUE	1	0.216843929586511	2		1346	1078	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681410	88681410	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780108	NA	P-0021331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	59	681	0	ENST00000372037.3:c.1300G>A	p.Gly434Ser	p.G434S	ENST00000372037	NM_004329.2	434	Ggc/Agc	11/13	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.216843929586511	2		681	531	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309819	104309819	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	53	752	0	ENST00000369902.3:c.410C>T	p.Pro137Leu	p.P137L	ENST00000369902	NM_016169.3	137	cCc/cTc	3/12	1	2	FACETS	0.76	0.647	0.884	0.76	0.647	0.884	SUBCLONAL	1	TRUE	1	0.216843929586511	2		752	643	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922294	100922294	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1315135533	NA	P-0021331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	35	530	1	ENST00000325455.5:c.2218C>T	p.Arg740Ter	p.R740*	ENST00000325455	NM_001202474.3	740	Cga/Tga	5/8	1	2	FACETS	0.735	0.603	0.884	0.735	0.603	0.884	SUBCLONAL	1	TRUE	1	0.216843929586511	2		531	439	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231457	46231457	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	39	550	0	ENST00000334344.6:c.1297T>G	p.Cys433Gly	p.C433G	ENST00000334344	NM_152641.2	433	Tgc/Ggc	10/21	1	2	FACETS	0.725	0.601	0.864	0.725	0.601	0.864	SUBCLONAL	1	TRUE	1	0.216843929586511	2		550	496	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246477	46246489	+	frameshift_variant	Frame_Shift_Del	DEL	GGGAAACAGTCGC	GGGAAACAGTCGC	-	novel	NA	P-0021331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	25	492	0	ENST00000334344.6:c.4571_4583del	p.Arg1524LysfsTer7	p.R1524Kfs*7	ENST00000334344	NM_152641.2	1524	aGGGAAACAGTCGCa/aa	15/21	1	2	FACETS	0.543	0.427	0.676	0.543	0.427	0.676	SUBCLONAL	1	TRUE	1	0.216843929586511	2		492	425	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622553	28622553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	47	627	0	ENST00000241453.7:c.1064C>T	p.Ser355Leu	p.S355L	ENST00000241453	NM_004119.2	355	tCa/tTa	9/24	1	2	FACETS	0.715	0.603	0.84	0.715	0.603	0.84	SUBCLONAL	1	TRUE	1	0.216843929586511	2		627	606	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99486260	99486260	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	64	1029	0	ENST00000268035.6:c.3566T>C	p.Phe1189Ser	p.F1189S	ENST00000268035	NM_000875.3	1189	tTc/tCc	19/21	0.216843929586511	3	FACETS	0.715	0.618	0.822	0.358	0.308	0.411	SUBCLONAL	1	TRUE	1	0.216843929586511	3		1029	915	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965111	81965111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	62	807	0	ENST00000359376.3:c.2591C>T	p.Pro864Leu	p.P864L	ENST00000359376	NM_002661.3	864	cCt/cTt	25/33	1	2	FACETS	0.869	0.75	0.998	0.869	0.75	0.998	CLONAL	1	TRUE	1	0.216843929586511	2		807	658	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560913	9560913	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559720359	NA	P-0021331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	69	778	2	ENST00000353224.5:c.869C>T	p.Ser290Leu	p.S290L	ENST00000353224	NM_177990.2	290	tCg/tTg	4/10	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.216843929586511	2		780	595	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955863	55955863	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868047715	NA	P-0021331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	52	655	0	ENST00000263923.4:c.3299C>T	p.Ser1100Phe	p.S1100F	ENST00000263923	NM_002253.2	1100	tCc/tTc	24/30	0.1664205641894	3	FACETS	0.953	0.811	1	0.476	0.405	0.554	CLONAL	1	TRUE	1	0.216843929586511	3		655	558	SUCCESS
APC	324	MSKCC	GRCh37	5	112116491	112116491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	27	438	0	ENST00000257430.4:c.536C>T	p.Ser179Phe	p.S179F	ENST00000257430	NM_000038.5	179	tCc/tTc	6/16	1	2	FACETS	0.776	0.618	0.956	0.776	0.618	0.956	CLONAL	1	TRUE	1	0.216843929586511	2		438	321	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450261	50450261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	53	896	0	ENST00000331340.3:c.445C>T	p.Gln149Ter	p.Q149*	ENST00000331340	NM_006060.4	149	Cag/Tag	5/8	0.185919193259255	4	FACETS	0.78	0.663	0.908	0.39	0.331	0.454	CLONAL	1	TRUE	2	0.216843929586511	4		896	763	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140449184	140449184	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	50	733	0	ENST00000288602.6:c.1895C>T	p.Pro632Leu	p.P632L	ENST00000288602	NM_004333.4	632	cCa/cTa	16/18	0.185919193259255	4	FACETS	0.813	0.689	0.951	0.407	0.344	0.476	CLONAL	1	TRUE	2	0.216843929586511	4		733	690	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874526	151874526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761335251	NA	P-0021331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	43	587	0	ENST00000262189.6:c.8012C>T	p.Thr2671Met	p.T2671M	ENST00000262189	NM_170606.2	2671	aCg/aTg	38/59	0.185919193259255	4	FACETS	0.796	0.665	0.942	0.398	0.332	0.471	CLONAL	1	TRUE	2	0.216843929586511	4		587	606	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80343498	80343498	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	101	823	0	ENST00000286548.4:c.821A>C	p.Asn274Thr	p.N274T	ENST00000286548	NM_002072.3	274	aAc/aCc	6/7	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.216843929586511	2		823	705	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242835	98242835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	121	755	1	ENST00000331920.6:c.782C>T	p.Pro261Leu	p.P261L	ENST00000331920	NM_000264.3	261	cCt/cTt	6/24	1	2	FACETS	0.848	0.768	0.933	1	0.987	1	CLONAL	2	TRUE	1	0.216843929586511	2		756	658	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0021333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	416	1047	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.441330895452415	5	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	TRUE	2	0.441330895452415	5		1049	1020	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0021333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	259	631	0	ENST00000269305.4:c.375+1G>T		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.441330895452415	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.441330895452415	2		631	549	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123695	11123695	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	329	913	0	ENST00000358026.2:c.2345G>A	p.Gly782Asp	p.G782D	ENST00000358026	NM_001128849.1	782	gGc/gAc	16/36	0.441330895452415	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.441330895452415	2		913	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0021334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	305	795	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.52498763806422	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.52498763806422	1		796	808	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913274	NA	P-0021334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	18	940	0	ENST00000263967.3:c.1634A>C	p.Glu545Ala	p.E545A	ENST00000263967	NM_006218.2	545	gAg/gCg	10/21	0.36742453317901	2	FACETS	0.187	0.14	0.242	0.093	0.07	0.121	SUBCLONAL	1	TRUE	0	0.52498763806422	2		940	367	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702205	47702205	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750047	NA	P-0021334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	183	777	0	ENST00000233146.2:c.1801C>T	p.Gln601Ter	p.Q601*	ENST00000233146	NM_000251.2	601	Cag/Tag	12/16	1	2	FACETS	0.935	0.865	1	0.935	0.865	1	CLONAL	1	TRUE	1	0.52498763806422	2		777	746	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0021341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	392	692	2	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.939	0.895	0.984	0.939	0.895	0.984	CLONAL	1	TRUE	1	0.79675811488351	2		694	1048	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0021341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	604	1043	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.778018810661396	1	FACETS	0.998	0.969	1	0.998	0.969	1	CLONAL	1	TRUE	0	0.79675811488351	1		1044	914	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0021341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	423	900	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	1	2	FACETS	0.998	0.953	1	0.998	0.953	1	CLONAL	1	TRUE	1	0.79675811488351	2		900	1064	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0021347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	80	1047	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.17182115319693	2	FACETS	0.88	0.776	0.991	0.88	0.776	0.991	CLONAL	2	FALSE	0	0.17182115319693	2		1049	529	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0021347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	60	891	3	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.948	0.815	1	0.948	0.815	1	CLONAL	1	FALSE	1	0.17182115319693	2		894	737	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285796	46285796	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	70	471	0	ENST00000334344.6:c.5064del	p.Asp1688GlufsTer13	p.D1688Efs*13	ENST00000334344	NM_152641.2	1688	gaT/ga	18/21	0.17182115319693	2	FACETS	0.939	0.821	1	0.939	0.821	1	CLONAL	2	FALSE	0	0.17182115319693	2		471	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578471	7578482	+	inframe_deletion	In_Frame_Del	DEL	GGGCGGGGGTGT	GGGCGGGGGTGT	-	rs137852790	NA	P-0021347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	151	937	2	ENST00000269305.4:c.448_459del	p.Thr150_Pro153del	p.T150_P153del	ENST00000269305	NM_001126112.2	150	ACACCCCCGCCC/-	5/11	1	2	FACETS	1	0.94	1	1	0.991	1	CLONAL	2	FALSE	1	0.17182115319693	2		939	850	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193800	106193800	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	46	479	0	ENST00000380013.4:c.4262A>G	p.Tyr1421Cys	p.Y1421C	ENST00000380013	NM_001127208.2	1421	tAc/tGc	10/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.17182115319693	2		479	369	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0021351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	423	1047	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	0.881	0.85	0.912			1	INDETERMINATE	2	TRUE	NA	0.715397397696705	2		1049	671	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0021351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	604	692	2	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.715397397696705	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.715397397696705	2		694	834	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245399	153245399	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	339	882	3	ENST00000281708.4:c.1792A>C	p.Asn598His	p.N598H	ENST00000281708	NM_033632.3	598	Aat/Cat	11/12	0.696964607260207	2	FACETS	0.901	0.866	0.935	0.901	0.866	0.935	CLONAL	2	TRUE	0	0.715397397696705	2		885	526	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163807	32163807	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751250725	NA	P-0021351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	366	861	0	ENST00000375023.3:c.5419G>A	p.Ala1807Thr	p.A1807T	ENST00000375023	NM_004557.3	1807	Gct/Act	30/30	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.715397397696705	2		861	948	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045969	47045969	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	354	985	5	ENST00000377604.3:c.2764A>G	p.Met922Val	p.M922V	ENST00000377604	NM_001204468.1	922	Atg/Gtg	24/24	0.715397397696705	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.715397397696705	1		990	635	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266068	41266098	+	protein_altering_variant	In_Frame_Del	DEL	TTAGTCACTGGCAGCAACAGTCTTACCTGGA	TTAGTCACTGGCAGCAACAGTCTTACCTGGA	G	novel	NA	P-0021351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	209	454	4	ENST00000349496.5:c.65_95delinsG	p.Val22_Asp32delinsGly	p.V22_D32delinsG	ENST00000349496	NM_001904.3	22	gTTAGTCACTGGCAGCAACAGTCTTACCTGGAc/gGc	3/15	0.679162885356558	2	FACETS	0.828	0.784	0.871	0.828	0.784	0.871	CLONAL	2	TRUE	0	0.715397397696705	2		458	353	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0021352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	229	710	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.454480405596457	2	FACETS	0.771	0.726	0.817	0.771	0.726	0.817	SUBCLONAL	2	TRUE	0	0.553967806606556	2		711	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0021352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	316	1104	3	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	0.553967806606556	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.553967806606556	1		1107	821	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266440	55266440	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	223	897	0	ENST00000275493.2:c.2732G>C	p.Gly911Ala	p.G911A	ENST00000275493	NM_005228.3	911	gGa/gCa	23/28	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.553967806606556	2		897	772	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968633	55968633	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200338299	NA	P-0021352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	234	991	2	ENST00000263923.4:c.2030C>T	p.Thr677Met	p.T677M	ENST00000263923	NM_002253.2	677	aCg/aTg	14/30	0.553967806606556	1	FACETS	0.982	0.922	1	0.982	0.922	1	CLONAL	1	TRUE	0	0.553967806606556	1		993	622	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432086	121432086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760640415	NA	P-0021352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	272	1058	0	ENST00000257555.6:c.833G>A	p.Arg278Gln	p.R278Q	ENST00000257555		278	cGg/cAg	4/10	1	2	FACETS	0.919	0.863	0.977	0.919	0.863	0.977	CLONAL	1	TRUE	1	0.553967806606556	2		1058	1068	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720866	89720887	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAATTTTAAGGTCAGTTAAATT	AAATTTTAAGGTCAGTTAAATT	-	novel	NA	P-0021352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	26	611	0	ENST00000371953.3:c.1020_1026+15del		p.X340_splice	ENST00000371953	NM_000314.4	340		8/9	0.553967806606556	1	FACETS	0.222	0.176	0.275	0.222	0.176	0.275	SUBCLONAL	1	TRUE	0	0.553967806606556	1		611	306	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112940014	112940014	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	273	1139	2	ENST00000351677.2:c.1666G>T	p.Asp556Tyr	p.D556Y	ENST00000351677	NM_002834.3	556	Gat/Tat	14/16	1	2	FACETS	0.858	0.805	0.912	0.858	0.805	0.912	CLONAL	1	TRUE	1	0.553967806606556	2		1141	1149	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928201	178928236	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTCTTCCATCTCTTAGGAAACTCCATGCTTAGAG	TTTTCTTCCATCTCTTAGGAAACTCCATGCTTAGAG	-	novel	NA	P-0021352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	96	489	0	ENST00000263967.3:c.1405-16_1424del		p.X469_splice	ENST00000263967	NM_006218.2	469		9/21	0.496655631980573	2	FACETS	0.889	0.798	0.984	0.444	0.399	0.492	CLONAL	1	TRUE	0	0.553967806606556	2		489	390	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588147	67588148	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0021352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	91	529	0	ENST00000274335.5:c.978_979del	p.Met326IlefsTer6	p.M326Ifs*6	ENST00000274335		326	aTG/a	7/15	0.478266374922198	1	FACETS	0.603	0.539	0.67	0.603	0.539	0.67	SUBCLONAL	1	TRUE	0	0.553967806606556	1		529	394	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248121	98248121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780705	NA	P-0021352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	182	788	2	ENST00000331920.6:c.430C>T	p.Arg144Cys	p.R144C	ENST00000331920	NM_000264.3	144	Cgc/Tgc	3/24	1	2	FACETS	0.865	0.799	0.932	0.865	0.799	0.932	CLONAL	1	TRUE	1	0.553967806606556	2		790	760	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858044	152858044	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557026036	NA	P-0021352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	169	594	4	ENST00000406277.2:c.571G>A	p.Val191Met	p.V191M	ENST00000406277	NM_152274.4	191	Gtg/Atg	6/7	0.478266374922198	1	FACETS	0.925	0.858	0.993	0.925	0.858	0.993	CLONAL	1	TRUE	0	0.553967806606556	1		598	477	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0021354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	187	1047	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.435507926834292	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.462251413810592	1		1049	540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0021354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	270	996	1	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.462251413810592	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.462251413810592	1		997	788	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33446177	33446177	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	136	689	0	ENST00000345365.6:c.97del	p.Ser33LeufsTer7	p.S33Lfs*7	ENST00000345365	NM_002878.3	33	Tct/ct	2/10	NA	2	FACETS	0.886	0.808	0.968			1	INDETERMINATE	1	TRUE	NA	0.462251413810592	2		689	664	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682386	37682386	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1412	130	689	0	ENST00000447079.4:c.3577G>C	p.Glu1193Gln	p.E1193Q	ENST00000447079	NM_015083.1	1193	Gaa/Caa	13/14	0.462251413810592	7	FACETS	0.786	0.71	0.867			1	SUBCLONAL	1	TRUE	NA	0.462251413810592	7		689	1542	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936983	48936983	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690863	NA	P-0021355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	25	583	1	ENST00000267163.4:c.751C>T	p.Arg251Ter	p.R251*	ENST00000267163	NM_000321.2	251	Cga/Tga	8/27	0.264942507484973	0	FACETS	0.91	0.729	1			1	CLONAL	1	FALSE	0	0.31048825953083	0		584	122	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022592	31022592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs373221034	NA	P-0021355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	106	846	1	ENST00000375687.4:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000375687	NM_015338.5	693	Cga/Tga	13/13	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	1	0.31048825953083	2		847	661	SUCCESS
AR	367	MSKCC	GRCh37	X	66937372	66937372	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	103	541	1	ENST00000374690.3:c.2226G>T	p.Trp742Cys	p.W742C	ENST00000374690	NM_000044.3	742	tgG/tgT	5/8	1	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	0	0.31048825953083	1		542	472	SUCCESS
AR	367	MSKCC	GRCh37	X	66943543	66943543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852581	NA	P-0021355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	92	349	0	ENST00000374690.3:c.2623C>T	p.His875Tyr	p.H875Y	ENST00000374690	NM_000044.3	875	Cat/Tat	8/8	1	1	FACETS	0.97	0.876	1	1	0.987	1	CLONAL	2	FALSE	0	0.31048825953083	1		349	258	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0021355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	39	359	4	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.31048825953083	2		363	192	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521299	187521299	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1166479124	NA	P-0021355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	102	993	1	ENST00000441802.2:c.11856del	p.Phe3952LeufsTer31	p.F3952Lfs*31	ENST00000441802	NM_005245.3	3952	ttT/tt	22/27	0.203413398758242	4	FACETS	1	0.969	1	0.611	0.546	0.679	CLONAL	1	FALSE	2	0.31048825953083	4		994	705	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457763	149457763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376495524	NA	P-0021355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	156	977	0	ENST00000286301.3:c.641G>A	p.Arg214Gln	p.R214Q	ENST00000286301	NM_005211.3	214	cGg/cAg	5/22	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.31048825953083	2		977	813	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11027109	11027109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173812039	NA	P-0021355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	169	1284	5	ENST00000327064.4:c.874G>A	p.Val292Ile	p.V292I	ENST00000327064	NM_199141.1	292	Gtc/Atc	7/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.31048825953083	2		1289	849	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425038	49425038	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783690	NA	P-0021355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	198	1214	1	ENST00000301067.7:c.13450C>T	p.Arg4484Ter	p.R4484*	ENST00000301067	NM_003482.3	4484	Cga/Tga	39/54	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.31048825953083	2		1215	972	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185545	27185545	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1564083506	NA	P-0021355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	103	1093	0	ENST00000380036.4:c.1250del	p.Pro417LeufsTer10	p.P417Lfs*10	ENST00000380036	NM_000459.3	415	ctC/ct	9/23	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	FALSE	1	0.31048825953083	2		1093	623	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977606	2977606	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	183	1271	3	ENST00000396946.4:c.1078A>G	p.Met360Val	p.M360V	ENST00000396946	NM_032415.4	360	Atg/Gtg	8/25	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.31048825953083	2		1274	1029	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242899	142242899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750252420	NA	P-0021355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	56	938	4	ENST00000350721.4:c.4088C>T	p.Ala1363Val	p.A1363V	ENST00000350721	NM_001184.3	1363	gCg/gTg	22/47	1	2	FACETS	0.855	0.734	0.986	0.855	0.734	0.986	CLONAL	1	FALSE	1	0.31048825953083	2		942	422	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845702	151845702	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771018478	NA	P-0021355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	126	904	1	ENST00000262189.6:c.13310C>T	p.Thr4437Met	p.T4437M	ENST00000262189	NM_170606.2	4437	aCg/aTg	52/59	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.31048825953083	2		905	647	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199493	16199493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752192287	NA	P-0021355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	72	531	0	ENST00000375759.3:c.266G>A	p.Arg89Gln	p.R89Q	ENST00000375759	NM_015001.2	89	cGg/cAg	2/15	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	FALSE	1	0.31048825953083	2		531	402	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462062	120462062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	144	909	0	ENST00000256646.2:c.5654C>T	p.Ala1885Val	p.A1885V	ENST00000256646	NM_024408.3	1885	gCc/gTc	31/34	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.31048825953083	2		909	851	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246027181	246027181	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	64	753	0	ENST00000388985.4:c.821A>G	p.Asp274Gly	p.D274G	ENST00000388985		274	gAt/gGt	9/12	NA	2	FACETS	0.998	0.868	1			1	INDETERMINATE	1	FALSE	NA	0.31048825953083	2		753	413	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102196003	102196003	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs571701272	NA	P-0021355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	11	521	0	ENST00000263464.3:c.763C>T	p.His255Tyr	p.H255Y	ENST00000263464	NM_001165.4	255	Cat/Tat	2/9	1	2	FACETS	0.36	0.248	0.498	0.36	0.248	0.498	SUBCLONAL	1	FALSE	1	0.31048825953083	2		521	197	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436073	49436073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs565881981	NA	P-0021355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	87	686	0	ENST00000301067.7:c.5908G>A	p.Asp1970Asn	p.D1970N	ENST00000301067	NM_003482.3	1970	Gac/Aac	28/54	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.31048825953083	2		686	449	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484150	50484150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	111	948	1	ENST00000394963.4:c.1000C>T	p.Arg334Trp	p.R334W	ENST00000394963	NM_003076.4	334	Cgg/Tgg	8/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.31048825953083	2		949	529	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118754	115118754	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	116	908	0	ENST00000257566.3:c.587A>G	p.Gln196Arg	p.Q196R	ENST00000257566	NM_016569.3	196	cAg/cGg	2/8	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	FALSE	1	0.31048825953083	2		908	733	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991300	41991301	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0021355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	53	934	0	ENST00000219905.7:c.2132_2133del	p.Ile711ArgfsTer33	p.I711Rfs*33	ENST00000219905	NM_001164273.1	711	ATa/a	5/24	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	1	0.31048825953083	2		934	282	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478548	99478548	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	93	439	0	ENST00000268035.6:c.3190C>T	p.Arg1064Ter	p.R1064*	ENST00000268035	NM_000875.3	1064	Cga/Tga	17/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.31048825953083	2		439	401	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50815196	50815196	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	124	894	0	ENST00000398568.2:c.1549G>T	p.Gly517Cys	p.G517C	ENST00000398568	NM_001042412.1	517	Ggc/Tgc	9/18	0.31048825953083	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	0	0.31048825953083	1		894	557	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41201169	41201169	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	62	1210	0	ENST00000357654.3:c.5375T>C	p.Val1792Ala	p.V1792A	ENST00000357654	NM_007294.3	1792	gTg/gCg	21/23	1	2	FACETS	0.615	0.531	0.707	0.615	0.531	0.707	SUBCLONAL	1	FALSE	1	0.31048825953083	2		1210	649	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55729505	55729505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1409691153	NA	P-0021355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	225	1194	2	ENST00000284073.2:c.773C>T	p.Ala258Val	p.A258V	ENST00000284073	NM_138962.2	258	gCg/gTg	11/14	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.31048825953083	2		1196	1148	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2220185	2220185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1212427702	NA	P-0021355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	142	1147	1	ENST00000398665.3:c.2770G>A	p.Gly924Ser	p.G924S	ENST00000398665	NM_032482.2	924	Ggt/Agt	23/28	0.31048825953083	1	FACETS	0.982	0.896	1	0.982	0.896	1	CLONAL	1	FALSE	0	0.31048825953083	1		1148	787	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793166	42793166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778778296	NA	P-0021355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	79	1234	4	ENST00000575354.2:c.1058G>A	p.Arg353Gln	p.R353Q	ENST00000575354	NM_015125.3	353	cGa/cAa	7/20	1	2	FACETS	0.631	0.554	0.713	0.631	0.554	0.713	SUBCLONAL	1	FALSE	1	0.31048825953083	2		1238	807	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944413	40944414	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0021355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	143	1048	4	ENST00000373198.4:c.2088_2089del	p.Leu698GlufsTer54	p.L698Efs*54	ENST00000373198	NM_133170.3	696	tcTCcc/tccc	12/32	0.31048825953083	3	FACETS	1	0.976	1	0.601	0.548	0.657	CLONAL	1	FALSE	1	0.31048825953083	3		1052	885	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713757	30713757	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	62	648	0	ENST00000295754.5:c.1082T>A	p.Leu361His	p.L361H	ENST00000295754	NM_003242.5	361	cTc/cAc	4/7	1	2	FACETS	0.734	0.635	0.842	0.734	0.635	0.842	SUBCLONAL	1	FALSE	1	0.31048825953083	2		648	544	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612083	189612083	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	142	930	0	ENST00000264731.3:c.1838del	p.Pro613LeufsTer91	p.P613Lfs*91	ENST00000264731	NM_003722.4	612	tCc/tc	14/14	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.31048825953083	2		930	836	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467758	66467758	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs879110644	NA	P-0021355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	35	549	0	ENST00000273854.3:c.511T>C	p.Tyr171His	p.Y171H	ENST00000273854	NM_004439.5	171	Tac/Cac	3/18	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	FALSE	1	0.31048825953083	2		549	216	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39002763	39002763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1303852277	NA	P-0021355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	14	512	0	ENST00000357387.3:c.266G>A	p.Arg89Gln	p.R89Q	ENST00000357387	NM_152756.3	89	cGg/cAg	5/38	0.31048825953083	3	FACETS	0.651	0.473	0.865	0.326	0.236	0.433	SUBCLONAL	1	FALSE	1	0.31048825953083	3		512	160	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432116	121432116	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1565885932	NA	P-0021355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	119	1053	3	ENST00000257555.6:c.863G>C	p.Gly288Ala	p.G288A	ENST00000257555		288	gGg/gCg	4/10	1	2	FACETS	0.938	0.847	1	0.938	0.847	1	CLONAL	1	FALSE	1	0.31048825953083	2		1056	817	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020703	37020703	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	65	847	0	ENST00000358127.4:c.142G>C	p.Gly48Arg	p.G48R	ENST00000358127	NM_001280556.1	48	Ggt/Cgt	2/10	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		847	818	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947560	48947560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690846	NA	P-0021358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	217	794	1	ENST00000267163.4:c.1147C>T	p.Gln383Ter	p.Q383*	ENST00000267163	NM_000321.2	383	Caa/Taa	12/27	0.279479352461575	3	FACETS	1	0.987	1	0.821	0.766	0.877	CLONAL	2	TRUE	0	0.279479352461575	3		795	719	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24134069	24134069	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	206	642	0	ENST00000263121.7:c.220C>G	p.Pro74Ala	p.P74A	ENST00000263121	NM_003073.3	74	Cct/Gct	2/9	0.279479352461575	5	FACETS	1	0.945	1			1	CLONAL	3	TRUE	NA	0.279479352461575	5		642	686	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041178	180041178	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs781205285	NA	P-0021358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	60	978	0	ENST00000261937.6:c.3221C>T	p.Ala1074Val	p.A1074V	ENST00000261937	NM_182925.4	1074	gCc/gTc	24/30	0.279479352461575	1	FACETS	0.784	0.677	0.901	0.784	0.677	0.901	CLONAL	1	TRUE	0	0.279479352461575	1		978	471	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936093	178936093	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913275	NA	P-0021360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	278	1099	2	ENST00000263967.3:c.1635G>T	p.Glu545Asp	p.E545D	ENST00000263967	NM_006218.2	545	gaG/gaT	10/21	0.714827287015448	4	FACETS	1	0.976	1	0.358	0.336	0.381	CLONAL	1	TRUE	1	0.867730826380214	4		1101	1114	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534285	534285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894226	NA	P-0021360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	197	1089	0	ENST00000451590.1:c.38G>A	p.Gly13Asp	p.G13D	ENST00000451590	NM_001130442.1	13	gGt/gAt	2/5	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.867730826380214	2		1089	426	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720711	89720712	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	28	179	0	ENST00000371953.3:c.867dup	p.Val290SerfsTer8	p.V290Sfs*8	ENST00000371953	NM_000314.4	288	gaa/gAaa	8/9	0.867730826380214	1	FACETS	0.468	0.387	0.554	0.468	0.387	0.554	SUBCLONAL	1	TRUE	0	0.867730826380214	1		179	78	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190709	108190709	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	305	963	2	ENST00000278616.4:c.6376G>T	p.Glu2126Ter	p.E2126*	ENST00000278616	NM_000051.3	2126	Gaa/Taa	44/63	1	2	FACETS	0.97	0.92	1	0.97	0.92	1	CLONAL	1	TRUE	1	0.867730826380214	2		965	725	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0021361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	54	662	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.638	0.545	0.74	0.638	0.545	0.74	SUBCLONAL	1	TRUE	1	0.30924020476237	2		663	547	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0021361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	173	748	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.253860974370431	2	FACETS	0.789	0.728	0.852	0.789	0.728	0.852	SUBCLONAL	2	TRUE	0	0.30924020476237	2		748	709	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437813	52437813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	102	796	1	ENST00000460680.1:c.1348G>A	p.Glu450Lys	p.E450K	ENST00000460680	NM_004656.3	450	Gag/Aag	13/17	1	2	FACETS	0.825	0.737	0.918	0.825	0.737	0.918	CLONAL	1	TRUE	1	0.30924020476237	2		797	800	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533701	63533701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	285	562	1	ENST00000307078.5:c.1453G>A	p.Gly485Ser	p.G485S	ENST00000307078	NM_004655.3	485	Ggc/Agc	6/11	0.661888201597458	3	FACETS	1	0.987	1	0.582	0.548	0.618	CLONAL	1	TRUE	1	0.661888201597458	3		563	984	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913471	NA	P-0021363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	11627	816	1	ENST00000269571.5:c.2329G>C	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ctg	20/27	0.661888201597458	23	FACETS	0.986	0.983	0.989			1	CLONAL	23	TRUE	NA	0.661888201597458	23		817	12319	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288969	212288969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148791072	NA	P-0021363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	135	680	0	ENST00000342788.4:c.2777C>T	p.Thr926Met	p.T926M	ENST00000342788	NM_005235.2	926	aCg/aTg	23/28	0.653962547986423	3	FACETS	1	0.92	1	0.504	0.46	0.549	CLONAL	1	TRUE	1	0.661888201597458	3		680	539	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014076	70014076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759306986	NA	P-0021363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	141	606	0	ENST00000394351.3:c.937C>T	p.Arg313Trp	p.R313W	ENST00000394351	NM_000248.3	313	Cgg/Tgg	9/9	1	2	FACETS	0.866	0.794	0.94	0.866	0.794	0.94	CLONAL	1	TRUE	1	0.661888201597458	2		606	492	SUCCESS
APC	324	MSKCC	GRCh37	5	112175242	112175243	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GATCCTGT	novel	NA	P-0021363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	101	260	0	ENST00000257430.4:c.3954_3961dup	p.Ser1321IlefsTer3	p.S1321Ifs*3	ENST00000257430	NM_000038.5	1317	-/GATCCTGT	16/16	0.661888201597458	2	FACETS	1	0.976	1	0.613	0.558	0.669	CLONAL	1	TRUE	0	0.661888201597458	2		260	249	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38148131	38148131	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	2044	767	0	ENST00000317025.8:c.2980G>A	p.Asp994Asn	p.D994N	ENST00000317025	NM_023034.1	994	Gac/Aac	17/24	0.661888201597458	12	FACETS	1	0.998	1			1	CLONAL	10	TRUE	NA	0.661888201597458	12		767	2538	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0021366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	158	1047	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.516265233058711	3	FACETS	0.97	0.89	1	0.485	0.445	0.527	CLONAL	1	TRUE	1	0.516265233058711	3		1047	794	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988393	36988393	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	98	278	0	ENST00000354822.5:c.260C>T	p.Ala87Val	p.A87V	ENST00000354822	NM_001079668.2	87	gCc/gTc	2/3	0.446496237839352	4	FACETS	0.765	0.688	0.846	0.765	0.688	0.846	SUBCLONAL	2	TRUE	2	0.516265233058711	4		278	376	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113114	+	missense_variant	Missense_Mutation	DNP	GA	GA	AG	novel	NA	P-0021366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	78	372	2	ENST00000345146.2:c.393_394delinsCT	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	131	ggTCgt/ggCTgt	4/10	0.516265233058711	3	FACETS	1	0.947	1	0.561	0.496	0.629	CLONAL	1	TRUE	1	0.516265233058711	3		374	339	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443750	52443750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	351	977	0	ENST00000460680.1:c.47C>T	p.Thr16Ile	p.T16I	ENST00000460680	NM_004656.3	16	aCc/aTc	2/17	0.505732054687927	2	FACETS	0.936	0.894	0.979	0.936	0.894	0.979	CLONAL	2	TRUE	0	0.516265233058711	2		977	726	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221320	1221320	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587776656	NA	P-0021367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	88	989	0	ENST00000326873.7:c.843del	p.Leu282SerfsTer5	p.L282Sfs*5	ENST00000326873	NM_000455.4	281	ccG/cc	6/10	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.16	2		989	1000	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435578	18435578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747513676	NA	P-0021367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	24	505	1	ENST00000266497.5:c.563C>T	p.Pro188Leu	p.P188L	ENST00000266497		188	cCg/cTg	1/31	0.3	2	FACETS	0.857	0.672	1			1	CLONAL	1	TRUE	NA	0.16	2		506	350	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175916366	175916366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	40	525	0	ENST00000367669.3:c.2143G>T	p.Val715Leu	p.V715L	ENST00000367669	NM_022457.5	715	Gtg/Ttg	19/20	1	2	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	TRUE	1	0.16	2		525	490	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136034	64136034	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1397460841	NA	P-0021367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	62	975	0	ENST00000334205.4:c.1295A>G	p.Gln432Arg	p.Q432R	ENST00000334205	NM_003942.2	432	cAg/cGg	11/17	1	2	FACETS	0.704	0.606	0.811	0.704	0.606	0.811	SUBCLONAL	1	TRUE	1	0.16	2		975	1101	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348769	118348769	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	42	643	0	ENST00000534358.1:c.3422C>T	p.Pro1141Leu	p.P1141L	ENST00000534358	NM_005933.3	1141	cCc/cTc	5/36	1	2	FACETS	0.772	0.643	0.916	0.772	0.643	0.916	CLONAL	1	TRUE	1	0.16	2		643	680	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680635	88680635	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	34	609	0	ENST00000360948.2:c.622G>T	p.Asp208Tyr	p.D208Y	ENST00000360948	NM_001012338.2	208	Gac/Tac	6/19	1	2	FACETS	0.685	0.559	0.829	0.685	0.559	0.829	SUBCLONAL	1	TRUE	1	0.16	2		609	620	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750720	39750720	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	29	502	1	ENST00000361337.2:c.2120A>T	p.Asp707Val	p.D707V	ENST00000361337	NM_003286.2	707	gAc/gTc	20/21	1	2	FACETS	0.684	0.548	0.84	0.684	0.548	0.84	SUBCLONAL	1	TRUE	1	0.16	2		503	530	SUCCESS
APC	324	MSKCC	GRCh37	5	112175604	112175604	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	27	555	0	ENST00000257430.4:c.4313C>G	p.Thr1438Arg	p.T1438R	ENST00000257430	NM_000038.5	1438	aCa/aGa	16/16	1	2	FACETS	0.675	0.536	0.835	0.675	0.536	0.835	SUBCLONAL	1	TRUE	1	0.16	2		555	500	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068105	94068105	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	22	514	0	ENST00000369303.4:c.857C>G	p.Ser286Cys	p.S286C	ENST00000369303	NM_004440.3	286	tCt/tGt	4/17	1	2	FACETS	0.65	0.503	0.822	0.65	0.503	0.822	SUBCLONAL	1	TRUE	1	0.16	2		514	423	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566315	141566315	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	47	823	0	ENST00000220592.5:c.1097G>T	p.Arg366Ile	p.R366I	ENST00000220592	NM_012154.3	366	aGa/aTa	9/19	1	2	FACETS	0.686	0.577	0.807	0.686	0.577	0.807	SUBCLONAL	1	TRUE	1	0.16	2		823	857	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0021368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	344	1047	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.664738898195907	4	FACETS	0.952	0.905	1	0.952	0.905	1	CLONAL	2	TRUE	2	0.671771609440353	4		1049	899	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0021369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	143	845	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.765	0.698	0.835	1	0.987	1	SUBCLONAL	2	TRUE	1	0.23	2		845	813	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795734	42795734	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	129	1221	0	ENST00000575354.2:c.2726del	p.Pro909ArgfsTer15	p.P909Rfs*15	ENST00000575354	NM_015125.3	908	gCc/gc	11/20	1	2	FACETS	0.974	0.881	1	0.974	0.881	1	CLONAL	1	TRUE	1	0.23	2		1221	1152	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023224	27023227	+	frameshift_variant	Frame_Shift_Del	DEL	GCCC	GCCC	-	novel	NA	P-0021369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	68	354	0	ENST00000324856.7:c.334_337del	p.Ala112Ter	p.A112*	ENST00000324856	NM_006015.4	110	agGCCC/ag	1/20	1	2	FACETS	0.774	0.677	0.878	1	0.975	1	SUBCLONAL	2	TRUE	1	0.23	2		354	382	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711897	89711914	+	inframe_deletion	In_Frame_Del	DEL	GGCGCTATGTGTATTATT	GGCGCTATGTGTATTATT	-	novel	NA	P-0021369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	49	731	0	ENST00000371953.3:c.515_532del	p.Arg172_Tyr178delinsAsn	p.R172_Y178delinsN	ENST00000371953	NM_000314.4	172	aGGCGCTATGTGTATTATTat/aat	6/9	1	2	FACETS	0.713	0.603	0.833	0.713	0.603	0.833	SUBCLONAL	1	TRUE	1	0.23	2		731	598	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541275	187541275	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	50	641	0	ENST00000441802.2:c.6465del	p.Ala2156GlnfsTer20	p.A2156Qfs*20	ENST00000441802	NM_005245.3	2155	gtT/gt	10/27	1	2	FACETS	0.677	0.574	0.791	0.677	0.574	0.791	SUBCLONAL	1	TRUE	1	0.23	2		641	642	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589224	67589224	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	34	620	0	ENST00000274335.5:c.1213del	p.Ile405Ter	p.I405*	ENST00000274335		404	ttA/tt	9/15	1	2	FACETS	0.531	0.433	0.642	0.531	0.433	0.642	SUBCLONAL	1	TRUE	1	0.23	2		620	557	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978499	70978499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141769540	NA	P-0021369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	68	634	0	ENST00000276594.2:c.1154C>T	p.Pro385Leu	p.P385L	ENST00000276594	NM_024504.3	385	cCg/cTg	5/8	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.23	2		634	582	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164810	123164810	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0021369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	37	281	0	ENST00000218089.9:c.124-1G>C		p.X42_splice	ENST00000218089	NM_001042749.1	42			1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.23	2		281	273	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0021373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	49	779	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.6	0.507	0.703	0.6	0.507	0.703	SUBCLONAL	1	TRUE	1	0.21	2		779	778	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0021373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	48	539	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	1	2	FACETS	0.989	0.837	1	0.989	0.837	1	CLONAL	1	TRUE	1	0.21	2		539	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579394	7579394	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	56	910	0	ENST00000269305.4:c.293del	p.Pro98LeufsTer25	p.P98Lfs*25	ENST00000269305	NM_001126112.2	98	cCt/ct	4/11	1	2	FACETS	0.625	0.534	0.725	0.625	0.534	0.725	SUBCLONAL	1	TRUE	1	0.21	2		910	853	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637974	39637974	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	56	826	0	ENST00000262039.4:c.2391G>C	p.Glu797Asp	p.E797D	ENST00000262039	NM_002647.2	797	gaG/gaC	22/25	1	2	FACETS	0.65	0.556	0.754	0.65	0.556	0.754	SUBCLONAL	1	TRUE	1	0.21	2		826	820	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604626	48604629	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GTCT	GTCT	-	novel	NA	P-0021373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	18	318	0	ENST00000342988.3:c.1451_1454del	p.Leu484GlnfsTer19	p.L484Qfs*19	ENST00000342988	NM_005359.5	483	aGTCTg/ag	12/12	1	2	FACETS	0.519	0.391	0.672	0.519	0.391	0.672	SUBCLONAL	1	TRUE	1	0.21	2		318	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659675	NA	P-0021374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	229	965	0	ENST00000269305.4:c.764T>C	p.Ile255Thr	p.I255T	ENST00000269305	NM_001126112.2	255	aTc/aCc	7/11	0.474255196028965	1	FACETS	0.871	0.813	0.93	0.871	0.813	0.93	CLONAL	1	TRUE	0	0.474255196028965	1		965	846	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916926	+	inframe_deletion	In_Frame_Del	DEL	CAG	CAG	-	novel	NA	P-0021374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	602	763	0	ENST00000263967.3:c.311_313del	p.Pro104_Val105delinsLeu	p.P104_V105delinsL	ENST00000263967	NM_006218.2	104	cCAGta/cta	2/21	0.474255196028965	3	FACETS	0.921	0.89	0.952	0.921	0.89	0.952	CLONAL	3	TRUE	0	0.474255196028965	3		763	1137	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0021376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	100	1047	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.3	2		1049	667	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0021376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	75	672	2	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.986	0.866	1	0.986	0.866	1	CLONAL	1	TRUE	1	0.3	2		674	507	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591132	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	rs1057519842	NA	P-0021376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	38	425	0	ENST00000274335.5:c.1727_1729del	p.Thr576del	p.T576del	ENST00000274335		575	aaGACg/aag	12/15	1	2	FACETS	0.799	0.663	0.95	0.799	0.663	0.95	CLONAL	1	TRUE	1	0.3	2		425	317	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100827	27100849	+	frameshift_variant	Frame_Shift_Del	DEL	AGCGGCCAATGGATGGCACATAT	AGCGGCCAATGGATGGCACATAT	CGC	novel	NA	P-0021376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	139	734	3	ENST00000324856.7:c.4109_4131delinsCGC	p.Lys1370ThrfsTer68	p.K1370Tfs*68	ENST00000324856	NM_006015.4	1370	aAGCGGCCAATGGATGGCACATAT/aCGC	18/20	0.275707759451166	2	FACETS	0.768	0.702	0.838	0.768	0.702	0.838	SUBCLONAL	2	TRUE	0	0.3	2		737	603	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717705	89717706	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	90	678	0	ENST00000371953.3:c.730_731insA	p.Pro244HisfsTer9	p.P244Hfs*9	ENST00000371953	NM_000314.4	244	cct/cAct	7/9	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.3	2		678	581	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466000	69466000	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	138	1111	1	ENST00000227507.2:c.838G>T	p.Glu280Ter	p.E280*	ENST00000227507	NM_053056.2	280	Gag/Tag	5/5	1	2	FACETS	0.924	0.84	1	0.924	0.84	1	CLONAL	1	TRUE	1	0.3	2		1112	996	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572967	41572967	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	123	937	0	ENST00000263253.7:c.5252C>G	p.Ala1751Gly	p.A1751G	ENST00000263253	NM_001429.3	1751	gCc/gGc	31/31	1	2	FACETS	0.928	0.838	1	0.928	0.838	1	CLONAL	1	TRUE	1	0.3	2		937	884	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916875	178916875	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	19	944	0	ENST00000263967.3:c.262C>G	p.Arg88Gly	p.R88G	ENST00000263967	NM_006218.2	88	Cga/Gga	2/21	1	2	FACETS	0.146	0.11	0.189	0.146	0.11	0.189	SUBCLONAL	1	TRUE	1	0.3	2		944	868	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	156	669	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.927	0.863	0.993	1	0.992	1	CLONAL	2	TRUE	1	0.488945936054664	2		669	344	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0021378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	32	772	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.383	0.311	0.464	0.383	0.311	0.464	SUBCLONAL	1	TRUE	1	0.488945936054664	2		772	342	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0021378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	128	546	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.488945936054664	2		546	426	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519922	NA	P-0021378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	254	946	6	ENST00000397062.3:c.235G>A	p.Glu79Lys	p.E79K	ENST00000397062	NM_006164.4	79	Gag/Aag	2/5	1	2	FACETS	0.796	0.749	0.842	1	0.994	1	SUBCLONAL	2	TRUE	1	0.488945936054664	2		952	653	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260516	16260517	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	104	570	5	ENST00000375759.3:c.7782dup	p.Glu2595Ter	p.E2595*	ENST00000375759	NM_015001.2	2594	tct/tcTt	11/15	1	2	FACETS	0.899	0.809	0.994	0.899	0.809	0.994	CLONAL	1	TRUE	1	0.488945936054664	2		575	473	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418470	49418470	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	127	783	1	ENST00000301067.7:c.15943C>G	p.Gln5315Glu	p.Q5315E	ENST00000301067	NM_003482.3	5315	Caa/Gaa	50/54	0.436225860265792	3	FACETS	0.816	0.74	0.897	0.408	0.37	0.449	CLONAL	1	TRUE	1	0.488945936054664	3		784	792	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426838	49426839	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0021378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	254	578	7	ENST00000301067.7:c.11649_11650del	p.His3883GlnfsTer128	p.H3883Qfs*128	ENST00000301067	NM_003482.3	3883	caCAgt/cagt	39/54	0.436225860265792	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.488945936054664	3		585	581	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431205	49431205	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1307868506	NA	P-0021378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	235	750	15	ENST00000301067.7:c.9934C>T	p.Gln3312Ter	p.Q3312*	ENST00000301067	NM_003482.3	3312	Cag/Tag	34/54	0.436225860265792	3	FACETS	0.766	0.717	0.816	0.766	0.717	0.816	SUBCLONAL	2	TRUE	1	0.488945936054664	3		765	781	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098642	47098642	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	208	732	3	ENST00000409792.3:c.6632G>C	p.Gly2211Ala	p.G2211A	ENST00000409792	NM_014159.6	2211	gGa/gCa	15/21	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.488945936054664	2		735	589	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896365	151896366	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	191	580	9	ENST00000262189.6:c.4271dup	p.His1424GlnfsTer5	p.H1424Qfs*5	ENST00000262189	NM_170606.2	1424	cac/caAc	27/59	0.436225860265792	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.488945936054664	3		589	421	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902207	151902208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	104	842	8	ENST00000262189.6:c.3944dup	p.Leu1315PhefsTer6	p.L1315Ffs*6	ENST00000262189	NM_170606.2	1315	tta/ttTa	25/59	0.436225860265792	3	FACETS	1	0.973	1	0.617	0.556	0.681	CLONAL	1	TRUE	1	0.488945936054664	3		850	429	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300966	137300966	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0021378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	180	710	6	ENST00000481739.1:c.610+1G>A		p.X204_splice	ENST00000481739	NM_002957.4	204			1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.488945936054664	2		716	576	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780828	9780828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1441813233	NA	P-0021381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	210	823	2	ENST00000377346.4:c.1550G>A	p.Arg517Gln	p.R517Q	ENST00000377346	NM_005026.3	517	cGg/cAg	13/24	0.291366646544155	3	FACETS	1	0.96	1	0.525	0.487	0.564	INDETERMINATE	1	TRUE	1	0.489475020500339	3		825	1018	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579319	7579348	+	inframe_deletion	In_Frame_Del	DEL	GTCACAGACTTGGCTGTCCCAGAATGCAAG	GTCACAGACTTGGCTGTCCCAGAATGCAAG	-	novel	NA	P-0021381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	446	638	2	ENST00000269305.4:c.339_368del	p.Leu114_Thr123del	p.L114_T123del	ENST00000269305	NM_001126112.2	113	ttCTTGCATTCTGGGACAGCCAAGTCTGTGACt/ttt	4/11	0.489475020500339	3	FACETS	0.889	0.854	0.923	0.889	0.854	0.923	CLONAL	3	TRUE	0	0.489475020500339	3		640	851	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732966	74732966	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	58	345	0	ENST00000359995.5:c.277G>C	p.Gly93Arg	p.G93R	ENST00000359995	NM_001195427.1	93	Ggc/Cgc	1/3	0.468910907358326	3	FACETS	0.696	0.599	0.8	0.348	0.299	0.4	SUBCLONAL	1	TRUE	1	0.489475020500339	3		345	424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0021383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	496	661	0	ENST00000269305.4:c.673-1G>C		p.X225_splice	ENST00000269305	NM_001126112.2	225			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		661	625	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0021384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	270	819	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		819	720	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696431	47696431	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519969	NA	P-0021386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	116	792	0	ENST00000347630.2:c.392G>C	p.Trp131Ser	p.W131S	ENST00000347630	NM_001007230.1	131	tGg/tCg	6/11	1	2	FACETS	0.847	0.765	0.934	0.847	0.765	0.934	CLONAL	1	TRUE	1	0.422634473946341	2		792	648	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413973	139413973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	197	1008	0	ENST00000277541.6:c.787G>C	p.Gly263Arg	p.G263R	ENST00000277541	NM_017617.3	263	Gga/Cga	5/34	1	2	FACETS	0.958	0.887	1	0.958	0.887	1	CLONAL	1	TRUE	1	0.422634473946341	2		1008	973	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485807	8485807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	43	380	2	ENST00000356435.5:c.3010C>A	p.Pro1004Thr	p.P1004T	ENST00000356435		1004	Cca/Aca	17/35	0.14894024479976	2	FACETS	0.788	0.663	0.926	0.788	0.663	0.926	CLONAL	2	TRUE	0	0.183616454656628	2		382	297	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007672	45007672	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	23	552	0	ENST00000558401.1:c.119C>G	p.Ser40Ter	p.S40*	ENST00000558401	NM_004048.2	40	tCa/tGa	2/4	0.183616454656628	2	FACETS	1	0.796	1	0.509	0.398	0.637	CLONAL	1	TRUE	0	0.183616454656628	2		552	246	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058093	27058093	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	115	519	0	ENST00000324856.7:c.1801C>T	p.Gln601Ter	p.Q601*	ENST00000324856	NM_006015.4	601	Cag/Tag	3/20	0.183616454656628	4	FACETS	1	0.951	1	1	0.951	1	CLONAL	3	TRUE	1	0.183616454656628	4		519	459	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211389	98211389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150850039	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	48	927	0	ENST00000331920.6:c.3766G>A	p.Val1256Met	p.V1256M	ENST00000331920	NM_000264.3	1256	Gtg/Atg	22/24	0.146389089338388	3	FACETS	0.802	0.676	0.94	0.401	0.338	0.47	CLONAL	1	TRUE	1	0.183616454656628	3		927	712	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293718	1293718	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	72	938	0	ENST00000310581.5:c.1283G>T	p.Arg428Leu	p.R428L	ENST00000310581	NM_198253.2	428	cGg/cTg	2/16	0.146389089338388	3	FACETS	1	0.933	1	0.555	0.484	0.631	CLONAL	1	TRUE	1	0.183616454656628	3		938	772	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958197	54958197	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	85	704	0	ENST00000312783.6:c.410G>T	p.Arg137Leu	p.R137L	ENST00000312783	NM_198436.1	137	cGc/cTc	6/10	0.183616454656628	4	FACETS	1	0.961	1	0.792	0.703	0.887	CLONAL	2	TRUE	1	0.183616454656628	4		704	461	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849141	156849141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1419179271	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	317	934	0	ENST00000524377.1:c.2033C>A	p.Thr678Asn	p.T678N	ENST00000524377	NM_002529.3	678	aCc/aAc	15/17	0.183616454656628	7	FACETS	1	0.96	1	1	0.96	1	CLONAL	5	TRUE	2	0.183616454656628	7		934	990	SUCCESS
FH	2271	MSKCC	GRCh37	1	241665777	241665777	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	27	586	0	ENST00000366560.3:c.1202G>T	p.Gly401Val	p.G401V	ENST00000366560	NM_000143.3	401	gGa/gTa	8/10	0.121458495960228	4	FACETS	0.739	0.587	0.913	0.37	0.293	0.457	CLONAL	1	TRUE	2	0.183616454656628	4		586	471	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924741	94924741	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	72	839	0	ENST00000536441.1:c.169G>A	p.Glu57Lys	p.E57K	ENST00000536441	NM_144665.3	57	Gaa/Aaa	3/10	0.152360818570094	3	FACETS	1	0.969	1	0.461	0.403	0.524	CLONAL	1	TRUE	0	0.183616454656628	3		839	619	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201867	102201867	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	84	498	0	ENST00000263464.3:c.1219G>T	p.Gly407Ter	p.G407*	ENST00000263464	NM_001165.4	407	Gga/Tga	6/9	0.152360818570094	3	FACETS	0.882	0.789	0.98	1	0.963	1	CLONAL	4	TRUE	0	0.183616454656628	3		498	283	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362012	118362012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555042415	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	47	528	0	ENST00000534358.1:c.4798G>A	p.Glu1600Lys	p.E1600K	ENST00000534358	NM_005933.3	1600	Gag/Aag	14/36	0.152360818570094	3	FACETS	0.787	0.667	0.919	0.525	0.444	0.613	CLONAL	2	TRUE	0	0.183616454656628	3		528	355	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50482303	50482303	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	72	617	0	ENST00000394963.4:c.655-1G>T		p.X219_splice	ENST00000394963	NM_003076.4	219			0.183616454656628	5	FACETS	1	0.942	1	0.753	0.66	0.852	CLONAL	2	TRUE	2	0.183616454656628	5		617	443	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233288	69233288	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769693191	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	15	409	0	ENST00000462284.1:c.1153G>A	p.Asp385Asn	p.D385N	ENST00000462284	NM_002392.5	385	Gat/Aat	11/11	0.183616454656628	5	FACETS	0.795	0.582	1	0.265	0.194	0.351	CLONAL	1	TRUE	2	0.183616454656628	5		409	262	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813355	102813355	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	69	664	1	ENST00000307046.8:c.334C>A	p.Leu112Ile	p.L112I	ENST00000307046	NM_001111285.1	112	Ctc/Atc	3/4	0.183616454656628	5	FACETS	0.929	0.81	1	0.619	0.54	0.704	CLONAL	2	TRUE	2	0.183616454656628	5		665	516	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913836	32913836	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs80358757	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	26	602	0	ENST00000380152.3:c.5344C>G	p.Gln1782Glu	p.Q1782E	ENST00000380152		1782	Caa/Gaa	11/27	0.183616454656628	6	FACETS	1	0.832	1	0.353	0.279	0.437	CLONAL	1	TRUE	3	0.183616454656628	6		602	366	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304252	91304252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	19	592	1	ENST00000355112.3:c.1649C>T	p.Ser550Phe	p.S550F	ENST00000355112	NM_000057.2	550	tCc/tTc	7/22	0.183616454656628	2	FACETS	0.704	0.534	0.903	0.352	0.267	0.452	CLONAL	1	TRUE	0	0.183616454656628	2		593	294	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645327	67645327	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	40	561	0	ENST00000264010.4:c.592C>G	p.Gln198Glu	p.Q198E	ENST00000264010	NM_006565.3	198	Cag/Gag	3/12	0.146389089338388	3	FACETS	1	0.904	1	0.566	0.471	0.672	CLONAL	1	TRUE	1	0.183616454656628	3		561	420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578396	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	GTGGGGGCAGCGCCTCACAACCTCCGTCATGTGCTGTGACTGCTTGT	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	91	792	0	ENST00000269305.4:c.488_534dup	p.His179ThrfsTer7	p.H179Tfs*7	ENST00000269305	NM_001126112.2	178	-/ACAAGCAGTCACAGCACATGACGGAGGTTGTGAGGCGCTGCCCCCAC	5/11	0.158935347999938	4	FACETS	0.874	0.777	0.978	0.437	0.388	0.489	CLONAL	2	TRUE	0	0.183616454656628	4		792	671	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7977017	7977017	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	43	810	0	ENST00000319144.4:c.1713C>G	p.Ile571Met	p.I571M	ENST00000319144	NM_001139.2	571	atC/atG	13/15	0.158935347999938	4	FACETS	0.803	0.671	0.951	0.201	0.167	0.238	CLONAL	1	TRUE	0	0.183616454656628	4		810	690	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602593	10602593	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	156	762	1	ENST00000171111.5:c.985T>A	p.Tyr329Asn	p.Y329N	ENST00000171111	NM_203500.1	329	Tac/Aac	3/6	0.183616454656628	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.183616454656628	2		763	713	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135059	11135059	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	138	961	3	ENST00000358026.2:c.3026G>T	p.Arg1009Leu	p.R1009L	ENST00000358026	NM_001128849.1	1009	cGc/cTc	21/36	0.183616454656628	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	0	0.183616454656628	2		964	722	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606119	47606119	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs770760223	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	18	706	0	ENST00000263735.4:c.583C>G	p.Leu195Val	p.L195V	ENST00000263735	NM_002354.2	195	Ctg/Gtg	6/9	0.146389089338388	3	FACETS	0.663	0.498	0.857	0.331	0.249	0.429	SUBCLONAL	1	TRUE	1	0.183616454656628	3		706	323	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018193	48018193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	43	865	0	ENST00000234420.5:c.388C>T	p.His130Tyr	p.H130Y	ENST00000234420	NM_000179.2	130	Cat/Tat	2/10	0.146389089338388	3	FACETS	0.722	0.603	0.855	0.361	0.301	0.428	SUBCLONAL	1	TRUE	1	0.183616454656628	3		865	708	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251872	212251872	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	17	318	0	ENST00000342788.4:c.3187C>A	p.Gln1063Lys	p.Q1063K	ENST00000342788	NM_005235.2	1063	Cag/Aag	27/28	0.183616454656628	5	FACETS	0.875	0.653	1	0.437	0.326	0.569	CLONAL	1	TRUE	3	0.183616454656628	5		318	270	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530064	212530064	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	34	343	0	ENST00000342788.4:c.1855C>T	p.Pro619Ser	p.P619S	ENST00000342788	NM_005235.2	619	Cca/Tca	15/28	0.183616454656628	5	FACETS	0.785	0.643	0.943	0.785	0.643	0.943	CLONAL	2	TRUE	3	0.183616454656628	5		343	301	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225449042	225449664	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGAGTTTGTAAAGTGCTTAGGAAGCTTGTAGGATGAAAGACGCTATAAATACACCCAATGTTACTAGTTTATGACCACGGAGCATTCCGTGGAACCACTGTCACTGCGTCGGGGGCAGGTTGATGGCATAGACCTTCCTGGGGAGGGGGGCAGAGAGAGAGGGCAGCCCCTTCATCACCCTAAAAGCTAGGCTGGGTAAATTTTCAAAGTGTAGCGAAACCCCACGTGAAAAGTTCCACACACGCCCCACACAGGGAGGACTCCGCGGCTGCTAGCAGCGCCGGAGACTGGGCCTACAACCCCGGCAACGTGGGGAGGCGTGGGGCGGCCGAGGGGCCCCGGCCGCAGCCGACGCCCGCGGAGCGGCTGAAGGAGCAGCTCCCGGACGGGGGCGCGGCGCCAGGCCCGGGCTCCCGGCGCGGGGAACGGCCCGGGAGGGCGGCCGCGCCGGGGCCCCGCGCCGCCCGGTTGCCGGGAAGGCTCGCGCCCCGCGGCCGGCGGGCGTGGGGGAGGGGAGGCCGGGCCTGCGGCCTGTTGGGGGACTTCAGCCCGGGCCTCGCGTGCGGCTCTCGGCCCGGCCCCCGGCCCCGGGGTCCCGGACGCCGAGGAGAGACTCACCGGA	AAGAGTTTGTAAAGTGCTTAGGAAGCTTGTAGGATGAAAGACGCTATAAATACACCCAATGTTACTAGTTTATGACCACGGAGCATTCCGTGGAACCACTGTCACTGCGTCGGGGGCAGGTTGATGGCATAGACCTTCCTGGGGAGGGGGGCAGAGAGAGAGGGCAGCCCCTTCATCACCCTAAAAGCTAGGCTGGGTAAATTTTCAAAGTGTAGCGAAACCCCACGTGAAAAGTTCCACACACGCCCCACACAGGGAGGACTCCGCGGCTGCTAGCAGCGCCGGAGACTGGGCCTACAACCCCGGCAACGTGGGGAGGCGTGGGGCGGCCGAGGGGCCCCGGCCGCAGCCGACGCCCGCGGAGCGGCTGAAGGAGCAGCTCCCGGACGGGGGCGCGGCGCCAGGCCCGGGCTCCCGGCGCGGGGAACGGCCCGGGAGGGCGGCCGCGCCGGGGCCCCGCGCCGCCCGGTTGCCGGGAAGGCTCGCGCCCCGCGGCCGGCGGGCGTGGGGGAGGGGAGGCCGGGCCTGCGGCCTGTTGGGGGACTTCAGCCCGGGCCTCGCGTGCGGCTCTCGGCCCGGCCCCCGGCCCCGGGGTCCCGGACGCCGAGGAGAGACTCACCGGA	-	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	0	51	0	0	ENST00000264414.4:c.63_66+619del		p.X21_splice	ENST00000264414	NM_003590.4	21		1/16	0.183616454656628	5	FACETS		NA	1	1	0.986	1	NA	14	TRUE	3	0.183616454656628	5		0	51	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663402	227663402	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	55	500	0	ENST00000305123.5:c.53A>G	p.Tyr18Cys	p.Y18C	ENST00000305123	NM_005544.2	18	tAc/tGc	1/2	0.183616454656628	5	FACETS	0.811	0.695	0.938	0.811	0.695	0.938	CLONAL	2	TRUE	3	0.183616454656628	5		500	471	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790021	40790021	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	42	665	0	ENST00000373198.4:c.2710C>A	p.Gln904Lys	p.Q904K	ENST00000373198	NM_133170.3	904	Cag/Aag	18/32	0.183616454656628	4	FACETS	0.782	0.652	0.928	0.261	0.217	0.31	CLONAL	1	TRUE	1	0.183616454656628	4		665	692	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513271	44513271	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	119	863	0	ENST00000291552.4:c.664G>T	p.Gly222Cys	p.G222C	ENST00000291552	NM_006758.2	222	Ggc/Tgc	8/8	0.146389089338388	3	FACETS	0.918	0.829	1	0.918	0.829	1	CLONAL	2	TRUE	1	0.183616454656628	3		863	771	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475584	12475584	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	42	621	0	ENST00000287820.6:c.1458G>C	p.Lys486Asn	p.K486N	ENST00000287820	NM_015869.4	486	aaG/aaC	7/7	0.159774143446771	3	FACETS	0.959	0.8	1			1	CLONAL	1	TRUE	NA	0.183616454656628	3		621	521	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259574	89259574	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	22	530	0	ENST00000336596.2:c.718C>A	p.Pro240Thr	p.P240T	ENST00000336596	NM_005233.5	240	Cca/Aca	3/17	0.121458495960228	4	FACETS	0.889	0.689	1	0.445	0.344	0.561	CLONAL	1	TRUE	2	0.183616454656628	4		530	319	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274802	142274802	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	81	691	0	ENST00000350721.4:c.2258G>C	p.Cys753Ser	p.C753S	ENST00000350721	NM_001184.3	753	tGt/tCt	10/47	0.152360818570094	3	FACETS	0.856	0.759	0.959	0.856	0.759	0.959	CLONAL	3	TRUE	0	0.183616454656628	3		691	375	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141100	55141100	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	74	613	0	ENST00000257290.5:c.1746T>A	p.Tyr582Ter	p.Y582*	ENST00000257290	NM_006206.4	582	taT/taA	12/23	0.107957356490718	3	FACETS	1	0.942	1	1	0.942	1	INDETERMINATE	2	TRUE	1	0.183616454656628	3		613	393	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201809	66201809	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	37	702	0	ENST00000273854.3:c.2693C>A	p.Pro898Gln	p.P898Q	ENST00000273854	NM_004439.5	898	cCa/cAa	16/18	0.107957356490718	3	FACETS	0.926	0.763	1	0.463	0.381	0.555	INDETERMINATE	1	TRUE	1	0.183616454656628	3		702	475	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226015	226015	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	11	166	0	ENST00000264932.6:c.474G>T	p.Met158Ile	p.M158I	ENST00000264932	NM_004168.2	158	atG/atT	5/15	0.146389089338388	3	FACETS	1	0.767	1	0.564	0.392	0.774	CLONAL	1	TRUE	1	0.183616454656628	3		166	116	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178562	56178562	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	13	359	0	ENST00000399503.3:c.3535G>C	p.Glu1179Gln	p.E1179Q	ENST00000399503	NM_005921.1	1179	Gag/Cag	14/20	0.183616454656628	2	FACETS	0.722	0.516	0.973	0.361	0.258	0.487	CLONAL	1	TRUE	0	0.183616454656628	2		359	196	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564327	86564327	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	47	471	1	ENST00000274376.6:c.59G>T	p.Gly20Val	p.G20V	ENST00000274376	NM_002890.2	20	gGa/gTa	1/25	0.183616454656628	2	FACETS	0.895	0.76	1	0.895	0.76	1	CLONAL	2	TRUE	0	0.183616454656628	2		472	286	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839790	27839790	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	55	722	0	ENST00000328488.2:c.304G>T	p.Val102Leu	p.V102L	ENST00000328488	NM_003533.2	102	Gtg/Ttg	1/1	0.183616454656628	6	FACETS	1	0.958	1	0.337	0.288	0.391	CLONAL	1	TRUE	2	0.183616454656628	6		722	607	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940142	31940142	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	44	1019	0	ENST00000375333.2:c.284C>G	p.Ser95Cys	p.S95C	ENST00000375333	NM_032454.1	95	tCt/tGt	2/8	0.183616454656628	6	FACETS	0.748	0.625	0.885	0.187	0.156	0.222	SUBCLONAL	1	TRUE	2	0.183616454656628	6		1019	876	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979213	93979213	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	46	521	0	ENST00000369303.4:c.1615A>C	p.Thr539Pro	p.T539P	ENST00000369303	NM_004440.3	539	Aca/Cca	7/17	0.183616454656628	5	FACETS	1	0.915	1	1	0.915	1	CLONAL	2	TRUE	3	0.183616454656628	5		521	285	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982063	93982063	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	55	616	0	ENST00000369303.4:c.1402C>A	p.His468Asn	p.H468N	ENST00000369303	NM_004440.3	468	Cat/Aat	6/17	0.183616454656628	5	FACETS	0.767	0.657	0.888	0.767	0.657	0.888	SUBCLONAL	2	TRUE	3	0.183616454656628	5		616	498	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631283	117631283	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs773896715	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	29	702	0	ENST00000368508.3:c.6395G>C	p.Ser2132Thr	p.S2132T	ENST00000368508	NM_002944.2	2132	aGt/aCt	40/43	0.183616454656628	5	FACETS	0.901	0.723	1	0.451	0.361	0.553	CLONAL	1	TRUE	3	0.183616454656628	5		702	447	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525479	137525479	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1422744046	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	18	682	0	ENST00000367739.4:c.536A>G	p.Asn179Ser	p.N179S	ENST00000367739	NM_000416.2	179	aAc/aGc	4/7	0.183616454656628	5	FACETS	0.7	0.527	0.907	0.35	0.263	0.454	SUBCLONAL	1	TRUE	3	0.183616454656628	5		682	357	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138201347	138201347	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	40	623	0	ENST00000237289.4:c.2046G>C	p.Gln682His	p.Q682H	ENST00000237289	NM_001270507.1	682	caG/caC	8/9	0.183616454656628	5	FACETS	0.909	0.754	1	0.455	0.377	0.542	CLONAL	1	TRUE	3	0.183616454656628	5		623	611	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959221	2959221	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	186	826	0	ENST00000396946.4:c.2295G>C	p.Met765Ile	p.M765I	ENST00000396946	NM_032415.4	765	atG/atC	18/25	0.121458495960228	4	FACETS	0.946	0.875	1	1	0.989	1	CLONAL	3	TRUE	2	0.183616454656628	4		826	845	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520027	106520027	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs370034420	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	48	481	0	ENST00000359195.3:c.2455G>T	p.Asp819Tyr	p.D819Y	ENST00000359195	NM_002649.2	819	Gat/Tat	6/11	0.121458495960228	4	FACETS	1	0.914	1	1	0.914	1	CLONAL	2	TRUE	2	0.183616454656628	4		481	279	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859797	151859797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	52	486	1	ENST00000262189.6:c.10865C>T	p.Pro3622Leu	p.P3622L	ENST00000262189	NM_170606.2	3622	cCa/cTa	43/59	0.183616454656628	8	FACETS	0.94	0.802	1	0.313	0.267	0.364	CLONAL	2	TRUE	2	0.183616454656628	8		487	467	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884356	151884356	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	22	326	0	ENST00000262189.6:c.4999G>C	p.Glu1667Gln	p.E1667Q	ENST00000262189	NM_170606.2	1667	Gaa/Caa	33/59	0.183616454656628	8	FACETS	1	0.869	1	0.198	0.153	0.25	CLONAL	1	TRUE	2	0.183616454656628	8		326	313	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007129	152007129	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	42	628	0	ENST00000262189.6:c.771G>T	p.Glu257Asp	p.E257D	ENST00000262189	NM_170606.2	257	gaG/gaT	6/59	0.183616454656628	8	FACETS	0.977	0.814	1	0.163	0.135	0.194	CLONAL	1	TRUE	2	0.183616454656628	8		628	726	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058461	69058461	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	29	658	1	ENST00000288368.4:c.4105C>T	p.Gln1369Ter	p.Q1369*	ENST00000288368	NM_024870.2	1369	Caa/Taa	34/40	0.121458495960228	4	FACETS	0.961	0.771	1	0.481	0.385	0.589	CLONAL	1	TRUE	2	0.183616454656628	4		659	389	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971145	21971145	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	69	493	0	ENST00000304494.5:c.213C>G	p.Asn71Lys	p.N71K	ENST00000304494	NM_000077.4	71	aaC/aaG	2/3	0.14894024479976	2	FACETS	0.984	0.861	1	0.984	0.861	1	CLONAL	2	TRUE	0	0.183616454656628	2		493	382	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128268662	128268663	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	101	842	0	ENST00000265960.3:c.992_993del	p.Pro331GlnfsTer5	p.P331Qfs*5	ENST00000265960	NM_001006617.1	331	cCC/c	8/12	0.146389089338388	3	FACETS	0.836	0.748	0.931	0.836	0.748	0.931	CLONAL	2	TRUE	1	0.183616454656628	3		842	718	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815632	139815632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	42	795	0	ENST00000247668.2:c.1103C>T	p.Ala368Val	p.A368V	ENST00000247668	NM_021138.3	368	gCt/gTt	9/11	0.146389089338388	3	FACETS	0.749	0.624	0.888	0.374	0.312	0.444	SUBCLONAL	1	TRUE	1	0.183616454656628	3		795	667	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044883	47044883	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	150	499	1	ENST00000377604.3:c.2209G>T	p.Asp737Tyr	p.D737Y	ENST00000377604	NM_001204468.1	737	Gac/Tac	20/24	0.183616454656628	2	FACETS	1	0.972	1			1	CLONAL	3	TRUE	NA	0.183616454656628	2		500	485	SUCCESS
AR	367	MSKCC	GRCh37	X	66765742	66765742	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	169	622	1	ENST00000374690.3:c.754G>T	p.Glu252Ter	p.E252*	ENST00000374690	NM_000044.3	252	Gag/Tag	1/8	0.183616454656628	2	FACETS	0.882	0.816	0.949			1	CLONAL	4	TRUE	NA	0.183616454656628	2		623	522	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593443	48593443	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	114	597	0	ENST00000342988.3:c.1194G>T	p.Trp398Cys	p.W398C	ENST00000342988	NM_005359.5	398	tgG/tgT	10/12	0.152360818570094	3	FACETS	1	0.91	1	1	0.91	1	CLONAL	3	TRUE	0	0.183616454656628	3		597	450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934576	NA	P-0021388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	184	988	0	ENST00000269305.4:c.818G>C	p.Arg273Pro	p.R273P	ENST00000269305	NM_001126112.2	273	cGt/cCt	8/11	0.209614375739705	1	FACETS	1	0.983	1	1	0.994	1	CLONAL	2	TRUE	0	0.209614375739705	1		988	653	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391107	89391107	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	59	754	0	ENST00000336596.2:c.1173C>G	p.Asn391Lys	p.N391K	ENST00000336596	NM_005233.5	391	aaC/aaG	5/17	1	2	FACETS	0.818	0.703	0.944	0.818	0.703	0.944	CLONAL	1	TRUE	1	0.209614375739705	2		754	688	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411360	63411360	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779976787	NA	P-0021388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	71	441	1	ENST00000330258.3:c.1807G>A	p.Ala603Thr	p.A603T	ENST00000330258	NM_152424.3	603	Gct/Act	2/2	0.209614375739705	0	FACETS	0.923	0.814	1			1	CLONAL	2	TRUE	NA	0.209614375739705	0		442	290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs17849781	NA	P-0021389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	312	916	0	ENST00000269305.4:c.832C>A	p.Pro278Thr	p.P278T	ENST00000269305	NM_001126112.2	278	Cct/Act	8/11	0.180850591132611	3	FACETS	0.88	0.832	0.928	0.88	0.832	0.928	CLONAL	3	TRUE	0	0.291630626922141	3		916	929	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202634	108202634	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs864622368	NA	P-0021390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	190	600	0	ENST00000278616.4:c.7658C>A	p.Pro2553His	p.P2553H	ENST00000278616	NM_000051.3	2553	cCc/cAc	52/63	1	2	FACETS	0.791	0.732	0.853	0.791	0.732	0.853	SUBCLONAL	1	TRUE	1	0.553144248633142	2		600	868	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503222	125503222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	170	489	1	ENST00000428830.2:c.589G>A	p.Val197Ile	p.V197I	ENST00000428830	NM_001114121.2	197	Gta/Ata	6/14	1	2	FACETS	0.927	0.856	1	0.927	0.856	1	CLONAL	1	TRUE	1	0.553144248633142	2		490	663	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923102	48923102	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	358	656	1	ENST00000267163.4:c.550G>T	p.Glu184Ter	p.E184*	ENST00000267163	NM_000321.2	184	Gaa/Taa	6/27	0.467733945752741	2	FACETS	0.759	0.722	0.795	0.759	0.722	0.795	SUBCLONAL	2	TRUE	0	0.553144248633142	2		657	853	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644940	67644940	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	167	664	1	ENST00000264010.4:c.205A>T	p.Thr69Ser	p.T69S	ENST00000264010	NM_006565.3	69	Acc/Tcc	3/12	1	2	FACETS	0.735	0.676	0.797	0.735	0.676	0.797	SUBCLONAL	1	TRUE	1	0.553144248633142	2		665	821	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0021390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	512	813	1	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	0.467733945752741	2	FACETS	0.791	0.76	0.823	0.791	0.76	0.823	SUBCLONAL	2	TRUE	0	0.553144248633142	2		814	1170	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39638005	39638005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	203	709	0	ENST00000262039.4:c.2422C>T	p.His808Tyr	p.H808Y	ENST00000262039	NM_002647.2	808	Cac/Tac	22/25	1	2	FACETS	0.788	0.731	0.847	0.788	0.731	0.847	SUBCLONAL	1	TRUE	1	0.553144248633142	2		709	932	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224517	36224517	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1297	300	953	0	ENST00000222270.7:c.6979A>G	p.Lys2327Glu	p.K2327E	ENST00000222270	NM_014727.1	2327	Aaa/Gaa	29/37	0.445638989890716	3	FACETS	0.867	0.814	0.922	0.434	0.407	0.461	CLONAL	1	TRUE	1	0.553144248633142	3		953	1597	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128028917	128028917	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	243	730	0	ENST00000285398.2:c.1940A>T	p.Lys647Ile	p.K647I	ENST00000285398	NM_000122.1	647	aAa/aTa	12/15	0.445638989890716	3	FACETS	0.944	0.881	1	0.472	0.44	0.505	CLONAL	1	TRUE	1	0.553144248633142	3		730	1188	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098936	178098936	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	538	582	0	ENST00000397062.3:c.109T>G	p.Phe37Val	p.F37V	ENST00000397062	NM_006164.4	37	Ttt/Gtt	2/5	0.445638989890716	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.553144248633142	3		582	1139	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379374	225379375	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1553523940	NA	P-0021390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	377	958	0	ENST00000264414.4:c.493_494del	p.Leu165IlefsTer37	p.L165Ifs*37	ENST00000264414	NM_003590.4	165	CTa/a	4/16	0.445638989890716	3	FACETS	1	0.993	1	0.652	0.619	0.687	CLONAL	1	TRUE	1	0.553144248633142	3		958	1334	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57474003	57474003	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	302	488	0	ENST00000371085.3:c.220G>A	p.Glu74Lys	p.E74K	ENST00000371085	NM_000516.4	74	Gaa/Aaa	3/13	0.445638989890716	3	FACETS	0.843	0.797	0.889	0.843	0.797	0.889	CLONAL	2	TRUE	1	0.553144248633142	3		488	827	SUCCESS
ATR	545	MSKCC	GRCh37	3	142212009	142212009	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	416	739	0	ENST00000350721.4:c.6043A>T	p.Asn2015Tyr	p.N2015Y	ENST00000350721	NM_001184.3	2015	Aac/Tac	35/47	0.421767726322767	4	FACETS	0.806	0.767	0.846	0.806	0.767	0.846	CLONAL	2	TRUE	2	0.553144248633142	4		739	1449	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535413	187535413	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	464	725	0	ENST00000441802.2:c.9161C>G	p.Ser3054Cys	p.S3054C	ENST00000441802	NM_005245.3	3054	tCt/tGt	12/27	0.467733945752741	2	FACETS	0.853	0.819	0.888	0.853	0.819	0.888	CLONAL	2	TRUE	0	0.553144248633142	2		725	983	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045769	26045769	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	346	596	0	ENST00000540144.1:c.131C>A	p.Pro44Gln	p.P44Q	ENST00000540144	NM_003531.2	44	cCg/cAg	1/1	0.467733945752741	2	FACETS	0.821	0.782	0.86	0.821	0.782	0.86	CLONAL	2	TRUE	0	0.553144248633142	2		596	762	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164103	32164103	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	227	818	0	ENST00000375023.3:c.5296A>G	p.Arg1766Gly	p.R1766G	ENST00000375023	NM_004557.3	1766	Agg/Ggg	29/30	0.467733945752741	2	FACETS	0.815	0.759	0.873	0.408	0.379	0.437	CLONAL	1	TRUE	0	0.553144248633142	2		818	1007	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954915	2954915	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	906	847	1	ENST00000396946.4:c.2795G>T	p.Arg932Leu	p.R932L	ENST00000396946	NM_032415.4	932	cGg/cTg	21/25	0.553144248633142	3	FACETS	0.916	0.893	0.94	0.916	0.893	0.94	CLONAL	3	TRUE	0	0.553144248633142	3		848	1521	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509848	106509848	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1043937061	NA	P-0021390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	202	821	0	ENST00000359195.3:c.1842G>T	p.Arg614Ser	p.R614S	ENST00000359195	NM_002649.2	614	agG/agT	2/11	1	2	FACETS	0.758	0.702	0.815	0.758	0.702	0.815	SUBCLONAL	1	TRUE	1	0.553144248633142	2		821	964	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127920550	127920550	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1331	191	752	0	ENST00000373547.4:c.349A>G	p.Arg117Gly	p.R117G	ENST00000373547	NM_002721.4	117	Aga/Gga	4/7	0.474231497379083	4	FACETS	0.705	0.649	0.763	0.235	0.216	0.255	SUBCLONAL	1	TRUE	1	0.553144248633142	4		752	1522	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760307	133760307	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	160	600	0	ENST00000318560.5:c.2630G>T	p.Arg877Met	p.R877M	ENST00000318560	NM_005157.4	877	aGg/aTg	11/11	0.474231497379083	4	FACETS	0.873	0.8	0.95	0.291	0.266	0.317	CLONAL	1	TRUE	1	0.553144248633142	4		600	1029	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928069	178928086	+	inframe_deletion	In_Frame_Del	DEL	TCATGGATTAGAAGATTT	TCATGGATTAGAAGATTT	-	novel	NA	P-0021391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1234	141	829	0	ENST00000263967.3:c.1347_1364del	p.His450_Leu455del	p.H450_L455del	ENST00000263967	NM_006218.2	449	ccTCATGGATTAGAAGATTTg/ccg	8/21	0.457516538306392	3	FACETS	0.551	0.5	0.604	0.275	0.25	0.302	SUBCLONAL	1	TRUE	1	0.457516538306392	3		829	1375	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982975	201982975	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	70	862	0	ENST00000359651.3:c.824T>C	p.Leu275Pro	p.L275P	ENST00000359651		275	cTg/cCg	7/8	1	2	FACETS	0.331	0.288	0.378	0.331	0.288	0.378	SUBCLONAL	1	TRUE	1	0.457516538306392	2		862	924	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494200	140494200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1213	100	936	0	ENST00000288602.6:c.1048G>A	p.Asp350Asn	p.D350N	ENST00000288602	NM_004333.4	350	Gat/Aat	8/18	1	2	FACETS	0.333	0.296	0.372	0.333	0.296	0.372	SUBCLONAL	1	TRUE	1	0.457516538306392	2		936	1313	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90976662	90976662	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	64	755	1	ENST00000265433.3:c.970G>A	p.Asp324Asn	p.D324N	ENST00000265433	NM_002485.4	324	Gat/Aat	8/16	1	2	FACETS	0.233	0.2	0.268	0.233	0.2	0.268	SUBCLONAL	1	TRUE	1	0.457516538306392	2		756	1203	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952064	76952064	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0021391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	67	648	0	ENST00000373344.5:c.370+1G>T		p.X124_splice	ENST00000373344	NM_000489.3	124			1	2	FACETS	0.294	0.254	0.337	0.294	0.254	0.337	SUBCLONAL	1	TRUE	1	0.457516538306392	2		648	997	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649912	88649912	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0121430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	73	612	0	ENST00000372037.3:c.161A>G	p.Asp54Gly	p.D54G	ENST00000372037	NM_004329.2	54	gAt/gGt	4/13	0.253636472947313	1	FACETS	0.38	0.332	0.43	0.38	0.332	0.43	INDETERMINATE	1	NA	0	0.552359170738188	1		612	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578507	7578507	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519977	NA	P-0021401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	824	759	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	0.657802667814252	2		759	1181	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750684	128750684	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	988	549	1	ENST00000377970.2:c.221C>A	p.Pro74Gln	p.P74Q	ENST00000377970	NM_002467.4	74	cCg/cAg	2/3	0.657802667814252	7	FACETS	0.933	0.913	0.953	0.933	0.913	0.953	CLONAL	6	TRUE	1	0.657802667814252	7		550	1419	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696461	47696461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	352	512	0	ENST00000347630.2:c.362G>A	p.Arg121Gln	p.R121Q	ENST00000347630	NM_001007230.1	121	cGg/cAg	6/11	0.651271628235542	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.657802667814252	3		512	444	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11032302	11032302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	133	499	0	ENST00000327064.4:c.1696G>A	p.Ala566Thr	p.A566T	ENST00000327064	NM_199141.1	566	Gcc/Acc	16/16	0.657802667814252	6	FACETS	0.752	0.681	0.827			1	SUBCLONAL	1	TRUE	NA	0.657802667814252	6		499	1245	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627279	14627279	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1735	143	744	1	ENST00000254322.2:c.791A>G	p.Glu264Gly	p.E264G	ENST00000254322	NM_006145.1	264	gAg/gGg	2/3	0.657802667814252	6	FACETS	0.536	0.486	0.589			1	SUBCLONAL	1	TRUE	NA	0.657802667814252	6		745	1878	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627472	14627472	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	92	549	2	ENST00000254322.2:c.598G>A	p.Glu200Lys	p.E200K	ENST00000254322	NM_006145.1	200	Gaa/Aaa	2/3	0.657802667814252	6	FACETS	0.578	0.512	0.649			1	SUBCLONAL	1	TRUE	NA	0.657802667814252	6		551	1120	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250694	26250694	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	163	500	0	ENST00000446824.2:c.140T>C	p.Val47Ala	p.V47A	ENST00000446824	NM_021018.2	47	gTc/gCc	1/1	0.625667104175942	4	FACETS	0.887	0.814	0.964	0.296	0.271	0.322	CLONAL	1	TRUE	1	0.657802667814252	4		500	926	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs199469669	NA	P-0021401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	11	579	0	ENST00000374080.3:c.130G>C	p.Gly44Arg	p.G44R	ENST00000374080		44	Ggt/Cgt	2/45	0.657802667814252	1	FACETS	0.043	0.029	0.061	0.043	0.029	0.061	SUBCLONAL	1	TRUE	0	0.657802667814252	1		579	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0021402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	232	960	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.481607851762575	2	FACETS	0.995	0.939	1	0.995	0.939	1	CLONAL	2	TRUE	0	0.481607851762575	2		960	484	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0021402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	31	573	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.388370367616217	5	FACETS	0.909	0.749	1	0.606	0.499	0.721	CLONAL	2	TRUE	2	0.481607851762575	5		573	122	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992630	72992630	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1189486286	NA	P-0021402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	55	651	0	ENST00000268489.5:c.1415C>A	p.Ala472Glu	p.A472E	ENST00000268489	NM_006885.3	472	gCg/gAg	2/10	1	2	FACETS	0.549	0.471	0.634	0.549	0.471	0.634	SUBCLONAL	1	TRUE	1	0.481607851762575	2		651	416	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462305	89462305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	29	659	0	ENST00000336596.2:c.1777C>T	p.Leu593Phe	p.L593F	ENST00000336596	NM_005233.5	593	Ctc/Ttc	10/17	0.481607851762575	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	2	TRUE	0	0.481607851762575	2		659	54	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074158	8074159	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0021402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	28	608	0	ENST00000377482.5:c.500_501del	p.Thr167ArgfsTer3	p.T167Rfs*3	ENST00000377482	NM_018948.3	167	aCA/a	4/4	1	2	FACETS	0.894	0.726	1	0.894	0.726	1	CLONAL	1	TRUE	1	0.481607851762575	2		608	130	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260126	10260126	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0021402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	64	919	0	ENST00000340748.4:c.2538+3G>A		p.X846_splice	ENST00000340748		846			0.481607851762575	2	FACETS	0.801	0.698	0.91	0.4	0.349	0.455	CLONAL	1	TRUE	0	0.481607851762575	2		919	332	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344505	118344508	+	frameshift_variant	Frame_Shift_Del	DEL	CCGG	CCGG	-	novel	NA	P-0021402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	18	412	1	ENST00000534358.1:c.2631_2634del	p.Asp877GlufsTer71	p.D877Efs*71	ENST00000534358	NM_005933.3	877	gaCCGG/ga	3/36	0.265753147393387	6	FACETS	0.492	0.37	0.637			1	INDETERMINATE	1	TRUE	NA	0.481607851762575	6		413	298	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0021404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	107	779	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.17645200554048	4	FACETS	1	0.933	1	0.526	0.472	0.583	INDETERMINATE	1	TRUE	2	0.412836678105847	4		779	696	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0021404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	35	753	2	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.137506812605899	4	FACETS	0.59	0.484	0.709	0.295	0.242	0.355	INDETERMINATE	1	TRUE	2	0.412836678105847	4		755	406	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969923	81969923	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773444784	NA	P-0021404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	40	817	1	ENST00000359376.3:c.2992G>A	p.Asp998Asn	p.D998N	ENST00000359376	NM_002661.3	998	Gac/Aac	27/33	1	2	FACETS	0.577	0.481	0.683	0.577	0.481	0.683	SUBCLONAL	1	TRUE	1	0.412836678105847	2		818	336	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671287	30671287	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	61	712	0	ENST00000376406.3:c.5590A>G	p.Arg1864Gly	p.R1864G	ENST00000376406	NM_014641.2	1864	Aga/Gga	11/15	0.412836678105847	5	FACETS	1	0.92	1			1	CLONAL	1	TRUE	NA	0.412836678105847	5		712	439	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900214	101900214	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs863223809	NA	P-0021404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	111	612	0	ENST00000374994.4:c.648T>G	p.Phe216Leu	p.F216L	ENST00000374994	NM_004612.2	216	ttT/ttG	4/9	0.232443135568622	5	FACETS	1	0.93	1			1	INDETERMINATE	2	TRUE	NA	0.412836678105847	5		612	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0021406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	21	824	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.396	0.304	0.506	0.396	0.304	0.506	SUBCLONAL	1	TRUE	1	0.13	2		825	815	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0021406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	12	672	2	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.617	0.433	0.846	0.617	0.433	0.846	SUBCLONAL	1	TRUE	1	0.13	2		674	299	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	42	690	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.107804954117922	3	FACETS	0.84	0.699	0.998	0.42	0.349	0.499	CLONAL	1	TRUE	1	0.13	3		690	819	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692961	89692961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060500122	NA	P-0021406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	18	570	0	ENST00000371953.3:c.445C>T	p.Gln149Ter	p.Q149*	ENST00000371953	NM_000314.4	149	Caa/Taa	5/9	1	2	FACETS	0.968	0.729	1	0.968	0.729	1	CLONAL	1	TRUE	1	0.13	2		570	286	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919595	28919595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs553261958	NA	P-0021406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	25	735	2	ENST00000282397.4:c.2342G>A	p.Arg781Gln	p.R781Q	ENST00000282397	NM_002019.4	781	cGa/cAa	16/30	1	2	FACETS	0.945	0.744	1	0.945	0.744	1	CLONAL	1	TRUE	1	0.13	2		737	407	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023408	27023408	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	38	627	0	ENST00000324856.7:c.514C>T	p.Gln172Ter	p.Q172*	ENST00000324856	NM_006015.4	172	Caa/Taa	1/20	1	2	FACETS	0.983	0.811	1	0.983	0.811	1	CLONAL	1	TRUE	1	0.13	2		627	595	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0021408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	24	916	3	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.198	0.154	0.249	0.198	0.154	0.249	SUBCLONAL	1	FALSE	1	0.204408616704901	2		919	1187	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934578	NA	P-0021408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	133	868	0	ENST00000269305.4:c.524G>T	p.Arg175Leu	p.R175L	ENST00000269305	NM_001126112.2	175	cGc/cTc	5/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.204408616704901	2		868	924	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154242	2154242	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755455183	NA	P-0021408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	64	1061	0	ENST00000434045.2:c.686del	p.Pro229GlnfsTer27	p.P229Qfs*27	ENST00000434045	NM_001127598.1	229	cCa/ca	5/5	1	2	FACETS	0.575	0.496	0.661	0.575	0.496	0.661	SUBCLONAL	1	FALSE	1	0.204408616704901	2		1061	1089	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	881	1147	2	ENST00000397752.3:c.3028G>A	p.Asp1010Asn	p.D1010N	ENST00000397752	NM_000245.2	1010	Gat/Aat	14/21	0.204408616704901	6	FACETS	0.949	0.921	0.976			1	CLONAL	7	FALSE	NA	0.204408616704901	6		1149	1829	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196902	108196902	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	106	702	0	ENST00000278616.4:c.6925C>G	p.Leu2309Val	p.L2309V	ENST00000278616	NM_000051.3	2309	Ctg/Gtg	47/63	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	1	0.204408616704901	2		702	901	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216540	108216540	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	59	772	0	ENST00000278616.4:c.8489T>G	p.Val2830Gly	p.V2830G	ENST00000278616	NM_000051.3	2830	gTt/gGt	58/63	1	2	FACETS	0.648	0.556	0.749	0.648	0.556	0.749	SUBCLONAL	1	FALSE	1	0.204408616704901	2		772	891	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245349	46245350	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	107	792	0	ENST00000334344.6:c.3444dup	p.Gln1149ThrfsTer11	p.Q1149Tfs*11	ENST00000334344	NM_152641.2	1148	tta/ttAa	15/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.204408616704901	2		792	784	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640010	3640010	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	166	1220	0	ENST00000294008.3:c.3629G>T	p.Ser1210Ile	p.S1210I	ENST00000294008	NM_032444.2	1210	aGc/aTc	12/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.204408616704901	2		1220	1161	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99179935	99179935	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	79	1076	1	ENST00000074304.5:c.1878G>C	p.Trp626Cys	p.W626C	ENST00000074304	NM_001134224.1	626	tgG/tgC	19/26	1	2	FACETS	0.638	0.559	0.724	0.638	0.559	0.724	SUBCLONAL	1	FALSE	1	0.204408616704901	2		1077	1211	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430956	181430956	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	220	1027	1	ENST00000325404.1:c.808C>A	p.Leu270Ile	p.L270I	ENST00000325404	NM_003106.3	270	Ctc/Atc	1/1	0.204408616704901	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	FALSE	2	0.204408616704901	4		1028	1249	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279473	1279473	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	69	1172	4	ENST00000310581.5:c.2063G>T	p.Arg688Met	p.R688M	ENST00000310581	NM_198253.2	688	aGg/aTg	5/16	1	2	FACETS	0.586	0.508	0.671	0.586	0.508	0.671	SUBCLONAL	1	FALSE	1	0.204408616704901	2		1176	1152	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372669	81372669	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	54	514	0	ENST00000222390.5:c.865G>T	p.Ala289Ser	p.A289S	ENST00000222390	NM_000601.4	289	Gct/Tct	7/18	0.204408616704901	1	FACETS	0.916	0.783	1	0.916	0.783	1	CLONAL	1	FALSE	0	0.204408616704901	1		514	518	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549364	5549364	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	127	801	1	ENST00000397747.3:c.391C>A	p.Leu131Ile	p.L131I	ENST00000397747	NM_025239.3	131	Cta/Ata	4/7	NA	2	FACETS	0.758	0.686	0.833			1	INDETERMINATE	2	FALSE	NA	0.204408616704901	2		802	820	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0021411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	29	573	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	0.452632386599298	2		573	107	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775467	39775467	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1048054600	NA	P-0021411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	10	768	3	ENST00000288319.7:c.553G>A	p.Ala185Thr	p.A185T	ENST00000288319	NM_182918.3	185	Gcc/Acc	4/10	0.330324118858017	3	FACETS	0.293	0.198	0.412	0.146	0.099	0.206	SUBCLONAL	1	TRUE	1	0.452632386599298	3		771	185	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115733	8115734	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CATCCAGA	novel	NA	P-0021411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	12	637	0	ENST00000346208.3:c.1081_1088dup	p.Arg364SerfsTer43	p.R364Sfs*43	ENST00000346208		360	ggc/ggCATCCAGAc	6/6	0.227708083802805	1	FACETS	0.21	0.148	0.287	0.21	0.148	0.287	INDETERMINATE	1	TRUE	0	0.452632386599298	1		637	195	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974394	93974394	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	35	624	0	ENST00000369303.4:c.1660C>A	p.Pro554Thr	p.P554T	ENST00000369303	NM_004440.3	554	Cct/Act	8/17	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.452632386599298	2		624	135	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247541	53247541	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	10	803	0	ENST00000375401.3:c.268G>T	p.Ala90Ser	p.A90S	ENST00000375401	NM_004187.3	90	Gcc/Tcc	3/26	0.150991103551122	0	FACETS	0.257	0.176	0.358			1	INDETERMINATE	1	TRUE	0	0.452632386599298	0		803	94	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0021418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	104	272	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.333215821322909	2	FACETS	1	0.979	1	0.659	0.596	0.724	CLONAL	1	TRUE	0	0.447148918156252	2		272	353	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32931894	32931894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358990	NA	P-0021418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	131	524	0	ENST00000380152.3:c.7633G>A	p.Val2545Ile	p.V2545I	ENST00000380152		2545	Gtt/Att	16/27	0.364986227985886	5	FACETS	1	0.98	1	0.321	0.291	0.352	CLONAL	1	TRUE	1	0.447148918156252	5		524	763	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63662128	63662128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	129	582	0	ENST00000279873.7:c.232C>T	p.Leu78Phe	p.L78F	ENST00000279873	NM_032199.2	78	Ctc/Ttc	2/10	0.333215821322909	2	FACETS	0.801	0.727	0.879	0.401	0.363	0.44	CLONAL	1	TRUE	0	0.447148918156252	2		582	720	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435253	110435253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771232244	NA	P-0021418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	200	500	2	ENST00000375856.3:c.3148G>A	p.Val1050Ile	p.V1050I	ENST00000375856	NM_003749.2	1050	Gtt/Att	1/2	0.364986227985886	5	FACETS	1	0.981	1	0.295	0.272	0.318	CLONAL	1	TRUE	1	0.447148918156252	5		502	1268	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858033	9858033	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1239554350	NA	P-0021418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	123	710	0	ENST00000330684.3:c.3368A>G	p.Glu1123Gly	p.E1123G	ENST00000330684	NM_001134407.1	1123	gAg/gGg	13/13	0.10312901824565	3	FACETS	0.718	0.649	0.792	0.359	0.324	0.396	INDETERMINATE	1	TRUE	1	0.447148918156252	3		710	937	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578378	7578392	+	inframe_deletion	In_Frame_Del	DEL	ATCTGAGCAGCGCTC	ATCTGAGCAGCGCTC	-	novel	NA	P-0021418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	306	564	2	ENST00000269305.4:c.538_552del	p.Glu180_Asp184del	p.E180_D184del	ENST00000269305	NM_001126112.2	180	GAGCGCTGCTCAGAT/-	5/11	0.333215821322909	2	FACETS	0.815	0.771	0.859	0.815	0.771	0.859	CLONAL	2	TRUE	0	0.447148918156252	2		566	840	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795607	42795607	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	215	821	0	ENST00000575354.2:c.2687C>A	p.Pro896Gln	p.P896Q	ENST00000575354	NM_015125.3	896	cCa/cAa	10/20	1	2	FACETS	0.821	0.762	0.882	0.821	0.762	0.882	CLONAL	1	TRUE	1	0.447148918156252	2		821	1172	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953837	55953837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	109	745	0	ENST00000263923.4:c.3599C>T	p.Ser1200Phe	p.S1200F	ENST00000263923	NM_002253.2	1200	tCc/tTc	27/30	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.26527946605556	2		745	796	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944914	31944914	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	48	300	0	ENST00000340398.3:c.187C>G	p.Arg63Gly	p.R63G	ENST00000340398	NM_001013699.2	63	Cgg/Ggg	1/1	1	2	FACETS	0.955	0.81	1	0.955	0.81	1	CLONAL	1	TRUE	1	0.26527946605556	2		300	379	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141507	11141507	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	87	723	2	ENST00000358026.2:c.3484G>T	p.Gly1162Cys	p.G1162C	ENST00000358026	NM_001128849.1	1162	Ggc/Tgc	25/36	0.26527946605556	1	FACETS	0.875	0.775	0.982	0.875	0.775	0.982	CLONAL	1	TRUE	0	0.26527946605556	1		725	650	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119624685	119624685	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	97	577	0	ENST00000316626.5:c.730G>T	p.Gly244Cys	p.G244C	ENST00000316626		244	Ggc/Tgc	7/12	1	2	FACETS	0.947	0.844	1	0.947	0.844	1	CLONAL	1	TRUE	1	0.26527946605556	2		577	772	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851274	156851274	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	54	718	0	ENST00000524377.1:c.2231G>C	p.Arg744Pro	p.R744P	ENST00000524377	NM_002529.3	744	cGt/cCt	17/17	0.26527946605556	3	FACETS	0.561	0.478	0.653	0.28	0.239	0.327	SUBCLONAL	1	TRUE	1	0.26527946605556	3		718	822	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451477	70451477	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	127	673	0	ENST00000373644.4:c.6317C>G	p.Ser2106Cys	p.S2106C	ENST00000373644	NM_030625.2	2106	tCt/tGt	12/12	0.242447203950431	3	FACETS	1	0.953	1	0.544	0.492	0.599	CLONAL	1	TRUE	1	0.26527946605556	3		673	997	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137198	64137198	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	45	773	0	ENST00000334205.4:c.1630G>T	p.Gly544Trp	p.G544W	ENST00000334205	NM_003942.2	544	Ggg/Tgg	14/17	0.185983485292238	2	FACETS	0.428	0.359	0.506	0.214	0.179	0.253	SUBCLONAL	1	TRUE	0	0.26527946605556	2		773	792	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518550	69518550	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	50	622	3	ENST00000294312.3:c.95C>T	p.Pro32Leu	p.P32L	ENST00000294312	NM_005117.2	32	cCc/cTc	1/3	0.233974748401306	3	FACETS	0.579	0.49	0.677	0.289	0.245	0.339	SUBCLONAL	1	TRUE	1	0.26527946605556	3		625	738	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998580	100998580	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	48	668	2	ENST00000325455.5:c.1222G>T	p.Gly408Cys	p.G408C	ENST00000325455	NM_001202474.3	408	Ggt/Tgt	1/8	0.233974748401306	3	FACETS	0.528	0.445	0.619	0.264	0.222	0.31	SUBCLONAL	1	TRUE	1	0.26527946605556	3		670	777	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125496701	125496701	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	150	464	0	ENST00000428830.2:c.38A>T	p.Gln13Leu	p.Q13L	ENST00000428830	NM_001114121.2	13	cAa/cTa	2/14	0.233974748401306	3	FACETS	0.811	0.742	0.883	0.811	0.742	0.883	CLONAL	2	TRUE	1	0.26527946605556	3		464	790	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022766	12022766	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	88	470	0	ENST00000396373.4:c.872G>T	p.Arg291Met	p.R291M	ENST00000396373	NM_001987.4	291	aGg/aTg	5/8	0.193238676562299	4	FACETS	1	0.917	1	0.348	0.308	0.391	CLONAL	1	TRUE	1	0.26527946605556	4		470	804	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861995	57861996	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	68	472	0	ENST00000228682.2:c.1297dup	p.Glu433GlyfsTer19	p.E433Gfs*19	ENST00000228682	NM_005269.2	432	-/G	10/12	1	2	FACETS	0.898	0.782	1	0.898	0.782	1	CLONAL	1	TRUE	1	0.26527946605556	2		472	571	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109795	115109795	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	96	839	1	ENST00000257566.3:c.2083C>A	p.Arg695Ser	p.R695S	ENST00000257566	NM_016569.3	695	Cgc/Agc	8/8	1	2	FACETS	0.841	0.748	0.939	0.841	0.748	0.939	CLONAL	1	TRUE	1	0.26527946605556	2		840	861	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895693	28895693	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	77	824	0	ENST00000282397.4:c.3081C>A	p.Asn1027Lys	p.N1027K	ENST00000282397	NM_002019.4	1027	aaC/aaA	23/30	0.26527946605556	2	FACETS	0.54	0.472	0.613	0.27	0.236	0.307	SUBCLONAL	1	TRUE	0	0.26527946605556	2		824	1075	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574405	95574405	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	49	338	0	ENST00000393063.1:c.2462G>T	p.Arg821Leu	p.R821L	ENST00000393063	NM_030621.3	821	cGc/cTc	17/28	1	2	FACETS	0.894	0.759	1	0.894	0.759	1	CLONAL	1	TRUE	1	0.26527946605556	2		338	413	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420272	88420272	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	94	634	1	ENST00000360948.2:c.2414G>T	p.Gly805Val	p.G805V	ENST00000360948	NM_001012338.2	805	gGg/gTg	19/19	1	2	FACETS	0.808	0.718	0.904	0.808	0.718	0.904	CLONAL	1	TRUE	1	0.26527946605556	2		635	877	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483911	88483911	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	116	745	0	ENST00000360948.2:c.1659C>A	p.Phe553Leu	p.F553L	ENST00000360948	NM_001012338.2	553	ttC/ttA	14/19	1	2	FACETS	0.816	0.734	0.903	0.816	0.734	0.903	CLONAL	1	TRUE	1	0.26527946605556	2		745	1072	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348175	348175	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	205	717	1	ENST00000262320.3:c.1331G>T	p.Trp444Leu	p.W444L	ENST00000262320	NM_003502.3	444	tGg/tTg	6/11	0.233974748401306	3	FACETS	0.96	0.891	1	0.96	0.891	1	CLONAL	2	TRUE	1	0.26527946605556	3		718	912	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213931	2213931	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	238	731	2	ENST00000326181.6:c.10G>T	p.Gly4Cys	p.G4C	ENST00000326181	NM_032271.2	4	Ggc/Tgc	2/21	0.233974748401306	3	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	1	0.26527946605556	3		733	994	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2221355	2221355	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	154	590	0	ENST00000326181.6:c.439G>T	p.Gly147Trp	p.G147W	ENST00000326181	NM_032271.2	147	Ggg/Tgg	6/21	0.233974748401306	3	FACETS	0.819	0.75	0.891	0.819	0.75	0.891	CLONAL	2	TRUE	1	0.26527946605556	3		590	803	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779157	3779157	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	178	616	1	ENST00000262367.5:c.5891G>T	p.Arg1964Leu	p.R1964L	ENST00000262367	NM_004380.2	1964	cGt/cTt	31/31	0.233974748401306	3	FACETS	0.937	0.865	1	0.937	0.865	1	CLONAL	2	TRUE	1	0.26527946605556	3		617	811	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991499	72991499	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	328	872	0	ENST00000268489.5:c.2546G>T	p.Gly849Val	p.G849V	ENST00000268489	NM_006885.3	849	gGc/gTc	2/10	0.233974748401306	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.26527946605556	3		872	1189	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578539	7578539	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782160	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	447	865	0	ENST00000269305.4:c.391A>T	p.Asn131Tyr	p.N131Y	ENST00000269305	NM_001126112.2	131	Aac/Tac	5/11	0.257071724916523	3	FACETS	0.972	0.928	1	0.972	0.928	1	CLONAL	3	TRUE	0	0.26527946605556	3		865	1309	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973761	15973761	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	172	553	0	ENST00000268712.3:c.4231A>T	p.Ser1411Cys	p.S1411C	ENST00000268712	NM_006311.3	1411	Agc/Tgc	31/46	0.257071724916523	3	FACETS	0.886	0.816	0.959	0.591	0.544	0.639	CLONAL	2	TRUE	0	0.26527946605556	3		553	829	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552227	29552227	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	84	649	0	ENST00000356175.3:c.1960C>A	p.Pro654Thr	p.P654T	ENST00000356175	NM_000267.3	654	Cct/Act	17/57	0.26527946605556	5	FACETS	0.836	0.736	0.943	0.279	0.245	0.315	CLONAL	1	TRUE	2	0.26527946605556	5		649	1059	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435485	56435485	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	255	772	0	ENST00000407977.2:c.1652A>C	p.His551Pro	p.H551P	ENST00000407977		551	cAc/cCc	9/10	0.26527946605556	5	FACETS	1	0.988	1	0.818	0.766	0.872	CLONAL	2	TRUE	2	0.26527946605556	5		772	1095	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39576688	39576688	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	141	492	0	ENST00000262039.4:c.978A>T	p.Gln326His	p.Q326H	ENST00000262039	NM_002647.2	326	caA/caT	9/25	0.233974748401306	3	FACETS	1	0.986	1	0.735	0.67	0.803	CLONAL	1	TRUE	1	0.26527946605556	3		492	819	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641522	47641522	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	47	483	0	ENST00000233146.2:c.907G>T	p.Asp303Tyr	p.D303Y	ENST00000233146	NM_000251.2	303	Gat/Tat	5/16	0.26527946605556	3	FACETS	0.456	0.383	0.537	0.228	0.191	0.269	SUBCLONAL	1	TRUE	1	0.26527946605556	3		483	880	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257747	198257747	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	123	558	1	ENST00000335508.6:c.3705G>T	p.Glu1235Asp	p.E1235D	ENST00000335508	NM_012433.2	1235	gaG/gaT	24/25	0.26527946605556	3	FACETS	1	0.965	1	0.571	0.516	0.63	CLONAL	1	TRUE	1	0.26527946605556	3		559	919	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257748	198257748	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	54	546	0	ENST00000335508.6:c.3704A>T	p.Glu1235Val	p.E1235V	ENST00000335508	NM_012433.2	1235	gAg/gTg	24/25	0.26527946605556	3	FACETS	0.508	0.433	0.592	0.254	0.216	0.296	SUBCLONAL	1	TRUE	1	0.26527946605556	3		546	907	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403190	213403190	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1300045748	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	92	625	0	ENST00000342788.4:c.65C>T	p.Pro22Leu	p.P22L	ENST00000342788	NM_005235.2	22	cCc/cTc	1/28	0.26527946605556	3	FACETS	1	0.938	1	0.541	0.481	0.606	CLONAL	1	TRUE	1	0.26527946605556	3		625	726	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793436	242793436	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	107	634	0	ENST00000334409.5:c.641C>A	p.Ser214Ter	p.S214*	ENST00000334409	NM_005018.2	214	tCa/tAa	5/5	0.26527946605556	3	FACETS	1	0.952	1	0.554	0.496	0.615	CLONAL	1	TRUE	1	0.26527946605556	3		634	825	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546651	9546651	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	224	629	0	ENST00000353224.5:c.1371A>T	p.Glu457Asp	p.E457D	ENST00000353224	NM_177990.2	457	gaA/gaT	5/10	0.26527946605556	5	FACETS	0.843	0.786	0.903			1	CLONAL	3	TRUE	NA	0.26527946605556	5		629	933	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017234	31017234	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	50	318	0	ENST00000375687.4:c.565G>C	p.Gly189Arg	p.G189R	ENST00000375687	NM_015338.5	189	Ggg/Cgg	7/13	0.233974748401306	3	FACETS	0.861	0.731	1	0.43	0.365	0.502	CLONAL	1	TRUE	1	0.26527946605556	3		318	496	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019162	31019162	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	125	684	1	ENST00000375687.4:c.757G>T	p.Glu253Ter	p.E253*	ENST00000375687	NM_015338.5	253	Gag/Tag	9/13	0.233974748401306	3	FACETS	0.944	0.852	1	0.472	0.426	0.521	CLONAL	1	TRUE	1	0.26527946605556	3		685	1131	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770556	40770556	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	88	613	0	ENST00000373198.4:c.2826del	p.Tyr943ThrfsTer6	p.Y943Tfs*6	ENST00000373198	NM_133170.3	942	tcC/tc	19/32	0.233974748401306	3	FACETS	0.966	0.855	1	0.483	0.427	0.542	CLONAL	1	TRUE	1	0.26527946605556	3		613	778	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458454	12458454	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	70	727	2	ENST00000287820.6:c.1071G>T	p.Met357Ile	p.M357I	ENST00000287820	NM_015869.4	357	atG/atT	6/7	0.233974748401306	3	FACETS	0.602	0.523	0.688	0.301	0.261	0.344	SUBCLONAL	1	TRUE	1	0.26527946605556	3		729	993	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72842131	72842131	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	75	591	0	ENST00000325599.8:c.1117G>T	p.Asp373Tyr	p.D373Y	ENST00000325599	NM_018130.2	373	Gac/Tac	10/11	0.233974748401306	3	FACETS	0.657	0.574	0.747	0.328	0.287	0.374	SUBCLONAL	1	TRUE	1	0.26527946605556	3		591	975	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447681	187447681	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	49	706	0	ENST00000232014.4:c.512G>T	p.Ser171Ile	p.S171I	ENST00000232014	NM_001130845.1	171	aGc/aTc	5/10	0.185983485292238	2	FACETS	0.529	0.447	0.62	0.265	0.223	0.31	SUBCLONAL	1	TRUE	0	0.26527946605556	2		706	698	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217307	66217307	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	34	366	0	ENST00000273854.3:c.2308G>T	p.Gly770Trp	p.G770W	ENST00000273854	NM_004439.5	770	Ggg/Tgg	14/18	1	2	FACETS	0.675	0.552	0.813	0.675	0.552	0.813	SUBCLONAL	1	TRUE	1	0.26527946605556	2		366	380	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627954	187627954	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	116	728	0	ENST00000441802.2:c.3028G>T	p.Val1010Phe	p.V1010F	ENST00000441802	NM_005245.3	1010	Gtt/Ttt	2/27	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.26527946605556	2		728	869	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679993	30679993	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	195	554	0	ENST00000376406.3:c.1726G>T	p.Asp576Tyr	p.D576Y	ENST00000376406	NM_014641.2	576	Gac/Tac	5/15	0.199967876397189	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.26527946605556	4		554	861	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117645554	117645554	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	105	626	0	ENST00000368508.3:c.5582G>T	p.Ser1861Ile	p.S1861I	ENST00000368508	NM_002944.2	1861	aGt/aTt	34/43	0.185983485292238	2	FACETS	1	0.925	1	0.519	0.465	0.577	CLONAL	1	TRUE	0	0.26527946605556	2		626	762	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200218	138200218	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	88	580	0	ENST00000237289.4:c.1636G>T	p.Glu546Ter	p.E546*	ENST00000237289	NM_001270507.1	546	Gag/Tag	7/9	0.185983485292238	2	FACETS	1	0.916	1	0.52	0.461	0.583	CLONAL	1	TRUE	0	0.26527946605556	2		580	638	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962930	2962930	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1349831751	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	422	888	0	ENST00000396946.4:c.1978C>G	p.Arg660Gly	p.R660G	ENST00000396946	NM_032415.4	660	Cgg/Ggg	16/25	0.26527946605556	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	1	0.26527946605556	4		888	1195	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355212	81355213	+	stop_gained	Nonsense_Mutation	DNP	CA	CA	AT	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	36	343	0	ENST00000222390.5:c.1161_1162delinsAT	p.His387_Gly388delinsGlnTer	p.H387_G388delinsQ*	ENST00000222390	NM_000601.4	387	caTGga/caATga	9/18	0.26527946605556	3	FACETS	0.642	0.527	0.77	0.321	0.263	0.385	SUBCLONAL	1	TRUE	1	0.26527946605556	3		343	479	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358944	81358944	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	46	601	0	ENST00000222390.5:c.1017G>T	p.Met339Ile	p.M339I	ENST00000222390	NM_000601.4	339	atG/atT	8/18	0.26527946605556	3	FACETS	0.447	0.375	0.527	0.223	0.187	0.264	SUBCLONAL	1	TRUE	1	0.26527946605556	3		601	879	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381579	81381579	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	23	319	1	ENST00000222390.5:c.483-1G>T		p.X161_splice	ENST00000222390	NM_000601.4	161			0.26527946605556	3	FACETS	0.469	0.365	0.59	0.234	0.182	0.295	SUBCLONAL	1	TRUE	1	0.26527946605556	3		320	419	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388037	81388037	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	108	721	0	ENST00000222390.5:c.338G>T	p.Gly113Val	p.G113V	ENST00000222390	NM_000601.4	113	gGc/gTc	3/18	0.26527946605556	3	FACETS	0.854	0.765	0.949	0.427	0.382	0.475	CLONAL	1	TRUE	1	0.26527946605556	3		721	1080	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345971	152345971	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	213	680	0	ENST00000359321.1:c.599A>G	p.Gln200Arg	p.Q200R	ENST00000359321	NM_005431.1	200	cAg/cGg	3/3	0.26527946605556	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.26527946605556	3		680	858	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162829	38162829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773861449	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	73	626	0	ENST00000317025.8:c.2377C>T	p.Arg793Cys	p.R793C	ENST00000317025	NM_023034.1	793	Cgc/Tgc	13/24	1	2	FACETS	0.603	0.526	0.686	0.603	0.526	0.686	SUBCLONAL	1	TRUE	1	0.26527946605556	2		626	913	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939487	68939487	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	67	631	0	ENST00000288368.4:c.472A>G	p.Thr158Ala	p.T158A	ENST00000288368	NM_024870.2	158	Aca/Gca	5/40	0.257071724916523	3	FACETS	0.6	0.52	0.687	0.2	0.173	0.229	SUBCLONAL	1	TRUE	0	0.26527946605556	3		631	954	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021727	69021727	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	143	601	3	ENST00000288368.4:c.3015G>T	p.Gln1005His	p.Q1005H	ENST00000288368	NM_024870.2	1005	caG/caT	25/40	0.257071724916523	3	FACETS	0.774	0.706	0.845	0.516	0.471	0.563	SUBCLONAL	2	TRUE	0	0.26527946605556	3		604	789	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376038	8376038	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	73	503	0	ENST00000356435.5:c.4559C>A	p.Pro1520His	p.P1520H	ENST00000356435		1520	cCt/cAt	28/35	0.26527946605556	1	FACETS	0.914	0.801	1	0.914	0.801	1	CLONAL	1	TRUE	0	0.26527946605556	1		503	522	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499645	8499645	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	64	452	0	ENST00000356435.5:c.2322+2T>A		p.X774_splice	ENST00000356435		774			0.26527946605556	1	FACETS	0.791	0.686	0.905	0.791	0.686	0.905	CLONAL	1	TRUE	0	0.26527946605556	1		452	529	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500843	8500843	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	92	637	0	ENST00000356435.5:c.2039G>T	p.Trp680Leu	p.W680L	ENST00000356435		680	tGg/tTg	13/35	0.26527946605556	1	FACETS	0.849	0.754	0.949	0.849	0.754	0.949	CLONAL	1	TRUE	0	0.26527946605556	1		637	709	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650170	93650170	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	42	575	0	ENST00000375746.1:c.1721G>T	p.Arg574Leu	p.R574L	ENST00000375746	NM_001174167.1	574	cGa/cTa	12/14	1	2	FACETS	0.484	0.403	0.574	0.484	0.403	0.574	SUBCLONAL	1	TRUE	1	0.26527946605556	2		575	654	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270604	98270604	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	23	105	0	ENST00000331920.6:c.40G>T	p.Gly14Cys	p.G14C	ENST00000331920	NM_000264.3	14	Ggc/Tgc	1/24	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.26527946605556	2		105	147	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921559	39921559	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	150	770	0	ENST00000378444.4:c.4261C>A	p.Arg1421Ser	p.R1421S	ENST00000378444	NM_001123385.1	1421	Cgc/Agc	10/15	0.188294825440183	4	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.26527946605556	4		770	1048	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933531	39933531	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	63	729	1	ENST00000378444.4:c.1068G>T	p.Glu356Asp	p.E356D	ENST00000378444	NM_001123385.1	356	gaG/gaT	4/15	0.188294825440183	4	FACETS	0.576	0.497	0.663			1	SUBCLONAL	1	TRUE	NA	0.26527946605556	4		730	1043	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038745	47038745	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	110	731	0	ENST00000377604.3:c.752C>A	p.Thr251Lys	p.T251K	ENST00000377604	NM_001204468.1	251	aCg/aAg	9/24	0.242447203950431	3	FACETS	0.992	0.89	1	0.496	0.445	0.55	CLONAL	1	TRUE	1	0.26527946605556	3		731	947	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245149	53245149	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1556851628	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	53	681	1	ENST00000375401.3:c.791G>T	p.Gly264Val	p.G264V	ENST00000375401	NM_004187.3	264	gGg/gTg	7/26	0.242447203950431	3	FACETS	0.6	0.511	0.699	0.3	0.255	0.35	SUBCLONAL	1	TRUE	1	0.26527946605556	3		682	754	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409862	63409862	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	80	503	1	ENST00000330258.3:c.3305A>T	p.Tyr1102Phe	p.Y1102F	ENST00000330258	NM_152424.3	1102	tAt/tTt	2/2	0.242447203950431	3	FACETS	0.997	0.878	1	0.499	0.439	0.563	CLONAL	1	TRUE	1	0.26527946605556	3		504	685	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410239	63410239	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	81	720	0	ENST00000330258.3:c.2928C>A	p.Ser976Arg	p.S976R	ENST00000330258	NM_152424.3	976	agC/agA	2/2	0.242447203950431	3	FACETS	0.809	0.712	0.914	0.404	0.356	0.457	CLONAL	1	TRUE	1	0.26527946605556	3		720	855	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411463	63411463	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	109	881	0	ENST00000330258.3:c.1704G>T	p.Leu568Phe	p.L568F	ENST00000330258	NM_152424.3	568	ttG/ttT	2/2	0.242447203950431	3	FACETS	0.809	0.725	0.899	0.405	0.362	0.45	CLONAL	1	TRUE	1	0.26527946605556	3		881	1150	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412468	63412468	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1174	154	832	0	ENST00000330258.3:c.699T>A	p.Asp233Glu	p.D233E	ENST00000330258	NM_152424.3	233	gaT/gaA	2/2	0.242447203950431	3	FACETS	0.99	0.904	1	0.495	0.452	0.541	CLONAL	1	TRUE	1	0.26527946605556	3		832	1328	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412988	63412988	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	123	843	0	ENST00000330258.3:c.179T>A	p.Phe60Tyr	p.F60Y	ENST00000330258	NM_152424.3	60	tTt/tAt	2/2	0.242447203950431	3	FACETS	0.871	0.785	0.962	0.435	0.392	0.481	CLONAL	1	TRUE	1	0.26527946605556	3		843	1206	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344161	70344161	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	79	666	0	ENST00000374080.3:c.1897C>G	p.Pro633Ala	p.P633A	ENST00000374080		633	Cct/Gct	13/45	0.242447203950431	3	FACETS	0.779	0.684	0.882	0.389	0.342	0.441	SUBCLONAL	1	TRUE	1	0.26527946605556	3		666	866	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360708	70360708	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	15	101	0	ENST00000374080.3:c.6267+1G>T		p.X2089_splice	ENST00000374080		2089			0.242447203950431	3	FACETS	0.935	0.689	1	0.467	0.344	0.613	CLONAL	1	TRUE	1	0.26527946605556	3		101	137	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76777865	76777865	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	73	514	0	ENST00000373344.5:c.6851G>T	p.Gly2284Val	p.G2284V	ENST00000373344	NM_000489.3	2284	gGa/gTa	32/35	0.242447203950431	3	FACETS	0.812	0.709	0.923	0.406	0.354	0.462	CLONAL	1	TRUE	1	0.26527946605556	3		514	768	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891418	76891418	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	104	594	0	ENST00000373344.5:c.4687C>A	p.His1563Asn	p.H1563N	ENST00000373344	NM_000489.3	1563	Cat/Aat	16/35	0.242447203950431	3	FACETS	1	0.911	1	0.51	0.456	0.568	CLONAL	1	TRUE	1	0.26527946605556	3		594	870	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019590	123019590	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	92	684	0	ENST00000355640.3:c.78G>T	p.Glu26Asp	p.E26D	ENST00000355640		26	gaG/gaT	2/7	0.242447203950431	3	FACETS	0.813	0.721	0.912	0.407	0.36	0.456	CLONAL	1	TRUE	1	0.26527946605556	3		684	966	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627697	37627698	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	T	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1214	67	806	0	ENST00000447079.4:c.1612_1613delinsT	p.Pro538PhefsTer72	p.P538Ffs*72	ENST00000447079	NM_015083.1	538	CCt/Tt	2/14	0.26527946605556	5	FACETS	0.551	0.477	0.632	0.184	0.159	0.211	SUBCLONAL	1	TRUE	2	0.26527946605556	5		806	1281	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39573238	39573240	+	missense_variant	Missense_Mutation	TNP	GTG	GTG	TTT	novel	NA	P-0021419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	95	565	4	ENST00000262039.4:c.719_721delinsTTT	p.Gly240_Asp241delinsValTyr	p.G240_D241delinsVY	ENST00000262039	NM_002647.2	240	gGTGat/gTTTat	7/25	0.233974748401306	3	FACETS	0.94	0.836	1	0.47	0.418	0.526	CLONAL	1	TRUE	1	0.26527946605556	3		569	863	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0021422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	281	857	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.271450116544182	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.271450116544182	4		857	1092	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915524	112915524	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121918455	NA	P-0021422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	123	749	0	ENST00000351677.2:c.923A>G	p.Asn308Ser	p.N308S	ENST00000351677	NM_002834.3	308	aAt/aGt	8/16	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.271450116544182	2		749	854	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0021424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	135	687	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.404233169216651	1	FACETS	0.981	0.896	1	0.981	0.896	1	CLONAL	1	TRUE	0	0.404233169216651	1		687	543	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0021424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	139	592	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.404233169216651	2		592	532	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612879	228612879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767647652	NA	P-0021424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	220	560	0	ENST00000366696.1:c.148C>T	p.Arg50Cys	p.R50C	ENST00000366696	NM_003493.2	50	Cgc/Tgc	1/1	0.192784641172747	4	FACETS	1	0.963	1	1	0.963	1	INDETERMINATE	2	TRUE	2	0.404233169216651	4		560	732	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057936	27057937	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0021424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	131	653	0	ENST00000324856.7:c.1649_1650dup	p.Tyr551ProfsTer69	p.Y551Pfs*69	ENST00000324856	NM_006015.4	548	-/CC	3/20	1	2	FACETS	0.835	0.758	0.916	0.835	0.758	0.916	CLONAL	1	TRUE	1	0.404233169216651	2		653	776	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878503	151878503	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	148	669	0	ENST00000262189.6:c.6442T>A	p.Ser2148Thr	p.S2148T	ENST00000262189	NM_170606.2	2148	Tct/Act	36/59	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.404233169216651	2		669	730	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0021425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2337	110	772	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.668307152582568	11	FACETS	0.539	0.482	0.601			1	SUBCLONAL	1	TRUE	NA	0.668307152582568	11		772	2447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0021425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	633	825	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.668307152582568	2	FACETS	0.998	0.97	1	0.998	0.97	1	CLONAL	2	TRUE	0	0.668307152582568	2		825	949	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869474	102869474	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	461	578	1	ENST00000307046.8:c.167C>A	p.Ala56Asp	p.A56D	ENST00000307046	NM_001111285.1	56	gCt/gAt	2/4	0.665854534839222	2	FACETS	0.991	0.959	1	0.991	0.959	1	CLONAL	2	TRUE	0	0.668307152582568	2		579	696	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610289	81610289	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	97	635	0	ENST00000298171.2:c.1887G>C	p.Leu629Phe	p.L629F	ENST00000298171	NM_000369.2	629	ttG/ttC	10/10	0.282312837370073	3	FACETS	0.502	0.447	0.56	0.251	0.223	0.28	INDETERMINATE	1	TRUE	1	0.668307152582568	3		635	772	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566139	95566139	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	235	659	0	ENST00000393063.1:c.4184A>G	p.Asp1395Gly	p.D1395G	ENST00000393063	NM_030621.3	1395	gAt/gGt	23/28	0.282312837370073	3	FACETS	1	0.978	1	0.55	0.514	0.587	INDETERMINATE	1	TRUE	1	0.668307152582568	3		659	853	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244876	41244876	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	567	744	0	ENST00000357654.3:c.2672C>G	p.Ser891Cys	p.S891C	ENST00000357654	NM_007294.3	891	tCc/tGc	10/23	0.668307152582568	2	FACETS	0.993	0.964	1	0.993	0.964	1	CLONAL	2	TRUE	0	0.668307152582568	2		744	854	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190717451	190717451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	257	679	0	ENST00000441310.2:c.770G>A	p.Arg257Lys	p.R257K	ENST00000441310	NM_000534.4	257	aGa/aAa	7/13	0.282312837370073	3	FACETS	1	0.986	1	0.584	0.548	0.621	INDETERMINATE	1	TRUE	1	0.668307152582568	3		679	879	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403630	138403630	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	443	612	0	ENST00000289153.2:c.2152A>C	p.Lys718Gln	p.K718Q	ENST00000289153	NM_006219.2	718	Aag/Cag	15/22	0.316232818974673	6	FACETS	0.943	0.902	0.984	0.943	0.902	0.984	INDETERMINATE	3	TRUE	3	0.668307152582568	6		612	1095	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555687605	NA	P-0021427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	77	554	0	ENST00000342988.3:c.1610A>G	p.Asp537Gly	p.D537G	ENST00000342988	NM_005359.5	537	gAc/gGc	12/12	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.226783668604693	2		554	616	SUCCESS
APC	324	MSKCC	GRCh37	5	112173947	112173947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs755806668	NA	P-0021427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	56	513	1	ENST00000257430.4:c.2656C>T	p.Gln886Ter	p.Q886*	ENST00000257430	NM_000038.5	886	Cag/Tag	16/16	1	2	FACETS	0.966	0.829	1	0.966	0.829	1	CLONAL	1	TRUE	1	0.226783668604693	2		514	511	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120181	70120182	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CG	novel	NA	P-0021427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	97	642	0	ENST00000245479.2:c.1185_1186dup	p.His396ArgfsTer8	p.H396Rfs*8	ENST00000245479	NM_000346.3	395	acg/aCGcg	3/3	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.226783668604693	2		642	641	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117962	70117963	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0021427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	52	383	0	ENST00000245479.2:c.431+1dup		p.R144fs	ENST00000245479	NM_000346.3	144	aga/aGga	1/3	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.226783668604693	2		383	335	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740668	58740668	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs759850701	NA	P-0021427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	65	773	1	ENST00000305921.3:c.1573G>T	p.Glu525Ter	p.E525*	ENST00000305921	NM_003620.3	525	Gaa/Taa	6/6	1	2	FACETS	0.834	0.723	0.956	0.834	0.723	0.956	CLONAL	1	TRUE	1	0.226783668604693	2		774	687	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922363	178922363	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	9	670	0	ENST00000263967.3:c.1132T>C	p.Cys378Arg	p.C378R	ENST00000263967	NM_006218.2	378	Tgt/Cgt	6/21	1	2	FACETS	0.183	0.12	0.264	0.183	0.12	0.264	SUBCLONAL	1	TRUE	1	0.226783668604693	2		670	434	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581348	48581348	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	61	662	0	ENST00000342988.3:c.653del	p.Pro218LeufsTer23	p.P218Lfs*23	ENST00000342988	NM_005359.5	218	Cct/ct	5/12	1	2	FACETS	0.952	0.822	1	0.952	0.822	1	CLONAL	1	TRUE	1	0.226783668604693	2		662	565	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573285	55573285	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	33	586	0	ENST00000288135.5:c.947T>C	p.Phe316Ser	p.F316S	ENST00000288135	NM_000222.2	316	tTc/tCc	6/21	1	2	FACETS	0.987	0.806	1	0.987	0.806	1	CLONAL	1	TRUE	1	0.226783668604693	2		586	295	SUCCESS
APC	324	MSKCC	GRCh37	5	112175778	112175779	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0021427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	41	458	0	ENST00000257430.4:c.4488_4489del	p.Pro1497ArgfsTer16	p.P1497Rfs*16	ENST00000257430	NM_000038.5	1496	aCT/a	16/16	1	2	FACETS	0.934	0.78	1	0.934	0.78	1	CLONAL	1	TRUE	1	0.226783668604693	2		458	387	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027813	152027813	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	71	687	2	ENST00000262189.6:c.262C>T	p.Gln88Ter	p.Q88*	ENST00000262189	NM_170606.2	88	Caa/Taa	3/59	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.226783668604693	2		689	500	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912366	97912366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	40	464	0	ENST00000289081.3:c.525G>A	p.Met175Ile	p.M175I	ENST00000289081	NM_000136.2	175	atG/atA	7/15	1	2	FACETS	0.757	0.629	0.899	0.757	0.629	0.899	SUBCLONAL	1	TRUE	1	0.226783668604693	2		464	466	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0021429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	98	757	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	1	2	FACETS	0.888	0.792	0.991	0.888	0.792	0.991	CLONAL	1	TRUE	1	0.272162085910751	2		757	811	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223422	53223422	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	166	982	1	ENST00000375401.3:c.3937C>T	p.Gln1313Ter	p.Q1313*	ENST00000375401	NM_004187.3	1313	Caa/Taa	23/26	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.272162085910751	2		983	1039	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0021430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	255	866	3	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.463093695963291	2		869	1090	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1427441061	NA	P-0021430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	210	658	3	ENST00000269305.4:c.560-2A>G		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.463093695963291	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.463093695963291	1		661	658	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770570	40770570	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	57	787	0	ENST00000373198.4:c.2812G>T	p.Gly938Trp	p.G938W	ENST00000373198	NM_133170.3	938	Ggg/Tgg	19/32	0.444550445563118	3	FACETS	0.283	0.241	0.328	0.094	0.08	0.11	SUBCLONAL	1	TRUE	0	0.463093695963291	3		787	1073	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980614	1980614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1560827075	NA	P-0021430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	159	553	3	ENST00000382891.5:c.4076G>A	p.Arg1359Gln	p.R1359Q	ENST00000382891	NM_133335.3	1359	cGg/cAg	22/22	1	2	FACETS	0.987	0.907	1	0.987	0.907	1	CLONAL	1	TRUE	1	0.463093695963291	2		556	696	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0021430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	152	614	4	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.865	0.792	0.941	0.865	0.792	0.941	CLONAL	1	TRUE	1	0.463093695963291	2		618	759	SUCCESS
APC	324	MSKCC	GRCh37	5	112175282	112175282	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0021430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	123	394	0	ENST00000257430.4:c.3991A>T	p.Arg1331Ter	p.R1331*	ENST00000257430	NM_000038.5	1331	Aga/Tga	16/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.463093695963291	2		394	499	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968317	2968317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781126781	NA	P-0021430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	203	829	3	ENST00000396946.4:c.1669C>T	p.Arg557Cys	p.R557C	ENST00000396946	NM_032415.4	557	Cgc/Tgc	13/25	0.442534325230113	3	FACETS	0.958	0.887	1	0.479	0.443	0.516	CLONAL	1	TRUE	1	0.463093695963291	3		832	1127	SUCCESS
AR	367	MSKCC	GRCh37	X	66765263	66765263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	135	619	10	ENST00000374690.3:c.275G>A	p.Gly92Asp	p.G92D	ENST00000374690	NM_000044.3	92	gGt/gAt	1/8	1	2	FACETS	0.827	0.753	0.905	0.827	0.753	0.905	CLONAL	1	TRUE	1	0.463093695963291	2		629	705	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0021431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	56	608	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	0.184502597242752	3	FACETS	0.603	0.517	0.696	0.302	0.258	0.348	INDETERMINATE	1	TRUE	1	0.49374036048502	3		608	469	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160653	56160654	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	178	468	0	ENST00000399503.3:c.930dup	p.Val311SerfsTer15	p.V311Sfs*15	ENST00000399503	NM_005921.1	309	-/A	4/20	0.284553287400997	3	FACETS	1	0.974	1	0.56	0.517	0.605	INDETERMINATE	1	TRUE	1	0.49374036048502	3		468	802	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184186	56184186	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0021431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	177	345	0	ENST00000399503.3:c.4389+2T>A		p.X1463_splice	ENST00000399503	NM_005921.1	1463			0.284553287400997	3	FACETS	0.953	0.887	1	0.953	0.887	1	INDETERMINATE	2	TRUE	1	0.49374036048502	3		345	469	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073542	8073542	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	124	530	0	ENST00000377482.5:c.1117G>C	p.Ala373Pro	p.A373P	ENST00000377482	NM_018948.3	373	Gcc/Ccc	4/4	1	2	FACETS	0.908	0.825	0.995	0.908	0.825	0.995	CLONAL	1	TRUE	1	0.503685202248142	2		530	542	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0021434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	199	857	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.232614418329325	2	FACETS	0.961	0.891	1	0.961	0.891	1	CLONAL	2	TRUE	0	0.235564269321473	2		859	879	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971199	21971199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894095	NA	P-0021434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	133	520	0	ENST00000304494.5:c.159G>A	p.Met53Ile	p.M53I	ENST00000304494	NM_000077.4	53	atG/atA	2/3	0.231440183776157	2	FACETS	0.917	0.835	1	0.917	0.835	1	CLONAL	2	TRUE	0	0.235564269321473	2		520	616	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519925	NA	P-0021434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	92	582	0	ENST00000263967.3:c.1357G>C	p.Glu453Gln	p.E453Q	ENST00000263967	NM_006218.2	453	Gaa/Caa	8/21	0.192967208615737	4	FACETS	0.794	0.706	0.887	0.794	0.706	0.887	SUBCLONAL	2	TRUE	2	0.235564269321473	4		582	608	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244616	46244616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	133	597	1	ENST00000334344.6:c.2710C>T	p.Gln904Ter	p.Q904*	ENST00000334344	NM_152641.2	904	Cag/Tag	15/21	0.232614418329325	2	FACETS	0.812	0.739	0.889	0.812	0.739	0.889	CLONAL	2	TRUE	0	0.235564269321473	2		598	695	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575107	48575107	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	127	490	1	ENST00000342988.3:c.301T>A	p.Trp101Arg	p.W101R	ENST00000342988	NM_005359.5	101	Tgg/Agg	3/12	0.147596543151811	3	FACETS	0.844	0.769	0.921	0.844	0.769	0.921	CLONAL	3	TRUE	0	0.235564269321473	3		491	476	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041032	42041032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	216	711	0	ENST00000219905.7:c.5410C>T	p.Pro1804Ser	p.P1804S	ENST00000219905	NM_001164273.1	1804	Cct/Tct	16/24	0.192967208615737	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	2	0.235564269321473	4		711	1047	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	397106	397355	+	splice_acceptor_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	CCTGTTGAAACCATTAAGAGGACAAGGATTAGGAAAGGTGGGTCCATGAAACACGACCAGAGGTTTTCTCAAGACAAGACTCACGATGACGCCCTCCCGCTCAAACTCAAAGCAAGAAACTCAGTTTAAATGTTCAATCAAGATATATTTTGGCCACAAGCATAGTTCTACTTTAAAGCAATTTCTGGAAACTTTTACAACTACAGGAATGCCTCTCATGCTAAGAAGGGATGCCCAGGACATGGGAATG	CCTGTTGAAACCATTAAGAGGACAAGGATTAGGAAAGGTGGGTCCATGAAACACGACCAGAGGTTTTCTCAAGACAAGACTCACGATGACGCCCTCCCGCTCAAACTCAAAGCAAGAAACTCAGTTTAAATGTTCAATCAAGATATATTTTGGCCACAAGCATAGTTCTACTTTAAAGCAATTTCTGGAAACTTTTACAACTACAGGAATGCCTCTCATGCTAAGAAGGGATGCCCAGGACATGGGAATG	-	novel	NA	P-0021434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	63	235	0	ENST00000262320.3:c.-81-249_-81del		p.X27_splice	ENST00000262320	NM_003502.3	27		2/11	0.183704075756055	4	FACETS	0.961	0.836	1			1	CLONAL	2	TRUE	NA	0.235564269321473	4		235	344	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913284	NA	P-0021434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	64	359	0	ENST00000263967.3:c.1035T>G	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaG	5/21	0.192967208615737	4	FACETS	0.841	0.732	0.959	0.841	0.732	0.959	CLONAL	2	TRUE	2	0.235564269321473	4		359	399	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140745	55140750	+	inframe_deletion	In_Frame_Del	DEL	GTGATT	GTGATT	-	novel	NA	P-0021434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	157	618	0	ENST00000257290.5:c.1611_1616del	p.Val538_Ile539del	p.V538_I539del	ENST00000257290	NM_006206.4	536	GTGATT/-	11/23	0.231440183776157	2	FACETS	0.908	0.833	0.986	0.908	0.833	0.986	CLONAL	2	TRUE	0	0.235564269321473	2		618	734	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536086	106536086	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	22	272	0	ENST00000369096.4:c.53A>T	p.Lys18Met	p.K18M	ENST00000369096	NM_001198.3	18	aAg/aTg	2/7	0.13982331915469	3	FACETS	0.496	0.383	0.627			1	INDETERMINATE	1	TRUE	NA	0.235564269321473	3		272	421	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437245	52437251	+	frameshift_variant	Frame_Shift_Del	DEL	TCCACTG	TCCACTG	-	novel	NA	P-0021435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	435	952	0	ENST00000460680.1:c.1793_1799del	p.Pro598ArgfsTer17	p.P598Rfs*17	ENST00000460680	NM_004656.3	598	cCAGTGGAg/cg	14/17	0.441964242979375	3	FACETS	0.961	0.923	0.999	0.961	0.923	0.999	CLONAL	3	TRUE	0	0.441964242979375	3		952	834	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857896	9857896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369878342	NA	P-0021436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	577	719	1	ENST00000330684.3:c.3505C>T	p.Arg1169Trp	p.R1169W	ENST00000330684	NM_001134407.1	1169	Cgg/Tgg	13/13	0.516760524509142	5	FACETS	1	0.994	1			1	CLONAL	3	TRUE	NA	0.516760524509142	5		720	1158	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098601	108098601	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1555054249	NA	P-0021436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	216	384	0	ENST00000278616.4:c.171G>T	p.Trp57Cys	p.W57C	ENST00000278616	NM_000051.3	57	tgG/tgT	3/63	0.508113794567861	3	FACETS	0.923	0.873	0.972	0.923	0.873	0.972	CLONAL	3	TRUE	0	0.516760524509142	3		384	380	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0021437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	179	772	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.389914707470046	3	FACETS	0.936	0.868	1	0.936	0.868	1	CLONAL	2	TRUE	1	0.389914707470046	3		772	586	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011152	12011152	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0021437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	168	599	1	ENST00000353533.5:c.559A>T	p.Lys187Ter	p.K187*	ENST00000353533	NM_003010.3	187	Aag/Tag	5/11	NA	2	FACETS	0.949	0.881	1			1	INDETERMINATE	2	TRUE	NA	0.389914707470046	2		600	454	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974793	15974794	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	168	546	0	ENST00000268712.3:c.4081dup	p.Thr1361AsnfsTer19	p.T1361Nfs*19	ENST00000268712	NM_006311.3	1361	act/aAct	30/46	NA	2	FACETS	0.86	0.797	0.925			1	INDETERMINATE	2	TRUE	NA	0.389914707470046	2		546	501	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012737	36012747	+	frameshift_variant	Frame_Shift_Del	DEL	CCCAAGCTGTT	CCCAAGCTGTT	-	novel	NA	P-0021437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	40	318	0	ENST00000358208.4:c.182_192del	p.Pro61ArgfsTer30	p.P61Rfs*30	ENST00000358208		61	CCCAAGCTGTTc/c	2/12	0.283013860250138	3	FACETS	0.885	0.74	1	0.443	0.37	0.523	CLONAL	1	TRUE	1	0.389914707470046	3		318	277	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0021438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	117	733	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	1	2	FACETS	0.734	0.662	0.809	0.734	0.662	0.809	SUBCLONAL	1	TRUE	1	0.437004381431208	2		733	730	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7141776	7141776	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	217	946	1	ENST00000302850.5:c.2594A>G	p.Asn865Ser	p.N865S	ENST00000302850	NM_000208.2	865	aAc/aGc	13/22	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.437004381431208	2		947	983	SUCCESS
ALK	238	MSKCC	GRCh37	2	29541192	29541192	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	45	832	0	ENST00000389048.3:c.1625C>G	p.Pro542Arg	p.P542R	ENST00000389048	NM_004304.4	542	cCg/cGg	8/29	1	2	FACETS	0.254	0.213	0.3	0.254	0.213	0.3	SUBCLONAL	1	TRUE	1	0.437004381431208	2		832	810	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344938	70344938	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	185	973	0	ENST00000374080.3:c.2168G>A	p.Gly723Glu	p.G723E	ENST00000374080		723	gGg/gAg	15/45	1	2	FACETS	0.932	0.861	1	0.932	0.861	1	CLONAL	1	TRUE	1	0.437004381431208	2		973	908	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713361	30713361	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	290	554	0	ENST00000295754.5:c.686C>T	p.Ser229Phe	p.S229F	ENST00000295754	NM_003242.5	229	tCc/tTc	4/7	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.644542932742281	2		554	785	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	14	669	0				ENST00000310581	NM_198253.2	-/1132			0.148253848741564	3	FACETS	0.783	0.596	0.982	0.783	0.596	0.982	INDETERMINATE	2	FALSE	1	0.637739807772772	3		669	37	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0021440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	141	710	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.515406188945502	6	FACETS	0.911	0.848	0.975	0.911	0.848	0.975	CLONAL	4	FALSE	2	0.637739807772772	6		711	276	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0021440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	60	419	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.337836654332245	3	FACETS	0.833	0.736	0.932	0.555	0.49	0.622	INDETERMINATE	2	FALSE	0	0.637739807772772	3		419	149	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267441	7267442	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	45	524	3	ENST00000302850.5:c.566_567delinsTT	p.Thr189Ile	p.T189I	ENST00000302850	NM_000208.2	189	aCC/aTT	2/22	0.24929009196812	4	FACETS	0.76	0.651	0.876	0.76	0.651	0.876	INDETERMINATE	2	FALSE	2	0.637739807772772	4		527	152	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212188	36212188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	60	515	1	ENST00000222270.7:c.1939C>T	p.Leu647Phe	p.L647F	ENST00000222270	NM_014727.1	647	Ctt/Ttt	3/37	0.637739807772772	4	FACETS	0.778	0.681	0.88	0.778	0.681	0.88	SUBCLONAL	2	FALSE	2	0.637739807772772	4		516	198	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131240	202131241	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	44	512	2	ENST00000358485.4:c.208_209delinsAA	p.Gly70Lys	p.G70K	ENST00000358485	NM_001080125.1	70	GGg/AAg	2/9	0.593127669276508	4	FACETS	1	0.944	1	0.624	0.531	0.724	CLONAL	1	FALSE	2	0.637739807772772	4		514	181	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0021441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	169	710	1	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	0.993	1	CLONAL	2	TRUE	1	0.329153988454025	2		711	497	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164508	47164508	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	185	564	0	ENST00000409792.3:c.1618del	p.Arg540AspfsTer39	p.R540Dfs*39	ENST00000409792	NM_014159.6	540	Cga/ga	3/21	0.329153988454025	0	FACETS	0.901	0.854	0.946			1	CLONAL	3	TRUE	0	0.329153988454025	0		564	279	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441268	52441269	+	missense_variant	Missense_Mutation	DNP	AC	AC	TG	novel	NA	P-0021441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	283	686	2	ENST00000460680.1:c.501_502delinsCA	p.Phe168Ile	p.F168I	ENST00000460680	NM_004656.3	167	gcGTtc/gcCAtc	7/17	0.329153988454025	0	FACETS	0.874	0.836	0.911			1	CLONAL	3	TRUE	0	0.329153988454025	0		688	440	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	168	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.442152900404715	3	FACETS	0.93	0.861	1	0.93	0.861	1	CLONAL	2	TRUE	1	0.442152900404715	3		434	499	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0021444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	96	692	2	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.92	0.824	1	0.92	0.824	1	CLONAL	1	TRUE	1	0.442152900404715	2		694	472	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552611	18552612	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0021444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	104	522	0	ENST00000266497.5:c.2024_2025dup	p.Tyr676AspfsTer19	p.Y676Dfs*19	ENST00000266497		674	-/AG	14/31	0.442152900404715	3	FACETS	0.928	0.833	1	0.464	0.416	0.515	CLONAL	1	TRUE	1	0.442152900404715	3		522	619	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879059	151879059	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	118	699	0	ENST00000262189.6:c.5886del	p.Tyr1963MetfsTer11	p.Y1963Mfs*11	ENST00000262189	NM_170606.2	1962	ccC/cc	36/59	0.442152900404715	3	FACETS	0.96	0.867	1	0.48	0.433	0.529	CLONAL	1	TRUE	1	0.442152900404715	3		699	679	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900706	3900722	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTGAAGAATCTCCCT	GGCTGAAGAATCTCCCT	-	novel	NA	P-0021449-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	295	582	0	ENST00000262367.5:c.374_390del	p.Gln125ProfsTer5	p.Q125Pfs*5	ENST00000262367	NM_004380.2	125	cAGGGAGATTCTTCAGCC/c	2/31	0.898419161043829	1	FACETS	0.94	0.907	0.97	0.94	0.907	0.97	CLONAL	1	TRUE	0	0.898419161043829	1		582	385	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069269	30069269	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021449-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	317	623	0	ENST00000338641.4:c.1135del	p.Glu379ArgfsTer47	p.E379Rfs*47	ENST00000338641	NM_000268.3	378	gaG/ga	12/16	0.898419161043829	1	FACETS	0.977	0.946	1	0.977	0.946	1	CLONAL	1	TRUE	0	0.898419161043829	1		623	398	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251982	153251985	+	frameshift_variant	Frame_Shift_Del	DEL	TTAC	TTAC	-	novel	NA	P-0021449-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	275	710	0	ENST00000281708.4:c.1021_1024del	p.Val341Ter	p.V341*	ENST00000281708	NM_033632.3	341	GTAAta/ta	7/12	0.898419161043829	1	FACETS	0.947	0.914	0.979	0.947	0.914	0.979	CLONAL	1	TRUE	0	0.898419161043829	1		710	356	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0021454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	340	916	3	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.342778902751934	5	FACETS	1	0.979	1			1	CLONAL	3	TRUE	NA	0.342778902751934	5		919	946	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578415	7578415	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	184	658	1	ENST00000269305.4:c.515T>A	p.Val172Asp	p.V172D	ENST00000269305	NM_001126112.2	172	gTt/gAt	5/11	0.291738039164701	2	FACETS	0.88	0.817	0.945	0.88	0.817	0.945	CLONAL	2	TRUE	0	0.342778902751934	2		659	610	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377024	118377024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781919840	NA	P-0021454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	98	369	1	ENST00000534358.1:c.10417C>T	p.Arg3473Cys	p.R3473C	ENST00000534358	NM_005933.3	3473	Cgt/Tgt	27/36	0.306851150551158	3	FACETS	0.772	0.692	0.855	0.772	0.692	0.855	SUBCLONAL	2	TRUE	1	0.342778902751934	3		370	434	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199700	11199700	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	358	520	2	ENST00000361445.4:c.4888G>T	p.Val1630Leu	p.V1630L	ENST00000361445	NM_004958.3	1630	Gta/Tta	35/58	0.342778902751934	5	FACETS	1	0.988	1			1	CLONAL	4	TRUE	NA	0.342778902751934	5		522	723	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259349	11259349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	461	667	0	ENST00000361445.4:c.4219G>T	p.Gly1407Cys	p.G1407C	ENST00000361445	NM_004958.3	1407	Ggc/Tgc	28/58	0.342778902751934	5	FACETS	1	0.992	1			1	CLONAL	4	TRUE	NA	0.342778902751934	5		667	916	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869515	102869515	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	129	456	1	ENST00000307046.8:c.126C>A	p.Phe42Leu	p.F42L	ENST00000307046	NM_001111285.1	42	ttC/ttA	2/4	0.305331960447388	2	FACETS	0.905	0.828	0.984	0.905	0.828	0.984	CLONAL	2	TRUE	0	0.342778902751934	2		457	416	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543626	29543626	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	89	567	1	ENST00000389048.3:c.1537G>T	p.Asp513Tyr	p.D513Y	ENST00000389048	NM_004304.4	513	Gac/Tac	7/29	NA	2	FACETS	0.921	0.818	1			1	INDETERMINATE	1	TRUE	NA	0.342778902751934	2		568	564	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876378	35876378	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	135	560	0	ENST00000303115.3:c.1170C>A	p.Cys390Ter	p.C390*	ENST00000303115	NM_002185.3	390	tgC/tgA	8/8	0.342778902751934	3	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.342778902751934	3		560	642	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617663	100617663	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	94	570	0	ENST00000308731.7:c.406A>C	p.Ser136Arg	p.S136R	ENST00000308731	NM_000061.2	136	Agt/Cgt	6/19	0.342778902751934	1	FACETS	0.992	0.887	1	0.992	0.887	1	CLONAL	1	TRUE	0	0.342778902751934	1		570	458	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	113	669	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.912	0.825	1	0.912	0.825	1	CLONAL	1	TRUE	1	0.510717388115331	2		669	485	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0021457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	78	772	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.618	0.545	0.697	0.618	0.545	0.697	SUBCLONAL	1	TRUE	1	0.510717388115331	2		772	494	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717778	89717778	+	splice_donor_variant	Splice_Site	SNP	T	T	A	rs1114167665	NA	P-0021457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	18	450	0	ENST00000371953.3:c.801+2T>A		p.X267_splice	ENST00000371953	NM_000314.4	267			1	2	FACETS	0.216	0.162	0.28	0.216	0.162	0.28	SUBCLONAL	1	TRUE	1	0.510717388115331	2		450	326	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0021458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	92	662	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.385467658914853	2		663	462	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546931	9546931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs562732119	NA	P-0021458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	108	590	1	ENST00000353224.5:c.1091C>T	p.Ser364Leu	p.S364L	ENST00000353224	NM_177990.2	364	tCg/tTg	5/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.385467658914853	2		591	462	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245843	46245843	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	72	504	0	ENST00000334344.6:c.3937C>T	p.Gln1313Ter	p.Q1313*	ENST00000334344	NM_152641.2	1313	Caa/Taa	15/21	0.385467658914853	1	FACETS	0.898	0.79	1	0.898	0.79	1	CLONAL	1	TRUE	0	0.385467658914853	1		504	336	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412941	63412941	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	167	492	3	ENST00000330258.3:c.226G>T	p.Gly76Ter	p.G76*	ENST00000330258	NM_152424.3	76	Gga/Tga	2/2	1	1	FACETS	0.825	0.766	0.884	1	0.992	1	CLONAL	2	TRUE	0	0.385467658914853	1		495	424	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341914	8341914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	76	731	0	ENST00000356435.5:c.4726G>A	p.Glu1576Lys	p.E1576K	ENST00000356435		1576	Gaa/Aaa	29/35	0.385467658914853	1	FACETS	0.786	0.693	0.885	0.786	0.693	0.885	SUBCLONAL	1	TRUE	0	0.385467658914853	1		731	405	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758315	41758315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	139	884	1	ENST00000301178.4:c.1771G>A	p.Glu591Lys	p.E591K	ENST00000301178	NM_021913.4	591	Gaa/Aaa	15/20	0.385467658914853	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.385467658914853	1		885	560	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468426	120468426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	106	641	2	ENST00000256646.2:c.4013C>T	p.Ser1338Phe	p.S1338F	ENST00000256646	NM_024408.3	1338	tCc/tTc	25/34	1	2	FACETS	0.935	0.841	1	0.935	0.841	1	CLONAL	1	TRUE	1	0.385467658914853	2		643	588	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741580	17741580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	93	604	0	ENST00000250003.3:c.251C>T	p.Pro84Leu	p.P84L	ENST00000250003	NM_002478.4	84	cCc/cTc	1/3	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.385467658914853	2		604	425	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376289	118376289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778675942	NA	P-0021458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	99	701	1	ENST00000534358.1:c.9682C>T	p.Arg3228Cys	p.R3228C	ENST00000534358	NM_005933.3	3228	Cgt/Tgt	27/36	0.385467658914853	1	FACETS	0.841	0.754	0.933	0.841	0.754	0.933	CLONAL	1	TRUE	0	0.385467658914853	1		702	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579329	7579329	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121912658	NA	P-0021458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	115	675	0	ENST00000269305.4:c.358A>C	p.Lys120Gln	p.K120Q	ENST00000269305	NM_001126112.2	120	Aag/Cag	4/11	0.385467658914853	1	FACETS	0.889	0.804	0.978	0.889	0.804	0.978	CLONAL	1	TRUE	0	0.385467658914853	1		675	542	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528097	29528097	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	79	477	0	ENST00000356175.3:c.1105C>G	p.Gln369Glu	p.Q369E	ENST00000356175	NM_000267.3	369	Cag/Gag	10/57	1	2	FACETS	0.983	0.869	1	0.983	0.869	1	CLONAL	1	TRUE	1	0.385467658914853	2		477	417	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602694	10602694	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	147	1005	1	ENST00000171111.5:c.884C>T	p.Ser295Phe	p.S295F	ENST00000171111	NM_203500.1	295	tCc/tTc	3/6	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.385467658914853	2		1006	739	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051693	13051693	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372777769	NA	P-0021458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	104	636	0	ENST00000316448.5:c.952C>T	p.Leu318Phe	p.L318F	ENST00000316448	NM_004343.3	318	Ctc/Ttc	7/9	1	2	FACETS	0.911	0.818	1	0.911	0.818	1	CLONAL	1	TRUE	1	0.385467658914853	2		636	592	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279980	18279980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	154	837	0	ENST00000222254.8:c.2063C>T	p.Ser688Leu	p.S688L	ENST00000222254	NM_005027.3	688	tCg/tTg	16/16	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.385467658914853	2		837	757	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057270	30057270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1015291245	NA	P-0021458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	90	676	0	ENST00000338641.4:c.752C>T	p.Thr251Ile	p.T251I	ENST00000338641	NM_000268.3	251	aCc/aTc	8/16	1	2	FACETS	0.691	0.613	0.774	0.691	0.613	0.774	SUBCLONAL	1	TRUE	1	0.385467658914853	2		676	676	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170002296	170002296	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772611163	NA	P-0021458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	28	157	1	ENST00000295797.4:c.1115G>A	p.Arg372Gln	p.R372Q	ENST00000295797	NM_002740.5	372	cGa/cAa	12/18	1	2	FACETS	0.865	0.698	1	0.865	0.698	1	CLONAL	1	TRUE	1	0.385467658914853	2		158	168	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564690	86564690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766535240	NA	P-0021458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	105	762	0	ENST00000274376.6:c.422C>T	p.Pro141Leu	p.P141L	ENST00000274376	NM_002890.2	141	cCt/cTt	1/25	1	2	FACETS	0.954	0.857	1	0.954	0.857	1	CLONAL	1	TRUE	1	0.385467658914853	2		762	571	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631171	176631171	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	102	662	0	ENST00000439151.2:c.1114C>T	p.Pro372Ser	p.P372S	ENST00000439151	NM_022455.4	372	Cct/Tct	4/23	0.38338556389074	2	FACETS	0.844	0.756	0.937	0.422	0.378	0.469	CLONAL	1	TRUE	0	0.385467658914853	2		662	627	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030199	180030199	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	90	616	2	ENST00000261937.6:c.4085G>A	p.Ser1362Asn	p.S1362N	ENST00000261937	NM_182925.4	1362	aGc/aAc	30/30	0.38338556389074	2	FACETS	0.981	0.874	1	0.491	0.437	0.547	CLONAL	1	TRUE	0	0.385467658914853	2		618	476	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170129	32170129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	100	928	3	ENST00000375023.3:c.3479C>T	p.Ser1160Phe	p.S1160F	ENST00000375023	NM_004557.3	1160	tCc/tTc	21/30	1	2	FACETS	0.765	0.684	0.851	0.765	0.684	0.851	SUBCLONAL	1	TRUE	1	0.385467658914853	2		931	678	SUCCESS
MET	4233	MSKCC	GRCh37	7	116399471	116399471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	95	611	1	ENST00000397752.3:c.2291G>A	p.Gly764Glu	p.G764E	ENST00000397752	NM_000245.2	764	gGg/gAg	10/21	1	2	FACETS	0.982	0.878	1	0.982	0.878	1	CLONAL	1	TRUE	1	0.385467658914853	2		612	502	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0021459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	126	1047	2	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	0.307174926222375	2		1049	700	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0021459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	123	647	0	ENST00000269305.4:c.559+1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.307174926222375	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.307174926222375	1		647	530	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932474	39932474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398124312	NA	P-0021459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	53	394	0	ENST00000378444.4:c.2125G>A	p.Gly709Ser	p.G709S	ENST00000378444	NM_001123385.1	709	Ggc/Agc	4/15	1	1	FACETS	0.721	0.617	0.835	0.721	0.617	0.835	SUBCLONAL	1	TRUE	0	0.307174926222375	1		394	405	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063717	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0021460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	40	376	0	ENST00000412916.2:c.165+1G>T		p.X55_splice	ENST00000412916		55			0.252408635516013	1	FACETS	0.675	0.563	0.797	0.675	0.563	0.797	SUBCLONAL	1	TRUE	0	0.33659450267833	1		376	293	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653835	89653835	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	49	527	0	ENST00000371953.3:c.133del	p.Val45TyrfsTer9	p.V45Yfs*9	ENST00000371953	NM_000314.4	45	Gta/ta	2/9	1	2	FACETS	0.538	0.456	0.629	0.538	0.456	0.629	SUBCLONAL	1	TRUE	1	0.33659450267833	2		527	541	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180528	56180528	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs371578161	NA	P-0021460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	51	396	0	ENST00000399503.3:c.3857A>T	p.Glu1286Val	p.E1286V	ENST00000399503	NM_005921.1	1286	gAa/gTa	16/20	1	2	FACETS	0.812	0.693	0.943	0.812	0.693	0.943	CLONAL	1	TRUE	1	0.33659450267833	2		396	373	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750945	128750945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	20	595	0	ENST00000377970.2:c.482C>T	p.Ser161Leu	p.S161L	ENST00000377970	NM_002467.4	161	tCa/tTa	2/3	1	2	FACETS	0.37	0.282	0.473	0.37	0.282	0.473	SUBCLONAL	1	TRUE	1	0.280739856250297	2		595	385	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969496	44969496	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0021461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	21	276	0	ENST00000377967.4:c.4176+2T>G		p.X1392_splice	ENST00000377967	NM_021140.2	1392			1	1	FACETS	0.531	0.41	0.672	0.531	0.41	0.672	SUBCLONAL	1	TRUE	0	0.280739856250297	1		276	242	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0021462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	18	381	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.449	0.337	0.583	0.449	0.337	0.583	SUBCLONAL	1	TRUE	1	0.18	2		381	445	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063717	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0021462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	35	376	0	ENST00000412916.2:c.165+1G>T		p.X55_splice	ENST00000412916		55			1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.18	2		376	374	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877822	151877822	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	29	341	0	ENST00000262189.6:c.7123C>T	p.Gln2375Ter	p.Q2375*	ENST00000262189	NM_170606.2	2375	Caa/Taa	36/59	1	2	FACETS	0.707	0.566	0.866	0.707	0.566	0.866	SUBCLONAL	1	TRUE	1	0.18	2		341	456	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041589	14041589	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	51	572	0	ENST00000311895.7:c.2136G>C	p.Glu712Asp	p.E712D	ENST00000311895	NM_005236.2	712	gaG/gaC	11/11	1	2	FACETS	0.182	0.154	0.212	0.182	0.154	0.212	SUBCLONAL	1	TRUE	1	0.93304587873719	2		572	602	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	99	669	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.341282832224643	2		669	571	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165942	118165942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749332682	NA	P-0021467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	79	446	0	ENST00000369448.3:c.452G>A	p.Arg151His	p.R151H	ENST00000369448	NM_017709.3	151	cGc/cAc	2/2	1	2	FACETS	0.928	0.818	1	0.928	0.818	1	CLONAL	1	TRUE	1	0.341282832224643	2		446	499	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879680	151879680	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0021467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	39	239	0	ENST00000262189.6:c.5266-1G>A		p.X1756_splice	ENST00000262189	NM_170606.2	1756			0.341282832224643	3	FACETS	0.949	0.79	1	0.474	0.395	0.562	CLONAL	1	TRUE	1	0.341282832224643	3		239	282	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537911	212537911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755861643	NA	P-0021469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	115	678	0	ENST00000342788.4:c.1694G>A	p.Gly565Asp	p.G565D	ENST00000342788	NM_005235.2	565	gGc/gAc	14/28	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.221281229058923	2		678	782	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432330	49432330	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	124	835	0	ENST00000301067.7:c.8809C>G	p.Pro2937Ala	p.P2937A	ENST00000301067	NM_003482.3	2937	Cca/Gca	34/54	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.221281229058923	2		835	863	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112097	115112097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	98	869	0	ENST00000257566.3:c.1643G>A	p.Gly548Glu	p.G548E	ENST00000257566	NM_016569.3	548	gGg/gAg	7/8	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.221281229058923	2		869	766	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0021470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	123	819	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.193442129662945	2	FACETS	1	0.979	1	0.647	0.586	0.711	CLONAL	1	TRUE	0	0.28	2		819	679	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0021470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	83	683	1	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.192316448553833	3	FACETS	1	0.971	1	0.664	0.587	0.745	CLONAL	1	TRUE	1	0.28	3		684	509	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675997	30675997	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148637924	NA	P-0021470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	85	761	1	ENST00000376406.3:c.2359G>A	p.Gly787Arg	p.G787R	ENST00000376406	NM_014641.2	787	Gga/Aga	8/15	0.250671815236152	4	FACETS	1	0.949	1	0.566	0.501	0.637	CLONAL	1	TRUE	2	0.28	4		762	686	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930687	32930687	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	53	583	0	ENST00000380152.3:c.7558C>G	p.Arg2520Gly	p.R2520G	ENST00000380152		2520	Cga/Gga	15/27	0.205415174141725	2	FACETS	0.682	0.582	0.792	0.341	0.291	0.396	SUBCLONAL	1	TRUE	0	0.28	2		583	555	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619842	1619842	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	56	956	0	ENST00000344749.5:c.1104G>T	p.Gln368His	p.Q368H	ENST00000344749	NM_001136139.2	368	caG/caT	14/19	0.128782335553757	5	FACETS	0.853	0.73	0.988	0.213	0.182	0.247	INDETERMINATE	1	TRUE	1	0.28	5		956	666	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267902	7267902	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs796678604	NA	P-0021470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	16	317	0	ENST00000302850.5:c.106C>G	p.Pro36Ala	p.P36A	ENST00000302850	NM_000208.2	36	Ccc/Gcc	2/22	0.128782335553757	5	FACETS	0.541	0.399	0.71	0.135	0.099	0.178	INDETERMINATE	1	TRUE	1	0.28	5		317	300	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441196	52441196	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	26	358	1	ENST00000460680.1:c.574G>T	p.Asp192Tyr	p.D192Y	ENST00000460680	NM_004656.3	192	Gac/Tac	7/17	0.192316448553833	3	FACETS	0.738	0.585	0.911	0.369	0.292	0.456	CLONAL	1	TRUE	1	0.28	3		359	287	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446328	187446328	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs775772146	NA	P-0021470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	52	602	0	ENST00000232014.4:c.1360A>G	p.Met454Val	p.M454V	ENST00000232014	NM_001130845.1	454	Atg/Gtg	6/10	0.192316448553833	3	FACETS	0.903	0.77	1	0.451	0.385	0.525	CLONAL	1	TRUE	1	0.28	3		602	469	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629146	187629147	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0021470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	89	607	3	ENST00000441802.2:c.1835_1836delinsCT	p.Leu612Pro	p.L612P	ENST00000441802	NM_005245.3	612	cTG/cCT	2/27	0.250671815236152	4	FACETS	1	0.96	1	0.591	0.524	0.663	CLONAL	1	TRUE	2	0.28	4		610	688	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176678767	176678767	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	35	627	0	ENST00000439151.2:c.4678G>C	p.Ala1560Pro	p.A1560P	ENST00000439151	NM_022455.4	1560	Gct/Cct	12/23	0.205415174141725	2	FACETS	0.428	0.35	0.516	0.214	0.175	0.258	SUBCLONAL	1	TRUE	0	0.28	2		627	584	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016210	150016210	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	33	466	0	ENST00000253339.5:c.496G>T	p.Gly166Trp	p.G166W	ENST00000253339		166	Ggg/Tgg	2/7	0.304501859698003	3	FACETS	0.545	0.443	0.66	0.273	0.221	0.33	SUBCLONAL	1	TRUE	1	0.28	3		466	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371409680	NA	P-0021471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	337	1121	0	ENST00000269305.4:c.848G>C	p.Arg283Pro	p.R283P	ENST00000269305	NM_001126112.2	283	cGc/cCc	8/11	0.393473136771596	3	FACETS	1	0.992	1	0.813	0.772	0.854	CLONAL	2	TRUE	0	0.393473136771596	3		1121	841	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426483	49426483	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	152	984	0	ENST00000301067.7:c.12005del	p.Pro4002GlnfsTer20	p.P4002Qfs*20	ENST00000301067	NM_003482.3	4002	cCa/ca	39/54	0.393473136771596	3	FACETS	0.906	0.828	0.989	0.453	0.414	0.495	CLONAL	1	TRUE	1	0.393473136771596	3		984	1020	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830631	72830631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753599043	NA	P-0021471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	368	769	1	ENST00000268489.5:c.5950G>A	p.Glu1984Lys	p.E1984K	ENST00000268489	NM_006885.3	1984	Gag/Aag	9/10	0.36040674895925	5	FACETS	1	0.966	1	0.611	0.582	0.642	CLONAL	3	TRUE	0	0.393473136771596	5		770	973	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234523	41234523	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs80357309	NA	P-0021471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	318	609	1	ENST00000357654.3:c.4255G>T	p.Glu1419Ter	p.E1419*	ENST00000357654	NM_007294.3	1419	Gaa/Taa	12/23	0.393473136771596	3	FACETS	0.835	0.793	0.878	0.835	0.793	0.878	CLONAL	3	TRUE	0	0.393473136771596	3		610	772	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917776	29917940	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTCCTCGGAGGGGATGCGGCGCCAGGACCAGCTCTGGTTCCTGAGGTCATGCAGTGGAGGGGAATACTCCAGCTCACAGGGGAAGTCAAAGCTGCACTCCAGACCTGCAATAATAGCCAAGGGTCAATGGAAAAAACCATTTCCCAAACGTGACTTTTCAGCCC	CCTCCTCGGAGGGGATGCGGCGCCAGGACCAGCTCTGGTTCCTGAGGTCATGCAGTGGAGGGGAATACTCCAGCTCACAGGGGAAGTCAAAGCTGCACTCCAGACCTGCAATAATAGCCAAGGGTCAATGGAAAAAACCATTTCCCAAACGTGACTTTTCAGCCC	-	novel	NA	P-0021471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	143	725	0	ENST00000389048.3:c.788-60_892del		p.X263_splice	ENST00000389048	NM_004304.4	263		3/29	0.393473136771596	3	FACETS	1	0.978	1	0.607	0.555	0.663	CLONAL	1	TRUE	1	0.393473136771596	3		725	716	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39725156	39725889	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTCTTGTTAAAAATGCAATTTCTGTATAGGATTCAGTAGGTCTAGGAGGGGGCCTGGGATTCTGCATTTCTAAACTCCCACATGATGCCAATGCTGCTGGTCTGTGAACCACTTGTTGAATAGCAAAGTTCTAGAAGAAGGTCTTATTAGGCTTTTCATATGGGAAATCTGGGCTTGCCTAGTATGGATATATATTTTTTTATTCATATTCCACCCACCTAACTTTGAAGAAGAAAGATGCCTATTTCTTTTCCCCACAATTCCTTTCTTCCACTCCCTGCCCTATCCCTTCCTCCCCTTCTTGAACAGAGGCTGCTTAGCTTAGCAGTGGCAGGAGTCCCTCTGAGGATTTGATTTTTAAAAACCATTGAAGAGGTGTAAAGGACCCTGCTTGCTGAAAGGAAAAGGAAGAGTGACTGGGCCTCCCCCAGGTCATCCCTGTCCTGAGCAGGCACCTGGGAACAATTAACTGGCATAGTCTCCAGAGAATGACCCAGGTAAATATATGCTAAAGAGAAGGAGAATTTGTACAAGTAGATATAAATCAGTATGTTGTCTTTGTTGTTGTTGCTACTATGTGTCACCAGACCTTTATATACCATGAGAAGGCAAACCATTATTAAAGAGAATTCGCTAGCCCTGGGTATTTATGCTTAGAACATGAATACTATACCTCACTTTTTGGAACCACTTTTTTCTCTAGGTAAAGTCATGAAGCTGAGCCCCAAAGCAG	AGTCTTGTTAAAAATGCAATTTCTGTATAGGATTCAGTAGGTCTAGGAGGGGGCCTGGGATTCTGCATTTCTAAACTCCCACATGATGCCAATGCTGCTGGTCTGTGAACCACTTGTTGAATAGCAAAGTTCTAGAAGAAGGTCTTATTAGGCTTTTCATATGGGAAATCTGGGCTTGCCTAGTATGGATATATATTTTTTTATTCATATTCCACCCACCTAACTTTGAAGAAGAAAGATGCCTATTTCTTTTCCCCACAATTCCTTTCTTCCACTCCCTGCCCTATCCCTTCCTCCCCTTCTTGAACAGAGGCTGCTTAGCTTAGCAGTGGCAGGAGTCCCTCTGAGGATTTGATTTTTAAAAACCATTGAAGAGGTGTAAAGGACCCTGCTTGCTGAAAGGAAAAGGAAGAGTGACTGGGCCTCCCCCAGGTCATCCCTGTCCTGAGCAGGCACCTGGGAACAATTAACTGGCATAGTCTCCAGAGAATGACCCAGGTAAATATATGCTAAAGAGAAGGAGAATTTGTACAAGTAGATATAAATCAGTATGTTGTCTTTGTTGTTGTTGCTACTATGTGTCACCAGACCTTTATATACCATGAGAAGGCAAACCATTATTAAAGAGAATTCGCTAGCCCTGGGTATTTATGCTTAGAACATGAATACTATACCTCACTTTTTGGAACCACTTTTTTCTCTAGGTAAAGTCATGAAGCTGAGCCCCAAAGCAG	-	novel	NA	P-0021471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	113	0	0	ENST00000361337.2:c.731-702_762del		p.X244_splice	ENST00000361337	NM_003286.2	244		10/21	0.338798989911983	5	FACETS	0.966	0.874	1	0.644	0.582	0.708	CLONAL	2	TRUE	2	0.393473136771596	5		0	473	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864364	151864364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	240	562	0	ENST00000262189.6:c.9617G>A	p.Arg3206Lys	p.R3206K	ENST00000262189	NM_170606.2	3206	aGa/aAa	42/59	0.284764194919255	3	FACETS	1	0.986	1	0.77	0.724	0.817	CLONAL	2	TRUE	0	0.393473136771596	3		562	632	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0021472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	59	1047	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.207405474812976	1	FACETS	0.854	0.735	0.984	0.854	0.735	0.984	CLONAL	1	TRUE	0	0.207405474812976	1		1049	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0021472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	116	963	0	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.207405474812976	1	FACETS	0.776	0.701	0.855	1	0.985	1	SUBCLONAL	2	TRUE	0	0.207405474812976	1		963	646	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571439	95571439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	29	383	0	ENST00000393063.1:c.3238G>A	p.Val1080Met	p.V1080M	ENST00000393063	NM_030621.3	1080	Gtg/Atg	21/28	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.207405474812976	2		383	256	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379657	17379657	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	22	599	0	ENST00000359435.4:c.42G>C	p.Glu14Asp	p.E14D	ENST00000359435	NM_001033549.1	14	gaG/gaC	2/9	1	2	FACETS	0.724	0.562	0.912	0.724	0.562	0.912	CLONAL	1	TRUE	1	0.207405474812976	2		599	293	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39550299	39550299	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374012011	NA	P-0021474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	56	328	0	ENST00000262039.4:c.410G>A	p.Arg137His	p.R137H	ENST00000262039	NM_002647.2	137	cGc/cAc	4/25	1	2	FACETS	0.461	0.396	0.533	0.461	0.396	0.533	SUBCLONAL	1	TRUE	1	0.522073447156264	2		328	465	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50482421	50482421	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0021474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	114	634	1	ENST00000394963.4:c.771+1G>A		p.X257_splice	ENST00000394963	NM_003076.4	257			0.292721582154384	3	FACETS	0.482	0.433	0.535	0.241	0.216	0.268	INDETERMINATE	1	TRUE	1	0.522073447156264	3		635	1142	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114253	115114272	+	frameshift_variant	Frame_Shift_Del	DEL	TGGACTGCAGGGTGAGCTGT	TGGACTGCAGGGTGAGCTGT	-	novel	NA	P-0021474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	165	649	0	ENST00000257566.3:c.945_964del	p.Lys315AsnfsTer5	p.K315Nfs*5	ENST00000257566	NM_016569.3	315	aaACAGCTCACCCTGCAGTCCAtg/aatg	6/8	0.292721582154384	3	FACETS	0.753	0.691	0.819	0.377	0.345	0.41	INDETERMINATE	1	TRUE	1	0.522073447156264	3		649	1058	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0021475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	106	875	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.987	0.883	1	0.987	0.883	1	CLONAL	1	TRUE	1	0.23	2		877	934	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0021475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	75	835	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.782	0.684	0.888	0.782	0.684	0.888	SUBCLONAL	1	TRUE	1	0.23	2		835	834	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448297	56448298	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1567880599	NA	P-0021475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	144	843	3	ENST00000407977.2:c.349dup	p.Arg117ProfsTer8	p.R117Pfs*8	ENST00000407977		117	cgc/cCgc	3/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.23	2		846	908	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057229	180057229	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754692331	NA	P-0021475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	71	743	1	ENST00000261937.6:c.509G>A	p.Arg170His	p.R170H	ENST00000261937	NM_182925.4	170	cGc/cAc	4/30	0.124850872229511	3	FACETS	0.905	0.789	1	0.452	0.394	0.515	INDETERMINATE	1	TRUE	1	0.23	3		744	761	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0021477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	218	789	4	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	1	0.985	1	1	0.995	1	CLONAL	2	TRUE	1	0.33	2		793	569	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0021478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	132	662	1				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.488537898173882	2		663	489	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653808	89653808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	164	761	0	ENST00000371953.3:c.106G>A	p.Gly36Arg	p.G36R	ENST00000371953	NM_000314.4	36	Gga/Aga	2/9	0.488537898173882	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.488537898173882	1		761	479	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665752	29665755	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1555535032	NA	P-0021478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	110	601	0	ENST00000356175.3:c.6789_6792del	p.Tyr2264ThrfsTer5	p.Y2264Tfs*5	ENST00000356175	NM_000267.3	2263	ACTTac/ac	45/57	0.488537898173882	1	FACETS	0.915	0.83	1	0.915	0.83	1	CLONAL	1	TRUE	0	0.488537898173882	1		601	372	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888162	112888162	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397507507	NA	P-0021478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	109	1036	0	ENST00000351677.2:c.178G>C	p.Gly60Arg	p.G60R	ENST00000351677	NM_002834.3	60	Ggt/Cgt	3/16	1	2	FACETS	0.69	0.62	0.763	0.69	0.62	0.763	SUBCLONAL	1	TRUE	1	0.488537898173882	2		1036	647	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	33	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.576	0.468	0.698	0.576	0.468	0.698	SUBCLONAL	1	TRUE	1	0.213507486255471	2		434	537	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0021480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	54	916	3	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.513	0.436	0.597	0.513	0.436	0.597	SUBCLONAL	1	TRUE	1	0.213507486255471	2		919	986	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0021480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	42	1062	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	0.396	0.329	0.471	0.396	0.329	0.471	SUBCLONAL	1	TRUE	1	0.213507486255471	2		1062	994	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654624	67654624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	102	788	0	ENST00000264010.4:c.1111C>T	p.Arg371Cys	p.R371C	ENST00000264010	NM_006565.3	371	Cgc/Tgc	6/12	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.213507486255471	2		788	860	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273029	55273029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770749711	NA	P-0021480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	91	977	1	ENST00000275493.2:c.3352G>A	p.Ala1118Thr	p.A1118T	ENST00000275493	NM_005228.3	1118	Gcg/Acg	28/28	0.213507486255471	2	FACETS	0.803	0.711	0.902	0.402	0.355	0.451	CLONAL	1	TRUE	0	0.213507486255471	2		978	1061	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845814	151845814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	231	1069	0	ENST00000262189.6:c.13198C>T	p.Arg4400Trp	p.R4400W	ENST00000262189	NM_170606.2	4400	Cgg/Tgg	52/59	0.213507486255471	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.213507486255471	2		1069	1018	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114166	115114166	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397514484	NA	P-0021480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	121	988	1	ENST00000257566.3:c.1051C>T	p.Gln351Ter	p.Q351*	ENST00000257566	NM_016569.3	351	Cag/Tag	6/8	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.213507486255471	2		989	1029	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116106	67116120	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTCTGACAGCAGGA	ATTCTGACAGCAGGA	GTC	novel	NA	P-0021480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	60	557	3	ENST00000412916.2:c.400-10_404delinsGTC		p.X134_splice	ENST00000412916		134		5/6	NA	2	FACETS	0.966	0.832	1			1	INDETERMINATE	1	TRUE	NA	0.213507486255471	2		560	582	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0021481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	100	900	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	1	2	FACETS	0.742	0.663	0.826	0.742	0.663	0.826	SUBCLONAL	1	TRUE	1	0.387057996579058	2		900	696	SUCCESS
APC	324	MSKCC	GRCh37	5	112175358	112175358	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1554085480	NA	P-0021481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	64	379	0	ENST00000257430.4:c.4067C>G	p.Ser1356Ter	p.S1356*	ENST00000257430	NM_000038.5	1356	tCa/tGa	16/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.387057996579058	2		379	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782620	NA	P-0021481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	208	1097	1	ENST00000269305.4:c.427G>A	p.Val143Met	p.V143M	ENST00000269305	NM_001126112.2	143	Gtg/Atg	5/11	0.387057996579058	1	FACETS	0.884	0.82	0.949	0.884	0.82	0.949	CLONAL	1	TRUE	0	0.387057996579058	1		1098	981	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384605	31384605	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	136	921	0	ENST00000328111.2:c.1307T>C	p.Leu436Ser	p.L436S	ENST00000328111	NM_006892.3	436	tTg/tCg	13/23	1	2	FACETS	0.848	0.771	0.928	0.848	0.771	0.928	CLONAL	1	TRUE	1	0.387057996579058	2		921	829	SUCCESS
APC	324	MSKCC	GRCh37	5	112173346	112173346	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	38	458	0	ENST00000257430.4:c.2055G>A	p.Trp685Ter	p.W685*	ENST00000257430	NM_000038.5	685	tgG/tgA	16/16	1	2	FACETS	0.581	0.481	0.691	0.581	0.481	0.691	SUBCLONAL	1	TRUE	1	0.387057996579058	2		458	338	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0021482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	118	465	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.692875859619075	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.711033570840797	1		465	212	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0021482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	218	931	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	0.894	0.835	0.954	0.894	0.835	0.954	CLONAL	1	TRUE	1	0.711033570840797	2		931	686	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	65	916	3	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.358	0.309	0.411	0.358	0.309	0.411	SUBCLONAL	1	TRUE	1	0.384272990352653	2		919	946	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	33	818	1	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.384272990352653	1	FACETS	0.138	0.112	0.169	0.138	0.112	0.169	SUBCLONAL	1	TRUE	0	0.384272990352653	1		819	1002	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508083	106508083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339698935	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	95	240	0	ENST00000359195.3:c.77G>A	p.Arg26His	p.R26H	ENST00000359195	NM_002649.2	26	cGc/cAc	2/11	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.384272990352653	2		240	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	252	815	0	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	0.384272990352653	1	FACETS	0.911	0.852	0.972	0.911	0.852	0.972	CLONAL	1	TRUE	0	0.384272990352653	1		815	1163	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649598	48649598	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1300	297	1076	1	ENST00000376670.3:c.82C>A	p.Pro28Thr	p.P28T	ENST00000376670	NM_002049.3	28	Cca/Aca	2/6	0.219431220185738	1	FACETS	0.782	0.734	0.831	0.782	0.734	0.831	INDETERMINATE	1	TRUE	0	0.384272990352653	1		1077	1597	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675302	241675302	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1553341598	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	124	719	2	ENST00000366560.3:c.520C>A	p.Pro174Thr	p.P174T	ENST00000366560	NM_000143.3	174	Cct/Act	4/10	1	2	FACETS	0.895	0.811	0.984	0.895	0.811	0.984	CLONAL	1	TRUE	1	0.384272990352653	2		721	721	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675346	241675346	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	126	766	0	ENST00000366560.3:c.476A>G	p.Asn159Ser	p.N159S	ENST00000366560	NM_000143.3	159	aAt/aGt	4/10	1	2	FACETS	0.866	0.785	0.952	0.866	0.785	0.952	CLONAL	1	TRUE	1	0.384272990352653	2		766	757	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998894	100998894	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	262	934	0	ENST00000325455.5:c.908T>A	p.Phe303Tyr	p.F303Y	ENST00000325455	NM_001202474.3	303	tTc/tAc	1/8	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.384272990352653	2		934	1356	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398282	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	143	751	1	ENST00000311936.3:c.37_38delinsTT	p.Gly13Phe	p.G13F	ENST00000311936	NM_004985.3	13	GGc/TTc	2/5	1	2	FACETS	0.799	0.728	0.874	0.799	0.728	0.874	SUBCLONAL	1	TRUE	1	0.384272990352653	2		752	931	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924316	112924316	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1317	138	757	1	ENST00000351677.2:c.1262G>T	p.Arg421Leu	p.R421L	ENST00000351677	NM_002834.3	421	cGg/cTg	11/16	0.384272990352653	3	FACETS	0.588	0.533	0.647	0.294	0.266	0.324	SUBCLONAL	1	TRUE	1	0.384272990352653	3		758	1455	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201299	133201299	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555300711	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	237	671	0	ENST00000320574.5:c.6845C>T	p.Pro2282Leu	p.P2282L	ENST00000320574	NM_006231.2	2282	cCa/cTa	49/49	0.384272990352653	2	FACETS	1	0.953	1	0.514	0.479	0.55	CLONAL	1	TRUE	0	0.384272990352653	2		671	1200	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129198	2129198	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	367	898	0	ENST00000219476.3:c.3131+1G>T		p.X1044_splice	ENST00000219476	NM_000548.3	1044			0.384272990352653	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.384272990352653	1		898	1267	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990455	81990455	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	248	708	0	ENST00000359376.3:c.3727del	p.Gln1243SerfsTer11	p.Q1243Sfs*11	ENST00000359376	NM_002661.3	1242	ctC/ct	32/33	0.384272990352653	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.384272990352653	1		708	978	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56412897	56412897	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	29	273	0	ENST00000348428.3:c.1912-1G>T		p.X638_splice	ENST00000348428	NM_006785.3	638			0.384272990352653	1	FACETS	0.592	0.478	0.719	0.592	0.478	0.719	SUBCLONAL	1	TRUE	0	0.384272990352653	1		273	206	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602565	10602565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	269	795	0	ENST00000171111.5:c.1013C>T	p.Ser338Leu	p.S338L	ENST00000171111	NM_203500.1	338	tCg/tTg	3/6	0.384272990352653	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.384272990352653	1		795	1100	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383134	42383134	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	760	814	0	ENST00000221972.3:c.154T>A	p.Phe52Ile	p.F52I	ENST00000221972	NM_021601.3	52	Ttc/Atc	2/5	0.384272990352653	3	FACETS	0.987	0.956	1	0.987	0.956	1	CLONAL	3	TRUE	0	0.384272990352653	3		814	1592	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940525	29940525	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	69	705	0	ENST00000389048.3:c.706C>T	p.Pro236Ser	p.P236S	ENST00000389048	NM_004304.4	236	Cct/Tct	2/29	0.168615625062009	1	FACETS	0.416	0.361	0.474	0.416	0.361	0.474	INDETERMINATE	1	TRUE	0	0.384272990352653	1		705	698	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248440	212248440	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	65	448	0	ENST00000342788.4:c.3827del	p.Pro1276LeufsTer15	p.P1276Lfs*15	ENST00000342788	NM_005235.2	1276	cCt/ct	28/28	0.168615625062009	1	FACETS	0.411	0.356	0.471	0.411	0.356	0.471	INDETERMINATE	1	TRUE	0	0.384272990352653	1		448	665	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285185	212285185	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	72	581	0	ENST00000342788.4:c.3116C>A	p.Ala1039Glu	p.A1039E	ENST00000342788	NM_005235.2	1039	gCa/gAa	25/28	0.168615625062009	1	FACETS	0.629	0.551	0.713	0.629	0.551	0.713	INDETERMINATE	1	TRUE	0	0.384272990352653	1		581	481	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543816	212543816	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	96	650	0	ENST00000342788.4:c.1583G>T	p.Arg528Ile	p.R528I	ENST00000342788	NM_005235.2	528	aGa/aTa	13/28	0.168615625062009	1	FACETS	0.445	0.395	0.497	0.445	0.395	0.497	INDETERMINATE	1	TRUE	0	0.384272990352653	1		650	908	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439454	220439454	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	82	518	1	ENST00000243786.2:c.307G>T	p.Ala103Ser	p.A103S	ENST00000243786	NM_002191.3	103	Gcc/Tcc	2/2	0.168615625062009	1	FACETS	0.45	0.396	0.507	0.45	0.396	0.507	INDETERMINATE	1	TRUE	0	0.384272990352653	1		519	767	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339071	225339071	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	31	589	0	ENST00000264414.4:c.2198G>T	p.Arg733Leu	p.R733L	ENST00000264414	NM_003590.4	733	cGa/cTa	16/16	0.168615625062009	1	FACETS	0.248	0.2	0.303	0.248	0.2	0.303	INDETERMINATE	1	TRUE	0	0.384272990352653	1		589	525	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660496	227660496	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	188	580	1	ENST00000305123.5:c.2959G>T	p.Gly987Cys	p.G987C	ENST00000305123	NM_005544.2	987	Ggt/Tgt	1/2	0.168615625062009	1	FACETS	0.807	0.746	0.871	0.807	0.746	0.871	INDETERMINATE	1	TRUE	0	0.384272990352653	1		581	979	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713238	30713238	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	74	455	0	ENST00000295754.5:c.563G>A	p.Cys188Tyr	p.C188Y	ENST00000295754	NM_003242.5	188	tGc/tAc	4/7	0.384272990352653	1	FACETS	0.474	0.415	0.538	0.474	0.415	0.538	SUBCLONAL	1	TRUE	0	0.384272990352653	1		455	656	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448579	89448579	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	61	754	0	ENST00000336596.2:c.1543G>C	p.Ala515Pro	p.A515P	ENST00000336596	NM_005233.5	515	Gct/Cct	7/17	0.168615625062009	1	FACETS	0.251	0.215	0.29	0.251	0.215	0.29	INDETERMINATE	1	TRUE	0	0.384272990352653	1		754	1023	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231233	142231233	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	50	708	0	ENST00000350721.4:c.4721G>T	p.Cys1574Phe	p.C1574F	ENST00000350721	NM_001184.3	1574	tGt/tTt	27/47	0.168615625062009	1	FACETS	0.241	0.203	0.282	0.241	0.203	0.282	INDETERMINATE	1	TRUE	0	0.384272990352653	1		708	873	SUCCESS
ATR	545	MSKCC	GRCh37	3	142238542	142238543	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	30	440	0	ENST00000350721.4:c.4350dup	p.Arg1451SerfsTer32	p.R1451Sfs*32	ENST00000350721	NM_001184.3	1450	-/T	24/47	0.168615625062009	1	FACETS	0.247	0.198	0.302	0.247	0.198	0.302	INDETERMINATE	1	TRUE	0	0.384272990352653	1		440	511	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532769	187532769	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	105	698	0	ENST00000441802.2:c.9624G>C	p.Arg3208Ser	p.R3208S	ENST00000441802	NM_005245.3	3208	agG/agC	14/27	0.168615625062009	1	FACETS	0.476	0.426	0.53	0.476	0.426	0.53	INDETERMINATE	1	TRUE	0	0.384272990352653	1		698	927	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584498	187584498	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs200917026	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	93	544	0	ENST00000441802.2:c.3535A>T	p.Thr1179Ser	p.T1179S	ENST00000441802	NM_005245.3	1179	Aca/Tca	3/27	0.168615625062009	1	FACETS	0.671	0.597	0.749	0.671	0.597	0.749	INDETERMINATE	1	TRUE	0	0.384272990352653	1		544	583	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190423	32190423	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	301	973	0	ENST00000375023.3:c.316del	p.Leu106SerfsTer146	p.L106Sfs*146	ENST00000375023	NM_004557.3	106	Ctc/tc	3/30	0.384272990352653	1	FACETS	0.987	0.929	1	0.987	0.929	1	CLONAL	1	TRUE	0	0.384272990352653	1		973	1282	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967817	93967817	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	180	529	0	ENST00000369303.4:c.2110G>T	p.Gly704Trp	p.G704W	ENST00000369303	NM_004440.3	704	Ggg/Tgg	11/17	0.26969834022503	2	FACETS	0.847	0.786	0.909	0.847	0.786	0.909	CLONAL	2	TRUE	0	0.384272990352653	2		529	553	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355228	81355229	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	111	425	0	ENST00000222390.5:c.1145dup	p.Asn382LysfsTer3	p.N382Kfs*3	ENST00000222390	NM_000601.4	382	aac/aaAc	9/18	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.384272990352653	2		425	568	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849974	151849974	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1027353520	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	121	455	0	ENST00000262189.6:c.12342G>T	p.Glu4114Asp	p.E4114D	ENST00000262189	NM_170606.2	4114	gaG/gaT	49/59	1	2	FACETS	0.818	0.739	0.901	0.818	0.739	0.901	CLONAL	1	TRUE	1	0.384272990352653	2		455	770	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917680	151917680	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	97	345	0	ENST00000262189.6:c.3640G>C	p.Val1214Leu	p.V1214L	ENST00000262189	NM_170606.2	1214	Gtg/Ctg	23/59	1	2	FACETS	0.913	0.816	1	0.913	0.816	1	CLONAL	1	TRUE	1	0.384272990352653	2		345	553	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162940	38162940	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1300563598	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	128	716	0	ENST00000317025.8:c.2266A>G	p.Lys756Glu	p.K756E	ENST00000317025	NM_023034.1	756	Aaa/Gaa	13/24	1	2	FACETS	0.73	0.661	0.802	0.73	0.661	0.802	SUBCLONAL	1	TRUE	1	0.384272990352653	2		716	913	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968182	68968182	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	76	778	0	ENST00000288368.4:c.1211C>A	p.Thr404Asn	p.T404N	ENST00000288368	NM_024870.2	404	aCt/aAt	10/40	1	2	FACETS	0.513	0.449	0.582	0.513	0.449	0.582	SUBCLONAL	1	TRUE	1	0.384272990352653	2		778	771	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002844	69002844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	36	442	0	ENST00000288368.4:c.2144C>T	p.Pro715Leu	p.P715L	ENST00000288368	NM_024870.2	715	cCt/cTt	20/40	1	2	FACETS	0.331	0.271	0.398	0.331	0.271	0.398	SUBCLONAL	1	TRUE	1	0.384272990352653	2		442	566	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869594	117869594	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	47	629	1	ENST00000297338.2:c.600C>A	p.Ser200Arg	p.S200R	ENST00000297338	NM_006265.2	200	agC/agA	6/14	0.384272990352653	3	FACETS	0.51	0.43	0.598	0.255	0.215	0.299	SUBCLONAL	1	TRUE	1	0.384272990352653	3		630	572	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518187	8518187	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	165	492	0	ENST00000356435.5:c.1204G>T	p.Gly402Trp	p.G402W	ENST00000356435		402	Ggg/Tgg	10/35	0.384272990352653	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.384272990352653	1		492	664	SUCCESS
AR	367	MSKCC	GRCh37	X	66765824	66765824	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1315	164	1198	0	ENST00000374690.3:c.836T>A	p.Val279Glu	p.V279E	ENST00000374690	NM_000044.3	279	gTg/gAg	1/8	0.219431220185738	1	FACETS	0.466	0.426	0.508	0.466	0.426	0.508	INDETERMINATE	1	TRUE	0	0.384272990352653	1		1198	1479	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344682	70344682	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	181	744	0	ENST00000374080.3:c.2043G>C	p.Lys681Asn	p.K681N	ENST00000374080		681	aaG/aaC	14/45	0.219431220185738	1	FACETS	0.813	0.75	0.879	0.813	0.75	0.879	INDETERMINATE	1	TRUE	0	0.384272990352653	1		744	936	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200071	123200071	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	48	621	0	ENST00000218089.9:c.2143C>A	p.Leu715Ile	p.L715I	ENST00000218089	NM_001042749.1	715	Ctc/Atc	22/35	0.149181855138365	3	FACETS	0.665	0.563	0.777	0.222	0.187	0.259	INDETERMINATE	1	TRUE	0	0.384272990352653	3		621	448	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279839	46279839	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	168	623	0	ENST00000371998.3:c.3765G>T	p.Gln1255His	p.Q1255H	ENST00000371998		1255	caG/caT	20/23	1	2	FACETS	0.782	0.718	0.85	0.782	0.718	0.85	SUBCLONAL	1	TRUE	1	0.384272990352653	2		623	1118	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0021485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	109	1049	1	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		1050	931	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	39	669	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.897	0.764	1	0.897	0.764	1	CLONAL	1	TRUE	1	0.797672656772998	2		669	109	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0021487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	94	418	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.906	0.819	0.996	0.906	0.819	0.996	CLONAL	1	TRUE	1	0.797672656772998	2		418	260	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791755	42791755	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	182	942	0	ENST00000575354.2:c.641A>G	p.His214Arg	p.H214R	ENST00000575354	NM_015125.3	214	cAc/cGc	5/20	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.797672656772998	2		942	378	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797134	42797135	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0021487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	26	1292	0	ENST00000575354.2:c.3501dup	p.Lys1168GlnfsTer26	p.K1168Qfs*26	ENST00000575354	NM_015125.3	1166	gcc/gCcc	15/20	NA	2	FACETS	0.128	0.1	0.159			1	INDETERMINATE	1	TRUE	NA	0.797672656772998	2		1292	511	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031970	26031970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	71	549	0	ENST00000244661.2:c.319G>A	p.Asp107Asn	p.D107N	ENST00000244661	NM_003537.3	107	Gac/Aac	1/1	0.318250909565398	2	FACETS	0.92	0.805	1	0.46	0.402	0.521	CLONAL	1	TRUE	0	0.342341735457008	2		549	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578463	7578463	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371524413	NA	P-0021498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	89	1149	0	ENST00000269305.4:c.467G>C	p.Arg156Pro	p.R156P	ENST00000269305	NM_001126112.2	156	cGc/cCc	5/11	1	2	FACETS	0.726	0.643	0.816	0.726	0.643	0.816	SUBCLONAL	1	TRUE	1	0.27	2		1149	908	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717609	89717609	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs876661024	NA	P-0021498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	51	703	0	ENST00000371953.3:c.635-1G>C		p.X212_splice	ENST00000371953	NM_000314.4	212			1	2	FACETS	0.748	0.636	0.871	0.748	0.636	0.871	SUBCLONAL	1	TRUE	1	0.27	2		703	505	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631183	69631183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	41	937	0	ENST00000334134.2:c.229G>A	p.Glu77Lys	p.E77K	ENST00000334134	NM_005247.2	77	Gag/Aag	2/3	1	2	FACETS	0.481	0.4	0.572	0.481	0.4	0.572	SUBCLONAL	1	TRUE	1	0.27	2		937	631	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0021500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	250	857	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.226526619628766	5	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	2	0.226526619628766	5		857	848	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577129	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519986	NA	P-0021500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	111	807	0	ENST00000269305.4:c.809T>G	p.Phe270Cys	p.F270C	ENST00000269305	NM_001126112.2	270	tTt/tGt	8/11	0.192304349739871	2	FACETS	0.789	0.711	0.872	0.789	0.711	0.872	SUBCLONAL	2	TRUE	0	0.226526619628766	2		807	621	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970895	21970899	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CCTCA	CCTCA	-	novel	NA	P-0021500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	110	917	0	ENST00000304494.5:c.457+2_457+6del		p.X153_splice	ENST00000304494	NM_000077.4	153			0.192304349739871	2	FACETS	0.797	0.718	0.881	0.797	0.718	0.881	SUBCLONAL	2	TRUE	0	0.226526619628766	2		917	609	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0021502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	439	942	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	0.574901607688997	7	FACETS	1	0.989	1	0.827	0.791	0.864	CLONAL	3	TRUE	3	0.574901607688997	7		942	1125	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0021502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	1362	1157	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.574901607688997	6	FACETS	1	0.997	1	1	0.997	1	CLONAL	6	TRUE	0	0.574901607688997	6		1157	1641	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505048	186505048	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	304	528	0	ENST00000323963.5:c.904G>C	p.Ala302Pro	p.A302P	ENST00000323963		302	Gct/Cct	8/11	0.574901607688997	6	FACETS	0.885	0.842	0.929	0.885	0.842	0.929	CLONAL	4	TRUE	2	0.574901607688997	6		528	642	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397159	397159	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781586995	NA	P-0021502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	259	670	0	ENST00000380956.4:c.544G>A	p.Val182Ile	p.V182I	ENST00000380956	NM_001195286.1	182	Gtc/Atc	5/9	0.574901607688997	4	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	2	0.574901607688997	4		670	702	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056641	26056641	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	103	355	0	ENST00000343677.2:c.16C>G	p.Pro6Ala	p.P6A	ENST00000343677	NM_005319.3	6	Cct/Gct	1/1	0.574901607688997	4	FACETS	0.919	0.833	1	0.919	0.833	1	CLONAL	2	TRUE	2	0.574901607688997	4		355	307	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133756045	133756045	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	259	701	0	ENST00000318560.5:c.1672G>A	p.Glu558Lys	p.E558K	ENST00000318560	NM_005157.4	558	Gag/Aag	10/11	0.574901607688997	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.574901607688997	4		701	676	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0021503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	422	662	1				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.674949892949284	2		663	1052	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0021503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	942	1025	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.686693475600491	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.674949892949284	2		1025	1208	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216545	108216545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779872	NA	P-0021503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	115	841	0	ENST00000278616.4:c.8494C>T	p.Arg2832Cys	p.R2832C	ENST00000278616	NM_000051.3	2832	Cgt/Tgt	58/63	0.409963954515215	2	FACETS	0.549	0.495	0.605	0.274	0.247	0.303	SUBCLONAL	1	TRUE	0	0.674949892949284	2		841	621	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059264	27059264	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0021503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	190	807	0	ENST00000324856.7:c.1901C>G	p.Ser634Ter	p.S634*	ENST00000324856	NM_006015.4	634	tCa/tGa	4/20	0.384509434828986	1	FACETS	0.47	0.435	0.506	0.47	0.435	0.506	INDETERMINATE	1	TRUE	0	0.674949892949284	1		807	793	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	131	846	1	ENST00000335508.6:c.2704G>A	p.Glu902Lys	p.E902K	ENST00000335508	NM_012433.2	902	Gaa/Aaa	18/25	0.359776159757697	3	FACETS	0.623	0.565	0.683	0.208	0.188	0.228	INDETERMINATE	1	TRUE	0	0.674949892949284	3		847	834	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170112	32170112	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	251	1025	3	ENST00000375023.3:c.3496C>T	p.Pro1166Ser	p.P1166S	ENST00000375023	NM_004557.3	1166	Cca/Tca	21/30	NA	2	FACETS	0.758	0.71	0.808			1	INDETERMINATE	1	TRUE	NA	0.674949892949284	2		1028	981	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197129	26197129	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	191	821	0	ENST00000356476.2:c.350G>C	p.Arg117Pro	p.R117P	ENST00000356476		117	cGa/cCa	1/1	0.47520996392695	1	FACETS	0.486	0.451	0.523	0.486	0.451	0.523	SUBCLONAL	1	TRUE	0	0.674949892949284	1		821	771	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059273	27059273	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	180	784	0	ENST00000324856.7:c.1910C>T	p.Ser637Phe	p.S637F	ENST00000324856	NM_006015.4	637	tCc/tTc	4/20	0.384509434828986	1	FACETS	0.469	0.433	0.506	0.469	0.433	0.506	INDETERMINATE	1	TRUE	0	0.674949892949284	1		784	754	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058649	72058649	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	129	566	0	ENST00000357731.5:c.791T>A	p.Leu264His	p.L264H	ENST00000357731	NM_173808.2	264	cTc/cAc	6/7	NA	2	FACETS	0.557	0.506	0.611			1	INDETERMINATE	1	TRUE	NA	0.674949892949284	2		566	686	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175987	176175987	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2065	176	551	3	ENST00000367669.3:c.128C>A	p.Ser43Ter	p.S43*	ENST00000367669	NM_022457.5	43	tCg/tAg	1/20	0.674949892949284	7	FACETS	0.625	0.573	0.681			1	SUBCLONAL	1	TRUE	NA	0.674949892949284	7		554	2241	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226549185	226549185	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	80	692	0	ENST00000366794.5:c.3021C>G	p.Phe1007Leu	p.F1007L	ENST00000366794	NM_001618.3	1007	ttC/ttG	23/23	NA	2	FACETS	0.331	0.291	0.374			1	INDETERMINATE	1	TRUE	NA	0.674949892949284	2		692	717	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999307	100999307	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	749	1077	3	ENST00000325455.5:c.495G>A	p.Met165Ile	p.M165I	ENST00000325455	NM_001202474.3	165	atG/atA	1/8	0.409963954515215	2	FACETS	0.879	0.854	0.903	0.879	0.854	0.903	CLONAL	2	TRUE	0	0.674949892949284	2		1080	1263	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123889486	123889486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61955123	NA	P-0021503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	85	317	2	ENST00000330479.4:c.713G>A	p.Arg238Gln	p.R238Q	ENST00000330479	NM_020382.3	238	cGg/cAg	7/9	1	2	FACETS	0.675	0.601	0.753	0.675	0.601	0.753	SUBCLONAL	1	TRUE	1	0.674949892949284	2		319	373	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73352435	73352435	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1388746108	NA	P-0021503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	172	1069	0	ENST00000377767.4:c.470A>G	p.Asn157Ser	p.N157S	ENST00000377767	NM_014953.3	157	aAt/aGt	3/21	NA	2	FACETS	0.476	0.438	0.517			1	INDETERMINATE	1	TRUE	NA	0.674949892949284	2		1069	1070	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784275	43784275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	171	1088	0	ENST00000382044.4:c.211G>A	p.Glu71Lys	p.E71K	ENST00000382044	NM_001141980.1	71	Gaa/Aaa	3/28	0.384509434828986	1	FACETS	0.409	0.377	0.443	0.409	0.377	0.443	INDETERMINATE	1	TRUE	0	0.674949892949284	1		1088	820	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868273	37868273	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	413	828	1	ENST00000269571.5:c.994G>C	p.Glu332Gln	p.E332Q	ENST00000269571		332	Gag/Cag	8/27	0.384509434828986	1	FACETS	1	0.966	1	1	0.966	1	INDETERMINATE	1	TRUE	0	0.674949892949284	1		829	804	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953253	17953253	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2709	195	1051	0	ENST00000458235.1:c.733C>A	p.Leu245Met	p.L245M	ENST00000458235	NM_000215.3	245	Ctg/Atg	6/24	0.674949892949284	6	FACETS	0.468	0.43	0.507			1	SUBCLONAL	1	TRUE	NA	0.674949892949284	6		1051	2904	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753717	42753717	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587777006	NA	P-0021503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	287	1100	0	ENST00000222329.4:c.547C>G	p.Arg183Gly	p.R183G	ENST00000222329	NM_006494.2	183	Cga/Gga	4/4	0.41553200759681	2	FACETS	0.627	0.589	0.667	0.314	0.294	0.334	SUBCLONAL	1	TRUE	0	0.674949892949284	2		1100	1356	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091771	29091771	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs886041172	NA	P-0021503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	668	709	0	ENST00000328354.6:c.1186C>G	p.Leu396Val	p.L396V	ENST00000328354	NM_007194.3	396	Ctt/Gtt	11/15	0.686693475600491	3	FACETS	0.901	0.878	0.925	1	0.998	1	CLONAL	3	TRUE	1	0.674949892949284	3		709	979	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31401631	31401631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1322275663	NA	P-0021503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	648	865	1	ENST00000344624.3:c.4033G>A	p.Glu1345Lys	p.E1345K	ENST00000344624		1345	Gaa/Aaa	33/33	0.519847504233228	4	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.674949892949284	4		866	1353	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839802	27839802	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	347	843	1	ENST00000328488.2:c.292G>C	p.Glu98Gln	p.E98Q	ENST00000328488	NM_003533.2	98	Gag/Cag	1/1	0.47520996392695	1	FACETS	0.907	0.865	0.95	0.907	0.865	0.95	CLONAL	1	TRUE	0	0.674949892949284	1		844	751	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004810	150004810	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	252	750	0	ENST00000253339.5:c.1415G>C	p.Arg472Thr	p.R472T	ENST00000253339		472	aGa/aCa	3/7	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.674949892949284	2		750	708	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502230	157502230	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	443	796	0	ENST00000346085.5:c.3263C>A	p.Ser1088Ter	p.S1088*	ENST00000346085	NM_020732.3	1088	tCa/tAa	12/20	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.674949892949284	2		796	1002	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161990410	161990410	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	131	788	0	ENST00000366898.1:c.910T>G	p.Phe304Val	p.F304V	ENST00000366898	NM_004562.2	304	Ttc/Gtc	8/12	1	2	FACETS	0.493	0.448	0.541	0.493	0.448	0.541	SUBCLONAL	1	TRUE	1	0.674949892949284	2		788	787	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509966	106509966	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	189	932	1	ENST00000359195.3:c.1960G>A	p.Asp654Asn	p.D654N	ENST00000359195	NM_002649.2	654	Gat/Aat	2/11	0.384509434828986	1	FACETS	0.449	0.415	0.483	0.449	0.415	0.483	INDETERMINATE	1	TRUE	0	0.674949892949284	1		933	827	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0021506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	29	832	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	0.694	0.555	0.854	0.694	0.555	0.854	SUBCLONAL	1	TRUE	1	0.12	2		832	696	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0021506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	18	931	1	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	1	2	FACETS	0.379	0.283	0.493	0.379	0.283	0.493	SUBCLONAL	1	TRUE	1	0.12	2		932	792	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876401	35876401	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	42	863	0	ENST00000303115.3:c.1193C>A	p.Pro398His	p.P398H	ENST00000303115	NM_002185.3	398	cCt/cAt	8/8	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.12	2		863	625	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246443	46246443	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0021506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	23	501	0	ENST00000334344.6:c.4537A>T	p.Lys1513Ter	p.K1513*	ENST00000334344	NM_152641.2	1513	Aaa/Taa	15/21	1	2	FACETS	0.854	0.664	1	0.854	0.664	1	CLONAL	1	TRUE	1	0.12	2		501	449	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846040	128846040	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	36	1039	0	ENST00000249373.3:c.970G>T	p.Ala324Ser	p.A324S	ENST00000249373	NM_005631.4	324	Gcc/Tcc	5/12	1	2	FACETS	0.836	0.685	1	0.836	0.685	1	CLONAL	1	TRUE	1	0.12	2		1039	718	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0021517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	44	367	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	0.281	0.235	0.331	0.281	0.235	0.331	SUBCLONAL	1	FALSE	1	0.665264416283975	2		367	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0021517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	105	760	1	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	1	2	FACETS	0.312	0.279	0.347	0.312	0.279	0.347	SUBCLONAL	1	FALSE	1	0.665264416283975	2		761	1012	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130367	2130367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397515225	NA	P-0021517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	108	860	4	ENST00000219476.3:c.3599G>A	p.Arg1200Gln	p.R1200Q	ENST00000219476	NM_000548.3	1200	cGg/cAg	30/42	1	2	FACETS	0.344	0.308	0.382	0.344	0.308	0.382	SUBCLONAL	1	FALSE	1	0.665264416283975	2		864	945	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212615399	212615399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369165560	NA	P-0021517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	247	476	4	ENST00000342788.4:c.587G>A	p.Arg196His	p.R196H	ENST00000342788	NM_005235.2	196	cGt/cAt	5/28	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.665264416283975	2		480	719	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737843	145737843	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs771326102	NA	P-0021517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	345	771	7	ENST00000428558.2:c.2987T>C	p.Met996Thr	p.M996T	ENST00000428558	NM_004260.3	996	aTg/aCg	18/22	NA	2	FACETS	0.986	0.935	1			1	INDETERMINATE	1	FALSE	NA	0.665264416283975	2		778	1052	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776310	76776310	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs122445099	NA	P-0021517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	64	628	1	ENST00000373344.5:c.7156C>T	p.Arg2386Ter	p.R2386*	ENST00000373344	NM_000489.3	2386	Cga/Tga	34/35	0.665264416283975	1	FACETS	0.29	0.251	0.331	0.29	0.251	0.331	SUBCLONAL	1	FALSE	0	0.665264416283975	1		629	443	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643784	52643784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	53	469	2	ENST00000394830.3:c.2112G>A	p.Met704Ile	p.M704I	ENST00000394830	NM_018313.4	704	atG/atA	17/30	1	2	FACETS	0.26	0.221	0.302	0.26	0.221	0.302	SUBCLONAL	1	FALSE	1	0.665264416283975	2		471	614	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0021528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	610	662	1				ENST00000310581	NM_198253.2	-/1132			0.621196513482586	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	1	0.621196513482586	4		663	1019	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0021528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	335	818	1	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.579721427154434	2	FACETS	0.89	0.851	0.929	0.89	0.851	0.929	CLONAL	2	TRUE	0	0.621196513482586	2		819	606	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256416	16256416	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1234631776	NA	P-0021528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	105	732	0	ENST00000375759.3:c.3681G>C	p.Lys1227Asn	p.K1227N	ENST00000375759	NM_015001.2	1227	aaG/aaC	11/15	1	2	FACETS	0.505	0.452	0.56	0.505	0.452	0.56	SUBCLONAL	1	TRUE	1	0.621196513482586	2		732	670	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43817949	43817949	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	217	771	0	ENST00000372470.3:c.1628T>G	p.Leu543Arg	p.L543R	ENST00000372470	NM_005373.2	543	cTt/cGt	11/12	1	2	FACETS	0.947	0.883	1	0.947	0.883	1	CLONAL	1	TRUE	1	0.621196513482586	2		771	738	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256151	133256151	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs374074035	NA	P-0021528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	97	748	0	ENST00000320574.5:c.510C>G	p.Ile170Met	p.I170M	ENST00000320574	NM_006231.2	170	atC/atG	6/49	0.315286342487882	3	FACETS	0.551	0.491	0.615	0.275	0.245	0.308	INDETERMINATE	1	TRUE	1	0.621196513482586	3		748	743	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030410	49030410	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	219	713	0	ENST00000267163.4:c.1885G>T	p.Glu629Ter	p.E629*	ENST00000267163	NM_000321.2	629	Gag/Tag	19/27	0.621196513482586	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.621196513482586	1		713	477	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021371	42021371	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	181	480	1	ENST00000219905.7:c.3667G>T	p.Glu1223Ter	p.E1223*	ENST00000219905	NM_001164273.1	1223	Gag/Tag	11/24	0.620664241355281	3	FACETS	0.985	0.911	1	0.493	0.455	0.532	CLONAL	1	TRUE	1	0.621196513482586	3		481	775	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993791	72993791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371690491	NA	P-0021528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	258	702	1	ENST00000268489.5:c.254C>T	p.Ser85Leu	p.S85L	ENST00000268489	NM_006885.3	85	tCg/tTg	2/10	0.300446060693729	2	FACETS	1	0.993	1	0.702	0.663	0.741	INDETERMINATE	1	TRUE	0	0.621196513482586	2		703	592	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138623	11138623	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	199	674	0	ENST00000358026.2:c.3379G>T	p.Asp1127Tyr	p.D1127Y	ENST00000358026	NM_001128849.1	1127	Gat/Tat	24/36	0.377419291262159	1	FACETS	0.821	0.767	0.876	0.821	0.767	0.876	CLONAL	1	TRUE	0	0.621196513482586	1		674	538	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868168	45868168	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	528	946	2	ENST00000391945.4:c.522C>G	p.Ile174Met	p.I174M	ENST00000391945	NM_000400.3	174	atC/atG	7/23	0.325508804646376	3	FACETS	1	0.995	1	0.773	0.746	0.8	INDETERMINATE	2	TRUE	0	0.621196513482586	3		948	961	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663157	227663157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs570775459	NA	P-0021528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	319	763	1	ENST00000305123.5:c.298G>A	p.Glu100Lys	p.E100K	ENST00000305123	NM_005544.2	100	Gag/Aag	1/2	0.579721427154434	2	FACETS	0.872	0.832	0.911	0.872	0.832	0.911	CLONAL	2	TRUE	0	0.621196513482586	2		764	589	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42848536	42848536	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	112	653	0	ENST00000398585.3:c.806C>A	p.Ser269Tyr	p.S269Y	ENST00000398585	NM_001135099.1	269	tCt/tAt	8/14	0.377419291262159	1	FACETS	0.433	0.39	0.478	0.433	0.39	0.478	SUBCLONAL	1	TRUE	0	0.621196513482586	1		653	574	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114547	73114547	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0021528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	104	358	0	ENST00000356692.5:c.929-1G>A		p.X310_splice	ENST00000356692		310			0.315286342487882	3	FACETS	1	0.975	1	0.622	0.562	0.683	INDETERMINATE	1	TRUE	1	0.621196513482586	3		358	353	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55962486	55962486	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	100	637	0	ENST00000263923.4:c.2638C>G	p.Arg880Gly	p.R880G	ENST00000263923	NM_002253.2	880	Cga/Gga	19/30	1	2	FACETS	0.53	0.474	0.59	0.53	0.474	0.59	SUBCLONAL	1	TRUE	1	0.621196513482586	2		637	607	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526849	31526849	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0021528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1521	162	1138	0	ENST00000344624.3:c.191C>G	p.Ser64Ter	p.S64*	ENST00000344624		64	tCa/tGa	2/33	0.621196513482586	4	FACETS	0.502	0.459	0.548	0.167	0.153	0.183	SUBCLONAL	1	TRUE	1	0.621196513482586	4		1138	1683	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935528	13935528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781723736	NA	P-0021528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	161	515	0	ENST00000405192.2:c.1328G>A	p.Cys443Tyr	p.C443Y	ENST00000405192	NM_001163147.1	443	tGc/tAc	12/12	0.621196513482586	1	FACETS	0.839	0.778	0.901	0.839	0.778	0.901	CLONAL	1	TRUE	0	0.621196513482586	1		515	426	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896463	151896463	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	310	632	0	ENST00000262189.6:c.4174C>T	p.Gln1392Ter	p.Q1392*	ENST00000262189	NM_170606.2	1392	Cag/Tag	27/59	0.315286342487882	3	FACETS	0.91	0.863	0.956	0.91	0.863	0.956	INDETERMINATE	2	TRUE	1	0.621196513482586	3		632	719	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	53	669	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.679	0.582	0.784	0.679	0.582	0.784	SUBCLONAL	1	TRUE	1	0.47	2		669	332	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0021529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	157	710	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.978	0.899	1	0.978	0.899	1	CLONAL	1	TRUE	1	0.47	2		711	683	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159755	20159755	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	80	300	0	ENST00000379607.5:c.4C>G	p.Pro2Ala	p.P2A	ENST00000379607	NM_001412.3	2	Ccc/Gcc	1/7	1	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.47	1		300	183	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0021531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	754	573	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.529538713002767	6	FACETS	0.981	0.954	1			1	CLONAL	5	TRUE	NA	0.529538713002767	6		573	1196	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0021531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	255	784	4	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.529538713002767	1	FACETS	0.99	0.932	1	0.99	0.932	1	CLONAL	1	TRUE	0	0.529538713002767	1		788	715	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0021531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	110	458	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.743	0.67	0.82	0.743	0.67	0.82	SUBCLONAL	1	TRUE	1	0.529538713002767	2		459	559	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0021531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	195	440	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.509035485388101	3	FACETS	0.875	0.817	0.935			1	CLONAL	2	TRUE	NA	0.529538713002767	3		440	532	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0021535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	159	779	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.354288151176974	2		779	764	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219413	1219413	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs730881971	NA	P-0021535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	95	663	0	ENST00000326873.7:c.464+1G>T		p.X155_splice	ENST00000326873	NM_000455.4	155			0.306176941524536	1	FACETS	0.842	0.752	0.937	0.842	0.752	0.937	CLONAL	1	TRUE	0	0.354288151176974	1		663	524	SUCCESS
RET	5979	MSKCC	GRCh37	10	43613917	43613917	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	97	744	0	ENST00000355710.3:c.2381G>T	p.Cys794Phe	p.C794F	ENST00000355710	NM_020975.4	794	tGc/tTc	13/20	1	2	FACETS	0.856	0.764	0.953	0.856	0.764	0.953	CLONAL	1	TRUE	1	0.354288151176974	2		744	640	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781902	3781903	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0021535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	100	830	1	ENST00000262367.5:c.4764_4765delinsTT	p.Lys1588_Asn1589delinsAsnTyr	p.K1588_N1589delinsNY	ENST00000262367	NM_004380.2	1588	aaGAac/aaTTac	29/31	1	2	FACETS	0.719	0.642	0.801	0.719	0.642	0.801	SUBCLONAL	1	TRUE	1	0.354288151176974	2		831	785	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805628	46805628	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	127	808	1	ENST00000290295.7:c.328C>A	p.Pro110Thr	p.P110T	ENST00000290295	NM_006361.5	110	Ccc/Acc	1/2	1	2	FACETS	0.871	0.789	0.957	0.871	0.789	0.957	CLONAL	1	TRUE	1	0.354288151176974	2		809	823	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117625	4117625	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	93	662	1	ENST00000262948.5:c.95C>T	p.Ala32Val	p.A32V	ENST00000262948	NM_030662.3	32	gCa/gTa	2/11	0.306176941524536	1	FACETS	0.842	0.751	0.938	0.842	0.751	0.938	CLONAL	1	TRUE	0	0.354288151176974	1		663	513	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602926	10602926	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	131	793	0	ENST00000171111.5:c.652G>C	p.Glu218Gln	p.E218Q	ENST00000171111	NM_203500.1	218	Gag/Cag	3/6	0.306176941524536	1	FACETS	0.819	0.744	0.898	0.819	0.744	0.898	CLONAL	1	TRUE	0	0.354288151176974	1		793	743	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312916	30312916	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	99	675	0	ENST00000262643.3:c.719G>T	p.Arg240Leu	p.R240L	ENST00000262643	NM_001238.2	240	cGt/cTt	9/12	1	2	FACETS	0.906	0.81	1	0.906	0.81	1	CLONAL	1	TRUE	1	0.354288151176974	2		675	617	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629234	187629234	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	131	775	0	ENST00000441802.2:c.1748G>T	p.Gly583Val	p.G583V	ENST00000441802	NM_005245.3	583	gGc/gTc	2/27	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.354288151176974	2		775	716	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31486597	31486597	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0021535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	123	640	0	ENST00000344624.3:c.1914+1G>T		p.X638_splice	ENST00000344624		638			1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.354288151176974	2		640	680	SUCCESS
APC	324	MSKCC	GRCh37	5	112179562	112179563	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0021535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	66	492	0	ENST00000257430.4:c.8271_8272delinsTT	p.Glu2758Ter	p.E2758*	ENST00000257430	NM_000038.5	2757	gtGGaa/gtTTaa	16/16	1	2	FACETS	0.77	0.67	0.878	0.77	0.67	0.878	SUBCLONAL	1	TRUE	1	0.354288151176974	2		492	484	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044957	47044957	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	126	446	0	ENST00000377604.3:c.2283T>G	p.Cys761Trp	p.C761W	ENST00000377604	NM_001204468.1	761	tgT/tgG	20/24	1	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.354288151176974	1		446	422	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046378	69046378	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375506738	NA	P-0021538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	77	800	0	ENST00000288368.4:c.3851C>T	p.Ala1284Val	p.A1284V	ENST00000288368	NM_024870.2	1284	gCg/gTg	32/40	1	2	FACETS	0.222	0.194	0.252	0.222	0.194	0.252	SUBCLONAL	1	TRUE	1	0.873865216119518	2		800	793	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112025268	112025268	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	367	791	0	ENST00000368678.4:c.481C>T	p.Arg161Ter	p.R161*	ENST00000368678		161	Cga/Tga	6/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.873865216119518	2		791	803	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932556	39932557	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0021538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	472	592	0	ENST00000378444.4:c.2042dup	p.His682SerfsTer58	p.H682Sfs*58	ENST00000378444	NM_001123385.1	681	cct/ccCt	4/15	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.873865216119518	1		592	590	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0021539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	175	681	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.183089062760887	2	FACETS	0.77	0.71	0.832	0.77	0.71	0.832	SUBCLONAL	2	TRUE	0	0.28	2		681	812	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986753	36986754	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	40	168	1	ENST00000354822.5:c.935dup	p.Gln313ThrfsTer126	p.Q313Tfs*126	ENST00000354822	NM_001079668.2	312	cta/ctTa	3/3	0.301342770202577	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	0	0.28	1		169	219	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56811531	56811531	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	139	648	0	ENST00000337432.4:c.1079A>C	p.Glu360Ala	p.E360A	ENST00000337432	NM_058216.2	360	gAa/gCa	9/9	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.28	2		648	958	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0021541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	801	857	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.46399907565049	4	FACETS	1	0.994	1			1	CLONAL	4	TRUE	NA	0.57603125701954	4		859	1052	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	161	690	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.57603125701954	3	FACETS	0.861	0.79	0.935	0.431	0.395	0.468	CLONAL	1	TRUE	1	0.57603125701954	3		690	836	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913351	NA	P-0021541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	150	682	0	ENST00000288602.6:c.1397G>T	p.Gly466Val	p.G466V	ENST00000288602	NM_004333.4	466	gGa/gTa	11/18	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.57603125701954	2		682	468	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564540	86564560	+	inframe_deletion	In_Frame_Del	DEL	CTGCTGCTGGCGTAGCTGGTG	CTGCTGCTGGCGTAGCTGGTG	-	rs745572583	NA	P-0021541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	147	682	0	ENST00000274376.6:c.285_305del	p.Ala100_Ala106del	p.A100_A106del	ENST00000274376	NM_002890.2	91	aCTGCTGCTGGCGTAGCTGGTGct/act	1/25	0.57603125701954	3	FACETS	1	0.986	1	0.676	0.622	0.732	CLONAL	1	TRUE	1	0.57603125701954	3		682	486	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696688	47696688	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519971	NA	P-0021542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	155	828	0	ENST00000347630.2:c.260A>G	p.Tyr87Cys	p.Y87C	ENST00000347630	NM_001007230.1	87	tAc/tGc	5/11	1	2	FACETS	0.85	0.783	0.919	0.85	0.783	0.919	CLONAL	1	TRUE	1	0.706944681166205	2		828	516	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200663	128200663	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	179	839	0	ENST00000341105.2:c.1142A>G	p.Asn381Ser	p.N381S	ENST00000341105	NM_032638.4	381	aAt/aGt	5/6	1	2	FACETS	0.931	0.864	0.999	0.931	0.864	0.999	CLONAL	1	TRUE	1	0.706944681166205	2		839	544	SUCCESS
APC	324	MSKCC	GRCh37	5	112102907	112102908	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0021542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	138	492	0	ENST00000257430.4:c.242_243del	p.Asn81IlefsTer57	p.N81Ifs*57	ENST00000257430	NM_000038.5	81	aAT/a	4/16	0.602618959186202	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.706944681166205	1		492	246	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864231	151864232	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0021542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	89	493	0	ENST00000262189.6:c.9748_9749dup	p.Gln3250HisfsTer13	p.Q3250Hfs*13	ENST00000262189	NM_170606.2	3250	cag/caCAg	42/59	1	2	FACETS	0.909	0.817	1	0.909	0.817	1	CLONAL	1	TRUE	1	0.706944681166205	2		493	277	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115965	8115974	+	frameshift_variant	Frame_Shift_Del	DEL	CATGGTCACC	CATGGTCACC	-	novel	NA	P-0021543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	54	455	0	ENST00000346208.3:c.1311_1320del	p.Ser437ArgfsTer35	p.S437Rfs*35	ENST00000346208		437	agCATGGTCACC/ag	6/6	1	2	FACETS	0.651	0.556	0.756	0.651	0.556	0.756	SUBCLONAL	1	TRUE	1	0.283912485796867	2		455	584	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575085	64575085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs794728624	NA	P-0021543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	161	779	0	ENST00000312049.6:c.722G>A	p.Cys241Tyr	p.C241Y	ENST00000312049	NM_130799.2	241	tGt/tAt	4/10	0.283912485796867	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.283912485796867	1		779	919	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	302	772	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.807450199118348	7	FACETS	0.91	0.871	0.949	1	0.991	1	CLONAL	5	TRUE	3	0.807450199118348	7		772	496	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258550	16258550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	217	697	0	ENST00000375759.3:c.5815C>T	p.Gln1939Ter	p.Q1939*	ENST00000375759	NM_015001.2	1939	Cag/Tag	11/15	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.807450199118348	2		697	535	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163711	72163711	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	83	812	0	ENST00000357731.5:c.647A>T	p.Lys216Ile	p.K216I	ENST00000357731	NM_173808.2	216	aAa/aTa	4/7	1	2	FACETS	0.832	0.746	0.922	0.832	0.746	0.922	CLONAL	1	TRUE	1	0.807450199118348	2		812	247	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841422	156841422	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	285	580	0	ENST00000524377.1:c.725G>T	p.Gly242Val	p.G242V	ENST00000524377	NM_002529.3	242	gGg/gTg	7/17	0.487573073188609	5	FACETS	0.934	0.888	0.98	0.934	0.888	0.98	CLONAL	3	TRUE	2	0.807450199118348	5		580	557	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724599	162724599	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	376	642	2	ENST00000367921.3:c.371G>T	p.Arg124Leu	p.R124L	ENST00000367921	NM_006182.2	124	cGg/cTg	5/18	0.487573073188609	5	FACETS	0.967	0.926	1	0.967	0.926	1	CLONAL	3	TRUE	2	0.807450199118348	5		644	710	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933462	100933462	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1565339096	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	142	389	0	ENST00000325455.5:c.1928A>G	p.Asn643Ser	p.N643S	ENST00000325455	NM_001202474.3	643	aAt/aGt	4/8	0.384992293680978	3	FACETS	1	0.985	1	0.769	0.724	0.813	INDETERMINATE	2	TRUE	0	0.807450199118348	3		389	214	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195845	102195845	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	269	578	0	ENST00000263464.3:c.605G>C	p.Arg202Thr	p.R202T	ENST00000263464	NM_001165.4	202	aGa/aCa	2/9	0.384992293680978	3	FACETS	1	0.991	1	0.757	0.724	0.789	INDETERMINATE	2	TRUE	0	0.807450199118348	3		578	412	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409095	4409095	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	297	599	0	ENST00000261254.3:c.790G>T	p.Asp264Tyr	p.D264Y	ENST00000261254	NM_001759.3	264	Gac/Tac	5/5	0.606569428659639	5	FACETS	1	0.985	1	0.735	0.696	0.774	CLONAL	2	TRUE	2	0.807450199118348	5		599	738	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446891	18446891	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	164	582	0	ENST00000266497.5:c.976C>A	p.Gln326Lys	p.Q326K	ENST00000266497		326	Cag/Aag	4/31	0.368420149298064	5	FACETS	0.839	0.782	0.896	0.839	0.782	0.896	INDETERMINATE	3	TRUE	2	0.807450199118348	5		582	357	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491390	18491390	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1377942847	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	50	564	1	ENST00000266497.5:c.1309del	p.Ile437TyrfsTer5	p.I437Yfs*5	ENST00000266497		435	Aaa/aa	8/31	0.368420149298064	5	FACETS	0.771	0.657	0.896	0.257	0.219	0.299	INDETERMINATE	1	TRUE	2	0.807450199118348	5		565	355	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435035	49435035	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765654409	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	173	694	0	ENST00000301067.7:c.6518C>T	p.Ser2173Leu	p.S2173L	ENST00000301067	NM_003482.3	2173	tCg/tTg	31/54	0.764590670931522	3	FACETS	0.841	0.776	0.908			1	CLONAL	1	TRUE	NA	0.807450199118348	3		694	715	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435453	49435453	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	95	834	0	ENST00000301067.7:c.6219C>G	p.Ile2073Met	p.I2073M	ENST00000301067	NM_003482.3	2073	atC/atG	30/54	0.764590670931522	3	FACETS	0.363	0.322	0.406			1	SUBCLONAL	1	TRUE	NA	0.807450199118348	3		834	910	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884623	111884623	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs778992065	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	412	793	0	ENST00000341259.2:c.799G>T	p.Glu267Ter	p.E267*	ENST00000341259	NM_005475.2	267	Gag/Tag	3/8	0.789550115623709	2	FACETS	0.976	0.948	1	0.976	0.948	1	CLONAL	2	TRUE	0	0.807450199118348	2		793	523	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926964	112926964	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	381	694	0	ENST00000351677.2:c.1584G>C	p.Arg528Ser	p.R528S	ENST00000351677	NM_002834.3	528	agG/agC	13/16	0.789550115623709	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.807450199118348	2		694	452	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256626	133256626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	269	609	0	ENST00000320574.5:c.337G>A	p.Glu113Lys	p.E113K	ENST00000320574	NM_006231.2	113	Gag/Aag	5/49	0.789550115623709	2	FACETS	0.989	0.955	1	0.989	0.955	1	CLONAL	2	TRUE	0	0.807450199118348	2		609	337	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636079	28636079	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	290	793	0	ENST00000241453.7:c.293C>A	p.Pro98Gln	p.P98Q	ENST00000241453	NM_004119.2	98	cCa/cAa	3/24	0.21306600296017	4	FACETS	0.926	0.877	0.976	0.926	0.877	0.976	INDETERMINATE	2	TRUE	2	0.807450199118348	4		793	701	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829881	72829881	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	530	825	0	ENST00000268489.5:c.6700C>G	p.Pro2234Ala	p.P2234A	ENST00000268489	NM_006885.3	2234	Cca/Gca	9/10	0.606569428659639	5	FACETS	1	0.995	1	0.804	0.772	0.835	CLONAL	2	TRUE	2	0.807450199118348	5		825	1204	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993858	72993858	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	416	503	0	ENST00000268489.5:c.187G>A	p.Glu63Lys	p.E63K	ENST00000268489	NM_006885.3	63	Gag/Aag	2/10	0.606569428659639	5	FACETS	0.868	0.831	0.905	0.868	0.831	0.905	CLONAL	3	TRUE	2	0.807450199118348	5		503	875	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	690	924	4	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	0.786081243848553	3	FACETS	0.948	0.928	0.966	0.948	0.928	0.966	CLONAL	3	TRUE	0	0.807450199118348	3		928	844	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315429	30315429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758186567	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	46	837	0	ENST00000322652.5:c.1114C>T	p.Pro372Ser	p.P372S	ENST00000322652	NM_015355.2	372	Cct/Tct	10/16	0.368420149298064	5	FACETS	0.328	0.275	0.386	0.109	0.091	0.129	INDETERMINATE	1	TRUE	2	0.807450199118348	5		837	769	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602619	10602619	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1239985410	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	611	644	0	ENST00000171111.5:c.959G>T	p.Arg320Leu	p.R320L	ENST00000171111	NM_203500.1	320	cGg/cTg	3/6	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.807450199118348	2		644	746	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794548	42794548	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	711	977	1	ENST00000575354.2:c.1628C>G	p.Ser543Ter	p.S543*	ENST00000575354	NM_015125.3	543	tCa/tGa	10/20	0.773885743805661	3	FACETS	0.941	0.922	0.959	0.941	0.922	0.959	CLONAL	3	TRUE	0	0.807450199118348	3		978	876	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505577	25505577	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	533	983	0	ENST00000264709.3:c.181G>T	p.Glu61Ter	p.E61*	ENST00000264709	NM_175629.2	61	Gaa/Taa	4/23	0.807450199118348	3	FACETS	0.953	0.92	0.986	0.953	0.92	0.986	CLONAL	2	TRUE	1	0.807450199118348	3		983	972	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641555	47641555	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1114167845	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	73	239	0	ENST00000233146.2:c.940C>T	p.Gln314Ter	p.Q314*	ENST00000233146	NM_000251.2	314	Cag/Tag	5/16	0.807450199118348	3	FACETS	0.913	0.826	1	0.913	0.826	1	CLONAL	2	TRUE	1	0.807450199118348	3		239	139	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022431	31022431	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	383	266	1	ENST00000375687.4:c.1916C>A	p.Thr639Asn	p.T639N	ENST00000375687	NM_015338.5	639	aCt/aAt	13/13	0.796002281559237	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	4	TRUE	0	0.807450199118348	4		267	415	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62325761	62325761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750539539	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	451	836	1	ENST00000360203.5:c.3029C>T	p.Thr1010Met	p.T1010M	ENST00000360203	NM_001283009.1	1010	aCg/aTg	31/35	0.780791149239764	6	FACETS	0.926	0.882	0.97	0.463	0.441	0.485	CLONAL	2	TRUE	2	0.807450199118348	6		837	1578	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866456	42866456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150502923	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	58	1041	2	ENST00000398585.3:c.176C>T	p.Pro59Leu	p.P59L	ENST00000398585	NM_001135099.1	59	cCg/cTg	3/14	0.104300683812039	3	FACETS	0.254	0.218	0.294	0.085	0.072	0.098	INDETERMINATE	1	TRUE	0	0.807450199118348	3		1043	793	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569662	41569662	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	88	420	0	ENST00000263253.7:c.4653G>C	p.Lys1551Asn	p.K1551N	ENST00000263253	NM_001429.3	1551	aaG/aaC	29/31	0.807450199118348	3	FACETS	0.838	0.748	0.933	0.419	0.374	0.467	CLONAL	1	TRUE	1	0.807450199118348	3		420	365	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183869	10183869	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	154	606	0	ENST00000256474.2:c.338G>A	p.Arg113Gln	p.R113Q	ENST00000256474	NM_000551.3	113	cGa/cAa	1/3	1	2	FACETS	0.741	0.682	0.801	0.741	0.682	0.801	SUBCLONAL	1	TRUE	1	0.807450199118348	2		606	515	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660150	12660150	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	179	746	1	ENST00000251849.4:c.71G>T	p.Gly24Val	p.G24V	ENST00000251849	NM_002880.3	24	gGc/gTc	2/17	1	2	FACETS	0.821	0.762	0.881	0.821	0.762	0.881	CLONAL	1	TRUE	1	0.807450199118348	2		747	540	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204909	128204909	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	891	1052	0	ENST00000341105.2:c.532C>A	p.Pro178Thr	p.P178T	ENST00000341105	NM_032638.4	178	Ccc/Acc	3/6	0.527302847217495	5	FACETS	1	0.986	1			1	CLONAL	3	TRUE	NA	0.807450199118348	5		1052	1595	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873098	134873098	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1401137889	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	290	738	1	ENST00000398015.3:c.1402G>A	p.Glu468Lys	p.E468K	ENST00000398015	NM_004441.4	468	Gag/Aag	6/16	0.527302847217495	5	FACETS	0.872	0.822	0.922			1	CLONAL	2	TRUE	NA	0.807450199118348	5		739	911	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953894	55953894	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	177	649	1	ENST00000263923.4:c.3542C>A	p.Ser1181Ter	p.S1181*	ENST00000263923	NM_002253.2	1181	tCa/tAa	27/30	0.310046896909119	3	FACETS	0.827	0.774	0.881	0.827	0.774	0.881	INDETERMINATE	2	TRUE	1	0.807450199118348	3		650	372	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627969	187627969	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	242	827	0	ENST00000441802.2:c.3013G>C	p.Asp1005His	p.D1005H	ENST00000441802	NM_005245.3	1005	Gac/Cac	2/27	0.310046896909119	3	FACETS	0.772	0.728	0.816	0.772	0.728	0.816	INDETERMINATE	2	TRUE	1	0.807450199118348	3		827	545	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633838	86633838	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	175	567	0	ENST00000274376.6:c.947G>T	p.Gly316Val	p.G316V	ENST00000274376	NM_002890.2	316	gGa/gTa	5/25	0.783386436872823	2	FACETS	0.914	0.871	0.955	0.914	0.871	0.955	CLONAL	2	TRUE	0	0.807450199118348	2		567	237	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149511584	149511584	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	407	840	0	ENST00000261799.4:c.1201G>A	p.Glu401Lys	p.E401K	ENST00000261799	NM_002609.3	401	Gag/Aag	8/23	0.783386436872823	2	FACETS	0.973	0.946	0.999	0.973	0.946	0.999	CLONAL	2	TRUE	0	0.807450199118348	2		840	518	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149511617	149511617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	396	789	0	ENST00000261799.4:c.1168G>A	p.Glu390Lys	p.E390K	ENST00000261799	NM_002609.3	390	Gag/Aag	8/23	0.783386436872823	2	FACETS	0.96	0.932	0.987	0.96	0.932	0.987	CLONAL	2	TRUE	0	0.807450199118348	2		789	511	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176684021	176684021	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	232	1039	0	ENST00000439151.2:c.4835G>T	p.Gly1612Val	p.G1612V	ENST00000439151	NM_022455.4	1612	gGa/gTa	13/23	0.783386436872823	2	FACETS	0.966	0.907	1	0.483	0.453	0.513	CLONAL	1	TRUE	0	0.807450199118348	2		1039	595	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680584	30680584	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	148	664	1	ENST00000376406.3:c.1135G>A	p.Asp379Asn	p.D379N	ENST00000376406	NM_014641.2	379	Gat/Aat	5/15	0.767244182836092	3	FACETS	0.929	0.853	1	0.31	0.284	0.336	CLONAL	1	TRUE	0	0.807450199118348	3		665	554	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323241	31323241	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	395	421	0	ENST00000412585.2:c.748C>T	p.Gln250Ter	p.Q250*	ENST00000412585	NM_005514.6	250	Cag/Tag	4/8	0.767244182836092	3	FACETS	0.94	0.915	0.964	0.94	0.915	0.964	CLONAL	3	TRUE	0	0.807450199118348	3		421	487	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005605	150005605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	79	469	0	ENST00000253339.5:c.620C>T	p.Ser207Leu	p.S207L	ENST00000253339		207	tCa/tTa	3/7	0.571186579293468	4	FACETS	0.956	0.846	1			1	CLONAL	1	TRUE	NA	0.807450199118348	4		469	370	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128849207	128849207	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	332	724	0	ENST00000249373.3:c.1435G>C	p.Glu479Gln	p.E479Q	ENST00000249373	NM_005631.4	479	Gag/Cag	8/12	0.296545290767422	4	FACETS	0.992	0.944	1	0.992	0.944	1	INDETERMINATE	2	TRUE	2	0.807450199118348	4		724	749	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913355	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	169	603	0	ENST00000288602.6:c.1406G>T	p.Gly469Val	p.G469V	ENST00000288602	NM_004333.4	469	gGa/gTa	11/18	0.296545290767422	4	FACETS	1	0.966	1	1	0.966	1	INDETERMINATE	2	TRUE	2	0.807450199118348	4		603	359	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874521	151874521	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	22	582	0	ENST00000262189.6:c.8017G>C	p.Asp2673His	p.D2673H	ENST00000262189	NM_170606.2	2673	Gat/Cat	38/59	0.296545290767422	4	FACETS	0.255	0.197	0.322	0.127	0.098	0.161	INDETERMINATE	1	TRUE	2	0.807450199118348	4		582	387	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995501	68995501	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	124	888	0	ENST00000288368.4:c.1905G>C	p.Lys635Asn	p.K635N	ENST00000288368	NM_024870.2	635	aaG/aaC	18/40	0.29764302178998	4	FACETS	0.809	0.741	0.879	0.809	0.741	0.879	INDETERMINATE	2	TRUE	2	0.807450199118348	4		888	343	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046311	69046311	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	196	518	0	ENST00000288368.4:c.3784C>G	p.Arg1262Gly	p.R1262G	ENST00000288368	NM_024870.2	1262	Cgt/Ggt	32/40	0.29764302178998	4	FACETS	0.966	0.905	1	0.966	0.905	1	INDETERMINATE	2	TRUE	2	0.807450199118348	4		518	454	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934320	39934320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	425	409	0	ENST00000378444.4:c.279G>T	p.Leu93Phe	p.L93F	ENST00000378444	NM_001123385.1	93	ttG/ttT	4/15	0.807450199118348	2	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.807450199118348	2		409	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0021545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	355	824	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.86274161463475	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.86274161463475	3		825	581	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0021545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	202	899	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.86274161463475	3	FACETS	1	0.974	1	0.544	0.507	0.582	CLONAL	1	TRUE	1	0.86274161463475	3		900	616	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033844	49033844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853294	NA	P-0021545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	609	695	0	ENST00000267163.4:c.1981C>T	p.Arg661Trp	p.R661W	ENST00000267163	NM_000321.2	661	Cgg/Tgg	20/27	0.86274161463475	5	FACETS	0.962	0.947	0.977	0.962	0.947	0.977	CLONAL	5	TRUE	0	0.86274161463475	5		695	673	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453375	40453375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1434706212	NA	P-0021545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	179	1080	3	ENST00000345506.4:c.1072G>A	p.Gly358Arg	p.G358R	ENST00000345506	NM_003152.3	358	Ggg/Agg	10/20	0.86274161463475	3	FACETS	0.992	0.919	1			1	CLONAL	1	TRUE	NA	0.86274161463475	3		1083	599	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259283	89259283	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	221	600	0	ENST00000336596.2:c.427A>T	p.Ile143Phe	p.I143F	ENST00000336596	NM_005233.5	143	Att/Ttt	3/17	0.281599379359808	3	FACETS	1	0.993	1	0.826	0.792	0.858	INDETERMINATE	2	TRUE	0	0.86274161463475	3		600	296	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164049	106164049	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	80	649	0	ENST00000380013.4:c.3559G>C	p.Gly1187Arg	p.G1187R	ENST00000380013	NM_001127208.2	1187	Ggc/Cgc	5/11	0.85370912110325	2	FACETS	0.793	0.709	0.879	0.396	0.354	0.44	SUBCLONAL	1	TRUE	0	0.86274161463475	2		649	234	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061232	38061232	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1486264414	NA	P-0021546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	73	947	0	ENST00000250448.2:c.757A>G	p.Met253Val	p.M253V	ENST00000250448	NM_004496.3	253	Atg/Gtg	2/2	0.225131611512793	4	FACETS	1	0.951	1	0.394	0.344	0.448	CLONAL	1	FALSE	1	0.229432946655503	4		947	662	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3094679	3094679	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	117	631	0	ENST00000078429.4:c.30C>G	p.Cys10Trp	p.C10W	ENST00000078429	NM_002067.2	10	tgC/tgG	1/7	0.229432946655503	5	FACETS	1	0.964	1	0.759	0.686	0.836	CLONAL	2	FALSE	2	0.229432946655503	5		631	602	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025955	48025955	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	160	608	0	ENST00000234420.5:c.833T>G	p.Ile278Arg	p.I278R	ENST00000234420	NM_000179.2	278	aTa/aGa	4/10	0.229432946655503	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	3	FALSE	1	0.229432946655503	4		608	525	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0021548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	468	785	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	NA	2	FACETS	0.985	0.947	1			1	INDETERMINATE	2	TRUE	NA	0.535783762851828	2		786	887	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673154	30673154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	153	629	0	ENST00000376406.3:c.3806C>T	p.Thr1269Ile	p.T1269I	ENST00000376406	NM_014641.2	1269	aCt/aTt	10/15	0.445636852063942	4	FACETS	0.887	0.811	0.967	0.443	0.405	0.484	CLONAL	1	TRUE	2	0.535783762851828	4		629	989	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855002	76855002	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	218	863	0	ENST00000373344.5:c.5834G>T	p.Gly1945Val	p.G1945V	ENST00000373344	NM_000489.3	1945	gGa/gTa	25/35	NA	2	FACETS	1	0.962	1			1	INDETERMINATE	1	TRUE	NA	0.535783762851828	2		863	778	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	95	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.547153055431919	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.547153055431919	1		434	247	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0021571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	175	786	3	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.547153055431919	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.547153055431919	1		789	432	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1485978447	NA	P-0021571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	187	597	1	ENST00000324856.7:c.5164C>T	p.Arg1722Ter	p.R1722*	ENST00000324856	NM_006015.4	1722	Cga/Tga	20/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.547153055431919	2		598	650	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158417	26158417	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs368384735	NA	P-0021571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	322	954	0	ENST00000289316.2:c.20C>G	p.Ser7Cys	p.S7C	ENST00000289316	NM_138720.2	7	tCt/tGt	1/2	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.547153055431919	2		954	1122	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40679368	40679368	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	170	587	0	ENST00000249776.8:c.446A>C	p.Lys149Thr	p.K149T	ENST00000249776	NM_033286.3	149	aAa/aCa	4/9	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.547153055431919	2		587	621	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842404	68842405	+	missense_variant	Missense_Mutation	DNP	CT	CT	TC	novel	NA	P-0021571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	194	718	1	ENST00000261769.5:c.465_466delinsTC	p.Trp156Arg	p.W156R	ENST00000261769	NM_004360.3	155	gaCTgg/gaTCgg	4/16	0.547153055431919	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.547153055431919	1		719	463	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682459	52682459	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0021571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	105	506	0	ENST00000394830.3:c.715-1G>C		p.X239_splice	ENST00000394830	NM_018313.4	239			0.547153055431919	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.547153055431919	1		506	250	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0021573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	155	815	1	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.279226639241815	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.279226639241815	1		816	903	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652056	36652056	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	113	883	2	ENST00000244741.5:c.178G>T	p.Glu60Ter	p.E60*	ENST00000244741	NM_000389.4	60	Gag/Tag	2/3	1	2	FACETS	0.719	0.645	0.797	0.719	0.645	0.797	SUBCLONAL	1	TRUE	1	0.279226639241815	2		885	1126	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135392	30135392	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	96	462	0	ENST00000331968.5:c.426T>G	p.Phe142Leu	p.F142L	ENST00000331968	NM_002742.2	142	ttT/ttG	3/18	0.279226639241815	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.279226639241815	1		462	540	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348318	89348318	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	225	1062	0	ENST00000301030.4:c.4632C>A	p.Asp1544Glu	p.D1544E	ENST00000301030	NM_001256183.1	1544	gaC/gaA	9/13	0.279226639241815	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.279226639241815	1		1062	1260	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950406	68950406	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	77	545	0	ENST00000288368.4:c.718A>T	p.Thr240Ser	p.T240S	ENST00000288368	NM_024870.2	240	Act/Tct	7/40	NA	2	FACETS	0.795	0.697	0.899			1	INDETERMINATE	1	TRUE	NA	0.279226639241815	2		545	694	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17380450	17380493	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGCTCCGCCAAGGGTTGTGGCCGGCAACCGGCGCCTCAAGGA	CAGGCTCCGCCAAGGGTTGTGGCCGGCAACCGGCGCCTCAAGGA	T	novel	NA	P-0021573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	55	722	0	ENST00000375499.3:c.22_65delinsA	p.Ser8ThrfsTer55	p.S8Tfs*55	ENST00000375499	NM_003000.2	8	TCCTTGAGGCGCCGGTTGCCGGCCACAACCCTTGGCGGAGCCTGc/Ac	1/8	0.279226639241815	1	FACETS	0.406	0.346	0.472	0.406	0.346	0.472	SUBCLONAL	1	TRUE	0	0.279226639241815	1		722	835	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0021574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	134	782	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.211438691482976	5	FACETS	0.94	0.861	1	0.94	0.861	1	CLONAL	4	TRUE	1	0.211438691482976	5		782	444	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864656	37864656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs950730453	NA	P-0021574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	76	801	1	ENST00000269571.5:c.308G>A	p.Arg103Gln	p.R103Q	ENST00000269571		103	cGa/cAa	3/27	0.0726893528004853	4	FACETS	1	0.951	1	0.587	0.514	0.665	INDETERMINATE	1	TRUE	2	0.211438691482976	4		802	742	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690306	117690306	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	36	449	0	ENST00000369458.3:c.823C>G	p.Leu275Val	p.L275V	ENST00000369458	NM_024626.3	275	Ctc/Gtc	5/6	0.210326577390644	2	FACETS	0.959	0.79	1	0.48	0.395	0.574	CLONAL	1	TRUE	0	0.211438691482976	2		449	355	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112035575	112035575	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1159797492	NA	P-0021574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	25	566	0	ENST00000368678.4:c.319G>C	p.Glu107Gln	p.E107Q	ENST00000368678		107	Gaa/Caa	4/13	0.211438691482976	5	FACETS	1	0.832	1	0.532	0.419	0.66	CLONAL	1	TRUE	3	0.211438691482976	5		566	293	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425644	49425644	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057517992	NA	P-0021574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	43	700	0	ENST00000301067.7:c.12844C>T	p.Arg4282Ter	p.R4282*	ENST00000301067	NM_003482.3	4282	Cga/Tga	39/54	0.0726893528004853	4	FACETS	1	0.856	1	0.512	0.428	0.605	INDETERMINATE	1	TRUE	2	0.211438691482976	4		700	481	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199864	138199864	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	56	444	0	ENST00000237289.4:c.1282G>C	p.Glu428Gln	p.E428Q	ENST00000237289	NM_001270507.1	428	Gag/Cag	7/9	0.211438691482976	3	FACETS	1	0.967	1	0.743	0.639	0.856	CLONAL	1	TRUE	1	0.211438691482976	3		444	394	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539885	187539885	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	26	451	1	ENST00000441802.2:c.7855C>A	p.Leu2619Ile	p.L2619I	ENST00000441802	NM_005245.3	2619	Ctt/Att	10/27	0.211438691482976	2	FACETS	0.878	0.697	1	0.439	0.348	0.543	CLONAL	1	TRUE	0	0.211438691482976	2		452	280	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448173	49448173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	56	629	0	ENST00000301067.7:c.427G>A	p.Ala143Thr	p.A143T	ENST00000301067	NM_003482.3	143	Gct/Act	4/54	0.0726893528004853	4	FACETS	1	0.946	1	0.611	0.524	0.706	INDETERMINATE	1	TRUE	2	0.211438691482976	4		629	525	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211836	2211836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	94	672	1	ENST00000398665.3:c.1552G>A	p.Glu518Lys	p.E518K	ENST00000398665	NM_032482.2	518	Gag/Aag	16/28	0.211438691482976	3	FACETS	0.968	0.864	1	0.968	0.864	1	CLONAL	2	TRUE	1	0.211438691482976	3		673	508	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	95	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.413218756573526	2		434	337	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491626	56491626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs576402458	NA	P-0021576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	175	493	0	ENST00000267101.3:c.2518G>A	p.Val840Met	p.V840M	ENST00000267101	NM_001982.3	840	Gtg/Atg	21/28	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.413218756573526	2		493	632	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373151	118373151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	157	486	0	ENST00000534358.1:c.6544G>A	p.Gly2182Ser	p.G2182S	ENST00000534358	NM_005933.3	2182	Ggt/Agt	27/36	0.771069262606805	3	FACETS	0.992	0.913	1	0.496	0.456	0.537	CLONAL	1	TRUE	1	0.771069262606805	3		486	569	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109764	115109764	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	282	941	0	ENST00000257566.3:c.2114C>T	p.Ser705Phe	p.S705F	ENST00000257566	NM_016569.3	705	tCc/tTc	8/8	0.764011463799844	4	FACETS	0.98	0.919	1	0.49	0.459	0.521	CLONAL	1	TRUE	2	0.771069262606805	4		941	1322	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1646408	1646408	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	195	724	0	ENST00000344749.5:c.91A>G	p.Thr31Ala	p.T31A	ENST00000344749	NM_001136139.2	31	Acc/Gcc	3/19	1	2	FACETS	0.863	0.804	0.924	0.863	0.804	0.924	CLONAL	1	TRUE	1	0.771069262606805	2		724	586	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542480	187542480	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763353583	NA	P-0021578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	171	568	0	ENST00000441802.2:c.5260C>T	p.His1754Tyr	p.H1754Y	ENST00000441802	NM_005245.3	1754	Cac/Tac	10/27	0.764011463799844	4	FACETS	0.896	0.824	0.97	0.448	0.412	0.485	CLONAL	1	TRUE	2	0.771069262606805	4		568	877	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0021579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	136	776	1	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.21771034471305	1	FACETS	1	0.918	1	1	0.918	1	INDETERMINATE	1	TRUE	0	0.428410631075262	1		777	497	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481478	140481478	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913371	NA	P-0021579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	167	1104	0	ENST00000288602.6:c.1330C>T	p.Arg444Trp	p.R444W	ENST00000288602	NM_004333.4	444	Cgg/Tgg	11/18	1	2	FACETS	0.867	0.797	0.94	0.867	0.797	0.94	CLONAL	1	TRUE	1	0.428410631075262	2		1104	899	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577507	7577507	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	201	910	0	ENST00000269305.4:c.774A>T	p.Glu258Asp	p.E258D	ENST00000269305	NM_001126112.2	258	gaA/gaT	7/11	0.428410631075262	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.428410631075262	1		910	688	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921551	178921551	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519939	NA	P-0021579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	251	433	0	ENST00000263967.3:c.1033A>C	p.Asn345His	p.N345H	ENST00000263967	NM_006218.2	345	Aat/Cat	5/21	0.417451721483408	4	FACETS	0.908	0.862	0.954	0.908	0.862	0.954	CLONAL	4	TRUE	0	0.428410631075262	4		433	461	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	325	479	0	ENST00000263967.3:c.3132T>G	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaG	21/21	0.417451721483408	4	FACETS	0.939	0.898	0.98	0.939	0.898	0.98	CLONAL	4	TRUE	0	0.428410631075262	4		479	577	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152857996	152857996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557026001	NA	P-0021579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	45	257	0	ENST00000406277.2:c.619G>A	p.Ala207Thr	p.A207T	ENST00000406277	NM_152274.4	207	Gcc/Acc	6/7	0.155742008251209	1	FACETS	0.655	0.555	0.764	0.655	0.555	0.764	INDETERMINATE	1	TRUE	0	0.428410631075262	1		257	252	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0021580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	233	692	2	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.319276889077569	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	1	0.319276889077569	3		694	828	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	134	699	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.319276889077569	3	FACETS	1	0.928	1	0.342	0.31	0.375	CLONAL	1	TRUE	0	0.319276889077569	3		699	949	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101300	27101300	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	144	796	0	ENST00000324856.7:c.4582C>T	p.Arg1528Ter	p.R1528*	ENST00000324856	NM_006015.4	1528	Cga/Tga	18/20	0.319276889077569	2	FACETS	1	0.965	1	0.556	0.507	0.607	CLONAL	1	TRUE	0	0.319276889077569	2		796	811	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771312	68771336	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	GCCAGCCATGGGCCCTTGGAGCCGC	GCCAGCCATGGGCCCTTGGAGCCGC	CCGG	novel	NA	P-0021580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	453	167	2	ENST00000261769.5:c.-7_18delinsCCGG		p.*3*	ENST00000261769	NM_004360.3	?-6/882		1/16	0.319276889077569	2	FACETS	0.896	0.863	0.929	1	0.997	1	CLONAL	4	TRUE	0	0.319276889077569	2		169	792	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350621	89350621	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs886041760	NA	P-0021580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1217	239	1334	0	ENST00000301030.4:c.2329G>T	p.Glu777Ter	p.E777*	ENST00000301030	NM_001256183.1	777	Gag/Tag	9/13	0.319276889077569	2	FACETS	1	0.952	1	0.514	0.478	0.551	CLONAL	1	TRUE	0	0.319276889077569	2		1334	1456	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905929	50905929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11550555	NA	P-0021580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	178	993	1	ENST00000440232.2:c.901G>A	p.Glu301Lys	p.E301K	ENST00000440232	NM_002691.3	301	Gaa/Aaa	8/27	0.309530582515682	4	FACETS	1	0.953	1	0.526	0.484	0.571	CLONAL	1	TRUE	2	0.319276889077569	4		994	1397	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252865	36252866	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGG	novel	NA	P-0021580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	151	493	0	ENST00000300305.3:c.496_497insCCC	p.Gly165_Arg166insPro	p.G165_R166insP	ENST00000300305		166	cga/cCCCga	4/8	0.319276889077569	3	FACETS	0.848	0.777	0.921	0.848	0.777	0.921	CLONAL	2	TRUE	1	0.319276889077569	3		493	647	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957014	1957014	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	128	700	2	ENST00000382891.5:c.2465G>A	p.Gly822Glu	p.G822E	ENST00000382891	NM_133335.3	822	gGg/gAg	13/22	NA	2	FACETS	1	0.928	1			1	INDETERMINATE	1	TRUE	NA	0.319276889077569	2		702	780	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	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	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.33	2		434	427	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193530	99193530	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	104	669	0	ENST00000074304.5:c.2725G>C	p.Glu909Gln	p.E909Q	ENST00000074304	NM_001134224.1	909	Gag/Cag	25/26	1	2	FACETS	0.883	0.791	0.98	0.883	0.791	0.98	CLONAL	1	TRUE	1	0.33	2		669	714	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287230	46287245	+	frameshift_variant	Frame_Shift_Del	DEL	AACTCCTAGAGCACAA	AACTCCTAGAGCACAA	-	novel	NA	P-0021582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	57	492	0	ENST00000334344.6:c.5177_5192del	p.Thr1726ArgfsTer4	p.T1726Rfs*4	ENST00000334344	NM_152641.2	1725	tcAACTCCTAGAGCACAA/tc	19/21	1	2	FACETS	0.785	0.675	0.905	0.785	0.675	0.905	CLONAL	1	TRUE	1	0.33	2		492	440	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470914	25470914	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	118	719	0	ENST00000264709.3:c.847G>C	p.Glu283Gln	p.E283Q	ENST00000264709	NM_175629.2	283	Gag/Cag	7/23	1	2	FACETS	0.926	0.836	1	0.926	0.836	1	CLONAL	1	TRUE	1	0.33	2		719	772	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879279	151879279	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0021582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	68	559	0	ENST00000262189.6:c.5666C>G	p.Ser1889Ter	p.S1889*	ENST00000262189	NM_170606.2	1889	tCa/tGa	36/59	1	2	FACETS	0.866	0.755	0.985	0.866	0.755	0.985	CLONAL	1	TRUE	1	0.33	2		559	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0021583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	64	875	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.14	2		877	738	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0021583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	36	1047	2	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	0.14	2		1049	506	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0021583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	14	379	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.69	0.498	0.923	0.69	0.498	0.923	SUBCLONAL	1	TRUE	1	0.14	2		379	290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0021585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	664	715	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.879655571769024	2	FACETS	0.988	0.971	1	0.988	0.971	1	CLONAL	2	TRUE	0	0.879655571769024	2		716	764	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857307	68857307	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs971882211	NA	P-0021585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	169	424	1	ENST00000261769.5:c.1942G>T	p.Glu648Ter	p.E648*	ENST00000261769	NM_004360.3	648	Gaa/Taa	13/16	0.879655571769024	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.879655571769024	1		425	201	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063666	67063685	+	frameshift_variant	Frame_Shift_Del	DEL	GAACGCCAGGCACGCTTCCA	GAACGCCAGGCACGCTTCCA	-	novel	NA	P-0021585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	176	583	0	ENST00000412916.2:c.122_141del	p.Gln41LeufsTer35	p.Q41Lfs*35	ENST00000412916		39	GAACGCCAGGCACGCTTCCAg/g	2/6	0.879655571769024	1	FACETS	0.919	0.874	0.961	0.919	0.874	0.961	CLONAL	1	TRUE	0	0.879655571769024	1		583	244	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676254	29676263	+	frameshift_variant	Frame_Shift_Del	DEL	GTGGCCTACT	GTGGCCTACT	CC	novel	NA	P-0021585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	274	502	1	ENST00000356175.3:c.7243_7252delinsCC	p.Val2415ProfsTer9	p.V2415Pfs*9	ENST00000356175	NM_000267.3	2415	GTGGCCTACTta/CCta	48/57	0.879655571769024	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.879655571769024	2		503	311	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910306	50910306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1341055535	NA	P-0021585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	345	929	2	ENST00000440232.2:c.1561C>T	p.Arg521Trp	p.R521W	ENST00000440232	NM_002691.3	521	Cgg/Tgg	13/27	0.702481156097461	3	FACETS	1	0.963	1			1	CLONAL	1	TRUE	NA	0.879655571769024	3		931	1107	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119595305	119595306	+	stop_gained	Nonsense_Mutation	DNP	GT	GT	TC	novel	NA	P-0021585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	127	507	3	ENST00000316626.5:c.863_864delinsGA	p.Tyr288Ter	p.Y288*	ENST00000316626		288	tAC/tGA	8/12	0.863955649151837	3	FACETS	0.815	0.742	0.891	0.408	0.371	0.446	CLONAL	1	TRUE	1	0.879655571769024	3		510	510	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127951955	127951955	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	350	855	0	ENST00000373547.4:c.43del	p.Leu15CysfsTer10	p.L15Cfs*10	ENST00000373547	NM_002721.4	15	Ctg/tg	1/7	1	2	FACETS	0.95	0.904	0.996	0.95	0.904	0.996	CLONAL	1	TRUE	1	0.879655571769024	2		855	838	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934874	NA	P-0021588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	884	1112	1	ENST00000269305.4:c.451C>G	p.Pro151Ala	p.P151A	ENST00000269305	NM_001126112.2	151	Ccc/Gcc	5/11	0.755914939610161	3	FACETS	0.989	0.972	1	0.989	0.972	1	CLONAL	3	TRUE	0	0.763616023195383	3		1113	1078	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061707	38061707	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1268419156	NA	P-0021588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	161	535	1	ENST00000250448.2:c.282C>A	p.Asn94Lys	p.N94K	ENST00000250448	NM_004496.3	94	aaC/aaA	2/2	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.763616023195383	2		536	369	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395746	45395746	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	150	555	1	ENST00000262160.6:c.388C>T	p.Arg130Ter	p.R130*	ENST00000262160	NM_005901.5	130	Cga/Tga	4/11	0.725141856166919	4	FACETS	0.829	0.758	0.903	0.276	0.252	0.301	CLONAL	1	TRUE	1	0.763616023195383	4		556	836	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860384	42860384	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	240	908	0	ENST00000398585.3:c.493A>C	p.Asn165His	p.N165H	ENST00000398585	NM_001135099.1	165	Aac/Cac	5/14	0.761411187759147	3	FACETS	1	0.944	1	0.504	0.472	0.538	CLONAL	1	TRUE	1	0.763616023195383	3		908	861	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15809050	15809114	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTCCAGCCACAAAAAGTACAGGGCCGCCCTGAAGAAGGAGAAACGAAAGAAACGTCGGCAGGAA	CTTCCAGCCACAAAAAGTACAGGGCCGCCCTGAAGAAGGAGAAACGAAAGAAACGTCGGCAGGAA	-	novel	NA	P-0021588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	43	569	0	ENST00000307771.7:c.42-4_102del		p.X14_splice	ENST00000307771	NM_005089.3	14		2/11	NA	2	FACETS	0.191	0.159	0.227			1	INDETERMINATE	1	TRUE	NA	0.763616023195383	2		569	589	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	168	669	0				ENST00000310581	NM_198253.2	-/1132			0.253782832709757	4	FACETS	0.882	0.814	0.952	0.882	0.814	0.952	CLONAL	2	TRUE	2	0.41463493803803	4		669	650	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906553	32906553	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	63	417	0	ENST00000380152.3:c.938C>G	p.Ser313Cys	p.S313C	ENST00000380152		313	tCt/tGt	10/27	0.41463493803803	3	FACETS	0.725	0.628	0.83	0.242	0.209	0.277	SUBCLONAL	1	TRUE	0	0.41463493803803	3		417	506	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40739825	40739825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759851333	NA	P-0021590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	301	937	2	ENST00000392038.2:c.1400G>A	p.Arg467Gln	p.R467Q	ENST00000392038	NM_001626.4	467	cGg/cAg	14/14	0.253782832709757	4	FACETS	0.787	0.74	0.835	0.787	0.74	0.835	SUBCLONAL	2	TRUE	2	0.41463493803803	4		939	1305	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0021591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	443	1047	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.158722817866756	5	FACETS	1	0.981	1	1	0.995	1	CLONAL	4	TRUE	2	0.244133184600821	5		1049	1183	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0021591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	301	1043	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.0781506630850097	4	FACETS	0.937	0.883	0.993			1	INDETERMINATE	3	TRUE	NA	0.244133184600821	4		1044	1091	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0021591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	146	624	1	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.162996907973187	2	FACETS	0.963	0.882	1	0.963	0.882	1	CLONAL	2	TRUE	0	0.244133184600821	2		625	621	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411246	63411246	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	163	826	3	ENST00000330258.3:c.1921C>T	p.Arg641Ter	p.R641*	ENST00000330258	NM_152424.3	641	Cga/Tga	2/2	0.0764667091325448	4	FACETS	0.823	0.755	0.895	0.823	0.755	0.895	INDETERMINATE	2	TRUE	2	0.244133184600821	4		829	1009	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867540	35867541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs869312857	NA	P-0021592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	116	442	0	ENST00000303115.3:c.361dup	p.Ile121AsnfsTer8	p.I121Nfs*8	ENST00000303115	NM_002185.3	118	-/A	3/8	1	2	FACETS	0.909	0.828	0.992	0.909	0.828	0.992	CLONAL	1	TRUE	1	0.703389439947706	2		442	363	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380338	14380339	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCCCACGCC	novel	NA	P-0021592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	342	474	1	ENST00000256196.4:c.70_78dup	p.Gly24_Gly26dup	p.G24_G26dup	ENST00000256196		24	-/GGCGTGGGC	1/6	0.667826506743654	2	FACETS	0.844	0.809	0.879	0.844	0.809	0.879	CLONAL	2	TRUE	0	0.703389439947706	2		475	576	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101002	27101002	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0021592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	268	817	0	ENST00000324856.7:c.4284C>G	p.Tyr1428Ter	p.Y1428*	ENST00000324856	NM_006015.4	1428	taC/taG	18/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.703389439947706	2		817	732	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106607	27106607	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	484	722	0	ENST00000324856.7:c.6218T>C	p.Leu2073Pro	p.L2073P	ENST00000324856	NM_006015.4	2073	cTa/cCa	20/20	0.257919698025699	5	FACETS	0.997	0.959	1			1	INDETERMINATE	3	TRUE	NA	0.703389439947706	5		722	946	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2206768	2206770	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0021592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	197	710	1	ENST00000398665.3:c.829_831del	p.Phe277del	p.F277del	ENST00000398665	NM_032482.2	276	aaCTTc/aac	10/28	0.357356715239975	1	FACETS	0.51	0.474	0.547	0.51	0.474	0.547	INDETERMINATE	1	TRUE	0	0.703389439947706	1		711	712	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061211	38061240	+	inframe_deletion	In_Frame_Del	DEL	AGTAGCAGCCGTTCTCGAACATGTTGCCGG	AGTAGCAGCCGTTCTCGAACATGTTGCCGG	-	novel	NA	P-0021594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	447	621	0	ENST00000250448.2:c.749_778del	p.Ser250_Tyr259del	p.S250_Y259del	ENST00000250448	NM_004496.3	250	tCCGGCAACATGTTCGAGAACGGCTGCTACTtg/ttg	2/2	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.691824642081939	2		621	962	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076782	72076782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373419972	NA	P-0021594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	307	712	0	ENST00000357731.5:c.715C>T	p.Arg239Cys	p.R239C	ENST00000357731	NM_173808.2	239	Cgc/Tgc	5/7	1	2	FACETS	0.984	0.93	1	0.984	0.93	1	CLONAL	1	TRUE	1	0.691824642081939	2		712	902	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162171	47162171	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs200956000	NA	P-0021594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	238	506	0	ENST00000409792.3:c.3955G>T	p.Val1319Leu	p.V1319L	ENST00000409792	NM_014159.6	1319	Gtg/Ttg	3/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.691824642081939	2		506	664	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	84	669	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.263977370730761	2		669	605	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192042	108192042	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	73	577	0	ENST00000278616.4:c.6467A>G	p.Glu2156Gly	p.E2156G	ENST00000278616	NM_000051.3	2156	gAa/gGa	45/63	1	2	FACETS	0.92	0.805	1	0.92	0.805	1	CLONAL	1	TRUE	1	0.263977370730761	2		577	601	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947576	48947576	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	94	631	1	ENST00000267163.4:c.1166del	p.Leu389Ter	p.L389*	ENST00000267163	NM_000321.2	388	aTt/at	12/27	0.263977370730761	1	FACETS	0.974	0.867	1	0.974	0.867	1	CLONAL	1	TRUE	0	0.263977370730761	1		632	635	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578470	7578470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852789	NA	P-0021595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	172	831	1	ENST00000269305.4:c.460G>A	p.Gly154Ser	p.G154S	ENST00000269305	NM_001126112.2	154	Ggc/Agc	5/11	0.263977370730761	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.263977370730761	1		832	896	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622252	162622252	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs781548251	NA	P-0021595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	53	469	0	ENST00000366898.1:c.445T>C	p.Tyr149His	p.Y149H	ENST00000366898	NM_004562.2	149	Tat/Cat	4/12	1	2	FACETS	0.717	0.611	0.833	0.717	0.611	0.833	SUBCLONAL	1	TRUE	1	0.263977370730761	2		469	560	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202220	108202220	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	434	572	0	ENST00000278616.4:c.7565A>C	p.Gln2522Pro	p.Q2522P	ENST00000278616	NM_000051.3	2522	cAa/cCa	51/63	0.794673582852081	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.791698918532798	4		572	943	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707970	47707970	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	432	578	0	ENST00000233146.2:c.2594T>G	p.Ile865Ser	p.I865S	ENST00000233146	NM_000251.2	865	aTc/aGc	15/16	0.794673582852081	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.791698918532798	2		578	545	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274655	198274655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1169	266	556	0	ENST00000335508.6:c.743C>T	p.Thr248Ile	p.T248I	ENST00000335508	NM_012433.2	248	aCc/aTc	7/25	0.669796324132028	6	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.791698918532798	6		556	1435	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0021600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	26	487	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	0.0320345662359514	3	FACETS	0.668	0.528	0.827	0.334	0.264	0.414	INDETERMINATE	1	TRUE	1	0.22	3		487	393	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0021600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	41	509	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.0320345662359514	3	FACETS	0.784	0.652	0.93	0.392	0.326	0.465	INDETERMINATE	1	TRUE	1	0.22	3		509	528	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	38	932	2	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.576	0.475	0.689	0.576	0.475	0.689	SUBCLONAL	1	TRUE	1	0.22	2		934	600	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900984	114900984	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778855667	NA	P-0021600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	47	753	2	ENST00000543371.1:c.598del	p.Leu200SerfsTer25	p.L200Sfs*25	ENST00000543371	NM_001198531.1	198	caC/ca	6/14	0.243455902537133	0	FACETS	0.736	0.621	0.862			1	SUBCLONAL	1	TRUE	0	0.22	0		755	453	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864309	117864309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301282588	NA	P-0021600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	43	531	0	ENST00000297338.2:c.1348C>T	p.Arg450Cys	p.R450C	ENST00000297338	NM_006265.2	450	Cgc/Tgc	11/14	0.0532209412676845	4	FACETS	1	0.908	1	0.564	0.472	0.665	INDETERMINATE	1	TRUE	2	0.22	4		531	423	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943348	17943348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148688786	NA	P-0021600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	58	809	0	ENST00000458235.1:c.2660G>A	p.Arg887His	p.R887H	ENST00000458235	NM_000215.3	887	cGt/cAt	19/24	0.126335868181594	5	FACETS	0.957	0.821	1			1	INDETERMINATE	1	TRUE	NA	0.22	5		809	733	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257169	19257169	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	37	756	0	ENST00000162023.5:c.794C>T	p.Pro265Leu	p.P265L	ENST00000162023		265	cCg/cTg	12/13	1	2	FACETS	0.793	0.654	0.949	0.793	0.654	0.949	CLONAL	1	TRUE	1	0.22	2		756	424	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368388	225368388	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1366667901	NA	P-0021600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	41	687	0	ENST00000264414.4:c.1358del	p.Asn453ThrfsTer2	p.N453Tfs*2	ENST00000264414	NM_003590.4	453	aAc/ac	9/16	1	2	FACETS	0.664	0.553	0.789	0.664	0.553	0.789	SUBCLONAL	1	TRUE	1	0.22	2		687	561	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428478	78428478	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	34	663	0	ENST00000370768.2:c.1321C>T	p.Gln441Ter	p.Q441*	ENST00000370768	NM_003902.3	441	Caa/Taa	14/20	0.0320345662359514	3	FACETS	0.559	0.455	0.676	0.279	0.227	0.338	INDETERMINATE	1	TRUE	1	0.22	3		663	614	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443512	49443512	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	61	698	0	ENST00000301067.7:c.3859del	p.Glu1287ArgfsTer43	p.E1287Rfs*43	ENST00000301067	NM_003482.3	1287	Gag/ag	11/54	0.106119529823898	6	FACETS	1	0.951	1	0.411	0.354	0.473	INDETERMINATE	1	TRUE	3	0.22	6		698	647	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199451	16199451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	22	412	1	ENST00000375759.3:c.224G>A	p.Arg75His	p.R75H	ENST00000375759	NM_015001.2	75	cGc/cAc	2/15	0.126335868181594	5	FACETS	0.643	0.497	0.812			1	INDETERMINATE	1	TRUE	NA	0.22	5		413	414	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692949	89692949	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167627	NA	P-0021600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	75	739	0	ENST00000371953.3:c.437del	p.Leu146Ter	p.L146*	ENST00000371953	NM_000314.4	145	Ttt/tt	5/9	0.0320345662359514	3	FACETS	1	0.909	1	0.523	0.458	0.594	INDETERMINATE	1	TRUE	1	0.22	3		739	723	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195733	102195733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	36	507	0	ENST00000263464.3:c.493G>A	p.Ala165Thr	p.A165T	ENST00000263464	NM_001165.4	165	Gca/Aca	2/9	0.126335868181594	5	FACETS	0.757	0.621	0.91			1	INDETERMINATE	1	TRUE	NA	0.22	5		507	575	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478846	56478846	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs201479792	NA	P-0021600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	53	1008	0	ENST00000267101.3:c.302A>G	p.Asn101Ser	p.N101S	ENST00000267101	NM_001982.3	101	aAc/aGc	3/28	0.106119529823898	6	FACETS	0.691	0.587	0.806	0.23	0.195	0.269	INDETERMINATE	1	TRUE	3	0.22	6		1008	1004	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861906	57861906	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs772813225	NA	P-0021600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	40	679	1	ENST00000228682.2:c.1207C>A	p.Leu403Met	p.L403M	ENST00000228682	NM_005269.2	403	Ctg/Atg	10/12	0.107465275435997	5	FACETS	0.669	0.554	0.797	0.223	0.184	0.266	INDETERMINATE	1	TRUE	2	0.22	5		680	723	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576248	88576248	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	36	592	0	ENST00000360948.2:c.1425G>T	p.Glu475Asp	p.E475D	ENST00000360948	NM_001012338.2	475	gaG/gaT	13/19	0.193373331766177	0	FACETS	0.963	0.796	1			1	CLONAL	1	TRUE	0	0.22	0		592	265	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216758	7216758	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1567615533	NA	P-0021600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	41	574	0	ENST00000380728.2:c.665T>C	p.Leu222Pro	p.L222P	ENST00000380728		222	cTa/cCa	8/11	0.0532209412676845	4	FACETS	0.644	0.535	0.766	0.322	0.267	0.383	INDETERMINATE	1	TRUE	2	0.22	4		574	706	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600020	10600020	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	52	957	0	ENST00000171111.5:c.1556T>C	p.Ile519Thr	p.I519T	ENST00000171111	NM_203500.1	519	aTc/aCc	5/6	1	2	FACETS	0.58	0.492	0.677	0.58	0.492	0.677	SUBCLONAL	1	TRUE	1	0.22	2		957	815	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918795	50918795	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777468034	NA	P-0021600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	60	975	0	ENST00000440232.2:c.2665C>T	p.Arg889Cys	p.R889C	ENST00000440232	NM_002691.3	889	Cgc/Tgc	21/27	1	2	FACETS	0.835	0.719	0.962	0.835	0.719	0.962	CLONAL	1	TRUE	1	0.22	2		975	653	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213366	39213366	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752395541	NA	P-0021600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	59	931	0	ENST00000402219.2:c.3601C>T	p.Arg1201Trp	p.R1201W	ENST00000402219	NM_005633.3	1201	Cgg/Tgg	23/23	0.0569408289040085	3	FACETS	0.821	0.705	0.948			1	INDETERMINATE	1	TRUE	NA	0.22	3		931	725	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484477	57484477	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	45	554	0	ENST00000371085.3:c.658C>T	p.His220Tyr	p.H220Y	ENST00000371085	NM_000516.4	220	Cac/Tac	8/13	1	2	FACETS	0.838	0.705	0.986	0.838	0.705	0.986	CLONAL	1	TRUE	1	0.22	2		554	488	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981468	55981468	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	41	639	0	ENST00000263923.4:c.469C>A	p.Leu157Ile	p.L157I	ENST00000263923	NM_002253.2	157	Ctc/Atc	4/30	0.3	1	FACETS	0.71	0.592	0.842	0.71	0.592	0.842	SUBCLONAL	1	TRUE	0	0.22	1		639	467	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539320	187539320	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761430021	NA	P-0021600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	34	549	0	ENST00000441802.2:c.8420C>T	p.Pro2807Leu	p.P2807L	ENST00000441802	NM_005245.3	2807	cCg/cTg	10/27	0.243455902537133	0	FACETS	0.886	0.728	1			1	CLONAL	1	TRUE	0	0.22	0		549	272	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961132	79961132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372073889	NA	P-0021600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	69	788	1	ENST00000265081.6:c.529G>A	p.Ala177Thr	p.A177T	ENST00000265081	NM_002439.4	177	Gca/Aca	3/24	0.0532209412676845	4	FACETS	1	0.948	1	0.59	0.513	0.672	INDETERMINATE	1	TRUE	2	0.22	4		789	649	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939072	131939072	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141989813	NA	P-0021600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	64	628	0	ENST00000265335.6:c.2288G>A	p.Arg763His	p.R763H	ENST00000265335		763	cGc/cAc	14/25	0.0532209412676845	4	FACETS	1	0.971	1	0.749	0.65	0.856	INDETERMINATE	1	TRUE	2	0.22	4		628	474	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524649	176524650	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0021600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	52	875	0	ENST00000292408.4:c.2385dup	p.Phe796LeufsTer18	p.F796Lfs*18	ENST00000292408	NM_213647.1	794	ttc/ttCc	18/18	1	2	FACETS	0.914	0.779	1	0.914	0.779	1	CLONAL	1	TRUE	1	0.22	2		875	517	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976766	2976766	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1562490836	NA	P-0021600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	73	1100	2	ENST00000396946.4:c.1246G>A	p.Glu416Lys	p.E416K	ENST00000396946	NM_032415.4	416	Gag/Aag	9/25	1	2	FACETS	0.958	0.837	1	0.958	0.837	1	CLONAL	1	TRUE	1	0.22	2		1102	693	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737786	145737786	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1366657913	NA	P-0021600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	44	899	0	ENST00000428558.2:c.3044A>G	p.Glu1015Gly	p.E1015G	ENST00000428558	NM_004260.3	1015	gAg/gGg	18/22	NA	2	FACETS	0.759	0.636	0.895			1	INDETERMINATE	1	TRUE	NA	0.22	2		899	527	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232134	98232134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199523893	NA	P-0021600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	47	525	1	ENST00000331920.6:c.1808G>A	p.Arg603His	p.R603H	ENST00000331920	NM_000264.3	603	cGc/cAc	13/24	1	2	FACETS	0.971	0.82	1	0.971	0.82	1	CLONAL	1	TRUE	1	0.22	2		526	440	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932084	39932084	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	47	415	0	ENST00000378444.4:c.2515A>G	p.Lys839Glu	p.K839E	ENST00000378444	NM_001123385.1	839	Aag/Gag	4/15	0.0569408289040085	2	FACETS	1	0.953	1			1	INDETERMINATE	1	TRUE	NA	0.22	2		415	316	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913140	44913140	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	41	465	0	ENST00000377967.4:c.815A>T	p.Tyr272Phe	p.Y272F	ENST00000377967	NM_021140.2	272	tAt/tTt	10/29	0.0569408289040085	2	FACETS	1	0.863	1			1	INDETERMINATE	1	TRUE	NA	0.22	2		465	359	SUCCESS
AR	367	MSKCC	GRCh37	X	66937356	66937356	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	61	386	0	ENST00000374690.3:c.2210T>C	p.Val737Ala	p.V737A	ENST00000374690	NM_000044.3	737	gTc/gCc	5/8	0.28674548131608	0	FACETS	0.949	0.829	1			1	CLONAL	2	TRUE	NA	0.22	0		386	228	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347844	70347844	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	56	425	0	ENST00000374080.3:c.3083A>G	p.Asn1028Ser	p.N1028S	ENST00000374080		1028	aAc/aGc	22/45	0.0569408289040085	2	FACETS	1	0.955	1			1	INDETERMINATE	1	TRUE	NA	0.22	2		425	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0021601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	385	1157	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.473246263461243	3	FACETS	0.917	0.873	0.961	0.917	0.873	0.961	CLONAL	2	TRUE	1	0.492920796267164	3		1157	1062	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577573	7577573	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0021601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	186	724	0	ENST00000269305.4:c.708C>G	p.Tyr236Ter	p.Y236*	ENST00000269305	NM_001126112.2	236	taC/taG	7/11	0.473246263461243	3	FACETS	0.961	0.887	1	0.48	0.443	0.519	CLONAL	1	TRUE	1	0.492920796267164	3		724	979	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121729	108121729	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs865985297	NA	P-0021601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	117	683	0	ENST00000278616.4:c.1537C>T	p.Gln513Ter	p.Q513*	ENST00000278616	NM_000051.3	513	Cag/Tag	10/63	0.455497133386123	2	FACETS	0.82	0.742	0.902	0.41	0.371	0.451	CLONAL	1	TRUE	0	0.492920796267164	2		683	579	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920369	134920369	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	139	620	0	ENST00000398015.3:c.2184C>G	p.Ile728Met	p.I728M	ENST00000398015	NM_004441.4	728	atC/atG	12/16	0.492920796267164	4	FACETS	0.856	0.778	0.937	0.285	0.259	0.313	CLONAL	1	TRUE	1	0.492920796267164	4		620	984	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171564	32171564	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	342	763	0	ENST00000375023.3:c.3214A>T	p.Ile1072Phe	p.I1072F	ENST00000375023	NM_004557.3	1072	Atc/Ttc	20/30	0.492920796267164	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.492920796267164	2		763	678	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38184352	38184352	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	124	598	0	ENST00000317025.8:c.1604T>G	p.Ile535Arg	p.I535R	ENST00000317025	NM_023034.1	535	aTa/aGa	7/24	0.492920796267164	1	FACETS	0.922	0.842	1	0.922	0.842	1	CLONAL	1	TRUE	0	0.492920796267164	1		598	411	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401825	139401825	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866251951	NA	P-0021601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	2550	928	1	ENST00000277541.6:c.3575G>T	p.Cys1192Phe	p.C1192F	ENST00000277541	NM_017617.3	1192	tGc/tTc	22/34	0.492920796267164	10	FACETS	1	0.998	1	1	0.998	1	CLONAL	10	TRUE	0	0.492920796267164	10		929	2972	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	788	916	0	ENST00000269305.4:c.517G>C	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ctg	5/11	0.505881206526127	4	FACETS	1	0.992	1			1	CLONAL	4	TRUE	NA	0.577338892422544	4		916	1046	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0021610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	309	600	10	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	0.577433877238976	4	FACETS	0.925	0.874	0.976	0.616	0.583	0.651	CLONAL	2	TRUE	1	0.577338892422544	4		610	913	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939536	71939536	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	268	1107	0	ENST00000298229.2:c.391G>C	p.Ala131Pro	p.A131P	ENST00000298229	NM_001567.3	131	Gcc/Ccc	3/28	0.577433877238976	2	FACETS	1	0.974	1	0.532	0.5	0.564	CLONAL	1	TRUE	0	0.577338892422544	2		1107	873	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949108	71949108	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs765003632	NA	P-0021610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	185	754	1	ENST00000298229.2:c.3575G>C	p.Arg1192Pro	p.R1192P	ENST00000298229	NM_001567.3	1192	cGg/cCg	27/28	0.577433877238976	2	FACETS	1	0.962	1	0.527	0.489	0.566	CLONAL	1	TRUE	0	0.577338892422544	2		755	608	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879842	37879842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	168	783	0	ENST00000269571.5:c.2137C>T	p.Arg713Trp	p.R713W	ENST00000269571		713	Cgg/Tgg	18/27	0.577338892422544	6	FACETS	0.947	0.868	1			1	CLONAL	1	TRUE	NA	0.577338892422544	6		783	1324	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220027	5220027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202004674	NA	P-0021610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	240	847	0	ENST00000357368.4:c.3688G>A	p.Gly1230Ser	p.G1230S	ENST00000357368	NM_002850.3	1230	Ggc/Agc	22/38	0.577433877238976	3	FACETS	1	0.977	1	0.547	0.511	0.584	CLONAL	1	TRUE	1	0.577338892422544	3		847	979	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158476	26158476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776467875	NA	P-0021610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	180	848	4	ENST00000289316.2:c.79G>A	p.Gly27Arg	p.G27R	ENST00000289316	NM_138720.2	27	Ggg/Agg	1/2	0.429949756713036	4	FACETS	1	0.956	1	0.526	0.485	0.569	CLONAL	1	TRUE	2	0.577338892422544	4		852	935	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800591	32800591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1453357528	NA	P-0021610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1173	432	858	0	ENST00000374899.4:c.956G>A	p.Arg319Gln	p.R319Q	ENST00000374899	NM_018833.2	319	cGg/cAg	6/12	0.577338892422544	6	FACETS	1	0.956	1			1	CLONAL	2	TRUE	NA	0.577338892422544	6		858	1605	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468041	50468041	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	123	505	0	ENST00000331340.3:c.1276C>A	p.Leu426Met	p.L426M	ENST00000331340	NM_006060.4	426	Ctg/Atg	8/8	0.577433877238976	3	FACETS	1	0.952	1	0.537	0.488	0.588	CLONAL	1	TRUE	1	0.577338892422544	3		505	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0021619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	77	1034	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.19	2		1037	718	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024989	31024989	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	47	625	0	ENST00000375687.4:c.4474A>T	p.Met1492Leu	p.M1492L	ENST00000375687	NM_015338.5	1492	Atg/Ttg	13/13	1	2	FACETS	0.856	0.722	1	0.856	0.722	1	CLONAL	1	TRUE	1	0.19	2		625	578	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409160	31409161	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	A	novel	NA	P-0021619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	30	610	0	ENST00000344624.3:c.3854+2dup		p.X1285_splice	ENST00000344624		1285			1	2	FACETS	0.566	0.455	0.693	0.566	0.455	0.693	SUBCLONAL	1	TRUE	1	0.19	2		610	558	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627744	37627744	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	109	1263	0	ENST00000447079.4:c.1661del	p.Leu554CysfsTer56	p.L554Cfs*56	ENST00000447079	NM_015083.1	553	ccT/cc	2/14	1	2	FACETS	0.989	0.886	1	0.989	0.886	1	CLONAL	1	TRUE	1	0.2	2		1263	1102	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061221	38061232	+	inframe_deletion	In_Frame_Del	DEL	GTTCTCGAACAT	GTTCTCGAACAT	-	novel	NA	P-0021620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	61	895	0	ENST00000250448.2:c.757_768del	p.Met253_Asn256del	p.M253_N256del	ENST00000250448	NM_004496.3	253	ATGTTCGAGAAC/-	2/2	1	2	FACETS	0.873	0.752	1	0.873	0.752	1	CLONAL	1	TRUE	1	0.2	2		895	699	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37055943	37055943	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	60	666	0	ENST00000231790.2:c.698G>A	p.Cys233Tyr	p.C233Y	ENST00000231790	NM_000249.3	233	tGt/tAt	9/19	1	2	FACETS	0.976	0.84	1	0.976	0.84	1	CLONAL	1	TRUE	1	0.2	2		666	615	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627446	37627452	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAATC	AAAAATC	-	novel	NA	P-0021620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	89	971	0	ENST00000447079.4:c.1361_1367del	p.Glu454ValfsTer8	p.E454Vfs*8	ENST00000447079	NM_015083.1	454	gAAAAATCt/gt	2/14	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.2	2		971	855	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250264	110250265	+	stop_gained	Nonsense_Mutation	DNP	CG	CG	TC	novel	NA	P-0021620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	49	998	0	ENST00000374672.4:c.410_411delinsGA	p.Ser137Ter	p.S137*	ENST00000374672	NM_004235.4	137	tCG/tGA	3/5	1	2	FACETS	0.593	0.5	0.695	0.593	0.5	0.695	SUBCLONAL	1	TRUE	1	0.2	2		998	827	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149917	202149917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	113	749	0	ENST00000358485.4:c.1358C>T	p.Pro453Leu	p.P453L	ENST00000358485	NM_001080125.1	453	cCg/cTg	8/9	0.342929291788826	1	FACETS	0.963	0.869	1	0.963	0.869	1	CLONAL	1	TRUE	0	0.342929291788826	1		749	567	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350532	15350532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748633137	NA	P-0021621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	176	1054	2	ENST00000263377.2:c.3383C>T	p.Ser1128Leu	p.S1128L	ENST00000263377	NM_058243.2	1128	tCg/tTg	16/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.342929291788826	2		1056	902	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50815298	50815298	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	125	863	1	ENST00000398568.2:c.1651C>T	p.Gln551Ter	p.Q551*	ENST00000398568	NM_001042412.1	551	Cag/Tag	9/18	0.317868090164609	1	FACETS	0.993	0.902	1	0.993	0.902	1	CLONAL	1	TRUE	0	0.342929291788826	1		864	608	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554805	106554806	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGCACCAGCAATCTCAAGACCCACCTGC	novel	NA	P-0021621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	59	569	0	ENST00000369096.4:c.1923_1951dup	p.Arg651ProfsTer34	p.R651Pfs*34	ENST00000369096	NM_001198.3	641	agc/agCAGCACCAGCAATCTCAAGACCCACCTGCc	7/7	1	2	FACETS	0.669	0.576	0.771	0.669	0.576	0.771	SUBCLONAL	1	TRUE	1	0.342929291788826	2		569	514	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	64	250	0	ENST00000304494.5:c.322G>C	p.Asp108His	p.D108H	ENST00000304494	NM_000077.4	108	Gat/Cat	2/3	0.282986543195557	4	FACETS	0.921	0.81	1			1	CLONAL	3	TRUE	NA	0.282986543195557	4		250	210	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0021622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	53	696	0	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.282986543195557	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.282986543195557	1		696	269	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656829	45656829	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	43	600	0	ENST00000407780.3:c.327G>C	p.Gln109His	p.Q109H	ENST00000407780	NM_001283052.1	109	caG/caC	3/7	0.250456939280125	3	FACETS	1	0.903	1	0.552	0.464	0.649	CLONAL	1	TRUE	1	0.282986543195557	3		600	314	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654605	29654605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555533569	NA	P-0021622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	30	282	0	ENST00000356175.3:c.5294C>T	p.Ser1765Leu	p.S1765L	ENST00000356175	NM_000267.3	1765	tCg/tTg	37/57	0.282986543195557	3	FACETS	0.627	0.505	0.765			1	SUBCLONAL	1	TRUE	NA	0.282986543195557	3		282	386	SUCCESS
RET	5979	MSKCC	GRCh37	10	43595988	43595988	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	51	657	0	ENST00000355710.3:c.155A>G	p.Tyr52Cys	p.Y52C	ENST00000355710	NM_020975.4	52	tAc/tGc	2/20	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.282986543195557	2		657	296	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427282	49427282	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	29	430	0	ENST00000301067.7:c.11206C>T	p.Gln3736Ter	p.Q3736*	ENST00000301067	NM_003482.3	3736	Cag/Tag	39/54	0.116155448190577	4	FACETS	1	0.914	1	0.629	0.508	0.764	INDETERMINATE	1	TRUE	2	0.282986543195557	4		430	209	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274055	10274055	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	21	659	0	ENST00000330684.3:c.214C>G	p.Leu72Val	p.L72V	ENST00000330684	NM_001134407.1	72	Ctg/Gtg	2/13	0.282986543195557	0	FACETS	0.429	0.331	0.543			1	SUBCLONAL	1	TRUE	0	0.282986543195557	0		659	248	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913286	NA	P-0021625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	23	813	0	ENST00000263967.3:c.1636C>G	p.Gln546Glu	p.Q546E	ENST00000263967	NM_006218.2	546	Cag/Gag	10/21	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.610162571741685	2		813	65	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	89	634	2	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.610162571741685	2		636	277	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0021625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	82	583	7	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	0.610162571741685	1	FACETS	0.939	0.846	1	0.939	0.846	1	CLONAL	1	TRUE	0	0.610162571741685	1		590	199	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176330	24176330	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1057517825	NA	P-0021625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	219	840	1	ENST00000263121.7:c.1121G>A	p.Arg374Gln	p.R374Q	ENST00000263121	NM_003073.3	374	cGg/cAg	9/9	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.610162571741685	2		841	703	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047314	77047314	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	28	564	0	ENST00000356341.3:c.1230C>A	p.Phe410Leu	p.F410L	ENST00000356341	NM_002576.4	410	ttC/ttA	13/15	1	2	FACETS	0.874	0.714	1	0.874	0.714	1	CLONAL	1	TRUE	1	0.610162571741685	2		564	105	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938748	76938748	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61752457	NA	P-0021625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	21	932	0	ENST00000373344.5:c.2000C>T	p.Pro667Leu	p.P667L	ENST00000373344	NM_000489.3	667	cCg/cTg	9/35	0.610162571741685	4	FACETS	1	0.914	1	0.456	0.36	0.562	CLONAL	1	TRUE	1	0.610162571741685	4		932	81	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612924	228612924	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs750944754	NA	P-0021625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	110	550	1	ENST00000366696.1:c.103G>T	p.Gly35Cys	p.G35C	ENST00000366696	NM_003493.2	35	Ggc/Tgc	1/1	1	2	FACETS	0.869	0.786	0.955	0.869	0.786	0.955	CLONAL	1	TRUE	1	0.610162571741685	2		551	415	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778611	3778668	+	frameshift_variant	Frame_Shift_Del	DEL	TGCATGGCATTCAGGTTCTGCAGGCTGGGCTGCTGGTGCATGCCAGGCTGGGGTTGCA	TGCATGGCATTCAGGTTCTGCAGGCTGGGCTGCTGGTGCATGCCAGGCTGGGGTTGCA	-	novel	NA	P-0021625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	152	706	0	ENST00000262367.5:c.6380_6437del	p.Met2127ArgfsTer19	p.M2127Rfs*19	ENST00000262367	NM_004380.2	2127	aTGCAACCCCAGCCTGGCATGCACCAGCAGCCCAGCCTGCAGAACCTGAATGCCATGCAg/ag	31/31	0.134911999733136	4	FACETS	1	0.95	1	1	0.95	1	INDETERMINATE	2	TRUE	2	0.610162571741685	4		706	388	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81927400	81927400	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0021625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	157	800	2	ENST00000359376.3:c.1072+1G>A		p.X358_splice	ENST00000359376	NM_002661.3	358			0.134911999733136	4	FACETS	1	0.988	1	0.726	0.668	0.785	INDETERMINATE	1	TRUE	2	0.610162571741685	4		802	571	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578467	7578468	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCGGGCG	novel	NA	P-0021625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	168	958	3	ENST00000269305.4:c.455_462dup	p.Thr155ArgfsTer18	p.T155Rfs*18	ENST00000269305	NM_001126112.2	154	-/CGCCCGGC	5/11	0.610162571741685	1	FACETS	0.653	0.603	0.704	0.653	0.603	0.704	SUBCLONAL	1	TRUE	0	0.610162571741685	1		961	586	SUCCESS
APC	324	MSKCC	GRCh37	5	112175700	112175700	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	13	435	0	ENST00000257430.4:c.4409del	p.Ala1470ValfsTer3	p.A1470Vfs*3	ENST00000257430	NM_000038.5	1470	gCt/gt	16/16	1	2	FACETS	1	0.83	1	1	0.83	1	CLONAL	1	TRUE	1	0.610162571741685	2		435	37	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505389	157505389	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	14	566	0	ENST00000346085.5:c.3370G>A	p.Glu1124Lys	p.E1124K	ENST00000346085	NM_020732.3	1124	Gag/Aag	13/20	1	2	FACETS	0.454	0.332	0.598	0.454	0.332	0.598	SUBCLONAL	1	TRUE	1	0.610162571741685	2		566	101	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089654	27089655	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	33	757	0	ENST00000324856.7:c.2612dup	p.Asn871LysfsTer65	p.N871Kfs*65	ENST00000324856	NM_006015.4	870	-/A	8/20	0.407314971194003	1	FACETS	0.226	0.183	0.274	0.226	0.183	0.274	SUBCLONAL	1	TRUE	0	0.445852608614195	1		757	510	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307199	65307199	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	30	834	1	ENST00000342505.4:c.2489A>G	p.Tyr830Cys	p.Y830C	ENST00000342505	NM_002227.2	830	tAt/tGt	18/25	0.389369238041892	1	FACETS	0.182	0.146	0.223	0.182	0.146	0.223	SUBCLONAL	1	TRUE	0	0.445852608614195	1		835	574	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061225	38061238	+	protein_altering_variant	In_Frame_Del	DEL	TCGAACATGTTGCC	TCGAACATGTTGCC	GA	novel	NA	P-0021626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	142	849	3	ENST00000250448.2:c.751_764delinsTC	p.Gly251_Glu255delinsSer	p.G251_E255delinsS	ENST00000250448	NM_004496.3	251	GGCAACATGTTCGAg/TCg	2/2	1	2	FACETS	0.985	0.9	1	0.985	0.9	1	CLONAL	1	TRUE	1	0.445852608614195	2		852	647	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696689	47696689	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	211	831	0	ENST00000347630.2:c.259T>G	p.Tyr87Asp	p.Y87D	ENST00000347630	NM_001007230.1	87	Tac/Gac	5/11	1	2	FACETS	0.943	0.879	1	0.943	0.879	1	CLONAL	1	TRUE	1	0.603836531727352	2		831	741	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149329	61149329	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	135	484	0	ENST00000295025.8:c.1519G>T	p.Gly507Ter	p.G507*	ENST00000295025	NM_002908.2	507	Gga/Tga	11/11	1	2	FACETS	0.933	0.854	1	0.933	0.854	1	CLONAL	1	TRUE	1	0.603836531727352	2		484	479	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735478	40735478	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	203	1030	0	ENST00000373198.4:c.3395T>C	p.Phe1132Ser	p.F1132S	ENST00000373198	NM_133170.3	1132	tTc/tCc	25/32	1	2	FACETS	0.917	0.853	0.983	0.917	0.853	0.983	CLONAL	1	TRUE	1	0.603836531727352	2		1030	733	SUCCESS
APC	324	MSKCC	GRCh37	5	112157641	112157647	+	frameshift_variant	Frame_Shift_Del	DEL	TGAAACT	TGAAACT	-	novel	NA	P-0021627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	227	757	0	ENST00000257430.4:c.1362_1368del	p.Met454IlefsTer11	p.M454Ifs*11	ENST00000257430	NM_000038.5	454	aTGAAACTt/at	11/16	0.53032705018319	1	FACETS	0.91	0.854	0.966	0.91	0.854	0.966	CLONAL	1	TRUE	0	0.603836531727352	1		757	577	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971091	21971116	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCTCCCGGGCAGCGTCGTGCACGG	GCCCTCCCGGGCAGCGTCGTGCACGG	-	novel	NA	P-0021629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	32	482	0	ENST00000304494.5:c.242_267del	p.Pro81LeufsTer30	p.P81Lfs*30	ENST00000304494	NM_000077.4	81	cCCGTGCACGACGCTGCCCGGGAGGGC/c	2/3	0.677498523441049	1	FACETS	0.425	0.351	0.507	0.425	0.351	0.507	SUBCLONAL	1	TRUE	0	0.702341760114898	1		482	139	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0021630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	36	363	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	0.259909458078747	2	FACETS	0.869	0.717	1	0.434	0.358	0.519	CLONAL	1	TRUE	0	0.283904961691899	2		363	292	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0021630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	58	878	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.283904961691899	4	FACETS	1	0.923	1	0.556	0.478	0.64	CLONAL	1	TRUE	2	0.283904961691899	4		878	472	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0021630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	77	733	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.283904961691899	4	FACETS	0.797	0.702	0.897	0.797	0.702	0.897	SUBCLONAL	2	TRUE	2	0.283904961691899	4		733	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519996	NA	P-0021630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	173	961	0	ENST00000269305.4:c.395A>T	p.Lys132Met	p.K132M	ENST00000269305	NM_001126112.2	132	aAg/aTg	5/11	0.259909458078747	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.283904961691899	2		961	557	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805584	46805584	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	120	852	0	ENST00000290295.7:c.372del	p.Thr125LeufsTer154	p.T125Lfs*154	ENST00000290295	NM_006361.5	124	ccC/cc	1/2	0.283904961691899	4	FACETS	0.855	0.773	0.94	0.855	0.773	0.94	CLONAL	2	TRUE	2	0.283904961691899	4		852	635	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604725	48604726	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs377767373	NA	P-0021630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	47	544	0	ENST00000342988.3:c.1549_1550del	p.Ser517HisfsTer9	p.S517Hfs*9	ENST00000342988	NM_005359.5	516	cAG/c	12/12	0.241408403148339	2	FACETS	1	0.943	1	0.62	0.527	0.721	CLONAL	1	TRUE	0	0.283904961691899	2		544	267	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38960080	38960080	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	72	267	0	ENST00000357387.3:c.1852G>A	p.Asp618Asn	p.D618N	ENST00000357387	NM_152756.3	618	Gat/Aat	21/38	0.283904961691899	6	FACETS	0.997	0.881	1	0.747	0.661	0.839	CLONAL	3	TRUE	2	0.283904961691899	6		267	266	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0021632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	248	1034	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.291747259987988	6	FACETS	1	0.959	1	0.841	0.8	0.881	CLONAL	5	FALSE	0	0.443848516999285	6		1037	418	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631632	119631632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759068324	NA	P-0021632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	12	591	1	ENST00000316626.5:c.634C>T	p.Pro212Ser	p.P212S	ENST00000316626		212	Ccc/Tcc	6/12	0.373174441552762	4	FACETS	0.365	0.256	0.498	0.182	0.128	0.249	SUBCLONAL	1	FALSE	2	0.443848516999285	4		592	214	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245381	153245381	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	107	962	0	ENST00000281708.4:c.1810A>G	p.Lys604Glu	p.K604E	ENST00000281708	NM_033632.3	604	Aaa/Gaa	11/12	0.190566897443767	2	FACETS	0.924	0.843	1	0.924	0.843	1	INDETERMINATE	2	FALSE	0	0.443848516999285	2		962	261	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	130	669	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.965	0.889	1	0.965	0.889	1	CLONAL	1	TRUE	1	0.877578031215245	2		669	307	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	100	1011	1	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	0.304	0.271	0.339	0.304	0.271	0.339	SUBCLONAL	1	TRUE	1	0.877578031215245	2		1012	749	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	221	772	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.941	0.884	0.999	0.941	0.884	0.999	CLONAL	1	TRUE	1	0.877578031215245	2		772	535	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665213	138665213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	192	1066	0	ENST00000330315.3:c.352G>A	p.Glu118Lys	p.E118K	ENST00000330315	NM_023067.3	118	Gag/Aag	1/1	1	2	FACETS	0.657	0.61	0.705	0.657	0.61	0.705	SUBCLONAL	1	TRUE	1	0.877578031215245	2		1066	666	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	79	546	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	NA	2	FACETS	0.35	0.308	0.394			1	INDETERMINATE	1	TRUE	NA	0.877578031215245	2		546	515	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247244	153247244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	196	587	0	ENST00000281708.4:c.1558G>A	p.Asp520Asn	p.D520N	ENST00000281708	NM_033632.3	520	Gat/Aat	10/12	1	2	FACETS	0.791	0.737	0.845	0.791	0.737	0.845	SUBCLONAL	1	TRUE	1	0.877578031215245	2		587	565	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	257	1052	0	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.877578031215245	2		1052	549	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370798	55370798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1406469266	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	66	852	1	ENST00000297316.4:c.100G>A	p.Glu34Lys	p.E34K	ENST00000297316	NM_022454.3	34	Gag/Aag	1/2	1	2	FACETS	0.33	0.287	0.376	0.33	0.287	0.376	SUBCLONAL	1	TRUE	1	0.877578031215245	2		853	456	SUCCESS
FH	2271	MSKCC	GRCh37	1	241683007	241683007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	114	641	0	ENST00000366560.3:c.16C>T	p.Arg6Trp	p.R6W	ENST00000366560	NM_000143.3	6	Cgg/Tgg	1/10	0.869566221557622	3	FACETS	0.572	0.516	0.632	0.286	0.258	0.316	SUBCLONAL	1	TRUE	1	0.877578031215245	3		641	653	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774771	73774771	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	148	741	0	ENST00000254810.4:c.316G>A	p.Glu106Lys	p.E106K	ENST00000254810	NM_005324.3	106	Gaa/Aaa	4/4	1	2	FACETS	0.677	0.623	0.734	0.677	0.623	0.734	SUBCLONAL	1	TRUE	1	0.877578031215245	2		741	498	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807890	1807890	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913105	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	188	889	0	ENST00000260795.2:c.1949A>T	p.Lys650Met	p.K650M	ENST00000260795		650	aAg/aTg	13/17	NA	2	FACETS	0.647	0.6	0.695			1	INDETERMINATE	1	TRUE	NA	0.877578031215245	2		889	662	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774148	56774148	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	210	805	2	ENST00000337432.4:c.499G>A	p.Asp167Asn	p.D167N	ENST00000337432	NM_058216.2	167	Gat/Aat	3/9	1	2	FACETS	0.739	0.689	0.789	0.739	0.689	0.789	SUBCLONAL	1	TRUE	1	0.877578031215245	2		807	648	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176686992	176686992	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	173	521	1	ENST00000439151.2:c.4969C>T	p.Arg1657Trp	p.R1657W	ENST00000439151	NM_022455.4	1657	Cgg/Tgg	14/23	1	2	FACETS	0.95	0.885	1	0.95	0.885	1	CLONAL	1	TRUE	1	0.877578031215245	2		522	415	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475599	12475599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	251	650	1	ENST00000287820.6:c.1473G>A	p.Met491Ile	p.M491I	ENST00000287820	NM_015869.4	491	atG/atA	7/7	0.219187992753832	3	FACETS	1	0.988	1	0.6	0.564	0.636	INDETERMINATE	1	TRUE	1	0.877578031215245	3		651	686	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618337	37618337	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	29	303	0	ENST00000447079.4:c.13G>A	p.Glu5Lys	p.E5K	ENST00000447079	NM_015083.1	5	Gag/Aag	1/14	1	2	FACETS	0.253	0.204	0.309	0.253	0.204	0.309	SUBCLONAL	1	TRUE	1	0.877578031215245	2		303	261	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933187	36933187	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	93	874	0	ENST00000361632.4:c.1930G>T	p.Gly644Ter	p.G644*	ENST00000361632		644	Gga/Tga	14/16	1	2	FACETS	0.351	0.313	0.393	0.351	0.313	0.393	SUBCLONAL	1	TRUE	1	0.877578031215245	2		874	603	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608372	43608372	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	94	1207	2	ENST00000355710.3:c.1720G>T	p.Glu574Ter	p.E574*	ENST00000355710	NM_020975.4	574	Gag/Tag	9/20	1	2	FACETS	0.293	0.26	0.327	0.293	0.26	0.327	SUBCLONAL	1	TRUE	1	0.877578031215245	2		1209	732	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852605	63852605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	59	648	1	ENST00000279873.7:c.3383G>A	p.Arg1128Lys	p.R1128K	ENST00000279873	NM_032199.2	1128	aGa/aAa	10/10	1	2	FACETS	0.294	0.253	0.338	0.294	0.253	0.338	SUBCLONAL	1	TRUE	1	0.877578031215245	2		649	458	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127829	64127829	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	186	886	0	ENST00000334205.4:c.322G>A	p.Asp108Asn	p.D108N	ENST00000334205	NM_003942.2	108	Gat/Aat	3/17	1	2	FACETS	0.709	0.658	0.761	0.709	0.658	0.761	SUBCLONAL	1	TRUE	1	0.877578031215245	2		886	598	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189500	94189500	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	218	570	0	ENST00000323929.3:c.1505G>C	p.Arg502Pro	p.R502P	ENST00000323929	NM_005591.3	502	cGt/cCt	14/20	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.877578031215245	2		570	495	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49419998	49419998	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	70	637	0	ENST00000301067.7:c.15751G>T	p.Glu5251Ter	p.E5251*	ENST00000301067	NM_003482.3	5251	Gag/Tag	48/54	1	2	FACETS	0.295	0.257	0.336	0.295	0.257	0.336	SUBCLONAL	1	TRUE	1	0.877578031215245	2		637	541	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420870	49420870	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370465399	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	64	681	0	ENST00000301067.7:c.14879G>A	p.Arg4960Gln	p.R4960Q	ENST00000301067	NM_003482.3	4960	cGa/cAa	48/54	1	2	FACETS	0.257	0.222	0.294	0.257	0.222	0.294	SUBCLONAL	1	TRUE	1	0.877578031215245	2		681	568	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21565530	21565530	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	57	702	0	ENST00000382592.4:c.356G>A	p.Arg119Gln	p.R119Q	ENST00000382592	NM_014572.2	119	cGa/cAa	3/8	1	2	FACETS	0.272	0.233	0.314	0.272	0.233	0.314	SUBCLONAL	1	TRUE	1	0.877578031215245	2		702	478	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923320	26923320	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	108	380	1	ENST00000381527.3:c.315+1G>A		p.X105_splice	ENST00000381527	NM_001260.1	105			1	2	FACETS	0.682	0.618	0.748	0.682	0.618	0.748	SUBCLONAL	1	TRUE	1	0.877578031215245	2		381	361	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81528539	81528539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	46	555	0	ENST00000298171.2:c.218C>T	p.Ser73Phe	p.S73F	ENST00000298171	NM_000369.2	73	tCt/tTt	2/10	0.868680962184866	3	FACETS	0.287	0.242	0.338	0.144	0.121	0.169	SUBCLONAL	1	TRUE	1	0.877578031215245	3		555	525	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023163	33023163	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1216397987	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	144	665	0	ENST00000300177.4:c.272G>A	p.Arg91Gln	p.R91Q	ENST00000300177	NM_001191322.1	91	cGa/cAa	2/2	1	2	FACETS	0.746	0.686	0.807	0.746	0.686	0.807	SUBCLONAL	1	TRUE	1	0.877578031215245	2		665	440	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40679401	40679401	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	173	706	0	ENST00000249776.8:c.479G>C	p.Arg160Thr	p.R160T	ENST00000249776	NM_033286.3	160	aGa/aCa	4/9	1	2	FACETS	0.653	0.604	0.703	0.653	0.604	0.703	SUBCLONAL	1	TRUE	1	0.877578031215245	2		706	604	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000307	42000325	+	frameshift_variant	Frame_Shift_Del	DEL	GGATTTCCCTTTGTTTCTA	GGATTTCCCTTTGTTTCTA	-	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	135	597	0	ENST00000219905.7:c.2329_2347del	p.Phe777GlnfsTer34	p.F777Qfs*34	ENST00000219905	NM_001164273.1	776	GGATTTCCCTTTGTTTCTAgg/gg	7/24	1	2	FACETS	0.789	0.725	0.855	0.789	0.725	0.855	SUBCLONAL	1	TRUE	1	0.877578031215245	2		597	390	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43766883	43766883	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	51	353	0	ENST00000382044.4:c.1168G>C	p.Glu390Gln	p.E390Q	ENST00000382044	NM_001141980.1	390	Gaa/Caa	10/28	1	2	FACETS	0.391	0.334	0.453	0.391	0.334	0.453	SUBCLONAL	1	TRUE	1	0.877578031215245	2		353	297	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618598	37618598	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	70	600	0	ENST00000447079.4:c.274G>C	p.Asp92His	p.D92H	ENST00000447079	NM_015083.1	92	Gac/Cac	1/14	1	2	FACETS	0.313	0.273	0.356	0.313	0.273	0.356	SUBCLONAL	1	TRUE	1	0.877578031215245	2		600	509	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805715	46805715	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	175	832	1	ENST00000290295.7:c.241G>A	p.Gly81Ser	p.G81S	ENST00000290295	NM_006361.5	81	Ggt/Agt	1/2	1	2	FACETS	0.701	0.649	0.754	0.701	0.649	0.754	SUBCLONAL	1	TRUE	1	0.877578031215245	2		833	569	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191188	2191188	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	351	936	1	ENST00000398665.3:c.442A>T	p.Ile148Phe	p.I148F	ENST00000398665	NM_032482.2	148	Att/Ttt	5/28	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.877578031215245	2		937	736	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082388	16082388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767463815	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	250	1029	2	ENST00000281043.3:c.202G>A	p.Ala68Thr	p.A68T	ENST00000281043	NM_005378.4	68	Gcg/Acg	2/3	1	2	FACETS	0.799	0.751	0.848	0.799	0.751	0.848	SUBCLONAL	1	TRUE	1	0.877578031215245	2		1031	713	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39239313	39239313	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	354	869	0	ENST00000402219.2:c.2344A>T	p.Ile782Leu	p.I782L	ENST00000402219	NM_005633.3	782	Ata/Tta	14/23	1	2	FACETS	0.997	0.95	1	0.997	0.95	1	CLONAL	1	TRUE	1	0.877578031215245	2		869	809	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202123070	202123070	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767472565	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	37	478	2	ENST00000358485.4:c.116C>T	p.Ser39Leu	p.S39L	ENST00000358485	NM_001080125.1	39	tCg/tTg	1/9	1	2	FACETS	0.238	0.196	0.284	0.238	0.196	0.284	SUBCLONAL	1	TRUE	1	0.877578031215245	2		480	355	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209101817	209101817	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	205	756	0	ENST00000345146.2:c.1231C>T	p.Gln411Ter	p.Q411*	ENST00000345146	NM_005896.2	411	Cag/Tag	10/10	1	2	FACETS	0.768	0.717	0.821	0.768	0.717	0.821	SUBCLONAL	1	TRUE	1	0.877578031215245	2		756	608	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466842	57466842	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	59	698	1	ENST00000371085.3:c.61G>A	p.Glu21Lys	p.E21K	ENST00000371085	NM_000516.4	21	Gag/Aag	1/13	1	2	FACETS	0.254	0.219	0.293	0.254	0.219	0.293	SUBCLONAL	1	TRUE	1	0.877578031215245	2		699	529	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655413	45655413	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	77	958	0	ENST00000407780.3:c.439C>T	p.His147Tyr	p.H147Y	ENST00000407780	NM_001283052.1	147	Cac/Tac	4/7	NA	2	FACETS	0.275	0.241	0.311			1	INDETERMINATE	1	TRUE	NA	0.877578031215245	2		958	639	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127165	22127165	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	112	587	0	ENST00000215832.6:c.963C>G	p.Asp321Glu	p.D321E	ENST00000215832	NM_002745.4	321	gaC/gaG	7/9	1	2	FACETS	0.566	0.512	0.622	0.566	0.512	0.622	SUBCLONAL	1	TRUE	1	0.877578031215245	2		587	451	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924826	49924826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	50	1038	2	ENST00000296474.3:c.4117G>A	p.Val1373Met	p.V1373M	ENST00000296474	NM_002447.2	1373	Gtg/Atg	20/20	0.219187992753832	3	FACETS	0.204	0.173	0.24	0.102	0.086	0.12	INDETERMINATE	1	TRUE	1	0.877578031215245	3		1040	802	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584476	52584476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	271	726	1	ENST00000394830.3:c.4537G>A	p.Glu1513Lys	p.E1513K	ENST00000394830	NM_018313.4	1513	Gag/Aag	29/30	0.219187992753832	3	FACETS	0.752	0.712	0.792	0.752	0.712	0.792	INDETERMINATE	2	TRUE	1	0.877578031215245	3		727	591	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803117	1803117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1330260382	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	195	943	0	ENST00000260795.2:c.469G>A	p.Glu157Lys	p.E157K	ENST00000260795		157	Gag/Aag	4/17	NA	2	FACETS	0.724	0.674	0.775			1	INDETERMINATE	1	TRUE	NA	0.877578031215245	2		943	614	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807568	1807568	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	222	961	0	ENST00000260795.2:c.1737C>G	p.Phe579Leu	p.F579L	ENST00000260795		579	ttC/ttG	12/17	NA	2	FACETS	0.765	0.716	0.816			1	INDETERMINATE	1	TRUE	NA	0.877578031215245	2		961	661	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156479	55156479	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	166	473	0	ENST00000257290.5:c.2881-1G>C		p.X961_splice	ENST00000257290	NM_006206.4	961			1	2	FACETS	0.998	0.93	1	0.998	0.93	1	CLONAL	1	TRUE	1	0.877578031215245	2		473	379	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971101	55971101	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	237	701	0	ENST00000263923.4:c.1696A>C	p.Ser566Arg	p.S566R	ENST00000263923	NM_002253.2	566	Agc/Cgc	13/30	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.877578031215245	2		701	530	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86681180	86681180	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	163	522	0	ENST00000274376.6:c.2821G>A	p.Ala941Thr	p.A941T	ENST00000274376	NM_002890.2	941	Gca/Aca	22/25	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.877578031215245	2		522	371	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652083	36652099	+	frameshift_variant	Frame_Shift_Del	DEL	CGGGGCCTTGGCCTGCC	CGGGGCCTTGGCCTGCC	-	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	278	894	0	ENST00000244741.5:c.206_222del	p.Arg69GlnfsTer14	p.R69Qfs*14	ENST00000244741	NM_000389.4	69	CGGGGCCTTGGCCTGCCc/c	2/3	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.877578031215245	2		894	628	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268026	55268026	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886026	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	220	782	0	ENST00000275493.2:c.2866G>A	p.Asp956Asn	p.D956N	ENST00000275493	NM_005228.3	956	Gat/Aat	24/28	1	2	FACETS	0.927	0.87	0.984	0.927	0.87	0.984	CLONAL	1	TRUE	1	0.877578031215245	2		782	541	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737407	145737407	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	187	870	1	ENST00000428558.2:c.3280G>A	p.Glu1094Lys	p.E1094K	ENST00000428558	NM_004260.3	1094	Gag/Aag	20/22	1	2	FACETS	0.701	0.651	0.752	0.701	0.651	0.752	SUBCLONAL	1	TRUE	1	0.877578031215245	2		871	608	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044518	5044518	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	174	524	0	ENST00000381652.3:c.466C>T	p.Gln156Ter	p.Q156*	ENST00000381652	NM_004972.3	156	Cag/Tag	5/25	1	2	FACETS	0.924	0.861	0.989	0.924	0.861	0.989	CLONAL	1	TRUE	1	0.877578031215245	2		524	429	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760969	133760969	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	301	874	1	ENST00000318560.5:c.3292C>T	p.Gln1098Ter	p.Q1098*	ENST00000318560	NM_005157.4	1098	Cag/Tag	11/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.877578031215245	2		875	657	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563060	21563061	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0021643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	214	889	0	ENST00000382592.4:c.857_858dup	p.Ala287ThrfsTer147	p.A287Tfs*147	ENST00000382592	NM_014572.2	286	-/AC	4/8	0.585325300013205	1	FACETS	0.961	0.901	1	0.961	0.901	1	CLONAL	1	TRUE	0	0.585325300013205	1		889	538	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983148	149983148	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0021643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	136	707	0	ENST00000253339.5:c.3110C>G	p.Ser1037Ter	p.S1037*	ENST00000253339		1037	tCa/tGa	7/7	0.585325300013205	1	FACETS	0.8	0.734	0.867	0.8	0.734	0.867	SUBCLONAL	1	TRUE	0	0.585325300013205	1		707	411	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983157	149983161	+	frameshift_variant	Frame_Shift_Del	DEL	GTTGG	GTTGG	-	novel	NA	P-0021643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	128	722	0	ENST00000253339.5:c.3097_3101del	p.Pro1033ArgfsTer6	p.P1033Rfs*6	ENST00000253339		1033	CCAACa/a	7/7	0.585325300013205	1	FACETS	0.762	0.697	0.829	0.762	0.697	0.829	SUBCLONAL	1	TRUE	0	0.585325300013205	1		722	406	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0021645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	328	824	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.389915999521068	2	FACETS	0.998	0.947	1	0.998	0.947	1	CLONAL	2	TRUE	0	0.389915999521068	2		825	843	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0021645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	63	380	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	1	2	FACETS	0.968	0.842	1	0.968	0.842	1	CLONAL	1	TRUE	1	0.389915999521068	2		380	334	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864388	162864388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368134308	NA	P-0021645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	186	688	1	ENST00000366898.1:c.125G>A	p.Arg42His	p.R42H	ENST00000366898	NM_004562.2	42	cGt/cAt	2/12	0.365729384687086	4	FACETS	0.877	0.812	0.944	0.585	0.541	0.63	CLONAL	2	TRUE	1	0.389915999521068	4		689	756	SUCCESS
APC	324	MSKCC	GRCh37	5	112173271	112173272	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	34	292	0	ENST00000257430.4:c.1981dup	p.Cys661LeufsTer13	p.C661Lfs*13	ENST00000257430	NM_000038.5	660	-/T	16/16	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.389915999521068	2		292	166	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465543	8465543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	114	754	2	ENST00000356435.5:c.3637G>A	p.Gly1213Arg	p.G1213R	ENST00000356435		1213	Gga/Aga	21/35	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.389915999521068	2		756	547	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0021646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	28	692	2	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.244316757668682	4	FACETS	0.699	0.56	0.856	0.35	0.28	0.428	SUBCLONAL	1	TRUE	2	0.398661316288865	4		694	281	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599321	55599321	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913507	NA	P-0021646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	24	551	0	ENST00000288135.5:c.2447A>T	p.Asp816Val	p.D816V	ENST00000288135	NM_000222.2	816	gAc/gTc	17/21	0.235227624745048	2	FACETS	0.185	0.144	0.232	0.092	0.072	0.116	INDETERMINATE	1	TRUE	0	0.398661316288865	2		551	651	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599338	55599338	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	226	506	0	ENST00000288135.5:c.2464A>T	p.Asn822Tyr	p.N822Y	ENST00000288135	NM_000222.2	822	Aat/Tat	17/21	0.235227624745048	2	FACETS	0.904	0.848	0.962	0.904	0.848	0.962	INDETERMINATE	2	TRUE	0	0.398661316288865	2		506	627	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592202	55592202	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	24	491	0	ENST00000288135.5:c.1526A>T	p.Lys509Ile	p.K509I	ENST00000288135	NM_000222.2	509	aAa/aTa	9/21	0.235227624745048	2	FACETS	0.248	0.193	0.311	0.124	0.096	0.156	INDETERMINATE	1	TRUE	0	0.398661316288865	2		491	486	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450270	50450270	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	21	554	0	ENST00000331340.3:c.454G>T	p.Ala152Ser	p.A152S	ENST00000331340	NM_006060.4	152	Gcc/Tcc	5/8	0.265133757936038	3	FACETS	0.425	0.328	0.539	0.213	0.164	0.27	SUBCLONAL	1	TRUE	1	0.398661316288865	3		554	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578234	7578234	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs786202222	NA	P-0021647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	390	733	0	ENST00000269305.4:c.615T>A	p.Tyr205Ter	p.Y205*	ENST00000269305	NM_001126112.2	205	taT/taA	6/11	0.756029684744414	2	FACETS	0.912	0.884	0.94	0.912	0.884	0.94	CLONAL	2	TRUE	0	0.814422059542881	2		733	525	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939436	36939436	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	234	783	1	ENST00000361632.4:c.414C>A	p.Ser138Arg	p.S138R	ENST00000361632		138	agC/agA	4/16	1	2	FACETS	0.967	0.909	1	0.967	0.909	1	CLONAL	1	TRUE	1	0.814422059542881	2		784	594	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696716	47696716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	89	518	0	ENST00000347630.2:c.232G>A	p.Glu78Lys	p.E78K	ENST00000347630	NM_001007230.1	78	Gaa/Aaa	5/11	0.203797993225799	3	FACETS	1	0.978	1	0.728	0.647	0.814	CLONAL	1	TRUE	1	0.25	3		518	550	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0021649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	35	321	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	0.886	0.728	1	0.886	0.728	1	CLONAL	1	TRUE	1	0.25	2		321	316	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0021649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	71	505	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	0.25	2		505	510	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857896	9857896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369878342	NA	P-0021649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	39	719	1	ENST00000330684.3:c.3505C>T	p.Arg1169Trp	p.R1169W	ENST00000330684	NM_001134407.1	1169	Cgg/Tgg	13/13	0.203797993225799	3	FACETS	0.593	0.49	0.708	0.296	0.245	0.354	SUBCLONAL	1	TRUE	1	0.25	3		720	592	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624266	89624268	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0021649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	23	342	0	ENST00000371953.3:c.42_44del	p.Arg15del	p.R15del	ENST00000371953	NM_000314.4	14	AGG/-	1/9	1	2	FACETS	0.479	0.373	0.602	0.479	0.373	0.602	SUBCLONAL	1	TRUE	1	0.25	2		342	384	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692820	89692820	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0021649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	16	281	0	ENST00000371953.3:c.304A>T	p.Lys102Ter	p.K102*	ENST00000371953	NM_000314.4	102	Aaa/Taa	5/9	1	2	FACETS	0.476	0.351	0.624	0.476	0.351	0.624	SUBCLONAL	1	TRUE	1	0.25	2		281	269	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111855999	111855999	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748515476	NA	P-0021649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	87	720	0	ENST00000341259.2:c.50C>T	p.Ala17Val	p.A17V	ENST00000341259	NM_005475.2	17	gCc/gTc	2/8	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.25	2		720	642	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526253	189526253	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	58	678	0	ENST00000264731.3:c.517G>A	p.Gly173Ser	p.G173S	ENST00000264731	NM_003722.4	173	Ggc/Agc	4/14	1	2	FACETS	0.824	0.708	0.951	0.824	0.708	0.951	CLONAL	1	TRUE	1	0.25	2		678	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0021652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	243	899	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.255098276748215	6	FACETS	0.919	0.867	0.971	0.613	0.578	0.648	INDETERMINATE	4	FALSE	0	0.473125206290713	6		900	544	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137779	64137779	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	223	1013	2	ENST00000334205.4:c.1880A>G	p.Lys627Arg	p.K627R	ENST00000334205	NM_003942.2	627	aAa/aGa	15/17	0.473125206290713	6	FACETS	0.939	0.879	1	0.705	0.659	0.751	CLONAL	3	FALSE	2	0.473125206290713	6		1015	651	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88672023	88672023	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	62	527	0	ENST00000372037.3:c.557G>T	p.Arg186Ile	p.R186I	ENST00000372037	NM_004329.2	186	aGa/aTa	8/13	0.473125206290713	5	FACETS	0.972	0.842	1	0.194	0.168	0.223	CLONAL	1	FALSE	0	0.473125206290713	5		527	461	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044465	128044465	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	301	690	3	ENST00000285398.2:c.1156G>T	p.Asp386Tyr	p.D386Y	ENST00000285398	NM_000122.1	386	Gac/Tac	8/15	0.473125206290713	7	FACETS	1	0.987	1	1	0.987	1	CLONAL	4	FALSE	3	0.473125206290713	7		693	624	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050374	37050374	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	35	474	0	ENST00000231790.2:c.526del	p.Ile176PhefsTer26	p.I176Ffs*26	ENST00000231790	NM_000249.3	175	Aaa/aa	6/19	0.472042672957018	5	FACETS	0.676	0.555	0.812	0.169	0.138	0.203	SUBCLONAL	1	FALSE	1	0.473125206290713	5		474	374	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271277	153271277	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs13146842	NA	P-0021652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	60	267	0	ENST00000281708.4:c.502-1G>A		p.X168_splice	ENST00000281708	NM_033632.3	168			0.176499578378244	5	FACETS	1	0.967	1	0.472	0.41	0.539	INDETERMINATE	1	FALSE	2	0.473125206290713	5		267	306	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589156	67589156	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	210	289	0	ENST00000274335.5:c.1147del	p.Ile383TyrfsTer14	p.I383Yfs*14	ENST00000274335		382	Aaa/aa	9/15	0.473125206290713	12	FACETS	1	0.953	1			1	CLONAL	5	FALSE	NA	0.473125206290713	12		289	584	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643348	52643348	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	143	608	1	ENST00000394830.3:c.2548C>T	p.Arg850Ter	p.R850*	ENST00000394830	NM_018313.4	850	Cga/Tga	17/30	0.485637932766025	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	0	0.485637932766025	1		609	322	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443883	52443887	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCT	GCCCT	CCCC	novel	NA	P-0021661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	135	1052	4	ENST00000460680.1:c.8_12delinsGGGG	p.Lys3ArgfsTer69	p.K3Rfs*69	ENST00000460680	NM_004656.3	3	aAGGGC/aGGGG	1/17	0.485637932766025	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	0	0.485637932766025	1		1056	397	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	92	669	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.542578367163492	2		669	319	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690846	89690846	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	43	630	2	ENST00000371953.3:c.253G>T	p.Val85Phe	p.V85F	ENST00000371953	NM_000314.4	85	Gtt/Ttt	4/9	0.542578367163492	1	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	0	0.542578367163492	1		632	109	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508804	29508804	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1060500274	NA	P-0021662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	32	660	1	ENST00000356175.3:c.730+1G>A		p.X244_splice	ENST00000356175	NM_000267.3	244			1	2	FACETS	0.698	0.573	0.835	0.698	0.573	0.835	SUBCLONAL	1	TRUE	1	0.542578367163492	2		661	169	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592358	29592358	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1085307819	NA	P-0021662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	43	700	0	ENST00000356175.3:c.4772+1G>A		p.X1591_splice	ENST00000356175	NM_000267.3	1591			1	2	FACETS	0.751	0.635	0.877	0.751	0.635	0.877	SUBCLONAL	1	TRUE	1	0.542578367163492	2		700	211	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0021663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	155	753	2	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.916	0.842	0.994	0.916	0.842	0.994	CLONAL	1	TRUE	1	0.526154561250843	2		755	643	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979530	7979530	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368323729	NA	P-0021663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	221	762	3	ENST00000319144.4:c.1495C>T	p.Arg499Cys	p.R499C	ENST00000319144	NM_001139.2	499	Cgc/Tgc	11/15	1	2	FACETS	0.992	0.925	1	0.992	0.925	1	CLONAL	1	TRUE	1	0.526154561250843	2		765	847	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100137	27100137	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	214	725	0	ENST00000324856.7:c.3934del	p.Ser1312ProfsTer169	p.S1312Pfs*169	ENST00000324856	NM_006015.4	1311	ccT/cc	16/20	1	2	FACETS	0.984	0.916	1	0.984	0.916	1	CLONAL	1	TRUE	1	0.526154561250843	2		725	827	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521415	8521415	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	261	875	0	ENST00000356435.5:c.823G>T	p.Asp275Tyr	p.D275Y	ENST00000356435		275	Gat/Tat	9/35	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.526154561250843	2		875	972	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748129	41748129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776131193	NA	P-0021664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	52	241	0	ENST00000226382.2:c.640G>A	p.Gly214Ser	p.G214S	ENST00000226382	NM_003924.3	214	Ggc/Agc	3/3	1	2	FACETS	0.797	0.688	0.913	0.797	0.688	0.913	CLONAL	1	TRUE	1	0.646166514709826	2		241	202	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	115	669	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.793828868330964	2		669	223	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888210	112888210	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121918464	NA	P-0021666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	32	814	0	ENST00000351677.2:c.226G>C	p.Glu76Gln	p.E76Q	ENST00000351677	NM_002834.3	76	Gag/Cag	3/16	1	2	FACETS	0.107	0.086	0.131	0.107	0.086	0.131	SUBCLONAL	1	TRUE	1	0.793828868330964	2		814	753	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888210	112888210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121918464	NA	P-0021666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	148	814	0	ENST00000351677.2:c.226G>A	p.Glu76Lys	p.E76K	ENST00000351677	NM_002834.3	76	Gag/Aag	3/16	1	2	FACETS	0.495	0.453	0.54	0.495	0.453	0.54	SUBCLONAL	1	TRUE	1	0.793828868330964	2		814	753	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888198	112888198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121918453	NA	P-0021666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	120	882	0	ENST00000351677.2:c.214G>A	p.Ala72Thr	p.A72T	ENST00000351677	NM_002834.3	72	Gcc/Acc	3/16	1	2	FACETS	0.382	0.345	0.422	0.382	0.345	0.422	SUBCLONAL	1	TRUE	1	0.793828868330964	2		882	791	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785690	50785690	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	150	834	0	ENST00000398568.2:c.680T>C	p.Leu227Pro	p.L227P	ENST00000398568	NM_001042412.1	227	cTt/cCt	4/18	1	2	FACETS	0.518	0.474	0.563	0.518	0.474	0.563	SUBCLONAL	1	TRUE	1	0.793828868330964	2		834	730	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593615	+	inframe_deletion	In_Frame_Del	DEL	AGTGGAAGGTTGTTG	AGTGGAAGGTTGTTG	-	novel	NA	P-0021667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	272	527	0	ENST00000288135.5:c.1669_1683del	p.Trp557_Glu561del	p.W557_E561del	ENST00000288135	NM_000222.2	556	cAGTGGAAGGTTGTTGag/cag	11/21	0.665631709708699	3	FACETS	1	0.992	1			1	CLONAL	1	TRUE	NA	0.811749443632966	3		527	728	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0021669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	159	662	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.882040836819645	2		663	331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578462	7578463	+	missense_variant	Missense_Mutation	DNP	GC	GC	AG	novel	NA	P-0021669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	23	1025	5	ENST00000269305.4:c.467_468delinsCT	p.Arg156Pro	p.R156P	ENST00000269305	NM_001126112.2	156	cGC/cCT	5/11	1	2	FACETS	0.053	0.04	0.067	0.053	0.04	0.067	SUBCLONAL	1	TRUE	1	0.882040836819645	2		1030	989	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041121	180041121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770869636	NA	P-0021669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	505	1492	3	ENST00000261937.6:c.3278C>T	p.Thr1093Met	p.T1093M	ENST00000261937	NM_182925.4	1093	aCg/aTg	24/30	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.882040836819645	2		1495	1127	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055982	180055982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147644625	NA	P-0021669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	384	960	4	ENST00000261937.6:c.1003G>A	p.Val335Ile	p.V335I	ENST00000261937	NM_182925.4	335	Gtc/Atc	8/30	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.882040836819645	2		964	865	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0021670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	126	487	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.872	0.797	0.949	0.872	0.797	0.949	CLONAL	1	TRUE	1	0.73	2		487	396	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0021670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	168	541	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.872	0.807	0.938	0.872	0.807	0.938	CLONAL	1	TRUE	1	0.73	2		541	528	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0021670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	200	600	10	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.933	0.871	0.998	0.933	0.871	0.998	CLONAL	1	TRUE	1	0.73	2		610	587	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0021670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	122	363	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	0.729957168395022	2	FACETS	0.823	0.751	0.898	0.412	0.375	0.449	CLONAL	1	TRUE	0	0.73	2		363	406	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	122	836	0	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	0.375	0.339	0.414	0.375	0.339	0.414	SUBCLONAL	1	TRUE	1	0.73	2		836	891	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	176	687	5	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.906	0.841	0.973	0.906	0.841	0.973	CLONAL	1	TRUE	1	0.73	2		692	532	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0021670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	530	937	4	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	0.83	0.802	0.857	1	0.997	1	CLONAL	2	TRUE	1	0.73	2		941	875	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636973	176636973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1215568879	NA	P-0021670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	212	857	0	ENST00000439151.2:c.1573C>T	p.Arg525Trp	p.R525W	ENST00000439151	NM_022455.4	525	Cgg/Tgg	5/23	1	2	FACETS	0.887	0.828	0.947	0.887	0.828	0.947	CLONAL	1	TRUE	1	0.73	2		857	655	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255883	16255883	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	85	599	2	ENST00000375759.3:c.3154del	p.Ile1052SerfsTer40	p.I1052Sfs*40	ENST00000375759	NM_015001.2	1050	Aaa/aa	11/15	1	2	FACETS	0.395	0.35	0.444	0.395	0.35	0.444	SUBCLONAL	1	TRUE	1	0.73	2		601	589	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693003	89693003	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs786204900	NA	P-0021670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	103	567	0	ENST00000371953.3:c.491del	p.Lys164ArgfsTer3	p.K164Rfs*3	ENST00000371953	NM_000314.4	163	Aaa/aa	5/9	1	2	FACETS	0.735	0.663	0.81	0.735	0.663	0.81	SUBCLONAL	1	TRUE	1	0.73	2		567	384	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913274	NA	P-0021670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	11	940	0	ENST00000263967.3:c.1634A>C	p.Glu545Ala	p.E545A	ENST00000263967	NM_006218.2	545	gAg/gCg	10/21	1	2	FACETS	0.072	0.049	0.1	0.072	0.049	0.1	SUBCLONAL	1	TRUE	1	0.73	2		940	421	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850704	63850705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	147	551	0	ENST00000279873.7:c.1489dup	p.Ile497AsnfsTer31	p.I497Nfs*31	ENST00000279873	NM_032199.2	494	-/A	10/10	1	2	FACETS	0.834	0.767	0.903	0.834	0.767	0.903	CLONAL	1	TRUE	1	0.73	2		551	483	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199945	138199945	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	162	564	0	ENST00000237289.4:c.1368del	p.Pro457LeufsTer20	p.P457Lfs*20	ENST00000237289	NM_001270507.1	455	Ggg/gg	7/9	1	2	FACETS	0.94	0.87	1	0.94	0.87	1	CLONAL	1	TRUE	1	0.73	2		564	472	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088681	27088682	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0021670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	326	1113	1	ENST00000324856.7:c.2296dup	p.Gln766ProfsTer51	p.Q766Pfs*51	ENST00000324856	NM_006015.4	764	tcc/tCcc	7/20	1	2	FACETS	0.893	0.845	0.942	0.893	0.845	0.942	CLONAL	1	TRUE	1	0.73	2		1114	1000	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306553	41306553	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	202	826	0	ENST00000373198.4:c.1106del	p.Gly369ValfsTer28	p.G369Vfs*28	ENST00000373198	NM_133170.3	369	gGt/gt	7/32	1	2	FACETS	0.865	0.806	0.925	0.865	0.806	0.925	CLONAL	1	TRUE	1	0.73	2		826	640	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426022	49426022	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	242	950	0	ENST00000301067.7:c.12466del	p.Gln4156AsnfsTer5	p.Q4156Nfs*5	ENST00000301067	NM_003482.3	4156	Caa/aa	39/54	1	2	FACETS	0.925	0.868	0.983	0.925	0.868	0.983	CLONAL	1	TRUE	1	0.73	2		950	717	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11172914	11172914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	201	789	0	ENST00000361445.4:c.7361C>T	p.Ser2454Leu	p.S2454L	ENST00000361445	NM_004958.3	2454	tCa/tTa	54/58	1	2	FACETS	0.821	0.764	0.879	0.821	0.764	0.879	CLONAL	1	TRUE	1	0.73	2		789	671	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903718	114903718	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241370314	NA	P-0021670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	333	1040	3	ENST00000543371.1:c.722C>T	p.Pro241Leu	p.P241L	ENST00000543371	NM_001198531.1	241	cCg/cTg	7/14	1	2	FACETS	0.981	0.93	1	0.981	0.93	1	CLONAL	1	TRUE	1	0.73	2		1043	930	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125088	46125088	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	88	308	0	ENST00000334344.6:c.275A>T	p.Tyr92Phe	p.Y92F	ENST00000334344	NM_152641.2	92	tAt/tTt	3/21	1	2	FACETS	0.867	0.779	0.959	0.867	0.779	0.959	CLONAL	1	TRUE	1	0.73	2		308	278	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434931	49434931	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	203	815	0	ENST00000301067.7:c.6622C>T	p.Gln2208Ter	p.Q2208*	ENST00000301067	NM_003482.3	2208	Cag/Tag	31/54	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.73	2		815	537	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885900	111885900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749430739	NA	P-0021670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	273	982	0	ENST00000341259.2:c.1522C>T	p.Arg508Trp	p.R508W	ENST00000341259	NM_005475.2	508	Cgg/Tgg	8/8	1	2	FACETS	0.971	0.916	1	0.971	0.916	1	CLONAL	1	TRUE	1	0.73	2		982	770	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112919947	112919947	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749523268	NA	P-0021670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	157	468	2	ENST00000351677.2:c.1162G>A	p.Val388Ile	p.V388I	ENST00000351677	NM_002834.3	388	Gtc/Atc	10/16	1	2	FACETS	0.952	0.88	1	0.952	0.88	1	CLONAL	1	TRUE	1	0.73	2		470	452	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347683	89347683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377219970	NA	P-0021670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	219	847	0	ENST00000301030.4:c.5267G>A	p.Cys1756Tyr	p.C1756Y	ENST00000301030	NM_001256183.1	1756	tGc/tAc	9/13	1	2	FACETS	0.902	0.844	0.962	0.902	0.844	0.962	CLONAL	1	TRUE	1	0.73	2		847	665	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145659	11145661	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	novel	NA	P-0021670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	274	949	2	ENST00000358026.2:c.4023_4025del	p.Asp1341del	p.D1341del	ENST00000358026	NM_001128849.1	1341	GAC/-	29/36	1	2	FACETS	0.93	0.876	0.985	0.93	0.876	0.985	CLONAL	1	TRUE	1	0.73	2		951	807	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029177	26029177	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	208	644	1	ENST00000435504.4:c.173C>T	p.Ala58Val	p.A58V	ENST00000435504		58	gCa/gTa	4/13	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.73	2		645	562	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557804	187557804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1321370436	NA	P-0021670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	204	646	0	ENST00000441802.2:c.3907G>A	p.Glu1303Lys	p.E1303K	ENST00000441802	NM_005245.3	1303	Gaa/Aaa	5/27	1	2	FACETS	0.935	0.872	0.998	0.935	0.872	0.998	CLONAL	1	TRUE	1	0.73	2		646	598	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935534	13935534	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	125	481	0	ENST00000405192.2:c.1322del	p.Gly441AlafsTer52	p.G441Afs*52	ENST00000405192	NM_001163147.1	441	gGc/gc	12/12	1	2	FACETS	0.837	0.765	0.912	0.837	0.765	0.912	CLONAL	1	TRUE	1	0.73	2		481	409	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372287	55372288	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1170462661	NA	P-0021670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	28	622	2	ENST00000297316.4:c.983dup	p.Gly331ArgfsTer34	p.G331Rfs*34	ENST00000297316	NM_022454.3	326	cac/caCc	2/2	1	2	FACETS	0.147	0.117	0.181	0.147	0.117	0.181	SUBCLONAL	1	TRUE	1	0.73	2		624	522	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742543	145742543	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1481180558	NA	P-0021670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	256	994	1	ENST00000428558.2:c.245T>A	p.Leu82Gln	p.L82Q	ENST00000428558	NM_004260.3	82	cTg/cAg	4/22	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.73	2		995	677	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950000	44950000	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	202	752	0	ENST00000377967.4:c.3769G>A	p.Glu1257Lys	p.E1257K	ENST00000377967	NM_021140.2	1257	Gaa/Aaa	26/29	1	2	FACETS	0.961	0.897	1	0.961	0.897	1	CLONAL	1	TRUE	1	0.73	2		752	576	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913503	NA	P-0021672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	171	839	0	ENST00000330062.3:c.515G>T	p.Arg172Met	p.R172M	ENST00000330062	NM_002168.2	172	aGg/aTg	4/11	0.415592830742582	3	FACETS	0.959	0.882	1	0.48	0.441	0.521	CLONAL	1	TRUE	1	0.415592830742582	3		839	1036	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0021675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	339	835	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.618626798952257	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.618626798952257	3		835	668	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219381	1219381	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	286	590	1	ENST00000326873.7:c.433G>T	p.Glu145Ter	p.E145*	ENST00000326873	NM_000455.4	145	Gag/Tag	3/10	0.591043248858902	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.618626798952257	2		591	440	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115460	115115460	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	108	448	0	ENST00000257566.3:c.866T>A	p.Ile289Lys	p.I289K	ENST00000257566	NM_016569.3	289	aTa/aAa	5/8	0.618626798952257	3	FACETS	1	0.903	1	0.5	0.451	0.551	CLONAL	1	TRUE	1	0.618626798952257	3		448	457	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	60	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.909	0.785	1	0.909	0.785	1	CLONAL	1	TRUE	1	0.308477158857363	2		434	428	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022592	31022592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs373221034	NA	P-0021677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	46	846	1	ENST00000375687.4:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000375687	NM_015338.5	693	Cga/Tga	13/13	1	2	FACETS	0.49	0.412	0.576	0.49	0.412	0.576	SUBCLONAL	1	TRUE	1	0.308477158857363	2		847	609	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063333	67063333	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	56	558	0	ENST00000412916.2:c.23A>G	p.Gln8Arg	p.Q8R	ENST00000412916		8	cAg/cGg	1/6	0.308477158857363	1	FACETS	0.817	0.702	0.94	0.817	0.702	0.94	CLONAL	1	TRUE	0	0.308477158857363	1		558	376	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0021678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	655	1047	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.864370747301477	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	FALSE	0	0.864370747301477	3		1049	719	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528647	89528647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536144760	NA	P-0021678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	103	242	0	ENST00000336596.2:c.2947G>A	p.Val983Met	p.V983M	ENST00000336596	NM_005233.5	983	Gtg/Atg	17/17	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.864370747301477	2		242	222	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405899	70405899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	248	922	1	ENST00000373644.4:c.3413C>T	p.Ser1138Leu	p.S1138L	ENST00000373644	NM_030625.2	1138	tCa/tTa	4/12	NA	2	FACETS	0.509	0.475	0.545			1	INDETERMINATE	1	TRUE	NA	0.78899348160519	2		923	1234	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592353	29592353	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500316	NA	P-0021679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	92	693	0	ENST00000356175.3:c.4768C>T	p.Arg1590Trp	p.R1590W	ENST00000356175	NM_000267.3	1590	Cgg/Tgg	35/57	0.404720774595311	1	FACETS	0.339	0.302	0.377	0.339	0.302	0.377	INDETERMINATE	1	TRUE	0	0.78899348160519	1		693	417	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405524	70405524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369726331	NA	P-0021679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	488	834	2	ENST00000373644.4:c.3038C>T	p.Ser1013Phe	p.S1013F	ENST00000373644	NM_030625.2	1013	tCc/tTc	4/12	NA	2	FACETS	0.896	0.857	0.935			1	INDETERMINATE	1	TRUE	NA	0.78899348160519	2		836	1381	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405595	70405595	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	447	806	2	ENST00000373644.4:c.3109C>A	p.Gln1037Lys	p.Q1037K	ENST00000373644	NM_030625.2	1037	Cag/Aag	4/12	NA	2	FACETS	0.861	0.822	0.901			1	INDETERMINATE	1	TRUE	NA	0.78899348160519	2		808	1316	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230526	46230526	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs750746147	NA	P-0021679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	102	573	0	ENST00000334344.6:c.775G>C	p.Gly259Arg	p.G259R	ENST00000334344	NM_152641.2	259	Ggt/Cgt	8/21	1	2	FACETS	0.519	0.466	0.575	0.519	0.466	0.575	SUBCLONAL	1	TRUE	1	0.78899348160519	2		573	498	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536706	120536706	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	170	927	0	ENST00000229340.5:c.386T>C	p.Val129Ala	p.V129A	ENST00000229340	NM_006861.6	129	gTg/gCg	5/6	1	2	FACETS	0.489	0.45	0.53	0.489	0.45	0.53	SUBCLONAL	1	TRUE	1	0.78899348160519	2		927	881	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457635	67457635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1429991069	NA	P-0021679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	349	952	5	ENST00000327367.4:c.445G>A	p.Glu149Lys	p.E149K	ENST00000327367	NM_005902.3	149	Gag/Aag	3/9	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.78899348160519	2		957	817	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88671946	88671946	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	84	595	0	ENST00000360948.2:c.1224C>G	p.Ile408Met	p.I408M	ENST00000360948	NM_001012338.2	408	atC/atG	10/19	1	2	FACETS	0.443	0.392	0.496	0.443	0.392	0.496	SUBCLONAL	1	TRUE	1	0.78899348160519	2		595	481	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679370	29679370	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1060500265	NA	P-0021679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	118	647	0	ENST00000356175.3:c.7490C>A	p.Ala2497Asp	p.A2497D	ENST00000356175	NM_000267.3	2497	gCc/gAc	50/57	0.404720774595311	1	FACETS	0.37	0.336	0.407	0.37	0.336	0.407	INDETERMINATE	1	TRUE	0	0.78899348160519	1		647	489	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383727	15383727	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	159	889	1	ENST00000263377.2:c.184C>T	p.Gln62Ter	p.Q62*	ENST00000263377	NM_058243.2	62	Caa/Taa	2/20	0.404720774595311	1	FACETS	0.398	0.366	0.431	0.398	0.366	0.431	INDETERMINATE	1	TRUE	0	0.78899348160519	1		890	613	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946133	55946133	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	103	570	0	ENST00000263923.4:c.4046C>A	p.Thr1349Asn	p.T1349N	ENST00000263923	NM_002253.2	1349	aCc/aAc	30/30	1	2	FACETS	0.549	0.493	0.607	0.549	0.493	0.607	SUBCLONAL	1	TRUE	1	0.78899348160519	2		570	476	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27205002	27205002	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	112	903	0	ENST00000380036.4:c.2303T>A	p.Ile768Asn	p.I768N	ENST00000380036	NM_000459.3	768	aTc/aAc	14/23	1	2	FACETS	0.438	0.394	0.484	0.438	0.394	0.484	SUBCLONAL	1	TRUE	1	0.78899348160519	2		903	648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747342068	NA	P-0021680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	97	1054	0	ENST00000269305.4:c.394A>G	p.Lys132Glu	p.K132E	ENST00000269305	NM_001126112.2	132	Aag/Gag	5/11	0.169176948962389	3	FACETS	0.742	0.66	0.83	0.371	0.33	0.415	INDETERMINATE	1	FALSE	1	0.3	3		1054	1002	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0021680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	77	843	1	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	0.169176948962389	3	FACETS	0.798	0.7	0.903	0.399	0.35	0.452	INDETERMINATE	1	FALSE	1	0.3	3		844	740	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456887	32456887	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1049509674	NA	P-0021680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	69	592	0	ENST00000332351.3:c.5A>G	p.Gln2Arg	p.Q2R	ENST00000332351	NM_024426.4	2	cAg/cGg	1/10	0.141044880029004	4	FACETS	1	0.906	1	0.524	0.456	0.596	INDETERMINATE	1	FALSE	2	0.3	4		592	571	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343922	118343922	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	32	524	0	ENST00000534358.1:c.2048A>T	p.His683Leu	p.H683L	ENST00000534358	NM_005933.3	683	cAt/cTt	3/36	0.141044880029004	4	FACETS	0.491	0.397	0.597	0.245	0.198	0.299	INDETERMINATE	1	FALSE	2	0.3	4		524	565	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120738	115120738	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	48	866	0	ENST00000257566.3:c.268T>G	p.Leu90Val	p.L90V	ENST00000257566	NM_016569.3	90	Ttg/Gtg	1/8	0.141044880029004	4	FACETS	0.509	0.429	0.598	0.255	0.214	0.299	INDETERMINATE	1	FALSE	2	0.3	4		866	817	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029154	14029154	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	49	385	0	ENST00000311895.7:c.1365G>T	p.Lys455Asn	p.K455N	ENST00000311895	NM_005236.2	455	aaG/aaT	8/11	0.141044880029004	4	FACETS	1	0.953	1	0.666	0.567	0.773	INDETERMINATE	1	FALSE	2	0.3	4		385	319	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89335070	89335070	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	48	475	1	ENST00000301030.4:c.7808C>T	p.Thr2603Ile	p.T2603I	ENST00000301030	NM_001256183.1	2603	aCt/aTt	13/13	0.141044880029004	4	FACETS	0.788	0.666	0.922	0.394	0.333	0.461	INDETERMINATE	1	FALSE	2	0.3	4		476	528	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40855816	40855816	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	67	806	3	ENST00000428826.2:c.2040del	p.Gly682GlufsTer11	p.G682Efs*11	ENST00000428826		680	cgG/cg	19/21	0.169176948962389	3	FACETS	0.785	0.682	0.897	0.393	0.341	0.449	INDETERMINATE	1	FALSE	1	0.3	3		809	654	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867666	78867666	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0021680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	49	795	0	ENST00000306801.3:c.2401+1G>T		p.X801_splice	ENST00000306801	NM_020761.2	801			0.169176948962389	3	FACETS	0.429	0.362	0.503	0.214	0.181	0.252	INDETERMINATE	1	FALSE	1	0.3	3		795	876	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191146	2191146	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	191	861	1	ENST00000398665.3:c.400G>T	p.Glu134Ter	p.E134*	ENST00000398665	NM_032482.2	134	Gag/Tag	5/28	0.3	3	FACETS	0.831	0.769	0.895	0.831	0.769	0.895	CLONAL	2	FALSE	1	0.3	3		862	881	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105657	11105657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	220	800	1	ENST00000358026.2:c.1573G>T	p.Glu525Ter	p.E525*	ENST00000358026	NM_001128849.1	525	Gag/Tag	9/36	0.3	3	FACETS	0.925	0.861	0.99	0.925	0.861	0.99	CLONAL	2	FALSE	1	0.3	3		801	912	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113217	209113217	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	92	625	0	ENST00000345146.2:c.290G>T	p.Gly97Val	p.G97V	ENST00000345146	NM_005896.2	97	gGc/gTc	4/10	0.124488067501386	5	FACETS	0.758	0.674	0.846	0.379	0.337	0.423	INDETERMINATE	2	FALSE	1	0.3	5		625	587	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812312	212812312	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	53	473	0	ENST00000342788.4:c.264A>C	p.Leu88Phe	p.L88F	ENST00000342788	NM_005235.2	88	ttA/ttC	3/28	0.124488067501386	5	FACETS	1	0.964	1	0.365	0.312	0.422	INDETERMINATE	1	FALSE	1	0.3	5		473	351	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225450	26225450	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	68	298	0	ENST00000360408.1:c.68C>A	p.Thr23Asn	p.T23N	ENST00000360408	NM_003532.2	23	aCt/aAt	1/1	0.219424605485324	4	FACETS	0.754	0.659	0.855	0.754	0.659	0.855	SUBCLONAL	2	FALSE	2	0.3	4		298	391	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190477	32190477	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	95	1105	2	ENST00000375023.3:c.262C>A	p.Leu88Ile	p.L88I	ENST00000375023	NM_004557.3	88	Cta/Ata	3/30	0.219424605485324	4	FACETS	0.807	0.717	0.904	0.404	0.358	0.452	CLONAL	1	FALSE	2	0.3	4		1107	1020	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542172	141542172	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	42	818	0	ENST00000220592.5:c.2551G>T	p.Asp851Tyr	p.D851Y	ENST00000220592	NM_012154.3	851	Gac/Tac	19/19	0.141044880029004	4	FACETS	0.447	0.372	0.531	0.224	0.186	0.266	INDETERMINATE	1	FALSE	2	0.3	4		818	814	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0021681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	159	1034	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.295045457893731	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.292190077099988	4		1037	654	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0021681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	408	1047	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.295045457893731	3	FACETS	1	0.959	1	1	0.996	1	CLONAL	3	TRUE	1	0.292190077099988	3		1049	1061	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0021681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	89	683	1	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.292190077099988	2		684	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	218	947	2	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	0.295045457893731	4	FACETS	0.856	0.799	0.915	1	0.989	1	CLONAL	3	TRUE	2	0.292190077099988	4		949	751	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858476	57858476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199685332	NA	P-0021681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	97	862	1	ENST00000228682.2:c.214C>T	p.Arg72Trp	p.R72W	ENST00000228682	NM_005269.2	72	Cgg/Tgg	4/12	0.295045457893731	3	FACETS	1	0.965	1	0.598	0.534	0.667	CLONAL	1	TRUE	1	0.292190077099988	3		863	636	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981156	201981169	+	frameshift_variant	Frame_Shift_Del	DEL	CAAGTGGAGAAGAA	CAAGTGGAGAAGAA	-	novel	NA	P-0021681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	82	1148	0	ENST00000359651.3:c.240_253del	p.Glu81ArgfsTer6	p.E81Rfs*6	ENST00000359651		79	CAAGTGGAGAAGAAc/c	2/8	0.295045457893731	3	FACETS	0.845	0.745	0.953	0.423	0.372	0.477	CLONAL	1	TRUE	1	0.292190077099988	3		1148	761	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855493	45855493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913026	NA	P-0021681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	253	1028	1	ENST00000391945.4:c.2164C>T	p.Arg722Trp	p.R722W	ENST00000391945	NM_000400.3	722	Cgg/Tgg	22/23	0.291616793884047	3	FACETS	0.986	0.928	1	0.986	0.928	1	CLONAL	3	TRUE	0	0.292190077099988	3		1029	671	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	164	699	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.936	0.864	1	0.936	0.864	1	CLONAL	1	TRUE	1	0.608302784571945	2		699	576	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835736	68835737	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	174	731	0	ENST00000261769.5:c.331dup	p.Ser111PhefsTer57	p.S111Ffs*57	ENST00000261769	NM_004360.3	109	-/T	3/16	0.608302784571945	1	FACETS	0.952	0.887	1	0.952	0.887	1	CLONAL	1	TRUE	0	0.608302784571945	1		731	418	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213849	66213849	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	89	722	1	ENST00000273854.3:c.2581G>A	p.Val861Ile	p.V861I	ENST00000273854	NM_004439.5	861	Gtc/Atc	15/18	1	2	FACETS	0.873	0.782	0.969	0.873	0.782	0.969	CLONAL	1	TRUE	1	0.608302784571945	2		723	335	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178120	56178120	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	87	446	0	ENST00000399503.3:c.3095del	p.Asn1032ThrfsTer50	p.N1032Tfs*50	ENST00000399503	NM_005921.1	1031	agA/ag	14/20	0.608302784571945	1	FACETS	0.952	0.861	1	0.952	0.861	1	CLONAL	1	TRUE	0	0.608302784571945	1		446	209	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069667	69069667	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	85	590	0	ENST00000288368.4:c.4342C>G	p.Leu1448Val	p.L1448V	ENST00000288368	NM_024870.2	1448	Ctc/Gtc	35/40	0.593309194446148	4	FACETS	0.786	0.696	0.882	0.262	0.232	0.294	SUBCLONAL	1	TRUE	1	0.608302784571945	4		590	572	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0021685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	134	672	2	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.365391653158417	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.365391653158417	2		674	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574026	7574026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	340	674	0	ENST00000269305.4:c.1001G>T	p.Gly334Val	p.G334V	ENST00000269305	NM_001126112.2	334	gGg/gTg	10/11	0.36531458989752	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	0	0.365391653158417	3		674	682	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17743005	17743005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	96	620	0	ENST00000250003.3:c.913C>T	p.Pro305Ser	p.P305S	ENST00000250003	NM_002478.4	305	Ccg/Tcg	3/3	0.365391653158417	3	FACETS	0.921	0.821	1	0.46	0.41	0.514	CLONAL	1	TRUE	1	0.365391653158417	3		620	675	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916753	48916753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	255	543	0	ENST00000267163.4:c.287del	p.Lys96ArgfsTer15	p.K96Rfs*15	ENST00000267163	NM_000321.2	95	Aaa/aa	3/27	0.365391653158417	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	4	TRUE	0	0.365391653158417	4		543	473	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564666	86564667	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0021685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	284	674	0	ENST00000274376.6:c.401_402dup	p.Pro135PhefsTer40	p.P135Ffs*40	ENST00000274376	NM_002890.2	133	ggt/ggTTt	1/25	0.32745570840587	3	FACETS	1	0.985	1	0.749	0.707	0.792	CLONAL	2	TRUE	0	0.365391653158417	3		674	818	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0021686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	416	1034	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	0.823	0.791	0.856			1	INDETERMINATE	2	TRUE	NA	0.67273237101906	2		1037	751	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	206	669	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.963	0.898	1	0.963	0.898	1	CLONAL	1	TRUE	1	0.67273237101906	2		669	636	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0021686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	2009	1047	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.67273237101906	7	FACETS	0.945	0.934	0.956			1	CLONAL	7	TRUE	NA	0.67273237101906	7		1047	2421	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455091	50455091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1422790468	NA	P-0021686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	194	599	2	ENST00000331340.3:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000331340	NM_006060.4	213	cGa/cAa	6/8	0.344119448164997	1	FACETS	0.781	0.73	0.833	0.781	0.73	0.833	INDETERMINATE	1	TRUE	0	0.67273237101906	1		601	490	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148726	20148726	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0021686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	164	276	0	ENST00000379607.5:c.338-1G>T		p.X113_splice	ENST00000379607	NM_001412.3	113			1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.67273237101906	1		276	260	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0021690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	187	726	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.917	0.851	0.986	0.917	0.851	0.986	CLONAL	1	TRUE	1	0.60492513546947	2		726	674	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944761	31944761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	80	274	1	ENST00000340398.3:c.340G>A	p.Ala114Thr	p.A114T	ENST00000340398	NM_001013699.2	114	Gct/Act	1/1	1	2	FACETS	0.948	0.845	1	0.948	0.845	1	CLONAL	1	TRUE	1	0.60492513546947	2		275	279	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794814	242794814	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756575544	NA	P-0021690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	104	524	0	ENST00000334409.5:c.395C>T	p.Ala132Val	p.A132V	ENST00000334409	NM_005018.2	132	gCg/gTg	2/5	1	2	FACETS	0.754	0.679	0.833	0.754	0.679	0.833	SUBCLONAL	1	TRUE	1	0.60492513546947	2		524	456	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916925	178916936	+	protein_altering_variant	In_Frame_Del	DEL	AGTAGGCAACCG	AGTAGGCAACCG	GTA	novel	NA	P-0021690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	404	627	5	ENST00000263967.3:c.312_323delinsGTA	p.Val105_Arg108delinsTyr	p.V105_R108delinsY	ENST00000263967	NM_006218.2	104	ccAGTAGGCAACCGt/ccGTAt	2/21	0.60492513546947	3	FACETS	0.843	0.811	0.875	0.843	0.811	0.875	CLONAL	3	TRUE	0	0.60492513546947	3		632	688	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0021692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	234	845	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	0.650039460683796	2		845	646	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0021692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	135	541	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.650039460683796	2		541	394	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101751	71101751	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	93	319	1	ENST00000318789.4:c.447del	p.Lys149AsnfsTer57	p.K149Nfs*57	ENST00000318789	NM_032682.5	149	aaA/aa	9/21	1	2	FACETS	0.829	0.744	0.918	0.829	0.744	0.918	CLONAL	1	TRUE	1	0.650039460683796	2		320	345	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0021692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	205	844	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.943	0.879	1	0.943	0.879	1	CLONAL	1	TRUE	1	0.650039460683796	2		846	669	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0021692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	222	786	3	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.923	0.862	0.985	0.923	0.862	0.985	CLONAL	1	TRUE	1	0.650039460683796	2		789	740	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	191	471	1	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.650039460683796	2		472	517	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0021692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	200	654	3	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.650039460683796	2		657	600	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717749	89717749	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	330	491	0	ENST00000371953.3:c.775del	p.His259ThrfsTer7	p.H259Tfs*7	ENST00000371953	NM_000314.4	258	ttC/tt	7/9	0.650039460683796	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.650039460683796	2		491	465	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027087	71027087	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	218	512	0	ENST00000318789.4:c.1240del	p.Leu414Ter	p.L414*	ENST00000318789	NM_032682.5	414	Ctg/tg	15/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.650039460683796	2		512	658	SUCCESS
APC	324	MSKCC	GRCh37	5	112173323	112173323	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	117	351	0	ENST00000257430.4:c.2032A>G	p.Ser678Gly	p.S678G	ENST00000257430	NM_000038.5	678	Agt/Ggt	16/16	1	2	FACETS	0.978	0.891	1	0.978	0.891	1	CLONAL	1	TRUE	1	0.650039460683796	2		351	368	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636766	8636766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776233840	NA	P-0021692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	173	638	0	ENST00000356435.5:c.143C>T	p.Thr48Met	p.T48M	ENST00000356435		48	aCg/aTg	2/35	1	2	FACETS	0.868	0.803	0.936	0.868	0.803	0.936	CLONAL	1	TRUE	1	0.650039460683796	2		638	613	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0021692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	221	695	0	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	1	2	FACETS	0.928	0.867	0.99	0.928	0.867	0.99	CLONAL	1	TRUE	1	0.650039460683796	2		695	733	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939797	71939797	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	296	943	0	ENST00000298229.2:c.428del	p.Pro143ArgfsTer36	p.P143Rfs*36	ENST00000298229	NM_001567.3	142	Ccc/cc	4/28	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.650039460683796	2		943	799	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852350	63852352	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0021692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	186	544	0	ENST00000279873.7:c.3130_3132del	p.Glu1044del	p.E1044del	ENST00000279873	NM_032199.2	1043	aAGGag/aag	10/10	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.650039460683796	2		544	570	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942558	71942559	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0021692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	221	470	0	ENST00000298229.2:c.1516_1517del	p.Trp506GlufsTer45	p.W506Efs*45	ENST00000298229	NM_001567.3	505	cTG/c	13/28	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.650039460683796	2		470	568	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563290	21563290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866451799	NA	P-0021692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	330	790	1	ENST00000382592.4:c.629C>T	p.Pro210Leu	p.P210L	ENST00000382592	NM_014572.2	210	cCg/cTg	4/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.650039460683796	2		791	900	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953734	48953734	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	148	375	1	ENST00000267163.4:c.1337A>G	p.Tyr446Cys	p.Y446C	ENST00000267163	NM_000321.2	446	tAc/tGc	14/27	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.650039460683796	2		376	410	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49280954	49280954	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0021692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	31	553	0	ENST00000282018.3:c.1A>G	p.Met1?	p.M1?	ENST00000282018	NM_020377.2	1	Atg/Gtg	1/1	1	2	FACETS	0.212	0.171	0.258	0.212	0.171	0.258	SUBCLONAL	1	TRUE	1	0.650039460683796	2		553	450	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435751	110435751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	89	168	0	ENST00000375856.3:c.2650C>T	p.Arg884Cys	p.R884C	ENST00000375856	NM_003749.2	884	Cgc/Tgc	1/2	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.650039460683796	2		168	219	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303942	91303942	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	191	700	0	ENST00000355112.3:c.1339G>T	p.Gly447Trp	p.G447W	ENST00000355112	NM_000057.2	447	Ggg/Tgg	7/22	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.650039460683796	2		700	527	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652192	3652192	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	342	840	1	ENST00000294008.3:c.877T>A	p.Leu293Met	p.L293M	ENST00000294008	NM_032444.2	293	Ttg/Atg	4/15	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.650039460683796	2		841	903	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584823	48584823	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	187	438	0	ENST00000342988.3:c.901T>A	p.Tyr301Asn	p.Y301N	ENST00000342988	NM_005359.5	301	Tac/Aac	7/12	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.650039460683796	2		438	540	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054604	13054605	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAG	novel	NA	P-0021692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	135	396	0	ENST00000316448.5:c.1142_1144dup	p.Glu381dup	p.E381dup	ENST00000316448	NM_004343.3	381	-/GAG	9/9	1	2	FACETS	0.911	0.834	0.99	0.911	0.834	0.99	CLONAL	1	TRUE	1	0.650039460683796	2		396	456	SUCCESS
ALK	238	MSKCC	GRCh37	2	29541195	29541195	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	209	650	0	ENST00000389048.3:c.1622C>T	p.Ala541Val	p.A541V	ENST00000389048	NM_004304.4	541	gCa/gTa	8/29	1	2	FACETS	0.964	0.899	1	0.964	0.899	1	CLONAL	1	TRUE	1	0.650039460683796	2		650	667	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119812281	119812281	+	start_lost	Translation_Start_Site	SNP	T	T	A	novel	NA	P-0021692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	173	439	0	ENST00000316626.5:c.1A>T	p.Met1?	p.M1?	ENST00000316626		1	Atg/Ttg	1/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.650039460683796	2		439	495	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204900	128204902	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0021692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	358	903	0	ENST00000341105.2:c.539_541del	p.Glu180del	p.E180del	ENST00000341105	NM_032638.4	180	gAAGtg/gtg	3/6	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.650039460683796	2		903	963	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80109476	80109476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	191	690	0	ENST00000265081.6:c.2729C>T	p.Ala910Val	p.A910V	ENST00000265081	NM_002439.4	910	gCa/gTa	20/24	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.650039460683796	2		690	532	SUCCESS
APC	324	MSKCC	GRCh37	5	112174728	112174728	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763486328	NA	P-0021692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	105	390	0	ENST00000257430.4:c.3437G>A	p.Arg1146His	p.R1146H	ENST00000257430	NM_000038.5	1146	cGt/cAt	16/16	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.650039460683796	2		390	304	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537237	80537237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	190	770	0	ENST00000286548.4:c.161C>T	p.Thr54Met	p.T54M	ENST00000286548	NM_002072.3	54	aCg/aTg	2/7	1	2	FACETS	0.958	0.891	1	0.958	0.891	1	CLONAL	1	TRUE	1	0.650039460683796	2		770	610	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209303	98209303	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	256	747	1	ENST00000331920.6:c.4235C>A	p.Pro1412His	p.P1412H	ENST00000331920	NM_000264.3	1412	cCc/cAc	23/24	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.650039460683796	2		748	688	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325426	1325426	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	228	586	0	ENST00000400841.2:c.249del	p.Cys84AlafsTer3	p.C84Afs*3	ENST00000400841		83	ggG/gg	3/6	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.650039460683796	2		586	664	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0021695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	225	363	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	0.987	0.928	1	0.987	0.928	1	CLONAL	1	TRUE	1	0.871960636591919	2		363	523	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957450	175957450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	293	538	0	ENST00000367669.3:c.1946C>T	p.Ala649Val	p.A649V	ENST00000367669	NM_022457.5	649	gCt/gTt	17/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.871960636591919	2		538	654	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004185	29004185	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0021695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	188	357	0	ENST00000282397.4:c.1106+2T>C		p.X369_splice	ENST00000282397	NM_002019.4	369			0.871960636591919	1	FACETS	0.989	0.946	1	0.989	0.946	1	CLONAL	1	TRUE	0	0.871960636591919	1		357	246	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99440037	99440037	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	338	545	0	ENST00000268035.6:c.1005A>C	p.Glu335Asp	p.E335D	ENST00000268035	NM_000875.3	335	gaA/gaC	4/21	1	2	FACETS	0.955	0.908	1	0.955	0.908	1	CLONAL	1	TRUE	1	0.871960636591919	2		545	812	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578441	7578441	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1567553246	NA	P-0021695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	439	726	0	ENST00000269305.4:c.489C>G	p.Tyr163Ter	p.Y163*	ENST00000269305	NM_001126112.2	163	taC/taG	5/11	0.864233819316548	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.871960636591919	1		726	559	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564748	86564749	+	stop_gained	Nonsense_Mutation	DNP	TG	TG	CT	novel	NA	P-0021695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	362	693	1	ENST00000274376.6:c.480_481delinsCT	p.Gly161Ter	p.G161*	ENST00000274376	NM_002890.2	160	gaTGga/gaCTga	1/25	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.871960636591919	2		694	810	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0021696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	123	832	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.2408009692441	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.249064188701161	1		832	764	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797777	42797777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778206	NA	P-0021696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	225	871	0	ENST00000575354.2:c.3829C>T	p.Arg1277Cys	p.R1277C	ENST00000575354	NM_015125.3	1277	Cgc/Tgc	16/20	0.249064188701161	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.249064188701161	3		871	904	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207204	1207204	+	splice_donor_variant	Splice_Site	SNP	T	T	G	rs112235354	NA	P-0021696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	73	782	0	ENST00000326873.7:c.290+2T>G		p.X97_splice	ENST00000326873	NM_000455.4	97			0.249064188701161	1	FACETS	0.841	0.736	0.955	0.841	0.736	0.955	CLONAL	1	TRUE	0	0.249064188701161	1		782	610	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28644695	28644695	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	97	819	0	ENST00000241453.7:c.98T>C	p.Ile33Thr	p.I33T	ENST00000241453	NM_004119.2	33	aTc/aCc	2/24	0.249064188701161	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.249064188701161	1		819	489	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81557484	81557484	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	69	632	0	ENST00000298171.2:c.464T>C	p.Ile155Thr	p.I155T	ENST00000298171	NM_000369.2	155	aTa/aCa	5/10	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.249064188701161	2		632	523	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097250	11097250	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	95	743	0	ENST00000358026.2:c.743del	p.Asn248IlefsTer55	p.N248Ifs*55	ENST00000358026	NM_001128849.1	247	ccA/cc	4/36	0.249064188701161	1	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	0	0.249064188701161	1		743	662	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793205	33793210	+	inframe_deletion	In_Frame_Del	DEL	GGGCCC	GGGCCC	-	novel	NA	P-0021696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	19	81	0	ENST00000498907.2:c.111_116del	p.Gly38_Pro39del	p.G38_P39del	ENST00000498907	NM_004364.3	37	gcGGGCCCc/gcc	1/1	0.249064188701161	3	FACETS	1	0.887	1	0.65	0.498	0.824	CLONAL	1	TRUE	1	0.249064188701161	3		81	132	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645649	215645649	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1559424451	NA	P-0021696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	81	649	0	ENST00000260947.4:c.949G>C	p.Glu317Gln	p.E317Q	ENST00000260947	NM_000465.2	317	Gaa/Caa	4/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.249064188701161	2		649	503	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572389	41572389	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	129	923	2	ENST00000263253.7:c.4918G>T	p.Glu1640Ter	p.E1640*	ENST00000263253	NM_001429.3	1640	Gag/Tag	30/31	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.249064188701161	2		925	809	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275229	41275229	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	83	445	0	ENST00000349496.5:c.1395C>G	p.Ile465Met	p.I465M	ENST00000349496	NM_001904.3	465	atC/atG	9/15	0.249064188701161	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.249064188701161	1		445	480	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0021698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	117	573	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.416436028172684	4	FACETS	1	0.961	1	0.564	0.509	0.622	CLONAL	1	TRUE	2	0.416436028172684	4		573	706	SUCCESS
EED	8726	MSKCC	GRCh37	11	85966309	85966309	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	64	569	1	ENST00000263360.6:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000263360	NM_003797.3	136	Caa/Taa	4/12	0.416436028172684	3	FACETS	0.785	0.681	0.897	0.393	0.34	0.449	SUBCLONAL	1	TRUE	1	0.416436028172684	3		570	473	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121566	108121566	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	329	727	0	ENST00000278616.4:c.1374C>G	p.Cys458Trp	p.C458W	ENST00000278616	NM_000051.3	458	tgC/tgG	10/63	0.388586634889727	3	FACETS	0.876	0.839	0.912			1	CLONAL	4	TRUE	NA	0.416436028172684	3		727	545	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060903	38060912	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGCTTATG	GGAGCTTATG	-	novel	NA	P-0021698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	96	662	0	ENST00000250448.2:c.1077_1086del	p.Ile360GlyfsTer26	p.I360Gfs*26	ENST00000250448	NM_004496.3	359	ccCATAAGCTCC/cc	2/2	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.416436028172684	2		662	419	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060913	38060913	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1243400765	NA	P-0021698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	114	642	0	ENST00000250448.2:c.1076C>T	p.Pro359Leu	p.P359L	ENST00000250448	NM_004496.3	359	cCc/cTc	2/2	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.416436028172684	2		642	394	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868320	45868320	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1488539972	NA	P-0021698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	161	1170	0	ENST00000391945.4:c.457C>T	p.Pro153Ser	p.P153S	ENST00000391945	NM_000400.3	153	Ccc/Tcc	6/23	0.354434556390261	5	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.416436028172684	5		1170	962	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0021700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	183	848	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	0.208994204660639	5	FACETS	0.989	0.914	1	0.659	0.609	0.711	INDETERMINATE	2	TRUE	2	0.357054747340508	5		848	796	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845518	128845518	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748004767	NA	P-0021700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	54	866	1	ENST00000249373.3:c.815C>T	p.Ala272Val	p.A272V	ENST00000249373	NM_005631.4	272	gCg/gTg	4/12	0.357054747340508	5	FACETS	0.479	0.408	0.558	0.12	0.102	0.14	SUBCLONAL	1	TRUE	1	0.357054747340508	5		867	969	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106400	27106405	+	inframe_deletion	In_Frame_Del	DEL	ACCCAG	ACCCAG	-	novel	NA	P-0021700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	128	612	0	ENST00000324856.7:c.6011_6016del	p.His2004_Gly2006delinsArg	p.H2004_G2006delinsR	ENST00000324856	NM_006015.4	2004	cACCCAGgg/cgg	20/20	0.343644220907972	3	FACETS	0.962	0.879	1	0.962	0.879	1	CLONAL	2	TRUE	1	0.357054747340508	3		612	439	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934873	9934873	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	72	858	0	ENST00000330684.3:c.1417T>C	p.Phe473Leu	p.F473L	ENST00000330684	NM_001134407.1	473	Ttt/Ctt	6/13	0.232455290134844	5	FACETS	0.883	0.771	1	0.294	0.257	0.335	CLONAL	1	TRUE	2	0.357054747340508	5		858	701	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170002257	170002257	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs554687623	NA	P-0021700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	58	232	0	ENST00000295797.4:c.1076C>G	p.Ser359Cys	p.S359C	ENST00000295797	NM_002740.5	359	tCt/tGt	12/18	0.357054747340508	5	FACETS	0.99	0.868	1	0.99	0.868	1	CLONAL	3	TRUE	2	0.357054747340508	5		232	168	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528630	8528630	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	46	542	0	ENST00000356435.5:c.502A>C	p.Thr168Pro	p.T168P	ENST00000356435		168	Aca/Cca	4/35	0.357054747340508	2	FACETS	0.734	0.62	0.859	0.367	0.31	0.43	SUBCLONAL	1	TRUE	0	0.357054747340508	2		542	351	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853407	151853407	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	130	599	0	ENST00000262189.6:c.11695A>G	p.Thr3899Ala	p.T3899A	ENST00000262189	NM_170606.2	3899	Aca/Gca	45/59	0.616483861689183	4	FACETS	0.719	0.651	0.789	0.359	0.325	0.395	SUBCLONAL	1	TRUE	2	0.69162736523671	4		599	885	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0021703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	24	967	2	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		969	773	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0021705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	138	779	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	0.992	1	CLONAL	2	TRUE	1	0.351819852903421	2		779	360	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0021705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	269	857	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.22902456016349	2	FACETS	1	0.99	1	0.641	0.601	0.682	CLONAL	1	TRUE	0	0.351819852903421	2		859	1193	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913384	NA	P-0021705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	281	663	0	ENST00000304494.5:c.262G>T	p.Glu88Ter	p.E88*	ENST00000304494	NM_000077.4	88	Gag/Tag	2/3	0.22902456016349	2	FACETS	0.886	0.835	0.939	0.886	0.835	0.939	CLONAL	2	TRUE	0	0.351819852903421	2		663	901	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115873	8115874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0021706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	142	883	0	ENST00000346208.3:c.1220dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tCcg	6/6	1	2	FACETS	0.676	0.616	0.738	0.676	0.616	0.738	SUBCLONAL	1	TRUE	1	0.515734857668379	2		883	815	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941662	48941681	+	frameshift_variant	Frame_Shift_Del	DEL	TTATCTTAAAAATAAAGATC	TTATCTTAAAAATAAAGATC	-	novel	NA	P-0021706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	46	487	0	ENST00000267163.4:c.973_992del	p.Tyr325ArgfsTer9	p.Y325Rfs*9	ENST00000267163	NM_000321.2	324	atTTATCTTAAAAATAAAGATCta/atta	10/27	0.368382222578626	1	FACETS	0.318	0.268	0.373	0.318	0.268	0.373	SUBCLONAL	1	TRUE	0	0.515734857668379	1		487	416	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340253	116340253	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	110	490	0	ENST00000397752.3:c.1115A>G	p.Asp372Gly	p.D372G	ENST00000397752	NM_000245.2	372	gAc/gGc	2/21	1	2	FACETS	0.874	0.789	0.963	0.874	0.789	0.963	CLONAL	1	TRUE	1	0.515734857668379	2		490	488	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069274	30069274	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	243	755	0	ENST00000338641.4:c.1139del	p.Thr380LysfsTer46	p.T380Kfs*46	ENST00000338641	NM_000268.3	380	aCa/aa	12/16	0.765723808824594	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.765723808824594	1		755	373	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412422	63412422	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	317	1189	0	ENST00000330258.3:c.745G>T	p.Ala249Ser	p.A249S	ENST00000330258	NM_152424.3	249	Gct/Tct	2/2	1	2	FACETS	0.955	0.905	1	0.955	0.905	1	CLONAL	1	TRUE	1	0.765723808824594	2		1189	867	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0021710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	133	367	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	0.234161041580101	1	FACETS	0.772	0.704	0.843	0.772	0.704	0.843	INDETERMINATE	1	TRUE	0	0.453194899933954	1		367	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0021716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	419	857	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.857219372700686	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.862160173219359	2		859	475	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0021716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	40	786	3	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.603564954406015	4	FACETS	0.271	0.224	0.323	0.135	0.112	0.162	SUBCLONAL	1	TRUE	2	0.862160173219359	4		789	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0021717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	259	853	0	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	0.341463086447044	2	FACETS	0.858	0.806	0.911	0.858	0.806	0.911	CLONAL	2	TRUE	0	0.36771853585773	2		853	821	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405761	70405761	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs569630690	NA	P-0021717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	53	609	0	ENST00000373644.4:c.3275A>G	p.Tyr1092Cys	p.Y1092C	ENST00000373644	NM_030625.2	1092	tAt/tGt	4/12	0.221042946087465	1	FACETS	0.465	0.397	0.54	0.465	0.397	0.54	SUBCLONAL	1	TRUE	0	0.36771853585773	1		609	506	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0021718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	201	967	2	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.415101850655073	2		969	960	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411063	63411063	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	166	876	0	ENST00000330258.3:c.2104G>T	p.Glu702Ter	p.E702*	ENST00000330258	NM_152424.3	702	Gag/Tag	2/2	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.415101850655073	2		876	797	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207092	1207092	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs778376925	NA	P-0021718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	153	1056	2	ENST00000326873.7:c.180C>A	p.Tyr60Ter	p.Y60*	ENST00000326873	NM_000455.4	60	taC/taA	1/10	0.415101850655073	1	FACETS	0.809	0.742	0.879	0.809	0.742	0.879	CLONAL	1	TRUE	0	0.415101850655073	1		1058	722	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748520	162748520	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0021718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	38	463	0	ENST00000367921.3:c.2433+1G>C		p.X811_splice	ENST00000367921	NM_006182.2	811			0.223936233989897	1	FACETS	0.299	0.247	0.358	0.299	0.247	0.358	INDETERMINATE	1	TRUE	0	0.415101850655073	1		463	485	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600473	10600473	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	135	819	0	ENST00000171111.5:c.1382T>G	p.Ile461Ser	p.I461S	ENST00000171111	NM_203500.1	461	aTc/aGc	4/6	0.415101850655073	1	FACETS	0.855	0.78	0.933	0.855	0.78	0.933	CLONAL	1	TRUE	0	0.415101850655073	1		819	603	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108652	8108652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777705809	NA	P-0021719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	205	937	1	ENST00000585124.1:c.743G>A	p.Arg248His	p.R248H	ENST00000585124	NM_004217.3	248	cGc/cAc	8/9	1	2	FACETS	0.933	0.866	1	0.933	0.866	1	CLONAL	1	TRUE	1	0.494833255074221	2		938	888	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0021719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	13	1042	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	0.153165467355836	0	FACETS	0.046	0.032	0.063			1	INDETERMINATE	1	TRUE	0	0.494833255074221	0		1042	580	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148546	119148554	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GTGACCCAG	GTGACCCAG	-	novel	NA	P-0021719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	102	642	0	ENST00000264033.4:c.1091_1095+4del		p.VTQdel	ENST00000264033	NM_005188.3	363	GTGACCCAG/-	7/16	1	2	FACETS	0.537	0.48	0.597	0.537	0.48	0.597	SUBCLONAL	1	TRUE	1	0.494833255074221	2		642	768	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550523	29550523	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	219	667	0	ENST00000356175.3:c.1783G>T	p.Glu595Ter	p.E595*	ENST00000356175	NM_000267.3	595	Gaa/Taa	16/57	1	2	FACETS	0.959	0.893	1	0.959	0.893	1	CLONAL	1	TRUE	1	0.494833255074221	2		667	923	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	35	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.71	0.58	0.858	0.71	0.58	0.858	SUBCLONAL	1	TRUE	1	0.13	2		434	758	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252994	36252995	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0021720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	54	764	0	ENST00000300305.3:c.366_367dup	p.Asp123GlyfsTer11	p.D123Gfs*11	ENST00000300305		123	gat/gGGat	4/8	1	2	FACETS	0.926	0.789	1	0.926	0.789	1	CLONAL	1	TRUE	1	0.13	2		764	897	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845366	151845366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	50	934	1	ENST00000262189.6:c.13646G>A	p.Arg4549His	p.R4549H	ENST00000262189	NM_170606.2	4549	cGc/cAc	52/59	1	2	FACETS	0.868	0.734	1	0.868	0.734	1	CLONAL	1	TRUE	1	0.13	2		935	886	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0021721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	141	779	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.191344211947936	5	FACETS	0.792	0.721	0.866	0.528	0.481	0.577	SUBCLONAL	2	FALSE	2	0.3	5		779	861	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0021721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	156	795	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.219054331031165	2	FACETS	0.791	0.727	0.858	0.791	0.727	0.858	SUBCLONAL	2	FALSE	0	0.3	2		796	657	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971026	21971054	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCAGGCATCGCGCACGTCCAGCCGCGC	CCCCAGGCATCGCGCACGTCCAGCCGCGC	-	novel	NA	P-0021721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	111	581	0	ENST00000304494.5:c.304_332del	p.Ala102ProfsTer8	p.A102Pfs*8	ENST00000304494	NM_000077.4	102	GCGCGGCTGGACGTGCGCGATGCCTGGGGc/c	2/3	0.220802114624152	2	FACETS	0.845	0.764	0.928	0.845	0.764	0.928	CLONAL	2	FALSE	0	0.3	2		581	438	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563428	87563428	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1564492351	NA	P-0021721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	130	823	1	ENST00000277120.3:c.1816G>A	p.Glu606Lys	p.E606K	ENST00000277120		606	Gag/Aag	16/19	0.220802114624152	2	FACETS	1	0.986	1	0.741	0.674	0.81	CLONAL	1	FALSE	0	0.3	2		824	585	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978946	25978946	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	97	672	0	ENST00000435504.4:c.977C>G	p.Ala326Gly	p.A326G	ENST00000435504		326	gCc/gGc	10/13	1	2	FACETS	0.406	0.362	0.454	0.406	0.362	0.454	SUBCLONAL	1	FALSE	1	0.568440700941042	2		672	840	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794117	242794117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773349951	NA	P-0021724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	329	1013	0	ENST00000334409.5:c.611G>A	p.Arg204His	p.R204H	ENST00000334409	NM_005018.2	204	cGc/cAc	4/5	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.591519121258078	2		1013	965	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587782272	NA	P-0021724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	262	804	0	ENST00000269305.4:c.994-1G>C		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.591519121258078	1	FACETS	0.987	0.932	1	0.987	0.932	1	CLONAL	1	TRUE	0	0.591519121258078	1		804	632	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73352418	73352418	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	104	861	1	ENST00000377767.4:c.487del	p.Met163CysfsTer12	p.M163Cfs*12	ENST00000377767	NM_014953.3	163	Atg/tg	3/21	0.591519121258078	5	FACETS	0.584	0.522	0.651	0.195	0.174	0.217	SUBCLONAL	1	TRUE	2	0.591519121258078	5		862	1136	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268731	46268731	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1366	229	865	0	ENST00000371998.3:c.3016C>G	p.Gln1006Glu	p.Q1006E	ENST00000371998		1006	Caa/Gaa	16/23	0.554353298004716	5	FACETS	0.916	0.851	0.984	0.229	0.212	0.246	CLONAL	1	TRUE	1	0.591519121258078	5		865	1595	SUCCESS
APC	324	MSKCC	GRCh37	5	112175137	112175143	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTGAA	AGCTGAA	-	novel	NA	P-0021724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	229	418	0	ENST00000257430.4:c.3846_3852del	p.Ala1283MetfsTer3	p.A1283Mfs*3	ENST00000257430	NM_000038.5	1282	tcAGCTGAA/tc	16/16	NA	2	FACETS	0.911	0.862	0.959			1	INDETERMINATE	2	TRUE	NA	0.591519121258078	2		418	425	SUCCESS
AR	367	MSKCC	GRCh37	X	66931352	66931352	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	93	891	0	ENST00000374690.3:c.1994T>A	p.Ile665Asn	p.I665N	ENST00000374690	NM_000044.3	665	aTt/aAt	4/8	0.591519121258078	2	FACETS	0.369	0.327	0.414	0.185	0.163	0.207	SUBCLONAL	1	TRUE	0	0.591519121258078	2		891	852	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74868172	74868172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1563677151	NA	P-0021725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	15	194	0	ENST00000284811.8:c.122C>T	p.Thr41Met	p.T41M	ENST00000284811		41	aCg/aTg	3/4	0.421503788373275	3	FACETS	0.504	0.37	0.664	0.252	0.185	0.332	SUBCLONAL	1	TRUE	1	0.421503788373275	3		194	171	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696435	47696435	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	245	1082	0	ENST00000347630.2:c.388G>A	p.Asp130Asn	p.D130N	ENST00000347630	NM_001007230.1	130	Gac/Aac	6/11	1	2	FACETS	0.811	0.761	0.861	1	0.994	1	CLONAL	2	TRUE	1	0.421503788373275	2		1082	717	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595381	141595381	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	332	1147	0	ENST00000220592.5:c.52A>T	p.Ile18Phe	p.I18F	ENST00000220592	NM_012154.3	18	Atc/Ttc	2/19	0.421503788373275	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.421503788373275	3		1147	887	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0021726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	1010	875	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.782999305508391	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.830224031821875	3		877	1126	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866099	37866099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs896171398	NA	P-0021726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	728	1025	2	ENST00000269571.5:c.608G>A	p.Arg203His	p.R203H	ENST00000269571		203	cGc/cAc	5/27	0.782999305508391	3	FACETS	0.973	0.956	0.989	0.973	0.956	0.989	CLONAL	3	TRUE	0	0.830224031821875	3		1027	850	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589223	67589225	+	inframe_deletion	In_Frame_Del	DEL	TAA	TAA	-	novel	NA	P-0021726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	550	627	0	ENST00000274335.5:c.1214_1216del	p.Ile405del	p.I405del	ENST00000274335		404	tTAAta/tta	9/15	0.583910003601122	4	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.830224031821875	4		627	1008	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0021730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	104	573	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.948	0.849	1	0.948	0.849	1	CLONAL	1	TRUE	1	0.31	2		573	708	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457243	25457243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377577594	NA	P-0021730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	31	735	1	ENST00000264709.3:c.2644C>T	p.Arg882Cys	p.R882C	ENST00000264709	NM_175629.2	882	Cgc/Tgc	23/23	1	2	FACETS	0.238	0.192	0.292	0.238	0.192	0.292	SUBCLONAL	1	TRUE	1	0.31	2		736	839	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs786202525	NA	P-0021733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	394	694	0	ENST00000269305.4:c.532del	p.His178ThrfsTer69	p.H178Tfs*69	ENST00000269305	NM_001126112.2	178	Cac/ac	5/11	0.817123780430788	2	FACETS	0.983	0.956	1	0.983	0.956	1	CLONAL	2	TRUE	0	0.826508400257539	2		694	485	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25462022	25462022	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	223	660	0	ENST00000264709.3:c.2385G>T	p.Trp795Cys	p.W795C	ENST00000264709	NM_175629.2	795	tgG/tgT	20/23	0.801138101405927	3	FACETS	1	0.953	1	0.513	0.479	0.547	CLONAL	1	TRUE	1	0.826508400257539	3		660	744	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129199	64129199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs545430280	NA	P-0021733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	218	828	0	ENST00000334205.4:c.737C>T	p.Thr246Met	p.T246M	ENST00000334205	NM_003942.2	246	aCg/aTg	7/17	0.826508400257539	3	FACETS	1	0.952	1	0.512	0.478	0.547	CLONAL	1	TRUE	1	0.826508400257539	3		828	728	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259723	11259723	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	330	567	0	ENST00000361445.4:c.3982G>C	p.Glu1328Gln	p.E1328Q	ENST00000361445	NM_004958.3	1328	Gaa/Caa	27/58	NA	2	FACETS	0.983	0.954	1			1	INDETERMINATE	2	TRUE	NA	0.826508400257539	2		567	406	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006401	12006401	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	275	741	0	ENST00000396373.4:c.369G>C	p.Gln123His	p.Q123H	ENST00000396373	NM_001987.4	123	caG/caC	4/8	0.710281769146653	3	FACETS	0.84	0.797	0.883	0.84	0.797	0.883	CLONAL	2	TRUE	1	0.826508400257539	3		741	560	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433362	49433362	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	187	842	0	ENST00000301067.7:c.8085C>G	p.Ile2695Met	p.I2695M	ENST00000301067	NM_003482.3	2695	atC/atG	32/54	0.826508400257539	3	FACETS	0.946	0.877	1	0.473	0.438	0.509	CLONAL	1	TRUE	1	0.826508400257539	3		842	676	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037951	49037951	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	358	703	0	ENST00000267163.4:c.2191C>G	p.Leu731Val	p.L731V	ENST00000267163	NM_000321.2	731	Ctt/Gtt	21/27	0.826508400257539	3	FACETS	0.986	0.962	1	0.986	0.962	1	CLONAL	3	TRUE	0	0.826508400257539	3		703	414	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039202	49039202	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	489	674	0	ENST00000267163.4:c.2280C>A	p.Phe760Leu	p.F760L	ENST00000267163	NM_000321.2	760	ttC/ttA	22/27	0.826508400257539	3	FACETS	0.959	0.938	0.98	0.959	0.938	0.98	CLONAL	3	TRUE	0	0.826508400257539	3		674	581	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680646	88680646	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	591	614	1	ENST00000360948.2:c.611T>A	p.Ile204Asn	p.I204N	ENST00000360948	NM_001012338.2	204	aTc/aAc	6/19	0.706540978608985	6	FACETS	0.947	0.917	0.976	0.947	0.917	0.976	CLONAL	4	TRUE	2	0.826508400257539	6		615	1002	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857413	9857413	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	339	642	0	ENST00000330684.3:c.3988A>T	p.Ser1330Cys	p.S1330C	ENST00000330684	NM_001134407.1	1330	Agt/Tgt	13/13	0.826508400257539	4	FACETS	0.962	0.915	1	0.962	0.915	1	CLONAL	2	TRUE	2	0.826508400257539	4		642	779	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271674	15271674	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	264	1066	1	ENST00000263388.2:c.6765G>T	p.Trp2255Cys	p.W2255C	ENST00000263388	NM_000435.2	2255	tgG/tgT	33/33	0.710281769146653	3	FACETS	1	0.962	1	0.516	0.485	0.548	CLONAL	1	TRUE	1	0.826508400257539	3		1067	875	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260062	19260062	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	508	879	0	ENST00000162023.5:c.231G>T	p.Glu77Asp	p.E77D	ENST00000162023		77	gaG/gaT	7/13	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.826508400257539	2		879	599	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25990551	25990551	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	159	781	0	ENST00000435504.4:c.676C>G	p.Gln226Glu	p.Q226E	ENST00000435504		226	Caa/Gaa	8/13	0.801138101405927	3	FACETS	0.973	0.897	1	0.486	0.448	0.526	CLONAL	1	TRUE	1	0.826508400257539	3		781	559	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566838	212566838	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	134	443	1	ENST00000342788.4:c.1343A>T	p.Gln448Leu	p.Q448L	ENST00000342788	NM_005235.2	448	cAg/cTg	12/28	0.826508400257539	3	FACETS	0.969	0.886	1	0.484	0.443	0.527	CLONAL	1	TRUE	1	0.826508400257539	3		444	473	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026981	71026981	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0021733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	604	622	0	ENST00000318789.4:c.1346C>G	p.Ser449Ter	p.S449*	ENST00000318789	NM_032682.5	449	tCa/tGa	15/21	0.826508400257539	3	FACETS	0.981	0.962	0.998	0.981	0.962	0.998	CLONAL	3	TRUE	0	0.826508400257539	3		622	702	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215889	142215890	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0021733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	414	568	1	ENST00000350721.4:c.5703_5704delinsTT	p.Ala1902Ser	p.A1902S	ENST00000350721	NM_001184.3	1901	ctGGct/ctTTct	33/47	0.826508400257539	6	FACETS	0.919	0.879	0.96			1	CLONAL	3	TRUE	NA	0.826508400257539	6		569	964	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155374	185155374	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	141	555	0	ENST00000265026.3:c.615C>G	p.Ile205Met	p.I205M	ENST00000265026	NM_004721.4	205	atC/atG	3/14	0.706540978608985	6	FACETS	1	0.953	1	0.267	0.243	0.293	CLONAL	1	TRUE	2	0.826508400257539	6		555	846	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628314	187628314	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	523	746	0	ENST00000441802.2:c.2668G>T	p.Glu890Ter	p.E890*	ENST00000441802	NM_005245.3	890	Gag/Tag	2/27	0.817123780430788	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.826508400257539	2		746	622	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982001	38982001	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	231	693	0	ENST00000357387.3:c.721C>G	p.Arg241Gly	p.R241G	ENST00000357387	NM_152756.3	241	Cga/Gga	8/38	0.80261096272978	2	FACETS	1	0.993	1	0.687	0.651	0.722	CLONAL	1	TRUE	0	0.826508400257539	2		693	407	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777889	27777889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768126021	NA	P-0021733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	410	464	0	ENST00000369163.2:c.38G>A	p.Gly13Asp	p.G13D	ENST00000369163	NM_003536.2	13	gGc/gAc	1/1	0.826508400257539	6	FACETS	0.938	0.897	0.98	0.938	0.897	0.98	CLONAL	3	TRUE	3	0.826508400257539	6		464	935	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671002	30671002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	500	777	3	ENST00000376406.3:c.5744G>A	p.Ser1915Asn	p.S1915N	ENST00000376406	NM_014641.2	1915	aGt/aAt	12/15	0.75429135639342	4	FACETS	0.971	0.932	1	0.971	0.932	1	CLONAL	2	TRUE	2	0.826508400257539	4		780	1138	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672305	30672305	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	449	782	0	ENST00000376406.3:c.4655C>T	p.Thr1552Ile	p.T1552I	ENST00000376406	NM_014641.2	1552	aCa/aTa	10/15	0.75429135639342	4	FACETS	0.95	0.91	0.991	0.95	0.91	0.991	CLONAL	2	TRUE	2	0.826508400257539	4		782	1044	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771169	161771169	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	833	756	1	ENST00000366898.1:c.1360A>T	p.Asn454Tyr	p.N454Y	ENST00000366898	NM_004562.2	454	Aac/Tac	12/12	0.826508400257539	4	FACETS	0.963	0.939	0.986			1	CLONAL	3	TRUE	NA	0.826508400257539	4		757	1275	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6038907	6038907	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0021733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	247	543	1	ENST00000265849.7:c.538-1G>T		p.X180_splice	ENST00000265849	NM_000535.5	180			0.352621997185221	6	FACETS	0.908	0.856	0.961	0.908	0.856	0.961	INDETERMINATE	3	TRUE	3	0.826508400257539	6		544	582	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345858	152345858	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	397	775	0	ENST00000359321.1:c.712A>T	p.Arg238Trp	p.R238W	ENST00000359321	NM_005431.1	238	Agg/Tgg	3/3	0.826508400257539	4	FACETS	0.971	0.927	1	0.971	0.927	1	CLONAL	2	TRUE	2	0.826508400257539	4		775	904	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56859043	56859043	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	140	741	0	ENST00000519728.1:c.169C>T	p.Gln57Ter	p.Q57*	ENST00000519728	NM_002350.3	57	Caa/Taa	3/13	NA	2	FACETS	1	0.941	1			1	INDETERMINATE	1	TRUE	NA	0.826508400257539	2		741	332	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864657	68864657	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	111	288	0	ENST00000288368.4:c.28C>A	p.Arg10Ser	p.R10S	ENST00000288368	NM_024870.2	10	Cgc/Agc	1/40	0.826508400257539	6	FACETS	1	0.954	1	0.276	0.248	0.305	CLONAL	1	TRUE	2	0.826508400257539	6		288	646	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080684	5080684	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0021733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	115	602	0	ENST00000381652.3:c.2434+1G>C		p.X812_splice	ENST00000381652	NM_004972.3	812			0.810985927403564	1	FACETS	0.878	0.817	0.937	0.878	0.817	0.937	CLONAL	1	TRUE	0	0.826508400257539	1		602	186	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750362	133750362	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	412	692	3	ENST00000318560.5:c.1193G>T	p.Gly398Val	p.G398V	ENST00000318560	NM_005157.4	398	gGa/gTa	7/11	0.817123780430788	2	FACETS	0.951	0.925	0.977	0.951	0.925	0.977	CLONAL	2	TRUE	0	0.826508400257539	2		695	524	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399774	139399790	+	frameshift_variant	Frame_Shift_Del	DEL	TCCGCACGCTGGCAGTC	TCCGCACGCTGGCAGTC	-	novel	NA	P-0021733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	204	626	0	ENST00000277541.6:c.4558_4574del	p.Asp1520ArgfsTer84	p.D1520Rfs*84	ENST00000277541	NM_017617.3	1520	GACTGCCAGCGTGCGGAa/a	25/34	0.820778347939771	2	FACETS	0.854	0.815	0.892	0.854	0.815	0.892	CLONAL	2	TRUE	0	0.826508400257539	2		626	289	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338683	70338683	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	601	381	0	ENST00000374080.3:c.79C>T	p.Gln27Ter	p.Q27*	ENST00000374080		27	Cag/Tag	1/45	0.772605543338397	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.826508400257539	2		381	671	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0021734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	318	692	2	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.44889713643714	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.44889713643714	2		694	698	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0021734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	149	565	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.44889713643714	2		565	660	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068366	26068368	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0021734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	370	589	0	ENST00000435504.4:c.122_124del	p.Glu41del	p.E41del	ENST00000435504		41	gAAGga/gga	2/13	0.44889713643714	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.44889713643714	2		589	804	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206882	36206883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	217	451	0	ENST00000300305.3:c.629dup	p.Asp211ArgfsTer2	p.D211Rfs*2	ENST00000300305		210	cta/ctTa	6/8	0.44889713643714	2	FACETS	0.987	0.927	1	0.987	0.927	1	CLONAL	2	TRUE	0	0.44889713643714	2		451	490	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151921101	151921102	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0021734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	12	19	0	ENST00000262189.6:c.3321_3322del	p.Asp1107GlufsTer13	p.D1107Efs*13	ENST00000262189	NM_170606.2	1107	gaTAga/gaga	20/59	0.44889713643714	3	FACETS	1	0.836	1	1	0.836	1	CLONAL	2	TRUE	1	0.44889713643714	3		19	28	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	163	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.421409344399203	2		434	638	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216702	36216702	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748120825	NA	P-0021738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	138	595	0	ENST00000222270.7:c.3868C>T	p.Arg1290Cys	p.R1290C	ENST00000222270	NM_014727.1	1290	Cgc/Tgc	13/37	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.421409344399203	2		595	633	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0021740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8383	2505	849	0	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.577591444991108	40	FACETS	0.954	0.934	0.974	0.238	0.233	0.244	CLONAL	10	TRUE	0	0.577591444991108	40		849	10888	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486101	29486101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199474728	NA	P-0021740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	96	638	0	ENST00000356175.3:c.278G>A	p.Cys93Tyr	p.C93Y	ENST00000356175	NM_000267.3	93	tGt/tAt	3/57	1	2	FACETS	0.947	0.852	1	0.947	0.852	1	CLONAL	1	TRUE	1	0.577591444991108	2		638	351	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29662033	29662033	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs974012306	NA	P-0021740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	68	558	0	ENST00000356175.3:c.5927G>A	p.Trp1976Ter	p.W1976*	ENST00000356175	NM_000267.3	1976	tGg/tAg	39/57	1	2	FACETS	0.875	0.77	0.987	0.875	0.77	0.987	CLONAL	1	TRUE	1	0.577591444991108	2		558	269	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31431786	31431786	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0021740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	27	488	0	ENST00000344624.3:c.3043-1G>A		p.X1015_splice	ENST00000344624		1015			1	2	FACETS	0.305	0.242	0.375	0.305	0.242	0.375	SUBCLONAL	1	TRUE	1	0.577591444991108	2		488	307	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0021742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	319	670	1	ENST00000269305.4:c.560-1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.700226293973537	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.700226293973537	1		671	562	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443818	18443818	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	49	572	0	ENST00000266497.5:c.791T>G	p.Val264Gly	p.V264G	ENST00000266497		264	gTt/gGt	3/31	1	2	FACETS	0.348	0.295	0.406	0.348	0.295	0.406	SUBCLONAL	1	TRUE	1	0.700226293973537	2		572	402	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243606	41243640	+	frameshift_variant	Frame_Shift_Del	DEL	ATCCTGGGTGTTTGTATTTGCAGTCAAGTCTTCCA	ATCCTGGGTGTTTGTATTTGCAGTCAAGTCTTCCA	-	novel	NA	P-0021742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	585	830	0	ENST00000357654.3:c.3908_3942del	p.Leu1303SerfsTer15	p.L1303Sfs*15	ENST00000357654	NM_007294.3	1303	tTGGAAGACTTGACTGCAAATACAAACACCCAGGAT/t	10/23	0.661419085560398	3	FACETS	0.906	0.881	0.93	0.906	0.881	0.93	CLONAL	3	TRUE	0	0.700226293973537	3		830	830	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218521	5218521	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	235	973	0	ENST00000357368.4:c.3958del	p.Arg1320AlafsTer6	p.R1320Afs*6	ENST00000357368	NM_002850.3	1320	Cgc/gc	25/38	1	2	FACETS	0.501	0.466	0.537	0.501	0.466	0.537	SUBCLONAL	1	TRUE	1	0.700226293973537	2		973	1341	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	179	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.22215951494945	3	FACETS	1	0.981	1	1	0.992	1	CLONAL	3	FALSE	1	0.22215951494945	3		434	515	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835794	68835794	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	267	654	0	ENST00000261769.5:c.385C>T	p.Gln129Ter	p.Q129*	ENST00000261769	NM_004360.3	129	Cag/Tag	3/16	0.22215951494945	1	FACETS	0.969	0.919	1	1	0.996	1	CLONAL	4	FALSE	0	0.22215951494945	1		654	551	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0021746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	13	772	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		772	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0021747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	98	815	1	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	1	2	FACETS	0.832	0.741	0.929	0.832	0.741	0.929	CLONAL	1	TRUE	1	0.260047510754342	2		816	906	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-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	116	585	0	ENST00000358487.5:c.749-183_801del		p.X250_splice	ENST00000358487	NM_000141.4	250		7/18	0.215651972329881	2	FACETS	1	0.98	1	0.676	0.61	0.745	CLONAL	1	TRUE	0	0.260047510754342	2		585	660	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214479	5214479	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	111	704	0	ENST00000357368.4:c.4507C>T	p.Gln1503Ter	p.Q1503*	ENST00000357368	NM_002850.3	1503	Cag/Tag	30/38	NA	2	FACETS	1	0.909	1			1	INDETERMINATE	1	TRUE	NA	0.260047510754342	2		704	843	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023640	31023640	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	94	782	0	ENST00000375687.4:c.3125C>A	p.Pro1042Gln	p.P1042Q	ENST00000375687	NM_015338.5	1042	cCa/cAa	13/13	NA	2	FACETS	0.794	0.706	0.889			1	INDETERMINATE	1	TRUE	NA	0.260047510754342	2		782	910	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938463	76938463	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	99	640	0	ENST00000373344.5:c.2285del	p.Lys762ArgfsTer6	p.K762Rfs*6	ENST00000373344	NM_000489.3	762	aAg/ag	9/35	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.328248758759982	2		640	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0021750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	368	815	1	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.408991588152071	3	FACETS	0.943	0.901	0.985	0.943	0.901	0.985	CLONAL	3	TRUE	0	0.408991588152071	3		816	766	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951110	17951110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777790283	NA	P-0021750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	77	822	0	ENST00000458235.1:c.1183C>T	p.Arg395Cys	p.R395C	ENST00000458235	NM_000215.3	395	Cgt/Tgt	9/24	0.293313339392012	3	FACETS	0.656	0.576	0.743	0.328	0.288	0.372	SUBCLONAL	1	TRUE	1	0.408991588152071	3		822	691	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	48	699	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.752	0.633	0.883	0.752	0.633	0.883	SUBCLONAL	1	TRUE	1	0.14	2		699	912	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0021751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	42	774	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.729	0.607	0.866	0.729	0.607	0.866	SUBCLONAL	1	TRUE	1	0.14	2		774	823	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0021751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	45	942	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.819	0.686	0.966	0.819	0.686	0.966	CLONAL	1	TRUE	1	0.14	2		942	785	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016634	12016634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	36	665	0	ENST00000353533.5:c.770C>T	p.Ser257Phe	p.S257F	ENST00000353533	NM_003010.3	257	tCt/tTt	7/11	1	2	FACETS	0.759	0.622	0.913	0.759	0.622	0.913	CLONAL	1	TRUE	1	0.14	2		665	678	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849456	68849456	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	72	898	0	ENST00000261769.5:c.1359del	p.His453GlnfsTer2	p.H453Qfs*2	ENST00000261769	NM_004360.3	453	caC/ca	10/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.14	2		898	849	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0021753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	122	772	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.948	0.857	1	0.948	0.857	1	CLONAL	1	TRUE	1	0.346941135655452	2		772	742	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844175	68844175	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	153	840	1	ENST00000261769.5:c.763C>T	p.Gln255Ter	p.Q255*	ENST00000261769	NM_004360.3	255	Cag/Tag	6/16	0.346941135655452	1	FACETS	0.992	0.909	1	0.992	0.909	1	CLONAL	1	TRUE	0	0.346941135655452	1		841	735	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186501406	186501406	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	82	515	1	ENST00000323963.5:c.7G>C	p.Gly3Arg	p.G3R	ENST00000323963		3	Ggt/Cgt	1/11	1	2	FACETS	0.9	0.796	1	0.9	0.796	1	CLONAL	1	TRUE	1	0.346941135655452	2		516	525	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923643	39923643	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	112	893	1	ENST00000378444.4:c.3448G>A	p.Glu1150Lys	p.E1150K	ENST00000378444	NM_001123385.1	1150	Gag/Aag	7/15	1	2	FACETS	0.762	0.685	0.844	0.762	0.685	0.844	SUBCLONAL	1	TRUE	1	0.346941135655452	2		894	847	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0021754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	132	857	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.3	3	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	3		857	756	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0021754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	49	1091	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		1091	663	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038756	47038756	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	48	1037	0	ENST00000377604.3:c.763C>T	p.Gln255Ter	p.Q255*	ENST00000377604	NM_001204468.1	255	Cag/Tag	9/24	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		1037	726	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213349	36213350	+	missense_variant	Missense_Mutation	DNP	TG	TG	GT	novel	NA	P-0021756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	251	1076	1	ENST00000222270.7:c.2546_2547delinsGT	p.Val849Gly	p.V849G	ENST00000222270	NM_014727.1	849	gTG/gGT	4/37	1	2	FACETS	0.792	0.74	0.845	0.792	0.74	0.845	SUBCLONAL	1	TRUE	1	0.570060592392832	2		1077	1112	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902386	1902386	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	206	786	0	ENST00000382891.5:c.5A>C	p.Glu2Ala	p.E2A	ENST00000382891	NM_133335.3	2	gAa/gCa	2/22	1	2	FACETS	0.896	0.833	0.96	0.896	0.833	0.96	CLONAL	1	TRUE	1	0.570060592392832	2		786	807	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0021757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	124	687	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.236457676546839	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.236457676546839	1		687	695	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627306	37627307	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs755536892	NA	P-0021757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	37	636	0	ENST00000447079.4:c.1233_1235dup	p.Ala413dup	p.A413dup	ENST00000447079	NM_015083.1	413	-/GCT	2/14	0.236457676546839	1	FACETS	0.879	0.727	1	0.879	0.727	1	CLONAL	1	TRUE	0	0.236457676546839	1		636	314	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31379407	31379407	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	337	587	0	ENST00000328111.2:c.814G>C	p.Val272Leu	p.V272L	ENST00000328111	NM_006892.3	272	Gtc/Ctc	8/23	0.236457676546839	5	FACETS	1	0.973	1	1	0.994	1	CLONAL	5	TRUE	1	0.236457676546839	5		587	749	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913517	NA	P-0021758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	147	560	0	ENST00000288135.5:c.1676T>G	p.Val559Gly	p.V559G	ENST00000288135	NM_000222.2	559	gTt/gGt	11/21	1	2	FACETS	0.963	0.884	1	0.963	0.884	1	CLONAL	1	TRUE	1	0.541216995179572	2		560	564	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438008	49438008	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	51	867	0	ENST00000301067.7:c.5163G>C	p.Leu1721Phe	p.L1721F	ENST00000301067	NM_003482.3	1721	ttG/ttC	21/54	1	2	FACETS	0.201	0.17	0.235	0.201	0.17	0.235	SUBCLONAL	1	TRUE	1	0.541216995179572	2		867	939	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158103	27158103	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	149	734	0	ENST00000380036.4:c.327G>C	p.Glu109Asp	p.E109D	ENST00000380036	NM_000459.3	109	gaG/gaC	2/23	1	2	FACETS	0.823	0.754	0.895	0.823	0.754	0.895	CLONAL	1	TRUE	1	0.541216995179572	2		734	669	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115272914	115272915	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0021758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	197	771	1	ENST00000438362.2:c.1458_1459del	p.Pro487Ter	p.P487*	ENST00000438362	NM_001242891.1	486	aaTCct/aact	12/20	0.541216995179572				0.807	0.927				CLONAL	1	TRUE	0	0.541216995179572	1		772	613	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665631	86665631	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs756634599	NA	P-0021768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	66	346	0	ENST00000274376.6:c.1612C>T	p.Pro538Ser	p.P538S	ENST00000274376	NM_002890.2	538	Cca/Tca	12/25	1	2	FACETS	0.916	0.815	1	0.916	0.815	1	CLONAL	1	TRUE	1	0.895425599445457	2		346	161	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371733	45371733	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	118	463	1	ENST00000262160.6:c.1258A>G	p.Lys420Glu	p.K420E	ENST00000262160	NM_005901.5	420	Aaa/Gaa	10/11	1	2	FACETS	0.9	0.824	0.976	0.9	0.824	0.976	CLONAL	1	TRUE	1	0.895425599445457	2		464	293	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0021771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	170	692	2	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.279320097651919	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	0	0.279320097651919	2		694	595	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0021771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	54	710	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.914	0.783	1	0.914	0.783	1	CLONAL	1	TRUE	1	0.279320097651919	2		711	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0021771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	144	784	4	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.279320097651919	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.279320097651919	1		788	862	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591888	48591888	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	151	794	1	ENST00000342988.3:c.1051G>T	p.Asp351Tyr	p.D351Y	ENST00000342988	NM_005359.5	351	Gat/Tat	9/12	0.232598045522054	2	FACETS	0.94	0.864	1	0.94	0.864	1	CLONAL	2	TRUE	0	0.279320097651919	2		795	575	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0021771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	79	465	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.279320097651919	3	FACETS	0.893	0.791	1	0.893	0.791	1	CLONAL	2	TRUE	1	0.279320097651919	3		465	361	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130352	2130352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773951533	NA	P-0021771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	109	1117	2	ENST00000219476.3:c.3584C>T	p.Ala1195Val	p.A1195V	ENST00000219476	NM_000548.3	1195	gCg/gTg	30/42	0.279320097651919	3	FACETS	0.965	0.865	1	0.482	0.432	0.535	CLONAL	1	TRUE	1	0.279320097651919	3		1119	922	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0021771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	55	713	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.279320097651919	3	FACETS	0.828	0.709	0.959	0.414	0.354	0.48	CLONAL	1	TRUE	1	0.279320097651919	3		714	542	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003812	45003812	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0021771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	87	660	0	ENST00000558401.1:c.67+1G>A		p.X23_splice	ENST00000558401	NM_004048.2	23			1	2	FACETS	0.937	0.83	1	0.937	0.83	1	CLONAL	1	TRUE	1	0.279320097651919	2		660	665	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088726	27088747	+	frameshift_variant	Frame_Shift_Del	DEL	GGACAGATACACACAGGCATGG	GGACAGATACACACAGGCATGG	-	novel	NA	P-0021771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	69	1095	0	ENST00000324856.7:c.2336_2357del	p.Gly779AlafsTer47	p.G779Afs*47	ENST00000324856	NM_006015.4	779	GGACAGATACACACAGGCATGGgc/gc	7/20	1	2	FACETS	0.629	0.546	0.718	0.629	0.546	0.718	SUBCLONAL	1	TRUE	1	0.279320097651919	2		1095	786	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873063	134873063	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	115	1127	0	ENST00000398015.3:c.1367A>T	p.Gln456Leu	p.Q456L	ENST00000398015	NM_004441.4	456	cAg/cTg	6/16	1	2	FACETS	0.983	0.885	1	0.983	0.885	1	CLONAL	1	TRUE	1	0.279320097651919	2		1127	838	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0021773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	160	916	3	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.291283992587591	2		919	806	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8252049	8252049	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs774615420	NA	P-0021773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	119	691	0	ENST00000335790.3:c.28G>T	p.Val10Leu	p.V10L	ENST00000335790	NM_002315.2	10	Gtg/Ttg	2/4	0.224584326964467	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	0	0.291283992587591	1		691	662	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845394	156845395	+	missense_variant	Missense_Mutation	DNP	CG	CG	AA	novel	NA	P-0021773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1227	68	872	3	ENST00000524377.1:c.1437_1438delinsAA	p.Glu480Lys	p.E480K	ENST00000524377	NM_002529.3	479	acCGag/acAAag	12/17	0.291283992587591	4	FACETS	0.466	0.403	0.534	0.155	0.134	0.178	SUBCLONAL	1	FALSE	1	0.291283992587591	4		875	1295	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450061	32450061	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	102	669	0	ENST00000332351.3:c.751G>C	p.Gly251Arg	p.G251R	ENST00000332351	NM_024426.4	251	Ggc/Cgc	2/10	0.224584326964467	1	FACETS	0.858	0.768	0.954	0.858	0.768	0.954	CLONAL	1	FALSE	0	0.291283992587591	1		669	697	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434544	49434544	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	92	756	0	ENST00000301067.7:c.7009C>G	p.Gln2337Glu	p.Q2337E	ENST00000301067	NM_003482.3	2337	Cag/Gag	31/54	1	2	FACETS	0.693	0.615	0.777	0.693	0.615	0.777	SUBCLONAL	1	FALSE	1	0.291283992587591	2		756	911	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115111985	115111985	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	77	906	0	ENST00000257566.3:c.1755C>G	p.His585Gln	p.H585Q	ENST00000257566	NM_016569.3	585	caC/caG	7/8	1	2	FACETS	0.526	0.46	0.597	0.526	0.46	0.597	SUBCLONAL	1	FALSE	1	0.291283992587591	2		906	1005	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426748	121426748	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	188	806	0	ENST00000257555.6:c.439C>A	p.His147Asn	p.H147N	ENST00000257555		147	Cac/Aac	2/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.291283992587591	2		806	892	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911973	32911973	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555283261	NA	P-0021773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	32	663	0	ENST00000380152.3:c.3481G>A	p.Asp1161Asn	p.D1161N	ENST00000380152		1161	Gat/Aat	11/27	0.224584326964467	1	FACETS	0.298	0.241	0.363	0.298	0.241	0.363	SUBCLONAL	1	FALSE	0	0.291283992587591	1		663	629	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614563	38614563	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	63	745	0	ENST00000299084.4:c.329G>T	p.Arg110Met	p.R110M	ENST00000299084	NM_152594.2	110	aGg/aTg	3/7	0.178010762894827	0	FACETS	0.412	0.355	0.473			1	SUBCLONAL	1	FALSE	0	0.291283992587591	0		745	745	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347363	89347363	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769501359	NA	P-0021773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	68	977	1	ENST00000301030.4:c.5587G>A	p.Asp1863Asn	p.D1863N	ENST00000301030	NM_001256183.1	1863	Gac/Aac	9/13	0.291283992587591	1	FACETS	0.449	0.389	0.513	0.449	0.389	0.513	SUBCLONAL	1	FALSE	0	0.291283992587591	1		978	889	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15374334	15374334	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	124	771	1	ENST00000263377.2:c.1238G>T	p.Arg413Leu	p.R413L	ENST00000263377	NM_058243.2	413	cGt/cTt	7/20	1	2	FACETS	0.92	0.832	1	0.92	0.832	1	CLONAL	1	FALSE	1	0.291283992587591	2		772	925	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241023	39241023	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	75	574	0	ENST00000402219.2:c.2048A>T	p.Gln683Leu	p.Q683L	ENST00000402219	NM_005633.3	683	cAg/cTg	12/23	1	2	FACETS	0.769	0.673	0.871	0.769	0.673	0.871	SUBCLONAL	1	FALSE	1	0.291283992587591	2		574	670	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624847	9624847	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	42	676	0	ENST00000353224.5:c.130G>C	p.Ala44Pro	p.A44P	ENST00000353224	NM_177990.2	44	Gca/Cca	3/10	0.233640650249243	3	FACETS	0.416	0.346	0.494	0.208	0.173	0.247	SUBCLONAL	1	FALSE	1	0.291283992587591	3		676	794	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467767	66467767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	37	416	0	ENST00000273854.3:c.502G>A	p.Glu168Lys	p.E168K	ENST00000273854	NM_004439.5	168	Gaa/Aaa	3/18	1	2	FACETS	0.53	0.437	0.635	0.53	0.437	0.635	SUBCLONAL	1	FALSE	1	0.291283992587591	2		416	479	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629693	187629693	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	54	761	0	ENST00000441802.2:c.1289A>T	p.Gln430Leu	p.Q430L	ENST00000441802	NM_005245.3	430	cAg/cTg	2/27	1	2	FACETS	0.455	0.387	0.529	0.455	0.387	0.529	SUBCLONAL	1	FALSE	1	0.291283992587591	2		761	815	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522646	67522646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	35	422	1	ENST00000274335.5:c.143C>T	p.Ala48Val	p.A48V	ENST00000274335		48	gCc/gTc	1/15	1	2	FACETS	0.439	0.359	0.529	0.439	0.359	0.529	SUBCLONAL	1	FALSE	1	0.291283992587591	2		423	548	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26021110	26021110	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	37	508	0	ENST00000357647.3:c.393C>G	p.Ile131Met	p.I131M	ENST00000357647	NM_003529.2	131	atC/atG	1/1	0.222597509000226	2	FACETS	0.39	0.321	0.468	0.195	0.16	0.234	SUBCLONAL	1	FALSE	0	0.291283992587591	2		508	651	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962924	2962924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	98	1086	0	ENST00000396946.4:c.1984C>T	p.Pro662Ser	p.P662S	ENST00000396946	NM_032415.4	662	Cca/Tca	16/25	1	2	FACETS	0.638	0.568	0.714	0.638	0.568	0.714	SUBCLONAL	1	FALSE	1	0.291283992587591	2		1086	1054	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521482	8521482	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs765489687	NA	P-0021773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	79	735	1	ENST00000356435.5:c.756C>A	p.Ser252Arg	p.S252R	ENST00000356435		252	agC/agA	9/35	1	2	FACETS	0.635	0.558	0.719	0.635	0.558	0.719	SUBCLONAL	1	FALSE	1	0.291283992587591	2		736	854	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228265	53228265	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	69	825	0	ENST00000375401.3:c.2137A>G	p.Thr713Ala	p.T713A	ENST00000375401	NM_004187.3	713	Acg/Gcg	15/26	0.224584326964467	1	FACETS	0.408	0.354	0.467	0.408	0.354	0.467	SUBCLONAL	1	FALSE	0	0.291283992587591	1		825	992	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0021777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	127	681	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	0.284134203392701	2		681	795	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0021777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	92	581	1	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.961	0.854	1	0.961	0.854	1	CLONAL	1	TRUE	1	0.284134203392701	2		582	674	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749415085	NA	P-0021777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	106	495	0	ENST00000263967.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000263967	NM_006218.2	38	Cgt/Tgt	2/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.284134203392701	2		495	567	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712013	89712014	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1114167663	NA	P-0021777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	110	278	0	ENST00000371953.3:c.632dup	p.Cys211TrpfsTer32	p.C211Wfs*32	ENST00000371953	NM_000314.4	211	tgc/tGgc	6/9	0.284134203392701	3	FACETS	1	0.976	1	0.826	0.749	0.905	CLONAL	2	TRUE	0	0.284134203392701	3		278	357	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100163	27100175	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCTAGCCGCTA	CTCCTAGCCGCTA	-	novel	NA	P-0021777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	146	622	0	ENST00000324856.7:c.3960_3972del	p.Ser1322ArgfsTer155	p.S1322Rfs*155	ENST00000324856	NM_006015.4	1320	tCTCCTAGCCGCTAc/tc	16/20	0.233015466027448	2	FACETS	0.775	0.709	0.844	0.775	0.709	0.844	SUBCLONAL	2	TRUE	0	0.284134203392701	2		622	663	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973133	25973133	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	97	517	0	ENST00000435504.4:c.1292G>A	p.Cys431Tyr	p.C431Y	ENST00000435504		431	tGt/tAt	12/13	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.284134203392701	2		517	663	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371712	55371713	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	100	797	0	ENST00000297316.4:c.403dup	p.Tyr135LeufsTer27	p.Y135Lfs*27	ENST00000297316	NM_022454.3	134	-/T	2/2	1	2	FACETS	0.82	0.732	0.915	0.82	0.732	0.915	CLONAL	1	TRUE	1	0.284134203392701	2		797	858	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0021778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	90	681	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.981	0.874	1	0.981	0.874	1	CLONAL	1	TRUE	1	0.377611503119029	2		681	486	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026112	71026112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs797045585	NA	P-0021778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	92	564	0	ENST00000318789.4:c.1510C>T	p.Arg504Cys	p.R504C	ENST00000318789	NM_032682.5	504	Cgc/Tgc	17/21	1	2	FACETS	0.805	0.717	0.9	0.805	0.717	0.9	CLONAL	1	TRUE	1	0.377611503119029	2		564	605	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218446	1218447	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	149	915	0	ENST00000326873.7:c.326dup	p.Asn109LysfsTer54	p.N109Kfs*54	ENST00000326873	NM_000455.4	107	-/A	2/10	0.377611503119029	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.377611503119029	1		915	581	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602754	10602754	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	173	910	5	ENST00000171111.5:c.824C>A	p.Ser275Ter	p.S275*	ENST00000171111	NM_203500.1	275	tCg/tAg	3/6	0.377611503119029	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.377611503119029	1		915	743	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530052	212530052	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	54	339	0	ENST00000342788.4:c.1867C>T	p.Gln623Ter	p.Q623*	ENST00000342788	NM_005235.2	623	Caa/Taa	15/28	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.377611503119029	2		339	218	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519331	176519331	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765722108	NA	P-0021778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	72	659	1	ENST00000292408.4:c.737C>T	p.Pro246Leu	p.P246L	ENST00000292408	NM_213647.1	246	cCg/cTg	7/18	1	2	FACETS	0.81	0.709	0.917	0.81	0.709	0.917	CLONAL	1	TRUE	1	0.377611503119029	2		660	471	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038793	47038794	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0021778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	94	470	0	ENST00000377604.3:c.803dup	p.Leu269ProfsTer32	p.L269Pfs*32	ENST00000377604	NM_001204468.1	267	cag/caGg	9/24	1	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.377611503119029	1		470	305	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412536	63412536	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1175084390	NA	P-0021778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	26	370	0	ENST00000330258.3:c.631G>A	p.Ala211Thr	p.A211T	ENST00000330258	NM_152424.3	211	Gcc/Acc	2/2	1	1	FACETS	0.486	0.386	0.598	0.486	0.386	0.598	SUBCLONAL	1	TRUE	0	0.377611503119029	1		370	230	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0021795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	197	662	1				ENST00000310581	NM_198253.2	-/1132			NA				0.823	0.918				INDETERMINATE	2	TRUE	NA	0.667423258645761	2		663	339	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244778	46244778	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057524391	NA	P-0021795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	67	723	4	ENST00000334344.6:c.2872C>T	p.Gln958Ter	p.Q958*	ENST00000334344	NM_152641.2	958	Cag/Tag	15/21	1	2	FACETS	0.426	0.371	0.486	0.426	0.371	0.486	SUBCLONAL	1	TRUE	1	0.667423258645761	2		727	471	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244389	46244389	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	93	649	0	ENST00000334344.6:c.2483C>G	p.Pro828Arg	p.P828R	ENST00000334344	NM_152641.2	828	cCt/cGt	15/21	1	2	FACETS	0.648	0.579	0.72	0.648	0.579	0.72	SUBCLONAL	1	TRUE	1	0.667423258645761	2		649	430	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336102	73336102	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	57	356	0	ENST00000377767.4:c.2301A>C	p.Leu767Phe	p.L767F	ENST00000377767	NM_014953.3	767	ttA/ttC	17/21	1	2	FACETS	0.867	0.756	0.984	0.867	0.756	0.984	CLONAL	1	TRUE	1	0.667423258645761	2		356	197	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509627	29509627	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	40	788	0	ENST00000356175.3:c.832C>G	p.Pro278Ala	p.P278A	ENST00000356175	NM_000267.3	278	Cca/Gca	8/57	1	2	FACETS	0.324	0.269	0.384	0.324	0.269	0.384	SUBCLONAL	1	TRUE	1	0.667423258645761	2		788	370	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069417	30069417	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	53	668	1	ENST00000338641.4:c.1282C>T	p.Gln428Ter	p.Q428*	ENST00000338641	NM_000268.3	428	Cag/Tag	12/16	1	2	FACETS	0.514	0.441	0.593	0.514	0.441	0.593	SUBCLONAL	1	TRUE	1	0.667423258645761	2		669	309	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555098	106555098	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756869725	NA	P-0021795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	202	686	3	ENST00000369096.4:c.2215G>A	p.Ala739Thr	p.A739T	ENST00000369096	NM_001198.3	739	Gct/Act	7/7	0.614003667055873	4	FACETS	0.791	0.737	0.846			1	SUBCLONAL	2	TRUE	NA	0.667423258645761	4		689	638	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	109	669	0				ENST00000310581	NM_198253.2	-/1132			0.210946332795601	3	FACETS	1	0.977	1	0.652	0.587	0.721	CLONAL	1	TRUE	1	0.32061684584692	3		669	605	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0021797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	79	784	4	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.32061684584692	1	FACETS	0.521	0.457	0.589	0.521	0.457	0.589	SUBCLONAL	1	TRUE	0	0.32061684584692	1		788	795	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0021797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	253	1033	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.32061684584692	3	FACETS	0.854	0.799	0.911	0.854	0.799	0.911	CLONAL	2	TRUE	1	0.32061684584692	3		1033	1072	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112106	115112106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	45	1043	0	ENST00000257566.3:c.1634C>T	p.Thr545Met	p.T545M	ENST00000257566	NM_016569.3	545	aCg/aTg	7/8	1	2	FACETS	0.318	0.266	0.376	0.318	0.266	0.376	SUBCLONAL	1	TRUE	1	0.32061684584692	2		1043	883	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0021800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	91	779	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.723150527855378	1	FACETS	0.929	0.849	1	0.929	0.849	1	CLONAL	1	TRUE	0	0.723150527855378	1		779	173	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252162	226252162	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	11	120	0	ENST00000366813.1:c.110A>G	p.Lys37Arg	p.K37R	ENST00000366813		37	aAg/aGg	1/3	0.723150527855378	3	FACETS	0.753	0.533	1	0.377	0.266	0.505	CLONAL	1	TRUE	1	0.723150527855378	3		120	55	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437332	121437332	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1418069323	NA	P-0021800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	36	1082	2	ENST00000257555.6:c.1670C>T	p.Thr557Met	p.T557M	ENST00000257555		557	aCg/aTg	9/10	0.723150527855378	1	FACETS	0.138	0.113	0.166	0.138	0.113	0.166	SUBCLONAL	1	TRUE	0	0.723150527855378	1		1084	461	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670628	67670628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	15	620	1	ENST00000264010.4:c.1873G>A	p.Glu625Lys	p.E625K	ENST00000264010	NM_006565.3	625	Gag/Aag	11/12	0.723150527855378	1	FACETS	0.098	0.071	0.13	0.098	0.071	0.13	SUBCLONAL	1	TRUE	0	0.723150527855378	1		621	270	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11999000	11999000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	75	445	0	ENST00000353533.5:c.502C>T	p.Leu168Phe	p.L168F	ENST00000353533	NM_003010.3	168	Ctc/Ttc	4/11	0.723150527855378	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.723150527855378	1		445	112	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519337	176519337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758837002	NA	P-0021800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	166	662	1	ENST00000292408.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000292408	NM_213647.1	248	cGg/cAg	7/18	0.49415543369949	1	FACETS	0.86	0.803	0.916	0.86	0.803	0.916	CLONAL	1	TRUE	0	0.723150527855378	1		663	341	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	404	690	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	NA	2	FACETS	0.754	0.722	0.787			1	INDETERMINATE	2	TRUE	NA	0.620590083948189	2		690	863	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456566	32456566	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1311557029	NA	P-0021804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	73	88	1	ENST00000332351.3:c.326C>A	p.Ala109Glu	p.A109E	ENST00000332351	NM_024426.4	109	gCg/gAg	1/10	0.612057739065652	2	FACETS	0.912	0.828	0.994	0.912	0.828	0.994	CLONAL	2	TRUE	0	0.620590083948189	2		89	129	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73352336	73352336	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	105	546	0	ENST00000377767.4:c.569C>A	p.Pro190Gln	p.P190Q	ENST00000377767	NM_014953.3	190	cCa/cAa	3/21	0.17543625889572	3	FACETS	0.956	0.861	1	0.478	0.43	0.528	INDETERMINATE	1	TRUE	1	0.620590083948189	3		546	464	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577537	7577538	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0021804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	497	785	1	ENST00000269305.4:c.743_744delinsCT	p.Arg248Pro	p.R248P	ENST00000269305	NM_001126112.2	248	cGG/cCT	7/11	0.612057739065652	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.620590083948189	2		786	776	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664523	29664523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	168	629	0	ENST00000356175.3:c.6502C>T	p.Pro2168Ser	p.P2168S	ENST00000356175	NM_000267.3	2168	Cct/Tct	42/57	0.610600742167391	3	FACETS	0.832	0.765	0.901	0.416	0.382	0.451	CLONAL	1	TRUE	1	0.620590083948189	3		629	853	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589563	67589586	+	inframe_deletion	In_Frame_Del	DEL	TGAAGCTGTAGGGAAAAAATTACA	TGAAGCTGTAGGGAAAAAATTACA	-	novel	NA	P-0021804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	55	304	0	ENST00000274335.5:c.1330_1353del	p.Ala444_Glu451del	p.A444_E451del	ENST00000274335		442	atTGAAGCTGTAGGGAAAAAATTACAt/att	10/15	0.620590083948189	1	FACETS	0.723	0.631	0.82	0.723	0.631	0.82	SUBCLONAL	1	TRUE	0	0.620590083948189	1		304	169	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0021805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	1907	779	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.421283058146083	14	FACETS	0.963	0.95	0.977			1	CLONAL	13	TRUE	NA	0.421283058146083	14		779	2550	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0021805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	285	651	0	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	NA	2	FACETS	0.928	0.877	0.979			1	INDETERMINATE	2	TRUE	NA	0.421283058146083	2		651	729	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681100	37681100	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	251	460	0	ENST00000447079.4:c.3269C>G	p.Ala1090Gly	p.A1090G	ENST00000447079	NM_015083.1	1090	gCt/gGt	12/14	0.336729116418795	4	FACETS	0.942	0.883	1	0.942	0.883	1	CLONAL	2	TRUE	2	0.421283058146083	4		460	899	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343507	343507	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567261095	NA	P-0021806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	14	942	0	ENST00000262320.3:c.2167C>T	p.Arg723Ter	p.R723*	ENST00000262320	NM_003502.3	723	Cga/Tga	8/11	0.781222039670447	2	FACETS	0.19	0.137	0.253	0.095	0.068	0.127	SUBCLONAL	1	FALSE	0	0.781222039670447	2		942	189	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88678953	88678953	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	117	395	0	ENST00000372037.3:c.893G>A	p.Gly298Asp	p.G298D	ENST00000372037	NM_004329.2	298	gGt/gAt	10/13	0.781222039670447	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	FALSE	2	0.781222039670447	4		395	239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0021822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	1047	1078	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.613034563395034	4	FACETS	0.979	0.96	0.997	0.979	0.96	0.997	CLONAL	4	TRUE	0	0.618805433661202	4		1078	1399	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779211	3779211	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783507	NA	P-0021822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	140	403	3	ENST00000262367.5:c.5837del	p.Pro1946HisfsTer30	p.P1946Hfs*30	ENST00000262367	NM_004380.2	1946	cCa/ca	31/31	0.289050906921224	3	FACETS	1	0.971	1	0.569	0.521	0.618	INDETERMINATE	1	TRUE	1	0.618805433661202	3		406	521	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318870	163318870	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1488666574	NA	P-0021822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	232	463	0	ENST00000271452.3:c.1260G>T	p.Gln420His	p.Q420H	ENST00000271452	NM_145697.2	420	caG/caT	13/14	0.441707492923991	3	FACETS	0.907	0.854	0.961	0.907	0.854	0.961	CLONAL	2	TRUE	1	0.618805433661202	3		463	541	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437125	121437125	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs749673816	NA	P-0021822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	335	1030	0	ENST00000257555.6:c.1556C>G	p.Pro519Arg	p.P519R	ENST00000257555		519	cCg/cGg	8/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.618805433661202	2		1030	1041	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039399	49039399	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0021822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	294	935	0	ENST00000267163.4:c.2384C>G	p.Ser795Ter	p.S795*	ENST00000267163	NM_000321.2	795	tCa/tGa	23/27	0.618805433661202	1	FACETS	0.991	0.94	1	0.991	0.94	1	CLONAL	1	TRUE	0	0.618805433661202	1		935	662	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808010	3808010	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	67	611	0	ENST00000262367.5:c.3409A>G	p.Thr1137Ala	p.T1137A	ENST00000262367	NM_004380.2	1137	Acc/Gcc	18/31	0.289050906921224	3	FACETS	0.364	0.316	0.417	0.182	0.158	0.209	INDETERMINATE	1	TRUE	1	0.618805433661202	3		611	778	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950423	17950423	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	226	784	0	ENST00000458235.1:c.1304C>A	p.Thr435Lys	p.T435K	ENST00000458235	NM_000215.3	435	aCa/aAa	10/24	0.618805433661202	1	FACETS	0.926	0.87	0.982	0.926	0.87	0.982	CLONAL	1	TRUE	0	0.618805433661202	1		784	545	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587236	212587236	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	326	555	0	ENST00000342788.4:c.765T>A	p.Ser255Arg	p.S255R	ENST00000342788	NM_005235.2	255	agT/agA	7/28	0.617400573445256	2	FACETS	0.972	0.931	1	0.972	0.931	1	CLONAL	2	TRUE	0	0.618805433661202	2		555	542	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652831	212652831	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	31	665	0	ENST00000342788.4:c.475G>C	p.Asp159His	p.D159H	ENST00000342788	NM_005235.2	159	Gac/Cac	4/28	0.617400573445256	2	FACETS	0.171	0.138	0.209	0.086	0.069	0.105	SUBCLONAL	1	TRUE	0	0.618805433661202	2		665	585	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225449662	225449662	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs867746441	NA	P-0021822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	101	483	1	ENST00000264414.4:c.65C>T	p.Pro22Leu	p.P22L	ENST00000264414	NM_003590.4	22	cCg/cTg	1/16	0.618805433661202	1	FACETS	0.711	0.643	0.782	0.711	0.643	0.782	SUBCLONAL	1	TRUE	0	0.618805433661202	1		484	317	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129978	55129979	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0021822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	87	798	3	ENST00000257290.5:c.512_513delinsTA	p.Ser171Leu	p.S171L	ENST00000257290	NM_006206.4	171	tCC/tTA	4/23	0.506745462015141	2	FACETS	0.336	0.297	0.378	0.168	0.148	0.189	SUBCLONAL	1	TRUE	0	0.618805433661202	2		801	837	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721882	176721882	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	209	751	0	ENST00000439151.2:c.7513G>C	p.Glu2505Gln	p.E2505Q	ENST00000439151	NM_022455.4	2505	Gag/Cag	23/23	0.617400573445256	2	FACETS	0.958	0.893	1	0.479	0.446	0.513	CLONAL	1	TRUE	0	0.618805433661202	2		751	705	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120756	94120756	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	26	735	0	ENST00000369303.4:c.295T>G	p.Phe99Val	p.F99V	ENST00000369303	NM_004440.3	99	Ttt/Gtt	3/17	0.618805433661202	1	FACETS	0.112	0.088	0.139	0.112	0.088	0.139	SUBCLONAL	1	TRUE	0	0.618805433661202	1		735	520	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138201364	138201364	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	238	640	0	ENST00000237289.4:c.2063A>G	p.Glu688Gly	p.E688G	ENST00000237289	NM_001270507.1	688	gAg/gGg	8/9	0.618805433661202	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.618805433661202	1		640	488	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450356	50450356	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0021822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	91	768	0	ENST00000331340.3:c.540C>G	p.Tyr180Ter	p.Y180*	ENST00000331340	NM_006060.4	180	taC/taG	5/8	0.287834857085038	1	FACETS	0.313	0.278	0.35	0.313	0.278	0.35	INDETERMINATE	1	TRUE	0	0.618805433661202	1		768	649	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56911020	56911020	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	317	733	0	ENST00000519728.1:c.1166C>G	p.Ala389Gly	p.A389G	ENST00000519728	NM_002350.3	389	gCt/gGt	11/13	0.618805433661202	3	FACETS	1	0.992	1	0.638	0.603	0.674	CLONAL	1	TRUE	1	0.618805433661202	3		733	1051	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930081	68930081	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	76	514	0	ENST00000288368.4:c.142G>A	p.Ala48Thr	p.A48T	ENST00000288368	NM_024870.2	48	Gca/Aca	2/40	0.54608112167217	4	FACETS	0.442	0.387	0.502	0.221	0.193	0.251	SUBCLONAL	1	TRUE	2	0.618805433661202	4		514	899	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564384	139564395	+	inframe_deletion	In_Frame_Del	DEL	GCCGGAACGGAG	GCCGGAACGGAG	-	novel	NA	P-0021822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	352	732	0	ENST00000308874.7:c.333_344del	p.Cys111_Gly115delinsTrp	p.C111_G115delinsW	ENST00000308874		111	tGCCGGAACGGAGgg/tgg	6/10	0.618805433661202	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.618805433661202	1		732	680	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624274	89624274	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs587782187	NA	P-0021823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	88	530	0	ENST00000371953.3:c.48T>A	p.Tyr16Ter	p.Y16*	ENST00000371953	NM_000314.4	16	taT/taA	1/9	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.223296046104965	2		530	645	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589663	67589663	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587777709	NA	P-0021823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	34	405	1	ENST00000274335.5:c.1425+1G>A		p.X475_splice	ENST00000274335		475			0.223296046104965	1	FACETS	0.649	0.53	0.782	0.649	0.53	0.782	SUBCLONAL	1	TRUE	0	0.223296046104965	1		406	417	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115463	115115463	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0021823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	75	623	0	ENST00000257566.3:c.865-2A>G		p.X289_splice	ENST00000257566	NM_016569.3	289			1	2	FACETS	0.883	0.773	1	0.883	0.773	1	CLONAL	1	TRUE	1	0.223296046104965	2		623	761	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1620978	1620979	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0021823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	105	923	0	ENST00000344749.5:c.1081dup	p.Gln361ProfsTer32	p.Q361Pfs*32	ENST00000344749	NM_001136139.2	361	cag/cCag	13/19	1	2	FACETS	0.874	0.781	0.973	0.874	0.781	0.973	CLONAL	1	TRUE	1	0.223296046104965	2		923	1076	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29106010	29106010	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	101	630	0	ENST00000328354.6:c.830del	p.Leu277Ter	p.L277*	ENST00000328354	NM_007194.3	277	tTg/tg	7/15	0.223296046104965	1	FACETS	0.978	0.873	1	0.978	0.873	1	CLONAL	1	TRUE	0	0.223296046104965	1		630	822	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912656	NA	P-0021824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	297	728	0	ENST00000269305.4:c.734G>C	p.Gly245Ala	p.G245A	ENST00000269305	NM_001126112.2	245	gGc/gCc	7/11	0.554129541226428	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.549685577660704	2		728	467	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974727	21974744	+	inframe_deletion	In_Frame_Del	DEL	CCTCCAGCAGCGCCCGCA	CCTCCAGCAGCGCCCGCA	-	novel	NA	P-0021824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	181	438	0	ENST00000304494.5:c.83_100del	p.Val28_Glu33del	p.V28_E33del	ENST00000304494	NM_000077.4	28	gTGCGGGCGCTGCTGGAGGcg/gcg	1/3	0.554129541226428	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.549685577660704	2		438	317	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467952	66467952	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	149	509	0	ENST00000273854.3:c.317A>G	p.Glu106Gly	p.E106G	ENST00000273854	NM_004439.5	106	gAa/gGa	3/18	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.549685577660704	2		509	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579315	7579315	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1555526478	NA	P-0021826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	585	552	1	ENST00000269305.4:c.372C>A	p.Cys124Ter	p.C124*	ENST00000269305	NM_001126112.2	124	tgC/tgA	4/11	0.696239815213295	4	FACETS	0.951	0.929	0.973	0.951	0.929	0.973	CLONAL	4	FALSE	0	0.696239815213295	4		553	749	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478604	99478604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	174	595	0	ENST00000268035.6:c.3246G>A	p.Met1082Ile	p.M1082I	ENST00000268035	NM_000875.3	1082	atG/atA	17/21	0.696239815213295	6	FACETS	0.945	0.868	1	0.189	0.173	0.205	CLONAL	1	FALSE	1	0.696239815213295	6		595	1266	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142853	7142853	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	154	605	0	ENST00000302850.5:c.2516A>T	p.Tyr839Phe	p.Y839F	ENST00000302850	NM_000208.2	839	tAc/tTc	12/22	0.696239815213295	6	FACETS	1	0.914	1	0.25	0.228	0.273	CLONAL	1	FALSE	2	0.696239815213295	6		605	1058	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430752	181430752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754986575	NA	P-0021826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	188	827	0	ENST00000325404.1:c.604G>A	p.Val202Met	p.V202M	ENST00000325404	NM_003106.3	202	Gtg/Atg	1/1	0.696239815213295	5	FACETS	0.996	0.919	1	0.249	0.229	0.269	CLONAL	1	FALSE	1	0.696239815213295	5		827	1109	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141567259	141567259	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1496	178	821	2	ENST00000220592.5:c.955G>T	p.Val319Phe	p.V319F	ENST00000220592	NM_012154.3	319	Gtt/Ttt	8/19	0.696239815213295	7	FACETS	0.837	0.768	0.909			1	CLONAL	1	FALSE	NA	0.696239815213295	7		823	1674	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0021828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	191	857	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.112522749681895	4	FACETS	0.925	0.861	0.992	0.925	0.861	0.992	INDETERMINATE	2	TRUE	2	0.527109187388477	4		859	598	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0021828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	48	272	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.0299155355891605	4	FACETS	0.786	0.675	0.903	0.786	0.675	0.903	INDETERMINATE	2	TRUE	2	0.527109187388477	4		272	177	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0021828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	166	772	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.0299155355891605	4	FACETS	0.983	0.911	1	0.983	0.911	1	INDETERMINATE	2	TRUE	2	0.527109187388477	4		772	489	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561423	9561423	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201131316	NA	P-0021828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	327	732	1	ENST00000353224.5:c.359C>T	p.Ala120Val	p.A120V	ENST00000353224	NM_177990.2	120	gCg/gTg	4/10	0.444966869473043	5	FACETS	1	0.99	1	0.852	0.812	0.892	CLONAL	3	TRUE	1	0.527109187388477	5		733	652	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242511	55242511	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs121913418	NA	P-0021828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	8	495	0	ENST00000275493.2:c.2281G>A	p.Asp761Asn	p.D761N	ENST00000275493	NM_005228.3	761	Gat/Aat	19/28	0.527109187388477	3	FACETS	0.108	0.069	0.159	0.054	0.034	0.08	SUBCLONAL	1	TRUE	1	0.527109187388477	3		495	355	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879580	37879580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	183	843	4	ENST00000269571.5:c.1955C>T	p.Thr652Met	p.T652M	ENST00000269571		652	aCg/aTg	17/27	0.112522749681895	4	FACETS	0.821	0.761	0.883	0.821	0.761	0.883	INDETERMINATE	2	TRUE	2	0.527109187388477	4		847	646	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778738	3778738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1489860615	NA	P-0021828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	156	933	0	ENST00000262367.5:c.6310C>T	p.Arg2104Cys	p.R2104C	ENST00000262367	NM_004380.2	2104	Cgc/Tgc	31/31	0.527109187388477	3	FACETS	1	0.923	1	0.503	0.462	0.547	CLONAL	1	TRUE	1	0.527109187388477	3		933	743	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574035	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GCTCACGCCCACGGATCT	GCTCACGCCCACGGATCT	-	novel	NA	P-0021828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	92	793	0	ENST00000269305.4:c.994-2_1009del		p.X332_splice	ENST00000269305	NM_001126112.2	332		10/11	0.112522749681895	4	FACETS	0.834	0.742	0.932	0.417	0.371	0.466	INDETERMINATE	1	TRUE	2	0.527109187388477	4		793	639	SUCCESS
APC	324	MSKCC	GRCh37	5	112137077	112137094	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCAGGTAAATAAATTATT	TCAGGTAAATAAATTATT	-	novel	NA	P-0021828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	48	464	0	ENST00000257430.4:c.832_834+15del		p.X278_splice	ENST00000257430	NM_000038.5	278		8/16	0.0299155355891605	4	FACETS	1	0.877	1	0.517	0.44	0.6	INDETERMINATE	1	TRUE	2	0.527109187388477	4		464	269	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469669	NA	P-0021829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	524	876	1	ENST00000374080.3:c.130G>A	p.Gly44Ser	p.G44S	ENST00000374080		44	Ggt/Agt	2/45	0.483983980192827	4	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.860185483282864	4		877	998	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465952	69465952	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	220	827	3	ENST00000227507.2:c.790C>T	p.Gln264Ter	p.Q264*	ENST00000227507	NM_053056.2	264	Cag/Tag	5/5	1	2	FACETS	0.995	0.935	1	0.995	0.935	1	CLONAL	1	TRUE	1	0.860185483282864	2		830	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	503	749	0	ENST00000269305.4:c.527G>C	p.Cys176Ser	p.C176S	ENST00000269305	NM_001126112.2	176	tGc/tCc	5/11	0.860185483282864	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.860185483282864	2		749	547	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076781	72076781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767198961	NA	P-0021829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	274	754	2	ENST00000357731.5:c.716G>A	p.Arg239His	p.R239H	ENST00000357731	NM_173808.2	239	cGc/cAc	5/7	0.860185483282864	3	FACETS	0.965	0.907	1	0.483	0.453	0.512	CLONAL	1	TRUE	1	0.860185483282864	3		756	944	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658227	18658227	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs778842175	NA	P-0021829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	14	619	0	ENST00000266497.5:c.3032C>A	p.Ala1011Asp	p.A1011D	ENST00000266497		1011	gCc/gAc	22/31	0.860185483282864	1	FACETS	0.068	0.049	0.092	0.068	0.049	0.092	SUBCLONAL	1	TRUE	0	0.860185483282864	1		619	272	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409255	31409255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	411	634	0	ENST00000344624.3:c.3762G>T	p.Leu1254Phe	p.L1254F	ENST00000344624		1254	ttG/ttT	30/33	0.812884203552513	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	2	0.860185483282864	4		634	803	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249017	55249018	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCA	rs1554350381	NA	P-0021831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	137	624	0	ENST00000275493.2:c.2317_2319dup	p.His773dup	p.H773dup	ENST00000275493	NM_005228.3	773	ccc/ccCCAc	20/28	0.3	3	FACETS	0.872	0.793	0.954	0.872	0.793	0.954	CLONAL	2	TRUE	1	0.22	3		624	793	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864355	57864355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765569651	NA	P-0021831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	54	723	0	ENST00000228682.2:c.1832G>A	p.Arg611Gln	p.R611Q	ENST00000228682	NM_005269.2	611	cGg/cAg	12/12	1	2	FACETS	0.61	0.519	0.709	0.61	0.519	0.709	SUBCLONAL	1	TRUE	1	0.22	2		723	805	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0021832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	222	1034	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.626016850433131	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.626016850433131	1		1037	435	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	36	669	0				ENST00000310581	NM_198253.2	-/1132			0.525556523331242	1	FACETS	0.374	0.31	0.445	0.374	0.31	0.445	SUBCLONAL	1	TRUE	0	0.626016850433131	1		669	211	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562710	29562710	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs863224660	NA	P-0021832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	95	738	1	ENST00000356175.3:c.3790G>T	p.Glu1264Ter	p.E1264*	ENST00000356175	NM_000267.3	1264	Gaa/Taa	28/57	0.626016850433131	1	FACETS	0.515	0.461	0.571	0.515	0.461	0.571	SUBCLONAL	1	TRUE	0	0.626016850433131	1		739	405	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027156	49027159	+	frameshift_variant	Frame_Shift_Del	DEL	CAAT	CAAT	-	novel	NA	P-0021832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	226	602	0	ENST00000267163.4:c.1726_1729del	p.Ser576ArgfsTer34	p.S576Rfs*34	ENST00000267163	NM_000321.2	575	CAATca/ca	18/27	0.626016850433131	1	FACETS	0.948	0.892	1	0.948	0.892	1	CLONAL	1	TRUE	0	0.626016850433131	1		602	523	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350108	89350108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768925695	NA	P-0021832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	241	951	1	ENST00000301030.4:c.2842G>A	p.Gly948Arg	p.G948R	ENST00000301030	NM_001256183.1	948	Ggg/Agg	9/13	0.448321017515076	1	FACETS	0.859	0.808	0.91	0.859	0.808	0.91	CLONAL	1	TRUE	0	0.626016850433131	1		952	616	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211849	123211850	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0021832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	220	331	0	ENST00000218089.9:c.2718_2719del	p.Lys906AsnfsTer11	p.K906Nfs*11	ENST00000218089	NM_001042749.1	906	AAa/a	27/35	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.626016850433131	1		331	374	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551931	150551931	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	76	570	0	ENST00000369026.2:c.76G>C	p.Gly26Arg	p.G26R	ENST00000369026	NM_021960.4	26	Ggc/Cgc	1/3	0.307495540071802	5	FACETS	0.58	0.507	0.658	0.193	0.169	0.22	INDETERMINATE	1	TRUE	2	0.533026837517492	5		570	885	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374664	118374664	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	452	524	0	ENST00000534358.1:c.8057A>T	p.Asn2686Ile	p.N2686I	ENST00000534358	NM_005933.3	2686	aAc/aTc	27/36	0.533026837517492	5	FACETS	1	0.991	1			1	CLONAL	3	TRUE	NA	0.533026837517492	5		524	916	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811777	102811777	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	328	638	0	ENST00000307046.8:c.407A>C	p.Gln136Pro	p.Q136P	ENST00000307046	NM_001111285.1	136	cAg/cCg	4/4	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.533026837517492	NA		638	834	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1567555907	NA	P-0021833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	421	783	1	ENST00000269305.4:c.314del	p.Gly105AlafsTer18	p.G105Afs*18	ENST00000269305	NM_001126112.2	105	gGc/gc	4/11	0.516871988135333	2	FACETS	0.963	0.924	1	0.963	0.924	1	CLONAL	2	TRUE	0	0.533026837517492	2		784	820	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579380	7579380	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555526589	NA	P-0021833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	435	793	0	ENST00000269305.4:c.307T>C	p.Tyr103His	p.Y103H	ENST00000269305	NM_001126112.2	103	Tac/Cac	4/11	0.516871988135333	2	FACETS	0.987	0.948	1	0.987	0.948	1	CLONAL	2	TRUE	0	0.533026837517492	2		793	827	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602818	10602818	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0021833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	268	804	0	ENST00000171111.5:c.760A>T	p.Lys254Ter	p.K254*	ENST00000171111	NM_203500.1	254	Aag/Tag	3/6	0.516871988135333	2	FACETS	0.931	0.873	0.99	0.466	0.436	0.495	CLONAL	1	TRUE	0	0.533026837517492	2		804	1080	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027854	48027854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761622304	NA	P-0021833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	133	488	0	ENST00000234420.5:c.2732G>A	p.Arg911Gln	p.R911Q	ENST00000234420	NM_000179.2	911	cGa/cAa	4/10	0.46217457623287	2	FACETS	1	0.971	1	0.568	0.52	0.618	CLONAL	1	TRUE	0	0.533026837517492	2		488	439	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485448	57485448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	71	453	0	ENST00000371085.3:c.1030G>A	p.Glu344Lys	p.E344K	ENST00000371085	NM_000516.4	344	Gag/Aag	12/13	0.373716236003909	5	FACETS	0.631	0.55	0.719			1	SUBCLONAL	1	TRUE	NA	0.533026837517492	5		453	760	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361263	66361263	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0021833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	42	327	1	ENST00000273854.3:c.911-2A>T		p.X304_splice	ENST00000273854	NM_004439.5	304			0.221599726134535	2	FACETS	0.381	0.318	0.45	0.19	0.159	0.225	INDETERMINATE	1	TRUE	0	0.533026837517492	2		328	414	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181842	56181842	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	111	565	0	ENST00000399503.3:c.4066G>T	p.Gly1356Cys	p.G1356C	ENST00000399503	NM_005921.1	1356	Ggc/Tgc	17/20	1	2	FACETS	0.761	0.687	0.84	0.761	0.687	0.84	SUBCLONAL	1	TRUE	1	0.533026837517492	2		565	547	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165260	32165260	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	117	774	0	ENST00000375023.3:c.4868G>T	p.Gly1623Val	p.G1623V	ENST00000375023	NM_004557.3	1623	gGg/gTg	27/30	0.307495540071802	5	FACETS	0.615	0.553	0.682	0.205	0.184	0.228	INDETERMINATE	1	TRUE	2	0.533026837517492	5		774	1284	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117737452	117737452	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	88	659	0	ENST00000368508.3:c.197C>G	p.Ser66Cys	p.S66C	ENST00000368508	NM_002944.2	66	tCt/tGt	3/43	0.46217457623287	2	FACETS	0.623	0.553	0.697	0.311	0.276	0.349	SUBCLONAL	1	TRUE	0	0.533026837517492	2		659	530	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372753	81372753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	285	525	0	ENST00000222390.5:c.781C>T	p.Arg261Cys	p.R261C	ENST00000222390	NM_000601.4	261	Cgc/Tgc	7/18	0.358978229519698	3	FACETS	1	0.976	1	0.701	0.664	0.738	CLONAL	2	TRUE	0	0.533026837517492	3		525	644	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864658	56864658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	57	643	1	ENST00000519728.1:c.621G>A	p.Met207Ile	p.M207I	ENST00000519728	NM_002350.3	207	atG/atA	7/13	0.533026837517492	3	FACETS	0.307	0.262	0.356	0.154	0.131	0.178	SUBCLONAL	1	TRUE	1	0.533026837517492	3		644	882	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410865	63410865	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	216	733	0	ENST00000330258.3:c.2302A>G	p.Ser768Gly	p.S768G	ENST00000330258	NM_152424.3	768	Agt/Ggt	2/2	0.221599726134535	2	FACETS	0.938	0.873	1	0.469	0.436	0.503	INDETERMINATE	1	TRUE	0	0.533026837517492	2		733	864	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345959	70345959	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	112	759	2	ENST00000374080.3:c.2496G>T	p.Lys832Asn	p.K832N	ENST00000374080		832	aaG/aaT	18/45	0.221599726134535	2	FACETS	0.504	0.453	0.559	0.252	0.226	0.28	INDETERMINATE	1	TRUE	0	0.533026837517492	2		761	833	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	253	699	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.366257624992826	2	FACETS	1	0.987	1	0.598	0.56	0.637	CLONAL	1	TRUE	0	0.421051141891985	2		699	1005	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998898	11998898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	274	336	2	ENST00000353533.5:c.400C>T	p.Arg134Trp	p.R134W	ENST00000353533	NM_003010.3	134	Cgg/Tgg	4/11	0.390915523399397	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.421051141891985	2		338	586	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2107149	2107149	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1366677287	NA	P-0021845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1540	98	702	0	ENST00000219476.3:c.818T>C	p.Ile273Thr	p.I273T	ENST00000219476	NM_000548.3	273	aTc/aCc	9/42	0.421051141891985	3	FACETS	0.344	0.305	0.386	0.172	0.152	0.193	SUBCLONAL	1	TRUE	1	0.421051141891985	3		702	1638	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158594957	158594957	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	111	480	0	ENST00000263640.3:c.1390G>T	p.Asp464Tyr	p.D464Y	ENST00000263640	NM_001105.4	464	Gac/Tac	10/11	1	2	FACETS	0.607	0.545	0.672	0.607	0.545	0.672	SUBCLONAL	1	TRUE	1	0.421051141891985	2		480	869	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420023	152420024	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0021845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	51	643	0	ENST00000206249.3:c.1711dup	p.Ala571GlyfsTer80	p.A571Gfs*80	ENST00000206249	NM_000125.3	570	-/G	8/8	0.366257624992826	2	FACETS	0.252	0.213	0.294	0.126	0.106	0.147	SUBCLONAL	1	TRUE	0	0.421051141891985	2		643	963	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504113	123504113	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	130	540	0	ENST00000371139.4:c.289C>T	p.Pro97Ser	p.P97S	ENST00000371139	NM_001114937.2	97	Cct/Tct	3/4	0.421051141891985	1	FACETS	0.666	0.605	0.73	0.666	0.605	0.73	SUBCLONAL	1	TRUE	0	0.421051141891985	1		540	732	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0021848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	120	662	1				ENST00000310581	NM_198253.2	-/1132			0.431930127216201	1	FACETS	0.983	0.898	1	0.983	0.898	1	CLONAL	1	TRUE	0	0.525132987666793	1		663	343	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252162	226252162	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	42	120	0	ENST00000366813.1:c.110A>G	p.Lys37Arg	p.K37R	ENST00000366813		37	aAg/aGg	1/3	1	2	FACETS	0.994	0.843	1	0.994	0.843	1	CLONAL	1	TRUE	1	0.525132987666793	2		120	161	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245077	133245077	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	188	787	0	ENST00000320574.5:c.2038C>G	p.Arg680Gly	p.R680G	ENST00000320574	NM_006231.2	680	Cgc/Ggc	19/49	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.525132987666793	2		787	685	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133695	2133695	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0021848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	199	809	1	ENST00000219476.3:c.3884-1G>T		p.X1295_splice	ENST00000219476	NM_000548.3	1295			NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.525132987666793	2		810	642	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136321	2136322	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0021848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	233	979	0	ENST00000219476.3:c.4792dup	p.Asp1598GlyfsTer5	p.D1598Gfs*5	ENST00000219476	NM_000548.3	1597	ctg/ctGg	37/42	NA	2	FACETS	0.989	0.924	1			1	INDETERMINATE	1	TRUE	NA	0.525132987666793	2		979	897	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401407	139401407	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1389804069	NA	P-0021848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	345	831	0	ENST00000277541.6:c.3662A>G	p.Asn1221Ser	p.N1221S	ENST00000277541	NM_017617.3	1221	aAc/aGc	23/34	0.525132987666793	2	FACETS	0.956	0.913	1	0.956	0.913	1	CLONAL	2	TRUE	0	0.525132987666793	2		831	687	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0021850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	538	681	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.99	1	1	0.998	1	CLONAL	2	TRUE	1	0.4	2		681	1243	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0021850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	555	825	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.886003563015236	1	FACETS	1	0.996	1	1	0.998	1	CLONAL	3	TRUE	0	0.4	1		825	669	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170016852	170016852	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1238	555	802	2	ENST00000295797.4:c.1657G>A	p.Asp553Asn	p.D553N	ENST00000295797	NM_002740.5	553	Gat/Aat	17/18	0.838071215212001	3	FACETS	0.929	0.89	0.968			1	CLONAL	2	TRUE	NA	0.4	3		804	1793	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567342	226567342	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	312	642	0	ENST00000366794.5:c.1544G>C	p.Gly515Ala	p.G515A	ENST00000366794	NM_001618.3	515	gGt/gCt	11/23	1	2	FACETS	0.841	0.796	0.888	1	0.995	1	CLONAL	2	TRUE	1	0.4	2		642	927	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953759	48953759	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0021850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	620	500	0	ENST00000267163.4:c.1362C>G	p.Tyr454Ter	p.Y454*	ENST00000267163	NM_000321.2	454	taC/taG	14/27	0.886003563015236	2	FACETS	1	0.997	1	1	0.998	1	CLONAL	4	TRUE	0	0.4	2		500	714	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609617	46609617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	690	997	6	ENST00000263734.3:c.2341C>T	p.Pro781Ser	p.P781S	ENST00000263734	NM_001430.4	781	Ccg/Tcg	15/16	1	2	FACETS	1	0.994	1	1	0.998	1	CLONAL	2	TRUE	1	0.4	2		1003	1553	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855214	76855214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1157154167	NA	P-0021850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	541	791	1	ENST00000373344.5:c.5773G>A	p.Asp1925Asn	p.D1925N	ENST00000373344	NM_000489.3	1925	Gat/Aat	24/35	1	2	FACETS	1	0.993	1	1	0.998	1	CLONAL	2	TRUE	1	0.4	2		792	1199	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	126	662	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.996	0.917	1	0.996	0.917	1	CLONAL	1	TRUE	1	0.857501413327633	2		663	295	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984021	2984021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766268425	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	647	870	0	ENST00000396946.4:c.509G>A	p.Arg170His	p.R170H	ENST00000396946	NM_032415.4	170	cGc/cAc	5/25	0.857501413327633	3	FACETS	0.994	0.978	1	0.994	0.978	1	CLONAL	3	TRUE	0	0.857501413327633	3		870	723	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106808	27106808	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	220	935	0	ENST00000324856.7:c.6419C>T	p.Pro2140Leu	p.P2140L	ENST00000324856	NM_006015.4	2140	cCc/cTc	20/20	1	2	FACETS	0.954	0.895	1	0.954	0.895	1	CLONAL	1	TRUE	1	0.857501413327633	2		935	538	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531815	46531815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	106	726	0	ENST00000262741.5:c.532G>A	p.Gly178Ser	p.G178S	ENST00000262741	NM_003629.3	178	Ggt/Agt	5/10	1	2	FACETS	0.77	0.699	0.844	0.77	0.699	0.844	SUBCLONAL	1	TRUE	1	0.857501413327633	2		726	321	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873223	71873223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	186	744	1	ENST00000357731.5:c.971G>A	p.Gly324Glu	p.G324E	ENST00000357731	NM_173808.2	324	gGg/gAg	7/7	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.857501413327633	2		745	415	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166160	118166160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	156	583	0	ENST00000369448.3:c.670G>A	p.Asp224Asn	p.D224N	ENST00000369448	NM_017709.3	224	Gac/Aac	2/2	1	2	FACETS	0.981	0.91	1	0.981	0.91	1	CLONAL	1	TRUE	1	0.857501413327633	2		583	371	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120478170	120478170	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	212	775	1	ENST00000256646.2:c.3580C>T	p.Gln1194Ter	p.Q1194*	ENST00000256646	NM_024408.3	1194	Cag/Tag	22/34	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.857501413327633	2		776	456	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843506	156843506	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1434897221	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	238	948	2	ENST00000524377.1:c.932C>T	p.Pro311Leu	p.P311L	ENST00000524377	NM_002529.3	311	cCg/cTg	8/17	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.857501413327633	2		950	554	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117004	193117004	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267598258	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	141	709	0	ENST00000367435.3:c.737C>T	p.Ser246Phe	p.S246F	ENST00000367435	NM_024529.4	246	tCc/tTc	8/17	1	2	FACETS	0.959	0.886	1	0.959	0.886	1	CLONAL	1	TRUE	1	0.857501413327633	2		709	343	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218890	193218890	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	68	513	0	ENST00000367435.3:c.1448T>C	p.Val483Ala	p.V483A	ENST00000367435	NM_024529.4	483	gTt/gCt	16/17	1	2	FACETS	0.797	0.706	0.891	0.797	0.706	0.891	SUBCLONAL	1	TRUE	1	0.857501413327633	2		513	199	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650147	206650147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	230	888	0	ENST00000367120.3:c.667C>T	p.Pro223Ser	p.P223S	ENST00000367120	NM_014002.3	223	Ccc/Tcc	7/22	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.857501413327633	2		888	502	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666400	206666400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	264	913	0	ENST00000367120.3:c.1880C>T	p.Ser627Phe	p.S627F	ENST00000367120	NM_014002.3	627	tCt/tTt	19/22	1		FACETS		0.955	1				CLONAL	1	TRUE	1	0.857501413327633	2		913	609	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680603	241680603	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1200934499	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	147	696	0	ENST00000366560.3:c.146C>T	p.Ser49Phe	p.S49F	ENST00000366560	NM_000143.3	49	tCc/tTc	2/10	1	2	FACETS	0.988	0.915	1	0.988	0.915	1	CLONAL	1	TRUE	1	0.857501413327633	2		696	347	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716070	243716070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	180	1025	1	ENST00000263826.5:c.1124C>T	p.Ser375Leu	p.S375L	ENST00000263826	NM_005465.4	375	tCa/tTa	10/13	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.857501413327633	2		1026	420	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63661484	63661484	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	345	627	0	ENST00000279873.7:c.16C>A	p.Leu6Ile	p.L6I	ENST00000279873	NM_032199.2	6	Ctc/Atc	1/10	0.857501413327633	3	FACETS	0.926	0.886	0.965	0.926	0.886	0.965	CLONAL	2	TRUE	1	0.857501413327633	3		627	621	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154749	2154749	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	192	936	0	ENST00000434045.2:c.472C>T	p.Pro158Ser	p.P158S	ENST00000434045	NM_001127598.1	158	Ccg/Tcg	4/5	1	2	FACETS	0.929	0.868	0.991	0.929	0.868	0.991	CLONAL	1	TRUE	1	0.857501413327633	2		936	482	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421575	32421575	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	212	873	0	ENST00000332351.3:c.1017C>A	p.Tyr339Ter	p.Y339*	ENST00000332351	NM_024426.4	339	taC/taA	6/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.857501413327633	2		873	486	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571979	64571979	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs794728631	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	288	1067	1	ENST00000312049.6:c.1660C>T	p.Gln554Ter	p.Q554*	ENST00000312049	NM_130799.2	554	Cag/Tag	10/10	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.857501413327633	2		1068	670	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588223	69588223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	163	870	0	ENST00000168712.1:c.475G>A	p.Glu159Lys	p.E159K	ENST00000168712	NM_002007.2	159	Gag/Aag	3/3	1	2	FACETS	0.927	0.861	0.995	0.927	0.861	0.995	CLONAL	1	TRUE	1	0.857501413327633	2		870	410	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949368	71949368	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144762578	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	210	918	0	ENST00000298229.2:c.3748C>T	p.Leu1250Phe	p.L1250F	ENST00000298229	NM_001567.3	1250	Ctt/Ttt	28/28	1	2	FACETS	0.899	0.841	0.957	0.899	0.841	0.957	CLONAL	1	TRUE	1	0.857501413327633	2		918	545	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912831	100912831	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	120	630	2	ENST00000325455.5:c.2491C>T	p.Pro831Ser	p.P831S	ENST00000325455	NM_001202474.3	831	Cct/Tct	7/8	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.857501413327633	2		632	267	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933421	100933421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	191	673	1	ENST00000325455.5:c.1969C>T	p.Pro657Ser	p.P657S	ENST00000325455	NM_001202474.3	657	Cca/Tca	4/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.857501413327633	2		674	417	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390751	118390751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	155	658	1	ENST00000534358.1:c.11401G>A	p.Glu3801Lys	p.E3801K	ENST00000534358	NM_005933.3	3801	Gag/Aag	33/36	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.857501413327633	2		659	354	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142518	119142518	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	170	864	2	ENST00000264033.4:c.517C>T	p.Leu173Phe	p.L173F	ENST00000264033	NM_005188.3	173	Ctc/Ttc	3/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.857501413327633	2		866	343	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420976	49420976	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	199	700	0	ENST00000301067.7:c.14773C>T	p.Pro4925Ser	p.P4925S	ENST00000301067	NM_003482.3	4925	Cct/Tct	48/54	1	2	FACETS	0.983	0.921	1	0.983	0.921	1	CLONAL	1	TRUE	1	0.857501413327633	2		700	472	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444720	49444720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	289	1224	0	ENST00000301067.7:c.2746C>T	p.Pro916Ser	p.P916S	ENST00000301067	NM_003482.3	916	Ccg/Tcg	10/54	1	2	FACETS	0.943	0.892	0.994	0.943	0.892	0.994	CLONAL	1	TRUE	1	0.857501413327633	2		1224	715	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445179	49445180	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	rs1463730553	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	56	1131	0	ENST00000301067.7:c.2286_2287del	p.Pro763AlafsTer3	p.P763Afs*3	ENST00000301067	NM_003482.3	762	tcTCcg/tccg	10/54	1	2	FACETS	0.199	0.17	0.231	0.199	0.17	0.231	SUBCLONAL	1	TRUE	1	0.857501413327633	2		1131	655	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562483	21562484	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGCAA	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	92	130	0	ENST00000382592.4:c.1435_1436insTTGCCC	p.Ala478_Pro479insLeuAla	p.A478_P479insLA	ENST00000382592	NM_014572.2	479	ccg/cTTGCCCcg	4/8	0.857501413327633	3	FACETS	0.97	0.892	1	0.97	0.892	1	CLONAL	2	TRUE	1	0.857501413327633	3		130	158	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506652	103506652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	221	524	0	ENST00000355739.4:c.395C>T	p.Pro132Leu	p.P132L	ENST00000355739	NM_000123.3	132	cCc/cTc	4/15	0.857501413327633	3	FACETS	0.949	0.899	0.999	0.949	0.899	0.999	CLONAL	2	TRUE	1	0.857501413327633	3		524	388	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514721	103514721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	155	543	1	ENST00000355739.4:c.1222G>A	p.Asp408Asn	p.D408N	ENST00000355739	NM_000123.3	408	Gat/Aat	8/15	0.857501413327633	3	FACETS	0.914	0.841	0.99	0.457	0.42	0.495	CLONAL	1	TRUE	1	0.857501413327633	3		544	565	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437865	110437865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs915146950	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	76	227	0	ENST00000375856.3:c.536G>A	p.Gly179Glu	p.G179E	ENST00000375856	NM_003749.2	179	gGg/gAg	1/2	0.857501413327633	3	FACETS	1	0.963	1	0.595	0.531	0.66	CLONAL	1	TRUE	1	0.857501413327633	3		227	213	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066713	30066713	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	120	687	0	ENST00000331968.5:c.2418G>T	p.Lys806Asn	p.K806N	ENST00000331968	NM_002742.2	806	aaG/aaT	16/18	1	2	FACETS	0.927	0.85	1	0.927	0.85	1	CLONAL	1	TRUE	1	0.857501413327633	2		687	302	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066721	30066721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1263767545	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	132	736	0	ENST00000331968.5:c.2410C>T	p.Pro804Ser	p.P804S	ENST00000331968	NM_002742.2	804	Ccc/Tcc	16/18	1	2	FACETS	0.903	0.831	0.976	0.903	0.831	0.976	CLONAL	1	TRUE	1	0.857501413327633	2		736	341	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105550	30105550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	336	1059	3	ENST00000331968.5:c.1136G>A	p.Ser379Asn	p.S379N	ENST00000331968	NM_002742.2	379	aGt/aAt	7/18	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.857501413327633	2		1062	731	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566179	95566179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1566761556	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	196	988	2	ENST00000393063.1:c.4144C>T	p.Pro1382Ser	p.P1382S	ENST00000393063	NM_030621.3	1382	Cct/Tct	23/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.857501413327633	2		990	411	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571415	95571415	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	81	329	0	ENST00000393063.1:c.3262G>A	p.Asp1088Asn	p.D1088N	ENST00000393063	NM_030621.3	1088	Gat/Aat	21/28	1	2	FACETS	0.904	0.812	0.998	0.904	0.812	0.998	CLONAL	1	TRUE	1	0.857501413327633	2		329	209	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213967	2213967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	223	933	0	ENST00000326181.6:c.46C>T	p.Pro16Ser	p.P16S	ENST00000326181	NM_032271.2	16	Ccc/Tcc	2/21	1	2	FACETS	0.965	0.907	1	0.965	0.907	1	CLONAL	1	TRUE	1	0.857501413327633	2		933	539	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640097	3640097	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	249	1273	0	ENST00000294008.3:c.3542C>T	p.Ala1181Val	p.A1181V	ENST00000294008	NM_032444.2	1181	gCt/gTt	12/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.857501413327633	2		1273	565	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858412	9858413	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	175	769	1	ENST00000330684.3:c.2988_2989delinsAA	p.Glu997Lys	p.E997K	ENST00000330684	NM_001134407.1	996	gtGGag/gtAAag	13/13	1	2	FACETS	0.954	0.888	1	0.954	0.888	1	CLONAL	1	TRUE	1	0.857501413327633	2		770	428	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813828	50813828	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	274	1027	0	ENST00000398568.2:c.1382C>T	p.Pro461Leu	p.P461L	ENST00000398568	NM_001042412.1	461	cCt/cTt	8/18	1	2	FACETS	0.958	0.906	1	0.958	0.906	1	CLONAL	1	TRUE	1	0.857501413327633	2		1027	667	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813884	50813884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	278	938	0	ENST00000398568.2:c.1438C>T	p.Pro480Ser	p.P480S	ENST00000398568	NM_001042412.1	480	Cct/Tct	8/18	1	2	FACETS	0.999	0.945	1	0.999	0.945	1	CLONAL	1	TRUE	1	0.857501413327633	2		938	649	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50821757	50821757	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	130	794	0	ENST00000398568.2:c.2093A>G	p.Lys698Arg	p.K698R	ENST00000398568	NM_001042412.1	698	aAa/aGa	13/18	1	2	FACETS	0.948	0.872	1	0.948	0.872	1	CLONAL	1	TRUE	1	0.857501413327633	2		794	320	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821572	72821572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457944892	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	110	303	0	ENST00000268489.5:c.10603G>A	p.Glu3535Lys	p.E3535K	ENST00000268489	NM_006885.3	3535	Gag/Aag	10/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.857501413327633	2		303	213	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829473	72829473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	213	881	0	ENST00000268489.5:c.7108G>A	p.Asp2370Asn	p.D2370N	ENST00000268489	NM_006885.3	2370	Gat/Aat	9/10	1	2	FACETS	0.986	0.925	1	0.986	0.925	1	CLONAL	1	TRUE	1	0.857501413327633	2		881	504	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993653	72993653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	269	916	1	ENST00000268489.5:c.392G>A	p.Gly131Glu	p.G131E	ENST00000268489	NM_006885.3	131	gGg/gAg	2/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.857501413327633	2		917	606	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81927366	81927366	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	264	1033	0	ENST00000359376.3:c.1039C>G	p.Arg347Gly	p.R347G	ENST00000359376	NM_002661.3	347	Cgc/Ggc	12/33	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.857501413327633	2		1033	609	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341586	89341587	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	145	591	2	ENST00000301030.4:c.7483_7484delinsTT	p.Pro2495Phe	p.P2495F	ENST00000301030	NM_001256183.1	2495	CCc/TTc	10/13	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.857501413327633	2		593	320	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347444	89347444	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529180532	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	221	917	1	ENST00000301030.4:c.5506C>T	p.Pro1836Ser	p.P1836S	ENST00000301030	NM_001256183.1	1836	Ccc/Tcc	9/13	1	2	FACETS	0.989	0.93	1	0.989	0.93	1	CLONAL	1	TRUE	1	0.857501413327633	2		918	521	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348106	89348106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	280	1195	2	ENST00000301030.4:c.4844C>T	p.Ser1615Phe	p.S1615F	ENST00000301030	NM_001256183.1	1615	tCc/tTc	9/13	1	2	FACETS	0.941	0.89	0.993	0.941	0.89	0.993	CLONAL	1	TRUE	1	0.857501413327633	2		1197	694	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357062	89357062	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	233	904	0	ENST00000301030.4:c.572G>A	p.Gly191Glu	p.G191E	ENST00000301030	NM_001256183.1	191	gGg/gAg	6/13	1	2	FACETS	0.97	0.913	1	0.97	0.913	1	CLONAL	1	TRUE	1	0.857501413327633	2		904	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577089	7577090	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	236	1004	3	ENST00000269305.4:c.848_849del	p.Arg283HisfsTer22	p.R283Hfs*22	ENST00000269305	NM_001126112.2	283	cGC/c	8/11	1	2	FACETS	0.913	0.858	0.968	0.913	0.858	0.968	CLONAL	1	TRUE	1	0.857501413327633	2		1007	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577548	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	240	928	3	ENST00000269305.4:c.733_734delinsAA	p.Gly245Asn	p.G245N	ENST00000269305	NM_001126112.2	245	GGc/AAc	7/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.857501413327633	2		931	542	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15967419	15967420	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	222	852	0	ENST00000268712.3:c.5183_5184delinsAA	p.Arg1728Gln	p.R1728Q	ENST00000268712	NM_006311.3	1728	cGG/cAA	35/46	1	2	FACETS	0.904	0.848	0.96	0.904	0.848	0.96	CLONAL	1	TRUE	1	0.857501413327633	2		852	573	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15978893	15978893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	192	965	1	ENST00000268712.3:c.3625C>T	p.His1209Tyr	p.H1209Y	ENST00000268712	NM_006311.3	1209	Cat/Tat	27/46	1	2	FACETS	0.941	0.879	1	0.941	0.879	1	CLONAL	1	TRUE	1	0.857501413327633	2		966	476	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619292	37619292	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	174	674	3	ENST00000447079.4:c.968C>T	p.Ser323Leu	p.S323L	ENST00000447079	NM_015083.1	323	tCg/tTg	1/14	1	2	FACETS	0.948	0.883	1	0.948	0.883	1	CLONAL	1	TRUE	1	0.857501413327633	2		677	428	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41258515	41258515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	174	991	1	ENST00000357654.3:c.170G>A	p.Gly57Glu	p.G57E	ENST00000357654	NM_007294.3	57	gGg/gAg	4/23	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.857501413327633	2		992	373	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761387	59761387	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	130	809	0	ENST00000259008.2:c.3020C>T	p.Ser1007Phe	p.S1007F	ENST00000259008	NM_032043.2	1007	tCt/tTt	20/20	1	2	FACETS	0.871	0.8	0.944	0.871	0.8	0.944	CLONAL	1	TRUE	1	0.857501413327633	2		809	348	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221299	1221300	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	216	997	2	ENST00000326873.7:c.822_823delinsTT	p.Pro275Ser	p.P275S	ENST00000326873	NM_000455.4	274	atCCcg/atTTcg	6/10	1	2	FACETS	0.879	0.824	0.936	0.879	0.824	0.936	CLONAL	1	TRUE	1	0.857501413327633	2		999	573	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226454	2226454	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424822653	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	307	1055	2	ENST00000398665.3:c.3934C>T	p.Pro1312Ser	p.P1312S	ENST00000398665	NM_032482.2	1312	Cct/Tct	27/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.857501413327633	2		1057	680	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101132	4101132	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	204	918	1	ENST00000262948.5:c.590C>T	p.Pro197Leu	p.P197L	ENST00000262948	NM_030662.3	197	cCc/cTc	6/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.857501413327633	2		919	443	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125473	7125473	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913144	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	234	1140	2	ENST00000302850.5:c.3079C>T	p.Arg1027Ter	p.R1027*	ENST00000302850	NM_000208.2	1027	Cga/Tga	17/22	1	2	FACETS	0.927	0.871	0.983	0.927	0.871	0.983	CLONAL	1	TRUE	1	0.857501413327633	2		1142	589	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096985	11096985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747458180	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	224	1055	1	ENST00000358026.2:c.476C>T	p.Pro159Leu	p.P159L	ENST00000358026	NM_001128849.1	159	cCc/cTc	4/36	1	2	FACETS	0.868	0.814	0.923	0.868	0.814	0.923	CLONAL	1	TRUE	1	0.857501413327633	2		1056	602	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289973	15289973	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759742938	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	246	1065	1	ENST00000263388.2:c.3581C>T	p.Pro1194Leu	p.P1194L	ENST00000263388	NM_000435.2	1194	cCc/cTc	22/33	1	2	FACETS	0.998	0.941	1	0.998	0.941	1	CLONAL	1	TRUE	1	0.857501413327633	2		1066	575	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292390	15292391	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	204	886	4	ENST00000263388.2:c.2788_2789delinsTT	p.Pro930Phe	p.P930F	ENST00000263388	NM_000435.2	930	CCc/TTc	17/33	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.857501413327633	2		890	474	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302469	15302469	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	225	897	0	ENST00000263388.2:c.803-1G>A		p.X268_splice	ENST00000263388	NM_000435.2	268			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.857501413327633	2		897	498	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223521	36223522	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	234	1090	2	ENST00000222270.7:c.6071_6072delinsTT	p.Ser2024Phe	p.S2024F	ENST00000222270	NM_014727.1	2024	tCC/tTT	28/37	1	2	FACETS	0.982	0.924	1	0.982	0.924	1	CLONAL	1	TRUE	1	0.857501413327633	2		1092	556	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912137	50912138	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	244	1119	5	ENST00000440232.2:c.1871_1872delinsTT	p.Pro624Leu	p.P624L	ENST00000440232	NM_002691.3	624	cCC/cTT	15/27	1	2	FACETS	0.995	0.938	1	0.995	0.938	1	CLONAL	1	TRUE	1	0.857501413327633	2		1124	572	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964912	25964912	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	171	650	0	ENST00000435504.4:c.4294C>T	p.Leu1432Phe	p.L1432F	ENST00000435504		1432	Ctt/Ttt	13/13	0.857501413327633	3	FACETS	1	0.93	1	0.502	0.465	0.541	CLONAL	1	TRUE	1	0.857501413327633	3		650	567	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967308	25967308	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	131	588	1	ENST00000435504.4:c.1898C>T	p.Pro633Leu	p.P633L	ENST00000435504		633	cCa/cTa	13/13	0.857501413327633	3	FACETS	0.804	0.733	0.878	0.402	0.366	0.439	CLONAL	1	TRUE	1	0.857501413327633	3		589	543	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462652	29462652	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	264	1172	0	ENST00000389048.3:c.2249C>T	p.Thr750Ile	p.T750I	ENST00000389048	NM_004304.4	750	aCc/aTc	13/29	0.857501413327633	3	FACETS	0.897	0.841	0.954	0.448	0.42	0.477	CLONAL	1	TRUE	1	0.857501413327633	3		1172	981	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136297	202136297	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	192	1019	1	ENST00000358485.4:c.541T>A	p.Phe181Ile	p.F181I	ENST00000358485	NM_001080125.1	181	Ttt/Att	3/9	1	2	FACETS	0.871	0.813	0.931	0.871	0.813	0.931	CLONAL	1	TRUE	1	0.857501413327633	2		1020	514	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248565	212248565	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	251	852	0	ENST00000342788.4:c.3702G>T	p.Lys1234Asn	p.K1234N	ENST00000342788	NM_005235.2	1234	aaG/aaT	28/28	1	2	FACETS	0.892	0.84	0.945	0.892	0.84	0.945	CLONAL	1	TRUE	1	0.857501413327633	2		852	656	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483981	212483981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	126	771	0	ENST00000342788.4:c.2222G>A	p.Gly741Glu	p.G741E	ENST00000342788	NM_005235.2	741	gGa/gAa	19/28	1	2	FACETS	0.93	0.855	1	0.93	0.855	1	CLONAL	1	TRUE	1	0.857501413327633	2		771	316	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543829	212543829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771154734	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	246	713	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	0.857501413327633	2		713	552	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566814	212566814	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	158	569	0	ENST00000342788.4:c.1367G>A	p.Gly456Glu	p.G456E	ENST00000342788	NM_005235.2	456	gGa/gAa	12/28	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.857501413327633	2		569	357	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538378	9538378	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	122	528	0	ENST00000353224.5:c.1620G>A	p.Met540Ile	p.M540I	ENST00000353224	NM_177990.2	540	atG/atA	7/10	1	2	FACETS	0.878	0.805	0.953	0.878	0.805	0.953	CLONAL	1	TRUE	1	0.857501413327633	2		528	324	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560812	9560812	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	162	656	0	ENST00000353224.5:c.970C>T	p.Pro324Ser	p.P324S	ENST00000353224	NM_177990.2	324	Ccc/Tcc	4/10	1	2	FACETS	0.842	0.779	0.905	0.842	0.779	0.905	CLONAL	1	TRUE	1	0.857501413327633	2		656	449	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561232	9561232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	228	816	1	ENST00000353224.5:c.550G>A	p.Glu184Lys	p.E184K	ENST00000353224	NM_177990.2	184	Gag/Aag	4/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.857501413327633	2		817	504	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561547	9561547	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	185	714	0	ENST00000353224.5:c.235G>A	p.Glu79Lys	p.E79K	ENST00000353224	NM_177990.2	79	Gaa/Aaa	4/10	1	2	FACETS	0.836	0.778	0.895	0.836	0.778	0.895	CLONAL	1	TRUE	1	0.857501413327633	2		714	516	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024515	31024515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	211	857	1	ENST00000375687.4:c.4000C>T	p.Pro1334Ser	p.P1334S	ENST00000375687	NM_015338.5	1334	Ccc/Tcc	13/13	1	2	FACETS	0.996	0.935	1	0.996	0.935	1	CLONAL	1	TRUE	1	0.857501413327633	2		858	494	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817358	39817358	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	179	792	0	ENST00000288319.7:c.205G>T	p.Glu69Ter	p.E69*	ENST00000288319	NM_182918.3	69	Gaa/Taa	2/10	1	2	FACETS	0.985	0.919	1	0.985	0.919	1	CLONAL	1	TRUE	1	0.857501413327633	2		792	424	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627424	37627424	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	200	893	0	ENST00000249071.6:c.295C>T	p.Pro99Ser	p.P99S	ENST00000249071	NM_002872.4	99	Cca/Tca	5/7	1	2	FACETS	0.984	0.922	1	0.984	0.922	1	CLONAL	1	TRUE	1	0.857501413327633	2		893	474	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422970	12422970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	165	883	0	ENST00000287820.6:c.460C>T	p.His154Tyr	p.H154Y	ENST00000287820	NM_015869.4	154	Cat/Tat	3/7	0.857501413327633	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.857501413327633	1		883	217	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437782	52437782	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	231	972	0	ENST00000460680.1:c.1379C>T	p.Ser460Leu	p.S460L	ENST00000460680	NM_004656.3	460	tCa/tTa	13/17	1	2	FACETS	0.971	0.913	1	0.971	0.913	1	CLONAL	1	TRUE	1	0.857501413327633	2		972	555	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987099	69987100	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	220	786	1	ENST00000394351.3:c.160_161delinsTT	p.Pro54Leu	p.P54L	ENST00000394351	NM_000248.3	54	CCa/TTa	2/9	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.857501413327633	2		787	507	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890344	72890344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	128	722	0	ENST00000325599.8:c.338C>T	p.Ser113Phe	p.S113F	ENST00000325599	NM_018130.2	113	tCt/tTt	4/11	1	2	FACETS	0.86	0.79	0.933	0.86	0.79	0.933	CLONAL	1	TRUE	1	0.857501413327633	2		722	347	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259167	89259167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753700696	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	140	581	0	ENST00000336596.2:c.311G>A	p.Arg104Gln	p.R104Q	ENST00000336596	NM_005233.5	104	cGa/cAa	3/17	1	2	FACETS	0.92	0.849	0.992	0.92	0.849	0.992	CLONAL	1	TRUE	1	0.857501413327633	2		581	355	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390968	89390968	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	184	827	1	ENST00000336596.2:c.1034G>A	p.Trp345Ter	p.W345*	ENST00000336596	NM_005233.5	345	tGg/tAg	5/17	1	2	FACETS	0.998	0.932	1	0.998	0.932	1	CLONAL	1	TRUE	1	0.857501413327633	2		828	430	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272074	142272074	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	120	691	0	ENST00000350721.4:c.2800T>C	p.Cys934Arg	p.C934R	ENST00000350721	NM_001184.3	934	Tgt/Cgt	13/47	1	2	FACETS	0.996	0.915	1	0.996	0.915	1	CLONAL	1	TRUE	1	0.857501413327633	2		691	281	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190956	185190956	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	312	1280	0	ENST00000265026.3:c.1837G>A	p.Glu613Lys	p.E613K	ENST00000265026	NM_004721.4	613	Gaa/Aaa	11/14	1	2	FACETS	0.995	0.945	1	0.995	0.945	1	CLONAL	1	TRUE	1	0.857501413327633	2		1280	731	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607210	189607210	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1200324125	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	299	1136	1	ENST00000264731.3:c.1589C>T	p.Ser530Phe	p.S530F	ENST00000264731	NM_003722.4	530	tCc/tTc	12/14	1	2	FACETS	0.94	0.89	0.99	0.94	0.89	0.99	CLONAL	1	TRUE	1	0.857501413327633	2		1137	742	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1918610	1918610	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	154	698	0	ENST00000382891.5:c.773G>T	p.Ser258Ile	p.S258I	ENST00000382891	NM_133335.3	258	aGt/aTt	4/22	1	2	FACETS	0.921	0.853	0.99	0.921	0.853	0.99	CLONAL	1	TRUE	1	0.857501413327633	2		698	390	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561863	55561863	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	137	551	1	ENST00000288135.5:c.253G>A	p.Glu85Lys	p.E85K	ENST00000288135	NM_000222.2	85	Gaa/Aaa	2/21	1	2	FACETS	0.88	0.811	0.951	0.88	0.811	0.951	CLONAL	1	TRUE	1	0.857501413327633	2		552	363	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589806	55589806	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502540	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	169	804	2	ENST00000288135.5:c.1288G>A	p.Ala430Thr	p.A430T	ENST00000288135	NM_000222.2	430	Gca/Aca	8/21	1	2	FACETS	0.892	0.828	0.956	0.892	0.828	0.956	CLONAL	1	TRUE	1	0.857501413327633	2		806	442	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599285	55599285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777616126	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	197	861	1	ENST00000288135.5:c.2411G>A	p.Arg804Gln	p.R804Q	ENST00000288135	NM_000222.2	804	cGg/cAg	17/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.857501413327633	2		862	404	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55603376	55603376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772159767	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	176	725	0	ENST00000288135.5:c.2732C>T	p.Pro911Leu	p.P911L	ENST00000288135	NM_000222.2	911	cCc/cTc	20/21	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.857501413327633	2		725	408	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953820	55953820	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	207	921	0	ENST00000263923.4:c.3616G>A	p.Glu1206Lys	p.E1206K	ENST00000263923	NM_002253.2	1206	Gaa/Aaa	27/30	1	2	FACETS	0.932	0.873	0.992	0.932	0.873	0.992	CLONAL	1	TRUE	1	0.857501413327633	2		921	518	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956220	55956220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190050670	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	213	831	1	ENST00000263923.4:c.3095G>A	p.Arg1032Gln	p.R1032Q	ENST00000263923	NM_002253.2	1032	cGa/cAa	23/30	1	2	FACETS	0.99	0.929	1	0.99	0.929	1	CLONAL	1	TRUE	1	0.857501413327633	2		832	502	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961109	55961109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374755237	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	241	927	0	ENST00000263923.4:c.2831G>A	p.Arg944Gln	p.R944Q	ENST00000263923	NM_002253.2	944	cGa/cAa	21/30	1	2	FACETS	0.971	0.914	1	0.971	0.914	1	CLONAL	1	TRUE	1	0.857501413327633	2		927	579	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964427	55964427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	189	783	0	ENST00000263923.4:c.2386G>A	p.Glu796Lys	p.E796K	ENST00000263923	NM_002253.2	796	Gaa/Aaa	17/30	1	2	FACETS	0.986	0.922	1	0.986	0.922	1	CLONAL	1	TRUE	1	0.857501413327633	2		783	447	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976627	55976627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	244	927	0	ENST00000263923.4:c.1198C>T	p.Leu400Phe	p.L400F	ENST00000263923	NM_002253.2	400	Ctt/Ttt	9/30	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.857501413327633	2		927	533	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197811	66197811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	188	638	0	ENST00000273854.3:c.2888G>A	p.Gly963Glu	p.G963E	ENST00000273854	NM_004439.5	963	gGa/gAa	17/18	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.857501413327633	2		638	427	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081525	143081525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	209	760	0	ENST00000262992.4:c.1549G>A	p.Asp517Asn	p.D517N	ENST00000262992	NM_001101669.1	517	Gat/Aat	15/24	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.857501413327633	2		760	468	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143181675	143181675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377427325	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	171	891	3	ENST00000262992.4:c.658G>A	p.Gly220Arg	p.G220R	ENST00000262992	NM_001101669.1	220	Gga/Aga	9/24	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.857501413327633	2		894	397	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534289	187534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	238	808	0	ENST00000441802.2:c.9437G>A	p.Arg3146Lys	p.R3146K	ENST00000441802	NM_005245.3	3146	aGa/aAa	13/27	0.857501413327633	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.857501413327633	1		808	313	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187558044	187558044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	123	479	0	ENST00000441802.2:c.3667C>T	p.Pro1223Ser	p.P1223S	ENST00000441802	NM_005245.3	1223	Ccc/Tcc	5/27	0.857501413327633	1	FACETS	0.999	0.944	1	0.999	0.944	1	CLONAL	1	TRUE	0	0.857501413327633	1		479	164	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	231076	231076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	220	856	0	ENST00000264932.6:c.856C>T	p.Pro286Ser	p.P286S	ENST00000264932	NM_004168.2	286	Cct/Tct	7/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.857501413327633	2		856	443	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271283	1271283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1169312254	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	134	673	2	ENST00000310581.5:c.2419G>A	p.Asp807Asn	p.D807N	ENST00000310581	NM_198253.2	807	Gac/Aac	8/16	1	2	FACETS	0.818	0.752	0.886	0.818	0.752	0.886	CLONAL	1	TRUE	1	0.857501413327633	2		675	382	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1272305	1272305	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1043358053	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	197	796	1	ENST00000310581.5:c.2377G>A	p.Glu793Lys	p.E793K	ENST00000310581	NM_198253.2	793	Gag/Aag	7/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.857501413327633	2		797	441	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278808	1278808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	230	1002	0	ENST00000310581.5:c.2234C>T	p.Ala745Val	p.A745V	ENST00000310581	NM_198253.2	745	gCc/gTc	6/16	1	2	FACETS	0.878	0.824	0.933	0.878	0.824	0.933	CLONAL	1	TRUE	1	0.857501413327633	2		1002	611	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294602	1294603	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	149	530	1	ENST00000310581.5:c.398_399delinsAA	p.Gly133Glu	p.G133E	ENST00000310581	NM_198253.2	133	gGG/gAA	2/16	1	2	FACETS	0.987	0.915	1	0.987	0.915	1	CLONAL	1	TRUE	1	0.857501413327633	2		531	352	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79966115	79966116	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	113	749	1	ENST00000265081.6:c.779_780delinsAA	p.Gly260Glu	p.G260E	ENST00000265081	NM_002439.4	260	gGG/gAA	4/24	1	2	FACETS	0.995	0.911	1	0.995	0.911	1	CLONAL	1	TRUE	1	0.857501413327633	2		750	265	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149511632	149511632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167658274	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	195	764	1	ENST00000261799.4:c.1153C>T	p.Arg385Cys	p.R385C	ENST00000261799	NM_002609.3	385	Cgc/Tgc	8/23	1	2	FACETS	0.962	0.899	1	0.962	0.899	1	CLONAL	1	TRUE	1	0.857501413327633	2		765	473	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721004	176721004	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	206	777	0	ENST00000439151.2:c.6635C>T	p.Pro2212Leu	p.P2212L	ENST00000439151	NM_022455.4	2212	cCt/cTt	23/23	0.857501413327633	1	FACETS	0.943	0.9	0.985	0.943	0.9	0.985	CLONAL	1	TRUE	0	0.857501413327633	1		777	291	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046363	180046363	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	182	782	0	ENST00000261937.6:c.2651G>A	p.Gly884Asp	p.G884D	ENST00000261937	NM_182925.4	884	gGc/gAc	19/30	NA	2	FACETS	0.894	0.832	0.956			1	INDETERMINATE	1	TRUE	NA	0.857501413327633	2		782	475	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056436	26056436	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	440	502	1	ENST00000343677.2:c.221A>T	p.Glu74Val	p.E74V	ENST00000343677	NM_005319.3	74	gAg/gTg	1/1	0.857501413327633	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.857501413327633	3		503	469	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31939838	31939838	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	832	1033	1	ENST00000375333.2:c.65C>T	p.Ser22Phe	p.S22F	ENST00000375333	NM_032454.1	22	tCc/tTc	1/8	0.857501413327633	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.857501413327633	3		1034	918	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36653561	36653561	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs981464191	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	735	830	1	ENST00000244741.5:c.479C>T	p.Ser160Phe	p.S160F	ENST00000244741	NM_000389.4	160	tCc/tTc	3/3	0.857501413327633	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.857501413327633	3		831	813	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93968002	93968002	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs766856886	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	476	588	0	ENST00000369303.4:c.1925G>A	p.Gly642Glu	p.G642E	ENST00000369303	NM_004440.3	642	gGa/gAa	11/17	0.857501413327633	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.857501413327633	3		588	514	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120366	94120366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1216099858	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	435	548	0	ENST00000369303.4:c.685G>A	p.Glu229Lys	p.E229K	ENST00000369303	NM_004440.3	229	Gag/Aag	3/17	0.857501413327633	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.857501413327633	3		548	460	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662453	117662453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	491	830	0	ENST00000368508.3:c.4924G>A	p.Glu1642Lys	p.E1642K	ENST00000368508	NM_002944.2	1642	Gaa/Aaa	30/43	0.857501413327633	3	FACETS	0.995	0.977	1	0.995	0.977	1	CLONAL	3	TRUE	0	0.857501413327633	3		830	548	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984104	2984104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	548	706	0	ENST00000396946.4:c.426G>A	p.Met142Ile	p.M142I	ENST00000396946	NM_032415.4	142	atG/atA	5/25	0.857501413327633	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.857501413327633	3		706	593	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467675	50467675	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759124417	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	633	834	0	ENST00000331340.3:c.910G>A	p.Glu304Lys	p.E304K	ENST00000331340	NM_006060.4	304	Gaa/Aaa	8/8	0.857501413327633	3	FACETS	0.995	0.978	1	0.995	0.978	1	CLONAL	3	TRUE	0	0.857501413327633	3		834	707	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860095	151860095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	306	678	1	ENST00000262189.6:c.10567C>T	p.Pro3523Ser	p.P3523S	ENST00000262189	NM_170606.2	3523	Cct/Tct	43/59	0.857501413327633	2	FACETS	0.997	0.97	1	0.997	0.97	1	CLONAL	2	TRUE	0	0.857501413327633	2		679	358	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945009	151945009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	24	140	0	ENST00000262189.6:c.2510C>T	p.Pro837Leu	p.P837L	ENST00000262189	NM_170606.2	837	cCt/cTt	14/59	0.857501413327633	2	FACETS	0.8	0.649	0.96	0.4	0.324	0.48	CLONAL	1	TRUE	0	0.857501413327633	2		140	70	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945058	151945058	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	56	1004	0	ENST00000262189.6:c.2461C>T	p.Pro821Ser	p.P821S	ENST00000262189	NM_170606.2	821	Cca/Tca	14/59	0.857501413327633	2	FACETS	0.217	0.185	0.251	0.108	0.092	0.126	SUBCLONAL	1	TRUE	0	0.857501413327633	2		1004	603	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981530	70981530	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	316	1338	0	ENST00000276594.2:c.566G>A	p.Gly189Glu	p.G189E	ENST00000276594	NM_024504.3	189	gGg/gAg	2/8	1	2	FACETS	0.983	0.933	1	0.983	0.933	1	CLONAL	1	TRUE	1	0.857501413327633	2		1338	750	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375969	8375969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1242333397	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	162	578	0	ENST00000356435.5:c.4628C>T	p.Pro1543Leu	p.P1543L	ENST00000356435		1543	cCt/cTt	28/35	0.857501413327633	3	FACETS	0.952	0.878	1	0.476	0.439	0.514	CLONAL	1	TRUE	1	0.857501413327633	3		578	567	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486058	8486058	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	257	876	1	ENST00000356435.5:c.2759G>A	p.Gly920Glu	p.G920E	ENST00000356435		920	gGa/gAa	17/35	0.857501413327633	3	FACETS	1	0.97	1	0.526	0.494	0.559	CLONAL	1	TRUE	1	0.857501413327633	3		877	814	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524925	8524925	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	347	541	0	ENST00000356435.5:c.679G>A	p.Glu227Lys	p.E227K	ENST00000356435		227	Gag/Aag	7/35	0.857501413327633	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.857501413327633	3		541	569	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636730	8636730	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	261	586	0	ENST00000356435.5:c.179A>G	p.Lys60Arg	p.K60R	ENST00000356435		60	aAa/aGa	2/35	0.857501413327633	3	FACETS	0.991	0.944	1	0.991	0.944	1	CLONAL	2	TRUE	1	0.857501413327633	3		586	439	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020726	37020726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs999324823	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	541	887	0	ENST00000358127.4:c.119G>A	p.Arg40Lys	p.R40K	ENST00000358127	NM_001280556.1	40	aGg/aAg	2/10	0.857501413327633	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.857501413327633	3		887	838	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248085	98248085	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	374	965	1	ENST00000331920.6:c.466C>T	p.Gln156Ter	p.Q156*	ENST00000331920	NM_000264.3	156	Caa/Taa	3/24	0.857501413327633	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.857501413327633	2		966	432	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900195	101900195	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	226	668	0	ENST00000374994.4:c.629G>A	p.Ser210Asn	p.S210N	ENST00000374994	NM_004612.2	210	aGc/aAc	4/9	0.857501413327633	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.857501413327633	2		668	258	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396800	139396800	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	480	1037	1	ENST00000277541.6:c.5308C>T	p.Pro1770Ser	p.P1770S	ENST00000277541	NM_017617.3	1770	Cct/Tct	28/34	0.857501413327633	2	FACETS	0.982	0.96	1	0.982	0.96	1	CLONAL	2	TRUE	0	0.857501413327633	2		1038	570	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403367	139403368	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	397	972	1	ENST00000277541.6:c.3125_3126delinsTT	p.Ser1042Phe	p.S1042F	ENST00000277541	NM_017617.3	1042	tCC/tTT	19/34	0.857501413327633	2	FACETS	0.985	0.961	1	0.985	0.961	1	CLONAL	2	TRUE	0	0.857501413327633	2		973	470	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321372	1321372	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1319865856	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	215	833	3	ENST00000400841.2:c.383C>T	p.Ser128Leu	p.S128L	ENST00000400841		128	tCg/tTg	4/6	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.857501413327633	1		836	276	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858412	9858412	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	175	764	0	ENST00000330684.3:c.2989G>A	p.Glu997Lys	p.E997K	ENST00000330684	NM_001134407.1	997	Gag/Aag	13/13	1	2	FACETS	0.954	0.888	1	0.954	0.888	1	CLONAL	1	TRUE	1	0.857501413327633	2		764	428	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292390	15292390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	203	868	0	ENST00000263388.2:c.2789C>T	p.Pro930Leu	p.P930L	ENST00000263388	NM_000435.2	930	cCc/cTc	17/33	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.857501413327633	2		868	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578188	7578188	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201592	NA	P-0021855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1171	69	893	0	ENST00000269305.4:c.661G>T	p.Glu221Ter	p.E221*	ENST00000269305	NM_001126112.2	221	Gag/Tag	6/11	1	2	FACETS	0.412	0.357	0.472	0.412	0.357	0.472	SUBCLONAL	1	TRUE	1	0.27	2		893	1240	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932136	36932136	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759549054	NA	P-0021855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	69	708	2	ENST00000361632.4:c.2333C>T	p.Ala778Val	p.A778V	ENST00000361632		778	gCg/gTg	16/16	1	2	FACETS	0.629	0.547	0.719	0.629	0.547	0.719	SUBCLONAL	1	TRUE	1	0.27	2		710	812	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420606	49420606	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	77	839	0	ENST00000301067.7:c.15143G>T	p.Arg5048Leu	p.R5048L	ENST00000301067	NM_003482.3	5048	cGt/cTt	48/54	1	2	FACETS	0.454	0.397	0.516	0.454	0.397	0.516	SUBCLONAL	1	TRUE	1	0.27	2		839	1257	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885512	111885512	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1253	90	912	0	ENST00000341259.2:c.1289A>C	p.His430Pro	p.H430P	ENST00000341259	NM_005475.2	430	cAc/cCc	7/8	1	2	FACETS	0.496	0.439	0.559	0.496	0.439	0.559	SUBCLONAL	1	TRUE	1	0.27	2		912	1343	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993509	72993509	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	64	852	2	ENST00000268489.5:c.536del	p.Gly179AlafsTer22	p.G179Afs*22	ENST00000268489	NM_006885.3	179	gGc/gc	2/10	1	2	FACETS	0.455	0.392	0.523	0.455	0.392	0.523	SUBCLONAL	1	TRUE	1	0.27	2		854	1042	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208253	5208253	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1458294662	NA	P-0021855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	53	741	0	ENST00000357368.4:c.5637C>G	p.His1879Gln	p.H1879Q	ENST00000357368	NM_002850.3	1879	caC/caG	36/38	1	2	FACETS	0.378	0.321	0.441	0.378	0.321	0.441	SUBCLONAL	1	TRUE	1	0.27	2		741	1038	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905596	50905596	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	81	898	1	ENST00000440232.2:c.724G>T	p.Ala242Ser	p.A242S	ENST00000440232	NM_002691.3	242	Gcg/Tcg	6/27	1	2	FACETS	0.493	0.433	0.558	0.493	0.433	0.558	SUBCLONAL	1	TRUE	1	0.27	2		899	1217	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031203	36031203	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	66	877	0	ENST00000358208.4:c.1322G>T	p.Arg441Leu	p.R441L	ENST00000358208		441	cGc/cTc	11/12	1	2	FACETS	0.397	0.343	0.456	0.397	0.343	0.456	SUBCLONAL	1	TRUE	1	0.27	2		877	1232	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287244	33287244	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	120	818	0	ENST00000374542.5:c.1853C>G	p.Ser618Cys	p.S618C	ENST00000374542	NM_001141970.1	618	tCt/tGt	6/8	1	2	FACETS	0.821	0.74	0.907	0.821	0.74	0.907	CLONAL	1	TRUE	1	0.27	2		818	1083	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577150	7577150	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	160	679	8	ENST00000269305.4:c.788del	p.Asn263IlefsTer82	p.N263Ifs*82	ENST00000269305	NM_001126112.2	263	aAt/at	8/11	0.427257237048583	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.461597734342792	1		687	467	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601944	43601944	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1172318035	NA	P-0021860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	170	880	2	ENST00000355710.3:c.988C>T	p.Arg330Trp	p.R330W	ENST00000355710	NM_020975.4	330	Cgg/Tgg	5/20	1	2	FACETS	0.981	0.904	1	0.981	0.904	1	CLONAL	1	TRUE	1	0.461597734342792	2		882	751	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186850	142186851	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0021860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	109	714	1	ENST00000350721.4:c.6612_6613del	p.Met2204IlefsTer17	p.M2204Ifs*17	ENST00000350721	NM_001184.3	2204	atGAaa/ataa	39/47	0.461597734342792	3	FACETS	0.855	0.768	0.946	0.427	0.384	0.473	CLONAL	1	TRUE	1	0.461597734342792	3		715	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	196	832	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.447564950438329	2		832	847	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412493	80412493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514698	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	16	538	0	ENST00000286548.4:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000286548	NM_002072.3	183	cGa/cAa	4/7	NA	2	FACETS	0.128	0.094	0.169			1	INDETERMINATE	1	TRUE	NA	0.447564950438329	2		538	560	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133483	55133483	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	783	697	4	ENST00000257290.5:c.787G>T	p.Glu263Ter	p.E263*	ENST00000257290	NM_006206.4	263	Gaa/Taa	6/23	0.447564950438329	7	FACETS	0.965	0.939	0.99			1	CLONAL	6	TRUE	NA	0.447564950438329	7		701	1281	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247267	153247267	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	116	604	0	ENST00000281708.4:c.1535G>A	p.Arg512Lys	p.R512K	ENST00000281708	NM_033632.3	512	aGg/aAg	10/12	1	2	FACETS	0.929	0.84	1	0.929	0.84	1	CLONAL	1	TRUE	1	0.447564950438329	2		604	558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579485	7579485	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs869312782	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	201	859	0	ENST00000269305.4:c.202G>T	p.Glu68Ter	p.E68*	ENST00000269305	NM_001126112.2	68	Gag/Tag	4/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.447564950438329	2		859	788	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163802	72163802	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	77	641	1	ENST00000357731.5:c.556C>T	p.Gln186Ter	p.Q186*	ENST00000357731	NM_173808.2	186	Caa/Taa	4/7	0.289823961107698	4	FACETS	0.759	0.667	0.859	0.38	0.333	0.43	SUBCLONAL	1	TRUE	2	0.447564950438329	4		642	656	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433876	78433876	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	96	630	0	ENST00000370768.2:c.223G>C	p.Ala75Pro	p.A75P	ENST00000370768	NM_003902.3	75	Gct/Cct	3/20	0.289823961107698	4	FACETS	0.83	0.74	0.927	0.415	0.37	0.464	CLONAL	1	TRUE	2	0.447564950438329	4		630	748	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054966	176054966	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	134	864	0	ENST00000367669.3:c.1087C>G	p.His363Asp	p.H363D	ENST00000367669	NM_022457.5	363	Cat/Gat	10/20	0.290291418232995	5	FACETS	0.84	0.761	0.923	0.28	0.253	0.308	CLONAL	1	TRUE	2	0.447564950438329	5		864	1192	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226561961	226561961	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	261	723	0	ENST00000366794.5:c.2036T>A	p.Val679Glu	p.V679E	ENST00000366794	NM_001618.3	679	gTg/gAg	14/23	0.447564950438329	5	FACETS	0.825	0.772	0.879	0.55	0.514	0.586	CLONAL	2	TRUE	2	0.447564950438329	5		723	1182	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77085377	77085377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	232	636	0	ENST00000356341.3:c.473C>T	p.Ala158Val	p.A158V	ENST00000356341	NM_002576.4	158	gCc/gTc	5/15	0.447564950438329	5	FACETS	0.909	0.848	0.972	0.606	0.565	0.648	CLONAL	2	TRUE	2	0.447564950438329	5		636	953	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871147	12871147	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	25	363	0	ENST00000228872.4:c.374C>A	p.Ser125Tyr	p.S125Y	ENST00000228872	NM_004064.3	125	tCt/tAt	1/3	0.447564950438329	1	FACETS	0.372	0.294	0.461	0.372	0.294	0.461	SUBCLONAL	1	TRUE	0	0.447564950438329	1		363	233	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378580	25378580	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	83	829	0	ENST00000311936.3:c.418C>T	p.Pro140Ser	p.P140S	ENST00000311936	NM_004985.3	140	Cct/Tct	4/5	0.347432275491639	5	FACETS	0.509	0.447	0.575			1	SUBCLONAL	1	TRUE	NA	0.447564950438329	5		829	1219	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557612	21557612	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	97	823	0	ENST00000382592.4:c.2233A>G	p.Met745Val	p.M745V	ENST00000382592	NM_014572.2	745	Atg/Gtg	5/8	0.44699973569228	2	FACETS	0.579	0.516	0.646	0.289	0.258	0.323	SUBCLONAL	1	TRUE	0	0.447564950438329	2		823	749	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28963971	28963971	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	97	568	1	ENST00000282397.4:c.1931G>T	p.Gly644Val	p.G644V	ENST00000282397	NM_002019.4	644	gGg/gTg	13/30	0.44699973569228	2	FACETS	0.957	0.858	1	0.478	0.429	0.531	CLONAL	1	TRUE	0	0.447564950438329	2		569	453	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912143	32912143	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	287	895	4	ENST00000380152.3:c.3651G>T	p.Arg1217Ser	p.R1217S	ENST00000380152		1217	agG/agT	11/27	0.44699973569228	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.447564950438329	2		899	618	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435854	110435854	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	241	639	0	ENST00000375856.3:c.2547G>T	p.Gln849His	p.Q849H	ENST00000375856	NM_003749.2	849	caG/caT	1/2	0.44699973569228	2	FACETS	0.995	0.939	1	0.995	0.939	1	CLONAL	2	TRUE	0	0.447564950438329	2		639	541	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041834	42041834	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	109	663	0	ENST00000219905.7:c.6032del	p.Asn2011ThrfsTer11	p.N2011Tfs*11	ENST00000219905	NM_001164273.1	2010	cAa/ca	17/24	0.447564950438329	2	FACETS	0.755	0.679	0.835	0.378	0.339	0.418	SUBCLONAL	1	TRUE	0	0.447564950438329	2		663	645	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678546	88678547	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs149187685	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	67	468	0	ENST00000360948.2:c.989dup	p.Pro331ThrfsTer76	p.P331Tfs*76	ENST00000360948	NM_001012338.2	330	cca/ccCa	9/19	0.447564950438329	2	FACETS	0.809	0.707	0.919	0.405	0.353	0.46	CLONAL	1	TRUE	0	0.447564950438329	2		468	370	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644830	67644830	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	263	568	2	ENST00000264010.4:c.95G>T	p.Gly32Val	p.G32V	ENST00000264010	NM_006565.3	32	gGc/gTc	3/12	0.341826316377797	3	FACETS	1	0.963	1			1	CLONAL	2	TRUE	NA	0.447564950438329	3		570	699	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579367	7579367	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782447	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	221	850	0	ENST00000269305.4:c.320A>G	p.Tyr107Cys	p.Y107C	ENST00000269305	NM_001126112.2	107	tAc/tGc	4/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.447564950438329	2		850	854	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118361	17118361	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	221	890	0	ENST00000285071.4:c.1476C>A	p.Asn492Lys	p.N492K	ENST00000285071	NM_144997.5	492	aaC/aaA	13/14	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.447564950438329	2		890	904	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741882	40741882	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	285	741	2	ENST00000392038.2:c.1090A>T	p.Met364Leu	p.M364L	ENST00000392038	NM_001626.4	364	Atg/Ttg	11/14	0.447564950438329	4	FACETS	0.8	0.752	0.85	0.8	0.752	0.85	SUBCLONAL	2	TRUE	2	0.447564950438329	4		743	1152	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799191	42799191	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	57	805	0	ENST00000575354.2:c.4675C>T	p.Pro1559Ser	p.P1559S	ENST00000575354	NM_015125.3	1559	Ccc/Tcc	20/20	0.447564950438329	4	FACETS	0.367	0.314	0.426	0.184	0.157	0.213	SUBCLONAL	1	TRUE	2	0.447564950438329	4		805	1004	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872199	45872199	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	44	799	0	ENST00000391945.4:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000391945	NM_000400.3	79	Gag/Cag	4/23	NA	2	FACETS	0.239	0.2	0.283			1	INDETERMINATE	1	TRUE	NA	0.447564950438329	2		799	822	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086069	16086069	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	260	745	3	ENST00000281043.3:c.1245G>T	p.Glu415Asp	p.E415D	ENST00000281043	NM_005378.4	415	gaG/gaT	3/3	0.349426450608199	3	FACETS	0.842	0.791	0.895	0.842	0.791	0.895	CLONAL	2	TRUE	1	0.447564950438329	3		748	844	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543695	29543695	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	126	872	0	ENST00000389048.3:c.1468A>C	p.Thr490Pro	p.T490P	ENST00000389048	NM_004304.4	490	Acc/Ccc	7/29	0.349426450608199	3	FACETS	0.668	0.603	0.736	0.334	0.301	0.368	SUBCLONAL	1	TRUE	1	0.447564950438329	3		872	1032	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285188	212285188	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	85	609	0	ENST00000342788.4:c.3113G>T	p.Arg1038Ile	p.R1038I	ENST00000342788	NM_005235.2	1038	aGa/aTa	25/28	0.295485519764704	3	FACETS	0.824	0.73	0.925	0.412	0.365	0.463	CLONAL	1	TRUE	1	0.447564950438329	3		609	564	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538358	9538358	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	116	517	1	ENST00000353224.5:c.1640C>A	p.Thr547Asn	p.T547N	ENST00000353224	NM_177990.2	547	aCt/aAt	7/10	0.143327571633467	5	FACETS	1	0.975	1			1	INDETERMINATE	1	TRUE	NA	0.447564950438329	5		518	692	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710653	40710653	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	107	608	1	ENST00000373198.4:c.4198G>T	p.Gly1400Trp	p.G1400W	ENST00000373198	NM_133170.3	1400	Ggg/Tgg	31/32	0.290291418232995	5	FACETS	1	0.899	1	0.334	0.299	0.371	CLONAL	1	TRUE	2	0.447564950438329	5		609	797	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827933	40827933	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	354	809	1	ENST00000373198.4:c.2495C>A	p.Ala832Asp	p.A832D	ENST00000373198	NM_133170.3	832	gCc/gAc	17/32	0.290291418232995	5	FACETS	1	0.989	1	0.768	0.728	0.809	CLONAL	2	TRUE	2	0.447564950438329	5		810	1147	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259009	89259009	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	47	226	0	ENST00000336596.2:c.154-1G>T		p.X52_splice	ENST00000336596	NM_005233.5	52			0.130430720772105	3	FACETS	1	0.911	1	0.549	0.468	0.637	INDETERMINATE	1	TRUE	1	0.447564950438329	3		226	234	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979564	55979564	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1415	122	756	0	ENST00000263923.4:c.883G>C	p.Asp295His	p.D295H	ENST00000263923	NM_002253.2	295	Gat/Cat	7/30	0.447564950438329	7	FACETS	0.752	0.677	0.831			1	SUBCLONAL	1	TRUE	NA	0.447564950438329	7		756	1537	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081512	143081512	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	99	563	0	ENST00000262992.4:c.1562G>T	p.Trp521Leu	p.W521L	ENST00000262992	NM_001101669.1	521	tGg/tTg	15/24	1	2	FACETS	0.903	0.809	1	0.903	0.809	1	CLONAL	1	TRUE	1	0.447564950438329	2		563	490	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094950	143094950	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	134	623	0	ENST00000262992.4:c.1194G>T	p.Gln398His	p.Q398H	ENST00000262992	NM_001101669.1	398	caG/caT	14/24	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.447564950438329	2		623	478	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518122	187518122	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs539779886	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	161	769	0	ENST00000441802.2:c.12572G>T	p.Gly4191Val	p.G4191V	ENST00000441802	NM_005245.3	4191	gGg/gTg	25/27	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.447564950438329	2		769	660	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861052	35861052	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	394	569	2	ENST00000303115.3:c.181G>T	p.Asp61Tyr	p.D61Y	ENST00000303115	NM_002185.3	61	Gac/Tac	2/8	0.447564950438329	7	FACETS	1	0.956	1			1	CLONAL	4	TRUE	NA	0.447564950438329	7		571	931	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876296	35876296	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	277	628	0	ENST00000303115.3:c.1088G>C	p.Arg363Thr	p.R363T	ENST00000303115	NM_002185.3	363	aGa/aCa	8/8	0.447564950438329	7	FACETS	0.834	0.784	0.886			1	CLONAL	3	TRUE	NA	0.447564950438329	7		628	1048	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659284	86659284	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	177	550	0	ENST00000274376.6:c.1573T>C	p.Cys525Arg	p.C525R	ENST00000274376	NM_002890.2	525	Tgt/Cgt	11/25	0.447564950438329	2	FACETS	0.901	0.839	0.963	0.901	0.839	0.963	CLONAL	2	TRUE	0	0.447564950438329	2		550	439	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106543551	106543551	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	77	495	0	ENST00000369096.4:c.353G>T	p.Gly118Val	p.G118V	ENST00000369096	NM_001198.3	118	gGt/gTt	3/7	0.15567351382775	2	FACETS	0.657	0.578	0.741	0.328	0.289	0.371	INDETERMINATE	1	TRUE	0	0.447564950438329	2		495	524	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555023	106555023	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	179	611	0	ENST00000369096.4:c.2140C>A	p.Pro714Thr	p.P714T	ENST00000369096	NM_001198.3	714	Ccg/Acg	7/7	0.15567351382775	2	FACETS	1	0.988	1	0.679	0.629	0.73	INDETERMINATE	1	TRUE	0	0.447564950438329	2		611	589	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729780	41729780	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	135	439	0	ENST00000242208.4:c.749G>C	p.Ser250Thr	p.S250T	ENST00000242208	NM_002192.2	250	aGt/aCt	3/3	0.290291418232995	5	FACETS	0.941	0.859	1	0.627	0.573	0.684	CLONAL	2	TRUE	2	0.447564950438329	5		439	536	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38314894	38314894	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	140	606	4	ENST00000425967.3:c.170C>A	p.Ser57Tyr	p.S57Y	ENST00000425967	NM_001174067.1	57	tCc/tAc	3/19	0.341826316377797	3	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.447564950438329	3		610	603	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891341	101891341	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	100	839	1	ENST00000374994.4:c.302G>T	p.Cys101Phe	p.C101F	ENST00000374994	NM_004612.2	101	tGc/tTc	2/9	0.447564950438329	3	FACETS	0.724	0.647	0.807	0.362	0.323	0.404	SUBCLONAL	1	TRUE	1	0.447564950438329	3		840	755	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0021862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	870	732	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.835722866764298	2	FACETS	0.988	0.972	1	0.988	0.972	1	CLONAL	2	TRUE	0	0.858473221507613	2		732	1026	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249002	55249003	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCGTGGA	rs397517109	NA	P-0021862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2002	4076	508	1	ENST00000275493.2:c.2303_2311dup	p.Ser768_Asp770dup	p.S768_D770dup	ENST00000275493	NM_005228.3	768	gcc/gcCAGCGTGGAc	20/28	0.858473221507613	14	FACETS	0.961	0.95	0.972			1	CLONAL	10	TRUE	NA	0.858473221507613	14		509	6078	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937103	36937103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1364558879	NA	P-0021862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	398	559	2	ENST00000361632.4:c.1216G>A	p.Val406Met	p.V406M	ENST00000361632		406	Gtg/Atg	9/16	0.858463173507213	3	FACETS	0.992	0.943	1	0.496	0.471	0.521	CLONAL	1	TRUE	1	0.858473221507613	3		561	1336	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831204	3831204	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0021862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	246	422	0	ENST00000262367.5:c.1676+1G>A		p.X559_splice	ENST00000262367	NM_004380.2	559			0.835722866764298	2	FACETS	0.826	0.776	0.877	0.413	0.388	0.439	CLONAL	1	TRUE	0	0.858473221507613	2		422	694	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7141701	7141701	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	357	636	0	ENST00000302850.5:c.2669G>T	p.Arg890Leu	p.R890L	ENST00000302850	NM_000208.2	890	cGa/cTa	13/22	1	2	FACETS	0.897	0.853	0.942	0.897	0.853	0.942	CLONAL	1	TRUE	1	0.858473221507613	2		636	927	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0021863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	213	486	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	0.436082682003275	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.436082682003275	2		486	480	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771828	135771828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779599439	NA	P-0021863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1509	84	876	0	ENST00000298552.3:c.3289C>T	p.Arg1097Cys	p.R1097C	ENST00000298552	NM_001162426.1	1097	Cgt/Tgt	23/23	0.436082682003275	5	FACETS	0.4	0.351	0.453	0.133	0.117	0.151	SUBCLONAL	1	TRUE	2	0.436082682003275	5		876	1593	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747342068	NA	P-0021863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	547	1054	0	ENST00000269305.4:c.394A>G	p.Lys132Glu	p.K132E	ENST00000269305	NM_001126112.2	132	Aag/Gag	5/11	0.436082682003275	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.436082682003275	2		1054	1188	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576213	88576213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	107	720	0	ENST00000360948.2:c.1460G>A	p.Gly487Asp	p.G487D	ENST00000360948	NM_001012338.2	487	gGc/gAc	13/19	0.201250325981003	3	FACETS	0.739	0.662	0.82	0.246	0.22	0.274	INDETERMINATE	1	TRUE	0	0.436082682003275	3		720	809	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252024	133252024	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	418	903	1	ENST00000320574.5:c.1186G>T	p.Glu396Ter	p.E396*	ENST00000320574	NM_006231.2	396	Gag/Tag	12/49	0.436082682003275	3	FACETS	0.994	0.948	1	0.994	0.948	1	CLONAL	2	TRUE	1	0.436082682003275	3		904	1175	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202789	133202789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771490182	NA	P-0021863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	63	773	2	ENST00000320574.5:c.6445C>T	p.Arg2149Cys	p.R2149C	ENST00000320574	NM_006231.2	2149	Cgc/Tgc	46/49	0.436082682003275	3	FACETS	0.346	0.298	0.399	0.173	0.149	0.2	SUBCLONAL	1	TRUE	1	0.436082682003275	3		775	1016	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16021290	16021290	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	339	609	1	ENST00000268712.3:c.1967C>T	p.Thr656Met	p.T656M	ENST00000268712	NM_006311.3	656	aCg/aTg	18/46	0.436082682003275	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.436082682003275	2		610	730	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117774	70117775	+	missense_variant	Missense_Mutation	DNP	TC	TC	GG	novel	NA	P-0021863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	473	827	0	ENST00000245479.2:c.242_243delinsGG	p.Leu81Arg	p.L81R	ENST00000245479	NM_000346.3	81	cTC/cGG	1/3	0.4337711263027	3	FACETS	0.994	0.957	1	0.994	0.957	1	CLONAL	3	TRUE	0	0.436082682003275	3		827	886	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62294213	62294213	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750794827	NA	P-0021863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	562	831	5	ENST00000360203.5:c.509G>A	p.Arg170His	p.R170H	ENST00000360203	NM_001283009.1	170	cGc/cAc	6/35	0.436082682003275	5	FACETS	0.901	0.864	0.937	0.901	0.864	0.937	CLONAL	3	TRUE	2	0.436082682003275	5		836	1578	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266054	41266078	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAAAAGCGGCTGTTAGTCACTGG	CAGAAAAGCGGCTGTTAGTCACTGG	-	novel	NA	P-0021863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	124	489	0	ENST00000349496.5:c.54_78del	p.Arg18SerfsTer21	p.R18Sfs*21	ENST00000349496	NM_001904.3	17	gaCAGAAAAGCGGCTGTTAGTCACTGG/ga	3/15	0.436082682003275	2	FACETS	1	0.979	1	0.626	0.57	0.684	CLONAL	1	TRUE	0	0.436082682003275	2		489	454	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266089	41266108	+	frameshift_variant	Frame_Shift_Del	DEL	CTTACCTGGACTCTGGAATC	CTTACCTGGACTCTGGAATC	-	novel	NA	P-0021863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	127	525	0	ENST00000349496.5:c.87_106del	p.Tyr30PhefsTer13	p.Y30Ffs*13	ENST00000349496	NM_001904.3	29	tCTTACCTGGACTCTGGAATC/t	3/15	0.436082682003275	2	FACETS	1	0.978	1	0.616	0.561	0.672	CLONAL	1	TRUE	0	0.436082682003275	2		525	473	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607169	189607169	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	154	946	0	ENST00000264731.3:c.1548G>C	p.Met516Ile	p.M516I	ENST00000264731	NM_003722.4	516	atG/atC	12/14	0.436082682003275	3	FACETS	0.666	0.608	0.727	0.333	0.304	0.364	SUBCLONAL	1	TRUE	1	0.436082682003275	3		946	1292	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0021865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	240	809	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.476849313967198	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	0	0.476849313967198	1		809	718	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578188	7578188	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	290	858	1	ENST00000269305.4:c.661del	p.Glu221SerfsTer26	p.E221Sfs*26	ENST00000269305	NM_001126112.2	221	Gag/ag	6/11	0.476849313967198	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	0	0.476849313967198	1		859	794	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604776	48604776	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs377767382	NA	P-0021865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	206	576	0	ENST00000342988.3:c.1598T>C	p.Leu533Pro	p.L533P	ENST00000342988	NM_005359.5	533	cTc/cCc	12/12	0.476849313967198	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	0	0.476849313967198	1		576	592	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059188	27059194	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTCTC	GGGTCTC	-	novel	NA	P-0021868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	321	722	2	ENST00000324856.7:c.1825_1831del	p.Gly609ArgfsTer8	p.G609Rfs*8	ENST00000324856	NM_006015.4	609	GGGTCTCag/ag	4/20	0.598370095278754	2	FACETS	0.842	0.813	0.869	1	0.995	1	CLONAL	3	TRUE	0	0.598370095278754	2		724	425	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0021870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	124	1047	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.217691091306415	1	FACETS	0.755	0.683	0.832	0.755	0.683	0.832	SUBCLONAL	1	TRUE	0	0.323428096207401	1		1049	851	SUCCESS
BLM	641	MSKCC	GRCh37	15	91290720	91290720	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs139282091	NA	P-0021870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	54	492	0	ENST00000355112.3:c.98C>T	p.Ser33Leu	p.S33L	ENST00000355112	NM_000057.2	33	tCa/tTa	2/22	0.268964689158815	1	FACETS	0.494	0.421	0.573	0.494	0.421	0.573	SUBCLONAL	1	TRUE	0	0.323428096207401	1		492	567	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577136	7577142	+	frameshift_variant	Frame_Shift_Del	DEL	TCCGTCC	TCCGTCC	-	novel	NA	P-0021870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	108	731	0	ENST00000269305.4:c.796_802del	p.Gly266ThrfsTer77	p.G266Tfs*77	ENST00000269305	NM_001126112.2	266	GGACGGAac/ac	8/11	0.217691091306415	1	FACETS	0.702	0.629	0.778	0.702	0.629	0.778	SUBCLONAL	1	TRUE	0	0.323428096207401	1		731	798	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039532	180039532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745459631	NA	P-0021871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	169	822	1	ENST00000261937.6:c.3511G>A	p.Asp1171Asn	p.D1171N	ENST00000261937	NM_182925.4	1171	Gac/Aac	26/30	0.116529262740918	5	FACETS	0.783	0.719	0.851	0.392	0.359	0.426	INDETERMINATE	2	TRUE	1	0.258060499411735	5		823	1160	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0021871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	232	603	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	0.207187551689259	4	FACETS	0.884	0.826	0.944	1	0.99	1	CLONAL	3	TRUE	2	0.258060499411735	4		603	853	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412252	139412252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057523819	NA	P-0021871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	350	1083	5	ENST00000277541.6:c.1393G>A	p.Ala465Thr	p.A465T	ENST00000277541	NM_017617.3	465	Gcc/Acc	8/34	0.218656243498461	4	FACETS	0.854	0.808	0.901	1	0.992	1	CLONAL	3	TRUE	2	0.258060499411735	4		1088	1332	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0021871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	152	692	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	0.207187551689259	4	FACETS	1	0.985	1	0.691	0.631	0.754	CLONAL	1	TRUE	2	0.258060499411735	4		692	1073	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207201	1207201	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0021871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	432	678	0	ENST00000326873.7:c.289A>T	p.Lys97Ter	p.K97*	ENST00000326873	NM_000455.4	97	Aag/Tag	1/10	0.258060499411735	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	3	TRUE	0	0.258060499411735	2		678	1029	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905112	50905112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781132734	NA	P-0021871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	145	739	0	ENST00000440232.2:c.394G>A	p.Asp132Asn	p.D132N	ENST00000440232	NM_002691.3	132	Gat/Aat	4/27	0.258060499411735	3	FACETS	1	0.977	1	0.611	0.556	0.668	CLONAL	1	TRUE	1	0.258060499411735	3		739	1039	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111445	8111445	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	146	535	1	ENST00000346208.3:c.931A>T	p.Arg311Trp	p.R311W	ENST00000346208		311	Agg/Tgg	5/6	0.206339950797438	4	FACETS	0.864	0.789	0.942	0.864	0.789	0.942	CLONAL	2	TRUE	2	0.258060499411735	4		536	824	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041817	42041817	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	50	505	2	ENST00000219905.7:c.6012G>T	p.Glu2004Asp	p.E2004D	ENST00000219905	NM_001164273.1	2004	gaG/gaT	17/24	1	2	FACETS	0.742	0.63	0.866	0.742	0.63	0.866	SUBCLONAL	1	TRUE	1	0.258060499411735	2		507	522	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242800987	242800987	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866088771	NA	P-0021871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	255	615	0	ENST00000334409.5:c.4C>T	p.Gln2Ter	p.Q2*	ENST00000334409	NM_005018.2	2	Cag/Tag	1/5	0.258060499411735	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.258060499411735	3		615	929	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445051	89445051	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	130	568	3	ENST00000336596.2:c.1371G>T	p.Trp457Cys	p.W457C	ENST00000336596	NM_005233.5	457	tgG/tgT	6/17	0.207187551689259	4	FACETS	0.943	0.857	1	0.943	0.857	1	CLONAL	2	TRUE	2	0.258060499411735	4		571	672	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441291	149441291	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	215	601	0	ENST00000286301.3:c.1748A>G	p.Gln583Arg	p.Q583R	ENST00000286301	NM_005211.3	583	cAg/cGg	12/22	0.116529262740918	5	FACETS	0.899	0.837	0.963	0.674	0.628	0.722	INDETERMINATE	3	TRUE	1	0.258060499411735	5		601	857	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180040033	180040033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	225	735	1	ENST00000261937.6:c.3409C>T	p.Pro1137Ser	p.P1137S	ENST00000261937	NM_182925.4	1137	Ccg/Tcg	25/30	0.116529262740918	5	FACETS	0.86	0.802	0.921	0.645	0.601	0.691	INDETERMINATE	3	TRUE	1	0.258060499411735	5		736	937	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908119	41908119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372683341	NA	P-0021871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	370	598	0	ENST00000372991.4:c.403C>T	p.Arg135Cys	p.R135C	ENST00000372991	NM_001760.3	135	Cgc/Tgc	2/5	0.258060499411735	3	FACETS	0.992	0.942	1	1	0.995	1	CLONAL	3	TRUE	1	0.258060499411735	3		598	1088	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750765	128750765	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1479	150	566	0	ENST00000377970.2:c.302A>T	p.Asn101Ile	p.N101I	ENST00000377970	NM_002467.4	101	aAc/aTc	2/3	0.258060499411735	12	FACETS	0.817	0.744	0.895	0.149	0.135	0.163	CLONAL	2	TRUE	1	0.258060499411735	12		566	1629	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93627380	93627380	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0021871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	124	596	0	ENST00000375746.1:c.846+1G>A		p.X282_splice	ENST00000375746	NM_001174167.1	282			0.258060499411735	2	FACETS	0.812	0.737	0.89	0.812	0.737	0.89	CLONAL	2	TRUE	0	0.258060499411735	2		596	592	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044549	47044549	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	107	667	1	ENST00000377604.3:c.2046C>A	p.Asp682Glu	p.D682E	ENST00000377604	NM_001204468.1	682	gaC/gaA	18/24	0.116529262740918	5	FACETS	1	0.954	1	0.279	0.25	0.311	INDETERMINATE	1	TRUE	1	0.258060499411735	5		668	1030	SUCCESS
AR	367	MSKCC	GRCh37	X	66942818	66942818	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs137852564	NA	P-0021871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	248	596	1	ENST00000374690.3:c.2599G>T	p.Val867Leu	p.V867L	ENST00000374690	NM_000044.3	867	Gtg/Ttg	7/8	0.116529262740918	5	FACETS	0.945	0.885	1	0.709	0.664	0.756	INDETERMINATE	3	TRUE	1	0.258060499411735	5		597	940	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0021873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	378	960	2	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	NA	2	FACETS	0.94	0.899	0.981			1	INDETERMINATE	2	TRUE	NA	0.524475448616748	2		962	767	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518183	8518183	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	1208	589	0	ENST00000356435.5:c.1208C>T	p.Pro403Leu	p.P403L	ENST00000356435		403	cCt/cTt	10/35	0.524475448616748	7	FACETS	0.994	0.978	1	0.994	0.978	1	CLONAL	7	TRUE	0	0.524475448616748	7		589	1530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs786201057	NA	P-0021873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	36	627	1	ENST00000269305.4:c.374C>A	p.Thr125Lys	p.T125K	ENST00000269305	NM_001126112.2	125	aCg/aAg	4/11	NA	2	FACETS	0.232	0.19	0.279			1	INDETERMINATE	1	TRUE	NA	0.524475448616748	2		628	593	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600324	10600324	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	308	699	0	ENST00000171111.5:c.1531G>T	p.Gly511Cys	p.G511C	ENST00000171111	NM_203500.1	511	Ggc/Tgc	4/6	0.520983360662077	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.524475448616748	2		699	566	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242768	66242768	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	307	488	0	ENST00000273854.3:c.1804G>T	p.Gly602Cys	p.G602C	ENST00000273854	NM_004439.5	602	Ggc/Tgc	9/18	0.520455977373679	4	FACETS	0.951	0.899	1			1	CLONAL	2	TRUE	NA	0.524475448616748	4		488	938	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52677289	52677289	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0021873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	452	922	0	ENST00000394830.3:c.970A>T	p.Arg324Ter	p.R324*	ENST00000394830	NM_018313.4	324	Aga/Tga	10/30	0.510848158108666	2	FACETS	0.965	0.927	1	0.965	0.927	1	CLONAL	2	TRUE	0	0.524475448616748	2		922	893	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467557	66467557	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1373753989	NA	P-0021873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	334	510	4	ENST00000273854.3:c.712C>T	p.Arg238Ter	p.R238*	ENST00000273854	NM_004439.5	238	Cga/Tga	3/18	0.520455977373679	4	FACETS	0.995	0.943	1			1	CLONAL	2	TRUE	NA	0.524475448616748	4		514	976	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073385	8073618	+	inframe_deletion	In_Frame_Del	DEL	GGCTGGATTTGGGCGCCTCCATTTGTTTCTTCTGCTTCCCTAAAAAATTTTTCATATTTGTCCAGGTATGGTGGTCGTTCAGGTAGTAGGTAATAATGTGTTGAACTAACCTTCTTCCCATTTTCAATAATGGGCAGAATGCAAGGAACCTTACTGGCAGATCCTTCGCTGTTCTGTCTTTGCAGTGCTTTGCTGCTGACATACTTGGGATCAGGGGCAAAGCTCTGTGTCGGG	GGCTGGATTTGGGCGCCTCCATTTGTTTCTTCTGCTTCCCTAAAAAATTTTTCATATTTGTCCAGGTATGGTGGTCGTTCAGGTAGTAGGTAATAATGTGTTGAACTAACCTTCTTCCCATTTTCAATAATGGGCAGAATGCAAGGAACCTTACTGGCAGATCCTTCGCTGTTCTGTCTTTGCAGTGCTTTGCTGCTGACATACTTGGGATCAGGGGCAAAGCTCTGTGTCGGG	-	novel	NA	P-0021873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	358	760	0	ENST00000377482.5:c.1041_1274del	p.Pro348_Pro425del	p.P348_P425del	ENST00000377482	NM_018948.3	347	ccCCCGACACAGAGCTTTGCCCCTGATCCCAAGTATGTCAGCAGCAAAGCACTGCAAAGACAGAACAGCGAAGGATCTGCCAGTAAGGTTCCTTGCATTCTGCCCATTATTGAAAATGGGAAGAAGGTTAGTTCAACACATTATTACCTACTACCTGAACGACCACCATACCTGGACAAATATGAAAAATTTTTTAGGGAAGCAGAAGAAACAAATGGAGGCGCCCAAATCCAGCCa/cca	4/4	0.510848158108666	2	FACETS	0.926	0.884	0.968	0.926	0.884	0.968	CLONAL	2	TRUE	0	0.524475448616748	2		760	737	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885917	23885917	+	start_lost	Translation_Start_Site	SNP	T	T	A	novel	NA	P-0021873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	167	417	0	ENST00000374561.5:c.1A>T	p.Met1?	p.M1?	ENST00000374561	NM_002167.4	1	Atg/Ttg	1/3	0.510848158108666	2	FACETS	0.827	0.77	0.885	0.827	0.77	0.885	CLONAL	2	TRUE	0	0.524475448616748	2		417	385	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46715696	46715696	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	448	842	1	ENST00000371975.4:c.115A>T	p.Ser39Cys	p.S39C	ENST00000371975	NM_003579.3	39	Agt/Tgt	3/18	0.510848158108666	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.524475448616748	2		843	816	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989033	85989033	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	115	548	0	ENST00000263360.6:c.1199A>G	p.Lys400Arg	p.K400R	ENST00000263360	NM_003797.3	400	aAa/aGa	11/12	0.245554927646186	3	FACETS	0.849	0.766	0.936			1	INDETERMINATE	1	TRUE	NA	0.524475448616748	3		548	652	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641544	18641544	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	334	637	0	ENST00000266497.5:c.2543C>G	p.Ala848Gly	p.A848G	ENST00000266497		848	gCc/gGc	17/31	0.216072507787693	5	FACETS	1	0.991	1	0.793	0.751	0.835	INDETERMINATE	2	TRUE	2	0.524475448616748	5		637	957	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440438	49440438	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	430	917	0	ENST00000301067.7:c.4372G>C	p.Asp1458His	p.D1458H	ENST00000301067	NM_003482.3	1458	Gac/Cac	15/54	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	2	TRUE	NA	0.524475448616748	2		917	816	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626755	28626755	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs750445891	NA	P-0021873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	392	746	0	ENST00000241453.7:c.541G>T	p.Ala181Ser	p.A181S	ENST00000241453	NM_004119.2	181	Gcc/Tcc	5/24	0.452971740805888	3	FACETS	0.976	0.931	1	0.976	0.931	1	CLONAL	2	TRUE	1	0.524475448616748	3		746	967	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28631559	28631559	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	178	716	1	ENST00000241453.7:c.409C>A	p.Gln137Lys	p.Q137K	ENST00000241453	NM_004119.2	137	Caa/Aaa	4/24	0.452971740805888	3	FACETS	0.957	0.883	1	0.479	0.441	0.518	CLONAL	1	TRUE	1	0.524475448616748	3		717	895	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042557	42042557	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	88	583	1	ENST00000219905.7:c.6752C>T	p.Ser2251Leu	p.S2251L	ENST00000219905	NM_001164273.1	2251	tCa/tTa	17/24	0.520983360662077	2	FACETS	0.508	0.451	0.57	0.254	0.225	0.285	SUBCLONAL	1	TRUE	0	0.524475448616748	2		584	660	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944136	81944136	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	230	681	1	ENST00000359376.3:c.1745G>T	p.Arg582Leu	p.R582L	ENST00000359376	NM_002661.3	582	cGg/cTg	18/33	0.369808397266523	4	FACETS	0.776	0.724	0.828	0.776	0.724	0.828	SUBCLONAL	2	TRUE	2	0.524475448616748	4		682	862	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618814	37618814	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	252	662	2	ENST00000447079.4:c.490G>T	p.Ala164Ser	p.A164S	ENST00000447079	NM_015083.1	164	Gcg/Tcg	1/14	0.24904452626041	5	FACETS	1	0.956	1	0.682	0.64	0.725	INDETERMINATE	2	TRUE	2	0.524475448616748	5		664	839	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051624	13051644	+	inframe_deletion	In_Frame_Del	DEL	GACAACCCCGAGTATTCTCCC	GACAACCCCGAGTATTCTCCC	-	novel	NA	P-0021873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	348	811	1	ENST00000316448.5:c.885_905del	p.Asn296_Asp302del	p.N296_D302del	ENST00000316448	NM_004343.3	295	GACAACCCCGAGTATTCTCCC/-	7/9	0.520983360662077	2	FACETS	0.864	0.823	0.905	0.864	0.823	0.905	CLONAL	2	TRUE	0	0.524475448616748	2		812	768	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376347	15376347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	203	1112	1	ENST00000263377.2:c.667C>T	p.His223Tyr	p.H223Y	ENST00000263377	NM_058243.2	223	Cac/Tac	5/20	0.3178899322453	5	FACETS	1	0.954	1	0.347	0.321	0.375	CLONAL	1	TRUE	2	0.524475448616748	5		1113	1327	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976464	25976464	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	200	847	0	ENST00000435504.4:c.1081G>C	p.Glu361Gln	p.E361Q	ENST00000435504		361	Gag/Cag	11/13	0.405370343206867	4	FACETS	0.993	0.919	1	0.331	0.306	0.357	CLONAL	1	TRUE	1	0.524475448616748	4		847	1171	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660775	227660775	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	503	735	1	ENST00000305123.5:c.2680G>T	p.Gly894Trp	p.G894W	ENST00000305123	NM_005544.2	894	Ggg/Tgg	1/2	0.482500734309272	3	FACETS	0.974	0.941	1	0.974	0.941	1	CLONAL	3	TRUE	0	0.524475448616748	3		736	829	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755437	39755437	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	336	716	0	ENST00000288319.7:c.1328C>A	p.Ser443Tyr	p.S443Y	ENST00000288319	NM_182918.3	443	tCc/tAc	10/10	0.524475448616748	2	FACETS	0.913	0.87	0.955	0.913	0.87	0.955	CLONAL	2	TRUE	0	0.524475448616748	2		716	702	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430722	181430722	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	814	689	1	ENST00000325404.1:c.574G>A	p.Ala192Thr	p.A192T	ENST00000325404	NM_003106.3	192	Gcg/Acg	1/1	0.524475448616748	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	4	TRUE	0	0.524475448616748	4		690	1181	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139775	55139775	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	86	744	0	ENST00000257290.5:c.1436G>C	p.Arg479Pro	p.R479P	ENST00000257290	NM_006206.4	479	cGa/cCa	10/23	0.520455977373679	4	FACETS	0.404	0.355	0.455			1	SUBCLONAL	1	TRUE	NA	0.524475448616748	4		744	1239	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984783	55984783	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	376	658	0	ENST00000263923.4:c.346G>T	p.Val116Phe	p.V116F	ENST00000263923	NM_002253.2	116	Gtc/Ttc	3/30	0.520455977373679	4	FACETS	0.965	0.917	1			1	CLONAL	2	TRUE	NA	0.524475448616748	4		658	1132	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156326	106156328	+	frameshift_variant	Frame_Shift_Del	DEL	TCC	TCC	CT	novel	NA	P-0021873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	229	541	2	ENST00000380013.4:c.1227_1229delinsCT	p.Pro410PhefsTer17	p.P410Ffs*17	ENST00000380013	NM_001127208.2	409	ccTCCt/ccCTt	3/11	0.524475448616748	3	FACETS	0.816	0.765	0.869	0.816	0.765	0.869	CLONAL	2	TRUE	1	0.524475448616748	3		543	675	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143033782	143033782	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	331	761	0	ENST00000262992.4:c.2189C>G	p.Pro730Arg	p.P730R	ENST00000262992	NM_001101669.1	730	cCt/cGt	20/24	0.524475448616748	5	FACETS	0.978	0.925	1	0.489	0.462	0.516	CLONAL	2	TRUE	1	0.524475448616748	5		761	1153	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564741	86564741	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs200949838	NA	P-0021873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	95	765	0	ENST00000274376.6:c.473C>G	p.Ser158Cys	p.S158C	ENST00000274376	NM_002890.2	158	tCt/tGt	1/25	0.499026852361888	2	FACETS	0.472	0.42	0.528	0.236	0.21	0.264	SUBCLONAL	1	TRUE	0	0.524475448616748	2		765	767	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681601	30681601	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	441	756	1	ENST00000376406.3:c.496G>C	p.Glu166Gln	p.E166Q	ENST00000376406	NM_014641.2	166	Gag/Cag	3/15	0.451418971578783	3	FACETS	0.918	0.883	0.952	0.918	0.883	0.952	CLONAL	3	TRUE	0	0.524475448616748	3		757	771	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873676	151873676	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	390	688	0	ENST00000262189.6:c.8862G>T	p.Leu2954Phe	p.L2954F	ENST00000262189	NM_170606.2	2954	ttG/ttT	38/59	0.369808397266523	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.524475448616748	4		688	1041	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0021874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	414	1006	1	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.544656578805455	1	FACETS	0.949	0.904	0.994	0.949	0.904	0.994	CLONAL	1	TRUE	0	0.544656578805455	1		1007	1166	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950208	38950208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs149611613	NA	P-0021874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	251	646	0	ENST00000357387.3:c.3742A>G	p.Met1248Val	p.M1248V	ENST00000357387	NM_152756.3	1248	Atg/Gtg	31/38	1	2	FACETS	0.945	0.885	1	0.945	0.885	1	CLONAL	1	TRUE	1	0.544656578805455	2		646	975	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0021875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	103	662	1				ENST00000310581	NM_198253.2	-/1132			0.186773270119235	5	FACETS	1	0.974	1			1	INDETERMINATE	2	FALSE	NA	0.551268953147938	5		663	283	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717615	89717615	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909227	NA	P-0021875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	287	374	0	ENST00000371953.3:c.640C>T	p.Gln214Ter	p.Q214*	ENST00000371953	NM_000314.4	214	Cag/Tag	7/9	0.551268953147938	2	FACETS	0.988	0.941	1	0.988	0.941	1	CLONAL	2	FALSE	0	0.551268953147938	2		374	527	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519988	NA	P-0021875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	322	510	0	ENST00000269305.4:c.808T>C	p.Phe270Leu	p.F270L	ENST00000269305	NM_001126112.2	270	Ttt/Ctt	8/11	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	2	FALSE	NA	0.551268953147938	2		510	572	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955481	48955481	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	341	448	1	ENST00000267163.4:c.1597del	p.Glu533LysfsTer10	p.E533Kfs*10	ENST00000267163	NM_000321.2	533	Gaa/aa	17/27	0.551268953147938	2	FACETS	0.947	0.905	0.989	0.947	0.905	0.989	CLONAL	2	FALSE	0	0.551268953147938	2		449	653	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0021876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	425	772	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.557116545604494	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.557116545604494	2		772	733	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0021876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	244	860	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.907	0.848	0.967	0.907	0.848	0.967	CLONAL	1	TRUE	1	0.557116545604494	2		860	966	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0021876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	214	845	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.857	0.798	0.919	0.857	0.798	0.919	CLONAL	1	TRUE	1	0.557116545604494	2		845	896	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692848	89692848	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	82	168	0	ENST00000371953.3:c.332G>A	p.Trp111Ter	p.W111*	ENST00000371953	NM_000314.4	111	tGg/tAg	5/9	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.557116545604494	2		168	291	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696716	47696716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	380	518	0	ENST00000347630.2:c.232G>A	p.Glu78Lys	p.E78K	ENST00000347630	NM_001007230.1	78	Gaa/Aaa	5/11	0.557116545604494	2	FACETS	0.943	0.904	0.983	0.943	0.904	0.983	CLONAL	2	TRUE	0	0.557116545604494	2		518	723	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371799	55371820	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCCGCGCTGGGCCCCGAG	GGCGGCCGCGCTGGGCCCCGAG	-	novel	NA	P-0021876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	68	96	0	ENST00000297316.4:c.499_520del	p.Leu167TrpfsTer213	p.L167Wfs*213	ENST00000297316	NM_022454.3	163	caGGCGGCCGCGCTGGGCCCCGAG/ca	2/2	0.557116545604494	3	FACETS	0.792	0.702	0.886	0.792	0.702	0.886	SUBCLONAL	2	TRUE	1	0.557116545604494	3		96	197	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107152	27107152	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	498	581	0	ENST00000324856.7:c.6763G>T	p.Glu2255Ter	p.E2255*	ENST00000324856	NM_006015.4	2255	Gaa/Taa	20/20	0.502786593561701	2	FACETS	0.937	0.902	0.972	0.937	0.902	0.972	CLONAL	2	TRUE	0	0.557116545604494	2		581	954	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720727	89720727	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	36	143	0	ENST00000371953.3:c.878G>T	p.Gly293Val	p.G293V	ENST00000371953	NM_000314.4	293	gGa/gTa	8/9	1	2	FACETS	0.793	0.661	0.936	0.793	0.661	0.936	CLONAL	1	TRUE	1	0.557116545604494	2		143	163	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350519	89350519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1360053875	NA	P-0021876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	81	785	0	ENST00000301030.4:c.2431G>A	p.Asp811Asn	p.D811N	ENST00000301030	NM_001256183.1	811	Gat/Aat	9/13	1	2	FACETS	0.234	0.205	0.265	0.234	0.205	0.265	SUBCLONAL	1	TRUE	1	0.557116545604494	2		785	1242	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396904	139396904	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs770247326	NA	P-0021876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	145	498	0	ENST00000277541.6:c.5204A>G	p.His1735Arg	p.H1735R	ENST00000277541	NM_017617.3	1735	cAc/cGc	28/34	1	2	FACETS	0.826	0.756	0.899	0.826	0.756	0.899	CLONAL	1	TRUE	1	0.557116545604494	2		498	630	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	61	936	0	ENST00000397752.3:c.3028G>C	p.Asp1010His	p.D1010H	ENST00000397752	NM_000245.2	1010	Gat/Cat	14/21	1	2	FACETS	0.91	0.786	1	0.91	0.786	1	CLONAL	1	FALSE	1	0.256795270033194	2		936	522	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521721	89521721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372594677	NA	P-0021877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	28	585	2	ENST00000336596.2:c.2798C>T	p.Thr933Met	p.T933M	ENST00000336596	NM_005233.5	933	aCg/aTg	16/17	1	2	FACETS	0.434	0.346	0.535	0.434	0.346	0.535	SUBCLONAL	1	FALSE	1	0.256795270033194	2		587	502	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039852	47039852	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	66	1060	0	ENST00000377604.3:c.1195del	p.Ala399LeufsTer86	p.A399Lfs*86	ENST00000377604	NM_001204468.1	399	Gct/ct	12/24	1	2	FACETS	0.556	0.481	0.637	0.556	0.481	0.637	SUBCLONAL	1	FALSE	1	0.256795270033194	2		1060	925	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541876	187541876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	82	681	0	ENST00000441802.2:c.5864C>T	p.Ser1955Phe	p.S1955F	ENST00000441802	NM_005245.3	1955	tCc/tTc	10/27	0.234376713051697	1	FACETS	0.598	0.527	0.674	0.598	0.527	0.674	SUBCLONAL	1	TRUE	0	0.318246503893731	1		681	725	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0021885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	184	1047	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.888	0.82	0.959	0.888	0.82	0.959	CLONAL	1	TRUE	1	0.444300871057516	2		1049	933	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0021885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	274	899	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.444300871057516	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.444300871057516	1		900	848	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0021885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	86	319	1	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.302372993476542	3	FACETS	0.886	0.786	0.993	0.443	0.393	0.497	CLONAL	1	TRUE	1	0.444300871057516	3		320	534	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381559	81381559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777026877	NA	P-0021885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	71	367	0	ENST00000222390.5:c.502C>T	p.Arg168Trp	p.R168W	ENST00000222390	NM_000601.4	168	Cgg/Tgg	5/18	0.444300871057516	3	FACETS	0.694	0.606	0.788	0.347	0.303	0.394	SUBCLONAL	1	TRUE	1	0.444300871057516	3		367	563	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022275	26022275	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	198	584	0	ENST00000435504.4:c.382A>C	p.Lys128Gln	p.K128Q	ENST00000435504		128	Aag/Cag	5/13	1	2	FACETS	0.981	0.909	1	0.981	0.909	1	CLONAL	1	TRUE	1	0.444300871057516	2		584	909	SUCCESS
APC	324	MSKCC	GRCh37	5	112175153	112175153	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	133	277	0	ENST00000257430.4:c.3863del	p.Gly1288AspfsTer17	p.G1288Dfs*17	ENST00000257430	NM_000038.5	1288	Gga/ga	16/16	0.302372993476542	3	FACETS	0.843	0.772	0.916	0.843	0.772	0.916	CLONAL	2	TRUE	1	0.444300871057516	3		277	434	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0021887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	154	662	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.769225386953218	2		663	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0021887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	509	736	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	NA	2	FACETS	0.771	0.745	0.797			1	INDETERMINATE	2	TRUE	NA	0.769225386953218	2		736	858	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354627	91354627	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs945181516	NA	P-0021887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	226	596	0	ENST00000355112.3:c.4067A>G	p.Lys1356Arg	p.K1356R	ENST00000355112	NM_000057.2	1356	aAg/aGg	21/22	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.769225386953218	2		596	573	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923197	39923197	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	73	667	0	ENST00000378444.4:c.3511C>G	p.Pro1171Ala	p.P1171A	ENST00000378444	NM_001123385.1	1171	Cct/Gct	8/15	NA	2	FACETS	0.307	0.268	0.348			1	INDETERMINATE	1	TRUE	NA	0.769225386953218	2		667	619	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0021889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	166	726	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.307280907116114	4	FACETS	0.878	0.808	0.952			1	CLONAL	2	TRUE	NA	0.307280907116114	4		726	804	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928072	178928098	+	inframe_deletion	In_Frame_Del	DEL	TGGATTAGAAGATTTGCTGAACCCTAT	TGGATTAGAAGATTTGCTGAACCCTAT	-	novel	NA	P-0021889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	127	571	0	ENST00000263967.3:c.1353_1379del	p.Leu452_Gly460del	p.L452_G460del	ENST00000263967	NM_006218.2	450	caTGGATTAGAAGATTTGCTGAACCCTATt/cat	8/21	0.307280907116114	5	FACETS	0.939	0.853	1	0.626	0.568	0.686	CLONAL	2	TRUE	2	0.307280907116114	5		571	643	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754320	57754320	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	135	507	0	ENST00000274289.3:c.531G>C	p.Leu177Phe	p.L177F	ENST00000274289	NM_006622.3	177	ttG/ttC	4/14	0.189980719419936	5	FACETS	0.974	0.887	1	0.649	0.591	0.71	CLONAL	2	TRUE	2	0.307280907116114	5		507	659	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034909	42034932	+	inframe_deletion	In_Frame_Del	DEL	CTGAGCCAGTTCAGGTGTGCAGCC	CTGAGCCAGTTCAGGTGTGCAGCC	-	novel	NA	P-0021889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	117	627	0	ENST00000219905.7:c.4754_4777del	p.Glu1585_Pro1592del	p.E1585_P1592del	ENST00000219905	NM_001164273.1	1584	tCTGAGCCAGTTCAGGTGTGCAGCCct/tct	15/24	0.235224027533206	4	FACETS	1	0.979	1	0.66	0.595	0.728	CLONAL	1	TRUE	2	0.307280907116114	4		627	754	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577560	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0021889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	240	735	0	ENST00000269305.4:c.721_722del	p.Ser241LeufsTer22	p.S241Lfs*22	ENST00000269305	NM_001126112.2	241	TCc/c	7/11	0.167585864277182	3	FACETS	1	0.982	1	0.754	0.706	0.803	INDETERMINATE	2	TRUE	0	0.307280907116114	3		735	797	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275810	38275810	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	78	650	2	ENST00000425967.3:c.1459A>T	p.Met487Leu	p.M487L	ENST00000425967	NM_001174067.1	487	Atg/Ttg	11/19	0.307280907116114	3	FACETS	0.856	0.752	0.968	0.428	0.376	0.484	CLONAL	1	TRUE	1	0.307280907116114	3		652	684	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578369	7578369	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0021891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	77	662	0	ENST00000269305.4:c.559+2T>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.533885043385078	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	0	0.533885043385078	2		662	138	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585382	29585383	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGAA	novel	NA	P-0021891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	77	861	0	ENST00000356175.3:c.4135_4139dup	p.Ser1380ArgfsTer7	p.S1380Rfs*7	ENST00000356175	NM_000267.3	1377	-/CAGAA	31/57	0.533885043385078	2	FACETS	1	0.976	1	0.68	0.608	0.755	CLONAL	1	TRUE	0	0.533885043385078	2		861	212	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	146	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.407437314344802	3	FACETS	0.936	0.861	1	0.936	0.861	1	CLONAL	2	TRUE	1	0.407437314344802	3		434	461	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164664	36164665	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0021893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	283	780	0	ENST00000300305.3:c.1210dup	p.His404ProfsTer196	p.H404Pfs*196	ENST00000300305		404	cac/cCac	8/8	0.407437314344802	3	FACETS	0.902	0.855	0.949	0.902	0.855	0.949	CLONAL	3	TRUE	0	0.407437314344802	3		780	618	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902742	50902742	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0021893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	29	803	1	ENST00000440232.2:c.316+1G>T		p.X106_splice	ENST00000440232	NM_002691.3	106			0.0756329054134244	3	FACETS	0.337	0.269	0.413			1	INDETERMINATE	1	TRUE	NA	0.407437314344802	3		804	509	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	68	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.98	0.852	1	0.98	0.852	1	CLONAL	1	TRUE	1	0.2	2		434	694	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	80	845	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	0.831	0.73	0.94	0.831	0.73	0.94	CLONAL	1	TRUE	1	0.2	2		845	963	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0021895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	64	509	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.997	0.863	1	0.997	0.863	1	CLONAL	1	TRUE	1	0.2	2		509	642	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005006	150005006	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	67	681	0	ENST00000253339.5:c.1219C>T	p.Gln407Ter	p.Q407*	ENST00000253339		407	Cag/Tag	3/7	1	2	FACETS	0.861	0.747	0.985	0.861	0.747	0.985	CLONAL	1	TRUE	1	0.2	2		681	778	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170952	56170953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0021895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	44	485	0	ENST00000399503.3:c.1783dup	p.Leu595ProfsTer51	p.L595Pfs*51	ENST00000399503	NM_005921.1	594	gcc/gCcc	10/20	1	2	FACETS	0.79	0.662	0.932	0.79	0.662	0.932	CLONAL	1	TRUE	1	0.2	2		485	557	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184160	56184163	+	frameshift_variant	Frame_Shift_Del	DEL	CAAT	CAAT	-	rs745497809	NA	P-0021895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	63	612	0	ENST00000399503.3:c.4367_4370del	p.Asn1456IlefsTer4	p.N1456Ifs*4	ENST00000399503	NM_005921.1	1455	tcCAAT/tc	19/20	1	2	FACETS	0.848	0.732	0.974	0.848	0.732	0.974	CLONAL	1	TRUE	1	0.2	2		612	743	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	260	967	2	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.258451202658091	4	FACETS	0.819	0.77	0.87	0.819	0.77	0.87	INDETERMINATE	2	TRUE	2	0.632501104337579	4		969	819	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578177	7578177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	674	878	0	ENST00000269305.4:c.672G>C	p.Glu224Asp	p.E224D	ENST00000269305	NM_001126112.2	224	gaG/gaC	6/11	0.632501104337579	3	FACETS	0.998	0.973	1	0.998	0.973	1	CLONAL	3	TRUE	0	0.632501104337579	3		878	937	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9787061	9787061	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	336	694	0	ENST00000377346.4:c.3092T>G	p.Val1031Gly	p.V1031G	ENST00000377346	NM_005026.3	1031	gTg/gGg	24/24	0.579024692663517	3	FACETS	0.913	0.869	0.957	0.913	0.869	0.957	CLONAL	2	TRUE	1	0.632501104337579	3		694	766	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322622	39322622	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	55	783	0	ENST00000373001.3:c.370T>C	p.Phe124Leu	p.F124L	ENST00000373001	NM_022157.3	124	Ttt/Ctt	2/7	0.579024692663517	3	FACETS	0.274	0.234	0.319	0.137	0.117	0.16	SUBCLONAL	1	TRUE	1	0.632501104337579	3		783	834	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830876	156830876	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	102	706	0	ENST00000524377.1:c.150C>A	p.Cys50Ter	p.C50*	ENST00000524377	NM_002529.3	50	tgC/tgA	1/17	0.323944471175285	3	FACETS	0.632	0.565	0.702	0.316	0.282	0.351	INDETERMINATE	1	TRUE	1	0.632501104337579	3		706	672	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982332	201982332	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	222	867	0	ENST00000359651.3:c.715del	p.Asp239IlefsTer15	p.D239Ifs*15	ENST00000359651		237	aaG/aa	6/8	0.323944471175285	3	FACETS	1	0.958	1	0.519	0.483	0.555	INDETERMINATE	1	TRUE	1	0.632501104337579	3		867	891	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154387	2154387	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	190	933	0	ENST00000434045.2:c.541C>G	p.Arg181Gly	p.R181G	ENST00000434045	NM_001127598.1	181	Cgc/Ggc	5/5	0.446073871707827	3	FACETS	0.868	0.803	0.936			1	CLONAL	1	TRUE	NA	0.632501104337579	3		933	911	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380196	25380196	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs953088090	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	90	650	1	ENST00000311936.3:c.262A>G	p.Lys88Glu	p.K88E	ENST00000311936	NM_004985.3	88	Aaa/Gaa	3/5	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.632501104337579	NA		651	808	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110783	2110783	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1567423658	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	225	869	0	ENST00000219476.3:c.1088A>G	p.Asn363Ser	p.N363S	ENST00000219476	NM_000548.3	363	aAc/aGc	11/42	0.614844205878632	2	FACETS	0.945	0.883	1	0.472	0.441	0.504	CLONAL	1	TRUE	0	0.632501104337579	2		869	753	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642720	3642720	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	194	822	0	ENST00000294008.3:c.2307G>T	p.Glu769Asp	p.E769D	ENST00000294008	NM_032444.2	769	gaG/gaT	11/15	0.614844205878632	2	FACETS	0.954	0.887	1	0.477	0.443	0.512	CLONAL	1	TRUE	0	0.632501104337579	2		822	643	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512261	38512261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	363	730	0	ENST00000254066.5:c.1172G>T	p.Gly391Val	p.G391V	ENST00000254066	NM_000964.3	391	gGg/gTg	9/9	0.629604310753227	3	FACETS	0.987	0.943	1	0.987	0.943	1	CLONAL	2	TRUE	1	0.632501104337579	3		730	765	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117895	70117895	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	137	536	0	ENST00000245479.2:c.363G>C	p.Arg121Ser	p.R121S	ENST00000245479	NM_000346.3	121	agG/agC	1/3	0.629604310753227	3	FACETS	0.99	0.904	1	0.495	0.452	0.54	CLONAL	1	TRUE	1	0.632501104337579	3		536	576	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743260	743260	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	627	858	0	ENST00000314574.4:c.880G>T	p.Gly294Ter	p.G294*	ENST00000314574	NM_005433.3	294	Gga/Tga	7/12	0.632501104337579	4	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.632501104337579	4		858	1467	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308434	30308434	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	678	766	0	ENST00000262643.3:c.448G>T	p.Asp150Tyr	p.D150Y	ENST00000262643	NM_001238.2	150	Gat/Tat	6/12	0.632501104337579	4	FACETS	0.912	0.883	0.941			1	CLONAL	3	TRUE	NA	0.632501104337579	4		766	1279	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741015	40741015	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	550	920	1	ENST00000392038.2:c.1303G>T	p.Asp435Tyr	p.D435Y	ENST00000392038	NM_001626.4	435	Gac/Tac	13/14	0.266590134991852	5	FACETS	0.985	0.949	1			1	INDETERMINATE	3	TRUE	NA	0.632501104337579	5		921	1147	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966456	25966456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866685548	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	268	819	1	ENST00000435504.4:c.2750C>T	p.Ser917Leu	p.S917L	ENST00000435504		917	tCg/tTg	13/13	0.579024692663517	3	FACETS	0.954	0.894	1	0.477	0.447	0.508	CLONAL	1	TRUE	1	0.632501104337579	3		820	1169	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259296	89259296	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	401	574	0	ENST00000336596.2:c.440del	p.Ala147GlufsTer16	p.A147Efs*16	ENST00000336596	NM_005233.5	147	gCa/ga	3/17	0.632501104337579	4	FACETS	0.952	0.914	0.989	0.952	0.914	0.989	CLONAL	3	TRUE	1	0.632501104337579	4		574	725	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278129	142278129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	189	740	1	ENST00000350721.4:c.1696G>A	p.Val566Met	p.V566M	ENST00000350721	NM_001184.3	566	Gtg/Atg	7/47	0.632501104337579	4	FACETS	0.873	0.805	0.943	0.291	0.268	0.315	CLONAL	1	TRUE	1	0.632501104337579	4		741	1118	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982091	38982091	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs201132232	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	574	637	0	ENST00000357387.3:c.631A>G	p.Ile211Val	p.I211V	ENST00000357387	NM_152756.3	211	Atc/Gtc	8/38	0.632501104337579	6	FACETS	0.935	0.903	0.967	0.935	0.903	0.967	CLONAL	4	TRUE	2	0.632501104337579	6		637	1099	SUCCESS
APC	324	MSKCC	GRCh37	5	112179752	112179752	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	138	447	0	ENST00000257430.4:c.8461G>C	p.Asp2821His	p.D2821H	ENST00000257430	NM_000038.5	2821	Gac/Cac	16/16	0.632501104337579	2	FACETS	0.938	0.86	1	0.469	0.43	0.51	CLONAL	1	TRUE	0	0.632501104337579	2		447	465	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394894	394894	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	171	618	0	ENST00000380956.4:c.290T>A	p.Leu97Gln	p.L97Q	ENST00000380956	NM_001195286.1	97	cTg/cAg	3/9	0.580592184210535	4	FACETS	0.914	0.84	0.99	0.457	0.42	0.495	CLONAL	1	TRUE	2	0.632501104337579	4		618	966	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190522	32190522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770403231	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	223	862	0	ENST00000375023.3:c.217C>T	p.Leu73Phe	p.L73F	ENST00000375023	NM_004557.3	73	Ctc/Ttc	3/30	0.580592184210535	4	FACETS	0.953	0.886	1	0.476	0.443	0.512	CLONAL	1	TRUE	2	0.632501104337579	4		862	1208	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652007	36652007	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	417	739	0	ENST00000244741.5:c.129G>T	p.Gln43His	p.Q43H	ENST00000244741	NM_000389.4	43	caG/caT	2/3	0.580592184210535	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.632501104337579	4		739	1036	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984065	2984065	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	332	613	0	ENST00000396946.4:c.465G>T	p.Arg155Ser	p.R155S	ENST00000396946	NM_032415.4	155	agG/agT	5/25	0.629604310753227	3	FACETS	0.934	0.889	0.979	0.934	0.889	0.979	CLONAL	2	TRUE	1	0.632501104337579	3		613	740	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971216	13971216	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs754217454	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	168	569	0	ENST00000405192.2:c.713A>G	p.His238Arg	p.H238R	ENST00000405192	NM_001163147.1	238	cAc/cGc	8/12	0.629604310753227	3	FACETS	0.907	0.835	0.982	0.453	0.417	0.491	CLONAL	1	TRUE	1	0.632501104337579	3		569	771	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273024	55273024	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	224	810	2	ENST00000275493.2:c.3347A>T	p.Asn1116Ile	p.N1116I	ENST00000275493	NM_005228.3	1116	aAc/aTc	28/28	0.629604310753227	3	FACETS	0.971	0.905	1	0.486	0.452	0.52	CLONAL	1	TRUE	1	0.632501104337579	3		812	960	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358979	81358979	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	271	736	2	ENST00000222390.5:c.982C>A	p.Arg328Ser	p.R328S	ENST00000222390	NM_000601.4	328	Cgt/Agt	8/18	0.629604310753227	3	FACETS	0.803	0.758	0.849	0.803	0.758	0.849	CLONAL	2	TRUE	1	0.632501104337579	3		738	702	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509625	106509625	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	189	640	0	ENST00000359195.3:c.1619G>T	p.Gly540Val	p.G540V	ENST00000359195	NM_002649.2	540	gGg/gTg	2/11	0.629604310753227	3	FACETS	0.988	0.915	1	0.494	0.457	0.532	CLONAL	1	TRUE	1	0.632501104337579	3		640	796	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863040	56863040	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	171	735	0	ENST00000519728.1:c.307A>T	p.Lys103Ter	p.K103*	ENST00000519728	NM_002350.3	103	Aag/Tag	5/13	0.629604310753227	3	FACETS	0.897	0.827	0.971	0.449	0.413	0.486	CLONAL	1	TRUE	1	0.632501104337579	3		735	793	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080555	5080555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	68	510	0	ENST00000381652.3:c.2306G>A	p.Arg769Lys	p.R769K	ENST00000381652	NM_004972.3	769	aGg/aAg	18/25	NA	2	FACETS	0.627	0.549	0.71			1	INDETERMINATE	1	TRUE	NA	0.632501104337579	2		510	343	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317318	87317318	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	177	787	0	ENST00000277120.3:c.343A>T	p.Ser115Cys	p.S115C	ENST00000277120		115	Agc/Tgc	4/19	1	2	FACETS	0.862	0.798	0.929	0.862	0.798	0.929	CLONAL	1	TRUE	1	0.632501104337579	2		787	649	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916521	39916521	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	474	873	1	ENST00000378444.4:c.4482C>A	p.Asp1494Glu	p.D1494E	ENST00000378444	NM_001123385.1	1494	gaC/gaA	11/15	0.372394994537734	3	FACETS	0.99	0.951	1			1	INDETERMINATE	2	TRUE	NA	0.632501104337579	3		874	996	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934394	39934394	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	372	726	0	ENST00000378444.4:c.205G>T	p.Ala69Ser	p.A69S	ENST00000378444	NM_001123385.1	69	Gca/Tca	4/15	0.372394994537734	3	FACETS	0.965	0.922	1			1	INDETERMINATE	2	TRUE	NA	0.632501104337579	3		726	802	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929072	44929072	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	102	624	0	ENST00000377967.4:c.2172A>G	p.Ile724Met	p.I724M	ENST00000377967	NM_021140.2	724	atA/atG	17/29	0.372394994537734	3	FACETS	0.661	0.592	0.734			1	INDETERMINATE	1	TRUE	NA	0.632501104337579	3		624	642	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650771	48650771	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	242	829	0	ENST00000376670.3:c.640C>A	p.Leu214Met	p.L214M	ENST00000376670	NM_002049.3	214	Ctg/Atg	4/6	0.372394994537734	3	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.632501104337579	3		829	843	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409860	63409860	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	121	531	0	ENST00000330258.3:c.3307G>T	p.Gly1103Trp	p.G1103W	ENST00000330258	NM_152424.3	1103	Ggg/Tgg	2/2	0.372394994537734	3	FACETS	0.859	0.779	0.944			1	INDETERMINATE	1	TRUE	NA	0.632501104337579	3		531	586	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0021897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	113	845	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.968	0.871	1	0.968	0.871	1	CLONAL	1	FALSE	1	0.275309113307525	2		845	848	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	104	379	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	FALSE	1	0.275309113307525	2		379	709	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0021897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	76	541	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.908	0.797	1	0.908	0.797	1	CLONAL	1	FALSE	1	0.275309113307525	2		541	608	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0021897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	86	667	1	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	1	2	FACETS	0.894	0.791	1	0.894	0.791	1	CLONAL	1	FALSE	1	0.275309113307525	2		668	699	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	160	918	1	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.275309113307525	2		919	896	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0021897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	84	728	5	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	1	2	FACETS	0.784	0.692	0.883	0.784	0.692	0.883	SUBCLONAL	1	FALSE	1	0.275309113307525	2		733	778	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0021897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	33	231	2	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	0.733	0.598	0.884	0.733	0.598	0.884	SUBCLONAL	1	FALSE	1	0.275309113307525	2		233	327	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0021897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	143	743	2	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	FALSE	1	0.275309113307525	2		745	977	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007332	143007332	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	71	772	0	ENST00000262992.4:c.2452del	p.Arg818GlufsTer4	p.R818Efs*4	ENST00000262992	NM_001101669.1	818	Aga/ga	22/24	1	2	FACETS	0.815	0.711	0.927	0.815	0.711	0.927	CLONAL	1	FALSE	1	0.275309113307525	2		772	633	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101751	71101751	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	68	319	1	ENST00000318789.4:c.447del	p.Lys149AsnfsTer57	p.K149Nfs*57	ENST00000318789	NM_032682.5	149	aaA/aa	9/21	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	FALSE	1	0.275309113307525	2		320	470	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720650	89720650	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1257124719	NA	P-0021897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	39	299	0	ENST00000371953.3:c.802-1G>A		p.X268_splice	ENST00000371953	NM_000314.4	268			1	2	FACETS	0.97	0.808	1	0.97	0.808	1	CLONAL	1	FALSE	1	0.275309113307525	2		299	292	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163554	32163554	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	86	703	3	ENST00000375023.3:c.5672del	p.Gly1891AlafsTer13	p.G1891Afs*13	ENST00000375023	NM_004557.3	1891	gGc/gc	30/30	1	2	FACETS	0.992	0.878	1	0.992	0.878	1	CLONAL	1	FALSE	1	0.275309113307525	2		706	630	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467573	66467573	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	78	585	0	ENST00000273854.3:c.696del	p.Lys232AsnfsTer36	p.K232Nfs*36	ENST00000273854	NM_004439.5	232	aaA/aa	3/18	1	2	FACETS	0.88	0.773	0.994	0.88	0.773	0.994	CLONAL	1	FALSE	1	0.275309113307525	2		585	644	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0021897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	146	844	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.275309113307525	2		846	981	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711875	89711875	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	rs587782603	NA	P-0021897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	49	578	0	ENST00000371953.3:c.493G>T	p.Gly165Ter	p.G165*	ENST00000371953	NM_000314.4	165	Gga/Tga	6/9	1	2	FACETS	0.749	0.635	0.875	0.749	0.635	0.875	SUBCLONAL	1	FALSE	1	0.275309113307525	2		578	475	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944698	71944698	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0021897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	149	976	1	ENST00000298229.2:c.2123-1G>T		p.X708_splice	ENST00000298229	NM_001567.3	708			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.275309113307525	2		977	966	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425838	49425840	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0021897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	129	732	0	ENST00000301067.7:c.12648_12650del	p.Gln4221del	p.Q4221del	ENST00000301067	NM_003482.3	4216	ccTCAg/ccg	39/54	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.275309113307525	2		732	864	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128302	30128302	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749988410	NA	P-0021897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	122	938	0	ENST00000263025.4:c.930G>A	p.Met310Ile	p.M310I	ENST00000263025	NM_002746.2	310	atG/atA	7/9	1	2	FACETS	0.895	0.808	0.988	0.895	0.808	0.988	CLONAL	1	FALSE	1	0.275309113307525	2		938	990	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828915	72828916	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0021897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	102	832	0	ENST00000268489.5:c.7665dup	p.Ala2556ArgfsTer23	p.A2556Rfs*23	ENST00000268489	NM_006885.3	2555	-/C	9/10	1	2	FACETS	0.837	0.748	0.932	0.837	0.748	0.932	CLONAL	1	FALSE	1	0.275309113307525	2		832	885	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376209	15376209	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	118	704	0	ENST00000263377.2:c.805C>T	p.Gln269Ter	p.Q269*	ENST00000263377	NM_058243.2	269	Cag/Tag	5/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.275309113307525	2		704	792	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103743	47103743	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	106	853	0	ENST00000409792.3:c.6203A>T	p.Gln2068Leu	p.Q2068L	ENST00000409792	NM_014159.6	2068	cAa/cTa	14/21	1	2	FACETS	0.873	0.782	0.97	0.873	0.782	0.97	CLONAL	1	FALSE	1	0.275309113307525	2		853	882	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280196	142280196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	95	818	0	ENST00000350721.4:c.1238G>A	p.Cys413Tyr	p.C413Y	ENST00000350721	NM_001184.3	413	tGc/tAc	5/47	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	FALSE	1	0.275309113307525	2		818	624	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589286	67589286	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	39	484	0	ENST00000274335.5:c.1276del	p.Tyr426IlefsTer20	p.Y426Ifs*20	ENST00000274335		425	cTt/ct	9/15	1	2	FACETS	0.752	0.624	0.893	0.752	0.624	0.893	SUBCLONAL	1	FALSE	1	0.275309113307525	2		484	377	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132796	152132796	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	148	766	0	ENST00000262189.6:c.76G>C	p.Ala26Pro	p.A26P	ENST00000262189	NM_170606.2	26	Gcc/Ccc	1/59	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.275309113307525	2		766	975	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0021921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	506	772	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.455782048187633	3	FACETS	0.942	0.912	0.972	0.942	0.912	0.972	CLONAL	3	TRUE	0	0.585167501544497	3		772	791	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0021921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	243	764	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.585167501544497	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.585167501544497	1		764	416	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729743	162729743	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	119	648	0	ENST00000367921.3:c.829C>T	p.Arg277Cys	p.R277C	ENST00000367921	NM_006182.2	277	Cgc/Tgc	8/18	0.354712323363943	1	FACETS	0.488	0.441	0.536	0.488	0.441	0.536	SUBCLONAL	1	TRUE	0	0.585167501544497	1		648	590	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779589	3779589	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	398	1165	0	ENST00000262367.5:c.5459A>G	p.Lys1820Arg	p.K1820R	ENST00000262367	NM_004380.2	1820	aAg/aGg	31/31	0.103734119343737	5	FACETS	1	0.991	1	0.771	0.735	0.808	INDETERMINATE	2	TRUE	2	0.585167501544497	5		1165	1104	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663299	227663301	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs753296153	NA	P-0021922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	195	650	0	ENST00000305123.5:c.154_156del	p.Lys52del	p.K52del	ENST00000305123	NM_005544.2	52	AAG/-	1/2	1	2	FACETS	0.821	0.766	0.877	0.821	0.766	0.877	CLONAL	1	TRUE	1	0.891527698318583	2		650	533	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294277	1294277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	36	347	0	ENST00000310581.5:c.724G>A	p.Ala242Thr	p.A242T	ENST00000310581	NM_198253.2	242	Gct/Act	2/16	1	2	FACETS	0.174	0.142	0.209	0.174	0.142	0.209	SUBCLONAL	1	TRUE	1	0.891527698318583	2		347	465	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261286	115261286	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	369	695	0	ENST00000438362.2:c.2435G>C	p.Ser812Thr	p.S812T	ENST00000438362	NM_001242891.1	812	aGt/aCt	19/20	1	2	FACETS	0.963	0.918	1	0.963	0.918	1	CLONAL	1	TRUE	1	0.891527698318583	2		695	860	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	70	669	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.947	0.834	1	0.947	0.834	1	CLONAL	1	TRUE	1	0.513452285025152	2		669	288	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0021925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	528	851	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	0.31223594148141	3	FACETS	0.958	0.919	0.997	0.958	0.919	0.997	CLONAL	2	TRUE	1	0.513452285025152	3		851	1349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	444	1001	2	ENST00000269305.4:c.472C>G	p.Arg158Gly	p.R158G	ENST00000269305	NM_001126112.2	158	Cgc/Ggc	5/11	0.513452285025152	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.513452285025152	1		1003	1041	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148710	20148729	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTTTCATTGATTTTAGCTAA	GTTTCATTGATTTTAGCTAA	TTGAG	novel	NA	P-0021925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	99	389	1	ENST00000379607.5:c.338-4_353delinsCTCAA		p.X113_splice	ENST00000379607	NM_001412.3	113		6/7	1	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.513452285025152	1		390	220	SUCCESS
APC	324	MSKCC	GRCh37	5	112173656	112173656	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123117	NA	P-0021926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	213	465	0	ENST00000257430.4:c.2365C>T	p.Gln789Ter	p.Q789*	ENST00000257430	NM_000038.5	789	Cag/Tag	16/16	0.272588668517366	5	FACETS	0.846	0.793	0.9	0.846	0.793	0.9	INDETERMINATE	3	TRUE	2	0.584370781950733	5		465	539	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0021926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	434	835	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.532769670561495	4	FACETS	0.924	0.887	0.961	0.924	0.887	0.961	CLONAL	3	TRUE	1	0.584370781950733	4		835	849	SUCCESS
APC	324	MSKCC	GRCh37	5	112175720	112175720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	145	486	0	ENST00000257430.4:c.4429C>T	p.Gln1477Ter	p.Q1477*	ENST00000257430	NM_000038.5	1477	Cag/Tag	16/16	0.272588668517366	5	FACETS	0.948	0.871	1	0.632	0.581	0.685	INDETERMINATE	2	TRUE	2	0.584370781950733	5		486	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs11575997	NA	P-0021926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	558	754	0	ENST00000269305.4:c.993+1G>T		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.540395995002859	3	FACETS	0.947	0.918	0.975	0.947	0.918	0.975	CLONAL	3	TRUE	0	0.584370781950733	3		754	869	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527775	103527775	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	176	548	0	ENST00000355739.4:c.3083A>C	p.Glu1028Ala	p.E1028A	ENST00000355739	NM_000123.3	1028	gAa/gCa	15/15	0.584370781950733	8	FACETS	1	0.987	1	0.232	0.213	0.252	CLONAL	1	TRUE	2	0.584370781950733	8		548	1189	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660730	227660730	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	242	964	1	ENST00000305123.5:c.2725T>A	p.Leu909Met	p.L909M	ENST00000305123	NM_005544.2	909	Ttg/Atg	1/2	0.584370781950733	3	FACETS	1	0.976	1	0.363	0.339	0.388	CLONAL	1	TRUE	0	0.584370781950733	3		965	983	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727171	40727171	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1414	367	728	0	ENST00000373198.4:c.3793T>C	p.Phe1265Leu	p.F1265L	ENST00000373198	NM_133170.3	1265	Ttc/Ctc	28/32	0.584370781950733	7	FACETS	0.868	0.82	0.916	0.434	0.41	0.458	CLONAL	2	TRUE	3	0.584370781950733	7		728	1781	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129409	152129409	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	254	496	0	ENST00000206249.3:c.362T>C	p.Leu121Pro	p.L121P	ENST00000206249	NM_000125.3	121	cTg/cCg	1/8	0.272588668517366	5	FACETS	1	0.984	1	0.752	0.707	0.798	INDETERMINATE	2	TRUE	2	0.584370781950733	5		496	723	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0021929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	73	916	3	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.107343520310945	3	FACETS	1	0.956	1	0.607	0.531	0.689	INDETERMINATE	1	TRUE	1	0.21	3		919	633	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0021929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	25	573	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.107343520310945	3	FACETS	0.453	0.356	0.565	0.226	0.178	0.283	INDETERMINATE	1	TRUE	1	0.21	3		573	581	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0021929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	45	666	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.847	0.712	0.997	0.847	0.712	0.997	CLONAL	1	TRUE	1	0.21	2		667	506	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936198	71936198	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	29	337	1	ENST00000298229.2:c.170C>A	p.Ala57Glu	p.A57E	ENST00000298229	NM_001567.3	57	gCg/gAg	1/28	1	2	FACETS	0.9	0.724	1	0.9	0.724	1	CLONAL	1	TRUE	1	0.21	2		338	307	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724630	112724631	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGAT	novel	NA	P-0021936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	131	660	0	ENST00000369452.4:c.516_519dup	p.Leu174AspfsTer3	p.L174Dfs*3	ENST00000369452	NM_007373.3	172	cgg/cGGATgg	2/9	0.498259967918648	1	FACETS	0.925	0.846	1	0.925	0.846	1	CLONAL	1	TRUE	0	0.498259967918648	1		660	427	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15374284	15374284	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	49	721	0	ENST00000263377.2:c.1288T>C	p.Tyr430His	p.Y430H	ENST00000263377	NM_058243.2	430	Tat/Cat	7/20	1	2	FACETS	0.309	0.261	0.362	0.309	0.261	0.362	SUBCLONAL	1	TRUE	1	0.498259967918648	2		721	637	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0021938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	160	772	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.972	0.891	1	0.972	0.891	1	CLONAL	1	TRUE	1	0.375905572289323	2		772	876	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435202	110435202	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1411255606	NA	P-0021941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	158	726	0	ENST00000375856.3:c.3199G>A	p.Gly1067Arg	p.G1067R	ENST00000375856	NM_003749.2	1067	Ggg/Agg	1/2	0.190557759888976	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	FALSE	2	0.20969178138329	4		726	778	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936983	48936983	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690863	NA	P-0021941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	103	583	1	ENST00000267163.4:c.751C>T	p.Arg251Ter	p.R251*	ENST00000267163	NM_000321.2	251	Cga/Tga	8/27	0.20969178138329	3	FACETS	1	0.922	1	1	0.922	1	CLONAL	2	FALSE	1	0.20969178138329	3		584	526	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610364	10610364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	221	1002	3	ENST00000171111.5:c.346C>T	p.Arg116Trp	p.R116W	ENST00000171111	NM_203500.1	116	Cgg/Tgg	2/6	0.20969178138329	2	FACETS	0.866	0.808	0.926	1	0.989	1	CLONAL	3	FALSE	0	0.20969178138329	2		1005	811	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670351	134670351	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	96	481	0	ENST00000398015.3:c.262G>A	p.Glu88Lys	p.E88K	ENST00000398015	NM_004441.4	88	Gag/Aag	3/16	0.20969178138329	6	FACETS	1	0.913	1			1	CLONAL	2	FALSE	NA	0.20969178138329	6		481	633	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447333	187447333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1369	81	722	1	ENST00000232014.4:c.860C>T	p.Ser287Leu	p.S287L	ENST00000232014	NM_001130845.1	287	tCa/tTa	5/10	0.20969178138329	14	FACETS	1	0.957	1	0.109	0.096	0.124	CLONAL	1	FALSE	3	0.20969178138329	14		723	1450	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38949832	38949832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746736711	NA	P-0021941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	38	408	0	ENST00000357387.3:c.4118C>T	p.Ser1373Phe	p.S1373F	ENST00000357387	NM_152756.3	1373	tCc/tTc	31/38	0.190557759888976	4	FACETS	1	0.832	1	0.503	0.416	0.6	CLONAL	1	FALSE	2	0.20969178138329	4		408	436	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499112	149499112	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs372042979	NA	P-0021941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	102	729	0	ENST00000261799.4:c.2716G>C	p.Glu906Gln	p.E906Q	ENST00000261799	NM_002609.3	906	Gag/Cag	20/23	0.190557759888976	4	FACETS	1	0.978	1	0.698	0.624	0.777	CLONAL	1	FALSE	2	0.20969178138329	4		729	843	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	191	699	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.207777658729375	4	FACETS	0.86	0.802	0.919	0.86	0.802	0.919	INDETERMINATE	2	FALSE	2	0.779156928571187	4		699	507	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0021943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	79	573	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.154124048138233	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.779156928571187	0		573	179	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948712	71948712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374001069	NA	P-0021943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	184	863	2	ENST00000298229.2:c.3424C>T	p.Arg1142Cys	p.R1142C	ENST00000298229	NM_001567.3	1142	Cgc/Tgc	26/28	0.604362990831208	6	FACETS	0.811	0.75	0.874	0.324	0.3	0.35	CLONAL	2	FALSE	1	0.779156928571187	6		865	745	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115717	8115718	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTATGAAGGG	novel	NA	P-0021943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	74	426	0	ENST00000346208.3:c.1071_1072insGGCTATGAAG	p.Lys358GlyfsTer16	p.K358Gfs*16	ENST00000346208		355	act/aCTATGAAGGGct	6/6	1	2	FACETS	0.648	0.573	0.727	0.648	0.573	0.727	SUBCLONAL	1	FALSE	1	0.779156928571187	2		426	293	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644948	67644963	+	frameshift_variant	Frame_Shift_Del	DEL	TCAGATGAAGACTGAA	TCAGATGAAGACTGAA	-	novel	NA	P-0021943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	139	651	0	ENST00000264010.4:c.213_228del	p.Gln72Ter	p.Q72*	ENST00000264010	NM_006565.3	71	ctTCAGATGAAGACTGAA/ct	3/12	0.779156928571187	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	0	0.779156928571187	1		651	197	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266567	198266567	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	91	592	0	ENST00000335508.6:c.2269A>G	p.Met757Val	p.M757V	ENST00000335508	NM_012433.2	757	Atg/Gtg	16/25	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.779156928571187	2		592	214	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0021944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	665	1034	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.455438766181387	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	4	TRUE	0	0.455438766181387	4		1037	1013	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659245	86659245	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554048066	NA	P-0021944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	139	549	0	ENST00000274376.6:c.1534C>T	p.Arg512Ter	p.R512*	ENST00000274376	NM_002890.2	512	Cga/Tga	11/25	0.45356795215374	2	FACETS	0.942	0.871	1	0.942	0.871	1	CLONAL	2	TRUE	0	0.455438766181387	2		549	324	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149710	202149710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	261	829	1	ENST00000358485.4:c.1151G>A	p.Gly384Asp	p.G384D	ENST00000358485	NM_001080125.1	384	gGc/gAc	8/9	0.240491391315139	5	FACETS	0.971	0.911	1	0.648	0.607	0.689	INDETERMINATE	2	TRUE	2	0.455438766181387	5		830	993	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913783	32913783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	165	655	0	ENST00000380152.3:c.5291C>T	p.Ser1764Leu	p.S1764L	ENST00000380152		1764	tCa/tTa	11/27	0.174647553352473	3	FACETS	0.818	0.756	0.882	0.545	0.504	0.588	INDETERMINATE	2	TRUE	0	0.455438766181387	3		655	544	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546065	29546065	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1135402815	NA	P-0021944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	281	766	0	ENST00000356175.3:c.1570G>T	p.Glu524Ter	p.E524*	ENST00000356175	NM_000267.3	524	Gaa/Taa	14/57	0.455438766181387	2	FACETS	0.997	0.945	1	0.997	0.945	1	CLONAL	2	TRUE	0	0.455438766181387	2		766	619	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165953	118165953	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	115	507	0	ENST00000369448.3:c.463A>G	p.Ile155Val	p.I155V	ENST00000369448	NM_017709.3	155	Atc/Gtc	2/2	0.455438766181387	3	FACETS	1	0.976	1	0.626	0.567	0.688	CLONAL	1	TRUE	1	0.455438766181387	3		507	495	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436662	49436662	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0021944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	139	667	0	ENST00000301067.7:c.5645-1G>T		p.X1882_splice	ENST00000301067	NM_003482.3	1882			0.455438766181387	3	FACETS	1	0.964	1	0.554	0.506	0.605	CLONAL	1	TRUE	1	0.455438766181387	3		667	676	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241043	133241043	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	120	744	0	ENST00000320574.5:c.2474G>C	p.Arg825Pro	p.R825P	ENST00000320574	NM_006231.2	825	cGc/cCc	22/49	0.455438766181387	3	FACETS	0.96	0.868	1	0.48	0.434	0.528	CLONAL	1	TRUE	1	0.455438766181387	3		744	674	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355957	73355957	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1301502111	NA	P-0021944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	168	1013	0	ENST00000377767.4:c.14A>G	p.Lys5Arg	p.K5R	ENST00000377767	NM_014953.3	5	aAg/aGg	1/21	0.174647553352473	3	FACETS	0.98	0.901	1	0.327	0.3	0.355	INDETERMINATE	1	TRUE	0	0.455438766181387	3		1013	924	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483955	88483955	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs547749746	NA	P-0021944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	293	851	0	ENST00000360948.2:c.1615G>A	p.Val539Met	p.V539M	ENST00000360948	NM_001012338.2	539	Gtg/Atg	14/19	0.240491391315139	5	FACETS	1	0.985	1	0.748	0.705	0.792	INDETERMINATE	2	TRUE	2	0.455438766181387	5		851	965	SUCCESS
BLM	641	MSKCC	GRCh37	15	91337439	91337439	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs369629509	NA	P-0021944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	178	656	0	ENST00000355112.3:c.3062A>G	p.Asn1021Ser	p.N1021S	ENST00000355112	NM_000057.2	1021	aAt/aGt	16/22	0.240491391315139	5	FACETS	1	0.969	1	0.722	0.669	0.777	INDETERMINATE	2	TRUE	2	0.455438766181387	5		656	607	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276627	15276627	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	176	1023	2	ENST00000263388.2:c.5638G>T	p.Val1880Phe	p.V1880F	ENST00000263388	NM_000435.2	1880	Gtc/Ttc	30/33	1	2	FACETS	0.981	0.905	1	0.981	0.905	1	CLONAL	1	TRUE	1	0.455438766181387	2		1025	788	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324736	31324736	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs151341086	NA	P-0021944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	34	140	0	ENST00000412585.2:c.74-2A>G		p.X25_splice	ENST00000412585	NM_005514.6	25			0.455438766181387	2	FACETS	0.829	0.7	0.964	0.829	0.7	0.964	CLONAL	2	TRUE	0	0.455438766181387	2		140	90	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651991	36651992	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0021944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	358	922	0	ENST00000244741.5:c.115dup	p.Ala39GlyfsTer9	p.A39Gfs*9	ENST00000244741	NM_000389.4	38	atg/atGg	2/3	0.455438766181387	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.455438766181387	2		922	752	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111995762	111995762	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	228	650	0	ENST00000368678.4:c.1336G>T	p.Val446Leu	p.V446L	ENST00000368678		446	Gtg/Ttg	12/13	0.449918452660639	2	FACETS	0.954	0.897	1	0.954	0.897	1	CLONAL	2	TRUE	0	0.455438766181387	2		650	525	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729597	41729597	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	217	715	1	ENST00000242208.4:c.932del	p.Gly311AlafsTer48	p.G311Afs*48	ENST00000242208	NM_002192.2	311	gGc/gc	3/3	0.455438766181387	3	FACETS	0.894	0.836	0.954	0.894	0.836	0.954	CLONAL	2	TRUE	1	0.455438766181387	3		716	654	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968158	68968159	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0021944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	303	826	4	ENST00000288368.4:c.1187_1188delinsAA	p.Ile396Lys	p.I396K	ENST00000288368	NM_024870.2	396	aTC/aAA	10/40	0.413731188106845	5	FACETS	1	0.989	1	0.795	0.751	0.84	CLONAL	2	TRUE	2	0.455438766181387	5		830	939	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519886	NA	P-0021945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	112	424	0	ENST00000349496.5:c.97T>C	p.Ser33Pro	p.S33P	ENST00000349496	NM_001904.3	33	Tct/Cct	3/15	0.25863237937111	2	FACETS	0.684	0.619	0.752	0.342	0.309	0.376	INDETERMINATE	1	TRUE	0	0.715045602800698	2		424	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574030	7574030	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	362	793	0	ENST00000269305.4:c.997del	p.Arg333ValfsTer12	p.R333Vfs*12	ENST00000269305	NM_001126112.2	333	Cgt/gt	10/11	0.715045602800698	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.715045602800698	1		793	559	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844172	68844172	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1555515445	NA	P-0021945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	628	847	1	ENST00000261769.5:c.760G>T	p.Asp254Tyr	p.D254Y	ENST00000261769	NM_004360.3	254	Gat/Tat	6/16	0.715045602800698	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.715045602800698	2		848	857	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984006	2984006	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	430	733	0	ENST00000396946.4:c.524C>G	p.Thr175Ser	p.T175S	ENST00000396946	NM_032415.4	175	aCc/aGc	5/25	0.417864246009215	4	FACETS	0.79	0.753	0.827	0.79	0.753	0.827	INDETERMINATE	2	TRUE	2	0.715045602800698	4		733	1306	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	32	663	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		663	543	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0021947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	390	857	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.988	0.943	1	0.988	0.943	1	CLONAL	1	TRUE	1	0.813579320867229	2		859	970	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0021947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	142	725	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.758010863546552	1	FACETS	0.338	0.309	0.368	0.338	0.309	0.368	SUBCLONAL	1	TRUE	0	0.813579320867229	1		725	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577115	7577115	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519983	NA	P-0021947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	446	872	4	ENST00000269305.4:c.823T>C	p.Cys275Arg	p.C275R	ENST00000269305	NM_001126112.2	275	Tgt/Cgt	8/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.813579320867229	2		876	1096	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916948	178916950	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0021947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	354	493	0	ENST00000263967.3:c.337_339del	p.Leu113del	p.L113del	ENST00000263967	NM_006218.2	112	aTCCtc/atc	2/21	0.737643336651422	3	FACETS	0.926	0.886	0.966	0.926	0.886	0.966	CLONAL	2	TRUE	1	0.813579320867229	3		493	661	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804231	43804231	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	99	533	0	ENST00000372470.3:c.231C>A	p.Cys77Ter	p.C77*	ENST00000372470	NM_005373.2	77	tgC/tgA	3/12	NA	2	FACETS	0.41	0.366	0.456			1	INDETERMINATE	1	TRUE	NA	0.813579320867229	2		533	594	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042385	42042386	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGAAAGAGGC	novel	NA	P-0021947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	392	673	0	ENST00000219905.7:c.6584_6593dup	p.Asp2198GlufsTer9	p.D2198Efs*9	ENST00000219905	NM_001164273.1	2194	aag/aAGAAAGAGGCag	17/24	NA	2	FACETS	0.781	0.752	0.809			1	INDETERMINATE	2	TRUE	NA	0.813579320867229	2		673	617	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480505	57480506	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGAGTACCAGCTGATTGACTGTGC	novel	NA	P-0021947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	74	434	0	ENST00000371085.3:c.502_525dup	p.Glu168_Ala175dup	p.E168_A175dup	ENST00000371085	NM_000516.4	168	aac/aaCGAGTACCAGCTGATTGACTGTGCc	6/13	0.47280164435252	1	FACETS	0.176	0.154	0.2	0.176	0.154	0.2	INDETERMINATE	1	TRUE	0	0.813579320867229	1		434	612	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132399	11132399	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0021965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	73	937	0	ENST00000358026.2:c.2617-2A>C		p.X873_splice	ENST00000358026	NM_001128849.1	873			0.215419247119354	2	FACETS	0.83	0.731	0.935	0.83	0.731	0.935	CLONAL	2	TRUE	0	0.25270134533387	2		937	348	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913315	NA	P-0021965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	98	841	0	ENST00000326873.7:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000326873	NM_000455.4	194	Gac/Tac	4/10	0.215419247119354	2	FACETS	0.972	0.873	1	0.972	0.873	1	CLONAL	2	TRUE	0	0.25270134533387	2		841	399	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782144	NA	P-0021965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	68	1114	0	ENST00000269305.4:c.473G>C	p.Arg158Pro	p.R158P	ENST00000269305	NM_001126112.2	158	cGc/cCc	5/11	0.203107856289035	2	FACETS	1	0.963	1	0.647	0.565	0.735	CLONAL	1	TRUE	0	0.25270134533387	2		1114	416	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974799	21974799	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	31	145	0	ENST00000304494.5:c.28G>T	p.Glu10Ter	p.E10*	ENST00000304494	NM_000077.4	10	Gag/Tag	1/3	0.215419247119354	2	FACETS	0.985	0.824	1	1	0.951	1	CLONAL	3	TRUE	0	0.25270134533387	2		145	83	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276619	115276619	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	28	908	0	ENST00000438362.2:c.840G>T	p.Lys280Asn	p.K280N	ENST00000438362	NM_001242891.1	280	aaG/aaT	8/20	0.152769615462351	4	FACETS	1	0.806	1	0.503	0.403	0.616	CLONAL	1	TRUE	2	0.25270134533387	4		908	276	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699312	117699312	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	65	845	0	ENST00000369458.3:c.329T>G	p.Val110Gly	p.V110G	ENST00000369458	NM_024626.3	110	gTt/gGt	3/6	0.152769615462351	4	FACETS	1	0.97	1	0.727	0.632	0.83	CLONAL	1	TRUE	2	0.25270134533387	4		845	443	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243859019	243859019	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0021965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	35	534	1	ENST00000263826.5:c.47-1G>T		p.X16_splice	ENST00000263826	NM_005465.4	16			0.152769615462351	4	FACETS	1	0.918	1	1	0.918	1	CLONAL	2	TRUE	2	0.25270134533387	4		535	147	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420218	49420218	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	68	995	0	ENST00000301067.7:c.15531G>T	p.Met5177Ile	p.M5177I	ENST00000301067	NM_003482.3	5177	atG/atT	48/54	0.183902060758297	3	FACETS	1	0.965	1	0.663	0.579	0.754	CLONAL	1	TRUE	1	0.25270134533387	3		995	457	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434078	49434078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767564144	NA	P-0021965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	52	803	0	ENST00000301067.7:c.7475G>A	p.Gly2492Glu	p.G2492E	ENST00000301067	NM_003482.3	2492	gGg/gAg	31/54	0.183902060758297	3	FACETS	1	0.959	1	0.684	0.585	0.791	CLONAL	1	TRUE	1	0.25270134533387	3		803	339	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865568	57865568	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	44	1031	0	ENST00000228682.2:c.3045G>T	p.Glu1015Asp	p.E1015D	ENST00000228682	NM_005269.2	1015	gaG/gaT	12/12	0.183902060758297	3	FACETS	0.932	0.782	1	0.466	0.391	0.548	CLONAL	1	TRUE	1	0.25270134533387	3		1031	421	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112424	115112424	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760237826	NA	P-0021965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	46	797	1	ENST00000257566.3:c.1316C>T	p.Pro439Leu	p.P439L	ENST00000257566	NM_016569.3	439	cCc/cTc	7/8	0.215419247119354	2	FACETS	1	0.914	1	0.562	0.475	0.657	CLONAL	1	TRUE	0	0.25270134533387	2		798	324	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68301849	68301849	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	23	822	0	ENST00000487270.1:c.251C>G	p.Ser84Cys	p.S84C	ENST00000487270	NM_133509.3	84	tCt/tGt	4/11	0.24089909613536	2	FACETS	0.587	0.458	0.736	0.294	0.229	0.368	SUBCLONAL	1	TRUE	0	0.25270134533387	2		822	310	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989151	41989151	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	37	813	0	ENST00000219905.7:c.1943G>C	p.Ser648Thr	p.S648T	ENST00000219905	NM_001164273.1	648	aGt/aCt	3/24	0.25270134533387	1	FACETS	0.867	0.718	1	0.867	0.718	1	CLONAL	1	TRUE	0	0.25270134533387	1		813	295	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727480	88727480	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	51	848	1	ENST00000360948.2:c.299A>T	p.Glu100Val	p.E100V	ENST00000360948	NM_001012338.2	100	gAg/gTg	3/19	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.25270134533387	2		849	373	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17129606	17129606	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	50	1220	1	ENST00000285071.4:c.280G>T	p.Gly94Ter	p.G94*	ENST00000285071	NM_144997.5	94	Gga/Tga	5/14	0.203107856289035	2	FACETS	0.984	0.837	1	0.492	0.418	0.573	CLONAL	1	TRUE	0	0.25270134533387	2		1221	402	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733029	74733029	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	53	730	0	ENST00000359995.5:c.214A>C	p.Met72Leu	p.M72L	ENST00000359995	NM_001195427.1	72	Atg/Ctg	1/3	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.25270134533387	2		730	362	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3114996	3114996	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	68	1319	0	ENST00000078429.4:c.531G>T	p.Gln177His	p.Q177H	ENST00000078429	NM_002067.2	177	caG/caT	4/7	0.215419247119354	2	FACETS	1	0.964	1	0.65	0.568	0.738	CLONAL	1	TRUE	0	0.25270134533387	2		1319	414	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905269	50905269	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	64	1234	0	ENST00000440232.2:c.477G>T	p.Glu159Asp	p.E159D	ENST00000440232	NM_002691.3	159	gaG/gaT	5/27	NA	2	FACETS	1	0.952	1			1	INDETERMINATE	1	TRUE	NA	0.25270134533387	2		1234	417	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505490	25505490	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	56	868	0	ENST00000264709.3:c.268A>T	p.Asn90Tyr	p.N90Y	ENST00000264709	NM_175629.2	90	Aat/Tat	4/23	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.25270134533387	2		868	390	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965842	25965842	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	44	886	0	ENST00000435504.4:c.3364G>T	p.Gly1122Trp	p.G1122W	ENST00000435504		1122	Ggg/Tgg	13/13	1	2	FACETS	0.921	0.775	1	0.921	0.775	1	CLONAL	1	TRUE	1	0.25270134533387	2		886	378	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100963	41100963	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	40	786	0	ENST00000373198.4:c.1393T>A	p.Ser465Thr	p.S465T	ENST00000373198	NM_133170.3	465	Tct/Act	8/32	0.237431360066052	0	FACETS	0.643	0.535	0.762			1	SUBCLONAL	1	TRUE	0	0.25270134533387	0		786	368	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143191861	143191861	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	46	746	0	ENST00000262992.4:c.570G>T	p.Glu190Asp	p.E190D	ENST00000262992	NM_001101669.1	190	gaG/gaT	8/24	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.25270134533387	2		746	331	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628949	187628949	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	39	821	0	ENST00000441802.2:c.2033G>T	p.Gly678Val	p.G678V	ENST00000441802	NM_005245.3	678	gGt/gTt	2/27	1	2	FACETS	0.944	0.785	1	0.944	0.785	1	CLONAL	1	TRUE	1	0.25270134533387	2		821	327	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036986	180036986	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	74	915	0	ENST00000261937.6:c.3726A>T	p.Arg1242Ser	p.R1242S	ENST00000261937	NM_182925.4	1242	agA/agT	28/30	0.25270134533387	1	FACETS	0.759	0.67	0.854	1	0.977	1	SUBCLONAL	2	TRUE	0	0.25270134533387	1		915	337	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641011	117641034	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTTCGAAGATTCACATTACCTTC	AGTTCGAAGATTCACATTACCTTC	-	novel	NA	P-0021965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	21	439	0	ENST00000368508.3:c.5937_5940+20del		p.X1979_splice	ENST00000368508	NM_002944.2	1979		36/43	0.25270134533387	1	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	0	0.25270134533387	1		439	128	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376059	8376059	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	21	458	0	ENST00000356435.5:c.4538A>T	p.Gln1513Leu	p.Q1513L	ENST00000356435		1513	cAa/cTa	28/35	0.215419247119354	2	FACETS	0.791	0.612	0.999	0.396	0.306	0.5	CLONAL	1	TRUE	0	0.25270134533387	2		458	210	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449745	8449745	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1172700321	NA	P-0021965-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	49	856	1	ENST00000356435.5:c.3968G>A	p.Arg1323His	p.R1323H	ENST00000356435		1323	cGc/cAc	23/35	0.215419247119354	2	FACETS	1	0.939	1	0.606	0.516	0.704	CLONAL	1	TRUE	0	0.25270134533387	2		857	320	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	137	669	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.702496344007263	2		669	342	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	670	554	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	0.702618458351589	3	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.702496344007263	3		554	1112	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186556	108186556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	144	373	1	ENST00000278616.4:c.6013C>T	p.Leu2005Phe	p.L2005F	ENST00000278616	NM_000051.3	2005	Ctc/Ttc	41/63	1	2	FACETS	0.93	0.855	1	0.93	0.855	1	CLONAL	1	TRUE	1	0.702496344007263	2		374	441	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149242	119149242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779039234	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	244	639	0	ENST00000264033.4:c.1250C>T	p.Pro417Leu	p.P417L	ENST00000264033	NM_005188.3	417	cCt/cTt	9/16	1	2	FACETS	0.944	0.886	1	0.944	0.886	1	CLONAL	1	TRUE	1	0.702496344007263	2		639	736	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851421	156851421	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	224	755	0	ENST00000524377.1:c.2378A>C	p.Asp793Ala	p.D793A	ENST00000524377	NM_002529.3	793	gAt/gCt	17/17	1	2	FACETS	0.986	0.923	1	0.986	0.923	1	CLONAL	1	TRUE	1	0.702496344007263	2		755	647	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246091305	246091306	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	193	550	3	ENST00000388985.4:c.629_630delinsTT	p.Pro210Leu	p.P210L	ENST00000388985		210	cCC/cTT	7/12	1	2	FACETS	0.947	0.882	1	0.947	0.882	1	CLONAL	1	TRUE	1	0.702496344007263	2		553	580	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948375	71948375	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	313	895	0	ENST00000298229.2:c.3087C>G	p.His1029Gln	p.H1029Q	ENST00000298229	NM_001567.3	1029	caC/caG	26/28	1	2	FACETS	0.901	0.851	0.952	0.901	0.851	0.952	CLONAL	1	TRUE	1	0.702496344007263	2		895	989	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192645	94192645	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	205	685	2	ENST00000323929.3:c.1429C>T	p.Gln477Ter	p.Q477*	ENST00000323929	NM_005591.3	477	Cag/Tag	13/20	1	2	FACETS	0.857	0.798	0.917	0.857	0.798	0.917	CLONAL	1	TRUE	1	0.702496344007263	2		687	681	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206798	102206798	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	231	576	1	ENST00000263464.3:c.1426G>A	p.Glu476Lys	p.E476K	ENST00000263464	NM_001165.4	476	Gaa/Aaa	7/9	1	2	FACETS	0.935	0.876	0.996	0.935	0.876	0.996	CLONAL	1	TRUE	1	0.702496344007263	2		577	703	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487653	56487653	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	228	653	0	ENST00000267101.3:c.1586G>C	p.Cys529Ser	p.C529S	ENST00000267101	NM_001982.3	529	tGt/tCt	13/28	1	2	FACETS	0.972	0.91	1	0.972	0.91	1	CLONAL	1	TRUE	1	0.702496344007263	2		653	668	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856488	111856488	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1327039356	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	105	388	0	ENST00000341259.2:c.539A>G	p.Lys180Arg	p.K180R	ENST00000341259	NM_005475.2	180	aAg/aGg	2/8	1	2	FACETS	0.81	0.732	0.891	0.81	0.732	0.891	CLONAL	1	TRUE	1	0.702496344007263	2		388	369	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219437	133219437	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	268	798	0	ENST00000320574.5:c.4697G>A	p.Arg1566Lys	p.R1566K	ENST00000320574	NM_006231.2	1566	aGa/aAa	36/49	1	2	FACETS	0.936	0.881	0.992	0.936	0.881	0.992	CLONAL	1	TRUE	1	0.702496344007263	2		798	815	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134312	41134312	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	208	591	0	ENST00000379561.5:c.1316del	p.Ile439AsnfsTer14	p.I439Nfs*14	ENST00000379561	NM_002015.3	439	aTa/aa	2/3	1	2	FACETS	0.895	0.834	0.956	0.895	0.834	0.956	CLONAL	1	TRUE	1	0.702496344007263	2		591	662	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457424	67457424	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	516	614	0	ENST00000327367.4:c.398C>T	p.Pro133Leu	p.P133L	ENST00000327367	NM_005902.3	133	cCa/cTa	2/9	0.695175411347925	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.702496344007263	2		614	690	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823777	3823777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150767375	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	230	526	1	ENST00000262367.5:c.2438C>T	p.Pro813Leu	p.P813L	ENST00000262367	NM_004380.2	813	cCg/cTg	13/31	1	2	FACETS	0.994	0.932	1	0.994	0.932	1	CLONAL	1	TRUE	1	0.702496344007263	2		527	659	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923416	9923416	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	261	747	0	ENST00000330684.3:c.1871G>A	p.Gly624Glu	p.G624E	ENST00000330684	NM_001134407.1	624	gGg/gAg	9/13	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.702496344007263	2		747	743	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780664	56780665	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	220	684	1	ENST00000337432.4:c.679_680delinsTT	p.Pro227Leu	p.P227L	ENST00000337432	NM_058216.2	227	CCa/TTa	4/9	1	2	FACETS	0.971	0.909	1	0.971	0.909	1	CLONAL	1	TRUE	1	0.702496344007263	2		685	645	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857767	78857767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372325672	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	217	608	0	ENST00000306801.3:c.1837C>T	p.Pro613Ser	p.P613S	ENST00000306801	NM_020761.2	613	Ccc/Tcc	16/34	1	2	FACETS	0.935	0.874	0.997	0.935	0.874	0.997	CLONAL	1	TRUE	1	0.702496344007263	2		608	661	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289699	15289699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	307	805	2	ENST00000263388.2:c.3772G>A	p.Gly1258Arg	p.G1258R	ENST00000263388	NM_000435.2	1258	Gga/Aga	23/33	1	2	FACETS	0.968	0.915	1	0.968	0.915	1	CLONAL	1	TRUE	1	0.702496344007263	2		807	903	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15374321	15374321	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	280	750	0	ENST00000263377.2:c.1251G>C	p.Glu417Asp	p.E417D	ENST00000263377	NM_058243.2	417	gaG/gaC	7/20	1	2	FACETS	0.977	0.921	1	0.977	0.921	1	CLONAL	1	TRUE	1	0.702496344007263	2		750	816	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214137	36214137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	303	867	1	ENST00000222270.7:c.2963C>T	p.Pro988Leu	p.P988L	ENST00000222270	NM_014727.1	988	cCc/cTc	6/37	1	2	FACETS	0.985	0.931	1	0.985	0.931	1	CLONAL	1	TRUE	1	0.702496344007263	2		868	876	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606708	29606708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768680011	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	234	597	0	ENST00000389048.3:c.1172G>A	p.Gly391Glu	p.G391E	ENST00000389048	NM_004304.4	391	gGa/gAa	5/29	1	2	FACETS	0.9	0.843	0.959	0.9	0.843	0.959	CLONAL	1	TRUE	1	0.702496344007263	2		597	740	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39214664	39214664	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	244	703	3	ENST00000402219.2:c.3460C>A	p.Pro1154Thr	p.P1154T	ENST00000402219	NM_005633.3	1154	Cct/Act	22/23	1	2	FACETS	0.886	0.831	0.943	0.886	0.831	0.943	CLONAL	1	TRUE	1	0.702496344007263	2		706	784	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607607	46607608	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	308	761	3	ENST00000263734.3:c.1796_1797delinsTT	p.Pro599Leu	p.P599L	ENST00000263734	NM_001430.4	599	cCC/cTT	12/16	1	2	FACETS	0.996	0.943	1	0.996	0.943	1	CLONAL	1	TRUE	1	0.702496344007263	2		764	880	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566701	212566701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	118	313	0	ENST00000342788.4:c.1480G>A	p.Glu494Lys	p.E494K	ENST00000342788	NM_005235.2	494	Gaa/Aaa	12/28	1	2	FACETS	0.794	0.722	0.869	0.794	0.722	0.869	SUBCLONAL	1	TRUE	1	0.702496344007263	2		313	423	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420092	41420093	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	121	330	0	ENST00000373198.4:c.228_229delinsAA	p.Met76_Val77delinsIleMet	p.M76_V77delinsIM	ENST00000373198	NM_133170.3	76	atGGtg/atAAtg	3/32	1	2	FACETS	0.794	0.722	0.868	0.794	0.722	0.868	SUBCLONAL	1	TRUE	1	0.702496344007263	2		330	434	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626725	12626725	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	229	599	0	ENST00000251849.4:c.1564A>G	p.Asn522Asp	p.N522D	ENST00000251849	NM_002880.3	522	Aac/Gac	15/17	1	2	FACETS	0.922	0.863	0.982	0.922	0.863	0.982	CLONAL	1	TRUE	1	0.702496344007263	2		599	707	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643768	52643768	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	300	694	0	ENST00000394830.3:c.2128C>G	p.Arg710Gly	p.R710G	ENST00000394830	NM_018313.4	710	Cga/Gga	17/30	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.702496344007263	2		694	842	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014127	70014629	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	CAGCATCATGCAGACCTAACCTGTACAACAACTCTCGATCTCACGGATGGCACCATCACCTTCAACAACAACCTCGGAACTGGGACTGAGGCCAACCAAGCCTATAGTGTCCCCACAAAAATGGGATCCAAACTGGAAGACATCCTGATGGACGACACCCTTTCTCCCGTCGGTGTCACTGATCCACTCCTTTCCTCAGTGTCCCCCGGAGCTTCCAAAACAAGCAGCCGGAGGAGCAGTATGAGCATGGAAGAGACGGAGCACACTTGTTAGCGAATCCTCCCTGCACTGCATTCGCACAAACTGCTTCCTTTCTTGATTCGTAGATTTAATAACTTACCTGAAGGGGTTTTCTTGATAATTTTCCTTTAATATGAAATTTTTTTTCATGCTTTATCAATAGCCCAGGATATATTTTATTTTTAGAATTTTGTGAAACAGACTTGTATATTCTATTTTACAACTACAAATGCCTCCAAAGTATTGTACAAATAAGTGTGCAG	CAGCATCATGCAGACCTAACCTGTACAACAACTCTCGATCTCACGGATGGCACCATCACCTTCAACAACAACCTCGGAACTGGGACTGAGGCCAACCAAGCCTATAGTGTCCCCACAAAAATGGGATCCAAACTGGAAGACATCCTGATGGACGACACCCTTTCTCCCGTCGGTGTCACTGATCCACTCCTTTCCTCAGTGTCCCCCGGAGCTTCCAAAACAAGCAGCCGGAGGAGCAGTATGAGCATGGAAGAGACGGAGCACACTTGTTAGCGAATCCTCCCTGCACTGCATTCGCACAAACTGCTTCCTTTCTTGATTCGTAGATTTAATAACTTACCTGAAGGGGTTTTCTTGATAATTTTCCTTTAATATGAAATTTTTTTTCATGCTTTATCAATAGCCCAGGATATATTTTATTTTTAGAATTTTGTGAAACAGACTTGTATATTCTATTTTACAACTACAAATGCCTCCAAAGTATTGTACAAATAAGTGTGCAG	-	novel	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	649	130	0	ENST00000394351.3:c.988_*230del		p.*330*	ENST00000394351	NM_000248.3	330		9/9	1	2	FACETS	0.773	0.748	0.798	1	0.998	1	SUBCLONAL	2	TRUE	1	0.702496344007263	2		130	1195	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390923	89390923	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	179	488	0	ENST00000336596.2:c.989G>A	p.Arg330Lys	p.R330K	ENST00000336596	NM_005233.5	330	aGa/aAa	5/17	1	2	FACETS	0.939	0.871	1	0.939	0.871	1	CLONAL	1	TRUE	1	0.702496344007263	2		488	543	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457270	89457270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	132	507	5	ENST00000336596.2:c.1751G>A	p.Gly584Asp	p.G584D	ENST00000336596	NM_005233.5	584	gGc/gAc	9/17	1	2	FACETS	0.808	0.739	0.88	0.808	0.739	0.88	CLONAL	1	TRUE	1	0.702496344007263	2		512	465	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612277	189612277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	151	402	0	ENST00000264731.3:c.2029G>A	p.Glu677Lys	p.E677K	ENST00000264731	NM_003722.4	677	Gag/Aag	14/14	1	2	FACETS	0.937	0.864	1	0.937	0.864	1	CLONAL	1	TRUE	1	0.702496344007263	2		402	459	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1959680	1959680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868806171	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	134	381	0	ENST00000382891.5:c.2902C>T	p.Arg968Cys	p.R968C	ENST00000382891	NM_133335.3	968	Cgt/Tgt	16/22	NA	2	FACETS	0.906	0.831	0.984			1	INDETERMINATE	1	TRUE	NA	0.702496344007263	2		381	421	SUCCESS
APC	324	MSKCC	GRCh37	5	112178465	112178465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881257	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	169	466	0	ENST00000257430.4:c.7174C>T	p.Pro2392Ser	p.P2392S	ENST00000257430	NM_000038.5	2392	Cca/Tca	16/16	0.261358524747407	5	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.702496344007263	5		466	690	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562391	176562391	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	281	735	1	ENST00000439151.2:c.287C>T	p.Ser96Phe	p.S96F	ENST00000439151	NM_022455.4	96	tCc/tTc	2/23	1	2	FACETS	0.989	0.933	1	0.989	0.933	1	CLONAL	1	TRUE	1	0.702496344007263	2		736	809	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673255	30673256	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	153	550	0	ENST00000376406.3:c.3704_3705delinsTT	p.Ser1235Phe	p.S1235F	ENST00000376406	NM_014641.2	1235	tCC/tTT	10/15	1	2	FACETS	0.721	0.662	0.782	0.721	0.662	0.782	SUBCLONAL	1	TRUE	1	0.702496344007263	2		550	604	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187506	32187506	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	254	826	0	ENST00000375023.3:c.1373C>T	p.Ser458Phe	p.S458F	ENST00000375023	NM_004557.3	458	tCc/tTc	8/30	1	2	FACETS	0.907	0.852	0.964	0.907	0.852	0.964	CLONAL	1	TRUE	1	0.702496344007263	2		826	797	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099313	157099333	+	inframe_deletion	In_Frame_Del	DEL	CACCACCACCACCACCATGCC	CACCACCACCACCACCATGCC	-	rs767952510	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	24	456	0	ENST00000346085.5:c.278_298del	p.His93_His99del	p.H93_H99del	ENST00000346085	NM_020732.3	84	CACCACCACCACCACCATGCC/-	1/20	0.702496344007263	1	FACETS	0.169	0.133	0.211	0.169	0.133	0.211	SUBCLONAL	1	TRUE	0	0.702496344007263	1		456	262	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523695	148523695	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	285	416	0	ENST00000320356.2:c.758C>T	p.Pro253Leu	p.P253L	ENST00000320356	NM_004456.4	253	cCa/cTa	8/20	0.702618458351589	3	FACETS	0.962	0.914	1	0.962	0.914	1	CLONAL	2	TRUE	1	0.702496344007263	3		416	570	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36846914	36846914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	190	581	3	ENST00000358127.4:c.1025C>T	p.Ser342Phe	p.S342F	ENST00000358127	NM_001280556.1	342	tCc/tTc	9/10	1	2	FACETS	0.716	0.664	0.771	0.716	0.664	0.771	SUBCLONAL	1	TRUE	1	0.702496344007263	2		584	755	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156728	20156728	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	243	253	0	ENST00000379607.5:c.29A>T	p.Lys10Ile	p.K10I	ENST00000379607	NM_001412.3	10	aAa/aTa	2/7	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.702496344007263	1		253	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0021975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	204	842	1	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.24567755667823	2	FACETS	0.751	0.698	0.806	0.751	0.698	0.806	SUBCLONAL	2	TRUE	0	0.334462626141117	2		843	812	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107180	27107180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1308037041	NA	P-0021975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	69	602	0	ENST00000324856.7:c.6791C>T	p.Ser2264Leu	p.S2264L	ENST00000324856	NM_006015.4	2264	tCa/tTa	20/20	1	2	FACETS	0.554	0.482	0.632	0.554	0.482	0.632	SUBCLONAL	1	TRUE	1	0.334462626141117	2		602	745	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845900	156845900	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	108	713	0	ENST00000524377.1:c.1530C>G	p.Ile510Met	p.I510M	ENST00000524377	NM_002529.3	510	atC/atG	13/17	0.21241991845397	5	FACETS	1	0.966	1	0.395	0.354	0.438	CLONAL	1	TRUE	2	0.334462626141117	5		713	819	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572084	64572084	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	63	575	1	ENST00000312049.6:c.1555C>A	p.Pro519Thr	p.P519T	ENST00000312049	NM_130799.2	519	Cct/Act	10/10	0.334462626141117	1	FACETS	0.486	0.42	0.557	0.486	0.42	0.557	SUBCLONAL	1	TRUE	0	0.334462626141117	1		576	646	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573799	64573799	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	72	685	0	ENST00000312049.6:c.954C>G	p.Ile318Met	p.I318M	ENST00000312049	NM_130799.2	318	atC/atG	7/10	0.334462626141117	1	FACETS	0.499	0.436	0.568	0.499	0.436	0.568	SUBCLONAL	1	TRUE	0	0.334462626141117	1		685	718	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438185	438185	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	88	377	0	ENST00000399788.2:c.1784G>C	p.Gly595Ala	p.G595A	ENST00000399788	NM_001042603.1	595	gGa/gCa	14/28	0.236865363580421	5	FACETS	1	0.971	1	0.435	0.385	0.487	CLONAL	1	TRUE	2	0.334462626141117	5		377	606	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2221334	2221334	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	169	711	0	ENST00000326181.6:c.418G>C	p.Asp140His	p.D140H	ENST00000326181	NM_032271.2	140	Gac/Cac	6/21	0.334462626141117	3	FACETS	0.843	0.777	0.911	0.843	0.777	0.911	CLONAL	2	TRUE	1	0.334462626141117	3		711	700	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752989	128752989	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	53	469	0	ENST00000377970.2:c.1150G>C	p.Glu384Gln	p.E384Q	ENST00000377970	NM_002467.4	384	Gag/Cag	3/3	0.334462626141117	4	FACETS	0.433	0.368	0.505	0.144	0.122	0.169	SUBCLONAL	1	TRUE	1	0.334462626141117	4		469	976	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577529	7577529	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs730882027	NA	P-0021982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	362	691	0	ENST00000269305.4:c.752T>G	p.Ile251Ser	p.I251S	ENST00000269305	NM_001126112.2	251	aTc/aGc	7/11	0.414837173647849	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.414837173647849	2		691	819	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455533	189455533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144315591	NA	P-0021982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	280	561	0	ENST00000264731.3:c.67G>A	p.Val23Ile	p.V23I	ENST00000264731	NM_003722.4	23	Gta/Ata	2/14	0.414837173647849	3	FACETS	0.835	0.79	0.88	1	0.992	1	CLONAL	3	TRUE	1	0.414837173647849	3		561	651	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284937	15284937	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1275632781	NA	P-0021982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1225	161	730	1	ENST00000263388.2:c.4678C>T	p.Arg1560Trp	p.R1560W	ENST00000263388	NM_000435.2	1560	Cgg/Tgg	25/33	0.414837173647849	5	FACETS	0.909	0.831	0.99	0.303	0.277	0.33	CLONAL	1	TRUE	2	0.414837173647849	5		731	1386	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0021985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	526	824	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.578702936254158	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.578702936254158	2		825	892	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101609	27101609	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	204	591	3	ENST00000324856.7:c.4891C>T	p.Gln1631Ter	p.Q1631*	ENST00000324856	NM_006015.4	1631	Cag/Tag	18/20	0.212790950359141	2	FACETS	0.695	0.644	0.747	0.347	0.322	0.374	INDETERMINATE	1	TRUE	0	0.578702936254158	2		594	1015	SUCCESS
APC	324	MSKCC	GRCh37	5	112175328	112175328	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	129	389	0	ENST00000257430.4:c.4037C>A	p.Ser1346Ter	p.S1346*	ENST00000257430	NM_000038.5	1346	tCa/tAa	16/16	0.578702936254158	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.578702936254158	1		389	237	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958231	11958231	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	144	318	0	ENST00000353533.5:c.144del	p.Phe48LeufsTer14	p.F48Lfs*14	ENST00000353533	NM_003010.3	47	aaT/aa	2/11	0.578702936254158	2	FACETS	0.908	0.846	0.97	0.908	0.846	0.97	CLONAL	2	TRUE	0	0.578702936254158	2		318	274	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641202	3641202	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770020510	NA	P-0021985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	378	723	0	ENST00000294008.3:c.2437G>A	p.Glu813Lys	p.E813K	ENST00000294008	NM_032444.2	813	Gag/Aag	12/15	0.578702936254158	3	FACETS	1	0.994	1	0.664	0.63	0.699	CLONAL	1	TRUE	1	0.578702936254158	3		723	1268	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349241	89349241	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1341	197	735	0	ENST00000301030.4:c.3709A>G	p.Lys1237Glu	p.K1237E	ENST00000301030	NM_001256183.1	1237	Aag/Gag	9/13	0.578702936254158	3	FACETS	0.571	0.527	0.617	0.285	0.263	0.309	SUBCLONAL	1	TRUE	1	0.578702936254158	3		735	1538	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652864	212652864	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	13	345	0	ENST00000342788.4:c.442T>A	p.Tyr148Asn	p.Y148N	ENST00000342788	NM_005235.2	148	Tat/Aat	4/28	0.212790950359141	2	FACETS	0.225	0.16	0.303	0.112	0.08	0.152	INDETERMINATE	1	TRUE	0	0.578702936254158	2		345	200	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182679046	182679046	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	64	419	0	ENST00000292782.4:c.488A>G	p.Asn163Ser	p.N163S	ENST00000292782	NM_020640.2	163	aAt/aGt	4/7	0.329597135023367	3	FACETS	0.682	0.593	0.779	0.227	0.197	0.26	INDETERMINATE	1	TRUE	0	0.578702936254158	3		419	418	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177504	56177504	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	64	367	0	ENST00000399503.3:c.2477T>C	p.Met826Thr	p.M826T	ENST00000399503	NM_005921.1	826	aTg/aCg	14/20	0.249320728527098	3	FACETS	0.597	0.518	0.682	0.298	0.259	0.341	INDETERMINATE	1	TRUE	1	0.578702936254158	3		367	478	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030329	180030329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142322370	NA	P-0021985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	356	496	1	ENST00000261937.6:c.3955C>T	p.Arg1319Trp	p.R1319W	ENST00000261937	NM_182925.4	1319	Cgg/Tgg	30/30	0.526022844374061	3	FACETS	1	0.995	1	0.494	0.469	0.52	CLONAL	1	TRUE	0	0.578702936254158	3		497	1070	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412733	63412733	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	190	476	1	ENST00000330258.3:c.434C>A	p.Thr145Lys	p.T145K	ENST00000330258	NM_152424.3	145	aCa/aAa	2/2	0.577977277703587	3	FACETS	0.953	0.882	1	0.477	0.441	0.514	CLONAL	1	TRUE	1	0.578702936254158	3		477	888	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111504	8111505	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	163	654	0	ENST00000346208.3:c.992dup	p.Asn331LysfsTer21	p.N331Kfs*21	ENST00000346208		330	-/A	5/6	1	2	FACETS	0.819	0.751	0.89	0.819	0.751	0.89	CLONAL	1	TRUE	1	0.395953511441984	2		654	1005	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220673	1220682	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTCCGGCT	TTCTCCGGCT	-	novel	NA	P-0021990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	150	661	0	ENST00000326873.7:c.692_701del	p.Phe231SerfsTer53	p.F231Sfs*53	ENST00000326873	NM_000455.4	231	TTCTCCGGCTtc/tc	5/10	0.347456840911041	1	FACETS	0.786	0.719	0.856	0.786	0.719	0.856	SUBCLONAL	1	TRUE	0	0.395953511441984	1		661	773	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0022000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	117	662	1				ENST00000310581	NM_198253.2	-/1132			0.544482209951805	6	FACETS	1	0.952	1	0.536	0.488	0.587	CLONAL	2	TRUE	2	0.620348480532836	6		663	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0022000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	415	819	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.53521688466616	3	FACETS	0.887	0.855	0.918	0.887	0.855	0.918	CLONAL	3	TRUE	0	0.620348480532836	3		819	659	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929487	44929487	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	198	356	0	ENST00000377967.4:c.2587C>T	p.Gln863Ter	p.Q863*	ENST00000377967	NM_021140.2	863	Cag/Tag	17/29	0.620348480532836	2	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.620348480532836	2		356	270	SUCCESS
FH	2271	MSKCC	GRCh37	1	241676926	241676926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776891545	NA	P-0022000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	230	612	0	ENST00000366560.3:c.355G>A	p.Ala119Thr	p.A119T	ENST00000366560	NM_000143.3	119	Gca/Aca	3/10	0.489544839092019	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.620348480532836	4		612	582	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129655	11129655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	236	713	1	ENST00000358026.2:c.2461G>A	p.Glu821Lys	p.E821K	ENST00000358026	NM_001128849.1	821	Gag/Aag	17/36	0.558438815590961	3	FACETS	0.905	0.852	0.958	0.905	0.852	0.958	CLONAL	2	TRUE	1	0.620348480532836	3		714	551	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871992	45871992	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	254	551	0	ENST00000391945.4:c.256G>C	p.Glu86Gln	p.E86Q	ENST00000391945	NM_000400.3	86	Gag/Cag	5/23	0.620348480532836	4	FACETS	0.882	0.829	0.936	0.882	0.829	0.936	CLONAL	2	TRUE	2	0.620348480532836	4		551	752	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922550	56922550	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	226	636	0	ENST00000519728.1:c.1420G>A	p.Asp474Asn	p.D474N	ENST00000519728	NM_002350.3	474	Gac/Aac	13/13	0.489544839092019	4	FACETS	0.936	0.877	0.995	0.936	0.877	0.995	CLONAL	2	TRUE	2	0.620348480532836	4		636	631	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46738442	46738442	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	131	698	0	ENST00000371975.4:c.1343C>A	p.Ser448Tyr	p.S448Y	ENST00000371975	NM_003579.3	448	tCt/tAt	12/18	0.489544839092019	4	FACETS	0.915	0.831	1	0.457	0.415	0.502	CLONAL	1	TRUE	2	0.620348480532836	4		698	748	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695961	117695961	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199701662	NA	P-0022000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	229	561	0	ENST00000369458.3:c.476A>G	p.Tyr159Cys	p.Y159C	ENST00000369458	NM_024626.3	159	tAt/tGt	4/6	0.489544839092019	4	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	2	0.620348480532836	4		561	593	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980347	201980347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	284	738	0	ENST00000359651.3:c.83C>T	p.Ser28Phe	p.S28F	ENST00000359651		28	tCt/tTt	1/8	0.489544839092019	4	FACETS	0.868	0.818	0.918	0.868	0.818	0.918	CLONAL	2	TRUE	2	0.620348480532836	4		738	855	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435505	18435505	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	33	322	0	ENST00000266497.5:c.490A>T	p.Asn164Tyr	p.N164Y	ENST00000266497		164	Aat/Tat	1/31	0.559844601222851	3	FACETS	0.661	0.542	0.792	0.33	0.271	0.396	SUBCLONAL	1	TRUE	1	0.620348480532836	3		322	211	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466935	18466935	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	86	570	0	ENST00000266497.5:c.1074T>A	p.Asp358Glu	p.D358E	ENST00000266497		358	gaT/gaA	5/31	0.559844601222851	3	FACETS	0.701	0.622	0.786	0.351	0.311	0.393	SUBCLONAL	1	TRUE	1	0.620348480532836	3		570	518	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830764	3830764	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	74	541	0	ENST00000262367.5:c.1792C>T	p.Gln598Ter	p.Q598*	ENST00000262367	NM_004380.2	598	Cag/Tag	8/31	0.558438815590961	3	FACETS	0.744	0.654	0.84	0.372	0.327	0.42	SUBCLONAL	1	TRUE	1	0.620348480532836	3		541	420	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351475	89351475	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1567581502	NA	P-0022000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	84	658	0	ENST00000301030.4:c.1475A>G	p.Asp492Gly	p.D492G	ENST00000301030	NM_001256183.1	492	gAc/gGc	9/13	0.558438815590961	3	FACETS	0.876	0.778	0.98	0.438	0.389	0.49	CLONAL	1	TRUE	1	0.620348480532836	3		658	405	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8109939	8109939	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	91	616	0	ENST00000585124.1:c.556G>C	p.Asp186His	p.D186H	ENST00000585124	NM_004217.3	186	Gat/Cat	7/9	0.53521688466616	3	FACETS	0.809	0.722	0.902	0.27	0.24	0.301	CLONAL	1	TRUE	0	0.620348480532836	3		616	475	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55334494	55334494	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	241	483	0	ENST00000284073.2:c.98C>T	p.Ser33Leu	p.S33L	ENST00000284073	NM_138962.2	33	tCa/tTa	2/14	0.557926946075751	3	FACETS	0.886	0.844	0.927	0.886	0.844	0.927	CLONAL	3	TRUE	0	0.620348480532836	3		483	383	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18963845	18963845	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	126	677	0	ENST00000262803.5:c.1022G>A	p.Arg341Lys	p.R341K	ENST00000262803	NM_002911.3	341	aGa/aAa	7/24	0.558438815590961	3	FACETS	1	0.927	1	0.511	0.465	0.559	CLONAL	1	TRUE	1	0.620348480532836	3		677	521	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753711	42753721	+	frameshift_variant	Frame_Shift_Del	DEL	AGCCTCGGCCC	AGCCTCGGCCC	-	novel	NA	P-0022000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	219	805	0	ENST00000222329.4:c.543_553del	p.Gly182SerfsTer3	p.G182Sfs*3	ENST00000222329	NM_006494.2	181	ctGGGCCGAGGCTca/ctca	4/4	0.620348480532836	4	FACETS	1	0.989	1	0.65	0.605	0.696	CLONAL	1	TRUE	2	0.620348480532836	4		805	880	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082436	16082436	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	90	722	0	ENST00000281043.3:c.250G>A	p.Glu84Lys	p.E84K	ENST00000281043	NM_005378.4	84	Gag/Aag	2/3	NA	2	FACETS	0.675	0.602	0.752			1	INDETERMINATE	1	TRUE	NA	0.620348480532836	2		722	430	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967074	25967074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	104	604	0	ENST00000435504.4:c.2132G>A	p.Arg711Lys	p.R711K	ENST00000435504		711	aGa/aAa	13/13	0.133296425089492	6	FACETS	0.918	0.828	1	0.612	0.552	0.675	INDETERMINATE	2	TRUE	3	0.620348480532836	6		604	409	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162666	47162666	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	81	517	0	ENST00000409792.3:c.3460G>C	p.Asp1154His	p.D1154H	ENST00000409792	NM_014159.6	1154	Gat/Cat	3/21	0.620348480532836	5	FACETS	0.642	0.565	0.725	0.214	0.188	0.242	SUBCLONAL	1	TRUE	2	0.620348480532836	5		517	785	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935084	49935084	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	446	698	0	ENST00000296474.3:c.1915G>A	p.Glu639Lys	p.E639K	ENST00000296474	NM_002447.2	639	Gag/Aag	6/20	0.620348480532836	5	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	2	0.620348480532836	5		698	866	SUCCESS
ATR	545	MSKCC	GRCh37	3	142234248	142234248	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	99	536	1	ENST00000350721.4:c.4492C>A	p.Leu1498Ile	p.L1498I	ENST00000350721	NM_001184.3	1498	Ctt/Att	25/47	0.620348480532836	5	FACETS	0.792	0.707	0.883	0.264	0.235	0.295	SUBCLONAL	1	TRUE	2	0.620348480532836	5		537	778	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670033	86670033	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0022000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	183	550	1	ENST00000274376.6:c.1833del	p.Phe611LeufsTer10	p.F611Lfs*10	ENST00000274376	NM_002890.2	610	caT/ca	14/25	0.525456206757718	2	FACETS	1	0.991	1	0.736	0.688	0.783	CLONAL	1	TRUE	0	0.620348480532836	2		551	401	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339698	116339698	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	77	428	0	ENST00000397752.3:c.560C>G	p.Ser187Cys	p.S187C	ENST00000397752	NM_000245.2	187	tCt/tGt	2/21	0.489544839092019	4	FACETS	0.86	0.757	0.969	0.43	0.378	0.485	CLONAL	1	TRUE	2	0.620348480532836	4		428	468	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054660	5054660	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1466480406	NA	P-0022000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	195	445	0	ENST00000381652.3:c.712C>T	p.Gln238Ter	p.Q238*	ENST00000381652	NM_004972.3	238	Cag/Tag	7/25	0.620348480532836	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.620348480532836	1		445	340	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900351	101900351	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	60	455	0	ENST00000374994.4:c.785T>A	p.Phe262Tyr	p.F262Y	ENST00000374994	NM_004612.2	262	tTt/tAt	4/9	0.558438815590961	3	FACETS	0.63	0.545	0.723	0.315	0.272	0.362	SUBCLONAL	1	TRUE	1	0.620348480532836	3		455	402	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755991	133755991	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	95	655	0	ENST00000318560.5:c.1618G>C	p.Glu540Gln	p.E540Q	ENST00000318560	NM_005157.4	540	Gag/Cag	10/11	0.558438815590961	3	FACETS	0.814	0.728	0.905	0.407	0.364	0.453	CLONAL	1	TRUE	1	0.620348480532836	3		655	493	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759395	133759395	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1194832601	NA	P-0022000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	142	776	0	ENST00000318560.5:c.1718C>T	p.Pro573Leu	p.P573L	ENST00000318560	NM_005157.4	573	cCt/cTt	11/11	0.558438815590961	3	FACETS	1	0.936	1	0.514	0.47	0.559	CLONAL	1	TRUE	1	0.620348480532836	3		776	584	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356231	70356231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	216	362	0	ENST00000374080.3:c.5126G>A	p.Arg1709Gln	p.R1709Q	ENST00000374080		1709	cGa/cAa	37/45	0.620348480532836	2	FACETS	1	0.969	1			1	CLONAL	2	TRUE	NA	0.620348480532836	2		362	339	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100007	157100007	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	21	238	0	ENST00000346085.5:c.944G>T	p.Gly315Val	p.G315V	ENST00000346085	NM_020732.3	315	gGa/gTa	1/20	0.202415009375739	0	FACETS	1	0.902	1			1	CLONAL	1	TRUE	0	0.202415009375739	0		238	125	SUCCESS
BTK	695	MSKCC	GRCh37	X	100625009	100625009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782731222	NA	P-0022002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	75	342	3	ENST00000308731.7:c.368G>A	p.Arg123Gln	p.R123Q	ENST00000308731	NM_000061.2	123	cGg/cAg	5/19	1	1	FACETS	0.895	0.802	0.991	1	0.988	1	CLONAL	4	TRUE	0	0.202415009375739	1		345	186	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587781525	NA	P-0022005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	515	788	0	ENST00000269305.4:c.842A>G	p.Asp281Gly	p.D281G	ENST00000269305	NM_001126112.2	281	gAc/gGc	8/11	0.842013631694151	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.85225244167503	1		788	609	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679577	86679577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	105	747	0	ENST00000274376.6:c.2738G>A	p.Arg913Gln	p.R913Q	ENST00000274376	NM_002890.2	913	cGg/cAg	21/25	0.837426099867367	2	FACETS	1	0.984	1	0.655	0.605	0.705	CLONAL	1	TRUE	0	0.85225244167503	2		747	188	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532623	46532623	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	52	535	0	ENST00000262741.5:c.455T>C	p.Leu152Pro	p.L152P	ENST00000262741	NM_003629.3	152	cTt/cCt	4/10	1	2	FACETS	0.616	0.532	0.706	0.616	0.532	0.706	SUBCLONAL	1	TRUE	1	0.85225244167503	2		535	198	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222338	2222338	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	132	690	0	ENST00000326181.6:c.622C>T	p.Arg208Ter	p.R208*	ENST00000326181	NM_032271.2	208	Cga/Tga	8/21	0.370367852389928	5	FACETS	0.765	0.694	0.84	0.255	0.231	0.28	INDETERMINATE	1	TRUE	2	0.85225244167503	5		690	922	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146547	185146547	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147690863	NA	P-0022005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	86	578	1	ENST00000265026.3:c.178G>A	p.Val60Met	p.V60M	ENST00000265026	NM_004721.4	60	Gtg/Atg	2/14	0.793330909203354	3	FACETS	0.559	0.496	0.626	0.279	0.248	0.313	SUBCLONAL	1	TRUE	1	0.85225244167503	3		579	515	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521468	187521468	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	38	566	1	ENST00000441802.2:c.11687C>A	p.Pro3896His	p.P3896H	ENST00000441802	NM_005245.3	3896	cCt/cAt	22/27	1	2	FACETS	0.339	0.282	0.402	0.339	0.282	0.402	SUBCLONAL	1	TRUE	1	0.85225244167503	2		567	263	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023150	27023150	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210287540	NA	P-0022007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	14	45	0	ENST00000324856.7:c.256G>A	p.Gly86Ser	p.G86S	ENST00000324856	NM_006015.4	86	Ggc/Agc	1/20	0.313024181194348	3	FACETS	0.526	0.382	0.698	0.263	0.191	0.349	SUBCLONAL	1	TRUE	1	0.446072604300052	3		45	146	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812486	43812486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	96	514	1	ENST00000372470.3:c.1189C>T	p.His397Tyr	p.H397Y	ENST00000372470	NM_005373.2	397	Cac/Tac	8/12	0.313024181194348	3	FACETS	0.866	0.773	0.965	0.433	0.386	0.483	CLONAL	1	TRUE	1	0.446072604300052	3		515	608	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163297298	163297298	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	74	688	0	ENST00000271452.3:c.144C>G	p.Ile48Met	p.I48M	ENST00000271452	NM_145697.2	48	atC/atG	3/14	0.368272372660452	3	FACETS	0.52	0.454	0.59	0.26	0.227	0.295	SUBCLONAL	1	TRUE	1	0.446072604300052	3		688	781	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201814	102201814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	58	596	0	ENST00000263464.3:c.1166G>A	p.Gly389Asp	p.G389D	ENST00000263464	NM_001165.4	389	gGc/gAc	6/9	0.382893729896901	5	FACETS	0.405	0.346	0.469			1	SUBCLONAL	1	TRUE	NA	0.446072604300052	5		596	1072	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363901	118363901	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	99	526	0	ENST00000534358.1:c.5134G>C	p.Glu1712Gln	p.E1712Q	ENST00000534358	NM_005933.3	1712	Gaa/Caa	16/36	0.149839112209878	5	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.446072604300052	5		526	611	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576850	7576861	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TACCTGAAGGGT	TACCTGAAGGGT	-	novel	NA	P-0022007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	296	712	0	ENST00000269305.4:c.985_993+3del		p.X329_splice	ENST00000269305	NM_001126112.2	329		9/11	0.358762506262578	3	FACETS	1	0.99	1			1	CLONAL	2	TRUE	NA	0.446072604300052	3		712	685	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505003	186505003	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	32	400	0	ENST00000323963.5:c.859G>C	p.Asp287His	p.D287H	ENST00000323963		287	Gac/Cac	8/11	0.368272372660452	3	FACETS	0.307	0.248	0.373	0.153	0.124	0.187	SUBCLONAL	1	TRUE	1	0.446072604300052	3		400	572	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858480	27858480	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	72	450	0	ENST00000359303.2:c.91C>A	p.Pro31Thr	p.P31T	ENST00000359303	NM_003535.2	31	Cca/Aca	1/1	0.368272372660452	3	FACETS	0.958	0.841	1	0.479	0.42	0.542	CLONAL	1	TRUE	1	0.446072604300052	3		450	412	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923385	36923385	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	81	679	0	ENST00000358127.4:c.877G>T	p.Val293Leu	p.V293L	ENST00000358127	NM_001280556.1	293	Gtg/Ttg	7/10	0.441676309701293	3	FACETS	0.463	0.406	0.523	0.231	0.203	0.262	SUBCLONAL	1	TRUE	1	0.446072604300052	3		679	960	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300953	137300968	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATGAAGCGGGAAGGTA	ATGAAGCGGGAAGGTA	CATG	novel	NA	P-0022007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	87	720	2	ENST00000481739.1:c.598_610+3delinsCATG		p.X200_splice	ENST00000481739	NM_002957.4	200		4/10	0.431060998743975	2	FACETS	0.699	0.62	0.783	0.35	0.31	0.392	SUBCLONAL	1	TRUE	0	0.446072604300052	2		722	558	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812486	43812486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	103	514	1	ENST00000372470.3:c.1189C>T	p.His397Tyr	p.H397Y	ENST00000372470	NM_005373.2	397	Cac/Tac	8/12	0.193837626018912	4	FACETS	1	0.918	1	0.514	0.461	0.571	INDETERMINATE	1	TRUE	2	0.449532713154779	4		515	646	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363901	118363901	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	85	526	0	ENST00000534358.1:c.5134G>C	p.Glu1712Gln	p.E1712Q	ENST00000534358	NM_005933.3	1712	Gaa/Caa	16/36	NA	2	FACETS	0.85	0.755	0.951			1	INDETERMINATE	1	TRUE	NA	0.449532713154779	2		526	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576850	7576861	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TACCTGAAGGGT	TACCTGAAGGGT	-	novel	NA	P-0022007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	170	712	0	ENST00000269305.4:c.985_993+3del		p.X329_splice	ENST00000269305	NM_001126112.2	329		9/11	0.333227855828414	4	FACETS	0.868	0.808	0.929			1	CLONAL	3	TRUE	NA	0.449532713154779	4		712	421	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858480	27858480	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	71	450	0	ENST00000359303.2:c.91C>A	p.Pro31Thr	p.P31T	ENST00000359303	NM_003535.2	31	Cca/Aca	1/1	0.449532713154779	3	FACETS	0.891	0.781	1	0.446	0.39	0.505	CLONAL	1	TRUE	1	0.449532713154779	3		450	434	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300953	137300968	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATGAAGCGGGAAGGTA	ATGAAGCGGGAAGGTA	CATG	novel	NA	P-0022007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	38	720	2	ENST00000481739.1:c.598_610+3delinsCATG		p.X200_splice	ENST00000481739	NM_002957.4	200		4/10	0.449532713154779	2	FACETS	0.325	0.268	0.388	0.162	0.134	0.194	SUBCLONAL	1	TRUE	0	0.449532713154779	2		722	521	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050943	13050943	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	118	571	0	ENST00000316448.5:c.474C>A	p.Asn158Lys	p.N158K	ENST00000316448	NM_004343.3	158	aaC/aaA	4/9	0.449532713154779	3	FACETS	0.655	0.59	0.724	0.327	0.295	0.362	SUBCLONAL	1	TRUE	1	0.449532713154779	3		571	982	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0022020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	802	715	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	2	TRUE	NA	0.878784274025963	2		716	883	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939046	48939052	+	frameshift_variant	Frame_Shift_Del	DEL	TCAAAAA	TCAAAAA	-	novel	NA	P-0022020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	164	531	2	ENST00000267163.4:c.879_885del	p.Lys294LeufsTer5	p.K294Lfs*5	ENST00000267163	NM_000321.2	293	tTCAAAAAt/tt	9/27	0.860438991750145	2	FACETS	0.837	0.796	0.876	0.837	0.796	0.876	CLONAL	2	TRUE	0	0.878784274025963	2		533	223	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556657	41556657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	284	787	1	ENST00000263253.7:c.3602G>A	p.Cys1201Tyr	p.C1201Y	ENST00000263253	NM_001429.3	1201	tGt/tAt	20/31	1	2	FACETS	0.918	0.868	0.968	0.918	0.868	0.968	CLONAL	1	TRUE	1	0.878784274025963	2		788	704	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595361	141595361	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	151	900	0	ENST00000220592.5:c.72G>C	p.Lys24Asn	p.K24N	ENST00000220592	NM_012154.3	24	aaG/aaC	2/19	0.878784274025963	3	FACETS	0.391	0.357	0.428	0.196	0.178	0.214	SUBCLONAL	1	TRUE	1	0.878784274025963	3		900	1264	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0022027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	571	860	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.361726078902025	9	FACETS	1	0.991	1	0.918	0.886	0.95	CLONAL	6	TRUE	2	0.361726078902025	9		860	1113	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591825	48591825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767342	NA	P-0022027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	139	521	0	ENST00000342988.3:c.988G>A	p.Glu330Lys	p.E330K	ENST00000342988	NM_005359.5	330	Gaa/Aaa	9/12	0.355736787627131	2	FACETS	0.913	0.839	0.989	0.913	0.839	0.989	CLONAL	2	TRUE	0	0.361726078902025	2		521	421	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576120	88576120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147160868	NA	P-0022027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	201	761	2	ENST00000360948.2:c.1553G>A	p.Arg518His	p.R518H	ENST00000360948	NM_001012338.2	518	cGt/cAt	13/19	0.256893773214162	4	FACETS	0.989	0.919	1	0.989	0.919	1	CLONAL	2	TRUE	2	0.361726078902025	4		763	765	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0022027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	243	761	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			NA	2	FACETS	0.922	0.865	0.979			1	INDETERMINATE	2	TRUE	NA	0.361726078902025	2		761	729	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053141	180053141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs907068772	NA	P-0022027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	70	608	0	ENST00000261937.6:c.1228C>T	p.Arg410Cys	p.R410C	ENST00000261937	NM_182925.4	410	Cgc/Tgc	9/30	1	2	FACETS	0.715	0.624	0.813	0.715	0.624	0.813	SUBCLONAL	1	TRUE	1	0.361726078902025	2		608	541	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980712	70980712	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs930655259	NA	P-0022027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	105	628	0	ENST00000276594.2:c.754+2T>C		p.X252_splice	ENST00000276594	NM_024504.3	252			0.361726078902025	1	FACETS	0.868	0.78	0.96	0.868	0.78	0.96	CLONAL	1	TRUE	0	0.361726078902025	1		628	548	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750776	128750776	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	85	534	0	ENST00000377970.2:c.313G>A	p.Gly105Ser	p.G105S	ENST00000377970	NM_002467.4	105	Ggc/Agc	2/3	0.323139953654232	3	FACETS	1	0.953	1	0.571	0.506	0.64	CLONAL	1	TRUE	1	0.361726078902025	3		534	486	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0022033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	69	772	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.339391324146347	5	FACETS	1	0.889	1	1	0.889	1	CLONAL	3	TRUE	2	0.339391324146347	5		772	204	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601926	43601926	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	433	797	0	ENST00000355710.3:c.970T>A	p.Trp324Arg	p.W324R	ENST00000355710	NM_020975.4	324	Tgg/Agg	5/20	0.224896206080195	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.339391324146347	4		797	1644	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125513686	125513686	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0022033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	52	420	0	ENST00000428830.2:c.815-1G>T		p.X272_splice	ENST00000428830	NM_001114121.2	272			0.224896206080195	4	FACETS	0.757	0.65	0.873	0.757	0.65	0.873	SUBCLONAL	2	TRUE	2	0.339391324146347	4		420	271	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0022033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	381	787	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	0.155056429562636	4	FACETS	1	0.954	1	1	0.954	1	INDETERMINATE	2	TRUE	2	0.339391324146347	4		787	1493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1265	475	806	0	ENST00000269305.4:c.481del	p.Ala161ProfsTer9	p.A161Pfs*9	ENST00000269305	NM_001126112.2	161	Gcc/cc	5/11	0.155056429562636	4	FACETS	1	0.986	1	1	0.986	1	INDETERMINATE	2	TRUE	2	0.339391324146347	4		806	1740	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633847	86633847	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	29	518	0	ENST00000274376.6:c.956G>A	p.Trp319Ter	p.W319*	ENST00000274376	NM_002890.2	319	tGg/tAg	5/25	0.307313740275396	2	FACETS	0.859	0.695	1	0.429	0.347	0.521	CLONAL	1	TRUE	0	0.339391324146347	2		518	199	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938965	76938965	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	53	808	0	ENST00000373344.5:c.1783C>A	p.Leu595Ile	p.L595I	ENST00000373344	NM_000489.3	595	Ctt/Att	9/35	0.189156263755275	4	FACETS	1	0.947	1	0.619	0.53	0.715	INDETERMINATE	1	TRUE	2	0.339391324146347	4		808	338	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0022052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	209	772	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.597797086137702	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	2	0.597797086137702	4		772	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577145	7577148	+	frameshift_variant	Frame_Shift_Del	DEL	GTAG	GTAG	-	novel	NA	P-0022052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	329	664	0	ENST00000269305.4:c.790_793del	p.Leu264TrpfsTer80	p.L264Wfs*80	ENST00000269305	NM_001126112.2	264	CTACtg/tg	8/11	0.592148334834149	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.597797086137702	2		664	534	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872012	37872012	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3343	426	787	0	ENST00000269571.5:c.1333C>A	p.Leu445Met	p.L445M	ENST00000269571		445	Ctg/Atg	12/27	0.597797086137702	21	FACETS	0.842	0.797	0.888			1	CLONAL	3	TRUE	NA	0.597797086137702	21		787	3769	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259259	36259260	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0022052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	305	453	0	ENST00000300305.3:c.230_231dup	p.Met78AlafsTer45	p.M78Afs*45	ENST00000300305		77	-/GC	3/8	0.597797086137702	4	FACETS	0.882	0.847	0.917			1	CLONAL	4	TRUE	NA	0.597797086137702	4		453	462	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722068	176722068	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	287	492	0	ENST00000439151.2:c.7699C>T	p.Pro2567Ser	p.P2567S	ENST00000439151	NM_022455.4	2567	Cca/Tca	23/23	0.597797086137702	7	FACETS	1	0.988	1	0.47	0.442	0.499	CLONAL	2	TRUE	2	0.597797086137702	7		492	1019	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0022059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	143	795	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.816342188945441	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.83051391859879	1		796	192	SUCCESS
FH	2271	MSKCC	GRCh37	1	241671989	241671989	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	45	710	2	ENST00000366560.3:c.652C>A	p.Leu218Ile	p.L218I	ENST00000366560	NM_000143.3	218	Ctt/Att	5/10	0.83051391859879	3	FACETS	0.748	0.636	0.869	0.374	0.318	0.435	SUBCLONAL	1	TRUE	1	0.83051391859879	3		712	205	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857787	9857787	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	108	653	0	ENST00000330684.3:c.3614A>T	p.Glu1205Val	p.E1205V	ENST00000330684	NM_001134407.1	1205	gAg/gTg	13/13	0.83051391859879	2	FACETS	1	0.965	1	0.551	0.505	0.598	CLONAL	1	TRUE	0	0.83051391859879	2		653	236	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929095	44929095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	54	616	0	ENST00000377967.4:c.2195G>A	p.Arg732Lys	p.R732K	ENST00000377967	NM_021140.2	732	aGg/aAg	17/29	0.388385539910953	3	FACETS	0.837	0.723	0.957	0.418	0.361	0.479	INDETERMINATE	1	TRUE	1	0.83051391859879	3		616	220	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0022061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	566	681	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.677162556164639	4	FACETS	0.89	0.861	0.919	0.89	0.861	0.919	CLONAL	3	TRUE	1	0.754017652101445	4		681	986	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724799	43724799	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	619	650	0	ENST00000382044.4:c.3268C>T	p.Gln1090Ter	p.Q1090*	ENST00000382044	NM_001141980.1	1090	Cag/Tag	17/28	0.696195610814161	3	FACETS	0.837	0.814	0.86	0.837	0.814	0.86	CLONAL	3	TRUE	0	0.754017652101445	3		650	900	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15967400	15967400	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	260	486	1	ENST00000268712.3:c.5203G>T	p.Asp1735Tyr	p.D1735Y	ENST00000268712	NM_006311.3	1735	Gac/Tac	35/46	0.442976745212239	4	FACETS	0.767	0.721	0.813	0.767	0.721	0.813	INDETERMINATE	2	TRUE	2	0.754017652101445	4		487	789	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532630	63532630	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199719878	NA	P-0022061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	72	660	2	ENST00000307078.5:c.1949G>A	p.Arg650His	p.R650H	ENST00000307078	NM_004655.3	650	cGc/cAc	8/11	0.556191374507078	4	FACETS	0.271	0.235	0.309	0.135	0.117	0.155	SUBCLONAL	1	TRUE	2	0.754017652101445	4		662	1238	SUCCESS
APC	324	MSKCC	GRCh37	5	112173723	112173726	+	frameshift_variant	Frame_Shift_Del	DEL	CAGA	CAGA	-	rs1131691136	NA	P-0022061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	358	375	0	ENST00000257430.4:c.2434_2437del	p.Asp812IlefsTer7	p.D812Ifs*7	ENST00000257430	NM_000038.5	811	tCAGAc/tc	16/16	0.397733489995856	6	FACETS	1	0.97	1	0.766	0.731	0.802	INDETERMINATE	3	TRUE	2	0.754017652101445	6		375	777	SUCCESS
APC	324	MSKCC	GRCh37	5	112175399	112175399	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0022061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	193	326	0	ENST00000257430.4:c.4108A>T	p.Lys1370Ter	p.K1370*	ENST00000257430	NM_000038.5	1370	Aaa/Taa	16/16	0.397733489995856	6	FACETS	1	0.945	1	0.509	0.474	0.546	INDETERMINATE	2	TRUE	2	0.754017652101445	6		326	630	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661882	29661882	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs587782088	NA	P-0022063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	225	686	0	ENST00000356175.3:c.5776G>T	p.Glu1926Ter	p.E1926*	ENST00000356175	NM_000267.3	1926	Gaa/Taa	39/57	0.321989571561833	5	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.437924105245304	5		686	1197	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677851	117677851	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	176	433	0	ENST00000368508.3:c.4082G>T	p.Trp1361Leu	p.W1361L	ENST00000368508	NM_002944.2	1361	tGg/tTg	25/43	0.331171858155621	2	FACETS	1	0.989	1	0.711	0.659	0.765	CLONAL	1	TRUE	0	0.437924105245304	2		433	565	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0022066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	791	993	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.679220438913936	8	FACETS	1	0.996	1			1	CLONAL	6	FALSE	NA	0.679220438913936	8		993	1095	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0022066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	41	516	1	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	0.419498003222244	4	FACETS	0.602	0.503	0.711	0.301	0.251	0.356	SUBCLONAL	1	FALSE	2	0.679220438913936	4		517	337	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061250	38061250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1459219194	NA	P-0022066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	227	607	1	ENST00000250448.2:c.739C>T	p.His247Tyr	p.H247Y	ENST00000250448	NM_004496.3	247	Cac/Tac	2/2	0.457937992830662	6	FACETS	0.887	0.827	0.948	0.591	0.551	0.632	CLONAL	2	FALSE	3	0.679220438913936	6		608	889	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842468	68842468	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1555515232	NA	P-0022066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	60	508	0	ENST00000261769.5:c.529C>T	p.Gln177Ter	p.Q177*	ENST00000261769	NM_004360.3	177	Cag/Tag	4/16	0.339826291503979	3	FACETS	1	0.889	1	0.34	0.296	0.386	INDETERMINATE	1	FALSE	0	0.679220438913936	3		508	232	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326690	62326690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375593361	NA	P-0022066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	35	703	1	ENST00000360203.5:c.3509G>A	p.Arg1170Gln	p.R1170Q	ENST00000360203	NM_001283009.1	1170	cGg/cAg	34/35	1	2	FACETS	0.44	0.363	0.526	0.44	0.363	0.526	SUBCLONAL	1	FALSE	1	0.679220438913936	2		704	234	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808247	99808247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	103	564	0	ENST00000280892.6:c.442C>T	p.Arg148Cys	p.R148C	ENST00000280892	NM_001130678.1	148	Cgc/Tgc	5/7	0.707441005534342	4	FACETS	0.823	0.738	0.913			1	CLONAL	1	FALSE	NA	0.679220438913936	4		564	619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	DEL	C	C	-	rs1567550969	NA	P-0022068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	244	809	0	ENST00000269305.4:c.672+1del		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.335469922030866	3	FACETS	1	0.958	1			1	CLONAL	3	TRUE	NA	0.366813127901296	3		809	516	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466300	120466300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761870508	NA	P-0022068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	46	622	0	ENST00000256646.2:c.4819C>T	p.Arg1607Cys	p.R1607C	ENST00000256646	NM_024408.3	1607	Cgc/Tgc	26/34	0.200487000591853	4	FACETS	0.934	0.789	1	0.467	0.394	0.547	INDETERMINATE	1	TRUE	2	0.366813127901296	4		622	367	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432738	49432738	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555191203	NA	P-0022068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	156	685	0	ENST00000301067.7:c.8401C>T	p.Arg2801Ter	p.R2801*	ENST00000301067	NM_003482.3	2801	Cga/Tga	34/54	0.11889570287689	3	FACETS	1	0.983	1			1	INDETERMINATE	2	TRUE	NA	0.366813127901296	3		685	411	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858130	9858130	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	66	775	0	ENST00000330684.3:c.3271G>C	p.Ala1091Pro	p.A1091P	ENST00000330684	NM_001134407.1	1091	Gcc/Ccc	13/13	0.366813127901296	3	FACETS	0.957	0.833	1	0.478	0.416	0.545	CLONAL	1	TRUE	1	0.366813127901296	3		775	445	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645342	67645342	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	51	505	0	ENST00000264010.4:c.607A>G	p.Lys203Glu	p.K203E	ENST00000264010	NM_006565.3	203	Aaa/Gaa	3/12	0.366813127901296	3	FACETS	1	0.893	1	0.527	0.451	0.611	CLONAL	1	TRUE	1	0.366813127901296	3		505	312	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645355	67645355	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	51	480	0	ENST00000264010.4:c.620C>G	p.Thr207Ser	p.T207S	ENST00000264010	NM_006565.3	207	aCc/aGc	3/12	0.366813127901296	3	FACETS	1	0.905	1	0.539	0.461	0.624	CLONAL	1	TRUE	1	0.366813127901296	3		480	305	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821274	72821274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767666978	NA	P-0022068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	134	663	0	ENST00000268489.5:c.10901C>T	p.Pro3634Leu	p.P3634L	ENST00000268489	NM_006885.3	3634	cCt/cTt	10/10	0.366813127901296	3	FACETS	0.992	0.908	1	0.992	0.908	1	CLONAL	2	TRUE	1	0.366813127901296	3		663	436	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679698	30679698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771332562	NA	P-0022068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	82	791	0	ENST00000376406.3:c.2021G>A	p.Arg674Lys	p.R674K	ENST00000376406	NM_014641.2	674	aGa/aAa	5/15	0.306746863823443	4	FACETS	1	0.922	1	0.529	0.467	0.595	CLONAL	1	TRUE	2	0.366813127901296	4		791	578	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	211	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.401778183518136	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.401778183518136	3		434	531	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0022069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	67	726	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.120641279275369	1	FACETS	0.445	0.387	0.508	0.445	0.387	0.508	INDETERMINATE	1	TRUE	0	0.401778183518136	1		726	599	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0022072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	472	1137	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.8652291668255	2		1137	1076	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121913370	NA	P-0022072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	201	575	0	ENST00000288602.6:c.1742A>G	p.Asn581Ser	p.N581S	ENST00000288602	NM_004333.4	581	aAt/aGt	15/18	1	2	FACETS	0.849	0.793	0.906	0.849	0.793	0.906	CLONAL	1	TRUE	1	0.8652291668255	2		575	547	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274911	41274911	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs868651538	NA	P-0022072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	366	782	0	ENST00000349496.5:c.1161T>A	p.Asn387Lys	p.N387K	ENST00000349496	NM_001904.3	387	aaT/aaA	8/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.8652291668255	2		782	815	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338671	70338671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	331	940	0	ENST00000374080.3:c.67G>T	p.Asp23Tyr	p.D23Y	ENST00000374080		23	Gat/Tat	1/45	1	2	FACETS	0.995	0.946	1	0.995	0.946	1	CLONAL	1	TRUE	1	0.8652291668255	2		940	769	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0022072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	725	868	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	0.8652291668255	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.8652291668255	2		868	805	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780684	9780684	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	263	663	1	ENST00000377346.4:c.1486C>T	p.Arg496Ter	p.R496*	ENST00000377346	NM_005026.3	496	Cga/Tga	12/24	0.110638235116087	5	FACETS	0.97	0.917	1			1	INDETERMINATE	3	TRUE	NA	0.576155055266633	5		664	585	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322590	30322590	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	118	609	1	ENST00000322652.5:c.1603C>T	p.Arg535Ter	p.R535*	ENST00000322652	NM_015355.2	535	Cga/Tga	14/16	0.576155055266633	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.576155055266633	1		610	252	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961555	54961555	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	101	561	0	ENST00000312783.6:c.77T>C	p.Leu26Pro	p.L26P	ENST00000312783	NM_198436.1	26	cTc/cCc	4/10	0.576155055266633	5	FACETS	0.978	0.875	1	0.326	0.291	0.363	CLONAL	1	TRUE	2	0.576155055266633	5		561	668	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945081	151945081	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	40	728	0	ENST00000262189.6:c.2438C>G	p.Pro813Arg	p.P813R	ENST00000262189	NM_170606.2	813	cCa/cGa	14/59	0.576155055266633	3	FACETS	0.405	0.336	0.481	0.202	0.168	0.241	SUBCLONAL	1	TRUE	1	0.576155055266633	3		728	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0022081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	532	1034	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.818292884837783	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.818292884837783	1		1037	721	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0022081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	360	529	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	1	2	FACETS	0.989	0.941	1	0.989	0.941	1	CLONAL	1	TRUE	1	0.818292884837783	2		529	890	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274794	123274794	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913478	NA	P-0022081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	916	608	0	ENST00000358487.5:c.1124A>G	p.Tyr375Cys	p.Y375C	ENST00000358487	NM_000141.4	375	tAc/tGc	9/18	0.10660024732314	4	FACETS	0.983	0.96	1			1	INDETERMINATE	3	TRUE	NA	0.818292884837783	4		608	1380	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829731	72829731	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs869312913	NA	P-0022081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	659	762	0	ENST00000268489.5:c.6850C>T	p.Arg2284Ter	p.R2284*	ENST00000268489	NM_006885.3	2284	Cga/Tga	9/10	0.818292884837783	1	FACETS	0.975	0.949	1	0.975	0.949	1	CLONAL	1	TRUE	0	0.818292884837783	1		762	976	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881620	37881620	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196082930	NA	P-0022081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1317	797	691	0	ENST00000269571.5:c.2690G>A	p.Arg897Gln	p.R897Q	ENST00000269571		897	cGg/cAg	22/27	0.328425663648638	5	FACETS	1	0.983	1			1	INDETERMINATE	2	TRUE	NA	0.818292884837783	5		691	2114	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057998	27058014	+	frameshift_variant	Frame_Shift_Del	DEL	CACCCTCGACGCTCTCC	CACCCTCGACGCTCTCC	-	novel	NA	P-0022081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	469	587	0	ENST00000324856.7:c.1708_1724del	p.Pro570AlafsTer47	p.P570Afs*47	ENST00000324856	NM_006015.4	569	gCACCCTCGACGCTCTCC/g	3/20	1	2	FACETS	0.962	0.921	1	0.962	0.921	1	CLONAL	1	TRUE	1	0.818292884837783	2		587	1192	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105594	27105598	+	frameshift_variant	Frame_Shift_Del	DEL	GGTGG	GGTGG	-	novel	NA	P-0022081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	382	584	0	ENST00000324856.7:c.5206_5210del	p.Val1736Ter	p.V1736*	ENST00000324856	NM_006015.4	1735	gaGGTGGgt/gagt	20/20	1	2	FACETS	0.864	0.822	0.906	0.864	0.822	0.906	CLONAL	1	TRUE	1	0.818292884837783	2		584	1081	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032336	42032336	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	432	637	0	ENST00000219905.7:c.4520C>G	p.Ser1507Cys	p.S1507C	ENST00000219905	NM_001164273.1	1507	tCt/tGt	14/24	1	2	FACETS	0.913	0.872	0.955	0.913	0.872	0.955	CLONAL	1	TRUE	1	0.818292884837783	2		637	1156	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372074	55372081	+	frameshift_variant	Frame_Shift_Del	DEL	AGGTCTCG	AGGTCTCG	-	novel	NA	P-0022081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	354	533	0	ENST00000297316.4:c.764_771del	p.Gln255ArgfsTer107	p.Q255Rfs*107	ENST00000297316	NM_022454.3	255	cAGGTCTCG/c	2/2	0.818292884837783	1	FACETS	0.866	0.831	0.901	0.866	0.831	0.901	CLONAL	1	TRUE	0	0.818292884837783	1		533	590	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238941	5238941	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs913402227	NA	P-0022084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	72	493	0	ENST00000357368.4:c.1838C>T	p.Thr613Met	p.T613M	ENST00000357368	NM_002850.3	613	aCg/aTg	13/38	0.394828774165336	2	FACETS	1	0.975	1	0.721	0.638	0.808	CLONAL	1	TRUE	0	0.394828774165336	2		493	253	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757274881	NA	P-0022084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	391	999	2	ENST00000269305.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	144	Cag/Tag	5/11	0.291222306500871	3	FACETS	0.88	0.841	0.92	0.88	0.841	0.92	CLONAL	3	TRUE	0	0.394828774165336	3		1001	898	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737142	145737142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61755067	NA	P-0022084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	229	894	1	ENST00000428558.2:c.3424G>A	p.Asp1142Asn	p.D1142N	ENST00000428558	NM_004260.3	1142	Gac/Aac	21/22	0.309049730571896	3	FACETS	1	0.968	1	0.702	0.657	0.747	CLONAL	2	TRUE	0	0.394828774165336	3		895	660	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	427	824	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	0.394828774165336	10	FACETS	0.976	0.929	1			1	CLONAL	4	TRUE	NA	0.394828774165336	10		824	1429	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941184	71941184	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	170	867	0	ENST00000298229.2:c.959T>C	p.Leu320Pro	p.L320P	ENST00000298229	NM_001567.3	320	cTg/cCg	9/28	0.394828774165336	5	FACETS	1	0.978	1	0.296	0.272	0.322	CLONAL	1	TRUE	1	0.394828774165336	5		867	1157	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817751	3817751	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	171	699	0	ENST00000262367.5:c.3220T>C	p.Ser1074Pro	p.S1074P	ENST00000262367	NM_004380.2	1074	Tca/Cca	16/31	0.394828774165336	2	FACETS	1	0.988	1	0.699	0.645	0.753	CLONAL	1	TRUE	0	0.394828774165336	2		699	620	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45864832	45864832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778436682	NA	P-0022084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	253	1115	1	ENST00000391945.4:c.1187C>T	p.Pro396Leu	p.P396L	ENST00000391945	NM_000400.3	396	cCg/cTg	12/23	0.212596412165414	4	FACETS	0.784	0.733	0.836			1	INDETERMINATE	2	TRUE	NA	0.394828774165336	4		1116	1140	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62311242	62311242	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	154	523	0	ENST00000360203.5:c.1078C>G	p.Gln360Glu	p.Q360E	ENST00000360203	NM_001283009.1	360	Cag/Gag	13/35	0.249409471416307	4	FACETS	0.953	0.876	1	0.953	0.876	1	CLONAL	2	TRUE	2	0.394828774165336	4		523	571	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755533	57755533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	326	688	0	ENST00000274289.3:c.254G>A	p.Gly85Asp	p.G85D	ENST00000274289	NM_006622.3	85	gGc/gAc	1/14	0.309049730571896	3	FACETS	1	0.992	1	0.817	0.775	0.859	CLONAL	2	TRUE	0	0.394828774165336	3		688	807	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5534978	5534978	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201840318	NA	P-0022084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	163	536	1	ENST00000397747.3:c.289G>A	p.Glu97Lys	p.E97K	ENST00000397747	NM_025239.3	97	Gaa/Aaa	3/7	0.249409471416307	4	FACETS	0.903	0.832	0.976	0.903	0.832	0.976	CLONAL	2	TRUE	2	0.394828774165336	4		537	638	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397675	139397675	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs886043624	NA	P-0022084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	142	855	0	ENST00000277541.6:c.5126T>C	p.Leu1709Pro	p.L1709P	ENST00000277541	NM_017617.3	1709	cTg/cCg	27/34	0.249409471416307	4	FACETS	1	0.983	1	0.666	0.608	0.727	CLONAL	1	TRUE	2	0.394828774165336	4		855	753	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041110	180041110	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781402372	NA	P-0022086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	167	1389	2	ENST00000261937.6:c.3289G>A	p.Val1097Met	p.V1097M	ENST00000261937	NM_182925.4	1097	Gtg/Atg	24/30	0.293975383778206	1	FACETS	0.966	0.886	1	0.966	0.886	1	CLONAL	1	TRUE	0	0.26	1		1391	1157	SUCCESS
CBL	867	MSKCC	GRCh37	11	119167662	119167662	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	36	617	1	ENST00000264033.4:c.2071C>T	p.Gln691Ter	p.Q691*	ENST00000264033	NM_005188.3	691	Caa/Taa	13/16	0.299704140340542	1	FACETS	0.41	0.336	0.494	0.41	0.336	0.494	SUBCLONAL	1	TRUE	0	0.26	1		618	587	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308047	30308064	+	inframe_deletion	In_Frame_Del	DEL	TGGGACAATAATGCAGTC	TGGGACAATAATGCAGTC	-	novel	NA	P-0022086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	61	567	0	ENST00000262643.3:c.186_203del	p.Trp62_Val67del	p.W62_V67del	ENST00000262643	NM_001238.2	62	TGGGACAATAATGCAGTC/-	5/12	1	2	FACETS	0.764	0.659	0.879	0.764	0.659	0.879	SUBCLONAL	1	TRUE	1	0.26	2		567	614	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043687	6043687	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	95	492	0	ENST00000265849.7:c.166C>A	p.Leu56Ile	p.L56I	ENST00000265849	NM_000535.5	56	Cta/Ata	3/15	0.293461537707842	3	FACETS	1	0.976	1	0.677	0.604	0.755	CLONAL	1	TRUE	1	0.26	3		492	610	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74868172	74868172	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	13	145	0	ENST00000284811.8:c.122C>G	p.Thr41Arg	p.T41R	ENST00000284811		41	aCg/aGg	3/4	0.293461537707842	3	FACETS	0.614	0.439	0.827	0.307	0.219	0.414	SUBCLONAL	1	TRUE	1	0.26	3		145	184	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245476	46245476	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	54	392	0	ENST00000334344.6:c.3572del	p.Asn1191MetfsTer13	p.N1191Mfs*13	ENST00000334344	NM_152641.2	1190	ggA/gg	15/21	0.301099644518532	9	FACETS	0.964	0.821	1			1	CLONAL	1	TRUE	NA	0.26	9		392	823	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	456	1047	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.353454808463396	6	FACETS	1	0.96	1	1	0.96	1	CLONAL	3	TRUE	3	0.572500152326663	6		1049	1135	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0022095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	516	857	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.393330946997074	2	FACETS	0.963	0.929	0.997	0.963	0.929	0.997	CLONAL	2	TRUE	0	0.572500152326663	2		859	936	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0022095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	107	272	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.449540255152798	4	FACETS	0.812	0.735	0.891	0.812	0.735	0.891	CLONAL	2	TRUE	2	0.572500152326663	4		272	362	SUCCESS
APC	324	MSKCC	GRCh37	5	112151263	112151263	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	275	406	1	ENST00000257430.4:c.907del	p.Arg303GlyfsTer2	p.R303Gfs*2	ENST00000257430	NM_000038.5	302	cgA/cg	9/16	0.449540255152798	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.572500152326663	4		407	730	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0022098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	370	824	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.546148952038365	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.546148952038365	1		825	850	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589589	67589591	+	inframe_deletion	In_Frame_Del	DEL	AAT	AAT	-	novel	NA	P-0022098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	59	389	0	ENST00000274335.5:c.1353_1355del	p.Glu451_Tyr452delinsAsp	p.E451_Y452delinsD	ENST00000274335		451	gAATat/gat	10/15	1	2	FACETS	0.679	0.588	0.777	0.679	0.588	0.777	SUBCLONAL	1	TRUE	1	0.546148952038365	2		389	318	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593360	67593363	+	frameshift_variant	Frame_Shift_Del	DEL	CCTT	CCTT	-	novel	NA	P-0022098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	124	387	0	ENST00000274335.5:c.2106_2109del	p.Leu703CysfsTer11	p.L703Cfs*11	ENST00000274335		702	tcCCTT/tc	15/15	1	2	FACETS	0.832	0.756	0.911	0.832	0.756	0.911	CLONAL	1	TRUE	1	0.546148952038365	2		387	546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579314	7579314	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs1057520003	NA	P-0022099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	25	549	0	ENST00000269305.4:c.373A>C	p.Thr125Pro	p.T125P	ENST00000269305	NM_001126112.2	125	Acg/Ccg	4/11	1	2	FACETS	0.36	0.282	0.45	0.36	0.282	0.45	SUBCLONAL	1	TRUE	1	0.200309087436236	2		549	694	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442712	99442712	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	42	614	0	ENST00000268035.6:c.1109T>G	p.Ile370Ser	p.I370S	ENST00000268035	NM_000875.3	370	aTt/aGt	5/21	1	2	FACETS	0.618	0.514	0.733	0.618	0.514	0.733	SUBCLONAL	1	TRUE	1	0.200309087436236	2		614	679	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979011	7979011	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs758813905	NA	P-0022099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	47	684	0	ENST00000319144.4:c.1556A>G	p.Tyr519Cys	p.Y519C	ENST00000319144	NM_001139.2	519	tAt/tGt	12/15	1	2	FACETS	0.513	0.431	0.604	0.513	0.431	0.604	SUBCLONAL	1	TRUE	1	0.200309087436236	2		684	915	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128036589	128036748	+	splice_donor_variant,intron_variant	Splice_Site	DEL	GGTCTTCCCTGGTTTCTGAGACCAGGGCCACAGAACAAGATCTTTGGAGCCCAAGAAGTTCCTGAGAGAAAAACAAAAAAACAAAACAACAGCCACCTTCTGCACTCTCAATGGGGAAGAGAAACTGGCCTGGAGGAAGCTCCAAGTTTTCAATTCTTAC	GGTCTTCCCTGGTTTCTGAGACCAGGGCCACAGAACAAGATCTTTGGAGCCCAAGAAGTTCCTGAGAGAAAAACAAAAAAACAAAACAACAGCCACCTTCTGCACTCTCAATGGGGAAGAGAAACTGGCCTGGAGGAAGCTCCAAGTTTTCAATTCTTAC	-	novel	NA	P-0022099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	24	56	0	ENST00000285398.2:c.1730+1_1730+160del		p.X577_splice	ENST00000285398	NM_000122.1	577			0.109153281699939	0	FACETS	0.887	0.719	1			1	INDETERMINATE	3	TRUE	0	0.200309087436236	0		56	72	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842623	68842623	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	104	673	0	ENST00000261769.5:c.560del	p.Lys187ArgfsTer28	p.K187Rfs*28	ENST00000261769	NM_004360.3	187	Aag/ag	5/16	0.266167404325829	1	FACETS	0.971	0.87	1	0.971	0.87	1	CLONAL	1	TRUE	0	0.266167404325829	1		673	698	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426693	212426693	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	76	568	0	ENST00000342788.4:c.2422G>A	p.Val808Ile	p.V808I	ENST00000342788	NM_005235.2	808	Gtc/Atc	20/28	1	2	FACETS	0.905	0.794	1	0.905	0.794	1	CLONAL	1	TRUE	1	0.266167404325829	2		568	631	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947443	38947443	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	31	412	0	ENST00000357387.3:c.4237G>T	p.Val1413Leu	p.V1413L	ENST00000357387	NM_152756.3	1413	Gtg/Ttg	32/38	1	2	FACETS	0.574	0.464	0.698	0.574	0.464	0.698	SUBCLONAL	1	TRUE	1	0.266167404325829	2		412	406	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0022117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	243	672	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.682830487741396	3	FACETS	1	0.99	1	0.772	0.734	0.81	CLONAL	2	FALSE	0	0.682830487741396	3		672	412	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856394	111856394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1194532448	NA	P-0022117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	107	216	0	ENST00000341259.2:c.445C>T	p.Arg149Cys	p.R149C	ENST00000341259	NM_005475.2	149	Cgc/Tgc	2/8	0.398417220326288	5	FACETS	0.948	0.87	1	0.948	0.87	1	INDETERMINATE	3	FALSE	2	0.682830487741396	5		216	223	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281855	49281855	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	138	691	0	ENST00000282018.3:c.902A>C	p.Asn301Thr	p.N301T	ENST00000282018	NM_020377.2	301	aAt/aCt	1/1	0.682830487741396	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	FALSE	1	0.682830487741396	3		691	249	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061023	38061024	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0022117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	52	362	0	ENST00000250448.2:c.964_965dup	p.Pro324ArgfsTer27	p.P324Rfs*27	ENST00000250448	NM_004496.3	322	ggc/ggGGc	2/2	0.439435673017222	5	FACETS	1	0.894	1	0.351	0.3	0.405	CLONAL	1	FALSE	2	0.682830487741396	5		362	293	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0022119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	95	772	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.835	0.742	0.933	0.835	0.742	0.933	CLONAL	1	TRUE	1	0.27	2		772	843	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057936	27057937	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1415146710	NA	P-0022119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	62	687	0	ENST00000324856.7:c.1650dup	p.Tyr551LeufsTer72	p.Y551Lfs*72	ENST00000324856	NM_006015.4	548	-/C	3/20	1	2	FACETS	0.566	0.488	0.652	0.566	0.488	0.652	SUBCLONAL	1	TRUE	1	0.27	2		687	811	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0022119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	19	552	0	ENST00000374080.3:c.3670C>T	p.Leu1224Phe	p.L1224F	ENST00000374080		1224	Ctc/Ttc	26/45	1	2	FACETS	0.16	0.12	0.207	0.16	0.12	0.207	SUBCLONAL	1	TRUE	1	0.27	2		552	881	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263973	104263974	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776579	NA	P-0022120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	112	258	0	ENST00000369902.3:c.71dup	p.Ala25GlyfsTer23	p.A25Gfs*23	ENST00000369902	NM_016169.3	22	gcc/gCcc	1/12	0.344857739476976	1	FACETS	0.761	0.691	0.833	0.761	0.691	0.833	INDETERMINATE	1	TRUE	0	0.577138090458961	1		258	363	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0022120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	129	638	7	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	0.577138090458961	1	FACETS	0.474	0.43	0.52	0.474	0.43	0.52	SUBCLONAL	1	TRUE	0	0.577138090458961	1		645	671	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0022120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	75	487	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	0.344857739476976	1	FACETS	0.438	0.385	0.494	0.438	0.385	0.494	INDETERMINATE	1	TRUE	0	0.577138090458961	1		487	422	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098455	11098455	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1361910224	NA	P-0022120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	197	516	1	ENST00000358026.2:c.973G>A	p.Val325Met	p.V325M	ENST00000358026	NM_001128849.1	325	Gtg/Atg	6/36	0.344857739476976	1	FACETS	0.934	0.872	0.997	0.934	0.872	0.997	INDETERMINATE	1	TRUE	0	0.577138090458961	1		517	520	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196880	108196880	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	608	491	0	ENST00000278616.4:c.6908del	p.Lys2303ArgfsTer7	p.K2303Rfs*7	ENST00000278616	NM_000051.3	2301	gcA/gc	47/63	0.577138090458961	3	FACETS	0.956	0.928	0.983			1	CLONAL	3	TRUE	NA	0.577138090458961	3		491	947	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30946592	30946594	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs752094508	NA	P-0022120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	175	352	0	ENST00000375687.4:c.25_27del	p.Lys9del	p.K9del	ENST00000375687	NM_015338.5	5	cAGAag/cag	1/13	1	2	FACETS	0.929	0.859	1	0.929	0.859	1	CLONAL	1	TRUE	1	0.577138090458961	2		352	653	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936349	49936349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755080567	NA	P-0022120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	216	685	0	ENST00000296474.3:c.1499G>A	p.Arg500Gln	p.R500Q	ENST00000296474	NM_002447.2	500	cGg/cAg	3/20	NA	2	FACETS	1	0.955	1			1	INDETERMINATE	1	TRUE	NA	0.577138090458961	2		685	727	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40457680	40457680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	155	679	1	ENST00000345506.4:c.1433C>T	p.Ala478Val	p.A478V	ENST00000345506	NM_003152.3	478	gCc/gTc	13/20	0.28347964596339	1	FACETS	0.501	0.459	0.544	0.501	0.459	0.544	INDETERMINATE	1	TRUE	0	0.577138090458961	1		680	763	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512402	38512402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	121	678	4	ENST00000254066.5:c.1319del	p.Pro440ArgfsTer203	p.P440Rfs*203	ENST00000254066	NM_000964.3	438	gCc/gc	9/9	0.28347964596339	1	FACETS	0.36	0.325	0.397	0.36	0.325	0.397	INDETERMINATE	1	TRUE	0	0.577138090458961	1		682	829	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945647	206945647	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550164520	NA	P-0022120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	204	576	0	ENST00000423557.1:c.134G>A	p.Arg45Gln	p.R45Q	ENST00000423557	NM_000572.2	45	cGa/cAa	1/5	1	2	FACETS	0.868	0.807	0.932	0.868	0.807	0.932	CLONAL	1	TRUE	1	0.577138090458961	2		576	814	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897444	78897444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746953724	NA	P-0022120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	110	824	1	ENST00000306801.3:c.2779C>T	p.Arg927Trp	p.R927W	ENST00000306801	NM_020761.2	927	Cgg/Tgg	23/34	1	2	FACETS	0.389	0.349	0.432	0.389	0.349	0.432	SUBCLONAL	1	TRUE	1	0.577138090458961	2		825	980	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258944	16258944	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	153	798	1	ENST00000375759.3:c.6215del	p.Asn2072ThrfsTer14	p.N2072Tfs*14	ENST00000375759	NM_015001.2	2070	gAa/ga	11/15	0.28347964596339	1	FACETS	0.388	0.355	0.424	0.388	0.355	0.424	INDETERMINATE	1	TRUE	0	0.577138090458961	1		799	971	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429367	78429367	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	159	591	0	ENST00000370768.2:c.1075C>T	p.Arg359Ter	p.R359*	ENST00000370768	NM_003902.3	359	Cga/Tga	13/20	0.28347964596339	1	FACETS	0.49	0.449	0.532	0.49	0.449	0.532	INDETERMINATE	1	TRUE	0	0.577138090458961	1		591	800	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239881	105239881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1165092690	NA	P-0022120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	285	666	0	ENST00000349310.3:c.739G>A	p.Glu247Lys	p.E247K	ENST00000349310	NM_001014432.1	247	Gag/Aag	10/15	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.577138090458961	2		666	836	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43767848	43767848	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	218	633	0	ENST00000382044.4:c.1000T>C	p.Cys334Arg	p.C334R	ENST00000382044	NM_001141980.1	334	Tgt/Cgt	9/28	1	2	FACETS	0.848	0.79	0.908	0.848	0.79	0.908	CLONAL	1	TRUE	1	0.577138090458961	2		633	891	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640766	3640766	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	114	626	0	ENST00000294008.3:c.2873G>A	p.Cys958Tyr	p.C958Y	ENST00000294008	NM_032444.2	958	tGc/tAc	12/15	0.344857739476976	1	FACETS	0.488	0.44	0.538	0.488	0.44	0.538	INDETERMINATE	1	TRUE	0	0.577138090458961	1		626	576	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789651	3789651	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	109	617	0	ENST00000262367.5:c.4208A>G	p.Asp1403Gly	p.D1403G	ENST00000262367	NM_004380.2	1403	gAc/gGc	25/31	0.344857739476976	1	FACETS	0.407	0.366	0.451	0.407	0.366	0.451	INDETERMINATE	1	TRUE	0	0.577138090458961	1		617	660	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024503	16024503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	111	509	0	ENST00000268712.3:c.1715G>A	p.Arg572Gln	p.R572Q	ENST00000268712	NM_006311.3	572	cGa/cAa	16/46	0.28347964596339	1	FACETS	0.377	0.339	0.418	0.377	0.339	0.418	INDETERMINATE	1	TRUE	0	0.577138090458961	1		509	725	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870471	40870471	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0022120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	104	427	1	ENST00000428826.2:c.931+1G>A		p.X311_splice	ENST00000428826		311			0.28347964596339	1	FACETS	0.469	0.421	0.519	0.469	0.421	0.519	INDETERMINATE	1	TRUE	0	0.577138090458961	1		428	547	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210457	2210457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751484453	NA	P-0022120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	234	838	0	ENST00000398665.3:c.1064C>T	p.Thr355Met	p.T355M	ENST00000398665	NM_032482.2	355	aCg/aTg	13/28	0.344857739476976	1	FACETS	0.815	0.764	0.867	0.815	0.764	0.867	INDETERMINATE	1	TRUE	0	0.577138090458961	1		838	708	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982474	10982474	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1324350170	NA	P-0022120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	33	115	0	ENST00000327064.4:c.99del	p.Gly34AlafsTer91	p.G34Afs*91	ENST00000327064	NM_199141.1	32	ttC/tt	1/16	0.344857739476976	1	FACETS	0.417	0.343	0.499	0.417	0.343	0.499	INDETERMINATE	1	TRUE	0	0.577138090458961	1		115	195	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257162	19257163	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0022120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	68	675	0	ENST00000162023.5:c.800dup	p.Gly268TrpfsTer17	p.G268Wfs*17	ENST00000162023		267	cct/ccCt	12/13	0.344857739476976	1	FACETS	0.26	0.226	0.297	0.26	0.226	0.297	INDETERMINATE	1	TRUE	0	0.577138090458961	1		675	644	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218825	36218825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777643588	NA	P-0022120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	142	858	1	ENST00000222270.7:c.4436C>T	p.Ser1479Leu	p.S1479L	ENST00000222270	NM_014727.1	1479	tCg/tTg	18/37	0.344857739476976	1	FACETS	0.402	0.366	0.44	0.402	0.366	0.44	INDETERMINATE	1	TRUE	0	0.577138090458961	1		859	871	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703577	47703577	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1558519728	NA	P-0022120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	267	694	0	ENST00000233146.2:c.2077T>C	p.Cys693Arg	p.C693R	ENST00000233146	NM_000251.2	693	Tgt/Cgt	13/16	0.577138090458961	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.577138090458961	1		694	648	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162704	47162704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142723093	NA	P-0022120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	83	576	2	ENST00000409792.3:c.3422C>T	p.Pro1141Leu	p.P1141L	ENST00000409792	NM_014159.6	1141	cCg/cTg	3/21	1	2	FACETS	0.365	0.322	0.412	0.365	0.322	0.412	SUBCLONAL	1	TRUE	1	0.577138090458961	2		578	787	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940126	49940126	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200046052	NA	P-0022120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	89	666	2	ENST00000296474.3:c.917G>A	p.Arg306His	p.R306H	ENST00000296474	NM_002447.2	306	cGc/cAc	1/20	NA	2	FACETS	0.446	0.396	0.501			1	INDETERMINATE	1	TRUE	NA	0.577138090458961	2		668	691	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631607	119631607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	100	492	1	ENST00000316626.5:c.659G>A	p.Arg220Gln	p.R220Q	ENST00000316626		220	cGg/cAg	6/12	1	2	FACETS	0.507	0.453	0.565	0.507	0.453	0.565	SUBCLONAL	1	TRUE	1	0.577138090458961	2		493	683	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958587	38958587	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs532413623	NA	P-0022120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	124	329	1	ENST00000357387.3:c.2378C>T	p.Ala793Val	p.A793V	ENST00000357387	NM_152756.3	793	gCg/gTg	24/38	1	2	FACETS	0.995	0.907	1	0.995	0.907	1	CLONAL	1	TRUE	1	0.577138090458961	2		330	432	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513317	149513317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147568171	NA	P-0022120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	97	487	0	ENST00000261799.4:c.766C>T	p.Arg256Trp	p.R256W	ENST00000261799	NM_002609.3	256	Cgg/Tgg	6/23	0.344857739476976	1	FACETS	0.5	0.448	0.556	0.5	0.448	0.556	INDETERMINATE	1	TRUE	0	0.577138090458961	1		487	478	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394915	394915	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	149	498	1	ENST00000380956.4:c.311G>T	p.Ser104Ile	p.S104I	ENST00000380956	NM_001195286.1	104	aGc/aTc	3/9	NA	2	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.577138090458961	2		499	494	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273120	55273120	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1476431328	NA	P-0022120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	138	675	0	ENST00000275493.2:c.3443A>G	p.Asn1148Ser	p.N1148S	ENST00000275493	NM_005228.3	1148	aAc/aGc	28/28	NA	2	FACETS	0.552	0.502	0.604			1	INDETERMINATE	1	TRUE	NA	0.577138090458961	2		675	867	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500946	8500946	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	77	490	0	ENST00000356435.5:c.1936T>C	p.Ser646Pro	p.S646P	ENST00000356435		646	Tcc/Ccc	13/35	0.344857739476976	1	FACETS	0.299	0.262	0.338	0.299	0.262	0.338	INDETERMINATE	1	TRUE	0	0.577138090458961	1		490	635	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357094	70357094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	203	480	0	ENST00000374080.3:c.5609C>T	p.Thr1870Ile	p.T1870I	ENST00000374080		1870	aCc/aTc	39/45	0.096033745240232	2	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.577138090458961	2		480	619	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	107	1047	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.379682459979214	2		1049	406	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577562	7577563	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGT	novel	NA	P-0022128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	187	770	0	ENST00000269305.4:c.716_718dup	p.Asn239dup	p.N239dup	ENST00000269305	NM_001126112.2	239	agt/aACAgt	7/11	0.379682459979214	2	FACETS	0.803	0.746	0.862	0.803	0.746	0.862	CLONAL	2	TRUE	0	0.379682459979214	2		770	613	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44935940	44935940	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0022128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	43	211	0	ENST00000377967.4:c.2703-2A>G		p.X901_splice	ENST00000377967	NM_021140.2	901			1	1	FACETS	1	0.932	1	1	0.977	1	CLONAL	2	TRUE	0	0.379682459979214	1		211	83	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492891	56492891	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	21	400	0	ENST00000407977.2:c.48del	p.Leu17Ter	p.L17*	ENST00000407977		16	ctG/ct	2/10	0.379682459979214	2	FACETS	0.306	0.235	0.388	0.153	0.117	0.194	SUBCLONAL	1	TRUE	0	0.379682459979214	2		400	362	SUCCESS
APC	324	MSKCC	GRCh37	5	112175328	112175328	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	90	389	0	ENST00000257430.4:c.4037C>A	p.Ser1346Ter	p.S1346*	ENST00000257430	NM_000038.5	1346	tCa/tAa	16/16	1	2	FACETS	0.909	0.813	1	0.909	0.813	1	CLONAL	1	TRUE	1	0.530890191612696	2		389	373	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0022137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	169	667	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	0.878	0.809	0.95	0.878	0.809	0.95	CLONAL	1	TRUE	1	0.530890191612696	2		667	725	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100133	30100133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370296777	NA	P-0022137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	172	972	0	ENST00000331968.5:c.1487C>T	p.Thr496Met	p.T496M	ENST00000331968	NM_002742.2	496	aCg/aTg	10/18	0.329382332465244	1	FACETS	0.517	0.475	0.56	0.517	0.475	0.56	SUBCLONAL	1	TRUE	0	0.530890191612696	1		972	921	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446455	49446455	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	103	657	0	ENST00000301067.7:c.1150G>C	p.Glu384Gln	p.E384Q	ENST00000301067	NM_003482.3	384	Gag/Cag	9/54	1	2	FACETS	0.487	0.436	0.542	0.487	0.436	0.542	SUBCLONAL	1	TRUE	1	0.530890191612696	2		657	796	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861162	57861162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564027387	NA	P-0022137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	258	795	0	ENST00000228682.2:c.959C>T	p.Thr320Met	p.T320M	ENST00000228682	NM_005269.2	320	aCg/aTg	9/12	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.530890191612696	2		795	897	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123880917	123880917	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372757608	NA	P-0022137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	197	600	0	ENST00000330479.4:c.535C>T	p.Arg179Cys	p.R179C	ENST00000330479	NM_020382.3	179	Cgc/Tgc	5/9	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.530890191612696	2		600	725	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41001278	41001287	+	frameshift_variant	Frame_Shift_Del	DEL	GACCCAGATC	GACCCAGATC	-	novel	NA	P-0022137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	126	849	0	ENST00000267868.3:c.399_408del	p.Lys133AsnfsTer5	p.K133Nfs*5	ENST00000267868	NM_002875.4	133	aaGACCCAGATC/aa	5/10	0.329382332465244	1	FACETS	0.416	0.376	0.458	0.416	0.376	0.458	SUBCLONAL	1	TRUE	0	0.530890191612696	1		849	838	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082206	16082206	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	186	1236	1	ENST00000281043.3:c.20C>A	p.Ser7Tyr	p.S7Y	ENST00000281043	NM_005378.4	7	tCc/tAc	2/3	1	2	FACETS	0.561	0.517	0.607	0.561	0.517	0.607	SUBCLONAL	1	TRUE	1	0.530890191612696	2		1237	1249	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976680	55976680	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	274	916	0	ENST00000263923.4:c.1145T>C	p.Val382Ala	p.V382A	ENST00000263923	NM_002253.2	382	gTa/gCa	9/30	0.41657274031186	1	FACETS	0.883	0.831	0.936	0.883	0.831	0.936	CLONAL	1	TRUE	0	0.530890191612696	1		916	859	SUCCESS
APC	324	MSKCC	GRCh37	5	112170770	112170770	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs876658355	NA	P-0022137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	288	941	0	ENST00000257430.4:c.1866C>A	p.Tyr622Ter	p.Y622*	ENST00000257430	NM_000038.5	622	taC/taA	15/16	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.530890191612696	2		941	1074	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0022145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	57	779	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.893	0.766	1	0.893	0.766	1	CLONAL	1	TRUE	1	0.202333147104233	2		779	631	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0022145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	83	1034	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.901	0.793	1	0.901	0.793	1	CLONAL	1	TRUE	1	0.202333147104233	2		1037	911	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528705	8528705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370111525	NA	P-0022147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	45	567	1	ENST00000356435.5:c.427G>A	p.Ala143Thr	p.A143T	ENST00000356435		143	Gcc/Acc	4/35	0.449343979118334	6	FACETS	0.468	0.392	0.553	0.156	0.13	0.185	SUBCLONAL	1	TRUE	3	0.449343979118334	6		568	812	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578530	7578533	+	frameshift_variant	Frame_Shift_Del	DEL	ACAT	ACAT	-	novel	NA	P-0022147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	391	1123	0	ENST00000269305.4:c.397_400del	p.Met133PhefsTer36	p.M133Ffs*36	ENST00000269305	NM_001126112.2	133	ATGTtt/tt	5/11	0.449343979118334	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.449343979118334	2		1123	841	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33446179	33446179	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	96	683	0	ENST00000345365.6:c.95T>G	p.Val32Gly	p.V32G	ENST00000345365	NM_002878.3	32	gTt/gGt	2/10	0.340726544444813	4	FACETS	0.854	0.761	0.953	0.427	0.38	0.477	CLONAL	1	TRUE	2	0.449343979118334	4		683	725	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78858903	78858903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1359463998	NA	P-0022147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	283	819	0	ENST00000306801.3:c.1938G>A	p.Met646Ile	p.M646I	ENST00000306801	NM_020761.2	646	atG/atA	17/34	0.340726544444813	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.449343979118334	4		819	828	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293497	1293497	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	195	1074	0	ENST00000310581.5:c.1504A>G	p.Lys502Glu	p.K502E	ENST00000310581	NM_198253.2	502	Aag/Gag	2/16	0.119899744420769	4	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.449343979118334	4		1074	914	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123234423	123234423	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0022147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	304	636	0	ENST00000218089.9:c.3784-1G>A		p.X1262_splice	ENST00000218089	NM_001042749.1	1262			0.225270456489391	6	FACETS	0.905	0.862	0.947			1	INDETERMINATE	5	TRUE	NA	0.449343979118334	6		636	568	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047524	49047527	+	splice_donor_variant,coding_sequence_variant	Splice_Site	ONP	GGGG	GGGG	AGGT	novel	NA	P-0022147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	109	505	0	ENST00000267163.4:c.2518_2520+1delinsAGGT		p.X840_splice	ENST00000267163	NM_000321.2	840		24/27	0.449343979118334	3	FACETS	1	0.953	1			1	CLONAL	2	TRUE	NA	0.449343979118334	3		505	278	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55569926	55569926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502570	NA	P-0022169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	29	321	1	ENST00000288135.5:c.793G>A	p.Gly265Ser	p.G265S	ENST00000288135	NM_000222.2	265	Ggt/Agt	5/21	1	2	FACETS	0.385	0.309	0.47	0.385	0.309	0.47	SUBCLONAL	1	TRUE	1	0.518324986843667	2		322	291	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245981	16245981	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758108044	NA	P-0022169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	37	433	0	ENST00000375759.3:c.1604G>A	p.Arg535Gln	p.R535Q	ENST00000375759	NM_015001.2	535	cGa/cAa	8/15	1	2	FACETS	0.313	0.258	0.375	0.313	0.258	0.375	SUBCLONAL	1	TRUE	1	0.518324986843667	2		433	456	SUCCESS
EED	8726	MSKCC	GRCh37	11	85961336	85961336	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0022169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	14	167	0	ENST00000263360.6:c.115-2A>T		p.X39_splice	ENST00000263360	NM_003797.3	39			1	2	FACETS	0.322	0.233	0.428	0.322	0.233	0.428	SUBCLONAL	1	TRUE	1	0.518324986843667	2		167	168	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577171	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTAGATTACCACTACTCAGGATAGGAA	AGTAGATTACCACTACTCAGGATAGGAA	-	novel	NA	P-0022169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	43	594	1	ENST00000269305.4:c.783-16_794del		p.X261_splice	ENST00000269305	NM_001126112.2	261		8/11	1	2	FACETS	0.366	0.306	0.433	0.366	0.306	0.433	SUBCLONAL	1	TRUE	1	0.518324986843667	2		595	453	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299868	15299871	+	frameshift_variant	Frame_Shift_Del	DEL	GACA	GACA	-	novel	NA	P-0022169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	60	834	0	ENST00000263388.2:c.1307_1310del	p.Leu436ArgfsTer14	p.L436Rfs*14	ENST00000263388	NM_000435.2	436	cTGTCg/cg	8/33	1	2	FACETS	0.39	0.335	0.449	0.39	0.335	0.449	SUBCLONAL	1	TRUE	1	0.518324986843667	2		834	594	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431026	181431026	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	39	772	0	ENST00000325404.1:c.878A>G	p.His293Arg	p.H293R	ENST00000325404	NM_003106.3	293	cAc/cGc	1/1	0.518324986843667	3	FACETS	0.257	0.212	0.308	0.129	0.106	0.154	SUBCLONAL	1	TRUE	1	0.518324986843667	3		772	737	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0022172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	26	875	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.106	0.083	0.132	0.106	0.083	0.132	SUBCLONAL	1	TRUE	1	0.61	2		877	808	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123694	11123694	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	294	889	1	ENST00000358026.2:c.2344G>A	p.Gly782Ser	p.G782S	ENST00000358026	NM_001128849.1	782	Ggc/Agc	16/36	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.61	2		890	859	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786791	3786791	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	91	575	0	ENST00000262367.5:c.4420T>C	p.Cys1474Arg	p.C1474R	ENST00000262367	NM_004380.2	1474	Tgt/Cgt	27/31	1	2	FACETS	0.651	0.581	0.726	0.651	0.581	0.726	SUBCLONAL	1	TRUE	1	0.61	2		575	458	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100102	27100103	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0022172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	286	842	0	ENST00000324856.7:c.3898_3899del	p.Met1300GlufsTer22	p.M1300Efs*22	ENST00000324856	NM_006015.4	1300	ATg/g	16/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.61	2		842	778	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175996762	175996762	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	46	729	0	ENST00000367669.3:c.1675T>G	p.Cys559Gly	p.C559G	ENST00000367669	NM_022457.5	559	Tgc/Ggc	15/20	1	2	FACETS	0.392	0.33	0.459	0.392	0.33	0.459	SUBCLONAL	1	TRUE	1	0.61	2		729	385	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651922	36651926	+	frameshift_variant	Frame_Shift_Del	DEL	GCAAG	GCAAG	-	novel	NA	P-0022172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	240	743	0	ENST00000244741.5:c.46_50del	p.Lys16LeufsTer18	p.K16Lfs*18	ENST00000244741	NM_000389.4	15	aGCAAG/a	2/3	0.0773543535337575	3	FACETS	1	0.992	1	0.692	0.649	0.736	INDETERMINATE	1	TRUE	1	0.61	3		743	742	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239938	53239938	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	117	851	0	ENST00000375401.3:c.1503G>C	p.Trp501Cys	p.W501C	ENST00000375401	NM_004187.3	501	tgG/tgC	11/26	1	2	FACETS	0.555	0.501	0.612	0.555	0.501	0.612	SUBCLONAL	1	TRUE	1	0.61	2		851	691	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115818	8115834	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCTCGTTTAACCCGG	CAGCTCGTTTAACCCGG	-	novel	NA	P-0022175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	225	549	0	ENST00000346208.3:c.1165_1181del	p.Ser389ArgfsTer112	p.S389Rfs*112	ENST00000346208		388	aaCAGCTCGTTTAACCCGGcc/aacc	6/6	1	2	FACETS	0.523	0.487	0.561	0.523	0.487	0.561	SUBCLONAL	1	TRUE	1	0.819459266512913	2		549	1049	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798408	42798408	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	504	668	0	ENST00000575354.2:c.4279C>T	p.Pro1427Ser	p.P1427S	ENST00000575354	NM_015125.3	1427	Ccc/Tcc	18/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.819459266512913	2		668	1221	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0022177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	271	710	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.345878411908386	3	FACETS	0.963	0.907	1	0.963	0.907	1	CLONAL	2	TRUE	1	0.433304309171991	3		711	790	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508728	148508728	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs267601395	NA	P-0022177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	304	612	0	ENST00000320356.2:c.1936T>A	p.Tyr646Asn	p.Y646N	ENST00000320356	NM_004456.4	646	Tac/Aac	16/20	0.345878411908386	3	FACETS	0.949	0.897	1	0.949	0.897	1	CLONAL	2	TRUE	1	0.433304309171991	3		612	899	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281203	15281203	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	186	864	1	ENST00000263388.2:c.5053G>A	p.Asp1685Asn	p.D1685N	ENST00000263388	NM_000435.2	1685	Gac/Aac	27/33	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.433304309171991	2		865	702	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917787	29917787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	174	716	2	ENST00000389048.3:c.881C>T	p.Pro294Leu	p.P294L	ENST00000389048	NM_004304.4	294	cCc/cTc	3/29	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.433304309171991	2		718	755	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303267	11303267	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	178	726	0	ENST00000361445.4:c.1316T>C	p.Leu439Pro	p.L439P	ENST00000361445	NM_004958.3	439	cTa/cCa	9/58	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.433304309171991	2		726	814	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156744	2156744	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	139	613	0	ENST00000434045.2:c.178C>T	p.Pro60Ser	p.P60S	ENST00000434045	NM_001127598.1	60	Cca/Tca	3/5	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.433304309171991	2		613	496	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893340	32893340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1566215861	NA	P-0022177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	156	623	0	ENST00000380152.3:c.194C>T	p.Pro65Leu	p.P65L	ENST00000380152		65	cCa/cTa	3/27	1	2	FACETS	0.946	0.868	1	0.946	0.868	1	CLONAL	1	TRUE	1	0.433304309171991	2		623	761	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911425	32911425	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	98	469	0	ENST00000380152.3:c.2933A>T	p.Asn978Ile	p.N978I	ENST00000380152		978	aAt/aTt	11/27	1	2	FACETS	0.792	0.708	0.881	0.792	0.708	0.881	SUBCLONAL	1	TRUE	1	0.433304309171991	2		469	571	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372693	81372693	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	204	466	0	ENST00000222390.5:c.841G>A	p.Glu281Lys	p.E281K	ENST00000222390	NM_000601.4	281	Gag/Aag	7/18	0.345878411908386	3	FACETS	0.872	0.812	0.933	0.872	0.812	0.933	CLONAL	2	TRUE	1	0.433304309171991	3		466	657	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521504	46521504	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	142	914	0	ENST00000262741.5:c.904C>G	p.Leu302Val	p.L302V	ENST00000262741	NM_003629.3	302	Ctg/Gtg	7/10	0.315790110650395	3	FACETS	0.701	0.638	0.768	0.351	0.319	0.384	SUBCLONAL	1	TRUE	1	0.463730447865156	3		914	1076	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218970	193218970	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	176	582	1	ENST00000367435.3:c.1528G>T	p.Val510Leu	p.V510L	ENST00000367435	NM_024529.4	510	Gtg/Ttg	16/17	0.315790110650395	3	FACETS	1	0.989	1	0.715	0.661	0.77	CLONAL	1	TRUE	1	0.463730447865156	3		583	654	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230694	46230694	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	228	635	1	ENST00000334344.6:c.943T>C	p.Phe315Leu	p.F315L	ENST00000334344	NM_152641.2	315	Ttc/Ctc	8/21	0.393925278651718	3	FACETS	0.796	0.744	0.849	0.796	0.744	0.849	SUBCLONAL	2	TRUE	1	0.463730447865156	3		636	761	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563095	21563095	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	60	1031	0	ENST00000382592.4:c.824T>C	p.Phe275Ser	p.F275S	ENST00000382592	NM_014572.2	275	tTc/tCc	4/8	0.463730447865156	1	FACETS	0.311	0.268	0.359	0.311	0.268	0.359	SUBCLONAL	1	TRUE	0	0.463730447865156	1		1031	639	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514608	103514608	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370885325	NA	P-0022178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	142	480	0	ENST00000355739.4:c.1109G>A	p.Arg370His	p.R370H	ENST00000355739	NM_000123.3	370	cGt/cAt	8/15	0.367467245924709	3	FACETS	0.787	0.723	0.854	0.525	0.482	0.57	SUBCLONAL	2	TRUE	0	0.463730447865156	3		480	479	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857854	9857854	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555482367	NA	P-0022178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	181	800	0	ENST00000330684.3:c.3547C>T	p.Gln1183Ter	p.Q1183*	ENST00000330684	NM_001134407.1	1183	Cag/Tag	13/13	0.315790110650395	3	FACETS	1	0.989	1	0.706	0.653	0.76	CLONAL	1	TRUE	1	0.463730447865156	3		800	681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	288	980	0	ENST00000269305.4:c.376T>C	p.Tyr126His	p.Y126H	ENST00000269305	NM_001126112.2	126	Tac/Cac	5/11	0.362194185807378	2	FACETS	0.772	0.729	0.816	0.772	0.729	0.816	SUBCLONAL	2	TRUE	0	0.463730447865156	2		980	804	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588751	29588751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760703505	NA	P-0022178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	161	469	0	ENST00000356175.3:c.4537C>T	p.Arg1513Ter	p.R1513*	ENST00000356175	NM_000267.3	1513	Cga/Tga	34/57	0.362194185807378	2	FACETS	0.825	0.765	0.886	0.825	0.765	0.886	CLONAL	2	TRUE	0	0.463730447865156	2		469	421	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752805	42752805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767131852	NA	P-0022178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	154	1008	1	ENST00000222329.4:c.1459C>T	p.Arg487Cys	p.R487C	ENST00000222329	NM_006494.2	487	Cgc/Tgc	4/4	0.389445450032825	4	FACETS	0.937	0.857	1			1	CLONAL	1	TRUE	NA	0.463730447865156	4		1009	1037	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527354	187527354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373193128	NA	P-0022178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	131	619	2	ENST00000441802.2:c.10220C>T	p.Thr3407Met	p.T3407M	ENST00000441802	NM_005245.3	3407	aCg/aTg	17/27	0.385288634353392	2	FACETS	0.937	0.853	1	0.468	0.426	0.513	CLONAL	1	TRUE	0	0.463730447865156	2		621	603	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31468126	31468126	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	138	801	1	ENST00000344624.3:c.2286C>G	p.Phe762Leu	p.F762L	ENST00000344624		762	ttC/ttG	15/33	0.164666302860915	5	FACETS	0.972	0.883	1	0.324	0.294	0.356	INDETERMINATE	1	TRUE	2	0.463730447865156	5		802	1038	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519721	137519721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	102	471	0	ENST00000367739.4:c.917C>T	p.Ser306Leu	p.S306L	ENST00000367739	NM_000416.2	306	tCa/tTa	7/7	1	2	FACETS	0.924	0.831	1	0.924	0.831	1	CLONAL	1	TRUE	1	0.463730447865156	2		471	476	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0022186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	151	916	3	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.329599010572809	2		919	813	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0022186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	69	806	1	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	0.632	0.55	0.72	0.632	0.55	0.72	SUBCLONAL	1	TRUE	1	0.329599010572809	2		807	663	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200151	128200151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	151	928	2	ENST00000341105.2:c.1154C>T	p.Pro385Leu	p.P385L	ENST00000341105	NM_032638.4	385	cCa/cTa	6/6	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.329599010572809	2		930	821	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265007	198265007	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	102	608	0	ENST00000335508.6:c.2870G>T	p.Arg957Leu	p.R957L	ENST00000335508	NM_012433.2	957	cGa/cTa	19/25	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.329599010572809	2		608	521	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560451	65560451	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	143	649	1	ENST00000358664.4:c.146C>A	p.Ser49Ter	p.S49*	ENST00000358664	NM_002382.4	49	tCa/tAa	3/5	0.329599010572809	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.329599010572809	1		650	582	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058313	42058313	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	70	548	0	ENST00000219905.7:c.8033G>T	p.Ser2678Ile	p.S2678I	ENST00000219905	NM_001164273.1	2678	aGc/aTc	24/24	1	2	FACETS	0.906	0.792	1	0.906	0.792	1	CLONAL	1	TRUE	1	0.329599010572809	2		548	469	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647077	23647077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	194	1155	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	0.329599010572809	2		1155	1082	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33430565	33430566	+	splice_acceptor_variant,intron_variant	Splice_Site	DNP	TG	TG	AT	novel	NA	P-0022186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	103	740	2	ENST00000345365.6:c.577-3_577-2delinsAT		p.X193_splice	ENST00000345365	NM_002878.3	193			0.145383511067957	3	FACETS	1	0.938	1	0.534	0.478	0.593	INDETERMINATE	1	TRUE	1	0.329599010572809	3		742	682	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39570515	39570515	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	29	511	0	ENST00000262039.4:c.711A>T	p.Glu237Asp	p.E237D	ENST00000262039	NM_002647.2	237	gaA/gaT	6/25	1	2	FACETS	0.421	0.337	0.516	0.421	0.337	0.516	SUBCLONAL	1	TRUE	1	0.329599010572809	2		511	418	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198264996	198264996	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	100	604	0	ENST00000335508.6:c.2881G>T	p.Val961Phe	p.V961F	ENST00000335508	NM_012433.2	961	Gtc/Ttc	19/25	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.329599010572809	2		604	507	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265019	198265019	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	108	628	0	ENST00000335508.6:c.2858A>C	p.Asp953Ala	p.D953A	ENST00000335508	NM_012433.2	953	gAc/gCc	19/25	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.329599010572809	2		628	556	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179414	56179414	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	122	529	0	ENST00000399503.3:c.3727T>C	p.Trp1243Arg	p.W1243R	ENST00000399503	NM_005921.1	1243	Tgg/Cgg	15/20	0.145383511067957	3	FACETS	0.834	0.757	0.914	0.834	0.757	0.914	INDETERMINATE	2	TRUE	1	0.329599010572809	3		529	517	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044499	47044499	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0022186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	144	967	0	ENST00000377604.3:c.1996A>T	p.Lys666Ter	p.K666*	ENST00000377604	NM_001204468.1	666	Aaa/Taa	18/24	1	2	FACETS	0.988	0.901	1	0.988	0.901	1	CLONAL	1	TRUE	1	0.329599010572809	2		967	884	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958118	54958118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	134	578	0	ENST00000312783.6:c.489del	p.Leu164TyrfsTer19	p.L164Yfs*19	ENST00000312783	NM_198436.1	163	gtG/gt	6/10	1	2	FACETS	0.811	0.741	0.885	0.811	0.741	0.885	CLONAL	1	TRUE	1	0.604918680491193	2		578	546	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0022190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	59	534	1	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.948	1	1	0.981	1	CLONAL	2	TRUE	1	0.1	2		535	484	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0022190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	54	733	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.896	0.764	1	1	0.973	1	CLONAL	2	TRUE	1	0.1	2		733	603	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0022190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	53	623	0	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	1	2	FACETS	0.759	0.646	0.883	1	0.965	1	SUBCLONAL	2	TRUE	1	0.1	2		623	698	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412095	63412095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852217	NA	P-0022190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	98	1105	0	ENST00000330258.3:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000330258	NM_152424.3	358	Cga/Tga	2/2	1	2	FACETS	0.836	0.744	0.935	1	0.983	1	CLONAL	2	TRUE	1	0.1	2		1105	1172	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0022193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	65	857	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.61584796220255	3	FACETS	0.244	0.21	0.28	0.122	0.105	0.14	SUBCLONAL	1	TRUE	1	0.61584796220255	3		857	1133	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153691	55153691	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	48	578	0	ENST00000257290.5:c.2657G>T	p.Trp886Leu	p.W886L	ENST00000257290	NM_006206.4	886	tGg/tTg	19/23	1	2	FACETS	0.857	0.723	1	0.857	0.723	1	CLONAL	1	TRUE	1	0.16	2		578	700	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100938	27100938	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	36	485	0	ENST00000324856.7:c.4220C>A	p.Pro1407Gln	p.P1407Q	ENST00000324856	NM_006015.4	1407	cCa/cAa	18/20	1	2	FACETS	0.783	0.642	0.941	0.783	0.642	0.941	CLONAL	1	TRUE	1	0.16	2		485	575	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813286	102813286	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0022195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	30	449	0	ENST00000307046.8:c.402+1G>T		p.X134_splice	ENST00000307046	NM_001111285.1	134			1	2	FACETS	0.781	0.629	0.955	0.781	0.629	0.955	CLONAL	1	TRUE	1	0.16	2		449	480	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443697	29443697	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs281864719	NA	P-0022195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	56	568	0	ENST00000389048.3:c.3520T>C	p.Phe1174Leu	p.F1174L	ENST00000389048	NM_004304.4	1174	Ttc/Ctc	23/29	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.16	2		568	667	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793742	89793742	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	45	493	1	ENST00000336032.3:c.811A>T	p.Thr271Ser	p.T271S	ENST00000336032	NM_006813.2	271	Act/Tct	2/2	1	2	FACETS	0.973	0.817	1	0.973	0.817	1	CLONAL	1	TRUE	1	0.16	2		494	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0022196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	367	875	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.609677824805319	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.609677824805319	1		877	814	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	232	669	0				ENST00000310581	NM_198253.2	-/1132			0.334339031507296	1	FACETS	0.742	0.695	0.79	0.742	0.695	0.79	INDETERMINATE	1	TRUE	0	0.609677824805319	1		669	713	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0022196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	535	710	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.609677824805319	3	FACETS	0.981	0.944	1	0.981	0.944	1	CLONAL	2	TRUE	1	0.609677824805319	3		711	1167	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913534	39913535	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0022196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	318	445	0	ENST00000378444.4:c.4792_4793dup	p.Trp1598CysfsTer21	p.W1598Cfs*21	ENST00000378444	NM_001123385.1	1598	tgg/tgTGg	13/15	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.609677824805319	1		445	575	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106058	8106058	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	205	646	0	ENST00000346208.3:c.878T>A	p.Met293Lys	p.M293K	ENST00000346208		293	aTg/aAg	4/6	0.330431162280602	2	FACETS	0.752	0.701	0.805	0.752	0.701	0.805	SUBCLONAL	2	TRUE	0	0.401324209128956	2		646	679	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794494	242794494	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	115	835	0	ENST00000334409.5:c.448G>C	p.Glu150Gln	p.E150Q	ENST00000334409	NM_005018.2	150	Gaa/Caa	3/5	NA	2	FACETS	0.737	0.664	0.814			1	INDETERMINATE	1	TRUE	NA	0.401324209128956	2		835	778	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274121	10274121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	35	720	0	ENST00000330684.3:c.148G>A	p.Glu50Lys	p.E50K	ENST00000330684	NM_001134407.1	50	Gaa/Aaa	2/13	1	2	FACETS	0.332	0.271	0.4	0.332	0.271	0.4	SUBCLONAL	1	TRUE	1	0.401324209128956	2		720	526	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11181402	11181402	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	120	835	0	ENST00000361445.4:c.6834G>C	p.Leu2278Phe	p.L2278F	ENST00000361445	NM_004958.3	2278	ttG/ttC	49/58	1	2	FACETS	0.916	0.829	1	0.916	0.829	1	CLONAL	1	TRUE	1	0.401324209128956	2		835	653	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307165	65307165	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	35	541	0	ENST00000342505.4:c.2523C>G	p.Ile841Met	p.I841M	ENST00000342505	NM_002227.2	841	atC/atG	18/25	1	2	FACETS	0.333	0.272	0.401	0.333	0.272	0.401	SUBCLONAL	1	TRUE	1	0.401324209128956	2		541	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578445	7578450	+	inframe_deletion	In_Frame_Del	DEL	ATGGCC	ATGGCC	-	novel	NA	P-0022231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	137	843	0	ENST00000269305.4:c.480_485del	p.Met160_Ala161del	p.M160_A161del	ENST00000269305	NM_001126112.2	160	atGGCCATc/atc	5/11	0.380144960861035	1	FACETS	0.786	0.717	0.859	0.786	0.717	0.859	SUBCLONAL	1	TRUE	0	0.401324209128956	1		843	694	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762481	41762481	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	35	582	0	ENST00000301178.4:c.2161C>G	p.Leu721Val	p.L721V	ENST00000301178	NM_021913.4	721	Cta/Gta	18/20	1	2	FACETS	0.311	0.254	0.375	0.311	0.254	0.375	SUBCLONAL	1	TRUE	1	0.401324209128956	2		582	561	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027227	48027227	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63751419	NA	P-0022231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	28	538	0	ENST00000234420.5:c.2105C>T	p.Ser702Leu	p.S702L	ENST00000234420	NM_000179.2	702	tCa/tTa	4/10	1	2	FACETS	0.264	0.21	0.326	0.264	0.21	0.326	SUBCLONAL	1	TRUE	1	0.401324209128956	2		538	528	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921404	178921404	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	44	750	0	ENST00000263967.3:c.886C>G	p.Gln296Glu	p.Q296E	ENST00000263967	NM_006218.2	296	Caa/Gaa	5/21	1	2	FACETS	0.387	0.324	0.457	0.387	0.324	0.457	SUBCLONAL	1	TRUE	1	0.401324209128956	2		750	566	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562347	176562347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	49	770	0	ENST00000439151.2:c.243G>A	p.Met81Ile	p.M81I	ENST00000439151	NM_022455.4	81	atG/atA	2/23	0.16441930323765	2	FACETS	0.326	0.275	0.382	0.163	0.137	0.191	INDETERMINATE	1	TRUE	0	0.401324209128956	2		770	749	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562849	176562849	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	46	663	0	ENST00000439151.2:c.745G>T	p.Glu249Ter	p.E249*	ENST00000439151	NM_022455.4	249	Gaa/Taa	2/23	0.16441930323765	2	FACETS	0.311	0.261	0.367	0.156	0.13	0.184	INDETERMINATE	1	TRUE	0	0.401324209128956	2		663	736	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552870	106552870	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	1353	844	0	ENST00000369096.4:c.835G>C	p.Asp279His	p.D279H	ENST00000369096	NM_001198.3	279	Gac/Cac	5/7	0.401324209128956	10	FACETS	1	0.993	1			1	CLONAL	8	TRUE	NA	0.401324209128956	10		844	2131	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129319	152129319	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1417351665	NA	P-0022231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	53	634	0	ENST00000206249.3:c.272C>G	p.Ser91Cys	p.S91C	ENST00000206249	NM_000125.3	91	tCc/tGc	1/8	0.322834098410286	1	FACETS	0.382	0.326	0.444	0.382	0.326	0.444	SUBCLONAL	1	TRUE	0	0.401324209128956	1		634	552	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913151	39913151	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	22	429	0	ENST00000378444.4:c.4964C>G	p.Ser1655Cys	p.S1655C	ENST00000378444	NM_001123385.1	1655	tCt/tGt	14/15	0.29362000946591	1	FACETS	0.223	0.172	0.282	0.223	0.172	0.282	SUBCLONAL	1	TRUE	0	0.401324209128956	1		429	393	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922945	39922945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	73	814	0	ENST00000378444.4:c.3763G>A	p.Glu1255Lys	p.E1255K	ENST00000378444	NM_001123385.1	1255	Gag/Aag	8/15	0.29362000946591	1	FACETS	0.397	0.346	0.451	0.397	0.346	0.451	SUBCLONAL	1	TRUE	0	0.401324209128956	1		814	733	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0022237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	565	931	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	0.486726878429997	3	FACETS	1	0.997	1	0.733	0.704	0.762	CLONAL	1	TRUE	1	0.713870508575803	3		931	1466	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599332	55599332	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519710	NA	P-0022237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1179	194	724	1	ENST00000288135.5:c.2458G>T	p.Asp820Tyr	p.D820Y	ENST00000288135	NM_000222.2	820	Gat/Tat	17/21	0.486726878429997	3	FACETS	0.537	0.496	0.581	0.269	0.247	0.291	SUBCLONAL	1	TRUE	1	0.713870508575803	3		725	1373	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	301	669	0				ENST00000310581	NM_198253.2	-/1132			0.338836798829097	1	FACETS	0.599	0.569	0.628	0.599	0.569	0.628	INDETERMINATE	1	TRUE	0	0.900438622916304	1		669	614	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699369	47699369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	428	462	0	ENST00000347630.2:c.139G>A	p.Glu47Lys	p.E47K	ENST00000347630	NM_001007230.1	47	Gaa/Aaa	4/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.900438622916304	2		462	941	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755470	39755470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	188	447	1	ENST00000288319.7:c.1295C>T	p.Ala432Val	p.A432V	ENST00000288319	NM_182918.3	432	gCg/gTg	10/10	1	2	FACETS	0.504	0.466	0.543	0.504	0.466	0.543	SUBCLONAL	1	TRUE	1	0.900438622916304	2		448	829	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426736	49426771	+	inframe_deletion	In_Frame_Del	DEL	GCTGCTGCTGCTGCTGAAGTTGCTGTTGCTGTTGCA	GCTGCTGCTGCTGCTGAAGTTGCTGTTGCTGTTGCA	-	rs1415174573	NA	P-0022240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	100	211	0	ENST00000301067.7:c.11717_11752del	p.Leu3906_Gln3917del	p.L3906_Q3917del	ENST00000301067	NM_003482.3	3906	cTGCAACAGCAACAGCAACTTCAGCAGCAGCAGCAGCag/cag	39/54	0.543977637495195	3	FACETS	0.734	0.659	0.812	0.367	0.329	0.406	SUBCLONAL	1	TRUE	1	0.900438622916304	3		211	439	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90634876	90634876	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	187	420	0	ENST00000330062.3:c.116A>G	p.Tyr39Cys	p.Y39C	ENST00000330062	NM_002168.2	39	tAt/tGt	2/11	0.441848381075117	1	FACETS	0.332	0.308	0.358	0.332	0.308	0.358	INDETERMINATE	1	TRUE	0	0.900438622916304	1		420	687	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0022241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	225	847	1	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.552354452794538	1	FACETS	0.98	0.919	1	0.98	0.919	1	CLONAL	1	TRUE	0	0.552354452794538	1		848	602	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs149680468	NA	P-0022241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	79	583	0	ENST00000281708.4:c.1513C>A	p.Arg505Ser	p.R505S	ENST00000281708	NM_033632.3	505	Cgc/Agc	10/12	0.552354452794538	1	FACETS	0.635	0.563	0.711	0.635	0.563	0.711	SUBCLONAL	1	TRUE	0	0.552354452794538	1		583	326	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28600614	28600614	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	225	864	1	ENST00000253063.3:c.965G>T	p.Gly322Val	p.G322V	ENST00000253063	NM_031459.4	322	gGa/gTa	7/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.552354452794538	2		865	752	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175898	176175898	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	40	167	1	ENST00000367669.3:c.217G>C	p.Ala73Pro	p.A73P	ENST00000367669	NM_022457.5	73	Gcc/Ccc	1/20	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.552354452794538	2		168	132	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347549	89347549	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	36	785	1	ENST00000301030.4:c.5401G>T	p.Glu1801Ter	p.E1801*	ENST00000301030	NM_001256183.1	1801	Gaa/Taa	9/13	1	2	FACETS	0.209	0.171	0.252	0.209	0.171	0.252	SUBCLONAL	1	TRUE	1	0.552354452794538	2		786	623	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659943	227659944	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0022241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	184	825	2	ENST00000305123.5:c.3511_3512delinsTT	p.Gly1171Leu	p.G1171L	ENST00000305123	NM_005544.2	1171	GGg/TTg	1/2	1	2	FACETS	0.918	0.85	0.988	0.918	0.85	0.988	CLONAL	1	TRUE	1	0.552354452794538	2		827	726	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518243	187518243	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	116	392	0	ENST00000441802.2:c.12451T>G	p.Cys4151Gly	p.C4151G	ENST00000441802	NM_005245.3	4151	Tgc/Ggc	25/27	0.552354452794538	1	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	0	0.552354452794538	1		392	304	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945316	151945316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	14	66	0	ENST00000262189.6:c.2203G>A	p.Gly735Arg	p.G735R	ENST00000262189	NM_170606.2	735	Gga/Aga	14/59	1	2	FACETS	0.611	0.449	0.799	0.611	0.449	0.799	SUBCLONAL	1	TRUE	1	0.552354452794538	2		66	83	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891249	101891249	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	270	706	0	ENST00000374994.4:c.210G>C	p.Met70Ile	p.M70I	ENST00000374994	NM_004612.2	70	atG/atC	2/9	0.552354452794538	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.552354452794538	1		706	542	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969392	44969393	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CC	CC	-	novel	NA	P-0022241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	129	424	0	ENST00000377967.4:c.4074_4075del	p.Cys1358Ter	p.C1358*	ENST00000377967	NM_021140.2	1358	tgCCaa/tgaa	28/29	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.552354452794538	1		424	265	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	253	669	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.898304544614347	2		669	550	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947596	48947596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1566196458	NA	P-0022244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	115	576	0	ENST00000267163.4:c.1183C>T	p.Gln395Ter	p.Q395*	ENST00000267163	NM_000321.2	395	Caa/Taa	12/27	0.876913948813505	1	FACETS	0.934	0.882	0.983	0.934	0.882	0.983	CLONAL	1	TRUE	0	0.898304544614347	1		576	151	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743864	41743864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753706427	NA	P-0022244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	370	689	0	ENST00000301178.4:c.799G>A	p.Asp267Asn	p.D267N	ENST00000301178	NM_021913.4	267	Gat/Aat	7/20	0.880477053581545	3	FACETS	0.964	0.915	1	0.482	0.457	0.508	CLONAL	1	TRUE	1	0.898304544614347	3		689	1238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0022244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	512	1488	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	1	2	FACETS	0.999	0.96	1	0.999	0.96	1	CLONAL	1	TRUE	1	0.898304544614347	2		1488	1141	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579331	7579331	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	343	620	0	ENST00000269305.4:c.356C>G	p.Ala119Gly	p.A119G	ENST00000269305	NM_001126112.2	119	gCc/gGc	4/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.898304544614347	2		620	758	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368239	45368239	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	243	630	0	ENST00000262160.6:c.1363C>T	p.Gln455Ter	p.Q455*	ENST00000262160	NM_005901.5	455	Cag/Tag	11/11	1	2	FACETS	0.936	0.882	0.991	0.936	0.882	0.991	CLONAL	1	TRUE	1	0.898304544614347	2		630	578	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870853	12870853	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	134	246	0	ENST00000228872.4:c.80C>A	p.Ser27Ter	p.S27*	ENST00000228872	NM_004064.3	27	tCg/tAg	1/3	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.898304544614347	2		246	298	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163313556	163313556	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	117	463	1	ENST00000271452.3:c.703G>T	p.Glu235Ter	p.E235*	ENST00000271452	NM_145697.2	235	Gaa/Taa	10/14	1	2	FACETS	0.857	0.784	0.931	0.857	0.784	0.931	CLONAL	1	TRUE	1	0.898304544614347	2		464	304	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226002	133226002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753514393	NA	P-0022244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	417	902	1	ENST00000320574.5:c.3895G>A	p.Glu1299Lys	p.E1299K	ENST00000320574	NM_006231.2	1299	Gag/Aag	31/49	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.898304544614347	2		903	921	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871860	12871860	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs73281150	NA	P-0022244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	166	264	0	ENST00000228872.4:c.577C>A	p.Leu193Ile	p.L193I	ENST00000228872	NM_004064.3	193	Ctc/Atc	2/3	1	2	FACETS	0.922	0.857	0.987	0.922	0.857	0.987	CLONAL	1	TRUE	1	0.898304544614347	2		264	401	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219234	133219234	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	308	694	1	ENST00000320574.5:c.4810G>T	p.Glu1604Ter	p.E1604*	ENST00000320574	NM_006231.2	1604	Gag/Tag	37/49	1	2	FACETS	0.934	0.886	0.983	0.934	0.886	0.983	CLONAL	1	TRUE	1	0.898304544614347	2		695	734	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906684	32906684	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	180	523	1	ENST00000380152.3:c.1069G>T	p.Glu357Ter	p.E357*	ENST00000380152		357	Gaa/Taa	10/27	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.898304544614347	2		524	387	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918141	50918141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753609023	NA	P-0022244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	429	772	1	ENST00000440232.2:c.2458G>A	p.Ala820Thr	p.A820T	ENST00000440232	NM_002691.3	820	Gcc/Acc	20/27	0.880477053581545	3	FACETS	1	0.987	1	0.544	0.519	0.57	CLONAL	1	TRUE	1	0.898304544614347	3		773	1272	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827885	40827885	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	1182	588	0	ENST00000373198.4:c.2543G>T	p.Gly848Val	p.G848V	ENST00000373198	NM_133170.3	848	gGa/gTa	17/32	0.898304544614347	5	FACETS	0.971	0.954	0.988	0.971	0.954	0.988	CLONAL	4	TRUE	1	0.898304544614347	5		588	1590	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994146	21994146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	368	673	0	ENST00000579755.1:c.185G>A	p.Arg62Lys	p.R62K	ENST00000579755		62	aGa/aAa	1/3	1		FACETS		0.932	1				CLONAL	1	TRUE	1	0.898304544614347	2		673	838	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579366	7579366	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0022283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	190	746	0	ENST00000269305.4:c.321C>G	p.Tyr107Ter	p.Y107*	ENST00000269305	NM_001126112.2	107	taC/taG	4/11	0.379297014540089	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.379297014540089	1		746	804	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222982	1222982	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs727504172	NA	P-0022283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	268	558	1	ENST00000326873.7:c.921-2A>T		p.X307_splice	ENST00000326873	NM_000455.4	307			0.358421795086123	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.379297014540089	2		559	671	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281778	39281778	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519963	NA	P-0022283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	75	633	0	ENST00000402219.2:c.697A>T	p.Asn233Tyr	p.N233Y	ENST00000402219	NM_005633.3	233	Aat/Tat	5/23	1	2	FACETS	0.81	0.712	0.916	0.81	0.712	0.916	CLONAL	1	TRUE	1	0.379297014540089	2		633	488	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248397	59248397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	99	397	1	ENST00000371222.2:c.346C>T	p.Arg116Cys	p.R116C	ENST00000371222	NM_002228.3	116	Cgc/Tgc	1/1	1	2	FACETS	0.985	0.882	1	0.985	0.882	1	CLONAL	1	TRUE	1	0.379297014540089	2		398	530	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180599	94180599	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	85	478	0	ENST00000323929.3:c.1569G>T	p.Met523Ile	p.M523I	ENST00000323929	NM_005591.3	523	atG/atT	15/20	0.268923004819736	1	FACETS	0.824	0.731	0.921	0.824	0.731	0.921	CLONAL	1	TRUE	0	0.379297014540089	1		478	441	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870945	12870977	+	inframe_deletion	In_Frame_Del	DEL	CGCAAGTGGAATTTCGATTTTCAGAATCACAAA	CGCAAGTGGAATTTCGATTTTCAGAATCACAAA	-	novel	NA	P-0022283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	68	325	0	ENST00000228872.4:c.173_205del	p.Arg58_Lys68del	p.R58_K68del	ENST00000228872	NM_004064.3	58	CGCAAGTGGAATTTCGATTTTCAGAATCACAAA/-	1/3	0.379297014540089	1	FACETS	0.867	0.76	0.982	0.867	0.76	0.982	CLONAL	1	TRUE	0	0.379297014540089	1		325	335	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003734	45003748	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	TTCGGGCCGAGATGT	TTCGGGCCGAGATGT	-	novel	NA	P-0022283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	464	85	0	ENST00000558401.1:c.-11_4del		p.*4*	ENST00000558401	NM_004048.2	?-2/119		1/4	0.379297014540089	1	FACETS	1	0.995	1	1	0.998	1	CLONAL	2	TRUE	0	0.379297014540089	1		85	824	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714651	52714651	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	171	711	1	ENST00000322088.6:c.409G>T	p.Gly137Cys	p.G137C	ENST00000322088	NM_014225.5	137	Ggc/Tgc	4/15	NA	2	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.379297014540089	2		712	820	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010475	48010475	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	155	610	0	ENST00000234420.5:c.103G>T	p.Ala35Ser	p.A35S	ENST00000234420	NM_000179.2	35	Gcc/Tcc	1/10	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.379297014540089	2		610	794	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415121	116415121	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	153	646	2	ENST00000397752.3:c.3215G>T	p.Gly1072Val	p.G1072V	ENST00000397752	NM_000245.2	1072	gGg/gTg	15/21	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.379297014540089	2		648	771	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759407	133759407	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	173	746	1	ENST00000318560.5:c.1730G>T	p.Arg577Leu	p.R577L	ENST00000318560	NM_005157.4	577	cGa/cTa	11/11	1	2	FACETS	0.96	0.884	1	0.96	0.884	1	CLONAL	1	TRUE	1	0.379297014540089	2		747	950	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4388007	4388007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775067994	NA	P-0022286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	78	482	1	ENST00000261254.3:c.493C>T	p.Arg165Cys	p.R165C	ENST00000261254	NM_001759.3	165	Cgc/Tgc	3/5	NA	2	FACETS	0.94	0.829	1			1	INDETERMINATE	1	TRUE	NA	0.368118394396532	2		483	451	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574381	95574381	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	45	293	0	ENST00000393063.1:c.2486T>G	p.Ile829Ser	p.I829S	ENST00000393063	NM_030621.3	829	aTt/aGt	17/28	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.368118394396532	2		293	223	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	495	1047	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.190409856829753	10	FACETS	0.964	0.924	1			1	CLONAL	8	TRUE	NA	0.190409856829753	10		1049	1188	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044965	47044966	+	missense_variant	Missense_Mutation	DNP	GC	GC	AT	novel	NA	P-0022290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	162	994	4	ENST00000377604.3:c.2291_2292delinsAT	p.Cys764Tyr	p.C764Y	ENST00000377604	NM_001204468.1	764	tGC/tAT	20/24	0.190409856829753	3	FACETS	0.805	0.737	0.877	0.805	0.737	0.877	CLONAL	2	TRUE	1	0.190409856829753	3		998	1157	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	71	669	0				ENST00000310581	NM_198253.2	-/1132			0.3	0	FACETS	0.877	0.785	0.969			1	CLONAL	4	TRUE	0	0.2	0		669	162	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0022293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	102	710	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.907	0.824	0.993	1	0.991	1	CLONAL	4	TRUE	1	0.2	2		711	281	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175836	24175837	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555881563	NA	P-0022293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	93	642	0	ENST00000263121.7:c.1066_1067del	p.Leu356AspfsTer4	p.L356Dfs*4	ENST00000263121	NM_003073.3	355	aCT/a	8/9	1	2	FACETS	1	0.954	1	1	0.99	1	CLONAL	3	TRUE	1	0.2	2		642	281	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880473	155880473	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	129	652	1	ENST00000368323.3:c.80T>A	p.Leu27Gln	p.L27Q	ENST00000368323	NM_006912.5	27	cTg/cAg	2/6	0.127777176718053	3	FACETS	0.885	0.81	0.962	1	0.989	1	CLONAL	4	TRUE	1	0.2	3		653	401	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366956	40366956	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	95	838	0	ENST00000397332.2:c.241G>C	p.Ala81Pro	p.A81P	ENST00000397332	NM_001033082.2	81	Gca/Cca	2/3	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.267070104271187	2		838	588	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120502102	120502102	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	32	666	0	ENST00000256646.2:c.1939G>C	p.Asp647His	p.D647H	ENST00000256646	NM_024408.3	647	Gat/Cat	12/34	1	2	FACETS	0.393	0.318	0.479	0.393	0.318	0.479	SUBCLONAL	1	TRUE	1	0.267070104271187	2		666	609	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0022301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	191	960	2	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.195751159591098	2	FACETS	0.765	0.707	0.825	0.765	0.707	0.825	SUBCLONAL	2	TRUE	0	0.267070104271187	2		962	935	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685621	29685621	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0022301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	53	652	1	ENST00000356175.3:c.8031C>G	p.Tyr2677Ter	p.Y2677*	ENST00000356175	NM_000267.3	2677	taC/taG	54/57	0.195751159591098	2	FACETS	1	0.948	1	0.622	0.533	0.718	CLONAL	1	TRUE	0	0.267070104271187	2		653	319	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098575	11098575	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	97	1098	1	ENST00000358026.2:c.1093G>T	p.Glu365Ter	p.E365*	ENST00000358026	NM_001128849.1	365	Gag/Tag	6/36	0.267070104271187	1	FACETS	0.746	0.664	0.833	0.746	0.664	0.833	SUBCLONAL	1	TRUE	0	0.267070104271187	1		1099	844	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15280933	15280933	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	134	1126	2	ENST00000263388.2:c.5163G>A	p.Trp1721Ter	p.W1721*	ENST00000263388	NM_000435.2	1721	tgG/tgA	28/33	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.267070104271187	2		1128	1003	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943426	17943426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	169	980	0	ENST00000458235.1:c.2582G>A	p.Gly861Glu	p.G861E	ENST00000458235	NM_000215.3	861	gGg/gAg	19/24	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.267070104271187	2		980	899	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278071	18278071	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	168	1068	0	ENST00000222254.8:c.1691A>G	p.Lys564Arg	p.K564R	ENST00000222254	NM_005027.3	564	aAg/aGg	13/16	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.267070104271187	2		1068	966	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229381	36229381	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	98	711	0	ENST00000222270.7:c.8071A>G	p.Lys2691Glu	p.K2691E	ENST00000222270	NM_014727.1	2691	Aag/Gag	37/37	0.0841629998774338	3	FACETS	1	0.967	1	0.605	0.54	0.674	INDETERMINATE	1	TRUE	1	0.267070104271187	3		711	688	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670292	134670292	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	43	495	0	ENST00000398015.3:c.203A>C	p.Gln68Pro	p.Q68P	ENST00000398015	NM_004441.4	68	cAg/cCg	3/16	0.267070104271187	2	FACETS	0.54	0.451	0.639	0.27	0.225	0.32	SUBCLONAL	1	TRUE	0	0.267070104271187	2		495	596	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461570	138461570	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0022301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	45	641	2	ENST00000289153.2:c.451A>T	p.Lys151Ter	p.K151*	ENST00000289153	NM_006219.2	151	Aaa/Taa	3/22	0.267070104271187	2	FACETS	0.757	0.637	0.89	0.379	0.318	0.445	SUBCLONAL	1	TRUE	0	0.267070104271187	2		643	445	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55524203	55524203	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	44	743	0	ENST00000288135.5:c.22T>C	p.Trp8Arg	p.W8R	ENST00000288135	NM_000222.2	8	Tgg/Cgg	1/21	1	2	FACETS	0.495	0.414	0.585	0.495	0.414	0.585	SUBCLONAL	1	TRUE	1	0.267070104271187	2		743	666	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594203	55594203	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	38	474	2	ENST00000288135.5:c.1906G>T	p.Ala636Ser	p.A636S	ENST00000288135	NM_000222.2	636	Gcc/Tcc	13/21	1	2	FACETS	0.668	0.552	0.797	0.668	0.552	0.797	SUBCLONAL	1	TRUE	1	0.267070104271187	2		476	426	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106194073	106194073	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	40	335	0	ENST00000380013.4:c.4535C>T	p.Ala1512Val	p.A1512V	ENST00000380013	NM_001127208.2	1512	gCa/gTa	10/11	1	2	FACETS	0.948	0.791	1	0.948	0.791	1	CLONAL	1	TRUE	1	0.267070104271187	2		335	316	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31401657	31401658	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	52	526	0	ENST00000344624.3:c.4006_4007insT	p.Gln1336LeufsTer33	p.Q1336Lfs*33	ENST00000344624		1336	cag/cTag	33/33	0.267070104271187	3	FACETS	0.897	0.764	1	0.449	0.382	0.521	CLONAL	1	TRUE	1	0.267070104271187	3		526	492	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564752	86564753	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGA	novel	NA	P-0022301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	109	805	0	ENST00000274376.6:c.485_488dup	p.Glu163AspfsTer18	p.E163Dfs*18	ENST00000274376	NM_002890.2	162	cca/cCAGAca	1/25	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.267070104271187	2		805	799	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522591	176522591	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	113	943	1	ENST00000292408.4:c.1688G>C	p.Arg563Pro	p.R563P	ENST00000292408	NM_213647.1	563	cGg/cCg	13/18	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.267070104271187	2		944	751	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109314049	109314049	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	44	672	0	ENST00000436639.2:c.1174A>C	p.Ser392Arg	p.S392R	ENST00000436639	NM_014454.2	392	Agt/Cgt	7/10	1	2	FACETS	0.779	0.654	0.917	0.779	0.654	0.917	CLONAL	1	TRUE	1	0.267070104271187	2		672	423	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477849	140477849	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	55	724	0	ENST00000288602.6:c.1459G>C	p.Val487Leu	p.V487L	ENST00000288602	NM_004333.4	487	Gtg/Ctg	12/18	0.182466784087273	5	FACETS	1	0.962	1	0.469	0.402	0.542	CLONAL	1	TRUE	2	0.267070104271187	5		724	410	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151850033	151850033	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	66	331	0	ENST00000262189.6:c.12283A>T	p.Ser4095Cys	p.S4095C	ENST00000262189	NM_170606.2	4095	Agc/Tgc	49/59	0.182466784087273	5	FACETS	0.956	0.835	1	0.637	0.556	0.724	CLONAL	2	TRUE	2	0.267070104271187	5		331	362	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29195901	29195901	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	58	966	0	ENST00000240100.2:c.697C>G	p.Pro233Ala	p.P233A	ENST00000240100	NM_001394.6	233	Cca/Gca	3/4	0.260180364456263	1	FACETS	0.393	0.337	0.455	0.393	0.337	0.455	SUBCLONAL	1	TRUE	0	0.267070104271187	1		966	957	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	63	669	0				ENST00000310581	NM_198253.2	-/1132			0.357392847109767	3	FACETS	0.896	0.776	1	0.448	0.388	0.512	CLONAL	1	TRUE	1	0.357392847109767	3		669	464	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0022302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	482	785	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.341857206542154	4	FACETS	0.896	0.86	0.931	0.896	0.86	0.931	CLONAL	4	TRUE	0	0.357392847109767	4		786	1022	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311619	15311621	+	inframe_deletion	In_Frame_Del	DEL	AGC	AGC	-	rs746497955	NA	P-0022302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	13	133	0	ENST00000263388.2:c.96_98del	p.Leu33del	p.L33del	ENST00000263388	NM_000435.2	32	ctGCTa/cta	1/33	0.260950562322686	4	FACETS	0.581	0.415	0.781	0.29	0.207	0.391	SUBCLONAL	1	TRUE	2	0.357392847109767	4		133	170	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208051	5208051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1477222866	NA	P-0022302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	91	663	1	ENST00000357368.4:c.5660C>T	p.Thr1887Met	p.T1887M	ENST00000357368	NM_002850.3	1887	aCg/aTg	37/38	0.260950562322686	4	FACETS	1	0.969	1	0.625	0.556	0.698	CLONAL	1	TRUE	2	0.357392847109767	4		664	553	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133729537	133729537	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	79	729	1	ENST00000318560.5:c.166G>T	p.Ala56Ser	p.A56S	ENST00000318560	NM_005157.4	56	Gct/Tct	2/11	0.260950562322686	4	FACETS	0.598	0.524	0.677	0.299	0.262	0.339	SUBCLONAL	1	TRUE	2	0.357392847109767	4		730	1004	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288526	15288526	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	51	236	0	ENST00000263388.2:c.4213T>G	p.Cys1405Gly	p.C1405G	ENST00000263388	NM_000435.2	1405	Tgc/Ggc	24/33	0.260950562322686	4	FACETS	0.918	0.79	1	0.918	0.79	1	CLONAL	2	TRUE	2	0.357392847109767	4		236	211	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21968242	21968242	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0022302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	196	509	0	ENST00000304494.5:c.458-1G>A		p.X153_splice	ENST00000304494	NM_000077.4	153			0.260950562322686	4	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	2	0.357392847109767	4		509	702	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412663	139412663	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1368532867	NA	P-0022302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	363	1041	1	ENST00000277541.6:c.1181G>T	p.Gly394Val	p.G394V	ENST00000277541	NM_017617.3	394	gGc/gTc	7/34	0.260950562322686	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	2	0.357392847109767	4		1042	1204	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413064	139413064	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	170	642	0	ENST00000277541.6:c.1078G>T	p.Glu360Ter	p.E360*	ENST00000277541	NM_017617.3	360	Gag/Tag	6/34	0.260950562322686	4	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	2	0.357392847109767	4		642	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577567	7577567	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920789	NA	P-0022307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	127	789	0	ENST00000269305.4:c.714T>G	p.Cys238Trp	p.C238W	ENST00000269305	NM_001126112.2	238	tgT/tgG	7/11	0.197870436114732	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.23	2		789	459	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256750	16256750	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760134992	NA	P-0022307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	116	653	0	ENST00000375759.3:c.4015C>T	p.Arg1339Cys	p.R1339C	ENST00000375759	NM_015001.2	1339	Cgt/Tgt	11/15	0.3	3	FACETS	0.987	0.892	1	0.987	0.892	1	CLONAL	2	TRUE	1	0.23	3		653	570	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344548	118344548	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	50	493	0	ENST00000534358.1:c.2674A>G	p.Lys892Glu	p.K892E	ENST00000534358	NM_005933.3	892	Aaa/Gaa	3/36	0.266865442071881	3	FACETS	1	0.922	1	0.378	0.321	0.441	CLONAL	1	TRUE	0	0.23	3		493	427	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481659	56481659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140656187	NA	P-0022307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	45	799	0	ENST00000267101.3:c.694G>A	p.Ala232Thr	p.A232T	ENST00000267101	NM_001982.3	232	Gcc/Acc	6/28	1	2	FACETS	0.776	0.652	0.913	0.776	0.652	0.913	CLONAL	1	TRUE	1	0.23	2		799	504	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762223	43762225	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs1278069153	NA	P-0022307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	80	810	0	ENST00000382044.4:c.1220_1222del	p.Gly407del	p.G407del	ENST00000382044	NM_001141980.1	407	gGAGag/gag	11/28	0.273913236034497	3	FACETS	1	0.964	1	0.628	0.553	0.708	CLONAL	1	TRUE	1	0.23	3		810	618	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645449	67645450	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0022307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	17	442	0	ENST00000264010.4:c.716_717del	p.Glu239GlyfsTer2	p.E239Gfs*2	ENST00000264010	NM_006565.3	238	tcAGag/tcag	3/12	1	2	FACETS	0.494	0.369	0.644	0.494	0.369	0.644	SUBCLONAL	1	TRUE	1	0.23	2		442	299	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660559	67660559	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	73	675	0	ENST00000264010.4:c.1459A>G	p.Lys487Glu	p.K487E	ENST00000264010	NM_006565.3	487	Aag/Gag	8/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.23	2		675	477	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553591	29553592	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0022307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	100	250	0	ENST00000356175.3:c.2142_2143del	p.Cys714Ter	p.C714*	ENST00000356175	NM_000267.3	714	TGt/t	18/57	0.3	3	FACETS	1	0.951	1			1	CLONAL	3	TRUE	NA	0.23	3		250	299	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220070	5220071	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0022307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	30	803	0	ENST00000357368.4:c.3644_3645del	p.Val1215AlafsTer18	p.V1215Afs*18	ENST00000357368	NM_002850.3	1215	gTG/g	22/38	0.3	1	FACETS	0.629	0.507	0.767	0.629	0.507	0.767	SUBCLONAL	1	TRUE	0	0.23	1		803	367	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262502	10262503	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0022307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	32	748	0	ENST00000340748.4:c.1992_1993del	p.Cys664TrpfsTer4	p.C664Wfs*4	ENST00000340748		664	tgTGgg/tggg	22/40	1	2	FACETS	0.561	0.455	0.682	0.561	0.455	0.682	SUBCLONAL	1	TRUE	1	0.23	2		748	496	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349988	15349988	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775138875	NA	P-0022307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	56	906	2	ENST00000263377.2:c.3664G>A	p.Asp1222Asn	p.D1222N	ENST00000263377	NM_058243.2	1222	Gac/Aac	18/20	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.23	2		908	486	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47612320	47612321	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0022307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	24	613	0	ENST00000263735.4:c.874_875del	p.Lys292GlufsTer6	p.K292Efs*6	ENST00000263735	NM_002354.2	292	AAg/g	8/9	0.3	3	FACETS	0.576	0.451	0.721	0.192	0.15	0.241	SUBCLONAL	1	TRUE	0	0.23	3		613	404	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54948511	54948512	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0022307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	28	517	0	ENST00000312783.6:c.806_807del	p.Glu269AlafsTer2	p.E269Afs*2	ENST00000312783	NM_198436.1	269	gAG/g	8/10	0.3	3	FACETS	0.667	0.533	0.82	0.334	0.266	0.41	SUBCLONAL	1	TRUE	1	0.23	3		517	407	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326461	62326462	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0022307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	68	1093	0	ENST00000360203.5:c.3388_3389del	p.Gln1130AspfsTer56	p.Q1130Dfs*56	ENST00000360203	NM_001283009.1	1129	tCA/t	33/35	0.3	3	FACETS	1	0.928	1	0.55	0.479	0.628	CLONAL	1	TRUE	1	0.23	3		1093	599	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202746	128202746	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	27	913	0	ENST00000341105.2:c.974T>C	p.Met325Thr	p.M325T	ENST00000341105	NM_032638.4	325	aTg/aCg	4/6	NA	2	FACETS	0.517	0.411	0.639			1	INDETERMINATE	1	TRUE	NA	0.23	2		913	454	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80168997	80168997	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	33	853	0	ENST00000265081.6:c.3193G>T	p.Ala1065Ser	p.A1065S	ENST00000265081	NM_002439.4	1065	Gca/Tca	23/24	1	2	FACETS	0.565	0.459	0.684	0.565	0.459	0.684	SUBCLONAL	1	TRUE	1	0.23	2		853	508	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170827847	170827847	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	19	242	0	ENST00000296930.5:c.587T>G	p.Ile196Arg	p.I196R	ENST00000296930	NM_002520.6	196	aTa/aGa	8/11	1	2	FACETS	0.879	0.67	1	0.879	0.67	1	CLONAL	1	TRUE	1	0.23	2		242	188	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983016	149983016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326200282	NA	P-0022307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	31	777	1	ENST00000253339.5:c.3242G>A	p.Arg1081Gln	p.R1081Q	ENST00000253339		1081	cGa/cAa	7/7	1	2	FACETS	0.535	0.432	0.652	0.535	0.432	0.652	SUBCLONAL	1	TRUE	1	0.23	2		778	504	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630146	100630146	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	66	311	0	ENST00000308731.7:c.127G>C	p.Asp43His	p.D43H	ENST00000308731	NM_000061.2	43	Gac/Cac	2/19	0.3	2	FACETS	1	0.885	1			1	CLONAL	2	TRUE	NA	0.23	2		311	284	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	177	669	0				ENST00000310581	NM_198253.2	-/1132			0.239776605452063	5	FACETS	1	0.977	1	1	0.99	1	CLONAL	5	FALSE	1	0.245338653816902	5		669	361	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0022314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	13	532	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	0.217349245706326	3	FACETS	0.26	0.184	0.353	0.13	0.092	0.177	SUBCLONAL	1	FALSE	1	0.245338653816902	3		532	458	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0022314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	320	641	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	0.140883284651979	3	FACETS	1	0.959	1			1	INDETERMINATE	5	FALSE	NA	0.245338653816902	3		641	583	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546721	9546721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	67	353	0	ENST00000353224.5:c.1301C>T	p.Ala434Val	p.A434V	ENST00000353224	NM_177990.2	434	gCg/gTg	5/10	0.157180297083027	4	FACETS	1	0.915	1	1	0.977	1	CLONAL	3	FALSE	2	0.245338653816902	4		353	217	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665041	138665041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	38	231	0	ENST00000330315.3:c.524G>A	p.Gly175Glu	p.G175E	ENST00000330315	NM_023067.3	175	gGg/gAg	1/1	0.157180297083027	4	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	FALSE	2	0.245338653816902	4		231	158	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856356	45856356	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	183	915	0	ENST00000391945.4:c.1816G>C	p.Glu606Gln	p.E606Q	ENST00000391945	NM_000400.3	606	Gag/Cag	19/23	0.245338653816902	5	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	FALSE	2	0.245338653816902	5		915	626	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729940	30729940	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752444160	NA	P-0022314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	131	544	0	ENST00000295754.5:c.1461G>A	p.Met487Ile	p.M487I	ENST00000295754	NM_003242.5	487	atG/atA	6/7	0.157180297083027	4	FACETS	1	0.967	1	1	0.989	1	CLONAL	3	FALSE	2	0.245338653816902	4		544	399	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188049	151188049	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519950	NA	P-0022314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	83	515	0	ENST00000262187.5:c.104A>G	p.Tyr35Cys	p.Y35C	ENST00000262187	NM_005614.3	35	tAc/tGc	2/8	1	2	FACETS	0.992	0.883	1	1	0.985	1	CLONAL	2	FALSE	1	0.245338653816902	2		515	341	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139268	108139268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55723361	NA	P-0022314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	96	944	1	ENST00000278616.4:c.2770C>T	p.Arg924Trp	p.R924W	ENST00000278616	NM_000051.3	924	Cgg/Tgg	18/63	0.191516400168843	2	FACETS	0.831	0.744	0.923	0.831	0.744	0.923	CLONAL	2	FALSE	0	0.245338653816902	2		945	471	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913409	NA	P-0022314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	96	363	0	ENST00000349496.5:c.134C>G	p.Ser45Cys	p.S45C	ENST00000349496	NM_001904.3	45	tCt/tGt	3/15	0.157180297083027	4	FACETS	1	0.95	1	1	0.985	1	CLONAL	3	FALSE	2	0.245338653816902	4		363	299	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481648	56481648	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs774589520	NA	P-0022314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	230	864	0	ENST00000267101.3:c.683A>G	p.His228Arg	p.H228R	ENST00000267101	NM_001982.3	228	cAt/cGt	6/28	0.157180297083027	4	FACETS	0.973	0.914	1	1	0.995	1	CLONAL	4	FALSE	2	0.245338653816902	4		864	600	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0022314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	231	1011	1	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.245338653816902	0	FACETS	0.822	0.778	0.866			1	CLONAL	4	FALSE	0	0.245338653816902	0		1012	432	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471679	120471679	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	42	554	0	ENST00000256646.2:c.3812A>G	p.Asn1271Ser	p.N1271S	ENST00000256646	NM_024408.3	1271	aAc/aGc	23/34	0.217349245706326	3	FACETS	1	0.881	1	0.532	0.445	0.628	CLONAL	1	FALSE	1	0.245338653816902	3		554	361	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982419	201982419	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	189	932	0	ENST00000359651.3:c.798del	p.Ser266ArgfsTer28	p.S266Rfs*28	ENST00000359651		266	agC/ag	6/8	0.245338653816902	6	FACETS	0.952	0.882	1	0.714	0.661	0.769	CLONAL	3	FALSE	2	0.245338653816902	6		932	804	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343199	118343199	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	90	405	0	ENST00000534358.1:c.1325G>C	p.Arg442Pro	p.R442P	ENST00000534358	NM_005933.3	442	cGa/cCa	3/36	0.191516400168843	2	FACETS	0.919	0.828	1	1	0.979	1	CLONAL	3	FALSE	0	0.245338653816902	2		405	266	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038881	12038881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	122	472	0	ENST00000396373.4:c.1174G>A	p.Glu392Lys	p.E392K	ENST00000396373	NM_001987.4	392	Gag/Aag	7/8	0.237597510059748	4	FACETS	0.978	0.892	1	1	0.985	1	CLONAL	3	FALSE	2	0.245338653816902	4		472	422	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486587	56486587	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	199	682	0	ENST00000267101.3:c.1166C>G	p.Thr389Arg	p.T389R	ENST00000267101	NM_001982.3	389	aCa/aGa	10/28	0.157180297083027	4	FACETS	0.917	0.856	0.979	1	0.993	1	CLONAL	4	FALSE	2	0.245338653816902	4		682	551	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489558	56489558	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	153	598	0	ENST00000267101.3:c.2023A>T	p.Arg675Trp	p.R675W	ENST00000267101	NM_001982.3	675	Agg/Tgg	17/28	0.157180297083027	4	FACETS	1	0.963	1	1	0.99	1	CLONAL	3	FALSE	2	0.245338653816902	4		598	482	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495477	56495477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1254014051	NA	P-0022314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	189	736	0	ENST00000267101.3:c.3667G>A	p.Glu1223Lys	p.E1223K	ENST00000267101	NM_001982.3	1223	Gag/Aag	28/28	0.157180297083027	4	FACETS	0.91	0.848	0.974	1	0.993	1	CLONAL	4	FALSE	2	0.245338653816902	4		736	527	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828809	3828824	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCTTGGACGCTGAAA	GGCTTGGACGCTGAAA	-	novel	NA	P-0022314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	150	676	1	ENST00000262367.5:c.1824-6_1833del		p.X608_splice	ENST00000262367	NM_004380.2	608		9/31	0.236798302298613	1	FACETS	0.839	0.775	0.906	1	0.993	1	CLONAL	3	FALSE	0	0.245338653816902	1		677	426	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985815	60985815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	35	616	0	ENST00000333681.4:c.85G>A	p.Glu29Lys	p.E29K	ENST00000333681		29	Gag/Aag	2/3	0.245338653816902	1	FACETS	0.86	0.708	1	0.86	0.708	1	CLONAL	1	FALSE	0	0.245338653816902	1		616	291	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210848	2210855	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CCCCAGGG	CCCCAGGG	-	novel	NA	P-0022314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	89	394	0	ENST00000398665.3:c.1345_1351+1del		p.X449_splice	ENST00000398665	NM_032482.2	449		14/28	0.191516400168843	2	FACETS	0.96	0.873	1	1	0.987	1	CLONAL	4	FALSE	0	0.245338653816902	2		394	189	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18960973	18960973	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	219	850	0	ENST00000262803.5:c.551A>C	p.Tyr184Ser	p.Y184S	ENST00000262803	NM_002911.3	184	tAc/tCc	4/24	0.191516400168843	2	FACETS	1	0.981	1	1	0.994	1	CLONAL	3	FALSE	0	0.245338653816902	2		850	536	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731539	47731539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	18	59	0	ENST00000449228.1:c.253C>T	p.Pro85Ser	p.P85S	ENST00000449228	NM_001127240.2	85	Ccc/Tcc	2/4	0.245338653816902	5	FACETS	1	0.833	1	1	0.916	1	CLONAL	4	FALSE	2	0.245338653816902	5		59	47	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082191	16082191	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs370558211	NA	P-0022314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	122	957	0	ENST00000281043.3:c.5C>G	p.Pro2Arg	p.P2R	ENST00000281043	NM_005378.4	2	cCg/cGg	2/3	0.245338653816902	5	FACETS	0.929	0.841	1	0.62	0.56	0.682	CLONAL	2	FALSE	2	0.245338653816902	5		957	732	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202123021	202123021	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	53	490	0	ENST00000358485.4:c.67C>A	p.Pro23Thr	p.P23T	ENST00000358485	NM_001080125.1	23	Ccc/Acc	1/9	0.236798302298613	1	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	FALSE	0	0.245338653816902	1		490	361	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374915	149374915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772542532	NA	P-0022314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	194	884	0	ENST00000360632.3:c.179C>T	p.Ser60Leu	p.S60L	ENST00000360632	NM_015472.4	60	tCg/tTg	2/7	0.157180297083027	4	FACETS	0.973	0.904	1	1	0.99	1	CLONAL	3	FALSE	2	0.245338653816902	4		884	675	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940638	131940678	+	frameshift_variant	Frame_Shift_Del	DEL	GAGCAGACTGTGGAATTATCCACTGAAGTTCAGTCTTTGTA	GAGCAGACTGTGGAATTATCCACTGAAGTTCAGTCTTTGTA	CAG	novel	NA	P-0022314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	67	586	2	ENST00000265335.6:c.2665_2705delinsCAG	p.Glu889GlnfsTer8	p.E889Qfs*8	ENST00000265335		889	GAGCAGACTGTGGAATTATCCACTGAAGTTCAGTCTTTGTAc/CAGc	16/25	0.217349245706326	3	FACETS	0.811	0.708	0.921	0.811	0.708	0.921	CLONAL	2	FALSE	1	0.245338653816902	3		588	378	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433718	149433718	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	125	875	0	ENST00000286301.3:c.2833G>A	p.Glu945Lys	p.E945K	ENST00000286301	NM_005211.3	945	Gag/Aag	22/22	0.236798302298613	1	FACETS	0.88	0.801	0.962	1	0.989	1	CLONAL	2	FALSE	0	0.245338653816902	1		875	508	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636787	176636787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	100	603	0	ENST00000439151.2:c.1387G>A	p.Asp463Asn	p.D463N	ENST00000439151	NM_022455.4	463	Gat/Aat	5/23	1	2	FACETS	0.941	0.846	1	1	0.987	1	CLONAL	2	FALSE	1	0.245338653816902	2		603	433	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821485	32821485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757941717	NA	P-0022314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	167	820	0	ENST00000354258.4:c.109C>T	p.Arg37Trp	p.R37W	ENST00000354258	NM_000593.5	37	Cgg/Tgg	1/11	0.204521125606028	4	FACETS	0.921	0.855	0.99	1	0.992	1	CLONAL	4	FALSE	2	0.245338653816902	4		820	460	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92462483	92462537	+	frameshift_variant	Frame_Shift_Del	DEL	TCCTCGCCGGTCTGCACCCGCACGCGCTTCAACGCCACGAAACGGCCTCCGTTCT	TCCTCGCCGGTCTGCACCCGCACGCGCTTCAACGCCACGAAACGGCCTCCGTTCT	-	novel	NA	P-0022314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	54	719	0	ENST00000265734.4:c.101_155del	p.Lys34ArgfsTer14	p.K34Rfs*14	ENST00000265734	NM_001259.6	34	aAGAACGGAGGCCGTTTCGTGGCGTTGAAGCGCGTGCGGGTGCAGACCGGCGAGGAg/ag	2/8	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	FALSE	1	0.245338653816902	2		719	432	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508872	106508872	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	16	435	0	ENST00000359195.3:c.866A>T	p.Asn289Ile	p.N289I	ENST00000359195	NM_002649.2	289	aAc/aTc	2/11	1	2	FACETS	0.456	0.337	0.599	0.456	0.337	0.599	SUBCLONAL	1	FALSE	1	0.245338653816902	2		435	286	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250394	110250394	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	165	954	0	ENST00000374672.4:c.281G>A	p.Arg94Lys	p.R94K	ENST00000374672	NM_004235.4	94	aGa/aAa	3/5	0.245338653816902	0	FACETS	0.883	0.822	0.945			1	CLONAL	3	FALSE	0	0.245338653816902	0		954	383	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0022319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	24	860	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.517	0.404	0.649	0.517	0.404	0.649	SUBCLONAL	1	TRUE	1	0.13	2		860	714	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575132	48575132	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	28	477	0	ENST00000342988.3:c.326T>G	p.Leu109Arg	p.L109R	ENST00000342988	NM_005359.5	109	cTa/cGa	3/12	1	2	FACETS	0.988	0.789	1	0.988	0.789	1	CLONAL	1	TRUE	1	0.13	2		477	436	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877837	151877852	+	frameshift_variant	Frame_Shift_Del	DEL	TATTCTGTGTATCAGT	TATTCTGTGTATCAGT	-	novel	NA	P-0022319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	37	424	0	ENST00000262189.6:c.7093_7108del	p.Thr2365LeufsTer2	p.T2365Lfs*2	ENST00000262189	NM_170606.2	2365	ACTGATACACAGAATAct/ct	36/59	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.13	2		424	482	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	144	669	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.638909585498605	2		669	393	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306536	41306536	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	159	634	2	ENST00000373198.4:c.1123C>A	p.Pro375Thr	p.P375T	ENST00000373198	NM_133170.3	375	Cct/Act	7/32	1	2	FACETS	0.957	0.883	1	0.957	0.883	1	CLONAL	1	TRUE	1	0.638909585498605	2		636	520	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	80	1047	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.893	0.785	1	0.893	0.785	1	CLONAL	1	TRUE	1	0.225668325163982	2		1049	794	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0022325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	119	960	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.225668325163982	1	FACETS	0.925	0.834	1	0.925	0.834	1	CLONAL	1	TRUE	0	0.225668325163982	1		960	1011	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723130	49723130	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	91	826	0	ENST00000449682.2:c.1286A>C	p.Glu429Ala	p.E429A	ENST00000449682	NM_020998.3	429	gAg/gCg	11/18	1	2	FACETS	0.831	0.736	0.932	0.831	0.736	0.932	CLONAL	1	TRUE	1	0.225668325163982	2		826	971	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0022328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	239	662	1				ENST00000310581	NM_198253.2	-/1132			0.523851937837601	3	FACETS	0.901	0.84	0.964	0.45	0.42	0.482	CLONAL	1	TRUE	1	0.523851937837601	3		663	1278	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416378	29416380	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs755556501	NA	P-0022328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1674	211	1030	0	ENST00000389048.3:c.4573_4575del	p.Lys1525del	p.K1525del	ENST00000389048	NM_004304.4	1525	AAG/-	29/29	0.523851937837601	5	FACETS	0.763	0.706	0.823	0.191	0.176	0.206	SUBCLONAL	1	TRUE	1	0.523851937837601	5		1030	1885	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057835	27057835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	780	1184	1	ENST00000324856.7:c.1543C>T	p.Gln515Ter	p.Q515*	ENST00000324856	NM_006015.4	515	Cag/Tag	3/20	0.515757270336396	4	FACETS	0.893	0.865	0.922			1	CLONAL	3	TRUE	NA	0.523851937837601	4		1185	1693	SUCCESS
ATM	472	MSKCC	GRCh37	11	108214063	108214063	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	141	505	0	ENST00000278616.4:c.8383G>C	p.Asp2795His	p.D2795H	ENST00000278616	NM_000051.3	2795	Gat/Cat	57/63	0.497223108840805	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.523851937837601	2		505	249	SUCCESS
APC	324	MSKCC	GRCh37	5	112179275	112179275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	76	486	0	ENST00000257430.4:c.7984G>A	p.Glu2662Lys	p.E2662K	ENST00000257430	NM_000038.5	2662	Gag/Aag	16/16	0.491170497693635	2	FACETS	1	0.976	1	0.691	0.617	0.767	CLONAL	1	TRUE	0	0.523851937837601	2		486	210	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350822	15350822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200902225	NA	P-0022328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	233	723	0	ENST00000263377.2:c.3181G>A	p.Glu1061Lys	p.E1061K	ENST00000263377	NM_058243.2	1061	Gaa/Aaa	15/20	0.523851937837601	3	FACETS	0.872	0.812	0.935	0.436	0.406	0.468	CLONAL	1	TRUE	1	0.523851937837601	3		723	1287	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745977	162745977	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0022328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	61	488	0	ENST00000367921.3:c.2100C>G	p.Tyr700Ter	p.Y700*	ENST00000367921	NM_006182.2	700	taC/taG	16/18	0.498442136231299	3	FACETS	0.639	0.552	0.733	0.319	0.276	0.367	SUBCLONAL	1	TRUE	1	0.523851937837601	3		488	460	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745987	162745987	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	67	510	0	ENST00000367921.3:c.2110C>A	p.Leu704Ile	p.L704I	ENST00000367921	NM_006182.2	704	Ctt/Att	16/18	0.498442136231299	3	FACETS	0.678	0.591	0.772	0.339	0.295	0.386	SUBCLONAL	1	TRUE	1	0.523851937837601	3		510	476	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981203	201981209	+	frameshift_variant	Frame_Shift_Del	DEL	ATGTGAC	ATGTGAC	-	novel	NA	P-0022328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	895	1040	0	ENST00000359651.3:c.285_291del	p.Cys95TrpfsTer58	p.C95Wfs*58	ENST00000359651		94	cgATGTGAC/cg	2/8	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.523851937837601	2		1040	1635	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226553737	226553737	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	129	540	0	ENST00000366794.5:c.2423C>A	p.Ser808Tyr	p.S808Y	ENST00000366794	NM_001618.3	808	tCt/tAt	18/23	0.523851937837601	3	FACETS	0.932	0.847	1	0.466	0.423	0.511	CLONAL	1	TRUE	1	0.523851937837601	3		540	667	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239406	123239406	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	85	505	0	ENST00000358487.5:c.2431C>T	p.Gln811Ter	p.Q811*	ENST00000358487	NM_000141.4	811	Cag/Tag	18/18	0.166005805436388	4	FACETS	1	0.976	1	0.345	0.307	0.385	INDETERMINATE	1	TRUE	0	0.523851937837601	4		505	358	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716350	18716350	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	132	524	0	ENST00000266497.5:c.3697A>C	p.Ser1233Arg	p.S1233R	ENST00000266497		1233	Agc/Cgc	26/31	0.523851937837601	3	FACETS	1	0.983	1	0.657	0.6	0.716	CLONAL	1	TRUE	1	0.523851937837601	3		524	484	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431684	49431684	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	239	911	0	ENST00000301067.7:c.9455T>G	p.Leu3152Arg	p.L3152R	ENST00000301067	NM_003482.3	3152	cTg/cGg	34/54	0.523851937837601	3	FACETS	0.919	0.857	0.984	0.459	0.428	0.492	CLONAL	1	TRUE	1	0.523851937837601	3		911	1253	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26927885	26927893	+	inframe_deletion	In_Frame_Del	DEL	CAAGTTTCA	CAAGTTTCA	-	novel	NA	P-0022328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	79	409	0	ENST00000381527.3:c.326_334del	p.Lys109_His111del	p.K109_H111del	ENST00000381527	NM_001260.1	108	atCAAGTTTCAc/atc	4/13	NA	2	FACETS	0.852	0.768	0.937			1	INDETERMINATE	2	TRUE	NA	0.523851937837601	2		409	177	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434553	110434553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	479	840	0	ENST00000375856.3:c.3848C>T	p.Ser1283Phe	p.S1283F	ENST00000375856	NM_003749.2	1283	tCc/tTc	1/2	0.497223108840805	2	FACETS	0.883	0.847	0.918	0.883	0.847	0.918	CLONAL	2	TRUE	0	0.523851937837601	2		840	1036	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104442	2104442	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs45488500	NA	P-0022328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	536	893	1	ENST00000219476.3:c.481+1G>T		p.X161_splice	ENST00000219476	NM_000548.3	161			0.523851937837601	3	FACETS	0.954	0.916	0.992	0.954	0.916	0.992	CLONAL	2	TRUE	1	0.523851937837601	3		894	1354	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788624	3788628	+	frameshift_variant	Frame_Shift_Del	DEL	AACGT	AACGT	-	novel	NA	P-0022328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	107	679	0	ENST00000262367.5:c.4326_4330del	p.Arg1443ProfsTer8	p.R1443Pfs*8	ENST00000262367	NM_004380.2	1442	ccACGTTgc/ccgc	26/31	0.523851937837601	3	FACETS	0.669	0.6	0.743	0.335	0.3	0.372	SUBCLONAL	1	TRUE	1	0.523851937837601	3		679	770	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881428	37881428	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375637720	NA	P-0022328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1353	225	867	4	ENST00000269571.5:c.2620G>A	p.Glu874Lys	p.E874K	ENST00000269571		874	Gag/Aag	21/27	0.523851937837601	4	FACETS	0.83	0.77	0.892	0.277	0.256	0.298	CLONAL	1	TRUE	1	0.523851937837601	4		871	1578	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872375	45872375	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	678	919	0	ENST00000391945.4:c.136A>G	p.Thr46Ala	p.T46A	ENST00000391945	NM_000400.3	46	Acc/Gcc	3/23	0.523851937837601	3	FACETS	0.989	0.955	1	0.989	0.955	1	CLONAL	2	TRUE	1	0.523851937837601	3		919	1651	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121076	29121076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	189	969	0	ENST00000328354.6:c.481G>A	p.Glu161Lys	p.E161K	ENST00000328354	NM_007194.3	161	Gaa/Aaa	4/15	0.204715154108313	4	FACETS	0.851	0.79	0.914	0.851	0.79	0.914	INDETERMINATE	2	TRUE	2	0.523851937837601	4		969	646	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547987	41548002	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGATACTCAGCCGG	GCAGATACTCAGCCGG	-	novel	NA	P-0022328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	138	841	0	ENST00000263253.7:c.2968_2983del	p.Ala990ArgfsTer25	p.A990Rfs*25	ENST00000263253	NM_001429.3	990	GCAGATACTCAGCCGGag/ag	15/31	0.204715154108313	4	FACETS	1	0.969	1	0.569	0.519	0.622	INDETERMINATE	1	TRUE	2	0.523851937837601	4		841	705	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090482	37090482	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	146	562	0	ENST00000231790.2:c.2077G>C	p.Glu693Gln	p.E693Q	ENST00000231790	NM_000249.3	693	Gag/Cag	18/19	0.488198016026617	1	FACETS	0.902	0.83	0.976	0.902	0.83	0.976	CLONAL	1	TRUE	0	0.523851937837601	1		562	456	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569249	67569249	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	205	654	0	ENST00000274335.5:c.366T>G	p.Phe122Leu	p.F122L	ENST00000274335		122	ttT/ttG	2/15	0.491170497693635	2	FACETS	0.855	0.794	0.919	0.428	0.397	0.46	CLONAL	1	TRUE	0	0.523851937837601	2		654	915	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149437075	149437075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	456	889	0	ENST00000286301.3:c.2213C>T	p.Ser738Phe	p.S738F	ENST00000286301	NM_005211.3	738	tCt/tTt	16/22	0.491170497693635	2	FACETS	0.896	0.86	0.933	0.896	0.86	0.933	CLONAL	2	TRUE	0	0.523851937837601	2		889	971	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687320	117687320	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1314684858	NA	P-0022328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	59	599	0	ENST00000368508.3:c.2731C>G	p.Gln911Glu	p.Q911E	ENST00000368508	NM_002944.2	911	Cag/Gag	18/43	0.523851937837601	3	FACETS	1	0.886	1	0.511	0.444	0.584	CLONAL	1	TRUE	1	0.523851937837601	3		599	278	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001419	150001419	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	82	832	0	ENST00000253339.5:c.2185del	p.Ala729LeufsTer37	p.A729Lfs*37	ENST00000253339		729	Gct/ct	4/7	0.176212207940353	4	FACETS	1	0.966	1	0.62	0.55	0.693	INDETERMINATE	1	TRUE	2	0.523851937837601	4		832	385	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004939	150004961	+	frameshift_variant	Frame_Shift_Del	DEL	AGTCCAGGTACACTAATGTTATA	AGTCCAGGTACACTAATGTTATA	-	novel	NA	P-0022328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	110	572	0	ENST00000253339.5:c.1264_1286del	p.Tyr422AlafsTer21	p.Y422Afs*21	ENST00000253339		422	TATAACATTAGTGTACCTGGACTg/g	3/7	0.176212207940353	4	FACETS	1	0.976	1	0.634	0.572	0.699	INDETERMINATE	1	TRUE	2	0.523851937837601	4		572	505	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274872	38274872	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	238	878	0	ENST00000425967.3:c.1708G>C	p.Gly570Arg	p.G570R	ENST00000425967	NM_001174067.1	570	Ggg/Cgg	13/19	0.504398487367462	2	FACETS	0.882	0.824	0.943	0.441	0.412	0.472	CLONAL	1	TRUE	0	0.523851937837601	2		878	1030	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90994972	90994993	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGTTAACACAGCATGATTTC	GCAGTTAACACAGCATGATTTC	-	novel	NA	P-0022328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	34	577	0	ENST00000265433.3:c.128_149del	p.Arg43LeufsTer5	p.R43Lfs*5	ENST00000265433	NM_002485.4	43	cGAAATCATGCTGTGTTAACTGCt/ct	2/16	0.504398487367462	2	FACETS	0.366	0.299	0.44	0.183	0.149	0.22	SUBCLONAL	1	TRUE	0	0.523851937837601	2		577	355	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044440	5044441	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0022328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	69	788	0	ENST00000381652.3:c.390_391del	p.Arg130SerfsTer11	p.R130Sfs*11	ENST00000381652	NM_004972.3	130	AGa/a	5/25	0.490182147035289	1	FACETS	0.554	0.485	0.627	0.554	0.485	0.627	SUBCLONAL	1	TRUE	0	0.523851937837601	1		788	351	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922816	44922825	+	frameshift_variant	Frame_Shift_Del	DEL	TCCTGCCTGC	TCCTGCCTGC	-	novel	NA	P-0022328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	375	317	0	ENST00000377967.4:c.1677_1686del	p.Pro560LeufsTer30	p.P560Lfs*30	ENST00000377967	NM_021140.2	559	cgTCCTGCCTGC/cg	16/29	0.523851937837601	2	FACETS	1	0.99	1			1	CLONAL	2	TRUE	NA	0.523851937837601	2		317	653	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426651	47426651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	472	369	0	ENST00000377045.4:c.896C>T	p.Ser299Leu	p.S299L	ENST00000377045	NM_001654.4	299	tCa/tTa	10/16	0.523851937837601	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.523851937837601	2		369	746	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	135	669	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.972	0.886	1	0.972	0.886	1	CLONAL	1	TRUE	1	0.420674836882121	2		669	660	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720826	89720826	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	48	384	0	ENST00000371953.3:c.977A>G	p.Asp326Gly	p.D326G	ENST00000371953	NM_000314.4	326	gAc/gGc	8/9	0.420674836882121	1	FACETS	0.78	0.666	0.903	0.78	0.666	0.903	CLONAL	1	TRUE	0	0.420674836882121	1		384	231	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515074	148515074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	148	607	2	ENST00000320356.2:c.1135G>A	p.Glu379Lys	p.E379K	ENST00000320356	NM_004456.4	379	Gaa/Aaa	10/20	0.420674836882121	3	FACETS	0.926	0.845	1	0.463	0.422	0.505	CLONAL	1	TRUE	1	0.420674836882121	3		609	920	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980554	70980554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576020321	NA	P-0022331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	143	694	2	ENST00000276594.2:c.823G>A	p.Ala275Thr	p.A275T	ENST00000276594	NM_024504.3	275	Gcc/Acc	4/8	1	2	FACETS	0.736	0.67	0.805	0.736	0.67	0.805	SUBCLONAL	1	TRUE	1	0.420674836882121	2		696	924	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188174	11188174	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	267	775	1	ENST00000361445.4:c.5920T>C	p.Tyr1974His	p.Y1974H	ENST00000361445	NM_004958.3	1974	Tac/Cac	43/58	0.377118243701383	1	FACETS	0.671	0.634	0.708	0.671	0.634	0.708	INDETERMINATE	1	TRUE	0	0.776432358571479	1		776	627	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148874	119148874	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0022355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	233	394	7	ENST00000264033.4:c.1096-2A>T		p.X366_splice	ENST00000264033	NM_005188.3	366			0.748429966653098	2	FACETS	0.944	0.905	0.981	0.944	0.905	0.981	CLONAL	2	TRUE	0	0.776432358571479	2		401	318	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099307	4099307	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	181	1170	0	ENST00000262948.5:c.811G>C	p.Asp271His	p.D271H	ENST00000262948	NM_030662.3	271	Gac/Cac	7/11	0.290028189503962	1	FACETS	0.29	0.267	0.314	0.29	0.267	0.314	INDETERMINATE	1	TRUE	0	0.776432358571479	1		1170	982	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215927	36215927	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs372271044	NA	P-0022355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	487	1238	1	ENST00000222270.7:c.3467A>G	p.Asn1156Ser	p.N1156S	ENST00000222270	NM_014727.1	1156	aAt/aGt	10/37	0.290028189503962	1	FACETS	0.707	0.678	0.735	0.707	0.678	0.735	INDETERMINATE	1	TRUE	0	0.776432358571479	1		1239	1086	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578493	7578493	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1206165503	NA	P-0022358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	428	874	0	ENST00000269305.4:c.437G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tGg/tAg	5/11	0.50546943960137	2	FACETS	0.762	0.73	0.794	0.762	0.73	0.794	SUBCLONAL	2	TRUE	0	0.622670346898316	2		874	902	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573886	18573886	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1410	205	532	0	ENST00000266497.5:c.2204A>T	p.Gln735Leu	p.Q735L	ENST00000266497		735	cAa/cTa	15/31	0.622670346898316	7	FACETS	1	0.953	1	0.174	0.16	0.188	CLONAL	1	TRUE	1	0.622670346898316	7		532	1615	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031765	11031765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	660	908	0	ENST00000327064.4:c.1577G>A	p.Ser526Asn	p.S526N	ENST00000327064	NM_199141.1	526	aGt/aAt	14/16	0.532391745105243	4	FACETS	0.883	0.854	0.912			1	CLONAL	3	TRUE	NA	0.622670346898316	4		908	1298	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111514	8111515	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0022364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	577	710	0	ENST00000346208.3:c.1002_1003del	p.Asp335ProfsTer16	p.D335Pfs*16	ENST00000346208		334	GGg/g	5/6	0.477119618410666	6	FACETS	0.982	0.943	1			1	CLONAL	3	FALSE	NA	0.477119618410666	6		710	1605	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120796817	120796817	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210336675	NA	P-0022364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	77	749	2	ENST00000257552.2:c.442C>T	p.Arg148Trp	p.R148W	ENST00000257552	NM_002442.3	148	Cgg/Tgg	7/15	0.227613434077826	4	FACETS	0.803	0.705	0.907	0.268	0.235	0.303	INDETERMINATE	1	FALSE	1	0.477119618410666	4		751	594	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497284	149497284	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	53	704	0	ENST00000261799.4:c.3034G>C	p.Val1012Leu	p.V1012L	ENST00000261799	NM_002609.3	1012	Gtg/Ctg	22/23	0.278218402867907	5	FACETS	0.67	0.571	0.778	0.223	0.19	0.26	INDETERMINATE	1	FALSE	2	0.477119618410666	5		704	569	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505048	149505053	+	inframe_deletion	In_Frame_Del	DEL	ATAGGG	ATAGGG	-	novel	NA	P-0022367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	317	594	0	ENST00000261799.4:c.1762_1767del	p.Pro588_Tyr589del	p.P588_Y589del	ENST00000261799	NM_002609.3	588	CCCTAT/-	12/23	0.41158945443848	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	3	TRUE	0	0.41158945443848	3		594	617	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0022369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	154	779	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.251781952284537	3	FACETS	0.881	0.807	0.958	0.881	0.807	0.958	CLONAL	2	TRUE	1	0.254215435778122	3		779	775	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0022373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	416	1034	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	1	0.972	1			1	INDETERMINATE	2	TRUE	NA	0.545721983685556	2		1037	752	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984021	2984021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766268425	NA	P-0022373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	26	870	0	ENST00000396946.4:c.509G>A	p.Arg170His	p.R170H	ENST00000396946	NM_032415.4	170	cGc/cAc	5/25	0.545721983685556	3	FACETS	0.109	0.086	0.136			1	SUBCLONAL	1	TRUE	NA	0.545721983685556	3		870	1111	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778441	3778470	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	GCTGCTGCTGCTGCAGCAGCTGCCTCCGTA	GCTGCTGCTGCTGCAGCAGCTGCCTCCGTA	-	novel	NA	P-0022373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	372	946	2	ENST00000262367.5:c.6578_6607del	p.Leu2193_Gln2203delinsTer	p.L2193_Q2203delins*	ENST00000262367	NM_004380.2	2193	tTACGGAGGCAGCTGCTGCAGCAGCAGCAGCaa/taa	31/31	0.306747065342031	3	FACETS	0.828	0.787	0.869	0.552	0.525	0.58	INDETERMINATE	2	TRUE	0	0.545721983685556	3		948	1048	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0022378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	370	857	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.909	0.862	0.956	0.909	0.862	0.956	CLONAL	1	TRUE	1	0.673701370619602	2		857	1209	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	384	707	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.613244042807434	1	FACETS	0.911	0.87	0.951	0.911	0.87	0.951	CLONAL	1	TRUE	0	0.673701370619602	1		707	830	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	118	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.341991024734202	1	FACETS	0.469	0.425	0.515	0.469	0.425	0.515	INDETERMINATE	1	TRUE	0	0.673701370619602	1		434	495	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446858	18446858	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1249018026	NA	P-0022378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	60	376	0	ENST00000266497.5:c.943A>G	p.Ile315Val	p.I315V	ENST00000266497		315	Att/Gtt	4/31	0.341991024734202	1	FACETS	0.353	0.305	0.403	0.353	0.305	0.403	INDETERMINATE	1	TRUE	0	0.673701370619602	1		376	335	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003024	42003057	+	frameshift_variant	Frame_Shift_Del	DEL	TGTACCAGCTTCCCACTAAGAGTACCAGTTATGT	TGTACCAGCTTCCCACTAAGAGTACCAGTTATGT	-	novel	NA	P-0022378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	405	791	1	ENST00000219905.7:c.2561_2594del	p.Val854AspfsTer8	p.V854Dfs*8	ENST00000219905	NM_001164273.1	854	gTGTACCAGCTTCCCACTAAGAGTACCAGTTATGTa/ga	8/24	0.341991024734202	1	FACETS	0.758	0.723	0.793	0.758	0.723	0.793	INDETERMINATE	1	TRUE	0	0.673701370619602	1		792	1052	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492812	56492812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	196	606	0	ENST00000407977.2:c.127G>A	p.Glu43Lys	p.E43K	ENST00000407977		43	Gaa/Aaa	2/10	1	2	FACETS	0.473	0.436	0.51	0.473	0.436	0.51	SUBCLONAL	1	TRUE	1	0.673701370619602	2		606	1231	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216416	2216416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1222825058	NA	P-0022378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	223	689	0	ENST00000398665.3:c.2060C>T	p.Ala687Val	p.A687V	ENST00000398665	NM_032482.2	687	gCc/gTc	20/28	1	2	FACETS	0.49	0.455	0.526	0.49	0.455	0.526	SUBCLONAL	1	TRUE	1	0.673701370619602	2		689	1352	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010433	48010433	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1223476490	NA	P-0022378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	394	656	0	ENST00000234420.5:c.61A>G	p.Asn21Asp	p.N21D	ENST00000234420	NM_000179.2	21	Aac/Gac	1/10	1	2	FACETS	0.932	0.886	0.979	0.932	0.886	0.979	CLONAL	1	TRUE	1	0.673701370619602	2		656	1255	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732741	204732741	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	177	583	0	ENST00000302823.3:c.76T>C	p.Phe26Leu	p.F26L	ENST00000302823	NM_005214.4	26	Ttt/Ctt	1/4	1	2	FACETS	0.541	0.498	0.585	0.541	0.498	0.585	SUBCLONAL	1	TRUE	1	0.673701370619602	2		583	972	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538994	187538994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	305	623	0	ENST00000441802.2:c.8746C>T	p.Pro2916Ser	p.P2916S	ENST00000441802	NM_005245.3	2916	Cca/Tca	10/27	0.673701370619602	1	FACETS	0.895	0.85	0.94	0.895	0.85	0.94	CLONAL	1	TRUE	0	0.673701370619602	1		623	671	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282109	38282109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779380483	NA	P-0022378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	479	990	0	ENST00000425967.3:c.947C>T	p.Pro316Leu	p.P316L	ENST00000425967	NM_001174067.1	316	cCg/cTg	8/19	0.673701370619602	1	FACETS	0.929	0.892	0.966	0.929	0.892	0.966	CLONAL	1	TRUE	0	0.673701370619602	1		990	1015	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038867	47038870	+	frameshift_variant	Frame_Shift_Del	DEL	GAGC	GAGC	-	novel	NA	P-0022378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	242	907	0	ENST00000377604.3:c.874_877del	p.Glu292GlnfsTer15	p.E292Qfs*15	ENST00000377604	NM_001204468.1	292	GAGCca/ca	9/24	0.381362585219802	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.673701370619602	0		907	945	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577095	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519984	NA	P-0022380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	139	768	0	ENST00000269305.4:c.843C>A	p.Asp281Glu	p.D281E	ENST00000269305	NM_001126112.2	281	gaC/gaA	8/11	0.263870257523413	3	FACETS	0.982	0.897	1	0.982	0.897	1	CLONAL	2	FALSE	1	0.263870257523413	3		768	607	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729399	41729399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	74	677	0	ENST00000242208.4:c.1130G>A	p.Arg377His	p.R377H	ENST00000242208	NM_002192.2	377	cGc/cAc	3/3	0.263870257523413	3	FACETS	1	0.972	1	0.705	0.62	0.797	CLONAL	1	FALSE	1	0.263870257523413	3		677	450	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933337	100933337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767006543	NA	P-0022380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	80	660	0	ENST00000325455.5:c.2053C>T	p.Pro685Ser	p.P685S	ENST00000325455	NM_001202474.3	685	Cca/Tca	4/8	0.263870257523413	7	FACETS	0.975	0.861	1	0.39	0.344	0.439	CLONAL	2	FALSE	2	0.263870257523413	7		660	516	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40872362	40872362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	124	890	0	ENST00000428826.2:c.593C>T	p.Ser198Leu	p.S198L	ENST00000428826		198	tCa/tTa	7/21	0.263870257523413	3	FACETS	0.914	0.83	1	0.914	0.83	1	CLONAL	2	FALSE	1	0.263870257523413	3		890	582	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998189	169998189	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	38	703	0	ENST00000295797.4:c.880G>C	p.Glu294Gln	p.E294Q	ENST00000295797	NM_002740.5	294	Gag/Cag	9/18	0.263870257523413	3	FACETS	0.898	0.744	1	0.449	0.372	0.535	CLONAL	1	FALSE	1	0.263870257523413	3		703	363	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934144	39934144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375342424	NA	P-0022380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	26	725	0	ENST00000378444.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000378444	NM_001123385.1	152	cCg/cTg	4/15	0.263870257523413	3	FACETS	0.52	0.411	0.645	0.173	0.137	0.215	SUBCLONAL	1	FALSE	0	0.263870257523413	3		725	429	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000152-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	170	157	1	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.416659465169389	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.416659465169389	1		158	625	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984848	11984848	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0000152-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	209	504	0	ENST00000353533.5:c.393+1G>A		p.X131_splice	ENST00000353533	NM_003010.3	131			0.407604971757575	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.416659465169389	2		504	496	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865491	57865491	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1184432538	NA	P-0000152-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	361	1043	1	ENST00000228682.2:c.2968C>T	p.Arg990Ter	p.R990*	ENST00000228682	NM_005269.2	990	Cga/Tga	12/12	0.416659465169389	3	FACETS	0.969	0.92	1	0.969	0.92	1	CLONAL	2	TRUE	1	0.416659465169389	3		1044	1080	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402513	139402513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370300490	NA	P-0000152-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	202	1196	0	ENST00000277541.6:c.3404C>T	p.Ala1135Val	p.A1135V	ENST00000277541	NM_017617.3	1135	gCg/gTg	21/34	1	2	FACETS	0.837	0.775	0.902	0.837	0.775	0.902	CLONAL	1	TRUE	1	0.416659465169389	2		1196	1158	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719930	18719930	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	172	760	1	ENST00000266497.5:c.3827G>T	p.Arg1276Ile	p.R1276I	ENST00000266497		1276	aGa/aTa	27/31	0.537497660795615	2	FACETS	0.868	0.802	0.937	0.434	0.401	0.469	CLONAL	1	TRUE	0	0.608443525076124	2		761	651	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303439	91303439	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1169	142	695	0	ENST00000355112.3:c.1150G>T	p.Asp384Tyr	p.D384Y	ENST00000355112	NM_000057.2	384	Gat/Tat	6/22	0.608443525076124	6	FACETS	0.789	0.717	0.865	0.132	0.119	0.145	SUBCLONAL	1	TRUE	0	0.608443525076124	6		695	1311	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646903	23646903	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1223	210	819	0	ENST00000261584.4:c.964G>C	p.Glu322Gln	p.E322Q	ENST00000261584	NM_024675.3	322	Gag/Cag	4/13	0.608443525076124	6	FACETS	1	0.964	1			1	CLONAL	1	TRUE	NA	0.608443525076124	6		819	1433	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663398	67663398	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	119	540	0	ENST00000264010.4:c.1799G>C	p.Arg600Thr	p.R600T	ENST00000264010	NM_006565.3	600	aGa/aCa	10/12	0.576478862351802	3	FACETS	0.862	0.78	0.947	0.431	0.39	0.474	CLONAL	1	TRUE	1	0.608443525076124	3		540	592	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683503	29683503	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	96	582	0	ENST00000356175.3:c.7578G>C	p.Leu2526Phe	p.L2526F	ENST00000356175	NM_000267.3	2526	ttG/ttC	51/57	0.608443525076124	6	FACETS	0.742	0.66	0.83			1	SUBCLONAL	1	TRUE	NA	0.608443525076124	6		582	943	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163720	32163720	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	125	555	0	ENST00000375023.3:c.5506G>C	p.Glu1836Gln	p.E1836Q	ENST00000375023	NM_004557.3	1836	Gag/Cag	30/30	0.561498183026507	4	FACETS	0.937	0.85	1	0.469	0.425	0.515	CLONAL	1	TRUE	2	0.608443525076124	4		555	705	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937516	76937516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	151	394	0	ENST00000373344.5:c.3232G>A	p.Glu1078Lys	p.E1078K	ENST00000373344	NM_000489.3	1078	Gag/Aag	9/35	0.577039488827949	2	FACETS	1	0.93	1			1	CLONAL	1	TRUE	NA	0.608443525076124	2		394	491	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307904	11307904	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	195	755	0	ENST00000361445.4:c.1088G>C	p.Arg363Thr	p.R363T	ENST00000361445	NM_004958.3	363	aGa/aCa	7/58	0.552116528503418	5	FACETS	0.999	0.923	1	0.333	0.307	0.36	CLONAL	1	TRUE	2	0.608443525076124	5		755	1227	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127687	2127687	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769527912	NA	P-0000184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	181	694	0	ENST00000219476.3:c.2926C>T	p.Arg976Trp	p.R976W	ENST00000219476	NM_000548.3	976	Cgg/Tgg	26/42	0.537497660795615	2	FACETS	0.92	0.852	0.989	0.46	0.426	0.495	CLONAL	1	TRUE	0	0.608443525076124	2		694	647	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351664	89351664	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370109948	NA	P-0000184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	232	973	1	ENST00000301030.4:c.1286C>T	p.Ser429Leu	p.S429L	ENST00000301030	NM_001256183.1	429	tCg/tTg	9/13	0.561498183026507	4	FACETS	0.945	0.88	1	0.472	0.44	0.507	CLONAL	1	TRUE	2	0.608443525076124	4		974	1298	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243698	41243698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	182	845	0	ENST00000357654.3:c.3850C>T	p.His1284Tyr	p.H1284Y	ENST00000357654	NM_007294.3	1284	Cac/Tac	10/23	0.545947942264627	4	FACETS	0.926	0.854	1	0.309	0.284	0.334	CLONAL	1	TRUE	1	0.608443525076124	4		845	1039	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629003	14629003	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1282	140	758	0	ENST00000254322.2:c.159C>G	p.Asp53Glu	p.D53E	ENST00000254322	NM_006145.1	53	gaC/gaG	1/3	0.608443525076124	6	FACETS	0.717	0.651	0.788			1	SUBCLONAL	1	TRUE	NA	0.608443525076124	6		758	1422	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383317	42383317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219765308	NA	P-0000184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	487	700	1	ENST00000221972.3:c.337G>A	p.Glu113Lys	p.E113K	ENST00000221972	NM_021601.3	113	Gag/Aag	2/5	0.608443525076124	3	FACETS	0.851	0.821	0.88	0.851	0.821	0.88	CLONAL	3	TRUE	0	0.608443525076124	3		701	818	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383653	42383653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555843732	NA	P-0000184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	208	805	0	ENST00000221972.3:c.428G>A	p.Arg143Gln	p.R143Q	ENST00000221972	NM_021601.3	143	cGa/cAa	3/5	0.608443525076124	3	FACETS	0.934	0.867	1	0.311	0.289	0.335	CLONAL	1	TRUE	0	0.608443525076124	3		805	955	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467155	25467155	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	178	717	0	ENST00000264709.3:c.1720del	p.Ala574GlnfsTer77	p.A574Qfs*77	ENST00000264709	NM_175629.2	574	Gca/ca	15/23	0.576478862351802	3	FACETS	1	0.956	1	0.525	0.485	0.566	CLONAL	1	TRUE	1	0.608443525076124	3		717	727	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096187	178096187	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	124	580	0	ENST00000397062.3:c.1144G>C	p.Asp382His	p.D382H	ENST00000397062	NM_006164.4	382	Gat/Cat	5/5	0.561498183026507	4	FACETS	0.818	0.741	0.901	0.409	0.37	0.451	CLONAL	1	TRUE	2	0.608443525076124	4		580	801	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309730	30309730	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1626	317	703	0	ENST00000307677.4:c.292G>A	p.Glu98Lys	p.E98K	ENST00000307677	NM_138578.1	98	Gaa/Aaa	2/3	0.608443525076124	9	FACETS	0.839	0.789	0.891			1	CLONAL	2	TRUE	NA	0.608443525076124	9		703	1943	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46271017	46271017	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	160	691	0	ENST00000371998.3:c.3141G>C	p.Gln1047His	p.Q1047H	ENST00000371998		1047	caG/caC	17/23	0.608443525076124	6	FACETS	0.845	0.772	0.921	0.211	0.193	0.231	CLONAL	1	TRUE	2	0.608443525076124	6		691	1380	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278224	142278224	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	182	785	0	ENST00000350721.4:c.1601G>A	p.Trp534Ter	p.W534*	ENST00000350721	NM_001184.3	534	tGg/tAg	7/47	0.552116528503418	5	FACETS	0.946	0.871	1	0.315	0.29	0.342	CLONAL	1	TRUE	2	0.608443525076124	5		785	1210	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151868347	151868347	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0000184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	761	615	0	ENST00000262189.6:c.9453+2T>C		p.X3151_splice	ENST00000262189	NM_170606.2	3151			0.608443525076124	5	FACETS	0.925	0.904	0.946	0.925	0.904	0.946	CLONAL	5	TRUE	0	0.608443525076124	5		615	1034	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021677	69021677	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	102	628	0	ENST00000288368.4:c.2965C>T	p.Gln989Ter	p.Q989*	ENST00000288368	NM_024870.2	989	Cag/Tag	25/40	0.51689331954709	4	FACETS	0.726	0.649	0.807	0.363	0.324	0.404	SUBCLONAL	1	TRUE	2	0.608443525076124	4		628	743	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27109596	27109596	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1179	192	829	0	ENST00000380036.4:c.8C>G	p.Ser3Cys	p.S3C	ENST00000380036	NM_000459.3	3	tCt/tGt	1/23	0.50080446225557	6	FACETS	1	0.939	1	0.255	0.235	0.276	CLONAL	1	TRUE	2	0.608443525076124	6		829	1371	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841120	15841120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	157	396	0	ENST00000307771.7:c.1204C>T	p.His402Tyr	p.H402Y	ENST00000307771	NM_005089.3	402	Cac/Tac	11/11	0.577039488827949	2	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.608443525076124	2		396	434	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0000293-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	196	369	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	0.184171807793142	4	FACETS	1	0.987	1	1	0.987	1	INDETERMINATE	2	TRUE	2	0.357958494829041	4		369	598	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106223	27106223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000293-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	70	148	0	ENST00000324856.7:c.5834C>T	p.Pro1945Leu	p.P1945L	ENST00000324856	NM_006015.4	1945	cCa/cTa	20/20	0.139135065960587	4	FACETS	1	0.893	1	1	0.893	1	INDETERMINATE	2	TRUE	2	0.357958494829041	4		148	262	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903709	41903709	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000293-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	96	238	0	ENST00000372991.4:c.848C>T	p.Thr283Ile	p.T283I	ENST00000372991	NM_001760.3	283	aCt/aTt	5/5	0.223205215432505	4	FACETS	1	0.909	1	1	0.909	1	CLONAL	2	TRUE	2	0.357958494829041	4		238	360	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846068	128846068	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000293-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	143	444	0	ENST00000249373.3:c.998T>G	p.Val333Gly	p.V333G	ENST00000249373	NM_005631.4	333	gTg/gGg	5/12	0.357958494829041	4	FACETS	0.771	0.704	0.84	0.514	0.469	0.56	SUBCLONAL	2	TRUE	1	0.357958494829041	4		444	704	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238318	98238318	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000293-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	203	125	0	ENST00000331920.6:c.1726C>T	p.Gln576Ter	p.Q576*	ENST00000331920	NM_000264.3	576	Cag/Tag	12/24	0.357958494829041	8	FACETS	1	0.977	1			1	CLONAL	8	TRUE	NA	0.357958494829041	8		125	283	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420637	49420637	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000293-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	74	143	0	ENST00000301067.7:c.15112G>T	p.Glu5038Ter	p.E5038*	ENST00000301067	NM_003482.3	5038	Gag/Tag	48/54	0.261920614339298	5	FACETS	0.958	0.853	1	0.958	0.853	1	CLONAL	3	TRUE	2	0.357958494829041	5		143	221	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912874	32912874	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000293-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	96	165	0	ENST00000380152.3:c.4382C>T	p.Ser1461Phe	p.S1461F	ENST00000380152		1461	tCc/tTc	11/27	0.223205215432505	4	FACETS	0.77	0.689	0.855	0.77	0.689	0.855	SUBCLONAL	2	TRUE	2	0.357958494829041	4		165	473	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874333	76874333	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000293-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	213	442	0	ENST00000373344.5:c.5389G>T	p.Val1797Phe	p.V1797F	ENST00000373344	NM_000489.3	1797	Gtc/Ttc	21/35	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.357958494829041	2		442	957	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435257	49435258	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0000293-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	16	171	0	ENST00000301067.7:c.6295dup	p.Arg2099ProfsTer56	p.R2099Pfs*56	ENST00000301067	NM_003482.3	2099	cga/cCga	31/54	0.261920614339298	5	FACETS	0.458	0.338	0.602	0.153	0.112	0.201	SUBCLONAL	1	TRUE	2	0.357958494829041	5		171	300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573996	7573997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCTCTCGGAACATCTC	novel	NA	P-0000293-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	85	314	0	ENST00000269305.4:c.1015_1030dup	p.Leu344ArgfsTer8	p.L344Rfs*8	ENST00000269305	NM_001126112.2	344	ctg/cGAGATGTTCCGAGAGCtg	10/11	0.357958494829041	3	FACETS	1	0.961	1			1	CLONAL	1	TRUE	NA	0.357958494829041	3		314	471	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984968	101984969	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0000293-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	88	101	0	ENST00000282441.5:c.415_416delinsTT	p.Pro139Phe	p.P139F	ENST00000282441	NM_001130145.2	139	CCt/TTt	2/9	0.139135065960587	4	FACETS	0.972	0.877	1	1	0.981	1	INDETERMINATE	3	TRUE	2	0.357958494829041	4		101	229	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0000573-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	115	607	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.351475779916453	1	FACETS	0.254	0.228	0.281	0.254	0.228	0.281	INDETERMINATE	1	TRUE	0	0.594674371199927	1		607	1072	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0000573-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	173	246	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	0.502101766173803	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.594674371199927	1		246	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0000573-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	341	525	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.351475779916453	1	FACETS	0.881	0.836	0.926	0.881	0.836	0.926	INDETERMINATE	1	TRUE	0	0.594674371199927	1		525	915	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258202	16258202	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs895443307	NA	P-0000573-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	84	332	0	ENST00000375759.3:c.5467C>T	p.Arg1823Cys	p.R1823C	ENST00000375759	NM_015001.2	1823	Cgt/Tgt	11/15	1	2	FACETS	0.292	0.257	0.329	0.292	0.257	0.329	SUBCLONAL	1	TRUE	1	0.594674371199927	2		332	969	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242457	55242457	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759256622	NA	P-0000573-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	139	281	0	ENST00000275493.2:c.2227G>A	p.Ala743Thr	p.A743T	ENST00000275493	NM_005228.3	743	Gct/Act	19/28	1	2	FACETS	0.677	0.617	0.739	0.677	0.617	0.739	SUBCLONAL	1	TRUE	1	0.594674371199927	2		281	691	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224170	98224170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs570091335	NA	P-0000573-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	40	245	0	ENST00000331920.6:c.2671G>A	p.Gly891Ser	p.G891S	ENST00000331920	NM_000264.3	891	Ggc/Agc	16/24	1	2	FACETS	0.227	0.188	0.271	0.227	0.188	0.271	SUBCLONAL	1	TRUE	1	0.594674371199927	2		245	592	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139408978	139408978	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199666126	NA	P-0000573-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	54	260	0	ENST00000277541.6:c.2191C>T	p.Arg731Trp	p.R731W	ENST00000277541	NM_017617.3	731	Cgg/Tgg	13/34	1	2	FACETS	0.306	0.261	0.355	0.306	0.261	0.355	SUBCLONAL	1	TRUE	1	0.594674371199927	2		260	594	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333833	70333833	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000573-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	155	455	0	ENST00000373644.4:c.1738C>A	p.Leu580Ile	p.L580I	ENST00000373644	NM_030625.2	580	Cta/Ata	2/12	1	2	FACETS	0.536	0.49	0.584	0.536	0.49	0.584	SUBCLONAL	1	TRUE	1	0.594674371199927	2		455	972	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659550	88659550	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0000573-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	235	357	0	ENST00000372037.3:c.334-1G>T		p.X112_splice	ENST00000372037	NM_004329.2	112			1	2	FACETS	0.882	0.824	0.942	0.882	0.824	0.942	CLONAL	1	TRUE	1	0.594674371199927	2		357	896	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953535	32953535	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000573-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	128	254	0	ENST00000380152.3:c.8836T>A	p.Leu2946Met	p.L2946M	ENST00000380152		2946	Ttg/Atg	22/27	1	2	FACETS	0.62	0.563	0.68	0.62	0.563	0.68	SUBCLONAL	1	TRUE	1	0.594674371199927	2		254	694	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943641	9943641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000573-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	86	380	0	ENST00000330684.3:c.1300G>A	p.Val434Met	p.V434M	ENST00000330684	NM_001134407.1	434	Gtg/Atg	5/13	NA	2	FACETS	0.315	0.278	0.355			1	INDETERMINATE	1	TRUE	NA	0.594674371199927	2		380	917	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2214487	2214487	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000573-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	106	233	0	ENST00000398665.3:c.1815G>T	p.Glu605Asp	p.E605D	ENST00000398665	NM_032482.2	605	gaG/gaT	19/28	1	2	FACETS	0.669	0.602	0.74	0.669	0.602	0.74	SUBCLONAL	1	TRUE	1	0.594674371199927	2		233	533	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216397	2216397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1386157480	NA	P-0000573-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	129	362	0	ENST00000398665.3:c.2041C>T	p.Arg681Cys	p.R681C	ENST00000398665	NM_032482.2	681	Cgc/Tgc	20/28	1	2	FACETS	0.635	0.577	0.696	0.635	0.577	0.696	SUBCLONAL	1	TRUE	1	0.594674371199927	2		362	683	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095989	11095989	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371056395	NA	P-0000573-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	218	462	0	ENST00000358026.2:c.263C>T	p.Pro88Leu	p.P88L	ENST00000358026	NM_001128849.1	88	cCg/cTg	3/36	1	2	FACETS	0.887	0.826	0.949	0.887	0.826	0.949	CLONAL	1	TRUE	1	0.594674371199927	2		462	827	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281200	15281200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000573-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	79	539	0	ENST00000263388.2:c.5056G>A	p.Val1686Met	p.V1686M	ENST00000263388	NM_000435.2	1686	Gtg/Atg	27/33	1	2	FACETS	0.269	0.236	0.305	0.269	0.236	0.305	SUBCLONAL	1	TRUE	1	0.594674371199927	2		539	987	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42870094	42870094	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0000573-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	223	282	0	ENST00000398585.3:c.78C>G	p.Tyr26Ter	p.Y26*	ENST00000398585	NM_001135099.1	26	taC/taG	2/14	0.117495651426874	5	FACETS	0.859	0.801	0.918			1	INDETERMINATE	2	TRUE	NA	0.594674371199927	5		282	826	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731104	162731105	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0000573-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	69	570	0	ENST00000367921.3:c.964dup	p.Leu322ProfsTer5	p.L322Pfs*5	ENST00000367921	NM_006182.2	320	ttc/ttCc	9/18	NA	2	FACETS	0.194	0.168	0.222			1	INDETERMINATE	1	TRUE	NA	0.594674371199927	2		570	1197	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541578	187541579	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0000573-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	236	381	1	ENST00000441802.2:c.6161_6162del	p.Thr2054ArgfsTer4	p.T2054Rfs*4	ENST00000441802	NM_005245.3	2054	aCA/a	10/27	0.585165363012514	1	FACETS	0.955	0.898	1	0.955	0.898	1	CLONAL	1	TRUE	0	0.594674371199927	1		382	584	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696802	176696802	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0000573-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	117	184	0	ENST00000439151.2:c.5508del	p.Ala1837LeufsTer12	p.A1837Lfs*12	ENST00000439151	NM_022455.4	1835	Aaa/aa	16/23	0.585165363012514	1	FACETS	0.82	0.749	0.894	0.82	0.749	0.894	CLONAL	1	TRUE	0	0.594674371199927	1		184	337	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874092	151874093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0000573-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1330	261	536	0	ENST00000262189.6:c.8445dup	p.Ser2816IlefsTer6	p.S2816Ifs*6	ENST00000262189	NM_170606.2	2815	-/A	38/59	1	2	FACETS	0.552	0.515	0.59	0.552	0.515	0.59	SUBCLONAL	1	TRUE	1	0.594674371199927	2		536	1591	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786045	3786045	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000573-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	209	572	0	ENST00000262367.5:c.4720del	p.Thr1574ProfsTer61	p.T1574Pfs*61	ENST00000262367	NM_004380.2	1574	Acc/cc	28/31	1	2	FACETS	0.551	0.511	0.594	0.551	0.511	0.594	SUBCLONAL	1	TRUE	1	0.594674371199927	2		572	1275	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0000607-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	138	303	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.32537594994419	2		303	703	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs104886003	NA	P-0000607-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	42	142	0	ENST00000263967.3:c.1633G>C	p.Glu545Gln	p.E545Q	ENST00000263967	NM_006218.2	545	Gag/Cag	10/21	1	2	FACETS	0.814	0.683	0.959	0.814	0.683	0.959	CLONAL	1	TRUE	1	0.32537594994419	2		142	317	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257143	16257143	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000607-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	154	449	0	ENST00000375759.3:c.4408C>T	p.Arg1470Ter	p.R1470*	ENST00000375759	NM_015001.2	1470	Cga/Tga	11/15	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.32537594994419	2		449	917	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662590	227662590	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000607-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	65	192	0	ENST00000305123.5:c.865C>T	p.Leu289Phe	p.L289F	ENST00000305123	NM_005544.2	289	Ctc/Ttc	1/2	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.32537594994419	2		192	292	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637603	52637603	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000607-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	241	601	0	ENST00000394830.3:c.2713G>C	p.Glu905Gln	p.E905Q	ENST00000394830	NM_018313.4	905	Gag/Cag	18/30	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.32537594994419	2		601	1151	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508075	106508075	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs893866491	NA	P-0000607-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	58	132	1	ENST00000359195.3:c.69G>A	p.Met23Ile	p.M23I	ENST00000359195	NM_002649.2	23	atG/atA	2/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.32537594994419	2		133	286	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251950	8251950	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000607-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	136	392	2	ENST00000335790.3:c.127T>C	p.Tyr43His	p.Y43H	ENST00000335790	NM_002315.2	43	Tac/Cac	2/4	0.234567342359622	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.32537594994419	1		394	633	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29002012	29002012	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000607-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	116	283	1	ENST00000282397.4:c.1153A>G	p.Thr385Ala	p.T385A	ENST00000282397	NM_002019.4	385	Act/Gct	9/30	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.32537594994419	2		284	700	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883987	37883987	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs758365405	NA	P-0000607-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	125	369	3	ENST00000269571.5:c.3458G>T	p.Arg1153Leu	p.R1153L	ENST00000269571		1153	cGa/cTa	27/27	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.32537594994419	2		372	629	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845736	68845737	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGGT	novel	NA	P-0000607-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	88	262	1	ENST00000261769.5:c.983_986dup	p.Thr330GlyfsTer21	p.T330Gfs*21	ENST00000261769	NM_004360.3	328	gtg/gTGGTtg	7/16	0.271649113287057	0	FACETS	0.822	0.732	0.917			1	CLONAL	1	TRUE	0	0.32537594994419	0		263	444	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419921	+	missense_variant	Missense_Mutation	DNP	TC	TC	AG	novel	NA	P-0000607-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	86	247	0	ENST00000206249.3:c.1607_1608delinsAG	p.Leu536Gln	p.L536Q	ENST00000206249	NM_000125.3	536	cTC/cAG	8/8	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.32537594994419	2		247	461	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0000624-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	327	346	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.778	0.736	0.822	0.778	0.736	0.822	SUBCLONAL	1	TRUE	1	0.761324750362634	2		346	1104	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544703	65544703	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs387906650	NA	P-0000624-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	578	537	2	ENST00000358664.4:c.223C>T	p.Arg75Ter	p.R75*	ENST00000358664	NM_002382.4	75	Cga/Tga	4/5	0.761324750362634	1	FACETS	0.993	0.962	1	0.993	0.962	1	CLONAL	1	TRUE	0	0.761324750362634	1		539	947	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0000624-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1307	701	524	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	0.917	0.884	0.951	0.917	0.884	0.951	CLONAL	1	TRUE	1	0.761324750362634	2		524	2008	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405171	139405171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs578228721	NA	P-0000624-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	473	584	0	ENST00000277541.6:c.2674C>T	p.Arg892Cys	p.R892C	ENST00000277541	NM_017617.3	892	Cgc/Tgc	17/34	1	2	FACETS	0.972	0.93	1	0.972	0.93	1	CLONAL	1	TRUE	1	0.761324750362634	2		584	1279	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0000739-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	151	685	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	NA	2	FACETS	0.963	0.887	1			1	INDETERMINATE	1	TRUE	NA	0.643908390415405	2		685	487	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0000739-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	343	340	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.643908390415405	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.643908390415405	1		340	631	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275738	41275738	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000739-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	369	548	0	ENST00000349496.5:c.1633C>A	p.Gln545Lys	p.Q545K	ENST00000349496	NM_001904.3	545	Cag/Aag	10/15	0.323321829847653	1	FACETS	0.766	0.728	0.804	0.766	0.728	0.804	INDETERMINATE	1	TRUE	0	0.643908390415405	1		548	1015	SUCCESS
APC	324	MSKCC	GRCh37	5	112157650	112157650	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1060503333	NA	P-0000739-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	154	448	0	ENST00000257430.4:c.1370C>G	p.Ser457Ter	p.S457*	ENST00000257430	NM_000038.5	457	tCa/tGa	11/16	0.389037412274263	1	FACETS	0.37	0.338	0.403	0.37	0.338	0.403	SUBCLONAL	1	TRUE	0	0.643908390415405	1		448	877	SUCCESS
APC	324	MSKCC	GRCh37	5	112175191	112175192	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554085382	NA	P-0000739-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	155	247	0	ENST00000257430.4:c.3901dup	p.Thr1301AsnfsTer14	p.T1301Nfs*14	ENST00000257430	NM_000038.5	1300	-/A	16/16	0.389037412274263	1	FACETS	0.848	0.786	0.911	0.848	0.786	0.911	CLONAL	1	TRUE	0	0.643908390415405	1		247	385	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748502	162748502	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1218815846	NA	P-0000739-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	96	322	0	ENST00000367921.3:c.2416C>T	p.Arg806Ter	p.R806*	ENST00000367921	NM_006182.2	806	Cga/Tga	17/18	0.636544573072821	2	FACETS	0.464	0.414	0.518	0.232	0.207	0.259	SUBCLONAL	1	TRUE	0	0.643908390415405	2		322	642	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719767	190719767	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000739-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	117	412	0	ENST00000441310.2:c.1769T>A	p.Leu590His	p.L590H	ENST00000441310	NM_000534.4	590	cTc/cAc	9/13	0.636544573072821	2	FACETS	0.496	0.447	0.547	0.248	0.223	0.274	SUBCLONAL	1	TRUE	0	0.643908390415405	2		412	733	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402809	139402809	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs547455916	NA	P-0000739-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	136	383	0	ENST00000277541.6:c.3200C>T	p.Pro1067Leu	p.P1067L	ENST00000277541	NM_017617.3	1067	cCc/cTc	20/34	0.389037412274263	1	FACETS	0.461	0.42	0.504	0.461	0.42	0.504	SUBCLONAL	1	TRUE	0	0.643908390415405	1		383	621	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164689	36164689	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000739-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	176	595	0	ENST00000300305.3:c.1186T>A	p.Phe396Ile	p.F396I	ENST00000300305		396	Ttc/Atc	8/8	1	2	FACETS	0.465	0.427	0.504	0.465	0.427	0.504	SUBCLONAL	1	TRUE	1	0.643908390415405	2		595	1176	SUCCESS
AR	367	MSKCC	GRCh37	X	66942698	66942698	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000739-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	255	509	0	ENST00000374690.3:c.2479T>C	p.Phe827Leu	p.F827L	ENST00000374690	NM_000044.3	827	Ttc/Ctc	7/8	0.2750673505922	2	FACETS	0.659	0.616	0.703			1	INDETERMINATE	1	TRUE	NA	0.643908390415405	2		509	1202	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	321	733	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.406496881661392	2	FACETS	0.809	0.775	0.844	0.809	0.775	0.844	INDETERMINATE	2	TRUE	0	0.731772956955385	2		733	542	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	119	485	0	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.813	0.74	0.888	0.813	0.74	0.888	CLONAL	1	TRUE	1	0.731772956955385	2		485	400	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	325	471	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.731772956955385	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.731772956955385	2		471	432	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	91	423	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.649	0.581	0.722	0.649	0.581	0.722	SUBCLONAL	1	TRUE	1	0.731772956955385	2		423	383	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	242	419	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	0.731772956955385	2	FACETS	0.87	0.83	0.91	0.87	0.83	0.91	CLONAL	2	TRUE	0	0.731772956955385	2		420	380	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	74	276	3	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	NA	2	FACETS	1	0.944	1			1	INDETERMINATE	1	TRUE	NA	0.731772956955385	2		279	186	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	97	843	1	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	0.635848323831412	1	FACETS	0.343	0.307	0.381	0.343	0.307	0.381	SUBCLONAL	1	TRUE	0	0.731772956955385	1		844	490	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782063	9782063	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	194	718	0	ENST00000377346.4:c.2086A>G	p.Asn696Asp	p.N696D	ENST00000377346	NM_005026.3	696	Aat/Gat	17/24	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.731772956955385	2		718	429	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101231	27101231	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs753094331	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	60	581	0	ENST00000324856.7:c.4513A>G	p.Thr1505Ala	p.T1505A	ENST00000324856	NM_006015.4	1505	Acc/Gcc	18/20	1	2	FACETS	0.384	0.332	0.441	0.384	0.332	0.441	SUBCLONAL	1	TRUE	1	0.731772956955385	2		581	427	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176145045	176145045	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	59	574	0	ENST00000367669.3:c.565+1G>A		p.X189_splice	ENST00000367669	NM_022457.5	189			0.294005874956342	1	FACETS	0.263	0.227	0.302	0.263	0.227	0.302	INDETERMINATE	1	TRUE	0	0.731772956955385	1		574	389	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085728	16085728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144939456	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	146	475	0	ENST00000281043.3:c.904C>T	p.Arg302Cys	p.R302C	ENST00000281043	NM_005378.4	302	Cgt/Tgt	3/3	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.731772956955385	2		475	395	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149551	202149551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139337151	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	75	563	0	ENST00000358485.4:c.992C>T	p.Thr331Met	p.T331M	ENST00000358485	NM_001080125.1	331	aCg/aTg	8/9	NA	2	FACETS	0.376	0.33	0.426			1	INDETERMINATE	1	TRUE	NA	0.731772956955385	2		563	545	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37061895	37061895	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782087	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	319	447	1	ENST00000231790.2:c.979C>T	p.Gln327Ter	p.Q327*	ENST00000231790	NM_000249.3	327	Cag/Tag	11/19	0.731772956955385	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.731772956955385	2		448	419	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749415085	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	65	606	0	ENST00000263967.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000263967	NM_006218.2	38	Cgt/Tgt	2/21	0.294005874956342	1	FACETS	0.25	0.217	0.285	0.25	0.217	0.285	INDETERMINATE	1	TRUE	0	0.731772956955385	1		606	451	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808581	1808581	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	50	619	0	ENST00000260795.2:c.2194C>T	p.His732Tyr	p.H732Y	ENST00000260795		732	Cat/Tat	16/17	0.431729550552324	1	FACETS	0.249	0.212	0.289	0.249	0.212	0.289	INDETERMINATE	1	TRUE	0	0.731772956955385	1		619	348	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549334	187549334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	88	607	1	ENST00000441802.2:c.4784C>A	p.Ala1595Asp	p.A1595D	ENST00000441802	NM_005245.3	1595	gCt/gAt	9/27	0.294005874956342	1	FACETS	0.288	0.256	0.323	0.288	0.256	0.323	INDETERMINATE	1	TRUE	0	0.731772956955385	1		608	529	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503915	149503915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201183721	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	49	440	0	ENST00000261799.4:c.1921C>T	p.Arg641Cys	p.R641C	ENST00000261799	NM_002609.3	641	Cgc/Tgc	14/23	1	2	FACETS	0.38	0.323	0.443	0.38	0.323	0.443	SUBCLONAL	1	TRUE	1	0.731772956955385	2		440	352	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518690	176518690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770565518	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	78	304	0	ENST00000292408.4:c.608G>A	p.Arg203His	p.R203H	ENST00000292408	NM_213647.1	203	cGc/cAc	6/18	1	2	FACETS	0.943	0.843	1	0.943	0.843	1	CLONAL	1	TRUE	1	0.731772956955385	2		304	226	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170027	32170027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746443332	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	89	740	0	ENST00000375023.3:c.3581C>T	p.Pro1194Leu	p.P1194L	ENST00000375023	NM_004557.3	1194	cCg/cTg	21/30	0.481442888347225	1	FACETS	0.365	0.325	0.407	0.365	0.325	0.407	SUBCLONAL	1	TRUE	0	0.731772956955385	1		740	423	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32191633	32191633	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs750820892	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	276	1180	0	ENST00000375023.3:c.73G>T	p.Gly25Trp	p.G25W	ENST00000375023	NM_004557.3	25	Ggg/Tgg	1/30	0.481442888347225	1	FACETS	0.86	0.817	0.904	0.86	0.817	0.904	CLONAL	1	TRUE	0	0.731772956955385	1		1180	556	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686336	117686336	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs770304963	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	145	356	0	ENST00000368508.3:c.3005T>C	p.Val1002Ala	p.V1002A	ENST00000368508	NM_002944.2	1002	gTa/gCa	20/43	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.731772956955385	2		356	326	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469898	157469898	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs794727977	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	152	516	0	ENST00000346085.5:c.2692C>T	p.Arg898Ter	p.R898*	ENST00000346085	NM_020732.3	898	Cga/Tga	9/20	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.731772956955385	2		516	405	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380038	116380038	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	102	807	0	ENST00000397752.3:c.1427A>G	p.His476Arg	p.H476R	ENST00000397752	NM_000245.2	476	cAt/cGt	4/21	1	2	FACETS	0.402	0.359	0.447	0.402	0.359	0.447	SUBCLONAL	1	TRUE	1	0.731772956955385	2		807	694	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624407	140624407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1458837905	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	33	89	0	ENST00000288602.6:c.97G>A	p.Ala33Thr	p.A33T	ENST00000288602	NM_004333.4	33	Gcc/Acc	1/18	1	2	FACETS	0.805	0.671	0.949	0.805	0.671	0.949	CLONAL	1	TRUE	1	0.731772956955385	2		89	112	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486320	8486320	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	45	258	0	ENST00000356435.5:c.2497C>A	p.His833Asn	p.H833N	ENST00000356435		833	Cac/Aac	17/35	1	2	FACETS	0.612	0.52	0.71	0.612	0.52	0.71	SUBCLONAL	1	TRUE	1	0.731772956955385	2		258	201	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428261	49428261	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	63	493	0	ENST00000301067.7:c.10441-2A>G		p.X3481_splice	ENST00000301067	NM_003482.3	3481			1	2	FACETS	0.419	0.363	0.479	0.419	0.363	0.479	SUBCLONAL	1	TRUE	1	0.731772956955385	2		493	411	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121438877	121438877	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	70	535	1	ENST00000257555.6:c.1778G>A	p.Ser593Asn	p.S593N	ENST00000257555		593	aGc/aAc	10/10	0.294005874956342	1	FACETS	0.3	0.263	0.34	0.3	0.263	0.34	INDETERMINATE	1	TRUE	0	0.731772956955385	1		536	404	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219196	133219196	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	65	499	0	ENST00000320574.5:c.4848G>T	p.Lys1616Asn	p.K1616N	ENST00000320574	NM_006231.2	1616	aaG/aaT	37/49	0.294005874956342	1	FACETS	0.315	0.274	0.358	0.315	0.274	0.358	INDETERMINATE	1	TRUE	0	0.731772956955385	1		499	358	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929312	32929312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358958	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	34	590	2	ENST00000380152.3:c.7322G>A	p.Gly2441Asp	p.G2441D	ENST00000380152		2441	gGc/gAc	14/27	1	2	FACETS	0.292	0.239	0.352	0.292	0.239	0.352	SUBCLONAL	1	TRUE	1	0.731772956955385	2		592	318	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358450	91358450	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	74	776	0	ENST00000355112.3:c.4195A>G	p.Met1399Val	p.M1399V	ENST00000355112	NM_000057.2	1399	Atg/Gtg	22/22	0.294005874956342	1	FACETS	0.224	0.196	0.254	0.224	0.196	0.254	INDETERMINATE	1	TRUE	0	0.731772956955385	1		776	572	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820866	3820866	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772653113	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	71	298	0	ENST00000262367.5:c.2585C>T	p.Thr862Met	p.T862M	ENST00000262367	NM_004380.2	862	aCg/aTg	14/31	1	2	FACETS	0.886	0.786	0.99	0.886	0.786	0.99	CLONAL	1	TRUE	1	0.731772956955385	2		298	219	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17129612	17129612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755107067	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	226	719	1	ENST00000285071.4:c.274C>T	p.His92Tyr	p.H92Y	ENST00000285071	NM_144997.5	92	Cac/Tac	5/14	0.294005874956342	1	FACETS	0.735	0.691	0.779	0.735	0.691	0.779	INDETERMINATE	1	TRUE	0	0.731772956955385	1		720	533	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39600632	39600632	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	82	962	2	ENST00000262039.4:c.1447G>T	p.Ala483Ser	p.A483S	ENST00000262039	NM_002647.2	483	Gcc/Tcc	13/25	0.273542260240575	1	FACETS	0.247	0.218	0.278	0.247	0.218	0.278	INDETERMINATE	1	TRUE	0	0.731772956955385	1		964	576	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584558	48584558	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764421512	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	40	503	0	ENST00000342988.3:c.731C>A	p.Pro244His	p.P244H	ENST00000342988	NM_005359.5	244	cCt/cAt	6/12	0.273542260240575	1	FACETS	0.127	0.105	0.151	0.127	0.105	0.151	INDETERMINATE	1	TRUE	0	0.731772956955385	1		503	548	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212456	5212456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1191088838	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	123	540	0	ENST00000357368.4:c.4661C>T	p.Ala1554Val	p.A1554V	ENST00000357368	NM_002850.3	1554	gCg/gTg	31/38	0.431729550552324	1	FACETS	0.562	0.514	0.613	0.562	0.514	0.613	INDETERMINATE	1	TRUE	0	0.731772956955385	1		540	379	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291061	15291061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367923081	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	184	557	0	ENST00000263388.2:c.3149G>A	p.Arg1050Gln	p.R1050Q	ENST00000263388	NM_000435.2	1050	cGg/cAg	20/33	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.731772956955385	2		557	460	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921451	39921451	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	34	805	0	ENST00000378444.4:c.4369A>G	p.Ile1457Val	p.I1457V	ENST00000378444	NM_001123385.1	1457	Att/Gtt	10/15	0.635848323831412	1	FACETS	0.114	0.093	0.139	0.114	0.093	0.139	SUBCLONAL	1	TRUE	0	0.731772956955385	1		805	515	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224207	53224207	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202160290	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	182	771	0	ENST00000375401.3:c.3344G>A	p.Arg1115His	p.R1115H	ENST00000375401	NM_004187.3	1115	cGc/cAc	22/26	0.635848323831412	1	FACETS	0.663	0.617	0.709	0.663	0.617	0.709	SUBCLONAL	1	TRUE	0	0.731772956955385	1		771	476	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888785	76888785	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	115	1205	0	ENST00000373344.5:c.5044G>T	p.Gly1682Cys	p.G1682C	ENST00000373344	NM_000489.3	1682	Ggc/Tgc	19/35	0.731772956955385	1	FACETS	0.371	0.335	0.409	0.371	0.335	0.409	SUBCLONAL	1	TRUE	0	0.731772956955385	1		1205	537	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608923	100608923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	152	900	0	ENST00000308731.7:c.1685G>A	p.Arg562Gln	p.R562Q	ENST00000308731	NM_000061.2	562	cGg/cAg	17/19	0.731772956955385	1	FACETS	0.411	0.377	0.446	0.411	0.377	0.446	SUBCLONAL	1	TRUE	0	0.731772956955385	1		900	641	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101268	27101268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	55	602	1	ENST00000324856.7:c.4555del	p.Gln1519ArgfsTer8	p.Q1519Rfs*8	ENST00000324856	NM_006015.4	1517	gCc/gc	18/20	1	2	FACETS	0.356	0.305	0.412	0.356	0.305	0.412	SUBCLONAL	1	TRUE	1	0.731772956955385	2		603	422	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149793	202149794	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	71	646	1	ENST00000358485.4:c.1235_1236del	p.Lys412SerfsTer11	p.K412Sfs*11	ENST00000358485	NM_001080125.1	412	AAa/a	8/9	NA	2	FACETS	0.336	0.293	0.382			1	INDETERMINATE	1	TRUE	NA	0.731772956955385	2		647	577	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103755	47103756	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	92	879	5	ENST00000409792.3:c.6190_6191del	p.Asp2064ProfsTer8	p.D2064Pfs*8	ENST00000409792	NM_014159.6	2064	GAc/c	14/21	0.731772956955385	2	FACETS	0.365	0.325	0.409	0.183	0.162	0.205	SUBCLONAL	1	TRUE	0	0.731772956955385	2		884	688	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539266	187539266	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	71	667	0	ENST00000441802.2:c.8474del	p.Gly2825GlufsTer4	p.G2825Efs*4	ENST00000441802	NM_005245.3	2825	gGa/ga	10/27	0.294005874956342	1	FACETS	0.232	0.203	0.264	0.232	0.203	0.264	INDETERMINATE	1	TRUE	0	0.731772956955385	1		667	530	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	37	230	3	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	0.744	0.625	0.871	0.744	0.625	0.871	SUBCLONAL	1	TRUE	1	0.731772956955385	2		233	136	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649922	88649922	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786201038	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	140	451	0	ENST00000372037.3:c.176del	p.Leu59Ter	p.L59*	ENST00000372037	NM_004329.2	57	ccT/cc	4/13	0.294005874956342	1	FACETS	0.758	0.702	0.816	0.758	0.702	0.816	INDETERMINATE	1	TRUE	0	0.731772956955385	1		451	320	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577222	64577224	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs794728657	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	209	648	0	ENST00000312049.6:c.358_360del	p.Lys120del	p.K120del	ENST00000312049	NM_130799.2	120	AAG/-	2/10	0.294005874956342	1	FACETS	0.735	0.689	0.781	0.735	0.689	0.781	INDETERMINATE	1	TRUE	0	0.731772956955385	1		648	493	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029457	16029457	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	88	1110	1	ENST00000268712.3:c.1573del	p.Thr525GlnfsTer30	p.T525Qfs*30	ENST00000268712	NM_006311.3	525	Aca/ca	15/46	0.294005874956342	1	FACETS	0.194	0.172	0.219	0.194	0.172	0.219	INDETERMINATE	1	TRUE	0	0.731772956955385	1		1111	785	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918921	76918921	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	108	1522	4	ENST00000373344.5:c.4070del	p.Lys1357ArgfsTer18	p.K1357Rfs*18	ENST00000373344	NM_000489.3	1357	aAg/ag	12/35	0.731772956955385	1	FACETS	0.255	0.229	0.283	0.255	0.229	0.283	SUBCLONAL	1	TRUE	0	0.731772956955385	1		1526	734	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953741	48953742	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0001121-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	205	353	0	ENST00000267163.4:c.1346dup	p.Val450SerfsTer13	p.V450Sfs*13	ENST00000267163	NM_000321.2	448	-/G	14/27	0.441912677019219	1	FACETS	0.891	0.832	0.952	0.891	0.832	0.952	CLONAL	1	TRUE	0	0.546325702042662	1		353	612	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0001211-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	108	589	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.321627445157307	2	FACETS	0.922	0.837	1	0.922	0.837	1	CLONAL	2	TRUE	0	0.354973846722037	2		589	330	SUCCESS
AR	367	MSKCC	GRCh37	X	66766350	66766351	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGT	rs746958859	NA	P-0001211-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	28	89	3	ENST00000374690.3:c.1368_1370dup	p.Gly473dup	p.G473dup	ENST00000374690	NM_000044.3	473	-/GGT	1/8	0.354973846722037	0	FACETS	0.834	0.699	0.971			1	CLONAL	2	TRUE	0	0.354973846722037	0		92	61	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148544383	148544383	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1035066688	NA	P-0001211-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	18	398	0	ENST00000320356.2:c.8A>T	p.Gln3Leu	p.Q3L	ENST00000320356	NM_004456.4	3	cAg/cTg	2/20	1	2	FACETS	0.321	0.241	0.415	0.321	0.241	0.415	SUBCLONAL	1	TRUE	1	0.354973846722037	2		398	316	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578274	7578274	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001211-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	61	475	0	ENST00000269305.4:c.575A>T	p.Gln192Leu	p.Q192L	ENST00000269305	NM_001126112.2	192	cAg/cTg	6/11	0.321627445157307	2	FACETS	1	0.913	1	0.534	0.463	0.609	CLONAL	1	TRUE	0	0.354973846722037	2		475	322	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39726872	39726872	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001211-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	41	302	0	ENST00000361337.2:c.870G>C	p.Glu290Asp	p.E290D	ENST00000361337	NM_003286.2	290	gaG/gaC	11/21	0.335365364200633	2	FACETS	0.822	0.689	0.969	0.411	0.344	0.485	CLONAL	1	TRUE	0	0.354973846722037	2		302	281	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246603	46246603	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001211-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	48	165	0	ENST00000334344.6:c.4697del	p.Ala1566ValfsTer3	p.A1566Vfs*3	ENST00000334344	NM_152641.2	1566	gCt/gt	15/21	0.354973846722037	3	FACETS	0.784	0.672	0.905	0.784	0.672	0.905	CLONAL	2	TRUE	1	0.354973846722037	3		165	203	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183833	10183833	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001659-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	103	220	0	ENST00000256474.2:c.302T>G	p.Leu101Arg	p.L101R	ENST00000256474	NM_000551.3	101	cTg/cGg	1/3	NA	2	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.321973929792584	2		220	533	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225202	53225202	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1414718926	NA	P-0001659-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	130	217	0	ENST00000375401.3:c.3016A>G	p.Ile1006Val	p.I1006V	ENST00000375401	NM_004187.3	1006	Atc/Gtc	20/26	0.268166811568354	0	FACETS	0.769	0.706	0.833			1	SUBCLONAL	2	TRUE	NA	0.321973929792584	0		217	356	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702527	52702527	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001659-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	58	360	0	ENST00000394830.3:c.371del	p.Lys124SerfsTer50	p.K124Sfs*50	ENST00000394830	NM_018313.4	124	aAg/ag	4/30	0.321973929792584	1	FACETS	0.861	0.744	0.988	0.861	0.744	0.988	CLONAL	1	TRUE	0	0.321973929792584	1		360	351	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228296	53228296	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001659-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	120	213	0	ENST00000375401.3:c.2106del	p.Asp702GlufsTer62	p.D702Efs*62	ENST00000375401	NM_004187.3	702	gaT/ga	15/26	0.268166811568354	0	FACETS	0.662	0.603	0.722			1	SUBCLONAL	2	TRUE	NA	0.321973929792584	0		213	382	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0001676-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	121	303	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.234672936081937	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.234672936081937	3		303	481	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0001676-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	182	396	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.20363232433639	4	FACETS	0.902	0.834	0.971	1	0.988	1	CLONAL	3	TRUE	2	0.234672936081937	4		396	708	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001676-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	138	218	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.234672936081937	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	0	0.234672936081937	2		218	570	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0001676-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	89	476	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.234672936081937	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	0	0.234672936081937	2		476	362	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451784	29451784	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs772809305	NA	P-0001676-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	87	540	2	ENST00000389048.3:c.2781del	p.Cys928AlafsTer11	p.C928Afs*11	ENST00000389048	NM_004304.4	927	ggG/gg	16/29	1	2	FACETS	0.888	0.785	0.998	0.888	0.785	0.998	CLONAL	1	TRUE	1	0.234672936081937	2		542	835	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0001752-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	424	1085	1	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.692161036211735	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.692161036211735	1		1086	705	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788651	3788651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001752-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	194	595	0	ENST00000262367.5:c.4303G>A	p.Asp1435Asn	p.D1435N	ENST00000262367	NM_004380.2	1435	Gat/Aat	26/31	0.692161036211735	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.692161036211735	1		595	313	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926257	112926257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001752-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	163	701	1	ENST00000351677.2:c.1390G>A	p.Gly464Ser	p.G464S	ENST00000351677	NM_002834.3	464	Ggc/Agc	12/16	0.405893495384556	1	FACETS	0.582	0.538	0.628	0.582	0.538	0.628	INDETERMINATE	1	TRUE	0	0.692161036211735	1		702	529	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924639	94924639	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001752-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	285	911	0	ENST00000536441.1:c.271C>G	p.Arg91Gly	p.R91G	ENST00000536441	NM_144665.3	91	Cgg/Ggg	3/10	0.320607149884101	3	FACETS	1	0.993	1	0.68	0.642	0.719	INDETERMINATE	1	TRUE	1	0.692161036211735	3		911	815	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436496	110436496	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1381339944	NA	P-0001752-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	125	1267	0	ENST00000375856.3:c.1905C>G	p.Ile635Met	p.I635M	ENST00000375856	NM_003749.2	635	atC/atG	1/2	NA	2	FACETS	0.451	0.408	0.496			1	INDETERMINATE	1	TRUE	NA	0.692161036211735	2		1267	801	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063658	67063658	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1189096167	NA	P-0001752-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	121	626	1	ENST00000412916.2:c.107C>T	p.Pro36Leu	p.P36L	ENST00000412916		36	cCc/cTc	2/6	0.692161036211735	1	FACETS	0.485	0.441	0.532	0.485	0.441	0.532	SUBCLONAL	1	TRUE	0	0.692161036211735	1		627	471	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229252	36229252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001752-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	70	792	2	ENST00000222270.7:c.7942G>A	p.Ala2648Thr	p.A2648T	ENST00000222270	NM_014727.1	2648	Gcc/Acc	37/37	1	2	FACETS	0.297	0.258	0.338	0.297	0.258	0.338	SUBCLONAL	1	TRUE	1	0.692161036211735	2		794	682	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607628	46607628	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001752-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	162	969	0	ENST00000263734.3:c.1817C>A	p.Ser606Tyr	p.S606Y	ENST00000263734	NM_001430.4	606	tCc/tAc	12/16	0.105181351857884	5	FACETS	1	0.985	1	0.332	0.305	0.36	INDETERMINATE	1	TRUE	1	0.692161036211735	5		969	719	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849236	76849236	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001752-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	32	775	0	ENST00000373344.5:c.6040T>G	p.Leu2014Val	p.L2014V	ENST00000373344	NM_000489.3	2014	Tta/Gta	26/35	0.692161036211735	1	FACETS	0.162	0.131	0.196	0.162	0.131	0.196	SUBCLONAL	1	TRUE	0	0.692161036211735	1		775	374	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0002040-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	43	328	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.497	0.415	0.589	0.497	0.415	0.589	SUBCLONAL	1	FALSE	1	0.264525316451109	2		328	654	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659891	227659891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002040-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	46	537	0	ENST00000305123.5:c.3564C>A	p.Phe1188Leu	p.F1188L	ENST00000305123	NM_005544.2	1188	ttC/ttA	1/2	1	2	FACETS	0.494	0.415	0.582	0.494	0.415	0.582	SUBCLONAL	1	FALSE	1	0.264525316451109	2		537	704	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579584	7579585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0002040-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	39	395	0	ENST00000269305.4:c.102dup	p.Pro36AlafsTer7	p.P36Afs*7	ENST00000269305	NM_001126112.2	34	-/C	4/11	0.0790886419101358	3	FACETS	0.698	0.579	0.832			1	INDETERMINATE	1	FALSE	NA	0.264525316451109	3		395	478	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120495	70120505	+	frameshift_variant	Frame_Shift_Del	DEL	ACAACCCGTCT	ACAACCCGTCT	-	novel	NA	P-0002040-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	76	543	0	ENST00000245479.2:c.1500_1510del	p.Gln500HisfsTer74	p.Q500Hfs*74	ENST00000245479	NM_000346.3	499	gaACAACCCGTCTac/gaac	3/3	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.264525316451109	2		543	462	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0002088-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	542	941	2	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		943	1226	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881001	37881002	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGCTCCCC	rs397516981	NA	P-0002088-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	879	671	0	ENST00000269571.5:c.2331_2339dup	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	gtg/gtGGGCTCCCCg	20/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		671	1554	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446269	187446270	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770320988	NA	P-0002088-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	145	751	0	ENST00000232014.4:c.1418dup	p.Lys474GlufsTer26	p.K474Efs*26	ENST00000232014	NM_001130845.1	473	ccg/ccCg	6/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		751	412	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423449	116423453	+	frameshift_variant	Frame_Shift_Del	DEL	GGTGC	GGTGC	-	novel	NA	P-0002088-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	165	757	0	ENST00000397752.3:c.3724_3728del	p.Gly1242LysfsTer43	p.G1242Kfs*43	ENST00000397752	NM_000245.2	1242	GGTGCa/a	19/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		757	470	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109946	115109946	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002088-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	120	428	0	ENST00000257566.3:c.1932del	p.Ile645SerfsTer244	p.I645Sfs*244	ENST00000257566	NM_016569.3	644	tcC/tc	8/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		428	319	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481601	40481601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763754846	NA	P-0002088-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	428	1725	4	ENST00000264657.5:c.1204G>A	p.Gly402Ser	p.G402S	ENST00000264657	NM_139276.2	402	Ggc/Agc	13/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1729	1350	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0002102-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	106	169	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.605901357232882	2		169	344	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945129	32945129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80359104	NA	P-0002102-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	147	323	0	ENST00000380152.3:c.8524C>T	p.Arg2842Cys	p.R2842C	ENST00000380152		2842	Cgc/Tgc	20/27	1	2	FACETS	0.794	0.728	0.863	0.794	0.728	0.863	SUBCLONAL	1	TRUE	1	0.605901357232882	2		323	611	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806599	1806599	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749083353	NA	P-0002102-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	351	371	0	ENST00000260795.2:c.1315C>T	p.Arg439Cys	p.R439C	ENST00000260795		439	Cgc/Tgc	9/17	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.605901357232882	2		371	1152	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504572	103504572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776140428	NA	P-0002102-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	238	455	0	ENST00000355739.4:c.193C>T	p.Leu65Phe	p.L65F	ENST00000355739	NM_000123.3	65	Ctc/Ttc	2/15	1	2	FACETS	0.905	0.847	0.965	0.905	0.847	0.965	CLONAL	1	TRUE	1	0.605901357232882	2		455	868	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249360	153249361	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002102-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	167	347	0	ENST00000281708.4:c.1417dup	p.Arg473LysfsTer4	p.R473Kfs*4	ENST00000281708	NM_033632.3	473	aga/aAga	9/12	1	2	FACETS	0.941	0.869	1	0.941	0.869	1	CLONAL	1	TRUE	1	0.605901357232882	2		347	586	SUCCESS
APC	324	MSKCC	GRCh37	5	112174459	112174459	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002102-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	149	259	0	ENST00000257430.4:c.3168del	p.Ile1056MetfsTer5	p.I1056Mfs*5	ENST00000257430	NM_000038.5	1056	atA/at	16/16	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.605901357232882	2		259	481	SUCCESS
APC	324	MSKCC	GRCh37	5	112175668	112175668	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002102-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	202	386	1	ENST00000257430.4:c.4377del	p.Ala1460LeufsTer13	p.A1460Lfs*13	ENST00000257430	NM_000038.5	1459	acT/ac	16/16	1	2	FACETS	0.897	0.834	0.962	0.897	0.834	0.962	CLONAL	1	TRUE	1	0.605901357232882	2		387	743	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0002155-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	80	613	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.801	0.705	0.904	0.801	0.705	0.904	CLONAL	1	FALSE	1	0.3	2		614	666	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782177	NA	P-0002155-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	105	225	1	ENST00000269305.4:c.644G>A	p.Ser215Asn	p.S215N	ENST00000269305	NM_001126112.2	215	aGt/aAt	6/11	0.3	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	0	0.3	1		226	521	SUCCESS
APC	324	MSKCC	GRCh37	5	112175492	112175493	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002155-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	114	158	0	ENST00000257430.4:c.4203dup	p.Ala1402CysfsTer7	p.A1402Cfs*7	ENST00000257430	NM_000038.5	1401	att/aTtt	16/16	0.258256614666035	2	FACETS	0.882	0.8	0.967	0.882	0.8	0.967	CLONAL	2	FALSE	0	0.3	2		158	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0002200-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	40	651	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	1	0.844	1	1	0.844	1	CLONAL	1	TRUE	1	0.13	2		651	604	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057936	27057937	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1415146710	NA	P-0002200-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	41	586	0	ENST00000324856.7:c.1650dup	p.Tyr551LeufsTer72	p.Y551Lfs*72	ENST00000324856	NM_006015.4	548	-/C	3/20	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.13	2		586	601	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478161	138478161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002200-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	27	611	0	ENST00000289153.2:c.25C>T	p.Pro9Ser	p.P9S	ENST00000289153	NM_006219.2	9	Cct/Tct	1/22	1	2	FACETS	0.959	0.763	1	0.959	0.763	1	CLONAL	1	TRUE	1	0.13	2		611	433	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950066	44950066	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs863224886	NA	P-0002245-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	62	474	1	ENST00000377967.4:c.3835C>T	p.Arg1279Ter	p.R1279*	ENST00000377967	NM_021140.2	1279	Cga/Tga	26/29	0.341284881332117	1	FACETS	0.277	0.239	0.317	0.277	0.239	0.317	INDETERMINATE	1	TRUE	0	0.643635774970324	1		475	472	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14015937	14015937	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs187435008	NA	P-0002245-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	101	308	0	ENST00000311895.7:c.257G>A	p.Arg86His	p.R86H	ENST00000311895	NM_005236.2	86	cGc/cAc	2/11	0.406539864206916	5	FACETS	0.731	0.653	0.814			1	SUBCLONAL	1	TRUE	NA	0.643635774970324	5		308	844	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0002245-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	438	337	0	ENST00000346208.3:c.1220_1221insA	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcAg	6/6	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.643635774970324	2		337	1056	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0002324-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	128	451	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.329201233259358	2		451	777	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002324-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	155	561	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	1	2	FACETS	0.917	0.838	0.999	0.917	0.838	0.999	CLONAL	1	TRUE	1	0.329201233259358	2		561	1027	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240732	53240732	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002324-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	191	653	0	ENST00000375401.3:c.1348G>C	p.Gly450Arg	p.G450R	ENST00000375401	NM_004187.3	450	Ggc/Cgc	10/26	1	2	FACETS	0.982	0.906	1	0.982	0.906	1	CLONAL	1	TRUE	1	0.329201233259358	2		653	1182	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94908684	94908684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760970492	NA	P-0002324-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	174	560	0	ENST00000536441.1:c.1370G>A	p.Arg457Gln	p.R457Q	ENST00000536441	NM_144665.3	457	cGg/cAg	9/10	0.329201233259358	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.329201233259358	1		560	855	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371409680	NA	P-0002435-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	503	378	0	ENST00000269305.4:c.848G>C	p.Arg283Pro	p.R283P	ENST00000269305	NM_001126112.2	283	cGc/cCc	8/11	0.832201831013058	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	FALSE	0	0.82808446655573	2		378	561	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255665	16255665	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002435-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	154	287	0	ENST00000375759.3:c.2930A>T	p.Asp977Val	p.D977V	ENST00000375759	NM_015001.2	977	gAt/gTt	11/15	NA	2	FACETS	0.964	0.893	1			1	INDETERMINATE	1	FALSE	NA	0.82808446655573	2		287	386	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261463	16261463	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002435-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	198	315	0	ENST00000375759.3:c.8728G>T	p.Glu2910Ter	p.E2910*	ENST00000375759	NM_015001.2	2910	Gag/Tag	11/15	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	FALSE	NA	0.82808446655573	2		315	416	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096484	178096484	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002435-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	239	333	0	ENST00000397062.3:c.847G>A	p.Asp283Asn	p.D283N	ENST00000397062	NM_006164.4	283	Gat/Aat	5/5	0.563050704393509	5	FACETS	0.803	0.752	0.855	0.535	0.501	0.57	CLONAL	2	FALSE	2	0.82808446655573	5		333	806	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12653503	12653503	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002435-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	247	398	0	ENST00000251849.4:c.266G>C	p.Arg89Thr	p.R89T	ENST00000251849	NM_002880.3	89	aGg/aCg	3/17	0.832201831013058	5	FACETS	1	0.944	1	0.203	0.189	0.217	CLONAL	1	FALSE	0	0.82808446655573	5		398	1320	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455141	50455141	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002435-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	132	267	0	ENST00000331340.3:c.688A>T	p.Met230Leu	p.M230L	ENST00000331340	NM_006060.4	230	Atg/Ttg	6/8	0.784023833719262	4	FACETS	1	0.963	1			1	CLONAL	1	FALSE	NA	0.82808446655573	4		267	528	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615069	43615069	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002435-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	332	349	0	ENST00000355710.3:c.2483G>C	p.Gly828Ala	p.G828A	ENST00000355710	NM_020975.4	828	gGc/gCc	14/20	0.620805942790472	4	FACETS	1	0.958	1			1	CLONAL	2	FALSE	NA	0.82808446655573	4		349	728	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615190	43615190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002435-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	73	172	0	ENST00000355710.3:c.2604G>A	p.Met868Ile	p.M868I	ENST00000355710	NM_020975.4	868	atG/atA	14/20	0.620805942790472	4	FACETS	0.68	0.596	0.77			1	SUBCLONAL	1	FALSE	NA	0.82808446655573	4		172	474	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042188	14042189	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0002435-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	247	218	0	ENST00000311895.7:c.2739dup	p.Gly914ArgfsTer26	p.G914Rfs*26	ENST00000311895	NM_005236.2	912	gga/ggAa	11/11	0.832201831013058	2	FACETS	0.984	0.951	1	0.984	0.951	1	CLONAL	2	FALSE	0	0.82808446655573	2		218	303	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584375	39584375	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002435-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	199	343	0	ENST00000262039.4:c.1040del	p.Gln347ArgfsTer14	p.Q347Rfs*14	ENST00000262039	NM_002647.2	347	cAg/cg	10/25	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.82808446655573	2		343	468	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0002678-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	128	207	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.324179603107441	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.324179603107441	1		207	607	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149434799	149434799	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0002678-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	241	441	0	ENST00000286301.3:c.2654+1G>T		p.X885_splice	ENST00000286301	NM_005211.3	885			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.324179603107441	2		441	1336	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575189	48575189	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002678-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	179	382	0	ENST00000342988.3:c.383T>C	p.Val128Ala	p.V128A	ENST00000342988	NM_005359.5	128	gTg/gCg	3/12	0.324179603107441	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.324179603107441	1		382	880	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218538	5218538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767763908	NA	P-0002678-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	203	374	0	ENST00000357368.4:c.3941G>A	p.Arg1314His	p.R1314H	ENST00000357368	NM_002850.3	1314	cGc/cAc	25/38	0.324179603107441	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.324179603107441	1		374	898	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344009	70344009	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs772155788	NA	P-0002678-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	257	235	0	ENST00000374080.3:c.1745C>T	p.Thr582Met	p.T582M	ENST00000374080		582	aCg/aTg	13/45	1	1	FACETS	0.894	0.841	0.948	1	0.995	1	CLONAL	2	TRUE	0	0.324179603107441	1		235	743	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578423	7578424	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0002678-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	173	298	0	ENST00000269305.4:c.506dup	p.Met169IlefsTer12	p.M169Ifs*12	ENST00000269305	NM_001126112.2	169	atg/atTg	5/11	0.324179603107441	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.324179603107441	1		298	796	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667850	37667850	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002796-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	63	323	0	ENST00000447079.4:c.2735G>C	p.Arg912Pro	p.R912P	ENST00000447079	NM_015083.1	912	cGt/cCt	8/14	1	2	FACETS	0.768	0.671	0.871	0.768	0.671	0.871	SUBCLONAL	1	FALSE	1	0.600998850456768	2		323	273	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386450	31386450	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0002796-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	34	118	0	ENST00000328111.2:c.1674+1G>C		p.X558_splice	ENST00000328111	NM_006892.3	558			1	2	FACETS	0.666	0.55	0.791	0.666	0.55	0.791	SUBCLONAL	1	FALSE	1	0.600998850456768	2		118	170	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627417	37627418	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0002796-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	51	235	0	ENST00000447079.4:c.1337dup	p.Leu447ValfsTer15	p.L447Vfs*15	ENST00000447079	NM_015083.1	444	-/A	2/14	1	2	FACETS	0.682	0.585	0.786	0.682	0.585	0.786	SUBCLONAL	1	FALSE	1	0.600998850456768	2		235	249	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439682	51439682	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002805-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	514	239	0	ENST00000262662.1:c.247C>A	p.Leu83Met	p.L83M	ENST00000262662		83	Ctg/Atg	4/4	0.881605755720071	1	FACETS	0.981	0.955	1	0.981	0.955	1	CLONAL	1	TRUE	0	0.881605755720071	1		239	665	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435443	56435443	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002805-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	464	210	0	ENST00000407977.2:c.1694A>G	p.His565Arg	p.H565R	ENST00000407977		565	cAt/cGt	9/10	1	2	FACETS	0.876	0.838	0.914	0.876	0.838	0.914	CLONAL	1	TRUE	1	0.881605755720071	2		210	1202	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226949	2226949	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002805-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	436	147	0	ENST00000398665.3:c.4429G>A	p.Gly1477Ser	p.G1477S	ENST00000398665	NM_032482.2	1477	Ggc/Agc	27/28	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.881605755720071	2		147	918	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737798	145737799	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCA	novel	NA	P-0002805-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	423	168	0	ENST00000428558.2:c.3029_3031dup	p.Leu1010dup	p.L1010dup	ENST00000428558	NM_004260.3	1010	cag/cTGCag	18/22	0.881605755720071	2	FACETS	0.91	0.87	0.951	0.455	0.435	0.476	CLONAL	1	TRUE	0	0.881605755720071	2		168	1054	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0002958-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	167	524	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	NA	2	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.596596391546791	2		524	516	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577196	64577196	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1565651223	NA	P-0002958-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	100	568	2	ENST00000312049.6:c.386del	p.Leu129ProfsTer56	p.L129Pfs*56	ENST00000312049	NM_130799.2	129	cTc/cc	2/10	0.596596391546791	1	FACETS	0.865	0.785	0.947	0.865	0.785	0.947	CLONAL	1	TRUE	0	0.596596391546791	1		570	272	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980435	7980435	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760428119	NA	P-0002961-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	91	441	0	ENST00000319144.4:c.1148C>T	p.Thr383Met	p.T383M	ENST00000319144	NM_001139.2	383	aCg/aTg	9/15	1	2	FACETS	0.944	0.842	1	1	0.985	1	CLONAL	2	TRUE	1	0.21	2		441	459	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366981	15366982	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002961-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	83	724	1	ENST00000263377.2:c.1644dup	p.Glu549ArgfsTer13	p.E549Rfs*13	ENST00000263377	NM_058243.2	548	-/A	9/20	0.167665362430373	0	FACETS	1	0.948	1			1	CLONAL	1	TRUE	0	0.21	0		725	553	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002975-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	117	157	1	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.425514413208132	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	2	TRUE	0	0.425514413208132	2		158	275	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002975-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	79	561	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	NA	2	FACETS	1	0.967	1			1	INDETERMINATE	1	TRUE	NA	0.425514413208132	2		561	297	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574690	64574690	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002975-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	92	147	0	ENST00000312049.6:c.785del	p.Lys262SerfsTer19	p.K262Sfs*19	ENST00000312049	NM_130799.2	262	aAg/ag	5/10	NA	2	FACETS	0.905	0.818	0.993			1	INDETERMINATE	2	TRUE	NA	0.425514413208132	2		147	239	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812172	212812172	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002975-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	35	213	0	ENST00000342788.4:c.404G>T	p.Gly135Val	p.G135V	ENST00000342788	NM_005235.2	135	gGa/gTa	3/28	0.425514413208132	3	FACETS	0.506	0.415	0.609	0.253	0.207	0.305	SUBCLONAL	1	TRUE	1	0.425514413208132	3		213	394	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198263184	198263184	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0121502-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	193	375	0	ENST00000335508.6:c.3134+1G>A		p.X1045_splice	ENST00000335508	NM_012433.2	1045			0.381045170321574	3	FACETS	0.67	0.619	0.723	0.335	0.309	0.362	INDETERMINATE	1	NA	1	0.725741618874096	3		375	1082	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146576	55146576	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs751123873	NA	P-0121502-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	143	372	0	ENST00000257290.5:c.2250G>T	p.Glu750Asp	p.E750D	ENST00000257290	NM_006206.4	750	gaG/gaT	16/23	0.278854226707859	3	FACETS	0.692	0.631	0.756	0.346	0.315	0.378	INDETERMINATE	1	NA	1	0.725741618874096	3		372	776	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170321	119170321	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs768228850	NA	P-0121502-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	216	281	2	ENST00000264033.4:c.2551G>T	p.Ala851Ser	p.A851S	ENST00000264033	NM_005188.3	851	Gcc/Tcc	16/16	0.725741618874096	2	FACETS	1	0.99	1	0.629	0.592	0.667	CLONAL	1	NA	0	0.725741618874096	2		283	473	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727908	41727909	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0121502-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	112	407	0	ENST00000301178.4:c.538dup	p.Leu180ProfsTer30	p.L180Pfs*30	ENST00000301178	NM_021913.4	178	gtc/gtCc	4/20	1	2	FACETS	0.433	0.39	0.479	0.433	0.39	0.479	SUBCLONAL	1	NA	1	0.725741618874096	2		407	712	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0003119-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	54	985	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	1	2	FACETS	0.724	0.616	0.844	0.724	0.616	0.844	SUBCLONAL	1	TRUE	1	0.14	2		985	1065	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665210	138665210	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003119-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	54	1055	1	ENST00000330315.3:c.355G>T	p.Gly119Cys	p.G119C	ENST00000330315	NM_023067.3	119	Ggc/Tgc	1/1	1	2	FACETS	0.726	0.618	0.846	0.726	0.618	0.846	SUBCLONAL	1	TRUE	1	0.14	2		1056	1062	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55143565	55143565	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003119-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	25	427	0	ENST00000257290.5:c.1797G>T	p.Leu599Phe	p.L599F	ENST00000257290	NM_006206.4	599	ttG/ttT	13/23	1	2	FACETS	0.788	0.62	0.982	0.788	0.62	0.982	CLONAL	1	TRUE	1	0.14	2		427	453	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600392	10600392	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003119-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	82	1031	0	ENST00000171111.5:c.1463A>T	p.Glu488Val	p.E488V	ENST00000171111	NM_203500.1	488	gAg/gTg	4/6	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.14	2		1031	1090	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0003162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	443	682	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	0.805522830895287	2	FACETS	0.931	0.907	0.954	0.931	0.907	0.954	CLONAL	2	TRUE	0	0.863275778606898	2		682	551	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544703	65544703	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs387906650	NA	P-0003162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	569	537	2	ENST00000358664.4:c.223C>T	p.Arg75Ter	p.R75*	ENST00000358664	NM_002382.4	75	Cga/Tga	4/5	0.863275778606898	1	FACETS	0.891	0.865	0.916	0.891	0.865	0.916	CLONAL	1	TRUE	0	0.863275778606898	1		539	841	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599341	55599341	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519761	NA	P-0003162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	273	898	0	ENST00000288135.5:c.2467T>G	p.Tyr823Asp	p.Y823D	ENST00000288135	NM_000222.2	823	Tat/Gat	17/21	0.805522830895287	2	FACETS	0.865	0.816	0.915	0.433	0.408	0.458	CLONAL	1	TRUE	0	0.863275778606898	2		898	731	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166103	118166103	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	202	525	0	ENST00000369448.3:c.613C>T	p.His205Tyr	p.H205Y	ENST00000369448	NM_017709.3	205	Cac/Tac	2/2	0.863275778606898	1	FACETS	0.933	0.89	0.975	0.933	0.89	0.975	CLONAL	1	TRUE	0	0.863275778606898	1		525	285	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10244910	10244910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	771	1489	1	ENST00000340748.4:c.4799C>T	p.Ala1600Val	p.A1600V	ENST00000340748		1600	gCc/gTc	39/40	0.438117428011934	3	FACETS	0.875	0.849	0.901	0.875	0.849	0.901	INDETERMINATE	2	TRUE	1	0.863275778606898	3		1490	1461	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0003247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	24	613	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.2120098410062	4	FACETS	1	0.898	1	0.629	0.496	0.782	CLONAL	1	FALSE	2	0.2120098410062	4		614	218	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457168	25457168	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	13	802	0	ENST00000264709.3:c.2719G>T	p.Glu907Ter	p.E907*	ENST00000264709	NM_175629.2	907	Gag/Tag	23/23	0.193978799033701	0	FACETS	0.572	0.409	0.769			1	SUBCLONAL	1	FALSE	0	0.2120098410062	0		802	169	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251839	212251839	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	15	403	1	ENST00000342788.4:c.3220G>A	p.Glu1074Lys	p.E1074K	ENST00000342788	NM_005235.2	1074	Gaa/Aaa	27/28	0.126615166434081	4	FACETS	0.849	0.629	1	0.849	0.629	1	INDETERMINATE	2	FALSE	2	0.2120098410062	4		404	101	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355224	81355224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745555932	NA	P-0003247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	17	480	0	ENST00000222390.5:c.1150G>A	p.Asp384Asn	p.D384N	ENST00000222390	NM_000601.4	384	Gat/Aat	9/18	0.2120098410062	1	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	FALSE	0	0.2120098410062	1		480	111	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577518	7577518	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519995	NA	P-0003247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	21	1140	0	ENST00000269305.4:c.763A>T	p.Ile255Phe	p.I255F	ENST00000269305	NM_001126112.2	255	Atc/Ttc	7/11	0.2120098410062	5	FACETS	0.811	0.629	1			1	CLONAL	2	FALSE	NA	0.2120098410062	5		1140	161	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131408	17131408	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	14	916	0	ENST00000285071.4:c.44G>T	p.Gly15Val	p.G15V	ENST00000285071	NM_144997.5	15	gGc/gTc	4/14	0.2120098410062	0	FACETS	0.897	0.655	1			1	CLONAL	1	FALSE	0	0.2120098410062	0		916	116	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019534	123019534	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	29	831	0	ENST00000355640.3:c.22G>A	p.Gly8Arg	p.G8R	ENST00000355640		8	Gga/Aga	2/7	0.2120098410062	0	FACETS	1	0.9	1			1	CLONAL	1	FALSE	0	0.2120098410062	0		831	182	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904946	101904947	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0003247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	15	495	1	ENST00000374994.4:c.934_935delinsTT	p.Gly312Phe	p.G312F	ENST00000374994	NM_004612.2	312	GGt/TTt	5/9	0.2120098410062	0	FACETS	0.899	0.664	1			1	CLONAL	1	FALSE	0	0.2120098410062	0		496	124	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17350503	17350503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201517260	NA	P-0003247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	10	1034	0	ENST00000375499.3:c.607G>A	p.Gly203Arg	p.G203R	ENST00000375499	NM_003000.2	203	Gga/Aga	6/8	1	2	FACETS	0.536	0.363	0.752	0.536	0.363	0.752	SUBCLONAL	1	FALSE	1	0.2120098410062	2		1034	176	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432575	49432575	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1285381948	NA	P-0003247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	25	1171	1	ENST00000301067.7:c.8564C>T	p.Ala2855Val	p.A2855V	ENST00000301067	NM_003482.3	2855	gCg/gTg	34/54	0.2120098410062	4	FACETS	0.882	0.702	1	0.882	0.702	1	CLONAL	2	FALSE	2	0.2120098410062	4		1172	162	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515195	31515195	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	15	1634	2	ENST00000344624.3:c.1190C>G	p.Pro397Arg	p.P397R	ENST00000344624		397	cCt/cGt	5/33	0.2120098410062	0	FACETS	0.796	0.587	1			1	CLONAL	1	FALSE	0	0.2120098410062	0		1636	140	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	142	685	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.337678046271382	3	FACETS	0.967	0.897	1	0.967	0.897	1	INDETERMINATE	2	TRUE	1	0.642329461174572	3		685	302	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	34	251	0				ENST00000310581	NM_198253.2	-/1132			0.356077116031416	1	FACETS	0.413	0.341	0.492	0.413	0.341	0.492	INDETERMINATE	1	TRUE	0	0.642329461174572	1		251	174	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	242	218	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.642329461174572	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.642329461174572	1		218	469	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338683	70338683	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	282	190	0	ENST00000374080.3:c.79C>G	p.Gln27Glu	p.Q27E	ENST00000374080		27	Cag/Gag	1/45	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.642329461174572	1		190	515	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938203	36938203	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	286	334	1	ENST00000361632.4:c.758G>A	p.Trp253Ter	p.W253*	ENST00000361632		253	tGg/tAg	6/16	1	2	FACETS	0.996	0.939	1	0.996	0.939	1	CLONAL	1	TRUE	1	0.642329461174572	2		335	894	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149808	202149808	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	87	277	0	ENST00000358485.4:c.1249C>G	p.Gln417Glu	p.Q417E	ENST00000358485	NM_001080125.1	417	Cag/Gag	8/9	0.416141370268208	1	FACETS	0.337	0.299	0.378	0.337	0.299	0.378	SUBCLONAL	1	TRUE	0	0.642329461174572	1		277	545	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662805	227662805	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	219	282	0	ENST00000305123.5:c.650C>A	p.Ser217Ter	p.S217*	ENST00000305123	NM_005544.2	217	tCg/tAg	1/2	0.416141370268208	1	FACETS	0.768	0.719	0.817	0.768	0.719	0.817	SUBCLONAL	1	TRUE	0	0.642329461174572	1		282	603	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294370	1294370	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	63	127	0	ENST00000310581.5:c.631G>A	p.Gly211Arg	p.G211R	ENST00000310581	NM_198253.2	211	Ggg/Agg	2/16	0.356077116031416	1	FACETS	0.376	0.327	0.429	0.376	0.327	0.429	INDETERMINATE	1	TRUE	0	0.642329461174572	1		127	354	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742824	145742824	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	69	54	0	ENST00000428558.2:c.187G>T	p.Glu63Ter	p.E63*	ENST00000428558	NM_004260.3	63	Gag/Tag	3/22	0.284213056879647	2	FACETS	0.888	0.784	0.997	0.444	0.392	0.499	INDETERMINATE	1	TRUE	0	0.642329461174572	2		54	242	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853288	68853288	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	114	224	0	ENST00000261769.5:c.1671G>C	p.Lys557Asn	p.K557N	ENST00000261769	NM_004360.3	557	aaG/aaC	11/16	0.310317510774986	0	FACETS	0.193	0.173	0.213			1	INDETERMINATE	1	TRUE	0	0.642329461174572	0		224	659	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272338	15272338	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751050359	NA	P-0003279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	159	143	0	ENST00000263388.2:c.6101C>T	p.Pro2034Leu	p.P2034L	ENST00000263388	NM_000435.2	2034	cCc/cTc	33/33	0.262076670330432	1	FACETS	0.757	0.7	0.815	0.757	0.7	0.815	INDETERMINATE	1	TRUE	0	0.642329461174572	1		143	444	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164851	36164852	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0003279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	136	163	0	ENST00000300305.3:c.1023dup	p.Ile342HisfsTer258	p.I342Hfs*258	ENST00000300305		341	-/C	8/8	1	2	FACETS	0.753	0.688	0.822	0.753	0.688	0.822	SUBCLONAL	1	TRUE	1	0.642329461174572	2		163	562	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440302	52440310	+	inframe_deletion	In_Frame_Del	DEL	CACCTTCAG	CACCTTCAG	-	novel	NA	P-0003279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	209	242	0	ENST00000460680.1:c.742_750del	p.Leu248_Val250del	p.L248_V250del	ENST00000460680	NM_004656.3	248	CTGAAGGTG/-	9/17	0.642329461174572	1	FACETS	0.92	0.864	0.977	0.92	0.864	0.977	CLONAL	1	TRUE	0	0.642329461174572	1		242	480	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248998	55248999	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCCAGCG	rs727504263	NA	P-0003282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	287	243	1	ENST00000275493.2:c.2300_2308dup	p.Ala767_Val769dup	p.A767_V769dup	ENST00000275493	NM_005228.3	767	atg/aTGGCCAGCGtg	20/28	0.582469101862715	3	FACETS	0.839	0.793	0.886	0.839	0.793	0.886	CLONAL	2	TRUE	1	0.592763354685848	3		244	748	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379455	225379455	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	199	243	0	ENST00000264414.4:c.413A>G	p.Asn138Ser	p.N138S	ENST00000264414	NM_003590.4	138	aAc/aGc	4/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.592763354685848	2		243	657	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250922	153250922	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	199	262	0	ENST00000281708.4:c.1138G>C	p.Asp380His	p.D380H	ENST00000281708	NM_033632.3	380	Gat/Cat	8/12	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.592763354685848	2		262	613	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3929856	3929856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1211983012	NA	P-0003282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	396	262	0	ENST00000262367.5:c.62G>A	p.Gly21Asp	p.G21D	ENST00000262367	NM_004380.2	21	gGt/gAt	1/31	0.371777535412044	5	FACETS	1	0.992	1	0.79	0.753	0.828	CLONAL	2	TRUE	2	0.592763354685848	5		262	1065	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836321	89836348	+	frameshift_variant	Frame_Shift_Del	DEL	CACCAGGTGCAGGAGGACCCACATCCAC	CACCAGGTGCAGGAGGACCCACATCCAC	-	novel	NA	P-0003282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	156	269	0	ENST00000389301.3:c.2401_2428del	p.Val801LeufsTer13	p.V801Lfs*13	ENST00000389301	NM_000135.2	801	GTGGATGTGGGTCCTCCTGCACCTGGTGct/ct	26/43	NA	2	FACETS	0.952	0.877	1			1	INDETERMINATE	1	TRUE	NA	0.592763354685848	2		269	553	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003329-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	46	574	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	0.846	0.715	0.989	0.846	0.715	0.989	CLONAL	1	TRUE	1	0.32	2		574	340	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338632	70338632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003329-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	108	922	0	ENST00000374080.3:c.28G>A	p.Glu10Lys	p.E10K	ENST00000374080		10	Gaa/Aaa	1/45	1	2	FACETS	0.846	0.759	0.938	0.846	0.759	0.938	CLONAL	1	TRUE	1	0.32	2		922	798	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484597	57484597	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs137854533	NA	P-0003329-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	106	748	0	ENST00000371085.3:c.681G>T	p.Gln227His	p.Q227H	ENST00000371085	NM_000516.4	227	caG/caT	9/13	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.32	2		748	603	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270138	66270138	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003329-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	87	740	1	ENST00000273854.3:c.1744G>A	p.Gly582Arg	p.G582R	ENST00000273854	NM_004439.5	582	Gga/Aga	8/18	1	2	FACETS	0.884	0.784	0.991	0.884	0.784	0.991	CLONAL	1	TRUE	1	0.32	2		741	615	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023858	27023858	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003329-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	60	496	0	ENST00000324856.7:c.964G>T	p.Asp322Tyr	p.D322Y	ENST00000324856	NM_006015.4	322	Gac/Tac	1/20	0.304922770469219	1	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	0	0.32	1		496	303	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852473	63852473	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003329-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	101	840	1	ENST00000279873.7:c.3251G>A	p.Gly1084Glu	p.G1084E	ENST00000279873	NM_032199.2	1084	gGg/gAg	10/10	1	2	FACETS	0.927	0.829	1	0.927	0.829	1	CLONAL	1	TRUE	1	0.32	2		841	681	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846326	156846326	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003329-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	150	1239	0	ENST00000524377.1:c.1767T>G	p.Phe589Leu	p.F589L	ENST00000524377	NM_002529.3	589	ttT/ttG	14/17	0.297657166945799	2	FACETS	0.905	0.826	0.988	0.452	0.413	0.494	CLONAL	1	TRUE	0	0.32	2		1239	1036	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	29	251	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.957	0.793	1	0.957	0.793	1	CLONAL	1	TRUE	1	0.73	2		251	83	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0003388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	77	187	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.811	0.722	0.905	0.811	0.722	0.905	CLONAL	1	TRUE	1	0.73	2		187	260	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	74	169	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.834	0.741	0.932	0.834	0.741	0.932	CLONAL	1	TRUE	1	0.73	2		169	243	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045688	26045688	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1350355423	NA	P-0003388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	165	702	2	ENST00000540144.1:c.50C>T	p.Pro17Leu	p.P17L	ENST00000540144	NM_003531.2	17	cCg/cTg	1/1	1	2	FACETS	0.48	0.441	0.522	0.48	0.441	0.522	SUBCLONAL	1	TRUE	1	0.73	2		704	941	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847400	68847400	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0003388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	199	337	0	ENST00000261769.5:c.1320+2T>G		p.X440_splice	ENST00000261769	NM_004360.3	440			1	2	FACETS	0.977	0.912	1	0.977	0.912	1	CLONAL	1	TRUE	1	0.73	2		337	558	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243995	41243995	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	78	379	0	ENST00000357654.3:c.3553G>C	p.Glu1185Gln	p.E1185Q	ENST00000357654	NM_007294.3	1185	Gag/Cag	10/23	0.3	1	FACETS	0.308	0.271	0.347	0.308	0.271	0.347	INDETERMINATE	1	TRUE	0	0.73	1		379	441	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566424	41566424	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	208	380	0	ENST00000263253.7:c.4301A>G	p.His1434Arg	p.H1434R	ENST00000263253	NM_001429.3	1434	cAt/cGt	27/31	1	2	FACETS	0.865	0.807	0.924	0.865	0.807	0.924	CLONAL	1	TRUE	1	0.73	2		380	659	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171455	123171455	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	89	490	0	ENST00000218089.9:c.367C>T	p.Gln123Ter	p.Q123*	ENST00000218089	NM_001042749.1	123	Cag/Tag	6/35	1	2	FACETS	0.33	0.293	0.371	0.33	0.293	0.371	SUBCLONAL	1	TRUE	1	0.73	2		490	738	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220546	123220546	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	118	610	0	ENST00000218089.9:c.3203C>A	p.Ser1068Ter	p.S1068*	ENST00000218089	NM_001042749.1	1068	tCa/tAa	30/35	1	2	FACETS	0.409	0.368	0.451	0.409	0.368	0.451	SUBCLONAL	1	TRUE	1	0.73	2		610	791	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574883	41574884	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0003388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	241	484	0	ENST00000263253.7:c.7170dup	p.Thr2391HisfsTer9	p.T2391Hfs*9	ENST00000263253	NM_001429.3	2390	gcc/gCcc	31/31	1	2	FACETS	0.954	0.896	1	0.954	0.896	1	CLONAL	1	TRUE	1	0.73	2		484	692	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820585	44820585	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	215	593	0	ENST00000377967.4:c.284del	p.Phe95SerfsTer5	p.F95Sfs*5	ENST00000377967	NM_021140.2	94	gaT/ga	3/29	1	2	FACETS	0.839	0.783	0.896	0.839	0.783	0.896	CLONAL	1	TRUE	1	0.73	2		593	702	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720625	89720687	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTCTTTTCTTTTTTTTTTTTTTTAGGACAAAATGTTTCACTTTTGGGTAAATACATTCTTCA	TTTCTTTTCTTTTTTTTTTTTTTTAGGACAAAATGTTTCACTTTTGGGTAAATACATTCTTCA	-	novel	NA	P-0003506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	53	107	0	ENST00000371953.3:c.802-25_839del		p.X268_splice	ENST00000371953	NM_000314.4	268		8/9	0.581781152262044	1	FACETS	0.742	0.648	0.84	0.742	0.648	0.84	SUBCLONAL	1	TRUE	0	0.66	1		107	145	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690296	117690297	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	110	306	0	ENST00000369458.3:c.832dup	p.Tyr278LeufsTer34	p.Y278Lfs*34	ENST00000369458	NM_024626.3	278	tac/tTac	5/6	0.129272263819761	3	FACETS	0.833	0.752	0.919	0.417	0.376	0.46	INDETERMINATE	1	TRUE	1	0.66	3		306	532	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0003523-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	116	392	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	1	0.389098315430591	2		392	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0003523-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	9	555	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.389098315430591	1	FACETS	0.113	0.074	0.163	0.113	0.074	0.163	SUBCLONAL	1	FALSE	0	0.389098315430591	1		555	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0003523-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	65	631	2	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.389098315430591	1	FACETS	0.739	0.644	0.841	0.739	0.644	0.841	SUBCLONAL	1	FALSE	0	0.389098315430591	1		633	364	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36934771	36934771	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003523-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	155	1030	0	ENST00000361632.4:c.1562A>G	p.Tyr521Cys	p.Y521C	ENST00000361632		521	tAc/tGc	11/16	1	2	FACETS	0.893	0.818	0.972	0.893	0.818	0.972	CLONAL	1	FALSE	1	0.389098315430591	2		1030	892	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256600	115256600	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003523-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	62	257	0	ENST00000369535.4:c.112-1G>A		p.X38_splice	ENST00000369535	NM_002524.4	38			0.133547162755045	3	FACETS	0.964	0.836	1	0.482	0.418	0.551	INDETERMINATE	1	FALSE	1	0.389098315430591	3		257	395	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163115	47163115	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003523-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	131	421	0	ENST00000409792.3:c.3011A>T	p.Asp1004Val	p.D1004V	ENST00000409792	NM_014159.6	1004	gAt/gTt	3/21	0.389098315430591	1	FACETS	0.902	0.822	0.987	0.902	0.822	0.987	CLONAL	1	FALSE	0	0.389098315430591	1		421	601	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624564	93624564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs968372087	NA	P-0003523-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	129	669	0	ENST00000375746.1:c.655G>A	p.Asp219Asn	p.D219N	ENST00000375746	NM_001174167.1	219	Gac/Aac	4/14	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	FALSE	1	0.389098315430591	2		669	653	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251991	8251991	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs760736132	NA	P-0003523-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	94	642	0	ENST00000335790.3:c.86G>T	p.Arg29Leu	p.R29L	ENST00000335790	NM_002315.2	29	cGc/cTc	2/4	0.174675545469298	1	FACETS	0.718	0.641	0.8	0.718	0.641	0.8	INDETERMINATE	1	FALSE	0	0.389098315430591	1		642	542	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352365	70352365	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003523-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	148	1131	0	ENST00000374080.3:c.4392A>T	p.Glu1464Asp	p.E1464D	ENST00000374080		1464	gaA/gaT	31/45	0.129720431893268	0	FACETS	0.526	0.48	0.574			1	INDETERMINATE	1	FALSE	0	0.389098315430591	0		1131	884	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99809063	99809064	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003523-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	134	470	0	ENST00000280892.6:c.321dup	p.Gly108TrpfsTer3	p.G108Wfs*3	ENST00000280892	NM_001130678.1	107	-/T	4/7	1	2	FACETS	0.763	0.693	0.837	0.763	0.693	0.837	SUBCLONAL	1	FALSE	1	0.389098315430591	2		470	903	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863217	57863218	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0003523-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	82	877	0	ENST00000228682.2:c.1312_1313delinsAA	p.Pro438Lys	p.P438K	ENST00000228682	NM_005269.2	438	CCa/AAa	11/12	0.389098315430591	1	FACETS	0.608	0.537	0.684	0.608	0.537	0.684	SUBCLONAL	1	FALSE	0	0.389098315430591	1		877	558	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	121	157	1	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.620032731789257	4	FACETS	1	0.974	1	0.6	0.544	0.658	CLONAL	1	TRUE	2	0.620032731789257	4		158	527	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677925	58677948	+	inframe_deletion	In_Frame_Del	DEL	TCCGCGGCCGTCGCCGGCCGCCCT	TCCGCGGCCGTCGCCGGCCGCCCT	-	novel	NA	P-0003581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	124	228	0	ENST00000305921.3:c.153_176del	p.Arg52_Pro59del	p.R52_P59del	ENST00000305921	NM_003620.3	50	ccTCCGCGGCCGTCGCCGGCCGCCCTt/cct	1/6	0.620032731789257	6	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.620032731789257	6		228	685	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111471	8111472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0003581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	150	289	0	ENST00000346208.3:c.958dup	p.Cys320LeufsTer32	p.C320Lfs*32	ENST00000346208		319	-/T	5/6	0.620032731789257	3	FACETS	0.995	0.913	1	0.498	0.456	0.541	CLONAL	1	TRUE	1	0.620032731789257	3		289	637	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115922	8115923	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCG	novel	NA	P-0003581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	74	185	0	ENST00000346208.3:c.1271_1274dup	p.Ser426AlafsTer82	p.S426Afs*82	ENST00000346208		423	cac/caCCCGc	6/6	0.620032731789257	3	FACETS	0.784	0.69	0.884	0.392	0.345	0.442	SUBCLONAL	1	TRUE	1	0.620032731789257	3		185	399	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0003690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	56	187	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.673638868538124	2		187	116	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0003690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	61	245	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.673638868538124	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.673638868538124	1		245	86	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514647	44514647	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	81	278	0	ENST00000291552.4:c.509A>G	p.Asn170Ser	p.N170S	ENST00000291552	NM_006758.2	170	aAc/aGc	7/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.673638868538124	2		278	162	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942719	44942719	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	49	373	0	ENST00000377967.4:c.3299T>C	p.Leu1100Pro	p.L1100P	ENST00000377967	NM_021140.2	1100	cTa/cCa	23/29	0.227086110992212	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.673638868538124	0		373	95	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952146	178952147	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587776802	NA	P-0003690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	57	214	0	ENST00000263967.3:c.3203dup	p.Asn1068LysfsTer5	p.N1068Kfs*5	ENST00000263967	NM_006218.2	1067	-/A	21/21	0.673638868538124	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	1	0.673638868538124	3		214	101	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418729	49418731	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GCT	GCT	-	novel	NA	P-0003690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	51	185	0	ENST00000301067.7:c.15785-2_15785del		p.X5262_splice	ENST00000301067	NM_003482.3	5262		49/54	1	2	FACETS	0.94	0.815	1	0.94	0.815	1	CLONAL	1	TRUE	1	0.673638868538124	2		185	161	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433091	49433092	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	62	338	0	ENST00000301067.7:c.8279dup	p.Leu2761ProfsTer8	p.L2761Pfs*8	ENST00000301067	NM_003482.3	2760	atc/atTc	33/54	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.673638868538124	2		338	129	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556651	41556652	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0003690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	50	185	0	ENST00000263253.7:c.3599dup	p.Cys1201LeufsTer2	p.C1201Lfs*2	ENST00000263253	NM_001429.3	1199	cat/caTt	20/31	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.673638868538124	2		185	115	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923055	44923056	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0003690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	35	295	0	ENST00000377967.4:c.1916_1917insTA	p.Gln641LeufsTer51	p.Q641Lfs*51	ENST00000377967	NM_021140.2	639	tcc/tcTAc	16/29	0.227086110992212	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.673638868538124	0		295	105	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059179	47059179	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	187	330	0	ENST00000409792.3:c.7482C>A	p.Cys2494Ter	p.C2494*	ENST00000409792	NM_014159.6	2494	tgC/tgA	20/21	0.748568559384429	1	FACETS	0.911	0.858	0.965	0.911	0.858	0.965	CLONAL	1	TRUE	0	0.748568559384429	1		330	343	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933739	39933740	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCTTTTGTCTGCGCAATG	novel	NA	P-0003724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	173	192	0	ENST00000378444.4:c.841_859dup	p.Leu287ProfsTer20	p.L287Pfs*20	ENST00000378444	NM_001123385.1	287	ctc/cCATTGCGCAGACAAAAGCCtc	4/15	1	1	FACETS	0.841	0.787	0.894	0.841	0.787	0.894	CLONAL	1	TRUE	0	0.748568559384429	1		192	344	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0004017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	151	303	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	NA	2	FACETS	1	0.93	1			1	INDETERMINATE	2	TRUE	NA	0.41	2		303	367	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0004017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	72	184	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	NA	2	FACETS	1	0.955	1			1	INDETERMINATE	1	TRUE	NA	0.41	2		184	298	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	15	400	0	ENST00000269305.4:c.380C>A	p.Ser127Tyr	p.S127Y	ENST00000269305	NM_001126112.2	127	tCc/tAc	5/11	1	2	FACETS	0.278	0.203	0.368	0.278	0.203	0.368	SUBCLONAL	1	TRUE	1	0.41	2		400	263	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712580	52712580	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	98	236	0	ENST00000394830.3:c.172C>T	p.Arg58Ter	p.R58*	ENST00000394830	NM_018313.4	58	Cga/Tga	3/30	NA	2	FACETS	0.919	0.823	1			1	INDETERMINATE	1	TRUE	NA	0.41	2		236	520	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916768	48916768	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	56	177	0	ENST00000267163.4:c.298G>T	p.Gly100Ter	p.G100*	ENST00000267163	NM_000321.2	100	Gga/Tga	3/27	1	2	FACETS	0.856	0.738	0.984	0.856	0.738	0.984	CLONAL	1	TRUE	1	0.41	2		177	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578691	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGATGGCCATGGCGCGGACGCGGGTGCCGGGCGGGGGTGTGGAATCAACCCACAGCTGCACAGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAAGCAACTGGAAGACGGCAGCAAAGAAACAAACATGCGTAAGCACCTCCTGCAACCCACTAGCGAGCTAGAGAGAGTTGGCGT	AGATGGCCATGGCGCGGACGCGGGTGCCGGGCGGGGGTGTGGAATCAACCCACAGCTGCACAGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAAGCAACTGGAAGACGGCAGCAAAGAAACAAACATGCGTAAGCACCTCCTGCAACCCACTAGCGAGCTAGAGAGAGTTGGCGT	-	novel	NA	P-0004017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	38	142	0	ENST00000269305.4:c.376-135_489del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	1	2	FACETS	0.633	0.525	0.752	0.633	0.525	0.752	SUBCLONAL	1	TRUE	1	0.41	2		142	293	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891116	151891117	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTGTTGG	novel	NA	P-0004017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	52	156	0	ENST00000262189.6:c.4630_4637dup	p.Gln1546HisfsTer20	p.Q1546Hfs*20	ENST00000262189	NM_170606.2	1546	cag/caCCAACACAg	31/59	1	2	FACETS	0.75	0.642	0.868	0.75	0.642	0.868	SUBCLONAL	1	TRUE	1	0.41	2		156	338	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106000	27106001	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	43	82	0	ENST00000324856.7:c.5612dup	p.His1871GlnfsTer30	p.H1871Qfs*30	ENST00000324856	NM_006015.4	1871	cac/cAac	20/20	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.41	2		82	186	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106927	27106928	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	55	153	0	ENST00000324856.7:c.6539dup	p.Ala2181GlyfsTer44	p.A2181Gfs*44	ENST00000324856	NM_006015.4	2180	ctg/cTtg	20/20	1	2	FACETS	0.823	0.708	0.947	0.823	0.708	0.947	CLONAL	1	TRUE	1	0.41	2		153	326	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039179	49039180	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	77	266	0	ENST00000267163.4:c.2258dup	p.Val754SerfsTer4	p.V754Sfs*4	ENST00000267163	NM_000321.2	753	ata/aTta	22/27	1	2	FACETS	0.827	0.729	0.932	0.827	0.729	0.932	CLONAL	1	TRUE	1	0.41	2		266	454	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0004045-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	234	384	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.389049332280349	4	FACETS	0.975	0.913	1	0.488	0.456	0.52	CLONAL	2	TRUE	0	0.449431313534922	4		384	774	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0004045-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	284	576	0	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	0.401969282642742	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.449431313534922	1		576	787	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61197647	61197647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004045-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	159	547	0	ENST00000301761.2:c.29C>T	p.Ser10Leu	p.S10L	ENST00000301761	NM_017841.2	10	tCg/tTg	1/4	0.159239537352111	2	FACETS	0.705	0.646	0.768	0.353	0.323	0.384	INDETERMINATE	1	TRUE	0	0.449431313534922	2		547	1003	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715407	61715407	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0004045-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	123	421	0	ENST00000401558.2:c.2207-1G>A		p.X736_splice	ENST00000401558	NM_003400.3	736			0.33105875922193	3	FACETS	0.593	0.535	0.654	0.198	0.178	0.218	SUBCLONAL	1	TRUE	0	0.449431313534922	3		421	1131	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131976439	131976439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660400	NA	P-0004045-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	106	369	0	ENST00000265335.6:c.3694G>A	p.Glu1232Lys	p.E1232K	ENST00000265335		1232	Gag/Aag	24/25	0.382285637798828	3	FACETS	0.634	0.568	0.705	0.317	0.284	0.353	SUBCLONAL	1	TRUE	1	0.449431313534922	3		369	911	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577519	7577519	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004045-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	100	203	0	ENST00000269305.4:c.762C>G	p.Ile254Met	p.I254M	ENST00000269305	NM_001126112.2	254	atC/atG	7/11	0.401969282642742	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.449431313534922	1		203	320	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	64	251	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.824	0.727	0.925	0.824	0.727	0.925	CLONAL	1	TRUE	1	0.817765677812403	2		251	190	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	476	589	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.817765677812403	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.817765677812403	1		589	666	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	187	169	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.817765677812403	2		169	447	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261520	16261520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	265	277	1	ENST00000375759.3:c.8785G>A	p.Val2929Met	p.V2929M	ENST00000375759	NM_015001.2	2929	Gtg/Atg	11/15	1	2	FACETS	0.997	0.941	1	0.997	0.941	1	CLONAL	1	TRUE	1	0.817765677812403	2		278	650	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933216	36933216	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238508233	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1343	233	507	1	ENST00000361632.4:c.1901G>A	p.Gly634Asp	p.G634D	ENST00000361632		634	gGc/gAc	14/16	0.664883525272218	3	FACETS	0.509	0.473	0.547			1	SUBCLONAL	1	TRUE	NA	0.817765677812403	3		508	1576	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804214	43804214	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	305	291	0	ENST00000372470.3:c.214G>A	p.Glu72Lys	p.E72K	ENST00000372470	NM_005373.2	72	Gag/Aag	3/12	0.664883525272218	3	FACETS	1	0.976	1			1	CLONAL	1	TRUE	NA	0.817765677812403	3		291	990	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870379	155870379	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	215	405	0	ENST00000368323.3:c.460C>T	p.Arg154Ter	p.R154*	ENST00000368323	NM_006912.5	154	Cga/Tga	6/6	1	2	FACETS	0.481	0.447	0.517	0.481	0.447	0.517	SUBCLONAL	1	TRUE	1	0.817765677812403	2		405	1093	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161310391	161310391	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1222	368	515	0	ENST00000367975.2:c.187C>T	p.Leu63Phe	p.L63F	ENST00000367975	NM_003001.3	63	Ctt/Ttt	4/6	1	2	FACETS	0.566	0.535	0.597	0.566	0.535	0.597	SUBCLONAL	1	TRUE	1	0.817765677812403	2		515	1590	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25536849	25536849	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	67	257	0	ENST00000264709.3:c.5C>T	p.Pro2Leu	p.P2L	ENST00000264709	NM_175629.2	2	cCc/cTc	2/23	0.431028267338398	1	FACETS	0.265	0.231	0.301	0.265	0.231	0.301	INDETERMINATE	1	TRUE	0	0.817765677812403	1		257	366	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972834	25972834	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	214	428	0	ENST00000435504.4:c.1591C>A	p.Pro531Thr	p.P531T	ENST00000435504		531	Cct/Act	12/13	0.431028267338398	1	FACETS	0.352	0.327	0.377	0.352	0.327	0.377	INDETERMINATE	1	TRUE	0	0.817765677812403	1		428	880	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451806	29451806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746643773	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	163	305	0	ENST00000389048.3:c.2759G>A	p.Gly920Asp	p.G920D	ENST00000389048	NM_004304.4	920	gGt/gAt	16/29	0.431028267338398	1	FACETS	0.436	0.402	0.47	0.436	0.402	0.47	INDETERMINATE	1	TRUE	0	0.817765677812403	1		305	541	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566773	212566773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	459	386	0	ENST00000342788.4:c.1408C>T	p.His470Tyr	p.H470Y	ENST00000342788	NM_005235.2	470	Cat/Tat	12/28	0.431028267338398	1	FACETS	0.732	0.704	0.761	0.732	0.704	0.761	INDETERMINATE	1	TRUE	0	0.817765677812403	1		386	906	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812293	212812293	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569995088	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	177	342	0	ENST00000342788.4:c.283C>T	p.Arg95Cys	p.R95C	ENST00000342788	NM_005235.2	95	Cgt/Tgt	3/28	0.431028267338398	1	FACETS	0.385	0.356	0.416	0.385	0.356	0.416	INDETERMINATE	1	TRUE	0	0.817765677812403	1		342	664	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277257	41277257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	337	315	0	ENST00000349496.5:c.1726G>A	p.Ala576Thr	p.A576T	ENST00000349496	NM_001904.3	576	Gcc/Acc	11/15	0.431028267338398	1	FACETS	0.726	0.693	0.759	0.726	0.693	0.759	INDETERMINATE	1	TRUE	0	0.817765677812403	1		315	671	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164700	47164700	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	335	361	0	ENST00000409792.3:c.1426C>T	p.His476Tyr	p.H476Y	ENST00000409792	NM_014159.6	476	Cat/Tat	3/21	0.431028267338398	1	FACETS	0.761	0.727	0.796	0.761	0.727	0.796	INDETERMINATE	1	TRUE	0	0.817765677812403	1		361	636	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156900	89156900	+	start_lost	Translation_Start_Site	SNP	T	T	A	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	306	386	1	ENST00000336596.2:c.2T>A	p.Met1?	p.M1?	ENST00000336596	NM_005233.5	1	aTg/aAg	1/17	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.817765677812403	NA		387	701	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664730	138664730	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	12	22	0	ENST00000330315.3:c.835G>A	p.Gly279Ser	p.G279S	ENST00000330315	NM_023067.3	279	Ggc/Agc	1/1	1	2	FACETS	0.652	0.475	0.853	0.652	0.475	0.853	SUBCLONAL	1	TRUE	1	0.817765677812403	2		22	45	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188402	142188402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751140070	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	109	227	0	ENST00000350721.4:c.6329C>T	p.Ser2110Phe	p.S2110F	ENST00000350721	NM_001184.3	2110	tCc/tTc	38/47	1	2	FACETS	0.454	0.409	0.502	0.454	0.409	0.502	SUBCLONAL	1	TRUE	1	0.817765677812403	2		227	587	SUCCESS
ATR	545	MSKCC	GRCh37	3	142259791	142259791	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	417	409	0	ENST00000350721.4:c.3536G>A	p.Arg1179Lys	p.R1179K	ENST00000350721	NM_001184.3	1179	aGa/aAa	18/47	1	2	FACETS	0.987	0.943	1	0.987	0.943	1	CLONAL	1	TRUE	1	0.817765677812403	2		409	1033	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447240	187447240	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763822826	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	236	263	0	ENST00000232014.4:c.953C>T	p.Pro318Leu	p.P318L	ENST00000232014	NM_001130845.1	318	cCc/cTc	5/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.817765677812403	2		263	538	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540968	187540968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	201	187	0	ENST00000441802.2:c.6772G>A	p.Asp2258Asn	p.D2258N	ENST00000441802	NM_005245.3	2258	Gac/Aac	10/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.817765677812403	2		187	444	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924381	131924381	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1341798216	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	95	191	0	ENST00000265335.6:c.1054C>T	p.Arg352Cys	p.R352C	ENST00000265335		352	Cgt/Tgt	8/25	1	2	FACETS	0.556	0.498	0.617	0.556	0.498	0.617	SUBCLONAL	1	TRUE	1	0.817765677812403	2		191	418	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149436918	149436918	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	144	346	0	ENST00000286301.3:c.2251G>A	p.Glu751Lys	p.E751K	ENST00000286301	NM_005211.3	751	Gag/Aag	17/22	1	2	FACETS	0.528	0.483	0.575	0.528	0.483	0.575	SUBCLONAL	1	TRUE	1	0.817765677812403	2		346	667	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149450117	149450117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568352098	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	100	258	0	ENST00000286301.3:c.1100C>T	p.Ser367Phe	p.S367F	ENST00000286301	NM_005211.3	367	tCt/tTt	8/22	1	2	FACETS	0.457	0.409	0.507	0.457	0.409	0.507	SUBCLONAL	1	TRUE	1	0.817765677812403	2		258	535	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721012	176721012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	271	340	0	ENST00000439151.2:c.6643C>T	p.Pro2215Ser	p.P2215S	ENST00000439151	NM_022455.4	2215	Cct/Tct	23/23	1	2	FACETS	0.928	0.876	0.981	0.928	0.876	0.981	CLONAL	1	TRUE	1	0.817765677812403	2		340	714	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722083	176722083	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	122	281	0	ENST00000439151.2:c.7714C>T	p.Gln2572Ter	p.Q2572*	ENST00000439151	NM_022455.4	2572	Caa/Taa	23/23	1	2	FACETS	0.563	0.511	0.617	0.563	0.511	0.617	SUBCLONAL	1	TRUE	1	0.817765677812403	2		281	530	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047899	180047899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	166	244	0	ENST00000261937.6:c.2276C>T	p.Ser759Phe	p.S759F	ENST00000261937	NM_182925.4	759	tCc/tTc	15/30	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.817765677812403	2		244	403	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680764	30680764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	343	405	0	ENST00000376406.3:c.955G>A	p.Glu319Lys	p.E319K	ENST00000376406	NM_014641.2	319	Gaa/Aaa	5/15	0.476951508495705	3	FACETS	1	0.984	1	0.545	0.516	0.575	INDETERMINATE	1	TRUE	1	0.817765677812403	3		405	1084	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32189001	32189001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	321	395	0	ENST00000375023.3:c.553G>A	p.Gly185Ser	p.G185S	ENST00000375023	NM_004557.3	185	Ggc/Agc	4/30	0.476951508495705	3	FACETS	1	0.99	1	0.598	0.566	0.63	INDETERMINATE	1	TRUE	1	0.817765677812403	3		395	925	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43745403	43745403	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	477	485	1	ENST00000523873.1:c.315+1G>T		p.X105_splice	ENST00000523873		105			0.476951508495705	3	FACETS	1	0.995	1	0.63	0.602	0.657	INDETERMINATE	1	TRUE	1	0.817765677812403	3		486	1305	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517424	157517424	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	185	342	0	ENST00000346085.5:c.3988C>T	p.Pro1330Ser	p.P1330S	ENST00000346085	NM_020732.3	1330	Ccc/Tcc	16/20	0.788704132671875	2	FACETS	0.662	0.614	0.713	0.331	0.307	0.357	SUBCLONAL	1	TRUE	0	0.817765677812403	2		342	683	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771188	161771188	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	155	309	0	ENST00000366898.1:c.1341G>A	p.Trp447Ter	p.W447*	ENST00000366898	NM_004562.2	447	tgG/tgA	12/12	0.788704132671875	2	FACETS	0.67	0.616	0.725	0.335	0.308	0.363	SUBCLONAL	1	TRUE	0	0.817765677812403	2		309	566	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985494	2985494	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	244	422	0	ENST00000396946.4:c.317T>A	p.Val106Glu	p.V106E	ENST00000396946	NM_032415.4	106	gTg/gAg	4/25	0.431028267338398	1	FACETS	0.395	0.369	0.421	0.395	0.369	0.421	INDETERMINATE	1	TRUE	0	0.817765677812403	1		422	893	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878610	151878610	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	93	204	0	ENST00000262189.6:c.6335C>T	p.Pro2112Leu	p.P2112L	ENST00000262189	NM_170606.2	2112	cCt/cTt	36/59	1	2	FACETS	0.456	0.407	0.508	0.456	0.407	0.508	SUBCLONAL	1	TRUE	1	0.817765677812403	2		204	499	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862964	117862964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	230	502	0	ENST00000297338.2:c.1513C>T	p.Pro505Ser	p.P505S	ENST00000297338	NM_006265.2	505	Ccc/Tcc	12/14	1	2	FACETS	0.449	0.417	0.481	0.449	0.417	0.481	SUBCLONAL	1	TRUE	1	0.817765677812403	2		502	1254	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391340	139391340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1341934554	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	140	382	0	ENST00000277541.6:c.6851C>T	p.Thr2284Ile	p.T2284I	ENST00000277541	NM_017617.3	2284	aCc/aTc	34/34	0.410921973694613	2	FACETS	0.491	0.447	0.536	0.245	0.223	0.268	INDETERMINATE	1	TRUE	0	0.817765677812403	2		382	698	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412368	139412368	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	95	197	1	ENST00000277541.6:c.1277C>A	p.Ala426Glu	p.A426E	ENST00000277541	NM_017617.3	426	gCg/gAg	8/34	0.410921973694613	2	FACETS	0.553	0.495	0.614	0.277	0.247	0.307	INDETERMINATE	1	TRUE	0	0.817765677812403	2		198	420	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615541	43615541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	143	246	0	ENST00000355710.3:c.2620G>A	p.Asp874Asn	p.D874N	ENST00000355710	NM_020975.4	874	Gac/Aac	15/20	0.431028267338398	1	FACETS	0.418	0.384	0.454	0.418	0.384	0.454	INDETERMINATE	1	TRUE	0	0.817765677812403	1		246	494	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710676	114710676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	297	591	0	ENST00000543371.1:c.161C>T	p.Thr54Met	p.T54M	ENST00000543371	NM_001198531.1	54	aCg/aTg	1/14	0.431028267338398	1	FACETS	0.375	0.353	0.398	0.375	0.353	0.398	INDETERMINATE	1	TRUE	0	0.817765677812403	1		591	1145	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274831	123274831	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	149	289	0	ENST00000358487.5:c.1087C>T	p.Pro363Ser	p.P363S	ENST00000358487	NM_000141.4	363	Cct/Tct	9/18	0.431028267338398	1	FACETS	0.441	0.406	0.478	0.441	0.406	0.478	INDETERMINATE	1	TRUE	0	0.817765677812403	1		289	488	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533471	533472	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	160	208	0	ENST00000451590.1:c.431_432delinsTT	p.Thr144Ile	p.T144I	ENST00000451590	NM_001130442.1	144	aCC/aTT	4/5	0.817765677812403	1	FACETS	0.922	0.869	0.973	0.922	0.869	0.973	CLONAL	1	TRUE	0	0.817765677812403	1		208	251	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385207	4385207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	176	348	1	ENST00000261254.3:c.232C>T	p.Pro78Ser	p.P78S	ENST00000261254	NM_001759.3	78	Cct/Tct	2/5	NA	2	FACETS	0.468	0.431	0.506			1	INDETERMINATE	1	TRUE	NA	0.817765677812403	2		349	920	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491465	18491465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	168	332	0	ENST00000266497.5:c.1378C>T	p.Leu460Phe	p.L460F	ENST00000266497		460	Ctt/Ttt	8/31	1	2	FACETS	0.477	0.438	0.517	0.477	0.438	0.517	SUBCLONAL	1	TRUE	1	0.817765677812403	2		332	862	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231149	46231149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	67	405	0	ENST00000334344.6:c.1069C>T	p.His357Tyr	p.H357Y	ENST00000334344	NM_152641.2	357	Cat/Tat	9/21	1	2	FACETS	0.142	0.123	0.164	0.142	0.123	0.164	SUBCLONAL	1	TRUE	1	0.817765677812403	2		405	1150	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431811	49431811	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773164595	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	82	188	0	ENST00000301067.7:c.9328C>T	p.Arg3110Cys	p.R3110C	ENST00000301067	NM_003482.3	3110	Cgc/Tgc	34/54	1	2	FACETS	0.557	0.495	0.623	0.557	0.495	0.623	SUBCLONAL	1	TRUE	1	0.817765677812403	2		188	360	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432741	49432741	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1315374796	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	86	159	0	ENST00000301067.7:c.8398C>T	p.Gln2800Ter	p.Q2800*	ENST00000301067	NM_003482.3	2800	Cag/Tag	34/54	1	2	FACETS	0.61	0.544	0.679	0.61	0.544	0.679	SUBCLONAL	1	TRUE	1	0.817765677812403	2		159	345	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445728	49445728	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	333	476	0	ENST00000301067.7:c.1738C>G	p.Pro580Ala	p.P580A	ENST00000301067	NM_003482.3	580	Ccc/Gcc	10/54	1	2	FACETS	0.906	0.859	0.953	0.906	0.859	0.953	CLONAL	1	TRUE	1	0.817765677812403	2		476	899	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69207357	69207357	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	353	312	2	ENST00000462284.1:c.123G>C	p.Leu41Phe	p.L41F	ENST00000462284	NM_002392.5	41	ttG/ttC	3/11	1	2	FACETS	0.936	0.89	0.983	0.936	0.89	0.983	CLONAL	1	TRUE	1	0.817765677812403	2		314	922	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109881	115109881	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	125	165	0	ENST00000257566.3:c.1997C>A	p.Ala666Asp	p.A666D	ENST00000257566	NM_016569.3	666	gCc/gAc	8/8	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.817765677812403	2		165	282	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118941	115118941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	234	237	0	ENST00000257566.3:c.400C>T	p.Pro134Ser	p.P134S	ENST00000257566	NM_016569.3	134	Cct/Tct	2/8	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.817765677812403	2		237	565	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335930	73335930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs961788436	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	135	203	0	ENST00000377767.4:c.2365C>T	p.Arg789Trp	p.R789W	ENST00000377767	NM_014953.3	789	Cgg/Tgg	18/21	1	2	FACETS	0.497	0.453	0.544	0.497	0.453	0.544	SUBCLONAL	1	TRUE	1	0.817765677812403	2		203	664	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73340177	73340177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35017269	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	199	342	0	ENST00000377767.4:c.1903C>T	p.Pro635Ser	p.P635S	ENST00000377767	NM_014953.3	635	Cct/Tct	15/21	1	2	FACETS	0.488	0.451	0.525	0.488	0.451	0.525	SUBCLONAL	1	TRUE	1	0.817765677812403	2		342	998	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437404	110437404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	91	81	0	ENST00000375856.3:c.997C>T	p.Pro333Ser	p.P333S	ENST00000375856	NM_003749.2	333	Ccc/Tcc	1/2	0.522366704956546	3	FACETS	1	0.941	1			1	CLONAL	1	TRUE	NA	0.817765677812403	3		81	294	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582022	95582022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	333	297	0	ENST00000393063.1:c.1889C>T	p.Ala630Val	p.A630V	ENST00000393063	NM_030621.3	630	gCc/gTc	12/28	1	2	FACETS	0.99	0.94	1	0.99	0.94	1	CLONAL	1	TRUE	1	0.817765677812403	2		297	823	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023126	33023126	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	432	570	0	ENST00000300177.4:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000300177	NM_001191322.1	79	Gag/Cag	2/2	0.431028267338398	1	FACETS	0.717	0.688	0.746	0.717	0.688	0.746	INDETERMINATE	1	TRUE	0	0.817765677812403	1		570	871	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961523	41961523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	356	746	0	ENST00000219905.7:c.431C>T	p.Pro144Leu	p.P144L	ENST00000219905	NM_001164273.1	144	cCt/cTt	2/24	0.431028267338398	1	FACETS	0.384	0.363	0.405	0.384	0.363	0.405	INDETERMINATE	1	TRUE	0	0.817765677812403	1		746	1341	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994833	73994833	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	100	121	0	ENST00000318443.5:c.317C>T	p.Ser106Phe	p.S106F	ENST00000318443	NM_001024736.1	106	tCc/tTc	3/10	0.431028267338398	1	FACETS	0.786	0.722	0.848	0.786	0.722	0.848	INDETERMINATE	1	TRUE	0	0.817765677812403	1		121	184	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483925	88483925	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	381	396	1	ENST00000360948.2:c.1645T>A	p.Phe549Ile	p.F549I	ENST00000360948	NM_001012338.2	549	Ttt/Att	14/19	0.431028267338398	1	FACETS	0.748	0.717	0.78	0.748	0.717	0.78	INDETERMINATE	1	TRUE	0	0.817765677812403	1		397	736	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99491805	99491806	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	142	346	0	ENST00000268035.6:c.3590_3591delinsTT	p.Ser1197Phe	p.S1197F	ENST00000268035	NM_000875.3	1197	tCC/tTT	20/21	0.431028267338398	1	FACETS	0.312	0.285	0.34	0.312	0.285	0.34	INDETERMINATE	1	TRUE	0	0.817765677812403	1		346	658	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	338190	338190	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs370661416	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	515	599	0	ENST00000262320.3:c.2521C>T	p.Arg841Ter	p.R841*	ENST00000262320	NM_003502.3	841	Cga/Tga	11/11	0.18535307575654	3	FACETS	1	0.992	1	0.383	0.366	0.4	INDETERMINATE	1	TRUE	0	0.817765677812403	3		599	1544	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225598	2225598	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	237	286	0	ENST00000326181.6:c.1601A>T	p.Tyr534Phe	p.Y534F	ENST00000326181	NM_032271.2	534	tAc/tTc	17/21	0.18535307575654	3	FACETS	1	0.99	1	0.419	0.393	0.445	INDETERMINATE	1	TRUE	0	0.817765677812403	3		286	650	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778014	3778014	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	351	344	0	ENST00000262367.5:c.7034C>T	p.Ser2345Phe	p.S2345F	ENST00000262367	NM_004380.2	2345	tCt/tTt	31/31	0.18535307575654	3	FACETS	1	0.994	1	0.449	0.427	0.472	INDETERMINATE	1	TRUE	0	0.817765677812403	3		344	897	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778057	3778057	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	246	326	0	ENST00000262367.5:c.6991C>T	p.Pro2331Ser	p.P2331S	ENST00000262367	NM_004380.2	2331	Cct/Tct	31/31	0.18535307575654	3	FACETS	1	0.967	1	0.349	0.327	0.371	INDETERMINATE	1	TRUE	0	0.817765677812403	3		326	810	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3799647	3799647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	755	427	0	ENST00000262367.5:c.3817G>A	p.Asp1273Asn	p.D1273N	ENST00000262367	NM_004380.2	1273	Gat/Aat	21/31	0.18535307575654	3	FACETS	0.847	0.821	0.874	0.565	0.547	0.583	INDETERMINATE	2	TRUE	0	0.817765677812403	3		427	1535	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801787	3801787	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	288	283	0	ENST00000262367.5:c.3719G>A	p.Cys1240Tyr	p.C1240Y	ENST00000262367	NM_004380.2	1240	tGt/tAt	20/31	0.18535307575654	3	FACETS	1	0.981	1	0.364	0.343	0.386	INDETERMINATE	1	TRUE	0	0.817765677812403	3		283	908	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819249	3819249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	169	412	0	ENST00000262367.5:c.2986G>A	p.Glu996Lys	p.E996K	ENST00000262367	NM_004380.2	996	Gaa/Aaa	15/31	0.18535307575654	3	FACETS	0.547	0.502	0.594	0.182	0.167	0.198	INDETERMINATE	1	TRUE	0	0.817765677812403	3		412	1064	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830785	3830785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	315	313	0	ENST00000262367.5:c.1771G>A	p.Gly591Ser	p.G591S	ENST00000262367	NM_004380.2	591	Ggc/Agc	8/31	0.18535307575654	3	FACETS	1	0.99	1	0.395	0.373	0.416	INDETERMINATE	1	TRUE	0	0.817765677812403	3		313	917	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857127	9857127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs976259560	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	387	407	0	ENST00000330684.3:c.4274C>T	p.Ser1425Leu	p.S1425L	ENST00000330684	NM_001134407.1	1425	tCg/tTg	13/13	0.18535307575654	3	FACETS	1	0.991	1	0.388	0.368	0.407	INDETERMINATE	1	TRUE	0	0.817765677812403	3		407	1147	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984935	9984935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	488	455	2	ENST00000330684.3:c.1030G>A	p.Asp344Asn	p.D344N	ENST00000330684	NM_001134407.1	344	Gat/Aat	4/13	0.18535307575654	3	FACETS	1	0.989	1	0.365	0.349	0.382	INDETERMINATE	1	TRUE	0	0.817765677812403	3		457	1534	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984943	9984943	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1229	219	443	1	ENST00000330684.3:c.1022T>A	p.Val341Asp	p.V341D	ENST00000330684	NM_001134407.1	341	gTt/gAt	4/13	0.18535307575654	3	FACETS	0.521	0.483	0.561	0.174	0.161	0.187	INDETERMINATE	1	TRUE	0	0.817765677812403	3		444	1448	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830409	72830409	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1411105490	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	135	320	0	ENST00000268489.5:c.6172C>T	p.Pro2058Ser	p.P2058S	ENST00000268489	NM_006885.3	2058	Ccg/Tcg	9/10	0.529188743684717	1	FACETS	0.427	0.391	0.464	0.427	0.391	0.464	SUBCLONAL	1	TRUE	0	0.817765677812403	1		320	457	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845352	89845352	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	201	341	0	ENST00000389301.3:c.1775T>C	p.Val592Ala	p.V592A	ENST00000389301	NM_000135.2	592	gTg/gCg	19/43	0.529188743684717	1	FACETS	0.406	0.377	0.435	0.406	0.377	0.435	SUBCLONAL	1	TRUE	0	0.817765677812403	1		341	716	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696719	47696719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	170	308	0	ENST00000347630.2:c.229G>A	p.Asp77Asn	p.D77N	ENST00000347630	NM_001007230.1	77	Gat/Aat	5/11	NA	2	FACETS	0.45	0.414	0.488			1	INDETERMINATE	1	TRUE	NA	0.817765677812403	2		308	923	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756673	756673	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	265	482	0	ENST00000314574.4:c.155T>G	p.Val52Gly	p.V52G	ENST00000314574	NM_005433.3	52	gTt/gGt	2/12	1	2	FACETS	0.491	0.46	0.524	0.491	0.46	0.524	SUBCLONAL	1	TRUE	1	0.817765677812403	2		482	1319	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117138	7117138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	342	428	0	ENST00000302850.5:c.4078C>T	p.Pro1360Ser	p.P1360S	ENST00000302850	NM_000208.2	1360	Cct/Tct	22/22	0.303768874151732	1	FACETS	0.521	0.494	0.548	0.521	0.494	0.548	INDETERMINATE	1	TRUE	0	0.817765677812403	1		428	949	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10244907	10244907	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767705266	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	226	506	0	ENST00000340748.4:c.4802G>A	p.Arg1601Gln	p.R1601Q	ENST00000340748		1601	cGa/cAa	39/40	1	2	FACETS	0.527	0.491	0.565	0.527	0.491	0.565	SUBCLONAL	1	TRUE	1	0.817765677812403	2		506	1048	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098420	11098420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752581107	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	124	264	0	ENST00000358026.2:c.938C>T	p.Pro313Leu	p.P313L	ENST00000358026	NM_001128849.1	313	cCc/cTc	6/36	1	2	FACETS	0.613	0.557	0.67	0.613	0.557	0.67	SUBCLONAL	1	TRUE	1	0.817765677812403	2		264	495	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297790	15297790	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	294	307	0	ENST00000263388.2:c.1850G>A	p.Cys617Tyr	p.C617Y	ENST00000263388	NM_000435.2	617	tGc/tAc	12/33	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.817765677812403	2		307	708	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297932	15297932	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	230	229	0	ENST00000263388.2:c.1824C>A	p.Cys608Ter	p.C608*	ENST00000263388	NM_000435.2	608	tgC/tgA	11/33	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.817765677812403	2		229	501	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302907	15302907	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	172	244	0	ENST00000263388.2:c.543C>G	p.Phe181Leu	p.F181L	ENST00000263388	NM_000435.2	181	ttC/ttG	4/33	1	2	FACETS	0.916	0.852	0.983	0.916	0.852	0.983	CLONAL	1	TRUE	1	0.817765677812403	2		244	459	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350792	15350792	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	171	264	0	ENST00000263377.2:c.3211C>T	p.Pro1071Ser	p.P1071S	ENST00000263377	NM_058243.2	1071	Ccc/Tcc	15/20	1	2	FACETS	0.694	0.641	0.748	0.694	0.641	0.748	SUBCLONAL	1	TRUE	1	0.817765677812403	2		264	603	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257134	19257134	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	59	106	0	ENST00000162023.5:c.829C>T	p.Pro277Ser	p.P277S	ENST00000162023		277	Ccc/Tcc	12/13	1	2	FACETS	0.82	0.719	0.925	0.82	0.719	0.925	CLONAL	1	TRUE	1	0.817765677812403	2		106	176	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520209	9520210	+	missense_variant	Missense_Mutation	DNP	TG	TG	AT	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	166	350	0	ENST00000353224.5:c.2059_2060delinsAT	p.Gln687Met	p.Q687M	ENST00000353224	NM_177990.2	687	CAg/ATg	10/10	0.431028267338398	1	FACETS	0.373	0.343	0.403	0.373	0.343	0.403	INDETERMINATE	1	TRUE	0	0.817765677812403	1		350	644	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46275850	46275850	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1206893490	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	301	654	0	ENST00000371998.3:c.3286C>T	p.Gln1096Ter	p.Q1096*	ENST00000371998		1096	Caa/Taa	18/23	0.431028267338398	1	FACETS	0.355	0.334	0.377	0.355	0.334	0.377	INDETERMINATE	1	TRUE	0	0.817765677812403	1		654	1225	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288158	21288158	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	55	435	0	ENST00000354336.3:c.403C>T	p.Pro135Ser	p.P135S	ENST00000354336	NM_005207.3	135	Cct/Tct	2/3	1	2	FACETS	0.135	0.115	0.158	0.135	0.115	0.158	SUBCLONAL	1	TRUE	1	0.817765677812403	2		435	994	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30090771	30090771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	223	360	0	ENST00000338641.4:c.1768G>A	p.Ala590Thr	p.A590T	ENST00000338641	NM_000268.3	590	Gcc/Acc	16/16	1	2	FACETS	0.578	0.538	0.619	0.578	0.538	0.619	SUBCLONAL	1	TRUE	1	0.817765677812403	2		360	944	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53253927	53253927	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556856112	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	321	159	0	ENST00000375401.3:c.145C>T	p.Pro49Ser	p.P49S	ENST00000375401	NM_004187.3	49	Ccc/Tcc	1/26	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.817765677812403	1		159	381	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347278	70347278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	208	227	0	ENST00000374080.3:c.2942C>T	p.Ser981Phe	p.S981F	ENST00000374080		981	tCc/tTc	21/45	1	1	FACETS	0.529	0.495	0.565	0.529	0.495	0.565	SUBCLONAL	1	TRUE	0	0.817765677812403	1		227	568	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352349	70352349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	154	229	0	ENST00000374080.3:c.4376C>T	p.Ser1459Phe	p.S1459F	ENST00000374080		1459	tCc/tTc	31/45	1	1	FACETS	0.352	0.323	0.382	0.352	0.323	0.382	SUBCLONAL	1	TRUE	0	0.817765677812403	1		229	633	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938304	76938304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	488	244	0	ENST00000373344.5:c.2444C>T	p.Ser815Phe	p.S815F	ENST00000373344	NM_000489.3	815	tCt/tTt	9/35	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.817765677812403	1		244	584	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615662	100615662	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	662	289	0	ENST00000308731.7:c.670G>A	p.Asp224Asn	p.D224N	ENST00000308731	NM_000061.2	224	Gat/Aat	8/19	1	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.817765677812403	1		289	780	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480623	123480623	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	75	98	2	ENST00000371139.4:c.131G>T	p.Cys44Phe	p.C44F	ENST00000371139	NM_001114937.2	44	tGt/tTt	1/4	1	1	FACETS	0.408	0.361	0.456	0.408	0.361	0.456	SUBCLONAL	1	TRUE	0	0.817765677812403	1		100	266	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919228	48919229	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	317	334	0	ENST00000267163.4:c.396dup	p.Asn133Ter	p.N133*	ENST00000267163	NM_000321.2	131	-/T	4/27	1	2	FACETS	0.9	0.853	0.949	0.9	0.853	0.949	CLONAL	1	TRUE	1	0.817765677812403	2		334	861	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0004154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	207	308	1	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	0.310845103005293	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.314717393426119	4		309	811	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713469	40713469	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528913627	NA	P-0004154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	120	168	1	ENST00000373198.4:c.4046G>A	p.Arg1349His	p.R1349H	ENST00000373198	NM_133170.3	1349	cGt/cAt	30/32	0.314717393426119	5	FACETS	1	0.923	1	0.51	0.462	0.56	CLONAL	2	TRUE	1	0.314717393426119	5		169	550	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738360	133738360	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	74	166	0	ENST00000318560.5:c.760G>A	p.Gly254Arg	p.G254R	ENST00000318560	NM_005157.4	254	Ggg/Agg	4/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.314717393426119	2		166	378	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445125	49445125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs565042425	NA	P-0004154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	52	112	0	ENST00000301067.7:c.2341G>A	p.Ala781Thr	p.A781T	ENST00000301067	NM_003482.3	781	Gct/Act	10/54	0.314717393426119	3	FACETS	1	0.964	1	0.722	0.619	0.832	CLONAL	1	TRUE	1	0.314717393426119	3		112	265	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265743	41266365	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGT	CACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGT	-	novel	NA	P-0004154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	61	20	0	ENST00000349496.5:c.13+174_242-77del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.251835866487625	3	FACETS	0.986	0.898	1	1	0.983	1	CLONAL	5	TRUE	0	0.314717393426119	3		20	91	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579567	7579573	+	frameshift_variant	Frame_Shift_Del	DEL	CATTGCT	CATTGCT	-	novel	NA	P-0004154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	137	210	0	ENST00000269305.4:c.114_120del	p.Ala39MetfsTer3	p.A39Mfs*3	ENST00000269305	NM_001126112.2	38	caAGCAATG/ca	4/11	0.303117256999578	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	0	0.314717393426119	2		210	424	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442810	442811	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	57	220	0	ENST00000399788.2:c.1495dup	p.Glu499GlyfsTer29	p.E499Gfs*29	ENST00000399788	NM_001042603.1	499	gag/gGag	12/28	NA	2	FACETS	0.705	0.605	0.813			1	INDETERMINATE	1	TRUE	NA	0.314717393426119	2		220	514	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250125	110250125	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	22	273	0	ENST00000374672.4:c.550C>G	p.Pro184Ala	p.P184A	ENST00000374672	NM_004235.4	184	Ccc/Gcc	3/5	0.444008897793997	3	FACETS	0.299	0.231	0.378	0.15	0.115	0.189	SUBCLONAL	1	TRUE	1	0.444008897793997	3		273	405	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418616	49418616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	72	499	0	ENST00000301067.7:c.15898G>A	p.Ala5300Thr	p.A5300T	ENST00000301067	NM_003482.3	5300	Gcc/Acc	49/54	0.385985461292622	3	FACETS	0.615	0.538	0.699	0.308	0.268	0.35	SUBCLONAL	1	TRUE	1	0.444008897793997	3		499	644	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871063	12871064	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	48	258	0	ENST00000228872.4:c.291dup	p.Ala98CysfsTer27	p.A98Cfs*27	ENST00000228872	NM_004064.3	97	ggt/ggTt	1/3	0.444008897793997	3	FACETS	0.775	0.658	0.903			1	CLONAL	1	TRUE	NA	0.444008897793997	3		258	341	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588751	29588751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760703505	NA	P-0004242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	125	448	1	ENST00000356175.3:c.4537C>T	p.Arg1513Ter	p.R1513*	ENST00000356175	NM_000267.3	1513	Cga/Tga	34/57	1	2	FACETS	0.756	0.69	0.825	0.756	0.69	0.825	SUBCLONAL	1	TRUE	1	0.76	2		449	435	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661945	29661945	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854552	NA	P-0004242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	39	755	0	ENST00000356175.3:c.5839C>T	p.Arg1947Ter	p.R1947*	ENST00000356175	NM_000267.3	1947	Cga/Tga	39/57	1	2	FACETS	0.14	0.115	0.167	0.14	0.115	0.167	SUBCLONAL	1	TRUE	1	0.76	2		755	735	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932171	39932171	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555918056	NA	P-0004242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	401	880	0	ENST00000378444.4:c.2428C>T	p.Arg810Ter	p.R810*	ENST00000378444	NM_001123385.1	810	Cga/Tga	4/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.76	2		880	1019	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29497003	29497003	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397514641	NA	P-0004242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	211	485	0	ENST00000356175.3:c.574C>T	p.Arg192Ter	p.R192*	ENST00000356175	NM_000267.3	192	Cga/Tga	5/57	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.76	2		485	483	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158132	27158132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773256013	NA	P-0004242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	243	500	2	ENST00000380036.4:c.356G>A	p.Arg119His	p.R119H	ENST00000380036	NM_000459.3	119	cGt/cAt	2/23	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.76	2		502	590	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45864839	45864842	+	frameshift_variant	Frame_Shift_Del	DEL	AGTC	AGTC	-	novel	NA	P-0004242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1215	70	1060	0	ENST00000391945.4:c.1177_1180del	p.Asp393SerfsTer90	p.D393Sfs*90	ENST00000391945	NM_000400.3	393	GACTtc/tc	12/23	1	2	FACETS	0.143	0.124	0.164	0.143	0.124	0.164	SUBCLONAL	1	TRUE	1	0.76	2		1060	1285	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031691	69031691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748595305	NA	P-0004242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	172	739	0	ENST00000288368.4:c.3446G>A	p.Arg1149His	p.R1149H	ENST00000288368	NM_024870.2	1149	cGc/cAc	28/40	1	2	FACETS	0.585	0.539	0.632	0.585	0.539	0.632	SUBCLONAL	1	TRUE	1	0.76	2		739	774	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574761	41574761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	13	894	0	ENST00000263253.7:c.7046C>T	p.Pro2349Leu	p.P2349L	ENST00000263253	NM_001429.3	2349	cCt/cTt	31/31	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.76	NA		894	210	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648328	206648328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782549877	NA	P-0004373-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	87	235	0	ENST00000367120.3:c.349C>T	p.Arg117Cys	p.R117C	ENST00000367120	NM_014002.3	117	Cgc/Tgc	5/22	0.524840582286058	4	FACETS	0.806	0.714	0.903	0.269	0.238	0.301	CLONAL	1	TRUE	1	0.546719518363011	4		235	611	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206943200	206943200	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004373-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	93	241	0	ENST00000423557.1:c.418G>C	p.Glu140Gln	p.E140Q	ENST00000423557	NM_000572.2	140	Gag/Cag	4/5	0.524840582286058	4	FACETS	0.933	0.832	1	0.311	0.277	0.347	CLONAL	1	TRUE	1	0.546719518363011	4		241	564	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884079	37884079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761715861	NA	P-0004373-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	154	392	0	ENST00000269571.5:c.3550G>A	p.Val1184Ile	p.V1184I	ENST00000269571		1184	Gtt/Att	27/27	0.546719518363011	3	FACETS	1	0.948	1			1	CLONAL	1	TRUE	NA	0.546719518363011	3		392	687	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685327	86685330	+	frameshift_variant	Frame_Shift_Del	DEL	GAGC	GAGC	-	novel	NA	P-0004373-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	39	121	0	ENST00000274376.6:c.3044_3047del	p.Glu1015ValfsTer8	p.E1015Vfs*8	ENST00000274376	NM_002890.2	1015	GAGCgt/gt	24/25	0.157253860515392	3	FACETS	0.956	0.802	1	0.319	0.267	0.375	INDETERMINATE	1	TRUE	0	0.546719518363011	3		121	190	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	168	692	4	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	0.717822768165429	1	FACETS	0.714	0.664	0.766	0.714	0.664	0.766	SUBCLONAL	1	TRUE	0	0.717822768165429	1		696	420	SUCCESS
AR	367	MSKCC	GRCh37	X	66943543	66943543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852581	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	177	400	0	ENST00000374690.3:c.2623C>T	p.His875Tyr	p.H875Y	ENST00000374690	NM_000044.3	875	Cat/Tat	8/8	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.717822768165429	1		400	256	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	234	556	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	0.19452779389991	1	FACETS	0.616	0.578	0.656	0.616	0.578	0.656	INDETERMINATE	1	TRUE	0	0.717822768165429	1		556	678	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	86	448	1	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.717822768165429	1	FACETS	0.925	0.843	1	0.925	0.843	1	CLONAL	1	TRUE	0	0.717822768165429	1		449	166	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	292	1169	12	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	NA	2	FACETS	0.813	0.766	0.861			1	INDETERMINATE	1	TRUE	NA	0.717822768165429	2		1181	1001	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	117	276	3	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	1	2	FACETS	0.801	0.728	0.876	0.801	0.728	0.876	CLONAL	1	TRUE	1	0.717822768165429	2		279	407	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	89	240	2	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.742	0.664	0.824	0.742	0.664	0.824	SUBCLONAL	1	TRUE	1	0.717822768165429	2		242	334	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660220	227660220	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148962208	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	223	510	0	ENST00000305123.5:c.3235C>T	p.Pro1079Ser	p.P1079S	ENST00000305123	NM_005544.2	1079	Cct/Tct	1/2	1	2	FACETS	0.975	0.914	1	0.975	0.914	1	CLONAL	1	TRUE	1	0.717822768165429	2		510	637	SUCCESS
AR	367	MSKCC	GRCh37	X	66943552	66943552	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137852578	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	178	416	0	ENST00000374690.3:c.2632A>G	p.Thr878Ala	p.T878A	ENST00000374690	NM_000044.3	878	Act/Gct	8/8	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.717822768165429	1		416	260	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	118	441	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	1	2	FACETS	0.898	0.819	0.98	0.898	0.819	0.98	CLONAL	1	TRUE	1	0.717822768165429	2		441	366	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209514	98209514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781539921	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	177	413	1	ENST00000331920.6:c.4024C>T	p.Arg1342Cys	p.R1342C	ENST00000331920	NM_000264.3	1342	Cgc/Tgc	23/24	1	2	FACETS	0.908	0.843	0.975	0.908	0.843	0.975	CLONAL	1	TRUE	1	0.717822768165429	2		414	543	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	157	570	5	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	1	2	FACETS	0.875	0.807	0.944	0.875	0.807	0.944	CLONAL	1	TRUE	1	0.717822768165429	2		575	500	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245587	41245587	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357522	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	122	706	1	ENST00000357654.3:c.1961del	p.Lys654SerfsTer47	p.K654Sfs*47	ENST00000357654	NM_007294.3	654	aAg/ag	10/23	1	2	FACETS	0.863	0.787	0.941	0.863	0.787	0.941	CLONAL	1	TRUE	1	0.717822768165429	2		707	394	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664761	138664761	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs797044528	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	44	99	0	ENST00000330315.3:c.804del	p.Gly269AlafsTer2	p.G269Afs*2	ENST00000330315	NM_023067.3	268	ccC/cc	1/1	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.717822768165429	2		99	111	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269074	142269074	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	183	578	0	ENST00000350721.4:c.2876T>C	p.Val959Ala	p.V959A	ENST00000350721	NM_001184.3	959	gTg/gCg	14/47	1	2	FACETS	0.96	0.893	1	0.96	0.893	1	CLONAL	1	TRUE	1	0.717822768165429	2		578	531	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187560916	187560916	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	175	542	0	ENST00000441802.2:c.3602G>T	p.Arg1201Met	p.R1201M	ENST00000441802	NM_005245.3	1201	aGg/aTg	4/27	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.717822768165429	2		542	450	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652015	36652015	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1309823433	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	215	448	2	ENST00000244741.5:c.137G>A	p.Arg46His	p.R46H	ENST00000244741	NM_000389.4	46	cGt/cAt	2/3	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.717822768165429	2		450	591	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864309	117864309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301282588	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	164	680	1	ENST00000297338.2:c.1348C>T	p.Arg450Cys	p.R450C	ENST00000297338	NM_006265.2	450	Cgc/Tgc	11/14	NA	2	FACETS	0.94	0.87	1			1	INDETERMINATE	1	TRUE	NA	0.717822768165429	2		681	486	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366990	118366990	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	198	633	1	ENST00000534358.1:c.5572C>T	p.Arg1858Ter	p.R1858*	ENST00000534358	NM_005933.3	1858	Cga/Tga	20/36	1	2	FACETS	0.929	0.866	0.993	0.929	0.866	0.993	CLONAL	1	TRUE	1	0.717822768165429	2		634	594	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117431	115117431	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	107	524	0	ENST00000257566.3:c.743A>G	p.Tyr248Cys	p.Y248C	ENST00000257566	NM_016569.3	248	tAc/tGc	4/8	1	2	FACETS	0.867	0.786	0.95	0.867	0.786	0.95	CLONAL	1	TRUE	1	0.717822768165429	2		524	344	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819655	81819655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	293	920	3	ENST00000359376.3:c.61G>A	p.Ala21Thr	p.A21T	ENST00000359376	NM_002661.3	21	Gcc/Acc	2/33	0.535176061932718	3	FACETS	0.923	0.868	0.979	0.461	0.434	0.49	CLONAL	1	TRUE	1	0.717822768165429	3		923	1202	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245891	5245891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1045893958	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	537	760	1	ENST00000357368.4:c.884G>A	p.Arg295Gln	p.R295Q	ENST00000357368	NM_002850.3	295	cGg/cAg	10/38	0.705691978068784	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.717822768165429	2		761	742	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118365074	118365075	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	143	501	0	ENST00000534358.1:c.5256dup	p.Ala1753SerfsTer32	p.A1753Sfs*32	ENST00000534358	NM_005933.3	1750	-/A	17/36	1	2	FACETS	0.878	0.807	0.951	0.878	0.807	0.951	CLONAL	1	TRUE	1	0.717822768165429	2		501	454	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444437	50444437	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	96	278	0	ENST00000331340.3:c.369del	p.Ile124SerfsTer69	p.I124Sfs*69	ENST00000331340	NM_006060.4	123	Ggg/gg	4/8	1	2	FACETS	0.836	0.753	0.922	0.836	0.753	0.922	CLONAL	1	TRUE	1	0.717822768165429	2		278	320	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042482	37042482	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587778998	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	249	711	0	ENST00000231790.2:c.244A>G	p.Thr82Ala	p.T82A	ENST00000231790	NM_000249.3	82	Act/Gct	3/19	1	2	FACETS	0.976	0.917	1	0.976	0.917	1	CLONAL	1	TRUE	1	0.717822768165429	2		711	711	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161434	55161434	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	135	621	0	ENST00000257290.5:c.3265C>A	p.Leu1089Met	p.L1089M	ENST00000257290	NM_006206.4	1089	Ctg/Atg	23/23	NA	2	FACETS	0.779	0.712	0.847			1	INDETERMINATE	1	TRUE	NA	0.717822768165429	2		621	483	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056413	26056413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs967486148	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	30	328	0	ENST00000343677.2:c.244C>T	p.Leu82Phe	p.L82F	ENST00000343677	NM_005319.3	82	Ctt/Ttt	1/1	1	2	FACETS	0.183	0.147	0.223	0.183	0.147	0.223	SUBCLONAL	1	TRUE	1	0.717822768165429	2		328	458	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98222053	98222053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	133	282	0	ENST00000331920.6:c.2716C>T	p.Arg906Cys	p.R906C	ENST00000331920	NM_000264.3	906	Cgt/Tgt	17/24	1	2	FACETS	0.986	0.905	1	0.986	0.905	1	CLONAL	1	TRUE	1	0.717822768165429	2		282	376	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615577	43615577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146838520	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	216	602	0	ENST00000355710.3:c.2656C>T	p.Arg886Trp	p.R886W	ENST00000355710	NM_020975.4	886	Cgg/Tgg	15/20	1	2	FACETS	0.961	0.899	1	0.961	0.899	1	CLONAL	1	TRUE	1	0.717822768165429	2		602	626	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94224039	94224039	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	149	513	0	ENST00000323929.3:c.113T>C	p.Val38Ala	p.V38A	ENST00000323929	NM_005591.3	38	gTa/gCa	3/20	0.19452779389991	1	FACETS	0.686	0.634	0.739	0.686	0.634	0.739	INDETERMINATE	1	TRUE	0	0.717822768165429	1		513	388	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437395	110437395	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	52	103	1	ENST00000375856.3:c.1006A>G	p.Thr336Ala	p.T336A	ENST00000375856	NM_003749.2	336	Acg/Gcg	1/2	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.717822768165429	2		104	136	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582064	95582064	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	143	637	0	ENST00000393063.1:c.1847T>C	p.Leu616Ser	p.L616S	ENST00000393063	NM_030621.3	616	tTg/tCg	12/28	1	2	FACETS	0.974	0.897	1	0.974	0.897	1	CLONAL	1	TRUE	1	0.717822768165429	2		637	409	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779131	3779131	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	21	357	0	ENST00000262367.5:c.5917T>C	p.Tyr1973His	p.Y1973H	ENST00000262367	NM_004380.2	1973	Tac/Cac	31/31	1	2	FACETS	0.139	0.107	0.177	0.139	0.107	0.177	SUBCLONAL	1	TRUE	1	0.717822768165429	2		357	420	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8109917	8109917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	198	483	0	ENST00000585124.1:c.578G>A	p.Gly193Glu	p.G193E	ENST00000585124	NM_004217.3	193	gGg/gAg	7/9	1	2	FACETS	0.822	0.765	0.881	0.822	0.765	0.881	CLONAL	1	TRUE	1	0.717822768165429	2		483	671	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512459	38512459	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536574354	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	124	384	0	ENST00000254066.5:c.1370C>T	p.Pro457Leu	p.P457L	ENST00000254066	NM_000964.3	457	cCg/cTg	9/9	NA	2	FACETS	0.732	0.666	0.8			1	INDETERMINATE	1	TRUE	NA	0.717822768165429	2		384	472	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210756	2210756	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	265	724	0	ENST00000398665.3:c.1253A>G	p.Asn418Ser	p.N418S	ENST00000398665	NM_032482.2	418	aAc/aGc	14/28	0.705691978068784	2	FACETS	1	0.971	1	0.523	0.493	0.554	CLONAL	1	TRUE	0	0.717822768165429	2		724	706	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946845	17946845	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	219	599	0	ENST00000458235.1:c.1802A>G	p.Glu601Gly	p.E601G	ENST00000458235	NM_000215.3	601	gAa/gGa	14/24	0.19452779389991	1	FACETS	0.638	0.597	0.68	0.638	0.597	0.68	INDETERMINATE	1	TRUE	0	0.717822768165429	1		599	613	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260198	19260198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	229	609	1	ENST00000162023.5:c.95C>T	p.Ala32Val	p.A32V	ENST00000162023		32	gCc/gTc	7/13	0.19452779389991	1	FACETS	0.668	0.627	0.71	0.668	0.627	0.71	INDETERMINATE	1	TRUE	0	0.717822768165429	1		610	612	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884218	37884218	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	195	481	1	ENST00000269571.5:c.3694del	p.Ala1232LeufsTer70	p.A1232Lfs*70	ENST00000269571		1230	cGg/cg	27/27	1	2	FACETS	0.862	0.802	0.924	0.862	0.802	0.924	CLONAL	1	TRUE	1	0.717822768165429	2		482	630	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646084	215646085	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs746325928	NA	P-0004910-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	19	469	1	ENST00000260947.4:c.513dup	p.Asp172ArgfsTer10	p.D172Rfs*10	ENST00000260947	NM_000465.2	171	-/A	4/11	1	2	FACETS	0.193	0.146	0.247	0.193	0.146	0.247	SUBCLONAL	1	TRUE	1	0.717822768165429	2		470	275	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938218	76938219	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004919-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	25	610	0	ENST00000373344.5:c.2529dup	p.Thr844TyrfsTer5	p.T844Yfs*5	ENST00000373344	NM_000489.3	843	-/T	9/35	0.333258046857756	0	FACETS	0.328	0.259	0.408			1	SUBCLONAL	1	TRUE	NA	0.333258046857756	0		610	305	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0004960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	87	685	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.248285180552081	3	FACETS	0.996	0.882	1	0.498	0.441	0.56	CLONAL	1	TRUE	1	0.258483036670165	3		685	763	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0004960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	123	448	1	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.844	0.762	0.932	0.844	0.762	0.932	CLONAL	1	TRUE	1	0.258483036670165	2		449	1127	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0004960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	382	586	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.247782362568241	2	FACETS	0.999	0.947	1	0.999	0.947	1	CLONAL	2	TRUE	0	0.258483036670165	2		586	1480	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs770248150	NA	P-0004960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	223	422	0	ENST00000311936.3:c.351A>T	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaT	4/5	0.248285180552081	3	FACETS	0.907	0.844	0.972	0.907	0.844	0.972	CLONAL	2	TRUE	1	0.258483036670165	3		422	1074	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400848	72400848	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1624	89	886	0	ENST00000357731.5:c.323T>C	p.Val108Ala	p.V108A	ENST00000357731	NM_173808.2	108	gTa/gCa	2/7	0.258483036670165	2	FACETS	0.402	0.355	0.453	0.201	0.177	0.227	SUBCLONAL	1	TRUE	0	0.258483036670165	2		886	1713	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245504	153245504	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	118	512	1	ENST00000281708.4:c.1687A>G	p.Ile563Val	p.I563V	ENST00000281708	NM_033632.3	563	Atc/Gtc	11/12	1	2	FACETS	0.89	0.801	0.984	0.89	0.801	0.984	CLONAL	1	TRUE	1	0.258483036670165	2		513	1026	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514200	69514200	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1444	170	746	0	ENST00000294312.3:c.481C>A	p.Pro161Thr	p.P161T	ENST00000294312	NM_005117.2	161	Cca/Aca	3/3	1	2	FACETS	0.815	0.747	0.887	0.815	0.747	0.887	CLONAL	1	TRUE	1	0.258483036670165	2		746	1614	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321390	1321390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769805287	NA	P-0004960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	574	533	1	ENST00000400841.2:c.365C>T	p.Pro122Leu	p.P122L	ENST00000400841		122	cCg/cTg	4/6	0.258483036670165	4	FACETS	1	0.991	1			1	CLONAL	3	TRUE	NA	0.258483036670165	4		534	1684	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412095	63412095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852217	NA	P-0004960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	531	519	2	ENST00000330258.3:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000330258	NM_152424.3	358	Cga/Tga	2/2	0.198861864708372	2	FACETS	1	0.986	1			1	CLONAL	3	TRUE	NA	0.258483036670165	2		521	1299	SUCCESS
AR	367	MSKCC	GRCh37	X	66937392	66937392	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	174	365	0	ENST00000374690.3:c.2246C>A	p.Ala749Asp	p.A749D	ENST00000374690	NM_000044.3	749	gCc/gAc	5/8	0.198861864708372	2	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.258483036670165	2		365	1155	SUCCESS
APC	324	MSKCC	GRCh37	5	112174694	112174695	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	rs864622086	NA	P-0004960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	165	610	0	ENST00000257430.4:c.3404_3405del	p.Tyr1135Ter	p.Y1135*	ENST00000257430	NM_000038.5	1135	TAt/t	16/16	1	2	FACETS	0.98	0.897	1	0.98	0.897	1	CLONAL	1	TRUE	1	0.258483036670165	2		610	1303	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0005163-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	125	733	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.320007062539974	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.320007062539974	1		733	637	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581157	48581157	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1555685624	NA	P-0005163-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	41	248	0	ENST00000342988.3:c.461C>G	p.Ser154Ter	p.S154*	ENST00000342988	NM_005359.5	154	tCa/tGa	5/12	0.320007062539974	1	FACETS	0.549	0.458	0.65	0.549	0.458	0.65	SUBCLONAL	1	TRUE	0	0.320007062539974	1		248	392	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0005163-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	121	207	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.320007062539974	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	0	0.320007062539974	2		207	370	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821760	72821760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150891901	NA	P-0005163-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	193	556	3	ENST00000268489.5:c.10415C>T	p.Ala3472Val	p.A3472V	ENST00000268489	NM_006885.3	3472	gCg/gTg	10/10	0.320007062539974	2	FACETS	1	0.988	1	0.667	0.617	0.719	CLONAL	1	TRUE	0	0.320007062539974	2		559	904	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864807	117864808	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCTGCTGT	novel	NA	P-0005163-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	133	544	0	ENST00000297338.2:c.1293_1301dup	p.Gln431_Gln433dup	p.Q431_Q433dup	ENST00000297338	NM_006265.2	431	cat/caACAGCAGCAt	10/14	0.320007062539974	5	FACETS	0.996	0.902	1	0.249	0.225	0.274	CLONAL	1	TRUE	1	0.320007062539974	5		544	1235	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114901017	114901018	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0005163-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	141	640	0	ENST00000543371.1:c.629_630del	p.His210LeufsTer117	p.H210Lfs*117	ENST00000543371	NM_001198531.1	209	gaACac/gaac	6/14	1	2	FACETS	0.957	0.871	1	0.957	0.871	1	CLONAL	1	TRUE	1	0.320007062539974	2		640	921	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0005225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	169	685	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.458000892924181	3	FACETS	0.875	0.811	0.942	0.875	0.811	0.942	CLONAL	2	FALSE	1	0.458000892924181	3		685	518	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0005225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	170	291	0	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	0.849	0.789	0.91	1	0.992	1	CLONAL	2	FALSE	1	0.458000892924181	2		291	437	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188164	11188164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777893	NA	P-0005225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	119	340	0	ENST00000361445.4:c.5930C>T	p.Thr1977Ile	p.T1977I	ENST00000361445	NM_004958.3	1977	aCa/aTa	43/58	NA	2	FACETS	1	0.939	1			1	INDETERMINATE	1	FALSE	NA	0.458000892924181	2		340	497	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630542	187630542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	168	611	1	ENST00000441802.2:c.440C>T	p.Pro147Leu	p.P147L	ENST00000441802	NM_005245.3	147	cCg/cTg	2/27	0.249382702597183	1	FACETS	0.774	0.713	0.837	0.774	0.713	0.837	INDETERMINATE	1	FALSE	0	0.458000892924181	1		612	731	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859436	57859436	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	1735	805	0	ENST00000228682.2:c.581C>G	p.Pro194Arg	p.P194R	ENST00000228682	NM_005269.2	194	cCc/cGc	6/12	0.458000892924181	8	FACETS	0.972	0.958	0.986			1	CLONAL	8	FALSE	NA	0.458000892924181	8		805	2313	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041074	42041074	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	106	850	1	ENST00000219905.7:c.5452C>T	p.Arg1818Ter	p.R1818*	ENST00000219905	NM_001164273.1	1818	Cga/Tga	16/24	0.458000892924181	1	FACETS	0.576	0.517	0.638	0.576	0.517	0.638	SUBCLONAL	1	FALSE	0	0.458000892924181	1		851	620	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482874	67482874	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	rs1555414506	NA	P-0005225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	95	329	0	ENST00000327367.4:c.1278G>C	p.Ter426TyrextTer6	p.*426Yext*6	ENST00000327367	NM_005902.3	426	taG/taC	9/9	0.458000892924181	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	0	0.458000892924181	1		329	307	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134461	30134461	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	48	428	0	ENST00000263025.4:c.70G>T	p.Val24Phe	p.V24F	ENST00000263025	NM_002746.2	24	Gtc/Ttc	1/9	1	2	FACETS	0.284	0.239	0.333	0.284	0.239	0.333	SUBCLONAL	1	FALSE	1	0.458000892924181	2		428	739	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867695	45867695	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	143	432	0	ENST00000391945.4:c.705G>T	p.Glu235Asp	p.E235D	ENST00000391945	NM_000400.3	235	gaG/gaT	8/23	0.137149061722124	0	FACETS	0.484	0.441	0.527			1	INDETERMINATE	1	FALSE	0	0.458000892924181	0		432	700	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045024	47045024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	202	285	0	ENST00000377604.3:c.2350C>T	p.His784Tyr	p.H784Y	ENST00000377604	NM_001204468.1	784	Cac/Tac	20/24	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	0	0.458000892924181	1		285	478	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870255	44870256	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	164	391	0	ENST00000377967.4:c.435dup	p.Phe146IlefsTer6	p.F146Ifs*6	ENST00000377967	NM_021140.2	145	gca/gcAa	5/29	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	0	0.458000892924181	1		391	442	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191480	10191480	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913346	NA	P-0005306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	246	338	0	ENST00000256474.2:c.473T>C	p.Leu158Pro	p.L158P	ENST00000256474	NM_000551.3	158	cTg/cCg	3/3	0.392067258744846	2	FACETS	0.903	0.85	0.957	0.903	0.85	0.957	CLONAL	2	TRUE	0	0.435694377451036	2		338	625	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696240	52696240	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	441	595	0	ENST00000394830.3:c.437G>C	p.Arg146Pro	p.R146P	ENST00000394830	NM_018313.4	146	cGa/cCa	5/30	0.392067258744846	2	FACETS	0.955	0.914	0.996	0.955	0.914	0.996	CLONAL	2	TRUE	0	0.435694377451036	2		595	1060	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969104	93969104	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1475	594	700	0	ENST00000369303.4:c.1892C>T	p.Ser631Phe	p.S631F	ENST00000369303	NM_004440.3	631	tCc/tTc	10/17	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.435694377451036	2		700	2069	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437292	121437292	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	182	509	0	ENST00000257555.6:c.1630A>G	p.Thr544Ala	p.T544A	ENST00000257555		544	Acc/Gcc	9/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.435694377451036	2		509	652	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985587	60985587	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs763718170	NA	P-0005306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	53	184	1	ENST00000333681.4:c.313T>C	p.Ser105Pro	p.S105P	ENST00000333681		105	Tcc/Ccc	2/3	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.435694377451036	2		185	228	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265492	46265492	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1248	381	748	0	ENST00000371998.3:c.2362G>C	p.Glu788Gln	p.E788Q	ENST00000371998		788	Gag/Cag	12/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.435694377451036	2		748	1629	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725047	89725062	+	frameshift_variant	Frame_Shift_Del	DEL	AAGCTGTACTTCACAA	AAGCTGTACTTCACAA	-	novel	NA	P-0005306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	179	394	0	ENST00000371953.3:c.1032_1047del	p.Leu345GlnfsTer2	p.L345Qfs*2	ENST00000371953	NM_000314.4	344	AAGCTGTACTTCACAAaa/aa	9/9	0.102562024852531	3	FACETS	0.9	0.828	0.974	0.45	0.414	0.487	INDETERMINATE	1	TRUE	1	0.435694377451036	3		394	1112	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441188	52441188	+	splice_donor_variant	Splice_Site	DEL	A	A	-	novel	NA	P-0005306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	224	440	0	ENST00000460680.1:c.580+2del		p.X194_splice	ENST00000460680	NM_004656.3	194			0.392067258744846	2	FACETS	0.938	0.881	0.996	0.938	0.881	0.996	CLONAL	2	TRUE	0	0.435694377451036	2		440	548	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693005	89693005	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	TT	novel	NA	P-0005306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	135	229	0	ENST00000371953.3:c.489delinsTT	p.Lys163AsnfsTer2	p.K163Nfs*2	ENST00000371953	NM_000314.4	163	aaA/aaTT	5/9	0.102562024852531	3	FACETS	1	0.977	1	0.605	0.551	0.661	INDETERMINATE	1	TRUE	1	0.435694377451036	3		229	624	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	59	613	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.838	0.721	0.966	0.838	0.721	0.966	CLONAL	1	TRUE	1	0.247781091061473	2		614	568	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	226	752	0	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.247781091061473	2		752	1267	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	135	577	4	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.247781091061473	2		581	866	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005515	150005515	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	81	399	1	ENST00000253339.5:c.710del	p.Pro237HisfsTer6	p.P237Hfs*6	ENST00000253339		237	cCa/ca	3/7	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.247781091061473	2		400	627	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807363	3807364	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	99	423	0	ENST00000262367.5:c.3623dup	p.Gln1209ThrfsTer25	p.Q1209Tfs*25	ENST00000262367	NM_004380.2	1208	cca/ccCa	19/31	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.247781091061473	2		423	669	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257144	19257144	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	36	239	1	ENST00000162023.5:c.819del	p.Thr274ProfsTer?	p.T274Pfs*?	ENST00000162023		273	ccC/cc	12/13	1	2	FACETS	0.978	0.807	1	0.978	0.807	1	CLONAL	1	TRUE	1	0.247781091061473	2		240	297	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	94	397	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.247781091061473	2		397	712	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007620	45007620	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs111947448	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	46	279	0	ENST00000558401.1:c.68-1G>T		p.X23_splice	ENST00000558401	NM_004048.2	23			1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.247781091061473	2		279	367	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	111	475	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.247781091061473	2		475	819	SUCCESS
APC	324	MSKCC	GRCh37	5	112173847	112173848	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	88	432	0	ENST00000257430.4:c.2563_2564dup	p.Arg856AsnfsTer6	p.R856Nfs*6	ENST00000257430	NM_000038.5	852	-/GA	16/16	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.247781091061473	2		432	659	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343507	343507	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567261095	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	135	561	1	ENST00000262320.3:c.2167C>T	p.Arg723Ter	p.R723*	ENST00000262320	NM_003502.3	723	Cga/Tga	8/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.247781091061473	2		562	864	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090327	77090327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196615739	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	145	613	0	ENST00000356341.3:c.398C>T	p.Ser133Leu	p.S133L	ENST00000356341	NM_002576.4	133	tCg/tTg	4/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.247781091061473	2		613	970	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	103	399	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.801	0.719	0.887	1	0.984	1	CLONAL	2	TRUE	1	0.247781091061473	2		400	519	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716217	52716217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1173183954	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	126	449	3	ENST00000322088.6:c.661C>T	p.Arg221Trp	p.R221W	ENST00000322088	NM_014225.5	221	Cgg/Tgg	6/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.247781091061473	2		452	784	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671655	67671655	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1400980130	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	124	514	2	ENST00000264010.4:c.2070del	p.Glu691SerfsTer30	p.E691Sfs*30	ENST00000264010	NM_006565.3	688	gtA/gt	12/12	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.247781091061473	2		516	898	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133801	2133801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397515209	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	110	435	0	ENST00000219476.3:c.3989C>T	p.Thr1330Met	p.T1330M	ENST00000219476	NM_000548.3	1330	aCg/aTg	33/42	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.247781091061473	2		435	615	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832688	3832688	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	118	449	0	ENST00000262367.5:c.1570del	p.Leu524TrpfsTer6	p.L524Wfs*6	ENST00000262367	NM_004380.2	524	Ctg/tg	6/31	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.247781091061473	2		449	783	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737820	145737820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs36023964	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	81	371	1	ENST00000428558.2:c.3010C>T	p.Arg1004Trp	p.R1004W	ENST00000428558	NM_004260.3	1004	Cgg/Tgg	18/22	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.247781091061473	2		372	568	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262654	16262654	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745684921	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	54	274	1	ENST00000375759.3:c.9919C>T	p.Arg3307Trp	p.R3307W	ENST00000375759	NM_015001.2	3307	Cgg/Tgg	11/15	1	2	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	TRUE	1	0.247781091061473	2		275	436	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990480	69990480	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	85	393	0	ENST00000394351.3:c.439A>G	p.Thr147Ala	p.T147A	ENST00000394351	NM_000248.3	147	Acg/Gcg	4/9	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.247781091061473	2		393	579	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803222	1803222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	123	552	1	ENST00000260795.2:c.574G>A	p.Gly192Ser	p.G192S	ENST00000260795		192	Ggc/Agc	4/17	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.247781091061473	2		553	719	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628571	187628571	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs549553973	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	159	580	2	ENST00000441802.2:c.2411C>T	p.Ala804Val	p.A804V	ENST00000441802	NM_005245.3	804	gCg/gTg	2/27	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.247781091061473	2		582	1006	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517774	176517774	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	187	727	1	ENST00000292408.4:c.384G>T	p.Glu128Asp	p.E128D	ENST00000292408	NM_213647.1	128	gaG/gaT	4/18	1	2	FACETS	0.765	0.706	0.826	1	0.99	1	SUBCLONAL	2	TRUE	1	0.247781091061473	2		728	987	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170313	32170313	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	104	481	0	ENST00000375023.3:c.3295G>T	p.Gly1099Ter	p.G1099*	ENST00000375023	NM_004557.3	1099	Gga/Tga	21/30	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.247781091061473	2		481	791	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41904359	41904359	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	102	462	0	ENST00000372991.4:c.649G>A	p.Ala217Thr	p.A217T	ENST00000372991	NM_001760.3	217	Gcc/Acc	4/5	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.247781091061473	2		462	822	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976706	2976706	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1044557293	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	114	351	0	ENST00000396946.4:c.1306C>T	p.Arg436Trp	p.R436W	ENST00000396946	NM_032415.4	436	Cgg/Tgg	9/25	1	2	FACETS	0.763	0.689	0.841	1	0.984	1	SUBCLONAL	2	TRUE	1	0.247781091061473	2		351	603	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93627378	93627378	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs201994789	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	83	500	0	ENST00000375746.1:c.845C>T	p.Ala282Val	p.A282V	ENST00000375746	NM_001174167.1	282	gCg/gTg	6/14	1	2	FACETS	0.975	0.861	1	0.975	0.861	1	CLONAL	1	TRUE	1	0.247781091061473	2		500	687	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249887	110249887	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	34	214	0	ENST00000374672.4:c.788T>C	p.Val263Ala	p.V263A	ENST00000374672	NM_004235.4	263	gTg/gCg	3/5	1	2	FACETS	0.88	0.721	1	0.88	0.721	1	CLONAL	1	TRUE	1	0.247781091061473	2		214	312	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437199	49437199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1483821975	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	127	504	1	ENST00000301067.7:c.5480C>T	p.Pro1827Leu	p.P1827L	ENST00000301067	NM_003482.3	1827	cCa/cTa	24/54	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.247781091061473	2		505	811	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339492	339492	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764818271	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	151	645	2	ENST00000262320.3:c.2410G>A	p.Ala804Thr	p.A804T	ENST00000262320	NM_003502.3	804	Gct/Act	10/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.247781091061473	2		647	916	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819346	3819346	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	84	279	1	ENST00000262367.5:c.2889G>T	p.Gln963His	p.Q963H	ENST00000262367	NM_004380.2	963	caG/caT	15/31	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.247781091061473	2		280	479	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584482	39584482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	77	447	1	ENST00000262039.4:c.1147C>T	p.Arg383Trp	p.R383W	ENST00000262039	NM_002647.2	383	Cgg/Tgg	10/25	1	2	FACETS	0.856	0.751	0.969	0.856	0.751	0.969	CLONAL	1	TRUE	1	0.247781091061473	2		448	726	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612346	1612346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769011342	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	191	700	0	ENST00000344749.5:c.1673G>A	p.Arg558His	p.R558H	ENST00000344749	NM_001136139.2	558	cGc/cAc	18/19	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.247781091061473	2		700	1221	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223251	5223251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199604489	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	77	238	1	ENST00000357368.4:c.2552G>A	p.Arg851His	p.R851H	ENST00000357368	NM_002850.3	851	cGc/cAc	18/38	1	2	FACETS	0.898	0.794	1	1	0.982	1	CLONAL	2	TRUE	1	0.247781091061473	2		239	346	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350470	15350470	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs779348570	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	73	311	0	ENST00000263377.2:c.3445C>T	p.Arg1149Trp	p.R1149W	ENST00000263377	NM_058243.2	1149	Cgg/Tgg	16/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.247781091061473	2		311	467	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858008	45858008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199778239	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	101	547	0	ENST00000391945.4:c.1645G>A	p.Val549Met	p.V549M	ENST00000391945	NM_000400.3	549	Gtg/Atg	17/23	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.247781091061473	2		547	773	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1620992	1620992	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	190	677	0	ENST00000344749.5:c.1068del	p.Val357TrpfsTer37	p.V357Wfs*37	ENST00000344749	NM_001136139.2	356	ccC/cc	13/19	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.247781091061473	2		677	1128	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251985	153251986	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	99	449	0	ENST00000281708.4:c.1020dup	p.Val341SerfsTer22	p.V341Sfs*22	ENST00000281708	NM_033632.3	340	-/A	7/12	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.247781091061473	2		449	752	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158465	26158467	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs766586530	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	127	441	0	ENST00000289316.2:c.73_75del	p.Lys25del	p.K25del	ENST00000289316	NM_138720.2	23	cAGAag/cag	1/2	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.247781091061473	2		441	877	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362311	40362311	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	152	725	4	ENST00000293328.3:c.1784del	p.Leu595TrpfsTer4	p.L595Wfs*4	ENST00000293328	NM_012448.3	595	tTg/tg	15/19	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.247781091061473	2		729	1124	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737107	145737109	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs780986647	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	126	546	1	ENST00000428558.2:c.3457_3459del	p.Glu1153del	p.E1153del	ENST00000428558	NM_004260.3	1153	GAG/-	21/22	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.247781091061473	2		547	848	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686901	37686901	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	146	422	0	ENST00000447079.4:c.3810del	p.Gly1271AspfsTer23	p.G1271Dfs*23	ENST00000447079	NM_015083.1	1269	Ccc/cc	14/14	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.247781091061473	2		422	877	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156070	119156070	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	153	544	0	ENST00000264033.4:c.1739del	p.Pro580LeufsTer35	p.P580Lfs*35	ENST00000264033	NM_005188.3	579	Ccc/cc	11/16	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.247781091061473	2		544	1037	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106162524	106162524	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	105	366	1	ENST00000380013.4:c.3442del	p.Tyr1148IlefsTer4	p.Y1148Ifs*4	ENST00000380013	NM_001127208.2	1146	ccT/cc	4/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.247781091061473	2		367	649	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	101	251	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.52595372946422	2		251	352	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	12	240	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.479763027164876	3	FACETS	0.153	0.107	0.211	0.077	0.053	0.106	SUBCLONAL	1	TRUE	1	0.52595372946422	3		240	376	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	29	493	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.141	0.112	0.173	0.141	0.112	0.173	SUBCLONAL	1	TRUE	1	0.52595372946422	2		493	784	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939183	36939183	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	250	784	0	ENST00000361632.4:c.526G>C	p.Asp176His	p.D176H	ENST00000361632		176	Gac/Cac	5/16	1	2	FACETS	0.96	0.899	1	0.96	0.899	1	CLONAL	1	TRUE	1	0.52595372946422	2		784	990	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519891	29519891	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	182	545	0	ENST00000389048.3:c.1680G>C	p.Leu560Phe	p.L560F	ENST00000389048	NM_004304.4	560	ttG/ttC	9/29	1	2	FACETS	0.99	0.917	1	0.99	0.917	1	CLONAL	1	TRUE	1	0.52595372946422	2		545	699	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149799	202149799	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	112	467	0	ENST00000358485.4:c.1240T>C	p.Phe414Leu	p.F414L	ENST00000358485	NM_001080125.1	414	Ttt/Ctt	8/9	0.52595372946422	1	FACETS	0.654	0.591	0.72	0.654	0.591	0.72	SUBCLONAL	1	TRUE	0	0.52595372946422	1		467	480	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643533	52643533	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	166	552	0	ENST00000394830.3:c.2363C>T	p.Ser788Leu	p.S788L	ENST00000394830	NM_018313.4	788	tCa/tTa	17/30	0.52595372946422	1	FACETS	0.903	0.836	0.973	0.903	0.836	0.973	CLONAL	1	TRUE	0	0.52595372946422	1		552	515	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189585728	189585728	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	245	301	0	ENST00000264731.3:c.989G>C	p.Arg330Thr	p.R330T	ENST00000264731	NM_003722.4	330	aGa/aCa	7/14	0.479763027164876	3	FACETS	0.929	0.875	0.985	0.929	0.875	0.985	CLONAL	2	TRUE	1	0.52595372946422	3		301	633	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500492	149500492	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	242	525	1	ENST00000261799.4:c.2545C>T	p.Arg849Ter	p.R849*	ENST00000261799	NM_002609.3	849	Cga/Tga	18/23	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.52595372946422	2		526	864	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056201	26056201	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs766517381	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	134	439	0	ENST00000343677.2:c.456G>C	p.Lys152Asn	p.K152N	ENST00000343677	NM_005319.3	152	aaG/aaC	1/1	1	2	FACETS	0.954	0.871	1	0.954	0.871	1	CLONAL	1	TRUE	1	0.52595372946422	2		439	534	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652017	36652017	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	177	528	1	ENST00000244741.5:c.139G>T	p.Glu47Ter	p.E47*	ENST00000244741	NM_000389.4	47	Gag/Tag	2/3	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.52595372946422	2		529	669	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652129	36652129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34916193	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	112	410	0	ENST00000244741.5:c.251G>A	p.Arg84Gln	p.R84Q	ENST00000244741	NM_000389.4	84	cGa/cAa	2/3	1	2	FACETS	0.885	0.801	0.974	0.885	0.801	0.974	CLONAL	1	TRUE	1	0.52595372946422	2		410	481	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150475	157150475	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	169	519	0	ENST00000346085.5:c.1657C>G	p.Pro553Ala	p.P553A	ENST00000346085	NM_020732.3	553	Cca/Gca	2/20	1	2	FACETS	0.993	0.917	1	0.993	0.917	1	CLONAL	1	TRUE	1	0.52595372946422	2		519	647	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738304	145738304	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1206178457	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	271	379	0	ENST00000428558.2:c.2681G>A	p.Arg894Lys	p.R894K	ENST00000428558	NM_004260.3	894	aGa/aAa	16/22	0.523672233354731	4	FACETS	0.908	0.861	0.956	0.908	0.861	0.956	CLONAL	3	TRUE	1	0.52595372946422	4		379	577	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507393	8507393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	28	517	0	ENST00000356435.5:c.1585G>A	p.Glu529Lys	p.E529K	ENST00000356435		529	Gaa/Aaa	11/35	0.52595372946422	1	FACETS	0.152	0.121	0.187	0.152	0.121	0.187	SUBCLONAL	1	TRUE	0	0.52595372946422	1		517	517	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615040	43615040	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	151	537	0	ENST00000355710.3:c.2454G>C	p.Glu818Asp	p.E818D	ENST00000355710	NM_020975.4	818	gaG/gaC	14/20	1	2	FACETS	0.901	0.827	0.979	0.901	0.827	0.979	CLONAL	1	TRUE	1	0.52595372946422	2		537	637	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438087	438087	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	176	516	0	ENST00000399788.2:c.1882G>C	p.Asp628His	p.D628H	ENST00000399788	NM_001042603.1	628	Gat/Cat	14/28	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.52595372946422	2		516	665	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442507	49442507	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	159	590	0	ENST00000301067.7:c.4066G>C	p.Asp1356His	p.D1356H	ENST00000301067	NM_003482.3	1356	Gat/Cat	13/54	1	2	FACETS	0.779	0.715	0.846	0.779	0.715	0.846	SUBCLONAL	1	TRUE	1	0.52595372946422	2		590	776	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442519	49442519	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	149	535	0	ENST00000301067.7:c.4054G>T	p.Glu1352Ter	p.E1352*	ENST00000301067	NM_003482.3	1352	Gag/Tag	13/54	1	2	FACETS	0.807	0.739	0.878	0.807	0.739	0.878	CLONAL	1	TRUE	1	0.52595372946422	2		535	702	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004241	29004241	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772440220	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	162	551	1	ENST00000282397.4:c.1052G>A	p.Arg351Gln	p.R351Q	ENST00000282397	NM_002019.4	351	cGg/cAg	8/30	1	2	FACETS	0.797	0.732	0.864	0.797	0.732	0.864	SUBCLONAL	1	TRUE	1	0.52595372946422	2		552	773	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060934	38060934	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	85	337	0	ENST00000250448.2:c.1055C>A	p.Pro352Gln	p.P352Q	ENST00000250448	NM_004496.3	352	cCa/cAa	2/2	NA	2	FACETS	0.988	0.882	1			1	INDETERMINATE	1	TRUE	NA	0.52595372946422	2		337	327	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41023306	41023306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	237	660	1	ENST00000267868.3:c.950C>T	p.Ser317Phe	p.S317F	ENST00000267868	NM_002875.4	317	tCt/tTt	10/10	1	2	FACETS	0.969	0.906	1	0.969	0.906	1	CLONAL	1	TRUE	1	0.52595372946422	2		661	930	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789661	3789661	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	210	579	0	ENST00000262367.5:c.4198G>C	p.Glu1400Gln	p.E1400Q	ENST00000262367	NM_004380.2	1400	Gag/Cag	25/31	1	2	FACETS	0.97	0.903	1	0.97	0.903	1	CLONAL	1	TRUE	1	0.52595372946422	2		579	823	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23640569	23640569	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555460219	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	178	563	0	ENST00000261584.4:c.2542G>C	p.Asp848His	p.D848H	ENST00000261584	NM_024675.3	848	Gat/Cat	6/13	1	2	FACETS	0.819	0.756	0.885	0.819	0.756	0.885	CLONAL	1	TRUE	1	0.52595372946422	2		563	826	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	235	723	0	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	1	2	FACETS	0.875	0.817	0.936	0.875	0.817	0.936	CLONAL	1	TRUE	1	0.52595372946422	2		723	1021	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7218277	7218277	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	170	495	0	ENST00000380728.2:c.94+1G>A		p.X32_splice	ENST00000380728		32			0.52595372946422	2	FACETS	1	0.99	1	0.733	0.681	0.786	CLONAL	1	TRUE	0	0.52595372946422	2		495	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	459	535	2	ENST00000269305.4:c.994-1G>T		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.52595372946422	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.52595372946422	2		537	858	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	33	622	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.52595372946422	2	FACETS	0.124	0.1	0.151	0.062	0.05	0.076	SUBCLONAL	1	TRUE	0	0.52595372946422	2		622	1013	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41228557	41228557	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	200	564	0	ENST00000357654.3:c.4432G>C	p.Glu1478Gln	p.E1478Q	ENST00000357654	NM_007294.3	1478	Gag/Cag	13/23	1	2	FACETS	0.85	0.788	0.914	0.85	0.788	0.914	CLONAL	1	TRUE	1	0.52595372946422	2		564	895	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243604	41243604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	167	562	0	ENST00000357654.3:c.3944C>T	p.Pro1315Leu	p.P1315L	ENST00000357654	NM_007294.3	1315	cCt/cTt	10/23	1	2	FACETS	0.774	0.712	0.839	0.774	0.712	0.839	SUBCLONAL	1	TRUE	1	0.52595372946422	2		562	820	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299893	15299893	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	199	598	0	ENST00000263388.2:c.1285G>A	p.Glu429Lys	p.E429K	ENST00000263388	NM_000435.2	429	Gag/Aag	8/33	1	2	FACETS	0.881	0.817	0.947	0.881	0.817	0.947	CLONAL	1	TRUE	1	0.52595372946422	2		598	859	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871995	45871995	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	105	346	0	ENST00000391945.4:c.253G>C	p.Glu85Gln	p.E85Q	ENST00000391945	NM_000400.3	85	Gaa/Caa	5/23	1	2	FACETS	0.868	0.782	0.958	0.868	0.782	0.958	CLONAL	1	TRUE	1	0.52595372946422	2		346	460	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252953	36252953	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775206089	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	151	421	0	ENST00000300305.3:c.409G>A	p.Asp137Asn	p.D137N	ENST00000300305		137	Gat/Aat	4/8	1	2	FACETS	0.943	0.865	1	0.943	0.865	1	CLONAL	1	TRUE	1	0.52595372946422	2		421	609	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36265261	36265261	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	101	357	0	ENST00000300305.3:c.59-1G>C		p.X20_splice	ENST00000300305		20			1	2	FACETS	0.641	0.574	0.712	0.641	0.574	0.712	SUBCLONAL	1	TRUE	1	0.52595372946422	2		357	599	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176451	123176451	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1569510978	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	192	368	0	ENST00000218089.9:c.418C>T	p.Gln140Ter	p.Q140*	ENST00000218089	NM_001042749.1	140	Cag/Tag	7/35	1	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.52595372946422	1		368	489	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426549	49426550	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	326	782	0	ENST00000301067.7:c.11938dup	p.Gln3980ProfsTer32	p.Q3980Pfs*32	ENST00000301067	NM_003482.3	3980	cag/cCag	39/54	1	2	FACETS	0.997	0.942	1	0.997	0.942	1	CLONAL	1	TRUE	1	0.52595372946422	2		782	1243	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922786	44922805	+	frameshift_variant	Frame_Shift_Del	DEL	AGTGCCTAGCGTCTCTCAGC	AGTGCCTAGCGTCTCTCAGC	-	novel	NA	P-0005449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	33	313	0	ENST00000377967.4:c.1647_1666del	p.Arg549SerfsTer25	p.R549Sfs*25	ENST00000377967	NM_021140.2	549	agAGTGCCTAGCGTCTCTCAGCct/agct	16/29	1	1	FACETS	0.198	0.161	0.24	0.198	0.161	0.24	SUBCLONAL	1	TRUE	0	0.52595372946422	1		313	467	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	58	251	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.35962204977513	2		251	275	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	167	400	0	ENST00000269305.4:c.380C>A	p.Ser127Tyr	p.S127Y	ENST00000269305	NM_001126112.2	127	tCc/tAc	5/11	0.35962204977513	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.35962204977513	2		400	455	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880257	37880257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	375	501	0	ENST00000269571.5:c.2301C>G	p.Ile767Met	p.I767M	ENST00000269571		767	atC/atG	19/27	0.35962204977513	6	FACETS	0.911	0.867	0.955			1	CLONAL	4	TRUE	NA	0.35962204977513	6		501	984	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444333	50444333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775004468	NA	P-0005490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	48	370	0	ENST00000331340.3:c.263C>T	p.Ser88Leu	p.S88L	ENST00000331340	NM_006060.4	88	tCg/tTg	4/8	1	2	FACETS	0.774	0.657	0.902	0.774	0.657	0.902	CLONAL	1	TRUE	1	0.35962204977513	2		370	345	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54963225	54963225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381110341	NA	P-0005490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	39	458	0	ENST00000312783.6:c.29C>T	p.Ser10Leu	p.S10L	ENST00000312783	NM_198436.1	10	tCa/tTa	3/10	0.138672562381192	3	FACETS	0.553	0.458	0.658	0.276	0.229	0.329	INDETERMINATE	1	TRUE	1	0.35962204977513	3		458	463	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247165	153247165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	30	271	0	ENST00000281708.4:c.1637C>T	p.Ser546Leu	p.S546L	ENST00000281708	NM_033632.3	546	tCa/tTa	10/12	1	2	FACETS	0.609	0.492	0.74	0.609	0.492	0.74	SUBCLONAL	1	TRUE	1	0.35962204977513	2		271	274	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074274	8074274	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	150	874	0	ENST00000377482.5:c.385C>T	p.Pro129Ser	p.P129S	ENST00000377482	NM_018948.3	129	Cca/Tca	4/4	1	2	FACETS	0.952	0.87	1	0.952	0.87	1	CLONAL	1	TRUE	1	0.35962204977513	2		874	876	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156836765	156836765	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	63	357	0	ENST00000524377.1:c.423G>T	p.Gln141His	p.Q141H	ENST00000524377	NM_002529.3	141	caG/caT	4/17	NA	2	FACETS	0.692	0.6	0.793			1	INDETERMINATE	1	TRUE	NA	0.35962204977513	2		357	506	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225343045	225343045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	126	464	0	ENST00000264414.4:c.2047G>A	p.Glu683Lys	p.E683K	ENST00000264414	NM_003590.4	683	Gaa/Aaa	15/16	0.270881291533335	2	FACETS	0.832	0.76	0.907	0.832	0.76	0.907	CLONAL	2	TRUE	0	0.35962204977513	2		464	421	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562130	176562130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	133	359	0	ENST00000439151.2:c.26G>A	p.Arg9Lys	p.R9K	ENST00000439151	NM_022455.4	9	aGa/aAa	2/23	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.35962204977513	2		359	545	SUCCESS
ATM	472	MSKCC	GRCh37	11	108154982	108154982	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	29	245	0	ENST00000278616.4:c.3775C>G	p.Leu1259Val	p.L1259V	ENST00000278616	NM_000051.3	1259	Ctg/Gtg	26/63	1	2	FACETS	0.862	0.698	1	0.862	0.698	1	CLONAL	1	TRUE	1	0.35962204977513	2		245	187	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433653	49433653	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	234	524	0	ENST00000301067.7:c.7900C>T	p.Gln2634Ter	p.Q2634*	ENST00000301067	NM_003482.3	2634	Cag/Tag	31/54	0.330500291308539	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.35962204977513	3		524	736	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263898	133263898	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	52	198	0	ENST00000320574.5:c.4T>C	p.Ser2Pro	p.S2P	ENST00000320574	NM_006231.2	2	Tct/Cct	1/49	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.35962204977513	NA		198	382	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610554	81610554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	25	472	0	ENST00000298171.2:c.2152G>A	p.Asp718Asn	p.D718N	ENST00000298171	NM_000369.2	718	Gat/Aat	10/10	1	2	FACETS	0.364	0.286	0.453	0.364	0.286	0.453	SUBCLONAL	1	TRUE	1	0.35962204977513	2		472	382	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216986	7216986	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	373	699	1	ENST00000380728.2:c.535C>T	p.Gln179Ter	p.Q179*	ENST00000380728		179	Caa/Taa	7/11	0.35962204977513	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.35962204977513	2		700	927	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942749	15942749	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0005490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	42	493	0	ENST00000268712.3:c.6953C>G	p.Ser2318Ter	p.S2318*	ENST00000268712	NM_006311.3	2318	tCa/tGa	44/46	0.35962204977513	2	FACETS	0.486	0.405	0.575	0.243	0.202	0.288	SUBCLONAL	1	TRUE	0	0.35962204977513	2		493	481	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923049	44923050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	63	195	0	ENST00000377967.4:c.1911dup	p.Asn638Ter	p.N638*	ENST00000377967	NM_021140.2	637	tct/tcTt	16/29	1	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.35962204977513	1		195	202	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097198	178097199	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0005490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	154	390	0	ENST00000397062.3:c.514_515dup	p.Ala173Ter	p.A173*	ENST00000397062	NM_006164.4	172	gta/gtGTa	4/5	0.181822072801599	3	FACETS	0.909	0.836	0.984			1	INDETERMINATE	2	TRUE	NA	0.35962204977513	3		390	556	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361163	70361164	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAA	novel	NA	P-0005490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	40	267	0	ENST00000374080.3:c.6353_6354insACA	p.Gln2123dup	p.Q2123dup	ENST00000374080		2123	-/CAA	43/45	0.353113168505065	2	FACETS	0.502	0.417	0.597			1	SUBCLONAL	1	TRUE	NA	0.35962204977513	2		267	443	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518111	8518111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	108	495	0	ENST00000356435.5:c.1280G>A	p.Arg427Gln	p.R427Q	ENST00000356435		427	cGa/cAa	10/35	0.277505013422843	4	FACETS	1	0.979	1	0.686	0.616	0.759	CLONAL	1	TRUE	2	0.327119929671408	4		495	639	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140507774	140507774	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	97	422	0	ENST00000288602.6:c.697A>C	p.Thr233Pro	p.T233P	ENST00000288602	NM_004333.4	233	Aca/Cca	5/18	0.327119929671408	3	FACETS	1	0.895	1	0.501	0.447	0.559	CLONAL	1	TRUE	1	0.327119929671408	3		422	688	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374267	118374267	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	118	689	0	ENST00000534358.1:c.7660G>C	p.Glu2554Gln	p.E2554Q	ENST00000534358	NM_005933.3	2554	Gag/Cag	27/36	0.327119929671408	3	FACETS	0.865	0.779	0.955			1	CLONAL	1	TRUE	NA	0.327119929671408	3		689	971	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891044	112891044	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	377	449	0	ENST00000351677.2:c.378A>T	p.Leu126Phe	p.L126F	ENST00000351677	NM_002834.3	126	ttA/ttT	4/16	0.327119929671408	5	FACETS	1	0.989	1			1	CLONAL	4	TRUE	NA	0.327119929671408	5		449	778	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs967461896	NA	P-0005533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	156	455	0	ENST00000269305.4:c.526T>A	p.Cys176Ser	p.C176S	ENST00000269305	NM_001126112.2	176	Tgc/Agc	5/11	0.327119929671408	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	0	0.327119929671408	2		455	469	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249012	55249013	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGT	novel	NA	P-0005533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	299	499	0	ENST00000275493.2:c.2310_2311insGGT	p.Asp770_Asn771insGly	p.D770_N771insG	ENST00000275493	NM_005228.3	770	-/GGT	20/28	0.266668863752139	5	FACETS	1	0.981	1			1	CLONAL	3	TRUE	NA	0.327119929671408	5		499	840	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0005558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	34	372	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.797	0.65	0.963	0.797	0.65	0.963	CLONAL	1	TRUE	1	0.16	2		373	533	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259263	89259263	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776350196	NA	P-0005558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	31	436	0	ENST00000336596.2:c.407G>A	p.Arg136Gln	p.R136Q	ENST00000336596	NM_005233.5	136	cGa/cAa	3/17	1	2	FACETS	0.719	0.58	0.877	0.719	0.58	0.877	SUBCLONAL	1	TRUE	1	0.16	2		436	539	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041025	112041025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779126684	NA	P-0005558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	81	591	0	ENST00000368678.4:c.230G>A	p.Arg77His	p.R77H	ENST00000368678		77	cGt/cAt	3/13	1	2	FACETS	0.784	0.688	0.887	0.784	0.688	0.887	SUBCLONAL	1	TRUE	1	0.16	2		591	1292	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163912	152163912	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	47	469	0	ENST00000206249.3:c.633A>T	p.Arg211Ser	p.R211S	ENST00000206249	NM_000125.3	211	agA/agT	2/8	1	2	FACETS	0.931	0.784	1	0.931	0.784	1	CLONAL	1	TRUE	1	0.16	2		469	631	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578191	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs530941076	NA	P-0005558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	71	599	0	ENST00000269305.4:c.658T>C	p.Tyr220His	p.Y220H	ENST00000269305	NM_001126112.2	220	Tat/Cat	6/11	1	2	FACETS	0.813	0.708	0.928	0.813	0.708	0.928	CLONAL	1	TRUE	1	0.16	2		599	1091	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627666	14627666	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1210	70	660	0	ENST00000254322.2:c.404C>G	p.Pro135Arg	p.P135R	ENST00000254322	NM_006145.1	135	cCt/cGt	2/3	1	2	FACETS	0.684	0.594	0.782	0.684	0.594	0.782	SUBCLONAL	1	TRUE	1	0.16	2		660	1280	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573523	48573524	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	46	592	0	ENST00000342988.3:c.112dup	p.Arg38LysfsTer4	p.R38Kfs*4	ENST00000342988	NM_005359.5	36	gca/gcAa	2/12	1	2	FACETS	0.651	0.546	0.768	0.651	0.546	0.768	SUBCLONAL	1	TRUE	1	0.16	2		592	883	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971207	21971216	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTGCCAGAG	CCTGCCAGAG	-	novel	NA	P-0005558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	32	169	0	ENST00000304494.5:c.151-9_151del		p.X51_splice	ENST00000304494	NM_000077.4	51		2/3	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.16	2		169	363	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971205	21971216	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GACCTGCCAGAG	GACCTGCCAGAG	CA	novel	NA	P-0005558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	32	170	0	ENST00000304494.5:c.151-9_153delinsTG		p.X51_splice	ENST00000304494	NM_000077.4	51		2/3	1				0.875	1				CLONAL	1	TRUE	1	0.16	2		170	363	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0005642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	73	360	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.882	0.771	1	0.882	0.771	1	CLONAL	1	FALSE	1	0.235094021902444	2		360	704	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0005642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	48	467	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	1	2	FACETS	0.873	0.738	1	0.873	0.738	1	CLONAL	1	FALSE	1	0.235094021902444	2		467	468	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479784	67479784	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	68	469	0	ENST00000327367.4:c.1091A>C	p.Tyr364Ser	p.Y364S	ENST00000327367	NM_005902.3	364	tAc/tCc	8/9	0.167664632045841	0	FACETS	0.751	0.654	0.857			1	SUBCLONAL	1	FALSE	0	0.235094021902444	0		469	589	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971079	21971080	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0005642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	49	215	0	ENST00000304494.5:c.277_278dup	p.Leu94ArgfsTer53	p.L94Rfs*53	ENST00000304494	NM_000077.4	93	acg/acACg	2/3	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	FALSE	1	0.235094021902444	2		215	370	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584475	187584475	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1163622953	NA	P-0006088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	65	457	0	ENST00000441802.2:c.3558C>A	p.Phe1186Leu	p.F1186L	ENST00000441802	NM_005245.3	1186	ttC/ttA	3/27	1	2	FACETS	0.477	0.413	0.547	0.477	0.413	0.547	SUBCLONAL	1	TRUE	1	0.330660078878887	2		457	824	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731205	162731205	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	68	523	0	ENST00000367921.3:c.1060G>C	p.Asp354His	p.D354H	ENST00000367921	NM_006182.2	354	Gat/Cat	9/18	1	2	FACETS	0.521	0.452	0.595	0.521	0.452	0.595	SUBCLONAL	1	TRUE	1	0.330660078878887	2		523	790	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630240	187630240	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	44	352	0	ENST00000441802.2:c.742G>C	p.Glu248Gln	p.E248Q	ENST00000441802	NM_005245.3	248	Gaa/Caa	2/27	1	2	FACETS	0.456	0.381	0.538	0.456	0.381	0.538	SUBCLONAL	1	TRUE	1	0.330660078878887	2		352	584	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120614	94120614	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1334	96	865	0	ENST00000369303.4:c.437T>G	p.Ile146Arg	p.I146R	ENST00000369303	NM_004440.3	146	aTa/aGa	3/17	1	2	FACETS	0.406	0.36	0.455	0.406	0.36	0.455	SUBCLONAL	1	TRUE	1	0.330660078878887	2		865	1430	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042709	42042709	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1256	297	1012	0	ENST00000219905.7:c.6904G>T	p.Glu2302Ter	p.E2302*	ENST00000219905	NM_001164273.1	2302	Gaa/Taa	17/24	0.330660078878887	1	FACETS	0.965	0.907	1	0.965	0.907	1	CLONAL	1	TRUE	0	0.330660078878887	1		1012	1553	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038726	47038726	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	105	245	0	ENST00000377604.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000377604	NM_001204468.1	245	Cag/Tag	9/24	1	1	FACETS	0.801	0.726	0.878	1	0.986	1	CLONAL	2	TRUE	0	0.330660078878887	1		245	331	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410946	63410946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781777369	NA	P-0006088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	96	357	0	ENST00000330258.3:c.2221C>T	p.Pro741Ser	p.P741S	ENST00000330258	NM_152424.3	741	Ccc/Tcc	2/2	1	1	FACETS	0.791	0.706	0.881	0.791	0.706	0.881	SUBCLONAL	1	TRUE	0	0.330660078878887	1		357	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576882	7576883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	132	537	0	ENST00000269305.4:c.963dup	p.Pro322ThrfsTer15	p.P322Tfs*15	ENST00000269305	NM_001126112.2	321	-/A	9/11	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.330660078878887	2		537	789	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0006181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	263	340	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.98	0.922	1	0.98	0.922	1	CLONAL	1	TRUE	1	0.664228850380496	2		340	808	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	375	482	1	ENST00000342988.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000342988	NM_005359.5	356	cCt/cTt	9/12	0.620642943041547	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.664228850380496	1		483	675	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197478	26197478	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0006181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1334	172	663	0	ENST00000356476.2:c.1A>G	p.Met1?	p.M1?	ENST00000356476		1	Atg/Gtg	1/1	0.217421609724811	2	FACETS	0.344	0.315	0.374	0.172	0.157	0.187	INDETERMINATE	1	TRUE	0	0.664228850380496	2		663	1506	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172151	32172151	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750365938	NA	P-0006181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	369	413	0	ENST00000375023.3:c.2881G>A	p.Asp961Asn	p.D961N	ENST00000375023	NM_004557.3	961	Gat/Aat	19/30	0.217421609724811	2	FACETS	1	0.995	1	0.673	0.641	0.704	INDETERMINATE	1	TRUE	0	0.664228850380496	2		413	826	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663588	117663588	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	69	277	0	ENST00000368508.3:c.4644G>T	p.Glu1548Asp	p.E1548D	ENST00000368508	NM_002944.2	1548	gaG/gaT	28/43	0.217421609724811	2	FACETS	0.377	0.328	0.429	0.189	0.164	0.215	INDETERMINATE	1	TRUE	0	0.664228850380496	2		277	551	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492755	56492755	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	402	456	0	ENST00000407977.2:c.184A>G	p.Asn62Asp	p.N62D	ENST00000407977		62	Aat/Gat	2/10	0.351300708200121	1	FACETS	0.777	0.741	0.813	0.777	0.741	0.813	INDETERMINATE	1	TRUE	0	0.664228850380496	1		456	1041	SUCCESS
APC	324	MSKCC	GRCh37	5	112175476	112175476	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	363	334	0	ENST00000257430.4:c.4188del	p.Phe1396LeufsTer19	p.F1396Lfs*19	ENST00000257430	NM_000038.5	1395	agT/ag	16/16	0.661475879850144	2	FACETS	0.95	0.914	0.986	0.95	0.914	0.986	CLONAL	2	TRUE	0	0.664228850380496	2		334	575	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710637	114710638	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	701	757	0	ENST00000543371.1:c.123dup	p.Ala42SerfsTer2	p.A42Sfs*2	ENST00000543371	NM_001198531.1	41	tta/ttAa	1/14	0.351300708200121	1	FACETS	0.833	0.804	0.862	0.833	0.804	0.862	INDETERMINATE	1	TRUE	0	0.664228850380496	1		757	1692	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876658468	NA	P-0006281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	181	171	0	ENST00000269305.4:c.577C>G	p.His193Asp	p.H193D	ENST00000269305	NM_001126112.2	193	Cat/Gat	6/11	0.437454799485728	3	FACETS	1	0.961	1			1	CLONAL	3	TRUE	NA	0.437454799485728	3		171	327	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	62	139	0	ENST00000335508.6:c.2704G>A	p.Glu902Lys	p.E902K	ENST00000335508	NM_012433.2	902	Gaa/Aaa	18/25	0.437454799485728	3	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	1	0.437454799485728	3		139	160	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462581	29462581	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	57	190	1	ENST00000389048.3:c.2320C>A	p.Leu774Met	p.L774M	ENST00000389048	NM_004304.4	774	Ctg/Atg	13/29	0.437454799485728	3	FACETS	1	0.873	1	0.506	0.437	0.58	CLONAL	1	TRUE	1	0.437454799485728	3		191	314	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047062	128047062	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772575791	NA	P-0006281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	43	194	0	ENST00000285398.2:c.673G>A	p.Glu225Lys	p.E225K	ENST00000285398	NM_000122.1	225	Gaa/Aaa	6/15	0.331902746590055	5	FACETS	0.933	0.783	1	0.311	0.261	0.366	CLONAL	1	TRUE	2	0.437454799485728	5		194	349	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662307	227662307	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	39	158	0	ENST00000305123.5:c.1148C>G	p.Ser383Trp	p.S383W	ENST00000305123	NM_005544.2	383	tCg/tGg	1/2	0.437454799485728	3	FACETS	0.873	0.728	1	0.436	0.364	0.516	CLONAL	1	TRUE	1	0.437454799485728	3		158	249	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267219	41267219	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	27	132	0	ENST00000349496.5:c.803G>C	p.Gly268Ala	p.G268A	ENST00000349496	NM_001904.3	268	gGa/gCa	6/15	0.437454799485728	3	FACETS	0.752	0.603	0.92	0.376	0.301	0.46	CLONAL	1	TRUE	1	0.437454799485728	3		132	200	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602909	55602909	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs766036617	NA	P-0006281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	43	122	0	ENST00000288135.5:c.2619G>T	p.Met873Ile	p.M873I	ENST00000288135	NM_000222.2	873	atG/atT	19/21	0.185714458329972	5	FACETS	1	0.952	1			1	INDETERMINATE	1	TRUE	NA	0.437454799485728	5		122	237	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955933	55955933	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	26	178	0	ENST00000263923.4:c.3229A>G	p.Ile1077Val	p.I1077V	ENST00000263923	NM_002253.2	1077	Att/Gtt	24/30	1	2	FACETS	0.597	0.476	0.734	0.597	0.476	0.734	SUBCLONAL	1	TRUE	1	0.437454799485728	2		178	199	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677894	117677894	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	40	168	0	ENST00000368508.3:c.4039C>G	p.Leu1347Val	p.L1347V	ENST00000368508	NM_002944.2	1347	Cta/Gta	25/43	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.437454799485728	2		168	177	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157520015	157520015	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	90	229	1	ENST00000346085.5:c.4084C>T	p.Gln1362Ter	p.Q1362*	ENST00000346085	NM_020732.3	1362	Cag/Tag	17/20	0.346956512895657	2	FACETS	0.939	0.85	1	0.939	0.85	1	CLONAL	2	TRUE	0	0.437454799485728	2		230	219	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523486	106523486	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	28	102	0	ENST00000359195.3:c.2638G>T	p.Glu880Ter	p.E880*	ENST00000359195	NM_002649.2	880	Gag/Tag	8/11	0.30372349698783	5	FACETS	1	0.911	1	0.416	0.335	0.505	CLONAL	1	TRUE	2	0.437454799485728	5		102	170	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446161	70446161	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	44	153	0	ENST00000373644.4:c.5101C>T	p.Gln1701Ter	p.Q1701*	ENST00000373644	NM_030625.2	1701	Caa/Taa	11/12	0.437454799485728	3	FACETS	1	0.891	1	0.533	0.451	0.622	CLONAL	1	TRUE	1	0.437454799485728	3		153	230	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999114	100999114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1482228418	NA	P-0006281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	52	256	2	ENST00000325455.5:c.688G>A	p.Glu230Lys	p.E230K	ENST00000325455	NM_001202474.3	230	Gag/Aag	1/8	1	2	FACETS	0.884	0.759	1	0.884	0.759	1	CLONAL	1	TRUE	1	0.437454799485728	2		258	269	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446785	49446785	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	38	184	0	ENST00000301067.7:c.1025A>G	p.Asn342Ser	p.N342S	ENST00000301067	NM_003482.3	342	aAc/aGc	8/54	0.294560642879602	5	FACETS	1	0.871	1			1	CLONAL	1	TRUE	NA	0.437454799485728	5		184	272	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110047	115110047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766569858	NA	P-0006281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	48	162	0	ENST00000257566.3:c.1831G>A	p.Ala611Thr	p.A611T	ENST00000257566	NM_016569.3	611	Gcg/Acg	8/8	0.437454799485728	3	FACETS	1	0.946	1	0.622	0.532	0.719	CLONAL	1	TRUE	1	0.437454799485728	3		162	215	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472444	88472444	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	25	143	0	ENST00000360948.2:c.2111T>G	p.Val704Gly	p.V704G	ENST00000360948	NM_001012338.2	704	gTc/gGc	16/19	0.437454799485728	3	FACETS	0.496	0.391	0.615	0.248	0.195	0.308	SUBCLONAL	1	TRUE	1	0.437454799485728	3		143	281	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786137	3786137	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	96	225	0	ENST00000262367.5:c.4628A>T	p.Asp1543Val	p.D1543V	ENST00000262367	NM_004380.2	1543	gAt/gTt	28/31	0.437454799485728	3	FACETS	0.854	0.77	0.942	0.854	0.77	0.942	CLONAL	2	TRUE	1	0.437454799485728	3		225	313	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831986	72831986	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs374743360	NA	P-0006281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	58	310	0	ENST00000268489.5:c.4595A>G	p.Asn1532Ser	p.N1532S	ENST00000268489	NM_006885.3	1532	aAt/aGt	9/10	1	2	FACETS	0.834	0.721	0.955	0.834	0.721	0.955	CLONAL	1	TRUE	1	0.437454799485728	2		310	318	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122406	17122406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1337576606	NA	P-0006281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	83	206	0	ENST00000285071.4:c.989C>T	p.Ser330Phe	p.S330F	ENST00000285071	NM_144997.5	330	tCc/tTc	9/14	0.232046892246586	3	FACETS	0.948	0.85	1			1	INDETERMINATE	2	TRUE	NA	0.437454799485728	3		206	244	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794509	42794509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1221840528	NA	P-0006281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	175	228	0	ENST00000575354.2:c.1589C>T	p.Ser530Phe	p.S530F	ENST00000575354	NM_015125.3	530	tCc/tTc	10/20	0.437454799485728	5	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	TRUE	2	0.437454799485728	5		228	409	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796747	42796747	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	68	125	0	ENST00000575354.2:c.3205C>T	p.Gln1069Ter	p.Q1069*	ENST00000575354	NM_015125.3	1069	Cag/Tag	14/20	0.437454799485728	5	FACETS	0.929	0.817	1	0.62	0.544	0.699	CLONAL	2	TRUE	2	0.437454799485728	5		125	277	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410355	63410355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	65	134	0	ENST00000330258.3:c.2812G>A	p.Gly938Arg	p.G938R	ENST00000330258	NM_152424.3	938	Gga/Aga	2/2	0.437454799485728	2	FACETS	1	0.965	1			1	CLONAL	1	TRUE	NA	0.437454799485728	2		134	230	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102069	27102069	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	43	242	0	ENST00000324856.7:c.4996del	p.Thr1666ProfsTer7	p.T1666Pfs*7	ENST00000324856	NM_006015.4	1665	ggA/gg	19/20	0.437454799485728	3	FACETS	0.768	0.645	0.902	0.384	0.322	0.451	CLONAL	1	TRUE	1	0.437454799485728	3		242	312	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425135	49425136	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	145	213	0	ENST00000301067.7:c.13352dup	p.Ala4452GlyfsTer35	p.A4452Gfs*35	ENST00000301067	NM_003482.3	4451	ctg/ctTg	39/54	0.294560642879602	5	FACETS	0.986	0.911	1			1	CLONAL	3	TRUE	NA	0.437454799485728	5		213	371	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404311	139404315	+	missense_variant	Missense_Mutation	ONP	TCGTT	TCGTT	CCGTC	novel	NA	P-0006281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	73	197	0	ENST00000277541.6:c.2839_2843delinsGACGG	p.Asn947_Glu948delinsAspGly	p.N947_E948delinsDG	ENST00000277541	NM_017617.3	947	AACGAg/GACGGg	18/34	0.437454799485728	3	FACETS	1	0.973	1	0.461	0.407	0.518	CLONAL	1	TRUE	0	0.437454799485728	3		197	294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0006405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	103	717	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.724	0.647	0.806	0.724	0.647	0.806	SUBCLONAL	1	FALSE	1	0.294906893773332	2		717	965	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046289	128046289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746827111	NA	P-0006405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	89	601	2	ENST00000285398.2:c.974G>A	p.Arg325Gln	p.R325Q	ENST00000285398	NM_000122.1	325	cGa/cAa	7/15	1	2	FACETS	0.641	0.567	0.721	0.641	0.567	0.721	SUBCLONAL	1	FALSE	1	0.294906893773332	2		603	941	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143191893	143191893	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	39	621	1	ENST00000262992.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000262992	NM_001101669.1	180	Gaa/Aaa	8/24	0.202608556421049	1	FACETS	0.298	0.246	0.356	0.298	0.246	0.356	SUBCLONAL	1	FALSE	0	0.294906893773332	1		622	757	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060823	38060823	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1575	88	1014	1	ENST00000250448.2:c.1166A>T	p.Lys389Ile	p.K389I	ENST00000250448	NM_004496.3	389	aAa/aTa	2/2	1	2	FACETS	0.359	0.316	0.405	0.359	0.316	0.405	SUBCLONAL	1	FALSE	1	0.294906893773332	2		1015	1663	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501219	140501220	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	94	448	0	ENST00000288602.6:c.852_853insA	p.Gln285ThrfsTer3	p.Q285Tfs*3	ENST00000288602	NM_004333.4	284	-/A	6/18	0.294906893773332	8	FACETS	1	0.964	1			1	CLONAL	1	FALSE	NA	0.294906893773332	8		448	994	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	62	240	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.869	0.759	0.987			1	INDETERMINATE	1	TRUE	NA	0.548619470789376	2		240	260	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	299	260	0	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.548619470789376	2		260	500	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188171	11188171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	110	254	0	ENST00000361445.4:c.5923C>T	p.Pro1975Ser	p.P1975S	ENST00000361445	NM_004958.3	1975	Cca/Tca	43/58	NA	2	FACETS	1	0.91	1			1	INDETERMINATE	1	TRUE	NA	0.548619470789376	2		254	399	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307955	11307955	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184637287	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	41	405	0	ENST00000361445.4:c.1037G>A	p.Gly346Glu	p.G346E	ENST00000361445	NM_004958.3	346	gGg/gAg	7/58	1	2	FACETS	0.287	0.239	0.341	0.287	0.239	0.341	SUBCLONAL	1	TRUE	1	0.548619470789376	2		405	520	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263836	16263836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	41	435	0	ENST00000375759.3:c.10205C>T	p.Pro3402Leu	p.P3402L	ENST00000375759	NM_015001.2	3402	cCt/cTt	12/15	1	2	FACETS	0.265	0.22	0.315	0.265	0.22	0.315	SUBCLONAL	1	TRUE	1	0.548619470789376	2		435	564	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101353	27101353	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	30	416	1	ENST00000324856.7:c.4635G>A	p.Trp1545Ter	p.W1545*	ENST00000324856	NM_006015.4	1545	tgG/tgA	18/20	0.547910498008625	2	FACETS	0.19	0.152	0.233	0.095	0.076	0.117	SUBCLONAL	1	TRUE	0	0.548619470789376	2		417	575	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106957	27106957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	28	294	0	ENST00000324856.7:c.6568G>A	p.Gly2190Ser	p.G2190S	ENST00000324856	NM_006015.4	2190	Ggc/Agc	20/20	0.547910498008625	2	FACETS	0.271	0.216	0.333	0.135	0.108	0.167	SUBCLONAL	1	TRUE	0	0.548619470789376	2		294	377	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521487	46521487	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	431	492	0	ENST00000262741.5:c.921G>C	p.Lys307Asn	p.K307N	ENST00000262741	NM_003629.3	307	aaG/aaC	7/10	0.547910498008625	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.548619470789376	2		492	703	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303648	65303648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	58	311	0	ENST00000342505.4:c.3107C>T	p.Thr1036Ile	p.T1036I	ENST00000342505	NM_002227.2	1036	aCc/aTc	22/25	NA	2	FACETS	0.306	0.262	0.353			1	INDETERMINATE	1	TRUE	NA	0.548619470789376	2		311	692	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65349059	65349059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	164	346	0	ENST00000342505.4:c.106G>A	p.Val36Met	p.V36M	ENST00000342505	NM_002227.2	36	Gtg/Atg	3/25	NA	2	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.548619470789376	2		346	547	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058500	72058500	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1428865181	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	199	434	0	ENST00000357731.5:c.940C>T	p.Pro314Ser	p.P314S	ENST00000357731	NM_173808.2	314	Cct/Tct	6/7	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.548619470789376	2		434	700	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849075	156849075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	159	367	1	ENST00000524377.1:c.1967G>A	p.Cys656Tyr	p.C656Y	ENST00000524377	NM_002529.3	656	tGt/tAt	15/17	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.548619470789376	2		368	533	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226580000	226580000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	34	303	0	ENST00000366794.5:c.302G>A	p.Gly101Glu	p.G101E	ENST00000366794	NM_001618.3	101	gGa/gAa	3/23	1	2	FACETS	0.232	0.189	0.28	0.232	0.189	0.28	SUBCLONAL	1	TRUE	1	0.548619470789376	2		303	535	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029115	26029115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	54	394	0	ENST00000435504.4:c.235G>A	p.Gly79Arg	p.G79R	ENST00000435504		79	Gga/Aga	4/13	1	2	FACETS	0.269	0.229	0.313	0.269	0.229	0.313	SUBCLONAL	1	TRUE	1	0.548619470789376	2		394	731	SUCCESS
ALK	238	MSKCC	GRCh37	2	29541183	29541183	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147033307	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	177	339	0	ENST00000389048.3:c.1634G>A	p.Ser545Asn	p.S545N	ENST00000389048	NM_004304.4	545	aGc/aAc	8/29	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.548619470789376	2		339	588	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754982	29754982	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs770893847	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	15	183	0	ENST00000389048.3:c.953G>A	p.Gly318Asp	p.G318D	ENST00000389048	NM_004304.4	318	gGc/gAc	4/29	1	2	FACETS	0.185	0.135	0.246	0.185	0.135	0.246	SUBCLONAL	1	TRUE	1	0.548619470789376	2		183	295	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026917	48026917	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	208	357	0	ENST00000234420.5:c.1795G>A	p.Gly599Arg	p.G599R	ENST00000234420	NM_000179.2	599	Gga/Aga	4/10	1	2	FACETS	0.963	0.897	1	0.963	0.897	1	CLONAL	1	TRUE	1	0.548619470789376	2		357	787	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044527	128044527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772229792	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	50	339	0	ENST00000285398.2:c.1094G>A	p.Gly365Asp	p.G365D	ENST00000285398	NM_000122.1	365	gGc/gAc	8/15	1	2	FACETS	0.309	0.262	0.362	0.309	0.262	0.362	SUBCLONAL	1	TRUE	1	0.548619470789376	2		339	589	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872632	136872632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	297	702	1	ENST00000241393.3:c.866C>T	p.Ala289Val	p.A289V	ENST00000241393	NM_003467.2	289	gCc/gTc	2/2	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.548619470789376	2		703	908	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257727	198257727	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	76	359	0	ENST00000335508.6:c.3725G>A	p.Gly1242Glu	p.G1242E	ENST00000335508	NM_012433.2	1242	gGa/gAa	24/25	1	2	FACETS	0.369	0.323	0.419	0.369	0.323	0.419	SUBCLONAL	1	TRUE	1	0.548619470789376	2		359	750	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265128	198265128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	46	240	0	ENST00000335508.6:c.2749G>A	p.Val917Met	p.V917M	ENST00000335508	NM_012433.2	917	Gtg/Atg	19/25	1	2	FACETS	0.293	0.246	0.344	0.293	0.246	0.344	SUBCLONAL	1	TRUE	1	0.548619470789376	2		240	573	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139648	202139648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	41	420	0	ENST00000358485.4:c.809C>T	p.Ser270Phe	p.S270F	ENST00000358485	NM_001080125.1	270	tCt/tTt	6/9	1	2	FACETS	0.211	0.175	0.251	0.211	0.175	0.251	SUBCLONAL	1	TRUE	1	0.548619470789376	2		420	708	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067308	37067308	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057517541	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	182	372	0	ENST00000231790.2:c.1219C>T	p.Gln407Ter	p.Q407*	ENST00000231790	NM_000249.3	407	Cag/Tag	12/19	0.548619470789376	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.548619470789376	1		372	451	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070351	37070351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	79	393	1	ENST00000231790.2:c.1486C>T	p.Pro496Ser	p.P496S	ENST00000231790	NM_000249.3	496	Ccc/Tcc	13/19	0.548619470789376	1	FACETS	0.464	0.41	0.523	0.464	0.41	0.523	SUBCLONAL	1	TRUE	0	0.548619470789376	1		394	450	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924747	49924747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	167	493	0	ENST00000296474.3:c.4196C>T	p.Pro1399Leu	p.P1399L	ENST00000296474	NM_002447.2	1399	cCc/cTc	20/20	0.548619470789376	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.548619470789376	1		493	399	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008462	70008462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	30	217	0	ENST00000394351.3:c.749C>T	p.Ser250Phe	p.S250F	ENST00000394351	NM_000248.3	250	tCc/tTc	8/9	0.548619470789376	1	FACETS	0.243	0.196	0.297	0.243	0.196	0.297	SUBCLONAL	1	TRUE	0	0.548619470789376	1		217	326	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202726	128202726	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	39	462	0	ENST00000341105.2:c.994C>T	p.Leu332Phe	p.L332F	ENST00000341105	NM_032638.4	332	Ctc/Ttc	4/6	1	2	FACETS	0.191	0.157	0.228	0.191	0.157	0.228	SUBCLONAL	1	TRUE	1	0.548619470789376	2		462	745	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938783	178938783	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs887627133	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	90	73	0	ENST00000263967.3:c.2025G>A	p.Met675Ile	p.M675I	ENST00000263967	NM_006218.2	675	atG/atA	14/21	0.467768291176758	4	FACETS	0.931	0.848	1			1	CLONAL	3	TRUE	NA	0.548619470789376	4		73	182	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431017	181431017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	138	292	0	ENST00000325404.1:c.869G>A	p.Ser290Asn	p.S290N	ENST00000325404	NM_003106.3	290	aGc/aAc	1/1	0.467768291176758	4	FACETS	1	0.957	1			1	CLONAL	1	TRUE	NA	0.548619470789376	4		292	721	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146518	185146518	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1358772216	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	125	314	0	ENST00000265026.3:c.149G>A	p.Gly50Glu	p.G50E	ENST00000265026	NM_004721.4	50	gGg/gAg	2/14	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.548619470789376	2		314	445	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573288	55573288	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	45	325	0	ENST00000288135.5:c.950C>T	p.Pro317Leu	p.P317L	ENST00000288135	NM_000222.2	317	cCc/cTc	6/21	1	2	FACETS	0.266	0.223	0.314	0.266	0.223	0.314	SUBCLONAL	1	TRUE	1	0.548619470789376	2		325	617	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979554	55979554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1355954905	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	51	416	0	ENST00000263923.4:c.893C>T	p.Thr298Ile	p.T298I	ENST00000263923	NM_002253.2	298	aCc/aTc	7/30	1	2	FACETS	0.255	0.216	0.298	0.255	0.216	0.298	SUBCLONAL	1	TRUE	1	0.548619470789376	2		416	728	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190819	106190819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs534309433	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	67	281	0	ENST00000380013.4:c.4097G>A	p.Arg1366His	p.R1366H	ENST00000380013	NM_001127208.2	1366	cGt/cAt	9/11	1	2	FACETS	0.366	0.317	0.418	0.366	0.317	0.418	SUBCLONAL	1	TRUE	1	0.548619470789376	2		281	668	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	231116	231116	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	30	260	0	ENST00000264932.6:c.895+1G>A		p.X299_splice	ENST00000264932	NM_004168.2	299			NA	2	FACETS	0.285	0.229	0.348			1	INDETERMINATE	1	TRUE	NA	0.548619470789376	2		260	384	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160574	56160574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	142	264	0	ENST00000399503.3:c.848G>A	p.Arg283Lys	p.R283K	ENST00000399503	NM_005921.1	283	aGa/aAa	4/20	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.548619470789376	2		264	497	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588113	67588113	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	32	244	0	ENST00000274335.5:c.943A>G	p.Thr315Ala	p.T315A	ENST00000274335		315	Act/Gct	7/15	1	2	FACETS	0.221	0.178	0.268	0.221	0.178	0.268	SUBCLONAL	1	TRUE	1	0.548619470789376	2		244	529	SUCCESS
APC	324	MSKCC	GRCh37	5	112173572	112173572	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	77	335	0	ENST00000257430.4:c.2281G>A	p.Glu761Lys	p.E761K	ENST00000257430	NM_000038.5	761	Gaa/Aaa	16/16	1	2	FACETS	0.454	0.399	0.514	0.454	0.399	0.514	SUBCLONAL	1	TRUE	1	0.548619470789376	2		335	618	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819780	170819780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	36	218	0	ENST00000296930.5:c.419G>A	p.Gly140Glu	p.G140E	ENST00000296930	NM_002520.6	140	gGa/gAa	5/11	1	2	FACETS	0.319	0.262	0.382	0.319	0.262	0.382	SUBCLONAL	1	TRUE	1	0.548619470789376	2		218	412	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405053	405053	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	127	350	1	ENST00000380956.4:c.1135C>T	p.Pro379Ser	p.P379S	ENST00000380956	NM_001195286.1	379	Cca/Tca	8/9	0.319354818305274	3	FACETS	1	0.946	1	0.528	0.48	0.578	INDETERMINATE	1	TRUE	1	0.548619470789376	3		351	559	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178660	32178660	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	66	304	0	ENST00000375023.3:c.2734C>T	p.Pro912Ser	p.P912S	ENST00000375023	NM_004557.3	912	Ccc/Tcc	18/30	1	2	FACETS	0.514	0.447	0.586	0.514	0.447	0.586	SUBCLONAL	1	TRUE	1	0.548619470789376	2		304	468	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138382	37138382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	62	367	0	ENST00000373509.5:c.31C>T	p.His11Tyr	p.H11Y	ENST00000373509	NM_002648.3	11	Cac/Tac	1/6	1	2	FACETS	0.446	0.385	0.511	0.446	0.385	0.511	SUBCLONAL	1	TRUE	1	0.548619470789376	2		367	507	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983142	111983142	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	159	402	0	ENST00000368678.4:c.1405A>T	p.Asn469Tyr	p.N469Y	ENST00000368678		469	Aac/Tac	13/13	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.548619470789376	2		402	560	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111995798	111995798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	72	542	1	ENST00000368678.4:c.1300G>A	p.Ala434Thr	p.A434T	ENST00000368678		434	Gca/Aca	12/13	1	2	FACETS	0.277	0.241	0.316	0.277	0.241	0.316	SUBCLONAL	1	TRUE	1	0.548619470789376	2		543	946	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112029124	112029124	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	211	410	1	ENST00000368678.4:c.443+1G>A		p.X148_splice	ENST00000368678		148			1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.548619470789376	2		411	723	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864368	162864368	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	182	316	0	ENST00000366898.1:c.145G>A	p.Glu49Lys	p.E49K	ENST00000366898	NM_004562.2	49	Gag/Aag	2/12	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.548619470789376	2		316	590	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946339	2946339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746125201	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	137	350	1	ENST00000396946.4:c.3398G>A	p.Arg1133His	p.R1133H	ENST00000396946	NM_032415.4	1133	cGc/cAc	25/25	0.548619470789376	3	FACETS	1	0.938	1	0.517	0.472	0.565	CLONAL	1	TRUE	1	0.548619470789376	3		351	615	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026816	6026816	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	58	135	0	ENST00000265849.7:c.1580G>A	p.Arg527Lys	p.R527K	ENST00000265849	NM_000535.5	527	aGg/aAg	11/15	0.548619470789376	3	FACETS	0.983	0.853	1	0.492	0.426	0.562	CLONAL	1	TRUE	1	0.548619470789376	3		135	274	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455073	50455073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	46	262	2	ENST00000331340.3:c.620G>A	p.Gly207Asp	p.G207D	ENST00000331340	NM_006060.4	207	gGc/gAc	6/8	0.548619470789376	3	FACETS	0.329	0.276	0.387	0.164	0.138	0.194	SUBCLONAL	1	TRUE	1	0.548619470789376	3		264	650	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508256	106508256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	16	150	0	ENST00000359195.3:c.250G>A	p.Ala84Thr	p.A84T	ENST00000359195	NM_002649.2	84	Gcg/Acg	2/11	1	2	FACETS	0.257	0.19	0.337	0.257	0.19	0.337	SUBCLONAL	1	TRUE	1	0.548619470789376	2		150	227	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524651	106524651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	30	278	0	ENST00000359195.3:c.2812G>A	p.Ala938Thr	p.A938T	ENST00000359195	NM_002649.2	938	Gca/Aca	9/11	1	2	FACETS	0.209	0.167	0.256	0.209	0.167	0.256	SUBCLONAL	1	TRUE	1	0.548619470789376	2		278	524	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411652	116411652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	72	272	0	ENST00000397752.3:c.2831C>T	p.Ala944Val	p.A944V	ENST00000397752	NM_000245.2	944	gCa/gTa	13/21	1	2	FACETS	0.372	0.325	0.424	0.372	0.325	0.424	SUBCLONAL	1	TRUE	1	0.548619470789376	2		272	705	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853310	151853310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	102	204	0	ENST00000262189.6:c.11792G>A	p.Gly3931Glu	p.G3931E	ENST00000262189	NM_170606.2	3931	gGa/gAa	45/59	1	2	FACETS	0.887	0.799	0.98	0.887	0.799	0.98	CLONAL	1	TRUE	1	0.548619470789376	2		204	419	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873582	151873582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1563253073	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	148	307	0	ENST00000262189.6:c.8956G>A	p.Gly2986Ser	p.G2986S	ENST00000262189	NM_170606.2	2986	Ggt/Agt	38/59	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.548619470789376	2		307	536	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117870641	117870641	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	120	548	0	ENST00000297338.2:c.431C>T	p.Thr144Ile	p.T144I	ENST00000297338	NM_006265.2	144	aCc/aTc	5/14	1	2	FACETS	0.438	0.395	0.484	0.438	0.395	0.484	SUBCLONAL	1	TRUE	1	0.548619470789376	2		548	999	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641077	93641077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	30	232	0	ENST00000375746.1:c.1423G>A	p.Val475Ile	p.V475I	ENST00000375746	NM_001174167.1	475	Gtt/Att	11/14	1	2	FACETS	0.237	0.19	0.29	0.237	0.19	0.29	SUBCLONAL	1	TRUE	1	0.548619470789376	2		232	462	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100289	8100289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	34	324	0	ENST00000346208.3:c.263C>T	p.Pro88Leu	p.P88L	ENST00000346208		88	cCt/cTt	3/6	0.548619470789376	1	FACETS	0.303	0.248	0.364	0.303	0.248	0.364	SUBCLONAL	1	TRUE	0	0.548619470789376	1		324	297	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596110	43596110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1477699803	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	23	278	0	ENST00000355710.3:c.277G>A	p.Gly93Ser	p.G93S	ENST00000355710	NM_020975.4	93	Ggc/Agc	2/20	0.548619470789376	1	FACETS	0.217	0.169	0.273	0.217	0.169	0.273	SUBCLONAL	1	TRUE	0	0.548619470789376	1		278	280	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606869	43606869	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	79	200	0	ENST00000355710.3:c.1478C>T	p.Ser493Phe	p.S493F	ENST00000355710	NM_020975.4	493	tCt/tTt	7/20	0.548619470789376	1	FACETS	0.889	0.795	0.987	0.889	0.795	0.987	CLONAL	1	TRUE	0	0.548619470789376	1		200	235	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692968	89692968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	48	200	0	ENST00000371953.3:c.452C>T	p.Ala151Val	p.A151V	ENST00000371953	NM_000314.4	151	gCc/gTc	5/9	0.548619470789376	1	FACETS	0.358	0.303	0.417	0.358	0.303	0.417	SUBCLONAL	1	TRUE	0	0.548619470789376	1		200	355	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94163097	94163097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765958437	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	224	449	0	ENST00000323929.3:c.2050G>A	p.Val684Ile	p.V684I	ENST00000323929	NM_005591.3	684	Gtt/Att	19/20	1	2	FACETS	0.966	0.902	1	0.966	0.902	1	CLONAL	1	TRUE	1	0.548619470789376	2		449	845	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025510	1025510	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	43	309	0	ENST00000358495.3:c.865G>A	p.Ala289Thr	p.A289T	ENST00000358495	NM_134424.2	289	Gca/Aca	9/12	1	2	FACETS	0.349	0.292	0.412	0.349	0.292	0.412	SUBCLONAL	1	TRUE	1	0.548619470789376	2		309	449	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211594	46211594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	223	392	0	ENST00000334344.6:c.560G>A	p.Ser187Asn	p.S187N	ENST00000334344	NM_152641.2	187	aGc/aAc	5/21	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.548619470789376	2		392	789	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244899	46244899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	44	488	1	ENST00000334344.6:c.2993G>A	p.Gly998Glu	p.G998E	ENST00000334344	NM_152641.2	998	gGa/gAa	15/21	1	2	FACETS	0.198	0.165	0.234	0.198	0.165	0.234	SUBCLONAL	1	TRUE	1	0.548619470789376	2		489	812	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420324	49420324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	43	394	0	ENST00000301067.7:c.15425G>A	p.Cys5142Tyr	p.C5142Y	ENST00000301067	NM_003482.3	5142	tGt/tAt	48/54	1	2	FACETS	0.242	0.201	0.286	0.242	0.201	0.286	SUBCLONAL	1	TRUE	1	0.548619470789376	2		394	649	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420700	49420700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	51	239	1	ENST00000301067.7:c.15049G>A	p.Gly5017Ser	p.G5017S	ENST00000301067	NM_003482.3	5017	Ggc/Agc	48/54	1	2	FACETS	0.431	0.367	0.502	0.431	0.367	0.502	SUBCLONAL	1	TRUE	1	0.548619470789376	2		240	431	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422649	49422649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	37	347	1	ENST00000301067.7:c.14344G>A	p.Val4782Met	p.V4782M	ENST00000301067	NM_003482.3	4782	Gtg/Atg	45/54	1	2	FACETS	0.232	0.191	0.279	0.232	0.191	0.279	SUBCLONAL	1	TRUE	1	0.548619470789376	2		348	581	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433847	49433847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	161	335	0	ENST00000301067.7:c.7706G>A	p.Gly2569Asp	p.G2569D	ENST00000301067	NM_003482.3	2569	gGc/gAc	31/54	1	2	FACETS	0.995	0.917	1	0.995	0.917	1	CLONAL	1	TRUE	1	0.548619470789376	2		335	590	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444445	49444445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	141	271	0	ENST00000301067.7:c.2926C>T	p.Pro976Ser	p.P976S	ENST00000301067	NM_003482.3	976	Ccc/Tcc	11/54	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.548619470789376	2		271	443	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487289	56487289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	31	206	0	ENST00000267101.3:c.1435G>A	p.Glu479Lys	p.E479K	ENST00000267101	NM_001982.3	479	Gaa/Aaa	12/28	1	2	FACETS	0.278	0.225	0.339	0.278	0.225	0.339	SUBCLONAL	1	TRUE	1	0.548619470789376	2		206	406	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202827	133202827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	33	281	0	ENST00000320574.5:c.6407G>A	p.Gly2136Asp	p.G2136D	ENST00000320574	NM_006231.2	2136	gGc/gAc	46/49	1	2	FACETS	0.262	0.213	0.317	0.262	0.213	0.317	SUBCLONAL	1	TRUE	1	0.548619470789376	2		281	460	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26911762	26911762	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	181	276	0	ENST00000381527.3:c.187G>A	p.Ala63Thr	p.A63T	ENST00000381527	NM_001260.1	63	Gca/Aca	2/13	1	2	FACETS	0.936	0.866	1	0.936	0.866	1	CLONAL	1	TRUE	1	0.548619470789376	2		276	705	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103520537	103520537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	222	423	0	ENST00000355739.4:c.2608G>A	p.Gly870Ser	p.G870S	ENST00000355739	NM_000123.3	870	Ggt/Agt	12/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.548619470789376	2		423	734	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434799	110434799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1487151455	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	33	349	0	ENST00000375856.3:c.3602C>T	p.Pro1201Leu	p.P1201L	ENST00000375856	NM_003749.2	1201	cCc/cTc	1/2	1	2	FACETS	0.254	0.206	0.308	0.254	0.206	0.308	SUBCLONAL	1	TRUE	1	0.548619470789376	2		349	474	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435600	110435600	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	63	134	0	ENST00000375856.3:c.2801C>T	p.Pro934Leu	p.P934L	ENST00000375856	NM_003749.2	934	cCc/cTc	1/2	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.548619470789376	2		134	203	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65569030	65569030	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	182	427	0	ENST00000358664.4:c.28G>A	p.Glu10Lys	p.E10K	ENST00000358664	NM_002382.4	10	Gag/Aag	1/5	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.548619470789376	2		427	611	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95556839	95556839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1220636958	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	35	292	0	ENST00000393063.1:c.5765G>A	p.Ser1922Asn	p.S1922N	ENST00000393063	NM_030621.3	1922	aGc/aAc	28/28	1	2	FACETS	0.286	0.234	0.344	0.286	0.234	0.344	SUBCLONAL	1	TRUE	1	0.548619470789376	2		292	446	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000370	42000370	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	61	522	1	ENST00000219905.7:c.2389G>A	p.Gly797Arg	p.G797R	ENST00000219905	NM_001164273.1	797	Gga/Aga	7/24	1	2	FACETS	0.265	0.228	0.306	0.265	0.228	0.306	SUBCLONAL	1	TRUE	1	0.548619470789376	2		523	838	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041423	42041423	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	234	666	1	ENST00000219905.7:c.5618C>T	p.Ser1873Phe	p.S1873F	ENST00000219905	NM_001164273.1	1873	tCt/tTt	17/24	1	2	FACETS	0.961	0.898	1	0.961	0.898	1	CLONAL	1	TRUE	1	0.548619470789376	2		667	888	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678629	88678629	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	63	127	0	ENST00000360948.2:c.908-1G>A		p.X303_splice	ENST00000360948	NM_001012338.2	303			1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.548619470789376	2		127	221	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346762	91346762	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	132	216	0	ENST00000355112.3:c.3370G>A	p.Ala1124Thr	p.A1124T	ENST00000355112	NM_000057.2	1124	Gca/Aca	18/22	1	2	FACETS	0.99	0.905	1	0.99	0.905	1	CLONAL	1	TRUE	1	0.548619470789376	2		216	486	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456451	99456451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	135	310	0	ENST00000268035.6:c.1768G>A	p.Glu590Lys	p.E590K	ENST00000268035	NM_000875.3	590	Gag/Aag	8/21	1	2	FACETS	0.984	0.9	1	0.984	0.9	1	CLONAL	1	TRUE	1	0.548619470789376	2		310	500	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134691	2134691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	81	174	0	ENST00000219476.3:c.4468G>A	p.Glu1490Lys	p.E1490K	ENST00000219476	NM_000548.3	1490	Gag/Aag	34/42	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.548619470789376	2		174	281	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992589	72992589	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	51	692	0	ENST00000268489.5:c.1456G>A	p.Glu486Lys	p.E486K	ENST00000268489	NM_006885.3	486	Gag/Aag	2/10	1	2	FACETS	0.226	0.192	0.265	0.226	0.192	0.265	SUBCLONAL	1	TRUE	1	0.548619470789376	2		692	821	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348640	89348640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567569519	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	279	788	0	ENST00000301030.4:c.4310C>T	p.Pro1437Leu	p.P1437L	ENST00000301030	NM_001256183.1	1437	cCt/cTt	9/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.548619470789376	2		788	981	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89865616	89865616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	45	247	0	ENST00000389301.3:c.851G>A	p.Gly284Glu	p.G284E	ENST00000389301	NM_000135.2	284	gGa/gAa	10/43	1	2	FACETS	0.382	0.322	0.449	0.382	0.322	0.449	SUBCLONAL	1	TRUE	1	0.548619470789376	2		247	429	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89869683	89869683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	55	451	0	ENST00000389301.3:c.776C>T	p.Pro259Leu	p.P259L	ENST00000389301	NM_000135.2	259	cCt/cTt	8/43	1	2	FACETS	0.258	0.22	0.3	0.258	0.22	0.3	SUBCLONAL	1	TRUE	1	0.548619470789376	2		451	777	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968891	15968891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1189020284	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	51	318	1	ENST00000268712.3:c.4859C>T	p.Ser1620Leu	p.S1620L	ENST00000268712	NM_006311.3	1620	tCa/tTa	33/46	1	2	FACETS	0.319	0.271	0.372	0.319	0.271	0.372	SUBCLONAL	1	TRUE	1	0.548619470789376	2		319	583	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33446159	33446159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	27	349	0	ENST00000345365.6:c.115G>A	p.Val39Ile	p.V39I	ENST00000345365	NM_002878.3	39	Gta/Ata	2/10	1	2	FACETS	0.185	0.146	0.229	0.185	0.146	0.229	SUBCLONAL	1	TRUE	1	0.548619470789376	2		349	533	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686902	37686902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	63	379	0	ENST00000447079.4:c.3806C>T	p.Pro1269Leu	p.P1269L	ENST00000447079	NM_015083.1	1269	cCc/cTc	14/14	1	2	FACETS	0.41	0.355	0.47	0.41	0.355	0.47	SUBCLONAL	1	TRUE	1	0.548619470789376	2		379	560	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223015	1223015	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781966	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	123	253	0	ENST00000326873.7:c.952G>A	p.Ala318Thr	p.A318T	ENST00000326873	NM_000455.4	318	Gca/Aca	8/10	0.548619470789376	2	FACETS	1	0.941	1	0.521	0.475	0.569	CLONAL	1	TRUE	0	0.548619470789376	2		253	430	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7167980	7167980	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	110	254	0	ENST00000302850.5:c.1609G>A	p.Ala537Thr	p.A537T	ENST00000302850	NM_000208.2	537	Gcc/Acc	7/22	0.548619470789376	2	FACETS	0.935	0.846	1	0.467	0.423	0.514	CLONAL	1	TRUE	0	0.548619470789376	2		254	429	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599952	10599952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	43	436	0	ENST00000171111.5:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000171111	NM_203500.1	542	Gag/Aag	5/6	0.548619470789376	2	FACETS	0.216	0.18	0.256	0.108	0.09	0.128	SUBCLONAL	1	TRUE	0	0.548619470789376	2		436	726	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097655	11097655	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356912496	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	58	350	1	ENST00000358026.2:c.835G>A	p.Gly279Arg	p.G279R	ENST00000358026	NM_001128849.1	279	Ggg/Agg	5/36	0.548619470789376	2	FACETS	0.482	0.415	0.554	0.241	0.207	0.277	SUBCLONAL	1	TRUE	0	0.548619470789376	2		351	439	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101838	11101838	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	21	264	0	ENST00000358026.2:c.1258G>A	p.Val420Met	p.V420M	ENST00000358026	NM_001128849.1	420	Gtg/Atg	8/36	0.548619470789376	2	FACETS	0.185	0.142	0.235	0.092	0.071	0.118	SUBCLONAL	1	TRUE	0	0.548619470789376	2		264	414	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276756	15276756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143617599	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	42	417	1	ENST00000263388.2:c.5509C>T	p.Arg1837Cys	p.R1837C	ENST00000263388	NM_000435.2	1837	Cgt/Tgt	30/33	0.548619470789376	2	FACETS	0.294	0.245	0.348	0.147	0.122	0.174	SUBCLONAL	1	TRUE	0	0.548619470789376	2		418	521	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349901	15349901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	26	184	0	ENST00000263377.2:c.3751G>A	p.Glu1251Lys	p.E1251K	ENST00000263377	NM_058243.2	1251	Gag/Aag	18/20	0.548619470789376	2	FACETS	0.348	0.276	0.43	0.174	0.138	0.215	SUBCLONAL	1	TRUE	0	0.548619470789376	2		184	272	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791527	42791527	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	57	377	0	ENST00000575354.2:c.508C>T	p.Arg170Trp	p.R170W	ENST00000575354	NM_015125.3	170	Cgg/Tgg	4/20	0.548619470789376	2	FACETS	0.291	0.249	0.338	0.146	0.124	0.169	SUBCLONAL	1	TRUE	0	0.548619470789376	2		377	713	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798091	42798091	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	148	378	0	ENST00000575354.2:c.4045G>A	p.Val1349Ile	p.V1349I	ENST00000575354	NM_015125.3	1349	Gtc/Atc	17/20	0.548619470789376	2	FACETS	1	0.959	1	0.534	0.491	0.579	CLONAL	1	TRUE	0	0.548619470789376	2		378	505	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731491	47731491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	20	66	0	ENST00000449228.1:c.301C>T	p.Arg101Cys	p.R101C	ENST00000449228	NM_001127240.2	101	Cgc/Tgc	2/4	0.548619470789376	2	FACETS	0.715	0.556	0.894	0.357	0.278	0.447	SUBCLONAL	1	TRUE	0	0.548619470789376	2		66	102	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560859	9560859	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	54	491	0	ENST00000353224.5:c.923C>T	p.Pro308Leu	p.P308L	ENST00000353224	NM_177990.2	308	cCc/cTc	4/10	1	2	FACETS	0.264	0.225	0.307	0.264	0.225	0.307	SUBCLONAL	1	TRUE	1	0.548619470789376	2		491	746	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024806	31024806	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	157	474	0	ENST00000375687.4:c.4291C>T	p.Pro1431Ser	p.P1431S	ENST00000375687	NM_015338.5	1431	Ccc/Tcc	13/13	1	2	FACETS	0.906	0.833	0.981	0.906	0.833	0.981	CLONAL	1	TRUE	1	0.548619470789376	2		474	632	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36024580	36024580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	37	351	0	ENST00000358208.4:c.569C>T	p.Ser190Leu	p.S190L	ENST00000358208		190	tCa/tTa	6/12	1	2	FACETS	0.245	0.201	0.294	0.245	0.201	0.294	SUBCLONAL	1	TRUE	1	0.548619470789376	2		351	551	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39725892	39725892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	71	264	0	ENST00000361337.2:c.763G>A	p.Glu255Lys	p.E255K	ENST00000361337	NM_003286.2	255	Gaa/Aaa	10/21	1	2	FACETS	0.442	0.386	0.503	0.442	0.386	0.503	SUBCLONAL	1	TRUE	1	0.548619470789376	2		264	585	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265274	46265274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	58	617	0	ENST00000371998.3:c.2144C>T	p.Ser715Phe	p.S715F	ENST00000371998		715	tCt/tTt	12/23	1	2	FACETS	0.243	0.208	0.281	0.243	0.208	0.281	SUBCLONAL	1	TRUE	1	0.548619470789376	2		617	871	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566534	41566534	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	39	379	0	ENST00000263253.7:c.4411C>T	p.Leu1471Phe	p.L1471F	ENST00000263253	NM_001429.3	1471	Ctt/Ttt	27/31	1	2	FACETS	0.21	0.173	0.251	0.21	0.173	0.251	SUBCLONAL	1	TRUE	1	0.548619470789376	2		379	678	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923188	39923188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	47	225	0	ENST00000378444.4:c.3520G>A	p.Glu1174Lys	p.E1174K	ENST00000378444	NM_001123385.1	1174	Gaa/Aaa	8/15	1	1	FACETS	0.353	0.299	0.413	0.353	0.299	0.413	SUBCLONAL	1	TRUE	0	0.548619470789376	1		225	352	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934133	39934133	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	44	253	1	ENST00000378444.4:c.466C>T	p.Gln156Ter	p.Q156*	ENST00000378444	NM_001123385.1	156	Caa/Taa	4/15	1	1	FACETS	0.314	0.263	0.369	0.314	0.263	0.369	SUBCLONAL	1	TRUE	0	0.548619470789376	1		254	371	SUCCESS
AR	367	MSKCC	GRCh37	X	66765259	66765259	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs112374098	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	17	192	0	ENST00000374690.3:c.271C>T	p.Gln91Ter	p.Q91*	ENST00000374690	NM_000044.3	91	Cag/Tag	1/8	1	1	FACETS	0.15	0.111	0.196	0.15	0.111	0.196	SUBCLONAL	1	TRUE	0	0.548619470789376	1		192	300	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469669	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	61	201	0	ENST00000374080.3:c.130G>A	p.Gly44Ser	p.G44S	ENST00000374080		44	Ggt/Agt	2/45	1	1	FACETS	0.424	0.367	0.485	0.424	0.367	0.485	SUBCLONAL	1	TRUE	0	0.548619470789376	1		201	381	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589619	67589620	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGAATATGATAGATTATATGA	novel	NA	P-0006441-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	64	161	0	ENST00000274335.5:c.1390_1410dup	p.Asp464_Tyr470dup	p.D464_Y470dup	ENST00000274335		464	cga/cgAGAATATGATAGATTATATGAa	10/15	1	2	FACETS	0.484	0.42	0.553	0.484	0.42	0.553	SUBCLONAL	1	TRUE	1	0.548619470789376	2		161	482	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0006548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	163	431	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.221032703467678	4	FACETS	0.861	0.793	0.933	0.861	0.793	0.933	CLONAL	3	FALSE	1	0.221032703467678	4		431	697	SUCCESS
APC	324	MSKCC	GRCh37	5	112154723	112154723	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775126020	NA	P-0006548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	113	288	0	ENST00000257430.4:c.994C>T	p.Arg332Ter	p.R332*	ENST00000257430	NM_000038.5	332	Cga/Tga	10/16	0.221032703467678	2	FACETS	0.968	0.881	1	1	0.984	1	CLONAL	3	FALSE	0	0.221032703467678	2		288	352	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28934577	NA	P-0006548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	164	456	0	ENST00000269305.4:c.770T>C	p.Leu257Pro	p.L257P	ENST00000269305	NM_001126112.2	257	cTg/cCg	7/11	0.221032703467678	3	FACETS	0.882	0.817	0.949	1	0.981	1	CLONAL	4	FALSE	0	0.221032703467678	3		456	467	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604790	48604790	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1568211615	NA	P-0006548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	152	380	1	ENST00000342988.3:c.1612G>T	p.Glu538Ter	p.E538*	ENST00000342988	NM_005359.5	538	Gaa/Taa	12/12	0.221032703467678	3	FACETS	0.938	0.862	1	0.938	0.862	1	CLONAL	3	FALSE	0	0.221032703467678	3		381	543	SUCCESS
APC	324	MSKCC	GRCh37	5	112178000	112178000	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768922431	NA	P-0006548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	194	467	1	ENST00000257430.4:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000257430	NM_000038.5	2237	Cga/Tga	16/16	0.221032703467678	2	FACETS	0.98	0.912	1	1	0.991	1	CLONAL	3	FALSE	0	0.221032703467678	2		468	597	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891590	151891590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778490	NA	P-0006548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	185	421	1	ENST00000262189.6:c.4442G>A	p.Arg1481Gln	p.R1481Q	ENST00000262189	NM_170606.2	1481	cGa/cAa	29/59	0.221032703467678	5	FACETS	0.948	0.877	1	0.948	0.877	1	CLONAL	3	FALSE	2	0.221032703467678	5		422	784	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244967	46244967	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1385086744	NA	P-0006548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	248	572	0	ENST00000334344.6:c.3061C>A	p.Pro1021Thr	p.P1021T	ENST00000334344	NM_152641.2	1021	Ccc/Acc	15/21	0.221032703467678	4	FACETS	1	0.946	1	1	0.946	1	CLONAL	3	FALSE	1	0.221032703467678	4		572	904	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40497630	40497630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	307	703	1	ENST00000264657.5:c.319C>T	p.Arg107Trp	p.R107W	ENST00000264657	NM_139276.2	107	Cgg/Tgg	4/24	0.221032703467678	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	FALSE	1	0.221032703467678	4		704	990	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296358	15296358	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202228716	NA	P-0006548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	143	493	2	ENST00000263388.2:c.2084C>T	p.Pro695Leu	p.P695L	ENST00000263388	NM_000435.2	695	cCg/cTg	13/33	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	2	FALSE	NA	0.221032703467678	2		495	549	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344125	70344125	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	108	646	2	ENST00000374080.3:c.1861C>T	p.Arg621Ter	p.R621*	ENST00000374080		621	Cga/Tga	13/45	0.21555232007803	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	0	0.221032703467678	1		648	709	SUCCESS
APC	324	MSKCC	GRCh37	5	112175879	112175880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	168	416	0	ENST00000257430.4:c.4592dup	p.Asn1531LysfsTer2	p.N1531Kfs*2	ENST00000257430	NM_000038.5	1530	gaa/gAaa	16/16	0.221032703467678	2	FACETS	0.838	0.773	0.904	1	0.984	1	CLONAL	3	FALSE	0	0.221032703467678	2		416	605	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0006676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	139	169	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.945	0.871	1	0.945	0.871	1	CLONAL	1	TRUE	1	0.817047557752761	2		169	360	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0006676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	501	456	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.817047557752761	2		456	1207	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115928	8115929	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	161	276	1	ENST00000346208.3:c.1275dup	p.Ser426IlefsTer81	p.S426Ifs*81	ENST00000346208		425	cca/ccAa	6/6	1	2	FACETS	0.659	0.607	0.713	0.659	0.607	0.713	SUBCLONAL	1	TRUE	1	0.817047557752761	2		277	598	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162722960	162722960	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0006676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	486	543	0	ENST00000367921.3:c.158C>G	p.Ser53Ter	p.S53*	ENST00000367921	NM_006182.2	53	tCa/tGa	4/18	1	2	FACETS	0.987	0.946	1	0.987	0.946	1	CLONAL	1	TRUE	1	0.817047557752761	2		543	1205	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713316	30713316	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	652	337	0	ENST00000295754.5:c.641A>G	p.Glu214Gly	p.E214G	ENST00000295754	NM_003242.5	214	gAg/gGg	4/7	0.810224162618265	2	FACETS	0.991	0.97	1	0.991	0.97	1	CLONAL	2	TRUE	0	0.817047557752761	2		337	805	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230405	46230405	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1391481708	NA	P-0006676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	265	320	0	ENST00000334344.6:c.739C>T	p.Arg247Cys	p.R247C	ENST00000334344	NM_152641.2	247	Cgt/Tgt	7/21	NA	2	FACETS	0.722	0.678	0.766			1	INDETERMINATE	1	TRUE	NA	0.817047557752761	2		320	899	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0006810-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1515	327	811	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.475973703815103	3	FACETS	0.653	0.615	0.693	0.327	0.307	0.347	SUBCLONAL	1	TRUE	1	0.746653195111168	3		812	1842	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0006810-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	549	710	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.475973703815103	3	FACETS	0.751	0.721	0.78	0.751	0.721	0.78	SUBCLONAL	2	TRUE	1	0.746653195111168	3		710	1345	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs863224683	NA	P-0006810-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1355	369	1193	0	ENST00000269305.4:c.388C>G	p.Leu130Val	p.L130V	ENST00000269305	NM_001126112.2	130	Ctc/Gtc	5/11	0.374568659432311	1	FACETS	0.359	0.34	0.38	0.359	0.34	0.38	INDETERMINATE	1	TRUE	0	0.746653195111168	1		1193	1724	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876658468	NA	P-0006810-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	531	171	0	ENST00000269305.4:c.577C>G	p.His193Asp	p.H193D	ENST00000269305	NM_001126112.2	193	Cat/Gat	6/11	0.374568659432311	1	FACETS	0.728	0.699	0.756	0.728	0.699	0.756	INDETERMINATE	1	TRUE	0	0.746653195111168	1		171	1225	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679811	88679811	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006810-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	441	698	0	ENST00000360948.2:c.652A>C	p.Asn218His	p.N218H	ENST00000360948	NM_001012338.2	218	Aac/Cac	7/19	0.374568659432311	1	FACETS	0.694	0.664	0.724	0.694	0.664	0.724	INDETERMINATE	1	TRUE	0	0.746653195111168	1		698	1067	SUCCESS
APC	324	MSKCC	GRCh37	5	112174357	112174358	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs876658724	NA	P-0006810-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	472	354	0	ENST00000257430.4:c.3067dup	p.Thr1023AsnfsTer6	p.T1023Nfs*6	ENST00000257430	NM_000038.5	1022	-/A	16/16	0.1691186517069	5	FACETS	1	0.995	1			1	INDETERMINATE	4	TRUE	NA	0.746653195111168	5		354	603	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420384	49420384	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006810-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1295	255	801	0	ENST00000301067.7:c.15365A>T	p.Lys5122Met	p.K5122M	ENST00000301067	NM_003482.3	5122	aAg/aTg	48/54	0.38239589260299	2	FACETS	0.441	0.411	0.471	0.22	0.205	0.236	INDETERMINATE	1	TRUE	0	0.746653195111168	2		801	1550	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679811	88679812	+	missense_variant	Missense_Mutation	DNP	TG	TG	GA	novel	NA	P-0006810-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	441	697	1	ENST00000360948.2:c.651_652delinsTC	p.Asn218His	p.N218H	ENST00000360948	NM_001012338.2	217	gtCAac/gtTCac	7/19	0.374568659432311	1	FACETS	0.694	0.664	0.724	0.694	0.664	0.724	INDETERMINATE	1	TRUE	0	0.746653195111168	1		698	1067	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	59	685	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.283725877049456	3	FACETS	1	0.965	1	0.694	0.601	0.795	CLONAL	1	TRUE	1	0.283725877049456	3		685	342	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	136	251	0				ENST00000310581	NM_198253.2	-/1132			0.283725877049456	3	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	1	0.283725877049456	3		251	536	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	246	381	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	0.283725877049456	2	FACETS	0.999	0.936	1	0.999	0.936	1	CLONAL	2	TRUE	0	0.283725877049456	2		381	868	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089562	27089562	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	195	451	1	ENST00000324856.7:c.2518C>T	p.Gln840Ter	p.Q840*	ENST00000324856	NM_006015.4	840	Caa/Taa	8/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.283725877049456	2		452	927	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs121913468	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	91	362	0	ENST00000269571.5:c.2305G>C	p.Asp769His	p.D769H	ENST00000269571		769	Gac/Cac	19/27	0.283725877049456	3	FACETS	0.816	0.723	0.915	0.408	0.361	0.458	CLONAL	1	TRUE	1	0.283725877049456	3		362	898	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569301	67569301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	34	267	0	ENST00000274335.5:c.418G>A	p.Glu140Lys	p.E140K	ENST00000274335		140	Gaa/Aaa	2/15	0.270174760605767	1	FACETS	0.366	0.298	0.442	0.366	0.298	0.442	SUBCLONAL	1	TRUE	0	0.283725877049456	1		267	562	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339409	116339409	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	37	263	0	ENST00000397752.3:c.271G>A	p.Glu91Lys	p.E91K	ENST00000397752	NM_000245.2	91	Gaa/Aaa	2/21	1	2	FACETS	0.455	0.374	0.546	0.455	0.374	0.546	SUBCLONAL	1	TRUE	1	0.283725877049456	2		263	573	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458507	120458507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	146	290	0	ENST00000256646.2:c.6838C>T	p.Pro2280Ser	p.P2280S	ENST00000256646	NM_024408.3	2280	Cct/Tct	34/34	0.189530524512454	4	FACETS	0.831	0.759	0.906	0.831	0.759	0.906	CLONAL	2	TRUE	2	0.283725877049456	4		290	795	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101170	41101170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41279256	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	70	238	0	ENST00000373198.4:c.1186G>A	p.Val396Ile	p.V396I	ENST00000373198	NM_133170.3	396	Gta/Ata	8/32	1	2	FACETS	0.977	0.854	1	0.977	0.854	1	CLONAL	1	TRUE	1	0.283725877049456	2		238	505	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651901	36651902	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	198	293	1	ENST00000244741.5:c.25dup	p.Arg9ProfsTer27	p.R9Pfs*27	ENST00000244741	NM_000389.4	8	gtc/gtCc	2/3	0.283725877049456	2	FACETS	0.977	0.908	1	0.977	0.908	1	CLONAL	2	TRUE	0	0.283725877049456	2		294	714	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818286	43818286	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	46	424	0	ENST00000372470.3:c.1751C>A	p.Ser584Tyr	p.S584Y	ENST00000372470	NM_005373.2	584	tCc/tAc	12/12	1	2	FACETS	0.373	0.313	0.44	0.373	0.313	0.44	SUBCLONAL	1	TRUE	1	0.283725877049456	2		424	870	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458878	120458878	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	234	445	0	ENST00000256646.2:c.6467C>G	p.Ser2156Cys	p.S2156C	ENST00000256646	NM_024408.3	2156	tCt/tGt	34/34	0.189530524512454	4	FACETS	0.937	0.873	1	0.937	0.873	1	CLONAL	2	TRUE	2	0.283725877049456	4		445	1130	SUCCESS
H3C13	653604	MSKCC	GRCh37	1	149784859	149784859	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	36	237	0	ENST00000331491.1:c.378G>C	p.Gln126His	p.Q126H	ENST00000331491	NM_001123375.2	126	caG/caC	1/1	0.189530524512454	4	FACETS	0.486	0.398	0.585	0.243	0.199	0.293	SUBCLONAL	1	TRUE	2	0.283725877049456	4		237	670	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874563	155874563	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	69	437	0	ENST00000368323.3:c.196G>A	p.Asp66Asn	p.D66N	ENST00000368323	NM_006912.5	66	Gat/Aat	4/6	0.189530524512454	4	FACETS	0.541	0.469	0.619	0.271	0.234	0.31	SUBCLONAL	1	TRUE	2	0.283725877049456	4		437	1154	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023174	48023174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1389	128	643	1	ENST00000234420.5:c.599C>T	p.Ser200Leu	p.S200L	ENST00000234420	NM_000179.2	200	tCa/tTa	3/10	1	2	FACETS	0.595	0.537	0.656	0.595	0.537	0.656	SUBCLONAL	1	TRUE	1	0.283725877049456	2		644	1517	SUCCESS
REL	5966	MSKCC	GRCh37	2	61148915	61148915	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	55	331	0	ENST00000295025.8:c.1105C>G	p.His369Asp	p.H369D	ENST00000295025	NM_002908.2	369	Cat/Gat	11/11	1	2	FACETS	0.508	0.434	0.59	0.508	0.434	0.59	SUBCLONAL	1	TRUE	1	0.283725877049456	2		331	763	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149036	61149036	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	65	385	0	ENST00000295025.8:c.1226C>T	p.Ser409Phe	p.S409F	ENST00000295025	NM_002908.2	409	tCt/tTt	11/11	1	2	FACETS	0.505	0.436	0.579	0.505	0.436	0.579	SUBCLONAL	1	TRUE	1	0.283725877049456	2		385	908	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209101841	209101841	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	51	410	0	ENST00000345146.2:c.1207G>C	p.Glu403Gln	p.E403Q	ENST00000345146	NM_005896.2	403	Gaa/Caa	10/10	1	2	FACETS	0.398	0.337	0.466	0.398	0.337	0.466	SUBCLONAL	1	TRUE	1	0.283725877049456	2		410	903	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183766	10183766	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs200885420	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	51	318	0	ENST00000256474.2:c.235C>G	p.Arg79Gly	p.R79G	ENST00000256474	NM_000551.3	79	Cgc/Ggc	1/3	0.283725877049456	2	FACETS	0.573	0.487	0.669	0.287	0.243	0.335	SUBCLONAL	1	TRUE	0	0.283725877049456	2		318	627	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933705	49933705	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751338048	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	68	516	0	ENST00000296474.3:c.2572C>T	p.Arg858Cys	p.R858C	ENST00000296474	NM_002447.2	858	Cgc/Tgc	10/20	0.283725877049456	3	FACETS	0.49	0.425	0.562	0.245	0.212	0.281	SUBCLONAL	1	TRUE	1	0.283725877049456	3		516	1116	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279187	142279187	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	78	332	0	ENST00000350721.4:c.1459A>T	p.Ile487Phe	p.I487F	ENST00000350721	NM_001184.3	487	Att/Ttt	6/47	0.283725877049456	3	FACETS	0.725	0.636	0.821	0.362	0.318	0.411	SUBCLONAL	1	TRUE	1	0.283725877049456	3		332	866	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279231	142279231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	82	318	0	ENST00000350721.4:c.1415C>T	p.Ser472Phe	p.S472F	ENST00000350721	NM_001184.3	472	tCc/tTc	6/47	0.283725877049456	3	FACETS	0.77	0.678	0.869	0.385	0.339	0.435	SUBCLONAL	1	TRUE	1	0.283725877049456	3		318	857	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106162516	106162516	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	45	261	0	ENST00000380013.4:c.3430G>A	p.Glu1144Lys	p.E1144K	ENST00000380013	NM_001127208.2	1144	Gaa/Aaa	4/11	1	2	FACETS	0.539	0.453	0.636	0.539	0.453	0.636	SUBCLONAL	1	TRUE	1	0.283725877049456	2		261	588	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535405	187535405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	48	277	0	ENST00000441802.2:c.9169G>A	p.Glu3057Lys	p.E3057K	ENST00000441802	NM_005245.3	3057	Gaa/Aaa	12/27	1	2	FACETS	0.449	0.379	0.528	0.449	0.379	0.528	SUBCLONAL	1	TRUE	1	0.283725877049456	2		277	753	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557767	187557767	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	40	293	0	ENST00000441802.2:c.3944C>G	p.Ser1315Ter	p.S1315*	ENST00000441802	NM_005245.3	1315	tCa/tGa	5/27	1	2	FACETS	0.409	0.338	0.487	0.409	0.338	0.487	SUBCLONAL	1	TRUE	1	0.283725877049456	2		293	690	SUCCESS
APC	324	MSKCC	GRCh37	5	112177050	112177050	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780599	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	57	487	0	ENST00000257430.4:c.5759G>A	p.Arg1920Gln	p.R1920Q	ENST00000257430	NM_000038.5	1920	cGa/cAa	16/16	0.270174760605767	1	FACETS	0.326	0.278	0.378	0.326	0.278	0.378	SUBCLONAL	1	TRUE	0	0.283725877049456	1		487	1059	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166818	32166818	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1441415979	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	45	359	0	ENST00000375023.3:c.4420C>T	p.Arg1474Ter	p.R1474*	ENST00000375023	NM_004557.3	1474	Cga/Tga	24/30	NA	2	FACETS	0.395	0.331	0.467			1	INDETERMINATE	1	TRUE	NA	0.283725877049456	2		359	803	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117650555	117650555	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	160	511	0	ENST00000368508.3:c.5303C>G	p.Ser1768Ter	p.S1768*	ENST00000368508	NM_002944.2	1768	tCa/tGa	32/43	0.270174760605767	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.283725877049456	1		511	965	SUCCESS
MET	4233	MSKCC	GRCh37	7	116381023	116381023	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	71	416	0	ENST00000397752.3:c.1645G>C	p.Glu549Gln	p.E549Q	ENST00000397752	NM_000245.2	549	Gag/Cag	5/21	1	2	FACETS	0.521	0.453	0.594	0.521	0.453	0.594	SUBCLONAL	1	TRUE	1	0.283725877049456	2		416	961	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395531	116395531	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	37	337	0	ENST00000397752.3:c.1824G>C	p.Glu608Asp	p.E608D	ENST00000397752	NM_000245.2	608	gaG/gaC	6/21	1	2	FACETS	0.367	0.301	0.441	0.367	0.301	0.441	SUBCLONAL	1	TRUE	1	0.283725877049456	2		337	711	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891579	151891579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	98	328	0	ENST00000262189.6:c.4453G>A	p.Glu1485Lys	p.E1485K	ENST00000262189	NM_170606.2	1485	Gaa/Aaa	29/59	1	2	FACETS	0.877	0.782	0.978	0.877	0.782	0.978	CLONAL	1	TRUE	1	0.283725877049456	2		328	788	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737112	145737112	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	50	374	0	ENST00000428558.2:c.3454G>T	p.Glu1152Ter	p.E1152*	ENST00000428558	NM_004260.3	1152	Gag/Tag	21/22	0.283725877049456	3	FACETS	0.413	0.349	0.484	0.207	0.174	0.242	SUBCLONAL	1	TRUE	1	0.283725877049456	3		374	974	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742108	145742108	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	25	186	0	ENST00000428558.2:c.395G>C	p.Arg132Thr	p.R132T	ENST00000428558	NM_004260.3	132	aGa/aCa	5/22	0.283725877049456	3	FACETS	0.451	0.355	0.562	0.226	0.177	0.281	SUBCLONAL	1	TRUE	1	0.283725877049456	3		186	446	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69456120	69456120	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	67	371	0	ENST00000227507.2:c.39C>G	p.Ile13Met	p.I13M	ENST00000227507	NM_053056.2	13	atC/atG	1/5	1	2	FACETS	0.567	0.492	0.649	0.567	0.492	0.649	SUBCLONAL	1	TRUE	1	0.283725877049456	2		371	833	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999539	100999539	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1209	96	626	0	ENST00000325455.5:c.263C>G	p.Ser88Cys	p.S88C	ENST00000325455	NM_001202474.3	88	tCc/tGc	1/8	1	2	FACETS	0.519	0.46	0.581	0.519	0.46	0.581	SUBCLONAL	1	TRUE	1	0.283725877049456	2		626	1305	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196110	108196110	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	64	279	0	ENST00000278616.4:c.6646G>C	p.Asp2216His	p.D2216H	ENST00000278616	NM_000051.3	2216	Gat/Cat	46/63	1	2	FACETS	0.683	0.591	0.782	0.683	0.591	0.782	SUBCLONAL	1	TRUE	1	0.283725877049456	2		279	661	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342821	118342821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555035714	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	52	344	0	ENST00000534358.1:c.947C>T	p.Ser316Leu	p.S316L	ENST00000534358	NM_005933.3	316	tCg/tTg	3/36	1	2	FACETS	0.422	0.358	0.492	0.422	0.358	0.492	SUBCLONAL	1	TRUE	1	0.283725877049456	2		344	869	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144697	119144697	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	44	316	0	ENST00000264033.4:c.710C>T	p.Ser237Leu	p.S237L	ENST00000264033	NM_005188.3	237	tCg/tTg	4/16	1	2	FACETS	0.457	0.383	0.541	0.457	0.383	0.541	SUBCLONAL	1	TRUE	1	0.283725877049456	2		316	678	SUCCESS
CBL	867	MSKCC	GRCh37	11	119146791	119146791	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	56	381	0	ENST00000264033.4:c.954C>G	p.Ile318Met	p.I318M	ENST00000264033	NM_005188.3	318	atC/atG	6/16	1	2	FACETS	0.441	0.376	0.511	0.441	0.376	0.511	SUBCLONAL	1	TRUE	1	0.283725877049456	2		381	896	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910767	32910767	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	54	469	0	ENST00000380152.3:c.2275C>G	p.Leu759Val	p.L759V	ENST00000380152		759	Ctt/Gtt	11/27	1	2	FACETS	0.375	0.319	0.437	0.375	0.319	0.437	SUBCLONAL	1	TRUE	1	0.283725877049456	2		469	1015	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972384	32972384	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	42	299	0	ENST00000380152.3:c.9734C>G	p.Ser3245Ter	p.S3245*	ENST00000380152		3245	tCa/tGa	27/27	1	2	FACETS	0.408	0.339	0.484	0.408	0.339	0.484	SUBCLONAL	1	TRUE	1	0.283725877049456	2		299	726	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003068	42003068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1179	102	568	1	ENST00000219905.7:c.2605G>A	p.Asp869Asn	p.D869N	ENST00000219905	NM_001164273.1	869	Gat/Aat	8/24	1	2	FACETS	0.561	0.5	0.627	0.561	0.5	0.627	SUBCLONAL	1	TRUE	1	0.283725877049456	2		569	1281	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465517	99465517	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	72	416	0	ENST00000268035.6:c.2342G>A	p.Arg781Lys	p.R781K	ENST00000268035	NM_000875.3	781	aGa/aAa	11/21	1	2	FACETS	0.528	0.46	0.601	0.528	0.46	0.601	SUBCLONAL	1	TRUE	1	0.283725877049456	2		416	962	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99482465	99482465	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	125	388	0	ENST00000268035.6:c.3333G>C	p.Lys1111Asn	p.K1111N	ENST00000268035	NM_000875.3	1111	aaG/aaC	18/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.283725877049456	2		388	801	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991611	72991611	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	55	498	0	ENST00000268489.5:c.2434G>C	p.Glu812Gln	p.E812Q	ENST00000268489	NM_006885.3	812	Gag/Cag	2/10	1	2	FACETS	0.364	0.31	0.424	0.364	0.31	0.424	SUBCLONAL	1	TRUE	1	0.283725877049456	2		498	1065	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992138	72992138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764598603	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	59	489	0	ENST00000268489.5:c.1907C>T	p.Ser636Leu	p.S636L	ENST00000268489	NM_006885.3	636	tCg/tTg	2/10	1	2	FACETS	0.468	0.401	0.541	0.468	0.401	0.541	SUBCLONAL	1	TRUE	1	0.283725877049456	2		489	889	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351286	89351286	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	66	535	0	ENST00000301030.4:c.1664C>G	p.Ser555Cys	p.S555C	ENST00000301030	NM_001256183.1	555	tCt/tGt	9/13	1	2	FACETS	0.406	0.351	0.467	0.406	0.351	0.467	SUBCLONAL	1	TRUE	1	0.283725877049456	2		535	1145	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89825063	89825063	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779162871	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	86	421	3	ENST00000389301.3:c.2903C>T	p.Ser968Leu	p.S968L	ENST00000389301	NM_000135.2	968	tCg/tTg	30/43	1	2	FACETS	0.667	0.589	0.751	0.667	0.589	0.751	SUBCLONAL	1	TRUE	1	0.283725877049456	2		424	909	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838108	89838108	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	75	397	0	ENST00000389301.3:c.2129G>C	p.Arg710Thr	p.R710T	ENST00000389301	NM_000135.2	710	aGa/aCa	23/43	1	2	FACETS	0.631	0.552	0.716	0.631	0.552	0.716	SUBCLONAL	1	TRUE	1	0.283725877049456	2		397	838	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31381365	31381365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752673059	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	36	289	0	ENST00000328111.2:c.1090C>T	p.Arg364Cys	p.R364C	ENST00000328111	NM_006892.3	364	Cgt/Tgt	10/23	1	2	FACETS	0.41	0.336	0.493	0.41	0.336	0.493	SUBCLONAL	1	TRUE	1	0.283725877049456	2		289	619	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46266522	46266522	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	42	313	0	ENST00000371998.3:c.2507C>G	p.Ser836Cys	p.S836C	ENST00000371998		836	tCt/tGt	13/23	1	2	FACETS	0.419	0.349	0.497	0.419	0.349	0.497	SUBCLONAL	1	TRUE	1	0.283725877049456	2		313	707	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160206	22160206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	76	361	0	ENST00000215832.6:c.425C>T	p.Ser142Leu	p.S142L	ENST00000215832	NM_002745.4	142	tCa/tTa	3/9	1	2	FACETS	0.586	0.513	0.665	0.586	0.513	0.665	SUBCLONAL	1	TRUE	1	0.283725877049456	2		361	914	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504098	123504098	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006926-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	34	192	0	ENST00000371139.4:c.274C>G	p.Gln92Glu	p.Q92E	ENST00000371139	NM_001114937.2	92	Caa/Gaa	3/4	1	1	FACETS	0.521	0.426	0.628	0.521	0.426	0.628	SUBCLONAL	1	TRUE	0	0.283725877049456	1		192	395	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0006928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	336	621	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	0.186659139347645	8	FACETS	1	0.975	1	1	0.995	1	CLONAL	6	FALSE	4	0.186659139347645	8		621	898	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250500	26250501	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACACAGGTTGGTGTCCTCAAAGAGCCCCACCAGGT	novel	NA	P-0006928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1684	209	1395	0	ENST00000446824.2:c.299_333dup	p.Ala112ThrfsTer19	p.A112Tfs*19	ENST00000446824	NM_021018.2	111	-/ACCTGGTGGGGCTCTTTGAGGACACCAACCTGTGT	1/1	0.186659139347645	15	FACETS	0.873	0.807	0.942			1	CLONAL	3	FALSE	NA	0.186659139347645	15		1395	1893	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0007072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	394	621	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	1	2	FACETS	0.956	0.912	1	1	0.997	1	CLONAL	3	TRUE	1	0.269280005133108	2		621	1020	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143129637	143129637	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	60	398	0	ENST00000262992.4:c.1013A>G	p.Glu338Gly	p.E338G	ENST00000262992	NM_001101669.1	338	gAa/gGa	12/24	1	2	FACETS	0.844	0.728	0.97	0.844	0.728	0.97	CLONAL	1	TRUE	1	0.269280005133108	2		398	528	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56477573	56477573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374953448	NA	P-0007072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1173	154	547	1	ENST00000267101.3:c.121G>A	p.Asp41Asn	p.D41N	ENST00000267101	NM_001982.3	41	Gat/Aat	2/28	0.269280005133108	9	FACETS	0.837	0.764	0.914			1	CLONAL	2	TRUE	NA	0.269280005133108	9		548	1327	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988228	36988228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771777676	NA	P-0007072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	13	131	0	ENST00000354822.5:c.425G>A	p.Gly142Glu	p.G142E	ENST00000354822	NM_001079668.2	142	gGa/gAa	2/3	0.270452434836475	0	FACETS	0.699	0.504	0.93			1	SUBCLONAL	1	TRUE	0	0.269280005133108	0		131	101	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807965	3807965	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1374209600	NA	P-0007072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	211	393	0	ENST00000262367.5:c.3454C>G	p.Gln1152Glu	p.Q1152E	ENST00000262367	NM_004380.2	1152	Cag/Gag	18/31	NA	2	FACETS	0.888	0.831	0.947			1	INDETERMINATE	3	TRUE	NA	0.269280005133108	2		393	588	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573434	48573453	+	frameshift_variant	Frame_Shift_Del	DEL	TACGAATACACCAACAAGTA	TACGAATACACCAACAAGTA	-	novel	NA	P-0007072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	30	401	1	ENST00000342988.3:c.18_37del	p.Thr7Ter	p.T7*	ENST00000342988	NM_005359.5	6	atTACGAATACACCAACAAGTAat/atat	2/12	0.242843832997544	0	FACETS	0.875	0.712	1			1	CLONAL	1	TRUE	0	0.269280005133108	0		402	186	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0007104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	85	1073	4	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	NA	2	FACETS	0.396	0.349	0.446			1	INDETERMINATE	1	FALSE	NA	0.448536355055112	2		1077	958	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371942	55371942	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	49	846	0	ENST00000297316.4:c.632C>T	p.Ala211Val	p.A211V	ENST00000297316	NM_022454.3	211	gCg/gTg	2/2	1	2	FACETS	0.291	0.245	0.341	0.291	0.245	0.341	SUBCLONAL	1	FALSE	1	0.448536355055112	2		846	751	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0007115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	258	585	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.397283662076812	1	FACETS	0.363	0.339	0.388	0.363	0.339	0.388	INDETERMINATE	1	TRUE	0	0.685778874206442	1		585	1361	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0007115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	614	396	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.685778874206442	2	FACETS	0.984	0.956	1	0.984	0.956	1	CLONAL	2	TRUE	0	0.685778874206442	2		396	910	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519936	NA	P-0007115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	419	408	0	ENST00000263967.3:c.3127A>T	p.Met1043Leu	p.M1043L	ENST00000263967	NM_006218.2	1043	Atg/Ttg	21/21	0.685778874206442	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.685778874206442	1		408	723	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438153	110438153	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1314168066	NA	P-0007115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	202	173	0	ENST00000375856.3:c.248G>A	p.Arg83Gln	p.R83Q	ENST00000375856	NM_003749.2	83	cGg/cAg	1/2	0.667100110212863	3	FACETS	1	0.965	1	0.53	0.493	0.569	CLONAL	1	TRUE	1	0.685778874206442	3		173	746	SUCCESS
APC	324	MSKCC	GRCh37	5	112174529	112174529	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	324	425	3	ENST00000257430.4:c.3238G>T	p.Glu1080Ter	p.E1080*	ENST00000257430	NM_000038.5	1080	Gag/Tag	16/16	0.397283662076812	1	FACETS	0.826	0.785	0.867	0.826	0.785	0.867	INDETERMINATE	1	TRUE	0	0.685778874206442	1		428	752	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0007115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	288	326	0	ENST00000269305.4:c.97-1G>A		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.685778874206442	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.685778874206442	1		326	466	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604673	48604673	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060500738	NA	P-0007115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	359	423	0	ENST00000342988.3:c.1495T>C	p.Cys499Arg	p.C499R	ENST00000342988	NM_005359.5	499	Tgc/Cgc	12/12	0.685778874206442	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.685778874206442	1		423	668	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717695	89717696	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1060500115	NA	P-0007115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	218	335	0	ENST00000371953.3:c.723dup	p.Glu242Ter	p.E242*	ENST00000371953	NM_000314.4	240	-/T	7/9	0.685778874206442	1	FACETS	0.908	0.855	0.961	0.908	0.855	0.961	CLONAL	1	TRUE	0	0.685778874206442	1		335	460	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856093	68856093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121964878	NA	P-0007129-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	631	541	0	ENST00000261769.5:c.1901C>T	p.Ala634Val	p.A634V	ENST00000261769	NM_004360.3	634	gCg/gTg	12/16	0.974845119006813	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.974845119006813	1		541	646	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542332	187542332	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0007129-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	413	339	0	ENST00000441802.2:c.5408C>G	p.Ser1803Ter	p.S1803*	ENST00000441802	NM_005245.3	1803	tCa/tGa	10/27	0.974845119006813	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.974845119006813	1		339	428	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578484	7578485	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1064793929	NA	P-0007129-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	624	508	0	ENST00000269305.4:c.445dup	p.Ser149PhefsTer32	p.S149Ffs*32	ENST00000269305	NM_001126112.2	149	tcc/tTcc	5/11	0.974845119006813	1	FACETS	0.987	0.974	0.998	0.987	0.974	0.998	CLONAL	1	TRUE	0	0.974845119006813	1		508	665	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786758	3786758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007129-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	731	671	2	ENST00000262367.5:c.4453C>T	p.His1485Tyr	p.H1485Y	ENST00000262367	NM_004380.2	1485	Cat/Tat	27/31	1	2	FACETS	0.959	0.928	0.99	0.959	0.928	0.99	CLONAL	1	TRUE	1	0.974845119006813	2		673	1564	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004625	150004625	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007129-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1359	108	621	0	ENST00000253339.5:c.1600G>A	p.Glu534Lys	p.E534K	ENST00000253339		534	Gag/Aag	3/7	1	2	FACETS	0.151	0.135	0.169	0.151	0.135	0.169	SUBCLONAL	1	TRUE	1	0.974845119006813	2		621	1467	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181377	38181377	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007129-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	505	427	0	ENST00000396334.3:c.390C>G	p.Ile130Met	p.I130M	ENST00000396334	NM_002468.4	130	atC/atG	2/5	NA	2	FACETS	0.979	0.942	1			1	INDETERMINATE	1	TRUE	NA	0.974845119006813	2		427	1058	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405872	49405872	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007129-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	691	621	0	ENST00000418115.1:c.266C>G	p.Pro89Arg	p.P89R	ENST00000418115	NM_001664.2	89	cCt/cGt	3/5	1	2	FACETS	0.962	0.931	0.994	0.962	0.931	0.994	CLONAL	1	TRUE	1	0.974845119006813	2		621	1473	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153624	55153624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007129-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	758	573	0	ENST00000257290.5:c.2590C>T	p.Pro864Ser	p.P864S	ENST00000257290	NM_006206.4	864	Cct/Tct	19/23	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.974845119006813	2		573	1481	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38966814	38966814	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007129-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	362	305	0	ENST00000357387.3:c.1228G>C	p.Glu410Gln	p.E410Q	ENST00000357387	NM_152756.3	410	Gaa/Caa	15/38	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.974845119006813	2		305	731	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180964	32180964	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007129-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	611	539	0	ENST00000375023.3:c.2386G>T	p.Gly796Cys	p.G796C	ENST00000375023	NM_004557.3	796	Ggc/Tgc	15/30	1	2	FACETS	0.977	0.943	1	0.977	0.943	1	CLONAL	1	TRUE	1	0.974845119006813	2		539	1283	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868486	117868486	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007129-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2277	326	523	0	ENST00000297338.2:c.856C>A	p.Pro286Thr	p.P286T	ENST00000297338	NM_006265.2	286	Cca/Aca	8/14	0.787415880754956	5	FACETS	0.633	0.594	0.672			1	SUBCLONAL	1	TRUE	NA	0.974845119006813	5		523	2603	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851515	63851515	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007129-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	54	289	0	ENST00000279873.7:c.2293G>C	p.Glu765Gln	p.E765Q	ENST00000279873	NM_032199.2	765	Gag/Cag	10/10	1	2	FACETS	0.138	0.117	0.161	0.138	0.117	0.161	SUBCLONAL	1	TRUE	1	0.974845119006813	2		289	803	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905397	11905397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007129-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	448	327	2	ENST00000396373.4:c.47C>T	p.Ser16Leu	p.S16L	ENST00000396373	NM_001987.4	16	tCa/tTa	2/8	0.974845119006813	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.974845119006813	1		329	463	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90634877	90634877	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0007129-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	474	451	0	ENST00000330062.3:c.116-1G>C		p.X39_splice	ENST00000330062	NM_002168.2	39			0.974845119006813	2	FACETS	0.944	0.906	0.982	0.472	0.453	0.491	CLONAL	1	TRUE	0	0.974845119006813	2		451	1030	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170805	11170805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1029465394	NA	P-0007129-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	300	448	0	ENST00000358026.2:c.4949G>A	p.Arg1650Gln	p.R1650Q	ENST00000358026	NM_001128849.1	1650	cGa/cAa	35/36	1	2	FACETS	0.568	0.535	0.601	0.568	0.535	0.601	SUBCLONAL	1	TRUE	1	0.974845119006813	2		448	1084	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0007231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	219	451	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.913	0.856	0.97	1	0.994	1	CLONAL	2	TRUE	1	0.433954437560013	2		451	553	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106058	8106058	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	122	869	0	ENST00000346208.3:c.878T>A	p.Met293Lys	p.M293K	ENST00000346208		293	aTg/aAg	4/6	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.433954437560013	2		869	523	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0007231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	139	456	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.433954437560013	2		456	631	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161254	56161254	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	124	824	0	ENST00000399503.3:c.1123T>G	p.Leu375Val	p.L375V	ENST00000399503	NM_005921.1	375	Tta/Gta	5/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.433954437560013	2		824	511	SUCCESS
ATR	545	MSKCC	GRCh37	3	142253986	142254009	+	inframe_deletion	In_Frame_Del	DEL	TGTTGAATGGCCTTCATAGAGAGC	TGTTGAATGGCCTTCATAGAGAGC	-	novel	NA	P-0007231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	67	908	0	ENST00000350721.4:c.3858_3881del	p.Gln1286_Gln1293del	p.Q1286_Q1293del	ENST00000350721	NM_001184.3	1286	caGCTCTCTATGAAGGCCATTCAACAt/cat	21/47	1	2	FACETS	0.63	0.549	0.718	0.63	0.549	0.718	SUBCLONAL	1	TRUE	1	0.433954437560013	2		908	490	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178385	56178397	+	frameshift_variant	Frame_Shift_Del	DEL	TGCAGATTAGATG	TGCAGATTAGATG	-	novel	NA	P-0007231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	66	546	0	ENST00000399503.3:c.3359_3371del	p.Cys1120SerfsTer24	p.C1120Sfs*24	ENST00000399503	NM_005921.1	1120	TGCAGATTAGATGtc/tc	14/20	1	2	FACETS	0.854	0.746	0.97	0.854	0.746	0.97	CLONAL	1	TRUE	1	0.433954437560013	2		546	356	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783248	9783248	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0007231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	144	1099	0	ENST00000377346.4:c.2492C>G	p.Ser831Ter	p.S831*	ENST00000377346	NM_005026.3	831	tCa/tGa	20/24	NA	2	FACETS	0.955	0.873	1			1	INDETERMINATE	1	TRUE	NA	0.433954437560013	2		1099	695	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783338	9783338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	108	844	0	ENST00000377346.4:c.2582C>T	p.Ser861Phe	p.S861F	ENST00000377346	NM_005026.3	861	tCc/tTc	20/24	NA	2	FACETS	0.91	0.819	1			1	INDETERMINATE	1	TRUE	NA	0.433954437560013	2		844	547	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285621	46285621	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	74	858	0	ENST00000334344.6:c.4981G>C	p.Asp1661His	p.D1661H	ENST00000334344	NM_152641.2	1661	Gat/Cat	17/21	1	2	FACETS	0.711	0.624	0.803	0.711	0.624	0.803	SUBCLONAL	1	TRUE	1	0.433954437560013	2		858	480	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576036	29576036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146306756	NA	P-0007231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	121	1000	4	ENST00000356175.3:c.4009C>T	p.Arg1337Trp	p.R1337W	ENST00000356175	NM_000267.3	1337	Cgg/Tgg	30/57	1	2	FACETS	0.966	0.876	1	0.966	0.876	1	CLONAL	1	TRUE	1	0.433954437560013	2		1004	577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0007298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	169	730	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.305250168634704	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.320171871172286	1		731	867	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097692	27097694	+	inframe_deletion	In_Frame_Del	DEL	AGC	AGC	-	novel	NA	P-0007298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	283	1085	0	ENST00000324856.7:c.3283_3285del	p.Gln1095del	p.Q1095del	ENST00000324856	NM_006015.4	1094	aAGCag/aag	12/20	0.320171871172286	2	FACETS	0.887	0.834	0.94	0.887	0.834	0.94	CLONAL	2	TRUE	0	0.320171871172286	2		1085	997	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72863677	72863677	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0007298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	169	1217	2	ENST00000268489.5:c.3529+1G>A		p.X1177_splice	ENST00000268489	NM_006885.3	1177			1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.320171871172286	2		1219	1016	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502313	157502313	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0007298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	87	585	3	ENST00000346085.5:c.3345+1G>T		p.X1115_splice	ENST00000346085	NM_020732.3	1115			1	2	FACETS	0.955	0.847	1	0.955	0.847	1	CLONAL	1	TRUE	1	0.320171871172286	2		588	569	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771154	161771154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	125	1142	0	ENST00000366898.1:c.1375G>A	p.Gly459Arg	p.G459R	ENST00000366898	NM_004562.2	459	Ggg/Agg	12/12	1	2	FACETS	0.817	0.738	0.9	0.817	0.738	0.9	CLONAL	1	TRUE	1	0.320171871172286	2		1142	956	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524997	8524997	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	88	721	0	ENST00000356435.5:c.607G>T	p.Gly203Ter	p.G203*	ENST00000356435		203	Gga/Tga	7/35	NA	2	FACETS	0.866	0.768	0.97			1	INDETERMINATE	1	TRUE	NA	0.320171871172286	2		721	635	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782082	NA	P-0007414-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	21	298	0	ENST00000269305.4:c.745A>T	p.Arg249Trp	p.R249W	ENST00000269305	NM_001126112.2	249	Agg/Tgg	7/11	0.159236667824796	0	FACETS	0.365	0.28	0.464			1	SUBCLONAL	1	TRUE	0	0.22	0		298	408	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578476	7578477	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGGT	novel	NA	P-0007414-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	24	314	0	ENST00000269305.4:c.450_453dup	p.Pro152ThrfsTer30	p.P152Tfs*30	ENST00000269305	NM_001126112.2	151	-/ACCC	5/11	0.159236667824796	0	FACETS	0.391	0.306	0.49			1	SUBCLONAL	1	TRUE	0	0.22	0		314	435	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16174572	16174572	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007685-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	32	353	0	ENST00000375759.3:c.10G>A	p.Glu4Lys	p.E4K	ENST00000375759	NM_015001.2	4	Gaa/Aaa	1/15	0.378916299288856	1	FACETS	0.485	0.395	0.586	0.485	0.395	0.586	SUBCLONAL	1	TRUE	0	0.382281176059018	1		353	279	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499619	18499619	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007685-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	112	491	0	ENST00000266497.5:c.1474C>T	p.Gln492Ter	p.Q492*	ENST00000266497		492	Cag/Tag	10/31	0.3645717080989	1	FACETS	0.725	0.653	0.801	0.725	0.653	0.801	SUBCLONAL	1	TRUE	0	0.382281176059018	1		491	654	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912918	32912918	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007685-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	138	792	0	ENST00000380152.3:c.4426G>C	p.Asp1476His	p.D1476H	ENST00000380152		1476	Gac/Cac	11/27	0.382281176059018	1	FACETS	0.495	0.449	0.544	0.495	0.449	0.544	SUBCLONAL	1	TRUE	0	0.382281176059018	1		792	1179	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5206820	5206820	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007685-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	62	376	0	ENST00000357368.4:c.5812G>C	p.Glu1938Gln	p.E1938Q	ENST00000357368	NM_002850.3	1938	Gag/Cag	38/38	0.180825659254151	1	FACETS	0.685	0.594	0.783	0.685	0.594	0.783	INDETERMINATE	1	TRUE	0	0.382281176059018	1		376	383	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578515	7578516	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCCAGTTGGCAAAACATCTTGTTGAG	novel	NA	P-0007685-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	57	293	0	ENST00000269305.4:c.388_414dup	p.Leu130_Ala138dup	p.L130_A138dup	ENST00000269305	NM_001126112.2	130	-/CTCAACAAGATGTTTTGCCAACTGGCC	5/11	0.382281176059018	1	FACETS	0.654	0.563	0.752	0.654	0.563	0.752	SUBCLONAL	1	TRUE	0	0.382281176059018	1		293	369	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911001	32911004	+	stop_gained	Nonsense_Mutation	ONP	GAAA	GAAA	CAAT	novel	NA	P-0007685-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	115	805	0	ENST00000380152.3:c.2509_2512delinsCAAT	p.Glu837_Lys838delinsGlnTer	p.E837_K838delinsQ*	ENST00000380152		837	GAAAaa/CAATaa	11/27	0.382281176059018	1	FACETS	0.446	0.401	0.494	0.446	0.401	0.494	SUBCLONAL	1	TRUE	0	0.382281176059018	1		805	1091	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	23	417	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.907	0.709	1	0.907	0.709	1	CLONAL	1	TRUE	1	0.19	2		418	267	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713853	30713853	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039106	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	36	269	0	ENST00000295754.5:c.1178G>A	p.Cys393Tyr	p.C393Y	ENST00000295754	NM_003242.5	393	tGc/tAc	4/7	1	2	FACETS	0.817	0.671	0.98	0.817	0.671	0.98	CLONAL	1	TRUE	1	0.19	2		269	464	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457242	25457242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147001633	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	28	260	0	ENST00000264709.3:c.2645G>A	p.Arg882His	p.R882H	ENST00000264709	NM_175629.2	882	cGc/cAc	23/23	1	2	FACETS	0.442	0.352	0.545	0.442	0.352	0.545	SUBCLONAL	1	TRUE	1	0.19	2		260	667	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	10	76	1	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	0.101690429956256	3	FACETS	0.753	0.512	1	0.377	0.256	0.528	INDETERMINATE	1	TRUE	1	0.19	3		77	153	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164805	36164805	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	34	273	0	ENST00000300305.3:c.1070del	p.Pro357ArgfsTer237	p.P357Rfs*237	ENST00000300305		357	cCg/cg	8/8	1	2	FACETS	0.595	0.485	0.719	0.595	0.485	0.719	SUBCLONAL	1	TRUE	1	0.19	2		273	602	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100425	8100425	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	79	436	0	ENST00000346208.3:c.404del	p.Pro135ArgfsTer60	p.P135Rfs*60	ENST00000346208		133	taC/ta	3/6	1	2	FACETS	0.856	0.751	0.969	0.856	0.751	0.969	CLONAL	1	TRUE	1	0.19	2		436	972	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970901	21970901	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs45476696	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	46	290	0	ENST00000304494.5:c.457G>A	p.Asp153Asn	p.D153N	ENST00000304494	NM_000077.4	153	Gac/Aac	2/3	1	2	FACETS	0.764	0.642	0.898	0.764	0.642	0.898	SUBCLONAL	1	TRUE	1	0.19	2		290	634	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	107	424	0	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	0.101690429956256	3	FACETS	1	0.971	1	0.618	0.553	0.687	INDETERMINATE	1	TRUE	1	0.19	3		424	998	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476733	140476733	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1278812236	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	27	445	0	ENST00000288602.6:c.1673G>A	p.Arg558Gln	p.R558Q	ENST00000288602	NM_004333.4	558	cGa/cAa	13/18	1	2	FACETS	1	0.84	1	1	0.84	1	CLONAL	1	TRUE	1	0.19	2		445	268	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499363	89499363	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1317589623	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	31	354	1	ENST00000336596.2:c.2538del	p.Met847TrpfsTer10	p.M847Wfs*10	ENST00000336596	NM_005233.5	845	Ccc/cc	15/17	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.19	2		355	241	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46714230	46714230	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	37	317	0	ENST00000371975.4:c.50G>A	p.Gly17Asp	p.G17D	ENST00000371975	NM_003579.3	17	gGc/gAc	2/18	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.19	2		317	344	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032104	48032104	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	24	478	1	ENST00000234420.5:c.3494G>A	p.Cys1165Tyr	p.C1165Y	ENST00000234420	NM_000179.2	1165	tGc/tAc	6/10	1	2	FACETS	0.714	0.559	0.892	0.714	0.559	0.892	SUBCLONAL	1	TRUE	1	0.19	2		479	354	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155421	99155421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769671156	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	40	374	0	ENST00000074304.5:c.647G>A	p.Arg216Gln	p.R216Q	ENST00000074304	NM_001134224.1	216	cGa/cAa	9/26	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.19	2		374	324	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736176	204736176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	30	563	1	ENST00000302823.3:c.533G>A	p.Ser178Asn	p.S178N	ENST00000302823	NM_005214.4	178	aGc/aAc	3/4	1	2	FACETS	0.681	0.548	0.832	0.681	0.548	0.832	SUBCLONAL	1	TRUE	1	0.19	2		564	464	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134514507	134514507	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs372758942	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	69	380	0	ENST00000398015.3:c.34G>T	p.Ala12Ser	p.A12S	ENST00000398015	NM_004441.4	12	Gca/Tca	1/16	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.19	2		380	706	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851765	134851765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	44	280	0	ENST00000398015.3:c.1171G>A	p.Val391Ile	p.V391I	ENST00000398015	NM_004441.4	391	Gtc/Atc	5/16	1	2	FACETS	0.877	0.735	1	0.877	0.735	1	CLONAL	1	TRUE	1	0.19	2		280	528	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226865	142226865	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1348702370	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	21	447	1	ENST00000350721.4:c.4939C>T	p.Arg1647Cys	p.R1647C	ENST00000350721	NM_001184.3	1647	Cgc/Tgc	28/47	1	2	FACETS	0.734	0.566	0.931	0.734	0.566	0.931	CLONAL	1	TRUE	1	0.19	2		448	301	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747979	41747979	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1320695099	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	20	57	0	ENST00000226382.2:c.790G>T	p.Ala264Ser	p.A264S	ENST00000226382	NM_003924.3	264	Gct/Tct	3/3	1	2	FACETS	0.915	0.71	1	1	0.935	1	CLONAL	2	TRUE	1	0.19	2		57	115	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197443	106197443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1452689450	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	42	541	0	ENST00000380013.4:c.5776C>T	p.Arg1926Cys	p.R1926C	ENST00000380013	NM_001127208.2	1926	Cgt/Tgt	11/11	1	2	FACETS	1	0.84	1	1	0.84	1	CLONAL	1	TRUE	1	0.19	2		541	440	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288891	33288891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776375824	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	29	155	0	ENST00000374542.5:c.661G>A	p.Ala221Thr	p.A221T	ENST00000374542	NM_001141970.1	221	Gca/Aca	3/8	0.101690429956256	3	FACETS	1	0.846	1	0.531	0.426	0.648	INDETERMINATE	1	TRUE	1	0.19	3		155	315	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527648	157527648	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	31	300	0	ENST00000346085.5:c.5373A>G	p.Ile1791Met	p.I1791M	ENST00000346085	NM_020732.3	1791	atA/atG	20/20	1	2	FACETS	0.712	0.576	0.868	0.712	0.576	0.868	SUBCLONAL	1	TRUE	1	0.19	2		300	458	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319959	8319959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745582718	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	27	289	1	ENST00000356435.5:c.5542G>A	p.Val1848Ile	p.V1848I	ENST00000356435		1848	Gtt/Att	34/35	1	2	FACETS	0.781	0.627	0.954	1	0.94	1	CLONAL	2	TRUE	1	0.19	2		290	182	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407988	139407988	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	49	212	0	ENST00000277541.6:c.2209T>C	p.Tyr737His	p.Y737H	ENST00000277541	NM_017617.3	737	Tac/Cac	14/34	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.19	2		212	460	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333671	70333671	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773322363	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	18	385	0	ENST00000373644.4:c.1576G>A	p.Ala526Thr	p.A526T	ENST00000373644	NM_030625.2	526	Gct/Act	2/12	1	2	FACETS	0.734	0.553	0.948	0.734	0.553	0.948	CLONAL	1	TRUE	1	0.19	2		385	258	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649934	88649934	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	21	370	0	ENST00000372037.3:c.183C>A	p.Cys61Ter	p.C61*	ENST00000372037	NM_004329.2	61	tgC/tgA	4/13	1	2	FACETS	0.899	0.694	1	0.899	0.694	1	CLONAL	1	TRUE	1	0.19	2		370	246	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125496668	125496668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	29	379	1	ENST00000428830.2:c.5C>T	p.Ala2Val	p.A2V	ENST00000428830	NM_001114121.2	2	gCa/gTa	2/14	1	2	FACETS	0.963	0.774	1	0.963	0.774	1	CLONAL	1	TRUE	1	0.19	2		380	317	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416994	416994	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	28	430	0	ENST00000399788.2:c.3556A>G	p.Asn1186Asp	p.N1186D	ENST00000399788	NM_001042603.1	1186	Aac/Gac	23/28	1	2	FACETS	0.797	0.637	0.979	0.797	0.637	0.979	CLONAL	1	TRUE	1	0.19	2		430	370	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424459	49424459	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	49	364	0	ENST00000301067.7:c.13764G>T	p.Gln4588His	p.Q4588H	ENST00000301067	NM_003482.3	4588	caG/caT	41/54	1	2	FACETS	0.831	0.703	0.972	0.831	0.703	0.972	CLONAL	1	TRUE	1	0.19	2		364	621	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425728	49425728	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	32	303	0	ENST00000301067.7:c.12760C>T	p.Gln4254Ter	p.Q4254*	ENST00000301067	NM_003482.3	4254	Cag/Tag	39/54	1	2	FACETS	0.529	0.428	0.643	0.529	0.428	0.643	SUBCLONAL	1	TRUE	1	0.19	2		303	637	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347941	347941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	101	391	2	ENST00000262320.3:c.1565C>T	p.Ala522Val	p.A522V	ENST00000262320	NM_003502.3	522	gCg/gTg	6/11	0.101690429956256	3	FACETS	1	0.973	1	0.647	0.578	0.722	INDETERMINATE	1	TRUE	1	0.19	3		393	899	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350069	89350069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758856347	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1361	120	647	0	ENST00000301030.4:c.2881C>T	p.Arg961Cys	p.R961C	ENST00000301030	NM_001256183.1	961	Cgc/Tgc	9/13	0.101690429956256	3	FACETS	0.934	0.84	1	0.467	0.42	0.517	INDETERMINATE	1	TRUE	1	0.19	3		647	1481	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983200	7983200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1308351316	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	65	400	0	ENST00000319144.4:c.814G>A	p.Val272Ile	p.V272I	ENST00000319144	NM_001139.2	272	Gtc/Atc	7/15	0.101690429956256	3	FACETS	0.904	0.782	1	0.452	0.391	0.518	INDETERMINATE	1	TRUE	1	0.19	3		400	829	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244209	5244209	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1181117492	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	63	269	0	ENST00000357368.4:c.1273G>T	p.Ala425Ser	p.A425S	ENST00000357368	NM_002850.3	425	Gcc/Tcc	11/38	0.101690429956256	3	FACETS	1	0.95	1	0.609	0.527	0.699	INDETERMINATE	1	TRUE	1	0.19	3		269	596	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7163174	7163174	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	59	462	0	ENST00000302850.5:c.1898A>G	p.Asn633Ser	p.N633S	ENST00000302850	NM_000208.2	633	aAc/aGc	9/22	0.101690429956256	3	FACETS	1	0.873	1	0.508	0.437	0.586	INDETERMINATE	1	TRUE	1	0.19	3		462	669	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098434	11098434	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758091260	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	48	224	0	ENST00000358026.2:c.952G>A	p.Val318Ile	p.V318I	ENST00000358026	NM_001128849.1	318	Gtc/Atc	6/36	0.101690429956256	3	FACETS	1	0.862	1	0.51	0.431	0.598	INDETERMINATE	1	TRUE	1	0.19	3		224	542	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953306	17953306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	71	275	0	ENST00000458235.1:c.680G>A	p.Cys227Tyr	p.C227Y	ENST00000458235	NM_000215.3	227	tGc/tAc	6/24	0.101690429956256	3	FACETS	1	0.966	1	0.666	0.582	0.758	INDETERMINATE	1	TRUE	1	0.19	3		275	614	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797344	42797344	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	66	311	0	ENST00000575354.2:c.3706C>T	p.Pro1236Ser	p.P1236S	ENST00000575354	NM_015125.3	1236	Cca/Tca	15/20	0.101690429956256	3	FACETS	1	0.881	1	0.509	0.441	0.582	INDETERMINATE	1	TRUE	1	0.19	3		311	748	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051643	30051643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1427589827	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	23	429	0	ENST00000338641.4:c.577G>A	p.Ala193Thr	p.A193T	ENST00000338641	NM_000268.3	193	Gca/Aca	6/16	1	2	FACETS	0.586	0.456	0.737	0.586	0.456	0.737	SUBCLONAL	1	TRUE	1	0.19	2		429	413	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335923	73335923	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	10	266	0	ENST00000377767.4:c.2372del	p.Leu791TrpfsTer14	p.L791Wfs*14	ENST00000377767	NM_014953.3	791	tTg/tg	18/21	1	2	FACETS	0.569	0.386	0.799	0.569	0.386	0.799	SUBCLONAL	1	TRUE	1	0.19	2		266	185	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354152	15354152	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs868796773	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	12	98	1	ENST00000263377.2:c.2728del	p.Gln910LysfsTer39	p.Q910Kfs*39	ENST00000263377	NM_058243.2	910	Caa/aa	14/20	0.101690429956256	3	FACETS	0.617	0.434	0.844	0.309	0.217	0.422	INDETERMINATE	1	TRUE	1	0.19	3		99	224	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172062	32172063	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	57	423	0	ENST00000375023.3:c.2969dup	p.His991ProfsTer14	p.H991Pfs*14	ENST00000375023	NM_004557.3	990	ttc/ttTc	19/30	0.101690429956256	3	FACETS	0.823	0.705	0.953	0.412	0.352	0.477	INDETERMINATE	1	TRUE	1	0.19	3		423	798	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998627	100998629	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	rs751489196	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	98	371	1	ENST00000325455.5:c.1173_1175del	p.Glu392del	p.E392del	ENST00000325455	NM_001202474.3	391	gaGGAa/gaa	1/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.19	2		372	794	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659789	88659789	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs762900005	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	33	427	0	ENST00000372037.3:c.441del	p.Phe147LeufsTer18	p.F147Lfs*18	ENST00000372037	NM_004329.2	146	Ttt/tt	7/13	1	2	FACETS	0.919	0.749	1	0.919	0.749	1	CLONAL	1	TRUE	1	0.19	2		427	378	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910923	32910923	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359329	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	50	825	0	ENST00000380152.3:c.2435del	p.Asn812IlefsTer13	p.N812Ifs*13	ENST00000380152		811	Aaa/aa	11/27	1	2	FACETS	0.904	0.767	1	0.904	0.767	1	CLONAL	1	TRUE	1	0.19	2		825	582	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063359	67063359	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	54	262	0	ENST00000412916.2:c.54del	p.Phe18LeufsTer4	p.F18Lfs*4	ENST00000412916		17	Ttt/tt	1/6	0.101690429956256	3	FACETS	0.91	0.776	1	0.455	0.388	0.529	INDETERMINATE	1	TRUE	1	0.19	3		262	684	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93607788	93607789	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1433438204	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	19	500	0	ENST00000375746.1:c.496dup	p.Met166AsnfsTer14	p.M166Nfs*14	ENST00000375746	NM_001174167.1	164	gaa/gAaa	3/14	1	2	FACETS	0.59	0.447	0.758	0.59	0.447	0.758	SUBCLONAL	1	TRUE	1	0.19	2		500	339	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332471	70332471	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	34	497	3	ENST00000373644.4:c.380del	p.Lys127ArgfsTer8	p.K127Rfs*8	ENST00000373644	NM_030625.2	126	Aaa/aa	2/12	1	2	FACETS	0.942	0.77	1	0.942	0.77	1	CLONAL	1	TRUE	1	0.19	2		500	380	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2493227	2493228	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0007831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	78	431	0	ENST00000355716.4:c.669_670del	p.Ile223MetfsTer10	p.I223Mfs*10	ENST00000355716	NM_003820.2	223	ATa/a	6/8	0.3	2	FACETS	0.883	0.774	1			1	CLONAL	1	TRUE	NA	0.19	2		431	930	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0007887-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	8	478	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	NA	2	FACETS	0.169	0.108	0.249			1	INDETERMINATE	1	TRUE	NA	0.25	2		478	378	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94179016	94179017	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs876660269	NA	P-0007887-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	76	687	0	ENST00000323929.3:c.1826dup	p.Thr610AspfsTer7	p.T610Dfs*7	ENST00000323929	NM_005591.3	609	aag/aaAg	16/20	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.25	2		687	589	SUCCESS
APC	324	MSKCC	GRCh37	5	112154817	112154817	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007887-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	85	710	0	ENST00000257430.4:c.1088A>G	p.Asn363Ser	p.N363S	ENST00000257430	NM_000038.5	363	aAt/aGt	10/16	1	2	FACETS	0.988	0.874	1	0.988	0.874	1	CLONAL	1	TRUE	1	0.25	2		710	688	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512260	120512260	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	454	362	0	ENST00000256646.2:c.982A>T	p.Asn328Tyr	p.N328Y	ENST00000256646	NM_024408.3	328	Aac/Tac	6/34	0.414761382116307	1	FACETS	0.711	0.682	0.74	0.711	0.682	0.74	INDETERMINATE	1	TRUE	0	0.810026342347043	1		362	938	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168704	56168704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	665	472	0	ENST00000399503.3:c.1558C>T	p.Gln520Ter	p.Q520*	ENST00000399503	NM_005921.1	520	Cag/Tag	9/20	0.410160655199379	2	FACETS	1	0.998	1	0.732	0.71	0.753	INDETERMINATE	1	TRUE	0	0.810026342347043	2		472	1122	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070595	67070595	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	585	540	0	ENST00000412916.2:c.219G>A	p.Trp73Ter	p.W73*	ENST00000412916		73	tgG/tgA	3/6	0.810026342347043	1	FACETS	0.984	0.956	1	0.984	0.956	1	CLONAL	1	TRUE	0	0.810026342347043	1		540	873	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGGGACCC	novel	NA	P-0007984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	434	485	0	ENST00000346208.3:c.1000_1007dup	p.Val337GlyfsTer21	p.V337Gfs*21	ENST00000346208		333	-/GGGGACCC	5/6	0.414761382116307	1	FACETS	0.623	0.596	0.651	0.623	0.596	0.651	INDETERMINATE	1	TRUE	0	0.810026342347043	1		485	1023	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0008068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	236	295	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	0.887	0.827	0.949	0.887	0.827	0.949	CLONAL	1	TRUE	1	0.455514685902373	2		295	1168	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0008068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	534	412	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.455514685902373	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.455514685902373	2		412	1162	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0008068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	362	240	2	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	0.419510247454588	5	FACETS	0.908	0.863	0.954	0.681	0.647	0.715	CLONAL	3	TRUE	1	0.455514685902373	5		242	982	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791533	42791533	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1318	402	382	0	ENST00000575354.2:c.514C>T	p.Gln172Ter	p.Q172*	ENST00000575354	NM_015125.3	172	Cag/Tag	4/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.455514685902373	2		382	1720	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	595	398	0	ENST00000269305.4:c.430del	p.Gln144SerfsTer26	p.Q144Sfs*26	ENST00000269305	NM_001126112.2	144	Cag/ag	5/11	0.455514685902373	2	FACETS	0.949	0.914	0.984	0.949	0.914	0.984	CLONAL	2	TRUE	0	0.455514685902373	2		398	1377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519980	NA	P-0008709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	135	245	0	ENST00000269305.4:c.528C>G	p.Cys176Trp	p.C176W	ENST00000269305	NM_001126112.2	176	tgC/tgG	5/11	0.220013977507186	3	FACETS	1	0.964	1	0.731	0.669	0.795	CLONAL	2	TRUE	0	0.297030305888987	3		245	476	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871063	12871063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	62	195	1	ENST00000228872.4:c.290G>A	p.Gly97Asp	p.G97D	ENST00000228872	NM_004064.3	97	gGt/gAt	1/3	0.297030305888987	9	FACETS	1	0.968	1			1	CLONAL	1	TRUE	NA	0.297030305888987	9		196	582	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732361	74732361	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1574	196	1052	0	ENST00000359995.5:c.548C>A	p.Ser183Tyr	p.S183Y	ENST00000359995	NM_001195427.1	183	tCc/tAc	2/3	0.297030305888987	4	FACETS	0.967	0.892	1	0.242	0.223	0.262	CLONAL	1	TRUE	0	0.297030305888987	4		1052	1770	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176329	24176329	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1568963596	NA	P-0008709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	106	503	1	ENST00000263121.7:c.1120C>T	p.Arg374Trp	p.R374W	ENST00000263121	NM_003073.3	374	Cgg/Tgg	9/9	0.297030305888987	3	FACETS	0.961	0.861	1	0.48	0.43	0.534	CLONAL	1	TRUE	1	0.297030305888987	3		504	853	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551082	41551082	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	163	787	0	ENST00000263253.7:c.3226C>A	p.Arg1076Ser	p.R1076S	ENST00000263253	NM_001429.3	1076	Cgt/Agt	17/31	0.297030305888987	3	FACETS	0.968	0.886	1	0.484	0.443	0.527	CLONAL	1	TRUE	1	0.297030305888987	3		787	1302	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074254	8074255	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0008709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1397	192	1272	0	ENST00000377482.5:c.403_404dup	p.Asn135LysfsTer41	p.N135Kfs*41	ENST00000377482	NM_018948.3	135	aac/aaAAc	4/4	0.297030305888987	3	FACETS	0.934	0.861	1	0.311	0.287	0.337	CLONAL	1	TRUE	0	0.297030305888987	3		1272	1589	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947901	178947901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773300933	NA	P-0008710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	11	393	0	ENST00000263967.3:c.2776G>A	p.Asp926Asn	p.D926N	ENST00000263967	NM_006218.2	926	Gat/Aat	19/21	1	2	FACETS	1	0.693	1	1	0.693	1	CLONAL	1	TRUE	1	0.12	2		393	183	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0009137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	42	328	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.129287702370884	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		328	572	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045814	180045814	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1262382099	NA	P-0009137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	24	514	0	ENST00000261937.6:c.2957C>G	p.Ser986Trp	p.S986W	ENST00000261937	NM_182925.4	986	tCg/tGg	21/30	0.3	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		514	469	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845985	151845985	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	32	463	0	ENST00000262189.6:c.13027G>A	p.Glu4343Lys	p.E4343K	ENST00000262189	NM_170606.2	4343	Gaa/Aaa	52/59	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		463	522	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0009167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	61	372	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.304309779361559	1	FACETS	0.693	0.599	0.795	0.693	0.599	0.795	SUBCLONAL	1	TRUE	0	0.31	1		373	480	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504432	186504432	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	94	519	0	ENST00000323963.5:c.769G>A	p.Glu257Lys	p.E257K	ENST00000323963		257	Gag/Aag	7/11	1	2	FACETS	0.978	0.872	1	0.978	0.872	1	CLONAL	1	TRUE	1	0.31	2		519	620	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619180	37619180	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	143	391	0	ENST00000447079.4:c.856C>G	p.Gln286Glu	p.Q286E	ENST00000447079	NM_015083.1	286	Cag/Gag	1/14	1	2	FACETS	0.955	0.87	1	0.955	0.87	1	CLONAL	1	TRUE	1	0.31	2		391	966	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117884	70117884	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1327802772	NA	P-0009167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	36	214	0	ENST00000245479.2:c.352G>A	p.Ala118Thr	p.A118T	ENST00000245479	NM_000346.3	118	Gcg/Acg	1/3	1	2	FACETS	0.389	0.319	0.468	0.389	0.319	0.468	SUBCLONAL	1	TRUE	1	0.31	2		214	597	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120202	70120203	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0009167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	120	340	0	ENST00000245479.2:c.1205dup	p.Ser403GlufsTer175	p.S403Efs*175	ENST00000245479	NM_000346.3	402	ctg/cTtg	3/3	1	2	FACETS	0.97	0.876	1	0.97	0.876	1	CLONAL	1	TRUE	1	0.31	2		340	798	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0009186-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	99	560	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.22	2		560	713	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0009186-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	82	479	1	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	1	2	FACETS	0.617	0.542	0.698	0.617	0.542	0.698	SUBCLONAL	1	TRUE	1	0.22	2		480	1208	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346637	81346637	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009186-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	32	558	0	ENST00000222390.5:c.1316A>G	p.Tyr439Cys	p.Y439C	ENST00000222390	NM_000601.4	439	tAc/tGc	11/18	1	2	FACETS	0.51	0.413	0.621	0.51	0.413	0.621	SUBCLONAL	1	TRUE	1	0.22	2		558	570	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904835	101904835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009186-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	72	503	0	ENST00000374994.4:c.823C>T	p.Gln275Ter	p.Q275*	ENST00000374994	NM_004612.2	275	Cag/Tag	5/9	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.22	2		503	616	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009447-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	62	251	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.965	0.855	1	0.965	0.855	1	CLONAL	1	FALSE	1	0.823349710328404	2		251	156	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0009447-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	225	303	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.999	0.939	1	0.999	0.939	1	CLONAL	1	FALSE	1	0.823349710328404	2		304	547	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410204	63410204	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009447-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	48	392	0	ENST00000330258.3:c.2963C>T	p.Pro988Leu	p.P988L	ENST00000330258	NM_152424.3	988	cCa/cTa	2/2	0.555439096875213	1	FACETS	0.168	0.142	0.197	0.168	0.142	0.197	SUBCLONAL	1	FALSE	0	0.823349710328404	1		392	408	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432627	78432627	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009447-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	32	242	0	ENST00000370768.2:c.356G>T	p.Gly119Val	p.G119V	ENST00000370768	NM_003902.3	119	gGa/gTa	6/20	0.823349710328404	1	FACETS	0.185	0.151	0.224	0.185	0.151	0.224	SUBCLONAL	1	FALSE	0	0.823349710328404	1		242	247	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797300	42797301	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0009447-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	193	315	0	ENST00000575354.2:c.3663_3664insTT	p.Glu1222LeufsTer81	p.E1222Lfs*81	ENST00000575354	NM_015125.3	1221	tct/tcTTt	15/20	0.823349710328404	1	FACETS	0.881	0.834	0.927	0.881	0.834	0.927	CLONAL	1	FALSE	0	0.823349710328404	1		315	313	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0009460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	152	561	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	0.236722814382122	5	FACETS	0.914	0.835	0.996	0.609	0.557	0.664	CLONAL	2	FALSE	2	0.236722814382122	5		561	952	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152219	99152219	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	29	360	0	ENST00000074304.5:c.298A>T	p.Ser100Cys	p.S100C	ENST00000074304	NM_001134224.1	100	Agt/Tgt	6/26	0.215700136511575	3	FACETS	0.476	0.381	0.584	0.238	0.19	0.292	SUBCLONAL	1	FALSE	1	0.236722814382122	3		360	576	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885945	111885945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761330967	NA	P-0009460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1404	85	565	1	ENST00000341259.2:c.1567G>A	p.Glu523Lys	p.E523K	ENST00000341259	NM_005475.2	523	Gag/Aag	8/8	0.223047663844578	4	FACETS	0.596	0.525	0.674	0.298	0.262	0.337	SUBCLONAL	1	FALSE	2	0.236722814382122	4		566	1489	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752411	57752412	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0009460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	28	185	0	ENST00000274289.3:c.1161_1162del	p.Arg387SerfsTer3	p.R387Sfs*3	ENST00000274289	NM_006622.3	387	agAGtg/agtg	9/14	0.157511763319146	4	FACETS	0.656	0.524	0.807	0.328	0.262	0.404	SUBCLONAL	1	FALSE	2	0.236722814382122	4		185	446	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	210	251	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.869705112753347	2		251	464	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0009511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	349	303	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.916	0.871	0.962	0.916	0.871	0.962	CLONAL	1	TRUE	1	0.869705112753347	2		304	876	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791995	42791995	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	95	641	0	ENST00000575354.2:c.799T>G	p.Trp267Gly	p.W267G	ENST00000575354	NM_015125.3	267	Tgg/Ggg	6/20	0.869705112753347	1	FACETS	0.181	0.16	0.202	0.181	0.16	0.202	SUBCLONAL	1	TRUE	0	0.869705112753347	1		641	684	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791796	42791796	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	296	506	0	ENST00000575354.2:c.682C>G	p.Arg228Gly	p.R228G	ENST00000575354	NM_015125.3	228	Cgg/Ggg	5/20	0.869705112753347	1	FACETS	0.63	0.598	0.661	0.63	0.598	0.661	SUBCLONAL	1	TRUE	0	0.869705112753347	1		506	611	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791747	42791747	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	33	476	0	ENST00000575354.2:c.633C>G	p.Ser211Arg	p.S211R	ENST00000575354	NM_015125.3	211	agC/agG	5/20	0.869705112753347	1	FACETS	0.07	0.057	0.086	0.07	0.057	0.086	SUBCLONAL	1	TRUE	0	0.869705112753347	1		476	611	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432411	78432412	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACCTTTCTGGAAGGCCACC	novel	NA	P-0009511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	253	512	0	ENST00000370768.2:c.421_439dup	p.Ser147TrpfsTer15	p.S147Wfs*15	ENST00000370768	NM_003902.3	147	tcc/tGGTGGCCTTCCAGAAAGGTcc	7/20	0.869705112753347	1	FACETS	0.684	0.648	0.719	0.684	0.648	0.719	SUBCLONAL	1	TRUE	0	0.869705112753347	1		512	481	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469766	157469767	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0009511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1235	167	676	0	ENST00000346085.5:c.2562dup	p.Arg855GlnfsTer6	p.R855Qfs*6	ENST00000346085	NM_020732.3	854	tcc/tCcc	9/20	1	2	FACETS	0.274	0.251	0.298	0.274	0.251	0.298	SUBCLONAL	1	TRUE	1	0.869705112753347	2		676	1402	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115873	8115874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0009594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	241	448	0	ENST00000346208.3:c.1220dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tCcg	6/6	1	2	FACETS	0.928	0.867	0.991	0.928	0.867	0.991	CLONAL	1	TRUE	1	0.510547761195506	2		448	1017	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577557	7577557	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519982	NA	P-0009594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	230	322	0	ENST00000269305.4:c.724T>C	p.Cys242Arg	p.C242R	ENST00000269305	NM_001126112.2	242	Tgc/Cgc	7/11	0.510547761195506	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.510547761195506	1		322	636	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579575	7579575	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	550	388	1	ENST00000269305.4:c.112C>T	p.Gln38Ter	p.Q38*	ENST00000269305	NM_001126112.2	38	Caa/Taa	4/11	0.337493444899491	3	FACETS	1	0.982	1			1	CLONAL	3	TRUE	NA	0.514277998765002	3		389	878	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207064	1207065	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1131690917	NA	P-0009684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	595	537	0	ENST00000326873.7:c.157dup	p.Asp53GlyfsTer110	p.D53Gfs*110	ENST00000326873	NM_000455.4	51	atg/atGg	1/10	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	2	TRUE	NA	0.514277998765002	2		537	1126	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458310	120458310	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	180	351	0	ENST00000256646.2:c.7035G>T	p.Met2345Ile	p.M2345I	ENST00000256646	NM_024408.3	2345	atG/atT	34/34	0.514277998765002	1	FACETS	0.949	0.881	1	0.949	0.881	1	CLONAL	1	TRUE	0	0.514277998765002	1		351	548	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965216	25965216	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs955754916	NA	P-0009684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	218	500	1	ENST00000435504.4:c.3990G>A	p.Met1330Ile	p.M1330I	ENST00000435504		1330	atG/atA	13/13	0.509000911998191	2	FACETS	0.994	0.926	1	0.497	0.463	0.532	CLONAL	1	TRUE	0	0.514277998765002	2		501	853	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96931046	96931046	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	62	130	0	ENST00000258439.3:c.74A>G	p.Lys25Arg	p.K25R	ENST00000258439	NM_001193304.2	25	aAg/aGg	2/4	0.514277998765002	3	FACETS	0.913	0.794	1	0.456	0.397	0.521	CLONAL	1	TRUE	1	0.514277998765002	3		130	332	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539324	187539324	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	198	523	0	ENST00000441802.2:c.8416A>T	p.Ser2806Cys	p.S2806C	ENST00000441802	NM_005245.3	2806	Agc/Tgc	10/27	0.357475614389479	1	FACETS	0.845	0.786	0.906	0.845	0.786	0.906	CLONAL	1	TRUE	0	0.514277998765002	1		523	677	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224520	224520	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	111	217	0	ENST00000264932.6:c.196G>C	p.Val66Leu	p.V66L	ENST00000264932	NM_004168.2	66	Gtg/Ctg	3/15	0.373633494088633	3	FACETS	1	0.959	1	0.557	0.503	0.614	CLONAL	1	TRUE	1	0.514277998765002	3		217	487	SUCCESS
APC	324	MSKCC	GRCh37	5	112178662	112178662	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	178	505	0	ENST00000257430.4:c.7371G>C	p.Glu2457Asp	p.E2457D	ENST00000257430	NM_000038.5	2457	gaG/gaC	16/16	0.373633494088633	3	FACETS	0.944	0.87	1	0.472	0.435	0.511	CLONAL	1	TRUE	1	0.514277998765002	3		505	922	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020874	26020874	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1446	413	1166	0	ENST00000357647.3:c.157C>T	p.Arg53Cys	p.R53C	ENST00000357647	NM_003529.2	53	Cgc/Tgc	1/1	0.514277998765002	2	FACETS	0.864	0.82	0.909	0.432	0.41	0.455	CLONAL	1	TRUE	0	0.514277998765002	2		1166	1859	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032169	26032169	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	650	811	2	ENST00000244661.2:c.120C>A	p.His40Gln	p.H40Q	ENST00000244661	NM_003537.3	40	caC/caA	1/1	0.514277998765002	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.514277998765002	2		813	1239	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710984	117710984	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	193	178	0	ENST00000368508.3:c.1288G>T	p.Gly430Cys	p.G430C	ENST00000368508	NM_002944.2	430	Ggc/Tgc	12/43	0.509000911998191	2	FACETS	0.998	0.939	1	0.998	0.939	1	CLONAL	2	TRUE	0	0.514277998765002	2		178	376	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509427	106509427	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	1478	652	0	ENST00000359195.3:c.1421T>A	p.Leu474His	p.L474H	ENST00000359195	NM_002649.2	474	cTc/cAc	2/11	0.514277998765002	7	FACETS	0.951	0.933	0.969			1	CLONAL	6	TRUE	NA	0.514277998765002	7		652	2302	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741242	145741242	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1289670420	NA	P-0009684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	520	631	0	ENST00000428558.2:c.1164G>C	p.Glu388Asp	p.E388D	ENST00000428558	NM_004260.3	388	gaG/gaC	6/22	0.233775531790391	5	FACETS	1	0.98	1			1	INDETERMINATE	2	TRUE	NA	0.514277998765002	5		631	1723	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115111970	115111970	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs1262807912	NA	P-0009684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	199	258	0	ENST00000257566.3:c.1770G>C	p.Gln590His	p.Q590H	ENST00000257566	NM_016569.3	590	caG/caC	7/8	0.503091659833066	3	FACETS	0.906	0.846	0.967	0.906	0.846	0.967	CLONAL	2	TRUE	1	0.514277998765002	3		258	537	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472468	88472468	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	228	573	1	ENST00000360948.2:c.2087G>T	p.Gly696Val	p.G696V	ENST00000360948	NM_001012338.2	696	gGg/gTg	16/19	1	2	FACETS	0.87	0.811	0.931	0.87	0.811	0.931	CLONAL	1	TRUE	1	0.514277998765002	2		574	1019	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993518	72993518	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1349	403	797	1	ENST00000268489.5:c.527G>T	p.Gly176Val	p.G176V	ENST00000268489	NM_006885.3	176	gGc/gTc	2/10	0.373633494088633	3	FACETS	1	0.988	1	0.562	0.533	0.592	CLONAL	1	TRUE	1	0.514277998765002	3		798	1752	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118883	70118883	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	632	629	0	ENST00000245479.2:c.455G>C	p.Arg152Pro	p.R152P	ENST00000245479	NM_000346.3	152	cGg/cCg	2/3	1	2	FACETS	0.867	0.837	0.898	1	0.998	1	CLONAL	2	TRUE	1	0.514277998765002	2		629	1417	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78704391	78704391	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	255	484	0	ENST00000306801.3:c.539A>G	p.Tyr180Cys	p.Y180C	ENST00000306801	NM_020761.2	180	tAt/tGt	5/34	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.514277998765002	2		484	852	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39623724	39623724	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	223	582	3	ENST00000262039.4:c.2131G>T	p.Glu711Ter	p.E711*	ENST00000262039	NM_002647.2	711	Gag/Tag	20/25	1	2	FACETS	0.927	0.863	0.992	0.927	0.863	0.992	CLONAL	1	TRUE	1	0.514277998765002	2		585	936	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600045	10600045	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0009684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	363	334	0	ENST00000171111.5:c.1532-1G>T		p.X511_splice	ENST00000171111	NM_203500.1	511			0.509000911998191	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.514277998765002	2		334	667	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735500	40735500	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1164153820	NA	P-0009684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	271	504	1	ENST00000373198.4:c.3373A>T	p.Asn1125Tyr	p.N1125Y	ENST00000373198	NM_133170.3	1125	Aat/Tat	25/32	0.514277998765002	3	FACETS	1	0.983	1	0.567	0.532	0.604	CLONAL	1	TRUE	1	0.514277998765002	3		505	1168	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101460	27101460	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	290	602	0	ENST00000324856.7:c.4742del	p.His1581ProfsTer31	p.H1581Pfs*31	ENST00000324856	NM_006015.4	1581	cAc/cc	18/20	1	2	FACETS	0.972	0.914	1	0.972	0.914	1	CLONAL	1	TRUE	1	0.514277998765002	2		602	1160	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1329443726	NA	P-0009684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	102	214	0	ENST00000304494.5:c.262del	p.Glu88ArgfsTer58	p.E88Rfs*58	ENST00000304494	NM_000077.4	88	Gag/ag	2/3	0.514277998765002	1	FACETS	0.915	0.828	1	0.915	0.828	1	CLONAL	1	TRUE	0	0.514277998765002	1		214	322	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0009700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	394	328	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.597371305347118	4	FACETS	0.921	0.883	0.959	0.921	0.883	0.959	CLONAL	3	TRUE	1	0.6253142634819	4		328	741	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0009700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	536	584	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.620891410649047	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.6253142634819	2		585	800	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279214	142279214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371017404	NA	P-0009700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	75	942	2	ENST00000350721.4:c.1432G>A	p.Glu478Lys	p.E478K	ENST00000350721	NM_001184.3	478	Gaa/Aaa	6/47	0.597371305347118	4	FACETS	0.359	0.313	0.409	0.12	0.104	0.137	SUBCLONAL	1	TRUE	1	0.6253142634819	4		944	1086	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042434	16042434	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1568277803	NA	P-0009700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	218	1050	2	ENST00000268712.3:c.1240C>T	p.Arg414Ter	p.R414*	ENST00000268712	NM_006311.3	414	Cga/Tga	12/46	NA	2	FACETS	0.922	0.861	0.986			1	INDETERMINATE	1	TRUE	NA	0.6253142634819	2		1052	756	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851653	63851653	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	165	790	0	ENST00000279873.7:c.2431G>C	p.Asp811His	p.D811H	ENST00000279873	NM_032199.2	811	Gat/Cat	10/10	0.6253142634819	2	FACETS	0.901	0.831	0.972	0.45	0.415	0.486	CLONAL	1	TRUE	0	0.6253142634819	2		790	586	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782901	66782901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371140798	NA	P-0009700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	124	823	0	ENST00000307102.5:c.1130C>T	p.Ser377Phe	p.S377F	ENST00000307102	NM_002755.3	377	tCc/tTc	11/11	0.6253142634819	3	FACETS	0.717	0.649	0.788	0.359	0.324	0.394	SUBCLONAL	1	TRUE	1	0.6253142634819	3		823	726	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641767	23641767	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786203747	NA	P-0009700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	130	516	0	ENST00000261584.4:c.1708G>C	p.Glu570Gln	p.E570Q	ENST00000261584	NM_024675.3	570	Gag/Cag	5/13	0.535793157292721	5	FACETS	0.959	0.87	1	0.32	0.29	0.351	CLONAL	1	TRUE	2	0.6253142634819	5		516	840	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346798	89346798	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0009700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	104	479	0	ENST00000301030.4:c.6152C>G	p.Ser2051Ter	p.S2051*	ENST00000301030	NM_001256183.1	2051	tCa/tGa	9/13	0.535793157292721	5	FACETS	1	0.9	1	0.335	0.3	0.372	CLONAL	1	TRUE	2	0.6253142634819	5		479	642	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349940	15349940	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	80	866	0	ENST00000263377.2:c.3712G>A	p.Glu1238Lys	p.E1238K	ENST00000263377	NM_058243.2	1238	Gag/Aag	18/20	0.6253142634819	3	FACETS	0.421	0.37	0.476	0.21	0.185	0.238	SUBCLONAL	1	TRUE	1	0.6253142634819	3		866	798	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949065	151949065	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0009700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	191	891	0	ENST00000262189.6:c.1580T>G	p.Leu527Ter	p.L527*	ENST00000262189	NM_170606.2	527	tTa/tGa	11/59	1	2	FACETS	0.853	0.791	0.917	0.853	0.791	0.917	CLONAL	1	TRUE	1	0.6253142634819	2		891	716	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0009826-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	327	742	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.422477452678869	2	FACETS	0.972	0.924	1	0.972	0.924	1	CLONAL	2	TRUE	0	0.422477452678869	2		742	796	SUCCESS
APC	324	MSKCC	GRCh37	5	112175223	112175223	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009826-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	104	361	0	ENST00000257430.4:c.3933del	p.Ile1311MetfsTer10	p.I1311Mfs*10	ENST00000257430	NM_000038.5	1311	aTt/at	16/16	0.422477452678869	2	FACETS	0.861	0.782	0.941	0.861	0.782	0.941	CLONAL	2	TRUE	0	0.422477452678869	2		361	286	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426736	49426771	+	inframe_deletion	In_Frame_Del	DEL	GCTGCTGCTGCTGCTGAAGTTGCTGTTGCTGTTGCA	GCTGCTGCTGCTGCTGAAGTTGCTGTTGCTGTTGCA	-	rs1415174573	NA	P-0009826-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	46	472	0	ENST00000301067.7:c.11717_11752del	p.Leu3906_Gln3917del	p.L3906_Q3917del	ENST00000301067	NM_003482.3	3906	cTGCAACAGCAACAGCAACTTCAGCAGCAGCAGCAGCag/cag	39/54	0.422477452678869	3	FACETS	0.646	0.545	0.758	0.323	0.272	0.379	SUBCLONAL	1	TRUE	1	0.422477452678869	3		472	408	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86686656	86686656	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009826-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	31	680	0	ENST00000274376.6:c.3100C>T	p.Gln1034Ter	p.Q1034*	ENST00000274376	NM_002890.2	1034	Caa/Taa	25/25	0.422477452678869	2	FACETS	0.304	0.245	0.37	0.152	0.122	0.185	SUBCLONAL	1	TRUE	0	0.422477452678869	2		680	483	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0009964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	136	328	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.0953780140327125	3	FACETS	0.847	0.77	0.927	0.847	0.77	0.927	INDETERMINATE	2	TRUE	1	0.208684182272321	3		328	850	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0009964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	62	314	0	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	0.0953780140327125	3	FACETS	0.733	0.632	0.844	0.367	0.316	0.422	INDETERMINATE	1	TRUE	1	0.208684182272321	3		314	895	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0009964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	174	417	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.977	0.901	1	1	0.992	1	CLONAL	2	TRUE	1	0.208684182272321	2		418	853	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015368	176015368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749542797	NA	P-0009964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	169	427	0	ENST00000367669.3:c.1370C>T	p.Ala457Val	p.A457V	ENST00000367669	NM_022457.5	457	gCa/gTa	12/20	1	2	FACETS	0.907	0.834	0.983	1	0.991	1	CLONAL	2	TRUE	1	0.208684182272321	2		427	893	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082449	16082449	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	100	329	0	ENST00000281043.3:c.263G>T	p.Trp88Leu	p.W88L	ENST00000281043	NM_005378.4	88	tGg/tTg	2/3	1	2	FACETS	1	0.928	1	1	0.988	1	CLONAL	2	TRUE	1	0.208684182272321	2		329	460	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966882	25966882	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	166	451	0	ENST00000435504.4:c.2324A>G	p.Gln775Arg	p.Q775R	ENST00000435504		775	cAa/cGa	13/13	1	2	FACETS	0.9	0.827	0.976	1	0.991	1	CLONAL	2	TRUE	1	0.208684182272321	2		451	884	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30730005	30730005	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0009964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	94	236	0	ENST00000295754.5:c.1524+2T>C		p.X508_splice	ENST00000295754	NM_003242.5	508			0.0963701668457018	4	FACETS	0.992	0.885	1	0.992	0.885	1	INDETERMINATE	2	TRUE	2	0.208684182272321	4		236	549	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205667	128205667	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	124	433	0	ENST00000341105.2:c.208G>A	p.Val70Ile	p.V70I	ENST00000341105	NM_032638.4	70	Gtc/Atc	2/6	0.208684182272321	1	FACETS	0.753	0.682	0.827	1	0.985	1	SUBCLONAL	2	TRUE	0	0.208684182272321	1		433	707	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518263	187518263	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	33	156	0	ENST00000441802.2:c.12431A>G	p.Asn4144Ser	p.N4144S	ENST00000441802	NM_005245.3	4144	aAc/aGc	25/27	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.208684182272321	2		156	272	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670355	30670355	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1381288014	NA	P-0009964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	255	566	0	ENST00000376406.3:c.6077T>C	p.Leu2026Pro	p.L2026P	ENST00000376406	NM_014641.2	2026	cTa/cCa	14/15	0.199820317548893	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	2	0.208684182272321	4		566	1390	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519568	137519568	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	203	497	0	ENST00000367739.4:c.1070C>T	p.Thr357Ile	p.T357I	ENST00000367739	NM_000416.2	357	aCt/aTt	7/7	0.208684182272321	6	FACETS	1	0.981	1			1	CLONAL	2	TRUE	NA	0.208684182272321	6		497	1178	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729888	41729888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1043609570	NA	P-0009964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	161	735	1	ENST00000242208.4:c.641G>A	p.Arg214Gln	p.R214Q	ENST00000242208	NM_002192.2	214	cGg/cAg	3/3	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.208684182272321	2		736	1053	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456636	32456636	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	32	69	0	ENST00000332351.3:c.256C>A	p.Leu86Met	p.L86M	ENST00000332351	NM_024426.4	86	Ctg/Atg	1/10	0.208684182272321	1	FACETS	1	0.839	1	1	0.963	1	CLONAL	2	TRUE	0	0.208684182272321	1		69	135	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456737	32456737	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	63	239	0	ENST00000332351.3:c.155G>A	p.Arg52His	p.R52H	ENST00000332351	NM_024426.4	52	cGt/cAt	1/10	0.208684182272321	1	FACETS	0.901	0.786	1	1	0.978	1	CLONAL	2	TRUE	0	0.208684182272321	1		239	300	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343913	118343913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264831726	NA	P-0009964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	171	360	1	ENST00000534358.1:c.2039C>T	p.Ser680Leu	p.S680L	ENST00000534358	NM_005933.3	680	tCg/tTg	3/36	0.0953780140327125	3	FACETS	0.977	0.899	1	0.977	0.899	1	INDETERMINATE	2	TRUE	1	0.208684182272321	3		361	926	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438528	49438528	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	131	389	0	ENST00000301067.7:c.4962A>C	p.Glu1654Asp	p.E1654D	ENST00000301067	NM_003482.3	1654	gaA/gaC	19/54	0.208684182272321	6	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.208684182272321	6		389	1290	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437073	121437073	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	71	390	0	ENST00000257555.6:c.1504C>A	p.Leu502Ile	p.L502I	ENST00000257555		502	Ctc/Atc	8/10	0.208684182272321	4	FACETS	0.822	0.715	0.937	0.274	0.238	0.313	CLONAL	1	TRUE	1	0.208684182272321	4		390	1001	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041174	29041174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	199	509	0	ENST00000282397.4:c.254G>A	p.Gly85Asp	p.G85D	ENST00000282397	NM_002019.4	85	gGc/gAc	3/30	0.109750577312643	4	FACETS	0.86	0.795	0.928			1	INDETERMINATE	2	TRUE	NA	0.208684182272321	4		509	1340	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052629	42052629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1312	335	717	2	ENST00000219905.7:c.7300C>T	p.Arg2434Trp	p.R2434W	ENST00000219905	NM_001164273.1	2434	Cgg/Tgg	20/24	0.0953780140327125	3	FACETS	1	0.979	1	1	0.979	1	INDETERMINATE	2	TRUE	1	0.208684182272321	3		719	1647	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953118	81953118	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	185	675	1	ENST00000359376.3:c.2084T>C	p.Ile695Thr	p.I695T	ENST00000359376	NM_002661.3	695	aTc/aCc	20/33	0.179517294990601	0	FACETS	1	0.985	1			1	CLONAL	1	TRUE	0	0.208684182272321	0		676	1093	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434959	56434959	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	205	541	0	ENST00000407977.2:c.2178G>A	p.Trp726Ter	p.W726*	ENST00000407977		726	tgG/tgA	9/10	1	2	FACETS	0.945	0.877	1	1	0.993	1	CLONAL	2	TRUE	1	0.208684182272321	2		541	1039	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436149	56436149	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	218	564	0	ENST00000407977.2:c.988C>T	p.Arg330Ter	p.R330*	ENST00000407977		330	Cga/Tga	9/10	1	2	FACETS	0.883	0.82	0.948	1	0.993	1	CLONAL	2	TRUE	1	0.208684182272321	2		564	1183	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519896	66519896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	179	433	1	ENST00000358598.2:c.379G>A	p.Ala127Thr	p.A127T	ENST00000358598	NM_212471.2	127	Gct/Act	4/11	1	2	FACETS	0.842	0.775	0.911	1	0.991	1	CLONAL	2	TRUE	1	0.208684182272321	2		434	1019	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796615	42796615	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	73	252	0	ENST00000575354.2:c.3172T>C	p.Ser1058Pro	p.S1058P	ENST00000575354	NM_015125.3	1058	Tca/Cca	13/20	1	2	FACETS	0.791	0.695	0.895	1	0.977	1	SUBCLONAL	2	TRUE	1	0.208684182272321	2		252	442	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730876	40730876	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372862828	NA	P-0009964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	96	345	1	ENST00000373198.4:c.3659G>A	p.Arg1220Gln	p.R1220Q	ENST00000373198	NM_133170.3	1220	cGg/cAg	27/32	0.208684182272321	0	FACETS	0.664	0.593	0.739			1	SUBCLONAL	2	TRUE	0	0.208684182272321	0		346	548	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874013	151874013	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1248944002	NA	P-0009964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	232	573	0	ENST00000262189.6:c.8525del	p.Asn2842MetfsTer21	p.N2842Mfs*21	ENST00000262189	NM_170606.2	2842	aAt/at	38/59	1	2	FACETS	0.854	0.795	0.915	1	0.993	1	CLONAL	2	TRUE	1	0.208684182272321	2		573	1302	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412308	139412308	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	176	421	0	ENST00000277541.6:c.1337del	p.Gly446AlafsTer185	p.G446Afs*185	ENST00000277541	NM_017617.3	446	gGc/gc	8/34	1	2	FACETS	0.927	0.854	1	1	0.992	1	CLONAL	2	TRUE	1	0.208684182272321	2		421	910	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286237	66286238	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0009964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	169	537	0	ENST00000273854.3:c.1448dup	p.Asn483LysfsTer21	p.N483Kfs*21	ENST00000273854	NM_004439.5	483	aac/aaAc	6/18	0.179517294990601	0	FACETS	1	0.983	1			1	CLONAL	1	TRUE	0	0.208684182272321	0		537	1022	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99439989	99439989	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	126	325	0	ENST00000268035.6:c.957del	p.Met319IlefsTer66	p.M319Ifs*66	ENST00000268035	NM_000875.3	319	atG/at	4/21	0.208684182272321	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.208684182272321	1		325	761	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	56	276	3	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.208684182272321	2		279	402	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345769	152345769	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs759063323	NA	P-0009964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	205	474	0	ENST00000359321.1:c.801del	p.Lys267AsnfsTer30	p.K267Nfs*30	ENST00000359321	NM_005431.1	267	aaA/aa	3/3	1	2	FACETS	0.865	0.801	0.931	1	0.992	1	CLONAL	2	TRUE	1	0.208684182272321	2		474	1136	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910372	29910372	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs41548119	NA	P-0009964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	62	429	0	ENST00000376809.5:c.46del	p.Ala16ProfsTer4	p.A16Pfs*4	ENST00000376809	NM_002116.7	14	tcG/tc	1/8	0.199820317548893	4	FACETS	0.801	0.69	0.922	0.4	0.345	0.461	CLONAL	1	TRUE	2	0.208684182272321	4		429	897	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687471	37687472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs760014508	NA	P-0009964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	43	240	0	ENST00000447079.4:c.4382dup	p.Thr1463AsnfsTer50	p.T1463Nfs*50	ENST00000447079	NM_015083.1	1459	tgg/tGgg	14/14	0.109750577312643	4	FACETS	0.801	0.669	0.947			1	INDETERMINATE	1	TRUE	NA	0.208684182272321	4		240	622	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151825	108151825	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	160	331	0	ENST00000278616.4:c.3510del	p.Lys1170AsnfsTer11	p.K1170Nfs*11	ENST00000278616	NM_000051.3	1169	gAa/ga	24/63	0.0953780140327125	3	FACETS	0.918	0.842	0.998	0.918	0.842	0.998	INDETERMINATE	2	TRUE	1	0.208684182272321	3		331	922	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0010201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	792	667	2	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.425265901602318	4	FACETS	0.964	0.934	0.993			1	CLONAL	3	TRUE	NA	0.481547295914833	4		669	1686	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878749	151878749	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1211949081	NA	P-0010201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	191	373	0	ENST00000262189.6:c.6196C>T	p.Arg2066Ter	p.R2066*	ENST00000262189	NM_170606.2	2066	Cga/Tga	36/59	1	2	FACETS	0.967	0.896	1	0.967	0.896	1	CLONAL	1	TRUE	1	0.481547295914833	2		373	820	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049724	16049724	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	469	857	0	ENST00000268712.3:c.1048C>T	p.Arg350Ter	p.R350*	ENST00000268712	NM_006311.3	350	Cga/Tga	10/46	0.478861431674781	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.481547295914833	1		857	1369	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164812	36164813	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0010201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	204	454	0	ENST00000300305.3:c.1062dup	p.Tyr355LeufsTer245	p.Y355Lfs*245	ENST00000300305		354	-/C	8/8	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.481547295914833	2		454	822	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120634	115120643	+	frameshift_variant	Frame_Shift_Del	DEL	GACCATCTCG	GACCATCTCG	-	novel	NA	P-0010201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	261	652	1	ENST00000257566.3:c.363_372del	p.Glu122LeufsTer14	p.E122Lfs*14	ENST00000257566	NM_016569.3	121	acCGAGATGGTC/ac	1/8	1	2	FACETS	0.862	0.806	0.919	0.862	0.806	0.919	CLONAL	1	TRUE	1	0.481547295914833	2		653	1258	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835728	68835729	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACAC	novel	NA	P-0010201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	266	538	0	ENST00000261769.5:c.322_323insCACA	p.Arg108ThrfsTer61	p.R108Tfs*61	ENST00000261769	NM_004360.3	107	tac/tACACac	3/16	0.46886693181997	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.481547295914833	1		538	784	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0010235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	163	328	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.570775939690301	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	1	0.570775939690301	4		328	268	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971107	21971107	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	52	194	0	ENST00000304494.5:c.251A>G	p.Asp84Gly	p.D84G	ENST00000304494	NM_000077.4	84	gAc/gGc	2/3	0.534914534126586	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	2	TRUE	0	0.570775939690301	2		194	86	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545060	41545060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	52	490	4	ENST00000263253.7:c.2260C>T	p.Arg754Cys	p.R754C	ENST00000263253	NM_001429.3	754	Cgt/Tgt	13/31	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.570775939690301	2		494	176	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190603	11190603	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	36	434	0	ENST00000361445.4:c.5596C>T	p.Gln1866Ter	p.Q1866*	ENST00000361445	NM_004958.3	1866	Cag/Tag	39/58	0.160226018541877	0	FACETS	0.433	0.363	0.508			1	INDETERMINATE	1	TRUE	0	0.570775939690301	0		434	125	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050349	176050349	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	12	539	2	ENST00000367669.3:c.1216C>T	p.Arg406Ter	p.R406*	ENST00000367669	NM_022457.5	406	Cga/Tga	11/20	0.570775939690301	3	FACETS	0.235	0.165	0.321	0.117	0.082	0.161	SUBCLONAL	1	TRUE	1	0.570775939690301	3		541	230	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185013	32185013	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	22	548	0	ENST00000375023.3:c.1655T>C	p.Ile552Thr	p.I552T	ENST00000375023	NM_004557.3	552	aTc/aCc	10/30	0.173896934471063	6	FACETS	0.86	0.67	1			1	INDETERMINATE	1	TRUE	NA	0.570775939690301	6		548	192	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710744	117710744	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1375443218	NA	P-0010235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	29	465	0	ENST00000368508.3:c.1528C>T	p.Leu510Phe	p.L510F	ENST00000368508	NM_002944.2	510	Ctt/Ttt	12/43	0.509894015818149	1	FACETS	0.554	0.452	0.666	0.554	0.452	0.666	SUBCLONAL	1	TRUE	0	0.570775939690301	1		465	131	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043624	6043624	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	13	238	0	ENST00000265849.7:c.229G>T	p.Glu77Ter	p.E77*	ENST00000265849	NM_000535.5	77	Gaa/Taa	3/15	0.552792407130481	3	FACETS	0.623	0.45	0.828	0.311	0.225	0.414	SUBCLONAL	1	TRUE	1	0.570775939690301	3		238	94	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578196	7578197	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0010235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	83	588	0	ENST00000269305.4:c.651_652dup	p.Val218GlyfsTer30	p.V218Gfs*30	ENST00000269305	NM_001126112.2	218	gtg/gGGtg	6/11	0.534914534126586	2	FACETS	0.817	0.74	0.895	0.817	0.74	0.895	CLONAL	2	TRUE	0	0.570775939690301	2		588	178	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0010369-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	99	303	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.255828844716111	3	FACETS	0.892	0.81	0.975	1	0.981	1	CLONAL	3	TRUE	1	0.345901123228676	3		304	251	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0010369-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	352	447	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.345901123228676	9	FACETS	1	0.983	1			1	CLONAL	11	TRUE	NA	0.345901123228676	9		447	405	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918898	76918899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010369-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	279	595	0	ENST00000373344.5:c.4092dup	p.Glu1365ArgfsTer13	p.E1365Rfs*13	ENST00000373344	NM_000489.3	1364	-/A	12/35	1	1	FACETS	0.909	0.876	0.94	1	0.997	1	CLONAL	4	TRUE	0	0.345901123228676	1		595	367	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519996	NA	P-0010391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	197	301	0	ENST00000269305.4:c.395A>T	p.Lys132Met	p.K132M	ENST00000269305	NM_001126112.2	132	aAg/aTg	5/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.330710699222164	2		301	871	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813031	76813031	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	83	697	0	ENST00000373344.5:c.6590G>A	p.Arg2197His	p.R2197H	ENST00000373344	NM_000489.3	2197	cGt/cAt	30/35	0.284683128559921	0	FACETS	0.783	0.694	0.877			1	SUBCLONAL	1	TRUE	0	0.330710699222164	0		697	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577586	7577587	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGTGGTACAGTCAG	novel	NA	P-0010391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	106	338	0	ENST00000269305.4:c.680_694dup	p.Thr231_Ile232insThrAspCysThrThr	p.T231_I232insTDCTT	ENST00000269305	NM_001126112.2	232	atc/aCTGACTGTACCACCAtc	7/11	1	2	FACETS	0.806	0.723	0.895	0.806	0.723	0.895	CLONAL	1	TRUE	1	0.330710699222164	2		338	795	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807565	1807567	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs778027676	NA	P-0010391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	240	504	0	ENST00000260795.2:c.1735_1737del	p.Phe579del	p.F579del	ENST00000260795		578	tcCTTc/tcc	12/17	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.330710699222164	2		504	1221	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0010406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	223	686	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.383336600007832	1	FACETS	0.91	0.848	0.974	0.91	0.848	0.974	CLONAL	1	TRUE	0	0.425869748128317	1		686	906	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131327	17131327	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	218	656	0	ENST00000285071.4:c.125G>T	p.Gly42Val	p.G42V	ENST00000285071	NM_144997.5	42	gGt/gTt	4/14	0.383336600007832	1	FACETS	0.932	0.868	0.997	0.932	0.868	0.997	CLONAL	1	TRUE	0	0.425869748128317	1		656	865	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41219661	41219661	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	367	588	2	ENST00000357654.3:c.5038A>G	p.Ile1680Val	p.I1680V	ENST00000357654	NM_007294.3	1680	Att/Gtt	16/23	0.39702582758661	2	FACETS	0.885	0.842	0.928	0.885	0.842	0.928	CLONAL	2	TRUE	0	0.425869748128317	2		590	974	SUCCESS
APC	324	MSKCC	GRCh37	5	112175918	112175919	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAGAATCAAATGAATCCAAGAGAAAGAGGCAG	novel	NA	P-0010406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	27	327	0	ENST00000257430.4:c.4641_4642insTCCAAGAGAAAGAGGCAGAAGAATCAAATGAA	p.Asn1548SerfsTer28	p.N1548Sfs*28	ENST00000257430	NM_000038.5	1543	aaa/aAAGAATCAAATGAATCCAAGAGAAAGAGGCAGaa	16/16	0.383336600007832	1	FACETS	0.26	0.206	0.321	0.26	0.206	0.321	SUBCLONAL	1	TRUE	0	0.425869748128317	1		327	384	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0010453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	104	328	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.573517162541913	3	FACETS	0.836	0.76	0.914	0.836	0.76	0.914	CLONAL	2	TRUE	1	0.573517162541913	3		328	279	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061240	38061240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	63	551	0	ENST00000250448.2:c.749C>T	p.Ser250Phe	p.S250F	ENST00000250448	NM_004496.3	250	tCc/tTc	2/2	1	2	FACETS	0.799	0.698	0.907	0.799	0.698	0.907	CLONAL	1	TRUE	1	0.573517162541913	2		551	275	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115746	8115746	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	106	683	0	ENST00000346208.3:c.1092A>T	p.Arg364Ser	p.R364S	ENST00000346208		364	agA/agT	6/6	NA	2	FACETS	0.913	0.824	1			1	INDETERMINATE	1	TRUE	NA	0.573517162541913	2		683	405	SUCCESS
BLM	641	MSKCC	GRCh37	15	91306287	91306287	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	55	424	0	ENST00000355112.3:c.1974T>G	p.Ile658Met	p.I658M	ENST00000355112	NM_000057.2	658	atT/atG	8/22	1	2	FACETS	0.913	0.792	1	0.913	0.792	1	CLONAL	1	TRUE	1	0.573517162541913	2		424	210	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178492	56178493	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTGTCTCCTG	novel	NA	P-0010453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	108	371	0	ENST00000399503.3:c.3466_3475dup	p.Glu1159AlafsTer4	p.E1159Afs*4	ENST00000399503	NM_005921.1	1155	-/CTGTCTCCTG	14/20	0.573517162541913	3	FACETS	0.853	0.778	0.931	0.853	0.778	0.931	CLONAL	2	TRUE	1	0.573517162541913	3		371	284	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180551	56180555	+	frameshift_variant	Frame_Shift_Del	DEL	GAGAT	GAGAT	-	novel	NA	P-0010453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	38	292	0	ENST00000399503.3:c.3880_3884del	p.Glu1294LysfsTer13	p.E1294Kfs*13	ENST00000399503	NM_005921.1	1294	GAGATa/a	16/20	0.573517162541913	3	FACETS	0.661	0.55	0.784	0.33	0.275	0.392	SUBCLONAL	1	TRUE	1	0.573517162541913	3		292	258	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061268	38061269	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTTGCCCGG	novel	NA	P-0010453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	80	615	0	ENST00000250448.2:c.712_720dup	p.Pro238_Lys240dup	p.P238_K240dup	ENST00000250448	NM_004496.3	238	-/CCGGGCAAG	2/2	1	2	FACETS	0.903	0.803	1	0.903	0.803	1	CLONAL	1	TRUE	1	0.573517162541913	2		615	309	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1213	253	692	4	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.27165004305601	2		696	1466	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	107	229	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.27165004305601	2		229	529	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589582	67589582	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	122	198	0	ENST00000274335.5:c.1345T>A	p.Leu449Ile	p.L449I	ENST00000274335		449	Tta/Ata	10/15	0.167301532796387	3	FACETS	1	0.921	1	1	0.921	1	CLONAL	2	TRUE	1	0.27165004305601	3		198	503	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	206	345	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.27165004305601	2		345	1168	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	159	304	3	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.27165004305601	2		307	844	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	146	355	0	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.765	0.699	0.833	1	0.988	1	SUBCLONAL	2	TRUE	1	0.27165004305601	2		355	703	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434070	121434070	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766770471	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	267	541	5	ENST00000257555.6:c.961C>T	p.Arg321Cys	p.R321C	ENST00000257555		321	Cgc/Tgc	5/10	1	2	FACETS	0.855	0.802	0.911	1	0.994	1	CLONAL	2	TRUE	1	0.27165004305601	2		546	1149	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	272	397	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.27165004305601	2		397	1339	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639995	93639995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	161	348	0	ENST00000375746.1:c.1324G>A	p.Glu442Lys	p.E442K	ENST00000375746	NM_001174167.1	442	Gag/Aag	10/14	1	2	FACETS	0.781	0.717	0.847	1	0.989	1	SUBCLONAL	2	TRUE	1	0.27165004305601	2		348	759	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533905	63533905	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	165	277	0	ENST00000307078.5:c.1249del	p.Ala417ArgfsTer41	p.A417Rfs*41	ENST00000307078	NM_004655.3	417	Gcg/cg	6/11	1	2	FACETS	0.899	0.828	0.972	1	0.991	1	CLONAL	2	TRUE	1	0.27165004305601	2		277	676	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875627	35875627	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369971728	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	150	311	0	ENST00000303115.3:c.814G>A	p.Val272Ile	p.V272I	ENST00000303115	NM_002185.3	272	Gta/Ata	7/8	0.167301532796387	3	FACETS	0.901	0.826	0.98	0.901	0.826	0.98	CLONAL	2	TRUE	1	0.27165004305601	3		311	696	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440904	56440904	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1458799446	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	287	526	0	ENST00000407977.2:c.433C>T	p.Arg145Ter	p.R145*	ENST00000407977		145	Cga/Tga	4/10	1	2	FACETS	0.824	0.774	0.876	1	0.994	1	CLONAL	2	TRUE	1	0.27165004305601	2		526	1282	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	16	167	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	0.284	0.209	0.374	0.284	0.209	0.374	SUBCLONAL	1	TRUE	1	0.27165004305601	2		167	415	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799098	42799098	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	147	365	0	ENST00000575354.2:c.4586del	p.Pro1529LeufsTer91	p.P1529Lfs*91	ENST00000575354	NM_015125.3	1528	Ccc/cc	20/20	1	2	FACETS	0.756	0.691	0.823	1	0.988	1	SUBCLONAL	2	TRUE	1	0.27165004305601	2		365	716	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119781	70119781	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1274036689	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	248	596	0	ENST00000245479.2:c.788del	p.Gly263AlafsTer16	p.G263Afs*16	ENST00000245479	NM_000346.3	261	gaG/ga	3/3	1	2	FACETS	0.888	0.831	0.947	1	0.994	1	CLONAL	2	TRUE	1	0.27165004305601	2		596	1028	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272337	15272337	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs771517374	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	129	281	2	ENST00000263388.2:c.6102del	p.Gly2035ValfsTer50	p.G2035Vfs*50	ENST00000263388	NM_000435.2	2034	ccC/cc	33/33	1	2	FACETS	0.879	0.801	0.961	1	0.989	1	CLONAL	2	TRUE	1	0.27165004305601	2		283	540	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588981	67588981	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	152	232	0	ENST00000274335.5:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000274335		358	Cga/Tga	8/15	0.167301532796387	3	FACETS	0.791	0.724	0.861	0.791	0.724	0.861	SUBCLONAL	2	TRUE	1	0.27165004305601	3		232	803	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679546	86679546	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554050230	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	109	177	0	ENST00000274376.6:c.2707C>T	p.Arg903Ter	p.R903*	ENST00000274376	NM_002890.2	903	Cga/Tga	21/25	0.167301532796387	3	FACETS	1	0.981	1	0.715	0.644	0.791	CLONAL	1	TRUE	1	0.27165004305601	3		177	637	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117594	70117594	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	203	424	0	ENST00000245479.2:c.66del	p.Ser23AlafsTer38	p.S23Afs*38	ENST00000245479	NM_000346.3	21	gCc/gc	1/3	1	2	FACETS	0.868	0.806	0.932	1	0.993	1	CLONAL	2	TRUE	1	0.27165004305601	2		424	861	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703538	47703538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63749932	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	216	476	2	ENST00000233146.2:c.2038C>T	p.Arg680Ter	p.R680*	ENST00000233146	NM_000251.2	680	Cga/Tga	13/16	0.27165004305601	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.27165004305601	1		478	982	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513012	106513012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758968659	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	117	302	0	ENST00000359195.3:c.2026G>A	p.Ala676Thr	p.A676T	ENST00000359195	NM_002649.2	676	Gcc/Acc	3/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.27165004305601	2		302	802	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210737	2210737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	190	532	1	ENST00000398665.3:c.1234G>A	p.Gly412Arg	p.G412R	ENST00000398665	NM_032482.2	412	Ggg/Agg	14/28	0.271691411919437	2	FACETS	1	0.988	1	0.673	0.622	0.727	CLONAL	1	TRUE	0	0.27165004305601	2		533	1039	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099103	27099103	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	161	359	0	ENST00000324856.7:c.3524del	p.Pro1175HisfsTer5	p.P1175Hfs*5	ENST00000324856	NM_006015.4	1173	atC/at	13/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.27165004305601	2		359	843	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372205	55372205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs904970570	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	49	131	0	ENST00000297316.4:c.895G>A	p.Ala299Thr	p.A299T	ENST00000297316	NM_022454.3	299	Gcg/Acg	2/2	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.27165004305601	2		131	296	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262680	16262680	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	115	254	0	ENST00000375759.3:c.9950del	p.Pro3317ArgfsTer83	p.P3317Rfs*83	ENST00000375759	NM_015001.2	3315	caC/ca	11/15	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.27165004305601	2		254	568	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435815	56435815	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755967475	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	122	218	0	ENST00000407977.2:c.1322del	p.Pro441LeufsTer61	p.P441Lfs*61	ENST00000407977		441	cCt/ct	9/10	1	2	FACETS	0.913	0.83	0.999	1	0.989	1	CLONAL	2	TRUE	1	0.27165004305601	2		218	492	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119910	70119910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1297203260	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	201	379	0	ENST00000245479.2:c.916del	p.Val306CysfsTer77	p.V306Cfs*77	ENST00000245479	NM_000346.3	304	ccG/cc	3/3	1	2	FACETS	0.846	0.785	0.909	1	0.992	1	CLONAL	2	TRUE	1	0.27165004305601	2		379	875	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822586	72822586	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	271	649	6	ENST00000268489.5:c.9589del	p.Gln3197SerfsTer44	p.Q3197Sfs*44	ENST00000268489	NM_006885.3	3197	Cag/ag	10/10	0.27165004305601	1	FACETS	0.755	0.708	0.803	1	0.993	1	SUBCLONAL	2	TRUE	0	0.27165004305601	1		655	1142	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745962	745963	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	94	276	0	ENST00000314574.4:c.559_560del	p.Ser187Ter	p.S187*	ENST00000314574	NM_005433.3	187	AGt/t	5/12	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.27165004305601	2		276	555	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11168304	11168304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1255967230	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	177	405	0	ENST00000361445.4:c.7568C>T	p.Thr2523Met	p.T2523M	ENST00000361445	NM_004958.3	2523	aCg/aTg	57/58	1	2	FACETS	0.794	0.732	0.857	1	0.99	1	SUBCLONAL	2	TRUE	1	0.27165004305601	2		405	821	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658344	206658344	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139758641	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	128	268	0	ENST00000367120.3:c.1438G>A	p.Val480Met	p.V480M	ENST00000367120	NM_014002.3	480	Gtg/Atg	14/22	1	2	FACETS	0.772	0.702	0.846	1	0.986	1	SUBCLONAL	2	TRUE	1	0.27165004305601	2		268	610	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680522	241680522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778578307	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	329	411	0	ENST00000366560.3:c.227C>T	p.Thr76Met	p.T76M	ENST00000366560	NM_000143.3	76	aCg/aTg	2/10	1	2	FACETS	0.965	0.911	1	1	0.996	1	CLONAL	2	TRUE	1	0.27165004305601	2		411	1255	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657020	47657020	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63751108	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	268	438	0	ENST00000233146.2:c.1216C>T	p.Arg406Ter	p.R406*	ENST00000233146	NM_000251.2	406	Cga/Tga	7/16	0.27165004305601	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.27165004305601	1		438	1236	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275192	41275192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	146	324	0	ENST00000349496.5:c.1358G>A	p.Arg453Gln	p.R453Q	ENST00000349496	NM_001904.3	453	cGg/cAg	9/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.27165004305601	2		324	718	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436344	52436344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765539314	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	223	490	0	ENST00000460680.1:c.2150G>A	p.Arg717Gln	p.R717Q	ENST00000460680	NM_004656.3	717	cGg/cAg	17/17	1	2	FACETS	0.772	0.719	0.828	1	0.992	1	SUBCLONAL	2	TRUE	1	0.27165004305601	2		490	1063	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008432	70008432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1195515853	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	80	167	0	ENST00000394351.3:c.719G>A	p.Arg240His	p.R240H	ENST00000394351	NM_000248.3	240	cGc/cAc	8/9	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.27165004305601	2		167	417	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247487	71247487	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	195	410	0	ENST00000318789.4:c.46A>C	p.Ile16Leu	p.I16L	ENST00000318789	NM_032682.5	16	Atc/Ctc	6/21	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.27165004305601	2		410	1038	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880871	134880871	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	210	451	0	ENST00000398015.3:c.1434G>T	p.Glu478Asp	p.E478D	ENST00000398015	NM_004441.4	478	gaG/gaT	7/16	1	2	FACETS	0.85	0.789	0.912	1	0.993	1	CLONAL	2	TRUE	1	0.27165004305601	2		451	910	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236606	236606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754893758	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	107	241	0	ENST00000264932.6:c.1324G>A	p.Ala442Thr	p.A442T	ENST00000264932	NM_004168.2	442	Gcc/Acc	10/15	1	2	FACETS	1	0.919	1	1	0.989	1	CLONAL	2	TRUE	1	0.27165004305601	2		241	387	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282640	1282640	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	215	454	0	ENST00000310581.5:c.1673G>T	p.Arg558Met	p.R558M	ENST00000310581	NM_198253.2	558	aGg/aTg	3/16	1	2	FACETS	0.822	0.764	0.881	1	0.992	1	CLONAL	2	TRUE	1	0.27165004305601	2		454	963	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950798	38950798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767497249	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	90	232	0	ENST00000357387.3:c.3152G>A	p.Arg1051Gln	p.R1051Q	ENST00000357387	NM_152756.3	1051	cGg/cAg	31/38	0.167301532796387	3	FACETS	1	0.932	1	0.535	0.475	0.6	CLONAL	1	TRUE	1	0.27165004305601	3		232	703	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953760	131953760	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	96	170	0	ENST00000265335.6:c.3165-2A>G		p.X1055_splice	ENST00000265335		1055			1	2	FACETS	0.93	0.835	1	1	0.986	1	CLONAL	2	TRUE	1	0.27165004305601	2		170	380	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679450	30679450	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	242	432	2	ENST00000376406.3:c.2122C>A	p.Leu708Met	p.L708M	ENST00000376406	NM_014641.2	708	Ctg/Atg	6/15	1	2	FACETS	0.772	0.72	0.825	1	0.993	1	SUBCLONAL	2	TRUE	1	0.27165004305601	2		434	1154	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166817	32166817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751686959	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	124	292	1	ENST00000375023.3:c.4421G>A	p.Arg1474Gln	p.R1474Q	ENST00000375023	NM_004557.3	1474	cGa/cAa	24/30	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.27165004305601	2		293	665	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652073	36652073	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	220	490	1	ENST00000244741.5:c.195G>A	p.Trp65Ter	p.W65*	ENST00000244741	NM_000389.4	65	tgG/tgA	2/3	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.27165004305601	2		491	1185	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748510	43748510	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774265827	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1563	456	806	2	ENST00000523873.1:c.464G>A	p.Arg155His	p.R155H	ENST00000523873		155	cGc/cAc	6/8	1	2	FACETS	0.831	0.791	0.873	1	0.996	1	CLONAL	2	TRUE	1	0.27165004305601	2		808	2019	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157488310	157488310	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	88	231	0	ENST00000346085.5:c.3016A>C	p.Ser1006Arg	p.S1006R	ENST00000346085	NM_020732.3	1006	Agc/Cgc	10/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.27165004305601	2		231	442	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367296	50367296	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1432663785	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	158	282	0	ENST00000331340.3:c.103G>A	p.Glu35Lys	p.E35K	ENST00000331340	NM_006060.4	35	Gag/Aag	3/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.27165004305601	2		282	935	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455073	50455073	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	200	321	0	ENST00000331340.3:c.620G>T	p.Gly207Val	p.G207V	ENST00000331340	NM_006060.4	207	gGc/gTc	6/8	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.27165004305601	2		321	1048	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850377	128850377	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771078092	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	126	285	0	ENST00000249373.3:c.1640G>A	p.Arg547His	p.R547H	ENST00000249373	NM_005631.4	547	cGt/cAt	9/12	1	2	FACETS	0.935	0.852	1	1	0.989	1	CLONAL	2	TRUE	1	0.27165004305601	2		285	496	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845364	151845364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	169	339	0	ENST00000262189.6:c.13648G>A	p.Val4550Met	p.V4550M	ENST00000262189	NM_170606.2	4550	Gtg/Atg	52/59	1	2	FACETS	0.751	0.691	0.814	1	0.989	1	SUBCLONAL	2	TRUE	1	0.27165004305601	2		339	828	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965824	90965824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	84	322	0	ENST00000265433.3:c.1493C>T	p.Pro498Leu	p.P498L	ENST00000265433	NM_002485.4	498	cCc/cTc	11/16	1	2	FACETS	0.622	0.548	0.702	0.622	0.548	0.702	SUBCLONAL	1	TRUE	1	0.27165004305601	2		322	994	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133747523	133747523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	143	342	0	ENST00000318560.5:c.830C>T	p.Thr277Ile	p.T277I	ENST00000318560	NM_005157.4	277	aCc/aTc	5/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.27165004305601	2		342	768	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622146	43622146	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1439440590	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	184	500	0	ENST00000355710.3:c.3163A>G	p.Thr1055Ala	p.T1055A	ENST00000355710	NM_020975.4	1055	Aca/Gca	19/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.27165004305601	2		500	1023	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912166	114912166	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1482	426	911	0	ENST00000543371.1:c.1236A>C	p.Gln412His	p.Q412H	ENST00000543371	NM_001198531.1	412	caA/caC	11/14	0.27165004305601	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.27165004305601	1		911	1908	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202621	67202621	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1271376042	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	165	317	1	ENST00000312629.5:c.1430G>A	p.Arg477His	p.R477H	ENST00000312629	NM_003952.2	477	cGt/cAt	15/15	1	2	FACETS	0.77	0.708	0.834	1	0.989	1	SUBCLONAL	2	TRUE	1	0.27165004305601	2		318	789	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420184	49420184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555185701	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	178	396	1	ENST00000301067.7:c.15565G>A	p.Gly5189Arg	p.G5189R	ENST00000301067	NM_003482.3	5189	Gga/Aga	48/54	1	2	FACETS	0.807	0.745	0.872	1	0.991	1	CLONAL	2	TRUE	1	0.27165004305601	2		397	812	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426817	49426817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886049476	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	126	269	0	ENST00000301067.7:c.11671G>A	p.Ala3891Thr	p.A3891T	ENST00000301067	NM_003482.3	3891	Gct/Act	39/54	1	2	FACETS	0.77	0.7	0.844	1	0.986	1	SUBCLONAL	2	TRUE	1	0.27165004305601	2		269	602	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484085	50484085	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	188	385	1	ENST00000394963.4:c.935G>A	p.Arg312His	p.R312H	ENST00000394963	NM_003076.4	312	cGt/cAt	8/13	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.27165004305601	2		386	978	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219839	133219839	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766511597	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	121	286	0	ENST00000320574.5:c.4522C>T	p.Arg1508Cys	p.R1508C	ENST00000320574	NM_006231.2	1508	Cgc/Tgc	35/49	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.27165004305601	2		286	672	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592606	28592606	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs535289665	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	278	609	0	ENST00000241453.7:c.2539A>G	p.Asn847Asp	p.N847D	ENST00000241453	NM_004119.2	847	Aat/Gat	20/24	1	2	FACETS	0.831	0.78	0.884	1	0.994	1	CLONAL	2	TRUE	1	0.27165004305601	2		609	1231	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105238767	105238767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs188580689	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	209	476	0	ENST00000349310.3:c.1195G>A	p.Ala399Thr	p.A399T	ENST00000349310	NM_001014432.1	399	Gcc/Acc	13/15	1	2	FACETS	0.769	0.714	0.827	1	0.991	1	SUBCLONAL	2	TRUE	1	0.27165004305601	2		476	1000	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457304	67457304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223765	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	205	397	0	ENST00000327367.4:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000327367	NM_005902.3	93	cGa/cAa	2/9	1	2	FACETS	0.75	0.696	0.807	1	0.991	1	SUBCLONAL	2	TRUE	1	0.27165004305601	2		397	1006	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292842	91292842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371100621	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	179	324	0	ENST00000355112.3:c.344C>T	p.Pro115Leu	p.P115L	ENST00000355112	NM_000057.2	115	cCg/cTg	3/22	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.27165004305601	2		324	934	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821324	72821324	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	280	609	0	ENST00000268489.5:c.10851G>A	p.Trp3617Ter	p.W3617*	ENST00000268489	NM_006885.3	3617	tgG/tgA	10/10	0.27165004305601	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.27165004305601	1		609	1405	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822285	72822285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781775682	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1285	406	1071	2	ENST00000268489.5:c.9890C>T	p.Ser3297Leu	p.S3297L	ENST00000268489	NM_006885.3	3297	tCg/tTg	10/10	0.27165004305601	1	FACETS	0.764	0.725	0.804	1	0.995	1	SUBCLONAL	2	TRUE	0	0.27165004305601	1		1073	1691	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832406	72832406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1207124526	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	339	776	0	ENST00000268489.5:c.4175C>T	p.Pro1392Leu	p.P1392L	ENST00000268489	NM_006885.3	1392	cCg/cTg	9/10	0.27165004305601	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.27165004305601	1		776	1473	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348309	89348309	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1749	492	1317	1	ENST00000301030.4:c.4641G>T	p.Lys1547Asn	p.K1547N	ENST00000301030	NM_001256183.1	1547	aaG/aaT	9/13	0.27165004305601	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.27165004305601	1		1318	2241	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979619	7979619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140306846	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	216	419	0	ENST00000319144.4:c.1406G>A	p.Arg469Gln	p.R469Q	ENST00000319144	NM_001139.2	469	cGg/cAg	11/15	1	2	FACETS	0.794	0.738	0.851	1	0.992	1	SUBCLONAL	2	TRUE	1	0.27165004305601	2		419	1002	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973496	15973496	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	203	349	0	ENST00000268712.3:c.4496T>C	p.Met1499Thr	p.M1499T	ENST00000268712	NM_006311.3	1499	aTg/aCg	31/46	1	2	FACETS	0.814	0.755	0.875	1	0.992	1	CLONAL	2	TRUE	1	0.27165004305601	2		349	918	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220394	1220394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	181	567	0	ENST00000326873.7:c.487G>A	p.Gly163Ser	p.G163S	ENST00000326873	NM_000455.4	163	Ggc/Agc	4/10	0.271691411919437	2	FACETS	1	0.984	1	0.635	0.585	0.687	CLONAL	1	TRUE	0	0.27165004305601	2		567	1050	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943427	17943427	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200784656	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	259	589	0	ENST00000458235.1:c.2581G>A	p.Gly861Arg	p.G861R	ENST00000458235	NM_000215.3	861	Ggg/Agg	19/24	1	2	FACETS	0.763	0.713	0.814	1	0.993	1	SUBCLONAL	2	TRUE	1	0.27165004305601	2		589	1250	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917119	50917119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057522945	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	290	892	0	ENST00000440232.2:c.2371C>T	p.Arg791Trp	p.R791W	ENST00000440232	NM_002691.3	791	Cgg/Tgg	19/27	1	2	FACETS	0.784	0.737	0.834	1	0.994	1	SUBCLONAL	2	TRUE	1	0.27165004305601	2		892	1361	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572305	41572305	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	200	409	0	ENST00000263253.7:c.4834A>G	p.Ile1612Val	p.I1612V	ENST00000263253	NM_001429.3	1612	Att/Gtt	30/31	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.27165004305601	2		409	1057	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929133	44929133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	280	534	1	ENST00000377967.4:c.2233G>A	p.Glu745Lys	p.E745K	ENST00000377967	NM_021140.2	745	Gag/Aag	17/29	0.27165004305601	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.27165004305601	1		535	1251	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426104	47426104	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	387	779	0	ENST00000377045.4:c.624G>T	p.Gln208His	p.Q208H	ENST00000377045	NM_001654.4	208	caG/caT	7/16	0.27165004305601	1	FACETS	0.77	0.73	0.812	1	0.995	1	SUBCLONAL	2	TRUE	0	0.27165004305601	1		779	1598	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428265	47428265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	209	538	1	ENST00000377045.4:c.1225G>A	p.Val409Met	p.V409M	ENST00000377045	NM_001654.4	409	Gtg/Atg	11/16	0.27165004305601	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.27165004305601	1		539	940	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347906	70347906	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1285	369	755	0	ENST00000374080.3:c.3145A>G	p.Asn1049Asp	p.N1049D	ENST00000374080		1049	Aac/Gac	22/45	0.27165004305601	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.27165004305601	1		755	1654	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873929	151873929	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	179	406	0	ENST00000262189.6:c.8609del	p.Leu2870CysfsTer36	p.L2870Cfs*36	ENST00000262189	NM_170606.2	2870	tTg/tg	38/59	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.27165004305601	2		406	1023	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231419	98231420	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	65	177	0	ENST00000331920.6:c.1863_1864del	p.Arg621SerfsTer5	p.R621Sfs*5	ENST00000331920	NM_000264.3	621	agAGtg/agtg	14/24	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.27165004305601	2		177	391	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572092	64572093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs767319284	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1270	268	719	0	ENST00000312049.6:c.1546dup	p.Arg516ProfsTer15	p.R516Pfs*15	ENST00000312049	NM_130799.2	516	cgg/cCgg	10/10	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.27165004305601	2		719	1538	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434354	49434354	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	154	359	2	ENST00000301067.7:c.7199del	p.Pro2400LeufsTer26	p.P2400Lfs*26	ENST00000301067	NM_003482.3	2400	cCt/ct	31/54	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.27165004305601	2		361	835	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617679	39617680	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	144	335	0	ENST00000262039.4:c.1869dup	p.Lys624Ter	p.K624*	ENST00000262039	NM_002647.2	621	-/T	17/25	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.27165004305601	2		335	924	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564680	86564680	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	164	380	1	ENST00000274376.6:c.416del	p.Pro139LeufsTer35	p.P139Lfs*35	ENST00000274376	NM_002890.2	138	Ccc/cc	1/25	0.167301532796387	3	FACETS	0.792	0.727	0.859	0.792	0.727	0.859	SUBCLONAL	2	TRUE	1	0.27165004305601	3		381	866	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991625	25991626	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	158	290	0	ENST00000435504.4:c.616_617del	p.Val206ThrfsTer13	p.V206Tfs*13	ENST00000435504		206	GTa/a	7/13	0.27165004305601	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.27165004305601	1		290	845	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643791	52643791	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	197	288	0	ENST00000394830.3:c.2105del	p.Lys702SerfsTer12	p.K702Sfs*12	ENST00000394830	NM_018313.4	702	aAg/ag	17/30	1	2	FACETS	0.825	0.765	0.888	1	0.992	1	CLONAL	2	TRUE	1	0.27165004305601	2		288	879	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0010671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	124	328	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.66	2		328	366	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0010671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	49	134	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.83	0.714	0.952	0.83	0.714	0.952	CLONAL	1	TRUE	1	0.66	2		134	179	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0010671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	110	423	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	0.193444402275803	3	FACETS	1	0.909	1			1	INDETERMINATE	1	TRUE	NA	0.66	3		423	441	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	163	295	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.762	0.702	0.825	0.762	0.702	0.825	SUBCLONAL	1	TRUE	1	0.66	2		295	648	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106936	27106936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	122	195	0	ENST00000324856.7:c.6547C>T	p.Arg2183Cys	p.R2183C	ENST00000324856	NM_006015.4	2183	Cgt/Tgt	20/20	1	2	FACETS	0.838	0.763	0.916	0.838	0.763	0.916	CLONAL	1	TRUE	1	0.66	2		195	441	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956147	175956147	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	161	435	0	ENST00000367669.3:c.2065A>G	p.Lys689Glu	p.K689E	ENST00000367669	NM_022457.5	689	Aaa/Gaa	18/20	1	2	FACETS	0.859	0.792	0.928	0.859	0.792	0.928	CLONAL	1	TRUE	1	0.66	2		435	568	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0010671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	123	280	2	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	0.817	0.744	0.893	0.817	0.744	0.893	CLONAL	1	TRUE	1	0.66	2		282	456	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249160	55249160	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	169	255	2	ENST00000275493.2:c.2458C>T	p.Gln820Ter	p.Q820*	ENST00000275493	NM_005228.3	820	Cag/Tag	20/28	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.66	2		257	497	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287386	38287386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1162148796	NA	P-0010671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	143	201	1	ENST00000425967.3:c.271C>T	p.Arg91Trp	p.R91W	ENST00000425967	NM_001174067.1	91	Cgg/Tgg	4/19	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.66	2		202	421	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683390	88683390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369966011	NA	P-0010671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	92	218	1	ENST00000372037.3:c.1513G>A	p.Ala505Thr	p.A505T	ENST00000372037	NM_004329.2	505	Gcc/Acc	13/13	1	2	FACETS	0.955	0.859	1	0.955	0.859	1	CLONAL	1	TRUE	1	0.66	2		219	292	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685316	89685316	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs878853937	NA	P-0010671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	97	234	0	ENST00000371953.3:c.209+2T>C		p.X70_splice	ENST00000371953	NM_000314.4	70			1	2	FACETS	0.996	0.9	1	0.996	0.9	1	CLONAL	1	TRUE	1	0.66	2		234	295	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112221	115112221	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	104	145	0	ENST00000257566.3:c.1519C>A	p.Leu507Met	p.L507M	ENST00000257566	NM_016569.3	507	Ctg/Atg	7/8	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.66	2		145	313	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457705	67457705	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	223	291	2	ENST00000327367.4:c.515C>A	p.Pro172His	p.P172H	ENST00000327367	NM_005902.3	172	cCc/cAc	3/9	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.66	2		293	611	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678385	88678385	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	395	743	1	ENST00000360948.2:c.1151T>G	p.Leu384Arg	p.L384R	ENST00000360948	NM_001012338.2	384	cTg/cGg	9/19	1	2	FACETS	0.978	0.93	1	0.978	0.93	1	CLONAL	1	TRUE	1	0.66	2		744	1224	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679712	88679712	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	157	308	0	ENST00000360948.2:c.751A>T	p.Ile251Phe	p.I251F	ENST00000360948	NM_001012338.2	251	Atc/Ttc	7/19	1	2	FACETS	0.891	0.821	0.963	0.891	0.821	0.963	CLONAL	1	TRUE	1	0.66	2		308	534	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654642	67654642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	209	373	3	ENST00000264010.4:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000264010	NM_006565.3	377	Cgt/Tgt	6/12	0.193444402275803	3	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.66	3		376	639	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098422	11098422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764188556	NA	P-0010671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	118	155	0	ENST00000358026.2:c.940G>A	p.Ala314Thr	p.A314T	ENST00000358026	NM_001128849.1	314	Gcg/Acg	6/36	0.217389028142389	3	FACETS	1	0.98	1	0.636	0.579	0.694	INDETERMINATE	1	TRUE	1	0.66	3		155	374	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344077	70344077	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	338	850	3	ENST00000374080.3:c.1813C>T	p.Arg605Ter	p.R605*	ENST00000374080		605	Cga/Tga	13/45	0.274736539586146	1	FACETS	0.601	0.568	0.634	0.601	0.568	0.634	INDETERMINATE	1	TRUE	0	0.66	1		853	1142	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088787	27088788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0010671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	170	288	2	ENST00000324856.7:c.2402dup	p.Gln802SerfsTer15	p.Q802Sfs*15	ENST00000324856	NM_006015.4	799	cag/caGg	7/20	1	2	FACETS	0.893	0.826	0.962	0.893	0.826	0.962	CLONAL	1	TRUE	1	0.66	2		290	577	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330629	65330630	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	177	388	0	ENST00000342505.4:c.1016dup	p.Asn339LysfsTer2	p.N339Kfs*2	ENST00000342505	NM_002227.2	339	aat/aaAt	8/25	1	2	FACETS	0.805	0.745	0.868	0.805	0.745	0.868	CLONAL	1	TRUE	1	0.66	2		388	666	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023904	27023904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1232964733	NA	P-0010671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	25	34	0	ENST00000324856.7:c.1015del	p.Ala339LeufsTer24	p.A339Lfs*24	ENST00000324856	NM_006015.4	337	tGg/tg	1/20	1	2	FACETS	0.851	0.688	1	0.851	0.688	1	CLONAL	1	TRUE	1	0.66	2		34	89	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0010671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	172	330	11	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	0.86	0.795	0.927	0.86	0.795	0.927	CLONAL	1	TRUE	1	0.66	2		341	606	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431722	49431722	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555190550	NA	P-0010671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	258	390	0	ENST00000301067.7:c.9417del	p.Lys3140ArgfsTer2	p.K3140Rfs*2	ENST00000301067	NM_003482.3	3139	ccC/cc	34/54	1	2	FACETS	0.914	0.859	0.972	0.914	0.859	0.972	CLONAL	1	TRUE	1	0.66	2		390	855	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281181	15281181	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	83	493	0	ENST00000263388.2:c.5075del	p.Gly1692AlafsTer13	p.G1692Afs*13	ENST00000263388	NM_000435.2	1692	gGc/gc	27/33	1	2	FACETS	0.249	0.219	0.281	0.249	0.219	0.281	SUBCLONAL	1	TRUE	1	0.66	2		493	1011	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923087	39923087	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	340	653	0	ENST00000378444.4:c.3621del	p.Lys1207AsnfsTer31	p.K1207Nfs*31	ENST00000378444	NM_001123385.1	1207	aaA/aa	8/15	1	2	FACETS	0.92	0.871	0.97	0.92	0.871	0.97	CLONAL	1	TRUE	1	0.66	2		653	1120	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	54	151	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.399	0.342	0.462	0.399	0.342	0.462	SUBCLONAL	1	TRUE	1	0.66	2		151	410	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295242	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1361	191	346	0				ENST00000310581	NM_198253.2	-/1132			0.386887403945762	9	FACETS	1	0.99	1	0.25	0.23	0.27	CLONAL	1	TRUE	3	0.386887403945762	9		346	1552	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485115	57485115	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754097818	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1347	204	504	0	ENST00000371085.3:c.949C>T	p.Arg317Cys	p.R317C	ENST00000371085	NM_000516.4	317	Cgc/Tgc	11/13	0.386887403945762	7	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.386887403945762	7		504	1551	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562747	21562747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747638434	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	55	193	0	ENST00000382592.4:c.1172G>A	p.Arg391His	p.R391H	ENST00000382592	NM_014572.2	391	cGc/cAc	4/8	0.316862377960855	3	FACETS	0.64	0.548	0.741			1	SUBCLONAL	1	TRUE	NA	0.386887403945762	3		193	530	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164040	108164040	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1034235291	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	125	242	1	ENST00000278616.4:c.4612G>T	p.Val1538Leu	p.V1538L	ENST00000278616	NM_000051.3	1538	Gta/Tta	31/63	0.269092831690601	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.386887403945762	1		243	425	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17355225	17355225	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	170	400	0	ENST00000375499.3:c.293G>C	p.Cys98Ser	p.C98S	ENST00000375499	NM_003000.2	98	tGt/tCt	4/8	0.386887403945762	3	FACETS	1	0.978	1	0.585	0.538	0.634	CLONAL	1	TRUE	1	0.386887403945762	3		400	896	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474059	29474059	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1204	162	641	1	ENST00000389048.3:c.2116C>T	p.Gln706Ter	p.Q706*	ENST00000389048	NM_004304.4	706	Cag/Tag	12/29	0.386887403945762	3	FACETS	0.732	0.669	0.797	0.366	0.334	0.399	SUBCLONAL	1	TRUE	1	0.386887403945762	3		642	1366	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248607	212248607	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	128	552	0	ENST00000342788.4:c.3660G>T	p.Glu1220Asp	p.E1220D	ENST00000342788	NM_005235.2	1220	gaG/gaT	28/28	0.18200032720578	2	FACETS	0.589	0.532	0.648	0.294	0.266	0.325	INDETERMINATE	1	TRUE	0	0.386887403945762	2		552	1124	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225343003	225343003	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1427	152	993	0	ENST00000264414.4:c.2089G>C	p.Asp697His	p.D697H	ENST00000264414	NM_003590.4	697	Gac/Cac	15/16	0.18200032720578	2	FACETS	0.498	0.453	0.545	0.249	0.226	0.273	INDETERMINATE	1	TRUE	0	0.386887403945762	2		993	1579	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067398	37067398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782273	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	282	486	0	ENST00000231790.2:c.1309C>T	p.Pro437Ser	p.P437S	ENST00000231790	NM_000249.3	437	Cct/Tct	12/19	0.151820800665999	2	FACETS	0.765	0.72	0.811	0.765	0.72	0.811	INDETERMINATE	2	TRUE	0	0.386887403945762	2		486	953	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467695	66467695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	274	482	1	ENST00000273854.3:c.574G>A	p.Val192Ile	p.V192I	ENST00000273854	NM_004439.5	192	Gtt/Att	3/18	0.151820800665999	2	FACETS	0.808	0.76	0.856	0.808	0.76	0.856	INDETERMINATE	2	TRUE	0	0.386887403945762	2		483	877	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244158	153244158	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	173	689	0	ENST00000281708.4:c.1999G>T	p.Gly667Trp	p.G667W	ENST00000281708	NM_033632.3	667	Ggg/Tgg	12/12	0.151820800665999	2	FACETS	0.724	0.665	0.786	0.362	0.332	0.393	INDETERMINATE	1	TRUE	0	0.386887403945762	2		689	1235	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293731	1293731	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1359	192	369	0	ENST00000310581.5:c.1270G>T	p.Gly424Cys	p.G424C	ENST00000310581	NM_198253.2	424	Ggt/Tgt	2/16	0.386887403945762	9	FACETS	0.753	0.694	0.815	0.251	0.231	0.272	SUBCLONAL	2	TRUE	3	0.386887403945762	9		369	1551	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964477	93964477	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	372	803	0	ENST00000369303.4:c.2420C>T	p.Ala807Val	p.A807V	ENST00000369303	NM_004440.3	807	gCc/gTc	14/17	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.386887403945762	2		803	1376	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554918	106554918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs529025464	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	249	476	1	ENST00000369096.4:c.2035C>T	p.Arg679Cys	p.R679C	ENST00000369096	NM_001198.3	679	Cgt/Tgt	7/7	0.307283114953206	4	FACETS	0.789	0.738	0.843			1	SUBCLONAL	2	TRUE	NA	0.386887403945762	4		477	1131	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415582	152415582	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	354	662	0	ENST00000206249.3:c.1432G>A	p.Val478Ile	p.V478I	ENST00000206249	NM_000125.3	478	Gtc/Atc	7/8	0.151820800665999	2	FACETS	1	0.995	1	0.737	0.698	0.777	INDETERMINATE	1	TRUE	0	0.386887403945762	2		662	1241	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968281	2968281	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	651	551	1	ENST00000396946.4:c.1705G>T	p.Gly569Ter	p.G569*	ENST00000396946	NM_032415.4	569	Gga/Tga	13/25	0.386887403945762	5	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	2	0.386887403945762	5		552	1736	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978345	2978345	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	562	552	0	ENST00000396946.4:c.985G>C	p.Glu329Gln	p.E329Q	ENST00000396946	NM_032415.4	329	Gag/Cag	7/25	0.386887403945762	5	FACETS	0.975	0.936	1	0.975	0.936	1	CLONAL	3	TRUE	2	0.386887403945762	5		552	1570	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221846	55221846	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1421	550	765	0	ENST00000275493.2:c.889+1G>T		p.X297_splice	ENST00000275493	NM_005228.3	297			0.38200056362683	5	FACETS	1	0.992	1	0.76	0.727	0.793	CLONAL	2	TRUE	2	0.386887403945762	5		765	1971	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372707	81372707	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	482	636	2	ENST00000222390.5:c.827C>A	p.Pro276His	p.P276H	ENST00000222390	NM_000601.4	276	cCt/cAt	7/18	0.264858690569162	3	FACETS	1	0.994	1	0.808	0.774	0.842	CLONAL	2	TRUE	0	0.386887403945762	3		638	1227	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508596	106508596	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	179	303	0	ENST00000359195.3:c.590C>A	p.Ala197Asp	p.A197D	ENST00000359195	NM_002649.2	197	gCc/gAc	2/11	0.264858690569162	3	FACETS	0.874	0.809	0.94	0.582	0.539	0.627	CLONAL	2	TRUE	0	0.386887403945762	3		303	632	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917629	151917629	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	69	333	0	ENST00000262189.6:c.3691G>T	p.Gly1231Cys	p.G1231C	ENST00000262189	NM_170606.2	1231	Ggt/Tgt	23/59	0.264858690569162	3	FACETS	0.73	0.636	0.832	0.243	0.212	0.278	SUBCLONAL	1	TRUE	0	0.386887403945762	3		333	583	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970994	21970994	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	123	455	0	ENST00000304494.5:c.364G>T	p.Gly122Cys	p.G122C	ENST00000304494	NM_000077.4	122	Ggc/Tgc	2/3	0.154586445565464	3	FACETS	0.86	0.777	0.948	0.43	0.388	0.474	INDETERMINATE	1	TRUE	1	0.386887403945762	3		455	882	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339151	87339151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	108	505	0	ENST00000277120.3:c.733C>T	p.His245Tyr	p.H245Y	ENST00000277120		245	Cac/Tac	8/19	0.154586445565464	3	FACETS	0.749	0.672	0.832	0.375	0.336	0.416	INDETERMINATE	1	TRUE	1	0.386887403945762	3		505	889	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106040	8106040	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	98	393	0	ENST00000346208.3:c.860G>T	p.Cys287Phe	p.C287F	ENST00000346208		287	tGc/tTc	4/6	0.281994243036252	3	FACETS	0.689	0.614	0.77	0.23	0.204	0.257	SUBCLONAL	1	TRUE	0	0.386887403945762	3		393	877	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111517	8111517	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	550	578	0	ENST00000346208.3:c.1003G>T	p.Asp335Tyr	p.D335Y	ENST00000346208		335	Gac/Tac	5/6	0.281994243036252	3	FACETS	0.884	0.85	0.918	0.884	0.85	0.918	CLONAL	3	TRUE	0	0.386887403945762	3		578	1280	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852473	63852473	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1359	313	463	0	ENST00000279873.7:c.3251G>T	p.Gly1084Val	p.G1084V	ENST00000279873	NM_032199.2	1084	gGg/gTg	10/10	0.386887403945762	7	FACETS	0.952	0.895	1			1	CLONAL	2	TRUE	NA	0.386887403945762	7		463	1672	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589785	69589785	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1468828259	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	47	173	1	ENST00000168712.1:c.68G>A	p.Trp23Ter	p.W23*	ENST00000168712	NM_002007.2	23	tGg/tAg	1/3	0.386887403945762	5	FACETS	0.863	0.729	1			1	CLONAL	1	TRUE	NA	0.386887403945762	5		174	445	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180397	94180397	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1862	165	633	0	ENST00000323929.3:c.1771C>G	p.Gln591Glu	p.Q591E	ENST00000323929	NM_005591.3	591	Caa/Gaa	15/20	0.386887403945762	6	FACETS	0.746	0.682	0.814			1	SUBCLONAL	1	TRUE	NA	0.386887403945762	6		633	2027	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145491	58145491	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1197	1308	358	0	ENST00000257904.6:c.10T>C	p.Ser4Pro	p.S4P	ENST00000257904	NM_000075.3	4	Tct/Cct	2/8	0.386887403945762	15	FACETS	1	0.995	1			1	CLONAL	9	TRUE	NA	0.386887403945762	15		358	2505	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73352440	73352440	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	158	628	0	ENST00000377767.4:c.465G>T	p.Trp155Cys	p.W155C	ENST00000377767	NM_014953.3	155	tgG/tgT	3/21	0.292351117849518	1	FACETS	0.742	0.68	0.807	0.742	0.68	0.807	SUBCLONAL	1	TRUE	0	0.386887403945762	1		628	888	SUCCESS
BLM	641	MSKCC	GRCh37	15	91290653	91290653	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	107	596	0	ENST00000355112.3:c.31G>C	p.Glu11Gln	p.E11Q	ENST00000355112	NM_000057.2	11	Gag/Cag	2/22	0.247536479964764	3	FACETS	0.566	0.506	0.63	0.189	0.168	0.21	SUBCLONAL	1	TRUE	0	0.386887403945762	3		596	1167	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831747	72831747	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1281	221	961	0	ENST00000268489.5:c.4834G>C	p.Glu1612Gln	p.E1612Q	ENST00000268489	NM_006885.3	1612	Gag/Cag	9/10	NA	2	FACETS	0.761	0.706	0.818			1	INDETERMINATE	1	TRUE	NA	0.386887403945762	2		961	1502	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682395	37682395	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	103	438	0	ENST00000447079.4:c.3586A>G	p.Thr1196Ala	p.T1196A	ENST00000447079	NM_015083.1	1196	Acc/Gcc	13/14	0.357096279024731	5	FACETS	0.679	0.605	0.757	0.136	0.121	0.152	SUBCLONAL	1	TRUE	0	0.386887403945762	5		438	1240	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985608	60985608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	55	183	0	ENST00000333681.4:c.292C>T	p.Arg98Cys	p.R98C	ENST00000333681		98	Cgc/Tgc	2/3	0.253292944259059	3	FACETS	0.945	0.812	1	0.473	0.406	0.545	CLONAL	1	TRUE	1	0.386887403945762	3		183	359	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219469	5219469	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	380	471	0	ENST00000357368.4:c.3775G>T	p.Ala1259Ser	p.A1259S	ENST00000357368	NM_002850.3	1259	Gcc/Tcc	23/38	0.386887403945762	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.386887403945762	2		471	840	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376310	15376310	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	319	632	0	ENST00000263377.2:c.704A>T	p.Gln235Leu	p.Q235L	ENST00000263377	NM_058243.2	235	cAg/cTg	5/20	0.386887403945762	2	FACETS	1	0.994	1	0.726	0.686	0.768	CLONAL	1	TRUE	0	0.386887403945762	2		632	1135	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793072	33793072	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1508	116	453	0	ENST00000498907.2:c.249G>C	p.Gln83His	p.Q83H	ENST00000498907	NM_004364.3	83	caG/caC	1/1	0.386887403945762	7	FACETS	0.726	0.652	0.806			1	SUBCLONAL	1	TRUE	NA	0.386887403945762	7		453	1624	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384656	31384656	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1246	992	649	2	ENST00000328111.2:c.1358G>T	p.Gly453Val	p.G453V	ENST00000328111	NM_006892.3	453	gGg/gTg	13/23	0.386887403945762	6	FACETS	1	0.983	1	1	0.983	1	CLONAL	4	TRUE	2	0.386887403945762	6		651	2238	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485103	57485103	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1425	251	528	1	ENST00000371085.3:c.937C>T	p.Pro313Ser	p.P313S	ENST00000371085	NM_000516.4	313	Cca/Tca	11/13	0.386887403945762	7	FACETS	0.761	0.71	0.815			1	SUBCLONAL	2	TRUE	NA	0.386887403945762	7		529	1676	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845319	42845319	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	143	532	0	ENST00000398585.3:c.943G>C	p.Val315Leu	p.V315L	ENST00000398585	NM_001135099.1	315	Gtc/Ctc	9/14	0.265639251021576	1	FACETS	0.655	0.597	0.716	0.655	0.597	0.716	SUBCLONAL	1	TRUE	0	0.386887403945762	1		532	910	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41999995	41999996	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	452	879	0	ENST00000219905.7:c.2261dup	p.Leu754PhefsTer6	p.L754Ffs*6	ENST00000219905	NM_001164273.1	753	cct/ccTt	6/24	0.386887403945762	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.386887403945762	1		879	1372	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224186	53224195	+	frameshift_variant	Frame_Shift_Del	DEL	TCCTTCTCCA	TCCTTCTCCA	-	novel	NA	P-0010904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	138	364	0	ENST00000375401.3:c.3356_3365del	p.Met1119SerfsTer25	p.M1119Sfs*25	ENST00000375401	NM_004187.3	1119	aTGGAGAAGGAg/ag	22/26	0.386887403945762	2	FACETS	0.669	0.607	0.733			1	SUBCLONAL	1	TRUE	NA	0.386887403945762	2		364	1067	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552821	226552821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182639036	NA	P-0011188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	129	397	0	ENST00000366794.5:c.2540G>A	p.Arg847His	p.R847H	ENST00000366794	NM_001618.3	847	cGt/cAt	19/23	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.418549002035842	2		397	583	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061211	38061212	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0011188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	142	309	0	ENST00000250448.2:c.777_778insAG	p.Leu260SerfsTer62	p.L260Sfs*62	ENST00000250448	NM_004496.3	259	-/AG	2/2	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.418549002035842	2		309	545	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252856	36252857	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	30	498	0	ENST00000300305.3:c.505dup	p.Arg169LysfsTer44	p.R169Kfs*44	ENST00000300305		169	aga/aAga	4/8	1	2	FACETS	0.803	0.646	0.982	0.803	0.646	0.982	CLONAL	1	FALSE	1	0.153337881910225	2		498	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	103	887	1	ENST00000269305.4:c.166G>T	p.Glu56Ter	p.E56*	ENST00000269305	NM_001126112.2	56	Gaa/Taa	4/11	0.153337881910225	2	FACETS	0.914	0.818	1	0.914	0.818	1	CLONAL	2	FALSE	0	0.153337881910225	2		888	735	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881002	37881003	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCTCCCCA	rs397516982	NA	P-0012081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	114	895	0	ENST00000269571.5:c.2332_2340dup	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	-/GGCTCCCCA	20/27	0.153337881910225	2	FACETS	0.963	0.867	1	0.963	0.867	1	CLONAL	2	FALSE	0	0.153337881910225	2		895	772	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155721	56155722	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0012081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	62	524	0	ENST00000399503.3:c.816_817del	p.Arg273SerfsTer27	p.R273Sfs*27	ENST00000399503	NM_005921.1	271	agAAaa/agaa	3/20	0.153337881910225	2	FACETS	0.919	0.796	1	0.919	0.796	1	CLONAL	2	FALSE	0	0.153337881910225	2		524	440	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965672	93965672	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	104	1039	0	ENST00000369303.4:c.2256G>T	p.Met752Ile	p.M752I	ENST00000369303	NM_004440.3	752	atG/atT	13/17	1	2	FACETS	0.64	0.573	0.711	0.64	0.573	0.711	SUBCLONAL	1	TRUE	1	0.411907618566999	2		1039	789	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507431	8507431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	59	501	1	ENST00000356435.5:c.1547C>T	p.Pro516Leu	p.P516L	ENST00000356435		516	cCa/cTa	11/35	0.355892943288318	3	FACETS	0.796	0.687	0.914	0.265	0.229	0.305	CLONAL	1	TRUE	0	0.411907618566999	3		502	434	SUCCESS
AXL	558	MSKCC	GRCh37	19	41737177	41737177	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	317	847	0	ENST00000301178.4:c.757T>A	p.Tyr253Asn	p.Y253N	ENST00000301178	NM_021913.4	253	Tac/Aac	6/20	0.319009791461519	2	FACETS	0.839	0.794	0.885	0.839	0.794	0.885	CLONAL	2	TRUE	0	0.411907618566999	2		847	917	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101044	41101044	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	88	604	0	ENST00000373198.4:c.1312G>T	p.Glu438Ter	p.E438*	ENST00000373198	NM_133170.3	438	Gag/Tag	8/32	0.369524330828999	4	FACETS	0.734	0.649	0.824	0.367	0.324	0.412	SUBCLONAL	1	TRUE	2	0.411907618566999	4		604	822	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412389	139412427	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTGGCGAGGGCACACGGGTGAGAGGCTGCTCCAGGCAC	CCTGGCGAGGGCACACGGGTGAGAGGCTGCTCCAGGCAC	-	novel	NA	P-0012257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	18	298	0	ENST00000277541.6:c.1256-38_1256del		p.X419_splice	ENST00000277541	NM_017617.3	419		8/34	0.349327448506137	2	FACETS	0.302	0.227	0.391	0.151	0.113	0.196	SUBCLONAL	1	TRUE	0	0.411907618566999	2		298	289	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0012368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	277	680	3	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	0.620826990068816	2	FACETS	0.935	0.891	0.977	0.935	0.891	0.977	CLONAL	2	FALSE	0	0.627979170262268	2		683	472	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61712943	61712943	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	569	565	0	ENST00000401558.2:c.2468T>G	p.Phe823Cys	p.F823C	ENST00000401558	NM_003400.3	823	tTt/tGt	20/25	0.627979170262268	4	FACETS	0.844	0.814	0.874	0.844	0.814	0.874	CLONAL	3	FALSE	1	0.627979170262268	4		565	1165	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267340	198267340	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	136	505	0	ENST00000335508.6:c.2017A>T	p.Ile673Phe	p.I673F	ENST00000335508	NM_012433.2	673	Att/Ttt	14/25	0.342868516512511	4	FACETS	0.739	0.671	0.811	0.37	0.335	0.406	INDETERMINATE	1	FALSE	2	0.627979170262268	4		505	954	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348741	11348741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773971612	NA	P-0012368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	231	515	1	ENST00000332029.2:c.595G>A	p.Val199Ile	p.V199I	ENST00000332029	NM_003745.1	199	Gtc/Atc	2/2	0.342868516512511	4	FACETS	1	0.99	1	0.677	0.632	0.723	INDETERMINATE	1	FALSE	2	0.627979170262268	4		516	885	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954342	48954343	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0012368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	22	259	0	ENST00000267163.4:c.1465_1466dup	p.Glu492LeufsTer4	p.E492Lfs*4	ENST00000267163	NM_000321.2	488	gcg/gcGTg	16/27	0.525111689936744	1	FACETS	0.194	0.15	0.244	0.194	0.15	0.244	SUBCLONAL	1	FALSE	0	0.627979170262268	1		259	248	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	488	584	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.805379243939679	2		585	1156	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	208	303	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.941	0.88	1	0.941	0.88	1	CLONAL	1	TRUE	1	0.805379243939679	2		304	549	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101267	27101268	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	78	644	1	ENST00000324856.7:c.4555dup	p.Gln1519ProfsTer13	p.Q1519Pfs*13	ENST00000324856	NM_006015.4	1517	gcc/gCcc	18/20	1	2	FACETS	0.162	0.141	0.184	0.162	0.141	0.184	SUBCLONAL	1	TRUE	1	0.805379243939679	2		645	1196	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	687	896	3	ENST00000269305.4:c.455C>A	p.Pro152Gln	p.P152Q	ENST00000269305	NM_001126112.2	152	cCg/cAg	5/11	1	2	FACETS	0.973	0.939	1	0.973	0.939	1	CLONAL	1	TRUE	1	0.805379243939679	2		899	1753	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392036	81392036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	29	354	0	ENST00000222390.5:c.241C>T	p.Pro81Ser	p.P81S	ENST00000222390	NM_000601.4	81	Cca/Tca	2/18	1	2	FACETS	0.133	0.106	0.164	0.133	0.106	0.164	SUBCLONAL	1	TRUE	1	0.805379243939679	2		354	542	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765783	41765783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	196	337	0	ENST00000301178.4:c.2659G>A	p.Ala887Thr	p.A887T	ENST00000301178	NM_021913.4	887	Gcc/Acc	20/20	0.805379243939679	1	FACETS	0.734	0.69	0.779	0.734	0.69	0.779	SUBCLONAL	1	TRUE	0	0.805379243939679	1		337	396	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120469123	120469123	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	434	523	1	ENST00000256646.2:c.4004del	p.Pro1335ArgfsTer15	p.P1335Rfs*15	ENST00000256646	NM_024408.3	1335	cCg/cg	24/34	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.805379243939679	2		524	1056	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851261	63851261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757997426	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	67	712	1	ENST00000279873.7:c.2039C>T	p.Ser680Phe	p.S680F	ENST00000279873	NM_032199.2	680	tCt/tTt	10/10	1	2	FACETS	0.138	0.119	0.159	0.138	0.119	0.159	SUBCLONAL	1	TRUE	1	0.805379243939679	2		713	1204	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606127	81606127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	52	611	0	ENST00000298171.2:c.797C>T	p.Ser266Phe	p.S266F	ENST00000298171	NM_000369.2	266	tCc/tTc	9/10	0.805379243939679	1	FACETS	0.098	0.082	0.114	0.098	0.082	0.114	SUBCLONAL	1	TRUE	0	0.805379243939679	1		611	790	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643770	38643770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	60	715	1	ENST00000299084.4:c.1240G>A	p.Val414Ile	p.V414I	ENST00000299084	NM_152594.2	414	Gta/Ata	7/7	0.748526493623092	1	FACETS	0.107	0.092	0.124	0.107	0.092	0.124	SUBCLONAL	1	TRUE	0	0.805379243939679	1		716	829	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122981	2122981	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	492	679	0	ENST00000219476.3:c.2352A>C	p.Lys784Asn	p.K784N	ENST00000219476	NM_000548.3	784	aaA/aaC	21/42	1	2	FACETS	0.995	0.954	1	0.995	0.954	1	CLONAL	1	TRUE	1	0.805379243939679	2		679	1228	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129670	2129670	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1555511031	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	63	693	1	ENST00000219476.3:c.3397G>A	p.Gly1133Arg	p.G1133R	ENST00000219476	NM_000548.3	1133	Ggg/Agg	29/42	1	2	FACETS	0.129	0.111	0.149	0.129	0.111	0.149	SUBCLONAL	1	TRUE	1	0.805379243939679	2		694	1210	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779214	3779214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	30	307	0	ENST00000262367.5:c.5834C>T	p.Pro1945Leu	p.P1945L	ENST00000262367	NM_004380.2	1945	cCc/cTc	31/31	1	2	FACETS	0.135	0.108	0.166	0.135	0.108	0.166	SUBCLONAL	1	TRUE	1	0.805379243939679	2		307	551	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790529	3790529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	80	581	0	ENST00000262367.5:c.4004G>A	p.Gly1335Glu	p.G1335E	ENST00000262367	NM_004380.2	1335	gGa/gAa	24/31	1	2	FACETS	0.176	0.154	0.199	0.176	0.154	0.199	SUBCLONAL	1	TRUE	1	0.805379243939679	2		581	1130	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804218	46804218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1319	98	721	1	ENST00000290295.7:c.789G>A	p.Trp263Ter	p.W263*	ENST00000290295	NM_006361.5	263	tgG/tgA	2/2	1	2	FACETS	0.172	0.152	0.193	0.172	0.152	0.193	SUBCLONAL	1	TRUE	1	0.805379243939679	2		722	1417	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368258	45368258	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	61	563	0	ENST00000262160.6:c.1344G>A	p.Trp448Ter	p.W448*	ENST00000262160	NM_005901.5	448	tgG/tgA	11/11	1	2	FACETS	0.146	0.125	0.169	0.146	0.125	0.169	SUBCLONAL	1	TRUE	1	0.805379243939679	2		563	1037	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17940987	17940987	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs916412541	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1520	454	892	0	ENST00000458235.1:c.3137C>T	p.Ala1046Val	p.A1046V	ENST00000458235	NM_000215.3	1046	gCc/gTc	23/24	0.805379243939679	3	FACETS	0.801	0.762	0.841	0.401	0.381	0.421	CLONAL	1	TRUE	1	0.805379243939679	3		892	1974	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214001	36214001	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	538	878	0	ENST00000222270.7:c.2827G>A	p.Gly943Arg	p.G943R	ENST00000222270	NM_014727.1	943	Ggg/Agg	6/37	NA	2	FACETS	0.784	0.751	0.818			1	INDETERMINATE	1	TRUE	NA	0.805379243939679	2		878	1704	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965022	25965022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	294	471	0	ENST00000435504.4:c.4184G>A	p.Gly1395Asp	p.G1395D	ENST00000435504		1395	gGc/gAc	13/13	1	2	FACETS	0.801	0.756	0.848	0.801	0.756	0.848	CLONAL	1	TRUE	1	0.805379243939679	2		471	911	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972791	25972791	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768548056	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	55	409	0	ENST00000435504.4:c.1634G>A	p.Gly545Asp	p.G545D	ENST00000435504		545	gGt/gAt	12/13	1	2	FACETS	0.182	0.155	0.212	0.182	0.155	0.212	SUBCLONAL	1	TRUE	1	0.805379243939679	2		409	749	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39294834	39294834	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	326	486	0	ENST00000402219.2:c.148G>A	p.Glu50Lys	p.E50K	ENST00000402219	NM_005633.3	50	Gaa/Aaa	2/23	1	2	FACETS	0.834	0.789	0.879	0.834	0.789	0.879	CLONAL	1	TRUE	1	0.805379243939679	2		486	971	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99169269	99169269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	67	600	1	ENST00000074304.5:c.1199C>T	p.Ser400Phe	p.S400F	ENST00000074304	NM_001134224.1	400	tCc/tTc	15/26	1	2	FACETS	0.137	0.118	0.158	0.137	0.118	0.158	SUBCLONAL	1	TRUE	1	0.805379243939679	2		601	1214	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662328	227662328	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1162078187	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	42	562	0	ENST00000305123.5:c.1127C>T	p.Pro376Leu	p.P376L	ENST00000305123	NM_005544.2	376	cCc/cTc	1/2	0.805379243939679	1	FACETS	0.1	0.083	0.119	0.1	0.083	0.119	SUBCLONAL	1	TRUE	0	0.805379243939679	1		562	625	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259268	36259268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	28	274	0	ENST00000300305.3:c.223G>A	p.Asp75Asn	p.D75N	ENST00000300305		75	Gac/Aac	3/8	1	2	FACETS	0.151	0.12	0.186	0.151	0.12	0.186	SUBCLONAL	1	TRUE	1	0.805379243939679	2		274	460	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448490	89448490	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	42	392	0	ENST00000336596.2:c.1454C>T	p.Thr485Ile	p.T485I	ENST00000336596	NM_005233.5	485	aCc/aTc	7/17	0.112372292852608	4	FACETS	0.254	0.211	0.302	0.127	0.105	0.151	INDETERMINATE	1	TRUE	2	0.805379243939679	4		392	741	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604218	189604218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147181964	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1182	111	758	0	ENST00000264731.3:c.1385G>A	p.Ser462Asn	p.S462N	ENST00000264731	NM_003722.4	462	aGc/aAc	11/14	0.112372292852608	4	FACETS	0.385	0.345	0.428	0.192	0.172	0.214	INDETERMINATE	1	TRUE	2	0.805379243939679	4		758	1293	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980608	1980608	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753305456	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	280	467	0	ENST00000382891.5:c.4070G>A	p.Gly1357Asp	p.G1357D	ENST00000382891	NM_133335.3	1357	gGc/gAc	22/22	1	2	FACETS	0.851	0.802	0.901	0.851	0.802	0.901	CLONAL	1	TRUE	1	0.805379243939679	2		467	817	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226065	226065	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	27	259	0	ENST00000264932.6:c.524G>A	p.Gly175Glu	p.G175E	ENST00000264932	NM_004168.2	175	gGa/gAa	5/15	1	2	FACETS	0.142	0.113	0.176	0.142	0.113	0.176	SUBCLONAL	1	TRUE	1	0.805379243939679	2		259	471	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294409	1294409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758442518	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	71	661	0	ENST00000310581.5:c.592G>A	p.Gly198Arg	p.G198R	ENST00000310581	NM_198253.2	198	Gga/Aga	2/16	1	2	FACETS	0.145	0.126	0.166	0.145	0.126	0.166	SUBCLONAL	1	TRUE	1	0.805379243939679	2		661	1215	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504347	149504347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1197	63	757	0	ENST00000261799.4:c.1855G>A	p.Ala619Thr	p.A619T	ENST00000261799	NM_002609.3	619	Gct/Act	13/23	1	2	FACETS	0.124	0.107	0.143	0.124	0.107	0.143	SUBCLONAL	1	TRUE	1	0.805379243939679	2		757	1260	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720847	176720847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	54	357	0	ENST00000439151.2:c.6478C>T	p.Pro2160Ser	p.P2160S	ENST00000439151	NM_022455.4	2160	Ccg/Tcg	23/23	NA	2	FACETS	0.17	0.144	0.198			1	INDETERMINATE	1	TRUE	NA	0.805379243939679	2		357	789	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197205	26197205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	222	357	0	ENST00000356476.2:c.274G>A	p.Ala92Thr	p.A92T	ENST00000356476		92	Gcg/Acg	1/1	1	2	FACETS	0.828	0.774	0.882	0.828	0.774	0.882	CLONAL	1	TRUE	1	0.805379243939679	2		357	666	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129288	152129288	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756487587	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	65	609	0	ENST00000206249.3:c.241G>A	p.Gly81Ser	p.G81S	ENST00000206249	NM_000125.3	81	Ggc/Agc	1/8	1	2	FACETS	0.143	0.123	0.164	0.143	0.123	0.164	SUBCLONAL	1	TRUE	1	0.805379243939679	2		609	1130	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829252	128829252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	63	625	1	ENST00000249373.3:c.260C>T	p.Ala87Val	p.A87V	ENST00000249373	NM_005631.4	87	gCc/gTc	1/12	1	2	FACETS	0.125	0.107	0.145	0.125	0.107	0.145	SUBCLONAL	1	TRUE	1	0.805379243939679	2		626	1250	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27209205	27209205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	406	612	0	ENST00000380036.4:c.2662C>T	p.Leu888Phe	p.L888F	ENST00000380036	NM_000459.3	888	Ctc/Ttc	16/23	0.805379243939679	1	FACETS	0.855	0.822	0.888	0.855	0.822	0.888	CLONAL	1	TRUE	0	0.805379243939679	1		612	704	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781424	135781424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564482313	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	63	513	0	ENST00000298552.3:c.1541G>A	p.Gly514Asp	p.G514D	ENST00000298552	NM_001162426.1	514	gGt/gAt	15/23	1	2	FACETS	0.16	0.138	0.185	0.16	0.138	0.185	SUBCLONAL	1	TRUE	1	0.805379243939679	2		513	975	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395167	139395167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1547	119	924	0	ENST00000277541.6:c.5771C>T	p.Thr1924Ile	p.T1924I	ENST00000277541	NM_017617.3	1924	aCa/aTa	31/34	1	2	FACETS	0.177	0.159	0.197	0.177	0.159	0.197	SUBCLONAL	1	TRUE	1	0.805379243939679	2		924	1666	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890195	76890195	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0012463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	324	514	0	ENST00000373344.5:c.4700-1G>C		p.X1567_splice	ENST00000373344	NM_000489.3	1567			0.209473758072194	1	FACETS	0.592	0.562	0.623	0.592	0.562	0.623	INDETERMINATE	1	TRUE	0	0.805379243939679	1		514	812	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443731	49443731	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012497-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	86	715	0	ENST00000301067.7:c.3640G>T	p.Gly1214Cys	p.G1214C	ENST00000301067	NM_003482.3	1214	Ggt/Tgt	11/54	1	2	FACETS	0.323	0.284	0.363	0.323	0.284	0.363	SUBCLONAL	1	TRUE	1	0.579059030797472	2		715	921	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226935	2226935	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012497-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	45	330	1	ENST00000398665.3:c.4415C>A	p.Pro1472Gln	p.P1472Q	ENST00000398665	NM_032482.2	1472	cCg/cAg	27/28	1	2	FACETS	0.297	0.249	0.35	0.297	0.249	0.35	SUBCLONAL	1	TRUE	1	0.579059030797472	2		331	523	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	87	372	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	0.225827860962606	2		373	752	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0012533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	120	642	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.225827860962606	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.225827860962606	1		642	909	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372220	55372220	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756723008	NA	P-0012533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	28	130	0	ENST00000297316.4:c.910G>A	p.Gly304Arg	p.G304R	ENST00000297316	NM_022454.3	304	Ggg/Agg	2/2	0.1541357842031	3	FACETS	1	0.871	1	0.559	0.448	0.683	CLONAL	1	TRUE	1	0.225827860962606	3		130	247	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151646	55151647	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	84	438	0	ENST00000257290.5:c.2438dup	p.Asn813LysfsTer6	p.N813Kfs*6	ENST00000257290	NM_006206.4	811	tca/tcAa	17/23	1	2	FACETS	0.789	0.695	0.89	0.789	0.695	0.89	SUBCLONAL	1	TRUE	1	0.225827860962606	2		438	943	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111502	8111503	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0012539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	440	634	0	ENST00000346208.3:c.990dup	p.Asn331GlufsTer21	p.N331Efs*21	ENST00000346208		330	agg/aGgg	5/6	1	2	FACETS	0.909	0.869	0.95	0.909	0.869	0.95	CLONAL	1	TRUE	1	0.829164437310987	2		634	1167	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509364	149509364	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs762039865	NA	P-0012539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	283	439	1	ENST00000261799.4:c.1535A>G	p.Asn512Ser	p.N512S	ENST00000261799	NM_002609.3	512	aAc/aGc	10/23	1	2	FACETS	0.933	0.881	0.984	0.933	0.881	0.984	CLONAL	1	TRUE	1	0.829164437310987	2		440	732	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs869320707	NA	P-0012629-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	39	278	0	ENST00000397752.3:c.3028+1G>T		p.X1010_splice	ENST00000397752	NM_000245.2	1010			1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.15	2		278	498	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92247520	92247520	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012629-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	50	422	0	ENST00000265734.4:c.700G>T	p.Val234Leu	p.V234L	ENST00000265734	NM_001259.6	234	Gtg/Ttg	7/8	1	2	FACETS	0.738	0.624	0.864	0.738	0.624	0.864	SUBCLONAL	1	TRUE	1	0.15	2		422	903	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149251	119149251	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012629-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	22	517	0	ENST00000264033.4:c.1259G>T	p.Arg420Leu	p.R420L	ENST00000264033	NM_005188.3	420	cGa/cTa	9/16	1	2	FACETS	0.273	0.21	0.347	0.273	0.21	0.347	SUBCLONAL	1	TRUE	1	0.15	2		517	1074	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	134	372	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.827	0.751	0.907	0.827	0.751	0.907	CLONAL	1	TRUE	1	0.366700766614322	2		373	884	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0012751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	158	530	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	0.366700766614322	1	FACETS	0.943	0.866	1	0.943	0.866	1	CLONAL	1	TRUE	0	0.366700766614322	1		530	746	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376187	225376187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773927741	NA	P-0012751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	229	645	1	ENST00000264414.4:c.767C>T	p.Thr256Met	p.T256M	ENST00000264414	NM_003590.4	256	aCg/aTg	6/16	1	2	FACETS	0.891	0.829	0.957	0.891	0.829	0.957	CLONAL	1	TRUE	1	0.366700766614322	2		646	1401	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929395	44929395	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	262	403	0	ENST00000377967.4:c.2496del	p.Thr833LeufsTer34	p.T833Lfs*34	ENST00000377967	NM_021140.2	832	tCc/tc	17/29	1	1	FACETS	0.781	0.735	0.828	1	0.994	1	SUBCLONAL	2	TRUE	0	0.366700766614322	1		403	747	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156354	106156354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	132	505	2	ENST00000380013.4:c.1255C>T	p.Pro419Ser	p.P419S	ENST00000380013	NM_001127208.2	419	Cct/Tct	3/11	0.199409920118595	2	FACETS	1	0.981	1	0.638	0.582	0.696	INDETERMINATE	1	TRUE	0	0.4	2		507	517	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609813	117609813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761155034	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	85	833	1	ENST00000368508.3:c.6886G>A	p.Glu2296Lys	p.E2296K	ENST00000368508	NM_002944.2	2296	Gaa/Aaa	43/43	1	2	FACETS	0.535	0.472	0.603	0.535	0.472	0.603	SUBCLONAL	1	TRUE	1	0.4	2		834	794	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561263	9561263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769939031	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	160	578	1	ENST00000353224.5:c.519G>A	p.Met173Ile	p.M173I	ENST00000353224	NM_177990.2	173	atG/atA	4/10	0.3	3	FACETS	0.85	0.783	0.918	0.85	0.783	0.918	CLONAL	2	TRUE	1	0.4	3		579	565	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561352	9561352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773981325	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	137	593	1	ENST00000353224.5:c.430G>A	p.Glu144Lys	p.E144K	ENST00000353224	NM_177990.2	144	Gaa/Aaa	4/10	0.3	3	FACETS	0.778	0.712	0.848	0.778	0.712	0.848	SUBCLONAL	2	TRUE	1	0.4	3		594	528	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622630	158622630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	216	972	1	ENST00000263640.3:c.869C>T	p.Ser290Leu	p.S290L	ENST00000263640	NM_001105.4	290	tCg/tTg	8/11	0.292622716893783	2	FACETS	1	0.984	1	0.597	0.556	0.64	CLONAL	1	TRUE	0	0.4	2		973	904	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199342	16199342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	257	775	0	ENST00000375759.3:c.115C>T	p.Pro39Ser	p.P39S	ENST00000375759	NM_015001.2	39	Ccc/Tcc	2/15	0.3	4	FACETS	0.844	0.79	0.899	0.844	0.79	0.899	CLONAL	2	TRUE	2	0.4	4		775	1066	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401389	139401389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754998450	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	91	440	1	ENST00000277541.6:c.3680C>T	p.Pro1227Leu	p.P1227L	ENST00000277541	NM_017617.3	1227	cCc/cTc	23/34	NA	2	FACETS	0.934	0.833	1			1	INDETERMINATE	1	TRUE	NA	0.4	2		441	487	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120377	94120377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	86	918	0	ENST00000369303.4:c.674C>T	p.Ser225Phe	p.S225F	ENST00000369303	NM_004440.3	225	tCc/tTc	3/17	1	2	FACETS	0.488	0.431	0.55	0.488	0.431	0.55	SUBCLONAL	1	TRUE	1	0.4	2		918	881	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508905	106508905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755134917	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	108	347	0	ENST00000359195.3:c.899G>A	p.Gly300Glu	p.G300E	ENST00000359195	NM_002649.2	300	gGa/gAa	2/11	0.186186619543753	2	FACETS	1	0.98	1	0.677	0.612	0.744	INDETERMINATE	1	TRUE	0	0.4	2		347	399	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492945	8492945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759831182	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	228	587	1	ENST00000356435.5:c.2384C>T	p.Ser795Phe	p.S795F	ENST00000356435		795	tCc/tTc	16/35	0.288882661069713	3	FACETS	1	0.971	1	0.707	0.663	0.752	CLONAL	2	TRUE	0	0.4	3		588	645	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961109	55961109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374755237	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1509	172	622	0	ENST00000263923.4:c.2831G>A	p.Arg944Gln	p.R944Q	ENST00000263923	NM_002253.2	944	cGa/cAa	21/30	0.3	13	FACETS	0.819	0.75	0.89			1	CLONAL	2	TRUE	NA	0.4	13		622	1681	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005419	29005419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55687105	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	59	501	0	ENST00000282397.4:c.842G>A	p.Arg281Gln	p.R281Q	ENST00000282397	NM_002019.4	281	cGa/cAa	7/30	0.3	1	FACETS	0.549	0.473	0.631	0.549	0.473	0.631	SUBCLONAL	1	TRUE	0	0.4	1		501	430	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577531	7577532	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	67	626	0	ENST00000269305.4:c.749_750delinsTT	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCC/cTT	7/11	0.298951465986185	3	FACETS	0.514	0.446	0.588	0.257	0.223	0.294	SUBCLONAL	1	TRUE	1	0.4	3		626	782	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385271	41385271	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	74	561	0	ENST00000373198.4:c.690G>A	p.Trp230Ter	p.W230*	ENST00000373198	NM_133170.3	230	tgG/tgA	6/32	0.3	3	FACETS	0.681	0.596	0.773	0.34	0.298	0.387	SUBCLONAL	1	TRUE	1	0.4	3		561	652	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953195	81953195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs187454354	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	113	907	1	ENST00000359376.3:c.2161G>A	p.Glu721Lys	p.E721K	ENST00000359376	NM_002661.3	721	Gag/Aag	20/33	1	2	FACETS	0.613	0.551	0.679	0.613	0.551	0.679	SUBCLONAL	1	TRUE	1	0.4	2		908	922	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117630069	117630069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	98	674	1	ENST00000368508.3:c.6457G>A	p.Glu2153Lys	p.E2153K	ENST00000368508	NM_002944.2	2153	Gag/Aag	41/43	1	2	FACETS	0.701	0.626	0.781	0.701	0.626	0.781	SUBCLONAL	1	TRUE	1	0.4	2		675	699	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286760	212286760	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763644012	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	108	607	1	ENST00000342788.4:c.2936G>A	p.Arg979Gln	p.R979Q	ENST00000342788	NM_005235.2	979	cGa/cAa	24/28	0.292622716893783	2	FACETS	1	0.916	1	0.509	0.459	0.563	CLONAL	1	TRUE	0	0.4	2		608	530	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11204752	11204752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	240	855	1	ENST00000361445.4:c.4825C>T	p.Pro1609Ser	p.P1609S	ENST00000361445	NM_004958.3	1609	Ccc/Tcc	34/58	0.298951465986185	3	FACETS	0.772	0.721	0.823	0.772	0.721	0.823	SUBCLONAL	2	TRUE	1	0.4	3		856	933	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258107	16258107	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	155	460	0	ENST00000375759.3:c.5372C>T	p.Ala1791Val	p.A1791V	ENST00000375759	NM_015001.2	1791	gCc/gTc	11/15	0.3	4	FACETS	0.86	0.79	0.932	0.86	0.79	0.932	CLONAL	2	TRUE	2	0.4	4		460	631	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363547	40363547	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1317819335	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	88	606	0	ENST00000397332.2:c.682C>T	p.Pro228Ser	p.P228S	ENST00000397332	NM_001033082.2	228	Ccc/Tcc	3/3	0.298951465986185	3	FACETS	0.779	0.69	0.873	0.389	0.345	0.437	SUBCLONAL	1	TRUE	1	0.4	3		606	678	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46725708	46725708	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	186	702	0	ENST00000371975.4:c.344A>C	p.Lys115Thr	p.K115T	ENST00000371975	NM_003579.3	115	aAa/aCa	5/18	0.298951465986185	3	FACETS	1	0.988	1	0.674	0.623	0.727	CLONAL	1	TRUE	1	0.4	3		702	828	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838323	156838323	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1219432341	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	106	663	2	ENST00000524377.1:c.601C>T	p.Pro201Ser	p.P201S	ENST00000524377	NM_002529.3	201	Ccc/Tcc	6/17	1	2	FACETS	0.826	0.741	0.915	0.826	0.741	0.915	CLONAL	1	TRUE	1	0.4	2		665	642	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966556	25966556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	177	648	0	ENST00000435504.4:c.2650C>T	p.Pro884Ser	p.P884S	ENST00000435504		884	Ccc/Tcc	13/13	0.298951465986185	3	FACETS	0.819	0.758	0.883	0.819	0.758	0.883	CLONAL	2	TRUE	1	0.4	3		648	648	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47612324	47612324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786204192	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	248	847	1	ENST00000263735.4:c.878G>A	p.Arg293Lys	p.R293K	ENST00000263735	NM_002354.2	293	aGa/aAa	8/9	0.298951465986185	3	FACETS	1	0.992	1	0.74	0.692	0.789	CLONAL	1	TRUE	1	0.4	3		848	1006	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164786	47164786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs998524208	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	127	429	0	ENST00000409792.3:c.1340C>T	p.Ser447Phe	p.S447F	ENST00000409792	NM_014159.6	447	tCt/tTt	3/21	0.298951465986185	3	FACETS	1	0.983	1	0.69	0.628	0.755	CLONAL	1	TRUE	1	0.4	3		429	552	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391088	89391088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767254790	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	73	595	1	ENST00000336596.2:c.1154G>A	p.Arg385Gln	p.R385Q	ENST00000336596	NM_005233.5	385	cGa/cAa	5/17	0.298951465986185	3	FACETS	0.676	0.591	0.767	0.338	0.295	0.384	SUBCLONAL	1	TRUE	1	0.4	3		596	648	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968305	134968305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	161	657	0	ENST00000398015.3:c.2818C>T	p.Leu940Phe	p.L940F	ENST00000398015	NM_004441.4	940	Ctc/Ttc	15/16	0.298951465986185	3	FACETS	1	0.984	1	0.643	0.591	0.698	CLONAL	1	TRUE	1	0.4	3		657	751	SUCCESS
ATR	545	MSKCC	GRCh37	3	142253975	142253975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1406692405	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	95	586	0	ENST00000350721.4:c.3892G>A	p.Asp1298Asn	p.D1298N	ENST00000350721	NM_001184.3	1298	Gat/Aat	21/47	0.298951465986185	3	FACETS	0.82	0.731	0.916	0.41	0.365	0.458	CLONAL	1	TRUE	1	0.4	3		586	695	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146647	185146647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	70	463	0	ENST00000265026.3:c.278C>T	p.Ser93Leu	p.S93L	ENST00000265026	NM_004721.4	93	tCa/tTa	2/14	0.298951465986185	3	FACETS	0.794	0.693	0.902	0.397	0.346	0.451	CLONAL	1	TRUE	1	0.4	3		463	529	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133459	55133459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553903204	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	998	634	0	ENST00000257290.5:c.763G>A	p.Gly255Ser	p.G255S	ENST00000257290	NM_006206.4	255	Ggc/Agc	6/23	0.3	13	FACETS	1	0.992	1			1	CLONAL	10	TRUE	NA	0.4	13		634	1550	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156621	55156621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	934	577	3	ENST00000257290.5:c.3022G>A	p.Asp1008Asn	p.D1008N	ENST00000257290	NM_006206.4	1008	Gat/Aat	22/23	0.3	13	FACETS	1	0.992	1			1	CLONAL	9	TRUE	NA	0.4	13		580	1595	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976920	55976920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1294722006	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	137	451	2	ENST00000263923.4:c.992C>T	p.Ala331Val	p.A331V	ENST00000263923	NM_002253.2	331	gCt/gTt	8/30	0.3	13	FACETS	0.844	0.766	0.927			1	CLONAL	2	TRUE	NA	0.4	13		453	1298	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242752	66242752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	136	575	0	ENST00000273854.3:c.1820C>T	p.Ser607Phe	p.S607F	ENST00000273854	NM_004439.5	607	tCt/tTt	9/18	0.198021907263667	3	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.4	3		575	587	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279483	1279483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	86	621	0	ENST00000310581.5:c.2053G>A	p.Asp685Asn	p.D685N	ENST00000310581	NM_198253.2	685	Gat/Aat	5/16	0.3	5	FACETS	0.755	0.667	0.85	0.252	0.222	0.284	SUBCLONAL	1	TRUE	2	0.4	5		621	911	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046037	180046037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	101	236	0	ENST00000261937.6:c.2834C>T	p.Ala945Val	p.A945V	ENST00000261937	NM_182925.4	945	gCc/gTc	20/30	0.292622716893783	2	FACETS	0.807	0.73	0.886	0.807	0.73	0.886	CLONAL	2	TRUE	0	0.4	2		236	313	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672734	30672734	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755710749	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	138	966	0	ENST00000376406.3:c.4226C>T	p.Pro1409Leu	p.P1409L	ENST00000376406	NM_014641.2	1409	cCc/cTc	10/15	0.298951465986185	3	FACETS	0.817	0.743	0.896	0.409	0.371	0.448	CLONAL	1	TRUE	1	0.4	3		966	1013	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673634	30673634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1386319473	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	140	883	1	ENST00000376406.3:c.3326C>T	p.Thr1109Ile	p.T1109I	ENST00000376406	NM_014641.2	1109	aCt/aTt	10/15	0.298951465986185	3	FACETS	0.805	0.732	0.882	0.402	0.366	0.441	CLONAL	1	TRUE	1	0.4	3		884	1044	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170216	32170216	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757487459	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	80	539	0	ENST00000375023.3:c.3392C>T	p.Pro1131Leu	p.P1131L	ENST00000375023	NM_004557.3	1131	cCt/cTt	21/30	0.298951465986185	3	FACETS	0.723	0.636	0.816	0.361	0.318	0.408	SUBCLONAL	1	TRUE	1	0.4	3		539	664	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120534	94120534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1562167396	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	220	1054	1	ENST00000369303.4:c.517G>A	p.Glu173Lys	p.E173K	ENST00000369303	NM_004440.3	173	Gag/Aag	3/17	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.4	2		1055	905	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536242	106536242	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	176	586	0	ENST00000369096.4:c.209G>A	p.Gly70Asp	p.G70D	ENST00000369096	NM_001198.3	70	gGt/gAt	2/7	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.4	2		586	707	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710984	117710984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	59	264	1	ENST00000368508.3:c.1288G>A	p.Gly430Ser	p.G430S	ENST00000368508	NM_002944.2	430	Ggc/Agc	12/43	1	2	FACETS	0.902	0.781	1	0.902	0.781	1	CLONAL	1	TRUE	1	0.4	2		265	327	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509857	106509857	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	201	868	0	ENST00000359195.3:c.1851G>A	p.Trp617Ter	p.W617*	ENST00000359195	NM_002649.2	617	tgG/tgA	2/11	0.186186619543753	2	FACETS	1	0.985	1	0.608	0.564	0.653	INDETERMINATE	1	TRUE	0	0.4	2		868	827	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878070	151878070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	29	497	0	ENST00000262189.6:c.6875C>T	p.Pro2292Leu	p.P2292L	ENST00000262189	NM_170606.2	2292	cCa/cTa	36/59	0.186186619543753	2	FACETS	0.304	0.243	0.373	0.152	0.121	0.187	INDETERMINATE	1	TRUE	0	0.4	2		497	477	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319902	8319902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	276	704	2	ENST00000356435.5:c.5599G>A	p.Glu1867Lys	p.E1867K	ENST00000356435		1867	Gaa/Aaa	34/35	0.288882661069713	3	FACETS	1	0.979	1	0.719	0.678	0.76	CLONAL	2	TRUE	0	0.4	3		706	768	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331723	8331723	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367558329	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	218	532	0	ENST00000356435.5:c.5393G>A	p.Arg1798Gln	p.R1798Q	ENST00000356435		1798	cGa/cAa	33/35	0.288882661069713	3	FACETS	1	0.977	1	0.725	0.679	0.773	CLONAL	2	TRUE	0	0.4	3		532	601	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406301	70406301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	210	676	1	ENST00000373644.4:c.3815C>T	p.Ser1272Phe	p.S1272F	ENST00000373644	NM_030625.2	1272	tCc/tTc	4/12	0.274933755938258	2	FACETS	0.772	0.72	0.825	0.772	0.72	0.825	SUBCLONAL	2	TRUE	0	0.4	2		677	680	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197310	94197310	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1555010853	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	72	526	0	ENST00000323929.3:c.1194T>A	p.Phe398Leu	p.F398L	ENST00000323929	NM_005591.3	398	ttT/ttA	11/20	0.298951465986185	3	FACETS	0.667	0.582	0.758	0.333	0.291	0.379	SUBCLONAL	1	TRUE	1	0.4	3		526	648	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933307	100933307	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	112	1020	1	ENST00000325455.5:c.2083G>A	p.Glu695Lys	p.E695K	ENST00000325455	NM_001202474.3	695	Gaa/Aaa	4/8	0.298951465986185	3	FACETS	0.63	0.565	0.699	0.315	0.282	0.35	SUBCLONAL	1	TRUE	1	0.4	3		1021	1067	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359384	118359384	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	79	655	0	ENST00000534358.1:c.4388A>T	p.Asn1463Ile	p.N1463I	ENST00000534358	NM_005933.3	1463	aAc/aTc	11/36	0.298951465986185	3	FACETS	0.63	0.554	0.713	0.315	0.277	0.357	SUBCLONAL	1	TRUE	1	0.4	3		655	752	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373893	118373893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	173	626	0	ENST00000534358.1:c.7286G>A	p.Arg2429Lys	p.R2429K	ENST00000534358	NM_005933.3	2429	aGa/aAa	27/36	0.298951465986185	3	FACETS	1	0.989	1	0.742	0.685	0.802	CLONAL	1	TRUE	1	0.4	3		626	699	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103179	119103179	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	205	556	1	ENST00000264033.4:c.217C>T	p.Pro73Ser	p.P73S	ENST00000264033	NM_005188.3	73	Cca/Tca	2/16	0.298951465986185	3	FACETS	0.869	0.809	0.93	0.869	0.809	0.93	CLONAL	2	TRUE	1	0.4	3		557	708	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149242	119149242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779039234	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	200	746	0	ENST00000264033.4:c.1250C>T	p.Pro417Leu	p.P417L	ENST00000264033	NM_005188.3	417	cCt/cTt	9/16	0.298951465986185	3	FACETS	1	0.991	1	0.746	0.693	0.801	CLONAL	1	TRUE	1	0.4	3		746	804	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427339	427339	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	75	607	1	ENST00000399788.2:c.2830G>A	p.Glu944Lys	p.E944K	ENST00000399788	NM_001042603.1	944	Gaa/Aaa	19/28	0.289842677713079	3	FACETS	0.592	0.518	0.672			1	SUBCLONAL	1	TRUE	NA	0.4	3		608	760	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435401	18435401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762537354	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	79	552	0	ENST00000266497.5:c.386C>T	p.Pro129Leu	p.P129L	ENST00000266497		129	cCc/cTc	1/31	NA	2	FACETS	0.761	0.671	0.857			1	INDETERMINATE	1	TRUE	NA	0.4	2		552	519	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492521	50492521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	81	592	1	ENST00000394963.4:c.1417C>T	p.Pro473Ser	p.P473S	ENST00000394963	NM_003076.4	473	Cca/Tca	12/13	0.298951465986185	3	FACETS	0.667	0.587	0.752	0.333	0.293	0.376	SUBCLONAL	1	TRUE	1	0.4	3		593	729	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859610	57859610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369404558	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	119	942	1	ENST00000228682.2:c.664G>A	p.Glu222Lys	p.E222K	ENST00000228682	NM_005269.2	222	Gag/Aag	7/12	0.3	4	FACETS	0.671	0.603	0.742			1	SUBCLONAL	1	TRUE	NA	0.4	4		943	1242	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865548	57865548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	305	940	0	ENST00000228682.2:c.3025C>T	p.Pro1009Ser	p.P1009S	ENST00000228682	NM_005269.2	1009	Ccc/Tcc	12/12	0.3	4	FACETS	0.792	0.745	0.84			1	SUBCLONAL	2	TRUE	NA	0.4	4		940	1348	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885850	111885850	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	117	1079	0	ENST00000341259.2:c.1472A>G	p.His491Arg	p.H491R	ENST00000341259	NM_005475.2	491	cAc/cGc	8/8	0.298951465986185	3	FACETS	0.674	0.607	0.746	0.337	0.303	0.373	SUBCLONAL	1	TRUE	1	0.4	3		1079	1041	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112311	115112311	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	24	111	0	ENST00000257566.3:c.1429G>A	p.Glu477Lys	p.E477K	ENST00000257566	NM_016569.3	477	Gag/Aag	7/8	0.298951465986185	3	FACETS	1	0.825	1	0.522	0.414	0.643	CLONAL	1	TRUE	1	0.4	3		111	138	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118836	115118836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1430142395	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	89	587	2	ENST00000257566.3:c.505C>T	p.Arg169Trp	p.R169W	ENST00000257566	NM_016569.3	169	Cgg/Tgg	2/8	0.298951465986185	3	FACETS	0.75	0.665	0.841	0.375	0.332	0.421	SUBCLONAL	1	TRUE	1	0.4	3		589	712	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249767	133249767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565972431	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	89	600	0	ENST00000320574.5:c.1456C>T	p.Pro486Ser	p.P486S	ENST00000320574	NM_006231.2	486	Ccc/Tcc	14/49	0.298951465986185	3	FACETS	0.712	0.631	0.799	0.356	0.315	0.4	SUBCLONAL	1	TRUE	1	0.4	3		600	750	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911782	32911782	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	99	1055	0	ENST00000380152.3:c.3290T>C	p.Phe1097Ser	p.F1097S	ENST00000380152		1097	tTt/tCt	11/27	0.3	1	FACETS	0.523	0.467	0.583	0.523	0.467	0.583	SUBCLONAL	1	TRUE	0	0.4	1		1055	757	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679835	88679835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	75	441	0	ENST00000360948.2:c.628C>T	p.Pro210Ser	p.P210S	ENST00000360948	NM_001012338.2	210	Cct/Tct	7/19	1	2	FACETS	0.731	0.642	0.826	0.731	0.642	0.826	SUBCLONAL	1	TRUE	1	0.4	2		441	513	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631950	90631950	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	97	637	0	ENST00000330062.3:c.403C>T	p.Pro135Ser	p.P135S	ENST00000330062	NM_002168.2	135	Ccc/Tcc	4/11	1	2	FACETS	0.68	0.607	0.759	0.68	0.607	0.759	SUBCLONAL	1	TRUE	1	0.4	2		637	713	SUCCESS
BLM	641	MSKCC	GRCh37	15	91352379	91352379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	80	531	1	ENST00000355112.3:c.3764C>T	p.Ser1255Phe	p.S1255F	ENST00000355112	NM_000057.2	1255	tCt/tTt	20/22	1	2	FACETS	0.694	0.612	0.783	0.694	0.612	0.783	SUBCLONAL	1	TRUE	1	0.4	2		532	576	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478567	99478567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	82	595	0	ENST00000268035.6:c.3209C>T	p.Ser1070Phe	p.S1070F	ENST00000268035	NM_000875.3	1070	tCc/tTc	17/21	1	2	FACETS	0.654	0.577	0.736	0.654	0.577	0.736	SUBCLONAL	1	TRUE	1	0.4	2		595	627	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347206	347206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	185	619	0	ENST00000262320.3:c.1805G>A	p.Cys602Tyr	p.C602Y	ENST00000262320	NM_003502.3	602	tGc/tAc	7/11	0.292622716893783	2	FACETS	1	0.99	1	0.714	0.662	0.767	CLONAL	1	TRUE	0	0.4	2		619	648	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56863005	56863005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	82	854	0	ENST00000308159.5:c.911C>T	p.Pro304Leu	p.P304L	ENST00000308159	NM_014669.4	304	cCc/cTc	9/22	0.3	3	FACETS	0.548	0.483	0.619	0.274	0.241	0.31	SUBCLONAL	1	TRUE	1	0.4	3		854	897	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984778	72984778	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	130	848	1	ENST00000268489.5:c.2806C>T	p.Gln936Ter	p.Q936*	ENST00000268489	NM_006885.3	936	Cag/Tag	3/10	1	2	FACETS	0.726	0.658	0.798	0.726	0.658	0.798	SUBCLONAL	1	TRUE	1	0.4	2		849	895	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347249	89347249	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	120	994	0	ENST00000301030.4:c.5701C>T	p.Pro1901Ser	p.P1901S	ENST00000301030	NM_001256183.1	1901	Cct/Tct	9/13	1	2	FACETS	0.618	0.557	0.682	0.618	0.557	0.682	SUBCLONAL	1	TRUE	1	0.4	2		994	971	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348011	89348011	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	150	1198	2	ENST00000301030.4:c.4939C>T	p.Pro1647Ser	p.P1647S	ENST00000301030	NM_001256183.1	1647	Cct/Tct	9/13	1	2	FACETS	0.672	0.613	0.734	0.672	0.613	0.734	SUBCLONAL	1	TRUE	1	0.4	2		1200	1116	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89383402	89383402	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	111	932	0	ENST00000301030.4:c.26C>A	p.Ala9Glu	p.A9E	ENST00000301030	NM_001256183.1	9	gCa/gAa	3/13	0.298951465986185	3	FACETS	0.632	0.567	0.702	0.316	0.283	0.351	SUBCLONAL	1	TRUE	1	0.4	3		932	1053	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577527	7577527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	71	626	0	ENST00000269305.4:c.754C>T	p.Leu252Phe	p.L252F	ENST00000269305	NM_001126112.2	252	Ctc/Ttc	7/11	0.298951465986185	3	FACETS	0.53	0.461	0.604	0.265	0.23	0.302	SUBCLONAL	1	TRUE	1	0.4	3		626	804	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990645	7990645	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	135	623	0	ENST00000319144.4:c.116A>G	p.Asn39Ser	p.N39S	ENST00000319144	NM_001139.2	39	aAc/aGc	1/15	0.298951465986185	3	FACETS	0.89	0.809	0.976	0.445	0.404	0.488	CLONAL	1	TRUE	1	0.4	3		623	910	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8109815	8109815	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	68	504	0	ENST00000585124.1:c.680C>T	p.Ser227Phe	p.S227F	ENST00000585124	NM_004217.3	227	tCc/tTc	7/9	0.298951465986185	3	FACETS	0.646	0.561	0.737	0.323	0.28	0.369	SUBCLONAL	1	TRUE	1	0.4	3		504	632	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226581	2226581	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	129	572	0	ENST00000398665.3:c.4061C>T	p.Pro1354Leu	p.P1354L	ENST00000398665	NM_032482.2	1354	cCc/cTc	27/28	0.270343818390983	4	FACETS	1	0.974	1	0.599	0.543	0.657	CLONAL	1	TRUE	2	0.4	4		572	754	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138474	11138474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	153	549	1	ENST00000358026.2:c.3230G>A	p.Arg1077Gln	p.R1077Q	ENST00000358026	NM_001128849.1	1077	cGa/cAa	24/36	0.298951465986185	3	FACETS	1	0.986	1	0.679	0.623	0.737	CLONAL	1	TRUE	1	0.4	3		550	676	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727938	41727938	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1320068051	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	127	599	0	ENST00000301178.4:c.563C>T	p.Pro188Leu	p.P188L	ENST00000301178	NM_021913.4	188	cCc/cTc	4/20	0.298951465986185	3	FACETS	0.925	0.838	1	0.462	0.419	0.508	CLONAL	1	TRUE	1	0.4	3		599	824	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650526	48650526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	237	497	0	ENST00000376670.3:c.496C>T	p.Pro166Ser	p.P166S	ENST00000376670	NM_002049.3	166	Cct/Tct	3/6	0.226215400254842	2	FACETS	1	0.978	1			1	INDETERMINATE	2	TRUE	NA	0.4	2		497	551	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411447	63411447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754938624	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	227	462	0	ENST00000330258.3:c.1720C>T	p.Arg574Trp	p.R574W	ENST00000330258	NM_152424.3	574	Cgg/Tgg	2/2	0.226215400254842	2	FACETS	1	0.985	1			1	INDETERMINATE	2	TRUE	NA	0.4	2		462	497	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344165	70344165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1355367439	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	203	375	0	ENST00000374080.3:c.1901C>T	p.Pro634Leu	p.P634L	ENST00000374080		634	cCc/cTc	13/45	0.226215400254842	2	FACETS	1	0.984	1			1	INDETERMINATE	2	TRUE	NA	0.4	2		375	443	SUCCESS
BTK	695	MSKCC	GRCh37	X	100625027	100625027	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	100	434	0	ENST00000308731.7:c.350C>T	p.Thr117Ile	p.T117I	ENST00000308731	NM_000061.2	117	aCt/aTt	5/19	0.226215400254842	2	FACETS	0.963	0.864	1			1	INDETERMINATE	1	TRUE	NA	0.4	2		434	519	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578139	7578177	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAACCCCTCCTCCCAGAGACCCCAGTTGCAAACCAGACC	TAACCCCTCCTCCCAGAGACCCCAGTTGCAAACCAGACC	-	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	176	577	1	ENST00000269305.4:c.672_672+38del		p.X224_splice	ENST00000269305	NM_001126112.2	224		6/11	0.298951465986185	3	FACETS	0.78	0.721	0.841	0.78	0.721	0.841	SUBCLONAL	2	TRUE	1	0.4	3		578	677	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395756	45395758	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	139	507	0	ENST00000262160.6:c.376_378del	p.Val126del	p.V126del	ENST00000262160	NM_005901.5	126	GTT/-	4/11	0.292622716893783	2	FACETS	1	0.982	1	0.641	0.587	0.698	CLONAL	1	TRUE	0	0.4	2		507	542	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677327	29677328	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	139	514	0	ENST00000356175.3:c.7387dup	p.Ser2463PhefsTer3	p.S2463Ffs*3	ENST00000356175	NM_000267.3	2462	cct/ccTt	49/57	0.292622716893783	2	FACETS	1	0.987	1	0.725	0.665	0.788	CLONAL	1	TRUE	0	0.4	2		514	479	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158215	47158215	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	77	448	0	ENST00000409792.3:c.4484del	p.Lys1495SerfsTer20	p.K1495Sfs*20	ENST00000409792	NM_014159.6	1495	aAg/ag	4/21	0.298951465986185	3	FACETS	0.802	0.705	0.906	0.401	0.352	0.453	CLONAL	1	TRUE	1	0.4	3		448	576	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257059	16257060	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	131	461	0	ENST00000375759.3:c.4324_4325delinsTT	p.Pro1442Leu	p.P1442L	ENST00000375759	NM_015001.2	1442	CCa/TTa	11/15	0.3	4	FACETS	1	0.984	1	0.692	0.629	0.757	CLONAL	1	TRUE	2	0.4	4		461	663	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257858	16257859	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	94	331	0	ENST00000375759.3:c.5123_5124delinsTT	p.Pro1708Leu	p.P1708L	ENST00000375759	NM_015001.2	1708	cCC/cTT	11/15	0.3	4	FACETS	1	0.978	1	0.693	0.619	0.77	CLONAL	1	TRUE	2	0.4	4		331	475	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31015958	31015959	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	78	430	0	ENST00000375687.4:c.280_281delinsTT	p.Pro94Leu	p.P94L	ENST00000375687	NM_015338.5	94	CCa/TTa	5/13	0.3	3	FACETS	0.902	0.794	1	0.451	0.397	0.509	CLONAL	1	TRUE	1	0.4	3		430	519	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879141	151879142	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	34	727	1	ENST00000262189.6:c.5803_5804delinsTT	p.Pro1935Phe	p.P1935F	ENST00000262189	NM_170606.2	1935	CCc/TTc	36/59	0.186186619543753	2	FACETS	0.254	0.206	0.307	0.127	0.103	0.154	INDETERMINATE	1	TRUE	0	0.4	2		728	670	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92354981	92354982	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	127	531	0	ENST00000265734.4:c.495_496delinsTT	p.Leu166Phe	p.L166F	ENST00000265734	NM_001259.6	165	ggCCtt/ggTTtt	4/8	0.186186619543753	2	FACETS	1	0.966	1	0.565	0.514	0.618	INDETERMINATE	1	TRUE	0	0.4	2		531	562	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535338	66535339	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	158	722	0	ENST00000273854.3:c.122_123delinsAA	p.Trp41Ter	p.W41*	ENST00000273854	NM_004439.5	41	tGG/tAA	1/18	0.198021907263667	3	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.4	3		722	696	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193529	99193530	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	89	570	1	ENST00000074304.5:c.2724_2725delinsAA	p.Glu909Lys	p.E909K	ENST00000074304	NM_001134224.1	908	ctGGag/ctAAag	25/26	0.298951465986185	3	FACETS	0.802	0.711	0.898	0.401	0.355	0.449	CLONAL	1	TRUE	1	0.4	3		571	666	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917671	151917672	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	71	267	0	ENST00000262189.6:c.3648_3649delinsTT	p.Leu1217Phe	p.L1217F	ENST00000262189	NM_170606.2	1216	gtCCtt/gtTTtt	23/59	0.186186619543753	2	FACETS	1	0.974	1	0.71	0.628	0.796	INDETERMINATE	1	TRUE	0	0.4	2		267	250	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633405	8633406	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	230	729	0	ENST00000356435.5:c.263_264delinsAA	p.Arg88Gln	p.R88Q	ENST00000356435		88	cGG/cAA	3/35	0.288882661069713	3	FACETS	0.952	0.891	1	0.634	0.594	0.676	CLONAL	2	TRUE	0	0.4	3		729	725	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045516	47045517	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	192	311	0	ENST00000377604.3:c.2483_2484delinsTT	p.Pro828Leu	p.P828L	ENST00000377604	NM_001204468.1	828	cCC/cTT	22/24	0.226215400254842	2	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.4	2		311	407	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295253	+	upstream_gene_variant	5'Flank	ONP	GAGG	GAGG	TTCT	novel	NA	P-0012860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	491	259	0				ENST00000310581	NM_198253.2	-/1132			0.3	5	FACETS	1	0.98	1	1	0.996	1	CLONAL	4	TRUE	2	0.4	5		259	956	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0013121-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	643	779	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.721335489700663	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.721335489700663	1		781	1120	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403244	213403244	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs748663394	NA	P-0013121-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	498	777	0	ENST00000342788.4:c.11C>A	p.Ala4Glu	p.A4E	ENST00000342788	NM_005235.2	4	gCg/gAg	1/28	NA	2	FACETS	0.993	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.721335489700663	2		777	1390	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372070	55372070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013121-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	239	345	1	ENST00000297316.4:c.760G>A	p.Ala254Thr	p.A254T	ENST00000297316	NM_022454.3	254	Gcg/Acg	2/2	0.691786689554762	3	FACETS	0.939	0.878	1	0.47	0.439	0.502	CLONAL	1	TRUE	1	0.721335489700663	3		346	960	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882073	36882073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1372104492	NA	P-0013121-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	538	732	1	ENST00000358127.4:c.940G>A	p.Gly314Arg	p.G314R	ENST00000358127	NM_001280556.1	314	Ggg/Agg	8/10	1	2	FACETS	0.99	0.949	1	0.99	0.949	1	CLONAL	1	TRUE	1	0.721335489700663	2		733	1507	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346901	89346901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1455558820	NA	P-0013121-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	377	560	0	ENST00000301030.4:c.6049G>A	p.Ala2017Thr	p.A2017T	ENST00000301030	NM_001256183.1	2017	Gcc/Acc	9/13	1	2	FACETS	0.985	0.937	1	0.985	0.937	1	CLONAL	1	TRUE	1	0.721335489700663	2		560	1061	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256445	46256445	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013121-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1304	761	1056	0	ENST00000371998.3:c.673C>T	p.Gln225Ter	p.Q225*	ENST00000371998		225	Cag/Tag	7/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.721335489700663	2		1056	2065	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923000	44923000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139486036	NA	P-0013121-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	610	950	0	ENST00000377967.4:c.1861C>T	p.Arg621Cys	p.R621C	ENST00000377967	NM_021140.2	621	Cgc/Tgc	16/29	NA	2	FACETS	0.975	0.938	1			1	INDETERMINATE	1	TRUE	NA	0.721335489700663	2		950	1734	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846342	156846342	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746049437	NA	P-0013121-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	568	730	1	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	0.721335489700663	2		731	1513	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930942	39930942	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013121-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1243	687	982	0	ENST00000378444.4:c.2999T>C	p.Met1000Thr	p.M1000T	ENST00000378444	NM_001123385.1	1000	aTg/aCg	5/15	NA	2	FACETS	0.987	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.721335489700663	2		982	1930	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0013121-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	331	779	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.518646618804184	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.531466683963337	1		781	874	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403244	213403244	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs748663394	NA	P-0013121-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	244	777	0	ENST00000342788.4:c.11C>A	p.Ala4Glu	p.A4E	ENST00000342788	NM_005235.2	4	gCg/gAg	1/28	1	2	FACETS	0.927	0.866	0.989	0.927	0.866	0.989	CLONAL	1	TRUE	1	0.531466683963337	2		777	991	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372070	55372070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013121-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	135	345	1	ENST00000297316.4:c.760G>A	p.Ala254Thr	p.A254T	ENST00000297316	NM_022454.3	254	Gcg/Acg	2/2	0.285732053282642	4	FACETS	1	0.984	1	0.68	0.621	0.742	INDETERMINATE	1	TRUE	2	0.531466683963337	4		346	572	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882073	36882073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1372104492	NA	P-0013121-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	291	732	1	ENST00000358127.4:c.940G>A	p.Gly314Arg	p.G314R	ENST00000358127	NM_001280556.1	314	Ggg/Agg	8/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.531466683963337	2		733	1018	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346901	89346901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1455558820	NA	P-0013121-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	139	560	0	ENST00000301030.4:c.6049G>A	p.Ala2017Thr	p.A2017T	ENST00000301030	NM_001256183.1	2017	Gcc/Acc	9/13	1	2	FACETS	0.969	0.886	1	0.969	0.886	1	CLONAL	1	TRUE	1	0.531466683963337	2		560	540	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256445	46256445	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013121-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	237	1056	0	ENST00000371998.3:c.673C>T	p.Gln225Ter	p.Q225*	ENST00000371998		225	Cag/Tag	7/23	1	2	FACETS	0.888	0.829	0.949	0.888	0.829	0.949	CLONAL	1	TRUE	1	0.531466683963337	2		1056	1004	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923000	44923000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139486036	NA	P-0013121-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	325	950	0	ENST00000377967.4:c.1861C>T	p.Arg621Cys	p.R621C	ENST00000377967	NM_021140.2	621	Cgc/Tgc	16/29	0.272696467865617	1	FACETS	0.687	0.648	0.726	0.687	0.648	0.726	INDETERMINATE	1	TRUE	0	0.531466683963337	1		950	1308	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881001	37881002	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGCTCCCC	rs397516981	NA	P-0013172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	402	671	0	ENST00000269571.5:c.2331_2339dup	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	gtg/gtGGGCTCCCCg	20/27	1	2	FACETS	0.838	0.796	0.881	0.838	0.796	0.881	CLONAL	1	TRUE	1	0.661143945181197	2		671	1451	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794788	42794788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs891723299	NA	P-0013172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	59	577	0	ENST00000575354.2:c.1868G>A	p.Gly623Glu	p.G623E	ENST00000575354	NM_015125.3	623	gGa/gAa	10/20	1	2	FACETS	0.169	0.145	0.196	0.169	0.145	0.196	SUBCLONAL	1	TRUE	1	0.661143945181197	2		577	1053	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118758	115118758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	409	647	0	ENST00000257566.3:c.583del	p.Glu195AsnfsTer13	p.E195Nfs*13	ENST00000257566	NM_016569.3	195	Gaa/aa	2/8	1	2	FACETS	0.977	0.93	1	0.977	0.93	1	CLONAL	1	TRUE	1	0.661143945181197	2		647	1267	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857530	68857531	+	splice_donor_variant	Splice_Site	DEL	GT	GT	-	novel	NA	P-0013172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	164	273	0	ENST00000261769.5:c.2164+1_2164+2del		p.X722_splice	ENST00000261769	NM_004360.3	722			0.661143945181197	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.661143945181197	1		273	332	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013196-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	214	251	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		251	882	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013196-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	119	251	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.846	0.768	0.928	0.846	0.768	0.928	CLONAL	1	TRUE	1	0.5717904636935	2		251	492	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476265	88476265	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013196-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	205	961	2	ENST00000360948.2:c.1867G>A	p.Gly623Arg	p.G623R	ENST00000360948	NM_001012338.2	623	Gga/Aga	15/19	1	2	FACETS	0.634	0.587	0.683	0.634	0.587	0.683	SUBCLONAL	1	TRUE	1	0.5717904636935	2		963	1131	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953741	48953742	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0013604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	181	353	0	ENST00000267163.4:c.1346dup	p.Val450SerfsTer13	p.V450Sfs*13	ENST00000267163	NM_000321.2	448	-/G	14/27	0.203281550483603	2	FACETS	0.991	0.915	1	0.991	0.915	1	CLONAL	2	TRUE	0	0.228695222197789	2		353	799	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0013604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	255	633	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.220219361255588	2	FACETS	0.971	0.909	1	0.971	0.909	1	CLONAL	2	TRUE	0	0.228695222197789	2		633	1148	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528276	157528276	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	86	559	0	ENST00000346085.5:c.6001G>A	p.Glu2001Lys	p.E2001K	ENST00000346085	NM_020732.3	2001	Gag/Aag	20/20	1	2	FACETS	0.691	0.61	0.779	0.691	0.61	0.779	SUBCLONAL	1	TRUE	1	0.228695222197789	2		559	1088	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845922	156845922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1400	171	651	0	ENST00000524377.1:c.1552G>A	p.Glu518Lys	p.E518K	ENST00000524377	NM_002529.3	518	Gag/Aag	13/17	0.228695222197789	5	FACETS	1	0.983	1	0.32	0.293	0.348	CLONAL	1	TRUE	1	0.228695222197789	5		651	1571	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16247363	16247363	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0013604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	70	287	0	ENST00000375759.3:c.1636-2A>T		p.X546_splice	ENST00000375759	NM_015001.2	546			1	2	FACETS	0.948	0.826	1	0.948	0.826	1	CLONAL	1	TRUE	1	0.228695222197789	2		287	646	SUCCESS
CBL	867	MSKCC	GRCh37	11	119077153	119077153	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs772525018	NA	P-0013604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	75	276	0	ENST00000264033.4:c.26C>G	p.Ser9Cys	p.S9C	ENST00000264033	NM_005188.3	9	tCt/tGt	1/16	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.228695222197789	2		276	584	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006361	12006361	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1264	80	488	1	ENST00000396373.4:c.329G>T	p.Gly110Val	p.G110V	ENST00000396373	NM_001987.4	110	gGt/gTt	4/8	0.228695222197789	3	FACETS	0.58	0.508	0.658			1	SUBCLONAL	1	TRUE	NA	0.228695222197789	3		489	1344	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900403	32900403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	102	607	0	ENST00000380152.3:c.500C>T	p.Thr167Ile	p.T167I	ENST00000380152		167	aCa/aTa	6/27	0.203281550483603	2	FACETS	0.777	0.693	0.867	0.389	0.346	0.434	SUBCLONAL	1	TRUE	0	0.228695222197789	2		607	1148	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060949	38060949	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	140	273	0	ENST00000250448.2:c.1040C>T	p.Ser347Leu	p.S347L	ENST00000250448	NM_004496.3	347	tCg/tTg	2/2	0.191084940638685	4	FACETS	0.925	0.847	1	0.925	0.847	1	CLONAL	3	TRUE	1	0.228695222197789	4		273	542	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396698	396698	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	96	538	0	ENST00000262320.3:c.328G>T	p.Gly110Cys	p.G110C	ENST00000262320	NM_003502.3	110	Ggc/Tgc	2/11	1	2	FACETS	0.844	0.75	0.944	0.844	0.75	0.944	CLONAL	1	TRUE	1	0.228695222197789	2		538	995	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14022087	14022087	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	80	331	0	ENST00000311895.7:c.787G>C	p.Asp263His	p.D263H	ENST00000311895	NM_005236.2	263	Gac/Cac	4/11	1	2	FACETS	0.99	0.871	1	0.99	0.871	1	CLONAL	1	TRUE	1	0.228695222197789	2		331	707	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226500	41226500	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202631	NA	P-0013604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	180	445	0	ENST00000357654.3:c.4523G>A	p.Trp1508Ter	p.W1508*	ENST00000357654	NM_007294.3	1508	tGg/tAg	14/23	0.15708667963233	3	FACETS	0.857	0.79	0.928	0.857	0.79	0.928	CLONAL	2	TRUE	1	0.228695222197789	3		445	1023	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40742002	40742002	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1556	271	425	0	ENST00000392038.2:c.970G>T	p.Asp324Tyr	p.D324Y	ENST00000392038	NM_001626.4	324	Gac/Tac	11/14	0.228695222197789	13	FACETS	0.976	0.913	1			1	CLONAL	3	TRUE	NA	0.228695222197789	13		425	1827	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181353	185181353	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1192	85	527	0	ENST00000265026.3:c.1294G>T	p.Glu432Ter	p.E432*	ENST00000265026	NM_004721.4	432	Gaa/Taa	8/14	0.191084940638685	4	FACETS	0.715	0.63	0.807	0.238	0.21	0.269	SUBCLONAL	1	TRUE	1	0.228695222197789	4		527	1277	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707641	176707641	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	106	434	0	ENST00000439151.2:c.5698A>G	p.Thr1900Ala	p.T1900A	ENST00000439151	NM_022455.4	1900	Act/Gct	18/23	0.203281550483603	2	FACETS	0.96	0.859	1	0.48	0.429	0.534	CLONAL	1	TRUE	0	0.228695222197789	2		434	966	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045806	180045806	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	100	546	0	ENST00000261937.6:c.2965G>T	p.Glu989Ter	p.E989*	ENST00000261937	NM_182925.4	989	Gag/Tag	21/30	0.203281550483603	2	FACETS	0.935	0.834	1	0.468	0.417	0.522	CLONAL	1	TRUE	0	0.228695222197789	2		546	935	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339262	116339262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	153	614	0	ENST00000397752.3:c.124C>T	p.Gln42Ter	p.Q42*	ENST00000397752	NM_000245.2	42	Cag/Tag	2/21	0.15708667963233	3	FACETS	1	0.976	1	0.594	0.541	0.648	CLONAL	1	TRUE	1	0.228695222197789	3		614	1256	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44733177	44733177	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	63	531	0	ENST00000377967.4:c.169T>C	p.Phe57Leu	p.F57L	ENST00000377967	NM_021140.2	57	Ttt/Ctt	2/29	0.228695222197789	1	FACETS	0.565	0.487	0.649	0.565	0.487	0.649	SUBCLONAL	1	TRUE	0	0.228695222197789	1		531	864	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76949368	76949369	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0013604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1316	77	767	0	ENST00000373344.5:c.428_429delinsTT	p.Gly143Val	p.G143V	ENST00000373344	NM_000489.3	143	gGG/gTT	6/35	0.228695222197789	1	FACETS	0.428	0.374	0.487	0.428	0.374	0.487	SUBCLONAL	1	TRUE	0	0.228695222197789	1		767	1393	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188261	10188261	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0013638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	356	943	0	ENST00000256474.2:c.404T>A	p.Leu135Ter	p.L135*	ENST00000256474	NM_000551.3	135	tTa/tAa	2/3	0.408814565807954	2	FACETS	0.951	0.904	0.998	0.951	0.904	0.998	CLONAL	2	TRUE	0	0.408814565807954	2		943	916	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334727	81334727	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	341	1029	0	ENST00000222390.5:c.1989G>T	p.Lys663Asn	p.K663N	ENST00000222390	NM_000601.4	663	aaG/aaT	17/18	0.339695982652719	4	FACETS	0.966	0.913	1	0.966	0.913	1	CLONAL	2	TRUE	2	0.408814565807954	4		1029	1217	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43806072	43806072	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	171	935	0	ENST00000372470.3:c.868C>A	p.Gln290Lys	p.Q290K	ENST00000372470	NM_005373.2	290	Caa/Aaa	6/12	0.409103956764316	3	FACETS	1	0.96	1	0.535	0.492	0.58	CLONAL	1	TRUE	1	0.408814565807954	3		935	941	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627531	37627531	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	261	842	0	ENST00000447079.4:c.1446del	p.Lys482AsnfsTer14	p.K482Nfs*14	ENST00000447079	NM_015083.1	482	aaG/aa	2/14	0.409103956764316	3	FACETS	0.903	0.848	0.958	0.903	0.848	0.958	CLONAL	2	TRUE	1	0.408814565807954	3		842	852	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623170	52623170	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	335	820	2	ENST00000394830.3:c.2881G>T	p.Gly961Ter	p.G961*	ENST00000394830	NM_018313.4	961	Gga/Tga	19/30	0.408814565807954	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.408814565807954	2		822	811	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687293	117687293	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs774104513	NA	P-0013638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	143	846	0	ENST00000368508.3:c.2758C>G	p.Pro920Ala	p.P920A	ENST00000368508	NM_002944.2	920	Cca/Gca	18/43	0.409103956764316	3	FACETS	1	0.927	1	0.509	0.464	0.557	CLONAL	1	TRUE	1	0.408814565807954	3		846	827	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163662	47163663	+	frameshift_variant	Frame_Shift_Ins	INS	TT	TT	CTTGAA	novel	NA	P-0013638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	137	567	0	ENST00000409792.3:c.2463_2464delinsTTCAAG	p.Asn822SerfsTer3	p.N822Sfs*3	ENST00000409792	NM_014159.6	821	tcAAat/tcTTCAAGat	3/21	0.408814565807954	2	FACETS	0.79	0.725	0.857	0.79	0.725	0.857	SUBCLONAL	2	TRUE	0	0.408814565807954	2		567	424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	122	302	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	0.29242531814924	3	FACETS	1	0.964	1			1	CLONAL	1	TRUE	NA	0.29242531814924	3		302	838	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175996746	175996746	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	124	486	1	ENST00000367669.3:c.1691G>A	p.Ser564Asn	p.S564N	ENST00000367669	NM_022457.5	564	aGc/aAc	15/20	1	2	FACETS	0.724	0.653	0.799	0.724	0.653	0.799	SUBCLONAL	1	TRUE	1	0.29242531814924	2		487	1172	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376659	31376659	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	53	255	0	ENST00000328111.2:c.655-1G>T		p.X219_splice	ENST00000328111	NM_006892.3	219			0.274486849909123	3	FACETS	0.496	0.422	0.578	0.248	0.211	0.289	SUBCLONAL	1	TRUE	1	0.29242531814924	3		255	837	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288925	11288925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	123	350	0	ENST00000361445.4:c.2830G>A	p.Asp944Asn	p.D944N	ENST00000361445	NM_004958.3	944	Gat/Aat	19/58	1	2	FACETS	0.861	0.778	0.949	0.861	0.778	0.949	CLONAL	1	TRUE	1	0.29242531814924	2		350	977	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106975	27106976	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	82	278	0	ENST00000324856.7:c.6587dup	p.Phe2198LeufsTer27	p.F2198Lfs*27	ENST00000324856	NM_006015.4	2196	ctg/cTtg	20/20	1	2	FACETS	0.714	0.629	0.806	0.714	0.629	0.806	SUBCLONAL	1	TRUE	1	0.29242531814924	2		278	785	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932865	36932865	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1457	183	703	0	ENST00000361632.4:c.2006G>T	p.Ser669Ile	p.S669I	ENST00000361632		669	aGc/aTc	15/16	1	2	FACETS	0.763	0.702	0.828	0.763	0.702	0.828	SUBCLONAL	1	TRUE	1	0.29242531814924	2		703	1640	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435677	18435677	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	59	208	0	ENST00000266497.5:c.662G>A	p.Trp221Ter	p.W221*	ENST00000266497		221	tGg/tAg	1/31	1	2	FACETS	0.797	0.687	0.918	0.797	0.687	0.918	CLONAL	1	TRUE	1	0.29242531814924	2		208	506	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246365	46246365	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	231	388	0	ENST00000334344.6:c.4461del	p.Asp1488ThrfsTer28	p.D1488Tfs*28	ENST00000334344	NM_152641.2	1487	Ccc/cc	15/21	0.29242531814924	3	FACETS	0.857	0.799	0.918	0.857	0.799	0.918	CLONAL	2	TRUE	1	0.29242531814924	3		388	1056	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478893	56478893	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1541	173	600	1	ENST00000267101.3:c.349A>T	p.Ile117Phe	p.I117F	ENST00000267101	NM_001982.3	117	Atc/Ttc	3/28	0.29242531814924	3	FACETS	0.791	0.725	0.861	0.396	0.362	0.431	SUBCLONAL	1	TRUE	1	0.29242531814924	3		601	1714	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864768	57864768	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1428	470	715	0	ENST00000228682.2:c.2245G>T	p.Gly749Cys	p.G749C	ENST00000228682	NM_005269.2	749	Ggc/Tgc	12/12	0.29242531814924	3	FACETS	0.971	0.925	1	0.971	0.925	1	CLONAL	2	TRUE	1	0.29242531814924	3		715	1898	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112047	115112047	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	79	369	0	ENST00000257566.3:c.1693G>T	p.Ala565Ser	p.A565S	ENST00000257566	NM_016569.3	565	Gct/Tct	7/8	0.146102366778474	2	FACETS	0.667	0.586	0.755	0.334	0.293	0.378	INDETERMINATE	1	TRUE	0	0.29242531814924	2		369	810	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566212	95566212	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	82	441	0	ENST00000393063.1:c.4111G>T	p.Val1371Leu	p.V1371L	ENST00000393063	NM_030621.3	1371	Gtg/Ttg	23/28	0.196165115367825	3	FACETS	0.609	0.536	0.689	0.305	0.268	0.345	SUBCLONAL	1	TRUE	1	0.29242531814924	3		441	1055	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557401	29557401	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs267606599	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	108	236	0	ENST00000356175.3:c.3113+1G>T		p.X1038_splice	ENST00000356175	NM_000267.3	1038			0.146102366778474	2	FACETS	1	0.977	1	0.648	0.583	0.716	INDETERMINATE	1	TRUE	0	0.29242531814924	2		236	570	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436001	56436001	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	36	241	0	ENST00000407977.2:c.1136A>T	p.Gln379Leu	p.Q379L	ENST00000407977		379	cAg/cTg	9/10	0.146102366778474	2	FACETS	0.415	0.34	0.499	0.207	0.17	0.25	INDETERMINATE	1	TRUE	0	0.29242531814924	2		241	594	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56798141	56798141	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	218	534	0	ENST00000337432.4:c.872A>T	p.Asp291Val	p.D291V	ENST00000337432	NM_058216.2	291	gAt/gTt	6/9	0.146102366778474	2	FACETS	1	0.977	1	0.561	0.52	0.603	INDETERMINATE	1	TRUE	0	0.29242531814924	2		534	1330	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59878765	59878765	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	153	372	0	ENST00000259008.2:c.989G>T	p.Gly330Val	p.G330V	ENST00000259008	NM_032043.2	330	gGg/gTg	8/20	0.146102366778474	2	FACETS	1	0.942	1	0.52	0.475	0.567	INDETERMINATE	1	TRUE	0	0.29242531814924	2		372	1007	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216598	2216598	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	172	419	1	ENST00000398665.3:c.2242G>T	p.Val748Leu	p.V748L	ENST00000398665	NM_032482.2	748	Gtg/Ttg	20/28	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.29242531814924	2		420	1096	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600330	10600330	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	183	425	0	ENST00000171111.5:c.1525G>T	p.Gly509Trp	p.G509W	ENST00000171111	NM_203500.1	509	Ggg/Tgg	4/6	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.29242531814924	2		425	1119	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47724980	47724980	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1369	151	547	0	ENST00000449228.1:c.764G>C	p.Gly255Ala	p.G255A	ENST00000449228	NM_001127240.2	255	gGg/gCg	4/4	1	2	FACETS	0.679	0.619	0.743	0.679	0.619	0.743	SUBCLONAL	1	TRUE	1	0.29242531814924	2		547	1520	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905993	50905993	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs980303681	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1228	179	557	0	ENST00000440232.2:c.965G>T	p.Arg322Leu	p.R322L	ENST00000440232	NM_002691.3	322	cGc/cTc	8/27	1	2	FACETS	0.87	0.8	0.944	0.87	0.8	0.944	CLONAL	1	TRUE	1	0.29242531814924	2		557	1407	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872776	136872776	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2166	142	809	0	ENST00000241393.3:c.722C>T	p.Thr241Ile	p.T241I	ENST00000241393	NM_003467.2	241	aCa/aTa	2/2	0.274486849909123	3	FACETS	0.482	0.437	0.53	0.241	0.218	0.265	SUBCLONAL	1	TRUE	1	0.29242531814924	3		809	2308	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295774	212295774	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	82	492	0	ENST00000342788.4:c.2539C>G	p.Arg847Gly	p.R847G	ENST00000342788	NM_005235.2	847	Cgt/Ggt	21/28	1	2	FACETS	0.547	0.481	0.618	0.547	0.481	0.618	SUBCLONAL	1	TRUE	1	0.29242531814924	2		492	1025	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546635	9546635	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1320	291	605	2	ENST00000353224.5:c.1387G>T	p.Val463Leu	p.V463L	ENST00000353224	NM_177990.2	463	Gta/Tta	5/10	0.274486849909123	3	FACETS	1	0.993	1	0.708	0.664	0.753	CLONAL	1	TRUE	1	0.29242531814924	3		607	1611	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735452	40735452	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	158	557	2	ENST00000373198.4:c.3421C>A	p.Gln1141Lys	p.Q1141K	ENST00000373198	NM_133170.3	1141	Caa/Aaa	25/32	NA	2	FACETS	0.918	0.84	1			1	INDETERMINATE	1	TRUE	NA	0.29242531814924	2		559	1177	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735461	40735461	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1222754595	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	98	538	0	ENST00000373198.4:c.3412C>A	p.Leu1138Ile	p.L1138I	ENST00000373198	NM_133170.3	1138	Ctc/Atc	25/32	NA	2	FACETS	0.587	0.522	0.657			1	INDETERMINATE	1	TRUE	NA	0.29242531814924	2		538	1141	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790149	40790149	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	56	196	0	ENST00000373198.4:c.2582C>A	p.Thr861Asn	p.T861N	ENST00000373198	NM_133170.3	861	aCc/aAc	18/32	NA	2	FACETS	0.796	0.683	0.92			1	INDETERMINATE	1	TRUE	NA	0.29242531814924	2		196	481	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259206	89259206	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	45	361	0	ENST00000336596.2:c.350A>T	p.Lys117Met	p.K117M	ENST00000336596	NM_005233.5	117	aAg/aTg	3/17	1	2	FACETS	0.355	0.297	0.42	0.355	0.297	0.42	SUBCLONAL	1	TRUE	1	0.29242531814924	2		361	866	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612212	189612212	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	96	367	0	ENST00000264731.3:c.1964G>T	p.Arg655Leu	p.R655L	ENST00000264731	NM_003722.4	655	cGa/cTa	14/14	0.196165115367825	3	FACETS	0.783	0.696	0.876	0.392	0.348	0.438	SUBCLONAL	1	TRUE	1	0.29242531814924	3		367	961	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946301	55946301	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	60	269	0	ENST00000263923.4:c.3878C>A	p.Ser1293Tyr	p.S1293Y	ENST00000263923	NM_002253.2	1293	tCt/tAt	30/30	1	2	FACETS	0.585	0.504	0.675	0.585	0.504	0.675	SUBCLONAL	1	TRUE	1	0.29242531814924	2		269	701	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356209	66356209	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	79	422	0	ENST00000273854.3:c.1288G>T	p.Asp430Tyr	p.D430Y	ENST00000273854	NM_004439.5	430	Gat/Tat	5/18	1	2	FACETS	0.544	0.477	0.616	0.544	0.477	0.616	SUBCLONAL	1	TRUE	1	0.29242531814924	2		422	994	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871262	35871262	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	146	332	0	ENST00000303115.3:c.484G>T	p.Val162Phe	p.V162F	ENST00000303115	NM_002185.3	162	Gtt/Ttt	4/8	0.196165115367825	3	FACETS	1	0.98	1	0.623	0.569	0.681	CLONAL	1	TRUE	1	0.29242531814924	3		332	918	SUCCESS
APC	324	MSKCC	GRCh37	5	112179493	112179493	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	131	569	1	ENST00000257430.4:c.8202A>T	p.Lys2734Asn	p.K2734N	ENST00000257430	NM_000038.5	2734	aaA/aaT	16/16	1	2	FACETS	0.724	0.655	0.797	0.724	0.655	0.797	SUBCLONAL	1	TRUE	1	0.29242531814924	2		570	1237	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457684	149457684	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	84	485	1	ENST00000286301.3:c.720C>A	p.Asn240Lys	p.N240K	ENST00000286301	NM_005211.3	240	aaC/aaA	5/22	1	2	FACETS	0.507	0.446	0.572	0.507	0.446	0.572	SUBCLONAL	1	TRUE	1	0.29242531814924	2		486	1134	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503812	149503812	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	120	472	0	ENST00000261799.4:c.2023+1G>T		p.X675_splice	ENST00000261799	NM_002609.3	675			1	2	FACETS	0.715	0.644	0.79	0.715	0.644	0.79	SUBCLONAL	1	TRUE	1	0.29242531814924	2		472	1148	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041076	112041076	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1446	78	735	0	ENST00000368678.4:c.179G>T	p.Gly60Val	p.G60V	ENST00000368678		60	gGa/gTa	3/13	1	2	FACETS	0.35	0.306	0.398	0.35	0.306	0.398	SUBCLONAL	1	TRUE	1	0.29242531814924	2		735	1524	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739732	41739732	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1669	187	786	0	ENST00000242208.4:c.241del	p.Ala81ArgfsTer4	p.A81Rfs*4	ENST00000242208	NM_002192.2	81	Gcg/cg	2/3	1	2	FACETS	0.689	0.634	0.747	0.689	0.634	0.747	SUBCLONAL	1	TRUE	1	0.29242531814924	2		786	1856	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842373	151842373	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	75	280	0	ENST00000262189.6:c.14039G>T	p.Gly4680Val	p.G4680V	ENST00000262189	NM_170606.2	4680	gGg/gTg	54/59	0.196165115367825	3	FACETS	0.805	0.705	0.914	0.403	0.352	0.457	CLONAL	1	TRUE	1	0.29242531814924	3		280	730	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371713	55371713	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	65	287	0	ENST00000297316.4:c.403T>A	p.Tyr135Asn	p.Y135N	ENST00000297316	NM_022454.3	135	Tac/Aac	2/2	0.2026609161837	4	FACETS	0.723	0.625	0.829	0.361	0.312	0.415	SUBCLONAL	1	TRUE	2	0.29242531814924	4		287	795	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372304	55372304	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	76	252	0	ENST00000297316.4:c.994C>A	p.Gln332Lys	p.Q332K	ENST00000297316	NM_022454.3	332	Cag/Aag	2/2	0.2026609161837	4	FACETS	0.957	0.839	1	0.478	0.419	0.542	CLONAL	1	TRUE	2	0.29242531814924	4		252	702	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331585	8331585	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	139	549	0	ENST00000356435.5:c.5531G>A	p.Cys1844Tyr	p.C1844Y	ENST00000356435		1844	tGc/tAc	33/35	1	2	FACETS	0.802	0.728	0.879	0.802	0.728	0.879	CLONAL	1	TRUE	1	0.29242531814924	2		549	1186	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341847	8341847	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	92	565	0	ENST00000356435.5:c.4793C>A	p.Thr1598Lys	p.T1598K	ENST00000356435		1598	aCa/aAa	29/35	1	2	FACETS	0.533	0.472	0.598	0.533	0.472	0.598	SUBCLONAL	1	TRUE	1	0.29242531814924	2		565	1181	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499774	8499774	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	67	478	0	ENST00000356435.5:c.2195G>T	p.Trp732Leu	p.W732L	ENST00000356435		732	tGg/tTg	14/35	1	2	FACETS	0.442	0.383	0.507	0.442	0.383	0.507	SUBCLONAL	1	TRUE	1	0.29242531814924	2		478	1037	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349009	70349009	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1340	128	646	1	ENST00000374080.3:c.3521G>T	p.Arg1174Leu	p.R1174L	ENST00000374080		1174	cGc/cTc	25/45	1	2	FACETS	0.596	0.538	0.658	0.596	0.538	0.658	SUBCLONAL	1	TRUE	1	0.29242531814924	2		647	1468	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	166	251	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.87	0.806	0.935	0.87	0.806	0.935	CLONAL	1	TRUE	1	0.8	2		251	477	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252155	226252155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	77	110	0	ENST00000366813.1:c.103G>T	p.Gly35Trp	p.G35W	ENST00000366813		35	Ggg/Tgg	1/3	1	2	FACETS	0.883	0.789	0.98	0.883	0.789	0.98	CLONAL	1	TRUE	1	0.8	2		110	218	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0013849-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	75	941	2	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.12	2		943	1186	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604656	48604656	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013849-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	33	427	0	ENST00000342988.3:c.1478A>G	p.Asp493Gly	p.D493G	ENST00000342988	NM_005359.5	493	gAt/gGt	12/12	1	2	FACETS	0.862	0.7	1	0.862	0.7	1	CLONAL	1	TRUE	1	0.12	2		427	638	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450267	50450267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013849-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	50	657	0	ENST00000331340.3:c.451G>A	p.Gly151Arg	p.G151R	ENST00000331340	NM_006060.4	151	Ggg/Agg	5/8	1	2	FACETS	0.836	0.707	0.979	0.836	0.707	0.979	CLONAL	1	TRUE	1	0.12	2		657	997	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492590	56492590	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013849-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	66	664	0	ENST00000267101.3:c.2740G>C	p.Gly914Arg	p.G914R	ENST00000267101	NM_001982.3	914	Ggg/Cgg	23/28	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.12	2		664	1092	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	196	328	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.127675938685569	4	FACETS	1	0.963	1	1	0.963	1	INDETERMINATE	2	TRUE	2	0.279815345566122	4		328	846	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	268	613	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.929	0.872	0.988	1	0.995	1	CLONAL	2	TRUE	1	0.279815345566122	2		614	1031	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0014168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	235	686	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.219827273824273	2	FACETS	1	0.992	1	0.732	0.682	0.783	CLONAL	1	TRUE	0	0.279815345566122	2		686	1148	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210451	2210451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138206172	NA	P-0014168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	90	460	1	ENST00000398665.3:c.1058C>T	p.Ala353Val	p.A353V	ENST00000398665	NM_032482.2	353	gCg/gTg	13/28	1	2	FACETS	0.782	0.693	0.877	0.782	0.693	0.877	SUBCLONAL	1	TRUE	1	0.279815345566122	2		461	823	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969884	81969884	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199840870	NA	P-0014168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1431	317	962	1	ENST00000359376.3:c.2953G>A	p.Val985Ile	p.V985I	ENST00000359376	NM_002661.3	985	Gtc/Atc	27/33	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.279815345566122	2		963	1748	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101179	41101179	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770753852	NA	P-0014168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	98	248	0	ENST00000373198.4:c.1177G>A	p.Val393Met	p.V393M	ENST00000373198	NM_133170.3	393	Gtg/Atg	8/32	0.127675938685569	4	FACETS	1	0.946	1	1	0.946	1	INDETERMINATE	2	TRUE	2	0.279815345566122	4		248	414	SUCCESS
APC	324	MSKCC	GRCh37	5	112175287	112175288	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0014168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	154	383	0	ENST00000257430.4:c.3999dup	p.Ser1334IlefsTer8	p.S1334Ifs*8	ENST00000257430	NM_000038.5	1332	-/A	16/16	0.279815345566122	2	FACETS	0.848	0.779	0.92	0.848	0.779	0.92	CLONAL	2	TRUE	0	0.279815345566122	2		383	649	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0014190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	58	169	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.969	0.832	1	0.969	0.832	1	CLONAL	1	TRUE	1	0.19	2		169	630	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0014190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	48	396	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.19	2		396	498	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0014190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	32	369	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.84	0.682	1	0.84	0.682	1	CLONAL	1	TRUE	1	0.19	2		369	401	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394805	45394805	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	35	287	0	ENST00000262160.6:c.544C>T	p.Arg182Ter	p.R182*	ENST00000262160	NM_005901.5	182	Cga/Tga	5/11	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.19	2		287	343	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395776	45395776	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	32	305	1	ENST00000262160.6:c.358C>T	p.Arg120Ter	p.R120*	ENST00000262160	NM_005901.5	120	Cga/Tga	4/11	1	2	FACETS	0.818	0.664	0.991	0.818	0.664	0.991	CLONAL	1	TRUE	1	0.19	2		306	412	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457226	67457227	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	TGGCAGGTCCCTGGATGGCCGG	novel	NA	P-0014190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	44	498	0	ENST00000327367.4:c.207-5_223dup		p.X69_splice	ENST00000327367	NM_005902.3	69			1	2	FACETS	0.78	0.653	0.92	0.78	0.653	0.92	CLONAL	1	TRUE	1	0.19	2		498	594	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59793405	59793405	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	34	452	0	ENST00000259008.2:c.2399A>G	p.Tyr800Cys	p.Y800C	ENST00000259008	NM_032043.2	800	tAc/tGc	17/20	1	2	FACETS	0.871	0.712	1	0.871	0.712	1	CLONAL	1	TRUE	1	0.19	2		452	411	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593520	48593520	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	28	270	0	ENST00000342988.3:c.1271A>T	p.Asp424Val	p.D424V	ENST00000342988	NM_005359.5	424	gAt/gTt	10/12	1	2	FACETS	1	0.822	1	1	0.822	1	CLONAL	1	TRUE	1	0.19	2		270	287	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593532	48593533	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0014190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	17	241	0	ENST00000342988.3:c.1284_1285del	p.Lys428AsnfsTer11	p.K428Nfs*11	ENST00000342988	NM_005359.5	428	aAG/a	10/12	1	2	FACETS	0.694	0.518	0.902	0.694	0.518	0.902	SUBCLONAL	1	TRUE	1	0.19	2		241	258	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273230	198273230	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	65	555	2	ENST00000335508.6:c.980C>T	p.Pro327Leu	p.P327L	ENST00000335508	NM_012433.2	327	cCg/cTg	8/25	1	2	FACETS	0.993	0.86	1	0.993	0.86	1	CLONAL	1	TRUE	1	0.19	2		557	689	SUCCESS
APC	324	MSKCC	GRCh37	5	112173893	112173893	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	37	303	0	ENST00000257430.4:c.2602G>T	p.Glu868Ter	p.E868*	ENST00000257430	NM_000038.5	868	Gaa/Taa	16/16	1	2	FACETS	0.891	0.735	1	0.891	0.735	1	CLONAL	1	TRUE	1	0.19	2		303	437	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0014224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	101	685	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.768	0.688	0.853	0.768	0.688	0.853	SUBCLONAL	1	TRUE	1	0.44	2		685	598	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0014224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	103	468	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.823	0.738	0.912	0.823	0.738	0.912	CLONAL	1	TRUE	1	0.44	2		468	569	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0014224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	54	556	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.398	0.34	0.463	0.398	0.34	0.463	SUBCLONAL	1	TRUE	1	0.44	2		556	616	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0014224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	27	528	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.266	0.211	0.329	0.266	0.211	0.329	SUBCLONAL	1	TRUE	1	0.44	2		528	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0014224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	33	680	3	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	1	2	FACETS	0.175	0.142	0.213	0.175	0.142	0.213	SUBCLONAL	1	TRUE	1	0.44	2		683	857	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725042	89725042	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0014224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	65	212	0	ENST00000371953.3:c.1027-2A>T		p.X343_splice	ENST00000371953	NM_000314.4	343			1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.44	2		212	265	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023151	27023179	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	-	novel	NA	P-0014224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	104	98	0	ENST00000324856.7:c.267_295del	p.Ser90ProfsTer11	p.S90Pfs*11	ENST00000324856	NM_006015.4	86	gGCGGAGCCGGCAGCGGCGGCGGGCCCGGC/g	1/20	1	2	FACETS	1	0.977	1	1	0.991	1	CLONAL	2	TRUE	1	0.44	2		98	199	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692929	89692929	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1554898159	NA	P-0014224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	120	603	0	ENST00000371953.3:c.413A>G	p.Tyr138Cys	p.Y138C	ENST00000371953	NM_000314.4	138	tAt/tGt	5/9	1	2	FACETS	0.959	0.869	1	0.959	0.869	1	CLONAL	1	TRUE	1	0.44	2		603	569	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105966	27105967	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0014224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	95	428	0	ENST00000324856.7:c.5581_5582dup	p.Ser1861ArgfsTer23	p.S1861Rfs*23	ENST00000324856	NM_006015.4	1859	-/GA	20/20	1	2	FACETS	0.837	0.748	0.931	0.837	0.748	0.931	CLONAL	1	TRUE	1	0.44	2		428	516	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380346	14380346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	134	440	0	ENST00000256196.4:c.71G>A	p.Gly24Asp	p.G24D	ENST00000256196		24	gGc/gAc	1/6	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.44	2		440	489	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118370604	118370605	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	10	343	0	ENST00000534358.1:c.6135dup	p.Lys2046Ter	p.K2046*	ENST00000534358	NM_005933.3	2045	gat/gaTt	24/36	1	2	FACETS	0.855	0.58	1	0.855	0.58	1	CLONAL	1	TRUE	1	0.15	2		343	156	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061211	38061240	+	inframe_deletion	In_Frame_Del	DEL	AGTAGCAGCCGTTCTCGAACATGTTGCCGG	AGTAGCAGCCGTTCTCGAACATGTTGCCGG	-	novel	NA	P-0014249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	47	623	0	ENST00000250448.2:c.749_778del	p.Ser250_Tyr259del	p.S250_Y259del	ENST00000250448	NM_004496.3	250	tCCGGCAACATGTTCGAGAACGGCTGCTACTtg/ttg	2/2	1	2	FACETS	0.972	0.819	1	0.972	0.819	1	CLONAL	1	TRUE	1	0.15	2		623	645	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0014361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	103	535	2	ENST00000269305.4:c.994-1G>T		p.X332_splice	ENST00000269305	NM_001126112.2	332			1	2	FACETS	0.905	0.808	1	0.905	0.808	1	CLONAL	1	TRUE	1	0.235269214600113	2		537	968	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177558	56177558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	114	277	0	ENST00000399503.3:c.2531C>T	p.Ser844Phe	p.S844F	ENST00000399503	NM_005921.1	844	tCc/tTc	14/20	0.199909171343257	2	FACETS	1	0.983	1	0.742	0.669	0.819	CLONAL	1	TRUE	0	0.235269214600113	2		277	653	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220634	2220634	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	154	761	0	ENST00000326181.6:c.251G>T	p.Arg84Leu	p.R84L	ENST00000326181	NM_032271.2	84	cGc/cTc	5/21	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.235269214600113	2		761	1279	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446398	70446398	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	105	532	2	ENST00000373644.4:c.5338C>T	p.Arg1780Ter	p.R1780*	ENST00000373644	NM_030625.2	1780	Cga/Tga	11/12	1	2	FACETS	0.812	0.726	0.904	0.812	0.726	0.904	CLONAL	1	TRUE	1	0.235269214600113	2		534	1099	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531793	46531793	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	81	383	0	ENST00000262741.5:c.554A>G	p.His185Arg	p.H185R	ENST00000262741	NM_003629.3	185	cAc/cGc	5/10	0.234903690272526	3	FACETS	0.916	0.806	1	0.458	0.403	0.518	CLONAL	1	TRUE	1	0.235269214600113	3		383	840	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203493	108203493	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs140263969	NA	P-0014361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	74	184	0	ENST00000278616.4:c.7793G>T	p.Arg2598Leu	p.R2598L	ENST00000278616	NM_000051.3	2598	cGa/cTa	53/63	0.235269214600113	3	FACETS	0.96	0.846	1	0.96	0.846	1	CLONAL	2	TRUE	1	0.235269214600113	3		184	366	SUCCESS
CBL	867	MSKCC	GRCh37	11	119145620	119145620	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755244263	NA	P-0014361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	185	411	1	ENST00000264033.4:c.826G>A	p.Glu276Lys	p.E276K	ENST00000264033	NM_005188.3	276	Gaa/Aaa	5/16	0.235269214600113	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.235269214600113	3		412	834	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022436	12022436	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1479	278	959	3	ENST00000396373.4:c.542G>T	p.Arg181Leu	p.R181L	ENST00000396373	NM_001987.4	181	cGc/cTc	5/8	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.235269214600113	2		962	1757	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061174	38061174	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1208147234	NA	P-0014361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	55	248	0	ENST00000250448.2:c.815C>T	p.Pro272Leu	p.P272L	ENST00000250448	NM_004496.3	272	cCg/cTg	2/2	1	2	FACETS	0.876	0.749	1	0.876	0.749	1	CLONAL	1	TRUE	1	0.235269214600113	2		248	534	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831843	72831843	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1205	68	697	0	ENST00000268489.5:c.4738T>C	p.Ser1580Pro	p.S1580P	ENST00000268489	NM_006885.3	1580	Tca/Cca	9/10	1	2	FACETS	0.454	0.393	0.52	0.454	0.393	0.52	SUBCLONAL	1	TRUE	1	0.235269214600113	2		697	1273	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351871	89351871	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1276	192	757	0	ENST00000301030.4:c.1079C>G	p.Pro360Arg	p.P360R	ENST00000301030	NM_001256183.1	360	cCg/cGg	9/13	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.235269214600113	2		757	1468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578199	7578199	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1313	162	739	0	ENST00000269305.4:c.650T>A	p.Val217Glu	p.V217E	ENST00000269305	NM_001126112.2	217	gTg/gAg	6/11	1	2	FACETS	0.934	0.854	1	0.934	0.854	1	CLONAL	1	TRUE	1	0.235269214600113	2		739	1475	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881623	37881623	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1248	150	587	0	ENST00000269571.5:c.2693G>T	p.Arg898Leu	p.R898L	ENST00000269571		898	cGg/cTg	22/27	0.234903690272526	3	FACETS	1	0.927	1	0.51	0.464	0.558	CLONAL	1	TRUE	1	0.235269214600113	3		587	1398	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56409195	56409195	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	85	418	1	ENST00000348428.3:c.1702G>T	p.Glu568Ter	p.E568*	ENST00000348428	NM_006785.3	568	Gaa/Taa	14/17	1	2	FACETS	0.832	0.735	0.938	0.832	0.735	0.938	CLONAL	1	TRUE	1	0.235269214600113	2		419	868	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221238	1221239	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	541	680	0	ENST00000326873.7:c.761_762insT	p.Phe255LeufsTer11	p.F255Lfs*11	ENST00000326873	NM_000455.4	254	ccc/ccTc	6/10	0.231850440761271	2	FACETS	0.945	0.906	0.985	1	0.996	1	CLONAL	3	TRUE	0	0.235269214600113	2		680	1622	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143056	30143056	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	119	814	2	ENST00000389048.3:c.470C>A	p.Pro157His	p.P157H	ENST00000389048	NM_004304.4	157	cCc/cAc	1/29	1	2	FACETS	0.755	0.68	0.836	0.755	0.68	0.836	SUBCLONAL	1	TRUE	1	0.235269214600113	2		816	1339	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448585	89448585	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	95	507	0	ENST00000336596.2:c.1549T>C	p.Tyr517His	p.Y517H	ENST00000336596	NM_005233.5	517	Tat/Cat	7/17	0.193154775956563	1	FACETS	0.731	0.649	0.818	0.731	0.649	0.818	SUBCLONAL	1	TRUE	0	0.235269214600113	1		507	975	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961815	55961815	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	76	329	0	ENST00000263923.4:c.2746G>T	p.Val916Leu	p.V916L	ENST00000263923	NM_002253.2	916	Gtg/Ttg	20/30	1	2	FACETS	0.884	0.775	1	0.884	0.775	1	CLONAL	1	TRUE	1	0.235269214600113	2		329	731	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876344	35876344	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	81	430	0	ENST00000303115.3:c.1136C>A	p.Ala379Asp	p.A379D	ENST00000303115	NM_002185.3	379	gCc/gAc	8/8	1	2	FACETS	0.865	0.761	0.977	0.865	0.761	0.977	CLONAL	1	TRUE	1	0.235269214600113	2		430	796	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227848	55227848	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	43	283	0	ENST00000275493.2:c.1315G>C	p.Ala439Pro	p.A439P	ENST00000275493	NM_005228.3	439	Gca/Cca	12/28	0.193154775956563	1	FACETS	0.644	0.538	0.761	0.644	0.538	0.761	SUBCLONAL	1	TRUE	0	0.235269214600113	1		283	501	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371741	55371741	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	75	513	0	ENST00000297316.4:c.431A>T	p.Gln144Leu	p.Q144L	ENST00000297316	NM_022454.3	144	cAg/cTg	2/2	NA	2	FACETS	0.745	0.651	0.846			1	INDETERMINATE	1	TRUE	NA	0.235269214600113	2		513	856	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798881	135798881	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0014361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	28	160	0	ENST00000298552.3:c.364-2A>G		p.X122_splice	ENST00000298552	NM_001162426.1	122			0.199909171343257	2	FACETS	0.604	0.483	0.743	0.302	0.241	0.372	SUBCLONAL	1	TRUE	0	0.235269214600113	2		160	394	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360540	70360540	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1202	328	809	0	ENST00000374080.3:c.6100A>T	p.Ser2034Cys	p.S2034C	ENST00000374080		2034	Agt/Tgt	42/45	0.235269214600113	1	FACETS	0.804	0.758	0.851	1	0.995	1	CLONAL	2	TRUE	0	0.235269214600113	1		809	1530	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	65	372	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.758	0.658	0.866	0.758	0.658	0.866	SUBCLONAL	1	TRUE	1	0.337045345297539	2		373	509	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0014495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	214	585	3	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	0.337045345297539	2		588	894	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0014495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	240	796	0	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.337045345297539	2		796	1127	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0014495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	67	565	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.648	0.563	0.739	0.648	0.563	0.739	SUBCLONAL	1	TRUE	1	0.337045345297539	2		565	614	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0014495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	101	346	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.337045345297539	2		346	565	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0014495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	65	243	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.337045345297539	2	FACETS	1	0.97	1	0.701	0.614	0.794	CLONAL	1	TRUE	0	0.337045345297539	2		243	275	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257144	19257144	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	55	239	1	ENST00000162023.5:c.819del	p.Thr274ProfsTer?	p.T274Pfs*?	ENST00000162023		273	ccC/cc	12/13	1	2	FACETS	0.637	0.546	0.738	0.637	0.546	0.738	SUBCLONAL	1	TRUE	1	0.337045345297539	2		240	512	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	45	295	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.584	0.491	0.687	0.584	0.491	0.687	SUBCLONAL	1	TRUE	1	0.337045345297539	2		295	457	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0014495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	18	604	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.153	0.114	0.2	0.153	0.114	0.2	SUBCLONAL	1	TRUE	1	0.337045345297539	2		604	697	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0014495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	133	573	1	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.883	0.801	0.969	0.883	0.801	0.969	CLONAL	1	TRUE	1	0.337045345297539	2		574	894	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744385	41744385	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	73	515	2	ENST00000301178.4:c.1010del	p.Pro337LeufsTer29	p.P337Lfs*29	ENST00000301178	NM_021913.4	335	ggC/gg	8/20	1	2	FACETS	0.568	0.496	0.646	0.568	0.496	0.646	SUBCLONAL	1	TRUE	1	0.337045345297539	2		517	763	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199957	128199957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370164300	NA	P-0014495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	33	383	1	ENST00000341105.2:c.1348G>A	p.Gly450Arg	p.G450R	ENST00000341105	NM_032638.4	450	Gga/Aga	6/6	1	2	FACETS	0.299	0.242	0.363	0.299	0.242	0.363	SUBCLONAL	1	TRUE	1	0.337045345297539	2		384	655	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435138	110435138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746947070	NA	P-0014495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	132	764	1	ENST00000375856.3:c.3263C>T	p.Ala1088Val	p.A1088V	ENST00000375856	NM_003749.2	1088	gCg/gTg	1/2	1	2	FACETS	0.713	0.646	0.784	0.713	0.646	0.784	SUBCLONAL	1	TRUE	1	0.337045345297539	2		765	1099	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218282	133218282	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1476621612	NA	P-0014495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	131	589	0	ENST00000320574.5:c.5329A>G	p.Ser1777Gly	p.S1777G	ENST00000320574	NM_006231.2	1777	Agt/Ggt	39/49	1	2	FACETS	0.893	0.811	0.981	0.893	0.811	0.981	CLONAL	1	TRUE	1	0.337045345297539	2		589	870	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991949	72991949	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs753977275	NA	P-0014495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	72	366	0	ENST00000268489.5:c.2096del	p.Gly699AlafsTer125	p.G699Afs*125	ENST00000268489	NM_006885.3	699	gGc/gc	2/10	1	2	FACETS	0.743	0.65	0.844	0.743	0.65	0.844	SUBCLONAL	1	TRUE	1	0.337045345297539	2		366	575	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260960	16260960	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	83	351	0	ENST00000375759.3:c.8225C>T	p.Thr2742Ile	p.T2742I	ENST00000375759	NM_015001.2	2742	aCa/aTa	11/15	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.337045345297539	2		351	484	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330565	65330565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	91	480	0	ENST00000342505.4:c.1081G>A	p.Glu361Lys	p.E361K	ENST00000342505	NM_002227.2	361	Gaa/Aaa	8/25	1	2	FACETS	0.762	0.676	0.853	0.762	0.676	0.853	SUBCLONAL	1	TRUE	1	0.337045345297539	2		480	709	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466027	69466035	+	inframe_deletion	In_Frame_Del	DEL	GACGTGCGG	GACGTGCGG	-	novel	NA	P-0014495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	100	685	0	ENST00000227507.2:c.871_879del	p.Arg291_Val293del	p.R291_V293del	ENST00000227507	NM_053056.2	289	GACGTGCGG/-	5/5	1	2	FACETS	0.654	0.583	0.729	0.654	0.583	0.729	SUBCLONAL	1	TRUE	1	0.337045345297539	2		685	908	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123616	108123616	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	26	330	0	ENST00000278616.4:c.1880del	p.Phe627SerfsTer22	p.F627Sfs*22	ENST00000278616	NM_000051.3	625	aaT/aa	12/63	1	2	FACETS	0.41	0.325	0.509	0.41	0.325	0.509	SUBCLONAL	1	TRUE	1	0.337045345297539	2		330	376	SUCCESS
ATM	472	MSKCC	GRCh37	11	108183212	108183212	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1188125296	NA	P-0014495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	48	303	0	ENST00000278616.4:c.5993G>T	p.Gly1998Val	p.G1998V	ENST00000278616	NM_000051.3	1998	gGa/gTa	40/63	1	2	FACETS	0.863	0.733	1	0.863	0.733	1	CLONAL	1	TRUE	1	0.337045345297539	2		303	330	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631606	90631606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	113	516	0	ENST00000330062.3:c.663G>A	p.Met221Ile	p.M221I	ENST00000330062	NM_002168.2	221	atG/atA	5/11	1	2	FACETS	0.893	0.804	0.987	0.893	0.804	0.987	CLONAL	1	TRUE	1	0.337045345297539	2		516	751	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207152	1207153	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAG	novel	NA	P-0014495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	107	738	1	ENST00000326873.7:c.250_252dup	p.Lys84dup	p.K84dup	ENST00000326873	NM_000455.4	84	-/AAG	1/10	1	2	FACETS	0.541	0.484	0.602	0.541	0.484	0.602	SUBCLONAL	1	TRUE	1	0.337045345297539	2		739	1174	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61708414	61708414	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1163918812	NA	P-0014495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	53	272	0	ENST00000401558.2:c.2975C>T	p.Ala992Val	p.A992V	ENST00000401558	NM_003400.3	992	gCt/gTt	24/25	1	2	FACETS	0.707	0.604	0.819	0.707	0.604	0.819	SUBCLONAL	1	TRUE	1	0.337045345297539	2		272	445	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467391	66467391	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	50	202	0	ENST00000273854.3:c.878C>T	p.Ala293Val	p.A293V	ENST00000273854	NM_004439.5	293	gCa/gTa	3/18	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.337045345297539	2		202	283	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948502	31948502	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201134143	NA	P-0014495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	50	311	0	ENST00000375333.2:c.985C>T	p.Arg329Trp	p.R329W	ENST00000375333	NM_032454.1	329	Cgg/Tgg	7/8	1	2	FACETS	0.563	0.478	0.657	0.563	0.478	0.657	SUBCLONAL	1	TRUE	1	0.337045345297539	2		311	527	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370949	55370950	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0014495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	171	685	0	ENST00000297316.4:c.252dup	p.Arg85AlafsTer77	p.R85Afs*77	ENST00000297316	NM_022454.3	84	aag/aaGg	1/2	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.337045345297539	2		685	993	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164817	123164817	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	45	253	0	ENST00000218089.9:c.135del	p.Gly46AlafsTer25	p.G46Afs*25	ENST00000218089	NM_001042749.1	44	Aaa/aa	5/35	1	2	FACETS	0.834	0.704	0.977	0.834	0.704	0.977	CLONAL	1	TRUE	1	0.337045345297539	2		253	320	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405905	157405905	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774701560	NA	P-0014557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	125	357	0	ENST00000346085.5:c.2147C>T	p.Ala716Val	p.A716V	ENST00000346085	NM_020732.3	716	gCg/gTg	6/20	0.33014697158342	3	FACETS	1	0.909	1	0.502	0.454	0.553	CLONAL	1	TRUE	1	0.370635162743018	3		357	796	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966872	25966873	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0014557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	95	401	0	ENST00000435504.4:c.2333dup	p.Val779SerfsTer25	p.V779Sfs*25	ENST00000435504		778	cca/ccCa	13/13	0.337959896479556	3	FACETS	0.796	0.709	0.89	0.398	0.354	0.445	SUBCLONAL	1	TRUE	1	0.370635162743018	3		401	763	SUCCESS
APC	324	MSKCC	GRCh37	5	112170772	112170772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765557332	NA	P-0014557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	120	575	0	ENST00000257430.4:c.1868G>A	p.Arg623Gln	p.R623Q	ENST00000257430	NM_000038.5	623	cGg/cAg	15/16	1	2	FACETS	0.925	0.836	1	0.925	0.836	1	CLONAL	1	TRUE	1	0.370635162743018	2		575	700	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249079	55249079	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	353	539	0	ENST00000275493.2:c.2377A>C	p.Met793Leu	p.M793L	ENST00000275493	NM_005228.3	793	Atg/Ctg	20/28	0.199939358921341	5	FACETS	0.836	0.792	0.881	0.836	0.792	0.881	INDETERMINATE	3	TRUE	2	0.370635162743018	5		539	1182	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	103	328	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.348253681268959	4	FACETS	0.614	0.548	0.683	0.307	0.274	0.342	INDETERMINATE	1	TRUE	2	0.58227474593107	4		328	912	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842748	68842748	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0014560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	42	360	0	ENST00000261769.5:c.684C>G	p.Tyr228Ter	p.Y228*	ENST00000261769	NM_004360.3	228	taC/taG	5/16	1	2	FACETS	0.315	0.263	0.373	0.315	0.263	0.373	SUBCLONAL	1	TRUE	1	0.58227474593107	2		360	458	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178641	56178641	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	93	229	0	ENST00000399503.3:c.3615del	p.Pro1206LeufsTer39	p.P1206Lfs*39	ENST00000399503	NM_005921.1	1205	gTt/gt	14/20	0.469126979695072	4	FACETS	0.724	0.644	0.81	0.362	0.322	0.405	SUBCLONAL	1	TRUE	2	0.58227474593107	4		229	698	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942029	44942030	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0014560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	93	273	0	ENST00000377967.4:c.3284dup	p.Trp1096ValfsTer7	p.W1096Vfs*7	ENST00000377967	NM_021140.2	1093	-/A	22/29	0.105583908122642	4	FACETS	0.727	0.647	0.813	0.364	0.323	0.407	INDETERMINATE	1	TRUE	2	0.58227474593107	4		273	695	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	48	328	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.693	0.598	0.793	0.693	0.598	0.793	SUBCLONAL	1	FALSE	1	0.922969983093124	2		328	150	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225060	NA	P-0014622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	53	617	0	ENST00000263967.3:c.311C>T	p.Pro104Leu	p.P104L	ENST00000263967	NM_006218.2	104	cCa/cTa	2/21	1	2	FACETS	0.499	0.43	0.573	0.499	0.43	0.573	SUBCLONAL	1	FALSE	1	0.922969983093124	2		617	230	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168686	56168687	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0014622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	143	533	0	ENST00000399503.3:c.1543dup	p.Leu515ProfsTer26	p.L515Pfs*26	ENST00000399503	NM_005921.1	514	tcc/tCcc	9/20	0.922969983093124	6	FACETS	1	0.965	1			1	CLONAL	2	FALSE	NA	0.922969983093124	6		533	407	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168803	56168804	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0014622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	205	576	0	ENST00000399503.3:c.1658dup	p.Tyr553Ter	p.Y553*	ENST00000399503	NM_005921.1	553	tac/tAac	9/20	0.922969983093124	6	FACETS	1	0.988	1			1	CLONAL	2	FALSE	NA	0.922969983093124	6		576	512	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	192	613	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.942	0.872	1	1	0.993	1	CLONAL	2	TRUE	1	0.240706662071337	2		614	847	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0014641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	108	609	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.236517965920084	1	FACETS	0.92	0.825	1	0.92	0.825	1	CLONAL	1	TRUE	0	0.240706662071337	1		610	858	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821817	59821817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780235	NA	P-0014641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	91	629	1	ENST00000259008.2:c.2233G>A	p.Ala745Thr	p.A745T	ENST00000259008	NM_032043.2	745	Gca/Aca	15/20	0.180460992413791	3	FACETS	0.879	0.779	0.986	0.439	0.389	0.493	CLONAL	1	TRUE	1	0.240706662071337	3		630	964	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0014641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	35	208	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	0.240706662071337	1	FACETS	0.955	0.786	1	0.955	0.786	1	CLONAL	1	TRUE	0	0.240706662071337	1		208	268	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306649	41306650	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0014641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	113	793	0	ENST00000373198.4:c.1008_1009dup	p.Thr337ArgfsTer4	p.T337Rfs*4	ENST00000373198	NM_133170.3	337	acc/aGAcc	7/32	1	2	FACETS	0.892	0.801	0.989	0.892	0.801	0.989	CLONAL	1	TRUE	1	0.240706662071337	2		793	1052	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0014694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	102	685	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.751	0.672	0.833	0.751	0.672	0.833	SUBCLONAL	1	TRUE	1	0.438328412461918	2		685	620	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	109	613	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.338250337332408	1	FACETS	0.747	0.673	0.824	0.747	0.673	0.824	SUBCLONAL	1	TRUE	0	0.438328412461918	1		614	520	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0014694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	109	692	4	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.597	0.536	0.662	0.597	0.536	0.662	SUBCLONAL	1	TRUE	1	0.438328412461918	2		696	833	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56855485	56855485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs79070284	NA	P-0014694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	141	585	0	ENST00000308159.5:c.634G>A	p.Val212Ile	p.V212I	ENST00000308159	NM_014669.4	212	Gtc/Atc	7/22	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.438328412461918	2		585	635	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579354	7579355	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0014694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	190	1019	0	ENST00000269305.4:c.332_333del	p.Leu111ArgfsTer37	p.L111Rfs*37	ENST00000269305	NM_001126112.2	111	cTG/c	4/11	0.427230867090385	1	FACETS	0.812	0.751	0.874	0.812	0.751	0.874	CLONAL	1	TRUE	0	0.438328412461918	1		1019	834	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222183	2222183	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs988817026	NA	P-0014694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	60	1070	2	ENST00000398665.3:c.3015G>T	p.Gln1005His	p.Q1005H	ENST00000398665	NM_032482.2	1005	caG/caT	24/28	1	2	FACETS	0.28	0.24	0.323	0.28	0.24	0.323	SUBCLONAL	1	TRUE	1	0.438328412461918	2		1072	979	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467526	66467526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	82	477	0	ENST00000273854.3:c.743C>T	p.Thr248Ile	p.T248I	ENST00000273854	NM_004439.5	248	aCt/aTt	3/18	1	2	FACETS	0.731	0.646	0.821	0.731	0.646	0.821	SUBCLONAL	1	TRUE	1	0.438328412461918	2		477	512	SUCCESS
APC	324	MSKCC	GRCh37	5	112175452	112175452	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0014694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	213	453	0	ENST00000257430.4:c.4161T>A	p.Cys1387Ter	p.C1387*	ENST00000257430	NM_000038.5	1387	tgT/tgA	16/16	0.438328412461918	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.438328412461918	2		453	471	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115751	8115751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1157	123	663	2	ENST00000346208.3:c.1097G>A	p.Arg366Gln	p.R366Q	ENST00000346208		366	cGa/cAa	6/6	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.183375048193849	2		665	1280	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639732	3639732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759828401	NA	P-0014703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1853	374	914	0	ENST00000294008.3:c.3907G>A	p.Glu1303Lys	p.E1303K	ENST00000294008	NM_032444.2	1303	Gaa/Aaa	12/15	0.183375048193849	8	FACETS	0.946	0.894	1	0.473	0.447	0.5	CLONAL	3	TRUE	2	0.183375048193849	8		914	2227	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176559	56176559	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	164	497	0	ENST00000399503.3:c.2109del	p.Ser704GlnfsTer21	p.S704Qfs*21	ENST00000399503	NM_005921.1	703	atA/at	12/20	0.183375048193849	6	FACETS	0.92	0.843	1			1	CLONAL	2	TRUE	NA	0.183375048193849	6		497	1328	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178486	56178487	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0014703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	208	315	0	ENST00000399503.3:c.3460dup	p.Ala1154GlyfsTer6	p.A1154Gfs*6	ENST00000399503	NM_005921.1	1153	-/G	14/20	0.183375048193849	6	FACETS	0.916	0.852	0.983			1	CLONAL	4	TRUE	NA	0.183375048193849	6		315	846	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611793	100611793	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs782133950	NA	P-0014703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	154	512	0	ENST00000308731.7:c.1328T>C	p.Ile443Thr	p.I443T	ENST00000308731	NM_000061.2	443	aTt/aCt	14/19	1	2	FACETS	0.886	0.81	0.965	1	0.99	1	CLONAL	2	TRUE	1	0.183375048193849	2		512	948	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0014809-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	188	340	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.173316456704344	2	FACETS	0.85	0.787	0.915	0.85	0.787	0.915	CLONAL	2	TRUE	0	0.279320306035274	2		340	792	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117732	115117732	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014809-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	66	541	0	ENST00000257566.3:c.703A>T	p.Ser235Cys	p.S235C	ENST00000257566	NM_016569.3	235	Agt/Tgt	3/8	0.173316456704344	2	FACETS	0.603	0.522	0.69	0.301	0.261	0.345	SUBCLONAL	1	TRUE	0	0.279320306035274	2		541	784	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957525	1957525	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014809-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	212	827	0	ENST00000382891.5:c.2624G>C	p.Gly875Ala	p.G875A	ENST00000382891	NM_133335.3	875	gGg/gCg	14/22	0.279320306035274	3	FACETS	1	0.99	1	0.711	0.659	0.764	CLONAL	1	TRUE	1	0.279320306035274	3		827	1217	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28901633	28901633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014809-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	61	648	0	ENST00000282397.4:c.2762T>C	p.Leu921Pro	p.L921P	ENST00000282397	NM_002019.4	921	cTc/cCc	20/30	0.279320306035274	1	FACETS	0.501	0.431	0.577	0.501	0.431	0.577	SUBCLONAL	1	TRUE	0	0.279320306035274	1		648	750	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423637	88423637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014809-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	111	488	2	ENST00000360948.2:c.2198C>T	p.Pro733Leu	p.P733L	ENST00000360948	NM_001012338.2	733	cCc/cTc	18/19	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.279320306035274	2		490	659	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220409	1220409	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014809-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	199	911	0	ENST00000326873.7:c.502C>T	p.His168Tyr	p.H168Y	ENST00000326873	NM_000455.4	168	Cat/Tat	4/10	0.279320306035274	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.279320306035274	1		911	934	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0014821-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	319	609	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.667259078554948	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.667259078554948	1		610	582	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755611	39755611	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014821-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	131	611	0	ENST00000288319.7:c.1154G>A	p.Arg385His	p.R385H	ENST00000288319	NM_182918.3	385	cGc/cAc	10/10	1	2	FACETS	0.513	0.466	0.563	0.513	0.466	0.563	SUBCLONAL	1	TRUE	1	0.667259078554948	2		611	765	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458147	120458147	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1325403451	NA	P-0014821-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	315	748	0	ENST00000256646.2:c.7198C>T	p.Arg2400Ter	p.R2400*	ENST00000256646	NM_024408.3	2400	Cga/Tga	34/34	0.667259078554948	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.667259078554948	1		748	543	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602620	10602620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014821-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	102	665	2	ENST00000171111.5:c.958C>T	p.Arg320Trp	p.R320W	ENST00000171111	NM_203500.1	320	Cgg/Tgg	3/6	0.667259078554948	1	FACETS	0.277	0.247	0.308	0.277	0.247	0.308	SUBCLONAL	1	TRUE	0	0.667259078554948	1		667	736	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881509	48881509	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014821-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	241	472	0	ENST00000267163.4:c.232del	p.Trp78GlyfsTer33	p.W78Gfs*33	ENST00000267163	NM_000321.2	77	acT/ac	2/27	0.667259078554948	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.667259078554948	1		472	445	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843302	128843302	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014821-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	389	859	0	ENST00000249373.3:c.409G>C	p.Asp137His	p.D137H	ENST00000249373	NM_005631.4	137	Gac/Cac	2/12	0.354228205685225	1	FACETS	0.791	0.754	0.829	0.791	0.754	0.829	INDETERMINATE	1	TRUE	0	0.667259078554948	1		859	982	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317451	1317451	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014821-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	350	822	0	ENST00000400841.2:c.614A>G	p.Glu205Gly	p.E205G	ENST00000400841		205	gAg/gGg	5/6	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.667259078554948	2		822	1007	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0014859-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	71	417	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.319573534181509	3	FACETS	1	0.902	1	0.518	0.453	0.588	CLONAL	1	TRUE	1	0.319573534181509	3		418	497	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591917	48591925	+	inframe_deletion	In_Frame_Del	DEL	TCGCTTTTG	TCGCTTTTG	-	novel	NA	P-0014859-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	104	722	0	ENST00000342988.3:c.1081_1089del	p.Arg361_Cys363del	p.R361_C363del	ENST00000342988	NM_005359.5	360	gaTCGCTTTTGt/gat	9/12	0.319573534181509	2	FACETS	0.771	0.695	0.851	0.771	0.695	0.851	SUBCLONAL	2	TRUE	0	0.319573534181509	2		722	422	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112214	115112214	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014859-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	57	849	0	ENST00000257566.3:c.1526G>C	p.Gly509Ala	p.G509A	ENST00000257566	NM_016569.3	509	gGc/gCc	7/8	0.319573534181509	3	FACETS	0.953	0.82	1	0.477	0.41	0.549	CLONAL	1	TRUE	1	0.319573534181509	3		849	434	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422428	47422428	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014859-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	57	964	0	ENST00000377045.4:c.62T>G	p.Val21Gly	p.V21G	ENST00000377045	NM_001654.4	21	gTc/gGc	2/16	1	2	FACETS	0.754	0.648	0.87	0.754	0.648	0.87	SUBCLONAL	1	TRUE	1	0.319573534181509	2		964	473	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954273	32954273	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359752	NA	P-0014885-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	52	570	1	ENST00000380152.3:c.9253del	p.Thr3085GlnfsTer19	p.T3085Qfs*19	ENST00000380152		3083	Aaa/aa	24/27	1	2	FACETS	0.916	0.778	1	0.916	0.778	1	CLONAL	1	TRUE	1	0.14	2		571	811	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630446	47630446	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs63750984	NA	P-0014885-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	58	818	2	ENST00000233146.2:c.119del	p.Gly40AlafsTer24	p.G40Afs*24	ENST00000233146	NM_000251.2	39	cGg/cg	1/16	0.18857261082951	3	FACETS	0.86	0.736	0.996	0.43	0.368	0.498	CLONAL	1	TRUE	1	0.14	3		820	1031	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630493	47630493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014885-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	58	826	0	ENST00000233146.2:c.163C>T	p.Arg55Trp	p.R55W	ENST00000233146	NM_000251.2	55	Cgg/Tgg	1/16	0.18857261082951	3	FACETS	0.917	0.785	1	0.458	0.392	0.531	CLONAL	1	TRUE	1	0.14	3		826	967	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46271069	46271069	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014885-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	50	730	0	ENST00000371998.3:c.3193G>C	p.Asp1065His	p.D1065H	ENST00000371998		1065	Gat/Cat	17/23	1	2	FACETS	0.867	0.733	1	0.867	0.733	1	CLONAL	1	TRUE	1	0.14	2		730	824	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437246	52437246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014885-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	70	935	0	ENST00000460680.1:c.1798G>A	p.Glu600Lys	p.E600K	ENST00000460680	NM_004656.3	600	Gag/Aag	14/17	1	2	FACETS	0.961	0.835	1	0.961	0.835	1	CLONAL	1	TRUE	1	0.14	2		935	1041	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0014885-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	73	240	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.815	0.713	0.925	1	0.977	1	CLONAL	2	TRUE	1	0.14	2		240	640	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241678	55241678	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517085	NA	P-0014885-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	67	851	0	ENST00000275493.2:c.2126A>C	p.Glu709Ala	p.E709A	ENST00000275493	NM_005228.3	709	gAa/gCa	18/28	1	2	FACETS	0.99	0.858	1	0.99	0.858	1	CLONAL	1	TRUE	1	0.14	2		851	967	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28929495	NA	P-0014885-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	54	825	0	ENST00000275493.2:c.2155G>A	p.Gly719Ser	p.G719S	ENST00000275493	NM_005228.3	719	Ggc/Agc	18/28	1	2	FACETS	0.838	0.713	0.975	0.838	0.713	0.975	CLONAL	1	TRUE	1	0.14	2		825	921	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911534	101911534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111426349	NA	P-0014885-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	60	695	2	ENST00000374994.4:c.1459C>T	p.Arg487Trp	p.R487W	ENST00000374994	NM_004612.2	487	Cgg/Tgg	9/9	0.18857261082951	3	FACETS	1	0.931	1	0.57	0.49	0.658	CLONAL	1	TRUE	1	0.14	3		697	804	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380283	25380283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913528	NA	P-0015576-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	121	1200	0	ENST00000311936.3:c.175G>A	p.Ala59Thr	p.A59T	ENST00000311936	NM_004985.3	59	Gca/Aca	3/5	1	2	FACETS	0.666	0.601	0.734	0.666	0.601	0.734	SUBCLONAL	1	TRUE	1	0.392175773914849	2		1200	927	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988276	41988277	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015576-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	35	1075	0	ENST00000219905.7:c.1069dup	p.Ile357AsnfsTer6	p.I357Nfs*6	ENST00000219905	NM_001164273.1	356	-/A	3/24	0.356365598508969	1	FACETS	0.209	0.171	0.253	0.209	0.171	0.253	SUBCLONAL	1	TRUE	0	0.392175773914849	1		1075	686	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602611	10602611	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015576-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	133	1362	0	ENST00000171111.5:c.967A>G	p.Lys323Glu	p.K323E	ENST00000171111	NM_203500.1	323	Aag/Gag	3/6	0.356365598508969	1	FACETS	0.74	0.673	0.81	0.74	0.673	0.81	SUBCLONAL	1	TRUE	0	0.392175773914849	1		1362	737	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378634	25378634	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015576-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	134	1220	0	ENST00000311936.3:c.364T>C	p.Ser122Pro	p.S122P	ENST00000311936	NM_004985.3	122	Tct/Cct	4/5	1	2	FACETS	0.774	0.703	0.849	0.774	0.703	0.849	SUBCLONAL	1	TRUE	1	0.392175773914849	2		1220	883	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042296	42042297	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0015576-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	27	849	0	ENST00000219905.7:c.6493_6494del	p.Asp2165LeufsTer29	p.D2165Lfs*29	ENST00000219905	NM_001164273.1	2164	gGA/g	17/24	0.356365598508969	1	FACETS	0.228	0.181	0.282	0.228	0.181	0.282	SUBCLONAL	1	TRUE	0	0.392175773914849	1		849	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0016423-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	378	923	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.713309798429812	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.745214121970493	1		923	619	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206667324	206667324	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016423-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	765	775	0	ENST00000367120.3:c.2117G>T	p.Arg706Leu	p.R706L	ENST00000367120	NM_014002.3	706	cGg/cTg	21/22	0.719456124200773	3	FACETS	0.925	0.904	0.944	0.925	0.904	0.944	CLONAL	3	TRUE	0	0.745214121970493	3		775	1016	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546575	9546575	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777430875	NA	P-0016423-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	228	803	2	ENST00000353224.5:c.1447C>T	p.Arg483Trp	p.R483W	ENST00000353224	NM_177990.2	483	Cgg/Tgg	5/10	1	2	FACETS	0.933	0.874	0.993	0.933	0.874	0.993	CLONAL	1	TRUE	1	0.745214121970493	2		805	656	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141105	55141105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016423-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	229	573	0	ENST00000257290.5:c.1751C>T	p.Ser584Leu	p.S584L	ENST00000257290	NM_006206.4	584	tCa/tTa	12/23	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.745214121970493	2		573	595	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681424	88681424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016423-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	195	630	0	ENST00000372037.3:c.1314G>T	p.Trp438Cys	p.W438C	ENST00000372037	NM_004329.2	438	tgG/tgT	11/13	1	2	FACETS	0.987	0.921	1	0.987	0.921	1	CLONAL	1	TRUE	1	0.745214121970493	2		630	530	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933379	100933379	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016423-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	284	753	0	ENST00000325455.5:c.2011C>A	p.Gln671Lys	p.Q671K	ENST00000325455	NM_001202474.3	671	Cag/Aag	4/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.745214121970493	2		753	727	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404794	404794	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016423-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	223	794	2	ENST00000399788.2:c.4400G>T	p.Arg1467Leu	p.R1467L	ENST00000399788	NM_001042603.1	1467	cGg/cTg	26/28	NA	2	FACETS	0.935	0.876	0.996			1	INDETERMINATE	1	TRUE	NA	0.745214121970493	2		796	640	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864465	57864465	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016423-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	320	683	0	ENST00000228682.2:c.1942C>A	p.Arg648Ser	p.R648S	ENST00000228682	NM_005269.2	648	Cgt/Agt	12/12	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.745214121970493	2		683	755	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112386	115112386	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016423-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	219	589	0	ENST00000257566.3:c.1354G>C	p.Glu452Gln	p.E452Q	ENST00000257566	NM_016569.3	452	Gag/Cag	7/8	1	2	FACETS	0.964	0.902	1	0.964	0.902	1	CLONAL	1	TRUE	1	0.745214121970493	2		589	610	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219531	133219531	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016423-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	314	793	0	ENST00000320574.5:c.4603G>C	p.Gly1535Arg	p.G1535R	ENST00000320574	NM_006231.2	1535	Ggc/Cgc	36/49	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.745214121970493	2		793	842	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560401	95560401	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016423-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	269	721	0	ENST00000393063.1:c.5188G>T	p.Gly1730Trp	p.G1730W	ENST00000393063	NM_030621.3	1730	Ggg/Tgg	25/28	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.745214121970493	2		721	698	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456348	99456348	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016423-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	228	606	0	ENST00000268035.6:c.1665C>A	p.Asp555Glu	p.D555E	ENST00000268035	NM_000875.3	555	gaC/gaA	8/21	1	2	FACETS	0.879	0.823	0.936	0.879	0.823	0.936	CLONAL	1	TRUE	1	0.745214121970493	2		606	696	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533364	29533364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016423-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	110	388	0	ENST00000356175.3:c.1367C>T	p.Ala456Val	p.A456V	ENST00000356175	NM_000267.3	456	gCa/gTa	12/57	1	2	FACETS	0.796	0.722	0.872	0.796	0.722	0.872	SUBCLONAL	1	TRUE	1	0.745214121970493	2		388	371	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098409	11098409	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016423-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	303	749	0	ENST00000358026.2:c.928del	p.Arg310AlafsTer16	p.R310Afs*16	ENST00000358026	NM_001128849.1	309	ggC/gg	6/36	0.745214121970493	1	FACETS	0.983	0.939	1	0.983	0.939	1	CLONAL	1	TRUE	0	0.745214121970493	1		749	519	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965881	25965881	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016423-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	289	748	0	ENST00000435504.4:c.3325G>T	p.Gly1109Cys	p.G1109C	ENST00000435504		1109	Ggt/Tgt	13/13	1	2	FACETS	0.967	0.913	1	0.967	0.913	1	CLONAL	1	TRUE	1	0.745214121970493	2		748	802	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519873	29519873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016423-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	288	777	0	ENST00000389048.3:c.1698G>T	p.Leu566Phe	p.L566F	ENST00000389048	NM_004304.4	566	ttG/ttT	9/29	1	2	FACETS	0.983	0.929	1	0.983	0.929	1	CLONAL	1	TRUE	1	0.745214121970493	2		777	786	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021091	31021091	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016423-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	226	678	0	ENST00000375687.4:c.1090G>T	p.Gly364Cys	p.G364C	ENST00000375687	NM_015338.5	364	Ggt/Tgt	12/13	1	2	FACETS	0.952	0.892	1	0.952	0.892	1	CLONAL	1	TRUE	1	0.745214121970493	2		678	637	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286231	66286231	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016423-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	153	661	0	ENST00000273854.3:c.1455C>G	p.Ile485Met	p.I485M	ENST00000273854	NM_004439.5	485	atC/atG	6/18	1	2	FACETS	0.973	0.899	1	0.973	0.899	1	CLONAL	1	TRUE	1	0.745214121970493	2		661	422	SUCCESS
APC	324	MSKCC	GRCh37	5	112177053	112177053	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786204093	NA	P-0016423-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	242	681	0	ENST00000257430.4:c.5762G>T	p.Gly1921Val	p.G1921V	ENST00000257430	NM_000038.5	1921	gGt/gTt	16/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.745214121970493	2		681	639	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274823	38274823	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0016423-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	214	587	0	ENST00000425967.3:c.1756+1G>T		p.X586_splice	ENST00000425967	NM_001174067.1	586			1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.745214121970493	2		587	567	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500810	8500810	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016423-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	277	673	1	ENST00000356435.5:c.2072C>G	p.Thr691Arg	p.T691R	ENST00000356435		691	aCa/aGa	13/35	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.745214121970493	2		674	735	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940056	76940056	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016423-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	268	391	1	ENST00000373344.5:c.692G>T	p.Cys231Phe	p.C231F	ENST00000373344	NM_000489.3	231	tGt/tTt	9/35	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.745214121970493	1		392	352	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106366	27106366	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016423-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	174	672	1	ENST00000324856.7:c.5979del	p.Phe1993LeufsTer22	p.F1993Lfs*22	ENST00000324856	NM_006015.4	1993	Ttt/tt	20/20	0.745214121970493	3	FACETS	0.647	0.596	0.702	0.324	0.298	0.351	SUBCLONAL	1	TRUE	1	0.745214121970493	3		673	990	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891231	101891231	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016423-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	27	624	2	ENST00000374994.4:c.192A>T	p.Lys64Asn	p.K64N	ENST00000374994	NM_004612.2	64	aaA/aaT	2/9	0.745214121970493	1	FACETS	0.129	0.102	0.159	0.129	0.102	0.159	SUBCLONAL	1	TRUE	0	0.745214121970493	1		626	353	SUCCESS
AR	367	MSKCC	GRCh37	X	66765047	66765047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1297947716	NA	P-0017478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	60	1040	1	ENST00000374690.3:c.59G>A	p.Arg20Gln	p.R20Q	ENST00000374690	NM_000044.3	20	cGa/cAa	1/8	1	2	FACETS	0.337	0.289	0.389	0.337	0.289	0.389	SUBCLONAL	1	TRUE	1	0.430580060077305	2		1041	828	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742646	39742646	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	22	486	1	ENST00000361337.2:c.1489G>A	p.Glu497Lys	p.E497K	ENST00000361337	NM_003286.2	497	Gaa/Aaa	15/21	1	2	FACETS	0.251	0.194	0.318	0.251	0.194	0.318	SUBCLONAL	1	TRUE	1	0.430580060077305	2		487	407	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467652	50467652	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	112	658	0	ENST00000331340.3:c.887G>A	p.Ser296Asn	p.S296N	ENST00000331340	NM_006060.4	296	aGc/aAc	8/8	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.430580060077305	2		658	514	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017638-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	37	251	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.831	1	1	0.831	1	CLONAL	1	TRUE	1	0.14	2		251	524	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0017638-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	22	528	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.445	0.343	0.565	0.445	0.343	0.565	SUBCLONAL	1	TRUE	1	0.14	2		528	706	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913499	NA	P-0017638-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	14	263	0	ENST00000345146.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000345146	NM_005896.2	132	Cgt/Ggt	4/10	1	2	FACETS	0.451	0.325	0.606	0.451	0.325	0.606	SUBCLONAL	1	TRUE	1	0.14	2		263	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0018860-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	28	706	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	1	2	FACETS	0.211	0.168	0.26	0.211	0.168	0.26	SUBCLONAL	1	TRUE	1	0.46	2		706	577	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0018913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	680	1016	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	0.912299113446297	2	FACETS	0.881	0.863	0.899	0.881	0.863	0.899	CLONAL	2	TRUE	0	0.912299113446297	2		1016	846	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951099	48951100	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0018913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	193	637	0	ENST00000267163.4:c.1265_1266dup	p.Gly423Ter	p.G423*	ENST00000267163	NM_000321.2	421	gat/gATat	13/27	0.912299113446297	1	FACETS	0.939	0.901	0.975	0.939	0.901	0.975	CLONAL	1	TRUE	0	0.912299113446297	1		637	245	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	240465	240471	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TGTTTTA	TGTTTTA	-	novel	NA	P-0018913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	40	359	0	ENST00000264932.6:c.1433-8_1433-2del		p.X478_splice	ENST00000264932	NM_004168.2	478			0.543959033610594	1	FACETS	0.213	0.178	0.251	0.213	0.178	0.251	INDETERMINATE	1	TRUE	0	0.912299113446297	1		359	224	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106654	2106654	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45517119	NA	P-0018967-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	76	820	1	ENST00000219476.3:c.658C>T	p.Gln220Ter	p.Q220*	ENST00000219476	NM_000548.3	220	Cag/Tag	8/42	1	2	FACETS	0.377	0.33	0.428	0.377	0.33	0.428	SUBCLONAL	1	TRUE	1	0.538160501742104	2		821	749	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999429	100999429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs191163476	NA	P-0019030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	281	1051	0	ENST00000325455.5:c.373G>A	p.Gly125Arg	p.G125R	ENST00000325455	NM_001202474.3	125	Ggg/Agg	1/8	1	2	FACETS	0.936	0.882	0.991	0.936	0.882	0.991	CLONAL	1	TRUE	1	0.690040965983268	2		1051	870	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26978189	26978189	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	200	627	0	ENST00000381527.3:c.1366C>T	p.Gln456Ter	p.Q456*	ENST00000381527	NM_001260.1	456	Cag/Tag	13/13	1	2	FACETS	0.913	0.85	0.977	0.913	0.85	0.977	CLONAL	1	TRUE	1	0.690040965983268	2		627	635	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	90	251	0				ENST00000310581	NM_198253.2	-/1132			0.327511296303719	3	FACETS	0.783	0.7	0.87			1	SUBCLONAL	2	TRUE	NA	0.373768174851238	3		251	365	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640644	3640644	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	194	1193	0	ENST00000294008.3:c.2995C>A	p.Gln999Lys	p.Q999K	ENST00000294008	NM_032444.2	999	Caa/Aaa	12/15	0.215364718180436	4	FACETS	0.862	0.799	0.928	0.862	0.799	0.928	INDETERMINATE	2	TRUE	2	0.373768174851238	4		1193	827	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989609	15989609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	42	449	0	ENST00000268712.3:c.3164G>A	p.Gly1055Asp	p.G1055D	ENST00000268712	NM_006311.3	1055	gGc/gAc	23/46	0.341753783278665	3	FACETS	0.745	0.624	0.879	0.373	0.312	0.44	SUBCLONAL	1	TRUE	1	0.373768174851238	3		449	358	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019407	31019407	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	149	757	0	ENST00000375687.4:c.904C>G	p.Arg302Gly	p.R302G	ENST00000375687	NM_015338.5	302	Cgt/Ggt	10/13	0.316903646866711	3	FACETS	1	0.988	1	0.746	0.684	0.811	CLONAL	1	TRUE	1	0.373768174851238	3		757	634	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191593	10191593	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs281860296	NA	P-0019793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	208	812	1	ENST00000256474.2:c.586A>T	p.Lys196Ter	p.K196*	ENST00000256474	NM_000551.3	196	Aaa/Taa	3/3	0.306174448947088	3	FACETS	1	0.984	1	0.779	0.729	0.831	CLONAL	2	TRUE	0	0.373768174851238	3		813	565	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440311	52440311	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	225	957	0	ENST00000460680.1:c.741del	p.Leu248Ter	p.L248*	ENST00000460680	NM_004656.3	247	gtG/gt	9/17	0.306174448947088	3	FACETS	1	0.985	1	0.778	0.73	0.828	CLONAL	2	TRUE	0	0.373768174851238	3		957	612	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458315	120458315	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	36	752	0	ENST00000256646.2:c.7030G>T	p.Glu2344Ter	p.E2344*	ENST00000256646	NM_024408.3	2344	Gaa/Taa	34/34	0.215364718180436	4	FACETS	0.577	0.474	0.692	0.288	0.237	0.346	INDETERMINATE	1	TRUE	2	0.373768174851238	4		752	459	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226590019	226590019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758791748	NA	P-0019793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	79	957	1	ENST00000366794.5:c.182G>A	p.Gly61Asp	p.G61D	ENST00000366794	NM_001618.3	61	gGc/gAc	2/23	0.341753783278665	3	FACETS	0.761	0.67	0.86	0.381	0.335	0.43	SUBCLONAL	1	TRUE	1	0.373768174851238	3		958	659	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0019905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	387	685	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.573121224982193	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.573121224982193	3		685	862	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	178	251	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.573121224982193	2		251	586	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0019905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	374	1002	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.571817683985357	2	FACETS	0.951	0.912	0.991	0.951	0.912	0.991	CLONAL	2	TRUE	0	0.573121224982193	2		1002	686	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0019905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	622	1108	1	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.573121224982193	2	FACETS	0.979	0.947	1	0.979	0.947	1	CLONAL	2	TRUE	0	0.573121224982193	2		1109	1109	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966753	18966753	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	279	1055	1	ENST00000262803.5:c.1564C>T	p.Pro522Ser	p.P522S	ENST00000262803	NM_002911.3	522	Ccg/Tcg	12/24	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.573121224982193	2		1056	937	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271291	1271291	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	193	718	1	ENST00000310581.5:c.2411G>A	p.Gly804Asp	p.G804D	ENST00000310581	NM_198253.2	804	gGc/gAc	8/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.573121224982193	2		719	610	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929147	44929148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0019905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	177	738	0	ENST00000377967.4:c.2248dup	p.His750ProfsTer14	p.H750Pfs*14	ENST00000377967	NM_021140.2	749	-/C	17/29	1	2	FACETS	0.852	0.787	0.919	0.852	0.787	0.919	CLONAL	1	TRUE	1	0.573121224982193	2		738	725	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034466	47034467	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	252	1085	0	ENST00000377604.3:c.552dup	p.Thr185TyrfsTer24	p.T185Yfs*24	ENST00000377604	NM_001204468.1	184	gct/gcTt	6/24	1	2	FACETS	0.895	0.838	0.953	0.895	0.838	0.953	CLONAL	1	TRUE	1	0.573121224982193	2		1085	983	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0019988-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	32	521	0	ENST00000262160.6:c.1391C>G	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tGa	11/11	1	2	FACETS	0.887	0.719	1	0.887	0.719	1	CLONAL	1	TRUE	1	0.13	2		521	555	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121913370	NA	P-0019988-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	21	438	0	ENST00000288602.6:c.1742A>G	p.Asn581Ser	p.N581S	ENST00000288602	NM_004333.4	581	aAt/aGt	15/18	1	2	FACETS	0.905	0.696	1	0.905	0.696	1	CLONAL	1	TRUE	1	0.13	2		438	357	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239530	123239530	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019988-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1378	76	1532	1	ENST00000358487.5:c.2307C>A	p.Tyr769Ter	p.Y769*	ENST00000358487	NM_000141.4	769	taC/taA	18/18	1	2	FACETS	0.804	0.702	0.915	0.804	0.702	0.915	CLONAL	1	TRUE	1	0.13	2		1533	1454	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019988-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	65	1012	0	ENST00000267101.3:c.850G>C	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Cga	7/28	1	2	FACETS	0.92	0.795	1	0.92	0.795	1	CLONAL	1	TRUE	1	0.13	2		1012	1087	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999024	100999024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778694496	NA	P-0019988-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	52	849	0	ENST00000325455.5:c.778G>A	p.Ala260Thr	p.A260T	ENST00000325455	NM_001202474.3	260	Gcg/Acg	1/8	1	2	FACETS	0.834	0.708	0.974	0.834	0.708	0.974	CLONAL	1	TRUE	1	0.13	2		849	959	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900206	101900206	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727503470	NA	P-0019988-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	40	573	1	ENST00000374994.4:c.640G>A	p.Gly214Ser	p.G214S	ENST00000374994	NM_004612.2	214	Ggt/Agt	4/9	1	2	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	TRUE	1	0.13	2		574	594	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929273	44929274	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0019988-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	59	557	0	ENST00000377967.4:c.2375_2376del	p.Val792GlyfsTer6	p.V792Gfs*6	ENST00000377967	NM_021140.2	791	aaTGtg/aatg	17/29	1	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.13	1		557	599	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376722	8376722	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019988-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	45	598	0	ENST00000356435.5:c.4391A>C	p.Lys1464Thr	p.K1464T	ENST00000356435		1464	aAg/aCg	27/35	1	2	FACETS	0.968	0.812	1	0.968	0.812	1	CLONAL	1	TRUE	1	0.13	2		598	715	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521295	8521295	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019988-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	27	426	0	ENST00000356435.5:c.943G>A	p.Ala315Thr	p.A315T	ENST00000356435		315	Gca/Aca	9/35	1	2	FACETS	0.968	0.77	1	0.968	0.77	1	CLONAL	1	TRUE	1	0.13	2		426	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0019993-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	495	742	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.92959851630708	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.92959851630708	1		742	546	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595519	55595519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913516	NA	P-0019993-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	33	618	1	ENST00000288135.5:c.2009C>T	p.Thr670Ile	p.T670I	ENST00000288135	NM_000222.2	670	aCa/aTa	14/21	0.92959851630708	2	FACETS	0.08	0.064	0.097	0.04	0.032	0.049	SUBCLONAL	1	TRUE	0	0.92959851630708	2		619	893	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720819	89720819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019993-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	512	376	1	ENST00000371953.3:c.970G>A	p.Asp324Asn	p.D324N	ENST00000371953	NM_000314.4	324	Gat/Aat	8/9	0.927274152642916	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.92959851630708	2		377	547	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720840	89720840	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019993-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	511	428	0	ENST00000371953.3:c.991G>A	p.Asp331Asn	p.D331N	ENST00000371953	NM_000314.4	331	Gac/Aac	8/9	0.927274152642916	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.92959851630708	2		428	547	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941630	48941630	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1566194312	NA	P-0019993-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	257	343	0	ENST00000267163.4:c.940G>T	p.Val314Phe	p.V314F	ENST00000267163	NM_000321.2	314	Gtt/Ttt	10/27	0.92959851630708	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.92959851630708	1		343	294	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593597	55593602	+	inframe_deletion	In_Frame_Del	DEL	GTACAG	GTACAG	-	novel	NA	P-0019993-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	579	519	0	ENST00000288135.5:c.1663_1668del	p.Val555_Gln556del	p.V555_Q556del	ENST00000288135	NM_000222.2	555	GTACAG/-	11/21	0.92959851630708	2	FACETS	0.995	0.98	1	0.995	0.98	1	CLONAL	2	TRUE	0	0.92959851630708	2		519	626	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410313	63410313	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs768563880	NA	P-0019993-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	568	449	0	ENST00000330258.3:c.2854C>A	p.Pro952Thr	p.P952T	ENST00000330258	NM_152424.3	952	Ccc/Acc	2/2	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.92959851630708	1		449	608	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599322	55599322	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019993-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	385	687	0	ENST00000288135.5:c.2448C>A	p.Asp816Glu	p.D816E	ENST00000288135	NM_000222.2	816	gaC/gaA	17/21	0.92959851630708	2	FACETS	0.78	0.742	0.818	0.39	0.371	0.409	SUBCLONAL	1	TRUE	0	0.92959851630708	2		687	1062	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599330	55599332	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	novel	NA	P-0019993-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	352	678	0	ENST00000288135.5:c.2458_2460del	p.Asp820del	p.D820del	ENST00000288135	NM_000222.2	819	aATGat/aat	17/21	0.92959851630708	2	FACETS	0.734	0.696	0.772	0.367	0.348	0.386	SUBCLONAL	1	TRUE	0	0.92959851630708	2		678	1032	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0020063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	88	468	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.768	0.679	0.863	0.768	0.679	0.863	SUBCLONAL	1	TRUE	1	0.263480071100392	2		468	870	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0020063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	47	346	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.463	0.389	0.544	0.463	0.389	0.544	SUBCLONAL	1	TRUE	1	0.263480071100392	2		346	771	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717615	89717615	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909227	NA	P-0020063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	96	558	0	ENST00000371953.3:c.640C>T	p.Gln214Ter	p.Q214*	ENST00000371953	NM_000314.4	214	Cag/Tag	7/9	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.263480071100392	2		558	678	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0020063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	53	381	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.602	0.513	0.701	0.602	0.513	0.701	SUBCLONAL	1	TRUE	1	0.263480071100392	2		381	668	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936096	178936096	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	64	736	0	ENST00000263967.3:c.1638G>C	p.Gln546His	p.Q546H	ENST00000263967	NM_006218.2	546	caG/caC	10/21	1	2	FACETS	0.678	0.587	0.778	0.678	0.587	0.778	SUBCLONAL	1	TRUE	1	0.263480071100392	2		736	716	SUCCESS
EED	8726	MSKCC	GRCh37	11	85979511	85979511	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	517	486	1	ENST00000263360.6:c.874C>T	p.Gln292Ter	p.Q292*	ENST00000263360	NM_003797.3	292	Cag/Tag	9/12	0.695334161608926	3	FACETS	0.965	0.94	0.99	0.965	0.94	0.99	CLONAL	3	TRUE	0	0.700656116777631	3		487	688	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923060	44923060	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	426	611	0	ENST00000377967.4:c.1921C>T	p.Gln641Ter	p.Q641*	ENST00000377967	NM_021140.2	641	Cag/Tag	16/29	0.688949162907877	2	FACETS	0.979	0.947	1	0.979	0.947	1	CLONAL	2	TRUE	0	0.700656116777631	2		611	621	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710981	114710981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	443	490	2	ENST00000543371.1:c.205C>T	p.Pro69Ser	p.P69S	ENST00000543371	NM_001198531.1	69	Ccg/Tcg	2/14	0.644371439487509	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.700656116777631	4		492	1012	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647287	23647287	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	452	884	3	ENST00000261584.4:c.580G>T	p.Glu194Ter	p.E194*	ENST00000261584	NM_024675.3	194	Gaa/Taa	4/13	0.644371439487509	4	FACETS	0.957	0.915	0.998	0.957	0.915	0.998	CLONAL	2	TRUE	2	0.700656116777631	4		887	1147	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619172	37619172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759485356	NA	P-0020214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	437	635	1	ENST00000447079.4:c.848C>T	p.Ser283Leu	p.S283L	ENST00000447079	NM_015083.1	283	tCg/tTg	1/14	0.644371439487509	4	FACETS	0.963	0.921	1	0.963	0.921	1	CLONAL	2	TRUE	2	0.700656116777631	4		636	1101	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41201164	41201164	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	540	949	0	ENST00000357654.3:c.5380G>C	p.Glu1794Gln	p.E1794Q	ENST00000357654	NM_007294.3	1794	Gag/Cag	21/23	0.644371439487509	4	FACETS	0.929	0.892	0.967	0.929	0.892	0.967	CLONAL	2	TRUE	2	0.700656116777631	4		949	1411	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020265-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	68	157	1	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.607	0.526	0.695	0.607	0.526	0.695	SUBCLONAL	1	TRUE	1	0.193186052176363	2		158	1160	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651642	48651642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020265-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1318	153	1019	1	ENST00000376670.3:c.808C>T	p.Arg270Trp	p.R270W	ENST00000376670	NM_002049.3	270	Cgg/Tgg	5/6	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.193186052176363	2		1020	1471	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266703	18266703	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020265-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	73	786	0	ENST00000222254.8:c.14A>T	p.Glu5Val	p.E5V	ENST00000222254	NM_005027.3	5	gAg/gTg	2/16	1	2	FACETS	0.611	0.533	0.697	0.611	0.533	0.697	SUBCLONAL	1	TRUE	1	0.193186052176363	2		786	1236	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118817	61118818	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	TT	novel	NA	P-0020265-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	31	236	1	ENST00000295025.8:c.11-1_11delinsTT		p.X4_splice	ENST00000295025	NM_002908.2	4		2/11	1	2	FACETS	0.715	0.578	0.87	0.715	0.578	0.87	SUBCLONAL	1	TRUE	1	0.193186052176363	2		237	449	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292678	62292678	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020265-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1637	121	809	0	ENST00000360203.5:c.130A>G	p.Thr44Ala	p.T44A	ENST00000360203	NM_001283009.1	44	Acg/Gcg	3/35	0.193186052176363	6	FACETS	0.988	0.889	1			1	CLONAL	1	TRUE	NA	0.193186052176363	6		809	1758	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622571	28622571	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs537215681	NA	P-0020283-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	88	484	0	ENST00000241453.7:c.1046T>A	p.Phe349Tyr	p.F349Y	ENST00000241453	NM_004119.2	349	tTt/tAt	9/24	NA	2	FACETS	0.823	0.733	0.917			1	INDETERMINATE	1	TRUE	NA	0.52420415698983	2		484	408	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578546	7578562	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGGGAGTACTGTAGGA	AGGGGAGTACTGTAGGA	-	novel	NA	P-0020367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	166	849	1	ENST00000269305.4:c.376-8_384del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		850	603	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	148	134	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.936	0.862	1	1	0.991	1	CLONAL	2	TRUE	1	0.3406693443991	2		134	464	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	160	619	8	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.934	0.855	1	0.934	0.855	1	CLONAL	1	TRUE	1	0.3406693443991	2		627	1006	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	223	1043	2	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	0.3406693443991	3	FACETS	1	0.983	1	0.59	0.548	0.633	CLONAL	1	TRUE	1	0.3406693443991	3		1045	1299	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	144	585	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.3406693443991	2		588	824	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	91	545	2	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.814	0.724	0.911	0.814	0.724	0.911	CLONAL	1	TRUE	1	0.3406693443991	2		547	656	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	155	229	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.3406693443991	2		229	899	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	186	524	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.3406693443991	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.3406693443991	2		524	483	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511094	148511094	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	106	518	0	ENST00000320356.2:c.1808del	p.Asn603MetfsTer72	p.N603Mfs*72	ENST00000320356	NM_004456.4	603	aAt/at	15/20	1	2	FACETS	0.977	0.877	1	0.977	0.877	1	CLONAL	1	TRUE	1	0.3406693443991	2		518	637	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	114	1018	4	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	0.848	0.764	0.938	0.848	0.764	0.938	CLONAL	1	TRUE	1	0.3406693443991	2		1022	789	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	137	1001	7	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	0.897	0.815	0.982	0.897	0.815	0.982	CLONAL	1	TRUE	1	0.3406693443991	2		1008	897	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	243	621	4	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.968	1	1	0.995	1	CLONAL	2	TRUE	1	0.3406693443991	2		625	682	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	98	702	13	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.3406693443991	2		715	558	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	103	601	1	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.3406693443991	2		602	577	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138915	64138915	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	156	931	2	ENST00000334205.4:c.2287del	p.Arg763AlafsTer21	p.R763Afs*21	ENST00000334205	NM_003942.2	761	gCc/gc	17/17	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.3406693443991	2		933	799	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798822	42798822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	387	1042	2	ENST00000575354.2:c.4394G>A	p.Arg1465His	p.R1465H	ENST00000575354	NM_015125.3	1465	cGc/cAc	19/20	0.3406693443991	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.3406693443991	3		1044	1101	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589582	67589582	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	78	198	0	ENST00000274335.5:c.1345T>A	p.Leu449Ile	p.L449I	ENST00000274335		449	Tta/Ata	10/15	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.3406693443991	2		198	444	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626461	12626461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs727504827	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	91	701	0	ENST00000251849.4:c.1688G>A	p.Arg563Gln	p.R563Q	ENST00000251849	NM_002880.3	563	cGa/cAa	16/17	0.3406693443991	2	FACETS	0.826	0.734	0.924	0.413	0.367	0.462	CLONAL	1	TRUE	0	0.3406693443991	2		701	647	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984672	11984672	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	61	319	0	ENST00000353533.5:c.219-1G>C		p.X73_splice	ENST00000353533	NM_003010.3	73			1	2	FACETS	0.984	0.853	1	0.984	0.853	1	CLONAL	1	TRUE	1	0.3406693443991	2		319	364	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442811	442811	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	72	481	0	ENST00000399788.2:c.1495del	p.Glu499SerfsTer19	p.E499Sfs*19	ENST00000399788	NM_001042603.1	499	Gag/ag	12/28	NA	2	FACETS	0.87	0.762	0.986			1	INDETERMINATE	1	TRUE	NA	0.3406693443991	2		481	486	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	219	1984	5	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.3406693443991	2		1989	1166	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708596	43708596	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	132	715	0	ENST00000382044.4:c.4700G>T	p.Arg1567Met	p.R1567M	ENST00000382044	NM_001141980.1	1567	aGg/aTg	22/28	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.3406693443991	2		715	731	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	120	690	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	0.885	0.799	0.976	0.885	0.799	0.976	CLONAL	1	TRUE	1	0.3406693443991	2		690	796	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223086	5223086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1251374260	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	197	1181	5	ENST00000357368.4:c.2717C>T	p.Ala906Val	p.A906V	ENST00000357368	NM_002850.3	906	gCg/gTg	18/38	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.3406693443991	2		1186	934	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32814948	32814948	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	137	839	0	ENST00000354258.4:c.2117del	p.Gly706ValfsTer12	p.G706Vfs*12	ENST00000354258	NM_000593.5	706	gGt/gt	10/11	1	2	FACETS	0.971	0.884	1	0.971	0.884	1	CLONAL	1	TRUE	1	0.3406693443991	2		839	828	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	114	577	4	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.966	0.871	1	0.966	0.871	1	CLONAL	1	TRUE	1	0.3406693443991	2		581	693	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323362	31323363	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748204482	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	136	730	0	ENST00000412585.2:c.626dup	p.Thr211AspfsTer10	p.T211Dfs*10	ENST00000412585	NM_005514.6	209	cca/ccCa	4/8	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.3406693443991	2		730	745	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248285	59248285	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	28	143	0	ENST00000371222.2:c.458del	p.Gly153AlafsTer29	p.G153Afs*29	ENST00000371222	NM_002228.3	153	gGc/gc	1/1	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.3406693443991	2		143	131	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494665	2494665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779181014	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	151	973	3	ENST00000355716.4:c.805G>A	p.Val269Met	p.V269M	ENST00000355716	NM_003820.2	269	Gtg/Atg	8/8	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.3406693443991	2		976	854	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941052	36941052	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	178	1016	2	ENST00000361632.4:c.287A>G	p.Gln96Arg	p.Q96R	ENST00000361632		96	cAg/cGg	3/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.3406693443991	2		1018	954	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726267	46726267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371935755	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	146	784	2	ENST00000371975.4:c.461G>A	p.Arg154Gln	p.R154Q	ENST00000371975	NM_003579.3	154	cGg/cAg	6/18	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.3406693443991	2		786	731	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248010	59248011	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	149	907	0	ENST00000371222.2:c.732dup	p.Ile245HisfsTer65	p.I245Hfs*65	ENST00000371222	NM_002228.3	244	-/C	1/1	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.3406693443991	2		907	858	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120478217	120478217	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	71	510	0	ENST00000256646.2:c.3533G>T	p.Gly1178Val	p.G1178V	ENST00000256646	NM_024408.3	1178	gGc/gTc	22/34	1	2	FACETS	0.859	0.752	0.975	0.859	0.752	0.975	CLONAL	1	TRUE	1	0.3406693443991	2		510	485	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588172	69588172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550329316	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	177	982	1	ENST00000168712.1:c.526G>A	p.Gly176Ser	p.G176S	ENST00000168712	NM_002007.2	176	Ggc/Agc	3/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.3406693443991	2		983	924	SUCCESS
CBL	867	MSKCC	GRCh37	11	119158638	119158638	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	151	832	0	ENST00000264033.4:c.2018T>G	p.Ile673Ser	p.I673S	ENST00000264033	NM_005188.3	673	aTt/aGt	12/16	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.3406693443991	2		832	876	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245474	133245474	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752076074	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	125	769	1	ENST00000320574.5:c.1846C>T	p.Arg616Cys	p.R616C	ENST00000320574	NM_006231.2	616	Cgc/Tgc	17/49	1	2	FACETS	0.854	0.773	0.94	0.854	0.773	0.94	CLONAL	1	TRUE	1	0.3406693443991	2		770	859	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134420	41134420	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753862295	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	145	739	0	ENST00000379561.5:c.1208C>T	p.Pro403Leu	p.P403L	ENST00000379561	NM_002015.3	403	cCg/cTg	2/3	1	2	FACETS	0.95	0.867	1	0.95	0.867	1	CLONAL	1	TRUE	1	0.3406693443991	2		739	896	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422059	81422059	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	117	652	0	ENST00000298171.2:c.35T>C	p.Leu12Pro	p.L12P	ENST00000298171	NM_000369.2	12	cTg/cCg	1/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.3406693443991	2		652	563	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828282	72828282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs967750771	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	156	729	0	ENST00000268489.5:c.8299G>A	p.Gly2767Arg	p.G2767R	ENST00000268489	NM_006885.3	2767	Gga/Aga	9/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.3406693443991	2		729	773	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81927337	81927337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1164040767	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	216	928	0	ENST00000359376.3:c.1010G>A	p.Arg337Gln	p.R337Q	ENST00000359376	NM_002661.3	337	cGg/cAg	12/33	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.3406693443991	2		928	994	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351205	89351205	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	169	904	1	ENST00000301030.4:c.1745A>G	p.Glu582Gly	p.E582G	ENST00000301030	NM_001256183.1	582	gAg/gGg	9/13	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.3406693443991	2		905	846	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15938157	15938157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	130	580	0	ENST00000268712.3:c.7057G>A	p.Val2353Ile	p.V2353I	ENST00000268712	NM_006311.3	2353	Gtc/Atc	45/46	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.3406693443991	2		580	667	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961294	15961294	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	149	728	0	ENST00000268712.3:c.6095del	p.Pro2032LeufsTer17	p.P2032Lfs*17	ENST00000268712	NM_006311.3	2032	cCt/ct	39/46	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.3406693443991	2		728	808	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17117042	17117042	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	167	948	0	ENST00000285071.4:c.1667G>A	p.Gly556Asp	p.G556D	ENST00000285071	NM_144997.5	556	gGc/gAc	14/14	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.3406693443991	2		948	968	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676243	37676243	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	199	845	1	ENST00000447079.4:c.2998A>G	p.Met1000Val	p.M1000V	ENST00000447079	NM_015083.1	1000	Atg/Gtg	11/14	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.3406693443991	2		846	970	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246531	41246532	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs80357569	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	78	1010	3	ENST00000357654.3:c.1016dup	p.Val340GlyfsTer6	p.V340Gfs*6	ENST00000357654	NM_007294.3	339	aag/aaAg	10/23	1	2	FACETS	0.493	0.432	0.559	0.493	0.432	0.559	SUBCLONAL	1	TRUE	1	0.3406693443991	2		1013	928	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39537693	39537693	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	32	450	1	ENST00000262039.4:c.227C>T	p.Thr76Ile	p.T76I	ENST00000262039	NM_002647.2	76	aCa/aTa	2/25	1	2	FACETS	0.424	0.344	0.515	0.424	0.344	0.515	SUBCLONAL	1	TRUE	1	0.3406693443991	2		451	443	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097659	11097659	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	83	1156	0	ENST00000358026.2:c.839C>A	p.Pro280His	p.P280H	ENST00000358026	NM_001128849.1	280	cCt/cAt	5/36	1	2	FACETS	0.52	0.458	0.587	0.52	0.458	0.587	SUBCLONAL	1	TRUE	1	0.3406693443991	2		1156	937	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353959	15353959	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1354137520	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	49	301	1	ENST00000263377.2:c.2921C>A	p.Pro974Gln	p.P974Q	ENST00000263377	NM_058243.2	974	cCg/cAg	14/20	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.3406693443991	2		302	263	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497933	25497934	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	90	695	0	ENST00000264709.3:c.515dup	p.Gly173TrpfsTer43	p.G173Wfs*43	ENST00000264709	NM_175629.2	172	ggt/ggGt	6/23	1	2	FACETS	0.823	0.731	0.921	0.823	0.731	0.921	CLONAL	1	TRUE	1	0.3406693443991	2		695	642	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966238	25966238	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	158	772	0	ENST00000435504.4:c.2968A>G	p.Met990Val	p.M990V	ENST00000435504		990	Atg/Gtg	13/13	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.3406693443991	2		772	839	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966733	25966733	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	115	849	0	ENST00000435504.4:c.2473A>G	p.Ser825Gly	p.S825G	ENST00000435504		825	Agt/Ggt	13/13	1	2	FACETS	0.871	0.785	0.962	0.871	0.785	0.962	CLONAL	1	TRUE	1	0.3406693443991	2		849	775	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446251	29446251	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	162	816	0	ENST00000389048.3:c.3316A>G	p.Ser1106Gly	p.S1106G	ENST00000389048	NM_004304.4	1106	Agt/Ggt	20/29	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.3406693443991	2		816	840	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721099	61721099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1458439158	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	120	723	0	ENST00000401558.2:c.1175C>T	p.Pro392Leu	p.P392L	ENST00000401558	NM_003400.3	392	cCg/cTg	12/25	1	2	FACETS	0.968	0.875	1	0.968	0.875	1	CLONAL	1	TRUE	1	0.3406693443991	2		723	728	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288564	198288564	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774397512	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	138	879	3	ENST00000335508.6:c.163G>A	p.Val55Met	p.V55M	ENST00000335508	NM_012433.2	55	Gtg/Atg	2/25	1	2	FACETS	0.855	0.777	0.936	0.855	0.777	0.936	CLONAL	1	TRUE	1	0.3406693443991	2		882	948	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279789	46279789	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs969825525	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	149	656	0	ENST00000371998.3:c.3715C>T	p.Arg1239Ter	p.R1239*	ENST00000371998		1239	Cga/Tga	20/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.3406693443991	2		656	698	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160198	22160198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	98	452	0	ENST00000215832.6:c.433G>A	p.Val145Ile	p.V145I	ENST00000215832	NM_002745.4	145	Gtt/Att	3/9	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.3406693443991	2		452	534	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035134	37035204	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAAAGAGATGATTGAGAACTGGTACGGAGGGAGTCGAGCCGGGCTCACTTAAGGGCTACGACTTAACGGGC	CAAAGAGATGATTGAGAACTGGTACGGAGGGAGTCGAGCCGGGCTCACTTAAGGGCTACGACTTAACGGGC	AT	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	97	506	2	ENST00000231790.2:c.96_116+50delinsAT		p.X32_splice	ENST00000231790	NM_000249.3	32		1/19	0.3406693443991	2	FACETS	1	0.97	1	0.616	0.552	0.684	CLONAL	1	TRUE	0	0.3406693443991	2		508	462	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933438	49933438	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	147	879	1	ENST00000296474.3:c.2752del	p.Leu918CysfsTer18	p.L918Cfs*18	ENST00000296474	NM_002447.2	918	Ctg/tg	11/20	0.3406693443991	2	FACETS	1	0.978	1	0.606	0.554	0.66	CLONAL	1	TRUE	0	0.3406693443991	2		880	712	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165701	185165701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	110	595	0	ENST00000265026.3:c.976C>T	p.Arg326Trp	p.R326W	ENST00000265026	NM_004721.4	326	Cgg/Tgg	5/14	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.3406693443991	2		595	608	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191001	185191001	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	254	1292	2	ENST00000265026.3:c.1882T>C	p.Tyr628His	p.Y628H	ENST00000265026	NM_004721.4	628	Tac/Cac	11/14	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.3406693443991	2		1294	1414	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286238	66286238	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	92	611	0	ENST00000273854.3:c.1448del	p.Asn483ThrfsTer18	p.N483Tfs*18	ENST00000273854	NM_004439.5	483	aAc/ac	6/18	1	2	FACETS	0.911	0.811	1	0.911	0.811	1	CLONAL	1	TRUE	1	0.3406693443991	2		611	593	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538990	187538990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755244994	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	160	779	1	ENST00000441802.2:c.8750G>A	p.Arg2917Gln	p.R2917Q	ENST00000441802	NM_005245.3	2917	cGa/cAa	10/27	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.3406693443991	2		780	830	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294318	1294318	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	154	882	2	ENST00000310581.5:c.683C>T	p.Ala228Val	p.A228V	ENST00000310581	NM_198253.2	228	gCc/gTc	2/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.3406693443991	2		884	792	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294696	1294696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	166	771	2	ENST00000310581.5:c.305C>T	p.Ala102Val	p.A102V	ENST00000310581	NM_198253.2	102	gCg/gTg	2/16	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.3406693443991	2		773	734	SUCCESS
APC	324	MSKCC	GRCh37	5	112164604	112164604	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554082118	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	87	404	0	ENST00000257430.4:c.1682del	p.Lys561ArgfsTer9	p.K561Rfs*9	ENST00000257430	NM_000038.5	560	Aaa/aa	14/16	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.3406693443991	2		404	511	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672067	30672067	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	143	1051	0	ENST00000376406.3:c.4893del	p.Lys1632SerfsTer44	p.K1632Sfs*44	ENST00000376406	NM_014641.2	1631	ccC/cc	10/15	1	2	FACETS	0.932	0.849	1	0.932	0.849	1	CLONAL	1	TRUE	1	0.3406693443991	2		1051	901	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323092	31323093	+	splice_donor_variant	Splice_Site	INS	-	-	C	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	128	924	0	ENST00000412585.2:c.895+1dup		p.X299_splice	ENST00000412585	NM_005514.6	299			1	2	FACETS	0.932	0.845	1	0.932	0.845	1	CLONAL	1	TRUE	1	0.3406693443991	2		924	806	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818837	32818837	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1336232266	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	170	945	3	ENST00000354258.4:c.1114C>T	p.Arg372Ter	p.R372*	ENST00000354258	NM_000593.5	372	Cga/Tga	4/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.3406693443991	2		948	887	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392174	81392174	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	60	446	0	ENST00000222390.5:c.103del	p.Arg35GlufsTer16	p.R35Efs*16	ENST00000222390	NM_000601.4	35	Aga/ga	2/18	1	2	FACETS	0.829	0.716	0.951	0.829	0.716	0.951	CLONAL	1	TRUE	1	0.3406693443991	2		446	425	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412639	116412641	+	intron_variant	Intron	DEL	TGT	TGT	-	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	160	1152	0	ENST00000397752.3:c.3028+600_3028+602del		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.837	0.766	0.912	0.837	0.766	0.912	CLONAL	1	TRUE	1	0.3406693443991	2		1152	1122	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486350	8486350	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0020399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	48	344	0	ENST00000356435.5:c.2468-1G>A		p.X823_splice	ENST00000356435		823			1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.3406693443991	2		344	268	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88679226	88679226	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs879254049	NA	P-0020420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	125	465	0	ENST00000372037.3:c.1166G>A	p.Ser389Asn	p.S389N	ENST00000372037	NM_004329.2	389	aGt/aAt	10/13	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.352098237075334	2		465	664	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418455	49418455	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1469731570	NA	P-0020420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1505	95	912	1	ENST00000301067.7:c.15958C>T	p.Arg5320Cys	p.R5320C	ENST00000301067	NM_003482.3	5320	Cgc/Tgc	50/54	0.352098237075334	3	FACETS	0.397	0.351	0.445	0.198	0.175	0.223	SUBCLONAL	1	TRUE	1	0.352098237075334	3		913	1600	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577481	7577507	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGCAAGTGGCTCCTGACCTGGAGTCT	TGGCAAGTGGCTCCTGACCTGGAGTCT	-	novel	NA	P-0020420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	158	729	0	ENST00000269305.4:c.774_782+18del		p.X258_splice	ENST00000269305	NM_001126112.2	258		7/11	0.352008621172798	2	FACETS	0.895	0.819	0.974	0.447	0.409	0.487	CLONAL	1	TRUE	0	0.352098237075334	2		729	1003	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	122	372	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.82	0.744	0.9	0.82	0.744	0.9	CLONAL	1	TRUE	1	0.532151553204607	2		373	559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0020423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	235	730	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.532376336356704	1	FACETS	0.825	0.772	0.879	0.825	0.772	0.879	CLONAL	1	TRUE	0	0.532151553204607	1		731	786	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921567	178921567	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553821144	NA	P-0020423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	79	347	0	ENST00000263967.3:c.1049A>G	p.Asp350Gly	p.D350G	ENST00000263967	NM_006218.2	350	gAc/gGc	5/21	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.532151553204607	2		347	260	SUCCESS
APC	324	MSKCC	GRCh37	5	112174466	112174466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253882360	NA	P-0020423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	134	306	0	ENST00000257430.4:c.3175G>A	p.Glu1059Lys	p.E1059K	ENST00000257430	NM_000038.5	1059	Gaa/Aaa	16/16	0.506510097365223	2	FACETS	0.899	0.833	0.966	0.899	0.833	0.966	CLONAL	2	TRUE	0	0.532151553204607	2		306	280	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2214510	2214510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756254147	NA	P-0020423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1185	82	951	0	ENST00000398665.3:c.1838C>T	p.Thr613Met	p.T613M	ENST00000398665	NM_032482.2	613	aCg/aTg	19/28	1	2	FACETS	0.243	0.213	0.276	0.243	0.213	0.276	SUBCLONAL	1	TRUE	1	0.532151553204607	2		951	1267	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661390	227661390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141094678	NA	P-0020423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	130	519	1	ENST00000305123.5:c.2065G>A	p.Val689Ile	p.V689I	ENST00000305123	NM_005544.2	689	Gtc/Atc	1/2	1	2	FACETS	0.817	0.744	0.894	0.817	0.744	0.894	CLONAL	1	TRUE	1	0.532151553204607	2		520	598	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436356	52436356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1435755592	NA	P-0020423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	354	798	0	ENST00000460680.1:c.2138G>A	p.Arg713Gln	p.R713Q	ENST00000460680	NM_004656.3	713	cGg/cAg	17/17	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.532151553204607	2		798	1101	SUCCESS
APC	324	MSKCC	GRCh37	5	112174460	112174460	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	128	299	0	ENST00000257430.4:c.3169G>T	p.Glu1057Ter	p.E1057*	ENST00000257430	NM_000038.5	1057	Gaa/Taa	16/16	0.506510097365223	2	FACETS	0.922	0.853	0.991	0.922	0.853	0.991	CLONAL	2	TRUE	0	0.532151553204607	2		299	261	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0020427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	21	565	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.871	0.676	1	1	0.933	1	CLONAL	2	FALSE	1	0.151717287973454	2		565	159	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431746	49431748	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs748239185	NA	P-0020427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	33	853	1	ENST00000301067.7:c.9391_9393del	p.Pro3131del	p.P3131del	ENST00000301067	NM_003482.3	3131	CCT/-	34/54	1	2	FACETS	1	0.887	1	1	0.965	1	CLONAL	2	FALSE	1	0.151717287973454	2		854	196	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115829	8115830	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	60	904	0	ENST00000346208.3:c.1178dup	p.Ala394GlyfsTer113	p.A394Gfs*113	ENST00000346208		392	aac/aaCc	6/6	1	2	FACETS	1	0.93	1	1	0.984	1	CLONAL	3	FALSE	1	0.151717287973454	2		904	239	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352601	118352602	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0020427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	16	590	0	ENST00000534358.1:c.3808_3809del	p.Lys1270GlufsTer2	p.K1270Efs*2	ENST00000534358	NM_005933.3	1269	gAA/g	7/36	1	2	FACETS	0.753	0.561	0.979	1	0.897	1	CLONAL	2	FALSE	1	0.151717287973454	2		590	140	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518194	103518194	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	12	358	0	ENST00000355739.4:c.2132A>T	p.Asp711Val	p.D711V	ENST00000355739	NM_000123.3	711	gAt/gTt	9/15	0.151717287973454	3	FACETS	0.915	0.651	1	0.915	0.651	1	CLONAL	2	FALSE	1	0.151717287973454	3		358	93	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0020428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	242	897	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.473427886231946	1	FACETS	0.925	0.866	0.985	0.925	0.866	0.985	CLONAL	1	TRUE	0	0.473427886231946	1		897	844	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416304	29416304	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	304	963	2	ENST00000389048.3:c.4649T>A	p.Leu1550His	p.L1550H	ENST00000389048	NM_004304.4	1550	cTt/cAt	29/29	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.473427886231946	2		965	1160	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840564	36840564	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771002648	NA	P-0020428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	292	1004	1	ENST00000358127.4:c.1169G>A	p.Arg390His	p.R390H	ENST00000358127	NM_001280556.1	390	cGt/cAt	10/10	1	2	FACETS	0.925	0.869	0.982	0.925	0.869	0.982	CLONAL	1	TRUE	1	0.473427886231946	2		1005	1334	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236649	236649	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs76896145	NA	P-0020434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	10	781	2	ENST00000264932.6:c.1367C>T	p.Ser456Leu	p.S456L	ENST00000264932	NM_004168.2	456	tCg/tTg	10/15	0.422897421758465	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.872741848831342	0		783	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577505	7577505	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs745425759	NA	P-0020434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	431	897	0	ENST00000269305.4:c.776A>T	p.Asp259Val	p.D259V	ENST00000269305	NM_001126112.2	259	gAc/gTc	7/11	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	2	FALSE	NA	0.872741848831342	2		897	471	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288969	212288969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148791072	NA	P-0020434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	84	923	0	ENST00000342788.4:c.2777C>T	p.Thr926Met	p.T926M	ENST00000342788	NM_005235.2	926	aCg/aTg	23/28	0.583313979588956	1	FACETS	0.362	0.323	0.402	0.362	0.323	0.402	SUBCLONAL	1	FALSE	0	0.872741848831342	1		923	300	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937989	36937989	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	107	1082	0	ENST00000361632.4:c.847G>C	p.Gly283Arg	p.G283R	ENST00000361632		283	Ggc/Cgc	7/16	0.583313979588956	1	FACETS	0.287	0.258	0.317	0.287	0.258	0.317	SUBCLONAL	1	FALSE	0	0.872741848831342	1		1082	482	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911736	32911736	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	91	919	0	ENST00000380152.3:c.3244A>G	p.Lys1082Glu	p.K1082E	ENST00000380152		1082	Aaa/Gaa	11/27	0.502995780330267	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.872741848831342	0		919	204	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131758	2131758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	309	1133	1	ENST00000219476.3:c.3773C>T	p.Ala1258Val	p.A1258V	ENST00000219476	NM_000548.3	1258	gCc/gTc	31/42	0.572625596818956	1	FACETS	0.584	0.555	0.614	0.584	0.555	0.614	SUBCLONAL	1	FALSE	0	0.872741848831342	1		1134	683	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376332	15376332	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	132	1215	0	ENST00000263377.2:c.682G>C	p.Val228Leu	p.V228L	ENST00000263377	NM_058243.2	228	Gtc/Ctc	5/20	0.583313979588956	1	FACETS	0.253	0.23	0.277	0.253	0.23	0.277	SUBCLONAL	1	FALSE	0	0.872741848831342	1		1215	674	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55124943	55124943	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	55	1000	1	ENST00000257290.5:c.8C>G	p.Thr3Ser	p.T3S	ENST00000257290	NM_006206.4	3	aCt/aGt	2/23	0.349958683918107	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.872741848831342	0		1001	303	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93973625	93973625	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	28	655	0	ENST00000369303.4:c.1751G>C	p.Gly584Ala	p.G584A	ENST00000369303	NM_004440.3	584	gGt/gCt	9/17	0.510095512435718	4	FACETS	0.395	0.316	0.485	0.099	0.079	0.122	INDETERMINATE	1	FALSE	0	0.872741848831342	4		655	304	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517392	157517392	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs763750480	NA	P-0020434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	78	838	0	ENST00000346085.5:c.3956C>G	p.Ser1319Cys	p.S1319C	ENST00000346085	NM_020732.3	1319	tCt/tGt	16/20	0.510095512435718	4	FACETS	0.513	0.45	0.58	0.128	0.112	0.145	INDETERMINATE	1	FALSE	0	0.872741848831342	4		838	653	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs869320707	NA	P-0020437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	32	278	0	ENST00000397752.3:c.3028+1G>T		p.X1010_splice	ENST00000397752	NM_000245.2	1010			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		278	590	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0020437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	95	340	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.97	0.864	1	0.97	0.864	1	CLONAL	1	TRUE	1	0.27137964355263	2		340	722	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359975	87359975	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	40	418	0	ENST00000277120.3:c.1283G>T	p.Arg428Leu	p.R428L	ENST00000277120		428	cGg/cTg	11/19	1	2	FACETS	0.673	0.559	0.799	0.673	0.559	0.799	SUBCLONAL	1	TRUE	1	0.27137964355263	2		418	438	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188182	11188182	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	45	591	1	ENST00000361445.4:c.5912C>T	p.Ala1971Val	p.A1971V	ENST00000361445	NM_004958.3	1971	gCc/gTc	43/58	1	2	FACETS	0.545	0.458	0.643	0.545	0.458	0.643	SUBCLONAL	1	TRUE	1	0.27137964355263	2		592	608	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317087	11317087	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	40	790	0	ENST00000361445.4:c.407C>T	p.Ala136Val	p.A136V	ENST00000361445	NM_004958.3	136	gCa/gTa	4/58	1	2	FACETS	0.402	0.333	0.48	0.402	0.333	0.48	SUBCLONAL	1	TRUE	1	0.27137964355263	2		790	733	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276942	123276942	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	56	498	1	ENST00000358487.5:c.975G>T	p.Glu325Asp	p.E325D	ENST00000358487	NM_000141.4	325	gaG/gaT	8/18	1	2	FACETS	0.736	0.63	0.851	0.736	0.63	0.851	SUBCLONAL	1	TRUE	1	0.27137964355263	2		499	561	SUCCESS
CBL	867	MSKCC	GRCh37	11	119146836	119146836	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	70	529	0	ENST00000264033.4:c.999G>T	p.Arg333Ser	p.R333S	ENST00000264033	NM_005188.3	333	agG/agT	6/16	0.165095725006196	3	FACETS	1	0.909	1	0.526	0.459	0.598	CLONAL	1	TRUE	1	0.27137964355263	3		529	557	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432401	49432401	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	61	913	0	ENST00000301067.7:c.8738C>G	p.Pro2913Arg	p.P2913R	ENST00000301067	NM_003482.3	2913	cCc/cGc	34/54	1	2	FACETS	0.585	0.504	0.674	0.585	0.504	0.674	SUBCLONAL	1	TRUE	1	0.27137964355263	2		913	768	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858896	57858896	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	117	896	0	ENST00000228682.2:c.392C>A	p.Pro131Gln	p.P131Q	ENST00000228682	NM_005269.2	131	cCa/cAa	5/12	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.27137964355263	2		896	833	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622419	28622419	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	37	660	0	ENST00000241453.7:c.1198G>T	p.Gly400Ter	p.G400*	ENST00000241453	NM_004119.2	400	Gga/Tga	9/24	1	2	FACETS	0.502	0.413	0.602	0.502	0.413	0.602	SUBCLONAL	1	TRUE	1	0.27137964355263	2		660	543	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420286	88420286	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0020437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	73	699	0	ENST00000360948.2:c.2400C>G	p.Tyr800Ter	p.Y800*	ENST00000360948	NM_001012338.2	800	taC/taG	19/19	1	2	FACETS	0.9	0.787	1	0.9	0.787	1	CLONAL	1	TRUE	1	0.27137964355263	2		699	598	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584416	39584416	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	59	487	0	ENST00000262039.4:c.1081G>T	p.Glu361Ter	p.E361*	ENST00000262039	NM_002647.2	361	Gag/Tag	10/25	1	2	FACETS	0.82	0.706	0.944	0.82	0.706	0.944	CLONAL	1	TRUE	1	0.27137964355263	2		487	530	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225338994	225338994	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	90	799	0	ENST00000264414.4:c.2275G>T	p.Glu759Ter	p.E759*	ENST00000264414	NM_003590.4	759	Gag/Tag	16/16	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.27137964355263	2		799	622	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098952	47098952	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	80	755	0	ENST00000409792.3:c.6322G>T	p.Val2108Leu	p.V2108L	ENST00000409792	NM_014159.6	2108	Gta/Tta	15/21	1	2	FACETS	0.707	0.621	0.799	0.707	0.621	0.799	SUBCLONAL	1	TRUE	1	0.27137964355263	2		755	834	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161937	47161937	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	70	551	0	ENST00000409792.3:c.4189G>T	p.Asp1397Tyr	p.D1397Y	ENST00000409792	NM_014159.6	1397	Gat/Tat	3/21	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.27137964355263	2		551	494	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278215	142278215	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0020437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	73	875	2	ENST00000350721.4:c.1610T>A	p.Leu537Ter	p.L537*	ENST00000350721	NM_001184.3	537	tTg/tAg	7/47	1	2	FACETS	0.692	0.605	0.787	0.692	0.605	0.787	SUBCLONAL	1	TRUE	1	0.27137964355263	2		877	777	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177686	56177686	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	81	491	0	ENST00000399503.3:c.2659G>T	p.Ala887Ser	p.A887S	ENST00000399503	NM_005921.1	887	Gca/Tca	14/20	0.241026443886785	3	FACETS	1	0.969	1	0.651	0.574	0.732	CLONAL	1	TRUE	1	0.27137964355263	3		491	521	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591249	67591257	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TGGTTGACT	TGGTTGACT	-	novel	NA	P-0020437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	47	597	0	ENST00000274335.5:c.1747_1755del	p.Trp583_Thr585del	p.W583_T585del	ENST00000274335		583	TGGTTGACT/-	13/15	0.241026443886785	3	FACETS	0.664	0.56	0.78	0.332	0.28	0.39	SUBCLONAL	1	TRUE	1	0.27137964355263	3		597	592	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508406	106508406	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	39	352	0	ENST00000359195.3:c.400C>A	p.Gln134Lys	p.Q134K	ENST00000359195	NM_002649.2	134	Cag/Aag	2/11	0.27137964355263	3	FACETS	0.846	0.702	1	0.423	0.351	0.503	CLONAL	1	TRUE	1	0.27137964355263	3		352	386	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486035	8486035	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1333477882	NA	P-0020437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	50	737	0	ENST00000356435.5:c.2782G>C	p.Glu928Gln	p.E928Q	ENST00000356435		928	Gaa/Caa	17/35	0.27137964355263	1	FACETS	0.555	0.47	0.648	0.555	0.47	0.648	SUBCLONAL	1	TRUE	0	0.27137964355263	1		737	574	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87475960	87475960	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	102	1070	0	ENST00000277120.3:c.1402T>A	p.Ser468Thr	p.S468T	ENST00000277120		468	Tca/Aca	13/19	1	2	FACETS	0.806	0.719	0.898	0.806	0.719	0.898	CLONAL	1	TRUE	1	0.27137964355263	2		1070	933	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249372	110249372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	86	1213	1	ENST00000374672.4:c.1201G>A	p.Ala401Thr	p.A401T	ENST00000374672	NM_004235.4	401	Gcg/Acg	4/5	1	2	FACETS	0.536	0.472	0.604	0.536	0.472	0.604	SUBCLONAL	1	TRUE	1	0.27137964355263	2		1214	1183	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044492	47044493	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	89	840	0	ENST00000377604.3:c.1992dup	p.Gln665ThrfsTer8	p.Q665Tfs*8	ENST00000377604	NM_001204468.1	663	-/A	18/24	1	2	FACETS	0.863	0.765	0.968	0.863	0.765	0.968	CLONAL	1	TRUE	1	0.27137964355263	2		840	760	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347807	70347807	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	44	790	0	ENST00000374080.3:c.3046C>A	p.Arg1016Ser	p.R1016S	ENST00000374080		1016	Cgc/Agc	22/45	1	2	FACETS	0.437	0.365	0.517	0.437	0.365	0.517	SUBCLONAL	1	TRUE	1	0.27137964355263	2		790	742	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813088	76813089	+	missense_variant	Missense_Mutation	DNP	CG	CG	AA	novel	NA	P-0020437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	35	807	3	ENST00000373344.5:c.6532_6533delinsTT	p.Arg2178Leu	p.R2178L	ENST00000373344	NM_000489.3	2178	CGg/TTg	30/35	1	2	FACETS	0.406	0.332	0.49	0.406	0.332	0.49	SUBCLONAL	1	TRUE	1	0.27137964355263	2		810	635	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106880	27106880	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	315	692	0	ENST00000324856.7:c.6493del	p.Glu2165ArgfsTer35	p.E2165Rfs*35	ENST00000324856	NM_006015.4	2164	cGg/cg	20/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.734868516178371	2		692	846	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538281	187538281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	309	913	1	ENST00000441802.2:c.8953G>A	p.Asp2985Asn	p.D2985N	ENST00000441802	NM_005245.3	2985	Gac/Aac	11/27	NA	2	FACETS	0.901	0.852	0.952			1	INDETERMINATE	1	TRUE	NA	0.734868516178371	2		914	933	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156742	20156742	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0020441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	213	570	0	ENST00000379607.5:c.17-2A>T		p.X6_splice	ENST00000379607	NM_001412.3	6			0.734868516178371	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.734868516178371	1		570	366	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0020452-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	149	444	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.672	0.616	0.73	0.672	0.616	0.73	SUBCLONAL	1	TRUE	1	0.711760594074618	2		444	623	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935669	15935669	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020452-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	191	384	1	ENST00000268712.3:c.7264C>T	p.Arg2422Ter	p.R2422*	ENST00000268712	NM_006311.3	2422	Cga/Tga	46/46	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.711760594074618	2		385	521	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118853	115118853	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020452-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	207	551	0	ENST00000257566.3:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000257566	NM_016569.3	163	tAt/tGt	2/8	1	2	FACETS	0.852	0.794	0.911	0.852	0.794	0.911	CLONAL	1	TRUE	1	0.711760594074618	2		551	683	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47607098	47607100	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs1424757619	NA	P-0020452-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	73	576	0	ENST00000263735.4:c.852_854del	p.Val285del	p.V285del	ENST00000263735	NM_002354.2	283	aTTGtt/att	7/9	1	2	FACETS	0.24	0.21	0.274	0.24	0.21	0.274	SUBCLONAL	1	TRUE	1	0.711760594074618	2		576	853	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252852	36252852	+	splice_donor_variant	Splice_Site	DEL	A	A	-	novel	NA	P-0020452-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	180	344	0	ENST00000300305.3:c.508+2del		p.X170_splice	ENST00000300305		170			0.106338832851229	5	FACETS	0.942	0.875	1	0.628	0.583	0.674	INDETERMINATE	2	TRUE	2	0.711760594074618	5		344	555	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252989	36252990	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020452-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	242	510	0	ENST00000300305.3:c.372dup	p.Pro125SerfsTer13	p.P125Sfs*13	ENST00000300305		124	-/T	4/8	0.106338832851229	5	FACETS	1	0.952	1	0.677	0.636	0.719	INDETERMINATE	2	TRUE	2	0.711760594074618	5		510	692	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772219	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCCT	novel	NA	P-0020456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	234	888	0	ENST00000261769.5:c.67_68insTCCT	p.Gln23LeufsTer12	p.Q23Lfs*12	ENST00000261769	NM_004360.3	23	cag/cTCCTag	2/16	0.475545229581915	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.475545229581915	1		888	743	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485813	57485813	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	177	535	0	ENST00000371085.3:c.1114A>T	p.Ile372Phe	p.I372F	ENST00000371085	NM_000516.4	372	Atc/Ttc	13/13	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.475545229581915	2		535	720	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578412	7578412	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519747	NA	P-0020457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	296	823	1	ENST00000269305.4:c.518T>C	p.Val173Ala	p.V173A	ENST00000269305	NM_001126112.2	173	gTg/gCg	5/11	0.448882528200079	1	FACETS	0.989	0.932	1	0.989	0.932	1	CLONAL	1	TRUE	0	0.448882528200079	1		824	1034	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106703	27106703	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	146	761	2	ENST00000324856.7:c.6316del	p.Leu2106TrpfsTer29	p.L2106Wfs*29	ENST00000324856	NM_006015.4	2105	aCc/ac	20/20	1	2	FACETS	0.544	0.495	0.596	0.544	0.495	0.596	SUBCLONAL	1	TRUE	1	0.448882528200079	2		763	1195	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0020458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	39	717	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.688231653164601	1	FACETS	0.176	0.146	0.21	0.176	0.146	0.21	SUBCLONAL	1	TRUE	0	0.688231653164601	1		717	422	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	279	372	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.298853447789025	5	FACETS	1	0.984	1			1	CLONAL	2	TRUE	NA	0.440206875433643	5		373	935	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0020461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	389	1017	1	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.43265289529664	2	FACETS	0.976	0.932	1	0.976	0.932	1	CLONAL	2	TRUE	0	0.440206875433643	2		1018	905	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587242	212587242	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	76	574	0	ENST00000342788.4:c.759T>A	p.Asn253Lys	p.N253K	ENST00000342788	NM_005235.2	253	aaT/aaA	7/28	0.413040458978779	3	FACETS	0.799	0.703	0.903	0.4	0.351	0.452	CLONAL	1	TRUE	1	0.440206875433643	3		574	527	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	262	482	1	ENST00000342988.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000342988	NM_005359.5	356	cCt/cTt	9/12	0.43265289529664	2	FACETS	0.971	0.917	1	0.971	0.917	1	CLONAL	2	TRUE	0	0.440206875433643	2		483	613	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411678	63411678	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	502	617	3	ENST00000330258.3:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000330258	NM_152424.3	497	Cga/Tga	2/2	0.440206875433643	2	FACETS	0.977	0.946	1			1	CLONAL	3	TRUE	NA	0.440206875433643	2		620	778	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830132	72830132	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	618	794	1	ENST00000268489.5:c.6449C>A	p.Thr2150Asn	p.T2150N	ENST00000268489	NM_006885.3	2150	aCc/aAc	9/10	0.255152629674841	6	FACETS	0.969	0.938	0.999	0.807	0.782	0.833	INDETERMINATE	5	TRUE	0	0.440206875433643	6		795	1090	SUCCESS
APC	324	MSKCC	GRCh37	5	112170699	112170700	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0020461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	247	742	0	ENST00000257430.4:c.1795_1796del	p.Cys599HisfsTer2	p.C599Hfs*2	ENST00000257430	NM_000038.5	599	TGc/c	15/16	0.377459941598849	2	FACETS	0.904	0.851	0.957	0.904	0.851	0.957	CLONAL	2	TRUE	0	0.440206875433643	2		742	621	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0020462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	438	717	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.644070939779309	1	FACETS	0.991	0.951	1	0.991	0.951	1	CLONAL	1	TRUE	0	0.65371360863362	1		717	910	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243006	41243013	+	frameshift_variant	Frame_Shift_Del	DEL	TTCAGAGA	TTCAGAGA	-	novel	NA	P-0020462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	678	746	0	ENST00000357654.3:c.4133_4140del	p.Val1378GlyfsTer10	p.V1378Gfs*10	ENST00000357654	NM_007294.3	1378	gTCTCTGAA/g	11/23	0.65371360863362	2	FACETS	0.978	0.951	1	0.978	0.951	1	CLONAL	2	TRUE	0	0.65371360863362	2		746	1060	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027386	48027386	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	407	508	0	ENST00000234420.5:c.2264A>C	p.Glu755Ala	p.E755A	ENST00000234420	NM_000179.2	755	gAa/gCa	4/10	0.58036236177098	3	FACETS	0.911	0.871	0.951			1	CLONAL	2	TRUE	NA	0.65371360863362	3		508	907	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339555	70339635	+	inframe_deletion	In_Frame_Del	DEL	GCATTATTGCAGAGAAATTACGTTGTAATACCCTTCCTGACACTGGTCGCAGGAAGCCCCAAGTGAACCAGAAGGATAACT	GCATTATTGCAGAGAAATTACGTTGTAATACCCTTCCTGACACTGGTCGCAGGAAGCCCCAAGTGAACCAGAAGGATAACT	-	novel	NA	P-0020462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	288	836	2	ENST00000374080.3:c.224_304del	p.Ser75_Phe102delinsIle	p.S75_F102delinsI	ENST00000374080		75	aGCATTATTGCAGAGAAATTACGTTGTAATACCCTTCCTGACACTGGTCGCAGGAAGCCCCAAGTGAACCAGAAGGATAACTtc/atc	3/45	0.65371360863362	1	FACETS	0.876	0.83	0.923	0.876	0.83	0.923	CLONAL	1	TRUE	0	0.65371360863362	1		838	677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0020472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	164	1111	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.758	0.694	0.825	0.758	0.694	0.825	SUBCLONAL	1	TRUE	1	0.34	2		1112	1273	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167577	NA	P-0020472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	30	515	0	ENST00000257430.4:c.4463del	p.Leu1488TyrfsTer19	p.L1488Yfs*19	ENST00000257430	NM_000038.5	1487	acT/ac	16/16	1	2	FACETS	0.339	0.272	0.415	0.339	0.272	0.415	SUBCLONAL	1	TRUE	1	0.34	2		515	521	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229545	5229545	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	64	336	1	ENST00000357368.4:c.2306G>A	p.Arg769His	p.R769H	ENST00000357368	NM_002850.3	769	cGc/cAc	15/38	1	2	FACETS	0.822	0.714	0.939	0.822	0.714	0.939	CLONAL	1	TRUE	1	0.34	2		337	458	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52663039	52663039	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	42	412	0	ENST00000394830.3:c.1314G>C	p.Lys438Asn	p.K438N	ENST00000394830	NM_018313.4	438	aaG/aaC	13/30	1	2	FACETS	0.47	0.392	0.556	0.47	0.392	0.556	SUBCLONAL	1	TRUE	1	0.34	2		412	526	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0020474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	171	560	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.243531185747871	2		560	965	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0020474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	65	626	1	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.243531185747871	2		627	514	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947540	48947540	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0020474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	186	880	0	ENST00000267163.4:c.1128-1G>C		p.X376_splice	ENST00000267163	NM_000321.2	376			0.243531185747871	2	FACETS	0.929	0.859	1	0.929	0.859	1	CLONAL	2	TRUE	0	0.243531185747871	2		880	822	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871652	35871652	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	61	610	0	ENST00000216797.5:c.854A>T	p.Asp285Val	p.D285V	ENST00000216797	NM_020529.2	285	gAt/gTt	5/6	1	2	FACETS	0.914	0.789	1	0.914	0.789	1	CLONAL	1	TRUE	1	0.243531185747871	2		610	548	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0020477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2466	225	796	0	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	0.350693408495296	5	FACETS	0.728	0.674	0.784			1	SUBCLONAL	1	TRUE	NA	0.350693408495296	5		796	2691	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0020477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	189	843	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.350693408495296	2		843	836	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578466	7578466	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786202752	NA	P-0020477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	298	1469	0	ENST00000269305.4:c.464C>A	p.Thr155Asn	p.T155N	ENST00000269305	NM_001126112.2	155	aCc/aAc	5/11	0.350693408495296	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.350693408495296	1		1469	1367	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416673	416673	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	231	594	0	ENST00000399788.2:c.3877G>T	p.Glu1293Ter	p.E1293*	ENST00000399788	NM_001042603.1	1293	Gaa/Taa	23/28	0.350693408495296	3	FACETS	0.927	0.866	0.99	0.927	0.866	0.99	CLONAL	2	TRUE	1	0.350693408495296	3		594	835	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115462	115115462	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0020477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	165	848	2	ENST00000257566.3:c.865-1G>T		p.X289_splice	ENST00000257566	NM_016569.3	289			1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.350693408495296	2		850	934	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039497	49039497	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0020477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	220	871	0	ENST00000267163.4:c.2482A>T	p.Arg828Ter	p.R828*	ENST00000267163	NM_000321.2	828	Aga/Tga	23/27	0.350693408495296	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.350693408495296	1		871	834	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059132	42059132	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	127	665	0	ENST00000219905.7:c.8852C>G	p.Thr2951Ser	p.T2951S	ENST00000219905	NM_001164273.1	2951	aCt/aGt	24/24	1	2	FACETS	0.968	0.878	1	0.968	0.878	1	CLONAL	1	TRUE	1	0.350693408495296	2		665	748	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979002	7979002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150371678	NA	P-0020477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	222	1130	2	ENST00000319144.4:c.1565C>T	p.Pro522Leu	p.P522L	ENST00000319144	NM_001139.2	522	cCg/cTg	12/15	0.350693408495296	1	FACETS	0.987	0.918	1	0.987	0.918	1	CLONAL	1	TRUE	0	0.350693408495296	1		1132	1058	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78935227	78935227	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	307	1368	0	ENST00000306801.3:c.3639G>C	p.Trp1213Cys	p.W1213C	ENST00000306801	NM_020761.2	1213	tgG/tgC	31/34	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.350693408495296	2		1368	1475	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736922	736922	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	178	1109	0	ENST00000314574.4:c.1177A>G	p.Ile393Val	p.I393V	ENST00000314574	NM_005433.3	393	Att/Gtt	10/12	1	2	FACETS	0.926	0.853	1	0.926	0.853	1	CLONAL	1	TRUE	1	0.350693408495296	2		1109	1096	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341793	8341793	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	220	1212	0	ENST00000356435.5:c.4847G>T	p.Gly1616Val	p.G1616V	ENST00000356435		1616	gGa/gTa	29/35	0.350693408495296	1	FACETS	0.853	0.792	0.916	0.853	0.792	0.916	CLONAL	1	TRUE	0	0.350693408495296	1		1212	1213	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0020478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	83	462	1	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	0.93	0.824	1	0.93	0.824	1	CLONAL	1	TRUE	1	0.396572630612237	2		463	450	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913476	NA	P-0020478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	373	931	0	ENST00000358487.5:c.1647T>G	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaG	12/18	0.396572630612237	3	FACETS	0.998	0.948	1	0.998	0.948	1	CLONAL	2	TRUE	1	0.396572630612237	3		931	1129	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0020478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	197	1108	1	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	1	2	FACETS	0.919	0.85	0.991	0.919	0.85	0.991	CLONAL	1	TRUE	1	0.396572630612237	2		1109	1081	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690802	89690802	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1114167621	NA	P-0020478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	202	657	0	ENST00000371953.3:c.210-1G>A		p.X70_splice	ENST00000371953	NM_000314.4	70			0.396572630612237	3	FACETS	0.955	0.89	1	0.955	0.89	1	CLONAL	2	TRUE	1	0.396572630612237	3		657	639	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107088	27107099	+	inframe_deletion	In_Frame_Del	DEL	GGCTGCCCGCGC	GGCTGCCCGCGC	-	novel	NA	P-0020478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	166	703	0	ENST00000324856.7:c.6700_6711del	p.Ala2234_Ala2237del	p.A2234_A2237del	ENST00000324856	NM_006015.4	2233	cgGGCTGCCCGCGCg/cgg	20/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.396572630612237	2		703	792	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653800	89653800	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1554893771	NA	P-0020478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	83	676	0	ENST00000371953.3:c.98T>C	p.Ile33Thr	p.I33T	ENST00000371953	NM_000314.4	33	aTt/aCt	2/9	0.396572630612237	3	FACETS	0.726	0.64	0.817	0.363	0.32	0.409	SUBCLONAL	1	TRUE	1	0.396572630612237	3		676	691	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996769	100996770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0020478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	125	833	0	ENST00000325455.5:c.1756_1757dup	p.Ser586ArgfsTer64	p.S586Rfs*64	ENST00000325455	NM_001202474.3	586	agc/agAGc	2/8	1	2	FACETS	0.822	0.744	0.904	0.822	0.744	0.904	CLONAL	1	TRUE	1	0.396572630612237	2		833	767	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588927	67588927	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0020478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	76	497	0	ENST00000274335.5:c.1020-2A>G		p.X340_splice	ENST00000274335		340			1	2	FACETS	0.794	0.698	0.896	0.794	0.698	0.896	SUBCLONAL	1	TRUE	1	0.396572630612237	2		497	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0020480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	183	686	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.17940208427536	2	FACETS	1	0.985	1	0.645	0.594	0.698	CLONAL	1	TRUE	0	0.227954094588334	2		686	1245	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251754	212251754	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	34	505	0	ENST00000342788.4:c.3305T>G	p.Phe1102Cys	p.F1102C	ENST00000342788	NM_005235.2	1102	tTt/tGt	27/28	1	2	FACETS	0.55	0.449	0.665	0.55	0.449	0.665	SUBCLONAL	1	TRUE	1	0.227954094588334	2		505	542	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11264705	11264705	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	105	1080	2	ENST00000361445.4:c.3857G>A	p.Arg1286Gln	p.R1286Q	ENST00000361445	NM_004958.3	1286	cGg/cAg	26/58	1	2	FACETS	0.822	0.734	0.915	0.822	0.734	0.915	CLONAL	1	TRUE	1	0.227954094588334	2		1082	1121	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910711	29910711	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs45523732	NA	P-0020480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1328	258	1430	1	ENST00000376809.5:c.251G>A	p.Trp84Ter	p.W84*	ENST00000376809	NM_002116.7	84	tGg/tAg	2/8	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.227954094588334	2		1431	1586	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs863224499	NA	P-0020481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	401	1096	1	ENST00000269305.4:c.672+1G>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.45328759327571	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.62553061403563	1		1097	722	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998214	100998215	+	missense_variant	Missense_Mutation	DNP	GC	GC	AG	novel	NA	P-0020481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	43	820	6	ENST00000325455.5:c.1587_1588delinsCT	p.Leu530Phe	p.L530F	ENST00000325455	NM_001202474.3	529	gtGCtc/gtCTtc	1/8	0.62553061403563	3	FACETS	0.249	0.207	0.295	0.124	0.103	0.148	SUBCLONAL	1	TRUE	1	0.62553061403563	3		826	725	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518158	103518158	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	49	420	0	ENST00000355739.4:c.2096G>C	p.Ser699Thr	p.S699T	ENST00000355739	NM_000123.3	699	aGc/aCc	9/15	0.62553061403563	3	FACETS	0.47	0.398	0.548	0.235	0.199	0.274	SUBCLONAL	1	TRUE	1	0.62553061403563	3		420	438	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590424	67590424	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	152	347	0	ENST00000274335.5:c.1486G>C	p.Glu496Gln	p.E496Q	ENST00000274335		496	Gaa/Caa	11/15	0.62553061403563	2	FACETS	0.942	0.883	0.999	0.942	0.883	0.999	CLONAL	2	TRUE	0	0.62553061403563	2		347	258	SUCCESS
APC	324	MSKCC	GRCh37	5	112173956	112173957	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0020481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	312	561	0	ENST00000257430.4:c.2666_2667del	p.Lys889SerfsTer22	p.K889Sfs*22	ENST00000257430	NM_000038.5	889	AAa/a	16/16	0.62553061403563	2	FACETS	0.978	0.937	1	0.978	0.937	1	CLONAL	2	TRUE	0	0.62553061403563	2		561	510	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371751	118371751	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	85	482	0	ENST00000534358.1:c.6208T>C	p.Tyr2070His	p.Y2070H	ENST00000534358	NM_005933.3	2070	Tat/Cat	25/36	0.438308836534447	1	FACETS	0.687	0.61	0.768	0.687	0.61	0.768	SUBCLONAL	1	TRUE	0	0.438308836534447	1		482	441	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436805	110436805	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	206	1059	0	ENST00000375856.3:c.1596C>G	p.Asp532Glu	p.D532E	ENST00000375856	NM_003749.2	532	gaC/gaG	1/2	NA	2	FACETS	1	0.929	1			1	INDETERMINATE	1	TRUE	NA	0.438308836534447	2		1059	939	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272209	15272209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	126	476	0	ENST00000263388.2:c.6230C>T	p.Pro2077Leu	p.P2077L	ENST00000263388	NM_000435.2	2077	cCc/cTc	33/33	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.438308836534447	2		476	454	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949753	151949765	+	frameshift_variant	Frame_Shift_Del	DEL	CCACTGAGAACTA	CCACTGAGAACTA	-	novel	NA	P-0020482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	188	608	0	ENST00000262189.6:c.1335_1347del	p.Ser446ThrfsTer5	p.S446Tfs*5	ENST00000262189	NM_170606.2	445	tcTAGTTCTCAGTGG/tc	10/59	0.278864432277473	3	FACETS	1	0.989	1	0.694	0.643	0.747	CLONAL	1	TRUE	1	0.438308836534447	3		608	753	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929565	44929565	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs748064342	NA	P-0020482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	59	271	0	ENST00000377967.4:c.2665A>G	p.Ile889Val	p.I889V	ENST00000377967	NM_021140.2	889	Ata/Gta	17/29	1	1	FACETS	0.657	0.569	0.752	0.657	0.569	0.752	SUBCLONAL	1	TRUE	0	0.438308836534447	1		271	320	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	79	613	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.983	0.863	1	0.983	0.863	1	CLONAL	1	TRUE	1	0.19	2		614	846	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0020483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	44	392	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.813	0.681	0.959	0.813	0.681	0.959	CLONAL	1	TRUE	1	0.19	2		392	570	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103408	77103408	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	50	612	0	ENST00000356341.3:c.158G>A	p.Arg53Gln	p.R53Q	ENST00000356341	NM_002576.4	53	cGa/cAa	2/15	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.19	2		612	518	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476309	88476309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	93	1186	1	ENST00000360948.2:c.1823G>A	p.Gly608Asp	p.G608D	ENST00000360948	NM_001012338.2	608	gGc/gAc	15/19	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.19	2		1187	781	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164176	108164176	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	27	542	0	ENST00000278616.4:c.4748A>G	p.Tyr1583Cys	p.Y1583C	ENST00000278616	NM_000051.3	1583	tAc/tGc	31/63	1	2	FACETS	0.581	0.461	0.719	0.581	0.461	0.719	SUBCLONAL	1	TRUE	1	0.19	2		542	489	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218084	108218084	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	52	754	0	ENST00000278616.4:c.8663T>G	p.Ile2888Arg	p.I2888R	ENST00000278616	NM_000051.3	2888	aTa/aGa	59/63	1	2	FACETS	0.921	0.784	1	0.921	0.784	1	CLONAL	1	TRUE	1	0.19	2		754	594	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0020484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	135	169	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.251754379372179	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.251754379372179	3		169	535	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578433	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555526101	NA	P-0020484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	190	951	0	ENST00000269305.4:c.497C>G	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	166	tCa/tGa	5/11	0.251754379372179	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.251754379372179	2		951	707	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724433	162724433	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	35	608	1	ENST00000367921.3:c.205G>T	p.Asp69Tyr	p.D69Y	ENST00000367921	NM_006182.2	69	Gat/Tat	5/18	0.251754379372179	5	FACETS	0.836	0.685	1	0.279	0.228	0.336	CLONAL	1	TRUE	2	0.251754379372179	5		609	458	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658289	18658289	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	48	797	0	ENST00000266497.5:c.3094T>G	p.Cys1032Gly	p.C1032G	ENST00000266497		1032	Tgt/Ggt	22/31	0.207286362809442	4	FACETS	0.805	0.68	0.943	0.402	0.34	0.472	CLONAL	1	TRUE	2	0.251754379372179	4		797	593	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485061	57485061	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	32	547	0	ENST00000371085.3:c.895G>A	p.Glu299Lys	p.E299K	ENST00000371085	NM_000516.4	299	Gag/Aag	11/13	0.207286362809442	4	FACETS	0.651	0.527	0.79	0.325	0.263	0.395	SUBCLONAL	1	TRUE	2	0.251754379372179	4		547	489	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800145	32800145	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	74	576	0	ENST00000374899.4:c.1237A>G	p.Met413Val	p.M413V	ENST00000374899	NM_018833.2	413	Atg/Gtg	7/12	0.241954129668503	3	FACETS	1	0.974	1	0.726	0.637	0.82	CLONAL	1	TRUE	1	0.251754379372179	3		576	456	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041429	47041429	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	42	900	0	ENST00000377604.3:c.1773C>A	p.Asp591Glu	p.D591E	ENST00000377604	NM_001204468.1	591	gaC/gaA	16/24	0.251754379372179	3	FACETS	0.548	0.457	0.651	0.274	0.228	0.326	SUBCLONAL	1	TRUE	1	0.251754379372179	3		900	685	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0020487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	107	938	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	0.317690079468604	1	FACETS	0.731	0.659	0.806	0.731	0.659	0.806	SUBCLONAL	1	TRUE	0	0.477382232702271	1		938	467	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261145	16261145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	180	672	0	ENST00000375759.3:c.8410G>A	p.Ala2804Thr	p.A2804T	ENST00000375759	NM_015001.2	2804	Gcg/Acg	11/15	0.477382232702271	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.477382232702271	1		672	454	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154246	2154246	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1322797114	NA	P-0020487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	101	1074	1	ENST00000434045.2:c.682C>T	p.Pro228Ser	p.P228S	ENST00000434045	NM_001127598.1	228	Ccc/Tcc	5/5	1	2	FACETS	0.434	0.387	0.485	0.434	0.387	0.485	SUBCLONAL	1	TRUE	1	0.477382232702271	2		1075	974	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920350	50920365	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGAGGTGAGAGGGCC	AGGAGGTGAGAGGGCC	-	novel	NA	P-0020487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	247	1235	0	ENST00000440232.2:c.3116_3120+11del		p.X1039_splice	ENST00000440232	NM_002691.3	1039		25/27	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.477382232702271	2		1235	994	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023402	31023403	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0020487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	162	796	0	ENST00000375687.4:c.2887_2888del	p.Pro963IlefsTer6	p.P963Ifs*6	ENST00000375687	NM_015338.5	963	CCa/a	13/13	0.477382232702271	5	FACETS	0.994	0.91	1	0.248	0.227	0.271	CLONAL	1	TRUE	1	0.477382232702271	5		796	1172	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31431706	31431706	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	158	867	1	ENST00000344624.3:c.3122C>A	p.Ala1041Asp	p.A1041D	ENST00000344624		1041	gCc/gAc	23/33	1	2	FACETS	0.925	0.849	1	0.925	0.849	1	CLONAL	1	TRUE	1	0.477382232702271	2		868	716	SUCCESS
APC	324	MSKCC	GRCh37	5	112137082	112137082	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0020487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	80	479	0	ENST00000257430.4:c.834+2T>G		p.X278_splice	ENST00000257430	NM_000038.5	278			1	2	FACETS	0.977	0.867	1	0.977	0.867	1	CLONAL	1	TRUE	1	0.477382232702271	2		479	343	SUCCESS
APC	324	MSKCC	GRCh37	5	112170683	112170683	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554083132	NA	P-0020487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	111	794	0	ENST00000257430.4:c.1779G>A	p.Trp593Ter	p.W593*	ENST00000257430	NM_000038.5	593	tgG/tgA	15/16	1	2	FACETS	0.869	0.784	0.958	0.869	0.784	0.958	CLONAL	1	TRUE	1	0.477382232702271	2		794	535	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119070	70119089	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCTCCGGCATGAGCGAGG	CTCCTCCGGCATGAGCGAGG	A	novel	NA	P-0020487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	45	718	1	ENST00000245479.2:c.642_661delinsA	p.Ser215CysfsTer32	p.S215Cfs*32	ENST00000245479	NM_000346.3	214	tcCTCCTCCGGCATGAGCGAGGtg/tcAtg	2/3	1	2	FACETS	0.356	0.299	0.42	0.356	0.299	0.42	SUBCLONAL	1	TRUE	1	0.477382232702271	2		719	529	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106793	27106793	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	221	910	0	ENST00000324856.7:c.6404T>G	p.Ile2135Ser	p.I2135S	ENST00000324856	NM_006015.4	2135	aTt/aGt	20/20	1	2	FACETS	0.936	0.873	1	0.936	0.873	1	CLONAL	1	TRUE	1	0.538365621009279	2		910	877	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0020488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	154	431	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.516275313619289	1	FACETS	0.957	0.884	1	0.957	0.884	1	CLONAL	1	TRUE	0	0.538365621009279	1		431	437	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951074	48951074	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	54	437	1	ENST00000267163.4:c.1236A>T	p.Lys412Asn	p.K412N	ENST00000267163	NM_000321.2	412	aaA/aaT	13/27	NA	2	FACETS	1	0.909	1			1	INDETERMINATE	1	TRUE	NA	0.538365621009279	2		438	189	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579534	7579535	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0020488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	252	1298	0	ENST00000269305.4:c.152_153del	p.Glu51AlafsTer5	p.E51Afs*5	ENST00000269305	NM_001126112.2	51	gAA/g	4/11	0.491969606946607	1	FACETS	0.913	0.858	0.97	0.913	0.858	0.97	CLONAL	1	TRUE	0	0.538365621009279	1		1298	749	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591853	48591853	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	131	842	0	ENST00000342988.3:c.1016T>C	p.Phe339Ser	p.F339S	ENST00000342988	NM_005359.5	339	tTt/tCt	9/12	0.538365621009279	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.538365621009279	1		842	343	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591886	48591886	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	150	862	0	ENST00000342988.3:c.1049T>G	p.Val350Gly	p.V350G	ENST00000342988	NM_005359.5	350	gTt/gGt	9/12	0.538365621009279	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.538365621009279	1		862	366	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200082	128200082	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	228	1308	0	ENST00000341105.2:c.1223A>C	p.Lys408Thr	p.K408T	ENST00000341105	NM_032638.4	408	aAg/aCg	6/6	NA	2	FACETS	0.827	0.771	0.885			1	INDETERMINATE	1	TRUE	NA	0.538365621009279	2		1308	1024	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197573	106197573	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	94	584	0	ENST00000380013.4:c.5906A>C	p.Lys1969Thr	p.K1969T	ENST00000380013	NM_001127208.2	1969	aAg/aCg	11/11	1	2	FACETS	0.734	0.656	0.816	0.734	0.656	0.816	SUBCLONAL	1	TRUE	1	0.538365621009279	2		584	476	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948527	31948527	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	66	363	0	ENST00000375333.2:c.1010T>G	p.Leu337Arg	p.L337R	ENST00000375333	NM_032454.1	337	cTt/cGt	7/8	0.132217256864245	3	FACETS	1	0.958	1	0.61	0.536	0.689	INDETERMINATE	1	TRUE	1	0.538365621009279	3		363	255	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001366	150001367	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGATTTC	novel	NA	P-0020488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	89	1027	0	ENST00000253339.5:c.2231_2237dup	p.Val747LysfsTer7	p.V747Kfs*7	ENST00000253339		746	caa/caGAAATCAa	4/7	0.132217256864245	3	FACETS	0.941	0.838	1	0.47	0.419	0.525	INDETERMINATE	1	TRUE	1	0.538365621009279	3		1027	446	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182920	123182920	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	38	587	0	ENST00000218089.9:c.885T>A	p.His295Gln	p.H295Q	ENST00000218089	NM_001042749.1	295	caT/caA	10/35	0.21675108749733	1	FACETS	0.291	0.241	0.347	0.291	0.241	0.347	INDETERMINATE	1	TRUE	0	0.538365621009279	1		587	354	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	96	613	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.849	0.757	0.945	0.849	0.757	0.945	CLONAL	1	TRUE	1	0.37456567892982	2		614	604	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0020490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	80	169	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.953	0.843	1	0.953	0.843	1	CLONAL	1	TRUE	1	0.37456567892982	2		169	448	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390473	118390473	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	59	819	0	ENST00000534358.1:c.11287C>A	p.Pro3763Thr	p.P3763T	ENST00000534358	NM_005933.3	3763	Cct/Act	32/36	1	2	FACETS	0.396	0.34	0.457	0.396	0.34	0.457	SUBCLONAL	1	TRUE	1	0.37456567892982	2		819	796	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528598	89528598	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	84	527	0	ENST00000336596.2:c.2898C>G	p.Ile966Met	p.I966M	ENST00000336596	NM_005233.5	966	atC/atG	17/17	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.37456567892982	2		527	391	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743859	40743859	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369430281	NA	P-0020491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	155	813	2	ENST00000373198.4:c.3136C>T	p.Arg1046Cys	p.R1046C	ENST00000373198	NM_133170.3	1046	Cgc/Tgc	23/32	0.155802636114922	2	FACETS	0.954	0.873	1	0.477	0.436	0.52	INDETERMINATE	1	TRUE	0	0.329591826927094	2		815	986	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057600	180057600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1267101992	NA	P-0020491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	187	1452	3	ENST00000261937.6:c.355C>T	p.Arg119Cys	p.R119C	ENST00000261937	NM_182925.4	119	Cgc/Tgc	3/30	0.329591826927094	1	FACETS	0.905	0.836	0.978	0.905	0.836	0.978	CLONAL	1	TRUE	0	0.329591826927094	1		1455	1047	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0020493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	20	328	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.891	0.68	1	0.891	0.68	1	CLONAL	1	TRUE	1	0.11	2		328	408	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	37	613	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.11	2		614	639	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	36	1134	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	0.731	0.598	0.88	0.731	0.598	0.88	SUBCLONAL	1	TRUE	1	0.11	2		1134	896	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412110	63412110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852216	NA	P-0020493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	97	767	0	ENST00000330258.3:c.1057C>T	p.Arg353Ter	p.R353*	ENST00000330258	NM_152424.3	353	Cga/Tga	2/2	0.3	2	FACETS	1	0.915	1	1	0.982	1	CLONAL	3	TRUE	0	0.11	2		767	572	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871940	45871940	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142462393	NA	P-0020493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	52	1124	3	ENST00000391945.4:c.308C>T	p.Pro103Leu	p.P103L	ENST00000391945	NM_000400.3	103	cCg/cTg	5/23	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.11	2		1127	926	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436802	52436802	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	238	1176	0	ENST00000460680.1:c.1976del	p.Lys659SerfsTer33	p.K659Sfs*33	ENST00000460680	NM_004656.3	659	aAg/ag	15/17	1	2	FACETS	1	0.976	1	1	0.995	1	CLONAL	2	TRUE	1	0.24	2		1176	911	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0020496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	80	680	3	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	0.183759375610013	1	FACETS	0.939	0.825	1	0.939	0.825	1	CLONAL	1	TRUE	0	0.183759375610013	1		683	842	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916925	178916927	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0020496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	47	788	0	ENST00000263967.3:c.314_316del	p.Val105del	p.V105del	ENST00000263967	NM_006218.2	104	ccAGTa/cca	2/21	1	2	FACETS	0.847	0.714	0.994	0.847	0.714	0.994	CLONAL	1	TRUE	1	0.183759375610013	2		788	604	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128201179	128201179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	70	971	0	ENST00000265960.3:c.1556C>T	p.Ser519Phe	p.S519F	ENST00000265960	NM_001006617.1	519	tCc/tTc	12/12	1	2	FACETS	0.91	0.792	1	0.91	0.792	1	CLONAL	1	TRUE	1	0.183759375610013	2		971	837	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0020497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	137	340	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.79	0.717	0.867	0.79	0.717	0.867	SUBCLONAL	1	TRUE	1	0.285037103488601	2		340	1217	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270593	98270595	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	rs756897237	NA	P-0020497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	11	154	0	ENST00000331920.6:c.49_51del	p.Gly17del	p.G17del	ENST00000331920	NM_000264.3	17	GGC/-	1/24	1	2	FACETS	0.482	0.334	0.666	0.482	0.334	0.666	SUBCLONAL	1	TRUE	1	0.285037103488601	2		154	160	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984428	201984428	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	137	1064	0	ENST00000359651.3:c.1093G>T	p.Glu365Ter	p.E365*	ENST00000359651		365	Gag/Tag	8/8	0.279004735270682	3	FACETS	0.844	0.766	0.927	0.422	0.383	0.464	CLONAL	1	TRUE	1	0.285037103488601	3		1064	1301	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104352340	104352340	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	88	816	0	ENST00000369902.3:c.456G>C	p.Glu152Asp	p.E152D	ENST00000369902	NM_016169.3	152	gaG/gaC	4/12	1	2	FACETS	0.73	0.646	0.82	0.73	0.646	0.82	SUBCLONAL	1	TRUE	1	0.285037103488601	2		816	846	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003191	42003191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs761227360	NA	P-0020497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	268	1138	1	ENST00000219905.7:c.2728C>T	p.Arg910Ter	p.R910*	ENST00000219905	NM_001164273.1	910	Cga/Tga	8/24	0.279004735270682	3	FACETS	0.795	0.744	0.848	0.795	0.744	0.848	SUBCLONAL	2	TRUE	1	0.285037103488601	3		1139	1351	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42026720	42026720	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	111	958	2	ENST00000219905.7:c.3844G>T	p.Glu1282Ter	p.E1282*	ENST00000219905	NM_001164273.1	1282	Gaa/Taa	12/24	0.279004735270682	3	FACETS	0.804	0.721	0.892	0.402	0.36	0.446	CLONAL	1	TRUE	1	0.285037103488601	3		960	1107	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220666	1220670	+	frameshift_variant	Frame_Shift_Del	DEL	GGACA	GGACA	-	novel	NA	P-0020497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1544	209	1878	0	ENST00000326873.7:c.684_688del	p.Asp229LeufsTer35	p.D229Lfs*35	ENST00000326873	NM_000455.4	228	ctGGACAcc/ctcc	5/10	0.285037103488601	1	FACETS	0.717	0.663	0.774	0.717	0.663	0.774	SUBCLONAL	1	TRUE	0	0.285037103488601	1		1878	1753	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602922	10602922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1412	232	1658	2	ENST00000171111.5:c.656A>T	p.Glu219Val	p.E219V	ENST00000171111	NM_203500.1	219	gAg/gTg	3/6	0.285037103488601	1	FACETS	0.849	0.789	0.912	0.849	0.789	0.912	CLONAL	1	TRUE	0	0.285037103488601	1		1660	1644	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144123	11144123	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	187	1564	0	ENST00000358026.2:c.3704A>T	p.Asp1235Val	p.D1235V	ENST00000358026	NM_001128849.1	1235	gAc/gTc	26/36	0.285037103488601	1	FACETS	0.828	0.763	0.896	0.828	0.763	0.896	CLONAL	1	TRUE	0	0.285037103488601	1		1564	1359	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420000	152420000	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs146924427	NA	P-0020497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	112	1023	0	ENST00000206249.3:c.1687A>G	p.Thr563Ala	p.T563A	ENST00000206249	NM_000125.3	563	Acg/Gcg	8/8	1	2	FACETS	0.732	0.657	0.812	0.732	0.657	0.812	SUBCLONAL	1	TRUE	1	0.285037103488601	2		1023	1074	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0020498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	53	455	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		455	243	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143994	11143994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	599	888	3	ENST00000358026.2:c.3575G>A	p.Arg1192His	p.R1192H	ENST00000358026	NM_001128849.1	1192	cGc/cAc	26/36	0.645920393354886	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.645920393354886	2		891	890	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0020499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	506	872	2	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	2	TRUE	NA	0.645920393354886	2		874	782	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935322	36935323	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs747437399	NA	P-0020499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1331	316	1421	3	ENST00000361632.4:c.1404dup	p.Ser469GlnfsTer5	p.S469Qfs*5	ENST00000361632		468	-/C	10/16	0.635937062511708	3	FACETS	0.786	0.739	0.834			1	SUBCLONAL	1	TRUE	NA	0.645920393354886	3		1424	1647	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023145	27023179	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGCGGCGGAGCCGGCAGCGGCGGCGGGCCCGGC	GCGGCGGCGGAGCCGGCAGCGGCGGCGGGCCCGGC	-	novel	NA	P-0020499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	870	110	1	ENST00000324856.7:c.255_289del	p.Gly86AlafsTer13	p.G86Afs*13	ENST00000324856	NM_006015.4	84	gGCGGCGGCGGAGCCGGCAGCGGCGGCGGGCCCGGC/g	1/20	0.645920393354886	2	FACETS	0.966	0.955	0.975	1	0.999	1	CLONAL	3	TRUE	0	0.645920393354886	2		111	930	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849053	156849053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369353892	NA	P-0020499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1255	812	1503	4	ENST00000524377.1:c.1945C>T	p.Arg649Trp	p.R649W	ENST00000524377	NM_002529.3	649	Cgg/Tgg	15/17	0.573961676480719	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.645920393354886	4		1507	2067	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597818	43597837	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCAAGGTCTTCCTGTCAC	CCTCAAGGTCTTCCTGTCAC	-	novel	NA	P-0020499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1285	381	1456	2	ENST00000355710.3:c.368_387del	p.Leu123HisfsTer5	p.L123Hfs*5	ENST00000355710	NM_020975.4	122	taCCTCAAGGTCTTCCTGTCACcc/tacc	3/20	0.645920393354886	3	FACETS	0.937	0.887	0.988	0.468	0.443	0.494	CLONAL	1	TRUE	1	0.645920393354886	3		1458	1666	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813276	89813276	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	293	1017	0	ENST00000389301.3:c.3371G>T	p.Gly1124Val	p.G1124V	ENST00000389301	NM_000135.2	1124	gGt/gTt	34/43	0.513021403578096	3	FACETS	0.988	0.929	1			1	CLONAL	1	TRUE	NA	0.645920393354886	3		1017	1215	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579587	7579624	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGACTGTAGATGGGTGAAAAGAGCAGTCAGAGGACCA	GGGACTGTAGATGGGTGAAAAGAGCAGTCAGAGGACCA	-	novel	NA	P-0020499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	385	952	2	ENST00000269305.4:c.97-34_100del		p.X33_splice	ENST00000269305	NM_001126112.2	33		4/11	0.645920393354886	2	FACETS	0.797	0.763	0.831	0.797	0.763	0.831	SUBCLONAL	2	TRUE	0	0.645920393354886	2		954	748	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069228	30069444	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CACTTCAGCTAAGAGCACTGTGCCCTCCAGATGCGGTCTGAGGAGACAGCTGACCTGTTGGCTGAAAAGGCCCAGATCACCGAGGAGGAGGCAAAACTTCTGGCCCAGAAGGCCGCAGAGGCTGAGCAGGAAATGCAGCGCATCAAGGCCACAGCGATTCGCACGGAGGAGGAGAAGCGCCTGATGGAGCAGAAGGTGCTGGAAGCCGAGGTGCTGG	CACTTCAGCTAAGAGCACTGTGCCCTCCAGATGCGGTCTGAGGAGACAGCTGACCTGTTGGCTGAAAAGGCCCAGATCACCGAGGAGGAGGCAAAACTTCTGGCCCAGAAGGCCGCAGAGGCTGAGCAGGAAATGCAGCGCATCAAGGCCACAGCGATTCGCACGGAGGAGGAGAAGCGCCTGATGGAGCAGAAGGTGCTGGAAGCCGAGGTGCTGG	-	novel	NA	P-0020499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	206	523	1	ENST00000338641.4:c.1123-26_1313del		p.X375_splice	ENST00000338641	NM_000268.3	375		12/16	0.644160640948961	3	FACETS	1	0.983	1	0.738	0.697	0.78	CLONAL	2	TRUE	0	0.645920393354886	3		524	381	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565566	41565566	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	641	928	1	ENST00000263253.7:c.4232C>A	p.Thr1411Asn	p.T1411N	ENST00000263253	NM_001429.3	1411	aCt/aAt	26/31	0.644160640948961	3	FACETS	0.947	0.922	0.972	0.947	0.922	0.972	CLONAL	3	TRUE	0	0.645920393354886	3		929	924	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751425	57751425	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	176	673	0	ENST00000274289.3:c.1566C>A	p.Asp522Glu	p.D522E	ENST00000274289	NM_006622.3	522	gaC/gaA	11/14	1	2	FACETS	0.869	0.804	0.936	0.869	0.804	0.936	CLONAL	1	TRUE	1	0.645920393354886	2		673	627	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860367	151860367	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	564	784	1	ENST00000262189.6:c.10295A>G	p.Glu3432Gly	p.E3432G	ENST00000262189	NM_170606.2	3432	gAg/gGg	43/59	0.645920393354886	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.645920393354886	2		785	801	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072495	5072495	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	192	425	0	ENST00000381652.3:c.1645G>C	p.Glu549Gln	p.E549Q	ENST00000381652	NM_004972.3	549	Gaa/Caa	13/25	0.645920393354886	2	FACETS	0.944	0.893	0.994	0.944	0.893	0.994	CLONAL	2	TRUE	0	0.645920393354886	2		425	315	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418303	139418303	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1201407249	NA	P-0020499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2509	363	1866	5	ENST00000277541.6:c.269C>T	p.Ala90Val	p.A90V	ENST00000277541	NM_017617.3	90	gCc/gTc	3/34	0.531447732389595	4	FACETS	0.644	0.607	0.682	0.322	0.303	0.341	SUBCLONAL	1	TRUE	2	0.645920393354886	4		1871	2872	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0020500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	240	685	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.333875901822236	2	FACETS	0.977	0.925	1	1	0.994	1	CLONAL	3	TRUE	0	0.344656793108525	2		685	475	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	168	372	1	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	2	TRUE	NA	0.344656793108525	2		373	409	SUCCESS
APC	324	MSKCC	GRCh37	5	112175246	112175246	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1057517558	NA	P-0020500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	28	402	0	ENST00000257430.4:c.3956del	p.Pro1319LeufsTer2	p.P1319Lfs*2	ENST00000257430	NM_000038.5	1319	Cct/ct	16/16	0.344656793108525	2	FACETS	0.697	0.56	0.852	0.349	0.28	0.426	SUBCLONAL	1	TRUE	0	0.344656793108525	2		402	233	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0020500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	160	491	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	0.344656793108525	2	FACETS	0.862	0.802	0.923	1	0.987	1	CLONAL	3	TRUE	0	0.344656793108525	2		491	359	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903763	114903763	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	314	969	0	ENST00000543371.1:c.767C>T	p.Pro256Leu	p.P256L	ENST00000543371	NM_001198531.1	256	cCg/cTg	7/14	0.337705721624199	3	FACETS	0.934	0.887	0.983	1	0.994	1	CLONAL	3	TRUE	1	0.344656793108525	3		969	762	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0020501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	187	609	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.194934849145854	2	FACETS	0.934	0.862	1	0.934	0.862	1	CLONAL	2	TRUE	0	0.206294335413544	2		610	971	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0020502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	114	451	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.181257426068602	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	0	0.16	2		451	670	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509436	106509436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200175951	NA	P-0020502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	39	796	1	ENST00000359195.3:c.1430G>A	p.Arg477His	p.R477H	ENST00000359195	NM_002649.2	477	cGt/cAt	2/11	1	2	FACETS	0.639	0.528	0.764	0.639	0.528	0.764	SUBCLONAL	1	TRUE	1	0.16	2		797	763	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063344	67063344	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	71	834	0	ENST00000412916.2:c.34T>A	p.Phe12Ile	p.F12I	ENST00000412916		12	Ttc/Atc	1/6	0.17343652964644	2	FACETS	0.777	0.679	0.883	0.777	0.679	0.883	SUBCLONAL	2	TRUE	0	0.16	2		834	571	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16062088	16062088	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	38	709	0	ENST00000268712.3:c.718T>G	p.Tyr240Asp	p.Y240D	ENST00000268712	NM_006311.3	240	Tat/Gat	6/46	1	2	FACETS	0.798	0.659	0.955	0.798	0.659	0.955	CLONAL	1	TRUE	1	0.16	2		709	595	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	275	251	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.791124967396828	2		251	684	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0020505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	334	451	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	0.791124967396828	2		451	837	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936115	178936115	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	237	1580	2	ENST00000263967.3:c.1657A>G	p.Ser553Gly	p.S553G	ENST00000263967	NM_006218.2	553	Agt/Ggt	10/21	1	2	FACETS	0.974	0.916	1	0.974	0.916	1	CLONAL	1	TRUE	1	0.791124967396828	2		1582	615	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700310	117700310	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	176	704	1	ENST00000368508.3:c.2509A>T	p.Thr837Ser	p.T837S	ENST00000368508	NM_002944.2	837	Act/Tct	17/43	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.791124967396828	2		705	437	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0020506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	338	710	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.286023860683103	7	FACETS	1	0.964	1	0.681	0.645	0.717	CLONAL	4	TRUE	1	0.286023860683103	7		710	992	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577561	7577566	+	inframe_deletion	In_Frame_Del	DEL	ACTGTT	ACTGTT	-	novel	NA	P-0020506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	327	886	1	ENST00000269305.4:c.715_720del	p.Asn239_Ser240del	p.N239_S240del	ENST00000269305	NM_001126112.2	239	AACAGT/-	7/11	0.286023860683103	4	FACETS	0.861	0.813	0.909	0.861	0.813	0.909	CLONAL	3	TRUE	1	0.286023860683103	4		887	1139	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187560938	187560938	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0020506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	33	533	0	ENST00000441802.2:c.3581-1G>A		p.X1194_splice	ENST00000441802	NM_005245.3	1194			0.286023860683103	3	FACETS	0.403	0.327	0.489	0.134	0.109	0.163	SUBCLONAL	1	TRUE	0	0.286023860683103	3		533	654	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0020508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	110	303	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.941	0.851	1	0.941	0.851	1	CLONAL	1	TRUE	1	0.53	2		304	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0020508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	182	609	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.53	2		610	674	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs967461896	NA	P-0020508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	207	1021	0	ENST00000269305.4:c.526T>C	p.Cys176Arg	p.C176R	ENST00000269305	NM_001126112.2	176	Tgc/Cgc	5/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.53	2		1021	670	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141448	11141448	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	206	1222	0	ENST00000358026.2:c.3425T>G	p.Phe1142Cys	p.F1142C	ENST00000358026	NM_001128849.1	1142	tTc/tGc	25/36	0.214057772333687	1	FACETS	0.754	0.701	0.808	0.754	0.701	0.808	INDETERMINATE	1	TRUE	0	0.53	1		1222	758	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909641	76909651	+	frameshift_variant	Frame_Shift_Del	DEL	TCTGTTTATAG	TCTGTTTATAG	-	novel	NA	P-0020508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	195	578	0	ENST00000373344.5:c.4254_4264del	p.Ser1418ArgfsTer8	p.S1418Rfs*8	ENST00000373344	NM_000489.3	1418	agCTATAAACAGAaa/agaa	14/35	1	1	FACETS	0.952	0.887	1	0.952	0.887	1	CLONAL	1	TRUE	0	0.53	1		578	568	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	260	613	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.269988242080744	2	FACETS	1	0.987	1	1	0.996	1	CLONAL	4	TRUE	0	0.269983867138555	2		614	436	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0020509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	86	585	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.845	0.753	0.942	1	0.983	1	CLONAL	2	TRUE	1	0.269983867138555	2		588	377	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0020509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	62	702	13	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.789	0.687	0.898	1	0.974	1	SUBCLONAL	2	TRUE	1	0.269983867138555	2		715	291	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	59	1984	5	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.746	0.642	0.859	0.746	0.642	0.859	SUBCLONAL	1	TRUE	1	0.269983867138555	2		1989	586	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0020509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	21	346	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.24644852094214	3	FACETS	0.452	0.347	0.574	0.226	0.173	0.287	SUBCLONAL	1	TRUE	1	0.269983867138555	3		346	391	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0020509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	140	843	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	1	2	FACETS	0.985	0.909	1	1	0.993	1	CLONAL	3	TRUE	1	0.269983867138555	2		843	351	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	105	295	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	0.24644852094214	3	FACETS	0.863	0.782	0.947	1	0.978	1	CLONAL	3	TRUE	1	0.269983867138555	3		295	341	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0020509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	34	884	2	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.679	0.555	0.818	0.679	0.555	0.818	SUBCLONAL	1	TRUE	1	0.269983867138555	2		886	371	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	85	876	4	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	0.24644852094214	3	FACETS	0.752	0.667	0.842	0.752	0.667	0.842	SUBCLONAL	2	TRUE	1	0.269983867138555	3		880	475	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934037	39934037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	21	916	0	ENST00000378444.4:c.562C>T	p.Arg188Trp	p.R188W	ENST00000378444	NM_001123385.1	188	Cgg/Tgg	4/15	0.236528527278647	0	FACETS	0.295	0.227	0.375			1	SUBCLONAL	1	TRUE	0	0.269983867138555	0		916	385	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	71	998	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.78	0.686	0.881	1	0.977	1	SUBCLONAL	2	TRUE	1	0.269983867138555	2		998	337	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0020509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	69	1169	12	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.269983867138555	2		1181	412	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720803	89720804	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs786204892	NA	P-0020509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	21	632	0	ENST00000371953.3:c.955dup	p.Thr319AsnfsTer6	p.T319Nfs*6	ENST00000371953	NM_000314.4	318	-/A	8/9	1	2	FACETS	1	0.837	1	1	0.837	1	CLONAL	1	TRUE	1	0.269983867138555	2		632	142	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209298	133209298	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060500809	NA	P-0020509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	71	1249	0	ENST00000320574.5:c.6088del	p.Ala2030ProfsTer18	p.A2030Pfs*18	ENST00000320574	NM_006231.2	2030	Gcc/cc	44/49	0.269983867138555	1	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	0	0.269983867138555	1		1249	442	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916726	178916726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772110575	NA	P-0020509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	97	685	0	ENST00000263967.3:c.113G>A	p.Arg38His	p.R38H	ENST00000263967	NM_006218.2	38	cGt/cAt	2/21	1	2	FACETS	0.887	0.803	0.974	1	0.99	1	CLONAL	3	TRUE	1	0.269983867138555	2		685	270	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038260	30038260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1185977513	NA	P-0020509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	25	674	1	ENST00000338641.4:c.433G>A	p.Ala145Thr	p.A145T	ENST00000338641	NM_000268.3	145	Gcc/Acc	4/16	1	2	FACETS	0.531	0.418	0.66	0.531	0.418	0.66	SUBCLONAL	1	TRUE	1	0.269983867138555	2		675	349	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72833968	72833968	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs529603227	NA	P-0020509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	134	792	0	ENST00000268489.5:c.3925C>T	p.Arg1309Ter	p.R1309*	ENST00000268489	NM_006885.3	1309	Cga/Tga	8/10	1	2	FACETS	1	0.924	1	1	0.993	1	CLONAL	3	TRUE	1	0.269983867138555	2		792	330	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939260	71939260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	74	1271	1	ENST00000298229.2:c.209G>A	p.Arg70His	p.R70H	ENST00000298229	NM_001567.3	70	cGc/cAc	2/28	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.269983867138555	2		1272	518	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752695	42752695	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1366176199	NA	P-0020509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	89	1106	10	ENST00000222329.4:c.1569del	p.Leu525SerfsTer6	p.L525Sfs*6	ENST00000222329	NM_006494.2	523	ggG/gg	4/4	0.177141457227901	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.269983867138555	1		1116	477	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980604	70980604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1036596459	NA	P-0020509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	28	789	0	ENST00000276594.2:c.773C>T	p.Thr258Met	p.T258M	ENST00000276594	NM_024504.3	258	aCg/aTg	4/8	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.269983867138555	2		789	193	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11177130	11177130	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371628273	NA	P-0020509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	18	704	0	ENST00000361445.4:c.6947G>A	p.Arg2316Gln	p.R2316Q	ENST00000361445	NM_004958.3	2316	cGa/cAa	50/58	1	2	FACETS	0.415	0.312	0.537	0.415	0.312	0.537	SUBCLONAL	1	TRUE	1	0.269983867138555	2		704	321	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804275	43804275	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1260365360	NA	P-0020509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	99	848	0	ENST00000372470.3:c.275T>C	p.Val92Ala	p.V92A	ENST00000372470	NM_005373.2	92	gTg/gCg	3/12	0.24644852094214	3	FACETS	0.837	0.751	0.929	0.837	0.751	0.929	CLONAL	2	TRUE	1	0.269983867138555	3		848	497	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571819	64571819	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	117	1367	4	ENST00000312049.6:c.1820G>A	p.Arg607His	p.R607H	ENST00000312049	NM_130799.2	607	cGc/cAc	10/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.269983867138555	2		1371	734	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90633748	90633748	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	115	856	0	ENST00000330062.3:c.336G>C	p.Lys112Asn	p.K112N	ENST00000330062	NM_002168.2	112	aaG/aaC	3/11	0.177141457227901	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.269983867138555	1		856	511	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101108	4101108	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	46	893	0	ENST00000262948.5:c.614G>T	p.Arg205Ile	p.R205I	ENST00000262948	NM_030662.3	205	aGa/aTa	6/11	0.177141457227901	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.269983867138555	1		893	260	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627582	14627582	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	77	743	2	ENST00000254322.2:c.488del	p.Pro163GlnfsTer21	p.P163Qfs*21	ENST00000254322	NM_006145.1	163	cCa/ca	2/3	0.177141457227901	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.269983867138555	1		745	371	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281566	142281566	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	90	1139	0	ENST00000350721.4:c.678A>C	p.Glu226Asp	p.E226D	ENST00000350721	NM_001184.3	226	gaA/gaC	4/47	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.269983867138555	2		1139	466	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447334	187447335	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	31	777	0	ENST00000232014.4:c.858dup	p.Ser287LeufsTer11	p.S287Lfs*11	ENST00000232014	NM_001130845.1	286	-/C	5/10	1	2	FACETS	0.577	0.467	0.702	0.577	0.467	0.702	SUBCLONAL	1	TRUE	1	0.269983867138555	2		777	398	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133829	55133829	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	15	643	0	ENST00000257290.5:c.1042T>G	p.Ser348Ala	p.S348A	ENST00000257290	NM_006206.4	348	Tcc/Gcc	7/23	0.204406609315687	0	FACETS	0.322	0.235	0.426			1	SUBCLONAL	1	TRUE	0	0.269983867138555	0		643	252	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180040015	180040015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564369853	NA	P-0020509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	19	1469	4	ENST00000261937.6:c.3427G>A	p.Ala1143Thr	p.A1143T	ENST00000261937	NM_182925.4	1143	Gcc/Acc	25/30	0.269983867138555	1	FACETS	0.361	0.274	0.464	0.361	0.274	0.464	SUBCLONAL	1	TRUE	0	0.269983867138555	1		1473	337	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92355083	92355083	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	16	346	0	ENST00000265734.4:c.394G>T	p.Gly132Cys	p.G132C	ENST00000265734	NM_001259.6	132	Ggt/Tgt	4/8	1	2	FACETS	0.482	0.356	0.632	0.482	0.356	0.632	SUBCLONAL	1	TRUE	1	0.269983867138555	2		346	246	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0020509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	78	1674	0	ENST00000220592.5:c.1805_1806dup	p.Ala603ProfsTer93	p.A603Pfs*93	ENST00000220592	NM_012154.3	602	-/CC	14/19	1	2	FACETS	0.877	0.771	0.991	0.877	0.771	0.991	CLONAL	1	TRUE	1	0.269983867138555	2		1674	659	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820183	139820183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1353820572	NA	P-0020509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	35	978	2	ENST00000247668.2:c.1336G>A	p.Ala446Thr	p.A446T	ENST00000247668	NM_021138.3	446	Gcc/Acc	11/11	1	2	FACETS	0.412	0.336	0.497	0.412	0.336	0.497	SUBCLONAL	1	TRUE	1	0.269983867138555	2		980	630	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121912651	NA	P-0020510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	651	1000	0	ENST00000269305.4:c.742C>G	p.Arg248Gly	p.R248G	ENST00000269305	NM_001126112.2	248	Cgg/Ggg	7/11	0.324120896432754	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.324120896432754	3		1000	1431	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913381	NA	P-0020510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	292	846	3	ENST00000304494.5:c.322G>A	p.Asp108Asn	p.D108N	ENST00000304494	NM_000077.4	108	Gat/Aat	2/3	0.297106883935107	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.324120896432754	2		849	851	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031979	10031979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	135	869	0	ENST00000330684.3:c.844G>A	p.Asp282Asn	p.D282N	ENST00000330684	NM_001134407.1	282	Gat/Aat	3/13	0.305743753441993	3	FACETS	0.909	0.825	0.998	0.454	0.412	0.499	CLONAL	1	TRUE	1	0.324120896432754	3		869	1065	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257720	16257720	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550078220	NA	P-0020510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	352	603	0	ENST00000375759.3:c.4985C>T	p.Thr1662Met	p.T1662M	ENST00000375759	NM_015001.2	1662	aCg/aTg	11/15	0.3173414850831	4	FACETS	0.963	0.914	1	0.963	0.914	1	CLONAL	3	TRUE	1	0.324120896432754	4		603	996	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325728	30325728	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	201	489	0	ENST00000322652.5:c.1926T>A	p.Asn642Lys	p.N642K	ENST00000322652	NM_015355.2	642	aaT/aaA	16/16	0.3173414850831	4	FACETS	0.834	0.777	0.893	0.834	0.777	0.893	CLONAL	3	TRUE	1	0.324120896432754	4		489	656	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929110	44929111	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACCT	novel	NA	P-0020510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	213	613	1	ENST00000377967.4:c.2212_2215dup	p.Asn739ThrfsTer2	p.N739Tfs*2	ENST00000377967	NM_021140.2	737	aca/acACCTa	17/29	NA	2	FACETS	0.883	0.823	0.945			1	INDETERMINATE	2	TRUE	NA	0.324120896432754	2		614	744	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0020511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	160	565	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.781	0.714	0.851	0.781	0.714	0.851	SUBCLONAL	1	TRUE	1	0.325943347189961	2		565	1257	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063655	67063655	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	39	1169	1	ENST00000412916.2:c.104G>C	p.Arg35Pro	p.R35P	ENST00000412916		35	cGg/cCg	2/6	0.325943347189961	1	FACETS	0.289	0.238	0.345	0.289	0.238	0.345	SUBCLONAL	1	TRUE	0	0.325943347189961	1		1170	694	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178151	56178152	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	78	626	0	ENST00000399503.3:c.3127dup	p.Ser1043PhefsTer14	p.S1043Ffs*14	ENST00000399503	NM_005921.1	1042	ctt/cTtt	14/20	1	2	FACETS	0.883	0.777	0.996	0.883	0.777	0.996	CLONAL	1	TRUE	1	0.325943347189961	2		626	542	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523067	176523067	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs969219254	NA	P-0020511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	156	1185	6	ENST00000292408.4:c.1831C>T	p.Arg611Trp	p.R611W	ENST00000292408	NM_213647.1	611	Cgg/Tgg	14/18	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.325943347189961	2		1191	857	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44733232	44733240	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTAAGGC	AGGTAAGGC	-	novel	NA	P-0020511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	58	719	0	ENST00000377967.4:c.225+1_225+9del		p.X75_splice	ENST00000377967	NM_021140.2	75		2/29	1	2	FACETS	0.741	0.638	0.854	0.741	0.638	0.854	SUBCLONAL	1	TRUE	1	0.325943347189961	2		719	480	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0020514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	194	1055	1	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	0.728653559765812	3	FACETS	0.993	0.922	1	0.497	0.461	0.534	CLONAL	1	TRUE	1	0.741444010322632	3		1056	722	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499740	18499740	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	70	585	0	ENST00000266497.5:c.1595C>A	p.Ala532Glu	p.A532E	ENST00000266497		532	gCa/gAa	10/31	0.741444010322632	7	FACETS	0.46	0.4	0.526			1	SUBCLONAL	1	TRUE	NA	0.741444010322632	7		585	1171	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425655	49425655	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	168	947	0	ENST00000301067.7:c.12833G>A	p.Gly4278Glu	p.G4278E	ENST00000301067	NM_003482.3	4278	gGg/gAg	39/54	0.728653559765812	3	FACETS	0.745	0.685	0.807	0.372	0.342	0.404	SUBCLONAL	1	TRUE	1	0.741444010322632	3		947	834	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988298	36988298	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	273	1049	0	ENST00000354822.5:c.355G>T	p.Gly119Cys	p.G119C	ENST00000354822	NM_001079668.2	119	Ggc/Tgc	2/3	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.741444010322632	2		1049	733	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042467	42042467	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	129	875	0	ENST00000219905.7:c.6662T>C	p.Ile2221Thr	p.I2221T	ENST00000219905	NM_001164273.1	2221	aTc/aCc	17/24	0.741444010322632	2	FACETS	0.717	0.654	0.783	0.359	0.327	0.392	SUBCLONAL	1	TRUE	0	0.741444010322632	2		875	485	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026928	48026932	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGG	AAAGG	-	novel	NA	P-0020514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	178	529	0	ENST00000234420.5:c.1809_1813del	p.Lys603AsnfsTer2	p.K603Nfs*2	ENST00000234420	NM_000179.2	602	tcAAAGGaa/tcaa	4/10	0.728653559765812	3	FACETS	0.943	0.884	1	0.943	0.884	1	CLONAL	2	TRUE	1	0.741444010322632	3		529	349	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326496	62326496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	802	1518	0	ENST00000360203.5:c.3421C>T	p.Pro1141Ser	p.P1141S	ENST00000360203	NM_001283009.1	1141	Ccg/Tcg	33/35	0.707531993092581	4	FACETS	0.971	0.94	1	0.647	0.626	0.668	CLONAL	2	TRUE	1	0.741444010322632	4		1518	1940	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0020515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	229	1035	1	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.242073658705441	2	FACETS	0.877	0.819	0.936	0.877	0.819	0.936	CLONAL	2	TRUE	0	0.31277810323914	2		1036	835	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420192	88420192	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	260	710	0	ENST00000360948.2:c.2494C>G	p.Pro832Ala	p.P832A	ENST00000360948	NM_001012338.2	832	Cca/Gca	19/19	0.31277810323914	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	0	0.31277810323914	3		710	584	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202989	27202989	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	54	904	1	ENST00000380036.4:c.2081T>C	p.Ile694Thr	p.I694T	ENST00000380036	NM_000459.3	694	aTc/aCc	13/23	0.294379137748395	3	FACETS	0.648	0.553	0.752	0.324	0.276	0.376	SUBCLONAL	1	TRUE	1	0.31277810323914	3		905	616	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465454	99465454	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1285343143	NA	P-0020517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	249	844	0	ENST00000268035.6:c.2279C>T	p.Ala760Val	p.A760V	ENST00000268035	NM_000875.3	760	gCa/gTa	11/21	0.39675011516734	3	FACETS	1	0.951	1	0.509	0.476	0.542	INDETERMINATE	1	TRUE	1	0.75853277040745	3		844	890	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0020521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	863	1002	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.229418406451159	9	FACETS	1	0.986	1			1	CLONAL	7	FALSE	NA	0.229418406451159	9		1002	1889	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0020521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	88	1302	0	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	1	2	FACETS	0.726	0.641	0.817	0.726	0.641	0.817	SUBCLONAL	1	FALSE	1	0.229418406451159	2		1302	1057	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28886179	28886181	+	inframe_deletion	In_Frame_Del	DEL	GCA	GCA	-	novel	NA	P-0020521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	87	1132	0	ENST00000282397.4:c.3441_3443del	p.Phe1147_Ala1148delinsLeu	p.F1147_A1148delinsL	ENST00000282397	NM_002019.4	1147	ttTGCa/tta	26/30	1	2	FACETS	0.734	0.648	0.826	0.734	0.648	0.826	SUBCLONAL	1	FALSE	1	0.229418406451159	2		1132	1034	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988359	36988359	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0020521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	87	905	0	ENST00000354822.5:c.294C>G	p.Tyr98Ter	p.Y98*	ENST00000354822	NM_001079668.2	98	taC/taG	2/3	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.229418406451159	2		905	599	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0020522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	70	303	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.972	0.864	1	0.972	0.864	1	CLONAL	1	TRUE	1	0.742732745856638	2		304	194	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0020522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	685	717	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.742732745856638	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.742732745856638	2		717	813	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909629	76909629	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs919106518	NA	P-0020522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	220	1192	3	ENST00000373344.5:c.4276C>T	p.Arg1426Ter	p.R1426*	ENST00000373344	NM_000489.3	1426	Cga/Tga	14/35	0.485002531927587	1	FACETS	0.789	0.743	0.835	0.789	0.743	0.835	SUBCLONAL	1	TRUE	0	0.742732745856638	1		1195	472	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030341	11030341	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	212	778	6	ENST00000327064.4:c.1091A>G	p.Glu364Gly	p.E364G	ENST00000327064	NM_199141.1	364	gAa/gGa	9/16	0.214865068821587	1	FACETS	0.667	0.625	0.71	0.667	0.625	0.71	INDETERMINATE	1	TRUE	0	0.742732745856638	1		784	538	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555526268	NA	P-0020524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	933	2013	0	ENST00000269305.4:c.406C>G	p.Gln136Glu	p.Q136E	ENST00000269305	NM_001126112.2	136	Caa/Gaa	5/11	0.841250096144725	1	FACETS	0.974	0.953	0.995	0.974	0.953	0.995	CLONAL	1	TRUE	0	0.841250096144725	1		2013	1319	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518352	204518352	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	357	997	1	ENST00000367182.3:c.1015C>A	p.His339Asn	p.H339N	ENST00000367182	NM_001278516.1	339	Cat/Aat	11/11	0.841250096144725	3	FACETS	0.998	0.946	1	0.499	0.473	0.526	CLONAL	1	TRUE	1	0.841250096144725	3		998	1208	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042265	42042265	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	312	964	0	ENST00000219905.7:c.6460C>G	p.Leu2154Val	p.L2154V	ENST00000219905	NM_001164273.1	2154	Cta/Gta	17/24	1	2	FACETS	0.968	0.918	1	0.968	0.918	1	CLONAL	1	TRUE	1	0.841250096144725	2		964	766	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8733781	8733781	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs1355550277	NA	P-0020524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	451	1081	0	ENST00000356435.5:c.63G>C	p.Glu21Asp	p.E21D	ENST00000356435		21	gaG/gaC	1/35	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.841250096144725	2		1081	1030	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	661	613	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.66299359842331	4	FACETS	0.936	0.907	0.964	0.936	0.907	0.964	CLONAL	3	TRUE	1	0.68713304635993	4		614	1156	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0020526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	559	730	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.68713304635993	2	FACETS	0.979	0.95	1	0.979	0.95	1	CLONAL	2	TRUE	0	0.68713304635993	2		731	831	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858313	9858313	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	40	555	0	ENST00000330684.3:c.3088C>A	p.Pro1030Thr	p.P1030T	ENST00000330684	NM_001134407.1	1030	Cca/Aca	13/13	0.513435931391945	3	FACETS	0.822	0.709	0.936			1	CLONAL	2	TRUE	NA	0.75295763661205	3		555	89	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115750	8115750	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs104894164	NA	P-0020530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	207	952	2	ENST00000346208.3:c.1096C>T	p.Arg366Ter	p.R366*	ENST00000346208		366	Cga/Tga	6/6	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.538866381719315	2		954	766	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937611	76937615	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTT	CTTTT	-	novel	NA	P-0020541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	95	265	0	ENST00000373344.5:c.3133_3137del	p.Lys1045Ter	p.K1045*	ENST00000373344	NM_000489.3	1045	AAAAGt/t	9/35	1	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.468385673170952	1		265	273	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577448	64577448	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	162	793	0	ENST00000312049.6:c.134A>C	p.Glu45Ala	p.E45A	ENST00000312049	NM_130799.2	45	gAg/gCg	2/10	0.468385673170952	1	FACETS	0.953	0.879	1	0.953	0.879	1	CLONAL	1	TRUE	0	0.468385673170952	1		793	556	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0020543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	37	1002	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.140413547243793	1	FACETS	0.924	0.762	1	0.924	0.762	1	CLONAL	1	TRUE	0	0.18	1		1002	405	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207021	1207021	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913324	NA	P-0020543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	28	1041	0	ENST00000326873.7:c.109C>T	p.Gln37Ter	p.Q37*	ENST00000326873	NM_000455.4	37	Cag/Tag	1/10	0.140413547243793	1	FACETS	0.697	0.557	0.857	0.697	0.557	0.857	SUBCLONAL	1	TRUE	0	0.18	1		1041	406	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94128963	94128963	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	28	614	0	ENST00000369303.4:c.97G>T	p.Val33Leu	p.V33L	ENST00000369303	NM_004440.3	33	Gta/Tta	1/17	0.140413547243793	3	FACETS	1	0.916	1	0.647	0.519	0.792	CLONAL	1	TRUE	1	0.18	3		614	262	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551324	150551324	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	35	1304	1	ENST00000369026.2:c.683T>A	p.Phe228Tyr	p.F228Y	ENST00000369026	NM_021960.4	228	tTc/tAc	1/3	1	2	FACETS	0.84	0.688	1	0.84	0.688	1	CLONAL	1	TRUE	1	0.18	2		1305	463	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28963999	28963999	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	17	582	0	ENST00000282397.4:c.1903G>T	p.Ala635Ser	p.A635S	ENST00000282397	NM_002019.4	635	Gcc/Tcc	13/30	1	2	FACETS	0.587	0.437	0.765	0.587	0.437	0.765	SUBCLONAL	1	TRUE	1	0.18	2		582	322	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357126	89357129	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	novel	NA	P-0020543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	34	1089	0	ENST00000301030.4:c.505_508del	p.Glu169ProfsTer58	p.E169Pfs*58	ENST00000301030	NM_001256183.1	169	GAGAcc/cc	6/13	1	2	FACETS	0.904	0.739	1	0.904	0.739	1	CLONAL	1	TRUE	1	0.18	2		1089	418	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024479	16024479	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	23	658	0	ENST00000268712.3:c.1739G>T	p.Arg580Leu	p.R580L	ENST00000268712	NM_006311.3	580	cGc/cTc	16/46	1	2	FACETS	0.704	0.548	0.884	0.704	0.548	0.884	SUBCLONAL	1	TRUE	1	0.18	2		658	363	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592321	29592321	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	22	814	0	ENST00000356175.3:c.4736A>G	p.Lys1579Arg	p.K1579R	ENST00000356175	NM_000267.3	1579	aAa/aGa	35/57	1	2	FACETS	0.666	0.516	0.841	0.666	0.516	0.841	SUBCLONAL	1	TRUE	1	0.18	2		814	367	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602617	10602617	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	23	1107	0	ENST00000171111.5:c.961del	p.Ala321ArgfsTer7	p.A321Rfs*7	ENST00000171111	NM_203500.1	321	Gcg/cg	3/6	0.140413547243793	1	FACETS	0.615	0.479	0.773	0.615	0.479	0.773	SUBCLONAL	1	TRUE	0	0.18	1		1107	378	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637891	176637891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	35	834	0	ENST00000439151.2:c.2491G>T	p.Gly831Trp	p.G831W	ENST00000439151	NM_022455.4	831	Ggg/Tgg	5/23	1	2	FACETS	0.98	0.804	1	0.98	0.804	1	CLONAL	1	TRUE	1	0.18	2		834	397	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200081	138200081	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs764389516	NA	P-0020543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	31	625	0	ENST00000237289.4:c.1499A>G	p.Asn500Ser	p.N500S	ENST00000237289	NM_001270507.1	500	aAc/aGc	7/9	1	2	FACETS	0.996	0.806	1	0.996	0.806	1	CLONAL	1	TRUE	1	0.18	2		625	346	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111543	8111545	+	inframe_deletion	In_Frame_Del	DEL	CTA	CTA	-	novel	NA	P-0020545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	109	1052	0	ENST00000346208.3:c.1033_1035del	p.Tyr345del	p.Y345del	ENST00000346208		343	ctCTAc/ctc	5/6	1	2	FACETS	0.895	0.804	0.991	0.895	0.804	0.991	CLONAL	1	TRUE	1	0.327069130184252	2		1052	745	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115865	8115866	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	162	1249	0	ENST00000346208.3:c.1213dup	p.His405ProfsTer102	p.H405Pfs*102	ENST00000346208		404	agc/agCc	6/6	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.327069130184252	2		1249	852	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176494	123176494	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	78	582	0	ENST00000218089.9:c.461A>T	p.Glu154Val	p.E154V	ENST00000218089	NM_001042749.1	154	gAg/gTg	7/35	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.327069130184252	2		582	473	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28931588	NA	P-0020547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	23	611	0	ENST00000349496.5:c.94G>C	p.Asp32His	p.D32H	ENST00000349496	NM_001904.3	32	Gac/Cac	3/15	1	2	FACETS	0.268	0.208	0.337	0.268	0.208	0.337	SUBCLONAL	1	TRUE	1	0.394957819414634	2		611	435	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378648	25378648	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	49	941	0	ENST00000311936.3:c.350A>C	p.Lys117Thr	p.K117T	ENST00000311936	NM_004985.3	117	aAa/aCa	4/5	0.153055311448299	3	FACETS	0.36	0.304	0.422	0.12	0.101	0.141	INDETERMINATE	1	TRUE	0	0.394957819414634	3		941	825	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627293	12627293	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs730881003	NA	P-0020547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	1046	723	0	ENST00000251849.4:c.1423T>C	p.Phe475Leu	p.F475L	ENST00000251849	NM_002880.3	475	Ttt/Ctt	14/17	0.394957819414634	15	FACETS	0.974	0.949	0.998			1	CLONAL	10	TRUE	NA	0.394957819414634	15		723	1940	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	103	613	1	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	0.939	1	CLONAL	1	TRUE	1	0.21	2		614	914	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913343	NA	P-0020548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	116	1050	0	ENST00000269305.4:c.817C>A	p.Arg273Ser	p.R273S	ENST00000269305	NM_001126112.2	273	Cgt/Agt	8/11	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.21	2		1050	1049	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106342	27106342	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	49	822	0	ENST00000324856.7:c.5953T>C	p.Ser1985Pro	p.S1985P	ENST00000324856	NM_006015.4	1985	Tcc/Ccc	20/20	1	2	FACETS	0.545	0.46	0.639	0.545	0.46	0.639	SUBCLONAL	1	TRUE	1	0.21	2		822	856	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223299	5223299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746587534	NA	P-0020548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	53	1126	0	ENST00000357368.4:c.2504G>A	p.Arg835His	p.R835H	ENST00000357368	NM_002850.3	835	cGc/cAc	18/38	1	2	FACETS	0.488	0.415	0.569	0.488	0.415	0.569	SUBCLONAL	1	TRUE	1	0.21	2		1126	1034	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289145	33289145	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	78	830	0	ENST00000374542.5:c.407C>G	p.Ala136Gly	p.A136G	ENST00000374542	NM_001141970.1	136	gCc/gGc	3/8	1	2	FACETS	0.893	0.783	1	0.893	0.783	1	CLONAL	1	TRUE	1	0.21	2		830	832	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0020550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	164	809	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.164525705561869	3	FACETS	1	0.934	1	1	0.994	1	CLONAL	6	FALSE	1	0.164525705561869	3		809	359	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29106013	29106054	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTTCTATTTCTGTTTCAACATTGAGAGCTGGGTCCTTTGAT	ATTTCTATTTCTGTTTCAACATTGAGAGCTGGGTCCTTTGAT	-	novel	NA	P-0020550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	19	614	0	ENST00000328354.6:c.793-7_827del		p.X265_splice	ENST00000328354	NM_007194.3	265		7/15	0.164525705561869	0	FACETS	1	0.788	1			1	CLONAL	3	FALSE	0	0.164525705561869	0		614	64	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0020551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	217	667	2	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.123660343630929	5	FACETS	1	0.987	1	0.616	0.574	0.658	INDETERMINATE	2	FALSE	1	0.368099839581599	5		669	743	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0020551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	50	493	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.123660343630929	5	FACETS	0.507	0.429	0.593	0.127	0.107	0.149	INDETERMINATE	1	FALSE	1	0.368099839581599	5		493	832	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0020551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	51	569	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	0.368099839581599	2	FACETS	0.684	0.583	0.795	0.342	0.291	0.398	SUBCLONAL	1	FALSE	0	0.368099839581599	2		569	405	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842656	68842657	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0020551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	276	929	0	ENST00000261769.5:c.597_598dup	p.Pro200HisfsTer16	p.P200Hfs*16	ENST00000261769	NM_004360.3	198	gac/gACac	5/16	0.368099839581599	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	FALSE	0	0.368099839581599	2		929	731	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433689	49433689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760968358	NA	P-0020551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	69	1239	1	ENST00000301067.7:c.7864G>A	p.Asp2622Asn	p.D2622N	ENST00000301067	NM_003482.3	2622	Gac/Aac	31/54	0.24742812500638	4	FACETS	0.468	0.406	0.535	0.234	0.203	0.268	SUBCLONAL	1	FALSE	2	0.368099839581599	4		1240	1096	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115111999	115112000	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0020551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	132	1146	0	ENST00000257566.3:c.1740_1741del	p.Phe580LeufsTer111	p.F580Lfs*111	ENST00000257566	NM_016569.3	580	ttCCac/ttac	7/8	0.123660343630929	5	FACETS	1	0.976	1	0.308	0.279	0.339	INDETERMINATE	1	FALSE	1	0.368099839581599	5		1146	903	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061137	38061144	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCCCGC	GCCCCCGC	-	novel	NA	P-0020551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	41	155	0	ENST00000250448.2:c.845_852del	p.Ser282LysfsTer8	p.S282Kfs*8	ENST00000250448	NM_004496.3	282	aGCGGGGGC/a	2/2	1	2	FACETS	1	0.91	1	1	0.974	1	CLONAL	2	FALSE	1	0.368099839581599	2		155	103	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820919	3820922	+	frameshift_variant	Frame_Shift_Del	DEL	AGGT	AGGT	-	novel	NA	P-0020551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	233	929	0	ENST00000262367.5:c.2529_2532del	p.Pro844AlafsTer4	p.P844Afs*4	ENST00000262367	NM_004380.2	843	ctACCT/ct	14/31	0.24742812500638	4	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	FALSE	2	0.368099839581599	4		929	850	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971215	18971215	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	68	901	0	ENST00000262803.5:c.2268G>C	p.Glu756Asp	p.E756D	ENST00000262803	NM_002911.3	756	gaG/gaC	16/24	0.123660343630929	5	FACETS	0.639	0.555	0.731	0.16	0.138	0.183	INDETERMINATE	1	FALSE	1	0.368099839581599	5		901	897	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663222	227663222	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs776250632	NA	P-0020551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	43	835	0	ENST00000305123.5:c.233C>G	p.Ser78Cys	p.S78C	ENST00000305123	NM_005544.2	78	tCc/tGc	1/2	0.123660343630929	5	FACETS	0.509	0.425	0.603	0.127	0.106	0.151	INDETERMINATE	1	FALSE	1	0.368099839581599	5		835	712	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860822	151860822	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	29	495	0	ENST00000262189.6:c.9840G>A	p.Met3280Ile	p.M3280I	ENST00000262189	NM_170606.2	3280	atG/atA	43/59	0.24742812500638	4	FACETS	0.391	0.313	0.481	0.196	0.156	0.241	SUBCLONAL	1	FALSE	2	0.368099839581599	4		495	551	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650610	48650610	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	43	807	1	ENST00000376670.3:c.580C>T	p.Leu194Phe	p.L194F	ENST00000376670	NM_002049.3	194	Ctc/Ttc	3/6	0.159827372206185	2	FACETS	0.302	0.252	0.358	0.151	0.126	0.179	INDETERMINATE	1	FALSE	0	0.368099839581599	2		808	773	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0020552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	57	169	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.181151793447241	3	FACETS	0.319	0.273	0.37	0.16	0.136	0.185	INDETERMINATE	1	TRUE	1	0.687569282454567	3		169	698	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579538	7579539	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0020552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	359	1161	0	ENST00000269305.4:c.148_149del	p.Ile50Ter	p.I50*	ENST00000269305	NM_001126112.2	50	ATt/t	4/11	0.687569282454567	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.687569282454567	1		1161	624	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10277337	10277337	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	378	1167	0	ENST00000340748.4:c.780G>C	p.Glu260Asp	p.E260D	ENST00000340748		260	gaG/gaC	10/40	0.331610559037267	1	FACETS	0.711	0.676	0.746	0.711	0.676	0.746	INDETERMINATE	1	TRUE	0	0.687569282454567	1		1167	1015	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0020553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	129	607	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.357461473905198	1	FACETS	0.885	0.804	0.97	0.885	0.804	0.97	CLONAL	1	TRUE	0	0.357461473905198	1		607	670	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989562	85989562	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs767548896	NA	P-0020553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	74	472	0	ENST00000263360.6:c.1321C>T	p.Arg441Ter	p.R441*	ENST00000263360	NM_003797.3	441	Cga/Tga	12/12	1	2	FACETS	0.89	0.782	1	0.89	0.782	1	CLONAL	1	TRUE	1	0.357461473905198	2		472	465	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0020554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	41	303	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.868	0.727	1	1	0.964	1	CLONAL	2	TRUE	1	0.168651885568901	2		303	280	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0020554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	11	421	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	0.321	0.221	0.447	0.321	0.221	0.447	SUBCLONAL	1	TRUE	1	0.168651885568901	2		421	406	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0020554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	95	528	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.168651885568901	2	FACETS	0.871	0.78	0.967	1	0.975	1	CLONAL	3	TRUE	0	0.168651885568901	2		528	431	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023534	27023534	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs766506741	NA	P-0020554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	98	831	0	ENST00000324856.7:c.640T>C	p.Ser214Pro	p.S214P	ENST00000324856	NM_006015.4	214	Tcc/Ccc	1/20	1	2	FACETS	0.805	0.718	0.897	1	0.983	1	CLONAL	2	TRUE	1	0.168651885568901	2		831	722	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554117	63554117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	123	936	0	ENST00000307078.5:c.622G>A	p.Ala208Thr	p.A208T	ENST00000307078	NM_004655.3	208	Gct/Act	2/11	1	2	FACETS	0.782	0.706	0.862	1	0.985	1	SUBCLONAL	2	TRUE	1	0.168651885568901	2		936	933	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216437	36216437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	148	1120	5	ENST00000222270.7:c.3700G>A	p.Glu1234Lys	p.E1234K	ENST00000222270	NM_014727.1	1234	Gag/Aag	12/37	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.168651885568901	2		1125	1282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057519990	NA	P-0020555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	336	792	0	ENST00000269305.4:c.796G>T	p.Gly266Ter	p.G266*	ENST00000269305	NM_001126112.2	266	Gga/Tga	8/11	0.626548992646965	2	FACETS	0.893	0.854	0.931	0.893	0.854	0.931	CLONAL	2	TRUE	0	0.635911401733822	2		792	592	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117875470	117875470	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	49	698	1	ENST00000297338.2:c.173A>T	p.His58Leu	p.H58L	ENST00000297338	NM_006265.2	58	cAt/cTt	3/14	0.450647058619416	3	FACETS	0.286	0.241	0.335	0.095	0.08	0.112	SUBCLONAL	1	TRUE	0	0.635911401733822	3		699	710	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	101	372	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.91	0.824	0.999	1	0.991	1	CLONAL	4	TRUE	1	0.181325539687632	2		373	306	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986986	36986986	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs137852692	NA	P-0020557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	58	804	1	ENST00000354822.5:c.703G>T	p.Val235Phe	p.V235F	ENST00000354822	NM_001079668.2	235	Gtc/Ttc	3/3	1	2	FACETS	0.758	0.65	0.877	0.758	0.65	0.877	SUBCLONAL	1	TRUE	1	0.181325539687632	2		805	844	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988508	36988511	+	frameshift_variant	Frame_Shift_Del	DEL	GACT	GACT	-	novel	NA	P-0020557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	98	1064	0	ENST00000354822.5:c.142_145del	p.Ser48ProfsTer52	p.S48Pfs*52	ENST00000354822	NM_001079668.2	48	AGTCcc/cc	2/3	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.181325539687632	2		1064	1039	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	294	372	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.272108729170081	5	FACETS	1	0.985	1	0.741	0.7	0.782	INDETERMINATE	2	TRUE	2	0.610899525947725	5		373	830	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0020558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	271	642	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.610899525947725	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.610899525947725	1		642	563	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0020558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	44	448	1	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.805	0.685	0.933	0.805	0.685	0.933	CLONAL	1	TRUE	1	0.610899525947725	2		449	179	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0020558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	574	711	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.610899525947725	2	FACETS	0.871	0.851	0.891	1	0.998	1	CLONAL	3	TRUE	0	0.610899525947725	2		711	719	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604789	48604789	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	115	644	0	ENST00000342988.3:c.1611C>A	p.Asp537Glu	p.D537E	ENST00000342988	NM_005359.5	537	gaC/gaA	12/12	0.610899525947725	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.610899525947725	1		644	227	SUCCESS
APC	324	MSKCC	GRCh37	5	112170813	112170813	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	130	1082	0	ENST00000257430.4:c.1911del	p.Ile638TyrfsTer8	p.I638Yfs*8	ENST00000257430	NM_000038.5	637	Ggg/gg	15/16	1	2	FACETS	0.929	0.849	1	0.929	0.849	1	CLONAL	1	TRUE	1	0.610899525947725	2		1082	458	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0020559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	212	169	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.586106555356678	2		169	611	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266605	198266605	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs754077338	NA	P-0020559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	121	542	1	ENST00000335508.6:c.2231C>A	p.Ala744Asp	p.A744D	ENST00000335508	NM_012433.2	744	gCt/gAt	16/25	1	2	FACETS	0.913	0.831	0.999	0.913	0.831	0.999	CLONAL	1	TRUE	1	0.586106555356678	2		543	452	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821755	72821761	+	frameshift_variant	Frame_Shift_Del	DEL	AGCCCGC	AGCCCGC	-	novel	NA	P-0020559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	75	708	0	ENST00000268489.5:c.10414_10420del	p.Ala3472SerfsTer11	p.A3472Sfs*11	ENST00000268489	NM_006885.3	3472	GCGGGCTtc/tc	10/10	0.251779243638095	3	FACETS	0.515	0.451	0.583	0.257	0.225	0.292	INDETERMINATE	1	TRUE	1	0.586106555356678	3		708	643	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183211	56183211	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	133	539	0	ENST00000399503.3:c.4121A>G	p.Asn1374Ser	p.N1374S	ENST00000399503	NM_005921.1	1374	aAt/aGt	18/20	0.515022400581025	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.586106555356678	1		539	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0020560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	529	589	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.737068019446307	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.737068019446307	1		589	794	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226556015	226556015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	464	292	3	ENST00000366794.5:c.2162C>T	p.Ser721Phe	p.S721F	ENST00000366794	NM_001618.3	721	tCt/tTt	16/23	0.737068019446307	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.737068019446307	3		295	561	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66777518	66777518	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	421	591	8	ENST00000307102.5:c.884G>A	p.Arg295Lys	p.R295K	ENST00000307102	NM_002755.3	295	aGg/aAg	7/11	0.382334892117549	4	FACETS	0.914	0.873	0.956	0.914	0.873	0.956	INDETERMINATE	2	TRUE	2	0.737068019446307	4		599	1085	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281626	198281626	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	276	414	3	ENST00000335508.6:c.505A>T	p.Arg169Trp	p.R169W	ENST00000335508	NM_012433.2	169	Agg/Tgg	6/25	0.597222245983354	3	FACETS	0.825	0.781	0.869	0.825	0.781	0.869	CLONAL	2	TRUE	1	0.737068019446307	3		417	621	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197808	66197808	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	77	626	1	ENST00000273854.3:c.2891C>A	p.Ser964Tyr	p.S964Y	ENST00000273854	NM_004439.5	964	tCt/tAt	17/18	0.438235003322305	1	FACETS	0.293	0.257	0.33	0.293	0.257	0.33	INDETERMINATE	1	TRUE	0	0.737068019446307	1		627	451	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045845	143045845	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	168	591	5	ENST00000262992.4:c.1789C>G	p.Arg597Gly	p.R597G	ENST00000262992	NM_001101669.1	597	Cga/Gga	17/24	1	2	FACETS	0.528	0.485	0.572	0.528	0.485	0.572	SUBCLONAL	1	TRUE	1	0.737068019446307	2		596	864	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37141792	37141792	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	736	692	9	ENST00000373509.5:c.867G>T	p.Trp289Cys	p.W289C	ENST00000373509	NM_002648.3	289	tgG/tgT	6/6	0.498848281855794	4	FACETS	1	0.988	1	0.697	0.674	0.72	CLONAL	2	TRUE	1	0.737068019446307	4		701	1660	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120275	94120275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	53	325	0	ENST00000369303.4:c.776C>T	p.Pro259Leu	p.P259L	ENST00000369303	NM_004440.3	259	cCc/cTc	3/17	0.449159642341813	2	FACETS	0.335	0.286	0.389	0.168	0.143	0.195	SUBCLONAL	1	TRUE	0	0.737068019446307	2		325	429	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11015635	11015635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	66	793	0	ENST00000327064.4:c.229G>A	p.Val77Met	p.V77M	ENST00000327064	NM_199141.1	77	Gtg/Atg	2/16	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.201692857994263	2		793	641	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62317180	62317180	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	123	1109	0	ENST00000360203.5:c.1303G>C	p.Ala435Pro	p.A435P	ENST00000360203	NM_001283009.1	435	Gct/Cct	16/35	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.201692857994263	2		1109	898	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051642	30051643	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0020561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	29	548	0	ENST00000338641.4:c.577_578del	p.Ala193ArgfsTer9	p.A193Rfs*9	ENST00000338641	NM_000268.3	192	taCGca/taca	6/16	0.201756767951648	1	FACETS	0.581	0.466	0.712	0.581	0.466	0.712	SUBCLONAL	1	TRUE	0	0.201692857994263	1		548	445	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	132	251	0				ENST00000310581	NM_198253.2	-/1132			0.195894099228039	1	FACETS	0.71	0.65	0.771	0.71	0.65	0.771	INDETERMINATE	1	TRUE	0	0.619904562669708	1		251	414	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0020564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	124	303	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.915	0.835	0.999	0.915	0.835	0.999	CLONAL	1	TRUE	1	0.619904562669708	2		304	437	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429802	78429805	+	frameshift_variant	Frame_Shift_Del	DEL	GGAG	GGAG	-	novel	NA	P-0020564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	190	566	0	ENST00000370768.2:c.983_986del	p.Pro328GlnfsTer62	p.P328Qfs*62	ENST00000370768	NM_003902.3	328	cCTCCa/ca	12/20	0.619904562669708	1	FACETS	0.951	0.889	1	0.951	0.889	1	CLONAL	1	TRUE	0	0.619904562669708	1		566	445	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798098	42798098	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0020564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	279	828	0	ENST00000575354.2:c.4052C>G	p.Ser1351Ter	p.S1351*	ENST00000575354	NM_015125.3	1351	tCa/tGa	17/20	0.619904562669708	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.619904562669708	1		828	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578204	7578204	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	214	927	1	ENST00000269305.4:c.645T>A	p.Ser215Arg	p.S215R	ENST00000269305	NM_001126112.2	215	agT/agA	6/11	0.260100903460632	2	FACETS	0.82	0.763	0.878	0.82	0.763	0.878	CLONAL	2	FALSE	0	0.303985943797549	2		928	859	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	242	555	0	ENST00000304494.5:c.143C>T	p.Pro48Leu	p.P48L	ENST00000304494	NM_000077.4	48	cCg/cTg	1/3	0.279663026810201	3	FACETS	0.949	0.893	1	0.949	0.893	1	CLONAL	3	FALSE	0	0.303985943797549	3		555	644	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045954	26045954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	67	536	2	ENST00000540144.1:c.316G>A	p.Glu106Lys	p.E106K	ENST00000540144	NM_003531.2	106	Gaa/Aaa	1/1	0.235870874861742	4	FACETS	0.863	0.75	0.986	0.432	0.375	0.493	CLONAL	1	FALSE	2	0.303985943797549	4		538	666	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740157	162740157	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	159	683	3	ENST00000367921.3:c.1359G>T	p.Met453Ile	p.M453I	ENST00000367921	NM_006182.2	453	atG/atT	12/18	0.235870874861742	4	FACETS	0.867	0.795	0.941	0.867	0.795	0.941	CLONAL	2	FALSE	2	0.303985943797549	4		686	787	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431570	49431597	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCCCGTGGCCCCAAAGGAGGCCTTCT	CCTCCCGTGGCCCCAAAGGAGGCCTTCT	TCG	novel	NA	P-0020569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	156	775	3	ENST00000301067.7:c.9542_9569delinsCGA	p.Glu3181AlafsTer8	p.E3181Afs*8	ENST00000301067	NM_003482.3	3181	gAGAAGGCCTCCTTTGGGGCCACGGGAGGa/gCGAa	34/54	0.298729554246516	5	FACETS	0.785	0.718	0.855	0.523	0.479	0.57	SUBCLONAL	2	FALSE	2	0.303985943797549	5		778	952	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443512	49443512	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	228	662	0	ENST00000301067.7:c.3859del	p.Glu1287ArgfsTer43	p.E1287Rfs*43	ENST00000301067	NM_003482.3	1287	Gag/ag	11/54	0.298729554246516	5	FACETS	0.834	0.778	0.891	0.834	0.778	0.891	CLONAL	3	FALSE	2	0.303985943797549	5		662	873	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911691	32911691	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203711	NA	P-0020569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	83	631	1	ENST00000380152.3:c.3199A>G	p.Thr1067Ala	p.T1067A	ENST00000380152		1067	Act/Gct	11/27	0.289791178347603	3	FACETS	1	0.975	1	0.693	0.614	0.777	CLONAL	1	FALSE	1	0.303985943797549	3		632	454	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635645	47635645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41295286	NA	P-0020569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	78	718	1	ENST00000233146.2:c.317G>A	p.Arg106Lys	p.R106K	ENST00000233146	NM_000251.2	106	aGa/aAa	2/16	0.102099666913621	5	FACETS	1	0.913	1	0.262	0.23	0.297	INDETERMINATE	1	FALSE	1	0.303985943797549	5		719	712	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602970	55602970	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141126803	NA	P-0020569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	113	438	0	ENST00000288135.5:c.2680C>T	p.His894Tyr	p.H894Y	ENST00000288135	NM_000222.2	894	Cac/Tac	19/21	0.289791178347603	3	FACETS	0.869	0.786	0.955	0.869	0.786	0.955	CLONAL	2	FALSE	1	0.303985943797549	3		438	493	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629127	86629127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	105	422	0	ENST00000274376.6:c.872C>T	p.Thr291Ile	p.T291I	ENST00000274376	NM_002890.2	291	aCa/aTa	4/25	0.184687080685673	3	FACETS	1	0.962	1	0.749	0.678	0.823	CLONAL	2	FALSE	0	0.303985943797549	3		422	354	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520479	176520479	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	117	1113	1	ENST00000292408.4:c.1324G>T	p.Gly442Cys	p.G442C	ENST00000292408	NM_213647.1	442	Ggc/Tgc	10/18	0.303985943797549	1	FACETS	0.796	0.718	0.879	0.796	0.718	0.879	SUBCLONAL	1	FALSE	0	0.303985943797549	1		1114	820	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978741	70978741	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0020569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	114	480	0	ENST00000276594.2:c.913-1G>T		p.X305_splice	ENST00000276594	NM_024504.3	305			0.303985943797549	5	FACETS	0.894	0.807	0.985	0.596	0.538	0.657	CLONAL	2	FALSE	2	0.303985943797549	5		480	611	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578179	7578179	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	157	1059	1	ENST00000269305.4:c.670G>T	p.Glu224Ter	p.E224*	ENST00000269305	NM_001126112.2	224	Gag/Tag	6/11	0.431919915714659	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.431919915714659	1		1060	562	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250211	133250211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115047349	NA	P-0020570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	133	1039	1	ENST00000320574.5:c.1309G>A	p.Val437Met	p.V437M	ENST00000320574	NM_006231.2	437	Gtg/Atg	13/49	1	2	FACETS	0.971	0.885	1	0.971	0.885	1	CLONAL	1	TRUE	1	0.431919915714659	2		1040	634	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220703	1220703	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	143	1063	0	ENST00000326873.7:c.721G>C	p.Ala241Pro	p.A241P	ENST00000326873	NM_000455.4	241	Gct/Cct	5/10	0.431919915714659	1	FACETS	0.904	0.828	0.984	0.904	0.828	0.984	CLONAL	1	TRUE	0	0.431919915714659	1		1063	574	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432362	432362	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	32	319	1	ENST00000399788.2:c.2161C>A	p.Pro721Thr	p.P721T	ENST00000399788	NM_001042603.1	721	Cca/Aca	16/28	1	2	FACETS	0.981	0.808	1	0.981	0.808	1	CLONAL	1	TRUE	1	0.431919915714659	2		320	151	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425771	49425771	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	103	823	0	ENST00000301067.7:c.12717G>T	p.Gln4239His	p.Q4239H	ENST00000301067	NM_003482.3	4239	caG/caT	39/54	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.431919915714659	2		823	413	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2105513	2105513	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	121	746	0	ENST00000219476.3:c.592A>T	p.Met198Leu	p.M198L	ENST00000219476	NM_000548.3	198	Atg/Ttg	6/42	1	2	FACETS	0.931	0.843	1	0.931	0.843	1	CLONAL	1	TRUE	1	0.431919915714659	2		746	602	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306800	41306800	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0020570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	50	306	0	ENST00000373198.4:c.860-1G>A		p.X287_splice	ENST00000373198	NM_133170.3	287			1	2	FACETS	0.985	0.845	1	0.985	0.845	1	CLONAL	1	TRUE	1	0.431919915714659	2		306	235	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0020571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	24	328	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.483	0.378	0.605	0.483	0.378	0.605	SUBCLONAL	1	TRUE	1	0.21	2		328	473	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842383	68842384	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0020571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	46	715	0	ENST00000261769.5:c.445_446insAC	p.Leu149HisfsTer67	p.L149Hfs*67	ENST00000261769	NM_004360.3	148	-/CA	4/16	1	2	FACETS	0.754	0.634	0.887	0.754	0.634	0.887	SUBCLONAL	1	TRUE	1	0.21	2		715	581	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879364	151879364	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765915364	NA	P-0020571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	51	499	0	ENST00000262189.6:c.5581C>T	p.Arg1861Trp	p.R1861W	ENST00000262189	NM_170606.2	1861	Cgg/Tgg	36/59	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.21	2		499	434	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0020572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	765	340	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.328659105740703	7	FACETS	1	0.989	1			1	CLONAL	6	TRUE	NA	0.328659105740703	7		340	1364	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246011	46246011	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	45	346	0	ENST00000334344.6:c.4106del	p.Gly1369ValfsTer4	p.G1369Vfs*4	ENST00000334344	NM_152641.2	1369	Ggt/gt	15/21	1	2	FACETS	0.746	0.629	0.875	0.746	0.629	0.875	SUBCLONAL	1	TRUE	1	0.328659105740703	2		346	367	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427699	72427699	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	68	439	2	ENST00000477973.2:c.791A>T	p.Glu264Val	p.E264V	ENST00000477973	NM_012234.5	264	gAa/gTa	4/4	1	2	FACETS	0.873	0.761	0.993	0.873	0.761	0.993	CLONAL	1	TRUE	1	0.328659105740703	2		441	474	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0020575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	15	686	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.102	0.074	0.136	0.102	0.074	0.136	SUBCLONAL	1	TRUE	1	0.666405900730351	2		686	442	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	276	613	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.26097423146505	4	FACETS	0.837	0.788	0.887			1	CLONAL	3	TRUE	NA	0.343452364014798	4		614	860	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268766	41268766	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	111	787	2	ENST00000349496.5:c.1004A>T	p.Lys335Ile	p.K335I	ENST00000349496	NM_001904.3	335	aAa/aTa	7/15	0.324933283250807	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.343452364014798	1		789	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0020578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	141	609	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.324933283250807	1	FACETS	0.951	0.868	1	0.951	0.868	1	CLONAL	1	TRUE	0	0.343452364014798	1		610	715	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652855	212652856	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0020578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	35	695	2	ENST00000342788.4:c.450_451delinsAA	p.Asp150_Gln151delinsGluLys	p.D150_Q151delinsEK	ENST00000342788	NM_005235.2	150	gaCCag/gaAAag	4/28	1	2	FACETS	0.731	0.601	0.874	0.731	0.601	0.874	SUBCLONAL	1	TRUE	1	0.343452364014798	2		697	279	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668785	52668785	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	92	695	0	ENST00000394830.3:c.1134del	p.Phe379LeufsTer25	p.F379Lfs*25	ENST00000394830	NM_018313.4	378	tcC/tc	12/30	0.324933283250807	1	FACETS	0.977	0.873	1	0.977	0.873	1	CLONAL	1	TRUE	0	0.343452364014798	1		695	454	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876320	35876320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	84	752	1	ENST00000303115.3:c.1112C>A	p.Ala371Asp	p.A371D	ENST00000303115	NM_002185.3	371	gCt/gAt	8/8	1	2	FACETS	0.845	0.747	0.949	0.845	0.747	0.949	CLONAL	1	TRUE	1	0.343452364014798	2		753	579	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665686	86665686	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	86	705	0	ENST00000274376.6:c.1667A>G	p.Tyr556Cys	p.Y556C	ENST00000274376	NM_002890.2	556	tAc/tGc	12/25	0.343452364014798	1	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	0	0.343452364014798	1		705	407	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448296	56448297	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	102	967	0	ENST00000407977.2:c.350_351insA	p.Cys119LeufsTer6	p.C119Lfs*6	ENST00000407977		117	cgc/cgAc	3/10	1	2	FACETS	0.667	0.596	0.743	0.667	0.596	0.743	SUBCLONAL	1	TRUE	1	0.343452364014798	2		967	890	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1555525585	NA	P-0020579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	204	923	0	ENST00000269305.4:c.673-2A>G		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.239646001735239	3	FACETS	1	0.962	1	0.7	0.651	0.75	CLONAL	2	FALSE	0	0.3	3		923	745	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221319	1221320	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	304	1030	0	ENST00000326873.7:c.842_843insT	p.Leu282AlafsTer3	p.L282Afs*3	ENST00000326873	NM_000455.4	281	ccg/ccTg	6/10	0.256333470982457	3	FACETS	0.847	0.8	0.895	0.847	0.8	0.895	CLONAL	3	FALSE	0	0.3	3		1030	917	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112344	115112344	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0020579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	72	308	1	ENST00000257566.3:c.1396A>T	p.Lys466Ter	p.K466*	ENST00000257566	NM_016569.3	466	Aag/Tag	7/8	0.235682192900871	3	FACETS	0.993	0.877	1	0.993	0.877	1	CLONAL	2	FALSE	1	0.3	3		309	278	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652920	29652920	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	136	657	0	ENST00000356175.3:c.4855G>T	p.Glu1619Ter	p.E1619*	ENST00000356175	NM_000267.3	1619	Gaa/Taa	36/57	0.254732722820807	2	FACETS	0.844	0.771	0.92	0.844	0.771	0.92	CLONAL	2	FALSE	0	0.3	2		657	537	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066472	94066472	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	95	534	0	ENST00000369303.4:c.1287G>T	p.Arg429Ser	p.R429S	ENST00000369303	NM_004440.3	429	agG/agT	5/17	0.235682192900871	3	FACETS	0.772	0.69	0.858	0.772	0.69	0.858	SUBCLONAL	2	FALSE	1	0.3	3		534	472	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54959353	54959353	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0020580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	178	815	0	ENST00000312783.6:c.347C>G	p.Ser116Ter	p.S116*	ENST00000312783	NM_198436.1	116	tCa/tGa	5/10	1	2	FACETS	0.507	0.468	0.547	0.507	0.468	0.547	SUBCLONAL	1	TRUE	1	0.907292034676058	2		815	774	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724586	112724586	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0020580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	120	989	1	ENST00000369452.4:c.470C>G	p.Ser157Ter	p.S157*	ENST00000369452	NM_007373.3	157	tCa/tGa	2/9	0.212222955642056	2	FACETS	0.328	0.296	0.362	0.164	0.148	0.181	INDETERMINATE	1	TRUE	0	0.907292034676058	2		990	807	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154255	2154255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554804044	NA	P-0020580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	522	1214	4	ENST00000434045.2:c.673G>A	p.Gly225Arg	p.G225R	ENST00000434045	NM_001127598.1	225	Ggg/Agg	5/5	0.907292034676058	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.907292034676058	1		1218	588	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427894	49427894	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	455	1237	0	ENST00000301067.7:c.10696C>G	p.Leu3566Val	p.L3566V	ENST00000301067	NM_003482.3	3566	Ctg/Gtg	38/54	1	2	FACETS	0.934	0.894	0.974	0.934	0.894	0.974	CLONAL	1	TRUE	1	0.907292034676058	2		1237	1074	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647335	23647335	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	392	1165	0	ENST00000261584.4:c.532G>A	p.Glu178Lys	p.E178K	ENST00000261584	NM_024675.3	178	Gaa/Aaa	4/13	1	2	FACETS	0.92	0.878	0.963	0.92	0.878	0.963	CLONAL	1	TRUE	1	0.907292034676058	2		1165	939	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259653	89259653	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	158	481	0	ENST00000336596.2:c.797G>C	p.Arg266Thr	p.R266T	ENST00000336596	NM_005233.5	266	aGa/aCa	3/17	1	2	FACETS	0.957	0.889	1	0.957	0.889	1	CLONAL	1	TRUE	1	0.907292034676058	2		481	364	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430385	181430385	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	85	1125	1	ENST00000325404.1:c.237G>T	p.Trp79Cys	p.W79C	ENST00000325404	NM_003106.3	79	tgG/tgT	1/1	1	2	FACETS	0.176	0.155	0.199	0.176	0.155	0.199	SUBCLONAL	1	TRUE	1	0.907292034676058	2		1126	1066	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413178	139413178	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	689	1594	0	ENST00000277541.6:c.964G>T	p.Val322Leu	p.V322L	ENST00000277541	NM_017617.3	322	Gtg/Ttg	6/34	1	2	FACETS	0.993	0.96	1	0.993	0.96	1	CLONAL	1	TRUE	1	0.907292034676058	2		1594	1529	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431028	49431028	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	139	995	0	ENST00000301067.7:c.10111C>T	p.Gln3371Ter	p.Q3371*	ENST00000301067	NM_003482.3	3371	Cag/Tag	34/54	1	2	FACETS	1	0.951	1	1	0.991	1	CLONAL	2	TRUE	1	0.235414002004607	2		995	558	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870241	44870241	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0020581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	203	483	0	ENST00000377967.4:c.420C>G	p.Tyr140Ter	p.Y140*	ENST00000377967	NM_021140.2	140	taC/taG	5/29	1	1	FACETS	1	0.977	1	1	0.996	1	CLONAL	5	TRUE	0	0.235414002004607	1		483	292	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398881	398881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	53	735	0	ENST00000380956.4:c.691C>T	p.Pro231Ser	p.P231S	ENST00000380956	NM_001195286.1	231	Ccc/Tcc	6/9	1	2	FACETS	0.479	0.407	0.558	0.479	0.407	0.558	SUBCLONAL	1	TRUE	1	0.27	2		735	820	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183871	10183871	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs869025636	NA	P-0020583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	87	682	0	ENST00000256474.2:c.340G>C	p.Gly114Arg	p.G114R	ENST00000256474	NM_000551.3	114	Ggt/Cgt	1/3	1	2	FACETS	0.925	0.819	1	0.925	0.819	1	CLONAL	1	TRUE	1	0.27	2		682	697	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105258942	105258942	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	61	1000	0	ENST00000349310.3:c.39C>G	p.His13Gln	p.H13Q	ENST00000349310	NM_001014432.1	13	caC/caG	3/15	1	2	FACETS	0.442	0.38	0.51	0.442	0.38	0.51	SUBCLONAL	1	TRUE	1	0.27	2		1000	1023	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127685	47127706	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CTCTTCCTGAAGCTTCTGGTTA	CTCTTCCTGAAGCTTCTGGTTA	-	novel	NA	P-0020583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	80	683	0	ENST00000409792.3:c.5376_5397del	p.Ser1792ArgfsTer3	p.S1792Rfs*3	ENST00000409792	NM_014159.6	1792	agTAACCAGAAGCTTCAGGAAGAG/ag	11/21	1	2	FACETS	0.798	0.702	0.901	0.798	0.702	0.901	CLONAL	1	TRUE	1	0.27	2		683	743	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442047	52442047	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	97	756	1	ENST00000460680.1:c.302T>C	p.Leu101Pro	p.L101P	ENST00000460680	NM_004656.3	101	cTg/cCg	5/17	1	2	FACETS	0.818	0.729	0.914	0.818	0.729	0.914	CLONAL	1	TRUE	1	0.27	2		757	878	SUCCESS
APC	324	MSKCC	GRCh37	5	112179432	112179432	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	32	610	0	ENST00000257430.4:c.8141G>C	p.Arg2714Pro	p.R2714P	ENST00000257430	NM_000038.5	2714	cGt/cCt	16/16	1	2	FACETS	0.388	0.314	0.472	0.388	0.314	0.472	SUBCLONAL	1	TRUE	1	0.27	2		610	611	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741934	145741934	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	83	860	1	ENST00000428558.2:c.569G>A	p.Trp190Ter	p.W190*	ENST00000428558	NM_004260.3	190	tGg/tAg	5/22	0.156022375033451	3	FACETS	0.674	0.593	0.761	0.337	0.296	0.381	INDETERMINATE	1	TRUE	1	0.27	3		861	1035	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855229	76855229	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs912772662	NA	P-0020583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	67	461	0	ENST00000373344.5:c.5758A>G	p.Met1920Val	p.M1920V	ENST00000373344	NM_000489.3	1920	Atg/Gtg	24/35	0.0579858648786038	2	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.27	2		461	363	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	144	251	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.412757405879006	2		251	523	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56376730	56376730	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	80	687	0	ENST00000348428.3:c.770A>G	p.His257Arg	p.H257R	ENST00000348428	NM_006785.3	257	cAc/cGc	5/17	1	2	FACETS	0.881	0.779	0.99	0.881	0.779	0.99	CLONAL	1	TRUE	1	0.412757405879006	2		687	440	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900288	101900288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111854391	NA	P-0020585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	96	586	0	ENST00000374994.4:c.722C>T	p.Ser241Leu	p.S241L	ENST00000374994	NM_004612.2	241	tCg/tTg	4/9	0.536654861794462	1	FACETS	0.847	0.764	0.934	0.847	0.764	0.934	CLONAL	1	TRUE	0	0.536654861794462	1		586	309	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390995	89390995	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144727411	NA	P-0020586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	38	725	1	ENST00000336596.2:c.1061G>A	p.Arg354Gln	p.R354Q	ENST00000336596	NM_005233.5	354	cGg/cAg	5/17	0.133656337764378	3	FACETS	0.544	0.449	0.652	0.272	0.224	0.326	INDETERMINATE	1	TRUE	1	0.23	3		726	677	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26970491	26970491	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs201577656	NA	P-0020586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	17	454	0	ENST00000381527.3:c.860C>T	p.Thr287Met	p.T287M	ENST00000381527	NM_001260.1	287	aCg/aTg	8/13	1	2	FACETS	0.536	0.4	0.697	0.536	0.4	0.697	SUBCLONAL	1	TRUE	1	0.23	2		454	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs587781702	NA	P-0020586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	184	832	1	ENST00000269305.4:c.920-1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			1	2	FACETS	0.861	0.795	0.93	1	0.992	1	CLONAL	2	TRUE	1	0.23	2		833	929	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385173	41385173	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	94	908	0	ENST00000373198.4:c.788G>C	p.Ser263Thr	p.S263T	ENST00000373198	NM_133170.3	263	aGc/aCc	6/32	0.133656337764378	3	FACETS	0.93	0.826	1	0.465	0.413	0.521	INDETERMINATE	1	TRUE	1	0.23	3		908	980	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928301	69928301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	35	577	0	ENST00000352241.4:c.121C>T	p.Pro41Ser	p.P41S	ENST00000352241	NM_198159.2	41	Cct/Tct	2/10	0.133656337764378	3	FACETS	0.487	0.398	0.588	0.243	0.199	0.294	INDETERMINATE	1	TRUE	1	0.23	3		577	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0020588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	626	1050	0	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	0.574301777225626	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.574301777225626	2		1050	1023	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589698	69589698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	63	177	0	ENST00000168712.1:c.155C>T	p.Ala52Val	p.A52V	ENST00000168712	NM_002007.2	52	gCg/gTg	1/3	0.574301777225626	14	FACETS	1	0.879	1			1	CLONAL	1	TRUE	NA	0.574301777225626	14		177	955	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101300	27101301	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0020588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	166	808	0	ENST00000324856.7:c.4582_4583del	p.Arg1528AsnfsTer3	p.R1528Nfs*3	ENST00000324856	NM_006015.4	1528	CGa/a	18/20	1	2	FACETS	0.792	0.729	0.857	0.792	0.729	0.857	SUBCLONAL	1	TRUE	1	0.574301777225626	2		808	730	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549394	21549394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148935054	NA	P-0020588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	42	624	0	ENST00000382592.4:c.2882G>A	p.Arg961Gln	p.R961Q	ENST00000382592	NM_014572.2	961	cGg/cAg	8/8	0.154040815696553	3	FACETS	0.312	0.26	0.37	0.104	0.086	0.124	INDETERMINATE	1	TRUE	0	0.574301777225626	3		624	604	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060664	38060664	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	769	1108	4	ENST00000250448.2:c.1325C>A	p.Ala442Asp	p.A442D	ENST00000250448	NM_004496.3	442	gCc/gAc	2/2	0.185631236455452	5	FACETS	0.909	0.883	0.935	0.727	0.706	0.748	INDETERMINATE	4	TRUE	0	0.574301777225626	5		1112	1371	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142898	30142898	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755697363	NA	P-0020588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	509	1018	0	ENST00000389048.3:c.628G>A	p.Ala210Thr	p.A210T	ENST00000389048	NM_004304.4	210	Gcc/Acc	1/29	0.154040815696553	3	FACETS	1	0.992	1	0.735	0.707	0.763	INDETERMINATE	2	TRUE	0	0.574301777225626	3		1018	1035	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141617	202141617	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs765352144	NA	P-0020588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	132	647	0	ENST00000358485.4:c.905A>G	p.Asn302Ser	p.N302S	ENST00000358485	NM_001080125.1	302	aAt/aGt	7/9	0.154040815696553	3	FACETS	0.956	0.87	1	0.319	0.29	0.349	INDETERMINATE	1	TRUE	0	0.574301777225626	3		647	619	SUCCESS
APC	324	MSKCC	GRCh37	5	112175069	112175069	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	98	295	0	ENST00000257430.4:c.3778C>T	p.Gln1260Ter	p.Q1260*	ENST00000257430	NM_000038.5	1260	Cag/Tag	16/16	0.556092162390401	2	FACETS	0.772	0.704	0.841	0.772	0.704	0.841	SUBCLONAL	2	TRUE	0	0.574301777225626	2		295	221	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0020590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	101	525	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	1	2	FACETS	0.673	0.602	0.749	0.673	0.602	0.749	SUBCLONAL	1	TRUE	1	0.4	2		525	750	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0020594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	131	464	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	0.600075094139084	3	FACETS	0.815	0.741	0.892	0.407	0.37	0.446	CLONAL	1	TRUE	1	0.67651412432907	3		464	636	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0020594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	833	260	0	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.576055740827458	4	FACETS	0.971	0.952	0.99			1	CLONAL	4	TRUE	NA	0.67651412432907	4		260	1063	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201815	66201815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764665078	NA	P-0020594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	168	593	0	ENST00000273854.3:c.2687G>A	p.Arg896His	p.R896H	ENST00000273854	NM_004439.5	896	cGt/cAt	16/18	1	2	FACETS	0.849	0.784	0.916	0.849	0.784	0.916	CLONAL	1	TRUE	1	0.67651412432907	2		593	585	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48921989	48921989	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	479	652	0	ENST00000267163.4:c.531del	p.Ser178AlafsTer8	p.S178Afs*8	ENST00000267163	NM_000321.2	177	Ccc/cc	5/27	0.632916456244004	4	FACETS	1	0.995	1	0.864	0.838	0.89	CLONAL	3	TRUE	0	0.67651412432907	4		652	687	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31381393	31381393	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	143	575	1	ENST00000328111.2:c.1118G>A	p.Arg373Lys	p.R373K	ENST00000328111	NM_006892.3	373	aGg/aAg	10/23	0.67651412432907	6	FACETS	0.807	0.734	0.885	0.202	0.183	0.222	CLONAL	1	TRUE	2	0.67651412432907	6		576	1232	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321784	62321784	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1219370345	NA	P-0020594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1335	136	596	0	ENST00000360203.5:c.2403G>C	p.Gln801His	p.Q801H	ENST00000360203	NM_001283009.1	801	caG/caC	26/35	0.67651412432907	6	FACETS	0.643	0.583	0.707	0.161	0.145	0.177	SUBCLONAL	1	TRUE	2	0.67651412432907	6		596	1471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0020594-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	89	260	0	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.16	2		260	961	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48921989	48921989	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020594-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	59	652	0	ENST00000267163.4:c.531del	p.Ser178AlafsTer8	p.S178Afs*8	ENST00000267163	NM_000321.2	177	Ccc/cc	5/27	1	2	FACETS	0.886	0.761	1	0.886	0.761	1	CLONAL	1	TRUE	1	0.16	2		652	832	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0020602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	62	451	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.339246151864428	5	FACETS	0.994	0.894	1	1	0.97	1	CLONAL	5	TRUE	1	0.339246151864428	5		451	111	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713345	30713345	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748195637	NA	P-0020602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	45	517	1	ENST00000295754.5:c.670C>T	p.Arg224Cys	p.R224C	ENST00000295754	NM_003242.5	224	Cgc/Tgc	4/7	0.339246151864428	3	FACETS	1	0.925	1	1	0.925	1	CLONAL	2	TRUE	1	0.339246151864428	3		518	138	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0020602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	12	444	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			0.339246151864428	3	FACETS	0.853	0.606	1	0.427	0.303	0.575	CLONAL	1	TRUE	1	0.339246151864428	3		444	97	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577564	+	frameshift_variant	Frame_Shift_Del	DEL	GGAACTG	GGAACTG	-	novel	NA	P-0020602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	16	722	0	ENST00000269305.4:c.717_723del	p.Ser240AlafsTer5	p.S240Afs*5	ENST00000269305	NM_001126112.2	239	aaCAGTTCC/aa	7/11	0.188813474591176	2	FACETS	1	0.886	1	0.674	0.51	0.858	INDETERMINATE	1	TRUE	0	0.339246151864428	2		722	70	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47079224	47079224	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	26	601	0	ENST00000409792.3:c.7282G>A	p.Asp2428Asn	p.D2428N	ENST00000409792	NM_014159.6	2428	Gat/Aat	18/21	0.339246151864428	3	FACETS	1	0.936	1	0.741	0.597	0.9	CLONAL	1	TRUE	1	0.339246151864428	3		601	121	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183734	10183734	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs869025617	NA	P-0020605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	134	898	0	ENST00000256474.2:c.203C>A	p.Ser68Ter	p.S68*	ENST00000256474	NM_000551.3	68	tCg/tAg	1/3	0.360658026584271	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.360658026584271	1		898	603	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916920	178916922	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0020605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	252	760	0	ENST00000263967.3:c.307_309del	p.Glu103del	p.E103del	ENST00000263967	NM_006218.2	103	GAA/-	2/21	0.353823189857071	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	0	0.360658026584271	2		760	692	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240976	53240980	+	frameshift_variant	Frame_Shift_Del	DEL	GGCAT	GGCAT	-	novel	NA	P-0020605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	97	334	0	ENST00000375401.3:c.1231_1235del	p.Met411ArgfsTer19	p.M411Rfs*19	ENST00000375401	NM_004187.3	411	ATGCCc/c	9/26	1	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.360658026584271	1		334	304	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0020607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	359	609	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.81	0.774	0.847	1	0.996	1	CLONAL	2	TRUE	1	0.59703174860197	2		610	742	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0020607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	229	396	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.500582099300236	3	FACETS	0.778	0.73	0.828	0.778	0.73	0.828	SUBCLONAL	2	TRUE	1	0.59703174860197	3		396	640	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0020607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	127	491	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	1	2	FACETS	0.826	0.752	0.903	0.826	0.752	0.903	CLONAL	1	TRUE	1	0.59703174860197	2		491	515	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0020607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	74	402	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	0.725	0.639	0.816	0.725	0.639	0.816	SUBCLONAL	1	TRUE	1	0.59703174860197	2		402	342	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913998	32913998	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	64	689	0	ENST00000380152.3:c.5506A>T	p.Asn1836Tyr	p.N1836Y	ENST00000380152		1836	Aat/Tat	11/27	0.59703174860197	7	FACETS	0.592	0.511	0.68	0.085	0.073	0.098	SUBCLONAL	1	TRUE	0	0.59703174860197	7		689	903	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610154	10610154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	245	801	0	ENST00000171111.5:c.556G>A	p.Gly186Ser	p.G186S	ENST00000171111	NM_203500.1	186	Ggc/Agc	2/6	1	2	FACETS	0.903	0.845	0.962	0.903	0.845	0.962	CLONAL	1	TRUE	1	0.59703174860197	2		801	909	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582295	119582295	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	545	428	0	ENST00000316626.5:c.1106C>G	p.Thr369Arg	p.T369R	ENST00000316626		369	aCa/aGa	10/12	0.59703174860197	3	FACETS	0.881	0.852	0.909	0.881	0.852	0.909	CLONAL	3	TRUE	0	0.59703174860197	3		428	897	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359987	87359987	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs200354354	NA	P-0020611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	10	474	0	ENST00000277120.3:c.1295C>T	p.Ser432Leu	p.S432L	ENST00000277120		432	tCg/tTg	11/19	1	2	FACETS	0.999	0.677	1	0.999	0.677	1	CLONAL	1	TRUE	1	0.11	2		474	182	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444311	50444311	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778251001	NA	P-0020611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	13	491	0	ENST00000331340.3:c.241G>A	p.Asp81Asn	p.D81N	ENST00000331340	NM_006060.4	81	Gat/Aat	4/8	1	2	FACETS	0.927	0.661	1	0.927	0.661	1	CLONAL	1	TRUE	1	0.11	2		491	255	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475064	40475064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	31	1004	0	ENST00000264657.5:c.1846G>A	p.Glu616Lys	p.E616K	ENST00000264657	NM_139276.2	616	Gaa/Aaa	20/24	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.11	2		1004	435	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61709581	61709581	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	15	665	0	ENST00000401558.2:c.2906A>G	p.Asn969Ser	p.N969S	ENST00000401558	NM_003400.3	969	aAc/aGc	23/25	1	2	FACETS	1	0.794	1	1	0.794	1	CLONAL	1	TRUE	1	0.11	2		665	247	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171920	32171920	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	17	423	0	ENST00000375023.3:c.3112C>A	p.His1038Asn	p.H1038N	ENST00000375023	NM_004557.3	1038	Cac/Aac	19/30	1	2	FACETS	0.923	0.688	1	0.923	0.688	1	CLONAL	1	TRUE	1	0.11	2		423	335	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710576	117710577	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0020611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	14	411	1	ENST00000368508.3:c.1695_1696delinsAA	p.Val566Met	p.V566M	ENST00000368508	NM_002944.2	565	tcGGtg/tcAAtg	12/43	1	2	FACETS	0.932	0.673	1	0.932	0.673	1	CLONAL	1	TRUE	1	0.11	2		412	273	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	33	613	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.661	0.536	0.803	0.661	0.536	0.803	SUBCLONAL	1	TRUE	1	0.13	2		614	768	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0020615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	349	985	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.457652054124307	2	FACETS	0.87	0.827	0.913	0.87	0.827	0.913	CLONAL	2	TRUE	0	0.468825154064876	2		985	856	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	96	702	6	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	0.255108154446992	2		708	644	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	65	462	1	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.255108154446992	2		463	430	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	158	1984	5	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.255108154446992	2		1989	1189	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919466	78919466	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	116	879	0	ENST00000306801.3:c.3026-1G>T		p.X1009_splice	ENST00000306801	NM_020761.2	1009			1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.255108154446992	2		879	853	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089706	27089706	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	113	937	0	ENST00000324856.7:c.2666del	p.Gly889AlafsTer2	p.G889Afs*2	ENST00000324856	NM_006015.4	888	Ggg/gg	8/20	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.255108154446992	2		937	829	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968322	2968323	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs762770988	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	119	969	4	ENST00000396946.4:c.1663dup	p.Arg555ProfsTer38	p.R555Pfs*38	ENST00000396946	NM_032415.4	555	cgg/cCgg	13/25	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.255108154446992	2		973	879	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123688	11123688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	127	1024	0	ENST00000358026.2:c.2338G>A	p.Glu780Lys	p.E780K	ENST00000358026	NM_001128849.1	780	Gag/Aag	16/36	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.255108154446992	2		1024	967	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882049	36882050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs780753361	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	130	1166	5	ENST00000358127.4:c.963dup	p.Ala322ArgfsTer19	p.A322Rfs*19	ENST00000358127	NM_001280556.1	321	-/C	8/10	0.255108154446992	3	FACETS	0.981	0.887	1	0.49	0.443	0.54	CLONAL	1	TRUE	1	0.255108154446992	3		1171	1172	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794441	42794441	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	116	1331	2	ENST00000575354.2:c.1526del	p.Pro509HisfsTer14	p.P509Hfs*14	ENST00000575354	NM_015125.3	507	cgC/cg	10/20	NA	2	FACETS	0.763	0.686	0.845			1	INDETERMINATE	1	TRUE	NA	0.255108154446992	2		1333	1192	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257144	19257144	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	97	239	1	ENST00000162023.5:c.819del	p.Thr274ProfsTer?	p.T274Pfs*?	ENST00000162023		273	ccC/cc	12/13	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.255108154446992	2		240	670	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793677	89793677	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	56	564	1	ENST00000336032.3:c.752del	p.Lys251SerfsTer14	p.K251Sfs*14	ENST00000336032	NM_006813.2	249	gAa/ga	2/2	1	2	FACETS	0.785	0.673	0.908	0.785	0.673	0.908	CLONAL	1	TRUE	1	0.255108154446992	2		565	559	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156823	106156823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199640757	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	113	787	1	ENST00000380013.4:c.1724C>T	p.Ala575Val	p.A575V	ENST00000380013	NM_001127208.2	575	gCg/gTg	3/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.255108154446992	2		788	769	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971053	21971053	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137854598	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	71	692	0	ENST00000304494.5:c.305C>T	p.Ala102Val	p.A102V	ENST00000304494	NM_000077.4	102	gCg/gTg	2/3	0.255108154446992	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.255108154446992	1		692	461	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264985	46264985	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	199	734	0	ENST00000371998.3:c.1860del	p.Lys620AsnfsTer18	p.K620Nfs*18	ENST00000371998		619	Aaa/aa	12/23	0.255108154446992	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.255108154446992	2		734	688	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467573	66467573	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	62	626	0	ENST00000273854.3:c.696del	p.Lys232AsnfsTer36	p.K232Nfs*36	ENST00000273854	NM_004439.5	232	aaA/aa	3/18	1	2	FACETS	0.856	0.739	0.982	0.856	0.739	0.982	CLONAL	1	TRUE	1	0.255108154446992	2		626	568	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346157	89346158	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs878855327	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	30	357	0	ENST00000301030.4:c.6792dup	p.Ala2265ArgfsTer8	p.A2265Rfs*8	ENST00000301030	NM_001256183.1	2264	-/C	9/13	1	2	FACETS	0.751	0.607	0.915	0.751	0.607	0.915	CLONAL	1	TRUE	1	0.255108154446992	2		357	313	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955111	17955112	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755706305	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	122	1097	1	ENST00000458235.1:c.115dup	p.Gln39ProfsTer13	p.Q39Pfs*13	ENST00000458235	NM_000215.3	39	cag/cCag	2/24	1	2	FACETS	0.901	0.813	0.995	0.901	0.813	0.995	CLONAL	1	TRUE	1	0.255108154446992	2		1098	1061	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217705	7217707	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs757139280	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	72	744	0	ENST00000380728.2:c.220_222del	p.Glu74del	p.E74del	ENST00000380728		74	GAG/-	4/11	0.255108154446992	1	FACETS	0.819	0.716	0.931	0.819	0.716	0.931	CLONAL	1	TRUE	0	0.255108154446992	1		744	601	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885578	111885578	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs751470371	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	123	1141	0	ENST00000341259.2:c.1355C>G	p.Ala452Gly	p.A452G	ENST00000341259	NM_005475.2	452	gCc/gGc	7/8	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.255108154446992	2		1141	903	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385108	41385108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776607737	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	122	941	1	ENST00000373198.4:c.853G>A	p.Val285Met	p.V285M	ENST00000373198	NM_133170.3	285	Gtg/Atg	6/32	0.255108154446992	3	FACETS	1	0.943	1	0.532	0.48	0.587	CLONAL	1	TRUE	1	0.255108154446992	3		942	1014	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	128	1099	7	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.255108154446992	2		1106	847	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317133	11317133	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	120	1016	0	ENST00000361445.4:c.361G>T	p.Val121Phe	p.V121F	ENST00000361445	NM_004958.3	121	Gtt/Ttt	4/58	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.255108154446992	2		1016	888	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195383	102195383	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	70	616	0	ENST00000263464.3:c.143G>T	p.Arg48Met	p.R48M	ENST00000263464	NM_001165.4	48	aGg/aTg	2/9	1	2	FACETS	0.976	0.852	1	0.976	0.852	1	CLONAL	1	TRUE	1	0.255108154446992	2		616	562	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434648	49434648	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	131	1316	2	ENST00000301067.7:c.6905del	p.Pro2302GlnfsTer20	p.P2302Qfs*20	ENST00000301067	NM_003482.3	2302	cCa/ca	31/54	1	2	FACETS	0.987	0.894	1	0.987	0.894	1	CLONAL	1	TRUE	1	0.255108154446992	2		1318	1041	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609983	81609983	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	62	430	0	ENST00000298171.2:c.1581G>T	p.Met527Ile	p.M527I	ENST00000298171	NM_000369.2	527	atG/atT	10/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.255108154446992	2		430	369	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576121	88576121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374272958	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	99	1154	4	ENST00000360948.2:c.1552C>T	p.Arg518Cys	p.R518C	ENST00000360948	NM_001012338.2	518	Cgt/Tgt	13/19	1	2	FACETS	0.862	0.769	0.962	0.862	0.769	0.962	CLONAL	1	TRUE	1	0.255108154446992	2		1158	900	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032068	10032068	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	114	821	1	ENST00000330684.3:c.755A>G	p.Asp252Gly	p.D252G	ENST00000330684	NM_001134407.1	252	gAt/gGt	3/13	0.255108154446992	3	FACETS	1	0.958	1	0.562	0.505	0.622	CLONAL	1	TRUE	1	0.255108154446992	3		822	897	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274173	10274173	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	84	690	4	ENST00000330684.3:c.96del	p.Ala33ArgfsTer2	p.A33Rfs*2	ENST00000330684	NM_001134407.1	32	ccC/cc	2/13	0.255108154446992	3	FACETS	1	0.922	1	0.529	0.467	0.595	CLONAL	1	TRUE	1	0.255108154446992	3		694	702	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347164	89347164	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	93	816	1	ENST00000301030.4:c.5786G>T	p.Ser1929Ile	p.S1929I	ENST00000301030	NM_001256183.1	1929	aGc/aTc	9/13	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.255108154446992	2		817	708	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029416	16029416	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	132	1022	1	ENST00000268712.3:c.1614del	p.Asp539MetfsTer16	p.D539Mfs*16	ENST00000268712	NM_006311.3	538	aaA/aa	15/46	0.255108154446992	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.255108154446992	1		1023	760	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663430	29663430	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	86	862	3	ENST00000356175.3:c.6023A>G	p.Glu2008Gly	p.E2008G	ENST00000356175	NM_000267.3	2008	gAg/gGg	40/57	1	2	FACETS	0.944	0.835	1	0.944	0.835	1	CLONAL	1	TRUE	1	0.255108154446992	2		865	714	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435455	56435455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs553934414	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	142	980	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	0.255108154446992	2		980	846	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228560	36228560	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1337884328	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	131	1127	0	ENST00000222270.7:c.7574A>G	p.Asn2525Ser	p.N2525S	ENST00000222270	NM_014727.1	2525	aAc/aGc	34/37	0.255108154446992	3	FACETS	0.977	0.885	1	0.489	0.442	0.538	CLONAL	1	TRUE	1	0.255108154446992	3		1127	1185	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762465	41762465	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	201	826	0	ENST00000301178.4:c.2145G>T	p.Trp715Cys	p.W715C	ENST00000301178	NM_021913.4	715	tgG/tgT	18/20	0.255108154446992	3	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	1	0.255108154446992	3		826	870	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795734	42795734	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	149	1208	1	ENST00000575354.2:c.2726del	p.Pro909ArgfsTer15	p.P909Rfs*15	ENST00000575354	NM_015125.3	908	gCc/gc	11/20	NA	2	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.255108154446992	2		1209	1100	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702326	47702326	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	86	852	0	ENST00000233146.2:c.1922del	p.Cys641LeufsTer44	p.C641Lfs*44	ENST00000233146	NM_000251.2	641	tGt/tt	12/16	0.255108154446992	1	FACETS	0.999	0.885	1	0.999	0.885	1	CLONAL	1	TRUE	0	0.255108154446992	1		852	589	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442033	52442033	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754385495	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	102	869	1	ENST00000460680.1:c.316G>A	p.Val106Met	p.V106M	ENST00000460680	NM_004656.3	106	Gtg/Atg	5/17	0.255108154446992	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.255108154446992	1		870	648	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134514496	134514496	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1245944825	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	99	817	0	ENST00000398015.3:c.23T>C	p.Leu8Pro	p.L8P	ENST00000398015	NM_004441.4	8	cTg/cCg	1/16	0.255108154446992	3	FACETS	1	0.926	1	0.525	0.468	0.585	CLONAL	1	TRUE	1	0.255108154446992	3		817	834	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177655	56177656	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	51	604	0	ENST00000399503.3:c.2629_2630del	p.Leu877GlyfsTer26	p.L877Gfs*26	ENST00000399503	NM_005921.1	876	acTTtg/actg	14/20	1	2	FACETS	0.742	0.63	0.864	0.742	0.63	0.864	SUBCLONAL	1	TRUE	1	0.255108154446992	2		604	539	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590386	67590386	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	39	284	2	ENST00000274335.5:c.1448C>T	p.Ala483Val	p.A483V	ENST00000274335		483	gCt/gTt	11/15	1	2	FACETS	0.98	0.815	1	0.98	0.815	1	CLONAL	1	TRUE	1	0.255108154446992	2		286	312	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324663	31324664	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	38	374	0	ENST00000412585.2:c.144_145del	p.Val49GlyfsTer49	p.V49Gfs*49	ENST00000412585	NM_005514.6	48	tcAGtg/tctg	2/8	0.255108154446992	1	FACETS	0.899	0.747	1	0.899	0.747	1	CLONAL	1	TRUE	0	0.255108154446992	1		374	289	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528013	157528013	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1476439304	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	106	797	1	ENST00000346085.5:c.5738A>G	p.His1913Arg	p.H1913R	ENST00000346085	NM_020732.3	1913	cAc/cGc	20/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.255108154446992	2		798	728	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528283	157528284	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	123	1061	0	ENST00000346085.5:c.6013dup	p.Val2005GlyfsTer7	p.V2005Gfs*7	ENST00000346085	NM_020732.3	2003	aag/aaGg	20/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.255108154446992	2		1061	921	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350061	81350061	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs867372392	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	73	588	0	ENST00000222390.5:c.1271G>A	p.Arg424His	p.R424H	ENST00000222390	NM_000601.4	424	cGt/cAt	10/18	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.255108154446992	2		588	546	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845472	128845472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1428746507	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	136	1026	6	ENST00000249373.3:c.769C>T	p.Arg257Trp	p.R257W	ENST00000249373	NM_005631.4	257	Cgg/Tgg	4/12	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.255108154446992	2		1032	965	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992720	68992721	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs764112302	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	210	1092	11	ENST00000288368.4:c.1693dup	p.Ser565PhefsTer3	p.S565Ffs*3	ENST00000288368	NM_024870.2	562	cgt/cgTt	16/40	0.255108154446992	3	FACETS	0.97	0.901	1	0.97	0.901	1	CLONAL	2	TRUE	1	0.255108154446992	3		1103	957	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554341	141554341	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564077207	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	161	1233	5	ENST00000220592.5:c.1810G>A	p.Gly604Arg	p.G604R	ENST00000220592	NM_012154.3	604	Ggg/Agg	14/19	0.255108154446992	3	FACETS	1	0.962	1	0.546	0.499	0.595	CLONAL	1	TRUE	1	0.255108154446992	3		1238	1303	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570409	87570409	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	96	1006	1	ENST00000277120.3:c.2149G>A	p.Val717Met	p.V717M	ENST00000277120		717	Gtg/Atg	17/19	0.255108154446992	3	FACETS	0.838	0.745	0.937	0.419	0.372	0.469	CLONAL	1	TRUE	1	0.255108154446992	3		1007	1013	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341286	70341286	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1278775881	NA	P-0020616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	96	376	0	ENST00000374080.3:c.845G>A	p.Arg282Gln	p.R282Q	ENST00000374080		282	cGa/cAa	6/45	1	1	FACETS	0.93	0.836	1	1	0.986	1	CLONAL	2	TRUE	0	0.255108154446992	1		376	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0020617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	105	661	1	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.246335797026586	1	FACETS	0.986	0.884	1	0.986	0.884	1	CLONAL	1	TRUE	0	0.246335797026586	1		662	758	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120795681	120795681	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	87	598	0	ENST00000257552.2:c.472G>C	p.Glu158Gln	p.E158Q	ENST00000257552	NM_002442.3	158	Gag/Cag	8/15	1	2	FACETS	0.816	0.721	0.917	0.816	0.721	0.917	CLONAL	1	TRUE	1	0.246335797026586	2		598	866	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693929	47693929	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	93	812	1	ENST00000233146.2:c.1643G>A	p.Gly548Asp	p.G548D	ENST00000233146	NM_000251.2	548	gGt/gAt	10/16	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.762281523635829	2		813	233	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0020620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	14	421	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	0.159113499710759	2	FACETS	0.362	0.261	0.486	0.181	0.13	0.243	SUBCLONAL	1	TRUE	0	0.229259000173061	2		421	337	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0020620-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	58	421	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	0.519890322200568	2	FACETS	0.497	0.428	0.571	0.248	0.214	0.286	SUBCLONAL	1	TRUE	0	0.568048405161797	2		421	411	SUCCESS
ATR	545	MSKCC	GRCh37	3	142234310	142234310	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020620-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	76	765	0	ENST00000350721.4:c.4430C>G	p.Pro1477Arg	p.P1477R	ENST00000350721	NM_001184.3	1477	cCa/cGa	25/47	0.519890322200568	2	FACETS	0.513	0.45	0.579	0.256	0.225	0.29	SUBCLONAL	1	TRUE	0	0.568048405161797	2		765	522	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578446	7578479	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCCATGGCGCGGACGCGGGTGCCGGGCGGGGG	TGGCCATGGCGCGGACGCGGGTGCCGGGCGGGGG	-	novel	NA	P-0020621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	520	893	0	ENST00000269305.4:c.451_484del	p.Pro151SerfsTer8	p.P151Sfs*8	ENST00000269305	NM_001126112.2	151	CCCCCGCCCGGCACCCGCGTCCGCGCCATGGCCAtc/tc	5/11	0.671907085894561	3	FACETS	0.938	0.911	0.964	0.938	0.911	0.964	CLONAL	3	TRUE	0	0.671907085894561	3		893	735	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218456	1218456	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	109	834	0	ENST00000326873.7:c.331A>T	p.Ile111Phe	p.I111F	ENST00000326873	NM_000455.4	111	Atc/Ttc	2/10	0.671907085894561	1	FACETS	0.525	0.475	0.578	0.525	0.475	0.578	SUBCLONAL	1	TRUE	0	0.671907085894561	1		834	410	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42843733	42843733	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs758128660	NA	P-0020621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	87	595	1	ENST00000398585.3:c.1186G>A	p.Asp396Asn	p.D396N	ENST00000398585	NM_001135099.1	396	Gac/Aac	10/14	0.187448829408231	3	FACETS	0.856	0.763	0.955	0.285	0.254	0.319	INDETERMINATE	1	TRUE	0	0.671907085894561	3		596	404	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86686687	86686687	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs764515827	NA	P-0020621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	97	450	0	ENST00000274376.6:c.3131A>G	p.Asn1044Ser	p.N1044S	ENST00000274376	NM_002890.2	1044	aAt/aGt	25/25	0.311610718660397	6	FACETS	1	0.98	1	0.362	0.324	0.402	INDETERMINATE	1	TRUE	2	0.671907085894561	6		450	467	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0020622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	40	390	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.186063869000885	5	FACETS	1	0.885	1	0.699	0.594	0.81	INDETERMINATE	2	TRUE	2	0.546093832894246	5		390	127	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37665992	37665992	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1293	74	554	0	ENST00000447079.4:c.2644C>T	p.Arg882Trp	p.R882W	ENST00000447079	NM_015083.1	882	Cgg/Tgg	7/14	0.546093832894246	38	FACETS	1	0.919	1			1	CLONAL	2	TRUE	NA	0.546093832894246	38		554	1367	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577563	7577565	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0020622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	63	758	1	ENST00000269305.4:c.716_718del	p.Asn239del	p.N239del	ENST00000269305	NM_001126112.2	239	aACAgt/agt	7/11	0.357625662997669	2	FACETS	1	0.964	1	0.634	0.559	0.712	CLONAL	1	TRUE	0	0.546093832894246	2		759	182	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900884	3900884	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	35	749	0	ENST00000262367.5:c.212C>G	p.Ser71Trp	p.S71W	ENST00000262367	NM_004380.2	71	tCg/tGg	2/31	1	2	FACETS	0.631	0.522	0.752	0.631	0.522	0.752	SUBCLONAL	1	TRUE	1	0.546093832894246	2		749	203	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50830294	50830294	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	26	575	1	ENST00000398568.2:c.2737T>A	p.Leu913Met	p.L913M	ENST00000398568	NM_001042412.1	913	Ttg/Atg	18/18	0.496310190473088	1	FACETS	0.641	0.518	0.776	0.641	0.518	0.776	SUBCLONAL	1	TRUE	0	0.546093832894246	1		576	108	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0020626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	209	637	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	0.132574322673865	3	FACETS	1	0.993	1	0.746	0.701	0.79	INDETERMINATE	1	TRUE	1	0.937797555609037	3		637	439	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412493	80412493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514698	NA	P-0020626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	228	618	0	ENST00000286548.4:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000286548	NM_002072.3	183	cGa/cAa	4/7	1	2	FACETS	0.904	0.85	0.958	0.904	0.85	0.958	CLONAL	1	TRUE	1	0.937797555609037	2		618	538	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582120	189582120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	103	734	0	ENST00000264731.3:c.679G>A	p.Ala227Thr	p.A227T	ENST00000264731	NM_003722.4	227	Gcc/Acc	5/14	0.937797555609037	1	FACETS	0.49	0.447	0.534	0.49	0.447	0.534	SUBCLONAL	1	TRUE	0	0.937797555609037	1		734	238	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652020	36652020	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1407742055	NA	P-0020626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	398	1044	1	ENST00000244741.5:c.142C>T	p.Arg48Ter	p.R48*	ENST00000244741	NM_000389.4	48	Cga/Tga	2/3	0.132574322673865	3	FACETS	0.757	0.725	0.79	0.757	0.725	0.79	INDETERMINATE	2	TRUE	1	0.937797555609037	3		1045	823	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229617	5229617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064295	NA	P-0020626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	60	162	1	ENST00000357368.4:c.2234C>T	p.Ala745Val	p.A745V	ENST00000357368	NM_002850.3	745	gCg/gTg	15/38	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.937797555609037	2		163	118	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803121	1803121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745863884	NA	P-0020626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	297	1036	0	ENST00000260795.2:c.473G>A	p.Arg158Gln	p.R158Q	ENST00000260795		158	cGg/cAg	4/17	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.937797555609037	2		1036	595	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127262	17127262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200168437	NA	P-0020626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	259	813	0	ENST00000285071.4:c.592G>A	p.Asp198Asn	p.D198N	ENST00000285071	NM_144997.5	198	Gat/Aat	6/14	0.333006492059378	3	FACETS	1	0.994	1	0.742	0.702	0.782	INDETERMINATE	1	TRUE	1	0.937797555609037	3		813	547	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158626924	158626924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760152551	NA	P-0020626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	35	795	0	ENST00000263640.3:c.746C>T	p.Thr249Met	p.T249M	ENST00000263640	NM_001105.4	249	aCg/aTg	7/11	0.132574322673865	3	FACETS	0.206	0.168	0.248	0.103	0.084	0.124	INDETERMINATE	1	TRUE	1	0.937797555609037	3		795	533	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442567	52442567	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1253151209	NA	P-0020626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	314	655	1	ENST00000460680.1:c.178C>T	p.Arg60Ter	p.R60*	ENST00000460680	NM_004656.3	60	Cga/Tga	4/17	0.928253315210312	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.937797555609037	1		656	340	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253953	133253953	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115786159	NA	P-0020626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	34	933	0	ENST00000320574.5:c.797G>A	p.Arg266Gln	p.R266Q	ENST00000320574	NM_006231.2	266	cGa/cAa	8/49	1	2	FACETS	0.116	0.094	0.141	0.116	0.094	0.141	SUBCLONAL	1	TRUE	1	0.937797555609037	2		933	623	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46736426	46736426	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150138364	NA	P-0020626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	301	818	0	ENST00000371975.4:c.1138C>T	p.Arg380Trp	p.R380W	ENST00000371975	NM_003579.3	380	Cgg/Tgg	10/18	1	2	FACETS	0.94	0.892	0.988	0.94	0.892	0.988	CLONAL	1	TRUE	1	0.937797555609037	2		818	683	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138082	64138082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1328444508	NA	P-0020626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	387	1067	2	ENST00000334205.4:c.2005C>T	p.Arg669Trp	p.R669W	ENST00000334205	NM_003942.2	669	Cgg/Tgg	16/17	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.937797555609037	2		1069	784	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416861	121416861	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374794304	NA	P-0020626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	310	1252	4	ENST00000257555.6:c.290C>T	p.Ala97Val	p.A97V	ENST00000257555		97	gCg/gTg	1/10	1	2	FACETS	0.953	0.905	1	0.953	0.905	1	CLONAL	1	TRUE	1	0.937797555609037	2		1256	694	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2115581	2115581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45471596	NA	P-0020626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	308	1144	0	ENST00000219476.3:c.1661C>T	p.Ser554Leu	p.S554L	ENST00000219476	NM_000548.3	554	tCg/tTg	16/42	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.937797555609037	2		1144	657	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828015	72828015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745989025	NA	P-0020626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	301	1161	0	ENST00000268489.5:c.8566G>A	p.Asp2856Asn	p.D2856N	ENST00000268489	NM_006885.3	2856	Gac/Aac	9/10	NA	2	FACETS	0.945	0.897	0.994			1	INDETERMINATE	1	TRUE	NA	0.937797555609037	2		1161	679	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806242	1806242	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	271	984	0	ENST00000260795.2:c.1261C>T	p.Arg421Ter	p.R421*	ENST00000260795		421	Cga/Tga	8/17	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.937797555609037	2		984	542	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818275	32818275	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754828996	NA	P-0020626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	323	851	0	ENST00000354258.4:c.1250G>A	p.Arg417Gln	p.R417Q	ENST00000354258	NM_000593.5	417	cGg/cAg	5/11	0.132574322673865	3	FACETS	1	0.994	1	0.673	0.639	0.707	INDETERMINATE	1	TRUE	1	0.937797555609037	3		851	752	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508236	106508236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	141	470	0	ENST00000359195.3:c.230G>A	p.Arg77Gln	p.R77Q	ENST00000359195	NM_002649.2	77	cGa/cAa	2/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.937797555609037	2		470	289	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781403	135781403	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759379027	NA	P-0020626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	251	865	0	ENST00000298552.3:c.1562C>T	p.Ser521Leu	p.S521L	ENST00000298552	NM_001162426.1	521	tCg/tTg	15/23	NA	2	FACETS	0.947	0.895	1			1	INDETERMINATE	1	TRUE	NA	0.937797555609037	2		865	565	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860121	152860121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782206940	NA	P-0020626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	122	985	0	ENST00000406277.2:c.307G>A	p.Gly103Ser	p.G103S	ENST00000406277	NM_152274.4	103	Ggt/Agt	5/7	0.634030520690276		FACETS		0.257	0.31				SUBCLONAL	1	TRUE	0	0.937797555609037	1		985	489	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152864483	152864483	+	synonymous_variant	Silent	SNP	C	C	T	rs1557027784	NA	P-0020626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	18	109	0	ENST00000406277.2:c.45G>A	p.Pro15=	p.P15=	ENST00000406277	NM_152274.4	15	ccG/ccA	2/7	0.634030520690276		FACETS		0.26	0.416				SUBCLONAL	1	TRUE	0	0.937797555609037	1		109	61	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0020628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	151	845	1	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	0.240136335683438	3	FACETS	0.782	0.716	0.851	0.782	0.716	0.851	SUBCLONAL	2	TRUE	1	0.3	3		846	740	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100669	8100669	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	51	1202	0	ENST00000346208.3:c.643A>G	p.Thr215Ala	p.T215A	ENST00000346208		215	Acc/Gcc	3/6	1	2	FACETS	0.394	0.334	0.461	0.394	0.334	0.461	SUBCLONAL	1	TRUE	1	0.3	2		1202	863	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37876038	37876038	+	splice_acceptor_variant	In_Frame_Del	SNP	A	A	G	novel	NA	P-0020628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	285	1073	0	ENST00000269571.5:c.1899-2A>G		p.C634_S649del	ENST00000269571		634			0.220545021464	5	FACETS	1	0.988	1	0.789	0.741	0.838	CLONAL	2	TRUE	2	0.3	5		1073	1164	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0020629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	8	328	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		328	364	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	178	251	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.832	0.767	0.901	0.832	0.767	0.901	CLONAL	1	TRUE	1	0.439591336836046	2		251	973	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591129	67591130	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0020630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	94	339	0	ENST00000274335.5:c.1723_1724del	p.Lys575AspfsTer26	p.K575Dfs*26	ENST00000274335		574	agAAag/agag	12/15	1	2	FACETS	0.822	0.734	0.916	0.822	0.734	0.916	CLONAL	1	TRUE	1	0.439591336836046	2		339	520	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	100	372	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.379745964718126	3	FACETS	0.84	0.761	0.922	0.84	0.761	0.922	CLONAL	2	TRUE	1	0.507565220592683	3		373	294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0020631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	731	651	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.428745504189407	2	FACETS	0.871	0.842	0.9	0.871	0.842	0.9	CLONAL	2	TRUE	0	0.507565220592683	2		651	1654	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258959	153258959	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0020631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	23	377	0	ENST00000281708.4:c.856A>T	p.Lys286Ter	p.K286*	ENST00000281708	NM_033632.3	286	Aaa/Taa	5/12	0.244953477937338	3	FACETS	1	0.865	1	0.715	0.585	0.848	INDETERMINATE	2	TRUE	0	0.507565220592683	3		377	53	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971206	21971219	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACCTGCCAGAGAGA	ACCTGCCAGAGAGA	-	novel	NA	P-0020631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	217	616	0	ENST00000304494.5:c.151-12_152del		p.X51_splice	ENST00000304494	NM_000077.4	51		2/3	0.395664310472739	1	FACETS	0.626	0.581	0.671	0.626	0.581	0.671	SUBCLONAL	1	TRUE	0	0.507565220592683	1		616	1020	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520006	NA	P-0020632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	294	870	0	ENST00000269305.4:c.821T>C	p.Val274Ala	p.V274A	ENST00000269305	NM_001126112.2	274	gTt/gCt	8/11	0.357454198162886	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.357454198162886	1		870	983	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	150	537	3	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.357454198162886	2		540	621	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779258	3779258	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	80	480	0	ENST00000262367.5:c.5790del	p.Thr1931ProfsTer45	p.T1931Pfs*45	ENST00000262367	NM_004380.2	1930	ccC/cc	31/31	1	2	FACETS	0.84	0.741	0.946	0.84	0.741	0.946	CLONAL	1	TRUE	1	0.357454198162886	2		480	533	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380272	25380273	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCTTGACCTGCTGTGTCGAGAATATCCAAGAGACAGGTTTCT	novel	NA	P-0020632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	60	696	0	ENST00000311936.3:c.144_185dup	p.Thr50_Glu63dup	p.T50_E63dup	ENST00000311936	NM_004985.3	50	gag/gaAGAAACCTGTCTCTTGGATATTCTCGACACAGCAGGTCAAGAg	3/5	1	2	FACETS	0.415	0.357	0.479	0.415	0.357	0.479	SUBCLONAL	1	TRUE	1	0.357454198162886	2		696	808	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211073	36211073	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	234	1019	0	ENST00000222270.7:c.824G>C	p.Gly275Ala	p.G275A	ENST00000222270	NM_014727.1	275	gGa/gCa	3/37	1	2	FACETS	0.97	0.903	1	0.97	0.903	1	CLONAL	1	TRUE	1	0.357454198162886	2		1019	1350	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40828013	40828013	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	69	413	0	ENST00000373198.4:c.2415G>T	p.Lys805Asn	p.K805N	ENST00000373198	NM_133170.3	805	aaG/aaT	17/32	1	2	FACETS	0.667	0.581	0.759	0.667	0.581	0.759	SUBCLONAL	1	TRUE	1	0.357454198162886	2		413	579	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205156	128205156	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	199	772	0	ENST00000341105.2:c.285G>C	p.Leu95Phe	p.L95F	ENST00000341105	NM_032638.4	95	ttG/ttC	3/6	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.357454198162886	2		772	1012	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	73	134	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.934	0.82	1	0.934	0.82	1	CLONAL	1	TRUE	1	0.359211137109049	2		134	435	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	183	619	8	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	0.359211137109049	2		627	946	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	197	229	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.359211137109049	2		229	1033	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188513	11188513	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	89	561	3	ENST00000361445.4:c.5908del	p.Gln1970ArgfsTer7	p.Q1970Rfs*7	ENST00000361445	NM_004958.3	1970	Cag/ag	42/58	1	2	FACETS	0.724	0.642	0.812	0.724	0.642	0.812	SUBCLONAL	1	TRUE	1	0.359211137109049	2		564	684	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551952	150551952	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	243	914	3	ENST00000369026.2:c.55del	p.Ala19ProfsTer30	p.A19Pfs*30	ENST00000369026	NM_021960.4	19	Gcc/cc	1/3	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.359211137109049	2		917	1078	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097739	8097739	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	259	996	0	ENST00000346208.3:c.121T>C	p.Tyr41His	p.Y41H	ENST00000346208		41	Tac/Cac	2/6	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.359211137109049	2		996	1197	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852118	63852118	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	166	757	3	ENST00000279873.7:c.2901del	p.Lys967AsnfsTer15	p.K967Nfs*15	ENST00000279873	NM_032199.2	966	Aaa/aa	10/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.359211137109049	2		760	882	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446284	70446284	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	203	784	0	ENST00000373644.4:c.5230del	p.Arg1744GlufsTer18	p.R1744Efs*18	ENST00000373644	NM_030625.2	1742	Aaa/aa	11/12	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.359211137109049	2		784	976	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	137	866	2	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.953	0.868	1	0.953	0.868	1	CLONAL	1	TRUE	1	0.359211137109049	2		868	800	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903745	114903745	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	234	870	0	ENST00000543371.1:c.749T>C	p.Val250Ala	p.V250A	ENST00000543371	NM_001198531.1	250	gTa/gCa	7/14	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.359211137109049	2		870	1176	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276964	123276964	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	86	426	0	ENST00000358487.5:c.953A>G	p.Asn318Ser	p.N318S	ENST00000358487	NM_000141.4	318	aAc/aGc	8/18	1	2	FACETS	0.917	0.814	1	0.917	0.814	1	CLONAL	1	TRUE	1	0.359211137109049	2		426	522	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	221	981	0	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.359211137109049	2		981	1096	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201783	102201783	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs776315214	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	120	654	0	ENST00000263464.3:c.1135A>G	p.Thr379Ala	p.T379A	ENST00000263464	NM_001165.4	379	Act/Gct	6/9	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.359211137109049	2		654	592	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124653	108124653	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs730881344	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	122	802	0	ENST00000278616.4:c.2011A>G	p.Ile671Val	p.I671V	ENST00000278616	NM_000051.3	671	Ata/Gta	13/63	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.359211137109049	2		802	643	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498235	498235	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	86	325	1	ENST00000399788.2:c.23del	p.Gly8AlafsTer58	p.G8Afs*58	ENST00000399788	NM_001042603.1	8	gGc/gc	1/28	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.359211137109049	2		326	351	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18649063	18649063	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761182298	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	81	663	3	ENST00000266497.5:c.2738G>A	p.Gly913Asp	p.G913D	ENST00000266497		913	gGc/gAc	19/31	1	2	FACETS	0.953	0.843	1	0.953	0.843	1	CLONAL	1	TRUE	1	0.359211137109049	2		666	473	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425056	49425056	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs562043836	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1213	315	1306	2	ENST00000301067.7:c.13432C>T	p.Arg4478Trp	p.R4478W	ENST00000301067	NM_003482.3	4478	Cgg/Tgg	39/54	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.359211137109049	2		1308	1528	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427275	49427275	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	171	823	0	ENST00000301067.7:c.11213A>C	p.Gln3738Pro	p.Q3738P	ENST00000301067	NM_003482.3	3738	cAg/cCg	39/54	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.359211137109049	2		823	857	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448480	49448480	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	209	841	0	ENST00000301067.7:c.231del	p.His77GlnfsTer53	p.H77Qfs*53	ENST00000301067	NM_003482.3	77	caC/ca	3/54	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.359211137109049	2		841	1013	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861886	57861886	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754780184	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	218	797	2	ENST00000228682.2:c.1187G>A	p.Arg396Gln	p.R396Q	ENST00000228682	NM_005269.2	396	cGg/cAg	10/12	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.359211137109049	2		799	956	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885554	111885554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768630945	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	288	1231	2	ENST00000341259.2:c.1331C>T	p.Ser444Leu	p.S444L	ENST00000341259	NM_005475.2	444	tCg/tTg	7/8	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.359211137109049	2		1233	1366	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240628	133240628	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs749012938	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	225	808	0	ENST00000320574.5:c.2668A>G	p.Ile890Val	p.I890V	ENST00000320574	NM_006231.2	890	Atc/Gtc	23/49	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.359211137109049	2		808	966	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953616	32953616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45469092	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	82	657	0	ENST00000380152.3:c.8917C>T	p.Arg2973Cys	p.R2973C	ENST00000380152		2973	Cgt/Tgt	22/27	1	2	FACETS	0.865	0.764	0.972	0.865	0.764	0.972	CLONAL	1	TRUE	1	0.359211137109049	2		657	528	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919327	48919327	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	48	341	0	ENST00000267163.4:c.492A>T	p.Lys164Asn	p.K164N	ENST00000267163	NM_000321.2	164	aaA/aaT	4/27	1	2	FACETS	0.791	0.671	0.921	0.791	0.671	0.921	CLONAL	1	TRUE	1	0.359211137109049	2		341	338	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434598	110434598	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759219550	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	364	1266	0	ENST00000375856.3:c.3803C>T	p.Pro1268Leu	p.P1268L	ENST00000375856	NM_003749.2	1268	cCg/cTg	1/2	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.359211137109049	2		1266	1447	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093360	30093360	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	130	754	0	ENST00000331968.5:c.1903C>T	p.Gln635Ter	p.Q635*	ENST00000331968	NM_002742.2	635	Cag/Tag	13/18	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.359211137109049	2		754	615	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571499	95571499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555370020	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	167	612	0	ENST00000393063.1:c.3178C>T	p.Arg1060Cys	p.R1060C	ENST00000393063	NM_030621.3	1060	Cgc/Tgc	21/28	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.359211137109049	2		612	824	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242084	105242084	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	316	1264	0	ENST00000349310.3:c.340G>C	p.Glu114Gln	p.E114Q	ENST00000349310	NM_001014432.1	114	Gag/Cag	6/15	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.359211137109049	2		1264	1457	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028724	42028724	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	170	831	0	ENST00000219905.7:c.4262T>A	p.Leu1421Ter	p.L1421*	ENST00000219905	NM_001164273.1	1421	tTg/tAg	13/24	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.359211137109049	2		831	767	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43700287	43700287	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	178	915	0	ENST00000382044.4:c.5601-1G>A		p.X1867_splice	ENST00000382044	NM_001141980.1	1867			1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.359211137109049	2		915	948	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007681	45007681	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	94	533	0	ENST00000558401.1:c.128T>C	p.Leu43Pro	p.L43P	ENST00000558401	NM_004048.2	43	cTg/cCg	2/4	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.359211137109049	2		533	520	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	126	345	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.359211137109049	2		345	554	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339452	339452	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	190	1140	0	ENST00000262320.3:c.2450A>G	p.Lys817Arg	p.K817R	ENST00000262320	NM_003502.3	817	aAg/aGg	10/11	1	2	FACETS	0.809	0.746	0.875	0.809	0.746	0.875	CLONAL	1	TRUE	1	0.359211137109049	2		1140	1308	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649272	23649272	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs202194596	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	28	569	0	ENST00000261584.4:c.110G>A	p.Arg37His	p.R37H	ENST00000261584	NM_024675.3	37	cGt/cAt	3/13	1	2	FACETS	0.321	0.256	0.396	0.321	0.256	0.396	SUBCLONAL	1	TRUE	1	0.359211137109049	2		569	485	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835781	68835781	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060501215	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	202	831	0	ENST00000261769.5:c.377del	p.Pro126ArgfsTer89	p.P126Rfs*89	ENST00000261769	NM_004360.3	124	cgC/cg	3/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.359211137109049	2		831	1045	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849467	68849467	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778170	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	219	904	1	ENST00000261769.5:c.1370C>T	p.Thr457Met	p.T457M	ENST00000261769	NM_004360.3	457	aCg/aTg	10/16	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.359211137109049	2		905	982	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989484	7989484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772959657	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	183	940	0	ENST00000319144.4:c.202C>T	p.Arg68Cys	p.R68C	ENST00000319144	NM_001139.2	68	Cgc/Tgc	2/15	1	2	FACETS	0.98	0.903	1	0.98	0.903	1	CLONAL	1	TRUE	1	0.359211137109049	2		940	1040	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028624	12028624	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	100	493	0	ENST00000353533.5:c.827A>T	p.Asp276Val	p.D276V	ENST00000353533	NM_003010.3	276	gAc/gTc	8/11	1	2	FACETS	0.991	0.887	1	0.991	0.887	1	CLONAL	1	TRUE	1	0.359211137109049	2		493	562	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961370	15961370	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	131	751	0	ENST00000268712.3:c.6019A>G	p.Thr2007Ala	p.T2007A	ENST00000268712	NM_006311.3	2007	Acc/Gcc	39/46	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.359211137109049	2		751	696	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17120460	17120460	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	256	886	0	ENST00000285071.4:c.1099C>T	p.His367Tyr	p.H367Y	ENST00000285071	NM_144997.5	367	Cac/Tac	10/14	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.359211137109049	2		886	1037	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490382	29490382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754096545	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	164	642	1	ENST00000356175.3:c.467G>A	p.Arg156His	p.R156H	ENST00000356175	NM_000267.3	156	cGc/cAc	4/57	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.359211137109049	2		643	746	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687472	37687472	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	110	498	1	ENST00000447079.4:c.4382del	p.Gly1461AlafsTer38	p.G1461Afs*38	ENST00000447079	NM_015083.1	1459	tGg/tg	14/14	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.359211137109049	2		499	515	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437531	56437531	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	240	951	0	ENST00000407977.2:c.931del	p.Leu311SerfsTer108	p.L311Sfs*108	ENST00000407977		311	Ctc/tc	8/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.359211137109049	2		951	1082	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	267	1020	3	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.359211137109049	2		1023	1239	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885827	59885827	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs587781655	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	104	533	1	ENST00000259008.2:c.918+1G>A		p.X306_splice	ENST00000259008	NM_032043.2	306			1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.359211137109049	2		534	562	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554390	63554390	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	178	955	0	ENST00000307078.5:c.349T>C	p.Phe117Leu	p.F117L	ENST00000307078	NM_004655.3	117	Ttc/Ctc	2/11	1	2	FACETS	0.959	0.884	1	0.959	0.884	1	CLONAL	1	TRUE	1	0.359211137109049	2		955	1033	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554645	63554645	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	164	718	1	ENST00000307078.5:c.94del	p.Glu32ArgfsTer44	p.E32Rfs*44	ENST00000307078	NM_004655.3	32	Gag/ag	2/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.359211137109049	2		719	824	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39535279	39535279	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	20	312	0	ENST00000262039.4:c.23A>G	p.His8Arg	p.H8R	ENST00000262039	NM_002647.2	8	cAc/cGc	1/25	1	2	FACETS	0.288	0.219	0.368	0.288	0.219	0.368	SUBCLONAL	1	TRUE	1	0.359211137109049	2		312	387	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11015725	11015725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374384654	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	198	794	0	ENST00000327064.4:c.319G>A	p.Val107Ile	p.V107I	ENST00000327064	NM_199141.1	107	Gtc/Atc	2/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.359211137109049	2		794	925	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101922	11101922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	315	1270	2	ENST00000358026.2:c.1342C>T	p.Arg448Cys	p.R448C	ENST00000358026	NM_001128849.1	448	Cgc/Tgc	8/36	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.359211137109049	2		1272	1449	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144844	11144844	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	218	836	0	ENST00000358026.2:c.3919G>T	p.Ala1307Ser	p.A1307S	ENST00000358026	NM_001128849.1	1307	Gcc/Tcc	28/36	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.359211137109049	2		836	1088	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626865	14626865	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	307	1035	0	ENST00000254322.2:c.910del	p.Leu304SerfsTer17	p.L304Sfs*17	ENST00000254322	NM_006145.1	304	Ctc/tc	3/3	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.359211137109049	2		1035	1323	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279675	18279675	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555815238	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	150	722	1	ENST00000222254.8:c.1948A>G	p.Ser650Gly	p.S650G	ENST00000222254	NM_005027.3	650	Agc/Ggc	15/16	1	2	FACETS	0.958	0.875	1	0.958	0.875	1	CLONAL	1	TRUE	1	0.359211137109049	2		723	872	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961039	18961039	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	165	752	0	ENST00000262803.5:c.617T>C	p.Val206Ala	p.V206A	ENST00000262803	NM_002911.3	206	gTg/gCg	4/24	1	2	FACETS	0.942	0.865	1	0.942	0.865	1	CLONAL	1	TRUE	1	0.359211137109049	2		752	975	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731527	47731527	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	39	123	0	ENST00000449228.1:c.265G>A	p.Ala89Thr	p.A89T	ENST00000449228	NM_001127240.2	89	Gcc/Acc	2/4	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.359211137109049	2		123	156	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910318	50910318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201804732	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	336	1277	1	ENST00000440232.2:c.1573C>T	p.Arg525Trp	p.R525W	ENST00000440232	NM_002691.3	525	Cgg/Tgg	13/27	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.359211137109049	2		1278	1481	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716322	52716322	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	27	890	0	ENST00000322088.6:c.766T>C	p.Ser256Pro	p.S256P	ENST00000322088	NM_014225.5	256	Tcc/Ccc	6/15	1	2	FACETS	0.152	0.12	0.189	0.152	0.12	0.189	SUBCLONAL	1	TRUE	1	0.359211137109049	2		890	988	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1318	313	1504	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	0.359211137109049	2		1509	1631	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009125	27009126	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	96	559	0	ENST00000335756.4:c.65dup	p.Thr23AspfsTer55	p.T23Dfs*55	ENST00000335756	NM_001809.3	21	acc/aCcc	1/5	1	2	FACETS	0.793	0.707	0.884	0.793	0.707	0.884	SUBCLONAL	1	TRUE	1	0.359211137109049	2		559	674	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498064	29498064	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs769942064	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	148	979	0	ENST00000389048.3:c.1942A>G	p.Thr648Ala	p.T648A	ENST00000389048	NM_004304.4	648	Aca/Gca	11/29	1	2	FACETS	0.732	0.667	0.8	0.732	0.667	0.8	SUBCLONAL	1	TRUE	1	0.359211137109049	2		979	1126	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635614	47635614	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1443234544	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	220	996	4	ENST00000233146.2:c.286C>T	p.Arg96Cys	p.R96C	ENST00000233146	NM_000251.2	96	Cgt/Tgt	2/16	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.359211137109049	2		1000	976	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147777	61147777	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	93	383	1	ENST00000295025.8:c.1087G>A	p.Glu363Lys	p.E363K	ENST00000295025	NM_002908.2	363	Gaa/Aaa	10/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.359211137109049	2		384	411	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738339	190738339	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs761809273	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	102	514	0	ENST00000441310.2:c.2591A>G	p.Glu864Gly	p.E864G	ENST00000441310	NM_000534.4	864	gAa/gGa	12/13	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.359211137109049	2		514	480	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267387	198267387	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	138	812	1	ENST00000335508.6:c.1970C>T	p.Ser657Phe	p.S657F	ENST00000335508	NM_012433.2	657	tCc/tTc	14/25	1	2	FACETS	0.836	0.76	0.916	0.836	0.76	0.916	CLONAL	1	TRUE	1	0.359211137109049	2		813	919	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149728	202149728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	173	906	2	ENST00000358485.4:c.1173del	p.Ile392SerfsTer4	p.I392Sfs*4	ENST00000358485	NM_001080125.1	390	gCc/gc	8/9	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.359211137109049	2		908	898	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209108175	209108175	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	139	645	0	ENST00000345146.2:c.674A>C	p.Asp225Ala	p.D225A	ENST00000345146	NM_005896.2	225	gAc/gCc	6/10	1	2	FACETS	0.766	0.702	0.833	1	0.988	1	SUBCLONAL	2	TRUE	1	0.359211137109049	2		645	505	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212522477	212522477	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	111	495	0	ENST00000342788.4:c.1946+2T>C		p.X649_splice	ENST00000342788	NM_005235.2	649			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.359211137109049	2		495	484	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812268	212812268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754487821	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	64	454	0	ENST00000342788.4:c.308G>A	p.Arg103His	p.R103H	ENST00000342788	NM_005235.2	103	cGc/cAc	3/28	1	2	FACETS	0.778	0.675	0.889	0.778	0.675	0.889	SUBCLONAL	1	TRUE	1	0.359211137109049	2		454	458	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812320	212812320	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs763138791	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	21	384	0	ENST00000342788.4:c.256T>C	p.Tyr86His	p.Y86H	ENST00000342788	NM_005235.2	86	Tac/Cac	3/28	1	2	FACETS	0.354	0.272	0.45	0.354	0.272	0.45	SUBCLONAL	1	TRUE	1	0.359211137109049	2		384	330	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989593	212989593	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	128	428	0	ENST00000342788.4:c.118T>C	p.Ser40Pro	p.S40P	ENST00000342788	NM_005235.2	40	Tct/Cct	2/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.359211137109049	2		428	520	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374386	31374386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	156	878	0	ENST00000328111.2:c.385G>A	p.Gly129Ser	p.G129S	ENST00000328111	NM_006892.3	129	Ggc/Agc	5/23	1	2	FACETS	0.871	0.797	0.949	0.871	0.797	0.949	CLONAL	1	TRUE	1	0.359211137109049	2		878	997	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46275918	46275918	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	140	851	0	ENST00000371998.3:c.3354G>T	p.Gln1118His	p.Q1118H	ENST00000371998		1118	caG/caT	18/23	1	2	FACETS	0.987	0.899	1	0.987	0.899	1	CLONAL	1	TRUE	1	0.359211137109049	2		851	790	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484607	57484607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	145	661	1	ENST00000371085.3:c.691C>T	p.Arg231Cys	p.R231C	ENST00000371085	NM_000516.4	231	Cgc/Tgc	9/13	1	2	FACETS	0.966	0.881	1	0.966	0.881	1	CLONAL	1	TRUE	1	0.359211137109049	2		662	836	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817378	39817378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	172	658	1	ENST00000288319.7:c.185C>T	p.Ala62Val	p.A62V	ENST00000288319	NM_182918.3	62	gCc/gTc	2/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.359211137109049	2		659	712	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191600	10191600	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs869025667	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	78	775	0	ENST00000256474.2:c.593T>C	p.Leu198Pro	p.L198P	ENST00000256474	NM_000551.3	198	cTg/cCg	3/3	1	2	FACETS	0.426	0.373	0.483	0.426	0.373	0.483	SUBCLONAL	1	TRUE	1	0.359211137109049	2		775	1019	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	131	419	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.359211137109049	2		420	564	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053591	37053591	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs267607778	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	124	643	0	ENST00000231790.2:c.677+1G>A		p.X226_splice	ENST00000231790	NM_000249.3	226			1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.359211137109049	2		643	599	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277885	41277885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1168206875	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	83	630	1	ENST00000349496.5:c.1849G>A	p.Val617Ile	p.V617I	ENST00000349496	NM_001904.3	617	Gtc/Atc	12/15	1	2	FACETS	0.741	0.654	0.833	0.741	0.654	0.833	SUBCLONAL	1	TRUE	1	0.359211137109049	2		631	624	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623187	52623187	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	177	775	0	ENST00000394830.3:c.2864del	p.Asn955ThrfsTer53	p.N955Tfs*53	ENST00000394830	NM_018313.4	955	aAc/ac	19/30	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.359211137109049	2		775	852	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374736	149374736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1435671374	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	236	1120	1	ENST00000360632.3:c.358G>A	p.Val120Met	p.V120M	ENST00000360632	NM_015472.4	120	Gtg/Atg	2/7	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.359211137109049	2		1121	1293	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181349	185181351	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	93	457	0	ENST00000265026.3:c.1295_1297del	p.Glu432del	p.E432del	ENST00000265026	NM_004721.4	430	agAGAa/aga	8/14	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.359211137109049	2		457	447	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446165	187446165	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	215	1104	0	ENST00000232014.4:c.1523A>G	p.Tyr508Cys	p.Y508C	ENST00000232014	NM_001130845.1	508	tAc/tGc	6/10	1	2	FACETS	0.99	0.919	1	0.99	0.919	1	CLONAL	1	TRUE	1	0.359211137109049	2		1104	1209	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806696	1806696	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	309	1218	2	ENST00000260795.2:c.1412G>A	p.Arg471Gln	p.R471Q	ENST00000260795		471	cGg/cAg	9/17	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.359211137109049	2		1220	1409	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1952803	1952803	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144714547	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	139	555	0	ENST00000382891.5:c.1886C>T	p.Ser629Leu	p.S629L	ENST00000382891	NM_133335.3	629	tCg/tTg	10/22	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.359211137109049	2		555	704	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980515	1980515	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	277	1293	2	ENST00000382891.5:c.3977A>G	p.His1326Arg	p.H1326R	ENST00000382891	NM_133335.3	1326	cAt/cGt	22/22	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.359211137109049	2		1295	1384	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748244	41748245	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1394	386	1387	1	ENST00000226382.2:c.524dup	p.Ser176ValfsTer2	p.S176Vfs*2	ENST00000226382	NM_003924.3	175	aag/aaAg	3/3	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.359211137109049	2		1388	1780	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391455	84391456	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	89	504	0	ENST00000321945.7:c.376dup	p.Ser126PhefsTer30	p.S126Ffs*30	ENST00000321945	NM_139076.2	126	tca/tTca	5/9	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.359211137109049	2		504	449	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157134	106157134	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	162	614	0	ENST00000380013.4:c.2035A>G	p.Thr679Ala	p.T679A	ENST00000380013	NM_001127208.2	679	Act/Gct	3/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.359211137109049	2		614	695	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247373	153247373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	97	369	0	ENST00000281708.4:c.1429G>A	p.Gly477Ser	p.G477S	ENST00000281708	NM_033632.3	477	Ggt/Agt	10/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.359211137109049	2		369	430	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539257	187539257	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	113	512	0	ENST00000441802.2:c.8483T>C	p.Val2828Ala	p.V2828A	ENST00000441802	NM_005245.3	2828	gTa/gCa	10/27	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.359211137109049	2		512	545	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557914	187557914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	202	704	0	ENST00000441802.2:c.3797C>T	p.Ala1266Val	p.A1266V	ENST00000441802	NM_005245.3	1266	gCc/gTc	5/27	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.359211137109049	2		704	923	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630794	187630794	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	49	797	0	ENST00000441802.2:c.188T>G	p.Ile63Ser	p.I63S	ENST00000441802	NM_005245.3	63	aTt/aGt	2/27	1	2	FACETS	0.299	0.252	0.351	0.299	0.252	0.351	SUBCLONAL	1	TRUE	1	0.359211137109049	2		797	912	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271301	1271301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	272	899	0	ENST00000310581.5:c.2401G>A	p.Ala801Thr	p.A801T	ENST00000310581	NM_198253.2	801	Gcc/Acc	8/16	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.359211137109049	2		899	1110	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295052	1295052	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	33	263	0	ENST00000310581.5:c.53A>G	p.Tyr18Cys	p.Y18C	ENST00000310581	NM_198253.2	18	tAc/tGc	1/16	1	2	FACETS	0.468	0.381	0.565	0.468	0.381	0.565	SUBCLONAL	1	TRUE	1	0.359211137109049	2		263	393	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31429580	31429580	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	29	644	0	ENST00000344624.3:c.3216+2T>C		p.X1072_splice	ENST00000344624		1072			1	2	FACETS	0.296	0.236	0.363	0.296	0.236	0.363	SUBCLONAL	1	TRUE	1	0.359211137109049	2		644	546	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588966	67588966	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766580706	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	75	408	0	ENST00000274335.5:c.1057G>A	p.Gly353Arg	p.G353R	ENST00000274335		353	Ggg/Agg	8/15	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.359211137109049	2		408	388	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590974	67590974	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	33	167	0	ENST00000274335.5:c.1569-2A>G		p.X523_splice	ENST00000274335		523			1	2	FACETS	0.923	0.759	1	0.923	0.759	1	CLONAL	1	TRUE	1	0.359211137109049	2		167	199	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672712	86672712	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	44	325	0	ENST00000274376.6:c.2199G>T	p.Lys733Asn	p.K733N	ENST00000274376	NM_002890.2	733	aaG/aaT	17/25	1	2	FACETS	0.907	0.766	1	0.907	0.766	1	CLONAL	1	TRUE	1	0.359211137109049	2		325	270	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675571	86675571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1561325048	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	115	333	1	ENST00000274376.6:c.2513del	p.Asn838MetfsTer4	p.N838Mfs*4	ENST00000274376	NM_002890.2	836	gAa/ga	19/25	1	2	FACETS	0.947	0.864	1	1	0.989	1	CLONAL	2	TRUE	1	0.359211137109049	2		334	338	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502657	149502657	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	186	779	0	ENST00000261799.4:c.2131C>G	p.Pro711Ala	p.P711A	ENST00000261799	NM_002609.3	711	Ccc/Gcc	15/23	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.359211137109049	2		779	987	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176719121	176719121	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	125	330	0	ENST00000439151.2:c.6425A>G	p.Tyr2142Cys	p.Y2142C	ENST00000439151	NM_022455.4	2142	tAc/tGc	22/23	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.359211137109049	2		330	546	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030253	180030253	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1243	274	1548	0	ENST00000261937.6:c.4031G>T	p.Ser1344Ile	p.S1344I	ENST00000261937	NM_182925.4	1344	aGc/aTc	30/30	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.359211137109049	2		1548	1517	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158645	26158645	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	73	260	0	ENST00000289316.2:c.248A>G	p.His83Arg	p.H83R	ENST00000289316	NM_138720.2	83	cAt/cGt	1/2	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.359211137109049	2		260	296	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670331	30670331	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	121	561	0	ENST00000376406.3:c.6101A>G	p.Lys2034Arg	p.K2034R	ENST00000376406	NM_014641.2	2034	aAg/aGg	14/15	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.359211137109049	2		561	612	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163668	32163668	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	113	696	0	ENST00000375023.3:c.5558A>G	p.His1853Arg	p.H1853R	ENST00000375023	NM_004557.3	1853	cAt/cGt	30/30	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.359211137109049	2		696	592	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821331	32821331	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1218	295	1339	1	ENST00000354258.4:c.263T>C	p.Leu88Pro	p.L88P	ENST00000354258	NM_000593.5	88	cTa/cCa	1/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.359211137109049	2		1340	1513	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793650	89793650	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	75	453	0	ENST00000336032.3:c.719T>A	p.Val240Asp	p.V240D	ENST00000336032	NM_006813.2	240	gTt/gAt	2/2	1	2	FACETS	0.861	0.757	0.973	0.861	0.757	0.973	CLONAL	1	TRUE	1	0.359211137109049	2		453	485	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956645	93956645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	151	565	0	ENST00000369303.4:c.2591G>A	p.Gly864Asp	p.G864D	ENST00000369303	NM_004440.3	864	gGc/gAc	15/17	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.359211137109049	2		565	662	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553095	106553095	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	234	888	0	ENST00000369096.4:c.1060A>C	p.Ser354Arg	p.S354R	ENST00000369096	NM_001198.3	354	Agc/Cgc	5/7	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.359211137109049	2		888	1068	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024139	112024139	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	133	851	0	ENST00000368678.4:c.646A>G	p.Thr216Ala	p.T216A	ENST00000368678		216	Acc/Gcc	7/13	1	2	FACETS	0.998	0.907	1	0.998	0.907	1	CLONAL	1	TRUE	1	0.359211137109049	2		851	742	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962324	2962324	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	285	1143	1	ENST00000396946.4:c.2213G>T	p.Trp738Leu	p.W738L	ENST00000396946	NM_032415.4	738	tGg/tTg	17/25	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.359211137109049	2		1144	1283	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	264	1118	5	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	0.359211137109049	2		1123	1278	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431650	6431650	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	212	1113	1	ENST00000356142.4:c.203G>A	p.Arg68His	p.R68H	ENST00000356142	NM_018890.3	68	cGc/cAc	3/7	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.359211137109049	2		1114	939	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946143	13946143	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	201	863	0	ENST00000405192.2:c.953del	p.Leu318TrpfsTer2	p.L318Wfs*2	ENST00000405192	NM_001163147.1	318	tTg/tg	10/12	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.359211137109049	2		863	915	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845702	151845702	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771018478	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	173	845	1	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	0.359211137109049	2		846	875	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874149	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	140	765	0	ENST00000262189.6:c.8389_8390del	p.Lys2797GlyfsTer11	p.K2797Gfs*11	ENST00000262189	NM_170606.2	2797	AAg/g	38/59	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.359211137109049	2		765	752	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38188987	38188987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760950336	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	182	1235	1	ENST00000317025.8:c.1027G>A	p.Ala343Thr	p.A343T	ENST00000317025	NM_023034.1	343	Gca/Aca	5/24	1	2	FACETS	0.959	0.884	1	0.959	0.884	1	CLONAL	1	TRUE	1	0.359211137109049	2		1236	1057	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56879301	56879301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	226	971	0	ENST00000519728.1:c.818C>T	p.Ala273Val	p.A273V	ENST00000519728	NM_002350.3	273	gCt/gTt	9/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.359211137109049	2		971	1150	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992721	68992721	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs764112302	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	194	1025	6	ENST00000288368.4:c.1693del	p.Ser565ArgfsTer10	p.S565Rfs*10	ENST00000288368	NM_024870.2	562	cgT/cg	16/40	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.359211137109049	2		1031	882	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566375	141566375	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1564084326	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	80	570	0	ENST00000220592.5:c.1037T>C	p.Ile346Thr	p.I346T	ENST00000220592	NM_012154.3	346	aTt/aCt	9/19	1	2	FACETS	0.649	0.571	0.733	0.649	0.571	0.733	SUBCLONAL	1	TRUE	1	0.359211137109049	2		570	686	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499765	8499765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	112	908	0	ENST00000356435.5:c.2204C>T	p.Pro735Leu	p.P735L	ENST00000356435		735	cCc/cTc	14/35	1	2	FACETS	0.698	0.627	0.774	0.698	0.627	0.774	SUBCLONAL	1	TRUE	1	0.359211137109049	2		908	893	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209593	98209593	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	226	919	0	ENST00000331920.6:c.3945del	p.Tyr1316ThrfsTer56	p.Y1316Tfs*56	ENST00000331920	NM_000264.3	1315	ccC/cc	23/24	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.359211137109049	2		919	933	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759623	133759623	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	271	1312	0	ENST00000318560.5:c.1950del	p.Leu651TrpfsTer43	p.L651Wfs*43	ENST00000318560	NM_005157.4	649	aCc/ac	11/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.359211137109049	2		1312	1342	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293526	137293526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1326	362	1608	1	ENST00000481739.1:c.77G>A	p.Gly26Asp	p.G26D	ENST00000481739	NM_002957.4	26	gGc/gAc	2/10	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.359211137109049	2		1609	1688	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139811026	139811026	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	267	1050	1	ENST00000247668.2:c.637C>T	p.Arg213Ter	p.R213*	ENST00000247668	NM_021138.3	213	Cga/Tga	7/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.359211137109049	2		1051	1289	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933400	39933400	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	208	941	0	ENST00000378444.4:c.1199del	p.Gly400AlafsTer42	p.G400Afs*42	ENST00000378444	NM_001123385.1	400	gGc/gc	4/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.359211137109049	2		941	1049	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934289	39934289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	258	1022	1	ENST00000378444.4:c.310G>A	p.Ala104Thr	p.A104T	ENST00000378444	NM_001123385.1	104	Gct/Act	4/15	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.359211137109049	2		1023	1121	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70350054	70350054	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs966195679	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	128	554	3	ENST00000374080.3:c.4037G>A	p.Arg1346His	p.R1346H	ENST00000374080		1346	cGc/cAc	28/45	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.359211137109049	2		557	590	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937797	76937797	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	126	902	0	ENST00000373344.5:c.2951A>G	p.Gln984Arg	p.Q984R	ENST00000373344	NM_000489.3	984	cAg/cGg	9/35	1	2	FACETS	0.887	0.803	0.975	0.887	0.803	0.975	CLONAL	1	TRUE	1	0.359211137109049	2		902	791	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220559	123220560	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	194	737	0	ENST00000218089.9:c.3222dup	p.Ser1075IlefsTer12	p.S1075Ifs*12	ENST00000218089	NM_001042749.1	1072	-/A	30/35	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.359211137109049	2		737	936	SUCCESS
CBL	867	MSKCC	GRCh37	11	119077232	119077233	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAC	rs373212940	NA	P-0020633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	161	1140	0	ENST00000264033.4:c.125_127dup	p.His42dup	p.H42dup	ENST00000264033	NM_005188.3	42	-/CAC	1/16	1	2	FACETS	0.755	0.691	0.822	0.755	0.691	0.822	SUBCLONAL	1	TRUE	1	0.359211137109049	2		1140	1188	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	192	613	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.887	0.824	0.952	0.887	0.824	0.952	CLONAL	1	TRUE	1	0.656586217814765	2		614	659	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0020638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	486	240	0				ENST00000310581	NM_198253.2	-/1132			0.663624958206107	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.663624958206107	1		240	828	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729163	66729163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516792	NA	P-0020638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	44	874	1	ENST00000307102.5:c.371C>T	p.Pro124Leu	p.P124L	ENST00000307102	NM_002755.3	124	cCg/cTg	3/11	1	2	FACETS	0.108	0.089	0.128	0.108	0.089	0.128	SUBCLONAL	1	TRUE	1	0.663624958206107	2		875	1233	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0020638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	184	441	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.663624958206107	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.663624958206107	1		441	356	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459531	50459531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	188	414	0	ENST00000331340.3:c.820C>T	p.Arg274Cys	p.R274C	ENST00000331340	NM_006060.4	274	Cgt/Tgt	7/8	1	2	FACETS	0.853	0.792	0.917	0.853	0.792	0.917	CLONAL	1	TRUE	1	0.663624958206107	2		414	664	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0020638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	178	472	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	1	2	FACETS	0.861	0.797	0.927	0.861	0.797	0.927	CLONAL	1	TRUE	1	0.663624958206107	2		472	623	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333555	70333555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150689919	NA	P-0020638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	41	597	0	ENST00000373644.4:c.1460C>T	p.Ser487Leu	p.S487L	ENST00000373644	NM_030625.2	487	tCa/tTa	2/12	1	2	FACETS	0.159	0.132	0.19	0.159	0.132	0.19	SUBCLONAL	1	TRUE	1	0.663624958206107	2		597	777	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992907	72992907	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	247	898	0	ENST00000268489.5:c.1138C>T	p.Pro380Ser	p.P380S	ENST00000268489	NM_006885.3	380	Cca/Tca	2/10	1	2	FACETS	0.555	0.517	0.593	0.555	0.517	0.593	SUBCLONAL	1	TRUE	1	0.663624958206107	2		898	1342	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453185	140453185	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	70	344	0	ENST00000288602.6:c.1750C>T	p.Leu584Phe	p.L584F	ENST00000288602	NM_004333.4	584	Ctt/Ttt	15/18	1	2	FACETS	0.453	0.396	0.514	0.453	0.396	0.514	SUBCLONAL	1	TRUE	1	0.663624958206107	2		344	466	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159748	20159748	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	395	445	0	ENST00000379607.5:c.11A>G	p.Asn4Ser	p.N4S	ENST00000379607	NM_001412.3	4	aAt/aGt	1/7	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.663624958206107	1		445	593	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381466	81381466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	101	362	0	ENST00000222390.5:c.595G>A	p.Glu199Lys	p.E199K	ENST00000222390	NM_000601.4	199	Gaa/Aaa	5/18	1	2	FACETS	0.49	0.439	0.545	0.49	0.439	0.545	SUBCLONAL	1	TRUE	1	0.663624958206107	2		362	621	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512473	38512473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1714	105	1451	1	ENST00000254066.5:c.1384C>T	p.Pro462Ser	p.P462S	ENST00000254066	NM_000964.3	462	Ccg/Tcg	9/9	1	2	FACETS	0.174	0.155	0.195	0.174	0.155	0.195	SUBCLONAL	1	TRUE	1	0.663624958206107	2		1452	1819	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044470	12044470	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	95	326	0	ENST00000353533.5:c.1093C>T	p.Pro365Ser	p.P365S	ENST00000353533	NM_003010.3	365	Ccc/Tcc	11/11	1	2	FACETS	0.548	0.49	0.611	0.548	0.49	0.611	SUBCLONAL	1	TRUE	1	0.663624958206107	2		326	522	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739001	40739001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	228	550	0	ENST00000373198.4:c.3283G>A	p.Glu1095Lys	p.E1095K	ENST00000373198	NM_133170.3	1095	Gaa/Aaa	24/32	0.663624958206107	3	FACETS	0.926	0.863	0.991	0.463	0.431	0.496	CLONAL	1	TRUE	1	0.663624958206107	3		550	988	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981315	68981315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866864487	NA	P-0020638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	69	474	0	ENST00000288368.4:c.1387C>T	p.Arg463Cys	p.R463C	ENST00000288368	NM_024870.2	463	Cgc/Tgc	12/40	1	2	FACETS	0.371	0.323	0.423	0.371	0.323	0.423	SUBCLONAL	1	TRUE	1	0.663624958206107	2		474	560	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857061	9857061	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	97	375	0	ENST00000330684.3:c.4340C>T	p.Ser1447Phe	p.S1447F	ENST00000330684	NM_001134407.1	1447	tCc/tTc	13/13	1	2	FACETS	0.608	0.544	0.675	0.608	0.544	0.675	SUBCLONAL	1	TRUE	1	0.663624958206107	2		375	481	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212484001	212484001	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0020638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	78	432	0	ENST00000342788.4:c.2203-1G>A		p.X735_splice	ENST00000342788	NM_005235.2	735			1	2	FACETS	0.474	0.417	0.534	0.474	0.417	0.534	SUBCLONAL	1	TRUE	1	0.663624958206107	2		432	496	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793461	18793461	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	66	545	0	ENST00000266497.5:c.4158A>T	p.Lys1386Asn	p.K1386N	ENST00000266497		1386	aaA/aaT	30/31	1	2	FACETS	0.355	0.308	0.406	0.355	0.308	0.406	SUBCLONAL	1	TRUE	1	0.663624958206107	2		545	560	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675068	40675068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	423	959	1	ENST00000249776.8:c.32G>A	p.Arg11Lys	p.R11K	ENST00000249776	NM_033286.3	11	aGa/aAa	1/9	1	2	FACETS	0.983	0.937	1	0.983	0.937	1	CLONAL	1	TRUE	1	0.663624958206107	2		960	1297	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40683699	40683699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	164	818	0	ENST00000249776.8:c.691G>A	p.Gly231Ser	p.G231S	ENST00000249776	NM_033286.3	231	Ggc/Agc	7/9	1	2	FACETS	0.429	0.393	0.467	0.429	0.393	0.467	SUBCLONAL	1	TRUE	1	0.663624958206107	2		818	1153	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916202	9916202	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	114	575	0	ENST00000330684.3:c.2087A>C	p.Asn696Thr	p.N696T	ENST00000330684	NM_001134407.1	696	aAt/aCt	10/13	1	2	FACETS	0.431	0.388	0.477	0.431	0.388	0.477	SUBCLONAL	1	TRUE	1	0.663624958206107	2		575	797	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934531	9934531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	257	594	0	ENST00000330684.3:c.1624G>A	p.Gly542Ser	p.G542S	ENST00000330684	NM_001134407.1	542	Ggc/Agc	7/13	1	2	FACETS	0.934	0.877	0.992	0.934	0.877	0.992	CLONAL	1	TRUE	1	0.663624958206107	2		594	829	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796005	78796005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	194	792	2	ENST00000306801.3:c.895C>T	p.Pro299Ser	p.P299S	ENST00000306801	NM_020761.2	299	Cct/Tct	8/34	1	2	FACETS	0.503	0.465	0.543	0.503	0.465	0.543	SUBCLONAL	1	TRUE	1	0.663624958206107	2		794	1162	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290300	15290300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780646145	NA	P-0020638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	157	990	0	ENST00000263388.2:c.3335C>T	p.Pro1112Leu	p.P1112L	ENST00000263388	NM_000435.2	1112	cCt/cTt	21/33	1	2	FACETS	0.377	0.344	0.411	0.377	0.344	0.411	SUBCLONAL	1	TRUE	1	0.663624958206107	2		990	1256	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543777	212543777	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs769734905	NA	P-0020638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	40	470	0	ENST00000342788.4:c.1622G>A	p.Gly541Asp	p.G541D	ENST00000342788	NM_005235.2	541	gGt/gAt	13/28	1	2	FACETS	0.156	0.129	0.186	0.156	0.129	0.186	SUBCLONAL	1	TRUE	1	0.663624958206107	2		470	774	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817534	39817534	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	166	608	0	ENST00000288319.7:c.29C>T	p.Ser10Leu	p.S10L	ENST00000288319	NM_182918.3	10	tCa/tTa	2/10	1	2	FACETS	0.563	0.517	0.611	0.563	0.517	0.611	SUBCLONAL	1	TRUE	1	0.663624958206107	2		608	889	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190813	185190813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	204	836	1	ENST00000265026.3:c.1694C>T	p.Thr565Ile	p.T565I	ENST00000265026	NM_004721.4	565	aCt/aTt	11/14	0.608132064147801	2	FACETS	0.592	0.548	0.637	0.296	0.274	0.319	SUBCLONAL	1	TRUE	0	0.663624958206107	2		837	1039	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957735	1957735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	358	896	0	ENST00000382891.5:c.2701C>T	p.Pro901Ser	p.P901S	ENST00000382891	NM_133335.3	901	Ccc/Tcc	15/22	1	2	FACETS	0.891	0.844	0.938	0.891	0.844	0.938	CLONAL	1	TRUE	1	0.663624958206107	2		896	1211	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133480	55133480	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376265745	NA	P-0020638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	86	632	0	ENST00000257290.5:c.784G>A	p.Glu262Lys	p.E262K	ENST00000257290	NM_006206.4	262	Gaa/Aaa	6/23	1	2	FACETS	0.319	0.281	0.359	0.319	0.281	0.359	SUBCLONAL	1	TRUE	1	0.663624958206107	2		632	813	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553411	106553411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1407187879	NA	P-0020638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	64	451	1	ENST00000369096.4:c.1376C>T	p.Pro459Leu	p.P459L	ENST00000369096	NM_001198.3	459	cCc/cTc	5/7	1	2	FACETS	0.359	0.311	0.411	0.359	0.311	0.411	SUBCLONAL	1	TRUE	1	0.663624958206107	2		452	537	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752842	128752842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	65	292	0	ENST00000377970.2:c.1003C>T	p.Pro335Ser	p.P335S	ENST00000377970	NM_002467.4	335	Cct/Tct	3/3	1	2	FACETS	0.362	0.314	0.414	0.362	0.314	0.414	SUBCLONAL	1	TRUE	1	0.663624958206107	2		292	541	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518223	8518223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	62	404	0	ENST00000356435.5:c.1168G>A	p.Glu390Lys	p.E390K	ENST00000356435		390	Gaa/Aaa	10/35	0.663624958206107	1	FACETS	0.396	0.345	0.452	0.396	0.345	0.452	SUBCLONAL	1	TRUE	0	0.663624958206107	1		404	315	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	197	619	8	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	0.31	2		627	1261	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	94	417	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.277967505876513	3	FACETS	0.969	0.862	1	0.484	0.431	0.542	CLONAL	1	TRUE	1	0.31	3		418	723	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	311	229	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.843	0.799	0.888	1	0.996	1	CLONAL	3	TRUE	1	0.31	2		229	793	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954273	32954273	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359752	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	131	570	1	ENST00000380152.3:c.9253del	p.Thr3085GlnfsTer19	p.T3085Qfs*19	ENST00000380152		3083	Aaa/aa	24/27	0.180081519154178	3	FACETS	1	0.982	1	0.674	0.612	0.739	INDETERMINATE	1	TRUE	1	0.31	3		571	724	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	210	419	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.882	0.821	0.944	1	0.993	1	CLONAL	2	TRUE	1	0.31	2		420	768	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675571	86675571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1561325048	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	74	333	1	ENST00000274376.6:c.2513del	p.Asn838MetfsTer4	p.N838Mfs*4	ENST00000274376	NM_002890.2	836	gAa/ga	19/25	0.3	4	FACETS	1	0.917	1			1	CLONAL	1	TRUE	NA	0.31	4		334	590	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	132	867	0	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	0.144604256946288	1	FACETS	1	0.946	1	1	0.946	1	INDETERMINATE	1	TRUE	0	0.31	1		867	682	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	80	392	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.3	2	FACETS	0.787	0.693	0.888			1	SUBCLONAL	1	TRUE	NA	0.31	2		392	656	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256768	19256769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1202792889	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	96	804	0	ENST00000162023.5:c.944dup	p.Val316SerfsTer6	p.V316Sfs*6	ENST00000162023		315	cca/ccCa	13/13	1	2	FACETS	0.895	0.798	0.998	0.895	0.798	0.998	CLONAL	1	TRUE	1	0.31	2		804	692	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	181	876	2	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.144604256946288	1	FACETS	1	0.984	1	1	0.984	1	INDETERMINATE	1	TRUE	0	0.31	1		878	793	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560514	65560514	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	151	589	0	ENST00000358664.4:c.83A>G	p.His28Arg	p.H28R	ENST00000358664	NM_002382.4	28	cAt/cGt	3/5	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.31	2		589	846	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574678	41574679	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs754418509	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	175	1262	2	ENST00000263253.7:c.6970dup	p.His2324ProfsTer55	p.H2324Pfs*55	ENST00000263253	NM_001429.3	2321	-/C	31/31	0.144604256946288	1	FACETS	0.924	0.851	1	0.924	0.851	1	INDETERMINATE	1	TRUE	0	0.31	1		1264	1032	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659182	86659182	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	71	240	0	ENST00000274376.6:c.1475del	p.Asn492IlefsTer6	p.N492Ifs*6	ENST00000274376	NM_002890.2	491	Aaa/aa	11/25	0.3	4	FACETS	0.848	0.745	0.957			1	CLONAL	2	TRUE	NA	0.31	4		240	354	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	175	1121	9	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	0.180081519154178	3	FACETS	0.986	0.906	1	0.329	0.302	0.357	INDETERMINATE	1	TRUE	0	0.31	3		1130	1322	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279516	1279516	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773813809	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	204	1250	2	ENST00000310581.5:c.2020G>A	p.Gly674Ser	p.G674S	ENST00000310581	NM_198253.2	674	Ggc/Agc	5/16	0.3	0	FACETS	1	0.973	1			1	CLONAL	1	TRUE	0	0.31	0		1252	831	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	152	1062	3	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.31	2		1065	899	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482927	140482927	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	144	701	2	ENST00000288602.6:c.1208del	p.Pro403LeufsTer8	p.P403Lfs*8	ENST00000288602	NM_004333.4	403	cCt/ct	10/18	0.277967505876513	3	FACETS	1	0.938	1	0.519	0.472	0.568	CLONAL	1	TRUE	1	0.31	3		703	1034	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	179	1103	6	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	0.180081519154178	3	FACETS	1	0.978	1	0.588	0.541	0.637	INDETERMINATE	1	TRUE	1	0.31	3		1109	1135	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805473	1805473	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188723332	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	174	1109	0	ENST00000260795.2:c.985G>A	p.Val329Ile	p.V329I	ENST00000260795		329	Gtc/Atc	7/17	0.3	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.31	1		1109	810	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030692	48030692	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs267608092	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	37	503	2	ENST00000234420.5:c.3312del	p.Phe1104LeufsTer11	p.F1104Lfs*11	ENST00000234420	NM_000179.2	1102	acT/ac	5/10	0.376786127534674	3	FACETS	0.41	0.337	0.492	0.205	0.168	0.246	SUBCLONAL	1	TRUE	1	0.31	3		505	673	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337296	89337296	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567537413	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	161	784	0	ENST00000301030.4:c.7735C>T	p.Arg2579Cys	p.R2579C	ENST00000301030	NM_001256183.1	2579	Cgc/Tgc	12/13	0.144604256946288	1	FACETS	1	0.967	1	1	0.967	1	INDETERMINATE	1	TRUE	0	0.31	1		784	798	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807363	3807364	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	84	423	0	ENST00000262367.5:c.3623dup	p.Gln1209ThrfsTer25	p.Q1209Tfs*25	ENST00000262367	NM_004380.2	1208	cca/ccCa	19/31	0.144604256946288	0	FACETS	0.739	0.655	0.829			1	INDETERMINATE	1	TRUE	0	0.31	0		423	506	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272378	15272378	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199620476	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	221	1544	6	ENST00000263388.2:c.6061G>A	p.Val2021Met	p.V2021M	ENST00000263388	NM_000435.2	2021	Gtg/Atg	33/33	0.144604256946288	0	FACETS	0.962	0.895	1			1	INDETERMINATE	1	TRUE	0	0.31	0		1550	1023	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405652	70405652	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	97	643	0	ENST00000373644.4:c.3171del	p.Lys1057AsnfsTer25	p.K1057Nfs*25	ENST00000373644	NM_030625.2	1056	Aaa/aa	4/12	1	2	FACETS	0.95	0.848	1	0.95	0.848	1	CLONAL	1	TRUE	1	0.31	2		643	659	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946150	13946150	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1226	72	756	2	ENST00000405192.2:c.946C>T	p.Gln316Ter	p.Q316*	ENST00000405192	NM_001163147.1	316	Cag/Tag	10/12	0.277967505876513	3	FACETS	0.413	0.359	0.472	0.207	0.179	0.236	SUBCLONAL	1	TRUE	1	0.31	3		758	1298	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944592	40944592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371723954	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	100	526	0	ENST00000373198.4:c.1910G>A	p.Arg637Gln	p.R637Q	ENST00000373198	NM_133170.3	637	cGg/cAg	12/32	0.3	0	FACETS	0.868	0.778	0.962			1	CLONAL	1	TRUE	0	0.31	0		526	513	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1042175	1042175	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	67	962	0	ENST00000358495.3:c.50C>T	p.Ala17Val	p.A17V	ENST00000358495	NM_134424.2	17	gCt/gTt	2/12	0.3	2	FACETS	0.401	0.347	0.459			1	SUBCLONAL	1	TRUE	NA	0.31	2		962	1079	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930730	32930730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs74047012	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	139	635	0	ENST00000380152.3:c.7601C>T	p.Ala2534Val	p.A2534V	ENST00000380152		2534	gCg/gTg	15/27	0.180081519154178	3	FACETS	1	0.973	1	0.588	0.535	0.644	INDETERMINATE	1	TRUE	1	0.31	3		635	881	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222209	2222209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	66	1319	1	ENST00000398665.3:c.3041G>A	p.Gly1014Glu	p.G1014E	ENST00000398665	NM_032482.2	1014	gGg/gAg	24/28	0.144604256946288	1	FACETS	0.375	0.324	0.43	0.375	0.324	0.43	INDETERMINATE	1	TRUE	0	0.31	1		1320	960	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119794	70119794	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	64	995	0	ENST00000245479.2:c.800del	p.Pro267LeufsTer12	p.P267Lfs*12	ENST00000245479	NM_000346.3	266	Ccc/cc	3/3	1	2	FACETS	0.545	0.471	0.625	0.545	0.471	0.625	SUBCLONAL	1	TRUE	1	0.31	2		995	758	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686900	37686901	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs772711685	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	36	661	0	ENST00000447079.4:c.3810dup	p.Gly1271ArgfsTer13	p.G1271Rfs*13	ENST00000447079	NM_015083.1	1268	-/C	14/14	1	2	FACETS	0.357	0.292	0.429	0.357	0.292	0.429	SUBCLONAL	1	TRUE	1	0.31	2		661	651	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288788	15288789	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	28	363	0	ENST00000263388.2:c.3950dup	p.Gly1318ArgfsTer245	p.G1318Rfs*245	ENST00000263388	NM_000435.2	1317	cca/ccCa	24/33	0.144604256946288	0	FACETS	0.44	0.353	0.54			1	INDETERMINATE	1	TRUE	0	0.31	0		363	283	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546324	46546324	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	98	513	0	ENST00000262741.5:c.205del	p.Asp69IlefsTer7	p.D69Ifs*7	ENST00000262741	NM_003629.3	69	Gat/at	2/10	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.31	2		513	589	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194905	29194905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375453930	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	231	1028	1	ENST00000240100.2:c.823C>T	p.Arg275Cys	p.R275C	ENST00000240100	NM_001394.6	275	Cgc/Tgc	4/4	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.31	2		1029	1241	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368388	225368388	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1366667901	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	145	513	0	ENST00000264414.4:c.1358del	p.Asn453ThrfsTer2	p.N453Tfs*2	ENST00000264414	NM_003590.4	453	aAc/ac	9/16	0.180081519154178	3	FACETS	1	0.982	1	0.435	0.397	0.475	INDETERMINATE	1	TRUE	0	0.31	3		513	828	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577523	7577523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	41	960	0	ENST00000269305.4:c.758C>T	p.Thr253Ile	p.T253I	ENST00000269305	NM_001126112.2	253	aCc/aTc	7/11	1	2	FACETS	0.28	0.232	0.333	0.28	0.232	0.333	SUBCLONAL	1	TRUE	1	0.31	2		960	946	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608300	43608300	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	195	1244	1	ENST00000355710.3:c.1649-1G>T		p.X550_splice	ENST00000355710	NM_020975.4	550			0.144604256946288	1	FACETS	1	0.954	1	1	0.954	1	INDETERMINATE	1	TRUE	0	0.31	1		1245	1020	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245539	16245539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1471081719	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	87	590	0	ENST00000375759.3:c.1514G>A	p.Arg505His	p.R505H	ENST00000375759	NM_015001.2	505	cGc/cAc	7/15	1	2	FACETS	0.785	0.695	0.882	0.785	0.695	0.882	SUBCLONAL	1	TRUE	1	0.31	2		590	715	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245932	16245932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760738868	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	91	440	0	ENST00000375759.3:c.1555G>A	p.Val519Met	p.V519M	ENST00000375759	NM_015001.2	519	Gtg/Atg	8/15	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.31	2		440	571	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262337	16262337	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	56	321	0	ENST00000375759.3:c.9602C>A	p.Pro3201Gln	p.P3201Q	ENST00000375759	NM_015001.2	3201	cCa/cAa	11/15	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.31	2		321	308	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937090	36937090	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	112	738	0	ENST00000361632.4:c.1229C>T	p.Ala410Val	p.A410V	ENST00000361632		410	gCc/gTc	9/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.31	2		738	650	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941121	36941121	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	133	913	0	ENST00000361632.4:c.218del	p.Gly73AlafsTer31	p.G73Afs*31	ENST00000361632		73	gGc/gc	3/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.31	2		913	785	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163309260	163309260	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	125	526	0	ENST00000271452.3:c.604del	p.Thr202ArgfsTer2	p.T202Rfs*2	ENST00000271452	NM_145697.2	200	cAa/ca	8/14	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.31	2		526	705	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451504	70451504	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	71	843	0	ENST00000373644.4:c.6344A>G	p.Asp2115Gly	p.D2115G	ENST00000373644	NM_030625.2	2115	gAc/gGc	12/12	1	2	FACETS	0.486	0.423	0.554	0.486	0.423	0.554	SUBCLONAL	1	TRUE	1	0.31	2		843	943	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376995	118376995	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	76	458	3	ENST00000534358.1:c.10388C>T	p.Ala3463Val	p.A3463V	ENST00000534358	NM_005933.3	3463	gCc/gTc	27/36	0.3	2	FACETS	1	0.909	1			1	CLONAL	1	TRUE	NA	0.31	2		461	472	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432872	432872	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	148	667	0	ENST00000399788.2:c.2044A>T	p.Thr682Ser	p.T682S	ENST00000399788	NM_001042603.1	682	Aca/Tca	15/28	0.3	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.31	1		667	797	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298731	46298731	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	109	437	0	ENST00000334344.6:c.5378A>G	p.His1793Arg	p.H1793R	ENST00000334344	NM_152641.2	1793	cAt/cGt	21/21	0.180081519154178	3	FACETS	1	0.981	1	0.706	0.636	0.78	INDETERMINATE	1	TRUE	1	0.31	3		437	575	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424524	49424524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	153	833	0	ENST00000301067.7:c.13699C>T	p.Pro4567Ser	p.P4567S	ENST00000301067	NM_003482.3	4567	Cct/Tct	41/54	0.180081519154178	3	FACETS	1	0.982	1	0.638	0.583	0.695	INDETERMINATE	1	TRUE	1	0.31	3		833	894	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440106	49440106	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	178	947	0	ENST00000301067.7:c.4520G>A	p.Cys1507Tyr	p.C1507Y	ENST00000301067	NM_003482.3	1507	tGc/tAc	16/54	0.180081519154178	3	FACETS	1	0.985	1	0.646	0.595	0.699	INDETERMINATE	1	TRUE	1	0.31	3		947	1027	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445149	49445149	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	225	1225	0	ENST00000301067.7:c.2317del	p.Gln773SerfsTer157	p.Q773Sfs*157	ENST00000301067	NM_003482.3	773	Cag/ag	10/54	0.180081519154178	3	FACETS	1	0.99	1	0.678	0.63	0.728	INDETERMINATE	1	TRUE	1	0.31	3		1225	1236	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49449088	49449088	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	172	726	2	ENST00000301067.7:c.20C>T	p.Ala7Val	p.A7V	ENST00000301067	NM_003482.3	7	gCt/gTt	1/54	0.180081519154178	3	FACETS	1	0.987	1	0.691	0.636	0.749	INDETERMINATE	1	TRUE	1	0.31	3		728	927	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492552	56492552	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	165	792	0	ENST00000267101.3:c.2702T>C	p.Val901Ala	p.V901A	ENST00000267101	NM_001982.3	901	gTt/gCt	23/28	0.180081519154178	3	FACETS	1	0.986	1	0.684	0.628	0.742	INDETERMINATE	1	TRUE	1	0.31	3		792	899	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495417	56495417	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1391637476	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	155	843	1	ENST00000267101.3:c.3607A>G	p.Arg1203Gly	p.R1203G	ENST00000267101	NM_001982.3	1203	Agg/Ggg	28/28	0.180081519154178	3	FACETS	1	0.976	1	0.59	0.539	0.643	INDETERMINATE	1	TRUE	1	0.31	3		844	979	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145478	58145478	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	134	450	0	ENST00000257904.6:c.23C>A	p.Pro8Gln	p.P8Q	ENST00000257904	NM_000075.3	8	cCa/cAa	2/8	0.180081519154178	3	FACETS	1	0.985	1	0.723	0.658	0.79	INDETERMINATE	1	TRUE	1	0.31	3		450	691	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32971137	32971137	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	128	737	0	ENST00000380152.3:c.9604C>A	p.Pro3202Thr	p.P3202T	ENST00000380152		3202	Ccg/Acg	26/27	0.180081519154178	3	FACETS	1	0.955	1	0.545	0.494	0.599	INDETERMINATE	1	TRUE	1	0.31	3		737	875	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30098282	30098282	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	129	711	0	ENST00000331968.5:c.1690A>G	p.Ile564Val	p.I564V	ENST00000331968	NM_002742.2	564	Att/Gtt	11/18	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.31	2		711	810	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477178	67477178	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	141	706	2	ENST00000327367.4:c.985G>A	p.Ala329Thr	p.A329T	ENST00000327367	NM_005902.3	329	Gcc/Acc	7/9	0.144604256946288	1	FACETS	1	0.961	1	1	0.961	1	INDETERMINATE	1	TRUE	0	0.31	1		708	703	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423545	88423545	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	152	826	0	ENST00000360948.2:c.2290T>C	p.Phe764Leu	p.F764L	ENST00000360948	NM_001012338.2	764	Ttc/Ctc	18/19	0.144604256946288	1	FACETS	1	0.923	1	1	0.923	1	INDETERMINATE	1	TRUE	0	0.31	1		826	821	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136381	2136381	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs45517375	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	153	802	2	ENST00000219476.3:c.4849+1G>A		p.X1617_splice	ENST00000219476	NM_000548.3	1617			0.144604256946288	0	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	0	0.31	0		804	622	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81891943	81891943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771121259	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	138	612	0	ENST00000359376.3:c.413C>T	p.Thr138Met	p.T138M	ENST00000359376	NM_002661.3	138	aCg/aTg	4/33	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.31	2		612	783	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357069	89357069	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	153	765	0	ENST00000301030.4:c.565A>G	p.Ser189Gly	p.S189G	ENST00000301030	NM_001256183.1	189	Agc/Ggc	6/13	0.144604256946288	1	FACETS	1	0.974	1	1	0.974	1	INDETERMINATE	1	TRUE	0	0.31	1		765	721	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004645	16004646	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	172	780	0	ENST00000268712.3:c.2608dup	p.Arg870LysfsTer9	p.R870Kfs*9	ENST00000268712	NM_006311.3	870	agg/aAgg	20/46	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.31	2		780	941	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627380	37627380	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	54	866	0	ENST00000447079.4:c.1295A>G	p.Asn432Ser	p.N432S	ENST00000447079	NM_015083.1	432	aAc/aGc	2/14	1	2	FACETS	0.398	0.338	0.463	0.398	0.338	0.463	SUBCLONAL	1	TRUE	1	0.31	2		866	876	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681117	37681117	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs144011843	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	44	552	0	ENST00000447079.4:c.3286T>G	p.Ser1096Ala	p.S1096A	ENST00000447079	NM_015083.1	1096	Tct/Gct	12/14	1	2	FACETS	0.462	0.387	0.546	0.462	0.387	0.546	SUBCLONAL	1	TRUE	1	0.31	2		552	614	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530129	63530132	+	frameshift_variant	Frame_Shift_Del	DEL	AAGT	AAGT	-	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	117	722	0	ENST00000307078.5:c.2303_2306del	p.Tyr768PhefsTer13	p.Y768Ffs*13	ENST00000307078	NM_004655.3	768	tACTTt/tt	10/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.31	2		722	705	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724461	724461	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	189	1068	0	ENST00000314574.4:c.1595C>A	p.Ala532Asp	p.A532D	ENST00000314574	NM_005433.3	532	gCt/gAt	12/12	1	2	FACETS	0.985	0.908	1	0.985	0.908	1	CLONAL	1	TRUE	1	0.31	2		1068	1238	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621158	1621158	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	163	1196	0	ENST00000344749.5:c.988del	p.Asp330MetfsTer64	p.D330Mfs*64	ENST00000344749	NM_001136139.2	330	Gat/at	12/19	0.144604256946288	1	FACETS	0.996	0.914	1	0.996	0.914	1	INDETERMINATE	1	TRUE	0	0.31	1		1196	892	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625669	1625669	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	213	1259	3	ENST00000344749.5:c.405del	p.Leu138CysfsTer6	p.L138Cfs*6	ENST00000344749	NM_001136139.2	135	ccC/cc	7/19	0.144604256946288	1	FACETS	1	0.987	1	1	0.987	1	INDETERMINATE	1	TRUE	0	0.31	1		1262	925	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031170	11031170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	199	1028	2	ENST00000327064.4:c.1255C>T	p.Arg419Trp	p.R419W	ENST00000327064	NM_199141.1	419	Cgg/Tgg	11/16	0.144604256946288	0	FACETS	0.947	0.878	1			1	INDETERMINATE	1	TRUE	0	0.31	0		1030	935	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627771	14627771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	177	810	0	ENST00000254322.2:c.299C>T	p.Ala100Val	p.A100V	ENST00000254322	NM_006145.1	100	gCc/gTc	2/3	0.144604256946288	0	FACETS	0.738	0.68	0.8			1	INDETERMINATE	1	TRUE	0	0.31	0		810	1067	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376248	15376248	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	110	683	0	ENST00000263377.2:c.766del	p.Gln256SerfsTer27	p.Q256Sfs*27	ENST00000263377	NM_058243.2	256	Cag/ag	5/20	0.144604256946288	0	FACETS	0.956	0.863	1			1	INDETERMINATE	1	TRUE	0	0.31	0		683	512	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17947959	17947959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886039394	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	198	1009	2	ENST00000458235.1:c.1765G>A	p.Gly589Ser	p.G589S	ENST00000458235	NM_000215.3	589	Ggc/Agc	13/24	0.144604256946288	0	FACETS	0.942	0.873	1			1	INDETERMINATE	1	TRUE	0	0.31	0		1011	936	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948772	17948772	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	216	1191	1	ENST00000458235.1:c.1670T>C	p.Val557Ala	p.V557A	ENST00000458235	NM_000215.3	557	gTc/gCc	12/24	0.144604256946288	0	FACETS	0.897	0.833	0.963			1	INDETERMINATE	1	TRUE	0	0.31	0		1192	1072	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214151	36214151	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	225	1189	0	ENST00000222270.7:c.2977C>G	p.Pro993Ala	p.P993A	ENST00000222270	NM_014727.1	993	Cct/Gct	6/37	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.31	2		1189	1110	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223124	36223124	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	239	1394	0	ENST00000222270.7:c.5674T>G	p.Ser1892Ala	p.S1892A	ENST00000222270	NM_014727.1	1892	Tct/Gct	28/37	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.31	2		1394	1284	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919053	50919054	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	171	1091	0	ENST00000440232.2:c.2792dup	p.Val933CysfsTer21	p.V933Cfs*21	ENST00000440232	NM_002691.3	930	-/A	22/27	0.3	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.31	1		1091	890	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716327	52716327	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	180	693	2	ENST00000322088.6:c.771G>A	p.Trp257Ter	p.W257*	ENST00000322088	NM_014225.5	257	tgG/tgA	6/15	0.3	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.31	1		695	693	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25536823	25536823	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1213222712	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	189	1184	3	ENST00000264709.3:c.31del	p.Asp11ThrfsTer61	p.D11Tfs*61	ENST00000264709	NM_175629.2	11	Gac/ac	2/23	0.376786127534674	3	FACETS	1	0.976	1	0.57	0.526	0.617	CLONAL	1	TRUE	1	0.31	3		1187	1235	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095565	178095565	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	123	486	1	ENST00000397062.3:c.1766G>T	p.Gly589Val	p.G589V	ENST00000397062	NM_006164.4	589	gGc/gTc	5/5	0.457526770144681	3	FACETS	1	0.941	1	0.529	0.478	0.582	CLONAL	1	TRUE	1	0.31	3		487	867	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209110147	209110147	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	47	579	0	ENST00000345146.2:c.416A>G	p.Tyr139Cys	p.Y139C	ENST00000345146	NM_005896.2	139	tAc/tGc	5/10	0.457526770144681	3	FACETS	0.387	0.325	0.455	0.193	0.162	0.228	SUBCLONAL	1	TRUE	1	0.31	3		579	906	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426734	212426734	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	65	663	0	ENST00000342788.4:c.2381T>C	p.Leu794Pro	p.L794P	ENST00000342788	NM_005235.2	794	cTg/cCg	20/28	0.457526770144681	3	FACETS	0.446	0.385	0.512	0.223	0.192	0.256	SUBCLONAL	1	TRUE	1	0.31	3		663	1087	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39706232	39706232	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	76	283	0	ENST00000361337.2:c.290C>A	p.Ser97Tyr	p.S97Y	ENST00000361337	NM_003286.2	97	tCt/tAt	5/21	0.144604256946288	1	FACETS	1	0.884	1	1	0.884	1	INDETERMINATE	1	TRUE	0	0.31	1		283	413	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62316928	62316928	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	126	813	0	ENST00000360203.5:c.1244T>C	p.Leu415Pro	p.L415P	ENST00000360203	NM_001283009.1	415	cTg/cCg	15/35	0.3	2	FACETS	1	0.956	1			1	CLONAL	1	TRUE	NA	0.31	2		813	745	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547973	41547973	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1232641756	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	125	745	0	ENST00000263253.7:c.2954A>G	p.Asp985Gly	p.D985G	ENST00000263253	NM_001429.3	985	gAt/gGt	15/31	0.144604256946288	1	FACETS	0.894	0.81	0.983	0.894	0.81	0.983	INDETERMINATE	1	TRUE	0	0.31	1		745	762	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568636	41568636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	86	488	0	ENST00000263253.7:c.4586G>A	p.Arg1529Gln	p.R1529Q	ENST00000263253	NM_001429.3	1529	cGa/cAa	28/31	0.144604256946288	1	FACETS	0.902	0.8	1	0.902	0.8	1	INDETERMINATE	1	TRUE	0	0.31	1		488	520	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932644	49932644	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	136	966	0	ENST00000296474.3:c.3227C>A	p.Pro1076His	p.P1076H	ENST00000296474	NM_002447.2	1076	cCc/cAc	14/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.31	2		966	818	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933268	49933268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	178	1110	0	ENST00000296474.3:c.2842C>T	p.Pro948Ser	p.P948S	ENST00000296474	NM_002447.2	948	Cca/Tca	12/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.31	2		1110	975	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72897490	72897490	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	78	289	0	ENST00000325599.8:c.2T>C	p.Met1?	p.M1?	ENST00000325599	NM_018130.2	1	aTg/aCg	1/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.31	2		289	386	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880956	134880956	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	131	654	0	ENST00000398015.3:c.1519C>T	p.Arg507Cys	p.R507C	ENST00000398015	NM_004441.4	507	Cgt/Tgt	7/16	0.3	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.31	1		654	650	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664649	138664649	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	11	163	0	ENST00000330315.3:c.916C>T	p.Pro306Ser	p.P306S	ENST00000330315	NM_023067.3	306	Ccg/Tcg	1/1	0.3	1	FACETS	0.306	0.211	0.423	0.306	0.211	0.423	SUBCLONAL	1	TRUE	0	0.31	1		163	196	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242732	66242732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	84	395	1	ENST00000273854.3:c.1840C>T	p.His614Tyr	p.H614Y	ENST00000273854	NM_004439.5	614	Cat/Tat	9/18	1	2	FACETS	0.996	0.882	1	0.996	0.882	1	CLONAL	1	TRUE	1	0.31	2		396	544	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383638	84383638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200281698	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	151	779	1	ENST00000321945.7:c.1214G>A	p.Arg405Gln	p.R405Q	ENST00000321945	NM_139076.2	405	cGg/cAg	9/9	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.31	2		780	951	SUCCESS
APC	324	MSKCC	GRCh37	5	112177423	112177423	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	66	351	0	ENST00000257430.4:c.6132C>A	p.Ser2044Arg	p.S2044R	ENST00000257430	NM_000038.5	2044	agC/agA	16/16	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.31	2		351	424	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819754	170819754	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	79	388	2	ENST00000296930.5:c.393G>T	p.Glu131Asp	p.E131D	ENST00000296930	NM_002520.6	131	gaG/gaT	5/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.31	2		390	447	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673065	30673065	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1362687413	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	217	1238	0	ENST00000376406.3:c.3895C>T	p.Arg1299Ter	p.R1299*	ENST00000376406	NM_014641.2	1299	Cga/Tga	10/15	0.180081519154178	4	FACETS	1	0.989	1	0.689	0.639	0.741	INDETERMINATE	1	TRUE	2	0.31	4		1238	1331	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790951	89790951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1321576244	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	56	588	1	ENST00000336032.3:c.338G>A	p.Arg113His	p.R113H	ENST00000336032	NM_006813.2	113	cGc/cAc	1/2	0.180081519154178	3	FACETS	0.544	0.465	0.631	0.272	0.232	0.316	INDETERMINATE	1	TRUE	1	0.31	3		589	767	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710533	117710533	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	18	216	0	ENST00000368508.3:c.1739C>T	p.Pro580Leu	p.P580L	ENST00000368508	NM_002944.2	580	cCt/cTt	12/43	1	2	FACETS	0.478	0.36	0.616	0.478	0.36	0.616	SUBCLONAL	1	TRUE	1	0.31	2		216	243	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192428	138192428	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1170624868	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	75	311	2	ENST00000237289.4:c.64C>T	p.Arg22Trp	p.R22W	ENST00000237289	NM_001270507.1	22	Cgg/Tgg	2/9	0.3	5	FACETS	1	0.94	1			1	CLONAL	1	TRUE	NA	0.31	5		313	632	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099403	157099408	+	inframe_deletion	In_Frame_Del	DEL	CAGCAG	CAGCAG	-	rs587779743	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	26	397	0	ENST00000346085.5:c.357_362del	p.Gln130_Gln131del	p.Q130_Q131del	ENST00000346085	NM_020732.3	114	CAGCAG/-	1/20	1	2	FACETS	0.368	0.291	0.457	0.368	0.291	0.457	SUBCLONAL	1	TRUE	1	0.31	2		397	456	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880087	151880088	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	121	613	0	ENST00000262189.6:c.5236_5237del	p.Glu1746ThrfsTer2	p.E1746Tfs*2	ENST00000262189	NM_170606.2	1746	GAa/a	35/59	0.277967505876513	3	FACETS	1	0.906	1	0.502	0.453	0.554	CLONAL	1	TRUE	1	0.31	3		613	898	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730440	133730440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777111369	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	98	481	0	ENST00000318560.5:c.506G>A	p.Gly169Glu	p.G169E	ENST00000318560	NM_005157.4	169	gGg/gAg	3/11	0.144604256946288	1	FACETS	1	0.917	1	1	0.917	1	INDETERMINATE	1	TRUE	0	0.31	1		481	520	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396503	139396503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs571739078	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	160	1096	3	ENST00000277541.6:c.5422G>A	p.Asp1808Asn	p.D1808N	ENST00000277541	NM_017617.3	1808	Gac/Aac	29/34	0.144604256946288	1	FACETS	0.85	0.779	0.925	0.85	0.779	0.925	INDETERMINATE	1	TRUE	0	0.31	1		1099	1026	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967841	93967841	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	50	659	0	ENST00000369303.4:c.2086del	p.His696IlefsTer13	p.H696Ifs*13	ENST00000369303	NM_004440.3	696	Cat/at	11/17	0.180081519154178	3	FACETS	0.429	0.362	0.502	0.214	0.181	0.251	INDETERMINATE	1	TRUE	1	0.31	3		659	869	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0020640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	94	303	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.797	0.718	0.878	0.797	0.718	0.878	SUBCLONAL	1	TRUE	1	0.805414555247736	2		304	293	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519990	NA	P-0020640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	642	825	0	ENST00000269305.4:c.796G>C	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Cga	8/11	0.805414555247736	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.805414555247736	2		825	780	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944368	76944369	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	250	837	0	ENST00000373344.5:c.536dup	p.Asn179LysfsTer10	p.N179Kfs*10	ENST00000373344	NM_000489.3	179	aat/aaAt	7/35	1	2	FACETS	0.973	0.916	1	0.973	0.916	1	CLONAL	1	TRUE	1	0.805414555247736	2		837	638	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020641-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	293	251	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.802568655970737	2		251	724	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453138	140453139	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTA	rs727502902	NA	P-0020641-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	792	650	0	ENST00000288602.6:c.1794_1796dup	p.Thr599dup	p.T599dup	ENST00000288602	NM_004333.4	599	aca/acTACa	15/18	0.771466901638176	4	FACETS	0.877	0.853	0.901	0.877	0.853	0.901	CLONAL	3	TRUE	1	0.802568655970737	4		650	1352	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772950	135772951	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs118203724	NA	P-0020641-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	33	597	1	ENST00000298552.3:c.2672dup	p.Asn891LysfsTer13	p.N891Kfs*13	ENST00000298552	NM_001162426.1	891	aac/aaAc	21/23	0.801708906474401	1	FACETS	0.114	0.093	0.139	0.114	0.093	0.139	SUBCLONAL	1	TRUE	0	0.802568655970737	1		598	431	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561340	9561340	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020641-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	330	610	0	ENST00000353224.5:c.442G>A	p.Glu148Lys	p.E148K	ENST00000353224	NM_177990.2	148	Gag/Aag	4/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.802568655970737	2		610	807	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244982	123244982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020641-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	436	793	0	ENST00000358487.5:c.2122C>T	p.Pro708Ser	p.P708S	ENST00000358487	NM_000141.4	708	Ccc/Tcc	16/18	0.801708906474401	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.802568655970737	1		793	612	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356850483	NA	P-0020641-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	307	594	2	ENST00000342505.4:c.1289C>T	p.Pro430Leu	p.P430L	ENST00000342505	NM_002227.2	430	cCg/cTg	9/25	1	2	FACETS	0.976	0.925	1	0.976	0.925	1	CLONAL	1	TRUE	1	0.802568655970737	2		596	784	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-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	165	630	1	ENST00000371953.3:c.470_492+43del		p.X157_splice	ENST00000371953	NM_000314.4	157		5/9	0.801708906474401	1	FACETS	0.889	0.836	0.94	0.889	0.836	0.94	CLONAL	1	TRUE	0	0.802568655970737	1		631	277	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857149	9857149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020641-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	261	458	0	ENST00000330684.3:c.4252G>A	p.Gly1418Ser	p.G1418S	ENST00000330684	NM_001134407.1	1418	Ggc/Agc	13/13	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.802568655970737	2		458	650	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995216	15995216	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020641-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	465	778	1	ENST00000268712.3:c.2977C>T	p.Pro993Ser	p.P993S	ENST00000268712	NM_006311.3	993	Cca/Tca	22/46	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.802568655970737	2		779	1133	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897322	78897322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020641-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	414	786	2	ENST00000306801.3:c.2657C>T	p.Ser886Phe	p.S886F	ENST00000306801	NM_020761.2	886	tCc/tTc	23/34	1	2	FACETS	0.947	0.904	0.991	0.947	0.904	0.991	CLONAL	1	TRUE	1	0.802568655970737	2		788	1089	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1623990	1623991	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020641-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	346	774	1	ENST00000344749.5:c.508_509delinsTT	p.Pro170Phe	p.P170F	ENST00000344749	NM_001136139.2	170	CCc/TTc	8/19	1	2	FACETS	0.914	0.868	0.961	0.914	0.868	0.961	CLONAL	1	TRUE	1	0.802568655970737	2		775	943	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260139	10260140	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0020641-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	402	794	1	ENST00000340748.4:c.2527_2528del	p.Trp843GlyfsTer27	p.W843Gfs*27	ENST00000340748		843	TGg/g	25/40	1	2	FACETS	0.996	0.95	1	0.996	0.95	1	CLONAL	1	TRUE	1	0.802568655970737	2		795	1006	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278102	15278102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143939165	NA	P-0020641-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	439	1001	0	ENST00000263388.2:c.5320G>A	p.Asp1774Asn	p.D1774N	ENST00000263388	NM_000435.2	1774	Gac/Aac	29/33	1	2	FACETS	0.967	0.924	1	0.967	0.924	1	CLONAL	1	TRUE	1	0.802568655970737	2		1001	1131	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723473	52723473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020641-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	359	757	0	ENST00000322088.6:c.1334C>T	p.Ser445Phe	p.S445F	ENST00000322088	NM_014225.5	445	tCc/tTc	11/15	1	2	FACETS	0.955	0.908	1	0.955	0.908	1	CLONAL	1	TRUE	1	0.802568655970737	2		757	937	SUCCESS
ALK	238	MSKCC	GRCh37	2	29473983	29473983	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020641-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	394	884	3	ENST00000389048.3:c.2192C>T	p.Thr731Ile	p.T731I	ENST00000389048	NM_004304.4	731	aCc/aTc	12/29	1	2	FACETS	0.955	0.91	1	0.955	0.91	1	CLONAL	1	TRUE	1	0.802568655970737	2		887	1028	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566814	212566814	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020641-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	263	459	1	ENST00000342788.4:c.1367G>A	p.Gly456Glu	p.G456E	ENST00000342788	NM_005235.2	456	gGa/gAa	12/28	1	2	FACETS	0.992	0.936	1	0.992	0.936	1	CLONAL	1	TRUE	1	0.802568655970737	2		460	661	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180624	32180624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1340588950	NA	P-0020641-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	353	641	1	ENST00000375023.3:c.2503G>A	p.Gly835Ser	p.G835S	ENST00000375023	NM_004557.3	835	Ggc/Agc	16/30	0.725128679263061	3	FACETS	1	0.966	1	0.513	0.486	0.541	CLONAL	1	TRUE	1	0.802568655970737	3		642	1202	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395430	116395430	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020641-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	361	704	0	ENST00000397752.3:c.1723C>T	p.Leu575Phe	p.L575F	ENST00000397752	NM_000245.2	575	Ctt/Ttt	6/21	0.771466901638176	4	FACETS	1	0.968	1	0.344	0.325	0.363	CLONAL	1	TRUE	1	0.802568655970737	4		704	1572	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399273	139399273	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020641-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	525	985	1	ENST00000277541.6:c.4870G>A	p.Glu1624Lys	p.E1624K	ENST00000277541	NM_017617.3	1624	Gag/Aag	26/34	0.801708906474401	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.802568655970737	1		986	778	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589642	67589642	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	64	442	0	ENST00000274335.5:c.1405G>T	p.Glu469Ter	p.E469*	ENST00000274335		469	Gaa/Taa	10/15	0.297933375018951	1	FACETS	0.891	0.776	1	0.891	0.776	1	CLONAL	1	TRUE	0	0.32	1		442	377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0020643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	117	1017	1	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.297933375018951	1	FACETS	0.77	0.694	0.85	0.77	0.694	0.85	SUBCLONAL	1	TRUE	0	0.32	1		1018	798	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191766	123191766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	94	726	0	ENST00000218089.9:c.1355G>A	p.Gly452Glu	p.G452E	ENST00000218089	NM_001042749.1	452	gGa/gAa	15/35	1	2	FACETS	0.848	0.755	0.947	0.848	0.755	0.947	CLONAL	1	TRUE	1	0.32	2		726	693	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263314	115263314	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	116	945	1	ENST00000438362.2:c.2036C>T	p.Pro679Leu	p.P679L	ENST00000438362	NM_001242891.1	679	cCa/cTa	17/20	1	2	FACETS	0.917	0.826	1	0.917	0.826	1	CLONAL	1	TRUE	1	0.32	2		946	791	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441821	49441821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202217665	NA	P-0020643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	118	812	1	ENST00000301067.7:c.4163G>A	p.Arg1388Gln	p.R1388Q	ENST00000301067	NM_003482.3	1388	cGg/cAg	14/54	0.254580358589495	1	FACETS	0.937	0.847	1	0.937	0.847	1	CLONAL	1	TRUE	0	0.32	1		813	661	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557612	95557612	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	115	741	0	ENST00000393063.1:c.5455A>G	p.Ile1819Val	p.I1819V	ENST00000393063	NM_030621.3	1819	Att/Gtt	26/28	0.297933375018951	1	FACETS	0.896	0.808	0.988	0.896	0.808	0.988	CLONAL	1	TRUE	0	0.32	1		741	674	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39623740	39623740	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	89	735	0	ENST00000262039.4:c.2147G>C	p.Gly716Ala	p.G716A	ENST00000262039	NM_002647.2	716	gGg/gCg	20/25	0.297933375018951	1	FACETS	0.8	0.711	0.895	0.8	0.711	0.895	SUBCLONAL	1	TRUE	0	0.32	1		735	584	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702268	47702268	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs63750280	NA	P-0020643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	110	789	0	ENST00000233146.2:c.1864C>G	p.Pro622Ala	p.P622A	ENST00000233146	NM_000251.2	622	Cca/Gca	12/16	1	2	FACETS	0.978	0.879	1	0.978	0.879	1	CLONAL	1	TRUE	1	0.32	2		789	703	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594030	55594030	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	82	569	0	ENST00000288135.5:c.1816G>T	p.Ala606Ser	p.A606S	ENST00000288135	NM_000222.2	606	Gca/Tca	12/21	1	2	FACETS	0.927	0.819	1	0.927	0.819	1	CLONAL	1	TRUE	1	0.32	2		569	553	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629739	187629739	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	84	908	1	ENST00000441802.2:c.1243del	p.Tyr415ThrfsTer9	p.Y415Tfs*9	ENST00000441802	NM_005245.3	415	Tac/ac	2/27	0.297933375018951	1	FACETS	0.689	0.609	0.775	0.689	0.609	0.775	SUBCLONAL	1	TRUE	0	0.32	1		909	640	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31529166	31529166	+	start_lost	Translation_Start_Site	SNP	T	T	C	rs1480768583	NA	P-0020643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	110	840	0	ENST00000344624.3:c.1A>G	p.Met1?	p.M1?	ENST00000344624		1	Atg/Gtg	1/33	1	2	FACETS	0.855	0.768	0.947	0.855	0.768	0.947	CLONAL	1	TRUE	1	0.32	2		840	804	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359039	81359039	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	52	823	0	ENST00000222390.5:c.922G>T	p.Gly308Cys	p.G308C	ENST00000222390	NM_000601.4	308	Ggt/Tgt	8/18	0.231384942287478	2	FACETS	0.477	0.405	0.556	0.239	0.202	0.278	SUBCLONAL	1	TRUE	0	0.32	2		823	681	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971053	21971054	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	71	870	0	ENST00000304494.5:c.304dup	p.Ala102GlyfsTer18	p.A102Gfs*18	ENST00000304494	NM_000077.4	102	gcg/gGcg	2/3	0.297933375018951	1	FACETS	0.589	0.514	0.67	0.589	0.514	0.67	SUBCLONAL	1	TRUE	0	0.32	1		870	633	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411872	63411872	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs754155510	NA	P-0020643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	192	1610	1	ENST00000330258.3:c.1295G>T	p.Gly432Val	p.G432V	ENST00000330258	NM_152424.3	432	gGc/gTc	2/2	1	2	FACETS	0.966	0.892	1	0.966	0.892	1	CLONAL	1	TRUE	1	0.32	2		1611	1242	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339327	70339328	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	CT	novel	NA	P-0020643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	83	618	0	ENST00000374080.3:c.204_204+1delinsCT		p.X68_splice	ENST00000374080		68		2/45	1	2	FACETS	0.899	0.795	1	0.899	0.795	1	CLONAL	1	TRUE	1	0.32	2		618	577	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200098	123200098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	92	911	0	ENST00000218089.9:c.2170G>A	p.Asp724Asn	p.D724N	ENST00000218089	NM_001042749.1	724	Gac/Aac	22/35	1	2	FACETS	0.776	0.689	0.869	0.776	0.689	0.869	SUBCLONAL	1	TRUE	1	0.32	2		911	741	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205060	123205060	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	94	818	1	ENST00000218089.9:c.2420G>T	p.Arg807Leu	p.R807L	ENST00000218089	NM_001042749.1	807	cGt/cTt	25/35	1	2	FACETS	0.918	0.818	1	0.918	0.818	1	CLONAL	1	TRUE	1	0.32	2		819	640	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861505	152861505	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	93	801	0	ENST00000406277.2:c.247G>T	p.Glu83Ter	p.E83*	ENST00000406277	NM_152274.4	83	Gag/Tag	4/7	1		FACETS		0.825	1				CLONAL	1	TRUE	1	0.32	2		801	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0020644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	264	1217	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.461898093343399	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.461898093343399	1		1217	874	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983784	15983784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150513105	NA	P-0020644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	211	844	3	ENST00000268712.3:c.3338G>A	p.Arg1113Gln	p.R1113Q	ENST00000268712	NM_006311.3	1113	cGa/cAa	25/46	0.461898093343399	1	FACETS	0.933	0.869	0.999	0.933	0.869	0.999	CLONAL	1	TRUE	0	0.461898093343399	1		847	753	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686985	37686985	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774869348	NA	P-0020644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	211	795	1	ENST00000447079.4:c.3889G>A	p.Val1297Met	p.V1297M	ENST00000447079	NM_015083.1	1297	Gtg/Atg	14/14	0.461898093343399	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.461898093343399	1		796	626	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47601175	47601175	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747098539	NA	P-0020644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	149	765	0	ENST00000263735.4:c.413G>A	p.Arg138Gln	p.R138Q	ENST00000263735	NM_002354.2	138	cGa/cAa	3/9	1	2	FACETS	0.957	0.877	1	0.957	0.877	1	CLONAL	1	TRUE	1	0.461898093343399	2		765	674	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971159	21971159	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758389471	NA	P-0020644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	188	956	1	ENST00000304494.5:c.199G>A	p.Gly67Ser	p.G67S	ENST00000304494	NM_000077.4	67	Ggc/Agc	2/3	0.461898093343399	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.461898093343399	1		957	602	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0020645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	29	328	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.815	1	1	0.815	1	CLONAL	1	TRUE	1	0.266179800242995	2		328	216	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0020645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	9	548	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	1	2	FACETS	0.319	0.211	0.457	0.319	0.211	0.457	SUBCLONAL	1	TRUE	1	0.266179800242995	2		548	212	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0020648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	44	328	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.229289395414886	2		328	377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0020648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	95	717	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.229289395414886	1	FACETS	0.89	0.792	0.995	0.89	0.792	0.995	CLONAL	1	TRUE	0	0.229289395414886	1		717	824	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001395	150001395	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	192	1064	1	ENST00000253339.5:c.2209C>T	p.Arg737Ter	p.R737*	ENST00000253339		737	Cga/Tga	4/7	0.803688904102525	1	FACETS	0.816	0.77	0.862	0.816	0.77	0.862	CLONAL	1	TRUE	0	0.823752805808263	1		1065	336	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105887	27105887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375198223	NA	P-0020649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	295	788	0	ENST00000324856.7:c.5498G>A	p.Arg1833His	p.R1833H	ENST00000324856	NM_006015.4	1833	cGt/cAt	20/20	NA	2	FACETS	0.985	0.933	1			1	INDETERMINATE	1	TRUE	NA	0.823752805808263	2		788	727	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0020651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	1003	560	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.497085931537137	10	FACETS	0.947	0.925	0.969			1	CLONAL	8	TRUE	NA	0.497085931537137	10		560	1591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs1202793339	NA	P-0020651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	189	862	0	ENST00000269305.4:c.560-1G>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			NA	2	FACETS	0.753	0.702	0.805			1	INDETERMINATE	2	TRUE	NA	0.497085931537137	2		862	505	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514475	103514475	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs959017243	NA	P-0020651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	43	332	0	ENST00000355739.4:c.976T>C	p.Cys326Arg	p.C326R	ENST00000355739	NM_000123.3	326	Tgt/Cgt	8/15	0.467026003110554	4	FACETS	0.676	0.567	0.797	0.338	0.283	0.399	SUBCLONAL	1	TRUE	2	0.497085931537137	4		332	383	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0020652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	82	328	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.621	0.549	0.698	0.621	0.549	0.698	SUBCLONAL	1	TRUE	1	0.497100758633321	2		328	531	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	148	251	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.96	0.88	1	0.96	0.88	1	CLONAL	1	TRUE	1	0.497100758633321	2		251	620	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684326	29684326	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201367	NA	P-0020652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	224	865	3	ENST00000356175.3:c.7846C>T	p.Arg2616Ter	p.R2616*	ENST00000356175	NM_000267.3	2616	Cga/Tga	53/57	1	2	FACETS	0.95	0.885	1	0.95	0.885	1	CLONAL	1	TRUE	1	0.497100758633321	2		868	949	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832913	3832913	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	119	572	0	ENST00000262367.5:c.1345C>A	p.Pro449Thr	p.P449T	ENST00000262367	NM_004380.2	449	Cca/Aca	6/31	1	2	FACETS	0.88	0.798	0.966	0.88	0.798	0.966	CLONAL	1	TRUE	1	0.497100758633321	2		572	544	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562746	29562746	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs199474742	NA	P-0020652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	190	777	0	ENST00000356175.3:c.3826C>G	p.Arg1276Gly	p.R1276G	ENST00000356175	NM_000267.3	1276	Cga/Gga	28/57	1	2	FACETS	0.943	0.873	1	0.943	0.873	1	CLONAL	1	TRUE	1	0.497100758633321	2		777	811	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0020661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	143	545	2	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.347650653580922	2	FACETS	1	0.985	1	0.681	0.624	0.74	CLONAL	1	TRUE	0	0.403074146640166	2		547	521	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0020661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	58	412	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.20215009433528	1	FACETS	0.387	0.332	0.447	0.387	0.332	0.447	INDETERMINATE	1	TRUE	0	0.403074146640166	1		412	594	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0020661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	243	1111	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.403074146640166	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.403074146640166	1		1112	812	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555687605	NA	P-0020661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	128	435	0	ENST00000342988.3:c.1610A>G	p.Asp537Gly	p.D537G	ENST00000342988	NM_005359.5	537	gAc/gGc	12/12	0.401036928055262	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.403074146640166	1		435	488	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858337	9858337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs560057284	NA	P-0020661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	159	371	0	ENST00000330684.3:c.3064C>T	p.Arg1022Cys	p.R1022C	ENST00000330684	NM_001134407.1	1022	Cgc/Tgc	13/13	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.403074146640166	2		371	607	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225896	2225896	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	253	793	0	ENST00000326181.6:c.1688A>G	p.Tyr563Cys	p.Y563C	ENST00000326181	NM_032271.2	563	tAc/tGc	18/21	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.403074146640166	2		793	1007	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311616	15311616	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	21	106	0	ENST00000263388.2:c.101C>A	p.Ala34Glu	p.A34E	ENST00000263388	NM_000435.2	34	gCg/gAg	1/33	1	2	FACETS	0.595	0.461	0.749	0.595	0.461	0.749	SUBCLONAL	1	TRUE	1	0.403074146640166	2		106	175	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939628	131939628	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	51	408	0	ENST00000265335.6:c.2414T>A	p.Val805Asp	p.V805D	ENST00000265335		805	gTt/gAt	15/25	0.20215009433528	1	FACETS	0.393	0.334	0.458	0.393	0.334	0.458	INDETERMINATE	1	TRUE	0	0.403074146640166	1		408	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0020662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	146	755	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.191818393266832	2	FACETS	0.923	0.845	1	0.923	0.845	1	CLONAL	2	TRUE	0	0.229180220312707	2		755	690	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591888	48591888	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	38	634	2	ENST00000342988.3:c.1051G>T	p.Asp351Tyr	p.D351Y	ENST00000342988	NM_005359.5	351	Gat/Tat	9/12	0.229180220312707	1	FACETS	0.555	0.458	0.663	0.555	0.458	0.663	SUBCLONAL	1	TRUE	0	0.229180220312707	1		636	529	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956772	68956772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199819614	NA	P-0020662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	78	898	0	ENST00000288368.4:c.890G>A	p.Arg297His	p.R297H	ENST00000288368	NM_024870.2	297	cGt/cAt	8/40	1	2	FACETS	0.691	0.606	0.783	0.691	0.606	0.783	SUBCLONAL	1	TRUE	1	0.229180220312707	2		898	985	SUCCESS
AR	367	MSKCC	GRCh37	X	66766568	66766568	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	109	1026	1	ENST00000374690.3:c.1580G>A	p.Trp527Ter	p.W527*	ENST00000374690	NM_000044.3	527	tGg/tAg	1/8	0.229180220312707	1	FACETS	0.906	0.812	1	0.906	0.812	1	CLONAL	1	TRUE	0	0.229180220312707	1		1027	930	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566300	141566300	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	59	613	0	ENST00000220592.5:c.1112C>G	p.Ser371Trp	p.S371W	ENST00000220592	NM_012154.3	371	tCg/tGg	9/19	1	2	FACETS	0.697	0.598	0.804	0.697	0.598	0.804	SUBCLONAL	1	TRUE	1	0.229180220312707	2		613	739	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063718	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0020663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	30	283	0	ENST00000412916.2:c.165+2dup		p.X55_splice	ENST00000412916		55			0.165957750705164	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		283	220	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847300	68847301	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	61	721	0	ENST00000261769.5:c.1223dup	p.Trp409ValfsTer10	p.W409Vfs*10	ENST00000261769	NM_004360.3	408	gcg/gCcg	9/16	0.165957750705164	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		721	625	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	53	372	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.309	0.264	0.358	0.309	0.264	0.358	SUBCLONAL	1	TRUE	1	0.841868983199281	2		373	408	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895610	28895610	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	24	524	0	ENST00000282397.4:c.3164G>A	p.Arg1055Lys	p.R1055K	ENST00000282397	NM_002019.4	1055	aGa/aAa	23/30	1	2	FACETS	0.15	0.117	0.188	0.15	0.117	0.188	SUBCLONAL	1	TRUE	1	0.841868983199281	2		524	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	rs786202799	NA	P-0020664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	57	771	1	ENST00000269305.4:c.376-2A>T		p.X126_splice	ENST00000269305	NM_001126112.2	126			NA	2	FACETS	0.217	0.185	0.251			1	INDETERMINATE	1	TRUE	NA	0.841868983199281	2		772	625	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017769	31017769	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	46	582	0	ENST00000375687.4:c.631G>T	p.Ala211Ser	p.A211S	ENST00000375687	NM_015338.5	211	Gcc/Tcc	8/13	1	2	FACETS	0.239	0.201	0.28	0.239	0.201	0.28	SUBCLONAL	1	TRUE	1	0.841868983199281	2		582	458	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863371	57863371	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	28	776	0	ENST00000228682.2:c.1466G>C	p.Gly489Ala	p.G489A	ENST00000228682	NM_005269.2	489	gGc/gCc	11/12	1	2	FACETS	0.123	0.097	0.151	0.123	0.097	0.151	SUBCLONAL	1	TRUE	1	0.841868983199281	2		776	543	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680722	88680722	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	39	679	2	ENST00000360948.2:c.535del	p.Glu179ArgfsTer24	p.E179Rfs*24	ENST00000360948	NM_001012338.2	179	Gag/ag	6/19	1	2	FACETS	0.209	0.173	0.249	0.209	0.173	0.249	SUBCLONAL	1	TRUE	1	0.841868983199281	2		681	443	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462640	29462640	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	71	801	0	ENST00000389048.3:c.2261C>A	p.Ser754Tyr	p.S754Y	ENST00000389048	NM_004304.4	754	tCc/tAc	13/29	1	2	FACETS	0.266	0.232	0.303	0.266	0.232	0.303	SUBCLONAL	1	TRUE	1	0.841868983199281	2		801	633	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536169	41536169	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	38	641	1	ENST00000263253.7:c.1786G>T	p.Asp596Tyr	p.D596Y	ENST00000263253	NM_001429.3	596	Gat/Tat	9/31	1	2	FACETS	0.186	0.153	0.223	0.186	0.153	0.223	SUBCLONAL	1	TRUE	1	0.841868983199281	2		642	485	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218783	66218783	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	29	430	0	ENST00000273854.3:c.2275G>C	p.Gly759Arg	p.G759R	ENST00000273854	NM_004439.5	759	Ggc/Cgc	13/18	1	2	FACETS	0.263	0.212	0.321	0.263	0.212	0.321	SUBCLONAL	1	TRUE	1	0.841868983199281	2		430	262	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797181	32797181	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	39	614	0	ENST00000374899.4:c.1928A>G	p.Gln643Arg	p.Q643R	ENST00000374899	NM_018833.2	643	cAg/cGg	11/12	1	2	FACETS	0.211	0.175	0.252	0.211	0.175	0.252	SUBCLONAL	1	TRUE	1	0.841868983199281	2		614	439	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444293	50444293	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	24	408	0	ENST00000331340.3:c.226del	p.Glu76LysfsTer17	p.E76Kfs*17	ENST00000331340	NM_006060.4	75	Ggg/gg	4/8	1	2	FACETS	0.169	0.132	0.212	0.169	0.132	0.212	SUBCLONAL	1	TRUE	1	0.841868983199281	2		408	337	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942842	68942842	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	59	690	0	ENST00000288368.4:c.654G>T	p.Met218Ile	p.M218I	ENST00000288368	NM_024870.2	218	atG/atT	6/40	1	2	FACETS	0.253	0.218	0.292	0.253	0.218	0.292	SUBCLONAL	1	TRUE	1	0.841868983199281	2		690	553	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223348	53223358	+	frameshift_variant	Frame_Shift_Del	DEL	TCTGAGGGGGT	TCTGAGGGGGT	-	novel	NA	P-0020664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	31	704	0	ENST00000375401.3:c.4001_4011del	p.Asp1334GlyfsTer9	p.D1334Gfs*9	ENST00000375401	NM_004187.3	1334	gACCCCCTCAGA/g	23/26	NA	2	FACETS	0.159	0.128	0.194			1	INDETERMINATE	1	TRUE	NA	0.841868983199281	2		704	464	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357441	70357441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	60	804	0	ENST00000374080.3:c.5782C>T	p.His1928Tyr	p.H1928Y	ENST00000374080		1928	Cat/Tat	40/45	1	2	FACETS	0.238	0.205	0.274	0.238	0.205	0.274	SUBCLONAL	1	TRUE	1	0.841868983199281	2		804	599	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0020665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	153	1002	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.259735178669664	3	FACETS	0.936	0.858	1	0.936	0.858	1	CLONAL	2	TRUE	1	0.259735178669664	3		1002	711	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579529	7579529	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658483	NA	P-0020665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	101	595	0	ENST00000269305.4:c.158G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tGg/tAg	4/11	0.196056569813834	1	FACETS	0.981	0.877	1	0.981	0.877	1	CLONAL	1	TRUE	0	0.259735178669664	1		595	690	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62298844	62298844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560281693	NA	P-0020665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	117	601	0	ENST00000360203.5:c.637C>T	p.Arg213Trp	p.R213W	ENST00000360203	NM_001283009.1	213	Cgg/Tgg	8/35	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.259735178669664	2		601	768	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0020667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	75	528	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.28	2		528	483	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0020667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	17	565	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.18	0.134	0.237	0.18	0.134	0.237	SUBCLONAL	1	TRUE	1	0.28	2		565	673	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121909229	NA	P-0020667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	26	613	0	ENST00000371953.3:c.389G>C	p.Arg130Pro	p.R130P	ENST00000371953	NM_000314.4	130	cGa/cCa	5/9	1	2	FACETS	0.385	0.304	0.478	0.385	0.304	0.478	SUBCLONAL	1	TRUE	1	0.28	2		613	483	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589594	67589596	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	novel	NA	P-0020667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	51	420	0	ENST00000274335.5:c.1358_1360del	p.Asn453del	p.N453del	ENST00000274335		453	AAC/-	10/15	1	2	FACETS	0.979	0.835	1	0.979	0.835	1	CLONAL	1	TRUE	1	0.28	2		420	372	SUCCESS
ATM	472	MSKCC	GRCh37	11	108100037	108100037	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555055319	NA	P-0020667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	40	437	0	ENST00000278616.4:c.318A>C	p.Lys106Asn	p.K106N	ENST00000278616	NM_000051.3	106	aaA/aaC	4/63	1	2	FACETS	0.796	0.663	0.943	0.796	0.663	0.943	CLONAL	1	TRUE	1	0.28	2		437	359	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0020668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	94	619	8	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.757	0.674	0.846	0.757	0.674	0.846	SUBCLONAL	1	TRUE	1	0.351553631108554	2		627	706	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0020668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	52	412	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.649	0.553	0.753	0.649	0.553	0.753	SUBCLONAL	1	TRUE	1	0.351553631108554	2		412	456	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106078	27106078	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	43	486	1	ENST00000324856.7:c.5693del	p.Pro1898HisfsTer25	p.P1898Hfs*25	ENST00000324856	NM_006015.4	1897	Ccc/cc	20/20	1	2	FACETS	0.481	0.402	0.568	0.481	0.402	0.568	SUBCLONAL	1	TRUE	1	0.351553631108554	2		487	509	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0020668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	45	304	3	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.444	0.372	0.523	0.444	0.372	0.523	SUBCLONAL	1	TRUE	1	0.351553631108554	2		307	577	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	70	515	1	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	0.71	0.619	0.807	0.71	0.619	0.807	SUBCLONAL	1	TRUE	1	0.351553631108554	2		516	561	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589589	67589591	+	inframe_deletion	In_Frame_Del	DEL	AAT	AAT	-	novel	NA	P-0020668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	60	343	0	ENST00000274335.5:c.1353_1355del	p.Glu451_Tyr452delinsAsp	p.E451_Y452delinsD	ENST00000274335		451	gAATat/gat	10/15	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.351553631108554	2		343	318	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098566	11098566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776534924	NA	P-0020668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	123	640	4	ENST00000358026.2:c.1084G>A	p.Asp362Asn	p.D362N	ENST00000358026	NM_001128849.1	362	Gac/Aac	6/36	1	2	FACETS	0.88	0.796	0.969	0.88	0.796	0.969	CLONAL	1	TRUE	1	0.351553631108554	2		644	795	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950099	38950099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757900166	NA	P-0020668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	92	524	0	ENST00000357387.3:c.3851C>T	p.Ser1284Leu	p.S1284L	ENST00000357387	NM_152756.3	1284	tCg/tTg	31/38	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.351553631108554	2		524	502	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653848	89653856	+	inframe_deletion	In_Frame_Del	DEL	ATATTGATG	ATATTGATG	-	novel	NA	P-0020668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	45	474	0	ENST00000371953.3:c.148_156del	p.Ile50_Asp52del	p.I50_D52del	ENST00000371953	NM_000314.4	49	aATATTGATGat/aat	2/9	0.312124845679972	3	FACETS	0.652	0.548	0.766	0.326	0.274	0.383	SUBCLONAL	1	TRUE	1	0.351553631108554	3		474	462	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690836	89690837	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0020668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	126	430	0	ENST00000371953.3:c.243_244del	p.Phe81LeufsTer10	p.F81Lfs*10	ENST00000371953	NM_000314.4	81	ttTAat/ttat	4/9	0.312124845679972	3	FACETS	0.953	0.87	1	0.953	0.87	1	CLONAL	2	TRUE	1	0.351553631108554	3		430	442	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	532688	532688	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	74	796	0	ENST00000451590.1:c.518del	p.Pro173LeufsTer10	p.P173Lfs*10	ENST00000451590	NM_001130442.1	173	cCt/ct	5/5	1	2	FACETS	0.488	0.426	0.555	0.488	0.426	0.555	SUBCLONAL	1	TRUE	1	0.351553631108554	2		796	863	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929239	32929240	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs397507907	NA	P-0020668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	55	566	0	ENST00000380152.3:c.7251_7252del	p.His2417GlnfsTer3	p.H2417Qfs*3	ENST00000380152		2417	CAc/c	14/27	1	2	FACETS	0.628	0.538	0.727	0.628	0.538	0.727	SUBCLONAL	1	TRUE	1	0.351553631108554	2		566	498	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11027412	11027412	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	96	757	1	ENST00000327064.4:c.979C>T	p.Arg327Ter	p.R327*	ENST00000327064	NM_199141.1	327	Cga/Tga	8/16	1	2	FACETS	0.625	0.556	0.699	0.625	0.556	0.699	SUBCLONAL	1	TRUE	1	0.351553631108554	2		758	874	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220069	36220069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1239076295	NA	P-0020668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	133	651	1	ENST00000222270.7:c.4789C>T	p.Arg1597Trp	p.R1597W	ENST00000222270	NM_014727.1	1597	Cgg/Tgg	22/37	1	2	FACETS	0.989	0.899	1	0.989	0.899	1	CLONAL	1	TRUE	1	0.351553631108554	2		652	765	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009113	27009118	+	inframe_deletion	In_Frame_Del	DEL	AGCCCG	AGCCCG	-	novel	NA	P-0020668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	12	155	0	ENST00000335756.4:c.56_61del	p.Ser19_Pro20del	p.S19_P20del	ENST00000335756	NM_001809.3	17	AGCCCG/-	1/5	1	2	FACETS	0.429	0.302	0.584	0.429	0.302	0.584	SUBCLONAL	1	TRUE	1	0.351553631108554	2		155	159	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027104	71027104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1454411756	NA	P-0020668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	91	533	0	ENST00000318789.4:c.1223C>T	p.Thr408Met	p.T408M	ENST00000318789	NM_032682.5	408	aCg/aTg	15/21	1	2	FACETS	0.843	0.75	0.943	0.843	0.75	0.943	CLONAL	1	TRUE	1	0.351553631108554	2		533	614	SUCCESS
APC	324	MSKCC	GRCh37	5	112174471	112174471	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	51	327	0	ENST00000257430.4:c.3183del	p.Lys1061AsnfsTer65	p.K1061Nfs*65	ENST00000257430	NM_000038.5	1060	atA/at	16/16	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.351553631108554	2		327	272	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250047	53250047	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	100	600	1	ENST00000375401.3:c.202del	p.Arg68GlufsTer5	p.R68Efs*5	ENST00000375401	NM_004187.3	68	Cga/ga	2/26	1	2	FACETS	0.739	0.66	0.823	0.739	0.66	0.823	SUBCLONAL	1	TRUE	1	0.351553631108554	2		601	770	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0020669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	79	492	0	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.341502357593247	2		492	391	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920785	100920785	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	63	574	0	ENST00000325455.5:c.2363G>T	p.Arg788Leu	p.R788L	ENST00000325455	NM_001202474.3	788	cGg/cTg	6/8	0.340190267275344	2	FACETS	1	0.881	1	0.507	0.44	0.578	CLONAL	1	TRUE	0	0.341502357593247	2		574	364	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933454	100933455	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	37	426	0	ENST00000325455.5:c.1935dup	p.Arg646GlnfsTer20	p.R646Qfs*20	ENST00000325455	NM_001202474.3	645	-/C	4/8	0.340190267275344	2	FACETS	0.576	0.476	0.688	0.288	0.238	0.344	SUBCLONAL	1	TRUE	0	0.341502357593247	2		426	376	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913111	44913113	+	frameshift_variant	Frame_Shift_Del	DEL	AGC	AGC	TT	novel	NA	P-0020669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	70	849	0	ENST00000377967.4:c.786_788delinsTT	p.Lys262AsnfsTer63	p.K262Nfs*63	ENST00000377967	NM_021140.2	262	aaAGCc/aaTTc	10/29	1	2	FACETS	0.93	0.813	1	0.93	0.813	1	CLONAL	1	TRUE	1	0.341502357593247	2		849	441	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338669	70338669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	117	845	1	ENST00000374080.3:c.65C>T	p.Pro22Leu	p.P22L	ENST00000374080		22	cCc/cTc	1/45	1	2	FACETS	0.969	0.875	1	0.969	0.875	1	CLONAL	1	TRUE	1	0.341502357593247	2		846	707	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0020673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	1067	685	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.827599552828897	14	FACETS	1	0.992	1			1	CLONAL	12	TRUE	NA	0.827599552828897	14		685	1267	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007332	143007332	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	269	593	7	ENST00000262992.4:c.2452del	p.Arg818GlufsTer4	p.R818Efs*4	ENST00000262992	NM_001101669.1	818	Aga/ga	22/24	0.827599552828897	3	FACETS	0.931	0.901	0.959	0.931	0.901	0.959	CLONAL	3	TRUE	0	0.827599552828897	3		600	329	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579396	7579405	+	frameshift_variant	Frame_Shift_Del	DEL	GACAGAAGAT	GACAGAAGAT	-	novel	NA	P-0020673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	203	777	6	ENST00000269305.4:c.282_291del	p.Ser95LeufsTer25	p.S95Lfs*25	ENST00000269305	NM_001126112.2	94	tcATCTTCTGTC/tc	4/11	0.827599552828897	2	FACETS	0.902	0.863	0.939	0.902	0.863	0.939	CLONAL	2	TRUE	0	0.827599552828897	2		783	272	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32968967	32968967	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0020673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	93	545	6	ENST00000380152.3:c.9398C>G	p.Ser3133Ter	p.S3133*	ENST00000380152		3133	tCa/tGa	25/27	0.827599552828897	7	FACETS	0.992	0.883	1			1	CLONAL	1	TRUE	NA	0.827599552828897	7		551	695	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591125	67591126	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAGAAAGAC	novel	NA	P-0020675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	117	479	0	ENST00000274335.5:c.1723_1731dup	p.Lys575_Arg577dup	p.K575_R577dup	ENST00000274335		575	ctg/ctGAGAAAGACg	12/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.394591375508165	2		479	439	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578509	7578509	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519978	NA	P-0020675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	413	1012	0	ENST00000269305.4:c.421T>C	p.Cys141Arg	p.C141R	ENST00000269305	NM_001126112.2	141	Tgc/Cgc	5/11	0.402125953872414	0	FACETS	1	0.986	1			1	CLONAL	1	TRUE	0	0.394591375508165	0		1012	1168	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843716	156843717	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	293	1037	0	ENST00000524377.1:c.1145dup	p.Glu384ArgfsTer18	p.E384Rfs*18	ENST00000524377	NM_002529.3	381	aac/aaCc	8/17	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.394591375508165	2		1037	1385	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589598	67589599	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0020675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	96	633	0	ENST00000274335.5:c.1362_1363del	p.Gln455ValfsTer9	p.Q455Vfs*9	ENST00000274335		454	aCT/a	10/15	1	2	FACETS	0.934	0.835	1	0.934	0.835	1	CLONAL	1	TRUE	1	0.394591375508165	2		633	521	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633319	8633319	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs778130827	NA	P-0020675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	44	778	0	ENST00000356435.5:c.350G>A	p.Arg117Gln	p.R117Q	ENST00000356435		117	cGg/cAg	3/35	1	2	FACETS	0.384	0.321	0.453	0.384	0.321	0.453	SUBCLONAL	1	TRUE	1	0.394591375508165	2		778	581	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721836	176721836	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	102	736	0	ENST00000439151.2:c.7467T>G	p.Ser2489Arg	p.S2489R	ENST00000439151	NM_022455.4	2489	agT/agG	23/23	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.29099293390566	2		736	694	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0020678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	54	685	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.486131864234086	4	FACETS	0.399	0.34	0.464	0.2	0.17	0.232	SUBCLONAL	1	TRUE	2	0.515797982723475	4		685	795	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	547	924	2	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.515797982723475	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.515797982723475	2		926	1052	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0020678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	2352	675	6	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	0.515797982723475	21	FACETS	1	0.996	1	0.914	0.904	0.925	CLONAL	18	TRUE	1	0.515797982723475	21		681	2943	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557642	95557642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	688	871	2	ENST00000393063.1:c.5425G>A	p.Gly1809Arg	p.G1809R	ENST00000393063	NM_030621.3	1809	Ggg/Agg	26/28	0.840609527114484	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.840609527114484	2		873	740	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577529	7577529	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs730882027	NA	P-0020679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	28	835	0	ENST00000269305.4:c.752T>A	p.Ile251Asn	p.I251N	ENST00000269305	NM_001126112.2	251	aTc/aAc	7/11	1	2	FACETS	0.078	0.062	0.097	0.078	0.062	0.097	SUBCLONAL	1	TRUE	1	0.840609527114484	2		835	851	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0020681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	102	340	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.292100776380612	3	FACETS	0.761	0.679	0.848			1	SUBCLONAL	1	TRUE	NA	0.322033065845279	3		340	967	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11177096	11177096	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878855328	NA	P-0020681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	56	778	0	ENST00000361445.4:c.6981G>A	p.Met2327Ile	p.M2327I	ENST00000361445	NM_004958.3	2327	atG/atA	50/58	1	2	FACETS	0.466	0.398	0.54	0.466	0.398	0.54	SUBCLONAL	1	TRUE	1	0.322033065845279	2		778	747	SUCCESS
APC	324	MSKCC	GRCh37	5	112175524	112175524	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	87	525	0	ENST00000257430.4:c.4233del	p.Ser1411ArgfsTer4	p.S1411Rfs*4	ENST00000257430	NM_000038.5	1411	agT/ag	16/16	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.322033065845279	2		525	514	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591825	48591825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767342	NA	P-0020681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	41	759	1	ENST00000342988.3:c.988G>A	p.Glu330Lys	p.E330K	ENST00000342988	NM_005359.5	330	Gaa/Aaa	9/12	1	2	FACETS	0.404	0.336	0.481	0.404	0.336	0.481	SUBCLONAL	1	TRUE	1	0.322033065845279	2		760	630	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs121913468	NA	P-0020681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	44	589	0	ENST00000269571.5:c.2305G>A	p.Asp769Asn	p.D769N	ENST00000269571		769	Gac/Aac	19/27	1	2	FACETS	0.452	0.379	0.534	0.452	0.379	0.534	SUBCLONAL	1	TRUE	1	0.322033065845279	2		589	604	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114799803	114799803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	65	844	2	ENST00000543371.1:c.470C>T	p.Pro157Leu	p.P157L	ENST00000543371	NM_001198531.1	157	cCa/cTa	5/14	1	2	FACETS	0.531	0.46	0.609	0.531	0.46	0.609	SUBCLONAL	1	TRUE	1	0.322033065845279	2		846	760	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0020682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	309	651	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.261940755327154	3	FACETS	0.834	0.792	0.875			1	INDETERMINATE	3	TRUE	NA	0.458141768005234	3		651	663	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493688	56493688	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	73	561	0	ENST00000267101.3:c.3004G>C	p.Glu1002Gln	p.E1002Q	ENST00000267101	NM_001982.3	1002	Gaa/Caa	25/28	0.408385999028004	2	FACETS	0.697	0.612	0.789	0.349	0.306	0.395	SUBCLONAL	1	TRUE	0	0.458141768005234	2		561	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0020683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	220	642	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.393183248015772	1	FACETS	0.998	0.93	1	0.998	0.93	1	CLONAL	1	TRUE	0	0.393183248015772	1		642	901	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577427	64577433	+	frameshift_variant	Frame_Shift_Del	DEL	CGGTTGA	CGGTTGA	-	novel	NA	P-0020684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	358	928	0	ENST00000312049.6:c.149_155del	p.Val50AlafsTer67	p.V50Afs*67	ENST00000312049	NM_130799.2	50	gTCAACCGc/gc	2/10	0.718634695669552	1	FACETS	0.877	0.837	0.916	0.877	0.837	0.916	CLONAL	1	TRUE	0	0.718634695669552	1		928	728	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219152	94219152	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	413	858	0	ENST00000323929.3:c.252G>A	p.Met84Ile	p.M84I	ENST00000323929	NM_005591.3	84	atG/atA	4/20	0.718634695669552	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.718634695669552	1		858	732	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158197	47158197	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	378	920	1	ENST00000409792.3:c.4502G>A	p.Cys1501Tyr	p.C1501Y	ENST00000409792	NM_014159.6	1501	tGt/tAt	4/21	0.718634695669552	1	FACETS	0.977	0.936	1	0.977	0.936	1	CLONAL	1	TRUE	0	0.718634695669552	1		921	690	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	152	303	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.909	0.842	0.977	0.909	0.842	0.977	CLONAL	1	TRUE	1	0.870992440320264	2		304	384	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	31	369	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	NA	2	FACETS	0.077	0.062	0.095			1	INDETERMINATE	1	TRUE	NA	0.870992440320264	2		369	922	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514007	103514007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	45	825	0	ENST00000355739.4:c.823G>A	p.Glu275Lys	p.E275K	ENST00000355739	NM_000123.3	275	Gag/Aag	7/15	1	2	FACETS	0.163	0.137	0.193	0.163	0.137	0.193	SUBCLONAL	1	TRUE	1	0.870992440320264	2		825	632	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032756	48032756	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	23	426	0	ENST00000234420.5:c.3557-1G>A		p.X1186_splice	ENST00000234420	NM_000179.2	1186			0.870992440320264	1	FACETS	0.143	0.112	0.179	0.143	0.112	0.179	SUBCLONAL	1	TRUE	0	0.870992440320264	1		426	208	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021817	71021817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs797045586	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	38	379	0	ENST00000318789.4:c.1541G>A	p.Arg514His	p.R514H	ENST00000318789	NM_032682.5	514	cGt/cAt	18/21	0.182658409115116	1	FACETS	0.185	0.154	0.22	0.185	0.154	0.22	INDETERMINATE	1	TRUE	0	0.870992440320264	1		379	266	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871249	12871249	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	22	249	0	ENST00000228872.4:c.475+1G>A		p.X159_splice	ENST00000228872	NM_004064.3	159			0.870992440320264	1	FACETS	0.213	0.167	0.265	0.213	0.167	0.265	SUBCLONAL	1	TRUE	0	0.870992440320264	1		249	134	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272287	15272287	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	47	960	1	ENST00000263388.2:c.6152C>T	p.Pro2051Leu	p.P2051L	ENST00000263388	NM_000435.2	2051	cCt/cTt	33/33	1	2	FACETS	0.162	0.136	0.19	0.162	0.136	0.19	SUBCLONAL	1	TRUE	1	0.870992440320264	2		961	667	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019408	31019408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769717271	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	159	740	0	ENST00000375687.4:c.905G>A	p.Arg302His	p.R302H	ENST00000375687	NM_015338.5	302	cGt/cAt	10/13	1	2	FACETS	0.539	0.496	0.585	0.539	0.496	0.585	SUBCLONAL	1	TRUE	1	0.870992440320264	2		740	677	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983994	2983994	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	390	1013	1	ENST00000396946.4:c.536G>A	p.Arg179Gln	p.R179Q	ENST00000396946	NM_032415.4	179	cGg/cAg	5/25	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.870992440320264	2		1014	842	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588876	29588876	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1555619056	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	81	480	2	ENST00000356175.3:c.4661+1G>A		p.X1554_splice	ENST00000356175	NM_000267.3	1554			1	2	FACETS	0.496	0.44	0.556	0.496	0.44	0.556	SUBCLONAL	1	TRUE	1	0.870992440320264	2		482	375	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027089	48027089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	162	713	0	ENST00000234420.5:c.1967C>T	p.Pro656Leu	p.P656L	ENST00000234420	NM_000179.2	656	cCc/cTc	4/10	0.870992440320264	1	FACETS	0.662	0.619	0.706	0.662	0.619	0.706	SUBCLONAL	1	TRUE	0	0.870992440320264	1		713	317	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945970	17945970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568403015	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	73	1066	3	ENST00000458235.1:c.1969C>T	p.Arg657Trp	p.R657W	ENST00000458235	NM_000215.3	657	Cgg/Tgg	15/24	1	2	FACETS	0.197	0.171	0.224	0.197	0.171	0.224	SUBCLONAL	1	TRUE	1	0.870992440320264	2		1069	853	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891010	112891010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	42	493	0	ENST00000351677.2:c.344G>A	p.Gly115Glu	p.G115E	ENST00000351677	NM_002834.3	115	gGa/gAa	4/16	1	2	FACETS	0.249	0.208	0.294	0.249	0.208	0.294	SUBCLONAL	1	TRUE	1	0.870992440320264	2		493	388	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435864	110435864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	38	757	0	ENST00000375856.3:c.2537G>A	p.Gly846Glu	p.G846E	ENST00000375856	NM_003749.2	846	gGg/gAg	1/2	1	2	FACETS	0.143	0.117	0.171	0.143	0.117	0.171	SUBCLONAL	1	TRUE	1	0.870992440320264	2		757	612	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29662034	29662034	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs876660696	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	110	636	1	ENST00000356175.3:c.5928G>A	p.Trp1976Ter	p.W1976*	ENST00000356175	NM_000267.3	1976	tgG/tgA	39/57	1	2	FACETS	0.537	0.485	0.592	0.537	0.485	0.592	SUBCLONAL	1	TRUE	1	0.870992440320264	2		637	470	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981515	70981515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745606576	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	50	1178	1	ENST00000276594.2:c.581G>A	p.Arg194Gln	p.R194Q	ENST00000276594	NM_024504.3	194	cGg/cAg	2/8	1	2	FACETS	0.123	0.103	0.144	0.123	0.103	0.144	SUBCLONAL	1	TRUE	1	0.870992440320264	2		1179	936	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489187	2489187	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	38	976	0	ENST00000355716.4:c.92G>A	p.Gly31Glu	p.G31E	ENST00000355716	NM_003820.2	31	gGa/gAa	2/8	1	2	FACETS	0.119	0.097	0.142	0.119	0.097	0.142	SUBCLONAL	1	TRUE	1	0.870992440320264	2		976	736	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778801	9778801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775700162	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	46	951	2	ENST00000377346.4:c.1070C>T	p.Thr357Met	p.T357M	ENST00000377346	NM_005026.3	357	aCg/aTg	9/24	1	2	FACETS	0.133	0.112	0.158	0.133	0.112	0.158	SUBCLONAL	1	TRUE	1	0.870992440320264	2		953	792	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202720	16202720	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	119	567	0	ENST00000375759.3:c.428C>T	p.Ala143Val	p.A143V	ENST00000375759	NM_015001.2	143	gCt/gTt	3/15	1	2	FACETS	0.567	0.514	0.622	0.567	0.514	0.622	SUBCLONAL	1	TRUE	1	0.870992440320264	2		567	482	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363457	40363457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	71	940	0	ENST00000397332.2:c.772G>A	p.Ala258Thr	p.A258T	ENST00000397332	NM_001033082.2	258	Gct/Act	3/3	1	2	FACETS	0.226	0.197	0.257	0.226	0.197	0.257	SUBCLONAL	1	TRUE	1	0.870992440320264	2		940	722	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799216	45799216	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064794128	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	145	782	0	ENST00000450313.1:c.217G>A	p.Glu73Lys	p.E73K	ENST00000450313	NM_012222.2	73	Gaa/Aaa	3/16	1	2	FACETS	0.547	0.5	0.595	0.547	0.5	0.595	SUBCLONAL	1	TRUE	1	0.870992440320264	2		782	609	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799240	45799240	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553130504	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	36	656	2	ENST00000450313.1:c.193C>T	p.Pro65Ser	p.P65S	ENST00000450313	NM_012222.2	65	Cca/Tca	3/16	1	2	FACETS	0.151	0.124	0.182	0.151	0.124	0.182	SUBCLONAL	1	TRUE	1	0.870992440320264	2		658	547	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321336	65321336	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	69	952	0	ENST00000342505.4:c.1504G>A	p.Val502Met	p.V502M	ENST00000342505	NM_002227.2	502	Gtg/Atg	11/25	1	2	FACETS	0.193	0.167	0.22	0.193	0.167	0.22	SUBCLONAL	1	TRUE	1	0.870992440320264	2		952	823	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555260	226555260	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	87	912	0	ENST00000366794.5:c.2327G>A	p.Ser776Asn	p.S776N	ENST00000366794	NM_001618.3	776	aGt/aAt	17/23	0.198115278100985	3	FACETS	0.385	0.34	0.433	0.192	0.17	0.217	INDETERMINATE	1	TRUE	1	0.870992440320264	3		912	745	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245912950	245912950	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	33	558	0	ENST00000388985.4:c.1202G>A	p.Arg401Lys	p.R401K	ENST00000388985		401	aGa/aAa	12/12	0.198115278100985	3	FACETS	0.22	0.179	0.267	0.11	0.089	0.134	INDETERMINATE	1	TRUE	1	0.870992440320264	3		558	494	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63816960	63816960	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	44	445	1	ENST00000279873.7:c.931G>A	p.Val311Ile	p.V311I	ENST00000279873	NM_032199.2	311	Gtt/Att	6/10	0.272688044760985	1	FACETS	0.18	0.151	0.211	0.18	0.151	0.211	INDETERMINATE	1	TRUE	0	0.870992440320264	1		446	317	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112764436	112764436	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	47	974	2	ENST00000369452.4:c.1045G>A	p.Gly349Ser	p.G349S	ENST00000369452	NM_007373.3	349	Ggt/Agt	5/9	0.272688044760985	1	FACETS	0.098	0.082	0.116	0.098	0.082	0.116	INDETERMINATE	1	TRUE	0	0.870992440320264	1		976	620	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156704	2156704	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	44	963	2	ENST00000434045.2:c.218C>T	p.Ala73Val	p.A73V	ENST00000434045	NM_001127598.1	73	gCc/gTc	3/5	0.870992440320264	1	FACETS	0.155	0.13	0.182	0.155	0.13	0.182	SUBCLONAL	1	TRUE	0	0.870992440320264	1		965	369	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942654	71942654	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	190	853	1	ENST00000298229.2:c.1610C>A	p.Thr537Asn	p.T537N	ENST00000298229	NM_001567.3	537	aCc/aAc	13/28	1	2	FACETS	0.607	0.563	0.652	0.607	0.563	0.652	SUBCLONAL	1	TRUE	1	0.870992440320264	2		854	719	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77051758	77051758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	91	886	1	ENST00000356341.3:c.1049G>A	p.Gly350Asp	p.G350D	ENST00000356341	NM_002576.4	350	gGc/gAc	11/15	1	2	FACETS	0.28	0.249	0.314	0.28	0.249	0.314	SUBCLONAL	1	TRUE	1	0.870992440320264	2		887	745	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383331	4383331	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	78	858	1	ENST00000261254.3:c.125C>T	p.Ser42Phe	p.S42F	ENST00000261254	NM_001759.3	42	tCc/tTc	1/5	0.870992440320264	3	FACETS	0.245	0.215	0.279			1	SUBCLONAL	1	TRUE	NA	0.870992440320264	3		859	1048	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945078	31945078	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	169	835	0	ENST00000340398.3:c.23C>T	p.Ala8Val	p.A8V	ENST00000340398	NM_001013699.2	8	gCt/gTt	1/1	1	2	FACETS	0.561	0.517	0.606	0.561	0.517	0.606	SUBCLONAL	1	TRUE	1	0.870992440320264	2		835	692	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222695	69222695	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	162	848	0	ENST00000462284.1:c.668G>A	p.Gly223Glu	p.G223E	ENST00000462284	NM_002392.5	223	gGg/gAg	8/11	1	2	FACETS	0.565	0.52	0.612	0.565	0.52	0.612	SUBCLONAL	1	TRUE	1	0.870992440320264	2		848	658	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249862	133249862	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	45	590	0	ENST00000320574.5:c.1361C>T	p.Thr454Ile	p.T454I	ENST00000320574	NM_006231.2	454	aCt/aTt	14/49	1	2	FACETS	0.203	0.17	0.239	0.203	0.17	0.239	SUBCLONAL	1	TRUE	1	0.870992440320264	2		590	509	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623596	28623596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	149	891	1	ENST00000241453.7:c.961G>A	p.Ala321Thr	p.A321T	ENST00000241453	NM_004119.2	321	Gca/Aca	8/24	1	2	FACETS	0.511	0.468	0.555	0.511	0.468	0.555	SUBCLONAL	1	TRUE	1	0.870992440320264	2		892	670	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046576	30046576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	173	845	0	ENST00000331968.5:c.2607G>A	p.Trp869Ter	p.W869*	ENST00000331968	NM_002742.2	869	tgG/tgA	18/18	1	2	FACETS	0.538	0.496	0.581	0.538	0.496	0.581	SUBCLONAL	1	TRUE	1	0.870992440320264	2		845	739	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986935	36986935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	207	779	1	ENST00000354822.5:c.754G>A	p.Asp252Asn	p.D252N	ENST00000354822	NM_001079668.2	252	Gac/Aac	3/3	1	2	FACETS	0.647	0.602	0.693	0.647	0.602	0.693	SUBCLONAL	1	TRUE	1	0.870992440320264	2		780	735	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560431	65560431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	106	563	0	ENST00000358664.4:c.166G>A	p.Glu56Lys	p.E56K	ENST00000358664	NM_002382.4	56	Gag/Aag	3/5	1	2	FACETS	0.569	0.513	0.627	0.569	0.513	0.627	SUBCLONAL	1	TRUE	1	0.870992440320264	2		563	428	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38641633	38641633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	62	771	2	ENST00000299084.4:c.593G>A	p.Gly198Asp	p.G198D	ENST00000299084	NM_152594.2	198	gGt/gAt	6/7	1	2	FACETS	0.253	0.219	0.291	0.253	0.219	0.291	SUBCLONAL	1	TRUE	1	0.870992440320264	2		773	562	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2090156	2090156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148474733	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	112	1021	1	ENST00000219066.1:c.793G>A	p.Ala265Thr	p.A265T	ENST00000219066	NM_002528.5	265	Gcc/Acc	5/6	1	2	FACETS	0.299	0.268	0.331	0.299	0.268	0.331	SUBCLONAL	1	TRUE	1	0.870992440320264	2		1022	860	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658503	3658503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	80	995	0	ENST00000294008.3:c.463G>A	p.Glu155Lys	p.E155K	ENST00000294008	NM_032444.2	155	Gaa/Aaa	2/15	1	2	FACETS	0.206	0.18	0.233	0.206	0.18	0.233	SUBCLONAL	1	TRUE	1	0.870992440320264	2		995	893	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777961	3777961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	223	1213	2	ENST00000262367.5:c.7087C>T	p.Pro2363Ser	p.P2363S	ENST00000262367	NM_004380.2	2363	Ccg/Tcg	31/31	1	2	FACETS	0.51	0.474	0.546	0.51	0.474	0.546	SUBCLONAL	1	TRUE	1	0.870992440320264	2		1215	1005	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821353	72821353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	146	392	0	ENST00000268489.5:c.10822G>A	p.Ala3608Thr	p.A3608T	ENST00000268489	NM_006885.3	3608	Gct/Act	10/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.870992440320264	2		392	299	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830421	72830421	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	56	356	0	ENST00000268489.5:c.6160G>A	p.Ala2054Thr	p.A2054T	ENST00000268489	NM_006885.3	2054	Gcg/Acg	9/10	1	2	FACETS	0.579	0.502	0.661	0.579	0.502	0.661	SUBCLONAL	1	TRUE	1	0.870992440320264	2		356	222	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89871796	89871796	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144917960	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	184	824	3	ENST00000389301.3:c.601C>T	p.Pro201Ser	p.P201S	ENST00000389301	NM_000135.2	201	Ccc/Tcc	7/43	1	2	FACETS	0.62	0.575	0.668	0.62	0.575	0.668	SUBCLONAL	1	TRUE	1	0.870992440320264	2		827	681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578386	7578386	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	615	772	1	ENST00000269305.4:c.544del	p.Cys182AlafsTer65	p.C182Afs*65	ENST00000269305	NM_001126112.2	182	Tgc/gc	5/11	0.870992440320264	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.870992440320264	2		773	671	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935656	15935656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	48	574	0	ENST00000268712.3:c.7277C>T	p.Pro2426Leu	p.P2426L	ENST00000268712	NM_006311.3	2426	cCa/cTa	46/46	0.870992440320264	2	FACETS	0.231	0.195	0.271	0.116	0.097	0.136	SUBCLONAL	1	TRUE	0	0.870992440320264	2		574	477	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246577	41246577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1462728426	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	245	1160	1	ENST00000357654.3:c.971G>A	p.Ser324Asn	p.S324N	ENST00000357654	NM_007294.3	324	aGt/aAt	10/23	1	2	FACETS	0.625	0.585	0.666	0.625	0.585	0.666	SUBCLONAL	1	TRUE	1	0.870992440320264	2		1161	900	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78704486	78704486	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	78	628	1	ENST00000306801.3:c.634C>T	p.Gln212Ter	p.Q212*	ENST00000306801	NM_020761.2	212	Cag/Tag	5/34	1	2	FACETS	0.319	0.28	0.36	0.319	0.28	0.36	SUBCLONAL	1	TRUE	1	0.870992440320264	2		629	562	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4123791	4123791	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	47	587	0	ENST00000262948.5:c.82G>A	p.Gly28Ser	p.G28S	ENST00000262948	NM_030662.3	28	Ggc/Agc	1/11	1	2	FACETS	0.224	0.189	0.263	0.224	0.189	0.263	SUBCLONAL	1	TRUE	1	0.870992440320264	2		587	482	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602652	10602652	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	217	1005	1	ENST00000171111.5:c.926C>T	p.Thr309Ile	p.T309I	ENST00000171111	NM_203500.1	309	aCc/aTc	3/6	1	2	FACETS	0.547	0.509	0.586	0.547	0.509	0.586	SUBCLONAL	1	TRUE	1	0.870992440320264	2		1006	911	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098452	11098452	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs926054421	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	143	499	1	ENST00000358026.2:c.970C>T	p.Pro324Ser	p.P324S	ENST00000358026	NM_001128849.1	324	Ccc/Tcc	6/36	1	2	FACETS	0.73	0.671	0.79	0.73	0.671	0.79	SUBCLONAL	1	TRUE	1	0.870992440320264	2		500	450	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946008	17946008	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1354716418	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	169	964	0	ENST00000458235.1:c.1931C>T	p.Pro644Leu	p.P644L	ENST00000458235	NM_000215.3	644	cCc/cTc	15/24	1	2	FACETS	0.542	0.499	0.586	0.542	0.499	0.586	SUBCLONAL	1	TRUE	1	0.870992440320264	2		964	716	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948832	17948832	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778413	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	50	919	3	ENST00000458235.1:c.1610G>A	p.Arg537Gln	p.R537Q	ENST00000458235	NM_000215.3	537	cGg/cAg	12/24	1	2	FACETS	0.139	0.117	0.163	0.139	0.117	0.163	SUBCLONAL	1	TRUE	1	0.870992440320264	2		922	825	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211643	36211643	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	22	594	1	ENST00000222270.7:c.1394G>A	p.Cys465Tyr	p.C465Y	ENST00000222270	NM_014727.1	465	tGc/tAc	3/37	NA	2	FACETS	0.126	0.097	0.16			1	INDETERMINATE	1	TRUE	NA	0.870992440320264	2		595	401	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214735	36214735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	40	651	2	ENST00000222270.7:c.3161C>T	p.Pro1054Leu	p.P1054L	ENST00000222270	NM_014727.1	1054	cCc/cTc	8/37	NA	2	FACETS	0.208	0.172	0.247			1	INDETERMINATE	1	TRUE	NA	0.870992440320264	2		653	442	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223821	36223821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1391834825	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	183	1209	2	ENST00000222270.7:c.6371C>T	p.Pro2124Leu	p.P2124L	ENST00000222270	NM_014727.1	2124	cCt/cTt	28/37	NA	2	FACETS	0.551	0.509	0.594			1	INDETERMINATE	1	TRUE	NA	0.870992440320264	2		1211	763	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793343	42793343	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	155	860	1	ENST00000575354.2:c.1145G>A	p.Gly382Asp	p.G382D	ENST00000575354	NM_015125.3	382	gGc/gAc	8/20	NA	2	FACETS	0.554	0.508	0.6			1	INDETERMINATE	1	TRUE	NA	0.870992440320264	2		861	643	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905315	50905315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1441	227	1081	0	ENST00000440232.2:c.523G>A	p.Asp175Asn	p.D175N	ENST00000440232	NM_002691.3	175	Gac/Aac	5/27	0.799096723755514	4	FACETS	0.585	0.543	0.629			1	SUBCLONAL	1	TRUE	NA	0.870992440320264	4		1081	1668	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702293	47702293	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	38	871	0	ENST00000233146.2:c.1889G>A	p.Gly630Glu	p.G630E	ENST00000233146	NM_000251.2	630	gGa/gAa	12/16	0.870992440320264	1	FACETS	0.104	0.086	0.125	0.104	0.086	0.125	SUBCLONAL	1	TRUE	0	0.870992440320264	1		871	473	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027853	48027853	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63751017	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	36	551	0	ENST00000234420.5:c.2731C>T	p.Arg911Ter	p.R911*	ENST00000234420	NM_000179.2	911	Cga/Tga	4/10	0.870992440320264	1	FACETS	0.145	0.119	0.174	0.145	0.119	0.174	SUBCLONAL	1	TRUE	0	0.870992440320264	1		551	322	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032823	48032823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	24	742	1	ENST00000234420.5:c.3623C>T	p.Ser1208Phe	p.S1208F	ENST00000234420	NM_000179.2	1208	tCt/tTt	7/10	0.870992440320264	1	FACETS	0.082	0.064	0.103	0.082	0.064	0.103	SUBCLONAL	1	TRUE	0	0.870992440320264	1		743	378	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182632	99182632	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	36	462	1	ENST00000074304.5:c.2435G>A	p.Arg812Lys	p.R812K	ENST00000074304	NM_001134224.1	812	aGg/aAg	22/26	1	2	FACETS	0.226	0.186	0.271	0.226	0.186	0.271	SUBCLONAL	1	TRUE	1	0.870992440320264	2		463	365	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044282	128044282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	120	640	0	ENST00000285398.2:c.1339C>T	p.Pro447Ser	p.P447S	ENST00000285398	NM_000122.1	447	Cca/Tca	8/15	1	2	FACETS	0.489	0.443	0.537	0.489	0.443	0.537	SUBCLONAL	1	TRUE	1	0.870992440320264	2		640	564	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044378	128044378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	166	876	1	ENST00000285398.2:c.1243C>T	p.His415Tyr	p.H415Y	ENST00000285398	NM_000122.1	415	Cac/Tac	8/15	1	2	FACETS	0.503	0.463	0.545	0.503	0.463	0.545	SUBCLONAL	1	TRUE	1	0.870992440320264	2		877	758	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495297	212495297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	57	786	0	ENST00000342788.4:c.1969G>A	p.Val657Ile	p.V657I	ENST00000342788	NM_005235.2	657	Gta/Ata	17/28	1	2	FACETS	0.246	0.211	0.284	0.246	0.211	0.284	SUBCLONAL	1	TRUE	1	0.870992440320264	2		786	532	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525071	9525071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	58	873	1	ENST00000353224.5:c.1814G>A	p.Gly605Asp	p.G605D	ENST00000353224	NM_177990.2	605	gGc/gAc	8/10	1	2	FACETS	0.192	0.164	0.222	0.192	0.164	0.222	SUBCLONAL	1	TRUE	1	0.870992440320264	2		874	694	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546985	9546985	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	42	539	0	ENST00000353224.5:c.1037G>A	p.Gly346Glu	p.G346E	ENST00000353224	NM_177990.2	346	gGg/gAg	5/10	1	2	FACETS	0.238	0.199	0.282	0.238	0.199	0.282	SUBCLONAL	1	TRUE	1	0.870992440320264	2		539	405	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39704908	39704908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	26	381	0	ENST00000361337.2:c.253G>A	p.Asp85Asn	p.D85N	ENST00000361337	NM_003286.2	85	Gac/Aac	4/21	1	2	FACETS	0.177	0.14	0.22	0.177	0.14	0.22	SUBCLONAL	1	TRUE	1	0.870992440320264	2		381	337	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091133	29091133	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	66	819	0	ENST00000328354.6:c.1357G>A	p.Ala453Thr	p.A453T	ENST00000328354	NM_007194.3	453	Gca/Aca	12/15	0.182658409115116	1	FACETS	0.164	0.142	0.187	0.164	0.142	0.187	INDETERMINATE	1	TRUE	0	0.870992440320264	1		819	523	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436818	52436818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	107	981	1	ENST00000460680.1:c.1960G>A	p.Val654Ile	p.V654I	ENST00000460680	NM_004656.3	654	Gta/Ata	15/17	0.182658409115116	1	FACETS	0.197	0.177	0.219	0.197	0.177	0.219	INDETERMINATE	1	TRUE	0	0.870992440320264	1		982	703	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890285	72890285	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	148	806	0	ENST00000325599.8:c.397C>T	p.Pro133Ser	p.P133S	ENST00000325599	NM_018130.2	133	Ccc/Tcc	4/11	1	2	FACETS	0.488	0.447	0.532	0.488	0.447	0.532	SUBCLONAL	1	TRUE	1	0.870992440320264	2		806	696	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200005	128200005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	69	939	2	ENST00000341105.2:c.1300G>A	p.Ala434Thr	p.A434T	ENST00000341105	NM_032638.4	434	Gct/Act	6/6	1	2	FACETS	0.226	0.197	0.259	0.226	0.197	0.259	SUBCLONAL	1	TRUE	1	0.870992440320264	2		941	700	SUCCESS
ATR	545	MSKCC	GRCh37	3	142238510	142238510	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	18	421	0	ENST00000350721.4:c.4382+1G>A		p.X1461_splice	ENST00000350721	NM_001184.3	1461			1	2	FACETS	0.123	0.092	0.16	0.123	0.092	0.16	SUBCLONAL	1	TRUE	1	0.870992440320264	2		421	336	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281211	142281211	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	66	758	0	ENST00000350721.4:c.1033G>A	p.Ala345Thr	p.A345T	ENST00000350721	NM_001184.3	345	Gct/Act	4/47	1	2	FACETS	0.242	0.209	0.277	0.242	0.209	0.277	SUBCLONAL	1	TRUE	1	0.870992440320264	2		758	627	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919275	178919275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	28	457	0	ENST00000263967.3:c.760G>A	p.Val254Met	p.V254M	ENST00000263967	NM_006218.2	254	Gtg/Atg	4/21	1	2	FACETS	0.15	0.12	0.185	0.15	0.12	0.185	SUBCLONAL	1	TRUE	1	0.870992440320264	2		457	428	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902707	1902707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	77	978	0	ENST00000382891.5:c.326G>A	p.Gly109Glu	p.G109E	ENST00000382891	NM_133335.3	109	gGg/gAg	2/22	1	2	FACETS	0.2	0.175	0.227	0.2	0.175	0.227	SUBCLONAL	1	TRUE	1	0.870992440320264	2		978	885	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84390260	84390260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	42	681	0	ENST00000321945.7:c.521C>T	p.Ser174Phe	p.S174F	ENST00000321945	NM_139076.2	174	tCt/tTt	6/9	0.870992440320264	1	FACETS	0.18	0.151	0.213	0.18	0.151	0.213	SUBCLONAL	1	TRUE	0	0.870992440320264	1		681	302	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249503	153249503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs767037353	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	147	924	0	ENST00000281708.4:c.1275G>A	p.Trp425Ter	p.W425*	ENST00000281708	NM_033632.3	425	tgG/tgA	9/12	0.870992440320264	1	FACETS	0.574	0.532	0.616	0.574	0.532	0.616	SUBCLONAL	1	TRUE	0	0.870992440320264	1		924	332	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524759	187524759	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1351067279	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	46	925	2	ENST00000441802.2:c.10921C>T	p.His3641Tyr	p.H3641Y	ENST00000441802	NM_005245.3	3641	Cac/Tac	19/27	0.870992440320264	1	FACETS	0.134	0.113	0.158	0.134	0.113	0.158	SUBCLONAL	1	TRUE	0	0.870992440320264	1		927	445	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628566	187628566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750719535	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	93	1087	1	ENST00000441802.2:c.2416C>T	p.Arg806Cys	p.R806C	ENST00000441802	NM_005245.3	806	Cgt/Tgt	2/27	0.870992440320264	1	FACETS	0.256	0.229	0.286	0.256	0.229	0.286	SUBCLONAL	1	TRUE	0	0.870992440320264	1		1088	470	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31483660	31483660	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	48	546	0	ENST00000344624.3:c.2071+1G>A		p.X691_splice	ENST00000344624		691			0.870992440320264	2	FACETS	0.319	0.271	0.373	0.16	0.135	0.187	SUBCLONAL	1	TRUE	0	0.870992440320264	2		546	345	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177695	56177695	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777039063	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	75	584	0	ENST00000399503.3:c.2668C>T	p.Pro890Ser	p.P890S	ENST00000399503	NM_005921.1	890	Ccc/Tcc	14/20	1	2	FACETS	0.418	0.368	0.472	0.418	0.368	0.472	SUBCLONAL	1	TRUE	1	0.870992440320264	2		584	412	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460546	149460546	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	158	836	0	ENST00000286301.3:c.91G>A	p.Val31Ile	p.V31I	ENST00000286301	NM_005211.3	31	Gtc/Atc	3/22	NA	2	FACETS	0.534	0.49	0.579			1	INDETERMINATE	1	TRUE	NA	0.870992440320264	2		836	680	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170827892	170827892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	39	625	0	ENST00000296930.5:c.632G>A	p.Gly211Glu	p.G211E	ENST00000296930	NM_002520.6	211	gGa/gAa	8/11	1	2	FACETS	0.175	0.144	0.208	0.175	0.144	0.208	SUBCLONAL	1	TRUE	1	0.870992440320264	2		625	513	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402623	20402623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	52	579	3	ENST00000346618.3:c.160C>T	p.Pro54Ser	p.P54S	ENST00000346618	NM_001949.4	54	Ccg/Tcg	1/7	1	2	FACETS	0.233	0.198	0.271	0.233	0.198	0.271	SUBCLONAL	1	TRUE	1	0.870992440320264	2		582	512	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169150	32169150	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	173	957	0	ENST00000375023.3:c.3883C>T	p.Pro1295Ser	p.P1295S	ENST00000375023	NM_004557.3	1295	Ccc/Tcc	22/30	1	2	FACETS	0.614	0.567	0.662	0.614	0.567	0.662	SUBCLONAL	1	TRUE	1	0.870992440320264	2		957	647	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289514	33289514	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	422	1174	1	ENST00000374542.5:c.189T>A	p.Asn63Lys	p.N63K	ENST00000374542	NM_001141970.1	63	aaT/aaA	2/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.870992440320264	2		1175	910	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652152	36652152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779054757	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	66	841	0	ENST00000244741.5:c.274G>A	p.Gly92Ser	p.G92S	ENST00000244741	NM_000389.4	92	Ggc/Agc	2/3	1	2	FACETS	0.248	0.215	0.284	0.248	0.215	0.284	SUBCLONAL	1	TRUE	1	0.870992440320264	2		841	611	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652219	36652219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1336878345	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	59	911	0	ENST00000244741.5:c.341C>T	p.Ser114Leu	p.S114L	ENST00000244741	NM_000389.4	114	tCa/tTa	2/3	1	2	FACETS	0.204	0.175	0.236	0.204	0.175	0.236	SUBCLONAL	1	TRUE	1	0.870992440320264	2		911	664	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909211	41909211	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	223	1080	4	ENST00000372991.4:c.177G>A	p.Met59Ile	p.M59I	ENST00000372991	NM_001760.3	59	atG/atA	1/5	1	2	FACETS	0.657	0.614	0.702	0.657	0.614	0.702	SUBCLONAL	1	TRUE	1	0.870992440320264	2		1084	779	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016210	150016210	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	26	581	1	ENST00000253339.5:c.496G>A	p.Gly166Arg	p.G166R	ENST00000253339		166	Ggg/Agg	2/7	1	2	FACETS	0.133	0.105	0.165	0.133	0.105	0.165	SUBCLONAL	1	TRUE	1	0.870992440320264	2		582	450	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527695	157527695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1201052597	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	155	773	1	ENST00000346085.5:c.5420G>A	p.Gly1807Glu	p.G1807E	ENST00000346085	NM_020732.3	1807	gGg/gAg	20/20	1	2	FACETS	0.489	0.448	0.531	0.489	0.448	0.531	SUBCLONAL	1	TRUE	1	0.870992440320264	2		774	728	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55269011	55269011	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	72	1059	0	ENST00000275493.2:c.3077G>A	p.Ser1026Asn	p.S1026N	ENST00000275493	NM_005228.3	1026	aGc/aAc	25/28	1	2	FACETS	0.218	0.19	0.249	0.218	0.19	0.249	SUBCLONAL	1	TRUE	1	0.870992440320264	2		1059	757	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523537	106523537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	39	594	0	ENST00000359195.3:c.2689G>A	p.Gly897Ser	p.G897S	ENST00000359195	NM_002649.2	897	Ggc/Agc	8/11	0.870992440320264	3	FACETS	0.177	0.146	0.211			1	SUBCLONAL	1	TRUE	NA	0.870992440320264	3		594	728	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512630	148512630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	54	648	1	ENST00000320356.2:c.1514C>T	p.Ala505Val	p.A505V	ENST00000320356	NM_004456.4	505	gCt/gTt	13/20	0.43257460779052	6	FACETS	0.323	0.275	0.377	0.108	0.091	0.126	INDETERMINATE	1	TRUE	3	0.870992440320264	6		649	1051	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860287	151860287	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	78	667	0	ENST00000262189.6:c.10375C>T	p.Pro3459Ser	p.P3459S	ENST00000262189	NM_170606.2	3459	Cct/Tct	43/59	0.43257460779052	6	FACETS	0.509	0.446	0.577	0.17	0.148	0.193	INDETERMINATE	1	TRUE	3	0.870992440320264	6		667	965	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486265	8486265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143196383	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	23	572	0	ENST00000356435.5:c.2552G>A	p.Gly851Glu	p.G851E	ENST00000356435		851	gGa/gAa	17/35	1	2	FACETS	0.138	0.107	0.173	0.138	0.107	0.173	SUBCLONAL	1	TRUE	1	0.870992440320264	2		572	384	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504263	8504263	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	48	607	0	ENST00000356435.5:c.1820C>T	p.Ser607Leu	p.S607L	ENST00000356435		607	tCa/tTa	12/35	1	2	FACETS	0.232	0.196	0.272	0.232	0.196	0.272	SUBCLONAL	1	TRUE	1	0.870992440320264	2		607	475	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020748	37020748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	68	901	0	ENST00000358127.4:c.97C>T	p.Leu33Phe	p.L33F	ENST00000358127	NM_001280556.1	33	Ctc/Ttc	2/10	1	2	FACETS	0.218	0.189	0.25	0.218	0.189	0.25	SUBCLONAL	1	TRUE	1	0.870992440320264	2		901	715	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128347847	128347847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	75	925	0	ENST00000265960.3:c.658G>A	p.Glu220Lys	p.E220K	ENST00000265960	NM_001006617.1	220	Gag/Aag	5/12	0.323553181165153	5	FACETS	0.35	0.305	0.398			1	INDETERMINATE	1	TRUE	NA	0.870992440320264	5		925	1135	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937112	39937112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	60	939	0	ENST00000378444.4:c.71G>A	p.Gly24Glu	p.G24E	ENST00000378444	NM_001123385.1	24	gGg/gAg	2/15	0.582720015320191	1	FACETS	0.129	0.111	0.149	0.129	0.111	0.149	SUBCLONAL	1	TRUE	0	0.870992440320264	1		939	601	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44920600	44920600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	37	899	2	ENST00000377967.4:c.1361C>T	p.Ala454Val	p.A454V	ENST00000377967	NM_021140.2	454	gCt/gTt	14/29	0.582720015320191	1	FACETS	0.09	0.074	0.108	0.09	0.074	0.108	SUBCLONAL	1	TRUE	0	0.870992440320264	1		901	534	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348147	70348147	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	67	769	0	ENST00000374080.3:c.3211G>A	p.Val1071Met	p.V1071M	ENST00000374080		1071	Gtg/Atg	23/45	0.182658409115116	1	FACETS	0.154	0.134	0.176	0.154	0.134	0.176	INDETERMINATE	1	TRUE	0	0.870992440320264	1		769	564	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937689	76937722	+	frameshift_variant	Frame_Shift_Del	DEL	GGTAACTTTTCAGTGCCATCAGATGAAGATTCAT	GGTAACTTTTCAGTGCCATCAGATGAAGATTCAT	-	novel	NA	P-0020686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	268	957	0	ENST00000373344.5:c.3026_3059del	p.Tyr1009LeufsTer13	p.Y1009Lfs*13	ENST00000373344	NM_000489.3	1009	tATGAATCTTCATCTGATGGCACTGAAAAGTTACCt/tt	9/35	0.182658409115116	1	FACETS	0.557	0.526	0.588	0.557	0.526	0.588	INDETERMINATE	1	TRUE	0	0.870992440320264	1		957	624	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579315	7579316	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1267047192	NA	P-0020688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	199	706	0	ENST00000269305.4:c.371dup	p.Cys124TrpfsTer25	p.C124Wfs*25	ENST00000269305	NM_001126112.2	124	tgc/tgGc	4/11	0.277660596693369	5	FACETS	0.935	0.875	0.996	0.748	0.7	0.797	CLONAL	4	TRUE	0	0.328870362735875	5		706	483	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399258	139399258	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	34	963	0	ENST00000277541.6:c.4885C>T	p.His1629Tyr	p.H1629Y	ENST00000277541	NM_017617.3	1629	Cac/Tac	26/34	0.28907539052364	1	FACETS	0.442	0.361	0.533	0.442	0.361	0.533	SUBCLONAL	1	TRUE	0	0.328870362735875	1		963	391	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625090	69625090	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	51	662	0	ENST00000334134.2:c.703G>C	p.Glu235Gln	p.E235Q	ENST00000334134	NM_005247.2	235	Gag/Cag	3/3	0.351679265157371	4	FACETS	1	0.892	1	0.526	0.45	0.609	CLONAL	1	TRUE	2	0.448331543016171	4		662	313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579485	7579485	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs869312782	NA	P-0020690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	132	973	2	ENST00000269305.4:c.202G>T	p.Glu68Ter	p.E68*	ENST00000269305	NM_001126112.2	68	Gag/Tag	4/11	0.439758761311702	2	FACETS	0.932	0.859	1	0.932	0.859	1	CLONAL	2	TRUE	0	0.448331543016171	2		975	316	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61713033	61713033	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	82	781	0	ENST00000401558.2:c.2378C>G	p.Pro793Arg	p.P793R	ENST00000401558	NM_003400.3	793	cCa/cGa	20/25	0.448331543016171	3	FACETS	1	0.94	1	0.547	0.485	0.613	CLONAL	1	TRUE	1	0.448331543016171	3		781	409	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161850	47161851	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0020690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	131	713	3	ENST00000409792.3:c.4275_4276del	p.Lys1426SerfsTer2	p.K1426Sfs*2	ENST00000409792	NM_014159.6	1425	aaGAaa/aaaa	3/21	0.448331543016171	2	FACETS	0.835	0.767	0.904	0.835	0.767	0.904	CLONAL	2	TRUE	0	0.448331543016171	2		716	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0020692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	369	742	1	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.595218845069979	2	FACETS	0.991	0.952	1	0.991	0.952	1	CLONAL	2	TRUE	0	0.603475998696255	2		743	617	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0020692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	140	530	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	0.590254917305529	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.603475998696255	1		530	320	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377270	118377270	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	115	548	0	ENST00000534358.1:c.10663G>C	p.Gly3555Arg	p.G3555R	ENST00000534358	NM_005933.3	3555	Ggc/Cgc	27/36	0.590254917305529	1	FACETS	0.899	0.822	0.977	0.899	0.822	0.977	CLONAL	1	TRUE	0	0.603475998696255	1		548	296	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867627	78867627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	256	982	2	ENST00000306801.3:c.2363G>A	p.Arg788His	p.R788H	ENST00000306801	NM_020761.2	788	cGc/cAc	20/34	0.595218845069979	2	FACETS	0.973	0.913	1	0.486	0.456	0.517	CLONAL	1	TRUE	0	0.603475998696255	2		984	872	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222455	2222455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1251069640	NA	P-0020692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	92	689	0	ENST00000398665.3:c.3287C>T	p.Thr1096Met	p.T1096M	ENST00000398665	NM_032482.2	1096	aCg/aTg	24/28	0.293165622975065	3	FACETS	0.656	0.584	0.733	0.328	0.292	0.367	INDETERMINATE	1	TRUE	1	0.603475998696255	3		689	605	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961503	54961503	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	250	709	0	ENST00000312783.6:c.129G>C	p.Gln43His	p.Q43H	ENST00000312783	NM_198436.1	43	caG/caC	4/10	0.603475998696255	3	FACETS	0.931	0.879	0.984	0.931	0.879	0.984	CLONAL	2	TRUE	1	0.603475998696255	3		709	579	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628376	187628376	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	385	999	0	ENST00000441802.2:c.2606C>A	p.Ser869Ter	p.S869*	ENST00000441802	NM_005245.3	869	tCa/tAa	2/27	0.595218845069979	2	FACETS	0.869	0.833	0.906	0.869	0.833	0.906	CLONAL	2	TRUE	0	0.603475998696255	2		999	734	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839984	27839984	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	170	680	1	ENST00000328488.2:c.110A>T	p.Lys37Met	p.K37M	ENST00000328488	NM_003533.2	37	aAg/aTg	1/1	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.603475998696255	2		681	507	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92355008	92355008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776044022	NA	P-0020692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	163	506	1	ENST00000265734.4:c.469G>A	p.Gly157Arg	p.G157R	ENST00000265734	NM_001259.6	157	Gga/Aga	4/8	0.603475998696255	5	FACETS	0.979	0.898	1			1	CLONAL	1	TRUE	NA	0.603475998696255	5		507	1051	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900201	101900201	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	111	595	1	ENST00000374994.4:c.635G>T	p.Gly212Val	p.G212V	ENST00000374994	NM_004612.2	212	gGc/gTc	4/9	0.603475998696255	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.603475998696255	1		596	247	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436297	110436302	+	inframe_deletion	In_Frame_Del	DEL	CGGCGG	CGGCGG	-	rs34412495	NA	P-0020693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	71	270	0	ENST00000375856.3:c.2099_2104del	p.Ala700_Ala701del	p.A700_A701del	ENST00000375856	NM_003749.2	700	gCCGCCGtg/gtg	1/2	0.192897426149092	3	FACETS	0.989	0.873	1	1	0.976	1	CLONAL	3	TRUE	1	0.192897426149092	3		270	272	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117820	70117821	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCTCCT	novel	NA	P-0020693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	51	710	0	ENST00000245479.2:c.294_295insTGGCTCC	p.Ser99TrpfsTer155	p.S99Wfs*155	ENST00000245479	NM_000346.3	96	-/GGCTCCT	1/3	0.192897426149092	3	FACETS	0.853	0.723	0.995	0.426	0.361	0.498	CLONAL	1	TRUE	1	0.192897426149092	3		710	680	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274778	142274780	+	missense_variant	Missense_Mutation	TNP	GAA	GAA	TTT	novel	NA	P-0020693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	36	759	0	ENST00000350721.4:c.2280_2282delinsAAA	p.Ser761Asn	p.S761N	ENST00000350721	NM_001184.3	760	gcTTCt/gcAAAt	10/47	0.192897426149092	3	FACETS	0.92	0.756	1	0.46	0.378	0.552	CLONAL	1	TRUE	1	0.192897426149092	3		759	445	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115873	8115874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	78	448	0	ENST00000346208.3:c.1220dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tCcg	6/6	0.250176637452882	1	FACETS	0.37	0.325	0.419	0.37	0.325	0.419	INDETERMINATE	1	FALSE	0	0.429597827293921	1		448	770	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0020695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	125	738	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	0.250176637452882	1	FACETS	0.757	0.687	0.83	0.757	0.687	0.83	INDETERMINATE	1	FALSE	0	0.429597827293921	1		738	604	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43700201	43700201	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	76	841	0	ENST00000382044.4:c.5686A>T	p.Ile1896Phe	p.I1896F	ENST00000382044	NM_001141980.1	1896	Atc/Ttc	27/28	1	2	FACETS	0.461	0.404	0.523	0.461	0.404	0.523	SUBCLONAL	1	FALSE	1	0.429597827293921	2		841	767	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50810162	50810162	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	204	888	0	ENST00000398568.2:c.986C>G	p.Ser329Cys	p.S329C	ENST00000398568	NM_001042412.1	329	tCc/tGc	6/18	0.397490446911841	2	FACETS	0.78	0.727	0.833	0.78	0.727	0.833	SUBCLONAL	2	FALSE	0	0.429597827293921	2		888	609	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950751	38950751	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	96	610	0	ENST00000357387.3:c.3199G>A	p.Asp1067Asn	p.D1067N	ENST00000357387	NM_152756.3	1067	Gat/Aat	31/38	0.250176637452882	1	FACETS	0.751	0.673	0.835	0.751	0.673	0.835	INDETERMINATE	1	FALSE	0	0.429597827293921	1		610	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782329	NA	P-0020696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	369	1086	0	ENST00000269305.4:c.746G>C	p.Arg249Thr	p.R249T	ENST00000269305	NM_001126112.2	249	aGg/aCg	7/11	0.313012592850145	2	FACETS	0.905	0.861	0.951	0.905	0.861	0.951	CLONAL	2	TRUE	0	0.390012174241279	2		1086	1045	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958127	2958127	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs769192567	NA	P-0020696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	80	1207	0	ENST00000396946.4:c.2605C>T	p.Arg869Trp	p.R869W	ENST00000396946	NM_032415.4	869	Cgg/Tgg	19/25	0.362002421223542	1	FACETS	0.418	0.367	0.472	0.418	0.367	0.472	SUBCLONAL	1	TRUE	0	0.390012174241279	1		1207	791	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834565	156834565	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	134	1327	0	ENST00000524377.1:c.333C>A	p.Phe111Leu	p.F111L	ENST00000524377	NM_002529.3	111	ttC/ttA	3/17	0.390012174241279	3	FACETS	0.701	0.635	0.771	0.351	0.317	0.386	SUBCLONAL	1	TRUE	1	0.390012174241279	3		1327	1171	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955439	48955602	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AATGTGCTTAATTTAAAAGCCTTTGATTTTTACAAAGTGATCGAAAGTTTTATCAAAGCAGAAGGCAACTTGACAAGAGAAATGATAAAACATTTAGAACGATGTGAACATCGAATCATGGAATCCCTTGCATGGCTCTCAGTAAGTAGCTAAATAATTGAAGA	AATGTGCTTAATTTAAAAGCCTTTGATTTTTACAAAGTGATCGAAAGTTTTATCAAAGCAGAAGGCAACTTGACAAGAGAAATGATAAAACATTTAGAACGATGTGAACATCGAATCATGGAATCCCTTGCATGGCTCTCAGTAAGTAGCTAAATAATTGAAGA	-	novel	NA	P-0020696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	42	634	1	ENST00000267163.4:c.1558_1695+26del		p.X520_splice	ENST00000267163	NM_000321.2	520		17/27	0.357115262989808	3	FACETS	0.504	0.42	0.596	0.168	0.14	0.199	SUBCLONAL	1	TRUE	0	0.390012174241279	3		635	511	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231085	98231085	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1311804361	NA	P-0020696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	68	762	0	ENST00000331920.6:c.2198C>T	p.Ser733Leu	p.S733L	ENST00000331920	NM_000264.3	733	tCa/tTa	14/24	1	2	FACETS	0.57	0.496	0.65	0.57	0.496	0.65	SUBCLONAL	1	TRUE	1	0.390012174241279	2		762	612	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	157	251	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.290716062757151	2		251	755	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0020701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	135	730	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.928	0.842	1	0.928	0.842	1	CLONAL	1	FALSE	1	0.290716062757151	2		731	1001	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353860	40353860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238042644	NA	P-0020701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	89	627	1	ENST00000293328.3:c.2260G>A	p.Asp754Asn	p.D754N	ENST00000293328	NM_012448.3	754	Gat/Aat	19/19	1	2	FACETS	0.758	0.671	0.851	0.758	0.671	0.851	SUBCLONAL	1	FALSE	1	0.290716062757151	2		628	808	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533790	63533790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	49	744	0	ENST00000307078.5:c.1364C>T	p.Pro455Leu	p.P455L	ENST00000307078	NM_004655.3	455	cCa/cTa	6/11	1	2	FACETS	0.369	0.311	0.433	0.369	0.311	0.433	SUBCLONAL	1	FALSE	1	0.290716062757151	2		744	913	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089590	27089591	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	75	704	0	ENST00000324856.7:c.2548dup	p.Tyr850LeufsTer22	p.Y850Lfs*22	ENST00000324856	NM_006015.4	849	cct/ccTt	8/20	1	2	FACETS	0.674	0.589	0.764	0.674	0.589	0.764	SUBCLONAL	1	FALSE	1	0.290716062757151	2		704	766	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999176	100999176	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	85	1022	0	ENST00000325455.5:c.626C>A	p.Pro209Gln	p.P209Q	ENST00000325455	NM_001202474.3	209	cCa/cAa	1/8	0.290716062757151	1	FACETS	0.505	0.445	0.57	0.505	0.445	0.57	SUBCLONAL	1	FALSE	0	0.290716062757151	1		1022	989	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734188	58734188	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	61	579	0	ENST00000305921.3:c.1246A>C	p.Thr416Pro	p.T416P	ENST00000305921	NM_003620.3	416	Aca/Cca	5/6	1	2	FACETS	0.59	0.508	0.68	0.59	0.508	0.68	SUBCLONAL	1	FALSE	1	0.290716062757151	2		579	711	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0020702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	2149	685	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.295755138104978	32	FACETS	1	0.991	1			1	CLONAL	27	TRUE	NA	0.44	32		685	2737	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0020702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	260	953	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.295755138104978	6	FACETS	0.85	0.798	0.903	0.638	0.599	0.678	CLONAL	3	TRUE	2	0.44	6		953	871	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100451	8100451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1266983268	NA	P-0020702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	364	1381	1	ENST00000346208.3:c.425C>T	p.Ser142Leu	p.S142L	ENST00000346208		142	tCg/tTg	3/6	0.295755138104978	6	FACETS	0.85	0.806	0.895	0.637	0.604	0.671	CLONAL	3	TRUE	2	0.44	6		1382	1220	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517733	187517733	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373442556	NA	P-0020702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	19	285	0	ENST00000441802.2:c.12961G>A	p.Asp4321Asn	p.D4321N	ENST00000441802	NM_005245.3	4321	Gac/Aac	25/27	0.295755138104978	6	FACETS	0.777	0.592	0.993	0.194	0.148	0.249	CLONAL	1	TRUE	2	0.44	6		285	209	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729844	41729844	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs908163566	NA	P-0020702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	155	660	0	ENST00000242208.4:c.685C>T	p.Arg229Trp	p.R229W	ENST00000242208	NM_002192.2	229	Cgg/Tgg	3/3	0.295755138104978	8	FACETS	1	0.96	1	0.532	0.49	0.575	CLONAL	3	TRUE	2	0.44	8		660	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0020702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	226	994	1	ENST00000269305.4:c.560-1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.221278006238401	3	FACETS	1	0.986	1	0.779	0.733	0.827	INDETERMINATE	2	TRUE	0	0.44	3		995	536	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431445	49431445	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	161	1288	0	ENST00000301067.7:c.9694G>A	p.Glu3232Lys	p.E3232K	ENST00000301067	NM_003482.3	3232	Gag/Aag	34/54	0.295755138104978	6	FACETS	1	0.98	1	0.308	0.282	0.336	CLONAL	1	TRUE	2	0.44	6		1288	1116	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220534	133220534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs778153462	NA	P-0020702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	108	969	1	ENST00000320574.5:c.4179G>T	p.Met1393Ile	p.M1393I	ENST00000320574	NM_006231.2	1393	atG/atT	33/49	0.295755138104978	6	FACETS	1	0.981	1	0.359	0.322	0.397	CLONAL	1	TRUE	2	0.44	6		970	643	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873256	136873256	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1251842734	NA	P-0020702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	78	515	0	ENST00000241393.3:c.242C>G	p.Ser81Ter	p.S81*	ENST00000241393	NM_003467.2	81	tCa/tGa	2/2	0.295755138104978	6	FACETS	1	0.969	1	0.329	0.29	0.372	CLONAL	1	TRUE	2	0.44	6		515	506	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206891	36206892	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0020702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	108	510	0	ENST00000300305.3:c.620_621del	p.Arg207ProfsTer5	p.R207Pfs*5	ENST00000300305		207	cGG/c	6/8	0.295755138104978	5	FACETS	0.979	0.886	1	0.653	0.59	0.718	CLONAL	2	TRUE	2	0.44	5		510	416	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007410	143007410	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0020702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	41	407	1	ENST00000262992.4:c.2375-1G>A		p.X792_splice	ENST00000262992	NM_001101669.1	792			0.295755138104978	6	FACETS	1	0.956	1	0.368	0.309	0.433	CLONAL	1	TRUE	2	0.44	6		408	238	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874365	151874365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746319127	NA	P-0020702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	71	809	0	ENST00000262189.6:c.8173G>A	p.Glu2725Lys	p.E2725K	ENST00000262189	NM_170606.2	2725	Gag/Aag	38/59	0.295755138104978	6	FACETS	1	0.966	1	0.33	0.288	0.374	CLONAL	1	TRUE	2	0.44	6		809	460	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0020703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	57	736	0	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	FALSE	1	NA	2		736	804	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156732	20156732	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	53	343	0	ENST00000379607.5:c.25G>C	p.Gly9Arg	p.G9R	ENST00000379607	NM_001412.3	9	Ggt/Cgt	2/7	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		343	472	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748602	40748602	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	66	679	2	ENST00000373198.4:c.2914C>T	p.Arg972Ter	p.R972*	ENST00000373198	NM_133170.3	972	Cga/Tga	21/32	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		681	747	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0020704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	109	771	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.29	2		771	503	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106519	27106523	+	frameshift_variant	Frame_Shift_Del	DEL	AACAA	AACAA	-	novel	NA	P-0020704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	107	1034	0	ENST00000324856.7:c.6131_6135del	p.Asn2044SerfsTer53	p.N2044Sfs*53	ENST00000324856	NM_006015.4	2044	AACAAa/a	20/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.29	2		1034	512	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922894	44922915	+	frameshift_variant	Frame_Shift_Del	DEL	GGGAAGTACAGACACTATTTTG	GGGAAGTACAGACACTATTTTG	-	novel	NA	P-0020704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	78	334	0	ENST00000377967.4:c.1755_1776del	p.Gly586Ter	p.G586*	ENST00000377967	NM_021140.2	585	ctGGGAAGTACAGACACTATTTTG/ct	16/29	0.301492465740932	2	FACETS	0.879	0.788	0.973			1	CLONAL	3	TRUE	NA	0.29	2		334	204	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629575	187629575	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	32	862	0	ENST00000441802.2:c.1407A>T	p.Lys469Asn	p.K469N	ENST00000441802	NM_005245.3	469	aaA/aaT	2/27	0.187628137464424	2	FACETS	0.671	0.549	0.806	0.336	0.274	0.403	INDETERMINATE	1	TRUE	0	0.46300671177126	2		862	206	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944886	131944886	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	19	429	0	ENST00000265335.6:c.2907A>T	p.Lys969Asn	p.K969N	ENST00000265335		969	aaA/aaT	18/25	1	2	FACETS	1	0.83	1	1	0.83	1	CLONAL	1	TRUE	1	0.46300671177126	2		429	76	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813902	50813902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1162538506	NA	P-0020715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	346	772	4	ENST00000398568.2:c.1456C>T	p.Arg486Cys	p.R486C	ENST00000398568	NM_001042412.1	486	Cgt/Tgt	8/18	0.102214742104759	1	FACETS	1	0.994	1	1	0.994	1	INDETERMINATE	1	TRUE	0	0.589961701717108	1		776	650	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579375	7579426	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGTAGGTTTTCTGGGAAGGGACAGAAGATGACAGGGGCCAGGAGGGGGCT	CTGGTAGGTTTTCTGGGAAGGGACAGAAGATGACAGGGGCCAGGAGGGGGCT	TCCTGGCCC	novel	NA	P-0020715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	228	865	5	ENST00000269305.4:c.261_312delinsGGGCCAGGA	p.Ala88GlyfsTer21	p.A88Gfs*21	ENST00000269305	NM_001126112.2	87	ccAGCCCCCTCCTGGCCCCTGTCATCTTCTGTCCCTTCCCAGAAAACCTACCAG/ccGGGCCAGGA	4/11	0.527382331591121	2	FACETS	1	0.99	1	0.64	0.6	0.68	CLONAL	1	TRUE	0	0.589961701717108	2		870	604	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440372	52440372	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	259	668	4	ENST00000460680.1:c.680G>T	p.Arg227Leu	p.R227L	ENST00000460680	NM_004656.3	227	cGc/cTc	9/17	0.529523808925752	3	FACETS	0.915	0.864	0.967	0.61	0.576	0.645	CLONAL	2	TRUE	0	0.589961701717108	3		672	621	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390935	89390935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	100	580	0	ENST00000336596.2:c.1001C>T	p.Ser334Phe	p.S334F	ENST00000336596	NM_005233.5	334	tCt/tTt	5/17	0.529523808925752	3	FACETS	0.78	0.698	0.866	0.26	0.232	0.289	SUBCLONAL	1	TRUE	0	0.589961701717108	3		580	563	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754292	57754292	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	173	714	1	ENST00000274289.3:c.559A>G	p.Arg187Gly	p.R187G	ENST00000274289	NM_006622.3	187	Agg/Ggg	4/14	1	2	FACETS	0.973	0.9	1	0.973	0.9	1	CLONAL	1	TRUE	1	0.589961701717108	2		715	603	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5066677	5066677	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0020715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	82	718	0	ENST00000381652.3:c.1215-1G>A		p.X405_splice	ENST00000381652	NM_004972.3	405			1	2	FACETS	0.882	0.786	0.984	0.882	0.786	0.984	CLONAL	1	TRUE	1	0.589961701717108	2		718	315	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0020716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	141	560	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.89	0.81	0.974	0.89	0.81	0.974	CLONAL	1	TRUE	1	0.318086349324203	2		560	996	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0020716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	207	1038	1	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.318086349324203	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.318086349324203	1		1039	966	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690819	89690820	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0020716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	111	708	0	ENST00000371953.3:c.227_228del	p.Tyr76Ter	p.Y76*	ENST00000371953	NM_000314.4	76	TAt/t	4/9	0.318086349324203	1	FACETS	0.906	0.816	1	0.906	0.816	1	CLONAL	1	TRUE	0	0.318086349324203	1		708	648	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713853	30713853	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039106	NA	P-0020716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	142	269	0	ENST00000295754.5:c.1178G>A	p.Cys393Tyr	p.C393Y	ENST00000295754	NM_003242.5	393	tGc/tAc	4/7	0.318086349324203	1	FACETS	0.925	0.843	1	0.925	0.843	1	CLONAL	1	TRUE	0	0.318086349324203	1		269	812	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683551	29683557	+	frameshift_variant	Frame_Shift_Del	DEL	CACAACA	CACAACA	-	novel	NA	P-0020716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	81	587	0	ENST00000356175.3:c.7627_7633del	p.Thr2543ProfsTer4	p.T2543Pfs*4	ENST00000356175	NM_000267.3	2542	atCACAACA/at	51/57	1	2	FACETS	0.753	0.664	0.85	0.753	0.664	0.85	SUBCLONAL	1	TRUE	1	0.318086349324203	2		587	676	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	33	613	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.483	0.392	0.587	0.483	0.392	0.587	SUBCLONAL	1	TRUE	1	0.16	2		614	854	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0020717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	35	340	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.512	0.418	0.619	0.512	0.418	0.619	SUBCLONAL	1	TRUE	1	0.16	2		340	854	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858327	27858327	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	50	642	2	ENST00000359303.2:c.244G>A	p.Asp82Asn	p.D82N	ENST00000359303	NM_003535.2	82	Gac/Aac	1/1	1	2	FACETS	0.875	0.741	1	0.875	0.741	1	CLONAL	1	TRUE	1	0.16	2		644	714	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041800	42041800	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	69	509	0	ENST00000219905.7:c.5995G>T	p.Glu1999Ter	p.E1999*	ENST00000219905	NM_001164273.1	1999	Gag/Tag	17/24	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.16	2		509	584	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041439	47041439	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	49	738	1	ENST00000377604.3:c.1783C>T	p.Gln595Ter	p.Q595*	ENST00000377604	NM_001204468.1	595	Cag/Tag	16/24	1	2	FACETS	0.782	0.661	0.917	0.782	0.661	0.917	CLONAL	1	TRUE	1	0.16	2		739	783	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776309	76776309	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	80	948	0	ENST00000373344.5:c.7157G>T	p.Arg2386Leu	p.R2386L	ENST00000373344	NM_000489.3	2386	cGa/cTa	34/35	1	2	FACETS	0.876	0.769	0.993	0.876	0.769	0.993	CLONAL	1	TRUE	1	0.16	2		948	1141	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0020721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	1004	340	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.673665494638074	8	FACETS	0.971	0.946	0.996	0.971	0.946	0.996	CLONAL	5	TRUE	3	0.673665494638074	8		340	1854	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11264742	11264742	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	428	968	0	ENST00000361445.4:c.3820A>G	p.Arg1274Gly	p.R1274G	ENST00000361445	NM_004958.3	1274	Agg/Ggg	26/58	0.673665494638074	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.673665494638074	4		968	1033	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023576	27023576	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	225	451	0	ENST00000324856.7:c.682G>T	p.Ala228Ser	p.A228S	ENST00000324856	NM_006015.4	228	Gcc/Tcc	1/20	0.673665494638074	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.673665494638074	4		451	521	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783685	50783685	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	397	856	0	ENST00000398568.2:c.76C>T	p.Gln26Ter	p.Q26*	ENST00000398568	NM_001042412.1	26	Caa/Taa	3/18	0.340419813417218	5	FACETS	0.899	0.859	0.939	0.899	0.859	0.939	INDETERMINATE	3	TRUE	2	0.673665494638074	5		856	879	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0020721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	376	759	0	ENST00000269305.4:c.560-2A>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.673665494638074	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.673665494638074	2		759	512	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221260	1221260	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	808	943	2	ENST00000326873.7:c.783C>A	p.Tyr261Ter	p.Y261*	ENST00000326873	NM_000455.4	261	taC/taA	6/10	0.59873320057187	4	FACETS	1	0.986	1			1	CLONAL	4	TRUE	NA	0.673665494638074	4		945	998	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530092	212530092	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	300	570	0	ENST00000342788.4:c.1827T>A	p.Asp609Glu	p.D609E	ENST00000342788	NM_005235.2	609	gaT/gaA	15/28	0.544515787277123	4	FACETS	0.927	0.885	0.969	0.927	0.885	0.969	CLONAL	3	TRUE	1	0.673665494638074	4		570	536	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177630	56177630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	315	565	1	ENST00000399503.3:c.2603C>T	p.Ala868Val	p.A868V	ENST00000399503	NM_005921.1	868	gCc/gTc	14/20	0.673665494638074	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.673665494638074	4		566	755	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816571	32816571	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0020721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	491	1053	0	ENST00000354258.4:c.1604C>G	p.Ser535Ter	p.S535*	ENST00000354258	NM_000593.5	535	tCa/tGa	7/11	0.673665494638074	5	FACETS	1	0.981	1	0.695	0.665	0.726	CLONAL	2	TRUE	2	0.673665494638074	5		1053	1405	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381507	81381507	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	144	628	0	ENST00000222390.5:c.554G>A	p.Gly185Glu	p.G185E	ENST00000222390	NM_000601.4	185	gGg/gAg	5/18	0.673665494638074	3	FACETS	0.99	0.907	1	0.495	0.453	0.539	CLONAL	1	TRUE	1	0.673665494638074	3		628	577	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202954	27202954	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs112475919	NA	P-0020721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	165	811	1	ENST00000380036.4:c.2046C>A	p.Asp682Glu	p.D682E	ENST00000380036	NM_000459.3	682	gaC/gaA	13/23	1	2	FACETS	0.94	0.869	1	0.94	0.869	1	CLONAL	1	TRUE	1	0.673665494638074	2		812	521	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	226	613	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.457362057619195	2	FACETS	0.917	0.862	0.972	0.917	0.862	0.972	CLONAL	2	TRUE	0	0.457362057619195	2		614	539	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	62	574	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	0.735	0.638	0.839	0.735	0.638	0.839	SUBCLONAL	1	TRUE	1	0.457362057619195	2		574	369	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983911	2983911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237589286	NA	P-0020723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	268	1204	1	ENST00000396946.4:c.619C>T	p.Arg207Cys	p.R207C	ENST00000396946	NM_032415.4	207	Cgc/Tgc	5/25	0.457958007718253	3	FACETS	1	0.985	1	0.583	0.546	0.621	CLONAL	1	TRUE	1	0.457362057619195	3		1205	1235	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601893	43601893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057521089	NA	P-0020723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	170	901	2	ENST00000355710.3:c.937C>T	p.Arg313Trp	p.R313W	ENST00000355710	NM_020975.4	313	Cgg/Tgg	5/20	1	2	FACETS	0.803	0.738	0.87	0.803	0.738	0.87	CLONAL	1	TRUE	1	0.457362057619195	2		903	926	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578369	7578369	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0020723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	288	714	0	ENST00000269305.4:c.559+2T>G		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.453073768978768	2	FACETS	0.922	0.873	0.971	0.922	0.873	0.971	CLONAL	2	TRUE	0	0.457362057619195	2		714	683	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380795	118380795	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	93	710	3	ENST00000534358.1:c.11033G>A	p.Ser3678Asn	p.S3678N	ENST00000534358	NM_005933.3	3678	aGt/aAt	30/36	0.457958007718253	3	FACETS	0.919	0.819	1	0.459	0.409	0.512	CLONAL	1	TRUE	1	0.457362057619195	3		713	544	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576096	88576096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371590703	NA	P-0020723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	122	1010	0	ENST00000360948.2:c.1577C>T	p.Pro526Leu	p.P526L	ENST00000360948	NM_001012338.2	526	cCg/cTg	13/19	0.193897619048724	2	FACETS	0.562	0.507	0.62	0.281	0.253	0.31	INDETERMINATE	1	TRUE	0	0.457362057619195	2		1010	950	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829165	128829165	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	91	91	0	ENST00000249373.3:c.173C>T	p.Pro58Leu	p.P58L	ENST00000249373	NM_005631.4	58	cCg/cTg	1/12	0.457958007718253	3	FACETS	0.836	0.76	0.912	1	0.977	1	CLONAL	3	TRUE	1	0.457362057619195	3		91	195	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0020724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	101	1016	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	1	2	FACETS	0.907	0.826	0.99	0.907	0.826	0.99	CLONAL	1	TRUE	1	0.897840572091599	2		1016	248	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	41	733	2	ENST00000347630.2:c.399C>A	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttA	6/11	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.244883322527606	2		735	264	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0020727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	139	685	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.25	2		685	823	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0020727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	52	260	0	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.302742577714307	1	FACETS	0.465	0.395	0.542	0.465	0.395	0.542	SUBCLONAL	1	TRUE	0	0.25	1		260	783	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063633	67063633	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0020727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	104	616	1	ENST00000412916.2:c.82A>T	p.Lys28Ter	p.K28*	ENST00000412916		28	Aag/Tag	2/6	0.302742577714307	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.25	1		617	563	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217614	7217614	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	104	630	1	ENST00000380728.2:c.313C>T	p.Gln105Ter	p.Q105*	ENST00000380728		105	Cag/Tag	4/11	0.302742577714307	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.25	1		631	593	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016558	12016558	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	114	551	0	ENST00000353533.5:c.694C>A	p.Pro232Thr	p.P232T	ENST00000353533	NM_003010.3	232	Cct/Act	7/11	0.302742577714307	1	FACETS	0.751	0.679	0.827	1	0.984	1	SUBCLONAL	2	TRUE	0	0.25	1		551	531	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977858	134977858	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	73	550	1	ENST00000398015.3:c.2851C>T	p.Leu951Phe	p.L951F	ENST00000398015	NM_004441.4	951	Ctc/Ttc	16/16	0.302742577714307	1	FACETS	0.992	0.87	1	0.992	0.87	1	CLONAL	1	TRUE	0	0.25	1		551	515	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	43	690	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	0.636	0.53	0.754	0.636	0.53	0.754	SUBCLONAL	1	TRUE	1	0.16	2		690	845	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211139	36211139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776148419	NA	P-0020729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1276	74	989	1	ENST00000222270.7:c.890G>A	p.Arg297Gln	p.R297Q	ENST00000222270	NM_014727.1	297	cGa/cAa	3/37	1	2	FACETS	0.685	0.597	0.781	0.685	0.597	0.781	SUBCLONAL	1	TRUE	1	0.16	2		990	1350	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0020729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	39	308	1	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	1	2	FACETS	0.61	0.504	0.729	0.61	0.504	0.729	SUBCLONAL	1	TRUE	1	0.16	2		309	799	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554355	81554355	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747687365	NA	P-0020729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	35	576	0	ENST00000298171.2:c.379del	p.Leu127SerfsTer2	p.L127Sfs*2	ENST00000298171	NM_000369.2	125	ctC/ct	4/10	1	2	FACETS	0.745	0.61	0.898	0.745	0.61	0.898	SUBCLONAL	1	TRUE	1	0.16	2		576	587	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0020729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	64	661	1	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.16	2		662	778	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672318	86672318	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	48	610	2	ENST00000274376.6:c.2120G>A	p.Arg707His	p.R707H	ENST00000274376	NM_002890.2	707	cGt/cAt	16/25	1	2	FACETS	0.951	0.803	1	0.951	0.803	1	CLONAL	1	TRUE	1	0.16	2		612	631	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	63	867	0	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	1	1	FACETS	0.763	0.661	0.873	1	0.971	1	SUBCLONAL	2	TRUE	0	0.16	1		867	475	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249361	153249361	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	26	586	1	ENST00000281708.4:c.1417del	p.Arg473GlufsTer25	p.R473Efs*25	ENST00000281708	NM_033632.3	473	Aga/ga	9/12	1	2	FACETS	0.693	0.548	0.86	0.693	0.548	0.86	SUBCLONAL	1	TRUE	1	0.16	2		587	469	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467197	25467197	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	39	547	1	ENST00000264709.3:c.1678G>A	p.Val560Met	p.V560M	ENST00000264709	NM_175629.2	560	Gtg/Atg	15/23	1	2	FACETS	0.67	0.553	0.8	0.67	0.553	0.8	SUBCLONAL	1	TRUE	1	0.16	2		548	728	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228172	53228172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	44	300	1	ENST00000375401.3:c.2230C>T	p.Arg744Trp	p.R744W	ENST00000375401	NM_004187.3	744	Cgg/Tgg	15/26	1	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.16	1		301	398	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27213538	27213538	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	45	680	0	ENST00000380036.4:c.2938del	p.Ile980Ter	p.I980*	ENST00000380036	NM_000459.3	978	gcA/gc	18/23	1	2	FACETS	0.78	0.654	0.92	0.78	0.654	0.92	CLONAL	1	TRUE	1	0.16	2		680	721	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614463	38614463	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	32	613	0	ENST00000299084.4:c.234del	p.Asp79ThrfsTer42	p.D79Tfs*42	ENST00000299084	NM_152594.2	77	Aaa/aa	3/7	1	2	FACETS	0.71	0.575	0.864	0.71	0.575	0.864	SUBCLONAL	1	TRUE	1	0.16	2		613	563	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303664	65303664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763865501	NA	P-0020729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	46	763	0	ENST00000342505.4:c.3091G>A	p.Asp1031Asn	p.D1031N	ENST00000342505	NM_002227.2	1031	Gat/Aat	22/25	1	2	FACETS	0.63	0.528	0.743	0.63	0.528	0.743	SUBCLONAL	1	TRUE	1	0.16	2		763	913	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998598	100998598	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1279278874	NA	P-0020729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	39	554	4	ENST00000325455.5:c.1204C>T	p.Arg402Cys	p.R402C	ENST00000325455	NM_001202474.3	402	Cgt/Tgt	1/8	1	2	FACETS	0.711	0.587	0.849	0.711	0.587	0.849	SUBCLONAL	1	TRUE	1	0.16	2		558	686	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856428	111856428	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	40	379	1	ENST00000341259.2:c.479C>T	p.Ala160Val	p.A160V	ENST00000341259	NM_005475.2	160	gCt/gTt	2/8	1	2	FACETS	0.98	0.814	1	0.98	0.814	1	CLONAL	1	TRUE	1	0.16	2		380	510	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476364	88476364	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780933441	NA	P-0020729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	48	751	0	ENST00000360948.2:c.1768G>A	p.Glu590Lys	p.E590K	ENST00000360948	NM_001012338.2	590	Gag/Aag	15/19	1	2	FACETS	0.74	0.624	0.869	0.74	0.624	0.869	SUBCLONAL	1	TRUE	1	0.16	2		751	811	SUCCESS
BLM	641	MSKCC	GRCh37	15	91308628	91308628	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	30	551	0	ENST00000355112.3:c.2177A>G	p.Lys726Arg	p.K726R	ENST00000355112	NM_000057.2	726	aAg/aGg	9/22	1	2	FACETS	0.653	0.525	0.8	0.653	0.525	0.8	SUBCLONAL	1	TRUE	1	0.16	2		551	574	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640550	3640550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774562724	NA	P-0020729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	68	818	0	ENST00000294008.3:c.3089C>T	p.Pro1030Leu	p.P1030L	ENST00000294008	NM_032444.2	1030	cCg/cTg	12/15	1	2	FACETS	0.825	0.716	0.944	0.825	0.716	0.944	CLONAL	1	TRUE	1	0.16	2		818	1030	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550577	29550577	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	18	373	0	ENST00000356175.3:c.1841del	p.Asn614IlefsTer17	p.N614Ifs*17	ENST00000356175	NM_000267.3	613	Aaa/aa	16/57	1	2	FACETS	0.643	0.483	0.832	0.643	0.483	0.832	SUBCLONAL	1	TRUE	1	0.16	2		373	350	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117613	70117614	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAG	novel	NA	P-0020729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	58	719	0	ENST00000245479.2:c.84_86dup	p.Glu28dup	p.E28dup	ENST00000245479	NM_000346.3	28	-/GAG	1/3	1	2	FACETS	0.906	0.777	1	0.906	0.777	1	CLONAL	1	TRUE	1	0.16	2		719	800	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252721	10252721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1316623288	NA	P-0020729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	71	652	0	ENST00000340748.4:c.3244C>T	p.Arg1082Cys	p.R1082C	ENST00000340748		1082	Cgc/Tgc	29/40	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.16	2		652	834	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18964066	18964066	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	52	522	2	ENST00000262803.5:c.1063C>T	p.Arg355Trp	p.R355W	ENST00000262803	NM_002911.3	355	Cgg/Tgg	8/24	1	2	FACETS	0.956	0.813	1	0.956	0.813	1	CLONAL	1	TRUE	1	0.16	2		524	680	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189340	99189340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867760971	NA	P-0020729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	101	724	0	ENST00000074304.5:c.2596G>A	p.Val866Met	p.V866M	ENST00000074304	NM_001134224.1	866	Gtg/Atg	24/26	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.16	2		724	919	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095826	178095826	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1434375367	NA	P-0020729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	89	598	0	ENST00000397062.3:c.1505G>A	p.Arg502His	p.R502H	ENST00000397062	NM_006164.4	502	cGt/cAt	5/5	1	2	FACETS	0.76	0.674	0.852	1	0.979	1	SUBCLONAL	2	TRUE	1	0.16	2		598	732	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803654	1803654	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	62	918	0	ENST00000260795.2:c.832T>C	p.Tyr278His	p.Y278H	ENST00000260795		278	Tac/Cac	6/17	1	2	FACETS	0.709	0.61	0.817	0.709	0.61	0.817	SUBCLONAL	1	TRUE	1	0.16	2		918	1093	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645047	86645047	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	28	441	0	ENST00000274376.6:c.1122del	p.Val376Ter	p.V376*	ENST00000274376	NM_002890.2	373	agT/ag	8/25	1	2	FACETS	0.914	0.73	1	0.914	0.73	1	CLONAL	1	TRUE	1	0.16	2		441	383	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671889	30671889	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	109	837	1	ENST00000376406.3:c.5071G>T	p.Ala1691Ser	p.A1691S	ENST00000376406	NM_014641.2	1691	Gct/Tct	10/15	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.16	2		838	1053	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638307	117638307	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs957947676	NA	P-0020729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	26	468	0	ENST00000368508.3:c.6134C>T	p.Thr2045Met	p.T2045M	ENST00000368508	NM_002944.2	2045	aCg/aTg	38/43	1	2	FACETS	0.629	0.497	0.781	0.629	0.497	0.781	SUBCLONAL	1	TRUE	1	0.16	2		468	517	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0020730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	118	328	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.25685477769995	3	FACETS	0.842	0.761	0.926	0.842	0.761	0.926	CLONAL	2	TRUE	1	0.25685477769995	3		328	616	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0020730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	144	829	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.248120534378681	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.25685477769995	1		829	705	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241726	55241726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767505234	NA	P-0020730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	57	736	1	ENST00000275493.2:c.2174C>T	p.Thr725Met	p.T725M	ENST00000275493	NM_005228.3	725	aCg/aTg	18/28	1	2	FACETS	0.669	0.574	0.774	0.669	0.574	0.774	SUBCLONAL	1	TRUE	1	0.25685477769995	2		737	663	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272146	142272146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	59	744	0	ENST00000350721.4:c.2728G>A	p.Glu910Lys	p.E910K	ENST00000350721	NM_001184.3	910	Gaa/Aaa	13/47	0.25685477769995	3	FACETS	0.603	0.518	0.697	0.302	0.259	0.349	SUBCLONAL	1	TRUE	1	0.25685477769995	3		744	859	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623782	28623782	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	39	830	0	ENST00000241453.7:c.872C>T	p.Ala291Val	p.A291V	ENST00000241453	NM_004119.2	291	gCa/gTa	7/24	0.162765206574861	0	FACETS	0.347	0.287	0.415			1	SUBCLONAL	1	TRUE	0	0.25685477769995	0		830	650	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41011095	41011095	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	36	734	0	ENST00000267868.3:c.528G>C	p.Glu176Asp	p.E176D	ENST00000267868	NM_002875.4	176	gaG/gaC	6/10	0.248120534378681	1	FACETS	0.392	0.321	0.472	0.392	0.321	0.472	SUBCLONAL	1	TRUE	0	0.25685477769995	1		734	623	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944253	81944253	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	55	915	0	ENST00000359376.3:c.1862A>C	p.His621Pro	p.H621P	ENST00000359376	NM_002661.3	621	cAc/cCc	18/33	0.25685477769995	3	FACETS	0.568	0.484	0.66	0.284	0.242	0.33	SUBCLONAL	1	TRUE	1	0.25685477769995	3		915	851	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130353	11130353	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	50	904	3	ENST00000358026.2:c.2592C>G	p.Ile864Met	p.I864M	ENST00000358026	NM_001128849.1	864	atC/atG	18/36	NA	2	FACETS	0.499	0.422	0.584			1	INDETERMINATE	1	TRUE	NA	0.25685477769995	2		907	780	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661935	227661935	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	78	869	0	ENST00000305123.5:c.1520C>A	p.Ala507Asp	p.A507D	ENST00000305123	NM_005544.2	507	gCt/gAt	1/2	0.111057592283242	4	FACETS	0.971	0.852	1	0.486	0.426	0.55	INDETERMINATE	1	TRUE	2	0.25685477769995	4		869	786	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183734	10183734	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	55	889	0	ENST00000256474.2:c.203C>G	p.Ser68Trp	p.S68W	ENST00000256474	NM_000551.3	68	tCg/tGg	1/3	1	2	FACETS	0.597	0.51	0.693	0.597	0.51	0.693	SUBCLONAL	1	TRUE	1	0.25685477769995	2		889	717	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158564	26158564	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	52	834	0	ENST00000289316.2:c.167C>G	p.Ser56Cys	p.S56C	ENST00000289316	NM_138720.2	56	tCt/tGt	1/2	0.25685477769995	4	FACETS	0.592	0.502	0.691			1	SUBCLONAL	1	TRUE	NA	0.25685477769995	4		834	860	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020086	123020086	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	54	1097	1	ENST00000355640.3:c.574A>T	p.Thr192Ser	p.T192S	ENST00000355640		192	Aca/Tca	2/7	NA	2	FACETS	0.45	0.383	0.524			1	INDETERMINATE	1	TRUE	NA	0.25685477769995	2		1098	935	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971177	21971177	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913382	NA	P-0020732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	543	651	0	ENST00000304494.5:c.181G>T	p.Glu61Ter	p.E61*	ENST00000304494	NM_000077.4	61	Gag/Tag	2/3	0.52740750869115	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.537596438044591	2		651	894	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549587	5549616	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCAGCATTGACCTTCAAAGTAAGAGCTGCC	CCAGCATTGACCTTCAAAGTAAGAGCTGCC	-	novel	NA	P-0020732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	118	858	0	ENST00000397747.3:c.616_631+14del		p.X206_splice	ENST00000397747	NM_025239.3	206		4/7	0.52740750869115	2	FACETS	0.53	0.478	0.585	0.265	0.239	0.293	SUBCLONAL	1	TRUE	0	0.537596438044591	2		858	828	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929416	44929417	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0020732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	303	516	0	ENST00000377967.4:c.2517_2518del	p.Asn839LysfsTer6	p.N839Kfs*6	ENST00000377967	NM_021140.2	839	aAC/a	17/29	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.537596438044591	1		516	590	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0020734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	8	303	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.242	0.155	0.354	0.242	0.155	0.354	SUBCLONAL	1	FALSE	1	0.344700195963063	2		304	192	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696644	47696644	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519964	NA	P-0020734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	78	992	0	ENST00000347630.2:c.304T>G	p.Phe102Val	p.F102V	ENST00000347630	NM_001007230.1	102	Ttc/Gtc	5/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.344700195963063	2		992	407	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0020735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	69	584	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.937	0.814	1	0.937	0.814	1	CLONAL	1	TRUE	1	0.14	2		585	1052	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589599	67589601	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	novel	NA	P-0020735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	33	524	0	ENST00000274335.5:c.1362_1364del	p.Gln455del	p.Q455del	ENST00000274335		454	acTCAg/acg	10/15	1	2	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	TRUE	1	0.14	2		524	455	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0020736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	314	451	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.549718939862813	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.549718939862813	3		451	715	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982318	201982318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140187152	NA	P-0020736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1704	204	852	1	ENST00000359651.3:c.697C>T	p.Arg233Cys	p.R233C	ENST00000359651		233	Cgt/Tgt	6/8	0.549718939862813	8	FACETS	1	0.946	1	0.172	0.158	0.186	CLONAL	1	TRUE	2	0.549718939862813	8		853	1908	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111469	8111469	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	406	930	0	ENST00000346208.3:c.956del	p.Asn319ThrfsTer36	p.N319Tfs*36	ENST00000346208		319	Aac/ac	5/6	0.549718939862813	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.549718939862813	3		930	873	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070602	67070602	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	237	449	0	ENST00000412916.2:c.226G>T	p.Glu76Ter	p.E76*	ENST00000412916		76	Gaa/Taa	3/6	0.549718939862813	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.549718939862813	2		449	423	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945496	151945497	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0020736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	682	1090	0	ENST00000262189.6:c.2022_2023del	p.Glu674AspfsTer30	p.E674Dfs*30	ENST00000262189	NM_170606.2	674	gaAAca/gaca	14/59	0.549718939862813	4	FACETS	0.944	0.913	0.974	0.944	0.913	0.974	CLONAL	3	TRUE	1	0.549718939862813	4		1090	1358	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0020739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	120	328	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.992	0.9	1	0.992	0.9	1	CLONAL	1	TRUE	1	0.455517277671315	2		328	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0020739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	218	651	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.4494524366257	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.455517277671315	1		651	707	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	161	415	3	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	0.455517277671315	2	FACETS	0.89	0.827	0.955	0.89	0.827	0.955	CLONAL	2	TRUE	0	0.455517277671315	2		418	397	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800978	243800978	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	199	978	5	ENST00000263826.5:c.496C>T	p.Arg166Ter	p.R166*	ENST00000263826	NM_005465.4	166	Cga/Tga	5/13	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.455517277671315	2		983	863	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154748	2154748	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs369122420	NA	P-0020739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	193	877	6	ENST00000434045.2:c.473C>T	p.Pro158Leu	p.P158L	ENST00000434045	NM_001127598.1	158	cCg/cTg	4/5	1	2	FACETS	0.922	0.853	0.993	0.922	0.853	0.993	CLONAL	1	TRUE	1	0.455517277671315	2		883	919	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508176	106508176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752039271	NA	P-0020739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	188	342	3	ENST00000359195.3:c.170C>T	p.Ala57Val	p.A57V	ENST00000359195	NM_002649.2	57	gCg/gTg	2/11	0.455517277671315	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.455517277671315	3		345	465	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188244	32188244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs996553122	NA	P-0020739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	207	1155	7	ENST00000375023.3:c.1097C>T	p.Pro366Leu	p.P366L	ENST00000375023	NM_004557.3	366	cCg/cTg	6/30	1	2	FACETS	0.976	0.906	1	0.976	0.906	1	CLONAL	1	TRUE	1	0.455517277671315	2		1162	931	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557376	21557376	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	48	459	0	ENST00000382592.4:c.2469A>T	p.Lys823Asn	p.K823N	ENST00000382592	NM_014572.2	823	aaA/aaT	5/8	0.71712506351094	1	FACETS	0.247	0.21	0.289	0.247	0.21	0.289	SUBCLONAL	1	TRUE	0	0.71712506351094	1		459	347	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057936	27057937	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1415146710	NA	P-0020746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	56	586	0	ENST00000324856.7:c.1650dup	p.Tyr551LeufsTer72	p.Y551Lfs*72	ENST00000324856	NM_006015.4	548	-/C	3/20	0.236871275831802	1	FACETS	0.474	0.405	0.55	0.474	0.405	0.55	SUBCLONAL	1	TRUE	0	0.236871275831802	1		586	879	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0020746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	177	295	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.218636729656555	3	FACETS	0.85	0.783	0.92	0.85	0.783	0.92	CLONAL	2	TRUE	1	0.236871275831802	3		295	983	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443625	29443625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751306825	NA	P-0020746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	87	724	0	ENST00000389048.3:c.3592C>T	p.Leu1198Phe	p.L1198F	ENST00000389048	NM_004304.4	1198	Ctc/Ttc	23/29	1	2	FACETS	0.712	0.629	0.802	0.712	0.629	0.802	SUBCLONAL	1	TRUE	1	0.236871275831802	2		724	1031	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0020747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	86	340	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	0.18	2		340	871	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695766	117695766	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	48	692	1	ENST00000369458.3:c.671C>A	p.Ser224Tyr	p.S224Y	ENST00000369458	NM_024626.3	224	tCc/tAc	4/6	1	2	FACETS	0.724	0.61	0.849	0.724	0.61	0.849	SUBCLONAL	1	TRUE	1	0.18	2		693	737	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205754	108205754	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	43	634	0	ENST00000278616.4:c.8069T>C	p.Phe2690Ser	p.F2690S	ENST00000278616	NM_000051.3	2690	tTt/tCt	55/63	1	2	FACETS	0.772	0.645	0.913	0.772	0.645	0.913	CLONAL	1	TRUE	1	0.18	2		634	619	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434404	49434404	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	77	987	0	ENST00000301067.7:c.7149G>T	p.Leu2383Phe	p.L2383F	ENST00000301067	NM_003482.3	2383	ttG/ttT	31/54	1	2	FACETS	0.778	0.681	0.884	0.778	0.681	0.884	SUBCLONAL	1	TRUE	1	0.18	2		987	1099	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647368	23647368	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	91	934	0	ENST00000261584.4:c.499G>T	p.Asp167Tyr	p.D167Y	ENST00000261584	NM_024675.3	167	Gat/Tat	4/13	1	2	FACETS	0.908	0.804	1	0.908	0.804	1	CLONAL	1	TRUE	1	0.18	2		934	1113	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17117027	17117027	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	94	932	0	ENST00000285071.4:c.1682A>G	p.Tyr561Cys	p.Y561C	ENST00000285071	NM_144997.5	561	tAc/tGc	14/14	1	2	FACETS	0.995	0.883	1	0.995	0.883	1	CLONAL	1	TRUE	1	0.18	2		932	1050	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243911	41243911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	72	952	1	ENST00000357654.3:c.3637G>A	p.Glu1213Lys	p.E1213K	ENST00000357654	NM_007294.3	1213	Gaa/Aaa	10/23	1	2	FACETS	0.845	0.736	0.963	0.845	0.736	0.963	CLONAL	1	TRUE	1	0.18	2		953	947	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857649	59857649	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	76	587	1	ENST00000259008.2:c.1908G>T	p.Glu636Asp	p.E636D	ENST00000259008	NM_032043.2	636	gaG/gaT	13/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.18	2		588	640	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920331	50920331	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1276328747	NA	P-0020747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1317	115	1178	3	ENST00000440232.2:c.3097G>T	p.Glu1033Ter	p.E1033*	ENST00000440232	NM_002691.3	1033	Gag/Tag	25/27	1	2	FACETS	0.892	0.801	0.99	0.892	0.801	0.99	CLONAL	1	TRUE	1	0.18	2		1181	1432	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72893542	72893543	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0020747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	51	978	2	ENST00000325599.8:c.175_176delinsTT	p.Gly59Leu	p.G59L	ENST00000325599	NM_018130.2	59	GGa/TTa	2/11	1	2	FACETS	0.713	0.604	0.833	0.713	0.604	0.833	SUBCLONAL	1	TRUE	1	0.18	2		980	795	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342675	70342675	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	75	970	1	ENST00000374080.3:c.1436C>A	p.Ser479Tyr	p.S479Y	ENST00000374080		479	tCc/tAc	10/45	0.0824369451776215	0	FACETS	0.65	0.568	0.739			1	INDETERMINATE	1	TRUE	0	0.18	0		971	1051	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020150	123020150	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	74	1198	1	ENST00000355640.3:c.638G>T	p.Cys213Phe	p.C213F	ENST00000355640		213	tGt/tTt	2/7	0.0824369451776215	0	FACETS	0.542	0.473	0.617			1	INDETERMINATE	1	TRUE	0	0.18	0		1199	1244	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0020749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	66	328	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	0.25	2		328	463	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028619	12028619	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	87	508	0	ENST00000353533.5:c.822A>T	p.Arg274Ser	p.R274S	ENST00000353533	NM_003010.3	274	agA/agT	8/11	0.241611167147963	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.25	1		508	521	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16040728	16040728	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0020749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	48	460	0	ENST00000268712.3:c.1408-2A>G		p.X470_splice	ENST00000268712	NM_006311.3	470			0.241611167147963	1	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	0	0.25	1		460	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0020750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	190	779	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA	2	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.312552526405066	2		781	1113	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053194	180053194	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	175	860	3	ENST00000261937.6:c.1175C>A	p.Ala392Asp	p.A392D	ENST00000261937	NM_182925.4	392	gCc/gAc	9/30	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.312552526405066	2		863	1077	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443695	29443695	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs863225281	NA	P-0020753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	45	760	0	ENST00000389048.3:c.3522C>A	p.Phe1174Leu	p.F1174L	ENST00000389048	NM_004304.4	1174	ttC/ttA	23/29	1	2	FACETS	0.562	0.471	0.664	0.562	0.471	0.664	SUBCLONAL	1	TRUE	1	0.173585253659537	2		760	922	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0020754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	47	733	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.172	0.144	0.203	0.172	0.144	0.203	SUBCLONAL	1	TRUE	1	0.463338884148824	2		733	1178	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0020754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	169	585	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.787	0.723	0.853	0.787	0.723	0.853	SUBCLONAL	1	TRUE	1	0.463338884148824	2		588	927	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0020754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	215	528	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.463338884148824	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.463338884148824	2		528	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0020754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	280	979	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.463338884148824	2		979	1128	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954198	48954198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123331	NA	P-0020754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	74	459	0	ENST00000267163.4:c.1399C>T	p.Arg467Ter	p.R467*	ENST00000267163	NM_000321.2	467	Cga/Tga	15/27	1	2	FACETS	0.793	0.697	0.894	0.793	0.697	0.894	SUBCLONAL	1	TRUE	1	0.463338884148824	2		459	403	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0020754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	109	421	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.463338884148824	2	FACETS	1	0.911	1	0.505	0.456	0.556	CLONAL	1	TRUE	0	0.463338884148824	2		421	466	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0020754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	104	423	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.92	0.828	1	0.92	0.828	1	CLONAL	1	TRUE	1	0.463338884148824	2		423	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577575	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782289	NA	P-0020754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	31	812	0	ENST00000269305.4:c.706T>C	p.Tyr236His	p.Y236H	ENST00000269305	NM_001126112.2	236	Tac/Cac	7/11	1	2	FACETS	0.127	0.102	0.156	0.127	0.102	0.156	SUBCLONAL	1	TRUE	1	0.463338884148824	2		812	1052	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057937	27057937	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	237	953	0	ENST00000324856.7:c.1650del	p.Tyr551ThrfsTer68	p.Y551Tfs*68	ENST00000324856	NM_006015.4	549	Ccc/cc	3/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.463338884148824	2		953	980	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005515	150005515	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	122	399	1	ENST00000253339.5:c.710del	p.Pro237HisfsTer6	p.P237Hfs*6	ENST00000253339		237	cCa/ca	3/7	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.463338884148824	2		400	512	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370957	55370957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	267	916	0	ENST00000297316.4:c.259G>A	p.Ala87Thr	p.A87T	ENST00000297316	NM_022454.3	87	Gcg/Acg	1/2	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.463338884148824	2		916	993	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881488	48881489	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0020754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	108	497	2	ENST00000267163.4:c.219_220dup	p.Ala74GlufsTer4	p.A74Efs*4	ENST00000267163	NM_000321.2	70	-/AG	2/27	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.463338884148824	2		499	445	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11168272	11168272	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	60	829	0	ENST00000361445.4:c.7600T>C	p.Ser2534Pro	p.S2534P	ENST00000361445	NM_004958.3	2534	Tcc/Ccc	57/58	1	2	FACETS	0.256	0.22	0.296	0.256	0.22	0.296	SUBCLONAL	1	TRUE	1	0.463338884148824	2		829	1010	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023089	27023090	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	36	112	0	ENST00000324856.7:c.197dup	p.Gln67AlafsTer44	p.Q67Afs*44	ENST00000324856	NM_006015.4	65	-/C	1/20	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.463338884148824	2		112	149	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936189	71936189	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	141	546	0	ENST00000298229.2:c.161G>T	p.Gly54Val	p.G54V	ENST00000298229	NM_001567.3	54	gGg/gTg	1/28	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.463338884148824	2		546	564	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343381	118343381	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	106	465	3	ENST00000534358.1:c.1507C>T	p.Arg503Trp	p.R503W	ENST00000534358	NM_005933.3	503	Cgg/Tgg	3/36	1	2	FACETS	0.899	0.809	0.993	0.899	0.809	0.993	CLONAL	1	TRUE	1	0.463338884148824	2		468	509	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541646	120541646	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167669994	NA	P-0020754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	90	774	1	ENST00000229340.5:c.211C>T	p.Arg71Cys	p.R71C	ENST00000229340	NM_006861.6	71	Cgc/Tgc	3/6	1	2	FACETS	0.408	0.361	0.458	0.408	0.361	0.458	SUBCLONAL	1	TRUE	1	0.463338884148824	2		775	952	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7128915	7128915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1280056812	NA	P-0020754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	125	772	1	ENST00000302850.5:c.2893G>A	p.Val965Ile	p.V965I	ENST00000302850	NM_000208.2	965	Gtc/Atc	15/22	1	2	FACETS	0.851	0.772	0.934	0.851	0.772	0.934	CLONAL	1	TRUE	1	0.463338884148824	2		773	634	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375428	15375430	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0020754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	182	926	0	ENST00000263377.2:c.997_999del	p.Lys333del	p.K333del	ENST00000263377	NM_058243.2	333	AAG/-	6/20	1	2	FACETS	0.731	0.673	0.791	0.731	0.673	0.791	SUBCLONAL	1	TRUE	1	0.463338884148824	2		926	1075	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574619	41574620	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0020754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	86	1115	2	ENST00000263253.7:c.6910_6911del	p.Ser2304GlnfsTer74	p.S2304Qfs*74	ENST00000263253	NM_001429.3	2302	TCt/t	31/31	1	2	FACETS	0.305	0.269	0.345	0.305	0.269	0.345	SUBCLONAL	1	TRUE	1	0.463338884148824	2		1117	1216	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591141	67591142	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATTG	novel	NA	P-0020754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	55	472	0	ENST00000274335.5:c.1734_1735insATTG	p.Gln579IlefsTer24	p.Q579Ifs*24	ENST00000274335		578	-/ATTG	12/15	1	2	FACETS	0.989	0.855	1	0.989	0.855	1	CLONAL	1	TRUE	1	0.463338884148824	2		472	240	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288207	33288207	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	70	717	0	ENST00000374542.5:c.1201A>T	p.Thr401Ser	p.T401S	ENST00000374542	NM_001141970.1	401	Acc/Tcc	4/8	1	2	FACETS	0.339	0.295	0.387	0.339	0.295	0.387	SUBCLONAL	1	TRUE	1	0.463338884148824	2		717	891	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492901	8492901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	99	777	0	ENST00000356435.5:c.2428G>A	p.Ala810Thr	p.A810T	ENST00000356435		810	Gct/Act	16/35	1	2	FACETS	0.464	0.414	0.519	0.464	0.414	0.519	SUBCLONAL	1	TRUE	1	0.463338884148824	2		777	920	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0020755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	261	742	1	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.324596406413206	2	FACETS	0.812	0.765	0.861	0.812	0.765	0.861	CLONAL	2	TRUE	0	0.430680037823152	2		743	746	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145656	11145656	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	206	866	0	ENST00000358026.2:c.4018G>T	p.Glu1340Ter	p.E1340*	ENST00000358026	NM_001128849.1	1340	Gag/Tag	29/36	0.351699748780141	2	FACETS	0.799	0.746	0.853	0.799	0.746	0.853	SUBCLONAL	2	TRUE	0	0.430680037823152	2		866	599	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732726	204732726	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	96	611	0	ENST00000302823.3:c.63del	p.Cys22AlafsTer50	p.C22Afs*50	ENST00000302823	NM_005214.4	21	Ccc/cc	1/4	0.111596675827578	5	FACETS	1	0.937	1			1	INDETERMINATE	1	TRUE	NA	0.430680037823152	5		611	683	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021815	71021815	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	91	332	0	ENST00000318789.4:c.1543C>T	p.His515Tyr	p.H515Y	ENST00000318789	NM_032682.5	515	Cat/Tat	18/21	0.324596406413206	2	FACETS	1	0.978	1	0.686	0.616	0.759	CLONAL	1	TRUE	0	0.430680037823152	2		332	308	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465645	8465645	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	142	678	0	ENST00000356435.5:c.3535A>G	p.Ser1179Gly	p.S1179G	ENST00000356435		1179	Agc/Ggc	21/35	0.324596406413206	2	FACETS	1	0.985	1	0.678	0.622	0.736	CLONAL	1	TRUE	0	0.430680037823152	2		678	486	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930306	39930306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	52	997	0	ENST00000378444.4:c.3158G>A	p.Arg1053Lys	p.R1053K	ENST00000378444	NM_001123385.1	1053	aGg/aAg	6/15	0.323342950290611	2	FACETS	0.284	0.241	0.332	0.142	0.12	0.166	SUBCLONAL	1	TRUE	0	0.430680037823152	2		997	850	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44911039	44911039	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	38	640	0	ENST00000377967.4:c.740A>T	p.Gln247Leu	p.Q247L	ENST00000377967	NM_021140.2	247	cAa/cTa	9/29	0.323342950290611	2	FACETS	0.252	0.207	0.302	0.126	0.103	0.151	SUBCLONAL	1	TRUE	0	0.430680037823152	2		640	701	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0020756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	43	455	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.619	0.518	0.731	0.619	0.518	0.731	SUBCLONAL	1	TRUE	1	0.267206385634422	2		455	520	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0020756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	77	861	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.638	0.559	0.724	0.638	0.559	0.724	SUBCLONAL	1	TRUE	1	0.267206385634422	2		861	903	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0020756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	77	396	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.644	0.564	0.73	0.644	0.564	0.73	SUBCLONAL	1	TRUE	1	0.267206385634422	2		396	895	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732957	30732957	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504421	NA	P-0020756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	59	587	0	ENST00000295754.5:c.1570G>A	p.Asp524Asn	p.D524N	ENST00000295754	NM_003242.5	524	Gac/Aac	7/7	1	2	FACETS	0.644	0.553	0.743	0.644	0.553	0.743	SUBCLONAL	1	TRUE	1	0.267206385634422	2		587	686	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0020762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	356	685	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.977	0.928	1	0.977	0.928	1	CLONAL	1	TRUE	1	0.745424073452428	2		685	978	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0020762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	425	456	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.745424073452428	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.745424073452428	1		456	691	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910683	32910683	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	170	757	0	ENST00000380152.3:c.2191G>T	p.Glu731Ter	p.E731*	ENST00000380152		731	Gaa/Taa	11/27	0.371729122507229	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.745424073452428	0		757	615	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562569	95562569	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	266	485	0	ENST00000393063.1:c.4688T>C	p.Val1563Ala	p.V1563A	ENST00000393063	NM_030621.3	1563	gTg/gCg	24/28	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.745424073452428	2		485	696	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879112	151879113	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	ATTTGCTGTTGTCTCATTCATTTGAAGGGGCC	novel	NA	P-0020762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	267	859	0	ENST00000262189.6:c.5801_5832dup	p.Arg1945GlyfsTer5	p.R1945Gfs*5	ENST00000262189	NM_170606.2	1944	-/GGCCCCTTCAAATGAATGAGACAACAGCAAAT	36/59	0.745424073452428	1	FACETS	0.547	0.514	0.58	0.547	0.514	0.58	SUBCLONAL	1	TRUE	0	0.745424073452428	1		859	822	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0020764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	47	328	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.961	0.811	1	0.961	0.811	1	CLONAL	1	TRUE	1	0.2	2		328	489	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285754	87285754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370304899	NA	P-0020764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	34	852	1	ENST00000277120.3:c.91G>A	p.Ala31Thr	p.A31T	ENST00000277120		31	Gcc/Acc	2/19	1	2	FACETS	0.561	0.457	0.678	0.561	0.457	0.678	SUBCLONAL	1	TRUE	1	0.2	2		853	606	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857275	9857275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426934537	NA	P-0020764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	97	719	0	ENST00000330684.3:c.4126C>T	p.Arg1376Cys	p.R1376C	ENST00000330684	NM_001134407.1	1376	Cgc/Tgc	13/13	1	2	FACETS	0.798	0.712	0.888	1	0.983	1	SUBCLONAL	2	TRUE	1	0.2	2		719	608	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39074470	39074470	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1454741396	NA	P-0020764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	31	591	0	ENST00000357387.3:c.10A>G	p.Ile4Val	p.I4V	ENST00000357387	NM_152756.3	4	Atc/Gtc	1/38	1	2	FACETS	0.736	0.595	0.896	0.736	0.595	0.896	SUBCLONAL	1	TRUE	1	0.2	2		591	421	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301852	65301852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	55	455	0	ENST00000342505.4:c.3187G>A	p.Asp1063Asn	p.D1063N	ENST00000342505	NM_002227.2	1063	Gac/Aac	23/25	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.2	2		455	516	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096655	178096655	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	36	513	0	ENST00000397062.3:c.676T>A	p.Tyr226Asn	p.Y226N	ENST00000397062	NM_006164.4	226	Tat/Aat	5/5	1	2	FACETS	0.526	0.431	0.633	0.526	0.431	0.633	SUBCLONAL	1	TRUE	1	0.2	2		513	684	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31495400	31495400	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	39	636	0	ENST00000344624.3:c.1748A>C	p.Asn583Thr	p.N583T	ENST00000344624		583	aAc/aCc	9/33	1	2	FACETS	0.546	0.451	0.653	0.546	0.451	0.653	SUBCLONAL	1	TRUE	1	0.2	2		636	714	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0020767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	889	779	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.929396557342733	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.929396557342733	3		781	929	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732951	30732951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223854	NA	P-0020767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	95	532	0	ENST00000295754.5:c.1564G>A	p.Asp522Asn	p.D522N	ENST00000295754	NM_003242.5	522	Gac/Aac	7/7	1	2	FACETS	0.831	0.753	0.911	0.831	0.753	0.911	CLONAL	1	TRUE	1	0.929396557342733	2		532	246	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197331	26197331	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	155	895	0	ENST00000356476.2:c.148C>G	p.Arg50Gly	p.R50G	ENST00000356476		50	Cgc/Ggc	1/1	0.692905864175808	6	FACETS	1	0.968	1	0.372	0.34	0.405	CLONAL	1	TRUE	3	0.929396557342733	6		895	855	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552990	106552990	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	136	963	0	ENST00000369096.4:c.955G>C	p.Glu319Gln	p.E319Q	ENST00000369096	NM_001198.3	319	Gag/Cag	5/7	0.5187149206085	3	FACETS	0.765	0.699	0.835			1	INDETERMINATE	1	TRUE	NA	0.929396557342733	3		963	560	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380076	116380077	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0020767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	120	979	2	ENST00000397752.3:c.1465_1466delinsTT	p.Glu489Leu	p.E489L	ENST00000397752	NM_000245.2	489	GAa/TTa	4/21	0.873696033712551	6	FACETS	0.79	0.712	0.872	0.263	0.237	0.291	SUBCLONAL	1	TRUE	3	0.929396557342733	6		981	935	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020117	123020117	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	75	1260	0	ENST00000355640.3:c.605G>T	p.Cys202Phe	p.C202F	ENST00000355640		202	tGt/tTt	2/7	0.929396557342733	3	FACETS	0.323	0.282	0.367	0.161	0.141	0.184	SUBCLONAL	1	TRUE	1	0.929396557342733	3		1260	732	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0020770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	163	730	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.459190729254705	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.459190729254705	1		731	531	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28897002	28897002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554058758	NA	P-0020770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	126	488	0	ENST00000282397.4:c.2878G>A	p.Val960Ile	p.V960I	ENST00000282397	NM_002019.4	960	Gtc/Atc	21/30	1	2	FACETS	0.9	0.817	0.986	0.9	0.817	0.986	CLONAL	1	TRUE	1	0.459190729254705	2		488	610	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658535	206658535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1281179215	NA	P-0020770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	49	280	0	ENST00000367120.3:c.1508C>T	p.Ala503Val	p.A503V	ENST00000367120	NM_014002.3	503	gCg/gTg	15/22	0.453523229242194	3	FACETS	0.578	0.49	0.675	0.193	0.163	0.225	SUBCLONAL	1	TRUE	0	0.459190729254705	3		280	454	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060568	38060571	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	AGCT	AGCT	-	novel	NA	P-0020770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	714	138	0	ENST00000250448.2:c.1418_*2del		p.*473*	ENST00000250448	NM_004496.3	473		2/2	1	2	FACETS	1	0.997	1	1	0.998	1	CLONAL	2	TRUE	1	0.459190729254705	2		138	1283	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467921	50467921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	43	372	0	ENST00000331340.3:c.1156C>T	p.Arg386Cys	p.R386C	ENST00000331340	NM_006060.4	386	Cgc/Tgc	8/8	1	2	FACETS	0.431	0.36	0.508	0.431	0.36	0.508	SUBCLONAL	1	TRUE	1	0.459190729254705	2		372	435	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56882298	56882298	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	228	527	0	ENST00000519728.1:c.996G>T	p.Lys332Asn	p.K332N	ENST00000519728	NM_002350.3	332	aaG/aaT	10/13	0.459190729254705	5	FACETS	0.912	0.851	0.976	0.608	0.567	0.651	CLONAL	2	TRUE	2	0.459190729254705	5		527	919	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912660	NA	P-0020773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1204	25	751	0	ENST00000269305.4:c.839G>T	p.Arg280Ile	p.R280I	ENST00000269305	NM_001126112.2	280	aGa/aTa	8/11	1	2	FACETS	0.239	0.187	0.3	0.239	0.187	0.3	SUBCLONAL	1	TRUE	1	0.17	2		751	1229	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0020774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	112	340	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.996	0.897	1	0.996	0.897	1	CLONAL	1	TRUE	1	0.313194110090693	2		340	718	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610229	10610229	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	170	1058	0	ENST00000171111.5:c.481A>G	p.Met161Val	p.M161V	ENST00000171111	NM_203500.1	161	Atg/Gtg	2/6	0.310761711886456	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.313194110090693	1		1058	852	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0020774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	78	477	0	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	1	2	FACETS	0.996	0.878	1	0.996	0.878	1	CLONAL	1	TRUE	1	0.313194110090693	2		477	500	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102196076	102196076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	47	373	0	ENST00000263464.3:c.836C>T	p.Ala279Val	p.A279V	ENST00000263464	NM_001165.4	279	gCg/gTg	2/9	1	2	FACETS	0.718	0.607	0.84	0.718	0.607	0.84	SUBCLONAL	1	TRUE	1	0.313194110090693	2		373	418	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28885773	28885773	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs776343811	NA	P-0020774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	86	727	1	ENST00000282397.4:c.3589A>T	p.Ser1197Cys	p.S1197C	ENST00000282397	NM_002019.4	1197	Agt/Tgt	27/30	1	2	FACETS	0.882	0.781	0.989	0.882	0.781	0.989	CLONAL	1	TRUE	1	0.313194110090693	2		728	623	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101967	11101967	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	137	937	1	ENST00000358026.2:c.1387G>T	p.Glu463Ter	p.E463*	ENST00000358026	NM_001128849.1	463	Gag/Tag	8/36	0.310761711886456	1	FACETS	0.994	0.906	1	0.994	0.906	1	CLONAL	1	TRUE	0	0.313194110090693	1		938	742	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	139	251	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.999	0.922	1	0.999	0.922	1	CLONAL	1	TRUE	1	0.792441176920186	2		251	351	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16040642	16040642	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	216	670	0	ENST00000268712.3:c.1492del	p.Arg498AlafsTer17	p.R498Afs*17	ENST00000268712	NM_006311.3	498	Cgc/gc	14/46	1	2	FACETS	0.898	0.84	0.957	0.898	0.84	0.957	CLONAL	1	TRUE	1	0.792441176920186	2		670	607	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245700	41245702	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs80358329	NA	P-0020775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	44	825	1	ENST00000357654.3:c.1846_1848del	p.Ser616del	p.S616del	ENST00000357654	NM_007294.3	616	TCT/-	10/23	1	2	FACETS	0.132	0.11	0.157	0.132	0.11	0.157	SUBCLONAL	1	TRUE	1	0.792441176920186	2		826	840	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158452	26158452	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	315	872	0	ENST00000289316.2:c.55G>C	p.Val19Leu	p.V19L	ENST00000289316	NM_138720.2	19	Gtg/Ctg	1/2	NA	2	FACETS	0.972	0.921	1			1	INDETERMINATE	1	TRUE	NA	0.792441176920186	2		872	818	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0020776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	58	500	0	ENST00000311936.3:c.34_35delinsTT	p.Gly12Phe	p.G12F	ENST00000311936	NM_004985.3	12	GGt/TTt	2/5	1	2	FACETS	0.76	0.652	0.878	0.76	0.652	0.878	SUBCLONAL	1	TRUE	1	0.215220664030159	2		500	709	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144564	55144564	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	49	376	1	ENST00000257290.5:c.2038G>A	p.Gly680Arg	p.G680R	ENST00000257290	NM_006206.4	680	Gga/Aga	15/23	1	2	FACETS	0.874	0.74	1	0.874	0.74	1	CLONAL	1	TRUE	1	0.215220664030159	2		377	521	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105820	27105820	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0020776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	52	387	1	ENST00000324856.7:c.5431A>T	p.Lys1811Ter	p.K1811*	ENST00000324856	NM_006015.4	1811	Aag/Tag	20/20	1	2	FACETS	0.966	0.823	1	0.966	0.823	1	CLONAL	1	TRUE	1	0.215220664030159	2		388	500	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193205420	193205420	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	64	382	0	ENST00000367435.3:c.1351G>C	p.Ala451Pro	p.A451P	ENST00000367435	NM_024529.4	451	Gca/Cca	15/17	0.215220664030159	4	FACETS	0.994	0.86	1	0.331	0.286	0.38	CLONAL	1	TRUE	1	0.215220664030159	4		382	727	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864847	57864847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	40	540	2	ENST00000228682.2:c.2324C>T	p.Pro775Leu	p.P775L	ENST00000228682	NM_005269.2	775	cCc/cTc	12/12	1	2	FACETS	0.539	0.446	0.642	0.539	0.446	0.642	SUBCLONAL	1	TRUE	1	0.215220664030159	2		542	690	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832775	3832775	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	48	401	0	ENST00000262367.5:c.1483C>T	p.Gln495Ter	p.Q495*	ENST00000262367	NM_004380.2	495	Cag/Tag	6/31	1	2	FACETS	0.787	0.665	0.921	0.787	0.665	0.921	CLONAL	1	TRUE	1	0.215220664030159	2		401	567	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220623	1220624	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	58	589	0	ENST00000326873.7:c.644dup	p.Ser216LeufsTer50	p.S216Lfs*50	ENST00000326873	NM_000455.4	214	cag/caGg	5/10	1	2	FACETS	0.904	0.777	1	0.904	0.777	1	CLONAL	1	TRUE	1	0.215220664030159	2		589	596	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602864	10602864	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	89	686	0	ENST00000171111.5:c.714C>G	p.Asn238Lys	p.N238K	ENST00000171111	NM_203500.1	238	aaC/aaG	3/6	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.215220664030159	2		686	813	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872901	136872901	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	54	282	0	ENST00000241393.3:c.597C>G	p.Phe199Leu	p.F199L	ENST00000241393	NM_003467.2	199	ttC/ttG	2/2	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.215220664030159	2		282	418	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215882	142215882	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	58	302	0	ENST00000350721.4:c.5711G>C	p.Arg1904Pro	p.R1904P	ENST00000350721	NM_001184.3	1904	cGg/cCg	33/47	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.215220664030159	2		302	452	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527319	187527319	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	71	388	0	ENST00000441802.2:c.10255C>G	p.Pro3419Ala	p.P3419A	ENST00000441802	NM_005245.3	3419	Ccc/Gcc	17/27	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.215220664030159	2		388	596	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978840	13978840	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	36	420	0	ENST00000405192.2:c.267G>C	p.Lys89Asn	p.K89N	ENST00000405192	NM_001163147.1	89	aaG/aaC	6/12	0.215220664030159	3	FACETS	0.675	0.554	0.811	0.337	0.277	0.406	SUBCLONAL	1	TRUE	1	0.215220664030159	3		420	549	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039709	47039709	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1556778444	NA	P-0020776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	57	548	0	ENST00000377604.3:c.1160+1G>T		p.X387_splice	ENST00000377604	NM_001204468.1	387			1	2	FACETS	0.75	0.643	0.868	0.75	0.643	0.868	SUBCLONAL	1	TRUE	1	0.215220664030159	2		548	706	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572535	95572535	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852978	NA	P-0020777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	205	391	1	ENST00000393063.1:c.2830C>T	p.Arg944Ter	p.R944*	ENST00000393063	NM_030621.3	944	Cga/Tga	19/28	0.187180323146144	5	FACETS	0.846	0.79	0.903	0.846	0.79	0.903	INDETERMINATE	3	TRUE	2	0.473203633476119	5		392	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578412	7578412	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519747	NA	P-0020777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	448	679	0	ENST00000269305.4:c.518T>G	p.Val173Gly	p.V173G	ENST00000269305	NM_001126112.2	173	gTg/gGg	5/11	0.452031994121056	2	FACETS	0.929	0.89	0.968	0.929	0.89	0.968	CLONAL	2	TRUE	0	0.473203633476119	2		679	1019	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436386	52436386	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	385	697	0	ENST00000460680.1:c.2108G>A	p.Gly703Glu	p.G703E	ENST00000460680	NM_004656.3	703	gGg/gAg	17/17	0.337601027765288	4	FACETS	0.88	0.835	0.926			1	CLONAL	2	TRUE	NA	0.473203633476119	4		697	1362	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374828	149374828	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	376	318	0	ENST00000360632.3:c.266C>G	p.Ser89Trp	p.S89W	ENST00000360632	NM_015472.4	89	tCg/tGg	2/7	0.473203633476119	5	FACETS	0.992	0.951	1	0.992	0.951	1	CLONAL	4	TRUE	1	0.473203633476119	5		318	685	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922328	178922328	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	713	556	0	ENST00000263967.3:c.1097C>G	p.Pro366Arg	p.P366R	ENST00000263967	NM_006218.2	366	cCc/cGc	6/21	0.473203633476119	6	FACETS	0.92	0.893	0.947			1	CLONAL	5	TRUE	NA	0.473203633476119	6		556	1275	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562124	176562124	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs995047182	NA	P-0020777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	344	608	0	ENST00000439151.2:c.20T>C	p.Leu7Pro	p.L7P	ENST00000439151	NM_022455.4	7	cTa/cCa	2/23	0.30791478948372	4	FACETS	0.939	0.89	0.99	0.939	0.89	0.99	CLONAL	2	TRUE	2	0.473203633476119	4		608	1140	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509447	106509447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	403	658	2	ENST00000359195.3:c.1441G>A	p.Val481Ile	p.V481I	ENST00000359195	NM_002649.2	481	Gtc/Atc	2/11	0.452031994121056	2	FACETS	0.934	0.893	0.975	0.934	0.893	0.975	CLONAL	2	TRUE	0	0.473203633476119	2		660	912	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542531	141542531	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1322	149	501	1	ENST00000220592.5:c.2455G>T	p.Asp819Tyr	p.D819Y	ENST00000220592	NM_012154.3	819	Gat/Tat	18/19	0.473203633476119	6	FACETS	0.833	0.759	0.912	0.167	0.151	0.183	CLONAL	1	TRUE	1	0.473203633476119	6		502	1471	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197027	123197027	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	41	648	0	ENST00000218089.9:c.1793A>T	p.Glu598Val	p.E598V	ENST00000218089	NM_001042749.1	598	gAa/gTa	19/35	1	2	FACETS	0.347	0.288	0.411	0.347	0.288	0.411	SUBCLONAL	1	TRUE	1	0.473203633476119	2		648	500	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	60	613	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.587	0.504	0.677	0.587	0.504	0.677	SUBCLONAL	1	TRUE	1	0.263218828523941	2		614	777	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471712	120471712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs75423398	NA	P-0020779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	46	487	0	ENST00000256646.2:c.3779G>A	p.Arg1260His	p.R1260H	ENST00000256646	NM_024408.3	1260	cGt/cAt	23/34	1	2	FACETS	0.605	0.509	0.711	0.605	0.509	0.711	SUBCLONAL	1	TRUE	1	0.263218828523941	2		487	578	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458813	120458813	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs375876845	NA	P-0020779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	61	627	0	ENST00000256646.2:c.6532G>T	p.Ala2178Ser	p.A2178S	ENST00000256646	NM_024408.3	2178	Gcc/Tcc	34/34	1	2	FACETS	0.612	0.527	0.705	0.612	0.527	0.705	SUBCLONAL	1	TRUE	1	0.263218828523941	2		627	757	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499723	18499723	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	60	476	0	ENST00000266497.5:c.1578C>A	p.Ser526Arg	p.S526R	ENST00000266497		526	agC/agA	10/31	1	2	FACETS	0.804	0.693	0.925	0.804	0.693	0.925	CLONAL	1	TRUE	1	0.263218828523941	2		476	567	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426411	49426411	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	97	1010	0	ENST00000301067.7:c.12077A>G	p.Gln4026Arg	p.Q4026R	ENST00000301067	NM_003482.3	4026	cAa/cGa	39/54	1	2	FACETS	0.65	0.578	0.727	0.65	0.578	0.727	SUBCLONAL	1	TRUE	1	0.263218828523941	2		1010	1134	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445379	49445379	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	104	974	1	ENST00000301067.7:c.2087C>T	p.Ser696Phe	p.S696F	ENST00000301067	NM_003482.3	696	tCc/tTc	10/54	1	2	FACETS	0.801	0.716	0.891	0.801	0.716	0.891	CLONAL	1	TRUE	1	0.263218828523941	2		975	987	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47602389	47602389	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	55	450	0	ENST00000263735.4:c.442C>G	p.Leu148Val	p.L148V	ENST00000263735	NM_002354.2	148	Cta/Gta	4/9	1	2	FACETS	0.664	0.568	0.77	0.664	0.568	0.77	SUBCLONAL	1	TRUE	1	0.263218828523941	2		450	629	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629316	187629316	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	86	695	0	ENST00000441802.2:c.1666A>G	p.Thr556Ala	p.T556A	ENST00000441802	NM_005245.3	556	Aca/Gca	2/27	1	2	FACETS	0.768	0.678	0.864	0.768	0.678	0.864	SUBCLONAL	1	TRUE	1	0.263218828523941	2		695	851	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260708	1260708	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370445231	NA	P-0020779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	62	530	1	ENST00000310581.5:c.2851C>T	p.Arg951Trp	p.R951W	ENST00000310581	NM_198253.2	951	Cgg/Tgg	12/16	0.203050667988723	5	FACETS	0.834	0.719	0.959	0.278	0.239	0.32	CLONAL	1	TRUE	2	0.263218828523941	5		531	788	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158743	26158743	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	116	616	0	ENST00000289316.2:c.346A>G	p.Thr116Ala	p.T116A	ENST00000289316	NM_138720.2	116	Acc/Gcc	1/2	0.23475764384778	3	FACETS	1	0.976	1	0.634	0.572	0.701	CLONAL	1	TRUE	1	0.263218828523941	3		616	786	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317891	8317891	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	55	467	0	ENST00000356435.5:c.5722G>T	p.Asp1908Tyr	p.D1908Y	ENST00000356435		1908	Gac/Tac	35/35	1	2	FACETS	0.702	0.6	0.814	0.702	0.6	0.814	SUBCLONAL	1	TRUE	1	0.263218828523941	2		467	595	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039350	47039369	+	frameshift_variant	Frame_Shift_Del	DEL	GTGCTGTCCTCCTCCAACGT	GTGCTGTCCTCCTCCAACGT	-	novel	NA	P-0020779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	52	379	0	ENST00000377604.3:c.974_993del	p.Val325AlafsTer49	p.V325Afs*49	ENST00000377604	NM_001204468.1	325	GTGCTGTCCTCCTCCAACGTg/g	10/24	1	1	FACETS	0.778	0.664	0.903	0.778	0.664	0.903	CLONAL	1	TRUE	0	0.263218828523941	1		379	441	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293558	1293558	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	98	951	0	ENST00000310581.5:c.1443del	p.Arg481SerfsTer28	p.R481Sfs*28	ENST00000310581	NM_198253.2	481	agG/ag	2/16	0.260732892898522	4	FACETS	0.866	0.771	0.969	0.433	0.385	0.485	CLONAL	1	TRUE	2	0.266198129011491	4		951	1076	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0020781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	240	685	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.420056199595432	11	FACETS	0.994	0.937	1	0.662	0.624	0.701	CLONAL	6	FALSE	2	0.420056199595432	11		685	554	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	153	1134	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	0.420056199595432	11	FACETS	1	0.981	1	0.277	0.253	0.301	CLONAL	2	FALSE	2	0.420056199595432	11		1134	846	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251907	153251907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	115	763	0	ENST00000281708.4:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000281708	NM_033632.3	367	Cga/Tga	7/12	0.24475955763146	5	FACETS	0.93	0.849	1	0.93	0.849	1	INDETERMINATE	3	FALSE	2	0.420056199595432	5		763	320	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739374	145739374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776218553	NA	P-0020781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	190	971	2	ENST00000428558.2:c.1996G>A	p.Gly666Arg	p.G666R	ENST00000428558	NM_004260.3	666	Ggg/Agg	12/22	0.420056199595432	6	FACETS	1	0.979	1	0.573	0.531	0.616	CLONAL	2	FALSE	2	0.420056199595432	6		973	726	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922694	44922694	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397514628	NA	P-0020781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	51	502	1	ENST00000377967.4:c.1555C>T	p.Arg519Ter	p.R519*	ENST00000377967	NM_021140.2	519	Cga/Tga	16/29	0.355427007228072	4	FACETS	1	0.939	1			1	CLONAL	1	FALSE	NA	0.420056199595432	4		503	289	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196791	108196791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039471	NA	P-0020781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	73	444	0	ENST00000278616.4:c.6814G>A	p.Glu2272Lys	p.E2272K	ENST00000278616	NM_000051.3	2272	Gaa/Aaa	47/63	0.230129384959534	2	FACETS	0.858	0.777	0.938	1	0.976	1	INDETERMINATE	3	FALSE	0	0.420056199595432	2		444	135	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128622	64128622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	172	778	0	ENST00000334205.4:c.479G>A	p.Arg160Gln	p.R160Q	ENST00000334205	NM_003942.2	160	cGa/cAa	5/17	0.420056199595432	8	FACETS	0.972	0.903	1			1	CLONAL	4	FALSE	NA	0.420056199595432	8		778	476	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136264	64136264	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	177	764	4	ENST00000334205.4:c.1423G>A	p.Asp475Asn	p.D475N	ENST00000334205	NM_003942.2	475	Gac/Aac	12/17	0.420056199595432	8	FACETS	1	0.968	1			1	CLONAL	4	FALSE	NA	0.420056199595432	8		768	446	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431680	431680	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	137	900	0	ENST00000399788.2:c.2329G>C	p.Glu777Gln	p.E777Q	ENST00000399788	NM_001042603.1	777	Gag/Cag	17/28	0.373009214399458	5	FACETS	0.886	0.814	0.96	0.886	0.814	0.96	CLONAL	3	FALSE	2	0.420056199595432	5		900	400	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427508	49427514	+	frameshift_variant	Frame_Shift_Del	DEL	CCCAGGG	CCCAGGG	-	novel	NA	P-0020781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	153	776	0	ENST00000301067.7:c.10974_10980del	p.Pro3659ValfsTer88	p.P3659Vfs*88	ENST00000301067	NM_003482.3	3658	acCCCTGGG/ac	39/54	0.420056199595432	8	FACETS	0.999	0.924	1	0.999	0.924	1	CLONAL	4	FALSE	4	0.420056199595432	8		776	412	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446774	49446775	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0020781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	189	736	0	ENST00000301067.7:c.1035_1036del	p.Cys346SerfsTer17	p.C346Sfs*17	ENST00000301067	NM_003482.3	345	ctCTgt/ctgt	8/54	0.420056199595432	8	FACETS	0.878	0.817	0.941	0.878	0.817	0.941	CLONAL	4	FALSE	4	0.420056199595432	8		736	579	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046488	30046488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	18	794	1	ENST00000331968.5:c.2695G>A	p.Glu899Lys	p.E899K	ENST00000331968	NM_002742.2	899	Gaa/Aaa	18/18	0.163199427904257	3	FACETS	0.757	0.575	0.967	0.378	0.287	0.484	INDETERMINATE	1	FALSE	1	0.420056199595432	3		795	137	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570180	95570180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150514959	NA	P-0020781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	32	460	0	ENST00000393063.1:c.3553G>A	p.Ala1185Thr	p.A1185T	ENST00000393063	NM_030621.3	1185	Gcc/Acc	22/28	0.163199427904257	3	FACETS	1	0.947	1	0.732	0.605	0.868	INDETERMINATE	1	FALSE	1	0.420056199595432	3		460	126	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740591	58740591	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	102	753	0	ENST00000305921.3:c.1496T>C	p.Val499Ala	p.V499A	ENST00000305921	NM_003620.3	499	gTg/gCg	6/6	0.420056199595432	6	FACETS	0.949	0.853	1	0.474	0.426	0.525	CLONAL	2	FALSE	2	0.420056199595432	6		753	471	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288229	33288229	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	305	786	0	ENST00000374542.5:c.1179G>C	p.Lys393Asn	p.K393N	ENST00000374542	NM_001141970.1	393	aaG/aaC	4/8	0.420056199595432	11	FACETS	1	0.976	1			1	CLONAL	4	FALSE	NA	0.420056199595432	11		786	991	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878769	151878769	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0020781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	50	568	0	ENST00000262189.6:c.6176C>G	p.Ser2059Ter	p.S2059*	ENST00000262189	NM_170606.2	2059	tCa/tGa	36/59	0.420056199595432	1	FACETS	0.855	0.75	0.961	1	0.976	1	CLONAL	2	FALSE	0	0.420056199595432	1		568	110	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878787	151878787	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	64	617	0	ENST00000262189.6:c.6158C>G	p.Ser2053Cys	p.S2053C	ENST00000262189	NM_170606.2	2053	tCt/tGt	36/59	0.420056199595432	1	FACETS	0.885	0.79	0.98	1	0.982	1	CLONAL	2	FALSE	0	0.420056199595432	1		617	136	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878839	151878839	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	93	731	0	ENST00000262189.6:c.6106C>G	p.Leu2036Val	p.L2036V	ENST00000262189	NM_170606.2	2036	Ctt/Gtt	36/59	0.420056199595432	1	FACETS	0.945	0.864	1	1	0.988	1	CLONAL	2	FALSE	0	0.420056199595432	1		731	185	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785992	135785992	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0020781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	96	906	0	ENST00000298552.3:c.1229C>G	p.Ser410Ter	p.S410*	ENST00000298552	NM_001162426.1	410	tCa/tGa	12/23	0.263003603878702	4	FACETS	1	0.902	1	1	0.902	1	CLONAL	2	FALSE	2	0.420056199595432	4		906	324	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0020782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	187	560	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.392079826224283	2		560	932	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267360	198267360	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs374250186	NA	P-0020782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	160	740	0	ENST00000335508.6:c.1997A>T	p.Lys666Met	p.K666M	ENST00000335508	NM_012433.2	666	aAg/aTg	14/25	1	2	FACETS	0.856	0.785	0.931	0.856	0.785	0.931	CLONAL	1	TRUE	1	0.392079826224283	2		740	953	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964202	28964202	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	90	453	0	ENST00000282397.4:c.1700C>A	p.Pro567Gln	p.P567Q	ENST00000282397	NM_002019.4	567	cCg/cAg	13/30	1	2	FACETS	0.873	0.777	0.975	0.873	0.777	0.975	CLONAL	1	TRUE	1	0.392079826224283	2		453	526	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7163193	7163193	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	147	750	2	ENST00000302850.5:c.1879G>T	p.Asp627Tyr	p.D627Y	ENST00000302850	NM_000208.2	627	Gat/Tat	9/22	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.392079826224283	2		752	748	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524474	44524474	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	91	399	0	ENST00000291552.4:c.83G>C	p.Arg28Pro	p.R28P	ENST00000291552	NM_006758.2	28	cGt/cCt	2/8	1	2	FACETS	0.871	0.775	0.972	0.871	0.775	0.972	CLONAL	1	TRUE	1	0.392079826224283	2		399	533	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	132	613	1	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	0.264467880425524	2		614	896	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0020790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	138	584	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.241006908050392	1	FACETS	0.945	0.859	1	0.945	0.859	1	CLONAL	1	TRUE	0	0.264467880425524	1		585	958	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934201	48934201	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	90	1008	0	ENST00000267163.4:c.656del	p.Met219SerfsTer45	p.M219Sfs*45	ENST00000267163	NM_000321.2	219	aTg/ag	7/27	0.264467880425524	1	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	0	0.264467880425524	1		1008	580	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44910994	44910994	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0020790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	109	905	0	ENST00000377967.4:c.695T>A	p.Leu232Ter	p.L232*	ENST00000377967	NM_021140.2	232	tTg/tAg	9/29	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.264467880425524	2		905	748	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	204	372	1	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	0.652193036008559	2		373	625	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0020791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	318	712	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.652193036008559	3	FACETS	0.928	0.882	0.973	0.928	0.882	0.973	CLONAL	2	TRUE	1	0.652193036008559	3		712	697	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0020791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	195	169	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.652193036008559	2		169	533	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0020791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	335	556	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.652193036008559	2		556	869	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368317	45368317	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1420438415	NA	P-0020791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	147	618	4	ENST00000262160.6:c.1285C>T	p.Gln429Ter	p.Q429*	ENST00000262160	NM_005901.5	429	Cag/Tag	11/11	0.652193036008559	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.652193036008559	1		622	266	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945129	32945129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80359104	NA	P-0020791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	78	323	0	ENST00000380152.3:c.8524C>T	p.Arg2842Cys	p.R2842C	ENST00000380152		2842	Cgc/Tgc	20/27	0.652193036008559	3	FACETS	0.755	0.667	0.849	0.378	0.333	0.425	SUBCLONAL	1	TRUE	1	0.652193036008559	3		323	420	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473719	67473719	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	603	958	1	ENST00000327367.4:c.799G>T	p.Glu267Ter	p.E267*	ENST00000327367	NM_005902.3	267	Gag/Tag	6/9	0.652193036008559	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.652193036008559	2		959	858	SUCCESS
AR	367	MSKCC	GRCh37	X	66943543	66943543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852581	NA	P-0020792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	84	400	0	ENST00000374690.3:c.2623C>T	p.His875Tyr	p.H875Y	ENST00000374690	NM_000044.3	875	Cat/Tat	8/8	1	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.736508674247637	1		400	112	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9928076	9928076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	77	489	1	ENST00000330684.3:c.1663G>A	p.Ala555Thr	p.A555T	ENST00000330684	NM_001134407.1	555	Gcc/Acc	8/13	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.736508674247637	2		490	194	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989481	85989481	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	119	731	0	ENST00000263360.6:c.1240C>G	p.Arg414Gly	p.R414G	ENST00000263360	NM_003797.3	414	Cga/Gga	12/12	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.736508674247637	2		731	275	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029190	26029190	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	71	646	2	ENST00000435504.4:c.160G>A	p.Ala54Thr	p.A54T	ENST00000435504		54	Gca/Aca	4/13	0.172177617154721	2	FACETS	0.918	0.815	1	0.459	0.407	0.513	INDETERMINATE	1	TRUE	0	0.736508674247637	2		648	210	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	116	613	1	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	0.263970331513778	2		614	744	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0020793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	153	1217	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.263970331513778	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.263970331513778	1		1217	865	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136019	64136019	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199674030	NA	P-0020793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	181	1148	2	ENST00000334205.4:c.1280G>A	p.Arg427His	p.R427H	ENST00000334205	NM_003942.2	427	cGc/cAc	11/17	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.263970331513778	2		1150	1116	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047163	77047163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	74	937	0	ENST00000356341.3:c.1381G>A	p.Glu461Lys	p.E461K	ENST00000356341	NM_002576.4	461	Gag/Aag	13/15	1	2	FACETS	0.617	0.539	0.702	0.617	0.539	0.702	SUBCLONAL	1	TRUE	1	0.263970331513778	2		937	908	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350447	89350447	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1464	108	1452	2	ENST00000301030.4:c.2503G>A	p.Asp835Asn	p.D835N	ENST00000301030	NM_001256183.1	835	Gac/Aac	9/13	0.263970331513778	3	FACETS	0.589	0.526	0.656	0.295	0.263	0.328	SUBCLONAL	1	TRUE	1	0.263970331513778	3		1454	1572	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944362	40944362	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0020793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	120	668	0	ENST00000373198.4:c.2139+1G>A		p.X713_splice	ENST00000373198	NM_133170.3	713			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.263970331513778	2		668	690	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045870	26045870	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	75	750	0	ENST00000540144.1:c.232G>C	p.Asp78His	p.D78H	ENST00000540144	NM_003531.2	78	Gac/Cac	1/1	1	2	FACETS	0.729	0.638	0.828	0.729	0.638	0.828	SUBCLONAL	1	TRUE	1	0.263970331513778	2		750	779	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0020799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	46	607	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		607	1062	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519988	NA	P-0020802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	259	1028	0	ENST00000269305.4:c.808T>G	p.Phe270Val	p.F270V	ENST00000269305	NM_001126112.2	270	Ttt/Gtt	8/11	0.442431519198509	1	FACETS	0.961	0.901	1	0.961	0.901	1	CLONAL	1	TRUE	0	0.442431519198509	1		1028	949	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81916891	81916891	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs763366111	NA	P-0020802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	138	1095	0	ENST00000359376.3:c.710A>T	p.Asp237Val	p.D237V	ENST00000359376	NM_002661.3	237	gAt/gTt	9/33	0.442431519198509	1	FACETS	0.5	0.455	0.548	0.5	0.455	0.548	SUBCLONAL	1	TRUE	0	0.442431519198509	1		1095	971	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753719	42753719	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	166	1212	2	ENST00000222329.4:c.545G>T	p.Gly182Val	p.G182V	ENST00000222329	NM_006494.2	182	gGc/gTc	4/4	1	2	FACETS	0.671	0.615	0.73	0.671	0.615	0.73	SUBCLONAL	1	TRUE	1	0.442431519198509	2		1214	1118	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114747	73114747	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	52	370	0	ENST00000356692.5:c.1128C>G	p.Asp376Glu	p.D376E	ENST00000356692		376	gaC/gaG	9/9	1	2	FACETS	0.864	0.742	0.996	0.864	0.742	0.996	CLONAL	1	TRUE	1	0.442431519198509	2		370	272	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465606	99465606	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	101	820	0	ENST00000268035.6:c.2431G>A	p.Glu811Lys	p.E811K	ENST00000268035	NM_000875.3	811	Gag/Aag	11/21	0.330315397318794	3	FACETS	0.879	0.785	0.978	0.439	0.392	0.489	CLONAL	1	TRUE	1	0.330315397318794	3		820	811	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0020803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	181	890	2	ENST00000269305.4:c.97-1G>T		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.295623087495094	2	FACETS	0.815	0.755	0.878	0.815	0.755	0.878	CLONAL	2	TRUE	0	0.330315397318794	2		892	672	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911491	114911491	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	88	277	0	ENST00000543371.1:c.1009C>G	p.Gln337Glu	p.Q337E	ENST00000543371	NM_001198531.1	337	Cag/Gag	10/14	0.295623087495094	2	FACETS	0.998	0.897	1	0.998	0.897	1	CLONAL	2	TRUE	0	0.330315397318794	2		277	267	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99192826	99192826	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199652097	NA	P-0020803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	48	793	0	ENST00000268035.6:c.16G>A	p.Gly6Arg	p.G6R	ENST00000268035	NM_000875.3	6	Gga/Aga	1/21	0.330315397318794	3	FACETS	0.374	0.315	0.439	0.187	0.157	0.22	SUBCLONAL	1	TRUE	1	0.330315397318794	3		793	906	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665346	138665346	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1272	197	1513	0	ENST00000330315.3:c.219G>C	p.Lys73Asn	p.K73N	ENST00000330315	NM_023067.3	73	aaG/aaC	1/1	0.330315397318794	3	FACETS	0.946	0.873	1	0.315	0.291	0.341	CLONAL	1	TRUE	0	0.330315397318794	3		1513	1469	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86681121	86681121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs574953066	NA	P-0020803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	86	548	0	ENST00000274376.6:c.2762C>T	p.Ser921Phe	p.S921F	ENST00000274376	NM_002890.2	921	tCt/tTt	22/25	0.285100598149928	4	FACETS	1	0.953	1	0.572	0.507	0.642	CLONAL	1	TRUE	2	0.330315397318794	4		548	605	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481452	20481452	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0020803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	51	487	0	ENST00000346618.3:c.521C>G	p.Ser174Ter	p.S174*	ENST00000346618	NM_001949.4	174	tCa/tGa	3/7	NA	2	FACETS	0.778	0.663	0.903			1	INDETERMINATE	1	TRUE	NA	0.330315397318794	2		487	397	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242481	+	protein_altering_variant	In_Frame_Del	DEL	GAATTAAGAGAAGCAA	GAATTAAGAGAAGCAA	ATTC	novel	NA	P-0020803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	119	876	3	ENST00000275493.2:c.2236_2251delinsATTC	p.Glu746_Thr751delinsIlePro	p.E746_T751delinsIP	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCAAca/ATTCca	19/28	0.22119176778686	4	FACETS	1	0.974	1	0.617	0.557	0.68	CLONAL	1	TRUE	2	0.330315397318794	4		879	777	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842267	151842267	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	64	669	0	ENST00000262189.6:c.14145G>C	p.Met4715Ile	p.M4715I	ENST00000262189	NM_170606.2	4715	atG/atC	54/59	0.22119176778686	4	FACETS	0.83	0.719	0.951	0.415	0.359	0.476	CLONAL	1	TRUE	2	0.330315397318794	4		669	621	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152357789	152357789	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	210	828	2	ENST00000359321.1:c.118C>T	p.His40Tyr	p.H40Y	ENST00000359321	NM_005431.1	40	Cat/Tat	2/3	0.22119176778686	4	FACETS	0.995	0.925	1	0.995	0.925	1	CLONAL	2	TRUE	2	0.330315397318794	4		830	850	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352389	70352389	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0020803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	146	616	0	ENST00000374080.3:c.4415+1G>C		p.X1472_splice	ENST00000374080		1472			0.140688244095132	4	FACETS	0.962	0.882	1	0.962	0.882	1	INDETERMINATE	2	TRUE	2	0.330315397318794	4		616	611	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0020806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	293	589	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.486147045095578	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	0	0.525050951227416	1		589	782	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0020806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	180	412	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.912	0.843	0.983	0.912	0.843	0.983	CLONAL	1	FALSE	1	0.525050951227416	2		412	752	SUCCESS
APC	324	MSKCC	GRCh37	5	112175324	112175324	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1211642532	NA	P-0020806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	96	351	2	ENST00000257430.4:c.4033G>T	p.Glu1345Ter	p.E1345*	ENST00000257430	NM_000038.5	1345	Gaa/Taa	16/16	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	FALSE	1	0.525050951227416	2		353	364	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566709	212566709	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	121	486	0	ENST00000342788.4:c.1472G>T	p.Arg491Ile	p.R491I	ENST00000342788	NM_005235.2	491	aGa/aTa	12/28	0.161419464076173	0	FACETS	0.421	0.382	0.462			1	INDETERMINATE	1	FALSE	0	0.525050951227416	0		486	520	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967567	26967567	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	913	883	0	ENST00000381527.3:c.710G>A	p.Arg237Gln	p.R237Q	ENST00000381527	NM_001260.1	237	cGa/cAa	7/13	0.525050951227416	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	FALSE	0	0.525050951227416	3		883	1300	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920444	114920444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1219807932	NA	P-0020806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	352	727	0	ENST00000543371.1:c.1385C>T	p.Pro462Leu	p.P462L	ENST00000543371	NM_001198531.1	462	cCg/cTg	13/14	NA	2	FACETS	0.902	0.861	0.944			1	INDETERMINATE	2	FALSE	NA	0.525050951227416	2		727	743	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0020810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	27	609	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.248196493157062	1	FACETS	0.851	0.681	1	0.851	0.681	1	CLONAL	1	TRUE	0	0.248196493157062	1		610	224	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672827	30672827	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	21	1338	0	ENST00000376406.3:c.4133C>T	p.Ser1378Phe	p.S1378F	ENST00000376406	NM_014641.2	1378	tCc/tTc	10/15	0.221643985525094	2	FACETS	0.572	0.44	0.725	0.286	0.22	0.363	SUBCLONAL	1	TRUE	0	0.248196493157062	2		1338	296	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	215	251	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.927	0.867	0.988	0.927	0.867	0.988	CLONAL	1	TRUE	1	0.753127682988012	2		251	616	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955423	48955423	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	161	661	0	ENST00000267163.4:c.1541del	p.Phe514SerfsTer5	p.F514Sfs*5	ENST00000267163	NM_000321.2	513	tcT/tc	17/27	0.753127682988012	1	FACETS	0.959	0.9	1	0.959	0.9	1	CLONAL	1	TRUE	0	0.753127682988012	1		661	278	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591141	67591153	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CCAATACTTGATG	CCAATACTTGATG	-	novel	NA	P-0020811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	279	426	0	ENST00000274335.5:c.1734_1745+1del		p.X578_splice	ENST00000274335		578		12/15	0.751912663509521	2	FACETS	0.943	0.906	0.978	0.943	0.906	0.978	CLONAL	2	TRUE	0	0.753127682988012	2		426	393	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247367	153247367	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	32	418	0	ENST00000281708.4:c.1435C>T	p.Arg479Ter	p.R479*	ENST00000281708	NM_033632.3	479	Cga/Tga	10/12	1	2	FACETS	0.566	0.459	0.686	0.566	0.459	0.686	SUBCLONAL	1	TRUE	1	0.276518031060674	2		418	409	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729880	30729881	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0020816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	44	392	0	ENST00000295754.5:c.1403_1404del	p.Lys468ArgfsTer3	p.K468Rfs*3	ENST00000295754	NM_003242.5	467	gtAAaa/gtaa	6/7	0.168737324416054	2	FACETS	0.749	0.629	0.881	0.374	0.314	0.441	SUBCLONAL	1	TRUE	0	0.276518031060674	2		392	425	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846036	68846036	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0020816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	152	813	0	ENST00000261769.5:c.1009-2A>G		p.X337_splice	ENST00000261769	NM_004360.3	337			0.176825590833879	2	FACETS	1	0.982	1	0.641	0.587	0.699	CLONAL	1	TRUE	0	0.276518031060674	2		813	857	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099901	27099901	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0020816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	65	754	0	ENST00000324856.7:c.3780C>G	p.Tyr1260Ter	p.Y1260*	ENST00000324856	NM_006015.4	1260	taC/taG	15/20	1	2	FACETS	0.649	0.562	0.744	0.649	0.562	0.744	SUBCLONAL	1	TRUE	1	0.276518031060674	2		754	724	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176085815	176085815	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	109	695	0	ENST00000367669.3:c.971G>C	p.Ser324Thr	p.S324T	ENST00000367669	NM_022457.5	324	aGt/aCt	9/20	0.227336716649942	3	FACETS	0.752	0.676	0.831	0.752	0.676	0.831	SUBCLONAL	2	TRUE	1	0.276518031060674	3		695	597	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991293	41991294	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0020816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	57	880	1	ENST00000219905.7:c.2124_2125delinsTT	p.Lys708_Glu709delinsAsnTer	p.K708_E709delinsN*	ENST00000219905	NM_001164273.1	708	aaGGaa/aaTTaa	5/24	1	2	FACETS	0.591	0.506	0.683	0.591	0.506	0.683	SUBCLONAL	1	TRUE	1	0.276518031060674	2		881	698	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412890	49412890	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	58	977	0	ENST00000418115.1:c.133G>C	p.Asp45His	p.D45H	ENST00000418115	NM_001664.2	45	Gat/Cat	2/5	1	2	FACETS	0.432	0.37	0.5	0.432	0.37	0.5	SUBCLONAL	1	TRUE	1	0.276518031060674	2		977	971	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	94	706	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	1	2	FACETS	0.9	0.8	1	0.9	0.8	1	CLONAL	1	TRUE	1	0.27	2		706	774	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733217	40733217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	61	678	0	ENST00000373198.4:c.3589G>A	p.Glu1197Lys	p.E1197K	ENST00000373198	NM_133170.3	1197	Gaa/Aaa	26/32	1	2	FACETS	0.694	0.598	0.798	0.694	0.598	0.798	SUBCLONAL	1	TRUE	1	0.27	2		678	651	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546761	9546761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768724288	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	30	322	0	ENST00000353224.5:c.1261G>A	p.Asp421Asn	p.D421N	ENST00000353224	NM_177990.2	421	Gac/Aac	5/10	1	2	FACETS	0.826	0.668	1	0.826	0.668	1	CLONAL	1	TRUE	1	0.27	2		322	269	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733211	40733211	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	52	673	0	ENST00000373198.4:c.3595C>T	p.Gln1199Ter	p.Q1199*	ENST00000373198	NM_133170.3	1199	Cag/Tag	26/32	1	2	FACETS	0.621	0.528	0.723	0.621	0.528	0.723	SUBCLONAL	1	TRUE	1	0.27	2		673	620	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562746	29562746	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs199474742	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	48	638	0	ENST00000356175.3:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000356175	NM_000267.3	1276	Cga/Tga	28/57	1	2	FACETS	0.57	0.481	0.668	0.57	0.481	0.668	SUBCLONAL	1	TRUE	1	0.27	2		638	624	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612073	189612073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142762485	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	113	745	2	ENST00000264731.3:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000264731	NM_003722.4	609	Gaa/Aaa	14/14	1	2	FACETS	0.875	0.786	0.969	0.875	0.786	0.969	CLONAL	1	TRUE	1	0.27	2		747	957	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953634	38953634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146765449	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	24	362	0	ENST00000357387.3:c.2719C>T	p.Arg907Cys	p.R907C	ENST00000357387	NM_152756.3	907	Cgt/Tgt	28/38	0.141318777768122	3	FACETS	0.534	0.418	0.667	0.267	0.209	0.334	INDETERMINATE	1	TRUE	1	0.27	3		362	378	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608648	189608648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	69	732	0	ENST00000264731.3:c.1723C>T	p.Gln575Ter	p.Q575*	ENST00000264731	NM_003722.4	575	Cag/Tag	13/14	1	2	FACETS	0.579	0.503	0.662	0.579	0.503	0.662	SUBCLONAL	1	TRUE	1	0.27	2		732	882	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922258	100922258	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	26	564	0	ENST00000325455.5:c.2254C>T	p.Gln752Ter	p.Q752*	ENST00000325455	NM_001202474.3	752	Cag/Tag	5/8	1	2	FACETS	0.473	0.374	0.587	0.473	0.374	0.587	SUBCLONAL	1	TRUE	1	0.27	2		564	407	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934887	9934887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	53	695	2	ENST00000330684.3:c.1403C>T	p.Ser468Phe	p.S468F	ENST00000330684	NM_001134407.1	468	tCc/tTc	6/13	1	2	FACETS	0.709	0.604	0.823	0.709	0.604	0.823	SUBCLONAL	1	TRUE	1	0.27	2		697	554	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956676	93956676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465960814	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	44	488	0	ENST00000369303.4:c.2560C>T	p.Arg854Cys	p.R854C	ENST00000369303	NM_004440.3	854	Cgt/Tgt	15/17	1	2	FACETS	0.679	0.569	0.8	0.679	0.569	0.8	SUBCLONAL	1	TRUE	1	0.27	2		488	480	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156354	106156354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	38	505	2	ENST00000380013.4:c.1255C>T	p.Pro419Ser	p.P419S	ENST00000380013	NM_001127208.2	419	Cct/Tct	3/11	1	2	FACETS	0.698	0.578	0.833	0.698	0.578	0.833	SUBCLONAL	1	TRUE	1	0.27	2		507	403	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050707	30050708	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	54	448	0	ENST00000338641.4:c.514dup	p.Arg172LysfsTer31	p.R172Kfs*31	ENST00000338641	NM_000268.3	170	cca/ccAa	5/16	0.141318777768122	1	FACETS	0.688	0.588	0.797	0.688	0.588	0.797	INDETERMINATE	1	TRUE	0	0.27	1		448	503	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222732	5222732	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772912033	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	100	881	0	ENST00000357368.4:c.3071C>T	p.Pro1024Leu	p.P1024L	ENST00000357368	NM_002850.3	1024	cCc/cTc	18/38	1	2	FACETS	0.992	0.886	1	0.992	0.886	1	CLONAL	1	TRUE	1	0.27	2		881	747	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515295	31515295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756537138	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	82	782	3	ENST00000344624.3:c.1090C>T	p.Arg364Cys	p.R364C	ENST00000344624		364	Cgt/Tgt	5/33	0.21164688568396	1	FACETS	0.66	0.581	0.745	0.66	0.581	0.745	SUBCLONAL	1	TRUE	0	0.27	1		785	796	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249666	110249666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140990946	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	379	1057	2	ENST00000374672.4:c.1009C>T	p.Pro337Ser	p.P337S	ENST00000374672	NM_004235.4	337	Cct/Tct	3/5	0.265509817459847	2	FACETS	0.936	0.888	0.986	0.936	0.888	0.986	CLONAL	2	TRUE	0	0.27	2		1059	1499	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251941	8251941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	107	804	1	ENST00000335790.3:c.136G>A	p.Glu46Lys	p.E46K	ENST00000335790	NM_002315.2	46	Gaa/Aaa	2/4	1	2	FACETS	0.921	0.825	1	0.921	0.825	1	CLONAL	1	TRUE	1	0.27	2		805	861	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359060	81359060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	51	569	0	ENST00000222390.5:c.901G>A	p.Glu301Lys	p.E301K	ENST00000222390	NM_000601.4	301	Gaa/Aaa	8/18	1	2	FACETS	0.672	0.571	0.783	0.672	0.571	0.783	SUBCLONAL	1	TRUE	1	0.27	2		569	562	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054037	42054037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1246555872	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	23	413	0	ENST00000219905.7:c.7499C>T	p.Ser2500Leu	p.S2500L	ENST00000219905	NM_001164273.1	2500	tCg/tTg	21/24	1	2	FACETS	0.503	0.392	0.631	0.503	0.392	0.631	SUBCLONAL	1	TRUE	1	0.27	2		413	339	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962334	2962334	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	66	861	0	ENST00000396946.4:c.2203G>A	p.Glu735Lys	p.E735K	ENST00000396946	NM_032415.4	735	Gaa/Aaa	17/25	1	2	FACETS	0.607	0.525	0.695	0.607	0.525	0.695	SUBCLONAL	1	TRUE	1	0.27	2		861	806	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69050711	69050711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	40	625	0	ENST00000288368.4:c.4046C>T	p.Ser1349Phe	p.S1349F	ENST00000288368	NM_024870.2	1349	tCc/tTc	33/40	0.21164688568396	1	FACETS	0.561	0.466	0.666	0.561	0.466	0.666	SUBCLONAL	1	TRUE	0	0.27	1		625	457	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715410	117715410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	40	596	0	ENST00000368508.3:c.1079G>A	p.Arg360Lys	p.R360K	ENST00000368508	NM_002944.2	360	aGa/aAa	10/43	1	2	FACETS	0.636	0.528	0.756	0.636	0.528	0.756	SUBCLONAL	1	TRUE	1	0.27	2		596	466	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321305	65321305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368776025	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	106	785	0	ENST00000342505.4:c.1535C>T	p.Ser512Leu	p.S512L	ENST00000342505	NM_002227.2	512	tCg/tTg	11/25	1	2	FACETS	0.729	0.652	0.811	0.729	0.652	0.811	SUBCLONAL	1	TRUE	1	0.27	2		785	1077	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259453	16259453	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1291646884	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	72	552	0	ENST00000375759.3:c.6718C>T	p.Pro2240Ser	p.P2240S	ENST00000375759	NM_015001.2	2240	Cct/Tct	11/15	1	2	FACETS	0.757	0.66	0.86	0.757	0.66	0.86	SUBCLONAL	1	TRUE	1	0.27	2		552	705	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260276	16260276	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	73	546	1	ENST00000375759.3:c.7541C>T	p.Pro2514Leu	p.P2514L	ENST00000375759	NM_015001.2	2514	cCa/cTa	11/15	1	2	FACETS	0.734	0.641	0.834	0.734	0.641	0.834	SUBCLONAL	1	TRUE	1	0.27	2		547	737	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262378	16262378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	61	352	0	ENST00000375759.3:c.9643G>A	p.Gly3215Arg	p.G3215R	ENST00000375759	NM_015001.2	3215	Ggg/Agg	11/15	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.27	2		352	429	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599253	28599254	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	151	1005	2	ENST00000253063.3:c.699_700delinsTT	p.Pro234Ser	p.P234S	ENST00000253063	NM_031459.4	233	ccCCct/ccTTct	5/10	1	2	FACETS	0.909	0.829	0.994	0.909	0.829	0.994	CLONAL	1	TRUE	1	0.27	2		1007	1230	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458234	120458234	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	105	723	0	ENST00000256646.2:c.7111C>T	p.Pro2371Ser	p.P2371S	ENST00000256646	NM_024408.3	2371	Cca/Tca	34/34	1	2	FACETS	0.917	0.821	1	0.917	0.821	1	CLONAL	1	TRUE	1	0.27	2		723	848	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451413	70451413	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	55	672	0	ENST00000373644.4:c.6253G>A	p.Asp2085Asn	p.D2085N	ENST00000373644	NM_030625.2	2085	Gac/Aac	12/12	1	2	FACETS	0.602	0.514	0.698	0.602	0.514	0.698	SUBCLONAL	1	TRUE	1	0.27	2		672	677	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274777	123274777	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	113	698	0	ENST00000358487.5:c.1141T>A	p.Tyr381Asn	p.Y381N	ENST00000358487	NM_000141.4	381	Tac/Aac	9/18	1	2	FACETS	0.921	0.828	1	0.921	0.828	1	CLONAL	1	TRUE	1	0.27	2		698	909	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161490	2161490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	65	740	1	ENST00000434045.2:c.37C>T	p.Pro13Ser	p.P13S	ENST00000434045	NM_001127598.1	13	Ccc/Tcc	2/5	1	2	FACETS	0.612	0.529	0.701	0.612	0.529	0.701	SUBCLONAL	1	TRUE	1	0.27	2		741	787	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128672	64128672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	106	767	0	ENST00000334205.4:c.529C>T	p.Leu177Phe	p.L177F	ENST00000334205	NM_003942.2	177	Ctc/Ttc	5/17	1	2	FACETS	0.786	0.703	0.874	0.786	0.703	0.874	SUBCLONAL	1	TRUE	1	0.27	2		767	999	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344888	118344888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	64	386	0	ENST00000534358.1:c.3014C>T	p.Ser1005Phe	p.S1005F	ENST00000534358	NM_005933.3	1005	tCc/tTc	3/36	1	2	FACETS	0.937	0.813	1	0.937	0.813	1	CLONAL	1	TRUE	1	0.27	2		386	506	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360543	118360543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	59	581	0	ENST00000534358.1:c.4516C>T	p.His1506Tyr	p.H1506Y	ENST00000534358	NM_005933.3	1506	Cac/Tac	12/36	1	2	FACETS	0.579	0.497	0.668	0.579	0.497	0.668	SUBCLONAL	1	TRUE	1	0.27	2		581	755	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392012	118392013	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	53	613	1	ENST00000534358.1:c.11523_11524delinsTT	p.His3842Tyr	p.H3842Y	ENST00000534358	NM_005933.3	3841	atCCat/atTTat	35/36	1	2	FACETS	0.566	0.481	0.658	0.566	0.481	0.658	SUBCLONAL	1	TRUE	1	0.27	2		614	694	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149244	119149244	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	67	657	0	ENST00000264033.4:c.1252T>A	p.Phe418Ile	p.F418I	ENST00000264033	NM_005188.3	418	Ttc/Atc	9/16	1	2	FACETS	0.545	0.472	0.624	0.545	0.472	0.624	SUBCLONAL	1	TRUE	1	0.27	2		657	911	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149294	119149294	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	95	669	0	ENST00000264033.4:c.1302T>G	p.Phe434Leu	p.F434L	ENST00000264033	NM_005188.3	434	ttT/ttG	9/16	1	2	FACETS	0.721	0.641	0.807	0.721	0.641	0.807	SUBCLONAL	1	TRUE	1	0.27	2		669	976	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155730	119155730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1385124529	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	118	860	0	ENST00000264033.4:c.1483C>T	p.Pro495Ser	p.P495S	ENST00000264033	NM_005188.3	495	Ccg/Tcg	10/16	1	2	FACETS	0.722	0.649	0.799	0.722	0.649	0.799	SUBCLONAL	1	TRUE	1	0.27	2		860	1211	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432844	432844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	66	735	0	ENST00000399788.2:c.2072C>T	p.Ser691Phe	p.S691F	ENST00000399788	NM_001042603.1	691	tCc/tTc	15/28	0.3	2	FACETS	0.642	0.557	0.736			1	SUBCLONAL	1	TRUE	NA	0.27	2		735	761	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644460	18644460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	34	714	1	ENST00000266497.5:c.2638C>T	p.Pro880Ser	p.P880S	ENST00000266497		880	Cct/Tct	18/31	1	2	FACETS	0.47	0.383	0.568	0.47	0.383	0.568	SUBCLONAL	1	TRUE	1	0.27	2		715	536	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926247	112926247	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	108	708	0	ENST00000351677.2:c.1380T>G	p.Ser460Arg	p.S460R	ENST00000351677	NM_002834.3	460	agT/agG	12/16	0.265509817459847	1	FACETS	0.929	0.834	1	0.929	0.834	1	CLONAL	1	TRUE	0	0.27	1		708	745	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610228	81610228	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139352934	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	49	523	0	ENST00000298171.2:c.1826G>A	p.Arg609Gln	p.R609Q	ENST00000298171	NM_000369.2	609	cGa/cAa	10/10	1	2	FACETS	0.608	0.514	0.711	0.608	0.514	0.711	SUBCLONAL	1	TRUE	1	0.27	2		523	597	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590864	95590864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	39	512	0	ENST00000393063.1:c.1045G>A	p.Asp349Asn	p.D349N	ENST00000393063	NM_030621.3	349	Gac/Aac	9/28	1	2	FACETS	0.615	0.509	0.732	0.615	0.509	0.732	SUBCLONAL	1	TRUE	1	0.27	2		512	470	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003357	42003357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	81	586	0	ENST00000219905.7:c.2894C>T	p.Pro965Leu	p.P965L	ENST00000219905	NM_001164273.1	965	cCa/cTa	8/24	1	2	FACETS	0.823	0.725	0.929	0.823	0.725	0.929	CLONAL	1	TRUE	1	0.27	2		586	729	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034789	42034789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1188527747	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	79	599	1	ENST00000219905.7:c.4631G>A	p.Ser1544Asn	p.S1544N	ENST00000219905	NM_001164273.1	1544	aGt/aAt	15/24	1	2	FACETS	0.732	0.643	0.828	0.732	0.643	0.828	SUBCLONAL	1	TRUE	1	0.27	2		600	799	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041524	42041525	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	59	699	0	ENST00000219905.7:c.5719_5720delinsTT	p.Pro1907Phe	p.P1907F	ENST00000219905	NM_001164273.1	1907	CCt/TTt	17/24	1	2	FACETS	0.561	0.482	0.648	0.561	0.482	0.648	SUBCLONAL	1	TRUE	1	0.27	2		699	779	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680731	88680731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	103	797	0	ENST00000360948.2:c.526G>A	p.Glu176Lys	p.E176K	ENST00000360948	NM_001012338.2	176	Gag/Aag	6/19	1	2	FACETS	0.916	0.819	1	0.916	0.819	1	CLONAL	1	TRUE	1	0.27	2		797	833	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312729	91312729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	70	495	1	ENST00000355112.3:c.2468C>T	p.Ser823Phe	p.S823F	ENST00000355112	NM_000057.2	823	tCt/tTt	12/22	1	2	FACETS	0.663	0.577	0.756	0.663	0.577	0.756	SUBCLONAL	1	TRUE	1	0.27	2		496	782	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396235	396235	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	141	794	1	ENST00000262320.3:c.791C>T	p.Pro264Leu	p.P264L	ENST00000262320	NM_003502.3	264	cCc/cTc	2/11	1	2	FACETS	0.969	0.881	1	0.969	0.881	1	CLONAL	1	TRUE	1	0.27	2		795	1078	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646219	3646219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	130	948	1	ENST00000294008.3:c.1859G>A	p.Arg620Lys	p.R620K	ENST00000294008	NM_032444.2	620	aGg/aAg	8/15	1	2	FACETS	0.952	0.862	1	0.952	0.862	1	CLONAL	1	TRUE	1	0.27	2		949	1012	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781431	3781431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	85	539	0	ENST00000262367.5:c.4934C>T	p.Thr1645Ile	p.T1645I	ENST00000262367	NM_004380.2	1645	aCc/aTc	30/31	1	2	FACETS	0.985	0.872	1	0.985	0.872	1	CLONAL	1	TRUE	1	0.27	2		539	639	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857506	9857506	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	52	498	0	ENST00000330684.3:c.3895C>T	p.Pro1299Ser	p.P1299S	ENST00000330684	NM_001134407.1	1299	Cct/Tct	13/13	1	2	FACETS	0.928	0.792	1	0.928	0.792	1	CLONAL	1	TRUE	1	0.27	2		498	415	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858032	9858032	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	54	676	0	ENST00000330684.3:c.3369G>T	p.Glu1123Asp	p.E1123D	ENST00000330684	NM_001134407.1	1123	gaG/gaT	13/13	1	2	FACETS	0.721	0.615	0.836	0.721	0.615	0.836	SUBCLONAL	1	TRUE	1	0.27	2		676	555	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993051	72993051	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	117	970	1	ENST00000268489.5:c.994G>A	p.Asp332Asn	p.D332N	ENST00000268489	NM_006885.3	332	Gac/Aac	2/10	1	2	FACETS	0.722	0.649	0.799	0.722	0.649	0.799	SUBCLONAL	1	TRUE	1	0.27	2		971	1201	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934290	81934290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs996161733	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	109	883	0	ENST00000359376.3:c.1267G>A	p.Glu423Lys	p.E423K	ENST00000359376	NM_002661.3	423	Gaa/Aaa	14/33	1	2	FACETS	0.841	0.754	0.934	0.841	0.754	0.934	CLONAL	1	TRUE	1	0.27	2		883	960	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990366	81990366	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	75	675	0	ENST00000359376.3:c.3637C>T	p.Gln1213Ter	p.Q1213*	ENST00000359376	NM_002661.3	1213	Cag/Tag	32/33	1	2	FACETS	0.755	0.661	0.856	0.755	0.661	0.856	SUBCLONAL	1	TRUE	1	0.27	2		675	736	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527574	29527580	+	frameshift_variant	Frame_Shift_Del	DEL	CATTTTC	CATTTTC	-	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	44	747	0	ENST00000356175.3:c.1024_1030del	p.Ile342TyrfsTer32	p.I342Yfs*32	ENST00000356175	NM_000267.3	341	gtCATTTTC/gt	9/57	1	2	FACETS	0.501	0.419	0.592	0.501	0.419	0.592	SUBCLONAL	1	TRUE	1	0.27	2		747	651	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244547	41244547	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	62	853	0	ENST00000357654.3:c.3001G>A	p.Glu1001Lys	p.E1001K	ENST00000357654	NM_007294.3	1001	Gaa/Aaa	10/23	1	2	FACETS	0.629	0.543	0.724	0.629	0.543	0.724	SUBCLONAL	1	TRUE	1	0.27	2		853	730	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59878769	59878769	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	53	552	1	ENST00000259008.2:c.985C>T	p.Gln329Ter	p.Q329*	ENST00000259008	NM_032043.2	329	Caa/Taa	8/20	1	2	FACETS	0.742	0.633	0.862	0.742	0.633	0.862	SUBCLONAL	1	TRUE	1	0.27	2		553	529	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532590	63532590	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730882193	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	123	879	1	ENST00000307078.5:c.1989G>A	p.Trp663Ter	p.W663*	ENST00000307078	NM_004655.3	663	tgG/tgA	8/11	1	2	FACETS	0.998	0.902	1	0.998	0.902	1	CLONAL	1	TRUE	1	0.27	2		880	913	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732310	74732310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	32	370	0	ENST00000359995.5:c.599C>T	p.Ser200Phe	p.S200F	ENST00000359995	NM_001195427.1	200	tCc/tTc	2/3	1	2	FACETS	0.424	0.343	0.516	0.424	0.343	0.516	SUBCLONAL	1	TRUE	1	0.27	2		370	559	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796897	78796897	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	91	618	0	ENST00000306801.3:c.1010T>G	p.Phe337Cys	p.F337C	ENST00000306801	NM_020761.2	337	tTc/tGc	9/34	1	2	FACETS	0.899	0.798	1	0.899	0.798	1	CLONAL	1	TRUE	1	0.27	2		618	750	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247910	10247910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	108	863	0	ENST00000340748.4:c.4292C>T	p.Ala1431Val	p.A1431V	ENST00000340748		1431	gCc/gTc	36/40	1	2	FACETS	0.78	0.698	0.866	0.78	0.698	0.866	SUBCLONAL	1	TRUE	1	0.27	2		863	1026	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610579	10610579	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	125	838	1	ENST00000171111.5:c.131C>T	p.Pro44Leu	p.P44L	ENST00000171111	NM_203500.1	44	cCc/cTc	2/6	1	2	FACETS	0.807	0.729	0.89	0.807	0.729	0.89	CLONAL	1	TRUE	1	0.27	2		839	1147	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272321	15272321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	144	1089	0	ENST00000263388.2:c.6118G>A	p.Gly2040Arg	p.G2040R	ENST00000263388	NM_000435.2	2040	Ggg/Agg	33/33	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.27	2		1089	1011	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349565	15349565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	146	1047	1	ENST00000263377.2:c.4009C>T	p.Arg1337Cys	p.R1337C	ENST00000263377	NM_058243.2	1337	Cgc/Tgc	19/20	1	2	FACETS	0.826	0.752	0.905	0.826	0.752	0.905	CLONAL	1	TRUE	1	0.27	2		1048	1309	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961502	18961502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	46	488	0	ENST00000262803.5:c.635C>T	p.Pro212Leu	p.P212L	ENST00000262803	NM_002911.3	212	cCc/cTc	5/24	1	2	FACETS	0.624	0.525	0.733	0.624	0.525	0.733	SUBCLONAL	1	TRUE	1	0.27	2		488	546	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223966	36223967	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1212	143	1021	4	ENST00000222270.7:c.6516_6517delinsTT	p.Arg2173Trp	p.R2173W	ENST00000222270	NM_014727.1	2172	gtCCgg/gtTTgg	28/37	1	2	FACETS	0.782	0.71	0.857	0.782	0.71	0.857	SUBCLONAL	1	TRUE	1	0.27	2		1025	1355	SUCCESS
AXL	558	MSKCC	GRCh37	19	41749522	41749522	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	52	543	0	ENST00000301178.4:c.1447G>A	p.Glu483Lys	p.E483K	ENST00000301178	NM_021913.4	483	Gaa/Aaa	12/20	1	2	FACETS	0.598	0.508	0.697	0.598	0.508	0.697	SUBCLONAL	1	TRUE	1	0.27	2		543	644	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50143307	50143307	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	22	198	0	ENST00000246792.3:c.49G>A	p.Gly17Arg	p.G17R	ENST00000246792	NM_006270.3	17	Ggg/Agg	1/6	1	2	FACETS	0.637	0.494	0.801	0.637	0.494	0.801	SUBCLONAL	1	TRUE	1	0.27	2		198	256	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46587882	46587882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	62	541	0	ENST00000263734.3:c.560C>T	p.Ser187Leu	p.S187L	ENST00000263734	NM_001430.4	187	tCa/tTa	5/16	1	2	FACETS	0.698	0.602	0.802	0.698	0.602	0.802	SUBCLONAL	1	TRUE	1	0.27	2		541	658	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587120	212587120	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	29	447	0	ENST00000342788.4:c.881C>T	p.Pro294Leu	p.P294L	ENST00000342788	NM_005235.2	294	cCa/cTa	7/28	1	2	FACETS	0.592	0.475	0.724	0.592	0.475	0.724	SUBCLONAL	1	TRUE	1	0.27	2		447	363	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624913	9624913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	60	624	0	ENST00000353224.5:c.64C>T	p.His22Tyr	p.H22Y	ENST00000353224	NM_177990.2	22	Cat/Tat	3/10	1	2	FACETS	0.72	0.62	0.829	0.72	0.62	0.829	SUBCLONAL	1	TRUE	1	0.27	2		624	617	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747137	40747138	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	54	579	3	ENST00000373198.4:c.2944_2945delinsTT	p.Pro982Leu	p.P982L	ENST00000373198	NM_133170.3	982	CCg/TTg	22/32	1	2	FACETS	0.634	0.541	0.736	0.634	0.541	0.736	SUBCLONAL	1	TRUE	1	0.27	2		582	631	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899063	40899063	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1405822046	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	118	648	1	ENST00000373198.4:c.2207G>A	p.Gly736Glu	p.G736E	ENST00000373198	NM_133170.3	736	gGg/gAg	14/32	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.27	2		649	718	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944364	40944364	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	65	558	1	ENST00000373198.4:c.2138G>A	p.Gly713Glu	p.G713E	ENST00000373198	NM_133170.3	713	gGa/gAa	12/32	1	2	FACETS	0.995	0.864	1	0.995	0.864	1	CLONAL	1	TRUE	1	0.27	2		559	484	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324601	62324601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146221660	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	110	785	0	ENST00000360203.5:c.2957G>A	p.Arg986Gln	p.R986Q	ENST00000360203	NM_001283009.1	986	cGa/cAa	30/35	1	2	FACETS	0.658	0.589	0.731	0.658	0.589	0.731	SUBCLONAL	1	TRUE	1	0.27	2		785	1238	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127238	22127238	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1289443802	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	260	871	0	ENST00000215832.6:c.890A>G	p.Asn297Ser	p.N297S	ENST00000215832	NM_002745.4	297	aAc/aGc	7/9	0.141318777768122	1	FACETS	1	0.992	1	1	0.992	1	INDETERMINATE	1	TRUE	0	0.27	1		871	1172	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545150	41545150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1352652949	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1394	114	777	0	ENST00000263253.7:c.2350C>T	p.Pro784Ser	p.P784S	ENST00000263253	NM_001429.3	784	Ccg/Tcg	13/31	0.3	5	FACETS	0.787	0.706	0.873			1	SUBCLONAL	1	TRUE	NA	0.27	5		777	1508	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715633	30715633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	52	373	0	ENST00000295754.5:c.1291G>A	p.Glu431Lys	p.E431K	ENST00000295754	NM_003242.5	431	Gaa/Aaa	5/7	1	2	FACETS	0.868	0.74	1	0.868	0.74	1	CLONAL	1	TRUE	1	0.27	2		373	444	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162137	47162137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	61	513	0	ENST00000409792.3:c.3989C>T	p.Ser1330Phe	p.S1330F	ENST00000409792	NM_014159.6	1330	tCc/tTc	3/21	1	2	FACETS	0.731	0.63	0.841	0.731	0.63	0.841	SUBCLONAL	1	TRUE	1	0.27	2		513	618	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164495	47164495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	44	492	1	ENST00000409792.3:c.1631C>T	p.Ser544Leu	p.S544L	ENST00000409792	NM_014159.6	544	tCa/tTa	3/21	1	2	FACETS	0.704	0.591	0.829	0.704	0.591	0.829	SUBCLONAL	1	TRUE	1	0.27	2		493	463	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119585450	119585451	+	missense_variant	Missense_Mutation	DNP	GT	GT	AA	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	27	474	3	ENST00000316626.5:c.934_935delinsTT	p.Thr312Phe	p.T312F	ENST00000316626		312	ACc/TTc	9/12	1	2	FACETS	0.445	0.354	0.551	0.445	0.354	0.551	SUBCLONAL	1	TRUE	1	0.27	2		477	449	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183534	185183534	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	63	341	0	ENST00000265026.3:c.1389-1G>A		p.X463_splice	ENST00000265026	NM_004721.4	463			1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.27	2		341	438	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590699	189590699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	70	645	1	ENST00000264731.3:c.1264G>A	p.Glu422Lys	p.E422K	ENST00000264731	NM_003722.4	422	Gaa/Aaa	10/14	1	2	FACETS	0.63	0.548	0.719	0.63	0.548	0.719	SUBCLONAL	1	TRUE	1	0.27	2		646	823	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612284	189612284	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	40	392	0	ENST00000264731.3:c.2036G>A	p.Gly679Glu	p.G679E	ENST00000264731	NM_003722.4	679	gGg/gAg	14/14	1	2	FACETS	0.663	0.551	0.787	0.663	0.551	0.787	SUBCLONAL	1	TRUE	1	0.27	2		392	447	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161385	55161385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	77	631	0	ENST00000257290.5:c.3216G>A	p.Met1072Ile	p.M1072I	ENST00000257290	NM_006206.4	1072	atG/atA	23/23	1	2	FACETS	0.731	0.641	0.828	0.731	0.641	0.828	SUBCLONAL	1	TRUE	1	0.27	2		631	780	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230905	66230905	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	28	493	0	ENST00000273854.3:c.2066T>A	p.Val689Asp	p.V689D	ENST00000273854	NM_004439.5	689	gTt/gAt	12/18	1	2	FACETS	0.599	0.479	0.736	0.599	0.479	0.736	SUBCLONAL	1	TRUE	1	0.27	2		493	346	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156321	106156321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	49	415	0	ENST00000380013.4:c.1222C>T	p.Pro408Ser	p.P408S	ENST00000380013	NM_001127208.2	408	Ccc/Tcc	3/11	1	2	FACETS	0.831	0.705	0.969	0.831	0.705	0.969	CLONAL	1	TRUE	1	0.27	2		415	437	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157923	106157923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	39	345	0	ENST00000380013.4:c.2824C>T	p.Pro942Ser	p.P942S	ENST00000380013	NM_001127208.2	942	Ccc/Tcc	3/11	1	2	FACETS	0.719	0.596	0.855	0.719	0.596	0.855	SUBCLONAL	1	TRUE	1	0.27	2		345	402	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295230	+	upstream_gene_variant	5'Flank	TNP	GGG	GGG	AAA	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	59	577	1				ENST00000310581	NM_198253.2	-/1132			0.21164688568396	1	FACETS	0.833	0.718	0.957	0.833	0.718	0.957	CLONAL	1	TRUE	0	0.27	1		578	454	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526801	31526801	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	87	798	0	ENST00000344624.3:c.239C>T	p.Pro80Leu	p.P80L	ENST00000344624		80	cCc/cTc	2/33	0.141318777768122	3	FACETS	0.815	0.721	0.917	0.408	0.36	0.459	INDETERMINATE	1	TRUE	1	0.27	3		798	897	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047200	180047200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	102	909	0	ENST00000261937.6:c.2515G>A	p.Glu839Lys	p.E839K	ENST00000261937	NM_182925.4	839	Gaa/Aaa	17/30	0.328737888221673	0	FACETS	0.673	0.602	0.75			1	SUBCLONAL	1	TRUE	0	0.27	0		909	819	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940126	31940126	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1489	198	966	0	ENST00000375333.2:c.268C>T	p.Pro90Ser	p.P90S	ENST00000375333	NM_032454.1	90	Cct/Tct	2/8	0.21164688568396	3	FACETS	0.987	0.91	1	0.493	0.455	0.534	CLONAL	1	TRUE	1	0.27	3		966	1687	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188203	32188203	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	101	719	0	ENST00000375023.3:c.1138C>G	p.Leu380Val	p.L380V	ENST00000375023	NM_004557.3	380	Ctc/Gtc	6/30	0.21164688568396	3	FACETS	1	0.925	1	0.522	0.466	0.582	CLONAL	1	TRUE	1	0.27	3		719	813	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288927	33288927	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370297398	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	78	436	0	ENST00000374542.5:c.625G>A	p.Glu209Lys	p.E209K	ENST00000374542	NM_001141970.1	209	Gag/Aag	3/8	0.3	5	FACETS	1	0.955	1			1	CLONAL	1	TRUE	NA	0.27	5		436	682	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609926	117609926	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	44	671	0	ENST00000368508.3:c.6773T>A	p.Ile2258Asn	p.I2258N	ENST00000368508	NM_002944.2	2258	aTt/aAt	43/43	1	2	FACETS	0.628	0.526	0.741	0.628	0.526	0.741	SUBCLONAL	1	TRUE	1	0.27	2		671	519	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662320	117662320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	49	827	0	ENST00000368508.3:c.5057G>A	p.Arg1686Lys	p.R1686K	ENST00000368508	NM_002944.2	1686	aGa/aAa	30/43	1	2	FACETS	0.594	0.502	0.695	0.594	0.502	0.695	SUBCLONAL	1	TRUE	1	0.27	2		827	611	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959005	2959005	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	41	571	0	ENST00000396946.4:c.2510+1G>A		p.X837_splice	ENST00000396946	NM_032415.4	837			1	2	FACETS	0.553	0.46	0.657	0.553	0.46	0.657	SUBCLONAL	1	TRUE	1	0.27	2		571	549	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978823	13978823	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	67	767	1	ENST00000405192.2:c.284C>T	p.Pro95Leu	p.P95L	ENST00000405192	NM_001163147.1	95	cCa/cTa	6/12	1	2	FACETS	0.719	0.624	0.822	0.719	0.624	0.822	SUBCLONAL	1	TRUE	1	0.27	2		768	690	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224334	55224335	+	missense_variant	Missense_Mutation	DNP	TG	TG	AT	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	38	565	2	ENST00000275493.2:c.1115_1116delinsAT	p.Leu372His	p.L372H	ENST00000275493	NM_005228.3	372	cTG/cAT	9/28	1	2	FACETS	0.453	0.373	0.542	0.453	0.373	0.542	SUBCLONAL	1	TRUE	1	0.27	2		567	622	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860100	151860100	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	28	439	0	ENST00000262189.6:c.10562C>T	p.Ser3521Leu	p.S3521L	ENST00000262189	NM_170606.2	3521	tCa/tTa	43/59	1	2	FACETS	0.416	0.331	0.512	0.416	0.331	0.512	SUBCLONAL	1	TRUE	1	0.27	2		439	499	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874754	151874754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775427298	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	62	413	0	ENST00000262189.6:c.7784C>T	p.Pro2595Leu	p.P2595L	ENST00000262189	NM_170606.2	2595	cCc/cTc	38/59	1	2	FACETS	0.764	0.66	0.877	0.764	0.66	0.877	SUBCLONAL	1	TRUE	1	0.27	2		413	601	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346392	152346392	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554410567	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	50	715	0	ENST00000359321.1:c.178C>T	p.His60Tyr	p.H60Y	ENST00000359321	NM_005431.1	60	Cac/Tac	3/3	1	2	FACETS	0.595	0.504	0.696	0.595	0.504	0.696	SUBCLONAL	1	TRUE	1	0.27	2		715	622	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340446	8340446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1329770480	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	58	550	1	ENST00000356435.5:c.5150C>T	p.Thr1717Ile	p.T1717I	ENST00000356435		1717	aCc/aTc	31/35	0.21164688568396	1	FACETS	0.624	0.535	0.72	0.624	0.535	0.72	SUBCLONAL	1	TRUE	0	0.27	1		551	596	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212740	27212740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	125	971	0	ENST00000380036.4:c.2722G>A	p.Gly908Arg	p.G908R	ENST00000380036	NM_000459.3	908	Gga/Aga	17/23	0.21164688568396	1	FACETS	0.832	0.752	0.916	0.832	0.752	0.916	CLONAL	1	TRUE	0	0.27	1		971	963	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606553	93606553	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267602311	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	69	751	0	ENST00000375746.1:c.373G>A	p.Glu125Lys	p.E125K	ENST00000375746	NM_001174167.1	125	Gaa/Aaa	2/14	0.21164688568396	1	FACETS	0.578	0.502	0.66	0.578	0.502	0.66	SUBCLONAL	1	TRUE	0	0.27	1		751	765	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228066	53228066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	79	356	2	ENST00000375401.3:c.2248C>T	p.Arg750Trp	p.R750W	ENST00000375401	NM_004187.3	750	Cgg/Tgg	16/26	1	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.27	1		358	434	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344170	70344170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	82	374	0	ENST00000374080.3:c.1906C>T	p.Pro636Ser	p.P636S	ENST00000374080		636	Ccc/Tcc	13/45	1	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.27	1		374	427	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858086	152858087	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AT	novel	NA	P-0020817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	114	418	1	ENST00000406277.2:c.528_529delinsAT	p.Tyr176_His177delinsTer	p.Y176_H177delins*	ENST00000406277	NM_152274.4	176	taCCat/taATat	6/7	1	1	FACETS	0.804	0.729	0.883	1	0.986	1	CLONAL	2	TRUE	0	0.27	1		419	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0020818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	868	733	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	2	TRUE	NA	0.739750934640371	2		733	1167	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0020818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	155	303	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.981	0.908	1	0.981	0.908	1	CLONAL	1	TRUE	1	0.739750934640371	2		304	427	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937833	76937836	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0020818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	328	414	0	ENST00000373344.5:c.2912_2915del	p.Lys971ThrfsTer31	p.K971Tfs*31	ENST00000373344	NM_000489.3	971	aAAGAc/ac	9/35	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.739750934640371	1		414	479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782144	NA	P-0020820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	608	1106	0	ENST00000269305.4:c.473G>C	p.Arg158Pro	p.R158P	ENST00000269305	NM_001126112.2	158	cGc/cCc	5/11	0.782961438614832	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.782961438614832	2		1106	750	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0020820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	562	246	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	0.782961438614832	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.782961438614832	2		246	646	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220649	1220649	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	700	1213	2	ENST00000326873.7:c.667G>T	p.Glu223Ter	p.E223*	ENST00000326873	NM_000455.4	223	Gag/Tag	5/10	0.782961438614832	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.782961438614832	2		1215	848	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0020820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	426	360	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.782961438614832	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	2	0.782961438614832	4		360	966	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602763	10602763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774469695	NA	P-0020820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	761	1209	4	ENST00000171111.5:c.815G>A	p.Arg272His	p.R272H	ENST00000171111	NM_203500.1	272	cGc/cAc	3/6	0.782961438614832	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.782961438614832	2		1213	904	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097782	27097782	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	408	630	0	ENST00000324856.7:c.3371A>T	p.Lys1124Met	p.K1124M	ENST00000324856	NM_006015.4	1124	aAg/aTg	12/20	0.521818431259117	4	FACETS	0.944	0.91	0.978	0.944	0.91	0.978	CLONAL	3	TRUE	1	0.782961438614832	4		630	656	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120460387	120460387	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0020820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	251	639	1	ENST00000256646.2:c.5930-2A>T		p.X1977_splice	ENST00000256646	NM_024408.3	1977			0.782961438614832	3	FACETS	0.993	0.944	1	0.993	0.944	1	CLONAL	2	TRUE	1	0.782961438614832	3		640	449	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999347	100999347	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	577	1178	3	ENST00000325455.5:c.455C>A	p.Pro152Gln	p.P152Q	ENST00000325455	NM_001202474.3	152	cCg/cAg	1/8	0.782961438614832	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.782961438614832	2		1181	682	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499689	18499689	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	199	855	0	ENST00000266497.5:c.1544C>G	p.Ser515Cys	p.S515C	ENST00000266497		515	tCc/tGc	10/31	0.782961438614832	4	FACETS	1	0.964	1	0.531	0.492	0.571	CLONAL	1	TRUE	2	0.782961438614832	4		855	854	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434067	49434067	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	386	727	0	ENST00000301067.7:c.7486G>T	p.Ala2496Ser	p.A2496S	ENST00000301067	NM_003482.3	2496	Gca/Tca	31/54	0.782961438614832	4	FACETS	0.991	0.946	1	0.991	0.946	1	CLONAL	2	TRUE	2	0.782961438614832	4		727	887	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446430	49446430	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	449	834	0	ENST00000301067.7:c.1175G>T	p.Cys392Phe	p.C392F	ENST00000301067	NM_003482.3	392	tGc/tTc	9/54	0.782961438614832	4	FACETS	0.949	0.909	0.99	0.949	0.909	0.99	CLONAL	2	TRUE	2	0.782961438614832	4		834	1077	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479833	67479833	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	236	689	2	ENST00000327367.4:c.1140G>T	p.Trp380Cys	p.W380C	ENST00000327367	NM_005902.3	380	tgG/tgT	8/9	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.782961438614832	2		691	566	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251761	212251761	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	270	476	0	ENST00000342788.4:c.3298G>T	p.Glu1100Ter	p.E1100*	ENST00000342788	NM_005235.2	1100	Gag/Tag	27/28	0.757290993123186	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.782961438614832	4		476	580	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750473	41750473	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	182	720	0	ENST00000226382.2:c.155G>C	p.Gly52Ala	p.G52A	ENST00000226382	NM_003924.3	52	gGg/gCg	1/3	0.782961438614832	3	FACETS	0.936	0.867	1	0.468	0.433	0.504	CLONAL	1	TRUE	1	0.782961438614832	3		720	691	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038562	47038562	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	564	928	0	ENST00000377604.3:c.724G>T	p.Glu242Ter	p.E242*	ENST00000377604	NM_001204468.1	242	Gag/Tag	8/24	0.782961438614832	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.782961438614832	2		928	698	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938611	76938611	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	274	888	1	ENST00000373344.5:c.2137C>A	p.Pro713Thr	p.P713T	ENST00000373344	NM_000489.3	713	Cct/Act	9/35	0.427715520694777	5	FACETS	1	0.95	1	0.672	0.634	0.711	INDETERMINATE	2	TRUE	2	0.782961438614832	5		889	755	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200032	123200032	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	108	438	0	ENST00000218089.9:c.2104G>C	p.Asp702His	p.D702H	ENST00000218089	NM_001042749.1	702	Gac/Cac	22/35	0.427715520694777	5	FACETS	0.934	0.849	1	0.623	0.566	0.682	INDETERMINATE	2	TRUE	2	0.782961438614832	5		438	321	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	109	251	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.29	2		251	740	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0020821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	202	584	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.29	2		585	1037	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243472	46243472	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	96	599	0	ENST00000334344.6:c.1825C>T	p.Gln609Ter	p.Q609*	ENST00000334344	NM_152641.2	609	Cag/Tag	14/21	0.220529864250141	2	FACETS	1	0.979	1	0.704	0.63	0.782	CLONAL	1	TRUE	0	0.29	2		599	470	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981195	201981202	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTCACG	TTCTCACG	-	novel	NA	P-0020821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	139	1048	1	ENST00000359651.3:c.274_281del	p.Phe92MetfsTer2	p.F92Mfs*2	ENST00000359651		92	TTCTCACGa/a	2/8	1	2	FACETS	0.81	0.736	0.889	0.81	0.736	0.889	CLONAL	1	TRUE	1	0.29	2		1049	1183	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343528	118343529	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	84	575	2	ENST00000534358.1:c.1660dup	p.Gln554ProfsTer27	p.Q554Pfs*27	ENST00000534358	NM_005933.3	552	gcc/gCcc	3/36	1	2	FACETS	0.861	0.76	0.968	0.861	0.76	0.968	CLONAL	1	TRUE	1	0.29	2		577	673	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048760	180048760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754245879	NA	P-0020821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	119	1042	1	ENST00000261937.6:c.1802C>T	p.Ala601Val	p.A601V	ENST00000261937	NM_182925.4	601	gCg/gTg	13/30	1	2	FACETS	0.688	0.62	0.762	0.688	0.62	0.762	SUBCLONAL	1	TRUE	1	0.29	2		1043	1192	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980520	70980520	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	194	1008	0	ENST00000276594.2:c.857A>C	p.Lys286Thr	p.K286T	ENST00000276594	NM_024504.3	286	aAa/aCa	4/8	0.3	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.29	1		1008	1033	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028758	47028758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	99	927	1	ENST00000377604.3:c.62G>A	p.Arg21His	p.R21H	ENST00000377604	NM_001204468.1	21	cGc/cAc	3/24	1	2	FACETS	0.618	0.55	0.691	0.618	0.55	0.691	SUBCLONAL	1	TRUE	1	0.29	2		928	1105	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	142	251	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.768	0.706	0.831	0.768	0.706	0.831	SUBCLONAL	1	TRUE	1	0.837064421242735	2		251	442	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0020824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	129	417	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.883	0.811	0.957	0.883	0.811	0.957	CLONAL	1	TRUE	1	0.837064421242735	2		418	349	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577279	64577295	+	frameshift_variant	Frame_Shift_Del	DEL	GACGGCGCCTCGGATCT	GACGGCGCCTCGGATCT	-	novel	NA	P-0020824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	283	943	2	ENST00000312049.6:c.287_303del	p.Gln96ArgfsTer15	p.Q96Rfs*15	ENST00000312049	NM_130799.2	96	cAGATCCGAGGCGCCGTC/c	2/10	0.837064421242735	1	FACETS	0.966	0.928	1	0.966	0.928	1	CLONAL	1	TRUE	0	0.837064421242735	1		945	407	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748768	43748768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	39	1230	2	ENST00000382044.4:c.2038C>T	p.Gln680Ter	p.Q680*	ENST00000382044	NM_001141980.1	680	Caa/Taa	12/28	1	2	FACETS	0.12	0.099	0.144	0.12	0.099	0.144	SUBCLONAL	1	TRUE	1	0.837064421242735	2		1232	775	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0020825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	264	716	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.626612067289978	3	FACETS	0.895	0.838	0.954	0.448	0.419	0.477	CLONAL	1	TRUE	1	0.626612067289978	3		716	1236	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0020825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	370	811	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.626612067289978	3	FACETS	1	0.978	1	0.53	0.502	0.559	CLONAL	1	TRUE	1	0.626612067289978	3		812	1464	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404576	8404576	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146844299	NA	P-0020825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	149	384	0	ENST00000356435.5:c.4171G>A	p.Ala1391Thr	p.A1391T	ENST00000356435		1391	Gca/Aca	25/35	1	2	FACETS	0.944	0.868	1	0.944	0.868	1	CLONAL	1	TRUE	1	0.626612067289978	2		384	504	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653780	89653781	+	splice_acceptor_variant	Splice_Site	DEL	AG	AG	-	rs1554893747	NA	P-0020825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	95	435	0	ENST00000371953.3:c.80-1_80del		p.X27_splice	ENST00000371953	NM_000314.4	27			0.626612067289978	1	FACETS	0.826	0.748	0.906	0.826	0.748	0.906	CLONAL	1	TRUE	0	0.626612067289978	1		435	252	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679790	88679790	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	299	728	0	ENST00000360948.2:c.673G>T	p.Asp225Tyr	p.D225Y	ENST00000360948	NM_001012338.2	225	Gac/Tac	7/19	1	2	FACETS	0.861	0.811	0.912	0.861	0.811	0.912	CLONAL	1	TRUE	1	0.626612067289978	2		728	1109	SUCCESS
APC	324	MSKCC	GRCh37	5	112154966	112154970	+	frameshift_variant	Frame_Shift_Del	DEL	ATACG	ATACG	C	novel	NA	P-0020825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	299	753	0	ENST00000257430.4:c.1237_1241delinsC	p.Ile413ProfsTer40	p.I413Pfs*40	ENST00000257430	NM_000038.5	413	ATACGc/Cc	10/16	0.626612067289978	1	FACETS	0.887	0.84	0.934	0.887	0.84	0.934	CLONAL	1	TRUE	0	0.626612067289978	1		753	739	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	260	372	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.264713484207442	2	FACETS	0.82	0.771	0.87	0.82	0.771	0.87	CLONAL	2	TRUE	0	0.40043377869449	2		373	792	SUCCESS
APC	324	MSKCC	GRCh37	5	112175171	112175171	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085373	NA	P-0020826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	106	324	1	ENST00000257430.4:c.3880C>T	p.Gln1294Ter	p.Q1294*	ENST00000257430	NM_000038.5	1294	Cag/Tag	16/16	0.40043377869449	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	0	0.40043377869449	2		325	259	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578177	7578177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	346	972	0	ENST00000269305.4:c.672G>C	p.Glu224Asp	p.E224D	ENST00000269305	NM_001126112.2	224	gaG/gaC	6/11	0.40043377869449	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.40043377869449	1		972	1015	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032594	12032594	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	203	732	0	ENST00000353533.5:c.1030G>T	p.Val344Phe	p.V344F	ENST00000353533	NM_003010.3	344	Gtc/Ttc	9/11	0.40043377869449	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.40043377869449	1		732	704	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019657	123019657	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	135	902	0	ENST00000355640.3:c.145C>T	p.Arg49Ter	p.R49*	ENST00000355640		49	Cga/Tga	2/7	0.211067683353596	3	FACETS	0.783	0.711	0.86	0.261	0.237	0.287	INDETERMINATE	1	TRUE	0	0.40043377869449	3		902	1033	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	272	613	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.951	0.894	1	0.951	0.894	1	CLONAL	1	TRUE	1	0.595351352576643	2		614	961	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0020827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	226	452	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	0.595351352576643	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.595351352576643	1		452	504	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149808	202149808	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	267	739	1	ENST00000358485.4:c.1249C>T	p.Gln417Ter	p.Q417*	ENST00000358485	NM_001080125.1	417	Cag/Tag	8/9	1	2	FACETS	0.954	0.896	1	0.954	0.896	1	CLONAL	1	TRUE	1	0.595351352576643	2		740	940	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44910953	44910953	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0020827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	204	223	0	ENST00000377967.4:c.655-1G>A		p.X219_splice	ENST00000377967	NM_021140.2	219			1	1	FACETS	0.766	0.728	0.804	1	0.994	1	SUBCLONAL	2	TRUE	0	0.595351352576643	1		223	314	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971048	21971058	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGCGCCCCG	GCCGCGCCCCG	-	novel	NA	P-0020827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	353	590	0	ENST00000304494.5:c.300_310del	p.Ala102ArgfsTer14	p.A102Rfs*14	ENST00000304494	NM_000077.4	100	gcCGGGGCGCGGCtg/gctg	2/3	0.595351352576643	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.595351352576643	1		590	698	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs878854073	NA	P-0020827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	304	677	1	ENST00000269305.4:c.673-1G>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.595351352576643	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.595351352576643	1		678	691	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738172	133738172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755144370	NA	P-0020827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	183	566	0	ENST00000318560.5:c.572G>A	p.Arg191His	p.R191H	ENST00000318560	NM_005157.4	191	cGc/cAc	4/11	0.595351352576643	1	FACETS	0.869	0.809	0.93	0.869	0.809	0.93	CLONAL	1	TRUE	0	0.595351352576643	1		566	497	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0020828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	318	340	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.333072157500708	2		340	1289	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893408	32893408	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	149	704	0	ENST00000380152.3:c.262C>G	p.Leu88Val	p.L88V	ENST00000380152		88	Ctg/Gtg	3/27	0.161388885122003	1	FACETS	0.919	0.841	1	0.919	0.841	1	INDETERMINATE	1	TRUE	0	0.333072157500708	1		704	811	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579592	7579602	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TGTAGATGGGT	TGTAGATGGGT	-	novel	NA	P-0020828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	141	832	1	ENST00000269305.4:c.97-12_97-2del		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.333072157500708	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.333072157500708	1		833	689	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483000	29483000	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0020828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	167	511	0	ENST00000356175.3:c.61-1G>A		p.X21_splice	ENST00000356175	NM_000267.3	21			0.333072157500708	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.333072157500708	1		511	562	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220418	1220419	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCATTGTGCACAAGGACATCAAGCC	novel	NA	P-0020828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	158	1283	0	ENST00000326873.7:c.513_537dup	p.Gly180HisfsTer94	p.G180Hfs*94	ENST00000326873	NM_000455.4	171	ggc/gGCATTGTGCACAAGGACATCAAGCCgc	4/10	0.143731263959106	1	FACETS	0.793	0.726	0.863	0.793	0.726	0.863	INDETERMINATE	1	TRUE	0	0.333072157500708	1		1283	997	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211139	36211139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776148419	NA	P-0020828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1329	217	989	1	ENST00000222270.7:c.890G>A	p.Arg297Gln	p.R297Q	ENST00000222270	NM_014727.1	297	cGa/cAa	3/37	1	2	FACETS	0.843	0.781	0.907	0.843	0.781	0.907	CLONAL	1	TRUE	1	0.333072157500708	2		990	1546	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564570	55564570	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	246	892	1	ENST00000288135.5:c.458G>T	p.Gly153Val	p.G153V	ENST00000288135	NM_000222.2	153	gGg/gTg	3/21	1	2	FACETS	0.813	0.761	0.866	1	0.993	1	CLONAL	2	TRUE	1	0.333072157500708	2		893	909	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912110	76912110	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	64	962	1	ENST00000373344.5:c.4154A>T	p.Gln1385Leu	p.Q1385L	ENST00000373344	NM_000489.3	1385	cAg/cTg	13/35	1	2	FACETS	0.352	0.304	0.405	0.352	0.304	0.405	SUBCLONAL	1	TRUE	1	0.333072157500708	2		963	1091	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	504	372	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.299661329443658	3	FACETS	0.97	0.935	1	0.97	0.935	1	INDETERMINATE	2	TRUE	1	0.77772763593357	3		373	928	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578412	7578413	+	missense_variant	Missense_Mutation	DNP	AC	AC	TG	novel	NA	P-0020829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	361	899	2	ENST00000269305.4:c.517_518delinsCA	p.Val173Gln	p.V173Q	ENST00000269305	NM_001126112.2	173	GTg/CAg	5/11	0.77772763593357	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.77772763593357	1		901	553	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196819	106196819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	170	626	0	ENST00000380013.4:c.5152G>A	p.Val1718Ile	p.V1718I	ENST00000380013	NM_001127208.2	1718	Gta/Ata	11/11	0.158973852291818	3	FACETS	1	0.988	1	0.447	0.415	0.479	INDETERMINATE	1	TRUE	0	0.77772763593357	3		626	453	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117684019	117684019	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	186	529	0	ENST00000368508.3:c.3128C>A	p.Ala1043Glu	p.A1043E	ENST00000368508	NM_002944.2	1043	gCa/gAa	21/43	0.77772763593357	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.77772763593357	1		529	258	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555526097	NA	P-0020831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	403	961	0	ENST00000269305.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000269305	NM_001126112.2	167	Cag/Tag	5/11	NA	2	FACETS	1	0.961	1			1	INDETERMINATE	2	TRUE	NA	0.461138743905164	2		961	870	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223115	41223115	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0020831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	217	818	1	ENST00000357654.3:c.4816A>T	p.Lys1606Ter	p.K1606*	ENST00000357654	NM_007294.3	1606	Aaa/Taa	15/23	0.461138743905164	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.461138743905164	1		819	625	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504357	186504357	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	83	489	0	ENST00000323963.5:c.694C>G	p.Pro232Ala	p.P232A	ENST00000323963		232	Cca/Gca	7/11	0.461138743905164	3	FACETS	0.735	0.649	0.826	0.367	0.324	0.413	SUBCLONAL	1	TRUE	1	0.461138743905164	3		489	603	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725519	117725519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	141	719	0	ENST00000368508.3:c.362C>T	p.Ser121Phe	p.S121F	ENST00000368508	NM_002944.2	121	tCt/tTt	5/43	0.461138743905164	1	FACETS	0.914	0.837	0.993	0.914	0.837	0.993	CLONAL	1	TRUE	0	0.461138743905164	1		719	515	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782329	NA	P-0020833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	345	1086	0	ENST00000269305.4:c.746G>C	p.Arg249Thr	p.R249T	ENST00000269305	NM_001126112.2	249	aGg/aCg	7/11	0.564816327479672	1	FACETS	0.878	0.833	0.923	0.878	0.833	0.923	CLONAL	1	TRUE	0	0.568008819880109	1		1086	991	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916776	48916776	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0020833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	170	784	0	ENST00000267163.4:c.306T>A	p.Cys102Ter	p.C102*	ENST00000267163	NM_000321.2	102	tgT/tgA	3/27	0.568008819880109	1	FACETS	0.755	0.698	0.813	0.755	0.698	0.813	SUBCLONAL	1	TRUE	0	0.568008819880109	1		784	568	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020835-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	196	251	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.832788466386558	2		251	466	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179050	123179050	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020835-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	393	447	0	ENST00000218089.9:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000218089	NM_001042749.1	167	Cag/Tag	8/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.832788466386558	1		447	469	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0020835-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	255	446	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.832788466386558	2		446	565	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651906	36651906	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020835-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	531	607	0	ENST00000244741.5:c.28C>T	p.Gln10Ter	p.Q10*	ENST00000244741	NM_000389.4	10	Cag/Tag	2/3	0.832077594843855	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.832788466386558	2		607	634	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102067	27102067	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0020835-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	70	577	0	ENST00000324856.7:c.4994-1G>T		p.X1665_splice	ENST00000324856	NM_006015.4	1665			1	2	FACETS	0.24	0.209	0.274	0.24	0.209	0.274	SUBCLONAL	1	TRUE	1	0.832788466386558	2		577	700	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982323	201982324	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020835-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	373	731	0	ENST00000359651.3:c.703dup	p.Cys235LeufsTer66	p.C235Lfs*66	ENST00000359651		234	-/T	6/8	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.832788466386558	2		731	884	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524142	18524143	+	missense_variant	Missense_Mutation	DNP	CT	CT	AG	novel	NA	P-0020835-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	114	514	1	ENST00000266497.5:c.1654_1655inv	p.Leu552Ser	p.L552S	ENST00000266497		552	CTt/AGt	11/31	1	2	FACETS	0.492	0.445	0.542	0.492	0.445	0.542	SUBCLONAL	1	TRUE	1	0.832788466386558	2		515	556	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245826	46245826	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0020835-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	215	398	0	ENST00000334344.6:c.3920C>G	p.Ser1307Ter	p.S1307*	ENST00000334344	NM_152641.2	1307	tCa/tGa	15/21	1	2	FACETS	0.909	0.852	0.968	0.909	0.852	0.968	CLONAL	1	TRUE	1	0.832788466386558	2		398	568	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287287	46287300	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGAGAGGATCAA	GAGGAGAGGATCAA	-	novel	NA	P-0020835-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	260	565	0	ENST00000334344.6:c.5234_5247del	p.Arg1745LysfsTer10	p.R1745Kfs*10	ENST00000334344	NM_152641.2	1744	ctGAGGAGAGGATCAAga/ctga	19/21	1	2	FACETS	0.875	0.824	0.926	0.875	0.824	0.926	CLONAL	1	TRUE	1	0.832788466386558	2		565	714	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458321	12458321	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020835-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	692	612	0	ENST00000287820.6:c.938G>T	p.Cys313Phe	p.C313F	ENST00000287820	NM_015869.4	313	tGc/tTc	6/7	0.804766619195056	2	FACETS	0.998	0.978	1	0.998	0.978	1	CLONAL	2	TRUE	0	0.832788466386558	2		612	833	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982123	38982123	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020835-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	138	347	0	ENST00000357387.3:c.599A>T	p.Glu200Val	p.E200V	ENST00000357387	NM_152756.3	200	gAg/gTg	8/38	1	2	FACETS	0.656	0.601	0.714	0.656	0.601	0.714	SUBCLONAL	1	TRUE	1	0.832788466386558	2		347	505	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs149680468	NA	P-0020835-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	223	446	0	ENST00000281708.4:c.1513C>A	p.Arg505Ser	p.R505S	ENST00000281708	NM_033632.3	505	Cgc/Agc	10/12	1	2	FACETS	0.948	0.89	1	0.948	0.89	1	CLONAL	1	TRUE	1	0.832788466386558	2		446	565	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	284	613	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.93	0.879	0.982	0.93	0.879	0.982	CLONAL	1	TRUE	1	0.82	2		614	745	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0020836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	367	1108	1	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	0.995	0.947	1	0.995	0.947	1	CLONAL	1	TRUE	1	0.82	2		1109	900	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981540	201981540	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	438	1151	0	ENST00000359651.3:c.454G>C	p.Glu152Gln	p.E152Q	ENST00000359651		152	Gag/Cag	3/8	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.82	2		1151	1065	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801726	3801726	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0020836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	282	794	0	ENST00000262367.5:c.3779+1G>T		p.X1260_splice	ENST00000262367	NM_004380.2	1260			1	2	FACETS	0.995	0.942	1	0.995	0.942	1	CLONAL	1	TRUE	1	0.82	2		794	691	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526081	189526082	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	289	806	0	ENST00000264731.3:c.346dup	p.Leu116ProfsTer20	p.L116Pfs*20	ENST00000264731	NM_003722.4	115	-/C	4/14	1	2	FACETS	0.878	0.829	0.927	0.878	0.829	0.927	CLONAL	1	TRUE	1	0.82	2		806	803	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338695	70338695	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	294	447	0	ENST00000374080.3:c.91C>A	p.Gln31Lys	p.Q31K	ENST00000374080		31	Cag/Aag	1/45	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.82	1		447	366	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259216	16259216	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757967848	NA	P-0020836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	220	755	0	ENST00000375759.3:c.6481G>A	p.Glu2161Lys	p.E2161K	ENST00000375759	NM_015001.2	2161	Gaa/Aaa	11/15	1	2	FACETS	0.933	0.875	0.992	0.933	0.875	0.992	CLONAL	1	TRUE	1	0.82	2		755	575	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981516	201981518	+	frameshift_variant	Frame_Shift_Del	DEL	GAG	GAG	AA	novel	NA	P-0020836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	419	1083	3	ENST00000359651.3:c.430_432delinsAA	p.Glu144LysfsTer11	p.E144Kfs*11	ENST00000359651		144	GAG/AA	3/8	1	2	FACETS	0.998	0.954	1	0.998	0.954	1	CLONAL	1	TRUE	1	0.82	2		1086	1024	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686883	37686883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	311	767	1	ENST00000447079.4:c.3787G>A	p.Glu1263Lys	p.E1263K	ENST00000447079	NM_015083.1	1263	Gag/Aag	14/14	1	2	FACETS	0.963	0.912	1	0.963	0.912	1	CLONAL	1	TRUE	1	0.82	2		768	788	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845814	151845814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	324	1019	4	ENST00000262189.6:c.13198C>T	p.Arg4400Trp	p.R4400W	ENST00000262189	NM_170606.2	4400	Cgg/Tgg	52/59	1	2	FACETS	0.971	0.921	1	0.971	0.921	1	CLONAL	1	TRUE	1	0.82	2		1023	814	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937664	44937665	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	223	390	0	ENST00000377967.4:c.2855dup	p.Phe953LeufsTer26	p.F953Lfs*26	ENST00000377967	NM_021140.2	951	gct/gcTt	19/29	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.82	1		390	294	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0020837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	382	524	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.511691357839735	5	FACETS	0.923	0.891	0.954	0.923	0.891	0.954	CLONAL	5	TRUE	0	0.536368471745797	5		524	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519998	NA	P-0020837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	336	967	1	ENST00000269305.4:c.581T>C	p.Leu194Pro	p.L194P	ENST00000269305	NM_001126112.2	194	cTt/cCt	6/11	0.535830129050175	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.536368471745797	2		968	625	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175836	24175837	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555881563	NA	P-0020837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	331	963	1	ENST00000263121.7:c.1066_1067del	p.Leu356AspfsTer4	p.L356Dfs*4	ENST00000263121	NM_003073.3	355	aCT/a	8/9	0.536368471745797	5	FACETS	0.888	0.843	0.933	0.888	0.843	0.933	CLONAL	3	TRUE	2	0.536368471745797	5		964	836	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196640	67196640	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	46	812	1	ENST00000312629.5:c.169G>T	p.Val57Phe	p.V57F	ENST00000312629	NM_003952.2	57	Gtt/Ttt	3/15	0.536368471745797	3	FACETS	0.282	0.237	0.333	0.141	0.118	0.167	SUBCLONAL	1	TRUE	1	0.536368471745797	3		813	771	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912711	32912711	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	355	635	0	ENST00000380152.3:c.4219G>C	p.Glu1407Gln	p.E1407Q	ENST00000380152		1407	Gaa/Caa	11/27	0.244546117458331	5	FACETS	0.924	0.885	0.964	0.74	0.708	0.771	INDETERMINATE	4	TRUE	0	0.536368471745797	5		635	646	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098728	2098728	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	85	927	0	ENST00000219476.3:c.112T>G	p.Phe38Val	p.F38V	ENST00000219476	NM_000548.3	38	Ttt/Gtt	2/42	0.454298176603682	5	FACETS	0.46	0.405	0.519	0.153	0.135	0.173	SUBCLONAL	1	TRUE	2	0.536368471745797	5		927	1244	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967993	93967993	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	56	607	0	ENST00000369303.4:c.1934G>C	p.Gly645Ala	p.G645A	ENST00000369303	NM_004440.3	645	gGt/gCt	11/17	1	2	FACETS	0.478	0.41	0.551	0.478	0.41	0.551	SUBCLONAL	1	TRUE	1	0.536368471745797	2		607	437	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0020838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	342	295	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.497412667719647	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.497412667719647	3		295	825	SUCCESS
APC	324	MSKCC	GRCh37	5	112173345	112173345	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	90	616	0	ENST00000257430.4:c.2054G>A	p.Trp685Ter	p.W685*	ENST00000257430	NM_000038.5	685	tGg/tAg	16/16	1	2	FACETS	0.933	0.833	1	0.933	0.833	1	CLONAL	1	TRUE	1	0.497412667719647	2		616	388	SUCCESS
APC	324	MSKCC	GRCh37	5	112175358	112175358	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1554085480	NA	P-0020838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	102	428	0	ENST00000257430.4:c.4067C>G	p.Ser1356Ter	p.S1356*	ENST00000257430	NM_000038.5	1356	tCa/tGa	16/16	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.497412667719647	2		428	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578537	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs879254214	NA	P-0020838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	691	1517	0	ENST00000269305.4:c.393_395del	p.Asn131del	p.N131del	ENST00000269305	NM_001126112.2	131	aaCAAg/aag	5/11	0.497412667719647	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.497412667719647	2		1517	1373	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217614	142217614	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	94	852	0	ENST00000350721.4:c.5383G>T	p.Gly1795Ter	p.G1795*	ENST00000350721	NM_001184.3	1795	Gga/Tga	32/47	0.169921095760015	5	FACETS	0.819	0.728	0.916	0.273	0.242	0.306	INDETERMINATE	1	TRUE	2	0.497412667719647	5		852	806	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189585691	189585691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1205536026	NA	P-0020838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	280	1004	0	ENST00000264731.3:c.952C>T	p.Arg318Cys	p.R318C	ENST00000264731	NM_003722.4	318	Cgc/Tgc	7/14	0.169921095760015	5	FACETS	0.908	0.853	0.964	0.605	0.568	0.643	INDETERMINATE	2	TRUE	2	0.497412667719647	5		1004	1083	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0020839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	90	717	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.224552420222516	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.24	1		717	539	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0020839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	22	437	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	0.227063744386744	4	FACETS	0.697	0.54	0.88	0.349	0.27	0.44	SUBCLONAL	1	TRUE	2	0.24	4		437	326	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715979	52715979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786205227	NA	P-0020839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	105	853	1	ENST00000322088.6:c.544C>T	p.Arg182Trp	p.R182W	ENST00000322088	NM_014225.5	182	Cgg/Tgg	5/15	1	2	FACETS	0.913	0.822	1	1	0.987	1	CLONAL	2	TRUE	1	0.24	2		854	479	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239218	105239218	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	27	859	0	ENST00000349310.3:c.1169A>G	p.Gln390Arg	p.Q390R	ENST00000349310	NM_001014432.1	390	cAg/cGg	12/15	1	2	FACETS	0.499	0.396	0.617	0.499	0.396	0.617	SUBCLONAL	1	TRUE	1	0.24	2		859	451	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44894199	44894200	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTA	novel	NA	P-0020839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	38	944	0	ENST00000377967.4:c.589_592dup	p.Asn198MetfsTer2	p.N198Mfs*2	ENST00000377967	NM_021140.2	196	-/TGTA	7/29	1	2	FACETS	0.579	0.478	0.692	0.579	0.478	0.692	SUBCLONAL	1	TRUE	1	0.24	2		944	547	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940025	49940025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201546006	NA	P-0020848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	29	1098	2	ENST00000296474.3:c.1018G>A	p.Ala340Thr	p.A340T	ENST00000296474	NM_002447.2	340	Gcc/Acc	1/20	0.404082677350469	1	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	0	0.404082677350469	1		1100	110	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440365	52440365	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	32	946	0	ENST00000460680.1:c.687C>G	p.Asn229Lys	p.N229K	ENST00000460680	NM_004656.3	229	aaC/aaG	9/17	0.404082677350469	1	FACETS	0.957	0.791	1	0.957	0.791	1	CLONAL	1	TRUE	0	0.404082677350469	1		946	132	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994234	21994234	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1287464120	NA	P-0020848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	27	959	1	ENST00000579755.1:c.97G>T	p.Glu33Ter	p.E33*	ENST00000579755		33	Gag/Tag	1/3	0.404082677350469		FACETS		0.714	1				CLONAL	1	TRUE	0	0.404082677350469	1		960	121	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0020849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	813	717	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.455717192224073	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	4	TRUE	0	0.455717192224073	4		717	1260	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	159	134	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.993	0.916	1	0.993	0.916	1	CLONAL	1	TRUE	1	0.572755565393469	2		134	559	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1259	143	1043	2	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.356	0.323	0.391	0.356	0.323	0.391	SUBCLONAL	1	TRUE	1	0.572755565393469	2		1045	1402	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736510	85736511	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs387906351	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	166	539	3	ENST00000370580.1:c.136dup	p.Ile46AsnfsTer4	p.I46Nfs*4	ENST00000370580	NM_003921.4	46	ata/aAta	2/3	1	2	FACETS	0.813	0.749	0.88	0.813	0.749	0.88	CLONAL	1	TRUE	1	0.572755565393469	2		542	713	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097751	27097751	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	69	833	1	ENST00000324856.7:c.3344del	p.Pro1115GlnfsTer46	p.P1115Qfs*46	ENST00000324856	NM_006015.4	1114	Ccc/cc	12/20	1	2	FACETS	0.245	0.212	0.28	0.245	0.212	0.28	SUBCLONAL	1	TRUE	1	0.572755565393469	2		834	985	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591085	67591085	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519839	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	261	355	0	ENST00000274335.5:c.1678G>T	p.Asp560Tyr	p.D560Y	ENST00000274335		560	Gac/Tac	12/15	0.572755565393469	2	FACETS	0.97	0.922	1	0.97	0.922	1	CLONAL	2	TRUE	0	0.572755565393469	2		355	470	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	145	243	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	0.979	0.899	1	0.979	0.899	1	CLONAL	1	TRUE	1	0.572755565393469	2		243	517	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789591	3789591	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	128	560	0	ENST00000262367.5:c.4268del	p.Pro1423LeufsTer36	p.P1423Lfs*36	ENST00000262367	NM_004380.2	1423	cCt/ct	25/31	1	2	FACETS	0.549	0.498	0.603	0.549	0.498	0.603	SUBCLONAL	1	TRUE	1	0.572755565393469	2		560	814	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835780	68835781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	290	760	0	ENST00000261769.5:c.377dup	p.Pro127AlafsTer41	p.P127Afs*41	ENST00000261769	NM_004360.3	124	cgc/cgCc	3/16	1	2	FACETS	0.817	0.767	0.867	0.817	0.767	0.867	CLONAL	1	TRUE	1	0.572755565393469	2		760	1240	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560464	95560464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	255	699	0	ENST00000393063.1:c.5125G>A	p.Asp1709Asn	p.D1709N	ENST00000393063	NM_030621.3	1709	Gat/Aat	25/28	1	2	FACETS	0.927	0.868	0.986	0.927	0.868	0.986	CLONAL	1	TRUE	1	0.572755565393469	2		699	961	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	76	692	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	1	2	FACETS	0.271	0.236	0.308	0.271	0.236	0.308	SUBCLONAL	1	TRUE	1	0.572755565393469	2		692	981	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928078	178928080	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs587776933	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	68	836	0	ENST00000263967.3:c.1359_1361del	p.Glu453del	p.E453del	ENST00000263967	NM_006218.2	452	ttAGAa/tta	8/21	0.270083777351291	3	FACETS	0.31	0.268	0.355	0.155	0.134	0.178	INDETERMINATE	1	TRUE	1	0.572755565393469	3		836	986	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645140	67645140	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	262	868	0	ENST00000264010.4:c.409del	p.Ala137LeufsTer17	p.A137Lfs*17	ENST00000264010	NM_006565.3	135	caG/ca	3/12	1	2	FACETS	0.841	0.788	0.895	0.841	0.788	0.895	CLONAL	1	TRUE	1	0.572755565393469	2		868	1088	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215357	5215357	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1440179947	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	152	819	0	ENST00000357368.4:c.4261C>T	p.Arg1421Cys	p.R1421C	ENST00000357368	NM_002850.3	1421	Cgc/Tgc	28/38	1	2	FACETS	0.522	0.477	0.57	0.522	0.477	0.57	SUBCLONAL	1	TRUE	1	0.572755565393469	2		819	1016	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226576366	226576366	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	186	950	0	ENST00000366794.5:c.708del	p.Ala237ProfsTer2	p.A237Pfs*2	ENST00000366794	NM_001618.3	236	aaA/aa	5/23	1	2	FACETS	0.505	0.465	0.546	0.505	0.465	0.546	SUBCLONAL	1	TRUE	1	0.572755565393469	2		950	1287	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431874	49431874	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	180	913	2	ENST00000301067.7:c.9265del	p.Val3089TrpfsTer30	p.V3089Wfs*30	ENST00000301067	NM_003482.3	3089	Gtg/tg	34/54	1	2	FACETS	0.527	0.485	0.571	0.527	0.485	0.571	SUBCLONAL	1	TRUE	1	0.572755565393469	2		915	1193	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554345	141554345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748399150	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1383	375	1005	4	ENST00000220592.5:c.1806del	p.Ala603ProfsTer92	p.A603Pfs*92	ENST00000220592	NM_012154.3	602	ccC/cc	14/19	0.554119840437022	3	FACETS	0.958	0.907	1	0.479	0.453	0.506	CLONAL	1	TRUE	1	0.572755565393469	3		1009	1758	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783260	9783260	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	373	860	0	ENST00000377346.4:c.2504C>A	p.Ala835Asp	p.A835D	ENST00000377346	NM_005026.3	835	gCc/gAc	20/24	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.572755565393469	2		860	1273	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601869	43601869	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	209	738	0	ENST00000355710.3:c.913C>T	p.Pro305Ser	p.P305S	ENST00000355710	NM_020975.4	305	Cct/Tct	5/20	1	2	FACETS	0.773	0.718	0.83	0.773	0.718	0.83	SUBCLONAL	1	TRUE	1	0.572755565393469	2		738	944	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710613	114710613	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	106	601	0	ENST00000543371.1:c.101del	p.Asn34ThrfsTer8	p.N34Tfs*8	ENST00000543371	NM_001198531.1	33	gAa/ga	1/14	1	2	FACETS	0.47	0.421	0.522	0.47	0.421	0.522	SUBCLONAL	1	TRUE	1	0.572755565393469	2		601	787	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609460	81609460	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	213	707	0	ENST00000298171.2:c.1058A>G	p.Tyr353Cys	p.Y353C	ENST00000298171	NM_000369.2	353	tAc/tGc	10/10	1	2	FACETS	0.895	0.833	0.959	0.895	0.833	0.959	CLONAL	1	TRUE	1	0.572755565393469	2		707	831	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574405	95574405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	120	376	1	ENST00000393063.1:c.2462G>A	p.Arg821His	p.R821H	ENST00000393063	NM_030621.3	821	cGc/cAc	17/28	1	2	FACETS	0.963	0.876	1	0.963	0.876	1	CLONAL	1	TRUE	1	0.572755565393469	2		377	435	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860650	3860650	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	188	886	0	ENST00000262367.5:c.929T>C	p.Phe310Ser	p.F310S	ENST00000262367	NM_004380.2	310	tTc/tCc	3/31	1	2	FACETS	0.514	0.473	0.556	0.514	0.473	0.556	SUBCLONAL	1	TRUE	1	0.572755565393469	2		886	1278	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584476	39584476	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	108	461	0	ENST00000262039.4:c.1141G>A	p.Val381Ile	p.V381I	ENST00000262039	NM_002647.2	381	Gtt/Att	10/25	1	2	FACETS	0.551	0.495	0.611	0.551	0.495	0.611	SUBCLONAL	1	TRUE	1	0.572755565393469	2		461	684	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210431	2210431	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	69	841	0	ENST00000398665.3:c.1038G>C	p.Gln346His	p.Q346H	ENST00000398665	NM_032482.2	346	caG/caC	13/28	1	2	FACETS	0.214	0.186	0.245	0.214	0.186	0.245	SUBCLONAL	1	TRUE	1	0.572755565393469	2		841	1125	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274310	5274310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1318	81	861	2	ENST00000357368.4:c.137C>T	p.Ser46Leu	p.S46L	ENST00000357368	NM_002850.3	46	tCg/tTg	3/38	1	2	FACETS	0.202	0.177	0.229	0.202	0.177	0.229	SUBCLONAL	1	TRUE	1	0.572755565393469	2		863	1399	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272238	15272238	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs760917811	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	260	804	2	ENST00000263388.2:c.6201del	p.Lys2069ArgfsTer16	p.K2069Rfs*16	ENST00000263388	NM_000435.2	2067	ccC/cc	33/33	1	2	FACETS	0.999	0.937	1	0.999	0.937	1	CLONAL	1	TRUE	1	0.572755565393469	2		806	909	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216188	36216189	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	157	928	0	ENST00000222270.7:c.3602dup	p.Met1202AspfsTer22	p.M1202Dfs*22	ENST00000222270	NM_014727.1	1199	ggc/ggCc	11/37	1	2	FACETS	0.483	0.441	0.526	0.483	0.441	0.526	SUBCLONAL	1	TRUE	1	0.572755565393469	2		928	1136	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912413	50912413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142361709	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	370	1060	0	ENST00000440232.2:c.1927G>A	p.Gly643Arg	p.G643R	ENST00000440232	NM_002691.3	643	Ggg/Agg	16/27	1	2	FACETS	0.995	0.943	1	0.995	0.943	1	CLONAL	1	TRUE	1	0.572755565393469	2		1060	1299	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485837	57485837	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	91	615	0	ENST00000371085.3:c.1138C>T	p.Arg380Cys	p.R380C	ENST00000371085	NM_000516.4	380	Cgt/Tgt	13/13	1	2	FACETS	0.328	0.291	0.369	0.328	0.291	0.369	SUBCLONAL	1	TRUE	1	0.572755565393469	2		615	968	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164728	36164728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	132	892	0	ENST00000300305.3:c.1147C>T	p.Pro383Ser	p.P383S	ENST00000300305		383	Ccg/Tcg	8/8	1	2	FACETS	0.388	0.351	0.427	0.388	0.351	0.427	SUBCLONAL	1	TRUE	1	0.572755565393469	2		892	1188	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1795713	1795713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs908992323	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	111	394	0	ENST00000260795.2:c.52G>A	p.Ala18Thr	p.A18T	ENST00000260795		18	Gcc/Acc	1/17	1	2	FACETS	0.938	0.85	1	0.938	0.85	1	CLONAL	1	TRUE	1	0.572755565393469	2		394	413	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517591	176517591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758477132	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	233	1000	1	ENST00000292408.4:c.292C>T	p.Arg98Cys	p.R98C	ENST00000292408	NM_213647.1	98	Cgc/Tgc	3/18	0.572755565393469	2	FACETS	0.646	0.601	0.692	0.323	0.3	0.346	SUBCLONAL	1	TRUE	0	0.572755565393469	2		1001	1260	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048670	180048670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1362559080	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	112	766	1	ENST00000261937.6:c.1892C>T	p.Ala631Val	p.A631V	ENST00000261937	NM_182925.4	631	gCg/gTg	13/30	0.572755565393469	2	FACETS	0.407	0.366	0.452	0.204	0.183	0.226	SUBCLONAL	1	TRUE	0	0.572755565393469	2		767	960	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407475	407477	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	34	628	0	ENST00000380956.4:c.1235_1237del	p.Gln412del	p.Q412del	ENST00000380956	NM_001195286.1	411	agACAa/aga	9/9	1	2	FACETS	0.189	0.153	0.229	0.189	0.153	0.229	SUBCLONAL	1	TRUE	1	0.572755565393469	2		628	629	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389269	8389269	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	64	918	0	ENST00000356435.5:c.4349C>T	p.Thr1450Ile	p.T1450I	ENST00000356435		1450	aCa/aTa	26/35	1	2	FACETS	0.196	0.169	0.226	0.196	0.169	0.226	SUBCLONAL	1	TRUE	1	0.572755565393469	2		918	1138	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537249	80537250	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	130	810	0	ENST00000286548.4:c.148_149del	p.Ser50TrpfsTer19	p.S50Wfs*19	ENST00000286548	NM_002072.3	50	AGt/t	2/7	1	2	FACETS	0.422	0.382	0.464	0.422	0.382	0.464	SUBCLONAL	1	TRUE	1	0.572755565393469	2		810	1076	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225097	53225097	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0020850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	110	660	0	ENST00000375401.3:c.3120+1G>A		p.X1040_splice	ENST00000375401	NM_004187.3	1040			0.572755565393469	1	FACETS	0.436	0.392	0.482	0.436	0.392	0.482	SUBCLONAL	1	TRUE	0	0.572755565393469	1		660	629	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207204	1207204	+	splice_donor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0020851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	313	1016	0	ENST00000326873.7:c.290+2del		p.X97_splice	ENST00000326873	NM_000455.4	97			0.801084865230324	1	FACETS	0.982	0.943	1	0.982	0.943	1	CLONAL	1	TRUE	0	0.801084865230324	1		1016	477	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271883	15271883	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	267	1335	0	ENST00000263388.2:c.6556del	p.Leu2186CysfsTer60	p.L2186Cfs*60	ENST00000263388	NM_000435.2	2186	Ctg/tg	33/33	1	2	FACETS	0.928	0.875	0.982	0.928	0.875	0.982	CLONAL	1	TRUE	1	0.801084865230324	2		1335	718	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637862	176637863	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0020851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	229	951	0	ENST00000439151.2:c.2466_2467dup	p.Pro823LeufsTer15	p.P823Lfs*15	ENST00000439151	NM_022455.4	821	ggc/ggCTc	5/23	0.801084865230324	1	FACETS	0.957	0.912	1	0.957	0.912	1	CLONAL	1	TRUE	0	0.801084865230324	1		951	358	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406621	70406622	+	missense_variant	Missense_Mutation	DNP	AG	AG	TT	novel	NA	P-0020860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1318	98	895	2	ENST00000373644.4:c.4135_4136delinsTT	p.Ser1379Phe	p.S1379F	ENST00000373644	NM_030625.2	1379	AGt/TTt	4/12	0.948212297624585	1	FACETS	0.077	0.068	0.086	0.077	0.068	0.086	SUBCLONAL	1	TRUE	0	0.948212297624585	1		897	1416	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788561	3788561	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	96	518	0	ENST00000262367.5:c.4393G>A	p.Gly1465Arg	p.G1465R	ENST00000262367	NM_004380.2	1465	Ggg/Agg	26/31	0.948212297624585	1	FACETS	0.139	0.123	0.156	0.139	0.123	0.156	SUBCLONAL	1	TRUE	0	0.948212297624585	1		518	766	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664578	29664578	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	61	562	0	ENST00000356175.3:c.6557A>G	p.Glu2186Gly	p.E2186G	ENST00000356175	NM_000267.3	2186	gAa/gGa	42/57	0.948212297624585	1	FACETS	0.063	0.054	0.073	0.063	0.054	0.073	SUBCLONAL	1	TRUE	0	0.948212297624585	1		562	1069	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104676	69104676	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	158	761	0	ENST00000288368.4:c.4520G>A	p.Gly1507Glu	p.G1507E	ENST00000288368	NM_024870.2	1507	gGg/gAg	37/40	0.948212297624585	1	FACETS	0.149	0.136	0.163	0.149	0.136	0.163	SUBCLONAL	1	TRUE	0	0.948212297624585	1		761	1178	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1204	109	372	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.247985542617033	5	FACETS	0.919	0.822	1			1	CLONAL	1	TRUE	NA	0.247985542617033	5		373	1313	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420311	88420311	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	86	561	2	ENST00000360948.2:c.2375C>T	p.Pro792Leu	p.P792L	ENST00000360948	NM_001012338.2	792	cCc/cTc	19/19	0.217104150898808	1	FACETS	0.794	0.702	0.893	0.794	0.702	0.893	SUBCLONAL	1	TRUE	0	0.247985542617033	1		563	765	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587780070	NA	P-0020861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	105	698	0	ENST00000269305.4:c.535C>A	p.His179Asn	p.H179N	ENST00000269305	NM_001126112.2	179	Cat/Aat	5/11	0.217104150898808	1	FACETS	0.777	0.695	0.864	0.777	0.695	0.864	SUBCLONAL	1	TRUE	0	0.247985542617033	1		698	955	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652386	206652386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781784265	NA	P-0020861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1269	86	738	0	ENST00000367120.3:c.1093G>A	p.Val365Ile	p.V365I	ENST00000367120	NM_014002.3	365	Gtc/Atc	10/22	0.247985542617033	3	FACETS	0.575	0.507	0.649	0.288	0.253	0.325	SUBCLONAL	1	TRUE	1	0.247985542617033	3		738	1355	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458261	120458262	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0020861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	151	710	0	ENST00000256646.2:c.7083_7084delinsAT	p.Asp2362Tyr	p.D2362Y	ENST00000256646	NM_024408.3	2361	caGGac/caATac	34/34	0.247985542617033	3	FACETS	1	0.972	1	0.579	0.528	0.633	CLONAL	1	TRUE	1	0.247985542617033	3		710	1182	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150217	108150217	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0020861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	49	580	0	ENST00000278616.4:c.3285-1G>T		p.X1095_splice	ENST00000278616	NM_000051.3	1095			0.217104150898808	1	FACETS	0.417	0.352	0.489	0.417	0.352	0.489	SUBCLONAL	1	TRUE	0	0.247985542617033	1		580	830	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435850	110435850	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	129	534	0	ENST00000375856.3:c.2551G>T	p.Ala851Ser	p.A851S	ENST00000375856	NM_003749.2	851	Gcc/Tcc	1/2	0.138672237331755	3	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.247985542617033	3		534	974	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606168	81606168	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	148	629	0	ENST00000298171.2:c.838C>G	p.Pro280Ala	p.P280A	ENST00000298171	NM_000369.2	280	Cca/Gca	9/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.247985542617033	2		629	951	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712518	43712518	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1233	123	814	1	ENST00000382044.4:c.4666G>A	p.Glu1556Lys	p.E1556K	ENST00000382044	NM_001141980.1	1556	Gag/Aag	21/28	0.214160967576962	3	FACETS	0.822	0.741	0.909	0.411	0.37	0.455	CLONAL	1	TRUE	1	0.247985542617033	3		815	1356	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828213	50828213	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	112	645	1	ENST00000398568.2:c.2551A>T	p.Ile851Phe	p.I851F	ENST00000398568	NM_001042412.1	851	Atc/Ttc	17/18	1	2	FACETS	0.919	0.825	1	0.919	0.825	1	CLONAL	1	TRUE	1	0.247985542617033	2		646	983	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543537	9543537	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0020861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	101	611	0	ENST00000353224.5:c.1616+1G>T		p.X539_splice	ENST00000353224	NM_177990.2	539			1	2	FACETS	0.931	0.831	1	0.931	0.831	1	CLONAL	1	TRUE	1	0.247985542617033	2		611	875	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253748	153253748	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	46	461	0	ENST00000281708.4:c.985G>T	p.Gly329Trp	p.G329W	ENST00000281708	NM_033632.3	329	Ggg/Tgg	6/12	1	2	FACETS	0.515	0.433	0.607	0.515	0.433	0.607	SUBCLONAL	1	TRUE	1	0.247985542617033	2		461	720	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0020862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1371	560	396	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.67473483767796	3	FACETS	1	0.993	1	0.575	0.55	0.6	CLONAL	1	TRUE	1	0.67473483767796	3		396	1931	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102131	27102131	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	477	873	0	ENST00000324856.7:c.5057G>A	p.Trp1686Ter	p.W1686*	ENST00000324856	NM_006015.4	1686	tGg/tAg	19/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.67473483767796	2		873	1355	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274911	41274911	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs868651538	NA	P-0020862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	431	722	1	ENST00000349496.5:c.1161T>A	p.Asn387Lys	p.N387K	ENST00000349496	NM_001904.3	387	aaT/aaA	8/15	0.266128898424195	3	FACETS	0.757	0.723	0.792	0.757	0.723	0.792	INDETERMINATE	2	TRUE	1	0.67473483767796	3		723	1128	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828125	243828125	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1289	76	909	0	ENST00000263826.5:c.233A>G	p.Gln78Arg	p.Q78R	ENST00000263826	NM_005465.4	78	cAg/cGg	3/13	1	2	FACETS	0.165	0.144	0.188	0.165	0.144	0.188	SUBCLONAL	1	TRUE	1	0.67473483767796	2		909	1365	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572851	41572852	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0020862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	559	886	0	ENST00000263253.7:c.5137_5138del	p.Asp1713Ter	p.D1713*	ENST00000263253	NM_001429.3	1712	ttAGat/ttat	31/31	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.67473483767796	2		886	1554	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637296	176637297	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0020862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	465	843	0	ENST00000439151.2:c.1896_1897del	p.Ser633Ter	p.S633*	ENST00000439151	NM_022455.4	632	cgAAgt/cggt	5/23	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.67473483767796	2		843	1364	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912075	127912077	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0020862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	60	605	0	ENST00000373547.4:c.793_795del	p.Cys265del	p.C265del	ENST00000373547	NM_002721.4	265	TGT/-	7/7	1	2	FACETS	0.176	0.151	0.204	0.176	0.151	0.204	SUBCLONAL	1	TRUE	1	0.67473483767796	2		605	1008	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912164	127912164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	272	442	0	ENST00000373547.4:c.706G>A	p.Ala236Thr	p.A236T	ENST00000373547	NM_002721.4	236	Gca/Aca	7/7	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.67473483767796	2		442	788	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915852	127915852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	506	749	1	ENST00000373547.4:c.629G>A	p.Arg210Gln	p.R210Q	ENST00000373547	NM_002721.4	210	cGa/cAa	6/7	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.67473483767796	2		750	1150	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412647	63412648	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	130	424	0	ENST00000330258.3:c.519dup	p.Ser174Ter	p.S174*	ENST00000330258	NM_152424.3	173	-/T	2/2	1	1	FACETS	0.375	0.341	0.412	0.375	0.341	0.412	SUBCLONAL	1	TRUE	0	0.67473483767796	1		424	680	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	199	372	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.94	0.871	1	0.94	0.871	1	CLONAL	1	TRUE	1	0.443287497130396	2		373	955	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0020863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	196	184	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.443287497130396	2		184	853	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473756	67473756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906852	NA	P-0020863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	69	944	1	ENST00000327367.4:c.836G>A	p.Arg279Lys	p.R279K	ENST00000327367	NM_005902.3	279	aGg/aAg	6/9	1	2	FACETS	0.315	0.273	0.36	0.315	0.273	0.36	SUBCLONAL	1	TRUE	1	0.443287497130396	2		945	989	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935384	36935384	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	223	993	1	ENST00000361632.4:c.1343G>A	p.Gly448Asp	p.G448D	ENST00000361632		448	gGc/gAc	10/16	1	2	FACETS	0.912	0.849	0.978	0.912	0.849	0.978	CLONAL	1	TRUE	1	0.443287497130396	2		994	1103	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581290	48581296	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTCTG	AGCTCTG	-	novel	NA	P-0020863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	418	901	0	ENST00000342988.3:c.594_600del	p.Ala199Ter	p.A199*	ENST00000342988	NM_005359.5	198	ccAGCTCTG/cc	5/12	0.426076942175374	2	FACETS	0.943	0.901	0.985	0.943	0.901	0.985	CLONAL	2	TRUE	0	0.443287497130396	2		901	1000	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164887	36164888	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGCT	novel	NA	P-0020863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	258	1052	0	ENST00000300305.3:c.984_987dup	p.Phe330SerfsTer271	p.F330Sfs*271	ENST00000300305		329	-/AGCG	8/8	1	2	FACETS	0.982	0.919	1	0.982	0.919	1	CLONAL	1	TRUE	1	0.443287497130396	2		1052	1185	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578515	7578515	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1212996409	NA	P-0020864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	232	686	1	ENST00000269305.4:c.415A>T	p.Lys139Ter	p.K139*	ENST00000269305	NM_001126112.2	139	Aag/Tag	5/11	1	2	FACETS	0.781	0.728	0.837	1	0.992	1	SUBCLONAL	2	TRUE	1	0.26441487869467	2		687	1123	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057803	27057804	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0020864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	337	769	0	ENST00000324856.7:c.1513_1514del	p.Gln505ValfsTer117	p.Q505Vfs*117	ENST00000324856	NM_006015.4	504	cCA/c	3/20	0.26441487869467	2	FACETS	0.959	0.906	1	0.959	0.906	1	CLONAL	2	TRUE	0	0.26441487869467	2		769	1329	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0020866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	30	369	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.587778701619324	1	FACETS	0.204	0.164	0.249	0.204	0.164	0.249	SUBCLONAL	1	TRUE	0	0.616259713941871	1		369	330	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696644	47696644	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519964	NA	P-0020866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	218	992	0	ENST00000347630.2:c.304T>G	p.Phe102Val	p.F102V	ENST00000347630	NM_001007230.1	102	Ttc/Gtc	5/11	1	2	FACETS	0.992	0.927	1	0.992	0.927	1	CLONAL	1	TRUE	1	0.616259713941871	2		992	713	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380350	14380350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	113	394	0	ENST00000256196.4:c.67G>A	p.Gly23Ser	p.G23S	ENST00000256196		23	Ggc/Agc	1/6	1	2	FACETS	0.853	0.773	0.936	0.853	0.773	0.936	CLONAL	1	TRUE	1	0.616259713941871	2		394	430	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506714	103506714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	98	347	1	ENST00000355739.4:c.457G>A	p.Glu153Lys	p.E153K	ENST00000355739	NM_000123.3	153	Gaa/Aaa	4/15	1	2	FACETS	0.862	0.776	0.952	0.862	0.776	0.952	CLONAL	1	TRUE	1	0.616259713941871	2		348	369	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009347	69009347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs190776975	NA	P-0020866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	254	685	0	ENST00000288368.4:c.2464G>A	p.Val822Met	p.V822M	ENST00000288368	NM_024870.2	822	Gtg/Atg	22/40	0.531085133260319	3	FACETS	1	0.957	1	0.514	0.481	0.548	CLONAL	1	TRUE	1	0.616259713941871	3		685	1049	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	121	372	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.873	0.791	0.96	0.873	0.791	0.96	CLONAL	1	TRUE	1	0.435761392149046	2		373	636	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0020867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	971	686	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.386513551953002	3	FACETS	1	0.995	1			1	CLONAL	3	TRUE	NA	0.435761392149046	3		686	1682	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226494	1226494	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752015385	NA	P-0020868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	123	1036	7	ENST00000326873.7:c.1150C>T	p.Arg384Trp	p.R384W	ENST00000326873	NM_000455.4	384	Cgg/Tgg	9/10	1	2	FACETS	0.98	0.884	1	0.98	0.884	1	CLONAL	1	TRUE	1	0.205482373683721	2		1043	1222	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281660	49281660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61735175	NA	P-0020868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	178	1115	2	ENST00000282018.3:c.707C>T	p.Ser236Leu	p.S236L	ENST00000282018	NM_020377.2	236	tCg/tTg	1/1	0.205482373683721	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.205482373683721	1		1117	1326	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332822	65332828	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCATC	CCGCATC	-	novel	NA	P-0020868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	71	519	0	ENST00000342505.4:c.711_717del	p.Met238Ter	p.M238*	ENST00000342505	NM_002227.2	237	agGATGCGG/ag	7/25	0.205482373683721	1	FACETS	0.849	0.741	0.967	0.849	0.741	0.967	CLONAL	1	TRUE	0	0.205482373683721	1		519	730	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323264	31323274	+	frameshift_variant	Frame_Shift_Del	DEL	TGCCAGGTCAG	TGCCAGGTCAG	-	novel	NA	P-0020868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	53	393	0	ENST00000412585.2:c.715_725del	p.Leu239AlafsTer11	p.L239Afs*11	ENST00000412585	NM_005514.6	239	CTGACCTGGCAg/g	4/8	1	2	FACETS	0.935	0.797	1	0.935	0.797	1	CLONAL	1	TRUE	1	0.205482373683721	2		393	552	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860737	151860753	+	frameshift_variant	Frame_Shift_Del	DEL	GTGGCACCATGGGAAAG	GTGGCACCATGGGAAAG	-	novel	NA	P-0020868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	92	610	0	ENST00000262189.6:c.9909_9925del	p.Phe3304AlafsTer16	p.F3304Afs*16	ENST00000262189	NM_170606.2	3303	acCTTTCCCATGGTGCCACag/acag	43/59	0.205482373683721	3	FACETS	1	0.912	1	0.516	0.458	0.579	CLONAL	1	TRUE	1	0.205482373683721	3		610	956	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0020874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	257	340	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	0.544266781459868	2		340	913	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228980	36228980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780852805	NA	P-0020874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	330	696	0	ENST00000222270.7:c.7760G>A	p.Arg2587Gln	p.R2587Q	ENST00000222270	NM_014727.1	2587	cGa/cAa	36/37	1	2	FACETS	0.991	0.936	1	0.991	0.936	1	CLONAL	1	TRUE	1	0.544266781459868	2		696	1224	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436695	110436695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	330	814	3	ENST00000375856.3:c.1706G>A	p.Arg569Gln	p.R569Q	ENST00000375856	NM_003749.2	569	cGa/cAa	1/2	1	2	FACETS	0.972	0.919	1	0.972	0.919	1	CLONAL	1	TRUE	1	0.544266781459868	2		817	1247	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731228	162731228	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	137	352	0	ENST00000367921.3:c.1083G>C	p.Glu361Asp	p.E361D	ENST00000367921	NM_006182.2	361	gaG/gaC	9/18	0.544266781459868	3	FACETS	0.862	0.785	0.943	0.431	0.392	0.472	CLONAL	1	TRUE	1	0.544266781459868	3		352	743	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193121509	193121509	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0020874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	95	349	0	ENST00000367435.3:c.908-1G>C		p.X303_splice	ENST00000367435	NM_024529.4	303			0.544266781459868	3	FACETS	0.876	0.783	0.974	0.438	0.391	0.487	CLONAL	1	TRUE	1	0.544266781459868	3		349	507	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349468	73349468	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	183	672	1	ENST00000377767.4:c.868G>T	p.Asp290Tyr	p.D290Y	ENST00000377767	NM_014953.3	290	Gat/Tat	6/21	1	2	FACETS	0.834	0.771	0.9	0.834	0.771	0.9	CLONAL	1	TRUE	1	0.544266781459868	2		673	806	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798872	42798872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	371	701	0	ENST00000575354.2:c.4444G>A	p.Gly1482Ser	p.G1482S	ENST00000575354	NM_015125.3	1482	Ggc/Agc	19/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.544266781459868	2		701	1319	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912299	29912299	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1431	97	896	0	ENST00000376809.5:c.921del	p.Ile308SerfsTer14	p.I308Sfs*14	ENST00000376809	NM_002116.7	306	atC/at	5/8	0.544266781459868	3	FACETS	0.297	0.263	0.333	0.148	0.131	0.167	SUBCLONAL	1	TRUE	1	0.544266781459868	3		896	1528	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981855	70981855	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446042463	NA	P-0020874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	566	792	0	ENST00000276594.2:c.241G>A	p.Gly81Ser	p.G81S	ENST00000276594	NM_024504.3	81	Ggt/Agt	2/8	0.544266781459868	2	FACETS	0.966	0.933	1	0.966	0.933	1	CLONAL	2	TRUE	0	0.544266781459868	2		792	1076	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0020876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	459	813	1	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.325380673081849	2	FACETS	0.964	0.92	1	0.964	0.92	1	CLONAL	2	TRUE	0	0.331621935995882	2		814	1436	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951053	48951053	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0020876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	115	294	0	ENST00000267163.4:c.1216-1G>C		p.X406_splice	ENST00000267163	NM_000321.2	406			0.331621935995882	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.331621935995882	1		294	486	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325798	65325798	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	146	542	0	ENST00000342505.4:c.1324G>T	p.Gly442Cys	p.G442C	ENST00000342505	NM_002227.2	442	Ggt/Tgt	9/25	1	2	FACETS	0.942	0.859	1	0.942	0.859	1	CLONAL	1	TRUE	1	0.331621935995882	2		542	935	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981086	201981086	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	261	567	0	ENST00000359651.3:c.165G>C	p.Glu55Asp	p.E55D	ENST00000359651		55	gaG/gaC	2/8	0.237749897927855	2	FACETS	0.864	0.811	0.918	0.864	0.811	0.918	CLONAL	2	TRUE	0	0.331621935995882	2		567	911	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118760	115118760	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	293	780	0	ENST00000257566.3:c.581G>T	p.Gly194Val	p.G194V	ENST00000257566	NM_016569.3	194	gGg/gTg	2/8	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.331621935995882	2		780	1284	SUCCESS
APC	324	MSKCC	GRCh37	5	112164656	112164656	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0020876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	80	351	0	ENST00000257430.4:c.1730T>A	p.Leu577Ter	p.L577*	ENST00000257430	NM_000038.5	577	tTa/tAa	14/16	0.331621935995882	1	FACETS	0.616	0.543	0.696	0.616	0.543	0.696	SUBCLONAL	1	TRUE	0	0.331621935995882	1		351	653	SUCCESS
APC	324	MSKCC	GRCh37	5	112175097	112175097	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	44	324	0	ENST00000257430.4:c.3806T>G	p.Ile1269Arg	p.I1269R	ENST00000257430	NM_000038.5	1269	aTa/aGa	16/16	0.331621935995882	1	FACETS	0.38	0.318	0.449	0.38	0.318	0.449	SUBCLONAL	1	TRUE	0	0.331621935995882	1		324	582	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0020877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	21	685	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.816	1	1	0.816	1	CLONAL	1	TRUE	1	0.619795145959914	2		685	66	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	26	251	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.619795145959914	2		251	66	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650051	206650051	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs782081148	NA	P-0020877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	38	771	0	ENST00000367120.3:c.571C>T	p.Arg191Ter	p.R191*	ENST00000367120	NM_014002.3	191	Cga/Tga	7/22	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.619795145959914	2		771	101	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023676	27023676	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	33	688	0	ENST00000324856.7:c.782C>G	p.Ser261Trp	p.S261W	ENST00000324856	NM_006015.4	261	tCg/tGg	1/20	1	2	FACETS	0.942	0.785	1	0.942	0.785	1	CLONAL	1	TRUE	1	0.619795145959914	2		688	113	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245965	46245965	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	30	518	0	ENST00000334344.6:c.4059G>C	p.Leu1353Phe	p.L1353F	ENST00000334344	NM_152641.2	1353	ttG/ttC	15/21	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.619795145959914	2		518	92	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420277	49420277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	36	839	1	ENST00000301067.7:c.15472G>A	p.Glu5158Lys	p.E5158K	ENST00000301067	NM_003482.3	5158	Gag/Aag	48/54	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.619795145959914	2		840	106	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914401	32914401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80358824	NA	P-0020877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	16	931	0	ENST00000380152.3:c.5909C>T	p.Ser1970Leu	p.S1970L	ENST00000380152		1970	tCa/tTa	11/27	0.14362126059857	0	FACETS	0.297	0.225	0.378			1	INDETERMINATE	1	TRUE	0	0.619795145959914	0		931	66	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988274	41988274	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	38	778	1	ENST00000219905.7:c.1066C>T	p.Leu356Phe	p.L356F	ENST00000219905	NM_001164273.1	356	Ctt/Ttt	3/24	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.619795145959914	2		779	119	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988560	41988560	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0020877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	33	758	0	ENST00000219905.7:c.1352C>G	p.Ser451Ter	p.S451*	ENST00000219905	NM_001164273.1	451	tCa/tGa	3/24	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.619795145959914	2		758	104	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72863744	72863747	+	missense_variant	Missense_Mutation	ONP	CTTC	CTTC	ATTT	novel	NA	P-0020877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	26	660	1	ENST00000268489.5:c.3460_3463delinsAAAT	p.Glu1154_Asp1155delinsLysTyr	p.E1154_D1155delinsKY	ENST00000268489	NM_006885.3	1154	GAAGat/AAATat	5/10	1	2	FACETS	0.902	0.732	1	0.902	0.732	1	CLONAL	1	TRUE	1	0.619795145959914	2		661	93	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72863756	72863756	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	20	574	1	ENST00000268489.5:c.3451G>T	p.Glu1151Ter	p.E1151*	ENST00000268489	NM_006885.3	1151	Gaa/Taa	5/10	1	2	FACETS	0.75	0.587	0.933	0.75	0.587	0.933	CLONAL	1	TRUE	1	0.619795145959914	2		575	86	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872380	45872380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	20	833	1	ENST00000391945.4:c.131C>T	p.Ser44Leu	p.S44L	ENST00000391945	NM_000400.3	44	tCa/tTa	3/23	1	2	FACETS	0.717	0.56	0.893	0.717	0.56	0.893	SUBCLONAL	1	TRUE	1	0.619795145959914	2		834	90	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47601171	47601171	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	44	734	0	ENST00000263735.4:c.409G>C	p.Glu137Gln	p.E137Q	ENST00000263735	NM_002354.2	137	Gag/Cag	3/9	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.619795145959914	2		734	124	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035147	37035147	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63751012	NA	P-0020877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	29	472	0	ENST00000231790.2:c.109G>A	p.Glu37Lys	p.E37K	ENST00000231790	NM_000249.3	37	Gag/Aag	1/19	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.619795145959914	2		472	81	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142984	47142984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	28	757	0	ENST00000409792.3:c.4979C>T	p.Ser1660Leu	p.S1660L	ENST00000409792	NM_014159.6	1660	tCa/tTa	8/21	1	2	FACETS	0.886	0.724	1	0.886	0.724	1	CLONAL	1	TRUE	1	0.619795145959914	2		757	102	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0020877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	42	291	0	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	0.194265539420418	1	FACETS	1	0.889	1	1	0.889	1	INDETERMINATE	1	TRUE	0	0.619795145959914	1		291	91	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542599	141542599	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	36	888	1	ENST00000220592.5:c.2387C>G	p.Ser796Cys	p.S796C	ENST00000220592	NM_012154.3	796	tCc/tGc	18/19	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.619795145959914	2		889	106	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391352	139391352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1190825232	NA	P-0020877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	20	1008	1	ENST00000277541.6:c.6839C>T	p.Ser2280Phe	p.S2280F	ENST00000277541	NM_017617.3	2280	tCt/tTt	34/34	0.619795145959914	1	FACETS	0.825	0.658	1	0.825	0.658	1	CLONAL	1	TRUE	0	0.619795145959914	1		1009	54	SUCCESS
AR	367	MSKCC	GRCh37	X	66765521	66765521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	30	483	0	ENST00000374690.3:c.533C>T	p.Ser178Phe	p.S178F	ENST00000374690	NM_000044.3	178	tCc/tTc	1/8	0.194265539420418	0	FACETS	0.694	0.595	0.791			1	INDETERMINATE	1	TRUE	NA	0.619795145959914	0		483	53	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1185	166	613	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.908	0.832	0.988	0.908	0.832	0.988	CLONAL	1	TRUE	1	0.270674889003676	2		614	1351	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640328	3640328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767093188	NA	P-0020878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1394	226	1100	0	ENST00000294008.3:c.3311G>A	p.Arg1104Gln	p.R1104Q	ENST00000294008	NM_032444.2	1104	cGg/cAg	12/15	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.270674889003676	2		1100	1620	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577541	7577541	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	229	864	0	ENST00000269305.4:c.740del	p.Asn247ThrfsTer98	p.N247Tfs*98	ENST00000269305	NM_001126112.2	247	aAc/ac	7/11	0.270674889003676	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.270674889003676	1		864	1247	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37045932	37045941	+	frameshift_variant	Frame_Shift_Del	DEL	CAACGAAAAC	CAACGAAAAC	-	novel	NA	P-0020880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	316	804	0	ENST00000231790.2:c.347_356del	p.Thr116LysfsTer17	p.T116Kfs*17	ENST00000231790	NM_000249.3	116	aCAACGAAAACa/aa	4/19	1	2	FACETS	0.844	0.799	0.89	0.844	0.799	0.89	CLONAL	1	TRUE	1	0.831649643034953	2		804	900	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0020881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	666	799	0	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	0.531358459874343	4	FACETS	1	0.996	1	1	0.996	1	CLONAL	4	TRUE	0	0.531358459874343	4		799	868	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0020881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	186	303	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.488544792248084	4	FACETS	0.839	0.784	0.894	1	0.988	1	CLONAL	3	TRUE	2	0.531358459874343	4		304	426	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909653	76909654	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCGCTGATTTTCTTACAGCG	novel	NA	P-0020881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	187	372	0	ENST00000373344.5:c.4251_4252insCGCTGTAAGAAAATCAGCGG	p.Ser1418ArgfsTer79	p.S1418Rfs*79	ENST00000373344	NM_000489.3	1417	-/CGCTGTAAGAAAATCAGCGG	14/35	0.51138319671926	2	FACETS	0.889	0.833	0.945			1	CLONAL	2	TRUE	NA	0.531358459874343	2		372	396	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164163	108164164	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs864622164	NA	P-0020882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	236	454	1	ENST00000278616.4:c.4741dup	p.Ile1581AsnfsTer5	p.I1581Nfs*5	ENST00000278616	NM_000051.3	1579	caa/cAaa	31/63	0.840264517720753	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	FALSE	0	0.840264517720753	1		455	284	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742852	145742853	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	927	521	0	ENST00000428558.2:c.158dup	p.Gln54ProfsTer83	p.Q54Pfs*83	ENST00000428558	NM_004260.3	53	ggc/ggGc	3/22	0.840264517720753	6	FACETS	0.953	0.929	0.977	0.953	0.929	0.977	CLONAL	4	FALSE	2	0.840264517720753	6		521	1551	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742945	17742945	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	30	744	4	ENST00000250003.3:c.853G>T	p.Ala285Ser	p.A285S	ENST00000250003	NM_002478.4	285	Gct/Tct	3/3	1	2	FACETS	0.446	0.358	0.545	0.446	0.358	0.545	SUBCLONAL	1	TRUE	1	0.26	2		748	518	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120647	115120647	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	205	1131	1	ENST00000257566.3:c.359G>T	p.Gly120Val	p.G120V	ENST00000257566	NM_016569.3	120	gGc/gTc	1/8	NA	2	FACETS	0.901	0.837	0.967			1	INDETERMINATE	2	TRUE	NA	0.26	2		1132	875	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515106	103515106	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1471960675	NA	P-0020883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	34	497	0	ENST00000355739.4:c.1607A>G	p.Asn536Ser	p.N536S	ENST00000355739	NM_000123.3	536	aAt/aGt	8/15	1	2	FACETS	0.657	0.537	0.792	0.657	0.537	0.792	SUBCLONAL	1	TRUE	1	0.26	2		497	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0020883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	215	887	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	0.272391389894743	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.26	2		887	692	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684285	29684285	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0020883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	161	654	0	ENST00000356175.3:c.7807-2A>T		p.X2603_splice	ENST00000356175	NM_000267.3	2603			0.272391389894743	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	0	0.26	2		654	598	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39576684	39576684	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	64	597	0	ENST00000262039.4:c.974A>T	p.Asn325Ile	p.N325I	ENST00000262039	NM_002647.2	325	aAt/aTt	9/25	1	2	FACETS	0.837	0.725	0.959	0.837	0.725	0.959	CLONAL	1	TRUE	1	0.26	2		597	588	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790086	40790086	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	63	750	0	ENST00000373198.4:c.2645A>G	p.Asp882Gly	p.D882G	ENST00000373198	NM_133170.3	882	gAc/gGc	18/32	0.105589921267532	4	FACETS	0.983	0.85	1	0.492	0.425	0.564	INDETERMINATE	1	TRUE	2	0.26	4		750	621	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039904	47039904	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	138	479	0	ENST00000377604.3:c.1247A>T	p.Gln416Leu	p.Q416L	ENST00000377604	NM_001204468.1	416	cAg/cTg	12/24	0.259713328879581	2	FACETS	1	0.981	1			1	CLONAL	2	TRUE	NA	0.26	2		479	426	SUCCESS
APC	324	MSKCC	GRCh37	5	112175328	112175328	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	163	396	0	ENST00000257430.4:c.4037C>A	p.Ser1346Ter	p.S1346*	ENST00000257430	NM_000038.5	1346	tCa/tAa	16/16	0.529374922698204	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.529374922698204	1		396	384	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962603	38962603	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	332	673	0	ENST00000357387.3:c.1652T>A	p.Ile551Lys	p.I551K	ENST00000357387	NM_152756.3	551	aTa/aAa	18/38	0.529374922698204	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.529374922698204	3		673	766	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0020886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	249	685	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.751283296169778	3	FACETS	0.993	0.93	1	0.497	0.465	0.529	CLONAL	1	TRUE	1	0.751283296169778	3		685	918	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247514	123247514	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	22	794	0	ENST00000358487.5:c.1977G>C	p.Lys659Asn	p.K659N	ENST00000358487	NM_000141.4	659	aaG/aaC	14/18	0.751283296169778	1	FACETS	0.071	0.055	0.09	0.071	0.055	0.09	SUBCLONAL	1	TRUE	0	0.751283296169778	1		794	514	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404893	70404893	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765094207	NA	P-0020886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	170	723	1	ENST00000373644.4:c.2407G>A	p.Ala803Thr	p.A803T	ENST00000373644	NM_030625.2	803	Gct/Act	4/12	0.751283296169778	1	FACETS	0.673	0.626	0.72	0.673	0.626	0.72	SUBCLONAL	1	TRUE	0	0.751283296169778	1		724	420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	368	950	0	ENST00000269305.4:c.376T>C	p.Tyr126His	p.Y126H	ENST00000269305	NM_001126112.2	126	Tac/Cac	5/11	1	2	FACETS	0.975	0.927	1	0.975	0.927	1	CLONAL	1	TRUE	1	0.751283296169778	2		950	1005	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410035	63410035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	174	724	0	ENST00000330258.3:c.3132G>A	p.Met1044Ile	p.M1044I	ENST00000330258	NM_152424.3	1044	atG/atA	2/2	0.249353381101628	1	FACETS	0.489	0.453	0.527	0.489	0.453	0.527	INDETERMINATE	1	TRUE	0	0.751283296169778	1		724	591	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741604	17741604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866359886	NA	P-0020886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	44	434	1	ENST00000250003.3:c.275G>A	p.Arg92His	p.R92H	ENST00000250003	NM_002478.4	92	cGc/cAc	1/3	1	2	FACETS	0.25	0.209	0.295	0.25	0.209	0.295	SUBCLONAL	1	TRUE	1	0.751283296169778	2		435	469	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409102	4409102	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778716956	NA	P-0020886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	179	575	0	ENST00000261254.3:c.797G>A	p.Arg266His	p.R266H	ENST00000261254	NM_001759.3	266	cGt/cAt	5/5	NA	2	FACETS	0.837	0.777	0.9			1	INDETERMINATE	1	TRUE	NA	0.751283296169778	2		575	569	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0020886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	350	777	25	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	0.751283296169778	2		802	651	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841419	156841419	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	182	483	0	ENST00000524377.1:c.722C>A	p.Ser241Tyr	p.S241Y	ENST00000524377	NM_002529.3	241	tCt/tAt	7/17	0.678277210863029	3	FACETS	0.93	0.86	1	0.465	0.43	0.501	CLONAL	1	TRUE	1	0.751283296169778	3		483	717	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717757	89717758	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1554825249	NA	P-0020886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	208	561	0	ENST00000371953.3:c.783_784del	p.Asn262GlnfsTer35	p.N262Qfs*35	ENST00000371953	NM_000314.4	261	cAG/c	7/9	0.751283296169778	1	FACETS	0.955	0.903	1	0.955	0.903	1	CLONAL	1	TRUE	0	0.751283296169778	1		561	362	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021366	42021366	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772780139	NA	P-0020886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	182	528	0	ENST00000219905.7:c.3662G>A	p.Arg1221Gln	p.R1221Q	ENST00000219905	NM_001164273.1	1221	cGg/cAg	11/24	0.594400647682417	1	FACETS	0.855	0.802	0.907	0.855	0.802	0.907	CLONAL	1	TRUE	0	0.751283296169778	1		528	354	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786740	3786740	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	302	832	0	ENST00000262367.5:c.4471C>G	p.Gln1491Glu	p.Q1491E	ENST00000262367	NM_004380.2	1491	Caa/Gaa	27/31	1	2	FACETS	0.84	0.793	0.888	0.84	0.793	0.888	CLONAL	1	TRUE	1	0.751283296169778	2		832	957	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905513	50905513	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	306	928	0	ENST00000440232.2:c.641T>G	p.Val214Gly	p.V214G	ENST00000440232	NM_002691.3	214	gTg/gGg	6/27	NA	2	FACETS	0.905	0.856	0.956			1	INDETERMINATE	1	TRUE	NA	0.751283296169778	2		928	900	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085673	16085673	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	300	842	0	ENST00000281043.3:c.849G>T	p.Glu283Asp	p.E283D	ENST00000281043	NM_005378.4	283	gaG/gaT	3/3	1	2	FACETS	0.892	0.843	0.943	0.892	0.843	0.943	CLONAL	1	TRUE	1	0.751283296169778	2		842	895	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089091	37089091	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	241	633	0	ENST00000231790.2:c.1813G>C	p.Glu605Gln	p.E605Q	ENST00000231790	NM_000249.3	605	Gaa/Caa	16/19	0.751283296169778	1	FACETS	0.894	0.847	0.941	0.894	0.847	0.941	CLONAL	1	TRUE	0	0.751283296169778	1		633	448	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089136	37089136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	231	676	0	ENST00000231790.2:c.1858G>A	p.Glu620Lys	p.E620K	ENST00000231790	NM_000249.3	620	Gag/Aag	16/19	0.751283296169778	1	FACETS	0.865	0.818	0.912	0.865	0.818	0.912	CLONAL	1	TRUE	0	0.751283296169778	1		676	444	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090410	37090410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	224	769	0	ENST00000231790.2:c.2005G>A	p.Glu669Lys	p.E669K	ENST00000231790	NM_000249.3	669	Gaa/Aaa	18/19	0.751283296169778	1	FACETS	0.908	0.859	0.956	0.908	0.859	0.956	CLONAL	1	TRUE	0	0.751283296169778	1		769	410	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1266601	1266601	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	197	765	0	ENST00000310581.5:c.2632A>G	p.Thr878Ala	p.T878A	ENST00000310581	NM_198253.2	878	Acc/Gcc	10/16	1	2	FACETS	0.806	0.749	0.863	0.806	0.749	0.863	CLONAL	1	TRUE	1	0.751283296169778	2		765	651	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55225358	55225358	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	306	731	0	ENST00000275493.2:c.1210T>C	p.Phe404Leu	p.F404L	ENST00000275493	NM_005228.3	404	Ttt/Ctt	11/28	1	2	FACETS	0.965	0.913	1	0.965	0.913	1	CLONAL	1	TRUE	1	0.751283296169778	2		731	844	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411576	116411576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759522148	NA	P-0020886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	169	497	1	ENST00000397752.3:c.2755G>A	p.Val919Ile	p.V919I	ENST00000397752	NM_000245.2	919	Gtc/Atc	13/21	1	2	FACETS	0.903	0.837	0.971	0.903	0.837	0.971	CLONAL	1	TRUE	1	0.751283296169778	2		498	498	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410237	63410237	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	212	832	0	ENST00000330258.3:c.2930C>G	p.Pro977Arg	p.P977R	ENST00000330258	NM_152424.3	977	cCc/cGc	2/2	0.249353381101628	1	FACETS	0.54	0.504	0.576	0.54	0.504	0.576	INDETERMINATE	1	TRUE	0	0.751283296169778	1		832	653	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623152	52623161	+	protein_altering_variant	In_Frame_Del	DEL	CCACATAGAC	CCACATAGAC	G	novel	NA	P-0020886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	301	818	0	ENST00000394830.3:c.2890_2899delinsC	p.Val964_Glu967delinsGln	p.V964_E967delinsQ	ENST00000394830	NM_018313.4	964	GTCTATGTGGaa/Caa	19/30	0.751283296169778	1	FACETS	0.889	0.847	0.93	0.889	0.847	0.93	CLONAL	1	TRUE	0	0.751283296169778	1		818	563	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	188	251	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.911	0.849	0.975	0.911	0.849	0.975	CLONAL	1	TRUE	1	0.78587777066496	2		251	525	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711874	89711874	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs786204862	NA	P-0020901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	30	547	0	ENST00000371953.3:c.493-1G>A		p.X165_splice	ENST00000371953	NM_000314.4	165			0.78587777066496	1	FACETS	0.154	0.124	0.188	0.154	0.124	0.188	SUBCLONAL	1	TRUE	0	0.78587777066496	1		547	301	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233034	55233034	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4271	8571	733	0	ENST00000275493.2:c.1784G>A	p.Cys595Tyr	p.C595Y	ENST00000275493	NM_005228.3	595	tGc/tAc	15/28	0.78587777066496	27	FACETS	1	0.998	1			1	CLONAL	18	TRUE	NA	0.78587777066496	27		733	12842	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15374316	15374316	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	373	831	0	ENST00000263377.2:c.1256G>T	p.Gly419Val	p.G419V	ENST00000263377	NM_058243.2	419	gGt/gTt	7/20	0.78587777066496	3	FACETS	1	0.976	1	0.524	0.497	0.551	CLONAL	1	TRUE	1	0.78587777066496	3		831	1262	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282584	1282584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1207489144	NA	P-0020901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	72	790	1	ENST00000310581.5:c.1729C>T	p.Arg577Trp	p.R577W	ENST00000310581	NM_198253.2	577	Cgg/Tgg	3/16	1	2	FACETS	0.231	0.201	0.264	0.231	0.201	0.264	SUBCLONAL	1	TRUE	1	0.78587777066496	2		791	792	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401429	401429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	15	270	0	ENST00000380956.4:c.751C>T	p.Arg251Trp	p.R251W	ENST00000380956	NM_001195286.1	251	Cgg/Tgg	7/9	1	2	FACETS	0.189	0.138	0.25	0.189	0.138	0.25	SUBCLONAL	1	TRUE	1	0.78587777066496	2		270	202	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0020905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	32	878	3	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		881	862	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027128	49027128	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0020907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	94	530	0	ENST00000267163.4:c.1696del		p.X566_splice	ENST00000267163	NM_000321.2	566			0.683749171512664	1	FACETS	0.887	0.809	0.965	0.887	0.809	0.965	CLONAL	1	TRUE	0	0.702056923444459	1		530	196	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900918	3900918	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	444	906	2	ENST00000262367.5:c.178G>A	p.Val60Ile	p.V60I	ENST00000262367	NM_004380.2	60	Gtt/Att	2/31	0.593359262195305	2	FACETS	0.81	0.779	0.84	0.81	0.779	0.84	CLONAL	2	TRUE	0	0.702056923444459	2		908	781	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510276	187510276	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	188	672	0	ENST00000441802.2:c.13237T>G	p.Tyr4413Asp	p.Y4413D	ENST00000441802	NM_005245.3	4413	Tac/Gac	27/27	0.229666764964944	3	FACETS	0.986	0.913	1	0.493	0.456	0.53	INDETERMINATE	1	TRUE	1	0.702056923444459	3		672	734	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410114	139410114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	238	905	0	ENST00000277541.6:c.1724G>A	p.Cys575Tyr	p.C575Y	ENST00000277541	NM_017617.3	575	tGc/tAc	11/34	1	2	FACETS	0.609	0.568	0.652	0.609	0.568	0.652	SUBCLONAL	1	TRUE	1	0.702056923444459	2		905	1113	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641113	117641113	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	160	817	0	ENST00000368508.3:c.5858G>T	p.Ser1953Ile	p.S1953I	ENST00000368508	NM_002944.2	1953	aGt/aTt	36/43	1	2	FACETS	0.906	0.834	0.981	0.906	0.834	0.981	CLONAL	1	TRUE	1	0.543153510769255	2		817	650	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0020910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	376	607	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.773306751724118	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.773306751724118	1		607	583	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735506	40735506	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	186	754	0	ENST00000373198.4:c.3367G>C	p.Ala1123Pro	p.A1123P	ENST00000373198	NM_133170.3	1123	Gcc/Ccc	25/32	NA	2	FACETS	0.934	0.87	1			1	INDETERMINATE	1	TRUE	NA	0.773306751724118	2		754	515	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991757	72991758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760959844	NA	P-0020912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	36	852	2	ENST00000268489.5:c.2287dup	p.Glu763GlyfsTer26	p.E763Gfs*26	ENST00000268489	NM_006885.3	763	gag/gGag	2/10	0.50668177218894	1	FACETS	0.209	0.171	0.251	0.209	0.171	0.251	SUBCLONAL	1	TRUE	0	0.50668177218894	1		854	508	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109918	115109918	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	265	1227	1	ENST00000257566.3:c.1960del	p.Ser654ValfsTer235	p.S654Vfs*235	ENST00000257566	NM_016569.3	654	Agt/gt	8/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.50668177218894	2		1228	973	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110076	115110082	+	frameshift_variant	Frame_Shift_Del	DEL	AACAGGC	AACAGGC	-	novel	NA	P-0020912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	338	1526	0	ENST00000257566.3:c.1796_1802del	p.Ser599ThrfsTer31	p.S599Tfs*31	ENST00000257566	NM_016569.3	599	aGCCTGTTc/ac	8/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.50668177218894	2		1526	1249	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847298	68847299	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	223	1018	1	ENST00000261769.5:c.1221dup	p.Ala408SerfsTer11	p.A408Sfs*11	ENST00000261769	NM_004360.3	407	cca/ccAa	9/16	0.50668177218894	1	FACETS	0.955	0.894	1	0.955	0.894	1	CLONAL	1	TRUE	0	0.50668177218894	1		1019	688	SUCCESS
APC	324	MSKCC	GRCh37	5	112177827	112177827	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	36	555	0	ENST00000257430.4:c.6536A>G	p.Lys2179Arg	p.K2179R	ENST00000257430	NM_000038.5	2179	aAa/aGa	16/16	1	2	FACETS	0.241	0.197	0.29	0.241	0.197	0.29	SUBCLONAL	1	TRUE	1	0.50668177218894	2		555	590	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0020914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	1189	187	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.813383997622263	5	FACETS	0.995	0.977	1			1	CLONAL	4	TRUE	NA	0.892690691076089	5		187	1566	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0020914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	175	478	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.864	0.803	0.925	0.864	0.803	0.925	CLONAL	1	TRUE	1	0.892690691076089	2		478	454	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244232	153244232	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	346	674	0	ENST00000281708.4:c.1925A>G	p.Asp642Gly	p.D642G	ENST00000281708	NM_033632.3	642	gAt/gGt	12/12	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.892690691076089	2		674	708	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631129	176631129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	71	782	1	ENST00000439151.2:c.1072C>T	p.Arg358Trp	p.R358W	ENST00000439151	NM_022455.4	358	Cgg/Tgg	4/23	1	2	FACETS	0.243	0.212	0.277	0.243	0.212	0.277	SUBCLONAL	1	TRUE	1	0.892690691076089	2		783	655	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023256	27023265	+	frameshift_variant	Frame_Shift_Del	DEL	CCGGCGGCGG	CCGGCGGCGG	-	novel	NA	P-0020914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	157	542	0	ENST00000324856.7:c.363_372del	p.Gly122ValfsTer107	p.G122Vfs*107	ENST00000324856	NM_006015.4	121	cCCGGCGGCGGc/cc	1/20	1	2	FACETS	0.709	0.654	0.765	0.709	0.654	0.765	SUBCLONAL	1	TRUE	1	0.892690691076089	2		542	496	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374210	118374210	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	284	632	0	ENST00000534358.1:c.7603G>C	p.Glu2535Gln	p.E2535Q	ENST00000534358	NM_005933.3	2535	Gag/Cag	27/36	1	2	FACETS	0.99	0.938	1	0.99	0.938	1	CLONAL	1	TRUE	1	0.892690691076089	2		632	643	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839819	27839819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1561942582	NA	P-0020914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	436	898	1	ENST00000328488.2:c.275C>T	p.Ala92Val	p.A92V	ENST00000328488	NM_003533.2	92	gCg/gTg	1/1	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.892690691076089	2		899	904	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891638	151891644	+	frameshift_variant	Frame_Shift_Del	DEL	GTGACAG	GTGACAG	-	novel	NA	P-0020914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	150	556	0	ENST00000262189.6:c.4388_4394del	p.Pro1463LeufsTer19	p.P1463Lfs*19	ENST00000262189	NM_170606.2	1463	cCTGTCACt/ct	29/59	1	2	FACETS	0.884	0.818	0.952	0.884	0.818	0.952	CLONAL	1	TRUE	1	0.892690691076089	2		556	380	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69050718	69050718	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1237289874	NA	P-0020914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	250	798	1	ENST00000288368.4:c.4053C>A	p.Tyr1351Ter	p.Y1351*	ENST00000288368	NM_024870.2	1351	taC/taA	33/40	0.892690691076089	3	FACETS	0.935	0.877	0.995	0.468	0.438	0.498	CLONAL	1	TRUE	1	0.892690691076089	3		799	866	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918642	44918642	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	386	997	0	ENST00000377967.4:c.1125C>A	p.Tyr375Ter	p.Y375*	ENST00000377967	NM_021140.2	375	taC/taA	12/29	0.836472192337685	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.892690691076089	1		997	455	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696431	47696431	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	102	898	1	ENST00000347630.2:c.392G>T	p.Trp131Leu	p.W131L	ENST00000347630	NM_001007230.1	131	tGg/tTg	6/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	1	0.258611959231104	2		899	683	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671462	30671462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	373	1187	1	ENST00000376406.3:c.5498C>T	p.Ser1833Phe	p.S1833F	ENST00000376406	NM_014641.2	1833	tCc/tTc	10/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.567410642256814	2		1188	1294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	245	841	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	0.567410642256814	1	FACETS	0.983	0.926	1	0.983	0.926	1	CLONAL	1	TRUE	0	0.567410642256814	1		841	629	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240362	98240362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767273237	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	91	598	2	ENST00000331920.6:c.1322G>A	p.Arg441His	p.R441H	ENST00000331920	NM_000264.3	441	cGc/cAc	9/24	0.228536187278832	2	FACETS	0.36	0.319	0.404	0.18	0.159	0.202	INDETERMINATE	1	TRUE	0	0.567410642256814	2		600	891	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532825	187532825	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	269	821	0	ENST00000441802.2:c.9568G>T	p.Glu3190Ter	p.E3190*	ENST00000441802	NM_005245.3	3190	Gaa/Taa	14/27	0.567410642256814	1	FACETS	0.958	0.904	1	0.958	0.904	1	CLONAL	1	TRUE	0	0.567410642256814	1		821	709	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950111	44950111	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	245	326	0	ENST00000377967.4:c.3878+2T>G		p.X1293_splice	ENST00000377967	NM_021140.2	1293			1	1	FACETS	0.777	0.74	0.813	1	0.995	1	SUBCLONAL	2	TRUE	0	0.567410642256814	1		326	398	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968219	134968219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759415643	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	323	884	1	ENST00000398015.3:c.2732C>T	p.Thr911Met	p.T911M	ENST00000398015	NM_004441.4	911	aCg/aTg	15/16	0.567410642256814	3	FACETS	1	0.967	1	0.519	0.489	0.549	CLONAL	1	TRUE	1	0.567410642256814	3		885	1409	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961867	41961867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	136	473	0	ENST00000219905.7:c.775C>T	p.Arg259Trp	p.R259W	ENST00000219905	NM_001164273.1	259	Cgg/Tgg	2/24	1	2	FACETS	0.947	0.867	1	0.947	0.867	1	CLONAL	1	TRUE	1	0.567410642256814	2		473	506	SUCCESS
BLM	641	MSKCC	GRCh37	15	91308637	91308637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866243946	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	174	623	0	ENST00000355112.3:c.2186C>T	p.Ser729Phe	p.S729F	ENST00000355112	NM_000057.2	729	tCc/tTc	9/22	1	2	FACETS	0.866	0.8	0.935	0.866	0.8	0.935	CLONAL	1	TRUE	1	0.567410642256814	2		623	708	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686895	117686895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	175	507	0	ENST00000368508.3:c.2822C>T	p.Ser941Phe	p.S941F	ENST00000368508	NM_002944.2	941	tCc/tTc	19/43	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.567410642256814	2		507	615	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589826	212589826	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	262	970	0	ENST00000342788.4:c.716C>T	p.Ser239Leu	p.S239L	ENST00000342788	NM_005235.2	239	tCa/tTa	6/28	1	2	FACETS	0.933	0.875	0.992	0.933	0.875	0.992	CLONAL	1	TRUE	1	0.567410642256814	2		970	990	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149274	119149274	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762677807	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	271	813	1	ENST00000264033.4:c.1282C>T	p.Pro428Ser	p.P428S	ENST00000264033	NM_005188.3	428	Ccc/Tcc	9/16	1	2	FACETS	0.91	0.854	0.967	0.91	0.854	0.967	CLONAL	1	TRUE	1	0.567410642256814	2		814	1050	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145598	24145598	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	304	911	1	ENST00000263121.7:c.617G>A	p.Trp206Ter	p.W206*	ENST00000263121	NM_003073.3	206	tGg/tAg	5/9	0.567410642256814	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.567410642256814	1		912	696	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709102	117709102	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1470291308	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	265	844	2	ENST00000368508.3:c.1855C>T	p.Pro619Ser	p.P619S	ENST00000368508	NM_002944.2	619	Cct/Tct	13/43	1	2	FACETS	0.97	0.911	1	0.97	0.911	1	CLONAL	1	TRUE	1	0.567410642256814	2		846	963	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650051	206650051	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs782081148	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	315	771	0	ENST00000367120.3:c.571C>T	p.Arg191Ter	p.R191*	ENST00000367120	NM_014002.3	191	Cga/Tga	7/22	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.567410642256814	2		771	1012	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471784	120471784	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	220	677	2	ENST00000256646.2:c.3707T>C	p.Leu1236Pro	p.L1236P	ENST00000256646	NM_024408.3	1236	cTt/cCt	23/34	1	2	FACETS	0.947	0.883	1	0.947	0.883	1	CLONAL	1	TRUE	1	0.567410642256814	2		679	819	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099317	193099317	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	188	621	1	ENST00000367435.3:c.251C>T	p.Pro84Leu	p.P84L	ENST00000367435	NM_024529.4	84	cCt/cTt	3/17	1	2	FACETS	0.87	0.805	0.936	0.87	0.805	0.936	CLONAL	1	TRUE	1	0.567410642256814	2		622	762	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204499930	204499930	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	282	749	0	ENST00000367182.3:c.272C>T	p.Ser91Phe	p.S91F	ENST00000367182	NM_001278516.1	91	tCc/tTc	4/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.567410642256814	2		749	937	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622078	43622078	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	227	638	0	ENST00000355710.3:c.3095G>A	p.Gly1032Asp	p.G1032D	ENST00000355710	NM_020975.4	1032	gGc/gAc	19/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.567410642256814	2		638	747	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850981	63850982	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	219	866	5	ENST00000279873.7:c.1759_1760delinsAT	p.Glu587Ile	p.E587I	ENST00000279873	NM_032199.2	587	GAa/ATa	10/10	1	2	FACETS	0.781	0.727	0.838	0.781	0.727	0.838	SUBCLONAL	1	TRUE	1	0.567410642256814	2		871	988	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274650	123274650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1291747099	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	209	677	0	ENST00000358487.5:c.1268C>T	p.Pro423Leu	p.P423L	ENST00000358487	NM_000141.4	423	cCc/cTc	9/18	1	2	FACETS	0.985	0.917	1	0.985	0.917	1	CLONAL	1	TRUE	1	0.567410642256814	2		677	748	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138933	64138933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	211	794	0	ENST00000334205.4:c.2300G>A	p.Gly767Asp	p.G767D	ENST00000334205	NM_003942.2	767	gGc/gAc	17/17	1	2	FACETS	0.832	0.773	0.892	0.832	0.773	0.892	CLONAL	1	TRUE	1	0.567410642256814	2		794	894	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233199	46233199	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	195	606	0	ENST00000334344.6:c.1418C>T	p.Ser473Phe	p.S473F	ENST00000334344	NM_152641.2	473	tCc/tTc	11/21	1	2	FACETS	0.876	0.812	0.941	0.876	0.812	0.941	CLONAL	1	TRUE	1	0.567410642256814	2		606	785	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440421	49440422	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	335	1070	3	ENST00000301067.7:c.4388_4389delinsTT	p.Thr1463Ile	p.T1463I	ENST00000301067	NM_003482.3	1463	aCC/aTT	15/54	1	2	FACETS	0.991	0.937	1	0.991	0.937	1	CLONAL	1	TRUE	1	0.567410642256814	2		1073	1191	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443560	49443561	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	277	915	0	ENST00000301067.7:c.3810_3811del	p.Leu1271IlefsTer14	p.L1271Ifs*14	ENST00000301067	NM_003482.3	1270	tcACta/tcta	11/54	1	2	FACETS	0.953	0.896	1	0.953	0.896	1	CLONAL	1	TRUE	1	0.567410642256814	2		915	1024	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832554	72832554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	224	715	0	ENST00000268489.5:c.4027G>A	p.Asp1343Asn	p.D1343N	ENST00000268489	NM_006885.3	1343	Gat/Aat	9/10	1	2	FACETS	0.997	0.931	1	0.997	0.931	1	CLONAL	1	TRUE	1	0.567410642256814	2		715	792	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577070	7577071	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	300	1091	2	ENST00000269305.4:c.867_868delinsTT	p.Arg290Cys	p.R290C	ENST00000269305	NM_001126112.2	289	ctCCgc/ctTTgc	8/11	0.567410642256814	1	FACETS	0.965	0.913	1	0.965	0.913	1	CLONAL	1	TRUE	0	0.567410642256814	1		1093	785	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256733	19256733	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	348	988	2	ENST00000162023.5:c.980C>G	p.Pro327Arg	p.P327R	ENST00000162023		327	cCc/cGc	13/13	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.567410642256814	2		990	1100	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791278	42791278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	351	1022	2	ENST00000575354.2:c.338C>T	p.Pro113Leu	p.P113L	ENST00000575354	NM_015125.3	113	cCt/cTt	3/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.567410642256814	2		1024	1194	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906751	50906752	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	339	1051	3	ENST00000440232.2:c.1139_1140delinsTT	p.Ala380Val	p.A380V	ENST00000440232	NM_002691.3	380	gCC/gTT	10/27	1	2	FACETS	0.997	0.943	1	0.997	0.943	1	CLONAL	1	TRUE	1	0.567410642256814	2		1054	1199	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967146	25967146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	193	553	0	ENST00000435504.4:c.2060G>A	p.Gly687Glu	p.G687E	ENST00000435504		687	gGa/gAa	13/13	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.567410642256814	2		553	623	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015676	27015676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	271	860	0	ENST00000335756.4:c.263C>T	p.Ala88Val	p.A88V	ENST00000335756	NM_001809.3	88	gCc/gTc	3/5	1	2	FACETS	0.953	0.895	1	0.953	0.895	1	CLONAL	1	TRUE	1	0.567410642256814	2		860	1002	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607369	46607369	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	344	1036	0	ENST00000263734.3:c.1558G>A	p.Asp520Asn	p.D520N	ENST00000263734	NM_001430.4	520	Gat/Aat	12/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.567410642256814	2		1036	1185	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288623	198288623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	361	1094	2	ENST00000335508.6:c.104C>T	p.Ser35Phe	p.S35F	ENST00000335508	NM_012433.2	35	tCt/tTt	2/25	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.567410642256814	2		1096	1265	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546762	9546763	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	39	402	1	ENST00000353224.5:c.1259_1260delinsTT	p.Ser420Phe	p.S420F	ENST00000353224	NM_177990.2	420	tCC/tTT	5/10	0.567410642256814	1	FACETS	0.312	0.259	0.37	0.312	0.259	0.37	SUBCLONAL	1	TRUE	0	0.567410642256814	1		403	316	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024015	31024015	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	298	811	0	ENST00000375687.4:c.3500C>T	p.Pro1167Leu	p.P1167L	ENST00000375687	NM_015338.5	1167	cCc/cTc	13/13	1	2	FACETS	0.99	0.933	1	0.99	0.933	1	CLONAL	1	TRUE	1	0.567410642256814	2		811	1061	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513337	44513337	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	423	947	4	ENST00000291552.4:c.598C>T	p.Arg200Trp	p.R200W	ENST00000291552	NM_006758.2	200	Cgg/Tgg	8/8	0.222003277434825	3	FACETS	0.812	0.775	0.85	0.812	0.775	0.85	INDETERMINATE	2	TRUE	1	0.567410642256814	3		951	1178	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565526	41565526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	275	725	1	ENST00000263253.7:c.4192C>T	p.Leu1398Phe	p.L1398F	ENST00000263253	NM_001429.3	1398	Ctc/Ttc	26/31	0.567410642256814	1	FACETS	0.996	0.941	1	0.996	0.941	1	CLONAL	1	TRUE	0	0.567410642256814	1		726	697	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924754	49924754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	341	974	0	ENST00000296474.3:c.4189C>T	p.Pro1397Ser	p.P1397S	ENST00000296474	NM_002447.2	1397	Cct/Tct	20/20	0.567410642256814	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.567410642256814	1		974	851	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502849	186502849	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	598	794	2	ENST00000323963.5:c.307C>T	p.Gln103Ter	p.Q103*	ENST00000323963		103	Caa/Taa	4/11	0.567410642256814	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	1	0.567410642256814	3		796	1210	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1953910	1953910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	387	1140	2	ENST00000382891.5:c.2089C>T	p.Leu697Phe	p.L697F	ENST00000382891	NM_133335.3	697	Ctt/Ttt	11/22	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.567410642256814	2		1142	1351	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564559	55564560	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	242	824	0	ENST00000288135.5:c.447_448delinsAA	p.Gly150Arg	p.G150R	ENST00000288135	NM_000222.2	149	aaGGgg/aaAAgg	3/21	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.567410642256814	2		824	846	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067041	143067041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	261	716	0	ENST00000262992.4:c.1672G>A	p.Gly558Arg	p.G558R	ENST00000262992	NM_001101669.1	558	Gga/Aga	16/24	0.567410642256814	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.567410642256814	1		716	655	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226130	226130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	362	1162	0	ENST00000264932.6:c.589G>A	p.Gly197Ser	p.G197S	ENST00000264932	NM_004168.2	197	Ggc/Agc	5/15	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.567410642256814	2		1162	1273	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293754	1293754	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	349	1138	1	ENST00000310581.5:c.1247G>T	p.Arg416Leu	p.R416L	ENST00000310581	NM_198253.2	416	cGa/cTa	2/16	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.567410642256814	2		1139	1204	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875613	35875613	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	172	573	0	ENST00000303115.3:c.801-1G>T		p.X267_splice	ENST00000303115	NM_002185.3	267			1	2	FACETS	0.846	0.78	0.913	0.846	0.78	0.913	CLONAL	1	TRUE	1	0.567410642256814	2		573	717	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271443	38271443	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	365	925	0	ENST00000425967.3:c.2378C>T	p.Ser793Phe	p.S793F	ENST00000425967	NM_001174067.1	793	tCc/tTc	18/19	0.567410642256814	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.567410642256814	1		925	825	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992708	68992708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	309	956	0	ENST00000288368.4:c.1673C>T	p.Pro558Leu	p.P558L	ENST00000288368	NM_024870.2	558	cCc/cTc	16/40	0.222003277434825	3	FACETS	1	0.981	1	0.546	0.514	0.578	INDETERMINATE	1	TRUE	1	0.567410642256814	3		956	1281	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561529	141561529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1177813535	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	294	623	0	ENST00000220592.5:c.1276G>A	p.Ala426Thr	p.A426T	ENST00000220592	NM_012154.3	426	Gct/Act	11/19	0.222003277434825	3	FACETS	0.832	0.787	0.879	0.832	0.787	0.879	INDETERMINATE	2	TRUE	1	0.567410642256814	3		623	799	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090464	5090464	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	152	463	1	ENST00000381652.3:c.2780T>C	p.Leu927Ser	p.L927S	ENST00000381652	NM_004972.3	927	tTa/tCa	21/25	0.567410642256814	1	FACETS	0.903	0.834	0.973	0.903	0.834	0.973	CLONAL	1	TRUE	0	0.567410642256814	1		464	425	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908819	101908819	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	164	729	0	ENST00000374994.4:c.1183T>C	p.Ser395Pro	p.S395P	ENST00000374994	NM_004612.2	395	Tcc/Ccc	7/9	0.228536187278832	2	FACETS	0.618	0.567	0.671	0.309	0.283	0.336	INDETERMINATE	1	TRUE	0	0.567410642256814	2		729	935	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417527	139417527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	584	1300	2	ENST00000277541.6:c.517C>T	p.Pro173Ser	p.P173S	ENST00000277541	NM_017617.3	173	Ccc/Tcc	4/34	0.228536187278832	2	FACETS	1	0.997	1	0.699	0.672	0.726	INDETERMINATE	1	TRUE	0	0.567410642256814	2		1302	1473	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240762	53240762	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	361	541	1	ENST00000375401.3:c.1318T>C	p.Tyr440His	p.Y440H	ENST00000375401	NM_004187.3	440	Tat/Cat	10/26	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.567410642256814	1		542	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0020921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	588	733	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.280552677096321	4	FACETS	0.968	0.939	0.997	1	0.997	1	CLONAL	6	FALSE	0	0.280552677096321	4		733	924	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0020921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	148	303	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.280552677096321	4	FACETS	1	0.97	1	1	0.99	1	CLONAL	3	FALSE	2	0.280552677096321	4		304	408	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582445	119582445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762651036	NA	P-0020921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	61	325	0	ENST00000316626.5:c.956G>A	p.Arg319Gln	p.R319Q	ENST00000316626		319	cGa/cAa	10/12	0.280552677096321	3	FACETS	1	0.968	1	0.712	0.618	0.814	CLONAL	1	FALSE	1	0.280552677096321	3		325	348	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40865275	40865275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	101	1044	0	ENST00000428826.2:c.1156G>A	p.Gly386Arg	p.G386R	ENST00000428826		386	Gga/Aga	11/21	0.280552677096321	5	FACETS	1	0.965	1	0.398	0.355	0.444	CLONAL	1	FALSE	2	0.280552677096321	5		1044	857	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62318991	62318991	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs759740295	NA	P-0020921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	56	974	0	ENST00000360203.5:c.1349G>A	p.Gly450Glu	p.G450E	ENST00000360203	NM_001283009.1	450	gGg/gAg	17/35	0.280552677096321	3	FACETS	0.737	0.631	0.853	0.368	0.315	0.427	SUBCLONAL	1	FALSE	1	0.280552677096321	3		974	618	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702531	52702531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	110	773	0	ENST00000394830.3:c.367G>A	p.Ala123Thr	p.A123T	ENST00000394830	NM_018313.4	123	Gca/Aca	4/30	0.280552677096321	4	FACETS	1	0.981	1	0.709	0.638	0.785	CLONAL	1	FALSE	2	0.280552677096321	4		773	708	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851612	128851612	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs757625155	NA	P-0020921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	82	857	2	ENST00000249373.3:c.1936+1G>A		p.X646_splice	ENST00000249373	NM_005631.4	646			0.280552677096321	5	FACETS	1	0.951	1	0.575	0.507	0.649	CLONAL	1	FALSE	3	0.280552677096321	5		859	722	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97879644	97879644	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	91	699	0	ENST00000289081.3:c.1025C>T	p.Pro342Leu	p.P342L	ENST00000289081	NM_000136.2	342	cCt/cTt	11/15	0.280552677096321	5	FACETS	1	0.975	1	0.454	0.403	0.508	CLONAL	1	FALSE	2	0.280552677096321	5		699	677	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855044	76855047	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TTCT	TTCT	-	novel	NA	P-0020921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	171	635	0	ENST00000373344.5:c.5789_5792del	p.Lys1930ArgfsTer24	p.K1930Rfs*24	ENST00000373344	NM_000489.3	1930	aAGAAg/ag	25/35	0.280552677096321	3	FACETS	0.861	0.798	0.927	1	0.986	1	CLONAL	3	FALSE	1	0.280552677096321	3		635	538	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	99	613	1	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	0.230405679406733	2		614	763	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440943	56440943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786205215	NA	P-0020922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	79	837	4	ENST00000407977.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000407977		132	Cga/Tga	4/10	1	2	FACETS	0.867	0.762	0.98	0.867	0.762	0.98	CLONAL	1	TRUE	1	0.230405679406733	2		841	791	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275669	41275669	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764576683	NA	P-0020922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	76	702	1	ENST00000349496.5:c.1564G>A	p.Ala522Thr	p.A522T	ENST00000349496	NM_001904.3	522	Gca/Aca	10/15	1	2	FACETS	0.948	0.831	1	0.948	0.831	1	CLONAL	1	TRUE	1	0.230405679406733	2		703	696	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106504	27106505	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	95	930	0	ENST00000324856.7:c.6117dup	p.Gly2040ArgfsTer59	p.G2040Rfs*59	ENST00000324856	NM_006015.4	2039	caa/cAaa	20/20	1	2	FACETS	0.936	0.832	1	0.936	0.832	1	CLONAL	1	TRUE	1	0.230405679406733	2		930	881	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107994	30107994	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	98	838	0	ENST00000331968.5:c.813C>G	p.His271Gln	p.H271Q	ENST00000331968	NM_002742.2	271	caC/caG	5/18	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.230405679406733	2		838	780	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143176	30143176	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201290745	NA	P-0020922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	69	833	0	ENST00000389048.3:c.350C>T	p.Pro117Leu	p.P117L	ENST00000389048	NM_004304.4	117	cCg/cTg	1/29	1	2	FACETS	0.877	0.763	1	0.877	0.763	1	CLONAL	1	TRUE	1	0.230405679406733	2		833	683	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412970	49412970	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	109	1018	0	ENST00000418115.1:c.53A>C	p.Lys18Thr	p.K18T	ENST00000418115	NM_001664.2	18	aAg/aCg	2/5	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.230405679406733	2		1018	816	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0020924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	62	857	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.229941583896835	4	FACETS	0.687	0.593	0.79	0.344	0.296	0.395	SUBCLONAL	1	TRUE	2	0.358933351848566	4		857	683	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873660	35873660	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs201559094	NA	P-0020924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	58	561	2	ENST00000303115.3:c.616C>T	p.Arg206Ter	p.R206*	ENST00000303115	NM_002185.3	206	Cga/Tga	5/8	0.208501817464085	4	FACETS	0.885	0.762	1	0.443	0.381	0.51	INDETERMINATE	1	TRUE	2	0.358933351848566	4		563	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0020926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	482	584	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.423389506659742	3	FACETS	1	0.994	1	0.789	0.759	0.82	CLONAL	2	TRUE	0	0.53046155114775	3		585	971	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0020926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	9	719	2	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.532844543920223	1	FACETS	0.112	0.074	0.161	0.112	0.074	0.161	SUBCLONAL	1	TRUE	0	0.53046155114775	1		721	222	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778425	3778436	+	inframe_deletion	In_Frame_Del	DEL	TGTTGCTGCTGC	TGTTGCTGCTGC	-	rs750150018	NA	P-0020926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	100	1134	0	ENST00000262367.5:c.6612_6623del	p.Gln2213_Gln2216del	p.Q2213_Q2216del	ENST00000262367	NM_004380.2	2204	caGCAGCAGCAACAa/caa	31/31	0.53046155114775	2	FACETS	0.552	0.493	0.614	0.276	0.246	0.307	SUBCLONAL	1	TRUE	0	0.53046155114775	2		1134	683	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494588	2494588	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs377222246	NA	P-0020926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	60	870	0	ENST00000355716.4:c.728G>A	p.Arg243Gln	p.R243Q	ENST00000355716	NM_003820.2	243	cGg/cAg	8/8	0.346454046002497	3	FACETS	0.373	0.321	0.431	0.124	0.107	0.144	SUBCLONAL	1	TRUE	0	0.53046155114775	3		870	767	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200918	67200918	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	88	1009	0	ENST00000312629.5:c.906G>C	p.Lys302Asn	p.K302N	ENST00000312629	NM_003952.2	302	aaG/aaC	10/15	1	2	FACETS	0.351	0.31	0.395	0.351	0.31	0.395	SUBCLONAL	1	TRUE	1	0.53046155114775	2		1009	945	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597444	10597444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866539542	NA	P-0020926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	305	1215	2	ENST00000171111.5:c.1759G>A	p.Asp587Asn	p.D587N	ENST00000171111	NM_203500.1	587	Gat/Aat	6/6	0.532844543920223	3	FACETS	0.981	0.923	1	0.491	0.461	0.521	CLONAL	1	TRUE	1	0.53046155114775	3		1217	1483	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0020937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	29	853	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.51	0.408	0.626	0.51	0.408	0.626	SUBCLONAL	1	TRUE	1	0.21	2		853	542	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562637	21562637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758639228	NA	P-0020937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	73	709	1	ENST00000382592.4:c.1282G>A	p.Ala428Thr	p.A428T	ENST00000382592	NM_014572.2	428	Gcc/Acc	4/8	1	2	FACETS	0.856	0.748	0.974	0.856	0.748	0.974	CLONAL	1	TRUE	1	0.21	2		710	812	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845586	63845596	+	frameshift_variant	Frame_Shift_Del	DEL	AACGCATCAAA	AACGCATCAAA	GTTC	novel	NA	P-0020937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	27	537	2	ENST00000279873.7:c.1325_1335delinsGTTC	p.Lys442SerfsTer35	p.K442Sfs*35	ENST00000279873	NM_032199.2	442	aAACGCATCAAA/aGTTC	9/10	1	2	FACETS	0.587	0.466	0.725	0.587	0.466	0.725	SUBCLONAL	1	TRUE	1	0.21	2		539	438	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720851	89720851	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	60	698	0	ENST00000371953.3:c.1003del	p.Arg335AspfsTer9	p.R335Dfs*9	ENST00000371953	NM_000314.4	334	aaC/aa	8/9	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.21	2		698	563	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274770	123274771	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCAGTAAATGGCTATCT	novel	NA	P-0020937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	62	1016	0	ENST00000358487.5:c.1130_1147dup	p.Cys382_Ile383insLysIleAlaIleTyrCys	p.C382_I383insKIAIYC	ENST00000358487	NM_000141.4	383	ata/aAGATAGCCATTTACTGCAta	9/18	1	2	FACETS	0.645	0.555	0.742	0.645	0.555	0.742	SUBCLONAL	1	TRUE	1	0.21	2		1016	916	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589627	67589630	+	frameshift_variant	Frame_Shift_Del	DEL	GATA	GATA	-	novel	NA	P-0020937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	48	615	0	ENST00000274335.5:c.1393_1396del	p.Arg465TyrfsTer14	p.R465Yfs*14	ENST00000274335		464	GATAga/ga	10/15	1	2	FACETS	0.989	0.837	1	0.989	0.837	1	CLONAL	1	TRUE	1	0.21	2		615	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs879253911	NA	P-0020938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	32	706	0	ENST00000269305.4:c.538G>T	p.Glu180Ter	p.E180*	ENST00000269305	NM_001126112.2	180	Gag/Tag	5/11	1	2	FACETS	0.91	0.742	1	0.91	0.742	1	CLONAL	1	FALSE	1	0.270555172788988	2		706	260	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577330	64577333	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	rs587776841	NA	P-0020939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	533	792	0	ENST00000312049.6:c.249_252del	p.Ile85SerfsTer33	p.I85Sfs*33	ENST00000312049	NM_130799.2	83	ctGTCT/ct	2/10	0.908858994615095	1	FACETS	0.983	0.961	1	0.983	0.961	1	CLONAL	1	TRUE	0	0.908858994615095	1		792	651	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289247	33289247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1455644209	NA	P-0020939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	446	547	1	ENST00000374542.5:c.305C>T	p.Ser102Leu	p.S102L	ENST00000374542	NM_001141970.1	102	tCg/tTg	3/8	0.908858994615095	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.908858994615095	1		548	522	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435542	18435542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223716645	NA	P-0020939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	132	319	0	ENST00000266497.5:c.527C>T	p.Pro176Leu	p.P176L	ENST00000266497		176	cCt/cTt	1/31	0.461368595755189	1	FACETS	0.349	0.319	0.38	0.349	0.319	0.38	INDETERMINATE	1	TRUE	0	0.908858994615095	1		319	454	SUCCESS
MET	4233	MSKCC	GRCh37	7	116422139	116422139	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	461	580	0	ENST00000397752.3:c.3620C>T	p.Ala1207Val	p.A1207V	ENST00000397752	NM_000245.2	1207	gCa/gTa	18/21	1	2	FACETS	0.962	0.923	1	0.962	0.923	1	CLONAL	1	TRUE	1	0.908858994615095	2		580	1054	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0020941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	264	717	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.203177203447601	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.203177203447601	2		717	1153	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0020941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	98	169	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.907	0.811	1	1	0.986	1	CLONAL	2	TRUE	1	0.203177203447601	2		169	532	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	174	993	2	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.185629208731069	3	FACETS	0.791	0.727	0.858	0.791	0.727	0.858	SUBCLONAL	2	TRUE	1	0.203177203447601	3		995	1193	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566460	41566460	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	216	782	0	ENST00000263253.7:c.4337A>G	p.Tyr1446Cys	p.Y1446C	ENST00000263253	NM_001429.3	1446	tAt/tGt	27/31	0.185629208731069	3	FACETS	0.888	0.827	0.951	1	0.989	1	CLONAL	3	TRUE	1	0.203177203447601	3		782	879	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007128	152007128	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	121	917	0	ENST00000262189.6:c.772T>C	p.Trp258Arg	p.W258R	ENST00000262189	NM_170606.2	258	Tgg/Cgg	6/59	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.203177203447601	2		917	838	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0020943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	217	912	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.511382832477352	3	FACETS	0.914	0.856	0.973	0.914	0.856	0.973	CLONAL	2	FALSE	1	0.511382832477352	3		912	583	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115715	8115715	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	161	476	0	ENST00000346208.3:c.1061del	p.Leu354ArgfsTer3	p.L354Rfs*3	ENST00000346208		354	cTg/cg	6/6	0.511382832477352	4	FACETS	0.856	0.789	0.924	0.856	0.789	0.924	CLONAL	2	FALSE	2	0.511382832477352	4		476	556	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118896	115118896	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	60	538	0	ENST00000257566.3:c.445T>A	p.Tyr149Asn	p.Y149N	ENST00000257566	NM_016569.3	149	Tac/Aac	2/8	0.443665217024972	3	FACETS	0.556	0.479	0.639	0.278	0.239	0.32	SUBCLONAL	1	FALSE	1	0.511382832477352	3		538	530	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063386	67063386	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	255	661	0	ENST00000412916.2:c.76G>T	p.Glu26Ter	p.E26*	ENST00000412916		26	Gag/Tag	1/6	0.394442174784492	3	FACETS	1	0.988	1	0.772	0.73	0.814	CLONAL	2	FALSE	0	0.511382832477352	3		661	541	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0020944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	55	1002	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.977	0.836	1	0.977	0.836	1	CLONAL	1	TRUE	1	0.2	2		1002	563	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207162	1207162	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs137853076	NA	P-0020944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	76	1119	0	ENST00000326873.7:c.250A>T	p.Lys84Ter	p.K84*	ENST00000326873	NM_000455.4	84	Aag/Tag	1/10	1	2	FACETS	0.785	0.687	0.891	0.785	0.687	0.891	SUBCLONAL	1	TRUE	1	0.2	2		1119	968	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221975	1221975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568710381	NA	P-0020944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	67	1127	0	ENST00000326873.7:c.890G>A	p.Arg297Lys	p.R297K	ENST00000326873	NM_000455.4	297	aGg/aAg	7/10	1	2	FACETS	0.755	0.654	0.864	0.755	0.654	0.864	SUBCLONAL	1	TRUE	1	0.2	2		1127	888	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287468	46287469	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	30	599	0	ENST00000334344.6:c.5333dup	p.Asn1778LysfsTer4	p.N1778Kfs*4	ENST00000334344	NM_152641.2	1776	tta/ttAa	20/21	1	2	FACETS	0.637	0.512	0.779	0.637	0.512	0.779	SUBCLONAL	1	TRUE	1	0.2	2		599	471	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134364	41134364	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	53	623	0	ENST00000379561.5:c.1264C>T	p.Gln422Ter	p.Q422*	ENST00000379561	NM_002015.3	422	Caa/Taa	2/3	1	2	FACETS	0.895	0.763	1	0.895	0.763	1	CLONAL	1	TRUE	1	0.2	2		623	592	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986783	36986784	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	25	356	0	ENST00000354822.5:c.905dup	p.Ala304CysfsTer135	p.A304Cfs*135	ENST00000354822	NM_001079668.2	302	gcg/gcCg	3/3	1	2	FACETS	0.926	0.732	1	0.926	0.732	1	CLONAL	1	TRUE	1	0.2	2		356	270	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295077	1295098	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCTCGGCAGCGGGGAGCGCG	CGGCTCGGCAGCGGGGAGCGCG	-	novel	NA	P-0020944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	21	217	0	ENST00000310581.5:c.7_28del	p.Arg3CysfsTer68	p.R3Cfs*68	ENST00000310581	NM_198253.2	3	CGCGCTCCCCGCTGCCGAGCCGtg/tg	1/16	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.2	2		217	166	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477806	140477806	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs180177039	NA	P-0020944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	40	782	0	ENST00000288602.6:c.1502A>T	p.Glu501Val	p.E501V	ENST00000288602	NM_004333.4	501	gAa/gTa	12/18	1	2	FACETS	0.786	0.653	0.934	0.786	0.653	0.934	CLONAL	1	TRUE	1	0.2	2		782	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	54	1249	0	ENST00000269305.4:c.377A>C	p.Tyr126Ser	p.Y126S	ENST00000269305	NM_001126112.2	126	tAc/tCc	5/11	1	2	FACETS	0.266	0.226	0.31	0.266	0.226	0.31	SUBCLONAL	1	TRUE	1	0.34016770139276	2		1249	1195	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781844	9781844	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	128	1183	0	ENST00000377346.4:c.1981G>T	p.Ala661Ser	p.A661S	ENST00000377346	NM_005026.3	661	Gcc/Tcc	16/24	1	2	FACETS	0.622	0.562	0.686	0.622	0.562	0.686	SUBCLONAL	1	TRUE	1	0.34016770139276	2		1183	1209	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435527	18435527	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	22	369	0	ENST00000266497.5:c.512T>C	p.Phe171Ser	p.F171S	ENST00000266497		171	tTt/tCt	1/31	1	2	FACETS	0.328	0.254	0.415	0.328	0.254	0.415	SUBCLONAL	1	TRUE	1	0.34016770139276	2		369	394	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424177	49424178	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	39	690	0	ENST00000301067.7:c.13884_13885insT	p.Thr4629TyrfsTer18	p.T4629Yfs*18	ENST00000301067	NM_003482.3	4628	-/T	42/54	1	2	FACETS	0.357	0.295	0.426	0.357	0.295	0.426	SUBCLONAL	1	TRUE	1	0.34016770139276	2		690	643	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012592	36012592	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	40	920	2	ENST00000358208.4:c.36C>G	p.Ser12Arg	p.S12R	ENST00000358208		12	agC/agG	2/12	1	2	FACETS	0.303	0.25	0.361	0.303	0.25	0.361	SUBCLONAL	1	TRUE	1	0.34016770139276	2		922	777	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973958	55973958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769193899	NA	P-0020945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	51	936	1	ENST00000263923.4:c.1358C>T	p.Pro453Leu	p.P453L	ENST00000263923	NM_002253.2	453	cCg/cTg	10/30	1	2	FACETS	0.361	0.306	0.422	0.361	0.306	0.422	SUBCLONAL	1	TRUE	1	0.34016770139276	2		937	831	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639068	176639068	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	51	845	0	ENST00000439151.2:c.3668A>G	p.His1223Arg	p.H1223R	ENST00000439151	NM_022455.4	1223	cAt/cGt	5/23	1	2	FACETS	0.387	0.328	0.452	0.387	0.328	0.452	SUBCLONAL	1	TRUE	1	0.34016770139276	2		845	775	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004220	150004220	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	34	560	0	ENST00000253339.5:c.2005A>T	p.Met669Leu	p.M669L	ENST00000253339		669	Atg/Ttg	3/7	1	2	FACETS	0.337	0.275	0.408	0.337	0.275	0.408	SUBCLONAL	1	TRUE	1	0.34016770139276	2		560	593	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891654	151891654	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0020945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	25	398	2	ENST00000262189.6:c.4379-1G>T		p.X1460_splice	ENST00000262189	NM_170606.2	1460			1	2	FACETS	0.379	0.298	0.472	0.379	0.298	0.472	SUBCLONAL	1	TRUE	1	0.34016770139276	2		400	388	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69011949	69011950	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0020945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	66	1190	0	ENST00000288368.4:c.2588_2589del	p.Phe863CysfsTer12	p.F863Cfs*12	ENST00000288368	NM_024870.2	862	caTTtt/catt	23/40	1	2	FACETS	0.326	0.281	0.374	0.326	0.281	0.374	SUBCLONAL	1	TRUE	1	0.34016770139276	2		1190	1191	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926885	112926885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507544	NA	P-0020949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	253	882	0	ENST00000351677.2:c.1505C>T	p.Ser502Leu	p.S502L	ENST00000351677	NM_002834.3	502	tCa/tTa	13/16	0.203658738951388	3	FACETS	0.798	0.748	0.85	0.798	0.748	0.85	INDETERMINATE	2	TRUE	1	0.406098646417612	3		882	939	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0020949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	29	126	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.406098646417612	2		126	117	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486101	29486101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199474728	NA	P-0020949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	88	684	0	ENST00000356175.3:c.278G>A	p.Cys93Tyr	p.C93Y	ENST00000356175	NM_000267.3	93	tGt/tAt	3/57	0.406098646417612	1	FACETS	0.771	0.686	0.861	0.771	0.686	0.861	SUBCLONAL	1	TRUE	0	0.406098646417612	1		684	448	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938785	76938788	+	frameshift_variant	Frame_Shift_Del	DEL	TTCG	TTCG	-	novel	NA	P-0020949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	148	508	0	ENST00000373344.5:c.1960_1963del	p.Arg654AspfsTer5	p.R654Dfs*5	ENST00000373344	NM_000489.3	654	CGAAga/ga	9/35	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.406098646417612	1		508	413	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0020951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	235	651	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.317082071726921	2	FACETS	0.974	0.912	1	0.974	0.912	1	CLONAL	2	TRUE	0	0.317082071726921	2		651	761	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115952	8115953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	76	539	0	ENST00000346208.3:c.1300dup	p.His434ProfsTer73	p.H434Pfs*73	ENST00000346208		433	cac/caCc	6/6	0.317082071726921	3	FACETS	0.918	0.806	1	0.459	0.403	0.52	CLONAL	1	TRUE	1	0.317082071726921	3		539	605	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685315	89685315	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0020951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	131	618	0	ENST00000371953.3:c.209+1G>C		p.X70_splice	ENST00000371953	NM_000314.4	70			NA	2	FACETS	0.943	0.863	1			1	INDETERMINATE	2	TRUE	NA	0.317082071726921	2		618	438	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863342	56863342	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	81	465	0	ENST00000519728.1:c.486A>C	p.Lys162Asn	p.K162N	ENST00000519728	NM_002350.3	162	aaA/aaC	6/13	0.317082071726921	3	FACETS	1	0.944	1	0.559	0.494	0.63	CLONAL	1	TRUE	1	0.317082071726921	3		465	529	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	99	372	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.624231009119846	3	FACETS	0.933	0.851	1	0.933	0.851	1	CLONAL	2	TRUE	1	0.624231009119846	3		373	223	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0020952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	232	880	1	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	0.624231009119846	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.624231009119846	1		881	501	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041266	47041266	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0020952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	216	531	2	ENST00000377604.3:c.1693+1G>A		p.X565_splice	ENST00000377604	NM_001204468.1	565			1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.624231009119846	1		533	384	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138473	11138473	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	98	659	1	ENST00000358026.2:c.3229C>T	p.Arg1077Ter	p.R1077*	ENST00000358026	NM_001128849.1	1077	Cga/Tga	24/36	0.499989997831806	1	FACETS	0.514	0.462	0.57	0.514	0.462	0.57	SUBCLONAL	1	TRUE	0	0.624231009119846	1		660	420	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643807	38643807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	248	949	2	ENST00000299084.4:c.1277G>T	p.Cys426Phe	p.C426F	ENST00000299084	NM_152594.2	426	tGc/tTc	7/7	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.624231009119846	2		951	760	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936345	49936345	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	77	583	0	ENST00000296474.3:c.1503T>A	p.Asp501Glu	p.D501E	ENST00000296474	NM_002447.2	501	gaT/gaA	3/20	0.520230913862408	1	FACETS	0.324	0.286	0.365	0.324	0.286	0.365	SUBCLONAL	1	TRUE	0	0.773088754219026	1		583	377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578376	7578379	+	frameshift_variant	Frame_Shift_Del	DEL	CTAT	CTAT	-	novel	NA	P-0020954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	182	736	0	ENST00000269305.4:c.551_554del	p.Asp184AlafsTer62	p.D184Afs*62	ENST00000269305	NM_001126112.2	184	gATAGc/gc	5/11	0.3544783593832	2	FACETS	0.952	0.885	1	0.952	0.885	1	CLONAL	2	TRUE	0	0.369004496525209	2		736	518	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268766	41268766	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	156	787	2	ENST00000349496.5:c.1004A>T	p.Lys335Ile	p.K335I	ENST00000349496	NM_001904.3	335	aAa/aTa	7/15	0.369004496525209	2	FACETS	0.905	0.836	0.976	0.905	0.836	0.976	CLONAL	2	TRUE	0	0.369004496525209	2		789	467	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278106	41278106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	159	607	1	ENST00000349496.5:c.1982G>A	p.Arg661Gln	p.R661Q	ENST00000349496	NM_001904.3	661	cGa/cAa	13/15	0.369004496525209	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.369004496525209	2		608	413	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651532	52651532	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	137	692	2	ENST00000394830.3:c.1564C>T	p.Arg522Ter	p.R522*	ENST00000394830	NM_018313.4	522	Cga/Tga	15/30	0.369004496525209	2	FACETS	0.912	0.838	0.988	0.912	0.838	0.988	CLONAL	2	TRUE	0	0.369004496525209	2		694	407	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0020954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	138	417	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.297802020349017	4	FACETS	0.943	0.862	1	0.943	0.862	1	CLONAL	2	TRUE	2	0.369004496525209	4		418	543	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220717	1220717	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587782018	NA	P-0020955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	306	744	3	ENST00000326873.7:c.734+1G>T		p.X245_splice	ENST00000326873	NM_000455.4	245			0.346021876433942	3	FACETS	0.9	0.853	0.947	0.9	0.853	0.947	CLONAL	3	TRUE	0	0.360201192217493	3		747	743	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657313	29657313	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0020955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	102	670	1	ENST00000356175.3:c.5547-1G>T		p.X1849_splice	ENST00000356175	NM_000267.3	1849			0.341181931064494	3	FACETS	0.89	0.796	0.99	0.445	0.398	0.495	CLONAL	1	TRUE	1	0.360201192217493	3		671	751	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143289	108143291	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0020955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	188	595	0	ENST00000278616.4:c.3108_3110del	p.Ser1037del	p.S1037del	ENST00000278616	NM_000051.3	1036	ttCTCt/ttt	21/63	0.322196604730611	2	FACETS	0.97	0.903	1	0.97	0.903	1	CLONAL	2	TRUE	0	0.360201192217493	2		595	538	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335623	73335623	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	63	444	1	ENST00000377767.4:c.2548G>T	p.Ala850Ser	p.A850S	ENST00000377767	NM_014953.3	850	Gcc/Tcc	19/21	0.341181931064494	3	FACETS	0.826	0.715	0.945	0.413	0.357	0.473	CLONAL	1	TRUE	1	0.360201192217493	3		445	500	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349420	73349420	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	91	692	0	ENST00000377767.4:c.916T>C	p.Ser306Pro	p.S306P	ENST00000377767	NM_014953.3	306	Tct/Cct	6/21	0.341181931064494	3	FACETS	0.834	0.74	0.934	0.417	0.37	0.467	CLONAL	1	TRUE	1	0.360201192217493	3		692	715	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483016	29483016	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	165	589	0	ENST00000356175.3:c.76G>T	p.Gly26Ter	p.G26*	ENST00000356175	NM_000267.3	26	Gga/Tga	2/57	0.341181931064494	3	FACETS	0.96	0.887	1	0.96	0.887	1	CLONAL	2	TRUE	1	0.360201192217493	3		589	563	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727066	40727066	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	89	585	0	ENST00000373198.4:c.3898G>T	p.Ala1300Ser	p.A1300S	ENST00000373198	NM_133170.3	1300	Gcc/Tcc	28/32	0.344823157091454	4	FACETS	0.974	0.864	1	0.325	0.288	0.364	CLONAL	1	TRUE	1	0.360201192217493	4		585	690	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339481	81339481	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	169	647	0	ENST00000222390.5:c.1523T>A	p.Met508Lys	p.M508K	ENST00000222390	NM_000601.4	508	aTg/aAg	13/18	0.336194195039823	2	FACETS	0.879	0.813	0.946	0.879	0.813	0.946	CLONAL	2	TRUE	0	0.360201192217493	2		647	534	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044925	47044925	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	300	509	3	ENST00000377604.3:c.2251G>T	p.Glu751Ter	p.E751*	ENST00000377604	NM_001204468.1	751	Gag/Tag	20/24	0.323853945664267	2	FACETS	0.951	0.905	0.996			1	CLONAL	3	TRUE	NA	0.360201192217493	2		512	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	906	1096	0	ENST00000269305.4:c.470T>G	p.Val157Gly	p.V157G	ENST00000269305	NM_001126112.2	157	gTc/gGc	5/11	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	2	TRUE	NA	0.753838965646142	2		1096	1199	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821080	72821080	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	398	929	0	ENST00000268489.5:c.11095G>C	p.Asp3699His	p.D3699H	ENST00000268489	NM_006885.3	3699	Gac/Cac	10/10	0.753838965646142	3	FACETS	0.885	0.839	0.931	0.442	0.419	0.466	CLONAL	1	TRUE	1	0.753838965646142	3		929	1643	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114342	143114392	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGAGCATCTGGAGTAGAAACAGACAAGGAGATGAACACTTTGCAAACATTT	AGAGCATCTGGAGTAGAAACAGACAAGGAGATGAACACTTTGCAAACATTT	-	novel	NA	P-0020958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	136	650	0	ENST00000262992.4:c.1073-44_1079del		p.X358_splice	ENST00000262992	NM_001101669.1	358		13/24	0.753838965646142	2	FACETS	0.591	0.539	0.645	0.295	0.269	0.323	SUBCLONAL	1	TRUE	0	0.753838965646142	2		650	611	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200084	138200084	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1042443197	NA	P-0020958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	241	567	0	ENST00000237289.4:c.1502C>A	p.Ala501Asp	p.A501D	ENST00000237289	NM_001270507.1	501	gCc/gAc	7/9	0.753838965646142	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.753838965646142	1		567	389	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964418	70964418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1040334034	NA	P-0020958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	604	696	2	ENST00000276594.2:c.1610G>A	p.Arg537Gln	p.R537Q	ENST00000276594	NM_024504.3	537	cGg/cAg	8/8	0.696592997651572	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.753838965646142	3		698	1059	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072541	5072541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368927897	NA	P-0020958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	291	675	2	ENST00000381652.3:c.1691G>A	p.Arg564Gln	p.R564Q	ENST00000381652	NM_004972.3	564	cGa/cAa	13/25	1	2	FACETS	0.913	0.862	0.965	0.913	0.862	0.965	CLONAL	1	TRUE	1	0.753838965646142	2		677	846	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76931752	76931752	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	469	932	1	ENST00000373344.5:c.3778G>A	p.Asp1260Asn	p.D1260N	ENST00000373344	NM_000489.3	1260	Gat/Aat	10/35	0.606696627541991	3	FACETS	1	0.983	1	0.53	0.505	0.555	CLONAL	1	TRUE	1	0.753838965646142	3		933	1617	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	72	613	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	0.408076937767303	2		614	311	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0020960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	144	245	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.408076937767303	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.408076937767303	1		245	553	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015732	112015732	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0020960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	60	442	0	ENST00000368678.4:c.1111-1G>A		p.X371_splice	ENST00000368678		371			1	2	FACETS	0.826	0.715	0.945	0.826	0.715	0.945	CLONAL	1	TRUE	1	0.408076937767303	2		442	356	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206782	27206782	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	103	449	0	ENST00000380036.4:c.2567G>A	p.Arg856Lys	p.R856K	ENST00000380036	NM_000459.3	856	aGa/aAa	15/23	0.408076937767303	6	FACETS	1	0.974	1	0.257	0.23	0.286	CLONAL	1	TRUE	1	0.408076937767303	6		449	714	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950040	44950041	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	54	321	0	ENST00000377967.4:c.3811dup	p.Val1271GlyfsTer20	p.V1271Gfs*20	ENST00000377967	NM_021140.2	1270	atg/atGg	26/29	1	1	FACETS	0.758	0.664	0.854	1	0.972	1	SUBCLONAL	2	TRUE	0	0.408076937767303	1		321	139	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0020961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	141	417	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.168804510700795	3	FACETS	0.816	0.747	0.888	0.816	0.747	0.888	INDETERMINATE	2	TRUE	1	0.360372502081214	3		418	566	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708603	43708603	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	291	653	2	ENST00000382044.4:c.4693G>T	p.Gly1565Ter	p.G1565*	ENST00000382044	NM_001141980.1	1565	Gga/Tga	22/28	0.360372502081214	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.360372502081214	2		655	750	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0020963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	133	471	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.677694517342672	1	FACETS	0.968	0.898	1	0.968	0.898	1	CLONAL	1	TRUE	0	0.677694517342672	1		471	268	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519999	NA	P-0020963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	301	806	0	ENST00000269305.4:c.716A>G	p.Asn239Ser	p.N239S	ENST00000269305	NM_001126112.2	239	aAc/aGc	7/11	0.669429206841263	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.677694517342672	1		806	562	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070640	67070643	+	frameshift_variant	Frame_Shift_Del	DEL	AGAA	AGAA	-	novel	NA	P-0020964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	100	366	0	ENST00000412916.2:c.267_270del	p.Arg90LysfsTer7	p.R90Kfs*7	ENST00000412916		88	ttAGAA/tt	3/6	0.621636099965467	1	FACETS	0.914	0.832	0.997	0.914	0.832	0.997	CLONAL	1	TRUE	0	0.62277048950984	1		366	242	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115707	8115719	+	frameshift_variant	Frame_Shift_Del	DEL	CAGACCCCTGACT	CAGACCCCTGACT	TCTAAACA	novel	NA	P-0020964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	61	579	4	ENST00000346208.3:c.1053_1065delinsTCTAAACA	p.Arg352LeufsTer17	p.R352Lfs*17	ENST00000346208		351	aaCAGACCCCTGACT/aaTCTAAACA	6/6	1	2	FACETS	0.377	0.325	0.433	0.377	0.325	0.433	SUBCLONAL	1	TRUE	1	0.62277048950984	2		583	520	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112390	115112390	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	220	829	0	ENST00000257566.3:c.1350del	p.Ala451ArgfsTer181	p.A451Rfs*181	ENST00000257566	NM_016569.3	450	ggC/gg	7/8	0.358763770461695	1	FACETS	0.786	0.736	0.837	0.786	0.736	0.837	INDETERMINATE	1	TRUE	0	0.62277048950984	1		829	619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0020965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	544	609	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.303091626838578	2	FACETS	0.835	0.802	0.868	1	0.995	1	CLONAL	3	TRUE	0	0.32	2		610	1357	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812204	43812204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs751975712	NA	P-0020965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	182	794	2	ENST00000372470.3:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000372470	NM_005373.2	357	Cga/Tga	7/12	1	2	FACETS	0.985	0.907	1	0.985	0.907	1	CLONAL	1	TRUE	1	0.32	2		796	1155	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130646	29130646	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	162	633	0	ENST00000328354.6:c.64del	p.His22MetfsTer39	p.H22Mfs*39	ENST00000328354	NM_007194.3	22	Cat/at	2/15	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.32	2		633	984	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166227	32166227	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1272	192	1008	0	ENST00000375023.3:c.4727A>G	p.Glu1576Gly	p.E1576G	ENST00000375023	NM_004557.3	1576	gAa/gGa	26/30	1	2	FACETS	0.82	0.756	0.887	0.82	0.756	0.887	CLONAL	1	TRUE	1	0.32	2		1008	1464	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6048631	6048631	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587780048	NA	P-0020965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1359	246	768	0	ENST00000265849.7:c.20C>G	p.Ser7Trp	p.S7W	ENST00000265849	NM_000535.5	7	tCg/tGg	1/15	1	2	FACETS	0.958	0.893	1	0.958	0.893	1	CLONAL	1	TRUE	1	0.32	2		768	1605	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575540	64575540	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	233	936	2	ENST00000312049.6:c.477del	p.Phe159LeufsTer26	p.F159Lfs*26	ENST00000312049	NM_130799.2	159	ttT/tt	3/10	0.442113063115062	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.442113063115062	1		938	790	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331911	81331911	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1487303636	NA	P-0020967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	27	507	0	ENST00000222390.5:c.2173G>T	p.Val725Leu	p.V725L	ENST00000222390	NM_000601.4	725	Gta/Tta	18/18	1	2	FACETS	0.388	0.309	0.478	0.388	0.309	0.478	SUBCLONAL	1	TRUE	1	0.442113063115062	2		507	315	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907819	76907819	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	55	161	0	ENST00000373344.5:c.4342del	p.Glu1448LysfsTer42	p.E1448Kfs*42	ENST00000373344	NM_000489.3	1448	Gaa/aa	15/35	1	1	FACETS	0.763	0.672	0.855	1	0.974	1	SUBCLONAL	2	TRUE	0	0.442113063115062	1		161	127	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579327	7579331	+	frameshift_variant	Frame_Shift_Del	DEL	CTTGG	CTTGG	-	novel	NA	P-0020968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	156	745	0	ENST00000269305.4:c.356_360del	p.Ala119ValfsTer28	p.A119Vfs*28	ENST00000269305	NM_001126112.2	119	gCCAAG/g	4/11	0.524965210622104	1	FACETS	0.945	0.873	1	0.945	0.873	1	CLONAL	1	TRUE	0	0.524965210622104	1		745	464	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	105	251	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.946	0.848	1	0.946	0.848	1	CLONAL	1	TRUE	1	0.306617991401538	2		251	724	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0020973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	70	729	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	NA	2	FACETS	0.51	0.443	0.582			1	INDETERMINATE	1	TRUE	NA	0.306617991401538	2		729	896	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0020973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	245	981	1	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.306617991401538	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.306617991401538	1		982	1081	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0020973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	64	527	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	1	2	FACETS	0.964	0.838	1	0.964	0.838	1	CLONAL	1	TRUE	1	0.306617991401538	2		527	433	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721622	49721622	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs200268600	NA	P-0020973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	12	60	0	ENST00000449682.2:c.2017G>A	p.Gly673Ser	p.G673S	ENST00000449682	NM_020998.3	673	Ggt/Agt	18/18	1	2	FACETS	1	0.717	1	1	0.717	1	CLONAL	1	TRUE	1	0.306617991401538	2		60	78	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107028	27107043	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCCTCCTCCACATG	CAGCCTCCTCCACATG	-	novel	NA	P-0020973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	157	751	1	ENST00000324856.7:c.6642_6657del	p.Ser2214ArgfsTer12	p.S2214Rfs*12	ENST00000324856	NM_006015.4	2213	gcCAGCCTCCTCCACATG/gc	20/20	0.200351876654799	3	FACETS	0.762	0.699	0.828	0.762	0.699	0.828	SUBCLONAL	2	TRUE	1	0.306617991401538	3		752	775	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202234	108202234	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	89	939	0	ENST00000278616.4:c.7579A>G	p.Met2527Val	p.M2527V	ENST00000278616	NM_000051.3	2527	Atg/Gtg	51/63	0.306617991401538	1	FACETS	0.895	0.796	1	0.895	0.796	1	CLONAL	1	TRUE	0	0.306617991401538	1		939	549	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111995819	111995820	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	71	620	0	ENST00000368678.4:c.1278dup	p.Ile427HisfsTer19	p.I427Hfs*19	ENST00000368678		426	-/C	12/13	1	2	FACETS	0.686	0.598	0.781	0.686	0.598	0.781	SUBCLONAL	1	TRUE	1	0.306617991401538	2		620	675	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	86	251	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.844	0.75	0.942	0.844	0.75	0.942	CLONAL	1	TRUE	1	0.478602593263694	2		251	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912664	NA	P-0020974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	139	1049	3	ENST00000269305.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000269305	NM_001126112.2	337	cGc/cAc	10/11	0.478602593263694	1	FACETS	0.87	0.797	0.946	0.87	0.797	0.946	CLONAL	1	TRUE	0	0.478602593263694	1		1052	508	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226992	2226992	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	144	908	1	ENST00000398665.3:c.4472C>T	p.Ser1491Phe	p.S1491F	ENST00000398665	NM_032482.2	1491	tCc/tTc	27/28	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.478602593263694	2		909	538	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561681	55561681	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	71	390	0	ENST00000288135.5:c.71C>G	p.Ser24Cys	p.S24C	ENST00000288135	NM_000222.2	24	tCt/tGt	2/21	1	2	FACETS	0.905	0.796	1	0.905	0.796	1	CLONAL	1	TRUE	1	0.478602593263694	2		390	328	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0020977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	225	560	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.27991992249814	4	FACETS	1	0.984	1	0.779	0.727	0.833	CLONAL	2	FALSE	1	0.278341430206059	4		560	884	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0020977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	338	1134	1	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.27991992249814	4	FACETS	0.999	0.946	1			1	CLONAL	3	FALSE	NA	0.278341430206059	4		1135	1036	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584513	48584514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs377767334	NA	P-0020977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	69	536	1	ENST00000342988.3:c.692dup	p.Ser232GlnfsTer3	p.S232Qfs*3	ENST00000342988	NM_005359.5	229	ctg/ctGg	6/12	0.206572495738492	3	FACETS	1	0.935	1			1	CLONAL	1	FALSE	NA	0.278341430206059	3		537	506	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779180	135779180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200827913	NA	P-0020977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	46	628	2	ENST00000298552.3:c.2066G>A	p.Arg689His	p.R689H	ENST00000298552	NM_001162426.1	689	cGc/cAc	17/23	1	2	FACETS	0.66	0.556	0.775	0.66	0.556	0.775	SUBCLONAL	1	FALSE	1	0.278341430206059	2		630	501	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636766	8636766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776233840	NA	P-0020977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	40	740	0	ENST00000356435.5:c.143C>T	p.Thr48Met	p.T48M	ENST00000356435		48	aCg/aTg	2/35	1	2	FACETS	0.383	0.317	0.457	0.383	0.317	0.457	SUBCLONAL	1	FALSE	1	0.278341430206059	2		740	750	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112448	115112448	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398394014	NA	P-0020977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	102	935	1	ENST00000257566.3:c.1292C>T	p.Ala431Val	p.A431V	ENST00000257566	NM_016569.3	431	gCg/gTg	7/8	0.27991992249814	3	FACETS	1	0.966	1	0.596	0.533	0.662	CLONAL	1	FALSE	1	0.278341430206059	3		936	701	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028610	12028610	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0020977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	83	519	1	ENST00000353533.5:c.814-1G>A		p.X272_splice	ENST00000353533	NM_003010.3	272			NA	2	FACETS	1	0.967	1			1	INDETERMINATE	1	FALSE	NA	0.278341430206059	2		520	473	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210899	36210899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757329299	NA	P-0020977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	75	919	2	ENST00000222270.7:c.650G>A	p.Arg217Gln	p.R217Q	ENST00000222270	NM_014727.1	217	cGg/cAg	3/37	0.27991992249814	3	FACETS	0.762	0.666	0.865	0.381	0.333	0.433	SUBCLONAL	1	FALSE	1	0.278341430206059	3		921	806	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965019	25965019	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750809033	NA	P-0020977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	34	686	2	ENST00000435504.4:c.4187C>T	p.Thr1396Met	p.T1396M	ENST00000435504		1396	aCg/aTg	13/13	0.230587518266838	2	FACETS	0.382	0.311	0.462	0.191	0.155	0.231	SUBCLONAL	1	FALSE	0	0.278341430206059	2		688	640	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379486	225379486	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	113	657	1	ENST00000264414.4:c.382C>A	p.Arg128Ser	p.R128S	ENST00000264414	NM_003590.4	128	Cgt/Agt	4/16	0.278341430206059	5	FACETS	0.76	0.684	0.841			1	SUBCLONAL	2	FALSE	NA	0.278341430206059	5		658	757	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111759	56111759	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265532691	NA	P-0020977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	27	96	0	ENST00000399503.3:c.359G>A	p.Gly120Asp	p.G120D	ENST00000399503	NM_005921.1	120	gGc/gAc	1/20	0.278341430206059	5	FACETS	0.899	0.731	1	0.899	0.731	1	CLONAL	3	FALSE	2	0.278341430206059	5		96	102	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971077	21971077	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	77	679	0	ENST00000304494.5:c.281T>G	p.Leu94Arg	p.L94R	ENST00000304494	NM_000077.4	94	cTg/cGg	2/3	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	FALSE	1	0.278341430206059	2		679	539	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971084	21971109	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGGAAGCCCTCCCGGGCAGCGTCG	CCAGGAAGCCCTCCCGGGCAGCGTCG	A	novel	NA	P-0020977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	42	674	0	ENST00000304494.5:c.249_274delinsT	p.Asp84ThrfsTer54	p.D84Tfs*54	ENST00000304494	NM_000077.4	83	caCGACGCTGCCCGGGAGGGCTTCCTGGac/caTac	2/3	1				0.49	0.695				SUBCLONAL	1	FALSE	1	0.278341430206059	2		674	514	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	28	251	0				ENST00000310581	NM_198253.2	-/1132			0.598057495695311	1	FACETS	0.411	0.332	0.499	0.411	0.332	0.499	SUBCLONAL	1	FALSE	0	0.594583679337333	1		251	161	SUCCESS
APC	324	MSKCC	GRCh37	5	112162804	112162804	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs863225313	NA	P-0020987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	70	487	0	ENST00000257430.4:c.1409-1G>A		p.X470_splice	ENST00000257430	NM_000038.5	470			0.459959395219626	4	FACETS	1	0.903	1	0.517	0.453	0.585	CLONAL	1	FALSE	2	0.594583679337333	4		487	363	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809341	243809341	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0020987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	60	604	0	ENST00000263826.5:c.285-2A>G		p.X95_splice	ENST00000263826	NM_005465.4	95			0.598057495695311	4	FACETS	0.56	0.482	0.644	0.187	0.16	0.215	SUBCLONAL	1	FALSE	1	0.594583679337333	4		604	575	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245320	46245339	+	frameshift_variant	Frame_Shift_Del	DEL	GGGAGTACAAACTGTGCCCA	GGGAGTACAAACTGTGCCCA	-	novel	NA	P-0020987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	125	612	0	ENST00000334344.6:c.3414_3433del	p.Gly1139PhefsTer14	p.G1139Ffs*14	ENST00000334344	NM_152641.2	1138	ggGGGAGTACAAACTGTGCCCAtt/ggtt	15/21	0.535230681505578	4	FACETS	1	0.975	1	0.604	0.549	0.662	CLONAL	1	FALSE	2	0.594583679337333	4		612	555	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47596649	47596649	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs201402370	NA	P-0020987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	74	465	0	ENST00000263735.4:c.5C>A	p.Ala2Glu	p.A2E	ENST00000263735	NM_002354.2	2	gCg/gAg	1/9	0.259540112707662	4	FACETS	0.837	0.744	0.935	0.837	0.744	0.935	INDETERMINATE	2	FALSE	2	0.594583679337333	4		465	237	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928534	69928534	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	82	886	0	ENST00000352241.4:c.354G>C	p.Lys118Asn	p.K118N	ENST00000352241	NM_198159.2	118	aaG/aaC	2/10	NA	2	FACETS	0.441	0.389	0.497			1	INDETERMINATE	1	FALSE	NA	0.594583679337333	2		886	625	SUCCESS
APC	324	MSKCC	GRCh37	5	112174712	112174725	+	frameshift_variant	Frame_Shift_Del	DEL	ACCAATTATAGTGA	ACCAATTATAGTGA	-	novel	NA	P-0020987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	62	464	0	ENST00000257430.4:c.3423_3436del	p.Asn1142LeufsTer3	p.N1142Lfs*3	ENST00000257430	NM_000038.5	1141	ACCAATTATAGTGAa/a	16/16	0.459959395219626	4	FACETS	0.873	0.757	0.997	0.436	0.378	0.499	CLONAL	1	FALSE	2	0.594583679337333	4		464	381	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	75	251	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.951	1			1	INDETERMINATE	1	FALSE	NA	0.808513731539186	2		251	169	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221710	55221710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4651	837	584	1	ENST00000275493.2:c.754C>T	p.Arg252Cys	p.R252C	ENST00000275493	NM_005228.3	252	Cgc/Tgc	7/28	0.808513731539186	39	FACETS	1	0.966	1			1	CLONAL	6	FALSE	NA	0.808513731539186	39		585	5488	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	321	613	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.30882820156886	1	FACETS	0.628	0.597	0.66	0.628	0.597	0.66	INDETERMINATE	1	TRUE	0	0.836157964584198	1		614	711	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023008	27023010	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs587779737	NA	P-0020990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	11	47	0	ENST00000324856.7:c.126_128del	p.Ala45del	p.A45del	ENST00000324856	NM_006015.4	38	gaGGCg/gag	1/20	NA	2	FACETS	0.283	0.197	0.387			1	INDETERMINATE	1	TRUE	NA	0.836157964584198	2		47	93	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0020990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	201	423	3	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	NA	2	FACETS	1	0.955	1			1	INDETERMINATE	1	TRUE	NA	0.836157964584198	2		426	470	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486587	56486587	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	161	764	0	ENST00000267101.3:c.1166C>A	p.Thr389Lys	p.T389K	ENST00000267101	NM_001982.3	389	aCa/aAa	10/28	0.30882820156886	1	FACETS	0.404	0.372	0.436	0.404	0.372	0.436	INDETERMINATE	1	TRUE	0	0.836157964584198	1		764	555	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873625	35873626	+	inframe_insertion,splice_region_variant	In_Frame_Ins	INS	-	-	GTCCCCGTCCTCGGT	novel	NA	P-0020990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	64	379	0	ENST00000216797.5:c.211_225dup	p.Thr71_Asp75dup	p.T71_D75dup	ENST00000216797	NM_020529.2	71	-/ACCGAGGACGGGGAC	1/6	0.822622823081169	2	FACETS	0.48	0.418	0.546	0.24	0.209	0.273	SUBCLONAL	1	TRUE	0	0.836157964584198	2		379	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578391	7578393	+	frameshift_variant	Frame_Shift_Del	DEL	TCA	TCA	AT	novel	NA	P-0020990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	412	743	0	ENST00000269305.4:c.537_539delinsAT	p.His179GlnfsTer68	p.H179Qfs*68	ENST00000269305	NM_001126112.2	179	caTGAg/caATg	5/11	0.836157964584198	2	FACETS	0.98	0.954	1	0.98	0.954	1	CLONAL	2	TRUE	0	0.836157964584198	2		743	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0020991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	191	733	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.210351873171741	2	FACETS	0.784	0.726	0.843	0.784	0.726	0.843	SUBCLONAL	2	FALSE	0	0.310478735958838	2		733	785	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971153	21971153	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913383	NA	P-0020991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	119	634	0	ENST00000304494.5:c.205G>T	p.Glu69Ter	p.E69*	ENST00000304494	NM_000077.4	69	Gag/Tag	2/3	0.310478735958838	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	0	0.310478735958838	1		634	517	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196830	123196830	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	119	355	0	ENST00000218089.9:c.1717C>T	p.Gln573Ter	p.Q573*	ENST00000218089	NM_001042749.1	573	Cag/Tag	18/35	0.303063941260205	2	FACETS	0.961	0.875	1			1	CLONAL	2	FALSE	NA	0.310478735958838	2		355	399	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913409	NA	P-0020991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	100	518	0	ENST00000349496.5:c.134C>G	p.Ser45Cys	p.S45C	ENST00000349496	NM_001904.3	45	tCt/tGt	3/15	0.310478735958838	3	FACETS	1	0.98	1	0.714	0.64	0.792	CLONAL	1	FALSE	1	0.310478735958838	3		518	521	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945150	44945150	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	162	390	0	ENST00000377967.4:c.3474T>G	p.Asn1158Lys	p.N1158K	ENST00000377967	NM_021140.2	1158	aaT/aaG	24/29	0.310478735958838	2	FACETS	1	0.981	1			1	CLONAL	2	FALSE	NA	0.310478735958838	2		390	445	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939217	76939217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	51	549	1	ENST00000373344.5:c.1531G>A	p.Glu511Lys	p.E511K	ENST00000373344	NM_000489.3	511	Gaa/Aaa	9/35	0.303063941260205	2	FACETS	0.523	0.444	0.61			1	SUBCLONAL	1	FALSE	NA	0.310478735958838	2		550	628	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0020994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	386	799	0	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	0.876739767907776	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.876739767907776	1		799	450	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935319	36935319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748675453	NA	P-0020994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	391	851	0	ENST00000361632.4:c.1408G>A	p.Ala470Thr	p.A470T	ENST00000361632		470	Gcg/Acg	10/16	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.876739767907776	2		851	825	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379426	225379427	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	487	891	0	ENST00000264414.4:c.441dup	p.Arg148SerfsTer11	p.R148Sfs*11	ENST00000264414	NM_003590.4	147	-/T	4/16	1	2	FACETS	0.947	0.908	0.986	0.947	0.908	0.986	CLONAL	1	TRUE	1	0.876739767907776	2		891	1173	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5077570	5077570	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	332	580	0	ENST00000381652.3:c.1982T>C	p.Met661Thr	p.M661T	ENST00000381652	NM_004972.3	661	aTg/aCg	15/25	0.876739767907776	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.876739767907776	1		580	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691025	NA	P-0021008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	371	632	0	ENST00000269305.4:c.785G>T	p.Gly262Val	p.G262V	ENST00000269305	NM_001126112.2	262	gGt/gTt	8/11	0.685434906412683	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.685434906412683	1		632	647	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099610	157099610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1246202974	NA	P-0021008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	50	140	0	ENST00000346085.5:c.547G>A	p.Gly183Ser	p.G183S	ENST00000346085	NM_020732.3	183	Ggc/Agc	1/20	1	2	FACETS	0.553	0.473	0.639	0.553	0.473	0.639	SUBCLONAL	1	TRUE	1	0.685434906412683	2		140	264	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319875	8319875	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	314	585	0	ENST00000356435.5:c.5626G>T	p.Val1876Phe	p.V1876F	ENST00000356435		1876	Gtc/Ttc	34/35	0.416579086581552	3	FACETS	1	0.982	1	0.546	0.515	0.578	CLONAL	1	TRUE	1	0.685434906412683	3		585	1126	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250373	110250373	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	54	683	0	ENST00000374672.4:c.302A>G	p.Asp101Gly	p.D101G	ENST00000374672	NM_004235.4	101	gAt/gGt	3/5	1	2	FACETS	0.916	0.779	1	0.916	0.779	1	CLONAL	1	TRUE	1	0.11	2		683	1072	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417616	139417616	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1228192276	NA	P-0021009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1266	68	732	0	ENST00000277541.6:c.428C>T	p.Pro143Leu	p.P143L	ENST00000277541	NM_017617.3	143	cCg/cTg	4/34	1	2	FACETS	0.927	0.803	1	0.927	0.803	1	CLONAL	1	TRUE	1	0.11	2		732	1334	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0021012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	18	725	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.259	0.194	0.337	0.259	0.194	0.337	SUBCLONAL	1	TRUE	1	0.18	2		725	772	SUCCESS
APC	324	MSKCC	GRCh37	5	112175288	112175288	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0021012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	25	335	0	ENST00000257430.4:c.3997A>T	p.Lys1333Ter	p.K1333*	ENST00000257430	NM_000038.5	1333	Aaa/Taa	16/16	1	2	FACETS	0.718	0.565	0.893	0.718	0.565	0.893	SUBCLONAL	1	TRUE	1	0.18	2		335	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579547	7579547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567557016	NA	P-0021012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	101	901	1	ENST00000269305.4:c.140del	p.Pro47ArgfsTer76	p.P47Rfs*76	ENST00000269305	NM_001126112.2	47	cCg/cg	4/11	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.18	2		902	1008	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120240	70120241	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0021012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	99	1030	0	ENST00000245479.2:c.1246dup	p.Gln416ProfsTer162	p.Q416Pfs*162	ENST00000245479	NM_000346.3	414	-/C	3/3	1	2	FACETS	0.997	0.888	1	0.997	0.888	1	CLONAL	1	TRUE	1	0.18	2		1030	1103	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0021015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	321	636	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.587102123695337	2	FACETS	0.973	0.932	1	0.973	0.932	1	CLONAL	2	TRUE	0	0.606145398439834	2		636	544	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508533	106508533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773456619	NA	P-0021015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	21	246	1	ENST00000359195.3:c.527C>T	p.Thr176Met	p.T176M	ENST00000359195	NM_002649.2	176	aCg/aTg	2/11	0.2247359641507	5	FACETS	0.675	0.522	0.851	0.135	0.104	0.171	INDETERMINATE	1	TRUE	0	0.606145398439834	5		247	196	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100934	27100952	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCCAGCCCAGCCCCAGC	CCCCCAGCCCAGCCCCAGC	-	novel	NA	P-0021015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	228	635	0	ENST00000324856.7:c.4217_4235del	p.Pro1406LeufsTer69	p.P1406Lfs*69	ENST00000324856	NM_006015.4	1406	CCCCCAGCCCAGCCCCAGCct/ct	18/20	0.587102123695337	2	FACETS	0.945	0.896	0.993	0.945	0.896	0.993	CLONAL	2	TRUE	0	0.606145398439834	2		635	398	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102196062	102196062	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	25	359	0	ENST00000263464.3:c.822G>T	p.Glu274Asp	p.E274D	ENST00000263464	NM_001165.4	274	gaG/gaT	2/9	0.606145398439834	1	FACETS	0.26	0.206	0.322	0.26	0.206	0.322	SUBCLONAL	1	TRUE	0	0.606145398439834	1		359	221	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646921	23646921	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	63	722	0	ENST00000261584.4:c.946C>A	p.Pro316Thr	p.P316T	ENST00000261584	NM_024675.3	316	Ccc/Acc	4/13	0.197150580487412	2	FACETS	0.381	0.329	0.436	0.19	0.164	0.218	INDETERMINATE	1	TRUE	0	0.606145398439834	2		722	546	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832563	72832563	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	29	451	0	ENST00000268489.5:c.4018C>A	p.Gln1340Lys	p.Q1340K	ENST00000268489	NM_006885.3	1340	Caa/Aaa	9/10	0.141660279367818	3	FACETS	0.304	0.244	0.373	0.101	0.081	0.125	INDETERMINATE	1	TRUE	0	0.606145398439834	3		451	410	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546784	9546784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1252319558	NA	P-0021015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	89	352	0	ENST00000353224.5:c.1238C>T	p.Pro413Leu	p.P413L	ENST00000353224	NM_177990.2	413	cCg/cTg	5/10	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.606145398439834	2		352	204	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182662958	182662958	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	37	419	1	ENST00000292782.4:c.704C>A	p.Ala235Glu	p.A235E	ENST00000292782	NM_020640.2	235	gCa/gAa	7/7	0.587102123695337	2	FACETS	0.335	0.277	0.401	0.168	0.138	0.201	SUBCLONAL	1	TRUE	0	0.606145398439834	2		420	364	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129363	152129363	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	70	553	0	ENST00000206249.3:c.316A>C	p.Ser106Arg	p.S106R	ENST00000206249	NM_000125.3	106	Agc/Cgc	1/8	0.197150580487412	2	FACETS	0.524	0.458	0.594	0.262	0.229	0.297	INDETERMINATE	1	TRUE	0	0.606145398439834	2		553	441	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863037	56863037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	301	607	0	ENST00000519728.1:c.304G>A	p.Ala102Thr	p.A102T	ENST00000519728	NM_002350.3	102	Gca/Aca	5/13	0.606145398439834	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.606145398439834	2		607	458	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859844	117859844	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	37	346	0	ENST00000297338.2:c.1791C>A	p.Phe597Leu	p.F597L	ENST00000297338	NM_006265.2	597	ttC/ttA	14/14	0.129168393244106	5	FACETS	0.578	0.477	0.691			1	INDETERMINATE	1	TRUE	NA	0.606145398439834	5		346	403	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974603	21974831	+	splice_donor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	TCCAATTCCCCTGCAAACTTCGTCCTCCAGAGTCGCCCGCCATCCCCTGCTCCCGCTGCAGACCCTCTACCCACCTGGATCGGCCTCCGACCGTAACTATTCGGTGCGTTGGGCAGCGCCCCCGCCTCCAGCAGCGCCCGCACCTCCTCTACCCGACCCCGGGCCGCGGCCGTGGCCAGCCAGTCAGCCGAAGGCTCCATGCTGCTCCCCGCCGCCGGCTCCATGCTGC	TCCAATTCCCCTGCAAACTTCGTCCTCCAGAGTCGCCCGCCATCCCCTGCTCCCGCTGCAGACCCTCTACCCACCTGGATCGGCCTCCGACCGTAACTATTCGGTGCGTTGGGCAGCGCCCCCGCCTCCAGCAGCGCCCGCACCTCCTCTACCCGACCCCGGGCCGCGGCCGTGGCCAGCCAGTCAGCCGAAGGCTCCATGCTGCTCCCCGCCGCCGGCTCCATGCTGC	-	novel	NA	P-0021015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	124	811	0	ENST00000304494.5:c.-5_150+74del		p.X2_splice	ENST00000304494	NM_000077.4	2		1/3	0.606145398439834	1	FACETS	0.779	0.713	0.847	0.779	0.713	0.847	SUBCLONAL	1	TRUE	0	0.606145398439834	1		811	366	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339940	70339940	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	29	575	1	ENST00000374080.3:c.473G>T	p.Trp158Leu	p.W158L	ENST00000374080		158	tGg/tTg	4/45	0.595283905316496	2	FACETS	0.194	0.155	0.239	0.097	0.077	0.12	SUBCLONAL	1	TRUE	0	0.606145398439834	2		576	492	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445349	49445349	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	66	1257	0	ENST00000301067.7:c.2117del	p.Pro706LeufsTer224	p.P706Lfs*224	ENST00000301067	NM_003482.3	706	cCt/ct	10/54	0.0783909653350792	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		1257	794	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0021026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	22	613	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.152348291634128	3	FACETS	0.762	0.589	0.964	0.381	0.294	0.482	CLONAL	1	TRUE	1	0.12	3		614	510	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912660	NA	P-0021026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	33	751	0	ENST00000269305.4:c.839G>T	p.Arg280Ile	p.R280I	ENST00000269305	NM_001126112.2	280	aGa/aTa	8/11	1	2	FACETS	0.755	0.613	0.917	0.755	0.613	0.917	CLONAL	1	TRUE	1	0.12	2		751	728	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397650	49397650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755060419	NA	P-0021026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	32	746	0	ENST00000418115.1:c.574G>A	p.Val192Ile	p.V192I	ENST00000418115	NM_001664.2	192	Gtc/Atc	5/5	1	2	FACETS	0.866	0.701	1	0.866	0.701	1	CLONAL	1	TRUE	1	0.12	2		746	616	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045901	180045901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	27	649	1	ENST00000261937.6:c.2870G>A	p.Arg957His	p.R957H	ENST00000261937	NM_182925.4	957	cGc/cAc	21/30	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.12	2		650	393	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0021029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	42	865	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	0.351	0.292	0.417	0.351	0.292	0.417	SUBCLONAL	1	TRUE	1	0.32	2		865	748	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221995	1221995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201090	NA	P-0021029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	47	845	0	ENST00000326873.7:c.910C>T	p.Arg304Trp	p.R304W	ENST00000326873	NM_000455.4	304	Cgg/Tgg	7/10	1	2	FACETS	0.391	0.329	0.46	0.391	0.329	0.46	SUBCLONAL	1	TRUE	1	0.32	2		845	751	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484221	8484221	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	31	751	0	ENST00000356435.5:c.3311C>A	p.Ala1104Glu	p.A1104E	ENST00000356435		1104	gCa/gAa	19/35	1	2	FACETS	0.314	0.253	0.383	0.314	0.253	0.383	SUBCLONAL	1	TRUE	1	0.32	2		751	617	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649598	48649598	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	51	913	1	ENST00000376670.3:c.82C>A	p.Pro28Thr	p.P28T	ENST00000376670	NM_002049.3	28	Cca/Aca	2/6	1	2	FACETS	0.437	0.371	0.511	0.437	0.371	0.511	SUBCLONAL	1	TRUE	1	0.32	2		914	729	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349597	70349597	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	40	844	2	ENST00000374080.3:c.3759G>T	p.Glu1253Asp	p.E1253D	ENST00000374080		1253	gaG/gaT	27/45	1	2	FACETS	0.333	0.276	0.397	0.333	0.276	0.397	SUBCLONAL	1	TRUE	1	0.32	2		846	751	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0021030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	366	775	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.918081516650157	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.922981005306133	2		775	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs17849781	NA	P-0021033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	158	1018	2	ENST00000269305.4:c.832C>A	p.Pro278Thr	p.P278T	ENST00000269305	NM_001126112.2	278	Cct/Act	8/11	0.23050901750156	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	FALSE	0	0.23050901750156	2		1020	592	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0021033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	51	799	1	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.23050901750156	3	FACETS	1	0.928	1	0.577	0.491	0.67	CLONAL	1	FALSE	1	0.23050901750156	3		800	428	SUCCESS
APC	324	MSKCC	GRCh37	5	112174885	112174886	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs864622106	NA	P-0021033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	71	528	0	ENST00000257430.4:c.3595_3596del	p.Lys1199GlufsTer8	p.K1199Efs*8	ENST00000257430	NM_000038.5	1198	tcAAag/tcag	16/16	0.23050901750156	3	FACETS	1	0.915	1	1	0.915	1	CLONAL	2	FALSE	1	0.23050901750156	3		528	327	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995569	68995569	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	60	978	3	ENST00000288368.4:c.1973C>A	p.Ser658Ter	p.S658*	ENST00000288368	NM_024870.2	658	tCg/tAg	18/40	0.23050901750156	3	FACETS	0.947	0.816	1	0.316	0.272	0.364	CLONAL	1	FALSE	0	0.23050901750156	3		981	613	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0021034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	200	1002	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.238727816248318	2	FACETS	0.821	0.762	0.883	0.821	0.762	0.883	CLONAL	2	TRUE	0	0.274597003061811	2		1002	887	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044711	47044711	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	95	1170	0	ENST00000377604.3:c.2112del	p.Glu705ArgfsTer97	p.E705Rfs*97	ENST00000377604	NM_001204468.1	704	gCc/gc	19/24	0.274597003061811	1	FACETS	0.801	0.713	0.895	0.801	0.713	0.895	CLONAL	1	TRUE	0	0.274597003061811	1		1170	745	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776131	9776131	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	60	952	0	ENST00000377346.4:c.595A>C	p.Ser199Arg	p.S199R	ENST00000377346	NM_005026.3	199	Agc/Cgc	5/24	0.274597003061811	1	FACETS	0.596	0.513	0.686	0.596	0.513	0.686	SUBCLONAL	1	TRUE	0	0.274597003061811	1		952	633	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150300	108150301	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0021034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	179	739	1	ENST00000278616.4:c.3367_3368delinsAA	p.Ala1123Lys	p.A1123K	ENST00000278616	NM_000051.3	1123	GCa/AAa	23/63	0.233532071655092	4	FACETS	1	0.952	1	0.694	0.641	0.749	CLONAL	2	TRUE	1	0.274597003061811	4		740	798	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160451	108160466	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAAGTGGCTTAGGA	AAAAAGTGGCTTAGGA	-	novel	NA	P-0021034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	91	926	0	ENST00000278616.4:c.4359_4374del	p.Ile1453MetfsTer15	p.I1453Mfs*15	ENST00000278616	NM_000051.3	1453	atAAAAAGTGGCTTAGGA/at	29/63	0.233532071655092	4	FACETS	0.737	0.653	0.828	0.246	0.217	0.276	SUBCLONAL	1	TRUE	1	0.274597003061811	4		926	1146	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37882020	37882020	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201399875	NA	P-0021034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	81	1025	4	ENST00000269571.5:c.2786G>A	p.Arg929Gln	p.R929Q	ENST00000269571		929	cGg/cAg	23/27	1	2	FACETS	0.771	0.679	0.871	0.771	0.679	0.871	SUBCLONAL	1	TRUE	1	0.274597003061811	2		1029	765	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637907	39637907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	161	862	1	ENST00000262039.4:c.2324C>T	p.Pro775Leu	p.P775L	ENST00000262039	NM_002647.2	775	cCa/cTa	22/25	0.238727816248318	2	FACETS	0.817	0.751	0.885	0.817	0.751	0.885	CLONAL	2	TRUE	0	0.274597003061811	2		863	718	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155393	47155393	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	82	943	0	ENST00000409792.3:c.4688G>T	p.Gly1563Val	p.G1563V	ENST00000409792	NM_014159.6	1563	gGc/gTc	5/21	1	2	FACETS	0.728	0.641	0.822	0.728	0.641	0.822	SUBCLONAL	1	TRUE	1	0.274597003061811	2		943	820	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164373	47164403	+	frameshift_variant	Frame_Shift_Del	DEL	ACTGTTTGATTTCTTCATTTAATTCTGTACA	ACTGTTTGATTTCTTCATTTAATTCTGTACA	-	novel	NA	P-0021034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	58	595	0	ENST00000409792.3:c.1723_1753del	p.Cys575LeufsTer16	p.C575Lfs*16	ENST00000409792	NM_014159.6	575	TGTACAGAATTAAATGAAGAAATCAAACAGTct/ct	3/21	1	2	FACETS	0.749	0.644	0.864	0.749	0.644	0.864	SUBCLONAL	1	TRUE	1	0.274597003061811	2		595	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0021035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	221	730	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.560393119072666	1	FACETS	0.913	0.855	0.972	0.913	0.855	0.972	CLONAL	1	TRUE	0	0.560393119072666	1		731	622	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922574	56922574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	152	778	1	ENST00000519728.1:c.1444G>A	p.Glu482Lys	p.E482K	ENST00000519728	NM_002350.3	482	Gaa/Aaa	13/13	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.560393119072666	2		779	534	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000085	30000086	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0021036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	380	988	0	ENST00000338641.4:c.100dup	p.Glu34GlyfsTer15	p.E34Gfs*15	ENST00000338641	NM_000268.3	33	atg/atGg	1/16	0.885729159525034	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.885729159525034	1		988	468	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430749	47430749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1275541592	NA	P-0021037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	253	538	0	ENST00000377045.4:c.1714C>T	p.Arg572Trp	p.R572W	ENST00000377045	NM_001654.4	572	Cgg/Tgg	16/16	1	1	FACETS	0.957	0.92	0.993	1	0.997	1	CLONAL	6	TRUE	0	0.23	1		538	339	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026137	48026137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	55	544	0	ENST00000234420.5:c.1015G>A	p.Ala339Thr	p.A339T	ENST00000234420	NM_000179.2	339	Gct/Act	4/10	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.184582665873338	2		544	447	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0021039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	94	303	1	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	0.665187876813144	2		304	260	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577586	7577586	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587781589	NA	P-0021039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	431	963	0	ENST00000269305.4:c.695T>G	p.Ile232Ser	p.I232S	ENST00000269305	NM_001126112.2	232	aTc/aGc	7/11	0.665187876813144	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.665187876813144	2		963	547	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207685	102207685	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	69	552	0	ENST00000263464.3:c.1667C>A	p.Thr556Lys	p.T556K	ENST00000263464	NM_001165.4	556	aCa/aAa	9/9	0.665187876813144	3	FACETS	1	0.907	1	0.518	0.456	0.583	CLONAL	1	TRUE	1	0.665187876813144	3		552	267	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298723	46298724	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0021039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	88	590	1	ENST00000334344.6:c.5371_5372del	p.Lys1791GlufsTer3	p.K1791Efs*3	ENST00000334344	NM_152641.2	1790	ttAAag/ttag	21/21	0.23244273028021	2	FACETS	1	0.953	1	0.549	0.494	0.605	INDETERMINATE	1	TRUE	0	0.665187876813144	2		591	241	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	62	328	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.878	0.759	1	0.878	0.759	1	CLONAL	1	TRUE	1	0.25	2		328	565	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914581	32914581	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	85	1106	0	ENST00000380152.3:c.6089A>T	p.Asn2030Ile	p.N2030I	ENST00000380152		2030	aAt/aTt	11/27	1	2	FACETS	0.705	0.622	0.795	0.705	0.622	0.795	SUBCLONAL	1	TRUE	1	0.25	2		1106	964	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270368	10270368	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867003508	NA	P-0021040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	109	1100	0	ENST00000340748.4:c.1198G>A	p.Glu400Lys	p.E400K	ENST00000340748		400	Gag/Aag	16/40	1	2	FACETS	0.944	0.846	1	0.944	0.846	1	CLONAL	1	TRUE	1	0.25	2		1100	924	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39214624	39214624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778109739	NA	P-0021040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	86	932	0	ENST00000402219.2:c.3500C>T	p.Ser1167Leu	p.S1167L	ENST00000402219	NM_005633.3	1167	tCa/tTa	22/23	1	2	FACETS	0.82	0.724	0.923	0.82	0.724	0.923	CLONAL	1	TRUE	1	0.25	2		932	839	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637282	47637282	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553350676	NA	P-0021040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	134	1046	0	ENST00000233146.2:c.416A>G	p.Asn139Ser	p.N139S	ENST00000233146	NM_000251.2	139	aAt/aGt	3/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.25	2		1046	935	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952108	178952108	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	58	660	0	ENST00000263967.3:c.3163A>T	p.Met1055Leu	p.M1055L	ENST00000263967	NM_006218.2	1055	Atg/Ttg	21/21	1	2	FACETS	0.884	0.76	1	0.884	0.76	1	CLONAL	1	TRUE	1	0.25	2		660	525	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577129	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519986	NA	P-0021041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	815	931	0	ENST00000269305.4:c.809T>C	p.Phe270Ser	p.F270S	ENST00000269305	NM_001126112.2	270	tTt/tCt	8/11	0.488991312591922	5	FACETS	0.998	0.975	1	0.998	0.975	1	CLONAL	5	TRUE	0	0.488991312591922	5		931	1158	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286529	33286787	+	splice_donor_variant,splice_acceptor_variant,frameshift_variant,stop_lost,intron_variant	Splice_Site	DEL	GTCTGAGAGCACGATGATCTCTTCTGGATCGCATTGTGTGGCCACACTTGTCTGCAGGGAAGTGAGAGACAAAGAGTCAAAGAGATCTGGAGTACAGGAGAAAAGAAACAGGAGGATTTAGAGGATAAAATGGGTGGGAAAAAGGAAGAGACAGGATGTGGCACGTGGAATATTCAGACAGAGCAGCTGAAACAGCCAATGAAAGAGAACAAATTGTCAGAGGAAACACGCCCTCCCCTTCTTACCTTGCAAGTACCAG	GTCTGAGAGCACGATGATCTCTTCTGGATCGCATTGTGTGGCCACACTTGTCTGCAGGGAAGTGAGAGACAAAGAGTCAAAGAGATCTGGAGTACAGGAGAAAAGAAACAGGAGGATTTAGAGGATAAAATGGGTGGGAAAAAGGAAGAGACAGGATGTGGCACGTGGAATATTCAGACAGAGCAGCTGAAACAGCCAATGAAAGAGAACAAATTGTCAGAGGAAACACGCCCTCCCCTTCTTACCTTGCAAGTACCAG	-	novel	NA	P-0021041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	215	685	0	ENST00000374542.5:c.2150_2214del		p.X717_splice	ENST00000374542	NM_001141970.1	717	cCTGGTACTTGCAAGGTAAGAAGGGGAGGGCGTGTTTCCTCTGACAATTTGTTCTCTTTCATTGGCTGTTTCAGCTGCTCTGTCTGAATATTCCACGTGCCACATCCTGTCTCTTCCTTTTTCCCACCCATTTTATCCTCTAAATCCTCCTGTTTCTTTTCTCCTGTACTCCAGATCTCTTTGACTCTTTGTCTCTCACTTCCCTGCAGACAAGTGTGGCCACACAATGCGATCCAGAAGAGATCATCGTGCTCTCAGAC/c	7-8/8	0.484569497937714	3	FACETS	1	0.973	1	0.71	0.666	0.754	CLONAL	2	TRUE	0	0.488991312591922	3		685	514	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0021044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	133	811	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.384897042387017	3	FACETS	1	0.963	1	0.557	0.506	0.61	CLONAL	1	TRUE	1	0.387946248320443	3		812	735	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971177	21971177	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913382	NA	P-0021044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	96	651	0	ENST00000304494.5:c.181G>T	p.Glu61Ter	p.E61*	ENST00000304494	NM_000077.4	61	Gag/Tag	2/3	0.386966741102838	1	FACETS	0.875	0.783	0.971	0.875	0.783	0.971	CLONAL	1	TRUE	0	0.387946248320443	1		651	456	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0021044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	147	791	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.384897042387017	3	FACETS	1	0.987	1	0.724	0.663	0.787	CLONAL	1	TRUE	1	0.387946248320443	3		791	625	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921555	178921555	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	54	523	1	ENST00000263967.3:c.1037T>A	p.Val346Glu	p.V346E	ENST00000263967	NM_006218.2	346	gTa/gAa	5/21	1	2	FACETS	0.765	0.656	0.883	0.765	0.656	0.883	SUBCLONAL	1	TRUE	1	0.387946248320443	2		524	364	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044898	47044898	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	329	1114	1	ENST00000377604.3:c.2224C>T	p.Gln742Ter	p.Q742*	ENST00000377604	NM_001204468.1	742	Cag/Tag	20/24	0.315922856244838	4	FACETS	0.998	0.943	1	0.998	0.943	1	CLONAL	2	TRUE	2	0.387946248320443	4		1115	1180	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137092	64137092	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0021044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	89	734	1	ENST00000334205.4:c.1602+1G>T		p.X534_splice	ENST00000334205	NM_003942.2	534			0.364196992093901	3	FACETS	0.936	0.832	1	0.468	0.416	0.524	CLONAL	1	TRUE	1	0.387946248320443	3		735	585	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885896	59885896	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	110	837	0	ENST00000259008.2:c.850G>T	p.Val284Phe	p.V284F	ENST00000259008	NM_032043.2	284	Gtc/Ttc	7/20	0.364196992093901	3	FACETS	0.899	0.808	0.996	0.45	0.404	0.498	CLONAL	1	TRUE	1	0.387946248320443	3		837	753	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611919	100611919	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	267	935	0	ENST00000308731.7:c.1202A>T	p.Asp401Val	p.D401V	ENST00000308731	NM_000061.2	401	gAc/gTc	14/19	0.315922856244838	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.387946248320443	4		935	908	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1131691023	NA	P-0021045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	155	964	0	ENST00000269305.4:c.470T>A	p.Val157Asp	p.V157D	ENST00000269305	NM_001126112.2	157	gTc/gAc	5/11	0.218842493841037	3	FACETS	1	0.977	1	0.396	0.362	0.43	INDETERMINATE	1	TRUE	0	0.402932068634018	3		964	779	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450156	32450156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779451877	NA	P-0021045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	45	752	1	ENST00000332351.3:c.656C>T	p.Thr219Met	p.T219M	ENST00000332351	NM_024426.4	219	aCg/aTg	2/10	0.403318884464013	3	FACETS	0.552	0.464	0.65	0.276	0.232	0.325	SUBCLONAL	1	TRUE	1	0.402932068634018	3		753	486	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434732	49434732	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767236217	NA	P-0021045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	81	995	2	ENST00000301067.7:c.6821C>T	p.Ser2274Leu	p.S2274L	ENST00000301067	NM_003482.3	2274	tCg/tTg	31/54	0.402932068634018	6	FACETS	1	0.957	1	0.397	0.35	0.447	CLONAL	1	TRUE	3	0.402932068634018	6		997	610	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278167	142278167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs952177176	NA	P-0021045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	131	916	0	ENST00000350721.4:c.1658C>T	p.Ser553Phe	p.S553F	ENST00000350721	NM_001184.3	553	tCt/tTt	7/47	0.179005335571858	6	FACETS	1	0.945	1	0.7	0.638	0.765	INDETERMINATE	2	TRUE	3	0.402932068634018	6		916	559	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0021047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	12	601	1	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		602	292	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579427	7579427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	91	913	3	ENST00000269305.4:c.260C>T	p.Pro87Leu	p.P87L	ENST00000269305	NM_001126112.2	87	cCa/cTa	4/11	1	2	FACETS	0.503	0.447	0.564	0.503	0.447	0.564	SUBCLONAL	1	TRUE	1	0.51	2		916	709	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577599	7577600	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1567550002	NA	P-0021048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	98	771	0	ENST00000269305.4:c.681dup	p.Asp228Ter	p.D228*	ENST00000269305	NM_001126112.2	227	-/T	7/11	1	2	FACETS	0.498	0.444	0.555	0.498	0.444	0.555	SUBCLONAL	1	TRUE	1	0.51	2		771	772	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710578	40710578	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	83	801	0	ENST00000373198.4:c.4273G>C	p.Val1425Leu	p.V1425L	ENST00000373198	NM_133170.3	1425	Gtg/Ctg	31/32	1	2	FACETS	0.997	0.878	1	0.997	0.878	1	CLONAL	1	TRUE	1	0.190282906612957	2		801	875	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325416	1325416	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	66	863	0	ENST00000400841.2:c.259G>A	p.Asp87Asn	p.D87N	ENST00000400841		87	Gac/Aac	3/6	1	2	FACETS	0.247	0.213	0.283	0.247	0.213	0.283	SUBCLONAL	1	TRUE	1	0.59328700813153	2		863	902	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200860	67200860	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	78	895	0	ENST00000312629.5:c.851del	p.Gly284AlafsTer21	p.G284Afs*21	ENST00000312629	NM_003952.2	283	aGg/ag	10/15	0.533762240853086	3	FACETS	0.266	0.233	0.302	0.133	0.116	0.151	SUBCLONAL	1	TRUE	1	0.59328700813153	3		895	1281	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343775	118343775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	511	836	0	ENST00000534358.1:c.1901C>T	p.Ser634Leu	p.S634L	ENST00000534358	NM_005933.3	634	tCa/tTa	3/36	0.59328700813153	3	FACETS	0.989	0.951	1	0.989	0.951	1	CLONAL	2	TRUE	1	0.59328700813153	3		836	1129	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912839	32912839	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	164	590	0	ENST00000380152.3:c.4347C>G	p.Phe1449Leu	p.F1449L	ENST00000380152		1449	ttC/ttG	11/27	1	2	FACETS	0.879	0.81	0.95	0.879	0.81	0.95	CLONAL	1	TRUE	1	0.59328700813153	2		590	629	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912895	32912895	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555283769	NA	P-0021054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	162	521	0	ENST00000380152.3:c.4403C>G	p.Ser1468Cys	p.S1468C	ENST00000380152		1468	tCt/tGt	11/27	1	2	FACETS	0.884	0.814	0.956	0.884	0.814	0.956	CLONAL	1	TRUE	1	0.59328700813153	2		521	618	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78617548	78617548	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	44	706	0	ENST00000306801.3:c.286C>G	p.Gln96Glu	p.Q96E	ENST00000306801	NM_020761.2	96	Cag/Gag	3/34	0.590380806939608	2	FACETS	0.213	0.178	0.252	0.106	0.089	0.126	SUBCLONAL	1	TRUE	0	0.59328700813153	2		706	697	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205017	123205017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	52	521	2	ENST00000218089.9:c.2377G>A	p.Asp793Asn	p.D793N	ENST00000218089	NM_001042749.1	793	Gat/Aat	25/35	0.59328700813153	3	FACETS	0.393	0.334	0.457	0.196	0.167	0.229	SUBCLONAL	1	TRUE	1	0.59328700813153	3		523	579	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599964	10599965	+	missense_variant	Missense_Mutation	DNP	CG	CG	GA	novel	NA	P-0021054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	256	1174	1	ENST00000171111.5:c.1611_1612delinsTC	p.Asp538His	p.D538H	ENST00000171111	NM_203500.1	537	taCGat/taTCat	5/6	1	2	FACETS	0.879	0.823	0.936	0.879	0.823	0.936	CLONAL	1	TRUE	1	0.59328700813153	2		1175	982	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593458	55593458	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	30	531	0	ENST00000288135.5:c.1615A>T	p.Ile539Phe	p.I539F	ENST00000288135	NM_000222.2	539	Att/Ttt	10/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		531	351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934874	NA	P-0021056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	549	1117	0	ENST00000269305.4:c.451C>G	p.Pro151Ala	p.P151A	ENST00000269305	NM_001126112.2	151	Ccc/Gcc	5/11	0.547065451300206	3	FACETS	0.983	0.952	1	0.983	0.952	1	CLONAL	3	TRUE	0	0.547065451300206	3		1117	867	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795094	45795094	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	103	702	1	ENST00000450313.1:c.1534C>T	p.Gln512Ter	p.Q512*	ENST00000450313	NM_012222.2	512	Cag/Tag	16/16	0.547065451300206	4	FACETS	0.899	0.806	0.998	0.45	0.403	0.499	CLONAL	1	TRUE	2	0.547065451300206	4		703	648	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375812	118375831	+	frameshift_variant	Frame_Shift_Del	DEL	ACCACTCCACCCCACCTGAA	ACCACTCCACCCCACCTGAA	-	novel	NA	P-0021056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	199	811	0	ENST00000534358.1:c.9205_9224del	p.Thr3069AlafsTer4	p.T3069Afs*4	ENST00000534358	NM_005933.3	3069	ACCACTCCACCCCACCTGAAg/g	27/36	0.524990646318666	2	FACETS	0.965	0.909	1	0.965	0.909	1	CLONAL	2	TRUE	0	0.547065451300206	2		811	377	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0021057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	267	1208	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.979	0.925	1	0.979	0.925	1	CLONAL	1	TRUE	1	0.850907737319551	2		1209	641	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572009	64572010	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	411	948	0	ENST00000312049.6:c.1629dup	p.Pro544ThrfsTer13	p.P544Tfs*13	ENST00000312049	NM_130799.2	543	-/A	10/10	0.891907224127085	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.891907224127085	1		948	495	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	148	251	0				ENST00000310581	NM_198253.2	-/1132			0.209743974305133	4	FACETS	0.868	0.797	0.942	0.868	0.797	0.942	INDETERMINATE	2	TRUE	2	0.421460168513593	4		251	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579494	7579494	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1555526721	NA	P-0021059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	233	1023	0	ENST00000269305.4:c.193A>T	p.Arg65Ter	p.R65*	ENST00000269305	NM_001126112.2	65	Aga/Tga	4/11	0.421460168513593	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.421460168513593	1		1023	775	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230892	53230892	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	234	442	2	ENST00000375401.3:c.1901G>T	p.Arg634Leu	p.R634L	ENST00000375401	NM_004187.3	634	cGc/cTc	14/26	0.367658956899898	2	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.421460168513593	2		444	475	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0021059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	87	492	0	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	0.421460168513593	3	FACETS	0.976	0.867	1	0.488	0.433	0.546	CLONAL	1	TRUE	1	0.421460168513593	3		492	512	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225628	225628	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876660259	NA	P-0021059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	124	563	3	ENST00000264932.6:c.407A>T	p.Gln136Leu	p.Q136L	ENST00000264932	NM_004168.2	136	cAg/cTg	4/15	0.209743974305133	4	FACETS	0.797	0.724	0.872	0.797	0.724	0.872	INDETERMINATE	2	TRUE	2	0.421460168513593	4		566	525	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023355	27023356	+	stop_gained	Nonsense_Mutation	DNP	AC	AC	GA	novel	NA	P-0021059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	199	545	3	ENST00000324856.7:c.461_462delinsGA	p.Tyr154Ter	p.Y154*	ENST00000324856	NM_006015.4	154	tAC/tGA	1/20	0.237893681401873	3	FACETS	1	0.986	1	0.796	0.745	0.847	INDETERMINATE	2	TRUE	0	0.421460168513593	3		548	479	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467791	99467791	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	51	525	1	ENST00000268035.6:c.2660A>T	p.Lys887Met	p.K887M	ENST00000268035	NM_000875.3	887	aAg/aTg	13/21	1	2	FACETS	0.52	0.443	0.606	0.52	0.443	0.606	SUBCLONAL	1	TRUE	1	0.421460168513593	2		526	465	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858334	59858334	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	190	759	0	ENST00000259008.2:c.1661A>C	p.Gln554Pro	p.Q554P	ENST00000259008	NM_032043.2	554	cAg/cCg	12/20	0.121897746561564	4	FACETS	0.78	0.722	0.839	0.78	0.722	0.839	INDETERMINATE	2	TRUE	2	0.421460168513593	4		759	822	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661206	227661206	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	192	964	0	ENST00000305123.5:c.2249A>G	p.Tyr750Cys	p.Y750C	ENST00000305123	NM_005544.2	750	tAc/tGc	1/2	0.121897746561564	4	FACETS	1	0.988	1	0.674	0.623	0.727	INDETERMINATE	1	TRUE	2	0.421460168513593	4		964	961	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224613	224613	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	122	458	0	ENST00000264932.6:c.289A>T	p.Arg97Trp	p.R97W	ENST00000264932	NM_004168.2	97	Agg/Tgg	3/15	0.209743974305133	4	FACETS	0.818	0.743	0.896	0.818	0.743	0.896	INDETERMINATE	2	TRUE	2	0.421460168513593	4		458	503	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528660	8528660	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	127	626	0	ENST00000356435.5:c.472A>G	p.Thr158Ala	p.T158A	ENST00000356435		158	Act/Gct	4/35	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.421460168513593	2		626	549	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0021070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	120	685	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.377704125855135	3	FACETS	0.925	0.835	1	0.463	0.417	0.51	CLONAL	1	TRUE	1	0.383057404515649	3		685	807	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030325	180030325	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115824945	NA	P-0021070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	197	851	1	ENST00000261937.6:c.3959G>A	p.Arg1320Gln	p.R1320Q	ENST00000261937	NM_182925.4	1320	cGg/cAg	30/30	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.383057404515649	2		852	849	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121566	2121566	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	90	943	0	ENST00000219476.3:c.1895C>G	p.Pro632Arg	p.P632R	ENST00000219476	NM_000548.3	632	cCc/cGc	18/42	1	2	FACETS	0.532	0.471	0.597	0.532	0.471	0.597	SUBCLONAL	1	TRUE	1	0.383057404515649	2		943	883	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089976	16089976	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	38	476	0	ENST00000268712.3:c.134C>T	p.Ser45Phe	p.S45F	ENST00000268712	NM_006311.3	45	tCc/tTc	3/46	1	2	FACETS	0.454	0.375	0.542	0.454	0.375	0.542	SUBCLONAL	1	TRUE	1	0.383057404515649	2		476	437	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0021071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	51	613	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.872	0.743	1	0.872	0.743	1	CLONAL	1	TRUE	1	0.289489590341775	2		614	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0021071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	124	1085	1	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.279291966920144	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.289489590341775	1		1086	660	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211161	2211161	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1404201020	NA	P-0021071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	92	891	1	ENST00000398665.3:c.1415C>A	p.Pro472His	p.P472H	ENST00000398665	NM_032482.2	472	cCc/cAc	15/28	1	2	FACETS	0.836	0.743	0.936	0.836	0.743	0.936	CLONAL	1	TRUE	1	0.289489590341775	2		892	760	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0021072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	208	717	0	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	0.197045671351242	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.312073247740014	2		717	617	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599990	10599990	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	101	853	0	ENST00000171111.5:c.1586A>T	p.Asp529Val	p.D529V	ENST00000171111	NM_203500.1	529	gAc/gTc	5/6	0.312073247740014	3	FACETS	0.919	0.821	1	0.46	0.41	0.512	CLONAL	1	TRUE	1	0.312073247740014	3		853	814	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0021074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	80	665	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.938	0.834	1	0.938	0.834	1	CLONAL	1	TRUE	1	0.564737078586189	2		665	302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0021074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	219	584	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.564737078586189	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.564737078586189	1		585	505	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925328	114925328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	160	731	0	ENST00000543371.1:c.1406G>A	p.Cys469Tyr	p.C469Y	ENST00000543371	NM_001198531.1	469	tGc/tAc	14/14	1	2	FACETS	0.948	0.873	1	0.948	0.873	1	CLONAL	1	TRUE	1	0.564737078586189	2		731	598	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196220	106196233	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGACCAGTCATG	CAGGACCAGTCATG	-	novel	NA	P-0021074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	68	347	0	ENST00000380013.4:c.4556_4569del	p.Gly1519AlafsTer54	p.G1519Afs*54	ENST00000380013	NM_001127208.2	1518	tCAGGACCAGTCATG/t	11/11	1	2	FACETS	0.857	0.753	0.967	0.857	0.753	0.967	CLONAL	1	TRUE	1	0.564737078586189	2		347	281	SUCCESS
APC	324	MSKCC	GRCh37	5	112175192	112175193	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0021074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	61	328	0	ENST00000257430.4:c.3903_3904dup	p.Leu1302ProfsTer4	p.L1302Pfs*4	ENST00000257430	NM_000038.5	1301	acc/aCCcc	16/16	1	2	FACETS	0.956	0.836	1	0.956	0.836	1	CLONAL	1	TRUE	1	0.564737078586189	2		328	226	SUCCESS
APC	324	MSKCC	GRCh37	5	112175328	112175328	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0021078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	141	514	0	ENST00000257430.4:c.4037C>G	p.Ser1346Ter	p.S1346*	ENST00000257430	NM_000038.5	1346	tCa/tGa	16/16	0.45420596172542	2	FACETS	0.932	0.862	1	0.932	0.862	1	CLONAL	2	TRUE	0	0.45420596172542	2		514	333	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129749	108129749	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs780619951	NA	P-0021078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	155	1022	0	ENST00000278616.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000278616	NM_000051.3	805	Cga/Tga	16/63	1	2	FACETS	0.978	0.897	1	0.978	0.897	1	CLONAL	1	TRUE	1	0.45420596172542	2		1022	698	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136976	64136976	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779990907	NA	P-0021078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	172	896	5	ENST00000334205.4:c.1487G>T	p.Arg496Leu	p.R496L	ENST00000334205	NM_003942.2	496	cGc/cTc	13/17	1	2	FACETS	0.961	0.886	1	0.961	0.886	1	CLONAL	1	TRUE	1	0.45420596172542	2		901	788	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192108	108192108	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	140	1012	0	ENST00000278616.4:c.6533C>A	p.Ala2178Asp	p.A2178D	ENST00000278616	NM_000051.3	2178	gCc/gAc	45/63	1	2	FACETS	0.871	0.794	0.951	0.871	0.794	0.951	CLONAL	1	TRUE	1	0.45420596172542	2		1012	708	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118848	70119119	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGCCCCGAGCAGACTTCTGAACGAGAGCGAGAAGCGGCCCTTCGTGGAGGAGGCGGAGCGGCTGCGCGTGCAGCACAAGAAGGACCACCCGGATTACAAGTACCAGCCGCGGCGGAGGAAGTCGGTGAAGAACGGGCAGGCGGAGGCAGAGGAGGCCACGGAGCAGACGCACATCTCCCCCAACGCCATCTTCAAGGCGCTGCAGGCCGACTCGCCACACTCCTCCTCCGGCATGAGCGAGGTGCACTCCCCCGGCGAGCACTCGGGTGAGT	CGCCCCGAGCAGACTTCTGAACGAGAGCGAGAAGCGGCCCTTCGTGGAGGAGGCGGAGCGGCTGCGCGTGCAGCACAAGAAGGACCACCCGGATTACAAGTACCAGCCGCGGCGGAGGAAGTCGGTGAAGAACGGGCAGGCGGAGGCAGAGGAGGCCACGGAGCAGACGCACATCTCCCCCAACGCCATCTTCAAGGCGCTGCAGGCCGACTCGCCACACTCCTCCTCCGGCATGAGCGAGGTGCACTCCCCCGGCGAGCACTCGGGTGAGT	-	novel	NA	P-0021078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	16	524	0	ENST00000245479.2:c.432-6_685+12del		p.X144_splice	ENST00000245479	NM_000346.3	144		2/3	0.45420596172542	2	FACETS	0.315	0.233	0.412	0.157	0.116	0.206	SUBCLONAL	1	TRUE	0	0.45420596172542	2		524	224	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725321	49725321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372289594	NA	P-0021078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	144	747	1	ENST00000449682.2:c.104C>T	p.Ser35Leu	p.S35L	ENST00000449682	NM_020998.3	35	tCg/tTg	2/18	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.45420596172542	2		748	600	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214410	55214410	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	151	1031	0	ENST00000275493.2:c.536A>G	p.Asp179Gly	p.D179G	ENST00000275493	NM_005228.3	179	gAc/gGc	4/28	0.315662127818742	3	FACETS	0.9	0.822	0.981	0.45	0.411	0.491	CLONAL	1	TRUE	1	0.45420596172542	3		1031	907	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	225	251	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.766	0.722	0.811	1	0.993	1	SUBCLONAL	2	TRUE	1	0.614288023107508	2		251	478	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0021079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	499	187	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.272297607249352	3	FACETS	0.95	0.932	0.966			1	INDETERMINATE	4	TRUE	NA	0.614288023107508	3		187	559	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0021079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	242	971	0	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	1	2	FACETS	0.813	0.76	0.868	0.813	0.76	0.868	CLONAL	1	TRUE	1	0.614288023107508	2		971	969	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420213	49420213	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	384	753	0	ENST00000301067.7:c.15536G>T	p.Arg5179Leu	p.R5179L	ENST00000301067	NM_003482.3	5179	cGt/cTt	48/54	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.614288023107508	2		753	843	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49423021	49423021	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0021079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	308	654	1	ENST00000301067.7:c.14076-2A>G		p.X4692_splice	ENST00000301067	NM_003482.3	4692			1	2	FACETS	0.753	0.715	0.79	1	0.995	1	SUBCLONAL	2	TRUE	1	0.614288023107508	2		655	666	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640662	3640662	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	444	907	0	ENST00000294008.3:c.2977G>C	p.Glu993Gln	p.E993Q	ENST00000294008	NM_032444.2	993	Gag/Cag	12/15	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.614288023107508	2		907	999	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216444	36216444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	247	980	0	ENST00000222270.7:c.3707C>T	p.Pro1236Leu	p.P1236L	ENST00000222270	NM_014727.1	1236	cCc/cTc	12/37	1	2	FACETS	0.828	0.775	0.883	0.828	0.775	0.883	CLONAL	1	TRUE	1	0.614288023107508	2		980	971	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40747846	40747846	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	318	690	0	ENST00000392038.2:c.572A>T	p.Lys191Met	p.K191M	ENST00000392038	NM_001626.4	191	aAg/aTg	6/14	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.614288023107508	2		690	729	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665411	176665412	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0021079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	271	521	0	ENST00000439151.2:c.4096dup	p.Ala1366GlyfsTer2	p.A1366Gfs*2	ENST00000439151	NM_022455.4	1365	-/G	7/23	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.614288023107508	2		521	616	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197157	26197158	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0021079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	251	697	0	ENST00000356476.2:c.321_322insTG	p.Thr108Ter	p.T108*	ENST00000356476		107	-/TG	1/1	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.614288023107508	2		697	597	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44970633	44970633	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	259	367	0	ENST00000377967.4:c.4184del	p.Pro1395HisfsTer143	p.P1395Hfs*143	ENST00000377967	NM_021140.2	1395	Cca/ca	29/29	1	1	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	0	0.614288023107508	1		367	281	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788596	3788596	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	TT	novel	NA	P-0021079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	221	602	0	ENST00000262367.5:c.4358delinsAA	p.Ile1453LysfsTer26	p.I1453Kfs*26	ENST00000262367	NM_004380.2	1453	aTc/aAAc	26/31	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.614288023107508	2		602	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0021080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	259	589	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.226540611680584	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.226540611680584	2		589	981	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385233	41385233	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	48	847	0	ENST00000373198.4:c.728T>C	p.Val243Ala	p.V243A	ENST00000373198	NM_133170.3	243	gTc/gCc	6/32	1	2	FACETS	0.597	0.503	0.7	0.597	0.503	0.7	SUBCLONAL	1	TRUE	1	0.226540611680584	2		847	710	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138400860	138400860	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	50	972	0	ENST00000289153.2:c.2453A>T	p.Gln818Leu	p.Q818L	ENST00000289153	NM_006219.2	818	cAa/cTa	17/22	0.155627862902187	4	FACETS	0.662	0.56	0.775	0.221	0.186	0.259	SUBCLONAL	1	TRUE	1	0.226540611680584	4		972	818	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759916	133759916	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	62	1041	0	ENST00000318560.5:c.2239T>C	p.Phe747Leu	p.F747L	ENST00000318560	NM_005157.4	747	Ttt/Ctt	11/11	0.168229435361429	1	FACETS	0.632	0.545	0.727	0.632	0.545	0.727	SUBCLONAL	1	TRUE	0	0.226540611680584	1		1041	768	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760877	133760877	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	56	1039	1	ENST00000318560.5:c.3200G>C	p.Cys1067Ser	p.C1067S	ENST00000318560	NM_005157.4	1067	tGc/tCc	11/11	0.168229435361429	1	FACETS	0.537	0.458	0.622	0.537	0.458	0.622	SUBCLONAL	1	TRUE	0	0.226540611680584	1		1040	817	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195076	123195076	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	39	590	1	ENST00000218089.9:c.1419A>T	p.Leu473Phe	p.L473F	ENST00000218089	NM_001042749.1	473	ttA/ttT	16/35	NA	2	FACETS	0.731	0.606	0.871			1	INDETERMINATE	1	TRUE	NA	0.226540611680584	2		591	471	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28595728	28595728	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769967309	NA	P-0021081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	379	1146	5	ENST00000253063.3:c.125G>A	p.Arg42Gln	p.R42Q	ENST00000253063	NM_031459.4	42	cGa/cAa	2/10	1	2	FACETS	1	0.99	1	1	0.997	1	CLONAL	2	FALSE	1	0.338480465037516	2		1151	984	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225677	26225677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	307	990	0	ENST00000360408.1:c.295G>A	p.Ala99Thr	p.A99T	ENST00000360408	NM_003532.2	99	Gcc/Acc	1/1	0.338480465037516	3	FACETS	0.998	0.941	1	0.998	0.941	1	CLONAL	2	FALSE	1	0.338480465037516	3		990	1063	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0021082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	151	240	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.68754942019991	2		240	415	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0021082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	202	303	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.68754942019991	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.68754942019991	1		303	343	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144146	55144146	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	205	946	0	ENST00000257290.5:c.1975A>T	p.Asn659Tyr	p.N659Y	ENST00000257290	NM_006206.4	659	Aac/Tac	14/23	1	2	FACETS	0.803	0.747	0.86	0.803	0.747	0.86	CLONAL	1	TRUE	1	0.68754942019991	2		946	743	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450048	32450048	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444869026	NA	P-0021082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	229	830	1	ENST00000332351.3:c.764C>T	p.Ser255Leu	p.S255L	ENST00000332351	NM_024426.4	255	tCg/tTg	2/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.68754942019991	2		831	563	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056397	180056397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368167894	NA	P-0021082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	207	915	2	ENST00000261937.6:c.847C>T	p.Arg283Cys	p.R283C	ENST00000261937	NM_182925.4	283	Cgc/Tgc	7/30	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.68754942019991	2		917	546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912660	NA	P-0021083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	123	751	0	ENST00000269305.4:c.839G>T	p.Arg280Ile	p.R280I	ENST00000269305	NM_001126112.2	280	aGa/aTa	8/11	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.25	2		751	966	SUCCESS
APC	324	MSKCC	GRCh37	5	112175754	112175754	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0021083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	28	540	0	ENST00000257430.4:c.4463T>A	p.Leu1488Ter	p.L1488*	ENST00000257430	NM_000038.5	1488	tTa/tAa	16/16	1	2	FACETS	0.429	0.342	0.529	0.429	0.342	0.529	SUBCLONAL	1	TRUE	1	0.25	2		540	522	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061227	38061235	+	inframe_deletion	In_Frame_Del	DEL	GAACATGTT	GAACATGTT	-	novel	NA	P-0021083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	47	789	0	ENST00000250448.2:c.754_762del	p.Asn252_Phe254del	p.N252_F254del	ENST00000250448	NM_004496.3	252	AACATGTTC/-	2/2	1	2	FACETS	0.498	0.419	0.586	0.498	0.419	0.586	SUBCLONAL	1	TRUE	1	0.25	2		789	755	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578206	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs886039484	NA	P-0021088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	207	1116	0	ENST00000269305.4:c.643A>G	p.Ser215Gly	p.S215G	ENST00000269305	NM_001126112.2	215	Agt/Ggt	6/11	0.531223267024145	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	0	0.555192135530154	2		1116	372	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741684	17741684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1384940737	NA	P-0021088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	67	726	5	ENST00000250003.3:c.355C>T	p.Arg119Trp	p.R119W	ENST00000250003	NM_002478.4	119	Cgg/Tgg	1/3	0.555192135530154	3	FACETS	1	0.929	1	0.543	0.476	0.614	CLONAL	1	TRUE	1	0.555192135530154	3		731	284	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125036	46125036	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	70	525	3	ENST00000334344.6:c.223G>T	p.Glu75Ter	p.E75*	ENST00000334344	NM_152641.2	75	Gag/Tag	3/21	0.555192135530154	3	FACETS	0.937	0.836	1	0.937	0.836	1	CLONAL	2	TRUE	1	0.555192135530154	3		528	172	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246497	46246509	+	frameshift_variant	Frame_Shift_Del	DEL	CCAAATAAAGTAG	CCAAATAAAGTAG	-	novel	NA	P-0021088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	43	388	0	ENST00000334344.6:c.4591_4603del	p.Pro1531GlufsTer31	p.P1531Efs*31	ENST00000334344	NM_152641.2	1531	CCAAATAAAGTAGga/ga	15/21	0.555192135530154	3	FACETS	0.842	0.711	0.985	0.421	0.355	0.493	CLONAL	1	TRUE	1	0.555192135530154	3		388	235	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435390	121435390	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	109	1184	2	ENST00000257555.6:c.1423C>A	p.Pro475Thr	p.P475T	ENST00000257555		475	Ccg/Acg	7/10	0.555192135530154	3	FACETS	1	0.94	1	0.528	0.477	0.582	CLONAL	1	TRUE	1	0.555192135530154	3		1186	475	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872934	35872934	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	141	857	0	ENST00000216797.5:c.298G>C	p.Asp100His	p.D100H	ENST00000216797	NM_020529.2	100	Gac/Cac	2/6	0.555192135530154	4	FACETS	0.973	0.895	1	0.973	0.895	1	CLONAL	2	TRUE	2	0.555192135530154	4		857	406	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562480	95562480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	54	713	2	ENST00000393063.1:c.4777G>A	p.Val1593Ile	p.V1593I	ENST00000393063	NM_030621.3	1593	Gta/Ata	24/28	0.555192135530154	4	FACETS	0.772	0.661	0.892	0.386	0.33	0.446	SUBCLONAL	1	TRUE	2	0.555192135530154	4		715	392	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034837	42034837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	145	839	0	ENST00000219905.7:c.4681del	p.Thr1561ProfsTer15	p.T1561Pfs*15	ENST00000219905	NM_001164273.1	1560	cAa/ca	15/24	0.555192135530154	4	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	2	0.555192135530154	4		839	397	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550586	29550586	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0021088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	45	346	0	ENST00000356175.3:c.1845+1G>T		p.X615_splice	ENST00000356175	NM_000267.3	615			0.555192135530154	3	FACETS	1	0.952	1	0.651	0.557	0.751	CLONAL	1	TRUE	1	0.555192135530154	3		346	159	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985602	60985602	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	69	329	0	ENST00000333681.4:c.298G>T	p.Ala100Ser	p.A100S	ENST00000333681		100	Gcc/Tcc	2/3	0.555192135530154	3	FACETS	0.913	0.813	1	0.913	0.813	1	CLONAL	2	TRUE	1	0.555192135530154	3		329	174	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40744873	40744873	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	58	983	0	ENST00000392038.2:c.647A>G	p.Lys216Arg	p.K216R	ENST00000392038	NM_001626.4	216	aAg/aGg	8/14	0.555192135530154	3	FACETS	0.834	0.721	0.956	0.417	0.36	0.478	CLONAL	1	TRUE	1	0.555192135530154	3		983	320	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54956497	54956497	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	126	705	0	ENST00000312783.6:c.697A>T	p.Thr233Ser	p.T233S	ENST00000312783	NM_198436.1	233	Act/Tct	7/10	0.555192135530154	3	FACETS	0.941	0.866	1	0.941	0.866	1	CLONAL	2	TRUE	1	0.555192135530154	3		705	308	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185200167	185200167	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	141	970	1	ENST00000265026.3:c.2824G>T	p.Asp942Tyr	p.D942Y	ENST00000265026	NM_004721.4	942	Gac/Tac	14/14	0.555192135530154	4	FACETS	0.874	0.803	0.947	0.874	0.803	0.947	CLONAL	2	TRUE	2	0.555192135530154	4		971	452	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197171	106197171	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	64	557	1	ENST00000380013.4:c.5504G>T	p.Gly1835Val	p.G1835V	ENST00000380013	NM_001127208.2	1835	gGt/gTt	11/11	1	2	FACETS	0.848	0.741	0.96	0.848	0.741	0.96	CLONAL	1	TRUE	1	0.555192135530154	2		558	272	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530351	187530351	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	86	535	0	ENST00000441802.2:c.10192C>G	p.Leu3398Val	p.L3398V	ENST00000441802	NM_005245.3	3398	Ctc/Gtc	16/27	0.555192135530154	3	FACETS	0.773	0.694	0.855	0.773	0.694	0.855	SUBCLONAL	2	TRUE	1	0.555192135530154	3		535	256	SUCCESS
AR	367	MSKCC	GRCh37	X	66765346	66765347	+	missense_variant	Missense_Mutation	DNP	CA	CA	AT	novel	NA	P-0021088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	59	625	1	ENST00000374690.3:c.358_359delinsAT	p.Gln120Met	p.Q120M	ENST00000374690	NM_000044.3	120	CAg/ATg	1/8	1	1	FACETS	0.942	0.828	1	0.942	0.828	1	CLONAL	1	TRUE	0	0.555192135530154	1		626	163	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9787030	9787030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397518423	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	137	855	1	ENST00000377346.4:c.3061G>A	p.Glu1021Lys	p.E1021K	ENST00000377346	NM_005026.3	1021	Gaa/Aaa	24/24	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.39	2		856	691	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261434	16261434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	133	904	0	ENST00000375759.3:c.8699C>T	p.Ser2900Leu	p.S2900L	ENST00000375759	NM_015001.2	2900	tCg/tTg	11/15	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.39	2		904	653	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089669	27089669	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	94	883	4	ENST00000324856.7:c.2625G>A	p.Met875Ile	p.M875I	ENST00000324856	NM_006015.4	875	atG/atA	8/20	1	2	FACETS	0.795	0.709	0.887	0.795	0.709	0.887	SUBCLONAL	1	TRUE	1	0.39	2		887	606	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100172	27100172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775802127	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	82	668	2	ENST00000324856.7:c.3968G>A	p.Arg1323His	p.R1323H	ENST00000324856	NM_006015.4	1323	cGc/cAc	16/20	1	2	FACETS	0.918	0.813	1	0.918	0.813	1	CLONAL	1	TRUE	1	0.39	2		670	458	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932400	36932400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764345289	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	142	1128	0	ENST00000361632.4:c.2069C>T	p.Thr690Met	p.T690M	ENST00000361632		690	aCg/aTg	16/16	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.39	2		1128	697	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812205	43812205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866559375	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	138	994	2	ENST00000372470.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000372470	NM_005373.2	357	cGa/cAa	7/12	1	2	FACETS	0.917	0.835	1	0.917	0.835	1	CLONAL	1	TRUE	1	0.39	2		996	772	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812214	43812214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs993382058	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	135	979	0	ENST00000372470.3:c.1079G>A	p.Ser360Asn	p.S360N	ENST00000372470	NM_005373.2	360	aGc/aAc	7/12	1	2	FACETS	0.882	0.802	0.966	0.882	0.802	0.966	CLONAL	1	TRUE	1	0.39	2		979	785	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163819	72163819	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	44	562	0	ENST00000357731.5:c.539A>G	p.Lys180Arg	p.K180R	ENST00000357731	NM_173808.2	180	aAa/aGa	4/7	1	2	FACETS	0.848	0.716	0.992	0.848	0.716	0.992	CLONAL	1	TRUE	1	0.39	2		562	266	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428511	78428511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408536007	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	102	935	0	ENST00000370768.2:c.1288C>T	p.Arg430Cys	p.R430C	ENST00000370768	NM_003902.3	430	Cgt/Tgt	14/20	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.39	2		935	521	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276472	115276472	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	75	762	2	ENST00000438362.2:c.856G>T	p.Glu286Ter	p.E286*	ENST00000438362	NM_001242891.1	286	Gaa/Taa	9/20	1	2	FACETS	0.782	0.687	0.883	0.782	0.687	0.883	SUBCLONAL	1	TRUE	1	0.39	2		764	492	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745593	162745593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769532262	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	106	814	0	ENST00000367921.3:c.2008G>A	p.Glu670Lys	p.E670K	ENST00000367921	NM_006182.2	670	Gag/Aag	15/18	1	2	FACETS	0.881	0.791	0.976	0.881	0.791	0.976	CLONAL	1	TRUE	1	0.39	2		814	617	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206943236	206943236	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs766492258	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	78	561	2	ENST00000423557.1:c.382C>T	p.Arg128Ter	p.R128*	ENST00000423557	NM_000572.2	128	Cga/Tga	4/5	1	2	FACETS	0.873	0.77	0.983	0.873	0.77	0.983	CLONAL	1	TRUE	1	0.39	2		563	458	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228613019	228613019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773567566	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	77	423	0	ENST00000366696.1:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000366696	NM_003493.2	3	cGa/cAa	1/1	1	2	FACETS	0.99	0.874	1	0.99	0.874	1	CLONAL	1	TRUE	1	0.39	2		423	399	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115778	8115778	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	113	903	3	ENST00000346208.3:c.1124G>A	p.Cys375Tyr	p.C375Y	ENST00000346208		375	tGc/tAc	6/6	1	2	FACETS	0.847	0.763	0.936	0.847	0.763	0.936	CLONAL	1	TRUE	1	0.39	2		906	684	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63829469	63829469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1206856276	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	49	586	4	ENST00000279873.7:c.1112G>A	p.Arg371His	p.R371H	ENST00000279873	NM_032199.2	371	cGc/cAc	8/10	1	2	FACETS	0.653	0.554	0.76	0.653	0.554	0.76	SUBCLONAL	1	TRUE	1	0.39	2		590	385	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63829541	63829541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	60	570	1	ENST00000279873.7:c.1184G>A	p.Arg395His	p.R395H	ENST00000279873	NM_032199.2	395	cGc/cAc	8/10	1	2	FACETS	0.752	0.65	0.862	0.752	0.65	0.862	SUBCLONAL	1	TRUE	1	0.39	2		571	409	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845613	63845613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1352309345	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	47	394	0	ENST00000279873.7:c.1352G>A	p.Ser451Asn	p.S451N	ENST00000279873	NM_032199.2	451	aGc/aAc	9/10	1	2	FACETS	0.801	0.679	0.933	0.801	0.679	0.933	CLONAL	1	TRUE	1	0.39	2		394	301	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850777	63850777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374377066	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	74	640	0	ENST00000279873.7:c.1555G>A	p.Glu519Lys	p.E519K	ENST00000279873	NM_032199.2	519	Gaa/Aaa	10/10	1	2	FACETS	0.904	0.795	1	0.904	0.795	1	CLONAL	1	TRUE	1	0.39	2		640	420	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852134	63852134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772815163	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	98	790	0	ENST00000279873.7:c.2912C>T	p.Ser971Leu	p.S971L	ENST00000279873	NM_032199.2	971	tCg/tTg	10/10	1	2	FACETS	0.931	0.833	1	0.931	0.833	1	CLONAL	1	TRUE	1	0.39	2		790	540	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405917	70405917	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	79	891	0	ENST00000373644.4:c.3431A>C	p.Asn1144Thr	p.N1144T	ENST00000373644	NM_030625.2	1144	aAc/aCc	4/12	1	2	FACETS	0.753	0.664	0.849	0.753	0.664	0.849	SUBCLONAL	1	TRUE	1	0.39	2		891	538	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711931	89711931	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876659227	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	28	795	0	ENST00000371953.3:c.549G>T	p.Lys183Asn	p.K183N	ENST00000371953	NM_000314.4	183	aaG/aaT	6/9	1	2	FACETS	0.297	0.236	0.366	0.297	0.236	0.366	SUBCLONAL	1	TRUE	1	0.39	2		795	484	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	90	752	0	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	1	2	FACETS	0.705	0.626	0.789	0.705	0.626	0.789	SUBCLONAL	1	TRUE	1	0.39	2		752	655	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944012	71944012	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs777831045	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	150	1017	0	ENST00000298229.2:c.1945C>T	p.Arg649Ter	p.R649*	ENST00000298229	NM_001567.3	649	Cga/Tga	16/28	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.39	2		1017	721	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77048440	77048440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1326439583	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	141	916	1	ENST00000356341.3:c.1145C>T	p.Ser382Leu	p.S382L	ENST00000356341	NM_002576.4	382	tCg/tTg	12/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.39	2		917	627	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115600	108115600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772821016	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	68	850	1	ENST00000278616.4:c.748C>T	p.Arg250Ter	p.R250*	ENST00000278616	NM_000051.3	250	Cga/Tga	7/63	1	2	FACETS	0.733	0.639	0.833	0.733	0.639	0.833	SUBCLONAL	1	TRUE	1	0.39	2		851	476	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205756	108205756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531980488	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	78	609	0	ENST00000278616.4:c.8071C>T	p.Arg2691Cys	p.R2691C	ENST00000278616	NM_000051.3	2691	Cgc/Tgc	55/63	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.39	2		609	380	SUCCESS
CBL	867	MSKCC	GRCh37	11	119168162	119168162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763213265	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	89	853	0	ENST00000264033.4:c.2222C>T	p.Ala741Val	p.A741V	ENST00000264033	NM_005188.3	741	gCg/gTg	14/16	1	2	FACETS	0.701	0.622	0.786	0.701	0.622	0.786	SUBCLONAL	1	TRUE	1	0.39	2		853	651	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699323	18699323	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199904184	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	77	658	0	ENST00000266497.5:c.3424C>T	p.Arg1142Cys	p.R1142C	ENST00000266497		1142	Cgt/Tgt	24/31	1	2	FACETS	0.947	0.835	1	0.947	0.835	1	CLONAL	1	TRUE	1	0.39	2		658	417	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636471	21636471	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	103	872	0	ENST00000421138.2:c.539A>C	p.Lys180Thr	p.K180T	ENST00000421138		180	aAa/aCa	7/16	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.39	2		872	473	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944961	31944961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1441610501	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	113	783	0	ENST00000340398.3:c.140C>T	p.Ala47Val	p.A47V	ENST00000340398	NM_001013699.2	47	gCg/gTg	1/1	1	2	FACETS	0.961	0.867	1	0.961	0.867	1	CLONAL	1	TRUE	1	0.39	2		783	603	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245076	46245076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1234210825	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	98	800	0	ENST00000334344.6:c.3170C>T	p.Ser1057Leu	p.S1057L	ENST00000334344	NM_152641.2	1057	tCg/tTg	15/21	1	2	FACETS	0.873	0.78	0.97	0.873	0.78	0.97	CLONAL	1	TRUE	1	0.39	2		800	576	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425893	49425893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1209563787	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	145	991	2	ENST00000301067.7:c.12595G>A	p.Ala4199Thr	p.A4199T	ENST00000301067	NM_003482.3	4199	Gca/Aca	39/54	1	2	FACETS	0.976	0.891	1	0.976	0.891	1	CLONAL	1	TRUE	1	0.39	2		993	762	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869501	102869501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs527983684	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	111	690	3	ENST00000307046.8:c.140C>T	p.Thr47Met	p.T47M	ENST00000307046	NM_001111285.1	47	aCg/aTg	2/4	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.39	2		693	532	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120969	115120969	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	81	754	0	ENST00000257566.3:c.37A>C	p.Thr13Pro	p.T13P	ENST00000257566	NM_016569.3	13	Aca/Cca	1/8	1	2	FACETS	0.844	0.746	0.949	0.844	0.746	0.949	CLONAL	1	TRUE	1	0.39	2		754	492	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	104	738	1	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.39	2		739	469	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28908194	28908194	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767930948	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	109	1005	2	ENST00000282397.4:c.2561C>T	p.Thr854Met	p.T854M	ENST00000282397	NM_002019.4	854	aCg/aTg	18/30	1	2	FACETS	0.811	0.729	0.898	0.811	0.729	0.898	CLONAL	1	TRUE	1	0.39	2		1007	689	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008329	29008329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	60	518	0	ENST00000282397.4:c.542G>A	p.Gly181Glu	p.G181E	ENST00000282397	NM_002019.4	181	gGa/gAa	5/30	1	2	FACETS	0.916	0.794	1	0.916	0.794	1	CLONAL	1	TRUE	1	0.39	2		518	336	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913279	32913279	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	54	861	0	ENST00000380152.3:c.4787A>C	p.Asn1596Thr	p.N1596T	ENST00000380152		1596	aAt/aCt	11/27	1	2	FACETS	0.618	0.529	0.715	0.618	0.529	0.715	SUBCLONAL	1	TRUE	1	0.39	2		861	448	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346368	73346368	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	57	807	0	ENST00000377767.4:c.1432G>A	p.Val478Ile	p.V478I	ENST00000377767	NM_014953.3	478	Gta/Ata	10/21	1	2	FACETS	0.704	0.606	0.811	0.704	0.606	0.811	SUBCLONAL	1	TRUE	1	0.39	2		807	415	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519117	103519117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770975661	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	95	821	0	ENST00000355739.4:c.2455C>T	p.Arg819Trp	p.R819W	ENST00000355739	NM_000123.3	819	Cgg/Tgg	11/15	1	2	FACETS	0.73	0.651	0.815	0.73	0.651	0.815	SUBCLONAL	1	TRUE	1	0.39	2		821	667	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434426	110434426	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs149826392	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	136	1035	1	ENST00000375856.3:c.3975C>A	p.Phe1325Leu	p.F1325L	ENST00000375856	NM_003749.2	1325	ttC/ttA	1/2	1	2	FACETS	0.896	0.816	0.981	0.896	0.816	0.981	CLONAL	1	TRUE	1	0.39	2		1036	778	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435634	110435634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	97	519	1	ENST00000375856.3:c.2767G>A	p.Asp923Asn	p.D923N	ENST00000375856	NM_003749.2	923	Gac/Aac	1/2	1	2	FACETS	0.928	0.83	1	0.928	0.83	1	CLONAL	1	TRUE	1	0.39	2		520	536	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987192	36987192	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	120	1034	0	ENST00000354822.5:c.497A>G	p.Asn166Ser	p.N166S	ENST00000354822	NM_001079668.2	166	aAc/aGc	3/3	1	2	FACETS	0.918	0.831	1	0.918	0.831	1	CLONAL	1	TRUE	1	0.39	2		1034	670	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40993358	40993358	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	78	593	1	ENST00000267868.3:c.184A>C	p.Asn62His	p.N62H	ENST00000267868	NM_002875.4	62	Aat/Cat	3/10	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.39	2		594	394	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003246	42003246	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	103	993	0	ENST00000219905.7:c.2783A>C	p.Lys928Thr	p.K928T	ENST00000219905	NM_001164273.1	928	aAa/aCa	8/24	1	2	FACETS	0.823	0.737	0.913	0.823	0.737	0.913	CLONAL	1	TRUE	1	0.39	2		993	642	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707977	43707977	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	164	1056	1	ENST00000382044.4:c.4904G>A	p.Arg1635His	p.R1635H	ENST00000382044	NM_001141980.1	1635	cGc/cAc	23/28	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.39	2		1057	840	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714237	43714237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1171556914	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	165	1210	0	ENST00000382044.4:c.3916G>A	p.Asp1306Asn	p.D1306N	ENST00000382044	NM_001141980.1	1306	Gat/Aat	19/28	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.39	2		1210	838	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007643	45007643	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	52	519	1	ENST00000558401.1:c.90C>A	p.Tyr30Ter	p.Y30*	ENST00000558401	NM_004048.2	30	taC/taA	2/4	1	2	FACETS	0.839	0.718	0.969	0.839	0.718	0.969	CLONAL	1	TRUE	1	0.39	2		520	318	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007672	45007672	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	78	587	0	ENST00000558401.1:c.119C>A	p.Ser40Ter	p.S40*	ENST00000558401	NM_004048.2	40	tCa/tAa	2/4	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.39	2		587	368	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007867	45007867	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	85	630	0	ENST00000558401.1:c.314T>C	p.Val105Ala	p.V105A	ENST00000558401	NM_004048.2	105	gTg/gCg	2/4	1	2	FACETS	0.969	0.86	1	0.969	0.86	1	CLONAL	1	TRUE	1	0.39	2		630	450	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457303	67457303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768713596	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	133	924	5	ENST00000327367.4:c.277C>T	p.Arg93Ter	p.R93*	ENST00000327367	NM_005902.3	93	Cga/Tga	2/9	1	2	FACETS	0.981	0.893	1	0.981	0.893	1	CLONAL	1	TRUE	1	0.39	2		929	695	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473635	67473635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906853	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	142	937	1	ENST00000327367.4:c.715G>A	p.Glu239Lys	p.E239K	ENST00000327367	NM_005902.3	239	Gag/Aag	6/9	1	2	FACETS	0.985	0.899	1	0.985	0.899	1	CLONAL	1	TRUE	1	0.39	2		938	739	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726711	88726711	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	80	742	1	ENST00000360948.2:c.333G>T	p.Lys111Asn	p.K111N	ENST00000360948	NM_001012338.2	111	aaG/aaT	4/19	1	2	FACETS	0.764	0.674	0.86	0.764	0.674	0.86	SUBCLONAL	1	TRUE	1	0.39	2		743	537	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293070	91293070	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs569086568	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	42	648	2	ENST00000355112.3:c.572G>T	p.Arg191Ile	p.R191I	ENST00000355112	NM_000057.2	191	aGa/aTa	3/22	1	2	FACETS	0.409	0.341	0.484	0.409	0.341	0.484	SUBCLONAL	1	TRUE	1	0.39	2		650	527	SUCCESS
BLM	641	MSKCC	GRCh37	15	91326066	91326066	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	64	680	0	ENST00000355112.3:c.2570T>G	p.Phe857Cys	p.F857C	ENST00000355112	NM_000057.2	857	tTt/tGt	13/22	1	2	FACETS	0.763	0.663	0.871	0.763	0.663	0.871	SUBCLONAL	1	TRUE	1	0.39	2		680	430	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250839	99250839	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774734018	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	107	690	1	ENST00000268035.6:c.143G>A	p.Arg48His	p.R48H	ENST00000268035	NM_000875.3	48	cGc/cAc	2/21	1	2	FACETS	0.964	0.868	1	0.964	0.868	1	CLONAL	1	TRUE	1	0.39	2		691	569	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465573	99465573	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1318014146	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	45	852	3	ENST00000268035.6:c.2398C>T	p.Arg800Cys	p.R800C	ENST00000268035	NM_000875.3	800	Cgc/Tgc	11/21	1	2	FACETS	0.335	0.281	0.395	0.335	0.281	0.395	SUBCLONAL	1	TRUE	1	0.39	2		855	689	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639366	3639366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766448056	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	155	1041	0	ENST00000294008.3:c.4273G>A	p.Asp1425Asn	p.D1425N	ENST00000294008	NM_032444.2	1425	Gac/Aac	12/15	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.39	2		1041	763	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778168	3778168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763223282	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	150	1082	1	ENST00000262367.5:c.6880C>T	p.Arg2294Trp	p.R2294W	ENST00000262367	NM_004380.2	2294	Cgg/Tgg	31/31	1	2	FACETS	0.923	0.844	1	0.923	0.844	1	CLONAL	1	TRUE	1	0.39	2		1083	833	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857197	9857197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866121846	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	109	705	1	ENST00000330684.3:c.4204C>T	p.Arg1402Trp	p.R1402W	ENST00000330684	NM_001134407.1	1402	Cgg/Tgg	13/13	1	2	FACETS	0.986	0.888	1	0.986	0.888	1	CLONAL	1	TRUE	1	0.39	2		706	567	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845934	72845934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759043061	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	75	632	3	ENST00000268489.5:c.3533C>T	p.Ser1178Leu	p.S1178L	ENST00000268489	NM_006885.3	1178	tCg/tTg	6/10	1	2	FACETS	0.892	0.785	1	0.892	0.785	1	CLONAL	1	TRUE	1	0.39	2		635	431	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888069	81888069	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	69	636	0	ENST00000359376.3:c.214G>A	p.Glu72Lys	p.E72K	ENST00000359376	NM_002661.3	72	Gaa/Aaa	3/33	1	2	FACETS	0.863	0.755	0.979	0.863	0.755	0.979	CLONAL	1	TRUE	1	0.39	2		636	410	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556080	29556080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762709897	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	49	395	1	ENST00000356175.3:c.2447G>A	p.Arg816Gln	p.R816Q	ENST00000356175	NM_000267.3	816	cGa/cAa	21/57	1	2	FACETS	0.92	0.785	1	0.92	0.785	1	CLONAL	1	TRUE	1	0.39	2		396	273	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557865	29557865	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	29	354	0	ENST00000356175.3:c.3119A>C	p.Lys1040Thr	p.K1040T	ENST00000356175	NM_000267.3	1040	aAg/aCg	24/57	1	2	FACETS	0.896	0.727	1	0.896	0.727	1	CLONAL	1	TRUE	1	0.39	2		354	166	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29579995	29579995	+	intron_variant	Intron	SNP	G	G	T	rs1387972895	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	78	698	3	ENST00000356175.3:c.4110+3858G>T		p.*1370*	ENST00000356175	NM_000267.3	1384/2839			1	2	FACETS	0.998	0.881	1	0.998	0.881	1	CLONAL	1	TRUE	1	0.39	2		701	401	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652960	29652960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763413441	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	91	735	0	ENST00000356175.3:c.4895G>A	p.Arg1632His	p.R1632H	ENST00000356175	NM_000267.3	1632	cGc/cAc	36/57	1	2	FACETS	0.832	0.74	0.929	0.832	0.74	0.929	CLONAL	1	TRUE	1	0.39	2		735	561	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654757	29654757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771597781	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	77	635	0	ENST00000356175.3:c.5446G>A	p.Asp1816Asn	p.D1816N	ENST00000356175	NM_000267.3	1816	Gac/Aac	37/57	1	2	FACETS	0.876	0.772	0.986	0.876	0.772	0.986	CLONAL	1	TRUE	1	0.39	2		635	451	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654820	29654820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786203416	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	70	498	1	ENST00000356175.3:c.5509G>A	p.Ala1837Thr	p.A1837T	ENST00000356175	NM_000267.3	1837	Gca/Aca	37/57	1	2	FACETS	0.983	0.863	1	0.983	0.863	1	CLONAL	1	TRUE	1	0.39	2		499	365	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372045	45372045	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	77	801	0	ENST00000262160.6:c.1124A>C	p.Lys375Thr	p.K375T	ENST00000262160	NM_005901.5	375	aAa/aCa	9/11	1	2	FACETS	0.889	0.784	1	0.889	0.784	1	CLONAL	1	TRUE	1	0.39	2		801	444	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374881	45374881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	112	967	1	ENST00000262160.6:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000262160	NM_005901.5	321	cGa/cAa	8/11	1	2	FACETS	0.906	0.816	1	0.906	0.816	1	CLONAL	1	TRUE	1	0.39	2		968	634	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395689	45395689	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	100	759	0	ENST00000262160.6:c.445T>G	p.Cys149Gly	p.C149G	ENST00000262160	NM_005901.5	149	Tgc/Ggc	4/11	1	2	FACETS	0.946	0.848	1	0.946	0.848	1	CLONAL	1	TRUE	1	0.39	2		759	542	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215538	5215538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267605547	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	148	1083	1	ENST00000357368.4:c.4165G>A	p.Asp1389Asn	p.D1389N	ENST00000357368	NM_002850.3	1389	Gac/Aac	27/38	1	2	FACETS	0.951	0.869	1	0.951	0.869	1	CLONAL	1	TRUE	1	0.39	2		1084	798	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968144	18968144	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	154	944	2	ENST00000262803.5:c.1984G>A	p.Asp662Asn	p.D662N	ENST00000262803	NM_002911.3	662	Gac/Aac	15/24	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.39	2		946	664	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211219	36211219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765836382	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	183	1445	1	ENST00000222270.7:c.970G>A	p.Glu324Lys	p.E324K	ENST00000222270	NM_014727.1	324	Gaa/Aaa	3/37	1	2	FACETS	0.878	0.809	0.949	0.878	0.809	0.949	CLONAL	1	TRUE	1	0.39	2		1446	1069	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719065	52719065	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	76	937	0	ENST00000322088.6:c.841A>C	p.Thr281Pro	p.T281P	ENST00000322088	NM_014225.5	281	Aca/Cca	7/15	1	2	FACETS	0.574	0.503	0.65	0.574	0.503	0.65	SUBCLONAL	1	TRUE	1	0.39	2		937	679	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470926	25470926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1203141216	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	144	1095	0	ENST00000264709.3:c.835G>A	p.Asp279Asn	p.D279N	ENST00000264709	NM_175629.2	279	Gat/Aat	7/23	1	2	FACETS	0.954	0.871	1	0.954	0.871	1	CLONAL	1	TRUE	1	0.39	2		1095	774	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068374	26068374	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	78	749	0	ENST00000435504.4:c.116A>C	p.Gln39Pro	p.Q39P	ENST00000435504		39	cAg/cCg	2/13	1	2	FACETS	0.883	0.779	0.994	0.883	0.779	0.994	CLONAL	1	TRUE	1	0.39	2		749	453	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416563	29416563	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs374135358	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	28	784	0	ENST00000389048.3:c.4390C>T	p.Arg1464Ter	p.R1464*	ENST00000389048	NM_004304.4	1464	Cga/Tga	29/29	1	2	FACETS	0.275	0.219	0.339	0.275	0.219	0.339	SUBCLONAL	1	TRUE	1	0.39	2		784	522	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606678	29606678	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs188859061	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	101	935	0	ENST00000389048.3:c.1202G>A	p.Arg401Gln	p.R401Q	ENST00000389048	NM_004304.4	401	cGa/cAa	5/29	1	2	FACETS	0.811	0.725	0.901	0.811	0.725	0.901	CLONAL	1	TRUE	1	0.39	2		935	639	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606679	29606679	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs865931787	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	132	948	2	ENST00000389048.3:c.1201C>T	p.Arg401Ter	p.R401*	ENST00000389048	NM_004304.4	401	Cga/Tga	5/29	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.39	2		950	647	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222425	39222425	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	62	1056	0	ENST00000402219.2:c.3185A>C	p.Lys1062Thr	p.K1062T	ENST00000402219	NM_005633.3	1062	aAa/aCa	20/23	1	2	FACETS	0.425	0.366	0.489	0.425	0.366	0.489	SUBCLONAL	1	TRUE	1	0.39	2		1056	748	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281837	39281837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374761537	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	78	863	1	ENST00000402219.2:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000402219	NM_005633.3	213	cGa/cAa	5/23	1	2	FACETS	0.738	0.65	0.833	0.738	0.65	0.833	SUBCLONAL	1	TRUE	1	0.39	2		864	542	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606099	47606099	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	61	640	0	ENST00000263735.4:c.563A>G	p.Asn188Ser	p.N188S	ENST00000263735	NM_002354.2	188	aAt/aGt	6/9	1	2	FACETS	0.836	0.725	0.956	0.836	0.725	0.956	CLONAL	1	TRUE	1	0.39	2		640	374	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635578	47635578	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	119	842	0	ENST00000233146.2:c.250A>G	p.Asn84Asp	p.N84D	ENST00000233146	NM_000251.2	84	Aat/Gat	2/16	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.39	2		842	582	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641426	47641426	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	90	747	0	ENST00000233146.2:c.811T>C	p.Ser271Pro	p.S271P	ENST00000233146	NM_000251.2	271	Tct/Cct	5/16	1	2	FACETS	0.772	0.686	0.863	0.772	0.686	0.863	SUBCLONAL	1	TRUE	1	0.39	2		747	598	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703539	47703539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1203462814	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	107	955	0	ENST00000233146.2:c.2039G>A	p.Arg680Gln	p.R680Q	ENST00000233146	NM_000251.2	680	cGa/cAa	13/16	1	2	FACETS	0.933	0.839	1	0.933	0.839	1	CLONAL	1	TRUE	1	0.39	2		955	588	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193587	99193587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	90	728	2	ENST00000074304.5:c.2782G>A	p.Ala928Thr	p.A928T	ENST00000074304	NM_001134224.1	928	Gcc/Acc	25/26	1	2	FACETS	0.912	0.812	1	0.912	0.812	1	CLONAL	1	TRUE	1	0.39	2		730	506	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050307	128050307	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	132	839	0	ENST00000285398.2:c.350A>C	p.Lys117Thr	p.K117T	ENST00000285398	NM_000122.1	117	aAa/aCa	3/15	1	2	FACETS	0.971	0.883	1	0.971	0.883	1	CLONAL	1	TRUE	1	0.39	2		839	697	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267680	198267680	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	89	649	0	ENST00000335508.6:c.1799T>C	p.Leu600Ser	p.L600S	ENST00000335508	NM_012433.2	600	tTg/tCg	13/25	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.39	2		649	445	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131412	202131412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339962485	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	90	749	2	ENST00000358485.4:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000358485	NM_001080125.1	127	cGa/cAa	2/9	1	2	FACETS	0.958	0.853	1	0.958	0.853	1	CLONAL	1	TRUE	1	0.39	2		751	482	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204737492	204737492	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	82	679	0	ENST00000302823.3:c.629A>C	p.Glu210Ala	p.E210A	ENST00000302823	NM_005214.4	210	gAa/gCa	4/4	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.39	2		679	410	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209103819	209103819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	78	861	1	ENST00000345146.2:c.1130C>T	p.Ala377Val	p.A377V	ENST00000345146	NM_005896.2	377	gCt/gTt	9/10	1	2	FACETS	0.762	0.671	0.859	0.762	0.671	0.859	SUBCLONAL	1	TRUE	1	0.39	2		862	525	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523279	9523279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763590647	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	141	946	0	ENST00000353224.5:c.1958G>A	p.Arg653Gln	p.R653Q	ENST00000353224	NM_177990.2	653	cGg/cAg	9/10	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.39	2		946	667	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019417	31019417	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	79	790	0	ENST00000375687.4:c.914G>A	p.Ser305Asn	p.S305N	ENST00000375687	NM_015338.5	305	aGc/aAc	10/13	1	2	FACETS	0.688	0.606	0.776	0.688	0.606	0.776	SUBCLONAL	1	TRUE	1	0.39	2		790	589	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021124	31021124	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748644253	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	150	931	1	ENST00000375687.4:c.1123G>A	p.Val375Met	p.V375M	ENST00000375687	NM_015338.5	375	Gtg/Atg	12/13	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.39	2		932	739	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713470	40713470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318044562	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	42	1016	1	ENST00000373198.4:c.4045C>T	p.Arg1349Cys	p.R1349C	ENST00000373198	NM_133170.3	1349	Cgt/Tgt	30/32	1	2	FACETS	0.335	0.279	0.398	0.335	0.279	0.398	SUBCLONAL	1	TRUE	1	0.39	2		1017	642	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899085	40899085	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	124	968	1	ENST00000373198.4:c.2185G>T	p.Gly729Cys	p.G729C	ENST00000373198	NM_133170.3	729	Ggc/Tgc	14/32	1	2	FACETS	0.924	0.838	1	0.924	0.838	1	CLONAL	1	TRUE	1	0.39	2		969	688	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265268	46265268	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	71	539	0	ENST00000371998.3:c.2138T>C	p.Ile713Thr	p.I713T	ENST00000371998		713	aTa/aCa	12/23	1	2	FACETS	0.936	0.821	1	0.936	0.821	1	CLONAL	1	TRUE	1	0.39	2		539	389	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485442	57485442	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	55	626	0	ENST00000371085.3:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000371085	NM_000516.4	342	Cga/Tga	12/13	1	2	FACETS	0.577	0.494	0.667	0.577	0.494	0.667	SUBCLONAL	1	TRUE	1	0.39	2		626	489	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171640	36171640	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752288830	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	115	641	0	ENST00000300305.3:c.925G>A	p.Gly309Ser	p.G309S	ENST00000300305		309	Ggc/Agc	7/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.39	2		641	502	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565543	41565543	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	30	814	1	ENST00000263253.7:c.4209C>A	p.Phe1403Leu	p.F1403L	ENST00000263253	NM_001429.3	1403	ttC/ttA	26/31	1	2	FACETS	0.294	0.236	0.359	0.294	0.236	0.359	SUBCLONAL	1	TRUE	1	0.39	2		815	524	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650277	12650277	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	118	904	0	ENST00000251849.4:c.569T>C	p.Ile190Thr	p.I190T	ENST00000251849	NM_002880.3	190	aTc/aCc	5/17	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.39	2		904	574	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098930	47098930	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	168	1068	2	ENST00000409792.3:c.6344A>G	p.Lys2115Arg	p.K2115R	ENST00000409792	NM_014159.6	2115	aAa/aGa	15/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.39	2		1070	746	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927394	49927394	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528985327	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	57	1031	1	ENST00000296474.3:c.3910C>T	p.Arg1304Trp	p.R1304W	ENST00000296474	NM_002447.2	1304	Cgg/Tgg	19/20	1	2	FACETS	0.419	0.359	0.485	0.419	0.359	0.485	SUBCLONAL	1	TRUE	1	0.39	2		1032	697	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584478	52584478	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142726131	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	111	822	4	ENST00000394830.3:c.4535C>T	p.Ala1512Val	p.A1512V	ENST00000394830	NM_018313.4	1512	gCg/gTg	29/30	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.39	2		826	556	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637717	52637717	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	93	792	2	ENST00000394830.3:c.2599G>T	p.Glu867Ter	p.E867*	ENST00000394830	NM_018313.4	867	Gaa/Taa	18/30	1	2	FACETS	0.924	0.825	1	0.924	0.825	1	CLONAL	1	TRUE	1	0.39	2		794	516	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990402	69990402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765051386	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	46	559	0	ENST00000394351.3:c.361G>A	p.Asp121Asn	p.D121N	ENST00000394351	NM_000248.3	121	Gat/Aat	4/9	1	2	FACETS	0.784	0.664	0.915	0.784	0.664	0.915	CLONAL	1	TRUE	1	0.39	2		559	301	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71008534	71008534	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	63	477	0	ENST00000318789.4:c.1898T>C	p.Val633Ala	p.V633A	ENST00000318789	NM_032682.5	633	gTa/gCa	21/21	1	2	FACETS	0.841	0.731	0.96	0.841	0.731	0.96	CLONAL	1	TRUE	1	0.39	2		477	384	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026984	71026984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763413735	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	97	670	0	ENST00000318789.4:c.1343C>T	p.Ser448Leu	p.S448L	ENST00000318789	NM_032682.5	448	tCg/tTg	15/21	1	2	FACETS	0.867	0.774	0.964	0.867	0.774	0.964	CLONAL	1	TRUE	1	0.39	2		670	574	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480466	89480466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446890859	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	67	527	0	ENST00000336596.2:c.2303C>T	p.Ser768Leu	p.S768L	ENST00000336596	NM_005233.5	768	tCg/tTg	13/17	1	2	FACETS	0.814	0.71	0.926	0.814	0.71	0.926	CLONAL	1	TRUE	1	0.39	2		527	422	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204593	128204593	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	136	1031	0	ENST00000341105.2:c.848G>A	p.Arg283His	p.R283H	ENST00000341105	NM_032638.4	283	cGc/cAc	3/6	1	2	FACETS	0.955	0.87	1	0.955	0.87	1	CLONAL	1	TRUE	1	0.39	2		1031	730	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670615	134670615	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781004053	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	127	1047	2	ENST00000398015.3:c.526G>A	p.Ala176Thr	p.A176T	ENST00000398015	NM_004441.4	176	Gct/Act	3/16	1	2	FACETS	0.84	0.762	0.923	0.84	0.762	0.923	CLONAL	1	TRUE	1	0.39	2		1049	775	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374251	138374251	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	85	854	0	ENST00000289153.2:c.3193C>T	p.Arg1065Trp	p.R1065W	ENST00000289153	NM_006219.2	1065	Cgg/Tgg	22/22	1	2	FACETS	0.724	0.641	0.813	0.724	0.641	0.813	SUBCLONAL	1	TRUE	1	0.39	2		854	602	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453486	138453486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451809865	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	53	616	1	ENST00000289153.2:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000289153	NM_006219.2	321	cGa/cAa	5/22	1	2	FACETS	0.777	0.665	0.897	0.777	0.665	0.897	SUBCLONAL	1	TRUE	1	0.39	2		617	350	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274748	142274749	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	60	627	0	ENST00000350721.4:c.2311_2312insC	p.Lys771ThrfsTer6	p.K771Tfs*6	ENST00000350721	NM_001184.3	771	aaa/aCaa	10/47	1	2	FACETS	0.862	0.746	0.986	0.862	0.746	0.986	CLONAL	1	TRUE	1	0.39	2		627	357	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274778	142274778	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	69	776	0	ENST00000350721.4:c.2282C>T	p.Ser761Phe	p.S761F	ENST00000350721	NM_001184.3	761	tCt/tTt	10/47	1	2	FACETS	0.929	0.813	1	0.929	0.813	1	CLONAL	1	TRUE	1	0.39	2		776	381	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169999726	169999726	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	82	706	1	ENST00000295797.4:c.1037G>A	p.Arg346Gln	p.R346Q	ENST00000295797	NM_002740.5	346	cGa/cAa	11/18	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.39	2		707	397	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504023	186504023	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	29	514	1	ENST00000323963.5:c.588A>C	p.Gln196His	p.Q196H	ENST00000323963		196	caA/caC	6/11	1	2	FACETS	0.426	0.342	0.521	0.426	0.342	0.521	SUBCLONAL	1	TRUE	1	0.39	2		515	349	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506913	186506913	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	38	361	0	ENST00000323963.5:c.1080-1G>T		p.X360_splice	ENST00000323963		360			1	2	FACETS	0.836	0.697	0.99	0.836	0.697	0.99	CLONAL	1	TRUE	1	0.39	2		361	233	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447384	187447384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780987785	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	119	937	1	ENST00000232014.4:c.809G>A	p.Arg270Gln	p.R270Q	ENST00000232014	NM_001130845.1	270	cGa/cAa	5/10	1	2	FACETS	0.888	0.803	0.978	0.888	0.803	0.978	CLONAL	1	TRUE	1	0.39	2		938	687	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587160	189587160	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs941268998	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	82	801	0	ENST00000264731.3:c.1177C>T	p.Arg393Ter	p.R393*	ENST00000264731	NM_003722.4	393	Cga/Tga	9/14	1	2	FACETS	0.863	0.764	0.97	0.863	0.764	0.97	CLONAL	1	TRUE	1	0.39	2		801	487	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612028	189612028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs900140738	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	115	738	0	ENST00000264731.3:c.1780C>T	p.Arg594Ter	p.R594*	ENST00000264731	NM_003722.4	594	Cga/Tga	14/14	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.39	2		738	576	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1952853	1952853	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	134	913	0	ENST00000382891.5:c.1936G>A	p.Glu646Lys	p.E646K	ENST00000382891	NM_133335.3	646	Gaa/Aaa	10/22	1	2	FACETS	0.954	0.868	1	0.954	0.868	1	CLONAL	1	TRUE	1	0.39	2		913	720	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564503	55564503	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1044091916	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	103	688	0	ENST00000288135.5:c.391G>A	p.Asp131Asn	p.D131N	ENST00000288135	NM_000222.2	131	Gac/Aac	3/21	1	2	FACETS	0.998	0.897	1	0.998	0.897	1	CLONAL	1	TRUE	1	0.39	2		688	529	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467751	66467751	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	45	559	1	ENST00000273854.3:c.518A>G	p.Lys173Arg	p.K173R	ENST00000273854	NM_004439.5	173	aAa/aGa	3/18	1	2	FACETS	0.546	0.459	0.641	0.546	0.459	0.641	SUBCLONAL	1	TRUE	1	0.39	2		560	423	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383654	84383654	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	91	1015	0	ENST00000321945.7:c.1198T>G	p.Phe400Val	p.F400V	ENST00000321945	NM_139076.2	400	Ttt/Gtt	9/9	1	2	FACETS	0.842	0.75	0.941	0.842	0.75	0.941	CLONAL	1	TRUE	1	0.39	2		1015	554	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156315	106156315	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	71	485	0	ENST00000380013.4:c.1216C>A	p.Leu406Ile	p.L406I	ENST00000380013	NM_001127208.2	406	Ctt/Att	3/11	1	2	FACETS	0.929	0.815	1	0.929	0.815	1	CLONAL	1	TRUE	1	0.39	2		485	392	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156370	106156370	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	42	504	0	ENST00000380013.4:c.1271G>T	p.Ser424Ile	p.S424I	ENST00000380013	NM_001127208.2	424	aGc/aTc	3/11	1	2	FACETS	0.637	0.534	0.751	0.637	0.534	0.751	SUBCLONAL	1	TRUE	1	0.39	2		504	338	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	93	849	4	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	1	2	FACETS	0.749	0.666	0.836	0.749	0.666	0.836	SUBCLONAL	1	TRUE	1	0.39	2		853	637	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539885	187539885	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	89	688	1	ENST00000441802.2:c.7855C>A	p.Leu2619Ile	p.L2619I	ENST00000441802	NM_005245.3	2619	Ctt/Att	10/27	1	2	FACETS	0.997	0.888	1	0.997	0.888	1	CLONAL	1	TRUE	1	0.39	2		689	458	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630501	187630501	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	162	952	0	ENST00000441802.2:c.481A>C	p.Asn161His	p.N161H	ENST00000441802	NM_005245.3	161	Aac/Cac	2/27	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.39	2		952	799	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630587	187630587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770123806	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	109	1064	0	ENST00000441802.2:c.395G>A	p.Arg132Gln	p.R132Q	ENST00000441802	NM_005245.3	132	cGa/cAa	2/27	1	2	FACETS	0.828	0.744	0.916	0.828	0.744	0.916	CLONAL	1	TRUE	1	0.39	2		1064	675	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1258719	1258719	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	165	1015	1	ENST00000310581.5:c.3026C>T	p.Ala1009Val	p.A1009V	ENST00000310581	NM_198253.2	1009	gCg/gTg	13/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.39	2		1016	772	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874590	35874591	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	109	863	0	ENST00000303115.3:c.752dup	p.Ser252LeufsTer18	p.S252Lfs*18	ENST00000303115	NM_002185.3	249	agt/agTt	6/8	1	2	FACETS	0.936	0.843	1	0.936	0.843	1	CLONAL	1	TRUE	1	0.39	2		863	597	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982057	38982057	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	76	893	3	ENST00000357387.3:c.665G>A	p.Arg222Gln	p.R222Q	ENST00000357387	NM_152756.3	222	cGa/cAa	8/38	1	2	FACETS	0.821	0.722	0.926	0.821	0.722	0.926	CLONAL	1	TRUE	1	0.39	2		896	475	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152566	56152566	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	53	392	1	ENST00000399503.3:c.622C>T	p.Arg208Ter	p.R208*	ENST00000399503	NM_005921.1	208	Cga/Tga	2/20	1	2	FACETS	0.885	0.76	1	0.885	0.76	1	CLONAL	1	TRUE	1	0.39	2		393	307	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	58	513	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	0.921	0.796	1	0.921	0.796	1	CLONAL	1	TRUE	1	0.39	2		513	323	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589618	67589618	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519838	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	55	516	0	ENST00000274335.5:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000274335		461	Cga/Tga	10/15	1	2	FACETS	0.901	0.776	1	0.901	0.776	1	CLONAL	1	TRUE	1	0.39	2		516	313	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591270	67591270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1289880098	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	79	623	0	ENST00000274335.5:c.1768C>T	p.Arg590Trp	p.R590W	ENST00000274335		590	Cgg/Tgg	13/15	1	2	FACETS	0.873	0.771	0.982	0.873	0.771	0.982	CLONAL	1	TRUE	1	0.39	2		623	464	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80168958	80168958	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	85	989	0	ENST00000265081.6:c.3154T>G	p.Phe1052Val	p.F1052V	ENST00000265081	NM_002439.4	1052	Ttt/Gtt	23/24	1	2	FACETS	0.731	0.647	0.821	0.731	0.647	0.821	SUBCLONAL	1	TRUE	1	0.39	2		989	596	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670706	86670706	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	17	417	0	ENST00000274376.6:c.1984A>C	p.Thr662Pro	p.T662P	ENST00000274376	NM_002890.2	662	Aca/Cca	15/25	1	2	FACETS	0.374	0.279	0.486	0.374	0.279	0.486	SUBCLONAL	1	TRUE	1	0.39	2		417	233	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	55	665	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.75	0.644	0.865	0.75	0.644	0.865	SUBCLONAL	1	TRUE	1	0.39	2		665	376	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	62	585	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.871	0.756	0.994	0.871	0.756	0.994	CLONAL	1	TRUE	1	0.39	2		585	365	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940522	131940522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375315737	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	62	591	0	ENST00000265335.6:c.2549G>A	p.Arg850His	p.R850H	ENST00000265335		850	cGt/cAt	16/25	1	2	FACETS	0.777	0.674	0.889	0.777	0.674	0.889	SUBCLONAL	1	TRUE	1	0.39	2		591	409	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562484	176562484	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	102	985	0	ENST00000439151.2:c.380A>C	p.Lys127Thr	p.K127T	ENST00000439151	NM_022455.4	127	aAa/aCa	2/23	1	2	FACETS	0.73	0.653	0.811	0.73	0.653	0.811	SUBCLONAL	1	TRUE	1	0.39	2		985	717	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721771	176721771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767815479	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	80	712	4	ENST00000439151.2:c.7402C>T	p.Arg2468Trp	p.R2468W	ENST00000439151	NM_022455.4	2468	Cgg/Tgg	23/23	1	2	FACETS	0.9	0.795	1	0.9	0.795	1	CLONAL	1	TRUE	1	0.39	2		716	456	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057039	180057039	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	134	1092	0	ENST00000261937.6:c.580T>C	p.Ser194Pro	p.S194P	ENST00000261937	NM_182925.4	194	Tcc/Ccc	5/30	1	2	FACETS	0.873	0.794	0.957	0.873	0.794	0.957	CLONAL	1	TRUE	1	0.39	2		1092	787	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056291	26056292	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	114	748	0	ENST00000343677.2:c.365dup	p.Ala123GlyfsTer7	p.A123Gfs*7	ENST00000343677	NM_005319.3	122	aag/aaAg	1/1	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.39	2		748	570	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662700	117662700	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	56	757	1	ENST00000368508.3:c.4765G>T	p.Glu1589Ter	p.E1589*	ENST00000368508	NM_002944.2	1589	Gaa/Taa	29/43	1	2	FACETS	0.62	0.532	0.716	0.62	0.532	0.716	SUBCLONAL	1	TRUE	1	0.39	2		758	463	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026666	6026666	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	186	1463	0	ENST00000265849.7:c.1730A>C	p.Lys577Thr	p.K577T	ENST00000265849	NM_000535.5	577	aAg/aCg	11/15	1	2	FACETS	0.909	0.839	0.982	0.909	0.839	0.982	CLONAL	1	TRUE	1	0.39	2		1463	1049	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224321	55224321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	89	698	0	ENST00000275493.2:c.1102G>A	p.Asp368Asn	p.D368N	ENST00000275493	NM_005228.3	368	Gat/Aat	9/28	1	2	FACETS	0.933	0.831	1	0.933	0.831	1	CLONAL	1	TRUE	1	0.39	2		698	489	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273205	55273205	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	126	873	1	ENST00000275493.2:c.3528C>A	p.Phe1176Leu	p.F1176L	ENST00000275493	NM_005228.3	1176	ttC/ttA	28/28	1	2	FACETS	0.981	0.89	1	0.981	0.89	1	CLONAL	1	TRUE	1	0.39	2		874	659	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509432	106509432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs567756361	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	106	911	0	ENST00000359195.3:c.1426C>T	p.Arg476Cys	p.R476C	ENST00000359195	NM_002649.2	476	Cgc/Tgc	2/11	1	2	FACETS	0.882	0.793	0.977	0.882	0.793	0.977	CLONAL	1	TRUE	1	0.39	2		911	616	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545636	106545636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752242795	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	64	874	0	ENST00000359195.3:c.3113G>A	p.Gly1038Glu	p.G1038E	ENST00000359195	NM_002649.2	1038	gGa/gAa	11/11	1	2	FACETS	0.701	0.609	0.801	0.701	0.609	0.801	SUBCLONAL	1	TRUE	1	0.39	2		874	468	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418997	116418997	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200754673	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	53	432	0	ENST00000397752.3:c.3508C>T	p.Arg1170Ter	p.R1170*	ENST00000397752	NM_000245.2	1170	Cga/Tga	17/21	1	2	FACETS	0.871	0.747	1	0.871	0.747	1	CLONAL	1	TRUE	1	0.39	2		432	312	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845086	128845086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761395599	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	188	1098	2	ENST00000249373.3:c.580G>A	p.Glu194Lys	p.E194K	ENST00000249373	NM_005631.4	194	Gaa/Aaa	3/12	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.39	2		1100	928	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140487360	140487360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507472	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	103	916	2	ENST00000288602.6:c.1165C>T	p.Arg389Cys	p.R389C	ENST00000288602	NM_004333.4	389	Cgt/Tgt	9/18	1	2	FACETS	0.904	0.811	1	0.904	0.811	1	CLONAL	1	TRUE	1	0.39	2		918	584	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860317	151860317	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	85	683	0	ENST00000262189.6:c.10345T>C	p.Ser3449Pro	p.S3449P	ENST00000262189	NM_170606.2	3449	Tcc/Ccc	43/59	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.39	2		683	409	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151871325	151871325	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	61	583	0	ENST00000262189.6:c.9265T>G	p.Phe3089Val	p.F3089V	ENST00000262189	NM_170606.2	3089	Ttt/Gtt	39/59	1	2	FACETS	0.951	0.826	1	0.951	0.826	1	CLONAL	1	TRUE	1	0.39	2		583	329	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878863	151878863	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1563288201	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	118	841	2	ENST00000262189.6:c.6082C>T	p.Arg2028Ter	p.R2028*	ENST00000262189	NM_170606.2	2028	Cga/Tga	36/59	1	2	FACETS	0.982	0.889	1	0.982	0.889	1	CLONAL	1	TRUE	1	0.39	2		843	616	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945021	151945021	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs756918375	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	10	217	0	ENST00000262189.6:c.2498G>T	p.Arg833Ile	p.R833I	ENST00000262189	NM_170606.2	833	aGa/aTa	14/59	1	2	FACETS	0.366	0.249	0.513	0.366	0.249	0.513	SUBCLONAL	1	TRUE	1	0.39	2		217	140	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287216	38287216	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	176	1155	0	ENST00000425967.3:c.441C>A	p.Phe147Leu	p.F147L	ENST00000425967	NM_001174067.1	147	ttC/ttA	4/19	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.39	2		1155	867	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995539	68995539	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	83	1018	0	ENST00000288368.4:c.1943C>A	p.Pro648His	p.P648H	ENST00000288368	NM_024870.2	648	cCt/cAt	18/40	1	2	FACETS	0.784	0.693	0.881	0.784	0.693	0.881	SUBCLONAL	1	TRUE	1	0.39	2		1018	543	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136820	69136820	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	84	753	0	ENST00000288368.4:c.4734G>T	p.Lys1578Asn	p.K1578N	ENST00000288368	NM_024870.2	1578	aaG/aaT	39/40	1	2	FACETS	0.807	0.714	0.905	0.807	0.714	0.905	CLONAL	1	TRUE	1	0.39	2		753	534	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141582961	141582961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	171	1167	2	ENST00000220592.5:c.286G>A	p.Gly96Ser	p.G96S	ENST00000220592	NM_012154.3	96	Ggc/Agc	3/19	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.39	2		1169	873	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340357	8340357	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324340491	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	99	775	0	ENST00000356435.5:c.5239C>T	p.Arg1747Cys	p.R1747C	ENST00000356435		1747	Cgt/Tgt	31/35	1	2	FACETS	0.889	0.796	0.988	0.889	0.796	0.988	CLONAL	1	TRUE	1	0.39	2		775	571	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971026	21971026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	88	445	1	ENST00000304494.5:c.332G>A	p.Gly111Asp	p.G111D	ENST00000304494	NM_000077.4	111	gGc/gAc	2/3	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.39	2		446	412	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27229184	27229184	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	111	826	0	ENST00000380036.4:c.3329A>C	p.Lys1110Thr	p.K1110T	ENST00000380036	NM_000459.3	1110	aAg/aCg	23/23	1	2	FACETS	0.958	0.864	1	0.958	0.864	1	CLONAL	1	TRUE	1	0.39	2		826	594	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231389	98231389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559293815	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	121	873	4	ENST00000331920.6:c.1894G>A	p.Asp632Asn	p.D632N	ENST00000331920	NM_000264.3	632	Gac/Aac	14/24	1	2	FACETS	0.999	0.905	1	0.999	0.905	1	CLONAL	1	TRUE	1	0.39	2		877	621	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268698	98268698	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	53	544	0	ENST00000331920.6:c.385T>C	p.Trp129Arg	p.W129R	ENST00000331920	NM_000264.3	129	Tgg/Cgg	2/24	1	2	FACETS	0.747	0.639	0.863	0.747	0.639	0.863	SUBCLONAL	1	TRUE	1	0.39	2		544	364	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912079	127912079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	62	588	1	ENST00000373547.4:c.791G>A	p.Arg264His	p.R264H	ENST00000373547	NM_002721.4	264	cGt/cAt	7/7	1	2	FACETS	0.839	0.728	0.958	0.839	0.728	0.958	CLONAL	1	TRUE	1	0.39	2		589	379	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915943	127915943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781486938	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	98	858	2	ENST00000373547.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000373547	NM_002721.4	180	Gaa/Aaa	6/7	1	2	FACETS	0.812	0.725	0.904	0.812	0.725	0.904	CLONAL	1	TRUE	1	0.39	2		860	619	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760790	133760790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367600262	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	129	936	0	ENST00000318560.5:c.3113C>T	p.Ala1038Val	p.A1038V	ENST00000318560	NM_005157.4	1038	gCg/gTg	11/11	1	2	FACETS	0.927	0.841	1	0.927	0.841	1	CLONAL	1	TRUE	1	0.39	2		936	714	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393575	139393575	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	171	1006	0	ENST00000277541.6:c.6071T>C	p.Val2024Ala	p.V2024A	ENST00000277541	NM_017617.3	2024	gTa/gCa	32/34	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.39	2		1006	822	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410085	139410085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775217381	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	200	1192	6	ENST00000277541.6:c.1753G>A	p.Ala585Thr	p.A585T	ENST00000277541	NM_017617.3	585	Gcc/Acc	11/34	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.39	2		1198	963	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411783	63411783	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	153	592	0	ENST00000330258.3:c.1384G>T	p.Glu462Ter	p.E462*	ENST00000330258	NM_152424.3	462	Gaa/Taa	2/2	1	1	FACETS	0.808	0.748	0.869	1	0.991	1	CLONAL	2	TRUE	0	0.39	1		592	391	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344018	70344018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747113641	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	125	524	0	ENST00000374080.3:c.1754G>A	p.Arg585Gln	p.R585Q	ENST00000374080		585	cGa/cAa	13/45	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.39	1		524	403	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938406	76938406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	91	501	0	ENST00000373344.5:c.2342G>A	p.Arg781Gln	p.R781Q	ENST00000373344	NM_000489.3	781	cGa/cAa	9/35	1	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.39	1		501	279	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210266	123210266	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	84	436	0	ENST00000218089.9:c.2618T>C	p.Val873Ala	p.V873A	ENST00000218089	NM_001042749.1	873	gTa/gCa	26/35	1	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.39	1		436	249	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252163	226252163	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	14	131	0	ENST00000366813.1:c.111G>T	p.Lys37Asn	p.K37N	ENST00000366813		37	aaG/aaT	1/3	1	2	FACETS	0.756	0.554	0.993	0.756	0.554	0.993	CLONAL	1	TRUE	1	0.39	2		131	95	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0021091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	465	613	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.273788728363698	5	FACETS	1	0.979	1			1	CLONAL	4	TRUE	NA	0.273788728363698	5		614	1158	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492902	56492902	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	53	431	0	ENST00000407977.2:c.37T>A	p.Trp13Arg	p.W13R	ENST00000407977		13	Tgg/Agg	2/10	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.273788728363698	2		431	380	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604748	48604748	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	88	698	0	ENST00000342988.3:c.1570T>A	p.Trp524Arg	p.W524R	ENST00000342988	NM_005359.5	524	Tgg/Agg	12/12	0.273788728363698	1	FACETS	0.994	0.883	1	0.994	0.883	1	CLONAL	1	TRUE	0	0.273788728363698	1		698	558	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185200166	185200166	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	122	947	0	ENST00000265026.3:c.2824del	p.Asp942ThrfsTer36	p.D942Tfs*36	ENST00000265026	NM_004721.4	941	tcG/tc	14/14	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.273788728363698	2		947	854	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371409680	NA	P-0021093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	304	378	0	ENST00000269305.4:c.848G>C	p.Arg283Pro	p.R283P	ENST00000269305	NM_001126112.2	283	cGc/cCc	8/11	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.397953004025783	2		378	1137	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987052	36987052	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886041466	NA	P-0021093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	260	1032	0	ENST00000354822.5:c.637C>T	p.Gln213Ter	p.Q213*	ENST00000354822	NM_001079668.2	213	Cag/Tag	3/3	0.270802610474676	2	FACETS	1	0.992	1	0.709	0.665	0.753	CLONAL	1	TRUE	0	0.397953004025783	2		1032	922	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828563	72828563	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	158	1192	0	ENST00000268489.5:c.8018A>C	p.His2673Pro	p.H2673P	ENST00000268489	NM_006885.3	2673	cAc/cCc	9/10	1	2	FACETS	0.735	0.672	0.8	0.735	0.672	0.8	SUBCLONAL	1	TRUE	1	0.397953004025783	2		1192	1081	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325684	30325684	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	35	473	1	ENST00000322652.5:c.1882G>T	p.Ala628Ser	p.A628S	ENST00000322652	NM_015355.2	628	Gct/Tct	16/16	0.299153815935585	3	FACETS	1	0.885	1	0.546	0.452	0.65	CLONAL	1	TRUE	1	0.397953004025783	3		474	193	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761401	59761401	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs546083449	NA	P-0021093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	43	868	0	ENST00000259008.2:c.3006G>T	p.Trp1002Cys	p.W1002C	ENST00000259008	NM_032043.2	1002	tgG/tgT	20/20	0.299153815935585	3	FACETS	0.5	0.418	0.591	0.25	0.209	0.296	SUBCLONAL	1	TRUE	1	0.397953004025783	3		868	518	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285089	15285089	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	164	1163	7	ENST00000263388.2:c.4526C>A	p.Ala1509Asp	p.A1509D	ENST00000263388	NM_000435.2	1509	gCc/gAc	25/33	1	2	FACETS	0.786	0.721	0.855	0.786	0.721	0.855	SUBCLONAL	1	TRUE	1	0.397953004025783	2		1170	1048	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100981	41100981	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs188436636	NA	P-0021093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	125	1031	0	ENST00000373198.4:c.1375C>G	p.Arg459Gly	p.R459G	ENST00000373198	NM_133170.3	459	Cgg/Ggg	8/32	1	2	FACETS	0.624	0.564	0.688	0.624	0.564	0.688	SUBCLONAL	1	TRUE	1	0.397953004025783	2		1031	1006	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967181	93967181	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	23	1018	1	ENST00000369303.4:c.2171G>A	p.Arg724Lys	p.R724K	ENST00000369303	NM_004440.3	724	aGg/aAg	12/17	1	2	FACETS	0.496	0.388	0.62	0.496	0.388	0.62	SUBCLONAL	1	TRUE	1	0.397953004025783	2		1019	233	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969328	44969328	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	16	319	2	ENST00000377967.4:c.4010A>T	p.Glu1337Val	p.E1337V	ENST00000377967	NM_021140.2	1337	gAg/gTg	28/29	1	1	FACETS	0.882	0.667	1	0.882	0.667	1	CLONAL	1	TRUE	0	0.397953004025783	1		321	73	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0021094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	31	340	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	0.09	2		340	630	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221320	1221320	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587776656	NA	P-0021094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	91	631	0	ENST00000326873.7:c.843del	p.Leu282SerfsTer5	p.L282Sfs*5	ENST00000326873	NM_000455.4	281	ccG/cc	6/10	0.3	2	FACETS	0.985	0.873	1			1	CLONAL	2	TRUE	NA	0.09	2		631	1026	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457608	67457608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	84	638	0	ENST00000327367.4:c.418G>A	p.Val140Met	p.V140M	ENST00000327367	NM_005902.3	140	Gtg/Atg	3/9	1	2	FACETS	0.871	0.767	0.983	1	0.981	1	CLONAL	2	TRUE	1	0.09	2		638	1072	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602334	10602334	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	116	707	0	ENST00000171111.5:c.1244G>T	p.Arg415Leu	p.R415L	ENST00000171111	NM_203500.1	415	cGc/cTc	3/6	1	2	FACETS	1	0.9	1	1	0.988	1	CLONAL	2	TRUE	1	0.09	2		707	1286	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105635	11105636	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0021094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	69	688	1	ENST00000358026.2:c.1554_1555del	p.Asn519ArgfsTer14	p.N519Rfs*14	ENST00000358026	NM_001128849.1	517	aaAGag/aaag	9/36	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.09	2		689	1049	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181312	123181312	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	19	324	0	ENST00000218089.9:c.776G>T	p.Arg259Leu	p.R259L	ENST00000218089	NM_001042749.1	259	cGa/cTa	9/35	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.09	2		324	301	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0021095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	73	685	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.262079092790948	2		685	554	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0021095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	177	990	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	0.262079092790948	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.262079092790948	1		990	938	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928872	44928872	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs755440519	NA	P-0021095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	73	620	2	ENST00000377967.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000377967	NM_021140.2	658	Cga/Tga	17/29	1	2	FACETS	0.906	0.793	1	0.906	0.793	1	CLONAL	1	TRUE	1	0.262079092790948	2		622	615	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490337	29490337	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	228	648	1	ENST00000356175.3:c.425del	p.Leu142TyrfsTer23	p.L142Yfs*23	ENST00000356175	NM_000267.3	141	gTt/gt	4/57	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	2	TRUE	NA	0.262079092790948	2		649	769	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	103	328	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	0.502208086633466	2		328	372	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	138	585	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.502208086633466	2		585	424	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	92	134	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.502208086633466	2		134	358	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	221	702	6	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	0.502208086633466	2		708	651	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	523	733	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.502208086633466	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.502208086633466	2		733	908	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217792	2217792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760010356	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	284	1077	2	ENST00000398665.3:c.2566G>A	p.Gly856Ser	p.G856S	ENST00000398665	NM_032482.2	856	Ggc/Agc	22/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.502208086633466	2		1079	1030	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226423	2226423	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	334	1020	1	ENST00000398665.3:c.3907del	p.Ala1303LeufsTer24	p.A1303Lfs*24	ENST00000398665	NM_032482.2	1301	tcG/tc	27/28	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.502208086633466	2		1021	1153	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420315	88420315	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773244598	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	161	572	0	ENST00000360948.2:c.2371C>T	p.Arg791Trp	p.R791W	ENST00000360948	NM_001012338.2	791	Cgg/Tgg	19/19	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.502208086633466	2		572	523	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	203	715	13	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.502208086633466	2		728	643	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678783	52678784	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	91	521	0	ENST00000394830.3:c.835dup	p.Ile279AsnfsTer8	p.I279Nfs*8	ENST00000394830	NM_018313.4	279	ata/aAta	9/30	1	2	FACETS	0.804	0.717	0.895	0.804	0.717	0.895	CLONAL	1	TRUE	1	0.502208086633466	2		521	451	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437730	110437730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1209394395	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	141	1025	2	ENST00000375856.3:c.671G>A	p.Arg224His	p.R224H	ENST00000375856	NM_003749.2	224	cGc/cAc	1/2	1	2	FACETS	0.515	0.468	0.565	0.515	0.468	0.565	SUBCLONAL	1	TRUE	1	0.502208086633466	2		1027	1090	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443880	52443880	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs916069743	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	315	944	0	ENST00000460680.1:c.15G>A	p.Trp5Ter	p.W5*	ENST00000460680	NM_004656.3	5	tgG/tgA	1/17	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.502208086633466	2		944	1091	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346158	89346158	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs878855327	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	66	247	1	ENST00000301030.4:c.6792del	p.Ala2265ProfsTer72	p.A2265Pfs*72	ENST00000301030	NM_001256183.1	2264	ccC/cc	9/13	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.502208086633466	2		248	223	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149799	202149799	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	119	815	0	ENST00000358485.4:c.1245del	p.Phe415LeufsTer26	p.F415Lfs*26	ENST00000358485	NM_001080125.1	414	Ttt/tt	8/9	1	2	FACETS	0.696	0.629	0.766	0.696	0.629	0.766	SUBCLONAL	1	TRUE	1	0.502208086633466	2		815	681	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	139	314	0	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	0.889	0.811	0.969	0.889	0.811	0.969	CLONAL	1	TRUE	1	0.502208086633466	2		314	623	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777134	9777134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1445282622	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	56	976	1	ENST00000377346.4:c.898C>T	p.Arg300Cys	p.R300C	ENST00000377346	NM_005026.3	300	Cgt/Tgt	7/24	1	2	FACETS	0.2	0.17	0.233	0.2	0.17	0.233	SUBCLONAL	1	TRUE	1	0.502208086633466	2		977	1115	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	464333	464334	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	185	873	0	ENST00000399788.2:c.860_861del	p.Ser287CysfsTer2	p.S287Cfs*2	ENST00000399788	NM_001042603.1	287	tCT/t	7/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.502208086633466	2		873	631	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986886	36986886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	80	254	0	ENST00000354822.5:c.803G>A	p.Gly268Asp	p.G268D	ENST00000354822	NM_001079668.2	268	gGc/gAc	3/3	1	2	FACETS	0.915	0.812	1	0.915	0.812	1	CLONAL	1	TRUE	1	0.502208086633466	2		254	348	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512377	38512377	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555574293	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	90	672	0	ENST00000254066.5:c.1293del	p.Arg432GlyfsTer211	p.R432Gfs*211	ENST00000254066	NM_000964.3	430	Ggg/gg	9/9	1	2	FACETS	0.508	0.45	0.569	0.508	0.45	0.569	SUBCLONAL	1	TRUE	1	0.502208086633466	2		672	706	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611771	1611771	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	266	1059	0	ENST00000344749.5:c.1891del	p.Gln631ArgfsTer11	p.Q631Rfs*11	ENST00000344749	NM_001136139.2	631	Cag/ag	19/19	NA	2	FACETS	1	0.953	1			1	INDETERMINATE	1	TRUE	NA	0.502208086633466	2		1059	1040	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781353	3781353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	228	1062	0	ENST00000262367.5:c.5012C>T	p.Ala1671Val	p.A1671V	ENST00000262367	NM_004380.2	1671	gCc/gTc	30/31	1	2	FACETS	0.781	0.727	0.837	0.781	0.727	0.837	SUBCLONAL	1	TRUE	1	0.502208086633466	2		1062	1162	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	213	619	8	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	0.502208086633466	2		627	676	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	191	610	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	0.502208086633466	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.502208086633466	1		610	468	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	213	1040	6	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	1	2	FACETS	0.958	0.892	1	0.958	0.892	1	CLONAL	1	TRUE	1	0.502208086633466	2		1046	885	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	203	914	3	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.502208086633466	NA		917	656	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993630	72993630	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780015879	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	233	794	2	ENST00000268489.5:c.415G>A	p.Gly139Ser	p.G139S	ENST00000268489	NM_006885.3	139	Ggc/Agc	2/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.502208086633466	2		796	808	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228145	36228145	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	617	949	0	ENST00000222270.7:c.7531C>T	p.Arg2511Trp	p.R2511W	ENST00000222270	NM_014727.1	2511	Cgg/Tgg	33/37	1	2	FACETS	1	0.996	1	1	0.998	1	CLONAL	2	TRUE	1	0.502208086633466	2		949	1044	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	83	1043	2	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.294	0.259	0.333	0.294	0.259	0.333	SUBCLONAL	1	TRUE	1	0.502208086633466	2		1045	1123	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	151	865	2	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	1	2	FACETS	0.725	0.663	0.789	0.725	0.663	0.789	SUBCLONAL	1	TRUE	1	0.502208086633466	2		867	830	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434454	110434454	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	138	662	1	ENST00000375856.3:c.3947del	p.Pro1316LeufsTer15	p.P1316Lfs*15	ENST00000375856	NM_003749.2	1316	cCt/ct	1/2	1	2	FACETS	0.77	0.702	0.841	0.77	0.702	0.841	SUBCLONAL	1	TRUE	1	0.502208086633466	2		663	714	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912173	29912173	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	51	193	0	ENST00000376809.5:c.894G>A	p.Trp298Ter	p.W298*	ENST00000376809	NM_002116.7	298	tgG/tgA	4/8	0.502208086633466	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.502208086633466	1		193	121	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692803	89692803	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	46	518	0	ENST00000371953.3:c.287C>A	p.Pro96Gln	p.P96Q	ENST00000371953	NM_000314.4	96	cCa/cAa	5/9	1	2	FACETS	0.852	0.725	0.988	0.852	0.725	0.988	CLONAL	1	TRUE	1	0.502208086633466	2		518	215	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202812	16202812	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	214	778	1	ENST00000375759.3:c.520C>T	p.Arg174Ter	p.R174*	ENST00000375759	NM_015001.2	174	Cga/Tga	3/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.502208086633466	2		779	800	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36931967	36931967	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	42	772	1	ENST00000361632.4:c.2502del	p.Ser835AlafsTer15	p.S835Afs*15	ENST00000361632		834	ggG/gg	16/16	1	2	FACETS	0.206	0.171	0.245	0.206	0.171	0.245	SUBCLONAL	1	TRUE	1	0.502208086633466	2		773	811	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117035	193117035	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	98	607	0	ENST00000367435.3:c.771del	p.Ala258ProfsTer61	p.A258Pfs*61	ENST00000367435	NM_024529.4	256	gtA/gt	8/17	1	2	FACETS	0.672	0.601	0.747	0.672	0.601	0.747	SUBCLONAL	1	TRUE	1	0.502208086633466	2		607	581	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203726	94203726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	43	483	0	ENST00000323929.3:c.928G>A	p.Glu310Lys	p.E310K	ENST00000323929	NM_005591.3	310	Gag/Aag	9/20	1	2	FACETS	0.741	0.626	0.867	0.741	0.626	0.867	SUBCLONAL	1	TRUE	1	0.502208086633466	2		483	231	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933468	100933468	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	46	345	0	ENST00000325455.5:c.1922del	p.Lys641SerfsTer8	p.K641Sfs*8	ENST00000325455	NM_001202474.3	641	aAg/ag	4/8	1	2	FACETS	0.76	0.646	0.884	0.76	0.646	0.884	SUBCLONAL	1	TRUE	1	0.502208086633466	2		345	241	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050886	49050886	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144668210	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	142	679	0	ENST00000267163.4:c.2570G>A	p.Arg857His	p.R857H	ENST00000267163	NM_000321.2	857	cGt/cAt	25/27	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.502208086633466	2		679	533	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281426	49281426	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	45	881	0	ENST00000282018.3:c.473T>G	p.Leu158Arg	p.L158R	ENST00000282018	NM_020377.2	158	cTc/cGc	1/1	1	2	FACETS	0.222	0.186	0.263	0.222	0.186	0.263	SUBCLONAL	1	TRUE	1	0.502208086633466	2		881	806	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434920	110434921	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	263	991	1	ENST00000375856.3:c.3480dup	p.Val1161ArgfsTer164	p.V1161Rfs*164	ENST00000375856	NM_003749.2	1160	-/C	1/2	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.502208086633466	2		992	1041	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046552	30046552	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	215	819	0	ENST00000331968.5:c.2631del	p.Leu878CysfsTer7	p.L878Cfs*7	ENST00000331968	NM_002742.2	877	ggG/gg	18/18	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.502208086633466	2		819	734	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900971	3900971	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	252	941	0	ENST00000262367.5:c.125A>G	p.Asp42Gly	p.D42G	ENST00000262367	NM_004380.2	42	gAt/gGt	2/31	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.502208086633466	2		941	852	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934570	9934570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	214	759	1	ENST00000330684.3:c.1585G>A	p.Val529Met	p.V529M	ENST00000330684	NM_001134407.1	529	Gtg/Atg	7/13	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.502208086633466	2		760	694	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830379	72830379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	102	434	0	ENST00000268489.5:c.6202G>A	p.Ala2068Thr	p.A2068T	ENST00000268489	NM_006885.3	2068	Gcc/Acc	9/10	1	2	FACETS	0.998	0.899	1	0.998	0.899	1	CLONAL	1	TRUE	1	0.502208086633466	2		434	407	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682336	37682336	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	64	910	0	ENST00000447079.4:c.3527A>C	p.Glu1176Ala	p.E1176A	ENST00000447079	NM_015083.1	1176	gAg/gCg	13/14	1	2	FACETS	0.328	0.283	0.377	0.328	0.283	0.377	SUBCLONAL	1	TRUE	1	0.502208086633466	2		910	777	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492832	56492832	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	180	797	0	ENST00000407977.2:c.107T>C	p.Val36Ala	p.V36A	ENST00000407977		36	gTg/gCg	2/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.502208086633466	2		797	688	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117600	70117601	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	253	819	0	ENST00000245479.2:c.71_72dup	p.Thr25ProfsTer37	p.T25Pfs*37	ENST00000245479	NM_000346.3	23	agc/agCCc	1/3	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.502208086633466	2		819	928	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56338883	56338883	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	22	61	0	ENST00000348428.3:c.8T>C	p.Leu3Pro	p.L3P	ENST00000348428	NM_006785.3	3	cTg/cCg	1/17	1	2	FACETS	0.782	0.633	0.938	1	0.939	1	CLONAL	2	TRUE	1	0.502208086633466	2		61	56	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226716	2226716	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs747161883	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	193	822	0	ENST00000398665.3:c.4196C>A	p.Pro1399His	p.P1399H	ENST00000398665	NM_032482.2	1399	cCc/cAc	27/28	1	2	FACETS	0.846	0.784	0.912	0.846	0.784	0.912	CLONAL	1	TRUE	1	0.502208086633466	2		822	908	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11022898	11022899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	208	1070	1	ENST00000327064.4:c.603dup	p.Ala202CysfsTer22	p.A202Cfs*22	ENST00000327064	NM_199141.1	199	-/T	5/16	1	2	FACETS	0.733	0.68	0.789	0.733	0.68	0.789	SUBCLONAL	1	TRUE	1	0.502208086633466	2		1071	1130	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101919	11101919	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	57	1025	0	ENST00000358026.2:c.1339C>A	p.Leu447Met	p.L447M	ENST00000358026	NM_001128849.1	447	Ctg/Atg	8/36	1	2	FACETS	0.214	0.183	0.249	0.214	0.183	0.249	SUBCLONAL	1	TRUE	1	0.502208086633466	2		1025	1060	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284970	15284970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	46	916	1	ENST00000263388.2:c.4645G>A	p.Ala1549Thr	p.A1549T	ENST00000263388	NM_000435.2	1549	Gcg/Acg	25/33	1	2	FACETS	0.203	0.17	0.239	0.203	0.17	0.239	SUBCLONAL	1	TRUE	1	0.502208086633466	2		917	904	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942515	17942515	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149452625	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	74	993	0	ENST00000458235.1:c.2773C>T	p.Arg925Cys	p.R925C	ENST00000458235	NM_000215.3	925	Cgc/Tgc	20/24	1	2	FACETS	0.291	0.253	0.331	0.291	0.253	0.331	SUBCLONAL	1	TRUE	1	0.502208086633466	2		993	1014	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974405	18974405	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	92	675	0	ENST00000262803.5:c.2759T>C	p.Val920Ala	p.V920A	ENST00000262803	NM_002911.3	920	gTc/gCc	19/24	1	2	FACETS	0.475	0.421	0.532	0.475	0.421	0.532	SUBCLONAL	1	TRUE	1	0.502208086633466	2		675	772	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25536798	25536798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1290646331	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	226	785	1	ENST00000264709.3:c.56G>A	p.Arg19Gln	p.R19Q	ENST00000264709	NM_175629.2	19	cGg/cAg	2/23	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.502208086633466	2		786	812	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719362	190719362	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	54	419	1	ENST00000441310.2:c.1364A>T	p.Lys455Ile	p.K455I	ENST00000441310	NM_000534.4	455	aAa/aTa	9/13	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.502208086633466	2		420	175	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274511	198274511	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	182	685	0	ENST00000335508.6:c.887C>A	p.Thr296Asn	p.T296N	ENST00000335508	NM_012433.2	296	aCc/aAc	7/25	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.502208086633466	2		685	645	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379328	225379328	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	18	644	0	ENST00000264414.4:c.539+1G>A		p.X180_splice	ENST00000264414	NM_003590.4	180			1	2	FACETS	0.202	0.152	0.262	0.202	0.152	0.262	SUBCLONAL	1	TRUE	1	0.502208086633466	2		644	354	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024465	31024465	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	220	889	0	ENST00000375687.4:c.3950C>A	p.Pro1317His	p.P1317H	ENST00000375687	NM_015338.5	1317	cCc/cAc	13/13	0.349663542210302	3	FACETS	1	0.985	1	0.603	0.561	0.646	CLONAL	1	TRUE	1	0.502208086633466	3		889	909	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723336	49723336	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	59	272	0	ENST00000449682.2:c.1207G>C	p.Val403Leu	p.V403L	ENST00000449682	NM_020998.3	403	Gtc/Ctc	10/18	1	2	FACETS	0.737	0.638	0.843	0.737	0.638	0.843	SUBCLONAL	1	TRUE	1	0.502208086633466	2		272	319	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247469	71247469	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs794727811	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	236	791	0	ENST00000318789.4:c.64G>A	p.Gly22Ser	p.G22S	ENST00000318789	NM_032682.5	22	Ggc/Agc	6/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.502208086633466	2		791	807	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449668	187449668	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	169	720	0	ENST00000232014.4:c.212T>C	p.Val71Ala	p.V71A	ENST00000232014	NM_001130845.1	71	gTg/gCg	4/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.502208086633466	2		720	592	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1936936	1936936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	240	885	0	ENST00000382891.5:c.1621G>A	p.Ala541Thr	p.A541T	ENST00000382891	NM_133335.3	541	Gct/Act	7/22	0.290756562479764	3	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.502208086633466	3		885	905	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189851	66189851	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	155	721	0	ENST00000273854.3:c.3095A>G	p.Asn1032Ser	p.N1032S	ENST00000273854	NM_004439.5	1032	aAc/aGc	18/18	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.502208086633466	2		721	552	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332733	153332733	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	44	705	0	ENST00000281708.4:c.223G>T	p.Gly75Ter	p.G75*	ENST00000281708	NM_033632.3	75	Gga/Tga	2/12	1	2	FACETS	0.26	0.217	0.307	0.26	0.217	0.307	SUBCLONAL	1	TRUE	1	0.502208086633466	2		705	674	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31521250	31521250	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	133	810	0	ENST00000344624.3:c.927del	p.Glu310SerfsTer42	p.E310Sfs*42	ENST00000344624		309	aaA/aa	3/33	1	2	FACETS	0.88	0.802	0.961	0.88	0.802	0.961	CLONAL	1	TRUE	1	0.502208086633466	2		810	602	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944647	38944647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	20	540	0	ENST00000357387.3:c.4814C>T	p.Thr1605Ile	p.T1605I	ENST00000357387	NM_152756.3	1605	aCa/aTa	36/38	1	2	FACETS	0.26	0.199	0.332	0.26	0.199	0.332	SUBCLONAL	1	TRUE	1	0.502208086633466	2		540	306	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569266	67569266	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	169	741	0	ENST00000274335.5:c.386del	p.Pro129ArgfsTer48	p.P129Rfs*48	ENST00000274335		128	gCc/gc	2/15	1	2	FACETS	0.93	0.857	1	0.93	0.857	1	CLONAL	1	TRUE	1	0.502208086633466	2		741	724	SUCCESS
APC	324	MSKCC	GRCh37	5	112103059	112103059	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	87	446	0	ENST00000257430.4:c.394G>T	p.Gly132Ter	p.G132*	ENST00000257430	NM_000038.5	132	Gga/Tga	4/16	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.502208086633466	2		446	333	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401559	401559	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1224284590	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	111	713	0	ENST00000380956.4:c.881A>G	p.Tyr294Cys	p.Y294C	ENST00000380956	NM_001195286.1	294	tAc/tGc	7/9	1	2	FACETS	0.734	0.662	0.811	0.734	0.662	0.811	SUBCLONAL	1	TRUE	1	0.502208086633466	2		713	602	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402713	20402713	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	170	547	0	ENST00000346618.3:c.250C>A	p.Leu84Ile	p.L84I	ENST00000346618	NM_001949.4	84	Ctc/Atc	1/7	1	2	FACETS	0.977	0.901	1	0.977	0.901	1	CLONAL	1	TRUE	1	0.502208086633466	2		547	693	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670340	30670340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199953525	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	203	592	0	ENST00000376406.3:c.6092G>A	p.Arg2031Gln	p.R2031Q	ENST00000376406	NM_014641.2	2031	cGg/cAg	14/15	0.502208086633466	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.502208086633466	1		592	456	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163874	32163874	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	59	643	0	ENST00000375023.3:c.5352G>T	p.Gln1784His	p.Q1784H	ENST00000375023	NM_004557.3	1784	caG/caT	30/30	1	2	FACETS	0.339	0.291	0.391	0.339	0.291	0.391	SUBCLONAL	1	TRUE	1	0.502208086633466	2		643	694	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166763	32166763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761314959	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	54	948	2	ENST00000375023.3:c.4475G>A	p.Arg1492Gln	p.R1492Q	ENST00000375023	NM_004557.3	1492	cGg/cAg	24/30	1	2	FACETS	0.217	0.184	0.253	0.217	0.184	0.253	SUBCLONAL	1	TRUE	1	0.502208086633466	2		950	992	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066540	94066540	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	32	594	1	ENST00000369303.4:c.1219G>T	p.Ala407Ser	p.A407S	ENST00000369303	NM_004440.3	407	Gcc/Tcc	5/17	1	2	FACETS	0.257	0.208	0.313	0.257	0.208	0.313	SUBCLONAL	1	TRUE	1	0.502208086633466	2		595	495	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710924	117710924	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	154	533	0	ENST00000368508.3:c.1348G>A	p.Val450Met	p.V450M	ENST00000368508	NM_002944.2	450	Gtg/Atg	12/43	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.502208086633466	2		533	576	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005131	150005131	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	187	678	0	ENST00000253339.5:c.1094C>T	p.Ala365Val	p.A365V	ENST00000253339		365	gCt/gTt	3/7	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.502208086633466	2		678	606	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729709	41729709	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	171	863	0	ENST00000242208.4:c.820G>T	p.Gly274Ter	p.G274*	ENST00000242208	NM_002192.2	274	Gga/Tga	3/3	1	2	FACETS	0.912	0.84	0.986	0.912	0.84	0.986	CLONAL	1	TRUE	1	0.502208086633466	2		863	747	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334804	81334804	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	115	725	0	ENST00000222390.5:c.1912G>T	p.Gly638Ter	p.G638*	ENST00000222390	NM_000601.4	638	Gga/Tga	17/18	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.502208086633466	2		725	441	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874713	151874713	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	175	587	2	ENST00000262189.6:c.7825C>T	p.Arg2609Ter	p.R2609*	ENST00000262189	NM_170606.2	2609	Cga/Tga	38/59	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.502208086633466	2		589	578	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189104	38189104	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	39	621	0	ENST00000317025.8:c.911-1G>T		p.X304_splice	ENST00000317025	NM_023034.1	304			1	2	FACETS	0.298	0.247	0.356	0.298	0.247	0.356	SUBCLONAL	1	TRUE	1	0.502208086633466	2		621	521	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759967	133759967	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773883545	NA	P-0021099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	387	1014	0	ENST00000318560.5:c.2290C>T	p.Arg764Trp	p.R764W	ENST00000318560	NM_005157.4	764	Cgg/Tgg	11/11	0.35757047707089	2	FACETS	0.768	0.732	0.805	0.768	0.732	0.805	SUBCLONAL	2	TRUE	0	0.502208086633466	2		1014	1003	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0021100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	263	340	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.318272085928813	8	FACETS	0.927	0.868	0.987			1	CLONAL	3	TRUE	NA	0.318272085928813	8		340	1162	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971292	13971292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772105404	NA	P-0021100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	73	645	0	ENST00000405192.2:c.637C>T	p.Arg213Cys	p.R213C	ENST00000405192	NM_001163147.1	213	Cgc/Tgc	8/12	0.156967870649404	4	FACETS	1	0.878	1	0.501	0.439	0.569	INDETERMINATE	1	TRUE	2	0.318272085928813	4		645	603	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204612	108204612	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1555126163	NA	P-0021100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	43	370	0	ENST00000278616.4:c.7928-1G>A		p.X2643_splice	ENST00000278616	NM_000051.3	2643			0.268408455594585	2	FACETS	0.941	0.792	1	0.471	0.396	0.553	CLONAL	1	TRUE	0	0.318272085928813	2		370	287	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206581	108206581	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	120	457	1	ENST00000278616.4:c.8161G>T	p.Asp2721Tyr	p.D2721Y	ENST00000278616	NM_000051.3	2721	Gac/Tac	56/63	0.268408455594585	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	0	0.318272085928813	2		458	364	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549330	21549330	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	97	835	0	ENST00000382592.4:c.2946C>G	p.Ile982Met	p.I982M	ENST00000382592	NM_014572.2	982	atC/atG	8/8	0.284783889562158	3	FACETS	1	0.921	1			1	CLONAL	1	TRUE	NA	0.318272085928813	3		835	680	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134463	41134463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199719831	NA	P-0021100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	143	742	1	ENST00000379561.5:c.1165G>A	p.Val389Ile	p.V389I	ENST00000379561	NM_002015.3	389	Gtt/Att	2/3	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.318272085928813	2		743	609	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040892	42040892	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	161	741	2	ENST00000219905.7:c.5270G>T	p.Arg1757Leu	p.R1757L	ENST00000219905	NM_001164273.1	1757	cGt/cTt	16/24	1	2	FACETS	0.754	0.694	0.816	1	0.989	1	SUBCLONAL	2	TRUE	1	0.318272085928813	2		743	671	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634384	23634384	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	159	871	1	ENST00000261584.4:c.2902G>T	p.Ala968Ser	p.A968S	ENST00000261584	NM_024675.3	968	Gct/Tct	9/13	0.268408455594585	2	FACETS	0.834	0.768	0.902	0.834	0.768	0.902	CLONAL	2	TRUE	0	0.318272085928813	2		872	599	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012199	16012199	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	93	715	0	ENST00000268712.3:c.2083G>A	p.Asp695Asn	p.D695N	ENST00000268712	NM_006311.3	695	Gat/Aat	19/46	1	2	FACETS	0.928	0.826	1	0.928	0.826	1	CLONAL	1	TRUE	1	0.318272085928813	2		715	630	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256249	41256249	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	74	554	0	ENST00000357654.3:c.331G>T	p.Glu111Ter	p.E111*	ENST00000357654	NM_007294.3	111	Gaa/Taa	6/23	0.318272085928813	3	FACETS	1	0.968	1	0.659	0.579	0.744	CLONAL	1	TRUE	1	0.318272085928813	3		554	409	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121316	29121317	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTT	novel	NA	P-0021100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	126	981	0	ENST00000328354.6:c.356_358dup	p.Lys119dup	p.K119dup	ENST00000328354	NM_007194.3	119	agc/aAAAgc	3/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.318272085928813	2		981	710	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670378	134670378	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	140	594	0	ENST00000398015.3:c.289A>T	p.Ser97Cys	p.S97C	ENST00000398015	NM_004441.4	97	Agc/Tgc	3/16	0.200748908661852	1	FACETS	0.794	0.728	0.861	1	0.989	1	SUBCLONAL	2	TRUE	0	0.318272085928813	1		594	466	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928061	178928061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs573490174	NA	P-0021100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	93	794	0	ENST00000263967.3:c.1339C>T	p.Pro447Ser	p.P447S	ENST00000263967	NM_006218.2	447	Cca/Tca	8/21	0.318272085928813	6	FACETS	1	0.966	1			1	CLONAL	1	TRUE	NA	0.318272085928813	6		794	781	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039888	47039888	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	92	937	2	ENST00000377604.3:c.1231C>T	p.Gln411Ter	p.Q411*	ENST00000377604	NM_001204468.1	411	Cag/Tag	12/24	NA	2	FACETS	0.871	0.774	0.973			1	INDETERMINATE	1	TRUE	NA	0.318272085928813	2		939	664	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89828421	89828423	+	stop_gained	Nonsense_Mutation	TNP	GGT	GGT	AGA	novel	NA	P-0021100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	108	583	1	ENST00000389301.3:c.2786_2788delinsTCT	p.Tyr929_Gln930delinsPheTer	p.Y929_Q930delinsF*	ENST00000389301	NM_000135.2	929	tACCaa/tTCTaa	29/43	0.318272085928813	3	FACETS	0.868	0.784	0.957	0.868	0.784	0.957	CLONAL	2	TRUE	1	0.318272085928813	3		584	453	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0021116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	450	983	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.567200403652873	3	FACETS	0.995	0.954	1	0.995	0.954	1	CLONAL	2	TRUE	1	0.599756177937234	3		983	980	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0021116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	23	1034	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.562599732061174	1	FACETS	0.071	0.055	0.09	0.071	0.055	0.09	SUBCLONAL	1	TRUE	0	0.599756177937234	1		1034	753	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0021116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	286	1075	2	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.562599732061174	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.599756177937234	1		1077	665	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735458	40735458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1243407933	NA	P-0021116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	202	1026	0	ENST00000373198.4:c.3415C>T	p.Arg1139Trp	p.R1139W	ENST00000373198	NM_133170.3	1139	Cgg/Tgg	25/32	0.184707420676084	2	FACETS	0.687	0.636	0.739	0.343	0.318	0.37	INDETERMINATE	1	TRUE	0	0.599756177937234	2		1026	981	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0021116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	492	725	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.593560656406052	3	FACETS	0.954	0.924	0.984	0.954	0.924	0.984	CLONAL	3	TRUE	0	0.599756177937234	3		725	745	SUCCESS
APC	324	MSKCC	GRCh37	5	112128202	112128203	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	TAGTC	novel	NA	P-0021116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	173	612	0	ENST00000257430.4:c.705_706insTAGTC	p.Gln236Ter	p.Q236*	ENST00000257430	NM_000038.5	235	-/TAGTC	7/16	1	2	FACETS	0.797	0.735	0.861	0.797	0.735	0.861	SUBCLONAL	1	TRUE	1	0.599756177937234	2		612	724	SUCCESS
APC	324	MSKCC	GRCh37	5	112175273	112175273	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123121	NA	P-0021116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	104	368	0	ENST00000257430.4:c.3982C>T	p.Gln1328Ter	p.Q1328*	ENST00000257430	NM_000038.5	1328	Cag/Tag	16/16	1	2	FACETS	0.935	0.845	1	0.935	0.845	1	CLONAL	1	TRUE	1	0.599756177937234	2		368	371	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287518	33287518	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	511	977	2	ENST00000374542.5:c.1579A>G	p.Ile527Val	p.I527V	ENST00000374542	NM_001141970.1	527	Ata/Gta	6/8	0.535858144759512	3	FACETS	0.916	0.879	0.953	0.916	0.879	0.953	CLONAL	2	TRUE	1	0.599756177937234	3		979	1209	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932980	39932980	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238996683	NA	P-0021116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	239	955	3	ENST00000378444.4:c.1619G>A	p.Arg540Gln	p.R540Q	ENST00000378444	NM_001123385.1	540	cGg/cAg	4/15	0.567200403652873	3	FACETS	0.909	0.848	0.972	0.454	0.424	0.486	CLONAL	1	TRUE	1	0.599756177937234	3		958	1140	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	36	492	0	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	1	2	FACETS	0.349	0.286	0.418	0.349	0.286	0.418	SUBCLONAL	1	TRUE	1	0.5	2		492	413	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	87	134	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.868	0.773	0.968	0.868	0.773	0.968	CLONAL	1	TRUE	1	0.5	2		134	401	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	148	692	4	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.787	0.72	0.857	0.787	0.72	0.857	SUBCLONAL	1	TRUE	1	0.5	2		696	752	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	208	998	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.5	2		998	817	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	34	490	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.325	0.266	0.393	0.325	0.266	0.393	SUBCLONAL	1	TRUE	1	0.5	2		490	418	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589168	67589168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	95	475	0	ENST00000274335.5:c.1156C>T	p.Arg386Ter	p.R386*	ENST00000274335		386	Cga/Tga	9/15	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.5	2		475	347	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138642	55138642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143344944	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	177	758	1	ENST00000257290.5:c.1319C>T	p.Thr440Met	p.T440M	ENST00000257290	NM_006206.4	440	aCg/aTg	9/23	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.5	2		759	682	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	79	462	1	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.5	2		463	310	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	144	485	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	0.5	2		485	562	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024001	27024002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	26	121	0	ENST00000324856.7:c.1113dup	p.Gln372AlafsTer28	p.Q372Afs*28	ENST00000324856	NM_006015.4	369	-/G	1/20	1	2	FACETS	0.954	0.771	1	0.954	0.771	1	CLONAL	1	TRUE	1	0.5	2		121	109	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464896	120464896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	198	638	2	ENST00000256646.2:c.5176C>T	p.Arg1726Cys	p.R1726C	ENST00000256646	NM_024408.3	1726	Cgt/Tgt	28/34	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.5	2		640	701	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073804	8073804	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1557463619	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	43	455	2	ENST00000377482.5:c.855del	p.Arg286GlufsTer9	p.R286Efs*9	ENST00000377482	NM_018948.3	285	ccC/cc	4/4	1	2	FACETS	0.454	0.38	0.535	0.454	0.38	0.535	SUBCLONAL	1	TRUE	1	0.5	2		457	379	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736510	85736511	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs387906351	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	97	539	3	ENST00000370580.1:c.136dup	p.Ile46AsnfsTer4	p.I46Nfs*4	ENST00000370580	NM_003921.4	46	ata/aAta	2/3	1	2	FACETS	0.683	0.61	0.76	0.683	0.61	0.76	SUBCLONAL	1	TRUE	1	0.5	2		542	568	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794685	42794685	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767618694	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	77	985	1	ENST00000575354.2:c.1765C>T	p.Arg589Trp	p.R589W	ENST00000575354	NM_015125.3	589	Cgg/Tgg	10/20	1	2	FACETS	0.337	0.295	0.382	0.337	0.295	0.382	SUBCLONAL	1	TRUE	1	0.5	2		986	915	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805041	89805041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772505725	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	295	1098	4	ENST00000389301.3:c.4336G>A	p.Ala1446Thr	p.A1446T	ENST00000389301	NM_000135.2	1446	Gct/Act	43/43	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.5	2		1102	1106	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033352	48033352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750949	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	137	667	0	ENST00000234420.5:c.3656C>T	p.Thr1219Ile	p.T1219I	ENST00000234420	NM_000179.2	1219	aCt/aTt	8/10	1	2	FACETS	0.968	0.885	1	0.968	0.885	1	CLONAL	1	TRUE	1	0.5	2		667	566	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910427	50910427	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750466994	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	180	975	1	ENST00000440232.2:c.1682G>A	p.Arg561Gln	p.R561Q	ENST00000440232	NM_002691.3	561	cGg/cAg	13/27	1	2	FACETS	0.727	0.67	0.786	0.727	0.67	0.786	SUBCLONAL	1	TRUE	1	0.5	2		976	991	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	62	585	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.331	0.285	0.381	0.331	0.285	0.381	SUBCLONAL	1	TRUE	1	0.5	2		588	750	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255020	16255020	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747601086	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	106	442	0	ENST00000375759.3:c.2285G>A	p.Arg762Gln	p.R762Q	ENST00000375759	NM_015001.2	762	cGg/cAg	11/15	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.5	2		442	413	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	243	796	0	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	1	2	FACETS	0.945	0.883	1	0.945	0.883	1	CLONAL	1	TRUE	1	0.5	2		796	1029	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316397	14316397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782457908	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	155	870	0	ENST00000256196.4:c.208G>A	p.Ala70Thr	p.A70T	ENST00000256196		70	Gca/Aca	3/6	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.5	2		870	603	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417910	32417910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	208	784	0	ENST00000332351.3:c.1142C>T	p.Ser381Leu	p.S381L	ENST00000332351	NM_024426.4	381	tCg/tTg	7/10	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.5	2		784	831	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784903	9784903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761274254	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	53	962	0	ENST00000377346.4:c.2906G>A	p.Arg969His	p.R969H	ENST00000377346	NM_005026.3	969	cGc/cAc	23/24	1	2	FACETS	0.228	0.194	0.267	0.228	0.194	0.267	SUBCLONAL	1	TRUE	1	0.5	2		962	928	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696345	47696345	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	129	595	1	ENST00000347630.2:c.478G>A	p.Glu160Lys	p.E160K	ENST00000347630	NM_001007230.1	160	Gag/Aag	6/11	1	2	FACETS	0.928	0.845	1	0.928	0.845	1	CLONAL	1	TRUE	1	0.5	2		596	556	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056227	27056227	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763630072	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	159	826	0	ENST00000324856.7:c.1223C>T	p.Pro408Leu	p.P408L	ENST00000324856	NM_006015.4	408	cCg/cTg	2/20	1	2	FACETS	0.909	0.835	0.985	0.909	0.835	0.985	CLONAL	1	TRUE	1	0.5	2		826	700	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429796	78429796	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778374	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	66	614	1	ENST00000370768.2:c.992G>A	p.Arg331Gln	p.R331Q	ENST00000370768	NM_003902.3	331	cGa/cAa	12/20	1	2	FACETS	0.533	0.464	0.609	0.533	0.464	0.609	SUBCLONAL	1	TRUE	1	0.5	2		615	495	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282367	115282367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	70	779	1	ENST00000438362.2:c.283C>T	p.Leu95Phe	p.L95F	ENST00000438362	NM_001242891.1	95	Ctt/Ttt	3/20	1	2	FACETS	0.444	0.387	0.506	0.444	0.387	0.506	SUBCLONAL	1	TRUE	1	0.5	2		780	630	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693008	89693008	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	rs1564830522	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	46	488	0	ENST00000371953.3:c.492+1del		p.K164fs	ENST00000371953	NM_000314.4	164	aaG/aa	5/9	1	2	FACETS	0.643	0.545	0.75	0.643	0.545	0.75	SUBCLONAL	1	TRUE	1	0.5	2		488	286	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4388026	4388026	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367874736	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	49	588	0	ENST00000261254.3:c.512G>A	p.Arg171Gln	p.R171Q	ENST00000261254	NM_001759.3	171	cGg/cAg	3/5	1	2	FACETS	0.344	0.291	0.402	0.344	0.291	0.402	SUBCLONAL	1	TRUE	1	0.5	2		588	570	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422933	49422933	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372296816	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	135	1001	1	ENST00000301067.7:c.14162G>A	p.Arg4721His	p.R4721H	ENST00000301067	NM_003482.3	4721	cGt/cAt	44/54	1	2	FACETS	0.675	0.614	0.739	0.675	0.614	0.739	SUBCLONAL	1	TRUE	1	0.5	2		1002	800	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133236021	133236021	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	214	852	0	ENST00000320574.5:c.3135T>A	p.Asp1045Glu	p.D1045E	ENST00000320574	NM_006231.2	1045	gaT/gaA	26/49	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.5	2		852	748	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133236046	133236046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1397985428	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	158	801	0	ENST00000320574.5:c.3110G>A	p.Arg1037His	p.R1037H	ENST00000320574	NM_006231.2	1037	cGt/cAt	26/49	1	2	FACETS	0.884	0.812	0.959	0.884	0.812	0.959	CLONAL	1	TRUE	1	0.5	2		801	715	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436815	110436815	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	160	1084	0	ENST00000375856.3:c.1586del	p.Pro529ArgfsTer15	p.P529Rfs*15	ENST00000375856	NM_003749.2	529	cCg/cg	1/2	1	2	FACETS	0.637	0.583	0.693	0.637	0.583	0.693	SUBCLONAL	1	TRUE	1	0.5	2		1084	1005	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477167	67477167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	180	828	3	ENST00000327367.4:c.974G>A	p.Gly325Asp	p.G325D	ENST00000327367	NM_005902.3	325	gGc/gAc	7/9	1	2	FACETS	0.893	0.825	0.964	0.893	0.825	0.964	CLONAL	1	TRUE	1	0.5	2		831	806	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865869	56865869	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761782738	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	130	508	1	ENST00000308159.5:c.1201G>A	p.Asp401Asn	p.D401N	ENST00000308159	NM_014669.4	401	Gac/Aac	11/22	1	2	FACETS	0.935	0.852	1	0.935	0.852	1	CLONAL	1	TRUE	1	0.5	2		509	556	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351914	89351914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	363	1389	2	ENST00000301030.4:c.1036G>A	p.Glu346Lys	p.E346K	ENST00000301030	NM_001256183.1	346	Gag/Aag	9/13	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.5	2		1391	1367	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556364	29556364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	72	733	1	ENST00000356175.3:c.2731C>T	p.Leu911Phe	p.L911F	ENST00000356175	NM_000267.3	911	Ctt/Ttt	21/57	1	2	FACETS	0.411	0.359	0.468	0.411	0.359	0.468	SUBCLONAL	1	TRUE	1	0.5	2		734	700	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40498610	40498610	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	159	708	0	ENST00000264657.5:c.250C>T	p.Arg84Ter	p.R84*	ENST00000264657	NM_139276.2	84	Cga/Tga	3/24	1	2	FACETS	0.986	0.907	1	0.986	0.907	1	CLONAL	1	TRUE	1	0.5	2		708	645	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492923	56492923	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	75	295	0	ENST00000407977.2:c.16C>T	p.Gln6Ter	p.Q6*	ENST00000407977		6	Cag/Tag	2/10	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.5	2		295	275	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78704435	78704435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	179	628	0	ENST00000306801.3:c.583G>A	p.Asp195Asn	p.D195N	ENST00000306801	NM_020761.2	195	Gac/Aac	5/34	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.5	2		628	619	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7126651	7126651	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	197	902	0	ENST00000302850.5:c.2957G>T	p.Gly986Val	p.G986V	ENST00000302850	NM_000208.2	986	gGg/gTg	16/22	1	2	FACETS	0.961	0.891	1	0.961	0.891	1	CLONAL	1	TRUE	1	0.5	2		902	820	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945780	17945780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1009464631	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	152	847	1	ENST00000458235.1:c.2080G>A	p.Glu694Lys	p.E694K	ENST00000458235	NM_000215.3	694	Gag/Aag	16/24	1	2	FACETS	0.708	0.647	0.771	0.708	0.647	0.771	SUBCLONAL	1	TRUE	1	0.5	2		848	859	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210925	36210925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531663002	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	262	1069	4	ENST00000222270.7:c.676C>T	p.Arg226Trp	p.R226W	ENST00000222270	NM_014727.1	226	Cgg/Tgg	3/37	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.5	2		1073	912	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158626969	158626969	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	116	652	0	ENST00000263640.3:c.701T>C	p.Val234Ala	p.V234A	ENST00000263640	NM_001105.4	234	gTg/gCg	7/11	1	2	FACETS	0.668	0.602	0.736	0.668	0.602	0.736	SUBCLONAL	1	TRUE	1	0.5	2		652	695	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095834	29095834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs864622371	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	161	877	1	ENST00000328354.6:c.1000G>A	p.Ala334Thr	p.A334T	ENST00000328354	NM_007194.3	334	Gct/Act	9/15	1	2	FACETS	0.804	0.738	0.873	0.804	0.738	0.873	CLONAL	1	TRUE	1	0.5	2		878	801	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114292	143114292	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	145	675	0	ENST00000262992.4:c.1129A>G	p.Lys377Glu	p.K377E	ENST00000262992	NM_001101669.1	377	Aag/Gag	13/24	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.5	2		675	525	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286886	33286886	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762346785	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	195	808	2	ENST00000374542.5:c.2051C>T	p.Thr684Met	p.T684M	ENST00000374542	NM_001141970.1	684	aCg/aTg	7/8	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.5	2		810	760	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271461	38271461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374473310	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	224	1103	3	ENST00000425967.3:c.2360G>A	p.Arg787His	p.R787H	ENST00000425967	NM_001174067.1	787	cGc/cAc	18/19	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.5	2		1106	894	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922009	39922009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	60	803	2	ENST00000378444.4:c.4163C>T	p.Ala1388Val	p.A1388V	ENST00000378444	NM_001123385.1	1388	gCc/gTc	9/15	1	2	FACETS	0.299	0.257	0.345	0.299	0.257	0.345	SUBCLONAL	1	TRUE	1	0.5	2		805	802	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341244	70341244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	151	815	1	ENST00000374080.3:c.803G>A	p.Gly268Glu	p.G268E	ENST00000374080		268	gGa/gAa	6/45	1	2	FACETS	0.912	0.837	0.991	0.912	0.837	0.991	CLONAL	1	TRUE	1	0.5	2		816	662	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0021119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	196	712	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.704427374914866	2		712	548	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0021119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	329	733	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.667180225865823	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.704427374914866	1		733	569	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0021119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	224	872	3	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.704427374914866	2		875	593	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398220	25398220	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	218	870	1	ENST00000311936.3:c.99T>A	p.Asp33Glu	p.D33E	ENST00000311936	NM_004985.3	33	gaT/gaA	2/5	1	2	FACETS	0.957	0.895	1	0.957	0.895	1	CLONAL	1	TRUE	1	0.704427374914866	2		871	647	SUCCESS
APC	324	MSKCC	GRCh37	5	112175761	112175761	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	145	593	5	ENST00000257430.4:c.4473del	p.Phe1491LeufsTer16	p.F1491Lfs*16	ENST00000257430	NM_000038.5	1490	caT/ca	16/16	1	2	FACETS	0.931	0.857	1	0.931	0.857	1	CLONAL	1	TRUE	1	0.704427374914866	2		598	442	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604745	48604745	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	191	726	4	ENST00000342988.3:c.1567T>C	p.Cys523Arg	p.C523R	ENST00000342988	NM_005359.5	523	Tgc/Cgc	12/12	0.704427374914866	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.704427374914866	1		730	344	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856019	111856019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs984848263	NA	P-0021119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	257	861	6	ENST00000341259.2:c.70C>T	p.Arg24Trp	p.R24W	ENST00000341259	NM_005475.2	24	Cgg/Tgg	2/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.704427374914866	2		867	662	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119829	70119830	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0021119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	418	1245	3	ENST00000245479.2:c.832_833dup	p.Ser279Ter	p.S279*	ENST00000245479	NM_000346.3	277	-/CT	3/3	0.347131151978052	2	FACETS	1	0.996	1	0.731	0.701	0.761	INDETERMINATE	1	TRUE	0	0.704427374914866	2		1248	812	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78931459	78931459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761590823	NA	P-0021119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	104	1091	0	ENST00000306801.3:c.3406G>A	p.Gly1136Ser	p.G1136S	ENST00000306801	NM_020761.2	1136	Ggc/Agc	29/34	0.347131151978052	2	FACETS	0.429	0.384	0.477	0.215	0.192	0.239	INDETERMINATE	1	TRUE	0	0.704427374914866	2		1091	688	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99812467	99812467	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	204	666	1	ENST00000280892.6:c.202T>C	p.Phe68Leu	p.F68L	ENST00000280892	NM_001130678.1	68	Ttt/Ctt	3/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.704427374914866	2		667	528	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940545	131940545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	212	645	2	ENST00000265335.6:c.2572G>A	p.Glu858Lys	p.E858K	ENST00000265335		858	Gaa/Aaa	16/25	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.704427374914866	2		647	590	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33290660	33290660	+	5_prime_UTR_variant	5'UTR	SNP	C	C	A	novel	NA	P-0021119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	37	963	0	ENST00000374542.5:c.-74G>T		p.*25*	ENST00000374542	NM_001141970.1	-/740		1/8	0.704427374914866	2	FACETS	0.147	0.12	0.177	0.073	0.06	0.089	SUBCLONAL	1	TRUE	0	0.704427374914866	2		963	715	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004221	150004221	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	75	623	0	ENST00000253339.5:c.2004G>A	p.Met668Ile	p.M668I	ENST00000253339		668	atG/atA	3/7	0.704427374914866	2	FACETS	0.382	0.335	0.432	0.191	0.167	0.216	SUBCLONAL	1	TRUE	0	0.704427374914866	2		623	558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782144	NA	P-0021120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	382	1106	0	ENST00000269305.4:c.473G>C	p.Arg158Pro	p.R158P	ENST00000269305	NM_001126112.2	158	cGc/cCc	5/11	1	2	FACETS	0.895	0.848	0.942	0.895	0.848	0.942	CLONAL	1	TRUE	1	0.561095925544851	2		1106	1522	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572986	7572986	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555524156	NA	P-0021120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	249	640	1	ENST00000269305.4:c.1123C>T	p.Gln375Ter	p.Q375*	ENST00000269305	NM_001126112.2	375	Cag/Tag	11/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.561095925544851	2		641	875	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843610	156843610	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1554	139	1162	0	ENST00000524377.1:c.1036C>G	p.Leu346Val	p.L346V	ENST00000524377	NM_002529.3	346	Ctg/Gtg	8/17	1	2	FACETS	0.293	0.265	0.322	0.293	0.265	0.322	SUBCLONAL	1	TRUE	1	0.561095925544851	2		1162	1693	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332915	70332915	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs768012438	NA	P-0021120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	143	994	0	ENST00000373644.4:c.820G>C	p.Gly274Arg	p.G274R	ENST00000373644	NM_030625.2	274	Ggt/Cgt	2/12	0.295903295760751	1	FACETS	0.496	0.452	0.541	0.496	0.452	0.541	INDETERMINATE	1	TRUE	0	0.561095925544851	1		994	740	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625297	69625297	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	364	1043	1	ENST00000334134.2:c.496G>T	p.Gly166Cys	p.G166C	ENST00000334134	NM_005247.2	166	Ggc/Tgc	3/3	0.279933023127559	1	FACETS	0.805	0.764	0.847	0.805	0.764	0.847	INDETERMINATE	1	TRUE	0	0.561095925544851	1		1044	1159	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434697	49434697	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	312	1087	0	ENST00000301067.7:c.6856G>C	p.Glu2286Gln	p.E2286Q	ENST00000301067	NM_003482.3	2286	Gag/Cag	31/54	1	2	FACETS	0.784	0.738	0.832	0.784	0.738	0.832	SUBCLONAL	1	TRUE	1	0.561095925544851	2		1087	1418	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485990	40485990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	339	1080	1	ENST00000264657.5:c.875C>T	p.Ser292Phe	p.S292F	ENST00000264657	NM_139276.2	292	tCc/tTc	9/24	1	2	FACETS	0.999	0.945	1	0.999	0.945	1	CLONAL	1	TRUE	1	0.561095925544851	2		1081	1210	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968303	134968303	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	270	999	1	ENST00000398015.3:c.2816C>A	p.Ser939Tyr	p.S939Y	ENST00000398015	NM_004441.4	939	tCc/tAc	15/16	0.358014983131166	1	FACETS	0.741	0.696	0.786	0.741	0.696	0.786	SUBCLONAL	1	TRUE	0	0.561095925544851	1		1000	935	SUCCESS
APC	324	MSKCC	GRCh37	5	112173912	112173912	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1554084318	NA	P-0021120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	179	546	0	ENST00000257430.4:c.2621C>G	p.Ser874Ter	p.S874*	ENST00000257430	NM_000038.5	874	tCa/tGa	16/16	0.561095925544851	1	FACETS	0.979	0.911	1	0.979	0.911	1	CLONAL	1	TRUE	0	0.561095925544851	1		546	469	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223550	55223551	+	missense_variant	Missense_Mutation	DNP	CG	CG	AC	novel	NA	P-0021120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	623	864	0	ENST00000275493.2:c.917_918delinsAC	p.Ser306Tyr	p.S306Y	ENST00000275493	NM_005228.3	306	tCG/tAC	8/28	0.344699321467692	5	FACETS	1	0.996	1	0.831	0.8	0.863	CLONAL	2	TRUE	2	0.561095925544851	5		864	1640	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345201	70345201	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	139	853	0	ENST00000374080.3:c.2227G>T	p.Glu743Ter	p.E743*	ENST00000374080		743	Gag/Tag	16/45	0.358014983131166	1	FACETS	0.394	0.358	0.431	0.394	0.358	0.431	SUBCLONAL	1	TRUE	0	0.561095925544851	1		853	905	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643213	38643213	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0021120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	59	476	0	ENST00000299084.4:c.685-2A>G		p.X229_splice	ENST00000299084	NM_152594.2	229			0.295903295760751	1	FACETS	0.513	0.445	0.586	0.513	0.445	0.586	INDETERMINATE	1	TRUE	0	0.561095925544851	1		476	295	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0021123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	53	510	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.25	2		510	408	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480551	50480552	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0021123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	75	714	0	ENST00000394963.4:c.421_422del	p.Val141ThrfsTer13	p.V141Tfs*13	ENST00000394963	NM_003076.4	141	GTa/a	4/13	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.25	2		714	548	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442578	52442578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1294552464	NA	P-0021123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	44	584	0	ENST00000460680.1:c.167G>A	p.Arg56His	p.R56H	ENST00000460680	NM_004656.3	56	cGc/cAc	4/17	1	2	FACETS	0.697	0.584	0.822	0.697	0.584	0.822	SUBCLONAL	1	TRUE	1	0.25	2		584	505	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442568	52442573	+	inframe_deletion	In_Frame_Del	DEL	CCGGGA	CCGGGA	-	novel	NA	P-0021123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	41	614	0	ENST00000460680.1:c.172_177del	p.Ser58_Arg59del	p.S58_R59del	ENST00000460680	NM_004656.3	58	TCCCGG/-	4/17	1	2	FACETS	0.609	0.506	0.722	0.609	0.506	0.722	SUBCLONAL	1	TRUE	1	0.25	2		614	539	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0021125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	674	903	3	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.599067200593586	3	FACETS	0.956	0.93	0.981	0.956	0.93	0.981	CLONAL	3	TRUE	0	0.599067200593586	3		906	1020	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226926	2226926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375062102	NA	P-0021125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	133	463	2	ENST00000398665.3:c.4406C>T	p.Pro1469Leu	p.P1469L	ENST00000398665	NM_032482.2	1469	cCg/cTg	27/28	NA	2	FACETS	0.982	0.899	1			1	INDETERMINATE	1	TRUE	NA	0.599067200593586	2		465	452	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039454	49039454	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs774744607	NA	P-0021125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	408	718	0	ENST00000267163.4:c.2439T>G	p.Tyr813Ter	p.Y813*	ENST00000267163	NM_000321.2	813	taT/taG	23/27	0.599067200593586	2	FACETS	0.967	0.93	1	0.967	0.93	1	CLONAL	2	TRUE	0	0.599067200593586	2		718	704	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162683	47162683	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	117	640	0	ENST00000409792.3:c.3443C>G	p.Ser1148Cys	p.S1148C	ENST00000409792	NM_014159.6	1148	tCc/tGc	3/21	0.599067200593586	3	FACETS	0.774	0.699	0.853	0.387	0.349	0.427	SUBCLONAL	1	TRUE	1	0.599067200593586	3		640	656	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0021126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	536	857	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.879292955638849	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.879292955638849	1		857	683	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937001	48937001	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	372	666	2	ENST00000267163.4:c.769C>T	p.Gln257Ter	p.Q257*	ENST00000267163	NM_000321.2	257	Cag/Tag	8/27	0.879292955638849	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.879292955638849	1		668	450	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713738	30713738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893813	NA	P-0021126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	305	593	1	ENST00000295754.5:c.1063G>A	p.Ala355Thr	p.A355T	ENST00000295754	NM_003242.5	355	Gcc/Acc	4/7	1	2	FACETS	0.984	0.934	1	0.984	0.934	1	CLONAL	1	TRUE	1	0.879292955638849	2		594	705	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420311	88420311	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	352	561	2	ENST00000360948.2:c.2375C>T	p.Pro792Leu	p.P792L	ENST00000360948	NM_001012338.2	792	cCc/cTc	19/19	1	2	FACETS	0.961	0.915	1	0.961	0.915	1	CLONAL	1	TRUE	1	0.879292955638849	2		563	833	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118350896	118350896	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0021126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	386	710	0	ENST00000534358.1:c.3577A>T	p.Lys1193Ter	p.K1193*	ENST00000534358	NM_005933.3	1193	Aaa/Taa	6/36	1	2	FACETS	0.935	0.892	0.979	0.935	0.892	0.979	CLONAL	1	TRUE	1	0.879292955638849	2		710	939	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135314	2135316	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs137854146	NA	P-0021126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	94	889	0	ENST00000219476.3:c.4655_4657del	p.Glu1552del	p.E1552del	ENST00000219476	NM_000548.3	1551	ggAGAa/gga	36/42	0.879292955638849	1	FACETS	0.167	0.148	0.187	0.167	0.148	0.187	SUBCLONAL	1	TRUE	0	0.879292955638849	1		889	716	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368212	+	missense_variant	Missense_Mutation	DNP	GA	GA	AG	novel	NA	P-0021126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	315	559	0	ENST00000262160.6:c.1390_1391delinsCT	p.Ser464Leu	p.S464L	ENST00000262160	NM_005901.5	464	TCa/CTa	11/11	1	2	FACETS	0.928	0.88	0.976	0.928	0.88	0.976	CLONAL	1	TRUE	1	0.879292955638849	2		559	772	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794506	242794506	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0021126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	542	963	0	ENST00000334409.5:c.437-1G>A		p.X146_splice	ENST00000334409	NM_005018.2	146			1	2	FACETS	0.961	0.924	0.998	0.961	0.924	0.998	CLONAL	1	TRUE	1	0.879292955638849	2		963	1283	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	129	328	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.252796230534101	2	FACETS	0.882	0.806	0.961	0.882	0.806	0.961	CLONAL	2	TRUE	0	0.324952327929921	2		328	450	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	128	157	1	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.324952327929921	1	FACETS	0.88	0.798	0.966	0.88	0.798	0.966	CLONAL	1	TRUE	0	0.324952327929921	1		158	750	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0021148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	78	384	0	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	0.252796230534101	2	FACETS	1	0.953	1	0.58	0.512	0.652	CLONAL	1	TRUE	0	0.324952327929921	2		384	414	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870985	12870986	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1555085549	NA	P-0021148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	59	345	0	ENST00000228872.4:c.215dup	p.Lys73GlnfsTer52	p.K73Qfs*52	ENST00000228872	NM_004064.3	71	gag/gaGg	1/3	1	2	FACETS	0.829	0.715	0.952	0.829	0.715	0.952	CLONAL	1	TRUE	1	0.324952327929921	2		345	438	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834161	156834169	+	inframe_deletion	In_Frame_Del	DEL	GCAGCATCT	GCAGCATCT	-	novel	NA	P-0021148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1246	67	727	0	ENST00000524377.1:c.238_246del	p.Gln80_Leu82del	p.Q80_L82del	ENST00000524377	NM_002529.3	76	caGCAGCATCTg/cag	2/17	0.251716302792239	4	FACETS	0.416	0.36	0.478	0.139	0.12	0.16	SUBCLONAL	1	TRUE	1	0.324952327929921	4		727	1313	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515129	103515129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	24	271	0	ENST00000355739.4:c.1630G>A	p.Glu544Lys	p.E544K	ENST00000355739	NM_000123.3	544	Gag/Aag	8/15	1	2	FACETS	0.36	0.282	0.451	0.36	0.282	0.451	SUBCLONAL	1	TRUE	1	0.324952327929921	2		271	410	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0021153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	238	372	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.944	0.884	1	0.944	0.884	1	CLONAL	1	TRUE	1	0.651523229987712	2		373	774	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0021153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	313	848	1	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.651523229987712	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.651523229987712	1		849	608	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0021153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	167	712	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	NA	2	FACETS	0.86	0.794	0.928			1	INDETERMINATE	1	TRUE	NA	0.651523229987712	2		712	596	SUCCESS
APC	324	MSKCC	GRCh37	5	112175419	112175419	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0021153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	182	337	0	ENST00000257430.4:c.4128T>G	p.Tyr1376Ter	p.Y1376*	ENST00000257430	NM_000038.5	1376	taT/taG	16/16	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.651523229987712	2		337	412	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39321401	39321401	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	193	678	2	ENST00000373001.3:c.620G>A	p.Gly207Glu	p.G207E	ENST00000373001	NM_022157.3	207	gGg/gAg	3/7	1	2	FACETS	0.911	0.847	0.978	0.911	0.847	0.978	CLONAL	1	TRUE	1	0.651523229987712	2		680	650	SUCCESS
ATR	545	MSKCC	GRCh37	3	142185227	142185227	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	208	772	0	ENST00000350721.4:c.6836A>C	p.Asn2279Thr	p.N2279T	ENST00000350721	NM_001184.3	2279	aAc/aCc	40/47	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.651523229987712	2		772	635	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980613	1980613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764374372	NA	P-0021153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	184	585	0	ENST00000382891.5:c.4075C>T	p.Arg1359Trp	p.R1359W	ENST00000382891	NM_133335.3	1359	Cgg/Tgg	22/22	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.651523229987712	2		585	459	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356358	66356358	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	164	636	0	ENST00000273854.3:c.1139C>T	p.Pro380Leu	p.P380L	ENST00000273854	NM_004439.5	380	cCt/cTt	5/18	1	2	FACETS	0.925	0.855	0.998	0.925	0.855	0.998	CLONAL	1	TRUE	1	0.651523229987712	2		636	544	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575562	67575562	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0021153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	133	362	0	ENST00000274335.5:c.634+1G>A		p.X212_splice	ENST00000274335		212			1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.651523229987712	2		362	399	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273515	38273515	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	42	952	1	ENST00000425967.3:c.1820G>T	p.Arg607Leu	p.R607L	ENST00000425967	NM_001174067.1	607	cGg/cTg	14/19	0.651523229987712	1	FACETS	0.196	0.164	0.232	0.196	0.164	0.232	SUBCLONAL	1	TRUE	0	0.651523229987712	1		953	443	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001256	150001256	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000023-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	91	584	0	ENST00000253339.5:c.2348A>T	p.Asp783Val	p.D783V	ENST00000253339		783	gAc/gTc	4/7	0.319935387586574	1	FACETS	0.9	0.801	1	0.9	0.801	1	CLONAL	1	TRUE	0	0.319935387586574	1		584	531	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023076	150023076	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs187759014	NA	P-0000023-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	38	659	0	ENST00000253339.5:c.187C>T	p.Arg63Ter	p.R63*	ENST00000253339		63	Cga/Tga	1/7	0.319935387586574	1	FACETS	0.363	0.3	0.435	0.363	0.3	0.435	SUBCLONAL	1	TRUE	0	0.319935387586574	1		659	549	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514647	44514647	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000023-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	60	386	0	ENST00000291552.4:c.509A>G	p.Asn170Ser	p.N170S	ENST00000291552	NM_006758.2	170	aAc/aGc	7/8	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.319935387586574	2		386	351	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439259	52439259	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000023-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	60	381	0	ENST00000460680.1:c.983del	p.Pro328LeufsTer7	p.P328Lfs*7	ENST00000460680	NM_004656.3	328	cCt/ct	11/17	0.319935387586574	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.319935387586574	1		381	239	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555731	21555732	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000023-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	119	581	0	ENST00000382592.4:c.2538dup	p.Asn847Ter	p.N847*	ENST00000382592	NM_014572.2	846	-/T	6/8	0.319935387586574	1	FACETS	0.89	0.813	0.97	1	0.989	1	CLONAL	2	TRUE	0	0.319935387586574	1		581	351	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0000160-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	217	409	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.577006535458053	2		409	700	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561122	9561122	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000160-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	166	337	0	ENST00000353224.5:c.660G>T	p.Gln220His	p.Q220H	ENST00000353224	NM_177990.2	220	caG/caT	4/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.577006535458053	2		337	542	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0000163-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	72	539	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.517248582000279	1	FACETS	0.856	0.759	0.959	0.856	0.759	0.959	CLONAL	1	TRUE	0	0.517248582000279	1		539	241	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0000163-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	132	371	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.517248582000279	3	FACETS	1	0.972	1	0.579	0.528	0.632	CLONAL	1	TRUE	1	0.517248582000279	3		371	555	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123760	11123760	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000163-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	113	236	0	ENST00000358026.2:c.2410G>A	p.Gly804Arg	p.G804R	ENST00000358026	NM_001128849.1	804	Ggg/Agg	16/36	0.218755086409105	2	FACETS	1	0.981	1	0.658	0.599	0.719	INDETERMINATE	1	TRUE	0	0.517248582000279	2		236	332	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0000193-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	258	384	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.987	1	1	0.996	1	CLONAL	2	TRUE	1	0.639103825065469	2		384	375	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106078	27106078	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000193-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	174	359	0	ENST00000324856.7:c.5693del	p.Pro1898HisfsTer25	p.P1898Hfs*25	ENST00000324856	NM_006015.4	1897	Ccc/cc	20/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.639103825065469	2		359	480	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913396	NA	P-0000193-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	356	400	0	ENST00000349496.5:c.95A>T	p.Asp32Val	p.D32V	ENST00000349496	NM_001904.3	32	gAc/gTc	3/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.639103825065469	2		400	1021	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647668	2647668	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000193-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	280	546	0	ENST00000342085.4:c.1571A>G	p.Tyr524Cys	p.Y524C	ENST00000342085	NM_002613.4	524	tAt/tGt	14/14	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.639103825065469	2		546	767	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058052	27058064	+	frameshift_variant	Frame_Shift_Del	DEL	CCCAGCAAACTGC	CCCAGCAAACTGC	-	novel	NA	P-0000193-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	40	145	0	ENST00000324856.7:c.1761_1773del	p.Gln588IlefsTer27	p.Q588Ifs*27	ENST00000324856	NM_006015.4	587	tCCCAGCAAACTGCc/tc	3/20	1	2	FACETS	0.517	0.433	0.61	0.517	0.433	0.61	SUBCLONAL	1	TRUE	1	0.639103825065469	2		145	242	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654669	67654670	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0000193-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	419	536	0	ENST00000264010.4:c.1157dup	p.Tyr386Ter	p.Y386*	ENST00000264010	NM_006565.3	386	tat/tAat	6/12	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.639103825065469	2		536	1138	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846087	68846102	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGGTTAAGCACAAC	AGGGGTTAAGCACAAC	-	novel	NA	P-0000193-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	239	479	0	ENST00000261769.5:c.1060_1075del	p.Gly354GlnfsTer4	p.G354Qfs*4	ENST00000261769	NM_004360.3	353	gAGGGGTTAAGCACAACa/ga	8/16	1	2	FACETS	0.807	0.754	0.861	0.807	0.754	0.861	CLONAL	1	TRUE	1	0.639103825065469	2		479	927	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567723	226567723	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs201371549	NA	P-0000228-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2317	132	699	1	ENST00000366794.5:c.1443G>T	p.Trp481Cys	p.W481C	ENST00000366794	NM_001618.3	481	tgG/tgT	10/23	0.411344586460902	8	FACETS	0.585	0.528	0.646	0.098	0.088	0.108	SUBCLONAL	1	TRUE	2	0.411344586460902	8		700	2449	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664911	138664911	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000228-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	41	156	0	ENST00000330315.3:c.654C>G	p.Cys218Trp	p.C218W	ENST00000330315	NM_023067.3	218	tgC/tgG	1/1	0.407316434840899	3	FACETS	0.846	0.709	0.997	0.423	0.354	0.499	CLONAL	1	TRUE	1	0.411344586460902	3		156	284	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31020771	31020771	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000228-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	129	308	0	ENST00000375687.4:c.1068A>T	p.Glu356Asp	p.E356D	ENST00000375687	NM_015338.5	356	gaA/gaT	11/13	0.331533601317194	3	FACETS	1	0.91	1	0.501	0.455	0.55	CLONAL	1	TRUE	1	0.411344586460902	3		308	754	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	465700	465701	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0000228-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1157	115	530	0	ENST00000399788.2:c.675dup	p.Glu226ArgfsTer7	p.E226Rfs*7	ENST00000399788	NM_001042603.1	225	-/A	6/28	0.310065710434215	2	FACETS	0.44	0.394	0.488	0.22	0.197	0.244	SUBCLONAL	1	TRUE	0	0.411344586460902	2		530	1272	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0000274-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	105	357	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.272912078007983	3	FACETS	1	0.937	1	1	0.937	1	CLONAL	3	TRUE	0	0.343630567087876	3		357	232	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024721	14024721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1340754747	NA	P-0000274-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	16	312	0	ENST00000311895.7:c.947C>T	p.Thr316Met	p.T316M	ENST00000311895	NM_005236.2	316	aCg/aTg	5/11	0.209744169298232	1	FACETS	0.349	0.258	0.457	0.349	0.258	0.457	SUBCLONAL	1	TRUE	0	0.343630567087876	1		312	221	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419870	152419871	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000274-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	23	138	0	ENST00000206249.3:c.1560dup	p.Gly521ArgfsTer18	p.G521Rfs*18	ENST00000206249	NM_000125.3	519	-/A	8/8	1	2	FACETS	1	0.812	1	1	0.812	1	CLONAL	1	TRUE	1	0.343630567087876	2		138	130	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578284	7578288	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CCAGA	CCAGA	-	novel	NA	P-0000274-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	15	381	0	ENST00000269305.4:c.561_565del	p.Leu188ProfsTer19	p.L188Pfs*19	ENST00000269305	NM_001126112.2	187	ggTCTGGcc/ggcc	6/11	0.343630567087876	1	FACETS	0.951	0.71	1	0.951	0.71	1	CLONAL	1	TRUE	0	0.343630567087876	1		381	76	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098944	178098944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000319-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	157	491	1	ENST00000397062.3:c.101G>A	p.Arg34Gln	p.R34Q	ENST00000397062	NM_006164.4	34	cGa/cAa	2/5	0.37525961241521	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	FALSE	2	0.37525961241521	4		492	544	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412375	139412375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1341448592	NA	P-0000319-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	27	238	0	ENST00000277541.6:c.1270G>A	p.Glu424Lys	p.E424K	ENST00000277541	NM_017617.3	424	Gag/Aag	8/34	NA	2	FACETS	0.842	0.704	0.98			1	INDETERMINATE	3	FALSE	NA	0.37525961241521	2		238	57	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913294	NA	P-0000319-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	90	402	0	ENST00000371953.3:c.518G>C	p.Arg173Pro	p.R173P	ENST00000371953	NM_000314.4	173	cGc/cCc	6/9	0.37525961241521	2	FACETS	0.799	0.718	0.885	0.799	0.718	0.885	SUBCLONAL	2	FALSE	0	0.37525961241521	2		402	300	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431639	49431639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377384903	NA	P-0000319-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	13	430	0	ENST00000301067.7:c.9500G>A	p.Arg3167Gln	p.R3167Q	ENST00000301067	NM_003482.3	3167	cGg/cAg	34/54	0.22720701768467	5	FACETS	1	0.839	1	0.42	0.304	0.557	CLONAL	1	FALSE	2	0.37525961241521	5		430	86	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416663	121416663	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137853247	NA	P-0000319-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	14	491	0	ENST00000257555.6:c.92G>A	p.Gly31Asp	p.G31D	ENST00000257555		31	gGt/gAt	1/10	0.252345706856163	1	FACETS	0.994	0.738	1	0.994	0.738	1	CLONAL	1	FALSE	0	0.37525961241521	1		491	61	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29686017	29686017	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000319-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	51	338	0	ENST00000356175.3:c.8081C>A	p.Ala2694Glu	p.A2694E	ENST00000356175	NM_000267.3	2694	gCa/gAa	55/57	0.345551611731684	5	FACETS	0.77	0.659	0.889	0.513	0.439	0.593	SUBCLONAL	2	FALSE	2	0.37525961241521	5		338	276	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540225	187540226	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0000319-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	47	606	0	ENST00000441802.2:c.7514dup	p.Pro2506SerfsTer29	p.P2506Sfs*29	ENST00000441802	NM_005245.3	2505	gct/gcCt	10/27	NA	2	FACETS	1	0.947	1			1	INDETERMINATE	1	FALSE	NA	0.37525961241521	2		606	200	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630745	187630757	+	frameshift_variant	Frame_Shift_Del	DEL	ACTGTCTCCGGAA	ACTGTCTCCGGAA	-	novel	NA	P-0000319-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	25	694	0	ENST00000441802.2:c.225_237del	p.Ser76LysfsTer17	p.S76Kfs*17	ENST00000441802	NM_005245.3	75	gtTTCCGGAGACAGT/gt	2/27	NA	2	FACETS	0.495	0.391	0.614			1	INDETERMINATE	1	FALSE	NA	0.37525961241521	2		694	269	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0000356-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	233	357	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	0.496361060015955	2		357	849	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0000356-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	263	707	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.496361060015955	2		707	922	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47684731	47684731	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000356-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	195	370	0	ENST00000347630.2:c.718C>T	p.Arg240Ter	p.R240*	ENST00000347630	NM_001007230.1	240	Cga/Tga	9/11	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.496361060015955	2		370	647	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016579	12016580	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0000356-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	259	434	0	ENST00000353533.5:c.716dup	p.Ser240LysfsTer5	p.S240Kfs*5	ENST00000353533	NM_003010.3	239	aga/aGga	7/11	0.496361060015955	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.496361060015955	1		434	724	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0000624-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	8	357	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.277813981964459	5	FACETS	0.361	0.232	0.529	0.181	0.116	0.265	SUBCLONAL	1	TRUE	3	0.277813981964459	5		357	226	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0000624-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	173	305	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	0.277813981964459	7	FACETS	1	0.976	1	1	0.976	1	CLONAL	4	TRUE	3	0.277813981964459	7		305	473	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0000624-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	73	267	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.277813981964459	5	FACETS	0.964	0.861	1	1	0.971	1	CLONAL	4	TRUE	2	0.277813981964459	5		267	193	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405171	139405171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs578228721	NA	P-0000624-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	21	498	0	ENST00000277541.6:c.2674C>T	p.Arg892Cys	p.R892C	ENST00000277541	NM_017617.3	892	Cgc/Tgc	17/34	0.176684157467561	0	FACETS	1	0.892	1			1	CLONAL	1	TRUE	0	0.277813981964459	0		498	88	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544703	65544703	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs387906650	NA	P-0000624-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	63	559	1	ENST00000358664.4:c.223C>T	p.Arg75Ter	p.R75*	ENST00000358664	NM_002382.4	75	Cga/Tga	4/5	0.277813981964459	2	FACETS	1	0.956	1	1	0.981	1	CLONAL	3	TRUE	0	0.277813981964459	2		560	132	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0000625-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	142	474	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.75	0.687	0.816	1	0.988	1	SUBCLONAL	2	TRUE	1	0.340527077259131	2		474	556	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0000625-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	59	302	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.340527077259131	2		302	275	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843613	156843613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561243137	NA	P-0000625-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	218	805	0	ENST00000524377.1:c.1039C>T	p.Arg347Cys	p.R347C	ENST00000524377	NM_002529.3	347	Cgc/Tgc	8/17	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.340527077259131	2		805	930	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143444	30143444	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500231	NA	P-0000625-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	14	84	0	ENST00000389048.3:c.82C>T	p.Arg28Cys	p.R28C	ENST00000389048	NM_004304.4	28	Cgc/Tgc	1/29	0.232477566950655	1	FACETS	0.487	0.354	0.646	0.487	0.354	0.646	SUBCLONAL	1	TRUE	0	0.340527077259131	1		84	140	SUCCESS
APC	324	MSKCC	GRCh37	5	112137048	112137048	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1326410920	NA	P-0000625-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	59	260	0	ENST00000257430.4:c.802G>T	p.Glu268Ter	p.E268*	ENST00000257430	NM_000038.5	268	Gaa/Taa	8/16	1	2	FACETS	0.847	0.731	0.973	0.847	0.731	0.973	CLONAL	1	TRUE	1	0.340527077259131	2		260	409	SUCCESS
APC	324	MSKCC	GRCh37	5	112170813	112170813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554083227	NA	P-0000625-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	130	703	0	ENST00000257430.4:c.1909G>A	p.Gly637Arg	p.G637R	ENST00000257430	NM_000038.5	637	Ggg/Agg	15/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.340527077259131	2		703	553	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518992	103518992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000625-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	173	259	1	ENST00000355739.4:c.2330G>A	p.Arg777His	p.R777H	ENST00000355739	NM_000123.3	777	cGc/cAc	11/15	0.33435134614697	3	FACETS	0.834	0.775	0.895	1	0.986	1	CLONAL	3	TRUE	1	0.340527077259131	3		260	475	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0000625-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	88	148	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.340527077259131	2		148	358	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44896903	44896903	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000625-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	48	1230	0	ENST00000377967.4:c.623A>T	p.Gln208Leu	p.Q208L	ENST00000377967	NM_021140.2	208	cAa/cTa	8/29	0.340527077259131	1	FACETS	0.311	0.262	0.365	0.311	0.262	0.365	SUBCLONAL	1	TRUE	0	0.340527077259131	1		1230	752	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0000658-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	193	96	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.587572807814123	3	FACETS	1	0.982	1	1	0.994	1	CLONAL	3	TRUE	1	0.587572807814123	3		96	267	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875096	151875097	+	splice_acceptor_variant	Splice_Site	INS	-	-	T	rs753425356	NA	P-0000658-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	63	107	2	ENST00000262189.6:c.7443-2dup		p.X2481_splice	ENST00000262189	NM_170606.2	2481			0.587572807814123	3	FACETS	1	0.975	1	0.746	0.657	0.838	CLONAL	1	TRUE	1	0.587572807814123	3		109	186	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578214	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs864309495	NA	P-0000658-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	337	537	0	ENST00000269305.4:c.635_636del	p.Phe212SerfsTer3	p.F212Sfs*3	ENST00000269305	NM_001126112.2	212	tTT/t	6/11	0.544494952500339	3	FACETS	0.891	0.855	0.927	0.891	0.855	0.927	CLONAL	3	TRUE	0	0.587572807814123	3		537	555	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049715	16049716	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0000658-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	939	715	0	ENST00000268712.3:c.1056_1057del	p.Glu354ThrfsTer21	p.E354Tfs*21	ENST00000268712	NM_006311.3	352	caAAga/caga	10/46	0.544494952500339	3	FACETS	0.967	0.944	0.989	0.967	0.944	0.989	CLONAL	3	TRUE	0	0.587572807814123	3		715	1426	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560181	29560181	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000726-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	38	181	0	ENST00000356175.3:c.3658G>T	p.Glu1220Ter	p.E1220*	ENST00000356175	NM_000267.3	1220	Gaa/Taa	27/57	1	2	FACETS	0.819	0.68	0.972	0.819	0.68	0.972	CLONAL	1	TRUE	1	0.329041600716048	2		181	282	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531827	46531827	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000726-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	74	469	0	ENST00000262741.5:c.520A>T	p.Ile174Phe	p.I174F	ENST00000262741	NM_003629.3	174	Att/Ttt	5/10	1	2	FACETS	0.989	0.868	1	0.989	0.868	1	CLONAL	1	TRUE	1	0.329041600716048	2		469	455	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206667324	206667324	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000726-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	60	303	0	ENST00000367120.3:c.2117G>T	p.Arg706Leu	p.R706L	ENST00000367120	NM_014002.3	706	cGg/cTg	21/22	0.329041600716048	3	FACETS	0.957	0.826	1	0.478	0.413	0.549	CLONAL	1	TRUE	1	0.329041600716048	3		303	444	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007332	143007332	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1553966592	NA	P-0000726-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	84	441	0	ENST00000262992.4:c.2452A>T	p.Arg818Ter	p.R818*	ENST00000262992	NM_001101669.1	818	Aga/Tga	22/24	1	2	FACETS	0.973	0.861	1	0.973	0.861	1	CLONAL	1	TRUE	1	0.329041600716048	2		441	525	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915589	131915589	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000726-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	40	163	0	ENST00000265335.6:c.587G>T	p.Arg196Leu	p.R196L	ENST00000265335		196	cGt/cTt	5/25	0.307429051304377	1	FACETS	0.932	0.782	1	0.932	0.782	1	CLONAL	1	TRUE	0	0.329041600716048	1		163	218	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710626	117710626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000726-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	66	218	0	ENST00000368508.3:c.1646G>A	p.Gly549Asp	p.G549D	ENST00000368508	NM_002944.2	549	gGc/gAc	12/43	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.329041600716048	2		218	360	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515161	106515161	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000726-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	66	306	0	ENST00000359195.3:c.2304A>T	p.Lys768Asn	p.K768N	ENST00000359195	NM_002649.2	768	aaA/aaT	5/11	0.329041600716048	3	FACETS	0.822	0.714	0.939	0.274	0.238	0.313	CLONAL	1	TRUE	0	0.329041600716048	3		306	568	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846052	128846052	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000726-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	83	510	0	ENST00000249373.3:c.982G>T	p.Gly328Cys	p.G328C	ENST00000249373	NM_005631.4	328	Ggt/Tgt	5/12	0.329041600716048	3	FACETS	0.986	0.871	1	0.329	0.29	0.37	CLONAL	1	TRUE	0	0.329041600716048	3		510	596	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38283714	38283714	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000726-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	58	285	0	ENST00000425967.3:c.764A>G	p.Asp255Gly	p.D255G	ENST00000425967	NM_001174067.1	255	gAc/gGc	7/19	1	2	FACETS	0.899	0.776	1	0.899	0.776	1	CLONAL	1	TRUE	1	0.329041600716048	2		285	392	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465473	8465473	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000726-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	54	319	0	ENST00000356435.5:c.3707C>A	p.Ala1236Glu	p.A1236E	ENST00000356435		1236	gCa/gAa	21/35	0.329041600716048	1	FACETS	0.779	0.668	0.899	0.779	0.668	0.899	SUBCLONAL	1	TRUE	0	0.329041600716048	1		319	352	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518406	8518406	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000726-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	27	101	0	ENST00000356435.5:c.985C>G	p.Pro329Ala	p.P329A	ENST00000356435		329	Cct/Gct	10/35	0.329041600716048	1	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	0	0.329041600716048	1		101	124	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115760	8115760	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000726-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	93	535	0	ENST00000346208.3:c.1106C>A	p.Ser369Tyr	p.S369Y	ENST00000346208		369	tCt/tAt	6/6	0.329041600716048	3	FACETS	0.892	0.793	0.998	0.446	0.396	0.499	CLONAL	1	TRUE	1	0.329041600716048	3		535	738	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604479	43604479	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000726-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	60	287	0	ENST00000355710.3:c.1064G>T	p.Arg355Met	p.R355M	ENST00000355710	NM_020975.4	355	aGg/aTg	6/20	0.329041600716048	3	FACETS	1	0.909	1	0.534	0.461	0.612	CLONAL	1	TRUE	1	0.329041600716048	3		287	398	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534285	534285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894226	NA	P-0000726-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	163	310	0	ENST00000451590.1:c.38G>T	p.Gly13Val	p.G13V	ENST00000451590	NM_001130442.1	13	gGt/gTt	2/5	1	2	FACETS	1	0.936	1	1	0.993	1	CLONAL	2	TRUE	1	0.329041600716048	2		310	489	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742507	17742507	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000726-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	88	516	0	ENST00000250003.3:c.689A>T	p.Tyr230Phe	p.Y230F	ENST00000250003	NM_002478.4	230	tAc/tTc	2/3	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.329041600716048	2		516	488	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343274	118343274	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000726-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	38	256	0	ENST00000534358.1:c.1400A>T	p.Gln467Leu	p.Q467L	ENST00000534358	NM_005933.3	467	cAg/cTg	3/36	1	2	FACETS	0.724	0.601	0.861	0.724	0.601	0.861	SUBCLONAL	1	TRUE	1	0.329041600716048	2		256	319	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623608	28623608	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000726-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	58	188	0	ENST00000241453.7:c.949G>T	p.Val317Leu	p.V317L	ENST00000241453	NM_004119.2	317	Gta/Tta	8/24	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.329041600716048	2		188	331	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436404	110436404	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000726-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	41	210	1	ENST00000375856.3:c.1997G>T	p.Gly666Val	p.G666V	ENST00000375856	NM_003749.2	666	gGg/gTg	1/2	0.258307236487599	4	FACETS	1	0.869	1	0.522	0.437	0.617	CLONAL	1	TRUE	2	0.329041600716048	4		211	317	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81558951	81558951	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000726-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	50	276	0	ENST00000298171.2:c.544C>A	p.Leu182Met	p.L182M	ENST00000298171	NM_000369.2	182	Ctg/Atg	6/10	1	2	FACETS	0.804	0.684	0.935	0.804	0.684	0.935	CLONAL	1	TRUE	1	0.329041600716048	2		276	378	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467225	99467225	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000726-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	64	322	0	ENST00000268035.6:c.2606A>C	p.Tyr869Ser	p.Y869S	ENST00000268035	NM_000875.3	869	tAc/tCc	12/21	0.329041600716048	1	FACETS	0.997	0.869	1	0.997	0.869	1	CLONAL	1	TRUE	0	0.329041600716048	1		322	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934578	NA	P-0000726-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	67	164	1	ENST00000269305.4:c.524G>T	p.Arg175Leu	p.R175L	ENST00000269305	NM_001126112.2	175	cGc/cTc	5/11	0.329041600716048	1	FACETS	0.766	0.676	0.861	1	0.976	1	SUBCLONAL	2	TRUE	0	0.329041600716048	1		165	222	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559870	29559870	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000726-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	46	205	0	ENST00000356175.3:c.3467A>T	p.Asn1156Ile	p.N1156I	ENST00000356175	NM_000267.3	1156	aAc/aTc	26/57	1	2	FACETS	0.981	0.831	1	0.981	0.831	1	CLONAL	1	TRUE	1	0.329041600716048	2		205	285	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730934	40730934	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000726-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	25	106	0	ENST00000373198.4:c.3601C>A	p.Leu1201Ile	p.L1201I	ENST00000373198	NM_133170.3	1201	Ctc/Atc	27/32	1	2	FACETS	1	0.831	1	1	0.831	1	CLONAL	1	TRUE	1	0.329041600716048	2		106	145	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969982	161969982	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000726-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	80	528	0	ENST00000366898.1:c.987del	p.Val330CysfsTer105	p.V330Cfs*105	ENST00000366898	NM_004562.2	329	ggC/gg	9/12	1	2	FACETS	0.969	0.855	1	0.969	0.855	1	CLONAL	1	TRUE	1	0.329041600716048	2		528	502	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560477	65560477	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000726-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	79	295	0	ENST00000358664.4:c.120del	p.Asp41ThrfsTer24	p.D41Tfs*24	ENST00000358664	NM_002382.4	40	aaA/aa	3/5	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.329041600716048	2		295	467	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0000726-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	89	331	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	0.329041600716048	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.329041600716048	1		331	424	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547992	41547993	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000726-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	45	165	0	ENST00000263253.7:c.2974dup	p.Thr992AsnfsTer10	p.T992Nfs*10	ENST00000263253	NM_001429.3	991	-/A	15/31	0.329041600716048	1	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	0	0.329041600716048	1		165	223	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143268	24143269	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	TT	novel	NA	P-0000726-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	83	460	1	ENST00000263121.7:c.500_500+1delinsTT		p.X167_splice	ENST00000263121	NM_003073.3	167		4/9	0.329041600716048	1	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	0	0.329041600716048	1		461	415	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476318	88476319	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0000726-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	43	281	0	ENST00000360948.2:c.1813_1814delinsTT	p.Gly605Leu	p.G605L	ENST00000360948	NM_001012338.2	605	GGa/TTa	15/19	0.329041600716048	1	FACETS	0.633	0.531	0.745	0.633	0.531	0.745	SUBCLONAL	1	TRUE	0	0.329041600716048	1		281	345	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0000739-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	540	379	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.652807723851864	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.665499977628381	3		379	703	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543850	212543850	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000739-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	52	184	0	ENST00000342788.4:c.1549C>G	p.Pro517Ala	p.P517A	ENST00000342788	NM_005235.2	517	Cca/Gca	13/28	0.665499977628381	2	FACETS	0.34	0.289	0.395	0.17	0.144	0.198	SUBCLONAL	1	TRUE	0	0.665499977628381	2		184	460	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275738	41275738	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000739-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	116	221	0	ENST00000349496.5:c.1633C>A	p.Gln545Lys	p.Q545K	ENST00000349496	NM_001904.3	545	Cag/Aag	10/15	0.229383731222159	2	FACETS	0.703	0.637	0.772	0.351	0.318	0.386	INDETERMINATE	1	TRUE	0	0.665499977628381	2		221	496	SUCCESS
APC	324	MSKCC	GRCh37	5	112157650	112157650	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1060503333	NA	P-0000739-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	146	241	0	ENST00000257430.4:c.1370C>G	p.Ser457Ter	p.S457*	ENST00000257430	NM_000038.5	457	tCa/tGa	11/16	0.229383731222159	2	FACETS	1	0.983	1	0.611	0.565	0.658	INDETERMINATE	1	TRUE	0	0.665499977628381	2		241	359	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480426	50480426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000739-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	81	172	0	ENST00000394963.4:c.388G>A	p.Asp130Asn	p.D130N	ENST00000394963	NM_003076.4	130	Gac/Aac	3/13	0.652807723851864	3	FACETS	0.612	0.54	0.689	0.204	0.18	0.23	SUBCLONAL	1	TRUE	0	0.665499977628381	3		172	530	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094984	11094984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000739-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	31	435	0	ENST00000358026.2:c.157G>A	p.Gly53Arg	p.G53R	ENST00000358026	NM_001128849.1	53	Gga/Aga	2/36	0.665499977628381	1	FACETS	0.165	0.133	0.201	0.165	0.133	0.201	SUBCLONAL	1	TRUE	0	0.665499977628381	1		435	376	SUCCESS
APC	324	MSKCC	GRCh37	5	112175191	112175192	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554085382	NA	P-0000739-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	23	117	0	ENST00000257430.4:c.3901dup	p.Thr1301AsnfsTer14	p.T1301Nfs*14	ENST00000257430	NM_000038.5	1300	-/A	16/16	0.229383731222159	2	FACETS	0.549	0.434	0.678	0.274	0.217	0.339	INDETERMINATE	1	TRUE	0	0.665499977628381	2		117	126	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0000755-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	105	170	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	0.3	1	FACETS	1	0.968	1	1	0.991	1	CLONAL	3	TRUE	0	0.25	1		171	219	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965666	90965666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000755-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	235	421	0	ENST00000265433.3:c.1651del	p.Arg551GlyfsTer8	p.R551Gfs*8	ENST00000265433	NM_002485.4	551	Agg/gg	11/16	0.161082481661254	4	FACETS	1	0.94	1	1	0.993	1	CLONAL	3	TRUE	2	0.25	4		421	780	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000755-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	349	431	2	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	0.133732702749185	4	FACETS	1	0.988	1	1	0.997	1	INDETERMINATE	5	TRUE	2	0.25	4		433	639	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0000755-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	193	247	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	1	2	FACETS	0.859	0.8	0.92	1	0.994	1	CLONAL	3	TRUE	1	0.25	2		247	599	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780197	9780197	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751570218	NA	P-0000755-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	135	304	1	ENST00000377346.4:c.1367C>T	p.Thr456Met	p.T456M	ENST00000377346	NM_005026.3	456	aCg/aTg	11/24	1	2	FACETS	1	0.954	1	1	0.991	1	CLONAL	2	TRUE	1	0.25	2		305	507	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199610	16199610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1405372960	NA	P-0000755-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	65	131	0	ENST00000375759.3:c.383G>A	p.Arg128His	p.R128H	ENST00000375759	NM_015001.2	128	cGt/cAt	2/15	1	2	FACETS	1	0.907	1	1	0.982	1	CLONAL	2	TRUE	1	0.25	2		131	250	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702265	47702265	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750508	NA	P-0000755-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	173	328	0	ENST00000233146.2:c.1861C>T	p.Arg621Ter	p.R621*	ENST00000233146	NM_000251.2	621	Cga/Tga	12/16	0.3	0	FACETS	0.948	0.886	1			1	CLONAL	3	TRUE	0	0.25	0		328	365	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285314	212285314	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000755-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	181	275	0	ENST00000342788.4:c.2987C>A	p.Pro996His	p.P996H	ENST00000342788	NM_005235.2	996	cCc/cAc	25/28	1	2	FACETS	1	0.981	1	1	0.994	1	CLONAL	2	TRUE	1	0.25	2		275	617	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646033	215646033	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202110	NA	P-0000755-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	202	297	0	ENST00000260947.4:c.565G>A	p.Ala189Thr	p.A189T	ENST00000260947	NM_000465.2	189	Gca/Aca	4/11	1	2	FACETS	0.842	0.784	0.901	1	0.995	1	CLONAL	3	TRUE	1	0.25	2		297	640	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098586	47098586	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000755-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	161	241	0	ENST00000409792.3:c.6688G>A	p.Ala2230Thr	p.A2230T	ENST00000409792	NM_014159.6	2230	Gca/Aca	15/21	0.288972721399372	1	FACETS	1	0.978	1	1	0.993	1	CLONAL	2	TRUE	0	0.25	1		241	489	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437440	52437440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761596789	NA	P-0000755-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	94	115	0	ENST00000460680.1:c.1721C>T	p.Ala574Val	p.A574V	ENST00000460680	NM_004656.3	574	gCg/gTg	13/17	0.247008369322185	4	FACETS	1	0.963	1			1	CLONAL	3	TRUE	NA	0.25	4		115	275	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119642254	119642254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757429682	NA	P-0000755-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	203	257	0	ENST00000316626.5:c.443G>A	p.Arg148Gln	p.R148Q	ENST00000316626		148	cGa/cAa	4/12	0.166193622206788	3	FACETS	1	0.971	1			1	CLONAL	3	TRUE	NA	0.25	3		257	568	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664460	138664460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000755-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	89	105	0	ENST00000330315.3:c.1105G>A	p.Ala369Thr	p.A369T	ENST00000330315	NM_023067.3	369	Gcg/Acg	1/1	0.204884071370662	1	FACETS	1	0.973	1	1	0.988	1	CLONAL	2	TRUE	0	0.25	1		105	251	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177626	56177626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530669321	NA	P-0000755-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	185	262	0	ENST00000399503.3:c.2599G>A	p.Glu867Lys	p.E867K	ENST00000399503	NM_005921.1	867	Gaa/Aaa	14/20	1	2	FACETS	1	0.986	1	1	0.994	1	CLONAL	2	TRUE	1	0.25	2		262	592	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2969697	2969697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367917190	NA	P-0000755-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	85	220	0	ENST00000396946.4:c.1582G>A	p.Glu528Lys	p.E528K	ENST00000396946	NM_032415.4	528	Gag/Aag	12/25	0.204884071370662	1	FACETS	0.891	0.794	0.992	1	0.984	1	CLONAL	2	TRUE	0	0.25	1		220	334	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508499	106508499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752602335	NA	P-0000755-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	44	78	0	ENST00000359195.3:c.493G>A	p.Val165Ile	p.V165I	ENST00000359195	NM_002649.2	165	Gtc/Atc	2/11	1	2	FACETS	1	0.909	1	1	0.975	1	CLONAL	2	TRUE	1	0.25	2		78	161	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155142	108155142	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000755-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	173	310	0	ENST00000278616.4:c.3935G>T	p.Arg1312Ile	p.R1312I	ENST00000278616	NM_000051.3	1312	aGa/aTa	26/63	1	2	FACETS	1	0.978	1	1	0.993	1	CLONAL	2	TRUE	1	0.25	2		310	602	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950861	32950861	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80359128	NA	P-0000755-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	209	315	0	ENST00000380152.3:c.8687G>A	p.Arg2896His	p.R2896H	ENST00000380152		2896	cGt/cAt	21/27	0.204884071370662	1	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	0	0.25	1		315	611	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646627	23646627	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs180177100	NA	P-0000755-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	105	235	0	ENST00000261584.4:c.1240C>T	p.Arg414Ter	p.R414*	ENST00000261584	NM_024675.3	414	Cga/Tga	4/13	0.3	0	FACETS	0.849	0.768	0.934			1	CLONAL	2	TRUE	0	0.25	0		235	371	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618997	37618997	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000755-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	23	202	0	ENST00000447079.4:c.673A>G	p.Arg225Gly	p.R225G	ENST00000447079	NM_015083.1	225	Agg/Ggg	1/14	NA	2	FACETS	0.48	0.374	0.604			1	INDETERMINATE	1	TRUE	NA	0.25	2		202	383	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248621	10248621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000755-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	109	261	0	ENST00000340748.4:c.4132C>T	p.Arg1378Trp	p.R1378W	ENST00000340748		1378	Cgg/Tgg	35/40	0.22768732356838	0	FACETS	0.811	0.734	0.892			1	CLONAL	2	TRUE	0	0.25	0		261	403	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485868	57485868	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000755-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	132	229	0	ENST00000371085.3:c.1169A>G	p.Gln390Arg	p.Q390R	ENST00000371085	NM_000516.4	390	cAg/cGg	13/13	1	2	FACETS	1	0.951	1	1	0.991	1	CLONAL	2	TRUE	1	0.25	2		229	498	SUCCESS
AR	367	MSKCC	GRCh37	X	66937372	66937372	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000755-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	272	230	0	ENST00000374690.3:c.2226G>T	p.Trp742Cys	p.W742C	ENST00000374690	NM_000044.3	742	tgG/tgT	5/8	0.204884071370662	0	FACETS	0.798	0.764	0.831			1	SUBCLONAL	5	TRUE	NA	0.25	0		230	409	SUCCESS
AR	367	MSKCC	GRCh37	X	66943552	66943552	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137852578	NA	P-0000755-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	297	188	0	ENST00000374690.3:c.2632A>G	p.Thr878Ala	p.T878A	ENST00000374690	NM_000044.3	878	Act/Gct	8/8	0.204884071370662	0	FACETS	0.773	0.741	0.805			1	SUBCLONAL	5	TRUE	NA	0.25	0		188	461	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339129	65339129	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000755-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	153	271	0	ENST00000342505.4:c.407del	p.Asn136MetfsTer32	p.N136Mfs*32	ENST00000342505	NM_002227.2	136	aAt/at	5/25	0.133732702749185	4	FACETS	0.86	0.79	0.932	1	0.984	1	INDETERMINATE	3	TRUE	2	0.25	4		271	593	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070349	37070349	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs63750855	NA	P-0000755-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	181	319	0	ENST00000231790.2:c.1489del	p.Arg497GlyfsTer11	p.R497Gfs*11	ENST00000231790	NM_000249.3	495	aCc/ac	13/19	1	2	FACETS	1	0.983	1	1	0.994	1	CLONAL	2	TRUE	1	0.25	2		319	606	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs767894241	NA	P-0000755-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	160	315	0	ENST00000358127.4:c.76dup	p.Val26GlyfsTer49	p.V26Gfs*49	ENST00000358127	NM_001280556.1	26	gtt/gGtt	2/10	1	2	FACETS	1	0.949	1	1	0.992	1	CLONAL	2	TRUE	1	0.25	2		315	615	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250508	110250508	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000755-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	71	131	0	ENST00000374672.4:c.167del	p.Pro56GlnfsTer58	p.P56Qfs*58	ENST00000374672	NM_004235.4	56	cCa/ca	3/5	1	2	FACETS	1	0.943	1	1	0.984	1	CLONAL	2	TRUE	1	0.25	2		131	255	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0000755-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	142	299	0	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.959	0.878	1	1	0.991	1	CLONAL	2	TRUE	1	0.25	2		299	592	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294372	1294372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	53	212	0	ENST00000310581.5:c.629C>T	p.Ala210Val	p.A210V	ENST00000310581	NM_198253.2	210	gCc/gTc	2/16	0.843357828584424	4	FACETS	0.298	0.253	0.347			1	SUBCLONAL	1	TRUE	NA	0.850965265926291	4		212	774	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	213	342	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	0.850965265926291	2		342	434	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	41	368	3	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	0.436643526907547	1	FACETS	0.082	0.068	0.098	0.082	0.068	0.098	INDETERMINATE	1	TRUE	0	0.850965265926291	1		371	672	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	553	191	0	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	0.850965265926291	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.850965265926291	2		191	627	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256768	19256769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1202792889	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	35	164	0	ENST00000162023.5:c.944dup	p.Val316SerfsTer6	p.V316Sfs*6	ENST00000162023		315	cca/ccCa	13/13	1	2	FACETS	0.265	0.217	0.317	0.265	0.217	0.317	SUBCLONAL	1	TRUE	1	0.850965265926291	2		164	311	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	337	379	0	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	0.850965265926291	2		379	706	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459239	120459239	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	162	135	0	ENST00000256646.2:c.6106C>T	p.Arg2036Ter	p.R2036*	ENST00000256646	NM_024408.3	2036	Cga/Tga	34/34	0.418093205156845	3	FACETS	0.812	0.758	0.867	0.812	0.758	0.867	INDETERMINATE	2	TRUE	1	0.850965265926291	3		135	334	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054983	176054983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs991566021	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	405	479	1	ENST00000367669.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000367669	NM_022457.5	357	cGa/cAa	10/20	0.418093205156845	3	FACETS	1	0.993	1	0.615	0.586	0.644	INDETERMINATE	1	TRUE	1	0.850965265926291	3		480	1103	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467188	25467188	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1299203502	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	111	264	0	ENST00000264709.3:c.1687G>A	p.Val563Met	p.V563M	ENST00000264709	NM_175629.2	563	Gtg/Atg	15/23	NA	2	FACETS	0.503	0.454	0.554			1	INDETERMINATE	1	TRUE	NA	0.850965265926291	2		264	519	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095601	178095601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	408	381	0	ENST00000397062.3:c.1730C>T	p.Ser577Phe	p.S577F	ENST00000397062	NM_006164.4	577	tCt/tTt	5/5	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.850965265926291	2		381	840	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719307	190719307	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	192	200	0	ENST00000441310.2:c.1309C>T	p.Gln437Ter	p.Q437*	ENST00000441310	NM_000534.4	437	Cag/Tag	9/13	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.850965265926291	2		200	433	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050304	37050304	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs193922370	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	257	221	0	ENST00000231790.2:c.454-1G>A		p.X152_splice	ENST00000231790	NM_000249.3	152			0.850965265926291	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.850965265926291	1		221	310	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230878	66230878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	304	364	0	ENST00000273854.3:c.2093G>A	p.Gly698Glu	p.G698E	ENST00000273854	NM_004439.5	698	gGa/gAa	12/18	0.634413584020272	1	FACETS	0.823	0.787	0.858	0.823	0.787	0.858	CLONAL	1	TRUE	0	0.850965265926291	1		364	499	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258992	153258992	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	300	347	0	ENST00000281708.4:c.823C>T	p.Gln275Ter	p.Q275*	ENST00000281708	NM_033632.3	275	Cag/Tag	5/12	0.634413584020272	1	FACETS	0.718	0.684	0.752	0.718	0.684	0.752	SUBCLONAL	1	TRUE	0	0.850965265926291	1		347	564	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165095	32165095	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	68	149	0	ENST00000375023.3:c.5033A>G	p.Asp1678Gly	p.D1678G	ENST00000375023	NM_004557.3	1678	gAt/gGt	27/30	0.850965265926291	3	FACETS	0.493	0.43	0.561	0.164	0.143	0.187	SUBCLONAL	1	TRUE	0	0.850965265926291	3		149	462	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652297	36652297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201631722	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	83	150	0	ENST00000244741.5:c.419G>A	p.Arg140Gln	p.R140Q	ENST00000244741	NM_000389.4	140	cGa/cAa	2/3	0.850965265926291	3	FACETS	0.526	0.465	0.591	0.175	0.155	0.197	SUBCLONAL	1	TRUE	0	0.850965265926291	3		150	529	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760582	133760582	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775585843	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	349	438	0	ENST00000318560.5:c.2905G>A	p.Ala969Thr	p.A969T	ENST00000318560	NM_005157.4	969	Gcc/Acc	11/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.850965265926291	2		438	732	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391119	139391119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780869345	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	110	137	0	ENST00000277541.6:c.7072G>A	p.Ala2358Thr	p.A2358T	ENST00000277541	NM_017617.3	2358	Gcc/Acc	34/34	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.850965265926291	2		137	244	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409935	139409935	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	191	243	0	ENST00000277541.6:c.1903G>A	p.Gly635Arg	p.G635R	ENST00000277541	NM_017617.3	635	Gga/Aga	11/34	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.850965265926291	2		243	439	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102033244	102033244	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	156	119	0	ENST00000282441.5:c.630G>C	p.Met210Ile	p.M210I	ENST00000282441	NM_001130145.2	210	atG/atC	3/9	0.850965265926291	3	FACETS	1	0.988	1	0.681	0.631	0.731	CLONAL	1	TRUE	1	0.850965265926291	3		119	384	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023692	1023692	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	19	142	0	ENST00000358495.3:c.872C>A	p.Pro291His	p.P291H	ENST00000358495	NM_134424.2	291	cCt/cAt	10/12	NA	2	FACETS	0.121	0.092	0.156			1	INDETERMINATE	1	TRUE	NA	0.850965265926291	2		142	368	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433247	49433247	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	282	352	0	ENST00000301067.7:c.8200C>T	p.Arg2734Ter	p.R2734*	ENST00000301067	NM_003482.3	2734	Cga/Tga	32/54	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.850965265926291	2		352	625	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480103	50480103	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	95	167	0	ENST00000394963.4:c.337C>T	p.Gln113Ter	p.Q113*	ENST00000394963	NM_003076.4	113	Cag/Tag	2/13	1	2	FACETS	0.497	0.445	0.552	0.497	0.445	0.552	SUBCLONAL	1	TRUE	1	0.850965265926291	2		167	449	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011194	12011194	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	197	251	0	ENST00000353533.5:c.601C>T	p.Pro201Ser	p.P201S	ENST00000353533	NM_003010.3	201	Cca/Tca	5/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.850965265926291	2		251	463	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120521	70120521	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	243	286	0	ENST00000245479.2:c.1523G>A	p.Arg508Gln	p.R508Q	ENST00000245479	NM_000346.3	508	cGa/cAa	3/3	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.850965265926291	2		286	511	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110622	4110622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	190	156	0	ENST00000262948.5:c.335G>A	p.Arg112Gln	p.R112Q	ENST00000262948	NM_030662.3	112	cGg/cAg	3/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.850965265926291	2		156	418	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796532	42796532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	97	261	0	ENST00000575354.2:c.3089C>T	p.Thr1030Ile	p.T1030I	ENST00000575354	NM_015125.3	1030	aCc/aTc	13/20	1	2	FACETS	0.429	0.383	0.477	0.429	0.383	0.477	SUBCLONAL	1	TRUE	1	0.850965265926291	2		261	532	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127163	22127163	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	330	320	0	ENST00000215832.6:c.965A>C	p.Glu322Ala	p.E322A	ENST00000215832	NM_002745.4	322	gAg/gCg	7/9	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.850965265926291	2		320	657	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175793	24175793	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772804160	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	293	249	0	ENST00000263121.7:c.1021C>T	p.Arg341Trp	p.R341W	ENST00000263121	NM_003073.3	341	Cgg/Tgg	8/9	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.850965265926291	2		249	648	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572961	41572961	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	253	279	0	ENST00000263253.7:c.5246G>T	p.Arg1749Leu	p.R1749L	ENST00000263253	NM_001429.3	1749	cGg/cTg	31/31	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.850965265926291	2		279	568	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	439	269	0	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	0.418093205156845	3	FACETS	0.884	0.849	0.918	0.884	0.849	0.918	INDETERMINATE	2	TRUE	1	0.850965265926291	3		269	832	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437697	52437697	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1553644922	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	230	249	1	ENST00000460680.1:c.1464del	p.Ser489AlafsTer82	p.S489Afs*82	ENST00000460680	NM_004656.3	488	ccC/cc	13/17	0.850965265926291	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.850965265926291	1		250	270	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094927	143094927	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	116	304	0	ENST00000262992.4:c.1217del	p.Asn406ThrfsTer19	p.N406Tfs*19	ENST00000262992	NM_001101669.1	406	aAc/ac	14/24	0.634413584020272	1	FACETS	0.339	0.307	0.372	0.339	0.307	0.372	SUBCLONAL	1	TRUE	0	0.850965265926291	1		304	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577537	7577538	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	192	191	0	ENST00000269305.4:c.743_744delinsAA	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGG/cAA	7/11	1	2	FACETS	0.994	0.93	1	0.994	0.93	1	CLONAL	1	TRUE	1	0.850965265926291	2		191	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579312	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	195	169	0	ENST00000269305.4:c.375_375+1delinsAA		p.X125_splice	ENST00000269305	NM_001126112.2	125		4/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.850965265926291	2		169	396	SUCCESS
AR	367	MSKCC	GRCh37	X	66766350	66766351	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGG	novel	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	36	42	1	ENST00000374690.3:c.1362_1363insTGG	p.Gly454_Gly455insTrp	p.G454_G455insW	ENST00000374690	NM_000044.3	454	-/TGG	1/8	1	1	FACETS	0.853	0.748	0.951	0.853	0.748	0.951	CLONAL	1	TRUE	0	0.850965265926291	1		43	57	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649052	86649053	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0000764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	256	182	0	ENST00000274376.6:c.1332_1332+1delinsAA		p.X444_splice	ENST00000274376	NM_002890.2	444		9/25	0.850965265926291	2	FACETS	0.964	0.933	0.994	0.964	0.933	0.994	CLONAL	2	TRUE	0	0.850965265926291	2		182	312	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0000914-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	99	410	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.44613440993828	2	FACETS	0.633	0.565	0.705	0.317	0.282	0.353	SUBCLONAL	1	TRUE	0	0.44613440993828	2		410	701	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089043	37089043	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000914-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	131	167	0	ENST00000231790.2:c.1765G>C	p.Ala589Pro	p.A589P	ENST00000231790	NM_000249.3	589	Gcc/Ccc	16/19	0.237901242485899	2	FACETS	1	0.972	1	0.578	0.527	0.631	INDETERMINATE	1	TRUE	0	0.44613440993828	2		167	508	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109854	115109854	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000914-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	21	128	0	ENST00000257566.3:c.2024C>T	p.Ala675Val	p.A675V	ENST00000257566	NM_016569.3	675	gCc/gTc	8/8	0.252979176178141	4	FACETS	0.33	0.253	0.419	0.165	0.126	0.21	INDETERMINATE	1	TRUE	2	0.44613440993828	4		128	413	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219309	133219309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500802	NA	P-0000914-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	98	194	0	ENST00000320574.5:c.4735C>T	p.Arg1579Cys	p.R1579C	ENST00000320574	NM_006231.2	1579	Cgc/Tgc	37/49	0.252979176178141	4	FACETS	0.958	0.856	1	0.479	0.428	0.534	INDETERMINATE	1	TRUE	2	0.44613440993828	4		194	663	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518231	187518232	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0000914-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	133	156	0	ENST00000441802.2:c.12462_12463insA	p.His4155ThrfsTer50	p.H4155Tfs*50	ENST00000441802	NM_005245.3	4154	-/A	25/27	0.188380379474256	2	FACETS	1	0.983	1	0.652	0.597	0.71	INDETERMINATE	1	TRUE	0	0.44613440993828	2		156	457	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0000934-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	257	809	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	0.977	0.917	1	0.977	0.917	1	CLONAL	1	TRUE	1	0.593800808193251	2		809	886	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024001	27024002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0000934-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	28	36	0	ENST00000324856.7:c.1113dup	p.Gln372AlafsTer28	p.Q372Afs*28	ENST00000324856	NM_006015.4	369	-/G	1/20	0.593800808193251	1	FACETS	0.626	0.511	0.75	0.626	0.511	0.75	SUBCLONAL	1	TRUE	0	0.593800808193251	1		36	106	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303457	91303457	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0000934-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	144	422	0	ENST00000355112.3:c.1170del	p.Lys390AsnfsTer2	p.K390Nfs*2	ENST00000355112	NM_000057.2	390	Aaa/aa	6/22	1	2	FACETS	0.796	0.729	0.867	0.796	0.729	0.867	SUBCLONAL	1	TRUE	1	0.593800808193251	2		422	609	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0000952-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	805	384	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.425750927098931	7	FACETS	0.965	0.946	0.983			1	CLONAL	8	TRUE	NA	0.425750927098931	7		384	1011	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0000952-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	171	324	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.425750927098931	2		324	551	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0000952-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	180	326	1	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	0.804	0.747	0.862	1	0.992	1	CLONAL	2	TRUE	1	0.425750927098931	2		327	526	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087503	27087503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000952-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	155	339	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	0.425750927098931	2		339	507	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554954	187554955	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0000952-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	190	432	0	ENST00000441802.2:c.4206_4207insA	p.Asp1403ArgfsTer16	p.D1403Rfs*16	ENST00000441802	NM_005245.3	1402	-/A	7/27	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.425750927098931	2		432	628	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117769	70117807	+	inframe_deletion	In_Frame_Del	DEL	GGTGCTCAAAGGCTACGACTGGACGCTGGTGCCCATGCC	GGTGCTCAAAGGCTACGACTGGACGCTGGTGCCCATGCC	-	novel	NA	P-0000952-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	44	511	0	ENST00000245479.2:c.242_280del	p.Leu81_Val93del	p.L81_V93del	ENST00000245479	NM_000346.3	79	caGGTGCTCAAAGGCTACGACTGGACGCTGGTGCCCATGCCg/cag	1/3	0.425750927098931	3	FACETS	0.305	0.255	0.361	0.153	0.127	0.181	SUBCLONAL	1	TRUE	1	0.425750927098931	3		511	821	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115928	8115929	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000985-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	44	138	0	ENST00000346208.3:c.1275dup	p.Ser426IlefsTer81	p.S426Ifs*81	ENST00000346208		425	cca/ccAa	6/6	0.240255096946439	4	FACETS	0.957	0.807	1			1	INDETERMINATE	1	TRUE	NA	0.411969324026997	4		138	315	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167709	185167709	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001010-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	44	634	0	ENST00000265026.3:c.1032G>A	p.Trp344Ter	p.W344*	ENST00000265026	NM_004721.4	344	tgG/tgA	6/14	0.484829877788865	2	FACETS	0.938	0.853	1	0.938	0.853	1	INDETERMINATE	2	TRUE	0	0.823380549520162	2		634	57	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554312	81554313	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTA	novel	NA	P-0001010-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	10	641	0	ENST00000298171.2:c.332_333insTTA	p.Thr111_Arg112insTyr	p.T111_R112insY	ENST00000298171	NM_000369.2	111	acc/acTTAc	4/10	1	2	FACETS	0.261	0.178	0.363	0.261	0.178	0.363	SUBCLONAL	1	TRUE	1	0.823380549520162	2		641	93	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0001020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	395	435	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.239467884590513	5	FACETS	0.94	0.9	0.98	1	0.996	1	CLONAL	6	TRUE	1	0.239467884590513	5		436	795	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0001020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	108	288	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	1	0.973	1	1	0.99	1	CLONAL	2	TRUE	1	0.239467884590513	2		288	372	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867541	35867541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	30	363	0	ENST00000303115.3:c.361del	p.Ile121Ter	p.I121*	ENST00000303115	NM_002185.3	119	Aaa/aa	3/8	1	2	FACETS	0.602	0.485	0.735	0.602	0.485	0.735	SUBCLONAL	1	TRUE	1	0.239467884590513	2		363	416	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935606	13935606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326846768	NA	P-0001020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	94	239	0	ENST00000405192.2:c.1250G>A	p.Arg417His	p.R417H	ENST00000405192	NM_001163147.1	417	cGt/cAt	12/12	1	2	FACETS	1	0.925	1	1	0.987	1	CLONAL	2	TRUE	1	0.239467884590513	2		239	378	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779211	3779211	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783507	NA	P-0001020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	24	110	0	ENST00000262367.5:c.5837del	p.Pro1946HisfsTer30	p.P1946Hfs*30	ENST00000262367	NM_004380.2	1946	cCa/ca	31/31	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.239467884590513	2		110	148	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266476	198266476	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	99	323	0	ENST00000335508.6:c.2360T>A	p.Ile787Asn	p.I787N	ENST00000335508	NM_012433.2	787	aTt/aAt	16/25	1	2	FACETS	0.984	0.884	1	1	0.987	1	CLONAL	2	TRUE	1	0.239467884590513	2		323	420	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248627	212248627	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	117	453	1	ENST00000342788.4:c.3640A>G	p.Asn1214Asp	p.N1214D	ENST00000342788	NM_005235.2	1214	Aac/Gac	28/28	1	2	FACETS	0.987	0.895	1	1	0.989	1	CLONAL	2	TRUE	1	0.239467884590513	2		454	495	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146702	185146702	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	56	268	0	ENST00000265026.3:c.333C>G	p.Ser111Arg	p.S111R	ENST00000265026	NM_004721.4	111	agC/agG	2/14	0.10678792868304	4	FACETS	1	0.939	1	0.59	0.506	0.682	INDETERMINATE	1	TRUE	2	0.239467884590513	4		268	491	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250883	153250883	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	28	423	0	ENST00000281708.4:c.1177C>T	p.Arg393Ter	p.R393*	ENST00000281708	NM_033632.3	393	Cga/Tga	8/12	1	2	FACETS	0.474	0.378	0.584	0.474	0.378	0.584	SUBCLONAL	1	TRUE	1	0.239467884590513	2		423	493	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549832	187549832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371598532	NA	P-0001020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	50	427	1	ENST00000441802.2:c.4409C>T	p.Ala1470Val	p.A1470V	ENST00000441802	NM_005245.3	1470	gCg/gTg	8/27	1	2	FACETS	0.785	0.666	0.916	0.785	0.666	0.916	CLONAL	1	TRUE	1	0.239467884590513	2		428	532	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39002713	39002713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	48	438	0	ENST00000357387.3:c.316G>A	p.Ala106Thr	p.A106T	ENST00000357387	NM_152756.3	106	Gcg/Acg	5/38	1	2	FACETS	0.721	0.609	0.844	0.721	0.609	0.844	SUBCLONAL	1	TRUE	1	0.239467884590513	2		438	556	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97888839	97888839	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	127	458	0	ENST00000289081.3:c.868A>G	p.Ile290Val	p.I290V	ENST00000289081	NM_000136.2	290	Ata/Gta	9/15	1	2	FACETS	0.94	0.855	1	1	0.989	1	CLONAL	2	TRUE	1	0.239467884590513	2		458	564	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624305	89624305	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	85	186	0	ENST00000371953.3:c.79T>C	p.Tyr27His	p.Y27H	ENST00000371953	NM_000314.4	27	Tat/Cat	1/9	0.102216861302485	0	FACETS	0.726	0.646	0.81			1	INDETERMINATE	2	TRUE	0	0.239467884590513	0		186	372	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741834	17741834	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	15	115	0	ENST00000250003.3:c.505G>A	p.Ala169Thr	p.A169T	ENST00000250003	NM_002478.4	169	Gcc/Acc	1/3	1	2	FACETS	1	0.821	1	1	0.821	1	CLONAL	1	TRUE	1	0.239467884590513	2		115	109	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417886	32417886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	114	397	1	ENST00000332351.3:c.1166G>A	p.Arg389His	p.R389H	ENST00000332351	NM_024426.4	389	cGc/cAc	7/10	1	2	FACETS	0.891	0.806	0.981	1	0.987	1	CLONAL	2	TRUE	1	0.239467884590513	2		398	534	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736952	736952	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	82	391	0	ENST00000314574.4:c.1147G>T	p.Gly383Cys	p.G383C	ENST00000314574	NM_005433.3	383	Ggt/Tgt	10/12	1	2	FACETS	0.998	0.888	1	1	0.985	1	CLONAL	2	TRUE	1	0.239467884590513	2		391	343	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272501	15272501	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367885841	NA	P-0001020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	77	250	0	ENST00000263388.2:c.5938G>A	p.Ala1980Thr	p.A1980T	ENST00000263388	NM_000435.2	1980	Gcc/Acc	33/33	0.102216861302485	0	FACETS	0.771	0.683	0.864			1	INDETERMINATE	2	TRUE	0	0.239467884590513	0		250	317	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374341	31374341	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749197342	NA	P-0001020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	134	444	0	ENST00000328111.2:c.340C>T	p.Arg114Trp	p.R114W	ENST00000328111	NM_006892.3	114	Cgg/Tgg	5/23	1	2	FACETS	1	0.979	1	1	0.992	1	CLONAL	2	TRUE	1	0.239467884590513	2		444	460	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656792	45656792	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	42	301	0	ENST00000407780.3:c.364T>C	p.Phe122Leu	p.F122L	ENST00000407780	NM_001283052.1	122	Ttc/Ctc	3/7	NA	2	FACETS	0.821	0.687	0.971			1	INDETERMINATE	1	TRUE	NA	0.239467884590513	2		301	427	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513541	41513541	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	65	253	1	ENST00000263253.7:c.445C>T	p.Gln149Ter	p.Q149*	ENST00000263253	NM_001429.3	149	Cag/Tag	2/31	NA	2	FACETS	0.862	0.753	0.978			1	INDETERMINATE	2	TRUE	NA	0.239467884590513	2		254	315	SUCCESS
APC	324	MSKCC	GRCh37	5	112154827	112154828	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs387906237	NA	P-0001020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	92	337	0	ENST00000257430.4:c.1100_1101del	p.Ser367CysfsTer10	p.S367Cfs*10	ENST00000257430	NM_000038.5	366	gaCTct/gact	10/16	1	2	FACETS	0.848	0.757	0.944	1	0.984	1	CLONAL	2	TRUE	1	0.239467884590513	2		337	453	SUCCESS
APC	324	MSKCC	GRCh37	5	112174674	112174675	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0001020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	93	371	0	ENST00000257430.4:c.3386dup	p.Leu1129PhefsTer6	p.L1129Ffs*6	ENST00000257430	NM_000038.5	1128	tct/tcTt	16/16	1	2	FACETS	0.947	0.848	1	1	0.986	1	CLONAL	2	TRUE	1	0.239467884590513	2		371	410	SUCCESS
APC	324	MSKCC	GRCh37	5	112176171	112176171	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	176	421	0	ENST00000257430.4:c.4883del	p.Lys1628SerfsTer22	p.K1628Sfs*22	ENST00000257430	NM_000038.5	1627	cAa/ca	16/16	1	2	FACETS	1	0.983	1	1	0.994	1	CLONAL	2	TRUE	1	0.239467884590513	2		421	610	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402096	402098	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs1226495098	NA	P-0001020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	115	557	0	ENST00000399788.2:c.4693_4695del	p.Lys1565del	p.K1565del	ENST00000399788	NM_001042603.1	1565	AAG/-	27/28	0.239467884590513	4	FACETS	1	0.983	1	0.369	0.332	0.408	CLONAL	1	TRUE	0	0.239467884590513	4		557	806	SUCCESS
AR	367	MSKCC	GRCh37	X	66765242	66765243	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCA	rs753526329	NA	P-0001020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	58	155	0	ENST00000374690.3:c.271_273dup	p.Gln91dup	p.Q91dup	ENST00000374690	NM_000044.3	91	agg/agGCAg	1/8	0.239467884590513	0	FACETS	1	0.889	1			1	CLONAL	2	TRUE	NA	0.239467884590513	0		155	181	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0001073-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	208	368	3	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	0.126635409139347	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.855296097522255	0		371	543	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001073-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	191	347	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.855296097522255	2		347	443	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535310	66535310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763862819	NA	P-0001073-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	214	488	0	ENST00000273854.3:c.151C>T	p.Arg51Trp	p.R51W	ENST00000273854	NM_004439.5	51	Cgg/Tgg	1/18	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.855296097522255	2		488	498	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333683	70333683	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs774136143	NA	P-0001073-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	201	525	0	ENST00000373644.4:c.1588A>G	p.Ile530Val	p.I530V	ENST00000373644	NM_030625.2	530	Ata/Gta	2/12	0.514196881483625	3	FACETS	1	0.975	1			1	CLONAL	1	FALSE	NA	0.855296097522255	3		525	614	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420288	49420288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886043497	NA	P-0001073-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	205	459	0	ENST00000301067.7:c.15461G>A	p.Arg5154Gln	p.R5154Q	ENST00000301067	NM_003482.3	5154	cGg/cAg	48/54	1	2	FACETS	0.968	0.907	1	0.968	0.907	1	CLONAL	1	FALSE	1	0.855296097522255	2		459	495	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554590	63554590	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001073-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	159	425	0	ENST00000307078.5:c.149C>A	p.Pro50His	p.P50H	ENST00000307078	NM_004655.3	50	cCt/cAt	2/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.855296097522255	NA		425	394	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226064	53226064	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs782405999	NA	P-0001073-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	151	578	0	ENST00000375401.3:c.2785C>T	p.Arg929Ter	p.R929*	ENST00000375401	NM_004187.3	929	Cga/Tga	19/26	0.855296097522255	1	FACETS	0.986	0.935	1	0.986	0.935	1	CLONAL	1	FALSE	0	0.855296097522255	1		578	205	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589581	67589583	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	novel	NA	P-0001073-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	284	435	0	ENST00000274335.5:c.1345_1347del	p.Leu449del	p.L449del	ENST00000274335		448	aaATTa/aaa	10/15	0.136481721787084	4	FACETS	0.911	0.863	0.961	0.911	0.863	0.961	INDETERMINATE	2	FALSE	2	0.855296097522255	4		435	676	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690830	89690831	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0001073-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	297	340	0	ENST00000371953.3:c.240dup	p.Phe81IlefsTer2	p.F81Ifs*2	ENST00000371953	NM_000314.4	79	-/A	4/9	0.413953574410261	5	FACETS	0.806	0.76	0.853			1	INDETERMINATE	2	FALSE	NA	0.855296097522255	5		340	984	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717616	89717617	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0001073-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	517	330	0	ENST00000371953.3:c.642dup	p.Phe215ValfsTer28	p.F215Vfs*28	ENST00000371953	NM_000314.4	214	cag/caGg	7/9	0.413953574410261	5	FACETS	1	0.98	1			1	INDETERMINATE	3	FALSE	NA	0.855296097522255	5		330	901	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0001094-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	35	360	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	FALSE	1	0.177172121455571	2		361	373	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344853	70344853	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001094-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	26	959	0	ENST00000374080.3:c.2083G>A	p.Gly695Arg	p.G695R	ENST00000374080		695	Ggg/Agg	15/45	0.177172121455571	0	FACETS	0.497	0.393	0.617			1	SUBCLONAL	1	FALSE	0	0.177172121455571	0		959	486	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591125	67591126	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAGAAAGAC	novel	NA	P-0001094-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	36	279	0	ENST00000274335.5:c.1723_1731dup	p.Lys575_Arg577dup	p.K575_R577dup	ENST00000274335		575	ctg/ctGAGAAAGACg	12/15	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	FALSE	1	0.177172121455571	2		279	349	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023329	27023330	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	A	novel	NA	P-0001094-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	10	50	0	ENST00000324856.7:c.435_436delinsA	p.Pro146GlnfsTer86	p.P146Qfs*86	ENST00000324856	NM_006015.4	145	ccCCca/ccAca	1/20	1	2	FACETS	0.733	0.498	1	0.733	0.498	1	CLONAL	1	FALSE	1	0.177172121455571	2		50	154	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0001102-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	300	298	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.667079711415326	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	FALSE	0	0.667079711415326	2		298	407	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0001102-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	1120	340	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.522586045464616	4	FACETS	1	0.995	1			1	CLONAL	3	FALSE	NA	0.667079711415326	4		340	1754	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172089	99172089	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001102-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	130	272	0	ENST00000074304.5:c.1655A>G	p.Glu552Gly	p.E552G	ENST00000074304	NM_001134224.1	552	gAg/gGg	17/26	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	1	0.667079711415326	2		272	361	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84388647	84388647	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001102-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	337	610	0	ENST00000321945.7:c.641A>T	p.Lys214Met	p.K214M	ENST00000321945	NM_139076.2	214	aAg/aTg	7/9	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.667079711415326	2		610	1000	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460401	149460401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001102-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	165	495	0	ENST00000286301.3:c.236C>T	p.Thr79Met	p.T79M	ENST00000286301	NM_005211.3	79	aCg/aTg	3/22	1	2	FACETS	0.997	0.923	1	0.997	0.923	1	CLONAL	1	FALSE	1	0.667079711415326	2		495	496	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339301	116339301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001102-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	383	564	0	ENST00000397752.3:c.163G>A	p.Val55Ile	p.V55I	ENST00000397752	NM_000245.2	55	Gtc/Atc	2/21	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.667079711415326	2		564	1028	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129374	64129374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142374327	NA	P-0001102-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	206	577	0	ENST00000334205.4:c.806C>T	p.Ala269Val	p.A269V	ENST00000334205	NM_003942.2	269	gCg/gTg	8/17	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.667079711415326	2		577	537	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178641	108178641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775036118	NA	P-0001102-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	167	164	0	ENST00000278616.4:c.5692C>T	p.Arg1898Ter	p.R1898*	ENST00000278616	NM_000051.3	1898	Cga/Tga	38/63	1	2	FACETS	0.957	0.886	1	0.957	0.886	1	CLONAL	1	FALSE	1	0.667079711415326	2		164	523	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482425	56482425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001102-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	359	302	0	ENST00000267101.3:c.973G>A	p.Gly325Arg	p.G325R	ENST00000267101	NM_001982.3	325	Gga/Aga	8/28	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	2	FALSE	NA	0.667079711415326	2		302	467	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019265	31019265	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001102-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	247	469	0	ENST00000375687.4:c.860T>C	p.Leu287Pro	p.L287P	ENST00000375687	NM_015338.5	287	cTc/cCc	9/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.667079711415326	2		469	692	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57470712	57470712	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001102-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	153	233	0	ENST00000371085.3:c.185T>C	p.Ile62Thr	p.I62T	ENST00000371085	NM_000516.4	62	aTc/aCc	2/13	1	2	FACETS	0.894	0.824	0.967	0.894	0.824	0.967	CLONAL	1	FALSE	1	0.667079711415326	2		233	513	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584513	48584514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs377767334	NA	P-0001102-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	296	264	1	ENST00000342988.3:c.692dup	p.Ser232GlnfsTer3	p.S232Qfs*3	ENST00000342988	NM_005359.5	229	ctg/ctGg	6/12	0.638717040077615	2	FACETS	0.932	0.892	0.972	0.932	0.892	0.972	CLONAL	2	FALSE	0	0.667079711415326	2		265	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0001104-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	245	607	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.577133521643621	1	FACETS	0.869	0.817	0.923	0.869	0.817	0.923	CLONAL	1	TRUE	0	0.577133521643621	1		607	695	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0001104-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	246	208	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.521658404476956	1	FACETS	0.807	0.757	0.857	0.807	0.757	0.857	CLONAL	1	TRUE	0	0.577133521643621	1		208	752	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038912	12038912	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001104-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	282	567	0	ENST00000396373.4:c.1205A>G	p.Tyr402Cys	p.Y402C	ENST00000396373	NM_001987.4	402	tAc/tGc	7/8	0.224980857589016	4	FACETS	1	0.991	1	0.661	0.621	0.702	INDETERMINATE	1	TRUE	2	0.577133521643621	4		567	1166	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782654	9782654	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001104-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	401	488	0	ENST00000377346.4:c.2416C>A	p.Leu806Met	p.L806M	ENST00000377346	NM_005026.3	806	Ctg/Atg	19/24	0.421873166843158	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.577133521643621	1		488	907	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917797	29917797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748854412	NA	P-0001104-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	213	537	0	ENST00000389048.3:c.871C>T	p.Arg291Cys	p.R291C	ENST00000389048	NM_004304.4	291	Cgc/Tgc	3/29	0.554124343462215	3	FACETS	0.826	0.767	0.888	0.413	0.383	0.444	CLONAL	1	TRUE	1	0.577133521643621	3		537	1151	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808647	1808647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373425119	NA	P-0001104-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	218	558	0	ENST00000260795.2:c.2260G>A	p.Val754Met	p.V754M	ENST00000260795		754	Gtg/Atg	16/17	1	2	FACETS	0.794	0.739	0.851	0.794	0.739	0.851	SUBCLONAL	1	TRUE	1	0.577133521643621	2		558	951	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213909	66213909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001104-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	260	635	0	ENST00000273854.3:c.2521C>T	p.Pro841Ser	p.P841S	ENST00000273854	NM_004439.5	841	Cca/Tca	15/18	1	2	FACETS	0.873	0.818	0.929	0.873	0.818	0.929	CLONAL	1	TRUE	1	0.577133521643621	2		635	1032	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468029	50468029	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001104-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	122	296	1	ENST00000331340.3:c.1264G>A	p.Ala422Thr	p.A422T	ENST00000331340	NM_006060.4	422	Gcg/Acg	8/8	1	2	FACETS	0.731	0.663	0.803	0.731	0.663	0.803	SUBCLONAL	1	TRUE	1	0.577133521643621	2		297	578	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504378	8504378	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001104-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	187	370	0	ENST00000356435.5:c.1705T>A	p.Ser569Thr	p.S569T	ENST00000356435		569	Tca/Aca	12/35	0.521658404476956	1	FACETS	0.823	0.766	0.882	0.823	0.766	0.882	CLONAL	1	TRUE	0	0.577133521643621	1		370	560	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231337	46231337	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001104-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	209	425	0	ENST00000334344.6:c.1177G>A	p.Glu393Lys	p.E393K	ENST00000334344	NM_152641.2	393	Gaa/Aaa	10/21	0.103996580350345	3	FACETS	1	0.979	1	0.565	0.525	0.606	INDETERMINATE	1	TRUE	1	0.577133521643621	3		425	826	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432110	121432110	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001104-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	215	468	0	ENST00000257555.6:c.857A>T	p.Tyr286Phe	p.Y286F	ENST00000257555		286	tAc/tTc	4/10	NA	2	FACETS	0.835	0.777	0.895			1	INDETERMINATE	1	TRUE	NA	0.577133521643621	2		468	892	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2218120	2218120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001104-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	352	678	0	ENST00000326181.6:c.182C>T	p.Ser61Phe	p.S61F	ENST00000326181	NM_032271.2	61	tCc/tTc	4/21	1	2	FACETS	0.89	0.842	0.94	0.89	0.842	0.94	CLONAL	1	TRUE	1	0.577133521643621	2		678	1370	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857029	9857029	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001104-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	279	693	0	ENST00000330684.3:c.4372C>G	p.Pro1458Ala	p.P1458A	ENST00000330684	NM_001134407.1	1458	Cct/Gct	13/13	1	2	FACETS	0.796	0.747	0.847	0.796	0.747	0.847	SUBCLONAL	1	TRUE	1	0.577133521643621	2		693	1214	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439988	56439993	+	frameshift_variant	Frame_Shift_Ins	INS	GGATCC	GGATCC	TCATAATCTG	novel	NA	P-0001104-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	97	450	1	ENST00000407977.2:c.599_604delinsCAGATTATGA	p.Trp200SerfsTer60	p.W200Sfs*60	ENST00000407977		200	tGGATCCta/tCAGATTATGAta	6/10	0.577133521643621	1	FACETS	0.463	0.414	0.514	0.463	0.414	0.514	SUBCLONAL	1	TRUE	0	0.577133521643621	1		451	517	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331719	68331719	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs751355274	NA	P-0001118-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	12	164	0	ENST00000487270.1:c.316-1G>T		p.X106_splice	ENST00000487270	NM_133509.3	106			0.241824101289614	2	FACETS	0.152	0.106	0.207	0.076	0.053	0.104	INDETERMINATE	1	TRUE	0	0.879767369916631	2		164	180	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115971	8115972	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGTG	novel	NA	P-0001118-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	234	164	0	ENST00000346208.3:c.1318_1319insGTGA	p.Thr440SerfsTer68	p.T440Sfs*68	ENST00000346208		439	-/AGTG	6/6	0.879767369916631	11	FACETS	0.954	0.898	1			1	CLONAL	5	TRUE	NA	0.879767369916631	11		164	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0001130-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	215	609	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.422121108077005	1	FACETS	0.992	0.927	1	0.992	0.927	1	CLONAL	1	TRUE	0	0.482723501487188	1		610	681	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467570	66467570	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001130-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	137	335	0	ENST00000273854.3:c.699C>A	p.Cys233Ter	p.C233*	ENST00000273854	NM_004439.5	233	tgC/tgA	3/18	0.191675891935632	2	FACETS	0.608	0.552	0.666	0.304	0.276	0.333	INDETERMINATE	1	TRUE	0	0.482723501487188	2		335	934	SUCCESS
APC	324	MSKCC	GRCh37	5	112154696	112154696	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001130-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	99	286	0	ENST00000257430.4:c.967G>T	p.Gly323Cys	p.G323C	ENST00000257430	NM_000038.5	323	Ggt/Tgt	10/16	0.245283394427794	1	FACETS	0.454	0.405	0.505	0.454	0.405	0.505	INDETERMINATE	1	TRUE	0	0.482723501487188	1		286	686	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610136	10610136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001130-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	348	392	0	ENST00000171111.5:c.574G>A	p.Glu192Lys	p.E192K	ENST00000171111	NM_203500.1	192	Gag/Aag	2/6	0.482723501487188	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.482723501487188	1		392	1006	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610217	10610217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752325770	NA	P-0001130-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	362	417	0	ENST00000171111.5:c.493G>A	p.Asp165Asn	p.D165N	ENST00000171111	NM_203500.1	165	Gac/Aac	2/6	0.482723501487188	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.482723501487188	1		417	1041	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52661309	52661310	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTATCAGT	novel	NA	P-0001130-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	252	472	0	ENST00000394830.3:c.1520_1521insACTGATAC	p.Gly508LeufsTer14	p.G508Lfs*14	ENST00000394830	NM_018313.4	507	act/acACTGATACt	14/30	0.422121108077005	1	FACETS	0.716	0.67	0.764	0.716	0.67	0.764	SUBCLONAL	1	TRUE	0	0.482723501487188	1		472	1106	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148541	119148546	+	inframe_deletion	In_Frame_Del	DEL	TCAAAG	TCAAAG	-	novel	NA	P-0001130-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	324	443	0	ENST00000264033.4:c.1083_1088del	p.Ile361_Val363delinsMet	p.I361_V363delinsM	ENST00000264033	NM_005188.3	361	aTCAAAGtg/atg	7/16	0.44228291835524	2	FACETS	1	0.994	1	0.688	0.651	0.725	CLONAL	1	TRUE	0	0.482723501487188	2		443	976	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218422	1218456	+	frameshift_variant	Frame_Shift_Del	DEL	TCAACTACTGAGGAGGTTACGGCACAAAAATGTCA	TCAACTACTGAGGAGGTTACGGCACAAAAATGTCA	-	novel	NA	P-0001130-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	49	355	0	ENST00000326873.7:c.299_333del	p.Gln100ProfsTer51	p.Q100Pfs*51	ENST00000326873	NM_000455.4	99	atTCAACTACTGAGGAGGTTACGGCACAAAAATGTCAtc/attc	2/10	0.482723501487188	1	FACETS	0.25	0.211	0.292	0.25	0.211	0.292	SUBCLONAL	1	TRUE	0	0.482723501487188	1		355	617	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097133	11097134	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0001130-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	261	343	0	ENST00000358026.2:c.626dup	p.Met210AspfsTer77	p.M210Dfs*77	ENST00000358026	NM_001128849.1	208	-/C	4/36	0.482723501487188	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.482723501487188	1		343	742	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001208-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	98	307	0	ENST00000263967.3:c.323G>T	p.Arg108Leu	p.R108L	ENST00000263967	NM_006218.2	108	cGt/cTt	2/21	0.348687125245127	3	FACETS	1	0.943	1	0.706	0.639	0.776	CLONAL	2	TRUE	0	0.38737659498281	3		307	285	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs869320707	NA	P-0001208-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	303	228	0	ENST00000397752.3:c.3028+1G>T		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.38737659498281	3	FACETS	1	0.978	1	1	0.995	1	CLONAL	4	TRUE	0	0.38737659498281	3		228	454	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197275	106197276	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0001208-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	53	261	0	ENST00000380013.4:c.5609dup	p.Ile1871AsnfsTer4	p.I1871Nfs*4	ENST00000380013	NM_001127208.2	1870	tca/tCca	11/11	0.349498215424661	1	FACETS	0.959	0.827	1	0.959	0.827	1	CLONAL	1	TRUE	0	0.38737659498281	1		261	230	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0001212-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	96	96	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.997	0.9	1	0.997	0.9	1	CLONAL	1	TRUE	1	0.650616203624511	2		96	296	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044463	12044463	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0001212-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	71	252	0	ENST00000353533.5:c.1087-1G>A		p.X363_splice	ENST00000353533	NM_003010.3	363			0.650616203624511	1	FACETS	0.409	0.359	0.462	0.409	0.359	0.462	SUBCLONAL	1	TRUE	0	0.650616203624511	1		252	360	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950348	17950348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199659728	NA	P-0001212-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	192	526	0	ENST00000458235.1:c.1379G>A	p.Gly460Glu	p.G460E	ENST00000458235	NM_000215.3	460	gGg/gAg	10/24	0.281660448279668	4	FACETS	0.982	0.908	1	0.246	0.227	0.265	INDETERMINATE	1	TRUE	0	0.650616203624511	4		526	992	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101053	27101053	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001212-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	69	617	0	ENST00000324856.7:c.4336del	p.Arg1446AspfsTer35	p.R1446Dfs*35	ENST00000324856	NM_006015.4	1445	cgC/cg	18/20	1	2	FACETS	0.242	0.21	0.277	0.242	0.21	0.277	SUBCLONAL	1	TRUE	1	0.650616203624511	2		617	875	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105617	27105618	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCTT	novel	NA	P-0001212-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	89	547	0	ENST00000324856.7:c.5231_5232insTGCT	p.Leu1745AlafsTer12	p.L1745Afs*12	ENST00000324856	NM_006015.4	1743	acg/acGCTTg	20/20	1	2	FACETS	0.311	0.275	0.349	0.311	0.275	0.349	SUBCLONAL	1	TRUE	1	0.650616203624511	2		547	881	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404556	70404558	+	inframe_deletion	In_Frame_Del	DEL	TAC	TAC	-	novel	NA	P-0001212-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	189	474	0	ENST00000373644.4:c.2071_2073del	p.Thr691del	p.T691del	ENST00000373644	NM_030625.2	690	caTACt/cat	4/12	1	2	FACETS	0.774	0.717	0.832	0.774	0.717	0.832	SUBCLONAL	1	TRUE	1	0.650616203624511	2		474	751	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847226	68847227	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0001212-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	196	375	0	ENST00000261769.5:c.1150dup	p.Val384GlyfsTer3	p.V384Gfs*3	ENST00000261769	NM_004360.3	383	cag/caGg	9/16	0.650616203624511	1	FACETS	0.937	0.878	0.996	0.937	0.878	0.996	CLONAL	1	TRUE	0	0.650616203624511	1		375	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0001278-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	287	497	2	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	0.558548533206937	1	FACETS	0.993	0.939	1	0.993	0.939	1	CLONAL	1	TRUE	0	0.558548533206937	1		499	746	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211065	55211065	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001278-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	555	413	0	ENST00000275493.2:c.308A>T	p.Asn103Ile	p.N103I	ENST00000275493	NM_005228.3	103	aAc/aTc	3/28	0.558548533206937	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.558548533206937	2		413	918	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246224	46246224	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs772995852	NA	P-0001278-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	85	357	0	ENST00000334344.6:c.4318C>G	p.Gln1440Glu	p.Q1440E	ENST00000334344	NM_152641.2	1440	Cag/Gag	15/21	0.130056245428644	3	FACETS	0.48	0.424	0.541	0.24	0.212	0.271	INDETERMINATE	1	TRUE	1	0.558548533206937	3		357	811	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923160	48923160	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587776789	NA	P-0001278-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	154	311	0	ENST00000267163.4:c.607+1G>T		p.X203_splice	ENST00000267163	NM_000321.2	203			0.558548533206937	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.558548533206937	1		311	375	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348223	348223	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001278-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	50	201	0	ENST00000262320.3:c.1283C>A	p.Ser428Ter	p.S428*	ENST00000262320	NM_003502.3	428	tCg/tAg	6/11	0.558548533206937	1	FACETS	0.29	0.246	0.338	0.29	0.246	0.338	SUBCLONAL	1	TRUE	0	0.558548533206937	1		201	445	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831395	89831395	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001278-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	80	369	0	ENST00000389301.3:c.2681G>C	p.Arg894Thr	p.R894T	ENST00000389301	NM_000135.2	894	aGa/aCa	28/43	0.558548533206937	1	FACETS	0.332	0.292	0.375	0.332	0.292	0.375	SUBCLONAL	1	TRUE	0	0.558548533206937	1		369	622	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490319	29490319	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500244	NA	P-0001278-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	254	377	1	ENST00000356175.3:c.404G>A	p.Arg135Gln	p.R135Q	ENST00000356175	NM_000267.3	135	cGg/cAg	4/57	1	2	FACETS	0.845	0.791	0.901	0.845	0.791	0.901	CLONAL	1	TRUE	1	0.558548533206937	2		378	1076	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444487	49444488	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0001278-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	230	253	0	ENST00000301067.7:c.2883dup	p.Gly962TrpfsTer7	p.G962Wfs*7	ENST00000301067	NM_003482.3	961	-/T	11/54	0.130056245428644	3	FACETS	1	0.992	1	0.713	0.667	0.76	INDETERMINATE	1	TRUE	1	0.558548533206937	3		253	739	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023720	27023720	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001292-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	221	261	0	ENST00000324856.7:c.826G>T	p.Gly276Ter	p.G276*	ENST00000324856	NM_006015.4	276	Gga/Tga	1/20	0.580292331597097	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.580292331597097	1		261	483	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812269	212812269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201152419	NA	P-0001292-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	243	342	0	ENST00000342788.4:c.307C>T	p.Arg103Cys	p.R103C	ENST00000342788	NM_005235.2	103	Cgc/Tgc	3/28	1	2	FACETS	0.911	0.853	0.972	0.911	0.853	0.972	CLONAL	1	TRUE	1	0.580292331597097	2		342	919	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645687	12645687	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397516828	NA	P-0001292-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	135	193	0	ENST00000251849.4:c.782C>G	p.Pro261Arg	p.P261R	ENST00000251849	NM_002880.3	261	cCt/cGt	7/17	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.580292331597097	2		193	459	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913355	NA	P-0001292-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	241	336	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	0.580292331597097	2		336	767	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495764	72495765	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0001292-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	197	248	0	ENST00000477973.2:c.305dup	p.Arg103LysfsTer15	p.R103Kfs*15	ENST00000477973	NM_012234.5	103	aga/aAga	1/4	1	2	FACETS	0.862	0.8	0.926	0.862	0.8	0.926	CLONAL	1	TRUE	1	0.580292331597097	2		248	788	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226859	2226879	+	inframe_deletion	In_Frame_Del	DEL	GCGGCGTCCTCCGCAGGCGGC	GCGGCGTCCTCCGCAGGCGGC	-	rs748637415	NA	P-0001292-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	33	98	0	ENST00000398665.3:c.4353_4373del	p.Gly1452_Ala1458del	p.G1452_A1458del	ENST00000398665	NM_032482.2	1447	GCGGCGTCCTCCGCAGGCGGC/-	27/28	NA	2	FACETS	0.586	0.482	0.702			1	INDETERMINATE	1	TRUE	NA	0.580292331597097	2		98	194	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0001302-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	192	678	1	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.695875201767339	3	FACETS	0.809	0.748	0.871	0.404	0.374	0.436	CLONAL	1	TRUE	1	0.695875201767339	3		679	920	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685344	86685344	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001302-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	77	144	0	ENST00000274376.6:c.3060G>C	p.Gln1020His	p.Q1020H	ENST00000274376	NM_002890.2	1020	caG/caC	24/25	0.695875201767339	3	FACETS	0.712	0.628	0.801	0.356	0.314	0.401	SUBCLONAL	1	TRUE	1	0.695875201767339	3		144	419	SUCCESS
APC	324	MSKCC	GRCh37	5	112174901	112174901	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001302-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	303	284	0	ENST00000257430.4:c.3610C>T	p.Gln1204Ter	p.Q1204*	ENST00000257430	NM_000038.5	1204	Caa/Taa	16/16	0.695875201767339	3	FACETS	0.82	0.777	0.863	0.82	0.777	0.863	CLONAL	2	TRUE	1	0.695875201767339	3		284	716	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579382	7579383	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0001302-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	257	287	0	ENST00000269305.4:c.304dup	p.Thr102AsnfsTer47	p.T102Nfs*47	ENST00000269305	NM_001126112.2	102	acc/aAcc	4/11	0.610083529915886	2	FACETS	0.875	0.834	0.915	0.875	0.834	0.915	CLONAL	2	TRUE	0	0.695875201767339	2		287	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0001317-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	47	695	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.746	0.627	0.878	0.746	0.627	0.878	SUBCLONAL	1	TRUE	1	0.14	2		695	900	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593532	48593532	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555686620	NA	P-0001317-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	37	286	0	ENST00000342988.3:c.1283A>C	p.Lys428Thr	p.K428T	ENST00000342988	NM_005359.5	428	aAg/aCg	10/12	1	2	FACETS	0.801	0.659	0.961	0.801	0.659	0.961	CLONAL	1	TRUE	1	0.14	2		286	660	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437564	56437565	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0001317-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	57	348	0	ENST00000407977.2:c.896_897dup	p.Asp300TrpfsTer120	p.D300Wfs*120	ENST00000407977		299	-/TG	8/10	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.14	2		348	718	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0001383-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	144	357	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.49969177930489	3	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	1	0.49969177930489	3		357	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0001383-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	76	609	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.49969177930489	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.49969177930489	1		610	172	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059260	27059260	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001383-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	106	394	0	ENST00000324856.7:c.1897C>T	p.Gln633Ter	p.Q633*	ENST00000324856	NM_006015.4	633	Cag/Tag	4/20	0.152269134136852	5	FACETS	0.961	0.869	1	0.641	0.579	0.705	INDETERMINATE	2	TRUE	2	0.49969177930489	5		394	386	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246671	46246671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001383-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	27	96	0	ENST00000334344.6:c.4765G>T	p.Val1589Phe	p.V1589F	ENST00000334344	NM_152641.2	1589	Gtc/Ttc	15/21	0.316317770449552	3	FACETS	0.965	0.778	1	0.482	0.389	0.586	CLONAL	1	TRUE	1	0.49969177930489	3		96	140	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447892	49447892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001383-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	29	139	0	ENST00000301067.7:c.542C>T	p.Ser181Phe	p.S181F	ENST00000301067	NM_003482.3	181	tCc/tTc	5/54	0.316317770449552	3	FACETS	0.924	0.751	1	0.462	0.375	0.558	CLONAL	1	TRUE	1	0.49969177930489	3		139	157	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491692	56491692	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001383-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	34	341	0	ENST00000267101.3:c.2584G>C	p.Asp862His	p.D862H	ENST00000267101	NM_001982.3	862	Gat/Cat	21/28	0.388270037983474	4	FACETS	0.759	0.623	0.91	0.379	0.311	0.455	CLONAL	1	TRUE	2	0.49969177930489	4		341	269	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623559	28623559	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0001383-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	25	251	0	ENST00000241453.7:c.998C>G	p.Ser333Ter	p.S333*	ENST00000241453	NM_004119.2	333	tCa/tGa	8/24	0.36350875171145	0	FACETS	0.35	0.279	0.43			1	SUBCLONAL	1	TRUE	0	0.49969177930489	0		251	143	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527709	103527709	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001383-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	87	267	0	ENST00000355739.4:c.3017A>C	p.Asp1006Ala	p.D1006A	ENST00000355739	NM_000123.3	1006	gAt/gCt	15/15	0.152269134136852	5	FACETS	0.989	0.885	1	0.659	0.59	0.732	INDETERMINATE	2	TRUE	2	0.49969177930489	5		267	308	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557904	29557904	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0001383-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	47	144	0	ENST00000356175.3:c.3158C>G	p.Ser1053Ter	p.S1053*	ENST00000356175	NM_000267.3	1053	tCa/tGa	24/57	0.375948613779781	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.49969177930489	1		144	119	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86658489	86658490	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0001383-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	39	278	0	ENST00000274376.6:c.1453+2dup		p.X485_splice	ENST00000274376	NM_002890.2	485			0.405942829547806	2	FACETS	0.587	0.489	0.694	0.293	0.244	0.347	SUBCLONAL	1	TRUE	0	0.49969177930489	2		278	266	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984696	11984697	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0001383-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	36	87	0	ENST00000353533.5:c.243_244insAT	p.Glu82MetfsTer7	p.E82Mfs*7	ENST00000353533	NM_003010.3	81	att/atTAt	3/11	0.49969177930489	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.49969177930489	1		87	95	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0001424-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	393	208	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA	2	FACETS	0.792	0.754	0.83			1	INDETERMINATE	2	TRUE	NA	0.470419592491605	2		208	1055	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0001424-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	65	673	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.83	0.724	0.943	0.83	0.724	0.943	CLONAL	1	TRUE	1	0.470419592491605	2		673	333	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0001424-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	62	302	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.267514115344415	1	FACETS	0.493	0.427	0.564	0.493	0.427	0.564	INDETERMINATE	1	TRUE	0	0.470419592491605	1		302	409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0001424-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	143	350	0	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	0.470419592491605	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.470419592491605	1		350	456	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285870	38285870	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs780153672	NA	P-0001424-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	238	706	1	ENST00000425967.3:c.541C>T	p.Pro181Ser	p.P181S	ENST00000425967	NM_001174067.1	181	Ccc/Tcc	5/19	0.254270334402595	1	FACETS	0.837	0.782	0.893	0.837	0.782	0.893	INDETERMINATE	1	TRUE	0	0.470419592491605	1		707	925	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19261493	19261493	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001424-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	265	708	0	ENST00000162023.5:c.52C>A	p.Gln18Lys	p.Q18K	ENST00000162023		18	Cag/Aag	6/13	0.433622519721915	1	FACETS	0.887	0.833	0.943	0.887	0.833	0.943	CLONAL	1	TRUE	0	0.470419592491605	1		708	971	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763953	76763953	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001424-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	200	796	0	ENST00000373344.5:c.7355A>T	p.Gln2452Leu	p.Q2452L	ENST00000373344	NM_000489.3	2452	cAg/cTg	35/35	0.358357131547213	1	FACETS	0.501	0.463	0.54	0.501	0.463	0.54	SUBCLONAL	1	TRUE	0	0.470419592491605	1		796	1299	SUCCESS
APC	324	MSKCC	GRCh37	5	112116586	112116587	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1561485947	NA	P-0001424-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	92	308	0	ENST00000257430.4:c.636dup	p.Arg213ThrfsTer39	p.R213Tfs*39	ENST00000257430	NM_000038.5	211	gaa/gAaa	6/16	0.267514115344415	1	FACETS	0.646	0.577	0.719	0.646	0.577	0.719	INDETERMINATE	1	TRUE	0	0.470419592491605	1		308	463	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201672	66201672	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001424-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	146	643	0	ENST00000273854.3:c.2830A>G	p.Thr944Ala	p.T944A	ENST00000273854	NM_004439.5	944	Acg/Gcg	16/18	0.358357131547213	1	FACETS	0.404	0.368	0.442	0.404	0.368	0.442	SUBCLONAL	1	TRUE	0	0.470419592491605	1		643	1175	SUCCESS
ATR	545	MSKCC	GRCh37	3	142211996	142211997	+	missense_variant	Missense_Mutation	DNP	TT	TT	AA	novel	NA	P-0001424-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	59	639	0	ENST00000350721.4:c.6055_6056inv	p.Asn2019Phe	p.N2019F	ENST00000350721	NM_001184.3	2019	AAt/TTt	35/47	0.254270334402595	1	FACETS	0.169	0.145	0.196	0.169	0.145	0.196	INDETERMINATE	1	TRUE	0	0.470419592491605	1		639	1134	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0001424-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	211	208	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	0.455280103704011	2		208	841	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0001424-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	184	673	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.378017886526307	3	FACETS	0.917	0.853	0.983	0.917	0.853	0.983	CLONAL	2	TRUE	1	0.455280103704011	3		673	541	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0001424-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	79	302	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.257586775853375	3	FACETS	0.856	0.755	0.963	0.428	0.377	0.482	INDETERMINATE	1	TRUE	1	0.455280103704011	3		302	498	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0001424-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	150	350	0	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	0.455280103704011	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.455280103704011	1		350	399	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285870	38285870	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs780153672	NA	P-0001424-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	184	706	1	ENST00000425967.3:c.541C>T	p.Pro181Ser	p.P181S	ENST00000425967	NM_001174067.1	181	Ccc/Tcc	5/19	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.455280103704011	2		707	691	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19261493	19261493	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001424-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	194	708	0	ENST00000162023.5:c.52C>A	p.Gln18Lys	p.Q18K	ENST00000162023		18	Cag/Aag	6/13	0.193016958320548	1	FACETS	0.978	0.909	1	0.978	0.909	1	INDETERMINATE	1	TRUE	0	0.455280103704011	1		708	673	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763953	76763953	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001424-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	172	796	0	ENST00000373344.5:c.7355A>T	p.Gln2452Leu	p.Q2452L	ENST00000373344	NM_000489.3	2452	cAg/cTg	35/35	0.372173455847207	0	FACETS	0.518	0.477	0.561			1	SUBCLONAL	1	TRUE	0	0.455280103704011	0		796	794	SUCCESS
APC	324	MSKCC	GRCh37	5	112116586	112116587	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1561485947	NA	P-0001424-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	163	308	0	ENST00000257430.4:c.636dup	p.Arg213ThrfsTer39	p.R213Tfs*39	ENST00000257430	NM_000038.5	211	gaa/gAaa	6/16	0.257586775853375	3	FACETS	1	0.989	1	0.725	0.669	0.784	INDETERMINATE	1	TRUE	1	0.455280103704011	3		308	606	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032129	26032130	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0001424-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	128	302	0	ENST00000244661.2:c.158_159dup	p.Arg54AlafsTer10	p.R54Afs*10	ENST00000244661	NM_003537.3	53	-/GC	1/1	0.455280103704011	5	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.455280103704011	5		302	750	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0001484-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	92	305	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	0.98	0.869	1	0.98	0.869	1	CLONAL	1	TRUE	1	0.205524678301446	2		305	914	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088787	27088788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0001484-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	44	608	0	ENST00000324856.7:c.2402dup	p.Gln802SerfsTer15	p.Q802Sfs*15	ENST00000324856	NM_006015.4	799	cag/caGg	7/20	1	2	FACETS	0.606	0.507	0.716	0.606	0.507	0.716	SUBCLONAL	1	TRUE	1	0.205524678301446	2		608	707	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164065	108164066	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GATA	novel	NA	P-0001484-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	34	467	0	ENST00000278616.4:c.4642_4645dup	p.Asn1549ArgfsTer2	p.N1549Rfs*2	ENST00000278616	NM_000051.3	1546	gtg/gtGATAg	31/63	1	2	FACETS	0.546	0.445	0.66	0.546	0.445	0.66	SUBCLONAL	1	TRUE	1	0.205524678301446	2		467	606	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0001500-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	97	435	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.237668429106375	1	FACETS	0.883	0.789	0.981	0.883	0.789	0.981	CLONAL	1	TRUE	0	0.341922311723715	1		436	533	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0001500-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	49	298	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	0.287506541280893	1	FACETS	0.66	0.561	0.768	0.66	0.561	0.768	SUBCLONAL	1	TRUE	0	0.341922311723715	1		298	360	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0001500-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	81	586	1	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.287506541280893	1	FACETS	0.559	0.492	0.63	0.559	0.492	0.63	SUBCLONAL	1	TRUE	0	0.341922311723715	1		587	703	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0001500-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	105	824	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	0.237668429106375	1	FACETS	0.533	0.477	0.593	0.533	0.477	0.593	SUBCLONAL	1	TRUE	0	0.341922311723715	1		824	955	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29120965	29120965	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs1555926708	NA	P-0001500-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	206	405	0	ENST00000328354.6:c.592G>C	p.Val198Leu	p.V198L	ENST00000328354	NM_007194.3	198	Gtt/Ctt	4/15	0.341922311723715	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.341922311723715	2		405	572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578464	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001500-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	230	457	1	ENST00000269305.4:c.466del	p.Arg156AlafsTer14	p.R156Afs*14	ENST00000269305	NM_001126112.2	156	Cgc/gc	5/11	0.341922311723715	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.341922311723715	2		458	607	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737142	145737142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61755067	NA	P-0001500-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	70	520	0	ENST00000428558.2:c.3424G>A	p.Asp1142Asn	p.D1142N	ENST00000428558	NM_004260.3	1142	Gac/Aac	21/22	0.216659287681429	3	FACETS	0.626	0.545	0.714	0.209	0.181	0.238	SUBCLONAL	1	TRUE	0	0.341922311723715	3		520	766	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89881001	89881001	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001500-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	243	682	0	ENST00000389301.3:c.210A>T	p.Lys70Asn	p.K70N	ENST00000389301	NM_000135.2	70	aaA/aaT	3/43	0.212704067901127	3	FACETS	0.75	0.701	0.802	0.75	0.701	0.802	SUBCLONAL	2	TRUE	1	0.341922311723715	3		682	1109	SUCCESS
APC	324	MSKCC	GRCh37	5	112175749	112175761	+	frameshift_variant	Frame_Shift_Del	DEL	TACTTTATTACAT	TACTTTATTACAT	-	novel	NA	P-0001500-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	79	305	0	ENST00000257430.4:c.4459_4471del	p.Thr1487LeufsTer16	p.T1487Lfs*16	ENST00000257430	NM_000038.5	1486	gaTACTTTATTACAT/ga	16/16	0.287506541280893	1	FACETS	0.879	0.776	0.988	0.879	0.776	0.988	CLONAL	1	TRUE	0	0.341922311723715	1		305	436	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988224	36988247	+	inframe_deletion	In_Frame_Del	DEL	CCATCCGGGGCCAGAGGCGCTGTT	CCATCCGGGGCCAGAGGCGCTGTT	-	novel	NA	P-0001500-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	54	290	0	ENST00000354822.5:c.406_429del	p.Asn136_Trp143del	p.N136_W143del	ENST00000354822	NM_001079668.2	136	AACAGCGCCTCTGGCCCCGGATGG/-	2/3	0.287506541280893	1	FACETS	0.945	0.814	1	0.945	0.814	1	CLONAL	1	TRUE	0	0.341922311723715	1		290	277	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122378	17122379	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0001500-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	238	632	0	ENST00000285071.4:c.1016dup	p.Pro340AlafsTer50	p.P340Afs*50	ENST00000285071	NM_144997.5	339	cag/caAg	9/14	0.341922311723715	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.341922311723715	2		632	672	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0001516-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	254	384	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.259876770947576	3	FACETS	0.903	0.843	0.965	1	0.991	1	CLONAL	3	TRUE	1	0.15	3		384	1344	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517201	NA	P-0001516-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	62	306	0	ENST00000263967.3:c.1637A>C	p.Gln546Pro	p.Q546P	ENST00000263967	NM_006218.2	546	cAg/cCg	10/21	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.15	2		306	725	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs483352695	NA	P-0001516-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1607	92	602	0	ENST00000269305.4:c.736A>C	p.Met246Leu	p.M246L	ENST00000269305	NM_001126112.2	246	Atg/Ctg	7/11	1	2	FACETS	0.722	0.639	0.812	0.722	0.639	0.812	SUBCLONAL	1	TRUE	1	0.15	2		602	1699	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644880	67644881	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGGT	novel	NA	P-0001516-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1704	176	620	1	ENST00000264010.4:c.146_149dup	p.Val51GlyfsTer27	p.V51Gfs*27	ENST00000264010	NM_006565.3	49	gag/gAGGTag	3/12	0.194110375648951	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.15	1		621	1880	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0001545-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	91	305	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	0.363631204685546	4	FACETS	0.691	0.613	0.776	0.346	0.306	0.388	SUBCLONAL	1	TRUE	2	0.390767691371531	4		305	937	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0001726-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	35	505	0	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	0.412318241782333	3	FACETS	0.315	0.257	0.379	0.157	0.128	0.19	SUBCLONAL	1	FALSE	1	0.636437610228609	3		505	461	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0001726-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	379	685	1	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.636437610228609	7	FACETS	0.997	0.949	1			1	CLONAL	3	FALSE	NA	0.636437610228609	7		686	1032	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0001742-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	17	435	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.817	1	1	0.817	1	CLONAL	1	TRUE	1	0.443080034506253	2		436	71	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0001742-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	12	172	0	ENST00000257430.4:c.3919dup	p.Ile1307AsnfsTer8	p.I1307Nfs*8	ENST00000257430	NM_000038.5	1306	gaa/gAaa	16/16	0.163303955596608	3	FACETS	1	0.751	1	0.525	0.377	0.698	INDETERMINATE	1	TRUE	1	0.443080034506253	3		172	63	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0001761-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	137	660	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.58476369109649	1	FACETS	0.789	0.725	0.855	0.789	0.725	0.855	SUBCLONAL	1	FALSE	0	0.610574865279173	1		660	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0001761-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	120	723	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.610574865279173	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	0	0.610574865279173	1		723	258	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332368	70332368	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001761-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	94	538	0	ENST00000373644.4:c.273T>A	p.Phe91Leu	p.F91L	ENST00000373644	NM_030625.2	91	ttT/ttA	2/12	NA	2	FACETS	0.825	0.74	0.915			1	INDETERMINATE	1	FALSE	NA	0.610574865279173	2		538	373	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120403	70120404	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0001761-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	144	649	1	ENST00000245479.2:c.1406dup	p.Met469IlefsTer109	p.M469Ifs*109	ENST00000245479	NM_000346.3	469	atg/aTtg	3/3	0.610574865279173	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	0	0.610574865279173	1		650	266	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097680	27097680	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	174	302	0	ENST00000324856.7:c.3269G>T	p.Ser1090Ile	p.S1090I	ENST00000324856	NM_006015.4	1090	aGc/aTc	12/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		302	539	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551862	150551862	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1312773225	NA	P-0001782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	105	155	0	ENST00000369026.2:c.145G>C	p.Gly49Arg	p.G49R	ENST00000369026	NM_021960.4	49	Ggg/Cgg	1/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		155	446	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670358	134670358	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1449079060	NA	P-0001782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	102	278	0	ENST00000398015.3:c.269G>A	p.Arg90His	p.R90H	ENST00000398015	NM_004441.4	90	cGc/cAc	3/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		278	660	SUCCESS
ATR	545	MSKCC	GRCh37	3	142254044	142254044	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	16	215	0	ENST00000350721.4:c.3823A>G	p.Thr1275Ala	p.T1275A	ENST00000350721	NM_001184.3	1275	Acc/Gcc	21/47	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		215	239	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961055	55961055	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	109	360	0	ENST00000263923.4:c.2885G>C	p.Arg962Pro	p.R962P	ENST00000263923	NM_002253.2	962	cGc/cCc	21/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		360	644	SUCCESS
APC	324	MSKCC	GRCh37	5	112174845	112174845	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	111	296	0	ENST00000257430.4:c.3554C>A	p.Thr1185Lys	p.T1185K	ENST00000257430	NM_000038.5	1185	aCa/aAa	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		296	612	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970913	21970913	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	106	283	0	ENST00000304494.5:c.445G>T	p.Glu149Ter	p.E149*	ENST00000304494	NM_000077.4	149	Gaa/Taa	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		283	507	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209320	98209320	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs372558350	NA	P-0001782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	103	342	0	ENST00000331920.6:c.4218C>A	p.His1406Gln	p.H1406Q	ENST00000331920	NM_000264.3	1406	caC/caA	23/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		342	605	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98244319	98244319	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs768776930	NA	P-0001782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	132	263	0	ENST00000331920.6:c.658A>G	p.Ile220Val	p.I220V	ENST00000331920	NM_000264.3	220	Ata/Gta	5/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		263	473	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450142	32450142	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	88	257	0	ENST00000332351.3:c.670G>T	p.Gly224Trp	p.G224W	ENST00000332351	NM_024426.4	224	Ggg/Tgg	2/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		257	481	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138878	64138878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	72	209	2	ENST00000334205.4:c.2245G>A	p.Ala749Thr	p.A749T	ENST00000334205	NM_003942.2	749	Gcc/Acc	17/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		211	382	SUCCESS
EED	8726	MSKCC	GRCh37	11	85966292	85966292	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	83	367	0	ENST00000263360.6:c.389G>T	p.Gly130Val	p.G130V	ENST00000263360	NM_003797.3	130	gGa/gTa	4/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		367	893	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153464	108153464	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	162	308	4	ENST00000278616.4:c.3604G>T	p.Gly1202Ter	p.G1202*	ENST00000278616	NM_000051.3	1202	Gga/Tga	25/63	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		312	597	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779644	3779644	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	297	226	0	ENST00000262367.5:c.5404G>A	p.Val1802Met	p.V1802M	ENST00000262367	NM_004380.2	1802	Gtg/Atg	31/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		226	800	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66518916	66518916	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	94	275	0	ENST00000358598.2:c.197A>T	p.Gln66Leu	p.Q66L	ENST00000358598	NM_212471.2	66	cAg/cTg	3/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		275	770	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119932	70119932	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	171	196	0	ENST00000245479.2:c.934C>T	p.Gln312Ter	p.Q312*	ENST00000245479	NM_000346.3	312	Cag/Tag	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		196	587	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016030	31016030	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	200	306	0	ENST00000375687.4:c.352A>C	p.Thr118Pro	p.T118P	ENST00000375687	NM_015338.5	118	Act/Cct	5/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		306	688	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252869	36252869	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	110	298	0	ENST00000300305.3:c.493G>T	p.Gly165Cys	p.G165C	ENST00000300305		165	Ggt/Tgt	4/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		298	682	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259143	36259143	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	97	318	0	ENST00000300305.3:c.348C>G	p.Phe116Leu	p.F116L	ENST00000300305		116	ttC/ttG	3/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		318	592	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325400	1325400	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	151	325	0	ENST00000400841.2:c.275A>T	p.Asp92Val	p.D92V	ENST00000400841		92	gAc/gTc	3/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		325	610	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044557	47044557	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	196	325	0	ENST00000377604.3:c.2054G>T	p.Arg685Leu	p.R685L	ENST00000377604	NM_001204468.1	685	cGg/cTg	18/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		325	743	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352694	70352694	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0001782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	71	299	1	ENST00000374080.3:c.4416-1G>T		p.X1472_splice	ENST00000374080		1472			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		300	558	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138116	64138117	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0001782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	77	272	0	ENST00000334205.4:c.2040dup	p.Ser681LeufsTer123	p.S681Lfs*123	ENST00000334205	NM_003942.2	680	cgc/cgCc	16/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		272	494	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219367	1219368	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGACAGCGTGCC	novel	NA	P-0001782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	92	284	0	ENST00000326873.7:c.423_434dup	p.Asp141_Pro144dup	p.D141_P144dup	ENST00000326873	NM_000455.4	141	ctg/ctGGACAGCGTGCCg	3/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		284	540	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141498	11141499	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0001782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	165	329	0	ENST00000358026.2:c.3475_3476delinsTT	p.Gly1159Leu	p.G1159L	ENST00000358026	NM_001128849.1	1159	GGg/TTg	25/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		329	565	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956239	175956240	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0001782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	72	216	0	ENST00000367669.3:c.1973-1_1973delinsTT		p.X658_splice	ENST00000367669	NM_022457.5	658		18/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		216	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577499	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0001782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	123	208	0	ENST00000269305.4:c.782_782+1delinsTT		p.X261_splice	ENST00000269305	NM_001126112.2	261		7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		208	432	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0001791-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	65	442	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.13995958483528	3	FACETS	1	0.909	1	1	0.987	1	CLONAL	7	TRUE	1	0.191635800695659	3		444	106	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001791-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	14	372	1	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	0.191635800695659	5	FACETS	0.887	0.649	1	0.444	0.324	0.585	CLONAL	2	TRUE	1	0.191635800695659	5		373	106	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0001791-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	22	498	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	1	0.861	1	1	0.95	1	CLONAL	2	TRUE	1	0.191635800695659	2		498	102	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0001791-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	16	550	1	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	0.13995958483528	3	FACETS	0.915	0.686	1	0.915	0.686	1	CLONAL	2	TRUE	1	0.191635800695659	3		551	100	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001791-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	24	376	0	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	0.163453896186857	4	FACETS	0.939	0.75	1	1	0.925	1	CLONAL	3	TRUE	2	0.191635800695659	4		376	106	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0001791-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	48	824	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	1	0.866	1	1	0.98	1	CLONAL	3	TRUE	1	0.191635800695659	2		824	166	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001791-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	10	431	2	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	0.13995958483528	3	FACETS	0.922	0.628	1	0.461	0.314	0.644	CLONAL	1	TRUE	1	0.191635800695659	3		433	124	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589619	67589620	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0001791-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	83	640	0	ENST00000274335.5:c.1384_1385del	p.Glu462IlefsTer2	p.E462Ifs*2	ENST00000274335		461	cGA/c	10/15	0.191635800695659	23	FACETS	1	0.895	1			1	CLONAL	10	TRUE	NA	0.191635800695659	23		640	261	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100195	27100195	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001791-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	28	553	1	ENST00000324856.7:c.3991C>T	p.Gln1331Ter	p.Q1331*	ENST00000324856	NM_006015.4	1331	Cag/Tag	16/20	0.13995958483528	3	FACETS	0.998	0.815	1	1	0.943	1	CLONAL	3	TRUE	1	0.191635800695659	3		554	107	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65311207	65311207	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001791-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	11	713	0	ENST00000342505.4:c.2104C>G	p.Leu702Val	p.L702V	ENST00000342505	NM_002227.2	702	Ctg/Gtg	15/25	0.13995958483528	3	FACETS	1	0.838	1	0.684	0.478	0.933	CLONAL	1	TRUE	1	0.191635800695659	3		713	92	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001791-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	33	732	0	ENST00000397062.3:c.246A>T	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaT	2/5	0.191635800695659	5	FACETS	1	0.921	1	0.616	0.507	0.736	CLONAL	2	TRUE	1	0.191635800695659	5		732	180	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165464	47165464	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001791-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	30	898	0	ENST00000409792.3:c.662T>C	p.Val221Ala	p.V221A	ENST00000409792	NM_014159.6	221	gTt/gCt	3/21	1	2	FACETS	0.957	0.789	1	1	0.968	1	CLONAL	3	TRUE	1	0.191635800695659	2		898	109	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158064	106158064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1412331007	NA	P-0001791-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	20	804	1	ENST00000380013.4:c.2965C>T	p.Pro989Ser	p.P989S	ENST00000380013	NM_001127208.2	989	Cca/Tca	3/11	1	2	FACETS	0.859	0.673	1	1	0.95	1	CLONAL	3	TRUE	1	0.191635800695659	2		805	81	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158277	106158277	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001791-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	21	734	1	ENST00000380013.4:c.3178G>T	p.Gly1060Trp	p.G1060W	ENST00000380013	NM_001127208.2	1060	Ggg/Tgg	3/11	1	2	FACETS	1	0.808	1	1	0.945	1	CLONAL	2	TRUE	1	0.191635800695659	2		735	106	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629483	187629483	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs766981976	NA	P-0001791-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	25	803	1	ENST00000441802.2:c.1499A>G	p.Tyr500Cys	p.Y500C	ENST00000441802	NM_005245.3	500	tAc/tGc	2/27	0.191635800695659	1	FACETS	1	0.883	1	1	0.957	1	CLONAL	2	TRUE	0	0.191635800695659	1		804	103	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485885	8485885	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs139259906	NA	P-0001791-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	17	861	0	ENST00000356435.5:c.2932A>G	p.Thr978Ala	p.T978A	ENST00000356435		978	Act/Gct	17/35	1	2	FACETS	1	0.861	1	1	0.939	1	CLONAL	2	TRUE	1	0.191635800695659	2		861	74	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779084	135779084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769566267	NA	P-0001791-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	31	708	0	ENST00000298552.3:c.2162G>A	p.Arg721His	p.R721H	ENST00000298552	NM_001162426.1	721	cGc/cAc	17/23	1	2	FACETS	1	0.88	1	1	0.971	1	CLONAL	3	TRUE	1	0.191635800695659	2		708	100	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332109	70332109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777837034	NA	P-0001791-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	15	760	0	ENST00000373644.4:c.14G>A	p.Arg5His	p.R5H	ENST00000373644	NM_030625.2	5	cGc/cAc	2/12	0.191635800695659	4	FACETS	1	0.768	1	0.691	0.513	0.897	CLONAL	2	TRUE	1	0.191635800695659	4		760	90	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256679	19256679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1357520436	NA	P-0001791-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	22	430	0	ENST00000162023.5:c.1034G>A	p.Arg345Gln	p.R345Q	ENST00000162023		345	cGg/cAg	13/13	1	2	FACETS	1	0.806	1	1	0.947	1	CLONAL	2	TRUE	1	0.191635800695659	2		430	112	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31020781	31020781	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001791-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	15	443	0	ENST00000375687.4:c.1078G>T	p.Gly360Ter	p.G360*	ENST00000375687	NM_015338.5	360	Gga/Tga	11/13	1	2	FACETS	1	0.837	1	1	0.931	1	CLONAL	2	TRUE	1	0.191635800695659	2		443	67	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566522	41566522	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs200897987	NA	P-0001791-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	32	865	0	ENST00000263253.7:c.4399T>A	p.Tyr1467Asn	p.Y1467N	ENST00000263253	NM_001429.3	1467	Tac/Aac	27/31	1	2	FACETS	1	0.903	1	1	0.966	1	CLONAL	2	TRUE	1	0.191635800695659	2		865	145	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593247	67593247	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001791-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	79	741	0	ENST00000274335.5:c.1994del	p.Gly665AlafsTer3	p.G665Afs*3	ENST00000274335		665	Ggc/gc	15/15	0.191635800695659	23	FACETS	1	0.909	1			1	CLONAL	12	TRUE	NA	0.191635800695659	23		741	204	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711887	89711887	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776673	NA	P-0001791-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	23	710	0	ENST00000371953.3:c.507del	p.Ser170ValfsTer13	p.S170Vfs*13	ENST00000371953	NM_000314.4	169	Ccc/cc	6/9	0.191635800695659	4	FACETS	1	0.855	1	0.739	0.584	0.913	CLONAL	2	TRUE	1	0.191635800695659	4		710	129	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0001804-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	55	516	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.289531592439412	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.438528650017915	1		517	162	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373209	118373209	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001804-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	52	599	0	ENST00000534358.1:c.6602C>T	p.Ser2201Phe	p.S2201F	ENST00000534358	NM_005933.3	2201	tCt/tTt	27/36	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.438528650017915	2		599	209	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330486	65330487	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0001804-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	57	506	0	ENST00000342505.4:c.1159_1160insT	p.Gln387LeufsTer66	p.Q387Lfs*66	ENST00000342505	NM_002227.2	387	cag/cTag	8/25	0.393774732543816	3	FACETS	1	0.965	1	0.686	0.596	0.782	CLONAL	1	TRUE	1	0.438528650017915	3		506	231	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097199	11097200	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCCCT	rs372601826	NA	P-0001832-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	129	337	0	ENST00000358026.2:c.708_713dup	p.Gly243_Pro244dup	p.G243_P244dup	ENST00000358026	NM_001128849.1	243	-/GGCCCT	4/36	0.186637682256118	2	FACETS	0.944	0.862	1	0.472	0.431	0.515	INDETERMINATE	1	TRUE	0	0.594247772010636	2		337	460	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372758	81372758	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001832-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	191	510	0	ENST00000222390.5:c.776A>G	p.Tyr259Cys	p.Y259C	ENST00000222390	NM_000601.4	259	tAt/tGt	7/18	0.594247772010636	3	FACETS	1	0.988	1	0.438	0.406	0.47	CLONAL	1	TRUE	0	0.594247772010636	3		510	635	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0001832-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	2472	507	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.594247772010636	35	FACETS	0.986	0.973	0.999			1	CLONAL	26	TRUE	NA	0.594247772010636	35		507	3506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578414	7578414	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001832-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	287	390	0	ENST00000269305.4:c.516del	p.Val173Ter	p.V173*	ENST00000269305	NM_001126112.2	172	gtT/gt	5/11	0.533251455607816	3	FACETS	0.945	0.905	0.984	0.945	0.905	0.984	CLONAL	3	TRUE	0	0.594247772010636	3		390	442	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266092	41266092	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001910-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	349	534	0	ENST00000349496.5:c.89A>C	p.Tyr30Ser	p.Y30S	ENST00000349496	NM_001904.3	30	tAc/tCc	3/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.833033094726116	2		534	822	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519886	NA	P-0001910-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	353	544	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	0.833033094726116	2		544	845	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157735	106157735	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001910-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	320	484	0	ENST00000380013.4:c.2636T>A	p.Leu879His	p.L879H	ENST00000380013	NM_001127208.2	879	cTt/cAt	3/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.833033094726116	2		484	728	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114181	115114182	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGCTG	novel	NA	P-0001910-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	324	594	0	ENST00000257566.3:c.1031_1035dup	p.Phe346GlnfsTer17	p.F346Qfs*17	ENST00000257566	NM_016569.3	345	-/CAGCT	6/8	1	2	FACETS	0.776	0.734	0.818	0.776	0.734	0.818	SUBCLONAL	1	TRUE	1	0.833033094726116	2		594	1003	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517201	NA	P-0001967-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	183	306	0	ENST00000263967.3:c.1637A>C	p.Gln546Pro	p.Q546P	ENST00000263967	NM_006218.2	546	cAg/cCg	10/21	1	2	FACETS	0.998	0.933	1	0.998	0.933	1	CLONAL	1	TRUE	1	0.89	2		306	412	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2193780	2193780	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001967-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	200	339	0	ENST00000398665.3:c.586G>C	p.Glu196Gln	p.E196Q	ENST00000398665	NM_032482.2	196	Gag/Cag	6/28	0.3	2	FACETS	0.979	0.918	1			1	INDETERMINATE	1	TRUE	NA	0.89	2		339	459	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179184	123179184	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001967-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	344	467	0	ENST00000218089.9:c.633A>C	p.Gln211His	p.Q211H	ENST00000218089	NM_001042749.1	211	caA/caC	8/35	0.3	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.89	2		467	710	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856027	68856028	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0001967-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	252	515	0	ENST00000261769.5:c.1838dup	p.Asn613LysfsTer4	p.N613Kfs*4	ENST00000261769	NM_004360.3	612	ata/atAa	12/16	0.3	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.89	0		515	322	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022490	31022490	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001996-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	65	142	0	ENST00000375687.4:c.1975G>C	p.Gly659Arg	p.G659R	ENST00000375687	NM_015338.5	659	Ggt/Cgt	13/13	0.8341019695743	6	FACETS	0.682	0.591	0.78	0.114	0.098	0.13	SUBCLONAL	1	TRUE	0	0.8341019695743	6		142	610	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426635	212426640	+	frameshift_variant	Frame_Shift_Del	DEL	ATCTGG	ATCTGG	TA	novel	NA	P-0001996-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	31	380	0	ENST00000342788.4:c.2475_2480delinsTA	p.Gln826LysfsTer5	p.Q826Kfs*5	ENST00000342788	NM_005235.2	825	gtCCAGATa/gtTAa	20/28	0.8341019695743	3	FACETS	0.479	0.39	0.578	0.239	0.195	0.289	SUBCLONAL	1	TRUE	1	0.8341019695743	3		380	220	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426679	212426684	+	inframe_deletion	In_Frame_Del	DEL	CTTGTG	CTTGTG	-	novel	NA	P-0001996-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	33	342	0	ENST00000342788.4:c.2431_2436del	p.His811_Lys812del	p.H811_K812del	ENST00000342788	NM_005235.2	811	CACAAG/-	20/28	0.8341019695743	3	FACETS	0.438	0.358	0.527	0.219	0.179	0.264	SUBCLONAL	1	TRUE	1	0.8341019695743	3		342	256	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0001996-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	302	363	1	ENST00000269305.4:c.810dup	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	270	-/T	8/11	0.825323219762448	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.8341019695743	2		364	353	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665804	29665830	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TACAGCCACTTCTTAATAAGGTAATTA	TACAGCCACTTCTTAATAAGGTAATTA	-	novel	NA	P-0001996-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	49	360	0	ENST00000356175.3:c.6839_6858+7del		p.X2280_splice	ENST00000356175	NM_000267.3	2280		45/57	0.460013338207845	6	FACETS	1	0.945	1	0.413	0.353	0.478	INDETERMINATE	1	TRUE	3	0.8341019695743	6		360	253	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514570	41514571	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0001996-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	42	244	0	ENST00000373198.4:c.90_91del	p.Gly31LeufsTer4	p.G31Lfs*4	ENST00000373198	NM_133170.3	30	ggTGgc/gggc	2/32	0.8341019695743	6	FACETS	0.724	0.606	0.855	0.121	0.101	0.143	SUBCLONAL	1	TRUE	0	0.8341019695743	6		244	371	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0002000-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	62	371	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		371	693	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0002051-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	196	299	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	0.553140617016237	2		299	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0002051-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	294	703	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.553140617016237	2		704	766	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520006	NA	P-0002051-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	326	555	0	ENST00000269305.4:c.821T>C	p.Val274Ala	p.V274A	ENST00000269305	NM_001126112.2	274	gTt/gCt	8/11	1	2	FACETS	0.767	0.729	0.806	1	0.995	1	SUBCLONAL	2	TRUE	1	0.553140617016237	2		555	768	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938229	76938230	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002051-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	175	361	0	ENST00000373344.5:c.2518dup	p.Arg840LysfsTer9	p.R840Kfs*9	ENST00000373344	NM_000489.3	840	aga/aAga	9/35	1	1	FACETS	0.787	0.741	0.831	1	0.993	1	SUBCLONAL	2	TRUE	0	0.553140617016237	1		361	291	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0002054-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	289	474	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.517369533362066	4	FACETS	0.976	0.921	1	0.976	0.921	1	CLONAL	2	TRUE	2	0.516597699722659	4		474	869	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002054-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	55	372	1	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	NA	2	FACETS	0.995	0.863	1			1	INDETERMINATE	1	TRUE	NA	0.516597699722659	2		373	214	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0002054-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	161	237	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.516597699722659	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.516597699722659	2		237	278	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602354	10602354	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002054-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	88	480	0	ENST00000171111.5:c.1224del	p.Met409Ter	p.M409*	ENST00000171111	NM_203500.1	408	ccC/cc	3/6	0.517369533362066	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.516597699722659	1		480	194	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426680	212426680	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002054-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	214	514	2	ENST00000342788.4:c.2435A>T	p.Lys812Met	p.K812M	ENST00000342788	NM_005235.2	812	aAg/aTg	20/28	0.517369533362066	4	FACETS	0.942	0.88	1	0.942	0.88	1	CLONAL	2	TRUE	2	0.516597699722659	4		516	667	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801190	1801190	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002054-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	30	426	0	ENST00000260795.2:c.319T>A	p.Tyr107Asn	p.Y107N	ENST00000260795		107	Tac/Aac	2/17	NA	2	FACETS	0.759	0.62	0.913			1	INDETERMINATE	1	TRUE	NA	0.516597699722659	2		426	153	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268023	55268023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201830126	NA	P-0002054-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	97	433	0	ENST00000275493.2:c.2863G>A	p.Ala955Thr	p.A955T	ENST00000275493	NM_005228.3	955	Gca/Aca	24/28	1	2	FACETS	0.965	0.867	1	0.965	0.867	1	CLONAL	1	TRUE	1	0.516597699722659	2		433	389	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61213439	61213439	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002054-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	111	486	0	ENST00000301761.2:c.397G>T	p.Glu133Ter	p.E133*	ENST00000301761	NM_017841.2	133	Gaa/Taa	4/4	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.516597699722659	2		486	424	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346365	73346365	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002054-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	144	483	0	ENST00000377767.4:c.1435G>T	p.Asp479Tyr	p.D479Y	ENST00000377767	NM_014953.3	479	Gac/Tac	10/21	0.130105477311881	4	FACETS	1	0.987	1	0.729	0.668	0.793	INDETERMINATE	1	TRUE	2	0.516597699722659	4		483	580	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95598870	95598870	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1566815070	NA	P-0002054-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	122	508	0	ENST00000393063.1:c.289G>T	p.Val97Leu	p.V97L	ENST00000393063	NM_030621.3	97	Gtg/Ttg	4/28	1	2	FACETS	0.853	0.774	0.935	0.853	0.774	0.935	CLONAL	1	TRUE	1	0.516597699722659	2		508	554	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2113037	2113037	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002054-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	45	488	0	ENST00000219476.3:c.1426A>G	p.Asn476Asp	p.N476D	ENST00000219476	NM_000548.3	476	Aac/Gac	14/42	0.332152844724192	2	FACETS	0.65	0.55	0.759	0.325	0.275	0.38	SUBCLONAL	1	TRUE	0	0.516597699722659	2		488	268	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578514	7578514	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002054-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	88	438	0	ENST00000269305.4:c.416A>C	p.Lys139Thr	p.K139T	ENST00000269305	NM_001126112.2	139	aAg/aCg	5/11	0.363352141752438	4	FACETS	0.844	0.756	0.936	0.844	0.756	0.936	CLONAL	2	TRUE	2	0.516597699722659	4		438	306	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220701	1220701	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs730881976	NA	P-0002054-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	107	432	2	ENST00000326873.7:c.719C>A	p.Ser240Ter	p.S240*	ENST00000326873	NM_000455.4	240	tCg/tAg	5/10	0.517369533362066	1	FACETS	0.858	0.795	0.92	1	0.989	1	CLONAL	2	TRUE	0	0.516597699722659	1		434	179	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134239	11134239	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002054-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	92	476	0	ENST00000358026.2:c.2905C>A	p.His969Asn	p.H969N	ENST00000358026	NM_001128849.1	969	Cac/Aac	20/36	0.517369533362066	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.516597699722659	1		476	215	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40742002	40742002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002054-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	200	397	0	ENST00000392038.2:c.970G>A	p.Asp324Asn	p.D324N	ENST00000392038	NM_001626.4	324	Gac/Aac	11/14	0.517369533362066	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	4	TRUE	0	0.516597699722659	4		397	275	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560805	9560805	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002054-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	142	380	0	ENST00000353224.5:c.977T>A	p.Met326Lys	p.M326K	ENST00000353224	NM_177990.2	326	aTg/aAg	4/10	0.393718389409913	3	FACETS	0.885	0.815	0.956	0.885	0.815	0.956	CLONAL	2	TRUE	1	0.516597699722659	3		380	391	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121015	29121015	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002054-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	131	562	0	ENST00000328354.6:c.542G>T	p.Arg181Leu	p.R181L	ENST00000328354	NM_007194.3	181	cGt/cTt	4/15	0.210935046700351	1	FACETS	0.811	0.741	0.883	0.811	0.741	0.883	INDETERMINATE	1	TRUE	0	0.516597699722659	1		562	464	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650822	48650822	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002054-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	69	576	0	ENST00000376670.3:c.691T>C	p.Tyr231His	p.Y231H	ENST00000376670	NM_002049.3	231	Tat/Cat	4/6	0.154574217014628	0	FACETS	0.557	0.492	0.625			1	INDETERMINATE	1	TRUE	0	0.516597699722659	0		576	232	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652531	48652531	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002054-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	33	368	0	ENST00000376670.3:c.1202C>G	p.Pro401Arg	p.P401R	ENST00000376670	NM_002049.3	401	cCc/cGc	6/6	0.154574217014628	0	FACETS	0.381	0.314	0.454			1	INDETERMINATE	1	TRUE	0	0.516597699722659	0		368	162	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543861	212543862	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0002054-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	286	436	0	ENST00000342788.4:c.1537dup	p.Trp513LeufsTer16	p.W513Lfs*16	ENST00000342788	NM_005235.2	513	tgg/tTgg	13/28	0.517369533362066	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.516597699722659	4		436	734	SUCCESS
ATM	472	MSKCC	GRCh37	11	108154976	108154976	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002054-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	80	274	0	ENST00000278616.4:c.3770del	p.Pro1257HisfsTer4	p.P1257Hfs*4	ENST00000278616	NM_000051.3	1257	Cca/ca	26/63	1	2	FACETS	0.919	0.816	1	0.919	0.816	1	CLONAL	1	TRUE	1	0.516597699722659	2		274	337	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881001	37881002	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGCTCCCC	rs397516981	NA	P-0002088-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	580	673	0	ENST00000269571.5:c.2331_2339dup	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	gtg/gtGGGCTCCCCg	20/27	0.294196732296327	6	FACETS	1	0.993	1			1	INDETERMINATE	3	TRUE	NA	0.801766575149962	6		673	1141	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446269	187446270	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770320988	NA	P-0002088-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	183	269	0	ENST00000232014.4:c.1418dup	p.Lys474GlufsTer26	p.K474Efs*26	ENST00000232014	NM_001130845.1	473	ccg/ccCg	6/10	1	2	FACETS	0.892	0.83	0.955	0.892	0.83	0.955	CLONAL	1	TRUE	1	0.801766575149962	2		269	512	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423449	116423453	+	frameshift_variant	Frame_Shift_Del	DEL	GGTGC	GGTGC	-	novel	NA	P-0002088-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	297	427	0	ENST00000397752.3:c.3724_3728del	p.Gly1242LysfsTer43	p.G1242Kfs*43	ENST00000397752	NM_000245.2	1242	GGTGCa/a	19/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.801766575149962	2		427	711	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109946	115109946	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002088-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	159	223	0	ENST00000257566.3:c.1932del	p.Ile645SerfsTer244	p.I645Sfs*244	ENST00000257566	NM_016569.3	644	tcC/tc	8/8	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.801766575149962	2		223	377	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002144-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	67	619	0	ENST00000418115.1:c.50G>T	p.Gly17Val	p.G17V	ENST00000418115	NM_001664.2	17	gGa/gTa	2/5	1	2	FACETS	0.594	0.515	0.679	0.594	0.515	0.679	SUBCLONAL	1	TRUE	1	0.3	2		619	752	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835780	68835781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0002144-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	46	477	1	ENST00000261769.5:c.377dup	p.Pro127AlafsTer41	p.P127Afs*41	ENST00000261769	NM_004360.3	124	cgc/cgCc	3/16	0.3	1	FACETS	0.453	0.38	0.532	0.453	0.38	0.532	SUBCLONAL	1	TRUE	0	0.3	1		478	576	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25458649	25458649	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1015295548	NA	P-0002144-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	80	519	0	ENST00000264709.3:c.2524C>T	p.Gln842Ter	p.Q842*	ENST00000264709	NM_175629.2	842	Cag/Tag	22/23	1	2	FACETS	0.704	0.619	0.795	0.704	0.619	0.795	SUBCLONAL	1	TRUE	1	0.3	2		519	758	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936059	44936068	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTAGTATT	ACCTAGTATT	-	novel	NA	P-0002144-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	95	581	0	ENST00000377967.4:c.2820_2829del	p.Pro941ThrfsTer26	p.P941Tfs*26	ENST00000377967	NM_021140.2	940	acACCTAGTATT/ac	18/29	1	2	FACETS	0.742	0.659	0.829	0.742	0.659	0.829	SUBCLONAL	1	TRUE	1	0.3	2		581	854	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0002222-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	336	211	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.555459530585328	3	FACETS	1	0.992	1			1	CLONAL	3	TRUE	NA	0.746802533923982	3		211	393	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849929	156849929	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002222-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	285	631	0	ENST00000524377.1:c.2185T>C	p.Tyr729His	p.Y729H	ENST00000524377	NM_002529.3	729	Tac/Cac	16/17	0.656757446883518	4	FACETS	0.974	0.914	1	0.325	0.304	0.346	CLONAL	1	TRUE	1	0.746802533923982	4		631	1369	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2972202	2972202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002222-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	227	496	0	ENST00000396946.4:c.1537C>T	p.Pro513Ser	p.P513S	ENST00000396946	NM_032415.4	513	Ccc/Tcc	11/25	1	2	FACETS	0.941	0.882	1	0.941	0.882	1	CLONAL	1	TRUE	1	0.746802533923982	2		496	646	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426093	49426094	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0002222-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	373	473	0	ENST00000301067.7:c.12393_12394dup	p.His4132ProfsTer11	p.H4132Pfs*11	ENST00000301067	NM_003482.3	4132	cac/cCCac	39/54	0.746802533923982	3	FACETS	0.855	0.817	0.894	0.855	0.817	0.894	CLONAL	2	TRUE	1	0.746802533923982	3		473	802	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0002235-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	250	379	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.299551501288115	4	FACETS	1	0.983	1	0.748	0.703	0.793	CLONAL	2	FALSE	1	0.458564922002648	4		379	709	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0002235-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	32	302	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.272375732780814	3	FACETS	0.386	0.313	0.469	0.129	0.104	0.157	INDETERMINATE	1	FALSE	0	0.458564922002648	3		302	444	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188164	11188164	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587777893	NA	P-0002235-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	89	386	0	ENST00000361445.4:c.5930C>A	p.Thr1977Lys	p.T1977K	ENST00000361445	NM_004958.3	1977	aCa/aAa	43/58	0.458564922002648	3	FACETS	0.603	0.534	0.677	0.302	0.267	0.339	SUBCLONAL	1	FALSE	1	0.458564922002648	3		386	791	SUCCESS
APC	324	MSKCC	GRCh37	5	112174144	112174144	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0002235-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	234	501	0	ENST00000257430.4:c.2853T>A	p.Tyr951Ter	p.Y951*	ENST00000257430	NM_000038.5	951	taT/taA	16/16	0.272375732780814	3	FACETS	1	0.984	1	0.748	0.704	0.793	INDETERMINATE	2	FALSE	0	0.458564922002648	3		501	559	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0002268-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	80	660	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.443250738302028	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.443250738302028	1		660	243	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0002268-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	48	263	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.304685476539706	1	FACETS	0.826	0.707	0.954	0.826	0.707	0.954	CLONAL	1	TRUE	0	0.443250738302028	1		263	204	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547958	41547958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774408703	NA	P-0002268-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	64	500	0	ENST00000263253.7:c.2939C>T	p.Ala980Val	p.A980V	ENST00000263253	NM_001429.3	980	gCc/gTc	15/31	NA	2	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.443250738302028	2		500	234	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173695	108173696	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1555106508	NA	P-0002268-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	42	484	0	ENST00000278616.4:c.5441dup	p.Leu1814PhefsTer9	p.L1814Ffs*9	ENST00000278616	NM_000051.3	1812	gct/gcTt	36/63	0.443250738302028	1	FACETS	0.776	0.656	0.906	0.776	0.656	0.906	CLONAL	1	TRUE	0	0.443250738302028	1		484	190	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119730	70119731	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0002268-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	115	595	0	ENST00000245479.2:c.733dup	p.Val245GlyfsTer7	p.V245Gfs*7	ENST00000245479	NM_000346.3	244	-/G	3/3	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.443250738302028	2		595	443	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597438	10597439	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002272-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	43	549	0	ENST00000171111.5:c.1764dup	p.Asp589ArgfsTer30	p.D589Rfs*30	ENST00000171111	NM_203500.1	588	-/A	6/6	0.253244380883816	1	FACETS	0.118	0.098	0.14	0.118	0.098	0.14	INDETERMINATE	1	TRUE	0	0.746030476141084	1		549	611	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0002281-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	67	567	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.92	0.8	1	0.92	0.8	1	CLONAL	1	TRUE	1	0.227856042167631	2		567	639	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097304	178097304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763097686	NA	P-0002281-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	57	436	0	ENST00000397062.3:c.410C>T	p.Ser137Leu	p.S137L	ENST00000397062	NM_006164.4	137	tCg/tTg	4/5	1	2	FACETS	0.903	0.775	1	0.903	0.775	1	CLONAL	1	TRUE	1	0.227856042167631	2		436	554	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247846	59247847	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002281-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	100	775	0	ENST00000371222.2:c.896dup	p.Asn299LysfsTer11	p.N299Kfs*11	ENST00000371222	NM_002228.3	299	aac/aaAc	1/1	0.227856042167631	4	FACETS	1	0.962	1			1	CLONAL	1	TRUE	NA	0.227856042167631	4		775	916	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063316	67063338	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCGTCGTGCCCGACCAGAGAA	GCGCGTCGTGCCCGACCAGAGAA	-	novel	NA	P-0002281-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	25	246	0	ENST00000412916.2:c.8_30del	p.Arg3GlnfsTer9	p.R3Qfs*9	ENST00000412916		2	ccGCGCGTCGTGCCCGACCAGAGAAgc/ccgc	1/6	0.227856042167631	1	FACETS	0.685	0.541	0.849	0.685	0.541	0.849	SUBCLONAL	1	TRUE	0	0.227856042167631	1		246	284	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202269	138202269	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002299-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	372	303	0	ENST00000237289.4:c.2186G>A	p.Ser729Asn	p.S729N	ENST00000237289	NM_001270507.1	729	aGc/aAc	9/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.502574825422593	NA		303	1043	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980426	7980426	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759484732	NA	P-0002299-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	156	329	0	ENST00000319144.4:c.1157G>A	p.Arg386His	p.R386H	ENST00000319144	NM_001139.2	386	cGc/cAc	9/15	0.231228021408957	3	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.502574825422593	3		329	625	SUCCESS
AR	367	MSKCC	GRCh37	X	66943583	66943583	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002299-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	120	473	0	ENST00000374690.3:c.2663T>A	p.Val888Glu	p.V888E	ENST00000374690	NM_000044.3	888	gTg/gAg	8/8	0.51078051186276	3	FACETS	0.785	0.709	0.865	0.393	0.354	0.433	SUBCLONAL	1	TRUE	1	0.502574825422593	3		473	761	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441202	52441203	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	GTAGACCTTCAGCCCATCCA	novel	NA	P-0002299-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	497	287	0	ENST00000460680.1:c.548_567dup	p.Pro190TrpfsTer4	p.P190Wfs*4	ENST00000460680	NM_004656.3	189	-/TGGATGGGCTGAAGGTCTAC	7/17	0.51078051186276	4	FACETS	1	0.967	1	0.754	0.725	0.782	CLONAL	3	TRUE	0	0.502574825422593	4		287	986	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15975536	15975536	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002316-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	181	367	0	ENST00000268712.3:c.3818T>A	p.Ile1273Lys	p.I1273K	ENST00000268712	NM_006311.3	1273	aTa/aAa	29/46	0.803672742430389	1	FACETS	0.92	0.869	0.969	0.92	0.869	0.969	CLONAL	1	TRUE	0	0.803672742430389	1		367	293	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906548	32906548	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002316-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	210	407	1	ENST00000380152.3:c.937del	p.Ser313LeufsTer11	p.S313Lfs*11	ENST00000380152		311	tgT/tg	10/27	NA	2	FACETS	1	0.945	1			1	INDETERMINATE	1	TRUE	NA	0.803672742430389	2		408	518	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974897	15974928	+	frameshift_variant	Frame_Shift_Del	DEL	TCGTATGGGAGGACTTTCCCTTTTAATTTGTT	TCGTATGGGAGGACTTTCCCTTTTAATTTGTT	-	novel	NA	P-0002316-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	255	450	0	ENST00000268712.3:c.3947_3978del	p.Lys1316SerfsTer3	p.K1316Sfs*3	ENST00000268712	NM_006311.3	1316	aAACAAATTAAAAGGGAAAGTCCTCCCATACGA/a	30/46	0.803672742430389	1	FACETS	0.908	0.865	0.95	0.908	0.865	0.95	CLONAL	1	TRUE	0	0.803672742430389	1		450	418	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939262	76939263	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTTCTTATG	novel	NA	P-0002316-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	175	292	0	ENST00000373344.5:c.1477_1485dup	p.His493_Lys495dup	p.H493_K495dup	ENST00000373344	NM_000489.3	493	-/CATAAGAAA	9/35	1	1	FACETS	0.824	0.775	0.874	0.824	0.775	0.874	CLONAL	1	TRUE	0	0.803672742430389	1		292	316	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939711	76939723	+	frameshift_variant	Frame_Shift_Del	DEL	AGTGCGGAATAAG	AGTGCGGAATAAG	-	novel	NA	P-0002316-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	266	317	0	ENST00000373344.5:c.1025_1037del	p.Ser342Ter	p.S342*	ENST00000373344	NM_000489.3	342	tCTTATTCCGCACTa/ta	9/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.803672742430389	1		317	333	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42842637	42842638	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0002316-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	453	438	0	ENST00000398585.3:c.1219_1220delinsTT	p.Gly407Phe	p.G407F	ENST00000398585	NM_001135099.1	407	GGc/TTc	11/14	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.803672742430389	2		438	1118	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0002390-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	549	305	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	0.456414049163807	6	FACETS	0.967	0.929	1	0.967	0.929	1	CLONAL	3	FALSE	3	0.609247887469721	6		305	1378	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0002487-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	167	208	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	TRUE	1	0.597711900259937	2		208	525	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458424	120458424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002487-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	79	190	0	ENST00000256646.2:c.6921C>A	p.Phe2307Leu	p.F2307L	ENST00000256646	NM_024408.3	2307	ttC/ttA	34/34	1	2	FACETS	0.947	0.843	1	0.947	0.843	1	CLONAL	1	TRUE	1	0.597711900259937	2		190	279	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553426	106553426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002487-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	150	228	0	ENST00000369096.4:c.1391C>T	p.Thr464Ile	p.T464I	ENST00000369096	NM_001198.3	464	aCt/aTt	5/7	0.477513442305864	3	FACETS	0.858	0.794	0.923	0.858	0.794	0.923	CLONAL	2	TRUE	1	0.597711900259937	3		228	380	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273940	10273940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002487-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	114	326	0	ENST00000330684.3:c.329C>T	p.Ala110Val	p.A110V	ENST00000330684	NM_001134407.1	110	gCc/gTc	2/13	0.597711900259937	2	FACETS	0.908	0.824	0.996	0.454	0.412	0.498	CLONAL	1	TRUE	0	0.597711900259937	2		326	420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578535	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002487-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	239	280	0	ENST00000269305.4:c.395dup	p.Met133AspfsTer16	p.M133Dfs*16	ENST00000269305	NM_001126112.2	132	aag/aaAg	5/11	0.597711900259937	2	FACETS	0.987	0.938	1	0.987	0.938	1	CLONAL	2	TRUE	0	0.597711900259937	2		280	405	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448331	56448339	+	frameshift_variant	Frame_Shift_Del	DEL	TGCTGATGA	TGCTGATGA	C	novel	NA	P-0002487-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	250	228	0	ENST00000407977.2:c.308_316delinsG	p.Phe103CysfsTer19	p.F103Cfs*19	ENST00000407977		103	tTCATCAGCAtc/tGtc	3/10	0.597711900259937	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.597711900259937	2		228	397	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453132	140453132	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913365	NA	P-0002545-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	115	400	0	ENST00000288602.6:c.1803A>T	p.Lys601Asn	p.K601N	ENST00000288602	NM_004333.4	601	aaA/aaT	15/18	1	2	FACETS	0.71	0.644	0.78	0.71	0.644	0.78	SUBCLONAL	1	TRUE	1	0.70383271597816	2		400	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574002	7574003	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0002545-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	188	507	0	ENST00000269305.4:c.1024_1025insTA	p.Arg342LeufsTer4	p.R342Lfs*4	ENST00000269305	NM_001126112.2	342	cga/cTAga	10/11	0.669815673819916	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.70383271597816	1		507	338	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248629	10248629	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002545-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	84	337	0	ENST00000340748.4:c.4124del	p.Pro1375ArgfsTer43	p.P1375Rfs*43	ENST00000340748		1375	cCg/cg	35/40	1	2	FACETS	0.562	0.498	0.629	0.562	0.498	0.629	SUBCLONAL	1	TRUE	1	0.70383271597816	2		337	425	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0002562-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	150	673	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.615257471217293	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.615257471217293	3		673	269	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519925	NA	P-0002562-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	206	247	0	ENST00000263967.3:c.1357G>C	p.Glu453Gln	p.E453Q	ENST00000263967	NM_006218.2	453	Gaa/Caa	8/21	0.615257471217293	3	FACETS	0.982	0.922	1	0.982	0.922	1	CLONAL	2	TRUE	1	0.615257471217293	3		247	446	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0002562-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	301	461	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.615257471217293	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.615257471217293	2		461	441	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161221	56161221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781300314	NA	P-0002562-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	150	348	1	ENST00000399503.3:c.1090C>T	p.Arg364Trp	p.R364W	ENST00000399503	NM_005921.1	364	Cgg/Tgg	5/20	0.285812866558825	5	FACETS	1	0.937	1	0.679	0.626	0.734	INDETERMINATE	2	TRUE	2	0.615257471217293	5		349	460	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829321	128829321	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs945428238	NA	P-0002562-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	86	153	0	ENST00000249373.3:c.329C>T	p.Ser110Leu	p.S110L	ENST00000249373	NM_005631.4	110	tCg/tTg	1/12	0.285812866558825	5	FACETS	1	0.968	1	0.793	0.714	0.873	INDETERMINATE	2	TRUE	2	0.615257471217293	5		153	226	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879670	151879670	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002562-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	94	114	1	ENST00000262189.6:c.5275C>T	p.Gln1759Ter	p.Q1759*	ENST00000262189	NM_170606.2	1759	Cag/Tag	36/59	0.422913607743812	4	FACETS	0.953	0.861	1	0.953	0.861	1	CLONAL	2	TRUE	2	0.615257471217293	4		115	259	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007799	45007799	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002562-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	85	231	0	ENST00000558401.1:c.246C>G	p.Phe82Leu	p.F82L	ENST00000558401	NM_004048.2	82	ttC/ttG	2/4	1	2	FACETS	0.953	0.852	1	0.953	0.852	1	CLONAL	1	TRUE	1	0.615257471217293	2		231	290	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645516	67645516	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002562-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	37	94	0	ENST00000264010.4:c.781G>A	p.Gly261Ser	p.G261S	ENST00000264010	NM_006565.3	261	Ggt/Agt	3/12	NA	2	FACETS	0.986	0.831	1			1	INDETERMINATE	1	TRUE	NA	0.615257471217293	2		94	122	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256794	16256795	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0002562-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	118	264	0	ENST00000375759.3:c.4060_4061del	p.Ser1354PhefsTer7	p.S1354Ffs*7	ENST00000375759	NM_015001.2	1353	gtGAgt/gtgt	11/15	0.615257471217293	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.615257471217293	1		264	227	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971199	21971200	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	ATCA	novel	NA	P-0002562-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	44	75	0	ENST00000579755.1:c.198_201dup	p.Asp68Ter	p.D68*	ENST00000579755		67	-/TGAT	2/3	0.615257471217293	2	FACETS	0.777	0.678	0.877	0.777	0.678	0.877	SUBCLONAL	2	TRUE	0	0.615257471217293	2		75	92	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061530	38061556	+	inframe_deletion	In_Frame_Del	DEL	CGCGCGGCTGCGGCCCAGGTTGGACGG	CGCGCGGCTGCGGCCCAGGTTGGACGG	-	novel	NA	P-0002562-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	36	95	0	ENST00000250448.2:c.433_459del	p.Pro145_Ala153del	p.P145_A153del	ENST00000250448	NM_004496.3	145	CCGTCCAACCTGGGCCGCAGCCGCGCG/-	2/2	0.615257471217293	3	FACETS	1	0.894	1			1	CLONAL	1	TRUE	NA	0.615257471217293	3		95	140	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788618	3788625	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGGCAA	GGAGGCAA	-	novel	NA	P-0002562-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	98	325	0	ENST00000262367.5:c.4329_4336del	p.Cys1444HisfsTer6	p.C1444Hfs*6	ENST00000262367	NM_004380.2	1443	cgTTGCCTCCgc/cggc	26/31	0.336457624346773	4	FACETS	1	0.973	1	0.631	0.566	0.698	INDETERMINATE	1	TRUE	2	0.615257471217293	4		325	408	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0002605-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	249	266	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.322523360646535	3	FACETS	0.777	0.727	0.829			1	SUBCLONAL	2	TRUE	NA	0.370205775742973	3		266	1026	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643972	52643972	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0002605-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	62	149	0	ENST00000394830.3:c.1925-1G>T		p.X642_splice	ENST00000394830	NM_018313.4	642			0.270535685493478	1	FACETS	0.78	0.677	0.89	0.78	0.677	0.89	SUBCLONAL	1	TRUE	0	0.370205775742973	1		149	350	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498521	89498521	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002605-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	88	207	0	ENST00000336596.2:c.2493G>T	p.Gln831His	p.Q831H	ENST00000336596	NM_005233.5	831	caG/caT	14/17	1	2	FACETS	0.861	0.765	0.964	0.861	0.765	0.964	CLONAL	1	TRUE	1	0.370205775742973	2		207	552	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217279	66217279	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002605-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	29	204	0	ENST00000273854.3:c.2336G>T	p.Gly779Val	p.G779V	ENST00000273854	NM_004439.5	779	gGc/gTc	14/18	0.270535685493478	1	FACETS	0.264	0.211	0.325	0.264	0.211	0.325	SUBCLONAL	1	TRUE	0	0.370205775742973	1		204	483	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542579	187542579	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs770944934	NA	P-0002605-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	76	317	0	ENST00000441802.2:c.5161A>C	p.Thr1721Pro	p.T1721P	ENST00000441802	NM_005245.3	1721	Act/Cct	10/27	0.270535685493478	1	FACETS	0.398	0.348	0.452	0.398	0.348	0.452	SUBCLONAL	1	TRUE	0	0.370205775742973	1		317	840	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588233	69588233	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002605-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	686	326	0	ENST00000168712.1:c.465C>A	p.Cys155Ter	p.C155*	ENST00000168712	NM_002007.2	155	tgC/tgA	3/3	0.370205775742973	5	FACETS	0.969	0.94	0.997			1	CLONAL	5	TRUE	NA	0.370205775742973	5		326	1190	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578242	7578242	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882003	NA	P-0002605-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	153	326	0	ENST00000269305.4:c.607G>T	p.Val203Leu	p.V203L	ENST00000269305	NM_001126112.2	203	Gtg/Ttg	6/11	0.350015592842885	1	FACETS	0.951	0.872	1	0.951	0.872	1	CLONAL	1	TRUE	0	0.370205775742973	1		326	708	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560019	29560019	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0002605-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	132	245	0	ENST00000356175.3:c.3497-1G>T		p.X1166_splice	ENST00000356175	NM_000267.3	1166			1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.370205775742973	2		245	644	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597401	10597401	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002605-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	129	358	0	ENST00000171111.5:c.1802G>T	p.Arg601Leu	p.R601L	ENST00000171111	NM_203500.1	601	cGg/cTg	6/6	0.370205775742973	1	FACETS	0.92	0.837	1	0.92	0.837	1	CLONAL	1	TRUE	0	0.370205775742973	1		358	617	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099447	157099448	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAACAGCAACATCCCATTT	novel	NA	P-0002605-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	18	83	0	ENST00000346085.5:c.386_404dup	p.Asn136ThrfsTer102	p.N136Tfs*102	ENST00000346085	NM_020732.3	128	-/CAACAGCAACATCCCATTT	1/20	0.370205775742973	1	FACETS	0.343	0.259	0.442	0.343	0.259	0.442	SUBCLONAL	1	TRUE	0	0.370205775742973	1		83	231	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0002614-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	121	221	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		221	479	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241678	55241678	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517085	NA	P-0002614-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	138	250	0	ENST00000275493.2:c.2126A>C	p.Glu709Ala	p.E709A	ENST00000275493	NM_005228.3	709	gAa/gCa	18/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		250	548	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896419	28896419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002614-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	103	254	0	ENST00000282397.4:c.3031G>A	p.Glu1011Lys	p.E1011K	ENST00000282397	NM_002019.4	1011	Gag/Aag	22/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		254	451	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652097	36652098	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0002614-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	22	515	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		515	305	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262026	16262026	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs970852367	NA	P-0002672-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	112	170	0	ENST00000375759.3:c.9291G>T	p.Glu3097Asp	p.E3097D	ENST00000375759	NM_015001.2	3097	gaG/gaT	11/15	1	2	FACETS	0.912	0.829	0.997	0.912	0.829	0.997	CLONAL	1	TRUE	1	0.705688774992705	2		170	348	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165515	47165515	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0002672-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	303	334	0	ENST00000409792.3:c.611C>G	p.Ser204Ter	p.S204*	ENST00000409792	NM_014159.6	204	tCa/tGa	3/21	1	2	FACETS	0.994	0.94	1	0.994	0.94	1	CLONAL	1	TRUE	1	0.705688774992705	2		334	864	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565874	55565874	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002672-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	224	301	1	ENST00000288135.5:c.698G>C	p.Cys233Ser	p.C233S	ENST00000288135	NM_000222.2	233	tGc/tCc	4/21	1	2	FACETS	0.917	0.858	0.978	0.917	0.858	0.978	CLONAL	1	TRUE	1	0.705688774992705	2		302	692	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755637	57755637	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002672-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	228	304	0	ENST00000274289.3:c.150A>C	p.Gln50His	p.Q50H	ENST00000274289	NM_006622.3	50	caA/caC	1/14	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.705688774992705	2		304	631	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846084	151846084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752636504	NA	P-0002672-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	56	286	0	ENST00000262189.6:c.12928C>T	p.Pro4310Ser	p.P4310S	ENST00000262189	NM_170606.2	4310	Cct/Tct	52/59	1	2	FACETS	0.268	0.229	0.31	0.268	0.229	0.31	SUBCLONAL	1	TRUE	1	0.705688774992705	2		286	593	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692829	89692829	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002672-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	44	77	0	ENST00000371953.3:c.313T>A	p.Cys105Ser	p.C105S	ENST00000371953	NM_000314.4	105	Tgt/Agt	5/9	0.705688774992705	1	FACETS	0.589	0.505	0.678	0.589	0.505	0.678	SUBCLONAL	1	TRUE	0	0.705688774992705	1		77	137	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741886	17741886	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002672-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	27	33	0	ENST00000250003.3:c.557C>A	p.Pro186Gln	p.P186Q	ENST00000250003	NM_002478.4	186	cCg/cAg	1/3	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.705688774992705	2		33	66	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435528	18435528	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002672-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	148	293	0	ENST00000266497.5:c.513T>G	p.Phe171Leu	p.F171L	ENST00000266497		171	ttT/ttG	1/31	0.26062900377277	1	FACETS	0.54	0.496	0.585	0.54	0.496	0.585	INDETERMINATE	1	TRUE	0	0.705688774992705	1		293	503	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881438	48881438	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002672-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	178	213	0	ENST00000267163.4:c.160G>T	p.Glu54Ter	p.E54*	ENST00000267163	NM_000321.2	54	Gaa/Taa	2/27	0.705688774992705	1	FACETS	0.873	0.817	0.929	0.873	0.817	0.929	CLONAL	1	TRUE	0	0.705688774992705	1		213	374	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823858	3823858	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002672-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	309	323	0	ENST00000262367.5:c.2357A>C	p.Gln786Pro	p.Q786P	ENST00000262367	NM_004380.2	786	cAg/cCg	13/31	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.705688774992705	2		323	801	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348804	11348804	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002672-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	64	83	0	ENST00000332029.2:c.532T>C	p.Cys178Arg	p.C178R	ENST00000332029	NM_003745.1	178	Tgc/Cgc	2/2	1	2	FACETS	0.93	0.82	1	0.93	0.82	1	CLONAL	1	TRUE	1	0.705688774992705	2		83	195	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490246	29490246	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0002672-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	240	296	0	ENST00000356175.3:c.331A>T	p.Lys111Ter	p.K111*	ENST00000356175	NM_000267.3	111	Aaa/Taa	4/57	1	2	FACETS	0.878	0.822	0.934	0.878	0.822	0.934	CLONAL	1	TRUE	1	0.705688774992705	2		296	775	SUCCESS
YES1	7525	MSKCC	GRCh37	18	739767	739767	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0002672-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	94	420	0	ENST00000314574.4:c.1105A>T	p.Lys369Ter	p.K369*	ENST00000314574	NM_005433.3	369	Aag/Tag	9/12	1	2	FACETS	0.299	0.265	0.335	0.299	0.265	0.335	SUBCLONAL	1	TRUE	1	0.705688774992705	2		420	892	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855003	76855003	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002672-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	309	233	0	ENST00000373344.5:c.5833G>C	p.Gly1945Arg	p.G1945R	ENST00000373344	NM_000489.3	1945	Gga/Cga	25/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.705688774992705	1		233	456	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593591	55593596	+	inframe_deletion	In_Frame_Del	DEL	TATGAA	TATGAA	-	novel	NA	P-0002672-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	270	355	0	ENST00000288135.5:c.1657_1662del	p.Tyr553_Glu554del	p.Y553_E554del	ENST00000288135	NM_000222.2	553	TATGAA/-	11/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.705688774992705	2		355	708	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574009	7574010	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0002672-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	593	386	1	ENST00000269305.4:c.1017dup	p.Met340AspfsTer7	p.M340Dfs*7	ENST00000269305	NM_001126112.2	339	-/G	10/11	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	2	TRUE	NA	0.705688774992705	2		387	826	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958549	175958549	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1271141729	NA	P-0002692-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	44	351	0	ENST00000367669.3:c.1796G>A	p.Arg599His	p.R599H	ENST00000367669	NM_022457.5	599	cGt/cAt	16/20	1	2	FACETS	0.5	0.419	0.589	0.5	0.419	0.589	SUBCLONAL	1	TRUE	1	0.333648783466487	2		351	528	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18439830	18439830	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs186647102	NA	P-0002692-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	76	301	0	ENST00000266497.5:c.728C>T	p.Thr243Met	p.T243M	ENST00000266497		243	aCg/aTg	2/31	0.306816362339166	4	FACETS	0.972	0.853	1	0.324	0.284	0.367	CLONAL	1	TRUE	1	0.333648783466487	4		301	625	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577567	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1567549651	NA	P-0002692-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	130	250	0	ENST00000269305.4:c.714dup	p.Asn239Ter	p.N239*	ENST00000269305	NM_001126112.2	238	-/T	7/11	0.333648783466487	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.333648783466487	1		250	479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0002710-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	23	379	0	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.260138373447475	0	FACETS	0.226	0.178	0.279			1	INDETERMINATE	1	TRUE	0	0.603450306152876	0		379	134	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0002710-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	23	505	0	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	0.260138373447475	0	FACETS	0.198	0.155	0.245			1	INDETERMINATE	1	TRUE	0	0.603450306152876	0		505	153	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771932	135771932	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755396992	NA	P-0002710-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	46	403	1	ENST00000298552.3:c.3185G>A	p.Arg1062Gln	p.R1062Q	ENST00000298552	NM_001162426.1	1062	cGg/cAg	23/23	0.165661916119382	2	FACETS	0.886	0.759	1	0.443	0.379	0.511	INDETERMINATE	1	TRUE	0	0.603450306152876	2		404	172	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878530	151878530	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1396109953	NA	P-0002710-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	59	96	0	ENST00000262189.6:c.6415C>T	p.Arg2139Ter	p.R2139*	ENST00000262189	NM_170606.2	2139	Cga/Tga	36/59	0.165661916119382	2	FACETS	0.936	0.817	1	0.468	0.408	0.531	INDETERMINATE	1	TRUE	0	0.603450306152876	2		96	209	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971065	21971065	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002710-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	23	367	0	ENST00000304494.5:c.293A>C	p.His98Pro	p.H98P	ENST00000304494	NM_000077.4	98	cAc/cCc	2/3	0.571810056075011	1	FACETS	0.532	0.423	0.653	0.532	0.423	0.653	SUBCLONAL	1	TRUE	0	0.603450306152876	1		367	100	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292560	15292560	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002710-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	30	542	0	ENST00000263388.2:c.2619C>A	p.Cys873Ter	p.C873*	ENST00000263388	NM_000435.2	873	tgC/tgA	17/33	0.241739787315986	1	FACETS	0.34	0.276	0.412	0.34	0.276	0.412	INDETERMINATE	1	TRUE	0	0.603450306152876	1		542	204	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045718	47045718	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002710-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	37	317	0	ENST00000377604.3:c.2599C>T	p.Gln867Ter	p.Q867*	ENST00000377604	NM_001204468.1	867	Cag/Tag	23/24	1	1	FACETS	0.973	0.832	1	0.973	0.832	1	CLONAL	1	TRUE	0	0.603450306152876	1		317	88	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032536	12032537	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0002710-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	24	417	0	ENST00000353533.5:c.974dup	p.Pro326SerfsTer5	p.P326Sfs*5	ENST00000353533	NM_003010.3	324	-/C	9/11	0.260138373447475	0	FACETS	0.319	0.255	0.389			1	INDETERMINATE	1	TRUE	0	0.603450306152876	0		417	99	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0002748-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	190	673	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.741411292642477	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.741411292642477	3		673	305	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002748-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	143	374	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.741411292642477	2		374	312	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576024	29576024	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002748-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	217	327	0	ENST00000356175.3:c.3997G>T	p.Glu1333Ter	p.E1333*	ENST00000356175	NM_000267.3	1333	Gag/Tag	30/57	0.193350685312784	4	FACETS	0.913	0.856	0.971	0.913	0.856	0.971	INDETERMINATE	2	TRUE	2	0.741411292642477	4		327	558	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784136	9784136	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002748-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	172	245	0	ENST00000377346.4:c.2704C>T	p.Arg902Ter	p.R902*	ENST00000377346	NM_005026.3	902	Cga/Tga	21/24	NA	2	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.741411292642477	2		245	424	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026811	71026811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002748-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	179	317	0	ENST00000318789.4:c.1411G>A	p.Ala471Thr	p.A471T	ENST00000318789	NM_032682.5	471	Gca/Aca	16/21	0.718385737312872	2	FACETS	1	0.966	1	0.531	0.494	0.568	CLONAL	1	TRUE	0	0.741411292642477	2		317	455	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274718	142274718	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0002748-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	69	191	0	ENST00000350721.4:c.2341+1G>C		p.X781_splice	ENST00000350721	NM_001184.3	781			0.741411292642477	3	FACETS	0.693	0.607	0.785	0.347	0.303	0.393	SUBCLONAL	1	TRUE	1	0.741411292642477	3		191	368	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588942	67588942	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002748-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	104	242	0	ENST00000274335.5:c.1033G>A	p.Glu345Lys	p.E345K	ENST00000274335		345	Gaa/Aaa	8/15	1	2	FACETS	0.899	0.815	0.986	0.899	0.815	0.986	CLONAL	1	TRUE	1	0.741411292642477	2		242	312	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514547	149514547	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002748-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	158	305	0	ENST00000261799.4:c.397G>A	p.Glu133Lys	p.E133K	ENST00000261799	NM_002609.3	133	Gag/Aag	4/23	0.365493084703659	1	FACETS	0.547	0.505	0.591	0.547	0.505	0.591	INDETERMINATE	1	TRUE	0	0.741411292642477	1		305	490	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874836	151874836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs992402398	NA	P-0002748-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	56	311	0	ENST00000262189.6:c.7702G>A	p.Gly2568Arg	p.G2568R	ENST00000262189	NM_170606.2	2568	Gga/Aga	38/59	0.199392302355174	1	FACETS	0.212	0.181	0.245	0.212	0.181	0.245	INDETERMINATE	1	TRUE	0	0.741411292642477	1		311	449	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390918	139390918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1364332299	NA	P-0002748-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	436	277	1	ENST00000277541.6:c.7273G>A	p.Ala2425Thr	p.A2425T	ENST00000277541	NM_017617.3	2425	Gcc/Acc	34/34	0.735019266741233	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.741411292642477	2		278	557	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683977	29683977	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002748-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	153	318	0	ENST00000356175.3:c.7676-1G>A		p.X2559_splice	ENST00000356175	NM_000267.3	2559			0.193350685312784	4	FACETS	0.763	0.704	0.824	0.763	0.704	0.824	INDETERMINATE	2	TRUE	2	0.741411292642477	4		318	471	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683985	29683985	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002748-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	164	355	0	ENST00000356175.3:c.7683G>C	p.Gln2561His	p.Q2561H	ENST00000356175	NM_000267.3	2561	caG/caC	52/57	0.193350685312784	4	FACETS	0.778	0.72	0.838	0.778	0.72	0.838	INDETERMINATE	2	TRUE	2	0.741411292642477	4		355	495	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687232	37687232	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs778399102	NA	P-0002748-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	231	291	0	ENST00000447079.4:c.4136C>G	p.Ser1379Cys	p.S1379C	ENST00000447079	NM_015083.1	1379	tCt/tGt	14/14	0.193350685312784	4	FACETS	0.826	0.774	0.878	0.826	0.774	0.878	INDETERMINATE	2	TRUE	2	0.741411292642477	4		291	657	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919914	50919914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs550922227	NA	P-0002748-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	179	432	0	ENST00000440232.2:c.3001G>A	p.Gly1001Ser	p.G1001S	ENST00000440232	NM_002691.3	1001	Ggc/Agc	24/27	NA	2	FACETS	0.704	0.651	0.758			1	INDETERMINATE	1	TRUE	NA	0.741411292642477	2		432	686	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045541	47045541	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002748-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	399	173	0	ENST00000377604.3:c.2508G>T	p.Arg836Ser	p.R836S	ENST00000377604	NM_001204468.1	836	agG/agT	22/24	0.339566541775465	2	FACETS	1	0.997	1			1	INDETERMINATE	2	TRUE	NA	0.741411292642477	2		173	450	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652089	36652090	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002748-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	315	310	0	ENST00000244741.5:c.213dup	p.Gly72TrpfsTer17	p.G72Wfs*17	ENST00000244741	NM_000389.4	71	ctt/cTtt	2/3	0.339566541775465	5	FACETS	1	0.967	1			1	INDETERMINATE	2	TRUE	NA	0.741411292642477	5		310	872	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162010	22162011	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0002748-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	66	374	0	ENST00000215832.6:c.243_244dup	p.Asn82ArgfsTer18	p.N82Rfs*18	ENST00000215832	NM_002745.4	82	aac/aGAac	2/9	1	2	FACETS	0.324	0.281	0.371	0.324	0.281	0.371	SUBCLONAL	1	TRUE	1	0.741411292642477	2		374	549	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651893	36651894	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0002748-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	322	236	0	ENST00000244741.5:c.18_19dup	p.Asp7GlyfsTer25	p.D7Gfs*25	ENST00000244741	NM_000389.4	5	-/GG	2/3	0.339566541775465	5	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.741411292642477	5		236	761	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0002770-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	41	346	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.324879795556397	2	FACETS	1	0.899	1	0.546	0.46	0.639	CLONAL	1	TRUE	0	0.379359344847327	2		346	198	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002770-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	43	368	0	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	0.324879795556397	2	FACETS	0.782	0.667	0.903	0.782	0.667	0.903	CLONAL	2	TRUE	0	0.379359344847327	2		368	145	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486094	29486095	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0002770-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	56	233	0	ENST00000356175.3:c.276dup	p.Cys93MetfsTer14	p.C93Mfs*14	ENST00000356175	NM_000267.3	91	gaa/gAaa	3/57	0.324879795556397	2	FACETS	1	0.915	1	0.541	0.467	0.62	CLONAL	1	TRUE	0	0.379359344847327	2		233	273	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0002787-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	125	168	1	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	1	2	FACETS	0.748	0.681	0.817	0.748	0.681	0.817	SUBCLONAL	1	TRUE	1	0.723492819547372	2		169	462	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0002787-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	269	279	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.707239337829107	3	FACETS	0.879	0.824	0.936	0.44	0.412	0.468	CLONAL	1	TRUE	1	0.723492819547372	3		279	1152	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331601	8331601	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002787-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	267	313	1	ENST00000356435.5:c.5515C>A	p.Pro1839Thr	p.P1839T	ENST00000356435		1839	Ccc/Acc	33/35	0.473953684138344	1	FACETS	0.713	0.673	0.753	0.713	0.673	0.753	SUBCLONAL	1	TRUE	0	0.723492819547372	1		314	661	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100496	102100496	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002787-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	356	265	0	ENST00000282441.5:c.1340C>A	p.Ala447Asp	p.A447D	ENST00000282441	NM_001130145.2	447	gCc/gAc	9/9	0.658130322848527	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.723492819547372	1		265	559	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434561	49434562	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0002787-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	138	204	0	ENST00000301067.7:c.6991dup	p.Leu2331ProfsTer46	p.L2331Pfs*46	ENST00000301067	NM_003482.3	2331	ctg/cCtg	31/54	1	2	FACETS	0.808	0.741	0.878	0.808	0.741	0.878	CLONAL	1	TRUE	1	0.723492819547372	2		204	472	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0002886-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	28	588	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.339	0.27	0.419	0.339	0.27	0.419	SUBCLONAL	1	TRUE	1	0.241585474298035	2		589	683	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123688	11123688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002886-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	34	410	1	ENST00000358026.2:c.2338G>A	p.Glu780Lys	p.E780K	ENST00000358026	NM_001128849.1	780	Gag/Aag	16/36	0.241585474298035	1	FACETS	0.388	0.316	0.469	0.388	0.316	0.469	SUBCLONAL	1	TRUE	0	0.241585474298035	1		411	638	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165212	47165213	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002886-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	121	409	0	ENST00000409792.3:c.913dup	p.Thr305AsnfsTer4	p.T305Nfs*4	ENST00000409792	NM_014159.6	305	aca/aAca	3/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.241585474298035	2		409	746	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0002886-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	59	371	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.241585474298035	1	FACETS	0.847	0.73	0.975	0.847	0.73	0.975	CLONAL	1	TRUE	0	0.241585474298035	1		371	507	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927568	131927568	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0002886-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	88	274	0	ENST00000265335.6:c.1636-1G>T		p.X546_splice	ENST00000265335		546			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.241585474298035	2		274	521	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551118	41551118	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0002886-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	123	450	0	ENST00000263253.7:c.3261+1G>C		p.X1087_splice	ENST00000263253	NM_001429.3	1087			NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.241585474298035	2		450	778	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552814	226552814	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002886-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	83	405	0	ENST00000366794.5:c.2547G>T	p.Lys849Asn	p.K849N	ENST00000366794	NM_001618.3	849	aaG/aaT	19/23	0.241585474298035	3	FACETS	0.876	0.772	0.988	0.438	0.386	0.494	CLONAL	1	TRUE	1	0.241585474298035	3		405	879	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248150	98248150	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002886-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	115	337	0	ENST00000331920.6:c.401G>T	p.Gly134Val	p.G134V	ENST00000331920	NM_000264.3	134	gGa/gTa	3/24	1	2	FACETS	0.763	0.689	0.841	1	0.984	1	SUBCLONAL	2	TRUE	1	0.241585474298035	2		337	624	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900387	32900387	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002886-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	128	440	0	ENST00000380152.3:c.484G>T	p.Gly162Trp	p.G162W	ENST00000380152		162	Ggg/Tgg	6/27	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.241585474298035	2		440	735	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223271	2223271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002886-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	43	389	1	ENST00000326181.6:c.883G>A	p.Asp295Asn	p.D295N	ENST00000326181	NM_032271.2	295	Gat/Aat	10/21	1	2	FACETS	0.591	0.494	0.7	0.591	0.494	0.7	SUBCLONAL	1	TRUE	1	0.241585474298035	2		390	602	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226395	41226395	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002886-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	154	489	0	ENST00000357654.3:c.4628G>T	p.Gly1543Val	p.G1543V	ENST00000357654	NM_007294.3	1543	gGg/gTg	14/23	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.241585474298035	2		489	894	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216763	2216763	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0002886-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	51	161	0	ENST00000398665.3:c.2407A>T	p.Arg803Ter	p.R803*	ENST00000398665	NM_032482.2	803	Aga/Tga	20/28	0.241585474298035	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.241585474298035	1		161	252	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597492	10597492	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002886-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	110	369	0	ENST00000171111.5:c.1711G>C	p.Gly571Arg	p.G571R	ENST00000171111	NM_203500.1	571	Ggc/Cgc	6/6	0.241585474298035	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.241585474298035	1		369	614	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273811	18273811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002886-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	146	458	1	ENST00000222254.8:c.1144C>T	p.His382Tyr	p.H382Y	ENST00000222254	NM_005027.3	382	Cac/Tac	10/16	1	2	FACETS	0.934	0.855	1	1	0.991	1	CLONAL	2	TRUE	1	0.241585474298035	2		459	647	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546626	9546626	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002886-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	136	507	0	ENST00000353224.5:c.1396G>C	p.Ala466Pro	p.A466P	ENST00000353224	NM_177990.2	466	Gcc/Ccc	5/10	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.241585474298035	2		507	883	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039669	47039669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002886-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	127	232	0	ENST00000377604.3:c.1121G>T	p.Gly374Val	p.G374V	ENST00000377604	NM_001204468.1	374	gGc/gTc	11/24	1	1	FACETS	0.939	0.863	1	1	0.992	1	CLONAL	3	TRUE	0	0.241585474298035	1		232	328	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480508	123480508	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002886-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	108	174	0	ENST00000371139.4:c.16G>T	p.Val6Leu	p.V6L	ENST00000371139	NM_001114937.2	6	Gtg/Ttg	1/4	1	1	FACETS	1	0.956	1	1	0.989	1	CLONAL	2	TRUE	0	0.241585474298035	1		174	360	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948136	178948136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002915-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	117	451	0	ENST00000263967.3:c.2908G>A	p.Glu970Lys	p.E970K	ENST00000263967	NM_006218.2	970	Gaa/Aaa	20/21	NA	2	FACETS	0.793	0.717	0.871			1	INDETERMINATE	2	TRUE	NA	0.271380254989243	2		451	544	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673008	30673008	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002915-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	49	307	0	ENST00000376406.3:c.3952T>G	p.Ser1318Ala	p.S1318A	ENST00000376406	NM_014641.2	1318	Tct/Gct	10/15	0.211919872399052	2	FACETS	0.792	0.678	0.915	0.792	0.678	0.915	CLONAL	2	TRUE	0	0.271380254989243	2		307	228	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875031	151875031	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002915-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	80	524	0	ENST00000262189.6:c.7507C>T	p.Gln2503Ter	p.Q2503*	ENST00000262189	NM_170606.2	2503	Cag/Tag	38/59	0.271380254989243	3	FACETS	1	0.948	1	0.38	0.334	0.428	CLONAL	1	TRUE	0	0.271380254989243	3		524	588	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18762554	18762554	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002915-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	116	483	0	ENST00000266497.5:c.4050G>C	p.Met1350Ile	p.M1350I	ENST00000266497		1350	atG/atC	29/31	0.232405949664211	4	FACETS	0.83	0.749	0.915	0.83	0.749	0.915	CLONAL	2	TRUE	2	0.271380254989243	4		483	655	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130306	2130306	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs751708490	NA	P-0002915-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	134	795	0	ENST00000219476.3:c.3538A>G	p.Lys1180Glu	p.K1180E	ENST00000219476	NM_000548.3	1180	Aag/Gag	30/42	0.271380254989243	1	FACETS	0.854	0.78	0.93	1	0.989	1	CLONAL	2	TRUE	0	0.271380254989243	1		795	500	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820773	3820773	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs142047649	NA	P-0002915-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	91	693	0	ENST00000262367.5:c.2678C>G	p.Ser893Trp	p.S893W	ENST00000262367	NM_004380.2	893	tCg/tGg	14/31	0.271380254989243	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.271380254989243	1		693	474	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170882	56170890	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCTTATT	CTGCTTATT	AATGGAA	novel	NA	P-0002915-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	47	592	0	ENST00000399503.3:c.1710_1718delinsAATGGAA	p.Cys571MetfsTer4	p.C571Mfs*4	ENST00000399503	NM_005921.1	570	ggCTGCTTATTt/ggAATGGAAt	10/20	0.202452150547584	2	FACETS	0.72	0.608	0.844	0.36	0.304	0.422	SUBCLONAL	1	TRUE	0	0.271380254989243	2		592	481	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111510	8111511	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0002915-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	177	768	0	ENST00000346208.3:c.998dup	p.Asn333LysfsTer19	p.N333Kfs*19	ENST00000346208		332	-/A	5/6	0.271380254989243	5	FACETS	1	0.977	1	0.766	0.707	0.827	CLONAL	2	TRUE	2	0.271380254989243	5		768	799	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245366	41245367	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0002915-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	156	803	0	ENST00000357654.3:c.2181_2182del	p.Glu729ArgfsTer10	p.E729Rfs*10	ENST00000357654	NM_007294.3	727	ccAAga/ccga	10/23	0.187048448033553	2	FACETS	0.801	0.735	0.869	0.801	0.735	0.869	CLONAL	2	TRUE	0	0.271380254989243	2		803	718	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0002950-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	231	674	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.592784761930292	2		674	767	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115974	8115975	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCAT	novel	NA	P-0002950-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	90	349	0	ENST00000346208.3:c.1322_1326dup	p.Gly443ProfsTer34	p.G443Pfs*34	ENST00000346208		440	-/GCCAT	6/6	1	2	FACETS	0.797	0.712	0.886	0.797	0.712	0.886	SUBCLONAL	1	TRUE	1	0.592784761930292	2		349	381	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0002985-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	165	588	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.318147360328922	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.318147360328922	1		589	749	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0002985-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	160	723	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.318147360328922	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.318147360328922	1		723	722	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729932	30729932	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002985-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	92	386	0	ENST00000295754.5:c.1453G>T	p.Glu485Ter	p.E485*	ENST00000295754	NM_003242.5	485	Gaa/Taa	6/7	0.318147360328922	1	FACETS	0.941	0.839	1	0.941	0.839	1	CLONAL	1	TRUE	0	0.318147360328922	1		386	517	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057809	27057810	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002985-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	161	807	1	ENST00000324856.7:c.1518dup	p.Gln507SerfsTer116	p.Q507Sfs*116	ENST00000324856	NM_006015.4	506	tct/tcTt	3/20	0.318147360328922	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.318147360328922	1		808	699	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0002987-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	192	244	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.891472753017859	1	FACETS	0.922	0.88	0.961	0.922	0.88	0.961	CLONAL	1	TRUE	0	0.891472753017859	1		244	259	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692786	89692787	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAAA	novel	NA	P-0002987-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	26	255	0	ENST00000371953.3:c.273_274insAGAA	p.Asp92ArgfsTer4	p.D92Rfs*4	ENST00000371953	NM_000314.4	90	-/GAAA	5/9	0.891472753017859	1	FACETS	0.119	0.094	0.147	0.119	0.094	0.147	SUBCLONAL	1	TRUE	0	0.891472753017859	1		255	272	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576917	7576917	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002987-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	353	303	0	ENST00000269305.4:c.929del	p.Asn310ThrfsTer35	p.N310Tfs*35	ENST00000269305	NM_001126112.2	310	aAc/ac	9/11	0.891472753017859	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.891472753017859	1		303	432	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0003006-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	102	588	1	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	0.232550985585535	2		589	769	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636973	176636973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1215568879	NA	P-0003006-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	65	356	0	ENST00000439151.2:c.1573C>T	p.Arg525Trp	p.R525W	ENST00000439151	NM_022455.4	525	Cgg/Tgg	5/23	1	2	FACETS	0.947	0.822	1	0.947	0.822	1	CLONAL	1	TRUE	1	0.232550985585535	2		356	590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577107	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACAGGC	novel	NA	P-0003006-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	104	526	0	ENST00000269305.4:c.826_831dup	p.Ala276_Cys277dup	p.A276_C277dup	ENST00000269305	NM_001126112.2	276	-/GCCTGT	8/11	0.218116100271028	1	FACETS	0.918	0.821	1	0.918	0.821	1	CLONAL	1	TRUE	0	0.232550985585535	1		526	861	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435675	56435676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TAGGC	novel	NA	P-0003006-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	34	211	0	ENST00000407977.2:c.1457_1461dup	p.Gln488AlafsTer16	p.Q488Afs*16	ENST00000407977		487	-/GCCTA	9/10	0.142867784132733	3	FACETS	0.796	0.651	0.96	0.398	0.325	0.48	CLONAL	1	TRUE	1	0.232550985585535	3		211	410	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0003009-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	99	588	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.559	0.498	0.623	0.559	0.498	0.623	SUBCLONAL	1	TRUE	1	0.429920789804118	2		589	824	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0003009-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	162	517	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.429920789804118	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.429920789804118	1		517	445	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014202	70014202	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003009-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	181	562	0	ENST00000394351.3:c.1063G>T	p.Gly355Ter	p.G355*	ENST00000394351	NM_000248.3	355	Gga/Tga	9/9	0.420229681216778	1	FACETS	0.922	0.853	0.993	0.922	0.853	0.993	CLONAL	1	TRUE	0	0.429920789804118	1		562	717	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143029327	143029327	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003009-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	184	358	0	ENST00000262992.4:c.2293T>A	p.Leu765Met	p.L765M	ENST00000262992	NM_001101669.1	765	Ttg/Atg	21/24	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.429920789804118	2		358	808	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615013	43615013	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003009-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	98	389	0	ENST00000355710.3:c.2427C>A	p.Tyr809Ter	p.Y809*	ENST00000355710	NM_020975.4	809	taC/taA	14/20	1	2	FACETS	0.985	0.883	1	0.985	0.883	1	CLONAL	1	TRUE	1	0.429920789804118	2		389	463	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357483	70357483	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003009-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	174	491	0	ENST00000374080.3:c.5824C>A	p.Gln1942Lys	p.Q1942K	ENST00000374080		1942	Cag/Aag	40/45	0.429920789804118	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.429920789804118	1		491	488	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023987	27023987	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003009-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	30	12	0	ENST00000324856.7:c.1095del	p.Ser366AlafsTer25	p.S366Afs*25	ENST00000324856	NM_006015.4	365	Ggg/gg	1/20	0.418480877024306	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	2	TRUE	0	0.429920789804118	2		12	69	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176710802	176710803	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0003009-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	333	474	0	ENST00000439151.2:c.6025_6026dup	p.Gly2010LeufsTer11	p.G2010Lfs*11	ENST00000439151	NM_022455.4	2008	-/GC	20/23	0.403136084343266	2	FACETS	0.953	0.905	1	0.953	0.905	1	CLONAL	2	TRUE	0	0.429920789804118	2		474	813	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941824	44941824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003031-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	110	235	1	ENST00000377967.4:c.3148G>A	p.Glu1050Lys	p.E1050K	ENST00000377967	NM_021140.2	1050	Gaa/Aaa	21/29	0.291498674245161	0	FACETS	0.97	0.889	1			1	CLONAL	1	TRUE	NA	0.475571149516628	0		236	250	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983320	149983320	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	TT	novel	NA	P-0003031-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	65	272	0	ENST00000253339.5:c.2938delinsAA	p.Glu980LysfsTer4	p.E980Kfs*4	ENST00000253339		980	Gaa/AAaa	7/7	0.466425642180967	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.475571149516628	1		272	196	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941830	44941830	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003031-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	109	247	1	ENST00000377967.4:c.3154del	p.Glu1052LysfsTer31	p.E1052Kfs*31	ENST00000377967	NM_021140.2	1052	Gaa/aa	21/29	0.291498674245161	0	FACETS	0.962	0.88	1			1	CLONAL	1	TRUE	NA	0.475571149516628	0		248	250	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637649	176637650	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0003031-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	184	419	0	ENST00000439151.2:c.2256_2257del	p.Pro753LysfsTer11	p.P753Kfs*11	ENST00000439151	NM_022455.4	750	gCT/g	5/23	0.448410294939709	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.475571149516628	2		419	372	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0003035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	286	678	1	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	NA	2	FACETS	0.897	0.849	0.945			1	INDETERMINATE	2	FALSE	NA	0.466902884023555	2		679	683	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754956	29754956	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	64	317	0	ENST00000389048.3:c.979G>C	p.Ala327Pro	p.A327P	ENST00000389048	NM_004304.4	327	Gct/Cct	4/29	0.36913682989307	3	FACETS	0.732	0.635	0.836			1	SUBCLONAL	1	FALSE	NA	0.466902884023555	3		317	462	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983994	2983994	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	449	788	0	ENST00000396946.4:c.536G>A	p.Arg179Gln	p.R179Q	ENST00000396946	NM_032415.4	179	cGg/cAg	5/25	0.466902884023555	5	FACETS	0.872	0.833	0.912	0.872	0.833	0.912	CLONAL	3	FALSE	2	0.466902884023555	5		788	1250	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467828	50467828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1040607869	NA	P-0003035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	253	367	0	ENST00000331340.3:c.1063G>A	p.Ala355Thr	p.A355T	ENST00000331340	NM_006060.4	355	Gcg/Acg	8/8	0.466902884023555	5	FACETS	0.87	0.818	0.923	0.87	0.818	0.923	CLONAL	3	FALSE	2	0.466902884023555	5		367	706	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164101	108164101	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	250	450	0	ENST00000278616.4:c.4673C>A	p.Thr1558Lys	p.T1558K	ENST00000278616	NM_000051.3	1558	aCg/aAg	31/63	0.437731204503262	5	FACETS	0.943	0.883	1			1	CLONAL	2	FALSE	NA	0.466902884023555	5		450	965	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398260	25398260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	330	587	0	ENST00000311936.3:c.59C>T	p.Thr20Met	p.T20M	ENST00000311936	NM_004985.3	20	aCg/aTg	2/5	0.36913682989307	3	FACETS	1	0.977	1			1	CLONAL	2	FALSE	NA	0.466902884023555	3		587	830	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590593	95590593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	353	753	0	ENST00000393063.1:c.1316C>T	p.Thr439Ile	p.T439I	ENST00000393063	NM_030621.3	439	aCc/aTc	9/28	0.466902884023555	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	FALSE	0	0.466902884023555	2		753	732	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348684	89348684	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs751159286	NA	P-0003035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	262	1131	0	ENST00000301030.4:c.4266G>T	p.Leu1422Phe	p.L1422F	ENST00000301030	NM_001256183.1	1422	ttG/ttT	9/13	0.222342935902227	2	FACETS	0.814	0.761	0.869	0.407	0.38	0.435	INDETERMINATE	1	FALSE	0	0.466902884023555	2		1131	1379	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016584	12016584	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	120	545	0	ENST00000353533.5:c.720T>A	p.Ser240Arg	p.S240R	ENST00000353533	NM_003010.3	240	agT/agA	7/11	0.466902884023555	2	FACETS	0.861	0.78	0.946	0.431	0.39	0.473	CLONAL	1	FALSE	0	0.466902884023555	2		545	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578467	7578468	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0003035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	223	405	0	ENST00000269305.4:c.462dup	p.Thr155HisfsTer26	p.T155Hfs*26	ENST00000269305	NM_001126112.2	154	-/C	5/11	0.466902884023555	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	FALSE	0	0.466902884023555	2		405	467	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81340796	81340796	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs564721078	NA	P-0003056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	81	306	0	ENST00000222390.5:c.1444+1G>A		p.X482_splice	ENST00000222390	NM_000601.4	482			0.170802774752035	4	FACETS	0.765	0.683	0.85	0.765	0.683	0.85	INDETERMINATE	2	TRUE	2	0.665509426551018	4		306	265	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434958	49434959	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1555192751	NA	P-0003056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	36	104	0	ENST00000301067.7:c.6594dup	p.Tyr2199LeufsTer3	p.Y2199Lfs*3	ENST00000301067	NM_003482.3	2198	-/C	31/54	0.146379801075387	3	FACETS	0.775	0.658	0.897	0.775	0.658	0.897	INDETERMINATE	2	TRUE	1	0.665509426551018	3		104	93	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0003122-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	154	588	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	0.9	0.828	0.975			1	INDETERMINATE	2	TRUE	NA	0.299598403583369	2		589	571	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0003122-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	119	175	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.299598403583369	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.299598403583369	2		175	356	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199402	16199402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003122-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	91	239	0	ENST00000375759.3:c.175G>A	p.Ala59Thr	p.A59T	ENST00000375759	NM_015001.2	59	Gca/Aca	2/15	0.299598403583369	3	FACETS	1	0.939	1	0.542	0.482	0.607	CLONAL	1	TRUE	1	0.299598403583369	3		239	644	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112064	115112064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757023811	NA	P-0003122-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	85	224	0	ENST00000257566.3:c.1676C>T	p.Thr559Met	p.T559M	ENST00000257566	NM_016569.3	559	aCg/aTg	7/8	0.299598403583369	3	FACETS	0.868	0.772	0.968	0.868	0.772	0.968	CLONAL	2	TRUE	1	0.299598403583369	3		224	376	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112349	115112349	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003122-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	19	56	0	ENST00000257566.3:c.1391C>T	p.Pro464Leu	p.P464L	ENST00000257566	NM_016569.3	464	cCg/cTg	7/8	0.299598403583369	3	FACETS	1	0.887	1	0.645	0.497	0.815	CLONAL	1	TRUE	1	0.299598403583369	3		56	113	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575121	48575122	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003122-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	168	295	0	ENST00000342988.3:c.320dup	p.Asn107LysfsTer2	p.N107Kfs*2	ENST00000342988	NM_005359.5	105	-/A	3/12	0.299598403583369	2	FACETS	0.913	0.843	0.986	0.913	0.843	0.986	CLONAL	2	TRUE	0	0.299598403583369	2		295	614	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0003137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	27	357	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.933	0.742	1	0.933	0.742	1	CLONAL	1	TRUE	1	0.13	2		357	445	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405969	49405969	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	128	403	0	ENST00000418115.1:c.169T>G	p.Leu57Val	p.L57V	ENST00000418115	NM_001664.2	57	Ttg/Gtg	3/5	0.198065303318415	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.13	3		403	918	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55143576	55143576	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553904813	NA	P-0003137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	35	324	3	ENST00000257290.5:c.1808C>T	p.Ala603Val	p.A603V	ENST00000257290	NM_006206.4	603	gCg/gTg	13/23	1	2	FACETS	0.799	0.653	0.964	0.799	0.653	0.964	CLONAL	1	TRUE	1	0.13	2		327	674	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932334	39932335	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	TT	novel	NA	P-0003137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	73	230	0	ENST00000378444.4:c.2264_2265insAA	p.Tyr755Ter	p.Y755*	ENST00000378444	NM_001123385.1	755	tac/taAAc	4/15	1	1	FACETS	0.97	0.85	1	1	0.982	1	CLONAL	2	TRUE	0	0.13	1		230	541	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870985	12870986	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1555085549	NA	P-0003137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	83	279	0	ENST00000228872.4:c.215dup	p.Lys73GlnfsTer52	p.K73Qfs*52	ENST00000228872	NM_004064.3	71	gag/gaGg	1/3	0.259010142040529	3	FACETS	0.958	0.845	1			1	CLONAL	2	TRUE	NA	0.13	3		279	710	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117739	70117739	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	160	397	0	ENST00000245479.2:c.210del	p.Val71CysfsTer39	p.V71Cfs*39	ENST00000245479	NM_000346.3	69	ttC/tt	1/3	0.2328977138431	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	3	TRUE	0	0.13	3		397	807	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	209	374	0				ENST00000310581	NM_198253.2	-/1132			0.829136089230593	4	FACETS	0.894	0.86	0.925	1	0.993	1	CLONAL	4	TRUE	1	0.829136089230593	4		374	258	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092809	27092809	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	311	296	0	ENST00000324856.7:c.2830C>T	p.Gln944Ter	p.Q944*	ENST00000324856	NM_006015.4	944	Cag/Tag	9/20	1	2	FACETS	0.925	0.876	0.974	0.925	0.876	0.974	CLONAL	1	TRUE	1	0.829136089230593	2		296	811	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93636487	93636487	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	179	367	0	ENST00000375746.1:c.917C>T	p.Ser306Phe	p.S306F	ENST00000375746	NM_001174167.1	306	tCc/tTc	8/14	0.829136089230593	1	FACETS	0.406	0.376	0.438	0.406	0.376	0.438	SUBCLONAL	1	TRUE	0	0.829136089230593	1		367	622	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787691	135787692	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0003140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	465	297	1	ENST00000298552.3:c.890dup	p.Tyr297Ter	p.Y297*	ENST00000298552	NM_001162426.1	297	tat/taAt	9/23	0.829136089230593	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.829136089230593	1		298	600	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633229	12633229	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs368807126	NA	P-0003146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	122	301	0	ENST00000251849.4:c.1171A>T	p.Arg391Trp	p.R391W	ENST00000251849	NM_002880.3	391	Agg/Tgg	11/17	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		301	702	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041070	112041070	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	169	441	2	ENST00000368678.4:c.185C>G	p.Thr62Ser	p.T62S	ENST00000368678		62	aCc/aGc	3/13	0.0982717172849254	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		443	1237	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778125	135778135	+	frameshift_variant	Frame_Shift_Del	DEL	CTAACCTTCCA	CTAACCTTCCA	T	novel	NA	P-0003146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	84	315	0	ENST00000298552.3:c.2248_2258delinsA	p.Trp750IlefsTer20	p.W750Ifs*20	ENST00000298552	NM_001162426.1	750	TGGAAGGTTAGt/At	18/23	0.247035104831823	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		315	773	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797242	135797242	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	AT	novel	NA	P-0003146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	85	294	0	ENST00000298552.3:c.627delinsAT	p.Met209IlefsTer2	p.M209Ifs*2	ENST00000298552	NM_001162426.1	209	atG/atAT	7/23	0.247035104831823	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		294	789	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0003183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	303	435	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	0.7	2		436	758	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0003183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	81	516	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.174003516323196	1	FACETS	0.184	0.162	0.209	0.184	0.162	0.209	INDETERMINATE	1	TRUE	0	0.7	1		517	816	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0003183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	127	363	1	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.832	0.76	0.907	0.832	0.76	0.907	CLONAL	1	TRUE	1	0.7	2		364	436	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913338	NA	P-0003183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	44	234	0	ENST00000288602.6:c.1781A>T	p.Asp594Val	p.D594V	ENST00000288602	NM_004333.4	594	gAt/gTt	15/18	1	2	FACETS	0.24	0.201	0.284	0.24	0.201	0.284	SUBCLONAL	1	TRUE	1	0.7	2		234	523	SUCCESS
APC	324	MSKCC	GRCh37	5	112175651	112175651	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0003183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	308	360	0	ENST00000257430.4:c.4364del	p.Asn1455IlefsTer18	p.N1455Ifs*18	ENST00000257430	NM_000038.5	1454	Aaa/aa	16/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.7	2		360	867	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920413	114920413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767830105	NA	P-0003183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	415	471	0	ENST00000543371.1:c.1354G>A	p.Gly452Arg	p.G452R	ENST00000543371	NM_001198531.1	452	Ggg/Agg	13/14	0.3	2	FACETS	0.95	0.905	0.996			1	INDETERMINATE	1	TRUE	NA	0.7	2		471	1248	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925435	114925435	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs375657594	NA	P-0003183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	349	508	0	ENST00000543371.1:c.1513C>T	p.Arg505Ter	p.R505*	ENST00000543371	NM_001198531.1	505	Cga/Tga	14/14	0.3	2	FACETS	0.825	0.782	0.87			1	INDETERMINATE	1	TRUE	NA	0.7	2		508	1208	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588835	29588836	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0003183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	55	410	0	ENST00000356175.3:c.4623dup	p.Asn1542Ter	p.N1542*	ENST00000356175	NM_000267.3	1541	ctt/cTtt	34/57	0.174003516323196	1	FACETS	0.126	0.107	0.147	0.126	0.107	0.147	INDETERMINATE	1	TRUE	0	0.7	1		410	810	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717703	89717703	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	85	161	1	ENST00000371953.3:c.728T>C	p.Phe243Ser	p.F243S	ENST00000371953	NM_000314.4	243	tTc/tCc	7/9	0.305455557923243	6	FACETS	0.914	0.815	1			1	CLONAL	3	TRUE	NA	0.305455557923243	6		162	327	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101566	27101567	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0003191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	63	270	0	ENST00000324856.7:c.4850dup	p.Pro1618SerfsTer30	p.P1618Sfs*30	ENST00000324856	NM_006015.4	1616	-/G	18/20	0.305852544121379	3	FACETS	0.831	0.725	0.944	0.831	0.725	0.944	CLONAL	2	TRUE	1	0.305455557923243	3		270	286	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0003210-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	347	474	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.378069149255539	4	FACETS	0.855	0.814	0.897			1	CLONAL	3	TRUE	NA	0.491177638353411	4		474	821	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630465	187630465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1439256953	NA	P-0003210-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	162	402	0	ENST00000441802.2:c.517G>A	p.Ala173Thr	p.A173T	ENST00000441802	NM_005245.3	173	Gcc/Acc	2/27	0.491177638353411	3	FACETS	0.953	0.875	1	0.477	0.437	0.518	CLONAL	1	TRUE	1	0.491177638353411	3		402	862	SUCCESS
APC	324	MSKCC	GRCh37	5	112175153	112175153	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003210-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	168	179	0	ENST00000257430.4:c.3862G>T	p.Gly1288Ter	p.G1288*	ENST00000257430	NM_000038.5	1288	Gga/Tga	16/16	0.446131387508086	4	FACETS	1	0.933	1	1	0.933	1	CLONAL	2	TRUE	2	0.491177638353411	4		179	506	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20488427	20488427	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756468217	NA	P-0003210-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	133	356	0	ENST00000346618.3:c.1083G>A	p.Met361Ile	p.M361I	ENST00000346618	NM_001949.4	361	atG/atA	6/7	0.48047932788344	3	FACETS	0.892	0.811	0.977	0.446	0.405	0.489	CLONAL	1	TRUE	1	0.491177638353411	3		356	756	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934918	9934918	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003210-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	119	329	0	ENST00000330684.3:c.1372G>A	p.Gly458Arg	p.G458R	ENST00000330684	NM_001134407.1	458	Ggg/Agg	6/13	0.48047932788344	3	FACETS	0.939	0.849	1	0.469	0.424	0.517	CLONAL	1	TRUE	1	0.491177638353411	3		329	643	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938562	76938562	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003210-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	117	412	1	ENST00000373344.5:c.2186C>A	p.Ser729Ter	p.S729*	ENST00000373344	NM_000489.3	729	tCa/tAa	9/35	NA	2	FACETS	0.689	0.622	0.76			1	INDETERMINATE	1	TRUE	NA	0.491177638353411	2		413	691	SUCCESS
APC	324	MSKCC	GRCh37	5	112111408	112111411	+	frameshift_variant	Frame_Shift_Del	DEL	ATAG	ATAG	-	rs387906231	NA	P-0003210-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	170	269	0	ENST00000257430.4:c.509_512del	p.Asp170ValfsTer4	p.D170Vfs*4	ENST00000257430	NM_000038.5	169	ATAGat/at	5/16	0.446131387508086	4	FACETS	0.762	0.703	0.823	0.762	0.703	0.823	SUBCLONAL	2	TRUE	2	0.491177638353411	4		269	677	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900944	114900945	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0003210-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	207	343	0	ENST00000543371.1:c.555dup	p.Asn186Ter	p.N186*	ENST00000543371	NM_001198531.1	185	tct/tcTt	6/14	0.491177638353411	3	FACETS	1	0.976	1	0.558	0.518	0.599	CLONAL	1	TRUE	1	0.491177638353411	3		343	941	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794972	42794973	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0003272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	243	257	0	ENST00000575354.2:c.2054_2055dup	p.Ile686ProfsTer43	p.I686Pfs*43	ENST00000575354	NM_015125.3	684	-/CC	10/20	1	2	FACETS	0.983	0.929	1	0.983	0.929	1	CLONAL	1	TRUE	1	0.963736203137169	2		257	513	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782177	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	83	461	0	ENST00000269305.4:c.644G>T	p.Ser215Ile	p.S215I	ENST00000269305	NM_001126112.2	215	aGt/aTt	6/11	0.256183034102826	1	FACETS	0.83	0.733	0.933	0.83	0.733	0.933	CLONAL	1	TRUE	0	0.29	1		461	590	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449582	149449582	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	69	356	0	ENST00000286301.3:c.1364C>A	p.Pro455His	p.P455H	ENST00000286301	NM_005211.3	455	cCt/cAt	10/22	0.256183034102826	1	FACETS	0.957	0.837	1	0.957	0.837	1	CLONAL	1	TRUE	0	0.29	1		356	425	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470480	25470480	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs760854242	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	49	345	0	ENST00000264709.3:c.994G>T	p.Gly332Ter	p.G332*	ENST00000264709	NM_175629.2	332	Gga/Tga	8/23	0.156698676317136	1	FACETS	0.602	0.51	0.703	0.602	0.51	0.703	INDETERMINATE	1	TRUE	0	0.29	1		345	480	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143404	30143404	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	16	119	0	ENST00000389048.3:c.122G>T	p.Arg41Leu	p.R41L	ENST00000389048	NM_004304.4	41	cGg/cTg	1/29	0.156698676317136	1	FACETS	0.565	0.42	0.737	0.565	0.42	0.737	INDETERMINATE	1	TRUE	0	0.29	1		119	167	SUCCESS
REL	5966	MSKCC	GRCh37	2	61128200	61128200	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	46	109	0	ENST00000295025.8:c.376G>T	p.Gly126Ter	p.G126*	ENST00000295025	NM_002908.2	126	Gga/Tga	4/11	1	2	FACETS	0.795	0.671	0.932	0.795	0.671	0.932	CLONAL	1	TRUE	1	0.29	2		109	399	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145682	61145682	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	58	280	0	ENST00000295025.8:c.794G>T	p.Arg265Ile	p.R265I	ENST00000295025	NM_002908.2	265	aGa/aTa	7/11	1	2	FACETS	0.765	0.658	0.882	0.765	0.658	0.882	SUBCLONAL	1	TRUE	1	0.29	2		280	523	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274712	198274712	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	76	242	0	ENST00000335508.6:c.686C>A	p.Ser229Tyr	p.S229Y	ENST00000335508	NM_012433.2	229	tCc/tAc	7/25	1	2	FACETS	0.996	0.876	1	0.996	0.876	1	CLONAL	1	TRUE	1	0.29	2		242	526	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662133	227662133	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	34	313	0	ENST00000305123.5:c.1322C>A	p.Ser441Tyr	p.S441Y	ENST00000305123	NM_005544.2	441	tCc/tAc	1/2	0.241766482805621	3	FACETS	0.554	0.452	0.668	0.277	0.226	0.334	SUBCLONAL	1	TRUE	1	0.29	3		313	485	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443571	52443571	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	39	294	1	ENST00000460680.1:c.121G>T	p.Gly41Cys	p.G41C	ENST00000460680	NM_004656.3	41	Ggc/Tgc	3/17	0.156698676317136	1	FACETS	0.572	0.475	0.68	0.572	0.475	0.68	INDETERMINATE	1	TRUE	0	0.29	1		295	402	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981462	55981462	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	98	267	0	ENST00000263923.4:c.475G>T	p.Val159Leu	p.V159L	ENST00000263923	NM_002253.2	159	Gtg/Ttg	4/30	0.156698676317136	1	FACETS	1	0.967	1	1	0.967	1	INDETERMINATE	1	TRUE	0	0.29	1		267	481	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519785	176519785	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	57	351	0	ENST00000292408.4:c.1057G>T	p.Glu353Ter	p.E353*	ENST00000292408	NM_213647.1	353	Gag/Tag	8/18	0.256183034102826	1	FACETS	0.906	0.781	1	0.906	0.781	1	CLONAL	1	TRUE	0	0.29	1		351	371	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652251	36652251	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	49	233	0	ENST00000244741.5:c.373G>T	p.Glu125Ter	p.E125*	ENST00000244741	NM_000389.4	125	Gag/Tag	2/3	1	2	FACETS	0.864	0.734	1	0.864	0.734	1	CLONAL	1	TRUE	1	0.29	2		233	391	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120364	94120364	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	99	531	0	ENST00000369303.4:c.687G>T	p.Glu229Asp	p.E229D	ENST00000369303	NM_004440.3	229	gaG/gaT	3/17	0.3	0	FACETS	0.712	0.636	0.793			1	SUBCLONAL	1	TRUE	0	0.29	0		531	681	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117630000	117630000	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	32	302	0	ENST00000368508.3:c.6526A>G	p.Thr2176Ala	p.T2176A	ENST00000368508	NM_002944.2	2176	Aca/Gca	41/43	0.3	1	FACETS	0.38	0.308	0.462	0.38	0.308	0.462	SUBCLONAL	1	TRUE	0	0.29	1		302	496	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405902	157405902	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	29	278	0	ENST00000346085.5:c.2144C>G	p.Pro715Arg	p.P715R	ENST00000346085	NM_020732.3	715	cCg/cGg	6/20	1	2	FACETS	0.488	0.391	0.598	0.488	0.391	0.598	SUBCLONAL	1	TRUE	1	0.29	2		278	410	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55272994	55272994	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	164	378	0	ENST00000275493.2:c.3317A>T	p.Gln1106Leu	p.Q1106L	ENST00000275493	NM_005228.3	1106	cAg/cTg	28/28	1	2	FACETS	0.893	0.823	0.966	1	0.991	1	CLONAL	2	TRUE	1	0.29	2		378	633	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391728	139391728	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	18	303	0	ENST00000277541.6:c.6463G>T	p.Gly2155Cys	p.G2155C	ENST00000277541	NM_017617.3	2155	Ggc/Tgc	34/34	0.256183034102826	1	FACETS	0.37	0.278	0.478	0.37	0.278	0.478	SUBCLONAL	1	TRUE	0	0.29	1		303	287	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604633	43604633	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	31	327	0	ENST00000355710.3:c.1218T>A	p.Ser406Arg	p.S406R	ENST00000355710	NM_020975.4	406	agT/agA	6/20	0.210092117463612	4	FACETS	0.696	0.563	0.847	0.348	0.281	0.424	SUBCLONAL	1	TRUE	2	0.29	4		327	396	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148875	119148875	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs397517076	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	71	157	0	ENST00000264033.4:c.1096-1G>T		p.X366_splice	ENST00000264033	NM_005188.3	366			0.198317533407246	2	FACETS	0.756	0.665	0.852	0.756	0.665	0.852	SUBCLONAL	2	TRUE	0	0.29	2		157	324	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491387	18491387	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	55	197	0	ENST00000266497.5:c.1300G>T	p.Val434Phe	p.V434F	ENST00000266497		434	Gtt/Ttt	8/31	1	2	FACETS	0.776	0.664	0.897	0.776	0.664	0.897	SUBCLONAL	1	TRUE	1	0.29	2		197	489	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691196	18691196	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	44	266	0	ENST00000266497.5:c.3307T>A	p.Tyr1103Asn	p.Y1103N	ENST00000266497		1103	Tat/Aat	23/31	1	2	FACETS	0.674	0.566	0.794	0.674	0.566	0.794	SUBCLONAL	1	TRUE	1	0.29	2		266	450	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112526	115112526	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	63	312	0	ENST00000257566.3:c.1214G>T	p.Arg405Leu	p.R405L	ENST00000257566	NM_016569.3	405	cGt/cTt	7/8	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.29	2		312	406	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432205	121432205	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	34	220	0	ENST00000257555.6:c.952C>A	p.His318Asn	p.H318N	ENST00000257555		318	Cac/Aac	4/10	1	2	FACETS	0.792	0.65	0.951	0.792	0.65	0.951	CLONAL	1	TRUE	1	0.29	2		220	296	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008057	29008057	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	59	226	0	ENST00000282397.4:c.712C>A	p.Arg238Ser	p.R238S	ENST00000282397	NM_002019.4	238	Cgc/Agc	6/30	0.3	1	FACETS	0.928	0.802	1	0.928	0.802	1	CLONAL	1	TRUE	0	0.29	1		226	375	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012474	29012474	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	59	194	1	ENST00000282397.4:c.397A>T	p.Arg133Ter	p.R133*	ENST00000282397	NM_002019.4	133	Aga/Tga	4/30	0.3	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.29	1		195	313	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727529	88727529	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	39	197	0	ENST00000360948.2:c.250C>A	p.His84Asn	p.H84N	ENST00000360948	NM_001012338.2	84	Cac/Aac	3/19	0.3	1	FACETS	0.59	0.489	0.701	0.59	0.489	0.701	SUBCLONAL	1	TRUE	0	0.29	1		197	390	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369266	40369266	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	108	545	0	ENST00000293328.3:c.1292G>T	p.Gly431Val	p.G431V	ENST00000293328	NM_012448.3	431	gGg/gTg	11/19	0.160090752672985	0	FACETS	0.589	0.528	0.654			1	INDETERMINATE	1	TRUE	0	0.29	0		545	898	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007547	62007547	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1567810193	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	73	409	0	ENST00000392795.3:c.320C>A	p.Thr107Asn	p.T107N	ENST00000392795	NM_001039933.1	107	aCc/aAc	3/6	1	2	FACETS	0.882	0.772	1	0.882	0.772	1	CLONAL	1	TRUE	1	0.29	2		409	571	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374884	45374884	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	41	316	0	ENST00000262160.6:c.959A>T	p.Asn320Ile	p.N320I	ENST00000262160	NM_005901.5	320	aAc/aTc	8/11	1	2	FACETS	0.535	0.445	0.635	0.535	0.445	0.635	SUBCLONAL	1	TRUE	1	0.29	2		316	529	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610541	10610541	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	61	351	0	ENST00000171111.5:c.169G>T	p.Glu57Ter	p.E57*	ENST00000171111	NM_203500.1	57	Gag/Tag	2/6	0.3	1	FACETS	0.901	0.781	1	0.901	0.781	1	CLONAL	1	TRUE	0	0.29	1		351	399	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710569	40710569	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1290388722	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	126	282	0	ENST00000373198.4:c.4282A>G	p.Ile1428Val	p.I1428V	ENST00000373198	NM_133170.3	1428	Atc/Gtc	31/32	NA	2	FACETS	0.957	0.873	1			1	INDETERMINATE	2	TRUE	NA	0.29	2		282	454	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710600	40710600	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	25	273	0	ENST00000373198.4:c.4251C>G	p.Ile1417Met	p.I1417M	ENST00000373198	NM_133170.3	1417	atC/atG	31/32	NA	2	FACETS	0.367	0.288	0.457			1	INDETERMINATE	1	TRUE	NA	0.29	2		273	470	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206809	36206809	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	16	165	0	ENST00000300305.3:c.703G>A	p.Ala235Thr	p.A235T	ENST00000300305		235	Gcc/Acc	6/8	1	2	FACETS	0.433	0.32	0.568	0.433	0.32	0.568	SUBCLONAL	1	TRUE	1	0.29	2		165	255	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889090	76889090	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	74	508	0	ENST00000373344.5:c.4920G>T	p.Lys1640Asn	p.K1640N	ENST00000373344	NM_000489.3	1640	aaG/aaT	18/35	0.180566957172327	1	FACETS	0.612	0.535	0.695	0.612	0.535	0.695	SUBCLONAL	1	TRUE	0	0.29	1		508	713	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76931795	76931795	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	87	332	0	ENST00000373344.5:c.3737-2A>T		p.X1246_splice	ENST00000373344	NM_000489.3	1246			0.180566957172327	1	FACETS	0.763	0.676	0.857	0.763	0.676	0.857	SUBCLONAL	1	TRUE	0	0.29	1		332	672	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200096	123200096	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1239113258	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	91	409	0	ENST00000218089.9:c.2168G>T	p.Gly723Val	p.G723V	ENST00000218089	NM_001042749.1	723	gGa/gTa	22/35	0.180566957172327	1	FACETS	0.654	0.58	0.734	0.654	0.58	0.734	SUBCLONAL	1	TRUE	0	0.29	1		409	820	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220500	123220500	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	125	464	0	ENST00000218089.9:c.3157G>T	p.Asp1053Tyr	p.D1053Y	ENST00000218089	NM_001042749.1	1053	Gat/Tat	30/35	0.180566957172327	1	FACETS	0.983	0.89	1	0.983	0.89	1	CLONAL	1	TRUE	0	0.29	1		464	750	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141497	11141498	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs797045982	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	57	349	0	ENST00000358026.2:c.3480dup	p.Leu1161AlafsTer15	p.L1161Afs*15	ENST00000358026	NM_001128849.1	1158	-/G	25/36	0.3	1	FACETS	0.901	0.776	1	0.901	0.776	1	CLONAL	1	TRUE	0	0.29	1		349	373	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974689	21974689	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	48	315	0	ENST00000304494.5:c.138del	p.Arg47GlyfsTer6	p.R47Gfs*6	ENST00000304494	NM_000077.4	46	cgG/cg	1/3	0.256183034102826	1	FACETS	0.806	0.684	0.94	0.806	0.684	0.94	CLONAL	1	TRUE	0	0.29	1		315	351	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045683	47045684	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0003311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	19	297	0	ENST00000377604.3:c.2564_2565delinsTT	p.Gly855Val	p.G855V	ENST00000377604	NM_001204468.1	855	gGG/gTT	23/24	0.3	1	FACETS	0.323	0.244	0.415	0.323	0.244	0.415	SUBCLONAL	1	TRUE	0	0.29	1		297	347	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514057	125514057	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003325-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	351	463	0	ENST00000428830.2:c.995C>T	p.Pro332Leu	p.P332L	ENST00000428830	NM_001114121.2	332	cCc/cTc	10/14	0.204151046046147	1	FACETS	0.539	0.514	0.564	0.539	0.514	0.564	INDETERMINATE	1	TRUE	0	0.921013592315762	1		463	763	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690169	47690169	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003325-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	293	279	0	ENST00000233146.2:c.1387-1G>A		p.X463_splice	ENST00000233146	NM_000251.2	463			1	2	FACETS	0.958	0.909	1	0.958	0.909	1	CLONAL	1	TRUE	1	0.921013592315762	2		279	664	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851697	134851697	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370730579	NA	P-0003325-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	277	283	0	ENST00000398015.3:c.1103G>A	p.Arg368Gln	p.R368Q	ENST00000398015	NM_004441.4	368	cGg/cAg	5/16	0.765227002291343	3	FACETS	1	0.99	1	0.6	0.566	0.634	CLONAL	1	TRUE	1	0.921013592315762	3		283	732	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056326	26056326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201575995	NA	P-0003325-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	29	262	0	ENST00000343677.2:c.331G>A	p.Ala111Thr	p.A111T	ENST00000343677	NM_005319.3	111	Gca/Aca	1/1	1	2	FACETS	0.118	0.094	0.145	0.118	0.094	0.145	SUBCLONAL	1	TRUE	1	0.921013592315762	2		262	533	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508322	106508322	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs931789610	NA	P-0003325-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	17	107	0	ENST00000359195.3:c.316T>A	p.Trp106Arg	p.W106R	ENST00000359195	NM_002649.2	106	Tgg/Agg	2/11	1	2	FACETS	0.185	0.138	0.24	0.185	0.138	0.24	SUBCLONAL	1	TRUE	1	0.921013592315762	2		107	200	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138092	64138092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003325-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	155	279	0	ENST00000334205.4:c.2015C>T	p.Ser672Leu	p.S672L	ENST00000334205	NM_003942.2	672	tCg/tTg	16/17	1	2	FACETS	0.831	0.769	0.894	0.831	0.769	0.894	CLONAL	1	TRUE	1	0.921013592315762	2		279	405	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32931924	32931924	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0003325-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	368	370	0	ENST00000380152.3:c.7663A>T	p.Lys2555Ter	p.K2555*	ENST00000380152		2555	Aaa/Taa	16/27	1	2	FACETS	0.967	0.923	1	0.967	0.923	1	CLONAL	1	TRUE	1	0.921013592315762	2		370	826	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035305	42035305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003325-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	91	627	0	ENST00000219905.7:c.5147C>T	p.Ser1716Phe	p.S1716F	ENST00000219905	NM_001164273.1	1716	tCt/tTt	15/24	NA	2	FACETS	0.197	0.174	0.222			1	INDETERMINATE	1	TRUE	NA	0.921013592315762	2		627	1002	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478647	99478647	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003325-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	237	281	0	ENST00000268035.6:c.3289G>C	p.Glu1097Gln	p.E1097Q	ENST00000268035	NM_000875.3	1097	Gaa/Caa	17/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.921013592315762	2		281	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0003325-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	320	419	0	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	0.881377177159651	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.921013592315762	1		419	360	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588876	29588876	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1555619056	NA	P-0003325-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	148	306	0	ENST00000356175.3:c.4661+1G>A		p.X1554_splice	ENST00000356175	NM_000267.3	1554			0.857007256940413	1	FACETS	0.504	0.467	0.542	0.504	0.467	0.542	SUBCLONAL	1	TRUE	0	0.921013592315762	1		306	344	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354779	40354779	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003325-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	216	401	0	ENST00000293328.3:c.2125C>T	p.Pro709Ser	p.P709S	ENST00000293328	NM_012448.3	709	Cct/Tct	17/19	0.921013592315762	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.921013592315762	1		401	251	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371744	45371744	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003325-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	71	321	0	ENST00000262160.6:c.1247T>G	p.Met416Arg	p.M416R	ENST00000262160	NM_005901.5	416	aTg/aGg	10/11	1	2	FACETS	0.205	0.178	0.234	0.205	0.178	0.234	SUBCLONAL	1	TRUE	1	0.921013592315762	2		321	753	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223169	1223169	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1230130092	NA	P-0003325-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	160	308	0	ENST00000326873.7:c.1106C>T	p.Pro369Leu	p.P369L	ENST00000326873	NM_000455.4	369	cCc/cTc	8/10	0.204151046046147	1	FACETS	0.493	0.458	0.529	0.493	0.458	0.529	INDETERMINATE	1	TRUE	0	0.921013592315762	1		308	380	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123716	11123716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003325-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	267	348	0	ENST00000358026.2:c.2366C>T	p.Thr789Ile	p.T789I	ENST00000358026	NM_001128849.1	789	aCc/aTc	16/36	0.204151046046147	1	FACETS	0.61	0.579	0.641	0.61	0.579	0.641	INDETERMINATE	1	TRUE	0	0.921013592315762	1		348	513	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942143	17942143	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003325-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	45	263	0	ENST00000458235.1:c.2872G>A	p.Glu958Lys	p.E958K	ENST00000458235	NM_000215.3	958	Gag/Aag	21/24	0.204151046046147	1	FACETS	0.14	0.117	0.164	0.14	0.117	0.164	INDETERMINATE	1	TRUE	0	0.921013592315762	1		263	377	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961443	54961443	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003325-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	87	142	0	ENST00000312783.6:c.189G>T	p.Lys63Asn	p.K63N	ENST00000312783	NM_198436.1	63	aaG/aaT	4/10	NA	2	FACETS	0.638	0.572	0.708			1	INDETERMINATE	1	TRUE	NA	0.921013592315762	2		142	296	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839758	42839758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003325-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	40	367	0	ENST00000398585.3:c.1481G>A	p.Gly494Glu	p.G494E	ENST00000398585	NM_001135099.1	494	gGg/gAg	13/14	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.921013592315762	NA		367	573	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325340	1325340	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003325-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	241	321	0	ENST00000400841.2:c.335G>T	p.Trp112Leu	p.W112L	ENST00000400841		112	tGg/tTg	3/6	1	2	FACETS	0.918	0.865	0.972	0.918	0.865	0.972	CLONAL	1	TRUE	1	0.921013592315762	2		321	570	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429317	47429317	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003325-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	328	485	0	ENST00000377045.4:c.1445A>C	p.Asp482Ala	p.D482A	ENST00000377045	NM_001654.4	482	gAc/gCc	14/16	1	2	FACETS	0.926	0.88	0.972	0.926	0.88	0.972	CLONAL	1	TRUE	1	0.921013592315762	2		485	769	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431309	49431310	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCTGCTGCTGGGCAGGCTGCAACTGTGATGAAA	novel	NA	P-0003325-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	67	173	1	ENST00000301067.7:c.9829_9830insTTTCATCACAGTTGCAGCCTGCCCAGCAGCAGC	p.Gln3276_Gln3277insLeuSerSerGlnLeuGlnProAlaGlnGlnGln	p.Q3276_Q3277insLSSQLQPAQQQ	ENST00000301067	NM_003482.3	3277	cag/cTTTCATCACAGTTGCAGCCTGCCCAGCAGCAGCag	34/54	1	2	FACETS	0.452	0.395	0.512	0.452	0.395	0.512	SUBCLONAL	1	TRUE	1	0.921013592315762	2		174	322	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953775	48953776	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0003325-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	540	268	0	ENST00000267163.4:c.1379dup	p.Met460IlefsTer3	p.M460Ifs*3	ENST00000267163	NM_000321.2	460	atg/aTtg	14/27	0.921013592315762	2	FACETS	0.969	0.952	0.985	0.969	0.952	0.985	CLONAL	2	TRUE	0	0.921013592315762	2		268	605	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082436	16082436	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	12	222	0	ENST00000281043.3:c.250G>C	p.Glu84Gln	p.E84Q	ENST00000281043	NM_005378.4	84	Gag/Cag	2/3	0.31085936505125	4	FACETS	0.847	0.599	1			1	CLONAL	1	TRUE	NA	0.312731171544881	4		222	119	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11552761	NA	P-0003353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	27	423	0	ENST00000418115.1:c.50G>C	p.Gly17Ala	p.G17A	ENST00000418115	NM_001664.2	17	gGa/gCa	2/5	0.237966327290748	1	FACETS	0.69	0.553	0.846	0.69	0.553	0.846	SUBCLONAL	1	TRUE	0	0.312731171544881	1		423	211	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505595	186505595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	107	399	0	ENST00000323963.5:c.1003C>T	p.Arg335Cys	p.R335C	ENST00000323963		335	Cgc/Tgc	10/11	0.312731171544881	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.312731171544881	3		399	359	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517758	176517758	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	44	488	0	ENST00000292408.4:c.368C>G	p.Ser123Cys	p.S123C	ENST00000292408	NM_213647.1	123	tCc/tGc	4/18	0.194339052609927	4	FACETS	1	0.955	1	0.702	0.593	0.821	CLONAL	1	TRUE	2	0.312731171544881	4		488	263	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225674	26225674	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	78	708	0	ENST00000360408.1:c.292G>C	p.Glu98Gln	p.E98Q	ENST00000360408	NM_003532.2	98	Gag/Cag	1/1	0.312731171544881	6	FACETS	1	0.969	1	0.444	0.39	0.501	CLONAL	1	TRUE	3	0.312731171544881	6		708	609	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485282	8485282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	27	357	0	ENST00000356435.5:c.3098C>T	p.Ser1033Phe	p.S1033F	ENST00000356435		1033	tCc/tTc	18/35	0.312731171544881	4	FACETS	0.667	0.531	0.822	0.333	0.265	0.411	SUBCLONAL	1	TRUE	2	0.312731171544881	4		357	340	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276914	123276914	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	31	304	0	ENST00000358487.5:c.1003G>C	p.Glu335Gln	p.E335Q	ENST00000358487	NM_000141.4	335	Gag/Cag	8/18	NA	2	FACETS	0.757	0.615	0.916			1	INDETERMINATE	1	TRUE	NA	0.312731171544881	2		304	262	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445534	49445534	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	10	117	0	ENST00000301067.7:c.1932G>A	p.Met644Ile	p.M644I	ENST00000301067	NM_003482.3	644	atG/atA	10/54	0.312731171544881	5	FACETS	0.949	0.649	1	0.316	0.216	0.44	CLONAL	1	TRUE	2	0.312731171544881	5		117	99	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891189	112891189	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	17	211	0	ENST00000351677.2:c.523C>T	p.Gln175Ter	p.Q175*	ENST00000351677	NM_002834.3	175	Cag/Tag	4/16	NA	2	FACETS	0.688	0.517	0.889			1	INDETERMINATE	1	TRUE	NA	0.312731171544881	2		211	158	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114205	115114205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1456819388	NA	P-0003353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	29	389	0	ENST00000257566.3:c.1012G>A	p.Glu338Lys	p.E338K	ENST00000257566	NM_016569.3	338	Gag/Aag	6/8	NA	2	FACETS	0.64	0.515	0.781			1	INDETERMINATE	1	TRUE	NA	0.312731171544881	2		389	290	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061264	38061264	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	52	369	0	ENST00000250448.2:c.725C>A	p.Ser242Tyr	p.S242Y	ENST00000250448	NM_004496.3	242	tCc/tAc	2/2	0.312731171544881	4	FACETS	0.785	0.674	0.906	0.785	0.674	0.906	CLONAL	2	TRUE	2	0.312731171544881	4		369	278	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061283	38061283	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	64	405	0	ENST00000250448.2:c.706G>A	p.Asp236Asn	p.D236N	ENST00000250448	NM_004496.3	236	Gac/Aac	2/2	0.312731171544881	4	FACETS	0.936	0.818	1	0.936	0.818	1	CLONAL	2	TRUE	2	0.312731171544881	4		405	287	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996086	73996086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	14	370	1	ENST00000318443.5:c.820C>T	p.Pro274Ser	p.P274S	ENST00000318443	NM_001024736.1	274	Cct/Tct	5/10	0.312731171544881	3	FACETS	0.815	0.594	1	0.272	0.198	0.36	CLONAL	1	TRUE	0	0.312731171544881	3		371	127	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857558	9857558	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	16	192	0	ENST00000330684.3:c.3843G>C	p.Lys1281Asn	p.K1281N	ENST00000330684	NM_001134407.1	1281	aaG/aaC	13/13	1	2	FACETS	0.581	0.431	0.759	0.581	0.431	0.759	SUBCLONAL	1	TRUE	1	0.312731171544881	2		192	176	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341344	89341344	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	15	267	0	ENST00000301030.4:c.7591G>C	p.Glu2531Gln	p.E2531Q	ENST00000301030	NM_001256183.1	2531	Gag/Cag	11/13	0.139625971635924	0	FACETS	0.568	0.42	0.743			1	INDETERMINATE	1	TRUE	0	0.312731171544881	0		267	116	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643617	52643618	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	42	265	0	ENST00000394830.3:c.2278_2279insT	p.Arg760LeufsTer8	p.R760Lfs*8	ENST00000394830	NM_018313.4	760	cgc/cTgc	17/30	0.312731171544881	3	FACETS	1	0.916	1	0.573	0.481	0.674	CLONAL	1	TRUE	1	0.312731171544881	3		265	271	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489499	56489499	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	38	256	0	ENST00000267101.3:c.1967del	p.Phe656SerfsTer2	p.F656Sfs*2	ENST00000267101	NM_001982.3	655	aTt/at	17/28	0.312731171544881	5	FACETS	1	0.931	1	0.418	0.347	0.496	CLONAL	1	TRUE	2	0.312731171544881	5		256	285	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335040	81335040	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751819844	NA	P-0003363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	83	228	0	ENST00000222390.5:c.1787C>T	p.Thr596Met	p.T596M	ENST00000222390	NM_000601.4	596	aCg/aTg	16/18	0.185464231455024	4	FACETS	0.822	0.732	0.917	0.822	0.732	0.917	INDETERMINATE	2	TRUE	2	0.433134766020837	4		228	334	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206593	108206593	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587782049	NA	P-0003363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	92	243	0	ENST00000278616.4:c.8173G>C	p.Asp2725His	p.D2725H	ENST00000278616	NM_000051.3	2725	Gat/Cat	56/63	0.433134766020837	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.433134766020837	1		243	301	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793211	139793212	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs748531430	NA	P-0003363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	176	409	1	ENST00000247668.2:c.26dup	p.Gly10TrpfsTer70	p.G10Wfs*70	ENST00000247668	NM_021138.3	7	acc/aCcc	2/11	0.0927792833820276	1	FACETS	0.798	0.745	0.851	1	0.992	1	INDETERMINATE	2	TRUE	0	0.433134766020837	1		410	399	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	18	673	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.93	0.726	1	1	0.948	1	CLONAL	3	TRUE	1	0.230496593410365	2		673	56	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0003391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	24	134	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.808	1	1	0.951	1	CLONAL	2	TRUE	1	0.230496593410365	2		134	103	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627736	187627736	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	11	507	0	ENST00000441802.2:c.3246C>A	p.Phe1082Leu	p.F1082L	ENST00000441802	NM_005245.3	1082	ttC/ttA	2/27	1	2	FACETS	0.994	0.694	1	0.994	0.694	1	CLONAL	1	TRUE	1	0.230496593410365	2		507	96	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765775	41765775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	10	236	0	ENST00000301178.4:c.2651C>T	p.Ser884Phe	p.S884F	ENST00000301178	NM_021913.4	884	tCc/tTc	20/20	1	2	FACETS	0.789	0.538	1	0.789	0.538	1	CLONAL	1	TRUE	1	0.230496593410365	2		236	110	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44911017	44911017	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	14	488	0	ENST00000377967.4:c.718C>T	p.Gln240Ter	p.Q240*	ENST00000377967	NM_021140.2	240	Caa/Taa	9/29	0.221183822967833	0	FACETS	0.786	0.573	1			1	CLONAL	1	TRUE	0	0.230496593410365	0		488	119	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949018	44949018	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	11	412	0	ENST00000377967.4:c.3579G>A	p.Trp1193Ter	p.W1193*	ENST00000377967	NM_021140.2	1193	tgG/tgA	25/29	0.221183822967833	0	FACETS	1	0.735	1			1	CLONAL	1	TRUE	0	0.230496593410365	0		412	70	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211866	123211867	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	41	507	0	ENST00000218089.9:c.2737dup	p.Ile913AsnfsTer5	p.I913Nfs*5	ENST00000218089	NM_001042749.1	911	-/A	27/35	0.221183822967833	0	FACETS	0.999	0.85	1			1	CLONAL	2	TRUE	0	0.230496593410365	0		507	137	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195623	123195624	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0003391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	17	189	0	ENST00000218089.9:c.1537_1538del	p.Leu513AsnfsTer3	p.L513Nfs*3	ENST00000218089	NM_001042749.1	513	CTa/a	17/35	0.221183822967833	0	FACETS	1	0.873	1			1	CLONAL	1	TRUE	0	0.230496593410365	0		189	90	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918538	44918539	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0003391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	44	480	0	ENST00000377967.4:c.1024_1025del	p.Ile342LeufsTer21	p.I342Lfs*21	ENST00000377967	NM_021140.2	341	TAt/t	12/29	0.221183822967833	0	FACETS	1	0.896	1			1	CLONAL	2	TRUE	0	0.230496593410365	0		480	139	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0003396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	58	66	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.962	1	1	0.984	1	CLONAL	2	TRUE	1	0.491248524888409	2		66	101	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0003396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	12	134	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.267	0.188	0.364	0.267	0.188	0.364	SUBCLONAL	1	TRUE	1	0.491248524888409	2		134	183	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0003396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	130	286	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	0.491248524888409	2		286	463	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806119	1806119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931614	NA	P-0003396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	64	344	0	ENST00000260795.2:c.1138G>A	p.Gly380Arg	p.G380R	ENST00000260795		380	Ggg/Agg	8/17	1	2	FACETS	0.5	0.433	0.572	0.5	0.433	0.572	SUBCLONAL	1	TRUE	1	0.491248524888409	2		344	521	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0003396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	13	244	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.087	0.061	0.119	0.087	0.061	0.119	SUBCLONAL	1	TRUE	1	0.491248524888409	2		244	607	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25536796	25536796	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781254365	NA	P-0003396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	129	242	0	ENST00000264709.3:c.58G>A	p.Glu20Lys	p.E20K	ENST00000264709	NM_175629.2	20	Gag/Aag	2/23	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.491248524888409	2		242	469	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682422	52682422	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	91	414	0	ENST00000394830.3:c.751G>C	p.Asp251His	p.D251H	ENST00000394830	NM_018313.4	251	Gat/Cat	8/30	1	2	FACETS	0.505	0.448	0.566	0.505	0.448	0.566	SUBCLONAL	1	TRUE	1	0.491248524888409	2		414	733	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421528	32421528	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	67	212	0	ENST00000332351.3:c.1064G>A	p.Arg355Lys	p.R355K	ENST00000332351	NM_024426.4	355	aGa/aAa	6/10	1	2	FACETS	0.523	0.455	0.596	0.523	0.455	0.596	SUBCLONAL	1	TRUE	1	0.491248524888409	2		212	522	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195295	102195295	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	121	505	0	ENST00000263464.3:c.55A>G	p.Thr19Ala	p.T19A	ENST00000263464	NM_001165.4	19	Acg/Gcg	2/9	1	2	FACETS	0.585	0.528	0.645	0.585	0.528	0.645	SUBCLONAL	1	TRUE	1	0.491248524888409	2		505	842	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619885	21619885	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	64	335	0	ENST00000382592.4:c.281C>G	p.Ser94Cys	p.S94C	ENST00000382592	NM_014572.2	94	tCt/tGt	2/8	NA	2	FACETS	0.41	0.354	0.47			1	INDETERMINATE	1	TRUE	NA	0.491248524888409	2		335	636	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828733	3828733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	73	306	0	ENST00000262367.5:c.1909G>A	p.Glu637Lys	p.E637K	ENST00000262367	NM_004380.2	637	Gaa/Aaa	9/31	1	2	FACETS	0.451	0.394	0.512	0.451	0.394	0.512	SUBCLONAL	1	TRUE	1	0.491248524888409	2		306	659	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618422	37618422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs796501956	NA	P-0003396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	54	240	0	ENST00000447079.4:c.98G>A	p.Arg33Lys	p.R33K	ENST00000447079	NM_015083.1	33	aGa/aAa	1/14	1	2	FACETS	0.444	0.379	0.515	0.444	0.379	0.515	SUBCLONAL	1	TRUE	1	0.491248524888409	2		240	495	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921117	50921117	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	71	370	0	ENST00000440232.2:c.3237C>G	p.Phe1079Leu	p.F1079L	ENST00000440232	NM_002691.3	1079	ttC/ttG	27/27	1	2	FACETS	0.494	0.431	0.562	0.494	0.431	0.562	SUBCLONAL	1	TRUE	1	0.491248524888409	2		370	585	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713434	40713434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	60	241	0	ENST00000373198.4:c.4081G>A	p.Ala1361Thr	p.A1361T	ENST00000373198	NM_133170.3	1361	Gcc/Acc	30/32	1	2	FACETS	0.562	0.485	0.644	0.562	0.485	0.644	SUBCLONAL	1	TRUE	1	0.491248524888409	2		241	435	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200213	123200214	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0003396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	44	325	0	ENST00000218089.9:c.2192_2193del	p.Ile731ThrfsTer16	p.I731Tfs*16	ENST00000218089	NM_001042749.1	731	aTT/a	23/35	1	2	FACETS	0.366	0.307	0.432	0.366	0.307	0.432	SUBCLONAL	1	TRUE	1	0.491248524888409	2		325	489	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202443	123202444	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	103	357	0	ENST00000218089.9:c.2296dup	p.Arg766LysfsTer19	p.R766Kfs*19	ENST00000218089	NM_001042749.1	765	-/A	24/35	1	2	FACETS	0.752	0.674	0.833	0.752	0.674	0.833	SUBCLONAL	1	TRUE	1	0.491248524888409	2		357	558	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	16	374	0				ENST00000310581	NM_198253.2	-/1132			0.285173907784405	1	FACETS	0.419	0.323	0.523	0.419	0.323	0.523	INDETERMINATE	1	TRUE	0	0.896584046118919	1		374	47	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0003408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	47	134	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.904	0.786	1	0.904	0.786	1	CLONAL	1	TRUE	1	0.896584046118919	2		134	116	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105604	27105604	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758075735	NA	P-0003408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	142	493	0	ENST00000324856.7:c.5215C>T	p.Pro1739Ser	p.P1739S	ENST00000324856	NM_006015.4	1739	Cca/Tca	20/20	1	2	FACETS	0.934	0.864	1	0.934	0.864	1	CLONAL	1	TRUE	1	0.896584046118919	2		493	339	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436054	49436054	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0003408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	46	203	0	ENST00000301067.7:c.5927C>G	p.Ser1976Ter	p.S1976*	ENST00000301067	NM_003482.3	1976	tCa/tGa	28/54	NA	2	FACETS	1	0.877	1			1	INDETERMINATE	1	TRUE	NA	0.896584046118919	2		203	102	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938412	44938412	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	270	339	0	ENST00000377967.4:c.2960A>G	p.Lys987Arg	p.K987R	ENST00000377967	NM_021140.2	987	aAa/aGa	20/29	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.896584046118919	1		339	296	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651893	36651894	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0003408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	119	423	0	ENST00000244741.5:c.19dup	p.Asp7GlyfsTer29	p.D7Gfs*29	ENST00000244741	NM_000389.4	5	-/G	2/3	0.103567784370591	4	FACETS	0.954	0.877	1	0.954	0.877	1	INDETERMINATE	2	TRUE	2	0.896584046118919	4		423	264	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	34	374	0				ENST00000310581	NM_198253.2	-/1132			0.292044855789872	3	FACETS	0.658	0.543	0.785	0.219	0.181	0.262	INDETERMINATE	1	TRUE	0	0.706079382083657	3		374	198	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0003434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	54	753	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	0.827	0.718	0.942	0.827	0.718	0.942	CLONAL	1	TRUE	1	0.706079382083657	2		753	185	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0003434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	134	532	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.781	0.727	0.834	1	0.99	1	SUBCLONAL	2	TRUE	1	0.706079382083657	2		532	243	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45873425	45873425	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	179	430	0	ENST00000391945.4:c.71A>G	p.Tyr24Cys	p.Y24C	ENST00000391945	NM_000400.3	24	tAc/tGc	2/23	0.483770292643606	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.706079382083657	3		430	329	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691889	30691889	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	57	285	0	ENST00000295754.5:c.391G>A	p.Glu131Lys	p.E131K	ENST00000295754	NM_003242.5	131	Gag/Aag	3/7	0.192953076277961	1	FACETS	0.741	0.653	0.831	0.741	0.653	0.831	INDETERMINATE	1	TRUE	0	0.706079382083657	1		285	141	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442080	52442080	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	52	309	0	ENST00000460680.1:c.269C>G	p.Ser90Cys	p.S90C	ENST00000460680	NM_004656.3	90	tCt/tGt	5/17	0.192953076277961	1	FACETS	0.476	0.411	0.546	0.476	0.411	0.546	INDETERMINATE	1	TRUE	0	0.706079382083657	1		309	200	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443892	52443892	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0003434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	115	341	0	ENST00000460680.1:c.3G>A	p.Met1?	p.M1?	ENST00000460680	NM_004656.3	1	atG/atA	1/17	0.192953076277961	1	FACETS	0.682	0.623	0.742	0.682	0.623	0.742	INDETERMINATE	1	TRUE	0	0.706079382083657	1		341	309	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668637	52668637	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs764729828	NA	P-0003434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	30	419	3	ENST00000394830.3:c.1282A>G	p.Ile428Val	p.I428V	ENST00000394830	NM_018313.4	428	Ata/Gta	12/30	0.192953076277961	1	FACETS	0.407	0.333	0.488	0.407	0.333	0.488	INDETERMINATE	1	TRUE	0	0.706079382083657	1		422	135	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119812218	119812218	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	47	391	0	ENST00000316626.5:c.64G>A	p.Ala22Thr	p.A22T	ENST00000316626		22	Gct/Act	1/12	0.192953076277961	1	FACETS	0.379	0.323	0.44	0.379	0.323	0.44	INDETERMINATE	1	TRUE	0	0.706079382083657	1		391	227	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157573	106157573	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1193321482	NA	P-0003434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	46	407	0	ENST00000380013.4:c.2474C>T	p.Ser825Leu	p.S825L	ENST00000380013	NM_001127208.2	825	tCa/tTa	3/11	1	2	FACETS	0.863	0.741	0.991	0.863	0.741	0.991	CLONAL	1	TRUE	1	0.706079382083657	2		407	151	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112569	115112569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180836314	NA	P-0003434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	139	410	0	ENST00000257566.3:c.1171G>A	p.Asp391Asn	p.D391N	ENST00000257566	NM_016569.3	391	Gac/Aac	7/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.706079382083657	2		410	333	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26927961	26927961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	27	387	0	ENST00000381527.3:c.400C>T	p.Gln134Ter	p.Q134*	ENST00000381527	NM_001260.1	134	Cag/Tag	4/13	0.651351524888588	1	FACETS	0.458	0.372	0.552	0.458	0.372	0.552	SUBCLONAL	1	TRUE	0	0.706079382083657	1		387	108	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28931751	28931751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	35	496	0	ENST00000282397.4:c.2188C>T	p.His730Tyr	p.H730Y	ENST00000282397	NM_002019.4	730	Cac/Tac	15/30	0.651351524888588	1	FACETS	0.573	0.481	0.67	0.573	0.481	0.67	SUBCLONAL	1	TRUE	0	0.706079382083657	1		496	112	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435153	110435153	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776792996	NA	P-0003434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	30	300	0	ENST00000375856.3:c.3248C>T	p.Pro1083Leu	p.P1083L	ENST00000375856	NM_003749.2	1083	cCg/cTg	1/2	0.651351524888588	1	FACETS	0.294	0.239	0.355	0.294	0.239	0.355	SUBCLONAL	1	TRUE	0	0.706079382083657	1		300	187	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005599	42005599	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	62	552	0	ENST00000219905.7:c.3335A>T	p.Asp1112Val	p.D1112V	ENST00000219905	NM_001164273.1	1112	gAt/gTt	9/24	0.706079382083657	1	FACETS	0.738	0.653	0.824	0.738	0.653	0.824	SUBCLONAL	1	TRUE	0	0.706079382083657	1		552	154	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942536	17942536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	44	301	0	ENST00000458235.1:c.2752C>T	p.Arg918Cys	p.R918C	ENST00000458235	NM_000215.3	918	Cgc/Tgc	20/24	0.53400400246828	1	FACETS	0.345	0.291	0.402	0.345	0.291	0.402	SUBCLONAL	1	TRUE	0	0.706079382083657	1		301	234	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024021	31024021	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1212204313	NA	P-0003434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	65	414	0	ENST00000375687.4:c.3506C>A	p.Ser1169Tyr	p.S1169Y	ENST00000375687	NM_015338.5	1169	tCt/tAt	13/13	0.338572009790004	2	FACETS	1	0.93	1	0.535	0.474	0.598	INDETERMINATE	1	TRUE	0	0.706079382083657	2		414	172	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167454	24167454	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	37	407	0	ENST00000263121.7:c.838G>A	p.Glu280Lys	p.E280K	ENST00000263121	NM_003073.3	280	Gag/Aag	7/9	0.192953076277961	1	FACETS	0.435	0.364	0.511	0.435	0.364	0.511	INDETERMINATE	1	TRUE	0	0.706079382083657	1		407	156	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035106	30035106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	25	417	0	ENST00000338641.4:c.268G>A	p.Glu90Lys	p.E90K	ENST00000338641	NM_000268.3	90	Gaa/Aaa	3/16	0.192953076277961	1	FACETS	0.369	0.295	0.452	0.369	0.295	0.452	INDETERMINATE	1	TRUE	0	0.706079382083657	1		417	124	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545855	41545855	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs867077693	NA	P-0003434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	80	519	0	ENST00000263253.7:c.2470C>T	p.Gln824Ter	p.Q824*	ENST00000263253	NM_001429.3	824	Caa/Taa	14/31	0.192953076277961	1	FACETS	0.646	0.578	0.716	0.646	0.578	0.716	INDETERMINATE	1	TRUE	0	0.706079382083657	1		519	227	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060819	38060820	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGGGA	novel	NA	P-0003434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	83	566	0	ENST00000250448.2:c.1169_1170insTCCCG	p.Asp391ProfsTer51	p.D391Pfs*51	ENST00000250448	NM_004496.3	390	ggg/ggTCCCGg	2/2	0.410560378304423	1	FACETS	0.724	0.652	0.798	0.724	0.652	0.798	INDETERMINATE	1	TRUE	0	0.706079382083657	1		566	210	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226087	226087	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	41	162	0	ENST00000264932.6:c.548del	p.Gly183AlafsTer43	p.G183Afs*43	ENST00000264932	NM_004168.2	182	aaG/aa	5/15	0.292044855789872	3	FACETS	1	0.894	1	0.356	0.302	0.414	INDETERMINATE	1	TRUE	0	0.706079382083657	3		162	147	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262227	16262231	+	frameshift_variant	Frame_Shift_Del	DEL	TCCTG	TCCTG	-	novel	NA	P-0003434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	28	73	0	ENST00000375759.3:c.9494_9498del	p.Pro3165ArgfsTer17	p.P3165Rfs*17	ENST00000375759	NM_015001.2	3164	ctTCCTGtc/cttc	11/15	1	2	FACETS	0.634	0.516	0.765	0.634	0.516	0.765	SUBCLONAL	1	TRUE	1	0.706079382083657	2		73	125	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944758	31944758	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003442-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	92	157	0	ENST00000340398.3:c.343A>G	p.Lys115Glu	p.K115E	ENST00000340398	NM_001013699.2	115	Aag/Gag	1/1	1	2	FACETS	0.951	0.861	1	0.951	0.861	1	CLONAL	1	TRUE	1	0.833602808662785	2		157	232	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578484	7578485	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1064793929	NA	P-0003442-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	224	264	0	ENST00000269305.4:c.445dup	p.Ser149PhefsTer32	p.S149Ffs*32	ENST00000269305	NM_001126112.2	149	tcc/tTcc	5/11	0.833602808662785	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.833602808662785	1		264	305	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050894	49050894	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0003442-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	185	264	0	ENST00000267163.4:c.2581del	p.Arg861GlufsTer12	p.R861Efs*12	ENST00000267163	NM_000321.2	860	Aaa/aa	25/27	0.833602808662785	1	FACETS	0.75	0.705	0.795	0.75	0.705	0.795	SUBCLONAL	1	TRUE	0	0.833602808662785	1		264	345	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004599	150004600	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0003442-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	41	429	0	ENST00000253339.5:c.1625_1626del	p.Val542AspfsTer6	p.V542Dfs*6	ENST00000253339		542	gTG/g	3/7	0.833602808662785	1	FACETS	0.132	0.11	0.157	0.132	0.11	0.157	SUBCLONAL	1	TRUE	0	0.833602808662785	1		429	435	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0003449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	125	299	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.411981935298019	4	FACETS	0.873	0.801	0.947	0.873	0.801	0.947	INDETERMINATE	2	TRUE	2	0.770683204050421	4		299	329	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111131	193111131	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	21	352	0	ENST00000367435.3:c.664C>T	p.Arg222Ter	p.R222*	ENST00000367435	NM_024529.4	222	Cga/Tga	7/17	0.168619161275713	5	FACETS	0.39	0.3	0.495	0.13	0.1	0.165	INDETERMINATE	1	TRUE	2	0.770683204050421	5		352	301	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793443	18793443	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	22	422	0	ENST00000266497.5:c.4140A>T	p.Lys1380Asn	p.K1380N	ENST00000266497		1380	aaA/aaT	30/31	0.390952273976292	4	FACETS	0.403	0.313	0.507			1	INDETERMINATE	1	TRUE	NA	0.770683204050421	4		422	251	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920172	76920173	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0003449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	108	220	0	ENST00000373344.5:c.3904dup	p.Arg1302LysfsTer7	p.R1302Kfs*7	ENST00000373344	NM_000489.3	1302	aga/aAga	11/35	1	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.770683204050421	1		220	159	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577576	7577582	+	frameshift_variant	Frame_Shift_Del	DEL	GTTGTAG	GTTGTAG	-	novel	NA	P-0003449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	93	229	0	ENST00000269305.4:c.699_705del	p.Tyr234ThrfsTer11	p.Y234Tfs*11	ENST00000269305	NM_001126112.2	233	caCTACAAC/ca	7/11	0.770683204050421	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	0	0.770683204050421	3		229	105	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0003467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	62	299	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.862	0.753	0.978	0.862	0.753	0.978	CLONAL	1	TRUE	1	0.561745824039196	2		299	256	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920172	76920173	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0003467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	66	220	0	ENST00000373344.5:c.3904dup	p.Arg1302LysfsTer7	p.R1302Kfs*7	ENST00000373344	NM_000489.3	1302	aga/aAga	11/35	0.245514428584982	0	FACETS	0.673	0.6	0.748			1	INDETERMINATE	1	TRUE	NA	0.561745824039196	0		220	153	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156719	20156719	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	81	199	0	ENST00000379607.5:c.38G>T	p.Arg13Leu	p.R13L	ENST00000379607	NM_001412.3	13	cGc/cTc	2/7	0.245514428584982	0	FACETS	0.866	0.789	0.941			1	INDETERMINATE	1	TRUE	NA	0.561745824039196	0		199	146	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912655	NA	P-0003467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	187	252	0	ENST00000269305.4:c.725G>C	p.Cys242Ser	p.C242S	ENST00000269305	NM_001126112.2	242	tGc/tCc	7/11	0.523323157176717	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.561745824039196	2		252	291	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0003467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	58	522	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	0.73	0.632	0.834	0.73	0.632	0.834	SUBCLONAL	1	TRUE	1	0.561745824039196	2		522	283	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143985	11143985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	51	280	0	ENST00000358026.2:c.3566G>A	p.Arg1189Gln	p.R1189Q	ENST00000358026	NM_001128849.1	1189	cGa/cAa	26/36	1	2	FACETS	0.837	0.72	0.962	0.837	0.72	0.962	CLONAL	1	TRUE	1	0.561745824039196	2		280	217	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0003482-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	238	384	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.590057508303251	5	FACETS	1	0.978	1			1	CLONAL	5	TRUE	NA	0.656058468885509	5		384	284	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576851	7576851	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0003482-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	124	199	0	ENST00000269305.4:c.993+2T>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.643689259884239	2	FACETS	0.995	0.931	1	0.995	0.931	1	CLONAL	2	TRUE	0	0.656058468885509	2		199	190	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027789	152027790	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTCAGCATCCTCTTCTGCAGATTGTTCTTTGA	novel	NA	P-0003482-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	152	359	1	ENST00000262189.6:c.254_285dup	p.Ala96SerfsTer20	p.A96Sfs*20	ENST00000262189	NM_170606.2	95	-/TCAAAGAACAATCTGCAGAAGAGGATGCTGAA	3/59	0.656058468885509	4	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.656058468885509	4		360	671	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0003515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	69	214	2	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.797	0.703	0.896	0.797	0.703	0.896	SUBCLONAL	1	TRUE	1	0.69	2		216	251	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1646359	1646359	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	284	462	0	ENST00000344749.5:c.140G>C	p.Gly47Ala	p.G47A	ENST00000344749	NM_001136139.2	47	gGt/gCt	3/19	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.69	2		462	726	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0003523-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	215	474	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.62215163944825	6	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	FALSE	3	0.62215163944825	6		474	492	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003523-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	98	274	0	ENST00000288602.6:c.1780G>T	p.Asp594Tyr	p.D594Y	ENST00000288602	NM_004333.4	594	Gat/Tat	15/18	0.62215163944825	4	FACETS	0.89	0.805	0.978	0.89	0.805	0.978	CLONAL	2	FALSE	2	0.62215163944825	4		274	287	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448309	56448309	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003523-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	107	209	0	ENST00000407977.2:c.338G>T	p.Arg113Leu	p.R113L	ENST00000407977		113	cGa/cTa	3/10	0.62215163944825	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	FALSE	2	0.62215163944825	4		209	261	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600329	10600329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003523-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	151	365	0	ENST00000171111.5:c.1526G>A	p.Gly509Glu	p.G509E	ENST00000171111	NM_203500.1	509	gGg/gAg	4/6	0.62215163944825	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	FALSE	0	0.62215163944825	2		365	221	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357597	70357597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003523-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	94	439	0	ENST00000374080.3:c.5848C>T	p.His1950Tyr	p.H1950Y	ENST00000374080		1950	Cat/Tat	41/45	0.279748044927491	3	FACETS	1	0.982	1	0.728	0.657	0.801	INDETERMINATE	1	FALSE	1	0.62215163944825	3		439	272	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205134	123205134	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003523-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	69	463	1	ENST00000218089.9:c.2494C>A	p.His832Asn	p.H832N	ENST00000218089	NM_001042749.1	832	Cat/Aat	25/35	0.279748044927491	3	FACETS	1	0.94	1	0.555	0.489	0.625	INDETERMINATE	1	FALSE	1	0.62215163944825	3		464	262	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969905	161969905	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003523-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	68	310	1	ENST00000366898.1:c.1064del	p.Gly355AlafsTer80	p.G355Afs*80	ENST00000366898	NM_004562.2	355	gGc/gc	9/12	0.304509346716215	4	FACETS	0.882	0.781	0.987	0.882	0.781	0.987	INDETERMINATE	2	FALSE	2	0.62215163944825	4		311	201	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220585	1220587	+	frameshift_variant	Frame_Shift_Ins	INS	GCA	GCA	TCCC	novel	NA	P-0003523-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	70	298	0	ENST00000326873.7:c.603_605delinsTCCC	p.His202ProfsTer64	p.H202Pfs*64	ENST00000326873	NM_000455.4	201	ctGCAc/ctTCCCc	5/10	0.62215163944825	2	FACETS	0.978	0.891	1	0.978	0.891	1	CLONAL	2	FALSE	0	0.62215163944825	2		298	115	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020768	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs926053251	NA	P-0003548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	118	339	2	ENST00000358127.4:c.77T>G	p.Val26Gly	p.V26G	ENST00000358127	NM_001280556.1	26	gTt/gGt	2/10	0.497581908174947	1	FACETS	0.472	0.426	0.52	0.472	0.426	0.52	SUBCLONAL	1	TRUE	0	0.527802987981639	1		341	698	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971101	21971101	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	142	154	0	ENST00000579755.1:c.300C>A	p.Cys100Ter	p.C100*	ENST00000579755		100	tgC/tgA	2/3	0.497581908174947	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.527802987981639	1		154	346	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778741	3778741	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	167	249	0	ENST00000262367.5:c.6307C>A	p.Gln2103Lys	p.Q2103K	ENST00000262367	NM_004380.2	2103	Cag/Aag	31/31	1	2	FACETS	0.966	0.891	1	0.966	0.891	1	CLONAL	1	TRUE	1	0.527802987981639	2		249	655	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7163165	7163165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	251	298	0	ENST00000302850.5:c.1907C>T	p.Ser636Phe	p.S636F	ENST00000302850	NM_000208.2	636	tCc/tTc	9/22	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.527802987981639	2		298	890	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579708	7579709	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0003548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	238	361	0	ENST00000269305.4:c.87_88del	p.Asn29LysfsTer13	p.N29Kfs*13	ENST00000269305	NM_001126112.2	29	aaCAac/aaac	3/11	0.497581908174947	1	FACETS	0.919	0.862	0.978	0.919	0.862	0.978	CLONAL	1	TRUE	0	0.527802987981639	1		361	722	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570304	95570305	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0003548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	136	214	0	ENST00000393063.1:c.3427_3428dup	p.Glu1144Ter	p.E1144*	ENST00000393063	NM_030621.3	1143	cta/ctCTa	22/28	1	2	FACETS	0.924	0.844	1	0.924	0.844	1	CLONAL	1	TRUE	1	0.527802987981639	2		214	558	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0003613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	28	588	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.448	0.358	0.55	0.448	0.358	0.55	SUBCLONAL	1	TRUE	1	0.382476180127118	2		589	327	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0003613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	33	208	1	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.382476180127118	1	FACETS	0.731	0.601	0.874	0.731	0.601	0.874	SUBCLONAL	1	TRUE	0	0.382476180127118	1		209	191	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0003613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	37	230	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.382476180127118	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.382476180127118	1		230	128	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012389	29012389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161996687	NA	P-0003613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	29	313	1	ENST00000282397.4:c.482C>T	p.Thr161Met	p.T161M	ENST00000282397	NM_002019.4	161	aCg/aTg	4/30	0.326130701638166	1	FACETS	0.908	0.741	1	0.908	0.741	1	CLONAL	1	TRUE	0	0.382476180127118	1		314	135	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467670	50467670	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	31	343	0	ENST00000331340.3:c.905A>G	p.Glu302Gly	p.E302G	ENST00000331340	NM_006060.4	302	gAg/gGg	8/8	1	2	FACETS	0.932	0.762	1	0.932	0.762	1	CLONAL	1	TRUE	1	0.382476180127118	2		343	174	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39729894	39729894	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	46	379	1	ENST00000361337.2:c.1209A>C	p.Glu403Asp	p.E403D	ENST00000361337	NM_003286.2	403	gaA/gaC	13/21	0.266046701350295	3	FACETS	1	0.959	1	0.709	0.605	0.822	CLONAL	1	TRUE	1	0.382476180127118	3		380	202	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41522006	41522006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	25	368	0	ENST00000263253.7:c.868G>A	p.Asp290Asn	p.D290N	ENST00000263253	NM_001429.3	290	Gac/Aac	3/31	0.233732705780779	1	FACETS	0.734	0.586	0.9	0.734	0.586	0.9	SUBCLONAL	1	TRUE	0	0.382476180127118	1		368	144	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117835	70117836	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	59	328	0	ENST00000245479.2:c.305dup	p.Pro103AlafsTer149	p.P103Afs*149	ENST00000245479	NM_000346.3	101	-/A	1/3	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.382476180127118	2		328	234	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0003687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	183	326	1	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	0.951	0.882	1	0.951	0.882	1	CLONAL	1	TRUE	1	0.590165004525977	2		327	652	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937001	48937001	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	208	308	0	ENST00000267163.4:c.769C>T	p.Gln257Ter	p.Q257*	ENST00000267163	NM_000321.2	257	Cag/Tag	8/27	0.590165004525977	1	FACETS	0.974	0.913	1	0.974	0.913	1	CLONAL	1	TRUE	0	0.590165004525977	1		308	510	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267481	198267481	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs769888451	NA	P-0003687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	172	230	0	ENST00000335508.6:c.1876A>G	p.Asn626Asp	p.N626D	ENST00000335508	NM_012433.2	626	Aac/Gac	14/25	1	2	FACETS	0.951	0.879	1	0.951	0.879	1	CLONAL	1	TRUE	1	0.590165004525977	2		230	613	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591105	67591106	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	123	189	0	ENST00000274335.5:c.1701dup	p.Pro568ThrfsTer34	p.P568Tfs*34	ENST00000274335		566	-/A	12/15	1	2	FACETS	0.844	0.767	0.923	0.844	0.767	0.923	CLONAL	1	TRUE	1	0.590165004525977	2		189	494	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196970	106196970	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	89	467	0	ENST00000380013.4:c.5303C>A	p.Ala1768Glu	p.A1768E	ENST00000380013	NM_001127208.2	1768	gCa/gAa	11/11	1	2	FACETS	0.957	0.859	1	0.957	0.859	1	CLONAL	1	TRUE	1	0.643588680884708	2		467	289	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210778	5210778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374377699	NA	P-0003710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	173	454	1	ENST00000357368.4:c.5273C>T	p.Ala1758Val	p.A1758V	ENST00000357368	NM_002850.3	1758	gCg/gTg	34/38	0.643588680884708	4	FACETS	0.902	0.837	0.968	0.902	0.837	0.968	CLONAL	2	TRUE	2	0.643588680884708	4		455	490	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735503	40735503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763584414	NA	P-0003710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	134	484	0	ENST00000373198.4:c.3370G>A	p.Glu1124Lys	p.E1124K	ENST00000373198	NM_133170.3	1124	Gag/Aag	25/32	0.643588680884708	8	FACETS	1	0.983	1	0.23	0.208	0.252	CLONAL	1	TRUE	2	0.643588680884708	8		484	885	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577571	7577572	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGTAGT	novel	NA	P-0003710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	135	361	0	ENST00000269305.4:c.704_709dup	p.Asn235_Tyr236dup	p.N235_Y236dup	ENST00000269305	NM_001126112.2	235	atg/aACTACAtg	7/11	0.637862589927844	2	FACETS	0.795	0.738	0.851	0.795	0.738	0.851	SUBCLONAL	2	TRUE	0	0.643588680884708	2		361	264	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0003725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	219	586	1	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.726185029853069	3	FACETS	0.983	0.929	1	0.983	0.929	1	CLONAL	2	TRUE	1	0.726185029853069	3		587	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0003725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	178	360	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.726185029853069	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.726185029853069	2		361	227	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0003725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	279	420	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	0.726185029853069	3	FACETS	0.954	0.906	1	0.954	0.906	1	CLONAL	2	TRUE	1	0.726185029853069	3		420	549	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851684	134851684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373293977	NA	P-0003725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	109	352	0	ENST00000398015.3:c.1090C>T	p.Arg364Trp	p.R364W	ENST00000398015	NM_004441.4	364	Cgg/Tgg	5/16	0.726185029853069	3	FACETS	0.952	0.86	1	0.476	0.43	0.524	CLONAL	1	TRUE	1	0.726185029853069	3		352	430	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629336	187629336	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	272	449	0	ENST00000441802.2:c.1646G>T	p.Arg549Leu	p.R549L	ENST00000441802	NM_005245.3	549	cGg/cTg	2/27	0.726185029853069	2	FACETS	0.925	0.886	0.963	0.925	0.886	0.963	CLONAL	2	TRUE	0	0.726185029853069	2		449	405	SUCCESS
APC	324	MSKCC	GRCh37	5	112175630	112175631	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	127	521	0	ENST00000257430.4:c.4342dup	p.Thr1448AsnfsTer7	p.T1448Nfs*7	ENST00000257430	NM_000038.5	1447	caa/cAaa	16/16	0.726185029853069	3	FACETS	0.821	0.746	0.899	0.41	0.373	0.45	CLONAL	1	TRUE	1	0.726185029853069	3		521	581	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411615	63411615	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0003725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	255	322	0	ENST00000330258.3:c.1552del	p.Ser518LeufsTer23	p.S518Lfs*23	ENST00000330258	NM_152424.3	518	Tct/ct	2/2	0.518760209983938	2	FACETS	1	0.99	1			1	CLONAL	2	TRUE	NA	0.726185029853069	2		322	325	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0003734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	48	439	1	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.736	0.622	0.86	0.736	0.622	0.86	SUBCLONAL	1	TRUE	1	0.28	2		440	466	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965020	25965020	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	45	447	0	ENST00000435504.4:c.4186A>T	p.Thr1396Ser	p.T1396S	ENST00000435504		1396	Acg/Tcg	13/13	1	2	FACETS	0.685	0.576	0.806	0.685	0.576	0.806	SUBCLONAL	1	TRUE	1	0.28	2		447	469	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663063	227663063	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	19	384	0	ENST00000305123.5:c.392G>T	p.Gly131Val	p.G131V	ENST00000305123	NM_005544.2	131	gGt/gTt	1/2	1	2	FACETS	0.445	0.337	0.571	0.445	0.337	0.571	SUBCLONAL	1	TRUE	1	0.28	2		384	305	SUCCESS
APC	324	MSKCC	GRCh37	5	112175871	112175871	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747209080	NA	P-0003734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	28	389	0	ENST00000257430.4:c.4580C>T	p.Pro1527Leu	p.P1527L	ENST00000257430	NM_000038.5	1527	cCa/cTa	16/16	1	2	FACETS	0.508	0.405	0.624	0.508	0.405	0.624	SUBCLONAL	1	TRUE	1	0.28	2		389	394	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562463	176562463	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	30	515	0	ENST00000439151.2:c.359G>C	p.Gly120Ala	p.G120A	ENST00000439151	NM_022455.4	120	gGt/gCt	2/23	1	2	FACETS	0.386	0.31	0.473	0.386	0.31	0.473	SUBCLONAL	1	TRUE	1	0.28	2		515	555	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481467	20481467	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	34	348	0	ENST00000346618.3:c.536A>G	p.Tyr179Cys	p.Y179C	ENST00000346618	NM_001949.4	179	tAt/tGt	3/7	1	2	FACETS	0.6	0.49	0.723	0.6	0.49	0.723	SUBCLONAL	1	TRUE	1	0.28	2		348	405	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88679195	88679195	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	14	276	0	ENST00000372037.3:c.1135G>C	p.Ala379Pro	p.A379P	ENST00000372037	NM_004329.2	379	Gct/Cct	10/13	1	2	FACETS	0.383	0.276	0.512	0.383	0.276	0.512	SUBCLONAL	1	TRUE	1	0.28	2		276	261	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112302	115112302	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	11	82	0	ENST00000257566.3:c.1438G>T	p.Ala480Ser	p.A480S	ENST00000257566	NM_016569.3	480	Gcg/Tcg	7/8	1	2	FACETS	0.995	0.697	1	0.995	0.697	1	CLONAL	1	TRUE	1	0.28	2		82	79	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436013	110436013	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	13	260	0	ENST00000375856.3:c.2388G>T	p.Arg796Ser	p.R796S	ENST00000375856	NM_003749.2	796	agG/agT	1/2	0.164372261776318	3	FACETS	0.412	0.293	0.557	0.206	0.146	0.279	INDETERMINATE	1	TRUE	1	0.28	3		260	257	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560464	95560464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	13	173	0	ENST00000393063.1:c.5125G>A	p.Asp1709Asn	p.D1709N	ENST00000393063	NM_030621.3	1709	Gat/Aat	25/28	1	2	FACETS	0.436	0.311	0.588	0.436	0.311	0.588	SUBCLONAL	1	TRUE	1	0.28	2		173	213	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483977	88483977	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	22	384	0	ENST00000360948.2:c.1593G>C	p.Gln531His	p.Q531H	ENST00000360948	NM_001012338.2	531	caG/caC	14/19	1	2	FACETS	0.445	0.345	0.562	0.445	0.345	0.562	SUBCLONAL	1	TRUE	1	0.28	2		384	353	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761283	59761283	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	39	566	0	ENST00000259008.2:c.3124G>T	p.Glu1042Ter	p.E1042*	ENST00000259008	NM_032043.2	1042	Gaa/Taa	20/20	1	2	FACETS	0.529	0.438	0.63	0.529	0.438	0.63	SUBCLONAL	1	TRUE	1	0.28	2		566	527	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207146	1207146	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	47	346	0	ENST00000326873.7:c.234G>T	p.Lys78Asn	p.K78N	ENST00000326873	NM_000455.4	78	aaG/aaT	1/10	1	2	FACETS	0.799	0.676	0.935	0.799	0.676	0.935	CLONAL	1	TRUE	1	0.28	2		346	420	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599888	10599888	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	38	603	0	ENST00000171111.5:c.1688A>G	p.Gln563Arg	p.Q563R	ENST00000171111	NM_203500.1	563	cAg/cGg	5/6	1	2	FACETS	0.428	0.353	0.513	0.428	0.353	0.513	SUBCLONAL	1	TRUE	1	0.28	2		603	634	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602446	10602446	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	32	385	0	ENST00000171111.5:c.1132G>T	p.Gly378Cys	p.G378C	ENST00000171111	NM_203500.1	378	Ggc/Tgc	3/6	1	2	FACETS	0.564	0.458	0.684	0.564	0.458	0.684	SUBCLONAL	1	TRUE	1	0.28	2		385	405	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525015	9525015	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	23	422	0	ENST00000353224.5:c.1869+1G>A		p.X623_splice	ENST00000353224	NM_177990.2	623			1	2	FACETS	0.428	0.333	0.538	0.428	0.333	0.538	SUBCLONAL	1	TRUE	1	0.28	2		422	384	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044901	47044901	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	36	221	0	ENST00000377604.3:c.2227G>T	p.Glu743Ter	p.E743*	ENST00000377604	NM_001204468.1	743	Gag/Tag	20/24	1	1	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	0	0.28	1		221	198	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360537	70360537	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs372606012	NA	P-0003734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	54	320	0	ENST00000374080.3:c.6097A>G	p.Met2033Val	p.M2033V	ENST00000374080		2033	Atg/Gtg	42/45	1	1	FACETS	0.945	0.811	1	0.945	0.811	1	CLONAL	1	TRUE	0	0.28	1		320	351	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599883	10599884	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	42	590	0	ENST00000171111.5:c.1692_1693insT	p.Arg565Ter	p.R565*	ENST00000171111	NM_203500.1	564	-/T	5/6	1	2	FACETS	0.473	0.394	0.561	0.473	0.394	0.561	SUBCLONAL	1	TRUE	1	0.28	2		590	634	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5055702	5055703	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0003734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	28	391	0	ENST00000381652.3:c.972dup	p.Asp325Ter	p.D325*	ENST00000381652	NM_004972.3	324	att/aTtt	8/25	0.264705542002915	1	FACETS	0.48	0.384	0.59	0.48	0.384	0.59	SUBCLONAL	1	TRUE	0	0.28	1		391	358	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0003767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	89	588	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.23	2		589	734	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0003767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	51	357	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.648	0.55	0.757	0.648	0.55	0.757	SUBCLONAL	1	TRUE	1	0.23	2		357	684	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0003767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	109	615	2	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	0.768	0.688	0.854	0.768	0.688	0.854	SUBCLONAL	1	TRUE	1	0.23	2		617	1234	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	82	454	2	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.795	0.7	0.898	0.795	0.7	0.898	SUBCLONAL	1	TRUE	1	0.23	2		456	897	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0003767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	108	734	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.23	2		734	914	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560514	65560514	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	68	403	0	ENST00000358664.4:c.83A>G	p.His28Arg	p.H28R	ENST00000358664	NM_002382.4	28	cAt/cGt	3/5	1	2	FACETS	0.851	0.74	0.971	0.851	0.74	0.971	CLONAL	1	TRUE	1	0.23	2		403	695	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713688	30713688	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752866783	NA	P-0003767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	37	237	0	ENST00000295754.5:c.1013C>T	p.Thr338Met	p.T338M	ENST00000295754	NM_003242.5	338	aCg/aTg	4/7	1	2	FACETS	0.863	0.712	1	0.863	0.712	1	CLONAL	1	TRUE	1	0.23	2		237	373	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298579	11298579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751242124	NA	P-0003767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	81	445	0	ENST00000361445.4:c.1882C>T	p.Arg628Cys	p.R628C	ENST00000361445	NM_004958.3	628	Cgc/Tgc	12/58	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.23	2		445	702	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45800117	45800117	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	107	565	0	ENST00000450313.1:c.103G>T	p.Gly35Trp	p.G35W	ENST00000450313	NM_012222.2	35	Ggg/Tgg	2/16	1	2	FACETS	0.92	0.824	1	0.92	0.824	1	CLONAL	1	TRUE	1	0.23	2		565	1011	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890203	72890203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758931723	NA	P-0003767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	83	448	1	ENST00000325599.8:c.479G>A	p.Arg160Gln	p.R160Q	ENST00000325599	NM_018130.2	160	cGg/cAg	4/11	1	2	FACETS	0.919	0.811	1	0.919	0.811	1	CLONAL	1	TRUE	1	0.23	2		449	785	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497351	149497351	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	84	380	0	ENST00000261799.4:c.2967G>T	p.Gln989His	p.Q989H	ENST00000261799	NM_002609.3	989	caG/caT	22/23	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.23	2		380	617	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665372	117665372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	73	419	0	ENST00000368508.3:c.4375G>A	p.Ala1459Thr	p.A1459T	ENST00000368508	NM_002944.2	1459	Gcc/Acc	27/43	1	2	FACETS	0.986	0.862	1	0.986	0.862	1	CLONAL	1	TRUE	1	0.23	2		419	644	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845135	128845135	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	86	574	0	ENST00000249373.3:c.629T>C	p.Val210Ala	p.V210A	ENST00000249373	NM_005631.4	210	gTg/gCg	3/12	1	2	FACETS	0.834	0.736	0.938	0.834	0.736	0.938	CLONAL	1	TRUE	1	0.23	2		574	897	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750639	128750639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775522201	NA	P-0003767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	82	462	1	ENST00000377970.2:c.176C>T	p.Ala59Val	p.A59V	ENST00000377970	NM_002467.4	59	gCg/gTg	2/3	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.23	2		463	673	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750770	128750770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	65	482	1	ENST00000377970.2:c.307G>A	p.Gly103Ser	p.G103S	ENST00000377970	NM_002467.4	103	Ggc/Agc	2/3	1	2	FACETS	0.768	0.665	0.88	0.768	0.665	0.88	SUBCLONAL	1	TRUE	1	0.23	2		483	736	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	76	385	0	ENST00000227507.2:c.859C>G	p.Pro287Ala	p.P287A	ENST00000227507	NM_053056.2	287	Ccc/Gcc	5/5	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.23	2		385	543	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435215	49435215	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	38	181	0	ENST00000301067.7:c.6338T>C	p.Leu2113Pro	p.L2113P	ENST00000301067	NM_003482.3	2113	cTg/cCg	31/54	1	2	FACETS	1	0.835	1	1	0.835	1	CLONAL	1	TRUE	1	0.23	2		181	328	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2107125	2107125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1188591008	NA	P-0003767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	88	506	3	ENST00000219476.3:c.794G>A	p.Gly265Asp	p.G265D	ENST00000219476	NM_000548.3	265	gGc/gAc	9/42	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.23	2		509	756	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868043	56868043	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	96	537	0	ENST00000308159.5:c.1541G>C	p.Ser514Thr	p.S514T	ENST00000308159	NM_014669.4	514	aGc/aCc	14/22	1	2	FACETS	0.918	0.817	1	0.918	0.817	1	CLONAL	1	TRUE	1	0.23	2		537	909	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346127	89346127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750990942	NA	P-0003767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	15	194	0	ENST00000301030.4:c.6823G>A	p.Ala2275Thr	p.A2275T	ENST00000301030	NM_001256183.1	2275	Gcc/Acc	9/13	1	2	FACETS	0.548	0.401	0.725	0.548	0.401	0.725	SUBCLONAL	1	TRUE	1	0.23	2		194	238	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89811395	89811395	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	105	582	0	ENST00000389301.3:c.3598C>A	p.Leu1200Ile	p.L1200I	ENST00000389301	NM_000135.2	1200	Cta/Ata	36/43	1	2	FACETS	0.914	0.817	1	0.914	0.817	1	CLONAL	1	TRUE	1	0.23	2		582	999	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556289	29556289	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	107	592	0	ENST00000356175.3:c.2656A>G	p.Asn886Asp	p.N886D	ENST00000356175	NM_000267.3	886	Aac/Gac	21/57	1	2	FACETS	0.956	0.856	1	0.956	0.856	1	CLONAL	1	TRUE	1	0.23	2		592	973	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243999	5243999	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144686472	NA	P-0003767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	67	469	1	ENST00000357368.4:c.1483G>A	p.Glu495Lys	p.E495K	ENST00000357368	NM_002850.3	495	Gag/Aag	11/38	1	2	FACETS	0.768	0.666	0.878	0.768	0.666	0.878	SUBCLONAL	1	TRUE	1	0.23	2		470	759	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928078	178928080	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs587776933	NA	P-0003767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	54	413	0	ENST00000263967.3:c.1359_1361del	p.Glu453del	p.E453del	ENST00000263967	NM_006218.2	452	ttAGAa/tta	8/21	1	2	FACETS	0.896	0.766	1	0.896	0.766	1	CLONAL	1	TRUE	1	0.23	2		413	524	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993730	72993731	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769936196	NA	P-0003767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	87	644	1	ENST00000268489.5:c.314dup	p.Pro106AlafsTer13	p.P106Afs*13	ENST00000268489	NM_006885.3	105	ccg/ccCg	2/10	1	2	FACETS	0.835	0.738	0.939	0.835	0.738	0.939	CLONAL	1	TRUE	1	0.23	2		645	906	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119017	70119018	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0003767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	64	437	0	ENST00000245479.2:c.591_592del	p.Ile198LeufsTer53	p.I198Lfs*53	ENST00000245479	NM_000346.3	197	CAc/c	2/3	1	2	FACETS	0.82	0.709	0.94	0.82	0.709	0.94	CLONAL	1	TRUE	1	0.23	2		437	679	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511329	157511329	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	36	253	0	ENST00000346085.5:c.3851del	p.Gly1284GlufsTer2	p.G1284Efs*2	ENST00000346085	NM_020732.3	1283	Ggg/gg	15/20	1	2	FACETS	0.915	0.754	1	0.915	0.754	1	CLONAL	1	TRUE	1	0.23	2		253	342	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0003768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	209	379	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.228219586925611	5	FACETS	1	0.984	1	0.796	0.741	0.852	CLONAL	2	TRUE	2	0.343028711346811	5		379	773	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0003768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	112	229	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.247741412324528	2	FACETS	1	0.982	1	0.693	0.627	0.763	CLONAL	1	TRUE	0	0.343028711346811	2		231	471	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573563	48573564	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs786203560	NA	P-0003768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	90	206	0	ENST00000342988.3:c.153dup	p.Asp52ArgfsTer2	p.D52Rfs*2	ENST00000342988	NM_005359.5	49	-/A	2/12	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.343028711346811	2		206	406	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271527	38271527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760882547	NA	P-0003768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	102	240	0	ENST00000425967.3:c.2294G>A	p.Arg765Gln	p.R765Q	ENST00000425967	NM_001174067.1	765	cGg/cAg	18/19	0.225897152194264	4	FACETS	1	0.957	1			1	CLONAL	2	TRUE	NA	0.343028711346811	4		240	360	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0003796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	110	588	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.973	0.874	1	0.973	0.874	1	CLONAL	1	TRUE	1	0.27	2		589	837	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260214	16260214	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	47	144	0	ENST00000375759.3:c.7484del	p.Pro2495LeufsTer4	p.P2495Lfs*4	ENST00000375759	NM_015001.2	2493	agC/ag	11/15	1	2	FACETS	0.839	0.709	0.981	0.839	0.709	0.981	CLONAL	1	TRUE	1	0.27	2		144	415	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0003796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	89	498	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.803	0.711	0.901	0.803	0.711	0.901	CLONAL	1	TRUE	1	0.27	2		498	821	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882049	36882050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs780753361	NA	P-0003796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	90	607	0	ENST00000358127.4:c.963dup	p.Ala322ArgfsTer19	p.A322Rfs*19	ENST00000358127	NM_001280556.1	321	-/C	8/10	1	2	FACETS	0.912	0.809	1	0.912	0.809	1	CLONAL	1	TRUE	1	0.27	2		607	731	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0003796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	96	646	6	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.676	0.601	0.757	0.676	0.601	0.757	SUBCLONAL	1	TRUE	1	0.27	2		652	1052	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0003796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	98	409	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.27	2		409	664	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294372	1294372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	48	212	0	ENST00000310581.5:c.629C>T	p.Ala210Val	p.A210V	ENST00000310581	NM_198253.2	210	gCc/gTc	2/16	1	2	FACETS	0.977	0.829	1	0.977	0.829	1	CLONAL	1	TRUE	1	0.27	2		212	364	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764146326	NA	P-0003796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	52	414	0	ENST00000269305.4:c.841G>A	p.Asp281Asn	p.D281N	ENST00000269305	NM_001126112.2	281	Gac/Aac	8/11	1	2	FACETS	0.388	0.329	0.454	0.388	0.329	0.454	SUBCLONAL	1	TRUE	1	0.27	2		414	992	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0003796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	92	346	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.891	0.791	0.997	0.891	0.791	0.997	CLONAL	1	TRUE	1	0.27	2		346	765	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402537	20402537	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	15	75	0	ENST00000346618.3:c.74T>C	p.Val25Ala	p.V25A	ENST00000346618	NM_001949.4	25	gTc/gCc	1/7	1	2	FACETS	0.374	0.273	0.496	0.374	0.273	0.496	SUBCLONAL	1	TRUE	1	0.27	2		75	297	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439924	56439924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780231969	NA	P-0003796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	52	134	1	ENST00000407977.2:c.668G>A	p.Arg223His	p.R223H	ENST00000407977		223	cGc/cAc	6/10	1	2	FACETS	0.978	0.835	1	0.978	0.835	1	CLONAL	1	TRUE	1	0.27	2		135	394	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0003796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	131	615	2	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	0.856	0.775	0.942	0.856	0.775	0.942	CLONAL	1	TRUE	1	0.27	2		617	1133	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058529	72058529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	151	460	0	ENST00000357731.5:c.911G>A	p.Gly304Asp	p.G304D	ENST00000357731	NM_173808.2	304	gGc/gAc	6/7	1	2	FACETS	0.934	0.852	1	0.934	0.852	1	CLONAL	1	TRUE	1	0.27	2		460	1198	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042530	37042530	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267607725	NA	P-0003796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	123	374	0	ENST00000231790.2:c.292G>A	p.Gly98Ser	p.G98S	ENST00000231790	NM_000249.3	98	Ggc/Agc	3/19	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.27	2		374	910	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294223	1294223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1279966046	NA	P-0003796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	52	170	0	ENST00000310581.5:c.778G>A	p.Gly260Ser	p.G260S	ENST00000310581	NM_198253.2	260	Ggc/Agc	2/16	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.27	2		170	351	SUCCESS
APC	324	MSKCC	GRCh37	5	112164611	112164611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587783034	NA	P-0003796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	74	241	0	ENST00000257430.4:c.1685C>T	p.Thr562Met	p.T562M	ENST00000257430	NM_000038.5	562	aCg/aTg	14/16	1	2	FACETS	0.854	0.748	0.968	0.854	0.748	0.968	CLONAL	1	TRUE	1	0.27	2		241	642	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739599	41739599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	120	368	0	ENST00000242208.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000242208	NM_002192.2	125	aCg/aTg	2/3	1	2	FACETS	0.856	0.771	0.945	0.856	0.771	0.945	CLONAL	1	TRUE	1	0.27	2		368	1039	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994291	21994291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241364288	NA	P-0003796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	61	240	0	ENST00000579755.1:c.40G>A	p.Ala14Thr	p.A14T	ENST00000579755		14	Gcg/Acg	1/3	1		FACETS		0.732	0.973				CLONAL	1	TRUE	1	0.27	2		240	533	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717778	89717778	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0003796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	21	146	0	ENST00000371953.3:c.801+2T>C		p.X267_splice	ENST00000371953	NM_000314.4	267			1	2	FACETS	0.488	0.375	0.619	0.488	0.375	0.619	SUBCLONAL	1	TRUE	1	0.27	2		146	319	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912171	114912171	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1272	78	485	0	ENST00000543371.1:c.1241A>G	p.Tyr414Cys	p.Y414C	ENST00000543371	NM_001198531.1	414	tAc/tGc	11/14	1	2	FACETS	0.428	0.374	0.486	0.428	0.374	0.486	SUBCLONAL	1	TRUE	1	0.27	2		485	1350	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416701	121416701	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	98	360	0	ENST00000257555.6:c.130C>G	p.Leu44Val	p.L44V	ENST00000257555		44	Ctg/Gtg	1/10	1	2	FACETS	0.972	0.867	1	0.972	0.867	1	CLONAL	1	TRUE	1	0.27	2		360	747	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435414	110435414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	46	138	0	ENST00000375856.3:c.2987G>A	p.Gly996Asp	p.G996D	ENST00000375856	NM_003749.2	996	gGc/gAc	1/2	1	2	FACETS	0.841	0.71	0.986	0.841	0.71	0.986	CLONAL	1	TRUE	1	0.27	2		138	405	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101401	27101402	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0003796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	39	860	0	ENST00000324856.7:c.4689dup	p.Met1564HisfsTer8	p.M1564Hfs*8	ENST00000324856	NM_006015.4	1561	-/C	18/20	1	2	FACETS	0.401	0.331	0.48	0.401	0.331	0.48	SUBCLONAL	1	TRUE	1	0.27	2		860	720	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265048	46265049	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0003796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	133	529	0	ENST00000371998.3:c.1924dup	p.Leu642ProfsTer6	p.L642Pfs*6	ENST00000371998		640	tcc/tCcc	12/23	1	2	FACETS	0.857	0.777	0.943	0.857	0.777	0.943	CLONAL	1	TRUE	1	0.27	2		529	1149	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247903	59247904	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1179	185	506	0	ENST00000371222.2:c.839dup	p.Glu281GlyfsTer29	p.E281Gfs*29	ENST00000371222	NM_002228.3	280	ctg/ctTg	1/1	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.27	2		506	1364	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964077	28964077	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1565998842	NA	P-0003796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	100	371	0	ENST00000282397.4:c.1825del	p.Met609TrpfsTer16	p.M609Wfs*16	ENST00000282397	NM_002019.4	609	Atg/tg	13/30	1	2	FACETS	0.929	0.83	1	0.929	0.83	1	CLONAL	1	TRUE	1	0.27	2		371	797	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794441	42794441	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	121	508	0	ENST00000575354.2:c.1526del	p.Pro509HisfsTer14	p.P509Hfs*14	ENST00000575354	NM_015125.3	507	cgC/cg	10/20	1	2	FACETS	0.806	0.726	0.89	0.806	0.726	0.89	CLONAL	1	TRUE	1	0.27	2		508	1112	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119781	70119781	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1274036689	NA	P-0003796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	107	381	0	ENST00000245479.2:c.788del	p.Gly263AlafsTer16	p.G263Afs*16	ENST00000245479	NM_000346.3	261	gaG/ga	3/3	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.27	2		381	783	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433874	49433875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0003796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	60	302	0	ENST00000301067.7:c.7678dup	p.His2560ProfsTer95	p.H2560Pfs*95	ENST00000301067	NM_003482.3	2560	cat/cCat	31/54	1	2	FACETS	0.601	0.517	0.693	0.601	0.517	0.693	SUBCLONAL	1	TRUE	1	0.27	2		302	739	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554355	81554355	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747687365	NA	P-0003796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	108	391	2	ENST00000298171.2:c.379del	p.Leu127SerfsTer2	p.L127Sfs*2	ENST00000298171	NM_000369.2	125	ctC/ct	4/10	1	2	FACETS	0.802	0.718	0.891	0.802	0.718	0.891	CLONAL	1	TRUE	1	0.27	2		393	998	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247812	59247813	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0003796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1370	225	511	0	ENST00000371222.2:c.930_931del	p.Lys311SerfsTer6	p.K311Sfs*6	ENST00000371222	NM_002228.3	310	caGAaa/caaa	1/1	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.27	2		511	1595	SUCCESS
APC	324	MSKCC	GRCh37	5	112174783	112174783	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0003796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	92	293	0	ENST00000257430.4:c.3495del	p.Lys1165AsnfsTer17	p.K1165Nfs*17	ENST00000257430	NM_000038.5	1164	atA/at	16/16	1	2	FACETS	0.964	0.857	1	0.964	0.857	1	CLONAL	1	TRUE	1	0.27	2		293	707	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0003805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	69	66	0				ENST00000310581	NM_198253.2	-/1132			0.184155370191771	5	FACETS	0.876	0.787	0.966	0.876	0.787	0.966	INDETERMINATE	3	TRUE	2	0.817074329289436	5		66	143	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0003805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	151	148	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			NA	2	FACETS	0.929	0.883	0.971			1	INDETERMINATE	2	TRUE	NA	0.817074329289436	2		148	199	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692881	89692881	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	136	130	0	ENST00000371953.3:c.365T>A	p.Ile122Asn	p.I122N	ENST00000371953	NM_000314.4	122	aTt/aAt	5/9	0.817074329289436	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.817074329289436	1		130	170	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195094	123195094	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0003805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	336	147	0	ENST00000218089.9:c.1437C>G	p.Tyr479Ter	p.Y479*	ENST00000218089	NM_001042749.1	479	taC/taG	16/35	0.56632621902535	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.817074329289436	2		147	374	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15273306	15273307	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0003805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	70	350	0	ENST00000263388.2:c.5882dup	p.Asn1961LysfsTer5	p.N1961Kfs*5	ENST00000263388	NM_000435.2	1961	aat/aaAt	32/33	0.243486621557305	3	FACETS	0.458	0.4	0.521	0.229	0.2	0.261	INDETERMINATE	1	TRUE	1	0.817074329289436	3		350	527	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	15	374	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.19	2		374	122	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs104886003	NA	P-0003809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	26	142	0	ENST00000263967.3:c.1633G>C	p.Glu545Gln	p.E545Q	ENST00000263967	NM_006218.2	545	Gag/Cag	10/21	1	2	FACETS	0.837	0.664	1	0.837	0.664	1	CLONAL	1	TRUE	1	0.19	2		142	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1555525429	NA	P-0003809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	30	211	0	ENST00000269305.4:c.782+1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	0.827	0.666	1	0.827	0.666	1	CLONAL	1	TRUE	1	0.19	2		211	382	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467058	25467058	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	51	232	0	ENST00000264709.3:c.1817A>G	p.Gln606Arg	p.Q606R	ENST00000264709	NM_175629.2	606	cAg/cGg	15/23	0.191172107093482	3	FACETS	1	0.924	1	0.571	0.485	0.665	CLONAL	1	TRUE	1	0.19	3		232	515	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537224	80537224	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	37	173	0	ENST00000286548.4:c.174G>C	p.Gln58His	p.Q58H	ENST00000286548	NM_002072.3	58	caG/caC	2/7	1	2	FACETS	0.948	0.782	1	0.948	0.782	1	CLONAL	1	TRUE	1	0.19	2		173	411	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380279	25380279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	51	299	2	ENST00000311936.3:c.179G>A	p.Gly60Asp	p.G60D	ENST00000311936	NM_004985.3	60	gGt/gAt	3/5	1	2	FACETS	0.794	0.674	0.927	0.794	0.674	0.927	CLONAL	1	TRUE	1	0.19	2		301	676	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763282	59763282	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	67	353	0	ENST00000259008.2:c.2820G>C	p.Lys940Asn	p.K940N	ENST00000259008	NM_032043.2	940	aaG/aaC	19/20	1	2	FACETS	0.921	0.799	1	0.921	0.799	1	CLONAL	1	TRUE	1	0.19	2		353	766	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763455	59763455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	32	218	0	ENST00000259008.2:c.2647G>A	p.Glu883Lys	p.E883K	ENST00000259008	NM_032043.2	883	Gaa/Aaa	19/20	1	2	FACETS	0.63	0.51	0.765	0.63	0.51	0.765	SUBCLONAL	1	TRUE	1	0.19	2		218	535	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621908	1621908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	58	374	0	ENST00000344749.5:c.884C>T	p.Ser295Leu	p.S295L	ENST00000344749	NM_001136139.2	295	tCa/tTa	11/19	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.19	2		374	550	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36421175	36421175	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	38	224	0	ENST00000300305.3:c.22G>C	p.Glu8Gln	p.E8Q	ENST00000300305		8	Gag/Cag	1/8	1	2	FACETS	0.687	0.567	0.822	0.687	0.567	0.822	SUBCLONAL	1	TRUE	1	0.19	2		224	582	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937721	44937721	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	55	160	0	ENST00000377967.4:c.2909T>G	p.Ile970Arg	p.I970R	ENST00000377967	NM_021140.2	970	aTa/aGa	19/29	1	1	FACETS	0.751	0.645	0.865	1	0.967	1	SUBCLONAL	2	TRUE	0	0.19	1		160	349	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088648	27088649	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0003809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	50	304	0	ENST00000324856.7:c.2258dup	p.Met753IlefsTer64	p.M753Ifs*64	ENST00000324856	NM_006015.4	753	atg/aTtg	7/20	1	2	FACETS	0.771	0.653	0.901	0.771	0.653	0.901	CLONAL	1	TRUE	1	0.19	2		304	683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0003839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	348	695	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.446329168033079	2	FACETS	0.895	0.853	0.936	0.895	0.853	0.936	CLONAL	2	TRUE	0	0.537344817863756	2		695	724	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0003839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	247	435	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.440365735382398	3	FACETS	0.785	0.737	0.834	0.785	0.737	0.834	SUBCLONAL	2	TRUE	1	0.537344817863756	3		436	743	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837898	156837898	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	182	332	1	ENST00000524377.1:c.431T>C	p.Val144Ala	p.V144A	ENST00000524377	NM_002529.3	144	gTc/gCc	5/17	0.470396757608453	5	FACETS	0.847	0.784	0.913	0.565	0.522	0.609	CLONAL	2	TRUE	2	0.537344817863756	5		333	722	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716032	243716032	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	280	254	0	ENST00000263826.5:c.1162C>T	p.Arg388Cys	p.R388C	ENST00000263826	NM_005465.4	388	Cgc/Tgc	10/13	0.470396757608453	5	FACETS	0.911	0.861	0.961	0.911	0.861	0.961	CLONAL	3	TRUE	2	0.537344817863756	5		254	689	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590774	189590774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746969135	NA	P-0003839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	122	367	0	ENST00000264731.3:c.1339C>T	p.Leu447Phe	p.L447F	ENST00000264731	NM_003722.4	447	Ctt/Ttt	10/14	0.440365735382398	3	FACETS	0.88	0.797	0.967	0.44	0.398	0.484	CLONAL	1	TRUE	1	0.537344817863756	3		367	655	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653805	89653805	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	95	266	0	ENST00000371953.3:c.103A>T	p.Met35Leu	p.M35L	ENST00000371953	NM_000314.4	35	Atg/Ttg	2/9	0.350658840533178	4	FACETS	0.9	0.803	1	0.45	0.401	0.502	CLONAL	1	TRUE	2	0.537344817863756	4		266	604	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670736	67670736	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	207	357	0	ENST00000264010.4:c.1981C>G	p.Gln661Glu	p.Q661E	ENST00000264010	NM_006565.3	661	Cag/Gag	11/12	0.506464086266648	3	FACETS	1	0.991	1	0.719	0.67	0.769	CLONAL	1	TRUE	1	0.537344817863756	3		357	680	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023720	31023720	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	66	309	0	ENST00000375687.4:c.3205G>T	p.Val1069Leu	p.V1069L	ENST00000375687	NM_015338.5	1069	Gta/Tta	13/13	0.537344817863756	5	FACETS	0.48	0.415	0.55	0.16	0.138	0.184	SUBCLONAL	1	TRUE	2	0.537344817863756	5		309	925	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386367	31386367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374520428	NA	P-0003839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	199	342	0	ENST00000328111.2:c.1592G>A	p.Arg531His	p.R531H	ENST00000328111	NM_006892.3	531	cGc/cAc	15/23	0.537344817863756	5	FACETS	0.792	0.735	0.852	0.528	0.49	0.568	SUBCLONAL	2	TRUE	2	0.537344817863756	5		342	844	SUCCESS
APC	324	MSKCC	GRCh37	5	112175749	112175750	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	88	323	0	ENST00000257430.4:c.4459dup	p.Thr1487AsnfsTer27	p.T1487Nfs*27	ENST00000257430	NM_000038.5	1486	-/A	16/16	0.506464086266648	3	FACETS	0.771	0.685	0.863	0.385	0.342	0.432	SUBCLONAL	1	TRUE	1	0.537344817863756	3		323	539	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0003870-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	278	474	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.354515752652544	3	FACETS	0.811	0.765	0.858	0.811	0.765	0.858	CLONAL	2	TRUE	1	0.534208352111456	3		474	813	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555526268	NA	P-0003870-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	191	289	0	ENST00000269305.4:c.406C>G	p.Gln136Glu	p.Q136E	ENST00000269305	NM_001126112.2	136	Caa/Gaa	5/11	0.425120342324494	2	FACETS	0.789	0.738	0.841	0.789	0.738	0.841	SUBCLONAL	2	TRUE	0	0.534208352111456	2		289	453	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610608	52610609	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0003870-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	296	534	0	ENST00000394830.3:c.3564dup	p.Glu1189ArgfsTer6	p.E1189Rfs*6	ENST00000394830	NM_018313.4	1188	-/A	23/30	0.425120342324494	2	FACETS	0.774	0.733	0.815	0.774	0.733	0.815	SUBCLONAL	2	TRUE	0	0.534208352111456	2		534	716	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919264	178919264	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003870-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	240	396	0	ENST00000263967.3:c.749A>T	p.Tyr250Phe	p.Y250F	ENST00000263967	NM_006218.2	250	tAt/tTt	4/21	0.404041347498103	4	FACETS	0.767	0.717	0.818	0.767	0.717	0.818	SUBCLONAL	2	TRUE	2	0.534208352111456	4		396	899	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217211	66217211	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003870-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	106	473	0	ENST00000273854.3:c.2404G>A	p.Ala802Thr	p.A802T	ENST00000273854	NM_004439.5	802	Gct/Act	14/18	0.235385381558052	4	FACETS	0.645	0.577	0.717	0.215	0.192	0.239	INDETERMINATE	1	TRUE	1	0.534208352111456	4		473	944	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137834	64137834	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003870-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	51	454	0	ENST00000334205.4:c.1935G>T	p.Glu645Asp	p.E645D	ENST00000334205	NM_003942.2	645	gaG/gaT	15/17	0.273849429882326	4	FACETS	0.33	0.279	0.386	0.165	0.139	0.193	INDETERMINATE	1	TRUE	2	0.534208352111456	4		454	888	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593507	48593507	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1367209662	NA	P-0003870-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	290	312	0	ENST00000342988.3:c.1258C>T	p.Arg420Cys	p.R420C	ENST00000342988	NM_005359.5	420	Cgt/Tgt	10/12	0.425120342324494	2	FACETS	0.774	0.733	0.816	0.774	0.733	0.816	SUBCLONAL	2	TRUE	0	0.534208352111456	2		312	701	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252875	36252875	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003870-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	195	436	0	ENST00000300305.3:c.487T>G	p.Phe163Val	p.F163V	ENST00000300305		163	Ttt/Gtt	4/8	0.21478761715756	3	FACETS	1	0.945	1	0.512	0.474	0.552	INDETERMINATE	1	TRUE	1	0.534208352111456	3		436	903	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106313	27106314	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0003870-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	141	362	0	ENST00000324856.7:c.5924_5925del	p.Asp1975ValfsTer23	p.D1975Vfs*23	ENST00000324856	NM_006015.4	1975	gAT/g	20/20	0.411979689902486	3	FACETS	0.821	0.748	0.897	0.41	0.374	0.449	CLONAL	1	TRUE	1	0.534208352111456	3		362	815	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646129	215646131	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	novel	NA	P-0003870-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1570	201	382	0	ENST00000260947.4:c.467_469del	p.Tyr156_Val157delinsPhe	p.Y156_V157delinsF	ENST00000260947	NM_000465.2	156	tATGtt/ttt	4/11	0.534208352111456	9	FACETS	1	0.983	1	0.174	0.16	0.189	CLONAL	1	TRUE	2	0.534208352111456	9		382	1771	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265908	16265908	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003877-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	127	461	0	ENST00000375759.3:c.10981A>T	p.Ile3661Phe	p.I3661F	ENST00000375759	NM_015001.2	3661	Att/Ttt	15/15	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.404338873686831	2		461	589	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003877-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	109	301	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.24024965785643	0	FACETS	1	0.956	1			1	INDETERMINATE	1	FALSE	0	0.404338873686831	0		301	297	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857311	68857312	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0003877-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	66	245	0	ENST00000261769.5:c.1947dup	p.Ile650TyrfsTer13	p.I650Yfs*13	ENST00000261769	NM_004360.3	649	tct/tcTt	13/16	0.362422327612224	0	FACETS	0.694	0.609	0.785			1	SUBCLONAL	1	FALSE	0	0.404338873686831	0		245	280	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0003894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	171	229	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.438667569092704	2	FACETS	0.898	0.838	0.957	0.898	0.838	0.957	CLONAL	2	TRUE	0	0.519123342079113	2		231	367	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288967	212288967	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs537458255	NA	P-0003894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	63	261	0	ENST00000342788.4:c.2779C>T	p.Arg927Ter	p.R927*	ENST00000342788	NM_005235.2	927	Cga/Tga	23/28	0.303219212666715	4	FACETS	0.803	0.696	0.919			1	INDETERMINATE	1	TRUE	NA	0.519123342079113	4		261	459	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881549	111881549	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs900605292	NA	P-0003894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	174	223	0	ENST00000393256.3:c.227G>A	p.Arg76Lys	p.R76K	ENST00000393256	NM_006538.4	76	aGa/aAa	2/4	0.423594649005342	5	FACETS	0.858	0.798	0.92	0.858	0.798	0.92	CLONAL	3	TRUE	2	0.519123342079113	5		223	463	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884819	134884819	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	43	180	0	ENST00000398015.3:c.1595A>T	p.Lys532Met	p.K532M	ENST00000398015	NM_004441.4	532	aAg/aTg	8/16	0.22375605956494	3	FACETS	1	0.857	1	0.506	0.428	0.591	INDETERMINATE	1	TRUE	1	0.519123342079113	3		180	206	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272212	142272212	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1559988588	NA	P-0003894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	103	227	0	ENST00000350721.4:c.2662G>T	p.Ala888Ser	p.A888S	ENST00000350721	NM_001184.3	888	Gca/Tca	13/47	0.22375605956494	3	FACETS	1	0.966	1	0.583	0.525	0.643	INDETERMINATE	1	TRUE	1	0.519123342079113	3		227	429	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008080	29008080	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	42	171	0	ENST00000282397.4:c.689T>C	p.Ile230Thr	p.I230T	ENST00000282397	NM_002019.4	230	aTa/aCa	6/30	0.417669722782681	3	FACETS	0.614	0.514	0.724	0.307	0.257	0.362	SUBCLONAL	1	TRUE	1	0.519123342079113	3		171	332	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678598	88678598	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	21	97	0	ENST00000360948.2:c.938C>A	p.Pro313His	p.P313H	ENST00000360948	NM_001012338.2	313	cCt/cAt	9/19	0.243290557006573	4	FACETS	0.793	0.616	0.995	0.396	0.308	0.498	INDETERMINATE	1	TRUE	2	0.519123342079113	4		97	155	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679708	88679708	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	107	214	0	ENST00000360948.2:c.755A>C	p.Asn252Thr	p.N252T	ENST00000360948	NM_001012338.2	252	aAc/aCc	7/19	0.243290557006573	4	FACETS	1	0.956	1	1	0.956	1	INDETERMINATE	2	TRUE	2	0.519123342079113	4		214	289	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587512	29587512	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	151	192	0	ENST00000356175.3:c.4493G>T	p.Gly1498Val	p.G1498V	ENST00000356175	NM_000267.3	1498	gGg/gTg	33/57	0.423594649005342	5	FACETS	1	0.945	1	0.688	0.634	0.745	CLONAL	2	TRUE	2	0.519123342079113	5		192	501	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211746	5211746	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	57	209	0	ENST00000357368.4:c.5089T>G	p.Phe1697Val	p.F1697V	ENST00000357368	NM_002850.3	1697	Ttc/Gtc	33/38	0.271896422367856	3	FACETS	0.846	0.73	0.971	0.282	0.243	0.324	INDETERMINATE	1	TRUE	0	0.519123342079113	3		209	327	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094333	27094334	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0003894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	89	187	0	ENST00000324856.7:c.3041_3042insCA	p.Gly1015ArgfsTer25	p.G1015Rfs*25	ENST00000324856	NM_006015.4	1014	ctg/ctCAg	11/20	0.210482829980928	4	FACETS	1	0.979	1	0.725	0.648	0.806	INDETERMINATE	1	TRUE	2	0.519123342079113	4		187	359	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21968233	21968243	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	CGGGGATGTCT	CGGGGATGTCT	G	novel	NA	P-0003894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	56	109	0	ENST00000304494.5:c.458-2_466delinsC		p.X153_splice	ENST00000304494	NM_000077.4	153		3/3	0.22375605956494	3	FACETS	1	0.953	1	0.615	0.533	0.701	INDETERMINATE	1	TRUE	1	0.519123342079113	3		109	221	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139504	47139505	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0003895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	125	641	0	ENST00000409792.3:c.5082_5083del	p.Arg1694SerfsTer17	p.R1694Sfs*17	ENST00000409792	NM_014159.6	1694	agAGtc/agtc	9/21	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.289736421724311	2		641	587	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266139	41266140	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0003895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	117	430	1	ENST00000349496.5:c.137dup	p.Ser47GlufsTer3	p.S47Efs*3	ENST00000349496	NM_001904.3	46	ctg/cTtg	3/15	NA	2	FACETS	0.838	0.76	0.919			1	INDETERMINATE	2	TRUE	NA	0.289736421724311	2		431	482	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441424	52441443	+	frameshift_variant	Frame_Shift_Del	DEL	CTATTATGGGCCTTGGCCAA	CTATTATGGGCCTTGGCCAA	-	novel	NA	P-0003895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	141	516	0	ENST00000460680.1:c.409_428del	p.Leu137ProfsTer11	p.L137Pfs*11	ENST00000460680	NM_004656.3	137	TTGGCCAAGGCCCATAATAGc/c	6/17	NA	2	FACETS	1	0.952	1			1	INDETERMINATE	2	TRUE	NA	0.289736421724311	2		516	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0003915-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	259	607	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.273950276737485	1	FACETS	0.905	0.846	0.967	0.905	0.846	0.967	CLONAL	1	TRUE	0	0.33	1		607	1448	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562482	21562483	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGGCG	rs550642106	NA	P-0003915-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	30	42	0	ENST00000382592.4:c.1431_1436dup	p.Pro479_Ala480dup	p.P479_A480dup	ENST00000382592	NM_014572.2	479	ccg/ccCGCCCCg	4/8	0.304875397531883	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.33	1		42	116	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163551	47163551	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003915-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	105	362	0	ENST00000409792.3:c.2575A>G	p.Thr859Ala	p.T859A	ENST00000409792	NM_014159.6	859	Act/Gct	3/21	0.273950276737485	1	FACETS	0.788	0.707	0.874	0.788	0.707	0.874	SUBCLONAL	1	TRUE	0	0.33	1		362	674	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956212	55956212	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003915-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	64	504	0	ENST00000263923.4:c.3103C>A	p.Leu1035Ile	p.L1035I	ENST00000263923	NM_002253.2	1035	Ctc/Atc	23/30	1	2	FACETS	0.317	0.273	0.365	0.317	0.273	0.365	SUBCLONAL	1	TRUE	1	0.33	2		504	1225	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845731	68845731	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003915-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	146	176	0	ENST00000261769.5:c.977T>A	p.Ile326Asn	p.I326N	ENST00000261769	NM_004360.3	326	aTc/aAc	7/16	1	2	FACETS	0.827	0.759	0.897	1	0.99	1	CLONAL	2	TRUE	1	0.33	2		176	535	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624263	89624282	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAGGAGATATCAAGAGGA	AAAAGGAGATATCAAGAGGA	-	novel	NA	P-0003915-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	52	138	0	ENST00000371953.3:c.37_56del	p.Lys13TrpfsTer24	p.K13Wfs*24	ENST00000371953	NM_000314.4	13	AAAAGGAGATATCAAGAGGAt/t	1/9	1	2	FACETS	0.767	0.654	0.889	0.767	0.654	0.889	SUBCLONAL	1	TRUE	1	0.33	2		138	411	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0003921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	370	208	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.992	0.947	1	0.992	0.947	1	CLONAL	1	TRUE	1	0.892074041373035	2		208	836	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	102	374	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.844	0.767	0.923	0.844	0.767	0.923	CLONAL	1	TRUE	1	0.892074041373035	2		374	271	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144880	47144880	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	214	231	0	ENST00000409792.3:c.4873C>T	p.Arg1625Cys	p.R1625C	ENST00000409792	NM_014159.6	1625	Cgt/Tgt	7/21	0.331129056092111	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.892074041373035	0		231	559	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272777	18272777	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	rs147990742	NA	P-0003921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	161	231	0	ENST00000222254.8:c.817A>T	p.Ser273Cys	p.S273C	ENST00000222254	NM_005027.3	273	Agt/Tgt	7/16	0.488471314791807	1	FACETS	0.334	0.308	0.362	0.334	0.308	0.362	INDETERMINATE	1	TRUE	0	0.892074041373035	1		231	598	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612073	189612073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142762485	NA	P-0003921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	264	299	0	ENST00000264731.3:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000264731	NM_003722.4	609	Gaa/Aaa	14/14	0.687258937645646	1	FACETS	0.588	0.556	0.619	0.588	0.556	0.619	SUBCLONAL	1	TRUE	0	0.892074041373035	1		299	558	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805764	43805764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	378	328	2	ENST00000372470.3:c.820C>T	p.Leu274Phe	p.L274F	ENST00000372470	NM_005373.2	274	Ctc/Ttc	5/12	0.318750584224129	1	FACETS	0.601	0.574	0.628	0.601	0.574	0.628	INDETERMINATE	1	TRUE	0	0.892074041373035	1		330	781	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518755	204518755	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	351	203	0	ENST00000367182.3:c.1418C>T	p.Ser473Leu	p.S473L	ENST00000367182	NM_001278516.1	473	tCa/tTa	11/11	0.34694018736716	2	FACETS	1	0.996	1	0.693	0.665	0.72	INDETERMINATE	1	TRUE	0	0.892074041373035	2		203	568	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651334	52651334	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1394528754	NA	P-0003921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	311	312	0	ENST00000394830.3:c.1762G>A	p.Glu588Lys	p.E588K	ENST00000394830	NM_018313.4	588	Gaa/Aaa	15/30	0.331129056092111	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.892074041373035	0		312	746	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535307	66535307	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	315	278	0	ENST00000273854.3:c.154A>G	p.Thr52Ala	p.T52A	ENST00000273854	NM_004439.5	52	Acc/Gcc	1/18	0.249916064043391	1	FACETS	0.581	0.553	0.61	0.581	0.553	0.61	INDETERMINATE	1	TRUE	0	0.892074041373035	1		278	673	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627771	187627771	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	321	341	0	ENST00000441802.2:c.3211T>G	p.Tyr1071Asp	p.Y1071D	ENST00000441802	NM_005245.3	1071	Tac/Gac	2/27	0.249916064043391	1	FACETS	0.396	0.374	0.418	0.396	0.374	0.418	INDETERMINATE	1	TRUE	0	0.892074041373035	1		341	1008	SUCCESS
APC	324	MSKCC	GRCh37	5	112178415	112178415	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	387	288	0	ENST00000257430.4:c.7124A>T	p.Gln2375Leu	p.Q2375L	ENST00000257430	NM_000038.5	2375	cAa/cTa	16/16	1	2	FACETS	0.938	0.895	0.981	0.938	0.895	0.981	CLONAL	1	TRUE	1	0.892074041373035	2		288	925	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965706	93965706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	608	483	0	ENST00000369303.4:c.2222G>A	p.Gly741Glu	p.G741E	ENST00000369303	NM_004440.3	741	gGa/gAa	13/17	0.892074041373035	1	FACETS	0.999	0.977	1	0.999	0.977	1	CLONAL	1	TRUE	0	0.892074041373035	1		483	756	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972514	81972514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs904052522	NA	P-0003921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	678	477	2	ENST00000359376.3:c.3307G>A	p.Val1103Ile	p.V1103I	ENST00000359376	NM_002661.3	1103	Gtt/Att	29/33	0.318750584224129	1	FACETS	0.657	0.636	0.678	0.657	0.636	0.678	INDETERMINATE	1	TRUE	0	0.892074041373035	1		479	1281	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39644733	39644733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	248	240	0	ENST00000262039.4:c.2462C>T	p.Ser821Phe	p.S821F	ENST00000262039	NM_002647.2	821	tCc/tTc	23/25	0.318750584224129	1	FACETS	0.407	0.382	0.433	0.407	0.382	0.433	INDETERMINATE	1	TRUE	0	0.892074041373035	1		240	756	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296145	15296145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	206	308	0	ENST00000263388.2:c.2219C>T	p.Ser740Phe	p.S740F	ENST00000263388	NM_000435.2	740	tCc/tTc	14/33	0.488471314791807	1	FACETS	0.36	0.335	0.386	0.36	0.335	0.386	INDETERMINATE	1	TRUE	0	0.892074041373035	1		308	711	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459072	120459073	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	341	236	0	ENST00000256646.2:c.6272dup	p.Leu2092ProfsTer13	p.L2092Pfs*13	ENST00000256646	NM_024408.3	2091	ttc/ttTc	34/34	0.318750584224129	1	FACETS	0.638	0.609	0.667	0.638	0.609	0.667	INDETERMINATE	1	TRUE	0	0.892074041373035	1		236	664	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0004010-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	12	673	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.361247012495354	4	FACETS	0.529	0.374	0.717	0.264	0.187	0.359	SUBCLONAL	1	FALSE	2	0.542649957638542	4		673	129	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0004010-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	45	302	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.542649957638542	4	FACETS	1	0.922	1	0.571	0.485	0.665	CLONAL	1	FALSE	2	0.542649957638542	4		302	224	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380277	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913238	NA	P-0004010-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	13	384	0	ENST00000311936.3:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	61	Caa/Aaa	3/5	0.288858898711884	4	FACETS	0.496	0.355	0.666	0.248	0.177	0.333	INDETERMINATE	1	FALSE	2	0.542649957638542	4		384	149	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372337	55372337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1281266243	NA	P-0004010-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	13	376	1	ENST00000297316.4:c.1027C>T	p.Arg343Trp	p.R343W	ENST00000297316	NM_022454.3	343	Cgg/Tgg	2/2	0.497655899453151	4	FACETS	0.891	0.645	1	0.445	0.322	0.59	CLONAL	1	FALSE	2	0.542649957638542	4		377	83	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247369	153247369	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004010-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	19	211	0	ENST00000281708.4:c.1433C>T	p.Ser478Phe	p.S478F	ENST00000281708	NM_033632.3	478	tCt/tTt	10/12	0.377326636733433	3	FACETS	0.503	0.384	0.641	0.251	0.192	0.321	SUBCLONAL	1	FALSE	1	0.542649957638542	3		211	177	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250822	153250822	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0004010-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	31	506	0	ENST00000281708.4:c.1236+2T>C		p.X412_splice	ENST00000281708	NM_033632.3	412			0.377326636733433	3	FACETS	0.353	0.285	0.429	0.176	0.142	0.215	SUBCLONAL	1	FALSE	1	0.542649957638542	3		506	412	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215772	98215772	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1398400648	NA	P-0004010-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	21	289	0	ENST00000331920.6:c.3437A>G	p.Asp1146Gly	p.D1146G	ENST00000331920	NM_000264.3	1146	gAc/gGc	20/24	0.377326636733433	3	FACETS	0.449	0.347	0.568	0.225	0.173	0.284	SUBCLONAL	1	FALSE	1	0.542649957638542	3		289	219	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004010-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	14	428	0	ENST00000342988.3:c.1610A>C	p.Asp537Ala	p.D537A	ENST00000342988	NM_005359.5	537	gAc/gCc	12/12	0.361247012495354	4	FACETS	0.45	0.326	0.598	0.225	0.163	0.299	SUBCLONAL	1	FALSE	2	0.542649957638542	4		428	177	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670943	30670943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	139	359	0	ENST00000376406.3:c.5803G>A	p.Val1935Ile	p.V1935I	ENST00000376406	NM_014641.2	1935	Gtc/Atc	12/15	0.531617744303486	1	FACETS	0.409	0.372	0.448	0.409	0.372	0.448	SUBCLONAL	1	TRUE	0	0.571261050604663	1		359	849	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851131	63851131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778262915	NA	P-0004026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	58	224	0	ENST00000279873.7:c.1909G>A	p.Asp637Asn	p.D637N	ENST00000279873	NM_032199.2	637	Gac/Aac	10/10	0.571261050604663	1	FACETS	0.304	0.261	0.35	0.304	0.261	0.35	SUBCLONAL	1	TRUE	0	0.571261050604663	1		224	477	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508183	38508183	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	72	391	0	ENST00000254066.5:c.491A>C	p.Lys164Thr	p.K164T	ENST00000254066	NM_000964.3	164	aAg/aCg	5/9	1	2	FACETS	0.255	0.221	0.291	0.255	0.221	0.291	SUBCLONAL	1	TRUE	1	0.571261050604663	2		391	990	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814213	76814213	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	138	620	0	ENST00000373344.5:c.6431A>G	p.Asp2144Gly	p.D2144G	ENST00000373344	NM_000489.3	2144	gAc/gGc	29/35	0.459621471023503	0	FACETS	0.549	0.506	0.594			1	SUBCLONAL	1	TRUE	0	0.571261050604663	0		620	377	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577281	64577282	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	221	294	0	ENST00000312049.6:c.300dup	p.Val101ArgfsTer16	p.V101Rfs*16	ENST00000312049	NM_130799.2	100	-/C	2/10	0.571261050604663	1	FACETS	0.975	0.914	1	0.975	0.914	1	CLONAL	1	TRUE	0	0.571261050604663	1		294	567	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0004030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	87	302	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.433827798146659	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.433827798146659	1		302	258	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0004030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	93	216	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	0.433827798146659	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.433827798146659	1		216	314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	88	523	0	ENST00000269305.4:c.313G>T	p.Gly105Cys	p.G105C	ENST00000269305	NM_001126112.2	105	Ggc/Tgc	4/11	0.433827798146659	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.433827798146659	1		523	255	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118835	115118835	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs772182165	NA	P-0004030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	135	248	0	ENST00000257566.3:c.506G>T	p.Arg169Leu	p.R169L	ENST00000257566	NM_016569.3	169	cGg/cTg	2/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.433827798146659	2		248	505	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885835	23885835	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	156	391	0	ENST00000374561.5:c.83G>T	p.Arg28Leu	p.R28L	ENST00000374561	NM_002167.4	28	cGa/cTa	1/3	1	2	FACETS	0.876	0.803	0.952	0.876	0.803	0.952	CLONAL	1	TRUE	1	0.433827798146659	2		391	821	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099093	27099093	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	129	227	0	ENST00000324856.7:c.3509A>C	p.His1170Pro	p.H1170P	ENST00000324856	NM_006015.4	1170	cAc/cCc	13/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.433827798146659	2		227	486	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935296	36935296	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs144323240	NA	P-0004030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	162	529	0	ENST00000361632.4:c.1431G>T	p.Trp477Cys	p.W477C	ENST00000361632		477	tgG/tgT	10/16	0.404127038654894	1	FACETS	0.849	0.781	0.919	0.849	0.781	0.919	CLONAL	1	TRUE	0	0.433827798146659	1		529	689	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458225	120458225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	44	170	0	ENST00000256646.2:c.7120C>T	p.His2374Tyr	p.H2374Y	ENST00000256646	NM_024408.3	2374	Cat/Tat	34/34	1	2	FACETS	0.818	0.691	0.956	0.818	0.691	0.956	CLONAL	1	TRUE	1	0.433827798146659	2		170	248	SUCCESS
ALK	238	MSKCC	GRCh37	2	29450512	29450512	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	83	319	0	ENST00000389048.3:c.2842C>A	p.Pro948Thr	p.P948T	ENST00000389048	NM_004304.4	948	Ccc/Acc	17/29	0.404127038654894	1	FACETS	0.642	0.568	0.72	0.642	0.568	0.72	SUBCLONAL	1	TRUE	0	0.433827798146659	1		319	467	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670645	134670645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1197104045	NA	P-0004030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	161	341	0	ENST00000398015.3:c.556C>T	p.Leu186Phe	p.L186F	ENST00000398015	NM_004441.4	186	Ctt/Ttt	3/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.433827798146659	2		341	595	SUCCESS
ATR	545	MSKCC	GRCh37	3	142204103	142204103	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	84	248	0	ENST00000350721.4:c.6100G>C	p.Glu2034Gln	p.E2034Q	ENST00000350721	NM_001184.3	2034	Gaa/Caa	36/47	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.433827798146659	2		248	384	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138612	55138612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202072966	NA	P-0004030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	103	189	0	ENST00000257290.5:c.1289G>A	p.Gly430Glu	p.G430E	ENST00000257290	NM_006206.4	430	gGa/gAa	9/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.433827798146659	2		189	387	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675664	30675664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	129	432	0	ENST00000376406.3:c.2692G>A	p.Glu898Lys	p.E898K	ENST00000376406	NM_014641.2	898	Gag/Aag	8/15	0.152362320156137	4	FACETS	1	0.985	1	0.714	0.65	0.782	INDETERMINATE	1	TRUE	2	0.433827798146659	4		432	597	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2949704	2949704	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs763963222	NA	P-0004030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	132	302	0	ENST00000396946.4:c.3240G>C	p.Glu1080Asp	p.E1080D	ENST00000396946	NM_032415.4	1080	gaG/gaC	24/25	0.433827798146659	3	FACETS	1	0.956	1	0.542	0.493	0.594	CLONAL	1	TRUE	1	0.433827798146659	3		302	683	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003799	45003799	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	116	226	0	ENST00000558401.1:c.55G>T	p.Glu19Ter	p.E19*	ENST00000558401	NM_004048.2	19	Gag/Tag	1/4	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.433827798146659	2		226	498	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588803	29588803	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	109	300	0	ENST00000356175.3:c.4589A>C	p.His1530Pro	p.H1530P	ENST00000356175	NM_000267.3	1530	cAc/cCc	34/57	1	2	FACETS	0.987	0.89	1	0.987	0.89	1	CLONAL	1	TRUE	1	0.433827798146659	2		300	509	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805846	46805846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	165	509	1	ENST00000290295.7:c.110C>T	p.Pro37Leu	p.P37L	ENST00000290295	NM_006361.5	37	cCa/cTa	1/2	0.433827798146659	1	FACETS	0.885	0.815	0.957	0.885	0.815	0.957	CLONAL	1	TRUE	0	0.433827798146659	1		510	673	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600472	10600472	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	122	293	0	ENST00000171111.5:c.1383C>G	p.Ile461Met	p.I461M	ENST00000171111	NM_203500.1	461	atC/atG	4/6	0.433827798146659	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.433827798146659	1		293	400	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298020	15298020	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	123	247	0	ENST00000263388.2:c.1736G>T	p.Cys579Phe	p.C579F	ENST00000263388	NM_000435.2	579	tGc/tTc	11/33	0.383550113907365	3	FACETS	1	0.972	1	0.59	0.535	0.647	CLONAL	1	TRUE	1	0.433827798146659	3		247	585	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988676	41988676	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	176	455	0	ENST00000219905.7:c.1468del	p.Met490CysfsTer33	p.M490Cfs*33	ENST00000219905	NM_001164273.1	490	Atg/tg	3/24	0.367094538988427	0	FACETS	0.785	0.727	0.845			1	SUBCLONAL	1	TRUE	0	0.433827798146659	0		455	585	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223038	1223082	+	inframe_deletion	In_Frame_Del	DEL	CCCAGACACCAAGGACCGGTGGCGCAGCATGACTGTGGTGCCGTA	CCCAGACACCAAGGACCGGTGGCGCAGCATGACTGTGGTGCCGTA	-	novel	NA	P-0004030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	130	265	0	ENST00000326873.7:c.976_1020del	p.Pro326_Tyr340del	p.P326_Y340del	ENST00000326873	NM_000455.4	325	agCCCAGACACCAAGGACCGGTGGCGCAGCATGACTGTGGTGCCGTAc/agc	8/10	0.433827798146659	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.433827798146659	1		265	387	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539568	187539568	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	71	210	0	ENST00000441802.2:c.8172del	p.Ile2725SerfsTer28	p.I2725Sfs*28	ENST00000441802	NM_005245.3	2724	ctC/ct	10/27	1	2	FACETS	0.927	0.815	1	0.927	0.815	1	CLONAL	1	TRUE	1	0.433827798146659	2		210	353	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223087	1223088	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	146	330	0	ENST00000326873.7:c.1025dup	p.Asp343GlyfsTer17	p.D343Gfs*17	ENST00000326873	NM_000455.4	342	gag/gAag	8/10	0.433827798146659	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.433827798146659	1		330	450	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435328	18435329	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0004030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	81	221	0	ENST00000266497.5:c.313_314delinsAA	p.Pro105Lys	p.P105K	ENST00000266497		105	CCa/AAa	1/31	1	2	FACETS	0.862	0.763	0.968	0.862	0.763	0.968	CLONAL	1	TRUE	1	0.433827798146659	2		221	433	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100956	41100957	+	missense_variant	Missense_Mutation	DNP	GG	GG	TC	novel	NA	P-0004030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	62	154	0	ENST00000373198.4:c.1399_1400delinsGA	p.Pro467Asp	p.P467D	ENST00000373198	NM_133170.3	467	CCc/GAc	8/32	1	2	FACETS	0.81	0.703	0.924	0.81	0.703	0.924	CLONAL	1	TRUE	1	0.433827798146659	2		154	353	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591115	67591116	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1561299903	NA	P-0004040-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	394	412	0	ENST00000274335.5:c.1710dup	p.Ile571TyrfsTer31	p.I571Yfs*31	ENST00000274335		570	ctt/cTtt	12/15	0.771329256410102	3	FACETS	0.897	0.859	0.935	0.897	0.859	0.935	CLONAL	2	TRUE	1	0.771329256410102	3		412	789	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004040-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	316	301	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.975	0.924	1	0.975	0.924	1	CLONAL	1	TRUE	1	0.771329256410102	2		301	840	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0004040-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	261	734	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.827	0.778	0.878	0.827	0.778	0.878	CLONAL	1	TRUE	1	0.771329256410102	2		734	818	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0004040-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	216	380	0	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	1	2	FACETS	0.957	0.897	1	0.957	0.897	1	CLONAL	1	TRUE	1	0.771329256410102	2		380	585	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831603	72831604	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCACTCACA	novel	NA	P-0004040-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	280	676	0	ENST00000268489.5:c.4977_4978insTGTGAGTGGC	p.Ser1660CysfsTer5	p.S1660Cfs*5	ENST00000268489	NM_006885.3	1659	-/TGTGAGTGGC	9/10	1	2	FACETS	0.819	0.771	0.867	0.819	0.771	0.867	CLONAL	1	TRUE	1	0.771329256410102	2		676	887	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330610	65330611	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004040-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	242	468	0	ENST00000342505.4:c.1035dup	p.Leu346ThrfsTer4	p.L346Tfs*4	ENST00000342505	NM_002227.2	345	-/A	8/25	0.771329256410102	1	FACETS	0.907	0.861	0.952	0.907	0.861	0.952	CLONAL	1	TRUE	0	0.771329256410102	1		468	425	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	85	359	0	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.888	0.787	0.994	0.888	0.787	0.994	CLONAL	1	TRUE	1	0.390828378148457	2		359	490	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0004083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	291	518	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.390638167145129	2	FACETS	0.956	0.903	1	0.956	0.903	1	CLONAL	2	TRUE	0	0.390828378148457	2		518	779	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	69	414	7	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.692	0.604	0.787	0.692	0.604	0.787	SUBCLONAL	1	TRUE	1	0.390828378148457	2		421	510	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769886672	NA	P-0004083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	59	237	1	ENST00000405192.2:c.414dup	p.Thr139HisfsTer24	p.T139Hfs*24	ENST00000405192	NM_001163147.1	138	-/C	7/12	1	2	FACETS	0.918	0.794	1	0.918	0.794	1	CLONAL	1	TRUE	1	0.390828378148457	2		238	329	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427265	49427266	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGC	rs398123707	NA	P-0004083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	49	406	1	ENST00000301067.7:c.11220_11222dup	p.Gln3745dup	p.Q3745dup	ENST00000301067	NM_003482.3	3745	caa/caGCAa	39/54	1	2	FACETS	0.636	0.54	0.742	0.636	0.54	0.742	SUBCLONAL	1	TRUE	1	0.390828378148457	2		407	394	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0004083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	110	410	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.896	0.807	0.991	0.896	0.807	0.991	CLONAL	1	TRUE	1	0.390828378148457	2		410	628	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0004083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	173	526	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.390828378148457	2		526	833	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0004083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	307	831	11	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.114657070001084	0	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	0	0.390828378148457	0		842	860	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741822	162741822	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs115169993	NA	P-0004083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	129	342	0	ENST00000367921.3:c.1513G>A	p.Gly505Ser	p.G505S	ENST00000367921	NM_006182.2	505	Ggt/Agt	13/18	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.390828378148457	2		342	471	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136293	202136293	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	203	548	0	ENST00000358485.4:c.537T>A	p.Phe179Leu	p.F179L	ENST00000358485	NM_001080125.1	179	ttT/ttA	3/9	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.390828378148457	2		548	1022	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165327	47165327	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs186148199	NA	P-0004083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	219	530	0	ENST00000409792.3:c.799G>A	p.Val267Ile	p.V267I	ENST00000409792	NM_014159.6	267	Gta/Ata	3/21	0.390638167145129	2	FACETS	1	0.975	1	0.55	0.512	0.59	CLONAL	1	TRUE	0	0.390828378148457	2		530	1018	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs770248150	NA	P-0004083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	358	495	0	ENST00000311936.3:c.351A>T	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaT	4/5	1	2	FACETS	0.836	0.793	0.879	1	0.996	1	CLONAL	2	TRUE	1	0.390828378148457	2		495	1096	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431469	121431469	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	130	477	0	ENST00000257555.6:c.673A>G	p.Ser225Gly	p.S225G	ENST00000257555		225	Agc/Ggc	3/10	0.164203749758277	1	FACETS	0.913	0.832	0.999	0.913	0.832	0.999	INDETERMINATE	1	TRUE	0	0.390828378148457	1		477	586	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007619	45007619	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs111482205	NA	P-0004083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	85	272	1	ENST00000558401.1:c.68-2A>G		p.X23_splice	ENST00000558401	NM_004048.2	23			1	2	FACETS	0.792	0.702	0.889	0.792	0.702	0.889	SUBCLONAL	1	TRUE	1	0.390828378148457	2		273	549	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805318	89805318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201494304	NA	P-0004083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	157	516	0	ENST00000389301.3:c.4232C>T	p.Pro1411Leu	p.P1411L	ENST00000389301	NM_000135.2	1411	cCg/cTg	42/43	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.390828378148457	2		516	787	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120455	70120455	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	168	680	0	ENST00000245479.2:c.1457T>C	p.Val486Ala	p.V486A	ENST00000245479	NM_000346.3	486	gTc/gCc	3/3	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.390828378148457	2		680	794	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573228	41573228	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	28	425	0	ENST00000263253.7:c.5513C>A	p.Thr1838Asn	p.T1838N	ENST00000263253	NM_001429.3	1838	aCt/aAt	31/31	1	2	FACETS	0.279	0.222	0.344	0.279	0.222	0.344	SUBCLONAL	1	TRUE	1	0.390828378148457	2		425	514	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006897	47006897	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	133	257	0	ENST00000377604.3:c.17G>A	p.Arg6His	p.R6H	ENST00000377604	NM_001204468.1	6	cGt/cAt	2/24	1	1	FACETS	0.84	0.774	0.907	1	0.99	1	CLONAL	2	TRUE	0	0.390828378148457	1		257	326	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396792	396792	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	37	516	1	ENST00000262320.3:c.234del	p.Thr79ProfsTer5	p.T79Pfs*5	ENST00000262320	NM_003502.3	78	ccC/cc	2/11	1	2	FACETS	0.283	0.232	0.339	0.283	0.232	0.339	SUBCLONAL	1	TRUE	1	0.390828378148457	2		517	670	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845553	63845553	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	165	514	0	ENST00000279873.7:c.1295del	p.Asn432MetfsTer47	p.N432Mfs*47	ENST00000279873	NM_032199.2	431	gAa/ga	9/10	1	2	FACETS	0.838	0.769	0.91	0.838	0.769	0.91	CLONAL	1	TRUE	1	0.390828378148457	2		514	1008	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251782	10251782	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	45	553	1	ENST00000340748.4:c.3345del	p.Lys1117ArgfsTer16	p.K1117Rfs*16	ENST00000340748		1115	aaA/aa	30/40	1	2	FACETS	0.276	0.231	0.326	0.276	0.231	0.326	SUBCLONAL	1	TRUE	1	0.390828378148457	2		554	834	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248998	55248999	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCCAGCG	rs727504263	NA	P-0004120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	69	264	0	ENST00000275493.2:c.2300_2308dup	p.Ala767_Val769dup	p.A767_V769dup	ENST00000275493	NM_005228.3	767	atg/aTGGCCAGCGtg	20/28	0.281231045383173	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		264	558	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	63	374	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.377343872467991	2		374	307	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965862	25965862	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1160343563	NA	P-0004162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	142	217	0	ENST00000435504.4:c.3344C>T	p.Thr1115Ile	p.T1115I	ENST00000435504		1115	aCa/aTa	13/13	1	2	FACETS	0.87	0.793	0.951	0.87	0.793	0.951	CLONAL	1	TRUE	1	0.377343872467991	2		217	865	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762513	41762513	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	96	167	0	ENST00000301178.4:c.2193T>G	p.Asp731Glu	p.D731E	ENST00000301178	NM_021913.4	731	gaT/gaG	18/20	1	2	FACETS	0.877	0.783	0.977	0.877	0.783	0.977	CLONAL	1	TRUE	1	0.377343872467991	2		167	580	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951075	48951076	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	103	168	0	ENST00000267163.4:c.1240dup	p.Ser414LysfsTer14	p.S414Kfs*14	ENST00000267163	NM_000321.2	413	gaa/gAaa	13/27	0.367781561573206	1	FACETS	0.774	0.695	0.858	0.774	0.695	0.858	SUBCLONAL	1	TRUE	0	0.377343872467991	1		168	572	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263850	133263850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	21	100	1	ENST00000320574.5:c.52G>A	p.Glu18Lys	p.E18K	ENST00000320574	NM_006231.2	18	Gag/Aag	1/49	0.238419191232644	4	FACETS	1	0.816	1			1	CLONAL	1	TRUE	NA	0.238419191232644	4		101	205	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193181212	193181212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773264613	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	173	314	0	ENST00000367435.3:c.1048C>T	p.Pro350Ser	p.P350S	ENST00000367435	NM_024529.4	350	Ccc/Tcc	12/17	0.238419191232644	5	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	3	0.238419191232644	5		314	840	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599868	10599868	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	175	409	1	ENST00000171111.5:c.1708G>T	p.Gly570Ter	p.G570*	ENST00000171111	NM_203500.1	570	Gga/Tga	5/6	0.211410397441768	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.238419191232644	2		410	624	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119789	70119789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778047936	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	53	359	0	ENST00000245479.2:c.791G>A	p.Arg264Lys	p.R264K	ENST00000245479	NM_000346.3	264	aGa/aAa	3/3	0.238419191232644	4	FACETS	0.985	0.84	1	0.492	0.42	0.572	CLONAL	1	TRUE	2	0.238419191232644	4		359	559	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437220	220437220	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	65	543	0	ENST00000243786.2:c.124G>T	p.Gly42Trp	p.G42W	ENST00000243786	NM_002191.3	42	Ggg/Tgg	1/2	1	2	FACETS	0.958	0.831	1	0.958	0.831	1	CLONAL	1	TRUE	1	0.238419191232644	2		543	569	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36945043	36945043	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	85	449	0	ENST00000361632.4:c.55C>A	p.Leu19Ile	p.L19I	ENST00000361632		19	Ctc/Atc	2/16	NA	2	FACETS	1	0.953	1			1	INDETERMINATE	1	TRUE	NA	0.238419191232644	2		449	620	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65300318	65300318	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	51	197	0	ENST00000342505.4:c.3392G>T	p.Cys1131Phe	p.C1131F	ENST00000342505	NM_002227.2	1131	tGc/tTc	25/25	0.227750812131769	4	FACETS	1	0.88	1			1	CLONAL	1	TRUE	NA	0.238419191232644	4		197	509	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845873	156845873	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	109	464	0	ENST00000524377.1:c.1503T>G	p.Cys501Trp	p.C501W	ENST00000524377	NM_002529.3	501	tgT/tgG	13/17	0.238419191232644	3	FACETS	0.781	0.702	0.864			1	SUBCLONAL	2	TRUE	NA	0.238419191232644	3		464	655	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204495523	204495523	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	148	292	0	ENST00000367182.3:c.114T>A	p.His38Gln	p.H38Q	ENST00000367182	NM_001278516.1	38	caT/caA	3/11	0.238419191232644	5	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	3	0.238419191232644	5		292	807	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518424	204518424	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	118	351	0	ENST00000367182.3:c.1087C>T	p.Arg363Ter	p.R363*	ENST00000367182	NM_001278516.1	363	Cga/Tga	11/11	0.238419191232644	5	FACETS	0.859	0.775	0.948	0.859	0.775	0.948	CLONAL	2	TRUE	3	0.238419191232644	5		351	782	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466852	25466852	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	75	267	0	ENST00000264709.3:c.1852-1G>T		p.X618_splice	ENST00000264709	NM_175629.2	618			0.238419191232644	4	FACETS	0.815	0.716	0.921	0.815	0.716	0.921	CLONAL	2	TRUE	2	0.238419191232644	4		267	478	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578362	212578362	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	80	265	0	ENST00000342788.4:c.895G>T	p.Val299Leu	p.V299L	ENST00000342788	NM_005235.2	299	Gta/Tta	8/28	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.238419191232644	2		265	531	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225367741	225367741	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	133	361	0	ENST00000264414.4:c.1426G>T	p.Asp476Tyr	p.D476Y	ENST00000264414	NM_003590.4	476	Gat/Tat	10/16	0.238419191232644	4	FACETS	0.942	0.857	1			1	CLONAL	2	TRUE	NA	0.238419191232644	4		361	733	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143043	47143043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	83	291	0	ENST00000409792.3:c.4920G>T	p.Trp1640Cys	p.W1640C	ENST00000409792	NM_014159.6	1640	tgG/tgT	8/21	0.238419191232644	3	FACETS	1	0.937	1	0.547	0.483	0.617	CLONAL	1	TRUE	1	0.238419191232644	3		291	712	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164215	47164215	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	124	243	0	ENST00000409792.3:c.1911G>T	p.Lys637Asn	p.K637N	ENST00000409792	NM_014159.6	637	aaG/aaT	3/21	0.238419191232644	3	FACETS	1	0.917	1	1	0.917	1	CLONAL	2	TRUE	1	0.238419191232644	3		243	576	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015147	71015147	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1292897246	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	116	279	0	ENST00000318789.4:c.1783C>G	p.Leu595Val	p.L595V	ENST00000318789	NM_032682.5	595	Ctg/Gtg	20/21	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.238419191232644	NA		279	620	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259328	89259328	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	95	360	0	ENST00000336596.2:c.472G>T	p.Gly158Trp	p.G158W	ENST00000336596	NM_005233.5	158	Ggg/Tgg	3/17	0.238419191232644	3	FACETS	1	0.979	1	0.718	0.64	0.801	CLONAL	1	TRUE	1	0.238419191232644	3		360	621	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200062	128200062	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	64	385	0	ENST00000341105.2:c.1243G>T	p.Glu415Ter	p.E415*	ENST00000341105	NM_032638.4	415	Gag/Tag	6/6	0.238419191232644	3	FACETS	0.974	0.843	1	0.487	0.421	0.558	CLONAL	1	TRUE	1	0.238419191232644	3		385	617	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825398	134825398	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	71	367	0	ENST00000398015.3:c.914C>A	p.Thr305Asn	p.T305N	ENST00000398015	NM_004441.4	305	aCc/aAc	4/16	0.238419191232644	3	FACETS	1	0.968	1	0.679	0.594	0.77	CLONAL	1	TRUE	1	0.238419191232644	3		367	491	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281672	142281672	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1235951658	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	139	332	0	ENST00000350721.4:c.572C>T	p.Ser191Leu	p.S191L	ENST00000350721	NM_001184.3	191	tCa/tTa	4/47	0.238419191232644	3	FACETS	0.983	0.897	1	0.983	0.897	1	CLONAL	2	TRUE	1	0.238419191232644	3		332	664	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521515	187521515	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	59	153	0	ENST00000441802.2:c.11641-1G>A		p.X3881_splice	ENST00000441802	NM_005245.3	3881			1	2	FACETS	0.801	0.694	0.916	1	0.973	1	CLONAL	2	TRUE	1	0.238419191232644	2		153	309	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873648	35873648	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	117	307	0	ENST00000303115.3:c.604G>C	p.Glu202Gln	p.E202Q	ENST00000303115	NM_002185.3	202	Gag/Cag	5/8	0.238419191232644	6	FACETS	0.983	0.887	1	0.393	0.355	0.434	CLONAL	2	TRUE	1	0.238419191232644	6		307	737	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675622	86675622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	81	243	0	ENST00000274376.6:c.2558C>T	p.Ser853Leu	p.S853L	ENST00000274376	NM_002890.2	853	tCa/tTa	19/25	0.126326135976774	4	FACETS	1	0.968	1	0.648	0.571	0.731	INDETERMINATE	1	TRUE	2	0.238419191232644	4		243	649	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131930682	131930682	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	63	251	0	ENST00000265335.6:c.1915G>T	p.Glu639Ter	p.E639*	ENST00000265335		639	Gaa/Taa	12/25	0.126326135976774	4	FACETS	1	0.935	1	0.569	0.492	0.653	INDETERMINATE	1	TRUE	2	0.238419191232644	4		251	575	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974161	2974161	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	96	334	0	ENST00000396946.4:c.1444G>A	p.Glu482Lys	p.E482K	ENST00000396946	NM_032415.4	482	Gag/Aag	10/25	0.238419191232644	3	FACETS	0.884	0.79	0.982	0.884	0.79	0.982	CLONAL	2	TRUE	1	0.238419191232644	3		334	510	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729279	41729279	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	112	514	0	ENST00000242208.4:c.1250A>G	p.Asn417Ser	p.N417S	ENST00000242208	NM_002192.2	417	aAc/aGc	3/3	0.238419191232644	3	FACETS	1	0.98	1	0.692	0.622	0.765	CLONAL	1	TRUE	1	0.238419191232644	3		514	760	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729875	41729875	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	89	544	0	ENST00000242208.4:c.654G>T	p.Trp218Cys	p.W218C	ENST00000242208	NM_002192.2	218	tgG/tgT	3/3	0.238419191232644	3	FACETS	1	0.966	1	0.617	0.547	0.692	CLONAL	1	TRUE	1	0.238419191232644	3		544	677	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372752	81372752	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	132	298	0	ENST00000222390.5:c.782G>T	p.Arg261Leu	p.R261L	ENST00000222390	NM_000601.4	261	cGc/cTc	7/18	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	2	TRUE	NA	0.238419191232644	2		298	468	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508185	106508185	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	33	122	0	ENST00000359195.3:c.179A>G	p.His60Arg	p.H60R	ENST00000359195	NM_002649.2	60	cAc/cGc	2/11	0.238419191232644	5	FACETS	1	0.928	1			1	CLONAL	1	TRUE	NA	0.238419191232644	5		122	289	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418854	116418854	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180415202	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	135	239	0	ENST00000397752.3:c.3365C>T	p.Ser1122Phe	p.S1122F	ENST00000397752	NM_000245.2	1122	tCc/tTc	17/21	NA	2	FACETS	1	0.969	1			1	INDETERMINATE	2	TRUE	NA	0.238419191232644	2		239	502	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271704	38271704	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	65	339	3	ENST00000425967.3:c.2245C>A	p.Arg749Ser	p.R749S	ENST00000425967	NM_001174067.1	749	Cgc/Agc	17/19	0.238419191232644	3	FACETS	1	0.959	1	0.636	0.552	0.726	CLONAL	1	TRUE	1	0.238419191232644	3		342	480	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371618	55371618	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	49	235	0	ENST00000297316.4:c.308G>T	p.Gly103Val	p.G103V	ENST00000297316	NM_022454.3	103	gGc/gTc	2/2	0.238419191232644	3	FACETS	1	0.914	1	0.557	0.473	0.649	CLONAL	1	TRUE	1	0.238419191232644	3		235	413	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739030	145739030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199562131	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	100	222	0	ENST00000428558.2:c.2125C>T	p.Arg709Trp	p.R709W	ENST00000428558	NM_004260.3	709	Cgg/Tgg	13/22	0.238419191232644	10	FACETS	1	0.963	1			1	CLONAL	2	TRUE	NA	0.238419191232644	10		222	696	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376024	8376024	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	49	310	0	ENST00000356435.5:c.4573C>A	p.Pro1525Thr	p.P1525T	ENST00000356435		1525	Cca/Aca	28/35	0.218272671869625	0	FACETS	0.787	0.668	0.916			1	CLONAL	1	TRUE	0	0.238419191232644	0		310	398	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333293	70333293	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	97	350	0	ENST00000373644.4:c.1198G>C	p.Gly400Arg	p.G400R	ENST00000373644	NM_030625.2	400	Ggt/Cgt	2/12	0.238419191232644	3	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.238419191232644	3		350	652	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246242	46246242	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	300	297	0	ENST00000334344.6:c.4336G>C	p.Asp1446His	p.D1446H	ENST00000334344	NM_152641.2	1446	Gat/Cat	15/21	0.238419191232644	6	FACETS	0.942	0.892	0.993	0.785	0.743	0.828	CLONAL	5	TRUE	0	0.238419191232644	6		297	789	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69210637	69210637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	410	324	0	ENST00000462284.1:c.220G>A	p.Asp74Asn	p.D74N	ENST00000462284	NM_002392.5	74	Gat/Aat	4/11	0.238419191232644	7	FACETS	1	0.982	1			1	CLONAL	5	TRUE	NA	0.238419191232644	7		324	1042	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220449	133220449	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	199	247	0	ENST00000320574.5:c.4264G>C	p.Asp1422His	p.D1422H	ENST00000320574	NM_006231.2	1422	Gac/Cac	33/49	0.238419191232644	5	FACETS	0.957	0.892	1			1	CLONAL	4	TRUE	NA	0.238419191232644	5		247	592	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134724	41134724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1391222229	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	147	532	0	ENST00000379561.5:c.904C>T	p.His302Tyr	p.H302Y	ENST00000379561	NM_002015.3	302	Cac/Tac	2/3	0.219202519749041	2	FACETS	0.829	0.758	0.903	0.829	0.758	0.903	CLONAL	2	TRUE	0	0.238419191232644	2		532	744	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042428	42042428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	73	582	0	ENST00000219905.7:c.6623G>A	p.Cys2208Tyr	p.C2208Y	ENST00000219905	NM_001164273.1	2208	tGt/tAt	17/24	0.238419191232644	1	FACETS	0.694	0.606	0.789	0.694	0.606	0.789	SUBCLONAL	1	TRUE	0	0.238419191232644	1		582	777	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054540	42054540	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	131	424	0	ENST00000219905.7:c.7724G>C	p.Arg2575Thr	p.R2575T	ENST00000219905	NM_001164273.1	2575	aGa/aCa	22/24	0.238419191232644	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.238419191232644	1		424	793	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274153	10274153	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	21	243	0	ENST00000330684.3:c.116T>G	p.Met39Arg	p.M39R	ENST00000330684	NM_001134407.1	39	aTg/aGg	2/13	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.238419191232644	NA		243	265	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845577	72845577	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1199718521	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	73	534	0	ENST00000268489.5:c.3763C>T	p.Pro1255Ser	p.P1255S	ENST00000268489	NM_006885.3	1255	Ccc/Tcc	7/10	0.187918739752645	1	FACETS	0.79	0.69	0.897	0.79	0.69	0.897	SUBCLONAL	1	TRUE	0	0.238419191232644	1		534	683	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89806439	89806439	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs151241802	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	157	373	0	ENST00000389301.3:c.3897G>C	p.Lys1299Asn	p.K1299N	ENST00000389301	NM_000135.2	1299	aaG/aaC	39/43	0.126326135976774	4	FACETS	1	0.98	1	1	0.98	1	INDETERMINATE	2	TRUE	2	0.238419191232644	4		373	677	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682139	37682139	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	123	282	0	ENST00000447079.4:c.3330G>T	p.Gln1110His	p.Q1110H	ENST00000447079	NM_015083.1	1110	caG/caT	13/14	0.238419191232644	4	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	2	0.238419191232644	4		282	598	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41209094	41209094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs80357442	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	155	445	0	ENST00000357654.3:c.5252G>T	p.Arg1751Leu	p.R1751L	ENST00000357654	NM_007294.3	1751	cGa/cTa	19/23	0.188217260433541	3	FACETS	1	0.964	1			1	CLONAL	2	TRUE	NA	0.238419191232644	3		445	668	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678098	58678098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	113	348	0	ENST00000305921.3:c.323G>A	p.Gly108Asp	p.G108D	ENST00000305921	NM_003620.3	108	gGc/gAc	1/6	NA	2	FACETS	0.821	0.741	0.906			1	INDETERMINATE	2	TRUE	NA	0.238419191232644	2		348	577	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223068	1223068	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	157	356	0	ENST00000326873.7:c.1005G>T	p.Met335Ile	p.M335I	ENST00000326873	NM_000455.4	335	atG/atT	8/10	0.211410397441768	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.238419191232644	2		356	606	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794048	42794048	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	125	286	0	ENST00000575354.2:c.1409G>T	p.Arg470Leu	p.R470L	ENST00000575354	NM_015125.3	470	cGg/cTg	9/20	0.219202519749041	2	FACETS	0.943	0.857	1	0.943	0.857	1	CLONAL	2	TRUE	0	0.238419191232644	2		286	556	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523321	9523321	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	93	354	0	ENST00000353224.5:c.1916G>T	p.Gly639Val	p.G639V	ENST00000353224	NM_177990.2	639	gGc/gTc	9/10	NA	2	FACETS	0.819	0.732	0.912			1	INDETERMINATE	2	TRUE	NA	0.238419191232644	2		354	476	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408885	41408885	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	80	346	0	ENST00000373198.4:c.541G>T	p.Glu181Ter	p.E181*	ENST00000373198	NM_133170.3	181	Gag/Tag	4/32	0.188217260433541	3	FACETS	1	0.97	1			1	CLONAL	1	TRUE	NA	0.238419191232644	3		346	568	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164509	36164509	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	84	166	0	ENST00000300305.3:c.1366G>A	p.Glu456Lys	p.E456K	ENST00000300305		456	Gag/Aag	8/8	0.234754483482678	4	FACETS	0.851	0.758	0.948	1	0.971	1	CLONAL	3	TRUE	2	0.238419191232644	4		166	342	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077474	30077474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	108	243	0	ENST00000338641.4:c.1621G>A	p.Glu541Lys	p.E541K	ENST00000338641	NM_000268.3	541	Gaa/Aaa	15/16	0.238419191232644	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.238419191232644	3		243	422	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41525962	41525962	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	153	346	0	ENST00000263253.7:c.1237G>T	p.Val413Leu	p.V413L	ENST00000263253	NM_001429.3	413	Gtg/Ttg	5/31	0.238419191232644	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	1	0.238419191232644	3		346	690	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045518	47045518	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	96	179	0	ENST00000377604.3:c.2485G>T	p.Glu829Ter	p.E829*	ENST00000377604	NM_001204468.1	829	Gag/Tag	22/24	0.227750812131769	2	FACETS	0.994	0.899	1			1	CLONAL	3	TRUE	NA	0.238419191232644	2		179	270	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696179	52696179	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	150	484	0	ENST00000394830.3:c.498del	p.Gln167LysfsTer7	p.Q167Kfs*7	ENST00000394830	NM_018313.4	166	ggG/gg	5/30	0.238419191232644	3	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	1	0.238419191232644	3		484	680	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047811	128047812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	129	367	0	ENST00000285398.2:c.509dup	p.Leu170PhefsTer9	p.L170Ffs*9	ENST00000285398	NM_000122.1	170	ttg/ttTg	4/15	0.238419191232644	3	FACETS	0.878	0.797	0.962	0.878	0.797	0.962	CLONAL	2	TRUE	1	0.238419191232644	3		367	690	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412247	63412248	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	104	251	0	ENST00000330258.3:c.919dup	p.Asp307GlyfsTer17	p.D307Gfs*17	ENST00000330258	NM_152424.3	307	gac/gGac	2/2	1	1	FACETS	1	0.948	1	1	0.989	1	CLONAL	2	TRUE	0	0.238419191232644	1		251	358	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411279	63411280	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	89	240	0	ENST00000330258.3:c.1887_1888delinsTT	p.Gln629_Ala630delinsHisSer	p.Q629_A630delinsHS	ENST00000330258	NM_152424.3	629	caGGcc/caTTcc	2/2	1	1	FACETS	1	0.967	1	1	0.988	1	CLONAL	2	TRUE	0	0.238419191232644	1		240	277	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579338	7579340	+	frameshift_variant	Frame_Shift_Del	DEL	CAG	CAG	AA	novel	NA	P-0004189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	90	239	0	ENST00000269305.4:c.347_349delinsTT	p.Ser116PhefsTer7	p.S116Ffs*7	ENST00000269305	NM_001126112.2	116	tCTGgg/tTTgg	4/11	0.238419191232644	3	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	1	0.238419191232644	3		239	395	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0004196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	175	357	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	0.994	1	CLONAL	3	FALSE	1	0.265459296007038	2		357	431	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061463	38061463	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	417	172	0	ENST00000250448.2:c.526A>G	p.Ile176Val	p.I176V	ENST00000250448	NM_004496.3	176	Atc/Gtc	2/2	0.265459296007038	16	FACETS	0.995	0.958	1			1	CLONAL	13	FALSE	NA	0.265459296007038	16		172	694	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948100	178948100	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	22	220	0	ENST00000263967.3:c.2872C>A	p.Gln958Lys	p.Q958K	ENST00000263967	NM_006218.2	958	Cag/Aag	20/21	1	2	FACETS	0.385	0.297	0.486	0.385	0.297	0.486	SUBCLONAL	1	FALSE	1	0.265459296007038	2		220	431	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011152	12011152	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0004196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	180	247	0	ENST00000353533.5:c.559A>T	p.Lys187Ter	p.K187*	ENST00000353533	NM_003010.3	187	Aag/Tag	5/11	0.265459296007038	1	FACETS	0.888	0.835	0.941	1	0.995	1	CLONAL	4	FALSE	0	0.265459296007038	1		247	331	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004618	16004619	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	218	350	0	ENST00000268712.3:c.2635dup	p.Ser879PhefsTer8	p.S879Ffs*8	ENST00000268712	NM_006311.3	879	tcc/tTcc	20/46	0.265459296007038	1	FACETS	0.945	0.895	0.994	1	0.996	1	CLONAL	4	FALSE	0	0.265459296007038	1		350	377	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349241	70349242	+	missense_variant	Missense_Mutation	DNP	GA	GA	CT	novel	NA	P-0004196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	99	465	0	ENST00000374080.3:c.3653_3654delinsCT	p.Gly1218Ala	p.G1218A	ENST00000374080		1218	gGA/gCT	26/45	0.265459296007038	0	FACETS	0.941	0.852	1			1	CLONAL	2	FALSE	0	0.265459296007038	0		465	291	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0004260-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	140	409	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.84	2		409	306	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0004260-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	165	368	3	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.992	0.923	1	0.992	0.923	1	CLONAL	1	TRUE	1	0.84	2		371	396	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216477	108216477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587782558	NA	P-0004260-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	98	413	1	ENST00000278616.4:c.8432del	p.Lys2811SerfsTer46	p.K2811Sfs*46	ENST00000278616	NM_000051.3	2809	cAa/ca	58/63	1	2	FACETS	0.807	0.73	0.887	0.807	0.73	0.887	CLONAL	1	TRUE	1	0.84	2		414	289	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0004260-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	142	314	2	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.84	2		316	325	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878530	151878530	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1396109953	NA	P-0004260-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	71	96	0	ENST00000262189.6:c.6415C>T	p.Arg2139Ter	p.R2139*	ENST00000262189	NM_170606.2	2139	Cga/Tga	36/59	1	2	FACETS	0.821	0.729	0.915	0.821	0.729	0.915	CLONAL	1	TRUE	1	0.84	2		96	206	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0004260-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	203	191	2	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.871	0.814	0.929	0.871	0.814	0.929	CLONAL	1	TRUE	1	0.84	2		193	555	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047231	77047231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004260-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	189	291	0	ENST00000356341.3:c.1313G>A	p.Arg438Gln	p.R438Q	ENST00000356341	NM_002576.4	438	cGa/cAa	13/15	1	2	FACETS	0.936	0.873	0.999	0.936	0.873	0.999	CLONAL	1	TRUE	1	0.84	2		291	481	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141498	11141498	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004260-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	227	226	0	ENST00000358026.2:c.3480del	p.Leu1161SerfsTer3	p.L1161Sfs*3	ENST00000358026	NM_001128849.1	1159	Ggg/gg	25/36	1	2	FACETS	0.798	0.748	0.85	0.798	0.748	0.85	SUBCLONAL	1	TRUE	1	0.84	2		226	677	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900060	151900060	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004260-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	142	195	0	ENST00000262189.6:c.4051del	p.Arg1351GlyfsTer23	p.R1351Gfs*23	ENST00000262189	NM_170606.2	1351	Agg/gg	26/59	1	2	FACETS	0.95	0.877	1	0.95	0.877	1	CLONAL	1	TRUE	1	0.84	2		195	356	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447773	49447773	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004260-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	159	320	0	ENST00000301067.7:c.661del	p.Ala221LeufsTer40	p.A221Lfs*40	ENST00000301067	NM_003482.3	221	Gct/ct	5/54	1	2	FACETS	0.949	0.88	1	0.949	0.88	1	CLONAL	1	TRUE	1	0.84	2		320	399	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073668	8073668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768497001	NA	P-0004260-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	344	460	0	ENST00000377482.5:c.991C>T	p.Arg331Cys	p.R331C	ENST00000377482	NM_018948.3	331	Cgc/Tgc	4/4	1	2	FACETS	0.966	0.918	1	0.966	0.918	1	CLONAL	1	TRUE	1	0.84	2		460	848	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795060	45795060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374655042	NA	P-0004260-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	217	181	0	ENST00000450313.1:c.1568G>A	p.Arg523His	p.R523H	ENST00000450313	NM_012222.2	523	cGc/cAc	16/16	1	2	FACETS	0.973	0.913	1	0.973	0.913	1	CLONAL	1	TRUE	1	0.84	2		181	531	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705491	47705491	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587779143	NA	P-0004260-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	178	264	0	ENST00000233146.2:c.2291G>A	p.Trp764Ter	p.W764*	ENST00000233146	NM_000251.2	764	tGg/tAg	14/16	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.84	2		264	419	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149974	202149974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301592633	NA	P-0004260-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	165	167	0	ENST00000358485.4:c.1415G>A	p.Arg472Gln	p.R472Q	ENST00000358485	NM_001080125.1	472	cGa/cAa	8/9	1	2	FACETS	0.98	0.911	1	0.98	0.911	1	CLONAL	1	TRUE	1	0.84	2		167	401	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098913	47098913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004260-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	134	185	0	ENST00000409792.3:c.6361C>T	p.Arg2121Cys	p.R2121C	ENST00000409792	NM_014159.6	2121	Cgc/Tgc	15/21	1	2	FACETS	0.814	0.747	0.882	0.814	0.747	0.882	CLONAL	1	TRUE	1	0.84	2		185	392	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442569	52442569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1298276806	NA	P-0004260-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	165	145	0	ENST00000460680.1:c.176G>A	p.Arg59Gln	p.R59Q	ENST00000460680	NM_004656.3	59	cGg/cAg	4/17	1	2	FACETS	0.992	0.923	1	0.992	0.923	1	CLONAL	1	TRUE	1	0.84	2		145	396	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748225	41748225	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1462979811	NA	P-0004260-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	259	275	0	ENST00000226382.2:c.544G>T	p.Asp182Tyr	p.D182Y	ENST00000226382	NM_003924.3	182	Gac/Tac	3/3	1	2	FACETS	0.95	0.896	1	0.95	0.896	1	CLONAL	1	TRUE	1	0.84	2		275	649	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672318	86672318	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004260-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	122	138	0	ENST00000274376.6:c.2120G>A	p.Arg707His	p.R707H	ENST00000274376	NM_002890.2	707	cGt/cAt	16/25	1	2	FACETS	0.773	0.705	0.842	0.773	0.705	0.842	SUBCLONAL	1	TRUE	1	0.84	2		138	376	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430668	80430668	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004260-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	101	155	0	ENST00000286548.4:c.340C>T	p.Arg114Ter	p.R114*	ENST00000286548	NM_002072.3	114	Cga/Tga	3/7	1	2	FACETS	0.939	0.854	1	0.939	0.854	1	CLONAL	1	TRUE	1	0.84	2		155	256	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211491	98211491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747181820	NA	P-0004260-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	198	198	0	ENST00000331920.6:c.3664G>A	p.Asp1222Asn	p.D1222N	ENST00000331920	NM_000264.3	1222	Gac/Aac	22/24	1	2	FACETS	0.958	0.896	1	0.958	0.896	1	CLONAL	1	TRUE	1	0.84	2		198	492	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198442	108198442	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004260-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	139	167	0	ENST00000278616.4:c.7046G>T	p.Cys2349Phe	p.C2349F	ENST00000278616	NM_000051.3	2349	tGc/tTc	48/63	1	2	FACETS	0.991	0.915	1	0.991	0.915	1	CLONAL	1	TRUE	1	0.84	2		167	334	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435778	110435778	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746678031	NA	P-0004260-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	23	11	0	ENST00000375856.3:c.2623G>A	p.Gly875Ser	p.G875S	ENST00000375856	NM_003749.2	875	Ggc/Agc	1/2	0.162466152437652	3	FACETS	1	0.929	1	0.682	0.556	0.814	INDETERMINATE	1	TRUE	1	0.84	3		11	57	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654624	67654624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004260-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	179	245	0	ENST00000264010.4:c.1111C>T	p.Arg371Cys	p.R371C	ENST00000264010	NM_006565.3	371	Cgc/Tgc	6/12	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.84	2		245	412	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821602	72821602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777045104	NA	P-0004260-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	63	41	0	ENST00000268489.5:c.10573G>A	p.Gly3525Ser	p.G3525S	ENST00000268489	NM_006885.3	3525	Ggc/Agc	10/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.84	2		41	130	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351359	89351359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756332789	NA	P-0004260-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	372	400	0	ENST00000301030.4:c.1591G>A	p.Ala531Thr	p.A531T	ENST00000301030	NM_001256183.1	531	Gcc/Acc	9/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.84	2		400	859	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024417	16024417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771531803	NA	P-0004260-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	215	128	0	ENST00000268712.3:c.1801G>A	p.Ala601Thr	p.A601T	ENST00000268712	NM_006311.3	601	Gca/Aca	16/46	1	2	FACETS	0.983	0.922	1	0.983	0.922	1	CLONAL	1	TRUE	1	0.84	2		128	521	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366260	15366260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1463941396	NA	P-0004260-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	260	239	2	ENST00000263377.2:c.1895G>A	p.Arg632His	p.R632H	ENST00000263377	NM_058243.2	632	cGc/cAc	10/20	1	2	FACETS	0.857	0.807	0.908	0.857	0.807	0.908	CLONAL	1	TRUE	1	0.84	2		241	722	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46252809	46252809	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004260-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	163	403	0	ENST00000371998.3:c.238C>T	p.Arg80Cys	p.R80C	ENST00000371998		80	Cgt/Tgt	4/23	0.3	1	FACETS	0.494	0.457	0.531	0.494	0.457	0.531	INDETERMINATE	1	TRUE	0	0.84	1		403	456	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435199	49435199	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004260-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	69	64	0	ENST00000301067.7:c.6354del	p.Ala2119LeufsTer25	p.A2119Lfs*25	ENST00000301067	NM_003482.3	2118	ccC/cc	31/54	1	2	FACETS	0.888	0.79	0.99	0.888	0.79	0.99	CLONAL	1	TRUE	1	0.84	2		64	185	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115853	8115854	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0004260-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	301	287	0	ENST00000346208.3:c.1200_1201insAG	p.Ser402ProfsTer3	p.S402Pfs*3	ENST00000346208		400	atg/atGAg	6/6	0.3	3	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.84	3		287	764	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370236	40370236	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs761761205	NA	P-0004260-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	314	500	11	ENST00000293328.3:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000293328	NM_012448.3	368	Cag/ag	9/19	0.3	1	FACETS	0.871	0.835	0.906	0.871	0.835	0.906	INDETERMINATE	1	TRUE	0	0.84	1		511	498	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517955	176517955	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs774203148	NA	P-0004260-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	226	226	0	ENST00000292408.4:c.457del	p.Gln153SerfsTer58	p.Q153Sfs*58	ENST00000292408	NM_213647.1	151	caC/ca	5/18	1	2	FACETS	0.959	0.901	1	0.959	0.901	1	CLONAL	1	TRUE	1	0.84	2		226	561	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	93	464	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	NA	2	FACETS	0.926	0.87	0.978			1	INDETERMINATE	2	TRUE	NA	0.836558131720054	2		464	120	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428562	78428562	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	54	306	0	ENST00000370768.2:c.1237C>T	p.Gln413Ter	p.Q413*	ENST00000370768	NM_003902.3	413	Cag/Tag	14/20	0.262829737960203	4	FACETS	1	0.932	1	0.718	0.636	0.801	INDETERMINATE	2	TRUE	1	0.836558131720054	4		306	110	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617439	158617439	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	43	629	0	ENST00000263640.3:c.1217C>G	p.Ala406Gly	p.A406G	ENST00000263640	NM_001105.4	406	gCc/gGc	9/11	0.771340441675391	3	FACETS	0.959	0.818	1	0.32	0.272	0.37	CLONAL	1	TRUE	0	0.836558131720054	3		629	152	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138400851	138400851	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	55	408	0	ENST00000289153.2:c.2462G>C	p.Arg821Pro	p.R821P	ENST00000289153	NM_006219.2	821	cGc/cCc	17/22	0.801130675432856	4	FACETS	0.978	0.845	1	0.326	0.281	0.373	CLONAL	1	TRUE	1	0.836558131720054	4		408	247	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35860989	35860989	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	60	243	0	ENST00000303115.3:c.118T>C	p.Phe40Leu	p.F40L	ENST00000303115	NM_002185.3	40	Ttc/Ctc	2/8	0.394562095532327	3	FACETS	0.933	0.837	1	0.622	0.558	0.685	INDETERMINATE	2	TRUE	0	0.836558131720054	3		243	109	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545620	106545620	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	81	314	0	ENST00000359195.3:c.3097A>C	p.Met1033Leu	p.M1033L	ENST00000359195	NM_002649.2	1033	Atg/Ctg	11/11	0.735329292341033	3	FACETS	0.832	0.754	0.91	0.555	0.503	0.607	CLONAL	2	TRUE	0	0.836558131720054	3		314	165	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545640	106545640	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	57	316	1	ENST00000359195.3:c.3117G>T	p.Met1039Ile	p.M1039I	ENST00000359195	NM_002649.2	1039	atG/atT	11/11	0.735329292341033	3	FACETS	1	0.95	1	0.393	0.344	0.444	CLONAL	1	TRUE	0	0.836558131720054	3		317	164	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015003	37015003	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	58	214	0	ENST00000358127.4:c.401C>T	p.Ser134Phe	p.S134F	ENST00000358127	NM_001280556.1	134	tCc/tTc	3/10	0.801812154494703	2	FACETS	1	0.905	1	0.514	0.454	0.574	CLONAL	1	TRUE	0	0.836558131720054	2		214	135	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962545	100962545	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	48	497	0	ENST00000325455.5:c.1852A>T	p.Asn618Tyr	p.N618Y	ENST00000325455	NM_001202474.3	618	Aac/Tac	3/8	0.836558131720054	3	FACETS	0.693	0.591	0.802	0.346	0.295	0.401	SUBCLONAL	1	TRUE	1	0.836558131720054	3		497	235	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151863	108151863	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs377349886	NA	P-0004278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	28	213	0	ENST00000278616.4:c.3544G>C	p.Glu1182Gln	p.E1182Q	ENST00000278616	NM_000051.3	1182	Gag/Cag	24/63	0.836558131720054	3	FACETS	0.659	0.534	0.798	0.33	0.267	0.399	SUBCLONAL	1	TRUE	1	0.836558131720054	3		213	144	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373445	118373445	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	31	307	0	ENST00000534358.1:c.6838A>T	p.Asn2280Tyr	p.N2280Y	ENST00000534358	NM_005933.3	2280	Aac/Tac	27/36	NA	2	FACETS	0.788	0.656	0.929			1	INDETERMINATE	1	TRUE	NA	0.836558131720054	2		307	94	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907526	32907526	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0004278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	92	203	2	ENST00000380152.3:c.1909+2T>C		p.X637_splice	ENST00000380152		637			0.803626151985903	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.836558131720054	2		205	101	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684070	29684070	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	41	268	0	ENST00000356175.3:c.7768A>C	p.Thr2590Pro	p.T2590P	ENST00000356175	NM_000267.3	2590	Act/Cct	52/57	0.836558131720054	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.836558131720054	1		268	55	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210728	2210728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745700742	NA	P-0004278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	68	333	0	ENST00000398665.3:c.1225C>T	p.Arg409Cys	p.R409C	ENST00000398665	NM_032482.2	409	Cgc/Tgc	14/28	0.803626151985903	2	FACETS	0.973	0.867	1	0.487	0.433	0.541	CLONAL	1	TRUE	0	0.836558131720054	2		333	167	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121047	3121047	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	163	309	0	ENST00000078429.4:c.950A>G	p.Asn317Ser	p.N317S	ENST00000078429	NM_002067.2	317	aAc/aGc	7/7	0.803626151985903	2	FACETS	0.989	0.949	1	0.989	0.949	1	CLONAL	2	TRUE	0	0.836558131720054	2		309	197	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162735773	162735805	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACCCTTGTTTTATAACAGATGCTGCAATGTACA	ACCCTTGTTTTATAACAGATGCTGCAATGTACA	-	novel	NA	P-0004278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	29	332	0	ENST00000367921.3:c.1100-16_1116del		p.X367_splice	ENST00000367921	NM_006182.2	367		10/18	0.812693510868145	2	FACETS	0.722	0.595	0.859	0.361	0.297	0.43	SUBCLONAL	1	TRUE	0	0.836558131720054	2		332	96	SUCCESS
APC	324	MSKCC	GRCh37	5	112174969	112174970	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0004278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	26	216	0	ENST00000257430.4:c.3678_3679insCC	p.Arg1227ProfsTer39	p.R1227Pfs*39	ENST00000257430	NM_000038.5	1226	-/CC	16/16	0.756231375391907	1	FACETS	0.952	0.822	1	0.952	0.822	1	CLONAL	1	TRUE	0	0.836558131720054	1		216	38	SUCCESS
APC	324	MSKCC	GRCh37	5	112174949	112174960	+	inframe_deletion	In_Frame_Del	DEL	ACACCTTCATCT	ACACCTTCATCT	-	novel	NA	P-0004278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	23	215	0	ENST00000257430.4:c.3659_3670del	p.Thr1220_Ser1223del	p.T1220_S1223del	ENST00000257430	NM_000038.5	1220	ACACCTTCATCT/-	16/16	0.756231375391907	1	FACETS	0.914	0.778	1	0.914	0.778	1	CLONAL	1	TRUE	0	0.836558131720054	1		215	35	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0004314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	230	357	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.614176868867616	4	FACETS	0.973	0.913	1	0.973	0.913	1	CLONAL	2	TRUE	2	0.614176868867616	4		357	621	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	119	301	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.614176868867616	5	FACETS	1	0.966	1	0.384	0.347	0.422	CLONAL	1	TRUE	2	0.614176868867616	5		301	647	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112641	115112641	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0004314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	165	238	0	ENST00000257566.3:c.1100-1G>A		p.X367_splice	ENST00000257566	NM_016569.3	367			0.614176868867616	5	FACETS	1	0.975	1	0.743	0.689	0.799	CLONAL	2	TRUE	2	0.614176868867616	5		238	463	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434825	99434825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398752572	NA	P-0004314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	76	170	0	ENST00000268035.6:c.912G>A	p.Met304Ile	p.M304I	ENST00000268035	NM_000875.3	304	atG/atA	3/21	0.614176868867616	3	FACETS	1	0.913	1	0.518	0.459	0.581	CLONAL	1	TRUE	1	0.614176868867616	3		170	312	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112449	115112450	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	237	203	0	ENST00000257566.3:c.1290dup	p.Ala431SerfsTer8	p.A431Sfs*8	ENST00000257566	NM_016569.3	430	-/A	7/8	0.614176868867616	5	FACETS	1	0.962	1	1	0.962	1	CLONAL	3	TRUE	2	0.614176868867616	5		203	483	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248589	59248590	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCAC	novel	NA	P-0004314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	144	378	0	ENST00000371222.2:c.153_154insGTGGG	p.His52ValfsTer30	p.H52Vfs*30	ENST00000371222	NM_002228.3	51	-/GTGGG	1/1	0.614176868867616	3	FACETS	1	0.96	1	0.54	0.495	0.588	CLONAL	1	TRUE	1	0.614176868867616	3		378	567	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750460	57750461	+	stop_gained	Nonsense_Mutation	DNP	TT	TT	AA	novel	NA	P-0004314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	230	462	0	ENST00000274289.3:c.2007_2008inv	p.Leu669_Lys670delinsPheTer	p.L669_K670delinsF*	ENST00000274289	NM_006622.3	669	ttAAaa/ttTTaa	14/14	0.614176868867616	7	FACETS	0.834	0.776	0.893	0.417	0.388	0.447	CLONAL	2	TRUE	3	0.614176868867616	7		462	1139	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160762	56160762	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0004316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	41	342	0	ENST00000399503.3:c.1035+1G>T		p.X345_splice	ENST00000399503	NM_005921.1	345			0.359623722039779	5	FACETS	1	0.892	1	1	0.892	1	CLONAL	3	TRUE	2	0.558880513321804	5		342	87	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549094	87549094	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	12	398	0	ENST00000277120.3:c.1651C>T	p.Arg551Ter	p.R551*	ENST00000277120		551	Cga/Tga	15/19	1	2	FACETS	0.558	0.398	0.747	0.558	0.398	0.747	SUBCLONAL	1	TRUE	1	0.558880513321804	2		398	77	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692791	89692791	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	30	473	0	ENST00000371953.3:c.275A>T	p.Asp92Val	p.D92V	ENST00000371953	NM_000314.4	92	gAc/gTc	5/9	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.558880513321804	2		473	87	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118706	115118706	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	27	400	0	ENST00000257566.3:c.635A>T	p.Asn212Ile	p.N212I	ENST00000257566	NM_016569.3	212	aAc/aTc	2/8	0.340929036360258	4	FACETS	1	0.94	1	0.738	0.601	0.888	CLONAL	1	TRUE	2	0.558880513321804	4		400	102	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164867	36164868	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	47	224	0	ENST00000300305.3:c.1007dup	p.Ala338ArgfsTer262	p.A338Rfs*262	ENST00000300305		336	ttc/ttTc	8/8	0.396376603018471	3	FACETS	1	0.89	1	0.525	0.448	0.607	CLONAL	1	TRUE	1	0.558880513321804	3		224	205	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170864	56170865	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	21	311	0	ENST00000399503.3:c.1694dup	p.Met566AsnfsTer10	p.M566Nfs*10	ENST00000399503	NM_005921.1	564	-/G	10/20	0.359623722039779	5	FACETS	0.987	0.768	1	0.329	0.256	0.412	CLONAL	1	TRUE	2	0.558880513321804	5		311	140	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881001	37881002	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGCTCCCC	rs397516981	NA	P-0004359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	789	673	0	ENST00000269571.5:c.2331_2339dup	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	gtg/gtGGGCTCCCCg	20/27	0.572560777244244	3	FACETS	1	0.997	1	0.815	0.792	0.838	CLONAL	2	TRUE	0	0.590656791708885	3		673	1415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0004359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	435	112	0	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	0.576590041763193	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.590656791708885	2		112	719	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40498697	40498697	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	381	364	0	ENST00000264657.5:c.163T>G	p.Leu55Val	p.L55V	ENST00000264657	NM_139276.2	55	Ttg/Gtg	3/24	0.590656791708885	2	FACETS	0.865	0.82	0.911	0.433	0.41	0.456	CLONAL	1	TRUE	0	0.590656791708885	2		364	1491	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546984	9546985	+	missense_variant	Missense_Mutation	DNP	CC	CC	GA	novel	NA	P-0004359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	18	93	0	ENST00000353224.5:c.1037_1038delinsTC	p.Gly346Val	p.G346V	ENST00000353224	NM_177990.2	346	gGG/gTC	5/10	NA	2	FACETS	0.173	0.129	0.224			1	INDETERMINATE	1	TRUE	NA	0.590656791708885	2		93	353	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	99	588	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.3	4	FACETS	0.828	0.747	0.912			1	INDETERMINATE	2	TRUE	NA	0.56	4		589	333	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	101	831	11	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.3	1	FACETS	1	0.927	1	1	0.927	1	INDETERMINATE	1	TRUE	0	0.56	1		842	254	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	45	368	3	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.744	0.632	0.865	0.744	0.632	0.865	SUBCLONAL	1	TRUE	1	0.56	2		371	216	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106648	27106648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553153748	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	84	325	0	ENST00000324856.7:c.6259G>A	p.Gly2087Arg	p.G2087R	ENST00000324856	NM_006015.4	2087	Gga/Aga	20/20	0.151590432245125	4	FACETS	0.983	0.883	1	0.983	0.883	1	INDETERMINATE	2	TRUE	2	0.56	4		325	238	SUCCESS
APC	324	MSKCC	GRCh37	5	112175675	112175676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	65	576	0	ENST00000257430.4:c.4393_4394dup	p.Ser1465ArgfsTer9	p.S1465Rfs*9	ENST00000257430	NM_000038.5	1462	aag/aAGag	16/16	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.56	2		576	227	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	71	285	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.56	2		285	218	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	47	542	2	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	0.151590432245125	4	FACETS	0.932	0.792	1	0.466	0.396	0.542	INDETERMINATE	1	TRUE	2	0.56	4		544	281	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509085	66509085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	26	378	1	ENST00000273854.3:c.242del	p.Asn81MetfsTer24	p.N81Mfs*24	ENST00000273854	NM_004439.5	81	aAt/at	2/18	0.248803685877996	0	FACETS	0.193	0.153	0.237			1	INDETERMINATE	1	TRUE	0	0.56	0		379	212	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838363	156838363	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200132482	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	45	288	0	ENST00000524377.1:c.641G>A	p.Arg214Gln	p.R214Q	ENST00000524377	NM_002529.3	214	cGg/cAg	6/17	0.3	1	FACETS	0.956	0.826	1	0.956	0.826	1	INDETERMINATE	1	TRUE	0	0.56	1		288	121	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574678	41574679	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs754418509	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	29	1105	3	ENST00000263253.7:c.6970dup	p.His2324ProfsTer55	p.H2324Pfs*55	ENST00000263253	NM_001429.3	2321	-/C	31/31	1	2	FACETS	0.458	0.37	0.558	0.458	0.37	0.558	SUBCLONAL	1	TRUE	1	0.56	2		1108	226	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	31	568	4	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	0.373269362942016	0	FACETS	0.443	0.366	0.525			1	SUBCLONAL	1	TRUE	0	0.56	0		572	110	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796744	42796744	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370377701	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	58	294	0	ENST00000575354.2:c.3202G>A	p.Gly1068Ser	p.G1068S	ENST00000575354	NM_015125.3	1068	Ggt/Agt	14/20	0.3	3	FACETS	0.808	0.709	0.911			1	INDETERMINATE	2	TRUE	NA	0.56	3		294	164	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741760	145741760	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759352592	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	95	373	1	ENST00000428558.2:c.743G>A	p.Arg248His	p.R248H	ENST00000428558	NM_004260.3	248	cGt/cAt	5/22	0.151590432245125	3	FACETS	0.928	0.842	1	0.928	0.842	1	INDETERMINATE	2	TRUE	1	0.56	3		374	234	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468158	50468158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	39	270	0	ENST00000331340.3:c.1393G>A	p.Glu465Lys	p.E465K	ENST00000331340	NM_006060.4	465	Gaa/Aaa	8/8	1	2	FACETS	0.882	0.742	1	0.882	0.742	1	CLONAL	1	TRUE	1	0.56	2		270	158	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785964	135785964	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs118203506	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	14	183	0	ENST00000298552.3:c.1257del	p.Arg420GlyfsTer20	p.R420Gfs*20	ENST00000298552	NM_001162426.1	419	ccC/cc	12/23	0.3	1	FACETS	0.343	0.25	0.452	0.343	0.25	0.452	INDETERMINATE	1	TRUE	0	0.56	1		183	105	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900984	114900984	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778855667	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	59	707	0	ENST00000543371.1:c.598del	p.Leu200SerfsTer25	p.L200Sfs*25	ENST00000543371	NM_001198531.1	198	caC/ca	6/14	0.3	1	FACETS	0.529	0.458	0.604	0.529	0.458	0.604	INDETERMINATE	1	TRUE	0	0.56	1		707	287	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61197631	61197631	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs775763888	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	49	438	0	ENST00000301761.2:c.13A>G	p.Thr5Ala	p.T5A	ENST00000301761	NM_017841.2	5	Aca/Gca	1/4	1	2	FACETS	0.587	0.5	0.682	0.587	0.5	0.682	SUBCLONAL	1	TRUE	1	0.56	2		438	298	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11264661	11264661	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	26	380	0	ENST00000361445.4:c.3901C>T	p.Arg1301Cys	p.R1301C	ENST00000361445	NM_004958.3	1301	Cgc/Tgc	26/58	0.3	0	FACETS	0.227	0.181	0.279			1	INDETERMINATE	1	TRUE	0	0.56	0		380	180	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11273503	11273503	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751901845	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	15	346	0	ENST00000361445.4:c.3238C>T	p.Arg1080Cys	p.R1080C	ENST00000361445	NM_004958.3	1080	Cgt/Tgt	21/58	0.3	0	FACETS	0.154	0.113	0.203			1	INDETERMINATE	1	TRUE	0	0.56	0		346	153	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319406	11319406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149221273	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	59	374	0	ENST00000361445.4:c.61G>A	p.Val21Ile	p.V21I	ENST00000361445	NM_004958.3	21	Gtc/Atc	2/58	0.3	0	FACETS	0.504	0.441	0.569			1	INDETERMINATE	1	TRUE	0	0.56	0		374	184	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255472	16255472	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	28	287	0	ENST00000375759.3:c.2737C>A	p.Leu913Met	p.L913M	ENST00000375759	NM_015001.2	913	Ctg/Atg	11/15	0.151590432245125	4	FACETS	0.687	0.552	0.839	0.344	0.276	0.42	INDETERMINATE	1	TRUE	2	0.56	4		287	227	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17371344	17371344	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202119350	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	39	348	1	ENST00000375499.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000375499	NM_003000.2	38	Cgt/Tgt	2/8	0.151590432245125	4	FACETS	0.845	0.705	1	0.423	0.352	0.5	INDETERMINATE	1	TRUE	2	0.56	4		349	257	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059227	27059227	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	54	405	0	ENST00000324856.7:c.1864A>G	p.Lys622Glu	p.K622E	ENST00000324856	NM_006015.4	622	Aag/Gag	4/20	0.151590432245125	4	FACETS	0.967	0.831	1	0.484	0.415	0.557	INDETERMINATE	1	TRUE	2	0.56	4		405	311	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841541	156841541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774654606	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	43	242	2	ENST00000524377.1:c.844G>A	p.Val282Ile	p.V282I	ENST00000524377	NM_002529.3	282	Gtc/Atc	7/17	0.3	1	FACETS	0.747	0.637	0.864	0.747	0.637	0.864	INDETERMINATE	1	TRUE	0	0.56	1		244	148	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015258	128015258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115312738	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	35	338	0	ENST00000285398.2:c.2263G>A	p.Asp755Asn	p.D755N	ENST00000285398	NM_000122.1	755	Gac/Aac	15/15	1	2	FACETS	0.899	0.75	1	0.899	0.75	1	CLONAL	1	TRUE	1	0.56	2		338	139	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158626970	158626970	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1198616498	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	78	567	1	ENST00000263640.3:c.700G>A	p.Val234Met	p.V234M	ENST00000263640	NM_001105.4	234	Gtg/Atg	7/11	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.56	2		568	249	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662401	227662401	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	28	168	0	ENST00000305123.5:c.1054A>G	p.Asn352Asp	p.N352D	ENST00000305123	NM_005544.2	352	Aac/Gac	1/2	1	2	FACETS	0.478	0.385	0.584	0.478	0.385	0.584	SUBCLONAL	1	TRUE	1	0.56	2		168	209	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713802	30713802	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	108	238	0	ENST00000295754.5:c.1127T>C	p.Val376Ala	p.V376A	ENST00000295754	NM_003242.5	376	gTg/gCg	4/7	0.3	3	FACETS	0.848	0.773	0.926			1	INDETERMINATE	2	TRUE	NA	0.56	3		238	291	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715613	30715613	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs878854610	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	113	212	0	ENST00000295754.5:c.1271A>G	p.Tyr424Cys	p.Y424C	ENST00000295754	NM_003242.5	424	tAc/tGc	5/7	0.3	3	FACETS	0.776	0.706	0.847			1	INDETERMINATE	2	TRUE	NA	0.56	3		212	333	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924781	49924781	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372825999	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	82	556	1	ENST00000296474.3:c.4162C>T	p.Arg1388Cys	p.R1388C	ENST00000296474	NM_002447.2	1388	Cgc/Tgc	20/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.56	2		557	211	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933744	49933744	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs750582514	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	69	524	0	ENST00000296474.3:c.2533C>T	p.Arg845Ter	p.R845*	ENST00000296474	NM_002447.2	845	Cga/Tga	10/20	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.56	2		524	230	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178078	142178078	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	17	222	0	ENST00000350721.4:c.7340C>A	p.Pro2447His	p.P2447H	ENST00000350721	NM_001184.3	2447	cCt/cAt	43/47	1	2	FACETS	0.244	0.182	0.317	0.244	0.182	0.317	SUBCLONAL	1	TRUE	1	0.56	2		222	249	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588981	67588981	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	56	229	0	ENST00000274335.5:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000274335		358	Cga/Tga	8/15	0.3	5	FACETS	1	0.922	1			1	INDETERMINATE	1	TRUE	NA	0.56	5		229	333	SUCCESS
APC	324	MSKCC	GRCh37	5	112177968	112177968	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1246580689	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	71	371	0	ENST00000257430.4:c.6677G>A	p.Arg2226Gln	p.R2226Q	ENST00000257430	NM_000038.5	2226	cGa/cAa	16/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.56	2		371	200	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047905	180047905	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	18	293	0	ENST00000261937.6:c.2270T>C	p.Val757Ala	p.V757A	ENST00000261937	NM_182925.4	757	gTc/gCc	15/30	0.3	0	FACETS	0.267	0.204	0.339			1	INDETERMINATE	1	TRUE	0	0.56	0		293	106	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225530	26225530	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	118	876	0	ENST00000360408.1:c.148C>T	p.Arg50Cys	p.R50C	ENST00000360408	NM_003532.2	50	Cgc/Tgc	1/1	0.297641976259369	5	FACETS	1	0.957	1	0.369	0.333	0.407	INDETERMINATE	1	TRUE	2	0.56	5		876	700	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536224	106536224	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	81	262	0	ENST00000369096.4:c.191A>G	p.Asp64Gly	p.D64G	ENST00000369096	NM_001198.3	64	gAc/gGc	2/7	0.3	4	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.56	4		262	333	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220390	98220390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	52	266	0	ENST00000331920.6:c.3073C>T	p.Arg1025Cys	p.R1025C	ENST00000331920	NM_000264.3	1025	Cgc/Tgc	18/24	0.151590432245125	3	FACETS	0.772	0.671	0.877	0.772	0.671	0.877	INDETERMINATE	2	TRUE	1	0.56	3		266	154	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251976	8251976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371807297	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	29	360	0	ENST00000335790.3:c.101G>A	p.Arg34His	p.R34H	ENST00000335790	NM_002315.2	34	cGc/cAc	2/4	1	2	FACETS	0.632	0.512	0.764	0.632	0.512	0.764	SUBCLONAL	1	TRUE	1	0.56	2		360	164	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588192	69588192	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	16	525	0	ENST00000168712.1:c.506A>G	p.Tyr169Cys	p.Y169C	ENST00000168712	NM_002007.2	169	tAc/tGc	3/3	1	2	FACETS	0.433	0.323	0.562	0.433	0.323	0.562	SUBCLONAL	1	TRUE	1	0.56	2		525	132	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920750	100920750	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	28	542	0	ENST00000325455.5:c.2398A>G	p.Thr800Ala	p.T800A	ENST00000325455	NM_001202474.3	800	Acc/Gcc	6/8	0.3	0	FACETS	0.203	0.163	0.248			1	INDETERMINATE	1	TRUE	0	0.56	0		542	217	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920785	100920785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371165895	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	51	463	0	ENST00000325455.5:c.2363G>A	p.Arg788Gln	p.R788Q	ENST00000325455	NM_001202474.3	788	cGg/cAg	6/8	0.3	0	FACETS	0.352	0.302	0.405			1	INDETERMINATE	1	TRUE	0	0.56	0		463	228	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385261	4385261	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	55	364	0	ENST00000261254.3:c.286T>A	p.Ser96Thr	p.S96T	ENST00000261254	NM_001759.3	96	Tcc/Acc	2/5	0.297641976259369	3	FACETS	0.731	0.628	0.842	0.365	0.314	0.421	INDETERMINATE	1	TRUE	1	0.56	3		364	344	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828032	3828032	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	42	329	0	ENST00000262367.5:c.2093C>T	p.Ala698Val	p.A698V	ENST00000262367	NM_004380.2	698	gCa/gTa	10/31	1	2	FACETS	0.701	0.591	0.82	0.701	0.591	0.82	SUBCLONAL	1	TRUE	1	0.56	2		329	214	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831284	3831284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	74	235	0	ENST00000262367.5:c.1597G>A	p.Ala533Thr	p.A533T	ENST00000262367	NM_004380.2	533	Gca/Aca	7/31	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.56	2		235	208	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934239	81934239	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	47	384	0	ENST00000359376.3:c.1216G>A	p.Glu406Lys	p.E406K	ENST00000359376	NM_002661.3	406	Gag/Aag	14/33	0.373269362942016	0	FACETS	0.395	0.338	0.456			1	SUBCLONAL	1	TRUE	0	0.56	0		384	187	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81941311	81941311	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	22	365	0	ENST00000359376.3:c.1489G>A	p.Ala497Thr	p.A497T	ENST00000359376	NM_002661.3	497	Gcc/Acc	16/33	0.373269362942016	0	FACETS	0.21	0.163	0.262			1	SUBCLONAL	1	TRUE	0	0.56	0		365	165	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646849	37646849	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	40	434	0	ENST00000447079.4:c.1971G>C	p.Glu657Asp	p.E657D	ENST00000447079	NM_015083.1	657	gaG/gaC	3/14	0.3	2	FACETS	0.547	0.458	0.646			1	INDETERMINATE	1	TRUE	NA	0.56	2		434	261	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682393	37682393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61741615	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	66	350	2	ENST00000447079.4:c.3584C>T	p.Thr1195Met	p.T1195M	ENST00000447079	NM_015083.1	1195	aCg/aTg	13/14	0.3	2	FACETS	1	0.949	1			1	INDETERMINATE	1	TRUE	NA	0.56	2		352	206	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63537616	63537616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	55	457	2	ENST00000307078.5:c.1016G>A	p.Arg339His	p.R339H	ENST00000307078	NM_004655.3	339	cGc/cAc	4/11	0.297641976259369	4	FACETS	0.926	0.796	1	0.463	0.398	0.533	INDETERMINATE	1	TRUE	2	0.56	4		459	331	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210735	2210735	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1238067958	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	36	394	0	ENST00000398665.3:c.1232G>A	p.Arg411His	p.R411H	ENST00000398665	NM_032482.2	411	cGc/cAc	14/28	0.3	1	FACETS	0.439	0.364	0.521	0.439	0.364	0.521	INDETERMINATE	1	TRUE	0	0.56	1		394	211	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222475	2222475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200919682	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	10	162	0	ENST00000398665.3:c.3307G>A	p.Val1103Met	p.V1103M	ENST00000398665	NM_032482.2	1103	Gtg/Atg	24/28	0.3	2	FACETS	0.226	0.153	0.317			1	INDETERMINATE	1	TRUE	NA	0.56	2		162	158	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243960	5243960	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1260947679	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	16	278	0	ENST00000357368.4:c.1522G>A	p.Gly508Ser	p.G508S	ENST00000357368	NM_002850.3	508	Ggc/Agc	11/38	0.3	0	FACETS	0.283	0.212	0.363			1	INDETERMINATE	1	TRUE	0	0.56	0		278	89	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7126648	7126648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866193541	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	46	258	0	ENST00000302850.5:c.2960C>T	p.Pro987Leu	p.P987L	ENST00000302850	NM_000208.2	987	cCg/cTg	16/22	0.3	0	FACETS	0.458	0.392	0.527			1	INDETERMINATE	1	TRUE	0	0.56	0		258	158	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142851	7142851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139912396	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	15	226	0	ENST00000302850.5:c.2518G>A	p.Val840Ile	p.V840I	ENST00000302850	NM_000208.2	840	Gtc/Atc	12/22	1	2	FACETS	0.267	0.195	0.352	0.267	0.195	0.352	SUBCLONAL	1	TRUE	1	0.56	2		226	201	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141534	11141534	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	21	424	0	ENST00000358026.2:c.3511G>A	p.Val1171Met	p.V1171M	ENST00000358026	NM_001128849.1	1171	Gtg/Atg	25/36	1	2	FACETS	0.342	0.264	0.433	0.342	0.264	0.433	SUBCLONAL	1	TRUE	1	0.56	2		424	219	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144017	11144017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	41	374	0	ENST00000358026.2:c.3598C>T	p.Arg1200Cys	p.R1200C	ENST00000358026	NM_001128849.1	1200	Cgt/Tgt	26/36	1	2	FACETS	0.729	0.613	0.853	0.729	0.613	0.853	SUBCLONAL	1	TRUE	1	0.56	2		374	201	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905873	50905873	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756829126	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	34	472	2	ENST00000440232.2:c.845C>T	p.Thr282Met	p.T282M	ENST00000440232	NM_002691.3	282	aCg/aTg	8/27	0.3	0	FACETS	0.408	0.339	0.482			1	INDETERMINATE	1	TRUE	0	0.56	0		474	131	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912125	50912125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1309243644	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	59	566	1	ENST00000440232.2:c.1859C>T	p.Thr620Met	p.T620M	ENST00000440232	NM_002691.3	620	aCg/aTg	15/27	0.3	0	FACETS	0.565	0.497	0.636			1	INDETERMINATE	1	TRUE	0	0.56	0		567	164	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428277	47428277	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	13	197	0	ENST00000377045.4:c.1237A>C	p.Thr413Pro	p.T413P	ENST00000377045	NM_001654.4	413	Act/Cct	11/16	1	1	FACETS	0.288	0.207	0.385	0.288	0.207	0.385	SUBCLONAL	1	TRUE	0	0.56	1		197	116	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	65	402	2	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	0.151590432245125	0	FACETS	0.402	0.352	0.455			1	INDETERMINATE	1	TRUE	0	0.56	0		404	254	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859859	151859859	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	10	244	0	ENST00000262189.6:c.10803del	p.Lys3604ArgfsTer26	p.K3604Rfs*26	ENST00000262189	NM_170606.2	3601	aaA/aa	43/59	1	2	FACETS	0.196	0.133	0.276	0.196	0.133	0.276	SUBCLONAL	1	TRUE	1	0.56	2		244	182	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129338	152129338	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1361952517	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	14	344	2	ENST00000206249.3:c.296del	p.Pro99HisfsTer10	p.P99Hfs*10	ENST00000206249	NM_000125.3	97	ttC/tt	1/8	0.151590432245125	3	FACETS	0.474	0.345	0.628	0.237	0.172	0.314	INDETERMINATE	1	TRUE	1	0.56	3		346	135	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19261529	19261529	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	52	428	0	ENST00000162023.5:c.16del	p.Ile6SerfsTer14	p.I6Sfs*14	ENST00000162023		6	Atc/tc	6/13	0.3	3	FACETS	1	0.944	1			1	INDETERMINATE	1	TRUE	NA	0.56	3		428	200	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987193	69987193	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	17	236	0	ENST00000394351.3:c.258del	p.Glu87ArgfsTer19	p.E87Rfs*19	ENST00000394351	NM_000248.3	85	gAa/ga	2/9	1	2	FACETS	0.446	0.336	0.575	0.446	0.336	0.575	SUBCLONAL	1	TRUE	1	0.56	2		236	136	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030307	180030308	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs772530628	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	14	464	0	ENST00000261937.6:c.3976dup	p.Ala1326GlyfsTer118	p.A1326Gfs*118	ENST00000261937	NM_182925.4	1326	gcc/gGcc	30/30	1	2	FACETS	0.325	0.236	0.431	0.325	0.236	0.431	SUBCLONAL	1	TRUE	1	0.56	2		464	154	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	46	253	0	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	0.3	0	FACETS	0.794	0.697	0.891			1	INDETERMINATE	1	TRUE	0	0.56	0		253	91	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660534	190660534	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	93	186	0	ENST00000441310.2:c.175del	p.Glu59ArgfsTer10	p.E59Rfs*10	ENST00000441310	NM_000534.4	58	Ggg/gg	3/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.56	2		186	266	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401034	139401034	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	28	355	0	ENST00000277541.6:c.3959del	p.Gly1320AlafsTer125	p.G1320Afs*125	ENST00000277541	NM_017617.3	1320	gGc/gc	24/34	0.151590432245125	3	FACETS	0.631	0.507	0.769	0.315	0.253	0.385	INDETERMINATE	1	TRUE	1	0.56	3		355	203	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257365	19257366	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	21	240	0	ENST00000162023.5:c.767dup	p.Glu257ArgfsTer28	p.E257Rfs*28	ENST00000162023		256	cca/ccCa	11/13	0.3	3	FACETS	0.828	0.647	1			1	INDETERMINATE	1	TRUE	NA	0.56	3		240	116	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0004367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	227	357	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	0.82	2		357	522	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0004367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	117	66	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.981	0.898	1	0.981	0.898	1	CLONAL	1	TRUE	1	0.82	2		66	291	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0004367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	133	134	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.924	0.85	1	0.924	0.85	1	CLONAL	1	TRUE	1	0.82	2		134	351	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057230	180057230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780661773	NA	P-0004367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	26	217	0	ENST00000261937.6:c.508C>T	p.Arg170Cys	p.R170C	ENST00000261937	NM_182925.4	170	Cgc/Tgc	4/30	1	2	FACETS	0.127	0.1	0.158	0.127	0.1	0.158	SUBCLONAL	1	TRUE	1	0.82	2		217	501	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929487	44929487	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	522	528	0	ENST00000377967.4:c.2587C>T	p.Gln863Ter	p.Q863*	ENST00000377967	NM_021140.2	863	Cag/Tag	17/29	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.82	2		528	1162	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432379	78432379	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	85	300	0	ENST00000370768.2:c.472C>T	p.Gln158Ter	p.Q158*	ENST00000370768	NM_003902.3	158	Cag/Tag	7/20	1	2	FACETS	0.323	0.286	0.364	0.323	0.286	0.364	SUBCLONAL	1	TRUE	1	0.82	2		300	641	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913250	NA	P-0004367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	417	339	0	ENST00000369535.4:c.34G>T	p.Gly12Cys	p.G12C	ENST00000369535	NM_002524.4	12	Ggt/Tgt	2/7	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.82	2		339	959	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426021	138426021	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	296	336	0	ENST00000289153.2:c.1510T>A	p.Tyr504Asn	p.Y504N	ENST00000289153	NM_006219.2	504	Tat/Aat	9/22	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.82	2		336	655	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882341	89882341	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	442	474	0	ENST00000389301.3:c.133G>C	p.Glu45Gln	p.E45Q	ENST00000389301	NM_000135.2	45	Gaa/Caa	2/43	0.3	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.82	2		474	953	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123199797	123199798	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0004367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	261	359	0	ENST00000218089.9:c.2096+2dup		p.X699_splice	ENST00000218089	NM_001042749.1	699			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.82	2		359	610	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937712	44937713	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	280	404	0	ENST00000377967.4:c.2900_2901insG	p.Thr968TyrfsTer11	p.T968Yfs*11	ENST00000377967	NM_021140.2	967	gtt/gtGt	19/29	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.82	2		404	619	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0004380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	10	498	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.359	0.243	0.503	0.359	0.243	0.503	SUBCLONAL	1	TRUE	1	0.34	2		498	164	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0004380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	9	309	2	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.280038487776152	3	FACETS	0.442	0.294	0.631	0.221	0.147	0.316	SUBCLONAL	1	TRUE	1	0.34	3		311	140	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0004380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	5	314	2	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	0.241922436309316	0	FACETS	0.353	0.202	0.557			1	SUBCLONAL	1	TRUE	0	0.34	0		316	55	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0004380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	17	47	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	0.3	3	FACETS	0.836	0.64	1			1	CLONAL	2	TRUE	NA	0.34	3		47	70	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	14	341	0	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	0.3	3	FACETS	0.484	0.35	0.645			1	SUBCLONAL	1	TRUE	NA	0.34	3		341	199	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444659	78444659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs908264837	NA	P-0004380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	71	239	0	ENST00000370768.2:c.30del	p.Ser11LeufsTer43	p.S11Lfs*43	ENST00000370768	NM_003902.3	10	ccC/cc	1/20	0.165825968067872	4	FACETS	1	0.971	1	0.701	0.615	0.794	INDETERMINATE	1	TRUE	2	0.34	4		239	399	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0004380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	11	191	2	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	0.241922436309316	4	FACETS	0.552	0.382	0.762	0.276	0.191	0.381	SUBCLONAL	1	TRUE	2	0.34	4		193	157	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021817	71021817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs797045586	NA	P-0004380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	11	313	1	ENST00000318789.4:c.1541G>A	p.Arg514His	p.R514H	ENST00000318789	NM_032682.5	514	cGt/cAt	18/21	0.241922436309316	4	FACETS	0.411	0.284	0.569	0.205	0.142	0.285	SUBCLONAL	1	TRUE	2	0.34	4		314	211	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	14	298	0	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.58	0.422	0.769	0.58	0.422	0.769	SUBCLONAL	1	TRUE	1	0.34	2		298	142	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790455	3790455	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783490	NA	P-0004380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	14	415	0	ENST00000262367.5:c.4078C>T	p.Arg1360Ter	p.R1360*	ENST00000262367	NM_004380.2	1360	Cga/Tga	24/31	0.3	0	FACETS	0.412	0.3	0.545			1	SUBCLONAL	1	TRUE	0	0.34	0		415	132	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273111	198273111	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1239271340	NA	P-0004380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	15	336	0	ENST00000335508.6:c.1099A>G	p.Met367Val	p.M367V	ENST00000335508	NM_012433.2	367	Atg/Gtg	8/25	1	2	FACETS	0.464	0.34	0.612	0.464	0.34	0.612	SUBCLONAL	1	TRUE	1	0.34	2		336	190	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104713	209104713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	32	289	0	ENST00000345146.2:c.865G>A	p.Gly289Ser	p.G289S	ENST00000345146	NM_005896.2	289	Ggc/Agc	8/10	1	2	FACETS	0.833	0.681	1	0.833	0.681	1	CLONAL	1	TRUE	1	0.34	2		289	226	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439208	52439208	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	19	302	0	ENST00000460680.1:c.1034G>T	p.Gly345Val	p.G345V	ENST00000460680	NM_004656.3	345	gGg/gTg	11/17	0.241922436309316	4	FACETS	0.749	0.571	0.956	0.374	0.285	0.478	CLONAL	1	TRUE	2	0.34	4		302	200	SUCCESS
ATR	545	MSKCC	GRCh37	3	142168290	142168290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	24	272	0	ENST00000350721.4:c.7916G>A	p.Gly2639Asp	p.G2639D	ENST00000350721	NM_001184.3	2639	gGt/gAt	47/47	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.34	NA		272	334	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251555	251555	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763766162	NA	P-0004380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	21	285	0	ENST00000264932.6:c.1766G>A	p.Arg589Gln	p.R589Q	ENST00000264932	NM_004168.2	589	cGg/cAg	13/15	0.3	2	FACETS	0.98	0.765	1			1	CLONAL	1	TRUE	NA	0.34	2		285	126	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679546	86679546	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554050230	NA	P-0004380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	49	312	0	ENST00000274376.6:c.2707C>T	p.Arg903Ter	p.R903*	ENST00000274376	NM_002890.2	903	Cga/Tga	21/25	0.3	7	FACETS	1	0.945	1			1	CLONAL	1	TRUE	NA	0.34	7		312	422	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40486032	40486032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	20	533	0	ENST00000264657.5:c.833G>A	p.Arg278His	p.R278H	ENST00000264657	NM_139276.2	278	cGt/cAt	9/24	0.3	5	FACETS	0.521	0.398	0.665			1	SUBCLONAL	1	TRUE	NA	0.34	5		533	341	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732469	74732469	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	57	488	0	ENST00000359995.5:c.440C>G	p.Ser147Trp	p.S147W	ENST00000359995	NM_001195427.1	147	tCg/tGg	2/3	0.3	14	FACETS	1	0.871	1			1	CLONAL	2	TRUE	NA	0.34	14		488	502	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44921908	44921908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778421870	NA	P-0004380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	27	480	0	ENST00000377967.4:c.1442G>A	p.Arg481His	p.R481H	ENST00000377967	NM_021140.2	481	cGc/cAc	15/29	0.3	2	FACETS	0.565	0.451	0.695			1	SUBCLONAL	1	TRUE	NA	0.34	2		480	281	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936072	44936072	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1135401809	NA	P-0004380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	43	411	0	ENST00000377967.4:c.2832+1G>A		p.X944_splice	ENST00000377967	NM_021140.2	944			0.3	2	FACETS	0.897	0.755	1			1	CLONAL	1	TRUE	NA	0.34	2		411	282	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949076	44949076	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	17	472	1	ENST00000377967.4:c.3637C>T	p.Arg1213Ter	p.R1213*	ENST00000377967	NM_021140.2	1213	Cga/Tga	25/29	0.3	2	FACETS	0.469	0.351	0.609			1	SUBCLONAL	1	TRUE	NA	0.34	2		473	213	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247102	53247102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	18	537	0	ENST00000375401.3:c.398G>A	p.Arg133Gln	p.R133Q	ENST00000375401	NM_004187.3	133	cGg/cAg	4/26	0.3	0	FACETS	0.429	0.325	0.55			1	SUBCLONAL	1	TRUE	0	0.34	0		537	163	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646981	23646981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	14	383	1	ENST00000261584.4:c.886del	p.Met296Ter	p.M296*	ENST00000261584	NM_024675.3	296	Atg/tg	4/13	0.3	1	FACETS	0.422	0.306	0.561	0.422	0.306	0.561	SUBCLONAL	1	TRUE	0	0.34	1		384	162	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	19	359	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	0.669	0.511	0.852	0.669	0.511	0.852	SUBCLONAL	1	TRUE	1	0.34	2		359	167	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042483	42042483	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	26	552	0	ENST00000219905.7:c.6682del	p.Ser2228ValfsTer10	p.S2228Vfs*10	ENST00000219905	NM_001164273.1	2226	ggA/gg	17/24	0.109200661191101	0	FACETS	0.439	0.349	0.541			1	INDETERMINATE	1	TRUE	0	0.34	0		552	230	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911443	32911443	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359365	NA	P-0004380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	16	496	0	ENST00000380152.3:c.2957del	p.Asn986IlefsTer5	p.N986Ifs*5	ENST00000380152		984	gAa/ga	11/27	0.109200661191101	0	FACETS	0.247	0.183	0.325			1	INDETERMINATE	1	TRUE	0	0.34	0		496	251	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0004406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	103	673	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.254266528103206	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	3	TRUE	1	0.254266528103206	4		673	310	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115427	115115427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	159	435	0	ENST00000257566.3:c.899C>T	p.Ala300Val	p.A300V	ENST00000257566	NM_016569.3	300	gCa/gTa	5/8	0.194587473250963	3	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	1	0.254266528103206	3		435	675	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845298	42845298	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	63	308	0	ENST00000398585.3:c.964A>G	p.Ile322Val	p.I322V	ENST00000398585	NM_001135099.1	322	Atc/Gtc	9/14	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.254266528103206	2		308	431	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118599	115118684	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGCTGAAACTCATGAAATGGGAAGCACTGCCTTTGACTGAGTGAAGGAGGAGAAAATTTTACTGAAGAGAGCAATGAAACTTACA	GGGCTGAAACTCATGAAATGGGAAGCACTGCCTTTGACTGAGTGAAGGAGGAGAAAATTTTACTGAAGAGAGCAATGAAACTTACA	-	novel	NA	P-0004406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	66	153	0	ENST00000257566.3:c.657_657+85del		p.X219_splice	ENST00000257566	NM_016569.3	219		2/8	0.194587473250963	3	FACETS	1	0.889	1	1	0.889	1	CLONAL	2	TRUE	1	0.254266528103206	3		153	288	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842612	68842613	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	138	368	0	ENST00000261769.5:c.549dup	p.Lys184GlnfsTer15	p.K184Qfs*15	ENST00000261769	NM_004360.3	183	gac/gaCc	5/16	0.254266528103206	1	FACETS	0.902	0.826	0.982	1	0.99	1	CLONAL	2	TRUE	0	0.254266528103206	1		368	525	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253418	226253419	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0004406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	23	75	0	ENST00000366813.1:c.191_192del	p.Arg64GlnfsTer16	p.R64Qfs*16	ENST00000366813		64	CGc/c	2/3	0.254266528103206	5	FACETS	0.806	0.635	1	0.403	0.317	0.5	CLONAL	2	TRUE	1	0.254266528103206	5		75	155	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	25	374	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.836	1			1	INDETERMINATE	2	TRUE	NA	0.370673502988417	2		374	66	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0004420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	40	286	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	0.995	0.834	1	0.995	0.834	1	CLONAL	1	TRUE	1	0.370673502988417	2		286	217	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244283	46244283	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	47	424	0	ENST00000334344.6:c.2377C>T	p.Gln793Ter	p.Q793*	ENST00000334344	NM_152641.2	793	Caa/Taa	15/21	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.370673502988417	2		424	231	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949985	44949985	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	77	222	0	ENST00000377967.4:c.3754G>C	p.Ala1252Pro	p.A1252P	ENST00000377967	NM_021140.2	1252	Gca/Cca	26/29	1	1	FACETS	1	0.937	1	1	0.986	1	CLONAL	2	TRUE	0	0.370673502988417	1		222	161	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035945	47035946	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	33	303	0	ENST00000377604.3:c.627dup	p.Lys210GlnfsTer6	p.K210Qfs*6	ENST00000377604	NM_001204468.1	208	gac/gaCc	7/24	1	1	FACETS	0.701	0.575	0.839	0.701	0.575	0.839	SUBCLONAL	1	TRUE	0	0.370673502988417	1		303	207	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522574	187522575	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	41	296	0	ENST00000441802.2:c.11488dup	p.Ser3830PhefsTer19	p.S3830Ffs*19	ENST00000441802	NM_005245.3	3830	tca/tTca	21/27	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.370673502988417	2		296	186	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230752	53230752	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	241	227	0	ENST00000375401.3:c.2041C>T	p.Arg681Ter	p.R681*	ENST00000375401	NM_004187.3	681	Cga/Tga	14/26	0.213706576383527	2	FACETS	0.959	0.904	1			1	CLONAL	3	TRUE	NA	0.306306415127389	2		227	547	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460515	149460515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777239066	NA	P-0004458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	167	217	0	ENST00000286301.3:c.122G>A	p.Arg41Gln	p.R41Q	ENST00000286301	NM_005211.3	41	cGa/cAa	3/22	0.306306415127389	6	FACETS	0.956	0.878	1	0.478	0.439	0.519	CLONAL	2	TRUE	2	0.306306415127389	6		217	920	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023052	31023052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148575778	NA	P-0004458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	116	324	0	ENST00000375687.4:c.2537G>A	p.Ser846Asn	p.S846N	ENST00000375687	NM_015338.5	846	aGt/aAt	13/13	0.209830630328379	5	FACETS	1	0.951	1	0.72	0.652	0.791	CLONAL	2	TRUE	2	0.306306415127389	5		324	512	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643328	52643329	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	CGATTCATCCTTCTTGCTCGTTCCAATACTT	novel	NA	P-0004458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	30	272	0	ENST00000394830.3:c.2537_2567dup	p.Thr857SerfsTer17	p.T857Sfs*17	ENST00000394830	NM_018313.4	856	cgg/cgAAGTATTGGAACGAGCAAGAAGGATGAATCGg		0.268929673840319	2	FACETS	1	0.895	1	0.576	0.469	0.695	CLONAL	1	TRUE	0	0.306306415127389	2		272	170	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197853	123197853	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	46	195	0	ENST00000218089.9:c.1977del	p.Asp659GlufsTer33	p.D659Efs*33	ENST00000218089	NM_001042749.1	659	gaT/ga	20/35	0.213706576383527	2	FACETS	0.95	0.815	1			1	CLONAL	2	TRUE	NA	0.306306415127389	2		195	158	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183865	10183866	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0004458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	83	76	0	ENST00000256474.2:c.335dup	p.Tyr112Ter	p.Y112*	ENST00000256474	NM_000551.3	112	tac/tAac	1/3	0.268929673840319	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.306306415127389	2		76	220	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108259	8108267	+	inframe_deletion	In_Frame_Del	DEL	GAGACCTGG	GAGACCTGG	-	novel	NA	P-0004458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	86	238	0	ENST00000585124.1:c.957_965del	p.Gln320_Ser322del	p.Q320_S322del	ENST00000585124	NM_004217.3	319	gcCCAGGTCTCa/gca	9/9	0.307006460997879	3	FACETS	0.841	0.743	0.946	0.42	0.371	0.473	CLONAL	1	TRUE	1	0.306306415127389	3		238	770	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0004462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	152	357	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.837	0.771	0.904	0.837	0.771	0.904	CLONAL	1	TRUE	1	0.764772593081543	2		357	475	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111502	8111503	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	162	689	0	ENST00000346208.3:c.990dup	p.Asn331GlufsTer21	p.N331Efs*21	ENST00000346208		330	agg/aGgg	5/6	NA	2	FACETS	0.941	0.872	1			1	INDETERMINATE	1	TRUE	NA	0.764772593081543	2		689	450	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719104	52719104	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	18	262	0	ENST00000322088.6:c.880T>C	p.Cys294Arg	p.C294R	ENST00000322088	NM_014225.5	294	Tgt/Cgt	7/15	0.680262326429985	1	FACETS	0.157	0.118	0.202	0.157	0.118	0.202	SUBCLONAL	1	TRUE	0	0.764772593081543	1		262	185	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972564	25972564	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0004462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	113	197	0	ENST00000435504.4:c.1860+1del		p.X620_splice	ENST00000435504		620			NA	2	FACETS	0.966	0.881	1			1	INDETERMINATE	1	TRUE	NA	0.764772593081543	2		197	306	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7218291	7218292	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	137	280	0	ENST00000380728.2:c.80dup	p.Arg28AlafsTer11	p.R28Afs*11	ENST00000380728		27	gag/gaAg	2/11	0.764772593081543	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.764772593081543	1		280	215	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154252	2154252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771138084	NA	P-0004595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	115	434	1	ENST00000434045.2:c.676G>A	p.Gly226Ser	p.G226S	ENST00000434045	NM_001127598.1	226	Ggc/Agc	5/5	0.873956363358351	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.873956363358351	1		435	144	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918997	76918997	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0004595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	145	573	1	ENST00000373344.5:c.3994A>T	p.Lys1332Ter	p.K1332*	ENST00000373344	NM_000489.3	1332	Aag/Tag	12/35	0.499672016325197	1	FACETS	0.662	0.617	0.708	0.662	0.617	0.708	INDETERMINATE	1	TRUE	0	0.873956363358351	1		574	282	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778819	3778820	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	141	270	0	ENST00000262367.5:c.6228dup	p.Pro2077AlafsTer264	p.P2077Afs*264	ENST00000262367	NM_004380.2	2076	-/G	31/31	0.873956363358351	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.873956363358351	1		270	168	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575546	64575547	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0004595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	254	346	0	ENST00000312049.6:c.470_471del	p.Val157GlyfsTer22	p.V157Gfs*22	ENST00000312049	NM_130799.2	157	gTG/g	3/10	0.873956363358351	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.873956363358351	1		346	306	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572931	7572932	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	49	1211	0	ENST00000269305.4:c.1177dup	p.Asp393GlyfsTer78	p.D393Gfs*78	ENST00000269305	NM_001126112.2	393	gac/gGac	11/11	0.207216066695094	1	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	0	0.207216066695094	1		1211	391	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0004623-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	9	96	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.075	0.049	0.107	0.075	0.049	0.107	SUBCLONAL	1	TRUE	1	0.907421284616424	2		96	266	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0004623-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	199	617	2	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.947	0.887	1	0.947	0.887	1	CLONAL	1	TRUE	1	0.907421284616424	2		619	463	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456496	99456496	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004623-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	23	217	0	ENST00000268035.6:c.1813C>A	p.Arg605Ser	p.R605S	ENST00000268035	NM_000875.3	605	Cgc/Agc	8/21	1	2	FACETS	0.147	0.114	0.185	0.147	0.114	0.185	SUBCLONAL	1	TRUE	1	0.907421284616424	2		217	345	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159751	20159751	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004623-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	195	286	0	ENST00000379607.5:c.8A>G	p.Lys3Arg	p.K3R	ENST00000379607	NM_001412.3	3	aAg/aGg	1/7	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.907421284616424	2		286	417	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027086	71027087	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs797044652	NA	P-0004623-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	147	245	0	ENST00000318789.4:c.1240dup	p.Leu414ProfsTer47	p.L414Pfs*47	ENST00000318789	NM_032682.5	414	ctg/cCtg	15/21	1	2	FACETS	0.991	0.919	1	0.991	0.919	1	CLONAL	1	TRUE	1	0.907421284616424	2		245	327	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089705	27089706	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1286891446	NA	P-0004623-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	124	272	0	ENST00000324856.7:c.2666dup	p.Met890HisfsTer46	p.M890Hfs*46	ENST00000324856	NM_006015.4	887	-/G	8/20	1	2	FACETS	0.737	0.674	0.802	0.737	0.674	0.802	SUBCLONAL	1	TRUE	1	0.907421284616424	2		272	371	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0004624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	149	474	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.881	0.804	0.962	0.881	0.804	0.962	CLONAL	1	TRUE	1	0.344147076561675	2		474	983	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573978	7573979	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	GTTCCAAGGCCTCATTCAGC	novel	NA	P-0004624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	124	601	0	ENST00000269305.4:c.1029_1048dup	p.Leu350ArgfsTer2	p.L350Rfs*2	ENST00000269305	NM_001126112.2	350	ctc/cGCTGAATGAGGCCTTGGAACtc	10/11	0.266075493859874	2	FACETS	0.994	0.9	1	0.497	0.45	0.547	CLONAL	1	TRUE	0	0.344147076561675	2		601	725	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560181	29560181	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	31	181	0	ENST00000356175.3:c.3658G>T	p.Glu1220Ter	p.E1220*	ENST00000356175	NM_000267.3	1220	Gaa/Taa	27/57	0.3	1	FACETS	0.661	0.536	0.801	0.661	0.536	0.801	SUBCLONAL	1	TRUE	0	0.28	1		181	288	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325822	65325822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	37	240	0	ENST00000342505.4:c.1300C>T	p.His434Tyr	p.H434Y	ENST00000342505	NM_002227.2	434	Cac/Tac	9/25	1	2	FACETS	0.89	0.737	1	0.89	0.737	1	CLONAL	1	TRUE	1	0.28	2		240	297	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630377	47630377	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs745771647	NA	P-0004643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	32	242	0	ENST00000233146.2:c.47A>C	p.Glu16Ala	p.E16A	ENST00000233146	NM_000251.2	16	gAg/gCg	1/16	1	2	FACETS	0.73	0.594	0.883	0.73	0.594	0.883	SUBCLONAL	1	TRUE	1	0.28	2		242	313	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37092115	37092115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374380262	NA	P-0004643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	51	475	0	ENST00000231790.2:c.2242G>A	p.Asp748Asn	p.D748N	ENST00000231790	NM_000249.3	748	Gat/Aat	19/19	1	2	FACETS	0.804	0.684	0.935	0.804	0.684	0.935	CLONAL	1	TRUE	1	0.28	2		475	453	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934333	81934333	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	24	462	0	ENST00000359376.3:c.1310G>C	p.Ser437Thr	p.S437T	ENST00000359376	NM_002661.3	437	aGt/aCt	14/33	0.196551260306756	0	FACETS	0.318	0.249	0.398			1	SUBCLONAL	1	TRUE	0	0.28	0		462	388	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245210	41245210	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs80356945	NA	P-0004643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	31	454	0	ENST00000357654.3:c.2338C>G	p.Gln780Glu	p.Q780E	ENST00000357654	NM_007294.3	780	Cag/Gag	10/23	0.3	1	FACETS	0.475	0.384	0.578	0.475	0.384	0.578	SUBCLONAL	1	TRUE	0	0.28	1		454	401	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375012	45375012	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	40	346	0	ENST00000262160.6:c.831A>G	p.Ile277Met	p.I277M	ENST00000262160	NM_005901.5	277	atA/atG	8/11	1	2	FACETS	0.752	0.626	0.892	0.752	0.626	0.892	SUBCLONAL	1	TRUE	1	0.28	2		346	380	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069132	5069178	+	frameshift_variant	Frame_Shift_Del	DEL	TTGTTACCAGATGGAAACTGTTCGCTCAGACAATATAATTTTCCAGT	TTGTTACCAGATGGAAACTGTTCGCTCAGACAATATAATTTTCCAGT	-	novel	NA	P-0004643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	34	416	0	ENST00000381652.3:c.1439_1485del	p.Cys480TyrfsTer2	p.C480Yfs*2	ENST00000381652	NM_004972.3	479	aaTTGTTACCAGATGGAAACTGTTCGCTCAGACAATATAATTTTCCAGTtt/aatt	11/25	0.160610779012033	1	FACETS	0.517	0.422	0.623	0.517	0.422	0.623	INDETERMINATE	1	TRUE	0	0.28	1		416	404	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210502	2210502	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	21	253	0	ENST00000398665.3:c.1113del	p.Met372TrpfsTer15	p.M372Wfs*15	ENST00000398665	NM_032482.2	370	gCc/gc	13/28	0.160610779012033	1	FACETS	0.52	0.401	0.658	0.52	0.401	0.658	INDETERMINATE	1	TRUE	0	0.28	1		253	248	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602501	10602511	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCAGGTCCG	CTGCAGGTCCG	-	novel	NA	P-0004643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	24	249	0	ENST00000171111.5:c.1067_1077del	p.Ala356GlyfsTer55	p.A356Gfs*55	ENST00000171111	NM_203500.1	356	gCGGACCTGCAG/g	3/6	0.160610779012033	1	FACETS	0.563	0.442	0.701	0.563	0.442	0.701	INDETERMINATE	1	TRUE	0	0.28	1		249	262	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86681204	86681204	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	38	255	0	ENST00000274376.6:c.2846del	p.Lys949ArgfsTer19	p.K949Rfs*19	ENST00000274376	NM_002890.2	949	Aag/ag	22/25	1	2	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	TRUE	1	0.28	2		255	264	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973912	55973913	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	25	231	0	ENST00000263923.4:c.1403dup	p.Asn468LysfsTer16	p.N468Kfs*16	ENST00000263923	NM_002253.2	468	aac/aaAc	10/30	1	2	FACETS	0.603	0.476	0.749	0.603	0.476	0.749	SUBCLONAL	1	TRUE	1	0.28	2		231	296	SUCCESS
MET	4233	MSKCC	GRCh37	7	116399449	116399449	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	43	484	0	ENST00000397752.3:c.2271del	p.Ser758AlafsTer3	p.S758Afs*3	ENST00000397752	NM_000245.2	757	Ggg/gg	10/21	1	2	FACETS	0.708	0.593	0.835	0.708	0.593	0.835	SUBCLONAL	1	TRUE	1	0.28	2		484	434	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523648	41523648	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	205	949	0	ENST00000263253.7:c.1064A>G	p.Glu355Gly	p.E355G	ENST00000263253	NM_001429.3	355	gAa/gGa	4/31	0.554639240310807	4	FACETS	1	0.947	1	0.513	0.475	0.551	CLONAL	1	TRUE	2	0.664387699000862	4		949	1002	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717727	89717728	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGAT	novel	NA	P-0004734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	187	457	0	ENST00000371953.3:c.753_756dup	p.Ile253Ter	p.I253*	ENST00000371953	NM_000314.4	251	ggt/ggTGATt	7/9	0.664387699000862	2	FACETS	0.964	0.913	1	0.964	0.913	1	CLONAL	2	TRUE	0	0.664387699000862	2		457	292	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427265	49427266	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGC	rs398123707	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	49	406	1	ENST00000301067.7:c.11220_11222dup	p.Gln3745dup	p.Q3745dup	ENST00000301067	NM_003482.3	3745	caa/caGCAa	39/54	0.265045431041429	3	FACETS	1	0.927	1	0.577	0.49	0.671	CLONAL	1	TRUE	1	0.28	3		407	346	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	82	435	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.265045431041429	3	FACETS	1	0.973	1	0.684	0.605	0.768	CLONAL	1	TRUE	1	0.28	3		436	488	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772950	135772951	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs118203724	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	38	392	1	ENST00000298552.3:c.2672dup	p.Asn891LysfsTer13	p.N891Kfs*13	ENST00000298552	NM_001162426.1	891	aac/aaAc	21/23	1	2	FACETS	0.7	0.579	0.834	0.7	0.579	0.834	SUBCLONAL	1	TRUE	1	0.28	2		393	388	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	124	646	6	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.825	0.749	0.903	1	0.987	1	CLONAL	2	TRUE	1	0.28	2		652	537	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	38	409	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.649	0.537	0.775	0.649	0.537	0.775	SUBCLONAL	1	TRUE	1	0.28	2		409	418	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	110	302	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.766	0.691	0.844	1	0.984	1	SUBCLONAL	2	TRUE	1	0.28	2		302	513	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	14	243	0	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	1	FACETS	0.705	0.514	0.932	0.705	0.514	0.932	CLONAL	1	TRUE	0	0.28	1		243	122	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	212	547	7	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	0.161913991803311	4	FACETS	0.936	0.874	1			1	INDETERMINATE	3	TRUE	NA	0.28	4		554	690	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	26	481	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			1	2	FACETS	0.413	0.326	0.512	0.413	0.326	0.512	SUBCLONAL	1	TRUE	1	0.28	2		481	450	SUCCESS
APC	324	MSKCC	GRCh37	5	112173847	112173848	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	107	451	0	ENST00000257430.4:c.2563_2564dup	p.Arg856AsnfsTer6	p.R856Nfs*6	ENST00000257430	NM_000038.5	852	-/GA	16/16	1	2	FACETS	0.758	0.683	0.837	1	0.983	1	SUBCLONAL	2	TRUE	1	0.28	2		451	504	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	20	724	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.172	0.13	0.221	0.172	0.13	0.221	SUBCLONAL	1	TRUE	1	0.28	2		724	832	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	102	574	0	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	0.265045431041429	3	FACETS	0.799	0.717	0.885	0.799	0.717	0.885	SUBCLONAL	2	TRUE	1	0.28	3		574	520	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129428	64129428	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61736650	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	31	509	0	ENST00000334205.4:c.860C>T	p.Ala287Val	p.A287V	ENST00000334205	NM_003942.2	287	gCg/gTg	8/17	1	2	FACETS	0.597	0.483	0.726	0.597	0.483	0.726	SUBCLONAL	1	TRUE	1	0.28	2		509	371	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	58	424	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	1	2	FACETS	0.776	0.667	0.894	0.776	0.667	0.894	SUBCLONAL	1	TRUE	1	0.28	2		424	534	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448407	49448408	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs797045661	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	27	513	0	ENST00000301067.7:c.303dup	p.Ser102GlufsTer6	p.S102Efs*6	ENST00000301067	NM_003482.3	101	-/G	3/54	0.265045431041429	3	FACETS	0.458	0.364	0.566	0.229	0.182	0.283	SUBCLONAL	1	TRUE	1	0.28	3		513	480	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161182	56161182	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370499041	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	71	449	0	ENST00000399503.3:c.1051C>T	p.Arg351Cys	p.R351C	ENST00000399503	NM_005921.1	351	Cgt/Tgt	5/20	1	2	FACETS	0.964	0.843	1	0.964	0.843	1	CLONAL	1	TRUE	1	0.28	2		449	526	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	37	404	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	0.553	0.455	0.662	0.553	0.455	0.662	SUBCLONAL	1	TRUE	1	0.28	2		404	478	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	48	426	0	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	1	2	FACETS	0.652	0.551	0.763	0.652	0.551	0.763	SUBCLONAL	1	TRUE	1	0.28	2		426	526	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442854	187442854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867576130	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	48	389	1	ENST00000232014.4:c.1852C>T	p.Arg618Cys	p.R618C	ENST00000232014	NM_001130845.1	618	Cgt/Tgt	9/10	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.28	2		390	327	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259852	16259852	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	39	512	0	ENST00000375759.3:c.7117A>G	p.Thr2373Ala	p.T2373A	ENST00000375759	NM_015001.2	2373	Aca/Gca	11/15	1	2	FACETS	0.637	0.528	0.759	0.637	0.528	0.759	SUBCLONAL	1	TRUE	1	0.28	2		512	437	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306989	65306989	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	52	446	0	ENST00000342505.4:c.2588C>A	p.Thr863Asn	p.T863N	ENST00000342505	NM_002227.2	863	aCt/aAt	19/25	1	2	FACETS	0.723	0.615	0.84	0.723	0.615	0.84	SUBCLONAL	1	TRUE	1	0.28	2		446	514	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015428	176015428	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1373217036	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	55	389	0	ENST00000367669.3:c.1310C>T	p.Ala437Val	p.A437V	ENST00000367669	NM_022457.5	437	gCg/gTg	12/20	1	2	FACETS	0.684	0.585	0.793	0.684	0.585	0.793	SUBCLONAL	1	TRUE	1	0.28	2		389	574	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082943	16082943	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs754768625	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	17	148	0	ENST00000281043.3:c.757A>G	p.Ser253Gly	p.S253G	ENST00000281043	NM_005378.4	253	Agt/Ggt	2/3	NA	2	FACETS	0.995	0.751	1			1	INDETERMINATE	1	TRUE	NA	0.28	2		148	122	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99163159	99163159	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	98	507	2	ENST00000074304.5:c.1163+2T>C		p.X388_splice	ENST00000074304	NM_001134224.1	388			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.28	2		509	492	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044377	128044377	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	61	616	0	ENST00000285398.2:c.1244A>G	p.His415Arg	p.H415R	ENST00000285398	NM_000122.1	415	cAc/cGc	8/15	1	2	FACETS	0.838	0.724	0.962	0.838	0.724	0.962	CLONAL	1	TRUE	1	0.28	2		616	520	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141632	202141632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764461240	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	88	520	1	ENST00000358485.4:c.920G>A	p.Arg307Gln	p.R307Q	ENST00000358485	NM_001080125.1	307	cGg/cAg	7/9	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.28	2		521	612	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149917	202149917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	51	466	0	ENST00000358485.4:c.1358C>T	p.Pro453Leu	p.P453L	ENST00000358485	NM_001080125.1	453	cCg/cTg	8/9	1	2	FACETS	0.806	0.686	0.937	0.806	0.686	0.937	CLONAL	1	TRUE	1	0.28	2		466	452	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209106796	209106796	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	55	516	0	ENST00000345146.2:c.772G>A	p.Ala258Thr	p.A258T	ENST00000345146	NM_005896.2	258	Gct/Act	7/10	1	2	FACETS	0.825	0.707	0.954	0.825	0.707	0.954	CLONAL	1	TRUE	1	0.28	2		516	476	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293208	212293208	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	20	297	0	ENST00000342788.4:c.2644A>G	p.Met882Val	p.M882V	ENST00000342788	NM_005235.2	882	Atg/Gtg	22/28	1	2	FACETS	0.384	0.293	0.491	0.384	0.293	0.491	SUBCLONAL	1	TRUE	1	0.28	2		297	372	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660957	227660957	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs779385759	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	51	560	0	ENST00000305123.5:c.2498A>C	p.His833Pro	p.H833P	ENST00000305123	NM_005544.2	833	cAc/cCc	1/2	1	2	FACETS	0.78	0.664	0.907	0.78	0.664	0.907	CLONAL	1	TRUE	1	0.28	2		560	467	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663375	227663375	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	11	207	0	ENST00000305123.5:c.80A>G	p.Lys27Arg	p.K27R	ENST00000305123	NM_005544.2	27	aAa/aGa	1/2	1	2	FACETS	0.479	0.332	0.661	0.479	0.332	0.661	SUBCLONAL	1	TRUE	1	0.28	2		207	164	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37091995	37091995	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	85	477	0	ENST00000231790.2:c.2122A>T	p.Ile708Phe	p.I708F	ENST00000231790	NM_000249.3	708	Att/Ttt	19/19	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.28	2		477	474	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928016	49928016	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	156	713	0	ENST00000296474.3:c.3712T>C	p.Tyr1238His	p.Y1238H	ENST00000296474	NM_002447.2	1238	Tac/Cac	18/20	1	2	FACETS	0.89	0.818	0.964	1	0.991	1	CLONAL	2	TRUE	1	0.28	2		713	626	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696160	52696160	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	45	492	0	ENST00000394830.3:c.517G>T	p.Val173Leu	p.V173L	ENST00000394830	NM_018313.4	173	Gtg/Ttg	5/30	1	2	FACETS	0.784	0.66	0.921	0.784	0.66	0.921	CLONAL	1	TRUE	1	0.28	2		492	410	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720964	119720964	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	75	541	0	ENST00000316626.5:c.211T>C	p.Tyr71His	p.Y71H	ENST00000316626		71	Tat/Cat	2/12	1	2	FACETS	0.769	0.673	0.872	0.769	0.673	0.872	SUBCLONAL	1	TRUE	1	0.28	2		541	697	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038428	180038428	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	34	575	0	ENST00000261937.6:c.3589G>T	p.Gly1197Cys	p.G1197C	ENST00000261937	NM_182925.4	1197	Ggc/Tgc	27/30	1	2	FACETS	0.684	0.56	0.823	0.684	0.56	0.823	SUBCLONAL	1	TRUE	1	0.28	2		575	355	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394893	394893	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	41	351	0	ENST00000380956.4:c.289C>A	p.Leu97Met	p.L97M	ENST00000380956	NM_001195286.1	97	Ctg/Atg	3/9	NA	2	FACETS	0.792	0.661	0.936			1	INDETERMINATE	1	TRUE	NA	0.28	2		351	370	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158605	26158605	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs768212529	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	24	205	0	ENST00000289316.2:c.208A>G	p.Ile70Val	p.I70V	ENST00000289316	NM_138720.2	70	Atc/Gtc	1/2	0.154633726772335	3	FACETS	0.913	0.72	1	0.304	0.24	0.378	INDETERMINATE	1	TRUE	0	0.28	3		205	214	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671994	30671994	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	35	692	0	ENST00000376406.3:c.4966G>A	p.Ala1656Thr	p.A1656T	ENST00000376406	NM_014641.2	1656	Gca/Aca	10/15	0.154633726772335	3	FACETS	0.49	0.4	0.59	0.163	0.133	0.197	INDETERMINATE	1	TRUE	0	0.28	3		692	582	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679708	30679708	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	50	590	0	ENST00000376406.3:c.2011G>T	p.Gly671Ter	p.G671*	ENST00000376406	NM_014641.2	671	Gga/Tga	5/15	0.154633726772335	3	FACETS	0.808	0.686	0.942	0.269	0.228	0.314	INDETERMINATE	1	TRUE	0	0.28	3		590	504	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956659	93956659	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	52	818	0	ENST00000369303.4:c.2577G>T	p.Met859Ile	p.M859I	ENST00000369303	NM_004440.3	859	atG/atT	15/17	1	2	FACETS	0.568	0.483	0.662	0.568	0.483	0.662	SUBCLONAL	1	TRUE	1	0.28	2		818	654	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066534	94066534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1402331883	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	115	695	3	ENST00000369303.4:c.1225G>A	p.Ala409Thr	p.A409T	ENST00000369303	NM_004440.3	409	Gct/Act	5/17	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.28	2		698	732	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658485	117658485	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	49	282	0	ENST00000368508.3:c.5098T>C	p.Tyr1700His	p.Y1700H	ENST00000368508	NM_002944.2	1700	Tac/Cac	31/43	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.28	2		282	252	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969968	161969968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746215864	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	41	494	1	ENST00000366898.1:c.1001G>A	p.Arg334His	p.R334H	ENST00000366898	NM_004562.2	334	cGc/cAc	9/12	1	2	FACETS	0.689	0.574	0.816	0.689	0.574	0.816	SUBCLONAL	1	TRUE	1	0.28	2		495	425	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951847	2951847	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868687398	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	54	512	0	ENST00000396946.4:c.3103G>A	p.Glu1035Lys	p.E1035K	ENST00000396946	NM_032415.4	1035	Gaa/Aaa	23/25	0.3	1	FACETS	0.819	0.702	0.947	0.819	0.702	0.947	CLONAL	1	TRUE	0	0.28	1		512	405	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951862	2951862	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	24	484	0	ENST00000396946.4:c.3088A>G	p.Asn1030Asp	p.N1030D	ENST00000396946	NM_032415.4	1030	Aac/Gac	23/25	0.3	1	FACETS	0.402	0.315	0.502	0.402	0.315	0.502	SUBCLONAL	1	TRUE	0	0.28	1		484	367	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636784	8636784	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	44	459	0	ENST00000356435.5:c.125C>T	p.Ser42Phe	p.S42F	ENST00000356435		42	tCt/tTt	2/35	1	2	FACETS	0.57	0.478	0.673	0.57	0.478	0.673	SUBCLONAL	1	TRUE	1	0.28	2		459	551	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759443	133759443	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376925416	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	44	747	0	ENST00000318560.5:c.1766G>A	p.Arg589His	p.R589H	ENST00000318560	NM_005157.4	589	cGc/cAc	11/11	1	2	FACETS	0.553	0.463	0.653	0.553	0.463	0.653	SUBCLONAL	1	TRUE	1	0.28	2		747	568	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77070034	77070034	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	60	400	1	ENST00000356341.3:c.506C>T	p.Ala169Val	p.A169V	ENST00000356341	NM_002576.4	169	gCa/gTa	6/15	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.28	2		401	417	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944961	31944961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1441610501	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	129	516	2	ENST00000340398.3:c.140C>T	p.Ala47Val	p.A47V	ENST00000340398	NM_001013699.2	47	gCg/gTg	1/1	0.265045431041429	3	FACETS	0.901	0.82	0.986	0.901	0.82	0.986	CLONAL	2	TRUE	1	0.28	3		518	583	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432135	49432135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	52	599	0	ENST00000301067.7:c.9004G>A	p.Ala3002Thr	p.A3002T	ENST00000301067	NM_003482.3	3002	Gcc/Acc	34/54	0.265045431041429	3	FACETS	0.817	0.696	0.95	0.409	0.348	0.475	CLONAL	1	TRUE	1	0.28	3		599	518	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478923	56478923	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1308361325	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	52	574	0	ENST00000267101.3:c.379T>C	p.Ser127Pro	p.S127P	ENST00000267101	NM_001982.3	127	Tcc/Ccc	3/28	0.265045431041429	3	FACETS	0.625	0.532	0.729	0.313	0.266	0.365	SUBCLONAL	1	TRUE	1	0.28	3		574	677	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252337	133252337	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	108	481	0	ENST00000320574.5:c.1090G>T	p.Gly364Trp	p.G364W	ENST00000320574	NM_006231.2	364	Ggg/Tgg	11/49	0.265045431041429	3	FACETS	0.922	0.832	1	0.922	0.832	1	CLONAL	2	TRUE	1	0.28	3		481	477	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007688	45007688	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	65	413	1	ENST00000558401.1:c.135C>A	p.Cys45Ter	p.C45*	ENST00000558401	NM_004048.2	45	tgC/tgA	2/4	1	2	FACETS	0.996	0.866	1	0.996	0.866	1	CLONAL	1	TRUE	1	0.28	2		414	466	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782067	66782067	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	33	457	0	ENST00000307102.5:c.1034A>C	p.Asn345Thr	p.N345T	ENST00000307102	NM_002755.3	345	aAc/aCc	10/11	1	2	FACETS	0.424	0.344	0.514	0.424	0.344	0.514	SUBCLONAL	1	TRUE	1	0.28	2		457	556	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029555	14029555	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750549531	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	15	205	1	ENST00000311895.7:c.1766G>A	p.Arg589Gln	p.R589Q	ENST00000311895	NM_005236.2	589	cGg/cAg	8/11	1	2	FACETS	0.489	0.358	0.646	0.489	0.358	0.646	SUBCLONAL	1	TRUE	1	0.28	2		206	219	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864597	56864597	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	69	656	1	ENST00000308159.5:c.1085G>T	p.Arg362Ile	p.R362I	ENST00000308159	NM_014669.4	362	aGa/aTa	10/22	1	2	FACETS	0.853	0.743	0.971	0.853	0.743	0.971	CLONAL	1	TRUE	1	0.28	2		657	578	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346403	89346403	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	52	617	0	ENST00000301030.4:c.6547G>T	p.Val2183Leu	p.V2183L	ENST00000301030	NM_001256183.1	2183	Gtg/Ttg	9/13	1	2	FACETS	0.829	0.707	0.962	0.829	0.707	0.962	CLONAL	1	TRUE	1	0.28	2		617	448	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849325	89849325	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	52	607	0	ENST00000389301.3:c.1568T>A	p.Val523Asp	p.V523D	ENST00000389301	NM_000135.2	523	gTt/gAt	17/43	1	2	FACETS	0.68	0.579	0.791	0.68	0.579	0.791	SUBCLONAL	1	TRUE	1	0.28	2		607	546	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664858	29664858	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs745945481	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	35	403	0	ENST00000356175.3:c.6601A>G	p.Thr2201Ala	p.T2201A	ENST00000356175	NM_000267.3	2201	Acg/Gcg	43/57	1	2	FACETS	0.556	0.455	0.668	0.556	0.455	0.668	SUBCLONAL	1	TRUE	1	0.28	2		403	450	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325991	30325991	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	36	431	0	ENST00000322652.5:c.2189T>C	p.Val730Ala	p.V730A	ENST00000322652	NM_015355.2	730	gTt/gCt	16/16	1	2	FACETS	0.501	0.411	0.602	0.501	0.411	0.602	SUBCLONAL	1	TRUE	1	0.28	2		431	513	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246352	41246352	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780794	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	36	551	0	ENST00000357654.3:c.1196A>G	p.His399Arg	p.H399R	ENST00000357654	NM_007294.3	399	cAt/cGt	10/23	1	2	FACETS	0.508	0.417	0.61	0.508	0.417	0.61	SUBCLONAL	1	TRUE	1	0.28	2		551	506	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119014	70119014	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	26	470	0	ENST00000245479.2:c.586A>G	p.Thr196Ala	p.T196A	ENST00000245479	NM_000346.3	196	Acg/Gcg	2/3	1	2	FACETS	0.523	0.414	0.648	0.523	0.414	0.648	SUBCLONAL	1	TRUE	1	0.28	2		470	355	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120178	70120178	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057518216	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	33	263	2	ENST00000245479.2:c.1180C>T	p.Arg394Ter	p.R394*	ENST00000245479	NM_000346.3	394	Cga/Tga	3/3	1	2	FACETS	0.907	0.742	1	0.907	0.742	1	CLONAL	1	TRUE	1	0.28	2		265	260	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612341	1612341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376471101	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	69	690	1	ENST00000344749.5:c.1678C>T	p.Arg560Trp	p.R560W	ENST00000344749	NM_001136139.2	560	Cgg/Tgg	18/19	1	2	FACETS	0.903	0.787	1	0.903	0.787	1	CLONAL	1	TRUE	1	0.28	2		691	546	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110228	3110228	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769019097	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	46	597	2	ENST00000078429.4:c.218G>A	p.Arg73His	p.R73H	ENST00000078429	NM_002067.2	73	cGc/cAc	2/7	1	2	FACETS	0.679	0.572	0.797	0.679	0.572	0.797	SUBCLONAL	1	TRUE	1	0.28	2		599	484	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355121	15355121	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	26	452	0	ENST00000263377.2:c.2502G>T	p.Glu834Asp	p.E834D	ENST00000263377	NM_058243.2	834	gaG/gaT	13/20	1	2	FACETS	0.575	0.456	0.711	0.575	0.456	0.711	SUBCLONAL	1	TRUE	1	0.28	2		452	323	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743944	41743944	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	35	627	0	ENST00000301178.4:c.879G>T	p.Gln293His	p.Q293H	ENST00000301178	NM_021913.4	293	caG/caT	7/20	1	2	FACETS	0.617	0.506	0.742	0.617	0.506	0.742	SUBCLONAL	1	TRUE	1	0.28	2		627	405	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860903	45860903	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	48	582	0	ENST00000391945.4:c.1292C>A	p.Pro431His	p.P431H	ENST00000391945	NM_000400.3	431	cCc/cAc	13/23	1	2	FACETS	0.779	0.66	0.911	0.779	0.66	0.911	CLONAL	1	TRUE	1	0.28	2		582	440	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723079	52723079	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	11	238	0	ENST00000322088.6:c.1264G>A	p.Ala422Thr	p.A422T	ENST00000322088	NM_014225.5	422	Gcc/Acc	10/15	1	2	FACETS	0.429	0.297	0.594	0.429	0.297	0.594	SUBCLONAL	1	TRUE	1	0.28	2		238	183	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309568	30309568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766818591	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	32	528	1	ENST00000307677.4:c.454G>A	p.Val152Met	p.V152M	ENST00000307677	NM_138578.1	152	Gtg/Atg	2/3	1	2	FACETS	0.458	0.371	0.557	0.458	0.371	0.557	SUBCLONAL	1	TRUE	1	0.28	2		529	499	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408879	41408879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776612407	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	28	527	1	ENST00000373198.4:c.547C>T	p.Arg183Trp	p.R183W	ENST00000373198	NM_133170.3	183	Cgg/Tgg	4/32	1	2	FACETS	0.456	0.364	0.561	0.456	0.364	0.561	SUBCLONAL	1	TRUE	1	0.28	2		528	439	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250089	53250089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	72	321	0	ENST00000375401.3:c.160C>T	p.Pro54Ser	p.P54S	ENST00000375401	NM_004187.3	54	Cca/Tca	2/26	1	1	FACETS	0.851	0.752	0.954	1	0.98	1	CLONAL	2	TRUE	0	0.28	1		321	260	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019579	123019579	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	94	351	0	ENST00000355640.3:c.67T>C	p.Phe23Leu	p.F23L	ENST00000355640		23	Ttt/Ctt	2/7	1	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.28	1		351	431	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491389	18491390	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	50	483	0	ENST00000266497.5:c.1309dup	p.Ile437AsnfsTer19	p.I437Nfs*19	ENST00000266497		434	-/A	8/31	0.265045431041429	3	FACETS	0.62	0.525	0.724	0.31	0.262	0.362	SUBCLONAL	1	TRUE	1	0.28	3		483	657	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686315	30686316	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	102	393	0	ENST00000295754.5:c.175dup	p.Ser59PhefsTer4	p.S59Ffs*4	ENST00000295754	NM_003242.5	57	-/T	2/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.28	2		393	549	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721164	176721165	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1562308992	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	16	310	0	ENST00000439151.2:c.6801dup	p.Ala2268SerfsTer13	p.A2268Sfs*13	ENST00000439151	NM_022455.4	2265	-/A	23/23	1	2	FACETS	0.398	0.294	0.523	0.398	0.294	0.523	SUBCLONAL	1	TRUE	1	0.28	2		310	287	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637539	52637540	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	34	418	0	ENST00000394830.3:c.2776dup	p.Arg926LysfsTer4	p.R926Kfs*4	ENST00000394830	NM_018313.4	926	aga/aAga	18/30	1	2	FACETS	0.536	0.438	0.647	0.536	0.438	0.647	SUBCLONAL	1	TRUE	1	0.28	2		418	453	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246158	41246158	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	52	440	0	ENST00000357654.3:c.1390del	p.Thr464ProfsTer11	p.T464Pfs*11	ENST00000357654	NM_007294.3	464	Acc/cc	10/23	1	2	FACETS	0.827	0.705	0.96	0.827	0.705	0.96	CLONAL	1	TRUE	1	0.28	2		440	449	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184150	56184150	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	62	458	0	ENST00000399503.3:c.4359del	p.Lys1453AsnfsTer8	p.K1453Nfs*8	ENST00000399503	NM_005921.1	1452	gAa/ga	19/20	1	2	FACETS	0.865	0.748	0.992	0.865	0.748	0.992	CLONAL	1	TRUE	1	0.28	2		458	512	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310208	91310208	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs747341586	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	77	566	2	ENST00000355112.3:c.2268del	p.Asp757ThrfsTer4	p.D757Tfs*4	ENST00000355112	NM_000057.2	754	tcA/tc	10/22	1	2	FACETS	0.752	0.66	0.852	0.752	0.66	0.852	SUBCLONAL	1	TRUE	1	0.28	2		568	731	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411001	63411002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	94	296	0	ENST00000330258.3:c.2165dup	p.Gln723ProfsTer3	p.Q723Pfs*3	ENST00000330258	NM_152424.3	722	ttc/ttTc	2/2	1	1	FACETS	1	0.971	1	1	0.989	1	CLONAL	2	TRUE	0	0.28	1		296	242	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029437	16029439	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	rs774778469	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	66	497	0	ENST00000268712.3:c.1591_1593del	p.Glu531del	p.E531del	ENST00000268712	NM_006311.3	531	GAA/-	15/46	1	2	FACETS	0.693	0.601	0.793	0.693	0.601	0.793	SUBCLONAL	1	TRUE	1	0.28	2		497	680	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16022738	16022738	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	84	496	3	ENST00000268712.3:c.1914del	p.Gly639ValfsTer2	p.G639Vfs*2	ENST00000268712	NM_006311.3	638	aaA/aa	17/46	1	2	FACETS	0.985	0.871	1	0.985	0.871	1	CLONAL	1	TRUE	1	0.28	2		499	609	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097624	11097625	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1165714406	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	34	604	1	ENST00000358026.2:c.810dup	p.Gly271ArgfsTer16	p.G271Rfs*16	ENST00000358026	NM_001128849.1	268	-/C	5/36	1	2	FACETS	0.558	0.456	0.673	0.558	0.456	0.673	SUBCLONAL	1	TRUE	1	0.28	2		605	435	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434361	121434361	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs193922576	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	36	356	0	ENST00000257555.6:c.1129del	p.Leu377SerfsTer7	p.L377Sfs*7	ENST00000257555		375	ggC/gg	6/10	0.265045431041429	3	FACETS	0.875	0.721	1	0.438	0.36	0.524	CLONAL	1	TRUE	1	0.28	3		356	335	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097808	27097808	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	48	392	0	ENST00000324856.7:c.3399del	p.Ser1134LeufsTer27	p.S1134Lfs*27	ENST00000324856	NM_006015.4	1133	Ccc/cc	12/20	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.28	2		392	325	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202752	16202753	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	54	553	1	ENST00000375759.3:c.465dup	p.Thr156AspfsTer5	p.T156Dfs*5	ENST00000375759	NM_015001.2	154	cgg/cGgg	3/15	1	2	FACETS	0.65	0.555	0.755	0.65	0.555	0.755	SUBCLONAL	1	TRUE	1	0.28	2		554	593	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94209523	94209523	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	65	563	0	ENST00000323929.3:c.591del	p.Val198Ter	p.V198*	ENST00000323929	NM_005591.3	197	aaA/aa	7/20	1	2	FACETS	0.822	0.713	0.94	0.822	0.713	0.94	CLONAL	1	TRUE	1	0.28	2		563	565	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740623	58740624	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs763475304	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	51	809	0	ENST00000305921.3:c.1535dup	p.Asn512LysfsTer16	p.N512Kfs*16	ENST00000305921	NM_003620.3	510	caa/cAaa	6/6	1	2	FACETS	0.469	0.398	0.548	0.469	0.398	0.548	SUBCLONAL	1	TRUE	1	0.28	2		809	776	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042278	42042278	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	61	915	0	ENST00000219905.7:c.6474del	p.Glu2160ArgfsTer19	p.E2160Rfs*19	ENST00000219905	NM_001164273.1	2158	gCc/gc	17/24	0.3	1	FACETS	0.576	0.497	0.663	0.576	0.497	0.663	SUBCLONAL	1	TRUE	0	0.28	1		915	650	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211615	46211615	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	54	487	0	ENST00000334344.6:c.585del	p.Asp196IlefsTer19	p.D196Ifs*19	ENST00000334344	NM_152641.2	194	gAa/ga	5/21	0.265045431041429	3	FACETS	0.718	0.613	0.834	0.359	0.306	0.417	SUBCLONAL	1	TRUE	1	0.28	3		487	612	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149655	61149656	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	18	204	0	ENST00000295025.8:c.1851dup	p.Gln618SerfsTer8	p.Q618Sfs*8	ENST00000295025	NM_002908.2	615	-/T	11/11	1	2	FACETS	0.67	0.506	0.861	0.67	0.506	0.861	SUBCLONAL	1	TRUE	1	0.28	2		204	192	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070577	67070578	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	57	537	2	ENST00000412916.2:c.207dup	p.Pro70SerfsTer13	p.P70Sfs*13	ENST00000412916		67	-/T	3/6	1	2	FACETS	0.646	0.554	0.747	0.646	0.554	0.747	SUBCLONAL	1	TRUE	1	0.28	2		539	630	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117594	70117594	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	56	500	0	ENST00000245479.2:c.66del	p.Ser23AlafsTer38	p.S23Afs*38	ENST00000245479	NM_000346.3	21	gCc/gc	1/3	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.28	2		500	387	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734176	58734177	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	69	774	0	ENST00000305921.3:c.1238dup	p.Cys414MetfsTer20	p.C414Mfs*20	ENST00000305921	NM_003620.3	412	tcc/tCcc	5/6	1	2	FACETS	0.663	0.577	0.757	0.663	0.577	0.757	SUBCLONAL	1	TRUE	1	0.28	2		774	743	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785963	135785964	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs118203506	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	28	362	0	ENST00000298552.3:c.1257dup	p.Arg420GlnfsTer22	p.R420Qfs*22	ENST00000298552	NM_001162426.1	419	-/C	12/23	1	2	FACETS	0.576	0.461	0.708	0.576	0.461	0.708	SUBCLONAL	1	TRUE	1	0.28	2		362	347	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874013	151874013	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1248944002	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	65	564	2	ENST00000262189.6:c.8525del	p.Asn2842MetfsTer21	p.N2842Mfs*21	ENST00000262189	NM_170606.2	2842	aAt/at	38/59	1	2	FACETS	0.9	0.781	1	0.9	0.781	1	CLONAL	1	TRUE	1	0.28	2		566	516	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733413	85733414	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	65	905	0	ENST00000370580.1:c.598dup	p.Ala200GlyfsTer20	p.A200Gfs*20	ENST00000370580	NM_003921.4	200	gct/gGct	3/3	1	2	FACETS	0.638	0.552	0.731	0.638	0.552	0.731	SUBCLONAL	1	TRUE	1	0.28	2		905	728	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932274	36932275	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	47	822	0	ENST00000361632.4:c.2194dup	p.Asp732GlyfsTer40	p.D732Gfs*40	ENST00000361632		732	gac/gGac	16/16	1	2	FACETS	0.704	0.594	0.825	0.704	0.594	0.825	SUBCLONAL	1	TRUE	1	0.28	2		822	477	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0004768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	244	673	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.337888312244035	6	FACETS	0.99	0.937	1			1	CLONAL	5	TRUE	NA	0.337888312244035	6		673	489	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491373	2491373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766903122	NA	P-0004768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	48	425	0	ENST00000355716.4:c.416G>A	p.Arg139His	p.R139H	ENST00000355716	NM_003820.2	139	cGc/cAc	4/8	0.310579516969111	4	FACETS	0.941	0.797	1	0.47	0.398	0.549	CLONAL	1	TRUE	2	0.337888312244035	4		425	404	SUCCESS
BTK	695	MSKCC	GRCh37	X	100625055	100625055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	222	519	0	ENST00000308731.7:c.322G>A	p.Glu108Lys	p.E108K	ENST00000308731	NM_000061.2	108	Gaa/Aaa	5/19	0.315091471084988	5	FACETS	0.962	0.9	1	0.962	0.9	1	CLONAL	3	TRUE	2	0.337888312244035	5		519	686	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717731	89717732	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1114167661	NA	P-0004768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	95	273	0	ENST00000371953.3:c.757dup	p.Ile253AsnfsTer45	p.I253Nfs*45	ENST00000371953	NM_000314.4	252	-/A	7/9	0.337888312244035	2	FACETS	0.829	0.746	0.917	0.829	0.746	0.917	CLONAL	2	TRUE	0	0.337888312244035	2		273	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579329	7579330	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	137	379	0	ENST00000269305.4:c.357dup	p.Lys120GlnfsTer29	p.K120Qfs*29	ENST00000269305	NM_001126112.2	119	-/C	4/11	0.337888312244035	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	0	0.337888312244035	2		379	394	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004771-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	30	374	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.947	0.765	1	0.947	0.765	1	CLONAL	1	TRUE	1	0.231345696337579	2		374	274	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39613897	39613897	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004771-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	67	490	0	ENST00000262039.4:c.1815T>G	p.Ile605Met	p.I605M	ENST00000262039	NM_002647.2	605	atT/atG	16/25	0.231345696337579	3	FACETS	0.725	0.629	0.83			1	SUBCLONAL	1	TRUE	NA	0.231345696337579	3		490	891	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667635	29667638	+	frameshift_variant	Frame_Shift_Del	DEL	TAGA	TAGA	-	novel	NA	P-0004771-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	60	420	0	ENST00000356175.3:c.6974_6977del	p.Asp2325ValfsTer49	p.D2325Vfs*49	ENST00000356175	NM_000267.3	2324	tTAGAt/tt	46/57	1	2	FACETS	0.746	0.642	0.86	0.746	0.642	0.86	SUBCLONAL	1	TRUE	1	0.231345696337579	2		420	695	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591313	67591314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0004771-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	79	308	0	ENST00000274335.5:c.1814_1814+1dup		p.E604fs	ENST00000274335		604	gaa/gaAGa	13/15	1	2	FACETS	0.993	0.873	1	0.993	0.873	1	CLONAL	1	TRUE	1	0.231345696337579	2		308	688	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0004809-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	124	435	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.270528667206304	2		436	648	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0004809-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	144	384	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.765	0.699	0.834	1	0.988	1	SUBCLONAL	2	TRUE	1	0.270528667206304	2		384	696	SUCCESS
APC	324	MSKCC	GRCh37	5	112175621	112175621	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004809-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	199	494	0	ENST00000257430.4:c.4330C>T	p.Gln1444Ter	p.Q1444*	ENST00000257430	NM_000038.5	1444	Caa/Taa	16/16	1	2	FACETS	0.811	0.752	0.872	1	0.992	1	CLONAL	2	TRUE	1	0.270528667206304	2		494	907	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0004809-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	121	262	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	1	2	FACETS	0.812	0.736	0.891	1	0.987	1	CLONAL	2	TRUE	1	0.270528667206304	2		262	551	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416139	29416139	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004809-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	105	345	0	ENST00000389048.3:c.4814A>T	p.Glu1605Val	p.E1605V	ENST00000389048	NM_004304.4	1605	gAg/gTg	29/29	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.270528667206304	2		345	617	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713744	30713744	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs104893814	NA	P-0004809-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	289	263	2	ENST00000295754.5:c.1069G>T	p.Gly357Trp	p.G357W	ENST00000295754	NM_003242.5	357	Ggg/Tgg	4/7	0.270528667206304	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	3	TRUE	0	0.270528667206304	2		265	625	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136031	64136031	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004809-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	183	273	0	ENST00000334205.4:c.1292G>C	p.Arg431Pro	p.R431P	ENST00000334205	NM_003942.2	431	cGc/cCc	11/17	1	2	FACETS	0.936	0.866	1	1	0.993	1	CLONAL	2	TRUE	1	0.270528667206304	2		273	723	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029218	14029218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41557814	NA	P-0004809-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	198	530	0	ENST00000311895.7:c.1429C>T	p.Arg477Trp	p.R477W	ENST00000311895	NM_005236.2	477	Cgg/Tgg	8/11	1	2	FACETS	0.809	0.749	0.87	1	0.992	1	CLONAL	2	TRUE	1	0.270528667206304	2		530	905	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091862	29091862	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1060502716	NA	P-0004809-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	29	73	0	ENST00000328354.6:c.1096-1G>T		p.X366_splice	ENST00000328354	NM_007194.3	366			1	2	FACETS	0.94	0.77	1	1	0.957	1	CLONAL	2	TRUE	1	0.270528667206304	2		73	114	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410021	63410021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1258291174	NA	P-0004809-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	259	306	0	ENST00000330258.3:c.3146G>A	p.Arg1049Gln	p.R1049Q	ENST00000330258	NM_152424.3	1049	cGa/cAa	2/2	0.0780620298730925	2	FACETS	1	0.985	1			1	INDETERMINATE	3	TRUE	NA	0.270528667206304	2		306	574	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411828	63411837	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGATAAGA	CAGGATAAGA	-	novel	NA	P-0004809-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	338	405	0	ENST00000330258.3:c.1330_1339del	p.Ser444AlafsTer2	p.S444Afs*2	ENST00000330258	NM_152424.3	444	TCTTATCCTGgc/gc	2/2	0.0780620298730925	2	FACETS	0.919	0.876	0.961			1	INDETERMINATE	4	TRUE	NA	0.270528667206304	2		405	680	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272489	11272489	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004809-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	122	318	0	ENST00000361445.4:c.3441T>G	p.Asp1147Glu	p.D1147E	ENST00000361445	NM_004958.3	1147	gaT/gaG	23/58	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.270528667206304	2		318	643	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2137925	2137958	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCTGCAGTGCAGGAAAGGTAGGGCCGGGTGGGG	CCCTGCAGTGCAGGAAAGGTAGGGCCGGGTGGGG	-	rs137854209	NA	P-0004809-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	46	463	0	ENST00000219476.3:c.5068+27_5069-47del		p.X1690_splice	ENST00000219476	NM_000548.3	1690		39/42	1	2	FACETS	0.417	0.35	0.492	0.417	0.35	0.492	SUBCLONAL	1	TRUE	1	0.270528667206304	2		463	815	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120206	70120207	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0004809-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	193	351	0	ENST00000245479.2:c.1211_1212dup	p.Ser405ProfsTer66	p.S405Pfs*66	ENST00000245479	NM_000346.3	403	agc/agCCc	3/3	1	2	FACETS	0.868	0.804	0.934	1	0.992	1	CLONAL	2	TRUE	1	0.270528667206304	2		351	822	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0004849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	113	566	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	0.262595747746304	1	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	0	0.332425624433705	1		566	559	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470459	25470459	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0004849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	65	550	0	ENST00000264709.3:c.1014+1G>T		p.X338_splice	ENST00000264709	NM_175629.2	338			0.332425624433705	1	FACETS	0.644	0.559	0.736	0.644	0.559	0.736	SUBCLONAL	1	TRUE	0	0.332425624433705	1		550	506	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591247	67591247	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0004849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	110	529	0	ENST00000274335.5:c.1746-1G>A		p.X582_splice	ENST00000274335		582			0.278550443499525	1	FACETS	0.82	0.738	0.907	0.82	0.738	0.907	CLONAL	1	TRUE	0	0.332425624433705	1		529	673	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562675	29562679	+	frameshift_variant	Frame_Shift_Del	DEL	TACTC	TACTC	-	novel	NA	P-0004849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	96	650	0	ENST00000356175.3:c.3758_3762del	p.Leu1253ProfsTer9	p.L1253Pfs*9	ENST00000356175	NM_000267.3	1252	tTACTC/t	28/57	0.262595747746304	1	FACETS	0.727	0.649	0.811	0.727	0.649	0.811	SUBCLONAL	1	TRUE	0	0.332425624433705	1		650	662	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829753	76829756	+	frameshift_variant	Frame_Shift_Del	DEL	CTTC	CTTC	-	novel	NA	P-0004849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	128	410	0	ENST00000373344.5:c.6285_6288del	p.Lys2096SerfsTer12	p.K2096Sfs*12	ENST00000373344	NM_000489.3	2095	agGAAG/ag	28/35	1	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.332425624433705	1		410	507	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470463	25470464	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0004849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	66	568	0	ENST00000264709.3:c.1009_1010dup	p.Val338GlnfsTer8	p.V338Qfs*8	ENST00000264709	NM_175629.2	337	tca/tcTCa	8/23	0.332425624433705	1	FACETS	0.635	0.552	0.725	0.635	0.552	0.725	SUBCLONAL	1	TRUE	0	0.332425624433705	1		568	521	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954307	48954316	+	protein_altering_variant	In_Frame_Del	DEL	TCTGAATGAC	TCTGAATGAC	A	novel	NA	P-0004849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	80	350	0	ENST00000267163.4:c.1428_1437delinsA	p.Leu477_Asp479del	p.L477_D479del	ENST00000267163	NM_000321.2	476	ctTCTGAATGAC/ctA	16/27	0.278550443499525	1	FACETS	0.759	0.669	0.854	0.759	0.669	0.854	SUBCLONAL	1	TRUE	0	0.332425624433705	1		350	529	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0004866-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	60	314	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.20810537824666	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.20810537824666	1		314	410	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0004866-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	67	356	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.122210723549541	3	FACETS	1	0.97	1	0.714	0.621	0.813	INDETERMINATE	1	TRUE	1	0.20810537824666	3		356	498	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0004866-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	57	216	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	1	2	FACETS	0.904	0.781	1	1	0.976	1	CLONAL	2	TRUE	1	0.20810537824666	2		216	303	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28883065	28883065	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0004866-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	48	181	0	ENST00000282397.4:c.3636-1G>C		p.X1212_splice	ENST00000282397	NM_002019.4	1212			0.20810537824666	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.20810537824666	1		181	318	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572986	7572986	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004866-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	30	147	0	ENST00000269305.4:c.1123C>A	p.Gln375Lys	p.Q375K	ENST00000269305	NM_001126112.2	375	Cag/Aag	11/11	0.153000302864344	2	FACETS	1	0.892	1	0.579	0.469	0.703	CLONAL	1	TRUE	0	0.20810537824666	2		147	249	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	161	588	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.224446844779097	3	FACETS	0.91	0.834	0.989	0.91	0.834	0.989	CLONAL	2	TRUE	1	0.19	3		589	1020	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244361	46244361	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	80	426	0	ENST00000334344.6:c.2455C>T	p.Gln819Ter	p.Q819*	ENST00000334344	NM_152641.2	819	Caa/Taa	15/21	0.224446844779097	3	FACETS	0.941	0.826	1	0.47	0.413	0.533	CLONAL	1	TRUE	1	0.19	3		426	980	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190742103	190742103	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	90	375	1	ENST00000441310.2:c.2740G>T	p.Glu914Ter	p.E914*	ENST00000441310	NM_000534.4	914	Gag/Tag	13/13	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.19	2		376	904	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841892	151841892	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	90	488	0	ENST00000262189.6:c.14249A>G	p.Tyr4750Cys	p.Y4750C	ENST00000262189	NM_170606.2	4750	tAt/tGt	55/59	1	2	FACETS	0.83	0.734	0.933	0.83	0.734	0.933	CLONAL	1	TRUE	1	0.19	2		488	1141	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317907	8317907	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	107	497	1	ENST00000356435.5:c.5706G>T	p.Glu1902Asp	p.E1902D	ENST00000356435		1902	gaG/gaT	35/35	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.19	2		498	1002	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602328	10602328	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	80	557	0	ENST00000171111.5:c.1250G>T	p.Gly417Val	p.G417V	ENST00000171111	NM_203500.1	417	gGg/gTg	3/6	0.3	1	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	0	0.19	1		557	740	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132542	11132542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	38	563	0	ENST00000358026.2:c.2758G>A	p.Glu920Lys	p.E920K	ENST00000358026	NM_001128849.1	920	Gag/Aag	19/36	0.3	1	FACETS	0.478	0.393	0.572	0.478	0.393	0.572	SUBCLONAL	1	TRUE	0	0.19	1		563	758	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17949183	17949183	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	86	574	0	ENST00000458235.1:c.1458C>G	p.Ile486Met	p.I486M	ENST00000458235	NM_000215.3	486	atC/atG	11/24	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.19	2		574	844	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419835	41419835	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	43	414	0	ENST00000373198.4:c.486G>T	p.Gln162His	p.Q162H	ENST00000373198	NM_133170.3	162	caG/caT	3/32	1	2	FACETS	0.636	0.531	0.753	0.636	0.531	0.753	SUBCLONAL	1	TRUE	1	0.19	2		414	712	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041007	47041007	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	80	308	0	ENST00000377604.3:c.1537G>T	p.Glu513Ter	p.E513*	ENST00000377604	NM_001204468.1	513	Gag/Tag	14/24	1	1	FACETS	0.778	0.687	0.875	1	0.978	1	SUBCLONAL	2	TRUE	0	0.19	1		308	490	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207042	1207057	+	frameshift_variant	Frame_Shift_Del	DEL	AAGCTCATCGGCAAGT	AAGCTCATCGGCAAGT	-	novel	NA	P-0004875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	62	476	0	ENST00000326873.7:c.131_146del	p.Lys44ThrfsTer2	p.K44Tfs*2	ENST00000326873	NM_000455.4	44	AAGCTCATCGGCAAGTac/ac	1/10	0.3	1	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	0	0.19	1		476	585	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137528122	137528123	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	77	428	0	ENST00000367739.4:c.177dup	p.Thr60TyrfsTer10	p.T60Yfs*10	ENST00000367739	NM_000416.2	59	-/T	2/7	1	2	FACETS	0.866	0.758	0.982	0.866	0.758	0.982	CLONAL	1	TRUE	1	0.19	2		428	936	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244268	153244271	+	frameshift_variant	Frame_Shift_Del	DEL	AAAC	AAAC	-	novel	NA	P-0004875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	50	305	0	ENST00000281708.4:c.1886_1889del	p.Cys629TyrfsTer8	p.C629Yfs*8	ENST00000281708	NM_033632.3	629	tGTTTa/ta	12/12	1	2	FACETS	0.672	0.569	0.786	0.672	0.569	0.786	SUBCLONAL	1	TRUE	1	0.19	2		305	783	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577093	7577093	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882008	NA	P-0004903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	112	544	0	ENST00000269305.4:c.845G>C	p.Arg282Pro	p.R282P	ENST00000269305	NM_001126112.2	282	cGg/cCg	8/11	0.254326061649041	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.254326061649041	1		544	738	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717673	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GACGGGAAGACAAGTTCATGTACTTT	novel	NA	P-0004903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	52	412	0	ENST00000371953.3:c.700_725dup	p.Glu242AspfsTer23	p.E242Dfs*23	ENST00000371953	NM_000314.4	233	cga/cGACGGGAAGACAAGTTCATGTACTTTga	7/9	0.254326061649041	1	FACETS	0.577	0.49	0.671	0.577	0.49	0.671	SUBCLONAL	1	TRUE	0	0.254326061649041	1		412	619	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913237	NA	P-0004904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	60	183	0	ENST00000369535.4:c.35G>C	p.Gly12Ala	p.G12A	ENST00000369535	NM_002524.4	12	gGt/gCt	2/7	1	2	FACETS	0.921	0.799	1	0.921	0.799	1	CLONAL	1	TRUE	1	0.410881963165467	2		183	317	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0004904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	114	186	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.410881963165467	2	FACETS	0.974	0.891	1	0.974	0.891	1	CLONAL	2	TRUE	0	0.410881963165467	2		186	285	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695892	117695892	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	59	204	0	ENST00000369458.3:c.545C>A	p.Ala182Glu	p.A182E	ENST00000369458	NM_024626.3	182	gCa/gAa	4/6	1	2	FACETS	0.754	0.651	0.865	0.754	0.651	0.865	SUBCLONAL	1	TRUE	1	0.410881963165467	2		204	381	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575150	48575150	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	84	285	0	ENST00000342988.3:c.344G>C	p.Cys115Ser	p.C115S	ENST00000342988	NM_005359.5	115	tGt/tCt	3/12	0.402350225380883	1	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	0	0.410881963165467	1		285	317	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741973	40741973	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1323113005	NA	P-0004904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	146	286	0	ENST00000392038.2:c.999G>C	p.Trp333Cys	p.W333C	ENST00000392038	NM_001626.4	333	tgG/tgC	11/14	0.159429819324046	3	FACETS	1	0.968	1	0.562	0.513	0.613	INDETERMINATE	1	TRUE	1	0.410881963165467	3		286	762	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069382	30069382	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	202	319	1	ENST00000338641.4:c.1247C>A	p.Ala416Glu	p.A416E	ENST00000338641	NM_000268.3	416	gCg/gAg	12/16	1	2	FACETS	0.967	0.896	1	0.967	0.896	1	CLONAL	1	TRUE	1	0.410881963165467	2		320	1017	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202212	108202213	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATGTACCAATTGGCTGCTAGAATGGGGACCA	novel	NA	P-0004904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	74	213	0	ENST00000278616.4:c.7559_7589dup	p.Lys2530AsnfsTer7	p.K2530Nfs*7	ENST00000278616	NM_000051.3	2519	-/ATGTACCAATTGGCTGCTAGAATGGGGACCA	51/63	0.361114608666977	2	FACETS	1	0.96	1	0.6	0.53	0.674	CLONAL	1	TRUE	0	0.410881963165467	2		213	300	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160638	56160638	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004908-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	228	512	0	ENST00000399503.3:c.914del	p.Asn305ThrfsTer7	p.N305Tfs*7	ENST00000399503	NM_005921.1	304	acA/ac	4/20	0.361116498105749	5	FACETS	0.986	0.919	1	0.657	0.613	0.704	CLONAL	2	TRUE	2	0.361116498105749	5		512	987	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881002	37881003	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCTCCCCA	rs397516982	NA	P-0004908-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	322	658	0	ENST00000269571.5:c.2332_2340dup	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	-/GGCTCCCCA	20/27	0.232752260129509	5	FACETS	1	0.979	1	0.716	0.675	0.758	CLONAL	2	TRUE	2	0.361116498105749	5		658	1280	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120880	115120880	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs746244654	NA	P-0004908-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	157	355	0	ENST00000257566.3:c.126del	p.Ala43ArgfsTer2	p.A43Rfs*2	ENST00000257566	NM_016569.3	42	ccC/cc	1/8	0.232752260129509	5	FACETS	1	0.937	1	0.682	0.627	0.74	CLONAL	2	TRUE	2	0.361116498105749	5		355	655	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177598	56177620	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTATTGCAGATGAGGTGGAAA	GGCTATTGCAGATGAGGTGGAAA	-	novel	NA	P-0004908-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	233	455	0	ENST00000399503.3:c.2571_2593del	p.Met857IlefsTer39	p.M857Ifs*39	ENST00000399503	NM_005921.1	857	atGGCTATTGCAGATGAGGTGGAAAtt/attt	14/20	0.361116498105749	5	FACETS	1	0.983	1	0.765	0.715	0.817	CLONAL	2	TRUE	2	0.361116498105749	5		455	867	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs760043106	NA	P-0004912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	123	335	0	ENST00000269305.4:c.584T>A	p.Ile195Asn	p.I195N	ENST00000269305	NM_001126112.2	195	aTc/aAc	6/11	0.364344516459573	2	FACETS	0.763	0.696	0.832	0.763	0.696	0.832	SUBCLONAL	2	TRUE	0	0.402013853191603	2		335	401	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278049	18278049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	78	373	0	ENST00000222254.8:c.1669G>A	p.Asp557Asn	p.D557N	ENST00000222254	NM_005027.3	557	Gac/Aac	13/16	0.402013853191603	3	FACETS	0.713	0.626	0.805	0.356	0.313	0.403	SUBCLONAL	1	TRUE	1	0.402013853191603	3		373	654	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115914	8115915	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	96	226	0	ENST00000346208.3:c.1262dup	p.Met422AspfsTer85	p.M422Dfs*85	ENST00000346208		420	-/C	6/6	0.244246766144619	6	FACETS	0.822	0.735	0.914			1	CLONAL	2	TRUE	NA	0.402013853191603	6		226	524	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0004946-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	67	344	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.605	0.526	0.69	0.605	0.526	0.69	SUBCLONAL	1	TRUE	1	0.383973010025804	2		344	577	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913339	28913339	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004946-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	46	861	3	ENST00000282397.4:c.2454C>A	p.Ser818Arg	p.S818R	ENST00000282397	NM_002019.4	818	agC/agA	17/30	1	2	FACETS	0.342	0.287	0.403	0.342	0.287	0.403	SUBCLONAL	1	TRUE	1	0.383973010025804	2		864	701	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29563009	29563009	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004946-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	44	843	0	ENST00000356175.3:c.3944A>C	p.Gln1315Pro	p.Q1315P	ENST00000356175	NM_000267.3	1315	cAa/cCa	29/57	NA	2	FACETS	0.3	0.251	0.355			1	INDETERMINATE	1	TRUE	NA	0.383973010025804	2		843	763	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15809096	15809097	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004946-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	122	412	0	ENST00000307771.7:c.81_82insC	p.Lys28GlnfsTer27	p.K28Qfs*27	ENST00000307771	NM_005089.3	27	-/C	2/11	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.383973010025804	1		412	362	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0004950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	83	357	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.547	0.483	0.614	0.547	0.483	0.614	SUBCLONAL	1	TRUE	1	0.54908858056679	2		357	553	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10286275	10286275	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	85	481	0	ENST00000340748.4:c.541C>G	p.Gln181Glu	p.Q181E	ENST00000340748		181	Cag/Gag	6/40	1	2	FACETS	0.369	0.325	0.415	0.369	0.325	0.415	SUBCLONAL	1	TRUE	1	0.54908858056679	2		481	840	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179366	56179367	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	82	426	0	ENST00000399503.3:c.3680dup	p.Pro1228ThrfsTer11	p.P1228Tfs*11	ENST00000399503	NM_005921.1	1227	cta/cTta	15/20	1	2	FACETS	0.519	0.459	0.585	0.519	0.459	0.585	SUBCLONAL	1	TRUE	1	0.54908858056679	2		426	575	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842631	68842632	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	112	588	0	ENST00000261769.5:c.568dup	p.Tyr190LeufsTer9	p.Y190Lfs*9	ENST00000261769	NM_004360.3	189	-/T	5/16	0.345972760872854	1	FACETS	0.412	0.371	0.456	0.412	0.371	0.456	SUBCLONAL	1	TRUE	0	0.54908858056679	1		588	718	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	259	442	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.832	0.785	0.879	1	0.994	1	CLONAL	2	TRUE	1	0.494988232411823	2		444	629	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	136	208	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.924	0.843	1	0.924	0.843	1	CLONAL	1	TRUE	1	0.494988232411823	2		208	595	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	324	831	11	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.494988232411823	2	FACETS	0.947	0.893	1	0.473	0.446	0.501	CLONAL	1	TRUE	0	0.494988232411823	2		842	1383	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	157	498	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.864	0.793	0.938	0.864	0.793	0.938	CLONAL	1	TRUE	1	0.494988232411823	2		498	734	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	143	448	0	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.697	0.636	0.761	0.697	0.636	0.761	SUBCLONAL	1	TRUE	1	0.494988232411823	2		448	829	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	245	479	9	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.99	0.926	1	0.99	0.926	1	CLONAL	1	TRUE	1	0.494988232411823	2		488	1000	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	179	509	9	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.494988232411823	2		518	716	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032090	26032090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1329616402	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1377	452	1012	2	ENST00000244661.2:c.199C>T	p.Pro67Ser	p.P67S	ENST00000244661	NM_003537.3	67	Ccg/Tcg	1/1	1	2	FACETS	0.999	0.951	1	0.999	0.951	1	CLONAL	1	TRUE	1	0.494988232411823	2		1014	1829	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	201	244	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.494988232411823	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.494988232411823	2		244	384	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429978	78429978	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	126	318	1	ENST00000370768.2:c.901del	p.Ile301TyrfsTer22	p.I301Yfs*22	ENST00000370768	NM_003902.3	301	Ata/ta	11/20	1	2	FACETS	0.977	0.889	1	0.977	0.889	1	CLONAL	1	TRUE	1	0.494988232411823	2		319	521	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533939	63533940	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs771001164	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	98	249	0	ENST00000307078.5:c.1214_1215del	p.Glu405GlyfsTer56	p.E405Gfs*56	ENST00000307078	NM_004655.3	405	gAG/g	6/11	1	2	FACETS	0.844	0.757	0.936	0.844	0.757	0.936	CLONAL	1	TRUE	1	0.494988232411823	2		249	469	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913559	32913559	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359479	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	282	817	1	ENST00000380152.3:c.5073del	p.Lys1691AsnfsTer15	p.K1691Nfs*15	ENST00000380152		1689	gcA/gc	11/27	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.494988232411823	2		818	1067	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649922	88649922	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786201038	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	99	334	1	ENST00000372037.3:c.176del	p.Leu59Ter	p.L59*	ENST00000372037	NM_004329.2	57	ccT/cc	4/13	0.494988232411823	2	FACETS	0.821	0.736	0.911	0.411	0.368	0.456	CLONAL	1	TRUE	0	0.494988232411823	2		335	487	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347983	347983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760961378	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	244	474	3	ENST00000262320.3:c.1523del	p.Gly508ValfsTer197	p.G508Vfs*197	ENST00000262320	NM_003502.3	508	gGt/gt	6/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.494988232411823	2		477	963	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226589917	226589917	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	149	277	0	ENST00000366794.5:c.284C>T	p.Thr95Ile	p.T95I	ENST00000366794	NM_001618.3	95	aCa/aTa	2/23	1	2	FACETS	0.9	0.824	0.978	0.9	0.824	0.978	CLONAL	1	TRUE	1	0.494988232411823	2		277	669	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928424	69928424	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	221	405	0	ENST00000352241.4:c.244G>A	p.Ala82Thr	p.A82T	ENST00000352241	NM_198159.2	82	Gcg/Acg	2/10	1	2	FACETS	0.956	0.89	1	0.956	0.89	1	CLONAL	1	TRUE	1	0.494988232411823	2		405	934	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518911	187518911	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	245	565	0	ENST00000441802.2:c.12293G>T	p.Cys4098Phe	p.C4098F	ENST00000441802	NM_005245.3	4098	tGt/tTt	24/27	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.494988232411823	2		565	860	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203770	94203770	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	115	391	0	ENST00000323929.3:c.884A>G	p.Asn295Ser	p.N295S	ENST00000323929	NM_005591.3	295	aAt/aGt	9/20	1	2	FACETS	0.987	0.894	1	0.987	0.894	1	CLONAL	1	TRUE	1	0.494988232411823	2		391	471	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359330	118359330	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	143	297	2	ENST00000534358.1:c.4334T>C	p.Phe1445Ser	p.F1445S	ENST00000534358	NM_005933.3	1445	tTt/tCt	11/36	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.494988232411823	2		299	553	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495415	56495415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373454755	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	300	652	0	ENST00000267101.3:c.3605G>A	p.Arg1202Gln	p.R1202Q	ENST00000267101	NM_001982.3	1202	cGg/cAg	28/28	1	2	FACETS	0.999	0.941	1	0.999	0.941	1	CLONAL	1	TRUE	1	0.494988232411823	2		652	1213	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052624	42052624	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	454	831	0	ENST00000219905.7:c.7295A>C	p.Glu2432Ala	p.E2432A	ENST00000219905	NM_001164273.1	2432	gAg/gCg	20/24	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.494988232411823	2		831	1517	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354482	91354482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768010078	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	222	459	1	ENST00000355112.3:c.3922G>A	p.Gly1308Arg	p.G1308R	ENST00000355112	NM_000057.2	1308	Gga/Aga	21/22	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.494988232411823	2		460	863	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781302	3781302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781364836	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	353	589	0	ENST00000262367.5:c.5063C>T	p.Thr1688Met	p.T1688M	ENST00000262367	NM_004380.2	1688	aCg/aTg	30/31	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.494988232411823	2		589	1358	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108611	8108611	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	277	483	1	ENST00000585124.1:c.784C>T	p.Leu262Phe	p.L262F	ENST00000585124	NM_004217.3	262	Ctt/Ttt	8/9	1	2	FACETS	0.975	0.915	1	0.975	0.915	1	CLONAL	1	TRUE	1	0.494988232411823	2		484	1148	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492937	56492937	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	57	113	0	ENST00000407977.2:c.2T>C	p.Met1?	p.M1?	ENST00000407977		1	aTg/aCg	2/10	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.494988232411823	2		113	206	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11102000	11102000	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	192	348	1	ENST00000358026.2:c.1419+1G>A		p.X473_splice	ENST00000358026	NM_001128849.1	473			1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.494988232411823	2		349	722	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145645	11145645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	282	480	0	ENST00000358026.2:c.4007G>A	p.Arg1336His	p.R1336H	ENST00000358026	NM_001128849.1	1336	cGc/cAc	29/36	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.494988232411823	2		480	1048	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866321	42866321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766047137	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	171	335	0	ENST00000398585.3:c.311C>T	p.Thr104Met	p.T104M	ENST00000398585	NM_001135099.1	104	aCg/aTg	3/14	1	2	FACETS	0.973	0.898	1	0.973	0.898	1	CLONAL	1	TRUE	1	0.494988232411823	2		335	710	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513598	41513598	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	352	567	1	ENST00000263253.7:c.502G>T	p.Gly168Trp	p.G168W	ENST00000263253	NM_001429.3	168	Ggg/Tgg	2/31	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.494988232411823	2		568	1256	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041044	29041047	+	frameshift_variant	Frame_Shift_Del	DEL	AATA	AATA	-	novel	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	106	313	0	ENST00000282397.4:c.381_384del	p.Phe127LeufsTer9	p.F127Lfs*9	ENST00000282397	NM_002019.4	127	ttTATT/tt	3/30	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.494988232411823	2		313	428	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851848	134851848	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	191	477	0	ENST00000398015.3:c.1259del	p.Pro420HisfsTer28	p.P420Hfs*28	ENST00000398015	NM_004441.4	418	ttC/tt	5/16	1	2	FACETS	0.86	0.796	0.927	0.86	0.796	0.927	CLONAL	1	TRUE	1	0.494988232411823	2		477	897	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259454	11259454	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	186	433	0	ENST00000361445.4:c.4114del	p.Leu1372CysfsTer3	p.L1372Cfs*3	ENST00000361445	NM_004958.3	1372	Ctg/tg	28/58	1	2	FACETS	0.9	0.832	0.97	0.9	0.832	0.97	CLONAL	1	TRUE	1	0.494988232411823	2		433	835	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268793	98268793	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1554708751	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	315	529	1	ENST00000331920.6:c.290del	p.Asn97ThrfsTer20	p.N97Tfs*20	ENST00000331920	NM_000264.3	97	aAc/ac	2/24	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.494988232411823	2		530	1211	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100405	157100406	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGT	novel	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	44	101	0	ENST00000346085.5:c.1344_1345insTCG	p.Pro448_Pro449insSer	p.P448_P449insS	ENST00000346085	NM_020732.3	448	ccg/cCGTcg	1/20	1	2	FACETS	0.78	0.66	0.909	0.78	0.66	0.909	CLONAL	1	TRUE	1	0.494988232411823	2		101	228	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831391	72831392	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGC	novel	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	173	557	0	ENST00000268489.5:c.5187_5189dup	p.Gln1741dup	p.Q1741dup	ENST00000268489	NM_006885.3	1741	caa/caGCAa	9/10	1	2	FACETS	0.691	0.636	0.749	0.691	0.636	0.749	SUBCLONAL	1	TRUE	1	0.494988232411823	2		557	1011	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132494	11132494	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	245	500	0	ENST00000358026.2:c.2713del	p.Arg905AlafsTer5	p.R905Afs*5	ENST00000358026	NM_001128849.1	904	Ccc/cc	19/36	1	2	FACETS	0.878	0.82	0.937	0.878	0.82	0.937	CLONAL	1	TRUE	1	0.494988232411823	2		500	1128	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132896	64132896	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	325	621	3	ENST00000334205.4:c.1034del	p.Pro345LeufsTer30	p.P345Lfs*30	ENST00000334205	NM_003942.2	344	Ccc/cc	9/17	1	2	FACETS	0.993	0.937	1	0.993	0.937	1	CLONAL	1	TRUE	1	0.494988232411823	2		624	1322	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456497	32456497	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	24	54	0	ENST00000332351.3:c.395del	p.Pro132ArgfsTer26	p.P132Rfs*26	ENST00000332351	NM_024426.4	132	cCg/cg	1/10	1	2	FACETS	0.622	0.492	0.768	0.622	0.492	0.768	SUBCLONAL	1	TRUE	1	0.494988232411823	2		54	156	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671478	30671478	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	317	552	0	ENST00000376406.3:c.5482del	p.Gln1828LysfsTer10	p.Q1828Kfs*10	ENST00000376406	NM_014641.2	1828	Caa/aa	10/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.494988232411823	2		552	1194	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139625	202139626	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	526	509	0	ENST00000358485.4:c.790dup	p.Val264GlyfsTer13	p.V264Gfs*13	ENST00000358485	NM_001080125.1	262	-/G	6/9	0.494988232411823	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.494988232411823	2		509	1047	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953630	38953630	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	59	266	0	ENST00000357387.3:c.2723A>G	p.Asn908Ser	p.N908S	ENST00000357387	NM_152756.3	908	aAt/aGt	28/38	1	2	FACETS	0.637	0.551	0.731	0.637	0.551	0.731	SUBCLONAL	1	TRUE	1	0.494988232411823	2		266	374	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730095	41730095	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1353	300	850	0	ENST00000242208.4:c.434G>A	p.Ser145Asn	p.S145N	ENST00000242208	NM_002192.2	145	aGt/aAt	3/3	1	2	FACETS	0.733	0.688	0.78	0.733	0.688	0.78	SUBCLONAL	1	TRUE	1	0.494988232411823	2		850	1653	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467765	50467765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770131976	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	127	444	0	ENST00000331340.3:c.1000C>T	p.Pro334Ser	p.P334S	ENST00000331340	NM_006060.4	334	Ccc/Tcc	8/8	1	2	FACETS	0.627	0.567	0.689	0.627	0.567	0.689	SUBCLONAL	1	TRUE	1	0.494988232411823	2		444	819	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456645	32456645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1410971862	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	66	127	0	ENST00000332351.3:c.247G>A	p.Val83Ile	p.V83I	ENST00000332351	NM_024426.4	83	Gtc/Atc	1/10	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.494988232411823	2		127	246	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714409	117714409	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	129	480	1	ENST00000368508.3:c.1240del	p.Ile414LeufsTer14	p.I414Lfs*14	ENST00000368508	NM_002944.2	414	Att/tt	11/43	1	2	FACETS	0.747	0.678	0.819	0.747	0.678	0.819	SUBCLONAL	1	TRUE	1	0.494988232411823	2		481	698	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660808	227660810	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	rs747646240	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	254	342	9	ENST00000305123.5:c.2645_2647del	p.Gln882del	p.Q882del	ENST00000305123	NM_005544.2	882	cAGCcc/ccc	1/2	0.494988232411823	2	FACETS	0.775	0.73	0.821	0.775	0.73	0.821	SUBCLONAL	2	TRUE	0	0.494988232411823	2		351	662	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45396914	45396915	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004954-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	95	310	0	ENST00000262160.6:c.257dup	p.Leu87ThrfsTer20	p.L87Tfs*20	ENST00000262160	NM_005901.5	86	gga/ggGa	3/11	1	2	FACETS	0.806	0.721	0.896	0.806	0.721	0.896	CLONAL	1	TRUE	1	0.494988232411823	2		310	476	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004957-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	356	588	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.425089590840671	3	FACETS	0.874	0.84	0.909			1	CLONAL	3	TRUE	NA	0.610918655918142	3		589	580	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0004957-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	145	214	2	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	0.54553637606158	5	FACETS	1	0.977	1	0.402	0.367	0.439	CLONAL	1	TRUE	2	0.610918655918142	5		216	754	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0004957-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	572	609	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.569734065481759	2	FACETS	0.933	0.903	0.964	0.933	0.903	0.964	CLONAL	2	TRUE	0	0.610918655918142	2		610	1003	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0004957-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	307	552	1	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.425089590840671	3	FACETS	0.782	0.74	0.825			1	SUBCLONAL	2	TRUE	NA	0.610918655918142	3		553	839	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073717	8073717	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004957-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	896	704	0	ENST00000377482.5:c.942C>A	p.Asp314Glu	p.D314E	ENST00000377482	NM_018948.3	314	gaC/gaA	4/4	0.610918655918142	3	FACETS	0.985	0.956	1	0.985	0.956	1	CLONAL	2	TRUE	1	0.610918655918142	3		704	1943	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832038	72832038	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004957-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1355	381	681	0	ENST00000268489.5:c.4543G>C	p.Glu1515Gln	p.E1515Q	ENST00000268489	NM_006885.3	1515	Gaa/Caa	9/10	0.610918655918142	3	FACETS	0.938	0.888	0.989	0.469	0.444	0.495	CLONAL	1	TRUE	1	0.610918655918142	3		681	1736	SUCCESS
APC	324	MSKCC	GRCh37	5	112174000	112174000	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004957-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	114	340	0	ENST00000257430.4:c.2709del	p.Asp903GlufsTer13	p.D903Efs*13	ENST00000257430	NM_000038.5	903	gaC/ga	16/16	0.425089590840671	3	FACETS	0.811	0.732	0.894			1	CLONAL	1	TRUE	NA	0.610918655918142	3		340	601	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0004977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	45	340	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.264353505824912	3	FACETS	0.754	0.634	0.888	0.377	0.317	0.444	SUBCLONAL	1	TRUE	1	0.264353505824912	3		340	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0004977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	176	360	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.249278701905713	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	0	0.264353505824912	3		361	459	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167577	NA	P-0004977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	103	246	0	ENST00000257430.4:c.4463del	p.Leu1488TyrfsTer19	p.L1488Yfs*19	ENST00000257430	NM_000038.5	1487	acT/ac	16/16	0.264353505824912	3	FACETS	0.893	0.803	0.988	0.893	0.803	0.988	CLONAL	2	TRUE	1	0.264353505824912	3		246	494	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180049782	180049782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1454135156	NA	P-0004977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	72	439	0	ENST00000261937.6:c.1606G>A	p.Val536Ile	p.V536I	ENST00000261937	NM_182925.4	536	Gtc/Atc	12/30	0.264353505824912	3	FACETS	0.839	0.732	0.954	0.42	0.366	0.477	CLONAL	1	TRUE	1	0.264353505824912	3		439	735	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485774	8485774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767662106	NA	P-0004977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	110	260	0	ENST00000356435.5:c.3043C>T	p.Pro1015Ser	p.P1015S	ENST00000356435		1015	Cct/Tct	17/35	0.264353505824912	3	FACETS	0.822	0.741	0.908	0.822	0.741	0.908	CLONAL	2	TRUE	1	0.264353505824912	3		260	573	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298024	15298024	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	92	387	0	ENST00000263388.2:c.1732C>A	p.Arg578Ser	p.R578S	ENST00000263388	NM_000435.2	578	Cgc/Agc	11/33	0.24721475340651	4	FACETS	1	0.948	1	0.372	0.33	0.417	CLONAL	1	TRUE	1	0.264353505824912	4		387	788	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15827437	15827437	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	46	175	0	ENST00000307771.7:c.553G>T	p.Asp185Tyr	p.D185Y	ENST00000307771	NM_005089.3	185	Gat/Tat	7/11	0.264353505824912	2	FACETS	1	0.913	1			1	CLONAL	1	TRUE	NA	0.264353505824912	2		175	311	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937705	76937705	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	119	187	0	ENST00000373344.5:c.3043G>C	p.Gly1015Arg	p.G1015R	ENST00000373344	NM_000489.3	1015	Ggc/Cgc	9/35	0.264353505824912	2	FACETS	0.857	0.783	0.934			1	CLONAL	3	TRUE	NA	0.264353505824912	2		187	350	SUCCESS
APC	324	MSKCC	GRCh37	5	112173689	112173690	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	52	251	0	ENST00000257430.4:c.2403dup	p.Asp802Ter	p.D802*	ENST00000257430	NM_000038.5	800	gtt/gTtt	16/16	0.264353505824912	3	FACETS	0.828	0.705	0.963	0.414	0.352	0.482	CLONAL	1	TRUE	1	0.264353505824912	3		251	538	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	80	673	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	0.691374049591555	2		673	229	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	81	301	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.691374049591555	1	FACETS	0.369	0.326	0.414	0.369	0.326	0.414	SUBCLONAL	1	TRUE	0	0.691374049591555	1		301	416	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055756	152055756	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1283285486	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	22	232	1	ENST00000262189.6:c.166C>T	p.Arg56Ter	p.R56*	ENST00000262189	NM_170606.2	56	Cga/Tga	2/59	1	2	FACETS	0.161	0.124	0.204	0.161	0.124	0.204	SUBCLONAL	1	TRUE	1	0.691374049591555	2		233	395	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192065	108192065	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1317619286	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	141	330	0	ENST00000278616.4:c.6490G>C	p.Glu2164Gln	p.E2164Q	ENST00000278616	NM_000051.3	2164	Gag/Cag	45/63	1	2	FACETS	0.666	0.609	0.726	0.666	0.609	0.726	SUBCLONAL	1	TRUE	1	0.691374049591555	2		330	612	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127693	47127693	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	40	263	0	ENST00000409792.3:c.5389C>T	p.Gln1797Ter	p.Q1797*	ENST00000409792	NM_014159.6	1797	Cag/Tag	11/21	1	2	FACETS	0.216	0.179	0.257	0.216	0.179	0.257	SUBCLONAL	1	TRUE	1	0.691374049591555	2		263	536	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317160	11317160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	154	416	0	ENST00000361445.4:c.334C>T	p.Arg112Trp	p.R112W	ENST00000361445	NM_004958.3	112	Cgg/Tgg	4/58	1	2	FACETS	0.605	0.555	0.658	0.605	0.555	0.658	SUBCLONAL	1	TRUE	1	0.691374049591555	2		416	736	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256933	16256933	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	155	363	0	ENST00000375759.3:c.4198G>T	p.Glu1400Ter	p.E1400*	ENST00000375759	NM_015001.2	1400	Gaa/Taa	11/15	1	2	FACETS	0.707	0.65	0.767	0.707	0.65	0.767	SUBCLONAL	1	TRUE	1	0.691374049591555	2		363	634	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257290	16257290	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	140	355	0	ENST00000375759.3:c.4555G>A	p.Glu1519Lys	p.E1519K	ENST00000375759	NM_015001.2	1519	Gag/Aag	11/15	1	2	FACETS	0.672	0.614	0.732	0.672	0.614	0.732	SUBCLONAL	1	TRUE	1	0.691374049591555	2		355	603	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120469217	120469217	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	206	304	0	ENST00000256646.2:c.3910T>C	p.Phe1304Leu	p.F1304L	ENST00000256646	NM_024408.3	1304	Ttc/Ctc	24/34	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.691374049591555	2		304	581	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251769	212251769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	45	252	0	ENST00000342788.4:c.3290C>T	p.Ala1097Val	p.A1097V	ENST00000342788	NM_005235.2	1097	gCt/gTt	27/28	1	2	FACETS	0.213	0.178	0.251	0.213	0.178	0.251	SUBCLONAL	1	TRUE	1	0.691374049591555	2		252	612	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626123	12626123	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs80338797	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	138	258	0	ENST00000251849.4:c.1837C>G	p.Leu613Val	p.L613V	ENST00000251849	NM_002880.3	613	Cta/Gta	17/17	1	2	FACETS	0.731	0.669	0.796	0.731	0.669	0.796	SUBCLONAL	1	TRUE	1	0.691374049591555	2		258	546	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12632338	12632338	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	145	375	0	ENST00000251849.4:c.1329C>G	p.Phe443Leu	p.F443L	ENST00000251849	NM_002880.3	443	ttC/ttG	12/17	1	2	FACETS	0.64	0.586	0.697	0.64	0.586	0.697	SUBCLONAL	1	TRUE	1	0.691374049591555	2		375	655	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098670	47098670	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	203	405	0	ENST00000409792.3:c.6604C>A	p.Pro2202Thr	p.P2202T	ENST00000409792	NM_014159.6	2202	Cct/Act	15/21	1	2	FACETS	0.761	0.707	0.816	0.761	0.707	0.816	SUBCLONAL	1	TRUE	1	0.691374049591555	2		405	772	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668771	52668771	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751885636	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	87	314	0	ENST00000394830.3:c.1148C>T	p.Ser383Leu	p.S383L	ENST00000394830	NM_018313.4	383	tCa/tTa	12/30	1	2	FACETS	0.352	0.312	0.396	0.352	0.312	0.396	SUBCLONAL	1	TRUE	1	0.691374049591555	2		314	714	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69988316	69988316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747126448	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	136	205	0	ENST00000394351.3:c.329G>A	p.Arg110Gln	p.R110Q	ENST00000394351	NM_000248.3	110	cGa/cAa	3/9	1	2	FACETS	0.765	0.7	0.833	0.765	0.7	0.833	SUBCLONAL	1	TRUE	1	0.691374049591555	2		205	514	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021828	71021828	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	31	214	0	ENST00000318789.4:c.1531-1G>C		p.X511_splice	ENST00000318789	NM_032682.5	511			1	2	FACETS	0.224	0.181	0.272	0.224	0.181	0.272	SUBCLONAL	1	TRUE	1	0.691374049591555	2		214	401	SUCCESS
ATR	545	MSKCC	GRCh37	3	142168330	142168330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	30	243	0	ENST00000350721.4:c.7876G>A	p.Glu2626Lys	p.E2626K	ENST00000350721	NM_001184.3	2626	Gaa/Aaa	47/47	1	2	FACETS	0.161	0.129	0.197	0.161	0.129	0.197	SUBCLONAL	1	TRUE	1	0.691374049591555	2		243	540	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612113	189612113	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	150	330	0	ENST00000264731.3:c.1865G>T	p.Ser622Ile	p.S622I	ENST00000264731	NM_003722.4	622	aGt/aTt	14/14	1	2	FACETS	0.603	0.552	0.656	0.603	0.552	0.656	SUBCLONAL	1	TRUE	1	0.691374049591555	2		330	720	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253817	153253817	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	32	254	0	ENST00000281708.4:c.916C>A	p.Gln306Lys	p.Q306K	ENST00000281708	NM_033632.3	306	Cag/Aag	6/12	1	2	FACETS	0.234	0.189	0.284	0.234	0.189	0.284	SUBCLONAL	1	TRUE	1	0.691374049591555	2		254	396	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541712	187541712	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	147	345	0	ENST00000441802.2:c.6028G>A	p.Glu2010Lys	p.E2010K	ENST00000441802	NM_005245.3	2010	Gag/Aag	10/27	1	2	FACETS	0.676	0.619	0.735	0.676	0.619	0.735	SUBCLONAL	1	TRUE	1	0.691374049591555	2		345	629	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149450135	149450135	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	145	385	0	ENST00000286301.3:c.1083-1G>A		p.X361_splice	ENST00000286301	NM_005211.3	361			0.538146269203919	4	FACETS	0.816	0.745	0.891	0.272	0.248	0.297	CLONAL	1	TRUE	1	0.691374049591555	4		385	869	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497266	149497266	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	157	428	0	ENST00000261799.4:c.3052G>T	p.Asp1018Tyr	p.D1018Y	ENST00000261799	NM_002609.3	1018	Gac/Tac	22/23	0.538146269203919	4	FACETS	0.743	0.68	0.809	0.248	0.226	0.27	SUBCLONAL	1	TRUE	1	0.691374049591555	4		428	1034	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522416	176522416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519792	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	136	311	0	ENST00000292408.4:c.1605C>A	p.Asn535Lys	p.N535K	ENST00000292408	NM_213647.1	535	aaC/aaA	12/18	0.538146269203919	4	FACETS	0.709	0.644	0.778	0.236	0.214	0.26	SUBCLONAL	1	TRUE	1	0.691374049591555	4		311	938	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032031	26032031	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1240	116	657	0	ENST00000244661.2:c.258G>C	p.Gln86His	p.Q86H	ENST00000244661	NM_003537.3	86	caG/caC	1/1	0.227692869764989	5	FACETS	0.504	0.453	0.559	0.168	0.151	0.187	INDETERMINATE	1	TRUE	2	0.691374049591555	5		657	1356	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056021	26056021	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs987043105	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	47	155	0	ENST00000343677.2:c.636G>C	p.Lys212Asn	p.K212N	ENST00000343677	NM_005319.3	212	aaG/aaC	1/1	0.227692869764989	5	FACETS	0.674	0.57	0.788	0.225	0.19	0.263	INDETERMINATE	1	TRUE	2	0.691374049591555	5		155	411	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185020	32185020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1438542721	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	56	363	0	ENST00000375023.3:c.1648G>A	p.Glu550Lys	p.E550K	ENST00000375023	NM_004557.3	550	Gag/Aag	10/30	0.227692869764989	5	FACETS	0.371	0.316	0.43	0.124	0.105	0.144	INDETERMINATE	1	TRUE	2	0.691374049591555	5		363	890	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004877	150004877	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	136	318	0	ENST00000253339.5:c.1348G>A	p.Glu450Lys	p.E450K	ENST00000253339		450	Gaa/Aaa	3/7	0.691374049591555	1	FACETS	0.523	0.479	0.569	0.523	0.479	0.569	SUBCLONAL	1	TRUE	0	0.691374049591555	1		318	492	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90947841	90947841	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	27	218	0	ENST00000265433.3:c.2235-1G>A		p.X745_splice	ENST00000265433	NM_002485.4	745			1	2	FACETS	0.18	0.143	0.223	0.18	0.143	0.223	SUBCLONAL	1	TRUE	1	0.691374049591555	2		218	434	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739635	145739635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	91	421	0	ENST00000428558.2:c.1816G>A	p.Glu606Lys	p.E606K	ENST00000428558	NM_004260.3	606	Gag/Aag	11/22	1	2	FACETS	0.406	0.36	0.454	0.406	0.36	0.454	SUBCLONAL	1	TRUE	1	0.691374049591555	2		421	649	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891647	28891647	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	191	446	0	ENST00000282397.4:c.3374C>G	p.Ser1125Cys	p.S1125C	ENST00000282397	NM_002019.4	1125	tCt/tGt	25/30	0.691374049591555	1	FACETS	0.719	0.67	0.768	0.719	0.67	0.768	SUBCLONAL	1	TRUE	0	0.691374049591555	1		446	503	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256945	41256945	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs80357350	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	41	266	0	ENST00000357654.3:c.241C>G	p.Gln81Glu	p.Q81E	ENST00000357654	NM_007294.3	81	Caa/Gaa	5/23	NA	2	FACETS	0.225	0.187	0.267			1	INDETERMINATE	1	TRUE	NA	0.691374049591555	2		266	527	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696716	47696716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	134	312	0	ENST00000347630.2:c.232G>A	p.Glu78Lys	p.E78K	ENST00000347630	NM_001007230.1	78	Gaa/Aaa	5/11	0.691374049591555	3	FACETS	0.651	0.592	0.714	0.326	0.296	0.357	SUBCLONAL	1	TRUE	1	0.691374049591555	3		312	801	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117320	7117320	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559399455	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	60	407	0	ENST00000302850.5:c.3896C>T	p.Pro1299Leu	p.P1299L	ENST00000302850	NM_000208.2	1299	cCa/cTa	22/22	1	2	FACETS	0.231	0.199	0.267	0.231	0.199	0.267	SUBCLONAL	1	TRUE	1	0.691374049591555	2		407	750	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872221	45872221	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	82	345	0	ENST00000391945.4:c.213C>G	p.Ile71Met	p.I71M	ENST00000391945	NM_000400.3	71	atC/atG	4/23	1	2	FACETS	0.372	0.328	0.42	0.372	0.328	0.42	SUBCLONAL	1	TRUE	1	0.691374049591555	2		345	637	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016191	31016191	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	70	335	0	ENST00000375687.4:c.437C>A	p.Ser146Tyr	p.S146Y	ENST00000375687	NM_015338.5	146	tCc/tAc	6/13	0.530099403411068	4	FACETS	0.361	0.314	0.413	0.12	0.104	0.138	SUBCLONAL	1	TRUE	1	0.691374049591555	4		335	948	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750725	39750725	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	106	163	0	ENST00000361337.2:c.2125G>C	p.Glu709Gln	p.E709Q	ENST00000361337	NM_003286.2	709	Gag/Cag	20/21	0.530099403411068	4	FACETS	1	0.908	1	0.336	0.302	0.372	CLONAL	1	TRUE	1	0.691374049591555	4		163	514	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39772526	39772526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	44	307	0	ENST00000288319.7:c.715G>A	p.Glu239Lys	p.E239K	ENST00000288319	NM_182918.3	239	Gaa/Aaa	6/10	1	2	FACETS	0.203	0.17	0.24	0.203	0.17	0.24	SUBCLONAL	1	TRUE	1	0.691374049591555	2		307	626	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922160	39922160	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	70	564	0	ENST00000378444.4:c.4012G>C	p.Glu1338Gln	p.E1338Q	ENST00000378444	NM_001123385.1	1338	Gaa/Caa	9/15	0.691374049591555	3	FACETS	0.228	0.198	0.261	0.114	0.099	0.131	SUBCLONAL	1	TRUE	1	0.691374049591555	3		564	1195	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045016	47045016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556782040	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	169	441	0	ENST00000377604.3:c.2342C>T	p.Ser781Leu	p.S781L	ENST00000377604	NM_001204468.1	781	tCa/tTa	20/24	0.691374049591555	3	FACETS	0.689	0.633	0.747	0.344	0.316	0.374	SUBCLONAL	1	TRUE	1	0.691374049591555	3		441	955	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650729	48650729	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	242	466	0	ENST00000376670.3:c.599-1G>C		p.X200_splice	ENST00000376670	NM_002049.3	200			0.691374049591555	3	FACETS	0.945	0.883	1	0.472	0.441	0.505	CLONAL	1	TRUE	1	0.691374049591555	3		466	997	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239915	53239915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	98	420	0	ENST00000375401.3:c.1526C>T	p.Ser509Leu	p.S509L	ENST00000375401	NM_004187.3	509	tCa/tTa	11/26	0.691374049591555	3	FACETS	0.327	0.29	0.366	0.163	0.145	0.183	SUBCLONAL	1	TRUE	1	0.691374049591555	3		420	1167	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352372	70352372	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	190	479	1	ENST00000374080.3:c.4399C>T	p.Arg1467Ter	p.R1467*	ENST00000374080		1467	Cga/Tga	31/45	0.691374049591555	3	FACETS	0.704	0.65	0.76	0.352	0.325	0.38	SUBCLONAL	1	TRUE	1	0.691374049591555	3		480	1051	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368488	225368489	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	101	227	0	ENST00000264414.4:c.1257dup	p.Arg420Ter	p.R420*	ENST00000264414	NM_003590.4	419	-/T	9/16	1	2	FACETS	0.652	0.586	0.722	0.652	0.586	0.722	SUBCLONAL	1	TRUE	1	0.691374049591555	2		227	448	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862100	68862100	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	218	356	0	ENST00000261769.5:c.2190del	p.Leu731PhefsTer39	p.L731Ffs*39	ENST00000261769	NM_004360.3	730	Ttt/tt	14/16	0.691374049591555	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.691374049591555	1		356	386	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0005024-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	315	379	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	0.47281737247522	2		379	1251	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207090	1207091	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs876661012	NA	P-0005024-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	748	581	1	ENST00000326873.7:c.179dup	p.Tyr60Ter	p.Y60*	ENST00000326873	NM_000455.4	60	tac/tAac	1/10	0.47281737247522	2	FACETS	0.965	0.934	0.996	0.965	0.934	0.996	CLONAL	2	TRUE	0	0.47281737247522	2		582	1640	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395910	395910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755460615	NA	P-0005024-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	300	526	0	ENST00000380956.4:c.467C>T	p.Thr156Met	p.T156M	ENST00000380956	NM_001195286.1	156	aCg/aTg	4/9	0.153677572873311	4	FACETS	0.76	0.715	0.806	0.76	0.715	0.806	INDETERMINATE	2	TRUE	2	0.47281737247522	4		526	1230	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316069	11316069	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005024-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	227	335	0	ENST00000361445.4:c.685C>T	p.Gln229Ter	p.Q229*	ENST00000361445	NM_004958.3	229	Cag/Tag	5/58	0.350951550200282	1	FACETS	0.8	0.746	0.855	0.8	0.746	0.855	SUBCLONAL	1	TRUE	0	0.47281737247522	1		335	917	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316081	11316081	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005024-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	247	366	0	ENST00000361445.4:c.673C>G	p.Pro225Ala	p.P225A	ENST00000361445	NM_004958.3	225	Ccg/Gcg	5/58	0.350951550200282	1	FACETS	0.818	0.766	0.872	0.818	0.766	0.872	CLONAL	1	TRUE	0	0.47281737247522	1		366	975	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572201	64572201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301120298	NA	P-0005024-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	170	441	2	ENST00000312049.6:c.1438C>T	p.Arg480Trp	p.R480W	ENST00000312049	NM_130799.2	480	Cgg/Tgg	10/10	1	2	FACETS	0.522	0.479	0.568	0.522	0.479	0.568	SUBCLONAL	1	TRUE	1	0.47281737247522	2		443	1377	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610211	10610211	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005024-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	776	628	0	ENST00000171111.5:c.499G>T	p.Val167Phe	p.V167F	ENST00000171111	NM_203500.1	167	Gtt/Ttt	2/6	0.47281737247522	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.47281737247522	2		628	1573	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041201	47041202	+	frameshift_variant	Frame_Shift_Ins	INS	CC	CC	TAT	novel	NA	P-0005024-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	376	325	0	ENST00000377604.3:c.1629_1630delinsTAT	p.His544IlefsTer3	p.H544Ifs*3	ENST00000377604	NM_001204468.1	543	acCCat/acTATat	15/24	1	1	FACETS	0.765	0.731	0.799	1	0.996	1	SUBCLONAL	2	TRUE	0	0.47281737247522	1		325	794	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0005036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	211	280	1	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.697120925196569	2		281	544	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859305	151859305	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0005036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	336	497	0	ENST00000262189.6:c.11357C>G	p.Ser3786Ter	p.S3786*	ENST00000262189	NM_170606.2	3786	tCa/tGa	43/59	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.697120925196569	2		497	907	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991331	72991331	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1250	229	750	0	ENST00000268489.5:c.2714C>G	p.Ala905Gly	p.A905G	ENST00000268489	NM_006885.3	905	gCt/gGt	2/10	0.680210424413627	2	FACETS	0.444	0.413	0.477	0.222	0.206	0.239	SUBCLONAL	1	TRUE	0	0.697120925196569	2		750	1479	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160677	56160678	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	410	610	0	ENST00000399503.3:c.953dup	p.Leu318PhefsTer8	p.L318Ffs*8	ENST00000399503	NM_005921.1	317	-/T	4/20	1	2	FACETS	0.995	0.948	1	0.995	0.948	1	CLONAL	1	TRUE	1	0.697120925196569	2		610	1182	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152576	56152577	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	279	503	0	ENST00000399503.3:c.633+1dup		p.V211fs	ENST00000399503	NM_005921.1	211	gtg/gtGg	2/20	1	2	FACETS	0.932	0.878	0.987	0.932	0.878	0.987	CLONAL	1	TRUE	1	0.697120925196569	2		503	859	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0005063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	2116	605	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	0.419923650994144	19	FACETS	1	0.993	1	0.951	0.939	0.964	CLONAL	16	TRUE	2	0.419923650994144	19		605	2847	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028660	12028660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	54	651	0	ENST00000353533.5:c.863C>T	p.Ser288Phe	p.S288F	ENST00000353533	NM_003010.3	288	tCt/tTt	8/11	0.262715175625866	1	FACETS	0.264	0.224	0.307	0.264	0.224	0.307	SUBCLONAL	1	TRUE	0	0.419923650994144	1		651	771	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574022	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	145	790	2	ENST00000269305.4:c.1005dup	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	335	-/T	10/11	0.262715175625866	1	FACETS	0.759	0.694	0.827	0.759	0.694	0.827	SUBCLONAL	1	TRUE	0	0.419923650994144	1		792	719	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728527	190728527	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	81	462	0	ENST00000441310.2:c.1915A>T	p.Ile639Phe	p.I639F	ENST00000441310	NM_000534.4	639	Att/Ttt	10/13	1	2	FACETS	0.595	0.524	0.672	0.595	0.524	0.672	SUBCLONAL	1	TRUE	1	0.333509225598849	2		462	816	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665359	138665359	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	160	531	0	ENST00000330315.3:c.206A>C	p.Glu69Ala	p.E69A	ENST00000330315	NM_023067.3	69	gAg/gCg	1/1	1	2	FACETS	0.839	0.768	0.914	0.839	0.768	0.914	CLONAL	1	TRUE	1	0.333509225598849	2		531	1143	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793116	33793116	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	143	430	0	ENST00000498907.2:c.205G>T	p.Asp69Tyr	p.D69Y	ENST00000498907	NM_004364.3	69	Gac/Tac	1/1	0.134993207130446	3	FACETS	1	0.937	1			1	INDETERMINATE	1	TRUE	NA	0.333509225598849	3		430	966	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577136	7577137	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0005092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1204	251	681	0	ENST00000269305.4:c.801dup	p.Asn268GlufsTer4	p.N268Efs*4	ENST00000269305	NM_001126112.2	267	-/G	8/11	0.295414166525365	1	FACETS	0.862	0.804	0.922	0.862	0.804	0.922	CLONAL	1	TRUE	0	0.333509225598849	1		681	1455	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0005117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	33	942	2	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	0.238011425637744	1	FACETS	0.561	0.462	0.67	0.561	0.462	0.67	INDETERMINATE	1	TRUE	0	0.503013763767952	1		944	175	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843414	3843415	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0005117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	17	446	0	ENST00000262367.5:c.1188dup	p.His397AlafsTer30	p.H397Afs*30	ENST00000262367	NM_004380.2	396	-/G	4/31	1	2	FACETS	0.644	0.487	0.824	0.644	0.487	0.824	SUBCLONAL	1	TRUE	1	0.503013763767952	2		446	105	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98244236	98244237	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0005117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	76	515	0	ENST00000331920.6:c.739_740dup	p.Leu248ThrfsTer3	p.L248Tfs*3	ENST00000331920	NM_000264.3	247	tac/taTAc	5/24	0.379768433044984	3	FACETS	0.84	0.76	0.92			1	CLONAL	3	TRUE	NA	0.503013763767952	3		515	150	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412308	139412308	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	30	574	1	ENST00000277541.6:c.1337del	p.Gly446AlafsTer185	p.G446Afs*185	ENST00000277541	NM_017617.3	446	gGc/gc	8/34	0.503013763767952	1	FACETS	0.538	0.438	0.648	0.538	0.438	0.648	SUBCLONAL	1	TRUE	0	0.503013763767952	1		575	166	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217650	7217651	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	81	692	0	ENST00000380728.2:c.276dup	p.Val93SerfsTer4	p.V93Sfs*4	ENST00000380728		92	-/A	4/11	0.316565860656307	4	FACETS	0.9	0.803	1			1	CLONAL	2	TRUE	NA	0.503013763767952	4		692	269	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183793	10183793	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1553619431	NA	P-0005133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	133	329	0	ENST00000256474.2:c.262T>C	p.Trp88Arg	p.W88R	ENST00000256474	NM_000551.3	88	Tgg/Cgg	1/3	0.469410551621759	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.469410551621759	1		329	395	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022628	12022628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	66	413	0	ENST00000396373.4:c.734G>A	p.Cys245Tyr	p.C245Y	ENST00000396373	NM_001987.4	245	tGc/tAc	5/8	1	2	FACETS	0.302	0.261	0.347	0.302	0.261	0.347	SUBCLONAL	1	TRUE	1	0.469410551621759	2		413	930	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828803	26828803	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	58	380	1	ENST00000381527.3:c.25C>A	p.Leu9Met	p.L9M	ENST00000381527	NM_001260.1	9	Ctg/Atg	1/13	0.469410551621759	1	FACETS	0.352	0.302	0.406	0.352	0.302	0.406	SUBCLONAL	1	TRUE	0	0.469410551621759	1		381	538	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006603	62006603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	143	428	0	ENST00000392795.3:c.676C>T	p.His226Tyr	p.H226Y	ENST00000392795	NM_001039933.1	226	Cac/Tac	6/6	0.191235366752849	1	FACETS	0.712	0.651	0.776	0.712	0.651	0.776	INDETERMINATE	1	TRUE	0	0.469410551621759	1		428	655	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52677329	52677330	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	152	462	1	ENST00000394830.3:c.929dup	p.Thr311AspfsTer7	p.T311Dfs*7	ENST00000394830	NM_018313.4	310	ctg/ctTg	10/30	0.469410551621759	1	FACETS	0.895	0.823	0.969	0.895	0.823	0.969	CLONAL	1	TRUE	0	0.469410551621759	1		463	554	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934916	9934916	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	125	464	0	ENST00000330684.3:c.1374del	p.Phe459SerfsTer6	p.F459Sfs*6	ENST00000330684	NM_001134407.1	458	ggG/gg	6/13	1	2	FACETS	0.897	0.814	0.983	0.897	0.814	0.983	CLONAL	1	TRUE	1	0.469410551621759	2		464	594	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067142	37067142	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	74	228	0	ENST00000231790.2:c.1053del	p.Ala353LeufsTer14	p.A353Lfs*14	ENST00000231790	NM_000249.3	351	ggA/gg	12/19	0.469410551621759	1	FACETS	0.844	0.746	0.946	0.844	0.746	0.946	CLONAL	1	TRUE	0	0.469410551621759	1		228	286	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480130	20480130	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	62	558	0	ENST00000346618.3:c.449del	p.Leu150Ter	p.L150*	ENST00000346618	NM_001949.4	149	ggT/gg	2/7	NA	2	FACETS	0.277	0.239	0.32			1	INDETERMINATE	1	TRUE	NA	0.469410551621759	2		558	952	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0005164-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	136	340	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.878	0.802	0.956	0.878	0.802	0.956	CLONAL	1	TRUE	1	0.557495069259845	2		340	556	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956221	55956221	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs767542615	NA	P-0005164-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	145	491	0	ENST00000263923.4:c.3094C>T	p.Arg1032Ter	p.R1032*	ENST00000263923	NM_002253.2	1032	Cga/Tga	23/30	0.441878848275828	1	FACETS	0.75	0.689	0.814	0.75	0.689	0.814	SUBCLONAL	1	TRUE	0	0.557495069259845	1		491	500	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005164-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	170	445	0	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.557495069259845	2		445	521	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001463	150001463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005164-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	131	427	0	ENST00000253339.5:c.2141G>A	p.Gly714Glu	p.G714E	ENST00000253339		714	gGa/gAa	4/7	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.557495069259845	2		427	469	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209060	133209061	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005164-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	84	460	0	ENST00000320574.5:c.6170dup	p.Asn2057LysfsTer2	p.N2057Kfs*2	ENST00000320574	NM_006231.2	2057	aat/aaAt	45/49	1	2	FACETS	0.517	0.457	0.581	0.517	0.457	0.581	SUBCLONAL	1	TRUE	1	0.557495069259845	2		460	583	SUCCESS
APC	324	MSKCC	GRCh37	5	112175756	112175756	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005164-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	117	370	0	ENST00000257430.4:c.4466del	p.Leu1489TyrfsTer18	p.L1489Yfs*18	ENST00000257430	NM_000038.5	1489	Tta/ta	16/16	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.557495069259845	2		370	412	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220705	1220706	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	116	318	0	ENST00000326873.7:c.727dup	p.Val243GlyfsTer23	p.V243Gfs*23	ENST00000326873	NM_000455.4	241	-/G	5/10	0.578232573250842	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.578232573250842	1		318	282	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0005190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	192	364	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.578232573250842	2		364	606	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597395	10597395	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	247	231	0	ENST00000171111.5:c.1808G>T	p.Gly603Val	p.G603V	ENST00000171111	NM_203500.1	603	gGg/gTg	6/6	0.32792349467031	1	FACETS	1	0.992	1	1	0.992	1	INDETERMINATE	1	TRUE	0	0.578232573250842	1		231	483	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031964	26031964	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	296	181	0	ENST00000244661.2:c.325A>G	p.Asn109Asp	p.N109D	ENST00000244661	NM_003537.3	109	Aac/Gac	1/1	0.313457120997134	4	FACETS	0.796	0.75	0.843			1	INDETERMINATE	2	TRUE	NA	0.578232573250842	4		181	1015	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0005201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	228	360	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.977	1	1	0.995	1	CLONAL	2	TRUE	1	0.505159162806212	2		361	426	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0005201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	385	454	2	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.505159162806212	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	1	0.505159162806212	4		456	739	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693002	89693003	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	34	300	0	ENST00000371953.3:c.491dup	p.Val166SerfsTer14	p.V166Sfs*14	ENST00000371953	NM_000314.4	162	-/A	5/9	0.505159162806212	1	FACETS	0.488	0.402	0.583	0.488	0.402	0.583	SUBCLONAL	1	TRUE	0	0.505159162806212	1		300	206	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076902	41076902	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	156	665	0	ENST00000373198.4:c.1518G>A	p.Trp506Ter	p.W506*	ENST00000373198	NM_133170.3	506	tgG/tgA	9/32	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.505159162806212	2		665	572	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534341	187534341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	162	577	0	ENST00000441802.2:c.9385C>T	p.Pro3129Ser	p.P3129S	ENST00000441802	NM_005245.3	3129	Cct/Tct	13/27	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.505159162806212	2		577	635	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495442	149495442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576668629	NA	P-0005201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	138	608	0	ENST00000261799.4:c.3205G>A	p.Glu1069Lys	p.E1069K	ENST00000261799	NM_002609.3	1069	Gaa/Aaa	23/23	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.505159162806212	2		608	528	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710963	117710963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	94	356	0	ENST00000368508.3:c.1309C>T	p.Pro437Ser	p.P437S	ENST00000368508	NM_002944.2	437	Cct/Tct	12/43	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.505159162806212	2		356	316	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851369	151851369	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1261796800	NA	P-0005201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	315	555	0	ENST00000262189.6:c.12122C>T	p.Pro4041Leu	p.P4041L	ENST00000262189	NM_170606.2	4041	cCt/cTt	47/59	0.505159162806212	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	3	TRUE	1	0.505159162806212	4		555	625	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915952	127915952	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs865855853	NA	P-0005201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	275	958	1	ENST00000373547.4:c.529C>T	p.Arg177Ter	p.R177*	ENST00000373547	NM_002721.4	177	Cga/Tga	6/7	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.505159162806212	2		959	854	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	39	588	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.871	0.724	1	0.871	0.724	1	CLONAL	1	TRUE	1	0.24	2		589	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0005211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	34	505	0	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	0.203894457180642	1	FACETS	0.71	0.581	0.855	0.71	0.581	0.855	SUBCLONAL	1	TRUE	0	0.24	1		505	351	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058652	72058652	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0005211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	28	525	0	ENST00000357731.5:c.789-1G>C		p.X263_splice	ENST00000357731	NM_173808.2	263			1	2	FACETS	0.588	0.469	0.723	0.588	0.469	0.723	SUBCLONAL	1	TRUE	1	0.24	2		525	397	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0005216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	259	214	2	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	0.555256022472266	3	FACETS	1	0.99	1	0.614	0.579	0.65	CLONAL	1	TRUE	1	0.916863407841774	3		216	671	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913351	NA	P-0005216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	775	600	1	ENST00000288602.6:c.1397G>A	p.Gly466Glu	p.G466E	ENST00000288602	NM_004333.4	466	gGa/gAa	11/18	0.78889554825395	4	FACETS	0.968	0.945	0.991	0.968	0.945	0.991	CLONAL	3	TRUE	1	0.916863407841774	4		601	1116	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243561	46243561	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0005216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	206	267	1	ENST00000334344.6:c.1912+2T>G		p.X638_splice	ENST00000334344	NM_152641.2	638			NA	2	FACETS	1	0.946	1			1	INDETERMINATE	1	TRUE	NA	0.916863407841774	2		268	446	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061193	38061193	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	170	367	0	ENST00000250448.2:c.796T>G	p.Phe266Val	p.F266V	ENST00000250448	NM_004496.3	266	Ttc/Gtc	2/2	0.468340342957785	1	FACETS	0.339	0.313	0.365	0.339	0.313	0.365	INDETERMINATE	1	TRUE	0	0.916863407841774	1		367	593	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857070	9857070	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	330	557	0	ENST00000330684.3:c.4331T>A	p.Val1444Asp	p.V1444D	ENST00000330684	NM_001134407.1	1444	gTt/gAt	13/13	0.185505853999565	5	FACETS	1	0.953	1			1	INDETERMINATE	2	TRUE	NA	0.916863407841774	5		557	851	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696435	47696435	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	373	512	0	ENST00000347630.2:c.388G>C	p.Asp130His	p.D130H	ENST00000347630	NM_001007230.1	130	Gac/Cac	6/11	0.143203269730241	5	FACETS	0.884	0.846	0.922	0.663	0.634	0.691	INDETERMINATE	3	TRUE	1	0.916863407841774	5		512	729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577518	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	473	514	0	ENST00000269305.4:c.763dup	p.Ile255AsnfsTer9	p.I255Nfs*9	ENST00000269305	NM_001126112.2	255	atc/aAtc	7/11	0.916863407841774	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.916863407841774	1		514	538	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196920	106196921	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	45	425	3	ENST00000380013.4:c.5258dup	p.Asn1753LysfsTer3	p.N1753Kfs*3	ENST00000380013	NM_001127208.2	1751	-/A	11/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		428	679	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0005282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	329	379	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.302592383093095	3	FACETS	0.897	0.852	0.944	1	0.994	1	CLONAL	3	TRUE	1	0.34	3		379	841	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0005282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	91	324	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.302592383093095	3	FACETS	0.872	0.774	0.977	0.436	0.387	0.489	CLONAL	1	TRUE	1	0.34	3		324	718	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0005282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	166	229	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.183334305693471	2	FACETS	0.858	0.793	0.926	0.858	0.793	0.926	INDETERMINATE	2	TRUE	0	0.34	2		231	569	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974782	21974783	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CAGT	novel	NA	P-0005282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	42	279	0	ENST00000304494.5:c.41_44dup	p.Trp15Ter	p.W15*	ENST00000304494	NM_000077.4	15	tgg/tgACTGg	1/3	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.34	2		279	239	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256670	16256670	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	79	438	0	ENST00000375759.3:c.3935A>T	p.Tyr1312Phe	p.Y1312F	ENST00000375759	NM_015001.2	1312	tAt/tTt	11/15	0.302592383093095	4	FACETS	1	0.963	1			1	CLONAL	1	TRUE	NA	0.34	4		438	505	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175996746	175996746	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	103	651	2	ENST00000367669.3:c.1691G>A	p.Ser564Asn	p.S564N	ENST00000367669	NM_022457.5	564	aGc/aAc	15/20	0.302592383093095	3	FACETS	0.912	0.816	1	0.456	0.408	0.507	CLONAL	1	TRUE	1	0.34	3		653	777	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965535	25965535	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	172	595	0	ENST00000435504.4:c.3671A>G	p.Asp1224Gly	p.D1224G	ENST00000435504		1224	gAt/gGt	13/13	0.221891414084121	3	FACETS	0.886	0.818	0.956	0.886	0.818	0.956	CLONAL	2	TRUE	1	0.34	3		595	668	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266898	41266898	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1172941347	NA	P-0005282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	85	555	0	ENST00000349496.5:c.569G>A	p.Arg190His	p.R190H	ENST00000349496	NM_001904.3	190	cGt/cAt	5/15	0.302592383093095	3	FACETS	0.785	0.694	0.883	0.393	0.347	0.442	SUBCLONAL	1	TRUE	1	0.34	3		555	745	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722927	49722927	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776261411	NA	P-0005282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	41	250	0	ENST00000449682.2:c.1400C>T	p.Pro467Leu	p.P467L	ENST00000449682	NM_020998.3	467	cCg/cTg	12/18	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.34	2		250	214	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160715	56160715	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	92	566	0	ENST00000399503.3:c.989G>C	p.Gly330Ala	p.G330A	ENST00000399503	NM_005921.1	330	gGa/gCa	4/20	0.221891414084121	3	FACETS	1	0.948	1	0.554	0.494	0.619	CLONAL	1	TRUE	1	0.34	3		566	571	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043926	180043926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	186	597	1	ENST00000261937.6:c.3070G>A	p.Gly1024Arg	p.G1024R	ENST00000261937	NM_182925.4	1024	Ggg/Agg	22/30	0.183334305693471	2	FACETS	0.993	0.923	1	0.993	0.923	1	INDETERMINATE	2	TRUE	0	0.34	2		598	551	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459536	50459536	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	55	404	0	ENST00000331340.3:c.825G>C	p.Lys275Asn	p.K275N	ENST00000331340	NM_006060.4	275	aaG/aaC	7/8	0.302592383093095	3	FACETS	0.583	0.498	0.676	0.292	0.249	0.338	SUBCLONAL	1	TRUE	1	0.34	3		404	649	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218405	69218405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	97	560	0	ENST00000462284.1:c.497C>T	p.Ser166Phe	p.S166F	ENST00000462284	NM_002392.5	166	tCt/tTt	7/11	0.302592383093095	5	FACETS	0.928	0.826	1	0.464	0.413	0.519	CLONAL	1	TRUE	3	0.34	5		560	928	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119945	70119945	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	62	320	0	ENST00000245479.2:c.947C>A	p.Thr316Lys	p.T316K	ENST00000245479	NM_000346.3	316	aCg/aAg	3/3	0.169686659041118	5	FACETS	0.765	0.664	0.873	0.51	0.443	0.582	INDETERMINATE	2	TRUE	2	0.34	5		320	360	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974678	21974684	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TGGATCG	TGGATCG	-	novel	NA	P-0005282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	65	421	0	ENST00000304494.5:c.143_149del	p.Pro48ArgfsTer3	p.P48Rfs*3	ENST00000304494	NM_000077.4	48	cCGATCCAg/cg	1/3	1				0.808	1				CLONAL	1	TRUE	1	0.34	2		421	412	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935625	15935626	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0005282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	66	424	0	ENST00000268712.3:c.7307_7308del	p.Ser2436Ter	p.S2436*	ENST00000268712	NM_006311.3	2436	tCG/t	46/46	0.183334305693471	2	FACETS	0.859	0.748	0.979	0.429	0.374	0.49	INDETERMINATE	1	TRUE	0	0.34	2		424	452	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0005285-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	47	340	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.969	0.816	1	0.969	0.816	1	CLONAL	1	TRUE	1	0.13	2		340	746	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0005285-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	59	734	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.814	0.698	0.942	0.814	0.698	0.942	CLONAL	1	TRUE	1	0.13	2		734	1115	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0005285-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	28	527	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	1	2	FACETS	0.5	0.398	0.618	0.5	0.398	0.618	SUBCLONAL	1	TRUE	1	0.13	2		527	861	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690847	89690847	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587776667	NA	P-0005285-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	32	207	0	ENST00000371953.3:c.253+1G>T		p.X85_splice	ENST00000371953	NM_000314.4	85			1	2	FACETS	0.993	0.805	1	0.993	0.805	1	CLONAL	1	TRUE	1	0.13	2		207	496	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466026	69466028	+	inframe_deletion	In_Frame_Del	DEL	CGA	CGA	-	novel	NA	P-0005285-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	86	543	0	ENST00000227507.2:c.866_868del	p.Asp289del	p.D289del	ENST00000227507	NM_053056.2	288	acCGAc/acc	5/5	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.13	2		543	1017	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692981	89692982	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0005285-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	28	289	0	ENST00000371953.3:c.468_469dup	p.Glu157GlyfsTer3	p.E157Gfs*3	ENST00000371953	NM_000314.4	155	-/GG	5/9	1	2	FACETS	0.83	0.662	1	0.83	0.662	1	CLONAL	1	TRUE	1	0.13	2		289	519	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107138	27107138	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005285-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	26	268	0	ENST00000324856.7:c.6749del	p.Glu2250GlyfsTer17	p.E2250Gfs*17	ENST00000324856	NM_006015.4	2250	gAg/gg	20/20	1	2	FACETS	0.866	0.685	1	0.866	0.685	1	CLONAL	1	TRUE	1	0.13	2		268	462	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440879	52440882	+	frameshift_variant	Frame_Shift_Del	DEL	CCCG	CCCG	-	novel	NA	P-0005319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	214	356	0	ENST00000460680.1:c.622_625del	p.Arg208SerfsTer22	p.R208Sfs*22	ENST00000460680	NM_004656.3	208	CGGGtc/tc	8/17	0.486149631720101	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.486149631720101	1		356	630	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577594	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0005319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	157	306	0	ENST00000269305.4:c.687T>A	p.Cys229Ter	p.C229*	ENST00000269305	NM_001126112.2	229	tgT/tgA	7/11	0.486149631720101	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.486149631720101	1		306	448	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2164248	2164248	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	222	401	1	ENST00000398665.3:c.65G>A	p.Trp22Ter	p.W22*	ENST00000398665	NM_032482.2	22	tGg/tAg	1/28	0.486149631720101	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.486149631720101	1		402	630	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786941	135787070	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAGAAGTAGCACACCCTAAAATGGAAGAGAAGAACACAGGGGGTTAGTGTGTGGTTTTAGGTTATTCTGGTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGATGGTCCTCTAGACCATTTGATAATA	TAGAAGTAGCACACCCTAAAATGGAAGAGAAGAACACAGGGGGTTAGTGTGTGGTTTTAGGTTATTCTGGTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGATGGTCCTCTAGACCATTTGATAATA	-	novel	NA	P-0005319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	98	322	0	ENST00000298552.3:c.914-115_928del		p.X305_splice	ENST00000298552	NM_001162426.1	305		10/23	0.486149631720101	1	FACETS	0.684	0.614	0.758	0.684	0.614	0.758	SUBCLONAL	1	TRUE	0	0.486149631720101	1		322	446	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183762	10183763	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0005319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	135	244	0	ENST00000256474.2:c.232_233dup	p.Asn78LysfsTer82	p.N78Kfs*82	ENST00000256474	NM_000551.3	77	-/AA	1/3	0.486149631720101	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.486149631720101	1		244	406	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446909	18446909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	48	341	0	ENST00000266497.5:c.994C>A	p.His332Asn	p.H332N	ENST00000266497		332	Cat/Aat	4/31	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.14	2		341	617	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98009792	98009792	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	36	286	1	ENST00000289081.3:c.172A>T	p.Asn58Tyr	p.N58Y	ENST00000289081	NM_000136.2	58	Aat/Tat	3/15	1	2	FACETS	0.82	0.673	0.986	0.82	0.673	0.986	CLONAL	1	TRUE	1	0.14	2		287	627	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17743005	17743005	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	30	247	0	ENST00000250003.3:c.913C>A	p.Pro305Thr	p.P305T	ENST00000250003	NM_002478.4	305	Ccg/Acg	3/3	1	2	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	TRUE	1	0.14	2		247	408	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732413	74732413	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1447	106	609	0	ENST00000359995.5:c.496G>T	p.Ala166Ser	p.A166S	ENST00000359995	NM_001195427.1	166	Gca/Tca	2/3	1	2	FACETS	0.975	0.871	1	0.975	0.871	1	CLONAL	1	TRUE	1	0.14	2		609	1553	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546581	9546581	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	38	296	0	ENST00000353224.5:c.1441G>T	p.Asp481Tyr	p.D481Y	ENST00000353224	NM_177990.2	481	Gac/Tac	5/10	1	2	FACETS	0.863	0.712	1	0.863	0.712	1	CLONAL	1	TRUE	1	0.14	2		296	629	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40828000	40828000	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	22	176	0	ENST00000373198.4:c.2428C>A	p.Gln810Lys	p.Q810K	ENST00000373198	NM_133170.3	810	Cag/Aag	17/32	1	2	FACETS	0.768	0.595	0.971	0.768	0.595	0.971	CLONAL	1	TRUE	1	0.14	2		176	409	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11114063	11114063	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	53	427	1	ENST00000358026.2:c.1992del	p.Glu665ArgfsTer109	p.E665Rfs*109	ENST00000358026	NM_001128849.1	664	gAa/ga	13/36	1	2	FACETS	0.873	0.743	1	0.873	0.743	1	CLONAL	1	TRUE	1	0.14	2		428	867	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578473	7578474	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	74	221	1	ENST00000269305.4:c.456_457insT	p.Pro153SerfsTer28	p.P153Sfs*28	ENST00000269305	NM_001126112.2	152	-/T	5/11	1	2	FACETS	0.941	0.824	1	1	0.981	1	CLONAL	2	TRUE	1	0.14	2		222	562	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	128	359	0	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	1	0.947	1	1	0.991	1	CLONAL	2	TRUE	1	0.27	2		359	451	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	260	831	11	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.956	0.896	1	1	0.995	1	CLONAL	2	TRUE	1	0.27	2		842	1007	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	174	547	7	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	NA	2	FACETS	0.809	0.746	0.874			1	INDETERMINATE	2	TRUE	NA	0.27	2		554	797	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	137	309	2	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	0.992	1	CLONAL	2	TRUE	1	0.27	2		311	431	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	231	552	1	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.861	0.803	0.921	1	0.993	1	CLONAL	2	TRUE	1	0.27	2		553	994	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743896	41743896	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	183	601	1	ENST00000301178.4:c.836del	p.Pro279GlnfsTer18	p.P279Qfs*18	ENST00000301178	NM_021913.4	277	gaC/ga	7/20	0.3	1	FACETS	0.841	0.779	0.905	1	0.992	1	CLONAL	2	TRUE	0	0.27	1		602	697	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	95	386	3	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.952	1	1	0.988	1	CLONAL	2	TRUE	1	0.27	2		389	321	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703538	47703538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63749932	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	204	623	1	ENST00000233146.2:c.2038C>T	p.Arg680Ter	p.R680*	ENST00000233146	NM_000251.2	680	Cga/Tga	13/16	1	2	FACETS	0.83	0.771	0.892	1	0.992	1	CLONAL	2	TRUE	1	0.27	2		624	910	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	213	427	4	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	0.973	0.906	1	1	0.994	1	CLONAL	2	TRUE	1	0.27	2		431	811	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429978	78429978	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	159	318	1	ENST00000370768.2:c.901del	p.Ile301TyrfsTer22	p.I301Yfs*22	ENST00000370768	NM_003902.3	301	Ata/ta	11/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.27	2		319	787	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736166	204736166	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	203	705	0	ENST00000302823.3:c.529del	p.Tyr177IlefsTer10	p.Y177Ifs*10	ENST00000302823	NM_005214.4	175	Ttt/tt	3/4	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.27	2		705	1362	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216560	2216560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777525091	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	111	461	0	ENST00000398665.3:c.2204C>T	p.Thr735Met	p.T735M	ENST00000398665	NM_032482.2	735	aCg/aTg	20/28	0.3	0	FACETS	0.684	0.619	0.752			1	SUBCLONAL	2	TRUE	0	0.27	0		461	439	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	105	267	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.27	2		267	550	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258817	16258817	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs746795233	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	183	618	0	ENST00000375759.3:c.6082A>G	p.Met2028Val	p.M2028V	ENST00000375759	NM_015001.2	2028	Atg/Gtg	11/15	1	2	FACETS	0.916	0.847	0.987	1	0.992	1	CLONAL	2	TRUE	1	0.27	2		618	740	SUCCESS
APC	324	MSKCC	GRCh37	5	112175068	112175069	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	103	328	0	ENST00000257430.4:c.3778_3779del	p.Gln1260AspfsTer15	p.Q1260Dfs*15	ENST00000257430	NM_000038.5	1259	atACag/atag	16/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.27	2		328	516	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279861	46279866	+	inframe_deletion	In_Frame_Del	DEL	CAGCAA	CAGCAA	-	rs748517056	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	111	320	0	ENST00000371998.3:c.3810_3815del	p.Gln1275_Gln1276del	p.Q1275_Q1276del	ENST00000371998		1263	CAGCAA/-	20/23	0.3	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.27	1		320	480	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270530	98270530	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs751977093	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	32	217	0	ENST00000331920.6:c.114del	p.Leu39CysfsTer41	p.L39Cfs*41	ENST00000331920	NM_000264.3	38	ggG/gg	1/24	1	2	FACETS	0.587	0.476	0.712	0.587	0.476	0.712	SUBCLONAL	1	TRUE	1	0.27	2		217	404	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375459	40375459	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1312	105	1184	0	ENST00000293328.3:c.491del	p.Lys164SerfsTer17	p.K164Sfs*17	ENST00000293328	NM_012448.3	164	aAg/ag	5/19	0.3	1	FACETS	0.475	0.424	0.53	0.475	0.424	0.53	SUBCLONAL	1	TRUE	0	0.27	1		1184	1417	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11292579	11292579	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	169	488	2	ENST00000361445.4:c.2428G>T	p.Gly810Cys	p.G810C	ENST00000361445	NM_004958.3	810	Ggc/Tgc	16/58	0.3	1	FACETS	0.777	0.716	0.84	1	0.99	1	SUBCLONAL	2	TRUE	0	0.27	1		490	697	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85741978	85741978	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs606231305	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1499	102	678	0	ENST00000370580.1:c.57+1G>A		p.X19_splice	ENST00000370580	NM_003921.4	19			1	2	FACETS	0.472	0.42	0.528	0.472	0.42	0.528	SUBCLONAL	1	TRUE	1	0.27	2		678	1601	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120479966	120479966	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367562640	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	216	496	0	ENST00000256646.2:c.3461C>T	p.Ala1154Val	p.A1154V	ENST00000256646	NM_024408.3	1154	gCg/gTg	21/34	1	2	FACETS	0.95	0.885	1	1	0.994	1	CLONAL	2	TRUE	1	0.27	2		496	842	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843724	156843724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	306	602	1	ENST00000524377.1:c.1150G>A	p.Glu384Lys	p.E384K	ENST00000524377	NM_002529.3	384	Gag/Aag	8/17	0.3	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	3	TRUE	0	0.27	2		603	654	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794355	242794355	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	75	475	0	ENST00000334409.5:c.587C>G	p.Ala196Gly	p.A196G	ENST00000334409	NM_005018.2	196	gCa/gGa	3/5	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.27	2		475	413	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412922	49412922	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	68	825	0	ENST00000418115.1:c.101A>G	p.Tyr34Cys	p.Y34C	ENST00000418115	NM_001664.2	34	tAt/tGt	2/5	1	2	FACETS	0.526	0.456	0.602	0.526	0.456	0.602	SUBCLONAL	1	TRUE	1	0.27	2		825	958	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439181	52439181	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	35	269	0	ENST00000460680.1:c.1061T>G	p.Val354Gly	p.V354G	ENST00000460680	NM_004656.3	354	gTc/gGc	11/17	1	2	FACETS	0.588	0.482	0.707	0.588	0.482	0.707	SUBCLONAL	1	TRUE	1	0.27	2		269	441	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090533	71090533	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	269	595	0	ENST00000318789.4:c.815A>G	p.Asn272Ser	p.N272S	ENST00000318789	NM_032682.5	272	aAc/aGc	11/21	1	2	FACETS	0.915	0.858	0.973	1	0.995	1	CLONAL	2	TRUE	1	0.27	2		595	1089	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090597	71090597	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	335	648	0	ENST00000318789.4:c.751A>G	p.Ser251Gly	p.S251G	ENST00000318789	NM_032682.5	251	Agt/Ggt	11/21	1	2	FACETS	0.969	0.916	1	1	0.996	1	CLONAL	2	TRUE	1	0.27	2		648	1280	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979624	55979624	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	187	545	1	ENST00000263923.4:c.823C>T	p.Arg275Ter	p.R275*	ENST00000263923	NM_002253.2	275	Cga/Tga	7/30	0.3	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.27	1		546	827	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510101	187510101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375425015	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	116	433	0	ENST00000441802.2:c.13412C>T	p.Ala4471Val	p.A4471V	ENST00000441802	NM_005245.3	4471	gCg/gTg	27/27	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.27	2		433	764	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282650	1282650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1413965241	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	198	665	0	ENST00000310581.5:c.1663G>A	p.Glu555Lys	p.E555K	ENST00000310581	NM_198253.2	555	Gag/Aag	3/16	1	2	FACETS	1	0.985	1	1	0.994	1	CLONAL	2	TRUE	1	0.27	2		665	605	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433887	149433887	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs202216061	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	77	350	0	ENST00000286301.3:c.2761C>T	p.Arg921Trp	p.R921W	ENST00000286301	NM_005211.3	921	Cgg/Tgg	21/22	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.27	2		350	396	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158654	26158654	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs140038730	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	13	47	0	ENST00000289316.2:c.257A>G	p.Lys86Arg	p.K86R	ENST00000289316	NM_138720.2	86	aAg/aGg	1/2	0.3	6	FACETS	1	0.87	1	0.48	0.346	0.639	CLONAL	1	TRUE	3	0.27	6		47	103	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910692	29910692	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs281864736	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	229	506	2	ENST00000376809.5:c.232C>T	p.Gln78Ter	p.Q78*	ENST00000376809	NM_002116.7	78	Cag/Tag	2/8	1	2	FACETS	0.963	0.899	1	1	0.994	1	CLONAL	2	TRUE	1	0.27	2		508	881	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967829	93967829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	151	734	1	ENST00000369303.4:c.2098G>A	p.Val700Ile	p.V700I	ENST00000369303	NM_004440.3	700	Gtt/Att	11/17	1	2	FACETS	0.872	0.795	0.953	0.872	0.795	0.953	CLONAL	1	TRUE	1	0.27	2		735	1283	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271516	38271516	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	147	721	0	ENST00000425967.3:c.2305C>T	p.His769Tyr	p.H769Y	ENST00000425967	NM_001174067.1	769	Cat/Tat	18/19	1	2	FACETS	0.787	0.72	0.856	1	0.988	1	SUBCLONAL	2	TRUE	1	0.27	2		721	692	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412526	80412526	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1393447827	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	304	502	1	ENST00000286548.4:c.515A>G	p.Tyr172Cys	p.Y172C	ENST00000286548	NM_002072.3	172	tAc/tGc	4/7	1	2	FACETS	1	0.986	1	1	0.996	1	CLONAL	2	TRUE	1	0.27	2		503	989	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100468	8100468	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	52	459	0	ENST00000346208.3:c.442C>A	p.Pro148Thr	p.P148T	ENST00000346208		148	Ccg/Acg	3/6	1	2	FACETS	0.622	0.529	0.725	0.622	0.529	0.725	SUBCLONAL	1	TRUE	1	0.27	2		459	619	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63661981	63661981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1191	66	326	1	ENST00000279873.7:c.85C>T	p.Leu29Phe	p.L29F	ENST00000279873	NM_032199.2	29	Ctt/Ttt	2/10	0.3	4	FACETS	0.494	0.427	0.567			1	SUBCLONAL	1	TRUE	NA	0.27	4		327	1257	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196059	67196059	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	58	575	0	ENST00000312629.5:c.43A>G	p.Ser15Gly	p.S15G	ENST00000312629	NM_003952.2	15	Agc/Ggc	1/15	1	2	FACETS	0.579	0.496	0.669	0.579	0.496	0.669	SUBCLONAL	1	TRUE	1	0.27	2		575	742	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375929	118375929	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	65	445	0	ENST00000534358.1:c.9322A>G	p.Thr3108Ala	p.T3108A	ENST00000534358	NM_005933.3	3108	Acc/Gcc	27/36	1	2	FACETS	0.732	0.634	0.838	0.732	0.634	0.838	SUBCLONAL	1	TRUE	1	0.27	2		445	658	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287273	46287273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	216	551	0	ENST00000334344.6:c.5218G>A	p.Ala1740Thr	p.A1740T	ENST00000334344	NM_152641.2	1740	Gca/Aca	19/21	1	2	FACETS	0.872	0.812	0.935	1	0.993	1	CLONAL	2	TRUE	1	0.27	2		551	917	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109731	115109731	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369538205	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	213	519	0	ENST00000257566.3:c.2147C>T	p.Ala716Val	p.A716V	ENST00000257566	NM_016569.3	716	gCg/gTg	8/8	0.3	1	FACETS	0.901	0.84	0.964	1	0.993	1	CLONAL	2	TRUE	0	0.27	1		519	757	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201534	133201534	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	147	566	0	ENST00000320574.5:c.6704A>G	p.Tyr2235Cys	p.Y2235C	ENST00000320574	NM_006231.2	2235	tAc/tGc	48/49	0.3	1	FACETS	0.839	0.77	0.911	1	0.99	1	CLONAL	2	TRUE	0	0.27	1		566	561	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033830	49033830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202031219	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	214	431	0	ENST00000267163.4:c.1967G>A	p.Arg656Gln	p.R656Q	ENST00000267163	NM_000321.2	656	cGg/cAg	20/27	1	2	FACETS	0.918	0.855	0.984	1	0.993	1	CLONAL	2	TRUE	1	0.27	2		431	863	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352648	68352648	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	206	413	0	ENST00000487270.1:c.515T>C	p.Leu172Ser	p.L172S	ENST00000487270	NM_133509.3	172	tTg/tCg	6/11	1	2	FACETS	0.82	0.761	0.88	1	0.992	1	CLONAL	2	TRUE	1	0.27	2		413	931	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467848	99467848	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	192	638	0	ENST00000268035.6:c.2717A>G	p.Gln906Arg	p.Q906R	ENST00000268035	NM_000875.3	906	cAg/cGg	13/21	1	2	FACETS	0.768	0.71	0.828	1	0.991	1	SUBCLONAL	2	TRUE	1	0.27	2		638	926	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2115574	2115574	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777121421	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	147	527	1	ENST00000219476.3:c.1654G>A	p.Ala552Thr	p.A552T	ENST00000219476	NM_000548.3	552	Gca/Aca	16/42	0.3	1	FACETS	0.841	0.772	0.913	1	0.99	1	CLONAL	2	TRUE	0	0.27	1		528	560	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778173	3778173	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	41	317	0	ENST00000262367.5:c.6875A>G	p.Gln2292Arg	p.Q2292R	ENST00000262367	NM_004380.2	2292	cAg/cGg	31/31	0.3	1	FACETS	0.977	0.819	1	0.977	0.819	1	CLONAL	1	TRUE	0	0.27	1		317	269	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992513	72992513	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	293	896	1	ENST00000268489.5:c.1532C>A	p.Pro511His	p.P511H	ENST00000268489	NM_006885.3	511	cCt/cAt	2/10	1	2	FACETS	1	0.966	1	1	0.996	1	CLONAL	2	TRUE	1	0.27	2		897	1047	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346357	89346357	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	105	614	0	ENST00000301030.4:c.6593G>T	p.Arg2198Leu	p.R2198L	ENST00000301030	NM_001256183.1	2198	cGg/cTg	9/13	0.3	1	FACETS	0.763	0.688	0.841	1	0.984	1	SUBCLONAL	2	TRUE	0	0.27	1		614	441	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348151	89348151	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs891050032	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	207	923	1	ENST00000301030.4:c.4799G>A	p.Arg1600Gln	p.R1600Q	ENST00000301030	NM_001256183.1	1600	cGg/cAg	9/13	0.3	1	FACETS	0.882	0.821	0.945	1	0.993	1	CLONAL	2	TRUE	0	0.27	1		924	752	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350245	89350245	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1390581742	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	282	919	0	ENST00000301030.4:c.2705A>G	p.Glu902Gly	p.E902G	ENST00000301030	NM_001256183.1	902	gAg/gGg	9/13	0.3	1	FACETS	0.883	0.831	0.937	1	0.995	1	CLONAL	2	TRUE	0	0.27	1		919	1023	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857940	89857940	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	146	414	0	ENST00000389301.3:c.1230G>T	p.Trp410Cys	p.W410C	ENST00000389301	NM_000135.2	410	tgG/tgT	14/43	0.3	1	FACETS	0.809	0.742	0.879	1	0.989	1	CLONAL	2	TRUE	0	0.27	1		414	578	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435491	56435491	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	211	516	0	ENST00000407977.2:c.1646A>G	p.His549Arg	p.H549R	ENST00000407977		549	cAc/cGc	9/10	1	2	FACETS	1	0.953	1	1	0.994	1	CLONAL	2	TRUE	1	0.27	2		516	759	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867630	78867630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374232748	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	174	578	2	ENST00000306801.3:c.2366G>A	p.Arg789His	p.R789H	ENST00000306801	NM_020761.2	789	cGc/cAc	20/34	1	2	FACETS	0.816	0.752	0.882	1	0.991	1	CLONAL	2	TRUE	1	0.27	2		580	790	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39623700	39623700	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	215	504	0	ENST00000262039.4:c.2107T>C	p.Phe703Leu	p.F703L	ENST00000262039	NM_002647.2	703	Ttt/Ctt	20/25	1	2	FACETS	0.875	0.814	0.938	1	0.993	1	CLONAL	2	TRUE	1	0.27	2		504	910	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222228	5222228	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372067337	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	131	469	0	ENST00000357368.4:c.3107C>T	p.Ser1036Leu	p.S1036L	ENST00000357368	NM_002850.3	1036	tCg/tTg	19/38	0.3	0	FACETS	0.955	0.876	1			1	CLONAL	2	TRUE	0	0.27	0		469	371	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245841	5245841	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532977374	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	72	604	1	ENST00000357368.4:c.934G>A	p.Val312Met	p.V312M	ENST00000357368	NM_002850.3	312	Gtg/Atg	10/38	0.3	0	FACETS	0.608	0.531	0.691			1	SUBCLONAL	1	TRUE	0	0.27	0		605	640	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278077	18278077	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	75	592	0	ENST00000222254.8:c.1697A>G	p.Asp566Gly	p.D566G	ENST00000222254	NM_005027.3	566	gAc/gGc	13/16	0.3	1	FACETS	0.604	0.528	0.685	0.604	0.528	0.685	SUBCLONAL	1	TRUE	0	0.27	1		592	796	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022961	31022961	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	162	538	0	ENST00000375687.4:c.2446T>C	p.Ser816Pro	p.S816P	ENST00000375687	NM_015338.5	816	Tct/Cct	13/13	0.3	1	FACETS	0.751	0.691	0.813	1	0.989	1	SUBCLONAL	2	TRUE	0	0.27	1		538	691	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159023	24159023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776693680	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	201	460	0	ENST00000263121.7:c.695C>T	p.Thr232Met	p.T232M	ENST00000263121	NM_003073.3	232	aCg/aTg	6/9	1	2	FACETS	1	0.955	1	1	0.994	1	CLONAL	2	TRUE	1	0.27	2		460	719	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573200	41573200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	31	406	0	ENST00000263253.7:c.5485C>T	p.Arg1829Cys	p.R1829C	ENST00000263253	NM_001429.3	1829	Cgc/Tgc	31/31	1	2	FACETS	0.617	0.499	0.75	0.617	0.499	0.75	SUBCLONAL	1	TRUE	1	0.27	2		406	372	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652558	48652558	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781880992	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	49	91	0	ENST00000376670.3:c.1229C>T	p.Pro410Leu	p.P410L	ENST00000376670	NM_002049.3	410	cCg/cTg	6/6	1	1	FACETS	1	0.941	1	1	0.983	1	CLONAL	3	TRUE	0	0.27	1		91	94	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342150	70342150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	374	364	0	ENST00000374080.3:c.1202C>T	p.Pro401Leu	p.P401L	ENST00000374080		401	cCg/cTg	8/45	1	1	FACETS	0.894	0.857	0.931	1	0.997	1	CLONAL	4	TRUE	0	0.27	1		364	670	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166916	32166916	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	51	183	2	ENST00000375023.3:c.4322del	p.Pro1441LeufsTer17	p.P1441Lfs*17	ENST00000375023	NM_004557.3	1441	cCt/ct	24/30	1	2	FACETS	0.8	0.687	0.922	1	0.969	1	CLONAL	2	TRUE	1	0.27	2		185	236	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178577	56178579	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs750747779	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	192	504	2	ENST00000399503.3:c.3560_3562del	p.Glu1187del	p.E1187del	ENST00000399503	NM_005921.1	1184	GAA/-	14/20	1	2	FACETS	0.795	0.735	0.856	1	0.991	1	SUBCLONAL	2	TRUE	1	0.27	2		506	895	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211795	2211795	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	68	732	1	ENST00000398665.3:c.1516del	p.Gln506SerfsTer51	p.Q506Sfs*51	ENST00000398665	NM_032482.2	504	aCc/ac	16/28	0.3	0	FACETS	0.537	0.466	0.613			1	SUBCLONAL	1	TRUE	0	0.27	0		733	685	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244596	41244596	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80357627	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	72	560	0	ENST00000357654.3:c.2952del	p.Ile986SerfsTer14	p.I986Sfs*14	ENST00000357654	NM_007294.3	984	ttT/tt	10/23	0.3	1	FACETS	0.575	0.502	0.655	0.575	0.502	0.655	SUBCLONAL	1	TRUE	0	0.27	1		560	802	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39629562	39629562	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	218	543	2	ENST00000262039.4:c.2260del	p.Thr754GlnfsTer7	p.T754Qfs*7	ENST00000262039	NM_002647.2	752	acA/ac	21/25	1	2	FACETS	0.827	0.77	0.887	1	0.993	1	CLONAL	2	TRUE	1	0.27	2		545	976	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914617	32914617	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359561	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1274	383	1039	0	ENST00000380152.3:c.6129del	p.Gly2044AlafsTer7	p.G2044Afs*7	ENST00000380152		2042	cAa/ca	11/27	1	2	FACETS	0.856	0.811	0.902	1	0.996	1	CLONAL	2	TRUE	1	0.27	2		1039	1657	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467855	99467856	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	262	622	0	ENST00000268035.6:c.2732_2733dup	p.Gly912LeufsTer26	p.G912Lfs*26	ENST00000268035	NM_000875.3	908	-/TC	13/21	1	2	FACETS	1	0.972	1	1	0.995	1	CLONAL	2	TRUE	1	0.27	2		622	916	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219487	133219487	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	172	574	0	ENST00000320574.5:c.4647del	p.Lys1550AsnfsTer12	p.K1550Nfs*12	ENST00000320574	NM_006231.2	1549	ccC/cc	36/49	0.3	1	FACETS	0.918	0.849	0.99	1	0.992	1	CLONAL	2	TRUE	0	0.27	1		574	600	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265522	152265522	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1467954450	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	125	360	0	ENST00000206249.3:c.975del	p.Ile326TyrfsTer17	p.I326Yfs*17	ENST00000206249	NM_000125.3	325	ccG/cc	4/8	1	2	FACETS	0.849	0.772	0.93	1	0.988	1	CLONAL	2	TRUE	1	0.27	2		360	545	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808898	1808898	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1416045205	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	166	671	4	ENST00000260795.2:c.2334del	p.Ser779AlafsTer41	p.S779Afs*41	ENST00000260795		777	aCc/ac	17/17	0.3	1	FACETS	0.923	0.853	0.996	1	0.992	1	CLONAL	2	TRUE	0	0.27	1		675	576	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163553	32163554	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs777647776	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	108	339	6	ENST00000375023.3:c.5672dup	p.Gly1892ArgfsTer24	p.G1892Rfs*24	ENST00000375023	NM_004557.3	1891	ggc/ggGc	30/30	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.27	2		345	566	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176719159	176719159	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	134	301	0	ENST00000439151.2:c.6463+1del		p.G2155fs	ENST00000439151	NM_022455.4	2155	Ggg/gg	22/23	1	2	FACETS	0.929	0.849	1	1	0.99	1	CLONAL	2	TRUE	1	0.27	2		301	534	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439880	49439881	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	217	676	0	ENST00000301067.7:c.4660_4661del	p.Val1554LeufsTer48	p.V1554Lfs*48	ENST00000301067	NM_003482.3	1554	GTc/c	17/54	1	2	FACETS	0.91	0.848	0.975	1	0.993	1	CLONAL	2	TRUE	1	0.27	2		676	883	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380780	118380780	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	264	585	0	ENST00000534358.1:c.11022del	p.Phe3674LeufsTer23	p.F3674Lfs*23	ENST00000534358	NM_005933.3	3673	gTt/gt	30/36	1	2	FACETS	0.91	0.853	0.968	1	0.994	1	CLONAL	2	TRUE	1	0.27	2		585	1075	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910346	29910346	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	250	556	0	ENST00000376809.5:c.19del	p.Arg7GlufsTer13	p.R7Efs*13	ENST00000376809	NM_002116.7	6	Ccc/cc	1/8	1	2	FACETS	0.884	0.827	0.943	1	0.994	1	CLONAL	2	TRUE	1	0.27	2		556	1047	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487896	56487897	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	193	511	0	ENST00000267101.3:c.1628_1629del	p.Phe543CysfsTer3	p.F543Cfs*3	ENST00000267101	NM_001982.3	543	TTt/t	14/28	1	2	FACETS	0.998	0.927	1	1	0.993	1	CLONAL	2	TRUE	1	0.27	2		511	716	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266651	142266651	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	238	490	1	ENST00000350721.4:c.3273del	p.Phe1091LeufsTer28	p.F1091Lfs*28	ENST00000350721	NM_001184.3	1091	ttT/tt	16/47	1	2	FACETS	0.889	0.83	0.949	1	0.994	1	CLONAL	2	TRUE	1	0.27	2		491	992	SUCCESS
APC	324	MSKCC	GRCh37	5	112154850	112154850	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876658538	NA	P-0005326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	244	464	0	ENST00000257430.4:c.1124del	p.Gly375AlafsTer79	p.G375Afs*79	ENST00000257430	NM_000038.5	374	cGg/cg	10/16	1	2	FACETS	1	0.946	1	1	0.995	1	CLONAL	2	TRUE	1	0.27	2		464	893	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654642	67654642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005386-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	363	529	1	ENST00000264010.4:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000264010	NM_006565.3	377	Cgt/Tgt	6/12	0.688117887197108	1	FACETS	0.704	0.671	0.736	0.704	0.671	0.736	SUBCLONAL	1	TRUE	0	0.787073846819777	1		530	795	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163012	47163012	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs115790187	NA	P-0005386-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	254	419	1	ENST00000409792.3:c.3114T>A	p.Tyr1038Ter	p.Y1038*	ENST00000409792	NM_014159.6	1038	taT/taA	3/21	1	2	FACETS	0.728	0.683	0.775	0.728	0.683	0.775	SUBCLONAL	1	TRUE	1	0.787073846819777	2		420	886	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56171077	56171078	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCA	novel	NA	P-0005386-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	228	375	0	ENST00000399503.3:c.1906_1909dup	p.Ser637MetfsTer10	p.S637Mfs*10	ENST00000399503	NM_005921.1	635	-/TGCA	10/20	0.503068623972624	1	FACETS	0.642	0.604	0.681	0.642	0.604	0.681	SUBCLONAL	1	TRUE	0	0.787073846819777	1		375	547	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0005423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	70	96	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.877	0.765	0.999	0.877	0.765	0.999	CLONAL	1	TRUE	1	0.24	2		96	665	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115875	8115879	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCT	GCCCT	-	novel	NA	P-0005423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	244	314	1	ENST00000346208.3:c.1221_1225del	p.Pro408GlnfsTer97	p.P408Qfs*97	ENST00000346208		407	tcGCCCTtc/tctc	6/6	1	2	FACETS	0.801	0.747	0.856	1	0.993	1	CLONAL	2	TRUE	1	0.24	2		315	1270	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660603	190660603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	104	190	0	ENST00000441310.2:c.241C>T	p.His81Tyr	p.H81Y	ENST00000441310	NM_000534.4	81	Cat/Tat	3/13	0.3	3	FACETS	0.794	0.709	0.885			1	SUBCLONAL	1	TRUE	NA	0.24	3		190	1222	SUCCESS
ATR	545	MSKCC	GRCh37	3	142168411	142168411	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1198	113	234	0	ENST00000350721.4:c.7795C>A	p.Leu2599Ile	p.L2599I	ENST00000350721	NM_001184.3	2599	Cta/Ata	47/47	1	2	FACETS	0.718	0.644	0.797	0.718	0.644	0.797	SUBCLONAL	1	TRUE	1	0.24	2		234	1311	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982040	38982040	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1192	110	269	0	ENST00000357387.3:c.682A>T	p.Ile228Phe	p.I228F	ENST00000357387	NM_152756.3	228	Att/Ttt	8/38	1	2	FACETS	0.704	0.63	0.783	0.704	0.63	0.783	SUBCLONAL	1	TRUE	1	0.24	2		269	1302	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991118	41991118	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs761422551	NA	P-0005423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1561	318	332	1	ENST00000219905.7:c.2071G>T	p.Ala691Ser	p.A691S	ENST00000219905	NM_001164273.1	691	Gca/Tca	4/24	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.24	2		333	1879	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41276046	41276047	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1555600897	NA	P-0005423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1362	129	295	0	ENST00000357654.3:c.67_68insC	p.Glu23AlafsTer18	p.E23Afs*18	ENST00000357654	NM_007294.3	23	gag/gCag	2/23	1	2	FACETS	0.721	0.651	0.795	0.721	0.651	0.795	SUBCLONAL	1	TRUE	1	0.24	2		295	1491	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722905	49722906	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0005452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	23	135	2	ENST00000449682.2:c.1420_1421dup	p.Asp475GlnfsTer52	p.D475Qfs*52	ENST00000449682	NM_020998.3	474	cca/ccCCa	12/18	1	2	FACETS	0.743	0.58	0.931	0.743	0.58	0.931	CLONAL	1	TRUE	1	0.212675302412296	2		137	291	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877175	151877175	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs535169721	NA	P-0005452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	53	355	0	ENST00000262189.6:c.7186C>T	p.Gln2396Ter	p.Q2396*	ENST00000262189	NM_170606.2	2396	Cag/Tag	37/59	NA	2	FACETS	0.773	0.658	0.899			1	INDETERMINATE	1	TRUE	NA	0.212675302412296	2		355	645	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219578	133219578	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	46	389	0	ENST00000320574.5:c.4556G>T	p.Arg1519Leu	p.R1519L	ENST00000320574	NM_006231.2	1519	cGc/cTc	36/49	1	2	FACETS	0.682	0.574	0.803	0.682	0.574	0.803	SUBCLONAL	1	TRUE	1	0.212675302412296	2		389	634	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115722	8115724	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0005452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	220	585	1	ENST00000346208.3:c.1072_1074del	p.Lys358del	p.K358del	ENST00000346208		356	atGAAg/atg	6/6	1	2	FACETS	0.914	0.849	0.981	1	0.993	1	CLONAL	2	TRUE	1	0.212675302412296	2		586	1132	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0005470-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	158	367	1	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	1	2	FACETS	0.979	0.897	1	0.979	0.897	1	CLONAL	1	TRUE	1	0.352701509426756	2		368	915	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0005470-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	208	469	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	0.985	0.912	1	0.985	0.912	1	CLONAL	1	TRUE	1	0.352701509426756	2		469	1198	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097199	11097200	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCCCT	rs372601826	NA	P-0005470-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	48	337	0	ENST00000358026.2:c.708_713dup	p.Gly243_Pro244dup	p.G243_P244dup	ENST00000358026	NM_001128849.1	243	-/GGCCCT	4/36	1	2	FACETS	0.367	0.309	0.431	0.367	0.309	0.431	SUBCLONAL	1	TRUE	1	0.352701509426756	2		337	742	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005479-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	103	588	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.809	0.723	0.9	0.809	0.723	0.9	CLONAL	1	TRUE	1	0.317942683798219	2		589	801	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0005479-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	149	229	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.317942683798219	1	FACETS	0.942	0.861	1	0.942	0.861	1	CLONAL	1	TRUE	0	0.317942683798219	1		231	837	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940507	131940507	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005479-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	132	418	0	ENST00000265335.6:c.2534A>T	p.Lys845Met	p.K845M	ENST00000265335		845	aAg/aTg	16/25	1	2	FACETS	0.908	0.824	0.997	0.908	0.824	0.997	CLONAL	1	TRUE	1	0.317942683798219	2		418	914	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593558	48593558	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587781618	NA	P-0005479-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	62	226	0	ENST00000342988.3:c.1308+1G>A		p.X436_splice	ENST00000342988	NM_005359.5	436			0.317942683798219	1	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	0	0.317942683798219	1		226	321	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919252	48919253	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005479-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	137	353	0	ENST00000267163.4:c.418dup	p.Thr140AsnfsTer6	p.T140Nfs*6	ENST00000267163	NM_000321.2	139	-/A	4/27	0.317942683798219	2	FACETS	1	0.984	1	0.686	0.626	0.749	CLONAL	1	TRUE	0	0.317942683798219	2		353	628	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0005487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	391	208	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.526785404235899	3	FACETS	1	0.968	1			1	CLONAL	2	TRUE	NA	0.577048688737586	3		208	860	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919511	78919511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757342290	NA	P-0005487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	233	602	0	ENST00000306801.3:c.3070G>A	p.Gly1024Ser	p.G1024S	ENST00000306801	NM_020761.2	1024	Ggc/Agc	26/34	0.577048688737586	2	FACETS	1	0.954	1	0.512	0.479	0.546	CLONAL	1	TRUE	0	0.577048688737586	2		602	789	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603148	48603148	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1060500740	NA	P-0005487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	147	327	0	ENST00000342988.3:c.1447+2T>C		p.X483_splice	ENST00000342988	NM_005359.5	483			0.577048688737586	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.577048688737586	1		327	349	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276860	15276861	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs753725730	NA	P-0005487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	44	492	0	ENST00000263388.2:c.5404dup	p.Ala1802GlyfsTer8	p.A1802Gfs*8	ENST00000263388	NM_000435.2	1802	gct/gGct	30/33	0.577048688737586	3	FACETS	0.241	0.201	0.285			1	SUBCLONAL	1	TRUE	NA	0.577048688737586	3		492	817	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448304	56448305	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCGT	novel	NA	P-0005487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	376	439	0	ENST00000407977.2:c.339_342dup	p.Ala115ThrfsTer11	p.A115Tfs*11	ENST00000407977		114	-/ACGG	3/10	0.577048688737586	2	FACETS	0.955	0.916	0.995	0.955	0.916	0.995	CLONAL	2	TRUE	0	0.577048688737586	2		439	682	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACAACCCCC	rs397517115	NA	P-0005504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1216	3238	459	0	ENST00000275493.2:c.2311_2319dup	p.Asn771_His773dup	p.N771_H773dup	ENST00000275493	NM_005228.3	771	gac/gACAACCCCCac	20/28	0.444906171567993	64	FACETS	1	0.994	1			1	CLONAL	48	FALSE	NA	0.444906171567993	64		459	4454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs483352695	NA	P-0005504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	119	508	0	ENST00000269305.4:c.736A>T	p.Met246Leu	p.M246L	ENST00000269305	NM_001126112.2	246	Atg/Ttg	7/11	NA	2	FACETS	0.811	0.741	0.882			1	INDETERMINATE	2	FALSE	NA	0.444906171567993	2		508	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0005525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	218	703	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.623814980516003	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.623814980516003	1		704	458	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131972891	131972891	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	127	497	0	ENST00000265335.6:c.3474A>T	p.Gln1158His	p.Q1158H	ENST00000265335		1158	caA/caT	22/25	0.505855565090186	1	FACETS	0.656	0.599	0.715	0.656	0.599	0.715	SUBCLONAL	1	TRUE	0	0.623814980516003	1		497	427	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518738	176518738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200232395	NA	P-0005525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	45	583	0	ENST00000292408.4:c.656G>A	p.Arg219His	p.R219H	ENST00000292408	NM_213647.1	219	cGc/cAc	6/18	0.505855565090186	1	FACETS	0.181	0.152	0.214	0.181	0.152	0.214	SUBCLONAL	1	TRUE	0	0.623814980516003	1		583	548	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779564	3779564	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	215	808	0	ENST00000262367.5:c.5484C>A	p.Tyr1828Ter	p.Y1828*	ENST00000262367	NM_004380.2	1828	taC/taA	31/31	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.623814980516003	2		808	594	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765801	41765801	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	13	268	0	ENST00000301178.4:c.2677G>T	p.Gly893Cys	p.G893C	ENST00000301178	NM_021913.4	893	Ggt/Tgt	20/20	1	2	FACETS	0.16	0.114	0.217	0.16	0.114	0.217	SUBCLONAL	1	TRUE	1	0.623814980516003	2		268	260	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239756	53239756	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	155	350	0	ENST00000375401.3:c.1586G>T	p.Gly529Val	p.G529V	ENST00000375401	NM_004187.3	529	gGt/gTt	12/26	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.623814980516003	1		350	263	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509552	29509590	+	inframe_deletion	In_Frame_Del	DEL	GTGGATGGTTTTGCTGAAAGCACCAAACGTAAAGCAGCA	GTGGATGGTTTTGCTGAAAGCACCAAACGTAAAGCAGCA	-	novel	NA	P-0005525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	67	579	0	ENST00000356175.3:c.759_797del	p.Asp254_Val266del	p.D254_V266del	ENST00000356175	NM_000267.3	253	GTGGATGGTTTTGCTGAAAGCACCAAACGTAAAGCAGCA/-	8/57	0.623814980516003	1	FACETS	0.714	0.631	0.801	0.714	0.631	0.801	SUBCLONAL	1	TRUE	0	0.623814980516003	1		579	207	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572153	64572166	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGCGGCGGGGGC	TGGGCGGCGGGGGC	-	novel	NA	P-0005525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	36	420	0	ENST00000312049.6:c.1473_1486del	p.Pro492GlufsTer34	p.P492Efs*34	ENST00000312049	NM_130799.2	491	gaGCCCCCGCCGCCCAag/gaag	10/10	0.623814980516003	1	FACETS	0.231	0.19	0.277	0.231	0.19	0.277	SUBCLONAL	1	TRUE	0	0.623814980516003	1		420	344	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110002	115110002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	219	628	0	ENST00000257566.3:c.1876del	p.His626ThrfsTer6	p.H626Tfs*6	ENST00000257566	NM_016569.3	626	Cac/ac	8/8	1	2	FACETS	0.959	0.896	1	0.959	0.896	1	CLONAL	1	TRUE	1	0.623814980516003	2		628	732	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66520205	66520206	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs281864790	NA	P-0005525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	110	496	0	ENST00000358598.2:c.491_492del	p.Val164AspfsTer5	p.V164Dfs*5	ENST00000358598	NM_212471.2	163	acTGtg/actg	5/11	0.623814980516003	1	FACETS	0.899	0.821	0.978	0.899	0.821	0.978	CLONAL	1	TRUE	0	0.623814980516003	1		496	270	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577329	64577330	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs386134253	NA	P-0005525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	69	651	2	ENST00000312049.6:c.252dup	p.Ile85TyrfsTer32	p.I85Yfs*32	ENST00000312049	NM_130799.2	84	-/T	2/10	0.623814980516003	1	FACETS	0.368	0.321	0.417	0.368	0.321	0.417	SUBCLONAL	1	TRUE	0	0.623814980516003	1		653	414	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	204	660	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.372791136489741	3	FACETS	1	0.969	1			1	CLONAL	1	TRUE	NA	0.372791136489741	3		660	1195	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	174	646	6	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	0.248685386574446	4	FACETS	1	0.964	1	0.542	0.498	0.588	CLONAL	1	TRUE	2	0.372791136489741	4		652	1182	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	238	678	1	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.372791136489741	3	FACETS	1	0.976	1			1	CLONAL	1	TRUE	NA	0.372791136489741	3		679	1376	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574678	41574679	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs754418509	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	139	1105	3	ENST00000263253.7:c.6970dup	p.His2324ProfsTer55	p.H2324Pfs*55	ENST00000263253	NM_001429.3	2321	-/C	31/31	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.372791136489741	2		1108	731	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	197	314	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.248685386574446	4	FACETS	1	0.984	1	0.621	0.574	0.669	CLONAL	1	TRUE	2	0.372791136489741	4		314	1169	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075612	8075612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	239	1470	1	ENST00000377482.5:c.68G>A	p.Gly23Asp	p.G23D	ENST00000377482	NM_018948.3	23	gGc/gAc	2/4	0.28630184229866	1	FACETS	0.806	0.751	0.862	0.806	0.751	0.862	CLONAL	1	TRUE	0	0.372791136489741	1		1471	1295	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261038	16261038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144525015	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	86	961	5	ENST00000375759.3:c.8303C>T	p.Ala2768Val	p.A2768V	ENST00000375759	NM_015001.2	2768	gCg/gTg	11/15	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.372791136489741	2		966	404	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076745	72076745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1171	219	1613	1	ENST00000357731.5:c.752C>T	p.Pro251Leu	p.P251L	ENST00000357731	NM_173808.2	251	cCg/cTg	5/7	0.248685386574446	4	FACETS	1	0.981	1	0.58	0.538	0.624	CLONAL	1	TRUE	2	0.372791136489741	4		1614	1390	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115251164	115251164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730880381	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	150	1322	2	ENST00000369535.4:c.562G>A	p.Val188Met	p.V188M	ENST00000369535	NM_002524.4	188	Gtg/Atg	5/7	0.248685386574446	4	FACETS	0.972	0.887	1	0.486	0.443	0.531	CLONAL	1	TRUE	2	0.372791136489741	4		1324	1136	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612819	228612819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761689329	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	157	1845	7	ENST00000366696.1:c.208C>T	p.Arg70Trp	p.R70W	ENST00000366696	NM_003493.2	70	Cgg/Tgg	1/1	0.325781973494454	4	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.372791136489741	4		1852	946	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976476	25976476	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	175	1132	5	ENST00000435504.4:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000435504		357	Cga/Tga	11/13	1	2	FACETS	0.892	0.821	0.967	0.892	0.821	0.967	CLONAL	1	TRUE	1	0.372791136489741	2		1137	1052	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982356	25982356	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	173	797	0	ENST00000435504.4:c.934C>T	p.Arg312Ter	p.R312*	ENST00000435504		312	Cga/Tga	9/13	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.372791136489741	2		797	921	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047007	128047007	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	154	1435	1	ENST00000285398.2:c.728A>T	p.Asp243Val	p.D243V	ENST00000285398	NM_000122.1	243	gAc/gTc	6/15	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.372791136489741	2		1436	819	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732969	30732969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893810	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	180	1067	1	ENST00000295754.5:c.1582C>T	p.Arg528Cys	p.R528C	ENST00000295754	NM_003242.5	528	Cgt/Tgt	7/7	0.218956199337714	4	FACETS	1	0.989	1	0.735	0.678	0.794	INDETERMINATE	1	TRUE	2	0.372791136489741	4		1068	902	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268762	41268762	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1245266458	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	158	1195	2	ENST00000349496.5:c.1000G>A	p.Glu334Lys	p.E334K	ENST00000349496	NM_001904.3	334	Gaa/Aaa	7/15	0.218956199337714	4	FACETS	1	0.948	1	0.525	0.48	0.572	INDETERMINATE	1	TRUE	2	0.372791136489741	4		1197	1108	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277275	41277275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	203	1119	3	ENST00000349496.5:c.1744C>T	p.Arg582Trp	p.R582W	ENST00000349496	NM_001904.3	582	Cgg/Tgg	11/15	0.218956199337714	4	FACETS	1	0.987	1	0.655	0.606	0.705	INDETERMINATE	1	TRUE	2	0.372791136489741	4		1122	1142	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390994	89390994	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779599137	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	185	1237	0	ENST00000336596.2:c.1060C>T	p.Arg354Trp	p.R354W	ENST00000336596	NM_005233.5	354	Cgg/Tgg	5/17	0.297969497119166	4	FACETS	1	0.983	1	0.619	0.57	0.669	CLONAL	1	TRUE	2	0.372791136489741	4		1237	1101	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374293	138374293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	191	1258	1	ENST00000289153.2:c.3151G>A	p.Glu1051Lys	p.E1051K	ENST00000289153	NM_006219.2	1051	Gaa/Aaa	22/22	0.195886472415377	3	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.372791136489741	3		1259	1043	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808338	1808338	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	113	1260	0	ENST00000260795.2:c.2096C>A	p.Pro699His	p.P699H	ENST00000260795		699	cCt/cAt	15/17	0.248685386574446	4	FACETS	0.791	0.715	0.871	0.791	0.715	0.871	SUBCLONAL	2	TRUE	2	0.372791136489741	4		1260	526	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808590	1808590	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	93	1215	0	ENST00000260795.2:c.2203C>A	p.Pro735Thr	p.P735T	ENST00000260795		735	Ccc/Acc	16/17	0.248685386574446	4	FACETS	1	0.977	1	0.686	0.612	0.764	CLONAL	1	TRUE	2	0.372791136489741	4		1215	499	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964866	55964866	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs777472312	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	180	1107	3	ENST00000263923.4:c.2371C>T	p.Arg791Trp	p.R791W	ENST00000263923	NM_002253.2	791	Cgg/Tgg	16/30	0.195886472415377	3	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.372791136489741	3		1110	869	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591125	67591125	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	207	922	0	ENST00000274335.5:c.1718T>C	p.Leu573Pro	p.L573P	ENST00000274335		573	cTg/cCg	12/15	0.372791136489741	4	FACETS	1	0.987	1	0.643	0.596	0.693	CLONAL	1	TRUE	2	0.372791136489741	4		922	1185	SUCCESS
APC	324	MSKCC	GRCh37	5	112173495	112173495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147655929	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	180	1044	0	ENST00000257430.4:c.2204C>T	p.Ala735Val	p.A735V	ENST00000257430	NM_000038.5	735	gCg/gTg	16/16	0.372791136489741	3	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.372791136489741	3		1044	935	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149450031	149450031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1234365943	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	68	1007	1	ENST00000286301.3:c.1186C>T	p.Leu396Phe	p.L396F	ENST00000286301	NM_005211.3	396	Ctc/Ttc	8/22	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.372791136489741	2		1008	337	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457763	149457763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376495524	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	58	873	0	ENST00000286301.3:c.641G>A	p.Arg214Gln	p.R214Q	ENST00000286301	NM_005211.3	214	cGg/cAg	5/22	1	2	FACETS	0.889	0.768	1	0.889	0.768	1	CLONAL	1	TRUE	1	0.372791136489741	2		873	350	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056632	26056632	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1393790972	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	50	288	0	ENST00000343677.2:c.25C>G	p.Pro9Ala	p.P9A	ENST00000343677	NM_005319.3	9	Ccc/Gcc	1/1	0.372791136489741	5	FACETS	0.804	0.688	0.93	0.536	0.459	0.62	CLONAL	2	TRUE	2	0.372791136489741	5		288	260	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163675	32163675	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1333116692	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	51	676	0	ENST00000375023.3:c.5551C>T	p.Pro1851Ser	p.P1851S	ENST00000375023	NM_004557.3	1851	Ccc/Tcc	30/30	1	2	FACETS	0.934	0.799	1	0.934	0.799	1	CLONAL	1	TRUE	1	0.372791136489741	2		676	293	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681061	117681061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749977900	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	222	1194	0	ENST00000368508.3:c.3559G>A	p.Val1187Ile	p.V1187I	ENST00000368508	NM_002944.2	1187	Gtt/Att	23/43	0.297969497119166	4	FACETS	1	0.989	1	0.67	0.623	0.719	CLONAL	1	TRUE	2	0.372791136489741	4		1194	1220	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202364	138202364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	97	565	0	ENST00000237289.4:c.2281C>T	p.Arg761Cys	p.R761C	ENST00000237289	NM_001270507.1	761	Cgt/Tgt	9/9	0.297969497119166	4	FACETS	0.787	0.705	0.873	0.787	0.705	0.873	SUBCLONAL	2	TRUE	2	0.372791136489741	4		565	454	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467663	50467663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	119	1057	0	ENST00000331340.3:c.898G>A	p.Glu300Lys	p.E300K	ENST00000331340	NM_006060.4	300	Gag/Aag	8/8	0.297969497119166	4	FACETS	1	0.932	1	0.521	0.47	0.575	CLONAL	1	TRUE	2	0.372791136489741	4		1057	841	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485917	8485917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757868633	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	191	1402	4	ENST00000356435.5:c.2900C>T	p.Pro967Leu	p.P967L	ENST00000356435		967	cCg/cTg	17/35	0.297969497119166	4	FACETS	1	0.985	1	0.633	0.585	0.684	CLONAL	1	TRUE	2	0.372791136489741	4		1406	1111	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006026	22006026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1256288325	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	218	1115	0	ENST00000276925.6:c.377G>A	p.Arg126His	p.R126H	ENST00000276925	NM_004936.3	126	cGc/cAc	2/2	0.297969497119166	4	FACETS	1	0.991	1	0.747	0.694	0.801	CLONAL	1	TRUE	2	0.372791136489741	4		1115	1075	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139563095	139563095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	36	1109	4	ENST00000308874.7:c.167G>A	p.Cys56Tyr	p.C56Y	ENST00000308874		56	tGc/tAc	4/10	0.372791136489741	1	FACETS	0.504	0.415	0.602	0.504	0.415	0.602	SUBCLONAL	1	TRUE	0	0.372791136489741	1		1113	312	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851671	63851671	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	72	894	2	ENST00000279873.7:c.2449A>G	p.Arg817Gly	p.R817G	ENST00000279873	NM_032199.2	817	Agg/Ggg	10/10	0.356982954692261	5	FACETS	0.844	0.736	0.959			1	CLONAL	1	TRUE	NA	0.372791136489741	5		896	714	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	167	1040	3	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.325781973494454	4	FACETS	1	0.961	1			1	CLONAL	1	TRUE	NA	0.372791136489741	4		1043	1140	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310860	123310860	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147987917	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	257	1164	5	ENST00000358487.5:c.568C>T	p.Arg190Trp	p.R190W	ENST00000358487	NM_000141.4	190	Cgg/Tgg	5/18	0.28470404613328	2	FACETS	0.824	0.773	0.875	0.824	0.773	0.875	CLONAL	2	TRUE	0	0.372791136489741	2		1169	837	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410618	32410618	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	138	1117	1	ENST00000332351.3:c.1540C>A	p.Gln514Lys	p.Q514K	ENST00000332351	NM_024426.4	514	Cag/Aag	10/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.372791136489741	2		1118	691	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905418	11905418	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	102	907	0	ENST00000396373.4:c.68C>A	p.Pro23Gln	p.P23Q	ENST00000396373	NM_001987.4	23	cCa/cAa	2/8	0.248685386574446	4	FACETS	1	0.915	1	0.513	0.459	0.571	CLONAL	1	TRUE	2	0.372791136489741	4		907	732	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434315	49434315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	100	1567	2	ENST00000301067.7:c.7238C>T	p.Ala2413Val	p.A2413V	ENST00000301067	NM_003482.3	2413	gCc/gTc	31/54	0.28630184229866	1	FACETS	0.876	0.786	0.972	0.876	0.786	0.972	CLONAL	1	TRUE	0	0.372791136489741	1		1569	498	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437175	49437175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368134008	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	90	1279	3	ENST00000301067.7:c.5504G>A	p.Arg1835His	p.R1835H	ENST00000301067	NM_003482.3	1835	cGt/cAt	24/54	0.28630184229866	1	FACETS	0.832	0.742	0.928	0.832	0.742	0.928	CLONAL	1	TRUE	0	0.372791136489741	1		1282	472	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233149	69233149	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	179	1369	0	ENST00000462284.1:c.1014A>C	p.Glu338Asp	p.E338D	ENST00000462284	NM_002392.5	338	gaA/gaC	11/11	0.218956199337714	4	FACETS	1	0.949	1	0.521	0.479	0.565	INDETERMINATE	1	TRUE	2	0.372791136489741	4		1369	1265	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562345	21562345	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1204055851	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	121	788	2	ENST00000382592.4:c.1574G>A	p.Arg525His	p.R525H	ENST00000382592	NM_014572.2	525	cGc/cAc	4/8	0.372791136489741	3	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.372791136489741	3		790	552	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052629	42052629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	455	1678	4	ENST00000219905.7:c.7300C>T	p.Arg2434Trp	p.R2434W	ENST00000219905	NM_001164273.1	2434	Cgg/Tgg	20/24	0.198780036893062	3	FACETS	0.943	0.899	0.987	0.628	0.599	0.658	INDETERMINATE	2	TRUE	0	0.372791136489741	3		1682	1536	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727451	66727451	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519729	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	209	1371	0	ENST00000307102.5:c.167A>C	p.Gln56Pro	p.Q56P	ENST00000307102	NM_002755.3	56	cAg/cCg	2/11	0.198780036893062	3	FACETS	0.912	0.85	0.976	0.608	0.567	0.651	INDETERMINATE	2	TRUE	0	0.372791136489741	3		1371	729	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641218	23641218	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs180177110	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	96	985	2	ENST00000261584.4:c.2257C>T	p.Arg753Ter	p.R753*	ENST00000261584	NM_024675.3	753	Cga/Tga	5/13	1	2	FACETS	0.736	0.656	0.821	0.736	0.656	0.821	SUBCLONAL	1	TRUE	1	0.372791136489741	2		987	700	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835630	68835630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761562625	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	136	1372	3	ENST00000261769.5:c.221G>A	p.Arg74Gln	p.R74Q	ENST00000261769	NM_004360.3	74	cGa/cAa	3/16	1	2	FACETS	0.999	0.91	1	0.999	0.91	1	CLONAL	1	TRUE	1	0.372791136489741	2		1375	730	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838087	89838087	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1367168899	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	62	1193	0	ENST00000389301.3:c.2150T>C	p.Met717Thr	p.M717T	ENST00000389301	NM_000135.2	717	aTg/aCg	23/43	1	2	FACETS	0.648	0.561	0.743	0.648	0.561	0.743	SUBCLONAL	1	TRUE	1	0.372791136489741	2		1193	513	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510723	38510723	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752501819	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	31	798	1	ENST00000254066.5:c.977C>T	p.Thr326Met	p.T326M	ENST00000254066	NM_000964.3	326	aCg/aTg	7/9	NA	2	FACETS	0.687	0.559	0.831			1	INDETERMINATE	1	TRUE	NA	0.372791136489741	2		799	242	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440757	56440757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774211426	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	69	817	1	ENST00000407977.2:c.461C>T	p.Pro154Leu	p.P154L	ENST00000407977		154	cCg/cTg	5/10	0.156403295281137	4	FACETS	1	0.974	1	0.745	0.653	0.843	INDETERMINATE	1	TRUE	2	0.372791136489741	4		818	341	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78811795	78811795	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	103	979	0	ENST00000306801.3:c.1210C>T	p.Arg404Trp	p.R404W	ENST00000306801	NM_020761.2	404	Cgg/Tgg	10/34	0.156403295281137	4	FACETS	1	0.98	1	0.704	0.632	0.78	INDETERMINATE	1	TRUE	2	0.372791136489741	4		979	539	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222982	5222982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201435229	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	66	914	1	ENST00000357368.4:c.2821G>A	p.Ala941Thr	p.A941T	ENST00000357368	NM_002850.3	941	Gcc/Acc	18/38	1	2	FACETS	0.887	0.774	1	0.887	0.774	1	CLONAL	1	TRUE	1	0.372791136489741	2		915	399	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229502	5229502	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	18	341	0	ENST00000357368.4:c.2349G>T	p.Gln783His	p.Q783H	ENST00000357368	NM_002850.3	783	caG/caT	15/38	1	2	FACETS	0.87	0.664	1	0.87	0.664	1	CLONAL	1	TRUE	1	0.372791136489741	2		341	111	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231554	5231554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755739102	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	38	730	1	ENST00000357368.4:c.1922C>T	p.Pro641Leu	p.P641L	ENST00000357368	NM_002850.3	641	cCg/cTg	14/38	1	2	FACETS	0.581	0.481	0.692	0.581	0.481	0.692	SUBCLONAL	1	TRUE	1	0.372791136489741	2		731	351	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152145	11152145	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775399739	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	116	1308	2	ENST00000358026.2:c.4429C>T	p.Arg1477Trp	p.R1477W	ENST00000358026	NM_001128849.1	1477	Cgg/Tgg	31/36	0.121443456150133	0	FACETS	0.641	0.579	0.706			1	INDETERMINATE	1	TRUE	0	0.372791136489741	0		1310	609	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260058	19260058	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143400241	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	72	1265	3	ENST00000162023.5:c.235C>T	p.Arg79Cys	p.R79C	ENST00000162023		79	Cgc/Tgc	7/13	0.121443456150133	0	FACETS	0.664	0.583	0.749			1	INDETERMINATE	1	TRUE	0	0.372791136489741	0		1268	365	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762839	40762839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1407888862	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	47	898	3	ENST00000392038.2:c.169G>A	p.Val57Ile	p.V57I	ENST00000392038	NM_001626.4	57	Gta/Ata	3/14	0.121443456150133	0	FACETS	0.452	0.382	0.528			1	INDETERMINATE	1	TRUE	0	0.372791136489741	0		901	350	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36028617	36028617	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	63	1177	0	ENST00000358208.4:c.959T>C	p.Leu320Pro	p.L320P	ENST00000358208		320	cTg/cCg	8/12	0.28630184229866	1	FACETS	0.666	0.578	0.761	0.666	0.578	0.761	SUBCLONAL	1	TRUE	0	0.372791136489741	1		1177	413	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39708802	39708802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	144	892	2	ENST00000361337.2:c.413G>A	p.Arg138Lys	p.R138K	ENST00000361337	NM_003286.2	138	aGa/aAa	6/21	0.237991227099729	3	FACETS	0.87	0.792	0.951	0.435	0.396	0.476	CLONAL	1	TRUE	1	0.372791136489741	3		894	1054	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739099	40739099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536918490	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	83	1163	3	ENST00000373198.4:c.3185G>A	p.Arg1062His	p.R1062H	ENST00000373198	NM_133170.3	1062	cGc/cAc	24/32	0.237991227099729	3	FACETS	0.978	0.865	1	0.489	0.432	0.55	CLONAL	1	TRUE	1	0.372791136489741	3		1166	540	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256696	46256696	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768977330	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1313	245	1794	1	ENST00000371998.3:c.752G>A	p.Arg251His	p.R251H	ENST00000371998		251	cGc/cAc	8/23	0.237991227099729	3	FACETS	1	0.933	1	0.5	0.466	0.536	CLONAL	1	TRUE	1	0.372791136489741	3		1795	1558	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41525915	41525915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	149	1040	0	ENST00000263253.7:c.1190G>A	p.Arg397Gln	p.R397Q	ENST00000263253	NM_001429.3	397	cGa/cAa	5/31	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.372791136489741	2		1040	786	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911597	39911597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761983121	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	163	701	5	ENST00000378444.4:c.5033G>A	p.Arg1678His	p.R1678H	ENST00000378444	NM_001123385.1	1678	cGc/cAc	15/15	0.372791136489741	2	FACETS	0.892	0.825	0.961			1	CLONAL	2	TRUE	NA	0.372791136489741	2		706	490	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931619	39931619	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	128	685	0	ENST00000378444.4:c.2980G>T	p.Glu994Ter	p.E994*	ENST00000378444	NM_001123385.1	994	Gag/Tag	4/15	0.372791136489741	2	FACETS	0.975	0.895	1			1	CLONAL	2	TRUE	NA	0.372791136489741	2		685	352	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007824	45007825	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	202	874	0	ENST00000558401.1:c.276dup	p.Thr93HisfsTer2	p.T93Hfs*2	ENST00000558401	NM_004048.2	91	acc/aCcc	2/4	0.198780036893062	3	FACETS	1	0.99	1	0.474	0.44	0.51	INDETERMINATE	1	TRUE	0	0.372791136489741	3		874	904	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	70	531	4	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	0.372791136489741	1	FACETS	0.915	0.803	1	0.915	0.803	1	CLONAL	1	TRUE	0	0.372791136489741	1		535	334	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088787	27088788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	89	608	0	ENST00000324856.7:c.2402dup	p.Gln802SerfsTer15	p.Q802Sfs*15	ENST00000324856	NM_006015.4	799	cag/caGg	7/20	1	2	FACETS	0.898	0.798	1	0.898	0.798	1	CLONAL	1	TRUE	1	0.372791136489741	2		608	532	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027926	48027927	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs876659189	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	185	1127	1	ENST00000234420.5:c.2805dup	p.Asp936Ter	p.D936*	ENST00000234420	NM_000179.2	935	tct/tcTt	4/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.372791136489741	2		1128	931	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687472	37687472	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	72	235	1	ENST00000447079.4:c.4382del	p.Gly1461AlafsTer38	p.G1461Afs*38	ENST00000447079	NM_015083.1	1459	tGg/tg	14/14	NA	2	FACETS	0.746	0.653	0.846			1	INDETERMINATE	1	TRUE	NA	0.372791136489741	2		236	518	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0005548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	177	427	4	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	0.218956199337714	4	FACETS	1	0.982	1	0.611	0.563	0.662	INDETERMINATE	1	TRUE	2	0.372791136489741	4		431	1066	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0005621-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	187	446	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.201303174972673	2	FACETS	0.897	0.83	0.966	0.897	0.83	0.966	CLONAL	2	TRUE	0	0.254931786518403	2		446	818	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164784	47164784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1245212934	NA	P-0005621-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	69	289	0	ENST00000409792.3:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000409792	NM_014159.6	448	Cgg/Tgg	3/21	0.23540725245136	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.254931786518403	1		289	403	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73991982	73991982	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0005621-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	84	476	0	ENST00000318443.5:c.2T>C	p.Met1?	p.M1?	ENST00000318443	NM_001024736.1	1	aTg/aCg	2/10	1	2	FACETS	0.745	0.657	0.84	0.745	0.657	0.84	SUBCLONAL	1	TRUE	1	0.254931786518403	2		476	884	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226574125	226574125	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005621-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	90	410	0	ENST00000366794.5:c.736T>A	p.Trp246Arg	p.W246R	ENST00000366794	NM_001618.3	246	Tgg/Agg	6/23	0.254931786518403	3	FACETS	1	0.967	1	0.621	0.551	0.695	CLONAL	1	TRUE	1	0.254931786518403	3		410	641	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225360671	225360671	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005621-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	72	324	0	ENST00000264414.4:c.1720G>T	p.Glu574Ter	p.E574*	ENST00000264414	NM_003590.4	574	Gaa/Taa	13/16	1	2	FACETS	0.956	0.836	1	0.956	0.836	1	CLONAL	1	TRUE	1	0.254931786518403	2		324	591	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205041	128205041	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005621-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	108	399	0	ENST00000341105.2:c.400C>A	p.Pro134Thr	p.P134T	ENST00000341105	NM_032638.4	134	Cct/Act	3/6	0.254931786518403	3	FACETS	0.955	0.856	1			1	CLONAL	1	TRUE	NA	0.254931786518403	3		399	1000	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851567	134851567	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005621-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	65	285	0	ENST00000398015.3:c.973G>C	p.Gly325Arg	p.G325R	ENST00000398015	NM_004441.4	325	Ggt/Cgt	5/16	0.254931786518403	3	FACETS	0.863	0.748	0.988			1	CLONAL	1	TRUE	NA	0.254931786518403	3		285	666	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281570	142281570	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005621-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	48	308	0	ENST00000350721.4:c.674A>T	p.Gln225Leu	p.Q225L	ENST00000350721	NM_001184.3	225	cAa/cTa	4/47	0.254931786518403	6	FACETS	1	0.872	1	0.259	0.218	0.303	CLONAL	1	TRUE	2	0.254931786518403	6		308	549	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169195	32169195	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005621-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	71	349	0	ENST00000375023.3:c.3838G>C	p.Asp1280His	p.D1280H	ENST00000375023	NM_004557.3	1280	Gat/Cat	22/30	0.1591176308161	1	FACETS	0.776	0.678	0.883	0.776	0.678	0.883	SUBCLONAL	1	TRUE	0	0.254931786518403	1		349	626	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969087	93969087	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005621-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	123	522	1	ENST00000369303.4:c.1909C>A	p.Arg637Ser	p.R637S	ENST00000369303	NM_004440.3	637	Cgt/Agt	10/17	0.1591176308161	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.254931786518403	1		523	798	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942864	15942864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005621-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	83	448	0	ENST00000268712.3:c.6838G>A	p.Glu2280Lys	p.E2280K	ENST00000268712	NM_006311.3	2280	Gag/Aag	44/46	0.201303174972673	2	FACETS	1	0.885	1	0.501	0.442	0.564	CLONAL	1	TRUE	0	0.254931786518403	2		448	650	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756806	756806	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs760359350	NA	P-0005621-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	54	372	0	ENST00000314574.4:c.22G>C	p.Glu8Gln	p.E8Q	ENST00000314574	NM_005433.3	8	Gaa/Caa	2/12	0.2526040624313	4	FACETS	0.733	0.625	0.852			1	SUBCLONAL	1	TRUE	NA	0.254931786518403	4		372	725	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023861	27023904	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGGCGCCGGCAAGGGCCCGGCGGACATGGCCTCGCAGTGTTG	GGGGGCGCCGGCAAGGGCCCGGCGGACATGGCCTCGCAGTGTTG	-	novel	NA	P-0005621-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	25	105	0	ENST00000324856.7:c.973_1016del	p.Ala325CysfsTer60	p.A325Cfs*60	ENST00000324856	NM_006015.4	323	GGGGGCGCCGGCAAGGGCCCGGCGGACATGGCCTCGCAGTGTTGg/g	1/20	1	2	FACETS	0.656	0.518	0.814	0.656	0.518	0.814	SUBCLONAL	1	TRUE	1	0.254931786518403	2		105	299	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971091	21971091	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005621-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	66	194	0	ENST00000304494.5:c.267del	p.Phe90SerfsTer56	p.F90Sfs*56	ENST00000304494	NM_000077.4	89	ggC/gg	2/3	0.23540725245136	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.254931786518403	1		194	383	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637670	52637671	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005621-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	61	425	0	ENST00000394830.3:c.2645dup	p.Asn882LysfsTer19	p.N882Kfs*19	ENST00000394830	NM_018313.4	882	aat/aaAt	18/30	0.160528614424896	2	FACETS	0.944	0.815	1	0.472	0.407	0.542	CLONAL	1	TRUE	0	0.254931786518403	2		425	507	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005623-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	232	588	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.347063268726699	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.415467165768077	3		589	635	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0005623-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	455	609	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.415467165768077	1	FACETS	0.963	0.925	1	1	0.997	1	CLONAL	2	TRUE	0	0.415467165768077	1		610	901	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912149	114912149	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005623-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1427	475	776	2	ENST00000543371.1:c.1219C>T	p.Arg407Ter	p.R407*	ENST00000543371	NM_001198531.1	407	Cga/Tga	11/14	0.415467165768077	3	FACETS	1	0.996	1	0.726	0.692	0.761	CLONAL	1	TRUE	1	0.415467165768077	3		778	1902	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266013	41266355	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	In_Frame_Del	DEL	ATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTA	ATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTA	-	novel	NA	P-0005623-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	138	348	0	ENST00000349496.5:c.15_242-85del		p.A5_D81del	ENST00000349496	NM_001904.3	5		3/15	0.415467165768077	3	FACETS	0.882	0.809	0.957	0.588	0.539	0.638	CLONAL	2	TRUE	0	0.415467165768077	3		348	455	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248320	59248321	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCTGC	novel	NA	P-0005623-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	64	81	0	ENST00000371222.2:c.418_422dup	p.Met142GlnfsTer8	p.M142Qfs*8	ENST00000371222	NM_002228.3	141	ggc/ggGCAGGc	1/1	0.347063268726699	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.415467165768077	3		81	158	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435160	56435161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755128667	NA	P-0005647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	83	195	1	ENST00000407977.2:c.1976dup	p.Pro660SerfsTer87	p.P660Sfs*87	ENST00000407977		659	ggt/ggGt	9/10	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.23	2		196	710	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207153	1207155	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs587782056	NA	P-0005647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1307	156	380	0	ENST00000326873.7:c.250_252del	p.Lys84del	p.K84del	ENST00000326873	NM_000455.4	81	AAG/-	1/10	0.102810352971652	0	FACETS	0.714	0.652	0.78			1	INDETERMINATE	1	TRUE	0	0.23	0		380	1463	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562657	29562660	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs1064794276	NA	P-0005647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1406	164	351	0	ENST00000356175.3:c.3739_3742del	p.Phe1247IlefsTer18	p.F1247Ifs*18	ENST00000356175	NM_000267.3	1246	cTGTTt/ct	28/57	1	2	FACETS	0.908	0.831	0.99	0.908	0.831	0.99	CLONAL	1	TRUE	1	0.23	2		351	1570	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470497	25470497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758881009	NA	P-0005647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	99	305	1	ENST00000264709.3:c.977G>A	p.Arg326His	p.R326H	ENST00000264709	NM_175629.2	326	cGc/cAc	8/23	1	2	FACETS	0.913	0.814	1	0.913	0.814	1	CLONAL	1	TRUE	1	0.23	2		306	943	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425230	49425230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199797812	NA	P-0005647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	105	289	0	ENST00000301067.7:c.13258C>T	p.Arg4420Trp	p.R4420W	ENST00000301067	NM_003482.3	4420	Cgg/Tgg	39/54	0.102810352971652	3	FACETS	0.997	0.892	1	0.499	0.446	0.555	INDETERMINATE	1	TRUE	1	0.23	3		289	1021	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684326	29684326	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201367	NA	P-0005647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1276	149	312	0	ENST00000356175.3:c.7846C>T	p.Arg2616Ter	p.R2616*	ENST00000356175	NM_000267.3	2616	Cga/Tga	53/57	1	2	FACETS	0.909	0.828	0.995	0.909	0.828	0.995	CLONAL	1	TRUE	1	0.23	2		312	1425	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564530	86564530	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	112	268	0	ENST00000274376.6:c.266del	p.Gly89GlufsTer7	p.G89Efs*7	ENST00000274376	NM_002890.2	88	Ggg/gg	1/25	0.204315897562358	4	FACETS	1	0.97	1	0.607	0.545	0.674	CLONAL	1	TRUE	2	0.23	4		268	986	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560085	29560087	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	novel	NA	P-0005647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1237	139	334	1	ENST00000356175.3:c.3565_3567del	p.Gln1189del	p.Q1189del	ENST00000356175	NM_000267.3	1188	CAA/-	27/57	1	2	FACETS	0.878	0.797	0.964	0.878	0.797	0.964	CLONAL	1	TRUE	1	0.23	2		335	1376	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564712	86564712	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	91	311	0	ENST00000274376.6:c.446del	p.Gly149AlafsTer25	p.G149Afs*25	ENST00000274376	NM_002890.2	148	gcG/gc	1/25	0.204315897562358	4	FACETS	0.999	0.885	1	0.5	0.442	0.561	CLONAL	1	TRUE	2	0.23	4		311	974	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37092023	37092036	+	frameshift_variant	Frame_Shift_Del	DEL	AACACATTGTCTAT	AACACATTGTCTAT	G	novel	NA	P-0005647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	114	325	0	ENST00000231790.2:c.2150_2163delinsG	p.Glu717GlyfsTer62	p.E717Gfs*62	ENST00000231790	NM_000249.3	717	gAACACATTGTCTAT/gG	19/19	1	2	FACETS	0.817	0.733	0.905	0.817	0.733	0.905	CLONAL	1	TRUE	1	0.23	2		325	1214	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155365	47155365	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0005682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	145	467	0	ENST00000409792.3:c.4715+1G>T		p.X1572_splice	ENST00000409792	NM_014159.6	1572			0.396043692595298	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.396043692595298	1		467	549	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511104	148511104	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	154	428	0	ENST00000320356.2:c.1798G>T	p.Asp600Tyr	p.D600Y	ENST00000320356	NM_004456.4	600	Gac/Tac	15/20	0.39021510295851	3	FACETS	1	0.974	1	0.577	0.528	0.627	CLONAL	1	TRUE	1	0.396043692595298	3		428	808	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191635	10191636	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	142	482	0	ENST00000256474.2:c.630dup	p.Met211AspfsTer45	p.M211Dfs*45	ENST00000256474	NM_000551.3	210	cgg/cGgg	3/3	0.396043692595298	1	FACETS	0.909	0.831	0.99	0.909	0.831	0.99	CLONAL	1	TRUE	0	0.396043692595298	1		482	633	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437879	52437879	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	299	893	2	ENST00000460680.1:c.1282del	p.Ala428HisfsTer2	p.A428Hfs*2	ENST00000460680	NM_004656.3	428	Gca/ca	13/17	0.396043692595298	1	FACETS	0.997	0.938	1	0.997	0.938	1	CLONAL	1	TRUE	0	0.396043692595298	1		895	1215	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720857	89720857	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	30	215	0	ENST00000371953.3:c.1008del	p.Ser338LeufsTer6	p.S338Lfs*6	ENST00000371953	NM_000314.4	336	taC/ta	8/9	0.168669754234072	1	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	0	0.17	1		215	297	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945665	206945665	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	45	625	0	ENST00000423557.1:c.116A>T	p.Asn39Ile	p.N39I	ENST00000423557	NM_000572.2	39	aAc/aTc	1/5	1	2	FACETS	0.818	0.686	0.965	0.818	0.686	0.965	CLONAL	1	TRUE	1	0.17	2		625	647	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183776	10183777	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	30	334	0	ENST00000256474.2:c.245_246insT	p.Val83ArgfsTer49	p.V83Rfs*49	ENST00000256474	NM_000551.3	82	cgc/cgTc	1/3	1	2	FACETS	0.859	0.692	1	0.859	0.692	1	CLONAL	1	TRUE	1	0.17	2		334	411	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106821	27106821	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	35	411	1	ENST00000324856.7:c.6433del	p.Glu2145ArgfsTer55	p.E2145Rfs*55	ENST00000324856	NM_006015.4	2144	ctG/ct	20/20	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.17	2		412	368	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	83	442	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.938	0.836	1	0.938	0.836	1	CLONAL	1	FALSE	1	0.547913177776093	2		444	323	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	231	435	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.547913177776093	2		436	810	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056588	26056590	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs751086925	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	88	159	0	ENST00000343677.2:c.67_69del	p.Lys23del	p.K23del	ENST00000343677	NM_005319.3	23	AAG/-	1/1	0.119618761749901	4	FACETS	0.863	0.774	0.956	0.863	0.774	0.956	INDETERMINATE	2	FALSE	2	0.547913177776093	4		159	288	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439586	51439586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1372032935	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	270	326	0	ENST00000262662.1:c.151G>A	p.Glu51Lys	p.E51K	ENST00000262662		51	Gag/Aag	4/4	1	2	FACETS	0.931	0.873	0.989	0.931	0.873	0.989	CLONAL	1	FALSE	1	0.547913177776093	2		326	1059	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846308	156846308	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	52	461	0	ENST00000524377.1:c.1753del	p.Leu585CysfsTer73	p.L585Cfs*73	ENST00000524377	NM_002529.3	583	cgC/cg	14/17	1	2	FACETS	0.388	0.33	0.451	0.388	0.33	0.451	SUBCLONAL	1	FALSE	1	0.547913177776093	2		461	489	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	293	401	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.547913177776093	2		401	1001	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	257	170	1	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	0.996	1	CLONAL	2	FALSE	1	0.547913177776093	2		171	427	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	40	243	0	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	1	FACETS	0.785	0.666	0.912	0.785	0.666	0.912	CLONAL	1	FALSE	0	0.547913177776093	1		243	135	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	124	342	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	FALSE	1	0.547913177776093	2		342	396	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	255	628	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	2	FALSE	NA	0.547913177776093	2		628	445	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247039	53247039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556852808	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	289	341	0	ENST00000375401.3:c.461G>A	p.Arg154His	p.R154H	ENST00000375401	NM_004187.3	154	cGc/cAc	4/26	1	1	FACETS	0.763	0.728	0.798	1	0.995	1	SUBCLONAL	2	FALSE	0	0.547913177776093	1		341	502	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849663	68849663	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587780113	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	118	314	0	ENST00000261769.5:c.1565+1G>A		p.X522_splice	ENST00000261769	NM_004360.3	522			1	2	FACETS	0.951	0.864	1	0.951	0.864	1	CLONAL	1	FALSE	1	0.547913177776093	2		314	453	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573505	48573506	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	342	600	0	ENST00000342988.3:c.94_95del	p.Ser32Ter	p.S32*	ENST00000342988	NM_005359.5	30	gGA/g	2/12	1	2	FACETS	0.996	0.942	1	0.996	0.942	1	CLONAL	1	FALSE	1	0.547913177776093	2		600	1253	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765459	41765459	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	152	379	0	ENST00000301178.4:c.2335T>C	p.Tyr779His	p.Y779H	ENST00000301178	NM_021913.4	779	Tat/Cat	20/20	0.155178620948969	0	FACETS	0.42	0.386	0.456			1	INDETERMINATE	1	FALSE	0	0.547913177776093	0		379	597	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287469	46287469	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	270	359	0	ENST00000334344.6:c.5333del	p.Asn1778IlefsTer13	p.N1778Ifs*13	ENST00000334344	NM_152641.2	1776	ttA/tt	20/21	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	1	0.547913177776093	2		359	985	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412913	49412913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	239	543	0	ENST00000418115.1:c.110C>T	p.Thr37Ile	p.T37I	ENST00000418115	NM_001664.2	37	aCa/aTa	2/5	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.547913177776093	2		543	786	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	213	463	1	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.547913177776093	2		464	757	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084146	47084146	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	195	307	0	ENST00000409792.3:c.7143del	p.Ser2382LeufsTer29	p.S2382Lfs*29	ENST00000409792	NM_014159.6	2381	ccC/cc	17/21	1	2	FACETS	0.93	0.863	1	0.93	0.863	1	CLONAL	1	FALSE	1	0.547913177776093	2		307	765	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648328	206648328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782549877	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	107	384	0	ENST00000367120.3:c.349C>T	p.Arg117Cys	p.R117C	ENST00000367120	NM_014002.3	117	Cgc/Tgc	5/22	1	2	FACETS	0.896	0.809	0.987	0.896	0.809	0.987	CLONAL	1	FALSE	1	0.547913177776093	2		384	436	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214591	5214591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770889503	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	139	471	1	ENST00000357368.4:c.4475G>A	p.Arg1492Gln	p.R1492Q	ENST00000357368	NM_002850.3	1492	cGg/cAg	29/38	0.155178620948969	0	FACETS	0.402	0.367	0.438			1	INDETERMINATE	1	FALSE	0	0.547913177776093	0		472	571	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188854	32188854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1183058401	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	98	422	0	ENST00000375023.3:c.700C>T	p.Arg234Trp	p.R234W	ENST00000375023	NM_004557.3	234	Cgg/Tgg	4/30	1	2	FACETS	0.89	0.8	0.984	0.89	0.8	0.984	CLONAL	1	FALSE	1	0.547913177776093	2		422	402	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780684	9780684	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	123	428	0	ENST00000377346.4:c.1486C>T	p.Arg496Ter	p.R496*	ENST00000377346	NM_005026.3	496	Cga/Tga	12/24	0.155178620948969	0	FACETS	0.49	0.447	0.535			1	INDETERMINATE	1	FALSE	0	0.547913177776093	0		428	414	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658601	206658601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879953097	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	187	484	0	ENST00000367120.3:c.1574G>A	p.Arg525Gln	p.R525Q	ENST00000367120	NM_014002.3	525	cGg/cAg	15/22	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.547913177776093	2		484	635	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523049	25523049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1367571644	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	134	413	0	ENST00000264709.3:c.136C>T	p.Arg46Trp	p.R46W	ENST00000264709	NM_175629.2	46	Cgg/Tgg	3/23	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	FALSE	1	0.547913177776093	2		413	487	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693887	47693887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778523	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	303	459	1	ENST00000233146.2:c.1601G>A	p.Arg534His	p.R534H	ENST00000233146	NM_000251.2	534	cGt/cAt	10/16	1	2	FACETS	0.979	0.922	1	0.979	0.922	1	CLONAL	1	FALSE	1	0.547913177776093	2		460	1130	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47709924	47709924	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	267	375	0	ENST00000233146.2:c.2641G>T	p.Glu881Ter	p.E881*	ENST00000233146	NM_000251.2	881	Gaa/Taa	16/16	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.547913177776093	2		375	942	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170929	99170929	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	194	439	1	ENST00000074304.5:c.1558G>A	p.Val520Met	p.V520M	ENST00000074304	NM_001134224.1	520	Gtg/Atg	16/26	1	2	FACETS	0.988	0.917	1	0.988	0.917	1	CLONAL	1	FALSE	1	0.547913177776093	2		440	717	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128036942	128036942	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	163	376	0	ENST00000285398.2:c.1537C>A	p.Pro513Thr	p.P513T	ENST00000285398	NM_000122.1	513	Cct/Act	10/15	1	2	FACETS	0.993	0.916	1	0.993	0.916	1	CLONAL	1	FALSE	1	0.547913177776093	2		376	599	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662554	227662554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866672328	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	84	345	1	ENST00000305123.5:c.901C>T	p.Arg301Cys	p.R301C	ENST00000305123	NM_005544.2	301	Cgc/Tgc	1/2	1	2	FACETS	0.506	0.447	0.569	0.506	0.447	0.569	SUBCLONAL	1	FALSE	1	0.547913177776093	2		346	606	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397700	49397700	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	218	463	0	ENST00000418115.1:c.524C>T	p.Thr175Met	p.T175M	ENST00000418115	NM_001664.2	175	aCg/aTg	5/5	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.547913177776093	2		463	774	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427588	72427588	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	228	402	2	ENST00000477973.2:c.902G>A	p.Arg301His	p.R301H	ENST00000477973	NM_012234.5	301	cGt/cAt	4/4	1	2	FACETS	0.999	0.933	1	0.999	0.933	1	CLONAL	1	FALSE	1	0.547913177776093	2		404	833	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003184	143003184	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	317	405	0	ENST00000262992.4:c.2642G>T	p.Arg881Ile	p.R881I	ENST00000262992	NM_001101669.1	881	aGa/aTa	23/24	0.547913177776093	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	0	0.547913177776093	1		405	771	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332544	153332544	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	373	436	0	ENST00000281708.4:c.412A>G	p.Thr138Ala	p.T138A	ENST00000281708	NM_033632.3	138	Aca/Gca	2/12	0.547913177776093	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	0	0.547913177776093	1		436	980	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628547	187628547	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	387	509	0	ENST00000441802.2:c.2435T>C	p.Val812Ala	p.V812A	ENST00000441802	NM_005245.3	812	gTt/gCt	2/27	0.547913177776093	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	FALSE	0	0.547913177776093	1		509	817	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293458	1293458	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	76	335	0	ENST00000310581.5:c.1543C>T	p.Arg515Trp	p.R515W	ENST00000310581	NM_198253.2	515	Cgg/Tgg	2/16	NA	2	FACETS	0.5	0.439	0.565			1	INDETERMINATE	1	FALSE	NA	0.547913177776093	2		335	555	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38991049	38991049	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	190	236	0	ENST00000357387.3:c.583+2T>C		p.X195_splice	ENST00000357387	NM_152756.3	195			0.119618761749901	4	FACETS	0.819	0.761	0.88	0.819	0.761	0.88	INDETERMINATE	2	FALSE	2	0.547913177776093	4		236	655	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131895051	131895051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370769989	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	124	199	0	ENST00000265335.6:c.205G>A	p.Asp69Asn	p.D69N	ENST00000265335		69	Gat/Aat	2/25	0.119618761749901	4	FACETS	1	0.982	1	0.672	0.611	0.736	INDETERMINATE	1	FALSE	2	0.547913177776093	4		199	521	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923258	131923258	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769196703	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	148	174	0	ENST00000265335.6:c.761G>A	p.Arg254His	p.R254H	ENST00000265335		254	cGt/cAt	6/25	0.119618761749901	4	FACETS	0.813	0.748	0.881	0.813	0.748	0.881	INDETERMINATE	2	FALSE	2	0.547913177776093	4		174	514	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441394	149441394	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370624765	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	100	302	1	ENST00000286301.3:c.1645C>T	p.Arg549Cys	p.R549C	ENST00000286301	NM_005211.3	549	Cgc/Tgc	12/22	1	2	FACETS	0.966	0.87	1	0.966	0.87	1	CLONAL	1	FALSE	1	0.547913177776093	2		303	378	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500865	149500865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	103	403	0	ENST00000261799.4:c.2365G>A	p.Ala789Thr	p.A789T	ENST00000261799	NM_002609.3	789	Gca/Aca	17/23	1	2	FACETS	0.767	0.69	0.849	0.767	0.69	0.849	SUBCLONAL	1	FALSE	1	0.547913177776093	2		403	490	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056284	26056284	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	205	327	0	ENST00000343677.2:c.373G>T	p.Gly125Ter	p.G125*	ENST00000343677	NM_005319.3	125	Gga/Tga	1/1	0.119618761749901	4	FACETS	0.824	0.767	0.882	0.824	0.767	0.882	INDETERMINATE	2	FALSE	2	0.547913177776093	4		327	703	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715871	117715871	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	283	348	0	ENST00000368508.3:c.887C>T	p.Ser296Phe	p.S296F	ENST00000368508	NM_002944.2	296	tCc/tTc	9/43	0.119618761749901	4	FACETS	1	0.993	1	0.739	0.695	0.784	INDETERMINATE	1	FALSE	2	0.547913177776093	4		348	1082	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527835	157527835	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	235	392	1	ENST00000346085.5:c.5560G>T	p.Gly1854Cys	p.G1854C	ENST00000346085	NM_020732.3	1854	Ggt/Tgt	20/20	0.119618761749901	4	FACETS	0.806	0.754	0.859	0.806	0.754	0.859	INDETERMINATE	2	FALSE	2	0.547913177776093	4		393	824	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940458	13940458	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	198	258	0	ENST00000405192.2:c.1048C>T	p.Arg350Ter	p.R350*	ENST00000405192	NM_001163147.1	350	Cga/Tga	11/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.547913177776093	2		258	666	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508556	106508556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1189118505	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	108	173	1	ENST00000359195.3:c.550C>T	p.Arg184Cys	p.R184C	ENST00000359195	NM_002649.2	184	Cgc/Tgc	2/11	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	1	0.547913177776093	2		174	382	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5081749	5081749	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	230	334	0	ENST00000381652.3:c.2459A>T	p.Asp820Val	p.D820V	ENST00000381652	NM_004972.3	820	gAc/gTc	19/25	1	2	FACETS	0.982	0.917	1	0.982	0.917	1	CLONAL	1	FALSE	1	0.547913177776093	2		334	855	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606431	93606431	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	122	320	0	ENST00000375746.1:c.251G>C	p.Ser84Thr	p.S84T	ENST00000375746	NM_001174167.1	84	aGc/aCc	2/14	1	2	FACETS	0.958	0.871	1	0.958	0.871	1	CLONAL	1	FALSE	1	0.547913177776093	2		320	465	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797289	135797289	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	363	407	0	ENST00000298552.3:c.580A>T	p.Met194Leu	p.M194L	ENST00000298552	NM_001162426.1	194	Atg/Ttg	7/23	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	1	0.547913177776093	2		407	1088	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406048	70406048	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199726871	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	250	400	0	ENST00000373644.4:c.3562G>A	p.Asp1188Asn	p.D1188N	ENST00000373644	NM_030625.2	1188	Gac/Aac	4/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.547913177776093	2		400	830	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518512	69518512	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	163	288	0	ENST00000294312.3:c.133C>T	p.Arg45Trp	p.R45W	ENST00000294312	NM_005117.2	45	Cgg/Tgg	1/3	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.547913177776093	2		288	521	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480404	56480404	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	214	536	0	ENST00000267101.3:c.511G>T	p.Asp171Tyr	p.D171Y	ENST00000267101	NM_001982.3	171	Gat/Tat	4/28	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.547913177776093	2		536	646	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926260	112926260	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	229	427	1	ENST00000351677.2:c.1393C>T	p.Arg465Trp	p.R465W	ENST00000351677	NM_002834.3	465	Cgg/Tgg	12/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.547913177776093	2		428	726	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434683	99434683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs577508225	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	223	405	0	ENST00000268035.6:c.770C>T	p.Ala257Val	p.A257V	ENST00000268035	NM_000875.3	257	gCc/gTc	3/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.547913177776093	2		405	760	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888138	81888138	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	246	606	0	ENST00000359376.3:c.283T>C	p.Cys95Arg	p.C95R	ENST00000359376	NM_002661.3	95	Tgc/Cgc	3/33	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.547913177776093	2		606	864	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969881	81969881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	272	561	0	ENST00000359376.3:c.2950C>T	p.Arg984Cys	p.R984C	ENST00000359376	NM_002661.3	984	Cgc/Tgc	27/33	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.547913177776093	2		561	940	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436026	56436026	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771831816	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	92	308	1	ENST00000407977.2:c.1111C>T	p.Arg371Ter	p.R371*	ENST00000407977		371	Cga/Tga	9/10	1	2	FACETS	0.898	0.804	0.996	0.898	0.804	0.996	CLONAL	1	FALSE	1	0.547913177776093	2		309	374	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439906	56439906	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs763974538	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	160	272	0	ENST00000407977.2:c.686C>T	p.Pro229Leu	p.P229L	ENST00000407977		229	cCg/cTg	6/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.547913177776093	2		272	503	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78854225	78854225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	168	428	2	ENST00000306801.3:c.1520C>T	p.Ala507Val	p.A507V	ENST00000306801	NM_020761.2	507	gCg/gTg	14/34	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.547913177776093	2		430	598	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867533	78867533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs185118480	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	148	457	0	ENST00000306801.3:c.2269G>A	p.Gly757Arg	p.G757R	ENST00000306801	NM_020761.2	757	Gga/Aga	20/34	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	FALSE	1	0.547913177776093	2		457	520	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919514	78919514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149834841	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	149	435	0	ENST00000306801.3:c.3073G>A	p.Val1025Ile	p.V1025I	ENST00000306801	NM_020761.2	1025	Gtc/Atc	26/34	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	FALSE	1	0.547913177776093	2		435	541	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210501	2210501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368335495	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	137	373	2	ENST00000398665.3:c.1108G>A	p.Ala370Thr	p.A370T	ENST00000398665	NM_032482.2	370	Gcc/Acc	13/28	0.155178620948969	0	FACETS	0.456	0.417	0.496			1	INDETERMINATE	1	FALSE	0	0.547913177776093	0		375	496	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145624	11145624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555785361	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	160	354	0	ENST00000358026.2:c.3986G>A	p.Arg1329His	p.R1329H	ENST00000358026	NM_001128849.1	1329	cGc/cAc	29/36	0.155178620948969	0	FACETS	0.516	0.476	0.557			1	INDETERMINATE	1	FALSE	0	0.547913177776093	0		354	512	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298730	15298730	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	53	427	0	ENST00000263388.2:c.1568T>C	p.Val523Ala	p.V523A	ENST00000263388	NM_000435.2	523	gTg/gCg	10/33	0.155178620948969	0	FACETS	0.192	0.164	0.223			1	INDETERMINATE	1	FALSE	0	0.547913177776093	0		427	455	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15365052	15365052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	135	409	1	ENST00000263377.2:c.2069C>T	p.Ala690Val	p.A690V	ENST00000263377	NM_058243.2	690	gCc/gTc	11/20	0.155178620948969	0	FACETS	0.451	0.412	0.491			1	INDETERMINATE	1	FALSE	0	0.547913177776093	0		410	494	SUCCESS
AXL	558	MSKCC	GRCh37	19	41737136	41737136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761251235	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	185	499	0	ENST00000301178.4:c.716C>T	p.Thr239Met	p.T239M	ENST00000301178	NM_021913.4	239	aCg/aTg	6/20	0.155178620948969	0	FACETS	0.513	0.476	0.551			1	INDETERMINATE	1	FALSE	0	0.547913177776093	0		499	595	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793416	42793416	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	119	319	0	ENST00000575354.2:c.1218G>T	p.Glu406Asp	p.E406D	ENST00000575354	NM_015125.3	406	gaG/gaT	8/20	0.155178620948969	0	FACETS	0.511	0.466	0.558			1	INDETERMINATE	1	FALSE	0	0.547913177776093	0		319	384	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797780	42797780	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771163344	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	98	398	1	ENST00000575354.2:c.3832G>A	p.Val1278Ile	p.V1278I	ENST00000575354	NM_015125.3	1278	Gtc/Atc	16/20	0.155178620948969	0	FACETS	0.387	0.347	0.429			1	INDETERMINATE	1	FALSE	0	0.547913177776093	0		399	418	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945355	54945355	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	162	277	0	ENST00000312783.6:c.1071G>T	p.Arg357Ser	p.R357S	ENST00000312783	NM_198436.1	357	agG/agT	10/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.547913177776093	2		277	517	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121241	29121241	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781667	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	463	517	0	ENST00000328354.6:c.434G>A	p.Arg145Gln	p.R145Q	ENST00000328354	NM_007194.3	145	cGg/cAg	3/15	0.494628615863541	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	FALSE	1	0.547913177776093	3		517	1067	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566519	41566519	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	250	549	0	ENST00000263253.7:c.4396T>C	p.Trp1466Arg	p.W1466R	ENST00000263253	NM_001429.3	1466	Tgg/Cgg	27/31	0.547913177776093	3	FACETS	0.82	0.765	0.877			1	CLONAL	1	FALSE	NA	0.547913177776093	3		549	1418	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70355041	70355041	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	203	300	0	ENST00000374080.3:c.4963G>T	p.Gly1655Cys	p.G1655C	ENST00000374080		1655	Ggc/Tgc	36/45	1	1	FACETS	0.758	0.716	0.799	1	0.993	1	SUBCLONAL	2	FALSE	0	0.547913177776093	1		300	355	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937084	76937084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782520515	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	432	283	0	ENST00000373344.5:c.3664G>A	p.Asp1222Asn	p.D1222N	ENST00000373344	NM_000489.3	1222	Gat/Aat	9/35	1	1	FACETS	0.766	0.738	0.795	1	0.997	1	SUBCLONAL	2	FALSE	0	0.547913177776093	1		283	747	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401385	139401385	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	124	269	2	ENST00000277541.6:c.3684del	p.Val1229LeufsTer216	p.V1229Lfs*216	ENST00000277541	NM_017617.3	1228	ccC/cc	23/34	1	2	FACETS	0.947	0.862	1	0.947	0.862	1	CLONAL	1	FALSE	1	0.547913177776093	2		271	478	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733513	85733513	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs387906350	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	392	769	2	ENST00000370580.1:c.499del	p.Ser167LeufsTer6	p.S167Lfs*6	ENST00000370580	NM_003921.4	167	Tct/ct	3/3	1	2	FACETS	0.994	0.944	1	0.994	0.944	1	CLONAL	1	FALSE	1	0.547913177776093	2		771	1439	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518488	69518488	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	175	259	0	ENST00000294312.3:c.157del	p.His53ThrfsTer93	p.H53Tfs*93	ENST00000294312	NM_005117.2	53	Cac/ac	1/3	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.547913177776093	2		259	499	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426729	49426730	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs576788910	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	27	150	0	ENST00000301067.7:c.11756_11758dup	p.Gln3919dup	p.Q3919dup	ENST00000301067	NM_003482.3	3919	cta/cAGCta	39/54	1	2	FACETS	0.857	0.695	1	0.857	0.695	1	CLONAL	1	FALSE	1	0.547913177776093	2		150	115	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760024	133760024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	167	460	3	ENST00000318560.5:c.2352del	p.Arg785GlyfsTer3	p.R785Gfs*3	ENST00000318560	NM_005157.4	783	Ccc/cc	11/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.547913177776093	2		463	578	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029193	26029195	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	226	343	0	ENST00000435504.4:c.155_157del	p.Pro52del	p.P52del	ENST00000435504		52	cCTCtt/ctt	4/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.547913177776093	2		343	737	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100331	27100331	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	185	496	0	ENST00000324856.7:c.4046del	p.Pro1349LeufsTer132	p.P1349Lfs*132	ENST00000324856	NM_006015.4	1348	aCc/ac	17/20	NA	2	FACETS	0.92	0.852	0.991			1	INDETERMINATE	1	FALSE	NA	0.547913177776093	2		496	734	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702391	47702399	+	inframe_deletion	In_Frame_Del	DEL	ATGTTCCAC	ATGTTCCAC	-	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	111	282	0	ENST00000233146.2:c.1989_1997del	p.Met663_His665del	p.M663_H665del	ENST00000233146	NM_000251.2	663	ATGTTCCAC/-	12/16	1	2	FACETS	0.73	0.658	0.805	0.73	0.658	0.805	SUBCLONAL	1	FALSE	1	0.547913177776093	2		282	555	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091793	29091793	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs758677815	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	159	287	0	ENST00000328354.6:c.1164del	p.Thr389ProfsTer25	p.T389Pfs*25	ENST00000328354	NM_007194.3	388	ccC/cc	11/15	0.494628615863541	3	FACETS	1	0.981	1	0.604	0.556	0.654	CLONAL	1	FALSE	1	0.547913177776093	3		287	612	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409036	139409036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	106	524	0	ENST00000277541.6:c.2133del	p.Thr712ProfsTer60	p.T712Pfs*60	ENST00000277541	NM_017617.3	711	ccC/cc	13/34	1	2	FACETS	0.636	0.572	0.705	0.636	0.572	0.705	SUBCLONAL	1	FALSE	1	0.547913177776093	2		524	608	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149802	202149805	+	frameshift_variant	Frame_Shift_Del	DEL	TTTA	TTTA	-	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	169	339	0	ENST00000358485.4:c.1245_1248del	p.Ile416ArgfsTer24	p.I416Rfs*24	ENST00000358485	NM_001080125.1	415	TTTAtt/tt	8/9	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	FALSE	1	0.547913177776093	2		339	613	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445374	49445375	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	94	379	0	ENST00000301067.7:c.2091dup	p.Thr698HisfsTer6	p.T698Hfs*6	ENST00000301067	NM_003482.3	697	-/C	10/54	1	2	FACETS	0.889	0.797	0.985	0.889	0.797	0.985	CLONAL	1	FALSE	1	0.547913177776093	2		379	386	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101259	27101259	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	150	428	0	ENST00000324856.7:c.4541del	p.Thr1514ArgfsTer13	p.T1514Rfs*13	ENST00000324856	NM_006015.4	1514	aCg/ag	18/20	NA	2	FACETS	1	0.929	1			1	INDETERMINATE	1	FALSE	NA	0.547913177776093	2		428	541	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007825	45007825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	219	505	0	ENST00000558401.1:c.276del	p.Thr93LeufsTer10	p.T93Lfs*10	ENST00000558401	NM_004048.2	91	aCc/ac	2/4	1	2	FACETS	0.944	0.88	1	0.944	0.88	1	CLONAL	1	FALSE	1	0.547913177776093	2		505	847	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1328	175	817	4	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	0.425	0.39	0.462	0.425	0.39	0.462	SUBCLONAL	1	FALSE	1	0.547913177776093	2		821	1503	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420202	88420202	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	194	429	0	ENST00000360948.2:c.2484del	p.Lys829ArgfsTer18	p.K829Rfs*18	ENST00000360948	NM_001012338.2	828	ggG/gg	19/19	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.547913177776093	2		429	687	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781901	3781903	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	rs751071525	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	128	459	0	ENST00000262367.5:c.4764_4766del	p.Lys1588del	p.K1588del	ENST00000262367	NM_004380.2	1588	aaGAAc/aac	29/31	1	2	FACETS	0.89	0.811	0.973	0.89	0.811	0.973	CLONAL	1	FALSE	1	0.547913177776093	2		459	525	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123837	46123837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	222	256	0	ENST00000334344.6:c.109del	p.Ile37SerfsTer21	p.I37Sfs*21	ENST00000334344	NM_152641.2	35	Aaa/aa	2/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.547913177776093	2		256	763	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937419	76937421	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	rs1225014954	NA	P-0005823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	342	232	0	ENST00000373344.5:c.3327_3329del	p.Ser1110del	p.S1110del	ENST00000373344	NM_000489.3	1109	tcATCt/tct	9/35	1	1	FACETS	0.78	0.747	0.812	1	0.996	1	SUBCLONAL	2	FALSE	0	0.547913177776093	1		232	581	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	161	435	1	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	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		436	825	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115600	108115600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772821016	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	187	497	0	ENST00000278616.4:c.748C>T	p.Arg250Ter	p.R250*	ENST00000278616	NM_000051.3	250	Cga/Tga	7/63	1	2	FACETS	1	0.97	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		497	936	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	216	530	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	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		530	1052	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143241	24143241	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1232172026	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	279	656	2	ENST00000263121.7:c.473G>A	p.Arg158Gln	p.R158Q	ENST00000263121	NM_003073.3	158	cGa/cAa	4/9	1	2	FACETS	0.96	0.901	1	1	0.996	1	CLONAL	4	TRUE	1	0.121712654762108	2		658	1194	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	264	723	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.966	1	1	0.996	1	CLONAL	3	TRUE	1	0.121712654762108	2		723	1377	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	128	480	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.949	0.861	1	1	0.992	1	CLONAL	3	TRUE	1	0.121712654762108	2		480	739	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	205	551	0	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	1	2	FACETS	1	0.967	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		551	1046	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307902	11307902	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	239	652	0	ENST00000361445.4:c.1090G>T	p.Asp364Tyr	p.D364Y	ENST00000361445	NM_004958.3	364	Gac/Tac	7/58	1	2	FACETS	1	0.982	1	1	0.996	1	CLONAL	3	TRUE	1	0.121712654762108	2		652	1142	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237703	16237703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	261	592	1	ENST00000375759.3:c.1150C>T	p.Arg384Trp	p.R384W	ENST00000375759	NM_015001.2	384	Cgg/Tgg	5/15	1	2	FACETS	0.931	0.871	0.992	1	0.996	1	CLONAL	4	TRUE	1	0.121712654762108	2		593	1152	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259962	16259962	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	294	571	0	ENST00000375759.3:c.7227G>T	p.Glu2409Asp	p.E2409D	ENST00000375759	NM_015001.2	2409	gaG/gaT	11/15	1	2	FACETS	1	0.953	1	1	0.997	1	CLONAL	4	TRUE	1	0.121712654762108	2		571	1190	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094291	27094291	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	168	404	0	ENST00000324856.7:c.2999C>A	p.Ser1000Tyr	p.S1000Y	ENST00000324856	NM_006015.4	1000	tCt/tAt	11/20	1	2	FACETS	1	0.971	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		404	826	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105694	27105694	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	179	586	2	ENST00000324856.7:c.5305C>A	p.Leu1769Ile	p.L1769I	ENST00000324856	NM_006015.4	1769	Cta/Ata	20/20	1	2	FACETS	0.996	0.918	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		588	984	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36826842	36826842	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	236	621	1	ENST00000373129.3:c.92G>T	p.Arg31Ile	p.R31I	ENST00000373129	NM_032017.1	31	aGa/aTa	3/12	1	2	FACETS	1	0.958	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		622	1246	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941155	36941155	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs145623142	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	267	752	1	ENST00000361632.4:c.184C>A	p.Leu62Met	p.L62M	ENST00000361632		62	Ctg/Atg	3/16	1	2	FACETS	1	0.984	1	1	0.996	1	CLONAL	3	TRUE	1	0.121712654762108	2		753	1277	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805719	43805719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528834914	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	78	571	0	ENST00000372470.3:c.775G>A	p.Glu259Lys	p.E259K	ENST00000372470	NM_005373.2	259	Gaa/Aaa	5/12	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.121712654762108	2		571	1102	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812274	43812274	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	206	436	0	ENST00000372470.3:c.1139G>C	p.Gly380Ala	p.G380A	ENST00000372470	NM_005373.2	380	gGc/gCc	7/12	1	2	FACETS	0.955	0.887	1	1	0.995	1	CLONAL	4	TRUE	1	0.121712654762108	2		436	886	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795032	45795032	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs768671057	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	237	599	1	ENST00000450313.1:c.1596C>A	p.Phe532Leu	p.F532L	ENST00000450313	NM_012222.2	532	ttC/ttA	16/16	1	2	FACETS	1	0.953	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		600	1262	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65300268	65300268	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	120	348	0	ENST00000342505.4:c.3442G>T	p.Gly1148Ter	p.G1148*	ENST00000342505	NM_002227.2	1148	Gga/Tga	25/25	1	2	FACETS	1	0.964	1	1	0.992	1	CLONAL	3	TRUE	1	0.121712654762108	2		348	581	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310506	65310506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	277	568	2	ENST00000342505.4:c.2182G>A	p.Asp728Asn	p.D728N	ENST00000342505	NM_002227.2	728	Gac/Aac	16/25	1	2	FACETS	0.95	0.891	1	1	0.996	1	CLONAL	4	TRUE	1	0.121712654762108	2		570	1198	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65316594	65316594	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	97	380	0	ENST00000342505.4:c.1649-1G>T		p.X550_splice	ENST00000342505	NM_002227.2	550			1	2	FACETS	0.988	0.88	1	1	0.986	1	CLONAL	2	TRUE	1	0.121712654762108	2		380	807	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321245	65321245	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771960711	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	173	435	0	ENST00000342505.4:c.1595G>A	p.Arg532His	p.R532H	ENST00000342505	NM_002227.2	532	cGc/cAc	11/25	1	2	FACETS	1	0.975	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		435	833	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65334993	65334993	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	67	399	0	ENST00000342505.4:c.647+1G>T		p.X216_splice	ENST00000342505	NM_002227.2	216			1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.121712654762108	2		399	809	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65348959	65348959	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	46	288	0	ENST00000342505.4:c.205+1G>A		p.X69_splice	ENST00000342505	NM_002227.2	69			1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.121712654762108	2		288	628	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163744	72163744	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1248852117	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	215	697	0	ENST00000357731.5:c.614C>T	p.Ala205Val	p.A205V	ENST00000357731	NM_173808.2	205	gCg/gTg	4/7	1	2	FACETS	0.924	0.857	0.993	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		697	1275	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166011	118166011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750792861	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	175	463	0	ENST00000369448.3:c.521G>A	p.Arg174Gln	p.R174Q	ENST00000369448	NM_017709.3	174	cGg/cAg	2/2	1	2	FACETS	0.888	0.818	0.959	1	0.994	1	CLONAL	4	TRUE	1	0.121712654762108	2		463	810	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870200	155870200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	214	567	0	ENST00000368323.3:c.639G>T	p.Lys213Asn	p.K213N	ENST00000368323	NM_006912.5	213	aaG/aaT	6/6	1	2	FACETS	1	0.958	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		567	1122	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834571	156834571	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	147	551	0	ENST00000524377.1:c.339C>A	p.Phe113Leu	p.F113L	ENST00000524377	NM_002529.3	113	ttC/ttA	3/17	1	2	FACETS	1	0.962	1	1	0.991	1	CLONAL	2	TRUE	1	0.121712654762108	2		551	1098	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849050	156849050	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	230	492	1	ENST00000524377.1:c.1942C>A	p.His648Asn	p.H648N	ENST00000524377	NM_002529.3	648	Cac/Aac	15/17	1	2	FACETS	1	0.963	1	1	0.996	1	CLONAL	4	TRUE	1	0.121712654762108	2		493	904	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162688884	162688884	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	162	504	0	ENST00000367921.3:c.31C>A	p.Leu11Met	p.L11M	ENST00000367921	NM_006182.2	11	Ctg/Atg	3/18	1	2	FACETS	0.928	0.851	1	1	0.993	1	CLONAL	3	TRUE	1	0.121712654762108	2		504	956	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741963	162741963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	221	632	0	ENST00000367921.3:c.1654G>A	p.Asp552Asn	p.D552N	ENST00000367921	NM_006182.2	552	Gat/Aat	13/18	1	2	FACETS	1	0.961	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		632	1153	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748475	162748475	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	152	467	0	ENST00000367921.3:c.2389G>T	p.Val797Phe	p.V797F	ENST00000367921	NM_006182.2	797	Gtt/Ttt	17/18	1	2	FACETS	1	0.966	1	1	0.993	1	CLONAL	3	TRUE	1	0.121712654762108	2		467	753	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099343	193099343	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	166	389	0	ENST00000367435.3:c.277G>T	p.Asp93Tyr	p.D93Y	ENST00000367435	NM_024529.4	93	Gat/Tat	3/17	1	2	FACETS	0.994	0.913	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		389	915	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119509	193119509	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	68	440	1	ENST00000367435.3:c.904G>T	p.Glu302Ter	p.E302*	ENST00000367435	NM_024529.4	302	Gaa/Taa	9/17	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.121712654762108	2		441	932	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228613019	228613019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773567566	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	106	592	1	ENST00000366696.1:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000366696	NM_003493.2	3	cGa/cAa	1/1	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.121712654762108	2		593	1183	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243675668	243675668	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	152	419	0	ENST00000263826.5:c.1312G>T	p.Glu438Ter	p.E438*	ENST00000263826	NM_005465.4	438	Gaa/Taa	12/13	1	2	FACETS	1	0.947	1	1	0.993	1	CLONAL	3	TRUE	1	0.121712654762108	2		419	796	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965982	25965982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs62130126	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	231	560	0	ENST00000435504.4:c.3224G>A	p.Arg1075Gln	p.R1075Q	ENST00000435504		1075	cGg/cAg	13/13	1	2	FACETS	1	0.979	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		560	1130	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994324	25994324	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	233	590	0	ENST00000435504.4:c.489G>T	p.Lys163Asn	p.K163N	ENST00000435504		163	aaG/aaT	6/13	1	2	FACETS	1	0.967	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		590	1202	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068357	26068357	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	128	421	0	ENST00000435504.4:c.133G>T	p.Glu45Ter	p.E45*	ENST00000435504		45	Gaa/Taa	2/13	1	2	FACETS	1	0.975	1	1	0.991	1	CLONAL	2	TRUE	1	0.121712654762108	2		421	859	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068393	26068393	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	190	467	0	ENST00000435504.4:c.97G>T	p.Glu33Ter	p.E33*	ENST00000435504		33	Gaa/Taa	2/13	1	2	FACETS	1	0.959	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		467	985	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446209	29446209	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs774951734	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	220	414	0	ENST00000389048.3:c.3358C>T	p.Arg1120Trp	p.R1120W	ENST00000389048	NM_004304.4	1120	Cgg/Tgg	20/29	1	2	FACETS	0.983	0.916	1	1	0.996	1	CLONAL	4	TRUE	1	0.121712654762108	2		414	919	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917726	29917726	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	164	478	1	ENST00000389048.3:c.942G>T	p.Glu314Asp	p.E314D	ENST00000389048	NM_004304.4	314	gaG/gaT	3/29	1	2	FACETS	1	0.952	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		479	854	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698180	47698180	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63751411	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	161	438	0	ENST00000233146.2:c.1738G>T	p.Glu580Ter	p.E580*	ENST00000233146	NM_000251.2	580	Gaa/Taa	11/16	1	2	FACETS	0.925	0.848	1	1	0.993	1	CLONAL	3	TRUE	1	0.121712654762108	2		438	953	SUCCESS
REL	5966	MSKCC	GRCh37	2	61128137	61128137	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	174	309	0	ENST00000295025.8:c.313T>G	p.Leu105Val	p.L105V	ENST00000295025	NM_002908.2	105	Ttg/Gtg	4/11	1	2	FACETS	0.897	0.827	0.969	1	0.994	1	CLONAL	4	TRUE	1	0.121712654762108	2		309	797	SUCCESS
REL	5966	MSKCC	GRCh37	2	61144142	61144142	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	58	387	0	ENST00000295025.8:c.525T>G	p.Ile175Met	p.I175M	ENST00000295025	NM_002908.2	175	atT/atG	5/11	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.121712654762108	2		387	800	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	152	356	2	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	1	2	FACETS	1	0.973	1	1	0.993	1	CLONAL	3	TRUE	1	0.121712654762108	2		358	724	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61753622	61753622	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	131	419	0	ENST00000401558.2:c.161A>C	p.Lys54Thr	p.K54T	ENST00000401558	NM_003400.3	54	aAg/aCg	3/25	1	2	FACETS	1	0.965	1	1	0.991	1	CLONAL	2	TRUE	1	0.121712654762108	2		419	949	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046948	128046948	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	199	543	0	ENST00000285398.2:c.787G>T	p.Glu263Ter	p.E263*	ENST00000285398	NM_000122.1	263	Gaa/Taa	6/15	1	2	FACETS	1	0.967	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		543	1011	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873097	136873097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	347	761	6	ENST00000241393.3:c.401G>A	p.Arg134His	p.R134H	ENST00000241393	NM_003467.2	134	cGc/cAc	2/2	1	2	FACETS	0.972	0.919	1	1	0.997	1	CLONAL	4	TRUE	1	0.121712654762108	2		767	1466	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617565	158617565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	112	632	1	ENST00000263640.3:c.1091G>A	p.Ser364Asn	p.S364N	ENST00000263640	NM_001105.4	364	aGc/aAc	9/11	1	2	FACETS	0.843	0.757	0.936	1	0.985	1	CLONAL	2	TRUE	1	0.121712654762108	2		633	1091	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158626972	158626972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	262	624	2	ENST00000263640.3:c.698C>T	p.Ala233Val	p.A233V	ENST00000263640	NM_001105.4	233	gCc/gTc	7/11	1	2	FACETS	0.91	0.852	0.97	1	0.996	1	CLONAL	4	TRUE	1	0.121712654762108	2		626	1183	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096592	178096592	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	125	365	2	ENST00000397062.3:c.739C>A	p.Leu247Ile	p.L247I	ENST00000397062	NM_006164.4	247	Ctt/Att	5/5	1	2	FACETS	1	0.92	1	1	0.992	1	CLONAL	3	TRUE	1	0.121712654762108	2		367	674	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682826	190682826	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	147	417	0	ENST00000441310.2:c.502G>T	p.Glu168Ter	p.E168*	ENST00000441310	NM_000534.4	168	Gaa/Taa	5/13	1	2	FACETS	1	0.941	1	1	0.993	1	CLONAL	3	TRUE	1	0.121712654762108	2		417	776	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728575	190728575	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	232	538	0	ENST00000441310.2:c.1963A>G	p.Lys655Glu	p.K655E	ENST00000441310	NM_000534.4	655	Aaa/Gaa	10/13	1	2	FACETS	1	0.965	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		538	1203	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198260916	198260916	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	165	608	0	ENST00000335508.6:c.3403G>A	p.Glu1135Lys	p.E1135K	ENST00000335508	NM_012433.2	1135	Gaa/Aaa	23/25	1	2	FACETS	0.878	0.806	0.954	1	0.993	1	CLONAL	3	TRUE	1	0.121712654762108	2		608	1029	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198263220	198263220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	179	486	0	ENST00000335508.6:c.3099G>T	p.Glu1033Asp	p.E1033D	ENST00000335508	NM_012433.2	1033	gaG/gaT	21/25	1	2	FACETS	0.948	0.873	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		486	1034	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270010	198270010	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	57	445	0	ENST00000335508.6:c.1426G>T	p.Asp476Tyr	p.D476Y	ENST00000335508	NM_012433.2	476	Gat/Tat	10/25	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.121712654762108	2		445	833	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202123091	202123091	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1279024876	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	184	290	0	ENST00000358485.4:c.137G>T	p.Gly46Val	p.G46V	ENST00000358485	NM_001080125.1	46	gGa/gTa	1/9	1	2	FACETS	0.929	0.861	0.999	1	0.995	1	CLONAL	5	TRUE	1	0.121712654762108	2		290	651	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131447	202131447	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	184	516	0	ENST00000358485.4:c.415A>C	p.Asn139His	p.N139H	ENST00000358485	NM_001080125.1	139	Aac/Cac	2/9	1	2	FACETS	0.983	0.907	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		516	1025	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149643	202149643	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	209	576	0	ENST00000358485.4:c.1084G>A	p.Asp362Asn	p.D362N	ENST00000358485	NM_001080125.1	362	Gac/Aac	8/9	1	2	FACETS	0.94	0.874	1	1	0.995	1	CLONAL	4	TRUE	1	0.121712654762108	2		576	913	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251606	212251606	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	59	377	0	ENST00000342788.4:c.3453G>T	p.Met1151Ile	p.M1151I	ENST00000342788	NM_005235.2	1151	atG/atT	27/28	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.121712654762108	2		377	830	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251747	212251747	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	89	427	0	ENST00000342788.4:c.3312C>A	p.Asp1104Glu	p.D1104E	ENST00000342788	NM_005235.2	1104	gaC/gaA	27/28	1	2	FACETS	0.926	0.82	1	1	0.984	1	CLONAL	2	TRUE	1	0.121712654762108	2		427	790	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251814	212251814	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	47	387	0	ENST00000342788.4:c.3245G>T	p.Arg1082Ile	p.R1082I	ENST00000342788	NM_005235.2	1082	aGa/aTa	27/28	1	2	FACETS	0.952	0.801	1	0.952	0.801	1	CLONAL	1	TRUE	1	0.121712654762108	2		387	811	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286805	212286805	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	143	405	0	ENST00000342788.4:c.2891G>T	p.Arg964Ile	p.R964I	ENST00000342788	NM_005235.2	964	aGa/aTa	24/28	1	2	FACETS	0.962	0.878	1	1	0.993	1	CLONAL	3	TRUE	1	0.121712654762108	2		405	814	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439839	220439839	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761479412	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	245	660	0	ENST00000243786.2:c.692G>A	p.Arg231Gln	p.R231Q	ENST00000243786	NM_002191.3	231	cGa/cAa	2/2	1	2	FACETS	0.904	0.845	0.966	1	0.996	1	CLONAL	4	TRUE	1	0.121712654762108	2		660	1113	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661897	227661897	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs544750977	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	141	331	0	ENST00000305123.5:c.1558C>T	p.Arg520Trp	p.R520W	ENST00000305123	NM_005544.2	520	Cgg/Tgg	1/2	1	2	FACETS	0.933	0.853	1	1	0.993	1	CLONAL	4	TRUE	1	0.121712654762108	2		331	621	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641652	12641652	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	40	341	0	ENST00000251849.4:c.989T>G	p.Ile330Ser	p.I330S	ENST00000251849	NM_002880.3	330	aTt/aGt	9/17	1	2	FACETS	0.825	0.683	0.983	0.825	0.683	0.983	CLONAL	1	TRUE	1	0.121712654762108	2		341	797	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144859	47144859	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	103	505	1	ENST00000409792.3:c.4894G>A	p.Glu1632Lys	p.E1632K	ENST00000409792	NM_014159.6	1632	Gaa/Aaa	7/21	1	2	FACETS	0.816	0.729	0.909	1	0.984	1	CLONAL	2	TRUE	1	0.121712654762108	2		506	1037	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162485	47162485	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	198	497	0	ENST00000409792.3:c.3641A>C	p.Asn1214Thr	p.N1214T	ENST00000409792	NM_014159.6	1214	aAt/aCt	3/21	1	2	FACETS	1	0.976	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		497	967	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163277	47163277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149265978	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	182	620	1	ENST00000409792.3:c.2849G>A	p.Arg950His	p.R950H	ENST00000409792	NM_014159.6	950	cGt/cAt	3/21	1	2	FACETS	0.946	0.872	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		621	1054	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165678	47165678	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	201	540	0	ENST00000409792.3:c.448C>A	p.His150Asn	p.H150N	ENST00000409792	NM_014159.6	150	Cat/Aat	3/21	1	2	FACETS	1	0.973	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		540	998	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643768	52643768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	160	540	0	ENST00000394830.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000394830	NM_018313.4	710	Cga/Tga	17/30	1	2	FACETS	0.991	0.909	1	1	0.993	1	CLONAL	3	TRUE	1	0.121712654762108	2		540	884	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696234	52696234	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	66	563	0	ENST00000394830.3:c.443G>T	p.Arg148Ile	p.R148I	ENST00000394830	NM_018313.4	148	aGa/aTa	5/30	1	2	FACETS	0.914	0.791	1	0.914	0.791	1	CLONAL	1	TRUE	1	0.121712654762108	2		563	1186	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008501	70008501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147148433	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	174	502	2	ENST00000394351.3:c.788G>A	p.Arg263His	p.R263H	ENST00000394351	NM_000248.3	263	cGc/cAc	8/9	1	2	FACETS	1	0.923	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		504	950	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015074	71015074	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	73	547	0	ENST00000318789.4:c.1856A>G	p.Asp619Gly	p.D619G	ENST00000318789	NM_032682.5	619	gAc/gGc	20/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.121712654762108	2		547	1047	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72873669	72873669	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	174	404	1	ENST00000325599.8:c.633G>T	p.Gln211His	p.Q211H	ENST00000325599	NM_018130.2	211	caG/caT	6/11	1	2	FACETS	1	0.954	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		405	907	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259649	89259649	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	35	209	0	ENST00000336596.2:c.793G>T	p.Glu265Ter	p.E265*	ENST00000336596	NM_005233.5	265	Gaa/Taa	3/17	1	2	FACETS	0.965	0.794	1	1	0.962	1	CLONAL	2	TRUE	1	0.121712654762108	2		209	298	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456518	89456518	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	127	500	0	ENST00000336596.2:c.1694G>T	p.Gly565Val	p.G565V	ENST00000336596	NM_005233.5	565	gGg/gTg	8/17	1	2	FACETS	1	0.947	1	1	0.99	1	CLONAL	2	TRUE	1	0.121712654762108	2		500	977	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498484	89498484	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	191	617	0	ENST00000336596.2:c.2456C>A	p.Ser819Tyr	p.S819Y	ENST00000336596	NM_005233.5	819	tCt/tAt	14/17	1	2	FACETS	1	0.953	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		617	1005	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670708	134670708	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	156	480	0	ENST00000398015.3:c.619C>A	p.Pro207Thr	p.P207T	ENST00000398015	NM_004441.4	207	Cca/Aca	3/16	1	2	FACETS	0.941	0.862	1	1	0.993	1	CLONAL	3	TRUE	1	0.121712654762108	2		480	908	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138376574	138376574	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	198	572	1	ENST00000289153.2:c.2900T>A	p.Val967Asp	p.V967D	ENST00000289153	NM_006219.2	967	gTc/gAc	20/22	1	2	FACETS	1	0.954	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		573	1042	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426112	138426112	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	172	432	0	ENST00000289153.2:c.1419G>T	p.Leu473Phe	p.L473F	ENST00000289153	NM_006219.2	473	ttG/ttT	9/22	1	2	FACETS	1	0.97	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		432	849	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453486	138453486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451809865	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	210	557	0	ENST00000289153.2:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000289153	NM_006219.2	321	cGa/cAa	5/22	1	2	FACETS	0.992	0.92	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		557	1159	SUCCESS
ATR	545	MSKCC	GRCh37	3	142204013	142204013	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	159	506	2	ENST00000350721.4:c.6190C>A	p.Leu2064Ile	p.L2064I	ENST00000350721	NM_001184.3	2064	Ctc/Atc	36/47	1	2	FACETS	0.867	0.794	0.944	1	0.993	1	CLONAL	3	TRUE	1	0.121712654762108	2		508	1004	SUCCESS
ATR	545	MSKCC	GRCh37	3	142253951	142253951	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	203	492	0	ENST00000350721.4:c.3916A>C	p.Ser1306Arg	p.S1306R	ENST00000350721	NM_001184.3	1306	Agc/Cgc	21/47	1	2	FACETS	0.895	0.83	0.962	1	0.995	1	CLONAL	4	TRUE	1	0.121712654762108	2		492	932	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278247	142278247	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	159	307	0	ENST00000350721.4:c.1578G>T	p.Lys526Asn	p.K526N	ENST00000350721	NM_001184.3	526	aaG/aaT	7/47	1	2	FACETS	0.976	0.898	1	1	0.994	1	CLONAL	4	TRUE	1	0.121712654762108	2		307	669	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917594	178917594	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	179	447	0	ENST00000263967.3:c.469A>G	p.Asn157Asp	p.N157D	ENST00000263967	NM_006218.2	157	Aat/Gat	3/21	1	2	FACETS	1	0.974	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		447	871	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504354	186504354	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	110	332	0	ENST00000323963.5:c.691G>T	p.Asp231Tyr	p.D231Y	ENST00000323963		231	Gat/Tat	7/11	1	2	FACETS	1	0.97	1	1	0.99	1	CLONAL	2	TRUE	1	0.121712654762108	2		332	746	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584501	189584501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908849	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	68	474	0	ENST00000264731.3:c.797G>A	p.Arg266Gln	p.R266Q	ENST00000264731	NM_003722.4	266	cGa/cAa	6/14	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.121712654762108	2		474	983	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749374	41749374	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	31	313	0	ENST00000226382.2:c.421C>T	p.Arg141Ter	p.R141*	ENST00000226382	NM_003924.3	141	Cga/Tga	2/3	NA	2	FACETS	0.877	0.707	1			1	INDETERMINATE	1	TRUE	NA	0.121712654762108	2		313	581	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133724	55133724	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	158	523	0	ENST00000257290.5:c.937G>T	p.Gly313Cys	p.G313C	ENST00000257290	NM_006206.4	313	Ggt/Tgt	7/23	0.121712654762108	1	FACETS	0.897	0.822	0.976	1	0.993	1	CLONAL	3	TRUE	0	0.121712654762108	1		523	906	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133884	55133884	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	146	459	0	ENST00000257290.5:c.1097A>C	p.Asp366Ala	p.D366A	ENST00000257290	NM_006206.4	366	gAt/gCt	7/23	0.121712654762108	1	FACETS	1	0.979	1	1	0.992	1	CLONAL	2	TRUE	0	0.121712654762108	1		459	906	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138675	55138675	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1178568199	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	132	434	0	ENST00000257290.5:c.1352A>C	p.Lys451Thr	p.K451T	ENST00000257290	NM_006206.4	451	aAa/aCa	9/23	0.121712654762108	1	FACETS	0.895	0.813	0.98	1	0.992	1	CLONAL	3	TRUE	0	0.121712654762108	1		434	759	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146497	55146497	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	139	445	0	ENST00000257290.5:c.2171C>A	p.Ser724Tyr	p.S724Y	ENST00000257290	NM_006206.4	724	tCt/tAt	16/23	0.121712654762108	1	FACETS	0.957	0.872	1	1	0.992	1	CLONAL	3	TRUE	0	0.121712654762108	1		445	747	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565863	55565863	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	66	581	1	ENST00000288135.5:c.687C>A	p.Phe229Leu	p.F229L	ENST00000288135	NM_000222.2	229	ttC/ttA	4/21	0.121712654762108	1	FACETS	0.931	0.805	1	0.931	0.805	1	CLONAL	1	TRUE	0	0.121712654762108	1		582	1094	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948151	55948151	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	195	518	0	ENST00000263923.4:c.3820G>T	p.Asp1274Tyr	p.D1274Y	ENST00000263923	NM_002253.2	1274	Gac/Tac	29/30	0.121712654762108	1	FACETS	1	0.971	1	1	0.995	1	CLONAL	3	TRUE	0	0.121712654762108	1		518	918	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956201	55956201	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	206	519	0	ENST00000263923.4:c.3114G>T	p.Glu1038Asp	p.E1038D	ENST00000263923	NM_002253.2	1038	gaG/gaT	23/30	0.121712654762108	1	FACETS	1	0.962	1	1	0.995	1	CLONAL	3	TRUE	0	0.121712654762108	1		519	1004	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968651	55968651	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149740758	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	157	480	0	ENST00000263923.4:c.2012G>A	p.Gly671Glu	p.G671E	ENST00000263923	NM_002253.2	671	gGa/gAa	14/30	0.121712654762108	1	FACETS	1	0.934	1	1	0.993	1	CLONAL	3	TRUE	0	0.121712654762108	1		480	791	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976831	55976831	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	162	411	0	ENST00000263923.4:c.1081G>T	p.Glu361Ter	p.E361*	ENST00000263923	NM_002253.2	361	Gaa/Taa	8/30	0.121712654762108	1	FACETS	1	0.969	1	1	0.994	1	CLONAL	3	TRUE	0	0.121712654762108	1		411	752	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980418	55980418	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs75079316	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	148	457	0	ENST00000263923.4:c.673G>T	p.Asp225Tyr	p.D225Y	ENST00000263923	NM_002253.2	225	Gat/Tat	6/30	0.121712654762108	1	FACETS	0.912	0.833	0.994	1	0.993	1	CLONAL	3	TRUE	0	0.121712654762108	1		457	835	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189906	66189906	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149835568	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	146	491	0	ENST00000273854.3:c.3040G>A	p.Gly1014Ser	p.G1014S	ENST00000273854	NM_004439.5	1014	Ggt/Agt	18/18	0.121712654762108	1	FACETS	1	0.919	1	1	0.993	1	CLONAL	3	TRUE	0	0.121712654762108	1		491	747	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280142	66280142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1327931544	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	36	349	0	ENST00000273854.3:c.1547C>T	p.Thr516Met	p.T516M	ENST00000273854	NM_004439.5	516	aCg/aTg	7/18	1	2	FACETS	1	0.837	1	1	0.837	1	CLONAL	1	TRUE	1	0.121712654762108	2		349	579	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509087	66509087	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	128	374	0	ENST00000273854.3:c.240A>C	p.Lys80Asn	p.K80N	ENST00000273854	NM_004439.5	80	aaA/aaC	2/18	1	2	FACETS	1	0.921	1	1	0.992	1	CLONAL	3	TRUE	1	0.121712654762108	2		374	690	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509097	66509097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760211156	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	112	386	0	ENST00000273854.3:c.230C>T	p.Ala77Val	p.A77V	ENST00000273854	NM_004439.5	77	gCt/gTt	2/18	1	2	FACETS	0.854	0.769	0.945	1	0.99	1	CLONAL	3	TRUE	1	0.121712654762108	2		386	718	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157352	106157352	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	171	496	0	ENST00000380013.4:c.2253G>T	p.Lys751Asn	p.K751N	ENST00000380013	NM_001127208.2	751	aaG/aaT	3/11	1	2	FACETS	0.99	0.911	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		496	946	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158014	106158014	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	172	485	0	ENST00000380013.4:c.2915C>A	p.Ser972Tyr	p.S972Y	ENST00000380013	NM_001127208.2	972	tCt/tAt	3/11	1	2	FACETS	1	0.947	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		485	909	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164011	106164011	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	199	581	0	ENST00000380013.4:c.3521C>T	p.Ala1174Val	p.A1174V	ENST00000380013	NM_001127208.2	1174	gCt/gTt	5/11	1	2	FACETS	1	0.963	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		581	1024	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143324204	143324204	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	155	361	0	ENST00000262992.4:c.259A>C	p.Thr87Pro	p.T87P	ENST00000262992	NM_001101669.1	87	Aca/Cca	5/24	1	2	FACETS	0.884	0.811	0.96	1	0.994	1	CLONAL	4	TRUE	1	0.121712654762108	2		361	720	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249457	153249457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	166	496	1	ENST00000281708.4:c.1321C>T	p.Arg441Trp	p.R441W	ENST00000281708	NM_033632.3	441	Cgg/Tgg	9/12	1	2	FACETS	0.934	0.858	1	1	0.993	1	CLONAL	3	TRUE	1	0.121712654762108	2		497	973	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510153	187510153	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367799188	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	246	675	0	ENST00000441802.2:c.13360G>A	p.Glu4454Lys	p.E4454K	ENST00000441802	NM_005245.3	4454	Gaa/Aaa	27/27	1	2	FACETS	1	0.963	1	1	0.996	1	CLONAL	3	TRUE	1	0.121712654762108	2		675	1286	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527368	187527368	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	91	183	0	ENST00000441802.2:c.10207-1G>T		p.X3403_splice	ENST00000441802	NM_005245.3	3403			1	2	FACETS	1	0.957	1	1	0.989	1	CLONAL	3	TRUE	1	0.121712654762108	2		183	436	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531020	187531020	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	225	535	0	ENST00000441802.2:c.10003T>C	p.Phe3335Leu	p.F3335L	ENST00000441802	NM_005245.3	3335	Ttc/Ctc	15/27	1	2	FACETS	1	0.98	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		535	1086	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532825	187532825	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	225	490	1	ENST00000441802.2:c.9568G>T	p.Glu3190Ter	p.E3190*	ENST00000441802	NM_005245.3	3190	Gaa/Taa	14/27	1	2	FACETS	1	0.978	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		491	1100	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539809	187539809	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	46	466	0	ENST00000441802.2:c.7931A>C	p.Glu2644Ala	p.E2644A	ENST00000441802	NM_005245.3	2644	gAg/gCg	10/27	1	2	FACETS	0.887	0.745	1	0.887	0.745	1	CLONAL	1	TRUE	1	0.121712654762108	2		466	852	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539852	187539852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765674305	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	173	435	2	ENST00000441802.2:c.7888G>A	p.Asp2630Asn	p.D2630N	ENST00000441802	NM_005245.3	2630	Gac/Aac	10/27	1	2	FACETS	1	0.973	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		437	844	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542531	187542531	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	114	631	0	ENST00000441802.2:c.5209A>C	p.Ile1737Leu	p.I1737L	ENST00000441802	NM_005245.3	1737	Ata/Cta	10/27	1	2	FACETS	0.881	0.792	0.976	1	0.986	1	CLONAL	2	TRUE	1	0.121712654762108	2		631	1063	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542842	187542842	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs772854140	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	53	510	1	ENST00000441802.2:c.4898A>G	p.Tyr1633Cys	p.Y1633C	ENST00000441802	NM_005245.3	1633	tAt/tGt	10/27	1	2	FACETS	0.943	0.801	1	0.943	0.801	1	CLONAL	1	TRUE	1	0.121712654762108	2		511	924	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293664	1293664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111952055	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	160	362	0	ENST00000310581.5:c.1337G>A	p.Arg446His	p.R446H	ENST00000310581	NM_198253.2	446	cGt/cAt	2/16	1	2	FACETS	1	0.941	1	1	0.994	1	CLONAL	4	TRUE	1	0.121712654762108	2		362	640	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873655	35873655	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	125	567	0	ENST00000303115.3:c.611A>C	p.Lys204Thr	p.K204T	ENST00000303115	NM_002185.3	204	aAa/aCa	5/8	1	2	FACETS	1	0.95	1	1	0.99	1	CLONAL	2	TRUE	1	0.121712654762108	2		567	952	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876361	35876361	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	35	378	0	ENST00000303115.3:c.1153T>G	p.Ser385Ala	p.S385A	ENST00000303115	NM_002185.3	385	Tcc/Gcc	8/8	1	2	FACETS	0.875	0.716	1	0.875	0.716	1	CLONAL	1	TRUE	1	0.121712654762108	2		378	657	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876393	35876393	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	135	390	2	ENST00000303115.3:c.1185G>T	p.Lys395Asn	p.K395N	ENST00000303115	NM_002185.3	395	aaG/aaT	8/8	1	2	FACETS	1	0.945	1	1	0.992	1	CLONAL	3	TRUE	1	0.121712654762108	2		392	703	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982073	38982073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	143	431	0	ENST00000357387.3:c.649G>A	p.Asp217Asn	p.D217N	ENST00000357387	NM_152756.3	217	Gat/Aat	8/38	1	2	FACETS	0.834	0.76	0.912	1	0.992	1	CLONAL	3	TRUE	1	0.121712654762108	2		431	939	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39002645	39002645	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	107	377	0	ENST00000357387.3:c.384A>C	p.Leu128Phe	p.L128F	ENST00000357387	NM_152756.3	128	ttA/ttC	5/38	1	2	FACETS	1	0.965	1	1	0.989	1	CLONAL	2	TRUE	1	0.121712654762108	2		377	747	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178439	56178439	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	49	536	1	ENST00000399503.3:c.3412G>T	p.Ala1138Ser	p.A1138S	ENST00000399503	NM_005921.1	1138	Gca/Tca	14/20	1	2	FACETS	0.833	0.703	0.977	0.833	0.703	0.977	CLONAL	1	TRUE	1	0.121712654762108	2		537	967	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	323	413	2	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	0.959	0.91	1	1	0.997	1	CLONAL	7	TRUE	1	0.121712654762108	2		415	791	SUCCESS
APC	324	MSKCC	GRCh37	5	112173350	112173350	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	167	571	0	ENST00000257430.4:c.2059C>A	p.Leu687Ile	p.L687I	ENST00000257430	NM_000038.5	687	Ctc/Atc	16/16	1	2	FACETS	0.907	0.832	0.984	1	0.993	1	CLONAL	3	TRUE	1	0.121712654762108	2		571	1009	SUCCESS
APC	324	MSKCC	GRCh37	5	112174236	112174236	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139773221	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	217	571	0	ENST00000257430.4:c.2945C>T	p.Ser982Leu	p.S982L	ENST00000257430	NM_000038.5	982	tCg/tTg	16/16	1	2	FACETS	1	0.937	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		571	1177	SUCCESS
APC	324	MSKCC	GRCh37	5	112174802	112174802	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201830995	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	166	476	0	ENST00000257430.4:c.3511C>T	p.Arg1171Cys	p.R1171C	ENST00000257430	NM_000038.5	1171	Cgt/Tgt	16/16	1	2	FACETS	0.989	0.909	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		476	919	SUCCESS
APC	324	MSKCC	GRCh37	5	112174959	112174959	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	158	426	0	ENST00000257430.4:c.3668C>A	p.Ser1223Tyr	p.S1223Y	ENST00000257430	NM_000038.5	1223	tCt/tAt	16/16	1	2	FACETS	0.987	0.904	1	1	0.993	1	CLONAL	3	TRUE	1	0.121712654762108	2		426	877	SUCCESS
APC	324	MSKCC	GRCh37	5	112176020	112176020	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	149	401	0	ENST00000257430.4:c.4729G>T	p.Glu1577Ter	p.E1577*	ENST00000257430	NM_000038.5	1577	Gaa/Taa	16/16	1	2	FACETS	1	0.963	1	1	0.993	1	CLONAL	3	TRUE	1	0.121712654762108	2		401	747	SUCCESS
APC	324	MSKCC	GRCh37	5	112176706	112176706	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	166	458	0	ENST00000257430.4:c.5415C>A	p.Phe1805Leu	p.F1805L	ENST00000257430	NM_000038.5	1805	ttC/ttA	16/16	1	2	FACETS	1	0.936	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		458	890	SUCCESS
APC	324	MSKCC	GRCh37	5	112177203	112177203	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs754691867	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	96	415	0	ENST00000257430.4:c.5912C>A	p.Ser1971Tyr	p.S1971Y	ENST00000257430	NM_000038.5	1971	tCt/tAt	16/16	1	2	FACETS	1	0.957	1	1	0.988	1	CLONAL	2	TRUE	1	0.121712654762108	2		415	688	SUCCESS
APC	324	MSKCC	GRCh37	5	112178606	112178606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1311878041	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	169	483	1	ENST00000257430.4:c.7315C>T	p.Arg2439Cys	p.R2439C	ENST00000257430	NM_000038.5	2439	Cgc/Tgc	16/16	1	2	FACETS	1	0.964	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		484	854	SUCCESS
APC	324	MSKCC	GRCh37	5	112179516	112179516	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	194	514	0	ENST00000257430.4:c.8225A>G	p.Gln2742Arg	p.Q2742R	ENST00000257430	NM_000038.5	2742	cAa/cGa	16/16	1	2	FACETS	1	0.975	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		514	946	SUCCESS
APC	324	MSKCC	GRCh37	5	112179520	112179520	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1561621557	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	171	509	0	ENST00000257430.4:c.8229T>G	p.Asn2743Lys	p.N2743K	ENST00000257430	NM_000038.5	2743	aaT/aaG	16/16	1	2	FACETS	1	0.936	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		509	919	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924411	131924411	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	145	417	0	ENST00000265335.6:c.1084G>T	p.Glu362Ter	p.E362*	ENST00000265335		362	Gaa/Taa	8/25	1	2	FACETS	1	0.954	1	1	0.993	1	CLONAL	3	TRUE	1	0.121712654762108	2		417	745	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939134	131939134	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	151	640	0	ENST00000265335.6:c.2350A>C	p.Ser784Arg	p.S784R	ENST00000265335		784	Agt/Cgt	14/25	1	2	FACETS	1	0.925	1	1	0.991	1	CLONAL	2	TRUE	1	0.121712654762108	2		640	1222	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495372	149495372	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146614144	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	180	435	0	ENST00000261799.4:c.3275C>T	p.Ser1092Leu	p.S1092L	ENST00000261799	NM_002609.3	1092	tCg/tTg	23/23	1	2	FACETS	0.976	0.902	1	1	0.995	1	CLONAL	4	TRUE	1	0.121712654762108	2		435	758	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637295	176637295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201702515	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	186	494	0	ENST00000439151.2:c.1895G>A	p.Arg632Gln	p.R632Q	ENST00000439151	NM_022455.4	632	cGa/cAa	5/23	1	2	FACETS	1	0.967	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		494	939	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673753	176673753	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	276	601	0	ENST00000439151.2:c.4453A>C	p.Lys1485Gln	p.K1485Q	ENST00000439151	NM_022455.4	1485	Aaa/Caa	10/23	1	2	FACETS	1	0.984	1	1	0.996	1	CLONAL	3	TRUE	1	0.121712654762108	2		601	1319	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20483060	20483060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750169257	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	182	520	1	ENST00000346618.3:c.793G>A	p.Glu265Lys	p.E265K	ENST00000346618	NM_001949.4	265	Gag/Aag	4/7	NA	2	FACETS	0.95	0.876	1			1	INDETERMINATE	3	TRUE	NA	0.121712654762108	2		521	1049	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056189	26056189	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	53	459	0	ENST00000343677.2:c.468G>T	p.Lys156Asn	p.K156N	ENST00000343677	NM_005319.3	156	aaG/aaT	1/1	0.121712654762108	6	FACETS	1	0.909	1			1	CLONAL	1	TRUE	NA	0.121712654762108	6		459	986	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671212	30671212	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1373	106	709	1	ENST00000376406.3:c.5665G>T	p.Glu1889Ter	p.E1889*	ENST00000376406	NM_014641.2	1889	Gaa/Taa	11/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.121712654762108	2		710	1479	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671985	30671985	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1370	75	669	0	ENST00000376406.3:c.4975G>T	p.Asp1659Tyr	p.D1659Y	ENST00000376406	NM_014641.2	1659	Gat/Tat	10/15	1	2	FACETS	0.853	0.744	0.971	0.853	0.744	0.971	CLONAL	1	TRUE	1	0.121712654762108	2		669	1445	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675596	30675596	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1247	311	879	0	ENST00000376406.3:c.2760G>T	p.Glu920Asp	p.E920D	ENST00000376406	NM_014641.2	920	gaG/gaT	8/15	1	2	FACETS	1	0.98	1	1	0.996	1	CLONAL	3	TRUE	1	0.121712654762108	2		879	1558	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166773	32166773	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1231739465	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	232	519	1	ENST00000375023.3:c.4465C>T	p.Arg1489Ter	p.R1489*	ENST00000375023	NM_004557.3	1489	Cga/Tga	24/30	1	2	FACETS	0.995	0.928	1	1	0.996	1	CLONAL	4	TRUE	1	0.121712654762108	2		520	958	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172162	32172162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	200	383	0	ENST00000375023.3:c.2870C>T	p.Ala957Val	p.A957V	ENST00000375023	NM_004557.3	957	gCc/gTc	19/30	1	2	FACETS	0.965	0.896	1	1	0.995	1	CLONAL	4	TRUE	1	0.121712654762108	2		383	851	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178537	32178537	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	159	435	0	ENST00000375023.3:c.2857C>A	p.Leu953Ile	p.L953I	ENST00000375023	NM_004557.3	953	Ctc/Atc	18/30	1	2	FACETS	1	0.967	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		435	791	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93973599	93973599	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750462795	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	257	652	2	ENST00000369303.4:c.1777G>A	p.Asp593Asn	p.D593N	ENST00000369303	NM_004440.3	593	Gat/Aat	9/17	1	2	FACETS	1	0.959	1	1	0.996	1	CLONAL	3	TRUE	1	0.121712654762108	2		654	1360	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553781	106553781	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	75	430	0	ENST00000369096.4:c.1746G>T	p.Lys582Asn	p.K582N	ENST00000369096	NM_001198.3	582	aaG/aaT	5/7	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.121712654762108	2		430	1136	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609933	117609933	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	88	537	0	ENST00000368508.3:c.6766G>T	p.Asp2256Tyr	p.D2256Y	ENST00000368508	NM_002944.2	2256	Gat/Tat	43/43	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.121712654762108	2		537	1013	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631345	117631345	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	183	586	0	ENST00000368508.3:c.6333A>C	p.Lys2111Asn	p.K2111N	ENST00000368508	NM_002944.2	2111	aaA/aaC	40/43	1	2	FACETS	1	0.961	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		586	940	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642486	117642486	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	231	652	0	ENST00000368508.3:c.5713G>T	p.Glu1905Ter	p.E1905*	ENST00000368508	NM_002944.2	1905	Gag/Tag	35/43	1	2	FACETS	1	0.967	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		652	1189	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662397	117662397	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	160	487	0	ENST00000368508.3:c.4980G>T	p.Glu1660Asp	p.E1660D	ENST00000368508	NM_002944.2	1660	gaG/gaT	30/43	1	2	FACETS	1	0.941	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		487	849	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687329	117687329	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	211	570	0	ENST00000368508.3:c.2722G>T	p.Glu908Ter	p.E908*	ENST00000368508	NM_002944.2	908	Gaa/Taa	18/43	1	2	FACETS	1	0.977	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		570	1029	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706977	117706977	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764959275	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	212	510	1	ENST00000368508.3:c.2173G>A	p.Asp725Asn	p.D725N	ENST00000368508	NM_002944.2	725	Gac/Aac	15/43	1	2	FACETS	0.875	0.813	0.94	1	0.995	1	CLONAL	4	TRUE	1	0.121712654762108	2		511	995	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715410	117715410	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs769599473	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	202	559	0	ENST00000368508.3:c.1079G>T	p.Arg360Ile	p.R360I	ENST00000368508	NM_002944.2	360	aGa/aTa	10/43	1	2	FACETS	0.887	0.822	0.953	1	0.995	1	CLONAL	4	TRUE	1	0.121712654762108	2		559	936	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519560	137519560	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	76	415	0	ENST00000367739.4:c.1078G>T	p.Glu360Ter	p.E360*	ENST00000367739	NM_000416.2	360	Gaa/Taa	7/7	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.121712654762108	2		415	924	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137528188	137528188	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	147	448	0	ENST00000367739.4:c.112G>T	p.Glu38Ter	p.E38*	ENST00000367739	NM_000416.2	38	Gaa/Taa	2/7	1	2	FACETS	0.902	0.823	0.984	1	0.993	1	CLONAL	3	TRUE	1	0.121712654762108	2		448	893	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196847	138196847	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	75	481	0	ENST00000237289.4:c.509A>C	p.Asn170Thr	p.N170T	ENST00000237289	NM_001270507.1	170	aAt/aCt	4/9	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.121712654762108	2		481	1055	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199594	138199594	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	81	351	0	ENST00000237289.4:c.1012G>T	p.Glu338Ter	p.E338*	ENST00000237289	NM_001270507.1	338	Gaa/Taa	7/9	1	2	FACETS	0.959	0.845	1	1	0.983	1	CLONAL	2	TRUE	1	0.121712654762108	2		351	694	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200479	138200479	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	127	295	0	ENST00000237289.4:c.1897G>T	p.Glu633Ter	p.E633*	ENST00000237289	NM_001270507.1	633	Gaa/Taa	7/9	1	2	FACETS	1	0.911	1	1	0.992	1	CLONAL	3	TRUE	1	0.121712654762108	2		295	693	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005269	150005269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1449883955	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	145	543	2	ENST00000253339.5:c.956G>A	p.Gly319Asp	p.G319D	ENST00000253339		319	gGc/gAc	3/7	1	2	FACETS	0.95	0.867	1	1	0.993	1	CLONAL	3	TRUE	1	0.121712654762108	2		545	836	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265313	152265313	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	106	462	0	ENST00000206249.3:c.766C>T	p.Arg256Ter	p.R256*	ENST00000206249	NM_000125.3	256	Cga/Tga	4/8	1	2	FACETS	0.891	0.798	0.991	1	0.986	1	CLONAL	2	TRUE	1	0.121712654762108	2		462	977	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415580	152415580	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs570661763	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	83	626	0	ENST00000206249.3:c.1430G>A	p.Arg477Gln	p.R477Q	ENST00000206249	NM_000125.3	477	cGa/cAa	7/8	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.121712654762108	2		626	1185	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683734	162683734	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs770994041	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	83	436	0	ENST00000366898.1:c.235G>T	p.Glu79Ter	p.E79*	ENST00000366898	NM_004562.2	79	Gaa/Taa	3/12	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.121712654762108	2		436	1077	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2949715	2949715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	238	651	2	ENST00000396946.4:c.3229C>T	p.Arg1077Trp	p.R1077W	ENST00000396946	NM_032415.4	1077	Cgg/Tgg	24/25	1	2	FACETS	1	0.953	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		653	1268	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026643	6026643	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs63750947	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	240	553	0	ENST00000265849.7:c.1753C>A	p.Leu585Ile	p.L585I	ENST00000265849	NM_000535.5	585	Ctt/Att	11/15	1	2	FACETS	1	0.973	1	1	0.996	1	CLONAL	3	TRUE	1	0.121712654762108	2		553	1216	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6029548	6029548	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	174	480	0	ENST00000265849.7:c.1027A>T	p.Ile343Phe	p.I343F	ENST00000265849	NM_000535.5	343	Att/Ttt	10/15	1	2	FACETS	1	0.976	1	1	0.993	1	CLONAL	2	TRUE	1	0.121712654762108	2		480	1236	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14026296	14026296	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	99	316	0	ENST00000405192.2:c.148C>A	p.Leu50Ile	p.L50I	ENST00000405192	NM_001163147.1	50	Cta/Ata	4/12	1	2	FACETS	0.895	0.8	0.995	1	0.989	1	CLONAL	3	TRUE	1	0.121712654762108	2		316	606	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729535	41729535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1467	106	743	0	ENST00000242208.4:c.994G>A	p.Asp332Asn	p.D332N	ENST00000242208	NM_002192.2	332	Gac/Aac	3/3	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.121712654762108	2		743	1573	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358932	81358932	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	115	440	0	ENST00000222390.5:c.1029T>A	p.Asn343Lys	p.N343K	ENST00000222390	NM_000601.4	343	aaT/aaA	8/18	1	2	FACETS	1	0.971	1	1	0.99	1	CLONAL	2	TRUE	1	0.121712654762108	2		440	781	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509045	106509045	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752896730	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	182	437	0	ENST00000359195.3:c.1039G>A	p.Glu347Lys	p.E347K	ENST00000359195	NM_002649.2	347	Gag/Aag	2/11	1	2	FACETS	1	0.97	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		437	906	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545740	106545740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	177	592	1	ENST00000359195.3:c.3217G>A	p.Glu1073Lys	p.E1073K	ENST00000359195	NM_002649.2	1073	Gaa/Aaa	11/11	1	2	FACETS	0.972	0.896	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		593	997	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140500207	140500207	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	168	458	0	ENST00000288602.6:c.935T>C	p.Leu312Pro	p.L312P	ENST00000288602	NM_004333.4	312	cTa/cCa	7/18	1	2	FACETS	1	0.973	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		458	817	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859941	151859941	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	173	541	0	ENST00000262189.6:c.10721C>A	p.Ser3574Tyr	p.S3574Y	ENST00000262189	NM_170606.2	3574	tCt/tAt	43/59	1	2	FACETS	0.941	0.866	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		541	1007	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873309	151873309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145953124	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	201	457	1	ENST00000262189.6:c.9229C>T	p.Arg3077Cys	p.R3077C	ENST00000262189	NM_170606.2	3077	Cgt/Tgt	38/59	1	2	FACETS	0.914	0.846	0.986	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		458	1204	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873626	151873626	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	41	369	0	ENST00000262189.6:c.8912C>A	p.Ser2971Tyr	p.S2971Y	ENST00000262189	NM_170606.2	2971	tCt/tAt	38/59	1	2	FACETS	0.835	0.693	0.993	0.835	0.693	0.993	CLONAL	1	TRUE	1	0.121712654762108	2		369	807	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874046	151874046	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	208	628	2	ENST00000262189.6:c.8492C>A	p.Ser2831Tyr	p.S2831Y	ENST00000262189	NM_170606.2	2831	tCt/tAt	38/59	1	2	FACETS	0.922	0.854	0.992	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		630	1236	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279458	38279458	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	124	378	0	ENST00000425967.3:c.1031C>T	p.Thr344Ile	p.T344I	ENST00000425967	NM_001174067.1	344	aCt/aTt	9/19	0.121712654762108	1	FACETS	0.933	0.848	1	1	0.992	1	CLONAL	4	TRUE	0	0.121712654762108	1		378	513	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90971022	90971022	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	201	491	0	ENST00000265433.3:c.1055T>G	p.Leu352Arg	p.L352R	ENST00000265433	NM_002485.4	352	cTa/cGa	9/16	0.121712654762108	3	FACETS	0.957	0.885	1	0.957	0.885	1	CLONAL	3	TRUE	0	0.121712654762108	3		491	1221	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866702	117866702	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	353	496	1	ENST00000297338.2:c.943G>T	p.Glu315Ter	p.E315*	ENST00000297338	NM_006265.2	315	Gaa/Taa	9/14	0.121712654762108	3	FACETS	1	0.985	1	1	0.996	1	CLONAL	5	TRUE	0	0.121712654762108	3		497	1123	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117875450	117875450	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	259	737	0	ENST00000297338.2:c.193C>T	p.Arg65Ter	p.R65*	ENST00000297338	NM_006265.2	65	Cga/Tga	3/14	0.121712654762108	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	0	0.121712654762108	3		737	1332	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436600	8436600	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	50	495	1	ENST00000356435.5:c.4078G>T	p.Glu1360Ter	p.E1360*	ENST00000356435		1360	Gaa/Taa	24/35	1	2	FACETS	0.895	0.757	1	0.895	0.757	1	CLONAL	1	TRUE	1	0.121712654762108	2		496	918	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521481	8521481	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760428875	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	157	511	1	ENST00000356435.5:c.757G>A	p.Val253Ile	p.V253I	ENST00000356435		253	Gtt/Att	9/35	1	2	FACETS	0.994	0.911	1	1	0.993	1	CLONAL	3	TRUE	1	0.121712654762108	2		512	865	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528711	8528711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774617096	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	65	514	0	ENST00000356435.5:c.421C>T	p.Arg141Cys	p.R141C	ENST00000356435		141	Cgc/Tgc	4/35	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.121712654762108	2		514	899	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80343439	80343439	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	140	295	0	ENST00000286548.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000286548	NM_002072.3	294	Gaa/Taa	6/7	1	2	FACETS	1	0.971	1	1	0.993	1	CLONAL	3	TRUE	1	0.121712654762108	2		295	669	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908829	101908829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200657153	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	175	498	0	ENST00000374994.4:c.1193G>A	p.Arg398His	p.R398H	ENST00000374994	NM_004612.2	398	cGt/cAt	7/9	1	2	FACETS	0.978	0.9	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		498	980	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908877	101908877	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1469620887	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	149	480	0	ENST00000374994.4:c.1241G>A	p.Arg414Gln	p.R414Q	ENST00000374994	NM_004612.2	414	cGa/cAa	7/9	1	2	FACETS	0.917	0.838	1	1	0.993	1	CLONAL	3	TRUE	1	0.121712654762108	2		480	890	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781416	135781416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1249	359	820	1	ENST00000298552.3:c.1549C>T	p.Arg517Trp	p.R517W	ENST00000298552	NM_001162426.1	517	Cgg/Tgg	15/23	1	2	FACETS	0.917	0.867	0.969	1	0.997	1	CLONAL	4	TRUE	1	0.121712654762108	2		821	1608	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115815	8115815	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	264	624	1	ENST00000346208.3:c.1161G>T	p.Lys387Asn	p.K387N	ENST00000346208		387	aaG/aaT	6/6	1	2	FACETS	1	0.979	1	1	0.996	1	CLONAL	3	TRUE	1	0.121712654762108	2		625	1313	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63829499	63829499	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	128	411	0	ENST00000279873.7:c.1142T>G	p.Leu381Ter	p.L381*	ENST00000279873	NM_032199.2	381	tTa/tGa	8/10	1	2	FACETS	0.924	0.838	1	1	0.992	1	CLONAL	3	TRUE	1	0.121712654762108	2		411	759	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333080	70333080	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	199	558	0	ENST00000373644.4:c.985T>C	p.Phe329Leu	p.F329L	ENST00000373644	NM_030625.2	329	Ttc/Ctc	2/12	1	2	FACETS	1	0.948	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		558	1058	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333863	70333863	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs750883311	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	154	464	1	ENST00000373644.4:c.1768C>T	p.Arg590Ter	p.R590*	ENST00000373644	NM_030625.2	590	Cga/Tga	2/12	1	2	FACETS	1	0.973	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		465	738	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404693	70404693	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756914683	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	91	479	0	ENST00000373644.4:c.2207C>T	p.Ser736Leu	p.S736L	ENST00000373644	NM_030625.2	736	tCg/tTg	4/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.121712654762108	2		479	1164	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404862	70404862	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	135	429	0	ENST00000373644.4:c.2376A>C	p.Lys792Asn	p.K792N	ENST00000373644	NM_030625.2	792	aaA/aaC	4/12	1	2	FACETS	0.854	0.776	0.936	1	0.992	1	CLONAL	3	TRUE	1	0.121712654762108	2		429	866	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405080	70405080	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	220	574	0	ENST00000373644.4:c.2594A>C	p.Lys865Thr	p.K865T	ENST00000373644	NM_030625.2	865	aAa/aCa	4/12	1	2	FACETS	1	0.954	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		574	1165	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405349	70405349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	175	476	0	ENST00000373644.4:c.2863C>T	p.His955Tyr	p.H955Y	ENST00000373644	NM_030625.2	955	Cac/Tac	4/12	1	2	FACETS	1	0.938	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		476	938	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70411602	70411602	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	153	420	0	ENST00000373644.4:c.4277-1G>T		p.X1426_splice	ENST00000373644	NM_030625.2	1426			1	2	FACETS	1	0.958	1	1	0.993	1	CLONAL	3	TRUE	1	0.121712654762108	2		420	780	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685311	89685311	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	60	268	0	ENST00000371953.3:c.206A>C	p.Asn69Thr	p.N69T	ENST00000371953	NM_000314.4	69	aAt/aCt	3/9	1	2	FACETS	0.851	0.734	0.98	1	0.974	1	CLONAL	2	TRUE	1	0.121712654762108	2		268	579	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720711	89720711	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	15	51	0	ENST00000371953.3:c.862G>T	p.Glu288Ter	p.E288*	ENST00000371953	NM_000314.4	288	Gaa/Taa	8/9	1	2	FACETS	0.893	0.663	1	1	0.934	1	CLONAL	3	TRUE	1	0.121712654762108	2		51	92	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239508	123239508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374993905	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1499	91	890	1	ENST00000358487.5:c.2329G>A	p.Glu777Lys	p.E777K	ENST00000358487	NM_000141.4	777	Gaa/Aaa	18/18	1	2	FACETS	0.94	0.831	1	0.94	0.831	1	CLONAL	1	TRUE	1	0.121712654762108	2		891	1590	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247555	123247555	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	236	504	0	ENST00000358487.5:c.1936G>T	p.Gly646Ter	p.G646*	ENST00000358487	NM_000141.4	646	Gga/Tga	14/18	1	2	FACETS	1	0.975	1	1	0.996	1	CLONAL	3	TRUE	1	0.121712654762108	2		504	1181	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310821	123310821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	209	558	0	ENST00000358487.5:c.607C>T	p.Arg203Cys	p.R203C	ENST00000358487	NM_000141.4	203	Cgc/Tgc	5/18	1	2	FACETS	0.984	0.913	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		558	1163	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742934	17742934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	27	333	1	ENST00000250003.3:c.842G>A	p.Arg281His	p.R281H	ENST00000250003	NM_002478.4	281	cGc/cAc	3/3	1	2	FACETS	0.889	0.706	1	0.889	0.706	1	CLONAL	1	TRUE	1	0.121712654762108	2		334	499	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573813	64573813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139936447	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	185	420	1	ENST00000312049.6:c.940C>T	p.Arg314Trp	p.R314W	ENST00000312049	NM_130799.2	314	Cgg/Tgg	7/10	1	2	FACETS	1	0.979	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		421	874	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047231	77047231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	170	291	0	ENST00000356341.3:c.1313G>A	p.Arg438Gln	p.R438Q	ENST00000356341	NM_002576.4	438	cGa/cAa	13/15	1	2	FACETS	1	0.937	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		291	911	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77085386	77085386	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	213	511	0	ENST00000356341.3:c.464C>A	p.Ser155Tyr	p.S155Y	ENST00000356341	NM_002576.4	155	tCt/tAt	5/15	1	2	FACETS	1	0.97	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		511	1079	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94170371	94170371	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745614941	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	189	420	1	ENST00000323929.3:c.1898G>A	p.Arg633Gln	p.R633Q	ENST00000323929	NM_005591.3	633	cGa/cAa	17/20	1	2	FACETS	1	0.969	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		421	948	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192696	94192696	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	152	355	0	ENST00000323929.3:c.1378G>T	p.Glu460Ter	p.E460*	ENST00000323929	NM_005591.3	460	Gaa/Taa	13/20	1	2	FACETS	1	0.96	1	1	0.993	1	CLONAL	3	TRUE	1	0.121712654762108	2		355	771	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94224018	94224018	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	200	497	0	ENST00000323929.3:c.134G>T	p.Arg45Ile	p.R45I	ENST00000323929	NM_005591.3	45	aGa/aTa	3/20	1	2	FACETS	1	0.965	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		497	1023	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933252	100933252	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	271	780	2	ENST00000325455.5:c.2138C>A	p.Ser713Tyr	p.S713Y	ENST00000325455	NM_001202474.3	713	tCt/tAt	4/8	1	2	FACETS	1	0.969	1	1	0.996	1	CLONAL	3	TRUE	1	0.121712654762108	2		782	1407	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933270	100933270	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	274	793	0	ENST00000325455.5:c.2120A>C	p.Lys707Thr	p.K707T	ENST00000325455	NM_001202474.3	707	aAa/aCa	4/8	1	2	FACETS	1	0.966	1	1	0.996	1	CLONAL	3	TRUE	1	0.121712654762108	2		793	1434	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996829	100996829	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	229	679	0	ENST00000325455.5:c.1698T>G	p.Ile566Met	p.I566M	ENST00000325455	NM_001202474.3	566	atT/atG	2/8	1	2	FACETS	1	0.958	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		679	1205	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102056798	102056798	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	195	541	0	ENST00000282441.5:c.738T>G	p.Ile246Met	p.I246M	ENST00000282441	NM_001130145.2	246	atT/atG	4/9	1	2	FACETS	1	0.938	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		541	1051	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201936	102201936	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1423	327	930	2	ENST00000263464.3:c.1288G>T	p.Glu430Ter	p.E430*	ENST00000263464	NM_001165.4	430	Gag/Tag	6/9	1	2	FACETS	1	0.959	1	1	0.997	1	CLONAL	3	TRUE	1	0.121712654762108	2		932	1750	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122668	108122668	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	164	518	0	ENST00000278616.4:c.1712C>A	p.Ser571Tyr	p.S571Y	ENST00000278616	NM_000051.3	571	tCt/tAt	11/63	1	2	FACETS	0.94	0.862	1	1	0.993	1	CLONAL	3	TRUE	1	0.121712654762108	2		518	956	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124599	108124599	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	169	489	0	ENST00000278616.4:c.1957C>A	p.Leu653Ile	p.L653I	ENST00000278616	NM_000051.3	653	Ctt/Att	13/63	1	2	FACETS	0.945	0.868	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		489	980	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196197	108196197	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	185	452	0	ENST00000278616.4:c.6733G>T	p.Glu2245Ter	p.E2245*	ENST00000278616	NM_000051.3	2245	Gaa/Taa	46/63	1	2	FACETS	1	0.971	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		452	919	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201008	108201008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881383	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	178	492	0	ENST00000278616.4:c.7375C>T	p.Arg2459Cys	p.R2459C	ENST00000278616	NM_000051.3	2459	Cgt/Tgt	50/63	1	2	FACETS	1	0.969	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		492	889	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205711	108205711	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	120	330	0	ENST00000278616.4:c.8026G>T	p.Glu2676Ter	p.E2676*	ENST00000278616	NM_000051.3	2676	Gaa/Taa	55/63	1	2	FACETS	1	0.952	1	1	0.992	1	CLONAL	3	TRUE	1	0.121712654762108	2		330	607	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342539	118342539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	218	661	1	ENST00000534358.1:c.665G>T	p.Arg222Ile	p.R222I	ENST00000534358	NM_005933.3	222	aGa/aTa	3/36	1	2	FACETS	0.918	0.852	0.986	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		662	1301	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373664	118373664	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	60	534	0	ENST00000534358.1:c.7057T>G	p.Ser2353Ala	p.S2353A	ENST00000534358	NM_005933.3	2353	Tcc/Gcc	27/36	1	2	FACETS	0.907	0.779	1	0.907	0.779	1	CLONAL	1	TRUE	1	0.121712654762108	2		534	1087	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373689	118373689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782524513	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	203	505	2	ENST00000534358.1:c.7082C>T	p.Ser2361Leu	p.S2361L	ENST00000534358	NM_005933.3	2361	tCg/tTg	27/36	1	2	FACETS	1	0.961	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		507	1053	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376455	118376455	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs781886946	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	165	455	1	ENST00000534358.1:c.9848G>T	p.Arg3283Leu	p.R3283L	ENST00000534358	NM_005933.3	3283	cGa/cTa	27/36	1	2	FACETS	1	0.97	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		456	811	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169238	119169238	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	91	301	0	ENST00000264033.4:c.2422G>T	p.Asp808Tyr	p.D808Y	ENST00000264033	NM_005188.3	808	Gat/Tat	15/16	1	2	FACETS	1	0.968	1	1	0.988	1	CLONAL	2	TRUE	1	0.121712654762108	2		301	602	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431665	431665	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs754467075	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	214	483	0	ENST00000399788.2:c.2344C>T	p.Arg782Ter	p.R782*	ENST00000399788	NM_001042603.1	782	Cga/Tga	17/28	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	3	TRUE	NA	0.121712654762108	2		483	1013	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023606	1023606	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	249	535	0	ENST00000358495.3:c.958G>T	p.Glu320Ter	p.E320*	ENST00000358495	NM_134424.2	320	Gaa/Taa	10/12	NA	2	FACETS	0.922	0.862	0.984			1	INDETERMINATE	4	TRUE	NA	0.121712654762108	2		535	1109	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650557	18650557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	147	498	0	ENST00000266497.5:c.2768G>A	p.Gly923Glu	p.G923E	ENST00000266497		923	gGa/gAa	20/31	1	2	FACETS	0.897	0.818	0.979	1	0.992	1	CLONAL	3	TRUE	1	0.121712654762108	2		498	898	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658375	18658375	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	143	472	0	ENST00000266497.5:c.3180A>C	p.Gln1060His	p.Q1060H	ENST00000266497		1060	caA/caC	22/31	1	2	FACETS	0.904	0.825	0.988	1	0.992	1	CLONAL	3	TRUE	1	0.121712654762108	2		472	866	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699296	18699296	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	175	557	0	ENST00000266497.5:c.3397G>T	p.Asp1133Tyr	p.D1133Y	ENST00000266497		1133	Gac/Tac	24/31	1	2	FACETS	0.972	0.895	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		557	986	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246026	46246026	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	151	563	0	ENST00000334344.6:c.4120A>G	p.Lys1374Glu	p.K1374E	ENST00000334344	NM_152641.2	1374	Aaa/Gaa	15/21	1	2	FACETS	0.925	0.846	1	1	0.993	1	CLONAL	3	TRUE	1	0.121712654762108	2		563	894	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425896	49425896	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783685	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	178	552	1	ENST00000301067.7:c.12592C>T	p.Arg4198Ter	p.R4198*	ENST00000301067	NM_003482.3	4198	Cga/Tga	39/54	1	2	FACETS	0.991	0.913	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		553	984	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426198	49426198	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	113	369	0	ENST00000301067.7:c.12290T>G	p.Leu4097Arg	p.L4097R	ENST00000301067	NM_003482.3	4097	cTt/cGt	39/54	1	2	FACETS	0.875	0.789	0.967	1	0.99	1	CLONAL	3	TRUE	1	0.121712654762108	2		369	707	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863296	57863296	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1321	110	800	2	ENST00000228682.2:c.1391G>T	p.Gly464Val	p.G464V	ENST00000228682	NM_005269.2	464	gGt/gTt	11/12	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.121712654762108	2		802	1431	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864647	57864647	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	216	855	0	ENST00000228682.2:c.2124A>C	p.Glu708Asp	p.E708D	ENST00000228682	NM_005269.2	708	gaA/gaC	12/12	1	2	FACETS	1	0.984	1	1	0.994	1	CLONAL	2	TRUE	1	0.121712654762108	2		855	1461	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256623	133256623	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555230189	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	207	505	2	ENST00000320574.5:c.340C>T	p.Arg114Ter	p.R114*	ENST00000320574	NM_006231.2	114	Cga/Tga	5/49	1	2	FACETS	0.908	0.843	0.975	1	0.995	1	CLONAL	4	TRUE	1	0.121712654762108	2		507	937	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601301	28601301	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	203	584	0	ENST00000241453.7:c.2131C>A	p.His711Asn	p.H711N	ENST00000241453	NM_004119.2	711	Cac/Aac	17/24	1	2	FACETS	1	0.936	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		584	1099	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601361	28601361	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	147	471	0	ENST00000241453.7:c.2071T>G	p.Phe691Val	p.F691V	ENST00000241453	NM_004119.2	691	Ttt/Gtt	17/24	1	2	FACETS	0.951	0.868	1	1	0.993	1	CLONAL	3	TRUE	1	0.121712654762108	2		471	847	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912484	32912484	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1279	129	760	0	ENST00000380152.3:c.3992C>A	p.Ser1331Tyr	p.S1331Y	ENST00000380152		1331	tCt/tAt	11/27	1	2	FACETS	0.753	0.68	0.83	1	0.985	1	SUBCLONAL	2	TRUE	1	0.121712654762108	2		760	1408	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912525	32912525	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1362	81	724	1	ENST00000380152.3:c.4033G>T	p.Asp1345Tyr	p.D1345Y	ENST00000380152		1345	Gat/Tat	11/27	1	2	FACETS	0.922	0.809	1	0.922	0.809	1	CLONAL	1	TRUE	1	0.121712654762108	2		725	1443	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915255	32915255	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1202	289	805	0	ENST00000380152.3:c.6763A>G	p.Thr2255Ala	p.T2255A	ENST00000380152		2255	Aca/Gca	11/27	1	2	FACETS	1	0.972	1	1	0.996	1	CLONAL	3	TRUE	1	0.121712654762108	2		805	1491	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953964	32953964	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	112	438	0	ENST00000380152.3:c.9031C>A	p.Leu3011Ile	p.L3011I	ENST00000380152		3011	Ctt/Att	23/27	1	2	FACETS	1	0.957	1	1	0.989	1	CLONAL	2	TRUE	1	0.121712654762108	2		438	823	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881438	48881438	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	150	410	0	ENST00000267163.4:c.160G>A	p.Glu54Lys	p.E54K	ENST00000267163	NM_000321.2	54	Gaa/Aaa	2/27	1	2	FACETS	0.903	0.825	0.985	1	0.993	1	CLONAL	3	TRUE	1	0.121712654762108	2		410	910	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939054	48939054	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	91	402	0	ENST00000267163.4:c.886T>G	p.Phe296Val	p.F296V	ENST00000267163	NM_000321.2	296	Ttt/Gtt	9/27	1	2	FACETS	0.898	0.796	1	1	0.984	1	CLONAL	2	TRUE	1	0.121712654762108	2		402	833	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033829	49033829	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142509759	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	139	441	1	ENST00000267163.4:c.1966C>T	p.Arg656Trp	p.R656W	ENST00000267163	NM_000321.2	656	Cgg/Tgg	20/27	1	2	FACETS	0.905	0.824	0.99	1	0.992	1	CLONAL	3	TRUE	1	0.121712654762108	2		442	841	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337650	73337650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	224	498	0	ENST00000377767.4:c.2066G>A	p.Arg689Gln	p.R689Q	ENST00000377767	NM_014953.3	689	cGa/cAa	16/21	1	2	FACETS	1	0.959	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		498	1176	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73351596	73351596	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760670933	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	235	472	0	ENST00000377767.4:c.616G>A	p.Glu206Lys	p.E206K	ENST00000377767	NM_014953.3	206	Gaa/Aaa	4/21	1	2	FACETS	1	0.979	1	1	0.996	1	CLONAL	3	TRUE	1	0.121712654762108	2		472	1147	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609467	81609467	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	205	654	0	ENST00000298171.2:c.1065C>A	p.Phe355Leu	p.F355L	ENST00000298171	NM_000369.2	355	ttC/ttA	10/10	1	2	FACETS	0.868	0.803	0.935	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		654	1294	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557672	95557672	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	126	422	0	ENST00000393063.1:c.5395G>T	p.Glu1799Ter	p.E1799*	ENST00000393063	NM_030621.3	1799	Gaa/Taa	26/28	1	2	FACETS	0.906	0.821	0.995	1	0.991	1	CLONAL	3	TRUE	1	0.121712654762108	2		422	762	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562462	95562462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778230	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	41	413	1	ENST00000393063.1:c.4795C>T	p.Arg1599Trp	p.R1599W	ENST00000393063	NM_030621.3	1599	Cgg/Tgg	24/28	1	2	FACETS	0.89	0.739	1	0.89	0.739	1	CLONAL	1	TRUE	1	0.121712654762108	2		414	757	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95577679	95577679	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	187	670	0	ENST00000393063.1:c.2231A>G	p.Lys744Arg	p.K744R	ENST00000393063	NM_030621.3	744	aAa/aGa	15/28	1	2	FACETS	1	0.979	1	1	0.993	1	CLONAL	2	TRUE	1	0.121712654762108	2		670	1308	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582819	95582819	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	117	347	0	ENST00000393063.1:c.1723G>A	p.Asp575Asn	p.D575N	ENST00000393063	NM_030621.3	575	Gac/Aac	11/28	1	2	FACETS	0.874	0.789	0.964	1	0.991	1	CLONAL	3	TRUE	1	0.121712654762108	2		347	733	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95595941	95595941	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749484792	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	136	355	0	ENST00000393063.1:c.602G>A	p.Arg201His	p.R201H	ENST00000393063	NM_030621.3	201	cGc/cAc	7/28	1	2	FACETS	0.925	0.842	1	1	0.992	1	CLONAL	3	TRUE	1	0.121712654762108	2		355	805	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961867	41961867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1224	202	811	4	ENST00000219905.7:c.775C>T	p.Arg259Trp	p.R259W	ENST00000219905	NM_001164273.1	259	Cgg/Tgg	2/24	1	2	FACETS	1	0.98	1	1	0.994	1	CLONAL	2	TRUE	1	0.121712654762108	2		815	1426	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988772	41988772	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs758005338	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1476	80	810	0	ENST00000219905.7:c.1564T>G	p.Leu522Val	p.L522V	ENST00000219905	NM_001164273.1	522	Tta/Gta	3/24	1	2	FACETS	0.845	0.74	0.958	0.845	0.74	0.958	CLONAL	1	TRUE	1	0.121712654762108	2		810	1556	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042178	42042178	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1353	399	959	1	ENST00000219905.7:c.6373G>T	p.Glu2125Ter	p.E2125*	ENST00000219905	NM_001164273.1	2125	Gaa/Taa	17/24	1	2	FACETS	0.936	0.887	0.985	1	0.997	1	CLONAL	4	TRUE	1	0.121712654762108	2		960	1752	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054338	42054338	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	156	655	0	ENST00000219905.7:c.7522G>T	p.Glu2508Ter	p.E2508*	ENST00000219905	NM_001164273.1	2508	Gaa/Taa	22/24	1	2	FACETS	1	0.925	1	1	0.991	1	CLONAL	2	TRUE	1	0.121712654762108	2		655	1265	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058765	42058765	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	247	701	1	ENST00000219905.7:c.8485G>T	p.Glu2829Ter	p.E2829*	ENST00000219905	NM_001164273.1	2829	Gaa/Taa	24/24	1	2	FACETS	1	0.979	1	1	0.996	1	CLONAL	3	TRUE	1	0.121712654762108	2		702	1215	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007763	45007763	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1258519454	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	174	560	0	ENST00000558401.1:c.210G>T	p.Glu70Asp	p.E70D	ENST00000558401	NM_004048.2	70	gaG/gaT	2/4	1	2	FACETS	1	0.971	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		560	856	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007876	45007876	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	65	342	1	ENST00000558401.1:c.323C>A	p.Ser108Ter	p.S108*	ENST00000558401	NM_004048.2	108	tCa/tAa	2/4	1	2	FACETS	0.827	0.716	0.946	1	0.975	1	CLONAL	2	TRUE	1	0.121712654762108	2		343	646	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729090	66729090	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	257	569	0	ENST00000307102.5:c.298C>A	p.His100Asn	p.H100N	ENST00000307102	NM_002755.3	100	Cat/Aat	3/11	1	2	FACETS	1	0.961	1	1	0.996	1	CLONAL	4	TRUE	1	0.121712654762108	2		569	1020	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782859	66782859	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	212	485	0	ENST00000307102.5:c.1088G>T	p.Arg363Ile	p.R363I	ENST00000307102	NM_002755.3	363	aGa/aTa	11/11	1	2	FACETS	1	0.976	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		485	1041	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483966	88483966	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	168	497	0	ENST00000360948.2:c.1604G>T	p.Arg535Met	p.R535M	ENST00000360948	NM_001012338.2	535	aGg/aTg	14/19	1	2	FACETS	1	0.928	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		497	911	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310233	91310233	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs896043726	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	171	439	0	ENST00000355112.3:c.2287C>A	p.Leu763Ile	p.L763I	ENST00000355112	NM_000057.2	763	Cta/Ata	10/22	1	2	FACETS	0.963	0.885	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		439	973	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99454583	99454583	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543853218	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	57	487	0	ENST00000268035.6:c.1502C>T	p.Ser501Leu	p.S501L	ENST00000268035	NM_000875.3	501	tCg/tTg	7/21	1	2	FACETS	0.947	0.81	1	0.947	0.81	1	CLONAL	1	TRUE	1	0.121712654762108	2		487	989	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347200	347200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	191	412	0	ENST00000262320.3:c.1811G>T	p.Arg604Ile	p.R604I	ENST00000262320	NM_003502.3	604	aGa/aTa	7/11	1	2	FACETS	0.948	0.878	1	1	0.995	1	CLONAL	4	TRUE	1	0.121712654762108	2		412	828	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396589	396589	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	182	498	0	ENST00000262320.3:c.437G>A	p.Arg146Gln	p.R146Q	ENST00000262320	NM_003502.3	146	cGa/cAa	2/11	1	2	FACETS	1	0.958	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		498	944	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098655	2098655	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs766814650	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1242	75	637	2	ENST00000219476.3:c.39G>T	p.Glu13Asp	p.E13D	ENST00000219476	NM_000548.3	13	gaG/gaT	2/42	1	2	FACETS	0.936	0.817	1	0.936	0.817	1	CLONAL	1	TRUE	1	0.121712654762108	2		639	1317	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900349	3900349	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1178134399	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	179	512	0	ENST00000262367.5:c.747A>C	p.Gln249His	p.Q249H	ENST00000262367	NM_004380.2	249	caA/caC	2/31	1	2	FACETS	0.87	0.801	0.942	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		512	1127	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857948	9857948	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	59	511	2	ENST00000330684.3:c.3453C>A	p.Tyr1151Ter	p.Y1151*	ENST00000330684	NM_001134407.1	1151	taC/taA	13/13	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.121712654762108	2		513	891	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934798	9934798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	233	649	2	ENST00000330684.3:c.1492G>A	p.Gly498Ser	p.G498S	ENST00000330684	NM_001134407.1	498	Ggt/Agt	6/13	1	2	FACETS	1	0.976	1	1	0.996	1	CLONAL	3	TRUE	1	0.121712654762108	2		651	1160	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641217	23641217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778586	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	131	421	0	ENST00000261584.4:c.2258G>A	p.Arg753Gln	p.R753Q	ENST00000261584	NM_024675.3	753	cGa/cAa	5/13	1	2	FACETS	0.892	0.81	0.979	1	0.992	1	CLONAL	3	TRUE	1	0.121712654762108	2		421	804	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646559	23646559	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	98	263	0	ENST00000261584.4:c.1308G>T	p.Lys436Asn	p.K436N	ENST00000261584	NM_024675.3	436	aaG/aaT	4/13	1	2	FACETS	0.905	0.812	1	1	0.99	1	CLONAL	4	TRUE	1	0.121712654762108	2		263	445	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647472	23647472	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	48	474	1	ENST00000261584.4:c.395T>C	p.Val132Ala	p.V132A	ENST00000261584	NM_024675.3	132	gTc/gCc	4/13	1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	1	0.121712654762108	2		475	784	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129459	30129459	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	314	637	0	ENST00000263025.4:c.569T>C	p.Ile190Thr	p.I190T	ENST00000263025	NM_002746.2	190	aTt/aCt	4/9	1	2	FACETS	1	0.961	1	1	0.997	1	CLONAL	4	TRUE	1	0.121712654762108	2		637	1259	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670592	67670592	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	75	483	3	ENST00000264010.4:c.1838-1G>T		p.X613_splice	ENST00000264010	NM_006565.3	613			1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.121712654762108	2		486	1007	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821095	72821095	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	283	683	1	ENST00000268489.5:c.11080A>G	p.Thr3694Ala	p.T3694A	ENST00000268489	NM_006885.3	3694	Acc/Gcc	10/10	1	2	FACETS	1	0.96	1	1	0.996	1	CLONAL	3	TRUE	1	0.121712654762108	2		684	1502	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827706	72827706	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	207	679	0	ENST00000268489.5:c.8875A>G	p.Lys2959Glu	p.K2959E	ENST00000268489	NM_006885.3	2959	Aag/Gag	9/10	1	2	FACETS	0.84	0.777	0.905	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		679	1350	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831953	72831953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1492	101	733	0	ENST00000268489.5:c.4628G>A	p.Arg1543His	p.R1543H	ENST00000268489	NM_006885.3	1543	cGc/cAc	9/10	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.121712654762108	2		733	1593	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832272	72832272	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs764523105	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	296	654	1	ENST00000268489.5:c.4309A>G	p.Ser1437Gly	p.S1437G	ENST00000268489	NM_006885.3	1437	Agt/Ggt	9/10	1	2	FACETS	1	0.986	1	1	0.996	1	CLONAL	3	TRUE	1	0.121712654762108	2		655	1395	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942093	81942093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs926237449	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1366	100	703	2	ENST00000359376.3:c.1630G>A	p.Glu544Lys	p.E544K	ENST00000359376	NM_002661.3	544	Gag/Aag	17/33	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.121712654762108	2		705	1466	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990302	81990302	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	178	494	0	ENST00000359376.3:c.3573G>T	p.Glu1191Asp	p.E1191D	ENST00000359376	NM_002661.3	1191	gaG/gaT	32/33	1	2	FACETS	1	0.97	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		494	884	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348329	89348329	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1366	373	900	2	ENST00000301030.4:c.4621G>T	p.Glu1541Ter	p.E1541*	ENST00000301030	NM_001256183.1	1541	Gaa/Taa	9/13	1	2	FACETS	0.881	0.834	0.93	1	0.997	1	CLONAL	4	TRUE	1	0.121712654762108	2		902	1739	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89866024	89866024	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs995966978	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	250	455	0	ENST00000389301.3:c.815G>T	p.Arg272Ile	p.R272I	ENST00000389301	NM_000135.2	272	aGa/aTa	9/43	1	2	FACETS	0.879	0.822	0.939	1	0.996	1	CLONAL	4	TRUE	1	0.121712654762108	2		455	1168	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217719	7217719	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1179	263	753	1	ENST00000380728.2:c.208C>A	p.Leu70Met	p.L70M	ENST00000380728		70	Ctg/Atg	4/11	1	2	FACETS	0.999	0.934	1	1	0.996	1	CLONAL	3	TRUE	1	0.121712654762108	2		754	1442	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974826	15974826	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	197	492	0	ENST00000268712.3:c.4049C>A	p.Ser1350Tyr	p.S1350Y	ENST00000268712	NM_006311.3	1350	tCc/tAc	30/46	1	2	FACETS	1	0.973	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		492	977	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508761	29508761	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	169	502	0	ENST00000356175.3:c.688G>T	p.Glu230Ter	p.E230*	ENST00000356175	NM_000267.3	230	Gaa/Taa	7/57	1	2	FACETS	0.893	0.82	0.969	1	0.993	1	CLONAL	3	TRUE	1	0.121712654762108	2		502	1037	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509612	29509612	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	132	552	0	ENST00000356175.3:c.817C>A	p.Leu273Ile	p.L273I	ENST00000356175	NM_000267.3	273	Ctc/Atc	8/57	1	2	FACETS	1	0.957	1	1	0.99	1	CLONAL	2	TRUE	1	0.121712654762108	2		552	991	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550566	29550566	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	142	423	0	ENST00000356175.3:c.1826A>C	p.Lys609Thr	p.K609T	ENST00000356175	NM_000267.3	609	aAa/aCa	16/57	1	2	FACETS	0.913	0.832	0.998	1	0.992	1	CLONAL	3	TRUE	1	0.121712654762108	2		423	852	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676219	29676219	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1555536029	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	57	394	3	ENST00000356175.3:c.7208G>T	p.Arg2403Ile	p.R2403I	ENST00000356175	NM_000267.3	2403	aGa/aTa	48/57	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.121712654762108	2		397	905	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37865572	37865572	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	261	593	0	ENST00000269571.5:c.441G>T	p.Glu147Asp	p.E147D	ENST00000269571		147	gaG/gaT	4/27	1	2	FACETS	0.924	0.865	0.985	1	0.996	1	CLONAL	4	TRUE	1	0.121712654762108	2		593	1160	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487645	38487645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774732066	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	60	496	1	ENST00000254066.5:c.175G>A	p.Ala59Thr	p.A59T	ENST00000254066	NM_000964.3	59	Gcc/Acc	2/9	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.121712654762108	2		497	888	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223001	41223001	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs397509205	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	70	639	0	ENST00000357654.3:c.4930G>T	p.Glu1644Ter	p.E1644*	ENST00000357654	NM_007294.3	1644	Gaa/Taa	15/23	1	2	FACETS	0.963	0.837	1	0.963	0.837	1	CLONAL	1	TRUE	1	0.121712654762108	2		639	1194	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243716	41243716	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	60	620	0	ENST00000357654.3:c.3832A>C	p.Lys1278Gln	p.K1278Q	ENST00000357654	NM_007294.3	1278	Aag/Cag	10/23	1	2	FACETS	0.824	0.707	0.952	0.824	0.707	0.952	CLONAL	1	TRUE	1	0.121712654762108	2		620	1197	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243770	41243770	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555587079	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	209	544	0	ENST00000357654.3:c.3778T>G	p.Leu1260Val	p.L1260V	ENST00000357654	NM_007294.3	1260	Tta/Gta	10/23	1	2	FACETS	1	0.976	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		544	1025	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245326	41245326	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	211	500	0	ENST00000357654.3:c.2222C>A	p.Ser741Tyr	p.S741Y	ENST00000357654	NM_007294.3	741	tCt/tAt	10/23	1	2	FACETS	0.933	0.867	1	1	0.995	1	CLONAL	4	TRUE	1	0.121712654762108	2		500	929	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245825	41245825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397508902	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	159	448	0	ENST00000357654.3:c.1723G>A	p.Glu575Lys	p.E575K	ENST00000357654	NM_007294.3	575	Gaa/Aaa	10/23	1	2	FACETS	1	0.96	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		448	810	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805697	46805697	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	69	392	1	ENST00000290295.7:c.259T>C	p.Tyr87His	p.Y87H	ENST00000290295	NM_006361.5	87	Tac/Cac	1/2	1	2	FACETS	0.889	0.774	1	1	0.978	1	CLONAL	2	TRUE	1	0.121712654762108	2		393	638	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440930	56440930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1227515515	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	255	538	1	ENST00000407977.2:c.407C>T	p.Ala136Val	p.A136V	ENST00000407977		136	gCt/gTt	4/10	1	2	FACETS	0.939	0.878	1	1	0.996	1	CLONAL	4	TRUE	1	0.121712654762108	2		539	1116	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772395	56772395	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	239	593	0	ENST00000337432.4:c.249G>T	p.Lys83Asn	p.K83N	ENST00000337432	NM_058216.2	83	aaG/aaT	2/9	1	2	FACETS	1	0.966	1	1	0.996	1	CLONAL	3	TRUE	1	0.121712654762108	2		593	1238	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772468	56772468	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	164	503	0	ENST00000337432.4:c.322G>T	p.Asp108Tyr	p.D108Y	ENST00000337432	NM_058216.2	108	Gat/Tat	2/9	1	2	FACETS	0.914	0.838	0.993	1	0.993	1	CLONAL	3	TRUE	1	0.121712654762108	2		503	983	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58725277	58725277	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	116	687	1	ENST00000305921.3:c.851T>C	p.Phe284Ser	p.F284S	ENST00000305921	NM_003620.3	284	tTc/tCc	4/6	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.121712654762108	2		688	1296	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761173	59761173	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs570238270	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	155	521	0	ENST00000259008.2:c.3234G>T	p.Lys1078Asn	p.K1078N	ENST00000259008	NM_032043.2	1078	aaG/aaT	20/20	1	2	FACETS	1	0.951	1	1	0.993	1	CLONAL	3	TRUE	1	0.121712654762108	2		521	806	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761411	59761411	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	68	378	0	ENST00000259008.2:c.2996G>T	p.Arg999Ile	p.R999I	ENST00000259008	NM_032043.2	999	aGa/aTa	20/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.121712654762108	2		378	789	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821930	59821930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200313471	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	167	456	0	ENST00000259008.2:c.2120G>A	p.Arg707His	p.R707H	ENST00000259008	NM_032043.2	707	cGt/cAt	15/20	1	2	FACETS	0.925	0.849	1	1	0.993	1	CLONAL	3	TRUE	1	0.121712654762108	2		456	989	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743272	743272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs188857712	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	187	558	1	ENST00000314574.4:c.868G>A	p.Glu290Lys	p.E290K	ENST00000314574	NM_005433.3	290	Gaa/Aaa	7/12	1	2	FACETS	0.902	0.832	0.975	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		559	1135	SUCCESS
YES1	7525	MSKCC	GRCh37	18	751726	751726	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1010928891	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	105	362	0	ENST00000314574.4:c.350G>T	p.Arg117Ile	p.R117I	ENST00000314574	NM_005433.3	117	aGa/aTa	3/12	1	2	FACETS	0.867	0.778	0.962	1	0.99	1	CLONAL	3	TRUE	1	0.121712654762108	2		362	663	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374881	45374881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	163	487	1	ENST00000262160.6:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000262160	NM_005901.5	321	cGa/cAa	8/11	1	2	FACETS	0.96	0.881	1	1	0.993	1	CLONAL	3	TRUE	1	0.121712654762108	2		488	930	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2180724	2180724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	256	580	0	ENST00000398665.3:c.94G>A	p.Asp32Asn	p.D32N	ENST00000398665	NM_032482.2	32	Gat/Aat	2/28	1	2	FACETS	0.907	0.849	0.968	1	0.996	1	CLONAL	4	TRUE	1	0.121712654762108	2		580	1159	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220045	5220045	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145842090	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	209	565	1	ENST00000357368.4:c.3670G>A	p.Asp1224Asn	p.D1224N	ENST00000357368	NM_002850.3	1224	Gac/Aac	22/38	1	2	FACETS	1	0.981	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		566	991	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265175	5265175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147257283	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	157	541	0	ENST00000357368.4:c.412G>A	p.Asp138Asn	p.D138N	ENST00000357368	NM_002850.3	138	Gac/Aac	5/38	1	2	FACETS	0.923	0.845	1	1	0.993	1	CLONAL	3	TRUE	1	0.121712654762108	2		541	932	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098351	11098351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763054014	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	158	474	1	ENST00000358026.2:c.869C>T	p.Ala290Val	p.A290V	ENST00000358026	NM_001128849.1	290	gCg/gTg	6/36	1	2	FACETS	1	0.958	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		475	809	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276316	15276316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372834264	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	163	452	0	ENST00000263388.2:c.5678G>A	p.Arg1893Gln	p.R1893Q	ENST00000263388	NM_000435.2	1893	cGa/cAa	31/33	1	2	FACETS	1	0.944	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		452	862	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291527	15291527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756527298	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	224	479	1	ENST00000263388.2:c.3107G>A	p.Arg1036Gln	p.R1036Q	ENST00000263388	NM_000435.2	1036	cGa/cAa	19/33	1	2	FACETS	1	0.932	1	1	0.996	1	CLONAL	4	TRUE	1	0.121712654762108	2		480	920	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745625	41745625	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	111	583	0	ENST00000301178.4:c.1312G>A	p.Val438Met	p.V438M	ENST00000301178	NM_021913.4	438	Gtg/Atg	10/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.121712654762108	2		583	1218	SUCCESS
AXL	558	MSKCC	GRCh37	19	41749591	41749591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1456382289	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	318	622	1	ENST00000301178.4:c.1516C>T	p.Arg506Cys	p.R506C	ENST00000301178	NM_021913.4	506	Cgt/Tgt	12/20	1	2	FACETS	0.956	0.901	1	1	0.997	1	CLONAL	4	TRUE	1	0.121712654762108	2		623	1366	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52729220	52729220	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1043254977	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	63	504	0	ENST00000322088.6:c.1756C>A	p.Leu586Met	p.L586M	ENST00000322088	NM_014225.5	586	Ctg/Atg	15/15	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.121712654762108	2		504	1002	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021700	31021700	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	79	255	2	ENST00000375687.4:c.1699C>A	p.Pro567Thr	p.P567T	ENST00000375687	NM_015338.5	567	Ccc/Acc	12/13	0.121712654762108	5	FACETS	1	0.96	1	0.608	0.535	0.687	CLONAL	2	TRUE	1	0.121712654762108	5		257	631	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36028627	36028627	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	214	630	0	ENST00000358208.4:c.969G>T	p.Glu323Asp	p.E323D	ENST00000358208		323	gaG/gaT	8/12	0.121712654762108	5	FACETS	1	0.969	1	0.812	0.753	0.873	CLONAL	3	TRUE	1	0.121712654762108	5		630	1281	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39729850	39729850	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	58	382	1	ENST00000361337.2:c.1165G>T	p.Asp389Tyr	p.D389Y	ENST00000361337	NM_003286.2	389	Gat/Tat	13/21	0.121712654762108	5	FACETS	1	0.951	1	0.315	0.27	0.365	CLONAL	1	TRUE	1	0.121712654762108	5		383	894	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39744970	39744970	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	428	579	0	ENST00000361337.2:c.1760A>G	p.Lys587Arg	p.K587R	ENST00000361337	NM_003286.2	587	aAg/aGg	17/21	0.121712654762108	5	FACETS	0.964	0.919	1	1	0.996	1	CLONAL	7	TRUE	1	0.121712654762108	5		579	1233	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733283	40733283	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	148	375	0	ENST00000373198.4:c.3523T>G	p.Phe1175Val	p.F1175V	ENST00000373198	NM_133170.3	1175	Ttc/Gtc	26/32	0.121712654762108	5	FACETS	1	0.958	1	0.811	0.74	0.884	CLONAL	3	TRUE	1	0.121712654762108	5		375	887	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743943	40743943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs763964405	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	249	405	1	ENST00000373198.4:c.3052C>T	p.Arg1018Ter	p.R1018*	ENST00000373198	NM_133170.3	1018	Cga/Tga	23/32	0.121712654762108	5	FACETS	0.977	0.917	1	1	0.993	1	CLONAL	6	TRUE	1	0.121712654762108	5		406	825	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877330	40877330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750253646	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	111	341	0	ENST00000373198.4:c.2366G>A	p.Arg789Lys	p.R789K	ENST00000373198	NM_133170.3	789	aGg/aAg	15/32	0.121712654762108	5	FACETS	0.853	0.766	0.945	0.64	0.575	0.709	CLONAL	3	TRUE	1	0.121712654762108	5		341	843	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101118	41101118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751886972	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	331	462	1	ENST00000373198.4:c.1238C>T	p.Ala413Val	p.A413V	ENST00000373198	NM_133170.3	413	gCg/gTg	8/32	0.121712654762108	5	FACETS	1	0.966	1	1	0.996	1	CLONAL	7	TRUE	1	0.121712654762108	5		463	898	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306638	41306638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	176	496	1	ENST00000373198.4:c.1021G>A	p.Asp341Asn	p.D341N	ENST00000373198	NM_133170.3	341	Gac/Aac	7/32	0.121712654762108	5	FACETS	0.99	0.91	1	0.742	0.682	0.805	CLONAL	3	TRUE	1	0.121712654762108	5		497	1152	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268450	46268450	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1436	188	781	0	ENST00000371998.3:c.2837A>C	p.Asn946Thr	p.N946T	ENST00000371998		946	aAt/aCt	15/23	0.121712654762108	5	FACETS	1	0.973	1	0.562	0.518	0.609	CLONAL	2	TRUE	1	0.121712654762108	5		781	1624	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485115	57485115	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754097818	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	335	414	0	ENST00000371085.3:c.949C>T	p.Arg317Cys	p.R317C	ENST00000371085	NM_000516.4	317	Cgc/Tgc	11/13	0.121712654762108	5	FACETS	0.968	0.916	1	1	0.994	1	CLONAL	6	TRUE	1	0.121712654762108	5		414	1121	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775575	39775575	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	95	451	1	ENST00000288319.7:c.445G>T	p.Glu149Ter	p.E149*	ENST00000288319	NM_182918.3	149	Gaa/Taa	4/10	1	2	FACETS	0.986	0.877	1	1	0.986	1	CLONAL	2	TRUE	1	0.121712654762108	2		452	792	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162055	22162055	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	55	490	1	ENST00000215832.6:c.200G>T	p.Arg67Ile	p.R67I	ENST00000215832	NM_002745.4	67	aGa/aTa	2/9	1	2	FACETS	0.936	0.798	1	0.936	0.798	1	CLONAL	1	TRUE	1	0.121712654762108	2		491	966	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064321	30064321	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	193	467	0	ENST00000338641.4:c.886-1G>A		p.X296_splice	ENST00000338641	NM_000268.3	296			1	2	FACETS	1	0.968	1	1	0.995	1	CLONAL	3	TRUE	1	0.121712654762108	2		467	974	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20153903	20153903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	207	182	0	ENST00000379607.5:c.157G>A	p.Asp53Asn	p.D53N	ENST00000379607	NM_001412.3	53	Gat/Aat	3/7	1	1	FACETS	1	0.964	1	1	0.996	1	CLONAL	7	TRUE	0	0.121712654762108	1		182	441	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933640	39933640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780396086	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	225	348	0	ENST00000378444.4:c.959C>T	p.Ala320Val	p.A320V	ENST00000378444	NM_001123385.1	320	gCg/gTg	4/15	1	1	FACETS	0.996	0.935	1	1	0.996	1	CLONAL	6	TRUE	0	0.121712654762108	1		348	581	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222800	53222800	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	77	280	0	ENST00000375401.3:c.4136C>T	p.Ser1379Leu	p.S1379L	ENST00000375401	NM_004187.3	1379	tCg/tTg	25/26	1	1	FACETS	1	0.946	1	1	0.985	1	CLONAL	2	TRUE	0	0.121712654762108	1		280	524	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245277	53245277	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	246	339	0	ENST00000375401.3:c.760G>T	p.Asp254Tyr	p.D254Y	ENST00000375401	NM_004187.3	254	Gac/Tac	6/26	1	1	FACETS	0.939	0.883	0.996	1	0.996	1	CLONAL	6	TRUE	0	0.121712654762108	1		339	674	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411576	63411576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	308	338	0	ENST00000330258.3:c.1591C>T	p.Arg531Ter	p.R531*	ENST00000330258	NM_152424.3	531	Cga/Tga	2/2	1	1	FACETS	1	0.954	1	1	0.997	1	CLONAL	6	TRUE	0	0.121712654762108	1		338	786	SUCCESS
AR	367	MSKCC	GRCh37	X	66765275	66765275	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	147	277	0	ENST00000374690.3:c.287C>A	p.Ser96Tyr	p.S96Y	ENST00000374690	NM_000044.3	96	tCt/tAt	1/8	1	1	FACETS	1	0.944	1	1	0.994	1	CLONAL	5	TRUE	0	0.121712654762108	1		277	440	SUCCESS
AR	367	MSKCC	GRCh37	X	66766441	66766441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	25	118	1	ENST00000374690.3:c.1453C>T	p.Arg485Trp	p.R485W	ENST00000374690	NM_000044.3	485	Cgg/Tgg	1/8	1	1	FACETS	0.936	0.742	1	1	0.947	1	CLONAL	2	TRUE	0	0.121712654762108	1		119	206	SUCCESS
AR	367	MSKCC	GRCh37	X	66863204	66863204	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	204	318	1	ENST00000374690.3:c.1723C>A	p.Leu575Ile	p.L575I	ENST00000374690	NM_000044.3	575	Ctc/Atc	2/8	1	1	FACETS	1	0.956	1	1	0.996	1	CLONAL	6	TRUE	0	0.121712654762108	1		319	511	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348545	70348545	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	265	334	1	ENST00000374080.3:c.3452C>T	p.Ala1151Val	p.A1151V	ENST00000374080		1151	gCc/gTc	24/45	1	1	FACETS	1	0.969	1	1	0.997	1	CLONAL	6	TRUE	0	0.121712654762108	1		335	656	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938090	76938090	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	27	245	0	ENST00000373344.5:c.2658G>T	p.Glu886Asp	p.E886D	ENST00000373344	NM_000489.3	886	gaG/gaT	9/35	1	1	FACETS	0.924	0.734	1	0.924	0.734	1	CLONAL	1	TRUE	0	0.121712654762108	1		245	451	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938330	76938330	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	134	221	0	ENST00000373344.5:c.2418G>T	p.Lys806Asn	p.K806N	ENST00000373344	NM_000489.3	806	aaG/aaT	9/35	1	1	FACETS	1	0.965	1	1	0.994	1	CLONAL	5	TRUE	0	0.121712654762108	1		221	378	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939584	76939584	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	229	322	0	ENST00000373344.5:c.1164A>C	p.Lys388Asn	p.K388N	ENST00000373344	NM_000489.3	388	aaA/aaC	9/35	1	1	FACETS	1	0.974	1	1	0.996	1	CLONAL	5	TRUE	0	0.121712654762108	1		322	658	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034413	123034413	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	274	294	0	ENST00000355640.3:c.1170G>T	p.Lys390Asn	p.K390N	ENST00000355640		390	aaG/aaT	6/7	0.121712654762108	2	FACETS	1	0.968	1			1	CLONAL	7	TRUE	NA	0.121712654762108	2		294	624	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176470	123176470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	405	345	1	ENST00000218089.9:c.437G>A	p.Arg146Gln	p.R146Q	ENST00000218089	NM_001042749.1	146	cGa/cAa	7/35	0.121712654762108	2	FACETS	1	0.962	1			1	CLONAL	8	TRUE	NA	0.121712654762108	2		346	828	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215264	123215264	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	332	258	0	ENST00000218089.9:c.2810A>C	p.Asn937Thr	p.N937T	ENST00000218089	NM_001042749.1	937	aAt/aCt	28/35	0.121712654762108	2	FACETS	1	0.967	1			1	CLONAL	7	TRUE	NA	0.121712654762108	2		258	763	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220441	123220441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	42	374	0	ENST00000218089.9:c.3098G>A	p.Arg1033Gln	p.R1033Q	ENST00000218089	NM_001042749.1	1033	cGa/cAa	30/35	0.121712654762108	2	FACETS	0.948	0.789	1			1	CLONAL	1	TRUE	NA	0.121712654762108	2		374	728	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568865	212568866	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	170	573	0	ENST00000342788.4:c.1252dup	p.Ser418PhefsTer2	p.S418Ffs*2	ENST00000342788	NM_005235.2	418	tct/tTct	11/28	1	2	FACETS	0.941	0.864	1	1	0.994	1	CLONAL	3	TRUE	1	0.121712654762108	2		573	990	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	255	409	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.891	0.839	0.945	0.891	0.839	0.945	CLONAL	1	TRUE	1	0.817503347439796	2		409	700	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	327	342	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.993	0.943	1	0.993	0.943	1	CLONAL	1	TRUE	1	0.817503347439796	2		342	806	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	429	368	3	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.917	0.876	0.959	0.917	0.876	0.959	CLONAL	1	TRUE	1	0.817503347439796	2		371	1144	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533904	63533904	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201460658	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	242	422	1	ENST00000307078.5:c.1250C>T	p.Ala417Val	p.A417V	ENST00000307078	NM_004655.3	417	gCg/gTg	6/11	1	2	FACETS	0.916	0.862	0.972	0.916	0.862	0.972	CLONAL	1	TRUE	1	0.817503347439796	2		423	646	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	204	343	1	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	1	2	FACETS	0.745	0.694	0.797	0.745	0.694	0.797	SUBCLONAL	1	TRUE	1	0.817503347439796	2		344	670	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216477	108216477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587782558	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	257	413	1	ENST00000278616.4:c.8432del	p.Lys2811SerfsTer46	p.K2811Sfs*46	ENST00000278616	NM_000051.3	2809	cAa/ca	58/63	1	2	FACETS	0.865	0.814	0.917	0.865	0.814	0.917	CLONAL	1	TRUE	1	0.817503347439796	2		414	727	SUCCESS
ATR	545	MSKCC	GRCh37	3	142241619	142241619	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1474267384	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	320	595	1	ENST00000350721.4:c.4217C>T	p.Ala1406Val	p.A1406V	ENST00000350721	NM_001184.3	1406	gCg/gTg	23/47	1	2	FACETS	0.945	0.897	0.995	0.945	0.897	0.995	CLONAL	1	TRUE	1	0.817503347439796	2		596	828	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	213	314	2	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.817503347439796	2		316	483	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	375	396	5	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.817503347439796	2		401	876	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	234	484	0	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	1	2	FACETS	0.961	0.903	1	0.961	0.903	1	CLONAL	1	TRUE	1	0.817503347439796	2		484	596	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230752	53230752	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	459	227	0	ENST00000375401.3:c.2041C>T	p.Arg681Ter	p.R681*	ENST00000375401	NM_004187.3	681	Cga/Tga	14/26	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.817503347439796	1		227	580	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944623	38944623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	299	588	1	ENST00000357387.3:c.4838G>A	p.Arg1613His	p.R1613H	ENST00000357387	NM_152756.3	1613	cGc/cAc	36/38	1	2	FACETS	0.881	0.833	0.93	0.881	0.833	0.93	CLONAL	1	TRUE	1	0.817503347439796	2		589	830	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918622	44918622	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	358	344	0	ENST00000377967.4:c.1105C>T	p.Gln369Ter	p.Q369*	ENST00000377967	NM_021140.2	369	Cag/Tag	12/29	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.817503347439796	1		344	409	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17124854	17124854	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767119281	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	348	561	1	ENST00000285071.4:c.868G>A	p.Ala290Thr	p.A290T	ENST00000285071	NM_144997.5	290	Gct/Act	8/14	1	2	FACETS	0.983	0.935	1	0.983	0.935	1	CLONAL	1	TRUE	1	0.817503347439796	2		562	866	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458420	120458420	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	165	363	1	ENST00000256646.2:c.6925C>T	p.Leu2309Phe	p.L2309F	ENST00000256646	NM_024408.3	2309	Ctc/Ttc	34/34	1	2	FACETS	0.827	0.766	0.89	0.827	0.766	0.89	CLONAL	1	TRUE	1	0.817503347439796	2		364	488	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656987	47656987	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750302	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	753	628	0	ENST00000233146.2:c.1183C>T	p.Gln395Ter	p.Q395*	ENST00000233146	NM_000251.2	395	Caa/Taa	7/16	0.813822531659692	2	FACETS	0.984	0.965	1	0.984	0.965	1	CLONAL	2	TRUE	0	0.817503347439796	2		628	936	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968219	134968219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759415643	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	321	562	2	ENST00000398015.3:c.2732C>T	p.Thr911Met	p.T911M	ENST00000398015	NM_004441.4	911	aCg/aTg	15/16	1	2	FACETS	0.939	0.891	0.989	0.939	0.891	0.989	CLONAL	1	TRUE	1	0.817503347439796	2		564	836	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417934	138417934	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1194965901	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	156	302	0	ENST00000289153.2:c.1585C>T	p.Arg529Ter	p.R529*	ENST00000289153	NM_006219.2	529	Cga/Tga	11/22	1	2	FACETS	0.961	0.891	1	0.961	0.891	1	CLONAL	1	TRUE	1	0.817503347439796	2		302	397	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973979	55973979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762221907	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	288	585	2	ENST00000263923.4:c.1337C>T	p.Thr446Met	p.T446M	ENST00000263923	NM_002253.2	446	aCg/aTg	10/30	1	2	FACETS	0.886	0.837	0.936	0.886	0.837	0.936	CLONAL	1	TRUE	1	0.817503347439796	2		587	795	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004616	150004616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150904756	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	480	789	4	ENST00000253339.5:c.1609G>A	p.Ala537Thr	p.A537T	ENST00000253339		537	Gct/Act	3/7	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.817503347439796	2		793	1030	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275752	38275752	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747333248	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	374	569	1	ENST00000425967.3:c.1517G>A	p.Arg506Gln	p.R506Q	ENST00000425967	NM_001174067.1	506	cGg/cAg	11/19	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.817503347439796	2		570	892	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132926	64132926	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	408	589	0	ENST00000334205.4:c.1060C>T	p.Arg354Ter	p.R354*	ENST00000334205	NM_003942.2	354	Cga/Tga	9/17	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.817503347439796	2		589	921	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202231	108202231	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	254	495	0	ENST00000278616.4:c.7576A>G	p.Arg2526Gly	p.R2526G	ENST00000278616	NM_000051.3	2526	Aga/Gga	51/63	1	2	FACETS	0.912	0.859	0.967	0.912	0.859	0.967	CLONAL	1	TRUE	1	0.817503347439796	2		495	681	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479838	67479838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779602560	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	386	543	0	ENST00000327367.4:c.1145C>T	p.Ala382Val	p.A382V	ENST00000327367	NM_005902.3	382	gCg/gTg	8/9	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.817503347439796	2		543	910	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788669	3788669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	299	578	0	ENST00000262367.5:c.4285G>A	p.Val1429Met	p.V1429M	ENST00000262367	NM_004380.2	1429	Gtg/Atg	26/31	1	2	FACETS	0.955	0.904	1	0.955	0.904	1	CLONAL	1	TRUE	1	0.817503347439796	2		578	766	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822363	72822363	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759418149	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	574	901	0	ENST00000268489.5:c.9812C>T	p.Thr3271Met	p.T3271M	ENST00000268489	NM_006885.3	3271	aCg/aTg	10/10	1	2	FACETS	0.981	0.944	1	0.981	0.944	1	CLONAL	1	TRUE	1	0.817503347439796	2		901	1431	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244079	5244079	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	147	731	0	ENST00000357368.4:c.1403C>T	p.Pro468Leu	p.P468L	ENST00000357368	NM_002850.3	468	cCg/cTg	11/38	1	2	FACETS	0.309	0.281	0.339	0.309	0.281	0.339	SUBCLONAL	1	TRUE	1	0.817503347439796	2		731	1163	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169019	11169019	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372893370	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	385	646	1	ENST00000358026.2:c.4609G>A	p.Val1537Met	p.V1537M	ENST00000358026	NM_001128849.1	1537	Gtg/Atg	32/36	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.817503347439796	2		647	938	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18276986	18276986	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748211099	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	341	510	0	ENST00000222254.8:c.1433G>A	p.Arg478His	p.R478H	ENST00000222254	NM_005027.3	478	cGt/cAt	12/16	1	2	FACETS	0.949	0.902	0.997	0.949	0.902	0.997	CLONAL	1	TRUE	1	0.817503347439796	2		510	879	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748487	40748487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143335817	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	382	637	1	ENST00000392038.2:c.395C>T	p.Thr132Met	p.T132M	ENST00000392038	NM_001626.4	132	aCg/aTg	5/14	1	2	FACETS	0.923	0.879	0.968	0.923	0.879	0.968	CLONAL	1	TRUE	1	0.817503347439796	2		638	1012	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030983	36030983	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	305	473	0	ENST00000358208.4:c.1262C>T	p.Ala421Val	p.A421V	ENST00000358208		421	gCg/gTg	10/12	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.817503347439796	2		473	701	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41489043	41489043	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	314	579	0	ENST00000263253.7:c.35C>A	p.Ser12Ter	p.S12*	ENST00000263253	NM_001429.3	12	tCa/tAa	1/31	1	2	FACETS	0.887	0.84	0.935	0.887	0.84	0.935	CLONAL	1	TRUE	1	0.817503347439796	2		579	866	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195552	123195648	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGTGGCATATAGGGAGAAGAAATAAGCTAACTCTTTCTGACTTTTTTTTTTTTTTTTTTTTTTTTTAGCACTAACAGATAGGCAAGAGAGTGCTCT	AAGTGGCATATAGGGAGAAGAAATAAGCTAACTCTTTCTGACTTTTTTTTTTTTTTTTTTTTTTTTTAGCACTAACAGATAGGCAAGAGAGTGCTCT	-	novel	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	341	57	0	ENST00000218089.9:c.1535-69_1562del		p.X512_splice	ENST00000218089	NM_001042749.1	512		17/35	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.817503347439796	1		57	348	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405953	157405954	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1554294674	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	299	601	0	ENST00000346085.5:c.2201dup	p.Ser736IlefsTer27	p.S736Ifs*27	ENST00000346085	NM_020732.3	732	ccg/ccGg	6/20	1	2	FACETS	0.86	0.812	0.908	0.86	0.812	0.908	CLONAL	1	TRUE	1	0.817503347439796	2		601	851	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666428	206666428	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	402	651	1	ENST00000367120.3:c.1912del	p.Val638SerfsTer31	p.V638Sfs*31	ENST00000367120	NM_014002.3	636	caG/ca	19/22	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.817503347439796	2		652	973	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420332	49420333	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	385	720	0	ENST00000301067.7:c.15416dup	p.Pro5141AlafsTer3	p.P5141Afs*3	ENST00000301067	NM_003482.3	5139	aag/aaAg	48/54	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.817503347439796	2		720	903	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100934	27100934	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	288	524	0	ENST00000324856.7:c.4220del	p.Pro1407GlnfsTer74	p.P1407Qfs*74	ENST00000324856	NM_006015.4	1406	Ccc/cc	18/20	1	2	FACETS	0.923	0.873	0.975	0.923	0.873	0.975	CLONAL	1	TRUE	1	0.817503347439796	2		524	763	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512401	38512402	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs745553450	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	202	446	2	ENST00000254066.5:c.1319dup	p.Pro441AlafsTer5	p.P441Afs*5	ENST00000254066	NM_000964.3	438	gcc/gCcc	9/9	1	2	FACETS	0.839	0.783	0.896	0.839	0.783	0.896	CLONAL	1	TRUE	1	0.817503347439796	2		448	589	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428510	72428510	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	260	450	0	ENST00000477973.2:c.492del	p.Pro165LeufsTer43	p.P165Lfs*43	ENST00000477973	NM_012234.5	165	cCt/ct	2/4	1	2	FACETS	0.94	0.886	0.994	0.94	0.886	0.994	CLONAL	1	TRUE	1	0.817503347439796	2		450	677	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645499	67645500	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	212	339	1	ENST00000264010.4:c.769dup	p.Ile257AsnfsTer2	p.I257Nfs*2	ENST00000264010	NM_006565.3	255	aca/acAa	3/12	1	2	FACETS	0.935	0.875	0.995	0.935	0.875	0.995	CLONAL	1	TRUE	1	0.817503347439796	2		340	555	SUCCESS
BLM	641	MSKCC	GRCh37	15	91295028	91295030	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs587779895	NA	P-0005842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	267	585	0	ENST00000355112.3:c.819_821del	p.Lys273del	p.K273del	ENST00000355112	NM_000057.2	271	AAG/-	4/22	1	2	FACETS	0.911	0.859	0.964	0.911	0.859	0.964	CLONAL	1	TRUE	1	0.817503347439796	2		585	717	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0005867-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	52	157	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.361315927256057	3	FACETS	0.787	0.671	0.913	0.393	0.335	0.457	CLONAL	1	TRUE	1	0.361315927256057	3		157	432	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991736	25991736	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs530632623	NA	P-0005867-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	99	249	2	ENST00000435504.4:c.506C>T	p.Ala169Val	p.A169V	ENST00000435504		169	gCg/gTg	7/13	1	2	FACETS	0.824	0.736	0.917	0.824	0.736	0.917	CLONAL	1	TRUE	1	0.361315927256057	2		251	665	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86682699	86682699	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005867-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	70	214	0	ENST00000274376.6:c.2904C>G	p.Ile968Met	p.I968M	ENST00000274376	NM_002890.2	968	atC/atG	23/25	NA	2	FACETS	0.646	0.563	0.735			1	INDETERMINATE	1	TRUE	NA	0.361315927256057	2		214	600	SUCCESS
APC	324	MSKCC	GRCh37	5	112179233	112179233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1195417407	NA	P-0005867-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	146	244	0	ENST00000257430.4:c.7942G>A	p.Ala2648Thr	p.A2648T	ENST00000257430	NM_000038.5	2648	Gca/Aca	16/16	NA	2	FACETS	1	0.922	1			1	INDETERMINATE	1	TRUE	NA	0.361315927256057	2		244	800	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934234	48934234	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005867-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	70	213	0	ENST00000267163.4:c.689C>A	p.Ser230Ter	p.S230*	ENST00000267163	NM_000321.2	230	tCa/tAa	7/27	0.287600053930463	1	FACETS	0.86	0.754	0.973	0.86	0.754	0.973	CLONAL	1	TRUE	0	0.361315927256057	1		213	369	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618561	37618561	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005867-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	259	240	0	ENST00000447079.4:c.238del	p.Ser80ProfsTer12	p.S80Pfs*12	ENST00000447079	NM_015083.1	79	gaT/ga	1/14	0.361315927256057	3	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	1	0.361315927256057	3		240	845	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137524703	137524705	+	frameshift_variant	Frame_Shift_Ins	INS	ATG	ATG	TTAC	novel	NA	P-0005867-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	114	250	0	ENST00000367739.4:c.664_666delinsGTAA	p.His222ValfsTer8	p.H222Vfs*8	ENST00000367739	NM_000416.2	222	CAT/GTAA	5/7	1	2	FACETS	0.916	0.826	1	0.916	0.826	1	CLONAL	1	TRUE	1	0.361315927256057	2		250	689	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0005876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	162	435	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.238548054009271	3	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.358336050550673	3		436	778	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0005876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	46	327	1	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.358336050550673	3	FACETS	0.3	0.251	0.354	0.15	0.125	0.177	SUBCLONAL	1	TRUE	1	0.358336050550673	3		328	1010	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0005876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	197	310	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.358336050550673	3	FACETS	1	0.99	1	0.741	0.687	0.797	CLONAL	1	TRUE	1	0.358336050550673	3		310	875	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0005876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1303	227	724	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	0.227489737525897	3	FACETS	0.976	0.907	1	0.488	0.453	0.525	CLONAL	1	TRUE	1	0.358336050550673	3		724	1530	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0005876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	442	320	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	0.358336050550673	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.358336050550673	3		320	917	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0005876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	66	237	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.358336050550673	3	FACETS	1	0.883	1	0.507	0.442	0.578	CLONAL	1	TRUE	1	0.358336050550673	3		237	428	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248599	212248599	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1281587425	NA	P-0005876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	255	349	0	ENST00000342788.4:c.3668A>G	p.Lys1223Arg	p.K1223R	ENST00000342788	NM_005235.2	1223	aAg/aGg	28/28	0.227489737525897	3	FACETS	0.942	0.883	1	0.942	0.883	1	CLONAL	2	TRUE	1	0.358336050550673	3		349	891	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368252	45368252	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	380	348	0	ENST00000262160.6:c.1350C>G	p.Asp450Glu	p.D450E	ENST00000262160	NM_005901.5	450	gaC/gaG	11/11	0.358336050550673	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.358336050550673	3		348	1089	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217364	123217364	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	273	382	0	ENST00000218089.9:c.3018T>G	p.Phe1006Leu	p.F1006L	ENST00000218089	NM_001042749.1	1006	ttT/ttG	29/35	0.227489737525897	3	FACETS	0.763	0.715	0.811	0.763	0.715	0.811	SUBCLONAL	2	TRUE	1	0.358336050550673	3		382	1178	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035925	47035926	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0005876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	388	348	0	ENST00000377604.3:c.606_607dup	p.Ser203CysfsTer64	p.S203Cfs*64	ENST00000377604	NM_001204468.1	201	-/GT	7/24	0.227489737525897	3	FACETS	0.957	0.909	1	0.957	0.909	1	CLONAL	2	TRUE	1	0.358336050550673	3		348	1334	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971147	21971148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	40	44	0	ENST00000304494.5:c.210dup	p.Asn71GlnfsTer49	p.N71Qfs*49	ENST00000304494	NM_000077.4	70	-/C	2/3	0.358336050550673				0.94	1				CLONAL	1	TRUE	1	0.358336050550673	3		44	206	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712514	52712514	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0005893-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	157	513	0	ENST00000394830.3:c.236+2T>C		p.X79_splice	ENST00000394830	NM_018313.4	79			0.3	1	FACETS	0.97	0.893	1	0.97	0.893	1	CLONAL	1	TRUE	0	0.43	1		513	591	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164067	47164067	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005893-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	73	408	0	ENST00000409792.3:c.2059del	p.Cys687AlafsTer9	p.C687Afs*9	ENST00000409792	NM_014159.6	687	Tgc/gc	3/21	0.3	1	FACETS	0.751	0.661	0.846	0.751	0.661	0.846	SUBCLONAL	1	TRUE	0	0.43	1		408	355	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53253991	53253992	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005893-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	193	480	0	ENST00000375401.3:c.80dup	p.Leu28SerfsTer47	p.L28Sfs*47	ENST00000375401	NM_004187.3	27	cct/ccCt	1/26	1	1	FACETS	0.758	0.708	0.808	1	0.992	1	SUBCLONAL	2	TRUE	0	0.43	1		480	465	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188217	10188217	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005893-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	146	558	0	ENST00000256474.2:c.360del	p.Asp121MetfsTer38	p.D121Mfs*38	ENST00000256474	NM_000551.3	120	agA/ag	2/3	0.3	1	FACETS	0.935	0.858	1	0.935	0.858	1	CLONAL	1	TRUE	0	0.43	1		558	570	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0005896-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	160	357	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.84	0.78	0.901	1	0.991	1	CLONAL	2	TRUE	1	0.48701690155011	2		357	391	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0005896-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	77	269	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.48701690155011	2		269	235	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0005896-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	801	734	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.48701690155011	3	FACETS	1	0.988	1			1	CLONAL	3	TRUE	NA	0.48701690155011	3		734	1329	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0005896-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	130	193	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.869	0.801	0.939	1	0.99	1	CLONAL	2	TRUE	1	0.48701690155011	2		193	307	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144146	11144146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005896-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	351	700	0	ENST00000358026.2:c.3727C>T	p.Arg1243Trp	p.R1243W	ENST00000358026	NM_001128849.1	1243	Cgg/Tgg	26/36	1	2	FACETS	0.855	0.814	0.897	1	0.996	1	CLONAL	2	TRUE	1	0.48701690155011	2		700	843	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107180	27107180	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0005896-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	121	252	0	ENST00000324856.7:c.6791C>G	p.Ser2264Ter	p.S2264*	ENST00000324856	NM_006015.4	2264	tCa/tGa	20/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.48701690155011	2		252	348	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720711	89720712	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005896-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	26	51	0	ENST00000371953.3:c.867dup	p.Val290SerfsTer8	p.V290Sfs*8	ENST00000371953	NM_000314.4	288	gaa/gAaa	8/9	1	2	FACETS	0.797	0.656	0.944	1	0.949	1	CLONAL	2	TRUE	1	0.48701690155011	2		51	67	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100139	27100139	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005896-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	273	513	0	ENST00000324856.7:c.3936del	p.Asn1313ThrfsTer168	p.N1313Tfs*168	ENST00000324856	NM_006015.4	1312	tCc/tc	16/20	1	2	FACETS	0.79	0.745	0.834	1	0.994	1	SUBCLONAL	2	TRUE	1	0.48701690155011	2		513	710	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910371	29910372	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005896-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	311	704	0	ENST00000376809.5:c.46dup	p.Ala16GlyfsTer83	p.A16Gfs*83	ENST00000376809	NM_002116.7	14	tcg/tcGg	1/8	1	2	FACETS	0.764	0.723	0.805	1	0.995	1	SUBCLONAL	2	TRUE	1	0.48701690155011	2		704	836	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115859	8115859	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1303	213	596	0	ENST00000346208.3:c.1205C>T	p.Ser402Phe	p.S402F	ENST00000346208		402	tCc/tTc	6/6	1	2	FACETS	0.54	0.5	0.582	0.54	0.5	0.582	SUBCLONAL	1	TRUE	1	0.52	2		596	1516	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102056791	102056791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771074378	NA	P-0005904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	211	420	0	ENST00000282441.5:c.731G>A	p.Gly244Glu	p.G244E	ENST00000282441	NM_001130145.2	244	gGa/gAa	4/9	1	2	FACETS	0.986	0.918	1	0.986	0.918	1	CLONAL	1	TRUE	1	0.52	2		420	823	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878354	151878355	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	337	465	0	ENST00000262189.6:c.6590dup	p.Arg2198GlufsTer4	p.R2198Efs*4	ENST00000262189	NM_170606.2	2197	cag/caAg	36/59	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.52	2		465	1256	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	182	588	1	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	0.494446993362887	2		589	539	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0005908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	263	660	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.494446993362887	2		660	845	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0005908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	160	346	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.494446993362887	2		346	503	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661845	227661845	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	184	334	0	ENST00000305123.5:c.1610A>G	p.Gln537Arg	p.Q537R	ENST00000305123	NM_005544.2	537	cAg/cGg	1/2	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.494446993362887	2		334	605	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180165	38180165	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	119	248	0	ENST00000396334.3:c.13C>T	p.Arg5Cys	p.R5C	ENST00000396334	NM_002468.4	5	Cgc/Tgc	1/5	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.494446993362887	2		248	433	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508490	106508490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	74	129	0	ENST00000359195.3:c.484G>A	p.Val162Ile	p.V162I	ENST00000359195	NM_002649.2	162	Gtc/Atc	2/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.494446993362887	2		129	244	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063672	67063672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	215	349	0	ENST00000412916.2:c.121C>T	p.Gln41Ter	p.Q41*	ENST00000412916		41	Cag/Tag	2/6	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.494446993362887	2		349	818	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411246	63411246	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	311	258	0	ENST00000330258.3:c.1921C>T	p.Arg641Ter	p.R641*	ENST00000330258	NM_152424.3	641	Cga/Tga	2/2	1	1	FACETS	0.897	0.858	0.935	1	0.996	1	CLONAL	2	TRUE	0	0.494446993362887	1		258	528	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098885	178098886	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	210	459	0	ENST00000397062.3:c.159dup	p.Leu54ThrfsTer2	p.L54Tfs*2	ENST00000397062	NM_006164.4	53	-/A	2/5	1	2	FACETS	0.935	0.869	1	0.935	0.869	1	CLONAL	1	TRUE	1	0.494446993362887	2		459	908	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522799	67522800	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0005908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	131	309	1	ENST00000274335.5:c.297_298dup	p.Gly100GlufsTer15	p.G100Efs*15	ENST00000274335		99	cca/ccAGa	1/15	0.494446993362887	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.494446993362887	1		310	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138729528	NA	P-0005913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	9	390	0	ENST00000269305.4:c.523C>T	p.Arg175Cys	p.R175C	ENST00000269305	NM_001126112.2	175	Cgc/Tgc	5/11	0.366695530557446	3	FACETS	0.207	0.137	0.298	0.104	0.068	0.149	SUBCLONAL	1	FALSE	1	0.366695530557446	3		390	280	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162353	47162353	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0005913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	41	312	0	ENST00000409792.3:c.3773T>G	p.Leu1258Ter	p.L1258*	ENST00000409792	NM_014159.6	1258	tTa/tGa	3/21	0.348961786875615	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	2	FALSE	0	0.366695530557446	2		312	104	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976637	55976637	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	106	619	1	ENST00000263923.4:c.1188C>A	p.Tyr396Ter	p.Y396*	ENST00000263923	NM_002253.2	396	taC/taA	9/30	0.166309681568265	4	FACETS	1	0.962	1	0.748	0.678	0.822	INDETERMINATE	2	FALSE	1	0.366695530557446	4		620	352	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273273	55273273	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs768074018	NA	P-0005913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	133	393	0	ENST00000275493.2:c.3596G>C	p.Arg1199Thr	p.R1199T	ENST00000275493	NM_005228.3	1199	aGg/aCg	28/28	0.366695530557446	5	FACETS	1	0.941	1	1	0.988	1	CLONAL	3	FALSE	3	0.366695530557446	5		393	364	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426393	49426393	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772049588	NA	P-0005913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	111	640	0	ENST00000301067.7:c.12095C>T	p.Ala4032Val	p.A4032V	ENST00000301067	NM_003482.3	4032	gCc/gTc	39/54	0.179415482388365	5	FACETS	1	0.951	1	0.719	0.651	0.79	INDETERMINATE	2	FALSE	2	0.366695530557446	5		640	435	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112553	115112553	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs768701023	NA	P-0005913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	56	435	0	ENST00000257566.3:c.1187C>G	p.Ser396Cys	p.S396C	ENST00000257566	NM_016569.3	396	tCc/tGc	7/8	0.179415482388365	5	FACETS	1	0.882	1	0.344	0.295	0.397	INDETERMINATE	1	FALSE	2	0.366695530557446	5		435	459	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123025111	123025111	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	112	302	0	ENST00000355640.3:c.1001A>T	p.Lys334Met	p.K334M	ENST00000355640		334	aAg/aTg	4/7	0.189527403542552	3	FACETS	1	0.978	1			1	INDETERMINATE	3	FALSE	NA	0.366695530557446	3		302	207	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188250	10188251	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAAA	novel	NA	P-0005913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	127	586	0	ENST00000256474.2:c.395_398dup	p.Glu134AsnfsTer2	p.E134Nfs*2	ENST00000256474	NM_000551.3	131	-/CAAA	2/3	0.348961786875615	2	FACETS	0.897	0.821	0.976	0.897	0.821	0.976	CLONAL	2	FALSE	0	0.366695530557446	2		586	386	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702588	52702589	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AT	novel	NA	P-0005913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	59	452	0	ENST00000394830.3:c.309_310delinsAT	p.Met103_Glu104delinsIleTer	p.M103_E104delinsI*	ENST00000394830	NM_018313.4	103	atGGaa/atATaa	4/30	0.348961786875615	2	FACETS	0.817	0.714	0.924	0.817	0.714	0.924	CLONAL	2	FALSE	0	0.366695530557446	2		452	197	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0005931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	158	336	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	NA	2	FACETS	0.994	0.914	1			1	INDETERMINATE	2	TRUE	NA	0.23750794374926	2		336	669	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076823	72076823	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	46	344	1	ENST00000357731.5:c.674C>A	p.Pro225His	p.P225H	ENST00000357731	NM_173808.2	225	cCt/cAt	5/7	0.234734524375779	3	FACETS	0.746	0.627	0.877	0.373	0.313	0.439	SUBCLONAL	1	TRUE	1	0.23750794374926	3		345	581	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247244	153247244	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	157	447	0	ENST00000281708.4:c.1558G>T	p.Asp520Tyr	p.D520Y	ENST00000281708	NM_033632.3	520	Gat/Tat	10/12	0.219087048323461	2	FACETS	0.955	0.877	1	0.955	0.877	1	CLONAL	2	TRUE	0	0.23750794374926	2		447	692	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845185	128845185	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770465007	NA	P-0005931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	239	401	1	ENST00000249373.3:c.679C>T	p.His227Tyr	p.H227Y	ENST00000249373	NM_005631.4	227	Cac/Tac	3/12	0.234734524375779	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.23750794374926	3		402	933	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97888819	97888819	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	92	518	0	ENST00000289081.3:c.888G>C	p.Glu296Asp	p.E296D	ENST00000289081	NM_000136.2	296	gaG/gaC	9/15	0.192520310470788	4	FACETS	0.913	0.809	1	0.457	0.404	0.512	CLONAL	1	TRUE	2	0.23750794374926	4		518	1050	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49423021	49423021	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0005931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	230	379	0	ENST00000301067.7:c.14076-2A>G		p.X4692_splice	ENST00000301067	NM_003482.3	4692			0.23750794374926	3	FACETS	0.993	0.93	1	0.993	0.93	1	CLONAL	3	TRUE	0	0.23750794374926	3		379	727	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906873	32906873	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	27	246	0	ENST00000380152.3:c.1258G>C	p.Asp420His	p.D420H	ENST00000380152		420	Gac/Cac	10/27	0.233321162631313	2	FACETS	0.673	0.536	0.829	0.336	0.268	0.415	SUBCLONAL	1	TRUE	0	0.23750794374926	2		246	338	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351185	89351185	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	131	531	0	ENST00000301030.4:c.1765C>G	p.Leu589Val	p.L589V	ENST00000301030	NM_001256183.1	589	Ctg/Gtg	9/13	0.234734524375779	3	FACETS	1	0.954	1	0.544	0.492	0.599	CLONAL	1	TRUE	1	0.23750794374926	3		531	1134	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971032	21971065	+	frameshift_variant	Frame_Shift_Del	DEL	GCATCGCGCACGTCCAGCCGCGCCCCGGCCCGGT	GCATCGCGCACGTCCAGCCGCGCCCCGGCCCGGT	-	novel	NA	P-0005931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	179	243	0	ENST00000304494.5:c.293_326del	p.His98ProfsTer37	p.H98Pfs*37	ENST00000304494	NM_000077.4	98	cACCGGGCCGGGGCGCGGCTGGACGTGCGCGATGCc/cc	2/3	0.219087048323461	2	FACETS	0.9	0.835	0.967	1	0.988	1	CLONAL	3	TRUE	0	0.23750794374926	2		243	558	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627744	187627745	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AACGCCAG	novel	NA	P-0005931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	148	416	0	ENST00000441802.2:c.3230_3237dup	p.Gly1080LeufsTer8	p.G1080Lfs*8	ENST00000441802	NM_005245.3	1079	-/CTGGCGTT	2/27	0.219087048323461	2	FACETS	0.923	0.845	1	0.923	0.845	1	CLONAL	2	TRUE	0	0.23750794374926	2		416	675	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs878854073	NA	P-0005938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	214	314	0	ENST00000269305.4:c.673-1G>A		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.401865864493345	2	FACETS	0.889	0.833	0.946	0.889	0.833	0.946	CLONAL	2	TRUE	0	0.436652768023725	2		314	551	SUCCESS
APC	324	MSKCC	GRCh37	5	112175378	112175378	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0005938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	171	263	0	ENST00000257430.4:c.4087A>T	p.Lys1363Ter	p.K1363*	ENST00000257430	NM_000038.5	1363	Aaa/Taa	16/16	0.292619958416456	2	FACETS	1	0.989	1	0.699	0.647	0.753	CLONAL	1	TRUE	0	0.436652768023725	2		263	560	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185789	32185789	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	189	565	0	ENST00000375023.3:c.1607A>T	p.Gln536Leu	p.Q536L	ENST00000375023	NM_004557.3	536	cAg/cTg	9/30	NA	2	FACETS	0.942	0.871	1			1	INDETERMINATE	1	TRUE	NA	0.436652768023725	2		565	919	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412679	139412679	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	112	509	0	ENST00000277541.6:c.1165A>C	p.Thr389Pro	p.T389P	ENST00000277541	NM_017617.3	389	Acc/Ccc	7/34	0.234724109935198	1	FACETS	0.435	0.39	0.482	0.435	0.39	0.482	INDETERMINATE	1	TRUE	0	0.436652768023725	1		509	922	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601917	43601917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767388	NA	P-0005938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	192	524	0	ENST00000355710.3:c.961G>A	p.Gly321Arg	p.G321R	ENST00000355710	NM_020975.4	321	Ggg/Agg	5/20	1	2	FACETS	0.931	0.861	1	0.931	0.861	1	CLONAL	1	TRUE	1	0.436652768023725	2		524	945	SUCCESS
ATM	472	MSKCC	GRCh37	11	108213967	108213967	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876659872	NA	P-0005938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	311	338	0	ENST00000278616.4:c.8287C>T	p.Arg2763Ter	p.R2763*	ENST00000278616	NM_000051.3	2763	Cga/Tga	57/63	0.406542740475709	2	FACETS	0.9	0.853	0.948	0.9	0.853	0.948	CLONAL	2	TRUE	0	0.436652768023725	2		338	791	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589729	28589729	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1231	118	505	0	ENST00000241453.7:c.2651T>C	p.Leu884Pro	p.L884P	ENST00000241453	NM_004119.2	884	cTt/cCt	21/24	0.434609417476909	4	FACETS	0.576	0.517	0.638	0.288	0.258	0.319	SUBCLONAL	1	TRUE	2	0.436652768023725	4		505	1349	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191015	2191015	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	64	330	0	ENST00000398665.3:c.269A>C	p.Lys90Thr	p.K90T	ENST00000398665	NM_032482.2	90	aAg/aCg	5/28	0.234818034535397	2	FACETS	0.361	0.311	0.414	0.18	0.155	0.207	INDETERMINATE	1	TRUE	0	0.436652768023725	2		330	813	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226770	2226770	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	44	427	0	ENST00000398665.3:c.4250A>T	p.Glu1417Val	p.E1417V	ENST00000398665	NM_032482.2	1417	gAg/gTg	27/28	0.234818034535397	2	FACETS	0.231	0.192	0.273	0.115	0.096	0.137	INDETERMINATE	1	TRUE	0	0.436652768023725	2		427	874	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220162	5220162	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs760546803	NA	P-0005938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	136	345	0	ENST00000357368.4:c.3553A>C	p.Ile1185Leu	p.I1185L	ENST00000357368	NM_002850.3	1185	Atc/Ctc	22/38	0.292619958416456	2	FACETS	0.92	0.838	1	0.46	0.419	0.503	CLONAL	1	TRUE	0	0.436652768023725	2		345	677	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636206	28636208	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	INS	CCT	CCT	ACCA	novel	NA	P-0005938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	152	387	0	ENST00000241453.7:c.166-2_166delinsTGGT		p.X56_splice	ENST00000241453	NM_004119.2	56		3/24	0.434609417476909	4	FACETS	0.834	0.761	0.911	0.417	0.38	0.456	CLONAL	1	TRUE	2	0.436652768023725	4		387	1199	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715345	117715345	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs145259410	NA	P-0005948-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	83	377	0	ENST00000368508.3:c.1144T>C	p.Tyr382His	p.Y382H	ENST00000368508	NM_002944.2	382	Tat/Cat	10/43	0.410081341602526	1	FACETS	0.605	0.536	0.678	0.605	0.536	0.678	SUBCLONAL	1	TRUE	0	0.484731728095004	1		377	429	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097755	8097756	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005948-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	489	595	0	ENST00000346208.3:c.139dup	p.Val47GlyfsTer6	p.V47Gfs*6	ENST00000346208		46	gag/gaGg	2/6	1	2	FACETS	0.836	0.801	0.871	1	0.997	1	CLONAL	2	TRUE	1	0.484731728095004	2		595	1207	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	103	374	0				ENST00000310581	NM_198253.2	-/1132			0.362716399283071	1	FACETS	0.755	0.684	0.828	1	0.984	1	SUBCLONAL	2	TRUE	0	0.362716399283071	1		374	308	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0005950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	272	703	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.362716399283071	1	FACETS	0.923	0.872	0.975	1	0.995	1	CLONAL	2	TRUE	0	0.362716399283071	1		704	665	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161795	56161795	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	58	340	0	ENST00000399503.3:c.1292C>A	p.Ser431Ter	p.S431*	ENST00000399503	NM_005921.1	431	tCa/tAa	6/20	0.362716399283071	1	FACETS	0.554	0.476	0.637	0.554	0.476	0.637	SUBCLONAL	1	TRUE	0	0.362716399283071	1		340	473	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527792	103527792	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	138	628	0	ENST00000355739.4:c.3100A>G	p.Ile1034Val	p.I1034V	ENST00000355739	NM_000123.3	1034	Ata/Gta	15/15	0.29472075006038	1	FACETS	0.767	0.698	0.839	0.767	0.698	0.839	SUBCLONAL	1	TRUE	0	0.362716399283071	1		628	812	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167801	56167802	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	142	513	0	ENST00000399503.3:c.1368dup	p.Thr457TyrfsTer4	p.T457Yfs*4	ENST00000399503	NM_005921.1	456	ctt/cTtt	7/20	0.362716399283071	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.362716399283071	1		513	448	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061218	38061235	+	inframe_deletion	In_Frame_Del	DEL	GCCGTTCTCGAACATGTT	GCCGTTCTCGAACATGTT	-	novel	NA	P-0005950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	131	368	0	ENST00000250448.2:c.754_771del	p.Asn252_Gly257del	p.N252_G257del	ENST00000250448	NM_004496.3	252	AACATGTTCGAGAACGGC/-	2/2	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.362716399283071	2		368	502	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240740	53240752	+	frameshift_variant	Frame_Shift_Del	DEL	TTGGAATGGATGT	TTGGAATGGATGT	GA	novel	NA	P-0005950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	294	741	0	ENST00000375401.3:c.1328_1340delinsTC	p.Asp443ValfsTer11	p.D443Vfs*11	ENST00000375401	NM_004187.3	443	gACATCCATTCCAAa/gTCa	10/26	0.268055797475305	0	FACETS	0.647	0.612	0.683			1	SUBCLONAL	2	TRUE	0	0.362716399283071	0		741	798	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188251	10188252	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005958-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	199	780	0	ENST00000256474.2:c.397dup	p.Thr133AsnfsTer2	p.T133Nfs*2	ENST00000256474	NM_000551.3	132	caa/cAaa	2/3	0.359997024868167	2	FACETS	1	0.987	1	0.63	0.587	0.674	CLONAL	1	TRUE	0	0.535240367061099	2		780	590	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155495	47155495	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0005958-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	77	435	0	ENST00000409792.3:c.4587-1G>T		p.X1529_splice	ENST00000409792	NM_014159.6	1529			0.359997024868167	2	FACETS	1	0.953	1	0.569	0.506	0.634	CLONAL	1	TRUE	0	0.535240367061099	2		435	253	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540157	23540164	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGCGGG	GGCGCGGG	-	novel	NA	P-0005958-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	55	187	0	ENST00000380871.4:c.239_246del	p.Pro80ArgfsTer25	p.P80Rfs*25	ENST00000380871	NM_006167.3	80	cCCCGCGCC/c	1/2	0.235052756020511	3	FACETS	0.697	0.598	0.803	0.348	0.299	0.402	INDETERMINATE	1	TRUE	1	0.535240367061099	3		187	374	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598078	52598080	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	novel	NA	P-0005958-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	121	689	0	ENST00000394830.3:c.3786_3788del	p.Glu1262_Ile1263delinsAsp	p.E1262_I1263delinsD	ENST00000394830	NM_018313.4	1262	gaAATt/gat	24/30	0.359997024868167	2	FACETS	1	0.976	1	0.6	0.547	0.654	CLONAL	1	TRUE	0	0.535240367061099	2		689	377	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	49	588	1	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	0.2	2		589	414	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0005960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	34	302	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.78	0.637	0.94	0.78	0.637	0.94	CLONAL	1	TRUE	1	0.2	2		302	436	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217304	11217305	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCCTCCCACTCG	novel	NA	P-0006020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	83	612	0	ENST00000361445.4:c.4362_4373dup	p.Glu1455_Asp1458dup	p.E1455_D1458dup	ENST00000361445	NM_004958.3	1455	gat/gaCGAGTGGGAGGAt	30/58	0.134099698907103	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		612	720	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217230	11217230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786205165	NA	P-0006055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	616	692	1	ENST00000361445.4:c.4448G>A	p.Cys1483Tyr	p.C1483Y	ENST00000361445	NM_004958.3	1483	tGc/tAc	30/58	0.509204867606969	2	FACETS	0.924	0.892	0.956	0.924	0.892	0.956	CLONAL	2	TRUE	0	0.524643052270844	2		693	1271	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188320	10188320	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	268	527	1	ENST00000256474.2:c.463G>T	p.Val155Leu	p.V155L	ENST00000256474	NM_000551.3	155	Gtg/Ttg	2/3	0.524643052270844	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.524643052270844	1		528	667	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52692298	52692298	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	248	730	1	ENST00000394830.3:c.562C>T	p.Gln188Ter	p.Q188*	ENST00000394830	NM_018313.4	188	Cag/Tag	6/30	0.524643052270844	1	FACETS	0.948	0.89	1	0.948	0.89	1	CLONAL	1	TRUE	0	0.524643052270844	1		731	736	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460502	149460502	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	270	574	0	ENST00000286301.3:c.135T>A	p.Asn45Lys	p.N45K	ENST00000286301	NM_005211.3	45	aaT/aaA	3/22	0.524643052270844	3	FACETS	0.909	0.851	0.969	0.455	0.425	0.485	CLONAL	1	TRUE	1	0.524643052270844	3		574	1429	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912310	29912310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	267	613	0	ENST00000376809.5:c.929G>A	p.Gly310Asp	p.G310D	ENST00000376809	NM_002116.7	310	gGc/gAc	5/8	1	2	FACETS	0.872	0.817	0.929	0.872	0.817	0.929	CLONAL	1	TRUE	1	0.524643052270844	2		613	1167	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101061	41101062	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0006055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	298	684	0	ENST00000373198.4:c.1294dup	p.Gln432ProfsTer35	p.Q432Pfs*35	ENST00000373198	NM_133170.3	432	cag/cCag	8/32	1	2	FACETS	0.937	0.881	0.993	0.937	0.881	0.993	CLONAL	1	TRUE	1	0.524643052270844	2		684	1213	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	795	530	0	ENST00000346208.3:c.1220_1221insA	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcAg	6/6	0.486935022345274	5	FACETS	0.973	0.943	1	0.973	0.943	1	CLONAL	3	TRUE	2	0.620593416055541	5		530	1694	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46715685	46715685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1320236099	NA	P-0006068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	587	640	0	ENST00000371975.4:c.104G>A	p.Arg35Gln	p.R35Q	ENST00000371975	NM_003579.3	35	cGg/cAg	3/18	0.303871294257114	3	FACETS	1	0.994	1	0.759	0.733	0.784	INDETERMINATE	2	TRUE	0	0.620593416055541	3		640	1089	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859467	151859467	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	201	396	0	ENST00000262189.6:c.11195A>T	p.Glu3732Val	p.E3732V	ENST00000262189	NM_170606.2	3732	gAg/gTg	43/59	0.620967648076301	3	FACETS	0.957	0.888	1	0.478	0.444	0.514	CLONAL	1	TRUE	1	0.620593416055541	3		396	887	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173586	108173586	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1555106321	NA	P-0006068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	165	213	0	ENST00000278616.4:c.5326G>T	p.Glu1776Ter	p.E1776*	ENST00000278616	NM_000051.3	1776	Gaa/Taa	36/63	0.616416022393042	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.620593416055541	2		213	252	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0006139-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	318	442	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.292651214510003	4	FACETS	0.961	0.905	1	0.961	0.905	1	CLONAL	2	TRUE	2	0.292651214510003	4		442	1462	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812583	43812583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006139-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	74	473	0	ENST00000372470.3:c.1286G>A	p.Gly429Glu	p.G429E	ENST00000372470	NM_005373.2	429	gGa/gAa	8/12	0.132694940395732	4	FACETS	0.604	0.527	0.688	0.302	0.263	0.344	INDETERMINATE	1	TRUE	2	0.292651214510003	4		473	1082	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226406	133226406	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs756246229	NA	P-0006139-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	97	437	0	ENST00000320574.5:c.3652G>T	p.Val1218Leu	p.V1218L	ENST00000320574	NM_006231.2	1218	Gta/Tta	30/49	1	2	FACETS	0.656	0.583	0.733	0.656	0.583	0.733	SUBCLONAL	1	TRUE	1	0.292651214510003	2		437	1011	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7152935	7152935	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006139-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	45	306	0	ENST00000302850.5:c.2033T>G	p.Leu678Arg	p.L678R	ENST00000302850	NM_000208.2	678	cTg/cGg	10/22	NA	2	FACETS	0.507	0.425	0.597			1	INDETERMINATE	1	TRUE	NA	0.292651214510003	2		306	607	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306700	41306700	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006139-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	148	429	0	ENST00000373198.4:c.959T>G	p.Ile320Ser	p.I320S	ENST00000373198	NM_133170.3	320	aTc/aGc	7/32	0.204846291394517	3	FACETS	1	0.967	1	0.56	0.511	0.612	CLONAL	1	TRUE	1	0.292651214510003	3		429	1035	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039658	47039659	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006139-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	246	477	0	ENST00000377604.3:c.1111dup	p.Thr371AsnfsTer10	p.T371Nfs*10	ENST00000377604	NM_001204468.1	370	-/A	11/24	0.233218593769833	4	FACETS	0.765	0.713	0.818	0.765	0.713	0.818	SUBCLONAL	2	TRUE	2	0.292651214510003	4		477	1421	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111524	8111525	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0006169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	352	516	0	ENST00000346208.3:c.1011dup	p.Cys338LeufsTer14	p.C338Lfs*14	ENST00000346208		337	gtc/gtCc	5/6	0.326823487886264	5	FACETS	0.986	0.934	1	0.657	0.623	0.693	INDETERMINATE	2	TRUE	2	0.550529977255758	5		516	1184	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46597593	46597593	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	166	519	0	ENST00000262741.5:c.32A>G	p.Asp11Gly	p.D11G	ENST00000262741	NM_003629.3	11	gAt/gGt	1/10	0.425805518344499	3	FACETS	0.959	0.882	1			1	CLONAL	1	TRUE	NA	0.550529977255758	3		519	802	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508190	106508190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	91	263	0	ENST00000359195.3:c.184G>A	p.Ala62Thr	p.A62T	ENST00000359195	NM_002649.2	62	Gcc/Acc	2/11	0.26122864280108	5	FACETS	0.867	0.777	0.962	0.578	0.518	0.641	INDETERMINATE	2	TRUE	2	0.550529977255758	5		263	348	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419923	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATGACC	novel	NA	P-0006169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	58	387	0	ENST00000206249.3:c.1610_1615dup	p.Asp538_Leu539insHisAsp	p.D538_L539insHD	ENST00000206249	NM_000125.3	537	tat/tATGACCat	8/8	0.550529977255758	3	FACETS	0.552	0.475	0.636	0.276	0.237	0.318	SUBCLONAL	1	TRUE	1	0.550529977255758	3		387	487	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419923	+	missense_variant	Missense_Mutation	DNP	TA	TA	AG	novel	NA	P-0006169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	57	388	0	ENST00000206249.3:c.1609_1610delinsAG	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	TAt/AGt	8/8	0.550529977255758	3	FACETS	0.547	0.47	0.631	0.273	0.235	0.316	SUBCLONAL	1	TRUE	1	0.550529977255758	3		388	483	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	86	410	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.672	0.594	0.756	0.672	0.594	0.756	SUBCLONAL	1	TRUE	1	0.3	2		410	853	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119781	70119781	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1274036689	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	142	381	0	ENST00000245479.2:c.788del	p.Gly263AlafsTer16	p.G263Afs*16	ENST00000245479	NM_000346.3	261	gaG/ga	3/3	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.3	2		381	855	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	60	302	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.759	0.654	0.873	0.759	0.654	0.873	SUBCLONAL	1	TRUE	1	0.3	2		302	527	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	177	463	1	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.965	0.887	1	0.965	0.887	1	CLONAL	1	TRUE	1	0.3	2		464	1223	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	63	296	2	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.3	2		298	382	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161939	47161939	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	57	282	0	ENST00000409792.3:c.4187del	p.Asn1396MetfsTer16	p.N1396Mfs*16	ENST00000409792	NM_014159.6	1396	aAt/at	3/21	1	2	FACETS	0.744	0.639	0.858	0.744	0.639	0.858	SUBCLONAL	1	TRUE	1	0.3	2		282	511	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	12	190	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	0.221	0.154	0.303	0.221	0.154	0.303	SUBCLONAL	1	TRUE	1	0.3	2		190	362	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19261529	19261529	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	120	428	0	ENST00000162023.5:c.16del	p.Ile6SerfsTer14	p.I6Sfs*14	ENST00000162023		6	Atc/tc	6/13	1	2	FACETS	0.918	0.829	1	0.918	0.829	1	CLONAL	1	TRUE	1	0.3	2		428	871	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015428	176015428	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1373217036	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	111	389	0	ENST00000367669.3:c.1310C>T	p.Ala437Val	p.A437V	ENST00000367669	NM_022457.5	437	gCg/gTg	12/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.3	2		389	702	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	150	379	0	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.3	2		379	929	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928036	49928036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199869962	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	91	416	0	ENST00000296474.3:c.3692G>A	p.Arg1231His	p.R1231H	ENST00000296474	NM_002447.2	1231	cGc/cAc	18/20	1	2	FACETS	0.607	0.538	0.682	0.607	0.538	0.682	SUBCLONAL	1	TRUE	1	0.3	2		416	999	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	68	263	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.921	0.803	1	0.921	0.803	1	CLONAL	1	TRUE	1	0.3	2		263	492	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913837	32913837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359507	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	125	945	2	ENST00000380152.3:c.5351del	p.Asn1784ThrfsTer7	p.N1784Tfs*7	ENST00000380152		1782	cAa/ca	11/27	1	2	FACETS	0.766	0.692	0.844	0.766	0.692	0.844	SUBCLONAL	1	TRUE	1	0.3	2		947	1088	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209616	98209617	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761353734	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	60	243	0	ENST00000331920.6:c.3921dup	p.Arg1308GlnfsTer17	p.R1308Qfs*17	ENST00000331920	NM_000264.3	1307	-/C	23/24	1	2	FACETS	0.92	0.794	1	0.92	0.794	1	CLONAL	1	TRUE	1	0.3	2		243	435	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933240	49933240	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143096514	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	209	499	2	ENST00000296474.3:c.2870C>T	p.Thr957Met	p.T957M	ENST00000296474	NM_002447.2	957	aCg/aTg	12/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.3	2		501	1119	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784085	9784085	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	126	377	2	ENST00000377346.4:c.2653G>A	p.Ala885Thr	p.A885T	ENST00000377346	NM_005026.3	885	Gcc/Acc	21/24	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.3	2		379	801	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637338	47637338	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63751226	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	108	485	0	ENST00000233146.2:c.472C>T	p.Gln158Ter	p.Q158*	ENST00000233146	NM_000251.2	158	Cag/Tag	3/16	1	2	FACETS	0.829	0.743	0.92	0.829	0.743	0.92	CLONAL	1	TRUE	1	0.3	2		485	869	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702269	47702269	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28929483	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	92	428	1	ENST00000233146.2:c.1865C>A	p.Pro622Gln	p.P622Q	ENST00000233146	NM_000251.2	622	cCa/cAa	12/16	1	2	FACETS	0.811	0.721	0.908	0.811	0.721	0.908	CLONAL	1	TRUE	1	0.3	2		429	756	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916838	178916838	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	79	559	0	ENST00000263967.3:c.225A>C	p.Gln75His	p.Q75H	ENST00000263967	NM_006218.2	75	caA/caC	2/21	1	2	FACETS	0.435	0.381	0.493	0.435	0.381	0.493	SUBCLONAL	1	TRUE	1	0.3	2		559	1211	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235390	235390	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs878854625	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	116	288	0	ENST00000264932.6:c.1196C>A	p.Pro399Gln	p.P399Q	ENST00000264932	NM_004168.2	399	cCg/cAg	9/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.3	2		288	671	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672848	30672848	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1265	199	685	1	ENST00000376406.3:c.4112C>A	p.Pro1371His	p.P1371H	ENST00000376406	NM_014641.2	1371	cCt/cAt	10/15	1	2	FACETS	0.906	0.837	0.979	0.906	0.837	0.979	CLONAL	1	TRUE	1	0.3	2		686	1464	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964481	93964481	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775779069	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	114	453	0	ENST00000369303.4:c.2416G>A	p.Glu806Lys	p.E806K	ENST00000369303	NM_004440.3	806	Gaa/Aaa	14/17	1	2	FACETS	0.866	0.779	0.958	0.866	0.779	0.958	CLONAL	1	TRUE	1	0.3	2		453	878	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099080	157099080	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	55	125	0	ENST00000346085.5:c.17G>C	p.Gly6Ala	p.G6A	ENST00000346085	NM_020732.3	6	gGc/gCc	1/20	1	2	FACETS	0.78	0.668	0.902	0.78	0.668	0.902	CLONAL	1	TRUE	1	0.3	2		125	470	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864801	117864801	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	111	407	0	ENST00000297338.2:c.1308G>C	p.Gln436His	p.Q436H	ENST00000297338	NM_006265.2	436	caG/caC	10/14	1	2	FACETS	0.855	0.768	0.948	0.855	0.768	0.948	CLONAL	1	TRUE	1	0.3	2		407	865	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596068	43596068	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537523906	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	105	375	1	ENST00000355710.3:c.235C>T	p.Arg79Trp	p.R79W	ENST00000355710	NM_020975.4	79	Cgg/Tgg	2/20	1	2	FACETS	0.914	0.819	1	0.914	0.819	1	CLONAL	1	TRUE	1	0.3	2		376	766	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852292	63852292	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	109	313	0	ENST00000279873.7:c.3070G>A	p.Ala1024Thr	p.A1024T	ENST00000279873	NM_032199.2	1024	Gca/Aca	10/10	1	2	FACETS	0.932	0.837	1	0.932	0.837	1	CLONAL	1	TRUE	1	0.3	2		313	780	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137198	64137198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1284865222	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	127	330	0	ENST00000334205.4:c.1630G>A	p.Gly544Arg	p.G544R	ENST00000334205	NM_003942.2	544	Ggg/Agg	14/17	1	2	FACETS	0.951	0.861	1	0.951	0.861	1	CLONAL	1	TRUE	1	0.3	2		330	890	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909984	100909984	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	121	469	0	ENST00000325455.5:c.2665C>A	p.Leu889Met	p.L889M	ENST00000325455	NM_001202474.3	889	Ctg/Atg	8/8	1	2	FACETS	0.903	0.815	0.996	0.903	0.815	0.996	CLONAL	1	TRUE	1	0.3	2		469	893	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307646	118307646	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	45	148	0	ENST00000534358.1:c.419G>T	p.Gly140Val	p.G140V	ENST00000534358	NM_005933.3	140	gGc/gTc	1/36	1	2	FACETS	0.806	0.68	0.946	0.806	0.68	0.946	CLONAL	1	TRUE	1	0.3	2		148	372	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416796	416796	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756725945	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	109	404	0	ENST00000399788.2:c.3754C>T	p.Arg1252Cys	p.R1252C	ENST00000399788	NM_001042603.1	1252	Cgt/Tgt	23/28	0.3	2	FACETS	0.919	0.825	1			1	CLONAL	1	TRUE	NA	0.3	2		404	791	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416647	49416647	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	93	284	0	ENST00000301067.7:c.16064T>G	p.Leu5355Arg	p.L5355R	ENST00000301067	NM_003482.3	5355	cTg/cGg	51/54	1	2	FACETS	0.951	0.846	1	0.951	0.846	1	CLONAL	1	TRUE	1	0.3	2		284	652	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433611	49433611	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	109	373	0	ENST00000301067.7:c.7942C>T	p.Pro2648Ser	p.P2648S	ENST00000301067	NM_003482.3	2648	Cca/Tca	31/54	1	2	FACETS	0.912	0.819	1	0.912	0.819	1	CLONAL	1	TRUE	1	0.3	2		373	797	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877305	28877305	+	stop_lost	Nonstop_Mutation	SNP	T	T	C	rs1468536790	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	89	229	0	ENST00000282397.4:c.4016A>G	p.Ter1339TrpextTer20	p.*1339Wext*20	ENST00000282397	NM_002019.4	1339	tAg/tGg	30/30	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.3	2		229	576	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95577766	95577766	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	114	354	0	ENST00000393063.1:c.2144T>C	p.Val715Ala	p.V715A	ENST00000393063	NM_030621.3	715	gTt/gCt	15/28	1	2	FACETS	0.935	0.841	1	0.935	0.841	1	CLONAL	1	TRUE	1	0.3	2		354	813	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007792	45007792	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	64	317	0	ENST00000558401.1:c.239G>A	p.Trp80Ter	p.W80*	ENST00000558401	NM_004048.2	80	tGg/tAg	2/4	1	2	FACETS	0.659	0.571	0.756	0.659	0.571	0.756	SUBCLONAL	1	TRUE	1	0.3	2		317	647	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354607	91354607	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	121	486	0	ENST00000355112.3:c.4047A>C	p.Lys1349Asn	p.K1349N	ENST00000355112	NM_000057.2	1349	aaA/aaC	21/22	1	2	FACETS	0.83	0.749	0.916	0.83	0.749	0.916	CLONAL	1	TRUE	1	0.3	2		486	972	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99486163	99486163	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	52	306	0	ENST00000268035.6:c.3469A>G	p.Thr1157Ala	p.T1157A	ENST00000268035	NM_000875.3	1157	Acg/Gcg	19/21	1	2	FACETS	0.522	0.444	0.608	0.522	0.444	0.608	SUBCLONAL	1	TRUE	1	0.3	2		306	664	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2224023	2224023	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	111	461	0	ENST00000326181.6:c.1237A>G	p.Ser413Gly	p.S413G	ENST00000326181	NM_032271.2	413	Agt/Ggt	13/21	1	2	FACETS	0.907	0.815	1	0.907	0.815	1	CLONAL	1	TRUE	1	0.3	2		461	816	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845511	72845511	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750527365	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	203	502	0	ENST00000268489.5:c.3829G>A	p.Val1277Met	p.V1277M	ENST00000268489	NM_006885.3	1277	Gtg/Atg	7/10	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.3	2		502	1293	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816187	89816187	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	94	354	0	ENST00000389301.3:c.3190A>G	p.Ser1064Gly	p.S1064G	ENST00000389301	NM_000135.2	1064	Agc/Ggc	32/43	1	2	FACETS	0.73	0.649	0.817	0.73	0.649	0.817	SUBCLONAL	1	TRUE	1	0.3	2		354	858	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33430327	33430327	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	149	422	0	ENST00000345365.6:c.684G>A	p.Met228Ile	p.M228I	ENST00000345365	NM_002878.3	228	atG/atA	8/10	1	2	FACETS	0.916	0.835	1	0.916	0.835	1	CLONAL	1	TRUE	1	0.3	2		422	1085	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883770	37883770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747888253	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	138	406	0	ENST00000269571.5:c.3382G>A	p.Val1128Ile	p.V1128I	ENST00000269571		1128	Gtt/Att	26/27	1	2	FACETS	0.95	0.864	1	0.95	0.864	1	CLONAL	1	TRUE	1	0.3	2		406	968	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249155	10249155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765098980	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	141	367	0	ENST00000340748.4:c.4027G>A	p.Val1343Met	p.V1343M	ENST00000340748		1343	Gtg/Atg	34/40	1	2	FACETS	0.947	0.861	1	0.947	0.861	1	CLONAL	1	TRUE	1	0.3	2		367	993	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278185	15278185	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	146	389	0	ENST00000263388.2:c.5237A>G	p.Asp1746Gly	p.D1746G	ENST00000263388	NM_000435.2	1746	gAt/gGt	29/33	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.3	2		389	843	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943670	17943670	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	109	339	0	ENST00000458235.1:c.2419C>T	p.Gln807Ter	p.Q807*	ENST00000458235	NM_000215.3	807	Cag/Tag	18/24	1	2	FACETS	0.847	0.76	0.939	0.847	0.76	0.939	CLONAL	1	TRUE	1	0.3	2		339	858	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42843771	42843771	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	101	341	0	ENST00000398585.3:c.1148T>C	p.Ile383Thr	p.I383T	ENST00000398585	NM_001135099.1	383	aTt/aCt	10/14	1	2	FACETS	0.906	0.81	1	0.906	0.81	1	CLONAL	1	TRUE	1	0.3	2		341	743	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409784	63409784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761170439	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	113	457	1	ENST00000330258.3:c.3383C>T	p.Ala1128Val	p.A1128V	ENST00000330258	NM_152424.3	1128	gCc/gTc	2/2	0.0778089651889264	0	FACETS	0.615	0.553	0.68			1	INDETERMINATE	1	TRUE	0	0.3	0		458	858	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411678	63411678	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	119	441	0	ENST00000330258.3:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000330258	NM_152424.3	497	Cga/Tga	2/2	0.0778089651889264	0	FACETS	0.735	0.663	0.81			1	INDETERMINATE	1	TRUE	0	0.3	0		441	756	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523310	9523311	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	116	402	0	ENST00000353224.5:c.1926dup	p.Tyr643LeufsTer4	p.Y643Lfs*4	ENST00000353224	NM_177990.2	642	-/C	9/10	1	2	FACETS	0.89	0.801	0.984	0.89	0.801	0.984	CLONAL	1	TRUE	1	0.3	2		402	869	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710595	114710597	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs754968616	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	212	511	1	ENST00000543371.1:c.85_87del	p.Glu29del	p.E29del	ENST00000543371	NM_001198531.1	27	cAGGag/cag	1/14	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.3	2		512	1200	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742462	17742463	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs781603622	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	106	390	0	ENST00000250003.3:c.650dup	p.Ser218GlufsTer60	p.S218Efs*60	ENST00000250003	NM_002478.4	215	ggc/ggCc	2/3	1	2	FACETS	0.819	0.733	0.91	0.819	0.733	0.91	CLONAL	1	TRUE	1	0.3	2		390	863	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400023	139400023	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	68	307	1	ENST00000277541.6:c.4325del	p.Pro1442ArgfsTer3	p.P1442Rfs*3	ENST00000277541	NM_017617.3	1442	cCg/cg	25/34	1	2	FACETS	0.706	0.614	0.806	0.706	0.614	0.806	SUBCLONAL	1	TRUE	1	0.3	2		308	642	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041976	14041977	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	53	301	0	ENST00000311895.7:c.2526_2527del	p.Lys843ValfsTer2	p.K843Vfs*2	ENST00000311895	NM_005236.2	841	tcAGag/tcag	11/11	1	2	FACETS	0.617	0.526	0.717	0.617	0.526	0.717	SUBCLONAL	1	TRUE	1	0.3	2		301	573	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368256	45368256	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	70	411	0	ENST00000262160.6:c.1346del	p.Leu449TrpfsTer5	p.L449Wfs*5	ENST00000262160	NM_005901.5	449	tTg/tg	11/11	1	2	FACETS	0.677	0.59	0.772	0.677	0.59	0.772	SUBCLONAL	1	TRUE	1	0.3	2		411	689	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245024	133245024	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs752846614	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	98	312	3	ENST00000320574.5:c.2091del	p.Leu698CysfsTer94	p.L698Cfs*94	ENST00000320574	NM_006231.2	697	ccC/cc	19/49	1	2	FACETS	0.872	0.778	0.973	0.872	0.778	0.973	CLONAL	1	TRUE	1	0.3	2		315	749	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795269	42795269	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs34000070	NA	P-0006170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	92	321	0	ENST00000575354.2:c.2353del	p.Ala785ProfsTer139	p.A785Pfs*139	ENST00000575354	NM_015125.3	783	caG/ca	10/20	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.3	2		321	556	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0006249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	429	357	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.491875823129866	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.523017440248667	3		357	624	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177011	56177014	+	frameshift_variant	Frame_Shift_Del	DEL	ATAG	ATAG	-	novel	NA	P-0006249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	111	426	0	ENST00000399503.3:c.2286_2289del	p.Arg763CysfsTer35	p.R763Cfs*35	ENST00000399503	NM_005921.1	761	ATAGat/at	13/20	1	2	FACETS	0.884	0.799	0.973	0.884	0.799	0.973	CLONAL	1	TRUE	1	0.523017440248667	2		426	480	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983017	149983017	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757876116	NA	P-0006249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	172	638	2	ENST00000253339.5:c.3241C>T	p.Arg1081Ter	p.R1081*	ENST00000253339		1081	Cga/Tga	7/7	0.1969406809455	3	FACETS	1	0.99	1	0.745	0.69	0.802	INDETERMINATE	1	TRUE	1	0.523017440248667	3		640	557	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499771	8499771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748340591	NA	P-0006249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	184	587	1	ENST00000356435.5:c.2198G>A	p.Arg733His	p.R733H	ENST00000356435		733	cGc/cAc	14/35	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.523017440248667	2		588	637	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491373	18491373	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	255	434	0	ENST00000266497.5:c.1286A>G	p.Asn429Ser	p.N429S	ENST00000266497		429	aAt/aGt	8/31	0.523017440248667	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.523017440248667	3		434	602	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859039	57859039	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0006249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	150	909	0	ENST00000228682.2:c.534+1G>A		p.X178_splice	ENST00000228682	NM_005269.2	178			0.368814482013485	3	FACETS	0.983	0.9	1	0.492	0.45	0.535	CLONAL	1	TRUE	1	0.523017440248667	3		909	736	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830754	3830754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	163	494	1	ENST00000262367.5:c.1802G>A	p.Arg601Gln	p.R601Q	ENST00000262367	NM_004380.2	601	cGg/cAg	8/31	0.418783838489799	4	FACETS	0.787	0.726	0.851			1	SUBCLONAL	2	TRUE	NA	0.523017440248667	4		495	603	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374853	45374853	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	71	427	0	ENST00000262160.6:c.990G>T	p.Arg330Ser	p.R330S	ENST00000262160	NM_005901.5	330	agG/agT	8/11	1	2	FACETS	0.624	0.547	0.707	0.624	0.547	0.707	SUBCLONAL	1	TRUE	1	0.523017440248667	2		427	435	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229569	5229569	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	40	168	0	ENST00000357368.4:c.2282T>A	p.Val761Glu	p.V761E	ENST00000357368	NM_002850.3	761	gTg/gAg	15/38	0.470126647401233	5	FACETS	1	0.916	1	0.289	0.242	0.341	CLONAL	1	TRUE	1	0.523017440248667	5		168	236	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184093	56184094	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	AC	novel	NA	P-0006249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	126	563	0	ENST00000399503.3:c.4298_4299insAC	p.Trp1433Ter	p.W1433*	ENST00000399503	NM_005921.1	1433	tgg/tgACg	19/20	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.523017440248667	2		563	480	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519920	NA	P-0006251-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	57	258	1	ENST00000397062.3:c.85G>T	p.Asp29Tyr	p.D29Y	ENST00000397062	NM_006164.4	29	Gat/Tat	2/5	1	2	FACETS	0.887	0.762	1	0.887	0.762	1	CLONAL	1	TRUE	1	0.267790521524828	2		259	480	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910355	29910356	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCGT	novel	NA	P-0006251-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	62	488	0	ENST00000376809.5:c.27_28insGTTC	p.Leu10ValfsTer90	p.L10Vfs*90	ENST00000376809	NM_002116.7	9	ctc/cTCGTtc	1/8	1	2	FACETS	0.498	0.429	0.574	0.498	0.429	0.574	SUBCLONAL	1	TRUE	1	0.267790521524828	2		488	930	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320284	30320284	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006251-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	60	553	0	ENST00000322652.5:c.1225del	p.Asp409IlefsTer18	p.D409Ifs*18	ENST00000322652	NM_015355.2	409	Gat/at	11/16	1	2	FACETS	0.507	0.435	0.585	0.507	0.435	0.585	SUBCLONAL	1	TRUE	1	0.267790521524828	2		553	884	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0006317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	24	340	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.283965251507418	4	FACETS	1	0.889	1	0.761	0.619	0.912	CLONAL	2	TRUE	1	0.456903318471602	4		340	67	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0006317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	13	285	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.456903318471602	2		285	43	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	14	311	0	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	1	2	FACETS	1	0.821	1	1	0.821	1	CLONAL	1	TRUE	1	0.456903318471602	2		311	54	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849033	156849033	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs920692665	NA	P-0006317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	37	423	0	ENST00000524377.1:c.1925C>T	p.Ala642Val	p.A642V	ENST00000524377	NM_002529.3	642	gCg/gTg	15/17	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.456903318471602	2		423	140	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215617281	215617281	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0006317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	18	278	0	ENST00000260947.4:c.1569-2A>G		p.X523_splice	ENST00000260947	NM_000465.2	523			1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.456903318471602	2		278	58	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508176	106508176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752039271	NA	P-0006317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	24	212	0	ENST00000359195.3:c.170C>T	p.Ala57Val	p.A57V	ENST00000359195	NM_002649.2	57	gCg/gTg	2/11	0.443094510026656	3	FACETS	1	0.859	1	0.552	0.439	0.676	CLONAL	1	TRUE	1	0.456903318471602	3		212	117	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500865	8500865	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748586269	NA	P-0006317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	22	364	0	ENST00000356435.5:c.2017C>T	p.Leu673Phe	p.L673F	ENST00000356435		673	Ctt/Ttt	13/35	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.456903318471602	2		364	76	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456780	32456780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1166553415	NA	P-0006317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	16	144	1	ENST00000332351.3:c.112G>A	p.Gly38Ser	p.G38S	ENST00000332351	NM_024426.4	38	Ggc/Agc	1/10	1	2	FACETS	1	0.758	1	1	0.758	1	CLONAL	1	TRUE	1	0.456903318471602	2		145	70	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	27	430	0	ENST00000342988.3:c.1067C>G	p.Pro356Arg	p.P356R	ENST00000342988	NM_005359.5	356	cCt/cGt	9/12	0.456903318471602	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	0	0.456903318471602	1		430	77	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870793	12870794	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	34	119	0	ENST00000228872.4:c.21dup	p.Asn8Ter	p.N8*	ENST00000228872	NM_004064.3	7	tct/tcTt	1/3	0.283965251507418	4	FACETS	0.86	0.729	0.997	0.86	0.729	0.997	CLONAL	3	TRUE	1	0.456903318471602	4		119	84	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577111	7577112	+	inframe_insertion	In_Frame_Ins	INS	-	-	CACAAA	novel	NA	P-0006317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	21	489	2	ENST00000269305.4:c.821_826dup	p.Val274_Cys275dup	p.V274_C275dup	ENST00000269305	NM_001126112.2	274	gcc/gTTTGTGcc	8/11	0.456903318471602	1	FACETS	0.591	0.461	0.738	0.591	0.461	0.738	SUBCLONAL	1	TRUE	0	0.456903318471602	1		491	120	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050398	13050398	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	181	691	0	ENST00000316448.5:c.350T>C	p.Leu117Ser	p.L117S	ENST00000316448	NM_004343.3	117	tTg/tCg	3/9	1	2	FACETS	0.922	0.849	0.999	0.922	0.849	0.999	CLONAL	1	TRUE	1	0.330687232852791	2		691	1187	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624879	9624879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	135	568	0	ENST00000353224.5:c.98C>T	p.Thr33Ile	p.T33I	ENST00000353224	NM_177990.2	33	aCc/aTc	3/10	0.275288582403493	3	FACETS	0.828	0.751	0.91	0.414	0.375	0.455	CLONAL	1	TRUE	1	0.330687232852791	3		568	1149	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188255	10188256	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGAATTATTTGTGCCATCTCTCAATGTTGACGGACAGCCTATT	novel	NA	P-0006387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	78	527	0	ENST00000256474.2:c.400_442dup	p.Phe148Ter	p.F148*	ENST00000256474	NM_000551.3	133	act/acTGAATTATTTGTGCCATCTCTCAATGTTGACGGACAGCCTATTt	2/3	0.330687232852791	1	FACETS	0.356	0.312	0.404	0.356	0.312	0.404	SUBCLONAL	1	TRUE	0	0.330687232852791	1		527	1106	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437886	52437892	+	frameshift_variant	Frame_Shift_Del	DEL	CTTCCCT	CTTCCCT	-	novel	NA	P-0006387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	160	638	0	ENST00000460680.1:c.1269_1275del	p.Gly424GlnfsTer4	p.G424Qfs*4	ENST00000460680	NM_004656.3	423	acAGGGAAG/ac	13/17	0.330687232852791	1	FACETS	0.882	0.808	0.958	0.882	0.808	0.958	CLONAL	1	TRUE	0	0.330687232852791	1		638	916	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52685766	52685777	+	protein_altering_variant	In_Frame_Del	DEL	TCTGGGCAATGG	TCTGGGCAATGG	CCC	novel	NA	P-0006387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	132	561	0	ENST00000394830.3:c.695_706delinsGGG	p.Thr232_Arg236delinsArgGly	p.T232_R236delinsRG	ENST00000394830	NM_018313.4	232	aCCATTGCCCAGAgg/aGGGgg	7/30	0.330687232852791	1	FACETS	0.751	0.682	0.825	0.751	0.682	0.825	SUBCLONAL	1	TRUE	0	0.330687232852791	1		561	887	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0006404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	782	607	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.737444230756088	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.737444230756088	1		607	1277	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562981	29562981	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs376576925	NA	P-0006404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	506	754	2	ENST00000356175.3:c.3916C>T	p.Arg1306Ter	p.R1306*	ENST00000356175	NM_000267.3	1306	Cga/Tga	29/57	0.737444230756088	1	FACETS	0.959	0.925	0.993	0.959	0.925	0.993	CLONAL	1	TRUE	0	0.737444230756088	1		756	903	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937914	76937914	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	326	577	0	ENST00000373344.5:c.2834del	p.Lys945ArgfsTer25	p.K945Rfs*25	ENST00000373344	NM_000489.3	945	aAg/ag	9/35	0.737444230756088	1	FACETS	0.927	0.886	0.968	0.927	0.886	0.968	CLONAL	1	TRUE	0	0.737444230756088	1		577	602	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092965	27092965	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	60	626	2	ENST00000324856.7:c.2896G>T	p.Glu966Ter	p.E966*	ENST00000324856	NM_006015.4	966	Gag/Tag	10/20	0.737444230756088	1	FACETS	0.132	0.113	0.153	0.132	0.113	0.153	SUBCLONAL	1	TRUE	0	0.737444230756088	1		628	778	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720801	89720802	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	22	166	2	ENST00000371953.3:c.954dup	p.Thr319TyrfsTer6	p.T319Yfs*6	ENST00000371953	NM_000314.4	318	ctt/cTtt	8/9	0.737444230756088	1	FACETS	0.253	0.198	0.316	0.253	0.198	0.316	SUBCLONAL	1	TRUE	0	0.737444230756088	1		168	149	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006428-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	90	374	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.928	0.833	1	1	0.986	1	CLONAL	2	TRUE	1	0.321005356199818	2		374	302	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0006428-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	39	190	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	0.853	0.71	1	0.853	0.71	1	CLONAL	1	TRUE	1	0.321005356199818	2		190	285	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233037	55233037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1477025000	NA	P-0006428-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	98	446	1	ENST00000275493.2:c.1787C>T	p.Pro596Leu	p.P596L	ENST00000275493	NM_005228.3	596	cCg/cTg	15/28	1	2	FACETS	0.864	0.771	0.962	0.864	0.771	0.962	CLONAL	1	TRUE	1	0.321005356199818	2		447	707	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0006428-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	598	492	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	0.321005356199818	2	FACETS	1	0.994	1	1	0.998	1	CLONAL	4	TRUE	0	0.321005356199818	2		492	865	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341317	89341317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555523386	NA	P-0006428-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	95	236	0	ENST00000301030.4:c.7618C>T	p.Arg2540Trp	p.R2540W	ENST00000301030	NM_001256183.1	2540	Cgg/Tgg	11/13	0.204898036969418	1	FACETS	0.941	0.851	1	1	0.987	1	CLONAL	2	TRUE	0	0.321005356199818	1		236	264	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412627	139412627	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006428-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	207	450	0	ENST00000277541.6:c.1217del	p.Gly406AlafsTer225	p.G406Afs*225	ENST00000277541	NM_017617.3	406	gGc/gc	7/34	1	2	FACETS	1	0.961	1	1	0.994	1	CLONAL	2	TRUE	1	0.321005356199818	2		450	619	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393672	139393673	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCGG	novel	NA	P-0006428-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	156	444	0	ENST00000277541.6:c.5970_5973dup	p.Met1992ProfsTer4	p.M1992Pfs*4	ENST00000277541	NM_017617.3	1991	-/CCGC	32/34	1	2	FACETS	0.857	0.789	0.927	1	0.991	1	CLONAL	2	TRUE	1	0.321005356199818	2		444	567	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930234	39930241	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTCGTT	CTTTCGTT	-	novel	NA	P-0006428-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	409	838	0	ENST00000378444.4:c.3223_3230del	p.Asn1075Ter	p.N1075*	ENST00000378444	NM_001123385.1	1075	AACGAAAGt/t	6/15	0.204898036969418	1	FACETS	0.916	0.873	0.96	1	0.996	1	CLONAL	2	TRUE	0	0.321005356199818	1		838	1168	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148504767	148504784	+	inframe_deletion	In_Frame_Del	DEL	CGACATACTTCAGGGCAT	CGACATACTTCAGGGCAT	-	novel	NA	P-0006428-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	146	550	0	ENST00000320356.2:c.2210_2227del	p.Asp737_Val742del	p.D737_V742del	ENST00000320356	NM_004456.4	737	gATGCCCTGAAGTATGTCGgc/ggc	20/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.321005356199818	2		550	636	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512203	120512203	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006428-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	76	554	0	ENST00000256646.2:c.1039T>C	p.Cys347Arg	p.C347R	ENST00000256646	NM_024408.3	347	Tgt/Cgt	6/34	1	2	FACETS	0.624	0.546	0.707	0.624	0.546	0.707	SUBCLONAL	1	TRUE	1	0.321005356199818	2		554	759	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221765	55221765	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006428-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	102	728	0	ENST00000275493.2:c.809A>G	p.Tyr270Cys	p.Y270C	ENST00000275493	NM_005228.3	270	tAc/tGc	7/28	1	2	FACETS	0.721	0.644	0.803	0.721	0.644	0.803	SUBCLONAL	1	TRUE	1	0.321005356199818	2		728	882	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0006441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	1088	539	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.703582809901702	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.738832962467605	2		539	1412	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0006441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	456	66	0				ENST00000310581	NM_198253.2	-/1132			0.234144014329142	3	FACETS	1	0.996	1	0.734	0.702	0.766	INDETERMINATE	1	TRUE	1	0.738832962467605	3		66	1152	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210077	55210077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1342	124	563	0	ENST00000275493.2:c.187G>A	p.Gly63Arg	p.G63R	ENST00000275493	NM_005228.3	63	Ggg/Agg	2/28	0.696318022768252	4	FACETS	0.398	0.359	0.44	0.133	0.119	0.147	SUBCLONAL	1	TRUE	1	0.738832962467605	4		563	1466	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027128	49027128	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs794727199	NA	P-0006441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	253	411	0	ENST00000267163.4:c.1696-1G>A		p.X566_splice	ENST00000267163	NM_000321.2	566			0.696937852475121	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.738832962467605	1		411	382	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589619	67589620	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGAATATGATAGATTATATGA	novel	NA	P-0006441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	105	360	0	ENST00000274335.5:c.1390_1410dup	p.Asp464_Tyr470dup	p.D464_Y470dup	ENST00000274335		464	cga/cgAGAATATGATAGATTATATGAa	10/15	1	2	FACETS	0.502	0.451	0.556	0.502	0.451	0.556	SUBCLONAL	1	TRUE	1	0.738832962467605	2		360	566	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0006447-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	144	343	1	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	0.783237908738285	1	FACETS	0.902	0.844	0.959	0.902	0.844	0.959	CLONAL	1	TRUE	0	0.783237908738285	1		344	248	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849453	68849454	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0006447-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	163	455	0	ENST00000261769.5:c.1358_1359del	p.His453ArgfsTer10	p.H453Rfs*10	ENST00000261769	NM_004360.3	452	ctACac/ctac	10/16	0.783237908738285	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.783237908738285	1		455	248	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0006468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	533	366	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.678265781323902	2	FACETS	0.997	0.968	1	0.997	0.968	1	CLONAL	2	TRUE	0	0.691401868084063	2		366	773	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687471	37687472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs760014508	NA	P-0006468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	256	262	0	ENST00000447079.4:c.4382dup	p.Thr1463AsnfsTer50	p.T1463Nfs*50	ENST00000447079	NM_015083.1	1459	tgg/tGgg	14/14	0.691401868084063	4	FACETS	1	0.993	1	0.749	0.703	0.796	CLONAL	1	TRUE	2	0.691401868084063	4		262	836	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647631	23647631	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs766710382	NA	P-0006468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	198	265	0	ENST00000261584.4:c.236A>T	p.Tyr79Phe	p.Y79F	ENST00000261584	NM_024675.3	79	tAt/tTt	4/13	0.590815044230568	4	FACETS	0.886	0.826	0.946	0.886	0.826	0.946	CLONAL	2	TRUE	2	0.691401868084063	4		265	547	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687665	29687665	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	315	351	0	ENST00000356175.3:c.8258C>G	p.Ala2753Gly	p.A2753G	ENST00000356175	NM_000267.3	2753	gCc/gGc	56/57	0.691401868084063	4	FACETS	0.918	0.87	0.967	0.918	0.87	0.967	CLONAL	2	TRUE	2	0.691401868084063	4		351	839	SUCCESS
APC	324	MSKCC	GRCh37	5	112175345	112175346	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	155	223	0	ENST00000257430.4:c.4056dup	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1352	gtt/gTtt	16/16	0.691401868084063	2	FACETS	0.954	0.9	1	0.954	0.9	1	CLONAL	2	TRUE	0	0.691401868084063	2		223	235	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0006491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	176	356	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.306524129802129	2		356	1056	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578530	7578530	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs267605077	NA	P-0006491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	188	472	0	ENST00000269305.4:c.400T>A	p.Phe134Ile	p.F134I	ENST00000269305	NM_001126112.2	134	Ttt/Att	5/11	0.284112553062685	1	FACETS	0.899	0.83	0.972	0.899	0.83	0.972	CLONAL	1	FALSE	0	0.306524129802129	1		472	1155	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101909981	101909982	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	135	410	0	ENST00000374994.4:c.1302dup	p.Asp435Ter	p.D435*	ENST00000374994	NM_004612.2	434	tct/tcTt	8/9	1	2	FACETS	0.946	0.859	1	0.946	0.859	1	CLONAL	1	FALSE	1	0.306524129802129	2		410	931	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0006505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	279	326	1	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	1	0.991	1	1	0.996	1	CLONAL	2	TRUE	1	0.28	2		327	799	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833934	44833935	+	stop_gained	Nonsense_Mutation	INS	-	-	AGG	novel	NA	P-0006505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	341	400	0	ENST00000377967.4:c.359_360insGGA	p.Tyr120delinsTer	p.Y120delins*	ENST00000377967	NM_021140.2	120	tac/tAGGac	4/29	1	1	FACETS	1	0.991	1	1	0.997	1	CLONAL	4	TRUE	0	0.28	1		400	483	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433394	49433394	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783727	NA	P-0006522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	22	260	0	ENST00000301067.7:c.8053C>T	p.Arg2685Ter	p.R2685*	ENST00000301067	NM_003482.3	2685	Cga/Tga	32/54	1	2	FACETS	0.185	0.143	0.233	0.185	0.143	0.233	SUBCLONAL	1	TRUE	1	0.776258290442299	2		260	307	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702391	47702391	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs752241362	NA	P-0006522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	17	279	0	ENST00000233146.2:c.1987A>T	p.Met663Leu	p.M663L	ENST00000233146	NM_000251.2	663	Atg/Ttg	12/16	1	2	FACETS	0.13	0.097	0.17	0.13	0.097	0.17	SUBCLONAL	1	TRUE	1	0.776258290442299	2		279	336	SUCCESS
APC	324	MSKCC	GRCh37	5	112177010	112177010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	185	562	0	ENST00000257430.4:c.5719G>A	p.Ala1907Thr	p.A1907T	ENST00000257430	NM_000038.5	1907	Gct/Act	16/16	1	2	FACETS	0.714	0.661	0.767	0.714	0.661	0.767	SUBCLONAL	1	TRUE	1	0.776258290442299	2		562	668	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905465	11905465	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1036410712	NA	P-0006522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	320	295	0	ENST00000396373.4:c.115C>T	p.Arg39Ter	p.R39*	ENST00000396373	NM_001987.4	39	Cga/Tga	2/8	0.419782401906919	3	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.776258290442299	3		295	856	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415904	49415904	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	36	522	0	ENST00000301067.7:c.16443T>G	p.Cys5481Trp	p.C5481W	ENST00000301067	NM_003482.3	5481	tgT/tgG	53/54	1	2	FACETS	0.137	0.112	0.165	0.137	0.112	0.165	SUBCLONAL	1	TRUE	1	0.776258290442299	2		522	679	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50482421	50482421	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0006522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	179	479	0	ENST00000394963.4:c.771+1G>T		p.X257_splice	ENST00000394963	NM_003076.4	257			1	2	FACETS	0.824	0.764	0.885	0.824	0.764	0.885	CLONAL	1	TRUE	1	0.776258290442299	2		479	560	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210418	2210418	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	156	413	0	ENST00000398665.3:c.1026del	p.Arg343AlafsTer44	p.R343Afs*44	ENST00000398665	NM_032482.2	342	cGg/cg	13/28	1	2	FACETS	0.356	0.325	0.388	0.356	0.325	0.388	SUBCLONAL	1	TRUE	1	0.776258290442299	2		413	1130	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398278	25398279	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGC	novel	NA	P-0006522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	159	386	0	ENST00000311936.3:c.38_40dup	p.Gly13dup	p.G13dup	ENST00000311936	NM_004985.3	13	gta/gGCGta	2/5	1	2	FACETS	0.864	0.799	0.931	0.864	0.799	0.931	CLONAL	1	TRUE	1	0.776258290442299	2		386	474	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0006570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	152	134	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	NA	2	FACETS	0.781	0.721	0.843			1	INDETERMINATE	1	TRUE	NA	0.861035758457282	2		134	452	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913104	44913105	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	342	230	0	ENST00000377967.4:c.780dup	p.Asp261ArgfsTer2	p.D261Rfs*2	ENST00000377967	NM_021140.2	260	gga/ggAa	10/29	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.861035758457282	1		230	442	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197900	123197901	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0006570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	163	147	0	ENST00000218089.9:c.2025+1dup		p.E675fs	ENST00000218089	NM_001042749.1	675	gag/gaGg	20/35	1	1	FACETS	0.808	0.76	0.854	0.808	0.76	0.854	CLONAL	1	TRUE	0	0.861035758457282	1		147	267	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	145	588	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	1	0.94	1			1	INDETERMINATE	1	TRUE	NA	0.410085889835156	2		589	684	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0006581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	19	673	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.274	0.208	0.353	0.274	0.208	0.353	SUBCLONAL	1	TRUE	1	0.410085889835156	2		673	338	SUCCESS
APC	324	MSKCC	GRCh37	5	112175600	112175600	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	426	564	0	ENST00000257430.4:c.4312del	p.Thr1438HisfsTer35	p.T1438Hfs*35	ENST00000257430	NM_000038.5	1437	Aaa/aa	16/16	0.410085889835156	2	FACETS	0.994	0.95	1	0.994	0.95	1	CLONAL	2	TRUE	0	0.410085889835156	2		564	1045	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	50	397	0	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	0.23593990107878	0	FACETS	0.22	0.186	0.257			1	INDETERMINATE	1	TRUE	0	0.410085889835156	0		397	654	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0006581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	38	350	0	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	NA	2	FACETS	0.283	0.233	0.339			1	INDETERMINATE	1	TRUE	NA	0.410085889835156	2		350	654	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0006581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	68	446	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	NA	2	FACETS	0.349	0.303	0.4			1	INDETERMINATE	1	TRUE	NA	0.410085889835156	2		446	949	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577575	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587782289	NA	P-0006581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	94	431	0	ENST00000269305.4:c.706T>A	p.Tyr236Asn	p.Y236N	ENST00000269305	NM_001126112.2	236	Tac/Aac	7/11	NA	2	FACETS	0.499	0.443	0.559			1	INDETERMINATE	1	TRUE	NA	0.410085889835156	2		431	918	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936076	178936076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	57	172	1	ENST00000263967.3:c.1618C>T	p.Leu540Phe	p.L540F	ENST00000263967	NM_006218.2	540	Ctc/Ttc	10/21	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.410085889835156	2		173	271	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509735	106509735	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	178	392	0	ENST00000359195.3:c.1729C>A	p.His577Asn	p.H577N	ENST00000359195	NM_002649.2	577	Cat/Aat	2/11	1	2	FACETS	0.957	0.882	1	0.957	0.882	1	CLONAL	1	TRUE	1	0.410085889835156	2		392	907	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643942	52643943	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	86	242	0	ENST00000394830.3:c.1953dup	p.Ser652IlefsTer13	p.S652Ifs*13	ENST00000394830	NM_018313.4	651	-/A	17/30	0.282785284670219	1	FACETS	0.873	0.777	0.973	0.873	0.777	0.973	CLONAL	1	TRUE	0	0.410085889835156	1		242	382	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	131	588	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.15	2		589	1327	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0006587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1262	95	660	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.933	0.828	1	0.933	0.828	1	CLONAL	1	TRUE	1	0.15	2		660	1357	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0006587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	89	609	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.15	2		610	892	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0006587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	117	532	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.922	0.831	1	1	0.988	1	CLONAL	2	TRUE	1	0.15	2		532	846	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0006587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	63	480	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.843	0.726	0.969	0.843	0.726	0.969	CLONAL	1	TRUE	1	0.15	2		480	997	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0006587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	35	733	1	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	1	2	FACETS	0.412	0.336	0.499	0.412	0.336	0.499	SUBCLONAL	1	TRUE	1	0.15	2		734	1132	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750945	128750945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	89	489	1	ENST00000377970.2:c.482C>T	p.Ser161Leu	p.S161L	ENST00000377970	NM_002467.4	161	tCa/tTa	2/3	0.3	4	FACETS	1	0.966	1	0.418	0.37	0.471	CLONAL	1	TRUE	1	0.15	4		490	1087	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411276	63411276	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	57	389	1	ENST00000330258.3:c.1891C>T	p.Arg631Ter	p.R631*	ENST00000330258	NM_152424.3	631	Cga/Tga	2/2	0.284854629679303	0	FACETS	0.796	0.685	0.916			1	CLONAL	2	TRUE	NA	0.15	0		390	406	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554214	63554246	+	inframe_deletion	In_Frame_Del	DEL	CTGCGCCTGGTCAAACATGATGGAATCAATCTG	CTGCGCCTGGTCAAACATGATGGAATCAATCTG	-	novel	NA	P-0006587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	231	619	0	ENST00000307078.5:c.493_525del	p.Gln165_Gln175del	p.Q165_Q175del	ENST00000307078	NM_004655.3	165	CAGATTGATTCCATCATGTTTGACCAGGCGCAG/-	2/11	0.3	3	FACETS	1	0.948	1			1	CLONAL	3	TRUE	NA	0.15	3		619	1082	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119752	70119753	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	225	707	0	ENST00000245479.2:c.755dup	p.Lys253GlufsTer43	p.K253Efs*43	ENST00000245479	NM_000346.3	252	ctg/cTtg	3/3	0.3	3	FACETS	1	0.971	1			1	CLONAL	3	TRUE	NA	0.15	3		707	999	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041428	47041429	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0006587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	101	379	0	ENST00000377604.3:c.1776dup	p.Asn593GlnfsTer35	p.N593Qfs*35	ENST00000377604	NM_001204468.1	591	gac/gaCc	16/24	1	1	FACETS	0.973	0.871	1	1	0.987	1	CLONAL	2	TRUE	0	0.15	1		379	640	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0006618-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	136	356	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.992	0.904	1	0.992	0.904	1	CLONAL	1	TRUE	1	0.421352411095096	2		356	651	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0006618-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	240	318	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.421352411095096	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.421352411095096	1		318	700	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553677	106553677	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006618-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	167	283	0	ENST00000369096.4:c.1642A>C	p.Asn548His	p.N548H	ENST00000369096	NM_001198.3	548	Aat/Cat	5/7	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.421352411095096	2		283	781	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573492	41573492	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006618-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	205	336	0	ENST00000263253.7:c.5777T>G	p.Val1926Gly	p.V1926G	ENST00000263253	NM_001429.3	1926	gTg/gGg	31/31	0.421352411095096	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.421352411095096	1		336	662	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949068	44949068	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006618-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	219	447	0	ENST00000377967.4:c.3629T>G	p.Phe1210Cys	p.F1210C	ENST00000377967	NM_021140.2	1210	tTt/tGt	25/29	1	2	FACETS	0.997	0.927	1	0.997	0.927	1	CLONAL	1	TRUE	1	0.421352411095096	2		447	1043	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971145	21971146	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006618-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	48	81	0	ENST00000304494.5:c.212dup	p.Asn71LysfsTer49	p.N71Kfs*49	ENST00000304494	NM_000077.4	71	aac/aaAc	2/3	0.421352411095096	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.421352411095096	1		81	161	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	29	374	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.914	1			1	INDETERMINATE	1	TRUE	NA	0.763214652230473	2		374	66	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0006628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	342	371	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.763214652230473	7	FACETS	0.977	0.933	1			1	CLONAL	4	TRUE	NA	0.763214652230473	7		371	667	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652129	36652136	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGCCGG	GAGGCCGG	-	novel	NA	P-0006628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	93	333	0	ENST00000244741.5:c.253_260del	p.Gly85Ter	p.G85*	ENST00000244741	NM_000389.4	84	cGAGGCCGG/c	2/3	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.763214652230473	2		333	233	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608664	189608664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1464459460	NA	P-0006628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	103	349	1	ENST00000264731.3:c.1739C>T	p.Ser580Phe	p.S580F	ENST00000264731	NM_003722.4	580	tCc/tTc	13/14	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.763214652230473	2		350	195	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564578	41564578	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	109	450	0	ENST00000263253.7:c.4000G>T	p.Glu1334Ter	p.E1334*	ENST00000263253	NM_001429.3	1334	Gaa/Taa	24/31	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.763214652230473	2		450	221	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0006651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	39	498	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	0.12257625934066	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		498	654	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	120	356	1	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	0.3	4	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	4		357	753	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524146	187524146	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368616927	NA	P-0006651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	62	447	0	ENST00000441802.2:c.11393C>T	p.Pro3798Leu	p.P3798L	ENST00000441802	NM_005245.3	3798	cCg/cTg	20/27	0.3	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		447	692	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101055	26101055	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	87	465	0	ENST00000435504.4:c.37del	p.Trp13GlyfsTer9	p.W13Gfs*9	ENST00000435504		13	Tgg/gg	1/13	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		465	964	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0006668-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	773	384	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.272395406317729	7	FACETS	0.977	0.949	1			1	CLONAL	7	TRUE	NA	0.272395406317729	7		384	1395	SUCCESS
ATR	545	MSKCC	GRCh37	3	142285073	142285073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006668-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	97	412	0	ENST00000350721.4:c.182C>T	p.Ser61Phe	p.S61F	ENST00000350721	NM_001184.3	61	tCt/tTt	3/47	0.219469399224176	3	FACETS	0.774	0.688	0.865			1	SUBCLONAL	1	TRUE	NA	0.272395406317729	3		412	1046	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	rs886039483	NA	P-0006668-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	204	321	0	ENST00000269305.4:c.376T>G	p.Tyr126Asp	p.Y126D	ENST00000269305	NM_001126112.2	126	Tac/Gac	5/11	0.272395406317729	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.272395406317729	3		321	736	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285913	38285914	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCA	rs138489552	NA	P-0006668-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1227	77	464	0	ENST00000425967.3:c.495_497dup	p.Asp166dup	p.D166dup	ENST00000425967	NM_001174067.1	166	gac/gaTGAc	5/19	0.198197588022698	4	FACETS	0.552	0.482	0.627			1	SUBCLONAL	1	TRUE	NA	0.272395406317729	4		464	1304	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0006722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	318	480	0	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	0.273970781018851	4	FACETS	0.929	0.876	0.984	0.929	0.876	0.984	CLONAL	2	TRUE	2	0.361419787100884	4		480	1289	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974744	21974775	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTCCTCTACCCGACCCCGGGCCGCGGCCGT	ACCTCCTCTACCCGACCCCGGGCCGCGGCCGT	-	novel	NA	P-0006722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	130	247	0	ENST00000304494.5:c.52_83del	p.Thr18AlafsTer15	p.T18Afs*15	ENST00000304494	NM_000077.4	18	ACGGCCGCGGCCCGGGGTCGGGTAGAGGAGGTg/g	1/3	0.34107875310647	2	FACETS	1	0.98	1	0.633	0.577	0.692	CLONAL	1	TRUE	0	0.361419787100884	2		247	568	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106247	27106247	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	59	370	0	ENST00000324856.7:c.5858A>G	p.Lys1953Arg	p.K1953R	ENST00000324856	NM_006015.4	1953	aAg/aGg	20/20	0.245502378639928	3	FACETS	0.37	0.317	0.428	0.185	0.158	0.214	SUBCLONAL	1	TRUE	1	0.361419787100884	3		370	1043	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947852	178947852	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1236	236	521	0	ENST00000263967.3:c.2727C>A	p.Phe909Leu	p.F909L	ENST00000263967	NM_006218.2	909	ttC/ttA	19/21	0.361419787100884	3	FACETS	1	0.961	1	0.349	0.325	0.375	CLONAL	1	TRUE	0	0.361419787100884	3		521	1472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587781702	NA	P-0006722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	219	401	0	ENST00000269305.4:c.920-1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.273970781018851	4	FACETS	0.788	0.733	0.845	0.788	0.733	0.845	SUBCLONAL	2	TRUE	2	0.361419787100884	4		401	1047	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368427	225368428	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTCTC	novel	NA	P-0006722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	332	396	1	ENST00000264414.4:c.1314_1318dup	p.Leu440ArgfsTer17	p.L440Rfs*17	ENST00000264414	NM_003590.4	440	ctt/cGAGACtt	9/16	0.361419787100884	3	FACETS	0.902	0.853	0.953			1	CLONAL	2	TRUE	NA	0.361419787100884	3		397	1202	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0006743-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	124	463	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.164709941435481	2	FACETS	1	0.976	1	0.623	0.564	0.686	CLONAL	1	TRUE	0	0.251614543016305	2		463	791	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578440	7578440	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs879254249	NA	P-0006743-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	147	409	0	ENST00000269305.4:c.490A>G	p.Lys164Glu	p.K164E	ENST00000269305	NM_001126112.2	164	Aag/Gag	5/11	0.213770097506639	2	FACETS	0.81	0.741	0.882	0.81	0.741	0.882	CLONAL	2	TRUE	0	0.251614543016305	2		409	721	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145615	11145615	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006743-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	80	371	0	ENST00000358026.2:c.3977A>G	p.Glu1326Gly	p.E1326G	ENST00000358026	NM_001128849.1	1326	gAg/gGg	29/36	1	2	FACETS	0.871	0.766	0.984	0.871	0.766	0.984	CLONAL	1	TRUE	1	0.251614543016305	2		371	730	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224178	53224179	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006743-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	89	550	0	ENST00000375401.3:c.3372_3373insA	p.Leu1125IlefsTer5	p.L1125Ifs*5	ENST00000375401	NM_004187.3	1124	-/A	22/26	1	2	FACETS	0.753	0.666	0.846	0.753	0.666	0.846	SUBCLONAL	1	TRUE	1	0.251614543016305	2		550	940	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120149	70120149	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006743-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	92	180	0	ENST00000245479.2:c.1151del	p.Thr384SerfsTer2	p.T384Sfs*2	ENST00000245479	NM_000346.3	384	aCg/ag	3/3	0.213770097506639	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.251614543016305	2		180	339	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874405	76874407	+	frameshift_variant	Frame_Shift_Del	DEL	TGG	TGG	AT	novel	NA	P-0006743-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	69	616	0	ENST00000373344.5:c.5315_5317delinsAT	p.Ser1772TyrfsTer10	p.S1772Yfs*10	ENST00000373344	NM_000489.3	1772	tCCAtt/tATtt	21/35	1	2	FACETS	0.608	0.528	0.695	0.608	0.528	0.695	SUBCLONAL	1	TRUE	1	0.251614543016305	2		616	902	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	75	442	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.904	0.797	1	1	0.981	1	CLONAL	2	TRUE	1	0.22	2		444	377	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	37	384	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.895	0.739	1	0.895	0.739	1	CLONAL	1	TRUE	1	0.22	2		384	376	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573505	48573506	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	76	600	0	ENST00000342988.3:c.94_95del	p.Ser32Ter	p.S32*	ENST00000342988	NM_005359.5	30	gGA/g	2/12	1	2	FACETS	0.741	0.648	0.841	0.741	0.648	0.841	SUBCLONAL	1	TRUE	1	0.22	2		600	933	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	151	463	1	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	0.131963582989561	3	FACETS	1	0.984	1	0.674	0.615	0.736	INDETERMINATE	1	TRUE	1	0.22	3		464	1130	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084146	47084146	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	64	307	0	ENST00000409792.3:c.7143del	p.Ser2382LeufsTer29	p.S2382Lfs*29	ENST00000409792	NM_014159.6	2381	ccC/cc	17/21	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.22	2		307	565	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56872937	56872937	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	105	626	0	ENST00000308159.5:c.2097del	p.Phe699LeufsTer19	p.F699Lfs*19	ENST00000308159	NM_014669.4	698	Ttt/tt	19/22	1	2	FACETS	0.873	0.781	0.972	0.873	0.781	0.972	CLONAL	1	TRUE	1	0.22	2		626	1093	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	64	357	0	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	0.3	3	FACETS	1	0.958	1			1	CLONAL	1	TRUE	NA	0.22	3		357	507	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687472	37687472	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	20	235	1	ENST00000447079.4:c.4382del	p.Gly1461AlafsTer38	p.G1461Afs*38	ENST00000447079	NM_015083.1	1459	tGg/tg	14/14	1	2	FACETS	0.57	0.436	0.727	0.57	0.436	0.727	SUBCLONAL	1	TRUE	1	0.22	2		236	319	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	71	379	0	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	0.0957697272153347	0	FACETS	0.773	0.675	0.88			1	INDETERMINATE	1	TRUE	0	0.22	0		379	651	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867541	35867541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	46	363	0	ENST00000303115.3:c.361del	p.Ile121Ter	p.I121*	ENST00000303115	NM_002185.3	119	Aaa/aa	3/8	1	2	FACETS	0.622	0.523	0.732	0.622	0.523	0.732	SUBCLONAL	1	TRUE	1	0.22	2		363	672	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606696	29606696	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769910087	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	53	391	0	ENST00000389048.3:c.1184G>A	p.Arg395His	p.R395H	ENST00000389048	NM_004304.4	395	cGt/cAt	5/29	0.3	1	FACETS	0.87	0.742	1	0.87	0.742	1	CLONAL	1	TRUE	0	0.22	1		391	493	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100425	8100425	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	48	423	6	ENST00000346208.3:c.404del	p.Pro135ArgfsTer60	p.P135Rfs*60	ENST00000346208		133	taC/ta	3/6	0.0957697272153347	0	FACETS	0.512	0.432	0.6			1	INDETERMINATE	1	TRUE	0	0.22	0		429	665	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930634	32930634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56070345	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	67	351	0	ENST00000380152.3:c.7505G>A	p.Arg2502His	p.R2502H	ENST00000380152		2502	cGc/cAc	15/27	0.131963582989561	3	FACETS	1	0.876	1	0.505	0.438	0.577	INDETERMINATE	1	TRUE	1	0.22	3		351	670	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39772564	39772564	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	33	237	0	ENST00000288319.7:c.677del	p.Gly226ValfsTer65	p.G226Vfs*65	ENST00000288319	NM_182918.3	226	gGt/gt	6/10	1	2	FACETS	0.792	0.645	0.956	0.792	0.645	0.956	CLONAL	1	TRUE	1	0.22	2		237	379	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992964	72992964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561634666	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	122	780	2	ENST00000268489.5:c.1081G>A	p.Gly361Arg	p.G361R	ENST00000268489	NM_006885.3	361	Gga/Aga	2/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.22	2		782	1015	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884218	37884218	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	66	430	0	ENST00000269571.5:c.3694del	p.Ala1232LeufsTer70	p.A1232Lfs*70	ENST00000269571		1230	cGg/cg	27/27	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.22	2		430	579	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154241	2154242	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755455183	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	39	403	1	ENST00000434045.2:c.686dup	p.Glu230ArgfsTer50	p.E230Rfs*50	ENST00000434045	NM_001127598.1	229	cca/ccCa	5/5	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.22	2		404	326	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530140	212530140	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	48	345	0	ENST00000342788.4:c.1779T>A	p.Cys593Ter	p.C593*	ENST00000342788	NM_005235.2	593	tgT/tgA	15/28	1	2	FACETS	0.732	0.618	0.858	0.732	0.618	0.858	SUBCLONAL	1	TRUE	1	0.22	2		345	596	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089145	37089145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	37	394	1	ENST00000231790.2:c.1867G>A	p.Ala623Thr	p.A623T	ENST00000231790	NM_000249.3	623	Gca/Aca	16/19	1	2	FACETS	0.487	0.4	0.584	0.487	0.4	0.584	SUBCLONAL	1	TRUE	1	0.22	2		395	691	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928034	49928034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1449563443	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	89	577	0	ENST00000296474.3:c.3694G>A	p.Asp1232Asn	p.D1232N	ENST00000296474	NM_002447.2	1232	Gac/Aac	18/20	1	2	FACETS	0.885	0.783	0.994	0.885	0.783	0.994	CLONAL	1	TRUE	1	0.22	2		577	914	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200118	128200118	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553770434	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	28	269	0	ENST00000341105.2:c.1187G>A	p.Arg396Gln	p.R396Q	ENST00000341105	NM_032638.4	396	cGg/cAg	6/6	1	2	FACETS	0.651	0.52	0.8	0.651	0.52	0.8	SUBCLONAL	1	TRUE	1	0.22	2		269	391	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430600	181430600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1372564199	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	40	299	1	ENST00000325404.1:c.452C>T	p.Ala151Val	p.A151V	ENST00000325404	NM_003106.3	151	gCg/gTg	1/1	1	2	FACETS	0.868	0.722	1	0.868	0.722	1	CLONAL	1	TRUE	1	0.22	2		300	419	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973836	131973836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369788398	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	63	399	1	ENST00000265335.6:c.3539G>A	p.Arg1180Gln	p.R1180Q	ENST00000265335		1180	cGg/cAg	23/25	1	2	FACETS	0.826	0.714	0.949	0.826	0.714	0.949	CLONAL	1	TRUE	1	0.22	2		400	693	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370957	55370957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	63	384	0	ENST00000297316.4:c.259G>A	p.Ala87Thr	p.A87T	ENST00000297316	NM_022454.3	87	Gcg/Acg	1/2	0.131963582989561	3	FACETS	1	0.909	1	0.533	0.461	0.612	INDETERMINATE	1	TRUE	1	0.22	3		384	596	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967614	90967614	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	47	361	0	ENST00000265433.3:c.1294T>C	p.Ser432Pro	p.S432P	ENST00000265433	NM_002485.4	432	Tca/Cca	10/16	0.131963582989561	3	FACETS	0.66	0.555	0.775	0.33	0.277	0.388	INDETERMINATE	1	TRUE	1	0.22	3		361	719	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220420	98220420	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	83	466	0	ENST00000331920.6:c.3043T>G	p.Phe1015Val	p.F1015V	ENST00000331920	NM_000264.3	1015	Ttc/Gtc	18/24	1	2	FACETS	0.94	0.828	1	0.94	0.828	1	CLONAL	1	TRUE	1	0.22	2		466	803	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427167	49427167	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1233681272	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	69	569	0	ENST00000301067.7:c.11321A>G	p.Gln3774Arg	p.Q3774R	ENST00000301067	NM_003482.3	3774	cAg/cGg	39/54	0.131963582989561	3	FACETS	0.925	0.804	1	0.462	0.402	0.528	INDETERMINATE	1	TRUE	1	0.22	3		569	753	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444783	49444783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	70	374	0	ENST00000301067.7:c.2683C>T	p.Leu895Phe	p.L895F	ENST00000301067	NM_003482.3	895	Ctt/Ttt	10/54	0.131963582989561	3	FACETS	1	0.889	1	0.511	0.445	0.582	INDETERMINATE	1	TRUE	1	0.22	3		374	691	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549239	21549239	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149434310	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	100	632	1	ENST00000382592.4:c.3037G>A	p.Asp1013Asn	p.D1013N	ENST00000382592	NM_014572.2	1013	Gat/Aat	8/8	0.3	1	FACETS	0.82	0.731	0.915	0.82	0.731	0.915	CLONAL	1	TRUE	0	0.22	1		633	987	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563017	21563017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	35	315	0	ENST00000382592.4:c.902G>A	p.Gly301Asp	p.G301D	ENST00000382592	NM_014572.2	301	gGc/gAc	4/8	0.3	1	FACETS	0.591	0.484	0.712	0.591	0.484	0.712	SUBCLONAL	1	TRUE	0	0.22	1		315	479	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41962049	41962049	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	135	773	2	ENST00000219905.7:c.957G>T	p.Lys319Asn	p.K319N	ENST00000219905	NM_001164273.1	319	aaG/aaT	2/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.22	2		775	1069	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054348	42054348	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	93	512	0	ENST00000219905.7:c.7532T>C	p.Leu2511Pro	p.L2511P	ENST00000219905	NM_001164273.1	2511	cTg/cCg	22/24	1	2	FACETS	0.838	0.743	0.939	0.838	0.743	0.939	CLONAL	1	TRUE	1	0.22	2		512	1009	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339582	339582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558178546	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	90	437	0	ENST00000262320.3:c.2320G>A	p.Gly774Ser	p.G774S	ENST00000262320	NM_003502.3	774	Ggc/Agc	10/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.22	2		437	572	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779496	3779496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs988000147	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	61	487	1	ENST00000262367.5:c.5552G>A	p.Arg1851His	p.R1851H	ENST00000262367	NM_004380.2	1851	cGc/cAc	31/31	1	2	FACETS	0.868	0.748	0.998	0.868	0.748	0.998	CLONAL	1	TRUE	1	0.22	2		488	639	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836302	89836302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756082739	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	111	553	3	ENST00000389301.3:c.2447C>T	p.Ala816Val	p.A816V	ENST00000389301	NM_000135.2	816	gCg/gTg	26/43	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.22	2		556	976	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350526	15350526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200703650	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	20	194	0	ENST00000263377.2:c.3389G>A	p.Arg1130Gln	p.R1130Q	ENST00000263377	NM_058243.2	1130	cGg/cAg	16/20	0.0957697272153347	0	FACETS	0.581	0.445	0.74			1	INDETERMINATE	1	TRUE	0	0.22	0		194	244	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731622	47731622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	23	108	0	ENST00000449228.1:c.170C>T	p.Ala57Val	p.A57V	ENST00000449228	NM_001127240.2	57	gCg/gTg	2/4	0.16155697531615	0	FACETS	0.694	0.543	0.867			1	SUBCLONAL	1	TRUE	0	0.22	0		108	235	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919935	50919935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1044937882	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	60	438	0	ENST00000440232.2:c.3022C>T	p.Arg1008Cys	p.R1008C	ENST00000440232	NM_002691.3	1008	Cgc/Tgc	24/27	0.16155697531615	0	FACETS	0.877	0.757	1			1	CLONAL	1	TRUE	0	0.22	0		438	485	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428125	47428125	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	80	239	0	ENST00000377045.4:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000377045	NM_001654.4	362	cGa/cAa	11/16	1	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.22	1		239	500	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243853	46243853	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	34	266	0	ENST00000334344.6:c.1950del	p.Gln651ArgfsTer12	p.Q651Rfs*12	ENST00000334344	NM_152641.2	649	caT/ca	15/21	0.131963582989561	3	FACETS	0.754	0.616	0.91	0.377	0.308	0.455	INDETERMINATE	1	TRUE	1	0.22	3		266	455	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793362	242793363	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0006752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	44	398	0	ENST00000334409.5:c.714dup	p.Val239ArgfsTer6	p.V239Rfs*6	ENST00000334409	NM_005018.2	238	-/C	5/5	1	2	FACETS	0.84	0.705	0.99	0.84	0.705	0.99	CLONAL	1	TRUE	1	0.22	2		398	476	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907421	32907421	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359306	NA	P-0006838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	438	346	3	ENST00000380152.3:c.1813del	p.Ile605TyrfsTer9	p.I605Yfs*9	ENST00000380152		602	ggA/gg	10/27	0.496066376691155	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.500258518872791	2		349	819	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398262	25398262	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913538	NA	P-0006838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	350	354	0	ENST00000311936.3:c.57G>C	p.Leu19Phe	p.L19F	ENST00000311936	NM_004985.3	19	ttG/ttC	2/5	NA	2	FACETS	0.981	0.937	1			1	INDETERMINATE	2	TRUE	NA	0.500258518872791	2		354	713	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168695	32168695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143103753	NA	P-0006838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	77	510	1	ENST00000375023.3:c.4228C>T	p.Arg1410Cys	p.R1410C	ENST00000375023	NM_004557.3	1410	Cgc/Tgc	23/30	0.34666854784013	6	FACETS	0.486	0.425	0.553	0.081	0.07	0.093	SUBCLONAL	1	TRUE	0	0.500258518872791	6		511	1266	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295444	1295444	+	upstream_gene_variant	5'Flank	SNP	C	C	T	rs1396901074	NA	P-0006838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	11	11	0				ENST00000310581	NM_198253.2	-/1132			0.500258518872791	3	FACETS	0.859	0.625	1	0.859	0.625	1	CLONAL	2	TRUE	1	0.500258518872791	3		11	32	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88677032	88677032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782400	NA	P-0006838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	196	141	0	ENST00000372037.3:c.817C>T	p.Arg273Ter	p.R273*	ENST00000372037	NM_004329.2	273	Cga/Tga	9/13	0.500258518872791	3	FACETS	1	0.964	1	1	0.993	1	CLONAL	3	TRUE	1	0.500258518872791	3		141	319	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685269	89685269	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0006838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	284	166	0	ENST00000371953.3:c.165-1G>T		p.X55_splice	ENST00000371953	NM_000314.4	55			0.500258518872791	3	FACETS	1	0.97	1	1	0.995	1	CLONAL	3	TRUE	1	0.500258518872791	3		166	464	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572152	64572152	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1270463727	NA	P-0006838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	128	299	0	ENST00000312049.6:c.1487A>G	p.Lys496Arg	p.K496R	ENST00000312049	NM_130799.2	496	aAg/aGg	10/10	0.260921884483218	4	FACETS	0.732	0.662	0.806	0.366	0.331	0.403	INDETERMINATE	1	TRUE	2	0.500258518872791	4		299	1049	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022638	31022638	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	64	457	0	ENST00000375687.4:c.2123A>G	p.Gln708Arg	p.Q708R	ENST00000375687	NM_015338.5	708	cAg/cGg	13/13	0.403254699696029	4	FACETS	0.315	0.272	0.363	0.158	0.136	0.182	SUBCLONAL	1	TRUE	2	0.500258518872791	4		457	1217	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736510	85736511	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs387906351	NA	P-0006838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	589	584	4	ENST00000370580.1:c.136dup	p.Ile46AsnfsTer4	p.I46Nfs*4	ENST00000370580	NM_003921.4	46	ata/aAta	2/3	0.500258518872791	3	FACETS	0.911	0.876	0.947	0.911	0.876	0.947	CLONAL	2	TRUE	1	0.500258518872791	3		588	1615	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842331	68842331	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	220	354	0	ENST00000261769.5:c.393del	p.Val132PhefsTer83	p.V132Ffs*83	ENST00000261769	NM_004360.3	131	tCc/tc	4/16	0.177500465879551	2	FACETS	0.877	0.816	0.94	0.438	0.408	0.47	INDETERMINATE	1	TRUE	0	0.500258518872791	2		354	1003	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121529	2121573	+	inframe_deletion	In_Frame_Del	DEL	CTGCTGCGGGCCGACTCACTGCACCGCCTGGGCCTGCCCAACAAG	CTGCTGCGGGCCGACTCACTGCACCGCCTGGGCCTGCCCAACAAG	-	novel	NA	P-0006838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	96	349	0	ENST00000219476.3:c.1858_1902del	p.Leu620_Lys634del	p.L620_K634del	ENST00000219476	NM_000548.3	620	CTGCTGCGGGCCGACTCACTGCACCGCCTGGGCCTGCCCAACAAG/-	18/42	0.177500465879551	2	FACETS	0.565	0.504	0.631	0.283	0.252	0.316	INDETERMINATE	1	TRUE	0	0.500258518872791	2		349	679	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069101	5069122	+	frameshift_variant	Frame_Shift_Del	DEL	AGAACTTCAGCAGTCTTAAAGA	AGAACTTCAGCAGTCTTAAAGA	-	novel	NA	P-0006838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	42	462	0	ENST00000381652.3:c.1406_1427del	p.Lys469IlefsTer3	p.K469Ifs*3	ENST00000381652	NM_004972.3	469	aAGAACTTCAGCAGTCTTAAAGAt/at	11/25	0.30410835077284	1	FACETS	0.154	0.128	0.184	0.154	0.128	0.184	SUBCLONAL	1	TRUE	0	0.500258518872791	1		462	815	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006930-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	125	474	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	0.251851744374758	2		474	948	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868412	117868412	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006930-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	116	422	0	ENST00000297338.2:c.930T>G	p.Asp310Glu	p.D310E	ENST00000297338	NM_006265.2	310	gaT/gaG	8/14	1	2	FACETS	0.785	0.705	0.869	0.785	0.705	0.869	SUBCLONAL	1	TRUE	1	0.251851744374758	2		422	1174	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356400	70356401	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0006930-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	88	527	1	ENST00000374080.3:c.5301dup	p.Lys1768GlnfsTer3	p.K1768Qfs*3	ENST00000374080		1765	-/C	37/45	1	2	FACETS	0.678	0.599	0.763	0.678	0.599	0.763	SUBCLONAL	1	TRUE	1	0.251851744374758	2		528	1031	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971124	21971124	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006930-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	82	304	0	ENST00000304494.5:c.234del	p.Thr79ProfsTer67	p.T79Pfs*67	ENST00000304494	NM_000077.4	78	ctC/ct	2/3	0.251851744374758	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.251851744374758	1		304	519	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579537	7579537	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006930-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	97	492	0	ENST00000269305.4:c.150del	p.Ile50MetfsTer73	p.I50Mfs*73	ENST00000269305	NM_001126112.2	50	atT/at	4/11	0.251851744374758	1	FACETS	0.791	0.705	0.884	0.791	0.705	0.884	SUBCLONAL	1	TRUE	0	0.251851744374758	1		492	851	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0006940-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	90	356	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.779	0.692	0.872	0.779	0.692	0.872	SUBCLONAL	1	FALSE	1	0.365687833233208	2		356	632	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659323	86659323	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0006940-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	49	475	0	ENST00000274376.6:c.1610+2T>C		p.X537_splice	ENST00000274376	NM_002890.2	537			1	2	FACETS	0.617	0.524	0.72	0.617	0.524	0.72	SUBCLONAL	1	FALSE	1	0.365687833233208	2		475	434	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971177	21971211	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCGCCACTCGGGCGCTGCCCATCATCATGACCTGC	CCGCCACTCGGGCGCTGCCCATCATCATGACCTGC	-	novel	NA	P-0006940-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	29	181	0	ENST00000304494.5:c.151-4_181del		p.X51_splice	ENST00000304494	NM_000077.4	51		2/3	1	2	FACETS	0.844	0.683	1	0.844	0.683	1	CLONAL	1	FALSE	1	0.365687833233208	2		181	188	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577552	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CATGCAGGAACTGTTACACATGTAGTTGTAGTGGATGGTGGTACAGT	novel	NA	P-0006940-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	40	629	0	ENST00000269305.4:c.683_729dup	p.Gly244ThrfsTer19	p.G244Tfs*19	ENST00000269305	NM_001126112.2	243	-/ACTGTACCACCATCCACTACAACTACATGTGTAACAGTTCCTGCATG	7/11	0.29140589259674	1	FACETS	0.315	0.261	0.376	0.315	0.261	0.376	SUBCLONAL	1	FALSE	0	0.365687833233208	1		629	567	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880984	37880985	+	inframe_insertion	In_Frame_Ins	INS	-	-	TACGTGATGGCT	rs397516977	NA	P-0006965-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	422	567	0	ENST00000269571.5:c.2314_2325dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/TACGTGATGGCT	20/27	0.430357492457517	3	FACETS	0.954	0.909	0.999	0.954	0.909	0.999	CLONAL	2	TRUE	1	0.442937783116438	3		567	1220	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577543	7577543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1019340046	NA	P-0006965-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	203	572	0	ENST00000269305.4:c.738G>A	p.Met246Ile	p.M246I	ENST00000269305	NM_001126112.2	246	atG/atA	7/11	0.442937783116438	1	FACETS	0.955	0.888	1	0.955	0.888	1	CLONAL	1	TRUE	0	0.442937783116438	1		572	747	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971179	21971179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs36204594	NA	P-0006965-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	33	197	0	ENST00000304494.5:c.179C>T	p.Ala60Val	p.A60V	ENST00000304494	NM_000077.4	60	gCg/gTg	2/3	0.370259880290529	0	FACETS	0.488	0.402	0.583			1	SUBCLONAL	1	TRUE	0	0.442937783116438	0		197	170	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870888	12870888	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	252	328	0	ENST00000228872.4:c.115G>T	p.Glu39Ter	p.E39*	ENST00000228872	NM_004064.3	39	Gaa/Taa	1/3	1	2	FACETS	1	0.942	1	1	0.995	1	CLONAL	2	TRUE	1	0.359126294163315	2		328	701	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961308	41961308	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	370	626	0	ENST00000219905.7:c.218del	p.Gly73ValfsTer23	p.G73Vfs*23	ENST00000219905	NM_001164273.1	72	gtG/gt	2/24	0.359126294163315	1	FACETS	0.844	0.802	0.885	1	0.996	1	CLONAL	2	TRUE	0	0.359126294163315	1		626	1002	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579837	7579838	+	splice_donor_variant	Splice_Site	INS	-	-	CAGTTTCC	novel	NA	P-0006994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	263	421	0	ENST00000269305.4:c.68_74+1dup		p.X23_splice	ENST00000269305	NM_001126112.2	23			0.297013368628163	0	FACETS	0.826	0.782	0.871			1	CLONAL	2	TRUE	0	0.359126294163315	0		421	568	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538906	23538907	+	inframe_insertion	In_Frame_Ins	INS	-	-	TATAGCGTC	novel	NA	P-0006994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	254	431	0	ENST00000380871.4:c.524_532dup	p.Arg175_Tyr177dup	p.R175_Y177dup	ENST00000380871	NM_006167.3	175	aag/aGACGCTATAag	2/2	0.305123553796372	1	FACETS	0.776	0.729	0.823	1	0.994	1	SUBCLONAL	2	TRUE	0	0.359126294163315	1		431	748	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0007025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	88	347	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.673075100947415	1	FACETS	0.908	0.825	0.993	0.908	0.825	0.993	CLONAL	1	TRUE	0	0.673075100947415	1		347	191	SUCCESS
APC	324	MSKCC	GRCh37	5	112157690	112157690	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0007025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	174	266	1	ENST00000257430.4:c.1408+2T>A		p.X470_splice	ENST00000257430	NM_000038.5	470			1	2	FACETS	0.987	0.915	1	0.987	0.915	1	CLONAL	1	TRUE	1	0.673075100947415	2		267	524	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	238	588	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.396425625317851	4	FACETS	1	0.957	1			1	CLONAL	2	TRUE	NA	0.411246331830877	4		589	794	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0007062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	221	723	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.411246331830877	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.411246331830877	2		723	533	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023633	27023634	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCGGCTC	novel	NA	P-0007062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	59	132	0	ENST00000324856.7:c.741_747dup	p.Lys250ArgfsTer152	p.K250Rfs*152	ENST00000324856	NM_006015.4	247	gcc/gCCGGCTCcc	1/20	0.411246331830877	3	FACETS	0.783	0.682	0.889	0.783	0.682	0.889	SUBCLONAL	2	TRUE	1	0.411246331830877	3		132	221	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0007069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	72	673	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.878	0.774	0.987	0.878	0.774	0.987	CLONAL	1	TRUE	1	0.536232170136798	2		673	306	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0007069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	162	214	2	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	0.278428970885251	3	FACETS	1	0.98	1	0.595	0.548	0.644	INDETERMINATE	1	TRUE	1	0.536232170136798	3		216	644	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0007069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	413	609	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.536232170136798	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.536232170136798	1		610	1014	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685288	89685289	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	166	194	0	ENST00000371953.3:c.188dup	p.Asn63LysfsTer11	p.N63Kfs*11	ENST00000371953	NM_000314.4	61	-/A	3/9	0.536232170136798	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.536232170136798	2		194	270	SUCCESS
APC	324	MSKCC	GRCh37	5	112174094	112174095	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs863225332	NA	P-0007069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	176	352	0	ENST00000257430.4:c.2804dup	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	tac/tAac	16/16	1	2	FACETS	0.943	0.872	1	0.943	0.872	1	CLONAL	1	TRUE	1	0.536232170136798	2		352	696	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200033	123200033	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	115	261	0	ENST00000218089.9:c.2105A>G	p.Asp702Gly	p.D702G	ENST00000218089	NM_001042749.1	702	gAc/gGc	22/35	0.227970808229075	0	FACETS	0.502	0.456	0.55			1	INDETERMINATE	1	TRUE	0	0.536232170136798	0		261	396	SUCCESS
APC	324	MSKCC	GRCh37	5	112175880	112175880	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	247	372	0	ENST00000257430.4:c.4592del	p.Asn1531MetfsTer34	p.N1531Mfs*34	ENST00000257430	NM_000038.5	1530	gAa/ga	16/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.536232170136798	2		372	871	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0007095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	98	341	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.551322614915661	2		341	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0007095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	419	461	2	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.551322614915661	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.551322614915661	1		463	949	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743930	41743930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141302305	NA	P-0007095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1256	330	550	2	ENST00000301178.4:c.865G>A	p.Val289Met	p.V289M	ENST00000301178	NM_021913.4	289	Gtg/Atg	7/20	1	2	FACETS	0.755	0.711	0.799	0.755	0.711	0.799	SUBCLONAL	1	TRUE	1	0.551322614915661	2		552	1586	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665719	86665719	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0007095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	53	275	0	ENST00000274376.6:c.1698+2T>G		p.X566_splice	ENST00000274376	NM_002890.2	566			0.432386601936631	0	FACETS	0.387	0.334	0.444			1	SUBCLONAL	1	TRUE	0	0.551322614915661	0		275	223	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912257	97912257	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	623	503	0	ENST00000289081.3:c.634C>T	p.Gln212Ter	p.Q212*	ENST00000289081	NM_000136.2	212	Cag/Tag	7/15	0.548100769339292	2	FACETS	0.988	0.956	1	0.988	0.956	1	CLONAL	2	TRUE	0	0.551322614915661	2		503	1144	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405953	70405953	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	345	505	0	ENST00000373644.4:c.3467G>C	p.Arg1156Thr	p.R1156T	ENST00000373644	NM_030625.2	1156	aGa/aCa	4/12	0.551322614915661	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.551322614915661	1		505	850	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593477	48593477	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	266	409	1	ENST00000342988.3:c.1228C>T	p.Gln410Ter	p.Q410*	ENST00000342988	NM_005359.5	410	Cag/Tag	10/12	0.551322614915661	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.551322614915661	1		410	671	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937626	17937626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747388225	NA	P-0007095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	54	550	0	ENST00000458235.1:c.3301G>A	p.Gly1101Arg	p.G1101R	ENST00000458235	NM_000215.3	1101	Gga/Aga	24/24	0.551322614915661	1	FACETS	0.137	0.116	0.16	0.137	0.116	0.16	SUBCLONAL	1	TRUE	0	0.551322614915661	1		550	1033	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032758	30032758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	127	427	0	ENST00000338641.4:c.133G>A	p.Asp45Asn	p.D45N	ENST00000338641	NM_000268.3	45	Gac/Aac	2/16	0.220450837480552	2	FACETS	0.505	0.457	0.555	0.252	0.228	0.278	INDETERMINATE	1	TRUE	0	0.551322614915661	2		427	913	SUCCESS
APC	324	MSKCC	GRCh37	5	112178813	112178814	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CACCTAATCTCAGTCCCACTATAGAGTATAATGATGGAAGA	novel	NA	P-0007095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	73	392	0	ENST00000257430.4:c.7524_7564dup	p.Pro2522HisfsTer8	p.P2522Hfs*8	ENST00000257430	NM_000038.5	2508	cca/cCACCTAATCTCAGTCCCACTATAGAGTATAATGATGGAAGAca	16/16	0.432386601936631	0	FACETS	0.194	0.17	0.221			1	SUBCLONAL	1	TRUE	0	0.551322614915661	0		392	611	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0007143-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	206	547	7	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	0.308008219706825	1	FACETS	0.917	0.853	0.983	0.917	0.853	0.983	CLONAL	1	TRUE	0	0.442880400291663	1		554	790	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0007143-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	99	322	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.442880400291663	1	FACETS	0.784	0.704	0.868	0.784	0.704	0.868	SUBCLONAL	1	TRUE	0	0.442880400291663	1		322	444	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874637	35874637	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007143-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	181	525	3	ENST00000303115.3:c.799del	p.Arg267GlyfsTer28	p.R267Gfs*28	ENST00000303115	NM_002185.3	265	Aaa/aa	6/8	0.442880400291663	3	FACETS	0.984	0.907	1	0.492	0.453	0.532	CLONAL	1	TRUE	1	0.442880400291663	3		528	1015	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420661	49420661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555185875	NA	P-0007143-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	114	352	0	ENST00000301067.7:c.15088C>T	p.Arg5030Cys	p.R5030C	ENST00000301067	NM_003482.3	5030	Cgt/Tgt	48/54	1	2	FACETS	0.724	0.652	0.8	0.724	0.652	0.8	SUBCLONAL	1	TRUE	1	0.442880400291663	2		352	711	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56878430	56878430	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771046738	NA	P-0007143-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	252	724	2	ENST00000308159.5:c.2369G>A	p.Arg790His	p.R790H	ENST00000308159	NM_014669.4	790	cGc/cAc	22/22	1	2	FACETS	0.935	0.874	0.998	0.935	0.874	0.998	CLONAL	1	TRUE	1	0.442880400291663	2		726	1217	SUCCESS
APC	324	MSKCC	GRCh37	5	112175650	112175651	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007143-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	194	575	0	ENST00000257430.4:c.4364dup	p.Asn1455LysfsTer2	p.N1455Kfs*2	ENST00000257430	NM_000038.5	1453	-/A	16/16	0.373812321610997	1	FACETS	0.839	0.778	0.902	0.839	0.778	0.902	CLONAL	1	TRUE	0	0.442880400291663	1		575	813	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551951	150551952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs750805885	NA	P-0007143-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	193	478	3	ENST00000369026.2:c.55dup	p.Ala19GlyfsTer91	p.A19Gfs*91	ENST00000369026	NM_021960.4	19	gcc/gGcc	1/3	1	2	FACETS	0.874	0.808	0.942	0.874	0.808	0.942	CLONAL	1	TRUE	1	0.442880400291663	2		481	997	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65304197	65304197	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007143-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	194	581	0	ENST00000342505.4:c.2918A>G	p.Asn973Ser	p.N973S	ENST00000342505	NM_002227.2	973	aAc/aGc	21/25	0.376997091146281	1	FACETS	0.838	0.777	0.901	0.838	0.777	0.901	CLONAL	1	TRUE	0	0.442880400291663	1		581	814	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197150	106197150	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007143-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	154	411	1	ENST00000380013.4:c.5483A>G	p.Gln1828Arg	p.Q1828R	ENST00000380013	NM_001127208.2	1828	cAg/cGg	11/11	1	2	FACETS	0.885	0.811	0.962	0.885	0.811	0.962	CLONAL	1	TRUE	1	0.442880400291663	2		412	786	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117725	108117725	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007143-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	155	397	0	ENST00000278616.4:c.936A>T	p.Leu312Phe	p.L312F	ENST00000278616	NM_000051.3	312	ttA/ttT	8/63	1	2	FACETS	0.891	0.816	0.968	0.891	0.816	0.968	CLONAL	1	TRUE	1	0.442880400291663	2		397	786	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446729	49446729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376475904	NA	P-0007143-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	169	402	0	ENST00000301067.7:c.1081G>A	p.Val361Ile	p.V361I	ENST00000301067	NM_003482.3	361	Gtt/Att	8/54	1	2	FACETS	0.924	0.85	1	0.924	0.85	1	CLONAL	1	TRUE	1	0.442880400291663	2		402	826	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489570	40489570	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1004741102	NA	P-0007143-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	266	742	0	ENST00000264657.5:c.680C>T	p.Ala227Val	p.A227V	ENST00000264657	NM_139276.2	227	gCg/gTg	8/24	1	2	FACETS	0.918	0.86	0.979	0.918	0.86	0.979	CLONAL	1	TRUE	1	0.442880400291663	2		742	1308	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265386	10265386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1003447106	NA	P-0007143-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	179	457	0	ENST00000340748.4:c.1660G>A	p.Ala554Thr	p.A554T	ENST00000340748		554	Gcg/Acg	20/40	1	2	FACETS	0.853	0.786	0.922	0.853	0.786	0.922	CLONAL	1	TRUE	1	0.442880400291663	2		457	948	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143232	24143232	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007143-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	231	581	1	ENST00000263121.7:c.464G>A	p.Arg155His	p.R155H	ENST00000263121	NM_003073.3	155	cGc/cAc	4/9	1	2	FACETS	0.941	0.876	1	0.941	0.876	1	CLONAL	1	TRUE	1	0.442880400291663	2		582	1109	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622192	1622193	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0007143-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	197	595	0	ENST00000344749.5:c.682_683del	p.Trp228GlufsTer25	p.W228Efs*25	ENST00000344749	NM_001136139.2	228	TGg/g	10/19	1	2	FACETS	0.873	0.808	0.941	0.873	0.808	0.941	CLONAL	1	TRUE	1	0.442880400291663	2		595	1019	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806204	1806204	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007143-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	192	559	0	ENST00000260795.2:c.1227del	p.Thr410ProfsTer22	p.T410Pfs*22	ENST00000260795		408	tCc/tc	8/17	1	2	FACETS	0.831	0.768	0.896	0.831	0.768	0.896	CLONAL	1	TRUE	1	0.442880400291663	2		559	1044	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0007276-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	89	360	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.324582378031269	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.324582378031269	1		361	379	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0007276-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	153	356	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.324582378031269	2		356	794	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681828	30681828	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007276-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	184	350	0	ENST00000376406.3:c.269G>T	p.Arg90Leu	p.R90L	ENST00000376406	NM_014641.2	90	cGa/cTa	3/15	0.289127748007718	4	FACETS	1	0.989	1			1	CLONAL	1	TRUE	NA	0.324582378031269	4		350	1021	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974690	21974691	+	inframe_insertion	In_Frame_Ins	INS	-	-	GACCGT	novel	NA	P-0007276-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	120	307	0	ENST00000304494.5:c.131_136dup	p.Gly45_Arg46insHisGly	p.G45_R46insHG	ENST00000304494	NM_000077.4	46	cgg/cACGGTCgg	1/3	0.324582378031269	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	0	0.324582378031269	1		307	617	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	414	301	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.775115459919346	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.775115459919346	1		301	642	SUCCESS
AR	367	MSKCC	GRCh37	X	66765149	66765151	+	inframe_deletion	In_Frame_Del	DEL	TGC	TGC	-	rs752055010	NA	P-0007282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	46	324	0	ENST00000374690.3:c.170_172del	p.Leu57del	p.L57del	ENST00000374690	NM_000044.3	54	tTGCtg/ttg	1/8	NA	2	FACETS	0.214	0.18	0.252			1	INDETERMINATE	1	TRUE	NA	0.775115459919346	2		324	554	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199958	138199958	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	57	195	4	ENST00000237289.4:c.1376C>T	p.Ser459Leu	p.S459L	ENST00000237289	NM_001270507.1	459	tCg/tTg	7/9	0.775115459919346	1	FACETS	0.273	0.235	0.314	0.273	0.235	0.314	SUBCLONAL	1	TRUE	0	0.775115459919346	1		199	330	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860143	151860143	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs747835958	NA	P-0007282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	268	427	0	ENST00000262189.6:c.10519C>T	p.Arg3507Ter	p.R3507*	ENST00000262189	NM_170606.2	3507	Cga/Tga	43/59	1	2	FACETS	0.717	0.673	0.761	0.717	0.673	0.761	SUBCLONAL	1	TRUE	1	0.775115459919346	2		427	965	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522551	176522551	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774571806	NA	P-0007282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	405	424	0	ENST00000292408.4:c.1648G>A	p.Val550Met	p.V550M	ENST00000292408	NM_213647.1	550	Gtg/Atg	13/18	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.775115459919346	2		424	1031	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184589	11184589	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	146	507	0	ENST00000361445.4:c.6628G>C	p.Ala2210Pro	p.A2210P	ENST00000361445	NM_004958.3	2210	Gcc/Ccc	47/58	0.775115459919346	1	FACETS	0.288	0.263	0.314	0.288	0.263	0.314	SUBCLONAL	1	TRUE	0	0.775115459919346	1		507	801	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508610	38508610	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1391	152	585	0	ENST00000254066.5:c.658C>G	p.Leu220Val	p.L220V	ENST00000254066	NM_000964.3	220	Ctg/Gtg	6/9	1	2	FACETS	0.254	0.231	0.278	0.254	0.231	0.278	SUBCLONAL	1	TRUE	1	0.775115459919346	2		585	1543	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243057	105243058	+	inframe_insertion	In_Frame_Ins	INS	-	-	GATGATGAAGGTGTTGGGCCGGGGCCGCTCCGT	novel	NA	P-0007282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1608	617	604	0	ENST00000349310.3:c.193_225dup	p.Thr65_Ile75dup	p.T65_I75dup	ENST00000349310	NM_001014432.1	65	-/ACGGAGCGGCCCCGGCCCAACACCTTCATCATC	5/15	0.219160624440884	6	FACETS	0.912	0.875	0.95			1	INDETERMINATE	2	TRUE	NA	0.775115459919346	6		604	2225	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555684	21555685	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0007282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	41	627	1	ENST00000382592.4:c.2585_2586delinsAA	p.Arg862Gln	p.R862Q	ENST00000382592	NM_014572.2	862	cGG/cAA	6/8	0.775115459919346	1	FACETS	0.084	0.069	0.1	0.084	0.069	0.1	SUBCLONAL	1	TRUE	0	0.775115459919346	1		628	773	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0007303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	341	302	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.220876842146333	5	FACETS	1	0.989	1	0.761	0.722	0.801	INDETERMINATE	2	TRUE	2	0.564784392107282	5		302	977	SUCCESS
APC	324	MSKCC	GRCh37	5	112173926	112173926	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060503287	NA	P-0007303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	347	487	0	ENST00000257430.4:c.2635C>T	p.Gln879Ter	p.Q879*	ENST00000257430	NM_000038.5	879	Cag/Tag	16/16	0.220876842146333	5	FACETS	1	0.986	1	0.74	0.702	0.779	INDETERMINATE	2	TRUE	2	0.564784392107282	5		487	1022	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0007303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	574	263	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.495254501304355	5	FACETS	1	0.993	1			1	CLONAL	5	TRUE	NA	0.564784392107282	5		263	720	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509436	106509436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200175951	NA	P-0007303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	209	594	1	ENST00000359195.3:c.1430G>A	p.Arg477His	p.R477H	ENST00000359195	NM_002649.2	477	cGt/cAt	2/11	0.291197946048106	4	FACETS	0.859	0.796	0.925	0.43	0.398	0.463	INDETERMINATE	1	TRUE	2	0.564784392107282	4		595	1348	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782128	9782128	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	104	681	0	ENST00000377346.4:c.2151G>T	p.Leu717Phe	p.L717F	ENST00000377346	NM_005026.3	717	ttG/ttT	17/24	NA	2	FACETS	0.394	0.352	0.439			1	INDETERMINATE	1	TRUE	NA	0.564784392107282	2		681	934	SUCCESS
APC	324	MSKCC	GRCh37	5	112174355	112174355	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	204	379	0	ENST00000257430.4:c.3064G>C	p.Asp1022His	p.D1022H	ENST00000257430	NM_000038.5	1022	Gat/Cat	16/16	0.220876842146333	5	FACETS	1	0.985	1	0.79	0.738	0.843	INDETERMINATE	2	TRUE	2	0.564784392107282	5		379	563	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188853	32188853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs192478549	NA	P-0007303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	419	625	0	ENST00000375023.3:c.701G>A	p.Arg234Gln	p.R234Q	ENST00000375023	NM_004557.3	234	cGg/cAg	4/30	0.280207509929064	5	FACETS	1	0.991	1	0.774	0.738	0.811	INDETERMINATE	2	TRUE	2	0.564784392107282	5		625	1180	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006218	22006218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1204549439	NA	P-0007303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	135	403	1	ENST00000276925.6:c.185C>T	p.Ala62Val	p.A62V	ENST00000276925	NM_004936.3	62	gCg/gTg	2/2	0.371573557404355	4	FACETS	0.916	0.832	1	0.458	0.416	0.502	CLONAL	1	TRUE	2	0.564784392107282	4		404	817	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578560	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGGAGTACTGTAG	GGGGAGTACTGTAG	-	novel	NA	P-0007303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	666	584	0	ENST00000269305.4:c.376-6_383del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	0.549028301983491	3	FACETS	0.937	0.91	0.964			1	CLONAL	3	TRUE	NA	0.564784392107282	3		584	1076	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0007305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	118	359	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.788	0.713	0.866	1	0.986	1	SUBCLONAL	2	TRUE	1	0.26	2		360	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577575	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587782289	NA	P-0007305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	44	380	0	ENST00000269305.4:c.706T>G	p.Tyr236Asp	p.Y236D	ENST00000269305	NM_001126112.2	236	Tac/Gac	7/11	0.156809212733708	1	FACETS	0.662	0.555	0.779	0.662	0.555	0.779	SUBCLONAL	1	TRUE	0	0.26	1		380	445	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161171	56161171	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	45	356	0	ENST00000399503.3:c.1040G>T	p.Cys347Phe	p.C347F	ENST00000399503	NM_005921.1	347	tGc/tTc	5/20	1	2	FACETS	0.547	0.459	0.645	0.547	0.459	0.645	SUBCLONAL	1	TRUE	1	0.26	2		356	633	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022609	12022609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	58	390	0	ENST00000396373.4:c.715C>T	p.Pro239Ser	p.P239S	ENST00000396373	NM_001987.4	239	Ccc/Tcc	5/8	0.3	3	FACETS	1	0.881	1			1	CLONAL	1	TRUE	NA	0.26	3		390	491	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120175	70120175	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	29	222	0	ENST00000245479.2:c.1177C>T	p.Gln393Ter	p.Q393*	ENST00000245479	NM_000346.3	393	Cag/Tag	3/3	0.156809212733708	4	FACETS	1	0.876	1	0.56	0.451	0.682	CLONAL	1	TRUE	2	0.26	4		222	251	SUCCESS
APC	324	MSKCC	GRCh37	5	112155031	112155032	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	29	374	0	ENST00000257430.4:c.1307dup	p.Asn436LysfsTer8	p.N436Kfs*8	ENST00000257430	NM_000038.5	434	-/A	10/16	0.156809212733708	1	FACETS	0.354	0.283	0.435	0.354	0.283	0.435	SUBCLONAL	1	TRUE	0	0.26	1		374	548	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	84	588	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.997	0.879	1	0.997	0.879	1	CLONAL	1	TRUE	1	0.19123348930819	2		589	881	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0007333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	65	480	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	NA	2	FACETS	0.883	0.764	1			1	INDETERMINATE	1	TRUE	NA	0.19123348930819	2		480	770	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974696	21974697	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	35	390	0	ENST00000304494.5:c.130dup	p.Tyr44LeufsTer76	p.Y44Lfs*76	ENST00000304494	NM_000077.4	44	tac/tTac	1/3	0.1780679445518	1	FACETS	0.742	0.608	0.893	0.742	0.608	0.893	SUBCLONAL	1	TRUE	0	0.19123348930819	1		390	446	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0007356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	113	384	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.888	0.801	0.979	1	0.987	1	CLONAL	2	TRUE	1	0.208280660451185	2		384	611	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258035	123258035	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs763017169	NA	P-0007356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	84	560	0	ENST00000358487.5:c.1646A>G	p.Asn549Ser	p.N549S	ENST00000358487	NM_000141.4	549	aAt/aGt	12/18	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.208280660451185	2		560	690	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287449	46287449	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	73	515	0	ENST00000334344.6:c.5308C>G	p.Leu1770Val	p.L1770V	ENST00000334344	NM_152641.2	1770	Cta/Gta	20/21	0.170167865532559	1	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	0	0.208280660451185	1		515	628	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989385	7989385	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200663524	NA	P-0007356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	91	381	2	ENST00000319144.4:c.301G>A	p.Ala101Thr	p.A101T	ENST00000319144	NM_001139.2	101	Gcc/Acc	2/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.208280660451185	2		383	661	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265024	46265024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1172968588	NA	P-0007356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	51	748	1	ENST00000371998.3:c.1894C>T	p.Arg632Trp	p.R632W	ENST00000371998		632	Cgg/Tgg	12/23	0.208280660451185	3	FACETS	0.536	0.454	0.628	0.179	0.151	0.21	SUBCLONAL	1	TRUE	0	0.208280660451185	3		749	1008	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855268	76855268	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	61	299	0	ENST00000373344.5:c.5719A>G	p.Met1907Val	p.M1907V	ENST00000373344	NM_000489.3	1907	Atg/Gtg	24/35	1	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.208280660451185	1		299	404	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211849	123211849	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0007356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	50	269	0	ENST00000218089.9:c.2716A>T	p.Lys906Ter	p.K906*	ENST00000218089	NM_001042749.1	906	Aaa/Taa	27/35	1	1	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	0	0.208280660451185	1		269	399	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579314	7579342	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TGCAAGTCACAGACTTGGCTGTCCCAGAA	TGCAAGTCACAGACTTGGCTGTCCCAGAA	-	novel	NA	P-0007356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	65	278	0	ENST00000269305.4:c.345_373del	p.Ser116ValfsTer23	p.S116Vfs*23	ENST00000269305	NM_001126112.2	115	caTTCTGGGACAGCCAAGTCTGTGACTTGCAcg/cacg	4/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.208280660451185	2		278	443	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427026	49427027	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0007356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	57	281	0	ENST00000301067.7:c.11461dup	p.Gln3821ProfsTer191	p.Q3821Pfs*191	ENST00000301067	NM_003482.3	3821	cag/cCag	39/54	0.170167865532559	1	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	0	0.208280660451185	1		281	484	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923008	44923008	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	46	273	0	ENST00000377967.4:c.1870del	p.Leu624Ter	p.L624*	ENST00000377967	NM_021140.2	623	aaC/aa	16/29	1	1	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	0	0.208280660451185	1		273	372	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0007361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	39	340	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.581	0.482	0.692	0.581	0.482	0.692	SUBCLONAL	1	TRUE	1	0.324823193632173	2		340	413	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0007361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	55	302	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.193118679771224	3	FACETS	1	0.958	1	0.66	0.569	0.759	INDETERMINATE	1	TRUE	1	0.324823193632173	3		302	298	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117799	108117799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202160435	NA	P-0007361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	8	367	0	ENST00000278616.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000278616	NM_000051.3	337	cGt/cAt	8/63	1	2	FACETS	0.144	0.092	0.212	0.144	0.092	0.212	SUBCLONAL	1	TRUE	1	0.324823193632173	2		367	342	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268766	41268766	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	81	449	0	ENST00000349496.5:c.1004A>T	p.Lys335Ile	p.K335I	ENST00000349496	NM_001904.3	335	aAa/aTa	7/15	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.324823193632173	2		449	433	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309760	65309760	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1356522608	NA	P-0007361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	20	344	0	ENST00000342505.4:c.2390A>G	p.Lys797Arg	p.K797R	ENST00000342505	NM_002227.2	797	aAg/aGg	17/25	1	2	FACETS	0.365	0.279	0.467	0.365	0.279	0.467	SUBCLONAL	1	TRUE	1	0.324823193632173	2		344	337	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236086	108236086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782292	NA	P-0007361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	30	349	0	ENST00000278616.4:c.9022C>T	p.Arg3008Cys	p.R3008C	ENST00000278616	NM_000051.3	3008	Cgt/Tgt	63/63	1	2	FACETS	0.6	0.484	0.73	0.6	0.484	0.73	SUBCLONAL	1	TRUE	1	0.324823193632173	2		349	308	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944375	40944375	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	18	329	0	ENST00000373198.4:c.2127C>A	p.Ser709Arg	p.S709R	ENST00000373198	NM_133170.3	709	agC/agA	12/32	1	2	FACETS	0.488	0.368	0.629	0.488	0.368	0.629	SUBCLONAL	1	TRUE	1	0.324823193632173	2		329	227	SUCCESS
APC	324	MSKCC	GRCh37	5	112173785	112173785	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	21	290	0	ENST00000257430.4:c.2496del	p.Ser833AlafsTer9	p.S833Afs*9	ENST00000257430	NM_000038.5	832	Ccc/cc	16/16	0.193118679771224	3	FACETS	0.522	0.402	0.661	0.261	0.201	0.331	INDETERMINATE	1	TRUE	1	0.324823193632173	3		290	288	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0007404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	334	344	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.7	2		344	876	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161774	47161775	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0007404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	339	490	0	ENST00000409792.3:c.4351dup	p.Met1451AsnfsTer3	p.M1451Nfs*3	ENST00000409792	NM_014159.6	1451	atg/aAtg	3/21	1	2	FACETS	0.97	0.919	1	0.97	0.919	1	CLONAL	1	TRUE	1	0.7	2		490	999	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0007495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	271	379	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.271355053366061	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.340773499365344	3		379	856	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469669	NA	P-0007495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	203	327	0	ENST00000374080.3:c.130G>A	p.Gly44Ser	p.G44S	ENST00000374080		44	Ggt/Agt	2/45	1	1	FACETS	0.825	0.77	0.882	1	0.993	1	CLONAL	2	TRUE	0	0.340773499365344	1		327	599	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0007495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	146	313	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.340773499365344	2	FACETS	0.904	0.831	0.979	0.904	0.831	0.979	CLONAL	2	TRUE	0	0.340773499365344	2		313	474	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249510	153249510	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1157879635	NA	P-0007495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	118	291	0	ENST00000281708.4:c.1268G>T	p.Gly423Val	p.G423V	ENST00000281708	NM_033632.3	423	gGa/gTa	9/12	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.340773499365344	2		291	650	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363231	40363231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768216635	NA	P-0007495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	133	396	2	ENST00000397332.2:c.998C>T	p.Ala333Val	p.A333V	ENST00000397332	NM_001033082.2	333	gCg/gTg	3/3	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.340773499365344	2		398	680	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55143618	55143618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377318745	NA	P-0007495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	113	469	0	ENST00000257290.5:c.1850G>A	p.Arg617Gln	p.R617Q	ENST00000257290	NM_006206.4	617	cGg/cAg	13/23	0.21415995779397	1	FACETS	0.684	0.616	0.757	0.684	0.616	0.757	SUBCLONAL	1	TRUE	0	0.340773499365344	1		469	804	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041065	112041065	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1385	241	995	0	ENST00000368678.4:c.190T>A	p.Phe64Ile	p.F64I	ENST00000368678		64	Ttt/Att	3/13	0.21415995779397	1	FACETS	0.722	0.672	0.774	0.722	0.672	0.774	SUBCLONAL	1	TRUE	0	0.340773499365344	1		995	1626	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912158	114912158	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1549	138	1004	1	ENST00000543371.1:c.1228C>A	p.His410Asn	p.H410N	ENST00000543371	NM_001198531.1	410	Cat/Aat	11/14	1	2	FACETS	0.48	0.435	0.528	0.48	0.435	0.528	SUBCLONAL	1	TRUE	1	0.340773499365344	2		1005	1687	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007645	45007645	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	169	282	0	ENST00000558401.1:c.92C>A	p.Ser31Ter	p.S31*	ENST00000558401	NM_004048.2	31	tCa/tAa	2/4	0.340773499365344	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.340773499365344	2		282	470	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117854	70117854	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	42	369	0	ENST00000245479.2:c.322C>T	p.Pro108Ser	p.P108S	ENST00000245479	NM_000346.3	108	Ccc/Tcc	1/3	1	2	FACETS	0.477	0.398	0.565	0.477	0.398	0.565	SUBCLONAL	1	TRUE	1	0.340773499365344	2		369	517	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119683	70119683	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0007495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	163	683	0	ENST00000245479.2:c.686-1G>A		p.X229_splice	ENST00000245479	NM_000346.3	229			1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.340773499365344	2		683	937	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591978	48591978	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0007495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	83	249	0	ENST00000342988.3:c.1139+2T>C		p.X380_splice	ENST00000342988	NM_005359.5	380			0.340773499365344	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.340773499365344	1		249	360	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610402	10610402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1186163503	NA	P-0007495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	99	440	0	ENST00000171111.5:c.308C>T	p.Ser103Phe	p.S103F	ENST00000171111	NM_203500.1	103	tCc/tTc	2/6	1	2	FACETS	0.904	0.808	1	0.904	0.808	1	CLONAL	1	TRUE	1	0.340773499365344	2		440	643	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011139	12011140	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	116	426	0	ENST00000353533.5:c.547dup	p.Thr183AsnfsTer4	p.T183Nfs*4	ENST00000353533	NM_003010.3	182	-/A	5/11	1	2	FACETS	0.974	0.879	1	0.974	0.879	1	CLONAL	1	TRUE	1	0.340773499365344	2		426	699	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0007519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	407	681	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	1	2	FACETS	0.866	0.824	0.908	0.866	0.824	0.908	CLONAL	1	TRUE	1	0.768131722451419	2		681	1224	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835904	151835904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	19	462	1	ENST00000262189.6:c.14620C>T	p.Arg4874Trp	p.R4874W	ENST00000262189	NM_170606.2	4874	Cgg/Tgg	58/59	1	2	FACETS	0.655	0.498	0.84	0.655	0.498	0.84	SUBCLONAL	1	FALSE	1	0.223911687233603	2		463	259	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460417	149460417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756076440	NA	P-0007538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	13	611	1	ENST00000286301.3:c.220G>A	p.Ala74Thr	p.A74T	ENST00000286301	NM_005211.3	74	Gct/Act	3/22	0.184280069335043	1	FACETS	0.493	0.352	0.665	0.493	0.352	0.665	SUBCLONAL	1	FALSE	0	0.223911687233603	1		612	209	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422384	47422384	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	14	352	2	ENST00000377045.4:c.23del	p.Pro8LeufsTer26	p.P8Lfs*26	ENST00000377045	NM_001654.4	6	ggC/gg	2/16	1	1	FACETS	0.673	0.488	0.895	0.673	0.488	0.895	SUBCLONAL	1	FALSE	0	0.223911687233603	1		354	165	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591115	67591116	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1561299903	NA	P-0007538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	23	412	0	ENST00000274335.5:c.1710dup	p.Ile571TyrfsTer31	p.I571Yfs*31	ENST00000274335		570	ctt/cTtt	12/15	0.223911687233603	3	FACETS	0.769	0.6	0.964	0.385	0.3	0.482	CLONAL	1	FALSE	1	0.223911687233603	3		412	297	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693003	89693003	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs786204900	NA	P-0007538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	18	219	0	ENST00000371953.3:c.491del	p.Lys164ArgfsTer3	p.K164Rfs*3	ENST00000371953	NM_000314.4	163	Aaa/aa	5/9	0.0951863117428271	4	FACETS	0.924	0.698	1			1	INDETERMINATE	1	FALSE	NA	0.223911687233603	4		219	213	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439586	51439586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1372032935	NA	P-0007538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	19	326	0	ENST00000262662.1:c.151G>A	p.Glu51Lys	p.E51K	ENST00000262662		51	Gag/Aag	4/4	1	2	FACETS	0.449	0.34	0.578	0.449	0.34	0.578	SUBCLONAL	1	FALSE	1	0.223911687233603	2		326	378	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	231046	231046	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751008647	NA	P-0007538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	17	518	3	ENST00000264932.6:c.826G>A	p.Gly276Ser	p.G276S	ENST00000264932	NM_004168.2	276	Ggc/Agc	7/15	0.184280069335043	1	FACETS	0.71	0.532	0.919	0.71	0.532	0.919	CLONAL	1	FALSE	0	0.223911687233603	1		521	190	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751979	57751979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763253230	NA	P-0007538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	19	449	0	ENST00000274289.3:c.1258C>T	p.Leu420Phe	p.L420F	ENST00000274289	NM_006622.3	420	Ctc/Ttc	10/14	0.223911687233603	3	FACETS	0.854	0.65	1	0.427	0.325	0.546	CLONAL	1	FALSE	1	0.223911687233603	3		449	221	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041117	42041117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747757361	NA	P-0007538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	22	894	3	ENST00000219905.7:c.5495G>A	p.Arg1832Gln	p.R1832Q	ENST00000219905	NM_001164273.1	1832	cGg/cAg	16/24	0.184280069335043	1	FACETS	0.492	0.381	0.621	0.492	0.381	0.621	SUBCLONAL	1	FALSE	0	0.223911687233603	1		897	355	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627177	37627177	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	16	450	0	ENST00000447079.4:c.1092A>T	p.Arg364Ser	p.R364S	ENST00000447079	NM_015083.1	364	agA/agT	2/14	1	2	FACETS	0.5	0.369	0.656	0.5	0.369	0.656	SUBCLONAL	1	FALSE	1	0.223911687233603	2		450	286	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273217	18273217	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0007538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	13	726	0	ENST00000222254.8:c.1011-1G>T		p.X337_splice	ENST00000222254	NM_005027.3	337			0.184280069335043	1	FACETS	0.417	0.297	0.564	0.417	0.297	0.564	SUBCLONAL	1	FALSE	0	0.223911687233603	1		726	247	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44515807	44515807	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	17	505	0	ENST00000291552.4:c.246del	p.Phe82LeufsTer15	p.F82Lfs*15	ENST00000291552	NM_006758.2	82	ttT/tt	4/8	0.223911687233603	1	FACETS	0.482	0.359	0.627	0.482	0.359	0.627	SUBCLONAL	1	FALSE	0	0.223911687233603	1		505	280	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321268	65321269	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0007538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	12	410	0	ENST00000342505.4:c.1571dup	p.Ser524ArgfsTer12	p.S524Rfs*12	ENST00000342505	NM_002227.2	524	agc/agGc	11/25	1	2	FACETS	0.464	0.326	0.634	0.464	0.326	0.634	SUBCLONAL	1	FALSE	1	0.223911687233603	2		410	231	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120708	115120709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0007559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	141	496	0	ENST00000257566.3:c.296_297dup	p.Glu100TrpfsTer40	p.E100Wfs*40	ENST00000257566	NM_016569.3	99	-/TG	1/8	1	2	FACETS	0.804	0.736	0.875	1	0.989	1	CLONAL	2	TRUE	1	0.308077261374642	2		496	569	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	72	226	0	ENST00000206249.3:c.1610A>G	p.Tyr537Cys	p.Y537C	ENST00000206249	NM_000125.3	537	tAt/tGt	8/8	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.308077261374642	2		226	423	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347546	89347546	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	63	568	0	ENST00000301030.4:c.5404G>A	p.Glu1802Lys	p.E1802K	ENST00000301030	NM_001256183.1	1802	Gaa/Aaa	9/13	0.308077261374642	0	FACETS	0.863	0.751	0.982			1	CLONAL	1	TRUE	0	0.308077261374642	0		568	328	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508903	106508903	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	41	163	1	ENST00000359195.3:c.897C>A	p.Asn299Lys	p.N299K	ENST00000359195	NM_002649.2	299	aaC/aaA	2/11	0.243387134462662	4	FACETS	1	0.894	1	0.547	0.458	0.646	CLONAL	1	TRUE	2	0.308077261374642	4		164	318	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411567	116411567	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	98	252	0	ENST00000397752.3:c.2746T>C	p.Ser916Pro	p.S916P	ENST00000397752	NM_000245.2	916	Tct/Cct	13/21	0.243387134462662	4	FACETS	0.968	0.869	1	0.968	0.869	1	CLONAL	2	TRUE	2	0.308077261374642	4		252	430	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864047	97864047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	61	398	1	ENST00000289081.3:c.1619G>A	p.Ser540Asn	p.S540N	ENST00000289081	NM_000136.2	540	aGc/aAc	15/15	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.308077261374642	2		399	372	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120668	115120668	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	132	558	0	ENST00000257566.3:c.338G>A	p.Trp113Ter	p.W113*	ENST00000257566	NM_016569.3	113	tGg/tAg	1/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.308077261374642	2		558	654	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936802	32936802	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	67	338	0	ENST00000380152.3:c.7948G>C	p.Glu2650Gln	p.E2650Q	ENST00000380152		2650	Gaa/Caa	17/27	0.308077261374642	1	FACETS	0.82	0.714	0.933	0.82	0.714	0.933	CLONAL	1	TRUE	0	0.308077261374642	1		338	449	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842724	68842724	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	76	379	0	ENST00000261769.5:c.661del	p.Asp221IlefsTer29	p.D221Ifs*29	ENST00000261769	NM_004360.3	220	ctG/ct	5/16	0.236215092885206	0	FACETS	0.841	0.741	0.947			1	CLONAL	1	TRUE	0	0.308077261374642	0		379	406	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0007584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	96	340	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.462342409061349	4	FACETS	0.799	0.719	0.882	0.799	0.719	0.882	SUBCLONAL	2	FALSE	2	0.539372451105846	4		340	343	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0007584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	142	480	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.475639694517498	3	FACETS	1	0.968	1	0.719	0.666	0.772	CLONAL	2	FALSE	0	0.539372451105846	3		480	310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882019	NA	P-0007584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	189	265	0	ENST00000269305.4:c.455dup	p.Pro153AlafsTer28	p.P153Afs*28	ENST00000269305	NM_001126112.2	152	ccg/ccCg	5/11	0.356084726507495	2	FACETS	1	0.989	1	0.671	0.625	0.718	CLONAL	1	FALSE	0	0.539372451105846	2		265	522	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733058	74733058	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	175	351	2	ENST00000359995.5:c.185T>G	p.Phe62Cys	p.F62C	ENST00000359995	NM_001195427.1	62	tTt/tGt	1/3	0.462342409061349	4	FACETS	1	0.988	1	0.694	0.64	0.749	CLONAL	1	FALSE	2	0.539372451105846	4		353	720	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012692	36012692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770744364	NA	P-0007584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	166	34	0	ENST00000358208.4:c.136G>A	p.Gly46Ser	p.G46S	ENST00000358208		46	Ggc/Agc	2/12	0.539372451105846	8	FACETS	1	0.946	1	1	0.946	1	CLONAL	4	FALSE	4	0.539372451105846	8		34	395	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495248	212495248	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	193	423	0	ENST00000342788.4:c.2018T>C	p.Val673Ala	p.V673A	ENST00000342788	NM_005235.2	673	gTt/gCt	17/28	0.243604304401368	2	FACETS	1	0.981	1	0.587	0.543	0.633	CLONAL	1	FALSE	0	0.341576901210887	2		423	963	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185195118	185195118	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	83	453	0	ENST00000265026.3:c.2435G>T	p.Gly812Val	p.G812V	ENST00000265026	NM_004721.4	812	gGa/gTa	12/14	0.333034379716836	2	FACETS	0.383	0.336	0.433	0.191	0.168	0.217	SUBCLONAL	1	FALSE	0	0.341576901210887	2		453	1270	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067824	30067824	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	172	233	1	ENST00000338641.4:c.1009C>T	p.Gln337Ter	p.Q337*	ENST00000338641	NM_000268.3	337	Cag/Tag	11/16	0.227813925248801	2	FACETS	1	0.987	1	0.678	0.625	0.733	CLONAL	1	FALSE	0	0.341576901210887	2		234	743	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597451	10597452	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs774071816	NA	P-0007595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	368	441	0	ENST00000171111.5:c.1751dup	p.Tyr584Ter	p.Y584*	ENST00000171111	NM_203500.1	584	tac/taAc	6/6	0.274836417952071	2	FACETS	0.785	0.743	0.827	0.785	0.743	0.827	SUBCLONAL	2	FALSE	0	0.341576901210887	2		441	1373	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	157	474	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.240054996224843	4	FACETS	0.893	0.819	0.971	0.595	0.546	0.647	CLONAL	2	TRUE	1	0.267467568572448	4		474	833	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	262	831	11	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.939	0.88	1	1	0.995	1	CLONAL	2	TRUE	1	0.267467568572448	2		842	1043	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743896	41743896	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	212	601	1	ENST00000301178.4:c.836del	p.Pro279GlnfsTer18	p.P279Qfs*18	ENST00000301178	NM_021913.4	277	gaC/ga	7/20	0.244860787942606	4	FACETS	0.943	0.876	1	0.629	0.584	0.676	CLONAL	2	TRUE	1	0.267467568572448	4		602	1065	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	44	359	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.267467568572448	4	FACETS	0.415	0.346	0.491	0.138	0.115	0.164	SUBCLONAL	1	TRUE	1	0.267467568572448	4		360	1006	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259674	11259674	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	78	371	0	ENST00000361445.4:c.4031C>T	p.Ala1344Val	p.A1344V	ENST00000361445	NM_004958.3	1344	gCc/gTc	27/58	1	2	FACETS	0.799	0.702	0.904	0.799	0.702	0.904	CLONAL	1	TRUE	1	0.267467568572448	2		371	730	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835780	68835781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	118	477	1	ENST00000261769.5:c.377dup	p.Pro127AlafsTer41	p.P127Afs*41	ENST00000261769	NM_004360.3	124	cgc/cgCc	3/16	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.267467568572448	2		478	837	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053023	180053023	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	45	386	0	ENST00000261937.6:c.1267del	p.Gln423ArgfsTer70	p.Q423Rfs*70	ENST00000261937	NM_182925.4	423	Cag/ag	10/30	1	2	FACETS	0.691	0.581	0.813	0.691	0.581	0.813	SUBCLONAL	1	TRUE	1	0.267467568572448	2		386	487	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444659	78444659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs908264837	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	151	239	0	ENST00000370768.2:c.30del	p.Ser11LeufsTer43	p.S11Lfs*43	ENST00000370768	NM_003902.3	10	ccC/cc	1/20	1	2	FACETS	1	0.938	1	1	0.992	1	CLONAL	2	TRUE	1	0.267467568572448	2		239	551	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418718	49418718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760369709	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	65	236	0	ENST00000301067.7:c.15796C>T	p.Arg5266Cys	p.R5266C	ENST00000301067	NM_003482.3	5266	Cgc/Tgc	49/54	0.240054996224843	4	FACETS	1	0.953	1	0.407	0.353	0.465	CLONAL	1	TRUE	1	0.267467568572448	4		236	505	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577290	64577290	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886039413	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	45	456	1	ENST00000312049.6:c.292C>T	p.Arg98Ter	p.R98*	ENST00000312049	NM_130799.2	98	Cga/Tga	2/10	1	2	FACETS	0.526	0.441	0.62	0.526	0.441	0.62	SUBCLONAL	1	TRUE	1	0.267467568572448	2		457	640	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782275	56782275	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1227243689	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	143	560	3	ENST00000308159.5:c.116C>T	p.Ala39Val	p.A39V	ENST00000308159	NM_014669.4	39	gCg/gTg	2/22	1	2	FACETS	0.955	0.869	1	0.955	0.869	1	CLONAL	1	TRUE	1	0.267467568572448	2		563	1120	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202858	16202858	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746614090	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	136	417	0	ENST00000375759.3:c.566G>A	p.Arg189Gln	p.R189Q	ENST00000375759	NM_015001.2	189	cGa/cAa	3/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.267467568572448	2		417	828	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649592	206649592	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	132	343	1	ENST00000367120.3:c.427C>T	p.Arg143Cys	p.R143C	ENST00000367120	NM_014002.3	143	Cgc/Tgc	6/22	1	2	FACETS	0.88	0.802	0.961	1	0.989	1	CLONAL	2	TRUE	1	0.267467568572448	2		344	561	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028285	48028285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587779254	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	97	318	0	ENST00000234420.5:c.3163G>A	p.Ala1055Thr	p.A1055T	ENST00000234420	NM_000179.2	1055	Gca/Aca	4/10	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.267467568572448	2		318	719	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265061	198265061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	196	401	0	ENST00000335508.6:c.2816G>A	p.Arg939His	p.R939H	ENST00000335508	NM_012433.2	939	cGt/cAt	19/25	1	2	FACETS	0.872	0.809	0.938	1	0.992	1	CLONAL	2	TRUE	1	0.267467568572448	2		401	840	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663034	227663034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779847464	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	115	292	0	ENST00000305123.5:c.421G>A	p.Gly141Ser	p.G141S	ENST00000305123	NM_005544.2	141	Ggc/Agc	1/2	1	2	FACETS	1	0.954	1	1	0.99	1	CLONAL	2	TRUE	1	0.267467568572448	2		292	398	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247373	71247373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758125097	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	39	317	1	ENST00000318789.4:c.160G>A	p.Ala54Thr	p.A54T	ENST00000318789	NM_032682.5	54	Gcc/Acc	6/21	0.267467568572448	3	FACETS	0.52	0.43	0.621	0.173	0.143	0.207	SUBCLONAL	1	TRUE	0	0.267467568572448	3		318	636	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480469	89480469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	81	388	1	ENST00000336596.2:c.2306G>A	p.Arg769His	p.R769H	ENST00000336596	NM_005233.5	769	cGt/cAt	13/17	0.267467568572448	3	FACETS	0.716	0.629	0.81	0.239	0.209	0.27	SUBCLONAL	1	TRUE	0	0.267467568572448	3		389	959	SUCCESS
APC	324	MSKCC	GRCh37	5	112178228	112178228	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	129	549	0	ENST00000257430.4:c.6937G>A	p.Ala2313Thr	p.A2313T	ENST00000257430	NM_000038.5	2313	Gcc/Acc	16/16	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.267467568572448	2		549	883	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638697	176638697	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	114	485	0	ENST00000439151.2:c.3297T>G	p.Ser1099Arg	p.S1099R	ENST00000439151	NM_022455.4	1099	agT/agG	5/23	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.267467568572448	2		485	730	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696757	176696757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752685166	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	127	421	1	ENST00000439151.2:c.5458G>A	p.Val1820Met	p.V1820M	ENST00000439151	NM_022455.4	1820	Gtg/Atg	16/23	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.267467568572448	2		422	690	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30682856	30682856	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113702536	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	503	672	1	ENST00000376406.3:c.97C>T	p.Arg33Trp	p.R33W	ENST00000376406	NM_014641.2	33	Cgg/Tgg	2/15	0.267467568572448	2	FACETS	1	0.987	1	1	0.997	1	CLONAL	3	TRUE	0	0.267467568572448	2		673	1182	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509063	106509063	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	73	383	0	ENST00000359195.3:c.1057T>C	p.Ser353Pro	p.S353P	ENST00000359195	NM_002649.2	353	Tcc/Ccc	2/11	1	2	FACETS	0.848	0.741	0.962	0.848	0.741	0.962	CLONAL	1	TRUE	1	0.267467568572448	2		383	644	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845233	128845233	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	30	217	0	ENST00000249373.3:c.727C>A	p.Leu243Ile	p.L243I	ENST00000249373	NM_005631.4	243	Ctc/Atc	3/12	1	2	FACETS	0.721	0.582	0.878	0.721	0.582	0.878	SUBCLONAL	1	TRUE	1	0.267467568572448	2		217	311	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845190	151845190	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764910946	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	126	450	0	ENST00000262189.6:c.13822C>T	p.Arg4608Cys	p.R4608C	ENST00000262189	NM_170606.2	4608	Cgc/Tgc	52/59	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.267467568572448	2		450	684	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540288	23540288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770792266	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	57	245	0	ENST00000380871.4:c.115G>A	p.Ala39Thr	p.A39T	ENST00000380871	NM_006167.3	39	Gcg/Acg	1/2	0.23931089254982	3	FACETS	1	0.926	1	0.561	0.482	0.646	CLONAL	1	TRUE	1	0.267467568572448	3		245	431	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878944	117878944	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	128	593	0	ENST00000297338.2:c.25A>G	p.Ser9Gly	p.S9G	ENST00000297338	NM_006265.2	9	Agt/Ggt	2/14	0.23931089254982	3	FACETS	0.906	0.819	0.998	0.453	0.409	0.499	CLONAL	1	TRUE	1	0.267467568572448	3		593	1198	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574661	64574661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149783078	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	34	321	0	ENST00000312049.6:c.814C>T	p.His272Tyr	p.H272Y	ENST00000312049	NM_130799.2	272	Cat/Tat	5/10	1	2	FACETS	0.473	0.386	0.572	0.473	0.386	0.572	SUBCLONAL	1	TRUE	1	0.267467568572448	2		321	537	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124701	108124701	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	73	448	0	ENST00000278616.4:c.2059A>G	p.Lys687Glu	p.K687E	ENST00000278616	NM_000051.3	687	Aag/Gag	13/63	1	2	FACETS	0.748	0.653	0.85	0.748	0.653	0.85	SUBCLONAL	1	TRUE	1	0.267467568572448	2		448	730	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245621	46245621	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	97	516	0	ENST00000334344.6:c.3715G>T	p.Gly1239Cys	p.G1239C	ENST00000334344	NM_152641.2	1239	Ggt/Tgt	15/21	0.240054996224843	4	FACETS	0.795	0.706	0.889	0.265	0.235	0.297	SUBCLONAL	1	TRUE	1	0.267467568572448	4		516	1157	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115398	115115398	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs779733514	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	540	611	0	ENST00000257566.3:c.928C>T	p.Arg310Ter	p.R310*	ENST00000257566	NM_016569.3	310	Cga/Tga	5/8	0.240054996224843	4	FACETS	0.936	0.899	0.974	1	0.995	1	CLONAL	4	TRUE	1	0.267467568572448	4		611	1367	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601297	28601297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs976218231	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1188	98	633	0	ENST00000241453.7:c.2135G>A	p.Arg712Lys	p.R712K	ENST00000241453	NM_004119.2	712	aGg/aAg	17/24	0.244860787942606	4	FACETS	0.722	0.642	0.808	0.241	0.214	0.27	SUBCLONAL	1	TRUE	1	0.267467568572448	4		633	1286	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801727	3801727	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs777015995	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	80	447	0	ENST00000262367.5:c.3779C>T	p.Thr1260Met	p.T1260M	ENST00000262367	NM_004380.2	1260	aCg/aTg	20/31	1	2	FACETS	0.636	0.558	0.719	0.636	0.558	0.719	SUBCLONAL	1	TRUE	1	0.267467568572448	2		447	941	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771320	68771320	+	start_lost	Translation_Start_Site	SNP	T	T	C	rs1555509623	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	37	229	0	ENST00000261769.5:c.2T>C	p.Met1?	p.M1?	ENST00000261769	NM_004360.3	1	aTg/aCg	1/16	1	2	FACETS	0.758	0.626	0.905	0.758	0.626	0.905	CLONAL	1	TRUE	1	0.267467568572448	2		229	365	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821829	72821829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140437495	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	158	719	2	ENST00000268489.5:c.10346C>T	p.Ala3449Val	p.A3449V	ENST00000268489	NM_006885.3	3449	gCg/gTg	10/10	1	2	FACETS	0.955	0.873	1	0.955	0.873	1	CLONAL	1	TRUE	1	0.267467568572448	2		721	1237	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822274	72822274	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	207	744	0	ENST00000268489.5:c.9901G>T	p.Ala3301Ser	p.A3301S	ENST00000268489	NM_006885.3	3301	Gca/Tca	10/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.267467568572448	2		744	1264	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216731	7216731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	110	667	0	ENST00000380728.2:c.692C>T	p.Ala231Val	p.A231V	ENST00000380728		231	gCt/gTt	8/11	0.172772193622875	2	FACETS	0.804	0.721	0.892	0.402	0.36	0.446	CLONAL	1	TRUE	0	0.267467568572448	2		667	1023	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879819	37879819	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	131	315	1	ENST00000269571.5:c.2114C>T	p.Ala705Val	p.A705V	ENST00000269571		705	gCg/gTg	18/27	0.172772193622875	2	FACETS	0.921	0.84	1	0.921	0.84	1	CLONAL	2	TRUE	0	0.267467568572448	2		316	532	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475607	40475607	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	182	694	4	ENST00000264657.5:c.1637G>T	p.Trp546Leu	p.W546L	ENST00000264657	NM_139276.2	546	tGg/tTg	18/24	0.172772193622875	2	FACETS	1	0.975	1	0.57	0.525	0.617	CLONAL	1	TRUE	0	0.267467568572448	2		698	1194	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696682	47696682	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	160	546	0	ENST00000347630.2:c.266T>C	p.Leu89Ser	p.L89S	ENST00000347630	NM_001007230.1	89	tTa/tCa	5/11	0.172772193622875	2	FACETS	1	0.974	1	0.577	0.528	0.628	CLONAL	1	TRUE	0	0.267467568572448	2		546	1037	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59878691	59878691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	155	582	0	ENST00000259008.2:c.1063G>A	p.Ala355Thr	p.A355T	ENST00000259008	NM_032043.2	355	Gcc/Acc	8/20	0.172772193622875	2	FACETS	1	0.975	1	0.587	0.536	0.639	CLONAL	1	TRUE	0	0.267467568572448	2		582	988	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238951	5238951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237159914	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	113	311	1	ENST00000357368.4:c.1828C>T	p.Arg610Trp	p.R610W	ENST00000357368	NM_002850.3	610	Cgg/Tgg	13/38	0.244860787942606	4	FACETS	0.823	0.741	0.908	0.548	0.494	0.606	CLONAL	2	TRUE	1	0.267467568572448	4		312	651	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303922	30303922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	140	317	1	ENST00000262643.3:c.158C>T	p.Ala53Val	p.A53V	ENST00000262643	NM_001238.2	53	gCg/gTg	4/12	0.244860787942606	4	FACETS	0.928	0.846	1	0.619	0.564	0.676	CLONAL	2	TRUE	1	0.267467568572448	4		318	715	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388006	31388006	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908943	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	120	533	1	ENST00000328111.2:c.1807G>A	p.Ala603Thr	p.A603T	ENST00000328111	NM_006892.3	603	Gct/Act	17/23	0.267467568572448	4	FACETS	0.896	0.806	0.99	0.299	0.268	0.33	CLONAL	1	TRUE	1	0.267467568572448	4		534	1270	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206814	36206814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150042294	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	71	239	1	ENST00000300305.3:c.698G>A	p.Arg233His	p.R233H	ENST00000300305		233	cGc/cAc	6/8	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.267467568572448	2		240	439	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574489	41574489	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	91	360	2	ENST00000263253.7:c.6774G>T	p.Gln2258His	p.Q2258H	ENST00000263253	NM_001429.3	2258	caG/caT	31/31	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.267467568572448	2		362	565	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929238	44929238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1429606535	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	108	638	1	ENST00000377967.4:c.2338C>T	p.Leu780Phe	p.L780F	ENST00000377967	NM_021140.2	780	Ctc/Ttc	17/29	0.267467568572448	1	FACETS	0.644	0.576	0.715	0.644	0.576	0.715	SUBCLONAL	1	TRUE	0	0.267467568572448	1		639	1087	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223548	53223548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	40	232	0	ENST00000375401.3:c.3811C>T	p.Arg1271Trp	p.R1271W	ENST00000375401	NM_004187.3	1271	Cgg/Tgg	23/26	0.267467568572448	1	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	0	0.267467568572448	1		232	239	SUCCESS
AR	367	MSKCC	GRCh37	X	66937402	66937402	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	163	652	0	ENST00000374690.3:c.2256G>A	p.Trp752Ter	p.W752*	ENST00000374690	NM_000044.3	752	tgG/tgA	5/8	0.267467568572448	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.267467568572448	1		652	923	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514671	44514672	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	117	331	0	ENST00000291552.4:c.484_485del	p.Glu162MetfsTer32	p.E162Mfs*32	ENST00000291552	NM_006758.2	162	GAa/a	7/8	1	2	FACETS	0.752	0.68	0.827	1	0.984	1	SUBCLONAL	2	TRUE	1	0.267467568572448	2		331	582	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971026	21971026	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	38	305	0	ENST00000304494.5:c.332del	p.Gly111AlafsTer35	p.G111Afs*35	ENST00000304494	NM_000077.4	111	gGc/gc	2/3	1	2	FACETS	0.634	0.524	0.757	0.634	0.524	0.757	SUBCLONAL	1	TRUE	1	0.267467568572448	2		305	448	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050034	13050036	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	246	601	1	ENST00000316448.5:c.181_183del	p.Glu61del	p.E61del	ENST00000316448	NM_004343.3	60	GAG/-	2/9	0.244860787942606	4	FACETS	0.841	0.784	0.9	0.561	0.523	0.6	CLONAL	2	TRUE	1	0.267467568572448	4		602	1386	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962854	2962854	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	58	401	1	ENST00000396946.4:c.2054del	p.Gly685AlafsTer31	p.G685Afs*31	ENST00000396946	NM_032415.4	685	gGc/gc	16/25	1	2	FACETS	0.657	0.564	0.759	0.657	0.564	0.759	SUBCLONAL	1	TRUE	1	0.267467568572448	2		402	660	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043349	6043349	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781716	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	52	170	1	ENST00000265849.7:c.325del	p.Glu109LysfsTer3	p.E109Kfs*3	ENST00000265849	NM_000535.5	109	Gaa/aa	4/15	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.267467568572448	2		171	315	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224251	98224251	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	61	358	0	ENST00000331920.6:c.2590del	p.Glu864LysfsTer39	p.E864Kfs*39	ENST00000331920	NM_000264.3	864	Gaa/aa	16/24	1	2	FACETS	0.648	0.558	0.746	0.648	0.558	0.746	SUBCLONAL	1	TRUE	1	0.267467568572448	2		358	704	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343529	118343529	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	53	328	2	ENST00000534358.1:c.1660del	p.Gln554SerfsTer13	p.Q554Sfs*13	ENST00000534358	NM_005933.3	552	gCc/gc	3/36	1	2	FACETS	0.633	0.539	0.736	0.633	0.539	0.736	SUBCLONAL	1	TRUE	1	0.267467568572448	2		330	626	SUCCESS
APC	324	MSKCC	GRCh37	5	112173837	112173838	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	171	415	0	ENST00000257430.4:c.2547_2548del	p.Asp849GlufsTer62	p.D849Efs*62	ENST00000257430	NM_000038.5	849	gAT/g	16/16	1	2	FACETS	0.857	0.79	0.926	1	0.991	1	CLONAL	2	TRUE	1	0.267467568572448	2		415	746	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989668	15989669	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	56	378	0	ENST00000268712.3:c.3104dup	p.Leu1036SerfsTer35	p.L1036Sfs*35	ENST00000268712	NM_006311.3	1035	cct/ccCt	23/46	0.172772193622875	2	FACETS	0.493	0.421	0.572	0.246	0.21	0.286	SUBCLONAL	1	TRUE	0	0.267467568572448	2		378	850	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123040836	123040837	+	splice_acceptor_variant	Splice_Site	DEL	AG	AG	-	novel	NA	P-0007596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	192	487	0	ENST00000355640.3:c.1302_1303del		p.X434_splice	ENST00000355640		434			0.267467568572448	1	FACETS	0.867	0.805	0.932	1	0.992	1	CLONAL	2	TRUE	0	0.267467568572448	1		487	717	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0007804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	150	208	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.988	0.91	1	0.988	0.91	1	CLONAL	1	TRUE	1	0.63	2		208	482	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0007804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	260	660	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.863	0.81	0.918	0.863	0.81	0.918	CLONAL	1	TRUE	1	0.63	2		660	956	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0007804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	100	322	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.63	2		322	286	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754826	57754826	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	203	487	0	ENST00000274289.3:c.364C>T	p.His122Tyr	p.H122Y	ENST00000274289	NM_006622.3	122	Cat/Tat	2/14	1	2	FACETS	0.956	0.89	1	0.956	0.89	1	CLONAL	1	TRUE	1	0.63	2		487	674	SUCCESS
APC	324	MSKCC	GRCh37	5	112174484	112174484	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	122	469	1	ENST00000257430.4:c.3193C>T	p.Gln1065Ter	p.Q1065*	ENST00000257430	NM_000038.5	1065	Caa/Taa	16/16	1	2	FACETS	0.765	0.695	0.838	0.765	0.695	0.838	SUBCLONAL	1	TRUE	1	0.63	2		470	506	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168969	32168969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs567483221	NA	P-0007804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	522	640	1	ENST00000375023.3:c.4064G>A	p.Arg1355Gln	p.R1355Q	ENST00000375023	NM_004557.3	1355	cGg/cAg	22/30	0.147350025802158	3	FACETS	1	0.996	1	0.716	0.686	0.746	INDETERMINATE	1	TRUE	1	0.63	3		641	1522	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600507	43600507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	424	514	0	ENST00000355710.3:c.733G>A	p.Val245Met	p.V245M	ENST00000355710	NM_020975.4	245	Gtg/Atg	4/20	0.11947075031874	1	FACETS	0.74	0.705	0.775	0.74	0.705	0.775	INDETERMINATE	1	TRUE	0	0.63	1		514	1246	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156719	20156719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	366	290	0	ENST00000379607.5:c.38G>A	p.Arg13His	p.R13H	ENST00000379607	NM_001412.3	13	cGc/cAc	2/7	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.63	1		290	542	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139804423	139804425	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs754950511	NA	P-0007804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	476	663	0	ENST00000247668.2:c.587_589del	p.Lys196del	p.K196del	ENST00000247668	NM_021138.3	194	AAG/-	6/11	1	2	FACETS	0.951	0.908	0.995	0.951	0.908	0.995	CLONAL	1	TRUE	1	0.63	2		663	1589	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119765	70119766	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0007804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	394	468	1	ENST00000245479.2:c.770_771dup	p.Pro258AlafsTer22	p.P258Afs*22	ENST00000245479	NM_000346.3	256	ggg/ggGCg	3/3	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.63	2		469	1234	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0007852-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	62	431	5	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	0.81	0.7	0.929	0.81	0.7	0.929	CLONAL	1	TRUE	1	0.271447242431812	2		436	564	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593660	55593661	+	protein_altering_variant	In_Frame_Ins	INS	CT	CT	ATGATCACAAATGGGAGTGA	novel	NA	P-0007852-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	110	484	8	ENST00000288135.5:c.1726_1727delinsATGATCACAAATGGGAGTGA	p.Leu576delinsMetIleThrAsnGlySerAsp	p.L576delinsMITNGSD	ENST00000288135	NM_000222.2	576	CTt/ATGATCACAAATGGGAGTGAt	11/21	0.271447242431812	9	FACETS	0.803	0.72	0.891	0.201	0.18	0.223	CLONAL	2	TRUE	1	0.271447242431812	9		492	984	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577035	7577036	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0007854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	80	423	0	ENST00000269305.4:c.902dup	p.Gly302ArgfsTer4	p.G302Rfs*4	ENST00000269305	NM_001126112.2	301	cca/ccCa	8/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.242093044564726	2		423	504	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818346	170818346	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1561864425	NA	P-0007854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	27	490	0	ENST00000296930.5:c.176T>C	p.Ile59Thr	p.I59T	ENST00000296930	NM_002520.6	59	aTt/aCt	3/11	0.205746872707014	3	FACETS	0.853	0.681	1	0.427	0.34	0.525	CLONAL	1	FALSE	1	0.242093044564726	3		490	293	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191482	10191497	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGAGCGATGCCTCC	AAAGAGCGATGCCTCC	-	novel	NA	P-0007854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	29	367	0	ENST00000256474.2:c.476_491del	p.Lys159ArgfsTer6	p.K159Rfs*6	ENST00000256474	NM_000551.3	159	AAAGAGCGATGCCTCCag/ag	3/3	0.242093044564726	1	FACETS	0.63	0.507	0.771	0.63	0.507	0.771	SUBCLONAL	1	FALSE	0	0.242093044564726	1		367	334	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436863	52436872	+	frameshift_variant	Frame_Shift_Del	DEL	CACACTTCAG	CACACTTCAG	-	novel	NA	P-0007854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	33	446	0	ENST00000460680.1:c.1906_1915del	p.Leu636TrpfsTer16	p.L636Wfs*16	ENST00000460680	NM_004656.3	636	CTGAAGTGTGtg/tg	15/17	0.242093044564726	1	FACETS	0.705	0.575	0.85	0.705	0.575	0.85	SUBCLONAL	1	FALSE	0	0.242093044564726	1		446	340	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007898-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	92	474	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.2	2		474	906	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0007898-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	51	360	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	0.2	2		361	470	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243668559	243668559	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007898-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	57	324	0	ENST00000263826.5:c.1432C>T	p.Arg478Ter	p.R478*	ENST00000263826	NM_005465.4	478	Cga/Tga	13/13	1	2	FACETS	0.693	0.593	0.802	0.693	0.593	0.802	SUBCLONAL	1	TRUE	1	0.2	2		324	823	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880169	151880169	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007898-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	98	436	0	ENST00000262189.6:c.5155C>T	p.Gln1719Ter	p.Q1719*	ENST00000262189	NM_170606.2	1719	Cag/Tag	35/59	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.2	2		436	980	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48586246	48586247	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007898-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	74	302	0	ENST00000342988.3:c.917dup	p.Asn306LysfsTer2	p.N306Kfs*2	ENST00000342988	NM_005359.5	305	-/A	8/12	1	2	FACETS	0.839	0.733	0.954	0.839	0.733	0.954	CLONAL	1	TRUE	1	0.2	2		302	882	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431257	49431267	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCTGGGCAG	GGCCTGGGCAG	-	novel	NA	P-0007898-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	38	191	0	ENST00000301067.7:c.9872_9882del	p.Pro3291HisfsTer6	p.P3291Hfs*6	ENST00000301067	NM_003482.3	3291	cCTGCCCAGGCC/c	34/54	1	2	FACETS	0.729	0.602	0.872	0.729	0.602	0.872	SUBCLONAL	1	TRUE	1	0.2	2		191	521	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0007902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	354	673	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.727742200403261	3	FACETS	0.97	0.94	0.998	0.97	0.94	0.998	CLONAL	3	TRUE	0	0.727742200403261	3		673	456	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651096	206651096	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868911910	NA	P-0007902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1451	182	513	0	ENST00000367120.3:c.706C>T	p.Arg236Trp	p.R236W	ENST00000367120	NM_014002.3	236	Cgg/Tgg	8/22	0.725003206244242	5	FACETS	0.641	0.589	0.695	0.128	0.117	0.139	SUBCLONAL	1	TRUE	0	0.727742200403261	5		513	1633	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847303	68847304	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0007902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	442	614	0	ENST00000261769.5:c.1228dup	p.Glu410GlyfsTer9	p.E410Gfs*9	ENST00000261769	NM_004360.3	409	tgg/tGgg	9/16	0.727742200403261	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.727742200403261	1		614	692	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934220	49934221	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0007902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	279	867	0	ENST00000296474.3:c.2286_2287delinsTT	p.Trp762_Thr763delinsCysSer	p.W762_T763delinsCS	ENST00000296474	NM_002447.2	762	tgGAcc/tgTTcc	8/20	NA	2	FACETS	0.516	0.483	0.55			1	INDETERMINATE	1	TRUE	NA	0.727742200403261	2		867	1486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0007903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	321	350	0	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	0.281439496524386	3	FACETS	1	0.975	1			1	CLONAL	3	TRUE	NA	0.281439496524386	3		350	829	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945969	17945969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758959409	NA	P-0007903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	247	423	1	ENST00000458235.1:c.1970G>A	p.Arg657Gln	p.R657Q	ENST00000458235	NM_000215.3	657	cGg/cAg	15/24	0.281439496524386	4	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	2	0.281439496524386	4		424	1109	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231584	5231584	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	84	136	0	ENST00000357368.4:c.1892G>A	p.Arg631His	p.R631H	ENST00000357368	NM_002850.3	631	cGc/cAc	14/38	0.253901572853785	2	FACETS	0.972	0.868	1	0.972	0.868	1	CLONAL	2	TRUE	0	0.281439496524386	2		136	307	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271338	26271339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0007903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1387	175	989	0	ENST00000305910.3:c.274dup	p.Ala92GlyfsTer15	p.A92Gfs*15	ENST00000305910	NM_003534.2	92	gcc/gGcc	1/1	0.250081963216568	2	FACETS	0.796	0.731	0.865	0.398	0.365	0.433	SUBCLONAL	1	TRUE	0	0.281439496524386	2		989	1562	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974796	21974805	+	frameshift_variant	Frame_Shift_Del	DEL	GCTCCATGCT	GCTCCATGCT	-	novel	NA	P-0007903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	63	134	0	ENST00000304494.5:c.22_31del	p.Ser8LeufsTer15	p.S8Lfs*15	ENST00000304494	NM_000077.4	8	AGCATGGAGCct/ct	1/3	0.281439496524386	2	FACETS	0.999	0.877	1	0.999	0.877	1	CLONAL	2	TRUE	0	0.281439496524386	2		134	224	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579315	7579316	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1267047192	NA	P-0007930-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	43	362	0	ENST00000269305.4:c.371dup	p.Cys124TrpfsTer25	p.C124Wfs*25	ENST00000269305	NM_001126112.2	124	tgc/tgGc	4/11	1	2	FACETS	0.945	0.791	1	0.945	0.791	1	CLONAL	1	TRUE	1	0.2	2		362	455	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779790	3779790	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007930-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	38	301	1	ENST00000262367.5:c.5258G>T	p.Gly1753Val	p.G1753V	ENST00000262367	NM_004380.2	1753	gGc/gTc	31/31	1	2	FACETS	0.755	0.624	0.903	0.755	0.624	0.903	CLONAL	1	TRUE	1	0.2	2		302	503	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78797006	78797025	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	GTACATGCACGCCATGTGGT	GTACATGCACGCCATGTGGT	-	novel	NA	P-0007930-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	35	237	0	ENST00000306801.3:c.1120_1136+3del		p.X374_splice	ENST00000306801	NM_020761.2	374		9/34	1	2	FACETS	0.771	0.632	0.927	0.771	0.632	0.927	CLONAL	1	TRUE	1	0.2	2		237	454	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271193	153271193	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0007971-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	214	529	0	ENST00000281708.4:c.584+1G>A		p.X195_splice	ENST00000281708	NM_033632.3	195			0.354134506648856	2	FACETS	0.961	0.898	1	0.961	0.898	1	CLONAL	2	TRUE	0	0.354134506648856	2		529	629	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88677077	88677077	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007971-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	70	669	0	ENST00000372037.3:c.862A>G	p.Ile288Val	p.I288V	ENST00000372037	NM_004329.2	288	Ata/Gta	9/13	0.354134506648856	3	FACETS	0.545	0.474	0.622	0.272	0.237	0.311	SUBCLONAL	1	TRUE	1	0.354134506648856	3		669	854	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576891	7576891	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0007971-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	290	722	0	ENST00000269305.4:c.955A>T	p.Lys319Ter	p.K319*	ENST00000269305	NM_001126112.2	319	Aag/Tag	9/11	0.289685197652108	4	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	2	0.354134506648856	4		722	1106	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578379	7578379	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1567552536	NA	P-0007971-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	164	487	0	ENST00000269305.4:c.551del	p.Asp184ValfsTer63	p.D184Vfs*63	ENST00000269305	NM_001126112.2	184	gAt/gt	5/11	0.289685197652108	4	FACETS	0.989	0.912	1	0.989	0.912	1	CLONAL	2	TRUE	2	0.354134506648856	4		487	634	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542062	187542063	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007971-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	215	534	0	ENST00000441802.2:c.5677dup	p.Tyr1893LeufsTer15	p.Y1893Lfs*15	ENST00000441802	NM_005245.3	1893	tac/tTac	10/27	0.354134506648856	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.354134506648856	2		534	564	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401001	139401001	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007981-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	321	332	0	ENST00000277541.6:c.3992G>T	p.Gly1331Val	p.G1331V	ENST00000277541	NM_017617.3	1331	gGg/gTg	24/34	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.787866666051455	2		332	733	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852092	63852093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007981-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	179	200	0	ENST00000279873.7:c.2871dup	p.Ser958IlefsTer9	p.S958Ifs*9	ENST00000279873	NM_032199.2	957	gta/gtAa	10/10	1	2	FACETS	0.981	0.914	1	0.981	0.914	1	CLONAL	1	TRUE	1	0.787866666051455	2		200	463	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0007995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	252	607	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.397077595855674	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.397077595855674	1		607	890	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0007995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	77	442	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.86	0.758	0.969	0.86	0.758	0.969	CLONAL	1	TRUE	1	0.397077595855674	2		444	451	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0007995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	152	435	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.397077595855674	2		436	758	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789591	3789591	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	137	530	1	ENST00000262367.5:c.4268del	p.Pro1423LeufsTer36	p.P1423Lfs*36	ENST00000262367	NM_004380.2	1423	cCt/ct	25/31	1	2	FACETS	0.82	0.745	0.897	0.82	0.745	0.897	CLONAL	1	TRUE	1	0.397077595855674	2		531	842	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0007995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	92	267	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.795	0.708	0.888	0.795	0.708	0.888	SUBCLONAL	1	TRUE	1	0.397077595855674	2		267	583	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	144	298	0	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	0.397077595855674	3	FACETS	1	0.961	1	0.546	0.498	0.596	CLONAL	1	TRUE	1	0.397077595855674	3		298	796	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	171	314	0	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS	0.927	0.853	1	0.927	0.853	1	CLONAL	1	TRUE	1	0.397077595855674	2		314	929	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0007995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	218	477	1	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.397077595855674	2		478	1092	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391214	89391214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs530556931	NA	P-0007995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	85	145	0	ENST00000336596.2:c.1280C>T	p.Ala427Val	p.A427V	ENST00000336596	NM_005233.5	427	gCg/gTg	5/17	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.397077595855674	2		145	398	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098591	11098591	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854197	NA	P-0007995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	160	339	0	ENST00000358026.2:c.1109G>A	p.Arg370His	p.R370H	ENST00000358026	NM_001128849.1	370	cGc/cAc	6/36	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.397077595855674	2		339	688	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310451	65310451	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	152	350	0	ENST00000342505.4:c.2237T>C	p.Val746Ala	p.V746A	ENST00000342505	NM_002227.2	746	gTg/gCg	16/25	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.397077595855674	2		350	752	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917852	29917852	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	166	480	0	ENST00000389048.3:c.816T>G	p.Cys272Trp	p.C272W	ENST00000389048	NM_004304.4	272	tgT/tgG	3/29	1	2	FACETS	0.983	0.903	1	0.983	0.903	1	CLONAL	1	TRUE	1	0.397077595855674	2		480	851	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186895	142186895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866304619	NA	P-0007995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	95	256	0	ENST00000350721.4:c.6568C>T	p.Arg2190Cys	p.R2190C	ENST00000350721	NM_001184.3	2190	Cgt/Tgt	39/47	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.397077595855674	2		256	465	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590400	67590400	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	168	404	0	ENST00000274335.5:c.1462A>G	p.Asn488Asp	p.N488D	ENST00000274335		488	Aat/Gat	11/15	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.397077595855674	2		404	838	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554253	106554253	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	163	297	0	ENST00000369096.4:c.1781T>C	p.Leu594Pro	p.L594P	ENST00000369096	NM_001198.3	594	cTg/cCg	6/7	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.397077595855674	2		297	776	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026954	6026954	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1168365577	NA	P-0007995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	25	38	0	ENST00000265849.7:c.1442C>A	p.Pro481His	p.P481H	ENST00000265849	NM_000535.5	481	cCc/cAc	11/15	0.397077595855674	3	FACETS	1	0.877	1	0.572	0.457	0.7	CLONAL	1	TRUE	1	0.397077595855674	3		38	132	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434931	49434931	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	97	183	0	ENST00000301067.7:c.6622C>T	p.Gln2208Ter	p.Q2208*	ENST00000301067	NM_003482.3	2208	Cag/Tag	31/54	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.397077595855674	2		183	431	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865159	57865159	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	327	814	0	ENST00000228682.2:c.2636C>A	p.Pro879His	p.P879H	ENST00000228682	NM_005269.2	879	cCt/cAt	12/12	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.397077595855674	2		814	1546	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562103	21562103	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1218	316	780	2	ENST00000382592.4:c.1816A>G	p.Met606Val	p.M606V	ENST00000382592	NM_014572.2	606	Atg/Gtg	4/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.397077595855674	2		782	1534	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105240257	105240257	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781232725	NA	P-0007995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	161	417	0	ENST00000349310.3:c.694G>A	p.Gly232Arg	p.G232R	ENST00000349310	NM_001014432.1	232	Ggg/Agg	9/15	0.397077595855674	1	FACETS	0.973	0.895	1	0.973	0.895	1	CLONAL	1	TRUE	0	0.397077595855674	1		417	668	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684342	29684342	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	225	579	0	ENST00000356175.3:c.7862A>G	p.Tyr2621Cys	p.Y2621C	ENST00000356175	NM_000267.3	2621	tAc/tGc	53/57	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.397077595855674	2		579	1016	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225231	53225231	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	216	558	0	ENST00000375401.3:c.2987A>C	p.Lys996Thr	p.K996T	ENST00000375401	NM_004187.3	996	aAg/aCg	20/26	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.397077595855674	2		558	1075	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918967	76918967	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781810958	NA	P-0007995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	308	684	1	ENST00000373344.5:c.4024C>T	p.Arg1342Trp	p.R1342W	ENST00000373344	NM_000489.3	1342	Cgg/Tgg	12/35	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.397077595855674	2		685	1272	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637537	52637538	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0007995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	178	512	0	ENST00000394830.3:c.2778_2779del	p.Glu927SerfsTer2	p.E927Sfs*2	ENST00000394830	NM_018313.4	926	agAGaa/agaa	18/30	0.397077595855674	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.397077595855674	1		512	702	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37056036	37056037	+	splice_donor_variant	Splice_Site	INS	-	-	T	rs267607791	NA	P-0007995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	111	325	0	ENST00000231790.2:c.790+2dup		p.X264_splice	ENST00000231790	NM_000249.3	264			0.397077595855674	1	FACETS	0.842	0.76	0.928	0.842	0.76	0.928	CLONAL	1	TRUE	0	0.397077595855674	1		325	532	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660075	227660075	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462380251	NA	P-0007995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	140	250	0	ENST00000305123.5:c.3380del	p.Gly1127AlafsTer12	p.G1127Afs*12	ENST00000305123	NM_005544.2	1127	gGc/gc	1/2	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.397077595855674	2		250	676	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112253	115112253	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	35	62	0	ENST00000257566.3:c.1487del	p.Gly496AlafsTer136	p.G496Afs*136	ENST00000257566	NM_016569.3	496	gGc/gc	7/8	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.397077595855674	2		62	145	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14026116	14026116	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	150	433	0	ENST00000311895.7:c.1081del	p.Met361TrpfsTer15	p.M361Wfs*15	ENST00000311895	NM_005236.2	359	gAa/ga	6/11	1	2	FACETS	0.894	0.817	0.974	0.894	0.817	0.974	CLONAL	1	TRUE	1	0.397077595855674	2		433	845	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155779	106155779	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	106	285	0	ENST00000380013.4:c.685del	p.Thr229HisfsTer21	p.T229Hfs*21	ENST00000380013	NM_001127208.2	227	gAa/ga	3/11	1	2	FACETS	0.742	0.665	0.823	0.742	0.665	0.823	SUBCLONAL	1	TRUE	1	0.397077595855674	2		285	720	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0007995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	224	443	0	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.397077595855674	2		443	1076	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453138	140453139	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTA	rs727502902	NA	P-0007998-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	42	389	0	ENST00000288602.6:c.1794_1796dup	p.Thr599dup	p.T599dup	ENST00000288602	NM_004333.4	599	aca/acTACa	15/18	1	2	FACETS	0.394	0.328	0.468	0.394	0.328	0.468	SUBCLONAL	1	FALSE	1	0.3	2		389	710	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0008039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	9	673	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.17130927654462	3	FACETS	0.514	0.34	0.736	0.257	0.17	0.368	SUBCLONAL	1	TRUE	1	0.17130927654462	3		673	222	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955087	93955087	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	44	409	0	ENST00000369303.4:c.2811G>T	p.Met937Ile	p.M937I	ENST00000369303	NM_004440.3	937	atG/atT	16/17	1	2	FACETS	0.604	0.504	0.714	0.604	0.504	0.714	SUBCLONAL	1	TRUE	1	0.17130927654462	2		409	851	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106199	27106200	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0008039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	110	197	0	ENST00000324856.7:c.5811dup	p.Lys1938GlnfsTer7	p.K1938Qfs*7	ENST00000324856	NM_006015.4	1937	agc/agCc	20/20	0.17130927654462	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.17130927654462	2		197	525	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	226	374	0				ENST00000310581	NM_198253.2	-/1132			0.840366284692977	5	FACETS	0.849	0.794	0.905	0.566	0.529	0.604	CLONAL	2	TRUE	2	0.840366284692977	5		374	716	SUCCESS
APC	324	MSKCC	GRCh37	5	112175749	112175750	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0008133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	427	323	0	ENST00000257430.4:c.4459dup	p.Thr1487AsnfsTer27	p.T1487Nfs*27	ENST00000257430	NM_000038.5	1486	-/A	16/16	NA	2	FACETS	0.964	0.939	0.988			1	INDETERMINATE	2	TRUE	NA	0.840366284692977	2		323	527	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0008133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	643	617	2	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.840366284692977	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.840366284692977	3		619	1011	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251907	153251907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	292	528	2	ENST00000281708.4:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000281708	NM_033632.3	367	Cga/Tga	7/12	1	2	FACETS	0.942	0.891	0.993	0.942	0.891	0.993	CLONAL	1	TRUE	1	0.840366284692977	2		530	738	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557639	95557639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775912475	NA	P-0008133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	599	463	0	ENST00000393063.1:c.5428G>A	p.Asp1810Asn	p.D1810N	ENST00000393063	NM_030621.3	1810	Gat/Aat	26/28	0.77596329075695	3	FACETS	1	0.972	1			1	CLONAL	2	TRUE	NA	0.840366284692977	3		463	1009	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0008133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	353	288	0	ENST00000269305.4:c.97-1G>C		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.840366284692977	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.840366284692977	2		288	395	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729175	66729175	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121908596	NA	P-0008133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	487	353	0	ENST00000307102.5:c.383G>T	p.Gly128Val	p.G128V	ENST00000307102	NM_002755.3	128	gGc/gTc	3/11	0.840366284692977	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.840366284692977	2		353	563	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78938074	78938074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371220837	NA	P-0008133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	591	447	0	ENST00000306801.3:c.3952G>A	p.Val1318Met	p.V1318M	ENST00000306801	NM_020761.2	1318	Gtg/Atg	34/34	0.840366284692977	3	FACETS	0.991	0.959	1	0.991	0.959	1	CLONAL	2	TRUE	1	0.840366284692977	3		447	1008	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101830	11101830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	170	406	0	ENST00000358026.2:c.1250G>A	p.Arg417His	p.R417H	ENST00000358026	NM_001128849.1	417	cGc/cAc	8/36	0.840366284692977	3	FACETS	0.814	0.75	0.88	0.407	0.375	0.44	CLONAL	1	TRUE	1	0.840366284692977	3		406	706	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099253	4099255	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs763469132	NA	P-0008133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	572	437	0	ENST00000262948.5:c.863_865del	p.Glu288del	p.E288del	ENST00000262948	NM_030662.3	288	gAAGga/gga	7/11	0.840366284692977	3	FACETS	0.951	0.92	0.983	0.951	0.92	0.983	CLONAL	2	TRUE	1	0.840366284692977	3		437	1016	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0008159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	19	360	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.899	0.699	1	1	0.933	1	CLONAL	2	FALSE	1	0.260817834305508	2		361	81	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911146	29911146	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41542119	NA	P-0008159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	12	312	0	ENST00000376809.5:c.445G>A	p.Ala149Thr	p.A149T	ENST00000376809	NM_002116.7	149	Gcc/Acc	3/8	0.260817834305508	4	FACETS	0.763	0.545	1	0.763	0.545	1	CLONAL	2	FALSE	2	0.260817834305508	4		312	76	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169934	32169934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759022399	NA	P-0008159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	19	699	0	ENST00000375023.3:c.3674G>A	p.Arg1225Gln	p.R1225Q	ENST00000375023	NM_004557.3	1225	cGg/cAg	21/30	0.260817834305508	1	FACETS	0.85	0.651	1	0.85	0.651	1	CLONAL	1	FALSE	0	0.260817834305508	1		699	149	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609338	81609338	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1368060812	NA	P-0008159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	12	628	0	ENST00000298171.2:c.939del	p.Lys313AsnfsTer3	p.K313Nfs*3	ENST00000298171	NM_000369.2	312	agA/ag	10/10	0.170859704107527	1	FACETS	0.748	0.53	1	0.748	0.53	1	CLONAL	1	FALSE	0	0.260817834305508	1		628	107	SUCCESS
APC	324	MSKCC	GRCh37	5	112174583	112174584	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs1064794228	NA	P-0008159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	14	587	0	ENST00000257430.4:c.3295_3296del	p.Val1099PhefsTer19	p.V1099Ffs*19	ENST00000257430	NM_000038.5	1098	TGt/t	16/16	1	2	FACETS	0.985	0.72	1	0.985	0.72	1	CLONAL	1	FALSE	1	0.260817834305508	2		587	109	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105927	27105928	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0008159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	18	365	0	ENST00000324856.7:c.5540dup	p.Gly1848TrpfsTer6	p.G1848Wfs*6	ENST00000324856	NM_006015.4	1846	-/G	20/20	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	FALSE	1	0.260817834305508	2		365	116	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061264	38061264	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008211-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	250	384	0	ENST00000250448.2:c.725C>T	p.Ser242Phe	p.S242F	ENST00000250448	NM_004496.3	242	tCc/tTc	2/2	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.442796556730276	2		384	882	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100687	8100688	+	protein_altering_variant	In_Frame_Ins	INS	AC	AC	CCTGCCTGTTGTGAGCTGCTCTACGTGCCCTACGTGCT	novel	NA	P-0008211-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	164	365	0	ENST00000346208.3:c.661_662delinsCCTGCCTGTTGTGAGCTGCTCTACGTGCCCTACGTGCT	p.Thr221delinsProAlaCysCysGluLeuLeuTyrValProTyrValLeu	p.T221delinsPACCELLYVPYVL	ENST00000346208		221	ACc/CCTGCCTGTTGTGAGCTGCTCTACGTGCCCTACGTGCTc	3/6	1	2	FACETS	0.874	0.802	0.948	0.874	0.802	0.948	CLONAL	1	TRUE	1	0.442796556730276	2		365	848	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008234-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	18	374	0				ENST00000310581	NM_198253.2	-/1132			0.0766864593853853	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		374	88	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0008234-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	61	942	2	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		944	1126	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028824	47028824	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0008234-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	19	228	0	ENST00000377604.3:c.128C>G	p.Ser43Ter	p.S43*	ENST00000377604	NM_001204468.1	43	tCa/tGa	3/24	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		228	346	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44911033	44911034	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0008234-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	106	292	0	ENST00000377967.4:c.735dup	p.Gln247ThrfsTer16	p.Q247Tfs*16	ENST00000377967	NM_021140.2	245	gtc/gtCc	9/29	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		292	461	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0008260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	73	588	1	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		589	923	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584513	48584514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs377767334	NA	P-0008260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	31	264	1	ENST00000342988.3:c.692dup	p.Ser232GlnfsTer3	p.S232Qfs*3	ENST00000342988	NM_005359.5	229	ctg/ctGg	6/12	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		265	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0008260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	41	360	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		361	549	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0008271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	227	298	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.561616718452234	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.561616718452234	1		298	413	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0008271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	26	360	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.561616718452234	1	FACETS	0.151	0.119	0.188	0.151	0.119	0.188	SUBCLONAL	1	TRUE	0	0.561616718452234	1		360	440	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563465	87563465	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs202136187	NA	P-0008271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	26	312	0	ENST00000277120.3:c.1853A>G	p.Lys618Arg	p.K618R	ENST00000277120		618	aAg/aGg	16/19	0.561616718452234	1	FACETS	0.224	0.178	0.277	0.224	0.178	0.277	SUBCLONAL	1	TRUE	0	0.561616718452234	1		312	297	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63661474	63661474	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs140010870	NA	P-0008271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	74	330	1	ENST00000279873.7:c.6G>T	p.Glu2Asp	p.E2D	ENST00000279873	NM_032199.2	2	gaG/gaT	1/10	0.265200862287082	6	FACETS	0.735	0.643	0.835			1	INDETERMINATE	1	TRUE	NA	0.561616718452234	6		331	761	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5239002	5239002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775100072	NA	P-0008271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	29	485	0	ENST00000357368.4:c.1777C>T	p.Arg593Cys	p.R593C	ENST00000357368	NM_002850.3	593	Cgc/Tgc	13/38	0.561616718452234	1	FACETS	0.28	0.225	0.342	0.28	0.225	0.342	SUBCLONAL	1	TRUE	0	0.561616718452234	1		485	265	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791802	42791802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	47	342	1	ENST00000575354.2:c.688G>A	p.Val230Ile	p.V230I	ENST00000575354	NM_015125.3	230	Gtc/Atc	5/20	0.208674522388022	5	FACETS	0.448	0.377	0.527			1	INDETERMINATE	1	TRUE	NA	0.561616718452234	5		343	688	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791971	42791972	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0008271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	348	472	0	ENST00000575354.2:c.778dup	p.His260ProfsTer55	p.H260Pfs*55	ENST00000575354	NM_015125.3	259	gcc/gCcc	6/20	0.208674522388022	5	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.561616718452234	5		472	922	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0008287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	77	208	1	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.941	0.826	1	0.941	0.826	1	CLONAL	1	TRUE	1	0.218677472971595	2		209	748	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738275	133738276	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	86	278	0	ENST00000318560.5:c.676dup	p.Tyr226LeufsTer72	p.Y226Lfs*72	ENST00000318560	NM_005157.4	225	-/T	4/11	1	2	FACETS	0.96	0.849	1	0.96	0.849	1	CLONAL	1	TRUE	1	0.218677472971595	2		278	819	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099884	27099884	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	78	239	0	ENST00000324856.7:c.3765del	p.Met1256TrpfsTer13	p.M1256Wfs*13	ENST00000324856	NM_006015.4	1255	Ggg/gg	15/20	0.218677472971595	1	FACETS	0.951	0.836	1	0.951	0.836	1	CLONAL	1	TRUE	0	0.218677472971595	1		239	668	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0008357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	92	586	1	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	0.897	0.801	0.999	0.897	0.801	0.999	CLONAL	1	TRUE	1	0.440234434584981	2		587	466	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890149	76890150	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	74	490	0	ENST00000373344.5:c.4744dup	p.Thr1582AsnfsTer19	p.T1582Nfs*19	ENST00000373344	NM_000489.3	1582	aca/aAca	17/35	0.169652814509315	2	FACETS	0.784	0.689	0.885			1	INDETERMINATE	1	TRUE	NA	0.440234434584981	2		490	429	SUCCESS
APC	324	MSKCC	GRCh37	5	112175148	112175148	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	36	249	0	ENST00000257430.4:c.3859del	p.Ile1287Ter	p.I1287*	ENST00000257430	NM_000038.5	1286	gAa/ga	16/16	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.440234434584981	2		249	148	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0008370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	864	340	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.561701122687796	3	FACETS	1	0.995	1			1	CLONAL	3	TRUE	NA	0.561701122687796	3		340	1235	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231773	36231773	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1569061762	NA	P-0008370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	133	545	1	ENST00000300305.3:c.611G>A	p.Arg204Gln	p.R204Q	ENST00000300305		204	cGa/cAa	5/8	1	2	FACETS	0.465	0.422	0.511	0.465	0.422	0.511	SUBCLONAL	1	TRUE	1	0.561701122687796	2		546	1018	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098957	178098957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	118	400	0	ENST00000397062.3:c.88C>T	p.Leu30Phe	p.L30F	ENST00000397062	NM_006164.4	30	Ctt/Ttt	2/5	1	2	FACETS	0.528	0.477	0.583	0.528	0.477	0.583	SUBCLONAL	1	TRUE	1	0.561701122687796	2		400	795	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435312	56435312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139405076	NA	P-0008370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	110	254	0	ENST00000407977.2:c.1825C>T	p.Arg609Trp	p.R609W	ENST00000407977		609	Cgg/Tgg	9/10	1	2	FACETS	0.992	0.898	1	0.992	0.898	1	CLONAL	1	TRUE	1	0.561701122687796	2		254	395	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482858	67482858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	90	361	0	ENST00000327367.4:c.1262G>A	p.Cys421Tyr	p.C421Y	ENST00000327367	NM_005902.3	421	tGt/tAt	9/9	1	2	FACETS	0.575	0.511	0.643	0.575	0.511	0.643	SUBCLONAL	1	TRUE	1	0.561701122687796	2		361	557	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023637	27023638	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTCCAAGCCGC	novel	NA	P-0008370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	69	268	0	ENST00000324856.7:c.743_744insTTCCAAGCCGC	p.Ser255ArgfsTer112	p.S255Rfs*112	ENST00000324856	NM_006015.4	248	ggc/ggTTCCAAGCCGCc	1/20	0.561701122687796	1	FACETS	0.526	0.461	0.595	0.526	0.461	0.595	SUBCLONAL	1	TRUE	0	0.561701122687796	1		268	336	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171672	36171672	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	103	442	0	ENST00000300305.3:c.893del	p.Pro298GlnfsTer13	p.P298Qfs*13	ENST00000300305		298	cCa/ca	7/8	1	2	FACETS	0.484	0.433	0.538	0.484	0.433	0.538	SUBCLONAL	1	TRUE	1	0.561701122687796	2		442	758	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0008375-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	680	279	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	1	0.793067873567285	2		279	757	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857910	9857910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008375-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	233	352	0	ENST00000330684.3:c.3491C>T	p.Thr1164Met	p.T1164M	ENST00000330684	NM_001134407.1	1164	aCg/aTg	13/13	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.793067873567285	2		352	571	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198264987	198264987	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008375-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	449	331	0	ENST00000335508.6:c.2890A>G	p.Thr964Ala	p.T964A	ENST00000335508	NM_012433.2	964	Act/Gct	19/25	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.793067873567285	2		331	974	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341878	8341878	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008375-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	504	527	0	ENST00000356435.5:c.4762A>G	p.Met1588Val	p.M1588V	ENST00000356435		1588	Atg/Gtg	29/35	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.793067873567285	2		527	1161	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149003	119149003	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008375-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	360	269	0	ENST00000264033.4:c.1223G>C	p.Trp408Ser	p.W408S	ENST00000264033	NM_005188.3	408	tGg/tCg	8/16	0.793412312818224	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.793067873567285	1		269	427	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687182	37687182	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008375-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	240	307	0	ENST00000447079.4:c.4086G>C	p.Leu1362Phe	p.L1362F	ENST00000447079	NM_015083.1	1362	ttG/ttC	14/14	0.793412312818224	1	FACETS	0.546	0.513	0.58	0.546	0.513	0.58	SUBCLONAL	1	TRUE	0	0.793067873567285	1		307	669	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687370	37687370	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008375-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	232	291	0	ENST00000447079.4:c.4274G>A	p.Gly1425Glu	p.G1425E	ENST00000447079	NM_015083.1	1425	gGa/gAa	14/14	0.793412312818224	1	FACETS	0.52	0.487	0.553	0.52	0.487	0.553	SUBCLONAL	1	TRUE	0	0.793067873567285	1		291	679	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687502	37687502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008375-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	150	217	0	ENST00000447079.4:c.4406G>A	p.Gly1469Glu	p.G1469E	ENST00000447079	NM_015083.1	1469	gGa/gAa	14/14	0.793412312818224	1	FACETS	0.489	0.45	0.529	0.489	0.45	0.529	SUBCLONAL	1	TRUE	0	0.793067873567285	1		217	467	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687526	37687526	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008375-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	140	191	0	ENST00000447079.4:c.4430G>T	p.Arg1477Ile	p.R1477I	ENST00000447079	NM_015083.1	1477	aGa/aTa	14/14	0.793412312818224	1	FACETS	0.473	0.434	0.514	0.473	0.434	0.514	SUBCLONAL	1	TRUE	0	0.793067873567285	1		191	450	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687417	37687417	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	AA	novel	NA	P-0008375-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	175	279	0	ENST00000447079.4:c.4321delinsAA	p.Gly1441LysfsTer72	p.G1441Kfs*72	ENST00000447079	NM_015083.1	1441	Ggg/AAgg	14/14	0.793412312818224	1	FACETS	0.486	0.45	0.523	0.486	0.45	0.523	SUBCLONAL	1	TRUE	0	0.793067873567285	1		279	548	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0008443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	168	379	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.184944345951244	3	FACETS	0.905	0.839	0.971	1	0.988	1	INDETERMINATE	3	TRUE	1	0.309414849066666	3		379	462	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220705	1220706	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0008443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	81	318	0	ENST00000326873.7:c.727dup	p.Val243GlyfsTer23	p.V243Gfs*23	ENST00000326873	NM_000455.4	241	-/G	5/10	0.309414849066666	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.309414849066666	1		318	373	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402702	20402702	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	80	293	0	ENST00000346618.3:c.239C>T	p.Ala80Val	p.A80V	ENST00000346618	NM_001949.4	80	gCc/gTc	1/7	0.184944345951244	3	FACETS	1	0.972	1	0.674	0.596	0.757	INDETERMINATE	1	TRUE	1	0.309414849066666	3		293	443	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446398	70446398	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	95	324	0	ENST00000373644.4:c.5338C>T	p.Arg1780Ter	p.R1780*	ENST00000373644	NM_030625.2	1780	Cga/Tga	11/12	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.309414849066666	2		324	533	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100988	41100988	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	36	218	0	ENST00000373198.4:c.1368G>T	p.Met456Ile	p.M456I	ENST00000373198	NM_133170.3	456	atG/atT	8/32	1	2	FACETS	0.684	0.564	0.819	0.684	0.564	0.819	SUBCLONAL	1	TRUE	1	0.309414849066666	2		218	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577093	7577094	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGG	novel	NA	P-0008443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	118	362	0	ENST00000269305.4:c.844_845insCCC	p.Asp281_Arg282insPro	p.D281_R282insP	ENST00000269305	NM_001126112.2	282	cgg/cCCCgg	8/11	0.168667432789079	2	FACETS	0.831	0.754	0.911	0.831	0.754	0.911	INDETERMINATE	2	TRUE	0	0.309414849066666	2		362	459	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0008449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	76	384	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.255411147537564	3	FACETS	0.888	0.783	0.999	0.888	0.783	0.999	CLONAL	2	TRUE	1	0.255411147537564	3		384	378	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112153	115112154	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0008449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	56	308	0	ENST00000257566.3:c.1586dup	p.Ala530ArgfsTer162	p.A530Rfs*162	ENST00000257566	NM_016569.3	529	ggc/ggGc	7/8	1	2	FACETS	0.947	0.813	1	0.947	0.813	1	CLONAL	1	TRUE	1	0.255411147537564	2		308	463	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0008485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	184	435	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.65448442689347	1	FACETS	0.984	0.922	1	0.984	0.922	1	CLONAL	1	TRUE	0	0.657250225965808	1		436	382	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204511954	204511954	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	148	360	0	ENST00000367182.3:c.554G>T	p.Arg185Met	p.R185M	ENST00000367182	NM_001278516.1	185	aGg/aTg	8/11	0.657250225965808	3	FACETS	0.874	0.8	0.95	0.437	0.4	0.475	CLONAL	1	TRUE	1	0.657250225965808	3		360	685	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873449	136873449	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	374	752	0	ENST00000241393.3:c.49G>T	p.Gly17Cys	p.G17C	ENST00000241393	NM_003467.2	17	Ggc/Tgc	2/2	1	2	FACETS	0.904	0.858	0.951	0.904	0.858	0.951	CLONAL	1	TRUE	1	0.657250225965808	2		752	1259	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120524	94120524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	282	675	1	ENST00000369303.4:c.527C>T	p.Pro176Leu	p.P176L	ENST00000369303	NM_004440.3	176	cCt/cTt	3/17	1	2	FACETS	0.861	0.81	0.913	0.861	0.81	0.913	CLONAL	1	TRUE	1	0.657250225965808	2		676	997	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220382	1220382	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	155	356	0	ENST00000326873.7:c.475C>T	p.Gln159Ter	p.Q159*	ENST00000326873	NM_000455.4	159	Cag/Tag	4/10	0.657250225965808	1	FACETS	0.858	0.796	0.921	0.858	0.796	0.921	CLONAL	1	TRUE	0	0.657250225965808	1		356	369	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610160	10610160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	34	383	0	ENST00000171111.5:c.550G>A	p.Ala184Thr	p.A184T	ENST00000171111	NM_203500.1	184	Gcc/Acc	2/6	0.657250225965808	1	FACETS	0.144	0.117	0.174	0.144	0.117	0.174	SUBCLONAL	1	TRUE	0	0.657250225965808	1		383	484	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045501	47045501	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	252	229	1	ENST00000377604.3:c.2471del	p.Lys824SerfsTer23	p.K824Sfs*23	ENST00000377604	NM_001204468.1	823	gAa/ga	22/24	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.657250225965808	1		230	438	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945045	151945045	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	TT	novel	NA	P-0008485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	30	220	0	ENST00000262189.6:c.2474delinsAA	p.Met825LysfsTer3	p.M825Kfs*3	ENST00000262189	NM_170606.2	825	aTg/aAAg	14/59	1	2	FACETS	0.288	0.232	0.351	0.288	0.232	0.351	SUBCLONAL	1	TRUE	1	0.657250225965808	2		220	317	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0008494-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	277	310	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.390429111466485	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.419864534304187	2		310	615	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602493	10602493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008494-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	236	261	2	ENST00000171111.5:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000171111	NM_203500.1	362	cGg/cAg	3/6	0.419864534304187	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.419864534304187	2		263	492	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678783	52678784	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008494-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	294	390	0	ENST00000394830.3:c.835dup	p.Ile279AsnfsTer8	p.I279Nfs*8	ENST00000394830	NM_018313.4	279	ata/aAta	9/30	0.419864534304187	2	FACETS	0.901	0.852	0.951	0.901	0.852	0.951	CLONAL	2	TRUE	0	0.419864534304187	2		390	777	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089611	27089611	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008494-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	278	421	0	ENST00000324856.7:c.2567G>A	p.Gly856Glu	p.G856E	ENST00000324856	NM_006015.4	856	gGg/gAg	8/20	0.38072628490245	3	FACETS	0.863	0.812	0.915	0.863	0.812	0.915	CLONAL	2	TRUE	1	0.419864534304187	3		421	928	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47600638	47600638	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768335421	NA	P-0008494-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	460	477	0	ENST00000263735.4:c.113G>A	p.Cys38Tyr	p.C38Y	ENST00000263735	NM_002354.2	38	tGc/tAc	2/9	0.419864534304187	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.419864534304187	2		477	1039	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436821	52436821	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008494-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	406	514	0	ENST00000460680.1:c.1957G>T	p.Glu653Ter	p.E653*	ENST00000460680	NM_004656.3	653	Gag/Tag	15/17	0.419864534304187	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.419864534304187	2		514	908	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383675	84383675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008494-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	449	542	0	ENST00000321945.7:c.1177G>A	p.Glu393Lys	p.E393K	ENST00000321945	NM_139076.2	393	Gaa/Aaa	9/9	0.419864534304187	2	FACETS	0.978	0.935	1	0.978	0.935	1	CLONAL	2	TRUE	0	0.419864534304187	2		542	1094	SUCCESS
APC	324	MSKCC	GRCh37	5	112154801	112154801	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs863224455	NA	P-0008494-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	276	371	0	ENST00000257430.4:c.1072C>T	p.Gln358Ter	p.Q358*	ENST00000257430	NM_000038.5	358	Cag/Tag	10/16	0.419864534304187	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.419864534304187	2		371	651	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912653	32912653	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008494-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1182	425	744	0	ENST00000380152.3:c.4161A>C	p.Leu1387Phe	p.L1387F	ENST00000380152		1387	ttA/ttC	11/27	0.148844384662875	4	FACETS	0.894	0.851	0.939	0.894	0.851	0.939	INDETERMINATE	2	TRUE	2	0.419864534304187	4		744	1607	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	103	374	0				ENST00000310581	NM_198253.2	-/1132			0.165312452230026	0	FACETS	0.486	0.44	0.535			1	INDETERMINATE	1	TRUE	0	0.559816976801132	0		374	333	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0008532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	123	134	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.260718325900675	1	FACETS	0.734	0.669	0.802	0.734	0.669	0.802	INDETERMINATE	1	TRUE	0	0.559816976801132	1		134	431	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238983	5238983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs554924044	NA	P-0008532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	88	438	0	ENST00000357368.4:c.1796C>T	p.Pro599Leu	p.P599L	ENST00000357368	NM_002850.3	599	cCg/cTg	13/38	1	2	FACETS	0.384	0.34	0.432	0.384	0.34	0.432	SUBCLONAL	1	TRUE	1	0.559816976801132	2		438	818	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937741	44937742	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	193	212	0	ENST00000377967.4:c.2931dup	p.Lys978Ter	p.K978*	ENST00000377967	NM_021140.2	977	ctt/cTtt	19/29	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.559816976801132	1		212	411	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254614	1254614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201330213	NA	P-0008570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	120	267	0	ENST00000310581.5:c.3164C>T	p.Ser1055Leu	p.S1055L	ENST00000310581	NM_198253.2	1055	tCg/tTg	15/16	NA	2	FACETS	0.994	0.901	1			1	INDETERMINATE	1	TRUE	NA	0.431210182899027	2		267	560	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111467	8111468	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0008570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	155	360	0	ENST00000346208.3:c.954dup	p.Asn319GlufsTer33	p.N319Efs*33	ENST00000346208		318	gcg/gcGg	5/6	1	2	FACETS	0.945	0.866	1	0.945	0.866	1	CLONAL	1	TRUE	1	0.431210182899027	2		360	761	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242448	55242449	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTCCCGTCGCTATCAAGG	novel	NA	P-0008602-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1290	517	553	0	ENST00000275493.2:c.2219_2236dup	p.Lys745_Glu746insValProValAlaIleLys	p.K745_E746insVPVAIK	ENST00000275493	NM_005228.3	740	att/aTTCCCGTCGCTATCAAGGtt	19/28	0.275938640001709	6	FACETS	1	0.986	1			1	CLONAL	3	TRUE	NA	0.275938640001709	6		553	1807	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121912651	NA	P-0008602-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	225	590	0	ENST00000269305.4:c.742C>G	p.Arg248Gly	p.R248G	ENST00000269305	NM_001126112.2	248	Cgg/Ggg	7/11	0.253353574008677	2	FACETS	0.816	0.76	0.874	0.816	0.76	0.874	CLONAL	2	TRUE	0	0.275938640001709	2		590	999	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715389	117715389	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008602-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	57	425	0	ENST00000368508.3:c.1100G>T	p.Gly367Val	p.G367V	ENST00000368508	NM_002944.2	367	gGa/gTa	10/43	1	2	FACETS	0.574	0.491	0.664	0.574	0.491	0.664	SUBCLONAL	1	TRUE	1	0.275938640001709	2		425	720	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246021942	246021942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1320812485	NA	P-0008602-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	72	596	1	ENST00000388985.4:c.932C>T	p.Ala311Val	p.A311V	ENST00000388985		311	gCa/gTa	10/12	1	2	FACETS	0.486	0.423	0.555	0.486	0.423	0.555	SUBCLONAL	1	TRUE	1	0.275938640001709	2		597	1073	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0008651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	38	302	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.160476842360885	0	FACETS	0.467	0.39	0.552			1	INDETERMINATE	1	TRUE	0	0.438845834069069	0		302	208	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0008651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	81	331	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.412605350115228	1	FACETS	0.951	0.847	1	0.951	0.847	1	CLONAL	1	TRUE	0	0.438845834069069	1		331	303	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420315	88420315	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773244598	NA	P-0008651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	33	209	1	ENST00000360948.2:c.2371C>T	p.Arg791Trp	p.R791W	ENST00000360948	NM_001012338.2	791	Cgg/Tgg	19/19	0.438845834069069	1	FACETS	0.495	0.406	0.595	0.495	0.406	0.595	SUBCLONAL	1	TRUE	0	0.438845834069069	1		210	237	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516908	187516908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	133	369	0	ENST00000441802.2:c.13073C>T	p.Ala4358Val	p.A4358V	ENST00000441802	NM_005245.3	4358	gCc/gTc	26/27	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.438845834069069	2		369	521	SUCCESS
APC	324	MSKCC	GRCh37	5	112174096	112174096	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs137854575	NA	P-0008651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	44	322	0	ENST00000257430.4:c.2805C>G	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	taC/taG	16/16	0.160476842360885	0	FACETS	0.389	0.328	0.456			1	INDETERMINATE	1	TRUE	0	0.438845834069069	0		322	289	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265596	152265596	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	60	213	0	ENST00000206249.3:c.1049C>A	p.Ala350Glu	p.A350E	ENST00000206249	NM_000125.3	350	gCa/gAa	4/8	NA	2	FACETS	1	0.917	1			1	INDETERMINATE	1	TRUE	NA	0.438845834069069	2		213	255	SUCCESS
APC	324	MSKCC	GRCh37	5	112154680	112154681	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	54	257	0	ENST00000257430.4:c.953dup	p.Leu318PhefsTer9	p.L318Ffs*9	ENST00000257430	NM_000038.5	317	-/T	10/16	0.160476842360885	0	FACETS	0.691	0.598	0.788			1	INDETERMINATE	1	TRUE	0	0.438845834069069	0		257	200	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0008712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	206	409	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	0.600286399605694	4	FACETS	1	0.986	1	0.619	0.576	0.664	CLONAL	1	FALSE	2	0.68972484499015	4		409	815	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	84	588	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.362199078530422	1	FACETS	0.636	0.565	0.712	0.636	0.565	0.712	SUBCLONAL	1	TRUE	0	0.479114626851071	1		589	419	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	140	442	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.9	0.822	0.982	0.9	0.822	0.982	CLONAL	1	TRUE	1	0.479114626851071	2		444	649	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	82	208	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.774	0.686	0.868	0.774	0.686	0.868	SUBCLONAL	1	TRUE	1	0.479114626851071	2		208	442	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	253	512	4	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	0.826	0.772	0.883	0.826	0.772	0.883	CLONAL	1	TRUE	1	0.479114626851071	2		516	1278	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	112	296	2	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.479114626851071	2		298	467	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058747	180058748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755445139	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	211	467	0	ENST00000261937.6:c.89dup	p.Thr31AspfsTer15	p.T31Dfs*15	ENST00000261937	NM_182925.4	30	ccg/ccCg	2/30	1	2	FACETS	0.814	0.755	0.875	0.814	0.755	0.875	CLONAL	1	TRUE	1	0.479114626851071	2		467	1082	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533939	63533940	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs771001164	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	80	249	0	ENST00000307078.5:c.1214_1215del	p.Glu405GlyfsTer56	p.E405Gfs*56	ENST00000307078	NM_004655.3	405	gAG/g	6/11	1	2	FACETS	0.886	0.785	0.993	0.886	0.785	0.993	CLONAL	1	TRUE	1	0.479114626851071	2		249	377	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913252	39913253	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs797044647	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	284	313	0	ENST00000378444.4:c.4862dup	p.Gly1622ArgfsTer7	p.G1622Rfs*7	ENST00000378444	NM_001123385.1	1621	cca/ccCa	14/15	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.479114626851071	1		313	676	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372389	55372389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1274955948	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	63	491	0	ENST00000297316.4:c.1079G>A	p.Arg360His	p.R360H	ENST00000297316	NM_022454.3	360	cGc/cAc	2/2	1	2	FACETS	0.251	0.216	0.289	0.251	0.216	0.289	SUBCLONAL	1	TRUE	1	0.479114626851071	2		491	1047	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729962	30729962	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs104893819	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	146	228	0	ENST00000295754.5:c.1483C>T	p.Arg495Ter	p.R495*	ENST00000295754	NM_003242.5	495	Cga/Tga	6/7	1	2	FACETS	0.868	0.794	0.946	0.868	0.794	0.946	CLONAL	1	TRUE	1	0.479114626851071	2		228	702	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493620	56493621	+	splice_acceptor_variant	Splice_Site	DEL	AG	AG	-	rs766102716	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	214	420	1	ENST00000267101.3:c.2944_2945del		p.X982_splice	ENST00000267101	NM_001982.3	982			1	2	FACETS	0.993	0.923	1	0.993	0.923	1	CLONAL	1	TRUE	1	0.479114626851071	2		421	900	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105667	27105667	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	243	481	0	ENST00000324856.7:c.5278G>T	p.Glu1760Ter	p.E1760*	ENST00000324856	NM_006015.4	1760	Gag/Tag	20/20	1	2	FACETS	0.98	0.916	1	0.98	0.916	1	CLONAL	1	TRUE	1	0.479114626851071	2		481	1035	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281545	198281545	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1559272961	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	270	533	1	ENST00000335508.6:c.586C>T	p.Arg196Ter	p.R196*	ENST00000335508	NM_012433.2	196	Cga/Tga	6/25	1	2	FACETS	0.95	0.89	1	0.95	0.89	1	CLONAL	1	TRUE	1	0.479114626851071	2		534	1187	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141596	202141596	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	216	442	0	ENST00000358485.4:c.884G>A	p.Cys295Tyr	p.C295Y	ENST00000358485	NM_001080125.1	295	tGt/tAt	7/9	1	2	FACETS	0.93	0.865	0.997	0.93	0.865	0.997	CLONAL	1	TRUE	1	0.479114626851071	2		442	970	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231267	142231267	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	230	459	0	ENST00000350721.4:c.4687A>G	p.Thr1563Ala	p.T1563A	ENST00000350721	NM_001184.3	1563	Acc/Gcc	27/47	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.479114626851071	2		459	939	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973914	131973914	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	176	256	0	ENST00000265335.6:c.3617A>G	p.Lys1206Arg	p.K1206R	ENST00000265335		1206	aAg/aGg	23/25	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.479114626851071	2		256	649	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513202	149513202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374864774	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	230	499	1	ENST00000261799.4:c.881C>T	p.Thr294Met	p.T294M	ENST00000261799	NM_002609.3	294	aCg/aTg	6/23	1	2	FACETS	0.908	0.846	0.972	0.908	0.846	0.972	CLONAL	1	TRUE	1	0.479114626851071	2		500	1057	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112029160	112029160	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1326	336	814	0	ENST00000368678.4:c.408T>G	p.Asn136Lys	p.N136K	ENST00000368678		136	aaT/aaG	5/13	1	2	FACETS	0.844	0.796	0.894	0.844	0.796	0.894	CLONAL	1	TRUE	1	0.479114626851071	2		814	1662	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729984	41729984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1889	617	1036	1	ENST00000242208.4:c.545C>T	p.Pro182Leu	p.P182L	ENST00000242208	NM_002192.2	182	cCg/cTg	3/3	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.479114626851071	2		1037	2506	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494169	140494169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730880415	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	216	582	0	ENST00000288602.6:c.1079G>A	p.Arg360Gln	p.R360Q	ENST00000288602	NM_004333.4	360	cGa/cAa	8/18	1	2	FACETS	0.84	0.781	0.902	0.84	0.781	0.902	CLONAL	1	TRUE	1	0.479114626851071	2		582	1073	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878836	117878836	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	271	714	0	ENST00000297338.2:c.133A>G	p.Ile45Val	p.I45V	ENST00000297338	NM_006265.2	45	Atc/Gtc	2/14	1	2	FACETS	0.842	0.788	0.897	0.842	0.788	0.897	CLONAL	1	TRUE	1	0.479114626851071	2		714	1344	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737842	145737842	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	140	347	1	ENST00000428558.2:c.2988G>T	p.Met996Ile	p.M996I	ENST00000428558	NM_004260.3	996	atG/atT	18/22	1	2	FACETS	0.794	0.724	0.867	0.794	0.724	0.867	SUBCLONAL	1	TRUE	1	0.479114626851071	2		348	736	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570285	87570285	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	61	326	1	ENST00000277120.3:c.2025G>T	p.Gln675His	p.Q675H	ENST00000277120		675	caG/caT	17/19	0.411152402325347	3	FACETS	0.347	0.298	0.4	0.173	0.149	0.2	SUBCLONAL	1	TRUE	1	0.479114626851071	3		327	910	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220318	98220318	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	198	291	2	ENST00000331920.6:c.3145A>G	p.Asn1049Asp	p.N1049D	ENST00000331920	NM_000264.3	1049	Aac/Gac	18/24	0.411152402325347	3	FACETS	1	0.974	1	0.556	0.515	0.598	CLONAL	1	TRUE	1	0.479114626851071	3		293	922	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845643	63845643	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	79	237	0	ENST00000279873.7:c.1382C>T	p.Pro461Leu	p.P461L	ENST00000279873	NM_032199.2	461	cCc/cTc	9/10	1	2	FACETS	0.751	0.663	0.845	0.751	0.663	0.845	SUBCLONAL	1	TRUE	1	0.479114626851071	2		237	439	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925513	114925513	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1241598518	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1590	492	978	0	ENST00000543371.1:c.1591A>G	p.Met531Val	p.M531V	ENST00000543371	NM_001198531.1	531	Atg/Gtg	14/14	1	2	FACETS	0.986	0.941	1	0.986	0.941	1	CLONAL	1	TRUE	1	0.479114626851071	2		978	2082	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076624	102076624	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	94	193	0	ENST00000282441.5:c.803C>T	p.Ala268Val	p.A268V	ENST00000282441	NM_001130145.2	268	gCc/gTc	5/9	1	2	FACETS	0.888	0.794	0.986	0.888	0.794	0.986	CLONAL	1	TRUE	1	0.479114626851071	2		193	442	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1022610	1022610	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	149	451	0	ENST00000358495.3:c.1204G>A	p.Glu402Lys	p.E402K	ENST00000358495	NM_134424.2	402	Gaa/Aaa	12/12	1	2	FACETS	0.849	0.777	0.924	0.849	0.777	0.924	CLONAL	1	TRUE	1	0.479114626851071	2		451	733	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444555	49444555	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	97	228	0	ENST00000301067.7:c.2816T>A	p.Leu939His	p.L939H	ENST00000301067	NM_003482.3	939	cTc/cAc	11/54	1	2	FACETS	0.799	0.715	0.887	0.799	0.715	0.887	SUBCLONAL	1	TRUE	1	0.479114626851071	2		228	507	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480106	50480106	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	180	338	0	ENST00000394963.4:c.340C>T	p.Gln114Ter	p.Q114*	ENST00000394963	NM_003076.4	114	Cag/Tag	2/13	1	2	FACETS	0.899	0.83	0.97	0.899	0.83	0.97	CLONAL	1	TRUE	1	0.479114626851071	2		338	836	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484373	50484373	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	187	326	0	ENST00000394963.4:c.1133G>T	p.Ser378Ile	p.S378I	ENST00000394963	NM_003076.4	378	aGt/aTt	9/13	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.479114626851071	2		326	777	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536891	120536891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1337798232	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1608	428	859	3	ENST00000229340.5:c.295G>A	p.Val99Ile	p.V99I	ENST00000229340	NM_006861.6	99	Gtc/Atc	4/6	1	2	FACETS	0.878	0.833	0.923	0.878	0.833	0.923	CLONAL	1	TRUE	1	0.479114626851071	2		862	2036	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435294	121435294	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	42	288	0	ENST00000257555.6:c.1327G>T	p.Ala443Ser	p.A443S	ENST00000257555		443	Gca/Tca	7/10	1	2	FACETS	0.271	0.225	0.321	0.271	0.225	0.321	SUBCLONAL	1	TRUE	1	0.479114626851071	2		288	648	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563156	21563156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1326904339	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	206	367	0	ENST00000382592.4:c.763C>T	p.Arg255Trp	p.R255W	ENST00000382592	NM_014572.2	255	Cgg/Tgg	4/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.479114626851071	2		367	779	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987067	36987067	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	158	312	0	ENST00000354822.5:c.622C>T	p.Arg208Ter	p.R208*	ENST00000354822	NM_001079668.2	208	Cga/Tga	3/3	1	2	FACETS	0.932	0.856	1	0.932	0.856	1	CLONAL	1	TRUE	1	0.479114626851071	2		312	708	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456376	99456376	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	199	349	0	ENST00000268035.6:c.1693G>T	p.Gly565Cys	p.G565C	ENST00000268035	NM_000875.3	565	Ggc/Tgc	8/21	1	2	FACETS	0.949	0.88	1	0.949	0.88	1	CLONAL	1	TRUE	1	0.479114626851071	2		349	875	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788672	3788672	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1387351570	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	185	384	0	ENST00000262367.5:c.4282C>T	p.Arg1428Cys	p.R1428C	ENST00000262367	NM_004380.2	1428	Cgt/Tgt	26/31	1	2	FACETS	0.856	0.791	0.924	0.856	0.791	0.924	CLONAL	1	TRUE	1	0.479114626851071	2		384	902	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845477	72845477	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1395722106	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	231	567	0	ENST00000268489.5:c.3863C>T	p.Thr1288Met	p.T1288M	ENST00000268489	NM_006885.3	1288	aCg/aTg	7/10	1	2	FACETS	0.787	0.732	0.843	0.787	0.732	0.843	SUBCLONAL	1	TRUE	1	0.479114626851071	2		567	1226	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244880	41244880	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	120	384	0	ENST00000357654.3:c.2668G>T	p.Gly890Trp	p.G890W	ENST00000357654	NM_007294.3	890	Ggg/Tgg	10/23	0.288162621165043	1	FACETS	0.661	0.599	0.727	0.661	0.599	0.727	SUBCLONAL	1	TRUE	0	0.479114626851071	1		384	576	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436128	56436128	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	373	621	0	ENST00000407977.2:c.1009C>T	p.Arg337Ter	p.R337*	ENST00000407977		337	Cga/Tga	9/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.479114626851071	2		621	1507	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353815	15353815	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780028668	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	183	462	1	ENST00000263377.2:c.3065C>T	p.Pro1022Leu	p.P1022L	ENST00000263377	NM_058243.2	1022	cCg/cTg	14/20	1	2	FACETS	0.812	0.749	0.877	0.812	0.749	0.877	CLONAL	1	TRUE	1	0.479114626851071	2		463	941	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651171	45651171	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	255	467	1	ENST00000407780.3:c.854G>T	p.Ser285Ile	p.S285I	ENST00000407780	NM_001283052.1	285	aGc/aTc	5/7	1	2	FACETS	0.916	0.857	0.977	0.916	0.857	0.977	CLONAL	1	TRUE	1	0.479114626851071	2		468	1162	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76764017	76764017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	60	389	1	ENST00000373344.5:c.7291G>A	p.Ala2431Thr	p.A2431T	ENST00000373344	NM_000489.3	2431	Gca/Aca	35/35	1	1	FACETS	0.232	0.199	0.268	0.232	0.199	0.268	SUBCLONAL	1	TRUE	0	0.479114626851071	1		390	820	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732484	74732519	+	inframe_deletion	In_Frame_Del	DEL	GATCGGCTGCGAGACCTGGAACGACTCCGACTCCGG	GATCGGCTGCGAGACCTGGAACGACTCCGACTCCGG	-	rs1270919613	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1437	258	745	0	ENST00000359995.5:c.390_425del	p.Ser132_Arg143del	p.S132_R143del	ENST00000359995	NM_001195427.1	130	tcCCGGAGTCGGAGTCGTTCCAGGTCTCGCAGCCGATCt/tct	2/3	1	2	FACETS	0.635	0.593	0.68	0.635	0.593	0.68	SUBCLONAL	1	TRUE	1	0.479114626851071	2		745	1695	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728564	190728565	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	131	488	0	ENST00000441310.2:c.1958dup	p.Ile654AspfsTer21	p.I654Dfs*21	ENST00000441310	NM_000534.4	651	aga/agAa	10/13	1	2	FACETS	0.825	0.75	0.903	0.825	0.75	0.903	CLONAL	1	TRUE	1	0.479114626851071	2		488	663	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369100	118369101	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	123	252	0	ENST00000534358.1:c.5822dup	p.Pro1942AlafsTer31	p.P1942Afs*31	ENST00000534358	NM_005933.3	1940	caa/cAaa	22/36	1	2	FACETS	0.844	0.766	0.927	0.844	0.766	0.927	CLONAL	1	TRUE	1	0.479114626851071	2		252	608	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957465	175957465	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	177	552	0	ENST00000367669.3:c.1931del	p.Asn644ThrfsTer3	p.N644Tfs*3	ENST00000367669	NM_022457.5	644	aAc/ac	17/20	1	2	FACETS	0.806	0.742	0.872	0.806	0.742	0.872	CLONAL	1	TRUE	1	0.479114626851071	2		552	917	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622183	1622183	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1553	86	741	0	ENST00000344749.5:c.692del	p.Pro231ArgfsTer53	p.P231Rfs*53	ENST00000344749	NM_001136139.2	231	cCg/cg	10/19	1	2	FACETS	0.219	0.193	0.248	0.219	0.193	0.248	SUBCLONAL	1	TRUE	1	0.479114626851071	2		741	1639	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617680	39617680	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	102	426	0	ENST00000262039.4:c.1869del	p.Phe623LeufsTer43	p.F623Lfs*43	ENST00000262039	NM_002647.2	622	Ttt/tt	17/25	1	2	FACETS	0.697	0.624	0.774	0.697	0.624	0.774	SUBCLONAL	1	TRUE	1	0.479114626851071	2		426	611	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372092	55372093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	28	179	2	ENST00000297316.4:c.788dup	p.Glu264GlyfsTer101	p.E264Gfs*101	ENST00000297316	NM_022454.3	261	ggc/ggCc	2/2	1	2	FACETS	0.245	0.195	0.302	0.245	0.195	0.302	SUBCLONAL	1	TRUE	1	0.479114626851071	2		181	477	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057961	27057962	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0008729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	213	398	0	ENST00000324856.7:c.1669_1670del	p.Gln557ValfsTer65	p.Q557Vfs*65	ENST00000324856	NM_006015.4	557	CAg/g	3/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.479114626851071	2		398	841	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0008745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	120	588	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.962	0.868	1	0.962	0.868	1	CLONAL	1	TRUE	1	0.289786872371319	2		589	861	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0008745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	131	363	1	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.289786872371319	2	FACETS	0.766	0.698	0.838	0.766	0.698	0.838	SUBCLONAL	2	TRUE	0	0.289786872371319	2		364	590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0008745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	176	609	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.289786872371319	2		610	1027	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0008745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	109	482	5	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	0.280997087683149	3	FACETS	0.969	0.869	1	0.484	0.434	0.538	CLONAL	1	TRUE	1	0.289786872371319	3		487	889	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0008745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	86	401	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	0.289786872371319	2	FACETS	0.786	0.695	0.884	0.393	0.347	0.442	SUBCLONAL	1	TRUE	0	0.289786872371319	2		401	755	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0008745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	95	299	0	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	0.280997087683149	3	FACETS	1	0.939	1	0.54	0.481	0.603	CLONAL	1	TRUE	1	0.289786872371319	3		299	695	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858492	27858492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1318	247	957	0	ENST00000359303.2:c.79C>T	p.Arg27Cys	p.R27C	ENST00000359303	NM_003535.2	27	Cgc/Tgc	1/1	0.289786872371319	3	FACETS	1	0.987	1	0.624	0.581	0.668	CLONAL	1	TRUE	1	0.289786872371319	3		957	1565	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831026	72831026	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs61737017	NA	P-0008745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1256	237	886	1	ENST00000268489.5:c.5555A>C	p.Gln1852Pro	p.Q1852P	ENST00000268489	NM_006885.3	1852	cAg/cCg	9/10	0.14340987553746	0	FACETS	0.778	0.724	0.834			1	INDETERMINATE	1	TRUE	0	0.289786872371319	0		887	1493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0008745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	111	366	0	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.289786872371319	2		366	733	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522720	176522720	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757092386	NA	P-0008745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	119	399	1	ENST00000292408.4:c.1817G>A	p.Arg606Gln	p.R606Q	ENST00000292408	NM_213647.1	606	cGg/cAg	13/18	0.289786872371319	2	FACETS	1	0.949	1	0.54	0.487	0.595	CLONAL	1	TRUE	0	0.289786872371319	2		400	761	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045726	26045726	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1561	268	984	4	ENST00000540144.1:c.88G>A	p.Ala30Thr	p.A30T	ENST00000540144	NM_003531.2	30	Gct/Act	1/1	0.289786872371319	3	FACETS	1	0.984	1	0.579	0.541	0.619	CLONAL	1	TRUE	1	0.289786872371319	3		988	1829	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671451	30671451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1270	186	604	0	ENST00000376406.3:c.5509G>A	p.Val1837Met	p.V1837M	ENST00000376406	NM_014641.2	1837	Gtg/Atg	10/15	0.289786872371319	3	FACETS	1	0.929	1	0.505	0.464	0.547	CLONAL	1	TRUE	1	0.289786872371319	3		604	1456	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513371	106513371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765080806	NA	P-0008745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	115	479	2	ENST00000359195.3:c.2275G>A	p.Val759Ile	p.V759I	ENST00000359195	NM_002649.2	759	Gtc/Atc	4/11	1	2	FACETS	0.856	0.77	0.947	0.856	0.77	0.947	CLONAL	1	TRUE	1	0.289786872371319	2		481	927	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917715	151917715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	29	157	0	ENST00000262189.6:c.3605C>T	p.Pro1202Leu	p.P1202L	ENST00000262189	NM_170606.2	1202	cCa/cTa	23/59	1	2	FACETS	0.791	0.638	0.964	0.791	0.638	0.964	CLONAL	1	TRUE	1	0.289786872371319	2		157	253	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738708	145738708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	56	437	0	ENST00000428558.2:c.2356G>A	p.Val786Met	p.V786M	ENST00000428558	NM_004260.3	786	Gtg/Atg	15/22	0.280997087683149	3	FACETS	0.503	0.429	0.584	0.251	0.214	0.292	SUBCLONAL	1	TRUE	1	0.289786872371319	3		437	880	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285694	87285694	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs78936193	NA	P-0008745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	98	494	0	ENST00000277120.3:c.31G>A	p.Ala11Thr	p.A11T	ENST00000277120		11	Gcc/Acc	2/19	0.137697157065918	3	FACETS	0.799	0.712	0.893	0.266	0.237	0.298	INDETERMINATE	1	TRUE	0	0.289786872371319	3		494	969	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636210	87636210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs957713208	NA	P-0008745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	123	459	0	ENST00000277120.3:c.2375G>A	p.Arg792His	p.R792H	ENST00000277120		792	cGc/cAc	19/19	0.137697157065918	3	FACETS	1	0.954	1	0.364	0.329	0.401	INDETERMINATE	1	TRUE	0	0.289786872371319	3		459	890	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401384	139401384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766198119	NA	P-0008745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	92	361	1	ENST00000277541.6:c.3685G>A	p.Val1229Ile	p.V1229I	ENST00000277541	NM_017617.3	1229	Gtt/Att	23/34	0.137697157065918	3	FACETS	0.904	0.803	1	0.301	0.267	0.338	INDETERMINATE	1	TRUE	0	0.289786872371319	3		362	804	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	532701	532701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151229168	NA	P-0008745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	204	687	3	ENST00000451590.1:c.505C>T	p.Arg169Trp	p.R169W	ENST00000451590	NM_001130442.1	169	Cgg/Tgg	5/5	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.289786872371319	NA		690	1290	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195752	102195752	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1351	263	909	0	ENST00000263464.3:c.512C>T	p.Ala171Val	p.A171V	ENST00000263464	NM_001165.4	171	gCc/gTc	2/9	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.289786872371319	2		909	1614	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237692	133237692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753759783	NA	P-0008745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	141	611	0	ENST00000320574.5:c.2923C>T	p.Arg975Cys	p.R975C	ENST00000320574	NM_006231.2	975	Cgc/Tgc	25/49	1	2	FACETS	0.783	0.711	0.858	0.783	0.711	0.858	SUBCLONAL	1	TRUE	1	0.289786872371319	2		611	1243	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134933	41134933	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1569	248	996	0	ENST00000379561.5:c.695G>A	p.Gly232Glu	p.G232E	ENST00000379561	NM_002015.3	232	gGa/gAa	2/3	0.280997087683149	3	FACETS	1	0.971	1	0.539	0.502	0.578	CLONAL	1	TRUE	1	0.289786872371319	3		996	1817	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122768	7122768	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	57	506	1	ENST00000302850.5:c.3386C>T	p.Pro1129Leu	p.P1129L	ENST00000302850	NM_000208.2	1129	cCt/cTt	19/22	1	2	FACETS	0.39	0.333	0.452	0.39	0.333	0.452	SUBCLONAL	1	TRUE	1	0.289786872371319	2		507	1009	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302277	15302277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137852641	NA	P-0008745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	176	584	0	ENST00000263388.2:c.994C>T	p.Arg332Cys	p.R332C	ENST00000263388	NM_000435.2	332	Cgc/Tgc	6/33	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.289786872371319	2		584	1166	SUCCESS
AXL	558	MSKCC	GRCh37	19	41725374	41725374	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	467	594	0	ENST00000301178.4:c.81del	p.Arg28GlyfsTer70	p.R28Gfs*70	ENST00000301178	NM_021913.4	26	gCc/gc	1/20	0.207315729143933	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	3	TRUE	1	0.289786872371319	4		594	1376	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524567	103524568	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs759551120	NA	P-0008745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	134	449	0	ENST00000355739.4:c.2705dup	p.Asn902LysfsTer7	p.N902Kfs*7	ENST00000355739	NM_000123.3	900	caa/cAaa	13/15	0.280997087683149	3	FACETS	0.95	0.861	1	0.475	0.43	0.522	CLONAL	1	TRUE	1	0.289786872371319	3		449	1115	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797261	135797261	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	80	496	2	ENST00000298552.3:c.608del	p.Leu203CysfsTer7	p.L203Cfs*7	ENST00000298552	NM_001162426.1	203	tTg/tg	7/23	0.137697157065918	3	FACETS	0.502	0.44	0.569	0.167	0.146	0.19	INDETERMINATE	1	TRUE	0	0.289786872371319	3		498	1260	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147770	61147771	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0008745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	93	351	0	ENST00000295025.8:c.1086dup	p.Glu363ArgfsTer8	p.E363Rfs*8	ENST00000295025	NM_002908.2	360	-/A	10/11	0.280997087683149	3	FACETS	0.884	0.785	0.99	0.442	0.392	0.495	CLONAL	1	TRUE	1	0.289786872371319	3		351	831	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0008864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	147	269	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.384649860160962	3	FACETS	0.994	0.929	1	0.994	0.929	1	INDETERMINATE	2	TRUE	1	0.77437418682276	3		269	265	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0008864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	308	734	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.935	0.885	0.986	0.935	0.885	0.986	CLONAL	1	TRUE	1	0.77437418682276	2		734	851	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	100	347	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	0.447	0.4	0.497	0.447	0.4	0.497	SUBCLONAL	1	TRUE	1	0.77437418682276	2		347	578	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0008864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	142	431	5	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	0.994	0.917	1	0.994	0.917	1	CLONAL	1	TRUE	1	0.77437418682276	2		436	369	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593415	67593415	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	29	258	0	ENST00000274335.5:c.2161C>T	p.Gln721Ter	p.Q721*	ENST00000274335		721	Cag/Tag	15/15	0.77437418682276	1	FACETS	0.244	0.197	0.296	0.244	0.197	0.296	SUBCLONAL	1	TRUE	0	0.77437418682276	1		258	188	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39725967	39725967	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	102	278	0	ENST00000361337.2:c.838A>G	p.Lys280Glu	p.K280E	ENST00000361337	NM_003286.2	280	Aaa/Gaa	10/21	0.351252302657921	2	FACETS	1	0.984	1	0.675	0.621	0.73	INDETERMINATE	1	TRUE	0	0.77437418682276	2		278	195	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097746	27097747	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0008864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	145	425	0	ENST00000324856.7:c.3338dup	p.Pro1114SerfsTer9	p.P1114Sfs*9	ENST00000324856	NM_006015.4	1112	gac/gaCc	12/20	0.405891188803899	1	FACETS	0.412	0.378	0.448	0.412	0.378	0.448	INDETERMINATE	1	TRUE	0	0.77437418682276	1		425	557	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591242	67591247	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TTTCAG	TTTCAG	-	novel	NA	P-0008864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	163	313	0	ENST00000274335.5:c.1746-6_1746-1del		p.X582_splice	ENST00000274335		582			0.77437418682276	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.77437418682276	1		313	218	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692903	89692906	+	missense_variant	Missense_Mutation	ONP	ACGA	ACGA	CAGT	novel	NA	P-0008864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	77	321	0	ENST00000371953.3:c.387_390delinsCAGT	p.Arg130Ser	p.R130S	ENST00000371953	NM_000314.4	129	ggACGA/ggCAGT	5/9	0.384649860160962	3	FACETS	1	0.919	1	0.521	0.463	0.581	INDETERMINATE	1	TRUE	1	0.77437418682276	3		321	265	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0008936-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	96	269	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.208242392696747	2	FACETS	0.859	0.769	0.952	0.859	0.769	0.952	CLONAL	2	TRUE	0	0.255873146858655	2		269	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0008936-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	167	310	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.255873146858655	2		310	959	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589589	67589606	+	inframe_deletion	In_Frame_Del	DEL	AATATAACACTCAGTTTC	AATATAACACTCAGTTTC	-	novel	NA	P-0008936-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	82	496	0	ENST00000274335.5:c.1354_1371del	p.Tyr452_Gln457del	p.Y452_Q457del	ENST00000274335		451	gAATATAACACTCAGTTTCaa/gaa	10/15	1	2	FACETS	0.876	0.772	0.987	0.876	0.772	0.987	CLONAL	1	TRUE	1	0.255873146858655	2		496	732	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592122	67592122	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008936-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	99	500	0	ENST00000274335.5:c.1938T>G	p.Phe646Leu	p.F646L	ENST00000274335		646	ttT/ttG	14/15	1	2	FACETS	0.858	0.765	0.957	0.858	0.765	0.957	CLONAL	1	TRUE	1	0.255873146858655	2		500	902	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101750	71101751	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008936-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	67	478	0	ENST00000318789.4:c.447dup	p.Gln150ThrfsTer20	p.Q150Tfs*20	ENST00000318789	NM_032682.5	149	-/A	9/21	0.255873146858655	1	FACETS	0.621	0.538	0.71	0.621	0.538	0.71	SUBCLONAL	1	TRUE	0	0.255873146858655	1		478	736	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0008945-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1463	433	409	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	0.489538614843548	6	FACETS	0.821	0.781	0.863			1	CLONAL	2	TRUE	NA	0.626130980559377	6		409	1896	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155725	56155726	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0008945-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	161	387	0	ENST00000399503.3:c.819_820del	p.Arg273SerfsTer27	p.R273Sfs*27	ENST00000399503	NM_005921.1	273	AGa/a	3/20	0.584970361817823	4	FACETS	0.825	0.762	0.889	0.825	0.762	0.889	CLONAL	2	TRUE	2	0.626130980559377	4		387	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs11575997	NA	P-0008945-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	219	512	0	ENST00000269305.4:c.993+1G>T		p.X331_splice	ENST00000269305	NM_001126112.2	331			NA	2	FACETS	1	0.952	1			1	INDETERMINATE	2	TRUE	NA	0.626130980559377	2		512	349	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394866	394866	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs144593192	NA	P-0008945-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	22	405	0	ENST00000380956.4:c.262C>G	p.Pro88Ala	p.P88A	ENST00000380956	NM_001195286.1	88	Ccg/Gcg	3/9	0.187627836669371	6	FACETS	0.371	0.286	0.469			1	INDETERMINATE	1	TRUE	NA	0.626130980559377	6		405	427	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0008998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	60	340	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.847	0.73	0.974	0.847	0.73	0.974	CLONAL	1	TRUE	1	0.26	2		340	545	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0008998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	23	280	1	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.66	0.516	0.827	0.66	0.516	0.827	SUBCLONAL	1	TRUE	1	0.26	2		281	268	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717674	89717675	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0008998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	54	439	0	ENST00000371953.3:c.700dup	p.Arg234ProfsTer9	p.R234Pfs*9	ENST00000371953	NM_000314.4	233	-/C	7/9	1	2	FACETS	0.771	0.658	0.894	0.771	0.658	0.894	SUBCLONAL	1	TRUE	1	0.26	2		439	539	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481417	140481417	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913348	NA	P-0008998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	37	521	0	ENST00000288602.6:c.1391G>T	p.Gly464Val	p.G464V	ENST00000288602	NM_004333.4	464	gGa/gTa	11/18	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.26	NA		521	673	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023732	31023732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs549552934	NA	P-0008998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	71	499	0	ENST00000375687.4:c.3217C>T	p.Arg1073Cys	p.R1073C	ENST00000375687	NM_015338.5	1073	Cgc/Tgc	13/13	0.234681796896184	3	FACETS	0.851	0.742	0.969	0.426	0.371	0.485	CLONAL	1	TRUE	1	0.26	3		499	725	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509469	46509469	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs200277706	NA	P-0008998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	51	421	0	ENST00000262741.5:c.1262T>C	p.Leu421Pro	p.L421P	ENST00000262741	NM_003629.3	421	cTg/cCg	10/10	1	2	FACETS	0.814	0.692	0.947	0.814	0.692	0.947	CLONAL	1	TRUE	1	0.26	2		421	482	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053236	180053236	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	96	548	0	ENST00000261937.6:c.1133G>T	p.Arg378Leu	p.R378L	ENST00000261937	NM_182925.4	378	cGc/cTc	9/30	0.234681796896184	3	FACETS	1	0.959	1	0.581	0.518	0.649	CLONAL	1	TRUE	1	0.26	3		548	718	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264108	46264108	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	95	674	0	ENST00000371998.3:c.1155A>C	p.Gln385His	p.Q385H	ENST00000371998		385	caA/caC	11/23	0.234681796896184	3	FACETS	0.692	0.614	0.775	0.346	0.307	0.388	SUBCLONAL	1	TRUE	1	0.26	3		674	1194	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692858	89692867	+	frameshift_variant	Frame_Shift_Del	DEL	AGATGACAAT	AGATGACAAT	-	novel	NA	P-0008998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	16	129	0	ENST00000371953.3:c.342_351del	p.Glu114AspfsTer17	p.E114Dfs*17	ENST00000371953	NM_000314.4	114	gaAGATGACAAT/ga	5/9	1	2	FACETS	0.867	0.645	1	0.867	0.645	1	CLONAL	1	TRUE	1	0.26	2		129	142	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0009053-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	112	409	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.147239804751405	2	FACETS	1	0.976	1	0.65	0.583	0.722	CLONAL	1	TRUE	0	0.15	2		409	1148	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0009053-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	162	364	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.3	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.15	3		364	1032	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341976	8341976	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs377463668	NA	P-0009053-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	32	256	1	ENST00000356435.5:c.4664C>T	p.Ala1555Val	p.A1555V	ENST00000356435		1555	gCg/gTg	29/35	1	2	FACETS	0.813	0.659	0.987	0.813	0.659	0.987	CLONAL	1	TRUE	1	0.15	2		257	525	SUCCESS
APC	324	MSKCC	GRCh37	5	112175475	112175476	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTTTGAGA	novel	NA	P-0009053-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	83	342	0	ENST00000257430.4:c.4185_4192dup	p.Ser1398IlefsTer20	p.S1398Ifs*20	ENST00000257430	NM_000038.5	1395	agt/agTTTTGAGAt	16/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.15	2		342	870	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591141	67591152	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CCAATACTTGAT	CCAATACTTGAT	-	novel	NA	P-0009053-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	66	280	0	ENST00000274335.5:c.1734_1745del	p.Asp578_Met582delinsGlu	p.D578_M582delinsE	ENST00000274335		578	gaCCAATACTTGATg/gag	12/15	0.144064690085983	4	FACETS	1	0.958	1	0.636	0.551	0.728	CLONAL	1	TRUE	2	0.15	4		280	796	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	93	442	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.32	2		444	535	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	154	342	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.141531442111027	3	FACETS	0.806	0.739	0.875	0.806	0.739	0.875	INDETERMINATE	2	TRUE	1	0.32	3		342	693	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	130	454	2	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.892	0.808	0.98	0.892	0.808	0.98	CLONAL	1	TRUE	1	0.32	2		456	911	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	126	568	4	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.32	2		572	645	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	33	47	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	1	2	FACETS	0.893	0.732	1	0.893	0.732	1	CLONAL	1	TRUE	1	0.32	2		47	231	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16022738	16022738	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	199	496	3	ENST00000268712.3:c.1914del	p.Gly639ValfsTer2	p.G639Vfs*2	ENST00000268712	NM_006311.3	638	aaA/aa	17/46	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.32	2		499	1102	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983785	15983785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs772070121	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	106	432	0	ENST00000268712.3:c.3337C>T	p.Arg1113Ter	p.R1113*	ENST00000268712	NM_006311.3	1113	Cga/Tga	25/46	1	2	FACETS	0.624	0.558	0.695	0.624	0.558	0.695	SUBCLONAL	1	TRUE	1	0.32	2		432	1061	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101090	26101090	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	242	639	1	ENST00000435504.4:c.2T>C	p.Met1?	p.M1?	ENST00000435504		1	aTg/aCg	1/13	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.32	2		640	1218	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845243	151845243	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1323051494	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	118	343	0	ENST00000262189.6:c.13769G>A	p.Arg4590His	p.R4590H	ENST00000262189	NM_170606.2	4590	cGc/cAc	52/59	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.32	2		343	592	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	111	291	1	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	1	2	FACETS	0.925	0.832	1	0.925	0.832	1	CLONAL	1	TRUE	1	0.32	2		292	750	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	147	489	2	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.32	2		491	840	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032090	26032090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1329616402	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1479	222	1012	2	ENST00000244661.2:c.199C>T	p.Pro67Ser	p.P67S	ENST00000244661	NM_003537.3	67	Ccg/Tcg	1/1	1	2	FACETS	0.816	0.756	0.878	0.816	0.756	0.878	CLONAL	1	TRUE	1	0.32	2		1014	1701	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347484	91347484	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	251	604	2	ENST00000355112.3:c.3651del	p.Lys1217AsnfsTer62	p.K1217Nfs*62	ENST00000355112	NM_000057.2	1216	Aaa/aa	19/22	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.32	2		606	1351	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850704	63850705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	174	390	3	ENST00000279873.7:c.1489dup	p.Ile497AsnfsTer31	p.I497Nfs*31	ENST00000279873	NM_032199.2	494	-/A	10/10	1	2	FACETS	0.891	0.818	0.966	0.891	0.818	0.966	CLONAL	1	TRUE	1	0.32	2		393	1221	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015094	37015094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	232	584	0	ENST00000358127.4:c.310C>T	p.Arg104Cys	p.R104C	ENST00000358127	NM_001280556.1	104	Cgc/Tgc	3/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.32	2		584	1141	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932750	39932750	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143744110	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1201	268	724	1	ENST00000378444.4:c.1849G>A	p.Ala617Thr	p.A617T	ENST00000378444	NM_001123385.1	617	Gcc/Acc	4/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.32	2		725	1469	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546703	9546703	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	146	389	0	ENST00000353224.5:c.1319T>C	p.Val440Ala	p.V440A	ENST00000353224	NM_177990.2	440	gTc/gCc	5/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.32	2		389	699	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641465	47641465	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1375	345	773	0	ENST00000233146.2:c.850T>C	p.Ser284Pro	p.S284P	ENST00000233146	NM_000251.2	284	Tcc/Ccc	5/16	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.32	2		773	1720	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678806	52678806	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	84	300	0	ENST00000394830.3:c.814-1G>T		p.X272_splice	ENST00000394830	NM_018313.4	272			1	2	FACETS	0.76	0.671	0.855	0.76	0.671	0.855	SUBCLONAL	1	TRUE	1	0.32	2		300	691	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752353	57752353	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs764769020	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	208	459	0	ENST00000274289.3:c.1220T>C	p.Ile407Thr	p.I407T	ENST00000274289	NM_006622.3	407	aTa/aCa	9/14	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.32	2		459	992	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170817079	170817079	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	214	443	0	ENST00000296930.5:c.83A>T	p.Asp28Val	p.D28V	ENST00000296930	NM_002520.6	28	gAt/gTt	2/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.32	2		443	1071	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910405	29910405	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	132	468	0	ENST00000376809.5:c.73+2T>C		p.X25_splice	ENST00000376809	NM_002116.7	25			0.141531442111027	3	FACETS	1	0.933	1	0.518	0.47	0.569	INDETERMINATE	1	TRUE	1	0.32	3		468	924	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710969	117710969	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	92	211	0	ENST00000368508.3:c.1303G>A	p.Asp435Asn	p.D435N	ENST00000368508	NM_002944.2	435	Gac/Aac	12/43	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.32	2		211	421	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202188	138202188	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	122	313	0	ENST00000237289.4:c.2105G>T	p.Arg702Ile	p.R702I	ENST00000237289	NM_001270507.1	702	aGa/aTa	9/9	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.32	2		313	608	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976760	2976760	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	244	619	2	ENST00000396946.4:c.1252A>G	p.Arg418Gly	p.R418G	ENST00000396946	NM_032415.4	418	Agg/Ggg	9/25	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.32	2		621	1288	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391772	139391772	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	48	244	0	ENST00000277541.6:c.6419G>A	p.Cys2140Tyr	p.C2140Y	ENST00000277541	NM_017617.3	2140	tGc/tAc	34/34	1	2	FACETS	0.515	0.434	0.603	0.515	0.434	0.603	SUBCLONAL	1	TRUE	1	0.32	2		244	583	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435374	18435374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369286185	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	185	483	0	ENST00000266497.5:c.359C>T	p.Thr120Met	p.T120M	ENST00000266497		120	aCg/aTg	1/31	0.141531442111027	3	FACETS	1	0.987	1	0.678	0.626	0.733	INDETERMINATE	1	TRUE	1	0.32	3		483	989	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112571	115112571	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	145	344	0	ENST00000257566.3:c.1169G>A	p.Cys390Tyr	p.C390Y	ENST00000257566	NM_016569.3	390	tGc/tAc	7/8	0.141531442111027	3	FACETS	1	0.987	1	0.749	0.684	0.816	INDETERMINATE	1	TRUE	1	0.32	3		344	702	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972569	32972569	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	171	380	0	ENST00000380152.3:c.9919A>G	p.Lys3307Glu	p.K3307E	ENST00000380152		3307	Aaa/Gaa	27/27	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.32	2		380	826	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527756	103527756	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1178958900	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	200	554	0	ENST00000355739.4:c.3064A>G	p.Met1022Val	p.M1022V	ENST00000355739	NM_000123.3	1022	Atg/Gtg	15/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.32	2		554	1190	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054013	42054013	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377036527	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	250	731	0	ENST00000219905.7:c.7475G>A	p.Arg2492Gln	p.R2492Q	ENST00000219905	NM_001164273.1	2492	cGg/cAg	21/24	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.32	2		731	1405	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135231	2135231	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	119	376	0	ENST00000219476.3:c.4570T>C	p.Ser1524Pro	p.S1524P	ENST00000219476	NM_000548.3	1524	Tca/Cca	36/42	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.32	2		376	722	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041701	14041701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374978891	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	199	605	0	ENST00000311895.7:c.2248C>T	p.Arg750Cys	p.R750C	ENST00000311895	NM_005236.2	750	Cgc/Tgc	11/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.32	2		605	1168	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918742	50918742	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	177	542	0	ENST00000440232.2:c.2612T>C	p.Leu871Pro	p.L871P	ENST00000440232	NM_002691.3	871	cTg/cCg	21/27	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.32	2		542	1042	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375144	31375144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1033838676	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	175	444	1	ENST00000328111.2:c.541C>T	p.Pro181Ser	p.P181S	ENST00000328111	NM_006892.3	181	Ccc/Tcc	6/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.32	2		445	917	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422697	47422697	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	251	605	0	ENST00000377045.4:c.169G>C	p.Asp57His	p.D57H	ENST00000377045	NM_001654.4	57	Gac/Cac	3/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.32	2		605	1376	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847286	68847286	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	223	536	2	ENST00000261769.5:c.1212del	p.Asn405IlefsTer12	p.N405Ifs*12	ENST00000261769	NM_004360.3	403	gCc/gc	9/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.32	2		538	1197	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522190	157522190	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	101	275	0	ENST00000346085.5:c.4466del	p.Pro1489LeufsTer5	p.P1489Lfs*5	ENST00000346085	NM_020732.3	1488	Ccc/cc	18/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.32	2		275	566	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401637	401637	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	133	360	0	ENST00000380956.4:c.963del	p.Asp322ThrfsTer62	p.D322Tfs*62	ENST00000380956	NM_001195286.1	320	gCc/gc	7/9	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.32	2		360	636	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588972	67588972	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	127	387	1	ENST00000274335.5:c.1067del	p.Leu356TrpfsTer17	p.L356Wfs*17	ENST00000274335		355	Ttt/tt	8/15	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.32	2		388	766	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120396	70120396	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	234	769	0	ENST00000245479.2:c.1398del	p.Phe466LeufsTer4	p.F466Lfs*4	ENST00000245479	NM_000346.3	466	ttC/tt	3/3	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.32	2		769	1298	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467573	66467573	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	179	490	0	ENST00000273854.3:c.696del	p.Lys232AsnfsTer36	p.K232Nfs*36	ENST00000273854	NM_004439.5	232	aaA/aa	3/18	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.32	2		490	982	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156936	106156936	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs763386429	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	138	427	0	ENST00000380013.4:c.1842del	p.Leu615SerfsTer24	p.L615Sfs*24	ENST00000380013	NM_001127208.2	613	Ggg/gg	3/11	1	2	FACETS	0.952	0.866	1	0.952	0.866	1	CLONAL	1	TRUE	1	0.32	2		427	906	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739906	41739907	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0009057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	201	692	0	ENST00000242208.4:c.66dup	p.Thr23HisfsTer84	p.T23Hfs*84	ENST00000242208	NM_002192.2	22	-/C	2/3	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.32	2		692	1229	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0009086-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	153	66	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.923	0.855	0.993			1	INDETERMINATE	1	TRUE	NA	0.836883769268692	2		66	396	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0009086-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	254	809	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	0.455174067232786	1	FACETS	0.696	0.659	0.733	0.696	0.659	0.733	INDETERMINATE	1	TRUE	0	0.836883769268692	1		809	507	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134513	30134514	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCC	rs572866415	NA	P-0009086-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	26	283	0	ENST00000263025.4:c.15_17dup	p.Ala6dup	p.A6dup	ENST00000263025	NM_002746.2	6	gct/gcGGCt	1/9	0.593539689971074	1	FACETS	0.124	0.098	0.153	0.124	0.098	0.153	SUBCLONAL	1	TRUE	0	0.836883769268692	1		283	292	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105920	27105920	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009086-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	288	292	0	ENST00000324856.7:c.5531G>A	p.Trp1844Ter	p.W1844*	ENST00000324856	NM_006015.4	1844	tGg/tAg	20/20	NA	2	FACETS	1	0.949	1			1	INDETERMINATE	1	TRUE	NA	0.836883769268692	2		292	687	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477813	140477813	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs180177037	NA	P-0009086-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	365	445	0	ENST00000288602.6:c.1495A>G	p.Lys499Glu	p.K499E	ENST00000288602	NM_004333.4	499	Aaa/Gaa	12/18	1	2	FACETS	0.969	0.923	1	0.969	0.923	1	CLONAL	1	TRUE	1	0.836883769268692	2		445	900	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621855	1621855	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754332007	NA	P-0009086-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	130	467	0	ENST00000344749.5:c.937G>A	p.Gly313Arg	p.G313R	ENST00000344749	NM_001136139.2	313	Ggg/Agg	11/19	0.182774716225553	2	FACETS	0.418	0.379	0.459	0.209	0.189	0.23	INDETERMINATE	1	TRUE	0	0.836883769268692	2		467	743	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	319	372	1	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	1	0.95	1	1	0.997	1	CLONAL	3	TRUE	1	0.22	2		373	963	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	312	414	7	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.985	1	1	0.997	1	CLONAL	3	TRUE	1	0.22	2		421	852	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	139	280	1	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	1	0.955	1	1	0.993	1	CLONAL	3	TRUE	1	0.22	2		281	399	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	302	550	1	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	1	2	FACETS	1	0.983	1	1	0.997	1	CLONAL	3	TRUE	1	0.22	2		551	837	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696802	176696802	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	212	255	0	ENST00000439151.2:c.5508del	p.Ala1837LeufsTer12	p.A1837Lfs*12	ENST00000439151	NM_022455.4	1835	Aaa/aa	16/23	1	2	FACETS	0.968	0.903	1	1	0.995	1	CLONAL	3	TRUE	1	0.22	2		255	664	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497245	149497245	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	393	435	0	ENST00000261799.4:c.3073del	p.Leu1025CysfsTer20	p.L1025Cfs*20	ENST00000261799	NM_002609.3	1025	Ctg/tg	22/23	1	2	FACETS	1	0.988	1	1	0.997	1	CLONAL	3	TRUE	1	0.22	2		435	1080	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	323	395	1	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	1	2	FACETS	1	0.97	1	1	0.997	1	CLONAL	3	TRUE	1	0.22	2		396	945	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789591	3789591	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	402	530	1	ENST00000262367.5:c.4268del	p.Pro1423LeufsTer36	p.P1423Lfs*36	ENST00000262367	NM_004380.2	1423	cCt/ct	25/31	1	2	FACETS	1	0.989	1	1	0.997	1	CLONAL	3	TRUE	1	0.22	2		531	1090	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913399	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	457	417	0	ENST00000349496.5:c.100G>C	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Cga	3/15	1	2	FACETS	0.888	0.849	0.927	1	0.998	1	CLONAL	4	TRUE	1	0.22	2		417	1170	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588758	52588758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	461	440	0	ENST00000394830.3:c.4270C>T	p.Pro1424Ser	p.P1424S	ENST00000394830	NM_018313.4	1424	Ccg/Tcg	27/30	1	2	FACETS	0.897	0.858	0.936	1	0.998	1	CLONAL	4	TRUE	1	0.22	2		440	1168	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	418	583	6	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	1	0.984	1	1	0.997	1	CLONAL	3	TRUE	1	0.22	2		589	1186	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	135	47	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	1	2	FACETS	0.889	0.819	0.961	1	0.993	1	CLONAL	4	TRUE	1	0.22	2		47	345	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197716	123197716	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	132	543	0	ENST00000218089.9:c.1840C>T	p.Arg614Ter	p.R614*	ENST00000218089	NM_001042749.1	614	Cga/Tga	20/35	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.22	2		543	958	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432028	121432028	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778074427	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	531	564	0	ENST00000257555.6:c.775G>A	p.Val259Ile	p.V259I	ENST00000257555		259	Gtc/Atc	4/10	1	2	FACETS	0.941	0.903	0.978	1	0.998	1	CLONAL	4	TRUE	1	0.22	2		564	1283	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78435689	78435689	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	217	286	0	ENST00000370768.2:c.131A>G	p.Lys44Arg	p.K44R	ENST00000370768	NM_003902.3	44	aAa/aGa	2/20	1	2	FACETS	0.956	0.897	1	1	0.996	1	CLONAL	4	TRUE	1	0.22	2		286	516	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166139	118166139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766689047	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	354	436	0	ENST00000369448.3:c.649G>A	p.Gly217Arg	p.G217R	ENST00000369448	NM_017709.3	217	Ggg/Agg	2/2	1	2	FACETS	1	0.986	1	1	0.997	1	CLONAL	3	TRUE	1	0.22	2		436	978	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808054	1808054	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	270	315	0	ENST00000260795.2:c.2030T>C	p.Val677Ala	p.V677A	ENST00000260795		677	gTc/gCc	14/17	1	2	FACETS	1	0.987	1	1	0.996	1	CLONAL	3	TRUE	1	0.22	2		315	713	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976873	55976873	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	445	437	0	ENST00000263923.4:c.1039C>A	p.Arg347Ser	p.R347S	ENST00000263923	NM_002253.2	347	Cgt/Agt	8/30	1	2	FACETS	0.878	0.839	0.917	1	0.998	1	CLONAL	4	TRUE	1	0.22	2		437	1152	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510914	157510914	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	271	298	0	ENST00000346085.5:c.3689G>T	p.Arg1230Ile	p.R1230I	ENST00000346085	NM_020732.3	1230	aGa/aTa	14/20	1	2	FACETS	1	0.985	1	1	0.996	1	CLONAL	3	TRUE	1	0.22	2		298	727	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730254	133730254	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	433	393	0	ENST00000318560.5:c.320G>A	p.Gly107Asp	p.G107D	ENST00000318560	NM_005157.4	107	gGc/gAc	3/11	1	2	FACETS	0.935	0.894	0.976	1	0.998	1	CLONAL	4	TRUE	1	0.22	2		393	1053	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781268	135781268	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	725	901	1	ENST00000298552.3:c.1697C>A	p.Pro566His	p.P566H	ENST00000298552	NM_001162426.1	566	cCt/cAt	15/23	1	2	FACETS	0.885	0.854	0.916	1	0.998	1	CLONAL	4	TRUE	1	0.22	2		902	1862	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342895	118342895	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	496	470	0	ENST00000534358.1:c.1021A>G	p.Thr341Ala	p.T341A	ENST00000534358	NM_005933.3	341	Aca/Gca	3/36	1	2	FACETS	0.886	0.849	0.923	1	0.998	1	CLONAL	4	TRUE	1	0.22	2		470	1272	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348769	118348769	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	598	473	1	ENST00000534358.1:c.3422C>A	p.Pro1141His	p.P1141H	ENST00000534358	NM_005933.3	1141	cCc/cAc	5/36	1	2	FACETS	0.877	0.843	0.911	1	0.998	1	CLONAL	4	TRUE	1	0.22	2		474	1550	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870820	12870820	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	206	192	0	ENST00000228872.4:c.47T>C	p.Met16Thr	p.M16T	ENST00000228872	NM_004064.3	16	aTg/aCg	1/3	0.3	3	FACETS	0.948	0.887	1			1	CLONAL	4	TRUE	NA	0.22	3		192	548	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380168	25380168	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	264	347	0	ENST00000311936.3:c.290G>T	p.Arg97Ile	p.R97I	ENST00000311936	NM_004985.3	97	aGa/aTa	3/5	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	3	TRUE	NA	0.22	2		347	736	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352572	89352572	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs773119403	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	301	594	0	ENST00000301030.4:c.767A>G	p.Tyr256Cys	p.Y256C	ENST00000301030	NM_001256183.1	256	tAc/tGc	8/13	1	2	FACETS	1	0.943	1	1	0.995	1	CLONAL	2	TRUE	1	0.22	2		594	1364	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733232	74733232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	537	464	0	ENST00000359995.5:c.11G>A	p.Gly4Asp	p.G4D	ENST00000359995	NM_001195427.1	4	gGc/gAc	1/3	1	2	FACETS	0.891	0.856	0.927	1	0.998	1	CLONAL	4	TRUE	1	0.22	2		464	1369	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101082	4101082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778895928	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	194	170	0	ENST00000262948.5:c.640G>A	p.Gly214Arg	p.G214R	ENST00000262948	NM_030662.3	214	Ggg/Agg	6/11	1	2	FACETS	0.922	0.862	0.983	1	0.995	1	CLONAL	4	TRUE	1	0.22	2		170	478	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040659	47040659	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	539	483	0	ENST00000377604.3:c.1294C>T	p.Pro432Ser	p.P432S	ENST00000377604	NM_001204468.1	432	Ccg/Tcg	13/24	1	2	FACETS	0.959	0.922	0.997	1	0.998	1	CLONAL	4	TRUE	1	0.22	2		483	1277	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337684	73337684	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771690280	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	213	390	3	ENST00000377767.4:c.2032del	p.Ile678PhefsTer59	p.I678Ffs*59	ENST00000377767	NM_014953.3	678	Att/tt	16/21	1	2	FACETS	0.968	0.9	1	1	0.994	1	CLONAL	2	TRUE	1	0.22	2		393	1000	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828257	72828257	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1295	762	979	0	ENST00000268489.5:c.8324del	p.Pro2775GlnfsTer14	p.P2775Qfs*14	ENST00000268489	NM_006885.3	2775	cCa/ca	9/10	1	2	FACETS	1	0.994	1	1	0.998	1	CLONAL	3	TRUE	1	0.22	2		979	2057	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845633	63845634	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	270	209	0	ENST00000279873.7:c.1376dup	p.Pro461AlafsTer26	p.P461Afs*26	ENST00000279873	NM_032199.2	458	gcc/gCcc	9/10	0.249205182435199	4	FACETS	1	0.966	1			1	CLONAL	4	TRUE	NA	0.22	4		209	725	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356305	70356305	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	435	597	0	ENST00000374080.3:c.5203del	p.Arg1735AlafsTer23	p.R1735Afs*23	ENST00000374080		1734	Ccc/cc	37/45	1	2	FACETS	1	0.966	1	1	0.997	1	CLONAL	3	TRUE	1	0.22	2		597	1299	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345769	152345769	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs759063323	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	167	244	0	ENST00000359321.1:c.801del	p.Lys267AsnfsTer30	p.K267Nfs*30	ENST00000359321	NM_005431.1	267	aaA/aa	3/3	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.22	2		244	1101	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215231	123215231	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	144	506	0	ENST00000218089.9:c.2781del	p.Phe927LeufsTer4	p.F927Lfs*4	ENST00000218089	NM_001042749.1	926	cTt/ct	28/35	1	2	FACETS	0.822	0.75	0.897	1	0.989	1	CLONAL	2	TRUE	1	0.22	2		506	796	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444933	49444933	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767415197	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	84	174	0	ENST00000301067.7:c.2533del	p.Arg845GlyfsTer85	p.R845Gfs*85	ENST00000301067	NM_003482.3	845	Cgg/gg	10/54	0.145439147156591	3	FACETS	0.898	0.796	1			1	CLONAL	2	TRUE	NA	0.22	3		174	472	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933456	49933456	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	617	759	2	ENST00000296474.3:c.2734del	p.Asp912ThrfsTer24	p.D912Tfs*24	ENST00000296474	NM_002447.2	912	Gac/ac	11/20	1	2	FACETS	1	0.993	1	1	0.998	1	CLONAL	3	TRUE	1	0.22	2		761	1667	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331582	8331583	+	stop_gained,protein_altering_variant,splice_region_variant	Nonsense_Mutation	INS	-	-	ATTCTTGAACTGTAACTTACA	novel	NA	P-0009087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	150	527	0	ENST00000356435.5:c.5533_5534insTGTAAGTTACAGTTCAAGAAT	p.Ser1845delinsMetTer	p.S1845delinsM*	ENST00000356435		1845	agc/aTGTAAGTTACAGTTCAAGAATgc	33/35	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.22	2		527	1226	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0009168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	16	734	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	1	FACETS	0.136	0.1	0.18	0.136	0.1	0.18	SUBCLONAL	1	TRUE	0	0.291574286974224	1		734	687	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596014	43596014	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	120	397	1	ENST00000355710.3:c.181G>A	p.Glu61Lys	p.E61K	ENST00000355710	NM_020975.4	61	Gag/Aag	2/20	0.291574286974224	1	FACETS	0.804	0.725	0.887	0.804	0.725	0.887	CLONAL	1	TRUE	0	0.291574286974224	1		398	875	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748290	41748290	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	48	340	1	ENST00000226382.2:c.479C>T	p.Ala160Val	p.A160V	ENST00000226382	NM_003924.3	160	gCg/gTg	3/3	0.291574286974224	1	FACETS	0.315	0.265	0.37	0.315	0.265	0.37	SUBCLONAL	1	TRUE	0	0.291574286974224	1		341	893	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370756	225370756	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	79	435	0	ENST00000264414.4:c.1123G>C	p.Glu375Gln	p.E375Q	ENST00000264414	NM_003590.4	375	Gag/Cag	8/16	1	2	FACETS	0.453	0.397	0.514	0.453	0.397	0.514	SUBCLONAL	1	TRUE	1	0.291574286974224	2		435	1195	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006898	47006898	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1556762493	NA	P-0009168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	106	177	0	ENST00000377604.3:c.17+1G>T		p.X6_splice	ENST00000377604	NM_001204468.1	6			1	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.291574286974224	1		177	490	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599904	10599904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	261	467	0	ENST00000171111.5:c.1672G>A	p.Gly558Arg	p.G558R	ENST00000171111	NM_203500.1	558	Ggg/Agg	5/6	0.291574286974224	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.291574286974224	1		467	1217	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11308012	11308012	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0009168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	124	472	0	ENST00000361445.4:c.980C>G	p.Ser327Ter	p.S327*	ENST00000361445	NM_004958.3	327	tCa/tGa	7/58	1	2	FACETS	0.806	0.728	0.889	0.806	0.728	0.889	CLONAL	1	TRUE	1	0.291574286974224	2		472	1055	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057850	27057850	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	266	605	0	ENST00000324856.7:c.1558C>T	p.Gln520Ter	p.Q520*	ENST00000324856	NM_006015.4	520	Cag/Tag	3/20	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.291574286974224	2		605	1346	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095755	178095755	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1213	94	450	0	ENST00000397062.3:c.1576G>C	p.Glu526Gln	p.E526Q	ENST00000397062	NM_006164.4	526	Gag/Cag	5/5	0.291574286974224	3	FACETS	0.565	0.501	0.634	0.283	0.25	0.317	SUBCLONAL	1	TRUE	1	0.291574286974224	3		450	1307	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342976	225342976	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1624	156	672	0	ENST00000264414.4:c.2116G>T	p.Ala706Ser	p.A706S	ENST00000264414	NM_003590.4	706	Gct/Tct	15/16	1	2	FACETS	0.601	0.548	0.657	0.601	0.548	0.657	SUBCLONAL	1	TRUE	1	0.291574286974224	2		672	1780	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661011	227661011	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	180	330	0	ENST00000305123.5:c.2444G>T	p.Ser815Ile	p.S815I	ENST00000305123	NM_005544.2	815	aGc/aTc	1/2	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.291574286974224	2		330	972	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644679	134644679	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	188	335	0	ENST00000398015.3:c.80C>A	p.Thr27Lys	p.T27K	ENST00000398015	NM_004441.4	27	aCg/aAg	2/16	0.130381304735655	3	FACETS	0.832	0.769	0.897			1	INDETERMINATE	2	TRUE	NA	0.291574286974224	3		335	888	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573447	55573447	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	87	241	0	ENST00000288135.5:c.1109A>T	p.Asn370Ile	p.N370I	ENST00000288135	NM_000222.2	370	aAt/aTt	6/21	0.291574286974224	1	FACETS	0.984	0.874	1	0.984	0.874	1	CLONAL	1	TRUE	0	0.291574286974224	1		241	518	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513266	149513266	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	63	420	1	ENST00000261799.4:c.817C>A	p.Arg273Ser	p.R273S	ENST00000261799	NM_002609.3	273	Cgc/Agc	6/23	1	2	FACETS	0.41	0.353	0.472	0.41	0.353	0.472	SUBCLONAL	1	TRUE	1	0.291574286974224	2		421	1054	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271234	26271234	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1827	239	799	1	ENST00000305910.3:c.379C>A	p.Leu127Ile	p.L127I	ENST00000305910	NM_003534.2	127	Ctc/Atc	1/1	1	2	FACETS	0.794	0.737	0.852	0.794	0.737	0.852	SUBCLONAL	1	TRUE	1	0.291574286974224	2		800	2066	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163282	32163282	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs577160458	NA	P-0009168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1539	85	566	0	ENST00000375023.3:c.5944C>G	p.Gln1982Glu	p.Q1982E	ENST00000375023	NM_004557.3	1982	Caa/Gaa	30/30	1	2	FACETS	0.359	0.316	0.406	0.359	0.316	0.406	SUBCLONAL	1	TRUE	1	0.291574286974224	2		566	1624	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969119	93969119	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1320	121	585	0	ENST00000369303.4:c.1877A>T	p.Lys626Met	p.K626M	ENST00000369303	NM_004440.3	626	aAg/aTg	10/17	0.217975123923443	1	FACETS	0.492	0.443	0.544	0.492	0.443	0.544	SUBCLONAL	1	TRUE	0	0.291574286974224	1		585	1441	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334783	81334783	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	274	454	0	ENST00000222390.5:c.1933C>A	p.His645Asn	p.H645N	ENST00000222390	NM_000601.4	645	Cat/Aat	17/18	0.153518181864586	2	FACETS	0.793	0.744	0.844	0.793	0.744	0.844	INDETERMINATE	2	TRUE	0	0.291574286974224	2		454	1185	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971093	21971093	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	67	161	0	ENST00000304494.5:c.265G>T	p.Gly89Cys	p.G89C	ENST00000304494	NM_000077.4	89	Ggc/Tgc	2/3	0.217975123923443	1	FACETS	0.965	0.842	1	0.965	0.842	1	CLONAL	1	TRUE	0	0.291574286974224	1		161	407	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604526	43604526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1242961674	NA	P-0009168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	163	417	0	ENST00000355710.3:c.1111C>A	p.Gln371Lys	p.Q371K	ENST00000355710	NM_020975.4	371	Cag/Aag	6/20	0.291574286974224	1	FACETS	0.913	0.837	0.993	0.913	0.837	0.993	CLONAL	1	TRUE	0	0.291574286974224	1		417	1046	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589519	69589519	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	53	88	0	ENST00000168712.1:c.334C>A	p.Arg112Ser	p.R112S	ENST00000168712	NM_002007.2	112	Cgc/Agc	1/3	1	2	FACETS	0.787	0.679	0.903	1	0.97	1	CLONAL	2	TRUE	1	0.291574286974224	2		88	231	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448535	49448535	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0009168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	77	311	0	ENST00000301067.7:c.177-1G>T		p.X59_splice	ENST00000301067	NM_003482.3	59			0.291574286974224	3	FACETS	0.607	0.531	0.689			1	SUBCLONAL	1	TRUE	NA	0.291574286974224	3		311	997	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546119	29546119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	106	316	0	ENST00000356175.3:c.1624G>A	p.Ala542Thr	p.A542T	ENST00000356175	NM_000267.3	542	Gct/Act	14/57	0.291574286974224	3	FACETS	0.833	0.745	0.927			1	CLONAL	1	TRUE	NA	0.291574286974224	3		316	1000	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627376	37627376	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1327	135	538	1	ENST00000447079.4:c.1291G>T	p.Glu431Ter	p.E431*	ENST00000447079	NM_015083.1	431	Gag/Tag	2/14	0.291574286974224	3	FACETS	0.726	0.657	0.798			1	SUBCLONAL	1	TRUE	NA	0.291574286974224	3		539	1462	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214599	5214599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	54	442	2	ENST00000357368.4:c.4467G>A	p.Met1489Ile	p.M1489I	ENST00000357368	NM_002850.3	1489	atG/atA	29/38	0.291574286974224	1	FACETS	0.304	0.259	0.355	0.304	0.259	0.355	SUBCLONAL	1	TRUE	0	0.291574286974224	1		444	1040	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504078	123504078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	50	230	0	ENST00000371139.4:c.254C>T	p.Ser85Leu	p.S85L	ENST00000371139	NM_001114937.2	85	tCa/tTa	3/4	1	1	FACETS	0.49	0.415	0.572	0.49	0.415	0.572	SUBCLONAL	1	TRUE	0	0.291574286974224	1		230	598	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641138	117641139	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0009168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1209	78	568	0	ENST00000368508.3:c.5832_5833insT	p.Leu1945SerfsTer17	p.L1945Sfs*17	ENST00000368508	NM_002944.2	1944	-/T	36/43	0.217975123923443	1	FACETS	0.355	0.311	0.403	0.355	0.311	0.403	SUBCLONAL	1	TRUE	0	0.291574286974224	1		568	1287	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030348	180030362	+	inframe_deletion	In_Frame_Del	DEL	GTGTGCCCTGGTCAC	GTGTGCCCTGGTCAC	-	novel	NA	P-0009168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	57	513	0	ENST00000261937.6:c.3922_3936del	p.Val1308_His1312del	p.V1308_H1312del	ENST00000261937	NM_182925.4	1308	GTGACCAGGGCACAC/-	30/30	1	2	FACETS	0.367	0.314	0.426	0.367	0.314	0.426	SUBCLONAL	1	TRUE	1	0.291574286974224	2		513	1065	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577137	7577137	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	275	446	0	ENST00000269305.4:c.801del	p.Asn268ThrfsTer77	p.N268Tfs*77	ENST00000269305	NM_001126112.2	267	cgG/cg	8/11	0.291574286974224	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.291574286974224	1		446	1217	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0009170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	35	208	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.66	0.54	0.793	0.66	0.54	0.793	SUBCLONAL	1	FALSE	1	0.243426377235335	2		208	436	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0009170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	42	302	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.679	0.567	0.804	0.679	0.567	0.804	SUBCLONAL	1	FALSE	1	0.243426377235335	2		302	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0009178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	68	323	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	1	2	FACETS	0.672	0.583	0.767	0.672	0.583	0.767	SUBCLONAL	1	TRUE	1	0.282470528075795	2		323	717	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544640	65544640	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	71	414	0	ENST00000358664.4:c.286G>T	p.Glu96Ter	p.E96*	ENST00000358664	NM_002382.4	96	Gag/Tag	4/5	1	2	FACETS	0.82	0.716	0.932	0.82	0.716	0.932	CLONAL	1	TRUE	1	0.282470528075795	2		414	613	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587777894	NA	P-0009178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	69	492	1	ENST00000361445.4:c.6644C>A	p.Ser2215Tyr	p.S2215Y	ENST00000361445	NM_004958.3	2215	tCt/tAt	47/58	0.282470528075795	1	FACETS	0.63	0.548	0.718	0.63	0.548	0.718	SUBCLONAL	1	TRUE	0	0.282470528075795	1		493	666	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845987	156845987	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	33	393	0	ENST00000524377.1:c.1617G>C	p.Met539Ile	p.M539I	ENST00000524377	NM_002529.3	539	atG/atC	13/17	1	2	FACETS	0.464	0.377	0.562	0.464	0.377	0.562	SUBCLONAL	1	TRUE	1	0.282470528075795	2		393	504	SUCCESS
APC	324	MSKCC	GRCh37	5	112170652	112170652	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0009178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	43	397	0	ENST00000257430.4:c.1748C>G	p.Ser583Ter	p.S583*	ENST00000257430	NM_000038.5	583	tCa/tGa	15/16	1	2	FACETS	0.638	0.534	0.754	0.638	0.534	0.754	SUBCLONAL	1	TRUE	1	0.282470528075795	2		397	477	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120241	94120241	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	86	719	0	ENST00000369303.4:c.810G>C	p.Gln270His	p.Q270H	ENST00000369303	NM_004440.3	270	caG/caC	3/17	1	2	FACETS	0.623	0.549	0.701	0.623	0.549	0.701	SUBCLONAL	1	TRUE	1	0.282470528075795	2		719	978	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8252049	8252049	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs774615420	NA	P-0009178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	47	303	0	ENST00000335790.3:c.28G>T	p.Val10Leu	p.V10L	ENST00000335790	NM_002315.2	10	Gtg/Ttg	2/4	1	2	FACETS	0.878	0.743	1	0.878	0.743	1	CLONAL	1	TRUE	1	0.282470528075795	2		303	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573009	7573009	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs876658982	NA	P-0009178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	76	446	0	ENST00000269305.4:c.1101-1G>A		p.X367_splice	ENST00000269305	NM_001126112.2	367			1	2	FACETS	0.795	0.697	0.9	0.795	0.697	0.9	SUBCLONAL	1	TRUE	1	0.282470528075795	2		446	677	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969485	44969485	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	48	244	0	ENST00000377967.4:c.4167A>T	p.Gln1389His	p.Q1389H	ENST00000377967	NM_021140.2	1389	caA/caT	28/29	1	1	FACETS	0.672	0.569	0.786	0.672	0.569	0.786	SUBCLONAL	1	TRUE	0	0.282470528075795	1		244	434	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519590	137519590	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	44	515	0	ENST00000367739.4:c.1048del	p.Ser350LeufsTer3	p.S350Lfs*3	ENST00000367739	NM_000416.2	350	Tct/ct	7/7	1	2	FACETS	0.371	0.31	0.439	0.371	0.31	0.439	SUBCLONAL	1	TRUE	1	0.282470528075795	2		515	839	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129694	11129695	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0009178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	76	407	0	ENST00000358026.2:c.2501dup	p.Tyr834Ter	p.Y834*	ENST00000358026	NM_001128849.1	834	tac/tAac	17/36	0.282470528075795	1	FACETS	0.856	0.752	0.967	0.856	0.752	0.967	CLONAL	1	TRUE	0	0.282470528075795	1		407	540	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974817	21974818	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGGCTCCATG	novel	NA	P-0009178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	22	116	0	ENST00000304494.5:c.-1_9dup	p.Ala4HisfsTer14	p.A4Hfs*14	ENST00000304494	NM_000077.4	3	-/CATGGAGCCG	1/3	0.282470528075795	1	FACETS	0.672	0.524	0.843	0.672	0.524	0.843	SUBCLONAL	1	TRUE	0	0.282470528075795	1		116	199	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133878	55133880	+	missense_variant	Missense_Mutation	TNP	CCA	CCA	ACC	novel	NA	P-0009178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	53	391	0	ENST00000257290.5:c.1091_1093delinsACC	p.Thr364_Thr365delinsAsnPro	p.T364_T365delinsNP	ENST00000257290	NM_006206.4	364	aCCAct/aACCct	7/23	1	2	FACETS	0.661	0.563	0.768	0.661	0.563	0.768	SUBCLONAL	1	TRUE	1	0.282470528075795	2		391	568	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442545	52442545	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009290-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	314	297	0	ENST00000460680.1:c.200A>G	p.Asp67Gly	p.D67G	ENST00000460680	NM_004656.3	67	gAt/gGt	4/17	0.56598786767021	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.565484436007395	2		297	503	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729399	41729399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009290-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	303	664	1	ENST00000242208.4:c.1130G>A	p.Arg377His	p.R377H	ENST00000242208	NM_002192.2	377	cGc/cAc	3/3	0.56598786767021	3	FACETS	1	0.964	1	0.517	0.486	0.549	CLONAL	1	TRUE	1	0.565484436007395	3		665	1329	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589335	28589336	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0009290-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	65	402	0	ENST00000241453.7:c.2711dup	p.Asn904LysfsTer4	p.N904Kfs*4	ENST00000241453	NM_004119.2	904	aat/aaAt	22/24	NA	2	FACETS	0.285	0.246	0.327			1	INDETERMINATE	1	TRUE	NA	0.565484436007395	2		402	808	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163986	47163992	+	frameshift_variant	Frame_Shift_Del	DEL	ATGCTTT	ATGCTTT	-	novel	NA	P-0009290-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	370	330	0	ENST00000409792.3:c.2134_2140del	p.Lys712AlafsTer53	p.K712Afs*53	ENST00000409792	NM_014159.6	712	AAAGCATgc/gc	3/21	0.56598786767021	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.565484436007395	2		330	542	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713707	52713709	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0009290-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	36	302	0	ENST00000394830.3:c.19_21del	p.Arg7del	p.R7del	ENST00000394830	NM_018313.4	7	AGA/-	2/30	0.56598786767021	2	FACETS	0.203	0.166	0.244	0.101	0.083	0.122	SUBCLONAL	1	TRUE	0	0.565484436007395	2		302	628	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922988	44922989	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0009290-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	393	277	0	ENST00000377967.4:c.1850dup	p.Pro618ThrfsTer3	p.P618Tfs*3	ENST00000377967	NM_021140.2	617	cta/cTta	16/29	1	1	FACETS	0.9	0.87	0.929	1	0.997	1	CLONAL	2	TRUE	0	0.565484436007395	1		277	554	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900610	3900616	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCAGC	CGCCAGC	-	novel	NA	P-0009290-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	253	344	0	ENST00000262367.5:c.480_486del	p.Thr163AlafsTer13	p.T163Afs*13	ENST00000262367	NM_004380.2	160	ggGCTGGCG/gg	2/31	0.326454307511742	2	FACETS	0.946	0.898	0.994	0.946	0.898	0.994	INDETERMINATE	2	TRUE	0	0.565484436007395	2		344	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0009294-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	1299	607	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.619464117852791	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	0	0.629431857712864	3		607	1808	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100499	8100499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009294-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	262	634	2	ENST00000346208.3:c.473C>T	p.Pro158Leu	p.P158L	ENST00000346208		158	cCg/cTg	3/6	0.599339626966868	3	FACETS	1	0.955	1	0.341	0.319	0.363	CLONAL	1	TRUE	0	0.629431857712864	3		636	1070	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217302	11217302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009294-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	330	581	0	ENST00000361445.4:c.4376C>A	p.Ala1459Asp	p.A1459D	ENST00000361445	NM_004958.3	1459	gCc/gAc	30/58	0.629431857712864	2	FACETS	0.924	0.873	0.975	0.462	0.436	0.488	CLONAL	1	TRUE	0	0.629431857712864	2		581	1135	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0009294-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	288	414	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.887	0.835	0.94	0.887	0.835	0.94	CLONAL	1	TRUE	1	0.629431857712864	2		414	1032	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741900	17741900	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009294-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	17	31	0	ENST00000250003.3:c.571G>A	p.Glu191Lys	p.E191K	ENST00000250003	NM_002478.4	191	Gag/Aag	1/3	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.629431857712864	2		31	41	SUCCESS
APC	324	MSKCC	GRCh37	5	112175531	112175532	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1554085654	NA	P-0009294-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	243	434	0	ENST00000257430.4:c.4241dup	p.Ser1415LysfsTer8	p.S1415Kfs*8	ENST00000257430	NM_000038.5	1414	gta/gTta	16/16	1	2	FACETS	0.909	0.852	0.969	0.909	0.852	0.969	CLONAL	1	TRUE	1	0.629431857712864	2		434	849	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0009341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	535	314	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.574569526808396	2	FACETS	0.996	0.962	1	0.996	0.962	1	CLONAL	2	TRUE	0	0.574569526808396	2		314	935	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0009341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	349	360	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.574569526808396	2	FACETS	0.986	0.944	1	0.986	0.944	1	CLONAL	2	TRUE	0	0.574569526808396	2		361	616	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998898	11998898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	338	325	1	ENST00000353533.5:c.400C>T	p.Arg134Trp	p.R134W	ENST00000353533	NM_003010.3	134	Cgg/Tgg	4/11	0.574569526808396	2	FACETS	0.925	0.884	0.966	0.925	0.884	0.966	CLONAL	2	TRUE	0	0.574569526808396	2		326	636	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344954	118344955	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0009341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	215	325	0	ENST00000534358.1:c.3086dup	p.Ala1030GlyfsTer9	p.A1030Gfs*9	ENST00000534358	NM_005933.3	1027	cta/ctAa	3/36	1	2	FACETS	0.853	0.794	0.914	0.853	0.794	0.914	CLONAL	1	TRUE	1	0.574569526808396	2		325	877	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0009356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	376	409	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	0.406135070931585	11	FACETS	1	0.983	1			1	CLONAL	5	TRUE	NA	0.406135070931585	11		409	978	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588123	69588123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751257747	NA	P-0009356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	105	659	3	ENST00000168712.1:c.575G>A	p.Arg192Gln	p.R192Q	ENST00000168712	NM_002007.2	192	cGa/cAa	3/3	0.406135070931585	5	FACETS	1	0.965	1	0.235	0.21	0.261	CLONAL	1	TRUE	0	0.406135070931585	5		662	708	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518482	69518482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	70	204	0	ENST00000294312.3:c.163C>T	p.Leu55Phe	p.L55F	ENST00000294312	NM_005117.2	55	Ctc/Ttc	1/3	0.406135070931585	5	FACETS	0.758	0.665	0.857	0.303	0.266	0.343	SUBCLONAL	2	TRUE	0	0.406135070931585	5		204	366	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911338	32911338	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	246	1058	0	ENST00000380152.3:c.2846A>G	p.Tyr949Cys	p.Y949C	ENST00000380152		949	tAt/tGt	11/27	0.351930732061724	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.406135070931585	4		1058	745	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579393	7579408	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGACAGAAGATGAC	AGGGACAGAAGATGAC	-	novel	NA	P-0009356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	168	424	0	ENST00000269305.4:c.279_294del	p.Ser94ProfsTer24	p.S94Pfs*24	ENST00000269305	NM_001126112.2	93	ctGTCATCTTCTGTCCCT/ct	4/11	NA	2	FACETS	0.849	0.794	0.902			1	INDETERMINATE	3	TRUE	NA	0.406135070931585	2		424	325	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023269	27023292	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCGGCAGCAGCGATGGGGTGGG	TGGCGGCAGCAGCGATGGGGTGGG	C	novel	NA	P-0009356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	59	236	0	ENST00000324856.7:c.375_398delinsC	p.Gly127AlafsTer265	p.G127Afs*265	ENST00000324856	NM_006015.4	125	ggTGGCGGCAGCAGCGATGGGGTGGGg/ggCg	1/20	0.375681357444006	4	FACETS	0.853	0.735	0.981	0.426	0.367	0.491	CLONAL	1	TRUE	2	0.406135070931585	4		236	479	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0009403-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	116	552	1	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.818	0.736	0.904	0.818	0.736	0.904	CLONAL	1	TRUE	1	0.326534095952027	2		553	869	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0009403-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	108	386	3	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.326534095952027	2		389	487	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0009403-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	165	691	0	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	1	2	FACETS	0.787	0.721	0.857	0.787	0.721	0.857	SUBCLONAL	1	TRUE	1	0.326534095952027	2		691	1284	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209108185	209108185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751364381	NA	P-0009403-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	129	621	1	ENST00000345146.2:c.664C>T	p.Arg222Cys	p.R222C	ENST00000345146	NM_005896.2	222	Cgt/Tgt	6/10	1	2	FACETS	0.887	0.804	0.975	0.887	0.804	0.975	CLONAL	1	TRUE	1	0.326534095952027	2		622	891	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791356	42791356	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760049446	NA	P-0009403-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	86	599	0	ENST00000575354.2:c.416G>A	p.Arg139Gln	p.R139Q	ENST00000575354	NM_015125.3	139	cGg/cAg	3/20	1	2	FACETS	0.913	0.809	1	0.913	0.809	1	CLONAL	1	TRUE	1	0.326534095952027	2		599	577	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245976	5245976	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009403-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	74	693	0	ENST00000357368.4:c.799G>A	p.Val267Met	p.V267M	ENST00000357368	NM_002850.3	267	Gtg/Atg	10/38	1	2	FACETS	0.748	0.655	0.848	0.748	0.655	0.848	SUBCLONAL	1	TRUE	1	0.326534095952027	2		693	606	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223376	2223376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009403-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	143	752	0	ENST00000398665.3:c.3492del	p.Val1165CysfsTer8	p.V1165Cfs*8	ENST00000398665	NM_032482.2	1163	Ccc/cc	25/28	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.326534095952027	2		752	840	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857549	57857549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009403-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	140	891	2	ENST00000228682.2:c.79del	p.Ala27ProfsTer51	p.A27Pfs*51	ENST00000228682	NM_005269.2	25	caG/ca	2/12	1	2	FACETS	0.945	0.861	1	0.945	0.861	1	CLONAL	1	TRUE	1	0.326534095952027	2		893	907	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257144	19257144	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009403-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	32	301	0	ENST00000162023.5:c.819del	p.Thr274ProfsTer?	p.T274Pfs*?	ENST00000162023		273	ccC/cc	12/13	1	2	FACETS	0.693	0.564	0.836	0.693	0.564	0.836	SUBCLONAL	1	TRUE	1	0.326534095952027	2		301	283	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0009403-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	125	668	0	ENST00000311936.3:c.180_181delinsAA	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggAAaa	3/5	NA	2	FACETS	0.799	0.722	0.88			1	INDETERMINATE	1	TRUE	NA	0.326534095952027	2		668	958	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851574	134851574	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747682274	NA	P-0009403-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	98	514	0	ENST00000398015.3:c.980G>A	p.Arg327His	p.R327H	ENST00000398015	NM_004441.4	327	cGc/cAc	5/16	1	2	FACETS	0.865	0.772	0.964	0.865	0.772	0.964	CLONAL	1	TRUE	1	0.326534095952027	2		514	694	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212130	5212130	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529643294	NA	P-0009403-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	98	736	0	ENST00000357368.4:c.4901C>T	p.Thr1634Met	p.T1634M	ENST00000357368	NM_002850.3	1634	aCg/aTg	32/38	1	2	FACETS	0.81	0.723	0.903	0.81	0.723	0.903	CLONAL	1	TRUE	1	0.326534095952027	2		736	741	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905061	50905061	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009403-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	66	806	1	ENST00000440232.2:c.347del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	115	Ccc/cc	4/27	1	2	FACETS	0.459	0.398	0.527	0.459	0.398	0.527	SUBCLONAL	1	TRUE	1	0.326534095952027	2		807	880	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733425	85733425	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009403-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1285	211	1199	0	ENST00000370580.1:c.587G>T	p.Gly196Val	p.G196V	ENST00000370580	NM_003921.4	196	gGg/gTg	3/3	1	2	FACETS	0.864	0.8	0.931	0.864	0.8	0.931	CLONAL	1	TRUE	1	0.326534095952027	2		1199	1496	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120493350	120493350	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009403-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	157	796	0	ENST00000256646.2:c.2476A>G	p.Thr826Ala	p.T826A	ENST00000256646	NM_024408.3	826	Aca/Gca	15/34	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.326534095952027	2		796	934	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724610	162724610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778566598	NA	P-0009403-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	110	671	0	ENST00000367921.3:c.382C>T	p.Arg128Cys	p.R128C	ENST00000367921	NM_006182.2	128	Cgc/Tgc	5/18	1	2	FACETS	0.845	0.759	0.937	0.845	0.759	0.937	CLONAL	1	TRUE	1	0.326534095952027	2		671	797	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967116	25967116	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009403-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	76	446	0	ENST00000435504.4:c.2090G>T	p.Gly697Val	p.G697V	ENST00000435504		697	gGt/gTt	13/13	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.326534095952027	2		446	431	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215351	142215351	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009403-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	157	567	0	ENST00000350721.4:c.5750A>C	p.Asn1917Thr	p.N1917T	ENST00000350721	NM_001184.3	1917	aAt/aCt	34/47	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.326534095952027	2		567	873	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808308	1808308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1455074121	NA	P-0009403-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	114	743	0	ENST00000260795.2:c.2066C>T	p.Thr689Met	p.T689M	ENST00000260795		689	aCg/aTg	15/17	1	2	FACETS	0.977	0.88	1	0.977	0.88	1	CLONAL	1	TRUE	1	0.326534095952027	2		743	715	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438658	49438658	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1285271258	NA	P-0009403-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	126	639	1	ENST00000301067.7:c.4832G>A	p.Arg1611Gln	p.R1611Q	ENST00000301067	NM_003482.3	1611	cGg/cAg	19/54	NA	2	FACETS	1	0.952	1			1	INDETERMINATE	1	TRUE	NA	0.326534095952027	2		640	716	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445586	49445586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764295994	NA	P-0009403-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	133	744	0	ENST00000301067.7:c.1880C>T	p.Ser627Phe	p.S627F	ENST00000301067	NM_003482.3	627	tCc/tTc	10/54	NA	2	FACETS	0.958	0.87	1			1	INDETERMINATE	1	TRUE	NA	0.326534095952027	2		744	850	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134183	41134183	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009403-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	180	1064	2	ENST00000379561.5:c.1445C>A	p.Pro482His	p.P482H	ENST00000379561	NM_002015.3	482	cCt/cAt	2/3	1	2	FACETS	0.909	0.836	0.985	0.909	0.836	0.985	CLONAL	1	TRUE	1	0.326534095952027	2		1066	1213	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436686	110436686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009403-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	90	521	1	ENST00000375856.3:c.1715G>A	p.Arg572His	p.R572H	ENST00000375856	NM_003749.2	572	cGc/cAc	1/2	0.23197136530981	3	FACETS	1	0.929	1	0.531	0.471	0.594	CLONAL	1	TRUE	1	0.326534095952027	3		522	604	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872017	37872017	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009403-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	116	683	0	ENST00000269571.5:c.1338A>T	p.Gln446His	p.Q446H	ENST00000269571		446	caA/caT	12/27	1	2	FACETS	0.941	0.849	1	0.941	0.849	1	CLONAL	1	TRUE	1	0.326534095952027	2		683	755	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40371806	40371806	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs992474490	NA	P-0009403-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	53	416	0	ENST00000293328.3:c.605C>T	p.Thr202Met	p.T202M	ENST00000293328	NM_012448.3	202	aCg/aTg	6/19	1	2	FACETS	0.826	0.707	0.956	0.826	0.707	0.956	CLONAL	1	TRUE	1	0.326534095952027	2		416	393	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210834	2210834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374446300	NA	P-0009403-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	40	347	0	ENST00000398665.3:c.1331C>T	p.Thr444Met	p.T444M	ENST00000398665	NM_032482.2	444	aCg/aTg	14/28	1	2	FACETS	0.723	0.602	0.856	0.723	0.602	0.856	SUBCLONAL	1	TRUE	1	0.326534095952027	2		347	339	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856409	45856409	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009403-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	100	607	0	ENST00000391945.4:c.1763G>A	p.Cys588Tyr	p.C588Y	ENST00000391945	NM_000400.3	588	tGc/tAc	19/23	1	2	FACETS	0.929	0.831	1	0.929	0.831	1	CLONAL	1	TRUE	1	0.326534095952027	2		607	659	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657002	45657002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009403-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	123	821	0	ENST00000407780.3:c.154G>A	p.Val52Ile	p.V52I	ENST00000407780	NM_001283052.1	52	Gta/Ata	3/7	0.23197136530981	3	FACETS	0.917	0.828	1	0.458	0.414	0.506	CLONAL	1	TRUE	1	0.326534095952027	3		821	956	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077493	30077493	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009403-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	113	554	0	ENST00000338641.4:c.1640A>G	p.Glu547Gly	p.E547G	ENST00000338641	NM_000268.3	547	gAg/gGg	15/16	1	2	FACETS	0.949	0.855	1	0.949	0.855	1	CLONAL	1	TRUE	1	0.326534095952027	2		554	729	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652248	48652248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057518396	NA	P-0009403-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	148	997	2	ENST00000376670.3:c.919C>T	p.Arg307Cys	p.R307C	ENST00000376670	NM_002049.3	307	Cgc/Tgc	6/6	1	2	FACETS	0.83	0.757	0.907	0.83	0.757	0.907	CLONAL	1	TRUE	1	0.326534095952027	2		999	1092	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889148	76889148	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs122445106	NA	P-0009403-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	199	909	2	ENST00000373344.5:c.4862C>T	p.Thr1621Met	p.T1621M	ENST00000373344	NM_000489.3	1621	aCg/aTg	18/35	1	2	FACETS	0.926	0.856	0.999	0.926	0.856	0.999	CLONAL	1	TRUE	1	0.326534095952027	2		911	1316	SUCCESS
APC	324	MSKCC	GRCh37	5	112151228	112151229	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0009403-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	140	675	0	ENST00000257430.4:c.875dup	p.Leu292PhefsTer4	p.L292Ffs*4	ENST00000257430	NM_000038.5	291	gtt/gTtt	9/16	1	2	FACETS	0.861	0.783	0.943	0.861	0.783	0.943	CLONAL	1	TRUE	1	0.326534095952027	2		675	996	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223239	5223239	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009403-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	30	309	1	ENST00000357368.4:c.2564del	p.Pro855ArgfsTer67	p.P855Rfs*67	ENST00000357368	NM_002850.3	855	cCg/cg	18/38	1	2	FACETS	0.572	0.462	0.697	0.572	0.462	0.697	SUBCLONAL	1	TRUE	1	0.326534095952027	2		310	321	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026752	48026753	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0009403-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	88	567	0	ENST00000234420.5:c.1635dup	p.Glu546ArgfsTer17	p.E546Rfs*17	ENST00000234420	NM_000179.2	544	gaa/gAaa	4/10	1	2	FACETS	0.881	0.781	0.987	0.881	0.781	0.987	CLONAL	1	TRUE	1	0.326534095952027	2		567	612	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106525	27106526	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0009403-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	148	919	0	ENST00000324856.7:c.6137_6138del	p.Val2046GlyfsTer52	p.V2046Gfs*52	ENST00000324856	NM_006015.4	2046	GTg/g	20/20	1	2	FACETS	0.82	0.748	0.897	0.82	0.748	0.897	CLONAL	1	TRUE	1	0.326534095952027	2		919	1105	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	347	299	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	0.914250894258799	2		299	722	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775936	9775936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	271	242	0	ENST00000377346.4:c.400C>T	p.Pro134Ser	p.P134S	ENST00000377346	NM_005026.3	134	Cca/Tca	5/24	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.914250894258799	2		242	591	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255388	16255388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	507	452	0	ENST00000375759.3:c.2653G>A	p.Glu885Lys	p.E885K	ENST00000375759	NM_015001.2	885	Gag/Aag	11/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.914250894258799	2		452	1077	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261571	16261571	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	314	268	0	ENST00000375759.3:c.8836C>T	p.Gln2946Ter	p.Q2946*	ENST00000375759	NM_015001.2	2946	Cag/Tag	11/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.914250894258799	2		268	679	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471662	120471662	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	326	288	1	ENST00000256646.2:c.3829G>A	p.Gly1277Ser	p.G1277S	ENST00000256646	NM_024408.3	1277	Ggc/Agc	23/34	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.914250894258799	2		289	656	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743343	162743343	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	316	328	0	ENST00000367921.3:c.1813G>A	p.Val605Met	p.V605M	ENST00000367921	NM_006182.2	605	Gtg/Atg	14/18	0.801017488255813	3	FACETS	0.888	0.838	0.939	0.444	0.419	0.47	CLONAL	1	TRUE	1	0.914250894258799	3		328	1134	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518362	204518362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746628364	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	474	456	0	ENST00000367182.3:c.1025C>T	p.Ser342Phe	p.S342F	ENST00000367182	NM_001278516.1	342	tCc/tTc	11/11	0.914250894258799	2	FACETS	0.917	0.879	0.955	0.458	0.439	0.478	CLONAL	1	TRUE	0	0.914250894258799	2		456	1131	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033352	48033352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750949	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	357	335	0	ENST00000234420.5:c.3656C>T	p.Thr1219Ile	p.T1219I	ENST00000234420	NM_000179.2	1219	aCt/aTt	8/10	1	2	FACETS	0.941	0.896	0.986	0.941	0.896	0.986	CLONAL	1	TRUE	1	0.914250894258799	2		335	830	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728920	190728920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1216508176	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	241	204	0	ENST00000441310.2:c.2308G>A	p.Glu770Lys	p.E770K	ENST00000441310	NM_000534.4	770	Gag/Aag	10/13	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.914250894258799	2		204	526	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12647758	12647758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	537	480	0	ENST00000251849.4:c.622G>A	p.Ala208Thr	p.A208T	ENST00000251849	NM_002880.3	208	Gca/Aca	6/17	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.914250894258799	2		480	1172	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098700	47098700	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	411	403	0	ENST00000409792.3:c.6574C>T	p.Pro2192Ser	p.P2192S	ENST00000409792	NM_014159.6	2192	Ccc/Tcc	15/21	1	2	FACETS	0.983	0.94	1	0.983	0.94	1	CLONAL	1	TRUE	1	0.914250894258799	2		403	915	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643834	52643834	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	321	306	0	ENST00000394830.3:c.2062C>T	p.Pro688Ser	p.P688S	ENST00000394830	NM_018313.4	688	Ccc/Tcc	17/30	1	2	FACETS	0.886	0.84	0.931	0.886	0.84	0.931	CLONAL	1	TRUE	1	0.914250894258799	2		306	793	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987198	69987198	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs764022326	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	176	203	0	ENST00000394351.3:c.259G>A	p.Glu87Lys	p.E87K	ENST00000394351	NM_000248.3	87	Gag/Aag	2/9	1	2	FACETS	0.953	0.889	1	0.953	0.889	1	CLONAL	1	TRUE	1	0.914250894258799	2		203	404	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474773	138474773	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	404	336	0	ENST00000289153.2:c.220G>A	p.Asp74Asn	p.D74N	ENST00000289153	NM_006219.2	74	Gat/Aat	2/22	1	2	FACETS	0.992	0.949	1	0.992	0.949	1	CLONAL	1	TRUE	1	0.914250894258799	2		336	891	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268506	142268506	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	217	242	0	ENST00000350721.4:c.2986C>T	p.Gln996Ter	p.Q996*	ENST00000350721	NM_001184.3	996	Caa/Taa	15/47	1	2	FACETS	0.897	0.842	0.953	0.897	0.842	0.953	CLONAL	1	TRUE	1	0.914250894258799	2		242	529	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593413	55593413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	454	481	1	ENST00000288135.5:c.1570C>T	p.Pro524Ser	p.P524S	ENST00000288135	NM_000222.2	524	Cct/Tct	10/21	1	2	FACETS	0.965	0.925	1	0.965	0.925	1	CLONAL	1	TRUE	1	0.914250894258799	2		482	1029	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197003	106197003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	294	278	0	ENST00000380013.4:c.5336C>T	p.Ala1779Val	p.A1779V	ENST00000380013	NM_001127208.2	1779	gCc/gTc	11/11	NA	2	FACETS	0.963	0.913	1			1	INDETERMINATE	1	TRUE	NA	0.914250894258799	2		278	668	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755675	57755675	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	302	288	0	ENST00000274289.3:c.112C>G	p.Pro38Ala	p.P38A	ENST00000274289	NM_006622.3	38	Ccc/Gcc	1/14	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.914250894258799	2		288	620	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86668013	86668013	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	310	311	0	ENST00000274376.6:c.1776+1G>A		p.X592_splice	ENST00000274376	NM_002890.2	592			1	2	FACETS	0.923	0.875	0.97	0.923	0.875	0.97	CLONAL	1	TRUE	1	0.914250894258799	2		311	735	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439611	140439611	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	247	293	0	ENST00000288602.6:c.2127+1G>A		p.X709_splice	ENST00000288602	NM_004333.4	709			0.913024811700165	3	FACETS	0.77	0.72	0.821	0.385	0.36	0.411	SUBCLONAL	1	TRUE	1	0.914250894258799	3		293	1023	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845135	151845135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	364	421	0	ENST00000262189.6:c.13877G>A	p.Ser4626Asn	p.S4626N	ENST00000262189	NM_170606.2	4626	aGt/aAt	52/59	0.913024811700165	3	FACETS	0.85	0.805	0.896	0.425	0.402	0.448	CLONAL	1	TRUE	1	0.914250894258799	3		421	1365	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915891	127915891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	581	589	1	ENST00000373547.4:c.590C>T	p.Ser197Leu	p.S197L	ENST00000373547	NM_002721.4	197	tCa/tTa	6/7	1	2	FACETS	0.92	0.885	0.954	0.92	0.885	0.954	CLONAL	1	TRUE	1	0.914250894258799	2		590	1382	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63829489	63829489	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	303	268	0	ENST00000279873.7:c.1132T>C	p.Tyr378His	p.Y378H	ENST00000279873	NM_032199.2	378	Tat/Cat	8/10	1	2	FACETS	0.968	0.918	1	0.968	0.918	1	CLONAL	1	TRUE	1	0.914250894258799	2		268	685	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104264045	104264045	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748377573	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	476	420	0	ENST00000369902.3:c.136C>T	p.Pro46Ser	p.P46S	ENST00000369902	NM_016169.3	46	Cct/Tct	1/12	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.914250894258799	2		420	985	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154403	2154403	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	232	445	0	ENST00000434045.2:c.525G>A	p.Trp175Ter	p.W175*	ENST00000434045	NM_001127598.1	175	tgG/tgA	5/5	1	2	FACETS	0.627	0.586	0.669	0.627	0.586	0.669	SUBCLONAL	1	TRUE	1	0.914250894258799	2		445	809	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404741	404741	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1210	303	313	0	ENST00000399788.2:c.4453G>A	p.Glu1485Lys	p.E1485K	ENST00000399788	NM_001042603.1	1485	Gag/Aag	26/28	0.914250894258799	4	FACETS	0.839	0.788	0.891			1	CLONAL	1	TRUE	NA	0.914250894258799	4		313	1513	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409047	4409047	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	292	277	0	ENST00000261254.3:c.742G>A	p.Glu248Lys	p.E248K	ENST00000261254	NM_001759.3	248	Gag/Aag	5/5	0.914250894258799	4	FACETS	0.863	0.81	0.917			1	CLONAL	1	TRUE	NA	0.914250894258799	4		277	1417	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123846	46123846	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	234	228	0	ENST00000334344.6:c.112C>T	p.Pro38Ser	p.P38S	ENST00000334344	NM_152641.2	38	Cct/Tct	2/21	1	2	FACETS	0.909	0.856	0.963	0.909	0.856	0.963	CLONAL	1	TRUE	1	0.914250894258799	2		228	563	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246383	46246383	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	388	368	0	ENST00000334344.6:c.4477G>A	p.Val1493Ile	p.V1493I	ENST00000334344	NM_152641.2	1493	Gta/Ata	15/21	1	2	FACETS	0.952	0.908	0.995	0.952	0.908	0.995	CLONAL	1	TRUE	1	0.914250894258799	2		368	892	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434452	121434452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	268	390	0	ENST00000257555.6:c.1216G>A	p.Ala406Thr	p.A406T	ENST00000257555		406	Gcc/Acc	6/10	1	2	FACETS	0.7	0.658	0.742	0.7	0.658	0.742	SUBCLONAL	1	TRUE	1	0.914250894258799	2		390	838	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911856	32911856	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	737	700	1	ENST00000380152.3:c.3364G>A	p.Gly1122Arg	p.G1122R	ENST00000380152		1122	Gga/Aga	11/27	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.914250894258799	2		701	1571	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609895	81609895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	247	238	0	ENST00000298171.2:c.1493G>A	p.Gly498Asp	p.G498D	ENST00000298171	NM_000369.2	498	gGt/gAt	10/10	1	2	FACETS	0.968	0.914	1	0.968	0.914	1	CLONAL	1	TRUE	1	0.914250894258799	2		238	558	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479829	67479829	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	283	294	2	ENST00000327367.4:c.1136G>A	p.Gly379Asp	p.G379D	ENST00000327367	NM_005902.3	379	gGc/gAc	8/9	1	2	FACETS	0.924	0.875	0.974	0.924	0.875	0.974	CLONAL	1	TRUE	1	0.914250894258799	2		296	670	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129190	2129190	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	308	316	0	ENST00000219476.3:c.3124C>T	p.Pro1042Ser	p.P1042S	ENST00000219476	NM_000548.3	1042	Ccg/Tcg	27/42	1	2	FACETS	0.942	0.894	0.991	0.942	0.894	0.991	CLONAL	1	TRUE	1	0.914250894258799	2		316	715	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822546	72822546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	461	457	0	ENST00000268489.5:c.9629C>T	p.Pro3210Leu	p.P3210L	ENST00000268489	NM_006885.3	3210	cCt/cTt	10/10	1	2	FACETS	0.974	0.934	1	0.974	0.934	1	CLONAL	1	TRUE	1	0.914250894258799	2		457	1035	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81957100	81957100	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	480	498	0	ENST00000359376.3:c.2318C>T	p.Thr773Ile	p.T773I	ENST00000359376	NM_002661.3	773	aCc/aTc	22/33	1	2	FACETS	0.946	0.907	0.985	0.946	0.907	0.985	CLONAL	1	TRUE	1	0.914250894258799	2		498	1110	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556993	29556993	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1135402836	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	165	217	0	ENST00000356175.3:c.2990+1G>A		p.X997_splice	ENST00000356175	NM_000267.3	997			1	2	FACETS	0.807	0.749	0.867	0.807	0.749	0.867	CLONAL	1	TRUE	1	0.914250894258799	2		217	447	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560231	29560231	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	209	182	0	ENST00000356175.3:c.3708G>A	p.Trp1236Ter	p.W1236*	ENST00000356175	NM_000267.3	1236	tgG/tgA	27/57	1	2	FACETS	0.914	0.857	0.972	0.914	0.857	0.972	CLONAL	1	TRUE	1	0.914250894258799	2		182	500	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657340	29657340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555533845	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	481	405	0	ENST00000356175.3:c.5573C>T	p.Ala1858Val	p.A1858V	ENST00000356175	NM_000267.3	1858	gCc/gTc	38/57	1	2	FACETS	0.921	0.883	0.96	0.921	0.883	0.96	CLONAL	1	TRUE	1	0.914250894258799	2		405	1142	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684088	29684088	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	360	318	0	ENST00000356175.3:c.7786G>A	p.Ala2596Thr	p.A2596T	ENST00000356175	NM_000267.3	2596	Gcg/Acg	52/57	1	2	FACETS	0.955	0.91	1	0.955	0.91	1	CLONAL	1	TRUE	1	0.914250894258799	2		318	825	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321596	30321596	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	328	317	0	ENST00000322652.5:c.1451G>A	p.Gly484Asp	p.G484D	ENST00000322652	NM_015355.2	484	gGt/gAt	13/16	1	2	FACETS	0.929	0.883	0.976	0.929	0.883	0.976	CLONAL	1	TRUE	1	0.914250894258799	2		317	772	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434840	56434840	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	310	286	0	ENST00000407977.2:c.2297C>A	p.Ser766Ter	p.S766*	ENST00000407977		766	tCg/tAg	9/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.914250894258799	2		286	667	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435131	56435131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1254699355	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	268	196	0	ENST00000407977.2:c.2006C>T	p.Pro669Leu	p.P669L	ENST00000407977		669	cCc/cTc	9/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.914250894258799	2		196	519	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10257046	10257046	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	325	267	0	ENST00000340748.4:c.2827C>T	p.Pro943Ser	p.P943S	ENST00000340748		943	Cct/Tct	27/40	1	2	FACETS	0.915	0.869	0.961	0.915	0.869	0.961	CLONAL	1	TRUE	1	0.914250894258799	2		267	777	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143966	11143966	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	226	199	0	ENST00000358026.2:c.3547G>A	p.Asp1183Asn	p.D1183N	ENST00000358026	NM_001128849.1	1183	Gac/Aac	26/36	1	2	FACETS	0.968	0.911	1	0.968	0.911	1	CLONAL	1	TRUE	1	0.914250894258799	2		199	511	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031643	36031643	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	387	421	0	ENST00000358208.4:c.1472C>T	p.Pro491Leu	p.P491L	ENST00000358208		491	cCc/cTc	12/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.914250894258799	2		421	834	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932513	39932513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	415	219	0	ENST00000378444.4:c.2086C>T	p.Leu696Phe	p.L696F	ENST00000378444	NM_001123385.1	696	Ctt/Ttt	4/15	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.914250894258799	1		219	453	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938760	76938760	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	509	234	2	ENST00000373344.5:c.1988C>T	p.Pro663Leu	p.P663L	ENST00000373344	NM_000489.3	663	cCc/cTc	9/35	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.914250894258799	1		236	573	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939468	76939468	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	33	186	0	ENST00000373344.5:c.1280A>G	p.Lys427Arg	p.K427R	ENST00000373344	NM_000489.3	427	aAa/aGa	9/35	1	1	FACETS	0.073	0.059	0.089	0.073	0.059	0.089	SUBCLONAL	1	TRUE	0	0.914250894258799	1		186	538	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939465	76939466	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	439	193	0	ENST00000373344.5:c.1282_1283del	p.Asn428TyrfsTer5	p.N428Yfs*5	ENST00000373344	NM_000489.3	428	AAt/t	9/35	1	1	FACETS	0.962	0.937	0.985	0.962	0.937	0.985	CLONAL	1	TRUE	0	0.914250894258799	1		193	542	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211576	46211577	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	407	423	0	ENST00000334344.6:c.545_546del	p.Leu182ProfsTer4	p.L182Pfs*4	ENST00000334344	NM_152641.2	181	aCT/a	5/21	1	2	FACETS	0.895	0.854	0.936	0.895	0.854	0.936	CLONAL	1	TRUE	1	0.914250894258799	2		423	995	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578196	7578197	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0009499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	1037	395	0	ENST00000269305.4:c.652dup	p.Val218GlyfsTer4	p.V218Gfs*4	ENST00000269305	NM_001126112.2	218	gtg/gGtg	6/11	NA	2	FACETS	0.939	0.925	0.952			1	INDETERMINATE	2	TRUE	NA	0.914250894258799	2		395	1208	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0009537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	154	66	0				ENST00000310581	NM_198253.2	-/1132			0.133792990324052	4	FACETS	1	0.953	1	1	0.953	1	INDETERMINATE	2	TRUE	2	0.782220271623154	4		66	340	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0009537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	271	299	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.133792990324052	4	FACETS	0.866	0.817	0.916	0.866	0.817	0.916	INDETERMINATE	2	TRUE	2	0.782220271623154	4		299	713	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430764	78430764	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0009537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	340	370	0	ENST00000370768.2:c.625A>T	p.Lys209Ter	p.K209*	ENST00000370768	NM_003902.3	209	Aaa/Taa	8/20	0.782220271623154	1	FACETS	0.819	0.783	0.856	0.819	0.783	0.856	CLONAL	1	TRUE	0	0.782220271623154	1		370	646	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265609	198265609	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	362	343	0	ENST00000335508.6:c.2548A>G	p.Ile850Val	p.I850V	ENST00000335508	NM_012433.2	850	Ata/Gta	18/25	0.133792990324052	4	FACETS	0.785	0.745	0.825	0.785	0.745	0.825	INDETERMINATE	2	TRUE	2	0.782220271623154	4		343	1051	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102080275	102080275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1388109117	NA	P-0009537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	58	276	1	ENST00000282441.5:c.1012G>A	p.Ala338Thr	p.A338T	ENST00000282441	NM_001130145.2	338	Gca/Aca	6/9	0.133792990324052	4	FACETS	0.298	0.255	0.345	0.149	0.127	0.173	INDETERMINATE	1	TRUE	2	0.782220271623154	4		277	887	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793332	42793332	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0009537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	58	326	0	ENST00000575354.2:c.1135-1G>T		p.X379_splice	ENST00000575354	NM_015125.3	379			0.782220271623154	1	FACETS	0.21	0.181	0.242	0.21	0.181	0.242	SUBCLONAL	1	TRUE	0	0.782220271623154	1		326	429	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794841	42794841	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	18	246	0	ENST00000575354.2:c.1921G>T	p.Glu641Ter	p.E641*	ENST00000575354	NM_015125.3	641	Gag/Tag	10/20	0.782220271623154	1	FACETS	0.091	0.068	0.118	0.091	0.068	0.118	SUBCLONAL	1	TRUE	0	0.782220271623154	1		246	307	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795732	42795733	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCCC	novel	NA	P-0009537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	47	422	0	ENST00000575354.2:c.2727_2731dup	p.Pro911ArgfsTer15	p.P911Rfs*15	ENST00000575354	NM_015125.3	907	-/GCCCC	11/20	0.782220271623154	1	FACETS	0.125	0.105	0.147	0.125	0.105	0.147	SUBCLONAL	1	TRUE	0	0.782220271623154	1		422	586	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795096	42795100	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTT	AGCTT	-	novel	NA	P-0009537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	106	317	0	ENST00000575354.2:c.2178_2182del	p.Leu727ValfsTer34	p.L727Vfs*34	ENST00000575354	NM_015125.3	726	AGCTTa/a	10/20	0.782220271623154	1	FACETS	0.302	0.271	0.334	0.302	0.271	0.334	SUBCLONAL	1	TRUE	0	0.782220271623154	1		317	547	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798121	42798121	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	37	372	0	ENST00000575354.2:c.4077del	p.Phe1359LeufsTer56	p.F1359Lfs*56	ENST00000575354	NM_015125.3	1359	Ttt/tt	17/20	0.782220271623154	1	FACETS	0.109	0.089	0.131	0.109	0.089	0.131	SUBCLONAL	1	TRUE	0	0.782220271623154	1		372	529	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795532	42795532	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	39	363	0	ENST00000575354.2:c.2613del	p.Thr872ProfsTer52	p.T872Pfs*52	ENST00000575354	NM_015125.3	871	tCc/tc	10/20	0.782220271623154	1	FACETS	0.099	0.082	0.119	0.099	0.082	0.119	SUBCLONAL	1	TRUE	0	0.782220271623154	1		363	611	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0009561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	266	208	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.554828608851245	3	FACETS	0.921	0.87	0.973	0.921	0.87	0.973	CLONAL	2	TRUE	1	0.585039299281064	3		208	638	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43749769	43749769	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1455	346	796	0	ENST00000523873.1:c.622A>C	p.Asn208His	p.N208H	ENST00000523873		208	Aac/Cac	7/8	0.487382184091924	4	FACETS	1	0.97	1	0.52	0.491	0.551	CLONAL	1	TRUE	2	0.585039299281064	4		796	1801	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665317	117665317	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1046794283	NA	P-0009561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	192	538	0	ENST00000368508.3:c.4430G>A	p.Trp1477Ter	p.W1477*	ENST00000368508	NM_002944.2	1477	tGg/tAg	27/43	NA	2	FACETS	0.843	0.781	0.906			1	INDETERMINATE	1	TRUE	NA	0.585039299281064	2		538	779	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118367013	118367013	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs782296960	NA	P-0009561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	182	584	0	ENST00000534358.1:c.5595C>G	p.Asn1865Lys	p.N1865K	ENST00000534358	NM_005933.3	1865	aaC/aaG	20/36	1	2	FACETS	0.769	0.711	0.83	0.769	0.711	0.83	SUBCLONAL	1	TRUE	1	0.585039299281064	2		584	809	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682254	37682254	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	422	523	2	ENST00000447079.4:c.3445C>T	p.Gln1149Ter	p.Q1149*	ENST00000447079	NM_015083.1	1149	Cag/Tag	13/14	0.547412187640344	2	FACETS	0.954	0.917	0.991	0.954	0.917	0.991	CLONAL	2	TRUE	0	0.585039299281064	2		525	756	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448310	56448310	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567880628	NA	P-0009561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	313	374	0	ENST00000407977.2:c.337C>T	p.Arg113Ter	p.R113*	ENST00000407977		113	Cga/Tga	3/10	0.547412187640344	2	FACETS	0.98	0.937	1	0.98	0.937	1	CLONAL	2	TRUE	0	0.585039299281064	2		374	546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577514	7577515	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGA	novel	NA	P-0009561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	321	490	0	ENST00000269305.4:c.764_766dup	p.Ile255dup	p.I255dup	ENST00000269305	NM_001126112.2	255	aca/aTCAca	7/11	0.547412187640344	2	FACETS	0.856	0.816	0.896	0.856	0.816	0.896	CLONAL	2	TRUE	0	0.585039299281064	2		490	641	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210181	123210181	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0009584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	202	464	1	ENST00000218089.9:c.2534-1G>T		p.X845_splice	ENST00000218089	NM_001042749.1	845			1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.700621779389137	2		465	471	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871058	12871059	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0009584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	193	195	0	ENST00000228872.4:c.288dup	p.Gly97ArgfsTer28	p.G97Rfs*28	ENST00000228872	NM_004064.3	95	-/A	1/3	1	2	FACETS	1	0.994	1	1	0.996	1	CLONAL	2	TRUE	1	0.700621779389137	2		195	223	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0009617-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	475	703	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.808489064440608	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.808489064440608	1		704	609	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0009617-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	188	480	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.992	0.926	1	0.992	0.926	1	CLONAL	1	TRUE	1	0.808489064440608	2		480	469	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0009617-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	248	424	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	1	2	FACETS	0.991	0.934	1	0.991	0.934	1	CLONAL	1	TRUE	1	0.808489064440608	2		424	619	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0009617-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	132	341	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	0.808489064440608	3	FACETS	0.816	0.744	0.891	0.408	0.372	0.446	CLONAL	1	TRUE	1	0.808489064440608	3		341	562	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258744	115258744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434596	NA	P-0009617-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	192	373	0	ENST00000369535.4:c.38G>A	p.Gly13Asp	p.G13D	ENST00000369535	NM_002524.4	13	gGt/gAt	2/7	0.808489064440608	3	FACETS	0.85	0.787	0.914	0.425	0.393	0.457	CLONAL	1	TRUE	1	0.808489064440608	3		373	785	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248552	10248552	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1323856557	NA	P-0009617-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	387	528	0	ENST00000340748.4:c.4201C>T	p.Arg1401Trp	p.R1401W	ENST00000340748		1401	Cgg/Tgg	35/40	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.808489064440608	2		528	925	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281257	15281257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009617-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	351	418	0	ENST00000263388.2:c.4999C>T	p.Arg1667Cys	p.R1667C	ENST00000263388	NM_000435.2	1667	Cgc/Tgc	27/33	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.808489064440608	2		418	795	SUCCESS
APC	324	MSKCC	GRCh37	5	112175969	112175970	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1114167552	NA	P-0009617-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	163	310	0	ENST00000257430.4:c.4682dup	p.Asp1562GlyfsTer5	p.D1562Gfs*5	ENST00000257430	NM_000038.5	1560	gaa/gAaa	16/16	1	2	FACETS	0.91	0.844	0.978	0.91	0.844	0.978	CLONAL	1	TRUE	1	0.808489064440608	2		310	443	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0009627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	303	371	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.418883281972123	4	FACETS	0.967	0.912	1	0.645	0.608	0.683	CLONAL	2	TRUE	1	0.425132985915289	4		371	1050	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051658	30051658	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555993345	NA	P-0009627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	166	408	0	ENST00000338641.4:c.592C>T	p.Arg198Ter	p.R198*	ENST00000338641	NM_000268.3	198	Cga/Tga	6/16	0.425132985915289	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.425132985915289	1		408	564	SUCCESS
APC	324	MSKCC	GRCh37	5	112176051	112176051	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	116	380	0	ENST00000257430.4:c.4760C>A	p.Ser1587Ter	p.S1587*	ENST00000257430	NM_000038.5	1587	tCa/tAa	16/16	0.425132985915289	1	FACETS	0.844	0.765	0.928	0.844	0.765	0.928	CLONAL	1	TRUE	0	0.425132985915289	1		380	509	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919565	78919565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1307148616	NA	P-0009627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	77	272	0	ENST00000306801.3:c.3124G>A	p.Asp1042Asn	p.D1042N	ENST00000306801	NM_020761.2	1042	Gac/Aac	26/34	0.418883281972123	4	FACETS	0.73	0.641	0.827	0.243	0.213	0.276	SUBCLONAL	1	TRUE	1	0.425132985915289	4		272	707	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039435	47039435	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	128	434	0	ENST00000377604.3:c.1058T>A	p.Ile353Asn	p.I353N	ENST00000377604	NM_001204468.1	353	aTc/aAc	10/24	1	2	FACETS	0.95	0.863	1	0.95	0.863	1	CLONAL	1	TRUE	1	0.425132985915289	2		434	634	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0009756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	154	302	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.459797928600558	1	FACETS	0.896	0.824	0.97	0.896	0.824	0.97	CLONAL	1	TRUE	0	0.459797928600558	1		302	576	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032138	26032138	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1276	329	1431	1	ENST00000244661.2:c.151G>A	p.Glu51Lys	p.E51K	ENST00000244661	NM_003537.3	51	Gag/Aag	1/1	0.439432177718286	2	FACETS	0.892	0.84	0.944	0.446	0.42	0.472	CLONAL	1	TRUE	0	0.459797928600558	2		1432	1605	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207090	1207091	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs876661012	NA	P-0009756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	504	581	1	ENST00000326873.7:c.179dup	p.Tyr60Ter	p.Y60*	ENST00000326873	NM_000455.4	60	tac/tAac	1/10	0.459797928600558	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.459797928600558	2		582	1046	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163768	32163768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	76	560	0	ENST00000375023.3:c.5458G>A	p.Glu1820Lys	p.E1820K	ENST00000375023	NM_004557.3	1820	Gaa/Aaa	30/30	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.459797928600558	NA		560	630	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602659	10602659	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	465	721	0	ENST00000171111.5:c.919G>T	p.Glu307Ter	p.E307*	ENST00000171111	NM_203500.1	307	Gag/Tag	3/6	0.459797928600558	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.459797928600558	2		721	955	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169464	11169464	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	467	830	3	ENST00000358026.2:c.4630G>T	p.Glu1544Ter	p.E1544*	ENST00000358026	NM_001128849.1	1544	Gag/Tag	33/36	0.459797928600558	2	FACETS	0.986	0.946	1	0.986	0.946	1	CLONAL	2	TRUE	0	0.459797928600558	2		833	1030	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221266	1221267	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0009785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	206	592	0	ENST00000326873.7:c.792dup	p.Glu265Ter	p.E265*	ENST00000326873	NM_000455.4	263	-/T	6/10	0.25029151073367	2	FACETS	0.795	0.738	0.854	0.795	0.738	0.854	SUBCLONAL	2	TRUE	0	0.276585670533587	2		592	937	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481661	40481661	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	286	708	0	ENST00000264657.5:c.1144del	p.Arg382GlyfsTer12	p.R382Gfs*12	ENST00000264657	NM_139276.2	382	Cgg/gg	13/24	0.25029151073367	2	FACETS	0.844	0.793	0.897	0.844	0.793	0.897	CLONAL	2	TRUE	0	0.276585670533587	2		708	1225	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0009822-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	321	653	2	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.324232113357786	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.326834696709929	2		655	864	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913471	NA	P-0009822-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	253	686	0	ENST00000269571.5:c.2329G>C	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ctg	20/27	0.244312509205825	5	FACETS	1	0.985	1	0.776	0.727	0.827	CLONAL	2	TRUE	2	0.326834696709929	5		686	991	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375079	31375079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764064020	NA	P-0009822-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	92	532	0	ENST00000328111.2:c.476C>T	p.Pro159Leu	p.P159L	ENST00000328111	NM_006892.3	159	cCg/cTg	6/23	0.105648852792481	5	FACETS	1	0.958	1	0.388	0.344	0.434	INDETERMINATE	1	TRUE	2	0.326834696709929	5		532	721	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857393	68857394	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0009822-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	228	472	0	ENST00000261769.5:c.2029_2030dup	p.Gln677HisfsTer3	p.Q677Hfs*3	ENST00000261769	NM_004360.3	676	-/CA	13/16	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.326834696709929	2		472	564	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0009829-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	70	371	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.211438595785554	5	FACETS	1	0.883	1	0.338	0.294	0.385	CLONAL	1	TRUE	2	0.279558133190759	5		371	701	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0009829-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	15	384	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.279558133190759	3	FACETS	0.591	0.433	0.78	0.295	0.216	0.39	SUBCLONAL	1	TRUE	1	0.279558133190759	3		384	207	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845697	151845697	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009829-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	50	367	0	ENST00000262189.6:c.13315G>T	p.Val4439Phe	p.V4439F	ENST00000262189	NM_170606.2	4439	Gtc/Ttc	52/59	0.246414669734907	4	FACETS	0.925	0.785	1	0.462	0.392	0.539	CLONAL	1	TRUE	2	0.279558133190759	4		367	495	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136887	55136888	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGCT	novel	NA	P-0009829-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	17	530	0	ENST00000257290.5:c.1211_1214dup	p.Tyr405Ter	p.Y405*	ENST00000257290	NM_006206.4	403	-/AGCT	8/23	0.279558133190759	3	FACETS	0.6	0.448	0.779	0.3	0.224	0.39	SUBCLONAL	1	TRUE	1	0.279558133190759	3		530	231	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165212	47165213	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	56	409	0	ENST00000409792.3:c.913dup	p.Thr305AsnfsTer4	p.T305Nfs*4	ENST00000409792	NM_014159.6	305	aca/aAca	3/21	0.232550476523523	1	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	0	0.15	1		409	638	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	35	435	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.881	0.721	1	0.881	0.721	1	CLONAL	1	TRUE	1	0.15	2		436	530	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	46	409	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.15	2		409	474	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	154	463	1	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	1	0.941	1	1	0.992	1	CLONAL	2	TRUE	1	0.15	2		464	991	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900984	114900984	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778855667	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	142	707	0	ENST00000543371.1:c.598del	p.Leu200SerfsTer25	p.L200Sfs*25	ENST00000543371	NM_001198531.1	198	caC/ca	6/14	1	2	FACETS	0.863	0.785	0.945	1	0.989	1	CLONAL	2	TRUE	1	0.15	2		707	1097	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	49	552	1	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.256484719391591	0	FACETS	1	0.923	1			1	CLONAL	1	TRUE	0	0.15	0		553	484	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	106	314	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.843	0.758	0.932	1	0.99	1	CLONAL	3	TRUE	1	0.15	2		314	559	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	21	123	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	0.782	0.606	0.984	1	0.923	1	CLONAL	2	TRUE	1	0.15	2		123	179	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	80	554	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	0.232550476523523	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.15	1		554	836	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910661	32910662	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs276174819	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	72	778	3	ENST00000380152.3:c.2175dup	p.Val726SerfsTer25	p.V726Sfs*25	ENST00000380152		723	-/A	11/27	0.256484719391591	0	FACETS	1	0.915	1			1	CLONAL	1	TRUE	0	0.15	0		781	767	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221711	55221711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760101437	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	110	331	0	ENST00000275493.2:c.755G>A	p.Arg252His	p.R252H	ENST00000275493	NM_005228.3	252	cGc/cAc	7/28	1	2	FACETS	1	0.945	1	1	0.989	1	CLONAL	2	TRUE	1	0.15	2		331	681	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	58	612	0	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.15	2		612	562	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245587	41245587	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357522	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	51	646	3	ENST00000357654.3:c.1961del	p.Lys654SerfsTer47	p.K654Sfs*47	ENST00000357654	NM_007294.3	654	aAg/ag	10/23	0.181510642958115	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.15	1		649	500	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743896	41743896	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	144	601	1	ENST00000301178.4:c.836del	p.Pro279GlnfsTer18	p.P279Qfs*18	ENST00000301178	NM_021913.4	277	gaC/ga	7/20	1	2	FACETS	1	0.952	1	1	0.991	1	CLONAL	2	TRUE	1	0.15	2		602	901	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187558039	187558039	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	51	308	0	ENST00000441802.2:c.3672del	p.Lys1225AsnfsTer9	p.K1225Nfs*9	ENST00000441802	NM_005245.3	1224	ccC/cc	5/27	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.15	2		308	578	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56872937	56872937	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	102	626	0	ENST00000308159.5:c.2097del	p.Phe699LeufsTer19	p.F699Lfs*19	ENST00000308159	NM_014669.4	698	Ttt/tt	19/22	1	2	FACETS	0.804	0.718	0.895	1	0.983	1	CLONAL	2	TRUE	1	0.15	2		626	846	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709485	176709485	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	84	646	0	ENST00000439151.2:c.5912A>G	p.Tyr1971Cys	p.Y1971C	ENST00000439151	NM_022455.4	1971	tAt/tGt	19/23	1	2	FACETS	0.751	0.663	0.845	1	0.977	1	SUBCLONAL	2	TRUE	1	0.15	2		646	746	SUCCESS
APC	324	MSKCC	GRCh37	5	112174910	112174910	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	43	429	0	ENST00000257430.4:c.3622del	p.Thr1208ProfsTer57	p.T1208Pfs*57	ENST00000257430	NM_000038.5	1207	Aaa/aa	16/16	0.256484719391591	0	FACETS	1	0.86	1			1	CLONAL	1	TRUE	0	0.15	0		429	473	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257915	16257915	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	107	211	0	ENST00000375759.3:c.5180A>G	p.Gln1727Arg	p.Q1727R	ENST00000375759	NM_015001.2	1727	cAg/cGg	11/15	1	2	FACETS	1	0.973	1	1	0.99	1	CLONAL	2	TRUE	1	0.15	2		211	575	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37045935	37045935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750781	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	60	499	0	ENST00000231790.2:c.350C>T	p.Thr117Met	p.T117M	ENST00000231790	NM_000249.3	117	aCg/aTg	4/19	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.15	2		499	592	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89478272	89478272	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	43	479	0	ENST00000336596.2:c.2091T>G	p.Ile697Met	p.I697M	ENST00000336596	NM_005233.5	697	atT/atG	12/17	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.15	2		479	527	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151655	55151655	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	68	457	0	ENST00000257290.5:c.2439+2T>C		p.X813_splice	ENST00000257290	NM_006206.4	813			0.232550476523523	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.15	1		457	667	SUCCESS
APC	324	MSKCC	GRCh37	5	112173962	112173962	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	46	318	0	ENST00000257430.4:c.2671A>G	p.Met891Val	p.M891V	ENST00000257430	NM_000038.5	891	Atg/Gtg	16/16	0.256484719391591	0	FACETS	0.703	0.593	0.823			1	SUBCLONAL	2	TRUE	0	0.15	0		318	371	SUCCESS
APC	324	MSKCC	GRCh37	5	112174369	112174369	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	39	369	0	ENST00000257430.4:c.3078T>A	p.Asn1026Lys	p.N1026K	ENST00000257430	NM_000038.5	1026	aaT/aaA	16/16	0.256484719391591	0	FACETS	1	0.89	1			1	CLONAL	1	TRUE	0	0.15	0		369	402	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520258	176520258	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	130	263	0	ENST00000292408.4:c.1177C>T	p.Gln393Ter	p.Q393*	ENST00000292408	NM_213647.1	393	Cag/Tag	9/18	1	2	FACETS	1	0.97	1	1	0.991	1	CLONAL	2	TRUE	1	0.15	2		263	747	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748503	43748503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs769957944	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	167	641	0	ENST00000523873.1:c.457C>T	p.Arg153Ter	p.R153*	ENST00000523873		153	Cga/Tga	6/8	0.115602901758794	4	FACETS	0.85	0.781	0.923	1	0.983	1	CLONAL	3	TRUE	2	0.15	4		641	1004	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268075	55268075	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	84	477	0	ENST00000275493.2:c.2915C>T	p.Ala972Val	p.A972V	ENST00000275493	NM_005228.3	972	gCc/gTc	24/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.15	2		477	756	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123095	5123095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1007272721	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	37	477	0	ENST00000381652.3:c.3151A>G	p.Ile1051Val	p.I1051V	ENST00000381652	NM_004972.3	1051	Att/Gtt	23/25	1	2	FACETS	1	0.836	1	1	0.836	1	CLONAL	1	TRUE	1	0.15	2		477	486	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390915	139390915	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1030823951	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	118	349	0	ENST00000277541.6:c.7276A>G	p.Ser2426Gly	p.S2426G	ENST00000277541	NM_017617.3	2426	Agc/Ggc	34/34	1	2	FACETS	0.835	0.755	0.919	1	0.991	1	CLONAL	3	TRUE	1	0.15	2		349	628	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399279	139399279	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747447584	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	119	358	1	ENST00000277541.6:c.4864C>T	p.Arg1622Cys	p.R1622C	ENST00000277541	NM_017617.3	1622	Cgc/Tgc	26/34	1	2	FACETS	0.871	0.789	0.958	1	0.991	1	CLONAL	3	TRUE	1	0.15	2		359	607	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925397	114925397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773530340	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	153	643	3	ENST00000543371.1:c.1475C>T	p.Ser492Leu	p.S492L	ENST00000543371	NM_001198531.1	492	tCg/tTg	14/14	1	2	FACETS	1	0.923	1	1	0.991	1	CLONAL	2	TRUE	1	0.15	2		646	1009	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279581	123279581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	122	437	1	ENST00000358487.5:c.851C>T	p.Ala284Val	p.A284V	ENST00000358487	NM_000141.4	284	gCc/gTc	7/18	1	2	FACETS	1	0.924	1	1	0.989	1	CLONAL	2	TRUE	1	0.15	2		438	793	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563018	21563018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs577331900	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	83	255	1	ENST00000382592.4:c.901G>A	p.Gly301Ser	p.G301S	ENST00000382592	NM_014572.2	301	Ggc/Agc	4/8	NA	2	FACETS	1	0.963	1			1	INDETERMINATE	2	TRUE	NA	0.15	2		256	455	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911797	32911797	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	55	662	0	ENST00000380152.3:c.3305A>G	p.Asn1102Ser	p.N1102S	ENST00000380152		1102	aAt/aGt	11/27	0.256484719391591	0	FACETS	0.968	0.827	1			1	CLONAL	1	TRUE	0	0.15	0		662	644	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346783	89346783	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	93	474	0	ENST00000301030.4:c.6167A>G	p.Tyr2056Cys	p.Y2056C	ENST00000301030	NM_001256183.1	2056	tAc/tGc	9/13	0.142424599641659	0	FACETS	0.774	0.688	0.865			1	SUBCLONAL	2	TRUE	0	0.15	0		474	681	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679273	29679273	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	56	346	0	ENST00000356175.3:c.7395-2A>C		p.X2465_splice	ENST00000356175	NM_000267.3	2465			1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.15	2		346	563	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435777	56435777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1055597951	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	85	239	0	ENST00000407977.2:c.1360C>T	p.Arg454Cys	p.R454C	ENST00000407977		454	Cgc/Tgc	9/10	1	2	FACETS	0.986	0.873	1	1	0.984	1	CLONAL	2	TRUE	1	0.15	2		239	575	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56411707	56411707	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	146	605	0	ENST00000348428.3:c.1891T>C	p.Tyr631His	p.Y631H	ENST00000348428	NM_006785.3	631	Tac/Cac	15/17	1	2	FACETS	1	0.947	1	1	0.993	1	CLONAL	3	TRUE	1	0.15	2		605	621	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313211	30313211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1449890888	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	82	638	0	ENST00000262643.3:c.905C>T	p.Ser302Leu	p.S302L	ENST00000262643	NM_001238.2	302	tCg/tTg	10/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.15	2		638	839	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830450	72830450	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	95	559	0	ENST00000268489.5:c.6131del	p.Pro2044LeufsTer57	p.P2044Lfs*57	ENST00000268489	NM_006885.3	2044	cCt/ct	9/10	0.142424599641659	0	FACETS	1	0.957	1			1	CLONAL	1	TRUE	0	0.15	0		559	932	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028648	12028650	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	novel	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	65	541	1	ENST00000353533.5:c.854_856del	p.Asp285del	p.D285del	ENST00000353533	NM_003010.3	284	tATGat/tat	8/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.15	2		542	685	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900401	3900401	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	132	432	0	ENST00000262367.5:c.695del	p.Gln232ArgfsTer12	p.Q232Rfs*12	ENST00000262367	NM_004380.2	232	cAg/cg	2/31	1	2	FACETS	1	0.945	1	1	0.99	1	CLONAL	2	TRUE	1	0.15	2		432	832	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151254	202151254	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	110	632	0	ENST00000358485.4:c.1557del	p.Lys520AsnfsTer10	p.K520Nfs*10	ENST00000358485	NM_001080125.1	518	atG/at	9/9	1	2	FACETS	0.846	0.759	0.938	1	0.985	1	CLONAL	2	TRUE	1	0.15	2		632	867	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846107	151846107	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	98	384	0	ENST00000262189.6:c.12905del	p.Pro4302LeufsTer24	p.P4302Lfs*24	ENST00000262189	NM_170606.2	4302	cCt/ct	52/59	1	2	FACETS	0.916	0.818	1	1	0.985	1	CLONAL	2	TRUE	1	0.15	2		384	713	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434759	49434759	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	128	358	2	ENST00000301067.7:c.6794del	p.Gly2265GlufsTer21	p.G2265Efs*21	ENST00000301067	NM_003482.3	2265	gGa/ga	31/54	1	2	FACETS	1	0.968	1	1	0.991	1	CLONAL	2	TRUE	1	0.15	2		360	743	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0009837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	148	379	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	0.207195513592866	2		379	1101	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0009837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	58	434	0	ENST00000311936.3:c.34_35delinsTT	p.Gly12Phe	p.G12F	ENST00000311936	NM_004985.3	12	GGt/TTt	2/5	1	2	FACETS	0.503	0.431	0.583	0.503	0.431	0.583	SUBCLONAL	1	TRUE	1	0.207195513592866	2		434	1112	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637339	47637339	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1285	128	615	0	ENST00000233146.2:c.473A>G	p.Gln158Arg	p.Q158R	ENST00000233146	NM_000251.2	158	cAg/cGg	3/16	1	2	FACETS	0.874	0.79	0.964	0.874	0.79	0.964	CLONAL	1	TRUE	1	0.207195513592866	2		615	1413	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427383	427383	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	93	497	0	ENST00000399788.2:c.2786G>T	p.Gly929Val	p.G929V	ENST00000399788	NM_001042603.1	929	gGg/gTg	19/28	1	2	FACETS	0.837	0.743	0.939	0.837	0.743	0.939	CLONAL	1	TRUE	1	0.207195513592866	2		497	1072	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041373	47041373	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1235	117	684	1	ENST00000377604.3:c.1717C>T	p.Gln573Ter	p.Q573*	ENST00000377604	NM_001204468.1	573	Cag/Tag	16/24	1	2	FACETS	0.835	0.751	0.925	0.835	0.751	0.925	CLONAL	1	TRUE	1	0.207195513592866	2		685	1352	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024406	31024407	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0009837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	86	493	0	ENST00000375687.4:c.3892_3893insGA	p.Thr1298ArgfsTer153	p.T1298Rfs*153	ENST00000375687	NM_015338.5	1297	-/AG	13/13	1	2	FACETS	0.836	0.738	0.942	0.836	0.738	0.942	CLONAL	1	TRUE	1	0.207195513592866	2		493	993	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0009845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	97	509	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.141301022600282	3	FACETS	0.801	0.713	0.895	0.4	0.356	0.448	INDETERMINATE	1	TRUE	1	0.285336763359757	3		509	970	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575209	48575209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767326	NA	P-0009845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	106	435	0	ENST00000342988.3:c.403C>T	p.Arg135Ter	p.R135*	ENST00000342988	NM_005359.5	135	Cga/Tga	3/12	0.259042940641531	1	FACETS	0.843	0.755	0.935	0.843	0.755	0.935	CLONAL	1	TRUE	0	0.285336763359757	1		435	756	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149962	202149962	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	95	436	0	ENST00000358485.4:c.1403G>A	p.Cys468Tyr	p.C468Y	ENST00000358485	NM_001080125.1	468	tGt/tAt	8/9	1	2	FACETS	0.883	0.786	0.987	0.883	0.786	0.987	CLONAL	1	TRUE	1	0.285336763359757	2		436	754	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44910975	44910975	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	192	699	2	ENST00000377967.4:c.676G>T	p.Glu226Ter	p.E226*	ENST00000377967	NM_021140.2	226	Gaa/Taa	9/29	0.259042940641531	1	FACETS	0.988	0.912	1	0.988	0.912	1	CLONAL	1	TRUE	0	0.285336763359757	1		701	1168	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457681	67457682	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1555412140	NA	P-0009845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	168	529	0	ENST00000327367.4:c.492dup	p.Asn165Ter	p.N165*	ENST00000327367	NM_005902.3	164	act/acTt	3/9	0.285336763359757	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.285336763359757	1		529	810	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	141	374	0				ENST00000310581	NM_198253.2	-/1132			0.16061978622496	5	FACETS	1	0.964	1	0.729	0.668	0.791	INDETERMINATE	2	TRUE	2	0.42788555825723	5		374	495	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0009846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	153	280	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	0.42788555825723	3	FACETS	0.942	0.869	1	0.942	0.869	1	CLONAL	2	TRUE	1	0.42788555825723	3		280	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0009846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	549	653	2	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.364279302581024	3	FACETS	0.866	0.834	0.899			1	CLONAL	3	TRUE	NA	0.42788555825723	3		655	1199	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0009846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	2473	327	1	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.42788555825723	15	FACETS	1	0.997	1			1	CLONAL	14	TRUE	NA	0.42788555825723	15		328	3063	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978935	25978935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	377	613	0	ENST00000435504.4:c.988G>A	p.Glu330Lys	p.E330K	ENST00000435504		330	Gaa/Aaa	10/13	0.3417068678996	5	FACETS	1	0.988	1	0.75	0.712	0.79	CLONAL	2	TRUE	2	0.42788555825723	5		613	1285	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222277	2222277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	236	626	0	ENST00000398665.3:c.3109C>T	p.Pro1037Ser	p.P1037S	ENST00000398665	NM_032482.2	1037	Cct/Tct	24/28	0.3417068678996	5	FACETS	0.787	0.734	0.843	0.525	0.489	0.562	SUBCLONAL	2	TRUE	2	0.42788555825723	5		626	1150	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430508	181430508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	65	459	0	ENST00000325404.1:c.360G>A	p.Met120Ile	p.M120I	ENST00000325404	NM_003106.3	120	atG/atA	1/1	0.42788555825723	3	FACETS	0.419	0.362	0.481	0.21	0.181	0.241	SUBCLONAL	1	TRUE	1	0.42788555825723	3		459	880	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359345	118359345	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	150	539	0	ENST00000534358.1:c.4349T>G	p.Val1450Gly	p.V1450G	ENST00000534358	NM_005933.3	1450	gTc/gGc	11/36	0.343463615849994	4	FACETS	0.922	0.841	1	0.307	0.28	0.336	CLONAL	1	TRUE	1	0.42788555825723	4		539	1086	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371743	118371743	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782768278	NA	P-0009846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	49	486	0	ENST00000534358.1:c.6200G>A	p.Arg2067His	p.R2067H	ENST00000534358	NM_005933.3	2067	cGc/cAc	25/36	0.343463615849994	4	FACETS	0.354	0.298	0.415	0.118	0.099	0.139	SUBCLONAL	1	TRUE	1	0.42788555825723	4		486	925	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061456	38061456	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	283	412	0	ENST00000250448.2:c.533T>C	p.Leu178Pro	p.L178P	ENST00000250448	NM_004496.3	178	cTc/cCc	2/2	0.3417068678996	5	FACETS	0.836	0.788	0.885	0.836	0.788	0.885	CLONAL	3	TRUE	2	0.42788555825723	5		412	866	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427023	49427032	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTGGGGGC	CCCTGGGGGC	-	novel	NA	P-0009846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	241	378	0	ENST00000301067.7:c.11456_11465del	p.Gly3819AlafsTer8	p.G3819Afs*8	ENST00000301067	NM_003482.3	3819	gGCCCCCAGGGc/gc	39/54	0.243032877417424	5	FACETS	1	0.983	1	0.76	0.712	0.81	INDETERMINATE	2	TRUE	2	0.42788555825723	5		378	811	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088654	27088655	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0009846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	565	695	0	ENST00000324856.7:c.2265dup	p.Asn756GlufsTer61	p.N756Efs*61	ENST00000324856	NM_006015.4	755	agg/aGgg	7/20	0.42788555825723	4	FACETS	0.96	0.923	0.996			1	CLONAL	3	TRUE	NA	0.42788555825723	4		695	1310	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149961	202149962	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs587776665	NA	P-0009846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	350	561	0	ENST00000358485.4:c.1405_1406del	p.Val469PhefsTer28	p.V469Ffs*28	ENST00000358485	NM_001080125.1	468	TGt/t	8/9	0.42788555825723	3	FACETS	0.904	0.857	0.951	0.904	0.857	0.951	CLONAL	2	TRUE	1	0.42788555825723	3		561	1099	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0009863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	84	208	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.23809091611548	3	FACETS	0.931	0.826	1	0.931	0.826	1	CLONAL	2	TRUE	1	0.22	3		208	455	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	46	450	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	0.101957713017823	0	FACETS	0.561	0.472	0.66			1	INDETERMINATE	1	TRUE	0	0.22	0		450	581	SUCCESS
ATM	472	MSKCC	GRCh37	11	108154953	108154953	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0009863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	17	137	0	ENST00000278616.4:c.3747-1G>T		p.X1249_splice	ENST00000278616	NM_000051.3	1249			1	2	FACETS	0.805	0.603	1	0.805	0.603	1	CLONAL	1	TRUE	1	0.22	2		137	192	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999758	100999758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2152	124	563	3	ENST00000325455.5:c.44C>T	p.Ala15Val	p.A15V	ENST00000325455	NM_001202474.3	15	gCg/gTg	1/8	1	2	FACETS	0.495	0.446	0.548	0.495	0.446	0.548	SUBCLONAL	1	TRUE	1	0.22	2		566	2276	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78938120	78938120	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1220113516	NA	P-0009863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1209	190	371	1	ENST00000306801.3:c.3998G>A	p.Arg1333His	p.R1333H	ENST00000306801	NM_020761.2	1333	cGt/cAt	34/34	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.22	2		372	1399	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074311	30074311	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0009863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	30	183	0	ENST00000338641.4:c.1573A>T	p.Lys525Ter	p.K525*	ENST00000338641	NM_000268.3	525	Aaa/Taa	14/16	1	2	FACETS	0.59	0.475	0.721	0.59	0.475	0.721	SUBCLONAL	1	TRUE	1	0.22	2		183	462	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871059	12871060	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAGGTGCCTGC	novel	NA	P-0009863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	77	183	0	ENST00000228872.4:c.295_305dup	p.Gln104ArgfsTer19	p.Q104Rfs*19	ENST00000228872	NM_004064.3	96	aaa/aAAGGTGCCTGCaa	1/3	0.23809091611548	1	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	0	0.22	1		183	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577061	7577062	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0009863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	169	417	0	ENST00000269305.4:c.876dup	p.Gly293ArgfsTer13	p.G293Rfs*13	ENST00000269305	NM_001126112.2	292	-/A	8/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.22	2		417	1173	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	151	214	2	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	0.474800465177367	3	FACETS	1	0.984	1	0.643	0.591	0.697	CLONAL	1	TRUE	1	0.550160664584303	3		216	544	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	158	322	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.550160664584303	2		322	556	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720805	89720808	+	frameshift_variant	Frame_Shift_Del	DEL	CTTT	CTTT	-	rs398123330	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	95	146	0	ENST00000371953.3:c.956_959del	p.Thr319LysfsTer24	p.T319Kfs*24	ENST00000371953	NM_000314.4	319	aCTTTa/aa	8/9	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.550160664584303	2		146	278	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	436	309	2	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.504953741244545	2	FACETS	0.935	0.897	0.972	0.935	0.897	0.972	CLONAL	2	TRUE	0	0.550160664584303	2		311	848	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257143	16257143	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	303	610	4	ENST00000375759.3:c.4408C>T	p.Arg1470Ter	p.R1470*	ENST00000375759	NM_015001.2	1470	Cga/Tga	11/15	1	2	FACETS	0.977	0.921	1	0.977	0.921	1	CLONAL	1	TRUE	1	0.550160664584303	2		614	1127	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519134	103519135	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	295	595	1	ENST00000355739.4:c.2478dup	p.Asn827Ter	p.N827*	ENST00000355739	NM_000123.3	824	-/T	11/15	1	2	FACETS	0.856	0.805	0.908	0.856	0.805	0.908	CLONAL	1	TRUE	1	0.550160664584303	2		596	1253	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776783	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	152	378	0	ENST00000267163.4:c.1215+1G>A		p.X405_splice	ENST00000267163	NM_000321.2	405			0.385047881290828	1	FACETS	0.808	0.744	0.873	0.808	0.744	0.873	CLONAL	1	TRUE	0	0.550160664584303	1		378	496	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830902	72830903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	388	988	1	ENST00000268489.5:c.5677_5678dup	p.Asp1894GlyfsTer21	p.D1894Gfs*21	ENST00000268489	NM_006885.3	1893	agg/agAGg	9/10	0.461553714222233	1	FACETS	0.749	0.711	0.787	0.749	0.711	0.787	SUBCLONAL	1	TRUE	0	0.550160664584303	1		989	1366	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041025	112041025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779126684	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	532	728	0	ENST00000368678.4:c.230G>A	p.Arg77His	p.R77H	ENST00000368678		77	cGt/cAt	3/13	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.550160664584303	2		728	1628	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249405	110249405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	348	761	0	ENST00000374672.4:c.1168C>T	p.Arg390Trp	p.R390W	ENST00000374672	NM_004235.4	390	Cgg/Tgg	4/5	1	2	FACETS	0.885	0.837	0.935	0.885	0.837	0.935	CLONAL	1	TRUE	1	0.550160664584303	2		761	1429	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251542	251542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200397144	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	157	362	1	ENST00000264932.6:c.1753C>T	p.Arg585Trp	p.R585W	ENST00000264932	NM_004168.2	585	Cgg/Tgg	13/15	1	2	FACETS	0.915	0.841	0.991	0.915	0.841	0.991	CLONAL	1	TRUE	1	0.550160664584303	2		363	624	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596032	43596032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749390385	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	199	482	0	ENST00000355710.3:c.199C>T	p.Arg67Cys	p.R67C	ENST00000355710	NM_020975.4	67	Cgc/Tgc	2/20	1	2	FACETS	0.885	0.822	0.951	0.885	0.822	0.951	CLONAL	1	TRUE	1	0.550160664584303	2		482	817	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016264	150016264	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	276	651	3	ENST00000253339.5:c.442C>T	p.Arg148Ter	p.R148*	ENST00000253339		148	Cga/Tga	2/7	1	2	FACETS	0.893	0.839	0.95	0.893	0.839	0.95	CLONAL	1	TRUE	1	0.550160664584303	2		654	1123	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258878	16258878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	310	666	0	ENST00000375759.3:c.6143C>T	p.Ala2048Val	p.A2048V	ENST00000375759	NM_015001.2	2048	gCt/gTt	11/15	1	2	FACETS	0.928	0.874	0.982	0.928	0.874	0.982	CLONAL	1	TRUE	1	0.550160664584303	2		666	1215	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118871	61118871	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372213094	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	261	500	0	ENST00000295025.8:c.64C>T	p.Arg22Cys	p.R22C	ENST00000295025	NM_002908.2	22	Cgt/Tgt	2/11	1	2	FACETS	0.877	0.822	0.934	0.877	0.822	0.934	CLONAL	1	TRUE	1	0.550160664584303	2		500	1082	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437229	220437229	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753969684	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	325	757	1	ENST00000243786.2:c.133G>A	p.Ala45Thr	p.A45T	ENST00000243786	NM_002191.3	45	Gcg/Acg	1/2	1	2	FACETS	0.906	0.855	0.958	0.906	0.855	0.958	CLONAL	1	TRUE	1	0.550160664584303	2		758	1304	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664664	138664664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	22	28	0	ENST00000330315.3:c.901G>A	p.Ala301Thr	p.A301T	ENST00000330315	NM_023067.3	301	Gcg/Acg	1/1	1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	1	0.550160664584303	2		28	77	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940596	131940596	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	356	562	0	ENST00000265335.6:c.2623C>G	p.Leu875Val	p.L875V	ENST00000265335		875	Ctt/Gtt	16/25	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.550160664584303	2		562	1284	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502659	149502659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs554645092	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	154	333	0	ENST00000261799.4:c.2129C>T	p.Pro710Leu	p.P710L	ENST00000261799	NM_002609.3	710	cCg/cTg	15/23	1	2	FACETS	0.844	0.775	0.916	0.844	0.775	0.916	CLONAL	1	TRUE	1	0.550160664584303	2		333	663	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206804	162206804	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1262180713	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	190	381	0	ENST00000366898.1:c.871G>A	p.Ala291Thr	p.A291T	ENST00000366898	NM_004562.2	291	Gct/Act	7/12	1	2	FACETS	0.834	0.772	0.898	0.834	0.772	0.898	CLONAL	1	TRUE	1	0.550160664584303	2		381	828	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6029581	6029581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1236095389	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	504	572	0	ENST00000265849.7:c.994G>A	p.Val332Ile	p.V332I	ENST00000265849	NM_000535.5	332	Gtt/Att	10/15	0.550160664584303	3	FACETS	0.897	0.86	0.935	0.897	0.86	0.935	CLONAL	2	TRUE	1	0.550160664584303	3		572	1302	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6038848	6038848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876658387	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	627	650	0	ENST00000265849.7:c.596G>A	p.Arg199His	p.R199H	ENST00000265849	NM_000535.5	199	cGt/cAt	6/15	0.550160664584303	3	FACETS	0.978	0.943	1	0.978	0.943	1	CLONAL	2	TRUE	1	0.550160664584303	3		650	1486	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802558	139802558	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773154383	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	175	714	0	ENST00000247668.2:c.403G>A	p.Glu135Lys	p.E135K	ENST00000247668	NM_021138.3	135	Gaa/Aaa	5/11	1	2	FACETS	0.489	0.449	0.531	0.489	0.449	0.531	SUBCLONAL	1	TRUE	1	0.550160664584303	2		714	1300	SUCCESS
RET	5979	MSKCC	GRCh37	10	43598056	43598056	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751572082	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	177	345	0	ENST00000355710.3:c.604G>A	p.Val202Met	p.V202M	ENST00000355710	NM_020975.4	202	Gtg/Atg	3/20	1	2	FACETS	0.938	0.867	1	0.938	0.867	1	CLONAL	1	TRUE	1	0.550160664584303	2		345	686	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451546	70451546	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768089885	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	288	586	0	ENST00000373644.4:c.6386C>T	p.Ala2129Val	p.A2129V	ENST00000373644	NM_030625.2	2129	gCg/gTg	12/12	1	2	FACETS	0.913	0.858	0.969	0.913	0.858	0.969	CLONAL	1	TRUE	1	0.550160664584303	2		586	1147	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438183	438183	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	78	453	0	ENST00000399788.2:c.1786C>T	p.Arg596Cys	p.R596C	ENST00000399788	NM_001042603.1	596	Cgt/Tgt	14/28	1	2	FACETS	0.342	0.3	0.388	0.342	0.3	0.388	SUBCLONAL	1	TRUE	1	0.550160664584303	2		453	828	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285669	46285669	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1368075571	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	203	501	0	ENST00000334344.6:c.5029C>T	p.Arg1677Ter	p.R1677*	ENST00000334344	NM_152641.2	1677	Cga/Tga	17/21	1	2	FACETS	0.831	0.771	0.893	0.831	0.771	0.893	CLONAL	1	TRUE	1	0.550160664584303	2		501	888	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602330	28602330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1338788116	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	290	552	0	ENST00000241453.7:c.2038G>A	p.Ala680Thr	p.A680T	ENST00000241453	NM_004119.2	680	Gcg/Acg	16/24	1	2	FACETS	0.92	0.865	0.976	0.92	0.865	0.976	CLONAL	1	TRUE	1	0.550160664584303	2		552	1146	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436413	110436413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868142479	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	176	414	0	ENST00000375856.3:c.1988C>T	p.Ala663Val	p.A663V	ENST00000375856	NM_003749.2	663	gCg/gTg	1/2	1	2	FACETS	0.91	0.841	0.982	0.91	0.841	0.982	CLONAL	1	TRUE	1	0.550160664584303	2		414	703	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778738	3778738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1489860615	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	66	452	2	ENST00000262367.5:c.6310C>T	p.Arg2104Cys	p.R2104C	ENST00000262367	NM_004380.2	2104	Cgc/Tgc	31/31	1	2	FACETS	0.324	0.281	0.371	0.324	0.281	0.371	SUBCLONAL	1	TRUE	1	0.550160664584303	2		454	740	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274018	10274018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1354238435	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	255	631	0	ENST00000330684.3:c.251C>T	p.Thr84Met	p.T84M	ENST00000330684	NM_001134407.1	84	aCg/aTg	2/13	1	2	FACETS	0.941	0.882	1	0.941	0.882	1	CLONAL	1	TRUE	1	0.550160664584303	2		631	985	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81939042	81939042	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	352	869	0	ENST00000359376.3:c.1397T>C	p.Val466Ala	p.V466A	ENST00000359376	NM_002661.3	466	gTc/gCc	15/33	1	2	FACETS	0.875	0.828	0.924	0.875	0.828	0.924	CLONAL	1	TRUE	1	0.550160664584303	2		869	1462	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351736	89351736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1261106013	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1224	411	911	3	ENST00000301030.4:c.1214G>A	p.Arg405His	p.R405H	ENST00000301030	NM_001256183.1	405	cGt/cAt	9/13	1	2	FACETS	0.914	0.868	0.961	0.914	0.868	0.961	CLONAL	1	TRUE	1	0.550160664584303	2		914	1635	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78858817	78858817	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779943676	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	188	595	0	ENST00000306801.3:c.1852G>A	p.Ala618Thr	p.A618T	ENST00000306801	NM_020761.2	618	Gca/Aca	17/34	1	2	FACETS	0.912	0.845	0.982	0.912	0.845	0.982	CLONAL	1	TRUE	1	0.550160664584303	2		595	749	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919548	78919548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769436510	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	40	443	0	ENST00000306801.3:c.3107C>T	p.Pro1036Leu	p.P1036L	ENST00000306801	NM_020761.2	1036	cCg/cTg	26/34	1	2	FACETS	0.183	0.151	0.218	0.183	0.151	0.218	SUBCLONAL	1	TRUE	1	0.550160664584303	2		443	796	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291562	10291562	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	116	610	0	ENST00000340748.4:c.118-1G>A		p.X40_splice	ENST00000340748		40			1	2	FACETS	0.372	0.334	0.412	0.372	0.334	0.412	SUBCLONAL	1	TRUE	1	0.550160664584303	2		610	1134	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291860	15291860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146214060	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	224	574	0	ENST00000263388.2:c.2906G>A	p.Arg969Gln	p.R969Q	ENST00000263388	NM_000435.2	969	cGg/cAg	18/33	1	2	FACETS	0.954	0.89	1	0.954	0.89	1	CLONAL	1	TRUE	1	0.550160664584303	2		574	854	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793159	42793159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	201	501	1	ENST00000575354.2:c.1051C>T	p.Arg351Trp	p.R351W	ENST00000575354	NM_015125.3	351	Cgg/Tgg	7/20	1	2	FACETS	0.857	0.795	0.92	0.857	0.795	0.92	CLONAL	1	TRUE	1	0.550160664584303	2		502	853	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797955	42797955	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140554618	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	313	749	2	ENST00000575354.2:c.4007C>T	p.Pro1336Leu	p.P1336L	ENST00000575354	NM_015125.3	1336	cCg/cTg	16/20	1	2	FACETS	0.923	0.87	0.977	0.923	0.87	0.977	CLONAL	1	TRUE	1	0.550160664584303	2		751	1233	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46277819	46277819	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1242239410	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1406	179	636	0	ENST00000371998.3:c.3617T>C	p.Met1206Thr	p.M1206T	ENST00000371998		1206	aTg/aCg	19/23	0.474800465177367	3	FACETS	0.523	0.481	0.568	0.262	0.24	0.284	SUBCLONAL	1	TRUE	1	0.550160664584303	3		636	1585	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39772519	39772519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	307	566	1	ENST00000288319.7:c.722C>T	p.Thr241Met	p.T241M	ENST00000288319	NM_182918.3	241	aCg/aTg	6/10	1	2	FACETS	0.931	0.877	0.986	0.931	0.877	0.986	CLONAL	1	TRUE	1	0.550160664584303	2		567	1199	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574253	41574253	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs201097711	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	245	598	1	ENST00000263253.7:c.6538C>T	p.Arg2180Ter	p.R2180*	ENST00000263253	NM_001429.3	2180	Cga/Tga	31/31	1	2	FACETS	0.872	0.815	0.931	0.872	0.815	0.931	CLONAL	1	TRUE	1	0.550160664584303	2		599	1021	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44894174	44894174	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	358	354	0	ENST00000377967.4:c.565-2A>G		p.X189_splice	ENST00000377967	NM_021140.2	189			1	1	FACETS	0.762	0.731	0.793	1	0.996	1	SUBCLONAL	2	TRUE	0	0.550160664584303	1		354	619	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039372	47039372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	334	322	1	ENST00000377604.3:c.995G>A	p.Arg332His	p.R332H	ENST00000377604	NM_001204468.1	332	cGc/cAc	10/24	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.550160664584303	1		323	621	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330647	65330648	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	104	434	0	ENST00000342505.4:c.998_999del	p.Ser333CysfsTer2	p.S333Cfs*2	ENST00000342505	NM_002227.2	333	tCT/t	8/25	0.522301198026824	1	FACETS	0.452	0.406	0.502	0.452	0.406	0.502	SUBCLONAL	1	TRUE	0	0.550160664584303	1		434	606	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018082	48018082	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	259	565	0	ENST00000234420.5:c.278del	p.Gly93GlufsTer56	p.G93Efs*56	ENST00000234420	NM_000179.2	93	Gga/ga	2/10	0.520614659945142	1	FACETS	0.859	0.807	0.911	0.859	0.807	0.911	CLONAL	1	TRUE	0	0.550160664584303	1		565	795	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	212	359	0	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.51	2		359	761	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	58	410	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.275	0.236	0.319	0.275	0.236	0.319	SUBCLONAL	1	TRUE	1	0.51	2		410	826	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	62	357	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.138850677554079	3	FACETS	0.405	0.349	0.466	0.202	0.174	0.233	INDETERMINATE	1	TRUE	1	0.51	3		357	754	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	223	615	2	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	0.776	0.722	0.832	0.776	0.722	0.832	SUBCLONAL	1	TRUE	1	0.51	2		617	1127	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	29	170	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.291	0.233	0.356	0.291	0.233	0.356	SUBCLONAL	1	TRUE	1	0.51	2		171	391	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	154	342	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.896	0.822	0.973	0.896	0.822	0.973	CLONAL	1	TRUE	1	0.51	2		342	674	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733513	85733513	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs387906350	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	347	769	2	ENST00000370580.1:c.499del	p.Ser167LeufsTer6	p.S167Lfs*6	ENST00000370580	NM_003921.4	167	Tct/ct	3/3	1	2	FACETS	0.91	0.859	0.961	0.91	0.859	0.961	CLONAL	1	TRUE	1	0.51	2		771	1496	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	261	817	4	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	0.846	0.792	0.902	0.846	0.792	0.902	CLONAL	1	TRUE	1	0.51	2		821	1210	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	353	331	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	0.138850677554079	3	FACETS	1	0.992	1	1	0.992	1	INDETERMINATE	2	TRUE	1	0.51	3		332	741	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	46	343	1	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	1	2	FACETS	0.207	0.173	0.244	0.207	0.173	0.244	SUBCLONAL	1	TRUE	1	0.51	2		344	873	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	204	360	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.269484555850298	2	FACETS	0.825	0.773	0.877	0.825	0.773	0.877	INDETERMINATE	2	TRUE	0	0.51	2		361	485	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185195118	185195118	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	255	453	0	ENST00000265026.3:c.2435G>T	p.Gly812Val	p.G812V	ENST00000265026	NM_004721.4	812	gGa/gTa	12/14	0.138850677554079	3	FACETS	1	0.981	1	0.561	0.525	0.599	INDETERMINATE	1	TRUE	1	0.51	3		453	1118	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	43	47	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	1	2	FACETS	0.998	0.848	1	0.998	0.848	1	CLONAL	1	TRUE	1	0.51	2		47	169	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	322	431	2	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.51	2		433	975	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508499	106508499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752602335	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	43	78	0	ENST00000359195.3:c.493G>A	p.Val165Ile	p.V165I	ENST00000359195	NM_002649.2	165	Gtc/Atc	2/11	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.51	2		78	143	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	383	619	1	ENST00000263967.3:c.333G>T	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaT	2/21	0.138850677554079	3	FACETS	0.756	0.718	0.794	0.756	0.718	0.794	INDETERMINATE	2	TRUE	1	0.51	3		620	1247	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	192	332	1	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	0.138850677554079	3	FACETS	0.768	0.714	0.824	0.768	0.714	0.824	INDETERMINATE	2	TRUE	1	0.51	3		333	615	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512383	38512383	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1188389540	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	89	206	1	ENST00000254066.5:c.1294C>T	p.Arg432Trp	p.R432W	ENST00000254066	NM_000964.3	432	Cgg/Tgg	9/9	1	2	FACETS	0.804	0.717	0.897	0.804	0.717	0.897	CLONAL	1	TRUE	1	0.51	2		207	434	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219838	133219838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142508245	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	139	260	0	ENST00000320574.5:c.4523G>A	p.Arg1508His	p.R1508H	ENST00000320574	NM_006231.2	1508	cGc/cAc	35/49	1	2	FACETS	0.995	0.91	1	0.995	0.91	1	CLONAL	1	TRUE	1	0.51	2		260	548	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	257	493	0	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	1	2	FACETS	0.916	0.858	0.976	0.916	0.858	0.976	CLONAL	1	TRUE	1	0.51	2		493	1100	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741427	17741427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	282	547	0	ENST00000250003.3:c.98C>T	p.Pro33Leu	p.P33L	ENST00000250003	NM_002478.4	33	cCg/cTg	1/3	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.51	2		547	1052	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	340	702	5	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	0.974	0.92	1	0.974	0.92	1	CLONAL	1	TRUE	1	0.51	2		707	1369	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222309	53222309	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	90	249	0	ENST00000375401.3:c.4523del	p.Pro1508LeufsTer36	p.P1508Lfs*36	ENST00000375401	NM_004187.3	1508	cCt/ct	26/26	1	1	FACETS	0.562	0.5	0.627	0.562	0.5	0.627	SUBCLONAL	1	TRUE	0	0.51	1		249	468	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446270	187446270	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	178	297	0	ENST00000232014.4:c.1418del	p.Pro473ArgfsTer117	p.P473Rfs*117	ENST00000232014	NM_001130845.1	473	cCg/cg	6/10	0.138850677554079	3	FACETS	1	0.99	1	0.736	0.682	0.792	INDETERMINATE	1	TRUE	1	0.51	3		297	595	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100577	157100577	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1289149988	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	47	210	0	ENST00000346085.5:c.1518del	p.Gly507AspfsTer16	p.G507Dfs*16	ENST00000346085	NM_020732.3	505	aCc/ac	1/20	1	2	FACETS	0.302	0.254	0.355	0.302	0.254	0.355	SUBCLONAL	1	TRUE	1	0.51	2		210	610	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858008	45858008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199778239	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	68	423	0	ENST00000391945.4:c.1645G>A	p.Val549Met	p.V549M	ENST00000391945	NM_000400.3	549	Gtg/Atg	17/23	0.3	2	FACETS	0.288	0.25	0.33	0.144	0.125	0.165	INDETERMINATE	1	TRUE	0	0.51	2		423	926	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968597	55968597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34038364	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	106	490	1	ENST00000263923.4:c.2066C>T	p.Thr689Met	p.T689M	ENST00000263923	NM_002253.2	689	aCg/aTg	14/30	1	2	FACETS	0.427	0.382	0.475	0.427	0.382	0.475	SUBCLONAL	1	TRUE	1	0.51	2		491	974	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259800	16259800	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	197	389	0	ENST00000375759.3:c.7065T>A	p.His2355Gln	p.H2355Q	ENST00000375759	NM_015001.2	2355	caT/caA	11/15	0.288889075960592	4	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.51	4		389	1000	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36934793	36934793	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1281481744	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	331	764	0	ENST00000361632.4:c.1540C>T	p.Pro514Ser	p.P514S	ENST00000361632		514	Ccc/Tcc	11/16	1	2	FACETS	0.994	0.939	1	0.994	0.939	1	CLONAL	1	TRUE	1	0.51	2		764	1306	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253490	226253490	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	305	426	0	ENST00000366813.1:c.262G>T	p.Ala88Ser	p.A88S	ENST00000366813		88	Gca/Tca	2/3	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.51	2		426	1013	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151205	202151205	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	270	423	0	ENST00000358485.4:c.1505T>C	p.Leu502Pro	p.L502P	ENST00000358485	NM_001080125.1	502	cTg/cCg	9/9	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.51	2		423	877	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662482	227662482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	115	216	0	ENST00000305123.5:c.973C>T	p.Arg325Cys	p.R325C	ENST00000305123	NM_005544.2	325	Cgt/Tgt	1/2	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.51	2		216	449	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524747	187524747	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	53	408	0	ENST00000441802.2:c.10933A>G	p.Ile3645Val	p.I3645V	ENST00000441802	NM_005245.3	3645	Atc/Gtc	19/27	1	2	FACETS	0.215	0.183	0.251	0.215	0.183	0.251	SUBCLONAL	1	TRUE	1	0.51	2		408	965	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149465957	149465957	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	264	486	1	ENST00000286301.3:c.34G>A	p.Ala12Thr	p.A12T	ENST00000286301	NM_005211.3	12	Gcc/Acc	2/22	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.51	2		487	957	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225519	26225519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1381	523	1002	0	ENST00000360408.1:c.137C>T	p.Thr46Ile	p.T46I	ENST00000360408	NM_003532.2	46	aCc/aTc	1/1	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.51	2		1002	1904	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910712	29910712	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	246	498	0	ENST00000376809.5:c.252G>T	p.Trp84Cys	p.W84C	ENST00000376809	NM_002116.7	84	tgG/tgT	2/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.51	2		498	911	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677989	117677989	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	233	641	0	ENST00000368508.3:c.3944C>T	p.Pro1315Leu	p.P1315L	ENST00000368508	NM_002944.2	1315	cCc/cTc	25/43	1	2	FACETS	0.89	0.83	0.951	0.89	0.83	0.951	CLONAL	1	TRUE	1	0.51	2		641	1027	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099650	157099650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	14	25	0	ENST00000346085.5:c.587C>T	p.Ala196Val	p.A196V	ENST00000346085	NM_020732.3	196	gCg/gTg	1/20	1	2	FACETS	0.722	0.532	0.943	0.722	0.532	0.943	CLONAL	1	TRUE	1	0.51	2		25	76	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150365	157150365	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	73	405	0	ENST00000346085.5:c.1547G>A	p.Ser516Asn	p.S516N	ENST00000346085	NM_020732.3	516	aGc/aAc	2/20	1	2	FACETS	0.372	0.324	0.423	0.372	0.324	0.423	SUBCLONAL	1	TRUE	1	0.51	2		405	770	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157519980	157519980	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	62	386	1	ENST00000346085.5:c.4049G>A	p.Gly1350Asp	p.G1350D	ENST00000346085	NM_020732.3	1350	gGc/gAc	17/20	1	2	FACETS	0.251	0.216	0.29	0.251	0.216	0.29	SUBCLONAL	1	TRUE	1	0.51	2		387	967	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987326	2987326	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	253	529	0	ENST00000396946.4:c.103C>T	p.Arg35Cys	p.R35C	ENST00000396946	NM_032415.4	35	Cgc/Tgc	3/25	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.51	NA		529	1083	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089807	5089807	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	180	411	0	ENST00000381652.3:c.2705T>C	p.Leu902Pro	p.L902P	ENST00000381652	NM_004972.3	902	cTg/cCg	20/25	1	2	FACETS	0.875	0.808	0.944	0.875	0.808	0.944	CLONAL	1	TRUE	1	0.51	2		411	807	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600609	43600609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777221273	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	212	461	0	ENST00000355710.3:c.835G>A	p.Ala279Thr	p.A279T	ENST00000355710	NM_020975.4	279	Gcc/Acc	4/20	1	2	FACETS	0.916	0.851	0.982	0.916	0.851	0.982	CLONAL	1	TRUE	1	0.51	2		461	908	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416960	416960	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs749506721	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	220	493	0	ENST00000399788.2:c.3590A>C	p.Gln1197Pro	p.Q1197P	ENST00000399788	NM_001042603.1	1197	cAa/cCa	23/28	1	2	FACETS	0.982	0.915	1	0.982	0.915	1	CLONAL	1	TRUE	1	0.51	2		493	879	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534755	18534755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776582655	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	259	460	0	ENST00000266497.5:c.1813G>A	p.Val605Ile	p.V605I	ENST00000266497		605	Gta/Ata	12/31	1	2	FACETS	0.952	0.892	1	0.952	0.892	1	CLONAL	1	TRUE	1	0.51	2		460	1067	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241987	133241987	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs765831166	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	257	411	0	ENST00000320574.5:c.2369A>G	p.Glu790Gly	p.E790G	ENST00000320574	NM_006231.2	790	gAg/gGg	21/49	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.51	2		411	895	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437427	110437427	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	90	192	0	ENST00000375856.3:c.974A>G	p.His325Arg	p.H325R	ENST00000375856	NM_003749.2	325	cAc/cGc	1/2	1	2	FACETS	0.821	0.732	0.914	0.821	0.732	0.914	CLONAL	1	TRUE	1	0.51	2		192	430	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437611	110437611	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	163	262	0	ENST00000375856.3:c.790G>A	p.Val264Ile	p.V264I	ENST00000375856	NM_003749.2	264	Gtc/Atc	1/2	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.51	2		262	544	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434668	99434668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751059746	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	206	398	0	ENST00000268035.6:c.755G>A	p.Arg252His	p.R252H	ENST00000268035	NM_000875.3	252	cGc/cAc	3/21	1	2	FACETS	0.978	0.909	1	0.978	0.909	1	CLONAL	1	TRUE	1	0.51	2		398	826	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500579	99500579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34102392	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	41	319	1	ENST00000268035.6:c.4012G>A	p.Ala1338Thr	p.A1338T	ENST00000268035	NM_000875.3	1338	Gcc/Acc	21/21	1	2	FACETS	0.247	0.205	0.293	0.247	0.205	0.293	SUBCLONAL	1	TRUE	1	0.51	2		320	652	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347093	347093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	287	633	0	ENST00000262320.3:c.1918G>A	p.Glu640Lys	p.E640K	ENST00000262320	NM_003502.3	640	Gaa/Aaa	7/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.51	2		633	1087	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016610	12016610	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	295	387	0	ENST00000353533.5:c.746G>A	p.Gly249Asp	p.G249D	ENST00000353533	NM_003010.3	249	gGc/gAc	7/11	0.269484555850298	2	FACETS	1	0.994	1	0.734	0.694	0.775	INDETERMINATE	1	TRUE	0	0.51	2		387	788	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40456447	40456447	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	301	709	0	ENST00000345506.4:c.1257G>A	p.Met419Ile	p.M419I	ENST00000345506	NM_003152.3	419	atG/atA	11/20	1	2	FACETS	0.947	0.892	1	0.947	0.892	1	CLONAL	1	TRUE	1	0.51	2		709	1246	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985583	60985583	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	99	193	0	ENST00000333681.4:c.317G>A	p.Arg106His	p.R106H	ENST00000333681		106	cGc/cAc	2/3	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.51	2		193	340	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795061	42795061	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	325	447	0	ENST00000575354.2:c.2141G>T	p.Gly714Val	p.G714V	ENST00000575354	NM_015125.3	714	gGg/gTg	10/20	0.3	2	FACETS	1	0.993	1	0.667	0.631	0.703	INDETERMINATE	1	TRUE	0	0.51	2		447	956	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164862	36164862	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1273605678	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	44	307	1	ENST00000300305.3:c.1013C>T	p.Ala338Val	p.A338V	ENST00000300305		338	gCg/gTg	8/8	1	2	FACETS	0.308	0.258	0.364	0.308	0.258	0.364	SUBCLONAL	1	TRUE	1	0.51	2		308	560	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934352	39934352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1420747737	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	204	229	2	ENST00000378444.4:c.247C>T	p.Arg83Trp	p.R83W	ENST00000378444	NM_001123385.1	83	Cgg/Tgg	4/15	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.51	1		231	408	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426493	47426493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1046676785	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	377	287	0	ENST00000377045.4:c.836G>A	p.Arg279His	p.R279H	ENST00000377045	NM_001654.4	279	cGc/cAc	9/16	1	1	FACETS	0.824	0.791	0.858	1	0.996	1	CLONAL	2	TRUE	0	0.51	1		287	668	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938776	76938776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1557140467	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	218	241	0	ENST00000373344.5:c.1972C>T	p.Arg658Cys	p.R658C	ENST00000373344	NM_000489.3	658	Cgt/Tgt	9/35	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.51	1		241	436	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686798	117686799	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	170	481	0	ENST00000368508.3:c.2918dup	p.Ala974CysfsTer14	p.A974Cfs*14	ENST00000368508	NM_002944.2	973	cct/ccCt	19/43	1	2	FACETS	0.809	0.745	0.876	0.809	0.745	0.876	CLONAL	1	TRUE	1	0.51	2		481	824	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048111	180048111	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	95	376	1	ENST00000261937.6:c.2162del	p.Lys721SerfsTer13	p.K721Sfs*13	ENST00000261937	NM_182925.4	721	aAg/ag	14/30	0.190082306586631	1	FACETS	0.421	0.375	0.47	0.421	0.375	0.47	INDETERMINATE	1	TRUE	0	0.51	1		377	659	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097671	11097671	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	204	425	0	ENST00000358026.2:c.852del	p.Trp284CysfsTer19	p.W284Cfs*19	ENST00000358026	NM_001128849.1	284	tGg/tg	5/36	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.51	2		425	723	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100210	157100210	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	12	36	0	ENST00000346085.5:c.1151del	p.Gly384AlafsTer46	p.G384Afs*46	ENST00000346085	NM_020732.3	383	Ggg/gg	1/20	1	2	FACETS	0.38	0.268	0.514	0.38	0.268	0.514	SUBCLONAL	1	TRUE	1	0.51	2		36	124	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0009921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	308	609	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.413345070087985	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.413345070087985	2		610	678	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165602	118165602	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs921184290	NA	P-0009921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	116	444	0	ENST00000369448.3:c.112C>T	p.Arg38Ter	p.R38*	ENST00000369448	NM_017709.3	38	Cga/Tga	2/2	1	2	FACETS	0.931	0.841	1	0.931	0.841	1	CLONAL	1	TRUE	1	0.413345070087985	2		444	603	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589598	67589599	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCAGTTTCAAGAAAAAAG	novel	NA	P-0009921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	109	453	0	ENST00000274335.5:c.1364_1381dup	p.Gln455_Ser460dup	p.Q455_S460dup	ENST00000274335		455	act/acTCAGTTTCAAGAAAAAAGt	10/15	1	2	FACETS	0.704	0.632	0.78	0.704	0.632	0.78	SUBCLONAL	1	TRUE	1	0.413345070087985	2		453	749	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	100	208	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.31	2		208	568	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	39	448	0	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.383	0.316	0.458	0.383	0.316	0.458	SUBCLONAL	1	TRUE	1	0.31	2		448	657	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	73	568	4	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.894	0.783	1	0.894	0.783	1	CLONAL	1	TRUE	1	0.31	2		572	527	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114817	108114817	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786204543	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	71	517	1	ENST00000278616.4:c.640del	p.Ser214ProfsTer16	p.S214Pfs*16	ENST00000278616	NM_000051.3	212	Ttt/tt	6/63	1	2	FACETS	0.7	0.611	0.797	0.7	0.611	0.797	SUBCLONAL	1	TRUE	1	0.31	2		518	654	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519896	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	129	561	0	ENST00000281708.4:c.1514G>A	p.Arg505His	p.R505H	ENST00000281708	NM_033632.3	505	cGc/cAc	10/12	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.31	2		561	676	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744385	41744385	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	148	1055	4	ENST00000301178.4:c.1010del	p.Pro337LeufsTer29	p.P337Lfs*29	ENST00000301178	NM_021913.4	335	ggC/gg	8/20	1	2	FACETS	0.992	0.905	1	0.992	0.905	1	CLONAL	1	TRUE	1	0.31	2		1059	963	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984024	2984024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	96	723	0	ENST00000396946.4:c.506C>T	p.Thr169Met	p.T169M	ENST00000396946	NM_032415.4	169	aCg/aTg	5/25	1	2	FACETS	0.837	0.746	0.934	0.837	0.746	0.934	CLONAL	1	TRUE	1	0.31	2		723	740	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	104	385	3	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	0.141877844761588	1	FACETS	0.931	0.835	1	0.931	0.835	1	INDETERMINATE	1	TRUE	0	0.31	1		388	609	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717629	89717629	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1554825165	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	104	432	0	ENST00000371953.3:c.654C>A	p.Cys218Ter	p.C218*	ENST00000371953	NM_000314.4	218	tgC/tgA	7/9	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.31	2		432	619	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	138	661	1	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.31	2		662	870	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348566	89348568	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs753054998	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1442	214	1892	5	ENST00000301030.4:c.4382_4384del	p.Lys1461del	p.K1461del	ENST00000301030	NM_001256183.1	1461	aAGAga/aga	9/13	0.141877844761588	3	FACETS	0.963	0.892	1	0.481	0.446	0.519	INDETERMINATE	1	TRUE	1	0.31	3		1897	1656	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446270	187446270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767642014	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	50	481	0	ENST00000232014.4:c.1418C>T	p.Pro473Leu	p.P473L	ENST00000232014	NM_001130845.1	473	cCg/cTg	6/10	1	2	FACETS	0.731	0.622	0.852	0.731	0.622	0.852	SUBCLONAL	1	TRUE	1	0.31	2		481	441	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012386	152012386	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	62	599	0	ENST00000262189.6:c.427del	p.Ser143ValfsTer3	p.S143Vfs*3	ENST00000262189	NM_170606.2	143	Agt/gt	4/59	1	2	FACETS	0.587	0.507	0.675	0.587	0.507	0.675	SUBCLONAL	1	TRUE	1	0.31	2		599	681	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572092	64572093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs767319284	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	119	1228	6	ENST00000312049.6:c.1546dup	p.Arg516ProfsTer15	p.R516Pfs*15	ENST00000312049	NM_130799.2	516	cgg/cCgg	10/10	1	2	FACETS	0.651	0.586	0.72	0.651	0.586	0.72	SUBCLONAL	1	TRUE	1	0.31	2		1234	1179	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242776	16242776	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	111	714	0	ENST00000375759.3:c.1395+2T>C		p.X465_splice	ENST00000375759	NM_015001.2	465			1	2	FACETS	0.901	0.81	0.997	0.901	0.81	0.997	CLONAL	1	TRUE	1	0.31	2		714	795	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128016909	128016909	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs944132286	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	157	843	0	ENST00000285398.2:c.2180A>T	p.Glu727Val	p.E727V	ENST00000285398	NM_000122.1	727	gAg/gTg	14/15	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.31	2		843	950	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799520	72799520	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	130	926	0	ENST00000325599.8:c.1649T>G	p.Val550Gly	p.V550G	ENST00000325599	NM_018130.2	550	gTt/gGt	11/11	1	2	FACETS	0.807	0.731	0.888	0.807	0.731	0.888	CLONAL	1	TRUE	1	0.31	2		926	1039	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612131	189612131	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	75	785	0	ENST00000264731.3:c.1883T>C	p.Val628Ala	p.V628A	ENST00000264731	NM_003722.4	628	gTg/gCg	14/14	1	2	FACETS	0.588	0.514	0.668	0.588	0.514	0.668	SUBCLONAL	1	TRUE	1	0.31	2		785	823	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524347	187524347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773283301	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	65	335	1	ENST00000441802.2:c.11333C>T	p.Ala3778Val	p.A3778V	ENST00000441802	NM_005245.3	3778	gCg/gTg	19/27	1	2	FACETS	0.944	0.821	1	0.944	0.821	1	CLONAL	1	TRUE	1	0.31	2		336	444	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251537	251537	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	31	405	0	ENST00000264932.6:c.1748A>G	p.Glu583Gly	p.E583G	ENST00000264932	NM_004168.2	583	gAg/gGg	13/15	1	2	FACETS	0.475	0.384	0.578	0.475	0.384	0.578	SUBCLONAL	1	TRUE	1	0.31	2		405	421	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041235	112041235	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	187	1292	0	ENST00000368678.4:c.20A>C	p.Lys7Thr	p.K7T	ENST00000368678		7	aAg/aCg	3/13	0.210188759758309	4	FACETS	1	0.979	1	0.588	0.541	0.636	CLONAL	1	TRUE	2	0.31	4		1292	1345	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829170	128829170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	55	277	0	ENST00000249373.3:c.178C>T	p.Pro60Ser	p.P60S	ENST00000249373	NM_005631.4	60	Ccg/Tcg	1/12	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.31	2		277	275	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482927	140482927	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	96	689	0	ENST00000288602.6:c.1208C>T	p.Pro403Leu	p.P403L	ENST00000288602	NM_004333.4	403	cCt/cTt	10/18	1	2	FACETS	0.785	0.699	0.877	0.785	0.699	0.877	SUBCLONAL	1	TRUE	1	0.31	2		689	789	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741685	145741685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1349749745	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	59	572	0	ENST00000428558.2:c.818C>T	p.Ala273Val	p.A273V	ENST00000428558	NM_004260.3	273	gCa/gTa	5/22	1	2	FACETS	0.745	0.642	0.857	0.745	0.642	0.857	SUBCLONAL	1	TRUE	1	0.31	2		572	511	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231238	98231238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1366288601	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	86	529	2	ENST00000331920.6:c.2045G>A	p.Arg682His	p.R682H	ENST00000331920	NM_000264.3	682	cGc/cAc	14/24	1	2	FACETS	0.97	0.86	1	0.97	0.86	1	CLONAL	1	TRUE	1	0.31	2		531	572	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342865	118342865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368926838	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	118	596	0	ENST00000534358.1:c.991C>T	p.Arg331Trp	p.R331W	ENST00000534358	NM_005933.3	331	Cgg/Tgg	3/36	1	2	FACETS	0.984	0.888	1	0.984	0.888	1	CLONAL	1	TRUE	1	0.31	2		596	774	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347875	73347875	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs917054849	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	110	604	1	ENST00000377767.4:c.1186C>T	p.Arg396Trp	p.R396W	ENST00000377767	NM_014953.3	396	Cgg/Tgg	8/21	1	2	FACETS	0.903	0.811	1	0.903	0.811	1	CLONAL	1	TRUE	1	0.31	2		605	786	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041629	14041629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777184889	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	125	724	0	ENST00000311895.7:c.2176C>T	p.Arg726Cys	p.R726C	ENST00000311895	NM_005236.2	726	Cgc/Tgc	11/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.31	2		724	735	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576875	7576875	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1177881399	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	97	496	0	ENST00000269305.4:c.971A>G	p.Asp324Gly	p.D324G	ENST00000269305	NM_001126112.2	324	gAt/gGt	9/11	1	2	FACETS	0.884	0.788	0.986	0.884	0.788	0.986	CLONAL	1	TRUE	1	0.31	2		496	708	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984672	11984672	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	37	237	0	ENST00000353533.5:c.219-1G>C		p.X73_splice	ENST00000353533	NM_003010.3	73			1	2	FACETS	0.748	0.619	0.892	0.748	0.619	0.892	SUBCLONAL	1	TRUE	1	0.31	2		237	319	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007695	62007695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375597674	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	58	307	0	ENST00000392795.3:c.172C>T	p.Arg58Trp	p.R58W	ENST00000392795	NM_001039933.1	58	Cgg/Tgg	3/6	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.31	2		307	351	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629091	14629091	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs373251842	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	62	769	0	ENST00000254322.2:c.71A>G	p.Tyr24Cys	p.Y24C	ENST00000254322	NM_006145.1	24	tAc/tGc	1/3	1	2	FACETS	0.564	0.487	0.649	0.564	0.487	0.649	SUBCLONAL	1	TRUE	1	0.31	2		769	709	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383164	42383164	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	238	1495	4	ENST00000221972.3:c.184G>T	p.Ala62Ser	p.A62S	ENST00000221972	NM_021601.3	62	Gcc/Tcc	2/5	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.31	2		1499	1299	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264910	46264910	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1363	230	1680	0	ENST00000371998.3:c.1780A>G	p.Ser594Gly	p.S594G	ENST00000371998		594	Agt/Ggt	12/23	1	2	FACETS	0.931	0.865	1	0.931	0.865	1	CLONAL	1	TRUE	1	0.31	2		1680	1593	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733061	74733064	+	frameshift_variant	Frame_Shift_Del	DEL	CGAA	CGAA	-	novel	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	126	1090	0	ENST00000359995.5:c.179_182del	p.Val60AlafsTer171	p.V60Afs*171	ENST00000359995	NM_001195427.1	60	gTTCGc/gc	1/3	1	2	FACETS	0.854	0.772	0.94	0.854	0.772	0.94	CLONAL	1	TRUE	1	0.31	2		1090	952	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492768	56492768	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	137	830	0	ENST00000407977.2:c.171del	p.Thr58GlnfsTer4	p.T58Qfs*4	ENST00000407977		57	ccC/cc	2/10	1	2	FACETS	0.949	0.863	1	0.949	0.863	1	CLONAL	1	TRUE	1	0.31	2		830	931	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119661	108119661	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1275066585	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	27	222	0	ENST00000278616.4:c.1071del	p.Phe357LeufsTer33	p.F357Lfs*33	ENST00000278616	NM_000051.3	356	gTt/gt	9/63	1	2	FACETS	0.643	0.513	0.79	0.643	0.513	0.79	SUBCLONAL	1	TRUE	1	0.31	2		222	271	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486050	29486050	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1438566555	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	54	343	2	ENST00000356175.3:c.233del	p.Asn78IlefsTer7	p.N78Ifs*7	ENST00000356175	NM_000267.3	76	gAa/ga	3/57	1	2	FACETS	0.785	0.671	0.908	0.785	0.671	0.908	CLONAL	1	TRUE	1	0.31	2		345	444	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528585	89528587	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs748710353	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	74	423	0	ENST00000336596.2:c.2891_2893del	p.Lys964del	p.K964del	ENST00000336596	NM_005233.5	962	cAGAag/cag	17/17	1	2	FACETS	0.925	0.812	1	0.925	0.812	1	CLONAL	1	TRUE	1	0.31	2		423	516	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054541	42054541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1458609443	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	139	973	3	ENST00000219905.7:c.7731del	p.Asp2578ThrfsTer10	p.D2578Tfs*10	ENST00000219905	NM_001164273.1	2575	agA/ag	22/24	0.141877844761588	3	FACETS	0.946	0.86	1	0.473	0.43	0.519	INDETERMINATE	1	TRUE	1	0.31	3		976	1095	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439979	56439980	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	153	795	0	ENST00000407977.2:c.612_613del	p.Val205GlyfsTer53	p.V205Gfs*53	ENST00000407977		204	acAGtg/actg	6/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.31	2		795	852	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188294	32188295	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs766348245	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	65	929	9	ENST00000375023.3:c.1046dup	p.Thr350HisfsTer4	p.T350Hfs*4	ENST00000375023	NM_004557.3	349	ggc/ggGc	6/30	1	2	FACETS	0.399	0.344	0.458	0.399	0.344	0.458	SUBCLONAL	1	TRUE	1	0.31	2		938	1052	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711908	89711910	+	inframe_deletion	In_Frame_Del	DEL	TAT	TAT	-	rs587780711	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	41	508	0	ENST00000371953.3:c.532_534del	p.Tyr178del	p.Y178del	ENST00000371953	NM_000314.4	176	TAT/-	6/9	1	2	FACETS	0.413	0.343	0.491	0.413	0.343	0.491	SUBCLONAL	1	TRUE	1	0.31	2		508	640	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21272366	21272367	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTGCTA	novel	NA	P-0009964-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	157	1250	1	ENST00000354336.3:c.149_150insAGTGCT	p.Val49_Leu50dup	p.V49_L50dup	ENST00000354336	NM_005207.3	49	-/GTGCTA	1/3	1	2	FACETS	0.912	0.834	0.994	0.912	0.834	0.994	CLONAL	1	TRUE	1	0.31	2		1251	1111	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0010010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	187	357	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.41044300056369	3	FACETS	1	0.985	1	0.799	0.746	0.853	CLONAL	2	FALSE	0	0.41044300056369	3		357	458	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164686	36164686	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	157	517	0	ENST00000300305.3:c.1189del	p.Gln397LysfsTer197	p.Q397Kfs*197	ENST00000300305		397	Caa/aa	8/8	0.41044300056369	8	FACETS	0.803	0.734	0.875	0.268	0.244	0.292	CLONAL	2	FALSE	2	0.41044300056369	8		517	1063	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054748	5054748	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	134	495	0	ENST00000381652.3:c.800C>T	p.Thr267Ile	p.T267I	ENST00000381652	NM_004972.3	267	aCa/aTa	7/25	0.41044300056369	5	FACETS	0.773	0.704	0.846	0.516	0.469	0.564	SUBCLONAL	2	FALSE	2	0.41044300056369	5		495	682	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252961	36252962	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0010010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	147	341	0	ENST00000300305.3:c.400dup	p.Ala134GlyfsTer4	p.A134Gfs*4	ENST00000300305		134	gct/gGct	4/8	0.41044300056369	8	FACETS	1	0.986	1	0.24	0.218	0.262	CLONAL	1	FALSE	2	0.41044300056369	8		341	1112	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867234	68867237	+	stop_gained	Nonsense_Mutation	DEL	TGAT	TGAT	A	novel	NA	P-0010010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	370	419	0	ENST00000261769.5:c.2481_2484delinsA	p.Tyr827_Asp828delinsTer	p.Y827_D828delins*	ENST00000261769	NM_004360.3	827	taTGAT/taA	16/16	0.27025937110652	5	FACETS	0.955	0.918	0.992			1	CLONAL	5	FALSE	NA	0.41044300056369	5		419	610	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0010072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	160	435	1	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	0.330758416176746	2		436	910	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0010072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	231	424	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	0.318531095857664	2	FACETS	0.948	0.887	1	0.948	0.887	1	CLONAL	2	TRUE	0	0.330758416176746	2		424	737	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991713	25991713	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs190136878	NA	P-0010072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	183	495	0	ENST00000435504.4:c.529A>C	p.Lys177Gln	p.K177Q	ENST00000435504		177	Aag/Cag	7/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.330758416176746	2		495	934	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030367	49030368	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	136	424	0	ENST00000267163.4:c.1848dup	p.Gly617ArgfsTer36	p.G617Rfs*36	ENST00000267163	NM_000321.2	614	-/A	19/27	1	2	FACETS	0.949	0.862	1	0.949	0.862	1	CLONAL	1	TRUE	1	0.330758416176746	2		424	867	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353819	15353819	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	59	377	0	ENST00000263377.2:c.3061del	p.His1021IlefsTer47	p.H1021Ifs*47	ENST00000263377	NM_058243.2	1021	Cat/at	14/20	1	2	FACETS	0.736	0.634	0.846	0.736	0.634	0.846	SUBCLONAL	1	TRUE	1	0.330758416176746	2		377	485	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148544345	148544345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	168	618	2	ENST00000320356.2:c.46C>T	p.Arg16Trp	p.R16W	ENST00000320356	NM_004456.4	16	Cgg/Tgg	2/20	1	2	FACETS	0.937	0.86	1	0.937	0.86	1	CLONAL	1	TRUE	1	0.330758416176746	2		620	1084	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913253	39913253	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	234	352	1	ENST00000378444.4:c.4862del	p.Pro1621GlnfsTer53	p.P1621Qfs*53	ENST00000378444	NM_001123385.1	1621	cCa/ca	14/15	0.0960827487203004	2	FACETS	1	0.969	1			1	INDETERMINATE	2	TRUE	NA	0.330758416176746	2		353	672	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434991	110434991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	31	386	0	ENST00000375856.3:c.3410G>A	p.Arg1137His	p.R1137H	ENST00000375856	NM_003749.2	1137	cGc/cAc	1/2	1	2	FACETS	0.304	0.245	0.371	0.304	0.245	0.371	SUBCLONAL	1	TRUE	1	0.330758416176746	2		386	617	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641430	47641430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs34136999	NA	P-0010072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	300	808	3	ENST00000233146.2:c.815C>T	p.Ala272Val	p.A272V	ENST00000233146	NM_000251.2	272	gCg/gTg	5/16	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.330758416176746	2		811	1487	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170750	99170750	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771424128	NA	P-0010072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	66	270	1	ENST00000074304.5:c.1379C>T	p.Thr460Met	p.T460M	ENST00000074304	NM_001134224.1	460	aCg/aTg	16/26	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.330758416176746	2		271	372	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182521	99182521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373911327	NA	P-0010072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	113	453	0	ENST00000074304.5:c.2324C>T	p.Pro775Leu	p.P775L	ENST00000074304	NM_001134224.1	775	cCg/cTg	22/26	1	2	FACETS	0.968	0.872	1	0.968	0.872	1	CLONAL	1	TRUE	1	0.330758416176746	2		453	706	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739882	41739882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	135	719	2	ENST00000242208.4:c.91G>A	p.Ala31Thr	p.A31T	ENST00000242208	NM_002192.2	31	Gcg/Acg	2/3	1	2	FACETS	0.869	0.789	0.953	0.869	0.789	0.953	CLONAL	1	TRUE	1	0.330758416176746	2		721	939	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526693	106526693	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	148	503	1	ENST00000359195.3:c.2986G>A	p.Gly996Arg	p.G996R	ENST00000359195	NM_002649.2	996	Gga/Aga	10/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.330758416176746	2		504	772	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518246	8518246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	75	454	0	ENST00000356435.5:c.1145G>A	p.Gly382Glu	p.G382E	ENST00000356435		382	gGa/gAa	10/35	0.330758416176746	1	FACETS	0.655	0.574	0.741	0.655	0.574	0.741	SUBCLONAL	1	TRUE	0	0.330758416176746	1		454	578	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396925	139396925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766358616	NA	P-0010072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	53	177	0	ENST00000277541.6:c.5183C>T	p.Pro1728Leu	p.P1728L	ENST00000277541	NM_017617.3	1728	cCg/cTg	28/34	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.330758416176746	2		177	316	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047327	77047327	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1488995878	NA	P-0010072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	134	480	0	ENST00000356341.3:c.1217C>T	p.Thr406Ile	p.T406I	ENST00000356341	NM_002576.4	406	aCt/aTt	13/15	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.330758416176746	2		480	767	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123621	108123621	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	137	456	0	ENST00000278616.4:c.1880T>C	p.Phe627Ser	p.F627S	ENST00000278616	NM_000051.3	627	tTc/tCc	12/63	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.330758416176746	2		456	819	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416875	121416875	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	33	475	0	ENST00000257555.6:c.304G>A	p.Ala102Thr	p.A102T	ENST00000257555		102	Gcc/Acc	1/10	1	2	FACETS	0.311	0.252	0.377	0.311	0.252	0.377	SUBCLONAL	1	TRUE	1	0.330758416176746	2		475	642	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207578	2207578	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	129	407	0	ENST00000398665.3:c.862G>A	p.Gly288Ser	p.G288S	ENST00000398665	NM_032482.2	288	Ggc/Agc	11/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.330758416176746	2		407	608	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56866243	56866244	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0010072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	161	812	0	ENST00000308159.5:c.1292dup	p.Gln432ThrfsTer42	p.Q432Tfs*42	ENST00000308159	NM_014669.4	430	tcc/tCcc	12/22	1	2	FACETS	0.781	0.715	0.851	0.781	0.715	0.851	SUBCLONAL	1	TRUE	1	0.330758416176746	2		812	1246	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249361	153249361	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	142	502	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	0.330758416176746	2		503	760	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663356	67663356	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	83	713	2	ENST00000264010.4:c.1760del	p.Asn587MetfsTer44	p.N587Mfs*44	ENST00000264010	NM_006565.3	586	gAa/ga	10/12	1	2	FACETS	0.395	0.347	0.447	0.395	0.347	0.447	SUBCLONAL	1	TRUE	1	0.330758416176746	2		715	1270	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039484	49039484	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	137	610	1	ENST00000267163.4:c.2473del	p.Met825Ter	p.M825*	ENST00000267163	NM_000321.2	823	acA/ac	23/27	1	2	FACETS	0.732	0.665	0.804	0.732	0.665	0.804	SUBCLONAL	1	TRUE	1	0.330758416176746	2		611	1131	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649056	37649056	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	68	594	0	ENST00000447079.4:c.2163del	p.Lys721AsnfsTer32	p.K721Nfs*32	ENST00000447079	NM_015083.1	721	Aaa/aa	4/14	1	2	FACETS	0.384	0.333	0.44	0.384	0.333	0.44	SUBCLONAL	1	TRUE	1	0.330758416176746	2		594	1071	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692922	89692922	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201044	NA	P-0010097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	28	367	0	ENST00000371953.3:c.406T>C	p.Cys136Arg	p.C136R	ENST00000371953	NM_000314.4	136	Tgt/Cgt	5/9	0.413873602901839	1	FACETS	0.184	0.146	0.227	0.184	0.146	0.227	SUBCLONAL	1	TRUE	0	0.413873602901839	1		367	583	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610695	52610695	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	59	512	0	ENST00000394830.3:c.3478C>T	p.Arg1160Ter	p.R1160*	ENST00000394830	NM_018313.4	1160	Cga/Tga	23/30	0.413873602901839	1	FACETS	0.307	0.264	0.355	0.307	0.264	0.355	SUBCLONAL	1	TRUE	0	0.413873602901839	1		512	736	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144835	47144835	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0010097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	203	500	0	ENST00000409792.3:c.4917+1G>A		p.X1639_splice	ENST00000409792	NM_014159.6	1639			0.413873602901839	1	FACETS	0.989	0.919	1	0.989	0.919	1	CLONAL	1	TRUE	0	0.413873602901839	1		500	787	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573524	41573524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	216	532	0	ENST00000263253.7:c.5809G>A	p.Glu1937Lys	p.E1937K	ENST00000263253	NM_001429.3	1937	Gag/Aag	31/31	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.413873602901839	2		532	830	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442506	52442507	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	131	367	0	ENST00000460680.1:c.238dup	p.Met80AsnfsTer46	p.M80Nfs*46	ENST00000460680	NM_004656.3	80	atg/aAtg	4/17	0.413873602901839	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.413873602901839	1		367	470	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0010109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	75	293	1	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	0.275169900162003	3	FACETS	0.961	0.843	1	0.481	0.421	0.545	CLONAL	1	TRUE	1	0.275169900162003	3		294	645	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527820	157527820	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs779490460	NA	P-0010109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	60	312	0	ENST00000346085.5:c.5545C>A	p.Pro1849Thr	p.P1849T	ENST00000346085	NM_020732.3	1849	Ccc/Acc	20/20	0.275169900162003	1	FACETS	0.891	0.77	1	0.891	0.77	1	CLONAL	1	TRUE	0	0.275169900162003	1		312	422	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593662	55593663	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCTTATGATCATTTG	novel	NA	P-0010109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	142	490	0	ENST00000288135.5:c.1739_1740insTTTGCCTTATGATCA	p.Leu576_His580dup	p.L576_H580dup	ENST00000288135	NM_000222.2	576	-/CCTTATGATCATTTG	11/21	0.227808900124945	3	FACETS	1	0.987	1	0.748	0.682	0.817	CLONAL	1	TRUE	1	0.275169900162003	3		490	785	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0010117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	502	298	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.607617953492719	2	FACETS	0.988	0.955	1	0.988	0.955	1	CLONAL	2	TRUE	0	0.612947590377161	2		298	829	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527306	187527306	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1282821100	NA	P-0010117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	84	282	1	ENST00000441802.2:c.10268C>T	p.Thr3423Met	p.T3423M	ENST00000441802	NM_005245.3	3423	aCg/aTg	17/27	1	2	FACETS	0.391	0.345	0.44	0.391	0.345	0.44	SUBCLONAL	1	TRUE	1	0.612947590377161	2		283	701	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968619	55968620	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCCTTT	novel	NA	P-0010117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1216	68	507	0	ENST00000263923.4:c.2043_2044insAAAGGG	p.Gly681_Glu682insLysGly	p.G681_E682insKG	ENST00000263923	NM_002253.2	681	-/AAAGGG	14/30	0.478203098522481	3	FACETS	0.226	0.195	0.259			1	SUBCLONAL	1	TRUE	NA	0.612947590377161	3		507	1284	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038526	47038526	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	703	612	2	ENST00000377604.3:c.688C>T	p.Arg230Ter	p.R230*	ENST00000377604	NM_001204468.1	230	Cga/Tga	8/24	0.426636246589555	4	FACETS	0.968	0.936	1	0.968	0.936	1	CLONAL	3	FALSE	1	0.455818170220402	4		614	1546	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100980	41100980	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868706902	NA	P-0010134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	812	329	0	ENST00000373198.4:c.1376G>A	p.Arg459Gln	p.R459Q	ENST00000373198	NM_133170.3	459	cGg/cAg	8/32	0.455818170220402	8	FACETS	1	0.995	1	0.925	0.901	0.949	CLONAL	6	FALSE	1	0.455818170220402	8		329	1303	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215327	123215327	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	151	541	0	ENST00000218089.9:c.2873C>A	p.Thr958Asn	p.T958N	ENST00000218089	NM_001042749.1	958	aCt/aAt	28/35	0.455818170220402	4	FACETS	0.791	0.722	0.865			1	SUBCLONAL	1	FALSE	NA	0.455818170220402	4		541	1219	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578533	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0010134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	291	374	0	ENST00000269305.4:c.396_397dup	p.Met133ArgfsTer38	p.M133Rfs*38	ENST00000269305	NM_001126112.2	133	atg/aGAtg	5/11	0.446609303033954	2	FACETS	0.917	0.869	0.966	0.917	0.869	0.966	CLONAL	2	FALSE	0	0.455818170220402	2		374	696	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0010209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	248	607	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.29584356952545	3	FACETS	0.979	0.917	1	0.979	0.917	1	CLONAL	2	TRUE	1	0.34	3		607	872	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272024	15272024	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	149	220	0	ENST00000263388.2:c.6415C>T	p.Gln2139Ter	p.Q2139*	ENST00000263388	NM_000435.2	2139	Cag/Tag	33/33	0.301928509175999	5	FACETS	0.996	0.918	1	0.996	0.918	1	CLONAL	3	TRUE	2	0.34	5		220	443	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056572	26056573	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	40	150	0	ENST00000343677.2:c.84dup	p.Gly29TrpfsTer6	p.G29Wfs*6	ENST00000343677	NM_005319.3	28	-/T	1/1	0.301928509175999	3	FACETS	0.726	0.605	0.861	0.363	0.302	0.431	SUBCLONAL	1	TRUE	1	0.34	3		150	379	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0010210-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	44	278	0	ENST00000397752.3:c.3028+1G>A		p.X1010_splice	ENST00000397752	NM_000245.2	1010			1	2	FACETS	0.892	0.75	1	0.892	0.75	1	CLONAL	1	TRUE	1	0.268847321267747	2		278	367	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105754	27105756	+	frameshift_variant	Frame_Shift_Ins	INS	GCC	GCC	ACCT	novel	NA	P-0010210-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	46	476	1	ENST00000324856.7:c.5365_5367delinsACCT	p.Ala1789ThrfsTer13	p.A1789Tfs*13	ENST00000324856	NM_006015.4	1789	GCC/ACCT	20/20	1	2	FACETS	0.567	0.476	0.666	0.567	0.476	0.666	SUBCLONAL	1	TRUE	1	0.268847321267747	2		477	604	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881001	37881002	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGCTCCCC	rs397516981	NA	P-0010215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	382	673	0	ENST00000269571.5:c.2331_2339dup	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	gtg/gtGGGCTCCCCg	20/27	0.183970209369892	3	FACETS	0.945	0.896	0.995	0.63	0.597	0.664	INDETERMINATE	2	TRUE	0	0.307676635080631	3		673	1516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782620	NA	P-0010215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	245	544	0	ENST00000269305.4:c.427G>A	p.Val143Met	p.V143M	ENST00000269305	NM_001126112.2	143	Gtg/Atg	5/11	0.272839441027704	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.307676635080631	1		544	1259	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629613	187629613	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	59	592	0	ENST00000441802.2:c.1369A>C	p.Asn457His	p.N457H	ENST00000441802	NM_005245.3	457	Aat/Cat	2/27	1	2	FACETS	0.599	0.515	0.691	0.599	0.515	0.691	SUBCLONAL	1	TRUE	1	0.307676635080631	2		592	640	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219096	133219096	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	125	510	0	ENST00000320574.5:c.4948A>T	p.Ser1650Cys	p.S1650C	ENST00000320574	NM_006231.2	1650	Agc/Tgc	37/49	0.242897869017765	2	FACETS	0.75	0.677	0.826	0.375	0.338	0.413	SUBCLONAL	1	TRUE	0	0.307676635080631	2		510	1084	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041710	14041710	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0010215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	111	611	0	ENST00000311895.7:c.2257A>T	p.Lys753Ter	p.K753*	ENST00000311895	NM_005236.2	753	Aag/Tag	11/11	0.185347227974507	3	FACETS	0.993	0.893	1	0.497	0.446	0.55	CLONAL	1	TRUE	1	0.307676635080631	3		611	838	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795364	42795364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	206	434	0	ENST00000575354.2:c.2444C>T	p.Ala815Val	p.A815V	ENST00000575354	NM_015125.3	815	gCc/gTc	10/20	0.185347227974507	3	FACETS	1	0.99	1	0.708	0.656	0.762	CLONAL	1	TRUE	1	0.307676635080631	3		434	1091	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937958	76937958	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	41	639	0	ENST00000373344.5:c.2790T>A	p.Ser930Arg	p.S930R	ENST00000373344	NM_000489.3	930	agT/agA	9/35	0.272839441027704	1	FACETS	0.447	0.372	0.53	0.447	0.372	0.53	SUBCLONAL	1	TRUE	0	0.307676635080631	1		639	505	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448551	89448551	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0010224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	319	514	0	ENST00000336596.2:c.1515C>G	p.Tyr505Ter	p.Y505*	ENST00000336596	NM_005233.5	505	taC/taG	7/17	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.683316507578375	2		514	920	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578470	7578502	+	inframe_deletion	In_Frame_Del	DEL	CGGGCGGGGGTGTGGAATCAACCCACAGCTGCA	CGGGCGGGGGTGTGGAATCAACCCACAGCTGCA	-	novel	NA	P-0010224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	244	341	0	ENST00000269305.4:c.428_460del	p.Val143_Pro153del	p.V143_P153del	ENST00000269305	NM_001126112.2	143	gTGCAGCTGTGGGTTGATTCCACACCCCCGCCCGgc/ggc	5/11	0.674263647220291	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.683316507578375	1		341	448	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039493	49039494	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0010224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	285	388	0	ENST00000267163.4:c.2480dup	p.Arg828LysfsTer10	p.R828Kfs*10	ENST00000267163	NM_000321.2	826	-/C	23/27	1	2	FACETS	0.932	0.878	0.987	0.932	0.878	0.987	CLONAL	1	TRUE	1	0.683316507578375	2		388	895	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0010245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	67	673	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.558501592383523	2		673	238	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522416	176522416	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519792	NA	P-0010245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	123	401	0	ENST00000292408.4:c.1605C>G	p.Asn535Lys	p.N535K	ENST00000292408	NM_213647.1	535	aaC/aaG	12/18	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.558501592383523	2		401	425	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4388046	4388046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1488421614	NA	P-0010245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	77	265	0	ENST00000261254.3:c.532C>T	p.Arg178Cys	p.R178C	ENST00000261254	NM_001759.3	178	Cgc/Tgc	3/5	NA	2	FACETS	1	0.923	1			1	INDETERMINATE	1	TRUE	NA	0.558501592383523	2		265	263	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856520	45856520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751318902	NA	P-0010245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	108	577	0	ENST00000391945.4:c.1738G>A	p.Ala580Thr	p.A580T	ENST00000391945	NM_000400.3	580	Gcc/Acc	18/23	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.558501592383523	2		577	381	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862134	68862135	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	115	560	0	ENST00000261769.5:c.2223dup	p.Leu742ThrfsTer6	p.L742Tfs*6	ENST00000261769	NM_004360.3	741	tta/ttAa	14/16	0.558501592383523	1	FACETS	0.916	0.836	0.998	0.916	0.836	0.998	CLONAL	1	TRUE	0	0.558501592383523	1		560	324	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913471	NA	P-0010278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	224	686	0	ENST00000269571.5:c.2329G>C	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ctg	20/27	0.15921770959235	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	FALSE	2	0.185062695751771	4		686	1382	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99154370	99154370	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	80	433	0	ENST00000074304.5:c.512G>A	p.Trp171Ter	p.W171*	ENST00000074304	NM_001134224.1	171	tGg/tAg	8/26	0.175655028919076	3	FACETS	0.927	0.814	1	0.463	0.407	0.525	CLONAL	1	FALSE	1	0.185062695751771	3		433	1019	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012373	152012373	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	119	514	1	ENST00000262189.6:c.440A>T	p.Gln147Leu	p.Q147L	ENST00000262189	NM_170606.2	147	cAa/cTa	4/59	0.175150291215284	2	FACETS	1	0.979	1	0.663	0.597	0.732	CLONAL	1	FALSE	0	0.185062695751771	2		515	970	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180495	94180495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	101	548	1	ENST00000323929.3:c.1673C>T	p.Ser558Phe	p.S558F	ENST00000323929	NM_005591.3	558	tCt/tTt	15/20	0.175655028919076	3	FACETS	1	0.926	1	0.525	0.468	0.586	CLONAL	1	FALSE	1	0.185062695751771	3		549	1136	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416131	416131	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	101	497	0	ENST00000399788.2:c.4055C>T	p.Thr1352Ile	p.T1352I	ENST00000399788	NM_001042603.1	1352	aCa/aTa	24/28	0.175655028919076	3	FACETS	1	0.946	1	0.55	0.49	0.614	CLONAL	1	FALSE	1	0.185062695751771	3		497	1084	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858775	9858775	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1399604502	NA	P-0010278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	62	283	0	ENST00000330684.3:c.2626A>T	p.Ile876Phe	p.I876F	ENST00000330684	NM_001134407.1	876	Att/Ttt	13/13	0.15921770959235	4	FACETS	1	0.923	1	0.552	0.476	0.635	CLONAL	1	FALSE	2	0.185062695751771	4		283	719	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983300	15983300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	208	521	0	ENST00000268712.3:c.3479C>T	p.Ser1160Phe	p.S1160F	ENST00000268712	NM_006311.3	1160	tCc/tTc	26/46	0.175150291215284	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	FALSE	0	0.185062695751771	2		521	1022	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359671	40359671	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1642	324	866	1	ENST00000293328.3:c.1982G>A	p.Gly661Glu	p.G661E	ENST00000293328	NM_012448.3	661	gGa/gAa	16/19	0.15921770959235	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	FALSE	2	0.185062695751771	4		867	1966	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59793330	59793330	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	106	550	0	ENST00000259008.2:c.2474T>C	p.Leu825Ser	p.L825S	ENST00000259008	NM_032043.2	825	tTa/tCa	17/20	0.185062695751771	6	FACETS	1	0.961	1	0.29	0.259	0.324	CLONAL	1	FALSE	2	0.185062695751771	6		550	1351	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231483	5231483	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	73	496	0	ENST00000357368.4:c.1993G>T	p.Asp665Tyr	p.D665Y	ENST00000357368	NM_002850.3	665	Gac/Tac	14/38	0.175655028919076	3	FACETS	0.854	0.745	0.973	0.427	0.372	0.487	CLONAL	1	FALSE	1	0.185062695751771	3		496	1009	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855991	68855992	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	195	617	0	ENST00000261769.5:c.1800dup	p.Phe601IlefsTer4	p.F601Ifs*4	ENST00000261769	NM_004360.3	600	ata/atAa	12/16	NA	2	FACETS	0.841	0.777	0.908			1	INDETERMINATE	2	FALSE	NA	0.185062695751771	2		617	1253	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579400	7579401	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	154	390	1	ENST00000269305.4:c.286_287insA	p.Ser96TyrfsTer53	p.S96Yfs*53	ENST00000269305	NM_001126112.2	96	tct/tAct	4/11	0.175150291215284	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	FALSE	0	0.185062695751771	2		391	777	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105978	27105979	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0010278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	37	214	0	ENST00000324856.7:c.5591_5592del	p.Glu1864AlafsTer36	p.E1864Afs*36	ENST00000324856	NM_006015.4	1863	acAGag/acag	20/20	0.175655028919076	3	FACETS	0.91	0.75	1	0.455	0.375	0.545	CLONAL	1	FALSE	1	0.185062695751771	3		214	480	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029455	16029456	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0010278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1363	306	897	0	ENST00000268712.3:c.1574_1575del	p.Thr525ArgfsTer10	p.T525Rfs*10	ENST00000268712	NM_006311.3	525	aCA/a	15/46	0.175150291215284	2	FACETS	0.991	0.931	1	0.991	0.931	1	CLONAL	2	FALSE	0	0.185062695751771	2		897	1669	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0010307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	52	379	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	FALSE	1	0.21997905730952	2		379	436	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881621	111881621	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs769177798	NA	P-0010307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	80	344	0	ENST00000393256.3:c.299A>G	p.Asp100Gly	p.D100G	ENST00000393256	NM_006538.4	100	gAc/gGc	2/4	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.21997905730952	2		344	632	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094874	143094874	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	52	638	0	ENST00000262992.4:c.1270A>T	p.Ile424Leu	p.I424L	ENST00000262992	NM_001101669.1	424	Ata/Tta	14/24	0.181127923758639	1	FACETS	0.667	0.567	0.777	0.667	0.567	0.777	SUBCLONAL	1	FALSE	0	0.21997905730952	1		638	631	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336102	73336102	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	31	436	1	ENST00000377767.4:c.2301A>T	p.Leu767Phe	p.L767F	ENST00000377767	NM_014953.3	767	ttA/ttT	17/21	0.159673022077898	1	FACETS	0.496	0.4	0.604	0.496	0.4	0.604	SUBCLONAL	1	FALSE	0	0.21997905730952	1		437	506	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858784	9858784	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1555482977	NA	P-0010307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	26	275	0	ENST00000330684.3:c.2617G>T	p.Gly873Ter	p.G873*	ENST00000330684	NM_001134407.1	873	Gga/Tga	13/13	1	2	FACETS	0.775	0.615	0.958	0.775	0.615	0.958	CLONAL	1	FALSE	1	0.21997905730952	2		275	305	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995212	15995213	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	53	605	0	ENST00000268712.3:c.2980dup	p.Cys994LeufsTer24	p.C994Lfs*24	ENST00000268712	NM_006311.3	994	tgt/tTgt	22/46	1	2	FACETS	0.808	0.689	0.94	0.808	0.689	0.94	CLONAL	1	FALSE	1	0.21997905730952	2		605	596	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220707	1220708	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0010307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	110	323	1	ENST00000326873.7:c.725_726delinsTT	p.Gly242Val	p.G242V	ENST00000326873	NM_000455.4	242	gGG/gTT	5/10	0.200650525662835	2	FACETS	0.804	0.724	0.888	0.804	0.724	0.888	CLONAL	2	FALSE	0	0.21997905730952	2		324	622	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466019	69466019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	182	363	1	ENST00000227507.2:c.857C>T	p.Thr286Ile	p.T286I	ENST00000227507	NM_053056.2	286	aCa/aTa	5/5	1	2	FACETS	0.923	0.855	0.992	0.923	0.855	0.992	CLONAL	1	TRUE	1	0.620313435425101	2		364	636	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699360	47699360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	244	618	0	ENST00000347630.2:c.148G>A	p.Glu50Lys	p.E50K	ENST00000347630	NM_001007230.1	50	Gaa/Aaa	4/11	1	2	FACETS	0.842	0.788	0.898	0.842	0.788	0.898	CLONAL	1	TRUE	1	0.620313435425101	2		618	934	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692920	89692921	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs398123323	NA	P-0010310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	342	362	1	ENST00000371953.3:c.405dup	p.Cys136MetfsTer44	p.C136Mfs*44	ENST00000371953	NM_000314.4	135	ata/atAa	5/9	0.620313435425101	3	FACETS	0.88	0.845	0.915	0.88	0.845	0.915	CLONAL	3	TRUE	0	0.620313435425101	3		363	547	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266112	41266112	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913228	NA	P-0010310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	172	441	1	ENST00000349496.5:c.109T>C	p.Ser37Pro	p.S37P	ENST00000349496	NM_001904.3	37	Tct/Cct	3/15	1	2	FACETS	0.89	0.823	0.96	0.89	0.823	0.96	CLONAL	1	TRUE	1	0.620313435425101	2		442	623	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879903	37879903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	325	500	0	ENST00000269571.5:c.2198C>T	p.Thr733Ile	p.T733I	ENST00000269571		733	aCa/aTa	18/27	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.620313435425101	2		500	971	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106489	27106489	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	638	556	5	ENST00000324856.7:c.6100G>T	p.Glu2034Ter	p.E2034*	ENST00000324856	NM_006015.4	2034	Gag/Tag	20/20	0.620313435425101	2	FACETS	0.985	0.956	1	0.985	0.956	1	CLONAL	2	TRUE	0	0.620313435425101	2		561	1044	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678097	58678097	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	422	561	0	ENST00000305921.3:c.322G>A	p.Gly108Ser	p.G108S	ENST00000305921	NM_003620.3	108	Ggc/Agc	1/6	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.620313435425101	2		561	1220	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469814	157469817	+	frameshift_variant	Frame_Shift_Del	DEL	CCAG	CCAG	-	novel	NA	P-0010310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	318	463	0	ENST00000346085.5:c.2608_2611del	p.Pro870GlyfsTer43	p.P870Gfs*43	ENST00000346085	NM_020732.3	870	CCAGgg/gg	9/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.620313435425101	2		463	959	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591076	67591090	+	inframe_deletion	In_Frame_Del	DEL	CGAGAAATTGACAAA	CGAGAAATTGACAAA	-	novel	NA	P-0010310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	245	270	0	ENST00000274335.5:c.1671_1685del	p.Glu558_Arg562del	p.E558_R562del	ENST00000274335		557	CGAGAAATTGACAAA/-	12/15	0.620313435425101	2	FACETS	0.91	0.864	0.955	0.91	0.864	0.955	CLONAL	2	TRUE	0	0.620313435425101	2		270	434	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798353	45798353	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010464-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	156	459	0	ENST00000450313.1:c.583G>T	p.Glu195Ter	p.E195*	ENST00000450313	NM_012222.2	195	Gag/Tag	8/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.365815211938315	2		459	792	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470474	25470474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024296111	NA	P-0010464-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	53	244	0	ENST00000264709.3:c.1000G>A	p.Gly334Ser	p.G334S	ENST00000264709	NM_175629.2	334	Ggc/Agc	8/23	1	2	FACETS	0.707	0.604	0.818	0.707	0.604	0.818	SUBCLONAL	1	TRUE	1	0.365815211938315	2		244	410	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554897	187554897	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0010464-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	174	641	0	ENST00000441802.2:c.4264A>T	p.Lys1422Ter	p.K1422*	ENST00000441802	NM_005245.3	1422	Aag/Tag	7/27	0.365815211938315	1	FACETS	0.97	0.895	1	0.97	0.895	1	CLONAL	1	TRUE	0	0.365815211938315	1		641	801	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518056	176518056	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010464-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	131	376	0	ENST00000292408.4:c.554T>G	p.Leu185Arg	p.L185R	ENST00000292408	NM_213647.1	185	cTt/cGt	5/18	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.365815211938315	2		376	656	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562895	95562895	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010464-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	70	238	0	ENST00000393063.1:c.4362T>G	p.Asp1454Glu	p.D1454E	ENST00000393063	NM_030621.3	1454	gaT/gaG	24/28	NA	2	FACETS	0.962	0.842	1			1	INDETERMINATE	1	TRUE	NA	0.365815211938315	2		238	398	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724361	52724361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010464-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	86	256	1	ENST00000322088.6:c.1493G>A	p.Arg498His	p.R498H	ENST00000322088	NM_014225.5	498	cGc/cAc	12/15	1	2	FACETS	0.88	0.781	0.987	0.88	0.781	0.987	CLONAL	1	TRUE	1	0.365815211938315	2		257	534	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652530	48652530	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010464-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	54	159	0	ENST00000376670.3:c.1201C>A	p.Pro401Thr	p.P401T	ENST00000376670	NM_002049.3	401	Ccc/Acc	6/6	0.365815211938315	1	FACETS	0.965	0.832	1	0.965	0.832	1	CLONAL	1	TRUE	0	0.365815211938315	1		159	250	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127802	47127866	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTTCTTTCATGGGGGAAGGGAGACACGATGCAGAGCATTGGGAGGCAATATCAGAATATTACAAA	GTTCTTTCATGGGGGAAGGGAGACACGATGCAGAGCATTGGGAGGCAATATCAGAATATTACAAA	-	novel	NA	P-0010464-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	36	124	0	ENST00000409792.3:c.5278-62_5280del		p.X1760_splice	ENST00000409792	NM_014159.6	1760		11/21	0.32937105499101	1	FACETS	0.919	0.765	1	0.919	0.765	1	CLONAL	1	TRUE	0	0.365815211938315	1		124	175	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906837	32906837	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	GCCAGG	novel	NA	P-0010464-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	97	458	0	ENST00000380152.3:c.1222delinsGCCAGG	p.Met408AlafsTer24	p.M408Afs*24	ENST00000380152		408	Atg/GCCAGGtg	10/27	0.365815211938315	1	FACETS	0.771	0.689	0.858	0.771	0.689	0.858	SUBCLONAL	1	TRUE	0	0.365815211938315	1		458	562	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577084	7577084	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121912667	NA	P-0010487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	226	473	0	ENST00000269305.4:c.854A>T	p.Glu285Val	p.E285V	ENST00000269305	NM_001126112.2	285	gAg/gTg	8/11	0.179530042596509	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.179530042596509	2		473	1203	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249002	55249003	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCGTGGA	rs397517109	NA	P-0010487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	274	254	0	ENST00000275493.2:c.2303_2311dup	p.Ser768_Asp770dup	p.S768_D770dup	ENST00000275493	NM_005228.3	768	gcc/gcCAGCGTGGAc	20/28	0.179530042596509	8	FACETS	0.971	0.913	1			1	CLONAL	5	TRUE	NA	0.179530042596509	8		254	967	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442788	187442788	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	203	398	0	ENST00000232014.4:c.1918C>T	p.Arg640Trp	p.R640W	ENST00000232014	NM_001130845.1	640	Cgg/Tgg	9/10	0.169551329410562	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.179530042596509	2		398	1070	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76919028	76919029	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010496-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	283	412	0	ENST00000373344.5:c.3962dup	p.Asn1321LysfsTer3	p.N1321Kfs*3	ENST00000373344	NM_000489.3	1321	aat/aaAt	12/35	0.680457541545141	2	FACETS	0.954	0.913	0.993	0.954	0.913	0.993	CLONAL	2	TRUE	0	0.680457541545141	2		412	436	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0010524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	643	371	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.786999912135476	3	FACETS	0.792	0.765	0.82			1	SUBCLONAL	2	TRUE	NA	0.786999912135476	3		371	1437	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278049	18278049	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs372272045	NA	P-0010560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	73	346	0	ENST00000222254.8:c.1669G>T	p.Asp557Tyr	p.D557Y	ENST00000222254	NM_005027.3	557	Gac/Tac	13/16	1	2	FACETS	0.591	0.517	0.672	0.591	0.517	0.672	SUBCLONAL	1	TRUE	1	0.359544801943072	2		346	687	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150549945	150549945	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	72	157	0	ENST00000369026.2:c.959A>G	p.His320Arg	p.H320R	ENST00000369026	NM_021960.4	320	cAt/cGt	3/3	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.359544801943072	2		157	328	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729893	30729893	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	48	222	0	ENST00000295754.5:c.1414C>A	p.Pro472Thr	p.P472T	ENST00000295754	NM_003242.5	472	Cct/Act	6/7	1	2	FACETS	0.637	0.54	0.744	0.637	0.54	0.744	SUBCLONAL	1	TRUE	1	0.359544801943072	2		222	419	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259489	89259489	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	160	516	0	ENST00000336596.2:c.633G>T	p.Met211Ile	p.M211I	ENST00000336596	NM_005233.5	211	atG/atT	3/17	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.359544801943072	2		516	804	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115919	8115920	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0010560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	53	189	0	ENST00000346208.3:c.1266dup	p.His423AlafsTer84	p.H423Afs*84	ENST00000346208		422	atg/atGg	6/6	1	2	FACETS	0.797	0.682	0.921	0.797	0.682	0.921	CLONAL	1	TRUE	1	0.359544801943072	2		189	370	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0010571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	152	379	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.401392862020953	3	FACETS	0.883	0.821	0.947	0.883	0.821	0.947	CLONAL	3	TRUE	0	0.407297992201674	3		379	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0010571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	374	491	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	0.349837474414509	2	FACETS	0.924	0.879	0.969	0.924	0.879	0.969	CLONAL	2	TRUE	0	0.407297992201674	2		491	994	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39721126	39721126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771318367	NA	P-0010571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	74	413	0	ENST00000361337.2:c.629G>A	p.Arg210His	p.R210H	ENST00000361337	NM_003286.2	210	cGc/cAc	9/21	0.218057539900081	4	FACETS	0.9	0.789	1	0.3	0.263	0.34	INDETERMINATE	1	TRUE	1	0.407297992201674	4		413	568	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346659	81346659	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	131	331	0	ENST00000222390.5:c.1294G>T	p.Ala432Ser	p.A432S	ENST00000222390	NM_000601.4	432	Gca/Tca	11/18	0.397496611815349	3	FACETS	0.817	0.746	0.89	0.817	0.746	0.89	CLONAL	2	TRUE	1	0.407297992201674	3		331	474	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508200	106508200	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	125	140	0	ENST00000359195.3:c.194G>C	p.Gly65Ala	p.G65A	ENST00000359195	NM_002649.2	65	gGc/gCc	2/11	0.397496611815349	3	FACETS	1	0.916	1	1	0.916	1	CLONAL	2	TRUE	1	0.407297992201674	3		140	369	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509240	106509240	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	174	509	0	ENST00000359195.3:c.1234G>T	p.Val412Leu	p.V412L	ENST00000359195	NM_002649.2	412	Gtg/Ttg	2/11	0.397496611815349	3	FACETS	1	0.966	1	0.545	0.501	0.59	CLONAL	1	TRUE	1	0.407297992201674	3		509	944	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310884	123310884	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs200766273	NA	P-0010571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	180	522	1	ENST00000358487.5:c.544G>T	p.Gly182Trp	p.G182W	ENST00000358487	NM_000141.4	182	Ggg/Tgg	5/18	1	2	FACETS	0.959	0.884	1	0.959	0.884	1	CLONAL	1	TRUE	1	0.407297992201674	2		523	922	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149219	119149219	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0010571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	232	472	1	ENST00000264033.4:c.1228-1G>T		p.X410_splice	ENST00000264033	NM_005188.3	410			0.198934106395039	6	FACETS	1	0.981	1	0.756	0.705	0.807	INDETERMINATE	2	TRUE	3	0.407297992201674	6		473	912	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207042	1207042	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0010571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	235	391	0	ENST00000326873.7:c.130A>T	p.Lys44Ter	p.K44*	ENST00000326873	NM_000455.4	44	Aag/Tag	1/10	0.407297992201674	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.407297992201674	2		391	561	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841307	15841307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	379	287	0	ENST00000307771.7:c.1391G>A	p.Arg464His	p.R464H	ENST00000307771	NM_005089.3	464	cGt/cAt	11/11	0.404331179126372	2	FACETS	0.893	0.856	0.929			1	CLONAL	3	TRUE	NA	0.407297992201674	2		287	695	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86658397	86658397	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	88	305	0	ENST00000274376.6:c.1363del	p.Asp455MetfsTer28	p.D455Mfs*28	ENST00000274376	NM_002890.2	454	gtG/gt	10/25	0.407297992201674	2	FACETS	0.927	0.836	1	0.927	0.836	1	CLONAL	2	TRUE	0	0.407297992201674	2		305	233	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599938	10599939	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	411	558	0	ENST00000171111.5:c.1637dup	p.Val547ArgfsTer27	p.V547Rfs*27	ENST00000171111	NM_203500.1	546	ttc/ttTc	5/6	0.407297992201674	2	FACETS	0.948	0.905	0.992	0.948	0.905	0.992	CLONAL	2	TRUE	0	0.407297992201674	2		558	1064	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334786	81334787	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0010571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	59	374	0	ENST00000222390.5:c.1929_1930delinsAA	p.Ser643_Gln644delinsArgLys	p.S643_Q644delinsRK	ENST00000222390	NM_000601.4	643	agCCag/agAAag	17/18	0.397496611815349	3	FACETS	1	0.914	1	0.538	0.466	0.616	CLONAL	1	TRUE	1	0.407297992201674	3		374	324	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	294	695	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.455696214853583	2		695	1243	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	206	359	0	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.988	0.917	1	0.988	0.917	1	CLONAL	1	TRUE	1	0.455696214853583	2		359	915	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	209	448	0	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.911	0.846	0.979	0.911	0.846	0.979	CLONAL	1	TRUE	1	0.455696214853583	2		448	1007	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	219	512	4	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	0.983	0.915	1	0.983	0.915	1	CLONAL	1	TRUE	1	0.455696214853583	2		516	978	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294665	1294665	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	64	140	2	ENST00000310581.5:c.336del	p.Glu113ArgfsTer15	p.E113Rfs*15	ENST00000310581	NM_198253.2	112	ccC/cc	2/16	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.455696214853583	2		142	256	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	172	454	2	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.866	0.797	0.937	0.866	0.797	0.937	CLONAL	1	TRUE	1	0.455696214853583	2		456	872	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	402	479	9	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	0.417986128962814	3	FACETS	0.9	0.857	0.944	0.9	0.857	0.944	CLONAL	2	TRUE	1	0.455696214853583	3		488	1203	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781324	3781326	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs587783502	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	255	676	2	ENST00000262367.5:c.5039_5041del	p.Ser1680del	p.S1680del	ENST00000262367	NM_004380.2	1680	tCCTtg/ttg	30/31	1	2	FACETS	0.934	0.874	0.997	0.934	0.874	0.997	CLONAL	1	TRUE	1	0.455696214853583	2		678	1198	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	195	559	4	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	0.417986128962814	3	FACETS	1	0.968	1	0.542	0.501	0.584	CLONAL	1	TRUE	1	0.455696214853583	3		563	970	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	186	356	1	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.996	0.921	1	0.996	0.921	1	CLONAL	1	TRUE	1	0.455696214853583	2		357	820	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610666	10610666	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144429440	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	128	248	0	ENST00000171111.5:c.44G>A	p.Arg15Gln	p.R15Q	ENST00000171111	NM_203500.1	15	cGa/cAa	2/6	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.455696214853583	2		248	472	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	96	296	2	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	0.851	0.761	0.946	0.851	0.761	0.946	CLONAL	1	TRUE	1	0.455696214853583	2		298	495	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958549	175958549	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1271141729	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	122	351	0	ENST00000367669.3:c.1796G>A	p.Arg599His	p.R599H	ENST00000367669	NM_022457.5	599	cGt/cAt	16/20	1	2	FACETS	0.803	0.727	0.883	0.803	0.727	0.883	CLONAL	1	TRUE	1	0.455696214853583	2		351	667	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156731	20156731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	163	313	0	ENST00000379607.5:c.26G>A	p.Gly9Asp	p.G9D	ENST00000379607	NM_001412.3	9	gGt/gAt	2/7	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.455696214853583	1		313	371	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586502	189586502	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757536818	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	93	294	0	ENST00000264731.3:c.1126C>T	p.Arg376Cys	p.R376C	ENST00000264731	NM_003722.4	376	Cgc/Tgc	8/14	1	2	FACETS	0.777	0.693	0.867	0.777	0.693	0.867	SUBCLONAL	1	TRUE	1	0.455696214853583	2		294	525	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677945	58677945	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770413280	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	221	491	2	ENST00000305921.3:c.170C>T	p.Ala57Val	p.A57V	ENST00000305921	NM_003620.3	57	gCc/gTc	1/6	0.450614935392471	2	FACETS	1	0.983	1	0.581	0.541	0.621	CLONAL	1	TRUE	0	0.455696214853583	2		493	835	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5465595	5465595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148141792	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	164	650	2	ENST00000381577.3:c.779G>A	p.Arg260His	p.R260H	ENST00000381577	NM_014143.3	260	cGt/cAt	5/7	1	2	FACETS	0.86	0.79	0.933	0.86	0.79	0.933	CLONAL	1	TRUE	1	0.455696214853583	2		652	837	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601873	43601873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	85	599	0	ENST00000355710.3:c.917C>T	p.Ala306Val	p.A306V	ENST00000355710	NM_020975.4	306	gCa/gTa	5/20	1	2	FACETS	0.394	0.348	0.445	0.394	0.348	0.445	SUBCLONAL	1	TRUE	1	0.455696214853583	2		599	946	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678053	58678053	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1446153777	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	217	482	0	ENST00000305921.3:c.278G>A	p.Arg93His	p.R93H	ENST00000305921	NM_003620.3	93	cGc/cAc	1/6	0.450614935392471	2	FACETS	1	0.983	1	0.582	0.542	0.623	CLONAL	1	TRUE	0	0.455696214853583	2		482	818	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439919	56439919	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	436	559	0	ENST00000407977.2:c.673del	p.Arg225AlafsTer194	p.R225Afs*194	ENST00000407977		225	Cgc/gc	6/10	0.450614935392471	2	FACETS	0.987	0.946	1	0.987	0.946	1	CLONAL	2	TRUE	0	0.455696214853583	2		559	969	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919786	50919786	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1555793361	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	181	547	0	ENST00000440232.2:c.2953+1G>A		p.X985_splice	ENST00000440232	NM_002691.3	985			1	2	FACETS	0.905	0.835	0.977	0.905	0.835	0.977	CLONAL	1	TRUE	1	0.455696214853583	2		547	878	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866710	37866710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1258412021	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	421	580	0	ENST00000269571.5:c.877G>A	p.Ala293Thr	p.A293T	ENST00000269571		293	Gcc/Acc	7/27	0.450614935392471	2	FACETS	0.955	0.914	0.997	0.955	0.914	0.997	CLONAL	2	TRUE	0	0.455696214853583	2		580	967	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261538	16261538	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	176	456	0	ENST00000375759.3:c.8803G>T	p.Gly2935Trp	p.G2935W	ENST00000375759	NM_015001.2	2935	Ggg/Tgg	11/15	1	2	FACETS	0.934	0.861	1	0.934	0.861	1	CLONAL	1	TRUE	1	0.455696214853583	2		456	827	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100837	27100837	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	189	690	1	ENST00000324856.7:c.4119G>T	p.Met1373Ile	p.M1373I	ENST00000324856	NM_006015.4	1373	atG/atT	18/20	1	2	FACETS	0.883	0.817	0.953	0.883	0.817	0.953	CLONAL	1	TRUE	1	0.455696214853583	2		691	939	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846307	156846307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762542314	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	237	712	2	ENST00000524377.1:c.1748G>A	p.Arg583His	p.R583H	ENST00000524377	NM_002529.3	583	cGc/cAc	14/17	1	2	FACETS	0.975	0.91	1	0.975	0.91	1	CLONAL	1	TRUE	1	0.455696214853583	2		714	1067	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149938	202149938	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	191	582	0	ENST00000358485.4:c.1379T>C	p.Leu460Pro	p.L460P	ENST00000358485	NM_001080125.1	460	cTg/cCg	8/9	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.455696214853583	2		582	785	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662191	227662191	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	163	712	0	ENST00000305123.5:c.1264G>A	p.Asp422Asn	p.D422N	ENST00000305123	NM_005544.2	422	Gat/Aat	1/2	1	2	FACETS	0.736	0.675	0.8	0.736	0.675	0.8	SUBCLONAL	1	TRUE	1	0.455696214853583	2		712	972	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103785	47103785	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139016283	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	215	916	0	ENST00000409792.3:c.6161C>T	p.Pro2054Leu	p.P2054L	ENST00000409792	NM_014159.6	2054	cCg/cTg	14/21	1	2	FACETS	0.883	0.82	0.948	0.883	0.82	0.948	CLONAL	1	TRUE	1	0.455696214853583	2		916	1069	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933294	49933294	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	275	789	1	ENST00000296474.3:c.2816G>T	p.Cys939Phe	p.C939F	ENST00000296474	NM_002447.2	939	tGt/tTt	12/20	1	2	FACETS	0.998	0.936	1	0.998	0.936	1	CLONAL	1	TRUE	1	0.455696214853583	2		790	1209	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446845	187446845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201771435	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	154	477	0	ENST00000232014.4:c.1348G>A	p.Val450Ile	p.V450I	ENST00000232014	NM_001130845.1	450	Gtt/Att	5/10	1	2	FACETS	0.951	0.872	1	0.951	0.872	1	CLONAL	1	TRUE	1	0.455696214853583	2		477	711	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158113	106158113	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	136	510	0	ENST00000380013.4:c.3014A>C	p.Lys1005Thr	p.K1005T	ENST00000380013	NM_001127208.2	1005	aAg/aCg	3/11	1	2	FACETS	0.865	0.788	0.946	0.865	0.788	0.946	CLONAL	1	TRUE	1	0.455696214853583	2		510	690	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512341	149512341	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	164	436	0	ENST00000261799.4:c.1099C>A	p.Leu367Met	p.L367M	ENST00000261799	NM_002609.3	367	Ctg/Atg	7/23	1	2	FACETS	0.938	0.863	1	0.938	0.863	1	CLONAL	1	TRUE	1	0.455696214853583	2		436	767	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051034	180051034	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	183	620	0	ENST00000261937.6:c.1449G>A	p.Met483Ile	p.M483I	ENST00000261937	NM_182925.4	483	atG/atA	11/30	1	2	FACETS	0.846	0.781	0.914	0.846	0.781	0.914	CLONAL	1	TRUE	1	0.455696214853583	2		620	949	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393351	393351	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	177	480	0	ENST00000380956.4:c.199G>A	p.Asp67Asn	p.D67N	ENST00000380956	NM_001195286.1	67	Gac/Aac	2/9	1	2	FACETS	0.975	0.9	1	0.975	0.9	1	CLONAL	1	TRUE	1	0.455696214853583	2		480	797	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407516	407516	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	135	595	0	ENST00000380956.4:c.1274T>C	p.Leu425Pro	p.L425P	ENST00000380956	NM_001195286.1	425	cTg/cCg	9/9	1	2	FACETS	0.804	0.732	0.88	0.804	0.732	0.88	CLONAL	1	TRUE	1	0.455696214853583	2		595	737	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100417	157100417	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	29	81	0	ENST00000346085.5:c.1354C>T	p.Gln452Ter	p.Q452*	ENST00000346085	NM_020732.3	452	Cag/Tag	1/20	1	2	FACETS	0.979	0.799	1	0.979	0.799	1	CLONAL	1	TRUE	1	0.455696214853583	2		81	130	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848622	151848622	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376118166	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	124	512	1	ENST00000262189.6:c.12571G>A	p.Ala4191Thr	p.A4191T	ENST00000262189	NM_170606.2	4191	Gca/Aca	50/59	1	2	FACETS	0.822	0.745	0.903	0.822	0.745	0.903	CLONAL	1	TRUE	1	0.455696214853583	2		513	662	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738440	145738440	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201661055	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	165	441	0	ENST00000428558.2:c.2545G>A	p.Val849Met	p.V849M	ENST00000428558	NM_004260.3	849	Gtg/Atg	16/22	1	2	FACETS	0.907	0.834	0.984	0.907	0.834	0.984	CLONAL	1	TRUE	1	0.455696214853583	2		441	798	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87338562	87338562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	130	737	0	ENST00000277120.3:c.658G>A	p.Val220Met	p.V220M	ENST00000277120		220	Gtg/Atg	7/19	1	2	FACETS	0.935	0.851	1	0.935	0.851	1	CLONAL	1	TRUE	1	0.455696214853583	2		737	610	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93607729	93607729	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	122	446	0	ENST00000375746.1:c.431A>G	p.Glu144Gly	p.E144G	ENST00000375746	NM_001174167.1	144	gAg/gGg	3/14	1	2	FACETS	0.821	0.744	0.903	0.821	0.744	0.903	CLONAL	1	TRUE	1	0.455696214853583	2		446	652	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102196076	102196076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	160	734	0	ENST00000263464.3:c.836C>T	p.Ala279Val	p.A279V	ENST00000263464	NM_001165.4	279	gCg/gTg	2/9	1	2	FACETS	0.817	0.75	0.888	0.817	0.75	0.888	CLONAL	1	TRUE	1	0.455696214853583	2		734	859	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497611	125497611	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	76	359	0	ENST00000428830.2:c.175A>G	p.Asn59Asp	p.N59D	ENST00000428830	NM_001114121.2	59	Aat/Gat	3/14	1	2	FACETS	0.866	0.764	0.975	0.866	0.764	0.975	CLONAL	1	TRUE	1	0.455696214853583	2		359	385	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432914	432914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	143	492	1	ENST00000399788.2:c.2002C>T	p.Leu668Phe	p.L668F	ENST00000399788	NM_001042603.1	668	Ctt/Ttt	15/28	0.417986128962814	3	FACETS	1	0.935	1	0.514	0.469	0.561	CLONAL	1	TRUE	1	0.455696214853583	3		493	749	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110049	115110049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	163	475	1	ENST00000257566.3:c.1829C>T	p.Ala610Val	p.A610V	ENST00000257566	NM_016569.3	610	gCa/gTa	8/8	0.417986128962814	3	FACETS	1	0.947	1	0.52	0.478	0.565	CLONAL	1	TRUE	1	0.455696214853583	3		476	844	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557675	21557675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	227	709	0	ENST00000382592.4:c.2170G>A	p.Asp724Asn	p.D724N	ENST00000382592	NM_014572.2	724	Gac/Aac	5/8	1	2	FACETS	0.982	0.915	1	0.982	0.915	1	CLONAL	1	TRUE	1	0.455696214853583	2		709	1015	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563059	21563059	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	193	511	0	ENST00000382592.4:c.860C>A	p.Ala287Asp	p.A287D	ENST00000382592	NM_014572.2	287	gCc/gAc	4/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.455696214853583	2		511	805	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28903782	28903782	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	236	704	0	ENST00000282397.4:c.2677A>T	p.Asn893Tyr	p.N893Y	ENST00000282397	NM_002019.4	893	Aac/Tac	19/30	1	2	FACETS	0.946	0.882	1	0.946	0.882	1	CLONAL	1	TRUE	1	0.455696214853583	2		704	1095	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042336	42042336	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1473325397	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	263	1189	0	ENST00000219905.7:c.6531T>A	p.His2177Gln	p.H2177Q	ENST00000219905	NM_001164273.1	2177	caT/caA	17/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.455696214853583	2		1189	1097	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042344	42042344	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375801764	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	266	1186	0	ENST00000219905.7:c.6539G>A	p.Gly2180Asp	p.G2180D	ENST00000219905	NM_001164273.1	2180	gGc/gAc	17/24	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.455696214853583	2		1186	1104	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042350	42042350	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	261	1203	0	ENST00000219905.7:c.6545T>A	p.Leu2182Ter	p.L2182*	ENST00000219905	NM_001164273.1	2182	tTa/tAa	17/24	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.455696214853583	2		1203	1102	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2218083	2218083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745522760	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	295	900	0	ENST00000326181.6:c.145G>A	p.Gly49Arg	p.G49R	ENST00000326181	NM_032271.2	49	Ggg/Agg	4/21	1	2	FACETS	0.951	0.893	1	0.951	0.893	1	CLONAL	1	TRUE	1	0.455696214853583	2		900	1362	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856028	68856028	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	252	822	0	ENST00000261769.5:c.1836A>G	p.Ile612Met	p.I612M	ENST00000261769	NM_004360.3	612	atA/atG	12/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.455696214853583	2		822	1064	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828860	72828860	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	271	973	0	ENST00000268489.5:c.7721T>C	p.Phe2574Ser	p.F2574S	ENST00000268489	NM_006885.3	2574	tTc/tCc	9/10	1	2	FACETS	0.875	0.819	0.932	0.875	0.819	0.932	CLONAL	1	TRUE	1	0.455696214853583	2		973	1360	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217689	7217689	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1455713693	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	175	866	0	ENST00000380728.2:c.238C>T	p.Gln80Ter	p.Q80*	ENST00000380728		80	Cag/Tag	4/11	1	2	FACETS	0.746	0.686	0.808	0.746	0.686	0.808	SUBCLONAL	1	TRUE	1	0.455696214853583	2		866	1030	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108241	8108241	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773142037	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	243	691	0	ENST00000585124.1:c.983G>A	p.Arg328Gln	p.R328Q	ENST00000585124	NM_004217.3	328	cGg/cAg	9/9	1	2	FACETS	0.946	0.884	1	0.946	0.884	1	CLONAL	1	TRUE	1	0.455696214853583	2		691	1127	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17125941	17125941	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367843558	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	166	480	0	ENST00000285071.4:c.653G>A	p.Arg218His	p.R218H	ENST00000285071	NM_144997.5	218	cGt/cAt	7/14	1	2	FACETS	0.86	0.791	0.933	0.86	0.791	0.933	CLONAL	1	TRUE	1	0.455696214853583	2		480	847	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511574	38511574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	206	678	0	ENST00000254066.5:c.1072G>A	p.Ala358Thr	p.A358T	ENST00000254066	NM_000964.3	358	Gcg/Acg	8/9	0.450614935392471	2	FACETS	0.94	0.872	1	0.47	0.436	0.505	CLONAL	1	TRUE	0	0.455696214853583	2		678	962	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273775	18273775	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	174	526	0	ENST00000222254.8:c.1110-2A>G		p.X370_splice	ENST00000222254	NM_005027.3	370			1	2	FACETS	0.953	0.879	1	0.953	0.879	1	CLONAL	1	TRUE	1	0.455696214853583	2		526	801	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101086	41101086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776769442	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	153	596	0	ENST00000373198.4:c.1270G>A	p.Val424Met	p.V424M	ENST00000373198	NM_133170.3	424	Gtg/Atg	8/32	1	2	FACETS	0.878	0.804	0.955	0.878	0.804	0.955	CLONAL	1	TRUE	1	0.455696214853583	2		596	765	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537115	41537115	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853039	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	157	576	0	ENST00000263253.7:c.1942C>T	p.Arg648Ter	p.R648*	ENST00000263253	NM_001429.3	648	Cga/Tga	10/31	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.455696214853583	2		576	674	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227706	53227706	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1135401800	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	259	366	1	ENST00000375401.3:c.2482C>T	p.Arg828Ter	p.R828*	ENST00000375401	NM_004187.3	828	Cga/Tga	17/26	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.455696214853583	1		367	620	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428704	49428705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	175	570	0	ENST00000301067.7:c.10245dup	p.Ala3416CysfsTer7	p.A3416Cfs*7	ENST00000301067	NM_003482.3	3415	-/T	35/54	0.417986128962814	3	FACETS	0.967	0.89	1	0.484	0.445	0.524	CLONAL	1	TRUE	1	0.455696214853583	3		570	975	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263974	104263974	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776579	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	111	306	0	ENST00000369902.3:c.71del	p.Pro24ArgfsTer72	p.P24Rfs*72	ENST00000369902	NM_016169.3	22	gCc/gc	1/12	1	2	FACETS	0.931	0.841	1	0.931	0.841	1	CLONAL	1	TRUE	1	0.455696214853583	2		306	523	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259480	16259480	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	117	356	2	ENST00000375759.3:c.6750del	p.Ala2251GlnfsTer102	p.A2251Qfs*102	ENST00000375759	NM_015001.2	2249	Ccc/cc	11/15	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.455696214853583	2		358	512	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435157	49435157	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	151	266	0	ENST00000301067.7:c.6396del	p.Ala2133ProfsTer11	p.A2133Pfs*11	ENST00000301067	NM_003482.3	2132	ccC/cc	31/54	0.417986128962814	3	FACETS	0.793	0.73	0.858	0.793	0.73	0.858	SUBCLONAL	2	TRUE	1	0.455696214853583	3		266	513	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248471	59248473	+	inframe_deletion	In_Frame_Del	DEL	GTG	GTG	-	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	193	596	0	ENST00000371222.2:c.270_272del	p.Thr91del	p.T91del	ENST00000371222	NM_002228.3	90	acCACg/acg	1/1	1	2	FACETS	0.895	0.828	0.965	0.895	0.828	0.965	CLONAL	1	TRUE	1	0.455696214853583	2		596	946	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8113516	8113516	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	243	748	0	ENST00000585124.1:c.27del	p.Trp10GlyfsTer12	p.W10Gfs*12	ENST00000585124	NM_004217.3	9	ccC/cc	2/9	1	2	FACETS	0.826	0.77	0.884	0.826	0.77	0.884	CLONAL	1	TRUE	1	0.455696214853583	2		748	1291	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434713	110434716	+	missense_variant	Missense_Mutation	ONP	CGAC	CGAC	TGAT	novel	NA	P-0010581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	133	506	0	ENST00000375856.3:c.3685_3688delinsATCA	p.Val1229_Gly1230delinsIleSer	p.V1229_G1230delinsIS	ENST00000375856	NM_003749.2	1229	GTCGgt/ATCAgt	1/2	1	2	FACETS	0.699	0.635	0.767	0.699	0.635	0.767	SUBCLONAL	1	TRUE	1	0.455696214853583	2		506	835	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	54	374	0				ENST00000310581	NM_198253.2	-/1132			0.197293243055433	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.305476097628385	1		374	253	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0010588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	130	360	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.222386749318148	2	FACETS	0.828	0.755	0.904	0.828	0.755	0.904	CLONAL	2	TRUE	0	0.305476097628385	2		361	514	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713807	30713807	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	117	357	0	ENST00000295754.5:c.1132A>T	p.Arg378Trp	p.R378W	ENST00000295754	NM_003242.5	378	Agg/Tgg	4/7	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.305476097628385	2		357	686	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472442	88472442	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1323245430	NA	P-0010588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	89	447	0	ENST00000360948.2:c.2113T>C	p.Tyr705His	p.Y705H	ENST00000360948	NM_001012338.2	705	Tac/Cac	16/19	0.259045650780791	1	FACETS	0.687	0.609	0.77	0.687	0.609	0.77	SUBCLONAL	1	TRUE	0	0.305476097628385	1		447	719	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33446156	33446161	+	inframe_deletion	In_Frame_Del	DEL	CTACCT	CTACCT	-	novel	NA	P-0010588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	46	456	0	ENST00000345365.6:c.113_118del	p.Glu38_Val39del	p.E38_V39del	ENST00000345365	NM_002878.3	38	gAGGTAGct/gct	2/10	1	2	FACETS	0.415	0.348	0.489	0.415	0.348	0.489	SUBCLONAL	1	TRUE	1	0.305476097628385	2		456	726	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540440	187540441	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	68	261	0	ENST00000441802.2:c.7299_7300insA	p.Asp2434ArgfsTer3	p.D2434Rfs*3	ENST00000441802	NM_005245.3	2433	-/A	10/27	0.305476097628385	1	FACETS	0.955	0.835	1	0.955	0.835	1	CLONAL	1	TRUE	0	0.305476097628385	1		261	395	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	53	673	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.381030737874447	3	FACETS	0.776	0.663	0.899	0.388	0.331	0.45	SUBCLONAL	1	TRUE	1	0.381030737874447	3		673	427	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	113	66	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.844	0.76	0.932	0.844	0.76	0.932	CLONAL	1	TRUE	1	0.381030737874447	2		66	703	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	204	646	6	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.855	0.791	0.921	0.855	0.791	0.921	CLONAL	1	TRUE	1	0.381030737874447	2		652	1253	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	252	463	1	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.977	0.912	1	0.977	0.912	1	CLONAL	1	TRUE	1	0.381030737874447	2		464	1354	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248027	59248027	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	135	334	0	ENST00000371222.2:c.716C>T	p.Thr239Ile	p.T239I	ENST00000371222	NM_002228.3	239	aCa/aTa	1/1	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.381030737874447	2		334	689	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335013	65335013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	151	445	0	ENST00000342505.4:c.628G>A	p.Glu210Lys	p.E210K	ENST00000342505	NM_002227.2	210	Gaa/Aaa	6/25	1	2	FACETS	0.911	0.833	0.993	0.911	0.833	0.993	CLONAL	1	TRUE	1	0.381030737874447	2		445	870	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873191	71873191	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	230	761	0	ENST00000357731.5:c.1003C>T	p.Leu335Phe	p.L335F	ENST00000357731	NM_173808.2	335	Ctt/Ttt	7/7	1	2	FACETS	0.923	0.859	0.99	0.923	0.859	0.99	CLONAL	1	TRUE	1	0.381030737874447	2		761	1308	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243777029	243777029	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	127	425	0	ENST00000263826.5:c.640T>C	p.Ser214Pro	p.S214P	ENST00000263826	NM_005465.4	214	Tcc/Ccc	7/13	1	2	FACETS	0.935	0.848	1	0.935	0.848	1	CLONAL	1	TRUE	1	0.381030737874447	2		425	713	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149180	61149180	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	109	379	0	ENST00000295025.8:c.1370C>A	p.Ala457Asp	p.A457D	ENST00000295025	NM_002908.2	457	gCt/gAt	11/11	1	2	FACETS	0.748	0.672	0.829	0.748	0.672	0.829	SUBCLONAL	1	TRUE	1	0.381030737874447	2		379	765	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046241	128046241	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1430093547	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	151	357	0	ENST00000285398.2:c.1022C>T	p.Pro341Leu	p.P341L	ENST00000285398	NM_000122.1	341	cCc/cTc	7/15	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.381030737874447	2		357	780	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095827	178095827	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs914770655	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	149	413	2	ENST00000397062.3:c.1504C>T	p.Arg502Cys	p.R502C	ENST00000397062	NM_006164.4	502	Cgt/Tgt	5/5	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.381030737874447	2		415	723	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270174	198270174	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	99	316	0	ENST00000335508.6:c.1262A>T	p.Tyr421Phe	p.Y421F	ENST00000335508	NM_012433.2	421	tAt/tTt	10/25	1	2	FACETS	0.87	0.779	0.968	0.87	0.779	0.968	CLONAL	1	TRUE	1	0.381030737874447	2		316	597	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116221	209116221	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554138	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	167	544	0	ENST00000345146.2:c.55A>G	p.Thr19Ala	p.T19A	ENST00000345146	NM_005896.2	19	Aca/Gca	3/10	1	2	FACETS	0.944	0.867	1	0.944	0.867	1	CLONAL	1	TRUE	1	0.381030737874447	2		544	929	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295705	212295705	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	148	462	0	ENST00000342788.4:c.2608G>A	p.Gly870Arg	p.G870R	ENST00000342788	NM_005235.2	870	Gga/Aga	21/28	1	2	FACETS	0.982	0.898	1	0.982	0.898	1	CLONAL	1	TRUE	1	0.381030737874447	2		462	791	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626101	12626101	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	136	346	1	ENST00000251849.4:c.1859C>A	p.Ala620Asp	p.A620D	ENST00000251849	NM_002880.3	620	gCt/gAt	17/17	0.381030737874447	1	FACETS	0.874	0.797	0.955	0.874	0.797	0.955	CLONAL	1	TRUE	0	0.381030737874447	1		347	661	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927994	49927994	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772999107	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	281	726	2	ENST00000296474.3:c.3734G>A	p.Arg1245His	p.R1245H	ENST00000296474	NM_002447.2	1245	cGc/cAc	18/20	0.381030737874447	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.381030737874447	1		728	1163	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427613	72427613	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	115	411	0	ENST00000477973.2:c.877G>C	p.Glu293Gln	p.E293Q	ENST00000477973	NM_012234.5	293	Gag/Cag	4/4	0.381030737874447	1	FACETS	0.779	0.703	0.859	0.779	0.703	0.859	SUBCLONAL	1	TRUE	0	0.381030737874447	1		411	627	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204968	128204968	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	162	438	0	ENST00000341105.2:c.473C>T	p.Ser158Phe	p.S158F	ENST00000341105	NM_032638.4	158	tCc/tTc	3/6	0.381030737874447	3	FACETS	0.981	0.899	1	0.49	0.449	0.534	CLONAL	1	TRUE	1	0.381030737874447	3		438	1032	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665213	138665213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	240	563	0	ENST00000330315.3:c.352G>A	p.Glu118Lys	p.E118K	ENST00000330315	NM_023067.3	118	Gag/Aag	1/1	0.381030737874447	3	FACETS	1	0.975	1	0.547	0.51	0.586	CLONAL	1	TRUE	1	0.381030737874447	3		563	1370	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266707	142266707	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	143	455	0	ENST00000350721.4:c.3217C>T	p.Gln1073Ter	p.Q1073*	ENST00000350721	NM_001184.3	1073	Caa/Taa	16/47	0.381030737874447	3	FACETS	0.94	0.856	1	0.47	0.428	0.514	CLONAL	1	TRUE	1	0.381030737874447	3		455	951	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806582	1806582	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs997891391	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	114	446	0	ENST00000260795.2:c.1298C>A	p.Ser433Tyr	p.S433Y	ENST00000260795		433	tCc/tAc	9/17	1	2	FACETS	0.639	0.575	0.708	0.639	0.575	0.708	SUBCLONAL	1	TRUE	1	0.381030737874447	2		446	936	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807186	1807186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	178	461	0	ENST00000260795.2:c.1517C>T	p.Ala506Val	p.A506V	ENST00000260795		506	gCc/gTc	10/17	1	2	FACETS	0.996	0.918	1	0.996	0.918	1	CLONAL	1	TRUE	1	0.381030737874447	2		461	938	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573285	55573285	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	115	369	0	ENST00000288135.5:c.947T>G	p.Phe316Cys	p.F316C	ENST00000288135	NM_000222.2	316	tTc/tGc	6/21	1	2	FACETS	0.96	0.866	1	0.96	0.866	1	CLONAL	1	TRUE	1	0.381030737874447	2		369	629	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968136	55968136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747362899	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	154	508	1	ENST00000263923.4:c.2194G>A	p.Glu732Lys	p.E732K	ENST00000263923	NM_002253.2	732	Gaa/Aaa	15/30	1	2	FACETS	0.825	0.754	0.899	0.825	0.754	0.899	CLONAL	1	TRUE	1	0.381030737874447	2		509	980	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467464	66467464	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773032839	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	132	386	0	ENST00000273854.3:c.805G>A	p.Asp269Asn	p.D269N	ENST00000273854	NM_004439.5	269	Gat/Aat	3/18	1	2	FACETS	0.962	0.875	1	0.962	0.875	1	CLONAL	1	TRUE	1	0.381030737874447	2		386	720	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84403325	84403325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	169	503	1	ENST00000321945.7:c.160G>A	p.Glu54Lys	p.E54K	ENST00000321945	NM_139076.2	54	Gaa/Aaa	2/9	1	2	FACETS	0.997	0.917	1	0.997	0.917	1	CLONAL	1	TRUE	1	0.381030737874447	2		504	890	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196580	106196580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	115	417	0	ENST00000380013.4:c.4913C>T	p.Ser1638Leu	p.S1638L	ENST00000380013	NM_001127208.2	1638	tCa/tTa	11/11	1	2	FACETS	0.668	0.601	0.74	0.668	0.601	0.74	SUBCLONAL	1	TRUE	1	0.381030737874447	2		417	903	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244110	153244110	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	112	496	0	ENST00000281708.4:c.2047G>A	p.Val683Met	p.V683M	ENST00000281708	NM_033632.3	683	Gtg/Atg	12/12	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.381030737874447	NA		496	1146	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539564	187539565	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	246	386	0	ENST00000441802.2:c.8175_8176delinsTT	p.Arg2726Ter	p.R2726*	ENST00000441802	NM_005245.3	2725	atCCga/atTTga	10/27	0.372888103022963	3	FACETS	0.964	0.904	1			1	CLONAL	2	TRUE	NA	0.381030737874447	3		386	797	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542864	187542864	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	85	350	0	ENST00000441802.2:c.4876G>C	p.Asp1626His	p.D1626H	ENST00000441802	NM_005245.3	1626	Gat/Cat	10/27	0.372888103022963	3	FACETS	0.657	0.58	0.74			1	SUBCLONAL	1	TRUE	NA	0.381030737874447	3		350	808	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557881	187557881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	358	541	0	ENST00000441802.2:c.3830C>T	p.Thr1277Ile	p.T1277I	ENST00000441802	NM_005245.3	1277	aCc/aTc	5/27	0.372888103022963	3	FACETS	0.925	0.877	0.974			1	CLONAL	2	TRUE	NA	0.381030737874447	3		541	1209	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233751	233751	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	96	231	0	ENST00000264932.6:c.1055G>T	p.Arg352Leu	p.R352L	ENST00000264932	NM_004168.2	352	cGa/cTa	8/15	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.381030737874447	2		231	471	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189379	56189379	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	183	489	1	ENST00000399503.3:c.4411C>A	p.Pro1471Thr	p.P1471T	ENST00000399503	NM_005921.1	1471	Cca/Aca	20/20	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.381030737874447	2		490	942	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576768	67576768	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	54	179	1	ENST00000274335.5:c.850G>A	p.Glu284Lys	p.E284K	ENST00000274335		284	Gaa/Aaa	6/15	1	2	FACETS	0.744	0.638	0.859	0.744	0.638	0.859	SUBCLONAL	1	TRUE	1	0.381030737874447	2		180	381	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056286	180056286	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759344198	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	184	571	0	ENST00000261937.6:c.958C>T	p.Arg320Trp	p.R320W	ENST00000261937	NM_182925.4	320	Cgg/Tgg	7/30	1	2	FACETS	0.873	0.805	0.944	0.873	0.805	0.944	CLONAL	1	TRUE	1	0.381030737874447	2		571	1106	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045806	26045806	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1417	321	1045	0	ENST00000540144.1:c.168G>C	p.Gln56His	p.Q56H	ENST00000540144	NM_003531.2	56	caG/caC	1/1	1	2	FACETS	0.969	0.912	1	0.969	0.912	1	CLONAL	1	TRUE	1	0.381030737874447	2		1045	1738	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839839	27839839	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1442	327	999	0	ENST00000328488.2:c.255C>A	p.Phe85Leu	p.F85L	ENST00000328488	NM_003533.2	85	ttC/ttA	1/1	1	2	FACETS	0.97	0.914	1	0.97	0.914	1	CLONAL	1	TRUE	1	0.381030737874447	2		999	1769	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181528	32181528	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	182	460	0	ENST00000375023.3:c.2257T>A	p.Cys753Ser	p.C753S	ENST00000375023	NM_004557.3	753	Tgc/Agc	14/30	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.381030737874447	2		460	854	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956529	93956529	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	216	718	0	ENST00000369303.4:c.2707C>T	p.Pro903Ser	p.P903S	ENST00000369303	NM_004440.3	903	Ccc/Tcc	15/17	1	2	FACETS	0.939	0.871	1	0.939	0.871	1	CLONAL	1	TRUE	1	0.381030737874447	2		718	1208	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956544	93956544	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	212	756	0	ENST00000369303.4:c.2692A>G	p.Asn898Asp	p.N898D	ENST00000369303	NM_004440.3	898	Aat/Gat	15/17	1	2	FACETS	0.902	0.837	0.971	0.902	0.837	0.971	CLONAL	1	TRUE	1	0.381030737874447	2		756	1233	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956676	93956676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465960814	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	220	711	0	ENST00000369303.4:c.2560C>T	p.Arg854Cys	p.R854C	ENST00000369303	NM_004440.3	854	Cgt/Tgt	15/17	1	2	FACETS	0.972	0.903	1	0.972	0.903	1	CLONAL	1	TRUE	1	0.381030737874447	2		711	1188	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965677	93965677	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	209	779	0	ENST00000369303.4:c.2251G>C	p.Asp751His	p.D751H	ENST00000369303	NM_004440.3	751	Gat/Cat	13/17	1	2	FACETS	0.91	0.843	0.979	0.91	0.843	0.979	CLONAL	1	TRUE	1	0.381030737874447	2		779	1206	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124437	94124437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	210	655	0	ENST00000369303.4:c.146C>T	p.Ser49Phe	p.S49F	ENST00000369303	NM_004440.3	49	tCc/tTc	2/17	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.381030737874447	2		655	1096	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674261	117674261	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	152	579	0	ENST00000368508.3:c.4213A>C	p.Thr1405Pro	p.T1405P	ENST00000368508	NM_002944.2	1405	Aca/Cca	26/43	1	2	FACETS	0.838	0.766	0.914	0.838	0.766	0.914	CLONAL	1	TRUE	1	0.381030737874447	2		579	952	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674321	117674321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	116	422	0	ENST00000368508.3:c.4153C>T	p.Leu1385Phe	p.L1385F	ENST00000368508	NM_002944.2	1385	Ctt/Ttt	26/43	1	2	FACETS	0.911	0.823	1	0.911	0.823	1	CLONAL	1	TRUE	1	0.381030737874447	2		422	668	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674323	117674323	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	103	406	0	ENST00000368508.3:c.4151C>T	p.Thr1384Ile	p.T1384I	ENST00000368508	NM_002944.2	1384	aCc/aTc	26/43	1	2	FACETS	0.828	0.742	0.919	0.828	0.742	0.919	CLONAL	1	TRUE	1	0.381030737874447	2		406	653	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686303	117686303	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	154	461	0	ENST00000368508.3:c.3038T>C	p.Leu1013Ser	p.L1013S	ENST00000368508	NM_002944.2	1013	tTa/tCa	20/43	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.381030737874447	2		461	800	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710563	117710563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751886816	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	159	363	0	ENST00000368508.3:c.1709C>T	p.Ser570Phe	p.S570F	ENST00000368508	NM_002944.2	570	tCt/tTt	12/43	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.381030737874447	2		363	741	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983275	149983275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	128	371	0	ENST00000253339.5:c.2983C>T	p.Arg995Cys	p.R995C	ENST00000253339		995	Cgc/Tgc	7/7	1	2	FACETS	0.87	0.789	0.956	0.87	0.789	0.956	CLONAL	1	TRUE	1	0.381030737874447	2		371	772	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004721	150004721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1034620976	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	181	438	0	ENST00000253339.5:c.1504C>T	p.Arg502Cys	p.R502C	ENST00000253339		502	Cgt/Tgt	3/7	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.381030737874447	2		438	890	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099485	157099485	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	166	422	0	ENST00000346085.5:c.422G>A	p.Gly141Asp	p.G141D	ENST00000346085	NM_020732.3	141	gGc/gAc	1/20	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.381030737874447	2		422	862	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508517	106508517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs549157001	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	89	101	0	ENST00000359195.3:c.511G>A	p.Asp171Asn	p.D171N	ENST00000359195	NM_002649.2	171	Gat/Aat	2/11	0.30738628209589	2	FACETS	0.961	0.867	1	0.961	0.867	1	CLONAL	2	TRUE	0	0.381030737874447	2		101	243	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846150	128846151	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	415	653	0	ENST00000249373.3:c.1080_1081delinsTT	p.His361Tyr	p.H361Y	ENST00000249373	NM_005631.4	360	ttCCac/ttTTac	5/12	0.30738628209589	2	FACETS	0.899	0.856	0.942	0.899	0.856	0.942	CLONAL	2	TRUE	0	0.381030737874447	2		653	1212	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494194	140494194	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	56	550	0	ENST00000288602.6:c.1054G>C	p.Asp352His	p.D352H	ENST00000288602	NM_004333.4	352	Gat/Cat	8/18	0.30738628209589	2	FACETS	0.264	0.225	0.307	0.132	0.112	0.154	SUBCLONAL	1	TRUE	0	0.381030737874447	2		550	1112	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860416	151860416	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	358	584	0	ENST00000262189.6:c.10246A>G	p.Met3416Val	p.M3416V	ENST00000262189	NM_170606.2	3416	Atg/Gtg	43/59	0.30738628209589	2	FACETS	0.898	0.853	0.944	0.898	0.853	0.944	CLONAL	2	TRUE	0	0.381030737874447	2		584	1046	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007140	152007140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	324	475	1	ENST00000262189.6:c.760C>T	p.Arg254Cys	p.R254C	ENST00000262189	NM_170606.2	254	Cgt/Tgt	6/59	0.30738628209589	2	FACETS	0.911	0.863	0.96	0.911	0.863	0.96	CLONAL	2	TRUE	0	0.381030737874447	2		476	933	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238366	98238366	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	122	412	0	ENST00000331920.6:c.1678T>G	p.Phe560Val	p.F560V	ENST00000331920	NM_000264.3	560	Ttc/Gtc	12/24	1	2	FACETS	0.773	0.699	0.852	0.773	0.699	0.852	SUBCLONAL	1	TRUE	1	0.381030737874447	2		412	828	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249930	110249930	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs746813034	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	49	180	0	ENST00000374672.4:c.745A>G	p.Ser249Gly	p.S249G	ENST00000374672	NM_004235.4	249	Agc/Ggc	3/5	1	2	FACETS	0.638	0.542	0.744	0.638	0.542	0.744	SUBCLONAL	1	TRUE	1	0.381030737874447	2		180	403	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139411771	139411771	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	228	567	0	ENST00000277541.6:c.1508G>A	p.Gly503Asp	p.G503D	ENST00000277541	NM_017617.3	503	gGc/gAc	9/34	1	2	FACETS	0.966	0.899	1	0.966	0.899	1	CLONAL	1	TRUE	1	0.381030737874447	2		567	1239	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114905810	114905810	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	265	777	0	ENST00000543371.1:c.829A>G	p.Arg277Gly	p.R277G	ENST00000543371	NM_001198531.1	277	Aga/Gga	8/14	1	2	FACETS	0.965	0.903	1	0.965	0.903	1	CLONAL	1	TRUE	1	0.381030737874447	2		777	1441	SUCCESS
EED	8726	MSKCC	GRCh37	11	85975303	85975303	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	135	467	0	ENST00000263360.6:c.724G>A	p.Ala242Thr	p.A242T	ENST00000263360	NM_003797.3	242	Gct/Act	7/12	1	2	FACETS	0.847	0.77	0.928	0.847	0.77	0.928	CLONAL	1	TRUE	1	0.381030737874447	2		467	837	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999392	100999392	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	270	683	2	ENST00000325455.5:c.410C>T	p.Thr137Ile	p.T137I	ENST00000325455	NM_001202474.3	137	aCc/aTc	1/8	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.381030737874447	2		685	1408	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025908	1025908	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	204	650	0	ENST00000358495.3:c.622T>C	p.Cys208Arg	p.C208R	ENST00000358495	NM_134424.2	208	Tgc/Cgc	8/12	NA	2	FACETS	0.899	0.832	0.968			1	INDETERMINATE	1	TRUE	NA	0.381030737874447	2		650	1191	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424198	49424198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1458446899	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	92	256	1	ENST00000301067.7:c.13864C>T	p.Pro4622Ser	p.P4622S	ENST00000301067	NM_003482.3	4622	Cca/Tca	42/54	1	2	FACETS	0.98	0.874	1	0.98	0.874	1	CLONAL	1	TRUE	1	0.381030737874447	2		257	493	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431198	49431198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1258642596	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	192	442	0	ENST00000301067.7:c.9941C>T	p.Ser3314Phe	p.S3314F	ENST00000301067	NM_003482.3	3314	tCc/tTc	34/54	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.381030737874447	2		442	992	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431610	49431610	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	151	436	0	ENST00000301067.7:c.9529G>A	p.Gly3177Arg	p.G3177R	ENST00000301067	NM_003482.3	3177	Ggg/Agg	34/54	1	2	FACETS	0.946	0.865	1	0.946	0.865	1	CLONAL	1	TRUE	1	0.381030737874447	2		436	838	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490547	56490547	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	122	438	0	ENST00000267101.3:c.2191G>C	p.Glu731Gln	p.E731Q	ENST00000267101	NM_001982.3	731	Gag/Cag	19/28	1	2	FACETS	0.759	0.685	0.836	0.759	0.685	0.836	SUBCLONAL	1	TRUE	1	0.381030737874447	2		438	844	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860117	57860117	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	246	700	1	ENST00000228682.2:c.857A>G	p.Tyr286Cys	p.Y286C	ENST00000228682	NM_005269.2	286	tAc/tGc	8/12	1	2	FACETS	0.933	0.87	0.998	0.933	0.87	0.998	CLONAL	1	TRUE	1	0.381030737874447	2		701	1384	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813316	102813316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1404671399	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	156	496	1	ENST00000307046.8:c.373C>T	p.Arg125Cys	p.R125C	ENST00000307046	NM_001111285.1	125	Cgc/Tgc	3/4	1	2	FACETS	0.847	0.775	0.922	0.847	0.775	0.922	CLONAL	1	TRUE	1	0.381030737874447	2		497	967	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562667	21562667	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs998820358	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	74	161	0	ENST00000382592.4:c.1252C>T	p.Pro418Ser	p.P418S	ENST00000382592	NM_014572.2	418	Ccg/Tcg	4/8	0.381030737874447	1	FACETS	0.98	0.865	1	0.98	0.865	1	CLONAL	1	TRUE	0	0.381030737874447	1		161	321	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930730	32930730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs74047012	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	80	350	0	ENST00000380152.3:c.7601C>T	p.Ala2534Val	p.A2534V	ENST00000380152		2534	gCg/gTg	15/27	0.381030737874447	1	FACETS	0.594	0.524	0.67	0.594	0.524	0.67	SUBCLONAL	1	TRUE	0	0.381030737874447	1		350	572	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954198	48954198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123331	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	98	342	0	ENST00000267163.4:c.1399C>T	p.Arg467Ter	p.R467*	ENST00000267163	NM_000321.2	467	Cga/Tga	15/27	0.381030737874447	1	FACETS	0.85	0.761	0.943	0.85	0.761	0.943	CLONAL	1	TRUE	0	0.381030737874447	1		342	490	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435597	110435597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762535630	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	44	113	0	ENST00000375856.3:c.2804C>T	p.Ala935Val	p.A935V	ENST00000375856	NM_003749.2	935	gCg/gTg	1/2	1	2	FACETS	0.928	0.784	1	0.928	0.784	1	CLONAL	1	TRUE	1	0.381030737874447	2		113	249	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061532	38061532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781269308	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	123	237	0	ENST00000250448.2:c.457G>A	p.Ala153Thr	p.A153T	ENST00000250448	NM_004496.3	153	Gcg/Acg	2/2	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.381030737874447	2		237	579	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609925	81609925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772490052	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	134	315	0	ENST00000298171.2:c.1523C>T	p.Ser508Leu	p.S508L	ENST00000298171	NM_000369.2	508	tCg/tTg	10/10	1	2	FACETS	0.938	0.853	1	0.938	0.853	1	CLONAL	1	TRUE	1	0.381030737874447	2		315	750	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989087	41989087	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	241	837	2	ENST00000219905.7:c.1879C>T	p.Arg627Ter	p.R627*	ENST00000219905	NM_001164273.1	627	Cga/Tga	3/24	NA	2	FACETS	0.968	0.902	1			1	INDETERMINATE	1	TRUE	NA	0.381030737874447	2		839	1307	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032342	42032342	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1152	275	807	0	ENST00000219905.7:c.4526C>G	p.Thr1509Ser	p.T1509S	ENST00000219905	NM_001164273.1	1509	aCt/aGt	14/24	NA	2	FACETS	1	0.947	1			1	INDETERMINATE	1	TRUE	NA	0.381030737874447	2		807	1427	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934945	9934945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	118	335	0	ENST00000330684.3:c.1345G>A	p.Gly449Arg	p.G449R	ENST00000330684	NM_001134407.1	449	Ggg/Agg	6/13	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.381030737874447	2		335	617	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641508	23641509	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	153	548	1	ENST00000261584.4:c.1966_1967delinsTT	p.Pro656Leu	p.P656L	ENST00000261584	NM_024675.3	656	CCa/TTa	5/13	1	2	FACETS	0.814	0.744	0.887	0.814	0.744	0.887	CLONAL	1	TRUE	1	0.381030737874447	2		549	987	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577106	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	185	544	0	ENST00000269305.4:c.832_833delinsTT	p.Pro278Phe	p.P278F	ENST00000269305	NM_001126112.2	278	CCt/TTt	8/11	0.381030737874447	1	FACETS	0.963	0.891	1	0.963	0.891	1	CLONAL	1	TRUE	0	0.381030737874447	1		544	816	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492894	56492894	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	93	214	0	ENST00000407977.2:c.45G>A	p.Trp15Ter	p.W15*	ENST00000407977		15	tgG/tgA	2/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.381030737874447	2		214	423	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533778	63533778	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368525111	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	140	380	0	ENST00000307078.5:c.1376G>A	p.Arg459His	p.R459H	ENST00000307078	NM_004655.3	459	cGc/cAc	6/11	1	2	FACETS	0.876	0.798	0.958	0.876	0.798	0.958	CLONAL	1	TRUE	1	0.381030737874447	2		380	839	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534420	63534421	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	114	357	0	ENST00000307078.5:c.1100_1101delinsTT	p.Pro367Leu	p.P367L	ENST00000307078	NM_004655.3	367	cCC/cTT	5/11	1	2	FACETS	0.753	0.678	0.832	0.753	0.678	0.832	SUBCLONAL	1	TRUE	1	0.381030737874447	2		357	795	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120524	70120524	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	113	308	0	ENST00000245479.2:c.1526C>T	p.Pro509Leu	p.P509L	ENST00000245479	NM_000346.3	509	cCt/cTt	3/3	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.381030737874447	2		308	579	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724557	724557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	66	168	0	ENST00000314574.4:c.1499C>T	p.Ser500Phe	p.S500F	ENST00000314574	NM_005433.3	500	tCc/tTc	12/12	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.381030737874447	2		168	309	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191215	2191215	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	228	584	0	ENST00000398665.3:c.469G>A	p.Asp157Asn	p.D157N	ENST00000398665	NM_032482.2	157	Gac/Aac	5/28	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.381030737874447	2		584	1167	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210526	5210526	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	187	559	0	ENST00000357368.4:c.5441A>G	p.Asn1814Ser	p.N1814S	ENST00000357368	NM_002850.3	1814	aAc/aGc	35/38	1	2	FACETS	0.986	0.911	1	0.986	0.911	1	CLONAL	1	TRUE	1	0.381030737874447	2		559	995	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247915	10247916	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	114	313	0	ENST00000340748.4:c.4286_4287delinsTT	p.Pro1429Leu	p.P1429L	ENST00000340748		1429	cCC/cTT	36/40	1	2	FACETS	0.885	0.798	0.977	0.885	0.798	0.977	CLONAL	1	TRUE	1	0.381030737874447	2		313	676	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610554	10610554	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	174	382	0	ENST00000171111.5:c.156C>A	p.Phe52Leu	p.F52L	ENST00000171111	NM_203500.1	52	ttC/ttA	2/6	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.381030737874447	2		382	885	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170811	11170811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	112	308	0	ENST00000358026.2:c.4955C>T	p.Ser1652Phe	p.S1652F	ENST00000358026	NM_001128849.1	1652	tCc/tTc	35/36	1	2	FACETS	0.975	0.879	1	0.975	0.879	1	CLONAL	1	TRUE	1	0.381030737874447	2		308	603	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276756	15276756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143617599	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	154	527	1	ENST00000263388.2:c.5509C>T	p.Arg1837Cys	p.R1837C	ENST00000263388	NM_000435.2	1837	Cgt/Tgt	30/33	1	2	FACETS	0.752	0.687	0.82	0.752	0.687	0.82	SUBCLONAL	1	TRUE	1	0.381030737874447	2		528	1075	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278172	15278173	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	177	627	0	ENST00000263388.2:c.5249_5250delinsAA	p.Trp1750Ter	p.W1750*	ENST00000263388	NM_000435.2	1750	tGG/tAA	29/33	1	2	FACETS	0.846	0.779	0.917	0.846	0.779	0.917	CLONAL	1	TRUE	1	0.381030737874447	2		627	1098	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295830	15295830	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	149	413	0	ENST00000263388.2:c.2297G>A	p.Gly766Glu	p.G766E	ENST00000263388	NM_000435.2	766	gGa/gAa	15/33	1	2	FACETS	0.973	0.889	1	0.973	0.889	1	CLONAL	1	TRUE	1	0.381030737874447	2		413	804	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952276	17952276	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1433720267	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	98	335	0	ENST00000458235.1:c.1064C>G	p.Ser355Cys	p.S355C	ENST00000458235	NM_000215.3	355	tCc/tGc	8/24	1	2	FACETS	0.695	0.62	0.775	0.695	0.62	0.775	SUBCLONAL	1	TRUE	1	0.381030737874447	2		335	740	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257848	19257848	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759447294	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	199	446	2	ENST00000162023.5:c.538C>T	p.Pro180Ser	p.P180S	ENST00000162023		180	Cca/Tca	9/13	1	2	FACETS	0.982	0.909	1	0.982	0.909	1	CLONAL	1	TRUE	1	0.381030737874447	2		448	1064	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725141	47725142	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	177	419	0	ENST00000449228.1:c.602_603delinsTT	p.Thr201Ile	p.T201I	ENST00000449228	NM_001127240.2	201	aCC/aTT	4/4	1	2	FACETS	0.96	0.884	1	0.96	0.884	1	CLONAL	1	TRUE	1	0.381030737874447	2		419	968	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731464	47731464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	54	89	0	ENST00000449228.1:c.328C>T	p.Pro110Ser	p.P110S	ENST00000449228	NM_001127240.2	110	Ccg/Tcg	2/4	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.381030737874447	2		89	221	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877349	40877349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747289224	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	95	251	0	ENST00000373198.4:c.2347G>A	p.Val783Met	p.V783M	ENST00000373198	NM_133170.3	783	Gtg/Atg	15/32	1	2	FACETS	0.989	0.884	1	0.989	0.884	1	CLONAL	1	TRUE	1	0.381030737874447	2		251	504	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650833	48650833	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	184	363	1	ENST00000376670.3:c.702G>A	p.Met234Ile	p.M234I	ENST00000376670	NM_002049.3	234	atG/atA	4/6	1	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.381030737874447	1		364	688	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37083760	37083763	+	protein_altering_variant,splice_region_variant	In_Frame_Del	DEL	GAAG	GAAG	A	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	124	530	0	ENST00000231790.2:c.1669_1672delinsA	p.Glu557_Glu558delinsLys	p.E557_E558delinsK	ENST00000231790	NM_000249.3	557	GAAGaa/Aaa	15/19	0.381030737874447	1	FACETS	0.785	0.712	0.862	0.785	0.712	0.862	SUBCLONAL	1	TRUE	0	0.381030737874447	1		530	671	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395260	139395260	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	122	315	0	ENST00000277541.6:c.5678del	p.Gly1893AlafsTer88	p.G1893Afs*88	ENST00000277541	NM_017617.3	1893	gGc/gc	31/34	1	2	FACETS	0.85	0.769	0.936	0.85	0.769	0.936	CLONAL	1	TRUE	1	0.381030737874447	2		315	753	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435725	49435727	+	frameshift_variant	Frame_Shift_Del	DEL	GGA	GGA	C	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	173	535	0	ENST00000301067.7:c.6156_6158delinsG	p.Pro2053SerfsTer3	p.P2053Sfs*3	ENST00000301067	NM_003482.3	2052	gtTCCa/gtGa	29/54	1	2	FACETS	0.795	0.731	0.863	0.795	0.731	0.863	SUBCLONAL	1	TRUE	1	0.381030737874447	2		535	1142	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399552	139399552	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	91	240	0	ENST00000277541.6:c.4591del	p.Leu1531CysfsTer49	p.L1531Cfs*49	ENST00000277541	NM_017617.3	1531	Ctg/tg	26/34	1	2	FACETS	0.898	0.799	1	0.898	0.799	1	CLONAL	1	TRUE	1	0.381030737874447	2		240	532	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444378	49444378	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	80	375	0	ENST00000301067.7:c.2993del	p.Pro998LeufsTer2	p.P998Lfs*2	ENST00000301067	NM_003482.3	998	cCt/ct	11/54	1	2	FACETS	0.61	0.537	0.689	0.61	0.537	0.689	SUBCLONAL	1	TRUE	1	0.381030737874447	2		375	688	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	49	372	1	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.594	0.503	0.695	0.594	0.503	0.695	SUBCLONAL	1	TRUE	1	0.31	2		373	532	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	60	414	7	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.671	0.578	0.772	0.671	0.578	0.772	SUBCLONAL	1	TRUE	1	0.31	2		421	577	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	298	831	11	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.91	0.858	0.964	1	0.995	1	CLONAL	2	TRUE	1	0.31	2		842	1056	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	64	498	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.528	0.456	0.606	0.528	0.456	0.606	SUBCLONAL	1	TRUE	1	0.31	2		498	782	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913351	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	129	600	1	ENST00000288602.6:c.1397G>A	p.Gly466Glu	p.G466E	ENST00000288602	NM_004333.4	466	gGa/gAa	11/18	1	2	FACETS	0.939	0.851	1	0.939	0.851	1	CLONAL	1	TRUE	1	0.31	2		601	886	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	25	170	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.449	0.354	0.559	0.449	0.354	0.559	SUBCLONAL	1	TRUE	1	0.31	2		171	359	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	164	463	1	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.935	0.857	1	0.935	0.857	1	CLONAL	1	TRUE	1	0.31	2		464	1132	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	33	454	2	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.343	0.279	0.417	0.343	0.279	0.417	SUBCLONAL	1	TRUE	1	0.31	2		456	620	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	61	984	2	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	1	2	FACETS	0.404	0.348	0.467	0.404	0.348	0.467	SUBCLONAL	1	TRUE	1	0.31	2		986	973	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	71	314	2	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.31	2		316	423	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	41	583	6	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	0.372	0.308	0.442	0.372	0.308	0.442	SUBCLONAL	1	TRUE	1	0.31	2		589	712	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867541	35867541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	31	363	0	ENST00000303115.3:c.361del	p.Ile121Ter	p.I121*	ENST00000303115	NM_002185.3	119	Aaa/aa	3/8	1	2	FACETS	0.346	0.279	0.422	0.346	0.279	0.422	SUBCLONAL	1	TRUE	1	0.31	2		363	578	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736166	204736166	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	169	705	0	ENST00000302823.3:c.529del	p.Tyr177IlefsTer10	p.Y177Ifs*10	ENST00000302823	NM_005214.4	175	Ttt/tt	3/4	1	2	FACETS	0.921	0.845	1	0.921	0.845	1	CLONAL	1	TRUE	1	0.31	2		705	1184	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296358	15296358	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	85	549	2	ENST00000263388.2:c.2084del	p.Pro695ArgfsTer165	p.P695Rfs*165	ENST00000263388	NM_000435.2	695	cCg/cg	13/33	1	2	FACETS	0.886	0.784	0.995	0.886	0.784	0.995	CLONAL	1	TRUE	1	0.31	2		551	619	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339111	65339111	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	145	682	2	ENST00000342505.4:c.425del	p.Lys142ArgfsTer26	p.K142Rfs*26	ENST00000342505	NM_002227.2	142	aAg/ag	5/25	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.31	2		684	935	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806119	1806119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931614	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	179	344	0	ENST00000260795.2:c.1138G>A	p.Gly380Arg	p.G380R	ENST00000260795		380	Ggg/Agg	8/17	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.31	2		344	937	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164711	47164711	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201984344	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	54	439	0	ENST00000409792.3:c.1415G>A	p.Arg472His	p.R472H	ENST00000409792	NM_014159.6	472	cGt/cAt	3/21	1	2	FACETS	0.555	0.473	0.644	0.555	0.473	0.644	SUBCLONAL	1	TRUE	1	0.31	2		439	628	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	89	482	1	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	1	2	FACETS	0.825	0.732	0.925	0.825	0.732	0.925	CLONAL	1	TRUE	1	0.31	2		483	696	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220116	5220116	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781371580	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	67	381	0	ENST00000357368.4:c.3599G>A	p.Arg1200His	p.R1200H	ENST00000357368	NM_002850.3	1200	cGt/cAt	22/38	1	2	FACETS	0.998	0.871	1	0.998	0.871	1	CLONAL	1	TRUE	1	0.31	2		381	433	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141492	11141492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	127	525	1	ENST00000358026.2:c.3469C>T	p.Arg1157Trp	p.R1157W	ENST00000358026	NM_001128849.1	1157	Cgg/Tgg	25/36	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.31	2		526	741	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138375075	138375075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1405576100	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	75	441	0	ENST00000289153.2:c.2984G>A	p.Arg995Gln	p.R995Q	ENST00000289153	NM_006219.2	995	cGg/cAg	21/22	1	2	FACETS	0.763	0.669	0.865	0.763	0.669	0.865	SUBCLONAL	1	TRUE	1	0.31	2		441	634	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609314	39609314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766344105	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	102	488	0	ENST00000262039.4:c.1616G>A	p.Arg539His	p.R539H	ENST00000262039	NM_002647.2	539	cGt/cAt	15/25	1	2	FACETS	0.873	0.781	0.971	0.873	0.781	0.971	CLONAL	1	TRUE	1	0.31	2		488	754	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743859	40743859	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369430281	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	90	575	0	ENST00000373198.4:c.3136C>T	p.Arg1046Cys	p.R1046C	ENST00000373198	NM_133170.3	1046	Cgc/Tgc	23/32	1	2	FACETS	0.747	0.663	0.838	0.747	0.663	0.838	SUBCLONAL	1	TRUE	1	0.31	2		575	777	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870205	155870205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs563231684	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	64	790	3	ENST00000368323.3:c.634C>T	p.Arg212Trp	p.R212W	ENST00000368323	NM_006912.5	212	Cgg/Tgg	6/6	1	2	FACETS	0.357	0.307	0.41	0.357	0.307	0.41	SUBCLONAL	1	TRUE	1	0.31	2		793	1158	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193892	106193892	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1049545383	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	56	496	0	ENST00000380013.4:c.4354C>T	p.Arg1452Ter	p.R1452*	ENST00000380013	NM_001127208.2	1452	Cga/Tga	10/11	1	2	FACETS	0.428	0.366	0.497	0.428	0.366	0.497	SUBCLONAL	1	TRUE	1	0.31	2		496	844	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569733	41569733	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs144547088	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	148	592	0	ENST00000263253.7:c.4724A>G	p.Asn1575Ser	p.N1575S	ENST00000263253	NM_001429.3	1575	aAt/aGt	29/31	1	2	FACETS	0.978	0.893	1	0.978	0.893	1	CLONAL	1	TRUE	1	0.31	2		592	976	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097625	11097625	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	150	718	0	ENST00000358026.2:c.810del	p.Met272CysfsTer31	p.M272Cfs*31	ENST00000358026	NM_001128849.1	269	Ccc/cc	5/36	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.31	2		718	891	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375016	45375016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226662382	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	71	329	0	ENST00000262160.6:c.827C>T	p.Ser276Leu	p.S276L	ENST00000262160	NM_005901.5	276	tCg/tTg	8/11	1	2	FACETS	0.814	0.711	0.924	0.814	0.711	0.924	CLONAL	1	TRUE	1	0.31	2		329	563	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427568	72427568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs912857100	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	93	345	0	ENST00000477973.2:c.922G>A	p.Asp308Asn	p.D308N	ENST00000477973	NM_012234.5	308	Gac/Aac	4/4	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.31	2		345	579	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265302	10265302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	115	501	0	ENST00000340748.4:c.1744C>T	p.Arg582Trp	p.R582W	ENST00000340748		582	Cgg/Tgg	20/40	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.31	2		501	674	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991757	72991758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760959844	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	25	371	0	ENST00000268489.5:c.2287dup	p.Glu763GlyfsTer26	p.E763Gfs*26	ENST00000268489	NM_006885.3	763	gag/gGag	2/10	1	2	FACETS	0.333	0.262	0.416	0.333	0.262	0.416	SUBCLONAL	1	TRUE	1	0.31	2		371	484	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484085	50484085	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	126	531	0	ENST00000394963.4:c.935G>A	p.Arg312His	p.R312H	ENST00000394963	NM_003076.4	312	cGt/cAt	8/13	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.31	2		531	758	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199365	11199365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587777895	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	85	509	1	ENST00000361445.4:c.5126G>A	p.Arg1709His	p.R1709H	ENST00000361445	NM_004958.3	1709	cGc/cAc	36/58	1	2	FACETS	0.865	0.765	0.972	0.865	0.765	0.972	CLONAL	1	TRUE	1	0.31	2		510	634	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256832	16256832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs887977680	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	92	400	0	ENST00000375759.3:c.4097G>A	p.Arg1366Gln	p.R1366Q	ENST00000375759	NM_015001.2	1366	cGa/cAa	11/15	1	2	FACETS	0.858	0.762	0.959	0.858	0.762	0.959	CLONAL	1	TRUE	1	0.31	2		400	692	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846354	156846354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772229945	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	115	554	1	ENST00000524377.1:c.1795C>T	p.Arg599Cys	p.R599C	ENST00000524377	NM_002529.3	599	Cgc/Tgc	14/17	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.31	2		555	661	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469633	25469633	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754459010	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	67	445	2	ENST00000264709.3:c.1135C>T	p.Arg379Cys	p.R379C	ENST00000264709	NM_175629.2	379	Cgc/Tgc	10/23	1	2	FACETS	0.672	0.584	0.768	0.672	0.584	0.768	SUBCLONAL	1	TRUE	1	0.31	2		447	643	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719743	61719743	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	70	662	0	ENST00000401558.2:c.1525C>T	p.His509Tyr	p.H509Y	ENST00000401558	NM_003400.3	509	Cat/Tat	14/25	1	2	FACETS	0.417	0.362	0.477	0.417	0.362	0.477	SUBCLONAL	1	TRUE	1	0.31	2		662	1083	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182505	99182505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	110	502	0	ENST00000074304.5:c.2308G>A	p.Val770Met	p.V770M	ENST00000074304	NM_001134224.1	770	Gtg/Atg	22/26	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.31	2		502	710	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149752	202149752	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs777112657	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	86	593	0	ENST00000358485.4:c.1193A>G	p.Gln398Arg	p.Q398R	ENST00000358485	NM_001080125.1	398	cAg/cGg	8/9	1	2	FACETS	0.657	0.581	0.74	0.657	0.581	0.74	SUBCLONAL	1	TRUE	1	0.31	2		593	844	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378306	225378306	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	58	535	0	ENST00000264414.4:c.589G>T	p.Gly197Ter	p.G197*	ENST00000264414	NM_003590.4	197	Gga/Tga	5/16	1	2	FACETS	0.381	0.326	0.442	0.381	0.326	0.442	SUBCLONAL	1	TRUE	1	0.31	2		535	981	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379486	225379486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	68	367	1	ENST00000264414.4:c.382C>T	p.Arg128Cys	p.R128C	ENST00000264414	NM_003590.4	128	Cgt/Tgt	4/16	1	2	FACETS	0.812	0.708	0.925	0.812	0.708	0.925	CLONAL	1	TRUE	1	0.31	2		368	540	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936083	178936083	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519927	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	48	230	0	ENST00000263967.3:c.1625A>T	p.Glu542Val	p.E542V	ENST00000263967	NM_006218.2	542	gAa/gTa	10/21	1	2	FACETS	0.919	0.78	1	0.919	0.78	1	CLONAL	1	TRUE	1	0.31	2		230	337	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146653	185146653	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs547600832	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	100	315	1	ENST00000265026.3:c.284C>T	p.Thr95Met	p.T95M	ENST00000265026	NM_004721.4	95	aCg/aTg	2/14	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.31	2		316	555	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946269	55946269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758952853	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	136	431	0	ENST00000263923.4:c.3910G>A	p.Gly1304Ser	p.G1304S	ENST00000263923	NM_002253.2	1304	Ggc/Agc	30/30	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.31	2		431	720	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629616	187629616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	140	507	0	ENST00000441802.2:c.1366G>A	p.Ala456Thr	p.A456T	ENST00000441802	NM_005245.3	456	Gca/Aca	2/27	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.31	2		507	817	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681587	30681587	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	82	626	0	ENST00000376406.3:c.510G>T	p.Glu170Asp	p.E170D	ENST00000376406	NM_014641.2	170	gaG/gaT	3/15	1	2	FACETS	0.527	0.464	0.596	0.527	0.464	0.596	SUBCLONAL	1	TRUE	1	0.31	2		626	1003	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974378	93974378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753621830	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	96	693	2	ENST00000369303.4:c.1676C>T	p.Ala559Val	p.A559V	ENST00000369303	NM_004440.3	559	gCt/gTt	8/17	1	2	FACETS	0.55	0.488	0.615	0.55	0.488	0.615	SUBCLONAL	1	TRUE	1	0.31	2		695	1127	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528252	157528252	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554237801	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	41	462	1	ENST00000346085.5:c.5977C>T	p.Gln1993Ter	p.Q1993*	ENST00000346085	NM_020732.3	1993	Cag/Tag	20/20	1	2	FACETS	0.422	0.35	0.502	0.422	0.35	0.502	SUBCLONAL	1	TRUE	1	0.31	2		463	627	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395454	116395454	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	66	558	0	ENST00000397752.3:c.1747A>C	p.Ile583Leu	p.I583L	ENST00000397752	NM_000245.2	583	Ata/Cta	6/21	1	2	FACETS	0.526	0.455	0.602	0.526	0.455	0.602	SUBCLONAL	1	TRUE	1	0.31	2		558	810	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372049	55372049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1254366651	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	29	156	0	ENST00000297316.4:c.739G>A	p.Ala247Thr	p.A247T	ENST00000297316	NM_022454.3	247	Gcg/Acg	2/2	1	2	FACETS	0.607	0.488	0.742	0.607	0.488	0.742	SUBCLONAL	1	TRUE	1	0.31	2		156	308	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982701	90982701	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	58	618	0	ENST00000265433.3:c.787T>C	p.Phe263Leu	p.F263L	ENST00000265433	NM_002485.4	263	Ttt/Ctt	7/16	1	2	FACETS	0.332	0.284	0.385	0.332	0.284	0.385	SUBCLONAL	1	TRUE	1	0.31	2		618	1126	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741959	145741959	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750986351	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	89	328	1	ENST00000428558.2:c.544C>T	p.Arg182Trp	p.R182W	ENST00000428558	NM_004260.3	182	Cgg/Tgg	5/22	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.31	2		329	531	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564074	139564074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773216266	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	132	670	1	ENST00000308874.7:c.214G>A	p.Ala72Thr	p.A72T	ENST00000308874		72	Gcc/Acc	5/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.31	2		671	731	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406565	70406565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	74	669	1	ENST00000373644.4:c.4079G>A	p.Cys1360Tyr	p.C1360Y	ENST00000373644	NM_030625.2	1360	tGt/tAt	4/12	1	2	FACETS	0.529	0.462	0.602	0.529	0.462	0.602	SUBCLONAL	1	TRUE	1	0.31	2		670	902	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625386	69625386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782272422	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	101	561	0	ENST00000334134.2:c.407C>T	p.Thr136Met	p.T136M	ENST00000334134	NM_005247.2	136	aCg/aTg	3/3	1	2	FACETS	0.885	0.791	0.985	0.885	0.791	0.985	CLONAL	1	TRUE	1	0.31	2		561	736	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77069963	77069963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370942329	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	170	643	0	ENST00000356341.3:c.577C>T	p.Arg193Cys	p.R193C	ENST00000356341	NM_002576.4	193	Cgc/Tgc	6/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.31	2		643	971	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170273	119170273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368696716	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	125	523	0	ENST00000264033.4:c.2503C>T	p.Arg835Trp	p.R835W	ENST00000264033	NM_005188.3	835	Cgg/Tgg	16/16	1	2	FACETS	0.996	0.901	1	0.996	0.901	1	CLONAL	1	TRUE	1	0.31	2		523	810	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536641	120536641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	98	851	2	ENST00000229340.5:c.451G>A	p.Ala151Thr	p.A151T	ENST00000229340	NM_006861.6	151	Gcc/Acc	5/6	1	2	FACETS	0.564	0.501	0.63	0.564	0.501	0.63	SUBCLONAL	1	TRUE	1	0.31	2		853	1122	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133238236	133238236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	112	534	0	ENST00000320574.5:c.2741C>T	p.Ala914Val	p.A914V	ENST00000320574	NM_006231.2	914	gCt/gTt	24/49	1	2	FACETS	0.994	0.895	1	0.994	0.895	1	CLONAL	1	TRUE	1	0.31	2		534	727	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623524	28623524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371030554	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	86	360	2	ENST00000241453.7:c.1033G>A	p.Val345Ile	p.V345I	ENST00000241453	NM_004119.2	345	Gta/Ata	8/24	1	2	FACETS	0.937	0.83	1	0.937	0.83	1	CLONAL	1	TRUE	1	0.31	2		362	592	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239892	105239892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	94	361	0	ENST00000349310.3:c.728G>A	p.Arg243His	p.R243H	ENST00000349310	NM_001014432.1	243	cGt/cAt	10/15	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.31	2		361	588	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473704	67473704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1201995588	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	104	548	1	ENST00000327367.4:c.784G>A	p.Asp262Asn	p.D262N	ENST00000327367	NM_005902.3	262	Gac/Aac	6/9	1	2	FACETS	0.997	0.894	1	0.997	0.894	1	CLONAL	1	TRUE	1	0.31	2		549	673	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779038	3779038	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886039331	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	29	302	0	ENST00000262367.5:c.6010C>T	p.Arg2004Ter	p.R2004*	ENST00000262367	NM_004380.2	2004	Cga/Tga	31/31	1	2	FACETS	0.535	0.429	0.654	0.535	0.429	0.654	SUBCLONAL	1	TRUE	1	0.31	2		302	350	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830936	72830936	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	268	1001	0	ENST00000268489.5:c.5645T>A	p.Ile1882Asn	p.I1882N	ENST00000268489	NM_006885.3	1882	aTc/aAc	9/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.31	2		1001	1421	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993737	72993737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776936617	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	153	639	1	ENST00000268489.5:c.308G>A	p.Arg103His	p.R103H	ENST00000268489	NM_006885.3	103	cGc/cAc	2/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.31	2		640	926	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219322	1219322	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	50	471	0	ENST00000326873.7:c.375-1C>T		p.X125_splice	ENST00000326873	NM_000455.4	125			1	2	FACETS	0.525	0.444	0.613	0.525	0.444	0.613	SUBCLONAL	1	TRUE	1	0.31	2		471	615	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280066	18280066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1387844256	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	25	90	0	ENST00000222254.8:c.2149C>T	p.Arg717Cys	p.R717C	ENST00000222254	NM_005027.3	717	Cgc/Tgc	16/16	1	2	FACETS	0.791	0.636	0.96	1	0.94	1	CLONAL	2	TRUE	1	0.31	2		90	102	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793441	42793441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769792673	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	59	375	0	ENST00000575354.2:c.1243C>T	p.Arg415Trp	p.R415W	ENST00000575354	NM_015125.3	415	Cgg/Tgg	8/20	1	2	FACETS	0.772	0.665	0.888	0.772	0.665	0.888	SUBCLONAL	1	TRUE	1	0.31	2		375	493	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130448	29130448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	113	502	0	ENST00000328354.6:c.262C>T	p.Pro88Ser	p.P88S	ENST00000328354	NM_007194.3	88	Cct/Tct	2/15	1	2	FACETS	0.941	0.847	1	0.941	0.847	1	CLONAL	1	TRUE	1	0.31	2		502	775	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038260	30038260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1185977513	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	140	559	3	ENST00000338641.4:c.433G>A	p.Ala145Thr	p.A145T	ENST00000338641	NM_000268.3	145	Gcc/Acc	4/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.31	2		562	823	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573224	41573224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1439243688	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	91	460	0	ENST00000263253.7:c.5509C>T	p.Arg1837Trp	p.R1837W	ENST00000263253	NM_001429.3	1837	Cgg/Tgg	31/31	1	2	FACETS	0.929	0.826	1	0.929	0.826	1	CLONAL	1	TRUE	1	0.31	2		460	632	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344613	70344613	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	88	430	0	ENST00000374080.3:c.1975-1G>T		p.X659_splice	ENST00000374080		659			1	1	FACETS	0.86	0.763	0.962	0.86	0.763	0.962	CLONAL	1	TRUE	0	0.31	1		430	558	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502210	157502211	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	103	381	0	ENST00000346085.5:c.3249_3250del	p.Gly1084LeufsTer33	p.G1084Lfs*33	ENST00000346085	NM_020732.3	1081	gaAGag/gaag	12/20	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.31	2		381	645	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023831	27023831	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1415214478	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	36	303	0	ENST00000324856.7:c.941del	p.Gly314AlafsTer49	p.G314Afs*49	ENST00000324856	NM_006015.4	313	Ggg/gg	1/20	1	2	FACETS	0.437	0.359	0.526	0.437	0.359	0.526	SUBCLONAL	1	TRUE	1	0.31	2		303	531	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637392	47637392	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	135	780	0	ENST00000233146.2:c.526del	p.Cys176ValfsTer38	p.C176Vfs*38	ENST00000233146	NM_000251.2	176	Tgt/gt	3/16	1	2	FACETS	0.87	0.79	0.955	0.87	0.79	0.955	CLONAL	1	TRUE	1	0.31	2		780	1001	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246532	41246532	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357569	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	164	692	3	ENST00000357654.3:c.1016del	p.Lys339ArgfsTer2	p.K339Rfs*2	ENST00000357654	NM_007294.3	339	aAg/ag	10/23	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.31	2		695	1004	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655413	45655413	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	47	453	0	ENST00000407780.3:c.439del	p.His147ThrfsTer15	p.H147Tfs*15	ENST00000407780	NM_001283052.1	147	Cac/ac	4/7	1	2	FACETS	0.509	0.429	0.597	0.509	0.429	0.597	SUBCLONAL	1	TRUE	1	0.31	2		453	596	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023518	27023519	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	76	647	1	ENST00000324856.7:c.626dup	p.Asn209LysfsTer191	p.N209Kfs*191	ENST00000324856	NM_006015.4	208	-/A	1/20	1	2	FACETS	0.566	0.495	0.642	0.566	0.495	0.642	SUBCLONAL	1	TRUE	1	0.31	2		648	867	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126529	2126529	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs34245038	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	54	676	0	ENST00000219476.3:c.2784del	p.Glu929ArgfsTer19	p.E929Rfs*19	ENST00000219476	NM_000548.3	927	aCc/ac	25/42	1	2	FACETS	0.375	0.319	0.436	0.375	0.319	0.436	SUBCLONAL	1	TRUE	1	0.31	2		676	930	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870961	12870962	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	72	410	0	ENST00000228872.4:c.192dup	p.Gln65SerfsTer60	p.Q65Sfs*60	ENST00000228872	NM_004064.3	63	gat/gaTt	1/3	1	2	FACETS	0.626	0.546	0.712	0.626	0.546	0.712	SUBCLONAL	1	TRUE	1	0.31	2		410	742	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253835	153253836	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	38	308	0	ENST00000281708.4:c.897dup	p.Asp300ArgfsTer17	p.D300Rfs*17	ENST00000281708	NM_033632.3	299	-/A	6/12	1	2	FACETS	0.443	0.365	0.529	0.443	0.365	0.529	SUBCLONAL	1	TRUE	1	0.31	2		308	554	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220560	123220560	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	212	474	0	ENST00000218089.9:c.3222del	p.Lys1074AsnfsTer31	p.K1074Nfs*31	ENST00000218089	NM_001042749.1	1073	Aaa/aa	30/35	1	1	FACETS	0.8	0.746	0.856	1	0.992	1	SUBCLONAL	2	TRUE	0	0.31	1		474	722	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983042	111983042	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1181	122	931	6	ENST00000368678.4:c.1505del	p.Lys502ArgfsTer53	p.K502Rfs*53	ENST00000368678		502	aAg/ag	13/13	1	2	FACETS	0.604	0.544	0.668	0.604	0.544	0.668	SUBCLONAL	1	TRUE	1	0.31	2		937	1303	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5077503	5077503	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	23	248	0	ENST00000381652.3:c.1919del	p.Lys640ArgfsTer6	p.K640Rfs*6	ENST00000381652	NM_004972.3	639	Aaa/aa	15/25	1	2	FACETS	0.381	0.297	0.48	0.381	0.297	0.48	SUBCLONAL	1	TRUE	1	0.31	2		248	389	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434026	49434027	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	71	367	0	ENST00000301067.7:c.7525_7526dup	p.Val2510ArgfsTer34	p.V2510Rfs*34	ENST00000301067	NM_003482.3	2509	aag/aaAAg	31/54	1	2	FACETS	0.916	0.801	1	0.916	0.801	1	CLONAL	1	TRUE	1	0.31	2		367	500	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923045	44923048	+	frameshift_variant	Frame_Shift_Del	DEL	CTAT	CTAT	-	rs398122969	NA	P-0010803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	112	245	0	ENST00000377967.4:c.1909_1912del	p.Ser637ThrfsTer53	p.S637Tfs*53	ENST00000377967	NM_021140.2	636	CTATct/ct	16/29	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.31	1		245	427	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	298	474	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.360418429083456	5	FACETS	0.969	0.913	1	0.646	0.608	0.684	CLONAL	2	TRUE	2	0.519321976420364	5		474	1054	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38318622	38318622	+	start_lost	Translation_Start_Site	SNP	C	C	A	novel	NA	P-0010824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	198	542	0	ENST00000425967.3:c.3G>T	p.Met1?	p.M1?	ENST00000425967	NM_001174067.1	1	atG/atT	2/19	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.519321976420364	2		542	762	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845359	89845359	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	356	595	0	ENST00000389301.3:c.1768C>A	p.Pro590Thr	p.P590T	ENST00000389301	NM_000135.2	590	Cct/Act	19/43	0.496831123912363	2	FACETS	0.955	0.912	0.998	0.955	0.912	0.998	CLONAL	2	TRUE	0	0.519321976420364	2		595	718	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942737	44942737	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	481	681	0	ENST00000377967.4:c.3317T>G	p.Leu1106Arg	p.L1106R	ENST00000377967	NM_021140.2	1106	cTt/cGt	23/29	NA	2	FACETS	0.961	0.924	0.998			1	INDETERMINATE	2	TRUE	NA	0.519321976420364	2		681	964	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404892	404893	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0010824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	435	561	0	ENST00000399788.2:c.4301_4302insTT	p.Leu1435CysfsTer16	p.L1435Cfs*16	ENST00000399788	NM_001042603.1	1434	gtg/gtTTg	26/28	0.360418429083456	5	FACETS	1	0.993	1	0.812	0.775	0.849	CLONAL	2	TRUE	2	0.519321976420364	5		561	1224	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404908	404912	+	frameshift_variant	Frame_Shift_Del	DEL	CTTCG	CTTCG	-	novel	NA	P-0010824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	408	549	0	ENST00000399788.2:c.4282_4286del	p.Arg1428PhefsTer13	p.R1428Ffs*13	ENST00000399788	NM_001042603.1	1428	CGAAGt/t	26/28	0.360418429083456	5	FACETS	1	0.992	1	0.789	0.752	0.827	CLONAL	2	TRUE	2	0.519321976420364	5		549	1181	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404900	404902	+	frameshift_variant	Frame_Shift_Del	DEL	GTT	GTT	CA	novel	NA	P-0010824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	427	550	0	ENST00000399788.2:c.4292_4294delinsTG	p.Glu1431ValfsTer19	p.E1431Vfs*19	ENST00000399788	NM_001042603.1	1431	gAACct/gTGct	26/28	0.360418429083456	5	FACETS	1	0.993	1	0.809	0.771	0.846	CLONAL	2	TRUE	2	0.519321976420364	5		550	1206	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0010833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	267	435	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.328196791039512	2	FACETS	0.999	0.941	1	0.999	0.941	1	CLONAL	2	TRUE	0	0.349418868467252	2		436	765	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263973	104263974	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776579	NA	P-0010833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	43	282	0	ENST00000369902.3:c.71dup	p.Ala25GlyfsTer23	p.A25Gfs*23	ENST00000369902	NM_016169.3	22	gcc/gCcc	1/12	1	2	FACETS	0.47	0.393	0.555	0.47	0.393	0.555	SUBCLONAL	1	TRUE	1	0.349418868467252	2		282	524	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	220	608	3	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.349418868467252	2		611	1205	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0010833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	75	673	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	0.349418868467252	2		673	339	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0010833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	175	500	5	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.349418868467252	2		505	939	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0010833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	180	660	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.896	0.825	0.97	0.896	0.825	0.97	CLONAL	1	TRUE	1	0.349418868467252	2		660	1150	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0010833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	124	498	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.895	0.81	0.985	0.895	0.81	0.985	CLONAL	1	TRUE	1	0.349418868467252	2		498	793	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882049	36882050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs780753361	NA	P-0010833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	169	607	0	ENST00000358127.4:c.963dup	p.Ala322ArgfsTer19	p.A322Rfs*19	ENST00000358127	NM_001280556.1	321	-/C	8/10	0.346310017456727	3	FACETS	0.896	0.822	0.974	0.448	0.411	0.487	CLONAL	1	TRUE	1	0.349418868467252	3		607	1268	SUCCESS
APC	324	MSKCC	GRCh37	5	112174466	112174466	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	82	262	0	ENST00000257430.4:c.3175G>T	p.Glu1059Ter	p.E1059*	ENST00000257430	NM_000038.5	1059	Gaa/Taa	16/16	1	2	FACETS	0.855	0.755	0.961	0.855	0.755	0.961	CLONAL	1	TRUE	1	0.349418868467252	2		262	549	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99204054	99204054	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs76257041	NA	P-0010833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	108	370	0	ENST00000074304.5:c.2917G>A	p.Gly973Arg	p.G973R	ENST00000074304	NM_001134224.1	973	Gga/Aga	26/26	1	2	FACETS	0.871	0.782	0.965	0.871	0.782	0.965	CLONAL	1	TRUE	1	0.349418868467252	2		370	710	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279324	38279324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774768179	NA	P-0010833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1438	240	792	2	ENST00000425967.3:c.1165G>A	p.Val389Ile	p.V389I	ENST00000425967	NM_001174067.1	389	Gtt/Att	9/19	0.346310017456727	3	FACETS	0.962	0.895	1	0.481	0.447	0.516	CLONAL	1	TRUE	1	0.349418868467252	3		794	1678	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371717	55371717	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	120	322	0	ENST00000297316.4:c.407A>T	p.Lys136Met	p.K136M	ENST00000297316	NM_022454.3	136	aAg/aTg	2/2	0.346310017456727	3	FACETS	0.903	0.814	0.996	0.451	0.407	0.498	CLONAL	1	TRUE	1	0.349418868467252	3		322	894	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402764	139402764	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758471372	NA	P-0010833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	182	467	0	ENST00000277541.6:c.3245G>A	p.Arg1082His	p.R1082H	ENST00000277541	NM_017617.3	1082	cGc/cAc	20/34	0.346310017456727	3	FACETS	1	0.975	1	0.568	0.523	0.614	CLONAL	1	TRUE	1	0.349418868467252	3		467	1078	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456756	32456756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	103	224	1	ENST00000332351.3:c.136G>A	p.Ala46Thr	p.A46T	ENST00000332351	NM_024426.4	46	Gcc/Acc	1/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.349418868467252	2		225	444	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180915	108180915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	47	247	0	ENST00000278616.4:c.5791G>A	p.Ala1931Thr	p.A1931T	ENST00000278616	NM_000051.3	1931	Gct/Act	39/63	1	2	FACETS	0.616	0.52	0.721	0.616	0.52	0.721	SUBCLONAL	1	TRUE	1	0.349418868467252	2		247	437	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495736	56495736	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747453114	NA	P-0010833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	113	314	0	ENST00000267101.3:c.3926G>A	p.Arg1309His	p.R1309H	ENST00000267101	NM_001982.3	1309	cGc/cAc	28/28	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.349418868467252	2		314	599	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914223	32914223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1360	265	952	0	ENST00000380152.3:c.5731G>A	p.Asp1911Asn	p.D1911N	ENST00000380152		1911	Gat/Aat	11/27	1	2	FACETS	0.933	0.872	0.997	0.933	0.872	0.997	CLONAL	1	TRUE	1	0.349418868467252	2		952	1625	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434494	110434494	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1174414481	NA	P-0010833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	150	360	0	ENST00000375856.3:c.3907G>A	p.Gly1303Ser	p.G1303S	ENST00000375856	NM_003749.2	1303	Ggc/Agc	1/2	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.349418868467252	2		360	700	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434682	110434682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	117	465	3	ENST00000375856.3:c.3719G>A	p.Arg1240His	p.R1240H	ENST00000375856	NM_003749.2	1240	cGc/cAc	1/2	1	2	FACETS	0.756	0.681	0.835	0.756	0.681	0.835	SUBCLONAL	1	TRUE	1	0.349418868467252	2		468	886	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99460087	99460087	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	88	449	0	ENST00000268035.6:c.2183A>G	p.Asn728Ser	p.N728S	ENST00000268035	NM_000875.3	728	aAc/aGc	10/21	1	2	FACETS	0.588	0.52	0.661	0.588	0.52	0.661	SUBCLONAL	1	TRUE	1	0.349418868467252	2		449	856	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944410	40944410	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs777227473	NA	P-0010833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	111	641	0	ENST00000373198.4:c.2092C>A	p.Leu698Met	p.L698M	ENST00000373198	NM_133170.3	698	Ctg/Atg	12/32	1	2	FACETS	0.523	0.468	0.581	0.523	0.468	0.581	SUBCLONAL	1	TRUE	1	0.349418868467252	2		641	1215	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0010852-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	349	356	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.909	0.86	0.959	0.909	0.86	0.959	CLONAL	1	TRUE	1	0.59885336075648	2		356	1282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577567	7577568	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CACATGTAGTTGT	novel	NA	P-0010852-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	358	464	0	ENST00000269305.4:c.701_713dup	p.Cys238Ter	p.C238*	ENST00000269305	NM_001126112.2	238	tgt/tgACAACTACATGTGt	7/11	0.577771832969686	1	FACETS	0.82	0.778	0.862	0.82	0.778	0.862	CLONAL	1	TRUE	0	0.59885336075648	1		464	1022	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575172	48575184	+	frameshift_variant	Frame_Shift_Del	DEL	ATGTGATAGTGTC	ATGTGATAGTGTC	TGT	novel	NA	P-0010852-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	210	405	0	ENST00000342988.3:c.366_378delinsTGT	p.Lys122AsnfsTer4	p.K122Nfs*4	ENST00000342988	NM_005359.5	122	aaATGTGATAGTGTC/aaTGT	3/12	0.59885336075648	1	FACETS	0.547	0.508	0.587	0.547	0.508	0.587	SUBCLONAL	1	TRUE	0	0.59885336075648	1		405	899	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576919	7576919	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	738	392	0	ENST00000269305.4:c.927del	p.Asn310ThrfsTer35	p.N310Tfs*35	ENST00000269305	NM_001126112.2	309	ccC/cc	9/11	0.709531095764692	2	FACETS	0.988	0.964	1	0.988	0.964	1	CLONAL	2	TRUE	0	0.72101178093584	2		392	1036	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708153	117708153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	367	374	2	ENST00000368508.3:c.2024C>T	p.Pro675Leu	p.P675L	ENST00000368508	NM_002944.2	675	cCa/cTa	14/43	0.637057067351747	3	FACETS	0.921	0.88	0.962	0.921	0.88	0.962	CLONAL	2	TRUE	1	0.72101178093584	3		376	752	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257865	133257865	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	246	352	1	ENST00000320574.5:c.63G>T	p.Arg21Ser	p.R21S	ENST00000320574	NM_006231.2	21	agG/agT	2/49	0.637057067351747	3	FACETS	0.871	0.814	0.93	0.435	0.407	0.465	CLONAL	1	TRUE	1	0.72101178093584	3		353	1066	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961958	41961958	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	526	726	1	ENST00000219905.7:c.866G>T	p.Gly289Val	p.G289V	ENST00000219905	NM_001164273.1	289	gGt/gTt	2/24	1	2	FACETS	0.964	0.924	1	0.964	0.924	1	CLONAL	1	TRUE	1	0.72101178093584	2		727	1514	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47679277	47679277	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1372	73	454	3	ENST00000347630.2:c.930C>A	p.Asp310Glu	p.D310E	ENST00000347630	NM_001007230.1	310	gaC/gaA	10/11	0.702477583740539	3	FACETS	0.191	0.166	0.218	0.095	0.083	0.109	SUBCLONAL	1	TRUE	1	0.72101178093584	3		457	1445	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428671	49428671	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	807	486	0	ENST00000301067.7:c.10279del	p.Ala3427ProfsTer6	p.A3427Pfs*6	ENST00000301067	NM_003482.3	3427	Gcc/cc	35/54	0.637871104285482	3	FACETS	0.905	0.877	0.932	0.905	0.877	0.932	CLONAL	2	TRUE	1	0.72101178093584	3		486	1683	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741450	145741451	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0010857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1562	423	613	0	ENST00000428558.2:c.1052dup	p.Asn352GlnfsTer20	p.N352Qfs*20	ENST00000428558	NM_004260.3	351	ggc/ggGc	5/22	0.702477583740539	3	FACETS	0.804	0.763	0.846	0.402	0.381	0.423	CLONAL	1	TRUE	1	0.72101178093584	3		613	1985	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098420	11098420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752581107	NA	P-0010862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	98	479	1	ENST00000358026.2:c.938C>T	p.Pro313Leu	p.P313L	ENST00000358026	NM_001128849.1	313	cCc/cTc	6/36	0.313072338931688	3	FACETS	0.995	0.887	1	0.497	0.443	0.555	CLONAL	1	TRUE	1	0.313072338931688	3		480	728	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098368	11098368	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	122	568	0	ENST00000358026.2:c.886A>T	p.Thr296Ser	p.T296S	ENST00000358026	NM_001128849.1	296	Acg/Tcg	6/36	0.313072338931688	3	FACETS	1	0.95	1	0.54	0.488	0.596	CLONAL	1	TRUE	1	0.313072338931688	3		568	834	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023152	31023153	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	216	552	0	ENST00000375687.4:c.2638dup	p.Thr880AsnfsTer2	p.T880Nfs*2	ENST00000375687	NM_015338.5	879	-/A	13/13	0.313072338931688	4	FACETS	1	0.942	1	0.676	0.629	0.724	CLONAL	2	TRUE	1	0.313072338931688	4		552	894	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098465	11098466	+	missense_variant	Missense_Mutation	DNP	CG	CG	TT	novel	NA	P-0010862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	96	358	0	ENST00000358026.2:c.983_984delinsTT	p.Pro328Leu	p.P328L	ENST00000358026	NM_001128849.1	328	cCG/cTT	6/36	0.313072338931688	3	FACETS	1	0.934	1	0.533	0.475	0.595	CLONAL	1	TRUE	1	0.313072338931688	3		358	665	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	123	374	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.98	0.891	1	0.98	0.891	1	CLONAL	1	TRUE	1	0.522038261274273	2		374	481	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	744	411	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.522038261274273	2		411	1328	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354179	15354179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1393147270	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	135	228	0	ENST00000263377.2:c.2701C>T	p.Pro901Ser	p.P901S	ENST00000263377	NM_058243.2	901	Cca/Tca	14/20	1	2	FACETS	0.892	0.814	0.973	0.892	0.814	0.973	CLONAL	1	TRUE	1	0.522038261274273	2		228	580	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982036	93982036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1165179670	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	277	432	1	ENST00000369303.4:c.1429G>A	p.Glu477Lys	p.E477K	ENST00000369303	NM_004440.3	477	Gaa/Aaa	6/17	1	2	FACETS	0.952	0.894	1	0.952	0.894	1	CLONAL	1	TRUE	1	0.522038261274273	2		433	1115	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561396	9561396	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1262495622	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	310	427	1	ENST00000353224.5:c.386C>T	p.Ser129Phe	p.S129F	ENST00000353224	NM_177990.2	129	tCc/tTc	4/10	0.522038261274273	1	FACETS	0.993	0.939	1	0.993	0.939	1	CLONAL	1	TRUE	0	0.522038261274273	1		428	884	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094261	193094261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540541696	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	245	362	0	ENST00000367435.3:c.151C>T	p.Pro51Ser	p.P51S	ENST00000367435	NM_024529.4	51	Ccc/Tcc	2/17	1	2	FACETS	0.991	0.927	1	0.991	0.927	1	CLONAL	1	TRUE	1	0.522038261274273	2		362	947	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306568	41306568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	234	375	1	ENST00000373198.4:c.1091G>A	p.Arg364Gln	p.R364Q	ENST00000373198	NM_133170.3	364	cGa/cAa	7/32	0.522038261274273	1	FACETS	0.919	0.861	0.978	0.919	0.861	0.978	CLONAL	1	TRUE	0	0.522038261274273	1		376	721	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861246	57861246	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745587766	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	386	573	0	ENST00000228682.2:c.1043G>A	p.Arg348Gln	p.R348Q	ENST00000228682	NM_005269.2	348	cGa/cAa	9/12	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.522038261274273	2		573	1413	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259244	89259244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	232	319	0	ENST00000336596.2:c.388G>A	p.Asp130Asn	p.D130N	ENST00000336596	NM_005233.5	130	Gat/Aat	3/17	1	2	FACETS	0.97	0.906	1	0.97	0.906	1	CLONAL	1	TRUE	1	0.522038261274273	2		319	916	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494160	140494160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	323	439	0	ENST00000288602.6:c.1088C>T	p.Ser363Phe	p.S363F	ENST00000288602	NM_004333.4	363	tCc/tTc	8/18	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.522038261274273	2		439	1218	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416221	29416221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	293	477	0	ENST00000389048.3:c.4732C>T	p.Pro1578Ser	p.P1578S	ENST00000389048	NM_004304.4	1578	Cct/Tct	29/29	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.522038261274273	2		477	1115	SUCCESS
ALK	238	MSKCC	GRCh37	2	29436901	29436901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200110351	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	281	462	0	ENST00000389048.3:c.3692G>A	p.Arg1231Gln	p.R1231Q	ENST00000389048	NM_004304.4	1231	cGg/cAg	24/29	1	2	FACETS	0.976	0.917	1	0.976	0.917	1	CLONAL	1	TRUE	1	0.522038261274273	2		462	1103	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872864	136872864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1270	436	694	0	ENST00000241393.3:c.634G>A	p.Gly212Ser	p.G212S	ENST00000241393	NM_003467.2	212	Ggt/Agt	2/2	1	2	FACETS	0.979	0.931	1	0.979	0.931	1	CLONAL	1	TRUE	1	0.522038261274273	2		694	1706	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163893	47163893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	305	405	0	ENST00000409792.3:c.2233C>T	p.Pro745Ser	p.P745S	ENST00000409792	NM_014159.6	745	Cca/Tca	3/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.522038261274273	2		405	1086	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589306	67589306	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	162	245	0	ENST00000274335.5:c.1294C>T	p.Gln432Ter	p.Q432*	ENST00000274335		432	Caa/Taa	9/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.522038261274273	2		245	569	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481633	20481633	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	251	352	0	ENST00000346618.3:c.702G>T	p.Lys234Asn	p.K234N	ENST00000346618	NM_001949.4	234	aaG/aaT	3/7	1	2	FACETS	0.985	0.923	1	0.985	0.923	1	CLONAL	1	TRUE	1	0.522038261274273	2		352	976	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709098	117709098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	265	466	1	ENST00000368508.3:c.1859C>T	p.Pro620Leu	p.P620L	ENST00000368508	NM_002944.2	620	cCt/cTt	13/43	NA	2	FACETS	0.894	0.837	0.952			1	INDETERMINATE	1	TRUE	NA	0.522038261274273	2		467	1136	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282101	38282101	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	197	467	1	ENST00000425967.3:c.955C>A	p.Gln319Lys	p.Q319K	ENST00000425967	NM_001174067.1	319	Cag/Aag	8/19	1	2	FACETS	0.686	0.635	0.74	0.686	0.635	0.74	SUBCLONAL	1	TRUE	1	0.522038261274273	2		468	1100	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220507	98220507	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	266	368	0	ENST00000331920.6:c.2956G>A	p.Asp986Asn	p.D986N	ENST00000331920	NM_000264.3	986	Gac/Aac	18/24	0.522038261274273	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.522038261274273	1		368	729	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417574	139417574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	324	453	1	ENST00000277541.6:c.470C>T	p.Pro157Leu	p.P157L	ENST00000277541	NM_017617.3	157	cCc/cTc	4/34	0.522038261274273	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.522038261274273	1		454	894	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123324982	123324982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	294	480	0	ENST00000358487.5:c.346G>A	p.Glu116Lys	p.E116K	ENST00000358487	NM_000141.4	116	Gaa/Aaa	3/18	0.522038261274273	1	FACETS	0.944	0.891	0.998	0.944	0.891	0.998	CLONAL	1	TRUE	0	0.522038261274273	1		480	882	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573716	64573716	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	225	383	0	ENST00000312049.6:c.1037C>T	p.Thr346Ile	p.T346I	ENST00000312049	NM_130799.2	346	aCt/aTt	7/10	0.438804319919882	1	FACETS	0.977	0.915	1	0.977	0.915	1	CLONAL	1	TRUE	0	0.522038261274273	1		383	652	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443881	18443881	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	195	342	0	ENST00000266497.5:c.854A>C	p.Lys285Thr	p.K285T	ENST00000266497		285	aAg/aCg	3/31	1	2	FACETS	0.857	0.794	0.922	0.857	0.794	0.922	CLONAL	1	TRUE	1	0.522038261274273	2		342	872	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534798	18534798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767852668	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	214	369	0	ENST00000266497.5:c.1856C>T	p.Ser619Phe	p.S619F	ENST00000266497		619	tCc/tTc	12/31	1	2	FACETS	0.934	0.869	1	0.934	0.869	1	CLONAL	1	TRUE	1	0.522038261274273	2		369	878	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431395	121431395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs893256143	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	199	388	0	ENST00000257555.6:c.599G>A	p.Arg200Gln	p.R200Q	ENST00000257555		200	cGg/cAg	3/10	1	2	FACETS	0.8	0.741	0.861	0.8	0.741	0.861	SUBCLONAL	1	TRUE	1	0.522038261274273	2		388	953	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241044	133241044	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200283666	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	199	328	0	ENST00000320574.5:c.2473C>T	p.Arg825Cys	p.R825C	ENST00000320574	NM_006231.2	825	Cgc/Tgc	22/49	1	2	FACETS	0.963	0.894	1	0.963	0.894	1	CLONAL	1	TRUE	1	0.522038261274273	2		328	792	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895604	28895604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	239	405	0	ENST00000282397.4:c.3170G>A	p.Gly1057Glu	p.G1057E	ENST00000282397	NM_002019.4	1057	gGa/gAa	23/30	0.464414764489967	3	FACETS	0.946	0.882	1	0.473	0.441	0.507	CLONAL	1	TRUE	1	0.522038261274273	3		405	1220	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934354	81934354	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	345	481	0	ENST00000359376.3:c.1331C>G	p.Pro444Arg	p.P444R	ENST00000359376	NM_002661.3	444	cCc/cGc	14/33	0.522038261274273	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.522038261274273	1		481	905	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853769	59853769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	261	416	0	ENST00000259008.2:c.2090C>T	p.Ser697Phe	p.S697F	ENST00000259008	NM_032043.2	697	tCt/tTt	14/20	1	2	FACETS	0.926	0.867	0.986	0.926	0.867	0.986	CLONAL	1	TRUE	1	0.522038261274273	2		416	1080	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797979	42797979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	329	553	1	ENST00000575354.2:c.4031C>T	p.Ser1344Phe	p.S1344F	ENST00000575354	NM_015125.3	1344	tCt/tTt	16/20	1	2	FACETS	0.849	0.8	0.899	0.849	0.8	0.899	CLONAL	1	TRUE	1	0.522038261274273	2		554	1485	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024339	31024339	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	825	386	0	ENST00000375687.4:c.3824C>T	p.Ser1275Leu	p.S1275L	ENST00000375687	NM_015338.5	1275	tCa/tTa	13/13	0.513857831060167	4	FACETS	1	0.989	1			1	CLONAL	3	TRUE	NA	0.522038261274273	4		386	1551	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945354	54945354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	410	271	0	ENST00000312783.6:c.1072G>A	p.Asp358Asn	p.D358N	ENST00000312783	NM_198436.1	358	Gac/Aac	10/10	0.143217235393745	5	FACETS	0.968	0.925	1			1	INDETERMINATE	3	TRUE	NA	0.522038261274273	5		271	964	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755506	39755506	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	255	459	0	ENST00000288319.7:c.1259C>T	p.Ser420Phe	p.S420F	ENST00000288319	NM_182918.3	420	tCc/tTc	10/10	1	2	FACETS	0.93	0.871	0.991	0.93	0.871	0.991	CLONAL	1	TRUE	1	0.522038261274273	2		459	1050	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044847	47044847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	200	167	0	ENST00000377604.3:c.2173C>T	p.Pro725Ser	p.P725S	ENST00000377604	NM_001204468.1	725	Ccg/Tcg	20/24	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.522038261274273	1		167	403	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223568	53223568	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	130	121	1	ENST00000375401.3:c.3791C>T	p.Ala1264Val	p.A1264V	ENST00000375401	NM_004187.3	1264	gCc/gTc	23/26	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.522038261274273	1		122	278	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527499	157527519	+	inframe_deletion	In_Frame_Del	DEL	GAGGAAGACGAGGAGGATGAG	GAGGAAGACGAGGAGGATGAG	-	novel	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	170	385	0	ENST00000346085.5:c.5233_5253del	p.Glu1745_Asp1751del	p.E1745_D1751del	ENST00000346085	NM_020732.3	1742	GAGGAAGACGAGGAGGATGAG/-	20/20	1	2	FACETS	0.678	0.624	0.736	0.678	0.624	0.736	SUBCLONAL	1	TRUE	1	0.522038261274273	2		385	960	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711896	89711897	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	244	296	1	ENST00000371953.3:c.516dup	p.Arg173AlafsTer7	p.R173Afs*7	ENST00000371953	NM_000314.4	172	agg/aGgg	6/9	0.522038261274273	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.522038261274273	1		297	654	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620142	21620143	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0010937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	188	280	2	ENST00000382592.4:c.23_24delinsTT	p.Ala8Val	p.A8V	ENST00000382592	NM_014572.2	8	gCC/gTT	2/8	0.464414764489967	3	FACETS	0.824	0.761	0.89	0.412	0.38	0.445	CLONAL	1	TRUE	1	0.522038261274273	3		282	1102	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073928	8073928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746056102	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	79	1133	2	ENST00000377482.5:c.731G>A	p.Arg244Gln	p.R244Q	ENST00000377482	NM_018948.3	244	cGa/cAa	4/4	1	2	FACETS	0.822	0.721	0.932	0.822	0.721	0.932	CLONAL	1	TRUE	1	0.16	2		1135	1201	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254608	16254608	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1350671357	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	52	656	1	ENST00000375759.3:c.1873G>A	p.Asp625Asn	p.D625N	ENST00000375759	NM_015001.2	625	Gac/Aac	11/15	1	2	FACETS	0.792	0.672	0.923	0.792	0.672	0.923	CLONAL	1	TRUE	1	0.16	2		657	821	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059183	27059183	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	72	710	0	ENST00000324856.7:c.1820C>A	p.Ser607Ter	p.S607*	ENST00000324856	NM_006015.4	607	tCa/tAa	4/20	1	2	FACETS	0.952	0.83	1	0.952	0.83	1	CLONAL	1	TRUE	1	0.16	2		710	945	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	29	456	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.673	0.538	0.826	0.673	0.538	0.826	SUBCLONAL	1	TRUE	1	0.16	2		456	539	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807378	36807378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780818464	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	33	452	1	ENST00000373129.3:c.1286C>T	p.Ala429Val	p.A429V	ENST00000373129	NM_032017.1	429	gCg/gTg	12/12	1	2	FACETS	0.745	0.605	0.902	0.745	0.605	0.902	CLONAL	1	TRUE	1	0.16	2		453	554	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43806095	43806095	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	68	688	1	ENST00000372470.3:c.891G>T	p.Lys297Asn	p.K297N	ENST00000372470	NM_005373.2	297	aaG/aaT	6/12	1	2	FACETS	0.994	0.863	1	0.994	0.863	1	CLONAL	1	TRUE	1	0.16	2		689	855	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163760	72163760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	67	1166	0	ENST00000357731.5:c.598G>A	p.Glu200Lys	p.E200K	ENST00000357731	NM_173808.2	200	Gaa/Aaa	4/7	1	2	FACETS	0.751	0.65	0.861	0.751	0.65	0.861	SUBCLONAL	1	TRUE	1	0.16	2		1166	1115	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740098	162740098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781104392	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	24	368	0	ENST00000367921.3:c.1300C>T	p.Arg434Trp	p.R434W	ENST00000367921	NM_006182.2	434	Cgg/Tgg	12/18	1	2	FACETS	0.726	0.569	0.909	0.726	0.569	0.909	CLONAL	1	TRUE	1	0.16	2		368	413	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518460	204518460	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	40	513	1	ENST00000367182.3:c.1123G>T	p.Asp375Tyr	p.D375Y	ENST00000367182	NM_001278516.1	375	Gat/Tat	11/11	1	2	FACETS	0.675	0.559	0.804	0.675	0.559	0.804	SUBCLONAL	1	TRUE	1	0.16	2		514	741	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972866	25972866	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	57	622	0	ENST00000435504.4:c.1559C>A	p.Ser520Tyr	p.S520Y	ENST00000435504		520	tCt/tAt	12/13	1	2	FACETS	0.85	0.728	0.985	0.85	0.728	0.985	CLONAL	1	TRUE	1	0.16	2		622	838	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143482	30143482	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs770134645	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	17	160	0	ENST00000389048.3:c.44C>A	p.Ser15Tyr	p.S15Y	ENST00000389048	NM_004304.4	15	tCc/tAc	1/29	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.16	2		160	154	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641516	47641516	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	42	603	0	ENST00000233146.2:c.901A>G	p.Lys301Glu	p.K301E	ENST00000233146	NM_000251.2	301	Aaa/Gaa	5/16	1	2	FACETS	0.809	0.674	0.959	0.809	0.674	0.959	CLONAL	1	TRUE	1	0.16	2		603	649	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707951	47707951	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63749830	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	35	510	0	ENST00000233146.2:c.2575G>T	p.Glu859Ter	p.E859*	ENST00000233146	NM_000251.2	859	Gaa/Taa	15/16	1	2	FACETS	0.727	0.594	0.876	0.727	0.594	0.876	SUBCLONAL	1	TRUE	1	0.16	2		510	602	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026896	48026896	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	53	577	0	ENST00000234420.5:c.1774G>T	p.Val592Leu	p.V592L	ENST00000234420	NM_000179.2	592	Gta/Tta	4/10	1	2	FACETS	0.873	0.743	1	0.873	0.743	1	CLONAL	1	TRUE	1	0.16	2		577	759	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027541	48027541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587779923	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	29	327	1	ENST00000234420.5:c.2419G>A	p.Glu807Lys	p.E807K	ENST00000234420	NM_000179.2	807	Gaa/Aaa	4/10	1	2	FACETS	0.809	0.649	0.992	0.809	0.649	0.992	CLONAL	1	TRUE	1	0.16	2		328	448	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118941	61118941	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1456684871	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	60	501	0	ENST00000295025.8:c.134G>A	p.Arg45Gln	p.R45Q	ENST00000295025	NM_002908.2	45	cGa/cAa	2/11	1	2	FACETS	0.856	0.736	0.988	0.856	0.736	0.988	CLONAL	1	TRUE	1	0.16	2		501	876	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630638	158630638	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs387906591	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	61	912	2	ENST00000263640.3:c.605G>T	p.Arg202Ile	p.R202I	ENST00000263640	NM_001105.4	202	aGa/aTa	6/11	1	2	FACETS	0.657	0.565	0.759	0.657	0.565	0.759	SUBCLONAL	1	TRUE	1	0.16	2		914	1160	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131412	202131412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339962485	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	66	541	2	ENST00000358485.4:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000358485	NM_001080125.1	127	cGa/cAa	2/9	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.16	2		543	703	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113347	209113347	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754316078	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	51	560	0	ENST00000345146.2:c.160G>A	p.Asp54Asn	p.D54N	ENST00000345146	NM_005896.2	54	Gac/Aac	4/10	1	2	FACETS	0.814	0.69	0.951	0.814	0.69	0.951	CLONAL	1	TRUE	1	0.16	2		560	783	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288964	212288964	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	42	596	0	ENST00000342788.4:c.2782G>T	p.Glu928Ter	p.E928*	ENST00000342788	NM_005235.2	928	Gaa/Taa	23/28	1	2	FACETS	0.699	0.582	0.83	0.699	0.582	0.83	SUBCLONAL	1	TRUE	1	0.16	2		596	751	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645381	215645381	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780014	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	51	886	2	ENST00000260947.4:c.1217G>A	p.Arg406Gln	p.R406Q	ENST00000260947	NM_000465.2	406	cGa/cAa	4/11	1	2	FACETS	0.683	0.579	0.799	0.683	0.579	0.799	SUBCLONAL	1	TRUE	1	0.16	2		888	933	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379410	225379410	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs972626651	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	43	625	0	ENST00000264414.4:c.458G>A	p.Arg153His	p.R153H	ENST00000264414	NM_003590.4	153	cGt/cAt	4/16	1	2	FACETS	0.719	0.6	0.851	0.719	0.6	0.851	SUBCLONAL	1	TRUE	1	0.16	2		625	748	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058740	47058740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	28	304	1	ENST00000409792.3:c.7538C>T	p.Thr2513Ile	p.T2513I	ENST00000409792	NM_014159.6	2513	aCt/aTt	21/21	1	2	FACETS	0.825	0.659	1	0.825	0.659	1	CLONAL	1	TRUE	1	0.16	2		305	424	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427709	72427709	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	59	455	0	ENST00000477973.2:c.781G>T	p.Asp261Tyr	p.D261Y	ENST00000477973	NM_012234.5	261	Gac/Tac	4/4	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.16	2		455	650	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427738	72427738	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	59	369	0	ENST00000477973.2:c.752C>A	p.Thr251Asn	p.T251N	ENST00000477973	NM_012234.5	251	aCt/aAt	4/4	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.16	2		369	499	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631610	119631610	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	58	704	1	ENST00000316626.5:c.656C>A	p.Ser219Tyr	p.S219Y	ENST00000316626		219	tCt/tAt	6/12	1	2	FACETS	0.837	0.717	0.968	0.837	0.717	0.968	CLONAL	1	TRUE	1	0.16	2		705	866	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119634961	119634961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	32	535	0	ENST00000316626.5:c.538C>T	p.Arg180Trp	p.R180W	ENST00000316626		180	Cgg/Tgg	5/12	1	2	FACETS	0.638	0.516	0.776	0.638	0.516	0.776	SUBCLONAL	1	TRUE	1	0.16	2		535	627	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898711	134898711	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	59	671	2	ENST00000398015.3:c.1769G>T	p.Gly590Val	p.G590V	ENST00000398015	NM_004441.4	590	gGg/gTg	10/16	1	2	FACETS	0.964	0.828	1	0.964	0.828	1	CLONAL	1	TRUE	1	0.16	2		673	765	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272680	142272680	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	55	704	0	ENST00000350721.4:c.2519G>T	p.Gly840Val	p.G840V	ENST00000350721	NM_001184.3	840	gGa/gTa	11/47	1	2	FACETS	0.942	0.804	1	0.942	0.804	1	CLONAL	1	TRUE	1	0.16	2		704	730	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1293	87	928	1	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	0.788	0.695	0.888	0.788	0.695	0.888	SUBCLONAL	1	TRUE	1	0.16	2		929	1380	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	86	1114	2	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.808	0.712	0.911	0.808	0.712	0.911	CLONAL	1	TRUE	1	0.16	2		1116	1331	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185169115	185169115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	77	846	0	ENST00000265026.3:c.1210C>T	p.Leu404Phe	p.L404F	ENST00000265026	NM_004721.4	404	Ctc/Ttc	7/14	1	2	FACETS	0.93	0.814	1	0.93	0.814	1	CLONAL	1	TRUE	1	0.16	2		846	1035	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505640	186505640	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	69	874	0	ENST00000323963.5:c.1048C>A	p.Leu350Ile	p.L350I	ENST00000323963		350	Cta/Ata	10/11	1	2	FACETS	0.844	0.733	0.965	0.844	0.733	0.965	CLONAL	1	TRUE	1	0.16	2		874	1022	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449600	187449600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781532443	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	36	439	0	ENST00000232014.4:c.280C>T	p.Arg94Trp	p.R94W	ENST00000232014	NM_001130845.1	94	Cgg/Tgg	4/10	1	2	FACETS	0.733	0.601	0.881	0.733	0.601	0.881	SUBCLONAL	1	TRUE	1	0.16	2		439	614	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55603381	55603381	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	45	686	0	ENST00000288135.5:c.2737A>C	p.Lys913Gln	p.K913Q	ENST00000288135	NM_000222.2	913	Aaa/Caa	20/21	1	2	FACETS	0.757	0.635	0.893	0.757	0.635	0.893	SUBCLONAL	1	TRUE	1	0.16	2		686	743	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143029269	143029269	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	32	376	0	ENST00000262992.4:c.2351T>G	p.Phe784Cys	p.F784C	ENST00000262992	NM_001101669.1	784	tTt/tGt	21/24	1	2	FACETS	0.762	0.617	0.926	0.762	0.617	0.926	CLONAL	1	TRUE	1	0.16	2		376	525	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251946	153251946	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	51	702	1	ENST00000281708.4:c.1060G>T	p.Ala354Ser	p.A354S	ENST00000281708	NM_033632.3	354	Gca/Tca	7/12	1	2	FACETS	0.766	0.649	0.895	0.766	0.649	0.895	SUBCLONAL	1	TRUE	1	0.16	2		703	832	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332699	153332699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780061054	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	63	783	1	ENST00000281708.4:c.257C>T	p.Ser86Leu	p.S86L	ENST00000281708	NM_033632.3	86	tCg/tTg	2/12	1	2	FACETS	0.84	0.725	0.967	0.84	0.725	0.967	CLONAL	1	TRUE	1	0.16	2		784	937	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539727	187539727	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	41	584	0	ENST00000441802.2:c.8013C>A	p.Phe2671Leu	p.F2671L	ENST00000441802	NM_005245.3	2671	ttC/ttA	10/27	1	2	FACETS	0.875	0.727	1	0.875	0.727	1	CLONAL	1	TRUE	1	0.16	2		584	586	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542861	187542861	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1340793072	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	37	476	2	ENST00000441802.2:c.4879C>T	p.Arg1627Ter	p.R1627*	ENST00000441802	NM_005245.3	1627	Cga/Tga	10/27	1	2	FACETS	0.85	0.7	1	0.85	0.7	1	CLONAL	1	TRUE	1	0.16	2		478	544	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630763	187630763	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	56	816	0	ENST00000441802.2:c.219A>C	p.Lys73Asn	p.K73N	ENST00000441802	NM_005245.3	73	aaA/aaC	2/27	1	2	FACETS	0.803	0.686	0.931	0.803	0.686	0.931	CLONAL	1	TRUE	1	0.16	2		816	872	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189383	56189383	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776167103	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	74	717	0	ENST00000399503.3:c.4415C>T	p.Ser1472Leu	p.S1472L	ENST00000399503	NM_005921.1	1472	tCg/tTg	20/20	1	2	FACETS	0.918	0.801	1	0.918	0.801	1	CLONAL	1	TRUE	1	0.16	2		717	1008	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750454	57750454	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	55	642	0	ENST00000274289.3:c.2014C>T	p.Arg672Ter	p.R672*	ENST00000274289	NM_006622.3	672	Cga/Tga	14/14	1	2	FACETS	0.892	0.761	1	0.892	0.761	1	CLONAL	1	TRUE	1	0.16	2		642	771	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752839	57752839	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	35	351	1	ENST00000274289.3:c.1089C>A	p.Phe363Leu	p.F363L	ENST00000274289	NM_006622.3	363	ttC/ttA	8/14	1	2	FACETS	0.9	0.737	1	0.9	0.737	1	CLONAL	1	TRUE	1	0.16	2		352	486	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645152	86645152	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	27	364	0	ENST00000274376.6:c.1224G>T	p.Gln408His	p.Q408H	ENST00000274376	NM_002890.2	408	caG/caT	8/25	1	2	FACETS	0.667	0.53	0.825	0.667	0.53	0.825	SUBCLONAL	1	TRUE	1	0.16	2		364	506	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649005	86649005	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	32	413	0	ENST00000274376.6:c.1285G>T	p.Glu429Ter	p.E429*	ENST00000274376	NM_002890.2	429	Gaa/Taa	9/25	1	2	FACETS	0.745	0.603	0.905	0.745	0.603	0.905	CLONAL	1	TRUE	1	0.16	2		413	537	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672371	86672371	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	38	368	0	ENST00000274376.6:c.2173G>T	p.Glu725Ter	p.E725*	ENST00000274376	NM_002890.2	725	Gaa/Taa	16/25	1	2	FACETS	0.813	0.671	0.973	0.813	0.671	0.973	CLONAL	1	TRUE	1	0.16	2		368	584	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931374	131931374	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	65	578	0	ENST00000265335.6:c.2079G>T	p.Glu693Asp	p.E693D	ENST00000265335		693	gaG/gaT	13/25	1	2	FACETS	0.963	0.833	1	0.963	0.833	1	CLONAL	1	TRUE	1	0.16	2		578	844	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500867	149500867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774032065	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	35	411	0	ENST00000261799.4:c.2363G>A	p.Arg788Gln	p.R788Q	ENST00000261799	NM_002609.3	788	cGa/cAa	17/23	1	2	FACETS	0.79	0.646	0.951	0.79	0.646	0.951	CLONAL	1	TRUE	1	0.16	2		411	554	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501508	149501508	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	51	655	0	ENST00000261799.4:c.2279A>G	p.Asp760Gly	p.D760G	ENST00000261799	NM_002609.3	760	gAc/gGc	16/23	1	2	FACETS	0.786	0.666	0.918	0.786	0.666	0.918	CLONAL	1	TRUE	1	0.16	2		655	811	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562387	176562387	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	44	384	0	ENST00000439151.2:c.283G>T	p.Glu95Ter	p.E95*	ENST00000439151	NM_022455.4	95	Gaa/Taa	2/23	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.16	2		384	480	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675248	176675248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201483724	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	45	666	0	ENST00000439151.2:c.4564G>A	p.Asp1522Asn	p.D1522N	ENST00000439151	NM_022455.4	1522	Gat/Aat	11/23	1	2	FACETS	0.697	0.584	0.823	0.697	0.584	0.823	SUBCLONAL	1	TRUE	1	0.16	2		666	807	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036019	180036019	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	52	680	3	ENST00000261937.6:c.3842C>T	p.Ser1281Leu	p.S1281L	ENST00000261937	NM_182925.4	1281	tCg/tTg	29/30	1	2	FACETS	0.909	0.773	1	0.909	0.773	1	CLONAL	1	TRUE	1	0.16	2		683	715	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20488443	20488443	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	55	720	2	ENST00000346618.3:c.1099G>T	p.Asp367Tyr	p.D367Y	ENST00000346618	NM_001949.4	367	Gac/Tac	6/7	0.114631933318408	3	FACETS	0.748	0.637	0.869	0.374	0.318	0.435	SUBCLONAL	1	TRUE	1	0.16	3		722	993	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225411	26225411	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1584	103	1263	0	ENST00000360408.1:c.29A>C	p.Lys10Thr	p.K10T	ENST00000360408	NM_003532.2	10	aAa/aCa	1/1	0.114631933318408	3	FACETS	0.824	0.734	0.921	0.412	0.367	0.461	CLONAL	1	TRUE	1	0.16	3		1263	1687	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672233	30672233	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	73	895	0	ENST00000376406.3:c.4727C>A	p.Pro1576His	p.P1576H	ENST00000376406	NM_014641.2	1576	cCt/cAt	10/15	0.114631933318408	3	FACETS	0.958	0.835	1	0.479	0.417	0.546	CLONAL	1	TRUE	1	0.16	3		895	1029	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024169	112024169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465963577	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	69	990	3	ENST00000368678.4:c.616C>T	p.Arg206Cys	p.R206C	ENST00000368678		206	Cgc/Tgc	7/13	1	2	FACETS	0.726	0.63	0.831	0.726	0.63	0.831	SUBCLONAL	1	TRUE	1	0.16	2		993	1188	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710657	117710657	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	51	596	1	ENST00000368508.3:c.1615G>T	p.Glu539Ter	p.E539*	ENST00000368508	NM_002944.2	539	Gaa/Taa	12/43	1	2	FACETS	0.932	0.791	1	0.932	0.791	1	CLONAL	1	TRUE	1	0.16	2		597	684	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117746794	117746794	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770579408	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	55	613	0	ENST00000368508.3:c.26C>T	p.Pro9Leu	p.P9L	ENST00000368508	NM_002944.2	9	cCg/cTg	1/43	1	2	FACETS	0.899	0.767	1	0.899	0.767	1	CLONAL	1	TRUE	1	0.16	2		613	765	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196096	138196096	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	81	609	0	ENST00000237289.4:c.410A>C	p.Asn137Thr	p.N137T	ENST00000237289	NM_001270507.1	137	aAc/aCc	3/9	1	2	FACETS	0.986	0.866	1	0.986	0.866	1	CLONAL	1	TRUE	1	0.16	2		609	1027	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149982971	149982971	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	34	513	0	ENST00000253339.5:c.3287C>A	p.Pro1096His	p.P1096H	ENST00000253339		1096	cCt/cAt	7/7	1	2	FACETS	0.744	0.607	0.9	0.744	0.607	0.9	SUBCLONAL	1	TRUE	1	0.16	2		513	571	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004349	150004349	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	53	831	1	ENST00000253339.5:c.1876C>T	p.Arg626Ter	p.R626*	ENST00000253339		626	Cga/Tga	3/7	1	2	FACETS	0.706	0.6	0.823	0.706	0.6	0.823	SUBCLONAL	1	TRUE	1	0.16	2		832	938	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150392	157150392	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1267507212	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	62	701	0	ENST00000346085.5:c.1574G>A	p.Arg525Lys	p.R525K	ENST00000346085	NM_020732.3	525	aGa/aAa	2/20	1	2	FACETS	0.952	0.821	1	0.952	0.821	1	CLONAL	1	TRUE	1	0.16	2		701	814	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527458	157527458	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	51	532	0	ENST00000346085.5:c.5183C>A	p.Ser1728Tyr	p.S1728Y	ENST00000346085	NM_020732.3	1728	tCt/tAt	20/20	1	2	FACETS	0.851	0.722	0.994	0.851	0.722	0.994	CLONAL	1	TRUE	1	0.16	2		532	749	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211170	55211170	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	44	426	0	ENST00000275493.2:c.413G>T	p.Arg138Ile	p.R138I	ENST00000275493	NM_005228.3	138	aGa/aTa	3/28	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.16	2		426	422	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140487360	140487360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507472	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	75	896	1	ENST00000288602.6:c.1165C>T	p.Arg389Cys	p.R389C	ENST00000288602	NM_004333.4	389	Cgt/Tgt	9/18	1	2	FACETS	0.875	0.765	0.995	0.875	0.765	0.995	CLONAL	1	TRUE	1	0.16	2		897	1071	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511220	148511220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1164610428	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	34	394	1	ENST00000320356.2:c.1682G>A	p.Arg561His	p.R561H	ENST00000320356	NM_004456.4	561	cGc/cAc	15/20	1	2	FACETS	0.702	0.573	0.849	0.702	0.573	0.849	SUBCLONAL	1	TRUE	1	0.16	2		395	605	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851403	151851403	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	51	758	0	ENST00000262189.6:c.12088G>T	p.Glu4030Ter	p.E4030*	ENST00000262189	NM_170606.2	4030	Gaa/Taa	47/59	1	2	FACETS	0.7	0.593	0.818	0.7	0.593	0.818	SUBCLONAL	1	TRUE	1	0.16	2		758	911	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874383	151874383	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	36	600	0	ENST00000262189.6:c.8155A>C	p.Asn2719His	p.N2719H	ENST00000262189	NM_170606.2	2719	Aac/Cac	38/59	1	2	FACETS	0.775	0.635	0.931	0.775	0.635	0.931	CLONAL	1	TRUE	1	0.16	2		600	581	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055755	152055755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1403418496	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	59	538	0	ENST00000262189.6:c.167G>A	p.Arg56Gln	p.R56Q	ENST00000262189	NM_170606.2	56	cGa/cAa	2/59	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.16	2		538	701	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370965	55370965	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	37	415	0	ENST00000297316.4:c.267G>T	p.Gln89His	p.Q89H	ENST00000297316	NM_022454.3	89	caG/caT	1/2	1	2	FACETS	0.958	0.789	1	0.958	0.789	1	CLONAL	1	TRUE	1	0.16	2		415	483	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5029830	5029830	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	49	505	0	ENST00000381652.3:c.274G>T	p.Glu92Ter	p.E92*	ENST00000381652	NM_004972.3	92	Gaa/Taa	4/25	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.16	2		505	599	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570332	87570332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	50	718	0	ENST00000277120.3:c.2072G>A	p.Arg691His	p.R691H	ENST00000277120		691	cGc/cAc	17/19	1	2	FACETS	0.864	0.732	1	0.864	0.732	1	CLONAL	1	TRUE	1	0.16	2		718	723	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778101	135778101	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1554815018	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	46	636	0	ENST00000298552.3:c.2282A>G	p.Tyr761Cys	p.Y761C	ENST00000298552	NM_001162426.1	761	tAc/tGc	18/23	1	2	FACETS	0.742	0.623	0.874	0.742	0.623	0.874	SUBCLONAL	1	TRUE	1	0.16	2		636	775	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649927	88649927	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	37	418	0	ENST00000372037.3:c.176T>G	p.Leu59Ter	p.L59*	ENST00000372037	NM_004329.2	59	tTa/tGa	4/13	1	2	FACETS	0.925	0.762	1	0.925	0.762	1	CLONAL	1	TRUE	1	0.16	2		418	500	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624245	89624245	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554890335	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	19	158	0	ENST00000371953.3:c.19G>T	p.Glu7Ter	p.E7*	ENST00000371953	NM_000314.4	7	Gag/Tag	1/9	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.16	2		158	200	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692856	89692856	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	14	152	0	ENST00000371953.3:c.340G>T	p.Glu114Ter	p.E114*	ENST00000371953	NM_000314.4	114	Gaa/Taa	5/9	1	2	FACETS	0.897	0.65	1	0.897	0.65	1	CLONAL	1	TRUE	1	0.16	2		152	195	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720862	89720862	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	29	291	0	ENST00000371953.3:c.1013C>A	p.Ser338Tyr	p.S338Y	ENST00000371953	NM_000314.4	338	tCt/tAt	8/9	1	2	FACETS	0.893	0.716	1	0.893	0.716	1	CLONAL	1	TRUE	1	0.16	2		291	406	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104386931	104386931	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	43	413	0	ENST00000369902.3:c.1297-1G>T		p.X433_splice	ENST00000369902	NM_016169.3	433			1	2	FACETS	0.784	0.654	0.928	0.784	0.654	0.928	CLONAL	1	TRUE	1	0.16	2		413	686	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912150	114912150	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	88	1031	4	ENST00000543371.1:c.1220G>A	p.Arg407Gln	p.R407Q	ENST00000543371	NM_001198531.1	407	cGa/cAa	11/14	1	2	FACETS	0.939	0.829	1	0.939	0.829	1	CLONAL	1	TRUE	1	0.16	2		1035	1172	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154868	2154868	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768105151	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	34	593	0	ENST00000434045.2:c.353G>A	p.Arg118His	p.R118H	ENST00000434045	NM_001127598.1	118	cGc/cAc	4/5	1	2	FACETS	0.692	0.564	0.837	0.692	0.564	0.837	SUBCLONAL	1	TRUE	1	0.16	2		593	614	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132774	64132774	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	46	599	0	ENST00000334205.4:c.908G>A	p.Gly303Asp	p.G303D	ENST00000334205	NM_003942.2	303	gGc/gAc	9/17	1	2	FACETS	0.887	0.746	1	0.887	0.746	1	CLONAL	1	TRUE	1	0.16	2		599	648	SUCCESS
EED	8726	MSKCC	GRCh37	11	85968608	85968608	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	47	582	2	ENST00000263360.6:c.604G>T	p.Asp202Tyr	p.D202Y	ENST00000263360	NM_003797.3	202	Gat/Tat	6/12	1	2	FACETS	0.879	0.741	1	0.879	0.741	1	CLONAL	1	TRUE	1	0.16	2		584	668	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219163	94219163	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	46	420	0	ENST00000323929.3:c.241A>C	p.Lys81Gln	p.K81Q	ENST00000323929	NM_005591.3	81	Aaa/Caa	4/20	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.16	2		420	547	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115600	108115600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772821016	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	34	497	0	ENST00000278616.4:c.748C>T	p.Arg250Ter	p.R250*	ENST00000278616	NM_000051.3	250	Cga/Tga	7/63	1	2	FACETS	0.634	0.517	0.767	0.634	0.517	0.767	SUBCLONAL	1	TRUE	1	0.16	2		497	670	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503180	125503180	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	38	552	0	ENST00000428830.2:c.547G>T	p.Glu183Ter	p.E183*	ENST00000428830	NM_001114121.2	183	Gaa/Taa	6/14	1	2	FACETS	0.652	0.537	0.78	0.652	0.537	0.78	SUBCLONAL	1	TRUE	1	0.16	2		552	729	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491472	18491472	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	25	390	0	ENST00000266497.5:c.1385G>T	p.Arg462Ile	p.R462I	ENST00000266497		462	aGa/aTa	8/31	0.3	1	FACETS	0.607	0.477	0.756	0.607	0.477	0.756	SUBCLONAL	1	TRUE	0	0.16	1		390	474	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478786	56478786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324972550	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	58	499	0	ENST00000267101.3:c.242G>A	p.Arg81Gln	p.R81Q	ENST00000267101	NM_001982.3	81	cGa/cAa	3/28	0.114631933318408	3	FACETS	1	0.931	1	0.572	0.49	0.66	CLONAL	1	TRUE	1	0.16	3		499	685	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478965	56478965	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	72	583	3	ENST00000267101.3:c.421G>T	p.Glu141Ter	p.E141*	ENST00000267101	NM_001982.3	141	Gag/Tag	3/28	0.114631933318408	3	FACETS	1	0.932	1	0.554	0.482	0.631	CLONAL	1	TRUE	1	0.16	3		586	878	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811604	102811604	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	71	943	0	ENST00000307046.8:c.580G>T	p.Gly194Ter	p.G194*	ENST00000307046	NM_001111285.1	194	Gga/Tga	4/4	0.114631933318408	3	FACETS	0.933	0.812	1	0.467	0.406	0.533	CLONAL	1	TRUE	1	0.16	3		943	1027	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891035	112891035	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs755619262	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	31	303	0	ENST00000351677.2:c.369G>T	p.Glu123Asp	p.E123D	ENST00000351677	NM_002834.3	123	gaG/gaT	4/16	1	2	FACETS	1	0.828	1	1	0.828	1	CLONAL	1	TRUE	1	0.16	2		303	378	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112939991	112939991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	69	569	0	ENST00000351677.2:c.1643C>T	p.Ser548Phe	p.S548F	ENST00000351677	NM_002834.3	548	tCt/tTt	14/16	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.16	2		569	750	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209337	133209337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs115452769	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	37	630	3	ENST00000320574.5:c.6049C>T	p.Arg2017Cys	p.R2017C	ENST00000320574	NM_006231.2	2017	Cgc/Tgc	44/49	1	2	FACETS	0.71	0.584	0.852	0.71	0.584	0.852	SUBCLONAL	1	TRUE	1	0.16	2		633	651	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220557	133220557	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747619107	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	29	314	0	ENST00000320574.5:c.4156C>T	p.Arg1386Trp	p.R1386W	ENST00000320574	NM_006231.2	1386	Cgg/Tgg	33/49	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.16	2		314	316	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226361	133226361	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs745750549	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	39	806	0	ENST00000320574.5:c.3697C>T	p.Arg1233Ter	p.R1233*	ENST00000320574	NM_006231.2	1233	Cga/Tga	30/49	1	2	FACETS	0.643	0.531	0.769	0.643	0.531	0.769	SUBCLONAL	1	TRUE	1	0.16	2		806	758	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	50	530	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	0.897	0.759	1	0.897	0.759	1	CLONAL	1	TRUE	1	0.16	2		530	697	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563383	21563383	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	84	898	0	ENST00000382592.4:c.536C>T	p.Ser179Leu	p.S179L	ENST00000382592	NM_014572.2	179	tCg/tTg	4/8	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.16	2		898	951	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26974661	26974661	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	46	603	1	ENST00000381527.3:c.1005C>A	p.Phe335Leu	p.F335L	ENST00000381527	NM_001260.1	335	ttC/ttA	10/13	1	2	FACETS	0.859	0.722	1	0.859	0.722	1	CLONAL	1	TRUE	1	0.16	2		604	669	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589756	28589756	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	43	669	2	ENST00000241453.7:c.2624G>T	p.Gly875Val	p.G875V	ENST00000241453	NM_004119.2	875	gGa/gTa	21/24	1	2	FACETS	0.702	0.585	0.831	0.702	0.585	0.831	SUBCLONAL	1	TRUE	1	0.16	2		671	766	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964160	28964160	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	29	502	0	ENST00000282397.4:c.1742A>C	p.Lys581Thr	p.K581T	ENST00000282397	NM_002019.4	581	aAg/aCg	13/30	1	2	FACETS	0.632	0.505	0.776	0.632	0.505	0.776	SUBCLONAL	1	TRUE	1	0.16	2		502	574	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964184	28964184	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	35	452	0	ENST00000282397.4:c.1718T>C	p.Leu573Pro	p.L573P	ENST00000282397	NM_002019.4	573	cTg/cCg	13/30	1	2	FACETS	0.837	0.685	1	0.837	0.685	1	CLONAL	1	TRUE	1	0.16	2		452	523	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911088	32911088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs864622476	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1217	68	1193	1	ENST00000380152.3:c.2596G>A	p.Glu866Lys	p.E866K	ENST00000380152		866	Gaa/Aaa	11/27	1	2	FACETS	0.661	0.573	0.758	0.661	0.573	0.758	SUBCLONAL	1	TRUE	1	0.16	2		1194	1285	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336269	73336269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	19	210	0	ENST00000377767.4:c.2134G>A	p.Glu712Lys	p.E712K	ENST00000377767	NM_014953.3	712	Gaa/Aaa	17/21	1	2	FACETS	1	0.784	1	1	0.784	1	CLONAL	1	TRUE	1	0.16	2		210	230	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103520501	103520501	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	55	607	0	ENST00000355739.4:c.2572C>A	p.Leu858Ile	p.L858I	ENST00000355739	NM_000123.3	858	Ctt/Att	12/15	1	2	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	TRUE	1	0.16	2		607	686	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68301849	68301849	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	70	629	0	ENST00000487270.1:c.251C>A	p.Ser84Tyr	p.S84Y	ENST00000487270	NM_133509.3	84	tCt/tAt	4/11	1	2	FACETS	0.943	0.82	1	0.943	0.82	1	CLONAL	1	TRUE	1	0.16	2		629	928	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609532	81609532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	50	597	0	ENST00000298171.2:c.1130C>T	p.Thr377Ile	p.T377I	ENST00000298171	NM_000369.2	377	aCt/aTt	10/10	1	2	FACETS	0.888	0.752	1	0.888	0.752	1	CLONAL	1	TRUE	1	0.16	2		597	704	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95599662	95599662	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	44	543	0	ENST00000393063.1:c.134G>T	p.Arg45Ile	p.R45I	ENST00000393063	NM_030621.3	45	aGa/aTa	3/28	1	2	FACETS	0.869	0.727	1	0.869	0.727	1	CLONAL	1	TRUE	1	0.16	2		543	633	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042400	42042400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1257	96	1332	1	ENST00000219905.7:c.6595G>A	p.Glu2199Lys	p.E2199K	ENST00000219905	NM_001164273.1	2199	Gag/Aag	17/24	1	2	FACETS	0.887	0.787	0.994	0.887	0.787	0.994	CLONAL	1	TRUE	1	0.16	2		1333	1353	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046766	42046766	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	63	814	0	ENST00000219905.7:c.7139+1G>A		p.X2380_splice	ENST00000219905	NM_001164273.1	2380			1	2	FACETS	0.74	0.638	0.852	0.74	0.638	0.852	SUBCLONAL	1	TRUE	1	0.16	2		814	1064	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007779	45007779	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	43	523	0	ENST00000558401.1:c.226T>G	p.Phe76Val	p.F76V	ENST00000558401	NM_004048.2	76	Ttc/Gtc	2/4	1	2	FACETS	0.687	0.573	0.814	0.687	0.573	0.814	SUBCLONAL	1	TRUE	1	0.16	2		523	782	SUCCESS
BLM	641	MSKCC	GRCh37	15	91352484	91352484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1031421025	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	30	272	0	ENST00000355112.3:c.3869C>T	p.Ser1290Leu	p.S1290L	ENST00000355112	NM_000057.2	1290	tCg/tTg	20/22	1	2	FACETS	0.762	0.613	0.932	0.762	0.613	0.932	CLONAL	1	TRUE	1	0.16	2		272	492	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129426	2129426	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514887	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	33	349	0	ENST00000219476.3:c.3281C>T	p.Ser1094Leu	p.S1094L	ENST00000219476	NM_000548.3	1094	tCg/tTg	28/42	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.16	2		349	365	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223241	2223241	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765441523	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	50	476	1	ENST00000326181.6:c.853G>A	p.Glu285Lys	p.E285K	ENST00000326181	NM_032271.2	285	Gag/Aag	10/21	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.16	2		477	538	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857834	9857834	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	75	892	1	ENST00000330684.3:c.3567G>T	p.Lys1189Asn	p.K1189N	ENST00000330684	NM_001134407.1	1189	aaG/aaT	13/13	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.16	2		893	842	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892164	9892164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776791010	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	56	677	3	ENST00000330684.3:c.2326G>A	p.Asp776Asn	p.D776N	ENST00000330684	NM_001134407.1	776	Gac/Aac	11/13	1	2	FACETS	0.975	0.834	1	0.975	0.834	1	CLONAL	1	TRUE	1	0.16	2		680	718	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619257	23619257	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	75	674	0	ENST00000261584.4:c.3278T>G	p.Ile1093Ser	p.I1093S	ENST00000261584	NM_024675.3	1093	aTt/aGt	12/13	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.16	2		674	836	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646545	23646545	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	23	313	0	ENST00000261584.4:c.1322A>C	p.Lys441Thr	p.K441T	ENST00000261584	NM_024675.3	441	aAa/aCa	4/13	1	2	FACETS	0.721	0.561	0.906	0.721	0.561	0.906	CLONAL	1	TRUE	1	0.16	2		313	399	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133282	30133282	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	74	842	0	ENST00000263025.4:c.216G>T	p.Lys72Asn	p.K72N	ENST00000263025	NM_002746.2	72	aaG/aaT	2/9	1	2	FACETS	0.93	0.812	1	0.93	0.812	1	CLONAL	1	TRUE	1	0.16	2		842	995	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650710	67650710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243010179	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	73	673	0	ENST00000264010.4:c.1015C>T	p.Arg339Trp	p.R339W	ENST00000264010	NM_006565.3	339	Cgg/Tgg	5/12	1	2	FACETS	0.912	0.795	1	0.912	0.795	1	CLONAL	1	TRUE	1	0.16	2		673	1001	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855985	68855985	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780759537	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	46	701	1	ENST00000261769.5:c.1793G>A	p.Arg598Gln	p.R598Q	ENST00000261769	NM_004360.3	598	cGa/cAa	12/16	1	2	FACETS	0.714	0.6	0.842	0.714	0.6	0.842	SUBCLONAL	1	TRUE	1	0.16	2		702	805	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827732	72827732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241554729	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	72	914	2	ENST00000268489.5:c.8849G>A	p.Arg2950His	p.R2950H	ENST00000268489	NM_006885.3	2950	cGc/cAc	9/10	1	2	FACETS	0.962	0.838	1	0.962	0.838	1	CLONAL	1	TRUE	1	0.16	2		916	936	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81939065	81939065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867345397	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	59	931	1	ENST00000359376.3:c.1420G>A	p.Glu474Lys	p.E474K	ENST00000359376	NM_002661.3	474	Gaa/Aaa	15/33	1	2	FACETS	0.743	0.638	0.86	0.743	0.638	0.86	SUBCLONAL	1	TRUE	1	0.16	2		932	992	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348352	89348352	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	69	1097	0	ENST00000301030.4:c.4598A>C	p.Lys1533Thr	p.K1533T	ENST00000301030	NM_001256183.1	1533	aAa/aCa	9/13	1	2	FACETS	0.763	0.662	0.872	0.763	0.662	0.872	SUBCLONAL	1	TRUE	1	0.16	2		1097	1131	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349860	89349860	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1241	85	1174	0	ENST00000301030.4:c.3090G>T	p.Glu1030Asp	p.E1030D	ENST00000301030	NM_001256183.1	1030	gaG/gaT	9/13	1	2	FACETS	0.801	0.706	0.905	0.801	0.706	0.905	CLONAL	1	TRUE	1	0.16	2		1174	1326	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976107	7976107	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	59	639	1	ENST00000319144.4:c.2088G>T	p.Glu696Asp	p.E696D	ENST00000319144	NM_001139.2	696	gaG/gaT	15/15	1	2	FACETS	0.889	0.763	1	0.889	0.763	1	CLONAL	1	TRUE	1	0.16	2		640	830	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16022796	16022796	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	31	472	0	ENST00000268712.3:c.1856C>A	p.Ser619Tyr	p.S619Y	ENST00000268712	NM_006311.3	619	tCt/tAt	17/46	1	2	FACETS	0.681	0.549	0.831	0.681	0.549	0.831	SUBCLONAL	1	TRUE	1	0.16	2		472	569	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042433	16042433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	33	631	3	ENST00000268712.3:c.1241G>A	p.Arg414Gln	p.R414Q	ENST00000268712	NM_006311.3	414	cGa/cAa	12/46	1	2	FACETS	0.632	0.513	0.766	0.632	0.513	0.766	SUBCLONAL	1	TRUE	1	0.16	2		634	653	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089995	16089995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150859090	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	22	267	0	ENST00000268712.3:c.115G>A	p.Ala39Thr	p.A39T	ENST00000268712	NM_006311.3	39	Gca/Aca	3/46	1	2	FACETS	0.743	0.575	0.939	0.743	0.575	0.939	CLONAL	1	TRUE	1	0.16	2		267	370	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118616	17118616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112980409	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	44	560	0	ENST00000285071.4:c.1315G>A	p.Val439Met	p.V439M	ENST00000285071	NM_144997.5	439	Gtg/Atg	12/14	1	2	FACETS	0.842	0.705	0.995	0.842	0.705	0.995	CLONAL	1	TRUE	1	0.16	2		560	653	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556403	29556403	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	36	440	3	ENST00000356175.3:c.2770G>T	p.Glu924Ter	p.E924*	ENST00000356175	NM_000267.3	924	Gaa/Taa	21/57	1	2	FACETS	0.835	0.685	1	0.835	0.685	1	CLONAL	1	TRUE	1	0.16	2		443	539	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683508	29683508	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	28	443	0	ENST00000356175.3:c.7583C>A	p.Ser2528Ter	p.S2528*	ENST00000356175	NM_000267.3	2528	tCa/tAa	51/57	1	2	FACETS	0.651	0.519	0.802	0.651	0.519	0.802	SUBCLONAL	1	TRUE	1	0.16	2		443	538	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740668	58740668	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs759850701	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	73	1176	1	ENST00000305921.3:c.1573G>T	p.Glu525Ter	p.E525*	ENST00000305921	NM_003620.3	525	Gaa/Taa	6/6	1	2	FACETS	0.748	0.652	0.853	0.748	0.652	0.853	SUBCLONAL	1	TRUE	1	0.16	2		1177	1220	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511714	66511714	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	42	348	0	ENST00000358598.2:c.174G>T	p.Glu58Asp	p.E58D	ENST00000358598	NM_212471.2	58	gaG/gaT	2/11	1	2	FACETS	0.91	0.759	1	0.91	0.759	1	CLONAL	1	TRUE	1	0.16	2		348	577	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229620	5229620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	31	118	0	ENST00000357368.4:c.2231C>T	p.Pro744Leu	p.P744L	ENST00000357368	NM_002850.3	744	cCc/cTc	15/38	1	2	FACETS	1	0.912	1	1	0.965	1	CLONAL	2	TRUE	1	0.16	2		118	161	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291167	10291167	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	51	729	1	ENST00000340748.4:c.304G>T	p.Glu102Ter	p.E102*	ENST00000340748		102	Gaa/Taa	4/40	1	2	FACETS	0.697	0.591	0.815	0.697	0.591	0.815	SUBCLONAL	1	TRUE	1	0.16	2		730	914	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291528	10291528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755995375	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	63	639	3	ENST00000340748.4:c.151G>A	p.Glu51Lys	p.E51K	ENST00000340748		51	Gaa/Aaa	3/40	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.16	2		642	778	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950294	17950294	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	51	568	0	ENST00000458235.1:c.1433G>T	p.Arg478Ile	p.R478I	ENST00000458235	NM_000215.3	478	aGa/aTa	10/24	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.16	2		568	626	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257874	19257874	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780635430	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	43	587	2	ENST00000162023.5:c.512G>A	p.Arg171Gln	p.R171Q	ENST00000162023		171	cGa/cAa	9/13	1	2	FACETS	0.78	0.651	0.924	0.78	0.651	0.924	CLONAL	1	TRUE	1	0.16	2		589	689	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906786	50906786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778843530	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	92	1060	1	ENST00000440232.2:c.1174G>A	p.Val392Met	p.V392M	ENST00000440232	NM_002691.3	392	Gtg/Atg	10/27	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.16	2		1061	1028	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52729224	52729224	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	56	545	2	ENST00000322088.6:c.1760C>A	p.Ser587Tyr	p.S587Y	ENST00000322088	NM_014225.5	587	tCt/tAt	15/15	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.16	2		547	570	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021439	31021439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs545224250	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	36	426	0	ENST00000375687.4:c.1438G>A	p.Glu480Lys	p.E480K	ENST00000375687	NM_015338.5	480	Gaa/Aaa	12/13	1	2	FACETS	0.9	0.739	1	0.9	0.739	1	CLONAL	1	TRUE	1	0.16	2		426	500	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023957	31023957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139435094	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	37	484	0	ENST00000375687.4:c.3442C>T	p.Arg1148Cys	p.R1148C	ENST00000375687	NM_015338.5	1148	Cgc/Tgc	13/13	1	2	FACETS	0.797	0.656	0.956	0.797	0.656	0.956	CLONAL	1	TRUE	1	0.16	2		484	580	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944523	40944523	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	30	632	1	ENST00000373198.4:c.1979C>A	p.Ser660Tyr	p.S660Y	ENST00000373198	NM_133170.3	660	tCt/tAt	12/32	1	2	FACETS	0.701	0.564	0.857	0.701	0.564	0.857	SUBCLONAL	1	TRUE	1	0.16	2		633	535	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306588	41306588	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	44	666	0	ENST00000373198.4:c.1071G>T	p.Glu357Asp	p.E357D	ENST00000373198	NM_133170.3	357	gaG/gaT	7/32	1	2	FACETS	0.995	0.833	1	0.995	0.833	1	CLONAL	1	TRUE	1	0.16	2		666	553	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268449	46268449	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	63	986	0	ENST00000371998.3:c.2836A>G	p.Asn946Asp	p.N946D	ENST00000371998		946	Aat/Gat	15/23	1	2	FACETS	0.781	0.674	0.899	0.781	0.674	0.899	SUBCLONAL	1	TRUE	1	0.16	2		986	1008	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231773	36231773	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1569061762	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	56	545	1	ENST00000300305.3:c.611G>A	p.Arg204Gln	p.R204Q	ENST00000300305		204	cGa/cAa	5/8	0.102146591090001	0	FACETS	0.741	0.634	0.86			1	SUBCLONAL	1	TRUE	0	0.16	0		546	793	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24134006	24134006	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	53	487	0	ENST00000263121.7:c.157C>T	p.Arg53Ter	p.R53*	ENST00000263121	NM_003073.3	53	Cga/Tga	2/9	1	2	FACETS	0.957	0.815	1	0.957	0.815	1	CLONAL	1	TRUE	1	0.16	2		487	692	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143241	24143241	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1232172026	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	50	656	2	ENST00000263121.7:c.473G>A	p.Arg158Gln	p.R158Q	ENST00000263121	NM_003073.3	158	cGa/cAa	4/9	1	2	FACETS	0.953	0.807	1	0.953	0.807	1	CLONAL	1	TRUE	1	0.16	2		658	656	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913563	39913563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754643148	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	55	763	0	ENST00000378444.4:c.4765C>T	p.Arg1589Cys	p.R1589C	ENST00000378444	NM_001123385.1	1589	Cgc/Tgc	13/15	0.102146591090001	0	FACETS	0.625	0.533	0.726			1	SUBCLONAL	1	TRUE	0	0.16	0		763	924	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044462	47044462	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	45	653	0	ENST00000377604.3:c.1959G>T	p.Lys653Asn	p.K653N	ENST00000377604	NM_001204468.1	653	aaG/aaT	18/24	0.102146591090001	0	FACETS	0.609	0.51	0.719			1	SUBCLONAL	1	TRUE	0	0.16	0		653	776	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650397	48650397	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	45	763	0	ENST00000376670.3:c.367G>T	p.Asp123Tyr	p.D123Y	ENST00000376670	NM_002049.3	123	Gat/Tat	3/6	0.102146591090001	0	FACETS	0.651	0.546	0.768			1	SUBCLONAL	1	TRUE	0	0.16	0		763	726	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224141	53224141	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	46	850	4	ENST00000375401.3:c.3410C>T	p.Ala1137Val	p.A1137V	ENST00000375401	NM_004187.3	1137	gCg/gTg	22/26	0.102146591090001	0	FACETS	0.581	0.488	0.685			1	SUBCLONAL	1	TRUE	0	0.16	0		854	831	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228018	53228018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199422238	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	59	853	3	ENST00000375401.3:c.2296C>T	p.Arg766Trp	p.R766W	ENST00000375401	NM_004187.3	766	Cgg/Tgg	16/26	0.102146591090001	0	FACETS	0.689	0.591	0.796			1	SUBCLONAL	1	TRUE	0	0.16	0		856	899	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410352	63410352	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	69	953	0	ENST00000330258.3:c.2815G>T	p.Glu939Ter	p.E939*	ENST00000330258	NM_152424.3	939	Gaa/Taa	2/2	0.102146591090001	0	FACETS	0.783	0.68	0.895			1	SUBCLONAL	1	TRUE	0	0.16	0		953	925	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412510	63412510	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	45	779	1	ENST00000330258.3:c.657G>T	p.Glu219Asp	p.E219D	ENST00000330258	NM_152424.3	219	gaG/gaT	2/2	0.102146591090001	0	FACETS	0.687	0.576	0.81			1	SUBCLONAL	1	TRUE	0	0.16	0		780	688	SUCCESS
AR	367	MSKCC	GRCh37	X	66943638	66943638	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	52	1053	2	ENST00000374690.3:c.2718G>T	p.Lys906Asn	p.K906N	ENST00000374690	NM_000044.3	906	aaG/aaT	8/8	0.102146591090001	0	FACETS	0.546	0.463	0.638			1	SUBCLONAL	1	TRUE	0	0.16	0		1055	1000	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339568	70339568	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	51	726	1	ENST00000374080.3:c.237G>T	p.Glu79Asp	p.E79D	ENST00000374080		79	gaG/gaT	3/45	0.102146591090001	0	FACETS	0.631	0.534	0.737			1	SUBCLONAL	1	TRUE	0	0.16	0		727	849	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608209	100608209	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	42	635	0	ENST00000308731.7:c.1881T>G	p.Tyr627Ter	p.Y627*	ENST00000308731	NM_000061.2	627	taT/taG	18/19	0.102146591090001	0	FACETS	0.625	0.52	0.741			1	SUBCLONAL	1	TRUE	0	0.16	0		635	706	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613381	100613381	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	44	608	1	ENST00000308731.7:c.1019C>A	p.Pro340His	p.P340H	ENST00000308731	NM_000061.2	340	cCt/cAt	12/19	0.102146591090001	0	FACETS	0.717	0.6	0.847			1	SUBCLONAL	1	TRUE	0	0.16	0		609	644	SUCCESS
BTK	695	MSKCC	GRCh37	X	100624989	100624989	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	53	542	0	ENST00000308731.7:c.388A>C	p.Asn130His	p.N130H	ENST00000308731	NM_000061.2	130	Aac/Cac	5/19	0.102146591090001	0	FACETS	0.875	0.745	1			1	CLONAL	1	TRUE	0	0.16	0		542	636	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179125	123179125	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	43	694	2	ENST00000218089.9:c.574T>C	p.Tyr192His	p.Y192H	ENST00000218089	NM_001042749.1	192	Tat/Cat	8/35	0.102146591090001	0	FACETS	0.728	0.608	0.862			1	SUBCLONAL	1	TRUE	0	0.16	0		696	620	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656332	18656333	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	27	385	0	ENST00000266497.5:c.3014dup	p.Ala1006GlyfsTer4	p.A1006Gfs*4	ENST00000266497		1004	tta/ttAa	21/31	0.3	1	FACETS	0.654	0.519	0.808	0.654	0.519	0.808	SUBCLONAL	1	TRUE	0	0.16	1		385	475	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0010980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	197	379	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.313771529660002	3	FACETS	0.878	0.815	0.943	0.878	0.815	0.943	CLONAL	2	TRUE	1	0.335544161868341	3		379	781	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11552822	NA	P-0010980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	100	344	0	ENST00000304494.5:c.250G>T	p.Asp84Tyr	p.D84Y	ENST00000304494	NM_000077.4	84	Gac/Tac	2/3	0.335544161868341	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.335544161868341	1		344	436	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222987	1222987	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	78	400	1	ENST00000326873.7:c.924G>T	p.Trp308Cys	p.W308C	ENST00000326873	NM_000455.4	308	tgG/tgT	8/10	0.335544161868341	1	FACETS	0.906	0.8	1	0.906	0.8	1	CLONAL	1	TRUE	0	0.335544161868341	1		401	427	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098601	11098601	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0010980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	131	518	0	ENST00000358026.2:c.1118+1G>T		p.X373_splice	ENST00000358026	NM_001128849.1	373			0.335544161868341	1	FACETS	0.966	0.878	1	0.966	0.878	1	CLONAL	1	TRUE	0	0.335544161868341	1		518	673	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164513	47164513	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	156	610	0	ENST00000409792.3:c.1613G>T	p.Gly538Val	p.G538V	ENST00000409792	NM_014159.6	538	gGa/gTa	3/21	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.335544161868341	2		610	922	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288645	33288645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs865973372	NA	P-0010980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	171	364	0	ENST00000374542.5:c.907G>A	p.Gly303Ser	p.G303S	ENST00000374542	NM_001141970.1	303	Ggc/Agc	3/8	0.313771529660002	3	FACETS	0.907	0.838	0.979	0.907	0.838	0.979	CLONAL	2	TRUE	1	0.335544161868341	3		364	656	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602737	10602737	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	185	602	0	ENST00000171111.5:c.841C>A	p.Leu281Met	p.L281M	ENST00000171111	NM_203500.1	281	Ctg/Atg	3/6	0.335544161868341	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.335544161868341	1		602	912	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411922	63411922	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1410	282	1187	1	ENST00000330258.3:c.1245G>T	p.Met415Ile	p.M415I	ENST00000330258	NM_152424.3	415	atG/atT	2/2	1	2	FACETS	0.993	0.93	1	0.993	0.93	1	CLONAL	1	TRUE	1	0.335544161868341	2		1188	1692	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845854	72845855	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1266	266	957	0	ENST00000268489.5:c.3612dup	p.Pro1205SerfsTer11	p.P1205Sfs*11	ENST00000268489	NM_006885.3	1204	-/T	6/10	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.335544161868341	2		957	1532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0011029-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	690	478	0	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	0.561407187742647	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.557440542662262	3		478	967	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55270295	55270295	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011029-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	543	646	0	ENST00000275493.2:c.3248A>G	p.Asp1083Gly	p.D1083G	ENST00000275493	NM_005228.3	1083	gAc/gGc	27/28	0.512822069669613	5	FACETS	1	0.98	1	0.691	0.662	0.72	CLONAL	2	TRUE	2	0.557440542662262	5		646	1726	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778879	76778880	+	stop_gained,inframe_insertion,splice_region_variant	Nonsense_Mutation	INS	-	-	TTA	novel	NA	P-0011029-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	324	521	0	ENST00000373344.5:c.6700-1_6700insTAA	p.Lys2233_Asp2234insTer	p.K2233_D2234ins*	ENST00000373344	NM_000489.3	2233	-/TAA		0.561407187742647	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.557440542662262	2		521	574	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	66	588	1	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	0.985	1	CLONAL	3	TRUE	1	0.11	2		589	399	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	76	442	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.143980858401617	3	FACETS	1	0.922	1	1	0.984	1	CLONAL	4	TRUE	1	0.11	3		444	345	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	118	703	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.143980858401617	3	FACETS	1	0.964	1	1	0.987	1	CLONAL	3	TRUE	1	0.11	3		704	661	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	92	463	1	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	0.272045305625353	4	FACETS	0.861	0.765	0.963	1	0.971	1	CLONAL	3	TRUE	2	0.11	4		464	719	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436026	56436026	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771831816	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	54	308	1	ENST00000407977.2:c.1111C>T	p.Arg371Ter	p.R371*	ENST00000407977		371	Cga/Tga	9/10	0.143980858401617	3	FACETS	1	0.919	1	1	0.979	1	CLONAL	4	TRUE	1	0.11	3		309	237	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216477	108216477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587782558	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	45	413	1	ENST00000278616.4:c.8432del	p.Lys2811SerfsTer46	p.K2811Sfs*46	ENST00000278616	NM_000051.3	2809	cAa/ca	58/63	1	2	FACETS	0.885	0.748	1	1	0.977	1	CLONAL	3	TRUE	1	0.11	2		414	308	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	42	359	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.913	1	1	0.972	1	CLONAL	2	TRUE	1	0.11	2		360	334	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	64	386	3	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	0.143980858401617	3	FACETS	0.909	0.796	1	1	0.982	1	CLONAL	5	TRUE	1	0.11	3		389	270	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850704	63850705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	50	390	3	ENST00000279873.7:c.1489dup	p.Ile497AsnfsTer31	p.I497Nfs*31	ENST00000279873	NM_032199.2	494	-/A	10/10	0.3	6	FACETS	1	0.924	1			1	CLONAL	2	TRUE	NA	0.11	6		393	483	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884218	37884218	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	98	430	0	ENST00000269571.5:c.3694del	p.Ala1232LeufsTer70	p.A1232Lfs*70	ENST00000269571		1230	cGg/cg	27/27	0.143980858401617	3	FACETS	1	0.916	1	1	0.987	1	CLONAL	4	TRUE	1	0.11	3		430	459	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279861	46279866	+	inframe_deletion	In_Frame_Del	DEL	CAGCAA	CAGCAA	-	rs748517056	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	16	320	0	ENST00000371998.3:c.3810_3815del	p.Gln1275_Gln1276del	p.Q1275_Q1276del	ENST00000371998		1263	CAGCAA/-	20/23	1	2	FACETS	1	0.801	1	1	0.801	1	CLONAL	1	TRUE	1	0.11	2		320	264	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	96	385	3	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.963	0.863	1	1	0.99	1	CLONAL	4	TRUE	1	0.11	2		388	453	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795103	242795104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs768249210	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	47	407	0	ENST00000334409.5:c.105dup	p.Thr36HisfsTer70	p.T36Hfs*70	ENST00000334409	NM_005018.2	35	-/C	2/5	1	2	FACETS	1	0.938	1	1	0.976	1	CLONAL	2	TRUE	1	0.11	2		407	349	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482927	140482927	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	42	380	2	ENST00000288602.6:c.1208del	p.Pro403LeufsTer8	p.P403Lfs*8	ENST00000288602	NM_004333.4	403	cCt/ct	10/18	1	2	FACETS	1	0.92	1	1	0.973	1	CLONAL	2	TRUE	1	0.11	2		382	327	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646085	215646085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	33	392	0	ENST00000260947.4:c.513del	p.Asp172MetfsTer40	p.D172Mfs*40	ENST00000260947	NM_000465.2	171	aaA/aa	4/11	1	2	FACETS	1	0.843	1	1	0.962	1	CLONAL	2	TRUE	1	0.11	2		392	290	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551677	150551679	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs587760643	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	72	204	0	ENST00000369026.2:c.328_330del	p.Glu110del	p.E110del	ENST00000369026	NM_021960.4	110	GAG/-	1/3	0.3	15	FACETS	1	0.915	1			1	CLONAL	5	TRUE	NA	0.11	15		204	426	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120326	94120326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370195460	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	58	610	2	ENST00000369303.4:c.725C>T	p.Ala242Val	p.A242V	ENST00000369303	NM_004440.3	242	gCg/gTg	3/17	0.143980858401617	3	FACETS	1	0.887	1	1	0.887	1	CLONAL	2	TRUE	1	0.11	3		612	537	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411071	63411071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750971248	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	48	272	0	ENST00000330258.3:c.2096G>A	p.Arg699His	p.R699H	ENST00000330258	NM_152424.3	699	cGt/cAt	2/2	1	1	FACETS	1	0.901	1	1	0.983	1	CLONAL	5	TRUE	0	0.11	1		272	156	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671654	67671655	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	61	495	1	ENST00000264010.4:c.2070dup	p.Glu691ArgfsTer5	p.E691Rfs*5	ENST00000264010	NM_006565.3	688	gta/gtAa	12/12	1	2	FACETS	1	0.901	1	1	0.984	1	CLONAL	3	TRUE	1	0.11	2		496	353	SUCCESS
APC	324	MSKCC	GRCh37	5	112164664	112164664	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1060503259	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	23	188	0	ENST00000257430.4:c.1742del	p.Lys581ArgfsTer9	p.K581Rfs*9	ENST00000257430	NM_000038.5	580	Aaa/aa	14/16	1	2	FACETS	0.877	0.69	1	1	0.955	1	CLONAL	3	TRUE	1	0.11	2		188	159	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480538	120480538	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	56	453	0	ENST00000256646.2:c.3279G>T	p.Trp1093Cys	p.W1093C	ENST00000256646	NM_024408.3	1093	tgG/tgT	20/34	1	2	FACETS	1	0.905	1	1	0.978	1	CLONAL	2	TRUE	1	0.11	2		453	475	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870264	155870264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376391961	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	122	619	0	ENST00000368323.3:c.575C>T	p.Ala192Val	p.A192V	ENST00000368323	NM_006912.5	192	gCc/gTc	6/6	1	2	FACETS	1	0.93	1	1	0.992	1	CLONAL	3	TRUE	1	0.11	2		619	716	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872663	136872663	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	142	748	0	ENST00000241393.3:c.835A>G	p.Thr279Ala	p.T279A	ENST00000241393	NM_003467.2	279	Act/Gct	2/2	1	2	FACETS	1	0.977	1	1	0.992	1	CLONAL	2	TRUE	1	0.11	2		748	1052	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151314	202151314	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	41	443	0	ENST00000358485.4:c.1614T>A	p.Asp538Glu	p.D538E	ENST00000358485	NM_001080125.1	538	gaT/gaA	9/9	1	2	FACETS	1	0.862	1	1	0.969	1	CLONAL	2	TRUE	1	0.11	2		443	360	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035151	37035151	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587778888	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	97	188	0	ENST00000231790.2:c.113A>G	p.Asn38Ser	p.N38S	ENST00000231790	NM_000249.3	38	aAc/aGc	1/19	0.391673603089027	3	FACETS	0.96	0.865	1	1	0.99	1	CLONAL	6	TRUE	1	0.11	3		188	323	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266190	41266190	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	36	381	0	ENST00000349496.5:c.187C>A	p.Leu63Met	p.L63M	ENST00000349496	NM_001904.3	63	Ctg/Atg	3/15	0.391673603089027	3	FACETS	1	0.915	1	1	0.915	1	CLONAL	2	TRUE	1	0.11	3		381	290	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094943	143094943	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	36	375	0	ENST00000262992.4:c.1201T>C	p.Tyr401His	p.Y401H	ENST00000262992	NM_001101669.1	401	Tac/Cac	14/24	1	2	FACETS	0.846	0.699	1	1	0.97	1	CLONAL	3	TRUE	1	0.11	2		375	258	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866579	117866579	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	74	768	0	ENST00000297338.2:c.1066C>T	p.Pro356Ser	p.P356S	ENST00000297338	NM_006265.2	356	Ccc/Tcc	9/14	1	2	FACETS	1	0.95	1	1	0.984	1	CLONAL	2	TRUE	1	0.11	2		768	575	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319965	8319965	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs141403124	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	23	292	0	ENST00000356435.5:c.5536G>A	p.Ala1846Thr	p.A1846T	ENST00000356435		1846	Gcg/Acg	34/35	1	2	FACETS	0.89	0.696	1	1	0.939	1	CLONAL	2	TRUE	1	0.11	2		292	235	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549230	21549230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113238499	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	87	703	0	ENST00000382592.4:c.3046G>A	p.Glu1016Lys	p.E1016K	ENST00000382592	NM_014572.2	1016	Gaa/Aaa	8/8	0.3	1	FACETS	0.837	0.742	0.939	1	0.987	1	CLONAL	3	TRUE	0	0.11	1		703	595	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865792	56865792	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	83	732	1	ENST00000308159.5:c.1124A>G	p.Tyr375Cys	p.Y375C	ENST00000308159	NM_014669.4	375	tAc/tGc	11/22	1	2	FACETS	0.858	0.759	0.965	1	0.987	1	CLONAL	3	TRUE	1	0.11	2		733	586	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127424	17127424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372918705	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	47	357	1	ENST00000285071.4:c.430G>A	p.Gly144Arg	p.G144R	ENST00000285071	NM_144997.5	144	Gga/Aga	6/14	0.143980858401617	3	FACETS	1	0.921	1	1	0.921	1	CLONAL	2	TRUE	1	0.11	3		358	393	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436098	56436098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780224400	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	134	521	1	ENST00000407977.2:c.1039G>A	p.Gly347Ser	p.G347S	ENST00000407977		347	Ggc/Agc	9/10	0.143980858401617	3	FACETS	0.945	0.86	1	1	0.99	1	CLONAL	4	TRUE	1	0.11	3		522	680	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210796	5210796	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758652323	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	42	389	0	ENST00000357368.4:c.5255C>T	p.Ala1752Val	p.A1752V	ENST00000357368	NM_002850.3	1752	gCg/gTg	34/38	1	2	FACETS	1	0.849	1	1	0.977	1	CLONAL	3	TRUE	1	0.11	2		389	252	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265313	10265313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762421501	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	57	420	0	ENST00000340748.4:c.1733C>T	p.Thr578Ile	p.T578I	ENST00000340748		578	aCa/aTa	20/40	1	2	FACETS	1	0.947	1	1	0.98	1	CLONAL	2	TRUE	1	0.11	2		420	424	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118683	11118683	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555771662	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	124	528	0	ENST00000358026.2:c.2107G>A	p.Ala703Thr	p.A703T	ENST00000358026	NM_001128849.1	703	Gcg/Acg	14/36	1	2	FACETS	1	0.956	1	1	0.992	1	CLONAL	3	TRUE	1	0.11	2		528	688	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52729010	52729010	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	53	434	0	ENST00000322088.6:c.1702A>G	p.Thr568Ala	p.T568A	ENST00000322088	NM_014225.5	568	Acc/Gcc	14/15	1	2	FACETS	0.857	0.733	0.991	1	0.98	1	CLONAL	3	TRUE	1	0.11	2		434	375	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504029	123504029	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	13	186	0	ENST00000371139.4:c.205G>A	p.Ala69Thr	p.A69T	ENST00000371139	NM_001114937.2	69	Gca/Aca	3/4	1	1	FACETS	0.955	0.687	1	1	0.904	1	CLONAL	2	TRUE	0	0.11	1		186	117	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725019	47725019	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs762488821	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	135	573	0	ENST00000449228.1:c.725del	p.Gly242AlafsTer48	p.G242Afs*48	ENST00000449228	NM_001127240.2	242	gGc/gc	4/4	1	2	FACETS	0.893	0.813	0.977	1	0.993	1	CLONAL	4	TRUE	1	0.11	2		573	687	SUCCESS
APC	324	MSKCC	GRCh37	5	112170660	112170660	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554083100	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	38	323	0	ENST00000257430.4:c.1759del	p.Ser587AlafsTer3	p.S587Afs*3	ENST00000257430	NM_000038.5	586	Aaa/aa	15/16	1	2	FACETS	0.98	0.816	1	1	0.974	1	CLONAL	3	TRUE	1	0.11	2		323	235	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240271	5240271	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	62	483	0	ENST00000357368.4:c.1643del	p.Pro548ArgfsTer37	p.P548Rfs*37	ENST00000357368	NM_002850.3	548	cCg/cg	12/38	1	2	FACETS	1	0.872	1	1	0.984	1	CLONAL	3	TRUE	1	0.11	2		483	374	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620442	52620442	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	43	355	0	ENST00000394830.3:c.3311del	p.Lys1104ArgfsTer30	p.K1104Rfs*30	ENST00000394830	NM_018313.4	1104	aAg/ag	21/30	0.391673603089027	3	FACETS	1	0.909	1	1	0.909	1	CLONAL	2	TRUE	1	0.11	3		355	366	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437288	220437288	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1190141661	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	100	712	2	ENST00000243786.2:c.197del	p.Gly66AlafsTer61	p.G66Afs*61	ENST00000243786	NM_002191.3	64	ctG/ct	1/2	1	2	FACETS	1	0.951	1	1	0.99	1	CLONAL	3	TRUE	1	0.11	2		714	549	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991709	72991711	+	inframe_deletion	In_Frame_Del	DEL	GCA	GCA	-	rs752963945	NA	P-0011068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	36	249	0	ENST00000268489.5:c.2334_2336del	p.Ala784del	p.A784del	ENST00000268489	NM_006885.3	778	gcTGCg/gcg	2/10	1	2	FACETS	1	0.923	1	1	0.97	1	CLONAL	2	TRUE	1	0.11	2		249	267	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0011149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	260	439	1	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.33507711580124	2		440	631	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849038	156849038	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	634	490	0	ENST00000524377.1:c.1930C>A	p.Leu644Met	p.L644M	ENST00000524377	NM_002529.3	644	Ctg/Atg	15/17	0.33507711580124	8	FACETS	0.996	0.962	1			1	CLONAL	6	TRUE	NA	0.33507711580124	8		490	1270	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735454	204735454	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	211	438	0	ENST00000302823.3:c.255T>G	p.Cys85Trp	p.C85W	ENST00000302823	NM_005214.4	85	tgT/tgG	2/4	0.33507711580124	3	FACETS	0.928	0.864	0.994	0.928	0.864	0.994	CLONAL	2	TRUE	1	0.33507711580124	3		438	792	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661425	227661425	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	179	349	0	ENST00000305123.5:c.2030G>T	p.Gly677Val	p.G677V	ENST00000305123	NM_005544.2	677	gGt/gTt	1/2	0.33507711580124	3	FACETS	0.931	0.861	1	0.931	0.861	1	CLONAL	2	TRUE	1	0.33507711580124	3		349	670	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249062	55249062	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	100	436	0	ENST00000275493.2:c.2360A>T	p.Gln787Leu	p.Q787L	ENST00000275493	NM_005228.3	787	cAg/cTg	20/28	0.32095701310142	4	FACETS	0.985	0.879	1	0.328	0.293	0.366	CLONAL	1	TRUE	1	0.33507711580124	4		436	809	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544180	18544180	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	205	413	0	ENST00000266497.5:c.1997C>A	p.Pro666His	p.P666H	ENST00000266497		666	cCc/cAc	13/31	NA	2	FACETS	0.841	0.788	0.894			1	INDETERMINATE	3	TRUE	NA	0.33507711580124	2		413	485	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434732	49434732	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767236217	NA	P-0011149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	218	477	0	ENST00000301067.7:c.6821C>T	p.Ser2274Leu	p.S2274L	ENST00000301067	NM_003482.3	2274	tCg/tTg	31/54	0.33507711580124	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	1	0.33507711580124	3		477	740	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858960	57858960	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	321	882	0	ENST00000228682.2:c.456G>C	p.Gln152His	p.Q152H	ENST00000228682	NM_005269.2	152	caG/caC	5/12	0.33507711580124	3	FACETS	0.945	0.893	1	0.945	0.893	1	CLONAL	2	TRUE	1	0.33507711580124	3		882	1183	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78811798	78811798	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0011149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	168	367	0	ENST00000306801.3:c.1212+1G>C		p.X404_splice	ENST00000306801	NM_020761.2	404			0.33507711580124	3	FACETS	0.912	0.841	0.985	0.912	0.841	0.985	CLONAL	2	TRUE	1	0.33507711580124	3		367	642	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218415	1218415	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs112675807	NA	P-0011149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	193	506	0	ENST00000326873.7:c.291-1G>T		p.X97_splice	ENST00000326873	NM_000455.4	97			0.31696778867138	2	FACETS	0.892	0.829	0.956	0.892	0.829	0.956	CLONAL	2	TRUE	0	0.33507711580124	2		506	646	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600471	10600471	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	208	455	0	ENST00000171111.5:c.1384G>T	p.Gly462Trp	p.G462W	ENST00000171111	NM_203500.1	462	Ggg/Tgg	4/6	0.31696778867138	2	FACETS	0.943	0.88	1	0.943	0.88	1	CLONAL	2	TRUE	0	0.33507711580124	2		455	658	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436854	110436855	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0011149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	71	294	0	ENST00000375856.3:c.1545_1546dup	p.His516ProfsTer29	p.H516Pfs*29	ENST00000375856	NM_003749.2	516	cac/cCCac	1/2	0.33507711580124	2	FACETS	0.938	0.821	1	0.469	0.41	0.531	CLONAL	1	TRUE	0	0.33507711580124	2		294	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0011181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	758	302	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.479393489290437	4	FACETS	1	0.993	1			1	CLONAL	4	TRUE	NA	0.535166322135443	4		302	1047	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941715	48941716	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0011181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	198	249	0	ENST00000267163.4:c.1027_1028del	p.Leu343SerfsTer3	p.L343Sfs*3	ENST00000267163	NM_000321.2	342	aCT/a	10/27	0.5251964912986	2	FACETS	0.849	0.796	0.902	0.849	0.796	0.902	CLONAL	2	TRUE	0	0.535166322135443	2		249	436	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970944	55970944	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	337	563	0	ENST00000263923.4:c.1853C>G	p.Ser618Cys	p.S618C	ENST00000263923	NM_002253.2	618	tCt/tGt	13/30	0.535166322135443	3	FACETS	1	0.985	1	0.561	0.529	0.593	CLONAL	1	TRUE	1	0.535166322135443	3		563	1423	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912163	29912163	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	68	101	0	ENST00000376809.5:c.884C>A	p.Thr295Asn	p.T295N	ENST00000376809	NM_002116.7	295	aCc/aAc	4/8	0.535166322135443	7	FACETS	0.923	0.802	1			1	CLONAL	1	TRUE	NA	0.535166322135443	7		101	644	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509606	106509606	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	304	489	0	ENST00000359195.3:c.1600C>A	p.Pro534Thr	p.P534T	ENST00000359195	NM_002649.2	534	Ccc/Acc	2/11	0.535166322135443	3	FACETS	1	0.966	1	0.519	0.488	0.551	CLONAL	1	TRUE	1	0.535166322135443	3		489	1388	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400006	139400006	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	907	485	1	ENST00000277541.6:c.4342G>A	p.Ala1448Thr	p.A1448T	ENST00000277541	NM_017617.3	1448	Gcg/Acg	25/34	0.529614539733798	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.535166322135443	3		486	1405	SUCCESS
CBL	867	MSKCC	GRCh37	11	119167705	119167705	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	674	587	0	ENST00000264033.4:c.2114C>G	p.Ser705Cys	p.S705C	ENST00000264033	NM_005188.3	705	tCc/tGc	13/16	0.535166322135443	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.535166322135443	3		587	1544	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480090	50480090	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	215	429	0	ENST00000394963.4:c.324C>G	p.Ile108Met	p.I108M	ENST00000394963	NM_003076.4	108	atC/atG	2/13	0.486174571211832	3	FACETS	0.981	0.912	1	0.491	0.456	0.527	CLONAL	1	TRUE	1	0.535166322135443	3		429	1038	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868097	45868097	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs767895008	NA	P-0011181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	231	433	0	ENST00000391945.4:c.593C>T	p.Ser198Leu	p.S198L	ENST00000391945	NM_000400.3	198	tCa/tTa	7/23	0.452664429287342	4	FACETS	0.933	0.867	1	0.466	0.433	0.501	CLONAL	1	TRUE	2	0.535166322135443	4		433	1421	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162475207	162475208	+	splice_acceptor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0011181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	324	415	0	ENST00000366898.1:c.535-2dup		p.X179_splice	ENST00000366898	NM_004562.2	179			0.535166322135443	4	FACETS	0.828	0.783	0.875	0.828	0.783	0.875	CLONAL	2	TRUE	2	0.535166322135443	4		415	1122	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0011235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	296	435	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.357997990644868	3	FACETS	0.885	0.833	0.937	0.885	0.833	0.937	CLONAL	2	TRUE	1	0.361480070373738	3		436	1093	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056588	26056590	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs751086925	NA	P-0011235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	63	159	0	ENST00000343677.2:c.67_69del	p.Lys23del	p.K23del	ENST00000343677	NM_005319.3	23	AAG/-	1/1	1	2	FACETS	0.901	0.782	1	0.901	0.782	1	CLONAL	1	TRUE	1	0.361480070373738	2		159	387	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772950	135772951	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs118203724	NA	P-0011235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	47	392	1	ENST00000298552.3:c.2672dup	p.Asn891LysfsTer13	p.N891Kfs*13	ENST00000298552	NM_001162426.1	891	aac/aaAc	21/23	1	2	FACETS	0.278	0.233	0.327	0.278	0.233	0.327	SUBCLONAL	1	TRUE	1	0.361480070373738	2		393	937	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759623	133759623	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	201	452	2	ENST00000318560.5:c.1950del	p.Leu651TrpfsTer43	p.L651Wfs*43	ENST00000318560	NM_005157.4	649	aCc/ac	11/11	1	2	FACETS	0.938	0.868	1	0.938	0.868	1	CLONAL	1	TRUE	1	0.361480070373738	2		454	1185	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612948	228612948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750781461	NA	P-0011235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	271	515	1	ENST00000366696.1:c.79C>T	p.Arg27Cys	p.R27C	ENST00000366696	NM_003493.2	27	Cgc/Tgc	1/1	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.361480070373738	2		516	1351	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268793	41268793	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	56	324	0	ENST00000349496.5:c.1031T>C	p.Leu344Pro	p.L344P	ENST00000349496	NM_001904.3	344	cTg/cCg	7/15	1	2	FACETS	0.313	0.267	0.363	0.313	0.267	0.363	SUBCLONAL	1	TRUE	1	0.361480070373738	2		324	991	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526163	189526163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	223	413	0	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	0.361480070373738	2		413	1184	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961103	55961103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140041720	NA	P-0011235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	169	359	0	ENST00000263923.4:c.2837G>A	p.Arg946His	p.R946H	ENST00000263923	NM_002253.2	946	cGt/cAt	21/30	1	2	FACETS	0.934	0.858	1	0.934	0.858	1	CLONAL	1	TRUE	1	0.361480070373738	2		359	1001	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967193	93967193	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs983485848	NA	P-0011235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	183	484	0	ENST00000369303.4:c.2159A>G	p.Asp720Gly	p.D720G	ENST00000369303	NM_004440.3	720	gAt/gGt	12/17	1	2	FACETS	0.831	0.765	0.899	0.831	0.765	0.899	CLONAL	1	TRUE	1	0.361480070373738	2		484	1219	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877208	151877208	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	92	188	0	ENST00000262189.6:c.7153C>T	p.Gln2385Ter	p.Q2385*	ENST00000262189	NM_170606.2	2385	Cag/Tag	37/59	0.357997990644868	3	FACETS	1	0.916	1	0.517	0.46	0.578	CLONAL	1	TRUE	1	0.361480070373738	3		188	581	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342437	118342437	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	52	350	0	ENST00000534358.1:c.563C>T	p.Ala188Val	p.A188V	ENST00000534358	NM_005933.3	188	gCt/gTt	3/36	1	2	FACETS	0.289	0.245	0.338	0.289	0.245	0.338	SUBCLONAL	1	TRUE	1	0.361480070373738	2		350	995	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432787	432787	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	141	286	0	ENST00000399788.2:c.2129C>A	p.Pro710His	p.P710H	ENST00000399788	NM_001042603.1	710	cCc/cAc	15/28	0.357997990644868	3	FACETS	0.989	0.901	1	0.495	0.45	0.542	CLONAL	1	TRUE	1	0.361480070373738	3		286	931	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235941	133235941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	174	360	0	ENST00000320574.5:c.3215C>T	p.Ala1072Val	p.A1072V	ENST00000320574	NM_006231.2	1072	gCa/gTa	26/49	0.357997990644868	3	FACETS	0.99	0.91	1	0.495	0.455	0.537	CLONAL	1	TRUE	1	0.361480070373738	3		360	1148	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28931807	28931807	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	166	373	0	ENST00000282397.4:c.2132C>T	p.Pro711Leu	p.P711L	ENST00000282397	NM_002019.4	711	cCa/cTa	15/30	1	2	FACETS	0.948	0.87	1	0.948	0.87	1	CLONAL	1	TRUE	1	0.361480070373738	2		373	969	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061484	38061484	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	177	314	0	ENST00000250448.2:c.505G>A	p.Ala169Thr	p.A169T	ENST00000250448	NM_004496.3	169	Gcc/Acc	2/2	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.361480070373738	2		314	881	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134632	2134632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500969	NA	P-0011235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	151	346	1	ENST00000219476.3:c.4409G>A	p.Arg1470His	p.R1470H	ENST00000219476	NM_000548.3	1470	cGc/cAc	34/42	1	2	FACETS	0.924	0.845	1	0.924	0.845	1	CLONAL	1	TRUE	1	0.361480070373738	2		347	904	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348806	11348806	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	19	108	0	ENST00000332029.2:c.530T>C	p.Leu177Pro	p.L177P	ENST00000332029	NM_003745.1	177	cTg/cCg	2/2	1	2	FACETS	0.322	0.244	0.414	0.322	0.244	0.414	SUBCLONAL	1	TRUE	1	0.361480070373738	2		108	326	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512401	38512401	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1441911200	NA	P-0011235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	67	308	0	ENST00000254066.5:c.1312G>C	p.Ala438Pro	p.A438P	ENST00000254066	NM_000964.3	438	Gcc/Ccc	9/9	1	2	FACETS	0.406	0.352	0.465	0.406	0.352	0.465	SUBCLONAL	1	TRUE	1	0.361480070373738	2		308	913	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120199	70120199	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	49	315	0	ENST00000245479.2:c.1201C>T	p.Gln401Ter	p.Q401*	ENST00000245479	NM_000346.3	401	Cag/Tag	3/3	1	2	FACETS	0.296	0.249	0.347	0.296	0.249	0.347	SUBCLONAL	1	TRUE	1	0.361480070373738	2		315	917	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291782	15291782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs940948912	NA	P-0011235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	159	298	0	ENST00000263388.2:c.2984C>T	p.Pro995Leu	p.P995L	ENST00000263388	NM_000435.2	995	cCg/cTg	18/33	1	2	FACETS	0.937	0.858	1	0.937	0.858	1	CLONAL	1	TRUE	1	0.361480070373738	2		298	939	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412635	63412635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376626895	NA	P-0011235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	153	432	2	ENST00000330258.3:c.532C>T	p.Arg178Cys	p.R178C	ENST00000330258	NM_152424.3	178	Cgt/Tgt	2/2	1	2	FACETS	0.777	0.709	0.847	0.777	0.709	0.847	SUBCLONAL	1	TRUE	1	0.361480070373738	2		434	1090	SUCCESS
CBL	867	MSKCC	GRCh37	11	119145603	119145604	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0011235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	201	331	0	ENST00000264033.4:c.815dup	p.Leu272PhefsTer4	p.L272Ffs*4	ENST00000264033	NM_005188.3	270	gct/gcTt	5/16	1	2	FACETS	0.966	0.894	1	0.966	0.894	1	CLONAL	1	TRUE	1	0.361480070373738	2		331	1151	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415640	152415641	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCA	novel	NA	P-0011235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	130	368	0	ENST00000206249.3:c.1500_1502dup	p.Gln500dup	p.Q500dup	ENST00000206249	NM_000125.3	500	ctg/ctGCAg	7/8	1	2	FACETS	0.751	0.68	0.825	0.751	0.68	0.825	SUBCLONAL	1	TRUE	1	0.361480070373738	2		368	958	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	254	526	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.944	0.885	1	0.944	0.885	1	CLONAL	1	TRUE	1	0.611126694120872	2		526	881	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	220	498	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.842	0.785	0.901	0.842	0.785	0.901	CLONAL	1	TRUE	1	0.611126694120872	2		498	855	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	261	302	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.913	0.868	0.957	1	0.995	1	CLONAL	2	TRUE	1	0.611126694120872	2		302	468	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	254	342	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.611126694120872	2		342	776	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573505	48573506	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	129	600	0	ENST00000342988.3:c.94_95del	p.Ser32Ter	p.S32*	ENST00000342988	NM_005359.5	30	gGA/g	2/12	NA	2	FACETS	0.395	0.357	0.434			1	INDETERMINATE	1	TRUE	NA	0.611126694120872	2		600	1070	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	346	368	3	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.973	0.921	1	0.973	0.921	1	CLONAL	1	TRUE	1	0.611126694120872	2		371	1164	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	21	359	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.086	0.065	0.11	0.086	0.065	0.11	SUBCLONAL	1	TRUE	1	0.611126694120872	2		360	799	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660469	67660469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	258	516	2	ENST00000264010.4:c.1369C>T	p.Arg457Ter	p.R457*	ENST00000264010	NM_006565.3	457	Cga/Tga	8/12	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.611126694120872	2		518	833	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	215	386	3	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.937	0.874	1	0.937	0.874	1	CLONAL	1	TRUE	1	0.611126694120872	2		389	751	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867541	35867541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	173	363	0	ENST00000303115.3:c.361del	p.Ile121Ter	p.I121*	ENST00000303115	NM_002185.3	119	Aaa/aa	3/8	1	2	FACETS	0.844	0.779	0.91	0.844	0.779	0.91	CLONAL	1	TRUE	1	0.611126694120872	2		363	671	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522741	67522741	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	54	450	0	ENST00000274335.5:c.244del	p.Ile82SerfsTer32	p.I82Sfs*32	ENST00000274335		80	Aaa/aa	1/15	1	2	FACETS	0.279	0.238	0.324	0.279	0.238	0.324	SUBCLONAL	1	TRUE	1	0.611126694120872	2		450	633	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874530	155874530	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs869025191	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	291	670	0	ENST00000368323.3:c.229G>A	p.Ala77Thr	p.A77T	ENST00000368323	NM_006912.5	77	Gct/Act	4/6	1	2	FACETS	0.925	0.872	0.981	0.925	0.872	0.981	CLONAL	1	TRUE	1	0.611126694120872	2		670	1029	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434367	121434367	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	227	490	1	ENST00000257555.6:c.1136del	p.Pro379LeufsTer5	p.P379Lfs*5	ENST00000257555		377	ctC/ct	6/10	1	2	FACETS	0.951	0.889	1	0.951	0.889	1	CLONAL	1	TRUE	1	0.611126694120872	2		491	781	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	623	768	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	0.611126694120872	3	FACETS	0.957	0.923	0.991	0.957	0.923	0.991	CLONAL	2	TRUE	1	0.611126694120872	3		768	1391	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935606	13935606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326846768	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	193	239	0	ENST00000405192.2:c.1250G>A	p.Arg417His	p.R417H	ENST00000405192	NM_001163147.1	417	cGt/cAt	12/12	1	2	FACETS	0.982	0.913	1	0.982	0.913	1	CLONAL	1	TRUE	1	0.611126694120872	2		239	643	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223866	53223866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	38	470	0	ENST00000375401.3:c.3493C>T	p.Arg1165Cys	p.R1165C	ENST00000375401	NM_004187.3	1165	Cgt/Tgt	23/26	1	1	FACETS	0.133	0.109	0.159	0.133	0.109	0.159	SUBCLONAL	1	TRUE	0	0.611126694120872	1		470	650	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	262	677	1	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	0.775	0.726	0.825	0.775	0.726	0.825	SUBCLONAL	1	TRUE	1	0.611126694120872	2		678	1107	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164892	36164892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757999827	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	158	322	0	ENST00000300305.3:c.983C>T	p.Thr328Ile	p.T328I	ENST00000300305		328	aCa/aTa	8/8	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.611126694120872	2		322	511	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	265	191	2	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.611126694120872	2		193	848	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480167	20480167	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	53	559	0	ENST00000346618.3:c.484C>T	p.Arg162Ter	p.R162*	ENST00000346618	NM_001949.4	162	Cga/Tga	2/7	NA	2	FACETS	0.204	0.173	0.238			1	INDETERMINATE	1	TRUE	NA	0.611126694120872	2		559	852	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533939	63533940	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs771001164	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	110	249	0	ENST00000307078.5:c.1214_1215del	p.Glu405GlyfsTer56	p.E405Gfs*56	ENST00000307078	NM_004655.3	405	gAG/g	6/11	1	2	FACETS	0.93	0.843	1	0.93	0.843	1	CLONAL	1	TRUE	1	0.611126694120872	2		249	387	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944947	31944947	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868835690	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	210	481	0	ENST00000340398.3:c.154C>T	p.Arg52Cys	p.R52C	ENST00000340398	NM_001013699.2	52	Cgt/Tgt	1/1	1	2	FACETS	0.978	0.911	1	0.978	0.911	1	CLONAL	1	TRUE	1	0.611126694120872	2		481	703	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940819	49940819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1489965247	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	429	960	0	ENST00000296474.3:c.224G>A	p.Arg75His	p.R75H	ENST00000296474	NM_002447.2	75	cGc/cAc	1/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.611126694120872	2		960	1402	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519505	137519506	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs780346130	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	400	433	6	ENST00000367739.4:c.1132_1133del	p.Ser378PhefsTer6	p.S378Ffs*6	ENST00000367739	NM_000416.2	378	AGt/t	7/7	1	2	FACETS	0.889	0.853	0.925	1	0.997	1	CLONAL	2	TRUE	1	0.611126694120872	2		439	736	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165720	185165720	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	54	393	0	ENST00000265026.3:c.999del	p.Val334LeufsTer14	p.V334Lfs*14	ENST00000265026	NM_004721.4	332	gAa/ga	5/14	1	2	FACETS	0.26	0.222	0.303	0.26	0.222	0.303	SUBCLONAL	1	TRUE	1	0.611126694120872	2		393	679	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202351	138202351	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	198	465	1	ENST00000237289.4:c.2274del	p.Lys759SerfsTer57	p.K759Sfs*57	ENST00000237289	NM_001270507.1	756	gaC/ga	9/9	1	2	FACETS	0.905	0.841	0.971	0.905	0.841	0.971	CLONAL	1	TRUE	1	0.611126694120872	2		466	716	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877452	28877452	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1566275328	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	369	346	0	ENST00000282397.4:c.3869C>A	p.Pro1290His	p.P1290H	ENST00000282397	NM_002019.4	1290	cCc/cAc	30/30	0.611126694120872	3	FACETS	0.973	0.929	1	0.973	0.929	1	CLONAL	2	TRUE	1	0.611126694120872	3		346	810	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851941	128851943	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs767361434	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	198	565	0	ENST00000249373.3:c.2021_2023del	p.Lys674del	p.K674del	ENST00000249373	NM_005631.4	671	cgGAAg/cgg	12/12	1	2	FACETS	0.736	0.683	0.792	0.736	0.683	0.792	SUBCLONAL	1	TRUE	1	0.611126694120872	2		565	880	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795609	42795609	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	289	707	5	ENST00000575354.2:c.2694del	p.Ala900ProfsTer24	p.A900Pfs*24	ENST00000575354	NM_015125.3	897	Ccc/cc	10/20	0.611126694120872	3	FACETS	0.944	0.887	1	0.472	0.443	0.502	CLONAL	1	TRUE	1	0.611126694120872	3		712	1308	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262451	16262451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	113	257	0	ENST00000375759.3:c.9716C>T	p.Ala3239Val	p.A3239V	ENST00000375759	NM_015001.2	3239	gCc/gTc	11/15	1	2	FACETS	0.978	0.889	1	0.978	0.889	1	CLONAL	1	TRUE	1	0.611126694120872	2		257	378	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115251276	115251276	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	187	409	0	ENST00000369535.4:c.451-1G>T		p.X151_splice	ENST00000369535	NM_002524.4	151			1	2	FACETS	0.927	0.86	0.996	0.927	0.86	0.996	CLONAL	1	TRUE	1	0.611126694120872	2		409	660	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25990590	25990590	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs754208910	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	201	409	0	ENST00000435504.4:c.637T>C	p.Trp213Arg	p.W213R	ENST00000435504		213	Tgg/Cgg	8/13	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.611126694120872	2		409	635	SUCCESS
ALK	238	MSKCC	GRCh37	2	29436911	29436911	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	298	587	1	ENST00000389048.3:c.3682C>T	p.His1228Tyr	p.H1228Y	ENST00000389048	NM_004304.4	1228	Cac/Tac	24/29	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.611126694120872	2		588	940	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99163087	99163087	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	284	535	3	ENST00000074304.5:c.1093G>A	p.Ala365Thr	p.A365T	ENST00000074304	NM_001134224.1	365	Gca/Aca	13/26	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.611126694120872	2		538	861	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137404	202137404	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	203	403	0	ENST00000358485.4:c.632T>C	p.Leu211Pro	p.L211P	ENST00000358485	NM_001080125.1	211	cTg/cCg	4/9	1	2	FACETS	0.987	0.919	1	0.987	0.919	1	CLONAL	1	TRUE	1	0.611126694120872	2		403	673	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686319	30686319	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1559456557	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	238	457	0	ENST00000295754.5:c.175T>C	p.Ser59Pro	p.S59P	ENST00000295754	NM_003242.5	59	Tcc/Ccc	2/7	1	2	FACETS	0.97	0.908	1	0.97	0.908	1	CLONAL	1	TRUE	1	0.611126694120872	2		457	803	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451453	187451453	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	186	419	0	ENST00000232014.4:c.29A>G	p.Gln10Arg	p.Q10R	ENST00000232014	NM_001130845.1	10	cAg/cGg	3/10	1	2	FACETS	0.936	0.869	1	0.936	0.869	1	CLONAL	1	TRUE	1	0.611126694120872	2		419	650	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179506	56179506	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	151	266	0	ENST00000399503.3:c.3819G>T	p.Gln1273His	p.Q1273H	ENST00000399503	NM_005921.1	1273	caG/caT	15/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.611126694120872	2		266	443	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86648973	86648973	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	148	359	0	ENST00000274376.6:c.1254-1G>A		p.X418_splice	ENST00000274376	NM_002890.2	418			1	2	FACETS	0.924	0.849	1	0.924	0.849	1	CLONAL	1	TRUE	1	0.611126694120872	2		359	524	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86668014	86668014	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	199	472	0	ENST00000274376.6:c.1776+2T>C		p.X592_splice	ENST00000274376	NM_002890.2	592			1	2	FACETS	0.919	0.854	0.985	0.919	0.854	0.985	CLONAL	1	TRUE	1	0.611126694120872	2		472	709	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512350	149512350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754790326	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	214	469	1	ENST00000261799.4:c.1090G>A	p.Glu364Lys	p.E364K	ENST00000261799	NM_002609.3	364	Gaa/Aaa	7/23	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.611126694120872	2		470	678	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051033	180051033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	272	541	1	ENST00000261937.6:c.1450C>T	p.Pro484Ser	p.P484S	ENST00000261937	NM_182925.4	484	Cca/Tca	11/30	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.611126694120872	2		542	882	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271606	26271606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763475502	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	394	987	0	ENST00000305910.3:c.7C>T	p.Arg3Cys	p.R3C	ENST00000305910	NM_003534.2	3	Cgc/Tgc	1/1	NA	2	FACETS	0.946	0.899	0.994			1	INDETERMINATE	1	TRUE	NA	0.611126694120872	2		987	1363	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178669	32178669	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766521222	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	280	599	1	ENST00000375023.3:c.2725G>A	p.Asp909Asn	p.D909N	ENST00000375023	NM_004557.3	909	Gac/Aac	18/30	1	2	FACETS	0.968	0.911	1	0.968	0.911	1	CLONAL	1	TRUE	1	0.611126694120872	2		600	947	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185807	32185807	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	352	665	0	ENST00000375023.3:c.1589A>C	p.Asp530Ala	p.D530A	ENST00000375023	NM_004557.3	530	gAc/gCc	9/30	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.611126694120872	2		665	1086	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420040	152420040	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201118302	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	245	649	0	ENST00000206249.3:c.1727C>T	p.Ser576Leu	p.S576L	ENST00000206249	NM_000125.3	576	tCg/tTg	8/8	1	2	FACETS	0.889	0.832	0.947	0.889	0.832	0.947	CLONAL	1	TRUE	1	0.611126694120872	2		649	902	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729411	41729411	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	446	1155	0	ENST00000242208.4:c.1118T>C	p.Ile373Thr	p.I373T	ENST00000242208	NM_002192.2	373	aTc/aCc	3/3	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.611126694120872	2		1155	1408	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508383	106508383	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	91	230	0	ENST00000359195.3:c.377A>G	p.Lys126Arg	p.K126R	ENST00000359195	NM_002649.2	126	aAg/aGg	2/11	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.611126694120872	2		230	279	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868894	117868894	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs376740145	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	242	550	0	ENST00000297338.2:c.805A>G	p.Asn269Asp	p.N269D	ENST00000297338	NM_006265.2	269	Aat/Gat	7/14	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.611126694120872	2		550	743	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006138	22006138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	212	461	0	ENST00000276925.6:c.265C>T	p.Arg89Trp	p.R89W	ENST00000276925	NM_004936.3	89	Cgg/Tgg	2/2	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.611126694120872	2		461	684	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401768	139401768	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756362905	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	52	611	0	ENST00000277541.6:c.3632G>A	p.Arg1211Gln	p.R1211Q	ENST00000277541	NM_017617.3	1211	cGg/cAg	22/34	1	2	FACETS	0.173	0.146	0.202	0.173	0.146	0.202	SUBCLONAL	1	TRUE	1	0.611126694120872	2		611	985	SUCCESS
EED	8726	MSKCC	GRCh37	11	85956282	85956282	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs766472086	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	113	320	1	ENST00000263360.6:c.11G>T	p.Arg4Met	p.R4M	ENST00000263360	NM_003797.3	4	aGg/aTg	1/12	1	2	FACETS	0.837	0.758	0.919	0.837	0.758	0.919	CLONAL	1	TRUE	1	0.611126694120872	2		321	442	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163374	108163374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754181173	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	255	563	0	ENST00000278616.4:c.4465C>T	p.Arg1489Cys	p.R1489C	ENST00000278616	NM_000051.3	1489	Cgt/Tgt	30/63	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.611126694120872	2		563	831	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498148	498148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	327	804	2	ENST00000399788.2:c.110G>A	p.Gly37Asp	p.G37D	ENST00000399788	NM_001042603.1	37	gGc/gAc	1/28	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.611126694120872	2		806	1046	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437695	49437695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565802308	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	483	977	0	ENST00000301067.7:c.5275C>T	p.Arg1759Cys	p.R1759C	ENST00000301067	NM_003482.3	1759	Cgc/Tgc	22/54	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.611126694120872	2		977	1554	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447064	49447064	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	94	691	0	ENST00000301067.7:c.880T>C	p.Cys294Arg	p.C294R	ENST00000301067	NM_003482.3	294	Tgt/Cgt	7/54	1	2	FACETS	0.287	0.254	0.322	0.287	0.254	0.322	SUBCLONAL	1	TRUE	1	0.611126694120872	2		691	1073	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514839	103514839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs577826260	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	321	356	1	ENST00000355739.4:c.1340C>T	p.Ala447Val	p.A447V	ENST00000355739	NM_000123.3	447	gCg/gTg	8/15	0.611126694120872	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.611126694120872	3		357	683	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436060	110436060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1270526175	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	257	549	0	ENST00000375856.3:c.2341C>T	p.Pro781Ser	p.P781S	ENST00000375856	NM_003749.2	781	Ccc/Tcc	1/2	0.611126694120872	3	FACETS	1	0.968	1	0.526	0.493	0.561	CLONAL	1	TRUE	1	0.611126694120872	3		549	1043	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434841	99434841	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	164	312	0	ENST00000268035.6:c.928G>T	p.Gly310Cys	p.G310C	ENST00000268035	NM_000875.3	310	Ggc/Tgc	3/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.611126694120872	2		312	518	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857311	9857311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1245573153	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	280	573	4	ENST00000330684.3:c.4090G>A	p.Asp1364Asn	p.D1364N	ENST00000330684	NM_001134407.1	1364	Gat/Aat	13/13	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.611126694120872	2		577	878	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350282	89350282	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1357840458	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1655	122	1172	1	ENST00000301030.4:c.2668C>T	p.Arg890Trp	p.R890W	ENST00000301030	NM_001256183.1	890	Cgg/Tgg	9/13	1	2	FACETS	0.225	0.202	0.249	0.225	0.202	0.249	SUBCLONAL	1	TRUE	1	0.611126694120872	2		1173	1777	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866689	37866689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149210045	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	300	611	0	ENST00000269571.5:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269571		286	Gag/Aag	7/27	1	2	FACETS	0.965	0.91	1	0.965	0.91	1	CLONAL	1	TRUE	1	0.611126694120872	2		611	1017	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883701	37883701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs111611886	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	60	864	3	ENST00000269571.5:c.3313G>A	p.Asp1105Asn	p.D1105N	ENST00000269571		1105	Gac/Aac	26/27	1	2	FACETS	0.172	0.147	0.199	0.172	0.147	0.199	SUBCLONAL	1	TRUE	1	0.611126694120872	2		867	1141	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1646352	1646352	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1418	369	834	0	ENST00000344749.5:c.145+2T>C		p.X49_splice	ENST00000344749	NM_001136139.2	49			0.611126694120872	3	FACETS	0.882	0.834	0.932	0.441	0.417	0.466	CLONAL	1	TRUE	1	0.611126694120872	3		834	1787	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121008	3121008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762218250	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	448	469	3	ENST00000078429.4:c.911C>T	p.Ala304Val	p.A304V	ENST00000078429	NM_002067.2	304	gCg/gTg	7/7	0.611126694120872	3	FACETS	0.995	0.954	1	0.995	0.954	1	CLONAL	2	TRUE	1	0.611126694120872	3		472	962	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7163201	7163201	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	555	528	0	ENST00000302850.5:c.1871T>C	p.Val624Ala	p.V624A	ENST00000302850	NM_000208.2	624	gTg/gCg	9/22	0.611126694120872	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.611126694120872	3		528	1171	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314643	30314643	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	117	604	0	ENST00000262643.3:c.1192C>T	p.Gln398Ter	p.Q398*	ENST00000262643	NM_001238.2	398	Cag/Tag	12/12	0.611126694120872	3	FACETS	0.405	0.364	0.449	0.203	0.182	0.225	SUBCLONAL	1	TRUE	1	0.611126694120872	3		604	1233	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860610	45860610	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs762354840	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	774	822	0	ENST00000391945.4:c.1397T>G	p.Ile466Ser	p.I466S	ENST00000391945	NM_000400.3	466	aTc/aGc	15/23	0.611126694120872	3	FACETS	0.909	0.879	0.939	0.909	0.879	0.939	CLONAL	2	TRUE	1	0.611126694120872	3		822	1819	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656917	45656917	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	354	811	0	ENST00000407780.3:c.239A>G	p.Tyr80Cys	p.Y80C	ENST00000407780	NM_001283052.1	80	tAc/tGc	3/7	1	2	FACETS	0.944	0.894	0.995	0.944	0.894	0.995	CLONAL	1	TRUE	1	0.611126694120872	2		811	1227	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566496	41566496	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	361	720	0	ENST00000263253.7:c.4373C>A	p.Pro1458His	p.P1458H	ENST00000263253	NM_001429.3	1458	cCc/cAc	27/31	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.611126694120872	2		720	1176	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030500	47030500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	57	445	0	ENST00000377604.3:c.275G>A	p.Gly92Asp	p.G92D	ENST00000377604	NM_001204468.1	92	gGc/gAc	4/24	1	1	FACETS	0.212	0.181	0.245	0.212	0.181	0.245	SUBCLONAL	1	TRUE	0	0.611126694120872	1		445	612	SUCCESS
AR	367	MSKCC	GRCh37	X	66942743	66942743	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs372780925	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	412	537	0	ENST00000374690.3:c.2524A>G	p.Ile842Val	p.I842V	ENST00000374690	NM_000044.3	842	Atc/Gtc	7/8	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.611126694120872	1		537	711	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210295	123210295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	83	299	0	ENST00000218089.9:c.2647G>A	p.Ala883Thr	p.A883T	ENST00000218089	NM_001042749.1	883	Gca/Aca	26/35	1	1	FACETS	0.37	0.327	0.415	0.37	0.327	0.415	SUBCLONAL	1	TRUE	0	0.611126694120872	1		299	510	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456554	189456554	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	196	453	0	ENST00000264731.3:c.318del	p.Met107CysfsTer11	p.M107Cfs*11	ENST00000264731	NM_003722.4	105	gaC/ga	3/14	1	2	FACETS	0.88	0.817	0.945	0.88	0.817	0.945	CLONAL	1	TRUE	1	0.611126694120872	2		453	729	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487503	38487504	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	285	596	0	ENST00000254066.5:c.38dup	p.Gly14ArgfsTer38	p.G14Rfs*38	ENST00000254066	NM_000964.3	11	-/G	2/9	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.611126694120872	2		596	911	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43749726	43749729	+	frameshift_variant	Frame_Shift_Del	DEL	TTTG	TTTG	-	rs755042290	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	417	853	0	ENST00000523873.1:c.584_587del	p.Phe195TyrfsTer25	p.F195Yfs*25	ENST00000523873		193	caTTTG/ca	7/8	1	2	FACETS	0.95	0.903	0.997	0.95	0.903	0.997	CLONAL	1	TRUE	1	0.611126694120872	2		853	1437	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119909	70119910	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	224	461	0	ENST00000245479.2:c.916dup	p.Val306GlyfsTer272	p.V306Gfs*272	ENST00000245479	NM_000346.3	304	ccg/ccGg	3/3	1	2	FACETS	0.95	0.887	1	0.95	0.887	1	CLONAL	1	TRUE	1	0.611126694120872	2		461	772	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981721	101981721	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555075353	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	71	226	1	ENST00000282441.5:c.147del	p.Ala50ProfsTer24	p.A50Pfs*24	ENST00000282441	NM_001130145.2	48	Ccc/cc	1/9	1	2	FACETS	0.788	0.694	0.887	0.788	0.694	0.887	SUBCLONAL	1	TRUE	1	0.611126694120872	2		227	295	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589610	67589610	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	111	258	0	ENST00000274335.5:c.1378del	p.Ser460ValfsTer20	p.S460Vfs*20	ENST00000274335		458	gAa/ga	10/15	1	2	FACETS	0.851	0.77	0.935	0.851	0.77	0.935	CLONAL	1	TRUE	1	0.611126694120872	2		258	427	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483054	29483055	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	303	630	0	ENST00000356175.3:c.116dup	p.Asn39LysfsTer28	p.N39Kfs*28	ENST00000356175	NM_000267.3	38	-/A	2/57	1	2	FACETS	0.977	0.922	1	0.977	0.922	1	CLONAL	1	TRUE	1	0.611126694120872	2		630	1015	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475035	40475037	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	84	767	1	ENST00000264657.5:c.1873_1875del	p.Glu625del	p.E625del	ENST00000264657	NM_139276.2	625	GAG/-	20/24	1	2	FACETS	0.237	0.209	0.268	0.237	0.209	0.268	SUBCLONAL	1	TRUE	1	0.611126694120872	2		768	1158	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005667	42005667	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	291	646	0	ENST00000219905.7:c.3407del	p.Lys1136ArgfsTer6	p.K1136Rfs*6	ENST00000219905	NM_001164273.1	1135	Aaa/aa	9/24	1	2	FACETS	0.943	0.888	0.999	0.943	0.888	0.999	CLONAL	1	TRUE	1	0.611126694120872	2		646	1010	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56338887	56338887	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	63	113	1	ENST00000348428.3:c.16del	p.Asp6ThrfsTer67	p.D6Tfs*67	ENST00000348428	NM_006785.3	4	ttG/tt	1/17	NA	2	FACETS	0.977	0.858	1			1	INDETERMINATE	1	TRUE	NA	0.611126694120872	2		114	211	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008194	29008195	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0011239-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	459	466	0	ENST00000282397.4:c.676dup	p.Thr226AsnfsTer19	p.T226Nfs*19	ENST00000282397	NM_002019.4	226	acc/aAcc		0.611126694120872	3	FACETS	0.947	0.908	0.987	0.947	0.908	0.987	CLONAL	2	TRUE	1	0.611126694120872	3		466	1035	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	202	556	2	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	0.15350405945779	4	FACETS	0.793	0.735	0.854	0.793	0.735	0.854	INDETERMINATE	2	TRUE	2	0.31	4		558	1076	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	79	170	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	0.244896274284026	3	FACETS	1	0.959	1			1	CLONAL	1	TRUE	NA	0.31	3		171	490	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	316	628	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	0.301325447751319	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	0	0.31	3		628	733	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084146	47084146	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	171	307	0	ENST00000409792.3:c.7143del	p.Ser2382LeufsTer29	p.S2382Lfs*29	ENST00000409792	NM_014159.6	2381	ccC/cc	17/21	0.15350405945779	4	FACETS	1	0.974	1	0.573	0.525	0.622	INDETERMINATE	1	TRUE	2	0.31	4		307	1262	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	127	454	2	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	0.181292045507322	4	FACETS	1	0.979	1	0.644	0.583	0.708	INDETERMINATE	1	TRUE	2	0.31	4		456	833	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144017	11144017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	132	374	0	ENST00000358026.2:c.3598C>T	p.Arg1200Cys	p.R1200C	ENST00000358026	NM_001128849.1	1200	Cgt/Tgt	26/36	0.244896274284026	3	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.31	3		374	681	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	57	347	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.244896274284026	3	FACETS	1	0.949	1			1	CLONAL	1	TRUE	NA	0.31	3		347	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	120	377	1	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	0.15350405945779	4	FACETS	1	0.979	1	0.662	0.598	0.73	INDETERMINATE	1	TRUE	2	0.31	4		378	766	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097751	27097751	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	172	453	0	ENST00000324856.7:c.3344del	p.Pro1115GlnfsTer46	p.P1115Qfs*46	ENST00000324856	NM_006015.4	1114	Ccc/cc	12/20	0.181292045507322	4	FACETS	0.774	0.712	0.839	0.774	0.712	0.839	INDETERMINATE	2	TRUE	2	0.31	4		453	939	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023079	27023079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	61	96	0	ENST00000324856.7:c.185C>T	p.Ala62Val	p.A62V	ENST00000324856	NM_006015.4	62	gCc/gTc	1/20	0.181292045507322	4	FACETS	0.868	0.755	0.989	0.868	0.755	0.989	INDETERMINATE	2	TRUE	2	0.31	4		96	297	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429757	78429757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755419864	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	202	330	0	ENST00000370768.2:c.1031G>A	p.Arg344Gln	p.R344Q	ENST00000370768	NM_003902.3	344	cGa/cAa	12/20	0.181292045507322	4	FACETS	0.777	0.72	0.837	0.777	0.72	0.837	INDETERMINATE	2	TRUE	2	0.31	4		330	1098	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716217	52716217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1173183954	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	99	347	3	ENST00000322088.6:c.661C>T	p.Arg221Trp	p.R221W	ENST00000322088	NM_014225.5	221	Cgg/Tgg	6/15	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.31	2		350	573	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	61	376	0	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	0.216308530021666	4	FACETS	1	0.97	1	0.747	0.648	0.853	CLONAL	1	TRUE	2	0.31	4		376	345	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652960	29652960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763413441	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	147	442	1	ENST00000356175.3:c.4895G>A	p.Arg1632His	p.R1632H	ENST00000356175	NM_000267.3	1632	cGc/cAc	36/57	0.15350405945779	4	FACETS	1	0.934	1	0.515	0.469	0.564	INDETERMINATE	1	TRUE	2	0.31	4		443	1206	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974721	21974721	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	315	308	0	ENST00000304494.5:c.106del	p.Ala36ArgfsTer17	p.A36Rfs*17	ENST00000304494	NM_000077.4	36	Gcg/cg	1/3	0.301325447751319	2	FACETS	0.89	0.845	0.936	1	0.994	1	CLONAL	3	TRUE	0	0.31	2		308	761	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	147	521	1	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	0.15350405945779	4	FACETS	1	0.985	1	0.7	0.639	0.764	INDETERMINATE	1	TRUE	2	0.31	4		522	887	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755427	39755427	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	84	475	2	ENST00000288319.7:c.1338del	p.Phe446LeufsTer59	p.F446Lfs*59	ENST00000288319	NM_182918.3	446	ttT/tt	10/10	1	2	FACETS	0.838	0.74	0.942	0.838	0.74	0.942	CLONAL	1	TRUE	1	0.31	2		477	647	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538269	187538269	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs748652484	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	193	453	1	ENST00000441802.2:c.8965del	p.Arg2989GlyfsTer20	p.R2989Gfs*20	ENST00000441802	NM_005245.3	2989	Agg/gg	11/27	0.128824046606559	3	FACETS	0.809	0.749	0.871			1	INDETERMINATE	2	TRUE	NA	0.31	3		454	889	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101031	4101031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375843855	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	61	237	0	ENST00000262948.5:c.691C>T	p.Arg231Cys	p.R231C	ENST00000262948	NM_030662.3	231	Cgc/Tgc	6/11	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.31	2		237	357	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	203	523	2	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	0.301325447751319	3	FACETS	1	0.988	1	0.443	0.41	0.478	CLONAL	1	TRUE	0	0.31	3		525	1137	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693947	47693947	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs63750597	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	122	417	1	ENST00000233146.2:c.1661G>A	p.Ser554Asn	p.S554N	ENST00000233146	NM_000251.2	554	aGc/aAc	10/16	0.128951781431472	3	FACETS	1	0.981	1	0.671	0.608	0.738	INDETERMINATE	1	TRUE	1	0.31	3		418	677	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920699	96920699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746831347	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	125	339	0	ENST00000258439.3:c.281G>A	p.Arg94Gln	p.R94Q	ENST00000258439	NM_001193304.2	94	cGg/cAg	3/4	0.128951781431472	3	FACETS	1	0.96	1	0.556	0.503	0.612	INDETERMINATE	1	TRUE	1	0.31	3		339	838	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131331	202131331	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	79	298	0	ENST00000358485.4:c.299C>A	p.Ala100Asp	p.A100D	ENST00000358485	NM_001080125.1	100	gCc/gAc	2/9	0.284461624476244	4	FACETS	0.753	0.661	0.852	0.376	0.33	0.426	SUBCLONAL	1	TRUE	2	0.31	4		298	887	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286760	212286760	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763644012	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	159	364	0	ENST00000342788.4:c.2936G>A	p.Arg979Gln	p.R979Q	ENST00000342788	NM_005235.2	979	cGa/cAa	24/28	0.15350405945779	4	FACETS	1	0.984	1	0.661	0.605	0.72	INDETERMINATE	1	TRUE	2	0.31	4		364	1016	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643399	52643399	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146395938	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	200	516	1	ENST00000394830.3:c.2497C>T	p.Arg833Cys	p.R833C	ENST00000394830	NM_018313.4	833	Cgc/Tgc	17/30	0.15350405945779	4	FACETS	1	0.99	1	0.748	0.692	0.806	INDETERMINATE	1	TRUE	2	0.31	4		517	1130	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193856	106193856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369911989	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	199	430	3	ENST00000380013.4:c.4318C>T	p.Arg1440Trp	p.R1440W	ENST00000380013	NM_001127208.2	1440	Cgg/Tgg	10/11	0.284461624476244	4	FACETS	1	0.986	1	0.643	0.594	0.694	CLONAL	1	TRUE	2	0.31	4		433	1308	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549761	187549761	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	207	349	0	ENST00000441802.2:c.4480C>T	p.Gln1494Ter	p.Q1494*	ENST00000441802	NM_005245.3	1494	Cag/Tag	8/27	0.128824046606559	3	FACETS	0.886	0.824	0.951			1	INDETERMINATE	2	TRUE	NA	0.31	3		349	870	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680388	30680388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748459364	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	221	453	0	ENST00000376406.3:c.1331G>A	p.Arg444Gln	p.R444Q	ENST00000376406	NM_014641.2	444	cGa/cAa	5/15	0.301325447751319	6	FACETS	1	0.98	1	0.759	0.707	0.814	CLONAL	2	TRUE	3	0.31	6		453	1014	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185886	32185886	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	68	381	1	ENST00000375023.3:c.1511-1G>T		p.X504_splice	ENST00000375023	NM_004557.3	504			0.216308530021666	4	FACETS	1	0.934	1	0.558	0.486	0.635	CLONAL	1	TRUE	2	0.31	4		382	515	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288786	33288786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752819224	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	129	248	1	ENST00000374542.5:c.766C>T	p.Arg256Cys	p.R256C	ENST00000374542	NM_001141970.1	256	Cgc/Tgc	3/8	0.216308530021666	4	FACETS	1	0.984	1	0.713	0.646	0.782	CLONAL	1	TRUE	2	0.31	4		249	765	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793893	89793893	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	110	167	0	ENST00000336032.3:c.962C>T	p.Thr321Met	p.T321M	ENST00000336032	NM_006813.2	321	aCg/aTg	2/2	0.216308530021666	4	FACETS	1	0.974	1	0.627	0.564	0.695	CLONAL	1	TRUE	2	0.31	4		167	741	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864427	162864427	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	137	364	0	ENST00000366898.1:c.86T>C	p.Val29Ala	p.V29A	ENST00000366898	NM_004562.2	29	gTg/gCg	2/12	0.181292045507322	4	FACETS	1	0.985	1	0.716	0.651	0.783	INDETERMINATE	1	TRUE	2	0.31	4		364	809	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467912	50467912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	47	216	0	ENST00000331340.3:c.1147C>T	p.Pro383Ser	p.P383S	ENST00000331340	NM_006060.4	383	Ccc/Tcc	8/8	1	2	FACETS	0.72	0.609	0.843	0.72	0.609	0.843	SUBCLONAL	1	TRUE	1	0.31	2		216	421	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240734	55240734	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426364365	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	125	430	2	ENST00000275493.2:c.1978G>A	p.Val660Met	p.V660M	ENST00000275493	NM_005228.3	660	Gtg/Atg	17/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.31	2		432	682	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92354974	92354974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1220056162	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	162	325	0	ENST00000265734.4:c.503G>A	p.Arg168His	p.R168H	ENST00000265734	NM_001259.6	168	cGc/cAc	4/8	0.181292045507322	4	FACETS	1	0.973	1	0.573	0.525	0.624	INDETERMINATE	1	TRUE	2	0.31	4		325	1194	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966593	36966593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	179	448	3	ENST00000358127.4:c.733C>T	p.His245Tyr	p.H245Y	ENST00000358127	NM_001280556.1	245	Cac/Tac	6/10	0.301325447751319	2	FACETS	0.972	0.901	1	0.972	0.901	1	CLONAL	2	TRUE	0	0.31	2		451	594	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482340	87482340	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	55	427	0	ENST00000277120.3:c.1627G>T	p.Asp543Tyr	p.D543Y	ENST00000277120		543	Gac/Tac	14/19	1	2	FACETS	0.435	0.371	0.505	0.435	0.371	0.505	SUBCLONAL	1	TRUE	1	0.31	2		427	816	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127920568	127920568	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs761088509	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	215	634	2	ENST00000373547.4:c.331C>T	p.Arg111Ter	p.R111*	ENST00000373547	NM_002721.4	111	Cga/Tga	4/7	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.31	2		636	1081	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431829	49431829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	137	285	1	ENST00000301067.7:c.9310G>A	p.Ala3104Thr	p.A3104T	ENST00000301067	NM_003482.3	3104	Gct/Act	34/54	0.301325447751319	5	FACETS	0.936	0.858	1	0.936	0.858	1	CLONAL	3	TRUE	2	0.31	5		286	461	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993303	72993303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	195	648	1	ENST00000268489.5:c.742G>A	p.Asp248Asn	p.D248N	ENST00000268489	NM_006885.3	248	Gac/Aac	2/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.31	2		649	958	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696461	47696461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	287	354	0	ENST00000347630.2:c.362G>A	p.Arg121Gln	p.R121Q	ENST00000347630	NM_001007230.1	121	cGg/cAg	6/11	0.301325447751319	3	FACETS	0.874	0.825	0.923	0.874	0.825	0.923	CLONAL	3	TRUE	0	0.31	3		354	816	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534419	63534419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772636882	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	85	325	0	ENST00000307078.5:c.1102G>A	p.Ala368Thr	p.A368T	ENST00000307078	NM_004655.3	368	Gcc/Acc	5/11	0.301325447751319	3	FACETS	1	0.967	1	0.416	0.368	0.466	CLONAL	1	TRUE	0	0.31	3		325	508	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226548	1226548	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	97	396	0	ENST00000326873.7:c.1204A>G	p.Thr402Ala	p.T402A	ENST00000326873	NM_000455.4	402	Acc/Gcc	9/10	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.31	2		396	544	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110245	3110245	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777099166	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	118	481	0	ENST00000078429.4:c.235G>A	p.Val79Ile	p.V79I	ENST00000078429	NM_002067.2	79	Gtc/Atc	2/7	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.31	2		481	703	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273800	18273800	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	166	429	0	ENST00000222254.8:c.1133T>G	p.Ile378Ser	p.I378S	ENST00000222254	NM_005027.3	378	aTc/aGc	10/16	0.181292045507322	4	FACETS	0.788	0.724	0.855	0.788	0.724	0.855	INDETERMINATE	2	TRUE	2	0.31	4		429	890	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909535	50909535	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	150	593	0	ENST00000440232.2:c.1339A>G	p.Lys447Glu	p.K447E	ENST00000440232	NM_002691.3	447	Aag/Gag	11/27	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.31	2		593	747	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945659	54945659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753238269	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	41	86	0	ENST00000312783.6:c.911G>A	p.Arg304Gln	p.R304Q	ENST00000312783	NM_198436.1	304	cGg/cAg	9/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.31	2		86	191	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923742	39923742	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374493655	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	173	499	2	ENST00000378444.4:c.3349G>A	p.Ala1117Thr	p.A1117T	ENST00000378444	NM_001123385.1	1117	Gca/Aca	7/15	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.31	2		501	827	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438262	49438262	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	243	395	0	ENST00000301067.7:c.5007del	p.Val1670SerfsTer52	p.V1670Sfs*52	ENST00000301067	NM_003482.3	1669	ccC/cc	20/54	0.301325447751319	5	FACETS	1	0.988	1	0.825	0.772	0.88	CLONAL	2	TRUE	2	0.31	5		395	928	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846342	156846342	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	89	410	0	ENST00000524377.1:c.1786del	p.Asp596ThrfsTer62	p.D596Tfs*62	ENST00000524377	NM_002529.3	595	Ggg/gg	14/17	NA	2	FACETS	1	0.915	1			1	INDETERMINATE	1	TRUE	NA	0.31	2		410	555	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657030	47657030	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0011262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	196	455	0	ENST00000233146.2:c.1226del	p.Gln409ArgfsTer3	p.Q409Rfs*3	ENST00000233146	NM_000251.2	409	cAg/cg	7/16	0.128951781431472	3	FACETS	0.795	0.737	0.856	0.795	0.737	0.856	INDETERMINATE	2	TRUE	1	0.31	3		455	918	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0011288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	150	703	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.579906046564898	1	FACETS	0.875	0.817	0.933	0.875	0.817	0.933	CLONAL	1	TRUE	0	0.757756089691364	1		704	281	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0011288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	13	1114	2	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.088	0.062	0.12	0.088	0.062	0.12	SUBCLONAL	1	TRUE	1	0.757756089691364	2		1116	388	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0011288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	62	285	3	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	1	2	FACETS	0.899	0.792	1	0.899	0.792	1	CLONAL	1	TRUE	1	0.757756089691364	2		288	182	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0011288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	92	415	1	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	1	2	FACETS	0.867	0.781	0.956	0.867	0.781	0.956	CLONAL	1	TRUE	1	0.757756089691364	2		416	280	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845371	156845371	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	45	648	0	ENST00000524377.1:c.1414G>T	p.Gly472Cys	p.G472C	ENST00000524377	NM_002529.3	472	Ggt/Tgt	12/17	1	2	FACETS	0.42	0.355	0.491	0.42	0.355	0.491	SUBCLONAL	1	TRUE	1	0.757756089691364	2		648	283	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014356	70014356	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1018390529	NA	P-0011288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	38	739	0	ENST00000394351.3:c.1217G>A	p.Arg406Gln	p.R406Q	ENST00000394351	NM_000248.3	406	cGg/cAg	9/9	1	2	FACETS	0.243	0.201	0.29	0.243	0.201	0.29	SUBCLONAL	1	TRUE	1	0.757756089691364	2		739	413	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361213	66361213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1410955850	NA	P-0011288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	55	366	1	ENST00000273854.3:c.959G>A	p.Gly320Asp	p.G320D	ENST00000273854	NM_004439.5	320	gGc/gAc	4/18	0.600983203101149	1	FACETS	0.515	0.449	0.585	0.515	0.449	0.585	SUBCLONAL	1	TRUE	0	0.757756089691364	1		367	175	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962670	38962670	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	11	325	0	ENST00000357387.3:c.1585T>A	p.Leu529Ile	p.L529I	ENST00000357387	NM_152756.3	529	Tta/Ata	18/38	1	2	FACETS	0.277	0.192	0.379	0.277	0.192	0.379	SUBCLONAL	1	TRUE	1	0.757756089691364	2		325	105	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099109	157099109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1294708279	NA	P-0011288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	10	121	0	ENST00000346085.5:c.46G>A	p.Ala16Thr	p.A16T	ENST00000346085	NM_020732.3	16	Gcc/Acc	1/20	1	2	FACETS	0.162	0.109	0.227	0.162	0.109	0.227	SUBCLONAL	1	TRUE	1	0.757756089691364	2		121	163	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229612	5229612	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1246891588	NA	P-0011288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	64	49	0	ENST00000357368.4:c.2239G>A	p.Gly747Ser	p.G747S	ENST00000357368	NM_002850.3	747	Ggc/Agc	15/38	0.728224866930562	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.757756089691364	2		49	72	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339352	116339353	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTTTAA	novel	NA	P-0011288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	43	376	0	ENST00000397752.3:c.215_220dup	p.Leu73_Asn74insIleLeu	p.L73_N74insIL	ENST00000397752	NM_000245.2	72	gtt/gTTTTAAtt	2/21	1	2	FACETS	0.53	0.448	0.619	0.53	0.448	0.619	SUBCLONAL	1	TRUE	1	0.757756089691364	2		376	214	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0011344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	397	539	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.890590400824035	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.890590400824035	1		539	491	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0011344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	228	298	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.988	0.931	1	0.988	0.931	1	CLONAL	1	TRUE	1	0.890590400824035	2		298	518	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927977	178927982	+	inframe_deletion	In_Frame_Del	DEL	CACTGT	CACTGT	-	novel	NA	P-0011344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	139	180	0	ENST00000263967.3:c.1256_1261del	p.His419_Cys420del	p.H419_C420del	ENST00000263967	NM_006218.2	419	CACTGT/-	8/21	1	2	FACETS	0.975	0.902	1	0.975	0.902	1	CLONAL	1	TRUE	1	0.890590400824035	2		180	320	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923143	48923144	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0011344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	166	255	0	ENST00000267163.4:c.596dup	p.Leu199PhefsTer4	p.L199Ffs*4	ENST00000267163	NM_000321.2	197	-/T	6/27	0.890590400824035	1	FACETS	0.971	0.927	1	0.971	0.927	1	CLONAL	1	TRUE	0	0.890590400824035	1		255	213	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686323	117686323	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	307	302	0	ENST00000368508.3:c.3018A>C	p.Glu1006Asp	p.E1006D	ENST00000368508	NM_002944.2	1006	gaA/gaC	20/43	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.890590400824035	2		302	686	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298137	123298143	+	frameshift_variant	Frame_Shift_Del	DEL	GGACCCG	GGACCCG	-	novel	NA	P-0011344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	355	402	0	ENST00000358487.5:c.711_717del	p.Tyr237Ter	p.Y237*	ENST00000358487	NM_000141.4	237	taCGGGTCC/ta	6/18	1	2	FACETS	0.862	0.819	0.905	0.862	0.819	0.905	CLONAL	1	TRUE	1	0.890590400824035	2		402	925	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0011369-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	498	516	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.632599835125185	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	FALSE	0	0.633638055657161	2		517	774	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547360	106547360	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011369-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	183	317	0	ENST00000369096.4:c.597G>C	p.Trp199Cys	p.W199C	ENST00000369096	NM_001198.3	199	tgG/tgC	4/7	0.3176885338774	6	FACETS	1	0.98	1	0.397	0.365	0.43	INDETERMINATE	1	FALSE	3	0.633638055657161	6		317	1100	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759701	133759701	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011369-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	110	184	0	ENST00000318560.5:c.2024A>C	p.Glu675Ala	p.E675A	ENST00000318560	NM_005157.4	675	gAg/gCg	11/11	0.633638055657161	4	FACETS	0.746	0.671	0.827			1	SUBCLONAL	1	FALSE	NA	0.633638055657161	4		184	760	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988192	36988192	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011369-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	98	134	0	ENST00000354822.5:c.461C>G	p.Ala154Gly	p.A154G	ENST00000354822	NM_001079668.2	154	gCc/gGc	2/3	0.633638055657161	2	FACETS	1	0.935	1	0.523	0.472	0.575	CLONAL	1	FALSE	0	0.633638055657161	2		134	296	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536249	106536341	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGCGGTACTTCGGTTCAGGCGGAGGCATCCTTACCAAGGAATCTGCTTTTCAAGTATGCCACCAACAGTGAAGAGGTAAGCCTCTGGTTTAT	TGGCGGTACTTCGGTTCAGGCGGAGGCATCCTTACCAAGGAATCTGCTTTTCAAGTATGCCACCAACAGTGAAGAGGTAAGCCTCTGGTTTAT	-	novel	NA	P-0011369-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	298	378	0	ENST00000369096.4:c.218_291+19del		p.X73_splice	ENST00000369096	NM_001198.3	73		2/7	0.3176885338774	6	FACETS	1	0.963	1	0.686	0.647	0.727	INDETERMINATE	2	FALSE	3	0.633638055657161	6		378	1036	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245492	41245493	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0011369-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	603	553	0	ENST00000357654.3:c.2055dup	p.Glu686Ter	p.E686*	ENST00000357654	NM_007294.3	685	-/T	10/23	0.633638055657161	2	FACETS	0.923	0.894	0.952	0.923	0.894	0.952	CLONAL	2	FALSE	0	0.633638055657161	2		553	1031	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs770248150	NA	P-0011380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	122	495	0	ENST00000311936.3:c.351A>T	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaT	4/5	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.228115571288017	2		495	1049	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0011380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	62	302	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.988	0.854	1	0.988	0.854	1	CLONAL	1	TRUE	1	0.228115571288017	2		302	550	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685307	89685307	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123317	NA	P-0011380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	72	242	0	ENST00000371953.3:c.202T>C	p.Tyr68His	p.Y68H	ENST00000371953	NM_000314.4	68	Tac/Cac	3/9	0.198581275995565	3	FACETS	1	0.971	1	0.702	0.614	0.796	CLONAL	1	TRUE	1	0.228115571288017	3		242	501	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729181	66729181	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121908595	NA	P-0011380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	92	492	0	ENST00000307102.5:c.389A>G	p.Tyr130Cys	p.Y130C	ENST00000307102	NM_002755.3	130	tAt/tGt	3/11	0.228115571288017	1	FACETS	0.893	0.793	1	0.893	0.793	1	CLONAL	1	TRUE	0	0.228115571288017	1		492	800	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122487	17122487	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0011380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	136	673	0	ENST00000285071.4:c.908del	p.Glu303GlyfsTer20	p.E303Gfs*20	ENST00000285071	NM_144997.5	303	gAg/gg	9/14	0.228115571288017	1	FACETS	0.96	0.872	1	0.96	0.872	1	CLONAL	1	TRUE	0	0.228115571288017	1		673	1100	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026116	71026117	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAGT	novel	NA	P-0011380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	47	400	0	ENST00000318789.4:c.1502_1505dup	p.Phe502LeufsTer16	p.F502Lfs*16	ENST00000318789	NM_032682.5	502	ttc/ttACTTc	17/21	1	2	FACETS	0.526	0.442	0.618	0.526	0.442	0.618	SUBCLONAL	1	TRUE	1	0.228115571288017	2		400	784	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	356	327	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.52135745301615	3	FACETS	0.894	0.856	0.931	0.894	0.856	0.931	CLONAL	3	TRUE	0	0.52135745301615	3		327	642	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551677	150551677	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1220651661	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	76	203	0	ENST00000369026.2:c.330G>C	p.Glu110Asp	p.E110D	ENST00000369026	NM_021960.4	110	gaG/gaC	1/3	0.481745711450709	5	FACETS	1	0.906	1	0.345	0.303	0.39	CLONAL	1	TRUE	2	0.52135745301615	5		203	502	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849083	156849083	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	381	627	0	ENST00000524377.1:c.1975G>T	p.Gly659Cys	p.G659C	ENST00000524377	NM_002529.3	659	Ggc/Tgc	15/17	0.481745711450709	5	FACETS	0.948	0.899	0.997	0.632	0.599	0.665	CLONAL	2	TRUE	2	0.52135745301615	5		627	1374	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440202	220440202	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1152	307	916	0	ENST00000243786.2:c.1055A>G	p.Tyr352Cys	p.Y352C	ENST00000243786	NM_002191.3	352	tAt/tGt	2/2	0.511110037212509	3	FACETS	1	0.955	1	0.509	0.478	0.54	CLONAL	1	TRUE	1	0.52135745301615	3		916	1459	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422567	225422567	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	158	210	0	ENST00000264414.4:c.73A>G	p.Met25Val	p.M25V	ENST00000264414	NM_003590.4	25	Atg/Gtg	2/16	0.511110037212509	3	FACETS	0.955	0.886	1	0.955	0.886	1	CLONAL	2	TRUE	1	0.52135745301615	3		210	400	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498397	89498397	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	432	394	0	ENST00000336596.2:c.2369G>T	p.Trp790Leu	p.W790L	ENST00000336596	NM_005233.5	790	tGg/tTg	14/17	0.481745711450709	5	FACETS	0.959	0.918	1	0.959	0.918	1	CLONAL	3	TRUE	2	0.52135745301615	5		394	1026	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741590	17741590	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	151	198	0	ENST00000250003.3:c.261C>A	p.His87Gln	p.H87Q	ENST00000250003	NM_002478.4	87	caC/caA	1/3	0.511110037212509	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	1	0.52135745301615	3		198	352	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136193	64136193	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	287	403	1	ENST00000334205.4:c.1352A>T	p.Gln451Leu	p.Q451L	ENST00000334205	NM_003942.2	451	cAg/cTg	12/17	0.482144734295337	4	FACETS	0.901	0.849	0.955	0.901	0.849	0.955	CLONAL	2	TRUE	2	0.52135745301615	4		404	929	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514163	69514163	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	351	545	0	ENST00000294312.3:c.518C>G	p.Pro173Arg	p.P173R	ENST00000294312	NM_005117.2	173	cCa/cGa	3/3	0.482144734295337	4	FACETS	0.906	0.858	0.954	0.906	0.858	0.954	CLONAL	2	TRUE	2	0.52135745301615	4		545	1131	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245210	46245210	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	133	371	0	ENST00000334344.6:c.3304G>T	p.Ala1102Ser	p.A1102S	ENST00000334344	NM_152641.2	1102	Gcc/Tcc	15/21	0.419558841669069	4	FACETS	0.973	0.884	1	0.324	0.294	0.356	CLONAL	1	TRUE	1	0.52135745301615	4		371	798	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416423	49416423	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	398	442	0	ENST00000301067.7:c.16288A>G	p.Ile5430Val	p.I5430V	ENST00000301067	NM_003482.3	5430	Atc/Gtc	51/54	0.419558841669069	4	FACETS	1	0.991	1	0.771	0.736	0.807	CLONAL	2	TRUE	1	0.52135745301615	4		442	1004	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433848	49433848	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	155	561	1	ENST00000301067.7:c.7705G>T	p.Gly2569Cys	p.G2569C	ENST00000301067	NM_003482.3	2569	Ggc/Tgc	31/54	0.419558841669069	4	FACETS	0.825	0.754	0.899	0.275	0.251	0.3	CLONAL	1	TRUE	1	0.52135745301615	4		562	1097	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257255	133257255	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	155	527	0	ENST00000320574.5:c.223G>A	p.Asp75Asn	p.D75N	ENST00000320574	NM_006231.2	75	Gat/Aat	3/49	0.419558841669069	4	FACETS	0.894	0.817	0.974	0.298	0.272	0.325	CLONAL	1	TRUE	1	0.52135745301615	4		527	1012	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953773	48953773	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	35	270	0	ENST00000267163.4:c.1376C>G	p.Ser459Cys	p.S459C	ENST00000267163	NM_000321.2	459	tCc/tGc	14/27	0.502765041663911	3	FACETS	0.315	0.257	0.379	0.105	0.085	0.127	SUBCLONAL	1	TRUE	0	0.52135745301615	3		270	538	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336139	73336139	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	506	464	0	ENST00000377767.4:c.2264G>T	p.Cys755Phe	p.C755F	ENST00000377767	NM_014953.3	755	tGt/tTt	17/21	0.502765041663911	3	FACETS	0.869	0.837	0.9	0.869	0.837	0.9	CLONAL	3	TRUE	0	0.52135745301615	3		464	939	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95577731	95577731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	855	798	0	ENST00000393063.1:c.2179G>A	p.Asp727Asn	p.D727N	ENST00000393063	NM_030621.3	727	Gat/Aat	15/28	0.52135745301615	3	FACETS	0.984	0.959	1	0.984	0.959	1	CLONAL	3	TRUE	0	0.52135745301615	3		798	1400	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678582	88678582	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	176	239	0	ENST00000360948.2:c.954G>C	p.Glu318Asp	p.E318D	ENST00000360948	NM_001012338.2	318	gaG/gaC	9/19	0.511110037212509	3	FACETS	0.917	0.853	0.982	0.917	0.853	0.982	CLONAL	2	TRUE	1	0.52135745301615	3		239	464	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679241	88679241	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1567498322	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	177	538	0	ENST00000360948.2:c.796A>G	p.Ile266Val	p.I266V	ENST00000360948	NM_001012338.2	266	Atc/Gtc	8/19	0.511110037212509	3	FACETS	0.859	0.791	0.93	0.43	0.395	0.465	CLONAL	1	TRUE	1	0.52135745301615	3		538	996	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	364640	364640	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	171	466	0	ENST00000262320.3:c.922G>A	p.Ala308Thr	p.A308T	ENST00000262320	NM_003502.3	308	Gcc/Acc	3/11	0.507252510165699	3	FACETS	1	0.933	1	0.507	0.467	0.549	CLONAL	1	TRUE	1	0.52135745301615	3		466	815	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923497	9923497	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	242	307	0	ENST00000330684.3:c.1790C>A	p.Pro597His	p.P597H	ENST00000330684	NM_001134407.1	597	cCt/cAt	9/13	0.507252510165699	3	FACETS	0.891	0.837	0.945	0.891	0.837	0.945	CLONAL	2	TRUE	1	0.52135745301615	3		307	657	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984951	9984951	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	188	549	1	ENST00000330684.3:c.1014G>T	p.Met338Ile	p.M338I	ENST00000330684	NM_001134407.1	338	atG/atT	4/13	0.507252510165699	3	FACETS	0.866	0.799	0.935	0.433	0.399	0.468	CLONAL	1	TRUE	1	0.52135745301615	3		550	1050	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877373	89877373	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs781401861	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	283	392	0	ENST00000389301.3:c.390G>C	p.Glu130Asp	p.E130D	ENST00000389301	NM_000135.2	130	gaG/gaC	4/43	0.507252510165699	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.52135745301615	3		392	655	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435348	56435348	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	243	361	0	ENST00000407977.2:c.1789C>T	p.Gln597Ter	p.Q597*	ENST00000407977		597	Caa/Taa	9/10	0.3615407755278	5	FACETS	1	0.955	1			1	CLONAL	2	TRUE	NA	0.52135745301615	5		361	812	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117639	70117639	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs765600450	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	160	442	1	ENST00000245479.2:c.107C>A	p.Pro36Gln	p.P36Q	ENST00000245479	NM_000346.3	36	cCg/cAg	1/3	0.511110037212509	3	FACETS	1	0.922	1	0.502	0.461	0.545	CLONAL	1	TRUE	1	0.52135745301615	3		443	771	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220691	1220691	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs878853247	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	321	546	0	ENST00000326873.7:c.709G>C	p.Asp237His	p.D237H	ENST00000326873	NM_000455.4	237	Gac/Cac	5/10	0.476262333817511	2	FACETS	0.891	0.848	0.934	0.891	0.848	0.934	CLONAL	2	TRUE	0	0.52135745301615	2		546	691	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270570	10270570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	278	420	0	ENST00000340748.4:c.1070G>A	p.Gly357Glu	p.G357E	ENST00000340748		357	gGg/gAg	15/40	0.476262333817511	2	FACETS	0.866	0.82	0.912	0.866	0.82	0.912	CLONAL	2	TRUE	0	0.52135745301615	2		420	616	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313370	30313370	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	406	578	0	ENST00000262643.3:c.970A>G	p.Ile324Val	p.I324V	ENST00000262643	NM_001238.2	324	Ata/Gta	11/12	0.481745711450709	5	FACETS	0.966	0.918	1	0.644	0.612	0.676	CLONAL	2	TRUE	2	0.52135745301615	5		578	1437	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932962	39932962	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	366	546	0	ENST00000378444.4:c.1637G>T	p.Arg546Leu	p.R546L	ENST00000378444	NM_001123385.1	546	cGc/cTc	4/15	0.296277925957535	5	FACETS	1	0.979	1	0.705	0.669	0.742	INDETERMINATE	2	TRUE	2	0.52135745301615	5		546	1183	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411396	63411396	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	377	680	0	ENST00000330258.3:c.1771A>T	p.Arg591Trp	p.R591W	ENST00000330258	NM_152424.3	591	Agg/Tgg	2/2	0.296277925957535	5	FACETS	1	0.976	1	0.697	0.662	0.733	INDETERMINATE	2	TRUE	2	0.52135745301615	5		680	1232	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411705	63411705	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	439	702	0	ENST00000330258.3:c.1462G>T	p.Gly488Trp	p.G488W	ENST00000330258	NM_152424.3	488	Ggg/Tgg	2/2	0.296277925957535	5	FACETS	1	0.988	1	0.734	0.7	0.769	INDETERMINATE	2	TRUE	2	0.52135745301615	5		702	1362	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412862	63412862	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	383	520	1	ENST00000330258.3:c.305C>A	p.Ala102Glu	p.A102E	ENST00000330258	NM_152424.3	102	gCa/gAa	2/2	0.296277925957535	5	FACETS	1	0.976	1	0.696	0.661	0.732	INDETERMINATE	2	TRUE	2	0.52135745301615	5		521	1254	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617192	100617192	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	470	713	0	ENST00000308731.7:c.557A>T	p.Lys186Met	p.K186M	ENST00000308731	NM_000061.2	186	aAg/aTg	7/19	0.296277925957535	5	FACETS	1	0.988	1	0.728	0.695	0.761	INDETERMINATE	2	TRUE	2	0.52135745301615	5		713	1472	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210312	123210312	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	603	454	0	ENST00000218089.9:c.2664G>T	p.Gln888His	p.Q888H	ENST00000218089	NM_001042749.1	888	caG/caT	26/35	0.52135745301615	5	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	2	0.52135745301615	5		454	1318	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145742	11145742	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	319	538	0	ENST00000358026.2:c.4105del	p.Arg1369ValfsTer15	p.R1369Vfs*15	ENST00000358026	NM_001128849.1	1368	ggC/gg	29/36	0.476262333817511	2	FACETS	0.904	0.86	0.948	0.904	0.86	0.948	CLONAL	2	TRUE	0	0.52135745301615	2		538	677	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604306	189604307	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	403	421	0	ENST00000264731.3:c.1473_1474delinsAA	p.Pro492Thr	p.P492T	ENST00000264731	NM_003722.4	491	acTCct/acAAct	11/14	0.481745711450709	5	FACETS	0.871	0.831	0.912	0.871	0.831	0.912	CLONAL	3	TRUE	2	0.52135745301615	5		421	1054	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954340	48954340	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	TT	novel	NA	P-0011471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	253	246	0	ENST00000267163.4:c.1461delinsTT	p.Leu487PhefsTer6	p.L487Ffs*6	ENST00000267163	NM_000321.2	487	ttG/ttTT	16/27	0.502765041663911	3	FACETS	1	0.99	1	0.798	0.756	0.841	CLONAL	2	TRUE	0	0.52135745301615	3		246	511	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	89	532	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.256239928119662	2		532	553	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1247	136	1114	2	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.768	0.696	0.844	0.768	0.696	0.844	SUBCLONAL	1	FALSE	1	0.256239928119662	2		1116	1383	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	22	542	2	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.273	0.211	0.347	0.273	0.211	0.347	SUBCLONAL	1	FALSE	1	0.256239928119662	2		544	628	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	147	660	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.256239928119662	2		660	819	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793663	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1286	51	1079	2	ENST00000263967.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000263967	NM_006218.2	93	cGg/cAg	2/21	1	2	FACETS	0.298	0.252	0.349	0.298	0.252	0.349	SUBCLONAL	1	FALSE	1	0.256239928119662	2		1081	1337	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	149	244	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.871	0.803	0.941	1	0.993	1	CLONAL	3	FALSE	1	0.256239928119662	2		244	445	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176671198	176671198	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	88	494	0	ENST00000439151.2:c.4305C>A	p.Cys1435Ter	p.C1435*	ENST00000439151	NM_022455.4	1435	tgC/tgA	9/23	1	2	FACETS	0.962	0.852	1	0.962	0.852	1	CLONAL	1	FALSE	1	0.256239928119662	2		494	714	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557629	95557629	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	27	664	0	ENST00000393063.1:c.5438A>G	p.Glu1813Gly	p.E1813G	ENST00000393063	NM_030621.3	1813	gAg/gGg	26/28	1	2	FACETS	0.235	0.186	0.292	0.235	0.186	0.292	SUBCLONAL	1	FALSE	1	0.256239928119662	2		664	897	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	49	621	0	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	1	2	FACETS	0.497	0.419	0.582	0.497	0.419	0.582	SUBCLONAL	1	FALSE	1	0.256239928119662	2		621	770	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	62	824	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.442	0.38	0.51	0.442	0.38	0.51	SUBCLONAL	1	FALSE	1	0.256239928119662	2		824	1095	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923645	39923645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368780561	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	54	757	3	ENST00000378444.4:c.3446C>T	p.Ala1149Val	p.A1149V	ENST00000378444	NM_001123385.1	1149	gCg/gTg	7/15	1	2	FACETS	0.412	0.35	0.479	0.412	0.35	0.479	SUBCLONAL	1	FALSE	1	0.256239928119662	2		760	1024	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	65	654	0	ENST00000227507.2:c.859C>T	p.Pro287Ser	p.P287S	ENST00000227507	NM_053056.2	287	Ccc/Tcc	5/5	1	2	FACETS	0.693	0.6	0.794	0.693	0.6	0.794	SUBCLONAL	1	FALSE	1	0.256239928119662	2		654	732	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578226	7578226	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1464727668	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	127	790	0	ENST00000269305.4:c.623A>T	p.Asp208Val	p.D208V	ENST00000269305	NM_001126112.2	208	gAc/gTc	6/11	1	2	FACETS	0.897	0.811	0.988	0.897	0.811	0.988	CLONAL	1	FALSE	1	0.256239928119662	2		790	1105	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100183	27100183	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1421112233	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	30	479	0	ENST00000324856.7:c.3979C>T	p.Gln1327Ter	p.Q1327*	ENST00000324856	NM_006015.4	1327	Cag/Tag	16/20	1	2	FACETS	0.463	0.372	0.566	0.463	0.372	0.566	SUBCLONAL	1	FALSE	1	0.256239928119662	2		479	506	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390982	89390982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	36	597	0	ENST00000336596.2:c.1048G>A	p.Asp350Asn	p.D350N	ENST00000336596	NM_005233.5	350	Gac/Aac	5/17	1	2	FACETS	0.397	0.326	0.479	0.397	0.326	0.479	SUBCLONAL	1	FALSE	1	0.256239928119662	2		597	707	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715979	52715979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786205227	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	66	726	4	ENST00000322088.6:c.544C>T	p.Arg182Trp	p.R182W	ENST00000322088	NM_014225.5	182	Cgg/Tgg	5/15	1	2	FACETS	0.523	0.452	0.6	0.523	0.452	0.6	SUBCLONAL	1	FALSE	1	0.256239928119662	2		730	985	SUCCESS
ATR	545	MSKCC	GRCh37	3	142168368	142168368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1034620994	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	61	537	0	ENST00000350721.4:c.7838C>T	p.Pro2613Leu	p.P2613L	ENST00000350721	NM_001184.3	2613	cCg/cTg	47/47	1	2	FACETS	0.715	0.616	0.823	0.715	0.616	0.823	SUBCLONAL	1	FALSE	1	0.256239928119662	2		537	666	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992292	72992292	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140602496	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1335	136	1256	4	ENST00000268489.5:c.1753G>A	p.Gly585Ser	p.G585S	ENST00000268489	NM_006885.3	585	Ggc/Agc	2/10	1	2	FACETS	0.722	0.654	0.794	0.722	0.654	0.794	SUBCLONAL	1	FALSE	1	0.256239928119662	2		1260	1471	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797852	45797852	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759822330	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	147	646	1	ENST00000450313.1:c.919C>T	p.Arg307Trp	p.R307W	ENST00000450313	NM_012222.2	307	Cgg/Tgg	10/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.256239928119662	2		647	1032	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095943	178095943	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1438982923	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	53	479	1	ENST00000397062.3:c.1388C>T	p.Ala463Val	p.A463V	ENST00000397062	NM_006164.4	463	gCt/gTt	5/5	1	2	FACETS	0.831	0.709	0.964	0.831	0.709	0.964	CLONAL	1	FALSE	1	0.256239928119662	2		480	498	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37081744	37081744	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	52	643	0	ENST00000231790.2:c.1626G>T	p.Gln542His	p.Q542H	ENST00000231790	NM_000249.3	542	caG/caT	14/19	1	2	FACETS	0.432	0.366	0.504	0.432	0.366	0.504	SUBCLONAL	1	FALSE	1	0.256239928119662	2		643	940	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200073	128200073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374457534	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	58	771	3	ENST00000341105.2:c.1232C>T	p.Ala411Val	p.A411V	ENST00000341105	NM_032638.4	411	gCg/gTg	6/6	1	2	FACETS	0.405	0.347	0.47	0.405	0.347	0.47	SUBCLONAL	1	FALSE	1	0.256239928119662	2		774	1117	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178942528	178942528	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	31	353	0	ENST00000263967.3:c.2335C>A	p.Leu779Met	p.L779M	ENST00000263967	NM_006218.2	779	Ctg/Atg	16/21	1	2	FACETS	0.442	0.357	0.54	0.442	0.357	0.54	SUBCLONAL	1	FALSE	1	0.256239928119662	2		353	547	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430614	181430614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	31	341	0	ENST00000325404.1:c.466C>T	p.Arg156Cys	p.R156C	ENST00000325404	NM_003106.3	156	Cgc/Tgc	1/1	1	2	FACETS	0.532	0.43	0.648	0.532	0.43	0.648	SUBCLONAL	1	FALSE	1	0.256239928119662	2		341	455	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176678775	176678775	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	50	653	0	ENST00000439151.2:c.4686C>A	p.Cys1562Ter	p.C1562*	ENST00000439151	NM_022455.4	1562	tgC/tgA	12/23	1	2	FACETS	0.454	0.384	0.531	0.454	0.384	0.531	SUBCLONAL	1	FALSE	1	0.256239928119662	2		653	860	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707797	176707797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886041219	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	121	557	0	ENST00000439151.2:c.5854C>T	p.Arg1952Trp	p.R1952W	ENST00000439151	NM_022455.4	1952	Cgg/Tgg	18/23	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.256239928119662	2		557	815	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528079	157528079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1282942992	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	56	264	0	ENST00000346085.5:c.5804C>T	p.Ala1935Val	p.A1935V	ENST00000346085	NM_020732.3	1935	gCg/gTg	20/20	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	FALSE	1	0.256239928119662	2		264	415	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864225	117864225	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	58	883	4	ENST00000297338.2:c.1432C>T	p.Arg478Ter	p.R478*	ENST00000297338	NM_006265.2	478	Cga/Tga	11/14	1	2	FACETS	0.413	0.353	0.478	0.413	0.353	0.478	SUBCLONAL	1	FALSE	1	0.256239928119662	2		887	1097	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737699	145737699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758008013	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	36	423	0	ENST00000428558.2:c.3064C>T	p.Arg1022Cys	p.R1022C	ENST00000428558	NM_004260.3	1022	Cgt/Tgt	19/22	1	2	FACETS	0.473	0.388	0.569	0.473	0.388	0.569	SUBCLONAL	1	FALSE	1	0.256239928119662	2		423	594	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412547	80412547	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	34	436	0	ENST00000286548.4:c.494A>T	p.Asp165Val	p.D165V	ENST00000286548	NM_002072.3	165	gAc/gTc	4/7	1	2	FACETS	0.408	0.332	0.494	0.408	0.332	0.494	SUBCLONAL	1	FALSE	1	0.256239928119662	2		436	650	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250065	110250065	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	34	389	0	ENST00000374672.4:c.610C>A	p.Leu204Met	p.L204M	ENST00000374672	NM_004235.4	204	Ctg/Atg	3/5	1	2	FACETS	0.518	0.423	0.626	0.518	0.423	0.626	SUBCLONAL	1	FALSE	1	0.256239928119662	2		389	512	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760066	133760066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1459798133	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	33	495	1	ENST00000318560.5:c.2389G>A	p.Val797Ile	p.V797I	ENST00000318560	NM_005157.4	797	Gtc/Atc	11/11	1	2	FACETS	0.413	0.336	0.502	0.413	0.336	0.502	SUBCLONAL	1	FALSE	1	0.256239928119662	2		496	623	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399225	139399225	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs976118697	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	30	362	4	ENST00000277541.6:c.4918G>A	p.Ala1640Thr	p.A1640T	ENST00000277541	NM_017617.3	1640	Gca/Aca	26/34	1	2	FACETS	0.484	0.389	0.592	0.484	0.389	0.592	SUBCLONAL	1	FALSE	1	0.256239928119662	2		366	484	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981765	101981765	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	36	469	0	ENST00000282441.5:c.186G>T	p.Glu62Asp	p.E62D	ENST00000282441	NM_001130145.2	62	gaG/gaT	1/9	1	2	FACETS	0.422	0.346	0.508	0.422	0.346	0.508	SUBCLONAL	1	FALSE	1	0.256239928119662	2		469	666	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124717	108124717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751515818	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	43	418	0	ENST00000278616.4:c.2075G>A	p.Arg692His	p.R692H	ENST00000278616	NM_000051.3	692	cGc/cAc	13/63	1	2	FACETS	0.582	0.486	0.688	0.582	0.486	0.688	SUBCLONAL	1	FALSE	1	0.256239928119662	2		418	577	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165786	108165786	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs753870656	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	42	392	0	ENST00000278616.4:c.4909G>A	p.Asp1637Asn	p.D1637N	ENST00000278616	NM_000051.3	1637	Gat/Aat	32/63	1	2	FACETS	0.644	0.537	0.763	0.644	0.537	0.763	SUBCLONAL	1	FALSE	1	0.256239928119662	2		392	509	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118339561	118339561	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	90	567	0	ENST00000534358.1:c.502+2T>C		p.X168_splice	ENST00000534358	NM_005933.3	168			1	2	FACETS	0.826	0.732	0.927	0.826	0.732	0.927	CLONAL	1	FALSE	1	0.256239928119662	2		567	850	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856209	111856209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	38	334	1	ENST00000341259.2:c.260G>A	p.Arg87His	p.R87H	ENST00000341259	NM_005475.2	87	cGc/cAc	2/8	1	2	FACETS	0.5	0.413	0.598	0.5	0.413	0.598	SUBCLONAL	1	FALSE	1	0.256239928119662	2		335	593	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856280	111856280	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	10	65	0	ENST00000341259.2:c.331G>A	p.Ala111Thr	p.A111T	ENST00000341259	NM_005475.2	111	Gcc/Acc	2/8	1	2	FACETS	0.531	0.361	0.744	0.531	0.361	0.744	SUBCLONAL	1	FALSE	1	0.256239928119662	2		65	147	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134160	41134160	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374723626	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	114	1095	3	ENST00000379561.5:c.1468C>T	p.Arg490Trp	p.R490W	ENST00000379561	NM_002015.3	490	Cgg/Tgg	2/3	1	2	FACETS	0.734	0.659	0.814	0.734	0.659	0.814	SUBCLONAL	1	FALSE	1	0.256239928119662	2		1098	1212	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983596	7983596	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	45	649	0	ENST00000319144.4:c.711G>T	p.Lys237Asn	p.K237N	ENST00000319144	NM_001139.2	237	aaG/aaT	6/15	1	2	FACETS	0.391	0.327	0.462	0.391	0.327	0.462	SUBCLONAL	1	FALSE	1	0.256239928119662	2		649	898	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119861	70119861	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	79	624	0	ENST00000245479.2:c.863C>T	p.Thr288Ile	p.T288I	ENST00000245479	NM_000346.3	288	aCc/aTc	3/3	1	2	FACETS	0.718	0.63	0.812	0.718	0.63	0.812	SUBCLONAL	1	FALSE	1	0.256239928119662	2		624	859	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602589	10602589	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1378587016	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	38	546	1	ENST00000171111.5:c.989C>T	p.Thr330Ile	p.T330I	ENST00000171111	NM_203500.1	330	aCc/aTc	3/6	1	2	FACETS	0.424	0.349	0.508	0.424	0.349	0.508	SUBCLONAL	1	FALSE	1	0.256239928119662	2		547	700	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259300	36259300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	26	185	1	ENST00000300305.3:c.191G>A	p.Gly64Asp	p.G64D	ENST00000300305		64	gGc/gAc	3/8	1	2	FACETS	0.769	0.611	0.949	0.769	0.611	0.949	CLONAL	1	FALSE	1	0.256239928119662	2		186	264	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045486	47045486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	48	647	0	ENST00000377604.3:c.2453C>T	p.Ala818Val	p.A818V	ENST00000377604	NM_001204468.1	818	gCa/gTa	22/24	1	2	FACETS	0.41	0.345	0.482	0.41	0.345	0.482	SUBCLONAL	1	FALSE	1	0.256239928119662	2		647	914	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517927	187517928	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	133	716	0	ENST00000441802.2:c.12766dup	p.Tyr4256LeufsTer8	p.Y4256Lfs*8	ENST00000441802	NM_005245.3	4256	tac/tTac	25/27	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	FALSE	1	0.256239928119662	2		716	1015	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424442	49424443	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs797044740	NA	P-0011569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	120	572	0	ENST00000301067.7:c.13780dup	p.Ala4594GlyfsTer12	p.A4594Gfs*12	ENST00000301067	NM_003482.3	4594	gcc/gGcc	41/54	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.256239928119662	2		572	733	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11193207	11193207	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	264	329	0	ENST00000361445.4:c.5294A>G	p.Asn1765Ser	p.N1765S	ENST00000361445	NM_004958.3	1765	aAt/aGt	38/58	0.416304341075596	1	FACETS	0.958	0.901	1	0.958	0.901	1	CLONAL	1	TRUE	0	0.489532373764091	1		329	850	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923738	72923738	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	69	651	2	ENST00000268489.5:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000268489	NM_006885.3	1114	Cga/Tga	4/10	0.489532373764091	1	FACETS	0.165	0.143	0.189	0.165	0.143	0.189	SUBCLONAL	1	TRUE	0	0.489532373764091	1		653	1289	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037923	49037924	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	37	349	0	ENST00000267163.4:c.2167dup	p.Ile723AsnfsTer28	p.I723Nfs*28	ENST00000267163	NM_000321.2	721	-/A	21/27	0.489532373764091	1	FACETS	0.239	0.196	0.286	0.239	0.196	0.286	SUBCLONAL	1	TRUE	0	0.489532373764091	1		349	478	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0012071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	424	517	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	NA	2	FACETS	1	0.962	1			1	INDETERMINATE	2	TRUE	NA	0.467851042761174	2		517	902	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436296	110436297	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGG	rs34412495	NA	P-0012071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	20	77	1	ENST00000375856.3:c.2102_2104dup	p.Ala701dup	p.A701dup	ENST00000375856	NM_003749.2	701	gtg/gCCGtg	1/2	0.467557237851638	2	FACETS	0.712	0.552	0.895	0.356	0.276	0.448	SUBCLONAL	1	TRUE	0	0.467851042761174	2		78	120	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528645	89528645	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1449229684	NA	P-0012071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	277	360	0	ENST00000336596.2:c.2945C>A	p.Pro982His	p.P982H	ENST00000336596	NM_005233.5	982	cCc/cAc	17/17	0.40455515957467	4	FACETS	1	0.951	1			1	CLONAL	2	TRUE	NA	0.467851042761174	4		360	860	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582334	119582334	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0012071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1267	167	507	0	ENST00000316626.5:c.1067T>G	p.Leu356Ter	p.L356*	ENST00000316626		356	tTa/tGa	10/12	0.467851042761174	6	FACETS	0.964	0.883	1	0.241	0.22	0.263	CLONAL	1	TRUE	2	0.467851042761174	6		507	1434	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665386	138665386	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	579	408	0	ENST00000330315.3:c.179T>C	p.Val60Ala	p.V60A	ENST00000330315	NM_023067.3	60	gTg/gCg	1/1	0.467851042761174	6	FACETS	0.884	0.851	0.917	0.884	0.851	0.917	CLONAL	4	TRUE	2	0.467851042761174	6		408	1355	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158255	106158255	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	386	502	0	ENST00000380013.4:c.3156G>T	p.Lys1052Asn	p.K1052N	ENST00000380013	NM_001127208.2	1052	aaG/aaT	3/11	0.467851042761174	3	FACETS	0.927	0.882	0.973	0.927	0.882	0.973	CLONAL	2	TRUE	1	0.467851042761174	3		502	1098	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630081	187630081	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	531	533	1	ENST00000441802.2:c.901C>T	p.Gln301Ter	p.Q301*	ENST00000441802	NM_005245.3	301	Cag/Tag	2/27	0.467557237851638	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.467851042761174	2		534	1010	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189427	56189427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	243	532	1	ENST00000399503.3:c.4459C>T	p.Arg1487Cys	p.R1487C	ENST00000399503	NM_005921.1	1487	Cgt/Tgt	20/20	0.467557237851638	2	FACETS	1	0.969	1	0.529	0.495	0.565	CLONAL	1	TRUE	0	0.467851042761174	2		533	981	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199870	138199870	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	43	332	0	ENST00000237289.4:c.1288C>A	p.Leu430Ile	p.L430I	ENST00000237289	NM_001270507.1	430	Ctc/Atc	7/9	0.456078559386517	4	FACETS	0.338	0.281	0.4	0.113	0.093	0.134	SUBCLONAL	1	TRUE	1	0.467851042761174	4		332	799	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435548	18435548	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	311	392	0	ENST00000266497.5:c.533C>A	p.Thr178Lys	p.T178K	ENST00000266497		178	aCa/aAa	1/31	0.4494878114082	5	FACETS	0.948	0.894	1	0.632	0.596	0.669	CLONAL	2	TRUE	2	0.467851042761174	5		392	1193	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864354	57864354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368078339	NA	P-0012071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1499	304	728	1	ENST00000228682.2:c.1831C>T	p.Arg611Trp	p.R611W	ENST00000228682	NM_005269.2	611	Cgg/Tgg	12/12	0.425172254295795	4	FACETS	1	0.972	1	0.529	0.496	0.563	CLONAL	1	TRUE	2	0.467851042761174	4		729	1803	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027127	49027127	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0012071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	399	465	0	ENST00000267163.4:c.1696-2A>T		p.X566_splice	ENST00000267163	NM_000321.2	566			0.467557237851638	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.467851042761174	2		465	841	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858550	9858550	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	399	577	0	ENST00000330684.3:c.2851G>T	p.Gly951Trp	p.G951W	ENST00000330684	NM_001134407.1	951	Ggg/Tgg	13/13	0.4105968068951	5	FACETS	0.921	0.874	0.969	0.614	0.583	0.646	CLONAL	2	TRUE	2	0.467851042761174	5		577	1576	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134488	30134488	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	153	469	0	ENST00000263025.4:c.43C>G	p.Arg15Gly	p.R15G	ENST00000263025	NM_002746.2	15	Cgt/Ggt	1/9	0.4105968068951	5	FACETS	0.898	0.82	0.981	0.299	0.273	0.327	CLONAL	1	TRUE	2	0.467851042761174	5		469	1239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs201744589	NA	P-0012071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	422	502	0	ENST00000269305.4:c.892G>C	p.Glu298Gln	p.E298Q	ENST00000269305	NM_001126112.2	298	Gag/Cag	8/11	NA	2	FACETS	0.968	0.926	1			1	INDETERMINATE	2	TRUE	NA	0.467851042761174	2		502	932	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714643	52714643	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	651	454	0	ENST00000322088.6:c.401G>C	p.Arg134Pro	p.R134P	ENST00000322088	NM_014225.5	134	cGg/cCg	4/15	0.467851042761174	6	FACETS	0.906	0.875	0.938	0.906	0.875	0.938	CLONAL	4	TRUE	2	0.467851042761174	6		454	1486	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419902	41419902	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	390	586	0	ENST00000373198.4:c.419G>C	p.Gly140Ala	p.G140A	ENST00000373198	NM_133170.3	140	gGg/gCg	3/32	0.467851042761174	3	FACETS	0.921	0.876	0.966	0.921	0.876	0.966	CLONAL	2	TRUE	1	0.467851042761174	3		586	1117	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321355	1321355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	504	534	0	ENST00000400841.2:c.400G>A	p.Val134Met	p.V134M	ENST00000400841		134	Gtg/Atg	4/6	0.40455515957467	2	FACETS	1	0.996	1			1	CLONAL	1	TRUE	NA	0.467851042761174	2		534	1487	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872105	76872105	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	278	385	0	ENST00000373344.5:c.5542C>A	p.Gln1848Lys	p.Q1848K	ENST00000373344	NM_000489.3	1848	Cag/Aag	22/35	0.40455515957467	2	FACETS	1	0.993	1			1	CLONAL	1	TRUE	NA	0.467851042761174	2		385	838	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579315	7579316	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1267047192	NA	P-0012074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	273	362	0	ENST00000269305.4:c.371dup	p.Cys124TrpfsTer25	p.C124Wfs*25	ENST00000269305	NM_001126112.2	124	tgc/tgGc	4/11	0.360220214007641	2	FACETS	0.909	0.857	0.962	0.909	0.857	0.962	CLONAL	2	TRUE	0	0.388631838528451	2		362	773	SUCCESS
APC	324	MSKCC	GRCh37	5	112175235	112175235	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0012074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	194	286	0	ENST00000257430.4:c.3944C>G	p.Ser1315Ter	p.S1315*	ENST00000257430	NM_000038.5	1315	tCa/tGa	16/16	0.360220214007641	2	FACETS	0.84	0.782	0.9	0.84	0.782	0.9	CLONAL	2	TRUE	0	0.388631838528451	2		286	594	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812239	212812239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	71	520	0	ENST00000342788.4:c.337G>A	p.Asp113Asn	p.D113N	ENST00000342788	NM_005235.2	113	Gat/Aat	3/28	0.1544038494279	4	FACETS	0.708	0.617	0.806	0.354	0.308	0.403	INDETERMINATE	1	TRUE	2	0.388631838528451	4		520	717	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268138	153268138	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1406877044	NA	P-0012074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	153	540	1	ENST00000281708.4:c.670C>T	p.Arg224Ter	p.R224*	ENST00000281708	NM_033632.3	224	Cga/Tga	4/12	1	2	FACETS	0.734	0.671	0.801	0.734	0.671	0.801	SUBCLONAL	1	TRUE	1	0.388631838528451	2		541	1072	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188194	108188194	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs587780631	NA	P-0012074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	80	465	0	ENST00000278616.4:c.6293T>G	p.Leu2098Arg	p.L2098R	ENST00000278616	NM_000051.3	2098	cTt/cGt	43/63	0.265576498195219	3	FACETS	0.792	0.697	0.893	0.396	0.348	0.447	SUBCLONAL	1	TRUE	1	0.388631838528451	3		465	621	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368319	45368319	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	144	486	0	ENST00000262160.6:c.1283G>A	p.Arg428Lys	p.R428K	ENST00000262160	NM_005901.5	428	aGg/aAg	11/11	0.324444198900107	2	FACETS	0.767	0.705	0.832	0.767	0.705	0.832	SUBCLONAL	2	TRUE	0	0.388631838528451	2		486	483	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0012090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	57	357	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.605	0.518	0.701	0.605	0.518	0.701	SUBCLONAL	1	TRUE	1	0.207646826786416	2		357	907	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0012090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	80	371	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	1	2	FACETS	0.661	0.58	0.749	0.661	0.58	0.749	SUBCLONAL	1	TRUE	1	0.207646826786416	2		371	1166	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1567555907	NA	P-0012090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	48	454	0	ENST00000269305.4:c.314del	p.Gly105AlafsTer18	p.G105Afs*18	ENST00000269305	NM_001126112.2	105	gGc/gc	4/11	NA	2	FACETS	0.566	0.477	0.665			1	INDETERMINATE	1	TRUE	NA	0.207646826786416	2		454	817	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448328	56448328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199909371	NA	P-0012090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	56	405	0	ENST00000407977.2:c.319G>A	p.Val107Ile	p.V107I	ENST00000407977		107	Gtc/Atc	3/10	1	2	FACETS	0.626	0.535	0.726	0.626	0.535	0.726	SUBCLONAL	1	TRUE	1	0.207646826786416	2		405	862	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223461	2223461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	30	321	0	ENST00000398665.3:c.3572C>T	p.Ser1191Phe	p.S1191F	ENST00000398665	NM_032482.2	1191	tCt/tTt	25/28	1	2	FACETS	0.525	0.422	0.643	0.525	0.422	0.643	SUBCLONAL	1	TRUE	1	0.207646826786416	2		321	550	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121292	29121292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781879	NA	P-0012090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1487	105	613	0	ENST00000328354.6:c.383C>T	p.Pro128Leu	p.P128L	ENST00000328354	NM_007194.3	128	cCa/cTa	3/15	1	2	FACETS	0.635	0.567	0.709	0.635	0.567	0.709	SUBCLONAL	1	TRUE	1	0.207646826786416	2		613	1592	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0012152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	54	500	5	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.819	0.707	0.94	1	0.972	1	CLONAL	2	FALSE	1	0.259434696522996	2		505	254	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101401	27101402	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0012152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	136	860	0	ENST00000324856.7:c.4689dup	p.Met1564HisfsTer8	p.M1564Hfs*8	ENST00000324856	NM_006015.4	1561	-/C	18/20	0.14516550078507	3	FACETS	1	0.985	1	0.728	0.662	0.798	INDETERMINATE	1	FALSE	1	0.259434696522996	3		860	813	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0012152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	76	547	7	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	0.986	0.874	1	1	0.984	1	CLONAL	2	FALSE	1	0.259434696522996	2		554	297	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0012152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	8	190	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	1	0.78	1	1	0.78	1	CLONAL	1	FALSE	1	0.259434696522996	2		190	48	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0012152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	143	734	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.149958804102604	0	FACETS	0.753	0.69	0.818			1	INDETERMINATE	2	FALSE	0	0.259434696522996	0		734	542	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0012152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	20	482	5	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	0.259434696522996	4	FACETS	0.796	0.616	1	0.531	0.411	0.667	CLONAL	2	FALSE	1	0.259434696522996	4		487	122	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0012152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	39	427	4	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	1	0.93	1	1	0.973	1	CLONAL	2	FALSE	1	0.259434696522996	2		431	127	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	62	732	0	ENST00000397062.3:c.246A>T	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaT	2/5	1	2	FACETS	1	0.95	1	1	0.983	1	CLONAL	2	FALSE	1	0.259434696522996	2		732	205	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	156	298	0	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	0.241989438856101	0	FACETS	0.757	0.697	0.82			1	SUBCLONAL	2	FALSE	0	0.259434696522996	0		298	588	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0012152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	107	193	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.259434696522996	2	FACETS	0.906	0.839	0.972	1	0.991	1	CLONAL	5	FALSE	0	0.259434696522996	2		193	182	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	40	512	0	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.838	0.705	0.982	1	0.964	1	CLONAL	2	FALSE	1	0.259434696522996	2		512	184	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508082	106508082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	61	237	1	ENST00000359195.3:c.76C>T	p.Arg26Cys	p.R26C	ENST00000359195	NM_002649.2	26	Cgc/Tgc	2/11	1	2	FACETS	0.937	0.817	1	1	0.979	1	CLONAL	2	FALSE	1	0.259434696522996	2		238	251	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630626	158630626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912678	NA	P-0012152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	73	876	1	ENST00000263640.3:c.617G>A	p.Arg206His	p.R206H	ENST00000263640	NM_001105.4	206	cGc/cAc	6/11	1	2	FACETS	1	0.964	1	1	0.986	1	CLONAL	2	FALSE	1	0.259434696522996	2		877	231	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955112	17955112	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755706305	NA	P-0012152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	125	558	2	ENST00000458235.1:c.115del	p.Gln39SerfsTer108	p.Q39Sfs*108	ENST00000458235	NM_000215.3	39	Cag/ag	2/24	1	2	FACETS	0.962	0.875	1	1	0.99	1	CLONAL	2	FALSE	1	0.259434696522996	2		560	501	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165283	47165283	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	42	464	0	ENST00000409792.3:c.843del	p.Glu282LysfsTer19	p.E282Kfs*19	ENST00000409792	NM_014159.6	281	aaA/aa	3/21	1	2	FACETS	0.778	0.657	0.91	1	0.961	1	CLONAL	2	FALSE	1	0.259434696522996	2		464	208	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37055943	37055943	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	44	573	0	ENST00000231790.2:c.698G>A	p.Cys233Tyr	p.C233Y	ENST00000231790	NM_000249.3	233	tGt/tAt	9/19	1	2	FACETS	0.796	0.675	0.927	1	0.964	1	CLONAL	2	FALSE	1	0.259434696522996	2		573	213	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266840	41266840	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	27	469	0	ENST00000349496.5:c.511G>A	p.Ala171Thr	p.A171T	ENST00000349496	NM_001904.3	171	Gct/Act	5/15	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	FALSE	1	0.259434696522996	2		469	161	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916903	178916903	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	56	1238	2	ENST00000263967.3:c.290C>A	p.Pro97His	p.P97H	ENST00000263967	NM_006218.2	97	cCc/cAc	2/21	1	2	FACETS	0.885	0.766	1	1	0.975	1	CLONAL	2	FALSE	1	0.259434696522996	2		1240	244	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501499	149501499	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	32	871	0	ENST00000261799.4:c.2288A>G	p.Tyr763Cys	p.Y763C	ENST00000261799	NM_002609.3	763	tAt/tGt	16/23	1	2	FACETS	0.386	0.312	0.47	0.386	0.312	0.47	SUBCLONAL	1	FALSE	1	0.259434696522996	2		871	639	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481529	20481529	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	75	552	0	ENST00000346618.3:c.598G>T	p.Gly200Trp	p.G200W	ENST00000346618	NM_001949.4	200	Ggg/Tgg	3/7	0.128236077390546	4	FACETS	0.944	0.838	1	1	0.975	1	INDETERMINATE	3	FALSE	2	0.259434696522996	4		552	257	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624413	140624413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	91	178	0	ENST00000288602.6:c.91G>A	p.Ala31Thr	p.A31T	ENST00000288602	NM_004333.4	31	Gcc/Acc	1/18	1	2	FACETS	1	0.941	1	1	0.99	1	CLONAL	3	FALSE	1	0.259434696522996	2		178	222	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685289	89685289	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0012152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	36	199	0	ENST00000371953.3:c.184A>T	p.Lys62Ter	p.K62*	ENST00000371953	NM_000314.4	62	Aaa/Taa	3/9	0.259434696522996	2	FACETS	0.974	0.855	1	1	0.976	1	CLONAL	5	FALSE	0	0.259434696522996	2		199	57	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821425	72821425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769841511	NA	P-0012152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	55	1458	3	ENST00000268489.5:c.10750G>A	p.Ala3584Thr	p.A3584T	ENST00000268489	NM_006885.3	3584	Gca/Aca	10/10	1	2	FACETS	0.392	0.333	0.456	0.392	0.333	0.456	SUBCLONAL	1	FALSE	1	0.259434696522996	2		1461	1083	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17117082	17117082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776389684	NA	P-0012152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	162	738	5	ENST00000285071.4:c.1627G>A	p.Glu543Lys	p.E543K	ENST00000285071	NM_144997.5	543	Gag/Aag	14/14	0.14516550078507	3	FACETS	1	0.977	1	1	0.977	1	INDETERMINATE	2	FALSE	1	0.259434696522996	3		743	608	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820532	44820532	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	33	627	0	ENST00000377967.4:c.229G>A	p.Val77Ile	p.V77I	ENST00000377967	NM_021140.2	77	Gtt/Att	3/29	0.149958804102604	0	FACETS	0.703	0.583	0.833			1	INDETERMINATE	2	FALSE	0	0.259434696522996	0		627	134	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466003	69466038	+	inframe_deletion	In_Frame_Del	DEL	GTGGACCTGGCTTGCACACCCACCGACGTGCGGGAC	GTGGACCTGGCTTGCACACCCACCGACGTGCGGGAC	-	novel	NA	P-0012152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	87	707	1	ENST00000227507.2:c.847_882del	p.Leu283_Asp294del	p.L283_D294del	ENST00000227507	NM_053056.2	281	GTGGACCTGGCTTGCACACCCACCGACGTGCGGGAC/-	5/5	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.259434696522996	2		708	548	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443915	49443916	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	153	570	0	ENST00000301067.7:c.3455_3456insA	p.Val1153CysfsTer31	p.V1153Cfs*31	ENST00000301067	NM_003482.3	1152	cct/ccAt	11/54	1	2	FACETS	1	0.961	1	1	0.992	1	CLONAL	2	FALSE	1	0.259434696522996	2		570	550	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023968	27023975	+	frameshift_variant	Frame_Shift_Del	DEL	CCACGCGC	CCACGCGC	-	novel	NA	P-0012152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	47	154	0	ENST00000324856.7:c.1077_1084del	p.Ala360GlufsTer37	p.A360Efs*37	ENST00000324856	NM_006015.4	358	caCCACGCGCcc/cacc	1/20	0.14516550078507	3	FACETS	0.812	0.691	0.943	0.812	0.691	0.943	INDETERMINATE	2	FALSE	1	0.259434696522996	3		154	252	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008516	70008516	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	67	359	0	ENST00000394351.3:c.806del	p.Asn269ThrfsTer43	p.N269Tfs*43	ENST00000394351	NM_000248.3	268	gAa/ga	8/9	1	2	FACETS	1	0.96	1	1	0.984	1	CLONAL	2	FALSE	1	0.259434696522996	2		359	213	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	179	442	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.84	0.782	0.9	1	0.992	1	CLONAL	2	TRUE	1	0.440967077172897	2		444	483	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	189	410	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.342414014174736	0	FACETS	0.707	0.656	0.759			1	SUBCLONAL	1	TRUE	0	0.440967077172897	0		410	678	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882049	36882050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs780753361	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	204	607	0	ENST00000358127.4:c.963dup	p.Ala322ArgfsTer19	p.A322Rfs*19	ENST00000358127	NM_001280556.1	321	-/C	8/10	1	2	FACETS	0.866	0.803	0.932	0.866	0.803	0.932	CLONAL	1	TRUE	1	0.440967077172897	2		607	1068	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	27	170	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.645	0.517	0.788	0.645	0.517	0.788	SUBCLONAL	1	TRUE	1	0.440967077172897	2		171	190	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	187	628	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.440967077172897	2		628	839	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	216	479	9	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	0.440967077172897	3	FACETS	1	0.965	1	0.531	0.493	0.57	CLONAL	1	TRUE	1	0.440967077172897	3		488	1126	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	139	547	7	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	0.988	0.902	1	0.988	0.902	1	CLONAL	1	TRUE	1	0.440967077172897	2		554	638	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509085	66509085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	47	378	1	ENST00000273854.3:c.242del	p.Asn81MetfsTer24	p.N81Mfs*24	ENST00000273854	NM_004439.5	81	aAt/at	2/18	0.283832781718723	3	FACETS	0.566	0.477	0.663	0.283	0.238	0.332	SUBCLONAL	1	TRUE	1	0.440967077172897	3		379	460	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	77	322	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.440967077172897	2		322	274	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	49	123	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.440967077172897	2		123	201	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443634	49443634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs112921115	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	171	624	0	ENST00000301067.7:c.3737C>T	p.Thr1246Met	p.T1246M	ENST00000301067	NM_003482.3	1246	aCg/aTg	11/54	0.440967077172897	3	FACETS	0.847	0.778	0.919	0.423	0.389	0.46	CLONAL	1	TRUE	1	0.440967077172897	3		624	1118	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431874	49431874	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	146	463	3	ENST00000301067.7:c.9265del	p.Val3089TrpfsTer30	p.V3089Wfs*30	ENST00000301067	NM_003482.3	3089	Gtg/tg	34/54	0.440967077172897	3	FACETS	0.925	0.844	1	0.462	0.422	0.505	CLONAL	1	TRUE	1	0.440967077172897	3		466	874	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	134	482	5	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	0.283832781718723	3	FACETS	0.843	0.772	0.916	0.843	0.772	0.916	CLONAL	2	TRUE	1	0.440967077172897	3		487	440	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851054	63851054	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs117757404	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	100	289	0	ENST00000279873.7:c.1832C>T	p.Thr611Met	p.T611M	ENST00000279873	NM_032199.2	611	aCg/aTg	10/10	1	2	FACETS	0.935	0.839	1	0.935	0.839	1	CLONAL	1	TRUE	1	0.440967077172897	2		289	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577091	7577091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149633775	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	248	722	0	ENST00000269305.4:c.847C>T	p.Arg283Cys	p.R283C	ENST00000269305	NM_001126112.2	283	Cgc/Tgc	8/11	1	2	FACETS	0.911	0.85	0.973	0.911	0.85	0.973	CLONAL	1	TRUE	1	0.440967077172897	2		722	1235	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	164	471	6	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.919	0.845	0.997	0.919	0.845	0.997	CLONAL	1	TRUE	1	0.440967077172897	2		477	809	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144880	47144880	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	87	231	0	ENST00000409792.3:c.4873C>T	p.Arg1625Cys	p.R1625C	ENST00000409792	NM_014159.6	1625	Cgt/Tgt	7/21	1	2	FACETS	0.841	0.748	0.94	0.841	0.748	0.94	CLONAL	1	TRUE	1	0.440967077172897	2		231	469	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	115	386	3	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.789	0.712	0.87	0.789	0.712	0.87	SUBCLONAL	1	TRUE	1	0.440967077172897	2		389	661	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	227	357	0	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.440967077172897	2		357	992	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	144	509	9	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.440967077172897	2		518	585	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703538	47703538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63749932	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	151	623	1	ENST00000233146.2:c.2038C>T	p.Arg680Ter	p.R680*	ENST00000233146	NM_000251.2	680	Cga/Tga	13/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.440967077172897	2		624	633	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794655	42794655	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	194	569	1	ENST00000575354.2:c.1739del	p.Gly580ValfsTer148	p.G580Vfs*148	ENST00000575354	NM_015125.3	579	Ggg/gg	10/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.440967077172897	2		570	847	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063359	67063359	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	217	539	0	ENST00000412916.2:c.54del	p.Phe18LeufsTer4	p.F18Lfs*4	ENST00000412916		17	Ttt/tt	1/6	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.440967077172897	2		539	931	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625159	69625159	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554980306	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	185	617	2	ENST00000334134.2:c.634C>T	p.Arg212Trp	p.R212W	ENST00000334134	NM_005247.2	212	Cgg/Tgg	3/3	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.440967077172897	2		619	832	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100499	8100499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	242	634	2	ENST00000346208.3:c.473C>T	p.Pro158Leu	p.P158L	ENST00000346208		158	cCg/cTg	3/6	1	2	FACETS	0.929	0.867	0.994	0.929	0.867	0.994	CLONAL	1	TRUE	1	0.440967077172897	2		636	1181	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649566	206649566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1464747771	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	154	340	0	ENST00000367120.3:c.401G>A	p.Arg134His	p.R134H	ENST00000367120	NM_014002.3	134	cGc/cAc	6/22	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.440967077172897	2		340	644	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921803	111921803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	154	441	1	ENST00000393256.3:c.592C>T	p.His198Tyr	p.H198Y	ENST00000393256	NM_006538.4	198	Cat/Tat	4/4	1	2	FACETS	0.987	0.905	1	0.987	0.905	1	CLONAL	1	TRUE	1	0.440967077172897	2		442	708	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641190	12641190	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	222	755	3	ENST00000251849.4:c.1108G>A	p.Gly370Arg	p.G370R	ENST00000251849	NM_002880.3	370	Gga/Aga	10/17	1	2	FACETS	0.916	0.852	0.982	0.916	0.852	0.982	CLONAL	1	TRUE	1	0.440967077172897	2		758	1099	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182749	38182749	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	197	530	1	ENST00000396334.3:c.902G>A	p.Arg301His	p.R301H	ENST00000396334	NM_002468.4	301	cGc/cAc	5/5	1	2	FACETS	0.967	0.896	1	0.967	0.896	1	CLONAL	1	TRUE	1	0.440967077172897	2		531	924	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431077	181431077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	77	224	0	ENST00000325404.1:c.929G>A	p.Gly310Asp	p.G310D	ENST00000325404	NM_003106.3	310	gGc/gAc	1/1	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.440967077172897	2		224	343	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155325	185155325	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746379057	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	227	576	0	ENST00000265026.3:c.566C>T	p.Ala189Val	p.A189V	ENST00000265026	NM_004721.4	189	gCg/gTg	3/14	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.440967077172897	2		576	943	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356134	66356134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756357402	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	279	530	0	ENST00000273854.3:c.1363C>T	p.Arg455Trp	p.R455W	ENST00000273854	NM_004439.5	455	Cgg/Tgg	5/18	0.283832781718723	3	FACETS	0.933	0.879	0.987	0.933	0.879	0.987	CLONAL	2	TRUE	1	0.440967077172897	3		530	828	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540977	187540977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200488891	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	87	284	0	ENST00000441802.2:c.6763C>T	p.Arg2255Cys	p.R2255C	ENST00000441802	NM_005245.3	2255	Cgc/Tgc	10/27	0.283832781718723	3	FACETS	1	0.914	1	0.517	0.459	0.578	CLONAL	1	TRUE	1	0.440967077172897	3		284	466	SUCCESS
APC	324	MSKCC	GRCh37	5	112177001	112177001	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	70	635	0	ENST00000257430.4:c.5710C>T	p.Gln1904Ter	p.Q1904*	ENST00000257430	NM_000038.5	1904	Caa/Taa	16/16	1	2	FACETS	0.568	0.496	0.646	0.568	0.496	0.646	SUBCLONAL	1	TRUE	1	0.440967077172897	2		635	559	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638513	176638513	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	145	386	0	ENST00000439151.2:c.3113T>C	p.Met1038Thr	p.M1038T	ENST00000439151	NM_022455.4	1038	aTg/aCg	5/23	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.440967077172897	2		386	626	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683613	162683613	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	158	516	0	ENST00000366898.1:c.356T>G	p.Leu119Arg	p.L119R	ENST00000366898	NM_004562.2	119	cTg/cGg	3/12	1	2	FACETS	0.921	0.845	1	0.921	0.845	1	CLONAL	1	TRUE	1	0.440967077172897	2		516	778	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983457	90983457	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	65	365	0	ENST00000265433.3:c.646C>T	p.Gln216Ter	p.Q216*	ENST00000265433	NM_002485.4	216	Cag/Tag	6/16	0.283832781718723	3	FACETS	0.816	0.71	0.93	0.408	0.355	0.465	CLONAL	1	TRUE	1	0.440967077172897	3		365	441	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820166	139820166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540379507	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1368	346	1103	2	ENST00000247668.2:c.1319G>A	p.Arg440Gln	p.R440Q	ENST00000247668	NM_021138.3	440	cGg/cAg	11/11	1	2	FACETS	0.916	0.864	0.969	0.916	0.864	0.969	CLONAL	1	TRUE	1	0.440967077172897	2		1105	1714	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114724330	114724330	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368705098	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	242	946	0	ENST00000543371.1:c.397G>A	p.Gly133Ser	p.G133S	ENST00000543371	NM_001198531.1	133	Ggc/Agc	4/14	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.440967077172897	2		946	1042	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161445	2161445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758689893	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1274	207	964	0	ENST00000434045.2:c.82G>A	p.Gly28Arg	p.G28R	ENST00000434045	NM_001127598.1	28	Ggg/Agg	2/5	1	2	FACETS	0.634	0.586	0.684	0.634	0.586	0.684	SUBCLONAL	1	TRUE	1	0.440967077172897	2		964	1481	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246417	46246417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778810498	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	140	601	1	ENST00000334344.6:c.4511G>A	p.Arg1504Gln	p.R1504Q	ENST00000334344	NM_152641.2	1504	cGg/cAg	15/21	1	2	FACETS	0.907	0.828	0.99	0.907	0.828	0.99	CLONAL	1	TRUE	1	0.440967077172897	2		602	700	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112071	115112071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	216	621	0	ENST00000257566.3:c.1669G>A	p.Asp557Asn	p.D557N	ENST00000257566	NM_016569.3	557	Gat/Aat	7/8	0.440967077172897	3	FACETS	1	0.938	1	0.505	0.469	0.543	CLONAL	1	TRUE	1	0.440967077172897	3		621	1183	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563012	21563012	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371362441	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	203	488	2	ENST00000382592.4:c.907G>A	p.Ala303Thr	p.A303T	ENST00000382592	NM_014572.2	303	Gct/Act	4/8	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.440967077172897	2		490	899	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435111	110435111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	115	316	1	ENST00000375856.3:c.3290G>A	p.Arg1097His	p.R1097H	ENST00000375856	NM_003749.2	1097	cGc/cAc	1/2	1	2	FACETS	0.988	0.894	1	0.988	0.894	1	CLONAL	1	TRUE	1	0.440967077172897	2		317	528	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679209	88679209	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	92	564	0	ENST00000360948.2:c.828G>T	p.Glu276Asp	p.E276D	ENST00000360948	NM_001012338.2	276	gaG/gaT	8/19	1	2	FACETS	0.424	0.376	0.476	0.424	0.376	0.476	SUBCLONAL	1	TRUE	1	0.440967077172897	2		564	984	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032460	12032460	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	31	340	0	ENST00000353533.5:c.896A>T	p.Glu299Val	p.E299V	ENST00000353533	NM_003010.3	299	gAg/gTg	9/11	1	2	FACETS	0.475	0.385	0.576	0.475	0.385	0.576	SUBCLONAL	1	TRUE	1	0.440967077172897	2		340	296	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024509	16024509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1379969902	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	271	712	1	ENST00000268712.3:c.1709G>A	p.Arg570Gln	p.R570Q	ENST00000268712	NM_006311.3	570	cGg/cAg	16/46	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.440967077172897	2		713	1196	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459708	40459708	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748298777	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1519	444	1151	2	ENST00000345506.4:c.1873G>A	p.Gly625Arg	p.G625R	ENST00000345506	NM_003152.3	625	Ggg/Agg	16/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.440967077172897	2		1153	1963	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214666	5214666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs116660613	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	252	730	1	ENST00000357368.4:c.4400C>T	p.Pro1467Leu	p.P1467L	ENST00000357368	NM_002850.3	1467	cCg/cTg	29/38	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.440967077172897	2		731	1140	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40828020	40828020	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465304165	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	95	311	0	ENST00000373198.4:c.2408C>T	p.Ala803Val	p.A803V	ENST00000373198	NM_133170.3	803	gCc/gTc	17/32	1	2	FACETS	0.881	0.788	0.98	0.881	0.788	0.98	CLONAL	1	TRUE	1	0.440967077172897	2		311	489	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130573	29130573	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	128	643	0	ENST00000328354.6:c.137T>C	p.Met46Thr	p.M46T	ENST00000328354	NM_007194.3	46	aTg/aCg	2/15	1	2	FACETS	0.523	0.472	0.576	0.523	0.472	0.576	SUBCLONAL	1	TRUE	1	0.440967077172897	2		643	1111	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949103	44949103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	93	823	2	ENST00000377967.4:c.3664G>A	p.Ala1222Thr	p.A1222T	ENST00000377967	NM_021140.2	1222	Gca/Aca	25/29	1	2	FACETS	0.505	0.448	0.565	0.505	0.448	0.565	SUBCLONAL	1	TRUE	1	0.440967077172897	2		825	836	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190046	123190046	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	150	771	1	ENST00000218089.9:c.1265G>A	p.Arg422Gln	p.R422Q	ENST00000218089	NM_001042749.1	422	cGg/cAg	14/35	1	2	FACETS	0.928	0.85	1	0.928	0.85	1	CLONAL	1	TRUE	1	0.440967077172897	2		772	733	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252023	133252024	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1154	233	689	0	ENST00000320574.5:c.1186dup	p.Glu396GlyfsTer28	p.E396Gfs*28	ENST00000320574	NM_006231.2	396	gag/gGag	12/49	0.440967077172897	3	FACETS	0.93	0.865	0.997	0.465	0.432	0.499	CLONAL	1	TRUE	1	0.440967077172897	3		689	1387	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402224	402225	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	208	973	1	ENST00000399788.2:c.4566_4567del	p.Lys1523ValfsTer11	p.K1523Vfs*11	ENST00000399788	NM_001042603.1	1522	caGAag/caag	27/28	1	2	FACETS	0.839	0.777	0.902	0.839	0.777	0.902	CLONAL	1	TRUE	1	0.440967077172897	2		974	1125	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845615	63845618	+	frameshift_variant	Frame_Shift_Del	DEL	AAGA	AAGA	-	novel	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	74	272	1	ENST00000279873.7:c.1360_1363del	p.Glu454LysfsTer24	p.E454Kfs*24	ENST00000279873	NM_032199.2	452	AAGAaa/aa	9/10	1	2	FACETS	0.869	0.765	0.98	0.869	0.765	0.98	CLONAL	1	TRUE	1	0.440967077172897	2		273	386	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639646	47639646	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	86	463	0	ENST00000233146.2:c.740del	p.Gly247AlafsTer7	p.G247Afs*7	ENST00000233146	NM_000251.2	247	Ggc/gc	4/16	1	2	FACETS	0.737	0.654	0.826	0.737	0.654	0.826	SUBCLONAL	1	TRUE	1	0.440967077172897	2		463	529	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40477076	40477076	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	306	882	0	ENST00000264657.5:c.1369del	p.His457ThrfsTer7	p.H457Tfs*7	ENST00000264657	NM_139276.2	457	Cac/ac	16/24	1	2	FACETS	0.963	0.906	1	0.963	0.906	1	CLONAL	1	TRUE	1	0.440967077172897	2		882	1441	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257132	16257133	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	70	501	0	ENST00000375759.3:c.4399dup	p.Trp1467LeufsTer14	p.W1467Lfs*14	ENST00000375759	NM_015001.2	1466	gat/gaTt	11/15	1	2	FACETS	0.6	0.524	0.682	0.6	0.524	0.682	SUBCLONAL	1	TRUE	1	0.440967077172897	2		501	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0012189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	592	695	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.99	0.953	1	0.99	0.953	1	CLONAL	1	TRUE	1	0.837420935946116	2		695	1428	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554965	187554965	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	599	457	0	ENST00000441802.2:c.4196A>G	p.Asp1399Gly	p.D1399G	ENST00000441802	NM_005245.3	1399	gAc/gGc	7/27	0.837420935946116	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.837420935946116	2		457	699	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456497	99456497	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45553041	NA	P-0012189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	276	296	1	ENST00000268035.6:c.1814G>A	p.Arg605His	p.R605H	ENST00000268035	NM_000875.3	605	cGc/cAc	8/21	1	2	FACETS	0.934	0.882	0.986	0.934	0.882	0.986	CLONAL	1	TRUE	1	0.837420935946116	2		297	706	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0012189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	473	593	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	1	2	FACETS	0.894	0.855	0.933	0.894	0.855	0.933	CLONAL	1	TRUE	1	0.837420935946116	2		593	1264	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56402459	56402459	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	326	524	0	ENST00000348428.3:c.1501A>C	p.Ile501Leu	p.I501L	ENST00000348428	NM_006785.3	501	Atc/Ctc	13/17	1	2	FACETS	0.921	0.874	0.969	0.921	0.874	0.969	CLONAL	1	TRUE	1	0.837420935946116	2		524	845	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010530	48010548	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGGCCTGGGCCCAGGCC	CTGGGCCTGGGCCCAGGCC	-	novel	NA	P-0012189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	401	242	0	ENST00000234420.5:c.160_178del	p.Gly54TrpfsTer21	p.G54Wfs*21	ENST00000234420	NM_000179.2	53	gCTGGGCCTGGGCCCAGGCCc/gc	1/10	0.837420935946116	3	FACETS	1	0.993	1	0.622	0.592	0.651	CLONAL	1	TRUE	1	0.837420935946116	3		242	1093	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974808	21974809	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0012189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	211	205	0	ENST00000304494.5:c.18dup	p.Ser7GlufsTer8	p.S7Efs*8	ENST00000304494	NM_000077.4	6	-/G	1/3	0.837420935946116	1	FACETS	0.948	0.904	0.991	0.948	0.904	0.991	CLONAL	1	TRUE	0	0.837420935946116	1		205	309	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524468	187524469	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0012189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	609	377	0	ENST00000441802.2:c.11211_11212del	p.Cys3738ArgfsTer12	p.C3738Rfs*12	ENST00000441802	NM_005245.3	3737	ctCTgc/ctgc	19/27	0.837420935946116	2	FACETS	0.979	0.958	0.999	0.979	0.958	0.999	CLONAL	2	TRUE	0	0.837420935946116	2		377	743	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	60	374	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.988	0.859	1			1	INDETERMINATE	1	TRUE	NA	0.433948904066883	2		374	280	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652097	36652098	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0012207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	98	515	0	ENST00000244741.5:c.222dup	p.Lys75GlnfsTer14	p.K75Qfs*14	ENST00000244741	NM_000389.4	73	-/C	2/3	1	2	FACETS	0.826	0.739	0.918	0.826	0.739	0.918	CLONAL	1	TRUE	1	0.433948904066883	2		515	547	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0012207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	216	134	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.411034556066233	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.433948904066883	2		134	478	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652198	36652199	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0012207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	91	471	0	ENST00000244741.5:c.322dup	p.Glu108GlyfsTer21	p.E108Gfs*21	ENST00000244741	NM_000389.4	107	gag/gaGg	2/3	1	2	FACETS	0.824	0.734	0.919	0.824	0.734	0.919	CLONAL	1	TRUE	1	0.433948904066883	2		471	509	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806567	1806567	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs138986264	NA	P-0012207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	300	521	0	ENST00000260795.2:c.1283A>G	p.Asn428Ser	p.N428S	ENST00000260795		428	aAc/aGc	9/17	0.411034556066233	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.433948904066883	2		521	595	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339836	116339836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	156	605	1	ENST00000397752.3:c.698C>T	p.Ser233Phe	p.S233F	ENST00000397752	NM_000245.2	233	tCc/tTc	2/21	1	2	FACETS	0.817	0.748	0.889	0.817	0.748	0.889	CLONAL	1	TRUE	1	0.433948904066883	2		606	880	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781005	135781005	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs75820036	NA	P-0012207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	220	974	0	ENST00000298552.3:c.1960C>T	p.Gln654Ter	p.Q654*	ENST00000298552	NM_001162426.1	654	Cag/Tag	15/23	0.433948904066883	1	FACETS	0.892	0.831	0.955	0.892	0.831	0.955	CLONAL	1	TRUE	0	0.433948904066883	1		974	890	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851692	63851692	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	155	527	0	ENST00000279873.7:c.2470A>T	p.Met824Leu	p.M824L	ENST00000279873	NM_032199.2	824	Atg/Ttg	10/10	1	2	FACETS	0.988	0.906	1	0.988	0.906	1	CLONAL	1	TRUE	1	0.433948904066883	2		527	723	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95583979	95583979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	88	365	0	ENST00000393063.1:c.1489G>A	p.Glu497Lys	p.E497K	ENST00000393063	NM_030621.3	497	Gaa/Aaa	10/28	1	2	FACETS	0.88	0.783	0.982	0.88	0.783	0.982	CLONAL	1	TRUE	1	0.433948904066883	2		365	461	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16022773	16022773	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	106	443	0	ENST00000268712.3:c.1879C>T	p.Arg627Ter	p.R627*	ENST00000268712	NM_006311.3	627	Cga/Tga	17/46	1	2	FACETS	0.738	0.662	0.818	0.738	0.662	0.818	SUBCLONAL	1	TRUE	1	0.433948904066883	2		443	662	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0012233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	488	609	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.682497723884364	2	FACETS	0.971	0.941	1	0.971	0.941	1	CLONAL	2	TRUE	0	0.682497723884364	2		610	736	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0012233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	499	617	2	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.682497723884364	2	FACETS	0.962	0.932	0.992	0.962	0.932	0.992	CLONAL	2	TRUE	0	0.682497723884364	2		619	760	SUCCESS
APC	324	MSKCC	GRCh37	5	112175273	112175273	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123121	NA	P-0012233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	353	400	0	ENST00000257430.4:c.3982C>T	p.Gln1328Ter	p.Q1328*	ENST00000257430	NM_000038.5	1328	Cag/Tag	16/16	0.682497723884364	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.682497723884364	2		400	491	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482926	140482927	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs777474487	NA	P-0012233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	205	569	2	ENST00000288602.6:c.1208dup	p.Ala404CysfsTer9	p.A404Cfs*9	ENST00000288602	NM_004333.4	403	cct/ccCt	10/18	0.682497723884364	3	FACETS	0.729	0.675	0.784	0.364	0.337	0.392	SUBCLONAL	1	TRUE	1	0.682497723884364	3		571	1106	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433879	78433879	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	178	534	0	ENST00000370768.2:c.220G>T	p.Asp74Tyr	p.D74Y	ENST00000370768	NM_003902.3	74	Gat/Tat	3/20	0.682497723884364	2	FACETS	0.789	0.73	0.85	0.395	0.365	0.425	SUBCLONAL	1	TRUE	0	0.682497723884364	2		534	661	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625107	69625107	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs782554596	NA	P-0012233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	188	362	0	ENST00000334134.2:c.686G>C	p.Arg229Thr	p.R229T	ENST00000334134	NM_005247.2	229	aGa/aCa	3/3	0.682497723884364	2	FACETS	1	0.949	1	0.512	0.476	0.548	CLONAL	1	TRUE	0	0.682497723884364	2		362	538	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913167	44913167	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	221	922	0	ENST00000377967.4:c.842C>G	p.Pro281Arg	p.P281R	ENST00000377967	NM_021140.2	281	cCt/cGt	10/29	0.551799200355497	2	FACETS	0.6	0.558	0.643	0.3	0.279	0.322	SUBCLONAL	1	TRUE	0	0.682497723884364	2		922	1080	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0012279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	146	638	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	NA	2	FACETS	1	0.945	1			1	INDETERMINATE	2	TRUE	NA	0.427103150679862	2		638	334	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183825	10183825	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	117	337	2	ENST00000256474.2:c.294C>A	p.Tyr98Ter	p.Y98*	ENST00000256474	NM_000551.3	98	taC/taA	1/3	0.427103150679862	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.427103150679862	2		339	253	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993300	72993300	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745631900	NA	P-0012279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	185	904	1	ENST00000268489.5:c.745G>A	p.Gly249Ser	p.G249S	ENST00000268489	NM_006885.3	249	Ggt/Agt	2/10	0.324148038166718	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.427103150679862	1		905	610	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058705	47058706	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	117	564	0	ENST00000409792.3:c.7572dup	p.Lys2525Ter	p.K2525*	ENST00000409792	NM_014159.6	2524	-/T	21/21	0.357379218829138	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.427103150679862	1		564	341	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143399	30143399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	47	319	1	ENST00000389048.3:c.127C>T	p.Pro43Ser	p.P43S	ENST00000389048	NM_004304.4	43	Cca/Tca	1/29	0.427103150679862	3	FACETS	0.881	0.748	1	0.441	0.374	0.514	CLONAL	1	TRUE	1	0.427103150679862	3		320	303	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025961	48025961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	235	791	0	ENST00000234420.5:c.839G>A	p.Ser280Asn	p.S280N	ENST00000234420	NM_000179.2	280	aGt/aAt	4/10	0.427103150679862	3	FACETS	0.91	0.852	0.968	0.91	0.852	0.968	CLONAL	2	TRUE	1	0.427103150679862	3		791	734	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223905	53223905	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	148	327	0	ENST00000375401.3:c.3454del	p.Glu1152ArgfsTer112	p.E1152Rfs*112	ENST00000375401	NM_004187.3	1152	Gag/ag	23/26	0.292702747757317	2	FACETS	0.878	0.821	0.935			1	CLONAL	3	TRUE	NA	0.427103150679862	2		327	263	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696263	52696266	+	frameshift_variant	Frame_Shift_Del	DEL	GCAA	GCAA	-	novel	NA	P-0012279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	189	621	0	ENST00000394830.3:c.411_414del	p.Cys138AsnfsTer35	p.C138Nfs*35	ENST00000394830	NM_018313.4	137	gcTTGC/gc	5/30	0.357379218829138	1	FACETS	0.833	0.78	0.886	1	0.993	1	CLONAL	2	TRUE	0	0.427103150679862	1		621	418	SUCCESS
MET	4233	MSKCC	GRCh37	7	116414995	116415006	+	inframe_deletion	In_Frame_Del	DEL	ACATGTCCCCCA	ACATGTCCCCCA	-	novel	NA	P-0012279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	286	704	0	ENST00000397752.3:c.3089_3100del	p.Asp1030_Ile1034delinsVal	p.D1030_I1034delinsV	ENST00000397752	NM_000245.2	1030	gACATGTCCCCCAtc/gtc	15/21	0.317595276400459	6	FACETS	0.89	0.839	0.943	0.668	0.629	0.707	CLONAL	3	TRUE	2	0.427103150679862	6		704	930	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0012307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	49	673	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.988	0.838	1	0.988	0.838	1	CLONAL	1	TRUE	1	0.22	2		673	451	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115972	8115973	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0012307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	33	261	0	ENST00000346208.3:c.1320dup	p.Ala441ArgfsTer66	p.A441Rfs*66	ENST00000346208		440	acc/aCcc	6/6	1	2	FACETS	0.962	0.785	1	0.962	0.785	1	CLONAL	1	TRUE	1	0.22	2		261	312	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180835	106180835	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	94	586	0	ENST00000380013.4:c.3863G>T	p.Gly1288Val	p.G1288V	ENST00000380013	NM_001127208.2	1288	gGt/gTt	7/11	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.22	2		586	849	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120554444	120554444	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	42	295	0	ENST00000229340.5:c.11A>G	p.Asp4Gly	p.D4G	ENST00000229340	NM_006861.6	4	gAc/gGc	1/6	0.204787363605625	3	FACETS	1	0.851	1	0.509	0.426	0.602	CLONAL	1	TRUE	1	0.22	3		295	416	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	111	374	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.335439910859179	2		374	620	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411702	63411703	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0012317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	205	855	0	ENST00000330258.3:c.1464dup	p.Leu489AlafsTer19	p.L489Afs*19	ENST00000330258	NM_152424.3	488	-/G	2/2	1	2	FACETS	0.901	0.834	0.972	0.901	0.834	0.972	CLONAL	1	TRUE	1	0.335439910859179	2		855	1356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs863224499	NA	P-0012317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	217	813	0	ENST00000269305.4:c.672+1G>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.332427538822844	1	FACETS	0.968	0.9	1	0.968	0.9	1	CLONAL	1	TRUE	0	0.335439910859179	1		813	1112	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853251	68853251	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	199	728	1	ENST00000261769.5:c.1634G>C	p.Arg545Pro	p.R545P	ENST00000261769	NM_004360.3	545	cGg/cCg	11/16	NA	2	FACETS	0.931	0.86	1			1	INDETERMINATE	1	TRUE	NA	0.335439910859179	2		729	1275	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2114990	2115536	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGCAATCCCAGCTGCTCAGGAGGCTGAGGCAGGAGAATCGCTTGAACCTAGGAGGTGAAGGTTGCAGTGAGCCAAGATTCTGCCACTGCACTCCAGCCTGGACGACAGAGCAAGACTCTGTCTCAAAAAGAAAAAAAAAAAGGGCCGGGCACGGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGCGGATCATGAGGTCAGGAGATCAAGACCATCCTGGCTAACACGGTGAAACCCCATCTCTACTAAAAATACAAAAAATTAGCTGGGCGTGGTGGCGGGCGCCTGTAGTCCTAGCTACTGGGGAGGCTGAGGCAGGAGAATGGCGTGAACCTGGGAGGCGGAGCTTGTAGTGAGCTGAGATTGTGCCACCGCACTCCAGCCTGGGCGACAGAGCAAGACTCGATCTCAAAAAAAAAAAAAAAAAAAAAAAAGGTGTTTGTGGTAGAAAGTGTTCTCACGGCTGCTGACTCAGAACCATGAGCCTGTGTGTAAGTCCTGGCCTTCTCTTCAAAGGTGATGGCCCGCTCCCT	CTGCAATCCCAGCTGCTCAGGAGGCTGAGGCAGGAGAATCGCTTGAACCTAGGAGGTGAAGGTTGCAGTGAGCCAAGATTCTGCCACTGCACTCCAGCCTGGACGACAGAGCAAGACTCTGTCTCAAAAAGAAAAAAAAAAAGGGCCGGGCACGGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGCGGATCATGAGGTCAGGAGATCAAGACCATCCTGGCTAACACGGTGAAACCCCATCTCTACTAAAAATACAAAAAATTAGCTGGGCGTGGTGGCGGGCGCCTGTAGTCCTAGCTACTGGGGAGGCTGAGGCAGGAGAATGGCGTGAACCTGGGAGGCGGAGCTTGTAGTGAGCTGAGATTGTGCCACCGCACTCCAGCCTGGGCGACAGAGCAAGACTCGATCTCAAAAAAAAAAAAAAAAAAAAAAAAGGTGTTTGTGGTAGAAAGTGTTCTCACGGCTGCTGACTCAGAACCATGAGCCTGTGTGTAAGTCCTGGCCTTCTCTTCAAAGGTGATGGCCCGCTCCCT	-	novel	NA	P-0012317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1	154	1	0	ENST00000219476.3:c.1600-528_1618del		p.X534_splice	ENST00000219476	NM_000548.3	534		16/42	0.332427538822844	1	FACETS		NA	1	1	0.995	1	NA	5	TRUE	0	0.335439910859179	1		1	155	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416696	121416696	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012323-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	65	673	2	ENST00000257555.6:c.125G>C	p.Gly42Ala	p.G42A	ENST00000257555		42	gGc/gCc	1/10	1	2	FACETS	0.873	0.756	1	0.873	0.756	1	CLONAL	1	TRUE	1	0.206252442819248	2		675	722	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031999	10031999	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012323-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	88	891	0	ENST00000330684.3:c.824G>T	p.Gly275Val	p.G275V	ENST00000330684	NM_001134407.1	275	gGa/gTa	3/13	0.118358202626529	1	FACETS	0.621	0.548	0.699	0.621	0.548	0.699	INDETERMINATE	1	TRUE	0	0.206252442819248	1		891	1233	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069336	30069336	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0012323-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	96	632	0	ENST00000338641.4:c.1201A>T	p.Lys401Ter	p.K401*	ENST00000338641	NM_000268.3	401	Aag/Tag	12/16	0.206252442819248	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.206252442819248	1		632	714	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163441	47163442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012323-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	108	578	0	ENST00000409792.3:c.2684dup	p.Thr896AsnfsTer20	p.T896Nfs*20	ENST00000409792	NM_014159.6	895	cta/ctTa	3/21	0.206252442819248	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.206252442819248	1		578	714	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440911	52440912	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1205668341	NA	P-0012323-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	126	681	0	ENST00000460680.1:c.592dup	p.Glu198GlyfsTer45	p.E198Gfs*45	ENST00000460680	NM_004656.3	198	gag/gGag	8/17	0.178225915024098	2	FACETS	0.815	0.738	0.895	0.815	0.738	0.895	CLONAL	2	TRUE	0	0.206252442819248	2		681	750	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0012383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	92	539	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.432234438963872	1	FACETS	0.525	0.467	0.587	0.525	0.467	0.587	SUBCLONAL	1	TRUE	0	0.432234438963872	1		539	636	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0012383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	52	360	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.432234438963872	1	FACETS	0.599	0.513	0.692	0.599	0.513	0.692	SUBCLONAL	1	TRUE	0	0.432234438963872	1		361	315	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857391	9857391	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	133	527	5	ENST00000330684.3:c.4010C>T	p.Ser1337Leu	p.S1337L	ENST00000330684	NM_001134407.1	1337	tCg/tTg	13/13	0.185616043246408	3	FACETS	1	0.975	1	0.596	0.543	0.652	INDETERMINATE	1	TRUE	1	0.432234438963872	3		532	628	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	182	477	0	ENST00000206249.3:c.1609T>C	p.Tyr537His	p.Y537H	ENST00000206249	NM_000125.3	537	Tat/Cat	8/8	0.0748146106466918	4	FACETS	0.873	0.808	0.94	0.873	0.808	0.94	INDETERMINATE	2	TRUE	2	0.432234438963872	4		477	691	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114917778	114917778	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0012383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	119	404	0	ENST00000543371.1:c.1270-2A>C		p.X424_splice	ENST00000543371	NM_001198531.1	424			0.398093555080444	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.432234438963872	1		404	414	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652533	48652533	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	104	379	0	ENST00000376670.3:c.1204A>C	p.Thr402Pro	p.T402P	ENST00000376670	NM_002049.3	402	Acc/Ccc	6/6	0.432234438963872	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.432234438963872	1		379	322	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80646045	80646066	+	frameshift_variant	Frame_Shift_Del	DEL	GCGTCCCGCTTGTCCCTGCGGA	GCGTCCCGCTTGTCCCTGCGGA	-	novel	NA	P-0012383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	29	279	0	ENST00000286548.4:c.86_107del	p.Leu29ProfsTer24	p.L29Pfs*24	ENST00000286548	NM_002072.3	29	cTCCGCAGGGACAAGCGGGACGCc/cc	1/7	0.185616043246408	3	FACETS	0.469	0.376	0.574	0.234	0.188	0.287	INDETERMINATE	1	TRUE	1	0.432234438963872	3		279	348	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087372	27087373	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0012383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	86	588	0	ENST00000324856.7:c.1950dup	p.Met651HisfsTer25	p.M651Hfs*25	ENST00000324856	NM_006015.4	649	ctc/ctCc	5/20	0.432234438963872	1	FACETS	0.641	0.568	0.717	0.641	0.568	0.717	SUBCLONAL	1	TRUE	0	0.432234438963872	1		588	487	SUCCESS
APC	324	MSKCC	GRCh37	5	112174909	112174910	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	173	425	0	ENST00000257430.4:c.3622dup	p.Thr1208AsnfsTer9	p.T1208Nfs*9	ENST00000257430	NM_000038.5	1206	-/A	16/16	0.432234438963872	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.432234438963872	1		425	468	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0012459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	487	681	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	1	2	FACETS	0.836	0.801	0.871	0.836	0.801	0.871	CLONAL	1	TRUE	1	0.959748604033295	2		681	1214	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435311	18435311	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	411	414	0	ENST00000266497.5:c.296A>T	p.His99Leu	p.H99L	ENST00000266497		99	cAt/cTt	1/31	1	2	FACETS	0.981	0.939	1	0.981	0.939	1	CLONAL	1	TRUE	1	0.959748604033295	2		414	873	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991140	41991141	+	splice_donor_variant	Splice_Site	DEL	GT	GT	-	novel	NA	P-0012459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	564	493	0	ENST00000219905.7:c.2092+1_2092+2del		p.X698_splice	ENST00000219905	NM_001164273.1	698			0.957797691363799	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.959748604033295	1		493	594	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	811	588	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.590439671328233	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	4	TRUE	0	0.640713576106332	4		589	1006	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906916	32906919	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	rs80359277	NA	P-0012505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	191	171	0	ENST00000380152.3:c.1310_1313del	p.Lys437IlefsTer22	p.K437Ifs*22	ENST00000380152		434	aAAAGa/aa	10/27	0.640713576106332	2	FACETS	1	0.991	1	0.698	0.654	0.743	CLONAL	1	TRUE	0	0.640713576106332	2		171	427	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354393	354393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1488869543	NA	P-0012505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	328	432	0	ENST00000262320.3:c.1165G>A	p.Ala389Thr	p.A389T	ENST00000262320	NM_003502.3	389	Gcg/Acg	5/11	1	2	FACETS	0.982	0.929	1	0.982	0.929	1	CLONAL	1	TRUE	1	0.640713576106332	2		432	1043	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830265	72830265	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	580	509	0	ENST00000268489.5:c.6316C>G	p.Pro2106Ala	p.P2106A	ENST00000268489	NM_006885.3	2106	Ccg/Gcg	9/10	0.605451616163988	3	FACETS	0.897	0.863	0.93	0.897	0.863	0.93	CLONAL	2	TRUE	1	0.640713576106332	3		509	1333	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39713150	39713150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	133	212	1	ENST00000361337.2:c.556C>T	p.Pro186Ser	p.P186S	ENST00000361337	NM_003286.2	186	Cct/Tct	8/21	0.551965966234037	4	FACETS	0.804	0.73	0.882	0.268	0.243	0.294	CLONAL	1	TRUE	1	0.640713576106332	4		213	847	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344629	70344629	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	276	533	0	ENST00000374080.3:c.1990G>C	p.Glu664Gln	p.E664Q	ENST00000374080		664	Gaa/Caa	14/45	NA	2	FACETS	0.584	0.547	0.622			1	INDETERMINATE	1	TRUE	NA	0.640713576106332	2		533	1476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577121	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTCCCAGGACAGGCACAAACACG	CTCTCCCAGGACAGGCACAAACACG	-	novel	NA	P-0012505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	575	439	0	ENST00000269305.4:c.817_841del	p.Arg273ThrfsTer64	p.R273Tfs*64	ENST00000269305	NM_001126112.2	273	CGTGTTTGTGCCTGTCCTGGGAGAGac/ac	8/11	0.640713576106332	2	FACETS	0.837	0.809	0.866	0.837	0.809	0.866	CLONAL	2	TRUE	0	0.640713576106332	2		439	1072	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560425	65560432	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CCTTCTCT	CCTTCTCT	-	novel	NA	P-0012505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	246	300	0	ENST00000358664.4:c.165_171+1del		p.X55_splice	ENST00000358664	NM_002382.4	55		3/5	0.605451616163988	3	FACETS	1	0.942	1	0.504	0.471	0.538	CLONAL	1	TRUE	1	0.640713576106332	3		300	1006	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906919	32906923	+	protein_altering_variant	In_Frame_Ins	INS	GAAAG	GAAAG	AGAAAAGA	novel	NA	P-0012505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	64	174	0	ENST00000380152.3:c.1304_1308delinsAGAAAAGA	p.Arg435_Lys436delinsLysLysArg	p.R435_K436delinsKKR	ENST00000380152		435	aGAAAG/aAGAAAAGA	10/27	0.640713576106332	2	FACETS	0.461	0.401	0.527	0.231	0.2	0.264	SUBCLONAL	1	TRUE	0	0.640713576106332	2		174	433	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643923	52643924	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	92	380	0	ENST00000394830.3:c.1972dup	p.Met658AsnfsTer7	p.M658Nfs*7	ENST00000394830	NM_018313.4	658	atg/aAtg	17/30	0.4371125853014	1	FACETS	0.763	0.682	0.849	0.763	0.682	0.849	SUBCLONAL	1	TRUE	0	0.4371125853014	1		380	431	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191570	10191570	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1559429824	NA	P-0012519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	445	503	0	ENST00000256474.2:c.563T>A	p.Leu188Gln	p.L188Q	ENST00000256474	NM_000551.3	188	cTg/cAg	3/3	NA	2	FACETS	0.939	0.899	0.98			1	INDETERMINATE	2	TRUE	NA	0.4371125853014	2		503	1084	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144904	47144904	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	71	352	0	ENST00000409792.3:c.4849G>C	p.Ala1617Pro	p.A1617P	ENST00000409792	NM_014159.6	1617	Gcc/Ccc	7/21	0.4371125853014	1	FACETS	0.653	0.572	0.738	0.653	0.572	0.738	SUBCLONAL	1	TRUE	0	0.4371125853014	1		352	389	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442503	52442503	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	146	394	0	ENST00000460680.1:c.242T>G	p.Phe81Cys	p.F81C	ENST00000460680	NM_004656.3	81	tTc/tGc	4/17	0.4371125853014	1	FACETS	0.827	0.758	0.9	0.827	0.758	0.9	CLONAL	1	TRUE	0	0.4371125853014	1		394	631	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459719	149459719	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1331	266	601	0	ENST00000286301.3:c.488C>G	p.Thr163Ser	p.T163S	ENST00000286301	NM_005211.3	163	aCc/aGc	4/22	0.4371125853014	3	FACETS	0.929	0.868	0.991	0.464	0.434	0.496	CLONAL	1	TRUE	1	0.4371125853014	3		601	1597	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0012543-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	101	371	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.413255356768214	3	FACETS	0.684	0.611	0.761	0.342	0.305	0.381	SUBCLONAL	1	TRUE	1	0.515164438374446	3		371	721	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061194	38061195	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTT	novel	NA	P-0012543-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	109	253	0	ENST00000250448.2:c.794_795insAAG	p.Arg265_Phe266insSer	p.R265_F266insS	ENST00000250448	NM_004496.3	265	cgc/cgAAGc	2/2	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.515164438374446	2		253	367	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38064155	38064155	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	294	513	2	ENST00000250448.2:c.23A>T	p.Glu8Val	p.E8V	ENST00000250448	NM_004496.3	8	gAa/gTa	1/2	0.746275033902211	3	FACETS	0.859	0.807	0.911	0.429	0.403	0.456	CLONAL	1	TRUE	1	0.770556852376754	3		515	1231	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624292	89624321	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTAGACTTGACCTGTATCCATTTCTGCGG	CTTAGACTTGACCTGTATCCATTTCTGCGG	-	novel	NA	P-0012632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	75	276	0	ENST00000371953.3:c.68_79+18del		p.X23_splice	ENST00000371953	NM_000314.4	23		1/9	NA	2	FACETS	1	0.902	1			1	INDETERMINATE	1	TRUE	NA	0.770556852376754	2		276	193	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164858	36164859	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGCGCGGGGAACT	novel	NA	P-0012632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	128	347	0	ENST00000300305.3:c.1004_1016dup	p.Pro340ValfsTer264	p.P340Vfs*264	ENST00000300305		339	ctg/ctAGTTCCCCGCGCTg	8/8	0.746275033902211	3	FACETS	0.572	0.518	0.628	0.286	0.259	0.314	SUBCLONAL	1	TRUE	1	0.770556852376754	3		347	805	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867178	68867196	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCCTTCTTCTTTAGAATC	TCCCTTCTTCTTTAGAATC	-	novel	NA	P-0012632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	268	218	0	ENST00000261769.5:c.2440-14_2444del		p.X814_splice	ENST00000261769	NM_004360.3	814		16/16	0.768519332936443	2	FACETS	0.948	0.911	0.983	0.948	0.911	0.983	CLONAL	2	TRUE	0	0.770556852376754	2		218	367	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0012634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	119	384	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.852	0.77	0.938	0.852	0.77	0.938	CLONAL	1	TRUE	1	0.408895546434878	2		384	683	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070577	67070578	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	161	537	2	ENST00000412916.2:c.207dup	p.Pro70SerfsTer13	p.P70Sfs*13	ENST00000412916		67	-/T	3/6	0.408895546434878	1	FACETS	0.778	0.715	0.845	0.778	0.715	0.845	SUBCLONAL	1	TRUE	0	0.408895546434878	1		539	805	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855995	68855996	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	209	650	0	ENST00000261769.5:c.1805dup	p.Cys603LeufsTer2	p.C603Lfs*2	ENST00000261769	NM_004360.3	601	-/T	12/16	0.408895546434878	1	FACETS	0.957	0.89	1	0.957	0.89	1	CLONAL	1	TRUE	0	0.408895546434878	1		650	850	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0012713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	288	357	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.294211650520751	6	FACETS	1	0.981	1	1	0.981	1	CLONAL	4	TRUE	2	0.294211650520751	6		357	719	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313266	65313266	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	93	798	0	ENST00000342505.4:c.1848G>C	p.Lys616Asn	p.K616N	ENST00000342505	NM_002227.2	616	aaG/aaC	13/25	1	2	FACETS	0.819	0.728	0.916	0.819	0.728	0.916	CLONAL	1	TRUE	1	0.294211650520751	2		798	772	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430334	181430334	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	70	374	0	ENST00000325404.1:c.186G>C	p.Glu62Asp	p.E62D	ENST00000325404	NM_003106.3	62	gaG/gaC	1/1	0.294211650520751	6	FACETS	1	0.961	1	0.319	0.278	0.363	CLONAL	1	TRUE	2	0.294211650520751	6		374	593	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503994	186503994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1346	107	834	1	ENST00000323963.5:c.559G>A	p.Glu187Lys	p.E187K	ENST00000323963		187	Gaa/Aaa	6/11	0.294211650520751	6	FACETS	0.795	0.71	0.886	0.199	0.177	0.222	SUBCLONAL	1	TRUE	2	0.294211650520751	6		835	1453	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911520	114911520	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	107	641	0	ENST00000543371.1:c.1038G>C	p.Lys346Asn	p.K346N	ENST00000543371	NM_001198531.1	346	aaG/aaC	10/14	NA	2	FACETS	1	0.907	1			1	INDETERMINATE	1	TRUE	NA	0.294211650520751	2		641	719	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633583	69633583	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	60	266	0	ENST00000334134.2:c.119G>T	p.Gly40Val	p.G40V	ENST00000334134	NM_005247.2	40	gGc/gTc	1/3	0.294211650520751	4	FACETS	1	0.968	1	0.721	0.624	0.826	CLONAL	1	TRUE	2	0.294211650520751	4		266	366	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14028090	14028090	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	57	383	0	ENST00000311895.7:c.1144G>A	p.Glu382Lys	p.E382K	ENST00000311895	NM_005236.2	382	Gag/Aag	7/11	0.294211650520751	3	FACETS	0.952	0.818	1	0.476	0.409	0.549	CLONAL	1	TRUE	1	0.294211650520751	3		383	467	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964726	15964726	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1567769714	NA	P-0012713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	87	482	0	ENST00000268712.3:c.5870C>G	p.Ser1957Cys	p.S1957C	ENST00000268712	NM_006311.3	1957	tCt/tGt	37/46	0.294211650520751	3	FACETS	1	0.943	1	0.552	0.489	0.62	CLONAL	1	TRUE	1	0.294211650520751	3		482	614	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657603	37657603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	104	545	1	ENST00000447079.4:c.2520G>A	p.Met840Ile	p.M840I	ENST00000447079	NM_015083.1	840	atG/atA	6/14	0.294211650520751	3	FACETS	1	0.947	1	0.546	0.489	0.606	CLONAL	1	TRUE	1	0.294211650520751	3		546	743	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39593527	39593527	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	51	489	0	ENST00000262039.4:c.1292C>T	p.Ser431Leu	p.S431L	ENST00000262039	NM_002647.2	431	tCa/tTa	11/25	0.294211650520751	2	FACETS	0.823	0.701	0.957	0.412	0.35	0.479	CLONAL	1	TRUE	0	0.294211650520751	2		489	421	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212192	5212192	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	108	547	1	ENST00000357368.4:c.4839G>C	p.Lys1613Asn	p.K1613N	ENST00000357368	NM_002850.3	1613	aaG/aaC	32/38	0.294211650520751	3	FACETS	1	0.947	1	0.543	0.487	0.602	CLONAL	1	TRUE	1	0.294211650520751	3		548	776	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428942	47428942	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	116	810	0	ENST00000377045.4:c.1305C>G	p.Ile435Met	p.I435M	ENST00000377045	NM_001654.4	435	atC/atG	13/16	0.288356169931097	4	FACETS	1	0.939	1	0.354	0.318	0.391	CLONAL	1	TRUE	1	0.294211650520751	4		810	962	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411066	63411066	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	93	681	0	ENST00000330258.3:c.2101C>G	p.Leu701Val	p.L701V	ENST00000330258	NM_152424.3	701	Ctg/Gtg	2/2	0.288356169931097	4	FACETS	0.956	0.849	1	0.319	0.283	0.357	CLONAL	1	TRUE	1	0.294211650520751	4		681	856	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178459	56178460	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	78	468	0	ENST00000399503.3:c.3433dup	p.Thr1145AsnfsTer6	p.T1145Nfs*6	ENST00000399503	NM_005921.1	1144	-/A	14/20	0.294211650520751	3	FACETS	0.953	0.838	1	0.477	0.419	0.539	CLONAL	1	TRUE	1	0.294211650520751	3		468	638	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0012740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	217	435	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.942	0.883	1	1	0.995	1	CLONAL	3	TRUE	1	0.280895970493355	2		436	547	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0012740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	198	498	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	1	0.985	1	1	0.994	1	CLONAL	2	TRUE	1	0.280895970493355	2		498	583	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106078	27106078	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	156	359	0	ENST00000324856.7:c.5693del	p.Pro1898HisfsTer25	p.P1898Hfs*25	ENST00000324856	NM_006015.4	1897	Ccc/cc	20/20	1	2	FACETS	0.972	0.901	1	1	0.994	1	CLONAL	3	TRUE	1	0.280895970493355	2		359	381	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0012740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	327	817	4	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	0.928	0.881	0.976	1	0.997	1	CLONAL	3	TRUE	1	0.280895970493355	2		821	836	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0012740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	237	723	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.904	0.85	0.96	1	0.996	1	CLONAL	3	TRUE	1	0.280895970493355	2		723	622	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	118	531	4	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	0.278993381951611	1	FACETS	0.879	0.799	0.961	1	0.988	1	CLONAL	2	TRUE	0	0.280895970493355	1		535	411	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789591	3789591	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	195	530	1	ENST00000262367.5:c.4268del	p.Pro1423LeufsTer36	p.P1423Lfs*36	ENST00000262367	NM_004380.2	1423	cCt/ct	25/31	1	2	FACETS	0.989	0.925	1	1	0.995	1	CLONAL	3	TRUE	1	0.280895970493355	2		531	468	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447773	49447773	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	125	320	0	ENST00000301067.7:c.661del	p.Ala221LeufsTer40	p.A221Lfs*40	ENST00000301067	NM_003482.3	221	Gct/ct	5/54	1	2	FACETS	0.886	0.812	0.961	1	0.992	1	CLONAL	3	TRUE	1	0.280895970493355	2		320	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882019	NA	P-0012740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	171	461	0	ENST00000269305.4:c.455del	p.Pro152ArgfsTer18	p.P152Rfs*18	ENST00000269305	NM_001126112.2	152	cCg/cg	5/11	1	2	FACETS	0.931	0.866	0.997	1	0.994	1	CLONAL	3	TRUE	1	0.280895970493355	2		461	436	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717608	89717608	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1564566706	NA	P-0012740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	212	316	0	ENST00000371953.3:c.635-2A>G		p.X212_splice	ENST00000371953	NM_000314.4	212			0.280895970493355	5	FACETS	0.97	0.905	1	0.728	0.678	0.779	CLONAL	3	TRUE	1	0.280895970493355	5		316	737	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956964	2956964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1395288944	NA	P-0012740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	164	399	0	ENST00000396946.4:c.2663G>A	p.Arg888His	p.R888H	ENST00000396946	NM_032415.4	888	cGt/cAt	20/25	1	2	FACETS	1	0.962	1	1	0.994	1	CLONAL	3	TRUE	1	0.280895970493355	2		399	371	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089730	27089730	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	115	310	0	ENST00000324856.7:c.2686G>T	p.Glu896Ter	p.E896*	ENST00000324856	NM_006015.4	896	Gaa/Taa	8/20	1	2	FACETS	0.951	0.871	1	1	0.992	1	CLONAL	3	TRUE	1	0.280895970493355	2		310	287	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690847	89690847	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776667	NA	P-0012740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	222	261	0	ENST00000371953.3:c.253+1G>A		p.X85_splice	ENST00000371953	NM_000314.4	85			0.280895970493355	5	FACETS	0.975	0.924	1	1	0.994	1	CLONAL	6	TRUE	1	0.280895970493355	5		261	384	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096504	178096504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1181990251	NA	P-0012740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	243	509	1	ENST00000397062.3:c.827C>T	p.Thr276Ile	p.T276I	ENST00000397062	NM_006164.4	276	aCa/aTa	5/5	1	2	FACETS	0.897	0.843	0.951	1	0.996	1	CLONAL	3	TRUE	1	0.280895970493355	2		510	643	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560476	95560476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	148	183	0	ENST00000393063.1:c.5113G>A	p.Glu1705Lys	p.E1705K	ENST00000393063	NM_030621.3	1705	Gaa/Aaa	25/28	0.280895970493355	5	FACETS	1	0.974	1	1	0.989	1	CLONAL	5	TRUE	1	0.280895970493355	5		183	275	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521525	46521525	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	279	725	2	ENST00000262741.5:c.883del	p.Met295Ter	p.M295*	ENST00000262741	NM_003629.3	295	Atg/tg	7/10	1	2	FACETS	0.908	0.858	0.959	1	0.996	1	CLONAL	3	TRUE	1	0.280895970493355	2		727	729	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265863	16265863	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	259	792	0	ENST00000375759.3:c.10936C>A	p.Leu3646Ile	p.L3646I	ENST00000375759	NM_015001.2	3646	Ctc/Atc	15/15	1	2	FACETS	0.956	0.902	1	1	0.996	1	CLONAL	3	TRUE	1	0.280895970493355	2		792	643	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582275	119582275	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	173	398	0	ENST00000316626.5:c.1126A>G	p.Thr376Ala	p.T376A	ENST00000316626		376	Acc/Gcc	10/12	1	2	FACETS	1	0.985	1	1	0.994	1	CLONAL	2	TRUE	1	0.280895970493355	2		398	501	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177074	56177074	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	117	259	0	ENST00000399503.3:c.2344T>G	p.Ser782Ala	p.S782A	ENST00000399503	NM_005921.1	782	Tca/Gca	13/20	1	2	FACETS	0.89	0.814	0.968	1	0.991	1	CLONAL	3	TRUE	1	0.280895970493355	2		259	312	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522778	67522778	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	162	363	0	ENST00000274335.5:c.275C>A	p.Pro92His	p.P92H	ENST00000274335		92	cCt/cAt	1/15	1	2	FACETS	0.913	0.847	0.981	1	0.994	1	CLONAL	3	TRUE	1	0.280895970493355	2		363	421	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200267	138200267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	173	357	0	ENST00000237289.4:c.1685G>A	p.Arg562His	p.R562H	ENST00000237289	NM_001270507.1	562	cGt/cAt	7/9	1	2	FACETS	1	0.97	1	1	0.995	1	CLONAL	3	TRUE	1	0.280895970493355	2		357	384	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266514	55266514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	183	579	0	ENST00000275493.2:c.2806C>T	p.Pro936Ser	p.P936S	ENST00000275493	NM_005228.3	936	Cca/Tca	23/28	1	2	FACETS	0.876	0.815	0.937	1	0.994	1	CLONAL	3	TRUE	1	0.280895970493355	2		579	496	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842307	151842307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752190553	NA	P-0012740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	228	591	1	ENST00000262189.6:c.14105C>T	p.Ala4702Val	p.A4702V	ENST00000262189	NM_170606.2	4702	gCc/gTc	54/59	1	2	FACETS	0.889	0.834	0.944	1	0.995	1	CLONAL	3	TRUE	1	0.280895970493355	2		592	609	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432275	49432275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	245	775	0	ENST00000301067.7:c.8864C>T	p.Pro2955Leu	p.P2955L	ENST00000301067	NM_003482.3	2955	cCt/cTt	34/54	1	2	FACETS	0.878	0.826	0.932	1	0.996	1	CLONAL	3	TRUE	1	0.280895970493355	2		775	662	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103498680	103498680	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	226	644	0	ENST00000355739.4:c.64C>A	p.Leu22Met	p.L22M	ENST00000355739	NM_000123.3	22	Ctg/Atg	1/15	1	2	FACETS	0.879	0.825	0.935	1	0.995	1	CLONAL	3	TRUE	1	0.280895970493355	2		644	610	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40462546	40462546	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	493	768	0	ENST00000345506.4:c.2244G>C	p.Gln748His	p.Q748H	ENST00000345506	NM_003152.3	748	caG/caC	20/20	0.280895970493355	6	FACETS	0.93	0.892	0.968			1	CLONAL	5	TRUE	NA	0.280895970493355	6		768	1179	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279754	46279754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	226	551	0	ENST00000371998.3:c.3680C>T	p.Ala1227Val	p.A1227V	ENST00000371998		1227	gCc/gTc	20/23	0.278993381951611	1	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	0	0.280895970493355	1		551	586	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21304087	21304087	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	271	614	0	ENST00000354336.3:c.866C>A	p.Thr289Lys	p.T289K	ENST00000354336	NM_005207.3	289	aCg/aAg	3/3	1	2	FACETS	0.964	0.911	1	1	0.996	1	CLONAL	3	TRUE	1	0.280895970493355	2		614	667	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591222	67591266	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTTCTCTTTTCAAAACTGTTTTTCAGGTGGTTGACTCAAAAAGGT	GTTCTCTTTTCAAAACTGTTTTTCAGGTGGTTGACTCAAAAAGGT	-	novel	NA	P-0012740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	118	351	0	ENST00000274335.5:c.1746-22_1768del		p.X582_splice	ENST00000274335		582		13/15	1	2	FACETS	1	0.922	1	1	0.99	1	CLONAL	2	TRUE	1	0.280895970493355	2		351	414	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073426	8073426	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	362	1189	2	ENST00000377482.5:c.1233del	p.Phe411LeufsTer41	p.F411Lfs*41	ENST00000377482	NM_018948.3	411	ttT/tt	4/4	1	2	FACETS	1	0.977	1	1	0.997	1	CLONAL	3	TRUE	1	0.280895970493355	2		1191	827	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098975	178098977	+	inframe_deletion	In_Frame_Del	DEL	AAA	AAA	-	novel	NA	P-0012740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	131	298	0	ENST00000397062.3:c.68_70del	p.Leu23_Trp24delinsArg	p.L23_W24delinsR	ENST00000397062	NM_006164.4	23	cTTTgg/cgg	2/5	1	2	FACETS	0.878	0.807	0.951	1	0.992	1	CLONAL	3	TRUE	1	0.280895970493355	2		298	354	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591087	67591088	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	166	316	0	ENST00000274335.5:c.1683dup	p.Arg562ThrfsTer6	p.R562Tfs*6	ENST00000274335		560	-/A	12/15	1	2	FACETS	0.959	0.891	1	1	0.994	1	CLONAL	3	TRUE	1	0.280895970493355	2		316	411	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859039	57859039	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	177	909	0	ENST00000228682.2:c.534+1G>A		p.X178_splice	ENST00000228682	NM_005269.2	178			1	2	FACETS	0.913	0.841	0.987	0.913	0.841	0.987	CLONAL	1	TRUE	1	0.428122220162935	2		909	906	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	404	607	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.365481729657309	3	FACETS	0.892	0.854	0.931			1	CLONAL	3	TRUE	NA	0.428122220162935	3		607	856	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573563	48573564	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs786203560	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	89	206	0	ENST00000342988.3:c.153dup	p.Asp52ArgfsTer2	p.D52Rfs*2	ENST00000342988	NM_005359.5	49	-/A	2/12	0.4191231656669	1	FACETS	0.786	0.7	0.875	0.786	0.7	0.875	SUBCLONAL	1	TRUE	0	0.428122220162935	1		206	416	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55569954	55569954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138585275	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	124	507	4	ENST00000288135.5:c.821C>T	p.Thr274Met	p.T274M	ENST00000288135	NM_000222.2	274	aCg/aTg	5/21	1	2	FACETS	0.817	0.74	0.898	0.817	0.74	0.898	CLONAL	1	TRUE	1	0.428122220162935	2		511	709	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938271	36938271	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	204	909	1	ENST00000361632.4:c.690del	p.Met231CysfsTer32	p.M231Cfs*32	ENST00000361632		230	ccC/cc	6/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.428122220162935	2		910	827	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905055	50905055	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	145	790	2	ENST00000440232.2:c.342del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	113	Ggg/gg	4/27	0.428999211697465	1	FACETS	0.752	0.687	0.819	0.752	0.687	0.819	SUBCLONAL	1	TRUE	0	0.428122220162935	1		792	708	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615698	1615698	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	203	1176	0	ENST00000344749.5:c.1573del	p.Arg525GlyfsTer18	p.R525Gfs*18	ENST00000344749	NM_001136139.2	525	Cgg/gg	17/19	0.428999211697465	1	FACETS	0.87	0.807	0.934	0.87	0.807	0.934	CLONAL	1	TRUE	0	0.428122220162935	1		1176	857	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979986	7979987	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs746723399	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	95	404	0	ENST00000319144.4:c.1350dup	p.Leu451AlafsTer27	p.L451Afs*27	ENST00000319144	NM_001139.2	450	-/G	10/15	0.365481729657309	3	FACETS	1	0.894	1			1	CLONAL	1	TRUE	NA	0.428122220162935	3		404	538	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237604	16237604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	32	278	1	ENST00000375759.3:c.1051C>T	p.Leu351Phe	p.L351F	ENST00000375759	NM_015001.2	351	Ctt/Ttt	5/15	1	2	FACETS	0.395	0.321	0.479	0.395	0.321	0.479	SUBCLONAL	1	TRUE	1	0.428122220162935	2		279	378	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612890	228612890	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757564822	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	148	1027	0	ENST00000366696.1:c.137C>T	p.Thr46Met	p.T46M	ENST00000366696	NM_003493.2	46	aCg/aTg	1/1	1	2	FACETS	0.715	0.652	0.781	0.715	0.652	0.781	SUBCLONAL	1	TRUE	1	0.428122220162935	2		1027	967	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736272	243736272	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	80	437	0	ENST00000263826.5:c.775T>G	p.Leu259Val	p.L259V	ENST00000263826	NM_005465.4	259	Ttg/Gtg	8/13	1	2	FACETS	0.58	0.511	0.655	0.58	0.511	0.655	SUBCLONAL	1	TRUE	1	0.428122220162935	2		437	644	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505319	25505319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	58	494	0	ENST00000264709.3:c.439G>A	p.Ala147Thr	p.A147T	ENST00000264709	NM_175629.2	147	Gca/Aca	4/23	0.184097117288446	1	FACETS	0.449	0.386	0.518	0.449	0.386	0.518	INDETERMINATE	1	TRUE	0	0.428122220162935	1		494	474	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149718	202149718	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	130	592	0	ENST00000358485.4:c.1159G>A	p.Gly387Arg	p.G387R	ENST00000358485	NM_001080125.1	387	Gga/Aga	8/9	0.184097117288446	1	FACETS	0.798	0.726	0.873	0.798	0.726	0.873	INDETERMINATE	1	TRUE	0	0.428122220162935	1		592	598	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242899	142242899	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	117	649	0	ENST00000350721.4:c.4088C>A	p.Ala1363Glu	p.A1363E	ENST00000350721	NM_001184.3	1363	gCg/gAg	22/47	1	2	FACETS	0.705	0.636	0.778	0.705	0.636	0.778	SUBCLONAL	1	TRUE	1	0.428122220162935	2		649	775	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928083	178928083	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	103	419	0	ENST00000263967.3:c.1361A>T	p.Asp454Val	p.D454V	ENST00000263967	NM_006218.2	454	gAt/gTt	8/21	1	2	FACETS	0.984	0.885	1	0.984	0.885	1	CLONAL	1	TRUE	1	0.428122220162935	2		419	489	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190884	185190884	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765513332	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	48	771	5	ENST00000265026.3:c.1765C>T	p.Arg589Cys	p.R589C	ENST00000265026	NM_004721.4	589	Cgc/Tgc	11/14	1	2	FACETS	0.245	0.206	0.288	0.245	0.206	0.288	SUBCLONAL	1	TRUE	1	0.428122220162935	2		776	917	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540554	187540554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs975459956	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	111	434	0	ENST00000441802.2:c.7186G>A	p.Glu2396Lys	p.E2396K	ENST00000441802	NM_005245.3	2396	Gaa/Aaa	10/27	1	2	FACETS	0.913	0.823	1	0.913	0.823	1	CLONAL	1	TRUE	1	0.428122220162935	2		434	568	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152567	56152567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375239979	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	39	315	0	ENST00000399503.3:c.623G>A	p.Arg208Gln	p.R208Q	ENST00000399503	NM_005921.1	208	cGa/cAa	2/20	1	2	FACETS	0.499	0.414	0.593	0.499	0.414	0.593	SUBCLONAL	1	TRUE	1	0.428122220162935	2		315	365	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225414	26225414	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1186055143	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	308	1169	0	ENST00000360408.1:c.32C>T	p.Ser11Phe	p.S11F	ENST00000360408	NM_003532.2	11	tCc/tTc	1/1	0.232424912968281	3	FACETS	1	0.991	1	0.638	0.601	0.677	INDETERMINATE	1	TRUE	1	0.428122220162935	3		1169	1368	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553246	106553246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	135	520	1	ENST00000369096.4:c.1211C>T	p.Pro404Leu	p.P404L	ENST00000369096	NM_001198.3	404	cCc/cTc	5/7	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.428122220162935	2		521	570	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662727	117662727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1165495915	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	96	372	1	ENST00000368508.3:c.4738G>A	p.Glu1580Lys	p.E1580K	ENST00000368508	NM_002944.2	1580	Gaa/Aaa	29/43	1	2	FACETS	0.992	0.889	1	0.992	0.889	1	CLONAL	1	TRUE	1	0.428122220162935	2		373	452	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965879	90965879	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	92	384	0	ENST00000265433.3:c.1438T>A	p.Ser480Thr	p.S480T	ENST00000265433	NM_002485.4	480	Tca/Aca	11/16	1	2	FACETS	0.881	0.786	0.981	0.881	0.786	0.981	CLONAL	1	TRUE	1	0.428122220162935	2		384	488	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742453	145742453	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	81	429	0	ENST00000428558.2:c.335A>C	p.Asn112Thr	p.N112T	ENST00000428558	NM_004260.3	112	aAt/aCt	4/22	1	2	FACETS	0.725	0.64	0.815	0.725	0.64	0.815	SUBCLONAL	1	TRUE	1	0.428122220162935	2		429	522	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486022	8486022	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	156	639	0	ENST00000356435.5:c.2795C>A	p.Ser932Ter	p.S932*	ENST00000356435		932	tCa/tAa	17/35	0.4191231656669	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.428122220162935	1		639	555	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730196	133730196	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	79	334	1	ENST00000318560.5:c.262C>A	p.Leu88Ile	p.L88I	ENST00000318560	NM_005157.4	88	Ctc/Atc	3/11	0.346953209614385	3	FACETS	0.867	0.764	0.976	0.433	0.382	0.488	CLONAL	1	TRUE	1	0.428122220162935	3		335	517	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802565	139802565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	158	921	0	ENST00000247668.2:c.410C>T	p.Pro137Leu	p.P137L	ENST00000247668	NM_021138.3	137	cCc/cTc	5/11	NA	2	FACETS	0.721	0.66	0.785			1	INDETERMINATE	1	TRUE	NA	0.428122220162935	2		921	1024	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70442732	70442732	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	74	347	0	ENST00000373644.4:c.5052+2T>C		p.X1684_splice	ENST00000373644	NM_030625.2	1684			0.428122220162935	1	FACETS	0.813	0.718	0.915	0.813	0.718	0.915	CLONAL	1	TRUE	0	0.428122220162935	1		347	334	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206729	102206729	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	163	788	0	ENST00000263464.3:c.1357G>A	p.Ala453Thr	p.A453T	ENST00000263464	NM_001165.4	453	Gca/Aca	7/9	1	2	FACETS	0.875	0.804	0.95	0.875	0.804	0.95	CLONAL	1	TRUE	1	0.428122220162935	2		788	870	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691152	18691152	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	116	471	0	ENST00000266497.5:c.3263A>C	p.Asn1088Thr	p.N1088T	ENST00000266497		1088	aAc/aCc	23/31	1	2	FACETS	0.918	0.83	1	0.918	0.83	1	CLONAL	1	TRUE	1	0.428122220162935	2		471	590	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427950	49427950	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775632051	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	148	609	0	ENST00000301067.7:c.10640G>A	p.Arg3547His	p.R3547H	ENST00000301067	NM_003482.3	3547	cGc/cAc	38/54	1	2	FACETS	0.937	0.857	1	0.937	0.857	1	CLONAL	1	TRUE	1	0.428122220162935	2		609	738	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435983	49435983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1565798715	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	148	556	3	ENST00000301067.7:c.5998C>T	p.Gln2000Ter	p.Q2000*	ENST00000301067	NM_003482.3	2000	Cag/Tag	28/54	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.428122220162935	2		559	669	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480112	50480112	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	81	365	0	ENST00000394963.4:c.346G>T	p.Val116Phe	p.V116F	ENST00000394963	NM_003076.4	116	Gtc/Ttc	2/13	1	2	FACETS	0.792	0.7	0.889	0.792	0.7	0.889	SUBCLONAL	1	TRUE	1	0.428122220162935	2		365	478	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562921	21562921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	88	417	0	ENST00000382592.4:c.998C>T	p.Ser333Phe	p.S333F	ENST00000382592	NM_014572.2	333	tCc/tTc	4/8	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.428122220162935	2		417	405	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563002	21563002	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	74	528	0	ENST00000382592.4:c.917C>A	p.Pro306His	p.P306H	ENST00000382592	NM_014572.2	306	cCc/cAc	4/8	1	2	FACETS	0.76	0.667	0.859	0.76	0.667	0.859	SUBCLONAL	1	TRUE	1	0.428122220162935	2		528	455	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050853	49050853	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	62	208	0	ENST00000267163.4:c.2537A>C	p.Gln846Pro	p.Q846P	ENST00000267163	NM_000321.2	846	cAg/cCg	25/27	1	2	FACETS	0.914	0.795	1	0.914	0.795	1	CLONAL	1	TRUE	1	0.428122220162935	2		208	317	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678491	88678491	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	115	530	0	ENST00000360948.2:c.1045C>A	p.His349Asn	p.H349N	ENST00000360948	NM_001012338.2	349	Cat/Aat	9/19	1	2	FACETS	0.997	0.901	1	0.997	0.901	1	CLONAL	1	TRUE	1	0.428122220162935	2		530	539	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339494	339494	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144411078	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	156	777	0	ENST00000262320.3:c.2408G>A	p.Arg803His	p.R803H	ENST00000262320	NM_003502.3	803	cGc/cAc	10/11	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.428122220162935	2		777	707	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778313	3778313	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	53	280	0	ENST00000262367.5:c.6735G>T	p.Gln2245His	p.Q2245H	ENST00000262367	NM_004380.2	2245	caG/caT	31/31	1	2	FACETS	0.839	0.721	0.967	0.839	0.721	0.967	CLONAL	1	TRUE	1	0.428122220162935	2		280	295	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993521	72993521	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	171	959	0	ENST00000268489.5:c.524C>T	p.Pro175Leu	p.P175L	ENST00000268489	NM_006885.3	175	cCt/cTt	2/10	0.143053509106318	0	FACETS	0.533	0.491	0.577			1	INDETERMINATE	1	TRUE	0	0.428122220162935	0		959	857	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877441	89877441	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761430527	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	148	678	1	ENST00000389301.3:c.322C>T	p.Pro108Ser	p.P108S	ENST00000389301	NM_000135.2	108	Ccc/Tcc	4/43	NA	2	FACETS	0.975	0.893	1			1	INDETERMINATE	1	TRUE	NA	0.428122220162935	2		679	709	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552198	29552198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	266	595	0	ENST00000356175.3:c.1931C>T	p.Ser644Phe	p.S644F	ENST00000356175	NM_000267.3	644	tCc/tTc	17/57	NA	2	FACETS	0.856	0.807	0.906			1	INDETERMINATE	2	TRUE	NA	0.428122220162935	2		595	726	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435999	56435999	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	72	345	0	ENST00000407977.2:c.1138G>A	p.Glu380Lys	p.E380K	ENST00000407977		380	Gag/Aag	9/10	0.38609812785538	2	FACETS	1	0.949	1	0.572	0.504	0.643	CLONAL	1	TRUE	0	0.428122220162935	2		345	294	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774941	73774941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	306	520	0	ENST00000254810.4:c.232G>A	p.Asp78Asn	p.D78N	ENST00000254810	NM_005324.3	78	Gat/Aat	3/4	0.38609812785538	2	FACETS	0.986	0.935	1	0.986	0.935	1	CLONAL	2	TRUE	0	0.428122220162935	2		520	725	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226986	2226986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1418469674	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	80	288	0	ENST00000398665.3:c.4466C>T	p.Ala1489Val	p.A1489V	ENST00000398665	NM_032482.2	1489	gCc/gTc	27/28	0.184097117288446	1	FACETS	0.849	0.753	0.95	0.849	0.753	0.95	INDETERMINATE	1	TRUE	0	0.428122220162935	1		288	346	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260254	10260254	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	128	471	0	ENST00000340748.4:c.2413C>T	p.Leu805Phe	p.L805F	ENST00000340748		805	Ctc/Ttc	25/40	0.184097117288446	1	FACETS	0.877	0.798	0.959	0.877	0.798	0.959	INDETERMINATE	1	TRUE	0	0.428122220162935	1		471	536	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272200	15272200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	20	170	0	ENST00000263388.2:c.6239G>T	p.Arg2080Leu	p.R2080L	ENST00000263388	NM_000435.2	2080	cGg/cTg	33/33	0.184097117288446	1	FACETS	0.448	0.345	0.566	0.448	0.345	0.566	INDETERMINATE	1	TRUE	0	0.428122220162935	1		170	164	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288468	15288468	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	51	350	1	ENST00000263388.2:c.4271C>T	p.Pro1424Leu	p.P1424L	ENST00000263388	NM_000435.2	1424	cCc/cTc	24/33	0.184097117288446	1	FACETS	0.594	0.508	0.688	0.594	0.508	0.688	INDETERMINATE	1	TRUE	0	0.428122220162935	1		351	315	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298728	15298728	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	112	539	0	ENST00000263388.2:c.1570G>T	p.Asp524Tyr	p.D524Y	ENST00000263388	NM_000435.2	524	Gac/Tac	10/33	0.184097117288446	1	FACETS	0.816	0.737	0.898	0.816	0.737	0.898	INDETERMINATE	1	TRUE	0	0.428122220162935	1		539	504	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17941383	17941383	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	96	457	0	ENST00000458235.1:c.3025G>A	p.Asp1009Asn	p.D1009N	ENST00000458235	NM_000215.3	1009	Gac/Aac	22/24	0.184097117288446	1	FACETS	0.65	0.581	0.724	0.65	0.581	0.724	INDETERMINATE	1	TRUE	0	0.428122220162935	1		457	542	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748808	41748808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	177	842	1	ENST00000301178.4:c.1333G>A	p.Ala445Thr	p.A445T	ENST00000301178	NM_021913.4	445	Gcc/Acc	11/20	0.184097117288446	1	FACETS	0.817	0.754	0.883	0.817	0.754	0.883	INDETERMINATE	1	TRUE	0	0.428122220162935	1		843	795	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101026	41101026	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	100	482	0	ENST00000373198.4:c.1330T>A	p.Ser444Thr	p.S444T	ENST00000373198	NM_133170.3	444	Tcc/Acc	8/32	1	2	FACETS	0.965	0.866	1	0.965	0.866	1	CLONAL	1	TRUE	1	0.428122220162935	2		482	484	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057296	30057296	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	90	538	0	ENST00000338641.4:c.778G>A	p.Glu260Lys	p.E260K	ENST00000338641	NM_000268.3	260	Gaa/Aaa	8/16	0.184097117288446	1	FACETS	0.592	0.526	0.662	0.592	0.526	0.662	INDETERMINATE	1	TRUE	0	0.428122220162935	1		538	558	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652334	48652334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	188	1011	0	ENST00000376670.3:c.1005G>A	p.Met335Ile	p.M335I	ENST00000376670	NM_002049.3	335	atG/atA	6/6	0.428999211697465	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.428122220162935	1		1011	676	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540229	187540229	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	152	682	0	ENST00000441802.2:c.7511del	p.Asn2504ThrfsTer8	p.N2504Tfs*8	ENST00000441802	NM_005245.3	2504	aAc/ac	10/27	1	2	FACETS	0.835	0.764	0.91	0.835	0.764	0.91	CLONAL	1	TRUE	1	0.428122220162935	2		682	850	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971058	21971058	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	80	315	0	ENST00000304494.5:c.300del	p.Ala102ArgfsTer44	p.A102Rfs*44	ENST00000304494	NM_000077.4	100	gcC/gc	2/3	0.4191231656669	1	FACETS	0.989	0.88	1	0.989	0.88	1	CLONAL	1	TRUE	0	0.428122220162935	1		315	297	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94224123	94224125	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	40	222	0	ENST00000323929.3:c.27_29del	p.Asp9del	p.D9del	ENST00000323929	NM_005591.3	9	gaTGAa/gaa	3/20	1	2	FACETS	0.795	0.666	0.936	0.795	0.666	0.936	CLONAL	1	TRUE	1	0.428122220162935	2		222	235	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812227	212812230	+	frameshift_variant	Frame_Shift_Del	DEL	AGGC	AGGC	-	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	28	569	0	ENST00000342788.4:c.346_349del	p.Ala116TrpfsTer5	p.A116Wfs*5	ENST00000342788	NM_005235.2	116	GCCTtg/tg	3/28	0.184097117288446	1	FACETS	0.2	0.159	0.246	0.2	0.159	0.246	INDETERMINATE	1	TRUE	0	0.428122220162935	1		569	515	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864587	57864588	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	165	1003	0	ENST00000228682.2:c.2070dup	p.Ser691GlnfsTer4	p.S691Qfs*4	ENST00000228682	NM_005269.2	688	-/C	12/12	1	2	FACETS	0.786	0.721	0.853	0.786	0.721	0.853	SUBCLONAL	1	TRUE	1	0.428122220162935	2		1003	981	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446827	49446828	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	98	428	0	ENST00000301067.7:c.982dup	p.Ala328GlyfsTer14	p.A328Gfs*14	ENST00000301067	NM_003482.3	328	gcg/gGcg	8/54	1	2	FACETS	0.905	0.81	1	0.905	0.81	1	CLONAL	1	TRUE	1	0.428122220162935	2		428	506	SUCCESS
APC	324	MSKCC	GRCh37	5	112175618	112175619	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	113	697	0	ENST00000257430.4:c.4327_4328delinsTT	p.Pro1443Phe	p.P1443F	ENST00000257430	NM_000038.5	1443	CCt/TTt	16/16	1	2	FACETS	0.703	0.633	0.777	0.703	0.633	0.777	SUBCLONAL	1	TRUE	1	0.428122220162935	2		697	751	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115711	8115712	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	126	550	1	ENST00000346208.3:c.1057_1058delinsTT	p.Pro353Phe	p.P353F	ENST00000346208		353	CCc/TTc	6/6	0.428999211697465	1	FACETS	0.847	0.771	0.927	0.847	0.771	0.927	CLONAL	1	TRUE	0	0.428122220162935	1		551	546	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021249	31021250	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	85	415	1	ENST00000375687.4:c.1248_1249delinsTT	p.Arg417Ter	p.R417*	ENST00000375687	NM_015338.5	416	ctCCga/ctTTga	12/13	1	2	FACETS	0.829	0.735	0.928	0.829	0.735	0.928	CLONAL	1	TRUE	1	0.428122220162935	2		416	479	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10273406	10273407	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	130	586	1	ENST00000340748.4:c.896_897delinsTT	p.Pro299Leu	p.P299L	ENST00000340748		299	cCC/cTT	12/40	0.184097117288446	1	FACETS	0.657	0.597	0.721	0.657	0.597	0.721	INDETERMINATE	1	TRUE	0	0.428122220162935	1		587	726	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444043	49444044	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	107	498	0	ENST00000301067.7:c.3327_3328delinsTT	p.Pro1110Ser	p.P1110S	ENST00000301067	NM_003482.3	1109	gcCCca/gcTTca	11/54	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.428122220162935	2		498	485	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0012821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	274	357	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.287677955652868	3	FACETS	0.966	0.906	1	0.966	0.906	1	CLONAL	2	TRUE	1	0.287677955652868	3		357	1128	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587781525	NA	P-0012821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	254	887	0	ENST00000269305.4:c.842A>G	p.Asp281Gly	p.D281G	ENST00000269305	NM_001126112.2	281	gAc/gGc	8/11	0.168910117992659	1	FACETS	1	0.98	1	1	0.98	1	INDETERMINATE	1	TRUE	0	0.287677955652868	1		887	1353	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462643	29462643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs187200776	NA	P-0012821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1337	237	1089	2	ENST00000389048.3:c.2258G>A	p.Arg753Gln	p.R753Q	ENST00000389048	NM_004304.4	753	cGg/cAg	13/29	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.287677955652868	2		1091	1574	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947467	38947467	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1397	82	844	1	ENST00000357387.3:c.4213C>T	p.Arg1405Ter	p.R1405*	ENST00000357387	NM_152756.3	1405	Cga/Tga	32/38	0.287677955652868	3	FACETS	0.441	0.387	0.499	0.22	0.193	0.25	SUBCLONAL	1	TRUE	1	0.287677955652868	3		845	1479	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874272	155874272	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs886041414	NA	P-0012821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	86	644	0	ENST00000368323.3:c.259G>C	p.Asp87His	p.D87H	ENST00000368323	NM_006912.5	87	Gac/Cac	5/6	0.175148035185213	3	FACETS	0.548	0.482	0.618	0.274	0.241	0.309	SUBCLONAL	1	TRUE	1	0.287677955652868	3		644	1249	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988403	36988403	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	68	276	0	ENST00000354822.5:c.250C>G	p.Gln84Glu	p.Q84E	ENST00000354822	NM_001079668.2	84	Cag/Gag	2/3	0.287677955652868	1	FACETS	0.992	0.867	1	0.992	0.867	1	CLONAL	1	TRUE	0	0.287677955652868	1		276	408	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593416	48593417	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAAT	novel	NA	P-0012821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	141	673	0	ENST00000342988.3:c.1169_1172dup	p.Cys391Ter	p.C391*	ENST00000342988	NM_005359.5	389	-/GAAT	10/12	0.287677955652868	1	FACETS	0.98	0.893	1	0.98	0.893	1	CLONAL	1	TRUE	0	0.287677955652868	1		673	856	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974775	21974775	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	151	381	0	ENST00000304494.5:c.52del	p.Thr18ArgfsTer8	p.T18Rfs*8	ENST00000304494	NM_000077.4	18	Acg/cg	1/3	0.287677955652868	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.287677955652868	1		381	665	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988381	36988402	+	frameshift_variant	Frame_Shift_Del	DEL	TGGTGCCCCACGGCGTGCTGCT	TGGTGCCCCACGGCGTGCTGCT	-	novel	NA	P-0012821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	67	220	0	ENST00000354822.5:c.251_272del	p.Gln84ProfsTer10	p.Q84Pfs*10	ENST00000354822	NM_001079668.2	84	cAGCAGCACGCCGTGGGGCACCAc/cc	2/3	0.287677955652868	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.287677955652868	1		220	346	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220306	98220307	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CGTCCAGGGGTTCAGAAGGAAGACAG	novel	NA	P-0012880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	100	426	0	ENST00000331920.6:c.3131_3156dup	p.Ala1053LeufsTer5	p.A1053Lfs*5	ENST00000331920	NM_000264.3	1052	-/CTGTCTTCCTTCTGAACCCCTGGACG	18/24	0.407686577799035	1	FACETS	0.734	0.658	0.815	0.734	0.658	0.815	SUBCLONAL	1	TRUE	0	0.407686577799035	1		426	532	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0012911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	47	280	1	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.553	0.467	0.648	0.553	0.467	0.648	SUBCLONAL	1	TRUE	1	0.339956707120914	2		281	500	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0012911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1383	141	724	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.544	0.494	0.598	0.544	0.494	0.598	SUBCLONAL	1	TRUE	1	0.339956707120914	2		724	1524	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070577	67070578	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	92	537	2	ENST00000412916.2:c.207dup	p.Pro70SerfsTer13	p.P70Sfs*13	ENST00000412916		67	-/T	3/6	0.305833979311755	1	FACETS	0.458	0.406	0.514	0.458	0.406	0.514	SUBCLONAL	1	TRUE	0	0.339956707120914	1		539	980	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917737	29917737	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs149837139	NA	P-0012911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	71	528	0	ENST00000389048.3:c.931C>A	p.Arg311Ser	p.R311S	ENST00000389048	NM_004304.4	311	Cgt/Agt	3/29	1	2	FACETS	0.476	0.414	0.543	0.476	0.414	0.543	SUBCLONAL	1	TRUE	1	0.339956707120914	2		528	878	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115706	8115707	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGAC	novel	NA	P-0012911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	81	434	0	ENST00000346208.3:c.1054_1058dup	p.Leu354AspfsTer3	p.L354Dfs*3	ENST00000346208		351	aac/aaCAGACc	6/6	1	2	FACETS	0.59	0.519	0.666	0.59	0.519	0.666	SUBCLONAL	1	TRUE	1	0.339956707120914	2		434	808	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	81	588	1	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	0.241787252548701	2		589	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0012921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	93	609	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.241787252548701	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.241787252548701	1		610	614	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593473	48593474	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0012921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	82	535	1	ENST00000342988.3:c.1225dup	p.Val409GlyfsTer20	p.V409Gfs*20	ENST00000342988	NM_005359.5	408	-/G	10/12	0.241787252548701	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.241787252548701	1		536	555	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0012974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	118	363	1	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.866	0.79	0.945	0.866	0.79	0.945	CLONAL	1	TRUE	1	0.754585253466209	2		364	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0012974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	252	284	1	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.754585253466209	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.754585253466209	1		285	377	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567643	226567643	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs764897410	NA	P-0012974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	198	337	2	ENST00000366794.5:c.1523A>C	p.Lys508Thr	p.K508T	ENST00000366794	NM_001618.3	508	aAg/aCg	10/23	1	2	FACETS	0.914	0.853	0.977	0.914	0.853	0.977	CLONAL	1	TRUE	1	0.754585253466209	2		339	574	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880962	134880962	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1290751781	NA	P-0012974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	205	287	0	ENST00000398015.3:c.1525C>T	p.Arg509Cys	p.R509C	ENST00000398015	NM_004441.4	509	Cgc/Tgc	7/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.754585253466209	2		287	517	SUCCESS
APC	324	MSKCC	GRCh37	5	112174098	112174098	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs878853433	NA	P-0012974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	177	294	1	ENST00000257430.4:c.2807A>G	p.Asn936Ser	p.N936S	ENST00000257430	NM_000038.5	936	aAt/aGt	16/16	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.754585253466209	2		295	464	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117614	70117614	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	527	342	1	ENST00000245479.2:c.82G>T	p.Glu28Ter	p.E28*	ENST00000245479	NM_000346.3	28	Gag/Tag	1/3	0.754585253466209	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.754585253466209	2		343	644	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281517	15281517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	238	444	2	ENST00000263388.2:c.4856G>A	p.Arg1619His	p.R1619H	ENST00000263388	NM_000435.2	1619	cGc/cAc	26/33	1	2	FACETS	0.972	0.913	1	0.972	0.913	1	CLONAL	1	TRUE	1	0.754585253466209	2		446	649	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013728	12013728	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	147	263	0	ENST00000353533.5:c.673del	p.Ile225LeufsTer51	p.I225Lfs*51	ENST00000353533	NM_003010.3	224	Aaa/aa	6/11	0.754585253466209	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.754585253466209	1		263	208	SUCCESS
APC	324	MSKCC	GRCh37	5	112175171	112175172	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0012974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	89	158	0	ENST00000257430.4:c.3881_3882insAA	p.Glu1295ArgfsTer11	p.E1295Rfs*11	ENST00000257430	NM_000038.5	1294	cag/cAAag	16/16	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.754585253466209	2		158	221	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0012989-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	213	302	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.871798702229453	1	FACETS	0.955	0.915	0.992	0.955	0.915	0.992	CLONAL	1	TRUE	0	0.88	1		302	284	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852002	63852002	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012989-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	202	254	1	ENST00000279873.7:c.2780C>G	p.Ser927Cys	p.S927C	ENST00000279873	NM_032199.2	927	tCc/tGc	10/10	1	2	FACETS	0.975	0.914	1	0.975	0.914	1	CLONAL	1	TRUE	1	0.88	2		255	471	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133234501	133234501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774028311	NA	P-0012989-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	343	401	1	ENST00000320574.5:c.3331C>T	p.Arg1111Trp	p.R1111W	ENST00000320574	NM_006231.2	1111	Cgg/Tgg	27/49	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.88	2		402	766	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0012999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	117	66	0				ENST00000310581	NM_198253.2	-/1132			0.305741804665341	1	FACETS	0.862	0.778	0.95	0.862	0.778	0.95	CLONAL	1	TRUE	0	0.323414521177952	1		66	704	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0012999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	128	486	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.323414521177952	1	FACETS	0.886	0.804	0.972	0.886	0.804	0.972	CLONAL	1	TRUE	0	0.323414521177952	1		486	749	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523606	106523606	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0012999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	100	307	0	ENST00000359195.3:c.2758A>T	p.Lys920Ter	p.K920*	ENST00000359195	NM_002649.2	920	Aag/Tag	8/11	0.273624393056193	3	FACETS	0.867	0.773	0.966	0.433	0.386	0.483	CLONAL	1	TRUE	1	0.323414521177952	3		307	829	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066482	94066482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542602078	NA	P-0012999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1601	296	917	1	ENST00000369303.4:c.1277G>A	p.Arg426Gln	p.R426Q	ENST00000369303	NM_004440.3	426	cGa/cAa	5/17	1	2	FACETS	0.965	0.905	1	0.965	0.905	1	CLONAL	1	TRUE	1	0.323414521177952	2		918	1897	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2492096	2492097	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs772088410	NA	P-0012999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1326	325	730	0	ENST00000355716.4:c.500dup	p.Thr169AspfsTer65	p.T169Dfs*65	ENST00000355716	NM_003820.2	165	tgc/tgCc	5/8	0.138163043257842	4	FACETS	0.806	0.759	0.854			1	INDETERMINATE	2	TRUE	NA	0.323414521177952	4		730	1651	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458456	120458456	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	92	352	0	ENST00000256646.2:c.6889C>T	p.Pro2297Ser	p.P2297S	ENST00000256646	NM_024408.3	2297	Cct/Tct	34/34	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.323414521177952	NA		352	614	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719163	190719163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	70	275	0	ENST00000441310.2:c.1165C>T	p.Pro389Ser	p.P389S	ENST00000441310	NM_000534.4	389	Cca/Tca	9/13	1	2	FACETS	0.809	0.706	0.92	0.809	0.706	0.92	CLONAL	1	TRUE	1	0.323414521177952	2		275	535	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127420	55127420	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	204	709	0	ENST00000257290.5:c.208G>A	p.Glu70Lys	p.E70K	ENST00000257290	NM_006206.4	70	Gaa/Aaa	3/23	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.323414521177952	2		709	1255	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955581	55955581	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1479	219	866	1	ENST00000263923.4:c.3364G>A	p.Gly1122Arg	p.G1122R	ENST00000263923	NM_002253.2	1122	Gga/Aga	25/30	1	2	FACETS	0.798	0.739	0.859	0.798	0.739	0.859	SUBCLONAL	1	TRUE	1	0.323414521177952	2		867	1698	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149453012	149453012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	150	561	0	ENST00000286301.3:c.934G>A	p.Glu312Lys	p.E312K	ENST00000286301	NM_005211.3	312	Gag/Aag	7/22	1	2	FACETS	0.983	0.898	1	0.983	0.898	1	CLONAL	1	TRUE	1	0.323414521177952	2		561	944	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681034	117681034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142826369	NA	P-0012999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	155	552	0	ENST00000368508.3:c.3586G>A	p.Gly1196Arg	p.G1196R	ENST00000368508	NM_002944.2	1196	Gga/Aga	23/43	1	2	FACETS	0.818	0.747	0.892	0.818	0.747	0.892	CLONAL	1	TRUE	1	0.323414521177952	2		552	1172	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001541	150001541	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	116	369	0	ENST00000253339.5:c.2063A>T	p.Lys688Ile	p.K688I	ENST00000253339		688	aAa/aTa	4/7	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.323414521177952	2		369	652	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	463370	463370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749556390	NA	P-0012999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	195	593	2	ENST00000399788.2:c.901C>T	p.Arg301Trp	p.R301W	ENST00000399788	NM_001042603.1	301	Cgg/Tgg	8/28	NA	2	FACETS	0.89	0.822	0.961			1	INDETERMINATE	1	TRUE	NA	0.323414521177952	2		595	1355	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435925	110435925	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs946536275	NA	P-0012999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	58	162	0	ENST00000375856.3:c.2476A>G	p.Met826Val	p.M826V	ENST00000375856	NM_003749.2	826	Atg/Gtg	1/2	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.323414521177952	2		162	296	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222516	2222516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	169	690	1	ENST00000326181.6:c.710C>T	p.Pro237Leu	p.P237L	ENST00000326181	NM_032271.2	237	cCc/cTc	9/21	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.323414521177952	2		691	969	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031883	10031883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	139	517	0	ENST00000330684.3:c.940C>T	p.Pro314Ser	p.P314S	ENST00000330684	NM_001134407.1	314	Ccc/Tcc	3/13	1	2	FACETS	0.844	0.768	0.925	0.844	0.768	0.925	CLONAL	1	TRUE	1	0.323414521177952	2		517	1018	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844122	68844122	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	143	511	0	ENST00000261769.5:c.710C>T	p.Ser237Phe	p.S237F	ENST00000261769	NM_004360.3	237	tCc/tTc	6/16	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.323414521177952	2		511	879	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968232	15968232	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	229	667	1	ENST00000268712.3:c.5053C>T	p.Gln1685Ter	p.Q1685*	ENST00000268712	NM_006311.3	1685	Cag/Tag	34/46	0.323414521177952	1	FACETS	0.931	0.866	0.998	0.931	0.866	0.998	CLONAL	1	TRUE	0	0.323414521177952	1		668	1275	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528441	29528441	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	196	484	0	ENST00000356175.3:c.1198C>T	p.Gln400Ter	p.Q400*	ENST00000356175	NM_000267.3	400	Cag/Tag	11/57	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.323414521177952	2		484	1006	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687321	37687321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	225	630	0	ENST00000447079.4:c.4225C>T	p.Pro1409Ser	p.P1409S	ENST00000447079	NM_015083.1	1409	Ccc/Tcc	14/14	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.323414521177952	2		630	1242	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867032	45867032	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	64	271	0	ENST00000391945.4:c.1087C>T	p.Gln363Ter	p.Q363*	ENST00000391945	NM_000400.3	363	Cag/Tag	11/23	0.323414521177952	1	FACETS	0.821	0.714	0.937	0.821	0.714	0.937	CLONAL	1	TRUE	0	0.323414521177952	1		271	404	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933083	39933083	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	215	380	0	ENST00000378444.4:c.1516C>T	p.Pro506Ser	p.P506S	ENST00000378444	NM_001123385.1	506	Ccc/Tcc	4/15	1	1	FACETS	0.828	0.773	0.884	1	0.993	1	CLONAL	2	TRUE	0	0.323414521177952	1		380	673	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683426	182683426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013086-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	53	435	0	ENST00000292782.4:c.119C>T	p.Ala40Val	p.A40V	ENST00000292782	NM_020640.2	40	gCa/gTa	2/7	1	2	FACETS	0.43	0.366	0.5	0.43	0.366	0.5	SUBCLONAL	1	TRUE	1	0.373796549508744	2		435	660	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343180	118343180	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013086-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	65	632	0	ENST00000534358.1:c.1306C>G	p.Pro436Ala	p.P436A	ENST00000534358	NM_005933.3	436	Cct/Gct	3/36	1	2	FACETS	0.364	0.314	0.418	0.364	0.314	0.418	SUBCLONAL	1	TRUE	1	0.373796549508744	2		632	956	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248284	59248285	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0013086-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	20	94	0	ENST00000371222.2:c.458dup	p.Ser154GlnfsTer156	p.S154Qfs*156	ENST00000371222	NM_002228.3	153	ggc/ggGc	1/1	1	2	FACETS	0.799	0.617	1	0.799	0.617	1	CLONAL	1	TRUE	1	0.373796549508744	2		94	134	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117799	108117799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202160435	NA	P-0013143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	194	367	0	ENST00000278616.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000278616	NM_000051.3	337	cGt/cAt	8/63	0.588570419498947	3	FACETS	0.934	0.864	1	0.467	0.432	0.503	CLONAL	1	TRUE	1	0.588570419498947	3		367	914	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242448	55242449	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTCCCGTCGCTATCAAGG	novel	NA	P-0013143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	383	553	0	ENST00000275493.2:c.2219_2236dup	p.Lys745_Glu746insValProValAlaIleLys	p.K745_E746insVPVAIK	ENST00000275493	NM_005228.3	740	att/aTTCCCGTCGCTATCAAGGtt	19/28	0.588570419498947	4	FACETS	1	0.993	1	0.64	0.606	0.675	CLONAL	1	TRUE	2	0.588570419498947	4		553	1615	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955100	55955100	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	334	666	0	ENST00000263923.4:c.3445C>T	p.Gln1149Ter	p.Q1149*	ENST00000263923	NM_002253.2	1149	Cag/Tag	26/30	0.530364225399464	3	FACETS	1	0.994	1	0.474	0.448	0.499	CLONAL	1	TRUE	0	0.588570419498947	3		666	1034	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	187	208	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	0.376495032808321	2		208	984	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1480	356	831	11	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	0.376495032808321	2		842	1836	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007825	45007825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	380	505	0	ENST00000558401.1:c.276del	p.Thr93LeufsTer10	p.T93Lfs*10	ENST00000558401	NM_004048.2	91	aCc/ac	2/4	1	2	FACETS	0.923	0.878	0.969	1	0.996	1	CLONAL	2	TRUE	1	0.376495032808321	2		505	1093	SUCCESS
APC	324	MSKCC	GRCh37	5	112175970	112175970	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1114167552	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	130	359	1	ENST00000257430.4:c.4682del	p.Lys1561ArgfsTer4	p.K1561Rfs*4	ENST00000257430	NM_000038.5	1560	gAa/ga	16/16	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.376495032808321	2		360	654	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965666	90965666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1327	311	421	0	ENST00000265433.3:c.1651del	p.Arg551GlyfsTer8	p.R551Gfs*8	ENST00000265433	NM_002485.4	551	Agg/gg	11/16	0.376495032808321	2	FACETS	1	0.948	1	0.504	0.474	0.536	CLONAL	1	TRUE	0	0.376495032808321	2		421	1638	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	273	331	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.807	0.759	0.856	1	0.994	1	CLONAL	2	TRUE	1	0.376495032808321	2		332	899	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165653	118165653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763834209	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	187	541	1	ENST00000369448.3:c.163G>A	p.Val55Ile	p.V55I	ENST00000369448	NM_017709.3	55	Gtc/Atc	2/2	1	2	FACETS	0.998	0.922	1	0.998	0.922	1	CLONAL	1	TRUE	1	0.376495032808321	2		542	995	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396889	139396889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777962754	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	160	430	0	ENST00000277541.6:c.5219C>T	p.Ala1740Val	p.A1740V	ENST00000277541	NM_017617.3	1740	gCg/gTg	28/34	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.376495032808321	2		430	721	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1424	357	984	2	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.376495032808321	2		986	1781	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636729	8636729	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	55	386	0	ENST00000356435.5:c.180del	p.Gly61GlufsTer11	p.G61Efs*11	ENST00000356435		60	aaA/aa	2/35	1	2	FACETS	0.329	0.28	0.382	0.329	0.28	0.382	SUBCLONAL	1	TRUE	1	0.376495032808321	2		386	889	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	299	547	7	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.376495032808321	2		554	1418	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851177	151851177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141966811	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	232	622	4	ENST00000262189.6:c.12194C>T	p.Ala4065Val	p.A4065V	ENST00000262189	NM_170606.2	4065	gCg/gTg	48/59	1	2	FACETS	0.975	0.908	1	0.975	0.908	1	CLONAL	1	TRUE	1	0.376495032808321	2		626	1264	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907421	32907421	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359306	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	191	346	3	ENST00000380152.3:c.1813del	p.Ile605TyrfsTer9	p.I605Yfs*9	ENST00000380152		602	ggA/gg	10/27	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.376495032808321	2		349	1003	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149799	202149799	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	422	584	0	ENST00000358485.4:c.1245del	p.Phe415LeufsTer26	p.F415Lfs*26	ENST00000358485	NM_001080125.1	414	Ttt/tt	8/9	0.376495032808321	2	FACETS	0.945	0.901	0.989	0.945	0.901	0.989	CLONAL	2	TRUE	0	0.376495032808321	2		584	1186	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161939	47161939	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	175	282	0	ENST00000409792.3:c.4187del	p.Asn1396MetfsTer16	p.N1396Mfs*16	ENST00000409792	NM_014159.6	1396	aAt/at	3/21	1	2	FACETS	0.862	0.792	0.934	0.862	0.792	0.934	CLONAL	1	TRUE	1	0.376495032808321	2		282	1079	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664903	138664903	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	36	150	2	ENST00000330315.3:c.662C>T	p.Ala221Val	p.A221V	ENST00000330315	NM_023067.3	221	gCg/gTg	1/1	1	2	FACETS	0.744	0.615	0.887	0.744	0.615	0.887	SUBCLONAL	1	TRUE	1	0.376495032808321	2		152	257	SUCCESS
APC	324	MSKCC	GRCh37	5	112173926	112173926	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060503287	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	180	487	0	ENST00000257430.4:c.2635C>T	p.Gln879Ter	p.Q879*	ENST00000257430	NM_000038.5	879	Cag/Tag	16/16	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.376495032808321	2		487	934	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130266	11130266	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	209	493	0	ENST00000358026.2:c.2506-1G>T		p.X836_splice	ENST00000358026	NM_001128849.1	836			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.376495032808321	2		493	990	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779578	3779578	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1243	320	890	1	ENST00000262367.5:c.5470G>A	p.Ala1824Thr	p.A1824T	ENST00000262367	NM_004380.2	1824	Gcc/Acc	31/31	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.376495032808321	2		891	1563	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058747	180058748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755445139	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	163	467	0	ENST00000261937.6:c.89dup	p.Thr31AspfsTer15	p.T31Dfs*15	ENST00000261937	NM_182925.4	30	ccg/ccCg	2/30	1	2	FACETS	0.75	0.687	0.816	0.75	0.687	0.816	SUBCLONAL	1	TRUE	1	0.376495032808321	2		467	1155	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020764	37020764	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1258	263	790	3	ENST00000358127.4:c.81del	p.Phe27LeufsTer2	p.F27Lfs*2	ENST00000358127	NM_001280556.1	27	ttT/tt	2/10	1	2	FACETS	0.919	0.858	0.981	0.919	0.858	0.981	CLONAL	1	TRUE	1	0.376495032808321	2		793	1521	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424178	49424178	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs886040960	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	176	480	3	ENST00000301067.7:c.13884del	p.Thr4629ProfsTer11	p.T4629Pfs*11	ENST00000301067	NM_003482.3	4628	ccC/cc	42/54	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.376495032808321	2		483	850	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11301679	11301679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	94	593	0	ENST00000361445.4:c.1472G>A	p.Arg491Gln	p.R491Q	ENST00000361445	NM_004958.3	491	cGa/cAa	10/58	1	2	FACETS	0.447	0.397	0.502	0.447	0.397	0.502	SUBCLONAL	1	TRUE	1	0.376495032808321	2		593	1116	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256981	16256981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762271842	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	214	559	1	ENST00000375759.3:c.4246C>T	p.Arg1416Cys	p.R1416C	ENST00000375759	NM_015001.2	1416	Cgt/Tgt	11/15	1	2	FACETS	0.993	0.922	1	0.993	0.922	1	CLONAL	1	TRUE	1	0.376495032808321	2		560	1145	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087893	27087893	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376482571	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	254	624	0	ENST00000324856.7:c.2180G>A	p.Arg727Gln	p.R727Q	ENST00000324856	NM_006015.4	727	cGg/cAg	6/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.376495032808321	2		624	1184	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36821030	36821030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1171838543	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	211	592	1	ENST00000373129.3:c.347G>A	p.Arg116His	p.R116H	ENST00000373129	NM_032017.1	116	cGc/cAc	6/12	1	2	FACETS	0.963	0.893	1	0.963	0.893	1	CLONAL	1	TRUE	1	0.376495032808321	2		593	1164	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165861	118165861	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	165	492	0	ENST00000369448.3:c.371T>C	p.Val124Ala	p.V124A	ENST00000369448	NM_017709.3	124	gTg/gCg	2/2	1	2	FACETS	0.963	0.885	1	0.963	0.885	1	CLONAL	1	TRUE	1	0.376495032808321	2		492	910	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483245	120483245	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61755044	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	60	573	0	ENST00000256646.2:c.3116C>T	p.Thr1039Met	p.T1039M	ENST00000256646	NM_024408.3	1039	aCg/aTg	19/34	1	2	FACETS	0.331	0.284	0.382	0.331	0.284	0.382	SUBCLONAL	1	TRUE	1	0.376495032808321	2		573	964	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091376	193091376	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	483	628	0	ENST00000367435.3:c.46A>C	p.Lys16Gln	p.K16Q	ENST00000367435	NM_024529.4	16	Aag/Cag	1/17	0.348623769973381	4	FACETS	0.871	0.833	0.909	0.871	0.833	0.909	CLONAL	3	TRUE	1	0.376495032808321	4		628	1352	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416544	29416544	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	227	568	0	ENST00000389048.3:c.4409C>T	p.Ala1470Val	p.A1470V	ENST00000389048	NM_004304.4	1470	gCc/gTc	29/29	0.376495032808321	2	FACETS	1	0.938	1	0.505	0.469	0.541	CLONAL	1	TRUE	0	0.376495032808321	2		568	1195	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47709945	47709945	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	221	611	2	ENST00000233146.2:c.2662C>A	p.Leu888Met	p.L888M	ENST00000233146	NM_000251.2	888	Ctg/Atg	16/16	0.376495032808321	2	FACETS	0.93	0.863	0.998	0.465	0.431	0.499	CLONAL	1	TRUE	0	0.376495032808321	2		613	1263	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163425	47163425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757476376	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	210	549	0	ENST00000409792.3:c.2701G>A	p.Gly901Arg	p.G901R	ENST00000409792	NM_014159.6	901	Gga/Aga	3/21	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.376495032808321	2		549	1104	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725021	49725021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs114429531	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1332	120	768	2	ENST00000449682.2:c.323G>A	p.Arg108His	p.R108H	ENST00000449682	NM_020998.3	108	cGt/cAt	3/18	1	2	FACETS	0.439	0.395	0.486	0.439	0.395	0.486	SUBCLONAL	1	TRUE	1	0.376495032808321	2		770	1452	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445028	89445028	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	259	657	0	ENST00000336596.2:c.1348A>T	p.Arg450Ter	p.R450*	ENST00000336596	NM_005233.5	450	Aga/Tga	6/17	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.376495032808321	2		657	1336	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665413	138665413	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	161	469	0	ENST00000330315.3:c.152C>T	p.Pro51Leu	p.P51L	ENST00000330315	NM_023067.3	51	cCg/cTg	1/1	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.376495032808321	2		469	820	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196255	106196255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	209	500	0	ENST00000380013.4:c.4588C>A	p.Pro1530Thr	p.P1530T	ENST00000380013	NM_001127208.2	1530	Cct/Act	11/11	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.376495032808321	2		500	1096	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673772	30673772	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	205	658	0	ENST00000376406.3:c.3188C>A	p.Pro1063His	p.P1063H	ENST00000376406	NM_014641.2	1063	cCt/cAt	10/15	1	2	FACETS	0.925	0.857	0.996	0.925	0.857	0.996	CLONAL	1	TRUE	1	0.376495032808321	2		658	1177	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6038873	6038873	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	234	697	0	ENST00000265849.7:c.571T>G	p.Tyr191Asp	p.Y191D	ENST00000265849	NM_000535.5	191	Tac/Gac	6/15	1	2	FACETS	0.934	0.869	1	0.934	0.869	1	CLONAL	1	TRUE	1	0.376495032808321	2		697	1331	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339523	81339523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1489	283	868	0	ENST00000222390.5:c.1481G>A	p.Arg494Gln	p.R494Q	ENST00000222390	NM_000601.4	494	cGa/cAa	13/18	1	2	FACETS	0.848	0.794	0.904	0.848	0.794	0.904	CLONAL	1	TRUE	1	0.376495032808321	2		868	1772	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151833933	151833933	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376468045	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	175	472	3	ENST00000262189.6:c.14720G>A	p.Arg4907Gln	p.R4907Q	ENST00000262189	NM_170606.2	4907	cGg/cAg	59/59	1	2	FACETS	0.896	0.824	0.97	0.896	0.824	0.97	CLONAL	1	TRUE	1	0.376495032808321	2		475	1038	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271528	38271528	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1329256283	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	250	704	0	ENST00000425967.3:c.2293C>T	p.Arg765Trp	p.R765W	ENST00000425967	NM_001174067.1	765	Cgg/Tgg	18/19	1	2	FACETS	0.976	0.911	1	0.976	0.911	1	CLONAL	1	TRUE	1	0.376495032808321	2		704	1361	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370819	55370819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	55	394	0	ENST00000297316.4:c.121G>A	p.Asp41Asn	p.D41N	ENST00000297316	NM_022454.3	41	Gac/Aac	1/2	1	2	FACETS	0.517	0.442	0.599	0.517	0.442	0.599	SUBCLONAL	1	TRUE	1	0.376495032808321	2		394	565	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209282	98209282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372686352	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1281	326	863	2	ENST00000331920.6:c.4256G>A	p.Arg1419Gln	p.R1419Q	ENST00000331920	NM_000264.3	1419	cGg/cAg	23/24	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.376495032808321	2		865	1607	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399131	139399131	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	129	468	0	ENST00000277541.6:c.5012T>C	p.Val1671Ala	p.V1671A	ENST00000277541	NM_017617.3	1671	gTc/gCc	26/34	1	2	FACETS	0.81	0.734	0.89	0.81	0.734	0.89	CLONAL	1	TRUE	1	0.376495032808321	2		468	846	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251848	8251848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1470323179	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	179	546	0	ENST00000335790.3:c.229G>A	p.Asp77Asn	p.D77N	ENST00000335790	NM_002315.2	77	Gac/Aac	2/4	1	2	FACETS	0.996	0.918	1	0.996	0.918	1	CLONAL	1	TRUE	1	0.376495032808321	2		546	955	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741565	17741565	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	82	293	0	ENST00000250003.3:c.236A>C	p.Glu79Ala	p.E79A	ENST00000250003	NM_002478.4	79	gAg/gCg	1/3	1	2	FACETS	0.898	0.795	1	0.898	0.795	1	CLONAL	1	TRUE	1	0.376495032808321	2		293	485	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865482	57865482	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1555	369	1169	0	ENST00000228682.2:c.2959G>C	p.Ala987Pro	p.A987P	ENST00000228682	NM_005269.2	987	Gca/Cca	12/12	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.376495032808321	2		1169	1924	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109845	115109845	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1490395317	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	159	430	0	ENST00000257566.3:c.2033C>T	p.Ala678Val	p.A678V	ENST00000257566	NM_016569.3	678	gCc/gTc	8/8	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.376495032808321	2		430	722	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133238231	133238231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	256	627	0	ENST00000320574.5:c.2746C>T	p.Pro916Ser	p.P916S	ENST00000320574	NM_006231.2	916	Ccg/Tcg	24/49	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.376495032808321	2		627	1209	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81574751	81574751	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs771936985	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	194	689	0	ENST00000298171.2:c.647T>C	p.Ile216Thr	p.I216T	ENST00000298171	NM_000369.2	216	aTt/aCt	8/10	1	2	FACETS	0.84	0.776	0.907	0.84	0.776	0.907	CLONAL	1	TRUE	1	0.376495032808321	2		689	1227	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571561	95571561	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	161	636	1	ENST00000393063.1:c.3116C>A	p.Ala1039Asp	p.A1039D	ENST00000393063	NM_030621.3	1039	gCt/gAt	21/28	1	2	FACETS	0.808	0.74	0.88	0.808	0.74	0.88	CLONAL	1	TRUE	1	0.376495032808321	2		637	1058	SUCCESS
BLM	641	MSKCC	GRCh37	15	91333927	91333927	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775006576	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1198	230	691	2	ENST00000355112.3:c.2872G>A	p.Val958Met	p.V958M	ENST00000355112	NM_000057.2	958	Gtg/Atg	15/22	1	2	FACETS	0.856	0.795	0.918	0.856	0.795	0.918	CLONAL	1	TRUE	1	0.376495032808321	2		693	1428	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108846	2108846	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	234	761	0	ENST00000219476.3:c.947C>T	p.Pro316Leu	p.P316L	ENST00000219476	NM_000548.3	316	cCg/cTg	10/42	1	2	FACETS	0.969	0.902	1	0.969	0.902	1	CLONAL	1	TRUE	1	0.376495032808321	2		761	1283	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136201	2136201	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	132	377	0	ENST00000219476.3:c.4670G>A	p.Ser1557Asn	p.S1557N	ENST00000219476	NM_000548.3	1557	aGc/aAc	37/42	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.376495032808321	2		377	633	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56872882	56872882	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1828	416	1034	0	ENST00000308159.5:c.2037A>G	p.Ile679Met	p.I679M	ENST00000308159	NM_014669.4	679	atA/atG	19/22	1	2	FACETS	0.985	0.934	1	0.985	0.934	1	CLONAL	1	TRUE	1	0.376495032808321	2		1034	2244	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81979858	81979858	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751544016	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1745	141	981	0	ENST00000359376.3:c.3560G>A	p.Arg1187Gln	p.R1187Q	ENST00000359376	NM_002661.3	1187	cGg/cAg	31/33	1	2	FACETS	0.397	0.36	0.437	0.397	0.36	0.437	SUBCLONAL	1	TRUE	1	0.376495032808321	2		981	1886	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346204	89346204	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201043388	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	188	540	1	ENST00000301030.4:c.6746G>A	p.Arg2249His	p.R2249H	ENST00000301030	NM_001256183.1	2249	cGc/cAc	9/13	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.376495032808321	2		541	925	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346891	89346891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	167	556	0	ENST00000301030.4:c.6059C>T	p.Ala2020Val	p.A2020V	ENST00000301030	NM_001256183.1	2020	gCc/gTc	9/13	1	2	FACETS	0.966	0.888	1	0.966	0.888	1	CLONAL	1	TRUE	1	0.376495032808321	2		556	918	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579716	7579716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526933	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1387	93	818	0	ENST00000269305.4:c.80C>T	p.Pro27Leu	p.P27L	ENST00000269305	NM_001126112.2	27	cCt/cTt	3/11	1	2	FACETS	0.334	0.295	0.375	0.334	0.295	0.375	SUBCLONAL	1	TRUE	1	0.376495032808321	2		818	1480	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78865613	78865613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752600548	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	240	582	1	ENST00000306801.3:c.2077G>A	p.Ala693Thr	p.A693T	ENST00000306801	NM_020761.2	693	Gcc/Acc	18/34	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.376495032808321	2		583	997	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170828	11170828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757412819	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	133	363	0	ENST00000358026.2:c.4972G>A	p.Val1658Met	p.V1658M	ENST00000358026	NM_001128849.1	1658	Gtg/Atg	35/36	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.376495032808321	2		363	650	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284877	15284877	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	65	483	0	ENST00000263388.2:c.4736+2T>C		p.X1579_splice	ENST00000263388	NM_000435.2	1579			1	2	FACETS	0.374	0.323	0.43	0.374	0.323	0.43	SUBCLONAL	1	TRUE	1	0.376495032808321	2		483	923	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919735	50919735	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	290	874	0	ENST00000440232.2:c.2903G>A	p.Arg968His	p.R968H	ENST00000440232	NM_002691.3	968	cGc/cAc	23/27	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.376495032808321	2		874	1439	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035923	47035923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1543	269	988	0	ENST00000377604.3:c.601A>G	p.Lys201Glu	p.K201E	ENST00000377604	NM_001204468.1	201	Aag/Gag	7/24	1	2	FACETS	0.789	0.737	0.842	0.789	0.737	0.842	SUBCLONAL	1	TRUE	1	0.376495032808321	2		988	1812	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888819	76888819	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1669	313	920	0	ENST00000373344.5:c.5010G>T	p.Gln1670His	p.Q1670H	ENST00000373344	NM_000489.3	1670	caG/caT	19/35	1	2	FACETS	0.839	0.788	0.891	0.839	0.788	0.891	CLONAL	1	TRUE	1	0.376495032808321	2		920	1982	SUCCESS
AR	367	MSKCC	GRCh37	X	66765779	66765779	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1422	304	1013	0	ENST00000374690.3:c.796del	p.Asp266IlefsTer30	p.D266Ifs*30	ENST00000374690	NM_000044.3	264	cGg/cg	1/8	1	2	FACETS	0.936	0.879	0.994	0.936	0.879	0.994	CLONAL	1	TRUE	1	0.376495032808321	2		1013	1726	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135800999	135800999	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs118203367	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	130	591	0	ENST00000298552.3:c.338del	p.Leu113CysfsTer5	p.L113Cfs*5	ENST00000298552	NM_001162426.1	113	tTg/tg	5/23	1	2	FACETS	0.568	0.514	0.626	0.568	0.514	0.626	SUBCLONAL	1	TRUE	1	0.376495032808321	2		591	1215	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39629500	39629514	+	inframe_deletion	In_Frame_Del	DEL	TATTGCGTGATCACC	TATTGCGTGATCACC	-	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	176	465	0	ENST00000262039.4:c.2197_2211del	p.Cys733_Tyr737del	p.C733_Y737del	ENST00000262039	NM_002647.2	732	TATTGCGTGATCACC/-	21/25	1	2	FACETS	0.903	0.831	0.978	0.903	0.831	0.978	CLONAL	1	TRUE	1	0.376495032808321	2		465	1035	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239384	105239385	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	264	724	0	ENST00000349310.3:c.1002dup	p.Leu335AlafsTer21	p.L335Afs*21	ENST00000349310	NM_001014432.1	334	-/G	12/15	1	2	FACETS	0.971	0.908	1	0.971	0.908	1	CLONAL	1	TRUE	1	0.376495032808321	2		724	1444	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120795	115120795	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	149	575	0	ENST00000257566.3:c.211del	p.Ala71ArgfsTer17	p.A71Rfs*17	ENST00000257566	NM_016569.3	71	Gcg/cg	1/8	1	2	FACETS	0.954	0.872	1	0.954	0.872	1	CLONAL	1	TRUE	1	0.376495032808321	2		575	830	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935370	36935371	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1374	315	1026	0	ENST00000361632.4:c.1356dup	p.Asn453GlnfsTer10	p.N453Qfs*10	ENST00000361632		452	-/C	10/16	1	2	FACETS	0.991	0.932	1	0.991	0.932	1	CLONAL	1	TRUE	1	0.376495032808321	2		1026	1689	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742952	17742952	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	123	377	0	ENST00000250003.3:c.864del	p.Ser289AlafsTer47	p.S289Afs*47	ENST00000250003	NM_002478.4	287	gCc/gc	3/3	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.376495032808321	2		377	610	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16052795	16052795	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	155	516	2	ENST00000268712.3:c.879del	p.Phe293LeufsTer33	p.F293Lfs*33	ENST00000268712	NM_006311.3	293	ttT/tt	9/46	1	2	FACETS	0.803	0.734	0.875	0.803	0.734	0.875	CLONAL	1	TRUE	1	0.376495032808321	2		518	1026	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035915	47035916	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	C	novel	NA	P-0013169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1566	241	994	0	ENST00000377604.3:c.593_594delinsC	p.Leu198ProfsTer68	p.L198Pfs*68	ENST00000377604	NM_001204468.1	198	cTG/cC	7/24	1	2	FACETS	0.708	0.659	0.76	0.708	0.659	0.76	SUBCLONAL	1	TRUE	1	0.376495032808321	2		994	1807	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0013186-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	108	314	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.248829622161064	1	FACETS	0.775	0.694	0.861	0.775	0.694	0.861	SUBCLONAL	1	TRUE	0	0.248829622161064	1		314	981	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026741	6026741	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013186-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	67	270	0	ENST00000265849.7:c.1655A>T	p.His552Leu	p.H552L	ENST00000265849	NM_000535.5	552	cAt/cTt	11/15	0.248829622161064	3	FACETS	0.915	0.794	1	0.457	0.397	0.523	CLONAL	1	TRUE	1	0.248829622161064	3		270	662	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579445	7579446	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013186-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	276	526	0	ENST00000269305.4:c.241dup	p.Thr81AsnfsTer68	p.T81Nfs*68	ENST00000269305	NM_001126112.2	81	aca/aAca	4/11	0.220358500038459	3	FACETS	0.847	0.796	0.899	0.847	0.796	0.899	CLONAL	3	TRUE	0	0.248829622161064	3		526	982	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0013187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	220	673	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.598883477297344	3	FACETS	0.966	0.909	1	0.966	0.909	1	CLONAL	2	TRUE	1	0.598883477297344	3		673	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1427441061	NA	P-0013187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	309	526	0	ENST00000269305.4:c.560-2A>G		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.598883477297344	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.598883477297344	1		526	717	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954315	48954317	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	rs587776788	NA	P-0013187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	109	297	0	ENST00000267163.4:c.1439_1441del	p.Asn480del	p.N480del	ENST00000267163	NM_000321.2	479	gACAac/gac	16/27	0.598883477297344	1	FACETS	0.704	0.639	0.772	0.704	0.639	0.772	SUBCLONAL	1	TRUE	0	0.598883477297344	1		297	362	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252852	36252853	+	splice_donor_variant	Splice_Site	INS	-	-	CCTCTT	novel	NA	P-0013187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	225	343	0	ENST00000300305.3:c.504_508+1dup		p.X168_splice	ENST00000300305		168			1	2	FACETS	0.851	0.794	0.91	0.851	0.794	0.91	CLONAL	1	TRUE	1	0.598883477297344	2		343	883	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0013223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	272	809	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.57	2		809	932	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433650	49433650	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs794727549	NA	P-0013223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	138	725	0	ENST00000301067.7:c.7903C>T	p.Arg2635Ter	p.R2635*	ENST00000301067	NM_003482.3	2635	Cga/Tga	31/54	1	2	FACETS	0.526	0.478	0.576	0.526	0.478	0.576	SUBCLONAL	1	TRUE	1	0.57	2		725	921	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041395	42041396	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1191	462	1303	0	ENST00000219905.7:c.5591dup	p.Met1864IlefsTer29	p.M1864Ifs*29	ENST00000219905	NM_001164273.1	1864	atg/aTtg	17/24	1	2	FACETS	0.981	0.935	1	0.981	0.935	1	CLONAL	1	TRUE	1	0.57	2		1303	1653	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0013306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	139	516	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.886	0.805	0.972	0.886	0.805	0.972	CLONAL	1	TRUE	1	0.279828423833832	2		517	1121	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0013306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	258	371	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.193780078905274	5	FACETS	1	0.977	1	0.727	0.68	0.775	CLONAL	2	TRUE	2	0.279828423833832	5		371	1201	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0013306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	92	551	0	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	1	2	FACETS	0.746	0.662	0.837	0.746	0.662	0.837	SUBCLONAL	1	TRUE	1	0.279828423833832	2		551	881	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193202215	193202215	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1553291033	NA	P-0013306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	311	608	0	ENST00000367435.3:c.1247G>C	p.Gly416Ala	p.G416A	ENST00000367435	NM_024529.4	416	gGc/gCc	14/17	0.23129152244578	5	FACETS	1	0.99	1	0.828	0.78	0.877	CLONAL	2	TRUE	2	0.279828423833832	5		608	1271	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426668	212426668	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	182	657	0	ENST00000342788.4:c.2447G>C	p.Gly816Ala	p.G816A	ENST00000342788	NM_005235.2	816	gGa/gCa	20/28	0.175836753340561	4	FACETS	1	0.989	1	0.75	0.691	0.812	CLONAL	1	TRUE	2	0.279828423833832	4		657	1110	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426680	212426680	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	193	694	0	ENST00000342788.4:c.2435A>G	p.Lys812Arg	p.K812R	ENST00000342788	NM_005235.2	812	aAg/aGg	20/28	0.175836753340561	4	FACETS	0.781	0.722	0.843	0.781	0.722	0.843	SUBCLONAL	2	TRUE	2	0.279828423833832	4		694	1130	SUCCESS
ATR	545	MSKCC	GRCh37	3	142177826	142177826	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	98	476	1	ENST00000350721.4:c.7477G>T	p.Val2493Leu	p.V2493L	ENST00000350721	NM_001184.3	2493	Gta/Tta	44/47	1	2	FACETS	0.798	0.711	0.891	0.798	0.711	0.891	SUBCLONAL	1	TRUE	1	0.279828423833832	2		477	878	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606887	43606887	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	53	276	0	ENST00000355710.3:c.1496A>T	p.Gln499Leu	p.Q499L	ENST00000355710	NM_020975.4	499	cAg/cTg	7/20	0.227609051198198	3	FACETS	0.842	0.718	0.977	0.421	0.359	0.489	CLONAL	1	TRUE	1	0.279828423833832	3		276	513	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472661	88472661	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	114	307	0	ENST00000360948.2:c.1894C>A	p.His632Asn	p.H632N	ENST00000360948	NM_001012338.2	632	Cat/Aat	16/19	0.22818970939386	2	FACETS	0.825	0.746	0.907	0.825	0.746	0.907	CLONAL	2	TRUE	0	0.279828423833832	2		307	494	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430639	181430640	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGC	novel	NA	P-0013306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	54	342	0	ENST00000325404.1:c.493_494insCCG	p.Asn164_Gly165insAla	p.N164_G165insA	ENST00000325404	NM_003106.3	164	aac/aaCGCc	1/1	1	2	FACETS	0.789	0.675	0.914	0.789	0.675	0.914	CLONAL	1	TRUE	1	0.279828423833832	2		342	489	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	143	588	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.0632850242610872	4	FACETS	1	0.978	1	1	0.978	1	INDETERMINATE	2	TRUE	2	0.222298832757251	4		589	649	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197710	66197710	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs147053536	NA	P-0013338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	52	499	0	ENST00000273854.3:c.2989G>T	p.Val997Leu	p.V997L	ENST00000273854	NM_004439.5	997	Gtg/Ttg	17/18	0.20161537621678	3	FACETS	1	0.872	1	0.513	0.436	0.596	CLONAL	1	TRUE	1	0.222298832757251	3		499	507	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045533	47045533	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0013338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	63	552	0	ENST00000377604.3:c.2500A>T	p.Lys834Ter	p.K834*	ENST00000377604	NM_001204468.1	834	Aag/Tag	22/24	0.222298832757251	0	FACETS	1	0.925	1			1	CLONAL	1	TRUE	0	0.222298832757251	0		552	402	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371984	55371985	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0013338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	199	258	0	ENST00000297316.4:c.676_677del	p.Pro226AlafsTer138	p.P226Afs*138	ENST00000297316	NM_022454.3	225	tCC/t	2/2	0.222298832757251	7	FACETS	1	0.95	1	1	0.95	1	CLONAL	6	TRUE	1	0.222298832757251	7		258	457	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61712946	61712947	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	71	761	0	ENST00000401558.2:c.2464dup	p.Ile822AsnfsTer3	p.I822Nfs*3	ENST00000401558	NM_003400.3	822	ata/aAta	20/25	0.163148680851724	3	FACETS	1	0.901	1	0.519	0.452	0.591	CLONAL	1	TRUE	1	0.222298832757251	3		761	684	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202262	108202271	+	frameshift_variant	Frame_Shift_Del	DEL	GATTTCATGA	GATTTCATGA	-	novel	NA	P-0013338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	106	427	0	ENST00000278616.4:c.7607_7616del	p.Gly2536GlufsTer6	p.G2536Efs*6	ENST00000278616	NM_000051.3	2536	gGATTTCATGAa/ga	51/63	0.199815026967436	4	FACETS	0.939	0.848	1	0.704	0.636	0.775	CLONAL	3	TRUE	0	0.222298832757251	4		427	414	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576132	88576133	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0013338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	67	624	1	ENST00000360948.2:c.1540_1541delinsAA	p.Pro514Asn	p.P514N	ENST00000360948	NM_001012338.2	514	CCc/AAc	13/19	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.222298832757251	2		625	489	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	287	442	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.924	0.878	0.97	1	0.996	1	CLONAL	2	TRUE	1	0.537284169612683	2		444	578	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	137	208	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.842	0.768	0.918	0.842	0.768	0.918	CLONAL	1	TRUE	1	0.537284169612683	2		208	606	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	178	414	7	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.963	0.891	1	0.963	0.891	1	CLONAL	1	TRUE	1	0.537284169612683	2		421	688	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794441	42794441	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	273	508	0	ENST00000575354.2:c.1526del	p.Pro509HisfsTer14	p.P509Hfs*14	ENST00000575354	NM_015125.3	507	cgC/cg	10/20	1	2	FACETS	0.881	0.826	0.937	0.881	0.826	0.937	CLONAL	1	TRUE	1	0.537284169612683	2		508	1154	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	339	817	4	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	0.948	0.896	1	0.948	0.896	1	CLONAL	1	TRUE	1	0.537284169612683	2		821	1331	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	333	331	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.968	0.925	1	1	0.996	1	CLONAL	2	TRUE	1	0.537284169612683	2		332	640	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	228	396	5	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	0.537284169612683	2		401	825	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	174	357	0	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	0.92	0.85	0.993	0.92	0.85	0.993	CLONAL	1	TRUE	1	0.537284169612683	2		357	704	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070577	67070578	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	262	537	2	ENST00000412916.2:c.207dup	p.Pro70SerfsTer13	p.P70Sfs*13	ENST00000412916		67	-/T	3/6	1	2	FACETS	0.959	0.899	1	0.959	0.899	1	CLONAL	1	TRUE	1	0.537284169612683	2		539	1017	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	329	523	2	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	0.537284169612683	2		525	1187	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	201	294	2	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.537284169612683	2		296	729	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	123	341	0	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	0.831	0.754	0.911	0.831	0.754	0.911	CLONAL	1	TRUE	1	0.537284169612683	2		341	551	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532678	187532678	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777770871	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	248	511	0	ENST00000441802.2:c.9715G>A	p.Val3239Met	p.V3239M	ENST00000441802	NM_005245.3	3239	Gtg/Atg	14/27	1	2	FACETS	0.976	0.914	1	0.976	0.914	1	CLONAL	1	TRUE	1	0.537284169612683	2		511	946	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36028680	36028680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	198	403	0	ENST00000358208.4:c.1022C>T	p.Thr341Met	p.T341M	ENST00000358208		341	aCg/aTg	8/12	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.537284169612683	2		403	709	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1272311	1272311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141425941	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	220	407	3	ENST00000310581.5:c.2371G>A	p.Val791Ile	p.V791I	ENST00000310581	NM_198253.2	791	Gtc/Atc	7/16	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.537284169612683	2		410	819	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340097	116340097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35776110	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	142	273	0	ENST00000397752.3:c.959C>T	p.Ala320Val	p.A320V	ENST00000397752	NM_000245.2	320	gCg/gTg	2/21	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.537284169612683	2		273	522	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864451	151864451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs535118581	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	118	276	0	ENST00000262189.6:c.9530G>A	p.Arg3177His	p.R3177H	ENST00000262189	NM_170606.2	3177	cGt/cAt	42/59	1	2	FACETS	0.861	0.781	0.945	0.861	0.781	0.945	CLONAL	1	TRUE	1	0.537284169612683	2		276	510	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727943	41727943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770407415	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	257	360	0	ENST00000301178.4:c.568C>T	p.Arg190Cys	p.R190C	ENST00000301178	NM_021913.4	190	Cgc/Tgc	4/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.537284169612683	2		360	825	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120460319	120460319	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1446995271	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	241	426	4	ENST00000256646.2:c.5996del	p.Asn1999MetfsTer32	p.N1999Mfs*32	ENST00000256646	NM_024408.3	1999	aAt/at	33/34	1	2	FACETS	0.879	0.821	0.938	0.879	0.821	0.938	CLONAL	1	TRUE	1	0.537284169612683	2		430	1021	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250425	10250425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748262646	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	218	417	1	ENST00000340748.4:c.3827G>A	p.Arg1276His	p.R1276H	ENST00000340748		1276	cGc/cAc	33/40	1	2	FACETS	0.994	0.927	1	0.994	0.927	1	CLONAL	1	TRUE	1	0.537284169612683	2		418	816	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652329	206652330	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782347019	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	51	464	1	ENST00000367120.3:c.1042dup	p.Arg348ProfsTer8	p.R348Pfs*8	ENST00000367120	NM_014002.3	346	gcc/gCcc	10/22	1	2	FACETS	0.208	0.176	0.244	0.208	0.176	0.244	SUBCLONAL	1	TRUE	1	0.537284169612683	2		465	912	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520141	9520141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560752200	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	203	422	0	ENST00000353224.5:c.2128G>A	p.Val710Ile	p.V710I	ENST00000353224	NM_177990.2	710	Gtc/Atc	10/10	1	2	FACETS	0.983	0.914	1	0.983	0.914	1	CLONAL	1	TRUE	1	0.537284169612683	2		422	769	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739880	46739880	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	282	500	0	ENST00000371975.4:c.1681A>G	p.Ser561Gly	p.S561G	ENST00000371975	NM_003579.3	561	Agt/Ggt	15/18	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.537284169612683	2		500	949	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247883	59247883	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	415	540	0	ENST00000371222.2:c.860T>C	p.Leu287Ser	p.L287S	ENST00000371222	NM_002228.3	287	tTg/tCg	1/1	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.537284169612683	2		540	1372	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015225	128015225	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	69	418	0	ENST00000285398.2:c.2296A>G	p.Ser766Gly	p.S766G	ENST00000285398	NM_000122.1	766	Agc/Ggc	15/15	0.537284169612683	2	FACETS	0.265	0.23	0.304	0.133	0.115	0.152	SUBCLONAL	1	TRUE	0	0.537284169612683	2		418	968	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149593	202149593	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	441	390	0	ENST00000358485.4:c.1034A>G	p.Asp345Gly	p.D345G	ENST00000358485	NM_001080125.1	345	gAc/gGc	8/9	0.537284169612683	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.537284169612683	2		390	786	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72893525	72893525	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	195	461	0	ENST00000325599.8:c.193T>C	p.Tyr65His	p.Y65H	ENST00000325599	NM_018130.2	65	Tat/Cat	2/11	1	2	FACETS	0.883	0.819	0.95	0.883	0.819	0.95	CLONAL	1	TRUE	1	0.537284169612683	2		461	822	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664475	138664475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	147	213	1	ENST00000330315.3:c.1090G>A	p.Asp364Asn	p.D364N	ENST00000330315	NM_023067.3	364	Gac/Aac	1/1	1	2	FACETS	0.957	0.878	1	0.957	0.878	1	CLONAL	1	TRUE	1	0.537284169612683	2		214	572	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250896	153250896	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	197	373	1	ENST00000281708.4:c.1164G>T	p.Gln388His	p.Q388H	ENST00000281708	NM_033632.3	388	caG/caT	8/12	1	2	FACETS	0.961	0.892	1	0.961	0.892	1	CLONAL	1	TRUE	1	0.537284169612683	2		374	763	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295329	1295329	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	166	270	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.942	0.868	1	0.942	0.868	1	CLONAL	1	TRUE	1	0.537284169612683	2		271	656	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722324	176722324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886038676	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	41	381	0	ENST00000439151.2:c.7955C>T	p.Ala2652Val	p.A2652V	ENST00000439151	NM_022455.4	2652	gCt/gTt	23/23	1	2	FACETS	0.192	0.159	0.229	0.192	0.159	0.229	SUBCLONAL	1	TRUE	1	0.537284169612683	2		381	794	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651985	36651985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746709171	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	215	364	0	ENST00000244741.5:c.107C>T	p.Ala36Val	p.A36V	ENST00000244741	NM_000389.4	36	gCg/gTg	2/3	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.537284169612683	2		364	757	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969151	93969151	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	282	564	1	ENST00000369303.4:c.1845G>T	p.Glu615Asp	p.E615D	ENST00000369303	NM_004440.3	615	gaG/gaT	10/17	1	2	FACETS	0.931	0.874	0.988	0.931	0.874	0.988	CLONAL	1	TRUE	1	0.537284169612683	2		565	1128	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982054	93982054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	271	541	0	ENST00000369303.4:c.1411G>A	p.Gly471Arg	p.G471R	ENST00000369303	NM_004440.3	471	Gga/Aga	6/17	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.537284169612683	2		541	979	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739671	41739671	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	305	583	0	ENST00000242208.4:c.302T>C	p.Val101Ala	p.V101A	ENST00000242208	NM_002192.2	101	gTg/gCg	2/3	1	2	FACETS	0.924	0.87	0.979	0.924	0.87	0.979	CLONAL	1	TRUE	1	0.537284169612683	2		583	1229	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513305	106513305	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	167	368	0	ENST00000359195.3:c.2209C>A	p.Gln737Lys	p.Q737K	ENST00000359195	NM_002649.2	737	Caa/Aaa	4/11	1	2	FACETS	0.795	0.731	0.861	0.795	0.731	0.861	SUBCLONAL	1	TRUE	1	0.537284169612683	2		368	782	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055719	152055719	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	296	591	2	ENST00000262189.6:c.203G>T	p.Ser68Ile	p.S68I	ENST00000262189	NM_170606.2	68	aGc/aTc	2/59	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.537284169612683	2		593	1100	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215773	98215773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749542089	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	214	358	1	ENST00000331920.6:c.3436G>A	p.Asp1146Asn	p.D1146N	ENST00000331920	NM_000264.3	1146	Gac/Aac	20/24	1	2	FACETS	0.921	0.857	0.987	0.921	0.857	0.987	CLONAL	1	TRUE	1	0.537284169612683	2		359	865	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402723	139402723	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369730402	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	42	347	0	ENST00000277541.6:c.3286G>A	p.Val1096Met	p.V1096M	ENST00000277541	NM_017617.3	1096	Gtg/Atg	20/34	1	2	FACETS	0.253	0.21	0.3	0.253	0.21	0.3	SUBCLONAL	1	TRUE	1	0.537284169612683	2		347	619	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741604	17741604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866359886	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	85	119	0	ENST00000250003.3:c.275G>A	p.Arg92His	p.R92H	ENST00000250003	NM_002478.4	92	cGc/cAc	1/3	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.537284169612683	2		119	278	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188247	108188247	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	131	260	0	ENST00000278616.4:c.6346A>C	p.Ser2116Arg	p.S2116R	ENST00000278616	NM_000051.3	2116	Agc/Cgc	43/63	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.537284169612683	2		260	475	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431760	49431760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748336297	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	44	341	0	ENST00000301067.7:c.9379C>T	p.Arg3127Cys	p.R3127C	ENST00000301067	NM_003482.3	3127	Cgc/Tgc	34/54	1	2	FACETS	0.262	0.219	0.31	0.262	0.219	0.31	SUBCLONAL	1	TRUE	1	0.537284169612683	2		341	624	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138499	2138499	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137854214	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	321	533	0	ENST00000219476.3:c.5312C>T	p.Pro1771Leu	p.P1771L	ENST00000219476	NM_000548.3	1771	cCg/cTg	42/42	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.537284169612683	2		533	1124	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81960687	81960687	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	262	489	0	ENST00000359376.3:c.2418G>A	p.Trp806Ter	p.W806*	ENST00000359376	NM_002661.3	806	tgG/tgA	23/33	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.537284169612683	2		489	939	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350353	89350353	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1237	111	612	0	ENST00000301030.4:c.2597G>T	p.Arg866Met	p.R866M	ENST00000301030	NM_001256183.1	866	aGg/aTg	9/13	1	2	FACETS	0.307	0.274	0.341	0.307	0.274	0.341	SUBCLONAL	1	TRUE	1	0.537284169612683	2		612	1348	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295797	15295797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1166093165	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	295	432	1	ENST00000263388.2:c.2330C>T	p.Pro777Leu	p.P777L	ENST00000263388	NM_000435.2	777	cCg/cTg	15/33	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.537284169612683	2		433	885	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872384	45872384	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	216	368	0	ENST00000391945.4:c.127C>T	p.Pro43Ser	p.P43S	ENST00000391945	NM_000400.3	43	Ccc/Tcc	3/23	1	2	FACETS	0.985	0.918	1	0.985	0.918	1	CLONAL	1	TRUE	1	0.537284169612683	2		368	816	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937521	76937521	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	30	400	0	ENST00000373344.5:c.3227C>A	p.Ser1076Tyr	p.S1076Y	ENST00000373344	NM_000489.3	1076	tCt/tAt	9/35	1	2	FACETS	0.187	0.15	0.229	0.187	0.15	0.229	SUBCLONAL	1	TRUE	1	0.537284169612683	2		400	597	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225574	133225574	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	225	464	0	ENST00000320574.5:c.4090del	p.Arg1364ValfsTer5	p.R1364Vfs*5	ENST00000320574	NM_006231.2	1364	Cgt/gt	32/49	1	2	FACETS	0.976	0.911	1	0.976	0.911	1	CLONAL	1	TRUE	1	0.537284169612683	2		464	858	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433960	49433960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	43	315	0	ENST00000301067.7:c.7593del	p.Ser2532LeufsTer11	p.S2532Lfs*11	ENST00000301067	NM_003482.3	2531	ccC/cc	31/54	1	2	FACETS	0.234	0.195	0.278	0.234	0.195	0.278	SUBCLONAL	1	TRUE	1	0.537284169612683	2		315	683	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967511	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	rs1349928568	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	202	326	0	ENST00000265433.3:c.1396dup	p.Arg466LysfsTer5	p.R466Kfs*5	ENST00000265433	NM_002485.4	466	agg/aAgg	10/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.537284169612683	2		326	702	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15821896	15821896	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1195	65	608	0	ENST00000307771.7:c.294del	p.Lys98AsnfsTer10	p.K98Nfs*10	ENST00000307771	NM_005089.3	97	Aaa/aa	4/11	1	2	FACETS	0.192	0.165	0.221	0.192	0.165	0.221	SUBCLONAL	1	TRUE	1	0.537284169612683	2		608	1260	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119070	70119071	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	G	novel	NA	P-0013357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	95	221	0	ENST00000245479.2:c.642_643delinsG	p.Ser215ProfsTer4	p.S215Pfs*4	ENST00000245479	NM_000346.3	214	tcCTcc/tcGcc	2/3	1	2	FACETS	0.898	0.805	0.995	0.898	0.805	0.995	CLONAL	1	TRUE	1	0.537284169612683	2		221	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0013387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	357	516	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.323876431281049	3	FACETS	1	0.989	1	0.748	0.712	0.784	CLONAL	2	FALSE	0	0.44144363033068	3		517	880	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0013387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	387	371	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.44144363033068	4	FACETS	0.881	0.836	0.927	0.881	0.836	0.927	CLONAL	2	FALSE	2	0.44144363033068	4		371	1435	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162742008	162742008	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	370	777	0	ENST00000367921.3:c.1699G>C	p.Glu567Gln	p.E567Q	ENST00000367921	NM_006182.2	567	Gag/Cag	13/18	0.44144363033068	4	FACETS	0.899	0.852	0.947	0.899	0.852	0.947	CLONAL	2	FALSE	2	0.44144363033068	4		777	1344	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41905105	41905105	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	310	529	0	ENST00000372991.4:c.442C>G	p.Leu148Val	p.L148V	ENST00000372991	NM_001760.3	148	Ctc/Gtc	3/5	0.44144363033068	4	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	FALSE	2	0.44144363033068	4		529	1010	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63553946	63553946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	381	774	0	ENST00000307078.5:c.793G>A	p.Glu265Lys	p.E265K	ENST00000307078	NM_004655.3	265	Gaa/Aaa	2/11	0.44144363033068	4	FACETS	0.908	0.862	0.956	0.908	0.862	0.956	CLONAL	2	FALSE	2	0.44144363033068	4		774	1370	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420060	41420060	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	148	610	2	ENST00000373198.4:c.261G>T	p.Lys87Asn	p.K87N	ENST00000373198	NM_133170.3	87	aaG/aaT	3/32	0.44144363033068	3	FACETS	0.93	0.849	1	0.465	0.424	0.508	CLONAL	1	FALSE	1	0.44144363033068	3		612	880	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21272506	21272506	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	386	776	1	ENST00000354336.3:c.284C>A	p.Thr95Asn	p.T95N	ENST00000354336	NM_005207.3	95	aCc/aAc	1/3	0.323876431281049	3	FACETS	1	0.991	1	0.773	0.737	0.809	CLONAL	2	FALSE	0	0.44144363033068	3		777	921	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233193	46233219	+	frameshift_variant	Frame_Shift_Del	DEL	CAAGTTCCAGTCATCAAATGTTATCTG	CAAGTTCCAGTCATCAAATGTTATCTG	AGAT	novel	NA	P-0013387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	328	740	0	ENST00000334344.6:c.1412_1438delinsAGAT	p.Pro471GlnfsTer4	p.P471Qfs*4	ENST00000334344	NM_152641.2	471	cCAAGTTCCAGTCATCAAATGTTATCTGaa/cAGATaa	11/21	0.44144363033068	3	FACETS	0.813	0.768	0.858	0.813	0.768	0.858	CLONAL	2	FALSE	1	0.44144363033068	3		740	1116	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	219	474	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.0752215752337166	0	FACETS	0.455	0.423	0.488			1	INDETERMINATE	1	TRUE	0	0.51	0		474	925	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	125	442	2	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	0.51	2		444	458	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	155	628	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.838	0.769	0.911	0.838	0.769	0.911	CLONAL	1	TRUE	1	0.51	2		628	725	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	14	296	2	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	0.351838567509313	0	FACETS	0.137	0.098	0.182			1	SUBCLONAL	1	TRUE	0	0.51	0		298	197	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	175	984	2	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	0.115504664958924	0	FACETS	0.464	0.428	0.501			1	INDETERMINATE	1	TRUE	0	0.51	0		986	725	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	330	678	1	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.51	2		679	1250	SUCCESS
APC	324	MSKCC	GRCh37	5	112175675	112175676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	162	576	0	ENST00000257430.4:c.4393_4394dup	p.Ser1465ArgfsTer9	p.S1465Rfs*9	ENST00000257430	NM_000038.5	1462	aag/aAGag	16/16	1	2	FACETS	0.755	0.693	0.82	0.755	0.693	0.82	SUBCLONAL	1	TRUE	1	0.51	2		576	841	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78858817	78858817	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779943676	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	107	595	0	ENST00000306801.3:c.1852G>A	p.Ala618Thr	p.A618T	ENST00000306801	NM_020761.2	618	Gca/Aca	17/34	0.291392830443909	0	FACETS	0.428	0.386	0.473			1	INDETERMINATE	1	TRUE	0	0.51	0		595	480	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	212	482	5	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	1	2	FACETS	0.962	0.895	1	0.962	0.895	1	CLONAL	1	TRUE	1	0.51	2		487	864	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	140	480	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.938	0.858	1	0.938	0.858	1	CLONAL	1	TRUE	1	0.51	2		480	585	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	149	450	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.999	0.917	1	0.999	0.917	1	CLONAL	1	TRUE	1	0.51	2		450	585	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913837	32913837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359507	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1293	350	945	2	ENST00000380152.3:c.5351del	p.Asn1784ThrfsTer7	p.N1784Tfs*7	ENST00000380152		1782	cAa/ca	11/27	1	2	FACETS	0.835	0.789	0.883	0.835	0.789	0.883	CLONAL	1	TRUE	1	0.51	2		947	1643	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457264	67457264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750707381	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	106	620	1	ENST00000327367.4:c.238C>T	p.Arg80Trp	p.R80W	ENST00000327367	NM_005902.3	80	Cgg/Tgg	2/9	1	2	FACETS	0.822	0.74	0.908	0.822	0.74	0.908	CLONAL	1	TRUE	1	0.51	2		621	506	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412110	63412110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852216	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	255	1136	0	ENST00000330258.3:c.1057C>T	p.Arg353Ter	p.R353*	ENST00000330258	NM_152424.3	353	Cga/Tga	2/2	1	2	FACETS	0.956	0.895	1	0.956	0.895	1	CLONAL	1	TRUE	1	0.51	2		1136	1046	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	38	328	4	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.538	0.447	0.639	0.538	0.447	0.639	SUBCLONAL	1	TRUE	1	0.51	2		332	277	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	317	1108	3	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	0.0752215752337166	0	FACETS	0.467	0.44	0.494			1	INDETERMINATE	1	TRUE	0	0.51	0		1111	1305	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139794917	139794917	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780195720	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	279	915	2	ENST00000247668.2:c.311C>T	p.Pro104Leu	p.P104L	ENST00000247668	NM_021138.3	104	cCg/cTg	4/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.51	2		917	954	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	248	931	3	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	1	2	FACETS	0.997	0.934	1	0.997	0.934	1	CLONAL	1	TRUE	1	0.51	2		934	975	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298226	123298226	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	121	450	2	ENST00000358487.5:c.628C>T	p.Arg210Ter	p.R210*	ENST00000358487	NM_000141.4	210	Cga/Tga	6/18	1	2	FACETS	0.9	0.817	0.987	0.9	0.817	0.987	CLONAL	1	TRUE	1	0.51	2		452	527	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190714	11190714	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199646470	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	42	650	0	ENST00000361445.4:c.5485A>G	p.Thr1829Ala	p.T1829A	ENST00000361445	NM_004958.3	1829	Acc/Gcc	39/58	0.3	0	FACETS	0.131	0.109	0.155			1	INDETERMINATE	1	TRUE	0	0.51	0		650	617	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298120	15298120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376606994	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	164	694	1	ENST00000263388.2:c.1636G>A	p.Val546Met	p.V546M	ENST00000263388	NM_000435.2	546	Gtg/Atg	11/33	0.115504664958924	0	FACETS	0.679	0.629	0.73			1	INDETERMINATE	1	TRUE	0	0.51	0		695	464	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836985	89836985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs539161141	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	85	596	2	ENST00000389301.3:c.2209G>A	p.Ala737Thr	p.A737T	ENST00000389301	NM_000135.2	737	Gct/Act	24/43	0.0752215752337166	0	FACETS	0.275	0.243	0.31			1	INDETERMINATE	1	TRUE	0	0.51	0		598	593	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619428	1619428	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757623802	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	68	774	0	ENST00000344749.5:c.1213C>T	p.Arg405Cys	p.R405C	ENST00000344749	NM_001136139.2	405	Cgc/Tgc	15/19	0.3	1	FACETS	0.324	0.281	0.369	0.324	0.281	0.369	INDETERMINATE	1	TRUE	0	0.51	1		774	614	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107231	193107231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	189	477	0	ENST00000367435.3:c.440G>A	p.Arg147His	p.R147H	ENST00000367435	NM_024529.4	147	cGc/cAc	6/17	1	2	FACETS	0.888	0.821	0.956	0.888	0.821	0.956	CLONAL	1	TRUE	1	0.51	2		477	835	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101624	27101624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1283627889	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	164	601	4	ENST00000324856.7:c.4906C>T	p.Arg1636Trp	p.R1636W	ENST00000324856	NM_006015.4	1636	Cgg/Tgg	18/20	1	2	FACETS	0.919	0.846	0.995	0.919	0.846	0.995	CLONAL	1	TRUE	1	0.51	2		605	700	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511647	46511647	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	213	638	0	ENST00000262741.5:c.1130A>G	p.Asp377Gly	p.D377G	ENST00000262741	NM_003629.3	377	gAt/gGt	9/10	1	2	FACETS	0.896	0.833	0.961	0.896	0.833	0.961	CLONAL	1	TRUE	1	0.51	2		638	932	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739871	46739871	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769214858	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	118	672	0	ENST00000371975.4:c.1672C>T	p.Arg558Cys	p.R558C	ENST00000371975	NM_003579.3	558	Cgc/Tgc	15/18	1	2	FACETS	0.446	0.402	0.494	0.446	0.402	0.494	SUBCLONAL	1	TRUE	1	0.51	2		672	1037	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630442	47630442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	198	592	1	ENST00000233146.2:c.112G>A	p.Asp38Asn	p.D38N	ENST00000233146	NM_000251.2	38	Gac/Aac	1/16	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.51	2		593	589	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47672702	47672702	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs63751315	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	230	656	0	ENST00000233146.2:c.1292T>A	p.Leu431Ter	p.L431*	ENST00000233146	NM_000251.2	431	tTa/tAa	8/16	1	2	FACETS	0.82	0.764	0.878	0.82	0.764	0.878	CLONAL	1	TRUE	1	0.51	2		656	1100	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99179952	99179952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1394330959	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	219	800	0	ENST00000074304.5:c.1895C>T	p.Pro632Leu	p.P632L	ENST00000074304	NM_001134224.1	632	cCg/cTg	19/26	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.51	2		800	858	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662916	227662916	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1392016929	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	244	802	0	ENST00000305123.5:c.539T>C	p.Ile180Thr	p.I180T	ENST00000305123	NM_005544.2	180	aTt/aCt	1/2	1	2	FACETS	0.942	0.88	1	0.942	0.88	1	CLONAL	1	TRUE	1	0.51	2		802	1016	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138431133	138431133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	209	513	0	ENST00000289153.2:c.1316C>T	p.Ala439Val	p.A439V	ENST00000289153	NM_006219.2	439	gCg/gTg	8/22	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.51	2		513	813	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55124955	55124955	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764472307	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	249	906	1	ENST00000257290.5:c.20C>T	p.Ala7Val	p.A7V	ENST00000257290	NM_006206.4	7	gCg/gTg	2/23	1	2	FACETS	0.857	0.8	0.914	0.857	0.8	0.914	CLONAL	1	TRUE	1	0.51	2		907	1140	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224547	224547	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs781764920	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	61	478	0	ENST00000264932.6:c.223C>T	p.Arg75Ter	p.R75*	ENST00000264932	NM_004168.2	75	Cga/Tga	3/15	0.3	1	FACETS	0.347	0.299	0.398	0.347	0.299	0.398	INDETERMINATE	1	TRUE	0	0.51	1		478	514	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38955712	38955712	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	217	638	1	ENST00000357387.3:c.2594G>A	p.Arg865His	p.R865H	ENST00000357387	NM_152756.3	865	cGt/cAt	26/38	1	2	FACETS	0.84	0.781	0.901	0.84	0.781	0.901	CLONAL	1	TRUE	1	0.51	2		639	1013	SUCCESS
APC	324	MSKCC	GRCh37	5	112179179	112179179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199688874	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	155	494	0	ENST00000257430.4:c.7888G>A	p.Val2630Ile	p.V2630I	ENST00000257430	NM_000038.5	2630	Gtt/Att	16/16	1	2	FACETS	0.855	0.784	0.928	0.855	0.784	0.928	CLONAL	1	TRUE	1	0.51	2		494	711	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722090	176722090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150977055	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	145	424	1	ENST00000439151.2:c.7721C>T	p.Pro2574Leu	p.P2574L	ENST00000439151	NM_022455.4	2574	cCg/cTg	23/23	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.51	2		425	517	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527698	157527698	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376758952	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	207	574	0	ENST00000346085.5:c.5423G>A	p.Arg1808His	p.R1808H	ENST00000346085	NM_020732.3	1808	cGt/cAt	20/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.51	2		574	768	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341820	8341820	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	93	686	0	ENST00000356435.5:c.4820A>G	p.Asp1607Gly	p.D1607G	ENST00000356435		1607	gAt/gGt	29/35	1	2	FACETS	0.369	0.327	0.414	0.369	0.327	0.414	SUBCLONAL	1	TRUE	1	0.51	2		686	989	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412544	80412544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	223	574	1	ENST00000286548.4:c.497G>A	p.Arg166His	p.R166H	ENST00000286548	NM_002072.3	166	cGc/cAc	4/7	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.51	2		575	805	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97873912	97873912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371897078	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	133	547	0	ENST00000289081.3:c.1162G>A	p.Gly388Arg	p.G388R	ENST00000289081	NM_000136.2	388	Gga/Aga	13/15	1	2	FACETS	0.948	0.865	1	0.948	0.865	1	CLONAL	1	TRUE	1	0.51	2		547	550	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759526	133759526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773475680	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	174	840	0	ENST00000318560.5:c.1849C>T	p.Arg617Cys	p.R617C	ENST00000318560	NM_005157.4	617	Cgc/Tgc	11/11	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.51	2		840	681	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759706	133759706	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs564161762	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	52	336	1	ENST00000318560.5:c.2029G>A	p.Gly677Arg	p.G677R	ENST00000318560	NM_005157.4	677	Ggg/Agg	11/11	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.51	2		337	195	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114917814	114917814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751365426	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	217	787	1	ENST00000543371.1:c.1304C>T	p.Pro435Leu	p.P435L	ENST00000543371	NM_001198531.1	435	cCg/cTg	12/14	1	2	FACETS	0.849	0.79	0.911	0.849	0.79	0.911	CLONAL	1	TRUE	1	0.51	2		788	1002	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431810	49431810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769315900	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	79	430	1	ENST00000301067.7:c.9329G>A	p.Arg3110His	p.R3110H	ENST00000301067	NM_003482.3	3110	cGc/cAc	34/54	0.147963438924818	3	FACETS	1	0.954	1	0.575	0.51	0.644	INDETERMINATE	1	TRUE	1	0.51	3		431	338	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030387	49030387	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373601944	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	171	499	0	ENST00000267163.4:c.1862G>A	p.Arg621His	p.R621H	ENST00000267163	NM_000321.2	621	cGt/cAt	19/27	1	2	FACETS	0.831	0.765	0.899	0.831	0.765	0.899	CLONAL	1	TRUE	1	0.51	2		499	807	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131647	2131647	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45517305	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	188	816	2	ENST00000219476.3:c.3662C>T	p.Ser1221Leu	p.S1221L	ENST00000219476	NM_000548.3	1221	tCg/tTg	31/42	0.0752215752337166	0	FACETS	0.525	0.487	0.565			1	INDETERMINATE	1	TRUE	0	0.51	0		818	688	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519008	66519008	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555813217	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	185	691	0	ENST00000358598.2:c.289C>T	p.Arg97Ter	p.R97*	ENST00000358598	NM_212471.2	97	Cga/Tga	3/11	1	2	FACETS	0.859	0.794	0.926	0.859	0.794	0.926	CLONAL	1	TRUE	1	0.51	2		691	845	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207168	1207168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520039	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	201	668	0	ENST00000326873.7:c.256C>T	p.Arg86Ter	p.R86*	ENST00000326873	NM_000455.4	86	Cga/Tga	1/10	0.3	1	FACETS	0.847	0.788	0.908	0.847	0.788	0.908	INDETERMINATE	1	TRUE	0	0.51	1		668	693	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794874	42794874	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770323488	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	24	433	2	ENST00000575354.2:c.1954G>A	p.Ala652Thr	p.A652T	ENST00000575354	NM_015125.3	652	Gcc/Acc	10/20	0.115504664958924	0	FACETS	0.146	0.114	0.183			1	INDETERMINATE	1	TRUE	0	0.51	0		435	315	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919695	50919695	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	187	867	1	ENST00000440232.2:c.2863C>T	p.Gln955Ter	p.Q955*	ENST00000440232	NM_002691.3	955	Cag/Tag	23/27	0.115504664958924	0	FACETS	0.5	0.464	0.539			1	INDETERMINATE	1	TRUE	0	0.51	0		868	718	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41818358	41818358	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	30	56	0	ENST00000373198.4:c.16G>A	p.Ala6Thr	p.A6T	ENST00000373198	NM_133170.3	6	Gcg/Acg	1/32	0.115504664958924	0	FACETS	0.977	0.83	1			1	INDETERMINATE	1	TRUE	0	0.51	0		56	59	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655428	45655428	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372772395	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	110	440	1	ENST00000407780.3:c.424G>A	p.Val142Ile	p.V142I	ENST00000407780	NM_001283052.1	142	Gtc/Atc	4/7	0.3	2	FACETS	0.893	0.807	0.984			1	INDETERMINATE	1	TRUE	NA	0.51	2		441	483	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321280	1321280	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763471203	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	89	378	1	ENST00000400841.2:c.475G>A	p.Glu159Lys	p.E159K	ENST00000400841		159	Gag/Aag	4/6	1	2	FACETS	0.837	0.746	0.933	0.837	0.746	0.933	CLONAL	1	TRUE	1	0.51	2		379	417	SUCCESS
AR	367	MSKCC	GRCh37	X	66942786	66942786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs9332971	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	234	951	3	ENST00000374690.3:c.2567G>A	p.Arg856His	p.R856H	ENST00000374690	NM_000044.3	856	cGc/cAc	7/8	1	2	FACETS	0.898	0.838	0.96	0.898	0.838	0.96	CLONAL	1	TRUE	1	0.51	2		954	1022	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057666	27057666	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	122	904	0	ENST00000324856.7:c.1377del	p.Ser460AlafsTer159	p.S460Afs*159	ENST00000324856	NM_006015.4	458	ggC/gg	3/20	1	2	FACETS	0.433	0.39	0.478	0.433	0.39	0.478	SUBCLONAL	1	TRUE	1	0.51	2		904	1105	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099311	4099312	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	131	781	0	ENST00000262948.5:c.806dup	p.Pro270AlafsTer43	p.P270Afs*43	ENST00000262948	NM_030662.3	269	ccg/ccCg	7/11	0.3	1	FACETS	0.626	0.57	0.685	0.626	0.57	0.685	INDETERMINATE	1	TRUE	0	0.51	1		781	611	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656840	45656840	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	53	502	0	ENST00000407780.3:c.316del	p.Gln106ArgfsTer11	p.Q106Rfs*11	ENST00000407780	NM_001283052.1	106	Cag/ag	3/7	0.3	2	FACETS	0.442	0.377	0.513			1	INDETERMINATE	1	TRUE	NA	0.51	2		502	470	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157385	106157385	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	112	446	0	ENST00000380013.4:c.2290del	p.Gln764LysfsTer49	p.Q764Kfs*49	ENST00000380013	NM_001127208.2	762	caC/ca	3/11	1	2	FACETS	0.588	0.529	0.65	0.588	0.529	0.65	SUBCLONAL	1	TRUE	1	0.51	2		446	747	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646922	37646922	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	229	798	2	ENST00000447079.4:c.2048del	p.Pro683GlnfsTer70	p.P683Qfs*70	ENST00000447079	NM_015083.1	682	Ccc/cc	3/14	1	2	FACETS	0.966	0.901	1	0.966	0.901	1	CLONAL	1	TRUE	1	0.51	2		800	930	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168478	56168479	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	181	320	0	ENST00000399503.3:c.1436_1437del	p.Cys479Ter	p.C479*	ENST00000399503	NM_005921.1	478	gaGTgt/gagt	8/20	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.51	2		320	699	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938088	76938089	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	158	639	0	ENST00000373344.5:c.2658_2659dup	p.Thr887ArgfsTer19	p.T887Rfs*19	ENST00000373344	NM_000489.3	887	act/aGAct	9/35	1	2	FACETS	0.679	0.622	0.739	0.679	0.622	0.739	SUBCLONAL	1	TRUE	1	0.51	2		639	912	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782131	135782131	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	467	708	0	ENST00000298552.3:c.1425del	p.Asp476IlefsTer56	p.D476Ifs*56	ENST00000298552	NM_001162426.1	475	aaA/aa	14/23	1	2	FACETS	0.954	0.916	0.992	1	0.997	1	CLONAL	2	TRUE	1	0.51	2		708	960	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625696	1625696	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	226	890	0	ENST00000344749.5:c.378del	p.Ser127GlnfsTer17	p.S127Qfs*17	ENST00000344749	NM_001136139.2	126	ctG/ct	7/19	0.3	1	FACETS	1	0.987	1	1	0.987	1	INDETERMINATE	1	TRUE	0	0.51	1		890	560	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	108	1004	1	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	0.881	0.793	0.973	0.881	0.793	0.973	CLONAL	1	TRUE	1	0.45	2		1005	545	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0013452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	141	442	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.97	0.898	1	1	0.992	1	CLONAL	2	TRUE	1	0.45	2		444	323	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868194	45868194	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1032384332	NA	P-0013452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	32	588	2	ENST00000391945.4:c.496C>T	p.Arg166Cys	p.R166C	ENST00000391945	NM_000400.3	166	Cgt/Tgt	7/23	1	2	FACETS	0.322	0.261	0.391	0.322	0.261	0.391	SUBCLONAL	1	TRUE	1	0.45	2		590	442	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018076	48018076	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	59	528	0	ENST00000234420.5:c.271T>G	p.Ser91Ala	p.S91A	ENST00000234420	NM_000179.2	91	Tca/Gca	2/10	1	2	FACETS	0.735	0.635	0.842	0.735	0.635	0.842	SUBCLONAL	1	TRUE	1	0.45	2		528	357	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212522509	212522509	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs532377012	NA	P-0013452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	23	465	2	ENST00000342788.4:c.1916C>T	p.Thr639Met	p.T639M	ENST00000342788	NM_005235.2	639	aCg/aTg	16/28	1	2	FACETS	0.285	0.222	0.358	0.285	0.222	0.358	SUBCLONAL	1	TRUE	1	0.45	2		467	359	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922363	178922363	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	57	548	0	ENST00000263967.3:c.1132T>C	p.Cys378Arg	p.C378R	ENST00000263967	NM_006218.2	378	Tgt/Cgt	6/21	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.45	2		548	227	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191223	185191223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	44	287	0	ENST00000265026.3:c.2104G>A	p.Ala702Thr	p.A702T	ENST00000265026	NM_004721.4	702	Gcc/Acc	11/14	1	2	FACETS	0.993	0.843	1	0.993	0.843	1	CLONAL	1	TRUE	1	0.45	2		287	197	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561915	55561915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	29	454	0	ENST00000288135.5:c.305G>A	p.Gly102Asp	p.G102D	ENST00000288135	NM_000222.2	102	gGc/gAc	2/21	1	2	FACETS	0.286	0.229	0.351	0.286	0.229	0.351	SUBCLONAL	1	TRUE	1	0.45	2		454	451	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503887	149503887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758280032	NA	P-0013452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	94	566	2	ENST00000261799.4:c.1949C>T	p.Ser650Leu	p.S650L	ENST00000261799	NM_002609.3	650	tCg/tTg	14/23	1	2	FACETS	0.811	0.724	0.903	0.811	0.724	0.903	CLONAL	1	TRUE	1	0.45	2		568	515	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979559	2979559	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	65	449	0	ENST00000396946.4:c.688G>A	p.Asp230Asn	p.D230N	ENST00000396946	NM_032415.4	230	Gat/Aat	6/25	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.45	2		449	250	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340003	116340003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	10	382	1	ENST00000397752.3:c.865C>T	p.His289Tyr	p.H289Y	ENST00000397752	NM_000245.2	289	Cat/Tat	2/21	1	2	FACETS	0.292	0.198	0.41	0.292	0.198	0.41	SUBCLONAL	1	TRUE	1	0.45	2		383	152	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132906	64132906	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868566063	NA	P-0013452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	44	824	0	ENST00000334205.4:c.1040G>A	p.Ser347Asn	p.S347N	ENST00000334205	NM_003942.2	347	aGc/aAc	9/17	1	2	FACETS	0.34	0.285	0.402	0.34	0.285	0.402	SUBCLONAL	1	TRUE	1	0.45	2		824	575	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988155	85988155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	65	632	0	ENST00000263360.6:c.1100G>T	p.Arg367Met	p.R367M	ENST00000263360	NM_003797.3	367	aGg/aTg	10/12	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.45	2		632	260	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215356	5215356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1420232605	NA	P-0013452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	146	675	0	ENST00000357368.4:c.4262G>A	p.Arg1421His	p.R1421H	ENST00000357368	NM_002850.3	1421	cGc/cAc	28/38	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.45	2		675	533	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285054	15285054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	25	311	0	ENST00000263388.2:c.4561C>T	p.Pro1521Ser	p.P1521S	ENST00000263388	NM_000435.2	1521	Cca/Tca	25/33	1	2	FACETS	0.45	0.356	0.557	0.45	0.356	0.557	SUBCLONAL	1	TRUE	1	0.45	2		311	247	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692796	89692820	+	frameshift_variant	Frame_Shift_Del	DEL	AACCCACCACAGCTAGAACTTATCA	AACCCACCACAGCTAGAACTTATCA	-	novel	NA	P-0013452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	28	289	0	ENST00000371953.3:c.285_309del	p.Pro96PhefsTer9	p.P96Ffs*9	ENST00000371953	NM_000314.4	94	AACCCACCACAGCTAGAACTTATCAaa/aa	5/9	1	2	FACETS	0.988	0.803	1	0.988	0.803	1	CLONAL	1	TRUE	1	0.45	2		289	126	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366654	40366667	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTTCGCCCAGCG	GGGTTCGCCCAGCG	-	novel	NA	P-0013452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	102	390	1	ENST00000397332.2:c.530_543del	p.Pro177GlnfsTer17	p.P177Qfs*17	ENST00000397332	NM_001033082.2	177	cCGCTGGGCGAACCC/c	2/3	1	2	FACETS	0.965	0.867	1	0.965	0.867	1	CLONAL	1	TRUE	1	0.45	2		391	470	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791282	42791282	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	24	459	0	ENST00000575354.2:c.346del	p.Val116TrpfsTer89	p.V116Wfs*89	ENST00000575354	NM_015125.3	114	ttG/tt	3/20	1	2	FACETS	0.28	0.219	0.35	0.28	0.219	0.35	SUBCLONAL	1	TRUE	1	0.45	2		459	381	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645943	67645944	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0013452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	34	534	0	ENST00000264010.4:c.875_876del	p.Arg292ThrfsTer22	p.R292Tfs*22	ENST00000264010	NM_006565.3	291	GAg/g	4/12	1	2	FACETS	0.297	0.242	0.359	0.297	0.242	0.359	SUBCLONAL	1	TRUE	1	0.45	2		534	508	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73342925	73342925	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs774491006	NA	P-0013452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	47	438	0	ENST00000377767.4:c.1881del	p.Ala629LeufsTer2	p.A629Lfs*2	ENST00000377767	NM_014953.3	627	aaA/aa	14/21	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.45	2		438	197	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368387	225368388	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	11	425	0	ENST00000264414.4:c.1358dup	p.Asn453LysfsTer5	p.N453Kfs*5	ENST00000264414	NM_003590.4	453	aac/aaAc	9/16	1	2	FACETS	0.3	0.207	0.414	0.3	0.207	0.414	SUBCLONAL	1	TRUE	1	0.45	2		425	163	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210766	2210766	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	48	574	0	ENST00000398665.3:c.1266del	p.Glu423SerfsTer66	p.E423Sfs*66	ENST00000398665	NM_032482.2	421	aaC/aa	14/28	1	2	FACETS	0.357	0.301	0.419	0.357	0.301	0.419	SUBCLONAL	1	TRUE	1	0.45	2		574	597	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	99	208	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	FALSE	1	0.260300767867178	2		208	747	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	78	357	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.723	0.634	0.819	0.723	0.634	0.819	SUBCLONAL	1	FALSE	1	0.260300767867178	2		357	829	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	141	661	1	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	0.886	0.805	0.971	0.886	0.805	0.971	CLONAL	1	FALSE	1	0.260300767867178	2		662	1223	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671654	67671655	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	85	495	1	ENST00000264010.4:c.2070dup	p.Glu691ArgfsTer5	p.E691Rfs*5	ENST00000264010	NM_006565.3	688	gta/gtAa	12/12	1	2	FACETS	0.734	0.647	0.827	0.734	0.647	0.827	SUBCLONAL	1	FALSE	1	0.260300767867178	2		496	890	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101268	27101268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	95	614	0	ENST00000324856.7:c.4555del	p.Gln1519ArgfsTer8	p.Q1519Rfs*8	ENST00000324856	NM_006015.4	1517	gCc/gc	18/20	1	2	FACETS	0.796	0.708	0.891	0.796	0.708	0.891	SUBCLONAL	1	FALSE	1	0.260300767867178	2		614	917	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061169	38061169	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1489466891	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	19	230	0	ENST00000250448.2:c.820del	p.Ala274ProfsTer47	p.A274Pfs*47	ENST00000250448	NM_004496.3	274	Gcc/cc	2/2	1	2	FACETS	0.564	0.428	0.722	0.564	0.428	0.722	SUBCLONAL	1	FALSE	1	0.260300767867178	2		230	259	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752960	128752960	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	74	555	0	ENST00000377970.2:c.1121A>G	p.His374Arg	p.H374R	ENST00000377970	NM_002467.4	374	cAc/cGc	3/3	0.136895585119356	3	FACETS	0.534	0.465	0.608	0.267	0.232	0.304	INDETERMINATE	1	FALSE	1	0.260300767867178	3		555	1204	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874163	155874163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs977405637	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1328	85	703	0	ENST00000368323.3:c.368G>A	p.Arg123His	p.R123H	ENST00000368323	NM_006912.5	123	cGt/cAt	5/6	1	2	FACETS	0.462	0.407	0.522	0.462	0.407	0.522	SUBCLONAL	1	FALSE	1	0.260300767867178	2		703	1413	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245399	153245399	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	90	603	0	ENST00000281708.4:c.1792A>C	p.Asn598His	p.N598H	ENST00000281708	NM_033632.3	598	Aat/Cat	11/12	1	2	FACETS	0.737	0.653	0.828	0.737	0.653	0.828	SUBCLONAL	1	FALSE	1	0.260300767867178	2		603	938	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742547	145742547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1426829329	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	62	377	0	ENST00000428558.2:c.241del	p.His81IlefsTer2	p.H81Ifs*2	ENST00000428558	NM_004260.3	81	Cat/at	4/22	0.136895585119356	3	FACETS	0.747	0.644	0.859	0.373	0.322	0.43	INDETERMINATE	1	FALSE	1	0.260300767867178	3		377	721	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732910	44732910	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	79	460	0	ENST00000377967.4:c.117del	p.Ser40AlafsTer2	p.S40Afs*2	ENST00000377967	NM_021140.2	38	tCc/tc	1/29	0.260300767867178	1	FACETS	0.71	0.624	0.802	0.71	0.624	0.802	SUBCLONAL	1	FALSE	0	0.260300767867178	1		460	744	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099286	157099287	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1234	153	725	0	ENST00000346085.5:c.228dup	p.Ala77ArgfsTer155	p.A77Rfs*155	ENST00000346085	NM_020732.3	75	gcc/gCcc	1/20	1	2	FACETS	0.848	0.773	0.926	0.848	0.773	0.926	CLONAL	1	FALSE	1	0.260300767867178	2		725	1387	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434889	49434889	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555192676	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	96	490	1	ENST00000301067.7:c.6664C>T	p.Gln2222Ter	p.Q2222*	ENST00000301067	NM_003482.3	2222	Cag/Tag	31/54	0.147762423514347	3	FACETS	1	0.919	1	0.519	0.462	0.58	INDETERMINATE	1	FALSE	1	0.260300767867178	3		491	803	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395665	31395665	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1182001726	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	98	594	0	ENST00000328111.2:c.2518C>T	p.Arg840Ter	p.R840*	ENST00000328111	NM_006892.3	840	Cga/Tga	23/23	0.0388328013417958	3	FACETS	0.858	0.764	0.958			1	INDETERMINATE	1	FALSE	NA	0.260300767867178	3		594	992	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403254	213403254	+	frameshift_variant,start_lost,start_retained_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	47	643	0	ENST00000342788.4:c.1del	p.Met1?	p.M1?	ENST00000342788	NM_005235.2	1	Atg/tg	1/28	0.260300767867178	1	FACETS	0.342	0.287	0.403	0.342	0.287	0.403	SUBCLONAL	1	FALSE	0	0.260300767867178	1		643	919	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199481	16199481	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764932472	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	115	578	0	ENST00000375759.3:c.254C>T	p.Pro85Leu	p.P85L	ENST00000375759	NM_015001.2	85	cCg/cTg	2/15	1	2	FACETS	0.829	0.745	0.918	0.829	0.745	0.918	CLONAL	1	FALSE	1	0.260300767867178	2		578	1066	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260200	16260200	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	48	246	0	ENST00000375759.3:c.7465A>G	p.Ile2489Val	p.I2489V	ENST00000375759	NM_015001.2	2489	Atc/Gtc	11/15	1	2	FACETS	0.858	0.726	1	0.858	0.726	1	CLONAL	1	FALSE	1	0.260300767867178	2		246	430	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445447	29445447	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	106	700	0	ENST00000389048.3:c.3386A>C	p.Glu1129Ala	p.E1129A	ENST00000389048	NM_004304.4	1129	gAg/gCg	21/29	1	2	FACETS	0.751	0.672	0.836	0.751	0.672	0.836	SUBCLONAL	1	FALSE	1	0.260300767867178	2		700	1084	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940456	29940456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771593278	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	66	478	0	ENST00000389048.3:c.775C>T	p.Arg259Cys	p.R259C	ENST00000389048	NM_004304.4	259	Cgc/Tgc	2/29	1	2	FACETS	0.779	0.676	0.891	0.779	0.676	0.891	SUBCLONAL	1	FALSE	1	0.260300767867178	2		478	651	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172158	99172158	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	120	692	0	ENST00000074304.5:c.1724A>G	p.Asn575Ser	p.N575S	ENST00000074304	NM_001134224.1	575	aAc/aGc	17/26	1	2	FACETS	0.785	0.707	0.868	0.785	0.707	0.868	SUBCLONAL	1	FALSE	1	0.260300767867178	2		692	1174	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182499	99182499	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	91	585	0	ENST00000074304.5:c.2302T>C	p.Phe768Leu	p.F768L	ENST00000074304	NM_001134224.1	768	Ttt/Ctt	22/26	1	2	FACETS	0.679	0.602	0.763	0.679	0.602	0.763	SUBCLONAL	1	FALSE	1	0.260300767867178	2		585	1029	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183253	56183253	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	63	400	0	ENST00000399503.3:c.4163A>C	p.Asp1388Ala	p.D1388A	ENST00000399503	NM_005921.1	1388	gAt/gCt	18/20	1	2	FACETS	0.621	0.536	0.714	0.621	0.536	0.714	SUBCLONAL	1	FALSE	1	0.260300767867178	2		400	779	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911164	29911164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41552413	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	44	270	0	ENST00000376809.5:c.463C>T	p.Arg155Cys	p.R155C	ENST00000376809	NM_002116.7	155	Cgc/Tgc	3/8	0.147762423514347	3	FACETS	0.862	0.724	1	0.431	0.362	0.508	INDETERMINATE	1	FALSE	1	0.260300767867178	3		270	443	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196045	138196045	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	87	455	0	ENST00000237289.4:c.359T>C	p.Leu120Ser	p.L120S	ENST00000237289	NM_001270507.1	120	tTg/tCg	3/9	1	2	FACETS	0.721	0.637	0.811	0.721	0.637	0.811	SUBCLONAL	1	FALSE	1	0.260300767867178	2		455	927	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739328	145739328	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1256191939	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	98	481	0	ENST00000428558.2:c.2042A>G	p.Asp681Gly	p.D681G	ENST00000428558	NM_004260.3	681	gAc/gGc	12/22	0.136895585119356	3	FACETS	0.89	0.793	0.994	0.445	0.396	0.497	INDETERMINATE	1	FALSE	1	0.260300767867178	3		481	956	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904987	101904987	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	54	330	0	ENST00000374994.4:c.973+2T>C		p.X325_splice	ENST00000374994	NM_004612.2	325			1	2	FACETS	0.771	0.659	0.894	0.771	0.659	0.894	SUBCLONAL	1	FALSE	1	0.260300767867178	2		330	538	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998747	100998747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11571148	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	177	862	2	ENST00000325455.5:c.1055C>T	p.Pro352Leu	p.P352L	ENST00000325455	NM_001202474.3	352	cCg/cTg	1/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.260300767867178	2		864	1106	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345041	73345041	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	48	385	0	ENST00000377767.4:c.1755+1G>C		p.X585_splice	ENST00000377767	NM_014953.3	585			1	2	FACETS	0.72	0.609	0.843	0.72	0.609	0.843	SUBCLONAL	1	FALSE	1	0.260300767867178	2		385	512	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566229	95566229	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	108	588	0	ENST00000393063.1:c.4094T>C	p.Leu1365Pro	p.L1365P	ENST00000393063	NM_030621.3	1365	cTa/cCa	23/28	1	2	FACETS	0.874	0.784	0.971	0.874	0.784	0.971	CLONAL	1	FALSE	1	0.260300767867178	2		588	949	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820570	3820570	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	53	305	0	ENST00000262367.5:c.2880+1G>A		p.X960_splice	ENST00000262367	NM_004380.2	960			1	2	FACETS	0.895	0.764	1	0.895	0.764	1	CLONAL	1	FALSE	1	0.260300767867178	2		305	455	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3824601	3824601	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	108	726	0	ENST00000262367.5:c.2252T>C	p.Val751Ala	p.V751A	ENST00000262367	NM_004380.2	751	gTc/gCc	12/31	1	2	FACETS	0.692	0.619	0.77	0.692	0.619	0.77	SUBCLONAL	1	FALSE	1	0.260300767867178	2		726	1199	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645064	67645064	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	117	703	0	ENST00000264010.4:c.329T>C	p.Ile110Thr	p.I110T	ENST00000264010	NM_006565.3	110	aTa/aCa	3/12	1	2	FACETS	0.778	0.7	0.862	0.778	0.7	0.862	SUBCLONAL	1	FALSE	1	0.260300767867178	2		703	1155	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108698	8108698	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs746401290	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	104	621	0	ENST00000585124.1:c.697A>G	p.Met233Val	p.M233V	ENST00000585124	NM_004217.3	233	Atg/Gtg	8/9	1	2	FACETS	0.724	0.647	0.807	0.724	0.647	0.807	SUBCLONAL	1	FALSE	1	0.260300767867178	2		621	1103	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440675	56440675	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1327	178	874	0	ENST00000407977.2:c.543G>T	p.Lys181Asn	p.K181N	ENST00000407977		181	aaG/aaT	5/10	1	2	FACETS	0.909	0.835	0.986	0.909	0.835	0.986	CLONAL	1	FALSE	1	0.260300767867178	2		874	1505	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252837	10252837	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1160158444	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	164	410	0	ENST00000340748.4:c.3128A>G	p.Tyr1043Cys	p.Y1043C	ENST00000340748		1043	tAc/tGc	29/40	0.233112291720746	2	FACETS	1	0.988	1	0.739	0.679	0.802	CLONAL	1	FALSE	0	0.260300767867178	2		410	852	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564603	41564603	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	97	611	0	ENST00000263253.7:c.4025G>T	p.Arg1342Met	p.R1342M	ENST00000263253	NM_001429.3	1342	aGg/aTg	24/31	1	2	FACETS	0.643	0.572	0.72	0.643	0.572	0.72	SUBCLONAL	1	FALSE	1	0.260300767867178	2		611	1159	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360612	70360617	+	inframe_deletion	In_Frame_Del	DEL	CAGCAA	CAGCAA	-	rs753370104	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	43	615	1	ENST00000374080.3:c.6183_6188del	p.Gln2075_Gln2076del	p.Q2075_Q2076del	ENST00000374080		2058	CAGCAA/-	42/45	0.260300767867178	1	FACETS	0.334	0.278	0.396	0.334	0.278	0.396	SUBCLONAL	1	FALSE	0	0.260300767867178	1		616	860	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349355	89349356	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2157	248	1382	0	ENST00000301030.4:c.3594dup	p.Glu1199ArgfsTer5	p.E1199Rfs*5	ENST00000301030	NM_001256183.1	1198	-/A	9/13	0.142317837875497	3	FACETS	0.895	0.833	0.961			1	INDETERMINATE	1	FALSE	NA	0.260300767867178	3		1382	2405	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900661	3900661	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	79	418	2	ENST00000262367.5:c.435del	p.Ala146LeufsTer6	p.A146Lfs*6	ENST00000262367	NM_004380.2	145	ccC/cc	2/31	1	2	FACETS	0.871	0.766	0.984	0.871	0.766	0.984	CLONAL	1	FALSE	1	0.260300767867178	2		420	697	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019143	31019144	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	105	820	0	ENST00000375687.4:c.742dup	p.Glu248GlyfsTer6	p.E248Gfs*6	ENST00000375687	NM_015338.5	246	-/G	9/13	0.0388328013417958	3	FACETS	0.722	0.645	0.804			1	INDETERMINATE	1	FALSE	NA	0.260300767867178	3		820	1263	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432686	49432687	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	71	569	0	ENST00000301067.7:c.8452_8453del	p.Trp2818AlafsTer26	p.W2818Afs*26	ENST00000301067	NM_003482.3	2818	TGg/g	34/54	0.147762423514347	3	FACETS	0.593	0.516	0.677	0.297	0.258	0.339	INDETERMINATE	1	FALSE	1	0.260300767867178	3		569	1039	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224248	98224248	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	71	490	0	ENST00000331920.6:c.2593del	p.Thr865ProfsTer38	p.T865Pfs*38	ENST00000331920	NM_000264.3	865	Acc/cc	16/24	1	2	FACETS	0.61	0.531	0.696	0.61	0.531	0.696	SUBCLONAL	1	FALSE	1	0.260300767867178	2		490	894	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933594	39933594	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	72	607	1	ENST00000378444.4:c.1005del	p.Ser336ArgfsTer42	p.S336Rfs*42	ENST00000378444	NM_001123385.1	335	ccC/cc	4/15	0.260300767867178	1	FACETS	0.635	0.554	0.722	0.635	0.554	0.722	SUBCLONAL	1	FALSE	0	0.260300767867178	1		608	758	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533517	63533517	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555577625	NA	P-0013462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	89	643	0	ENST00000307078.5:c.1637del	p.Gly546AlafsTer143	p.G546Afs*143	ENST00000307078	NM_004655.3	546	gGc/gc	6/11	1	2	FACETS	0.786	0.696	0.883	0.786	0.696	0.883	SUBCLONAL	1	FALSE	1	0.260300767867178	2		643	870	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	51	588	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.666	0.566	0.776	0.666	0.566	0.776	SUBCLONAL	1	TRUE	1	0.277050267187181	2		589	553	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	177	789	1	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	0.277050267187181	2	FACETS	0.931	0.861	1	0.931	0.861	1	CLONAL	2	TRUE	0	0.277050267187181	2		790	686	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0013495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	49	427	1	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	1	2	FACETS	0.941	0.799	1	0.941	0.799	1	CLONAL	1	TRUE	1	0.277050267187181	2		428	376	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0013495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	27	365	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.699	0.557	0.859	0.699	0.557	0.859	SUBCLONAL	1	TRUE	1	0.277050267187181	2		365	279	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578206	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs886039484	NA	P-0013495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	87	866	0	ENST00000269305.4:c.643A>C	p.Ser215Arg	p.S215R	ENST00000269305	NM_001126112.2	215	Agt/Cgt	6/11	0.277050267187181	1	FACETS	0.866	0.767	0.971	0.866	0.767	0.971	CLONAL	1	TRUE	0	0.277050267187181	1		866	625	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251659	212251659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139785964	NA	P-0013495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	84	811	2	ENST00000342788.4:c.3400G>A	p.Val1134Met	p.V1134M	ENST00000342788	NM_005235.2	1134	Gtg/Atg	27/28	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.277050267187181	2		813	565	SUCCESS
APC	324	MSKCC	GRCh37	5	112174349	112174349	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	36	511	0	ENST00000257430.4:c.3058G>T	p.Glu1020Ter	p.E1020*	ENST00000257430	NM_000038.5	1020	Gaa/Taa	16/16	1	2	FACETS	0.931	0.769	1	0.931	0.769	1	CLONAL	1	TRUE	1	0.277050267187181	2		511	279	SUCCESS
APC	324	MSKCC	GRCh37	5	112177665	112177665	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	48	538	0	ENST00000257430.4:c.6374C>T	p.Ser2125Phe	p.S2125F	ENST00000257430	NM_000038.5	2125	tCt/tTt	16/16	1	2	FACETS	0.847	0.718	0.989	0.847	0.718	0.989	CLONAL	1	TRUE	1	0.277050267187181	2		538	409	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575137	48575137	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	63	713	0	ENST00000342988.3:c.331C>G	p.His111Asp	p.H111D	ENST00000342988	NM_005359.5	111	Cat/Gat	3/12	0.277050267187181	1	FACETS	0.83	0.719	0.95	0.83	0.719	0.95	CLONAL	1	TRUE	0	0.277050267187181	1		713	472	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931954	39931955	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	98	366	0	ENST00000378444.4:c.2644dup	p.Ser882LysfsTer35	p.S882Kfs*35	ENST00000378444	NM_001123385.1	882	agt/aAgt	4/15	1	1	FACETS	0.881	0.793	0.972	1	0.986	1	CLONAL	2	TRUE	0	0.277050267187181	1		366	346	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0013596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	878	454	2	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.449137522389002	9	FACETS	1	0.993	1	1	0.993	1	CLONAL	8	TRUE	1	0.449137522389002	9		456	1213	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0013596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	118	141	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.977	1	1	0.992	1	CLONAL	2	TRUE	1	0.449137522389002	2		142	227	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6439806	6439806	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	630	519	1	ENST00000356142.4:c.332A>T	p.Asn111Ile	p.N111I	ENST00000356142	NM_018890.3	111	aAt/aTt	5/7	0.449137522389002	9	FACETS	0.948	0.914	0.983	0.593	0.571	0.614	CLONAL	5	TRUE	1	0.449137522389002	9		520	1522	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609951	43609951	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377767410	NA	P-0013596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	231	897	0	ENST00000355710.3:c.1903C>T	p.Arg635Cys	p.R635C	ENST00000355710	NM_020975.4	635	Cgc/Tgc	11/20	0.449137522389002	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.449137522389002	1		897	750	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28908189	28908189	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	293	567	0	ENST00000282397.4:c.2566C>G	p.Arg856Gly	p.R856G	ENST00000282397	NM_002019.4	856	Cgg/Ggg	18/30	1	2	FACETS	0.939	0.889	0.988	1	0.996	1	CLONAL	2	TRUE	1	0.449137522389002	2		567	695	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350427	89350427	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	439	872	1	ENST00000301030.4:c.2523G>A	p.Trp841Ter	p.W841*	ENST00000301030	NM_001256183.1	841	tgG/tgA	9/13	1	2	FACETS	0.995	0.953	1	1	0.997	1	CLONAL	2	TRUE	1	0.449137522389002	2		873	982	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4102429	4102429	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	244	531	0	ENST00000262948.5:c.473T>A	p.Val158Glu	p.V158E	ENST00000262948	NM_030662.3	158	gTg/gAg	4/11	1	2	FACETS	0.948	0.894	1	1	0.995	1	CLONAL	2	TRUE	1	0.449137522389002	2		531	573	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383892	15383892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	195	417	0	ENST00000263377.2:c.19C>T	p.Pro7Ser	p.P7S	ENST00000263377	NM_058243.2	7	Cct/Tct	2/20	1	2	FACETS	0.967	0.905	1	1	0.994	1	CLONAL	2	TRUE	1	0.449137522389002	2		417	449	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022357	31022358	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCAGACA	novel	NA	P-0013596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	150	364	0	ENST00000375687.4:c.1843_1849dup	p.Ile617SerfsTer4	p.I617Sfs*4	ENST00000375687	NM_015338.5	614	-/GCAGACA	13/13	1	2	FACETS	0.761	0.702	0.821	1	0.989	1	SUBCLONAL	2	TRUE	1	0.449137522389002	2		364	439	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725190	49725190	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	67	178	0	ENST00000449682.2:c.235G>A	p.Asp79Asn	p.D79N	ENST00000449682	NM_020998.3	79	Gac/Aac	2/18	1	2	FACETS	0.802	0.711	0.896	1	0.979	1	CLONAL	2	TRUE	1	0.449137522389002	2		178	186	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389278	8389278	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752508898	NA	P-0013596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	312	642	2	ENST00000356435.5:c.4340G>A	p.Arg1447Gln	p.R1447Q	ENST00000356435		1447	cGg/cAg	26/35	1	2	FACETS	0.969	0.92	1	1	0.996	1	CLONAL	2	TRUE	1	0.449137522389002	2		644	717	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006225	22006225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751427195	NA	P-0013596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	147	259	0	ENST00000276925.6:c.178C>T	p.Arg60Cys	p.R60C	ENST00000276925	NM_004936.3	60	Cgc/Tgc	2/2	1	2	FACETS	1	0.929	1	1	0.992	1	CLONAL	2	TRUE	1	0.449137522389002	2		259	327	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849152	156849152	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs768180688	NA	P-0013651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1396	192	596	0	ENST00000524377.1:c.2044C>T	p.Arg682Cys	p.R682C	ENST00000524377	NM_002529.3	682	Cgt/Tgt	15/17	0.81832410557423	6	FACETS	0.779	0.718	0.843			1	SUBCLONAL	1	TRUE	NA	0.81832410557423	6		596	1588	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999087	100999087	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1299240489	NA	P-0013651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	212	617	0	ENST00000325455.5:c.715G>A	p.Gly239Ser	p.G239S	ENST00000325455	NM_001202474.3	239	Ggc/Agc	1/8	1	2	FACETS	0.996	0.934	1	0.996	0.934	1	CLONAL	1	TRUE	1	0.81832410557423	2		617	520	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	332	474	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.81832410557423	2	FACETS	0.971	0.941	0.999	0.971	0.941	0.999	CLONAL	2	TRUE	0	0.81832410557423	2		474	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0013651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	545	607	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.812401099729419	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.81832410557423	2		607	663	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505568	25505568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	246	554	1	ENST00000264709.3:c.190G>A	p.Asp64Asn	p.D64N	ENST00000264709	NM_175629.2	64	Gac/Aac	4/23	0.723604441310223	4	FACETS	0.962	0.899	1			1	CLONAL	1	TRUE	NA	0.81832410557423	4		555	1136	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967304	134967304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1422590121	NA	P-0013651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	202	498	1	ENST00000398015.3:c.2643G>A	p.Met881Ile	p.M881I	ENST00000398015	NM_004441.4	881	atG/atA	14/16	0.81832410557423	3	FACETS	0.876	0.814	0.94	0.438	0.407	0.47	CLONAL	1	TRUE	1	0.81832410557423	3		499	794	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526294	189526295	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCAA	novel	NA	P-0013651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	122	317	0	ENST00000264731.3:c.560_564dup	p.Ser189ProfsTer12	p.S189Pfs*12	ENST00000264731	NM_003722.4	186	-/GCCAA	4/14	0.81832410557423	3	FACETS	0.932	0.848	1	0.466	0.424	0.51	CLONAL	1	TRUE	1	0.81832410557423	3		317	451	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372248	55372248	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	44	258	0	ENST00000297316.4:c.938T>C	p.Met313Thr	p.M313T	ENST00000297316	NM_022454.3	313	aTg/aCg	2/2	0.720360324072095	3	FACETS	0.489	0.412	0.573			1	SUBCLONAL	1	TRUE	NA	0.81832410557423	3		258	310	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0013651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	169	214	1	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.81832410557423	2	FACETS	0.947	0.905	0.987	0.947	0.905	0.987	CLONAL	2	TRUE	0	0.81832410557423	2		215	218	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933145	39933146	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0013651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	275	678	0	ENST00000378444.4:c.1453_1454insC	p.Glu485AlafsTer14	p.E485Afs*14	ENST00000378444	NM_001123385.1	485	gaa/gCaa	4/15	0.81832410557423	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.81832410557423	1		678	372	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373848	118373848	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	65	396	1	ENST00000534358.1:c.7241C>T	p.Ser2414Leu	p.S2414L	ENST00000534358	NM_005933.3	2414	tCa/tTa	27/36	0.147792379685055	5	FACETS	1	0.932	1			1	CLONAL	1	TRUE	NA	0.147792379685055	5		397	952	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945034	31945034	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1185	163	672	0	ENST00000340398.3:c.67A>T	p.Thr23Ser	p.T23S	ENST00000340398	NM_001013699.2	23	Acg/Tcg	1/1	0.147792379685055	2	FACETS	0.818	0.749	0.891	0.818	0.749	0.891	CLONAL	2	TRUE	0	0.147792379685055	2		672	1348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577101	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0013656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	167	610	1	ENST00000269305.4:c.837_838insT	p.Arg280Ter	p.R280*	ENST00000269305	NM_001126112.2	279	-/T	8/11	1	2	FACETS	1	0.933	1	1	0.992	1	CLONAL	2	TRUE	1	0.147792379685055	2		611	1108	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486027	29486027	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0013656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	112	307	0	ENST00000356175.3:c.205-1G>A		p.X69_splice	ENST00000356175	NM_000267.3	69			1	2	FACETS	1	0.967	1	1	0.99	1	CLONAL	2	TRUE	1	0.147792379685055	2		307	649	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	56	374	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.338857750314444	2		374	222	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919598	96919598	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373951977	NA	P-0013705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	106	704	1	ENST00000258439.3:c.665C>T	p.Ala222Val	p.A222V	ENST00000258439	NM_001193304.2	222	gCg/gTg	4/4	1	2	FACETS	0.598	0.535	0.666	0.598	0.535	0.666	SUBCLONAL	1	TRUE	1	0.338857750314444	2		705	1046	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249018	55249019	+	inframe_insertion	In_Frame_Ins	INS	-	-	CACCAT	novel	NA	P-0013705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	146	569	0	ENST00000275493.2:c.2319_2320insCATCAC	p.His773_Val774insHisHis	p.H773_V774insHH	ENST00000275493	NM_005228.3	772	-/CACCAT	20/28	1	2	FACETS	0.989	0.903	1	0.989	0.903	1	CLONAL	1	TRUE	1	0.338857750314444	2		569	871	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730371	133730371	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs774952482	NA	P-0013705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	92	552	0	ENST00000318560.5:c.437A>G	p.Asn146Ser	p.N146S	ENST00000318560	NM_005157.4	146	aAt/aGt	3/11	0.338857750314444	1	FACETS	0.774	0.689	0.864	0.774	0.689	0.864	SUBCLONAL	1	TRUE	0	0.338857750314444	1		552	583	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0013714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	327	356	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.342859704969756	3	FACETS	0.869	0.825	0.914	0.869	0.825	0.914	CLONAL	3	TRUE	0	0.355095089971646	3		356	832	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579350	7579350	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587781642	NA	P-0013714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	274	518	0	ENST00000269305.4:c.337T>G	p.Phe113Val	p.F113V	ENST00000269305	NM_001126112.2	113	Ttc/Gtc	4/11	0.323461769703025	2	FACETS	0.959	0.903	1	0.959	0.903	1	CLONAL	2	TRUE	0	0.355095089971646	2		518	805	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971069	21971070	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0013714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	64	80	0	ENST00000304494.5:c.288dup	p.Leu97AlafsTer23	p.L97Afs*23	ENST00000304494	NM_000077.4	96	-/G	2/3	0.341230121822202	2	FACETS	1	0.972	1	0.724	0.634	0.819	CLONAL	1	TRUE	0	0.355095089971646	2		80	249	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	49	673	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.261141790675131	3	FACETS	0.737	0.623	0.861	0.368	0.311	0.431	SUBCLONAL	1	TRUE	1	0.261141790675131	3		673	576	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	133	374	0				ENST00000310581	NM_198253.2	-/1132			0.261141790675131	3	FACETS	0.944	0.86	1	0.944	0.86	1	CLONAL	2	TRUE	1	0.261141790675131	3		374	610	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1764	164	928	1	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	0.261141790675131	3	FACETS	0.737	0.673	0.804	0.368	0.336	0.402	SUBCLONAL	1	TRUE	1	0.261141790675131	3		929	1928	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	167	691	0	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	0.261141790675131	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.261141790675131	1		691	1052	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420788	49420788	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	106	486	0	ENST00000301067.7:c.14961G>A	p.Trp4987Ter	p.W4987*	ENST00000301067	NM_003482.3	4987	tgG/tgA	48/54	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.261141790675131	2		486	785	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686252	30686252	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	100	429	0	ENST00000295754.5:c.108G>C	p.Met36Ile	p.M36I	ENST00000295754	NM_003242.5	36	atG/atC	2/7	0.184409899967614	3	FACETS	0.99	0.883	1	0.495	0.441	0.552	CLONAL	1	TRUE	1	0.261141790675131	3		429	875	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518010	8518010	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	172	739	0	ENST00000356435.5:c.1381C>T	p.Gln461Ter	p.Q461*	ENST00000356435		461	Caa/Taa	10/35	0.261141790675131	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.261141790675131	1		739	1046	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313213	65313213	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	116	695	2	ENST00000342505.4:c.1899+2C>T		p.X633_splice	ENST00000342505	NM_002227.2	633			1	2	FACETS	0.832	0.748	0.921	0.832	0.748	0.921	CLONAL	1	TRUE	1	0.261141790675131	2		697	1068	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335148	65335148	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	76	486	0	ENST00000342505.4:c.493G>C	p.Asp165His	p.D165H	ENST00000342505	NM_002227.2	165	Gat/Cat	6/25	1	2	FACETS	0.778	0.682	0.882	0.778	0.682	0.882	SUBCLONAL	1	TRUE	1	0.261141790675131	2		486	748	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050364	176050364	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	53	597	0	ENST00000367669.3:c.1201C>T	p.Arg401Ter	p.R401*	ENST00000367669	NM_022457.5	401	Cga/Tga	11/20	0.261141790675131	3	FACETS	0.446	0.379	0.521	0.149	0.126	0.174	SUBCLONAL	1	TRUE	0	0.261141790675131	3		597	1028	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133238201	133238201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1452902479	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	101	740	0	ENST00000320574.5:c.2776G>A	p.Glu926Lys	p.E926K	ENST00000320574	NM_006231.2	926	Gag/Aag	24/49	1	2	FACETS	0.706	0.629	0.788	0.706	0.629	0.788	SUBCLONAL	1	TRUE	1	0.261141790675131	2		740	1096	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28644711	28644711	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	97	462	0	ENST00000241453.7:c.82C>T	p.Gln28Ter	p.Q28*	ENST00000241453	NM_004119.2	28	Caa/Taa	2/24	1	2	FACETS	0.916	0.816	1	0.916	0.816	1	CLONAL	1	TRUE	1	0.261141790675131	2		462	811	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913406	28913406	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	118	540	0	ENST00000282397.4:c.2387C>G	p.Ser796Ter	p.S796*	ENST00000282397	NM_002019.4	796	tCa/tGa	17/30	1	2	FACETS	0.989	0.891	1	0.989	0.891	1	CLONAL	1	TRUE	1	0.261141790675131	2		540	914	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726689	88726689	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	95	552	0	ENST00000360948.2:c.355C>T	p.Gln119Ter	p.Q119*	ENST00000360948	NM_001012338.2	119	Cag/Tag	4/19	1	2	FACETS	0.781	0.695	0.874	0.781	0.695	0.874	SUBCLONAL	1	TRUE	1	0.261141790675131	2		552	931	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508218	38508218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	151	692	0	ENST00000254066.5:c.526G>A	p.Glu176Lys	p.E176K	ENST00000254066	NM_000964.3	176	Gag/Aag	5/9	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.261141790675131	2		692	986	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740432	58740432	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	189	818	0	ENST00000305921.3:c.1337C>T	p.Ser446Leu	p.S446L	ENST00000305921	NM_003620.3	446	tCa/tTa	6/6	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.261141790675131	2		818	1340	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756598	756598	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	66	635	0	ENST00000314574.4:c.230C>G	p.Ser77Ter	p.S77*	ENST00000314574	NM_005433.3	77	tCa/tGa	2/12	1	2	FACETS	0.554	0.479	0.635	0.554	0.479	0.635	SUBCLONAL	1	TRUE	1	0.261141790675131	2		635	913	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350573	15350573	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	42	457	0	ENST00000263377.2:c.3342G>C	p.Lys1114Asn	p.K1114N	ENST00000263377	NM_058243.2	1114	aaG/aaC	16/20	1	2	FACETS	0.46	0.383	0.546	0.46	0.383	0.546	SUBCLONAL	1	TRUE	1	0.261141790675131	2		457	699	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022340	26022340	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	142	630	0	ENST00000435504.4:c.317C>G	p.Ser106Ter	p.S106*	ENST00000435504		106	tCa/tGa	5/13	1	2	FACETS	0.998	0.908	1	0.998	0.908	1	CLONAL	1	TRUE	1	0.261141790675131	2		630	1090	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054221	30054221	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	246	668	0	ENST00000338641.4:c.643G>C	p.Glu215Gln	p.E215Q	ENST00000338641	NM_000268.3	215	Gag/Cag	7/16	0.261141790675131	2	FACETS	0.903	0.844	0.964	0.903	0.844	0.964	CLONAL	2	TRUE	0	0.261141790675131	2		668	1043	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928919	49928919	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	93	834	0	ENST00000296474.3:c.3447C>G	p.Ile1149Met	p.I1149M	ENST00000296474	NM_002447.2	1149	atC/atG	16/20	1	2	FACETS	0.569	0.504	0.639	0.569	0.504	0.639	SUBCLONAL	1	TRUE	1	0.261141790675131	2		834	1251	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138375052	138375052	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	61	534	0	ENST00000289153.2:c.3007C>G	p.Leu1003Val	p.L1003V	ENST00000289153	NM_006219.2	1003	Ctc/Gtc	21/22	0.261141790675131	3	FACETS	0.497	0.427	0.574	0.249	0.213	0.287	SUBCLONAL	1	TRUE	1	0.261141790675131	3		534	1062	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586422	189586422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866267914	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	63	352	0	ENST00000264731.3:c.1046G>A	p.Gly349Glu	p.G349E	ENST00000264731	NM_003722.4	349	gGa/gAa	8/14	0.261141790675131	3	FACETS	0.928	0.803	1	0.464	0.401	0.532	CLONAL	1	TRUE	1	0.261141790675131	3		352	588	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467746	66467746	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	107	593	0	ENST00000273854.3:c.523G>C	p.Asp175His	p.D175H	ENST00000273854	NM_004439.5	175	Gat/Cat	3/18	1	2	FACETS	0.887	0.794	0.985	0.887	0.794	0.985	CLONAL	1	TRUE	1	0.261141790675131	2		593	924	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562906	176562906	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	245	513	0	ENST00000439151.2:c.802G>C	p.Glu268Gln	p.E268Q	ENST00000439151	NM_022455.4	268	Gaa/Caa	2/23	0.245956475938268	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	0	0.261141790675131	2		513	924	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225622	26225622	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1451	431	1282	0	ENST00000360408.1:c.240G>C	p.Lys80Asn	p.K80N	ENST00000360408	NM_003532.2	80	aaG/aaC	1/1	0.261141790675131	3	FACETS	0.991	0.942	1	0.991	0.942	1	CLONAL	2	TRUE	1	0.261141790675131	3		1282	1882	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519721	137519721	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	50	404	0	ENST00000367739.4:c.917C>G	p.Ser306Ter	p.S306*	ENST00000367739	NM_000416.2	306	tCa/tGa	7/7	0.261141790675131	1	FACETS	0.628	0.533	0.733	0.628	0.533	0.733	SUBCLONAL	1	TRUE	0	0.261141790675131	1		404	530	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005546	150005546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	87	599	0	ENST00000253339.5:c.679C>T	p.His227Tyr	p.H227Y	ENST00000253339		227	Cac/Tac	3/7	0.261141790675131	1	FACETS	0.717	0.634	0.806	0.717	0.634	0.806	SUBCLONAL	1	TRUE	0	0.261141790675131	1		599	808	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528033	157528033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	59	299	1	ENST00000346085.5:c.5758G>A	p.Glu1920Lys	p.E1920K	ENST00000346085	NM_020732.3	1920	Gag/Aag	20/20	0.261141790675131	1	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	0	0.261141790675131	1		300	387	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742144	145742144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779891153	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	88	219	0	ENST00000428558.2:c.359G>A	p.Gly120Glu	p.G120E	ENST00000428558	NM_004260.3	120	gGa/gAa	5/22	1	2	FACETS	0.955	0.853	1	1	0.985	1	CLONAL	2	TRUE	1	0.261141790675131	2		219	353	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504293	8504293	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	119	586	0	ENST00000356435.5:c.1790C>T	p.Thr597Ile	p.T597I	ENST00000356435		597	aCt/aTt	12/35	0.261141790675131	1	FACETS	0.892	0.805	0.985	0.892	0.805	0.985	CLONAL	1	TRUE	0	0.261141790675131	1		586	888	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864041	97864041	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	118	634	0	ENST00000289081.3:c.1625G>C	p.Arg542Thr	p.R542T	ENST00000289081	NM_000136.2	542	aGa/aCa	15/15	1	2	FACETS	0.937	0.844	1	0.937	0.844	1	CLONAL	1	TRUE	1	0.261141790675131	2		634	965	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417503	139417503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780209394	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	119	632	1	ENST00000277541.6:c.541G>A	p.Glu181Lys	p.E181K	ENST00000277541	NM_017617.3	181	Gag/Aag	4/34	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.261141790675131	2		633	858	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972667	76972667	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	189	744	0	ENST00000373344.5:c.74C>G	p.Ser25Ter	p.S25*	ENST00000373344	NM_000489.3	25	tCa/tGa	2/35	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.261141790675131	2		744	1312	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191741	123191741	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	123	759	1	ENST00000218089.9:c.1330G>A	p.Glu444Lys	p.E444K	ENST00000218089	NM_001042749.1	444	Gag/Aag	15/35	1	2	FACETS	0.866	0.781	0.955	0.866	0.781	0.955	CLONAL	1	TRUE	1	0.261141790675131	2		760	1088	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191748	123191748	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	124	781	0	ENST00000218089.9:c.1337G>C	p.Gly446Ala	p.G446A	ENST00000218089	NM_001042749.1	446	gGa/gCa	15/35	1	2	FACETS	0.852	0.769	0.94	0.852	0.769	0.94	CLONAL	1	TRUE	1	0.261141790675131	2		781	1115	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0013784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	103	552	1	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.261191261199674	2		553	717	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0013784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	97	480	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	0.261191261199674	2		480	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934576	NA	P-0013784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	43	672	0	ENST00000269305.4:c.818G>C	p.Arg273Pro	p.R273P	ENST00000269305	NM_001126112.2	273	cGt/cCt	8/11	0.261177399645979	1	FACETS	0.431	0.36	0.511	0.431	0.36	0.511	SUBCLONAL	1	TRUE	0	0.261191261199674	1		672	664	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946355	2946355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372251654	NA	P-0013784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	69	637	1	ENST00000396946.4:c.3382G>A	p.Val1128Ile	p.V1128I	ENST00000396946	NM_032415.4	1128	Gta/Ata	25/25	NA	2	FACETS	0.783	0.681	0.893			1	INDETERMINATE	1	TRUE	NA	0.261191261199674	2		638	675	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001244	150001244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	185	622	0	ENST00000253339.5:c.2360G>A	p.Gly787Glu	p.G787E	ENST00000253339		787	gGg/gAg	4/7	1	2	FACETS	0.88	0.814	0.948	1	0.992	1	CLONAL	2	TRUE	1	0.261191261199674	2		622	805	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398287	25398288	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTC	novel	NA	P-0013784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	157	537	0	ENST00000311936.3:c.29_31dup	p.Gly10dup	p.G10dup	ENST00000311936	NM_004985.3	10	gct/gGAGct	2/5	0.166205864364181	2	FACETS	0.836	0.767	0.907	0.836	0.767	0.907	CLONAL	2	TRUE	0	0.261191261199674	2		537	719	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56839482	56839482	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1054056220	NA	P-0013784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1267	70	841	0	ENST00000308159.5:c.427C>T	p.Arg143Ter	p.R143*	ENST00000308159	NM_014669.4	143	Cga/Tga	5/22	1	2	FACETS	0.401	0.348	0.459	0.401	0.348	0.459	SUBCLONAL	1	TRUE	1	0.261191261199674	2		841	1337	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828308	72828308	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	153	928	0	ENST00000268489.5:c.8273T>G	p.Leu2758Arg	p.L2758R	ENST00000268489	NM_006885.3	2758	cTc/cGc	9/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.261191261199674	2		928	947	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578220	7578220	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	109	709	0	ENST00000269305.4:c.629del	p.Asn210ThrfsTer37	p.N210Tfs*37	ENST00000269305	NM_001126112.2	210	aAc/ac	6/11	0.261177399645979	1	FACETS	0.949	0.852	1	0.949	0.852	1	CLONAL	1	TRUE	0	0.261191261199674	1		709	765	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041175	180041175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1400220848	NA	P-0013784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	106	542	0	ENST00000261937.6:c.3224G>A	p.Arg1075Gln	p.R1075Q	ENST00000261937	NM_182925.4	1075	cGg/cAg	24/30	0.199136538206392	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.261191261199674	1		542	565	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017620	112017620	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	52	815	0	ENST00000368678.4:c.893T>G	p.Leu298Arg	p.L298R	ENST00000368678		298	cTt/cGt	9/13	0.261191261199674	1	FACETS	0.378	0.32	0.441	0.378	0.32	0.441	SUBCLONAL	1	TRUE	0	0.261191261199674	1		815	916	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040969	47040970	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCT	novel	NA	P-0013784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	104	588	0	ENST00000377604.3:c.1501_1504dup	p.Gly502AlafsTer17	p.G502Afs*17	ENST00000377604	NM_001204468.1	500	cag/caGCCTg	14/24	0.261177399645979	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.261191261199674	1		588	561	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579349	7579349	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1567555667	NA	P-0013795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	297	692	0	ENST00000269305.4:c.338T>G	p.Phe113Cys	p.F113C	ENST00000269305	NM_001126112.2	113	tTc/tGc	4/11	0.336430807645042	2	FACETS	0.891	0.843	0.941	0.891	0.843	0.941	CLONAL	2	TRUE	0	0.408885722434573	2		692	815	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591104	67591115	+	inframe_deletion	In_Frame_Del	DEL	TTAAACCAGACC	TTAAACCAGACC	-	novel	NA	P-0013795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	82	340	0	ENST00000274335.5:c.1700_1711del	p.Lys567_Leu570del	p.K567_L570del	ENST00000274335		566	aTTAAACCAGACCtt/att	12/15	1	2	FACETS	0.844	0.747	0.948	0.844	0.747	0.948	CLONAL	1	TRUE	1	0.408885722434573	2		340	475	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122904	7122904	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1229730671	NA	P-0013795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	167	573	2	ENST00000302850.5:c.3355C>T	p.Arg1119Trp	p.R1119W	ENST00000302850	NM_000208.2	1119	Cgg/Tgg	18/22	0.303055843844801	3	FACETS	0.978	0.898	1	0.489	0.449	0.531	CLONAL	1	TRUE	1	0.408885722434573	3		575	1006	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593667	55593668	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGATCTCCCTTG	novel	NA	P-0013795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	269	441	0	ENST00000288135.5:c.1738_1739insTCCCTTGTGATC	p.Asp579_His580insLeuProCysAsp	p.D579_H580insLPCD	ENST00000288135	NM_000222.2	578	tat/taTGATCTCCCTTGt	11/21	0.408885722434573	3	FACETS	0.997	0.939	1	0.997	0.939	1	CLONAL	2	TRUE	1	0.408885722434573	3		441	795	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196207	106196207	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	94	316	0	ENST00000380013.4:c.4540C>A	p.Leu1514Ile	p.L1514I	ENST00000380013	NM_001127208.2	1514	Ctt/Att	11/11	1	2	FACETS	0.896	0.8	0.998	0.896	0.8	0.998	CLONAL	1	TRUE	1	0.408885722434573	2		316	513	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0013813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	94	439	1	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.21	2		440	887	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221830	55221830	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	128	964	3	ENST00000275493.2:c.874G>T	p.Val292Leu	p.V292L	ENST00000275493	NM_005228.3	292	Gtg/Ttg	7/28	1	2	FACETS	0.933	0.843	1	0.933	0.843	1	CLONAL	1	TRUE	1	0.21	2		967	1306	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546997	9546997	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	45	378	0	ENST00000353224.5:c.1025C>A	p.Pro342His	p.P342H	ENST00000353224	NM_177990.2	342	cCt/cAt	5/10	1	2	FACETS	0.861	0.723	1	0.861	0.723	1	CLONAL	1	TRUE	1	0.21	2		378	498	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099362	193099362	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1060500017	NA	P-0013813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	77	536	0	ENST00000367435.3:c.296A>G	p.Asn99Ser	p.N99S	ENST00000367435	NM_024529.4	99	aAt/aGt	3/17	1	2	FACETS	0.83	0.727	0.941	0.83	0.727	0.941	CLONAL	1	TRUE	1	0.21	2		536	884	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137748	64137748	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs201085797	NA	P-0013813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	89	765	1	ENST00000334205.4:c.1849G>T	p.Gly617Trp	p.G617W	ENST00000334205	NM_003942.2	617	Ggg/Tgg	15/17	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.21	2		766	697	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121525	108121526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	74	593	0	ENST00000278616.4:c.1333_1334insT	p.Gln445LeufsTer42	p.Q445Lfs*42	ENST00000278616	NM_000051.3	445	caa/cTaa	10/63	1	2	FACETS	0.769	0.672	0.875	0.769	0.672	0.875	SUBCLONAL	1	TRUE	1	0.21	2		593	916	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677993	58677993	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	66	466	0	ENST00000305921.3:c.218G>T	p.Arg73Leu	p.R73L	ENST00000305921	NM_003620.3	73	cGa/cTa	1/6	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.21	2		466	626	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383775	15383775	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1331613863	NA	P-0013813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	71	865	4	ENST00000263377.2:c.136C>T	p.Pro46Ser	p.P46S	ENST00000263377	NM_058243.2	46	Ccg/Tcg	2/20	1	2	FACETS	0.772	0.672	0.88	0.772	0.672	0.88	SUBCLONAL	1	TRUE	1	0.21	2		869	876	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466853	25466853	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0013813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	41	568	2	ENST00000264709.3:c.1852-2A>G		p.X618_splice	ENST00000264709	NM_175629.2	618			1	2	FACETS	0.667	0.555	0.793	0.667	0.555	0.793	SUBCLONAL	1	TRUE	1	0.21	2		570	585	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440180	220440180	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	109	1030	1	ENST00000243786.2:c.1033G>A	p.Asp345Asn	p.D345N	ENST00000243786	NM_002191.3	345	Gat/Aat	2/2	1	2	FACETS	0.912	0.817	1	0.912	0.817	1	CLONAL	1	TRUE	1	0.21	2		1031	1138	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510024	187510024	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	76	700	0	ENST00000441802.2:c.13489G>C	p.Asp4497His	p.D4497H	ENST00000441802	NM_005245.3	4497	Gat/Cat	27/27	1	2	FACETS	0.831	0.727	0.943	0.831	0.727	0.943	CLONAL	1	TRUE	1	0.21	2		700	871	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439746	140439746	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	48	468	0	ENST00000288602.6:c.1993A>G	p.Ile665Val	p.I665V	ENST00000288602	NM_004333.4	665	Ata/Gta	17/18	1	2	FACETS	0.711	0.6	0.834	0.711	0.6	0.834	SUBCLONAL	1	TRUE	1	0.21	2		468	643	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90994952	90994952	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	99	559	0	ENST00000265433.3:c.169C>G	p.Leu57Val	p.L57V	ENST00000265433	NM_002485.4	57	Ctg/Gtg	2/16	1	2	FACETS	0.856	0.762	0.956	0.856	0.762	0.956	CLONAL	1	TRUE	1	0.21	2		559	1102	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918990	76918990	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	112	423	0	ENST00000373344.5:c.4001C>G	p.Pro1334Arg	p.P1334R	ENST00000373344	NM_000489.3	1334	cCa/cGa	12/35	0.207889436406815	2	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.21	2		423	791	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0013822-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	203	585	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.170062577686688	3	FACETS	0.991	0.919	1	0.991	0.919	1	CLONAL	3	TRUE	0	0.15	3		585	979	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579323	7579324	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0013822-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	52	471	0	ENST00000269305.4:c.363dup	p.Val122CysfsTer27	p.V122Cfs*27	ENST00000269305	NM_001126112.2	121	-/T	4/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.15	2		471	512	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427119	49427143	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTGCTGGACCAGGAGGCCTTGGT	AGCTGCTGGACCAGGAGGCCTTGGT	-	novel	NA	P-0013861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	65	784	0	ENST00000301067.7:c.11345_11369del	p.His3782ArgfsTer40	p.H3782Rfs*40	ENST00000301067	NM_003482.3	3782	cACCAAGGCCTCCTGGTCCAGCAGCTg/cg	39/54	1	2	FACETS	0.488	0.422	0.56	0.488	0.422	0.56	SUBCLONAL	1	TRUE	1	0.32	2		784	832	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790401	3790402	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	47	517	0	ENST00000262367.5:c.4131dup	p.Arg1378ThrfsTer10	p.R1378Tfs*10	ENST00000262367	NM_004380.2	1377	-/A	24/31	1	2	FACETS	0.513	0.432	0.602	0.513	0.432	0.602	SUBCLONAL	1	TRUE	1	0.32	2		517	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578448	7578461	+	frameshift_variant	Frame_Shift_Del	DEL	GCCATGGCGCGGAC	GCCATGGCGCGGAC	-	novel	NA	P-0013861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	75	580	0	ENST00000269305.4:c.469_482del	p.Val157HisfsTer19	p.V157Hfs*19	ENST00000269305	NM_001126112.2	157	GTCCGCGCCATGGCc/c	5/11	0.180602258739378	1	FACETS	0.591	0.518	0.67	0.591	0.518	0.67	INDETERMINATE	1	TRUE	0	0.32	1		580	666	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398287	25398288	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTC	novel	NA	P-0013932-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	48	537	0	ENST00000311936.3:c.29_31dup	p.Gly10dup	p.G10dup	ENST00000311936	NM_004985.3	10	gct/gGAGct	2/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		537	759	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0013993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	42	707	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.204203655712402	5	FACETS	0.448	0.372	0.533	0.149	0.124	0.178	SUBCLONAL	1	FALSE	2	0.204203655712402	5		707	1200	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0013993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	211	379	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.158856862621901	4	FACETS	1	0.975	1	0.74	0.686	0.796	CLONAL	2	FALSE	1	0.204203655712402	4		379	1121	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0013993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	92	175	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.204203655712402	3	FACETS	1	0.966	1	0.615	0.546	0.689	CLONAL	1	FALSE	1	0.204203655712402	3		175	807	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18439857	18439858	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0013993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	77	577	1	ENST00000266497.5:c.761dup	p.Ile255AsnfsTer9	p.I255Nfs*9	ENST00000266497		252	gta/gtAa	2/31	0.158856862621901	4	FACETS	0.772	0.675	0.876	0.257	0.225	0.292	SUBCLONAL	1	FALSE	1	0.204203655712402	4		578	1177	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128292	30128292	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1796	294	1291	0	ENST00000263025.4:c.940A>C	p.Asn314His	p.N314H	ENST00000263025	NM_002746.2	314	Aac/Cac	7/9	0.204203655712402	6	FACETS	0.97	0.909	1	0.485	0.454	0.517	CLONAL	2	FALSE	2	0.204203655712402	6		1291	2090	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985521	60985521	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	137	759	4	ENST00000333681.4:c.379C>T	p.Arg127Trp	p.R127W	ENST00000333681		127	Cgg/Tgg	2/3	0.163661315134938	3	FACETS	0.792	0.719	0.868	0.792	0.719	0.868	SUBCLONAL	2	FALSE	1	0.204203655712402	3		763	934	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561764	55561764	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	36	641	3	ENST00000288135.5:c.154G>T	p.Asp52Tyr	p.D52Y	ENST00000288135	NM_000222.2	52	Gac/Tac	2/21	0.0997147399921836	4	FACETS	0.453	0.371	0.546	0.227	0.185	0.273	INDETERMINATE	1	FALSE	2	0.204203655712402	4		644	937	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394430	162394430	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	174	741	0	ENST00000366898.1:c.638G>C	p.Gly213Ala	p.G213A	ENST00000366898	NM_004562.2	213	gGa/gCa	6/12	0.204203655712402	3	FACETS	0.921	0.847	0.998	0.921	0.847	0.998	CLONAL	2	FALSE	1	0.204203655712402	3		741	1020	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428200	47428200	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs749435690	NA	P-0013993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	320	1157	0	ENST00000377045.4:c.1160G>T	p.Gly387Val	p.G387V	ENST00000377045	NM_001654.4	387	gGc/gTc	11/16	0.163568705089496	3	FACETS	1	0.988	1	0.788	0.742	0.835	CLONAL	2	FALSE	0	0.204203655712402	3		1157	1461	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	112	474	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.215943675939985	1	FACETS	0.905	0.818	0.997	1	0.988	1	CLONAL	2	FALSE	0	0.215943675939985	1		474	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0014042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	142	519	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.215943675939985	0	FACETS	0.986	0.904	1			1	CLONAL	2	FALSE	0	0.215943675939985	0		519	523	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022592	31022592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs373221034	NA	P-0014042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	147	647	4	ENST00000375687.4:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000375687	NM_015338.5	693	Cga/Tga	13/13	1	2	FACETS	0.81	0.74	0.884	1	0.989	1	CLONAL	2	FALSE	1	0.215943675939985	2		651	840	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119838	70119839	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0014042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	175	682	0	ENST00000245479.2:c.841dup	p.Asp281GlyfsTer15	p.D281Gfs*15	ENST00000245479	NM_000346.3	280	-/G	3/3	0.215943675939985	1	FACETS	0.96	0.886	1	1	0.992	1	CLONAL	2	FALSE	0	0.215943675939985	1		682	753	SUCCESS
APC	324	MSKCC	GRCh37	5	112175100	112175101	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	22	281	0	ENST00000257430.4:c.3814dup	p.Ser1272PhefsTer4	p.S1272Ffs*4	ENST00000257430	NM_000038.5	1270	tgt/tgTt	16/16	0.215943675939985	1	FACETS	0.707	0.549	0.89	0.707	0.549	0.89	SUBCLONAL	1	FALSE	0	0.215943675939985	1		281	257	SUCCESS
APC	324	MSKCC	GRCh37	5	112175429	112175430	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0014042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	80	406	0	ENST00000257430.4:c.4142dup	p.Leu1382ThrfsTer4	p.L1382Tfs*4	ENST00000257430	NM_000038.5	1380	acc/aCcc	16/16	0.215943675939985	1	FACETS	0.824	0.729	0.924	1	0.981	1	CLONAL	2	FALSE	0	0.215943675939985	1		406	401	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399796	139399796	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760875144	NA	P-0014042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	214	452	1	ENST00000277541.6:c.4552G>A	p.Gly1518Ser	p.G1518S	ENST00000277541	NM_017617.3	1518	Ggc/Agc	25/34	0.19727837466075	2	FACETS	0.976	0.911	1	1	0.992	1	CLONAL	3	FALSE	0	0.215943675939985	2		453	677	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	226	357	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.449782785253885	3	FACETS	0.902	0.847	0.959	0.902	0.847	0.959	CLONAL	2	TRUE	1	0.534377875039963	3		357	594	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928036	49928036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199869962	NA	P-0014092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	429	416	0	ENST00000296474.3:c.3692G>A	p.Arg1231His	p.R1231H	ENST00000296474	NM_002447.2	1231	cGc/cAc	18/20	0.449782785253885	3	FACETS	0.859	0.82	0.899	0.859	0.82	0.899	CLONAL	2	TRUE	1	0.534377875039963	3		416	1184	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877860	151877878	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGTTGGCACAGGTCCAG	GAAGTTGGCACAGGTCCAG	-	novel	NA	P-0014092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	187	642	0	ENST00000262189.6:c.7067_7085del	p.Pro2356GlnfsTer3	p.P2356Qfs*3	ENST00000262189	NM_170606.2	2356	cCTGGACCTGTGCCAACTTCa/ca	36/59	0.449782785253885	3	FACETS	1	0.989	1	0.695	0.645	0.747	CLONAL	1	TRUE	1	0.534377875039963	3		642	638	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257899	19257899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374422850	NA	P-0014092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	235	853	3	ENST00000162023.5:c.487G>A	p.Ala163Thr	p.A163T	ENST00000162023		163	Gcc/Acc	9/13	0.440939950042449	2	FACETS	0.834	0.778	0.892	0.417	0.389	0.446	CLONAL	1	TRUE	0	0.534377875039963	2		856	1054	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540233	187540233	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	144	949	0	ENST00000441802.2:c.7507G>A	p.Glu2503Lys	p.E2503K	ENST00000441802	NM_005245.3	2503	Gaa/Aaa	10/27	0.449782785253885	3	FACETS	0.822	0.75	0.897	0.411	0.375	0.449	CLONAL	1	TRUE	1	0.534377875039963	3		949	831	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160564	56160565	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0014092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	172	465	0	ENST00000399503.3:c.838_839del	p.Gln280GlufsTer20	p.Q280Efs*20	ENST00000399503	NM_005921.1	280	CAg/g	4/20	0.434008029323526	5	FACETS	0.809	0.746	0.874	0.539	0.497	0.583	CLONAL	2	TRUE	2	0.534377875039963	5		465	717	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177840	56177841	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	234	573	0	ENST00000399503.3:c.2815dup	p.Ser939PhefsTer2	p.S939Ffs*2	ENST00000399503	NM_005921.1	938	cct/ccTt	14/20	0.434008029323526	5	FACETS	1	0.98	1	0.74	0.693	0.787	CLONAL	2	TRUE	2	0.534377875039963	5		573	711	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225929	53225929	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	389	966	1	ENST00000375401.3:c.2920C>T	p.Gln974Ter	p.Q974*	ENST00000375401	NM_004187.3	974	Cag/Tag	19/26	0.422880612242916	3	FACETS	0.782	0.744	0.821	0.782	0.744	0.821	SUBCLONAL	2	TRUE	1	0.534377875039963	3		967	1179	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	93	442	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.191131706119693	2	FACETS	0.968	0.87	1	1	0.981	1	CLONAL	3	FALSE	0	0.191131706119693	2		444	335	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	74	556	2	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	1	2	FACETS	1	0.914	1	1	0.984	1	CLONAL	2	FALSE	1	0.191131706119693	2		558	370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057520000	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	159	485	5	ENST00000269305.4:c.452C>A	p.Pro151His	p.P151H	ENST00000269305	NM_001126112.2	151	cCc/cAc	5/11	1	2	FACETS	0.871	0.801	0.943	1	0.993	1	CLONAL	3	FALSE	1	0.191131706119693	2		490	637	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	25	410	1	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	1	2	FACETS	0.651	0.512	0.81	0.651	0.512	0.81	SUBCLONAL	1	FALSE	1	0.191131706119693	2		411	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	94	435	0	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	1	2	FACETS	1	0.966	1	1	0.988	1	CLONAL	2	FALSE	1	0.191131706119693	2		435	413	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855984	68855984	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121964877	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	104	658	0	ENST00000261769.5:c.1792C>T	p.Arg598Ter	p.R598*	ENST00000261769	NM_004360.3	598	Cga/Tga	12/16	0.191131706119693	0	FACETS	0.83	0.762	0.899			1	CLONAL	5	FALSE	0	0.191131706119693	0		658	212	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	81	427	0	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	1	2	FACETS	1	0.904	1	1	0.985	1	CLONAL	2	FALSE	1	0.191131706119693	2		427	414	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	88	306	0	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	1	2	FACETS	0.94	0.846	1	1	0.99	1	CLONAL	4	FALSE	1	0.191131706119693	2		306	245	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	110	372	1	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.909	0.823	0.999	1	0.991	1	CLONAL	3	FALSE	1	0.191131706119693	2		373	422	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123688	11123688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	43	410	1	ENST00000358026.2:c.2338G>A	p.Glu780Lys	p.E780K	ENST00000358026	NM_001128849.1	780	Gag/Aag	16/36	1	2	FACETS	0.821	0.686	0.971	0.821	0.686	0.971	CLONAL	1	FALSE	1	0.191131706119693	2		411	548	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260214	16260214	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	10	144	0	ENST00000375759.3:c.7484del	p.Pro2495LeufsTer4	p.P2495Lfs*4	ENST00000375759	NM_015001.2	2493	agC/ag	11/15	1	2	FACETS	0.539	0.365	0.758	0.539	0.365	0.758	SUBCLONAL	1	FALSE	1	0.191131706119693	2		144	194	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1131691023	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	43	461	0	ENST00000269305.4:c.470T>C	p.Val157Ala	p.V157A	ENST00000269305	NM_001126112.2	157	gTc/gCc	5/11	1	2	FACETS	0.751	0.628	0.889	0.751	0.628	0.889	SUBCLONAL	1	FALSE	1	0.191131706119693	2		461	599	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440135	49440136	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	28	486	1	ENST00000301067.7:c.4490_4491del	p.His1497LeufsTer30	p.H1497Lfs*30	ENST00000301067	NM_003482.3	1497	cAC/c	16/54	1	2	FACETS	0.637	0.508	0.784	0.637	0.508	0.784	SUBCLONAL	1	FALSE	1	0.191131706119693	2		487	460	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202283	133202283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764457707	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	172	635	0	ENST00000320574.5:c.6605C>T	p.Thr2202Met	p.T2202M	ENST00000320574	NM_006231.2	2202	aCg/aTg	47/49	1	2	FACETS	1	0.976	1	1	0.994	1	CLONAL	3	FALSE	1	0.191131706119693	2		635	535	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987087	36987087	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	71	308	1	ENST00000354822.5:c.602C>T	p.Ala201Val	p.A201V	ENST00000354822	NM_001079668.2	201	gCg/gTg	3/3	1	2	FACETS	0.964	0.851	1	1	0.986	1	CLONAL	3	FALSE	1	0.191131706119693	2		309	257	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11270924	11270924	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	66	475	1	ENST00000361445.4:c.3601C>T	p.Arg1201Ter	p.R1201*	ENST00000361445	NM_004958.3	1201	Cga/Tga	24/58	1	2	FACETS	0.94	0.826	1	1	0.985	1	CLONAL	3	FALSE	1	0.191131706119693	2		476	245	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288900	11288900	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	89	488	0	ENST00000361445.4:c.2855T>C	p.Met952Thr	p.M952T	ENST00000361445	NM_004958.3	952	aTg/aCg	19/58	1	2	FACETS	1	0.97	1	1	0.988	1	CLONAL	2	FALSE	1	0.191131706119693	2		488	373	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023768	27023769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	109	627	0	ENST00000324856.7:c.879dup	p.Thr294HisfsTer106	p.T294Hfs*106	ENST00000324856	NM_006015.4	292	acc/aCcc	1/20	1	2	FACETS	1	0.904	1	1	0.988	1	CLONAL	2	FALSE	1	0.191131706119693	2		627	568	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023913	27023913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	110	148	1	ENST00000324856.7:c.1019C>T	p.Ala340Val	p.A340V	ENST00000324856	NM_006015.4	340	gCg/gTg	1/20	1	2	FACETS	1	0.959	1	1	0.992	1	CLONAL	4	FALSE	1	0.191131706119693	2		149	266	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101278	27101278	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	131	560	0	ENST00000324856.7:c.4563del	p.Ala1522ProfsTer5	p.A1522Pfs*5	ENST00000324856	NM_006015.4	1520	ggC/gg	18/20	1	2	FACETS	1	0.918	1	1	0.992	1	CLONAL	3	FALSE	1	0.191131706119693	2		560	455	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106887	27106887	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	96	446	0	ENST00000324856.7:c.6498G>T	p.Met2166Ile	p.M2166I	ENST00000324856	NM_006015.4	2166	atG/atT	20/20	1	2	FACETS	1	0.957	1	1	0.988	1	CLONAL	2	FALSE	1	0.191131706119693	2		446	444	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458326	120458326	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	84	386	0	ENST00000256646.2:c.7019A>G	p.Tyr2340Cys	p.Y2340C	ENST00000256646	NM_024408.3	2340	tAc/tGc	34/34	1	2	FACETS	1	0.943	1	1	0.989	1	CLONAL	3	FALSE	1	0.191131706119693	2		386	271	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462945	120462945	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	144	572	0	ENST00000256646.2:c.5386G>T	p.Ala1796Ser	p.A1796S	ENST00000256646	NM_024408.3	1796	Gct/Tct	30/34	1	2	FACETS	1	0.974	1	1	0.993	1	CLONAL	3	FALSE	1	0.191131706119693	2		572	442	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759977	63759977	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	114	413	0	ENST00000279873.7:c.635del	p.Gly212AlafsTer24	p.G212Afs*24	ENST00000279873	NM_032199.2	210	ctG/ct	4/10	1	2	FACETS	1	0.942	1	1	0.991	1	CLONAL	3	FALSE	1	0.191131706119693	2		413	379	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137021	64137021	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	181	399	2	ENST00000334205.4:c.1532G>A	p.Arg511His	p.R511H	ENST00000334205	NM_003942.2	511	cGc/cAc	13/17	1	2	FACETS	1	0.978	1	1	0.995	1	CLONAL	3	FALSE	1	0.191131706119693	2		401	558	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343355	118343355	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	11	390	0	ENST00000534358.1:c.1481A>T	p.Glu494Val	p.E494V	ENST00000534358	NM_005933.3	494	gAg/gTg	3/36	1	2	FACETS	0.546	0.377	0.755	0.546	0.377	0.755	SUBCLONAL	1	FALSE	1	0.191131706119693	2		390	211	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409035	4409035	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	91	514	0	ENST00000261254.3:c.730A>G	p.Lys244Glu	p.K244E	ENST00000261254	NM_001759.3	244	Aaa/Gaa	5/5	1	2	FACETS	0.842	0.753	0.935	1	0.988	1	CLONAL	3	FALSE	1	0.191131706119693	2		514	377	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420593	49420598	+	inframe_deletion	In_Frame_Del	DEL	CAGGTT	CAGGTT	-	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	82	474	0	ENST00000301067.7:c.15151_15156del	p.Asn5051_Leu5052del	p.N5051_L5052del	ENST00000301067	NM_003482.3	5051	AACCTG/-	48/54	1	2	FACETS	0.898	0.794	1	1	0.983	1	CLONAL	2	FALSE	1	0.191131706119693	2		474	478	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443830	49443830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767932583	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	240	645	0	ENST00000301067.7:c.3541C>T	p.Pro1181Ser	p.P1181S	ENST00000301067	NM_003482.3	1181	Cca/Tca	11/54	1	2	FACETS	0.967	0.909	1	1	0.996	1	CLONAL	4	FALSE	1	0.191131706119693	2		645	649	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447881	49447881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201796530	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	146	337	2	ENST00000301067.7:c.553C>T	p.Arg185Cys	p.R185C	ENST00000301067	NM_003482.3	185	Cgc/Tgc	5/54	1	2	FACETS	1	0.976	1	1	0.993	1	CLONAL	3	FALSE	1	0.191131706119693	2		339	443	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988303	36988303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	62	196	0	ENST00000354822.5:c.350G>A	p.Cys117Tyr	p.C117Y	ENST00000354822	NM_001079668.2	117	tGc/tAc	2/3	1	2	FACETS	0.896	0.789	1	1	0.986	1	CLONAL	4	FALSE	1	0.191131706119693	2		196	181	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961895	41961896	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	58	1008	1	ENST00000219905.7:c.808_809del	p.Asp270TrpfsTer8	p.D270Wfs*8	ENST00000219905	NM_001164273.1	268	cAG/c	2/24	0.191131706119693	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	0	0.191131706119693	1		1009	395	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817720	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	137	625	0	ENST00000262367.5:c.3250dup	p.Ile1084AsnfsTer3	p.I1084Nfs*3	ENST00000262367	NM_004380.2	1084	atc/aAtc		1	2	FACETS	1	0.97	1	1	0.993	1	CLONAL	3	FALSE	1	0.191131706119693	2		625	426	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440931	56440931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	185	581	0	ENST00000407977.2:c.406G>A	p.Ala136Thr	p.A136T	ENST00000407977		136	Gct/Act	4/10	0.191131706119693	2	FACETS	1	0.979	1	1	0.992	1	CLONAL	3	FALSE	0	0.191131706119693	2		581	567	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276768	15276768	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1270568992	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	184	613	0	ENST00000263388.2:c.5497G>A	p.Ala1833Thr	p.A1833T	ENST00000263388	NM_000435.2	1833	Gca/Aca	30/33	1	2	FACETS	0.88	0.818	0.943	1	0.995	1	CLONAL	4	FALSE	1	0.191131706119693	2		613	547	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902194	50902194	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	246	994	0	ENST00000440232.2:c.86C>A	p.Pro29His	p.P29H	ENST00000440232	NM_002691.3	29	cCt/cAt	2/27	1	2	FACETS	0.878	0.824	0.933	1	0.996	1	CLONAL	4	FALSE	1	0.191131706119693	2		994	733	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149769	202149769	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	18	570	0	ENST00000358485.4:c.1210T>C	p.Cys404Arg	p.C404R	ENST00000358485	NM_001080125.1	404	Tgc/Cgc	8/9	1	2	FACETS	0.708	0.533	0.914	0.708	0.533	0.914	CLONAL	1	FALSE	1	0.191131706119693	2		570	266	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252959	36252959	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	70	428	0	ENST00000300305.3:c.403G>A	p.Gly135Ser	p.G135S	ENST00000300305		135	Ggc/Agc	4/8	0.191131706119693	1	FACETS	1	0.894	1	1	0.982	1	CLONAL	2	FALSE	0	0.191131706119693	1		428	325	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057288	30057288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753300935	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	31	499	0	ENST00000338641.4:c.770C>T	p.Pro257Leu	p.P257L	ENST00000338641	NM_000268.3	257	cCg/cTg	8/16	0.191131706119693	0	FACETS	0.896	0.726	1			1	CLONAL	1	FALSE	0	0.191131706119693	0		499	293	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275291	41275291	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750554859	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	21	358	1	ENST00000349496.5:c.1457G>A	p.Arg486His	p.R486H	ENST00000349496	NM_001904.3	486	cGc/cAc	9/15	1	2	FACETS	0.664	0.511	0.842	0.664	0.511	0.842	SUBCLONAL	1	FALSE	1	0.191131706119693	2		359	331	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52685804	52685804	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	21	557	0	ENST00000394830.3:c.668T>C	p.Ile223Thr	p.I223T	ENST00000394830	NM_018313.4	223	aTa/aCa	7/30	1	2	FACETS	1	0.845	1	1	0.845	1	CLONAL	1	FALSE	1	0.191131706119693	2		557	196	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920454	134920454	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	96	739	1	ENST00000398015.3:c.2269G>C	p.Val757Leu	p.V757L	ENST00000398015	NM_004441.4	757	Gtg/Ctg	12/16	1	2	FACETS	1	0.948	1	1	0.988	1	CLONAL	2	FALSE	1	0.191131706119693	2		740	459	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538941	187538941	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs113224498	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	92	626	0	ENST00000441802.2:c.8799del	p.Gly2934ValfsTer3	p.G2934Vfs*3	ENST00000441802	NM_005245.3	2933	caA/ca	10/27	0.191131706119693	1	FACETS	0.924	0.83	1	1	0.989	1	CLONAL	3	FALSE	0	0.191131706119693	1		626	314	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251519	251519	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	123	245	0	ENST00000264932.6:c.1730A>G	p.Gln577Arg	p.Q577R	ENST00000264932	NM_004168.2	577	cAg/cGg	13/15	0.191131706119693	3	FACETS	1	0.967	1	1	0.992	1	CLONAL	5	FALSE	1	0.191131706119693	3		245	259	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522545	176522545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199694646	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	141	549	0	ENST00000292408.4:c.1642G>A	p.Val548Met	p.V548M	ENST00000292408	NM_213647.1	548	Gtg/Atg	13/18	0.191131706119693	3	FACETS	0.955	0.879	1	1	0.991	1	CLONAL	4	FALSE	1	0.191131706119693	3		549	423	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523292	176523292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1172824038	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	148	551	1	ENST00000292408.4:c.1949G>A	p.Arg650His	p.R650H	ENST00000292408	NM_213647.1	650	cGc/cAc	15/18	0.191131706119693	3	FACETS	1	0.974	1	1	0.99	1	CLONAL	3	FALSE	1	0.191131706119693	3		552	495	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839907	27839907	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	671	1435	2	ENST00000328488.2:c.187A>T	p.Ile63Phe	p.I63F	ENST00000328488	NM_003533.2	63	Atc/Ttc	1/1	0.191131706119693	3	FACETS	1	0.992	1	1	0.998	1	CLONAL	7	FALSE	0	0.191131706119693	3		1437	1040	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405806	157405806	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	124	342	0	ENST00000346085.5:c.2048G>A	p.Gly683Asp	p.G683D	ENST00000346085	NM_020732.3	683	gGc/gAc	6/20	0.191131706119693	5	FACETS	1	0.925	1	1	0.988	1	CLONAL	6	FALSE	1	0.191131706119693	5		342	277	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468021	50468021	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	160	445	0	ENST00000331340.3:c.1259del	p.Pro420ArgfsTer40	p.P420Rfs*40	ENST00000331340	NM_006060.4	419	gCc/gc	8/8	1	2	FACETS	0.916	0.847	0.986	1	0.994	1	CLONAL	4	FALSE	1	0.191131706119693	2		445	457	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405176	139405176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1199428564	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	182	718	2	ENST00000277541.6:c.2669G>A	p.Gly890Asp	p.G890D	ENST00000277541	NM_017617.3	890	gGc/gAc	17/34	1	2	FACETS	0.953	0.883	1	1	0.994	1	CLONAL	3	FALSE	1	0.191131706119693	2		720	666	SUCCESS
AR	367	MSKCC	GRCh37	X	66931268	66931268	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	67	822	0	ENST00000374690.3:c.1910A>T	p.Asn637Ile	p.N637I	ENST00000374690	NM_000044.3	637	aAt/aTt	4/8	0.191131706119693	1	FACETS	0.941	0.823	1	1	0.98	1	CLONAL	2	FALSE	0	0.191131706119693	1		822	337	SUCCESS
AR	367	MSKCC	GRCh37	X	66931335	66931335	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	111	810	0	ENST00000374690.3:c.1977G>T	p.Lys659Asn	p.K659N	ENST00000374690	NM_000044.3	659	aaG/aaT	4/8	0.191131706119693	1	FACETS	1	0.964	1	1	0.992	1	CLONAL	3	FALSE	0	0.191131706119693	1		810	314	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181277	123181277	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	59	569	0	ENST00000218089.9:c.741A>T	p.Gln247His	p.Q247H	ENST00000218089	NM_001042749.1	247	caA/caT	9/35	0.191131706119693	1	FACETS	1	0.931	1	1	0.981	1	CLONAL	2	FALSE	0	0.191131706119693	1		569	251	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0014170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	88	410	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.43456261493342	2		410	399	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574678	41574679	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs754418509	NA	P-0014170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	51	1105	3	ENST00000263253.7:c.6970dup	p.His2324ProfsTer55	p.H2324Pfs*55	ENST00000263253	NM_001429.3	2321	-/C	31/31	1	2	FACETS	0.309	0.262	0.361	0.309	0.262	0.361	SUBCLONAL	1	TRUE	1	0.43456261493342	2		1108	760	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518992	103518992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	42	259	1	ENST00000355739.4:c.2330G>A	p.Arg777His	p.R777H	ENST00000355739	NM_000123.3	777	cGc/cAc	11/15	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.43456261493342	2		260	191	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100171	157100172	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0014170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	10	169	0	ENST00000346085.5:c.1114dup	p.Arg372ProfsTer163	p.R372Pfs*163	ENST00000346085	NM_020732.3	370	tcc/tCcc	1/20	1	2	FACETS	0.293	0.199	0.411	0.293	0.199	0.411	SUBCLONAL	1	TRUE	1	0.43456261493342	2		169	157	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254929	16254929	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs751475729	NA	P-0014170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	80	482	0	ENST00000375759.3:c.2194C>T	p.Arg732Ter	p.R732*	ENST00000375759	NM_015001.2	732	Cga/Tga	11/15	1	2	FACETS	0.92	0.815	1	0.92	0.815	1	CLONAL	1	TRUE	1	0.43456261493342	2		482	400	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692911	89692911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909241	NA	P-0014170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	71	383	0	ENST00000371953.3:c.395G>A	p.Gly132Asp	p.G132D	ENST00000371953	NM_000314.4	132	gGt/gAt	5/9	0.43456261493342	2	FACETS	0.801	0.712	0.893	0.801	0.712	0.893	CLONAL	2	TRUE	0	0.43456261493342	2		383	204	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913396	NA	P-0014170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	93	652	0	ENST00000349496.5:c.95A>C	p.Asp32Ala	p.D32A	ENST00000349496	NM_001904.3	32	gAc/gCc	3/15	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.43456261493342	2		652	405	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023827	27023827	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	85	616	0	ENST00000324856.7:c.936del	p.Gly314AlafsTer49	p.G314Afs*49	ENST00000324856	NM_006015.4	311	taC/ta	1/20	1	2	FACETS	0.849	0.753	0.95	0.849	0.753	0.95	CLONAL	1	TRUE	1	0.43456261493342	2		616	461	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522741	67522741	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	82	450	0	ENST00000274335.5:c.244del	p.Ile82SerfsTer32	p.I82Sfs*32	ENST00000274335		80	Aaa/aa	1/15	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.43456261493342	2		450	350	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916824	178916824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201269904	NA	P-0014170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	141	1305	3	ENST00000263967.3:c.211G>A	p.Val71Ile	p.V71I	ENST00000263967	NM_006218.2	71	Gta/Ata	2/21	1	2	FACETS	0.871	0.795	0.951	0.871	0.795	0.951	CLONAL	1	TRUE	1	0.43456261493342	2		1308	745	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836879	151836879	+	splice_region_variant,intron_variant	Splice_Region	DEL	A	A	-	rs369965395	NA	P-0014170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	68	511	6	ENST00000262189.6:c.14344-3del		p.X4782_splice	ENST00000262189	NM_170606.2	4782			1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.43456261493342	2		517	278	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023290	27023290	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	97	380	0	ENST00000324856.7:c.400del	p.Ala134ArgfsTer98	p.A134Rfs*98	ENST00000324856	NM_006015.4	132	gtG/gt	1/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.43456261493342	2		380	348	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987169	36987169	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	33	328	0	ENST00000354822.5:c.520G>T	p.Gly174Cys	p.G174C	ENST00000354822	NM_001079668.2	174	Ggc/Tgc	3/3	1	2	FACETS	0.791	0.65	0.946	0.791	0.65	0.946	CLONAL	1	TRUE	1	0.43456261493342	2		328	192	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007741	45007742	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0014170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	55	521	0	ENST00000558401.1:c.194_195del	p.Arg65AsnfsTer2	p.R65Nfs*2	ENST00000558401	NM_004048.2	63	gGA/g	2/4	1	2	FACETS	0.717	0.616	0.826	0.717	0.616	0.826	SUBCLONAL	1	TRUE	1	0.43456261493342	2		521	353	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210774	2210774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772047684	NA	P-0014170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	36	560	0	ENST00000398665.3:c.1271G>A	p.Arg424Gln	p.R424Q	ENST00000398665	NM_032482.2	424	cGg/cAg	14/28	1	2	FACETS	0.297	0.244	0.358	0.297	0.244	0.358	SUBCLONAL	1	TRUE	1	0.43456261493342	2		560	557	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303186	15303186	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0014170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	141	630	0	ENST00000263388.2:c.340+2T>C		p.X114_splice	ENST00000263388	NM_000435.2	114			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.43456261493342	2		630	564	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965612	25965612	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	93	605	0	ENST00000435504.4:c.3594G>T	p.Glu1198Asp	p.E1198D	ENST00000435504		1198	gaG/gaT	13/13	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.43456261493342	2		605	375	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540101	187540101	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	64	691	1	ENST00000441802.2:c.7639C>T	p.Gln2547Ter	p.Q2547*	ENST00000441802	NM_005245.3	2547	Cag/Tag	10/27	1	2	FACETS	0.777	0.676	0.886	0.777	0.676	0.886	SUBCLONAL	1	TRUE	1	0.43456261493342	2		692	379	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140454013	140454013	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	44	486	0	ENST00000288602.6:c.1715T>G	p.Ile572Ser	p.I572S	ENST00000288602	NM_004333.4	572	aTc/aGc	14/18	1	2	FACETS	0.614	0.517	0.72	0.614	0.517	0.72	SUBCLONAL	1	TRUE	1	0.43456261493342	2		486	330	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115873	8115874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0014219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	295	662	0	ENST00000346208.3:c.1220dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tCcg	6/6	0.345408981711487	6	FACETS	0.913	0.86	0.967			1	CLONAL	3	FALSE	NA	0.345408981711487	6		662	1055	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820862	36820862	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	63	624	0	ENST00000373129.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000373129	NM_032017.1	172	aGg/aAg	6/12	0.267963923417991	5	FACETS	0.801	0.692	0.92	0.267	0.23	0.307	CLONAL	1	FALSE	2	0.345408981711487	5		624	691	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163310151	163310154	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAGA	TAGA	-	rs775999824	NA	P-0014219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	69	458	0	ENST00000271452.3:c.607_610del		p.X203_splice	ENST00000271452	NM_145697.2	203		9/14	0.345945813703896	3	FACETS	0.913	0.797	1	0.457	0.398	0.52	CLONAL	1	FALSE	1	0.345408981711487	3		458	513	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	65	474	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.964	0.834	1	0.964	0.834	1	CLONAL	1	TRUE	1	0.15	2		474	899	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346338	73346338	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	51	370	0	ENST00000377767.4:c.1462G>C	p.Asp488His	p.D488H	ENST00000377767	NM_014953.3	488	Gat/Cat	10/21	1	2	FACETS	0.895	0.759	1	0.895	0.759	1	CLONAL	1	TRUE	1	0.15	2		370	760	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207202	1207203	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0014234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	60	687	0	ENST00000326873.7:c.290_290+1insTT	p.Lys97AsnfsTer7	p.K97Nfs*7	ENST00000326873	NM_000455.4	97	aag/aaTTg		1	2	FACETS	0.695	0.596	0.803	0.695	0.596	0.803	SUBCLONAL	1	TRUE	1	0.15	2		687	1151	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221319	1221320	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	58	598	0	ENST00000326873.7:c.842_843insT	p.Leu282AlafsTer3	p.L282Afs*3	ENST00000326873	NM_000455.4	281	ccg/ccTg	6/10	1	2	FACETS	0.822	0.704	0.951	0.822	0.704	0.951	CLONAL	1	TRUE	1	0.15	2		598	941	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0014235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	520	703	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.505796989292241	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.505796989292241	2		704	992	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745620	162745620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	64	500	2	ENST00000367921.3:c.2035G>A	p.Val679Ile	p.V679I	ENST00000367921	NM_006182.2	679	Gta/Ata	15/18	0.336507411256045	4	FACETS	0.431	0.372	0.495			1	SUBCLONAL	1	TRUE	NA	0.505796989292241	4		502	884	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100727	8100728	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs771019738	NA	P-0014235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	187	768	3	ENST00000346208.3:c.708dup	p.Ser237GlnfsTer66	p.S237Qfs*66	ENST00000346208		234	ttc/ttCc	3/6	NA	2	FACETS	0.757	0.699	0.817			1	INDETERMINATE	1	TRUE	NA	0.505796989292241	2		771	977	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998753	100998753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	340	672	0	ENST00000325455.5:c.1049C>T	p.Ser350Phe	p.S350F	ENST00000325455	NM_001202474.3	350	tCc/tTc	1/8	0.275540800075384	3	FACETS	0.909	0.862	0.956	0.909	0.862	0.956	INDETERMINATE	2	TRUE	1	0.505796989292241	3		672	927	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061218	38061230	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGTTCTCGAAC	GCCGTTCTCGAAC	-	novel	NA	P-0014235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	300	560	0	ENST00000250448.2:c.759_771del	p.Met253IlefsTer64	p.M253Ifs*64	ENST00000250448	NM_004496.3	253	atGTTCGAGAACGGC/at	2/2	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.505796989292241	2		560	906	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061836	38061862	+	inframe_deletion	In_Frame_Del	DEL	GTTCATGGTCATGTAGGTGTTCATGGA	GTTCATGGTCATGTAGGTGTTCATGGA	-	novel	NA	P-0014235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1361	394	1121	3	ENST00000250448.2:c.127_153del	p.Ser43_Asn51del	p.S43_N51del	ENST00000250448	NM_004496.3	43	TCCATGAACACCTACATGACCATGAAC/-	2/2	1	2	FACETS	0.888	0.841	0.935	0.888	0.841	0.935	CLONAL	1	TRUE	1	0.505796989292241	2		1124	1755	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873587	151873588	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0014235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	77	537	0	ENST00000262189.6:c.8950dup	p.Ser2984PhefsTer18	p.S2984Ffs*18	ENST00000262189	NM_170606.2	2984	tct/tTct	38/59	0.506512651588811	4	FACETS	0.468	0.409	0.531	0.234	0.204	0.266	SUBCLONAL	1	TRUE	2	0.505796989292241	4		537	980	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591115	67591115	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561299896	NA	P-0014239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	52	362	1	ENST00000274335.5:c.1708C>T	p.Leu570Phe	p.L570F	ENST00000274335		570	Ctt/Ttt	12/15	1	2	FACETS	0.872	0.742	1	0.872	0.742	1	CLONAL	1	TRUE	1	0.225960733578772	2		363	528	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974696	21974696	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	100	358	0	ENST00000304494.5:c.131del	p.Tyr44SerfsTer9	p.Y44Sfs*9	ENST00000304494	NM_000077.4	44	tAc/tc	1/3	0.225960733578772	2	FACETS	0.896	0.804	0.993	0.896	0.804	0.993	CLONAL	2	TRUE	0	0.225960733578772	2		358	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0014239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	180	615	1	ENST00000269305.4:c.215_216insTG	p.Val73AlafsTer51	p.V73Afs*51	ENST00000269305	NM_001126112.2	72	ccc/ccTGc	4/11	0.2117304636316	2	FACETS	0.963	0.889	1	0.963	0.889	1	CLONAL	2	TRUE	0	0.225960733578772	2		616	827	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579477	7579477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	178	626	0	ENST00000269305.4:c.210del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	70	gcT/gc	4/11	0.2117304636316	2	FACETS	0.93	0.858	1	0.93	0.858	1	CLONAL	2	TRUE	0	0.225960733578772	2		626	847	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921499	39921499	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	328	314	0	ENST00000378444.4:c.4321C>T	p.Gln1441Ter	p.Q1441*	ENST00000378444	NM_001123385.1	1441	Cag/Tag	10/15	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.908954505677759	1		314	353	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733606	85733607	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0014245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	105	481	0	ENST00000370580.1:c.404_405dup	p.Ser136AspfsTer13	p.S136Dfs*13	ENST00000370580	NM_003921.4	135	-/GA	3/3	1	2	FACETS	0.939	0.858	1	0.939	0.858	1	CLONAL	1	TRUE	1	0.908954505677759	2		481	246	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	115	588	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.803	0.724	0.887	0.803	0.724	0.887	CLONAL	1	TRUE	1	0.392877510019625	2		589	729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578552	7578553	+	stop_gained,splice_region_variant	Nonsense_Mutation	INS	-	-	TAC	novel	NA	P-0014252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	284	1404	1	ENST00000269305.4:c.376-1_377dup	p.Thr125_Tyr126insTer	p.T125_Y126ins*	ENST00000269305	NM_001126112.2	126	tac/taGTAc	5/11	0.392877510019625	1	FACETS	0.882	0.828	0.938	0.882	0.828	0.938	CLONAL	1	TRUE	0	0.392877510019625	1		1405	1317	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259362	89259362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	100	451	0	ENST00000336596.2:c.506G>A	p.Arg169Lys	p.R169K	ENST00000336596	NM_005233.5	169	aGa/aAa	3/17	1	2	FACETS	0.941	0.843	1	0.941	0.843	1	CLONAL	1	TRUE	1	0.392877510019625	2		451	541	SUCCESS
APC	324	MSKCC	GRCh37	5	112175759	112175760	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0014252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	167	269	0	ENST00000257430.4:c.4469_4470insAA	p.His1490GlnfsTer18	p.H1490Qfs*18	ENST00000257430	NM_000038.5	1490	cat/cAAat	16/16	0.392877510019625	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.392877510019625	2		269	374	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014285-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	159	588	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.783	0.718	0.851	1	0.989	1	SUBCLONAL	2	FALSE	1	0.244078466579265	2		589	832	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0014285-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	46	370	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	1	2	FACETS	0.656	0.551	0.771	0.656	0.551	0.771	SUBCLONAL	1	FALSE	1	0.244078466579265	2		370	575	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164447	47164447	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0014285-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	40	279	0	ENST00000409792.3:c.1679C>G	p.Ser560Ter	p.S560*	ENST00000409792	NM_014159.6	560	tCa/tGa	3/21	1	2	FACETS	0.792	0.659	0.94	0.792	0.659	0.94	CLONAL	1	FALSE	1	0.244078466579265	2		279	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579582	7579583	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0014285-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	97	506	0	ENST00000269305.4:c.104dup	p.Leu35PhefsTer8	p.L35Ffs*8	ENST00000269305	NM_001126112.2	35	ttg/ttTg	4/11	0.244078466579265	1	FACETS	0.81	0.722	0.905	0.81	0.722	0.905	CLONAL	1	FALSE	0	0.244078466579265	1		506	861	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945025	31945025	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014285-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	241	638	0	ENST00000340398.3:c.76G>A	p.Ala26Thr	p.A26T	ENST00000340398	NM_001013699.2	26	Gcc/Acc	1/1	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	1	0.244078466579265	2		638	1378	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107749	30107749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760459161	NA	P-0014285-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	66	440	0	ENST00000331968.5:c.931C>T	p.Arg311Cys	p.R311C	ENST00000331968	NM_002742.2	311	Cgt/Tgt	6/18	1	2	FACETS	0.699	0.605	0.8	0.699	0.605	0.8	SUBCLONAL	1	FALSE	1	0.244078466579265	2		440	774	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042026	42042027	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014285-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	97	527	0	ENST00000219905.7:c.6222dup	p.Lys2075Ter	p.K2075*	ENST00000219905	NM_001164273.1	2074	cgt/cgTt	17/24	0.244078466579265	1	FACETS	0.874	0.779	0.976	0.874	0.779	0.976	CLONAL	1	FALSE	0	0.244078466579265	1		527	798	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528146	29528146	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1350329837	NA	P-0014285-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	54	596	1	ENST00000356175.3:c.1154G>A	p.Arg385His	p.R385H	ENST00000356175	NM_000267.3	385	cGt/cAt	10/57	0.244078466579265	1	FACETS	0.505	0.43	0.587	0.505	0.43	0.587	SUBCLONAL	1	FALSE	0	0.244078466579265	1		597	769	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619427	1619427	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014285-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	114	663	1	ENST00000344749.5:c.1214G>T	p.Arg405Leu	p.R405L	ENST00000344749	NM_001136139.2	405	cGc/cTc	15/19	1	2	FACETS	0.772	0.693	0.856	0.772	0.693	0.856	SUBCLONAL	1	FALSE	1	0.244078466579265	2		664	1210	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573963	41573963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014285-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	93	517	0	ENST00000263253.7:c.6248C>T	p.Ala2083Val	p.A2083V	ENST00000263253	NM_001429.3	2083	gCa/gTa	31/31	0.244078466579265	1	FACETS	0.741	0.658	0.83	0.741	0.658	0.83	SUBCLONAL	1	FALSE	0	0.244078466579265	1		517	903	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679731	30679731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014285-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	105	491	2	ENST00000376406.3:c.1988G>A	p.Arg663Lys	p.R663K	ENST00000376406	NM_014641.2	663	aGa/aAa	5/15	0.211986667837838	3	FACETS	0.876	0.783	0.975	0.292	0.261	0.325	CLONAL	1	FALSE	0	0.244078466579265	3		493	1102	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184124	123184124	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014285-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	37	374	0	ENST00000218089.9:c.982T>G	p.Tyr328Asp	p.Y328D	ENST00000218089	NM_001042749.1	328	Tat/Gat	11/35	NA	2	FACETS	0.609	0.501	0.729			1	INDETERMINATE	1	FALSE	NA	0.244078466579265	2		374	498	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	244	474	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.484272250094702	4	FACETS	0.861	0.807	0.917	0.861	0.807	0.917	CLONAL	2	TRUE	2	0.526847814281502	4		474	821	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577573	7577573	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	394	595	2	ENST00000269305.4:c.708C>A	p.Tyr236Ter	p.Y236*	ENST00000269305	NM_001126112.2	236	taC/taA	7/11	0.477379139736827	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.526847814281502	2		597	737	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971011	21971012	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0014329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	261	369	0	ENST00000304494.5:c.346_347insT	p.Asp116ValfsTer4	p.D116Vfs*4	ENST00000304494	NM_000077.4	116	gac/gTac	2/3	0.488523024186335	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.526847814281502	2		369	471	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0014332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	90	96	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.504124650225008	2		96	284	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65312350	65312351	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0014332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	286	629	0	ENST00000342505.4:c.1968_1969del	p.Val658ProfsTer50	p.V658Pfs*50	ENST00000342505	NM_002227.2	656	gtCTgt/gtgt	14/25	0.384765176170402	1	FACETS	0.897	0.845	0.95	0.897	0.845	0.95	CLONAL	1	TRUE	0	0.504124650225008	1		629	946	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40683741	40683741	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs772662981	NA	P-0014332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	57	657	0	ENST00000249776.8:c.733C>G	p.His245Asp	p.H245D	ENST00000249776	NM_033286.3	245	Cac/Gac	7/9	0.504124650225008	1	FACETS	0.173	0.148	0.201	0.173	0.148	0.201	SUBCLONAL	1	TRUE	0	0.504124650225008	1		657	975	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579388	7579389	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0014332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	388	687	0	ENST00000269305.4:c.298dup	p.Gln100ProfsTer49	p.Q100Pfs*49	ENST00000269305	NM_001126112.2	100	cag/cCag	4/11	0.504124650225008	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.504124650225008	1		687	1040	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724485	724485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444974817	NA	P-0014332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	132	581	1	ENST00000314574.4:c.1571C>T	p.Ser524Phe	p.S524F	ENST00000314574	NM_005433.3	524	tCc/tTc	12/12	1	2	FACETS	0.67	0.608	0.734	0.67	0.608	0.734	SUBCLONAL	1	TRUE	1	0.504124650225008	2		582	782	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584503	48584521	+	frameshift_variant	Frame_Shift_Del	DEL	GCCAGTATACTGGGGGGCA	GCCAGTATACTGGGGGGCA	-	novel	NA	P-0014332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	21	354	0	ENST00000342988.3:c.680_698del	p.Ser227IlefsTer8	p.S227Ifs*8	ENST00000342988	NM_005359.5	226	GCCAGTATACTGGGGGGCAgc/gc	6/12	0.504124650225008	1	FACETS	0.169	0.129	0.215	0.169	0.129	0.215	SUBCLONAL	1	TRUE	0	0.504124650225008	1		354	369	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591792	48591792	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0014332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	20	395	0	ENST00000342988.3:c.956-1G>C		p.X319_splice	ENST00000342988	NM_005359.5	319			0.504124650225008	1	FACETS	0.218	0.167	0.278	0.218	0.167	0.278	SUBCLONAL	1	TRUE	0	0.504124650225008	1		395	272	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464501	25464501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	80	601	1	ENST00000264709.3:c.2012C>T	p.Thr671Met	p.T671M	ENST00000264709	NM_175629.2	671	aCg/aTg	17/23	1	2	FACETS	0.261	0.229	0.296	0.261	0.229	0.296	SUBCLONAL	1	TRUE	1	0.504124650225008	2		602	1215	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799490	72799490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1559656763	NA	P-0014332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	243	719	0	ENST00000325599.8:c.1679C>T	p.Ala560Val	p.A560V	ENST00000325599	NM_018130.2	560	gCt/gTt	11/11	0.267635555040944	1	FACETS	0.699	0.653	0.746	0.699	0.653	0.746	INDETERMINATE	1	TRUE	0	0.504124650225008	1		719	1032	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525527	137525527	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	75	732	0	ENST00000367739.4:c.488C>A	p.Pro163His	p.P163H	ENST00000367739	NM_000416.2	163	cCc/cAc	4/7	0.32601312868144	1	FACETS	0.286	0.25	0.325	0.286	0.25	0.325	SUBCLONAL	1	TRUE	0	0.504124650225008	1		732	779	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930119	68930119	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	194	533	0	ENST00000288368.4:c.180A>T	p.Lys60Asn	p.K60N	ENST00000288368	NM_024870.2	60	aaA/aaT	2/40	1	2	FACETS	0.922	0.854	0.992	0.922	0.854	0.992	CLONAL	1	TRUE	1	0.504124650225008	2		533	835	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559236	141559236	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	164	661	1	ENST00000220592.5:c.1565T>C	p.Leu522Pro	p.L522P	ENST00000220592	NM_012154.3	522	cTg/cCg	12/19	1	2	FACETS	0.518	0.474	0.564	0.518	0.474	0.564	SUBCLONAL	1	TRUE	1	0.504124650225008	2		662	1257	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249397	110249397	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs748447033	NA	P-0014332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1728	191	982	0	ENST00000374672.4:c.1176G>C	p.Arg392Ser	p.R392S	ENST00000374672	NM_004235.4	392	agG/agC	4/5	0.486734734700222	2	FACETS	0.395	0.363	0.428	0.197	0.181	0.214	SUBCLONAL	1	TRUE	0	0.504124650225008	2		982	1919	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	235	357	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.472653586116865	3	FACETS	0.949	0.895	1	0.949	0.895	1	CLONAL	2	FALSE	1	0.615663587856626	3		357	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579349	7579349	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1567555667	NA	P-0014362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	371	692	0	ENST00000269305.4:c.338T>G	p.Phe113Cys	p.F113C	ENST00000269305	NM_001126112.2	113	tTc/tGc	4/11	0.615663587856626	1	FACETS	0.927	0.883	0.971	0.927	0.883	0.971	CLONAL	1	FALSE	0	0.615663587856626	1		692	900	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684385	29684386	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0014362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	84	335	0	ENST00000356175.3:c.7905_7906insAA	p.Val2636LysfsTer23	p.V2636Kfs*23	ENST00000356175	NM_000267.3	2635	-/AA	53/57	0.615663587856626	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	FALSE	0	0.615663587856626	1		335	188	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922341	178922341	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	272	515	0	ENST00000263967.3:c.1110T>A	p.Asn370Lys	p.N370K	ENST00000263967	NM_006218.2	370	aaT/aaA	6/21	0.472653586116865	3	FACETS	0.818	0.772	0.865	0.818	0.772	0.865	CLONAL	2	FALSE	1	0.615663587856626	3		515	706	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0014404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	61	628	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.14	2		628	728	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436026	56436026	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771831816	NA	P-0014404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	34	308	1	ENST00000407977.2:c.1111C>T	p.Arg371Ter	p.R371*	ENST00000407977		371	Cga/Tga	9/10	1	2	FACETS	0.858	0.704	1	1	0.956	1	CLONAL	2	TRUE	1	0.14	2		309	283	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345769	152345769	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs759063323	NA	P-0014404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	23	244	0	ENST00000359321.1:c.801del	p.Lys267AsnfsTer30	p.K267Nfs*30	ENST00000359321	NM_005431.1	267	aaA/aa	3/3	0.3	1	FACETS	0.964	0.752	1	0.964	0.752	1	CLONAL	1	TRUE	0	0.14	1		244	317	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630905	187630905	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs75367100	NA	P-0014404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	43	412	1	ENST00000441802.2:c.77G>A	p.Arg26Gln	p.R26Q	ENST00000441802	NM_005245.3	26	cGa/cAa	2/27	1	2	FACETS	0.964	0.806	1	0.964	0.806	1	CLONAL	1	TRUE	1	0.14	2		413	637	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63537656	63537656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201387209	NA	P-0014404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	45	423	1	ENST00000307078.5:c.976C>T	p.Arg326Cys	p.R326C	ENST00000307078	NM_004655.3	326	Cgt/Tgt	4/11	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.14	2		424	606	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266503	55266503	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	38	497	0	ENST00000275493.2:c.2795G>A	p.Arg932His	p.R932H	ENST00000275493	NM_005228.3	932	cGc/cAc	23/28	0.0932444766916559	0	FACETS	0.682	0.562	0.816			1	SUBCLONAL	1	TRUE	0	0.14	0		497	685	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204842	128204842	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs768767517	NA	P-0014404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	38	655	0	ENST00000341105.2:c.599del	p.Gly200ValfsTer18	p.G200Vfs*18	ENST00000341105	NM_032638.4	200	gGt/gt	3/6	0.3	1	FACETS	0.733	0.604	0.877	0.733	0.604	0.877	SUBCLONAL	1	TRUE	0	0.14	1		655	689	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628026	187628026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750746155	NA	P-0014404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	38	579	0	ENST00000441802.2:c.2956G>A	p.Val986Ile	p.V986I	ENST00000441802	NM_005245.3	986	Gtc/Atc	2/27	1	2	FACETS	0.754	0.621	0.903	0.754	0.621	0.903	CLONAL	1	TRUE	1	0.14	2		579	720	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466004	69466004	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	34	657	1	ENST00000227507.2:c.842T>A	p.Val281Glu	p.V281E	ENST00000227507	NM_053056.2	281	gTg/gAg	5/5	0.3	0	FACETS	0.686	0.559	0.829			1	SUBCLONAL	1	TRUE	0	0.14	0		658	609	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678499	88678499	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	26	424	0	ENST00000360948.2:c.1037A>G	p.Lys346Arg	p.K346R	ENST00000360948	NM_001012338.2	346	aAg/aGg	9/19	0.3	1	FACETS	0.919	0.728	1	0.919	0.728	1	CLONAL	1	TRUE	0	0.14	1		424	376	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867216	68867216	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	42	412	0	ENST00000261769.5:c.2466del	p.Thr823GlnfsTer23	p.T823Qfs*23	ENST00000261769	NM_004360.3	821	gaC/ga	16/16	1	2	FACETS	0.96	0.8	1	0.96	0.8	1	CLONAL	1	TRUE	1	0.14	2		412	625	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7132211	7132211	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	45	582	0	ENST00000302850.5:c.2800G>A	p.Gly934Ser	p.G934S	ENST00000302850	NM_000208.2	934	Ggc/Agc	14/22	0.0932444766916559	0	FACETS	0.751	0.63	0.886			1	SUBCLONAL	1	TRUE	0	0.14	0		582	736	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139929	50139929	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374650566	NA	P-0014404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	66	690	1	ENST00000246792.3:c.400G>A	p.Asp134Asn	p.D134N	ENST00000246792	NM_006270.3	134	Gac/Aac	4/6	0.0932444766916559	0	FACETS	0.804	0.695	0.922			1	CLONAL	1	TRUE	0	0.14	0		691	1009	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639621	47639621	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0014404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	28	518	0	ENST00000233146.2:c.714T>G	p.Tyr238Ter	p.Y238*	ENST00000233146	NM_000251.2	238	taT/taG	4/16	1	2	FACETS	0.839	0.669	1	0.839	0.669	1	CLONAL	1	TRUE	1	0.14	2		518	477	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62320438	62320438	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752318462	NA	P-0014404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	37	543	0	ENST00000360203.5:c.1831G>A	p.Ala611Thr	p.A611T	ENST00000360203	NM_001283009.1	611	Gcc/Acc	22/35	0.3	2	FACETS	0.891	0.733	1			1	CLONAL	1	TRUE	NA	0.14	2		543	593	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067821	30067821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140266312	NA	P-0014404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	17	242	0	ENST00000338641.4:c.1006C>T	p.Arg336Trp	p.R336W	ENST00000338641	NM_000268.3	336	Cgg/Tgg	11/16	1	2	FACETS	0.846	0.631	1	0.846	0.631	1	CLONAL	1	TRUE	1	0.14	2		242	287	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526976	31526976	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1485879154	NA	P-0014404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	40	618	1	ENST00000344624.3:c.64C>T	p.Arg22Ter	p.R22*	ENST00000344624		22	Cga/Tga	2/33	0.3	2	FACETS	0.757	0.627	0.902			1	CLONAL	1	TRUE	NA	0.14	2		619	755	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467870	50467870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1483931742	NA	P-0014404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	16	272	0	ENST00000331340.3:c.1105G>A	p.Ala369Thr	p.A369T	ENST00000331340	NM_006060.4	369	Gcc/Acc	8/8	0.0932444766916559	0	FACETS	0.624	0.461	0.82			1	SUBCLONAL	1	TRUE	0	0.14	0		272	315	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468092	50468092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	21	242	0	ENST00000331340.3:c.1327G>A	p.Glu443Lys	p.E443K	ENST00000331340	NM_006060.4	443	Gag/Aag	8/8	0.0932444766916559	0	FACETS	0.794	0.611	1			1	CLONAL	1	TRUE	0	0.14	0		242	325	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133980	38133981	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	46	465	0	ENST00000317025.8:c.3905dup	p.Asn1302LysfsTer3	p.N1302Kfs*3	ENST00000317025	NM_023034.1	1302	aat/aaAt	23/24	1	2	FACETS	0.796	0.668	0.937	0.796	0.668	0.937	CLONAL	1	TRUE	1	0.14	2		465	826	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739029	145739029	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs947223466	NA	P-0014404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	35	475	1	ENST00000428558.2:c.2126G>A	p.Arg709Gln	p.R709Q	ENST00000428558	NM_004260.3	709	cGg/cAg	13/22	1	2	FACETS	0.77	0.63	0.929	0.77	0.63	0.929	CLONAL	1	TRUE	1	0.14	2		476	649	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492897	8492897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs544419494	NA	P-0014404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	31	351	0	ENST00000356435.5:c.2432G>A	p.Arg811His	p.R811H	ENST00000356435		811	cGc/cAc	16/35	1	2	FACETS	0.919	0.742	1	0.919	0.742	1	CLONAL	1	TRUE	1	0.14	2		351	482	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779102	135779102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs986350787	NA	P-0014404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	30	345	0	ENST00000298552.3:c.2144G>A	p.Arg715Gln	p.R715Q	ENST00000298552	NM_001162426.1	715	cGg/cAg	17/23	1	2	FACETS	0.974	0.784	1	0.974	0.784	1	CLONAL	1	TRUE	1	0.14	2		345	440	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	81	357	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	0.232015791509662	2		357	652	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106592	27106592	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	136	640	0	ENST00000324856.7:c.6203C>G	p.Ser2068Trp	p.S2068W	ENST00000324856	NM_006015.4	2068	tCg/tGg	20/20	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.232015791509662	2		640	1131	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944953	31944953	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376467484	NA	P-0014434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	43	513	1	ENST00000340398.3:c.148G>A	p.Glu50Lys	p.E50K	ENST00000340398	NM_001013699.2	50	Gag/Aag	1/1	1	2	FACETS	0.48	0.4	0.569	0.48	0.4	0.569	SUBCLONAL	1	TRUE	1	0.232015791509662	2		514	772	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161757	56161758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CATACATTGTCATCATCTAGTA	novel	NA	P-0014434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	120	576	0	ENST00000399503.3:c.1256_1277dup	p.Ser427TyrfsTer6	p.S427Yfs*6	ENST00000399503	NM_005921.1	418	-/CATACATTGTCATCATCTAGTA	6/20	1	2	FACETS	0.981	0.885	1	0.981	0.885	1	CLONAL	1	TRUE	1	0.232015791509662	2		576	1054	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189395	56189396	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	147	532	0	ENST00000399503.3:c.4430dup	p.Leu1477PhefsTer46	p.L1477Ffs*46	ENST00000399503	NM_005921.1	1476	cat/caTt	20/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.232015791509662	2		532	987	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0014465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	341	434	0				ENST00000310581	NM_198253.2	-/1132			0.378326825063887	7	FACETS	0.99	0.94	1	0.99	0.94	1	CLONAL	4	TRUE	3	0.378326825063887	7		434	886	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578191	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs530941076	NA	P-0014465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	260	735	0	ENST00000269305.4:c.658T>G	p.Tyr220Asp	p.Y220D	ENST00000269305	NM_001126112.2	220	Tat/Gat	6/11	0.37548123090972	4	FACETS	0.987	0.926	1	0.987	0.926	1	CLONAL	2	TRUE	2	0.378326825063887	4		735	960	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092739	27092740	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0014465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	218	479	0	ENST00000324856.7:c.2765dup	p.Met923HisfsTer13	p.M923Hfs*13	ENST00000324856	NM_006015.4	920	-/G	9/20	0.37548123090972	4	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	2	0.378326825063887	4		479	756	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233163	69233163	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	162	379	0	ENST00000462284.1:c.1028A>G	p.Asp343Gly	p.D343G	ENST00000462284	NM_002392.5	343	gAt/gGt	11/11	0.37548123090972	4	FACETS	0.974	0.898	1	0.974	0.898	1	CLONAL	2	TRUE	2	0.378326825063887	4		379	606	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670374	134670375	+	missense_variant	Missense_Mutation	DNP	CT	CT	AA	novel	NA	P-0014465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	37	403	0	ENST00000398015.3:c.285_286delinsAA	p.Asp95_Cys96delinsGluSer	p.D95_C96delinsES	ENST00000398015	NM_004441.4	95	gaCTgc/gaAAgc	3/16	0.374417197351721	4	FACETS	0.459	0.377	0.55	0.115	0.094	0.138	SUBCLONAL	1	TRUE	0	0.378326825063887	4		403	588	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685212	86685222	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TGTACCTGAAC	TGTACCTGAAC	-	novel	NA	P-0014465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	171	217	0	ENST00000274376.6:c.2929_2939del	p.Val977SerfsTer8	p.V977Sfs*8	ENST00000274376	NM_002890.2	976	aaTGTACCTGAACtt/aatt	24/25	0.374417197351721	4	FACETS	1	0.958	1	0.779	0.726	0.833	CLONAL	3	TRUE	0	0.378326825063887	4		217	400	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877996	151877996	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	178	276	0	ENST00000262189.6:c.6949C>G	p.Gln2317Glu	p.Q2317E	ENST00000262189	NM_170606.2	2317	Caa/Gaa	36/59	0.378326825063887	4	FACETS	1	0.982	1			1	CLONAL	2	TRUE	NA	0.378326825063887	4		276	551	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399960	139399960	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	260	678	1	ENST00000277541.6:c.4388G>T	p.Cys1463Phe	p.C1463F	ENST00000277541	NM_017617.3	1463	tGc/tTc	25/34	0.222854599733589	5	FACETS	1	0.987	1	0.794	0.746	0.844	INDETERMINATE	2	TRUE	2	0.378326825063887	5		679	904	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349946	70349946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	267	371	0	ENST00000374080.3:c.3929C>T	p.Pro1310Leu	p.P1310L	ENST00000374080		1310	cCa/cTa	28/45	0.187555136841581	2	FACETS	0.939	0.892	0.986			1	INDETERMINATE	3	TRUE	NA	0.378326825063887	2		371	501	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938434	76938434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	33	234	0	ENST00000373344.5:c.2314G>A	p.Gly772Arg	p.G772R	ENST00000373344	NM_000489.3	772	Ggg/Agg	9/35	0.187555136841581	2	FACETS	0.53	0.433	0.64			1	INDETERMINATE	1	TRUE	NA	0.378326825063887	2		234	329	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867540	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs11466445	NA	P-0014493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	12	24	0	ENST00000374994.4:c.76_78del	p.Ala26del	p.A26del	ENST00000374994	NM_004612.2	17	ctGGCg/ctg	1/9	0.486493832933143	2	FACETS	0.73	0.526	0.966	0.365	0.263	0.483	CLONAL	1	TRUE	0	0.567029258437998	2		24	58	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881414	37881414	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1131692237	NA	P-0014493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	373	574	0	ENST00000269571.5:c.2606T>G	p.Leu869Arg	p.L869R	ENST00000269571		869	cTg/cGg	21/27	0.482296295192889	3	FACETS	0.898	0.855	0.941	0.898	0.855	0.941	CLONAL	2	TRUE	1	0.567029258437998	3		574	940	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862105	68862106	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0014493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	257	365	0	ENST00000261769.5:c.2193_2194insG	p.Arg732AlafsTer16	p.R732Afs*16	ENST00000261769	NM_004360.3	731	-/G	14/16	0.486493832933143	2	FACETS	0.88	0.834	0.926	0.88	0.834	0.926	CLONAL	2	TRUE	0	0.567029258437998	2		365	515	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952006	178952006	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	301	379	0	ENST00000263967.3:c.3061T>A	p.Tyr1021Asn	p.Y1021N	ENST00000263967	NM_006218.2	1021	Tac/Aac	21/21	0.567029258437998	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.567029258437998	3		379	609	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178044	56178044	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	291	358	0	ENST00000399503.3:c.3018del	p.Gln1007ArgfsTer75	p.Q1007Rfs*75	ENST00000399503	NM_005921.1	1006	cTt/ct	14/20	0.567029258437998	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.567029258437998	3		358	598	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123040864	123040864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1489246570	NA	P-0014493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	485	763	0	ENST00000355640.3:c.1327C>T	p.Arg443Cys	p.R443C	ENST00000355640		443	Cgc/Tgc	7/7	0.567029258437998	4	FACETS	0.957	0.916	1	0.957	0.916	1	CLONAL	2	TRUE	2	0.567029258437998	4		763	1400	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0014558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	302	96	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.99	0.938	1	0.99	0.938	1	CLONAL	1	TRUE	1	0.846315389181572	2		96	721	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0014558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	529	621	0	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	0.846315389181572	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.846315389181572	1		621	717	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291056	15291056	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1302	586	711	0	ENST00000263388.2:c.3154G>C	p.Glu1052Gln	p.E1052Q	ENST00000263388	NM_000435.2	1052	Gag/Cag	20/33	0.659072127777076	3	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.846315389181572	3		711	1888	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292602	15292603	+	missense_variant	Missense_Mutation	DNP	CA	CA	TC	novel	NA	P-0014558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	432	582	2	ENST00000263388.2:c.2576_2577delinsGA	p.Leu859Arg	p.L859R	ENST00000263388	NM_000435.2	859	cTG/cGA	17/33	0.659072127777076	3	FACETS	0.909	0.865	0.954			1	CLONAL	1	TRUE	NA	0.846315389181572	3		584	1598	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864236	151864239	+	frameshift_variant	Frame_Shift_Del	DEL	CTAG	CTAG	-	novel	NA	P-0014558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	206	197	0	ENST00000262189.6:c.9742_9745del	p.Leu3248AsnfsTer13	p.L3248Nfs*13	ENST00000262189	NM_170606.2	3248	CTAGaa/aa	42/59	0.839670066509948	3	FACETS	1	0.969	1	0.534	0.498	0.571	CLONAL	1	TRUE	1	0.846315389181572	3		197	649	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900080	151900081	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	241	294	0	ENST00000262189.6:c.4030dup	p.Ile1344AsnfsTer11	p.I1344Nfs*11	ENST00000262189	NM_170606.2	1344	ata/aAta	26/59	0.839670066509948	3	FACETS	0.807	0.754	0.862	0.404	0.377	0.431	CLONAL	1	TRUE	1	0.846315389181572	3		294	1004	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931463	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622007	NA	P-0014566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	173	307	0	ENST00000374690.3:c.2105T>A	p.Leu702His	p.L702H	ENST00000374690	NM_000044.3	702	cTc/cAc	4/8	0.405323988506965	2	FACETS	0.762	0.701	0.827			1	SUBCLONAL	1	TRUE	NA	0.422157302441568	2		307	1075	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405566	70405566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760786464	NA	P-0014566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	237	489	1	ENST00000373644.4:c.3080C>T	p.Thr1027Ile	p.T1027I	ENST00000373644	NM_030625.2	1027	aCt/aTt	4/12	NA	2	FACETS	0.966	0.901	1			1	INDETERMINATE	1	TRUE	NA	0.422157302441568	2		490	1162	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888076	81888076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1353659689	NA	P-0014566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	167	376	0	ENST00000359376.3:c.221G>A	p.Arg74His	p.R74H	ENST00000359376	NM_002661.3	74	cGc/cAc	3/33	0.353365374792396	3	FACETS	0.941	0.864	1	0.471	0.432	0.511	CLONAL	1	TRUE	1	0.422157302441568	3		376	1018	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619130	37619130	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	274	484	0	ENST00000447079.4:c.807del	p.Ser270ArgfsTer68	p.S270Rfs*68	ENST00000447079	NM_015083.1	269	aCc/ac	1/14	NA	2	FACETS	1	0.963	1			1	INDETERMINATE	1	TRUE	NA	0.422157302441568	2		484	1252	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37671993	37671994	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0014566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	321	407	0	ENST00000447079.4:c.2782dup	p.Glu928GlyfsTer27	p.E928Gfs*27	ENST00000447079	NM_015083.1	926	-/G	9/14	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.422157302441568	2		407	1105	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969177	93969177	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	67	298	0	ENST00000369303.4:c.1819A>T	p.Thr607Ser	p.T607S	ENST00000369303	NM_004440.3	607	Acc/Tcc	10/17	1	2	FACETS	0.419	0.363	0.479	0.419	0.363	0.479	SUBCLONAL	1	TRUE	1	0.422157302441568	2		298	758	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061228	38061240	+	protein_altering_variant	In_Frame_Del	DEL	AACATGTTGCCGG	AACATGTTGCCGG	C	novel	NA	P-0014566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1568	222	533	0	ENST00000250448.2:c.749_761delinsG	p.Ser250_Phe254delinsCys	p.S250_F254delinsC	ENST00000250448	NM_004496.3	250	tCCGGCAACATGTTc/tGc	2/2	0.425718587034879	3	FACETS	0.712	0.66	0.766			1	SUBCLONAL	1	TRUE	NA	0.422157302441568	3		533	1790	SUCCESS
APC	324	MSKCC	GRCh37	5	112178000	112178000	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768922431	NA	P-0014570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	261	381	0	ENST00000257430.4:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000257430	NM_000038.5	2237	Cga/Tga	16/16	0.639373551376245	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.639373551376245	1		381	470	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982331	201982332	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0014570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	483	762	0	ENST00000359651.3:c.715dup	p.Asp239GlyfsTer62	p.D239Gfs*62	ENST00000359651		237	aag/aaGg	6/8	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.639373551376245	2		762	1250	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941711	48941711	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587778844	NA	P-0014570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	100	284	0	ENST00000267163.4:c.1024del	p.Thr342LeufsTer7	p.T342Lfs*7	ENST00000267163	NM_000321.2	341	Aaa/aa	10/27	0.639373551376245	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.639373551376245	1		284	188	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68301804	68301804	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	49	326	0	ENST00000487270.1:c.206G>A	p.Gly69Glu	p.G69E	ENST00000487270	NM_133509.3	69	gGg/gAg	4/11	0.639373551376245	1	FACETS	0.294	0.249	0.342	0.294	0.249	0.342	SUBCLONAL	1	TRUE	0	0.639373551376245	1		326	355	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993811	72993811	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs771934671	NA	P-0014570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	44	363	0	ENST00000268489.5:c.234G>T	p.Glu78Asp	p.E78D	ENST00000268489	NM_006885.3	78	gaG/gaT	2/10	0.639373551376245	1	FACETS	0.181	0.151	0.214	0.181	0.151	0.214	SUBCLONAL	1	TRUE	0	0.639373551376245	1		363	518	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729411	41729411	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	54	464	0	ENST00000242208.4:c.1118T>A	p.Ile373Asn	p.I373N	ENST00000242208	NM_002192.2	373	aTc/aAc	3/3	0.630487181511205	2	FACETS	0.187	0.159	0.218	0.094	0.079	0.109	SUBCLONAL	1	TRUE	0	0.639373551376245	2		464	902	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717777	89717777	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0014571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	140	244	0	ENST00000371953.3:c.801+1G>T		p.X267_splice	ENST00000371953	NM_000314.4	267			0.244050823043355	1	FACETS	1	0.978	1	1	0.978	1	INDETERMINATE	1	TRUE	0	0.445044168049215	1		244	415	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371708	225371708	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	346	481	0	ENST00000264414.4:c.896T>G	p.Met299Arg	p.M299R	ENST00000264414	NM_003590.4	299	aTg/aGg	7/16	0.445044168049215	3	FACETS	0.861	0.816	0.907	0.861	0.816	0.907	CLONAL	2	TRUE	1	0.445044168049215	3		481	1104	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570325	87570325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	331	521	0	ENST00000277120.3:c.2065G>A	p.Val689Met	p.V689M	ENST00000277120		689	Gtg/Atg	17/19	0.21809809490162	5	FACETS	0.891	0.841	0.942	0.594	0.56	0.628	INDETERMINATE	2	TRUE	2	0.445044168049215	5		521	1392	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427878	49427879	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0014571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	191	517	0	ENST00000301067.7:c.10711dup	p.Gln3571ProfsTer20	p.Q3571Pfs*20	ENST00000301067	NM_003482.3	3571	cag/cCag	38/54	0.445044168049215	3	FACETS	0.863	0.796	0.932	0.431	0.398	0.466	CLONAL	1	TRUE	1	0.445044168049215	3		517	1216	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43700219	43700219	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	220	475	0	ENST00000382044.4:c.5668del	p.Leu1890TrpfsTer9	p.L1890Wfs*9	ENST00000382044	NM_001141980.1	1890	Ctg/tg	27/28	0.445044168049215	1	FACETS	0.983	0.917	1	0.983	0.917	1	CLONAL	1	TRUE	0	0.445044168049215	1		475	782	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	284	374	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.881	0.832	0.931	0.881	0.832	0.931	CLONAL	1	TRUE	1	0.816821532947546	2		374	789	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0014648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	611	926	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.816821532947546	1	FACETS	0.969	0.942	0.996	0.969	0.942	0.996	CLONAL	1	TRUE	0	0.816821532947546	1		926	913	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955399	48955399	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	161	316	0	ENST00000267163.4:c.1515del	p.Asp507IlefsTer12	p.D507Ifs*12	ENST00000267163	NM_000321.2	505	aaT/aa	17/27	0.816821532947546	1	FACETS	0.904	0.851	0.955	0.904	0.851	0.955	CLONAL	1	TRUE	0	0.816821532947546	1		316	258	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821973	72821973	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	263	372	0	ENST00000268489.5:c.10202C>A	p.Thr3401Asn	p.T3401N	ENST00000268489	NM_006885.3	3401	aCc/aAc	10/10	1	2	FACETS	0.971	0.916	1	0.971	0.916	1	CLONAL	1	TRUE	1	0.816821532947546	2		372	663	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030058	36030058	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	419	742	0	ENST00000358208.4:c.1093C>T	p.Gln365Ter	p.Q365*	ENST00000358208		365	Cag/Tag	9/12	1	2	FACETS	0.934	0.891	0.976	0.934	0.891	0.976	CLONAL	1	TRUE	1	0.816821532947546	2		742	1099	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568557	41568557	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	505	805	0	ENST00000263253.7:c.4507T>A	p.Tyr1503Asn	p.Y1503N	ENST00000263253	NM_001429.3	1503	Tat/Aat	28/31	1	2	FACETS	0.983	0.943	1	0.983	0.943	1	CLONAL	1	TRUE	1	0.816821532947546	2		805	1258	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249012	55249013	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGTTA	novel	NA	P-0014648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	274	626	0	ENST00000275493.2:c.2310_2311insGGGTTA	p.Asp770_Asn771insGlyLeu	p.D770_N771insGL	ENST00000275493	NM_005228.3	770	-/GGGTTA	20/28	1	2	FACETS	0.738	0.694	0.783	0.738	0.694	0.783	SUBCLONAL	1	TRUE	1	0.816821532947546	2		626	909	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	96	474	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	0.16	2		474	838	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692791	89692791	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	65	473	0	ENST00000371953.3:c.275A>T	p.Asp92Val	p.D92V	ENST00000371953	NM_000314.4	92	gAc/gTc	5/9	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.16	2		473	771	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0014650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	102	734	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.16	2		734	1097	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0014650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	37	347	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	0.942	0.776	1	0.942	0.776	1	CLONAL	1	TRUE	1	0.16	2		347	491	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660469	67660469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	62	516	2	ENST00000264010.4:c.1369C>T	p.Arg457Ter	p.R457*	ENST00000264010	NM_006565.3	457	Cga/Tga	8/12	1	2	FACETS	0.858	0.739	0.988	0.858	0.739	0.988	CLONAL	1	TRUE	1	0.16	2		518	903	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101005	27101005	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1171	86	765	0	ENST00000324856.7:c.4288del	p.Gln1430SerfsTer51	p.Q1430Sfs*51	ENST00000324856	NM_006015.4	1429	aaC/aa	18/20	1	2	FACETS	0.855	0.754	0.964	0.855	0.754	0.964	CLONAL	1	TRUE	1	0.16	2		765	1257	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105904	27105905	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0014650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	83	617	0	ENST00000324856.7:c.5515_5516del	p.Ser1839TrpfsTer14	p.S1839Wfs*14	ENST00000324856	NM_006015.4	1839	AGt/t	20/20	1	2	FACETS	0.993	0.874	1	0.993	0.874	1	CLONAL	1	TRUE	1	0.16	2		617	1045	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40476777	40476777	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1287	91	758	1	ENST00000264657.5:c.1552C>T	p.Arg518Ter	p.R518*	ENST00000264657	NM_139276.2	518	Cga/Tga	17/24	1	2	FACETS	0.825	0.73	0.928	0.825	0.73	0.928	CLONAL	1	TRUE	1	0.16	2		759	1378	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39573265	39573265	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773500037	NA	P-0014650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	47	474	0	ENST00000262039.4:c.746G>A	p.Ser249Asn	p.S249N	ENST00000262039	NM_002647.2	249	aGt/aAt	7/25	1	2	FACETS	0.797	0.671	0.937	0.797	0.671	0.937	CLONAL	1	TRUE	1	0.16	2		474	737	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214666	133214667	+	missense_variant	Missense_Mutation	DNP	AT	AT	CC	novel	NA	P-0014655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	256	550	0	ENST00000320574.5:c.5611_5612delinsGG	p.Ile1871Gly	p.I1871G	ENST00000320574	NM_006231.2	1871	ATc/GGc	41/49	1	2	FACETS	0.808	0.757	0.861	0.808	0.757	0.861	CLONAL	1	TRUE	1	0.623463713106411	2		550	1016	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726560	41726561	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0014655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	540	594	0	ENST00000301178.4:c.108dup	p.Phe37LeufsTer54	p.F37Lfs*54	ENST00000301178	NM_021913.4	35	-/C	2/20	0.333048514518842	2	FACETS	1	0.997	1	0.732	0.704	0.76	INDETERMINATE	1	TRUE	0	0.623463713106411	2		594	1183	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143237	24143237	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	408	760	0	ENST00000263121.7:c.469G>C	p.Gly157Arg	p.G157R	ENST00000263121	NM_003073.3	157	Ggc/Cgc	4/9	0.236995102638587	1	FACETS	0.744	0.708	0.78	0.744	0.708	0.78	INDETERMINATE	1	TRUE	0	0.623463713106411	1		760	1211	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960102	134960111	+	frameshift_variant	Frame_Shift_Del	DEL	TTGGAGAGAG	TTGGAGAGAG	-	novel	NA	P-0014655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	80	684	0	ENST00000398015.3:c.2459_2468del	p.Phe820TyrfsTer56	p.F820Yfs*56	ENST00000398015	NM_004441.4	820	tTTGGAGAGAGa/ta	13/16	1	2	FACETS	0.214	0.187	0.243	0.214	0.187	0.243	SUBCLONAL	1	TRUE	1	0.623463713106411	2		684	1200	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38314891	38314891	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	428	364	0	ENST00000425967.3:c.173C>G	p.Pro58Arg	p.P58R	ENST00000425967	NM_001174067.1	58	cCg/cGg	3/19	0.42339309432991	3	FACETS	0.961	0.92	1	0.961	0.92	1	CLONAL	2	TRUE	1	0.623463713106411	3		364	937	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882100	36882100	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1214797180	NA	P-0014655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	148	653	0	ENST00000358127.4:c.913C>T	p.Arg305Cys	p.R305C	ENST00000358127	NM_001280556.1	305	Cgt/Tgt	8/10	1	2	FACETS	0.471	0.43	0.515	0.471	0.43	0.515	SUBCLONAL	1	TRUE	1	0.623463713106411	2		653	1007	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611834	100611843	+	frameshift_variant	Frame_Shift_Del	DEL	GATGGCCACG	GATGGCCACG	-	novel	NA	P-0014655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	123	582	0	ENST00000308731.7:c.1278_1287del	p.Asp426GlufsTer3	p.D426Efs*3	ENST00000308731	NM_000061.2	426	gaCGTGGCCATC/ga	14/19	0.623463713106411	1	FACETS	0.311	0.281	0.343	0.311	0.281	0.343	SUBCLONAL	1	TRUE	0	0.623463713106411	1		582	873	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0014680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	199	673	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	0.41	2		673	825	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0014680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	128	340	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.94	0.854	1	0.94	0.854	1	CLONAL	1	TRUE	1	0.41	2		340	664	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0014680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	92	347	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	0.863	0.769	0.962	0.863	0.769	0.962	CLONAL	1	TRUE	1	0.41	2		347	520	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0014680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	121	427	4	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.41	2		431	563	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533905	63533905	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	129	454	0	ENST00000307078.5:c.1249del	p.Ala417ArgfsTer41	p.A417Rfs*41	ENST00000307078	NM_004655.3	417	Gcg/cg	6/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.41	2		454	576	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0014680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	163	581	4	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	0.836	0.767	0.908	0.836	0.767	0.908	CLONAL	1	TRUE	1	0.41	2		585	951	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586101	29586101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876658127	NA	P-0014680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	34	471	0	ENST00000356175.3:c.4321C>T	p.Arg1441Trp	p.R1441W	ENST00000356175	NM_000267.3	1441	Cgg/Tgg	32/57	1	2	FACETS	0.268	0.218	0.325	0.268	0.218	0.325	SUBCLONAL	1	TRUE	1	0.41	2		471	618	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059230	27059230	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs267598525	NA	P-0014680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	153	574	0	ENST00000324856.7:c.1867G>T	p.Gly623Ter	p.G623*	ENST00000324856	NM_006015.4	623	Gga/Tga	4/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.41	2		574	698	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462983	120462983	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	52	457	0	ENST00000256646.2:c.5348C>T	p.Pro1783Leu	p.P1783L	ENST00000256646	NM_024408.3	1783	cCc/cTc	30/34	1	2	FACETS	0.443	0.377	0.516	0.443	0.377	0.516	SUBCLONAL	1	TRUE	1	0.41	2		457	572	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653835	89653836	+	inframe_insertion	In_Frame_Ins	INS	-	-	TATACAGGA	novel	NA	P-0014680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	100	520	0	ENST00000371953.3:c.134_142dup	p.Arg47_Asn48insIleTyrArg	p.R47_N48insIYR	ENST00000371953	NM_000314.4	45	gta/gTATACAGGAta	2/9	1	2	FACETS	0.874	0.783	0.971	0.874	0.783	0.971	CLONAL	1	TRUE	1	0.41	2		520	558	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109969	115109969	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	81	848	0	ENST00000257566.3:c.1909C>T	p.Arg637Trp	p.R637W	ENST00000257566	NM_016569.3	637	Cgg/Tgg	8/8	1	2	FACETS	0.333	0.292	0.378	0.333	0.292	0.378	SUBCLONAL	1	TRUE	1	0.41	2		848	1185	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28903769	28903769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	39	533	0	ENST00000282397.4:c.2690C>T	p.Ala897Val	p.A897V	ENST00000282397	NM_002019.4	897	gCc/gTc	19/30	1	2	FACETS	0.271	0.223	0.324	0.271	0.223	0.324	SUBCLONAL	1	TRUE	1	0.41	2		533	703	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347830	89347830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776489753	NA	P-0014680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	94	454	0	ENST00000301030.4:c.5120C>T	p.Thr1707Met	p.T1707M	ENST00000301030	NM_001256183.1	1707	aCg/aTg	9/13	1	2	FACETS	0.848	0.756	0.944	0.848	0.756	0.944	CLONAL	1	TRUE	1	0.41	2		454	541	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099245	157099245	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	146	555	4	ENST00000346085.5:c.182C>T	p.Thr61Met	p.T61M	ENST00000346085	NM_020732.3	61	aCg/aTg	1/20	1	2	FACETS	0.89	0.813	0.971	0.89	0.813	0.971	CLONAL	1	TRUE	1	0.41	2		559	800	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002647	37002647	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1041485987	NA	P-0014680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	146	427	0	ENST00000358127.4:c.602A>G	p.Glu201Gly	p.E201G	ENST00000358127	NM_001280556.1	201	gAa/gGa	5/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.41	2		427	631	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0014702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1223	509	753	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.336513748094855	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	FALSE	1	0.336513748094855	3		753	1732	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1568	215	347	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.336513748094855	5	FACETS	1	0.967	1	0.359	0.332	0.388	CLONAL	1	FALSE	2	0.336513748094855	5		347	1783	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	353	574	0	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	0.336513748094855	3	FACETS	0.984	0.931	1	0.984	0.931	1	CLONAL	2	FALSE	1	0.336513748094855	3		574	1246	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748502	162748502	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1218815846	NA	P-0014702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	11	340	1	ENST00000367921.3:c.2416C>T	p.Arg806Ter	p.R806*	ENST00000367921	NM_006182.2	806	Cga/Tga	17/18	0.336513748094855	6	FACETS	0.679	0.47	0.937	0.136	0.094	0.188	SUBCLONAL	1	FALSE	1	0.336513748094855	6		341	161	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107046	27107047	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0014702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	151	390	0	ENST00000324856.7:c.6659dup	p.Asn2220LysfsTer5	p.N2220Kfs*5	ENST00000324856	NM_006015.4	2219	-/A	20/20	1	2	FACETS	0.947	0.865	1	0.947	0.865	1	CLONAL	1	FALSE	1	0.336513748094855	2		390	948	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244824	46244824	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0014702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	132	751	0	ENST00000334344.6:c.2918C>G	p.Ser973Ter	p.S973*	ENST00000334344	NM_152641.2	973	tCa/tGa	15/21	0.336513748094855	3	FACETS	0.744	0.673	0.819	0.372	0.336	0.41	SUBCLONAL	1	FALSE	1	0.336513748094855	3		751	1232	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246668	46246668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	28	168	0	ENST00000334344.6:c.4762G>A	p.Val1588Met	p.V1588M	ENST00000334344	NM_152641.2	1588	Gtg/Atg	15/21	0.336513748094855	3	FACETS	0.817	0.665	0.983	0.817	0.665	0.983	CLONAL	2	FALSE	1	0.336513748094855	3		168	119	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118782	115118783	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0014702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	92	550	0	ENST00000257566.3:c.558dup	p.His187SerfsTer40	p.H187Sfs*40	ENST00000257566	NM_016569.3	186	-/T	2/8	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.336513748094855	2		550	491	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99451941	99451941	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	132	436	0	ENST00000268035.6:c.1275C>G	p.Asn425Lys	p.N425K	ENST00000268035	NM_000875.3	425	aaC/aaG	6/21	NA	2	FACETS	0.859	0.779	0.943			1	INDETERMINATE	1	FALSE	NA	0.336513748094855	2		436	913	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877455	89877455	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0014702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1664	92	785	0	ENST00000389301.3:c.308C>G	p.Ser103Ter	p.S103*	ENST00000389301	NM_000135.2	103	tCa/tGa	4/43	0.336513748094855	3	FACETS	0.364	0.321	0.409	0.182	0.16	0.205	SUBCLONAL	1	FALSE	1	0.336513748094855	3		785	1756	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628392	187628392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	51	693	1	ENST00000441802.2:c.2590G>A	p.Asp864Asn	p.D864N	ENST00000441802	NM_005245.3	864	Gac/Aac	2/27	0.336513748094855	5	FACETS	0.896	0.762	1	0.224	0.19	0.261	CLONAL	1	FALSE	1	0.336513748094855	5		694	509	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178310	56178310	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	51	369	0	ENST00000399503.3:c.3285del	p.Phe1095LeufsTer22	p.F1095Lfs*22	ENST00000399503	NM_005921.1	1095	Ttt/tt	14/20	0.336513748094855	0	FACETS	0.852	0.747	0.959			1	CLONAL	2	FALSE	0	0.336513748094855	0		369	118	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976741	2976741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564294642	NA	P-0014702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1951	290	714	0	ENST00000396946.4:c.1271G>A	p.Arg424Gln	p.R424Q	ENST00000396946	NM_032415.4	424	cGg/cAg	9/25	0.336513748094855	4	FACETS	1	0.957	1	0.514	0.481	0.548	CLONAL	1	FALSE	2	0.336513748094855	4		714	2241	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441589	6441589	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	68	231	0	ENST00000356142.4:c.436G>C	p.Glu146Gln	p.E146Q	ENST00000356142	NM_018890.3	146	Gag/Cag	6/7	0.336513748094855	4	FACETS	1	0.918	1	0.536	0.467	0.61	CLONAL	1	FALSE	2	0.336513748094855	4		231	504	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481390	140481390	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	37	377	0	ENST00000288602.6:c.1418A>T	p.Lys473Met	p.K473M	ENST00000288602	NM_004333.4	473	aAg/aTg	11/18	0.336513748094855	1	FACETS	0.5	0.413	0.597	0.5	0.413	0.597	SUBCLONAL	1	FALSE	0	0.336513748094855	1		377	366	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18439842	18439843	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	50	411	0	ENST00000266497.5:c.745dup	p.Cys249LeufsTer15	p.C249Lfs*15	ENST00000266497		247	tct/tcTt	2/31	1	2	FACETS	0.823	0.708	0.945	1	0.971	1	CLONAL	2	TRUE	1	0.316496138341538	2		411	192	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441322	52441322	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	244	433	0	ENST00000460680.1:c.448del	p.Arg150AlafsTer37	p.R150Afs*37	ENST00000460680	NM_004656.3	150	Cgc/gc	7/17	0.316496138341538	2	FACETS	0.899	0.853	0.943	1	0.995	1	CLONAL	4	TRUE	0	0.316496138341538	2		433	429	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	88	588	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.213440066983915	1	FACETS	0.543	0.48	0.61	0.543	0.48	0.61	SUBCLONAL	1	TRUE	0	0.32	1		589	851	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0014738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	147	674	1	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	1	2	FACETS	0.855	0.779	0.934	0.855	0.779	0.934	CLONAL	1	TRUE	1	0.32	2		675	1075	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591966	48591967	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0014738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	35	216	0	ENST00000342988.3:c.1130dup	p.Arg378GlufsTer15	p.R378Efs*15	ENST00000342988	NM_005359.5	377	gag/gAag	9/12	1	2	FACETS	0.547	0.448	0.657	0.547	0.448	0.657	SUBCLONAL	1	TRUE	1	0.32	2		216	400	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916933	178916933	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	267	470	0	ENST00000263967.3:c.320A>T	p.Asn107Ile	p.N107I	ENST00000263967	NM_006218.2	107	aAc/aTc	2/21	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.546185320775564	2		470	960	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844247	68844247	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	G	rs1555515469	NA	P-0014785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	241	474	0	ENST00000261769.5:c.832+3A>G		p.X278_splice	ENST00000261769	NM_004360.3	278			0.546185320775564	1	FACETS	0.991	0.932	1	0.991	0.932	1	CLONAL	1	TRUE	0	0.546185320775564	1		474	647	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037933	49037934	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	272	501	0	ENST00000267163.4:c.2174dup	p.Thr726AsnfsTer25	p.T726Nfs*25	ENST00000267163	NM_000321.2	725	gta/gTta	21/27	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.546185320775564	2		501	993	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089929	16089940	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	GCTGTTGCTGCA	GCTGTTGCTGCA	-	novel	NA	P-0014785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	211	433	1	ENST00000268712.3:c.170_181del	p.Leu57_Gln61delinsTer	p.L57_Q61delins*	ENST00000268712	NM_006311.3	57	tTGCAGCAACAGCag/tag	3/46	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.546185320775564	NA		434	592	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0014814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	649	384	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.338436280414534	3	FACETS	1	0.995	1	0.774	0.749	0.799	INDETERMINATE	2	TRUE	0	0.599176735867317	3		384	1212	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111499	8111500	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0014814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	200	643	0	ENST00000346208.3:c.987dup	p.Arg330GlufsTer22	p.R330Efs*22	ENST00000346208		329	agg/aGgg	5/6	0.306700665821822	2	FACETS	0.489	0.452	0.528	0.245	0.226	0.264	INDETERMINATE	1	TRUE	0	0.599176735867317	2		643	1365	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129169	64129169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746466314	NA	P-0014814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	231	616	1	ENST00000334205.4:c.707C>T	p.Ser236Leu	p.S236L	ENST00000334205	NM_003942.2	236	tCg/tTg	7/17	0.306700665821822	2	FACETS	0.591	0.55	0.634	0.296	0.275	0.317	INDETERMINATE	1	TRUE	0	0.599176735867317	2		617	1304	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199339	16199339	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	123	319	0	ENST00000375759.3:c.112C>T	p.Leu38Phe	p.L38F	ENST00000375759	NM_015001.2	38	Ctt/Ttt	2/15	0.325537346209362	1	FACETS	0.491	0.445	0.539	0.491	0.445	0.539	INDETERMINATE	1	TRUE	0	0.599176735867317	1		319	586	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483247	120483263	+	frameshift_variant	Frame_Shift_Del	DEL	TCCCTCATTCAGGCATG	TCCCTCATTCAGGCATG	-	novel	NA	P-0014814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	262	429	0	ENST00000256646.2:c.3098_3114del	p.Pro1033HisfsTer4	p.P1033Hfs*4	ENST00000256646	NM_024408.3	1033	cCATGCCTGAATGAGGGA/c	19/34	0.325537346209362	1	FACETS	0.767	0.721	0.813	0.767	0.721	0.813	INDETERMINATE	1	TRUE	0	0.599176735867317	1		429	799	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961416	1961416	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	337	571	0	ENST00000382891.5:c.3204C>G	p.Ile1068Met	p.I1068M	ENST00000382891	NM_133335.3	1068	atC/atG	17/22	1	2	FACETS	0.94	0.889	0.992	0.94	0.889	0.992	CLONAL	1	TRUE	1	0.599176735867317	2		571	1197	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630152	187630152	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	203	519	0	ENST00000441802.2:c.830C>G	p.Thr277Arg	p.T277R	ENST00000441802	NM_005245.3	277	aCa/aGa	2/27	1	2	FACETS	0.627	0.581	0.675	0.627	0.581	0.675	SUBCLONAL	1	TRUE	1	0.599176735867317	2		519	1081	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0014823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	200	356	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.277167545427214	2	FACETS	1	0.991	1	0.744	0.692	0.799	CLONAL	1	TRUE	0	0.355416647035334	2		356	756	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577086	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	275	574	0	ENST00000269305.4:c.852dup	p.Glu285ArgfsTer21	p.E285Rfs*21	ENST00000269305	NM_001126112.2	284	-/A	8/11	0.280146890452257	2	FACETS	1	0.993	1	0.73	0.685	0.776	CLONAL	1	TRUE	0	0.355416647035334	2		574	1060	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	290	474	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.489644165599996	2	FACETS	0.915	0.868	0.962	0.915	0.868	0.962	CLONAL	2	TRUE	0	0.499838825574827	2		474	634	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0014827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	168	298	0	ENST00000262160.6:c.1391C>G	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tGa	11/11	0.472389306258368	2	FACETS	0.787	0.731	0.844	0.787	0.731	0.844	SUBCLONAL	2	TRUE	0	0.499838825574827	2		298	427	SUCCESS
APC	324	MSKCC	GRCh37	5	112154942	112154942	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779780	NA	P-0014827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	235	527	1	ENST00000257430.4:c.1213C>T	p.Arg405Ter	p.R405*	ENST00000257430	NM_000038.5	405	Cga/Tga	10/16	0.328457650716582	3	FACETS	1	0.958	1	0.519	0.483	0.555	CLONAL	1	TRUE	1	0.499838825574827	3		528	1133	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0014827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	121	320	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	0.328457650716582	3	FACETS	0.855	0.773	0.941	0.427	0.386	0.471	CLONAL	1	TRUE	1	0.499838825574827	3		320	708	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912125	114912125	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	181	379	0	ENST00000543371.1:c.1195T>A	p.Tyr399Asn	p.Y399N	ENST00000543371	NM_001198531.1	399	Tac/Aac	11/14	1	2	FACETS	0.98	0.906	1	0.98	0.906	1	CLONAL	1	TRUE	1	0.499838825574827	2		379	739	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151830	108151830	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876659067	NA	P-0014827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	135	382	0	ENST00000278616.4:c.3511C>T	p.Gln1171Ter	p.Q1171*	ENST00000278616	NM_000051.3	1171	Cag/Tag	24/63	1	2	FACETS	0.809	0.737	0.884	0.809	0.737	0.884	CLONAL	1	TRUE	1	0.499838825574827	2		382	668	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205784	108205784	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	94	281	0	ENST00000278616.4:c.8099A>C	p.Lys2700Thr	p.K2700T	ENST00000278616	NM_000051.3	2700	aAa/aCa	55/63	1	2	FACETS	0.771	0.689	0.858	0.771	0.689	0.858	SUBCLONAL	1	TRUE	1	0.499838825574827	2		281	488	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457652	67457653	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GACT	novel	NA	P-0014827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	422	650	0	ENST00000327367.4:c.463_466dup	p.Tyr156Ter	p.Y156*	ENST00000327367	NM_005902.3	154	-/GACT	3/9	0.472389306258368	2	FACETS	0.868	0.83	0.906	0.868	0.83	0.906	CLONAL	2	TRUE	0	0.499838825574827	2		650	973	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434685	99434685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs543792941	NA	P-0014827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	426	464	0	ENST00000268035.6:c.772G>A	p.Gly258Ser	p.G258S	ENST00000268035	NM_000875.3	258	Ggt/Agt	3/21	0.472389306258368	2	FACETS	0.94	0.9	0.979	0.94	0.9	0.979	CLONAL	2	TRUE	0	0.499838825574827	2		464	907	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78704418	78704418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	143	367	1	ENST00000306801.3:c.566C>T	p.Pro189Leu	p.P189L	ENST00000306801	NM_020761.2	189	cCg/cTg	5/34	1	2	FACETS	0.938	0.858	1	0.938	0.858	1	CLONAL	1	TRUE	1	0.499838825574827	2		368	610	SUCCESS
APC	324	MSKCC	GRCh37	5	112174061	112174061	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0014827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	148	274	0	ENST00000257430.4:c.2770A>T	p.Arg924Ter	p.R924*	ENST00000257430	NM_000038.5	924	Aga/Tga	16/16	0.328457650716582	3	FACETS	1	0.987	1	0.717	0.659	0.777	CLONAL	1	TRUE	1	0.499838825574827	3		274	516	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242827	98242827	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	198	360	0	ENST00000331920.6:c.790T>C	p.Phe264Leu	p.F264L	ENST00000331920	NM_000264.3	264	Ttc/Ctc	6/24	0.328457650716582	3	FACETS	1	0.984	1	0.601	0.557	0.646	CLONAL	1	TRUE	1	0.499838825574827	3		360	824	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0014842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	52	280	1	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	1	0.946	1	1	0.979	1	CLONAL	2	TRUE	1	0.12	2		281	349	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097760	8097760	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	55	732	0	ENST00000346208.3:c.142G>A	p.Asp48Asn	p.D48N	ENST00000346208		48	Gat/Aat	2/6	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.12	2		732	717	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202314	133202314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	40	614	0	ENST00000320574.5:c.6574del	p.Ala2192ArgfsTer10	p.A2192Rfs*10	ENST00000320574	NM_006231.2	2192	Gcg/cg	47/49	1	2	FACETS	0.968	0.802	1	0.968	0.802	1	CLONAL	1	TRUE	1	0.12	2		614	689	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835732	68835733	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0014842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	59	661	0	ENST00000261769.5:c.326dup	p.Phe110ValfsTer58	p.F110Vfs*58	ENST00000261769	NM_004360.3	108	aga/agAa	3/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.12	2		661	692	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206838	36206838	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	87	447	0	ENST00000300305.3:c.674del	p.Leu225ProfsTer12	p.L225Pfs*12	ENST00000300305		225	cTc/cc	6/8	0.179972276734468	3	FACETS	0.907	0.804	1	1	0.974	1	CLONAL	3	TRUE	1	0.12	3		447	565	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125381	47125382	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0014842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	26	382	0	ENST00000409792.3:c.5888_5889del	p.Lys1963ArgfsTer12	p.K1963Rfs*12	ENST00000409792	NM_014159.6	1963	aAA/a	12/21	1	2	FACETS	0.856	0.677	1	0.856	0.677	1	CLONAL	1	TRUE	1	0.12	2		382	506	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0014866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	128	707	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.518	0.469	0.568	0.518	0.469	0.568	SUBCLONAL	1	TRUE	1	0.681206721661687	2		707	726	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0014866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	125	595	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.57	0.517	0.626	0.57	0.517	0.626	SUBCLONAL	1	TRUE	1	0.681206721661687	2		595	644	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469672	NA	P-0014866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	17	858	0	ENST00000374080.3:c.131G>A	p.Gly44Asp	p.G44D	ENST00000374080		44	gGt/gAt	2/45	1	2	FACETS	0.059	0.044	0.078	0.059	0.044	0.078	SUBCLONAL	1	TRUE	1	0.681206721661687	2		858	839	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100660	8100660	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	186	966	0	ENST00000346208.3:c.634T>G	p.Ser212Ala	p.S212A	ENST00000346208		212	Tcc/Gcc	3/6	1	2	FACETS	0.556	0.513	0.6	0.556	0.513	0.6	SUBCLONAL	1	TRUE	1	0.681206721661687	2		966	983	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856094	68856095	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGTGCCAACTGGACCATTC	novel	NA	P-0014866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	106	821	0	ENST00000261769.5:c.1906_1924dup	p.Tyr642CysfsTer27	p.Y642Cfs*27	ENST00000261769	NM_004360.3	634	-/AGTGCCAACTGGACCATTC	12/16	0.410385646339023	1	FACETS	0.302	0.271	0.335	0.302	0.271	0.335	SUBCLONAL	1	TRUE	0	0.681206721661687	1		821	679	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984681	11984684	+	frameshift_variant	Frame_Shift_Del	DEL	TGAG	TGAG	-	novel	NA	P-0014866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	29	504	1	ENST00000353533.5:c.227_230del	p.Leu76GlnfsTer11	p.L76Qfs*11	ENST00000353533	NM_003010.3	76	cTGAGa/ca	3/11	0.374610620248359	1	FACETS	0.159	0.127	0.194	0.159	0.127	0.194	INDETERMINATE	1	TRUE	0	0.681206721661687	1		505	354	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183253	56183253	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	134	620	0	ENST00000399503.3:c.4163A>G	p.Asp1388Gly	p.D1388G	ENST00000399503	NM_005921.1	1388	gAt/gGt	18/20	1	2	FACETS	0.535	0.487	0.586	0.535	0.487	0.586	SUBCLONAL	1	TRUE	1	0.681206721661687	2		620	735	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114237	115114239	+	frameshift_variant	Frame_Shift_Ins	INS	TCA	TCA	CCAT	novel	NA	P-0014866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	130	806	0	ENST00000257566.3:c.978_980delinsATGG	p.Asp326GlufsTer12	p.D326Efs*12	ENST00000257566	NM_016569.3	326	gaTGAa/gaATGGa	6/8	1	2	FACETS	0.488	0.443	0.536	0.488	0.443	0.536	SUBCLONAL	1	TRUE	1	0.681206721661687	2		806	782	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0014899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	442	208	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.359638660394744	4	FACETS	1	0.99	1			1	CLONAL	3	FALSE	NA	0.358855029968874	4		208	1008	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0014899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	468	703	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.359638660394744	3	FACETS	0.939	0.9	0.978			1	CLONAL	3	FALSE	NA	0.358855029968874	3		704	1092	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052636	42052636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1054243525	NA	P-0014899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	323	523	1	ENST00000219905.7:c.7307G>A	p.Arg2436His	p.R2436H	ENST00000219905	NM_001164273.1	2436	cGt/cAt	20/24	0.359638660394744	4	FACETS	1	0.988	1			1	CLONAL	2	FALSE	NA	0.358855029968874	4		524	1061	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376446	118376446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	281	550	0	ENST00000534358.1:c.9839C>T	p.Ser3280Leu	p.S3280L	ENST00000534358	NM_005933.3	3280	tCa/tTa	27/36	0.358855029968874	5	FACETS	1	0.987	1			1	CLONAL	2	FALSE	NA	0.358855029968874	5		550	1024	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041097	42041098	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0014899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	277	637	0	ENST00000219905.7:c.5476_5477dup	p.Leu1826PhefsTer13	p.L1826Ffs*13	ENST00000219905	NM_001164273.1	1825	-/TT	16/24	0.359638660394744	4	FACETS	0.853	0.801	0.908			1	CLONAL	2	FALSE	NA	0.358855029968874	4		637	1229	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008476	70008476	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057517966	NA	P-0014899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	92	533	0	ENST00000394351.3:c.763C>T	p.Arg255Ter	p.R255*	ENST00000394351	NM_000248.3	255	Cga/Tga	8/9	NA	2	FACETS	0.678	0.602	0.759			1	INDETERMINATE	1	FALSE	NA	0.358855029968874	2		533	756	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0014907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	335	461	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.649267137874325	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.649267137874325	1		461	595	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252852	36252853	+	splice_donor_variant	Splice_Site	INS	-	-	CCTCTT	novel	NA	P-0014907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	124	343	0	ENST00000300305.3:c.504_508+1dup		p.X168_splice	ENST00000300305		168			0.338796980389278	1	FACETS	0.419	0.38	0.46	0.419	0.38	0.46	INDETERMINATE	1	TRUE	0	0.649267137874325	1		343	616	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149036	61149036	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	111	399	1	ENST00000295025.8:c.1226C>T	p.Ser409Phe	p.S409F	ENST00000295025	NM_002908.2	409	tCt/tTt	11/11	0.273300349440015	3	FACETS	0.619	0.556	0.685	0.206	0.185	0.229	INDETERMINATE	1	TRUE	0	0.649267137874325	3		400	732	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288194	33288194	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs375524506	NA	P-0014907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	90	424	0	ENST00000374542.5:c.1214C>G	p.Ser405Cys	p.S405C	ENST00000374542	NM_001141970.1	405	tCt/tGt	4/8	1	2	FACETS	0.374	0.332	0.42	0.374	0.332	0.42	SUBCLONAL	1	TRUE	1	0.649267137874325	2		424	741	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0014907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	134	595	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			0.299286526822638	0	FACETS	0.255	0.232	0.278			1	INDETERMINATE	1	TRUE	0	0.649267137874325	0		595	568	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458042	120458042	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	101	477	0	ENST00000256646.2:c.7303G>C	p.Asp2435His	p.D2435H	ENST00000256646	NM_024408.3	2435	Gac/Cac	34/34	0.35288078176512	1	FACETS	0.369	0.33	0.409	0.369	0.33	0.409	INDETERMINATE	1	TRUE	0	0.649267137874325	1		477	570	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206661320	206661320	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	149	636	0	ENST00000367120.3:c.1686G>A	p.Met562Ile	p.M562I	ENST00000367120	NM_014002.3	562	atG/atA	16/22	0.601274578962894	4	FACETS	0.583	0.531	0.638	0.194	0.177	0.213	SUBCLONAL	1	TRUE	1	0.649267137874325	4		636	1298	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137170	64137170	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0014907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	111	572	0	ENST00000334205.4:c.1603-1G>A		p.X535_splice	ENST00000334205	NM_003942.2	535			0.385182567714169	1	FACETS	0.399	0.359	0.44	0.399	0.359	0.44	INDETERMINATE	1	TRUE	0	0.649267137874325	1		572	579	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242132	105242132	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	119	538	0	ENST00000349310.3:c.292G>T	p.Glu98Ter	p.E98*	ENST00000349310	NM_001014432.1	98	Gag/Tag	6/15	1	2	FACETS	0.517	0.467	0.57	0.517	0.467	0.57	SUBCLONAL	1	TRUE	1	0.649267137874325	2		538	709	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748606	43748606	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	193	1060	0	ENST00000382044.4:c.2200C>G	p.Gln734Glu	p.Q734E	ENST00000382044	NM_001141980.1	734	Caa/Gaa	12/28	0.568683476188339	1	FACETS	0.455	0.421	0.49	0.455	0.421	0.49	SUBCLONAL	1	TRUE	0	0.649267137874325	1		1060	883	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835617	68835629	+	frameshift_variant	Frame_Shift_Del	DEL	TCCCTCGACACCC	TCCCTCGACACCC	-	novel	NA	P-0014907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	258	596	0	ENST00000261769.5:c.208_220del	p.Ser70AspfsTer9	p.S70Dfs*9	ENST00000261769	NM_004360.3	70	TCCCTCGACACCCga/ga	3/16	0.649267137874325	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.649267137874325	1		596	484	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929489	81929489	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	154	617	0	ENST00000359376.3:c.1150G>A	p.Asp384Asn	p.D384N	ENST00000359376	NM_002661.3	384	Gac/Aac	13/33	0.649267137874325	1	FACETS	0.571	0.525	0.618	0.571	0.525	0.618	SUBCLONAL	1	TRUE	0	0.649267137874325	1		617	561	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585516	29585516	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555618566	NA	P-0014907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	36	158	0	ENST00000356175.3:c.4265C>T	p.Ser1422Leu	p.S1422L	ENST00000356175	NM_000267.3	1422	tCa/tTa	31/57	1	2	FACETS	0.427	0.352	0.509	0.427	0.352	0.509	SUBCLONAL	1	TRUE	1	0.649267137874325	2		158	260	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564515	55564515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754738766	NA	P-0014907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	103	510	3	ENST00000288135.5:c.403C>T	p.Arg135Cys	p.R135C	ENST00000288135	NM_000222.2	135	Cgc/Tgc	3/21	0.35288078176512	1	FACETS	0.318	0.284	0.353	0.318	0.284	0.353	INDETERMINATE	1	TRUE	0	0.649267137874325	1		513	674	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630870	187630870	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751034262	NA	P-0014907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	139	591	1	ENST00000441802.2:c.112G>A	p.Glu38Lys	p.E38K	ENST00000441802	NM_005245.3	38	Gag/Aag	2/27	0.649267137874325	1	FACETS	0.496	0.453	0.541	0.496	0.453	0.541	SUBCLONAL	1	TRUE	0	0.649267137874325	1		592	583	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961067	79961067	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	158	556	0	ENST00000265081.6:c.464C>G	p.Ser155Cys	p.S155C	ENST00000265081	NM_002439.4	155	tCt/tGt	3/24	0.200872862554718	2	FACETS	0.58	0.532	0.631	0.29	0.266	0.316	INDETERMINATE	1	TRUE	0	0.649267137874325	2		556	839	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542624	141542624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759574901	NA	P-0014907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	180	728	0	ENST00000220592.5:c.2362C>T	p.His788Tyr	p.H788Y	ENST00000220592	NM_012154.3	788	Cac/Tac	18/19	0.338796980389278	1	FACETS	0.521	0.481	0.562	0.521	0.481	0.562	INDETERMINATE	1	TRUE	0	0.649267137874325	1		728	719	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776983	135776983	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	97	395	0	ENST00000298552.3:c.2495C>T	p.Ser832Phe	p.S832F	ENST00000298552	NM_001162426.1	832	tCc/tTc	19/23	0.508350441156305	1	FACETS	0.416	0.372	0.462	0.416	0.372	0.462	SUBCLONAL	1	TRUE	0	0.649267137874325	1		395	485	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111502	8111503	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0014913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1265	472	689	0	ENST00000346208.3:c.990dup	p.Asn331GlufsTer21	p.N331Efs*21	ENST00000346208		330	agg/aGgg	5/6	0.843225283027305	4	FACETS	1	0.992	1			1	CLONAL	1	TRUE	NA	0.843225283027305	4		689	1737	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295773	212295773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1299031105	NA	P-0014913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	376	536	0	ENST00000342788.4:c.2540G>A	p.Arg847His	p.R847H	ENST00000342788	NM_005235.2	847	cGt/cAt	21/28	0.465392647576534	4	FACETS	1	0.992	1	0.413	0.392	0.435	INDETERMINATE	1	TRUE	1	0.843225283027305	4		536	1326	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023211	27023227	+	frameshift_variant	Frame_Shift_Del	DEL	ACGCGGGCCCTAGGCCC	ACGCGGGCCCTAGGCCC	CGCGGGCCTA	novel	NA	P-0014913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	170	282	2	ENST00000324856.7:c.317_333delinsCGCGGGCCTA	p.Asn106ThrfsTer4	p.N106Tfs*4	ENST00000324856	NM_006015.4	106	aACGCGGGCCCTAGGCCC/aCGCGGGCCTA	1/20	0.437192240283429	4	FACETS	1	0.983	1	0.409	0.378	0.442	INDETERMINATE	1	TRUE	1	0.843225283027305	4		284	605	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434384	49434384	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866926540	NA	P-0014913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	157	640	0	ENST00000301067.7:c.7169C>T	p.Pro2390Leu	p.P2390L	ENST00000301067	NM_003482.3	2390	cCg/cTg	31/54	0.843225283027305	3	FACETS	0.777	0.714	0.843			1	SUBCLONAL	1	TRUE	NA	0.843225283027305	3		640	681	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120148	70120148	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	162	227	0	ENST00000245479.2:c.1150A>G	p.Thr384Ala	p.T384A	ENST00000245479	NM_000346.3	384	Acg/Gcg	3/3	0.843225283027305	10	FACETS	0.882	0.808	0.958			1	CLONAL	2	TRUE	NA	0.843225283027305	10		227	953	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52693373	52693373	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	273	615	0	ENST00000322088.6:c.24C>G	p.Asp8Glu	p.D8E	ENST00000322088	NM_014225.5	8	gaC/gaG	1/15	0.843225283027305	3	FACETS	0.962	0.904	1	0.481	0.452	0.511	CLONAL	1	TRUE	1	0.843225283027305	3		615	957	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0014928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	62	288	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.628	0.543	0.721	0.628	0.543	0.721	SUBCLONAL	1	TRUE	1	0.35	2		288	564	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730075	41730075	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748897120	NA	P-0014928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	82	456	0	ENST00000242208.4:c.454C>T	p.Arg152Cys	p.R152C	ENST00000242208	NM_002192.2	152	Cgt/Tgt	3/3	1	2	FACETS	0.8	0.706	0.9	0.8	0.706	0.9	SUBCLONAL	1	TRUE	1	0.35	2		456	586	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128266	30128266	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	96	712	0	ENST00000263025.4:c.966G>T	p.Glu322Asp	p.E322D	ENST00000263025	NM_002746.2	322	gaG/gaT	7/9	0.3	2	FACETS	0.774	0.69	0.863			1	SUBCLONAL	1	TRUE	NA	0.35	2		712	709	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070575	67070575	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	57	282	0	ENST00000412916.2:c.199C>T	p.Gln67Ter	p.Q67*	ENST00000412916		67	Cag/Tag	3/6	0.347604248734207	1	FACETS	0.628	0.54	0.723	0.628	0.54	0.723	SUBCLONAL	1	TRUE	0	0.35	1		282	428	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178340	56178341	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	57	410	0	ENST00000399503.3:c.3315dup	p.Ile1106TyrfsTer4	p.I1106Yfs*4	ENST00000399503	NM_005921.1	1105	gtt/gTtt	14/20	0.149461229336752	3	FACETS	0.641	0.55	0.741	0.321	0.275	0.371	INDETERMINATE	1	TRUE	1	0.35	3		410	597	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178379	56178379	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	72	400	0	ENST00000399503.3:c.3352G>T	p.Glu1118Ter	p.E1118*	ENST00000399503	NM_005921.1	1118	Gag/Tag	14/20	0.149461229336752	3	FACETS	0.798	0.697	0.906	0.399	0.348	0.453	INDETERMINATE	1	TRUE	1	0.35	3		400	606	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0014938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	275	673	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	0.7	2		673	760	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	347	598	0	ENST00000269305.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	336	Gag/Tag	10/11	0.681248811068649	1	FACETS	0.969	0.926	1	0.969	0.926	1	CLONAL	1	TRUE	0	0.7	1		598	665	SUCCESS
FH	2271	MSKCC	GRCh37	1	241683007	241683007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	274	494	0	ENST00000366560.3:c.16C>T	p.Arg6Trp	p.R6W	ENST00000366560	NM_000143.3	6	Cgg/Tgg	1/10	0.626040332524506	3	FACETS	0.99	0.93	1	0.495	0.465	0.527	CLONAL	1	TRUE	1	0.7	3		494	1067	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107195	27107195	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0014938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	283	486	0	ENST00000324856.7:c.6806C>G	p.Ser2269Ter	p.S2269*	ENST00000324856	NM_006015.4	2269	tCa/tGa	20/20	0.681248811068649	1	FACETS	0.917	0.871	0.963	0.917	0.871	0.963	CLONAL	1	TRUE	0	0.7	1		486	573	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061461	38061461	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	275	507	0	ENST00000250448.2:c.528C>G	p.Ile176Met	p.I176M	ENST00000250448	NM_004496.3	176	atC/atG	2/2	1	2	FACETS	0.905	0.852	0.959	0.905	0.852	0.959	CLONAL	1	TRUE	1	0.7	2		507	868	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845741	68845742	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0014938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	288	414	2	ENST00000261769.5:c.988dup	p.Thr330AsnfsTer20	p.T330Nfs*20	ENST00000261769	NM_004360.3	329	-/A	7/16	0.681248811068649	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.7	1		416	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579714	7579714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	263	585	0	ENST00000269305.4:c.82G>A	p.Glu28Lys	p.E28K	ENST00000269305	NM_001126112.2	28	Gaa/Aaa	3/11	0.681248811068649	1	FACETS	0.815	0.771	0.86	0.815	0.771	0.86	CLONAL	1	TRUE	0	0.7	1		585	599	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216319	2216319	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs755460094	NA	P-0014938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	302	584	0	ENST00000398665.3:c.1963G>C	p.Glu655Gln	p.E655Q	ENST00000398665	NM_032482.2	655	Gag/Cag	20/28	1	2	FACETS	0.921	0.87	0.973	0.921	0.87	0.973	CLONAL	1	TRUE	1	0.7	2		584	937	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216484	2216484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	384	699	0	ENST00000398665.3:c.2128G>A	p.Glu710Lys	p.E710K	ENST00000398665	NM_032482.2	710	Gag/Aag	20/28	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.7	2		699	1094	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216586	2216586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	421	708	0	ENST00000398665.3:c.2230G>A	p.Asp744Asn	p.D744N	ENST00000398665	NM_032482.2	744	Gac/Aac	20/28	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.7	2		708	1195	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911464	134911464	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	297	608	0	ENST00000398015.3:c.1929G>C	p.Lys643Asn	p.K643N	ENST00000398015	NM_004441.4	643	aaG/aaC	11/16	1	2	FACETS	0.869	0.82	0.92	0.869	0.82	0.92	CLONAL	1	TRUE	1	0.7	2		608	976	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179353	56179353	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0014938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	107	207	0	ENST00000399503.3:c.3667-1G>A		p.X1223_splice	ENST00000399503	NM_005921.1	1223			1	2	FACETS	0.886	0.803	0.972	0.886	0.803	0.972	CLONAL	1	TRUE	1	0.7	2		207	345	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639025	176639025	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	345	615	0	ENST00000439151.2:c.3625C>G	p.Pro1209Ala	p.P1209A	ENST00000439151	NM_022455.4	1209	Cct/Gct	5/23	1	2	FACETS	0.996	0.945	1	0.996	0.945	1	CLONAL	1	TRUE	1	0.7	2		615	990	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639119	176639119	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1385474455	NA	P-0014938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	343	563	0	ENST00000439151.2:c.3719C>G	p.Ser1240Cys	p.S1240C	ENST00000439151	NM_022455.4	1240	tCc/tGc	5/23	1	2	FACETS	0.997	0.946	1	0.997	0.946	1	CLONAL	1	TRUE	1	0.7	2		563	983	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148526919	148526919	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	230	428	0	ENST00000320356.2:c.385C>G	p.His129Asp	p.H129D	ENST00000320356	NM_004456.4	129	Cat/Gat	5/20	1	2	FACETS	0.94	0.881	1	0.94	0.881	1	CLONAL	1	TRUE	1	0.7	2		428	699	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151850018	151850018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776705063	NA	P-0014938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	121	367	2	ENST00000262189.6:c.12298G>A	p.Ala4100Thr	p.A4100T	ENST00000262189	NM_170606.2	4100	Gca/Aca	49/59	1	2	FACETS	0.625	0.567	0.686	0.625	0.567	0.686	SUBCLONAL	1	TRUE	1	0.7	2		369	553	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787747	135787747	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	318	509	0	ENST00000298552.3:c.835C>A	p.His279Asn	p.H279N	ENST00000298552	NM_001162426.1	279	Cac/Aac	9/23	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.7	2		509	864	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207468	29207471	+	stop_gained	Nonsense_Mutation	ONP	CGTC	CGTC	AGTT	novel	NA	P-0014938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	224	343	0	ENST00000240100.2:c.325_328delinsAACT	p.Asp109_Glu110delinsAsnTer	p.D109_E110delinsN*	ENST00000240100	NM_001394.6	109	GACGag/AACTag	1/4	1	2	FACETS	0.988	0.925	1	0.988	0.925	1	CLONAL	1	TRUE	1	0.7	2		343	648	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0014954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	429	673	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.682558780356313	4	FACETS	0.945	0.903	0.988	0.473	0.451	0.494	CLONAL	2	TRUE	0	0.682558780356313	4		673	1119	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469603	25469603	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1470594184	NA	P-0014954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1571	269	751	0	ENST00000264709.3:c.1165G>A	p.Asp389Asn	p.D389N	ENST00000264709	NM_175629.2	389	Gac/Aac	10/23	0.682558780356313	6	FACETS	1	0.945	1	0.253	0.236	0.271	CLONAL	1	TRUE	2	0.682558780356313	6		751	1840	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115985	8115989	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	AGAGC	AGAGC	-	novel	NA	P-0014954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	104	311	0	ENST00000346208.3:c.1331_*3del		p.*444*	ENST00000346208		444		6/6	0.68265522613645	3	FACETS	0.881	0.793	0.973	0.44	0.396	0.487	CLONAL	1	TRUE	1	0.682558780356313	3		311	464	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512297	38512298	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0014954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	63	786	0	ENST00000254066.5:c.1211dup	p.Ser405LeufsTer41	p.S405Lfs*41	ENST00000254066	NM_000964.3	403	ccg/ccGg	9/9	NA	2	FACETS	0.2	0.172	0.23			1	INDETERMINATE	1	TRUE	NA	0.682558780356313	2		786	923	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637714	176637714	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1385	311	815	0	ENST00000439151.2:c.2314G>T	p.Ala772Ser	p.A772S	ENST00000439151	NM_022455.4	772	Gca/Tca	5/23	0.68265522613645	5	FACETS	1	0.979	1	0.362	0.34	0.385	CLONAL	1	TRUE	2	0.682558780356313	5		815	1696	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287398	38287398	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778531708	NA	P-0014954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2380	214	660	0	ENST00000425967.3:c.259C>T	p.Arg87Cys	p.R87C	ENST00000425967	NM_001174067.1	87	Cgc/Tgc	4/19	0.682558780356313	10	FACETS	0.902	0.833	0.973			1	CLONAL	1	TRUE	NA	0.682558780356313	10		660	2594	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044450	5044450	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	226	718	0	ENST00000381652.3:c.399del	p.His134MetfsTer33	p.H134Mfs*33	ENST00000381652	NM_004972.3	133	cGg/cg	5/25	1	2	FACETS	0.987	0.924	1	0.987	0.924	1	CLONAL	1	TRUE	1	0.682558780356313	2		718	671	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588238	69588241	+	missense_variant	Missense_Mutation	ONP	CATC	CATC	GATT	novel	NA	P-0014954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	165	469	0	ENST00000168712.1:c.457_460delinsAATC	p.Asp153_Glu154delinsAsnGln	p.D153_E154delinsNQ	ENST00000168712	NM_002007.2	153	GATGag/AATCag	3/3	0.574230298224873	6	FACETS	0.882	0.807	0.959	0.294	0.269	0.32	CLONAL	1	TRUE	3	0.682558780356313	6		469	1297	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	161	588	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.885	0.814	0.957	0.885	0.814	0.957	CLONAL	1	TRUE	1	0.56968626513698	2		589	639	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0015020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	110	314	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.56968626513698	1	FACETS	0.894	0.814	0.976	0.894	0.814	0.976	CLONAL	1	TRUE	0	0.56968626513698	1		314	309	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204864	NA	P-0015020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	176	414	0	ENST00000371953.3:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000371953	NM_000314.4	171	Cag/Tag	6/9	0.56968626513698	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.56968626513698	1		414	433	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0015020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	138	348	1	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	0.56968626513698	1	FACETS	0.888	0.817	0.961	0.888	0.817	0.961	CLONAL	1	TRUE	0	0.56968626513698	1		349	390	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559780	29559780	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	145	288	0	ENST00000356175.3:c.3377A>G	p.Gln1126Arg	p.Q1126R	ENST00000356175	NM_000267.3	1126	cAa/cGa	26/57	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.56968626513698	2		288	464	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293439	1293439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060503002	NA	P-0015020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	43	552	0	ENST00000310581.5:c.1562G>A	p.Arg521His	p.R521H	ENST00000310581	NM_198253.2	521	cGc/cAc	2/16	1	2	FACETS	0.218	0.182	0.259	0.218	0.182	0.259	SUBCLONAL	1	TRUE	1	0.56968626513698	2		552	691	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410856	31410856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	215	486	0	ENST00000344624.3:c.3664G>A	p.Glu1222Lys	p.E1222K	ENST00000344624		1222	Gaa/Aaa	28/33	1	2	FACETS	0.975	0.909	1	0.975	0.909	1	CLONAL	1	TRUE	1	0.56968626513698	2		486	774	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589214	67589215	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACA	novel	NA	P-0015020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	120	321	0	ENST00000274335.5:c.1202_1203insACA	p.Val401_Val402insGln	p.V401_V402insQ	ENST00000274335		401	gtg/gtACAg	9/15	1	2	FACETS	0.92	0.836	1	0.92	0.836	1	CLONAL	1	TRUE	1	0.56968626513698	2		321	458	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039405	47039405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	48	321	0	ENST00000377604.3:c.1028G>A	p.Arg343His	p.R343H	ENST00000377604	NM_001204468.1	343	cGc/cAc	10/24	1	1	FACETS	0.28	0.237	0.328	0.28	0.237	0.328	SUBCLONAL	1	TRUE	0	0.56968626513698	1		321	430	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0000024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	317	783	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.985	0.932	1	0.985	0.932	1	CLONAL	1	TRUE	1	0.667676553953993	2		783	964	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0000024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	231	248	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.589403799093764	3	FACETS	0.857	0.799	0.917	0.428	0.399	0.459	CLONAL	1	TRUE	1	0.667676553953993	3		248	1077	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913403	NA	P-0000024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	280	600	0	ENST00000349496.5:c.110C>A	p.Ser37Tyr	p.S37Y	ENST00000349496	NM_001904.3	37	tCt/tAt	3/15	0.589403799093764	3	FACETS	0.899	0.843	0.956	0.449	0.421	0.478	CLONAL	1	TRUE	1	0.667676553953993	3		600	1245	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105878	27105881	+	frameshift_variant	Frame_Shift_Del	DEL	AGCT	AGCT	-	novel	NA	P-0000024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	234	588	0	ENST00000324856.7:c.5489_5492del	p.Lys1830MetfsTer52	p.K1830Mfs*52	ENST00000324856	NM_006015.4	1830	aAGCTt/at	20/20	1	2	FACETS	0.921	0.862	0.981	0.921	0.862	0.981	CLONAL	1	TRUE	1	0.667676553953993	2		588	761	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591238	67591248	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTTTTTCAGG	TGTTTTTCAGG	-	novel	NA	P-0000024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	445	442	0	ENST00000274335.5:c.1746-8_1748del		p.X582_splice	ENST00000274335		582		13/15	0.56348386974771	4	FACETS	0.921	0.88	0.962	0.614	0.586	0.642	CLONAL	2	TRUE	1	0.667676553953993	4		442	1207	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720720	89720721	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs786204905	NA	P-0000024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	53	88	0	ENST00000371953.3:c.875dup	p.Asn292LysfsTer6	p.N292Kfs*6	ENST00000371953	NM_000314.4	291	gaa/gAaa	8/9	0.589403799093764	3	FACETS	0.95	0.82	1	0.475	0.41	0.544	CLONAL	1	TRUE	1	0.667676553953993	3		88	223	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0000069-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	217	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.151007178263749	3	FACETS	1	0.974	1	0.548	0.51	0.588	INDETERMINATE	1	TRUE	1	0.54	3		311	931	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0000069-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	137	338	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.884	0.807	0.964	0.884	0.807	0.964	CLONAL	1	TRUE	1	0.54	2		338	574	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106648	27106648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553153748	NA	P-0000069-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	246	455	0	ENST00000324856.7:c.6259G>A	p.Gly2087Arg	p.G2087R	ENST00000324856	NM_006015.4	2087	Gga/Aga	20/20	1	2	FACETS	0.95	0.889	1	0.95	0.889	1	CLONAL	1	TRUE	1	0.54	2		455	959	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567674	226567674	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000069-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	206	395	0	ENST00000366794.5:c.1492A>G	p.Lys498Glu	p.K498E	ENST00000366794	NM_001618.3	498	Aag/Gag	10/23	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.54	2		395	619	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0000069-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	147	379	2	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.904	0.829	0.983	0.904	0.829	0.983	CLONAL	1	TRUE	1	0.54	2		381	602	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149982928	149982928	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000069-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	215	540	0	ENST00000253339.5:c.3330G>C	p.Gln1110His	p.Q1110H	ENST00000253339		1110	caG/caC	7/7	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.54	2		540	780	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465997	69465997	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000069-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	242	337	0	ENST00000227507.2:c.835G>T	p.Glu279Ter	p.E279*	ENST00000227507	NM_053056.2	279	Gag/Tag	5/5	0.3	4	FACETS	0.943	0.885	1			1	INDETERMINATE	2	TRUE	NA	0.54	4		337	732	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158444	108158444	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0000069-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	116	214	0	ENST00000278616.4:c.4109+2T>C		p.X1370_splice	ENST00000278616	NM_000051.3	1370			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.54	2		214	381	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287293	46287293	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000069-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	158	432	0	ENST00000334344.6:c.5238A>C	p.Arg1746Ser	p.R1746S	ENST00000334344	NM_152641.2	1746	agA/agC	19/21	0.151007178263749	3	FACETS	1	0.986	1	0.664	0.611	0.718	INDETERMINATE	1	TRUE	1	0.54	3		432	560	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936984	48936984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772678500	NA	P-0000069-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	181	420	0	ENST00000267163.4:c.752G>A	p.Arg251Gln	p.R251Q	ENST00000267163	NM_000321.2	251	cGa/cAa	8/27	1	2	FACETS	0.932	0.862	1	0.932	0.862	1	CLONAL	1	TRUE	1	0.54	2		420	719	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631872	90631872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000069-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	229	404	0	ENST00000330062.3:c.481G>A	p.Val161Ile	p.V161I	ENST00000330062	NM_002168.2	161	Gtc/Atc	4/11	1	2	FACETS	0.963	0.899	1	0.963	0.899	1	CLONAL	1	TRUE	1	0.54	2		404	881	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44527561	44527561	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000069-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	237	391	0	ENST00000291552.4:c.44A>G	p.Lys15Arg	p.K15R	ENST00000291552	NM_006758.2	15	aAa/aGa	1/8	0.3	3	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.54	3		391	920	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087346	27087346	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0000069-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	144	395	1	ENST00000324856.7:c.1921del		p.X641_splice	ENST00000324856	NM_006015.4	641			1	2	FACETS	0.808	0.739	0.88	0.808	0.739	0.88	CLONAL	1	TRUE	1	0.54	2		396	660	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000069-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	199	240	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.816	0.757	0.878	0.816	0.757	0.878	CLONAL	1	TRUE	1	0.54	2		240	903	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378266	225378266	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0000069-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	235	626	2	ENST00000264414.4:c.629del	p.Leu210TrpfsTer16	p.L210Wfs*16	ENST00000264414	NM_003590.4	210	tTg/tg	5/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.54	2		628	840	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371929	55371930	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000069-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	124	104	0	ENST00000297316.4:c.620dup	p.Ser208GlufsTer157	p.S208Efs*157	ENST00000297316	NM_022454.3	207	cag/cAag	2/2	0.151007178263749	3	FACETS	0.788	0.721	0.858	0.788	0.721	0.858	INDETERMINATE	2	TRUE	1	0.54	3		104	370	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0000069-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	102	201	2	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.54	2		203	333	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0000069-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	101	230	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	0.941	1	CLONAL	1	TRUE	1	0.54	2		230	353	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132428	11132430	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0000069-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	253	567	0	ENST00000358026.2:c.2645_2647del	p.Glu882del	p.E882del	ENST00000358026	NM_001128849.1	882	GAA/-	19/36	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.54	2		567	937	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951996	178951996	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000107-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	80	370	0	ENST00000263967.3:c.3051T>G	p.Asp1017Glu	p.D1017E	ENST00000263967	NM_006218.2	1017	gaT/gaG	21/21	0.212771372693627	1	FACETS	0.749	0.658	0.847	0.749	0.658	0.847	SUBCLONAL	1	FALSE	0	0.212771372693627	1		370	897	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952000	178952000	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1328031338	NA	P-0000107-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	81	369	0	ENST00000263967.3:c.3055A>G	p.Ile1019Val	p.I1019V	ENST00000263967	NM_006218.2	1019	Att/Gtt	21/21	0.212771372693627	1	FACETS	0.756	0.665	0.854	0.756	0.665	0.854	SUBCLONAL	1	FALSE	0	0.212771372693627	1		369	900	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952006	178952006	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000107-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	88	371	0	ENST00000263967.3:c.3061T>C	p.Tyr1021His	p.Y1021H	ENST00000263967	NM_006218.2	1021	Tac/Cac	21/21	0.212771372693627	1	FACETS	0.828	0.732	0.93	0.828	0.732	0.93	CLONAL	1	FALSE	0	0.212771372693627	1		371	893	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559886	29559887	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1555614977	NA	P-0000107-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	106	184	0	ENST00000356175.3:c.3484dup	p.Met1162AsnfsTer33	p.M1162Nfs*33	ENST00000356175	NM_000267.3	1161	-/A	26/57	0.212771372693627	0	FACETS	0.834	0.752	0.921			1	CLONAL	2	FALSE	0	0.212771372693627	0		184	470	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383210	4383210	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000190-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	210	252	0	ENST00000261254.3:c.4G>A	p.Glu2Lys	p.E2K	ENST00000261254	NM_001759.3	2	Gag/Aag	1/5	0.703918579617604	4	FACETS	0.948	0.888	1			1	CLONAL	2	TRUE	NA	0.703918579617604	4		252	536	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155365	47155365	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0000190-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	543	402	0	ENST00000409792.3:c.4715+1G>T		p.X1572_splice	ENST00000409792	NM_014159.6	1572			0.703918579617604	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.703918579617604	2		402	748	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008036	29008036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754160537	NA	P-0000190-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	620	440	0	ENST00000282397.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000282397	NM_002019.4	245	Ggc/Agc	6/30	0.703918579617604	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.703918579617604	2		440	844	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866420	37866420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000190-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	399	420	0	ENST00000269571.5:c.725C>T	p.Ala242Val	p.A242V	ENST00000269571		242	gCc/gTc	6/27	0.703918579617604	4	FACETS	0.991	0.945	1	0.991	0.945	1	CLONAL	2	TRUE	2	0.703918579617604	4		420	975	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288858	15288858	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000190-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	24	18	0	ENST00000263388.2:c.3881G>T	p.Arg1294Leu	p.R1294L	ENST00000263388	NM_000435.2	1294	cGg/cTg	24/33	0.517999749625918	4	FACETS	0.901	0.755	1	1	0.94	1	CLONAL	3	TRUE	2	0.703918579617604	4		18	43	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300207	15300207	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000190-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	506	431	0	ENST00000263388.2:c.1069A>T	p.Ser357Cys	p.S357C	ENST00000263388	NM_000435.2	357	Agc/Tgc	7/33	0.517999749625918	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	2	0.703918579617604	4		431	1081	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938952	76938952	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000190-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1401	849	857	0	ENST00000373344.5:c.1796C>A	p.Pro599Gln	p.P599Q	ENST00000373344	NM_000489.3	599	cCa/cAa	9/35	0.517999749625918	4	FACETS	0.913	0.884	0.943	0.913	0.884	0.943	CLONAL	2	TRUE	2	0.703918579617604	4		857	2250	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050874	49050875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0000190-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	396	344	1	ENST00000267163.4:c.2559dup	p.Asn854Ter	p.N854*	ENST00000267163	NM_000321.2	853	tgt/tgTt	25/27	0.703918579617604	2	FACETS	0.91	0.877	0.943	0.91	0.877	0.943	CLONAL	2	TRUE	0	0.703918579617604	2		345	618	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0000209-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	215	248	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.520499802270322	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.520499802270322	1		248	576	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660536	67660536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000209-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	315	376	0	ENST00000264010.4:c.1436G>A	p.Arg479His	p.R479H	ENST00000264010	NM_006565.3	479	cGc/cAc	8/12	0.341996419606566	1	FACETS	0.903	0.853	0.953	0.903	0.853	0.953	CLONAL	1	TRUE	0	0.520499802270322	1		376	992	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556481	29556481	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1060500357	NA	P-0000209-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	123	132	0	ENST00000356175.3:c.2848C>T	p.Gln950Ter	p.Q950*	ENST00000356175	NM_000267.3	950	Cag/Tag	21/57	0.520499802270322	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.520499802270322	1		132	327	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589618	67589619	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAGAATATGATAGATTATATGAAG	novel	NA	P-0000209-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	177	323	0	ENST00000274335.5:c.1382_1405dup	p.Glu468_Glu469insGlyGluTyrAspArgLeuTyrGlu	p.E468_E469insGEYDRLYE	ENST00000274335		461	cga/cGAGAATATGATAGATTATATGAAGga	10/15	1	2	FACETS	0.675	0.622	0.731	0.675	0.622	0.731	SUBCLONAL	1	TRUE	1	0.520499802270322	2		323	1007	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573970	7573994	+	frameshift_variant	Frame_Shift_Del	DEL	CATCCTTGAGTTCCAAGGCCTCATT	CATCCTTGAGTTCCAAGGCCTCATT	-	novel	NA	P-0000209-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	306	331	0	ENST00000269305.4:c.1033_1057del	p.Asn345ProfsTer17	p.N345Pfs*17	ENST00000269305	NM_001126112.2	345	AATGAGGCCTTGGAACTCAAGGATGcc/cc	10/11	0.520499802270322	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.520499802270322	1		331	751	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162722894	162722894	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000242-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	80	256	0	ENST00000367921.3:c.92G>T	p.Arg31Leu	p.R31L	ENST00000367921	NM_006182.2	31	cGc/cTc	4/18	0.574670269855269	4	FACETS	1	0.978	1			1	INDETERMINATE	1	FALSE	NA	0.968228070106163	4		256	231	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520006	NA	P-0000242-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	68	466	0	ENST00000269305.4:c.821T>G	p.Val274Gly	p.V274G	ENST00000269305	NM_001126112.2	274	gTt/gGt	8/11	0.880812251770231	3	FACETS	0.899	0.793	1	0.449	0.396	0.505	CLONAL	1	FALSE	1	0.968228070106163	3		466	232	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252962	36252962	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs74315451	NA	P-0000242-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	62	150	0	ENST00000300305.3:c.400G>C	p.Ala134Pro	p.A134P	ENST00000300305		134	Gct/Cct	4/8	0.392325797009846	5	FACETS	0.73	0.633	0.836	0.243	0.211	0.279	INDETERMINATE	1	FALSE	2	0.968228070106163	5		150	430	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860461	151860462	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000242-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	61	363	0	ENST00000262189.6:c.10200dup	p.Lys3401Ter	p.K3401*	ENST00000262189	NM_170606.2	3400	-/T	43/59	0.357210626935177	6	FACETS	1	0.958	1	0.422	0.367	0.481	INDETERMINATE	1	FALSE	3	0.968228070106163	6		363	292	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023036	48023036	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1553411391	NA	P-0000247-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	40	260	0	ENST00000234420.5:c.461C>G	p.Ser154Ter	p.S154*	ENST00000234420	NM_000179.2	154	tCa/tGa	3/10	1	2	FACETS	0.488	0.405	0.582	0.488	0.405	0.582	SUBCLONAL	1	TRUE	1	0.262967891504445	2		260	623	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370981	55370982	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0000247-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	36	192	0	ENST00000297316.4:c.283_284insT	p.Asn95IlefsTer67	p.N95Ifs*67	ENST00000297316	NM_022454.3	95	aac/aTac	1/2	0.262967891504445	4	FACETS	0.545	0.447	0.656	0.182	0.149	0.219	SUBCLONAL	1	TRUE	1	0.262967891504445	4		192	634	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278102	142278102	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000271-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	403	272	0	ENST00000350721.4:c.1723T>C	p.Tyr575His	p.Y575H	ENST00000350721	NM_001184.3	575	Tat/Cat	7/47	0.565157275765424	3	FACETS	0.898	0.859	0.937	0.898	0.859	0.937	CLONAL	2	TRUE	1	0.688610871603628	3		272	876	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720808	89720808	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000271-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	194	89	0	ENST00000371953.3:c.959T>C	p.Leu320Ser	p.L320S	ENST00000371953	NM_000314.4	320	tTa/tCa	8/9	0.688610871603628	2	FACETS	0.862	0.814	0.908	0.862	0.814	0.908	CLONAL	2	TRUE	0	0.688610871603628	2		89	327	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508773	148508774	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0000271-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	61	254	0	ENST00000320356.2:c.1890dup	p.Ile631AspfsTer11	p.I631Dfs*11	ENST00000320356	NM_004456.4	630	-/G	16/20	1	2	FACETS	0.265	0.228	0.305	0.265	0.228	0.305	SUBCLONAL	1	TRUE	1	0.688610871603628	2		254	668	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889072	76889073	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0000271-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	534	334	0	ENST00000373344.5:c.4937_4938del	p.Lys1646ArgfsTer2	p.K1646Rfs*2	ENST00000373344	NM_000489.3	1646	aAA/a	18/35	0.248822535352298	2	FACETS	1	0.996	1	0.662	0.637	0.688	INDETERMINATE	1	TRUE	0	0.688610871603628	2		334	1171	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490980	56490980	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs931676601	NA	P-0000342-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	79	265	0	ENST00000267101.3:c.2426A>G	p.Gln809Arg	p.Q809R	ENST00000267101	NM_001982.3	809	cAg/cGg	20/28	1	2	FACETS	0.739	0.652	0.832	0.739	0.652	0.832	SUBCLONAL	1	TRUE	1	0.432895152044329	2		265	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0000342-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	243	521	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.337041764614717	2	FACETS	0.857	0.806	0.909	0.857	0.806	0.909	CLONAL	2	TRUE	0	0.432895152044329	2		521	655	SUCCESS
AXL	558	MSKCC	GRCh37	19	41749547	41749547	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000342-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	124	669	0	ENST00000301178.4:c.1472G>C	p.Arg491Thr	p.R491T	ENST00000301178	NM_021913.4	491	aGa/aCa	12/20	1	2	FACETS	0.642	0.58	0.707	0.642	0.58	0.707	SUBCLONAL	1	TRUE	1	0.432895152044329	2		669	893	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064394	30064394	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315497	NA	P-0000342-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	28	291	0	ENST00000338641.4:c.958C>T	p.Gln320Ter	p.Q320*	ENST00000338641	NM_000268.3	320	Cag/Tag	10/16	0.353871595571558	1	FACETS	0.247	0.197	0.304	0.247	0.197	0.304	SUBCLONAL	1	TRUE	0	0.432895152044329	1		291	411	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120206	70120207	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0000342-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	27	373	0	ENST00000245479.2:c.1212dup	p.Ser405GlnfsTer173	p.S405Qfs*173	ENST00000245479	NM_000346.3	403	agc/agCc	3/3	0.41424803927438	2	FACETS	0.266	0.211	0.329	0.133	0.105	0.165	SUBCLONAL	1	TRUE	0	0.432895152044329	2		373	469	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226549757	226549757	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000345-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	169	283	0	ENST00000366794.5:c.2876C>T	p.Ser959Leu	p.S959L	ENST00000366794	NM_001618.3	959	tCa/tTa	22/23	0.564140123797643	5	FACETS	0.875	0.803	0.951	0.292	0.267	0.317	CLONAL	1	TRUE	2	0.564140123797643	5		283	1264	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591085	67591085	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519839	NA	P-0000345-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	130	153	0	ENST00000274335.5:c.1678G>T	p.Asp560Tyr	p.D560Y	ENST00000274335		560	Gac/Tac	12/15	0.549578634131833	2	FACETS	0.895	0.816	0.977	0.447	0.408	0.489	CLONAL	1	TRUE	0	0.564140123797643	2		153	515	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89839769	89839769	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000345-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	484	385	1	ENST00000389301.3:c.1924G>A	p.Glu642Lys	p.E642K	ENST00000389301	NM_000135.2	642	Gaa/Aaa	22/43	0.564140123797643	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.564140123797643	3		386	1093	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325858	65325859	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0000345-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	288	246	0	ENST00000342505.4:c.1262_1263dup	p.Tyr422IlefsTer11	p.Y422Ifs*11	ENST00000342505	NM_002227.2	421	-/AT	9/25	NA	2	FACETS	0.862	0.819	0.906			1	INDETERMINATE	2	TRUE	NA	0.564140123797643	2		246	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579360	7579365	+	inframe_deletion	In_Frame_Del	DEL	GAAACC	GAAACC	-	novel	NA	P-0000345-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	231	271	0	ENST00000269305.4:c.322_327del	p.Gly108_Phe109del	p.G108_F109del	ENST00000269305	NM_001126112.2	108	GGTTTC/-	4/11	0.564140123797643	2	FACETS	1	0.993	1	0.744	0.7	0.789	CLONAL	1	TRUE	0	0.564140123797643	2		271	550	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553210	41553211	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0000345-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	209	345	0	ENST00000263253.7:c.3300dup	p.Thr1101TyrfsTer3	p.T1101Yfs*3	ENST00000263253	NM_001429.3	1100	tct/tcTt	18/31	0.185862398077545	6	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.564140123797643	6		345	1112	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519893	NA	P-0000346-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	332	525	3	ENST00000267101.3:c.310G>T	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ttg	3/28	0.474021109785068	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	2	0.474021109785068	4		528	1020	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231437	46231437	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000346-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	189	397	0	ENST00000334344.6:c.1277C>A	p.Thr426Lys	p.T426K	ENST00000334344	NM_152641.2	426	aCg/aAg	10/21	0.474021109785068	4	FACETS	0.846	0.784	0.909	0.846	0.784	0.909	CLONAL	2	TRUE	2	0.474021109785068	4		397	695	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944607	40944607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766880457	NA	P-0000346-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	96	251	0	ENST00000373198.4:c.1895G>A	p.Arg632Gln	p.R632Q	ENST00000373198	NM_133170.3	632	cGa/cAa	12/32	0.474021109785068	7	FACETS	0.849	0.759	0.945			1	CLONAL	2	TRUE	NA	0.474021109785068	7		251	521	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106519966	106519967	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0000346-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	137	351	0	ENST00000359195.3:c.2395_2396dup	p.Cys801AsnfsTer4	p.C801Nfs*4	ENST00000359195	NM_002649.2	798	-/GA	6/11	0.474021109785068	6	FACETS	0.972	0.888	1	0.486	0.444	0.53	CLONAL	2	TRUE	2	0.474021109785068	6		351	579	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000351-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	225	323	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.696746692467612	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.696746692467612	2		323	320	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917765	29917765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000351-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	129	433	0	ENST00000389048.3:c.903G>A	p.Met301Ile	p.M301I	ENST00000389048	NM_004304.4	301	atG/atA	3/29	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.696746692467612	2		433	272	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095743	178095743	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000351-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	522	475	0	ENST00000397062.3:c.1588G>C	p.Asp530His	p.D530H	ENST00000397062	NM_006164.4	530	Gat/Cat	5/5	0.696746692467612	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.696746692467612	3		475	995	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095822	178095822	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000351-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	402	309	0	ENST00000397062.3:c.1509G>C	p.Arg503Ser	p.R503S	ENST00000397062	NM_006164.4	503	agG/agC	5/5	0.696746692467612	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.696746692467612	3		309	776	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096076	178096076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000351-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	297	237	0	ENST00000397062.3:c.1255G>A	p.Asp419Asn	p.D419N	ENST00000397062	NM_006164.4	419	Gat/Aat	5/5	0.696746692467612	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.696746692467612	3		237	552	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519922	NA	P-0000351-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	594	638	0	ENST00000397062.3:c.235G>A	p.Glu79Lys	p.E79K	ENST00000397062	NM_006164.4	79	Gag/Aag	2/5	0.696746692467612	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.696746692467612	3		638	1063	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974783	21974784	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000351-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	169	234	0	ENST00000304494.5:c.43dup	p.Trp15LeufsTer29	p.W15Lfs*29	ENST00000304494	NM_000077.4	15	tgg/tTgg	1/3	0.696746692467612	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.696746692467612	2		234	236	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682399	52682400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0000368-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	518	390	0	ENST00000394830.3:c.773dup	p.Asn258LysfsTer6	p.N258Kfs*6	ENST00000394830	NM_018313.4	258	aat/aaAt	8/30	0.642818107550393	1	FACETS	0.951	0.914	0.988	0.951	0.914	0.988	CLONAL	1	TRUE	0	0.642818107550393	1		390	1150	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685288	89685289	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000442-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	357	291	0	ENST00000371953.3:c.188dup	p.Asn63LysfsTer11	p.N63Kfs*11	ENST00000371953	NM_000314.4	61	-/A	3/9	NA	2	FACETS	0.775	0.744	0.806			1	INDETERMINATE	2	TRUE	NA	0.772657379461598	2		291	596	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0000452-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	227	328	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.451056108025305	6	FACETS	0.98	0.916	1	0.49	0.458	0.523	INDETERMINATE	2	TRUE	2	0.765991609449097	6		328	766	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342421	70342421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771266719	NA	P-0000452-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	82	733	0	ENST00000374080.3:c.1312C>T	p.Arg438Cys	p.R438C	ENST00000374080		438	Cgc/Tgc	9/45	0.220946190777711	3	FACETS	0.314	0.276	0.355	0.157	0.138	0.178	INDETERMINATE	1	TRUE	1	0.765991609449097	3		733	942	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151289	202151290	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000452-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	364	854	0	ENST00000358485.4:c.1596dup	p.Leu533ThrfsTer6	p.L533Tfs*6	ENST00000358485	NM_001080125.1	530	aga/agAa	9/9	0.727267687197898	1	FACETS	0.803	0.768	0.839	0.803	0.768	0.839	CLONAL	1	TRUE	0	0.765991609449097	1		854	730	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743519	46743519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368491231	NA	P-0000452-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	259	501	0	ENST00000371975.4:c.1900C>T	p.Arg634Cys	p.R634C	ENST00000371975	NM_003579.3	634	Cgt/Tgt	17/18	0.518905441557946	6	FACETS	1	0.963	1	0.517	0.485	0.549	CLONAL	2	TRUE	2	0.765991609449097	6		501	828	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440903	52440903	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000452-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	491	501	0	ENST00000460680.1:c.601G>T	p.Glu201Ter	p.E201*	ENST00000460680	NM_004656.3	201	Gag/Tag	8/17	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	2	TRUE	NA	0.765991609449097	2		501	637	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866987936	NA	P-0000452-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	350	373	0	ENST00000281708.4:c.1436G>C	p.Arg479Pro	p.R479P	ENST00000281708	NM_033632.3	479	cGa/cCa	10/12	0.289610237442257	4	FACETS	0.787	0.747	0.828	0.787	0.747	0.828	INDETERMINATE	2	TRUE	2	0.765991609449097	4		373	1025	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735578	204735578	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000523-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	57	69	0	ENST00000302823.3:c.379T>A	p.Tyr127Asn	p.Y127N	ENST00000302823	NM_005214.4	127	Tac/Aac	2/4	0.222825606003465	3	FACETS	1	0.962	1	0.454	0.392	0.522	CLONAL	1	TRUE	0	0.269630378857058	3		69	352	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713703	52713703	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000523-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	63	156	0	ENST00000394830.3:c.25A>G	p.Thr9Ala	p.T9A	ENST00000394830	NM_018313.4	9	Acc/Gcc	2/30	0.105067742327975	4	FACETS	0.851	0.735	0.977	0.426	0.367	0.489	INDETERMINATE	1	TRUE	2	0.269630378857058	4		156	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0000523-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	39	251	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	1	2	FACETS	0.751	0.624	0.893	0.751	0.624	0.893	SUBCLONAL	1	TRUE	1	0.269630378857058	2		251	385	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0000523-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	58	174	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.566	0.485	0.655	0.566	0.485	0.655	SUBCLONAL	1	TRUE	1	0.269630378857058	2		174	760	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244781	46244782	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0000523-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	207	278	0	ENST00000334344.6:c.2876dup	p.Val960SerfsTer8	p.V960Sfs*8	ENST00000334344	NM_152641.2	959	aca/aCca	15/21	0.231581289116382	4	FACETS	1	0.99	1	0.717	0.663	0.772	CLONAL	1	TRUE	2	0.269630378857058	4		278	1360	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029527	14029527	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000570-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	37	191	0	ENST00000311895.7:c.1738C>G	p.Leu580Val	p.L580V	ENST00000311895	NM_005236.2	580	Ctt/Gtt	8/11	0.244034461014076	5	FACETS	1	0.872	1	0.356	0.294	0.425	CLONAL	1	TRUE	2	0.29	5		191	343	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0000570-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	347	392	0	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.3	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	1	0.29	4		392	883	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120205	70120206	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCCC	novel	NA	P-0000570-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	44	407	0	ENST00000245479.2:c.1208_1212dup	p.Ser405AlafsTer67	p.S405Afs*67	ENST00000245479	NM_000346.3	403	agc/aGCCCCgc	3/3	0.3	3	FACETS	0.556	0.465	0.657	0.185	0.155	0.219	SUBCLONAL	1	TRUE	0	0.29	3		407	625	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0000594-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	150	590	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.564032268082198	1	FACETS	0.784	0.722	0.848	0.784	0.722	0.848	SUBCLONAL	1	TRUE	0	0.564032268082198	1		590	487	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0000594-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	291	327	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.564032268082198	4	FACETS	0.839	0.79	0.888			1	CLONAL	2	TRUE	NA	0.564032268082198	4		327	962	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138409905	138409905	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000594-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	220	322	0	ENST00000289153.2:c.1973G>C	p.Arg658Thr	p.R658T	ENST00000289153	NM_006219.2	658	aGa/aCa	13/22	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.564032268082198	2		322	745	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092966	29092966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000594-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	109	264	0	ENST00000328354.6:c.1018G>A	p.Glu340Lys	p.E340K	ENST00000328354	NM_007194.3	340	Gaa/Aaa	10/15	1	2	FACETS	0.853	0.771	0.939	0.853	0.771	0.939	CLONAL	1	TRUE	1	0.564032268082198	2		264	453	SUCCESS
CBL	867	MSKCC	GRCh37	11	119168143	119168144	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0000594-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	122	278	0	ENST00000264033.4:c.2205_2206del	p.Tyr735Ter	p.Y735*	ENST00000264033	NM_005188.3	735	TAt/t	14/16	1	2	FACETS	0.768	0.697	0.843	0.768	0.697	0.843	SUBCLONAL	1	TRUE	1	0.564032268082198	2		278	563	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0000614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	503	295	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	0.3	2	FACETS	1	0.996	1	1	0.996	1	INDETERMINATE	2	TRUE	0	0.62	2		295	701	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226579931	226579931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765535441	NA	P-0000614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	271	607	0	ENST00000366794.5:c.371C>T	p.Thr124Met	p.T124M	ENST00000366794	NM_001618.3	124	aCg/aTg	3/23	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.62	2		607	762	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0000614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	331	280	2	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	1	2	FACETS	0.803	0.766	0.84	1	0.996	1	CLONAL	2	TRUE	1	0.62	2		282	665	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0000614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	82	168	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.3	2	FACETS	0.816	0.741	0.891	0.816	0.741	0.891	INDETERMINATE	2	TRUE	0	0.62	2		168	162	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11177098	11177098	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	47	574	0	ENST00000361445.4:c.6979A>G	p.Met2327Val	p.M2327V	ENST00000361445	NM_004958.3	2327	Atg/Gtg	50/58	1	2	FACETS	0.238	0.2	0.279	0.238	0.2	0.279	SUBCLONAL	1	TRUE	1	0.62	2		574	638	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101099	27101099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	74	498	0	ENST00000324856.7:c.4381C>T	p.Arg1461Ter	p.R1461*	ENST00000324856	NM_006015.4	1461	Cga/Tga	18/20	1	2	FACETS	0.237	0.207	0.27	0.237	0.207	0.27	SUBCLONAL	1	TRUE	1	0.62	2		498	1007	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461933	120461933	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0000614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	134	201	0	ENST00000256646.2:c.5781+2T>C		p.X1927_splice	ENST00000256646	NM_024408.3	1927			1	2	FACETS	0.91	0.833	0.99	0.91	0.833	0.99	CLONAL	1	TRUE	1	0.62	2		201	475	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641433	47641433	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs144288433	NA	P-0000614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	68	489	0	ENST00000233146.2:c.818T>C	p.Val273Ala	p.V273A	ENST00000233146	NM_000251.2	273	gTa/gCa	5/16	1	2	FACETS	0.369	0.321	0.421	0.369	0.321	0.421	SUBCLONAL	1	TRUE	1	0.62	2		489	595	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215235	142215235	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	114	408	0	ENST00000350721.4:c.5866T>A	p.Tyr1956Asn	p.Y1956N	ENST00000350721	NM_001184.3	1956	Tac/Aac	34/47	1	2	FACETS	0.737	0.667	0.81	0.737	0.667	0.81	SUBCLONAL	1	TRUE	1	0.62	2		408	499	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131976413	131976413	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	204	372	0	ENST00000265335.6:c.3668T>C	p.Leu1223Pro	p.L1223P	ENST00000265335		1223	cTc/cCc	24/25	1	2	FACETS	0.858	0.798	0.92	0.858	0.798	0.92	CLONAL	1	TRUE	1	0.62	2		372	767	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6037056	6037056	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	rs745487791	NA	P-0000614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	145	314	0	ENST00000265849.7:c.706-2A>C		p.X236_splice	ENST00000265849	NM_000535.5	236			1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.62	2		314	465	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787774	135787774	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	156	358	0	ENST00000298552.3:c.808T>C	p.Ser270Pro	p.S270P	ENST00000298552	NM_001162426.1	270	Tca/Cca	9/23	1	2	FACETS	0.814	0.749	0.882	0.814	0.749	0.882	CLONAL	1	TRUE	1	0.62	2		358	618	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022819	12022819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465114480	NA	P-0000614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	135	193	0	ENST00000396373.4:c.925C>T	p.Arg309Trp	p.R309W	ENST00000396373	NM_001987.4	309	Cgg/Tgg	5/8	0.3	4	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.62	4		193	509	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434449	121434449	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	296	450	0	ENST00000257555.6:c.1213A>G	p.Met405Val	p.M405V	ENST00000257555		405	Atg/Gtg	6/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.62	2		450	882	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252733	133252733	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	253	440	0	ENST00000320574.5:c.967A>G	p.Thr323Ala	p.T323A	ENST00000320574	NM_006231.2	323	Acc/Gcc	10/49	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.62	2		440	685	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21565453	21565453	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1444567100	NA	P-0000614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	409	601	0	ENST00000382592.4:c.433A>G	p.Arg145Gly	p.R145G	ENST00000382592	NM_014572.2	145	Agg/Ggg	3/8	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.62	2		601	1087	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763414	59763414	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	20	384	0	ENST00000259008.2:c.2688A>G	p.Ile896Met	p.I896M	ENST00000259008	NM_032043.2	896	atA/atG	19/20	1	2	FACETS	0.194	0.148	0.248	0.194	0.148	0.248	SUBCLONAL	1	TRUE	1	0.62	2		384	332	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0000614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	72	441	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.66	0.58	0.744	0.66	0.58	0.744	SUBCLONAL	1	TRUE	1	0.62	2		441	352	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122684	7122684	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs957304581	NA	P-0000614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	262	398	0	ENST00000302850.5:c.3470A>G	p.His1157Arg	p.H1157R	ENST00000302850	NM_000208.2	1157	cAt/cGt	19/22	1	2	FACETS	0.918	0.861	0.975	0.918	0.861	0.975	CLONAL	1	TRUE	1	0.62	2		398	921	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860915	45860915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs563069969	NA	P-0000614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	219	333	1	ENST00000391945.4:c.1280C>T	p.Thr427Ile	p.T427I	ENST00000391945	NM_000400.3	427	aCc/aTc	13/23	1	2	FACETS	0.868	0.809	0.928	0.868	0.809	0.928	CLONAL	1	TRUE	1	0.62	2		334	814	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357474	70357474	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs867091628	NA	P-0000614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	290	573	1	ENST00000374080.3:c.5815C>T	p.Gln1939Ter	p.Q1939*	ENST00000374080		1939	Cag/Tag	40/45	0.250641487143669	0	FACETS	0.445	0.421	0.471			1	INDETERMINATE	1	TRUE	0	0.62	0		574	798	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361105	70361105	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	231	288	0	ENST00000374080.3:c.6293A>C	p.Gln2098Pro	p.Q2098P	ENST00000374080		2098	cAg/cCg	43/45	0.250641487143669	0	FACETS	0.407	0.381	0.433			1	INDETERMINATE	1	TRUE	0	0.62	0		288	696	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182129	11182132	+	frameshift_variant	Frame_Shift_Del	DEL	CCAG	CCAG	-	novel	NA	P-0000614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	47	332	0	ENST00000361445.4:c.6714_6717del	p.Trp2239PhefsTer39	p.W2239Ffs*39	ENST00000361445	NM_004958.3	2238	ggCTGG/gg	48/58	1	2	FACETS	0.172	0.144	0.203	0.172	0.144	0.203	SUBCLONAL	1	TRUE	1	0.62	2		332	882	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256205	16256205	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0000614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	150	367	0	ENST00000375759.3:c.3475del	p.Ile1159LeufsTer28	p.I1159Lfs*28	ENST00000375759	NM_015001.2	1157	gAa/ga	11/15	1	2	FACETS	0.766	0.702	0.832	0.766	0.702	0.832	SUBCLONAL	1	TRUE	1	0.62	2		367	632	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259042	16259043	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0000614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	35	229	0	ENST00000375759.3:c.6313dup	p.Ala2105GlyfsTer18	p.A2105Gfs*18	ENST00000375759	NM_015001.2	2103	agg/aGgg	11/15	1	2	FACETS	0.187	0.152	0.226	0.187	0.152	0.226	SUBCLONAL	1	TRUE	1	0.62	2		229	604	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088787	27088788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0000614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	202	277	0	ENST00000324856.7:c.2402dup	p.Gln802SerfsTer15	p.Q802Sfs*15	ENST00000324856	NM_006015.4	799	cag/caGg	7/20	1	2	FACETS	0.97	0.903	1	0.97	0.903	1	CLONAL	1	TRUE	1	0.62	2		277	672	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106809	27106810	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	259	336	0	ENST00000324856.7:c.6420_6421insA	p.Phe2141IlefsTer9	p.F2141Ifs*9	ENST00000324856	NM_006015.4	2140	-/A	20/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.62	2		336	794	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455289	29455290	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0000614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	160	318	0	ENST00000389048.3:c.2512dup	p.Leu838ProfsTer27	p.L838Pfs*27	ENST00000389048	NM_004304.4	838	ctg/cCtg	15/29	1	2	FACETS	0.726	0.667	0.787	0.726	0.667	0.787	SUBCLONAL	1	TRUE	1	0.62	2		318	711	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589610	67589612	+	inframe_deletion	In_Frame_Del	DEL	AAA	AAA	-	novel	NA	P-0000614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	77	202	0	ENST00000274335.5:c.1376_1378del	p.Lys459del	p.K459del	ENST00000274335		458	gAAAaa/gaa	10/15	1	2	FACETS	0.927	0.824	1	0.927	0.824	1	CLONAL	1	TRUE	1	0.62	2		202	268	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6037056	6037056	+	splice_acceptor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0000614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	30	314	0	ENST00000265849.7:c.706-2del		p.X236_splice	ENST00000265849	NM_000535.5	236			1	2	FACETS	0.208	0.167	0.255	0.208	0.167	0.255	SUBCLONAL	1	TRUE	1	0.62	2		314	465	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434073	49434074	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1555192051	NA	P-0000614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	148	221	0	ENST00000301067.7:c.7479dup	p.Phe2494ValfsTer12	p.F2494Vfs*12	ENST00000301067	NM_003482.3	2493	-/G	31/54	1	2	FACETS	0.848	0.778	0.92	0.848	0.778	0.92	CLONAL	1	TRUE	1	0.62	2		221	563	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0000614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	142	498	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.929	0.853	1	0.929	0.853	1	CLONAL	1	TRUE	1	0.62	2		498	493	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486049	29486050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	112	264	0	ENST00000356175.3:c.233dup	p.Asn78LysfsTer29	p.N78Kfs*29	ENST00000356175	NM_000267.3	76	gaa/gAaa	3/57	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.62	2		264	343	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0000616-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	737	365	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.611581215894827	10	FACETS	1	0.993	1			1	CLONAL	6	FALSE	NA	0.611581215894827	10		365	1295	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435160	56435161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755128667	NA	P-0000616-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	155	375	0	ENST00000407977.2:c.1976dup	p.Pro660SerfsTer87	p.P660Sfs*87	ENST00000407977		659	ggt/ggGt	9/10	0.439165553122837	4	FACETS	0.929	0.868	0.99			1	CLONAL	3	FALSE	NA	0.611581215894827	4		375	293	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268766	41268766	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000616-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	219	480	0	ENST00000349496.5:c.1004A>T	p.Lys335Ile	p.K335I	ENST00000349496	NM_001904.3	335	aAa/aTa	7/15	0.611581215894827	3	FACETS	0.884	0.83	0.939	0.884	0.83	0.939	CLONAL	2	FALSE	1	0.611581215894827	3		480	529	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528031	157528031	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000616-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	88	340	0	ENST00000346085.5:c.5756T>A	p.Leu1919Gln	p.L1919Q	ENST00000346085	NM_020732.3	1919	cTg/cAg	20/20	0.611581215894827	3	FACETS	1	0.961	1	0.58	0.519	0.644	CLONAL	1	FALSE	1	0.611581215894827	3		340	324	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245419	41245419	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000616-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	133	602	0	ENST00000357654.3:c.2129C>T	p.Thr710Ile	p.T710I	ENST00000357654	NM_007294.3	710	aCt/aTt	10/23	0.611581215894827	2	FACETS	0.843	0.77	0.919	0.421	0.385	0.46	CLONAL	1	FALSE	0	0.611581215894827	2		602	516	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216376	2216376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs573741033	NA	P-0000616-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	42	512	0	ENST00000398665.3:c.2020C>T	p.Arg674Cys	p.R674C	ENST00000398665	NM_032482.2	674	Cgt/Tgt	20/28	0.611581215894827	1	FACETS	0.596	0.506	0.692	0.596	0.506	0.692	SUBCLONAL	1	FALSE	0	0.611581215894827	1		512	160	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578244	7578261	+	inframe_deletion	In_Frame_Del	DEL	CGCAAATTTCCTTCCACT	CGCAAATTTCCTTCCACT	-	novel	NA	P-0000616-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	113	611	0	ENST00000269305.4:c.588_605del	p.Gly199_Glu204del	p.G199_E204del	ENST00000269305	NM_001126112.2	196	cgAGTGGAAGGAAATTTGCGt/cgt	6/11	0.611581215894827	2	FACETS	1	0.985	1	0.705	0.646	0.765	CLONAL	1	FALSE	0	0.611581215894827	2		611	262	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944429	40944429	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000616-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	80	586	0	ENST00000373198.4:c.2073G>T	p.Trp691Cys	p.W691C	ENST00000373198	NM_133170.3	691	tgG/tgT	12/32	0.611581215894827	5	FACETS	0.708	0.623	0.8	0.236	0.207	0.267	SUBCLONAL	1	FALSE	2	0.611581215894827	5		586	708	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	57	245	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.953	1			1	INDETERMINATE	1	TRUE	NA	0.22	2		245	410	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0000627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	123	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.22	2		311	942	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445061	89445061	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs764806570	NA	P-0000627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	87	583	0	ENST00000336596.2:c.1381G>C	p.Glu461Gln	p.E461Q	ENST00000336596	NM_005233.5	461	Gaa/Caa	6/17	1	2	FACETS	0.815	0.719	0.917	0.815	0.719	0.917	CLONAL	1	TRUE	1	0.22	2		583	971	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955141	55955141	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0000627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	76	440	0	ENST00000263923.4:c.3405-1G>T		p.X1135_splice	ENST00000263923	NM_002253.2	1135			1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.22	2		440	636	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519237	187519237	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	111	508	0	ENST00000441802.2:c.12146G>C	p.Cys4049Ser	p.C4049S	ENST00000441802	NM_005245.3	4049	tGt/tCt	23/27	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.22	2		508	895	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523142	176523142	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	74	554	0	ENST00000292408.4:c.1906G>C	p.Gly636Arg	p.G636R	ENST00000292408	NM_213647.1	636	Ggc/Cgc	14/18	NA	2	FACETS	0.923	0.807	1			1	INDETERMINATE	1	TRUE	NA	0.22	2		554	729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579589	7579589	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	77	418	0	ENST00000269305.4:c.98C>T	p.Ser33Phe	p.S33F	ENST00000269305	NM_001126112.2	33	tCc/tTc	4/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.22	2		418	576	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15821910	15821910	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1369	180	938	0	ENST00000307771.7:c.303A>T	p.Glu101Asp	p.E101D	ENST00000307771	NM_005089.3	101	gaA/gaT	4/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.22	2		938	1549	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922264	39922264	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	75	473	0	ENST00000378444.4:c.3908G>T	p.Gly1303Val	p.G1303V	ENST00000378444	NM_001123385.1	1303	gGc/gTc	9/15	1	2	FACETS	0.943	0.826	1	0.943	0.826	1	CLONAL	1	TRUE	1	0.22	2		473	723	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968644	55968645	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	142	607	0	ENST00000263923.4:c.2018dup	p.Glu674GlyfsTer29	p.E674Gfs*29	ENST00000263923	NM_002253.2	673	ctg/ctTg	14/30	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.22	2		607	1110	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0000628-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	3348	310	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.81866053815032	22	FACETS	1	0.998	1			1	CLONAL	20	TRUE	NA	0.81866053815032	22		310	3704	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0000628-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	626	485	1	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.81866053815032	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.81866053815032	2		486	760	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151625	55151625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571523023	NA	P-0000628-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	875	601	0	ENST00000257290.5:c.2411G>A	p.Arg804Gln	p.R804Q	ENST00000257290	NM_006206.4	804	cGa/cAa	17/23	0.81866053815032	2	FACETS	0.997	0.979	1	0.997	0.979	1	CLONAL	2	TRUE	0	0.81866053815032	2		601	1072	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143040	47143041	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTCCACT	novel	NA	P-0000628-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	244	436	0	ENST00000409792.3:c.4918-2_4922dup	p.Asn1643AspfsTer25	p.N1643Dfs*25	ENST00000409792	NM_014159.6	1641	act/acAGTGGACt	8/21	0.81866053815032	2	FACETS	0.549	0.513	0.587	0.275	0.256	0.294	SUBCLONAL	1	TRUE	0	0.81866053815032	2		436	1085	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0000630-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	26	328	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.288609544910433	1	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	0	0.288609544910433	1		328	140	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28929495	NA	P-0000630-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	100	563	1	ENST00000275493.2:c.2155G>A	p.Gly719Ser	p.G719S	ENST00000275493	NM_005228.3	719	Ggc/Agc	18/28	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.288609544910433	2		564	605	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241677	55241677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504256	NA	P-0000630-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	109	443	0	ENST00000275493.2:c.2125G>A	p.Glu709Lys	p.E709K	ENST00000275493	NM_005228.3	709	Gaa/Aaa	18/28	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.288609544910433	2		443	697	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937179	76937179	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000630-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	39	1224	0	ENST00000373344.5:c.3569G>A	p.Arg1190Lys	p.R1190K	ENST00000373344	NM_000489.3	1190	aGa/aAa	9/35	0.288609544910433	0	FACETS	0.262	0.216	0.314			1	SUBCLONAL	1	TRUE	0	0.288609544910433	0		1224	733	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059128	47059129	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0000630-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	173	521	0	ENST00000409792.3:c.7532dup	p.Leu2512AlafsTer8	p.L2512Afs*8	ENST00000409792	NM_014159.6	2511	aag/aaAg	20/21	0.288609544910433	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.288609544910433	1		521	693	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577035	7577036	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0000632-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	149	569	0	ENST00000269305.4:c.902dup	p.Gly302ArgfsTer4	p.G302Rfs*4	ENST00000269305	NM_001126112.2	301	cca/ccCa	8/11	0.379617228296981	1	FACETS	0.806	0.737	0.878	0.806	0.737	0.878	CLONAL	1	TRUE	0	0.379617228296981	1		569	789	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0000637-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	193	625	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.878	0.816	0.943	0.878	0.816	0.943	CLONAL	1	TRUE	1	0.65490184754662	2		625	671	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0000637-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	86	284	0	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	0.25395729639269	1	FACETS	0.261	0.231	0.293	0.261	0.231	0.293	INDETERMINATE	1	TRUE	0	0.65490184754662	1		284	677	SUCCESS
AR	367	MSKCC	GRCh37	X	66766350	66766351	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGT	rs746958859	NA	P-0000637-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	63	78	1	ENST00000374690.3:c.1368_1370dup	p.Gly473dup	p.G473dup	ENST00000374690	NM_000044.3	473	-/GGT	1/8	0.65490184754662	1	FACETS	0.892	0.793	0.993	0.892	0.793	0.993	CLONAL	1	TRUE	0	0.65490184754662	1		79	145	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598108	52598108	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000637-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	324	758	0	ENST00000394830.3:c.3758C>A	p.Ser1253Ter	p.S1253*	ENST00000394830	NM_018313.4	1253	tCa/tAa	24/30	0.65490184754662	1	FACETS	0.935	0.889	0.98	0.935	0.889	0.98	CLONAL	1	TRUE	0	0.65490184754662	1		758	712	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685321	86685321	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs993477801	NA	P-0000637-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	75	181	0	ENST00000274376.6:c.3037A>G	p.Ser1013Gly	p.S1013G	ENST00000274376	NM_002890.2	1013	Agt/Ggt	24/25	1	2	FACETS	0.478	0.42	0.54	0.478	0.42	0.54	SUBCLONAL	1	TRUE	1	0.65490184754662	2		181	479	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527589	157527589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000637-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	24	186	0	ENST00000346085.5:c.5314G>A	p.Ala1772Thr	p.A1772T	ENST00000346085	NM_020732.3	1772	Gca/Aca	20/20	0.65490184754662	1	FACETS	0.139	0.108	0.174	0.139	0.108	0.174	SUBCLONAL	1	TRUE	0	0.65490184754662	1		186	355	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951891	2951891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs116583746	NA	P-0000637-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	299	387	0	ENST00000396946.4:c.3059C>T	p.Thr1020Met	p.T1020M	ENST00000396946	NM_032415.4	1020	aCg/aTg	23/25	0.463108554905248	3	FACETS	1	0.989	1	0.591	0.557	0.625	CLONAL	1	TRUE	1	0.65490184754662	3		387	1026	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436635	52436641	+	frameshift_variant	Frame_Shift_Del	DEL	GAGATAA	GAGATAA	-	novel	NA	P-0000637-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	135	297	0	ENST00000460680.1:c.2033_2039del	p.Phe678SerfsTer12	p.F678Sfs*12	ENST00000460680	NM_004656.3	678	tTTATCTCc/tc	16/17	0.65490184754662	1	FACETS	0.823	0.758	0.888	0.823	0.758	0.888	CLONAL	1	TRUE	0	0.65490184754662	1		297	337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0000670-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	19	245	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.147322794264108	4	FACETS	1	0.836	1	0.567	0.431	0.726	CLONAL	1	TRUE	2	0.16	4		245	243	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606715	29606715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000670-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	18	231	1	ENST00000389048.3:c.1165C>T	p.Leu389Phe	p.L389F	ENST00000389048	NM_004304.4	389	Ctc/Ttc	5/29	1	2	FACETS	0.733	0.552	0.947	0.733	0.552	0.947	CLONAL	1	TRUE	1	0.16	2		232	307	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024518	16024518	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780814332	NA	P-0000670-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	39	438	0	ENST00000268712.3:c.1700C>T	p.Ala567Val	p.A567V	ENST00000268712	NM_006311.3	567	gCc/gTc	16/46	NA	2	FACETS	0.634	0.524	0.758			1	INDETERMINATE	1	TRUE	NA	0.16	2		438	769	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249013	55249014	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACCCCC	novel	NA	P-0000670-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	43	236	0	ENST00000275493.2:c.2314_2319dup	p.Pro772_His773dup	p.P772_H773dup	ENST00000275493	NM_005228.3	772	aac/aACCCCCac	20/28	0.236616200670139	3	FACETS	0.829	0.696	0.976	0.829	0.696	0.976	CLONAL	2	TRUE	1	0.16	3		236	350	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974712	21974720	+	inframe_deletion	In_Frame_Del	DEL	TGGGCAGCG	TGGGCAGCG	-	novel	NA	P-0000670-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	17	219	0	ENST00000304494.5:c.107_115del	p.Ala36_Asn39delinsAsp	p.A36_N39delinsD	ENST00000304494	NM_000077.4	36	gCGCTGCCCAac/gac	1/3	1	2	FACETS	0.874	0.653	1	0.874	0.653	1	CLONAL	1	TRUE	1	0.16	2		219	243	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692894	89692895	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGAAAGGGAC	novel	NA	P-0000728-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	34	106	0	ENST00000371953.3:c.380_389dup	p.Thr131LysfsTer52	p.T131Kfs*52	ENST00000371953	NM_000314.4	126	-/GGAAAGGGAC	5/9	0.567703029802867	1	FACETS	0.393	0.324	0.471	0.393	0.324	0.471	SUBCLONAL	1	TRUE	0	0.567703029802867	1		106	218	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0000729-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	138	437	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.432553863052947	2		437	635	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884866	134884866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000729-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	170	365	0	ENST00000398015.3:c.1642G>A	p.Ala548Thr	p.A548T	ENST00000398015	NM_004441.4	548	Gcc/Acc	8/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.432553863052947	2		365	678	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459525	50459525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778820674	NA	P-0000729-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	75	209	0	ENST00000331340.3:c.814G>A	p.Ala272Thr	p.A272T	ENST00000331340	NM_006060.4	272	Gcc/Acc	7/8	1	2	FACETS	0.705	0.619	0.797	0.705	0.619	0.797	SUBCLONAL	1	TRUE	1	0.432553863052947	2		209	492	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433896	49433896	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000729-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	115	239	0	ENST00000301067.7:c.7657C>T	p.Gln2553Ter	p.Q2553*	ENST00000301067	NM_003482.3	2553	Cag/Tag	31/54	1	2	FACETS	0.994	0.899	1	0.994	0.899	1	CLONAL	1	TRUE	1	0.432553863052947	2		239	535	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434618	49434618	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0000729-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	112	244	0	ENST00000301067.7:c.6935C>G	p.Ser2312Ter	p.S2312*	ENST00000301067	NM_003482.3	2312	tCa/tGa	31/54	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.432553863052947	2		244	499	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012398	29012398	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000729-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	98	427	0	ENST00000282397.4:c.473G>T	p.Cys158Phe	p.C158F	ENST00000282397	NM_002019.4	158	tGc/tTc	4/30	0.387178157010664	1	FACETS	0.618	0.552	0.687	0.618	0.552	0.687	SUBCLONAL	1	TRUE	0	0.432553863052947	1		427	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579386	7579386	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0000729-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	147	256	0	ENST00000269305.4:c.301A>T	p.Lys101Ter	p.K101*	ENST00000269305	NM_001126112.2	101	Aaa/Taa	4/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.432553863052947	2		256	563	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602475	10602475	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000729-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	152	318	1	ENST00000171111.5:c.1103G>T	p.Cys368Phe	p.C368F	ENST00000171111	NM_203500.1	368	tGc/tTc	3/6	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.432553863052947	2		319	647	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950343	17950344	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0000729-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	163	357	0	ENST00000458235.1:c.1383dup	p.Leu462AlafsTer58	p.L462Afs*58	ENST00000458235	NM_000215.3	461	-/G	10/24	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.432553863052947	2		357	720	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610287	10610299	+	frameshift_variant	Frame_Shift_Del	DEL	GTAGGCGAATTCA	GTAGGCGAATTCA	CC	novel	NA	P-0000729-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	69	379	0	ENST00000171111.5:c.411_423delinsGG	p.Ile137MetfsTer33	p.I137Mfs*33	ENST00000171111	NM_203500.1	137	atTGAATTCGCCTAC/atGG	2/6	1	2	FACETS	0.503	0.438	0.574	0.503	0.438	0.574	SUBCLONAL	1	TRUE	1	0.432553863052947	2		379	634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0000751-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	134	590	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.48751050518161	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.48751050518161	1		590	356	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0000751-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	71	286	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.360451888614439	2	FACETS	1	0.953	1	0.578	0.511	0.648	CLONAL	1	TRUE	0	0.48751050518161	2		286	252	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0000751-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	106	621	1	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.87	0.783	0.961	0.87	0.783	0.961	CLONAL	1	TRUE	1	0.48751050518161	2		622	500	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641527	23641527	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000751-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	150	566	0	ENST00000261584.4:c.1948G>C	p.Glu650Gln	p.E650Q	ENST00000261584	NM_024675.3	650	Gag/Cag	5/13	0.48751050518161	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.48751050518161	1		566	382	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984788	11984788	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000751-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	78	232	0	ENST00000353533.5:c.334G>T	p.Ala112Ser	p.A112S	ENST00000353533	NM_003010.3	112	Gct/Tct	3/11	0.48751050518161	1	FACETS	0.903	0.803	1	0.903	0.803	1	CLONAL	1	TRUE	0	0.48751050518161	1		232	268	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221946	1221946	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0000751-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	124	492	0	ENST00000326873.7:c.863-2A>C		p.X288_splice	ENST00000326873	NM_000455.4	288			0.48751050518161	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.48751050518161	1		492	338	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0000802-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	357	697	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.805290013485997	4	FACETS	0.873	0.839	0.906	0.873	0.839	0.906	CLONAL	3	TRUE	1	0.949447611114419	4		697	560	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844747	156844747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771342578	NA	P-0000802-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1426	518	398	0	ENST00000524377.1:c.1301C>T	p.Thr434Met	p.T434M	ENST00000524377	NM_002529.3	434	aCg/aTg	11/17	0.949447611114419	6	FACETS	0.814	0.777	0.85	0.407	0.388	0.425	CLONAL	2	TRUE	2	0.949447611114419	6		398	1944	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175972	176175972	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000802-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	20	50	0	ENST00000367669.3:c.143T>C	p.Val48Ala	p.V48A	ENST00000367669	NM_022457.5	48	gTg/gCg	1/20	0.949447611114419	6	FACETS	0.639	0.491	0.811	0.16	0.122	0.203	SUBCLONAL	1	TRUE	2	0.949447611114419	6		50	191	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570070	212570070	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745408040	NA	P-0000802-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	134	370	0	ENST00000342788.4:c.1171G>A	p.Val391Ile	p.V391I	ENST00000342788	NM_005235.2	391	Gtc/Atc	10/28	0.699077629655444	4	FACETS	0.88	0.802	0.962	0.293	0.267	0.321	CLONAL	1	TRUE	1	0.949447611114419	4		370	625	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564590	86564590	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000802-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	140	274	0	ENST00000274376.6:c.322G>T	p.Ala108Ser	p.A108S	ENST00000274376	NM_002890.2	108	Gct/Tct	1/25	0.803143713145923	4	FACETS	0.841	0.767	0.917	0.42	0.383	0.459	CLONAL	1	TRUE	2	0.949447611114419	4		274	684	SUCCESS
APC	324	MSKCC	GRCh37	5	112174400	112174400	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0000802-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	59	112	0	ENST00000257430.4:c.3110del	p.Asn1037ThrfsTer19	p.N1037Tfs*19	ENST00000257430	NM_000038.5	1037	Aac/ac	16/16	0.803143713145923	4	FACETS	0.787	0.693	0.883	0.787	0.693	0.883	SUBCLONAL	2	TRUE	2	0.949447611114419	4		112	154	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196695	67196696	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0000802-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	170	145	0	ENST00000312629.5:c.230dup	p.Tyr78LeufsTer42	p.Y78Lfs*42	ENST00000312629	NM_003952.2	75	aag/aaGg	3/15	0.780386424820869	3	FACETS	0.8	0.749	0.851	0.8	0.749	0.851	SUBCLONAL	2	TRUE	1	0.949447611114419	3		145	330	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117958	70117959	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0000802-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	229	91	0	ENST00000245479.2:c.427dup	p.Trp143LeufsTer109	p.W143Lfs*109	ENST00000245479	NM_000346.3	142	-/T	1/3	0.949447611114419	4	FACETS	0.925	0.883	0.965	0.925	0.883	0.965	CLONAL	3	TRUE	1	0.949447611114419	4		91	339	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231863	36231879	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTGAAGCTTTTCCCTGT	GTGAAGCTTTTCCCTGT	-	novel	NA	P-0000802-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	178	240	0	ENST00000300305.3:c.509-4_521del		p.X170_splice	ENST00000300305		170		5/8	0.580349739372313	6	FACETS	0.827	0.765	0.891	0.551	0.51	0.594	CLONAL	2	TRUE	3	0.949447611114419	6		240	657	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0000820-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	298	586	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.474382144546967	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.711298566781112	1		586	515	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252994	36252995	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0000820-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	67	173	0	ENST00000300305.3:c.367dup	p.Asp123GlyfsTer15	p.D123Gfs*15	ENST00000300305		123	gat/gGat	4/8	0.276025250037041	3	FACETS	1	0.913	1	0.523	0.46	0.589	INDETERMINATE	1	TRUE	1	0.711298566781112	3		173	244	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254815	16254815	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000820-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	51	293	1	ENST00000375759.3:c.2080G>T	p.Glu694Ter	p.E694*	ENST00000375759	NM_015001.2	694	Gaa/Taa	11/15	0.711298566781112	1	FACETS	0.464	0.4	0.533	0.464	0.4	0.533	SUBCLONAL	1	TRUE	0	0.711298566781112	1		294	199	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	290	872	2	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.848175524457981	2		874	675	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	47	349	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	0.167	0.14	0.196	0.167	0.14	0.196	SUBCLONAL	1	TRUE	1	0.848175524457981	2		349	664	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725198	49725198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759497617	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	32	132	1	ENST00000449682.2:c.227C>T	p.Pro76Leu	p.P76L	ENST00000449682	NM_020998.3	76	cCc/cTc	2/18	1	2	FACETS	0.253	0.206	0.306	0.253	0.206	0.306	SUBCLONAL	1	TRUE	1	0.848175524457981	2		133	298	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553703	29553703	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1555613843	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	28	222	0	ENST00000356175.3:c.2251+1G>A		p.X751_splice	ENST00000356175	NM_000267.3	751			1	2	FACETS	0.159	0.126	0.196	0.159	0.126	0.196	SUBCLONAL	1	TRUE	1	0.848175524457981	2		222	416	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023352	27023352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769828930	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	57	254	1	ENST00000324856.7:c.458C>T	p.Pro153Leu	p.P153L	ENST00000324856	NM_006015.4	153	cCc/cTc	1/20	1	2	FACETS	0.256	0.219	0.296	0.256	0.219	0.296	SUBCLONAL	1	TRUE	1	0.848175524457981	2		255	525	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163760	72163760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	39	676	2	ENST00000357731.5:c.598G>A	p.Glu200Lys	p.E200K	ENST00000357731	NM_173808.2	200	Gaa/Aaa	4/7	1	2	FACETS	0.143	0.118	0.171	0.143	0.118	0.171	SUBCLONAL	1	TRUE	1	0.848175524457981	2		678	643	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635539	47635539	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs267607914	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	160	247	0	ENST00000233146.2:c.212-1G>A		p.X71_splice	ENST00000233146	NM_000251.2	71			1	2	FACETS	0.796	0.736	0.857	0.796	0.736	0.857	SUBCLONAL	1	TRUE	1	0.848175524457981	2		247	474	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702268	47702268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	238	491	1	ENST00000233146.2:c.1864C>T	p.Pro622Ser	p.P622S	ENST00000233146	NM_000251.2	622	Cca/Tca	12/16	1	2	FACETS	0.815	0.764	0.866	0.815	0.764	0.866	CLONAL	1	TRUE	1	0.848175524457981	2		492	689	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212289026	212289026	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	67	353	0	ENST00000342788.4:c.2720G>A	p.Gly907Glu	p.G907E	ENST00000342788	NM_005235.2	907	gGa/gAa	23/28	1	2	FACETS	0.354	0.308	0.403	0.354	0.308	0.403	SUBCLONAL	1	TRUE	1	0.848175524457981	2		353	446	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749371	41749371	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	27	192	0	ENST00000226382.2:c.424G>A	p.Val142Ile	p.V142I	ENST00000226382	NM_003924.3	142	Gtc/Atc	2/3	1	2	FACETS	0.128	0.101	0.158	0.128	0.101	0.158	SUBCLONAL	1	TRUE	1	0.848175524457981	2		192	498	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161308	55161308	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	222	309	0	ENST00000257290.5:c.3139G>A	p.Glu1047Lys	p.E1047K	ENST00000257290	NM_006206.4	1047	Gag/Aag	23/23	1	2	FACETS	0.78	0.73	0.832	0.78	0.73	0.832	SUBCLONAL	1	TRUE	1	0.848175524457981	2		309	671	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564602	55564602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	63	429	0	ENST00000288135.5:c.490C>T	p.Pro164Ser	p.P164S	ENST00000288135	NM_000222.2	164	Cct/Tct	3/21	1	2	FACETS	0.16	0.137	0.184	0.16	0.137	0.184	SUBCLONAL	1	TRUE	1	0.848175524457981	2		429	931	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532678	187532678	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777770871	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	83	457	0	ENST00000441802.2:c.9715G>A	p.Val3239Met	p.V3239M	ENST00000441802	NM_005245.3	3239	Gtg/Atg	14/27	1	2	FACETS	0.284	0.251	0.321	0.284	0.251	0.321	SUBCLONAL	1	TRUE	1	0.848175524457981	2		457	688	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630960	187630960	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	71	316	0	ENST00000441802.2:c.22C>T	p.Leu8Phe	p.L8F	ENST00000441802	NM_005245.3	8	Ctc/Ttc	2/27	1	2	FACETS	0.286	0.25	0.326	0.286	0.25	0.326	SUBCLONAL	1	TRUE	1	0.848175524457981	2		316	585	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176516646	176516646	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776518605	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	50	330	2	ENST00000292408.4:c.43C>T	p.Pro15Ser	p.P15S	ENST00000292408	NM_213647.1	15	Cct/Tct	2/18	1	2	FACETS	0.154	0.13	0.18	0.154	0.13	0.18	SUBCLONAL	1	TRUE	1	0.848175524457981	2		332	768	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517827	176517827	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	67	404	0	ENST00000292408.4:c.436+1G>A		p.X146_splice	ENST00000292408	NM_213647.1	146			1	2	FACETS	0.212	0.183	0.243	0.212	0.183	0.243	SUBCLONAL	1	TRUE	1	0.848175524457981	2		404	746	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046758	180046758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	39	222	0	ENST00000261937.6:c.2554G>A	p.Gly852Ser	p.G852S	ENST00000261937	NM_182925.4	852	Ggc/Agc	18/30	1	2	FACETS	0.155	0.128	0.186	0.155	0.128	0.186	SUBCLONAL	1	TRUE	1	0.848175524457981	2		222	592	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680022	30680022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	105	491	0	ENST00000376406.3:c.1697C>T	p.Ser566Phe	p.S566F	ENST00000376406	NM_014641.2	566	tCt/tTt	5/15	1	2	FACETS	0.244	0.218	0.272	0.244	0.218	0.272	SUBCLONAL	1	TRUE	1	0.848175524457981	2		491	1015	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288912	33288912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	90	210	0	ENST00000374542.5:c.640G>A	p.Glu214Lys	p.E214K	ENST00000374542	NM_001141970.1	214	Gaa/Aaa	3/8	1	2	FACETS	0.4	0.355	0.447	0.4	0.355	0.447	SUBCLONAL	1	TRUE	1	0.848175524457981	2		210	531	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508481	106508481	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	20	92	0	ENST00000359195.3:c.475G>A	p.Gly159Ser	p.G159S	ENST00000359195	NM_002649.2	159	Ggc/Agc	2/11	1	2	FACETS	0.227	0.174	0.288	0.227	0.174	0.288	SUBCLONAL	1	TRUE	1	0.848175524457981	2		92	208	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514971	148514971	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	285	483	0	ENST00000320356.2:c.1238C>T	p.Ser413Phe	p.S413F	ENST00000320356	NM_004456.4	413	tCt/tTt	10/20	1	2	FACETS	0.851	0.803	0.899	0.851	0.803	0.899	CLONAL	1	TRUE	1	0.848175524457981	2		483	790	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317114	87317114	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	60	409	0	ENST00000277120.3:c.253G>A	p.Asp85Asn	p.D85N	ENST00000277120		85	Gat/Aat	3/19	1	2	FACETS	0.199	0.171	0.23	0.199	0.171	0.23	SUBCLONAL	1	TRUE	1	0.848175524457981	2		409	710	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482301	87482301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	55	504	0	ENST00000277120.3:c.1588C>T	p.Pro530Ser	p.P530S	ENST00000277120		530	Ccc/Tcc	14/19	1	2	FACETS	0.162	0.137	0.188	0.162	0.137	0.188	SUBCLONAL	1	TRUE	1	0.848175524457981	2		504	803	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911547	101911547	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	47	353	0	ENST00000374994.4:c.1472C>T	p.Thr491Ile	p.T491I	ENST00000374994	NM_004612.2	491	aCa/aTa	9/9	1	2	FACETS	0.185	0.155	0.217	0.185	0.155	0.217	SUBCLONAL	1	TRUE	1	0.848175524457981	2		353	600	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175481	108175481	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501568	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	85	392	0	ENST00000278616.4:c.5576G>A	p.Arg1859Lys	p.R1859K	ENST00000278616	NM_000051.3	1859	aGa/aAa	37/63	1	2	FACETS	0.376	0.333	0.422	0.376	0.333	0.422	SUBCLONAL	1	TRUE	1	0.848175524457981	2		392	533	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374511	118374511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	96	377	1	ENST00000534358.1:c.7904C>T	p.Thr2635Ile	p.T2635I	ENST00000534358	NM_005933.3	2635	aCc/aTc	27/36	1	2	FACETS	0.315	0.281	0.352	0.315	0.281	0.352	SUBCLONAL	1	TRUE	1	0.848175524457981	2		378	718	SUCCESS
CBL	867	MSKCC	GRCh37	11	119146748	119146748	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	45	494	0	ENST00000264033.4:c.911C>T	p.Ala304Val	p.A304V	ENST00000264033	NM_005188.3	304	gCt/gTt	6/16	1	2	FACETS	0.129	0.108	0.153	0.129	0.108	0.153	SUBCLONAL	1	TRUE	1	0.848175524457981	2		494	821	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944832	31944832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	419	620	1	ENST00000340398.3:c.269G>A	p.Gly90Asp	p.G90D	ENST00000340398	NM_001013699.2	90	gGt/gAt	1/1	1	2	FACETS	0.746	0.71	0.782	0.746	0.71	0.782	SUBCLONAL	1	TRUE	1	0.848175524457981	2		621	1325	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864316	57864316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376908129	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	386	588	1	ENST00000228682.2:c.1793G>A	p.Gly598Glu	p.G598E	ENST00000228682	NM_005269.2	598	gGg/gAg	12/12	1	2	FACETS	0.72	0.684	0.757	0.72	0.684	0.757	SUBCLONAL	1	TRUE	1	0.848175524457981	2		589	1264	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915466	112915466	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	313	575	2	ENST00000351677.2:c.865A>G	p.Arg289Gly	p.R289G	ENST00000351677	NM_002834.3	289	Agg/Ggg	8/16	1	2	FACETS	0.939	0.89	0.988	0.939	0.89	0.988	CLONAL	1	TRUE	1	0.848175524457981	2		577	786	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239278	105239278	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746272761	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	123	360	4	ENST00000349310.3:c.1109G>A	p.Arg370His	p.R370H	ENST00000349310	NM_001014432.1	370	cGc/cAc	12/15	1	2	FACETS	0.347	0.313	0.382	0.347	0.313	0.382	SUBCLONAL	1	TRUE	1	0.848175524457981	2		364	836	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304399	91304399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	160	361	0	ENST00000355112.3:c.1796G>A	p.Arg599Lys	p.R599K	ENST00000355112	NM_000057.2	599	aGa/aAa	7/22	1	2	FACETS	0.837	0.774	0.9	0.837	0.774	0.9	CLONAL	1	TRUE	1	0.848175524457981	2		361	451	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588728	29588728	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	75	402	0	ENST00000356175.3:c.4515-1G>A		p.X1505_splice	ENST00000356175	NM_000267.3	1505			1	2	FACETS	0.275	0.24	0.311	0.275	0.24	0.311	SUBCLONAL	1	TRUE	1	0.848175524457981	2		402	644	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872075	37872075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	107	487	0	ENST00000269571.5:c.1396G>A	p.Ala466Thr	p.A466T	ENST00000269571		466	Gcc/Acc	12/27	1	2	FACETS	0.236	0.21	0.262	0.236	0.21	0.262	SUBCLONAL	1	TRUE	1	0.848175524457981	2		487	1071	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62008737	62008737	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	93	361	0	ENST00000392795.3:c.79G>A	p.Val27Ile	p.V27I	ENST00000392795	NM_001039933.1	27	Gta/Ata	2/6	1	2	FACETS	0.294	0.261	0.33	0.294	0.261	0.33	SUBCLONAL	1	TRUE	1	0.848175524457981	2		361	745	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30090741	30090741	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs749475992	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	96	384	0	ENST00000338641.4:c.1738C>T	p.Leu580Phe	p.L580F	ENST00000338641	NM_000268.3	580	Ctc/Ttc	16/16	1	2	FACETS	0.237	0.21	0.265	0.237	0.21	0.265	SUBCLONAL	1	TRUE	1	0.848175524457981	2		384	956	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776955	76776955	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	34	274	1	ENST00000373344.5:c.6997G>A	p.Glu2333Lys	p.E2333K	ENST00000373344	NM_000489.3	2333	Gaa/Aaa	33/35	1	1	FACETS	0.164	0.134	0.198	0.164	0.134	0.198	SUBCLONAL	1	TRUE	0	0.848175524457981	1		275	281	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220410	123220410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	41	246	0	ENST00000218089.9:c.3067G>A	p.Glu1023Lys	p.E1023K	ENST00000218089	NM_001042749.1	1023	Gaa/Aaa	30/35	1	1	FACETS	0.177	0.148	0.21	0.177	0.148	0.21	SUBCLONAL	1	TRUE	0	0.848175524457981	1		246	314	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528062	29528062	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	14	106	0	ENST00000356175.3:c.1074del	p.Phe358LeufsTer18	p.F358Lfs*18	ENST00000356175	NM_000267.3	357	cTt/ct	10/57	1	2	FACETS	0.268	0.195	0.355	0.268	0.195	0.355	SUBCLONAL	1	TRUE	1	0.848175524457981	2		106	123	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677324	29677325	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0000883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	52	379	0	ENST00000356175.3:c.7385dup	p.Ser2463PhefsTer3	p.S2463Ffs*3	ENST00000356175	NM_000267.3	2461	gac/gaCc	49/57	1	2	FACETS	0.286	0.244	0.332	0.286	0.244	0.332	SUBCLONAL	1	TRUE	1	0.848175524457981	2		379	429	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0000885-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	108	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.375868960301313	4	FACETS	0.926	0.832	1	0.463	0.416	0.513	CLONAL	1	TRUE	2	0.482164995362326	4		311	717	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0000885-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	48	286	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.45266136299139	4	FACETS	0.878	0.746	1	0.439	0.373	0.512	CLONAL	1	TRUE	2	0.482164995362326	4		286	336	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167736	56167736	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0000885-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	68	262	0	ENST00000399503.3:c.1302-1G>C		p.X434_splice	ENST00000399503	NM_005921.1	434			0.45266136299139	4	FACETS	0.81	0.706	0.923	0.405	0.353	0.462	CLONAL	1	TRUE	2	0.482164995362326	4		262	516	SUCCESS
APC	324	MSKCC	GRCh37	5	112154942	112154942	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779780	NA	P-0000885-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	57	290	1	ENST00000257430.4:c.1213C>T	p.Arg405Ter	p.R405*	ENST00000257430	NM_000038.5	405	Cga/Tga	10/16	0.45266136299139	4	FACETS	0.901	0.776	1	0.45	0.388	0.518	CLONAL	1	TRUE	2	0.482164995362326	4		291	389	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127730	64127730	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000885-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	36	203	0	ENST00000334205.4:c.223C>T	p.Arg75Cys	p.R75C	ENST00000334205	NM_003942.2	75	Cgc/Tgc	3/17	0.482164995362326	3	FACETS	1	0.846	1	0.509	0.423	0.603	CLONAL	1	TRUE	1	0.482164995362326	3		203	182	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473730	67473730	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000885-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	49	407	0	ENST00000327367.4:c.810C>G	p.Cys270Trp	p.C270W	ENST00000327367	NM_005902.3	270	tgC/tgG	6/9	0.334941587342172	4	FACETS	0.981	0.836	1	0.491	0.418	0.57	CLONAL	1	TRUE	2	0.482164995362326	4		407	307	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479810	67479810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863223746	NA	P-0000885-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	64	447	1	ENST00000327367.4:c.1117C>T	p.Arg373Cys	p.R373C	ENST00000327367	NM_005902.3	373	Cgc/Tgc	8/9	0.334941587342172	4	FACETS	0.955	0.83	1	0.478	0.415	0.545	CLONAL	1	TRUE	2	0.482164995362326	4		448	412	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879798	37879798	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000885-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	37	186	0	ENST00000269571.5:c.2093A>T	p.Glu698Val	p.E698V	ENST00000269571		698	gAg/gTg	18/27	0.175029844667307	4	FACETS	0.768	0.644	0.902	0.768	0.644	0.902	INDETERMINATE	2	TRUE	2	0.482164995362326	4		186	148	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375019	45375019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000885-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	61	308	0	ENST00000262160.6:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000262160	NM_005901.5	275	tGt/tAt	8/11	0.375868960301313	4	FACETS	0.817	0.706	0.937	0.409	0.353	0.469	CLONAL	1	TRUE	2	0.482164995362326	4		308	459	SUCCESS
APC	324	MSKCC	GRCh37	5	112170782	112170782	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0000885-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	72	484	0	ENST00000257430.4:c.1880del	p.Asn627ThrfsTer3	p.N627Tfs*3	ENST00000257430	NM_000038.5	626	acA/ac	15/16	0.45266136299139	4	FACETS	0.962	0.843	1	0.481	0.421	0.545	CLONAL	1	TRUE	2	0.482164995362326	4		484	460	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0000933-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	38	175	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.350898189745275	2		175	202	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0000933-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	197	406	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.350898189745275	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.350898189745275	3		406	542	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0000933-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	89	668	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.187156706373398	3	FACETS	1	0.947	1	0.555	0.493	0.621	INDETERMINATE	1	TRUE	1	0.350898189745275	3		668	537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579314	7579314	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000933-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	48	314	0	ENST00000269305.4:c.373A>G	p.Thr125Ala	p.T125A	ENST00000269305	NM_001126112.2	125	Acg/Gcg	4/11	1	2	FACETS	0.812	0.689	0.946	0.812	0.689	0.946	CLONAL	1	TRUE	1	0.350898189745275	2		314	337	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248583	59248584	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0000933-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	163	520	0	ENST00000371222.2:c.158_159dup	p.Arg54SerfsTer27	p.R54Sfs*27	ENST00000371222	NM_002228.3	53	-/TC	1/1	0.307499596691033	3	FACETS	1	0.971	1	0.564	0.517	0.613	CLONAL	1	TRUE	1	0.350898189745275	3		520	968	SUCCESS
APC	324	MSKCC	GRCh37	5	112174113	112174113	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554084511	NA	P-0000933-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	84	427	0	ENST00000257430.4:c.2825del	p.Asn942IlefsTer13	p.N942Ifs*13	ENST00000257430	NM_000038.5	941	gAa/ga	16/16	0.187156706373398	3	FACETS	1	0.946	1	0.557	0.493	0.625	INDETERMINATE	1	TRUE	1	0.350898189745275	3		427	505	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807905	3807906	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTCTTG	novel	NA	P-0001030-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	171	364	0	ENST00000262367.5:c.3507_3513dup	p.Ser1172GlnfsTer7	p.S1172Qfs*7	ENST00000262367	NM_004380.2	1171	-/CAAGACA	18/31	0.23678373701451	0	FACETS	0.647	0.597	0.698			1	SUBCLONAL	2	FALSE	0	0.286387086247839	0		364	659	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741694	17741694	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001090-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	405	373	0	ENST00000250003.3:c.365T>G	p.Leu122Arg	p.L122R	ENST00000250003	NM_002478.4	122	cTg/cGg	1/3	0.553706420554065	3	FACETS	0.995	0.977	1	1	0.997	1	CLONAL	4	TRUE	0	0.6	3		373	441	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916946	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0001090-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	232	272	0	ENST00000263967.3:c.332_334del	p.Lys111del	p.K111del	ENST00000263967	NM_006218.2	111	AAG/-	2/21	0.3	3	FACETS	0.934	0.88	0.99			1	INDETERMINATE	2	TRUE	NA	0.6	3		272	538	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922896	39922896	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	AA	novel	NA	P-0001090-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	173	286	0	ENST00000378444.4:c.3812delinsTT	p.Ser1271PhefsTer6	p.S1271Ffs*6	ENST00000378444	NM_001123385.1	1271	tCg/tTTg	8/15	1	1	FACETS	0.985	0.947	1	1	0.995	1	CLONAL	2	TRUE	0	0.6	1		286	205	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0001104-T05-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	249	365	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.588031315205918	1	FACETS	0.929	0.877	0.98	0.929	0.877	0.98	CLONAL	1	TRUE	0	0.660295775347393	1		365	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0001104-T05-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	277	654	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.660295775347393	1	FACETS	0.869	0.822	0.916	0.869	0.822	0.916	CLONAL	1	TRUE	0	0.660295775347393	1		655	647	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038912	12038912	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001104-T05-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	231	639	0	ENST00000396373.4:c.1205A>G	p.Tyr402Cys	p.Y402C	ENST00000396373	NM_001987.4	402	tAc/tGc	7/8	0.182324695818311	6	FACETS	1	0.947	1	0.677	0.632	0.722	INDETERMINATE	2	TRUE	3	0.660295775347393	6		639	800	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782654	9782654	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001104-T05-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	448	555	0	ENST00000377346.4:c.2416C>A	p.Leu806Met	p.L806M	ENST00000377346	NM_005026.3	806	Ctg/Atg	19/24	NA	2	FACETS	0.902	0.87	0.934			1	INDETERMINATE	2	TRUE	NA	0.660295775347393	2		555	752	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917797	29917797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748854412	NA	P-0001104-T05-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	198	542	0	ENST00000389048.3:c.871C>T	p.Arg291Cys	p.R291C	ENST00000389048	NM_004304.4	291	Cgc/Tgc	3/29	0.331569403338361	1	FACETS	0.58	0.539	0.622	0.58	0.539	0.622	INDETERMINATE	1	TRUE	0	0.660295775347393	1		542	693	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808647	1808647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373425119	NA	P-0001104-T05-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	186	486	0	ENST00000260795.2:c.2260G>A	p.Val754Met	p.V754M	ENST00000260795		754	Gtg/Atg	16/17	1	2	FACETS	0.846	0.784	0.909	0.846	0.784	0.909	CLONAL	1	TRUE	1	0.660295775347393	2		486	666	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213909	66213909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001104-T05-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	212	661	0	ENST00000273854.3:c.2521C>T	p.Pro841Ser	p.P841S	ENST00000273854	NM_004439.5	841	Cca/Tca	15/18	1	2	FACETS	0.889	0.829	0.951	0.889	0.829	0.951	CLONAL	1	TRUE	1	0.660295775347393	2		661	722	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468029	50468029	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001104-T05-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	194	362	1	ENST00000331340.3:c.1264G>A	p.Ala422Thr	p.A422T	ENST00000331340	NM_006060.4	422	Gcg/Acg	8/8	1	2	FACETS	0.973	0.905	1	0.973	0.905	1	CLONAL	1	TRUE	1	0.660295775347393	2		363	604	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504378	8504378	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001104-T05-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	155	426	0	ENST00000356435.5:c.1705T>A	p.Ser569Thr	p.S569T	ENST00000356435		569	Tca/Aca	12/35	0.660295775347393	1	FACETS	0.767	0.71	0.825	0.767	0.71	0.825	SUBCLONAL	1	TRUE	0	0.660295775347393	1		426	410	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231337	46231337	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001104-T05-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	182	516	1	ENST00000334344.6:c.1177G>A	p.Glu393Lys	p.E393K	ENST00000334344	NM_152641.2	393	Gaa/Aaa	10/21	0.312682359427239	3	FACETS	1	0.981	1	0.588	0.545	0.633	INDETERMINATE	1	TRUE	1	0.660295775347393	3		517	623	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432110	121432110	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001104-T05-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	222	528	0	ENST00000257555.6:c.857A>T	p.Tyr286Phe	p.Y286F	ENST00000257555		286	tAc/tTc	4/10	NA	2	FACETS	0.889	0.831	0.95			1	INDETERMINATE	1	TRUE	NA	0.660295775347393	2		528	756	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2218120	2218120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001104-T05-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	275	600	0	ENST00000326181.6:c.182C>T	p.Ser61Phe	p.S61F	ENST00000326181	NM_032271.2	61	tCc/tTc	4/21	1	2	FACETS	0.985	0.927	1	0.985	0.927	1	CLONAL	1	TRUE	1	0.660295775347393	2		600	846	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857029	9857029	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001104-T05-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	201	617	0	ENST00000330684.3:c.4372C>G	p.Pro1458Ala	p.P1458A	ENST00000330684	NM_001134407.1	1458	Cct/Gct	13/13	1	2	FACETS	0.853	0.793	0.914	0.853	0.793	0.914	CLONAL	1	TRUE	1	0.660295775347393	2		617	714	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47087987	47087987	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001104-T05-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	218	463	0	ENST00000409792.3:c.7088C>A	p.Pro2363His	p.P2363H	ENST00000409792	NM_014159.6	2363	cCc/cAc	16/21	1	2	FACETS	0.933	0.871	0.996	0.933	0.871	0.996	CLONAL	1	TRUE	1	0.660295775347393	2		463	708	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750450	41750450	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001104-T05-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	188	550	0	ENST00000226382.2:c.178C>G	p.Leu60Val	p.L60V	ENST00000226382	NM_003924.3	60	Ctc/Gtc	1/3	1	2	FACETS	0.888	0.825	0.954	0.888	0.825	0.954	CLONAL	1	TRUE	1	0.660295775347393	2		550	641	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954272	32954273	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359752	NA	P-0001104-T05-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	202	582	2	ENST00000380152.3:c.9253dup	p.Thr3085AsnfsTer26	p.T3085Nfs*26	ENST00000380152		3082	-/A	24/27	0.665167059373897	3	FACETS	0.844	0.783	0.908	0.422	0.391	0.454	CLONAL	1	TRUE	1	0.660295775347393	3		584	964	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439988	56439993	+	frameshift_variant	Frame_Shift_Ins	INS	GGATCC	GGATCC	TCATAATCTG	novel	NA	P-0001104-T05-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	219	472	0	ENST00000407977.2:c.599_604delinsCAGATTATGA	p.Trp200SerfsTer60	p.W200Sfs*60	ENST00000407977		200	tGGATCCta/tCAGATTATGAta	6/10	0.660295775347393	1	FACETS	0.883	0.83	0.937	0.883	0.83	0.937	CLONAL	1	TRUE	0	0.660295775347393	1		472	503	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222765	53222766	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0001205-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	488	468	0	ENST00000375401.3:c.4170dup	p.Leu1391ThrfsTer3	p.L1391Tfs*3	ENST00000375401	NM_004187.3	1390	-/A	25/26	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		468	708	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	76	590	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.716	0.628	0.811	0.716	0.628	0.811	SUBCLONAL	1	TRUE	1	0.31	2		590	685	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518099	8518099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764400127	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	33	381	0	ENST00000356435.5:c.1292C>T	p.Ser431Leu	p.S431L	ENST00000356435		431	tCg/tTg	10/35	1	2	FACETS	0.63	0.514	0.76	0.63	0.514	0.76	SUBCLONAL	1	TRUE	1	0.31	2		381	338	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982356	25982356	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	42	264	0	ENST00000435504.4:c.934C>T	p.Arg312Ter	p.R312*	ENST00000435504		312	Cga/Tga	9/13	0.172678218878313	1	FACETS	0.774	0.649	0.91	0.774	0.649	0.91	INDETERMINATE	1	TRUE	0	0.31	1		264	296	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443345	187443345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	55	417	1	ENST00000232014.4:c.1781G>A	p.Arg594Gln	p.R594Q	ENST00000232014	NM_001130845.1	594	cGa/cAa	8/10	1	2	FACETS	0.878	0.754	1	0.878	0.754	1	CLONAL	1	TRUE	1	0.31	2		418	404	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980345	55980345	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	71	624	0	ENST00000263923.4:c.746G>T	p.Arg249Ile	p.R249I	ENST00000263923	NM_002253.2	249	aGa/aTa	6/30	0.214239690486705	0	FACETS	0.594	0.519	0.675			1	SUBCLONAL	1	TRUE	0	0.31	0		624	532	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720870	89720870	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1554825652	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	51	285	0	ENST00000371953.3:c.1021T>G	p.Phe341Val	p.F341V	ENST00000371953	NM_000314.4	341	Ttt/Gtt	8/9	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.31	2		285	283	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143551	108143551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201780199	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	67	548	0	ENST00000278616.4:c.3256C>T	p.Arg1086Cys	p.R1086C	ENST00000278616	NM_000051.3	1086	Cgc/Tgc	22/63	1	2	FACETS	0.849	0.739	0.968	0.849	0.739	0.968	CLONAL	1	TRUE	1	0.31	2		548	509	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276250	15276250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747223569	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	66	472	0	ENST00000263388.2:c.5744G>A	p.Arg1915His	p.R1915H	ENST00000263388	NM_000435.2	1915	cGc/cAc	31/33	1	2	FACETS	0.803	0.698	0.917	0.803	0.698	0.917	CLONAL	1	TRUE	1	0.31	2		472	530	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	60	441	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.172678218878313	1	FACETS	0.796	0.688	0.912	0.796	0.688	0.912	INDETERMINATE	1	TRUE	0	0.31	1		441	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520006	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	20	708	1	ENST00000269305.4:c.821T>C	p.Val274Ala	p.V274A	ENST00000269305	NM_001126112.2	274	gTt/gCt	8/11	1	2	FACETS	0.207	0.157	0.265	0.207	0.157	0.265	SUBCLONAL	1	TRUE	1	0.31	2		709	624	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037474	12037474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	50	272	0	ENST00000396373.4:c.1105C>T	p.Arg369Trp	p.R369W	ENST00000396373	NM_001987.4	369	Cgg/Tgg	6/8	0.3	6	FACETS	1	0.963	1	0.491	0.418	0.57	CLONAL	1	TRUE	3	0.31	6		272	355	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453486	138453486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451809865	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	65	619	0	ENST00000289153.2:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000289153	NM_006219.2	321	cGa/cAa	5/22	1	2	FACETS	0.819	0.711	0.936	0.819	0.711	0.936	CLONAL	1	TRUE	1	0.31	2		619	512	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	74	444	1	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.31	2		445	472	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586470	189586470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147148566	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	33	200	0	ENST00000264731.3:c.1094C>T	p.Ser365Leu	p.S365L	ENST00000264731	NM_003722.4	365	tCg/tTg	8/14	1	2	FACETS	0.825	0.675	0.992	0.825	0.675	0.992	CLONAL	1	TRUE	1	0.31	2		200	258	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294163	1294163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199701877	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	55	427	0	ENST00000310581.5:c.838G>A	p.Glu280Lys	p.E280K	ENST00000310581	NM_198253.2	280	Gaa/Aaa	2/16	1	2	FACETS	0.964	0.828	1	0.964	0.828	1	CLONAL	1	TRUE	1	0.31	2		427	368	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856014	45856014	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751084702	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	62	388	1	ENST00000391945.4:c.1892G>A	p.Arg631His	p.R631H	ENST00000391945	NM_000400.3	631	cGc/cAc	20/23	1	2	FACETS	0.911	0.789	1	0.911	0.789	1	CLONAL	1	TRUE	1	0.31	2		389	439	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	75	460	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.31	2		460	477	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777640	9777640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148703447	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	60	372	0	ENST00000377346.4:c.976G>A	p.Glu326Lys	p.E326K	ENST00000377346	NM_005026.3	326	Gag/Aag	8/24	1	2	FACETS	0.805	0.695	0.924	0.805	0.695	0.924	CLONAL	1	TRUE	1	0.31	2		372	481	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781582	9781582	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	90	608	0	ENST00000377346.4:c.1892A>C	p.Lys631Thr	p.K631T	ENST00000377346	NM_005026.3	631	aAa/aCa	15/24	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.31	2		608	528	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169362	11169362	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	85	764	0	ENST00000361445.4:c.7513C>T	p.Arg2505Ter	p.R2505*	ENST00000361445	NM_004958.3	2505	Cga/Tga	56/58	1	2	FACETS	0.828	0.732	0.931	0.828	0.732	0.931	CLONAL	1	TRUE	1	0.31	2		764	662	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186818	11186818	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	52	356	0	ENST00000361445.4:c.6387A>C	p.Lys2129Asn	p.K2129N	ENST00000361445	NM_004958.3	2129	aaA/aaC	46/58	1	2	FACETS	0.791	0.675	0.918	0.791	0.675	0.918	CLONAL	1	TRUE	1	0.31	2		356	424	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16174607	16174607	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	52	496	0	ENST00000375759.3:c.45G>T	p.Glu15Asp	p.E15D	ENST00000375759	NM_015001.2	15	gaG/gaT	1/15	1	2	FACETS	0.899	0.769	1	0.899	0.769	1	CLONAL	1	TRUE	1	0.31	2		496	373	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237703	16237703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	88	448	0	ENST00000375759.3:c.1150C>T	p.Arg384Trp	p.R384W	ENST00000375759	NM_015001.2	384	Cgg/Tgg	5/15	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.31	2		448	536	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254758	16254758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758419650	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	69	456	0	ENST00000375759.3:c.2023G>A	p.Asp675Asn	p.D675N	ENST00000375759	NM_015001.2	675	Gat/Aat	11/15	1	2	FACETS	0.914	0.798	1	0.914	0.798	1	CLONAL	1	TRUE	1	0.31	2		456	487	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256942	16256942	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	70	522	0	ENST00000375759.3:c.4207C>T	p.Arg1403Ter	p.R1403*	ENST00000375759	NM_015001.2	1403	Cga/Tga	11/15	1	2	FACETS	0.868	0.759	0.987	0.868	0.759	0.987	CLONAL	1	TRUE	1	0.31	2		522	520	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521530	46521530	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs747237909	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	105	947	0	ENST00000262741.5:c.878A>C	p.Lys293Thr	p.K293T	ENST00000262741	NM_003629.3	293	aAa/aCa	7/10	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.31	2		947	672	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546353	46546353	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	83	690	0	ENST00000262741.5:c.176C>A	p.Ser59Tyr	p.S59Y	ENST00000262741	NM_003629.3	59	tCt/tAt	2/10	1	2	FACETS	0.894	0.79	1	0.894	0.79	1	CLONAL	1	TRUE	1	0.31	2		690	599	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325843	65325843	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1369499617	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	31	300	0	ENST00000342505.4:c.1279G>A	p.Val427Met	p.V427M	ENST00000342505	NM_002227.2	427	Gtg/Atg	9/25	1	2	FACETS	0.592	0.479	0.719	0.592	0.479	0.719	SUBCLONAL	1	TRUE	1	0.31	2		300	338	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428480	78428480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs569795654	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	63	561	1	ENST00000370768.2:c.1319G>A	p.Arg440Gln	p.R440Q	ENST00000370768	NM_003902.3	440	cGg/cAg	14/20	1	2	FACETS	0.915	0.794	1	0.915	0.794	1	CLONAL	1	TRUE	1	0.31	2		562	444	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429757	78429757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755419864	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	43	326	1	ENST00000370768.2:c.1031G>A	p.Arg344Gln	p.R344Q	ENST00000370768	NM_003902.3	344	cGa/cAa	12/20	1	2	FACETS	0.746	0.626	0.878	0.746	0.626	0.878	SUBCLONAL	1	TRUE	1	0.31	2		327	372	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699267	117699267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	59	567	1	ENST00000369458.3:c.374C>T	p.Ala125Val	p.A125V	ENST00000369458	NM_024626.3	125	gCt/gTt	3/6	1	2	FACETS	0.827	0.713	0.951	0.827	0.713	0.951	CLONAL	1	TRUE	1	0.31	2		568	460	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166273	118166273	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	45	435	0	ENST00000369448.3:c.783A>C	p.Glu261Asp	p.E261D	ENST00000369448	NM_017709.3	261	gaA/gaC	2/2	1	2	FACETS	0.802	0.676	0.94	0.802	0.676	0.94	CLONAL	1	TRUE	1	0.31	2		435	362	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464967	120464967	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs999822357	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	47	243	0	ENST00000256646.2:c.5105G>A	p.Arg1702Gln	p.R1702Q	ENST00000256646	NM_024408.3	1702	cGa/cAa	28/34	1	2	FACETS	0.963	0.816	1	0.963	0.816	1	CLONAL	1	TRUE	1	0.31	2		243	315	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497753	120497753	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	68	283	0	ENST00000256646.2:c.2129A>C	p.Glu710Ala	p.E710A	ENST00000256646	NM_024408.3	710	gAg/gCg	13/34	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.31	2		283	359	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161332117	161332117	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	64	507	0	ENST00000367975.2:c.406-2A>C		p.X136_splice	ENST00000367975	NM_003001.3	136			1	2	FACETS	0.997	0.867	1	0.997	0.867	1	CLONAL	1	TRUE	1	0.31	2		507	414	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050363	176050363	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1301409514	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	54	481	0	ENST00000367669.3:c.1202G>A	p.Arg401Gln	p.R401Q	ENST00000367669	NM_022457.5	401	cGa/cAa	11/20	1	2	FACETS	0.702	0.6	0.814	0.702	0.6	0.814	SUBCLONAL	1	TRUE	1	0.31	2		481	496	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091375	193091375	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	32	397	1	ENST00000367435.3:c.45G>T	p.Lys15Asn	p.K15N	ENST00000367435	NM_024529.4	15	aaG/aaT	1/17	1	2	FACETS	0.605	0.492	0.733	0.605	0.492	0.733	SUBCLONAL	1	TRUE	1	0.31	2		398	341	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099338	193099338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	60	397	0	ENST00000367435.3:c.272G>A	p.Arg91Gln	p.R91Q	ENST00000367435	NM_024529.4	91	cGa/cAa	3/17	1	2	FACETS	0.776	0.669	0.891	0.776	0.669	0.891	SUBCLONAL	1	TRUE	1	0.31	2		397	499	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518519	204518519	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	51	286	0	ENST00000367182.3:c.1182C>A	p.Phe394Leu	p.F394L	ENST00000367182	NM_001278516.1	394	ttC/ttA	11/11	1	2	FACETS	0.887	0.756	1	0.887	0.756	1	CLONAL	1	TRUE	1	0.31	2		286	371	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068357	26068357	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	81	598	0	ENST00000435504.4:c.133G>T	p.Glu45Ter	p.E45*	ENST00000435504		45	Gaa/Taa	2/13	0.172678218878313	1	FACETS	0.747	0.659	0.842	0.747	0.659	0.842	INDETERMINATE	1	TRUE	0	0.31	1		598	591	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693862	47693862	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	35	606	0	ENST00000233146.2:c.1576A>G	p.Thr526Ala	p.T526A	ENST00000233146	NM_000251.2	526	Acc/Gcc	10/16	1	2	FACETS	0.387	0.317	0.467	0.387	0.317	0.467	SUBCLONAL	1	TRUE	1	0.31	2		606	583	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705472	47705472	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658254	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	95	604	0	ENST00000233146.2:c.2272G>A	p.Asp758Asn	p.D758N	ENST00000233146	NM_000251.2	758	Gat/Aat	14/16	1	2	FACETS	0.998	0.89	1	0.998	0.89	1	CLONAL	1	TRUE	1	0.31	2		604	614	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026357	48026357	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587781508	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	75	502	0	ENST00000234420.5:c.1235A>C	p.Lys412Thr	p.K412T	ENST00000234420	NM_000179.2	412	aAg/aCg	4/10	1	2	FACETS	0.934	0.82	1	0.934	0.82	1	CLONAL	1	TRUE	1	0.31	2		502	518	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61717848	61717848	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	151	723	0	ENST00000401558.2:c.1951G>A	p.Glu651Lys	p.E651K	ENST00000401558	NM_003400.3	651	Gaa/Aaa	17/25	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.31	2		723	671	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128018845	128018845	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	73	708	0	ENST00000285398.2:c.2023A>G	p.Lys675Glu	p.K675E	ENST00000285398	NM_000122.1	675	Aag/Gag	13/15	1	2	FACETS	0.823	0.721	0.934	0.823	0.721	0.934	CLONAL	1	TRUE	1	0.31	2		708	572	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046337	128046337	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	62	485	0	ENST00000285398.2:c.926A>C	p.Asp309Ala	p.D309A	ENST00000285398	NM_000122.1	309	gAc/gCc	7/15	1	2	FACETS	0.881	0.763	1	0.881	0.763	1	CLONAL	1	TRUE	1	0.31	2		485	454	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095726	178095726	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	75	725	0	ENST00000397062.3:c.1605A>C	p.Glu535Asp	p.E535D	ENST00000397062	NM_006164.4	535	gaA/gaC	5/5	1	2	FACETS	0.966	0.848	1	0.966	0.848	1	CLONAL	1	TRUE	1	0.31	2		725	501	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719461	190719461	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	46	316	0	ENST00000441310.2:c.1463A>C	p.Glu488Ala	p.E488A	ENST00000441310	NM_000534.4	488	gAa/gCa	9/13	1	2	FACETS	0.853	0.721	0.997	0.853	0.721	0.997	CLONAL	1	TRUE	1	0.31	2		316	348	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198264812	198264812	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	68	647	0	ENST00000335508.6:c.2980C>A	p.Leu994Ile	p.L994I	ENST00000335508	NM_012433.2	994	Ctt/Att	20/25	1	2	FACETS	0.829	0.722	0.945	0.829	0.722	0.945	CLONAL	1	TRUE	1	0.31	2		647	529	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198269855	198269855	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	90	685	1	ENST00000335508.6:c.1484G>T	p.Arg495Ile	p.R495I	ENST00000335508	NM_012433.2	495	aGa/aTa	11/25	1	2	FACETS	0.991	0.881	1	0.991	0.881	1	CLONAL	1	TRUE	1	0.31	2		686	586	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274641	198274641	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	81	579	1	ENST00000335508.6:c.757A>G	p.Ile253Val	p.I253V	ENST00000335508	NM_012433.2	253	Ata/Gta	7/25	1	2	FACETS	0.957	0.845	1	0.957	0.845	1	CLONAL	1	TRUE	1	0.31	2		580	546	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116206	209116206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	47	648	0	ENST00000345146.2:c.70G>A	p.Glu24Lys	p.E24K	ENST00000345146	NM_005896.2	24	Gaa/Aaa	3/10	0.139055684806642	0	FACETS	0.541	0.457	0.632			1	INDETERMINATE	1	TRUE	0	0.31	0		648	387	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632230	215632230	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	53	540	0	ENST00000260947.4:c.1544C>T	p.Ser515Phe	p.S515F	ENST00000260947	NM_000465.2	515	tCc/tTc	6/11	0.139055684806642	0	FACETS	0.61	0.521	0.706			1	INDETERMINATE	1	TRUE	0	0.31	0		540	387	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645948	215645948	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	79	893	1	ENST00000260947.4:c.650A>C	p.Lys217Thr	p.K217T	ENST00000260947	NM_000465.2	217	aAa/aCa	4/11	0.139055684806642	0	FACETS	0.69	0.608	0.777			1	INDETERMINATE	1	TRUE	0	0.31	0		894	510	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732997	30732997	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057524810	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	50	326	0	ENST00000295754.5:c.1610G>A	p.Arg537His	p.R537H	ENST00000295754	NM_003242.5	537	cGc/cAc	7/7	0.251947839625436	3	FACETS	1	0.921	1	0.563	0.48	0.653	CLONAL	1	TRUE	1	0.31	3		326	331	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147608	47147608	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	50	285	0	ENST00000409792.3:c.4718A>C	p.Asn1573Thr	p.N1573T	ENST00000409792	NM_014159.6	1573	aAc/aCc	6/21	1	2	FACETS	0.899	0.765	1	0.899	0.765	1	CLONAL	1	TRUE	1	0.31	2		285	359	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090635	71090635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765483458	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	55	374	0	ENST00000318789.4:c.713C>T	p.Ala238Val	p.A238V	ENST00000318789	NM_032682.5	238	gCt/gTt	11/21	1	2	FACETS	0.88	0.756	1	0.88	0.756	1	CLONAL	1	TRUE	1	0.31	2		374	403	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474598	138474598	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	68	430	2	ENST00000289153.2:c.395A>C	p.Lys132Thr	p.K132T	ENST00000289153	NM_006219.2	132	aAa/aCa	2/22	1	2	FACETS	0.931	0.812	1	0.931	0.812	1	CLONAL	1	TRUE	1	0.31	2		432	471	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178136	142178136	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	56	384	0	ENST00000350721.4:c.7282C>A	p.Leu2428Ile	p.L2428I	ENST00000350721	NM_001184.3	2428	Ctc/Atc	43/47	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.31	2		384	355	SUCCESS
ATR	545	MSKCC	GRCh37	3	142224143	142224143	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	36	436	0	ENST00000350721.4:c.5034A>C	p.Lys1678Asn	p.K1678N	ENST00000350721	NM_001184.3	1678	aaA/aaC	29/47	1	2	FACETS	0.495	0.407	0.594	0.495	0.407	0.594	SUBCLONAL	1	TRUE	1	0.31	2		436	469	SUCCESS
ATR	545	MSKCC	GRCh37	3	142241619	142241619	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1474267384	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	76	530	0	ENST00000350721.4:c.4217C>T	p.Ala1406Val	p.A1406V	ENST00000350721	NM_001184.3	1406	gCg/gTg	23/47	1	2	FACETS	0.975	0.857	1	0.975	0.857	1	CLONAL	1	TRUE	1	0.31	2		530	503	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266652	142266652	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	68	441	0	ENST00000350721.4:c.3272T>G	p.Phe1091Cys	p.F1091C	ENST00000350721	NM_001184.3	1091	tTt/tGt	16/47	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.31	2		441	434	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268448	142268448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564283952	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	76	388	1	ENST00000350721.4:c.3044G>A	p.Arg1015Gln	p.R1015Q	ENST00000350721	NM_001184.3	1015	cGa/cAa	15/47	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.31	2		389	470	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178943780	178943780	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	63	492	1	ENST00000263967.3:c.2447T>A	p.Ile816Asn	p.I816N	ENST00000263967	NM_006218.2	816	aTt/aAt	17/21	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.31	2		493	374	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951919	178951919	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	54	413	0	ENST00000263967.3:c.2974C>T	p.Arg992Ter	p.R992*	ENST00000263967	NM_006218.2	992	Cga/Tga	21/21	1	2	FACETS	0.81	0.694	0.937	0.81	0.694	0.937	CLONAL	1	TRUE	1	0.31	2		413	430	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807288	1807288	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs121913112	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	68	447	3	ENST00000260795.2:c.1537G>A	p.Asp513Asn	p.D513N	ENST00000260795		513	Gat/Aat	11/17	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.31	2		450	394	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748309	41748309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs894529129	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	68	519	0	ENST00000226382.2:c.460C>T	p.Arg154Cys	p.R154C	ENST00000226382	NM_003924.3	154	Cgc/Tgc	3/3	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.31	2		519	419	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133854	55133854	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	64	472	1	ENST00000257290.5:c.1067T>C	p.Leu356Pro	p.L356P	ENST00000257290	NM_006206.4	356	cTg/cCg	7/23	1	2	FACETS	0.932	0.81	1	0.932	0.81	1	CLONAL	1	TRUE	1	0.31	2		473	443	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599341	55599341	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519761	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	44	380	0	ENST00000288135.5:c.2467T>G	p.Tyr823Asp	p.Y823D	ENST00000288135	NM_000222.2	823	Tat/Gat	17/21	0.214239690486705	0	FACETS	0.522	0.439	0.614			1	SUBCLONAL	1	TRUE	0	0.31	0		380	375	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233120	66233120	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	41	647	0	ENST00000273854.3:c.1879A>C	p.Lys627Gln	p.K627Q	ENST00000273854	NM_004439.5	627	Aaa/Caa	10/18	0.214239690486705	0	FACETS	0.401	0.334	0.476			1	SUBCLONAL	1	TRUE	0	0.31	0		647	455	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242774	66242774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151302542	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	35	229	0	ENST00000273854.3:c.1798G>A	p.Glu600Lys	p.E600K	ENST00000273854	NM_004439.5	600	Gaa/Aaa	9/18	0.214239690486705	0	FACETS	0.599	0.494	0.716			1	SUBCLONAL	1	TRUE	0	0.31	0		229	260	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467503	66467503	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	34	420	0	ENST00000273854.3:c.766C>T	p.Leu256Phe	p.L256F	ENST00000273854	NM_004439.5	256	Ctc/Ttc	3/18	0.214239690486705	0	FACETS	0.517	0.423	0.62			1	SUBCLONAL	1	TRUE	0	0.31	0		420	293	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155526	106155526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749618735	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	48	271	0	ENST00000380013.4:c.427G>A	p.Asp143Asn	p.D143N	ENST00000380013	NM_001127208.2	143	Gat/Aat	3/11	NA	2	FACETS	0.898	0.762	1			1	INDETERMINATE	1	TRUE	NA	0.31	2		271	345	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197255	106197255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1222260506	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	37	296	0	ENST00000380013.4:c.5588C>T	p.Ala1863Val	p.A1863V	ENST00000380013	NM_001127208.2	1863	gCc/gTc	11/11	NA	2	FACETS	0.853	0.706	1			1	INDETERMINATE	1	TRUE	NA	0.31	2		296	280	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244184	153244184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759610249	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	55	632	0	ENST00000281708.4:c.1973G>A	p.Arg658Gln	p.R658Q	ENST00000281708	NM_033632.3	658	cGa/cAa	12/12	0.3	1	FACETS	0.668	0.572	0.772	0.668	0.572	0.772	SUBCLONAL	1	TRUE	0	0.31	1		632	449	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542717	187542717	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	91	623	0	ENST00000441802.2:c.5023G>T	p.Glu1675Ter	p.E1675*	ENST00000441802	NM_005245.3	1675	Gaa/Taa	10/27	0.3	1	FACETS	0.988	0.881	1	0.988	0.881	1	CLONAL	1	TRUE	0	0.31	1		623	502	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627971	187627971	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	98	707	0	ENST00000441802.2:c.3011A>C	p.Lys1004Thr	p.K1004T	ENST00000441802	NM_005245.3	1004	aAa/aCa	2/27	0.3	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.31	1		707	482	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628149	187628149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377150532	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	124	548	0	ENST00000441802.2:c.2833G>A	p.Val945Ile	p.V945I	ENST00000441802	NM_005245.3	945	Gtc/Atc	2/27	0.3	1	FACETS	0.793	0.724	0.866	1	0.987	1	SUBCLONAL	2	TRUE	0	0.31	1		548	426	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628529	187628529	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	32	699	0	ENST00000441802.2:c.2453A>G	p.Asn818Ser	p.N818S	ENST00000441802	NM_005245.3	818	aAt/aGt	2/27	0.3	1	FACETS	0.339	0.275	0.413	0.339	0.275	0.413	SUBCLONAL	1	TRUE	0	0.31	1		699	514	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293662	1293662	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1304418053	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	67	364	0	ENST00000310581.5:c.1339C>T	p.Arg447Cys	p.R447C	ENST00000310581	NM_198253.2	447	Cgc/Tgc	2/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.31	2		364	331	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944624	38944624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1377027840	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	91	454	0	ENST00000357387.3:c.4837C>T	p.Arg1613Cys	p.R1613C	ENST00000357387	NM_152756.3	1613	Cgc/Tgc	36/38	0.3	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.31	1		454	392	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950310	38950310	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	52	591	0	ENST00000357387.3:c.3640A>C	p.Lys1214Gln	p.K1214Q	ENST00000357387	NM_152756.3	1214	Aag/Cag	31/38	0.3	1	FACETS	0.672	0.573	0.779	0.672	0.573	0.779	SUBCLONAL	1	TRUE	0	0.31	1		591	422	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155587	56155587	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	56	265	0	ENST00000399503.3:c.679C>A	p.His227Asn	p.H227N	ENST00000399503	NM_005921.1	227	Cac/Aac	3/20	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.31	2		265	353	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180561	56180561	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	59	307	0	ENST00000399503.3:c.3890T>C	p.Met1297Thr	p.M1297T	ENST00000399503	NM_005921.1	1297	aTg/aCg	16/20	1	2	FACETS	0.898	0.775	1	0.898	0.775	1	CLONAL	1	TRUE	1	0.31	2		307	424	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750818	57750818	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	46	390	0	ENST00000274289.3:c.1786C>T	p.Arg596Ter	p.R596*	ENST00000274289	NM_006622.3	596	Cga/Tga	13/14	1	2	FACETS	0.822	0.694	0.962	0.822	0.694	0.962	CLONAL	1	TRUE	1	0.31	2		390	361	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754238	57754238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	66	378	2	ENST00000274289.3:c.613G>A	p.Asp205Asn	p.D205N	ENST00000274289	NM_006622.3	205	Gat/Aat	4/14	1	2	FACETS	0.983	0.857	1	0.983	0.857	1	CLONAL	1	TRUE	1	0.31	2		380	433	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590457	67590457	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554051161	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	56	313	1	ENST00000274335.5:c.1519G>T	p.Glu507Ter	p.E507*	ENST00000274335		507	Gaa/Taa	11/15	1	2	FACETS	0.838	0.72	0.967	0.838	0.72	0.967	CLONAL	1	TRUE	1	0.31	2		314	431	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685258	86685258	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	67	348	0	ENST00000274376.6:c.2974T>C	p.Ser992Pro	p.S992P	ENST00000274376	NM_002890.2	992	Tcc/Ccc	24/25	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.31	2		348	386	SUCCESS
APC	324	MSKCC	GRCh37	5	112157650	112157650	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1060503333	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	87	460	0	ENST00000257430.4:c.1370C>A	p.Ser457Ter	p.S457*	ENST00000257430	NM_000038.5	457	tCa/tAa	11/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.31	2		460	466	SUCCESS
APC	324	MSKCC	GRCh37	5	112175897	112175897	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	43	233	2	ENST00000257430.4:c.4606G>T	p.Glu1536Ter	p.E1536*	ENST00000257430	NM_000038.5	1536	Gaa/Taa	16/16	1	2	FACETS	0.967	0.813	1	0.967	0.813	1	CLONAL	1	TRUE	1	0.31	2		235	287	SUCCESS
APC	324	MSKCC	GRCh37	5	112176261	112176261	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	57	609	0	ENST00000257430.4:c.4970T>G	p.Leu1657Arg	p.L1657R	ENST00000257430	NM_000038.5	1657	cTa/cGa	16/16	1	2	FACETS	0.776	0.667	0.895	0.776	0.667	0.895	SUBCLONAL	1	TRUE	1	0.31	2		609	474	SUCCESS
APC	324	MSKCC	GRCh37	5	112176639	112176639	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	59	417	1	ENST00000257430.4:c.5348C>A	p.Thr1783Asn	p.T1783N	ENST00000257430	NM_000038.5	1783	aCt/aAt	16/16	1	2	FACETS	0.956	0.826	1	0.956	0.826	1	CLONAL	1	TRUE	1	0.31	2		418	398	SUCCESS
APC	324	MSKCC	GRCh37	5	112177189	112177189	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	23	427	0	ENST00000257430.4:c.5898T>G	p.Asn1966Lys	p.N1966K	ENST00000257430	NM_000038.5	1966	aaT/aaG	16/16	1	2	FACETS	0.351	0.273	0.441	0.351	0.273	0.441	SUBCLONAL	1	TRUE	1	0.31	2		427	423	SUCCESS
APC	324	MSKCC	GRCh37	5	112177677	112177677	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782301	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	44	312	0	ENST00000257430.4:c.6386C>T	p.Ser2129Leu	p.S2129L	ENST00000257430	NM_000038.5	2129	tCg/tTg	16/16	1	2	FACETS	0.786	0.661	0.924	0.786	0.661	0.924	CLONAL	1	TRUE	1	0.31	2		312	361	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923272	131923272	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	36	226	0	ENST00000265335.6:c.775G>T	p.Glu259Ter	p.E259*	ENST00000265335		259	Gaa/Taa	6/25	1	2	FACETS	0.767	0.632	0.916	0.767	0.632	0.916	CLONAL	1	TRUE	1	0.31	2		226	303	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944853	131944853	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	66	288	0	ENST00000265335.6:c.2874G>T	p.Met958Ile	p.M958I	ENST00000265335		958	atG/atT	18/25	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.31	2		288	408	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131951771	131951771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	60	310	0	ENST00000265335.6:c.3113G>A	p.Arg1038Lys	p.R1038K	ENST00000265335		1038	aGa/aAa	20/25	1	2	FACETS	0.953	0.824	1	0.953	0.824	1	CLONAL	1	TRUE	1	0.31	2		310	406	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435618	149435618	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	44	479	0	ENST00000286301.3:c.2525G>T	p.Gly842Val	p.G842V	ENST00000286301	NM_005211.3	842	gGc/gTc	19/22	1	2	FACETS	0.842	0.709	0.989	0.842	0.709	0.989	CLONAL	1	TRUE	1	0.31	2		479	337	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441324	149441324	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1334063870	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	55	601	0	ENST00000286301.3:c.1715A>C	p.Asn572Thr	p.N572T	ENST00000286301	NM_005211.3	572	aAc/aCc	12/22	1	2	FACETS	0.792	0.679	0.915	0.792	0.679	0.915	CLONAL	1	TRUE	1	0.31	2		601	448	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456932	149456932	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148357861	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	58	442	0	ENST00000286301.3:c.796G>A	p.Asp266Asn	p.D266N	ENST00000286301	NM_005211.3	266	Gat/Aat	6/22	1	2	FACETS	0.856	0.738	0.985	0.856	0.738	0.985	CLONAL	1	TRUE	1	0.31	2		442	437	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457758	149457758	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs758322216	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	51	259	0	ENST00000286301.3:c.646C>T	p.Arg216Ter	p.R216*	ENST00000286301	NM_005211.3	216	Cga/Tga	5/22	1	2	FACETS	0.864	0.736	1	0.864	0.736	1	CLONAL	1	TRUE	1	0.31	2		259	381	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149465977	149465977	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	65	441	0	ENST00000286301.3:c.14T>C	p.Val5Ala	p.V5A	ENST00000286301	NM_005211.3	5	gTt/gCt	2/22	1	2	FACETS	0.896	0.779	1	0.896	0.779	1	CLONAL	1	TRUE	1	0.31	2		441	468	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500783	149500783	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	27	437	0	ENST00000261799.4:c.2447T>G	p.Phe816Cys	p.F816C	ENST00000261799	NM_002609.3	816	tTt/tGt	17/23	1	2	FACETS	0.472	0.375	0.582	0.472	0.375	0.582	SUBCLONAL	1	TRUE	1	0.31	2		437	369	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639103	176639103	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	50	168	0	ENST00000439151.2:c.3703A>C	p.Asn1235His	p.N1235H	ENST00000439151	NM_022455.4	1235	Aat/Cat	5/23	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.31	2		168	291	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721223	176721223	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	43	303	0	ENST00000439151.2:c.6854G>T	p.Arg2285Ile	p.R2285I	ENST00000439151	NM_022455.4	2285	aGa/aTa	23/23	1	2	FACETS	0.779	0.654	0.917	0.779	0.654	0.917	CLONAL	1	TRUE	1	0.31	2		303	356	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038377	180038377	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs935819804	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	81	543	0	ENST00000261937.6:c.3640G>A	p.Ala1214Thr	p.A1214T	ENST00000261937	NM_182925.4	1214	Gct/Act	27/30	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.31	2		543	471	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046038	180046038	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	32	141	0	ENST00000261937.6:c.2833G>A	p.Ala945Thr	p.A945T	ENST00000261937	NM_182925.4	945	Gcc/Acc	20/30	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.31	2		141	156	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680986	30680986	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	59	565	1	ENST00000376406.3:c.733G>A	p.Ala245Thr	p.A245T	ENST00000376406	NM_014641.2	245	Gca/Aca	5/15	1	2	FACETS	0.782	0.673	0.899	0.782	0.673	0.899	SUBCLONAL	1	TRUE	1	0.31	2		566	487	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288764	33288764	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1429735040	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	39	272	0	ENST00000374542.5:c.788G>A	p.Arg263His	p.R263H	ENST00000374542	NM_001141970.1	263	cGc/cAc	3/8	1	2	FACETS	0.747	0.621	0.886	0.747	0.621	0.886	SUBCLONAL	1	TRUE	1	0.31	2		272	337	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790793	89790793	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	73	741	1	ENST00000336032.3:c.180C>A	p.Phe60Leu	p.F60L	ENST00000336032	NM_006813.2	60	ttC/ttA	1/2	1	2	FACETS	0.861	0.754	0.976	0.861	0.754	0.976	CLONAL	1	TRUE	1	0.31	2		742	547	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793710	89793710	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	82	446	0	ENST00000336032.3:c.779A>C	p.Lys260Thr	p.K260T	ENST00000336032	NM_006813.2	260	aAa/aCa	2/2	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.31	2		446	455	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554871	106554871	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	53	303	1	ENST00000369096.4:c.1988T>G	p.Val663Gly	p.V663G	ENST00000369096	NM_001198.3	663	gTg/gGg	7/7	0.139055684806642	0	FACETS	0.814	0.699	0.937			1	INDETERMINATE	1	TRUE	0	0.31	0		304	290	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117746728	117746728	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	76	467	0	ENST00000368508.3:c.92A>C	p.Asn31Thr	p.N31T	ENST00000368508	NM_002944.2	31	aAt/aCt	1/43	0.139055684806642	0	FACETS	0.669	0.588	0.755			1	INDETERMINATE	1	TRUE	0	0.31	0		467	506	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004280	150004280	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	60	776	0	ENST00000253339.5:c.1945A>C	p.Asn649His	p.N649H	ENST00000253339		649	Aat/Cat	3/7	1	2	FACETS	0.672	0.579	0.773	0.672	0.579	0.773	SUBCLONAL	1	TRUE	1	0.31	2		776	576	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004430	150004430	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	29	613	0	ENST00000253339.5:c.1795A>C	p.Asn599His	p.N599H	ENST00000253339		599	Aat/Cat	3/7	1	2	FACETS	0.352	0.281	0.432	0.352	0.281	0.432	SUBCLONAL	1	TRUE	1	0.31	2		613	532	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265629	152265629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	25	184	0	ENST00000206249.3:c.1082C>T	p.Ala361Val	p.A361V	ENST00000206249	NM_000125.3	361	gCg/gTg	4/8	1	2	FACETS	0.881	0.7	1	0.881	0.7	1	CLONAL	1	TRUE	1	0.31	2		184	183	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505438	157505438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	62	445	0	ENST00000346085.5:c.3419C>T	p.Ser1140Phe	p.S1140F	ENST00000346085	NM_020732.3	1140	tCc/tTc	13/20	1	2	FACETS	0.952	0.825	1	0.952	0.825	1	CLONAL	1	TRUE	1	0.31	2		445	420	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527333	157527333	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	50	437	0	ENST00000346085.5:c.5058C>A	p.Tyr1686Ter	p.Y1686*	ENST00000346085	NM_020732.3	1686	taC/taA	20/20	1	2	FACETS	0.748	0.636	0.871	0.748	0.636	0.871	SUBCLONAL	1	TRUE	1	0.31	2		437	431	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528142	157528142	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	55	294	0	ENST00000346085.5:c.5867C>A	p.Ser1956Ter	p.S1956*	ENST00000346085	NM_020732.3	1956	tCa/tAa	20/20	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.31	2		294	320	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979448	2979448	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	97	736	2	ENST00000396946.4:c.799C>A	p.Leu267Met	p.L267M	ENST00000396946	NM_032415.4	267	Ctg/Atg	6/25	0.251947839625436	3	FACETS	1	0.9	1	0.505	0.45	0.563	CLONAL	1	TRUE	1	0.31	3		738	716	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431640	6431640	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	35	258	0	ENST00000356142.4:c.193G>T	p.Asp65Tyr	p.D65Y	ENST00000356142	NM_018890.3	65	Gac/Tac	3/7	0.251947839625436	3	FACETS	0.902	0.743	1	0.451	0.371	0.54	CLONAL	1	TRUE	1	0.31	3		258	289	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467988	50467988	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	77	390	0	ENST00000331340.3:c.1223G>T	p.Arg408Leu	p.R408L	ENST00000331340	NM_006060.4	408	cGc/cTc	8/8	0.251947839625436	3	FACETS	0.851	0.753	0.955	0.851	0.753	0.955	CLONAL	2	TRUE	1	0.31	3		390	337	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273297	55273297	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1301373415	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	42	244	0	ENST00000275493.2:c.3620T>G	p.Phe1207Cys	p.F1207C	ENST00000275493	NM_005228.3	1207	tTt/tGt	28/28	0.251947839625436	3	FACETS	0.819	0.685	0.967	0.41	0.342	0.484	CLONAL	1	TRUE	1	0.31	3		244	382	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509539	106509539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	80	433	2	ENST00000359195.3:c.1533G>T	p.Glu511Asp	p.E511D	ENST00000359195	NM_002649.2	511	gaG/gaT	2/11	0.251947839625436	3	FACETS	0.812	0.72	0.91	0.812	0.72	0.91	CLONAL	2	TRUE	1	0.31	3		435	367	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339746	116339746	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	56	479	0	ENST00000397752.3:c.608C>A	p.Ser203Tyr	p.S203Y	ENST00000397752	NM_000245.2	203	tCt/tAt	2/21	0.251947839625436	3	FACETS	0.879	0.754	1	0.439	0.377	0.507	CLONAL	1	TRUE	1	0.31	3		479	475	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411953	116411953	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	51	406	0	ENST00000397752.3:c.2938T>G	p.Leu980Val	p.L980V	ENST00000397752	NM_000245.2	980	Ttg/Gtg	14/21	0.251947839625436	3	FACETS	0.874	0.744	1	0.437	0.372	0.508	CLONAL	1	TRUE	1	0.31	3		406	435	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140449181	140449181	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	93	360	0	ENST00000288602.6:c.1898A>G	p.Tyr633Cys	p.Y633C	ENST00000288602	NM_004333.4	633	tAc/tGc	16/18	0.251947839625436	3	FACETS	0.817	0.731	0.908	0.817	0.731	0.908	CLONAL	2	TRUE	1	0.31	3		360	424	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140500260	140500260	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	43	302	0	ENST00000288602.6:c.882C>A	p.Phe294Leu	p.F294L	ENST00000288602	NM_004333.4	294	ttC/ttA	7/18	0.251947839625436	3	FACETS	0.859	0.721	1	0.43	0.36	0.506	CLONAL	1	TRUE	1	0.31	3		302	373	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151866289	151866289	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	44	374	1	ENST00000262189.6:c.9499T>G	p.Phe3167Val	p.F3167V	ENST00000262189	NM_170606.2	3167	Ttt/Gtt	41/59	0.251947839625436	3	FACETS	0.689	0.578	0.812	0.344	0.289	0.406	SUBCLONAL	1	TRUE	1	0.31	3		375	476	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874277	151874277	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	66	518	0	ENST00000262189.6:c.8261T>G	p.Phe2754Cys	p.F2754C	ENST00000262189	NM_170606.2	2754	tTt/tGt	38/59	0.251947839625436	3	FACETS	0.937	0.814	1	0.468	0.407	0.535	CLONAL	1	TRUE	1	0.31	3		518	525	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884352	151884352	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	58	327	0	ENST00000262189.6:c.5003T>C	p.Phe1668Ser	p.F1668S	ENST00000262189	NM_170606.2	1668	tTc/tCc	33/59	0.251947839625436	3	FACETS	1	0.948	1	0.607	0.524	0.697	CLONAL	1	TRUE	1	0.31	3		327	356	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945565	151945565	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	29	83	0	ENST00000262189.6:c.1954A>C	p.Asn652His	p.N652H	ENST00000262189	NM_170606.2	652	Aac/Cac	14/59	0.251947839625436	3	FACETS	1	0.843	1	1	0.843	1	CLONAL	2	TRUE	1	0.31	3		83	105	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274861	38274861	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	67	499	0	ENST00000425967.3:c.1719G>T	p.Lys573Asn	p.K573N	ENST00000425967	NM_001174067.1	573	aaG/aaT	13/19	1	2	FACETS	0.851	0.741	0.97	0.851	0.741	0.97	CLONAL	1	TRUE	1	0.31	2		499	508	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285566	38285566	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	56	506	0	ENST00000425967.3:c.587T>G	p.Leu196Trp	p.L196W	ENST00000425967	NM_001174067.1	196	tTg/tGg	6/19	1	2	FACETS	0.852	0.732	0.983	0.852	0.732	0.983	CLONAL	1	TRUE	1	0.31	2		506	424	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022060	5022060	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	80	548	0	ENST00000381652.3:c.73A>G	p.Ile25Val	p.I25V	ENST00000381652	NM_004972.3	25	Att/Gtt	3/25	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.31	2		548	493	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069199	5069199	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	47	413	0	ENST00000381652.3:c.1504A>C	p.Lys502Gln	p.K502Q	ENST00000381652	NM_004972.3	502	Aag/Cag	11/25	1	2	FACETS	0.902	0.765	1	0.902	0.765	1	CLONAL	1	TRUE	1	0.31	2		413	336	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072495	5072495	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	32	177	0	ENST00000381652.3:c.1645G>T	p.Glu549Ter	p.E549*	ENST00000381652	NM_004972.3	549	Gaa/Taa	13/25	1	2	FACETS	0.85	0.693	1	0.85	0.693	1	CLONAL	1	TRUE	1	0.31	2		177	243	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341860	8341860	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs920031806	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	67	712	0	ENST00000356435.5:c.4780T>G	p.Tyr1594Asp	p.Y1594D	ENST00000356435		1594	Tat/Gat	29/35	1	2	FACETS	0.891	0.776	1	0.891	0.776	1	CLONAL	1	TRUE	1	0.31	2		712	485	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404555	8404555	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	59	599	0	ENST00000356435.5:c.4192C>A	p.Leu1398Ile	p.L1398I	ENST00000356435		1398	Ctc/Atc	25/35	1	2	FACETS	0.879	0.758	1	0.879	0.758	1	CLONAL	1	TRUE	1	0.31	2		599	433	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471038	8471038	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	60	546	0	ENST00000356435.5:c.3461T>C	p.Phe1154Ser	p.F1154S	ENST00000356435		1154	tTt/tCt	20/35	1	2	FACETS	0.868	0.75	0.996	0.868	0.75	0.996	CLONAL	1	TRUE	1	0.31	2		546	446	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020745	37020745	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	76	616	2	ENST00000358127.4:c.100C>A	p.Pro34Thr	p.P34T	ENST00000358127	NM_001280556.1	34	Ccg/Acg	2/10	1	2	FACETS	0.995	0.875	1	0.995	0.875	1	CLONAL	1	TRUE	1	0.31	2		618	493	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97897778	97897778	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	64	377	0	ENST00000289081.3:c.693G>T	p.Lys231Asn	p.K231N	ENST00000289081	NM_000136.2	231	aaG/aaT	8/15	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.31	2		377	411	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405675	139405675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	76	494	0	ENST00000277541.6:c.2516G>A	p.Arg839Lys	p.R839K	ENST00000277541	NM_017617.3	839	aGa/aAa	16/34	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.31	2		494	457	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333539	70333539	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs570151139	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	65	566	0	ENST00000373644.4:c.1444A>C	p.Asn482His	p.N482H	ENST00000373644	NM_030625.2	482	Aac/Cac	2/12	1	2	FACETS	0.821	0.713	0.937	0.821	0.713	0.937	CLONAL	1	TRUE	1	0.31	2		566	511	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404538	70404538	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	83	559	0	ENST00000373644.4:c.2052A>C	p.Lys684Asn	p.K684N	ENST00000373644	NM_030625.2	684	aaA/aaC	4/12	1	2	FACETS	0.92	0.813	1	0.92	0.813	1	CLONAL	1	TRUE	1	0.31	2		559	582	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405377	70405377	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	67	526	0	ENST00000373644.4:c.2891C>A	p.Ser964Ter	p.S964*	ENST00000373644	NM_030625.2	964	tCa/tAa	4/12	1	2	FACETS	0.873	0.76	0.995	0.873	0.76	0.995	CLONAL	1	TRUE	1	0.31	2		526	495	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405996	70405996	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	67	484	0	ENST00000373644.4:c.3510A>C	p.Glu1170Asp	p.E1170D	ENST00000373644	NM_030625.2	1170	gaA/gaC	4/12	1	2	FACETS	0.976	0.851	1	0.976	0.851	1	CLONAL	1	TRUE	1	0.31	2		484	443	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406690	70406690	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	72	637	0	ENST00000373644.4:c.4204T>G	p.Phe1402Val	p.F1402V	ENST00000373644	NM_030625.2	1402	Ttc/Gtc	4/12	1	2	FACETS	0.9	0.788	1	0.9	0.788	1	CLONAL	1	TRUE	1	0.31	2		637	516	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70441196	70441196	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536711369	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	82	579	0	ENST00000373644.4:c.4865G>A	p.Arg1622Gln	p.R1622Q	ENST00000373644	NM_030625.2	1622	cGa/cAa	9/12	1	2	FACETS	0.849	0.749	0.956	0.849	0.749	0.956	CLONAL	1	TRUE	1	0.31	2		579	623	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451077	70451077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	62	420	0	ENST00000373644.4:c.5917G>A	p.Glu1973Lys	p.E1973K	ENST00000373644	NM_030625.2	1973	Gaa/Aaa	12/12	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.31	2		420	394	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310821	123310821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	92	697	1	ENST00000358487.5:c.607C>T	p.Arg203Cys	p.R203C	ENST00000358487	NM_000141.4	203	Cgc/Tgc	5/18	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.31	2		698	547	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090327	77090327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196615739	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	65	771	1	ENST00000356341.3:c.398C>T	p.Ser133Leu	p.S133L	ENST00000356341	NM_002576.4	133	tCg/tTg	4/15	1	2	FACETS	0.717	0.622	0.82	0.717	0.622	0.82	SUBCLONAL	1	TRUE	1	0.31	2		772	585	SUCCESS
EED	8726	MSKCC	GRCh37	11	85967528	85967528	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	58	417	0	ENST00000263360.6:c.526A>C	p.Asn176His	p.N176H	ENST00000263360	NM_003797.3	176	Aat/Cat	5/12	1	2	FACETS	0.854	0.736	0.983	0.854	0.736	0.983	CLONAL	1	TRUE	1	0.31	2		417	438	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118370076	118370076	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	70	293	0	ENST00000534358.1:c.6020T>G	p.Ile2007Ser	p.I2007S	ENST00000534358	NM_005933.3	2007	aTc/aGc	23/36	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.31	2		293	425	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375297	118375297	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	63	395	0	ENST00000534358.1:c.8690T>G	p.Phe2897Cys	p.F2897C	ENST00000534358	NM_005933.3	2897	tTt/tGt	27/36	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.31	2		395	379	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376958	118376958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139366882	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	52	382	0	ENST00000534358.1:c.10351G>A	p.Glu3451Lys	p.E3451K	ENST00000534358	NM_005933.3	3451	Gaa/Aaa	27/36	1	2	FACETS	0.841	0.718	0.975	0.841	0.718	0.975	CLONAL	1	TRUE	1	0.31	2		382	399	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125499333	125499333	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	45	398	0	ENST00000428830.2:c.402A>C	p.Glu134Asp	p.E134D	ENST00000428830	NM_001114121.2	134	gaA/gaC	5/14	1	2	FACETS	0.772	0.651	0.906	0.772	0.651	0.906	CLONAL	1	TRUE	1	0.31	2		398	376	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402073	402073	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs373843135	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	71	673	2	ENST00000399788.2:c.4718T>C	p.Val1573Ala	p.V1573A	ENST00000399788	NM_001042603.1	1573	gTt/gCt	27/28	0.180051060938801	1	FACETS	0.792	0.692	0.898	0.792	0.692	0.898	INDETERMINATE	1	TRUE	0	0.31	1		675	489	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402188	402188	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	102	1174	0	ENST00000399788.2:c.4603A>C	p.Lys1535Gln	p.K1535Q	ENST00000399788	NM_001042603.1	1535	Aag/Cag	27/28	0.180051060938801	1	FACETS	0.829	0.742	0.921	0.829	0.742	0.921	INDETERMINATE	1	TRUE	0	0.31	1		1174	671	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416138	416138	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	73	561	0	ENST00000399788.2:c.4048C>T	p.Arg1350Ter	p.R1350*	ENST00000399788	NM_001042603.1	1350	Cga/Tga	24/28	0.180051060938801	1	FACETS	0.734	0.643	0.832	0.734	0.643	0.832	INDETERMINATE	1	TRUE	0	0.31	1		561	542	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431664	431664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	76	645	0	ENST00000399788.2:c.2345G>A	p.Arg782Gln	p.R782Q	ENST00000399788	NM_001042603.1	782	cGa/cAa	17/28	0.180051060938801	1	FACETS	0.717	0.629	0.811	0.717	0.629	0.811	INDETERMINATE	1	TRUE	0	0.31	1		645	578	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432371	432371	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs763650631	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	27	175	0	ENST00000399788.2:c.2152T>C	p.Tyr718His	p.Y718H	ENST00000399788	NM_001042603.1	718	Tat/Cat	16/28	0.180051060938801	1	FACETS	0.791	0.635	0.967	0.791	0.635	0.967	INDETERMINATE	1	TRUE	0	0.31	1		175	186	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438052	438052	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	62	412	0	ENST00000399788.2:c.1917G>T	p.Leu639Phe	p.L639F	ENST00000399788	NM_001042603.1	639	ttG/ttT	14/28	0.180051060938801	1	FACETS	0.761	0.659	0.871	0.761	0.659	0.871	INDETERMINATE	1	TRUE	0	0.31	1		412	444	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	493276	493276	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	89	679	0	ENST00000399788.2:c.287A>C	p.Lys96Thr	p.K96T	ENST00000399788	NM_001042603.1	96	aAa/aCa	3/28	0.180051060938801	1	FACETS	0.793	0.704	0.888	0.793	0.704	0.888	INDETERMINATE	1	TRUE	0	0.31	1		679	612	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378558	25378558	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	65	421	0	ENST00000311936.3:c.440A>C	p.Lys147Thr	p.K147T	ENST00000311936	NM_004985.3	147	aAg/aCg	4/5	0.172678218878313	1	FACETS	0.879	0.765	1	0.879	0.765	1	INDETERMINATE	1	TRUE	0	0.31	1		421	403	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398279	25398279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894365	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	60	527	0	ENST00000311936.3:c.40G>A	p.Val14Ile	p.V14I	ENST00000311936	NM_004985.3	14	Gta/Ata	2/5	0.172678218878313	1	FACETS	0.732	0.632	0.84	0.732	0.632	0.84	INDETERMINATE	1	TRUE	0	0.31	1		527	447	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231466	46231466	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	44	360	0	ENST00000334344.6:c.1306A>C	p.Ile436Leu	p.I436L	ENST00000334344	NM_152641.2	436	Att/Ctt	10/21	0.172678218878313	1	FACETS	0.537	0.45	0.632	0.537	0.45	0.632	INDETERMINATE	1	TRUE	0	0.31	1		360	447	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244131	46244131	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	48	407	0	ENST00000334344.6:c.2225C>T	p.Ser742Phe	p.S742F	ENST00000334344	NM_152641.2	742	tCt/tTt	15/21	0.172678218878313	1	FACETS	0.727	0.617	0.847	0.727	0.617	0.847	INDETERMINATE	1	TRUE	0	0.31	1		407	360	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244266	46244266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	48	375	0	ENST00000334344.6:c.2360C>T	p.Thr787Ile	p.T787I	ENST00000334344	NM_152641.2	787	aCt/aTt	15/21	0.172678218878313	1	FACETS	0.776	0.659	0.904	0.776	0.659	0.904	INDETERMINATE	1	TRUE	0	0.31	1		375	337	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447923	49447923	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs770105193	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	19	138	0	ENST00000301067.7:c.511C>T	p.Arg171Cys	p.R171C	ENST00000301067	NM_003482.3	171	Cgc/Tgc	5/54	0.251947839625436	3	FACETS	0.778	0.594	0.992	0.389	0.297	0.496	CLONAL	1	TRUE	1	0.31	3		138	182	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480122	50480122	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	50	263	0	ENST00000394963.4:c.356G>A	p.Arg119Gln	p.R119Q	ENST00000394963	NM_003076.4	119	cGa/cAa	2/13	0.251947839625436	3	FACETS	1	0.916	1	0.556	0.474	0.646	CLONAL	1	TRUE	1	0.31	3		263	335	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891035	112891035	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs755619262	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	58	324	0	ENST00000351677.2:c.369G>T	p.Glu123Asp	p.E123D	ENST00000351677	NM_002834.3	123	gaG/gaT	4/16	0.251947839625436	3	FACETS	0.976	0.84	1	0.488	0.42	0.561	CLONAL	1	TRUE	1	0.31	3		324	443	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	65	411	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	0.866	0.753	0.989	0.866	0.753	0.989	CLONAL	1	TRUE	1	0.31	2		411	484	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923215	26923215	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs769996123	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	55	521	4	ENST00000381527.3:c.211C>T	p.Arg71Ter	p.R71*	ENST00000381527	NM_001260.1	71	Cga/Tga	3/13	1	2	FACETS	0.816	0.699	0.942	0.816	0.699	0.942	CLONAL	1	TRUE	1	0.31	2		525	435	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588668	28588668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	75	501	0	ENST00000241453.7:c.2780C>T	p.Ala927Val	p.A927V	ENST00000241453	NM_004119.2	927	gCt/gTt	23/24	1	2	FACETS	0.976	0.857	1	0.976	0.857	1	CLONAL	1	TRUE	1	0.31	2		501	496	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623610	28623610	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	50	359	1	ENST00000241453.7:c.947T>G	p.Phe316Cys	p.F316C	ENST00000241453	NM_004119.2	316	tTt/tGt	8/24	1	2	FACETS	0.757	0.644	0.882	0.757	0.644	0.882	SUBCLONAL	1	TRUE	1	0.31	2		360	426	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29002051	29002051	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	39	220	0	ENST00000282397.4:c.1114G>T	p.Asp372Tyr	p.D372Y	ENST00000282397	NM_002019.4	372	Gat/Tat	9/30	1	2	FACETS	0.902	0.751	1	0.902	0.751	1	CLONAL	1	TRUE	1	0.31	2		220	279	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005302	29005302	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	77	455	0	ENST00000282397.4:c.959A>C	p.Lys320Thr	p.K320T	ENST00000282397	NM_002019.4	320	aAa/aCa	7/30	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.31	2		455	415	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911450	32911450	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	30	291	0	ENST00000380152.3:c.2958T>G	p.Asn986Lys	p.N986K	ENST00000380152		986	aaT/aaG	11/27	1	2	FACETS	0.639	0.516	0.777	0.639	0.516	0.777	SUBCLONAL	1	TRUE	1	0.31	2		291	303	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912817	32912817	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs80358670	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	43	422	0	ENST00000380152.3:c.4325C>A	p.Ser1442Ter	p.S1442*	ENST00000380152		1442	tCa/tAa	11/27	1	2	FACETS	0.724	0.607	0.853	0.724	0.607	0.853	SUBCLONAL	1	TRUE	1	0.31	2		422	383	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914483	32914483	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	60	395	0	ENST00000380152.3:c.5991A>C	p.Arg1997Ser	p.R1997S	ENST00000380152		1997	agA/agC	11/27	1	2	FACETS	0.868	0.75	0.996	0.868	0.75	0.996	CLONAL	1	TRUE	1	0.31	2		395	446	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945208	32945208	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	48	316	0	ENST00000380152.3:c.8603A>C	p.Lys2868Thr	p.K2868T	ENST00000380152		2868	aAa/aCa	20/27	1	2	FACETS	0.712	0.603	0.832	0.712	0.603	0.832	SUBCLONAL	1	TRUE	1	0.31	2		316	435	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953977	32953977	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	68	571	0	ENST00000380152.3:c.9044A>C	p.Lys3015Thr	p.K3015T	ENST00000380152		3015	aAa/aCa	23/27	1	2	FACETS	0.87	0.759	0.991	0.87	0.759	0.991	CLONAL	1	TRUE	1	0.31	2		571	504	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955395	48955395	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	37	236	1	ENST00000267163.4:c.1511A>C	p.Gln504Pro	p.Q504P	ENST00000267163	NM_000321.2	504	cAg/cCg	17/27	1	2	FACETS	0.751	0.621	0.895	0.751	0.621	0.895	SUBCLONAL	1	TRUE	1	0.31	2		237	318	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73333938	73333938	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	70	531	0	ENST00000377767.4:c.2872A>C	p.Lys958Gln	p.K958Q	ENST00000377767	NM_014953.3	958	Aaa/Caa	21/21	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.31	2		531	384	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73343019	73343019	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	42	410	0	ENST00000377767.4:c.1787G>T	p.Arg596Ile	p.R596I	ENST00000377767	NM_014953.3	596	aGa/aTa	14/21	1	2	FACETS	0.772	0.646	0.91	0.772	0.646	0.91	CLONAL	1	TRUE	1	0.31	2		410	351	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524607	103524607	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	58	520	0	ENST00000355739.4:c.2738A>C	p.Lys913Thr	p.K913T	ENST00000355739	NM_000123.3	913	aAa/aCa	13/15	NA	2	FACETS	0.998	0.861	1			1	INDETERMINATE	1	TRUE	NA	0.31	2		520	375	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562587	95562587	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	47	395	0	ENST00000393063.1:c.4670A>G	p.Lys1557Arg	p.K1557R	ENST00000393063	NM_030621.3	1557	aAa/aGa	24/28	1	2	FACETS	0.806	0.682	0.942	0.806	0.682	0.942	CLONAL	1	TRUE	1	0.31	2		395	376	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572534	95572534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555370340	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	51	374	0	ENST00000393063.1:c.2831G>A	p.Arg944Gln	p.R944Q	ENST00000393063	NM_030621.3	944	cGa/cAa	19/28	1	2	FACETS	0.846	0.721	0.982	0.846	0.721	0.982	CLONAL	1	TRUE	1	0.31	2		374	389	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95599691	95599691	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	67	479	0	ENST00000393063.1:c.105A>T	p.Glu35Asp	p.E35D	ENST00000393063	NM_030621.3	35	gaA/gaT	3/28	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.31	2		479	413	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239674	105239674	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	84	696	0	ENST00000349310.3:c.871A>G	p.Thr291Ala	p.T291A	ENST00000349310	NM_001014432.1	291	Aca/Gca	11/15	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.31	2		696	501	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023238	33023238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756849803	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	75	541	2	ENST00000300177.4:c.347G>A	p.Arg116His	p.R116H	ENST00000300177	NM_001191322.1	116	cGc/cAc	2/2	1	2	FACETS	0.889	0.781	1	0.889	0.781	1	CLONAL	1	TRUE	1	0.31	2		543	544	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40993392	40993392	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	56	307	0	ENST00000267868.3:c.218A>C	p.Lys73Thr	p.K73T	ENST00000267868	NM_002875.4	73	aAa/aCa	3/10	1	2	FACETS	0.86	0.739	0.992	0.86	0.739	0.992	CLONAL	1	TRUE	1	0.31	2		307	420	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358680	67358680	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	56	466	0	ENST00000327367.4:c.188A>C	p.Lys63Thr	p.K63T	ENST00000327367	NM_005902.3	63	aAg/aCg	1/9	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.31	2		466	343	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669532	88669532	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	58	653	0	ENST00000360948.2:c.1366T>C	p.Tyr456His	p.Y456H	ENST00000360948	NM_001012338.2	456	Tat/Cat	12/19	1	2	FACETS	0.768	0.661	0.885	0.768	0.661	0.885	SUBCLONAL	1	TRUE	1	0.31	2		653	487	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727521	88727521	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	50	343	0	ENST00000360948.2:c.258G>T	p.Glu86Asp	p.E86D	ENST00000360948	NM_001012338.2	86	gaG/gaT	3/19	1	2	FACETS	0.99	0.844	1	0.99	0.844	1	CLONAL	1	TRUE	1	0.31	2		343	326	SUCCESS
BLM	641	MSKCC	GRCh37	15	91290715	91290715	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	82	585	0	ENST00000355112.3:c.93A>C	p.Lys31Asn	p.K31N	ENST00000355112	NM_000057.2	31	aaA/aaC	2/22	1	2	FACETS	0.941	0.832	1	0.941	0.832	1	CLONAL	1	TRUE	1	0.31	2		585	562	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292703	91292703	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746195311	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	89	434	0	ENST00000355112.3:c.205G>A	p.Glu69Lys	p.E69K	ENST00000355112	NM_000057.2	69	Gaa/Aaa	3/22	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.31	2		434	490	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310195	91310195	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	75	678	0	ENST00000355112.3:c.2249A>C	p.Tyr750Ser	p.Y750S	ENST00000355112	NM_000057.2	750	tAc/tCc	10/22	1	2	FACETS	0.88	0.772	0.995	0.88	0.772	0.995	CLONAL	1	TRUE	1	0.31	2		678	550	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358449	91358449	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	86	709	2	ENST00000355112.3:c.4194T>G	p.Ile1398Met	p.I1398M	ENST00000355112	NM_000057.2	1398	atT/atG	22/22	1	2	FACETS	0.973	0.863	1	0.973	0.863	1	CLONAL	1	TRUE	1	0.31	2		711	570	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100477	2100477	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	95	361	0	ENST00000219476.3:c.215A>T	p.Lys72Ile	p.K72I	ENST00000219476	NM_000548.3	72	aAa/aTa	3/42	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.31	2		361	576	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916248	9916248	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397518472	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	56	438	0	ENST00000330684.3:c.2041C>T	p.Arg681Ter	p.R681*	ENST00000330684	NM_001134407.1	681	Cga/Tga	10/13	1	2	FACETS	0.858	0.737	0.99	0.858	0.737	0.99	CLONAL	1	TRUE	1	0.31	2		438	421	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23635351	23635351	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1567214357	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	40	539	0	ENST00000261584.4:c.2813A>G	p.Asn938Ser	p.N938S	ENST00000261584	NM_024675.3	938	aAt/aGt	8/13	1	2	FACETS	0.418	0.346	0.497	0.418	0.346	0.497	SUBCLONAL	1	TRUE	1	0.31	2		539	618	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645350	67645350	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	49	296	0	ENST00000264010.4:c.615G>T	p.Lys205Asn	p.K205N	ENST00000264010	NM_006565.3	205	aaG/aaT	3/12	1	2	FACETS	0.703	0.596	0.82	0.703	0.596	0.82	SUBCLONAL	1	TRUE	1	0.31	2		296	450	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660578	67660578	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	113	691	0	ENST00000264010.4:c.1478A>C	p.Lys493Thr	p.K493T	ENST00000264010	NM_006565.3	493	aAg/aCg	8/12	1	2	FACETS	0.902	0.812	0.998	0.902	0.812	0.998	CLONAL	1	TRUE	1	0.31	2		691	808	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663392	67663392	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	85	350	0	ENST00000264010.4:c.1793G>T	p.Arg598Ile	p.R598I	ENST00000264010	NM_006565.3	598	aGa/aTa	10/12	1	2	FACETS	0.917	0.812	1	0.917	0.812	1	CLONAL	1	TRUE	1	0.31	2		350	598	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579349	7579349	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	65	370	0	ENST00000269305.4:c.338T>C	p.Phe113Ser	p.F113S	ENST00000269305	NM_001126112.2	113	tTc/tCc	4/11	1	2	FACETS	0.866	0.753	0.989	0.866	0.753	0.989	CLONAL	1	TRUE	1	0.31	2		370	484	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965543	15965543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	43	422	0	ENST00000268712.3:c.5263C>T	p.Arg1755Cys	p.R1755C	ENST00000268712	NM_006311.3	1755	Cgc/Tgc	36/46	1	2	FACETS	0.87	0.731	1	0.87	0.731	1	CLONAL	1	TRUE	1	0.31	2		422	319	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508742	29508742	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057517967	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	79	603	0	ENST00000356175.3:c.669G>A	p.Trp223Ter	p.W223*	ENST00000356175	NM_000267.3	223	tgG/tgA	7/57	1	2	FACETS	0.766	0.674	0.866	0.766	0.674	0.866	SUBCLONAL	1	TRUE	1	0.31	2		603	665	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663915	29663915	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	71	512	0	ENST00000356175.3:c.6347C>A	p.Ser2116Ter	p.S2116*	ENST00000356175	NM_000267.3	2116	tCa/tAa	41/57	1	2	FACETS	0.97	0.849	1	0.97	0.849	1	CLONAL	1	TRUE	1	0.31	2		512	472	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665080	29665080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	46	285	0	ENST00000356175.3:c.6679G>A	p.Ala2227Thr	p.A2227T	ENST00000356175	NM_000267.3	2227	Gct/Act	44/57	1	2	FACETS	0.93	0.787	1	0.93	0.787	1	CLONAL	1	TRUE	1	0.31	2		285	319	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322645	30322645	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	75	368	0	ENST00000322652.5:c.1658A>G	p.Gln553Arg	p.Q553R	ENST00000322652	NM_015355.2	553	cAg/cGg	14/16	1	2	FACETS	0.91	0.798	1	0.91	0.798	1	CLONAL	1	TRUE	1	0.31	2		368	532	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649111	37649111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	81	348	0	ENST00000447079.4:c.2216G>A	p.Gly739Asp	p.G739D	ENST00000447079	NM_015083.1	739	gGc/gAc	4/14	1	2	FACETS	0.955	0.843	1	0.955	0.843	1	CLONAL	1	TRUE	1	0.31	2		348	547	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883701	37883701	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	73	772	0	ENST00000269571.5:c.3313G>T	p.Asp1105Tyr	p.D1105Y	ENST00000269571		1105	Gac/Tac	26/27	1	2	FACETS	0.785	0.687	0.891	0.785	0.687	0.891	SUBCLONAL	1	TRUE	1	0.31	2		772	600	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435887	56435887	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	34	273	0	ENST00000407977.2:c.1250G>A	p.Gly417Glu	p.G417E	ENST00000407977		417	gGa/gAa	9/10	1	2	FACETS	0.91	0.748	1	0.91	0.748	1	CLONAL	1	TRUE	1	0.31	2		273	241	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554108	63554108	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	88	697	1	ENST00000307078.5:c.631A>C	p.Ser211Arg	p.S211R	ENST00000307078	NM_004655.3	211	Agt/Cgt	2/11	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.31	2		698	556	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66522024	66522024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	37	222	0	ENST00000358598.2:c.679G>A	p.Asp227Asn	p.D227N	ENST00000358598	NM_212471.2	227	Gac/Aac	7/11	1	2	FACETS	0.978	0.812	1	0.978	0.812	1	CLONAL	1	TRUE	1	0.31	2		222	244	SUCCESS
YES1	7525	MSKCC	GRCh37	18	742921	742921	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs758709210	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	85	523	0	ENST00000314574.4:c.1057A>G	p.Lys353Glu	p.K353E	ENST00000314574	NM_005433.3	353	Aaa/Gaa	8/12	0.3	1	FACETS	0.99	0.879	1	0.99	0.879	1	CLONAL	1	TRUE	0	0.31	1		523	468	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617684	39617684	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	38	474	0	ENST00000262039.4:c.1868T>G	p.Phe623Cys	p.F623C	ENST00000262039	NM_002647.2	623	tTt/tGt	17/25	0.172678218878313	1	FACETS	0.45	0.372	0.538	0.45	0.372	0.538	INDETERMINATE	1	TRUE	0	0.31	1		474	460	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604736	48604736	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	73	468	0	ENST00000342988.3:c.1558G>T	p.Glu520Ter	p.E520*	ENST00000342988	NM_005359.5	520	Gaa/Taa	12/12	0.172678218878313	1	FACETS	0.898	0.789	1	0.898	0.789	1	INDETERMINATE	1	TRUE	0	0.31	1		468	443	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099282	4099282	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	70	693	0	ENST00000262948.5:c.836T>G	p.Phe279Cys	p.F279C	ENST00000262948	NM_030662.3	279	tTt/tGt	7/11	1	2	FACETS	0.914	0.799	1	0.914	0.799	1	CLONAL	1	TRUE	1	0.31	2		693	494	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208010	5208010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	95	700	2	ENST00000357368.4:c.5701C>T	p.Arg1901Trp	p.R1901W	ENST00000357368	NM_002850.3	1901	Cgg/Tgg	37/38	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.31	2		702	602	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214576	5214576	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	69	544	0	ENST00000357368.4:c.4490C>A	p.Ser1497Ter	p.S1497*	ENST00000357368	NM_002850.3	1497	tCa/tAa	29/38	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.31	2		544	410	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219479	5219479	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	24	269	0	ENST00000357368.4:c.3766-1G>T		p.X1256_splice	ENST00000357368	NM_002850.3	1256			1	2	FACETS	0.492	0.385	0.614	0.492	0.385	0.614	SUBCLONAL	1	TRUE	1	0.31	2		269	315	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231606	5231606	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	21	122	0	ENST00000357368.4:c.1870G>T	p.Asp624Tyr	p.D624Y	ENST00000357368	NM_002850.3	624	Gac/Tac	14/38	1	2	FACETS	1	0.838	1	1	0.838	1	CLONAL	1	TRUE	1	0.31	2		122	124	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251852	10251852	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	79	608	0	ENST00000340748.4:c.3275A>C	p.Lys1092Thr	p.K1092T	ENST00000340748		1092	aAg/aCg	30/40	1	2	FACETS	0.865	0.762	0.976	0.865	0.762	0.976	CLONAL	1	TRUE	1	0.31	2		608	589	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10292721	10292721	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	80	382	0	ENST00000340748.4:c.113A>C	p.Glu38Ala	p.E38A	ENST00000340748		38	gAa/gCa	2/40	1	2	FACETS	0.89	0.784	1	0.89	0.784	1	CLONAL	1	TRUE	1	0.31	2		382	580	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758348	41758348	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs762510681	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	47	461	0	ENST00000301178.4:c.1804G>A	p.Gly602Ser	p.G602S	ENST00000301178	NM_021913.4	602	Ggt/Agt	15/20	1	2	FACETS	0.62	0.523	0.727	0.62	0.523	0.727	SUBCLONAL	1	TRUE	1	0.31	2		461	489	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765552	41765552	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	93	613	0	ENST00000301178.4:c.2428T>G	p.Leu810Val	p.L810V	ENST00000301178	NM_021913.4	810	Ttg/Gtg	20/20	1	2	FACETS	0.96	0.855	1	0.96	0.855	1	CLONAL	1	TRUE	1	0.31	2		613	625	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021610	31021610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369425922	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	48	315	0	ENST00000375687.4:c.1609G>A	p.Glu537Lys	p.E537K	ENST00000375687	NM_015338.5	537	Gaa/Aaa	12/13	1	2	FACETS	0.867	0.736	1	0.867	0.736	1	CLONAL	1	TRUE	1	0.31	2		315	357	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31372655	31372655	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	58	416	1	ENST00000328111.2:c.296A>C	p.Glu99Ala	p.E99A	ENST00000328111	NM_006892.3	99	gAa/gCa	4/23	1	2	FACETS	0.864	0.744	0.994	0.864	0.744	0.994	CLONAL	1	TRUE	1	0.31	2		417	433	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394021	31394021	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	45	351	0	ENST00000328111.2:c.2308A>G	p.Lys770Glu	p.K770E	ENST00000328111	NM_006892.3	770	Aaa/Gaa	22/23	1	2	FACETS	0.717	0.603	0.842	0.717	0.603	0.842	SUBCLONAL	1	TRUE	1	0.31	2		351	405	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742679	39742679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	72	400	0	ENST00000361337.2:c.1522C>T	p.Arg508Cys	p.R508C	ENST00000361337	NM_003286.2	508	Cgt/Tgt	15/21	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.31	2		400	440	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40864896	40864896	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	84	465	0	ENST00000373198.4:c.2372G>T	p.Arg791Ile	p.R791I	ENST00000373198	NM_133170.3	791	aGa/aTa	16/32	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.31	2		465	476	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419935	41419935	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	58	641	0	ENST00000373198.4:c.386G>T	p.Gly129Val	p.G129V	ENST00000373198	NM_133170.3	129	gGc/gTc	3/32	1	2	FACETS	0.872	0.751	1	0.872	0.751	1	CLONAL	1	TRUE	1	0.31	2		641	429	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21304053	21304053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	78	600	0	ENST00000354336.3:c.832G>A	p.Glu278Lys	p.E278K	ENST00000354336	NM_005207.3	278	Gaa/Aaa	3/3	0.251947839625436	3	FACETS	0.997	0.877	1	0.498	0.438	0.563	CLONAL	1	TRUE	1	0.31	3		600	583	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035126	30035126	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	89	520	0	ENST00000338641.4:c.288C>A	p.Phe96Leu	p.F96L	ENST00000338641	NM_000268.3	96	ttC/ttA	3/16	NA	2	FACETS	1	0.946	1			1	INDETERMINATE	1	TRUE	NA	0.31	2		520	519	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41542787	41542787	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	97	713	0	ENST00000263253.7:c.2098A>T	p.Asn700Tyr	p.N700Y	ENST00000263253	NM_001429.3	700	Aac/Tac	11/31	NA	2	FACETS	0.927	0.827	1			1	INDETERMINATE	1	TRUE	NA	0.31	2		713	675	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573284	41573284	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	63	603	0	ENST00000263253.7:c.5569A>C	p.Thr1857Pro	p.T1857P	ENST00000263253	NM_001429.3	1857	Aca/Cca	31/31	NA	2	FACETS	0.917	0.796	1			1	INDETERMINATE	1	TRUE	NA	0.31	2		603	443	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034444	47034444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	94	356	0	ENST00000377604.3:c.529G>A	p.Glu177Lys	p.E177K	ENST00000377604	NM_001204468.1	177	Gag/Aag	6/24	0.235072706367038	0	FACETS	0.636	0.572	0.703			1	SUBCLONAL	2	TRUE	NA	0.31	0		356	329	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247028	53247028	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	70	369	0	ENST00000375401.3:c.472G>A	p.Glu158Lys	p.E158K	ENST00000375401	NM_004187.3	158	Gaa/Aaa	4/26	0.235072706367038	0	FACETS	1	0.943	1			1	CLONAL	1	TRUE	NA	0.31	0		369	278	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778812	76778812	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	66	424	0	ENST00000373344.5:c.6767C>A	p.Ser2256Tyr	p.S2256Y	ENST00000373344	NM_000489.3	2256	tCt/tAt	31/35	0.235072706367038	0	FACETS	1	0.934	1			1	CLONAL	1	TRUE	NA	0.31	0		424	267	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938229	76938229	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs191682105	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	94	369	0	ENST00000373344.5:c.2519G>T	p.Arg840Ile	p.R840I	ENST00000373344	NM_000489.3	840	aGa/aTa	9/35	0.235072706367038	0	FACETS	0.739	0.667	0.814			1	SUBCLONAL	2	TRUE	NA	0.31	0		369	283	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938595	76938595	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	70	405	0	ENST00000373344.5:c.2153A>C	p.Lys718Thr	p.K718T	ENST00000373344	NM_000489.3	718	aAa/aCa	9/35	0.235072706367038	0	FACETS	1	0.958	1			1	CLONAL	1	TRUE	NA	0.31	0		405	260	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939169	76939169	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	69	393	1	ENST00000373344.5:c.1579G>A	p.Asp527Asn	p.D527N	ENST00000373344	NM_000489.3	527	Gac/Aac	9/35	0.235072706367038	0	FACETS	1	0.959	1			1	CLONAL	1	TRUE	NA	0.31	0		394	254	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123025128	123025128	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	102	366	0	ENST00000355640.3:c.1018A>C	p.Asn340His	p.N340H	ENST00000355640		340	Aac/Cac	4/7	0.180051060938801	0	FACETS	0.69	0.624	0.759			1	INDETERMINATE	2	TRUE	NA	0.31	0		366	329	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224596	123224596	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs765683304	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	87	404	0	ENST00000218089.9:c.3449A>G	p.Gln1150Arg	p.Q1150R	ENST00000218089	NM_001042749.1	1150	cAa/cGa	31/35	0.180051060938801	0	FACETS	0.643	0.576	0.714			1	INDETERMINATE	2	TRUE	NA	0.31	0		404	301	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030753	48030754	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1553331659	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	58	319	0	ENST00000234420.5:c.3371dup	p.Asn1124LysfsTer40	p.N1124Kfs*40	ENST00000234420	NM_000179.2	1123	gaa/gAaa	5/10	1	2	FACETS	0.812	0.699	0.934	0.812	0.699	0.934	CLONAL	1	TRUE	1	0.31	2		319	461	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380244	25380246	+	missense_variant	Missense_Mutation	TNP	TGT	TGT	CGG	novel	NA	P-0001215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	53	504	1	ENST00000311936.3:c.212_214delinsCCG	p.Tyr71_Met72delinsSerVal	p.Y71_M72delinsSV	ENST00000311936	NM_004985.3	71	tACAtg/tCCGtg	3/5	0.172678218878313	1	FACETS	0.578	0.493	0.671	0.578	0.493	0.671	INDETERMINATE	1	TRUE	0	0.31	1		505	500	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381541	81381541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	62	917	0	ENST00000222390.5:c.520G>A	p.Glu174Lys	p.E174K	ENST00000222390	NM_000601.4	174	Gaa/Aaa	5/18	0.214657886077992	3	FACETS	1	0.93	1	0.552	0.481	0.628	INDETERMINATE	1	TRUE	1	0.482131467754712	3		917	289	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316237	11316237	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748631718	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	64	389	0	ENST00000361445.4:c.517C>T	p.Arg173Cys	p.R173C	ENST00000361445	NM_004958.3	173	Cgt/Tgt	5/58	0.130717022042882	1	FACETS	1	0.913	1	1	0.913	1	INDETERMINATE	1	TRUE	0	0.482131467754712	1		389	193	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099090	27099090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1482721698	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	57	424	0	ENST00000324856.7:c.3506C>T	p.Pro1169Leu	p.P1169L	ENST00000324856	NM_006015.4	1169	cCa/cTa	13/20	0.260177284658015	4	FACETS	0.881	0.767	1	0.881	0.767	1	INDETERMINATE	2	TRUE	2	0.482131467754712	4		424	199	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100178	27100178	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	45	517	0	ENST00000324856.7:c.3974C>T	p.Pro1325Leu	p.P1325L	ENST00000324856	NM_006015.4	1325	cCc/cTc	16/20	0.260177284658015	4	FACETS	1	0.955	1	0.685	0.582	0.795	INDETERMINATE	1	TRUE	2	0.482131467754712	4		517	202	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458380	120458380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	31	231	0	ENST00000256646.2:c.6965C>T	p.Pro2322Leu	p.P2322L	ENST00000256646	NM_024408.3	2322	cCc/cTc	34/34	0.260177284658015	4	FACETS	0.908	0.752	1	0.908	0.752	1	INDETERMINATE	2	TRUE	2	0.482131467754712	4		231	105	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741940	162741940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150835897	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	52	555	0	ENST00000367921.3:c.1631C>T	p.Thr544Ile	p.T544I	ENST00000367921	NM_006182.2	544	aCc/aTc	13/18	NA	2	FACETS	1	0.9	1			1	INDETERMINATE	1	TRUE	NA	0.482131467754712	2		555	205	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497898	25497898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	38	504	0	ENST00000264709.3:c.551C>T	p.Pro184Leu	p.P184L	ENST00000264709	NM_175629.2	184	cCc/cTc	6/23	1	2	FACETS	0.838	0.701	0.988	0.838	0.701	0.988	CLONAL	1	TRUE	1	0.482131467754712	2		504	188	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248411	212248411	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	47	673	0	ENST00000342788.4:c.3856T>A	p.Ser1286Thr	p.S1286T	ENST00000342788	NM_005235.2	1286	Tct/Act	28/28	0.201610476919183	0	FACETS	0.472	0.402	0.546			1	INDETERMINATE	1	TRUE	0	0.482131467754712	0		673	214	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578371	212578371	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	35	513	0	ENST00000342788.4:c.886A>C	p.Asn296His	p.N296H	ENST00000342788	NM_005235.2	296	Aac/Cac	8/28	0.201610476919183	0	FACETS	0.427	0.354	0.507			1	INDETERMINATE	1	TRUE	0	0.482131467754712	0		513	176	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391000	89391000	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	118	656	0	ENST00000336596.2:c.1066G>A	p.Asp356Asn	p.D356N	ENST00000336596	NM_005233.5	356	Gat/Aat	5/17	0.288225302155438	2	FACETS	1	0.982	1	0.663	0.604	0.724	INDETERMINATE	1	TRUE	0	0.482131467754712	2		656	369	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468535	89468535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	49	431	0	ENST00000336596.2:c.2069C>T	p.Thr690Ile	p.T690I	ENST00000336596	NM_005233.5	690	aCc/aTc	11/17	0.288225302155438	2	FACETS	0.764	0.652	0.885	0.382	0.326	0.443	INDETERMINATE	1	TRUE	0	0.482131467754712	2		431	266	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202807	128202807	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	40	455	0	ENST00000341105.2:c.913C>T	p.Leu305Phe	p.L305F	ENST00000341105	NM_032638.4	305	Ctc/Ttc	4/6	0.147165082197821	4	FACETS	0.809	0.684	0.943	0.809	0.684	0.943	INDETERMINATE	2	TRUE	2	0.482131467754712	4		455	152	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808641	1808641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	79	765	1	ENST00000260795.2:c.2254C>T	p.Leu752Phe	p.L752F	ENST00000260795		752	Ctt/Ttt	16/17	0.147165082197821	4	FACETS	0.848	0.762	0.935	1	0.973	1	INDETERMINATE	3	TRUE	2	0.482131467754712	4		766	191	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953837	55953837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	33	630	0	ENST00000263923.4:c.3599C>T	p.Ser1200Phe	p.S1200F	ENST00000263923	NM_002253.2	1200	tCc/tTc	27/30	0.435885705532062	1	FACETS	0.597	0.492	0.713	0.597	0.492	0.713	SUBCLONAL	1	TRUE	0	0.482131467754712	1		630	174	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230813	66230813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748201189	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	43	859	0	ENST00000273854.3:c.2158G>A	p.Asp720Asn	p.D720N	ENST00000273854	NM_004439.5	720	Gat/Aat	12/18	0.435885705532062	1	FACETS	0.517	0.435	0.606	0.517	0.435	0.606	SUBCLONAL	1	TRUE	0	0.482131467754712	1		859	262	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467848	66467848	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1217481114	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	46	732	0	ENST00000273854.3:c.421C>T	p.Pro141Ser	p.P141S	ENST00000273854	NM_004439.5	141	Cct/Tct	3/18	0.435885705532062	1	FACETS	0.563	0.478	0.656	0.563	0.478	0.656	SUBCLONAL	1	TRUE	0	0.482131467754712	1		732	257	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197429	106197429	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	67	655	0	ENST00000380013.4:c.5762T>C	p.Met1921Thr	p.M1921T	ENST00000380013	NM_001127208.2	1921	aTg/aCg	11/11	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.482131467754712	2		655	252	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876398	35876398	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	38	481	0	ENST00000303115.3:c.1190G>A	p.Gly397Glu	p.G397E	ENST00000303115	NM_002185.3	397	gGg/gAg	8/8	0.147165082197821	4	FACETS	1	0.923	1	0.596	0.498	0.703	INDETERMINATE	1	TRUE	2	0.482131467754712	4		481	196	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177731	56177731	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1160631626	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	82	469	0	ENST00000399503.3:c.2704C>T	p.Pro902Ser	p.P902S	ENST00000399503	NM_005921.1	902	Cct/Tct	14/20	0.478602221967948	4	FACETS	0.84	0.749	0.936	0.84	0.749	0.936	CLONAL	2	TRUE	2	0.482131467754712	4		469	300	SUCCESS
APC	324	MSKCC	GRCh37	5	112173647	112173647	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1165139414	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	52	565	0	ENST00000257430.4:c.2356C>T	p.Arg786Cys	p.R786C	ENST00000257430	NM_000038.5	786	Cgt/Tgt	16/16	0.214657886077992	3	FACETS	1	0.947	1	0.608	0.524	0.698	INDETERMINATE	1	TRUE	1	0.482131467754712	3		565	220	SUCCESS
APC	324	MSKCC	GRCh37	5	112176824	112176824	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060503338	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	57	763	0	ENST00000257430.4:c.5533C>T	p.His1845Tyr	p.H1845Y	ENST00000257430	NM_000038.5	1845	Cat/Tat	16/16	0.214657886077992	3	FACETS	1	0.957	1	0.632	0.549	0.721	INDETERMINATE	1	TRUE	1	0.482131467754712	3		763	232	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927070	131927070	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	113	660	0	ENST00000265335.6:c.1607C>T	p.Thr536Ile	p.T536I	ENST00000265335		536	aCc/aTc	10/25	0.214657886077992	3	FACETS	1	0.984	1	0.736	0.668	0.807	INDETERMINATE	1	TRUE	1	0.482131467754712	3		660	395	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176710810	176710810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	54	728	0	ENST00000439151.2:c.6032C>T	p.Pro2011Leu	p.P2011L	ENST00000439151	NM_022455.4	2011	cCc/cTc	20/23	0.214657886077992	3	FACETS	0.936	0.805	1	0.468	0.402	0.539	INDETERMINATE	1	TRUE	1	0.482131467754712	3		728	297	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056964	180056964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	36	788	0	ENST00000261937.6:c.655C>T	p.Pro219Ser	p.P219S	ENST00000261937	NM_182925.4	219	Ccc/Tcc	5/30	0.460882410035956	0	FACETS	0.758	0.641	0.881			1	SUBCLONAL	1	TRUE	0	0.482131467754712	0		788	102	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704518	117704518	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	102	729	0	ENST00000368508.3:c.2458C>T	p.Leu820Phe	p.L820F	ENST00000368508	NM_002944.2	820	Ctt/Ttt	16/43	0.435885705532062	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.482131467754712	1		729	271	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150422	157150422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	64	652	1	ENST00000346085.5:c.1604C>T	p.Pro535Leu	p.P535L	ENST00000346085	NM_020732.3	535	cCt/cTt	2/20	NA	2	FACETS	1	0.877	1			1	INDETERMINATE	1	TRUE	NA	0.482131467754712	2		653	265	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527802	157527802	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1369594791	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	51	353	0	ENST00000346085.5:c.5527C>T	p.Arg1843Cys	p.R1843C	ENST00000346085	NM_020732.3	1843	Cgc/Tgc	20/20	NA	2	FACETS	1	0.957	1			1	INDETERMINATE	1	TRUE	NA	0.482131467754712	2		353	165	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940460	13940460	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	128	516	0	ENST00000405192.2:c.1046C>T	p.Ala349Val	p.A349V	ENST00000405192	NM_001163147.1	349	gCc/gTc	11/12	0.297138104647236	6	FACETS	0.896	0.826	0.967	0.896	0.826	0.967	CLONAL	4	TRUE	2	0.482131467754712	6		516	291	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459549	50459549	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	26	341	0	ENST00000331340.3:c.838C>T	p.Gln280Ter	p.Q280*	ENST00000331340	NM_006060.4	280	Cag/Tag	7/8	0.214657886077992	3	FACETS	0.943	0.756	1	0.471	0.378	0.575	INDETERMINATE	1	TRUE	1	0.482131467754712	3		341	142	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376024	8376024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	39	504	0	ENST00000356435.5:c.4573C>T	p.Pro1525Ser	p.P1525S	ENST00000356435		1525	Cca/Tca	28/35	0.460882410035956	0	FACETS	0.548	0.461	0.64			1	SUBCLONAL	1	TRUE	0	0.482131467754712	0		504	153	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	57	383	0	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	0.482131467754712	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.482131467754712	1		383	123	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98241391	98241391	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	42	454	0	ENST00000331920.6:c.1106C>T	p.Pro369Leu	p.P369L	ENST00000331920	NM_000264.3	369	cCc/cTc	8/24	0.482131467754712	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.482131467754712	1		454	94	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851285	63851285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	76	468	0	ENST00000279873.7:c.2063C>T	p.Ser688Phe	p.S688F	ENST00000279873	NM_032199.2	688	tCc/tTc	10/10	0.482131467754712	6	FACETS	1	0.898	1			1	CLONAL	2	TRUE	NA	0.482131467754712	6		468	305	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88635779	88635779	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	18	484	1	ENST00000372037.3:c.4C>T	p.Pro2Ser	p.P2S	ENST00000372037	NM_004329.2	2	Cct/Tct	3/13	1	2	FACETS	0.491	0.372	0.629	0.491	0.372	0.629	SUBCLONAL	1	TRUE	1	0.482131467754712	2		485	152	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239513	123239513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1032609119	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	69	716	0	ENST00000358487.5:c.2324C>T	p.Pro775Leu	p.P775L	ENST00000358487	NM_000141.4	775	cCt/cTt	18/18	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.482131467754712	2		716	282	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575494	64575494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	43	604	0	ENST00000312049.6:c.523C>T	p.Leu175Phe	p.L175F	ENST00000312049	NM_130799.2	175	Ctc/Ttc	3/10	0.241641024685758	4	FACETS	1	0.885	1			1	INDETERMINATE	1	TRUE	NA	0.482131467754712	4		604	249	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139269	108139269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782298	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	59	705	0	ENST00000278616.4:c.2771G>A	p.Arg924Gln	p.R924Q	ENST00000278616	NM_000051.3	924	cGg/cAg	18/63	0.147165082197821	4	FACETS	0.806	0.703	0.916	0.806	0.703	0.916	INDETERMINATE	2	TRUE	2	0.482131467754712	4		705	225	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944926	31944926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768639345	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	14	186	0	ENST00000340398.3:c.175G>A	p.Glu59Lys	p.E59K	ENST00000340398	NM_001013699.2	59	Gag/Aag	1/1	0.164011202907161	1	FACETS	0.648	0.479	0.842	0.648	0.479	0.842	INDETERMINATE	1	TRUE	0	0.482131467754712	1		186	68	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592680	28592680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	48	768	0	ENST00000241453.7:c.2465G>A	p.Gly822Glu	p.G822E	ENST00000241453	NM_004119.2	822	gGg/gAg	20/24	0.416632480521648	0	FACETS	0.867	0.754	0.982			1	CLONAL	1	TRUE	0	0.482131467754712	0		768	119	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436240	110436240	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774858350	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	19	282	0	ENST00000375856.3:c.2161C>T	p.Pro721Ser	p.P721S	ENST00000375856	NM_003749.2	721	Ccg/Tcg	1/2	0.435667607846836	1	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	0	0.482131467754712	1		282	49	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778935	3778935	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	20	231	0	ENST00000262367.5:c.6113C>T	p.Pro2038Leu	p.P2038L	ENST00000262367	NM_004380.2	2038	cCt/cTt	31/31	0.435885705532062	1	FACETS	0.797	0.625	0.987	0.797	0.625	0.987	CLONAL	1	TRUE	0	0.482131467754712	1		231	79	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857742	9857742	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	35	695	0	ENST00000330684.3:c.3659A>G	p.Asn1220Ser	p.N1220S	ENST00000330684	NM_001134407.1	1220	aAc/aGc	13/13	0.435885705532062	1	FACETS	0.875	0.732	1	0.875	0.732	1	CLONAL	1	TRUE	0	0.482131467754712	1		695	126	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858787	9858787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	20	340	0	ENST00000330684.3:c.2614C>T	p.His872Tyr	p.H872Y	ENST00000330684	NM_001134407.1	872	Cat/Tat	13/13	0.435885705532062	1	FACETS	0.75	0.586	0.931	0.75	0.586	0.931	CLONAL	1	TRUE	0	0.482131467754712	1		340	84	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862896	9862896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1198247451	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	27	435	0	ENST00000330684.3:c.2407G>A	p.Glu803Lys	p.E803K	ENST00000330684	NM_001134407.1	803	Gag/Aag	12/13	0.435885705532062	1	FACETS	0.486	0.39	0.593	0.486	0.39	0.593	SUBCLONAL	1	TRUE	0	0.482131467754712	1		435	175	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862939	9862939	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1163381321	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	25	368	0	ENST00000330684.3:c.2364G>A	p.Met788Ile	p.M788I	ENST00000330684	NM_001134407.1	788	atG/atA	12/13	0.435885705532062	1	FACETS	0.579	0.462	0.709	0.579	0.462	0.709	SUBCLONAL	1	TRUE	0	0.482131467754712	1		368	136	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89825073	89825073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	22	579	0	ENST00000389301.3:c.2893C>T	p.Pro965Ser	p.P965S	ENST00000389301	NM_000135.2	965	Cct/Tct	30/43	0.233266242508697	1	FACETS	0.325	0.253	0.408	0.325	0.253	0.408	INDETERMINATE	1	TRUE	0	0.482131467754712	1		579	213	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553484	29553484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs17881753	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	64	723	0	ENST00000356175.3:c.2033C>T	p.Pro678Leu	p.P678L	ENST00000356175	NM_000267.3	678	cCg/cTg	18/57	0.147165082197821	4	FACETS	1	0.958	1	0.625	0.545	0.71	INDETERMINATE	1	TRUE	2	0.482131467754712	4		723	315	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559842	29559842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	66	474	0	ENST00000356175.3:c.3439C>T	p.Leu1147Phe	p.L1147F	ENST00000356175	NM_000267.3	1147	Ctt/Ttt	26/57	0.147165082197821	4	FACETS	0.786	0.69	0.888	0.786	0.69	0.888	INDETERMINATE	2	TRUE	2	0.482131467754712	4		474	258	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533581	63533581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	47	1097	0	ENST00000307078.5:c.1573C>T	p.Pro525Ser	p.P525S	ENST00000307078	NM_004655.3	525	Ccc/Tcc	6/11	0.459009812045366	1	FACETS	0.791	0.677	0.913	0.791	0.677	0.913	CLONAL	1	TRUE	0	0.482131467754712	1		1097	187	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591837	48591837	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs867764109	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	100	723	1	ENST00000342988.3:c.1000C>T	p.Gln334Ter	p.Q334*	ENST00000342988	NM_005359.5	334	Cag/Tag	9/12	0.296238093050389	2	FACETS	0.792	0.719	0.866	0.792	0.719	0.866	SUBCLONAL	2	TRUE	0	0.482131467754712	2		724	262	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117084	7117084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	36	761	1	ENST00000302850.5:c.4132C>T	p.Arg1378Trp	p.R1378W	ENST00000302850	NM_000208.2	1378	Cgg/Tgg	22/22	0.430955348855787	0	FACETS	0.273	0.225	0.326			1	SUBCLONAL	1	TRUE	0	0.482131467754712	0		762	283	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355080	15355080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	35	244	0	ENST00000263377.2:c.2543C>T	p.Pro848Leu	p.P848L	ENST00000263377	NM_058243.2	848	cCa/cTa	13/20	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.482131467754712	2		244	116	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948818	17948818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	30	865	0	ENST00000458235.1:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000458235	NM_000215.3	542	Gag/Aag	12/24	1	2	FACETS	0.741	0.603	0.893	0.741	0.603	0.893	SUBCLONAL	1	TRUE	1	0.482131467754712	2		865	168	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257388	19257388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	29	473	0	ENST00000162023.5:c.745C>T	p.Pro249Ser	p.P249S	ENST00000162023		249	Ccc/Tcc	11/13	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.482131467754712	2		473	92	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525051	9525051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	38	801	0	ENST00000353224.5:c.1834C>T	p.Pro612Ser	p.P612S	ENST00000353224	NM_177990.2	612	Cct/Tct	8/10	0.214657886077992	3	FACETS	1	0.866	1	0.52	0.435	0.613	INDETERMINATE	1	TRUE	1	0.482131467754712	3		801	188	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017788	31017788	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	35	527	0	ENST00000375687.4:c.650T>A	p.Ile217Asn	p.I217N	ENST00000375687	NM_015338.5	217	aTt/aAt	8/13	0.214657886077992	3	FACETS	1	0.933	1	0.63	0.525	0.744	INDETERMINATE	1	TRUE	1	0.482131467754712	3		527	143	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42840342	42840342	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs570454392	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	56	475	0	ENST00000398585.3:c.1406G>A	p.Gly469Glu	p.G469E	ENST00000398585	NM_001135099.1	469	gGg/gAg	12/14	0.233266242508697	1	FACETS	0.753	0.653	0.86	0.753	0.653	0.86	INDETERMINATE	1	TRUE	0	0.482131467754712	1		475	234	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938022	76938022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	56	482	0	ENST00000373344.5:c.2726C>T	p.Pro909Leu	p.P909L	ENST00000373344	NM_000489.3	909	cCt/cTt	9/35	0.32277678480597	0	FACETS	0.797	0.699	0.898			1	SUBCLONAL	1	TRUE	NA	0.482131467754712	0		482	151	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274876	142274877	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	31	588	0	ENST00000350721.4:c.2183dup	p.Leu728PhefsTer7	p.L728Ffs*7	ENST00000350721	NM_001184.3	728	tta/ttTa	10/47	0.214657886077992	3	FACETS	0.512	0.414	0.621	0.256	0.207	0.311	INDETERMINATE	1	TRUE	1	0.482131467754712	3		588	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579547	7579552	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGAC	GGGGAC	AGCA	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	25	501	0	ENST00000269305.4:c.135_140delinsTGCT	p.Ser46AlafsTer5	p.S46Afs*5	ENST00000269305	NM_001126112.2	45	ctGTCCCCg/ctTGCTg	4/11	0.482131467754712	1	FACETS	0.679	0.544	0.827	0.679	0.544	0.827	SUBCLONAL	1	TRUE	0	0.482131467754712	1		501	116	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953135	17953136	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	13	410	0	ENST00000458235.1:c.850_851delinsAA	p.Gly284Lys	p.G284K	ENST00000458235	NM_000215.3	284	GGa/AAa	6/24	1	2	FACETS	0.556	0.401	0.739	0.556	0.401	0.739	SUBCLONAL	1	TRUE	1	0.482131467754712	2		410	97	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171735	36171736	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	69	408	0	ENST00000300305.3:c.829_830delinsTT	p.Pro277Leu	p.P277L	ENST00000300305		277	CCa/TTa	7/8	0.353228981659461	5	FACETS	0.752	0.66	0.85			1	SUBCLONAL	2	TRUE	NA	0.482131467754712	5		408	328	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509102	66509103	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	62	702	0	ENST00000273854.3:c.224_225delinsAA	p.Trp75Ter	p.W75*	ENST00000273854	NM_004439.5	75	tGG/tAA	2/18	0.435885705532062	1	FACETS	0.875	0.767	0.99	0.875	0.767	0.99	CLONAL	1	TRUE	0	0.482131467754712	1		702	223	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239111	98239112	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0001229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	59	482	0	ENST00000331920.6:c.1531_1532delinsAA	p.Gly511Asn	p.G511N	ENST00000331920	NM_000264.3	511	GGt/AAt	11/24	0.482131467754712	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.482131467754712	1		482	154	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0001286-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	102	697	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.212487807560831	2		697	681	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023060	27023060	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001286-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	15	34	0	ENST00000324856.7:c.166C>T	p.Gln56Ter	p.Q56*	ENST00000324856	NM_006015.4	56	Cag/Tag	1/20	NA	2	FACETS	0.967	0.723	1			1	INDETERMINATE	2	FALSE	NA	0.212487807560831	2		34	73	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105841	27105841	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001286-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	88	222	0	ENST00000324856.7:c.5452C>T	p.Gln1818Ter	p.Q1818*	ENST00000324856	NM_006015.4	1818	Cag/Tag	20/20	NA	2	FACETS	0.874	0.777	0.976			1	INDETERMINATE	2	FALSE	NA	0.212487807560831	2		222	474	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141084	55141084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778015444	NA	P-0001286-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	101	243	1	ENST00000257290.5:c.1730C>T	p.Pro577Leu	p.P577L	ENST00000257290	NM_006206.4	577	cCg/cTg	12/23	1	2	FACETS	0.813	0.728	0.902	1	0.984	1	CLONAL	2	FALSE	1	0.212487807560831	2		244	585	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835904	151835904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001286-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	51	246	0	ENST00000262189.6:c.14620C>T	p.Arg4874Trp	p.R4874W	ENST00000262189	NM_170606.2	4874	Cgg/Tgg	58/59	0.212487807560831	5	FACETS	0.769	0.652	0.899	0.256	0.217	0.3	SUBCLONAL	1	FALSE	2	0.212487807560831	5		246	823	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692848	89692848	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001286-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	33	68	0	ENST00000371953.3:c.332G>A	p.Trp111Ter	p.W111*	ENST00000371953	NM_000314.4	111	tGg/tAg	5/9	1	2	FACETS	0.919	0.758	1	1	0.96	1	CLONAL	2	FALSE	1	0.212487807560831	2		68	169	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104637	209104638	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0001286-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	124	324	0	ENST00000345146.2:c.940dup	p.Arg314ProfsTer34	p.R314Pfs*34	ENST00000345146	NM_005896.2	314	cgt/cCgt	8/10	0.212487807560831	4	FACETS	0.789	0.713	0.869	0.526	0.475	0.579	SUBCLONAL	2	FALSE	1	0.212487807560831	4		324	897	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591077	67591090	+	frameshift_variant	Frame_Shift_Del	DEL	GAGAAATTGACAAA	GAGAAATTGACAAA	-	novel	NA	P-0001286-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	20	115	0	ENST00000274335.5:c.1670_1683del	p.Arg557ProfsTer6	p.R557Pfs*6	ENST00000274335		557	cGAGAAATTGACAAA/c	12/15	0.19058832976896	3	FACETS	0.649	0.496	0.828	0.324	0.248	0.414	SUBCLONAL	1	FALSE	1	0.212487807560831	3		115	321	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692984	89692985	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0001286-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	91	175	0	ENST00000371953.3:c.468_469insT	p.Glu157Ter	p.E157*	ENST00000371953	NM_000314.4	156	-/T	5/9	1	2	FACETS	0.919	0.82	1	1	0.985	1	CLONAL	2	FALSE	1	0.212487807560831	2		175	466	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0001303-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	249	322	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.48165658269438	5	FACETS	0.805	0.753	0.859	0.537	0.502	0.573	CLONAL	2	TRUE	2	0.48165658269438	5		322	1106	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657167	215657167	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001303-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	33	225	0	ENST00000260947.4:c.218A>G	p.Asn73Ser	p.N73S	ENST00000260947	NM_000465.2	73	aAt/aGt	3/11	0.364334394636036	3	FACETS	0.328	0.267	0.398	0.109	0.089	0.133	SUBCLONAL	1	TRUE	0	0.48165658269438	3		225	518	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259311	89259311	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001303-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	53	365	0	ENST00000336596.2:c.455T>C	p.Phe152Ser	p.F152S	ENST00000336596	NM_005233.5	152	tTc/tCc	3/17	NA	2	FACETS	0.302	0.257	0.352			1	INDETERMINATE	1	TRUE	NA	0.48165658269438	2		365	728	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806176	1806176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370064407	NA	P-0001303-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	67	432	0	ENST00000260795.2:c.1195C>T	p.Arg399Cys	p.R399C	ENST00000260795		399	Cgc/Tgc	8/17	0.364334394636036	3	FACETS	0.38	0.329	0.435	0.127	0.109	0.145	SUBCLONAL	1	TRUE	0	0.48165658269438	3		432	909	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241617	55241617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001303-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	265	315	0	ENST00000275493.2:c.2065G>A	p.Val689Met	p.V689M	ENST00000275493	NM_005228.3	689	Gtg/Atg	18/28	0.48165658269438	5	FACETS	0.809	0.757	0.861	0.539	0.505	0.574	CLONAL	2	TRUE	2	0.48165658269438	5		315	1172	SUCCESS
AR	367	MSKCC	GRCh37	X	66863213	66863213	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001303-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	148	441	0	ENST00000374690.3:c.1732G>T	p.Gly578Ter	p.G578*	ENST00000374690	NM_000044.3	578	Gga/Tga	2/8	0.248157459427736	2	FACETS	0.691	0.63	0.753	0.345	0.315	0.377	INDETERMINATE	1	TRUE	0	0.48165658269438	2		441	890	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938397	76938397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001303-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	94	483	0	ENST00000373344.5:c.2351C>T	p.Ser784Phe	p.S784F	ENST00000373344	NM_000489.3	784	tCt/tTt	9/35	0.248157459427736	2	FACETS	0.339	0.301	0.38	0.17	0.15	0.19	INDETERMINATE	1	TRUE	0	0.48165658269438	2		483	1151	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597942	43597942	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001303-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	60	495	0	ENST00000355710.3:c.490G>A	p.Glu164Lys	p.E164K	ENST00000355710	NM_020975.4	164	Gag/Aag	3/20	0.301405639671584	4	FACETS	0.416	0.357	0.48	0.208	0.178	0.24	SUBCLONAL	1	TRUE	2	0.48165658269438	4		495	888	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579577	7579580	+	frameshift_variant	Frame_Shift_Ins	INS	GACG	GACG	ACGAC	novel	NA	P-0001303-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	103	247	0	ENST00000269305.4:c.107_110delinsGTCGT	p.Pro36ArgfsTer7	p.P36Rfs*7	ENST00000269305	NM_001126112.2	36	cCGTCc/cGTCGTc	4/11	0.385888246364959	1	FACETS	0.792	0.714	0.874	0.792	0.714	0.874	SUBCLONAL	1	TRUE	0	0.48165658269438	1		247	410	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837904	156837904	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001348-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	134	364	1	ENST00000524377.1:c.437C>A	p.Ser146Ter	p.S146*	ENST00000524377	NM_002529.3	146	tCg/tAg	5/17	0.672074245761104	3	FACETS	0.894	0.828	0.961	0.894	0.828	0.961	CLONAL	2	TRUE	1	0.726864695524461	3		365	281	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746110	162746110	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001348-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	128	289	2	ENST00000367921.3:c.2233G>T	p.Gly745Cys	p.G745C	ENST00000367921	NM_006182.2	745	Ggc/Tgc	16/18	0.672074245761104	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.726864695524461	3		291	228	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871274	35871274	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001348-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	38	371	0	ENST00000303115.3:c.496G>T	p.Asp166Tyr	p.D166Y	ENST00000303115	NM_002185.3	166	Gat/Tat	4/8	0.254761520091438	4	FACETS	1	0.869	1			1	INDETERMINATE	1	TRUE	NA	0.726864695524461	4		371	173	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32191699	32191699	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1046272476	NA	P-0001348-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	205	398	0	ENST00000375023.3:c.7C>G	p.Pro3Ala	p.P3A	ENST00000375023	NM_004557.3	3	Ccc/Gcc	1/30	0.726864695524461	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	3	TRUE	1	0.726864695524461	4		398	323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691003	NA	P-0001348-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	129	419	1	ENST00000269305.4:c.96+1G>T		p.X32_splice	ENST00000269305	NM_001126112.2	32			0.402864826077145	5	FACETS	0.871	0.804	0.938	0.871	0.804	0.938	INDETERMINATE	3	TRUE	2	0.726864695524461	5		420	284	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33446586	33446586	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs797044943	NA	P-0001348-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	134	579	0	ENST00000345365.6:c.47T>C	p.Met16Thr	p.M16T	ENST00000345365	NM_002878.3	16	aTg/aCg	1/10	0.402864826077145	5	FACETS	1	0.96	1	0.714	0.656	0.772	INDETERMINATE	2	TRUE	2	0.726864695524461	5		579	360	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899194	78899194	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001348-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	30	251	0	ENST00000306801.3:c.2833G>T	p.Ala945Ser	p.A945S	ENST00000306801	NM_020761.2	945	Gct/Tct	24/34	0.402864826077145	5	FACETS	0.548	0.442	0.667	0.183	0.147	0.223	INDETERMINATE	1	TRUE	2	0.726864695524461	5		251	315	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222983	1222983	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs398123406	NA	P-0001348-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	100	196	0	ENST00000326873.7:c.921-1G>T		p.X307_splice	ENST00000326873	NM_000455.4	307			0.678831650288662	2	FACETS	0.969	0.905	1	0.969	0.905	1	CLONAL	2	TRUE	0	0.726864695524461	2		196	142	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602773	10602773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001348-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	184	382	0	ENST00000171111.5:c.805C>T	p.Arg269Trp	p.R269W	ENST00000171111	NM_203500.1	269	Cgg/Tgg	3/6	0.678831650288662	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.726864695524461	2		382	224	SUCCESS
APC	324	MSKCC	GRCh37	5	112173628	112173628	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1561576308	NA	P-0001348-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	107	328	0	ENST00000257430.4:c.2338del	p.Ser780ValfsTer40	p.S780Vfs*40	ENST00000257430	NM_000038.5	779	ttA/tt	16/16	0.66356055703612	2	FACETS	0.956	0.894	1	0.956	0.894	1	CLONAL	2	TRUE	0	0.726864695524461	2		328	154	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974795	21974796	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCTC	novel	NA	P-0001348-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	52	148	0	ENST00000304494.5:c.28_31dup	p.Pro11ArgfsTer5	p.P11Rfs*5	ENST00000304494	NM_000077.4	11	cct/cGAGCct	1/3	0.678831650288662	2	FACETS	1	0.959	1	0.617	0.542	0.692	CLONAL	1	TRUE	0	0.726864695524461	2		148	116	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577061	7577084	+	inframe_deletion	In_Frame_Del	DEL	CTTTCTTGCGGAGATTCTCTTCCT	CTTTCTTGCGGAGATTCTCTTCCT	-	novel	NA	P-0001348-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	64	451	0	ENST00000269305.4:c.854_877del	p.Glu285_Lys292del	p.E285_K292del	ENST00000269305	NM_001126112.2	285	gAGGAAGAGAATCTCCGCAAGAAAGgg/ggg	8/11	0.402864826077145	5	FACETS	1	0.939	1	0.378	0.329	0.429	INDETERMINATE	1	TRUE	2	0.726864695524461	5		451	325	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561818	55561818	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001393-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	31	452	2	ENST00000288135.5:c.208A>T	p.Ile70Phe	p.I70F	ENST00000288135	NM_000222.2	70	Atc/Ttc	2/21	0.602786211827341	2	FACETS	0.217	0.175	0.265	0.109	0.087	0.133	SUBCLONAL	1	TRUE	0	0.602786211827341	2		454	473	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527471	157527471	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001393-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	64	493	0	ENST00000346085.5:c.5196G>C	p.Glu1732Asp	p.E1732D	ENST00000346085	NM_020732.3	1732	gaG/gaC	20/20	0.351060327407568	5	FACETS	0.469	0.405	0.539			1	INDETERMINATE	1	TRUE	NA	0.602786211827341	5		493	862	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396800	139396800	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001393-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	82	503	0	ENST00000277541.6:c.5308C>A	p.Pro1770Thr	p.P1770T	ENST00000277541	NM_017617.3	1770	Cct/Act	28/34	0.589344242369896	3	FACETS	0.551	0.486	0.62			1	SUBCLONAL	1	TRUE	NA	0.602786211827341	3		503	643	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342381	118342381	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001393-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	86	735	0	ENST00000534358.1:c.507A>T	p.Lys169Asn	p.K169N	ENST00000534358	NM_005933.3	169	aaA/aaT	3/36	1	2	FACETS	0.431	0.381	0.484	0.431	0.381	0.484	SUBCLONAL	1	TRUE	1	0.602786211827341	2		735	662	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240345	5240345	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0001393-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	31	437	0	ENST00000357368.4:c.1571-2A>T		p.X524_splice	ENST00000357368	NM_002850.3	524			0.213426236749442	2	FACETS	0.227	0.183	0.277	0.114	0.091	0.139	INDETERMINATE	1	TRUE	0	0.602786211827341	2		437	453	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928084	+	inframe_deletion	In_Frame_Del	DEL	GAAGAT	GAAGAT	-	novel	NA	P-0001393-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	129	562	0	ENST00000263967.3:c.1357_1362del	p.Glu453_Asp454del	p.E453_D454del	ENST00000263967	NM_006218.2	453	GAAGAT/-	8/21	0.602786211827341	2	FACETS	0.758	0.69	0.828	0.379	0.345	0.414	SUBCLONAL	1	TRUE	0	0.602786211827341	2		562	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577520	7577521	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGG	novel	NA	P-0001393-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	235	431	0	ENST00000269305.4:c.758_760dup	p.Thr253dup	p.T253dup	ENST00000269305	NM_001126112.2	253	atc/aCCAtc	7/11	0.602786211827341	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.602786211827341	2		431	390	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0001394-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	129	402	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.179368939808927	3	FACETS	0.925	0.84	1	0.925	0.84	1	CLONAL	2	TRUE	1	0.22	3		402	704	SUCCESS
APC	324	MSKCC	GRCh37	5	112174835	112174835	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0001394-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	80	341	0	ENST00000257430.4:c.3544A>T	p.Lys1182Ter	p.K1182*	ENST00000257430	NM_000038.5	1182	Aaa/Taa	16/16	0.179368939808927	3	FACETS	1	0.951	1	0.578	0.509	0.653	CLONAL	1	TRUE	1	0.22	3		341	698	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152503	56152503	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001394-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	80	371	0	ENST00000399503.3:c.559G>T	p.Glu187Ter	p.E187*	ENST00000399503	NM_005921.1	187	Gag/Tag	2/20	0.179368939808927	3	FACETS	0.903	0.793	1	0.451	0.396	0.511	CLONAL	1	TRUE	1	0.22	3		371	894	SUCCESS
ATM	472	MSKCC	GRCh37	11	108225552	108225552	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001394-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	62	333	0	ENST00000278616.4:c.8801C>A	p.Thr2934Asn	p.T2934N	ENST00000278616	NM_000051.3	2934	aCc/aAc	61/63	1	2	FACETS	0.7	0.603	0.806	0.7	0.603	0.806	SUBCLONAL	1	TRUE	1	0.22	2		333	805	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028660	12028660	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1334746981	NA	P-0001394-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	88	421	0	ENST00000353533.5:c.863C>G	p.Ser288Cys	p.S288C	ENST00000353533	NM_003010.3	288	tCt/tGt	8/11	1	2	FACETS	0.948	0.839	1	0.948	0.839	1	CLONAL	1	TRUE	1	0.22	2		421	844	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245021	41245021	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs80357435	NA	P-0001394-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	56	404	0	ENST00000357654.3:c.2527A>G	p.Thr843Ala	p.T843A	ENST00000357654	NM_007294.3	843	Aca/Gca	10/23	0.3	1	FACETS	0.716	0.613	0.829	0.716	0.613	0.829	SUBCLONAL	1	TRUE	0	0.22	1		404	633	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117627	70117628	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0001394-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	81	302	1	ENST00000245479.2:c.96dup	p.Ser33LeufsTer219	p.S33Lfs*219	ENST00000245479	NM_000346.3	32	ggc/ggCc	1/3	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.22	2		303	564	SUCCESS
APC	324	MSKCC	GRCh37	5	112176186	112176187	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TACACCG	novel	NA	P-0001394-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	80	369	0	ENST00000257430.4:c.4896_4902dup	p.Gly1635TyrfsTer5	p.G1635Yfs*5	ENST00000257430	NM_000038.5	1632	ttt/ttTACACCGt	16/16	0.179368939808927	3	FACETS	1	0.931	1	0.543	0.478	0.614	CLONAL	1	TRUE	1	0.22	3		369	743	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436570	49436571	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0001430-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	115	314	0	ENST00000301067.7:c.5735_5736insA	p.Gly1913TrpfsTer44	p.G1913Wfs*44	ENST00000301067	NM_003482.3	1912	cct/ccAt	26/54	0.470428249388779	5	FACETS	1	0.939	1	0.353	0.317	0.39	CLONAL	1	TRUE	2	0.470428249388779	5		314	788	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953632	32953633	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359732	NA	P-0001449-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	24	163	0	ENST00000380152.3:c.8940dup	p.Glu2981ArgfsTer37	p.E2981Rfs*37	ENST00000380152		2978	tca/tcAa	22/27	0.144621177182325	0	FACETS	0.187	0.147	0.232			1	INDETERMINATE	1	TRUE	0	0.553637096483604	0		163	207	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751237	57751237	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001449-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	41	245	0	ENST00000274289.3:c.1630G>C	p.Val544Leu	p.V544L	ENST00000274289	NM_006622.3	544	Gtt/Ctt	12/14	0.300331171154124	3	FACETS	0.489	0.408	0.578	0.244	0.204	0.289	INDETERMINATE	1	TRUE	1	0.553637096483604	3		245	387	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	443454	443454	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001449-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	50	261	0	ENST00000399788.2:c.1443C>A	p.Cys481Ter	p.C481*	ENST00000399788	NM_001042603.1	481	tgC/tgA	11/28	NA	2	FACETS	0.475	0.404	0.553			1	INDETERMINATE	1	TRUE	NA	0.553637096483604	2		261	380	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175996825	175996825	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0001467-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	122	307	0	ENST00000367669.3:c.1613-1G>T		p.X538_splice	ENST00000367669	NM_022457.5	538			0.16581707796358	3	FACETS	0.777	0.703	0.855	0.259	0.234	0.285	INDETERMINATE	1	TRUE	0	0.569647022697564	3		307	708	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422472	225422472	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001467-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	541	491	1	ENST00000264414.4:c.168G>C	p.Glu56Asp	p.E56D	ENST00000264414	NM_003590.4	56	gaG/gaC	2/16	0.569647022697564	2	FACETS	0.931	0.898	0.964	0.931	0.898	0.964	CLONAL	2	TRUE	0	0.569647022697564	2		492	1020	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55987337	55987337	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1195910028	NA	P-0001467-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	223	252	0	ENST00000263923.4:c.88G>T	p.Asp30Tyr	p.D30Y	ENST00000263923	NM_002253.2	30	Gat/Tat	2/30	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.569647022697564	2		252	590	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953162	38953162	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs200255149	NA	P-0001467-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	193	219	0	ENST00000357387.3:c.2822A>G	p.Asn941Ser	p.N941S	ENST00000357387	NM_152756.3	941	aAt/aGt	29/38	0.569647022697564	4	FACETS	1	0.932	1	0.336	0.31	0.363	CLONAL	1	TRUE	1	0.569647022697564	4		219	1055	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169961	32169961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1321236504	NA	P-0001467-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	468	472	0	ENST00000375023.3:c.3647C>T	p.Ser1216Phe	p.S1216F	ENST00000375023	NM_004557.3	1216	tCc/tTc	21/30	0.569647022697564	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.569647022697564	3		472	972	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609949	43609949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs75996173	NA	P-0001467-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	508	441	1	ENST00000355710.3:c.1901G>A	p.Cys634Tyr	p.C634Y	ENST00000355710	NM_020975.4	634	tGc/tAc	11/20	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.569647022697564	2		442	814	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033828	49033828	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0001467-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	876	479	4	ENST00000267163.4:c.1965T>A	p.Tyr655Ter	p.Y655*	ENST00000267163	NM_000321.2	655	taT/taA	20/27	0.512622615106953	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.569647022697564	3		483	1253	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574000	7574000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001467-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	248	495	2	ENST00000269305.4:c.1027G>T	p.Glu343Ter	p.E343*	ENST00000269305	NM_001126112.2	343	Gag/Tag	10/11	1	2	FACETS	0.953	0.892	1	0.953	0.892	1	CLONAL	1	TRUE	1	0.569647022697564	2		497	914	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736889	736889	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001467-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	649	643	4	ENST00000314574.4:c.1210G>T	p.Val404Leu	p.V404L	ENST00000314574	NM_005433.3	404	Gta/Tta	10/12	0.307957057045683	4	FACETS	0.974	0.938	1	0.974	0.938	1	INDETERMINATE	2	TRUE	2	0.569647022697564	4		647	1836	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292450	15292450	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001467-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	323	324	0	ENST00000263388.2:c.2729G>C	p.Cys910Ser	p.C910S	ENST00000263388	NM_000435.2	910	tGc/tCc	17/33	0.444211196719869	3	FACETS	1	0.974	1			1	CLONAL	2	TRUE	NA	0.569647022697564	3		324	703	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230892	53230892	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001467-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	143	382	0	ENST00000375401.3:c.1901G>T	p.Arg634Leu	p.R634L	ENST00000375401	NM_004187.3	634	cGc/cTc	14/26	0.278386486390762	2	FACETS	0.784	0.717	0.854	0.392	0.358	0.427	INDETERMINATE	1	TRUE	0	0.569647022697564	2		382	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578470	7578471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0001467-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	196	245	2	ENST00000269305.4:c.459dup	p.Gly154ArgfsTer27	p.G154Rfs*27	ENST00000269305	NM_001126112.2	153	-/C	5/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.569647022697564	2		247	527	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552592	18552606	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GACTCTCTGAAGAAA	GACTCTCTGAAGAAA	CAAAG	novel	NA	P-0001467-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	442	71	0	ENST00000266497.5:c.2004-1_2017delinsCAAAG		p.X668_splice	ENST00000266497		668		14/31	0.191167960434911	3	FACETS	1	0.995	1			1	INDETERMINATE	1	TRUE	NA	0.569647022697564	3		71	1487	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088787	27088788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0001484-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	62	277	0	ENST00000324856.7:c.2402dup	p.Gln802SerfsTer15	p.Q802Sfs*15	ENST00000324856	NM_006015.4	799	cag/caGg	7/20	1	2	FACETS	0.653	0.562	0.751	0.653	0.562	0.751	SUBCLONAL	1	TRUE	1	0.225619359614647	2		277	842	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0001484-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	130	480	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.225619359614647	2		480	1085	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164065	108164066	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GATA	novel	NA	P-0001484-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	50	290	0	ENST00000278616.4:c.4642_4645dup	p.Asn1549ArgfsTer2	p.N1549Rfs*2	ENST00000278616	NM_000051.3	1546	gtg/gtGATAg	31/63	1	2	FACETS	0.589	0.498	0.689	0.589	0.498	0.689	SUBCLONAL	1	TRUE	1	0.225619359614647	2		290	753	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710595	114710597	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs754968616	NA	P-0001484-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	92	872	0	ENST00000543371.1:c.85_87del	p.Glu29del	p.E29del	ENST00000543371	NM_001198531.1	27	cAGGag/cag	1/14	1	2	FACETS	0.61	0.54	0.685	0.61	0.54	0.685	SUBCLONAL	1	TRUE	1	0.225619359614647	2		872	1337	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134248	2134250	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs878854100	NA	P-0001484-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	50	384	0	ENST00000219476.3:c.4030_4032del	p.Glu1344del	p.E1344del	ENST00000219476	NM_000548.3	1342	cAGGag/cag	34/42	1	2	FACETS	0.543	0.459	0.636	0.543	0.459	0.636	SUBCLONAL	1	TRUE	1	0.225619359614647	2		384	816	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631656	90631682	+	protein_altering_variant	In_Frame_Del	DEL	TGACACCACTGCCATCTTTTGGGGTGA	TGACACCACTGCCATCTTTTGGGGTGA	GTG	novel	NA	P-0001484-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	103	414	0	ENST00000330062.3:c.587_613delinsCAC	p.Phe196_Lys205delinsSerGln	p.F196_K205delinsSQ	ENST00000330062	NM_002168.2	196	tTCACCCCAAAAGATGGCAGTGGTGTCAag/tCACag	5/11	0.225619359614647	3	FACETS	1	0.928	1			1	CLONAL	1	TRUE	NA	0.225619359614647	3		414	968	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	151	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.942	0.864	1	0.942	0.864	1	CLONAL	1	TRUE	1	0.48699416232746	2		311	658	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	133	226	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	1	2	FACETS	0.937	0.854	1	0.937	0.854	1	CLONAL	1	TRUE	1	0.48699416232746	2		226	583	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	162	476	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.654	0.599	0.711	0.654	0.599	0.711	SUBCLONAL	1	TRUE	1	0.48699416232746	2		476	1018	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671655	67671655	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1400980130	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	140	228	0	ENST00000264010.4:c.2070del	p.Glu691SerfsTer30	p.E691Sfs*30	ENST00000264010	NM_006565.3	688	gtA/gt	12/12	1	2	FACETS	0.983	0.899	1	0.983	0.899	1	CLONAL	1	TRUE	1	0.48699416232746	2		228	585	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	54	196	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.478	0.409	0.554	0.478	0.409	0.554	SUBCLONAL	1	TRUE	1	0.48699416232746	2		196	464	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370945	55370945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	173	268	0	ENST00000297316.4:c.247C>T	p.Arg83Cys	p.R83C	ENST00000297316	NM_022454.3	83	Cgc/Tgc	1/2	0.369638661115288	3	FACETS	1	0.985	1	0.638	0.589	0.689	CLONAL	1	TRUE	1	0.48699416232746	3		268	692	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045918	180045920	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CTC	CTC	-	rs746341092	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	59	190	0	ENST00000261937.6:c.2851_2853del	p.Glu951del	p.E951del	ENST00000261937	NM_182925.4	951	GAG/-	21/30	1	2	FACETS	0.797	0.691	0.911	0.797	0.691	0.911	CLONAL	1	TRUE	1	0.48699416232746	2		190	304	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	84	148	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	0.876	0.778	0.979	0.876	0.778	0.979	CLONAL	1	TRUE	1	0.48699416232746	2		148	394	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238958	5238958	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	130	334	0	ENST00000357368.4:c.1821del	p.Val608TrpfsTer30	p.V608Wfs*30	ENST00000357368	NM_002850.3	607	ccC/cc	13/38	1	2	FACETS	0.996	0.908	1	0.996	0.908	1	CLONAL	1	TRUE	1	0.48699416232746	2		334	536	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491337	2491337	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	194	340	0	ENST00000355716.4:c.380G>A	p.Cys127Tyr	p.C127Y	ENST00000355716	NM_003820.2	127	tGc/tAc	4/8	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.48699416232746	2		340	750	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726436	46726436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139448277	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	89	160	0	ENST00000371975.4:c.515G>A	p.Arg172His	p.R172H	ENST00000371975	NM_003579.3	172	cGc/cAc	7/18	1	2	FACETS	0.856	0.763	0.954	0.856	0.763	0.954	CLONAL	1	TRUE	1	0.48699416232746	2		160	427	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652792	212652792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375307182	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	98	391	1	ENST00000342788.4:c.514C>T	p.Pro172Ser	p.P172S	ENST00000342788	NM_005235.2	172	Cct/Tct	4/28	1	2	FACETS	0.786	0.704	0.873	0.786	0.704	0.873	SUBCLONAL	1	TRUE	1	0.48699416232746	2		392	512	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794881	242794881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs190602950	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	135	344	1	ENST00000334409.5:c.328G>A	p.Val110Met	p.V110M	ENST00000334409	NM_005018.2	110	Gtg/Atg	2/5	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.48699416232746	2		345	549	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37038192	37038192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750206	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	258	257	0	ENST00000231790.2:c.199G>A	p.Gly67Arg	p.G67R	ENST00000231790	NM_000249.3	67	Ggg/Agg	2/19	0.48699416232746	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.48699416232746	2		257	527	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71019919	71019919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760742879	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	181	236	1	ENST00000318789.4:c.1690G>A	p.Ala564Thr	p.A564T	ENST00000318789	NM_032682.5	564	Gcc/Acc	19/21	0.48699416232746	2	FACETS	0.982	0.908	1	0.491	0.454	0.53	CLONAL	1	TRUE	0	0.48699416232746	2		237	757	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057042	180057042	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	121	207	0	ENST00000261937.6:c.577G>A	p.Val193Met	p.V193M	ENST00000261937	NM_182925.4	193	Gtg/Atg	5/30	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.48699416232746	2		207	424	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935634	13935634	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	81	197	0	ENST00000405192.2:c.1222C>T	p.Arg408Cys	p.R408C	ENST00000405192	NM_001163147.1	408	Cgt/Tgt	12/12	1	2	FACETS	0.502	0.443	0.567	0.502	0.443	0.567	SUBCLONAL	1	TRUE	1	0.48699416232746	2		197	662	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399155	139399155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749490844	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	138	315	0	ENST00000277541.6:c.4988G>A	p.Arg1663Gln	p.R1663Q	ENST00000277541	NM_017617.3	1663	cGg/cAg	26/34	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.48699416232746	2		315	524	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410121	139410121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781682670	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	113	234	1	ENST00000277541.6:c.1717G>A	p.Asp573Asn	p.D573N	ENST00000277541	NM_017617.3	573	Gac/Aac	11/34	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.48699416232746	2		235	405	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850736	63850736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149466999	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	143	292	2	ENST00000279873.7:c.1514C>T	p.Ala505Val	p.A505V	ENST00000279873	NM_032199.2	505	gCg/gTg	10/10	1	2	FACETS	0.92	0.842	1	0.92	0.842	1	CLONAL	1	TRUE	1	0.48699416232746	2		294	638	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852248	63852248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145564601	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	114	198	1	ENST00000279873.7:c.3026C>T	p.Ala1009Val	p.A1009V	ENST00000279873	NM_032199.2	1009	gCg/gTg	10/10	1	2	FACETS	0.885	0.8	0.974	0.885	0.8	0.974	CLONAL	1	TRUE	1	0.48699416232746	2		199	529	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653835	89653835	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1382752324	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	105	302	0	ENST00000371953.3:c.133G>A	p.Val45Ile	p.V45I	ENST00000371953	NM_000314.4	45	Gta/Ata	2/9	1	2	FACETS	0.942	0.848	1	0.942	0.848	1	CLONAL	1	TRUE	1	0.48699416232746	2		302	458	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155024	108155024	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876660767	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	113	322	0	ENST00000278616.4:c.3817A>G	p.Asn1273Asp	p.N1273D	ENST00000278616	NM_000051.3	1273	Aat/Gat	26/63	1	2	FACETS	0.903	0.816	0.994	0.903	0.816	0.994	CLONAL	1	TRUE	1	0.48699416232746	2		322	514	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244968	133244968	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567031389	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	227	406	2	ENST00000320574.5:c.2147C>T	p.Ala716Val	p.A716V	ENST00000320574	NM_006231.2	716	gCg/gTg	19/49	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.48699416232746	2		408	890	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955538	48955538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913303	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	102	280	0	ENST00000267163.4:c.1654C>T	p.Arg552Ter	p.R552*	ENST00000267163	NM_000321.2	552	Cga/Tga	17/27	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.48699416232746	2		280	411	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250904	99250904	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1567086828	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	204	391	0	ENST00000268035.6:c.208T>C	p.Tyr70His	p.Y70H	ENST00000268035	NM_000875.3	70	Tac/Cac	2/21	1	2	FACETS	0.99	0.92	1	0.99	0.92	1	CLONAL	1	TRUE	1	0.48699416232746	2		391	846	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106749	2106749	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	83	389	0	ENST00000219476.3:c.753G>T	p.Glu251Asp	p.E251D	ENST00000219476	NM_000548.3	251	gaG/gaT	8/42	1	2	FACETS	0.464	0.409	0.523	0.464	0.409	0.523	SUBCLONAL	1	TRUE	1	0.48699416232746	2		389	734	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556292	29556292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1251621684	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	228	339	0	ENST00000356175.3:c.2659G>A	p.Ala887Thr	p.A887T	ENST00000356175	NM_000267.3	887	Gca/Aca	21/57	1	2	FACETS	0.964	0.899	1	0.964	0.899	1	CLONAL	1	TRUE	1	0.48699416232746	2		339	971	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440943	56440943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786205215	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	346	219	2	ENST00000407977.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000407977		132	Cga/Tga	4/10	0.48699416232746	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.48699416232746	2		221	639	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117869	70117869	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	147	253	0	ENST00000245479.2:c.337A>G	p.Met113Val	p.M113V	ENST00000245479	NM_000346.3	113	Atg/Gtg	1/3	0.48699416232746	2	FACETS	1	0.955	1	0.53	0.486	0.576	CLONAL	1	TRUE	0	0.48699416232746	2		253	569	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118913	70118913	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774639088	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	252	419	0	ENST00000245479.2:c.485G>A	p.Arg162His	p.R162H	ENST00000245479	NM_000346.3	162	cGc/cAc	2/3	0.48699416232746	2	FACETS	1	0.981	1	0.559	0.523	0.595	CLONAL	1	TRUE	0	0.48699416232746	2		419	926	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4090603	4090603	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs912154933	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	62	340	0	ENST00000262948.5:c.1196C>T	p.Ala399Val	p.A399V	ENST00000262948	NM_030662.3	399	gCc/gTc	11/11	1	2	FACETS	0.427	0.369	0.491	0.427	0.369	0.491	SUBCLONAL	1	TRUE	1	0.48699416232746	2		340	596	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281289	15281289	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	76	138	0	ENST00000263388.2:c.4967T>C	p.Val1656Ala	p.V1656A	ENST00000263388	NM_000435.2	1656	gTc/gCc	27/33	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.48699416232746	2		138	282	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950393	17950393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777849274	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	181	266	0	ENST00000458235.1:c.1334G>A	p.Arg445Gln	p.R445Q	ENST00000458235	NM_000215.3	445	cGa/cAa	10/24	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.48699416232746	2		266	737	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716217	52716217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1173183954	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	153	267	0	ENST00000322088.6:c.661C>T	p.Arg221Trp	p.R221W	ENST00000322088	NM_014225.5	221	Cgg/Tgg	6/15	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.48699416232746	2		267	607	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306676	41306676	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754008236	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	91	258	1	ENST00000373198.4:c.983G>A	p.Arg328His	p.R328H	ENST00000373198	NM_133170.3	328	cGc/cAc	7/32	1	2	FACETS	0.445	0.395	0.5	0.445	0.395	0.5	SUBCLONAL	1	TRUE	1	0.48699416232746	2		259	839	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514609	44514609	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	158	257	0	ENST00000291552.4:c.547C>T	p.Arg183Trp	p.R183W	ENST00000291552	NM_006758.2	183	Cgg/Tgg	7/8	0.158965589961019	3	FACETS	0.757	0.698	0.818	0.757	0.698	0.818	INDETERMINATE	2	TRUE	1	0.48699416232746	3		257	533	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938562	44938562	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	137	151	0	ENST00000377967.4:c.3110A>G	p.Gln1037Arg	p.Q1037R	ENST00000377967	NM_021140.2	1037	cAg/cGg	20/29	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.48699416232746	1		151	319	SUCCESS
AR	367	MSKCC	GRCh37	X	66766276	66766276	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755088348	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	110	111	0	ENST00000374690.3:c.1288G>A	p.Ala430Thr	p.A430T	ENST00000374690	NM_000044.3	430	Gcc/Acc	1/8	1	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.48699416232746	1		111	296	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641440	47641441	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	202	457	1	ENST00000233146.2:c.830dup	p.Leu277PhefsTer7	p.L277Ffs*7	ENST00000233146	NM_000251.2	275	-/T	5/16	1	2	FACETS	0.942	0.874	1	0.942	0.874	1	CLONAL	1	TRUE	1	0.48699416232746	2		458	881	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266476	198266477	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1394586762	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	132	268	0	ENST00000335508.6:c.2359dup	p.Ile787AsnfsTer21	p.I787Nfs*21	ENST00000335508	NM_012433.2	787	att/aAtt	16/25	1	2	FACETS	0.97	0.884	1	0.97	0.884	1	CLONAL	1	TRUE	1	0.48699416232746	2		268	559	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443613	52443613	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	144	209	0	ENST00000460680.1:c.79del	p.Val27CysfsTer45	p.V27Cfs*45	ENST00000460680	NM_004656.3	27	Gtg/tg	3/17	0.48699416232746	2	FACETS	0.911	0.834	0.992	0.456	0.417	0.496	CLONAL	1	TRUE	0	0.48699416232746	2		209	649	SUCCESS
FIP1L1	81608	MSKCC	GRCh37	4	54257658	54257658	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	97	269	0	ENST00000358575.5:c.657del	p.Phe219LeufsTer74	p.F219Lfs*74	ENST00000358575	NM_001134937.1	218	cTt/ct	8/18	1	2	FACETS	0.887	0.795	0.984	0.887	0.795	0.984	CLONAL	1	TRUE	1	0.48699416232746	2		269	449	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467646	66467646	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	143	213	0	ENST00000273854.3:c.623del	p.Lys208ArgfsTer60	p.K208Rfs*60	ENST00000273854	NM_004439.5	208	aAg/ag	3/18	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.48699416232746	2		213	549	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158100	106158100	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	75	233	0	ENST00000380013.4:c.3004del	p.Thr1002HisfsTer5	p.T1002Hfs*5	ENST00000380013	NM_001127208.2	1001	Aaa/aa	3/11	1	2	FACETS	0.474	0.415	0.537	0.474	0.415	0.537	SUBCLONAL	1	TRUE	1	0.48699416232746	2		233	650	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129329	152129329	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	180	380	0	ENST00000206249.3:c.287del	p.Gly96ValfsTer13	p.G96Vfs*13	ENST00000206249	NM_000125.3	94	ctG/ct	1/8	0.158965589961019	3	FACETS	1	0.972	1	0.554	0.512	0.599	INDETERMINATE	1	TRUE	1	0.48699416232746	3		380	829	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968322	2968323	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs762770988	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	98	229	0	ENST00000396946.4:c.1663dup	p.Arg555ProfsTer38	p.R555Pfs*38	ENST00000396946	NM_032415.4	555	cgg/cCgg	13/25	1	2	FACETS	0.768	0.688	0.853	0.768	0.688	0.853	SUBCLONAL	1	TRUE	1	0.48699416232746	2		229	524	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123245002	123245002	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	80	333	0	ENST00000358487.5:c.2102del	p.Gly701AlafsTer16	p.G701Afs*16	ENST00000358487	NM_000141.4	701	gGc/gc	16/18	1	2	FACETS	0.442	0.389	0.5	0.442	0.389	0.5	SUBCLONAL	1	TRUE	1	0.48699416232746	2		333	743	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878069	48878069	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	58	123	0	ENST00000267163.4:c.25del	p.Thr9ArgfsTer56	p.T9Rfs*56	ENST00000267163	NM_000321.2	7	cgA/cg	1/27	1	2	FACETS	0.628	0.542	0.722	0.628	0.542	0.722	SUBCLONAL	1	TRUE	1	0.48699416232746	2		123	379	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346884	73346884	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	94	301	0	ENST00000377767.4:c.1333del	p.Ser445HisfsTer20	p.S445Hfs*20	ENST00000377767	NM_014953.3	445	Tca/ca	9/21	1	2	FACETS	0.648	0.577	0.723	0.648	0.577	0.723	SUBCLONAL	1	TRUE	1	0.48699416232746	2		301	596	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435908	110435908	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	43	77	0	ENST00000375856.3:c.2493del	p.Arg832AlafsTer34	p.R832Afs*34	ENST00000375856	NM_003749.2	831	ggG/gg	1/2	1	2	FACETS	0.965	0.819	1	0.965	0.819	1	CLONAL	1	TRUE	1	0.48699416232746	2		77	183	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14026115	14026116	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs769120755	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	130	194	0	ENST00000311895.7:c.1081dup	p.Met361AsnfsTer4	p.M361Nfs*4	ENST00000311895	NM_005236.2	359	gaa/gAaa	6/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.48699416232746	2		194	517	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924284	11924285	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	23	19	0	ENST00000353533.5:c.81_82del	p.Pro29ArgfsTer11	p.P29Rfs*11	ENST00000353533	NM_003010.3	27	ccGGcg/cccg	1/11	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.48699416232746	2		19	64	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438206	56438207	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	359	331	0	ENST00000407977.2:c.786_787del	p.Gly263GlufsTer18	p.G263Efs*18	ENST00000407977		262	tcAGgg/tcgg	7/10	0.48699416232746	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.48699416232746	2		331	709	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533905	63533905	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	305	187	0	ENST00000307078.5:c.1249del	p.Ala417ArgfsTer41	p.A417Rfs*41	ENST00000307078	NM_004655.3	417	Gcg/cg	6/11	0.48699416232746	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.48699416232746	2		187	554	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273105	18273105	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	72	330	0	ENST00000222254.8:c.1000del	p.Asp334ThrfsTer7	p.D334Tfs*7	ENST00000222254	NM_005027.3	332	tGg/tg	8/16	1	2	FACETS	0.439	0.383	0.5	0.439	0.383	0.5	SUBCLONAL	1	TRUE	1	0.48699416232746	2		330	673	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221709	22221714	+	inframe_deletion	In_Frame_Del	DEL	CCGCCG	CCGCCG	-	rs751880548	NA	P-0001494-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	11	65	0	ENST00000215832.6:c.17_22del	p.Ala6_Ala7del	p.A6_A7del	ENST00000215832	NM_002745.4	6	gCGGCGGgc/ggc	1/9	1	2	FACETS	0.299	0.207	0.413	0.299	0.207	0.413	SUBCLONAL	1	TRUE	1	0.48699416232746	2		65	151	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0001500-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	109	454	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.461349595944182	2	FACETS	0.592	0.532	0.655	0.296	0.266	0.328	SUBCLONAL	1	FALSE	0	0.579279420765005	2		454	636	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0001500-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	331	402	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.457623076970206	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	FALSE	0	0.579279420765005	2		402	502	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0001500-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	303	528	3	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	0.457623076970206	2	FACETS	0.773	0.727	0.82	0.386	0.363	0.41	SUBCLONAL	1	FALSE	0	0.579279420765005	2		531	1354	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29120965	29120965	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs1555926708	NA	P-0001500-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	229	267	0	ENST00000328354.6:c.592G>C	p.Val198Leu	p.V198L	ENST00000328354	NM_007194.3	198	Gtt/Ctt	4/15	0.305139673667445	2	FACETS	0.859	0.812	0.907	0.859	0.812	0.907	INDETERMINATE	2	FALSE	0	0.579279420765005	2		267	460	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0001500-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	140	249	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	0.511660747236222	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	0	0.579279420765005	1		249	262	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578464	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001500-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	501	534	0	ENST00000269305.4:c.466del	p.Arg156AlafsTer14	p.R156Afs*14	ENST00000269305	NM_001126112.2	156	Cgc/gc	5/11	0.579279420765005	1	FACETS	1	0.996	1	1	0.998	1	CLONAL	2	FALSE	0	0.579279420765005	1		534	572	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737142	145737142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61755067	NA	P-0001500-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	445	667	0	ENST00000428558.2:c.3424G>A	p.Asp1142Asn	p.D1142N	ENST00000428558	NM_004260.3	1142	Gac/Aac	21/22	0.484368147628417	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	FALSE	2	0.579279420765005	4		667	1138	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89881001	89881001	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001500-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	297	455	0	ENST00000389301.3:c.210A>T	p.Lys70Asn	p.K70N	ENST00000389301	NM_000135.2	70	aaA/aaT	3/43	0.300550401458646	3	FACETS	1	0.993	1	0.464	0.437	0.491	INDETERMINATE	1	FALSE	0	0.579279420765005	3		455	951	SUCCESS
APC	324	MSKCC	GRCh37	5	112175749	112175761	+	frameshift_variant	Frame_Shift_Del	DEL	TACTTTATTACAT	TACTTTATTACAT	-	novel	NA	P-0001500-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	181	254	0	ENST00000257430.4:c.4459_4471del	p.Thr1487LeufsTer16	p.T1487Lfs*16	ENST00000257430	NM_000038.5	1486	gaTACTTTATTACAT/ga	16/16	0.461349595944182	2	FACETS	0.979	0.922	1	0.979	0.922	1	CLONAL	2	FALSE	0	0.579279420765005	2		254	319	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988224	36988247	+	inframe_deletion	In_Frame_Del	DEL	CCATCCGGGGCCAGAGGCGCTGTT	CCATCCGGGGCCAGAGGCGCTGTT	-	novel	NA	P-0001500-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	90	375	0	ENST00000354822.5:c.406_429del	p.Asn136_Trp143del	p.N136_W143del	ENST00000354822	NM_001079668.2	136	AACAGCGCCTCTGGCCCCGGATGG/-	2/3	0.511660747236222	1	FACETS	0.876	0.79	0.965	0.876	0.79	0.965	CLONAL	1	FALSE	0	0.579279420765005	1		375	252	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122378	17122379	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0001500-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	535	708	0	ENST00000285071.4:c.1016dup	p.Pro340AlafsTer50	p.P340Afs*50	ENST00000285071	NM_144997.5	339	cag/caAg	9/14	0.579279420765005	1	FACETS	1	0.994	1	1	0.998	1	CLONAL	2	FALSE	0	0.579279420765005	1		708	627	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528707	8528707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs545049137	NA	P-0001500-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	137	502	0	ENST00000356435.5:c.425C>T	p.Thr142Met	p.T142M	ENST00000356435		142	aCg/aTg	4/35	0.579279420765005	1	FACETS	0.684	0.626	0.744	0.684	0.626	0.744	SUBCLONAL	1	FALSE	0	0.579279420765005	1		502	491	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47168147	47168147	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001500-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	92	246	0	ENST00000409792.3:c.78A>C	p.Glu26Asp	p.E26D	ENST00000409792	NM_014159.6	26	gaA/gaC	2/21	NA	2	FACETS	1	0.911	1			1	INDETERMINATE	1	FALSE	NA	0.579279420765005	2		246	313	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576455	67576455	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001500-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	103	280	0	ENST00000274335.5:c.734A>C	p.Lys245Thr	p.K245T	ENST00000274335		245	aAa/aCa	5/15	0.461349595944182	2	FACETS	0.659	0.591	0.73	0.329	0.295	0.365	SUBCLONAL	1	FALSE	0	0.579279420765005	2		280	540	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449802	8449802	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs750416132	NA	P-0001500-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	134	379	0	ENST00000356435.5:c.3911T>C	p.Ile1304Thr	p.I1304T	ENST00000356435		1304	aTa/aCa	23/35	0.579279420765005	1	FACETS	0.685	0.626	0.745	0.685	0.626	0.745	SUBCLONAL	1	FALSE	0	0.579279420765005	1		379	480	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641180	93641180	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001500-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	113	385	0	ENST00000375746.1:c.1526A>G	p.Lys509Arg	p.K509R	ENST00000375746	NM_001174167.1	509	aAg/aGg	11/14	1	2	FACETS	0.613	0.553	0.677	0.613	0.553	0.677	SUBCLONAL	1	FALSE	1	0.579279420765005	2		385	636	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851674	63851674	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001500-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	101	393	0	ENST00000279873.7:c.2452G>T	p.Ala818Ser	p.A818S	ENST00000279873	NM_032199.2	818	Gcc/Tcc	10/10	0.430800504947233	3	FACETS	0.583	0.521	0.649	0.292	0.26	0.325	SUBCLONAL	1	FALSE	1	0.579279420765005	3		393	771	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404963	70404963	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001500-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	88	356	0	ENST00000373644.4:c.2477A>G	p.Gln826Arg	p.Q826R	ENST00000373644	NM_030625.2	826	cAg/cGg	4/12	0.430800504947233	3	FACETS	0.662	0.587	0.741	0.331	0.293	0.371	SUBCLONAL	1	FALSE	1	0.579279420765005	3		356	592	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031648	36031648	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001500-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1767	227	982	1	ENST00000358208.4:c.1477T>A	p.Ser493Thr	p.S493T	ENST00000358208		493	Tcc/Acc	12/12	0.579279420765005	4	FACETS	0.621	0.576	0.668	0.31	0.288	0.334	SUBCLONAL	1	FALSE	2	0.579279420765005	4		983	1994	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651679	206651679	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001622-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	684	393	0	ENST00000367120.3:c.989A>G	p.Asn330Ser	p.N330S	ENST00000367120	NM_014002.3	330	aAc/aGc	9/22	0.773877220393922	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.799929520775629	3		393	796	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612124	189612124	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001622-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3903	933	608	1	ENST00000264731.3:c.1876G>T	p.Val626Phe	p.V626F	ENST00000264731	NM_003722.4	626	Gtc/Ttc	14/14	0.799929520775629	10	FACETS	1	0.975	1			1	CLONAL	2	TRUE	NA	0.799929520775629	10		609	4836	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172139	32172139	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001622-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	40	498	0	ENST00000375023.3:c.2893T>A	p.Cys965Ser	p.C965S	ENST00000375023	NM_004557.3	965	Tgc/Agc	19/30	0.799929520775629	2	FACETS	0.131	0.108	0.157	0.066	0.054	0.079	SUBCLONAL	1	TRUE	0	0.799929520775629	2		498	761	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325164	123325164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001622-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1252	161	502	0	ENST00000358487.5:c.164G>A	p.Gly55Glu	p.G55E	ENST00000358487	NM_000141.4	55	gGg/gAg	3/18	0.796663479833568	4	FACETS	0.513	0.469	0.559	0.128	0.117	0.14	SUBCLONAL	1	TRUE	0	0.799929520775629	4		502	1413	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001978	29001978	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001622-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	204	520	0	ENST00000282397.4:c.1187C>G	p.Thr396Ser	p.T396S	ENST00000282397	NM_002019.4	396	aCt/aGt	9/30	0.796636642862214	2	FACETS	0.57	0.529	0.612	0.285	0.264	0.306	SUBCLONAL	1	TRUE	0	0.799929520775629	2		520	895	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0001622-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	1218	441	1	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	0.796663479833568	4	FACETS	0.99	0.978	1	0.99	0.978	1	CLONAL	4	TRUE	0	0.799929520775629	4		442	1384	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528073	29528073	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001622-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	109	197	0	ENST00000356175.3:c.1081A>T	p.Ser361Cys	p.S361C	ENST00000356175	NM_000267.3	361	Agt/Tgt	10/57	0.796663479833568	4	FACETS	0.729	0.655	0.807	0.182	0.163	0.202	SUBCLONAL	1	TRUE	0	0.799929520775629	4		197	673	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610359	10610359	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001622-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	706	558	0	ENST00000171111.5:c.351G>T	p.Glu117Asp	p.E117D	ENST00000171111	NM_203500.1	117	gaG/gaT	2/6	0.568849396737507	3	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.799929520775629	3		558	1192	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650778	48650778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104894809	NA	P-0001622-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	798	344	1	ENST00000376670.3:c.647G>A	p.Arg216Gln	p.R216Q	ENST00000376670	NM_002049.3	216	cGg/cAg	4/6	0.758163010132993	2	FACETS	1	0.998	1			1	CLONAL	2	TRUE	NA	0.799929520775629	2		345	892	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440430	49440431	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0001622-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	516	455	0	ENST00000301067.7:c.4379dup	p.Leu1461ThrfsTer30	p.L1461Tfs*30	ENST00000301067	NM_003482.3	1460	cca/ccCa	15/54	0.551068841226543	4	FACETS	1	0.993	1	0.747	0.719	0.775	CLONAL	2	TRUE	1	0.799929520775629	4		455	1036	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518477	69518478	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0001622-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	247	303	0	ENST00000294312.3:c.167_168delinsAA	p.Ser56Ter	p.S56*	ENST00000294312	NM_005117.2	56	tCC/tAA	1/3	0.394141035131592	3	FACETS	0.889	0.842	0.937			1	INDETERMINATE	2	TRUE	NA	0.799929520775629	3		303	486	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147551	47147551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001656-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	325	382	0	ENST00000409792.3:c.4775G>A	p.Arg1592Gln	p.R1592Q	ENST00000409792	NM_014159.6	1592	cGa/cAa	6/21	0.618044600030656	1	FACETS	0.959	0.911	1	0.959	0.911	1	CLONAL	1	TRUE	0	0.618044600030656	1		382	758	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668736	52668736	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001656-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	396	497	0	ENST00000394830.3:c.1183A>C	p.Ser395Arg	p.S395R	ENST00000394830	NM_018313.4	395	Agt/Cgt	12/30	0.618044600030656	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.618044600030656	1		497	834	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519741	176519741	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001656-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	611	365	0	ENST00000292408.4:c.1013C>T	p.Ser338Phe	p.S338F	ENST00000292408	NM_213647.1	338	tCc/tTc	8/18	0.618044600030656	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.618044600030656	3		365	1294	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064335	30064336	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0001656-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	245	445	0	ENST00000338641.4:c.901_902dup	p.Gly302SerfsTer8	p.G302Sfs*8	ENST00000338641	NM_000268.3	300	tgt/tgTAt	10/16	0.618044600030656	1	FACETS	0.834	0.784	0.884	0.834	0.784	0.884	CLONAL	1	TRUE	0	0.618044600030656	1		445	657	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0001679-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	110	413	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.696836586230511	2		413	311	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594221	55594221	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913512	NA	P-0001679-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	1026	539	0	ENST00000288135.5:c.1924A>G	p.Lys642Glu	p.K642E	ENST00000288135	NM_000222.2	642	Aaa/Gaa	13/21	0.599166030568727	6	FACETS	1	0.991	1			1	CLONAL	5	TRUE	NA	0.696836586230511	6		539	1385	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940572	131940572	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001679-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	212	571	0	ENST00000265335.6:c.2599A>T	p.Thr867Ser	p.T867S	ENST00000265335		867	Aca/Tca	16/25	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.696836586230511	2		571	593	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41554452	41554452	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001679-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	216	593	0	ENST00000263253.7:c.3538A>G	p.Lys1180Glu	p.K1180E	ENST00000263253	NM_001429.3	1180	Aaa/Gaa	19/31	0.696836586230511	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.696836586230511	1		593	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578397	7578398	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0001679-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	129	369	0	ENST00000269305.4:c.532dup	p.His178ProfsTer3	p.H178Pfs*3	ENST00000269305	NM_001126112.2	178	cac/cCac	5/11	0.696836586230511	1	FACETS	0.985	0.914	1	0.985	0.914	1	CLONAL	1	TRUE	0	0.696836586230511	1		369	245	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641522	47641522	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001687-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	75	301	0	ENST00000233146.2:c.907G>C	p.Asp303His	p.D303H	ENST00000233146	NM_000251.2	303	Gat/Cat	5/16	0.531265835474123	4	FACETS	0.926	0.814	1	0.463	0.407	0.523	CLONAL	1	TRUE	2	0.532939857041234	4		301	466	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399484	139399484	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001687-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	63	420	0	ENST00000277541.6:c.4659G>C	p.Glu1553Asp	p.E1553D	ENST00000277541	NM_017617.3	1553	gaG/gaC	26/34	0.532939857041234	8	FACETS	0.665	0.573	0.765	0.166	0.143	0.192	SUBCLONAL	1	TRUE	4	0.532939857041234	8		420	924	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945219	32945219	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001687-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	196	363	0	ENST00000380152.3:c.8614G>T	p.Glu2872Ter	p.E2872*	ENST00000380152		2872	Gaa/Taa	20/27	0.478570408331971	4	FACETS	0.984	0.917	1			1	CLONAL	2	TRUE	NA	0.532939857041234	4		363	573	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857739	9857739	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs767067753	NA	P-0001687-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	137	496	0	ENST00000330684.3:c.3662T>C	p.Met1221Thr	p.M1221T	ENST00000330684	NM_001134407.1	1221	aTg/aCg	13/13	0.251018762929464	5	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.532939857041234	5		496	653	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061705	38061706	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0001687-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	93	194	0	ENST00000250448.2:c.283dup	p.Ser95LysfsTer132	p.S95Kfs*132	ENST00000250448	NM_004496.3	95	agc/aAgc	2/2	0.532939857041234	6	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.532939857041234	6		194	511	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218423	1218423	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001687-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	348	420	0	ENST00000326873.7:c.298del	p.Gln100AsnfsTer3	p.Q100Nfs*3	ENST00000326873	NM_000455.4	100	Caa/aa	2/10	0.536516362981355	5	FACETS	0.934	0.888	0.979	0.934	0.888	0.979	CLONAL	3	TRUE	2	0.532939857041234	5		420	839	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0001757-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	457	245	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.461260474394239	2		245	925	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936768	78936768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs987417975	NA	P-0001757-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1314	258	366	1	ENST00000306801.3:c.3850G>A	p.Gly1284Arg	p.G1284R	ENST00000306801	NM_020761.2	1284	Gga/Aga	33/34	0.317152174730471	5	FACETS	1	0.986	1	0.401	0.374	0.429	CLONAL	1	TRUE	2	0.461260474394239	5		367	1572	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259278	36259279	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0001757-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	152	148	0	ENST00000300305.3:c.212dup	p.Arg72GlufsTer66	p.R72Efs*66	ENST00000300305		71	ctg/ctTg	3/8	1	2	FACETS	0.934	0.856	1	0.934	0.856	1	CLONAL	1	TRUE	1	0.461260474394239	2		148	706	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0001769-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	389	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.508628454063911	3	FACETS	0.978	0.932	1	0.978	0.932	1	CLONAL	2	TRUE	1	0.508628454063911	3		311	981	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0001769-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	217	265	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.918	0.854	0.983	0.918	0.854	0.983	CLONAL	1	TRUE	1	0.508628454063911	2		265	930	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0001769-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	177	501	1	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	0.133752654962968	0	FACETS	0.563	0.522	0.606			1	INDETERMINATE	1	TRUE	0	0.508628454063911	0		502	607	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0001769-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	201	476	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.786	0.728	0.846	0.786	0.728	0.846	SUBCLONAL	1	TRUE	1	0.508628454063911	2		476	1006	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0001769-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	465	284	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	0.508628454063911	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.508628454063911	3		284	1036	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247250	153247250	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001769-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	207	306	2	ENST00000281708.4:c.1552G>A	p.Ala518Thr	p.A518T	ENST00000281708	NM_033632.3	518	Gca/Aca	10/12	1	2	FACETS	0.925	0.859	0.993	0.925	0.859	0.993	CLONAL	1	TRUE	1	0.508628454063911	2		308	880	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222555	157222555	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554265269	NA	P-0001769-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	234	265	0	ENST00000346085.5:c.1822C>T	p.Gln608Ter	p.Q608*	ENST00000346085	NM_020732.3	608	Cag/Tag	4/20	0.499997440164829	3	FACETS	1	0.952	1	0.513	0.478	0.549	CLONAL	1	TRUE	1	0.508628454063911	3		265	1125	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907164	101907164	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001769-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	261	177	0	ENST00000374994.4:c.1124C>G	p.Thr375Arg	p.T375R	ENST00000374994	NM_004612.2	375	aCa/aGa	6/9	0.502958960171561	2	FACETS	0.972	0.921	1	0.972	0.921	1	CLONAL	2	TRUE	0	0.508628454063911	2		177	528	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022961	33022961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001769-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	180	213	0	ENST00000300177.4:c.70G>A	p.Gly24Arg	p.G24R	ENST00000300177	NM_001191322.1	24	Ggg/Agg	2/2	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.508628454063911	2		213	619	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007681	45007681	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001769-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	247	236	0	ENST00000558401.1:c.128T>G	p.Leu43Arg	p.L43R	ENST00000558401	NM_004048.2	43	cTg/cGg	2/4	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.508628454063911	2		236	948	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138570	2138570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45517423	NA	P-0001769-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	99	242	0	ENST00000219476.3:c.5383C>T	p.Arg1795Cys	p.R1795C	ENST00000219476	NM_000548.3	1795	Cgc/Tgc	42/42	0.32702561580946	0	FACETS	0.484	0.435	0.535			1	SUBCLONAL	1	TRUE	0	0.508628454063911	0		242	395	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118996	70118996	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001769-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	239	270	0	ENST00000245479.2:c.568G>T	p.Glu190Ter	p.E190*	ENST00000245479	NM_000346.3	190	Gag/Tag	2/3	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.508628454063911	2		270	731	SUCCESS
APC	324	MSKCC	GRCh37	5	112174005	112174006	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0001769-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	120	246	0	ENST00000257430.4:c.2716dup	p.Ser906PhefsTer6	p.S906Ffs*6	ENST00000257430	NM_000038.5	905	agt/agTt	16/16	1	2	FACETS	0.789	0.715	0.867	0.789	0.715	0.867	SUBCLONAL	1	TRUE	1	0.508628454063911	2		246	598	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717769	89717770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	132	192	0	ENST00000371953.3:c.800dup	p.Asp268GlyfsTer30	p.D268Gfs*30	ENST00000371953	NM_000314.4	265	cta/ctAa	7/9	1	2	FACETS	0.937	0.859	1	0.937	0.859	1	CLONAL	1	TRUE	1	0.697510351903042	2		192	404	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	256	1035	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.697510351903042	2		1036	720	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	145	498	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.904	0.831	0.978	0.904	0.831	0.978	CLONAL	1	TRUE	1	0.697510351903042	2		498	460	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	174	275	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.697510351903042	2		275	492	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	211	592	0	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.697510351903042	2		592	533	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	240	444	1	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.697510351903042	2		445	670	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1485978447	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	234	511	0	ENST00000324856.7:c.5164C>T	p.Arg1722Ter	p.R1722*	ENST00000324856	NM_006015.4	1722	Cga/Tga	20/20	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.697510351903042	2		511	666	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248024	59248024	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	215	360	0	ENST00000371222.2:c.719C>A	p.Pro240Gln	p.P240Q	ENST00000371222	NM_002228.3	240	cCg/cAg	1/1	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.697510351903042	2		360	601	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874275	155874275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1420077819	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	462	361	2	ENST00000368323.3:c.256C>T	p.Arg86Trp	p.R86W	ENST00000368323	NM_006912.5	86	Cgg/Tgg	5/6	0.697510351903042	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	1	0.697510351903042	4		363	736	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226589968	226589968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139202063	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	236	477	0	ENST00000366794.5:c.233G>A	p.Arg78Gln	p.R78Q	ENST00000366794	NM_001618.3	78	cGg/cAg	2/23	0.697510351903042	4	FACETS	1	0.968	1	0.354	0.329	0.378	CLONAL	1	TRUE	1	0.697510351903042	4		477	1083	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469630	25469630	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762563426	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	153	383	0	ENST00000264709.3:c.1138G>A	p.Ala380Thr	p.A380T	ENST00000264709	NM_175629.2	380	Gcg/Acg	10/23	0.697510351903042	3	FACETS	0.935	0.858	1	0.312	0.286	0.338	CLONAL	1	TRUE	0	0.697510351903042	3		383	633	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637507	47637507	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs763298811	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	190	268	0	ENST00000233146.2:c.641G>T	p.Arg214Ile	p.R214I	ENST00000233146	NM_000251.2	214	aGa/aTa	3/16	0.697510351903042	3	FACETS	0.94	0.882	0.998	0.626	0.588	0.665	CLONAL	2	TRUE	0	0.697510351903042	3		268	391	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032094	48032094	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587779266	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	739	455	0	ENST00000234420.5:c.3484G>C	p.Ala1162Pro	p.A1162P	ENST00000234420	NM_000179.2	1162	Gct/Cct	6/10	0.697510351903042	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.697510351903042	3		455	910	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164721	47164721	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	156	364	0	ENST00000409792.3:c.1405T>C	p.Tyr469His	p.Y469H	ENST00000409792	NM_014159.6	469	Tac/Cac	3/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.697510351903042	2		364	413	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643734	52643734	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs142097913	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	30	408	0	ENST00000394830.3:c.2162T>C	p.Ile721Thr	p.I721T	ENST00000394830	NM_018313.4	721	aTt/aCt	17/30	1	2	FACETS	0.177	0.142	0.216	0.177	0.142	0.216	SUBCLONAL	1	TRUE	1	0.697510351903042	2		408	487	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936096	178936096	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519940	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	145	253	0	ENST00000263967.3:c.1638G>T	p.Gln546His	p.Q546H	ENST00000263967	NM_006218.2	546	caG/caT	10/21	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.697510351903042	2		253	412	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430690	181430690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs890516076	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	156	254	0	ENST00000325404.1:c.542C>T	p.Pro181Leu	p.P181L	ENST00000325404	NM_003106.3	181	cCg/cTg	1/1	1	2	FACETS	0.977	0.902	1	0.977	0.902	1	CLONAL	1	TRUE	1	0.697510351903042	2		254	458	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807129	1807129	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	23	432	0	ENST00000260795.2:c.1460T>C	p.Val487Ala	p.V487A	ENST00000260795		487	gTc/gCc	10/17	0.697510351903042	1	FACETS	0.142	0.11	0.178	0.142	0.11	0.178	SUBCLONAL	1	TRUE	0	0.697510351903042	1		432	303	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541874	187541874	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs549753426	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	214	543	0	ENST00000441802.2:c.5866G>A	p.Asp1956Asn	p.D1956N	ENST00000441802	NM_005245.3	1956	Gat/Aat	10/27	NA	2	FACETS	1	0.967	1			1	INDETERMINATE	1	TRUE	NA	0.697510351903042	2		543	584	SUCCESS
APC	324	MSKCC	GRCh37	5	112175603	112175603	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	125	459	0	ENST00000257430.4:c.4312A>G	p.Thr1438Ala	p.T1438A	ENST00000257430	NM_000038.5	1438	Aca/Gca	16/16	1	2	FACETS	0.481	0.436	0.529	0.481	0.436	0.529	SUBCLONAL	1	TRUE	1	0.697510351903042	2		459	745	SUCCESS
APC	324	MSKCC	GRCh37	5	112179471	112179471	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	261	552	0	ENST00000257430.4:c.8180A>G	p.Gln2727Arg	p.Q2727R	ENST00000257430	NM_000038.5	2727	cAg/cGg	16/16	1	2	FACETS	0.902	0.847	0.957	0.902	0.847	0.957	CLONAL	1	TRUE	1	0.697510351903042	2		552	830	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176710828	176710828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587784177	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	230	525	1	ENST00000439151.2:c.6050G>A	p.Arg2017Gln	p.R2017Q	ENST00000439151	NM_022455.4	2017	cGg/cAg	20/23	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.697510351903042	2		526	642	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169914	32169914	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1345231909	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	198	470	0	ENST00000375023.3:c.3694C>T	p.Gln1232Ter	p.Q1232*	ENST00000375023	NM_004557.3	1232	Cag/Tag	21/30	1	2	FACETS	0.986	0.919	1	0.986	0.919	1	CLONAL	1	TRUE	1	0.697510351903042	2		470	576	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710720	117710720	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	44	441	2	ENST00000368508.3:c.1552T>C	p.Phe518Leu	p.F518L	ENST00000368508	NM_002944.2	518	Ttc/Ctc	12/43	1	2	FACETS	0.191	0.159	0.226	0.191	0.159	0.226	SUBCLONAL	1	TRUE	1	0.697510351903042	2		443	661	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157519961	157519961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554234953	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	245	414	0	ENST00000346085.5:c.4030C>T	p.Gln1344Ter	p.Q1344*	ENST00000346085	NM_020732.3	1344	Cag/Tag	17/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.697510351903042	2		414	650	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527938	157527938	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1554237565	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	223	296	0	ENST00000346085.5:c.5663T>A	p.Leu1888Ter	p.L1888*	ENST00000346085	NM_020732.3	1888	tTg/tAg	20/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.697510351903042	2		296	553	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946339	2946339	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	144	478	0	ENST00000396946.4:c.3398G>T	p.Arg1133Leu	p.R1133L	ENST00000396946	NM_032415.4	1133	cGc/cTc	25/25	0.1336855402467	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.697510351903042	0		478	456	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977554	2977554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs992263343	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	147	446	0	ENST00000396946.4:c.1130G>A	p.Arg377Gln	p.R377Q	ENST00000396946	NM_032415.4	377	cGg/cAg	8/25	0.1336855402467	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.697510351903042	0		446	434	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266503	55266503	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	164	477	0	ENST00000275493.2:c.2795G>A	p.Arg932His	p.R932H	ENST00000275493	NM_005228.3	932	cGc/cAc	23/28	1	2	FACETS	0.926	0.856	0.997	0.926	0.856	0.997	CLONAL	1	TRUE	1	0.697510351903042	2		477	508	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513206	106513206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	149	299	0	ENST00000359195.3:c.2110G>A	p.Ala704Thr	p.A704T	ENST00000359195	NM_002649.2	704	Gcc/Acc	4/11	1	2	FACETS	0.868	0.799	0.94	0.868	0.799	0.94	CLONAL	1	TRUE	1	0.697510351903042	2		299	492	SUCCESS
MET	4233	MSKCC	GRCh37	7	116409779	116409779	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	259	375	0	ENST00000397752.3:c.2664T>A	p.His888Gln	p.H888Q	ENST00000397752	NM_000245.2	888	caT/caA	12/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.697510351903042	2		375	693	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859704	151859704	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	218	378	1	ENST00000262189.6:c.10958C>G	p.Pro3653Arg	p.P3653R	ENST00000262189	NM_170606.2	3653	cCt/cGt	43/59	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.697510351903042	2		379	574	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5055789	5055789	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	184	347	0	ENST00000381652.3:c.1056+1G>A		p.X352_splice	ENST00000381652	NM_004972.3	352			1	2	FACETS	0.972	0.903	1	0.972	0.903	1	CLONAL	1	TRUE	1	0.697510351903042	2		347	543	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970967	21970967	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755927351	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	235	407	0	ENST00000304494.5:c.391C>T	p.Arg131Cys	p.R131C	ENST00000304494	NM_000077.4	131	Cgc/Tgc	2/3	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.697510351903042	2		407	647	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882082	36882082	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	48	387	0	ENST00000358127.4:c.931A>G	p.Thr311Ala	p.T311A	ENST00000358127	NM_001280556.1	311	Acc/Gcc	8/10	1	2	FACETS	0.296	0.25	0.346	0.296	0.25	0.346	SUBCLONAL	1	TRUE	1	0.697510351903042	2		387	465	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882104	36882104	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	163	384	0	ENST00000358127.4:c.911-2A>G		p.X304_splice	ENST00000358127	NM_001280556.1	304			1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.697510351903042	2		384	465	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401774	139401774	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	101	450	0	ENST00000277541.6:c.3626G>A	p.Cys1209Tyr	p.C1209Y	ENST00000277541	NM_017617.3	1209	tGc/tAc	22/34	0.346555566754485	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.697510351903042	0		450	302	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741363	17741363	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	192	456	1	ENST00000250003.3:c.34G>T	p.Asp12Tyr	p.D12Y	ENST00000250003	NM_002478.4	12	Gac/Tac	1/3	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.697510351903042	2		457	471	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127755	64127755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	131	288	0	ENST00000334205.4:c.248G>A	p.Arg83His	p.R83H	ENST00000334205	NM_003942.2	83	cGc/cAc	3/17	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.697510351903042	2		288	286	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	117	361	0	ENST00000227507.2:c.859C>T	p.Pro287Ser	p.P287S	ENST00000227507	NM_053056.2	287	Ccc/Tcc	5/5	0.663710613749044	1	FACETS	0.635	0.579	0.693	0.635	0.579	0.693	SUBCLONAL	1	TRUE	0	0.697510351903042	1		361	344	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342736	118342736	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	192	455	0	ENST00000534358.1:c.862G>T	p.Gly288Trp	p.G288W	ENST00000534358	NM_005933.3	288	Ggg/Tgg	3/36	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.697510351903042	2		455	519	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404794	404794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371387810	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	226	464	0	ENST00000399788.2:c.4400G>A	p.Arg1467Gln	p.R1467Q	ENST00000399788	NM_001042603.1	1467	cGg/cAg	26/28	NA	2	FACETS	0.943	0.883	1			1	INDETERMINATE	1	TRUE	NA	0.697510351903042	2		464	687	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211462	46211462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	202	374	0	ENST00000334344.6:c.428G>A	p.Arg143His	p.R143H	ENST00000334344	NM_152641.2	143	cGt/cAt	5/21	1	2	FACETS	0.931	0.868	0.996	0.931	0.868	0.996	CLONAL	1	TRUE	1	0.697510351903042	2		374	622	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233162	46233162	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	216	414	0	ENST00000334344.6:c.1381G>T	p.Ala461Ser	p.A461S	ENST00000334344	NM_152641.2	461	Gca/Tca	11/21	1	2	FACETS	0.824	0.768	0.881	0.824	0.768	0.881	CLONAL	1	TRUE	1	0.697510351903042	2		414	752	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950870	32950870	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	250	551	0	ENST00000380152.3:c.8696A>G	p.Gln2899Arg	p.Q2899R	ENST00000380152		2899	cAa/cGa	21/27	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.697510351903042	2		551	676	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99491870	99491870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1185222113	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	181	516	1	ENST00000268035.6:c.3655G>A	p.Glu1219Lys	p.E1219K	ENST00000268035	NM_000875.3	1219	Gag/Aag	20/21	1	2	FACETS	0.917	0.851	0.984	0.917	0.851	0.984	CLONAL	1	TRUE	1	0.697510351903042	2		517	566	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341245	341245	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1189783498	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	82	394	0	ENST00000262320.3:c.2239G>A	p.Ala747Thr	p.A747T	ENST00000262320	NM_003502.3	747	Gcg/Acg	9/11	0.306240461665834	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.697510351903042	0		394	269	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647704	2647704	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	165	471	0	ENST00000342085.4:c.1607G>A	p.Cys536Tyr	p.C536Y	ENST00000342085	NM_002613.4	536	tGc/tAc	14/14	1	2	FACETS	0.982	0.909	1	0.982	0.909	1	CLONAL	1	TRUE	1	0.697510351903042	2		471	482	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857047	9857047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568622613	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	216	449	0	ENST00000330684.3:c.4354C>T	p.Arg1452Cys	p.R1452C	ENST00000330684	NM_001134407.1	1452	Cgc/Tgc	13/13	1	2	FACETS	0.98	0.916	1	0.98	0.916	1	CLONAL	1	TRUE	1	0.697510351903042	2		449	632	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068415	16068415	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	29	57	0	ENST00000268712.3:c.496G>T	p.Gly166Ter	p.G166*	ENST00000268712	NM_006311.3	166	Gga/Tga	5/46	1	2	FACETS	0.832	0.684	0.99	0.832	0.684	0.99	CLONAL	1	TRUE	1	0.697510351903042	2		57	100	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556100	29556100	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	133	266	0	ENST00000356175.3:c.2467G>T	p.Gly823Ter	p.G823*	ENST00000356175	NM_000267.3	823	Gga/Tga	21/57	1	2	FACETS	0.953	0.875	1	0.953	0.875	1	CLONAL	1	TRUE	1	0.697510351903042	2		266	400	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556103	29556103	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	131	247	0	ENST00000356175.3:c.2470G>T	p.Gly824Ter	p.G824*	ENST00000356175	NM_000267.3	824	Gga/Tga	21/57	1	2	FACETS	0.996	0.914	1	0.996	0.914	1	CLONAL	1	TRUE	1	0.697510351903042	2		247	377	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101030	4101030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730880511	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	55	222	0	ENST00000262948.5:c.692G>A	p.Arg231His	p.R231H	ENST00000262948	NM_030662.3	231	cGc/cAc	6/11	0.212389921646979	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.697510351903042	0		222	170	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219369	5219369	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	153	402	0	ENST00000357368.4:c.3875C>T	p.Ala1292Val	p.A1292V	ENST00000357368	NM_002850.3	1292	gCc/gTc	23/38	0.212389921646979	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.697510351903042	0		402	452	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15365002	15365002	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	160	433	0	ENST00000263377.2:c.2119A>C	p.Ser707Arg	p.S707R	ENST00000263377	NM_058243.2	707	Agt/Cgt	11/20	1	2	FACETS	0.968	0.895	1	0.968	0.895	1	CLONAL	1	TRUE	1	0.697510351903042	2		433	474	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765459	41765459	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	219	410	0	ENST00000301178.4:c.2335T>C	p.Tyr779His	p.Y779H	ENST00000301178	NM_021913.4	779	Tat/Cat	20/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.697510351903042	2		410	560	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791320	42791320	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754556504	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	36	364	0	ENST00000575354.2:c.380C>T	p.Thr127Met	p.T127M	ENST00000575354	NM_015125.3	127	aCg/aTg	3/20	1	2	FACETS	0.227	0.186	0.273	0.227	0.186	0.273	SUBCLONAL	1	TRUE	1	0.697510351903042	2		364	455	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041601	47041601	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	79	548	0	ENST00000377604.3:c.1826A>T	p.Asp609Val	p.D609V	ENST00000377604	NM_001204468.1	609	gAt/gTt	17/24	0.1336855402467	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.697510351903042	0		548	507	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210266	123210266	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	298	482	0	ENST00000218089.9:c.2618T>C	p.Val873Ala	p.V873A	ENST00000218089	NM_001042749.1	873	gTa/gCa	26/35	0.1336855402467	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.697510351903042	0		482	692	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983058	149983058	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	223	560	0	ENST00000253339.5:c.3200del	p.Asn1067MetfsTer61	p.N1067Mfs*61	ENST00000253339		1067	aAt/at	7/7	1	2	FACETS	0.933	0.873	0.995	0.933	0.873	0.995	CLONAL	1	TRUE	1	0.697510351903042	2		560	685	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069060	5069060	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	223	450	1	ENST00000381652.3:c.1370del	p.Asn457MetfsTer22	p.N457Mfs*22	ENST00000381652	NM_004972.3	455	acA/ac	11/25	1	2	FACETS	0.988	0.925	1	0.988	0.925	1	CLONAL	1	TRUE	1	0.697510351903042	2		451	647	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287469	46287469	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	242	495	2	ENST00000334344.6:c.5333del	p.Asn1778IlefsTer13	p.N1778Ifs*13	ENST00000334344	NM_152641.2	1776	ttA/tt	20/21	1	2	FACETS	0.98	0.92	1	0.98	0.92	1	CLONAL	1	TRUE	1	0.697510351903042	2		497	708	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022443	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	rs750318549	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	66	272	0	ENST00000375687.4:c.1933_1934del	p.Gly645TrpfsTer12	p.G645Wfs*12	ENST00000375687	NM_015338.5	643	GGg/g	13/13	1	2	FACETS	0.776	0.682	0.874	0.776	0.682	0.874	SUBCLONAL	1	TRUE	1	0.697510351903042	2		272	244	SUCCESS
AR	367	MSKCC	GRCh37	X	66765149	66765151	+	inframe_deletion	In_Frame_Del	DEL	TGC	TGC	-	rs752055010	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	27	284	1	ENST00000374690.3:c.170_172del	p.Leu57del	p.L57del	ENST00000374690	NM_000044.3	54	tTGCtg/ttg	1/8	0.1336855402467	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.697510351903042	0		285	314	SUCCESS
BTK	695	MSKCC	GRCh37	X	100624988	100624988	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs864321664	NA	P-0001821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	246	503	0	ENST00000308731.7:c.389del	p.Asn130ThrfsTer2	p.N130Tfs*2	ENST00000308731	NM_000061.2	130	aAc/ac	5/19	0.1336855402467	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.697510351903042	0		503	592	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0001830-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	177	403	1	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.952	0.879	1	1	0.992	1	CLONAL	2	TRUE	1	0.226631951602372	2		404	820	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001830-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	30	472	0	ENST00000263967.3:c.3129G>C	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atC	21/21	0.176476321621708	1	FACETS	0.514	0.413	0.628	0.514	0.413	0.628	SUBCLONAL	1	TRUE	0	0.226631951602372	1		472	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0001830-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	64	391	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	0.176476321621708	1	FACETS	0.921	0.798	1	0.921	0.798	1	CLONAL	1	TRUE	0	0.226631951602372	1		391	544	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16248762	16248762	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001830-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	42	457	0	ENST00000375759.3:c.1768G>A	p.Glu590Lys	p.E590K	ENST00000375759	NM_015001.2	590	Gaa/Aaa	10/15	1	2	FACETS	0.617	0.514	0.731	0.617	0.514	0.731	SUBCLONAL	1	TRUE	1	0.226631951602372	2		457	601	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963931	2963931	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1286585074	NA	P-0001830-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	156	489	0	ENST00000396946.4:c.1876G>T	p.Glu626Ter	p.E626*	ENST00000396946	NM_032415.4	626	Gag/Tag	15/25	0.16138921261157	2	FACETS	1	0.987	1	0.726	0.664	0.791	CLONAL	1	TRUE	0	0.226631951602372	2		489	948	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426738	49426738	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001830-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	35	185	0	ENST00000301067.7:c.11750A>G	p.Gln3917Arg	p.Q3917R	ENST00000301067	NM_003482.3	3917	cAg/cGg	39/54	1	2	FACETS	1	0.838	1	1	0.838	1	CLONAL	1	TRUE	1	0.226631951602372	2		185	303	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219341	1219341	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001830-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	143	376	0	ENST00000326873.7:c.393C>A	p.Tyr131Ter	p.Y131*	ENST00000326873	NM_000455.4	131	taC/taA	3/10	0.226631951602372	1	FACETS	0.782	0.715	0.853	1	0.988	1	SUBCLONAL	2	TRUE	0	0.226631951602372	1		376	715	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527514	41527514	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001830-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	99	515	0	ENST00000263253.7:c.1405G>T	p.Ala469Ser	p.A469S	ENST00000263253	NM_001429.3	469	Gca/Tca	6/31	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.226631951602372	2		515	736	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181341	123181341	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001830-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	75	482	0	ENST00000218089.9:c.805C>T	p.Gln269Ter	p.Q269*	ENST00000218089	NM_001042749.1	269	Caa/Taa	9/35	0.226631951602372	1	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	0	0.226631951602372	1		482	585	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467713	66467713	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001830-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	46	669	0	ENST00000273854.3:c.556del	p.Asp187IlefsTer7	p.D187Ifs*7	ENST00000273854	NM_004439.5	186	Ctt/tt	3/18	0.176476321621708	1	FACETS	0.431	0.361	0.508	0.431	0.361	0.508	SUBCLONAL	1	TRUE	0	0.226631951602372	1		669	836	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332004	81332005	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0001830-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	35	650	0	ENST00000222390.5:c.2079dup	p.Gly694TrpfsTer31	p.G694Wfs*31	ENST00000222390	NM_000601.4	693	-/T	18/18	1	2	FACETS	0.468	0.382	0.565	0.468	0.382	0.565	SUBCLONAL	1	TRUE	1	0.226631951602372	2		650	660	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0001875-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	177	338	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	0.9	2		338	375	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645922	67645922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001875-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	131	319	0	ENST00000264010.4:c.850C>T	p.His284Tyr	p.H284Y	ENST00000264010	NM_006565.3	284	Cac/Tac	4/12	0.893826395583916	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.9	1		319	160	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538852	23538852	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001875-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	31	310	0	ENST00000380871.4:c.587C>T	p.Ser196Phe	p.S196F	ENST00000380871	NM_006167.3	196	tCt/tTt	2/2	0.147499356210784	3	FACETS	0.274	0.221	0.333	0.137	0.11	0.167	INDETERMINATE	1	TRUE	1	0.9	3		310	365	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016585	12016585	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001875-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	173	343	0	ENST00000353533.5:c.721G>T	p.Gly241Ter	p.G241*	ENST00000353533	NM_003010.3	241	Gga/Tga	7/11	0.893826395583916	1	FACETS	0.965	0.924	1	0.965	0.924	1	CLONAL	1	TRUE	0	0.9	1		343	219	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101695	71101698	+	frameshift_variant	Frame_Shift_Del	DEL	GGCT	GGCT	-	novel	NA	P-0001875-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	120	399	0	ENST00000318789.4:c.500_503del	p.Gln167LeufsTer38	p.Q167Lfs*38	ENST00000318789	NM_032682.5	167	cAGCCt/ct	9/21	0.893826395583916	1	FACETS	0.838	0.786	0.888	0.838	0.786	0.888	CLONAL	1	TRUE	0	0.9	1		399	175	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111475	8111476	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0001875-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	267	377	2	ENST00000346208.3:c.962dup	p.Thr322AspfsTer30	p.T322Dfs*30	ENST00000346208		321	cag/cAag	5/6	0.147499356210784	5	FACETS	1	0.989	1	0.779	0.736	0.821	INDETERMINATE	2	TRUE	2	0.9	5		379	597	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0001903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	70	328	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.395440628800153	4	FACETS	0.806	0.712	0.904	0.403	0.356	0.452	CLONAL	2	TRUE	0	0.556620042392539	4		328	243	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156981	106156981	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	20	341	0	ENST00000380013.4:c.1882G>T	p.Glu628Ter	p.E628*	ENST00000380013	NM_001127208.2	628	Gag/Tag	3/11	0.271711191993221	3	FACETS	0.481	0.369	0.61	0.24	0.184	0.305	INDETERMINATE	1	TRUE	1	0.556620042392539	3		341	191	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002645	37002645	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	23	300	0	ENST00000358127.4:c.604G>T	p.Gly202Cys	p.G202C	ENST00000358127	NM_001280556.1	202	Ggt/Tgt	5/10	0.555045742709345	1	FACETS	0.493	0.39	0.608	0.493	0.39	0.608	SUBCLONAL	1	TRUE	0	0.556620042392539	1		300	121	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926314	112926314	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	38	315	0	ENST00000351677.2:c.1447G>T	p.Gly483Cys	p.G483C	ENST00000351677	NM_002834.3	483	Ggt/Tgt	12/16	NA	2	FACETS	0.553	0.46	0.655			1	INDETERMINATE	1	TRUE	NA	0.556620042392539	2		315	247	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515223	103515223	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	50	410	0	ENST00000355739.4:c.1724C>G	p.Ser575Cys	p.S575C	ENST00000355739	NM_000123.3	575	tCt/tGt	8/15	0.556620042392539	3	FACETS	0.776	0.662	0.899	0.388	0.331	0.45	SUBCLONAL	1	TRUE	1	0.556620042392539	3		410	296	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579492	7579493	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0001903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	57	310	0	ENST00000269305.4:c.194dup	p.Met66AsnfsTer83	p.M66Nfs*83	ENST00000269305	NM_001126112.2	65	aga/agGa	4/11	0.366850594150057	3	FACETS	1	0.935	1	0.721	0.64	0.804	CLONAL	2	TRUE	0	0.556620042392539	3		310	121	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0001918-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	273	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.674641701735427	4	FACETS	0.955	0.894	1	0.318	0.298	0.34	CLONAL	1	TRUE	1	0.674641701735427	4		311	1419	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023007	27023008	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGC	rs587779737	NA	P-0001918-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	12	9	0	ENST00000324856.7:c.126_128dup	p.Ala45dup	p.A45dup	ENST00000324856	NM_006015.4	45	gag/gaGGCg	1/20	0.674641701735427	3	FACETS	1	0.861	1	0.661	0.487	0.851	CLONAL	1	TRUE	1	0.674641701735427	3		9	36	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426908	6426908	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001918-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1223	81	291	0	ENST00000356142.4:c.101C>G	p.Pro34Arg	p.P34R	ENST00000356142	NM_018890.3	34	cCt/cGt	2/7	0.635770420892984	4	FACETS	0.308	0.27	0.349	0.154	0.135	0.175	SUBCLONAL	1	TRUE	2	0.674641701735427	4		291	1304	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594221	55594221	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913512	NA	P-0001918-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	42	298	0	ENST00000288135.5:c.1924A>C	p.Lys642Gln	p.K642Q	ENST00000288135	NM_000222.2	642	Aaa/Caa	13/21	1	2	FACETS	0.189	0.157	0.225	0.189	0.157	0.225	SUBCLONAL	1	TRUE	1	0.674641701735427	2		298	658	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0001937-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	310	286	0	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	0.822706741000015	2	FACETS	0.976	0.946	1	0.976	0.946	1	CLONAL	2	TRUE	0	0.822706741000015	2		286	386	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46543187	46543187	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1296227284	NA	P-0001937-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	574	328	0	ENST00000262741.5:c.314G>T	p.Arg105Leu	p.R105L	ENST00000262741	NM_003629.3	105	cGg/cTg	3/10	0.561799467530813	4	FACETS	0.891	0.862	0.918	0.891	0.862	0.918	CLONAL	3	TRUE	1	0.822706741000015	4		328	952	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519787	29519787	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001937-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	188	273	0	ENST00000389048.3:c.1784G>A	p.Trp595Ter	p.W595*	ENST00000389048	NM_004304.4	595	tGg/tAg	9/29	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.822706741000015	2		273	408	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732712	204732712	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs772433747	NA	P-0001937-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	332	360	0	ENST00000302823.3:c.47C>A	p.Ala16Asp	p.A16D	ENST00000302823	NM_005214.4	16	gCt/gAt	1/4	0.193980811241057	4	FACETS	0.994	0.946	1	0.994	0.946	1	INDETERMINATE	2	TRUE	2	0.822706741000015	4		360	740	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812204	212812204	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001937-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	386	318	0	ENST00000342788.4:c.372A>T	p.Arg124Ser	p.R124S	ENST00000342788	NM_005235.2	124	agA/agT	3/28	0.193980811241057	4	FACETS	0.989	0.944	1	0.989	0.944	1	INDETERMINATE	2	TRUE	2	0.822706741000015	4		318	865	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117632220	117632220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001937-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	298	308	0	ENST00000368508.3:c.6196G>T	p.Gly2066Cys	p.G2066C	ENST00000368508	NM_002944.2	2066	Ggc/Tgc	39/43	0.142951458530501	4	FACETS	0.984	0.934	1	0.984	0.934	1	INDETERMINATE	2	TRUE	2	0.822706741000015	4		308	671	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63810661	63810661	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001937-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	214	253	1	ENST00000279873.7:c.748G>T	p.Gly250Cys	p.G250C	ENST00000279873	NM_032199.2	250	Ggc/Tgc	5/10	0.822706741000015	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.822706741000015	1		254	281	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409042	4409042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001937-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	168	265	1	ENST00000261254.3:c.737G>A	p.Cys246Tyr	p.C246Y	ENST00000261254	NM_001759.3	246	tGc/tAc	5/5	0.822706741000015	3	FACETS	0.939	0.867	1			1	CLONAL	1	TRUE	NA	0.822706741000015	3		266	614	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435026	49435026	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001937-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	182	160	0	ENST00000301067.7:c.6527C>T	p.Pro2176Leu	p.P2176L	ENST00000301067	NM_003482.3	2176	cCc/cTc	31/54	0.561799467530813	4	FACETS	0.911	0.861	0.96	0.911	0.861	0.96	CLONAL	3	TRUE	1	0.822706741000015	4		160	295	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916734	48916734	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0001937-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	228	229	0	ENST00000267163.4:c.265-1G>T		p.X89_splice	ENST00000267163	NM_000321.2	89			0.822706741000015	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.822706741000015	1		229	313	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514853	103514853	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001937-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	196	213	0	ENST00000355739.4:c.1354A>T	p.Asn452Tyr	p.N452Y	ENST00000355739	NM_000123.3	452	Aac/Tac	8/15	0.822706741000015	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.822706741000015	1		213	260	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434924	49434924	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001937-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	193	178	0	ENST00000301067.7:c.6629del	p.Pro2210ArgfsTer54	p.P2210Rfs*54	ENST00000301067	NM_003482.3	2210	cCg/cg	31/54	0.561799467530813	4	FACETS	0.877	0.829	0.925	0.877	0.829	0.925	CLONAL	3	TRUE	1	0.822706741000015	4		178	325	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839685	42839686	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0001937-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	166	272	0	ENST00000398585.3:c.1553dup	p.Asp519GlyfsTer40	p.D519Gfs*40	ENST00000398585	NM_001135099.1	518	acg/acCg	13/14	0.170227557744395	3	FACETS	1	0.986	1	0.633	0.587	0.68	INDETERMINATE	1	TRUE	1	0.822706741000015	3		272	450	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201670	66201671	+	missense_variant	Missense_Mutation	DNP	CG	CG	AA	novel	NA	P-0001937-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	303	304	0	ENST00000273854.3:c.2831_2832delinsTT	p.Thr944Ile	p.T944I	ENST00000273854	NM_004439.5	944	aCG/aTT	16/18	0.822706741000015	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.822706741000015	1		304	426	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0002081-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	378	348	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA	2	FACETS	0.925	0.886	0.965			1	INDETERMINATE	2	TRUE	NA	0.549719769058111	2		348	743	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0002081-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	116	331	0	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	0.549719769058111	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.549719769058111	1		331	246	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221293	1221293	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002081-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	122	252	0	ENST00000326873.7:c.816C>A	p.Tyr272Ter	p.Y272*	ENST00000326873	NM_000455.4	272	taC/taA	6/10	0.549719769058111	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.549719769058111	1		252	260	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141472	11141473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0002081-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	133	293	0	ENST00000358026.2:c.3450dup	p.Ile1151HisfsTer25	p.I1151Hfs*25	ENST00000358026	NM_001128849.1	1150	ttc/ttCc	25/36	0.549719769058111	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.549719769058111	1		293	271	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0002085-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	353	322	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.286788517849374	5	FACETS	1	0.985	1	0.738	0.698	0.778	CLONAL	2	TRUE	2	0.402173274271593	5		322	1272	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0002085-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	154	668	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.286788517849374	5	FACETS	1	0.982	1	0.424	0.387	0.462	CLONAL	1	TRUE	2	0.402173274271593	5		669	966	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259502	55259502	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002085-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	346	490	1	ENST00000275493.2:c.2560A>T	p.Thr854Ser	p.T854S	ENST00000275493	NM_005228.3	854	Aca/Tca	21/28	0.286788517849374	5	FACETS	1	0.983	1	0.727	0.688	0.767	CLONAL	2	TRUE	2	0.402173274271593	5		491	1265	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678619	88678619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148888023	NA	P-0002085-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	55	171	1	ENST00000360948.2:c.917G>A	p.Arg306His	p.R306H	ENST00000360948	NM_001012338.2	306	cGt/cAt	9/19	NA	2	FACETS	0.8	0.688	0.921			1	INDETERMINATE	1	TRUE	NA	0.402173274271593	2		172	342	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0002085-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	279	398	0	ENST00000269305.4:c.560-2A>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.402173274271593	2	FACETS	0.953	0.9	1	0.953	0.9	1	CLONAL	2	TRUE	0	0.402173274271593	2		398	728	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702569	52702569	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002085-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	259	390	0	ENST00000394830.3:c.329del	p.Asn110IlefsTer3	p.N110Ifs*3	ENST00000394830	NM_018313.4	110	aAt/at	4/30	0.402173274271593	2	FACETS	0.986	0.93	1	0.986	0.93	1	CLONAL	2	TRUE	0	0.402173274271593	2		390	653	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717713	89717714	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002085-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	211	262	0	ENST00000371953.3:c.740dup	p.Leu247PhefsTer6	p.L247Ffs*6	ENST00000371953	NM_000314.4	246	-/T	7/9	0.402173274271593	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.402173274271593	2		262	517	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138584	11138584	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002085-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	291	422	0	ENST00000358026.2:c.3340G>C	p.Asp1114His	p.D1114H	ENST00000358026	NM_001128849.1	1114	Gat/Cat	24/36	0.35661397525379	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.402173274271593	3		422	787	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138623	11138623	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002085-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	214	332	0	ENST00000358026.2:c.3379G>C	p.Asp1127His	p.D1127H	ENST00000358026	NM_001128849.1	1127	Gat/Cat	24/36	0.35661397525379	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	1	0.402173274271593	3		332	631	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911288	29911289	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0002085-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	28	153	0	ENST00000376809.5:c.589dup	p.Glu197GlyfsTer24	p.E197Gfs*24	ENST00000376809	NM_002116.7	196	ctg/ctGg	3/8	1	2	FACETS	0.428	0.343	0.526	0.428	0.343	0.526	SUBCLONAL	1	TRUE	1	0.402173274271593	2		153	325	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851693	134851693	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1042789	NA	P-0002118-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	107	364	0	ENST00000398015.3:c.1099C>T	p.Arg367Cys	p.R367C	ENST00000398015	NM_004441.4	367	Cgc/Tgc	5/16	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.34813321247349	2		364	613	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131930650	131930650	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002118-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	56	516	1	ENST00000265335.6:c.1883A>T	p.Lys628Met	p.K628M	ENST00000265335		628	aAg/aTg	12/25	1	2	FACETS	0.389	0.332	0.451	0.389	0.332	0.451	SUBCLONAL	1	TRUE	1	0.34813321247349	2		517	827	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106099	27106100	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0002118-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	62	522	0	ENST00000324856.7:c.5715dup	p.Arg1906ThrfsTer8	p.R1906Tfs*8	ENST00000324856	NM_006015.4	1904	gaa/gAaa	20/20	1	2	FACETS	0.599	0.517	0.687	0.599	0.517	0.687	SUBCLONAL	1	TRUE	1	0.34813321247349	2		522	595	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577563	+	inframe_deletion	In_Frame_Del	DEL	GGAACT	GGAACT	-	novel	NA	P-0002118-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	39	418	0	ENST00000269305.4:c.718_723del	p.Ser240_Ser241del	p.S240_S241del	ENST00000269305	NM_001126112.2	240	AGTTCC/-	7/11	0.305875093752416	1	FACETS	0.307	0.254	0.367	0.307	0.254	0.367	SUBCLONAL	1	TRUE	0	0.34813321247349	1		418	602	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0002171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	99	286	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.238820746420763	1	FACETS	0.988	0.882	1	0.988	0.882	1	CLONAL	1	TRUE	0	0.238820746420763	1		286	739	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680656	88680656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761690006	NA	P-0002171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	97	428	0	ENST00000360948.2:c.601C>T	p.Arg201Cys	p.R201C	ENST00000360948	NM_001012338.2	201	Cgc/Tgc	6/19	0.238820746420763	1	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	0	0.238820746420763	1		428	704	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591925	48591925	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	83	412	0	ENST00000342988.3:c.1088G>T	p.Cys363Phe	p.C363F	ENST00000342988	NM_005359.5	363	tGt/tTt	9/12	1	2	FACETS	0.928	0.818	1	0.928	0.818	1	CLONAL	1	TRUE	1	0.238820746420763	2		412	749	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002209-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	39	245	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.496836819915564	2		245	138	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0002209-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	116	295	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	1	2	FACETS	0.841	0.761	0.926	0.841	0.761	0.926	CLONAL	1	TRUE	1	0.496836819915564	2		295	555	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141586	202141586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760898260	NA	P-0002209-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	134	302	0	ENST00000358485.4:c.874C>T	p.Arg292Trp	p.R292W	ENST00000358485	NM_001080125.1	292	Cgg/Tgg	7/9	1	2	FACETS	0.968	0.884	1	0.968	0.884	1	CLONAL	1	TRUE	1	0.496836819915564	2		302	557	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806633	1806633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56240927	NA	P-0002209-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	207	485	0	ENST00000260795.2:c.1349C>T	p.Thr450Met	p.T450M	ENST00000260795		450	aCg/aTg	9/17	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.496836819915564	2		485	779	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467650	66467650	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1369888289	NA	P-0002209-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	113	245	0	ENST00000273854.3:c.619A>G	p.Lys207Glu	p.K207E	ENST00000273854	NM_004439.5	207	Aaa/Gaa	3/18	1	2	FACETS	0.993	0.899	1	0.993	0.899	1	CLONAL	1	TRUE	1	0.496836819915564	2		245	458	SUCCESS
APC	324	MSKCC	GRCh37	5	112177460	112177460	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0002209-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	126	286	0	ENST00000257430.4:c.6169A>T	p.Lys2057Ter	p.K2057*	ENST00000257430	NM_000038.5	2057	Aag/Tag	16/16	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.496836819915564	2		286	497	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168766	32168767	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0002209-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	111	457	0	ENST00000375023.3:c.4156_4157delinsAA	p.Gly1386Asn	p.G1386N	ENST00000375023	NM_004557.3	1386	GGt/AAt	23/30	1	2	FACETS	0.763	0.687	0.842	0.763	0.687	0.842	SUBCLONAL	1	TRUE	1	0.496836819915564	2		457	586	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188368	32188368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs551594218	NA	P-0002209-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	126	302	0	ENST00000375023.3:c.973C>T	p.His325Tyr	p.H325Y	ENST00000375023	NM_004557.3	325	Cac/Tac	6/30	1	2	FACETS	0.911	0.828	0.997	0.911	0.828	0.997	CLONAL	1	TRUE	1	0.496836819915564	2		302	557	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509474	106509474	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002209-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	261	305	0	ENST00000359195.3:c.1468A>C	p.Lys490Gln	p.K490Q	ENST00000359195	NM_002649.2	490	Aag/Cag	2/11	0.496836819915564	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.496836819915564	3		305	626	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0002209-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	211	271	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	0.474615355572595	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.496836819915564	2		271	388	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759718	133759718	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002209-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	64	192	0	ENST00000318560.5:c.2041T>C	p.Phe681Leu	p.F681L	ENST00000318560	NM_005157.4	681	Ttc/Ctc	11/11	1	2	FACETS	0.98	0.857	1	0.98	0.857	1	CLONAL	1	TRUE	1	0.496836819915564	2		192	263	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406261	70406261	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002209-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	143	387	0	ENST00000373644.4:c.3775C>T	p.Pro1259Ser	p.P1259S	ENST00000373644	NM_030625.2	1259	Cca/Tca	4/12	1	2	FACETS	0.855	0.782	0.932	0.855	0.782	0.932	CLONAL	1	TRUE	1	0.496836819915564	2		387	673	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94168996	94168996	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0002209-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	136	267	0	ENST00000323929.3:c.1994+2T>A		p.X665_splice	ENST00000323929	NM_005591.3	665			1	2	FACETS	0.919	0.838	1	0.919	0.838	1	CLONAL	1	TRUE	1	0.496836819915564	2		267	596	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124739	108124740	+	missense_variant	Missense_Mutation	DNP	AC	AC	TG	novel	NA	P-0002209-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	77	220	0	ENST00000278616.4:c.2097_2098delinsTG	p.Glu699_Gln700delinsAspGlu	p.E699_Q700delinsDE	ENST00000278616	NM_000051.3	699	gaACag/gaTGag	13/63	1	2	FACETS	0.814	0.719	0.914	0.814	0.719	0.914	CLONAL	1	TRUE	1	0.496836819915564	2		220	381	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557636	95557636	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002209-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	118	352	0	ENST00000393063.1:c.5431A>G	p.Ile1811Val	p.I1811V	ENST00000393063	NM_030621.3	1811	Att/Gtt	26/28	1	2	FACETS	0.822	0.744	0.904	0.822	0.744	0.904	CLONAL	1	TRUE	1	0.496836819915564	2		352	578	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740665	58740665	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002209-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	270	929	1	ENST00000305921.3:c.1570C>T	p.Gln524Ter	p.Q524*	ENST00000305921	NM_003620.3	524	Caa/Taa	6/6	1	2	FACETS	0.876	0.821	0.933	0.876	0.821	0.933	CLONAL	1	TRUE	1	0.496836819915564	2		930	1241	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47710049	47710050	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0002209-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	88	232	0	ENST00000233146.2:c.2767_2768del	p.Val923LysfsTer2	p.V923Kfs*2	ENST00000233146	NM_000251.2	922	ttTGta/ttta	16/16	1	2	FACETS	0.8	0.712	0.892	0.8	0.712	0.892	SUBCLONAL	1	TRUE	1	0.496836819915564	2		232	443	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051633	13051633	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	CA	novel	NA	P-0002209-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	262	891	0	ENST00000316448.5:c.892delinsCA	p.Glu298GlnfsTer12	p.E298Qfs*12	ENST00000316448	NM_004343.3	298	Gag/CAag	7/9	1	2	FACETS	0.848	0.794	0.905	0.848	0.794	0.905	CLONAL	1	TRUE	1	0.496836819915564	2		891	1243	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0002232-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	238	494	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.974	0.911	1	0.974	0.911	1	CLONAL	1	TRUE	1	0.586216794836788	2		494	834	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002232-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	458	218	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.476166385546313	4	FACETS	0.853	0.819	0.888			1	CLONAL	3	TRUE	NA	0.586216794836788	4		218	968	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459514	50459514	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002232-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	144	347	0	ENST00000331340.3:c.803C>A	p.Ala268Glu	p.A268E	ENST00000331340	NM_006060.4	268	gCa/gAa	7/8	0.232301907569426	0	FACETS	0.326	0.298	0.355			1	INDETERMINATE	1	TRUE	0	0.586216794836788	0		347	623	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042476	16042476	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002232-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	339	519	0	ENST00000268712.3:c.1198C>A	p.Leu400Ile	p.L400I	ENST00000268712	NM_006311.3	400	Ctc/Atc	12/46	0.148532288225412	3	FACETS	1	0.994	1	0.677	0.641	0.714	INDETERMINATE	1	TRUE	1	0.586216794836788	3		519	1105	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856033	68856034	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0002232-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	315	546	0	ENST00000261769.5:c.1842dup	p.Ile615HisfsTer2	p.I615Hfs*2	ENST00000261769	NM_004360.3	614	atc/atCc	12/16	0.586216794836788	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.586216794836788	1		546	744	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177446	56177450	+	frameshift_variant	Frame_Shift_Del	DEL	AATTC	AATTC	GGTT	novel	NA	P-0002232-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	333	504	0	ENST00000399503.3:c.2419_2423delinsGGTT	p.Asn807GlyfsTer15	p.N807Gfs*15	ENST00000399503	NM_005921.1	807	AATTCc/GGTTc	14/20	NA	2	FACETS	0.975	0.922	1			1	INDETERMINATE	1	TRUE	NA	0.586216794836788	2		504	1165	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0002286-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	18	328	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.337	0.253	0.437	0.337	0.253	0.437	SUBCLONAL	1	TRUE	1	0.25	2		328	427	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0002286-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	16	255	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.267	0.196	0.352	0.267	0.196	0.352	SUBCLONAL	1	TRUE	1	0.25	2		255	480	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682399	52682400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002286-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	128	390	0	ENST00000394830.3:c.773dup	p.Asn258LysfsTer6	p.N258Kfs*6	ENST00000394830	NM_018313.4	258	aat/aaAt	8/30	0.297529231432857	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.25	1		390	882	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0002286-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	82	179	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	1	2	FACETS	0.978	0.862	1	0.978	0.862	1	CLONAL	1	TRUE	1	0.25	2		179	671	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442542	52442542	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1194652468	NA	P-0002286-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	75	390	2	ENST00000460680.1:c.203A>G	p.Asp68Gly	p.D68G	ENST00000460680	NM_004656.3	68	gAt/gGt	4/17	0.297529231432857	1	FACETS	0.969	0.85	1	0.969	0.85	1	CLONAL	1	TRUE	0	0.25	1		392	542	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197505	106197506	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0002286-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	105	566	0	ENST00000380013.4:c.5844dup	p.Val1949SerfsTer7	p.V1949Sfs*7	ENST00000380013	NM_001127208.2	1946	-/A	11/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.25	2		566	778	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0002321-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	358	485	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	0.766632606449276	2		485	876	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0002321-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	231	286	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.84	0.787	0.895	0.84	0.787	0.895	CLONAL	1	TRUE	1	0.766632606449276	2		286	717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002321-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	242	308	0	ENST00000269305.4:c.313G>T	p.Gly105Cys	p.G105C	ENST00000269305	NM_001126112.2	105	Ggc/Tgc	4/11	1	2	FACETS	0.977	0.919	1	0.977	0.919	1	CLONAL	1	TRUE	1	0.766632606449276	2		308	646	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719113	190719113	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002321-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	260	279	0	ENST00000441310.2:c.1115A>G	p.Lys372Arg	p.K372R	ENST00000441310	NM_000534.4	372	aAa/aGa	9/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.766632606449276	2		279	612	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070402	37070402	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002321-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	235	301	0	ENST00000231790.2:c.1537A>G	p.Ile513Val	p.I513V	ENST00000231790	NM_000249.3	513	Att/Gtt	13/19	1	2	FACETS	0.923	0.866	0.981	0.923	0.866	0.981	CLONAL	1	TRUE	1	0.766632606449276	2		301	664	SUCCESS
APC	324	MSKCC	GRCh37	5	112174119	112174119	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0002321-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	295	372	0	ENST00000257430.4:c.2828C>G	p.Ser943Ter	p.S943*	ENST00000257430	NM_000038.5	943	tCa/tGa	16/16	1	2	FACETS	0.905	0.855	0.956	0.905	0.855	0.956	CLONAL	1	TRUE	1	0.766632606449276	2		372	850	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593417	48593417	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002321-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	296	307	0	ENST00000342988.3:c.1168G>T	p.Glu390Ter	p.E390*	ENST00000342988	NM_005359.5	390	Gaa/Taa	10/12	0.766632606449276	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.766632606449276	1		307	470	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024023	31024023	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002321-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	287	386	0	ENST00000375687.4:c.3508T>A	p.Leu1170Ile	p.L1170I	ENST00000375687	NM_015338.5	1170	Tta/Ata	13/13	0.766632606449276	3	FACETS	0.978	0.92	1	0.489	0.46	0.519	CLONAL	1	TRUE	1	0.766632606449276	3		386	1059	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0002321-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	340	402	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.977	0.927	1	0.977	0.927	1	CLONAL	1	TRUE	1	0.766632606449276	2		402	908	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0002330-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	1046	420	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.908980506259259	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.929053066329066	3		420	1641	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0002330-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	830	672	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.929053066329066	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.929053066329066	2		672	889	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0002330-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	489	778	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.977	0.938	1	0.977	0.938	1	CLONAL	1	TRUE	1	0.929053066329066	2		778	1078	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554278	29554278	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199474777	NA	P-0002330-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	499	390	2	ENST00000356175.3:c.2294G>A	p.Arg765His	p.R765H	ENST00000356175	NM_000267.3	765	cGc/cAc	19/57	0.719303258653413	3	FACETS	1	0.989	1			1	CLONAL	1	TRUE	NA	0.929053066329066	3		392	1441	SUCCESS
APC	324	MSKCC	GRCh37	5	112175354	112175418	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTCAGGAGCGAAATCTCCCTCCAAAAGTGGTGCTCAGACACCCAAAAGTCCACCTGAACACTA	TCTTCAGGAGCGAAATCTCCCTCCAAAAGTGGTGCTCAGACACCCAAAAGTCCACCTGAACACTA	-	novel	NA	P-0002330-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	361	364	0	ENST00000257430.4:c.4064_4128del	p.Ser1355CysfsTer9	p.S1355Cfs*9	ENST00000257430	NM_000038.5	1355	TCTTCAGGAGCGAAATCTCCCTCCAAAAGTGGTGCTCAGACACCCAAAAGTCCACCTGAACACTAt/t	16/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.929053066329066	2		364	741	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030478	49030479	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1566234123	NA	P-0002330-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	339	340	0	ENST00000267163.4:c.1959dup	p.Val654SerfsTer14	p.V654Sfs*14	ENST00000267163	NM_000321.2	651	-/A	19/27	0.929053066329066	1	FACETS	0.89	0.862	0.917	0.89	0.862	0.917	CLONAL	1	TRUE	0	0.929053066329066	1		340	439	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0002332-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	547	406	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.574864239036649	4	FACETS	0.953	0.925	0.98	0.953	0.925	0.98	CLONAL	3	TRUE	1	0.914887387986827	4		406	801	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491351	2491351	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002332-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	876	336	1	ENST00000355716.4:c.394G>T	p.Gly132Trp	p.G132W	ENST00000355716	NM_003820.2	132	Ggg/Tgg	4/8	0.795837869478124	4	FACETS	1	0.996	1			1	CLONAL	4	TRUE	NA	0.914887387986827	4		337	910	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12647788	12647788	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1208112942	NA	P-0002332-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	531	377	0	ENST00000251849.4:c.592A>G	p.Asn198Asp	p.N198D	ENST00000251849	NM_002880.3	198	Aat/Gat	6/17	0.914887387986827	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.914887387986827	2		377	571	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619279	37619280	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0002332-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	286	212	0	ENST00000447079.4:c.956dup	p.Tyr319Ter	p.Y319*	ENST00000447079	NM_015083.1	319	tac/tAac	1/14	0.851182352357226	4	FACETS	0.906	0.858	0.954	0.906	0.858	0.954	CLONAL	2	TRUE	2	0.914887387986827	4		212	661	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0002339-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	273	365	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.163919835614685	3	FACETS	0.967	0.909	1	1	0.995	1	CLONAL	4	TRUE	1	0.163919835614685	3		365	932	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0002339-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	295	441	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.160569456737794	0	FACETS	1	0.952	1			1	CLONAL	4	TRUE	0	0.163919835614685	0		441	748	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0002339-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	205	433	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.160569456737794	0	FACETS	0.937	0.876	0.999			1	CLONAL	4	TRUE	0	0.163919835614685	0		436	558	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245542	16245542	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002339-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	171	335	0	ENST00000375759.3:c.1517T>G	p.Leu506Arg	p.L506R	ENST00000375759	NM_015001.2	506	cTc/cGc	7/15	1	2	FACETS	0.899	0.828	0.972	1	0.994	1	CLONAL	3	TRUE	1	0.163919835614685	2		335	774	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405045	405045	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377483798	NA	P-0002339-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	90	407	1	ENST00000380956.4:c.1127G>A	p.Arg376His	p.R376H	ENST00000380956	NM_001195286.1	376	cGc/cAc	8/9	0.130968941921775	3	FACETS	1	0.963	1			1	CLONAL	1	TRUE	NA	0.163919835614685	3		408	981	SUCCESS
AR	367	MSKCC	GRCh37	X	66766105	66766105	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002339-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	79	260	0	ENST00000374690.3:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000374690	NM_000044.3	373	Gga/Aga	1/8	0.163919835614685	1	FACETS	1	0.921	1	1	0.984	1	CLONAL	2	TRUE	0	0.163919835614685	1		260	420	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436071	56436072	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0002339-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	261	378	1	ENST00000407977.2:c.1065dup	p.Ala356CysfsTer87	p.A356Cfs*87	ENST00000407977		355	-/T	9/10	0.163919835614685	3	FACETS	1	0.981	1	1	0.996	1	CLONAL	5	TRUE	1	0.163919835614685	3		379	634	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0002361-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	232	441	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.471868320954695	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.527405866092193	2		441	435	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358353	91358353	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs752989757	NA	P-0002361-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	67	462	0	ENST00000355112.3:c.4098G>C	p.Lys1366Asn	p.K1366N	ENST00000355112	NM_000057.2	1366	aaG/aaC	22/22	0.178897724255263	3	FACETS	0.701	0.611	0.798	0.234	0.203	0.266	INDETERMINATE	1	TRUE	0	0.527405866092193	3		462	458	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134515	2134515	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002361-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	83	571	0	ENST00000219476.3:c.4292C>A	p.Ser1431Ter	p.S1431*	ENST00000219476	NM_000548.3	1431	tCg/tAg	34/42	0.173894702113981	4	FACETS	0.819	0.724	0.921	0.409	0.362	0.461	INDETERMINATE	1	TRUE	2	0.527405866092193	4		571	587	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132428	11132428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002361-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	40	633	0	ENST00000358026.2:c.2644G>A	p.Glu882Lys	p.E882K	ENST00000358026	NM_001128849.1	882	Gaa/Aaa	19/36	0.528015043191971	1	FACETS	0.232	0.193	0.276	0.232	0.193	0.276	SUBCLONAL	1	TRUE	0	0.527405866092193	1		633	481	SUCCESS
EED	8726	MSKCC	GRCh37	11	85979542	85979543	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGACATAC	novel	NA	P-0002361-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	166	362	1	ENST00000263360.6:c.907_914dup	p.His305GlnfsTer14	p.H305Qfs*14	ENST00000263360	NM_003797.3	302	aga/agAGACATACa	9/12	0.525710170461427	2	FACETS	1	0.986	1	0.645	0.597	0.694	CLONAL	1	TRUE	0	0.527405866092193	2		363	488	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190744	108190745	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0002361-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	213	409	0	ENST00000278616.4:c.6412dup	p.Arg2138LysfsTer8	p.R2138Kfs*8	ENST00000278616	NM_000051.3	2137	-/A	44/63	0.525710170461427	2	FACETS	0.92	0.866	0.974	0.92	0.866	0.974	CLONAL	2	TRUE	0	0.527405866092193	2		409	439	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0002399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	169	387	0	ENST00000346208.3:c.1220_1221insA	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcAg	6/6	1	2	FACETS	0.878	0.808	0.951	0.878	0.808	0.951	CLONAL	1	TRUE	1	0.475675233311541	2		387	809	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0002523-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	4388	322	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.889458028148613	20	FACETS	1	0.998	1			1	CLONAL	19	TRUE	NA	0.889458028148613	20		322	4647	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498400	89498400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002523-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	71	344	0	ENST00000336596.2:c.2372C>T	p.Thr791Ile	p.T791I	ENST00000336596	NM_005233.5	791	aCa/aTa	14/17	NA	2	FACETS	0.331	0.29	0.376			1	INDETERMINATE	1	TRUE	NA	0.889458028148613	2		344	482	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356145	66356145	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002523-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	491	419	0	ENST00000273854.3:c.1352G>T	p.Ser451Ile	p.S451I	ENST00000273854	NM_004439.5	451	aGc/aTc	5/18	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	2	TRUE	NA	0.889458028148613	2		419	526	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793911	89793911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002523-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	84	216	0	ENST00000336032.3:c.980C>T	p.Thr327Ile	p.T327I	ENST00000336032	NM_006813.2	327	aCt/aTt	2/2	NA	2	FACETS	0.415	0.368	0.465			1	INDETERMINATE	1	TRUE	NA	0.889458028148613	2		216	455	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392068	81392068	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002523-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	214	438	0	ENST00000222390.5:c.209G>T	p.Cys70Phe	p.C70F	ENST00000222390	NM_000601.4	70	tGt/tTt	2/18	0.274857017663853	3	FACETS	1	0.981	1	0.565	0.528	0.603	INDETERMINATE	1	TRUE	1	0.889458028148613	3		438	615	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934575	NA	P-0002523-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	360	295	0	ENST00000269305.4:c.733G>C	p.Gly245Arg	p.G245R	ENST00000269305	NM_001126112.2	245	Ggc/Cgc	7/11	0.859965229964048	2	FACETS	0.987	0.964	1	0.987	0.964	1	CLONAL	2	TRUE	0	0.889458028148613	2		295	410	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032587	47032587	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0002523-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	271	361	0	ENST00000377604.3:c.493A>T	p.Lys165Ter	p.K165*	ENST00000377604	NM_001204468.1	165	Aaa/Taa	5/24	0.629396267407773	1	FACETS	0.907	0.872	0.941	0.907	0.872	0.941	CLONAL	1	TRUE	0	0.889458028148613	1		361	373	SUCCESS
AR	367	MSKCC	GRCh37	X	66765177	66765177	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002523-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	66	179	0	ENST00000374690.3:c.189G>T	p.Gln63His	p.Q63H	ENST00000374690	NM_000044.3	63	caG/caT	1/8	0.719680818303772	1	FACETS	0.197	0.171	0.224	0.197	0.171	0.224	SUBCLONAL	1	TRUE	0	0.889458028148613	1		179	419	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589589	67589606	+	inframe_deletion	In_Frame_Del	DEL	AATATAACACTCAGTTTC	AATATAACACTCAGTTTC	-	novel	NA	P-0002523-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	235	354	0	ENST00000274335.5:c.1354_1371del	p.Tyr452_Gln457del	p.Y452_Q457del	ENST00000274335		451	gAATATAACACTCAGTTTCaa/gaa	10/15	0.272243493010268	5	FACETS	0.796	0.745	0.848	0.53	0.496	0.565	INDETERMINATE	2	TRUE	2	0.889458028148613	5		354	775	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974774	21974775	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCCA	novel	NA	P-0002523-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	120	154	0	ENST00000304494.5:c.47_52dup	p.Ala17_Thr18insMetAla	p.A17_T18insMA	ENST00000304494	NM_000077.4	18	acg/aTGGCCAcg	1/3	0.889458028148613	1	FACETS	0.797	0.744	0.848	0.797	0.744	0.848	SUBCLONAL	1	TRUE	0	0.889458028148613	1		154	188	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0002529-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	196	402	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.424318972641486	2		402	731	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	443491	443491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002529-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	169	335	0	ENST00000399788.2:c.1406C>T	p.Pro469Leu	p.P469L	ENST00000399788	NM_001042603.1	469	cCg/cTg	11/28	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.424318972641486	2		335	664	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849800	156849800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41358549	NA	P-0002529-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	161	287	2	ENST00000524377.1:c.2056C>T	p.Arg686Cys	p.R686C	ENST00000524377	NM_002529.3	686	Cgc/Tgc	16/17	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.424318972641486	2		289	575	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164914	106164914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771761785	NA	P-0002529-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	150	176	0	ENST00000380013.4:c.3782G>A	p.Arg1261His	p.R1261H	ENST00000380013	NM_001127208.2	1261	cGc/cAc	6/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.424318972641486	2		176	523	SUCCESS
APC	324	MSKCC	GRCh37	5	112137082	112137082	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0002529-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	130	252	0	ENST00000257430.4:c.834+2T>A		p.X278_splice	ENST00000257430	NM_000038.5	278			0.424318972641486	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.424318972641486	1		252	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064794618	NA	P-0002529-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	191	285	0	ENST00000269305.4:c.159G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgG/tgA	4/11	0.424318972641486	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.424318972641486	1		285	501	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416365	49416379	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTCATACCTGCTCT	GCTCATACCTGCTCT	-	novel	NA	P-0002529-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	120	221	0	ENST00000301067.7:c.16332_16338+8del		p.X5444_splice	ENST00000301067	NM_003482.3	5444		51/54	1	2	FACETS	0.957	0.867	1	0.957	0.867	1	CLONAL	1	TRUE	1	0.424318972641486	2		221	591	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119730	70119731	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0002529-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	327	404	0	ENST00000245479.2:c.734_735dup	p.Gln246CysfsTer8	p.Q246Cfs*8	ENST00000245479	NM_000346.3	244	-/GT	3/3	0.380323240962126	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.424318972641486	3		404	890	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0002562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	225	328	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.268656154132529	1	FACETS	0.761	0.716	0.806	0.761	0.716	0.806	INDETERMINATE	1	TRUE	0	0.737703926327932	1		328	506	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519925	NA	P-0002562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	433	387	0	ENST00000263967.3:c.1357G>C	p.Glu453Gln	p.E453Q	ENST00000263967	NM_006218.2	453	Gaa/Caa	8/21	0.268656154132529	1	FACETS	0.731	0.7	0.763	0.731	0.7	0.763	INDETERMINATE	1	TRUE	0	0.737703926327932	1		387	1013	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161221	56161221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781300314	NA	P-0002562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	553	382	0	ENST00000399503.3:c.1090C>T	p.Arg364Trp	p.R364W	ENST00000399503	NM_005921.1	364	Cgg/Tgg	5/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.737703926327932	2		382	1477	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879670	151879670	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	154	129	0	ENST00000262189.6:c.5275C>T	p.Gln1759Ter	p.Q1759*	ENST00000262189	NM_170606.2	1759	Cag/Tag	36/59	1	2	FACETS	0.932	0.861	1	0.932	0.861	1	CLONAL	1	TRUE	1	0.737703926327932	2		129	448	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256794	16256795	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0002562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	438	316	0	ENST00000375759.3:c.4060_4061del	p.Ser1354PhefsTer7	p.S1354Ffs*7	ENST00000375759	NM_015001.2	1353	gtGAgt/gtgt	11/15	0.737703926327932	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.737703926327932	1		316	698	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971199	21971200	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	ATCA	novel	NA	P-0002562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	103	92	0	ENST00000579755.1:c.198_201dup	p.Asp68Ter	p.D68*	ENST00000579755		67	-/TGAT	2/3	0.737703926327932	1	FACETS	0.89	0.818	0.962	0.89	0.818	0.962	CLONAL	1	TRUE	0	0.737703926327932	1		92	198	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788618	3788625	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGGCAA	GGAGGCAA	-	novel	NA	P-0002562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1210	660	499	0	ENST00000262367.5:c.4329_4336del	p.Cys1444HisfsTer6	p.C1444Hfs*6	ENST00000262367	NM_004380.2	1443	cgTTGCCTCCgc/cggc	26/31	0.307583129858651	3	FACETS	1	0.996	1	0.655	0.63	0.68	INDETERMINATE	1	TRUE	1	0.737703926327932	3		499	1870	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717655	89717655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs905615413	NA	P-0002562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	383	316	1	ENST00000371953.3:c.680C>T	p.Ser227Phe	p.S227F	ENST00000371953	NM_000314.4	227	tCc/tTc	7/9	0.168367326749701	1	FACETS	0.674	0.642	0.706	0.674	0.642	0.706	INDETERMINATE	1	TRUE	0	0.737703926327932	1		317	973	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165732	185165746	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TATGGTGAGTGGCGC	TATGGTGAGTGGCGC	-	novel	NA	P-0002562-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	48	241	0	ENST00000265026.3:c.1007_1010+11del		p.X336_splice	ENST00000265026	NM_004721.4	336		5/14	0.268656154132529	1	FACETS	0.126	0.106	0.148	0.126	0.106	0.148	INDETERMINATE	1	TRUE	0	0.737703926327932	1		241	653	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0002609-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	128	365	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.167808300525567	2	FACETS	1	0.951	1	1	0.988	1	CLONAL	3	TRUE	0	0.167808300525567	2		365	478	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0002609-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	55	286	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.141256552159975	3	FACETS	0.965	0.829	1	0.965	0.829	1	CLONAL	2	TRUE	1	0.167808300525567	3		286	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0002609-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	110	375	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	NA	2	FACETS	0.947	0.86	1			1	INDETERMINATE	4	TRUE	NA	0.167808300525567	2		375	346	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162742002	162742002	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002609-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	67	529	0	ENST00000367921.3:c.1693T>A	p.Phe565Ile	p.F565I	ENST00000367921	NM_006182.2	565	Ttc/Atc	13/18	1	2	FACETS	0.891	0.777	1	1	0.978	1	CLONAL	2	TRUE	1	0.167808300525567	2		529	448	SUCCESS
FH	2271	MSKCC	GRCh37	1	241665743	241665743	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002609-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	33	624	0	ENST00000366560.3:c.1236G>A	p.Met412Ile	p.M412I	ENST00000366560	NM_000143.3	412	atG/atA	8/10	1	2	FACETS	0.88	0.716	1	0.88	0.716	1	CLONAL	1	TRUE	1	0.167808300525567	2		624	447	SUCCESS
APC	324	MSKCC	GRCh37	5	112174825	112174825	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002609-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	81	532	0	ENST00000257430.4:c.3535del	p.Tyr1179IlefsTer3	p.Y1179Ifs*3	ENST00000257430	NM_000038.5	1178	gaT/ga	16/16	0.141256552159975	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.167808300525567	3		532	448	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0002622-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	109	201	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.243063534580904	1	FACETS	0.811	0.733	0.891	1	0.986	1	CLONAL	2	TRUE	0	0.28	1		201	413	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917707	151917707	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0002622-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	15	115	0	ENST00000262189.6:c.3613A>T	p.Lys1205Ter	p.K1205*	ENST00000262189	NM_170606.2	1205	Aaa/Taa	23/59	1	2	FACETS	0.661	0.486	0.87	0.661	0.486	0.87	SUBCLONAL	1	TRUE	1	0.28	2		115	162	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070594	67070594	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002622-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	86	490	0	ENST00000412916.2:c.218G>A	p.Trp73Ter	p.W73*	ENST00000412916		73	tGg/tAg	3/6	0.301448901409538	1	FACETS	0.807	0.714	0.906	0.807	0.714	0.906	CLONAL	1	TRUE	0	0.28	1		490	655	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654689	29654690	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0002622-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	82	387	0	ENST00000356175.3:c.5380dup	p.Gln1794ProfsTer4	p.Q1794Pfs*4	ENST00000356175	NM_000267.3	1793	cac/caCc	37/57	0.15830895193532	0	FACETS	0.575	0.506	0.648			1	INDETERMINATE	1	TRUE	0	0.28	0		387	734	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0002630-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	166	363	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.101239640004114	5	FACETS	1	0.927	1			1	INDETERMINATE	3	TRUE	NA	0.241971969075264	5		363	620	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161270	56161270	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002630-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	192	393	0	ENST00000399503.3:c.1139T>C	p.Leu380Ser	p.L380S	ENST00000399503	NM_005921.1	380	tTa/tCa	5/20	0.16870051562643	4	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	2	0.241971969075264	4		393	949	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637723	176637723	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1310684026	NA	P-0002630-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	84	371	0	ENST00000439151.2:c.2323C>G	p.Gln775Glu	p.Q775E	ENST00000439151	NM_022455.4	775	Caa/Gaa	5/23	0.16870051562643	4	FACETS	1	0.909	1	0.518	0.456	0.583	CLONAL	1	TRUE	2	0.241971969075264	4		371	833	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41001291	41001291	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002630-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	93	383	0	ENST00000267868.3:c.412C>G	p.His138Asp	p.H138D	ENST00000267868	NM_002875.4	138	Cat/Gat	5/10	0.101087839838091	4	FACETS	1	0.942	1	0.547	0.486	0.613	INDETERMINATE	1	TRUE	2	0.241971969075264	4		383	872	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842658	68842659	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0002630-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	229	395	0	ENST00000261769.5:c.595dup	p.Thr199AsnfsTer10	p.T199Nfs*10	ENST00000261769	NM_004360.3	198	-/A	5/16	0.241971969075264	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.241971969075264	2		395	764	SUCCESS
APC	324	MSKCC	GRCh37	5	112175246	112175246	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1057517558	NA	P-0002728-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	99	487	0	ENST00000257430.4:c.3956del	p.Pro1319LeufsTer2	p.P1319Lfs*2	ENST00000257430	NM_000038.5	1319	Cct/ct	16/16	0.13662933613133	1	FACETS	0.642	0.574	0.713	0.642	0.574	0.713	INDETERMINATE	1	TRUE	0	0.430151187815912	1		487	563	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0002728-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	125	668	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.13662933613133	1	FACETS	0.661	0.599	0.726	0.661	0.599	0.726	INDETERMINATE	1	TRUE	0	0.430151187815912	1		668	690	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0002728-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	197	697	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.275646082336516	1	FACETS	0.898	0.833	0.965	0.898	0.833	0.965	CLONAL	1	TRUE	0	0.430151187815912	1		697	801	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0002728-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	53	509	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.184260410109694	0	FACETS	0.315	0.269	0.365			1	INDETERMINATE	1	TRUE	0	0.430151187815912	0		509	446	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579419	7579420	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs587783062	NA	P-0002728-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	52	483	0	ENST00000269305.4:c.267dup	p.Ser90LeufsTer59	p.S90Lfs*59	ENST00000269305	NM_001126112.2	89	-/C	4/11	0.184260410109694	0	FACETS	0.35	0.298	0.406			1	INDETERMINATE	1	TRUE	0	0.430151187815912	0		483	394	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076949	41076949	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002728-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	165	647	0	ENST00000373198.4:c.1471G>T	p.Glu491Ter	p.E491*	ENST00000373198	NM_133170.3	491	Gaa/Taa	9/32	0.430151187815912	3	FACETS	1	0.975	1	0.576	0.529	0.625	CLONAL	1	TRUE	1	0.430151187815912	3		647	809	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119814	70119815	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0002728-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	173	655	0	ENST00000245479.2:c.818_819dup	p.Asp274TrpfsTer6	p.D274Wfs*6	ENST00000245479	NM_000346.3	272	-/GT	3/3	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.430151187815912	2		655	605	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0002740-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	103	245	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	1	2	FACETS	0.968	0.873	1	1	0.988	1	CLONAL	2	TRUE	1	0.27860757452217	2		245	382	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11204749	11204749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199612643	NA	P-0002740-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	53	690	0	ENST00000361445.4:c.4828G>A	p.Glu1610Lys	p.E1610K	ENST00000361445	NM_004958.3	1610	Gag/Aag	34/58	1	2	FACETS	0.73	0.623	0.848	0.73	0.623	0.848	SUBCLONAL	1	TRUE	1	0.27860757452217	2		690	521	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109949	115109950	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0002740-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	39	405	0	ENST00000257566.3:c.1927_1928dup	p.Ser644ThrfsTer246	p.S644Tfs*246	ENST00000257566	NM_016569.3	643	tac/taTAc	8/8	1	2	FACETS	0.804	0.668	0.955	0.804	0.668	0.955	CLONAL	1	TRUE	1	0.27860757452217	2		405	348	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90627545	90627545	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002740-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	109	646	0	ENST00000330062.3:c.1312del	p.Leu438SerfsTer30	p.L438Sfs*30	ENST00000330062	NM_002168.2	438	Ctc/tc	11/11	1	2	FACETS	0.827	0.747	0.911	1	0.986	1	CLONAL	2	TRUE	1	0.27860757452217	2		646	473	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555667	21555683	+	frameshift_variant	Frame_Shift_Del	DEL	CACCTCTGGTGCTGCTT	CACCTCTGGTGCTGCTT	-	novel	NA	P-0002864-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	118	510	0	ENST00000382592.4:c.2587_2603del	p.Lys863ProfsTer27	p.K863Pfs*27	ENST00000382592	NM_014572.2	863	AAGCAGCACCAGAGGTGc/c	6/8	0.273303032612986	1	FACETS	0.525	0.473	0.581	0.525	0.473	0.581	SUBCLONAL	1	TRUE	0	0.381152728120266	1		510	954	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050681	30050682	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002864-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	82	415	0	ENST00000338641.4:c.488dup	p.Leu163PhefsTer40	p.L163Ffs*40	ENST00000338641	NM_000268.3	161	-/T	5/16	0.34717261084985	1	FACETS	0.492	0.433	0.555	0.492	0.433	0.555	SUBCLONAL	1	TRUE	0	0.381152728120266	1		415	708	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965526	25965527	+	missense_variant	Missense_Mutation	DNP	GC	GC	CT	novel	NA	P-0002864-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	159	537	0	ENST00000435504.4:c.3679_3680delinsAG	p.Ala1227Ser	p.A1227S	ENST00000435504		1227	GCt/AGt	13/13	1	2	FACETS	0.83	0.76	0.903	0.83	0.76	0.903	CLONAL	1	TRUE	1	0.381152728120266	2		537	1005	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0002874-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	431	348	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.98	0.934	1	0.98	0.934	1	CLONAL	1	TRUE	1	0.676098739933146	2		348	1301	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0002874-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	303	251	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.676098739933146	1	FACETS	0.926	0.88	0.972	0.926	0.88	0.972	CLONAL	1	TRUE	0	0.676098739933146	1		251	641	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597401	10597401	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002874-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	452	326	0	ENST00000171111.5:c.1802G>T	p.Arg601Leu	p.R601L	ENST00000171111	NM_203500.1	601	cGg/cTg	6/6	0.676098739933146	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.676098739933146	1		326	869	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288910	212288910	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002874-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	276	248	0	ENST00000342788.4:c.2836A>G	p.Thr946Ala	p.T946A	ENST00000342788	NM_005235.2	946	Act/Gct	23/28	1	2	FACETS	0.869	0.818	0.922	0.869	0.818	0.922	CLONAL	1	TRUE	1	0.676098739933146	2		248	939	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71050182	71050182	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002874-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	336	262	0	ENST00000318789.4:c.1003G>C	p.Asp335His	p.D335H	ENST00000318789	NM_032682.5	335	Gat/Cat	13/21	0.676098739933146	1	FACETS	0.933	0.889	0.977	0.933	0.889	0.977	CLONAL	1	TRUE	0	0.676098739933146	1		262	705	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720972	119720972	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002874-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	550	353	0	ENST00000316626.5:c.203G>T	p.Gly68Val	p.G68V	ENST00000316626		68	gGt/gTt	2/12	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.676098739933146	2		353	1475	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993602	90993602	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0002874-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	317	242	0	ENST00000265433.3:c.320+1G>T		p.X107_splice	ENST00000265433	NM_002485.4	107			0.607927110493202	3	FACETS	0.905	0.853	0.959	0.453	0.426	0.48	CLONAL	1	TRUE	1	0.676098739933146	3		242	1386	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741834	17741834	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs763127710	NA	P-0002874-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	129	105	0	ENST00000250003.3:c.505G>T	p.Ala169Ser	p.A169S	ENST00000250003	NM_002478.4	169	Gcc/Tcc	1/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.676098739933146	2		105	316	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491436	18491436	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002874-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	358	276	0	ENST00000266497.5:c.1349C>A	p.Thr450Lys	p.T450K	ENST00000266497		450	aCa/aAa	8/31	1	2	FACETS	0.867	0.822	0.914	0.867	0.822	0.914	CLONAL	1	TRUE	1	0.676098739933146	2		276	1221	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420207	88420207	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002874-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	363	340	0	ENST00000360948.2:c.2479T>A	p.Leu827Met	p.L827M	ENST00000360948	NM_001012338.2	827	Ttg/Atg	19/19	1	2	FACETS	0.974	0.925	1	0.974	0.925	1	CLONAL	1	TRUE	1	0.676098739933146	2		340	1102	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99460084	99460084	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002874-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	284	252	0	ENST00000268035.6:c.2180A>C	p.His727Pro	p.H727P	ENST00000268035	NM_000875.3	727	cAc/cCc	10/21	1	2	FACETS	0.917	0.864	0.971	0.917	0.864	0.971	CLONAL	1	TRUE	1	0.676098739933146	2		252	916	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713333	30713334	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002874-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	288	240	0	ENST00000295754.5:c.659dup	p.Glu221GlyfsTer3	p.E221Gfs*3	ENST00000295754	NM_003242.5	220	ctg/cTtg	4/7	0.676098739933146	1	FACETS	0.902	0.856	0.949	0.902	0.856	0.949	CLONAL	1	TRUE	0	0.676098739933146	1		240	625	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508533	106508533	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002874-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	152	104	0	ENST00000359195.3:c.527del	p.Thr176SerfsTer6	p.T176Sfs*6	ENST00000359195	NM_002649.2	176	aCg/ag	2/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.676098739933146	2		104	428	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0002907-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	1825	420	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.629699616034726	12	FACETS	1	0.997	1			1	CLONAL	10	TRUE	NA	0.629699616034726	12		420	2328	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974769	21974770	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCCGT	rs1563892769	NA	P-0002907-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	61	215	0	ENST00000304494.5:c.52_57dup	p.Thr18_Ala19dup	p.T18_A19dup	ENST00000304494	NM_000077.4	18	-/ACGGCC	1/3	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.629699616034726	2		215	171	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551772	150551772	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002907-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	49	64	0	ENST00000369026.2:c.235C>G	p.Pro79Ala	p.P79A	ENST00000369026	NM_021960.4	79	Ccg/Gcg	1/3	0.231929413744568	5	FACETS	0.834	0.727	0.944			1	INDETERMINATE	3	TRUE	NA	0.629699616034726	5		64	121	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412233	139412233	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs753964476	NA	P-0002907-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	90	437	0	ENST00000277541.6:c.1412T>C	p.Ile471Thr	p.I471T	ENST00000277541	NM_017617.3	471	aTt/aCt	8/34	0.559304085679803	3	FACETS	0.815	0.727	0.909	0.408	0.363	0.455	CLONAL	1	TRUE	1	0.629699616034726	3		437	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576872	7576872	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002907-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	265	380	0	ENST00000269305.4:c.974del	p.Gly325GlufsTer20	p.G325Efs*20	ENST00000269305	NM_001126112.2	325	gGa/ga	9/11	0.533888665268749	3	FACETS	1	0.993	1	0.825	0.786	0.864	CLONAL	2	TRUE	0	0.629699616034726	3		380	447	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183866	10183866	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs869025633	NA	P-0002908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	18	220	0	ENST00000256474.2:c.335A>G	p.Tyr112Cys	p.Y112C	ENST00000256474	NM_000551.3	112	tAc/tGc	1/3	0.529981554832514	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	2	TRUE	0	0.529981554832514	2		220	30	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197368	106197369	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0002908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	26	452	0	ENST00000380013.4:c.5703_5704del	p.Phe1901LeufsTer4	p.F1901Lfs*4	ENST00000380013	NM_001127208.2	1901	TTt/t	11/11	0.529981554832514	4	FACETS	1	0.82	1	1	0.82	1	CLONAL	2	TRUE	2	0.529981554832514	4		452	75	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577329	64577330	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	rs386134253	NA	P-0002908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	55	335	0	ENST00000312049.6:c.252_253insTT	p.Ile85LeufsTer35	p.I85Lfs*35	ENST00000312049	NM_130799.2	84	-/TT	2/10	0.481403657216079	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	3	TRUE	0	0.529981554832514	3		335	78	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829718	76829718	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	32	264	0	ENST00000373344.5:c.6323del	p.Val2108GlyfsTer15	p.V2108Gfs*15	ENST00000373344	NM_000489.3	2108	gTg/gg	28/35	0.529981554832514	2	FACETS	1	0.938	1			1	CLONAL	2	TRUE	NA	0.529981554832514	2		264	52	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0002911-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	77	201	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.405287146691207	4	FACETS	0.929	0.82	1			1	CLONAL	1	TRUE	NA	0.636697004381118	4		201	426	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469179	25469179	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0002911-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	151	574	0	ENST00000264709.3:c.1280-1G>A		p.X427_splice	ENST00000264709	NM_175629.2	427			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.636697004381118	2		574	426	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984951	55984951	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002911-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	119	672	0	ENST00000263923.4:c.178G>C	p.Asp60His	p.D60H	ENST00000263923	NM_002253.2	60	Gac/Cac	3/30	1	2	FACETS	0.829	0.753	0.908	0.829	0.753	0.908	CLONAL	1	TRUE	1	0.636697004381118	2		672	451	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628667	187628667	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002911-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	122	604	0	ENST00000441802.2:c.2315G>T	p.Gly772Val	p.G772V	ENST00000441802	NM_005245.3	772	gGa/gTa	2/27	1	2	FACETS	0.84	0.765	0.919	0.84	0.765	0.919	CLONAL	1	TRUE	1	0.636697004381118	2		604	456	SUCCESS
APC	324	MSKCC	GRCh37	5	112176893	112176893	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002911-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	162	672	0	ENST00000257430.4:c.5602G>C	p.Asp1868His	p.D1868H	ENST00000257430	NM_000038.5	1868	Gat/Cat	16/16	1	2	FACETS	0.996	0.92	1	0.996	0.92	1	CLONAL	1	TRUE	1	0.636697004381118	2		672	511	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293050	91293050	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002911-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	131	545	0	ENST00000355112.3:c.552G>C	p.Gln184His	p.Q184H	ENST00000355112	NM_000057.2	184	caG/caC	3/22	NA	2	FACETS	0.933	0.854	1			1	INDETERMINATE	1	TRUE	NA	0.636697004381118	2		545	441	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041626	14041626	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002911-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	122	759	1	ENST00000311895.7:c.2173G>A	p.Glu725Lys	p.E725K	ENST00000311895	NM_005236.2	725	Gag/Aag	11/11	1	2	FACETS	0.741	0.673	0.812	0.741	0.673	0.812	SUBCLONAL	1	TRUE	1	0.636697004381118	2		760	517	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849586	68849586	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002911-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	165	766	0	ENST00000261769.5:c.1489G>T	p.Glu497Ter	p.E497*	ENST00000261769	NM_004360.3	497	Gag/Tag	10/16	0.636697004381118	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.636697004381118	1		766	328	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604701	48604701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555687572	NA	P-0002911-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	143	616	0	ENST00000342988.3:c.1523G>A	p.Gly508Asp	p.G508D	ENST00000342988	NM_005359.5	508	gGc/gAc	12/12	0.581987567956922	1	FACETS	0.963	0.892	1	0.963	0.892	1	CLONAL	1	TRUE	0	0.636697004381118	1		616	318	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604799	48604799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002911-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	35	532	0	ENST00000342988.3:c.1621C>T	p.His541Tyr	p.H541Y	ENST00000342988	NM_005359.5	541	Cat/Tat	12/12	0.581987567956922	1	FACETS	0.222	0.182	0.266	0.222	0.182	0.266	SUBCLONAL	1	TRUE	0	0.636697004381118	1		532	338	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10267111	10267111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002911-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	125	613	0	ENST00000340748.4:c.1307C>T	p.Ser436Phe	p.S436F	ENST00000340748		436	tCt/tTt	17/40	1	2	FACETS	0.88	0.803	0.961	0.88	0.803	0.961	CLONAL	1	TRUE	1	0.636697004381118	2		613	446	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123505218	123505218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002911-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	125	561	0	ENST00000371139.4:c.364G>A	p.Asp122Asn	p.D122N	ENST00000371139	NM_001114937.2	122	Gat/Aat	4/4	0.136133974589564	0	FACETS	0.287	0.261	0.314			1	INDETERMINATE	1	TRUE	0	0.636697004381118	0		561	497	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255092	16255093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0002911-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	113	493	0	ENST00000375759.3:c.2363dup	p.Asn788LysfsTer2	p.N788Kfs*2	ENST00000375759	NM_015001.2	786	aca/acAa	11/15	1	2	FACETS	0.805	0.729	0.884	0.805	0.729	0.884	CLONAL	1	TRUE	1	0.636697004381118	2		493	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0002960-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	117	455	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.212883556802222	1	FACETS	0.617	0.557	0.681	0.617	0.557	0.681	INDETERMINATE	1	TRUE	0	0.397129834492339	1		457	765	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71008412	71008412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368167189	NA	P-0002960-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	108	570	0	ENST00000318789.4:c.2020G>A	p.Glu674Lys	p.E674K	ENST00000318789	NM_032682.5	674	Gag/Aag	21/21	1	2	FACETS	0.617	0.553	0.685	0.617	0.553	0.685	SUBCLONAL	1	TRUE	1	0.397129834492339	2		570	881	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664942	138664942	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002960-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	21	110	0	ENST00000330315.3:c.623A>G	p.Gln208Arg	p.Q208R	ENST00000330315	NM_023067.3	208	cAg/cGg	1/1	1	2	FACETS	0.433	0.334	0.548	0.433	0.334	0.548	SUBCLONAL	1	TRUE	1	0.397129834492339	2		110	244	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386537	81386537	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002960-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	42	654	0	ENST00000222390.5:c.450G>T	p.Gln150His	p.Q150H	ENST00000222390	NM_000601.4	150	caG/caT	4/18	1	2	FACETS	0.529	0.442	0.625	0.529	0.442	0.625	SUBCLONAL	1	TRUE	1	0.397129834492339	2		654	400	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098894	178098895	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002960-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	67	578	0	ENST00000397062.3:c.150dup	p.Gln51ThrfsTer5	p.Q51Tfs*5	ENST00000397062	NM_006164.4	50	-/A	2/5	NA	2	FACETS	0.581	0.505	0.663			1	INDETERMINATE	1	TRUE	NA	0.397129834492339	2		578	581	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436028	56436028	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002960-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	69	267	0	ENST00000407977.2:c.1109del	p.Pro370HisfsTer49	p.P370Hfs*49	ENST00000407977		370	cCa/ca	9/10	0.212883556802222	1	FACETS	0.543	0.473	0.618	0.543	0.473	0.618	INDETERMINATE	1	TRUE	0	0.397129834492339	1		267	513	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586450	189586451	+	missense_variant	Missense_Mutation	DNP	CA	CA	AT	novel	NA	P-0002964-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	166	232	0	ENST00000264731.3:c.1074_1075delinsAT	p.Ser358_Ile359delinsArgPhe	p.S358_I359delinsRF	ENST00000264731	NM_003722.4	358	agCAtc/agATtc	8/14	0.315874428237836	3	FACETS	1	0.98	1	0.588	0.543	0.635	INDETERMINATE	1	TRUE	1	0.668708905414296	3		232	563	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556696	41556696	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002964-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	165	266	0	ENST00000263253.7:c.3641C>A	p.Ser1214Tyr	p.S1214Y	ENST00000263253	NM_001429.3	1214	tCt/tAt	20/31	0.668708905414296	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.668708905414296	1		266	278	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099403	157099429	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAGCAGCAACAG	CAGCAGCAGCAGCAGCAGCAGCAACAG	-	rs910569810	NA	P-0002964-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	69	84	0	ENST00000346085.5:c.360_386del	p.Gln123_Gln131del	p.Q123_Q131del	ENST00000346085	NM_020732.3	114	CAGCAGCAGCAGCAGCAGCAGCAACAG/-	1/20	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.668708905414296	2		84	202	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069355	30069356	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0002964-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	231	268	0	ENST00000338641.4:c.1221_1222dup	p.Glu408GlyfsTer19	p.E408Gfs*19	ENST00000338641	NM_000268.3	407	cag/caGGg	12/16	0.668708905414296	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.668708905414296	1		268	452	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929387	44929393	+	frameshift_variant	Frame_Shift_Del	DEL	TCCAAAA	TCCAAAA	-	novel	NA	P-0002964-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	218	208	0	ENST00000377967.4:c.2491_2497del	p.Lys831LeufsTer34	p.K831Lfs*34	ENST00000377967	NM_021140.2	829	tcTCCAAAA/tc	17/29	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.668708905414296	1		208	305	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	127	124	0	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	0.945	0.864	1	0.945	0.864	1	CLONAL	1	TRUE	1	0.678969311493277	2		124	396	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	259	498	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.929	0.873	0.987	0.929	0.873	0.987	CLONAL	1	TRUE	1	0.678969311493277	2		498	821	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	609	240	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.98	0.952	1	1	0.998	1	CLONAL	2	TRUE	1	0.678969311493277	2		240	915	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	114	182	0	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	1	2	FACETS	0.735	0.666	0.807	0.735	0.666	0.807	SUBCLONAL	1	TRUE	1	0.678969311493277	2		182	457	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	391	243	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.958	0.924	0.992	1	0.997	1	CLONAL	2	TRUE	1	0.678969311493277	2		244	601	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	291	340	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.678969311493277	2		340	852	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749500	41749500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	97	271	0	ENST00000226382.2:c.295C>T	p.Arg99Trp	p.R99W	ENST00000226382	NM_003924.3	99	Cgg/Tgg	2/3	1	2	FACETS	0.388	0.345	0.433	0.388	0.345	0.433	SUBCLONAL	1	TRUE	1	0.678969311493277	2		271	737	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056236	27056236	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750719742	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	68	236	0	ENST00000324856.7:c.1232C>T	p.Pro411Leu	p.P411L	ENST00000324856	NM_006015.4	411	cCg/cTg	2/20	1	2	FACETS	0.24	0.208	0.274	0.24	0.208	0.274	SUBCLONAL	1	TRUE	1	0.678969311493277	2		236	836	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845390	156845390	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1355	349	289	0	ENST00000524377.1:c.1433C>A	p.Pro478His	p.P478H	ENST00000524377	NM_002529.3	478	cCc/cAc	12/17	0.678969311493277	4	FACETS	1	0.955	1	0.338	0.318	0.357	CLONAL	1	TRUE	1	0.678969311493277	4		289	1704	SUCCESS
FH	2271	MSKCC	GRCh37	1	241676953	241676953	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1338	291	362	0	ENST00000366560.3:c.328T>C	p.Tyr110His	p.Y110H	ENST00000366560	NM_000143.3	110	Tat/Cat	3/10	0.678969311493277	4	FACETS	0.883	0.829	0.94	0.294	0.276	0.314	CLONAL	1	TRUE	1	0.678969311493277	4		362	1629	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543689	29543689	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	318	315	0	ENST00000389048.3:c.1474G>T	p.Gly492Cys	p.G492C	ENST00000389048	NM_004304.4	492	Ggc/Tgc	7/29	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.678969311493277	2		315	907	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661393	227661393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751466820	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	240	269	0	ENST00000305123.5:c.2062G>A	p.Ala688Thr	p.A688T	ENST00000305123	NM_005544.2	688	Gcc/Acc	1/2	1	2	FACETS	0.934	0.875	0.994	0.934	0.875	0.994	CLONAL	1	TRUE	1	0.678969311493277	2		269	757	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	28	132	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	0.348	0.279	0.426	0.348	0.279	0.426	SUBCLONAL	1	TRUE	1	0.678969311493277	2		132	237	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430950	181430950	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	338	337	0	ENST00000325404.1:c.802G>A	p.Gly268Arg	p.G268R	ENST00000325404	NM_003106.3	268	Ggg/Agg	1/1	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.678969311493277	2		337	886	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803676	1803676	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	154	330	0	ENST00000260795.2:c.854T>C	p.Ile285Thr	p.I285T	ENST00000260795		285	aTc/aCc	6/17	1	2	FACETS	0.569	0.521	0.619	0.569	0.521	0.619	SUBCLONAL	1	TRUE	1	0.678969311493277	2		330	797	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649012	86649012	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	247	253	0	ENST00000274376.6:c.1292T>C	p.Ile431Thr	p.I431T	ENST00000274376	NM_002890.2	431	aTt/aCt	9/25	1	2	FACETS	0.921	0.864	0.979	0.921	0.864	0.979	CLONAL	1	TRUE	1	0.678969311493277	2		253	790	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056305	26056305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1256677846	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	306	313	0	ENST00000343677.2:c.352C>T	p.Pro118Ser	p.P118S	ENST00000343677	NM_005319.3	118	Ccc/Tcc	1/1	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.678969311493277	2		313	869	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30676047	30676047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529970009	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	293	272	0	ENST00000376406.3:c.2309C>T	p.Thr770Met	p.T770M	ENST00000376406	NM_014641.2	770	aCg/aTg	8/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.678969311493277	2		272	793	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382214	152382214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	307	221	1	ENST00000206249.3:c.1324G>A	p.Gly442Arg	p.G442R	ENST00000206249	NM_000125.3	442	Gga/Aga	6/8	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.678969311493277	2		222	886	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90971013	90971013	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	479	351	0	ENST00000265433.3:c.1064G>T	p.Ser355Ile	p.S355I	ENST00000265433	NM_002485.4	355	aGc/aTc	9/16	0.401979994662415	3	FACETS	0.832	0.797	0.866	0.832	0.797	0.866	INDETERMINATE	2	TRUE	1	0.678969311493277	3		351	1136	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741917	145741917	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	127	217	0	ENST00000428558.2:c.586A>G	p.Ser196Gly	p.S196G	ENST00000428558	NM_004260.3	196	Agt/Ggt	5/22	0.401979994662415	3	FACETS	0.55	0.498	0.605	0.275	0.249	0.303	INDETERMINATE	1	TRUE	1	0.678969311493277	3		217	911	SUCCESS
RET	5979	MSKCC	GRCh37	10	43598042	43598042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	267	292	0	ENST00000355710.3:c.590G>A	p.Cys197Tyr	p.C197Y	ENST00000355710	NM_020975.4	197	tGc/tAc	3/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.678969311493277	2		292	715	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717730	89717730	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121909239	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	237	233	0	ENST00000371953.3:c.755A>T	p.Asp252Val	p.D252V	ENST00000371953	NM_000314.4	252	gAt/gTt	7/9	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.678969311493277	2		233	674	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310914	123310914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	364	346	0	ENST00000358487.5:c.514G>A	p.Ala172Thr	p.A172T	ENST00000358487	NM_000141.4	172	Gcc/Acc	5/18	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.678969311493277	2		346	979	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416685	416685	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	389	272	0	ENST00000399788.2:c.3865C>T	p.Arg1289Ter	p.R1289*	ENST00000399788	NM_001042603.1	1289	Cga/Tga	23/28	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.678969311493277	2		272	1012	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274114	10274114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	297	321	1	ENST00000330684.3:c.155G>A	p.Arg52Gln	p.R52Q	ENST00000330684	NM_001134407.1	52	cGa/cAa	2/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.678969311493277	2		322	834	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974847	15974847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	334	410	0	ENST00000268712.3:c.4028C>T	p.Thr1343Ile	p.T1343I	ENST00000268712	NM_006311.3	1343	aCc/aTc	30/46	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.678969311493277	2		410	977	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271546	15271546	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	335	360	0	ENST00000263388.2:c.6893G>T	p.Ser2298Ile	p.S2298I	ENST00000263388	NM_000435.2	2298	aGc/aTc	33/33	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.678969311493277	2		360	951	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551013	41551013	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	139	299	0	ENST00000263253.7:c.3157G>T	p.Glu1053Ter	p.E1053*	ENST00000263253	NM_001429.3	1053	Gaa/Taa	17/31	1	2	FACETS	0.455	0.414	0.498	0.455	0.414	0.498	SUBCLONAL	1	TRUE	1	0.678969311493277	2		299	900	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222716	53222716	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	318	342	0	ENST00000375401.3:c.4220A>G	p.Asp1407Gly	p.D1407G	ENST00000375401	NM_004187.3	1407	gAc/gGc	25/26	0.379913186070203	3	FACETS	1	0.987	1	0.57	0.538	0.603	INDETERMINATE	1	TRUE	1	0.678969311493277	3		342	1100	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022274	26022274	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	411	370	0	ENST00000435504.4:c.383del	p.Lys128ArgfsTer39	p.K128Rfs*39	ENST00000435504		128	aAg/ag	5/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.678969311493277	2		370	1206	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007332	143007332	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	129	328	2	ENST00000262992.4:c.2452del	p.Arg818GlufsTer4	p.R818Efs*4	ENST00000262992	NM_001101669.1	818	Aga/ga	22/24	1	2	FACETS	0.407	0.369	0.448	0.407	0.369	0.448	SUBCLONAL	1	TRUE	1	0.678969311493277	2		330	933	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528825	157528825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	85	210	0	ENST00000346085.5:c.6554del	p.Pro2185ArgfsTer8	p.P2185Rfs*8	ENST00000346085	NM_020732.3	2184	Ccc/cc	20/20	1	2	FACETS	0.355	0.314	0.4	0.355	0.314	0.4	SUBCLONAL	1	TRUE	1	0.678969311493277	2		210	705	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690842	89690843	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	167	150	0	ENST00000371953.3:c.252_253dup	p.Val85GlufsTer15	p.V85Efs*15	ENST00000371953	NM_000314.4	83	-/AG	4/9	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.678969311493277	2		150	470	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444452	49444453	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	132	219	0	ENST00000301067.7:c.2918dup	p.Leu973PhefsTer17	p.L973Ffs*17	ENST00000301067	NM_003482.3	973	ttg/ttTg	11/54	1	2	FACETS	0.569	0.518	0.623	0.569	0.518	0.623	SUBCLONAL	1	TRUE	1	0.678969311493277	2		219	683	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	258	320	3	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	0.949	0.892	1	0.949	0.892	1	CLONAL	1	TRUE	1	0.678969311493277	2		323	801	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353819	15353819	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	68	277	1	ENST00000263377.2:c.3061del	p.His1021IlefsTer47	p.H1021Ifs*47	ENST00000263377	NM_058243.2	1021	Cat/at	14/20	1	2	FACETS	0.762	0.67	0.858	0.762	0.67	0.858	SUBCLONAL	1	TRUE	1	0.678969311493277	2		278	263	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573051	41573052	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0003014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	272	253	0	ENST00000263253.7:c.5340dup	p.Ile1781HisfsTer102	p.I1781Hfs*102	ENST00000263253	NM_001429.3	1779	tgc/tgCc	31/31	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.678969311493277	2		253	737	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0003023-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	95	485	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		485	952	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438210	49438211	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1555194303	NA	P-0003023-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	64	542	0	ENST00000301067.7:c.5058dup	p.Arg1687ThrfsTer4	p.R1687Tfs*4	ENST00000301067	NM_003482.3	1686	-/A	20/54	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		542	941	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711927	89711928	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554900593	NA	P-0003052-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	72	416	1	ENST00000371953.3:c.548dup	p.Asn184GlufsTer6	p.N184Efs*6	ENST00000371953	NM_000314.4	182	tta/ttAa	6/9	0.386084195139002	1	FACETS	0.813	0.715	0.918	0.813	0.715	0.918	CLONAL	1	TRUE	0	0.386084195139002	1		417	370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003052-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	64	291	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.386084195139002	1	FACETS	0.945	0.826	1	0.945	0.826	1	CLONAL	1	TRUE	0	0.386084195139002	1		291	283	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0003070-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	109	494	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.225733462367412	3	FACETS	1	0.978	1	0.671	0.602	0.744	CLONAL	1	TRUE	1	0.225733462367412	3		494	801	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0003070-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	84	654	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.225733462367412	3	FACETS	0.795	0.7	0.897	0.397	0.35	0.449	SUBCLONAL	1	TRUE	1	0.225733462367412	3		654	1042	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0003070-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	88	668	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.225733462367412	3	FACETS	0.884	0.781	0.994	0.442	0.39	0.497	CLONAL	1	TRUE	1	0.225733462367412	3		669	982	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17941409	17941409	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003070-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	196	428	1	ENST00000458235.1:c.2999C>A	p.Ser1000Ter	p.S1000*	ENST00000458235	NM_000215.3	1000	tCg/tAg	22/24	0.199909254467515	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.225733462367412	3		429	775	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577121	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCA	novel	NA	P-0003070-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	199	721	0	ENST00000269305.4:c.815_817dup	p.Val272_Arg273insLeu	p.V272_R273insL	ENST00000269305	NM_001126112.2	273	cgt/cTGCgt	8/11	0.225733462367412	2	FACETS	0.834	0.772	0.898	0.834	0.772	0.898	CLONAL	2	TRUE	0	0.225733462367412	2		721	1057	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0003130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	124	276	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.160275842642981	2	FACETS	0.884	0.802	0.97	0.884	0.802	0.97	CLONAL	2	FALSE	0	0.225551691824283	2		276	622	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0003130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	46	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	1	0.225551691824283	2		311	317	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0003130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	19	407	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.225551691824283	0	FACETS	0.514	0.39	0.658			1	SUBCLONAL	1	FALSE	0	0.225551691824283	0		407	254	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0003130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	116	376	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	FALSE	1	0.225551691824283	2		376	893	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808979	1808979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751115449	NA	P-0003130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	69	372	0	ENST00000260795.2:c.2411C>T	p.Ser804Leu	p.S804L	ENST00000260795		804	tCg/tTg	17/17	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	1	0.225551691824283	2		372	554	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554665	63554665	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	112	197	0	ENST00000307078.5:c.74C>G	p.Pro25Arg	p.P25R	ENST00000307078	NM_004655.3	25	cCa/cGa	2/11	1	2	FACETS	0.805	0.725	0.888	1	0.985	1	CLONAL	2	FALSE	1	0.225551691824283	2		197	617	SUCCESS
APC	324	MSKCC	GRCh37	5	112175465	112175466	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	AA	novel	NA	P-0003130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	32	301	0	ENST00000257430.4:c.4174_4175insAA	p.Ser1392Ter	p.S1392*	ENST00000257430	NM_000038.5	1392	tca/tAAca	16/16	0.225551691824283	0	FACETS	0.755	0.615	0.912			1	CLONAL	1	FALSE	0	0.225551691824283	0		301	291	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740216	162740216	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775098890	NA	P-0003133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	270	300	1	ENST00000367921.3:c.1418G>A	p.Arg473His	p.R473H	ENST00000367921	NM_006182.2	473	cGc/cAc	12/18	0.710054498048357	3	FACETS	1	0.968	1	0.524	0.492	0.556	CLONAL	1	TRUE	1	0.710054498048357	3		301	984	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934190	39934190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146403660	NA	P-0003133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	95	418	0	ENST00000378444.4:c.409G>A	p.Val137Ile	p.V137I	ENST00000378444	NM_001123385.1	137	Gtc/Atc	4/15	1	2	FACETS	0.288	0.256	0.323	0.288	0.256	0.323	SUBCLONAL	1	TRUE	1	0.710054498048357	2		418	928	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115907	8115908	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0003133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	199	215	0	ENST00000346208.3:c.1254dup	p.Pro419AlafsTer88	p.P419Afs*88	ENST00000346208		418	acg/acGg	6/6	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.710054498048357	2		215	550	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	20	245	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.763	0.587	0.964	0.763	0.587	0.964	CLONAL	1	TRUE	1	0.317902454988824	2		245	165	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0003161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	103	365	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	1	2	FACETS	0.761	0.68	0.846	0.761	0.68	0.846	SUBCLONAL	1	TRUE	1	0.317902454988824	2		365	852	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0003161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	65	313	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			1	2	FACETS	0.65	0.563	0.744	0.65	0.563	0.744	SUBCLONAL	1	TRUE	1	0.317902454988824	2		313	629	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873835	35873835	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs923187160	NA	P-0003161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	37	152	0	ENST00000216797.5:c.16G>A	p.Glu6Lys	p.E6K	ENST00000216797	NM_020529.2	6	Gag/Aag	1/6	1	2	FACETS	0.82	0.679	0.976	0.82	0.679	0.976	CLONAL	1	TRUE	1	0.317902454988824	2		152	284	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242679	16242679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	205	431	1	ENST00000375759.3:c.1300C>T	p.Pro434Ser	p.P434S	ENST00000375759	NM_015001.2	434	Ccc/Tcc	6/15	0.317902454988824	3	FACETS	1	0.989	1	0.69	0.639	0.743	CLONAL	1	TRUE	1	0.317902454988824	3		432	1083	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468180	120468180	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1290072854	NA	P-0003161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	44	214	0	ENST00000256646.2:c.4259C>T	p.Thr1420Ile	p.T1420I	ENST00000256646	NM_024408.3	1420	aCc/aTc	25/34	1	2	FACETS	0.658	0.552	0.774	0.658	0.552	0.774	SUBCLONAL	1	TRUE	1	0.317902454988824	2		214	421	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370675	225370675	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	37	232	0	ENST00000264414.4:c.1204G>A	p.Gly402Arg	p.G402R	ENST00000264414	NM_003590.4	402	Ggg/Agg	8/16	1	2	FACETS	0.377	0.31	0.452	0.377	0.31	0.452	SUBCLONAL	1	TRUE	1	0.317902454988824	2		232	618	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431100	181431100	+	stop_lost	Nonstop_Mutation	SNP	T	T	G	novel	NA	P-0003161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	25	137	0	ENST00000325404.1:c.952T>G	p.Ter318GlyextTer27	p.*318Gext*27	ENST00000325404	NM_003106.3	318	Tga/Gga	1/1	1	2	FACETS	0.587	0.464	0.728	0.587	0.464	0.728	SUBCLONAL	1	TRUE	1	0.317902454988824	2		137	268	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535490	187535490	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0003161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	26	168	0	ENST00000441802.2:c.9084T>A	p.Tyr3028Ter	p.Y3028*	ENST00000441802	NM_005245.3	3028	taT/taA	12/27	1	2	FACETS	0.362	0.286	0.449	0.362	0.286	0.449	SUBCLONAL	1	TRUE	1	0.317902454988824	2		168	452	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540887	187540887	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	43	271	0	ENST00000441802.2:c.6853C>T	p.Gln2285Ter	p.Q2285*	ENST00000441802	NM_005245.3	2285	Cag/Tag	10/27	1	2	FACETS	0.514	0.43	0.608	0.514	0.43	0.608	SUBCLONAL	1	TRUE	1	0.317902454988824	2		271	526	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459867	149459867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	33	203	0	ENST00000286301.3:c.340G>A	p.Glu114Lys	p.E114K	ENST00000286301	NM_005211.3	114	Gag/Aag	4/22	1	2	FACETS	0.552	0.45	0.667	0.552	0.45	0.667	SUBCLONAL	1	TRUE	1	0.317902454988824	2		203	376	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459558	50459558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	38	197	0	ENST00000331340.3:c.847C>T	p.Leu283Phe	p.L283F	ENST00000331340	NM_006060.4	283	Ctt/Ttt	7/8	1	2	FACETS	0.474	0.392	0.567	0.474	0.392	0.567	SUBCLONAL	1	TRUE	1	0.317902454988824	2		197	504	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797229	135797229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	191	318	0	ENST00000298552.3:c.640G>A	p.Glu214Lys	p.E214K	ENST00000298552	NM_001162426.1	214	Gag/Aag	7/23	0.263504450747159	2	FACETS	1	0.989	1	0.705	0.653	0.76	CLONAL	1	TRUE	0	0.317902454988824	2		318	852	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400050	139400050	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	96	337	0	ENST00000277541.6:c.4298G>A	p.Gly1433Glu	p.G1433E	ENST00000277541	NM_017617.3	1433	gGg/gAg	25/34	0.263504450747159	2	FACETS	1	0.945	1	0.546	0.488	0.608	CLONAL	1	TRUE	0	0.317902454988824	2		337	553	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412248	139412248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1352568382	NA	P-0003161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	155	368	0	ENST00000277541.6:c.1397C>T	p.Thr466Ile	p.T466I	ENST00000277541	NM_017617.3	466	aCc/aTc	8/34	0.263504450747159	2	FACETS	1	0.987	1	0.708	0.649	0.768	CLONAL	1	TRUE	0	0.317902454988824	2		368	689	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128011	64128011	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	55	302	0	ENST00000334205.4:c.409G>C	p.Glu137Gln	p.E137Q	ENST00000334205	NM_003942.2	137	Gag/Cag	4/17	1	2	FACETS	0.628	0.537	0.727	0.628	0.537	0.727	SUBCLONAL	1	TRUE	1	0.317902454988824	2		302	551	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572548	64572548	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	45	227	0	ENST00000312049.6:c.1308G>A	p.Trp436Ter	p.W436*	ENST00000312049	NM_130799.2	436	tgG/tgA	9/10	1	2	FACETS	0.564	0.474	0.664	0.564	0.474	0.664	SUBCLONAL	1	TRUE	1	0.317902454988824	2		227	502	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196836	108196836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1181779478	NA	P-0003161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	55	271	0	ENST00000278616.4:c.6859G>A	p.Gly2287Arg	p.G2287R	ENST00000278616	NM_000051.3	2287	Gga/Aga	47/63	1	2	FACETS	0.573	0.49	0.664	0.573	0.49	0.664	SUBCLONAL	1	TRUE	1	0.317902454988824	2		271	604	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041397	42041397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1216	132	653	0	ENST00000219905.7:c.5592G>A	p.Met1864Ile	p.M1864I	ENST00000219905	NM_001164273.1	1864	atG/atA	17/24	1	2	FACETS	0.616	0.557	0.678	0.616	0.557	0.678	SUBCLONAL	1	TRUE	1	0.317902454988824	2		653	1348	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821176	72821176	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	153	601	1	ENST00000268489.5:c.10999G>A	p.Asp3667Asn	p.D3667N	ENST00000268489	NM_006885.3	3667	Gat/Aat	10/10	1	2	FACETS	0.838	0.765	0.914	0.838	0.765	0.914	CLONAL	1	TRUE	1	0.317902454988824	2		602	1149	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441451	40441451	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	58	365	0	ENST00000345506.4:c.22C>T	p.Gln8Ter	p.Q8*	ENST00000345506	NM_003152.3	8	Cag/Tag	3/20	0.175041689177797	1	FACETS	0.481	0.413	0.556	0.481	0.413	0.556	INDETERMINATE	1	TRUE	0	0.317902454988824	1		365	638	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448279	56448279	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	26	164	0	ENST00000407977.2:c.368C>T	p.Ala123Val	p.A123V	ENST00000407977		123	gCt/gTt	3/10	1	2	FACETS	0.499	0.395	0.617	0.499	0.395	0.617	SUBCLONAL	1	TRUE	1	0.317902454988824	2		164	328	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14628978	14628978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	53	471	0	ENST00000254322.2:c.184G>A	p.Glu62Lys	p.E62K	ENST00000254322	NM_006145.1	62	Gag/Aag	1/3	1	2	FACETS	0.421	0.358	0.49	0.421	0.358	0.49	SUBCLONAL	1	TRUE	1	0.317902454988824	2		471	792	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39690033	39690033	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	27	139	0	ENST00000361337.2:c.59-1G>A		p.X20_splice	ENST00000361337	NM_003286.2	20			1	2	FACETS	0.449	0.357	0.555	0.449	0.357	0.555	SUBCLONAL	1	TRUE	1	0.317902454988824	2		139	378	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306677	41306677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs724159835	NA	P-0003161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	44	285	0	ENST00000373198.4:c.982C>T	p.Arg328Cys	p.R328C	ENST00000373198	NM_133170.3	328	Cgc/Tgc	7/32	1	2	FACETS	0.474	0.397	0.56	0.474	0.397	0.56	SUBCLONAL	1	TRUE	1	0.317902454988824	2		285	584	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045671	47045671	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	31	268	0	ENST00000377604.3:c.2552C>T	p.Pro851Leu	p.P851L	ENST00000377604	NM_001204468.1	851	cCt/cTt	23/24	1	2	FACETS	0.39	0.315	0.476	0.39	0.315	0.476	SUBCLONAL	1	TRUE	1	0.317902454988824	2		268	500	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938551	76938551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	78	452	0	ENST00000373344.5:c.2197G>A	p.Glu733Lys	p.E733K	ENST00000373344	NM_000489.3	733	Gaa/Aaa	9/35	1	2	FACETS	0.499	0.437	0.566	0.499	0.437	0.566	SUBCLONAL	1	TRUE	1	0.317902454988824	2		452	983	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400250	139400251	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0003161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	60	163	0	ENST00000277541.6:c.4097dup	p.Arg1368AlafsTer37	p.R1368Afs*37	ENST00000277541	NM_017617.3	1366	ggc/ggGc	25/34	0.263504450747159	2	FACETS	0.817	0.713	0.927	0.817	0.713	0.927	CLONAL	2	TRUE	0	0.317902454988824	2		163	231	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073824	8073825	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0003203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	398	508	0	ENST00000377482.5:c.834dup	p.Asp279ArgfsTer4	p.D279Rfs*4	ENST00000377482	NM_018948.3	278	-/A	4/4	0.698985323566319	1	FACETS	0.895	0.856	0.933	0.895	0.856	0.933	CLONAL	1	TRUE	0	0.698985323566319	1		508	828	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	72	389	2	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	1	2	FACETS	0.795	0.695	0.903	1	0.976	1	CLONAL	2	TRUE	1	0.151128726303238	2		391	599	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	39	809	0	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	0.149854806792149	3	FACETS	0.818	0.676	0.976	0.409	0.338	0.488	CLONAL	1	TRUE	1	0.151128726303238	3		809	679	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288437	15288437	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	32	181	0	ENST00000263388.2:c.4302G>A	p.Trp1434Ter	p.W1434*	ENST00000263388	NM_000435.2	1434	tgG/tgA	24/33	0.149854806792149	3	FACETS	0.752	0.612	0.909	0.752	0.612	0.909	CLONAL	2	TRUE	1	0.151128726303238	3		181	303	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097733	27097733	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	31	332	0	ENST00000324856.7:c.3322G>T	p.Glu1108Ter	p.E1108*	ENST00000324856	NM_006015.4	1108	Gaa/Taa	12/20	1	2	FACETS	0.773	0.624	0.942	0.773	0.624	0.942	CLONAL	1	TRUE	1	0.151128726303238	2		332	531	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099406	27099406	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	28	322	0	ENST00000324856.7:c.3643A>C	p.Met1215Leu	p.M1215L	ENST00000324856	NM_006015.4	1215	Atg/Ctg	14/20	1	2	FACETS	0.715	0.57	0.881	0.715	0.57	0.881	SUBCLONAL	1	TRUE	1	0.151128726303238	2		322	518	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106090	27106090	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	23	236	0	ENST00000324856.7:c.5701G>T	p.Gly1901Ter	p.G1901*	ENST00000324856	NM_006015.4	1901	Gga/Tga	20/20	1	2	FACETS	0.687	0.535	0.864	0.687	0.535	0.864	SUBCLONAL	1	TRUE	1	0.151128726303238	2		236	443	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400804	72400804	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	41	445	0	ENST00000357731.5:c.367C>T	p.Gln123Ter	p.Q123*	ENST00000357731	NM_173808.2	123	Caa/Taa	2/7	0.141150239328656	4	FACETS	1	0.856	1	0.516	0.429	0.613	CLONAL	1	TRUE	2	0.151128726303238	4		445	605	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966982	25966982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	51	276	0	ENST00000435504.4:c.2224G>T	p.Glu742Ter	p.E742*	ENST00000435504		742	Gag/Tag	13/13	0.149854806792149	3	FACETS	1	0.923	1	0.572	0.485	0.667	CLONAL	1	TRUE	1	0.151128726303238	3		276	635	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455315	29455315	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1311699420	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	54	191	1	ENST00000389048.3:c.2488-1G>A		p.X830_splice	ENST00000389048	NM_004304.4	830			0.149854806792149	3	FACETS	0.78	0.666	0.903	0.78	0.666	0.903	CLONAL	2	TRUE	1	0.151128726303238	3		192	493	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025771	48025771	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs950036621	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	42	273	1	ENST00000234420.5:c.649G>T	p.Asp217Tyr	p.D217Y	ENST00000234420	NM_000179.2	217	Gat/Tat	4/10	0.149854806792149	3	FACETS	1	0.941	1	0.653	0.545	0.772	CLONAL	1	TRUE	1	0.151128726303238	3		274	458	SUCCESS
ATR	545	MSKCC	GRCh37	3	142253927	142253927	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	28	298	1	ENST00000350721.4:c.3940A>G	p.Asn1314Asp	p.N1314D	ENST00000350721	NM_001184.3	1314	Aat/Gat	21/47	1	2	FACETS	0.816	0.651	1	0.816	0.651	1	CLONAL	1	TRUE	1	0.151128726303238	2		299	454	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156682	55156682	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs765476521	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	22	172	0	ENST00000257290.5:c.3083T>C	p.Val1028Ala	p.V1028A	ENST00000257290	NM_006206.4	1028	gTc/gCc	22/23	0.149854806792149	3	FACETS	0.789	0.61	0.997	0.394	0.305	0.499	CLONAL	1	TRUE	1	0.151128726303238	3		172	397	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356216	66356216	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	89	267	0	ENST00000273854.3:c.1281G>T	p.Met427Ile	p.M427I	ENST00000273854	NM_004439.5	427	atG/atT	5/18	0.149854806792149	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	1	0.151128726303238	3		267	555	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045834	143045834	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	55	275	0	ENST00000262992.4:c.1800G>T	p.Gln600His	p.Q600H	ENST00000262992	NM_001101669.1	600	caG/caT	17/24	0.149854806792149	3	FACETS	1	0.963	1	0.713	0.61	0.826	CLONAL	1	TRUE	1	0.151128726303238	3		275	549	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629880	187629880	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	78	318	0	ENST00000441802.2:c.1102G>C	p.Glu368Gln	p.E368Q	ENST00000441802	NM_005245.3	368	Gaa/Caa	2/27	0.149854806792149	3	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	1	0.151128726303238	3		318	509	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157256628	157256628	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	49	277	0	ENST00000346085.5:c.1955G>C	p.Arg652Thr	p.R652T	ENST00000346085	NM_020732.3	652	aGa/aCa	5/20	0.149854806792149	3	FACETS	1	0.95	1	0.66	0.559	0.772	CLONAL	1	TRUE	1	0.151128726303238	3		277	528	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860765	151860765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	32	240	0	ENST00000262189.6:c.9897G>A	p.Met3299Ile	p.M3299I	ENST00000262189	NM_170606.2	3299	atG/atA	43/59	0.141150239328656	4	FACETS	0.899	0.729	1	0.45	0.364	0.547	CLONAL	1	TRUE	2	0.151128726303238	4		240	542	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331612	8331612	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	66	420	0	ENST00000356435.5:c.5504G>C	p.Gly1835Ala	p.G1835A	ENST00000356435		1835	gGc/gCc	33/35	0.151128726303238	2	FACETS	1	0.966	1	0.687	0.596	0.785	CLONAL	1	TRUE	0	0.151128726303238	2		420	636	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	36	151	0	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	0.151128726303238	2	FACETS	1	0.946	1	0.717	0.591	0.858	CLONAL	1	TRUE	0	0.151128726303238	2		151	332	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189441	94189441	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	55	328	0	ENST00000323929.3:c.1563+1G>C		p.X521_splice	ENST00000323929	NM_005591.3	521			0.141150239328656	4	FACETS	1	0.96	1	0.696	0.595	0.806	CLONAL	1	TRUE	2	0.151128726303238	4		328	602	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922163	100922163	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs112862471	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	30	379	0	ENST00000325455.5:c.2349A>G	p.Ile783Met	p.I783M	ENST00000325455	NM_001202474.3	783	atA/atG	5/8	0.141150239328656	4	FACETS	0.779	0.626	0.953	0.389	0.313	0.477	CLONAL	1	TRUE	2	0.151128726303238	4		379	587	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114757	108114757	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587780629	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	33	280	0	ENST00000278616.4:c.574C>A	p.His192Asn	p.H192N	ENST00000278616	NM_000051.3	192	Cat/Aat	6/63	0.141150239328656	4	FACETS	0.956	0.777	1	0.478	0.388	0.579	CLONAL	1	TRUE	2	0.151128726303238	4		280	526	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218372	69218372	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	36	374	0	ENST00000462284.1:c.464C>A	p.Ser155Tyr	p.S155Y	ENST00000462284	NM_002392.5	155	tCt/tAt	7/11	1	2	FACETS	0.819	0.672	0.984	0.819	0.672	0.984	CLONAL	1	TRUE	1	0.151128726303238	2		374	582	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112884201	112884201	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	33	248	0	ENST00000351677.2:c.136A>G	p.Arg46Gly	p.R46G	ENST00000351677	NM_002834.3	46	Aga/Gga	2/16	1	2	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	TRUE	1	0.151128726303238	2		248	412	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915528	112915528	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	43	441	0	ENST00000351677.2:c.927C>G	p.Ile309Met	p.I309M	ENST00000351677	NM_002834.3	309	atC/atG	8/16	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.151128726303238	2		441	501	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250250	133250250	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs483352909	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	34	354	0	ENST00000320574.5:c.1270C>G	p.Leu424Val	p.L424V	ENST00000320574	NM_006231.2	424	Ctc/Gtc	13/49	1	2	FACETS	0.703	0.573	0.85	0.703	0.573	0.85	SUBCLONAL	1	TRUE	1	0.151128726303238	2		354	640	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964125	28964125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377395740	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	30	332	0	ENST00000282397.4:c.1777C>T	p.Arg593Trp	p.R593W	ENST00000282397	NM_002019.4	593	Cgg/Tgg	13/30	0.149854806792149	3	FACETS	0.8	0.643	0.978	0.4	0.321	0.489	CLONAL	1	TRUE	1	0.151128726303238	3		332	534	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355839	73355839	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	35	146	0	ENST00000377767.4:c.132G>T	p.Glu44Asp	p.E44D	ENST00000377767	NM_014953.3	44	gaG/gaT	1/21	0.149854806792149	3	FACETS	1	0.94	1	0.692	0.568	0.831	CLONAL	1	TRUE	1	0.151128726303238	3		146	360	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41021830	41021830	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	33	292	1	ENST00000267868.3:c.772G>C	p.Glu258Gln	p.E258Q	ENST00000267868	NM_002875.4	258	Gag/Cag	8/10	0.151128726303238	1	FACETS	0.671	0.545	0.813	0.671	0.545	0.813	SUBCLONAL	1	TRUE	0	0.151128726303238	1		293	602	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041920	42041920	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	42	445	0	ENST00000219905.7:c.6115G>T	p.Glu2039Ter	p.E2039*	ENST00000219905	NM_001164273.1	2039	Gaa/Taa	17/24	0.151128726303238	1	FACETS	0.914	0.763	1	0.914	0.763	1	CLONAL	1	TRUE	0	0.151128726303238	1		445	562	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304040	91304040	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	28	426	1	ENST00000355112.3:c.1437C>A	p.Phe479Leu	p.F479L	ENST00000355112	NM_000057.2	479	ttC/ttA	7/22	0.149854806792149	3	FACETS	0.808	0.645	0.995	0.404	0.322	0.498	CLONAL	1	TRUE	1	0.151128726303238	3		427	493	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442709	99442709	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1567185393	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	34	251	0	ENST00000268035.6:c.1106A>G	p.Asn369Ser	p.N369S	ENST00000268035	NM_000875.3	369	aAc/aGc	5/21	0.149854806792149	3	FACETS	1	0.839	1	0.515	0.42	0.621	CLONAL	1	TRUE	1	0.151128726303238	3		251	470	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864492	56864492	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	75	411	0	ENST00000308159.5:c.980G>T	p.Arg327Leu	p.R327L	ENST00000308159	NM_014669.4	327	cGc/cTc	10/22	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.151128726303238	2		411	743	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013719	12013719	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	43	304	1	ENST00000353533.5:c.661G>T	p.Glu221Ter	p.E221*	ENST00000353533	NM_003010.3	221	Gaa/Taa	6/11	1	2	FACETS	0.777	0.652	0.915	1	0.96	1	CLONAL	2	TRUE	1	0.151128726303238	2		305	366	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16021323	16021323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	40	319	0	ENST00000268712.3:c.1934G>A	p.Arg645His	p.R645H	ENST00000268712	NM_006311.3	645	cGt/cAt	18/46	1	2	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	TRUE	1	0.151128726303238	2		319	512	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560097	29560097	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	31	329	0	ENST00000356175.3:c.3574G>T	p.Glu1192Ter	p.E1192*	ENST00000356175	NM_000267.3	1192	Gaa/Taa	27/57	0.149854806792149	3	FACETS	0.86	0.695	1	0.43	0.347	0.524	CLONAL	1	TRUE	1	0.151128726303238	3		329	513	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435290	56435290	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	22	164	0	ENST00000407977.2:c.1847C>T	p.Pro616Leu	p.P616L	ENST00000407977		616	cCc/cTc	9/10	0.149854806792149	3	FACETS	0.867	0.672	1	0.434	0.336	0.548	CLONAL	1	TRUE	1	0.151128726303238	3		164	361	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448277	56448277	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	42	160	0	ENST00000407977.2:c.370A>T	p.Ser124Cys	p.S124C	ENST00000407977		124	Agc/Tgc	3/10	0.149854806792149	3	FACETS	1	0.905	1	0.564	0.47	0.668	CLONAL	1	TRUE	1	0.151128726303238	3		160	530	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740371	58740371	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	28	339	0	ENST00000305921.3:c.1276C>A	p.Pro426Thr	p.P426T	ENST00000305921	NM_003620.3	426	Cca/Aca	6/6	0.149854806792149	3	FACETS	0.73	0.582	0.9	0.365	0.291	0.45	SUBCLONAL	1	TRUE	1	0.151128726303238	3		339	546	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926556	59926556	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	33	378	0	ENST00000259008.2:c.441C>G	p.Tyr147Ter	p.Y147*	ENST00000259008	NM_032043.2	147	taC/taG	5/20	0.149854806792149	3	FACETS	0.815	0.663	0.988	0.408	0.331	0.494	CLONAL	1	TRUE	1	0.151128726303238	3		378	576	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213543	2213543	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	72	263	0	ENST00000398665.3:c.1563G>C	p.Lys521Asn	p.K521N	ENST00000398665	NM_032482.2	521	aaG/aaC	17/28	0.149854806792149	3	FACETS	0.803	0.702	0.913	0.803	0.702	0.913	CLONAL	2	TRUE	1	0.151128726303238	3		263	638	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350787	15350787	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	26	196	0	ENST00000263377.2:c.3216G>C	p.Gln1072His	p.Q1072H	ENST00000263377	NM_058243.2	1072	caG/caC	15/20	0.149854806792149	3	FACETS	0.887	0.702	1	0.444	0.351	0.55	CLONAL	1	TRUE	1	0.151128726303238	3		196	417	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952282	17952282	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	57	269	1	ENST00000458235.1:c.1058C>A	p.Thr353Lys	p.T353K	ENST00000458235	NM_000215.3	353	aCg/aAg	8/24	0.149854806792149	3	FACETS	1	0.95	1	0.626	0.536	0.724	CLONAL	1	TRUE	1	0.151128726303238	3		270	648	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797948	42797948	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1380205137	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	66	208	1	ENST00000575354.2:c.4000C>T	p.Arg1334Trp	p.R1334W	ENST00000575354	NM_015125.3	1334	Cgg/Tgg	16/20	0.149854806792149	3	FACETS	0.989	0.86	1	0.989	0.86	1	CLONAL	2	TRUE	1	0.151128726303238	3		209	475	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164611	36164611	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	45	174	0	ENST00000300305.3:c.1264G>A	p.Glu422Lys	p.E422K	ENST00000300305		422	Gag/Aag	8/8	1	2	FACETS	0.8	0.674	0.939	1	0.963	1	CLONAL	2	TRUE	1	0.151128726303238	2		174	372	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223892	53223892	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	27	184	0	ENST00000375401.3:c.3467A>C	p.Lys1156Thr	p.K1156T	ENST00000375401	NM_004187.3	1156	aAg/aCg	23/26	1	1	FACETS	1	0.831	1	1	0.831	1	CLONAL	1	TRUE	0	0.151128726303238	1		184	315	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287215	46287216	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	16	216	0	ENST00000334344.6:c.5165dup	p.Thr1723HisfsTer6	p.T1723Hfs*6	ENST00000334344	NM_152641.2	1720	-/G	19/21	1	2	FACETS	0.67	0.495	0.88	0.67	0.495	0.88	SUBCLONAL	1	TRUE	1	0.151128726303238	2		216	316	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099023	27099023	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	58	293	0	ENST00000324856.7:c.3442del	p.Gln1148SerfsTer13	p.Q1148Sfs*13	ENST00000324856	NM_006015.4	1147	Ccc/cc	13/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.151128726303238	2		293	530	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022924	31022925	+	missense_variant	Missense_Mutation	DNP	AG	AG	TA	novel	NA	P-0003229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	43	305	0	ENST00000375687.4:c.2409_2410delinsTA	p.Gln803_Gly804delinsHisArg	p.Q803_G804delinsHR	ENST00000375687	NM_015338.5	803	caAGga/caTAga	13/13	0.149854806792149	3	FACETS	1	0.949	1	0.686	0.575	0.81	CLONAL	1	TRUE	1	0.151128726303238	3		305	446	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0003237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	27	697	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	0.844	0.676	1			1	INDETERMINATE	1	TRUE	NA	0.310650936644927	2		697	206	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680588	241680588	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1270054582	NA	P-0003237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	32	400	0	ENST00000366560.3:c.161A>G	p.Tyr54Cys	p.Y54C	ENST00000366560	NM_000143.3	54	tAt/tGt	2/10	0.310650936644927	3	FACETS	0.895	0.73	1	0.447	0.365	0.54	CLONAL	1	TRUE	1	0.310650936644927	3		400	266	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25368469	25368469	+	intron_variant	Intron	SNP	A	A	G	novel	NA	P-0003237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	16	373	0	ENST00000311936.3:c.451-5624T>C		p.*151*	ENST00000311936	NM_004985.3	159/189			NA	2	FACETS	0.56	0.415	0.731			1	INDETERMINATE	1	TRUE	NA	0.310650936644927	2		373	184	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971150	21971151	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTCC	novel	NA	P-0003237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	12	93	0	ENST00000304494.5:c.204_207dup	p.Pro70GlyfsTer51	p.P70Gfs*51	ENST00000304494	NM_000077.4	69	-/GGAG	2/3	0.310650936644927	3	FACETS	0.93	0.661	1	0.465	0.33	0.626	CLONAL	1	TRUE	1	0.310650936644927	3		93	96	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0003289-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	7040	618	6	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.617157581823776	33	FACETS	0.992	0.987	0.997			1	CLONAL	31	TRUE	NA	0.617157581823776	33		624	7841	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900144	101900144	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003289-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	62	465	0	ENST00000374994.4:c.578T>C	p.Leu193Ser	p.L193S	ENST00000374994	NM_004612.2	193	tTa/tCa	4/9	0.617157581823776	3	FACETS	1	0.936	1	0.557	0.487	0.631	CLONAL	1	TRUE	1	0.617157581823776	3		465	236	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860036	57860036	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003289-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	33	801	0	ENST00000228682.2:c.776A>G	p.Glu259Gly	p.E259G	ENST00000228682	NM_005269.2	259	gAg/gGg	8/12	0.617157581823776	1	FACETS	0.185	0.151	0.224	0.185	0.151	0.224	SUBCLONAL	1	TRUE	0	0.617157581823776	1		801	399	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68934893	68934893	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003289-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	26	671	0	ENST00000487270.1:c.962T>G	p.Leu321Arg	p.L321R	ENST00000487270	NM_133509.3	321	cTt/cGt	10/11	0.609372930366992	2	FACETS	0.301	0.239	0.372	0.15	0.119	0.186	SUBCLONAL	1	TRUE	0	0.617157581823776	2		671	280	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383144	42383144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764758292	NA	P-0003289-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	215	852	2	ENST00000221972.3:c.164C>T	p.Pro55Leu	p.P55L	ENST00000221972	NM_021601.3	55	cCg/cTg	2/5	0.139765227151178	1	FACETS	0.694	0.648	0.742	0.694	0.648	0.742	INDETERMINATE	1	TRUE	0	0.617157581823776	1		854	694	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573999	7573999	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003289-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	254	763	2	ENST00000269305.4:c.1028del	p.Glu343GlyfsTer2	p.E343Gfs*2	ENST00000269305	NM_001126112.2	343	gAg/gg	10/11	0.609372930366992	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.617157581823776	2		765	401	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56363640	56363641	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGACAGTT	novel	NA	P-0003289-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	61	712	1	ENST00000348428.3:c.422_430dup	p.Gly141_Phe143dup	p.G141_F143dup	ENST00000348428	NM_006785.3	141	gct/gcTGGACAGTTt	3/17	0.602282968637848	1	FACETS	0.694	0.609	0.783	0.694	0.609	0.783	SUBCLONAL	1	TRUE	0	0.617157581823776	1		713	197	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249017	55249018	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCA	rs1554350381	NA	P-0003319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	185	265	0	ENST00000275493.2:c.2317_2319dup	p.His773dup	p.H773dup	ENST00000275493	NM_005228.3	773	ccc/ccCCAc	20/28	0.215824963769595	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		265	493	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088787	27088788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0003347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	122	277	0	ENST00000324856.7:c.2402dup	p.Gln802SerfsTer15	p.Q802Sfs*15	ENST00000324856	NM_006015.4	799	cag/caGg	7/20	1	2	FACETS	0.909	0.827	0.995	0.909	0.827	0.995	CLONAL	1	TRUE	1	0.564008039621473	2		277	476	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971029	21971029	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519852	NA	P-0003347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	125	185	0	ENST00000304494.5:c.329G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tGg/tAg	2/3	0.534284570022358	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.564008039621473	1		185	254	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43817936	43817936	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	113	470	0	ENST00000372470.3:c.1615C>A	p.Leu539Ile	p.L539I	ENST00000372470	NM_005373.2	539	Cta/Ata	11/12	1	2	FACETS	0.54	0.486	0.597	0.54	0.486	0.597	SUBCLONAL	1	TRUE	1	0.564008039621473	2		470	742	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843526	156843526	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	103	362	0	ENST00000524377.1:c.952A>T	p.Asn318Tyr	p.N318Y	ENST00000524377	NM_002529.3	318	Aat/Tat	8/17	0.336428845985564	4	FACETS	0.749	0.67	0.832	0.187	0.167	0.208	INDETERMINATE	1	TRUE	0	0.564008039621473	4		362	763	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085918	16085918	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs150742977	NA	P-0003347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	106	228	0	ENST00000281043.3:c.1094C>A	p.Pro365Gln	p.P365Q	ENST00000281043	NM_005378.4	365	cCa/cAa	3/3	0.440982675923109	3	FACETS	0.972	0.875	1	0.486	0.437	0.537	CLONAL	1	TRUE	1	0.564008039621473	3		228	496	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551342	29551342	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	119	276	0	ENST00000389048.3:c.1288T>A	p.Ser430Thr	p.S430T	ENST00000389048	NM_004304.4	430	Tcc/Acc	6/29	0.440982675923109	3	FACETS	1	0.911	1	0.503	0.455	0.552	CLONAL	1	TRUE	1	0.564008039621473	3		276	538	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127579	55127579	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	58	116	0	ENST00000257290.5:c.367G>C	p.Asp123His	p.D123H	ENST00000257290	NM_006206.4	123	Gac/Cac	3/23	0.440982675923109	3	FACETS	0.829	0.717	0.95	0.415	0.358	0.475	CLONAL	1	TRUE	1	0.564008039621473	3		116	318	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706968	117706968	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	378	330	0	ENST00000368508.3:c.2182G>T	p.Val728Leu	p.V728L	ENST00000368508	NM_002944.2	728	Gtg/Ttg	15/43	0.558060320748818	2	FACETS	0.962	0.922	1	0.962	0.922	1	CLONAL	2	TRUE	0	0.564008039621473	2		330	697	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624510	93624510	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	346	234	1	ENST00000375746.1:c.601G>T	p.Gly201Cys	p.G201C	ENST00000375746	NM_001174167.1	201	Ggc/Tgc	4/14	0.564008039621473	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.564008039621473	3		235	645	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066821	77066821	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1319725019	NA	P-0003347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	188	379	0	ENST00000356341.3:c.664A>G	p.Ile222Val	p.I222V	ENST00000356341	NM_002576.4	222	Att/Gtt	7/15	0.531354333115963	2	FACETS	0.935	0.867	1	0.468	0.433	0.503	CLONAL	1	TRUE	0	0.564008039621473	2		379	713	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699411	47699411	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	123	233	0	ENST00000347630.2:c.97T>G	p.Ser33Ala	p.S33A	ENST00000347630	NM_001007230.1	33	Tcc/Gcc	4/11	0.564008039621473	3	FACETS	0.832	0.754	0.914	0.416	0.377	0.457	CLONAL	1	TRUE	1	0.564008039621473	3		233	672	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600393	10600393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	372	453	0	ENST00000171111.5:c.1462G>A	p.Glu488Lys	p.E488K	ENST00000171111	NM_203500.1	488	Gag/Aag	4/6	0.558060320748818	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.564008039621473	2		453	623	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726580	41726580	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	129	338	0	ENST00000301178.4:c.125G>A	p.Gly42Glu	p.G42E	ENST00000301178	NM_021913.4	42	gGg/gAg	2/20	0.312262542454228	5	FACETS	1	0.931	1	0.344	0.312	0.378	INDETERMINATE	1	TRUE	2	0.564008039621473	5		338	818	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907683	111907684	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0003347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	174	305	0	ENST00000393256.3:c.458_459insTG	p.Arg154GlyfsTer17	p.R154Gfs*17	ENST00000393256	NM_006538.4	153	cgg/cGTgg	3/4	0.564008039621473	3	FACETS	1	0.926	1	0.502	0.463	0.543	CLONAL	1	TRUE	1	0.564008039621473	3		305	788	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579472	7579473	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	C	novel	NA	P-0003347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	188	186	0	ENST00000269305.4:c.214_215delinsG	p.Pro72AlafsTer51	p.P72Afs*51	ENST00000269305	NM_001126112.2	72	CCc/Gc	4/11	0.531354333115963	2	FACETS	0.952	0.896	1	0.952	0.896	1	CLONAL	2	TRUE	0	0.564008039621473	2		186	350	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884488	151884488	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	180	244	0	ENST00000262189.6:c.4867G>T	p.Glu1623Ter	p.E1623*	ENST00000262189	NM_170606.2	1623	Gaa/Taa	33/59	0.283660794509882	4	FACETS	0.886	0.817	0.957	0.886	0.817	0.957	CLONAL	2	TRUE	2	0.293440661999453	4		244	896	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022962	33022962	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	104	382	0	ENST00000300177.4:c.71G>C	p.Gly24Ala	p.G24A	ENST00000300177	NM_001191322.1	24	gGg/gCg	2/2	1	2	FACETS	0.96	0.86	1	0.96	0.86	1	CLONAL	1	TRUE	1	0.293440661999453	2		382	738	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115939	8115940	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0003394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	49	168	0	ENST00000346208.3:c.1287dup	p.Phe430LeufsTer77	p.F430Lfs*77	ENST00000346208		429	tcc/tCcc	6/6	1	2	FACETS	0.915	0.778	1	0.915	0.778	1	CLONAL	1	TRUE	1	0.293440661999453	2		168	365	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	87	328	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.727711163022943	2		328	235	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610608	52610609	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0003403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	165	358	0	ENST00000394830.3:c.3564dup	p.Glu1189ArgfsTer6	p.E1189Rfs*6	ENST00000394830	NM_018313.4	1188	-/A	23/30	0.727711163022943	1	FACETS	0.6	0.555	0.645	0.6	0.555	0.645	SUBCLONAL	1	TRUE	0	0.727711163022943	1		358	481	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0003403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	288	318	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.727711163022943	2		318	755	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195116	123195117	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0003403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	334	210	1	ENST00000218089.9:c.1459_1460insC	p.Cys487SerfsTer4	p.C487Sfs*4	ENST00000218089	NM_001042749.1	487	tgt/tCgt	16/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.727711163022943	1		211	449	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440347	52440356	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCACCACT	GGGCACCACT	-	novel	NA	P-0003403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	226	299	0	ENST00000460680.1:c.696_705del	p.Val233ThrfsTer13	p.V233Tfs*13	ENST00000460680	NM_004656.3	232	gcAGTGGTGCCC/gc	9/17	0.727711163022943	1	FACETS	0.971	0.919	1	0.971	0.919	1	CLONAL	1	TRUE	0	0.727711163022943	1		299	407	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	22	245	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.57781381529709	2		245	63	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636290	87636290	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	136	498	0	ENST00000277120.3:c.2455A>T	p.Ile819Phe	p.I819F	ENST00000277120		819	Atc/Ttc	19/19	1	2	FACETS	0.847	0.773	0.923	0.847	0.773	0.923	CLONAL	1	TRUE	1	0.57781381529709	2		498	556	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97876984	97876984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768508859	NA	P-0003409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	88	350	1	ENST00000289081.3:c.1081C>T	p.Arg361Trp	p.R361W	ENST00000289081	NM_000136.2	361	Cgg/Tgg	12/15	1	2	FACETS	0.739	0.659	0.824	0.739	0.659	0.824	SUBCLONAL	1	TRUE	1	0.57781381529709	2		351	412	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955563	48955563	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	134	319	0	ENST00000267163.4:c.1681del	p.Ala562HisfsTer49	p.A562Hfs*49	ENST00000267163	NM_000321.2	560	tCc/tc	17/27	0.400424350392192	1	FACETS	0.932	0.857	1	0.932	0.857	1	CLONAL	1	TRUE	0	0.57781381529709	1		319	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576900	7576901	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0003409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	107	263	0	ENST00000269305.4:c.945_946del	p.Gln317AlafsTer19	p.Q317Afs*19	ENST00000269305	NM_001126112.2	315	tcTCcc/tccc	9/11	0.57781381529709	1	FACETS	0.893	0.812	0.975	0.893	0.812	0.975	CLONAL	1	TRUE	0	0.57781381529709	1		263	295	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44911036	44911037	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	196	311	0	ENST00000377967.4:c.738dup	p.Gln247ThrfsTer16	p.Q247Tfs*16	ENST00000377967	NM_021140.2	246	tta/ttAa	9/29	0.274172606660226	0	FACETS	0.858	0.81	0.904			1	INDETERMINATE	1	TRUE	NA	0.57781381529709	0		311	334	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	321	328	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.75350922782914	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.75350922782914	3		328	582	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061463	38061463	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	217	275	0	ENST00000250448.2:c.526A>G	p.Ile176Val	p.I176V	ENST00000250448	NM_004496.3	176	Atc/Gtc	2/2	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.75350922782914	2		275	540	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627889	37627889	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	376	438	1	ENST00000447079.4:c.1804C>T	p.Gln602Ter	p.Q602*	ENST00000447079	NM_015083.1	602	Cag/Tag	2/14	0.75350922782914	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.75350922782914	1		439	580	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117409	115117410	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	301	299	0	ENST00000257566.3:c.764dup	p.Arg256LysfsTer4	p.R256Kfs*4	ENST00000257566	NM_016569.3	255	gta/gtTa	4/8	1	2	FACETS	0.963	0.91	1	0.963	0.91	1	CLONAL	1	TRUE	1	0.75350922782914	2		299	830	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25990499	25990503	+	frameshift_variant	Frame_Shift_Del	DEL	AGTAA	AGTAA	-	novel	NA	P-0003522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	289	347	0	ENST00000435504.4:c.724_728del	p.Leu242ArgfsTer11	p.L242Rfs*11	ENST00000435504		242	TTACTa/a	8/13	0.741299335036555	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.75350922782914	1		347	438	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0003536-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	510	351	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	0.649135914236391	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.649135914236391	3		351	646	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0003536-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	352	607	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.649135914236391	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.649135914236391	1		607	552	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012465	29012465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373801409	NA	P-0003536-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	294	425	0	ENST00000282397.4:c.406G>A	p.Val136Ile	p.V136I	ENST00000282397	NM_002019.4	136	Gta/Ata	4/30	0.446334663999276	3	FACETS	0.955	0.907	1	0.955	0.907	1	CLONAL	2	TRUE	1	0.649135914236391	3		425	628	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007741	45007741	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003536-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	285	465	0	ENST00000558401.1:c.188G>T	p.Gly63Val	p.G63V	ENST00000558401	NM_004048.2	63	gGa/gTa	2/4	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.649135914236391	2		465	774	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500832	8500832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756198535	NA	P-0003536-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	61	522	0	ENST00000356435.5:c.2050C>T	p.Arg684Trp	p.R684W	ENST00000356435		684	Cgg/Tgg	13/35	0.649135914236391	3	FACETS	0.274	0.236	0.316	0.091	0.078	0.106	SUBCLONAL	1	TRUE	0	0.649135914236391	3		522	908	SUCCESS
RET	5979	MSKCC	GRCh37	10	43598011	43598011	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003536-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	34	413	0	ENST00000355710.3:c.559C>A	p.Gln187Lys	p.Q187K	ENST00000355710	NM_020975.4	187	Cag/Aag	3/20	NA	2	FACETS	0.18	0.146	0.218			1	INDETERMINATE	1	TRUE	NA	0.649135914236391	2		413	582	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222698	69222698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755256189	NA	P-0003536-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	74	594	0	ENST00000462284.1:c.671C>T	p.Thr224Met	p.T224M	ENST00000462284	NM_002392.5	224	aCg/aTg	8/11	1	2	FACETS	0.3	0.262	0.341	0.3	0.262	0.341	SUBCLONAL	1	TRUE	1	0.649135914236391	2		594	759	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0003582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	73	668	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.881	0.773	0.996	0.881	0.773	0.996	CLONAL	1	TRUE	1	0.358780803049168	2		668	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0003582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	60	433	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.358780803049168	1	FACETS	0.956	0.831	1	0.956	0.831	1	CLONAL	1	TRUE	0	0.358780803049168	1		436	287	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727455	66727455	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs869025608	NA	P-0003582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	129	272	0	ENST00000307102.5:c.171G>T	p.Lys57Asn	p.K57N	ENST00000307102	NM_002755.3	57	aaG/aaT	2/11	0.346848519873647	2	FACETS	0.871	0.796	0.947	0.871	0.796	0.947	CLONAL	2	TRUE	0	0.358780803049168	2		272	413	SUCCESS
APC	324	MSKCC	GRCh37	5	112175191	112175192	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554085382	NA	P-0003582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	64	176	0	ENST00000257430.4:c.3901dup	p.Thr1301AsnfsTer14	p.T1301Nfs*14	ENST00000257430	NM_000038.5	1300	-/A	16/16	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.358780803049168	2		176	321	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667364	241667364	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	57	485	0	ENST00000366560.3:c.1086A>T	p.Glu362Asp	p.E362D	ENST00000366560	NM_000143.3	362	gaA/gaT	7/10	0.267952551298809	3	FACETS	0.499	0.427	0.578	0.249	0.213	0.289	SUBCLONAL	1	TRUE	1	0.358780803049168	3		485	751	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	58	261	1	ENST00000281708.4:c.1393C>A	p.Arg465Ser	p.R465S	ENST00000281708	NM_033632.3	465	Cgt/Agt	9/12	1	2	FACETS	0.717	0.617	0.825	0.717	0.617	0.825	SUBCLONAL	1	TRUE	1	0.358780803049168	2		262	451	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391848	139391848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777219891	NA	P-0003582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	57	304	1	ENST00000277541.6:c.6343G>A	p.Glu2115Lys	p.E2115K	ENST00000277541	NM_017617.3	2115	Gag/Aag	34/34	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.358780803049168	2		305	305	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750420	41750420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	74	269	0	ENST00000226382.2:c.208del	p.Leu70SerfsTer64	p.L70Sfs*64	ENST00000226382	NM_003924.3	70	Ctc/tc	1/3	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.358780803049168	2		269	369	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457270	67457270	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	TTCCGA	novel	NA	P-0003582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	107	231	0	ENST00000327367.4:c.244delinsTTCCGA	p.Gly82PhefsTer36	p.G82Ffs*36	ENST00000327367	NM_005902.3	82	Ggg/TTCCGAgg	2/9	0.346848519873647	2	FACETS	0.857	0.777	0.94	0.857	0.777	0.94	CLONAL	2	TRUE	0	0.358780803049168	2		231	348	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519893	NA	P-0003618-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	173	525	3	ENST00000267101.3:c.310G>T	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ttg	3/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.527451415245211	2		528	532	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0003618-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	201	402	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	FALSE	1	0.527451415245211	2		402	603	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039374	49039374	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853293	NA	P-0003618-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	166	495	0	ENST00000267163.4:c.2359C>T	p.Arg787Ter	p.R787*	ENST00000267163	NM_000321.2	787	Cga/Tga	23/27	0.527451415245211	1	FACETS	0.772	0.725	0.82	1	0.992	1	SUBCLONAL	2	FALSE	0	0.527451415245211	1		495	300	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444172	49444172	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003618-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	122	421	0	ENST00000301067.7:c.3199G>T	p.Glu1067Ter	p.E1067*	ENST00000301067	NM_003482.3	1067	Gag/Tag	11/54	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.527451415245211	2		421	357	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476391	88476391	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003618-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	167	222	0	ENST00000360948.2:c.1741G>T	p.Ala581Ser	p.A581S	ENST00000360948	NM_001012338.2	581	Gcc/Tcc	15/19	0.527451415245211	2	FACETS	0.891	0.845	0.934	1	0.992	1	CLONAL	3	FALSE	0	0.527451415245211	2		222	237	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243925	41243925	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003618-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	235	339	0	ENST00000357654.3:c.3623A>C	p.Lys1208Thr	p.K1208T	ENST00000357654	NM_007294.3	1208	aAa/aCa	10/23	0.223663041243186	2	FACETS	0.913	0.862	0.964	0.913	0.862	0.964	INDETERMINATE	2	FALSE	0	0.527451415245211	2		339	488	SUCCESS
APC	324	MSKCC	GRCh37	5	112175665	112175666	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003618-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	176	417	0	ENST00000257430.4:c.4375dup	p.Thr1459AsnfsTer3	p.T1459Nfs*3	ENST00000257430	NM_000038.5	1458	-/A	16/16	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.527451415245211	2		417	463	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578471	7578483	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCGGGGGTGTG	GGGCGGGGGTGTG	-	rs137852790	NA	P-0003618-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	92	290	0	ENST00000269305.4:c.447_459del	p.Thr150AlafsTer16	p.T150Afs*16	ENST00000269305	NM_001126112.2	149	tcCACACCCCCGCCC/tc	5/11	0.43454960387276	0	FACETS		NA	1			1	NA	2	FALSE	0	0.527451415245211	0		290	170	SUCCESS
APC	324	MSKCC	GRCh37	5	112174092	112174093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0003618-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	145	315	0	ENST00000257430.4:c.2803dup	p.Tyr935LeufsTer5	p.Y935Lfs*5	ENST00000257430	NM_000038.5	934	act/acTt	16/16	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.527451415245211	2		315	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0003636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	9	276	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.194118741077883	3	FACETS	0.86	0.584	1	0.573	0.389	0.795	CLONAL	2	TRUE	0	0.239134593427076	3		276	49	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653796	89653798	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs1554893765	NA	P-0003636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	13	267	0	ENST00000371953.3:c.97_99del	p.Ile33del	p.I33del	ENST00000371953	NM_000314.4	32	ATT/-	2/9	0.194118741077883	3	FACETS	1	0.752	1	0.35	0.251	0.467	CLONAL	1	TRUE	0	0.239134593427076	3		267	116	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486063	29486064	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs771115661	NA	P-0003636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	13	192	0	ENST00000356175.3:c.246_247del	p.Gln83ValfsTer23	p.Q83Vfs*23	ENST00000356175	NM_000267.3	80	taTCtc/tatc	3/57	0.194118741077883	3	FACETS	1	0.822	1	0.402	0.29	0.535	CLONAL	1	TRUE	0	0.239134593427076	3		192	101	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890149	76890150	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0003636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	31	554	0	ENST00000373344.5:c.4744dup	p.Thr1582AsnfsTer19	p.T1582Nfs*19	ENST00000373344	NM_000489.3	1582	aca/aAca	17/35	0.239134593427076	1	FACETS	0.865	0.711	1	1	0.956	1	CLONAL	2	TRUE	0	0.239134593427076	1		554	132	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033421	48033421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750119	NA	P-0003636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	18	343	0	ENST00000234420.5:c.3725G>A	p.Arg1242His	p.R1242H	ENST00000234420	NM_000179.2	1242	cGt/cAt	8/10	0.239134593427076	3	FACETS	0.81	0.619	1	0.81	0.619	1	CLONAL	2	TRUE	1	0.239134593427076	3		343	104	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050398	37050398	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0003636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	18	248	0	ENST00000231790.2:c.545+2T>C		p.X182_splice	ENST00000231790	NM_000249.3	182			0.194118741077883	3	FACETS	1	0.814	1	0.711	0.548	0.894	CLONAL	2	TRUE	0	0.239134593427076	3		248	79	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406040	70406040	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	16	369	0	ENST00000373644.4:c.3554C>T	p.Thr1185Ile	p.T1185I	ENST00000373644	NM_030625.2	1185	aCa/aTa	4/12	0.194118741077883	3	FACETS	0.948	0.715	1	0.632	0.477	0.809	CLONAL	2	TRUE	0	0.239134593427076	3		369	79	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	29	291	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	1	2	FACETS	0.942	0.755	1	0.942	0.755	1	CLONAL	1	TRUE	1	0.14	2		291	440	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125044	46125045	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0003683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	37	306	0	ENST00000334344.6:c.234dup	p.Pro79SerfsTer6	p.P79Sfs*6	ENST00000334344	NM_152641.2	77	-/T	3/21	1	2	FACETS	0.827	0.68	0.992	0.827	0.68	0.992	CLONAL	1	TRUE	1	0.14	2		306	639	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003790-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	79	245	0				ENST00000310581	NM_198253.2	-/1132			0.362049091520615	5	FACETS	1	0.956	1	0.761	0.679	0.847	CLONAL	2	TRUE	2	0.476303933553166	5		245	249	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199821	138199821	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003790-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	62	419	0	ENST00000237289.4:c.1239G>C	p.Lys413Asn	p.K413N	ENST00000237289	NM_001270507.1	413	aaG/aaC	7/9	0.109574827461833	3	FACETS	0.631	0.545	0.723	0.21	0.181	0.241	INDETERMINATE	1	TRUE	0	0.476303933553166	3		419	511	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504321	8504321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200847027	NA	P-0003790-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	223	557	2	ENST00000356435.5:c.1762C>T	p.Arg588Cys	p.R588C	ENST00000356435		588	Cgc/Tgc	12/35	0.476303933553166	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.476303933553166	1		559	629	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130707	29130707	+	start_lost	Translation_Start_Site	SNP	C	C	A	rs786203977	NA	P-0003790-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	77	277	1	ENST00000328354.6:c.3G>T	p.Met1?	p.M1?	ENST00000328354	NM_007194.3	1	atG/atT	2/15	0.476303933553166	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.476303933553166	1		278	210	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023529	27023530	+	frameshift_variant	Frame_Shift_Ins	INS	AC	AC	TGT	novel	NA	P-0003790-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	318	542	0	ENST00000324856.7:c.635_636delinsTGT	p.Tyr212LeufsTer2	p.Y212Lfs*2	ENST00000324856	NM_006015.4	212	tAC/tTGT	1/20	0.109574827461833	3	FACETS	1	0.989	1	0.756	0.718	0.794	INDETERMINATE	2	TRUE	0	0.476303933553166	3		542	729	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262685	16262685	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564799201	NA	P-0003790-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	13	179	0	ENST00000375759.3:c.9950C>T	p.Pro3317Leu	p.P3317L	ENST00000375759	NM_015001.2	3317	cCg/cTg	11/15	0.109574827461833	3	FACETS	0.299	0.213	0.404	0.1	0.071	0.135	INDETERMINATE	1	TRUE	0	0.476303933553166	3		179	226	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604659	55604659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139694927	NA	P-0003790-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	107	546	0	ENST00000288135.5:c.2867G>A	p.Arg956Gln	p.R956Q	ENST00000288135	NM_000222.2	956	cGg/cAg	21/21	0.352283210060782	3	FACETS	0.738	0.662	0.818	0.369	0.331	0.409	SUBCLONAL	1	TRUE	1	0.476303933553166	3		546	754	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196627	106196627	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003790-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	64	417	0	ENST00000380013.4:c.4960C>G	p.Gln1654Glu	p.Q1654E	ENST00000380013	NM_001127208.2	1654	Cag/Gag	11/11	0.352283210060782	3	FACETS	0.746	0.648	0.852	0.373	0.324	0.426	SUBCLONAL	1	TRUE	1	0.476303933553166	3		417	446	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860613	151860613	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003790-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	174	729	1	ENST00000262189.6:c.10049G>C	p.Arg3350Thr	p.R3350T	ENST00000262189	NM_170606.2	3350	aGa/aCa	43/59	0.255981644238972	1	FACETS	0.742	0.685	0.802	0.742	0.685	0.802	INDETERMINATE	1	TRUE	0	0.476303933553166	1		730	750	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371801	55371801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746536924	NA	P-0003790-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	10	97	0	ENST00000297316.4:c.491C>T	p.Ala164Val	p.A164V	ENST00000297316	NM_022454.3	164	gCg/gTg	2/2	0.243660587662054	4	FACETS	0.512	0.349	0.715	0.171	0.116	0.239	INDETERMINATE	1	TRUE	1	0.476303933553166	4		97	121	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	459891	459891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003790-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	133	656	0	ENST00000399788.2:c.1204G>A	p.Glu402Lys	p.E402K	ENST00000399788	NM_001042603.1	402	Gaa/Aaa	10/28	1	2	FACETS	0.931	0.848	1	0.931	0.848	1	CLONAL	1	TRUE	1	0.476303933553166	2		656	600	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039407	47039407	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003790-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	157	351	0	ENST00000377604.3:c.1030G>T	p.Gly344Cys	p.G344C	ENST00000377604	NM_001204468.1	344	Ggc/Tgc	10/24	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.476303933553166	1		351	349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0003811-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	239	227	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.589864833451643	3	FACETS	0.98	0.936	1	0.98	0.936	1	CLONAL	3	TRUE	0	0.589864833451643	3		227	357	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0003811-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	176	282	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.589864833451643	2	FACETS	0.991	0.934	1	0.991	0.934	1	CLONAL	2	TRUE	0	0.589864833451643	2		282	301	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428410	49428411	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1284500089	NA	P-0003811-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	81	368	0	ENST00000301067.7:c.10394dup	p.Pro3466ThrfsTer2	p.P3466Tfs*2	ENST00000301067	NM_003482.3	3465	gga/ggGa	36/54	0.589864833451643	3	FACETS	0.814	0.72	0.913	0.407	0.36	0.457	CLONAL	1	TRUE	1	0.589864833451643	3		368	437	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729968	30729968	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs863223852	NA	P-0003811-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	172	209	0	ENST00000295754.5:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000295754	NM_003242.5	497	Cga/Tga	6/7	0.58630069995554	2	FACETS	0.966	0.908	1	0.966	0.908	1	CLONAL	2	TRUE	0	0.589864833451643	2		209	302	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468488	89468488	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003811-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	115	329	0	ENST00000336596.2:c.2022G>T	p.Met674Ile	p.M674I	ENST00000336596	NM_005233.5	674	atG/atT	11/17	0.589864833451643	3	FACETS	1	0.965	1	0.566	0.513	0.621	CLONAL	1	TRUE	1	0.589864833451643	3		329	446	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136837	55136837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003811-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	151	403	0	ENST00000257290.5:c.1159G>A	p.Glu387Lys	p.E387K	ENST00000257290	NM_006206.4	387	Gaa/Aaa	8/23	0.551416469867646	3	FACETS	0.875	0.81	0.941	0.875	0.81	0.941	CLONAL	2	TRUE	1	0.589864833451643	3		403	379	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55962432	55962432	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003811-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	192	371	0	ENST00000263923.4:c.2692G>A	p.Val898Met	p.V898M	ENST00000263923	NM_002253.2	898	Gtg/Atg	19/30	0.551416469867646	3	FACETS	0.891	0.833	0.95	0.891	0.833	0.95	CLONAL	2	TRUE	1	0.589864833451643	3		371	473	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164916	106164916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1361899165	NA	P-0003811-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	124	168	0	ENST00000380013.4:c.3784C>T	p.Arg1262Trp	p.R1262W	ENST00000380013	NM_001127208.2	1262	Cgg/Tgg	6/11	0.589864833451643	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.589864833451643	2		168	200	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38955731	38955731	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003811-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	97	376	0	ENST00000357387.3:c.2575G>C	p.Asp859His	p.D859H	ENST00000357387	NM_152756.3	859	Gat/Cat	26/38	0.589864833451643	6	FACETS	1	0.931	1	0.212	0.189	0.236	CLONAL	1	TRUE	1	0.589864833451643	6		376	677	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521392	8521392	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003811-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	185	401	0	ENST00000356435.5:c.846G>T	p.Met282Ile	p.M282I	ENST00000356435		282	atG/atT	9/35	0.589864833451643	2	FACETS	0.931	0.876	0.985	0.931	0.876	0.985	CLONAL	2	TRUE	0	0.589864833451643	2		401	337	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869477	102869477	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003811-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	72	212	0	ENST00000307046.8:c.164G>C	p.Gly55Ala	p.G55A	ENST00000307046	NM_001111285.1	55	gGg/gCg	2/4	0.589864833451643	3	FACETS	1	0.882	1	0.5	0.441	0.563	CLONAL	1	TRUE	1	0.589864833451643	3		212	316	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884578	111884578	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764246459	NA	P-0003811-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	215	418	0	ENST00000341259.2:c.754G>A	p.Ala252Thr	p.A252T	ENST00000341259	NM_005475.2	252	Gca/Aca	3/8	0.589864833451643	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	1	0.589864833451643	3		418	465	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68290288	68290288	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003811-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	52	407	0	ENST00000487270.1:c.28G>T	p.Gly10Cys	p.G10C	ENST00000487270	NM_133509.3	10	Ggt/Tgt	2/11	0.589864833451643	3	FACETS	0.577	0.492	0.669	0.288	0.246	0.335	SUBCLONAL	1	TRUE	1	0.589864833451643	3		407	396	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682473	37682473	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003811-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	269	267	0	ENST00000447079.4:c.3664G>T	p.Glu1222Ter	p.E1222*	ENST00000447079	NM_015083.1	1222	Gag/Tag	13/14	0.589864833451643	3	FACETS	0.987	0.945	1	0.987	0.945	1	CLONAL	3	TRUE	0	0.589864833451643	3		267	399	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899176	78899176	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003811-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	22	193	0	ENST00000306801.3:c.2815G>T	p.Asp939Tyr	p.D939Y	ENST00000306801	NM_020761.2	939	Gac/Tac	24/34	0.589864833451643	3	FACETS	0.243	0.187	0.307	0.081	0.062	0.103	SUBCLONAL	1	TRUE	0	0.589864833451643	3		193	398	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410892	63410892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369264970	NA	P-0003811-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	252	518	0	ENST00000330258.3:c.2275G>A	p.Val759Ile	p.V759I	ENST00000330258	NM_152424.3	759	Gtt/Att	2/2	0.589864833451643	1	FACETS	0.751	0.716	0.785	1	0.995	1	SUBCLONAL	2	TRUE	0	0.589864833451643	1		518	401	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448529	49448529	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003811-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	150	233	0	ENST00000301067.7:c.182del	p.Gly61ValfsTer69	p.G61Vfs*69	ENST00000301067	NM_003482.3	61	gGt/gt	3/54	0.589864833451643	3	FACETS	0.853	0.789	0.918	0.853	0.789	0.918	CLONAL	2	TRUE	1	0.589864833451643	3		233	386	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	11	340	0	ENST00000335508.6:c.2704G>A	p.Glu902Lys	p.E902K	ENST00000335508	NM_012433.2	902	Gaa/Aaa	18/25	0.314698804851077	3	FACETS	0.801	0.559	1	0.401	0.279	0.548	CLONAL	1	TRUE	1	0.314698804851077	3		340	101	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778134	27778134	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	47	867	0	ENST00000369163.2:c.283G>A	p.Glu95Lys	p.E95K	ENST00000369163	NM_003536.2	95	Gag/Aag	1/1	0.314698804851077	4	FACETS	1	0.932	1			1	CLONAL	2	TRUE	NA	0.314698804851077	4		867	170	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415025	116415025	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs781686908	NA	P-0003832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	10	300	0	ENST00000397752.3:c.3119C>G	p.Ser1040Cys	p.S1040C	ENST00000397752	NM_000245.2	1040	tCt/tGt	15/21	0.314698804851077	3	FACETS	0.855	0.586	1	0.428	0.293	0.593	CLONAL	1	TRUE	1	0.314698804851077	3		300	86	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870922	12870922	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	15	227	0	ENST00000228872.4:c.149G>C	p.Arg50Thr	p.R50T	ENST00000228872	NM_004064.3	50	aGa/aCa	1/3	0.314698804851077	7	FACETS	1	0.878	1			1	CLONAL	1	TRUE	NA	0.314698804851077	7		227	122	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871758	12871758	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0003832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	17	136	0	ENST00000228872.4:c.476-1G>C		p.X159_splice	ENST00000228872	NM_004064.3	159			0.314698804851077	7	FACETS	1	0.883	1			1	CLONAL	1	TRUE	NA	0.314698804851077	7		136	143	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936059	44936060	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0003832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	10	246	0	ENST00000377967.4:c.2822dup	p.Ser942Ter	p.S942*	ENST00000377967	NM_021140.2	940	-/C	18/29	1	1	FACETS	0.956	0.663	1	0.956	0.663	1	CLONAL	1	TRUE	0	0.314698804851077	1		246	56	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0003950-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	253	287	1	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.750497462639834	1	FACETS	0.932	0.885	0.978	0.932	0.885	0.978	CLONAL	1	TRUE	0	0.750497462639834	1		288	452	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003950-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	152	293	1	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	0.750497462639834	1	FACETS	0.373	0.342	0.406	0.373	0.342	0.406	SUBCLONAL	1	TRUE	0	0.750497462639834	1		294	678	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115750	8115750	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs104894164	NA	P-0003950-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1458	753	580	0	ENST00000346208.3:c.1096C>T	p.Arg366Ter	p.R366*	ENST00000346208		366	Cga/Tga	6/6	0.47888218486417	3	FACETS	1	0.996	1	0.624	0.602	0.646	CLONAL	1	TRUE	1	0.750497462639834	3		580	2211	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100663	67100663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003950-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	759	445	2	ENST00000412916.2:c.361G>A	p.Gly121Ser	p.G121S	ENST00000412916		121	Ggt/Agt	4/6	NA	2	FACETS	0.939	0.916	0.961			1	INDETERMINATE	2	TRUE	NA	0.750497462639834	2		447	1077	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40761126	40761127	+	inframe_insertion	In_Frame_Ins	INS	-	-	TATGACAAAGGTGTTGGGTCGCGGCCTCTCGGTCTTCATCAGCTGGCA	novel	NA	P-0003950-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1442	436	406	0	ENST00000392038.2:c.178_225dup	p.Cys60_Ile75dup	p.C60_I75dup	ENST00000392038	NM_001626.4	60	-/TGCCAGCTGATGAAGACCGAGAGGCCGCGACCCAACACCTTTGTCATA	4/14	0.535730482532472	3	FACETS	0.851	0.809	0.894	0.284	0.269	0.298	CLONAL	1	TRUE	0	0.750497462639834	3		406	1878	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749497	41749497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003950-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	105	266	0	ENST00000226382.2:c.298C>T	p.Arg100Cys	p.R100C	ENST00000226382	NM_003924.3	100	Cgc/Tgc	2/3	0.516734407909314	1	FACETS	0.26	0.233	0.289	0.26	0.233	0.289	SUBCLONAL	1	TRUE	0	0.750497462639834	1		266	672	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164152	108164152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs550552791	NA	P-0003950-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	146	262	0	ENST00000278616.4:c.4724G>A	p.Arg1575His	p.R1575H	ENST00000278616	NM_000051.3	1575	cGt/cAt	31/63	0.329411254424657	3	FACETS	0.511	0.465	0.558	0.255	0.232	0.279	INDETERMINATE	1	TRUE	1	0.750497462639834	3		262	1048	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857362	9857362	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003950-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	142	303	0	ENST00000330684.3:c.4039G>T	p.Gly1347Cys	p.G1347C	ENST00000330684	NM_001134407.1	1347	Ggt/Tgt	13/13	0.47888218486417	3	FACETS	0.406	0.368	0.445	0.203	0.184	0.223	SUBCLONAL	1	TRUE	1	0.750497462639834	3		303	1283	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264440	46264440	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003950-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1748	247	588	0	ENST00000371998.3:c.1487A>G	p.Gln496Arg	p.Q496R	ENST00000371998		496	cAg/cGg	11/23	NA	2	FACETS	0.33	0.307	0.354			1	INDETERMINATE	1	TRUE	NA	0.750497462639834	2		588	1995	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	26	245	0				ENST00000310581	NM_198253.2	-/1132			0.230526486696459	1	FACETS	0.941	0.787	1	1	0.969	1	CLONAL	4	FALSE	0	0.230526486696459	1		245	53	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0004029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	217	237	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	0.230526486696459	4	FACETS	1	0.981	1	1	0.995	1	CLONAL	5	FALSE	2	0.230526486696459	4		237	425	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53241030	53241031	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0004029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	223	429	0	ENST00000375401.3:c.1180_1181del	p.Leu394AlafsTer11	p.L394Afs*11	ENST00000375401	NM_004187.3	394	CTg/g	9/26	0.230526486696459	1	FACETS	1	0.977	1	1	0.995	1	CLONAL	2	FALSE	0	0.230526486696459	1		429	777	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435412	18435412	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	66	212	0	ENST00000266497.5:c.397C>T	p.His133Tyr	p.H133Y	ENST00000266497		133	Cat/Tat	1/31	0.205826305324866	0	FACETS	1	0.955	1			1	CLONAL	1	FALSE	0	0.230526486696459	0		212	363	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171722	36171723	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0004029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	96	135	0	ENST00000300305.3:c.842dup	p.Tyr281Ter	p.Y281*	ENST00000300305		281	tac/taAc	7/8	0.230526486696459	1	FACETS	1	0.943	1	1	0.988	1	CLONAL	2	FALSE	0	0.230526486696459	1		135	344	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0004040-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	76	783	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.260723338412569	1	FACETS	0.665	0.583	0.754	0.665	0.583	0.754	SUBCLONAL	1	FALSE	0	0.260723338412569	1		783	762	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004040-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	62	218	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.849	0.734	0.974	0.849	0.734	0.974	CLONAL	1	FALSE	1	0.260723338412569	2		218	560	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0004040-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	67	628	0	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	0.238398717069638	3	FACETS	0.818	0.71	0.935	0.409	0.355	0.468	CLONAL	1	FALSE	1	0.260723338412569	3		628	710	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831603	72831604	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCACTCACA	novel	NA	P-0004040-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	84	411	0	ENST00000268489.5:c.4977_4978insTGTGAGTGGC	p.Ser1660CysfsTer5	p.S1660Cfs*5	ENST00000268489	NM_006885.3	1659	-/TGTGAGTGGC	9/10	0.254637311340915	0	FACETS	0.497	0.438	0.561			1	SUBCLONAL	1	FALSE	0	0.260723338412569	0		411	958	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591115	67591116	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1561299903	NA	P-0004040-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	96	235	0	ENST00000274335.5:c.1710dup	p.Ile571TyrfsTer31	p.I571Yfs*31	ENST00000274335		570	ctt/cTtt	12/15	0.238398717069638	3	FACETS	1	0.966	1	0.605	0.539	0.675	CLONAL	1	FALSE	1	0.260723338412569	3		235	688	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330610	65330611	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004040-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	55	587	0	ENST00000342505.4:c.1035dup	p.Leu346ThrfsTer4	p.L346Tfs*4	ENST00000342505	NM_002227.2	345	-/A	8/25	0.260723338412569	1	FACETS	0.607	0.519	0.704	0.607	0.519	0.704	SUBCLONAL	1	FALSE	0	0.260723338412569	1		587	604	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	43	201	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.55	2		201	145	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907683	111907683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146318804	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	77	239	0	ENST00000393256.3:c.457C>T	p.Arg153Trp	p.R153W	ENST00000393256	NM_006538.4	153	Cgg/Tgg	3/4	1	2	FACETS	0.87	0.77	0.974	0.87	0.77	0.974	CLONAL	1	TRUE	1	0.55	2		239	322	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	97	365	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.921	0.828	1	0.921	0.828	1	CLONAL	1	TRUE	1	0.55	2		365	383	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	76	476	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.801	0.708	0.9	0.801	0.708	0.9	CLONAL	1	TRUE	1	0.55	2		476	345	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	30	333	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.88	0.722	1	0.88	0.722	1	CLONAL	1	TRUE	1	0.55	2		335	124	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	109	299	7	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	0.168646998979885	3	FACETS	1	0.96	1	0.56	0.506	0.617	INDETERMINATE	1	TRUE	1	0.55	3		306	451	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	122	623	6	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	0.3	1	FACETS	0.759	0.691	0.828	0.759	0.691	0.828	INDETERMINATE	1	TRUE	0	0.55	1		629	424	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	58	197	0	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.55	2		197	208	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	108	250	1	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.956	0.864	1	0.956	0.864	1	CLONAL	1	TRUE	1	0.55	2		251	411	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821959	72821960	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs762108866	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	48	248	1	ENST00000268489.5:c.10215dup	p.Gly3406ArgfsTer25	p.G3406Rfs*25	ENST00000268489	NM_006885.3	3405	-/C	10/10	0.168646998979885	0	FACETS	0.271	0.23	0.315			1	INDETERMINATE	1	TRUE	0	0.55	0		249	290	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70441157	70441157	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	rs764225020	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	134	312	0	ENST00000373644.4:c.4832del	p.Asn1611ThrfsTer13	p.N1611Tfs*13	ENST00000373644	NM_030625.2	1609	gAa/ga	9/12	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.55	2		312	457	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625281	69625281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35983315	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	62	359	1	ENST00000334134.2:c.512G>A	p.Arg171His	p.R171H	ENST00000334134	NM_005247.2	171	cGc/cAc	3/3	1	2	FACETS	0.928	0.811	1	0.928	0.811	1	CLONAL	1	TRUE	1	0.55	2		360	243	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625080	69625080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782166974	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	18	130	0	ENST00000334134.2:c.713C>T	p.Ala238Val	p.A238V	ENST00000334134	NM_005247.2	238	gCg/gTg	3/3	1	2	FACETS	0.85	0.655	1	0.85	0.655	1	CLONAL	1	TRUE	1	0.55	2		130	77	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203691	94203691	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	125	277	2	ENST00000323929.3:c.963del	p.Phe321LeufsTer8	p.F321Lfs*8	ENST00000323929	NM_005591.3	321	ttT/tt	9/20	1	2	FACETS	0.988	0.901	1	0.988	0.901	1	CLONAL	1	TRUE	1	0.55	2		279	460	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885643	23885643	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	131	477	0	ENST00000374561.5:c.275C>A	p.Pro92His	p.P92H	ENST00000374561	NM_002167.4	92	cCt/cAt	1/3	0.124661773991986	0	FACETS	0.439	0.401	0.479			1	INDETERMINATE	1	TRUE	0	0.55	0		477	488	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076815	72076815	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	123	247	1	ENST00000357731.5:c.682C>G	p.Gln228Glu	p.Q228E	ENST00000357731	NM_173808.2	228	Cag/Gag	5/7	1	2	FACETS	0.99	0.901	1	0.99	0.901	1	CLONAL	1	TRUE	1	0.55	2		248	452	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150030	202150030	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs931648756	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	47	152	0	ENST00000358485.4:c.1471C>T	p.Arg491Ter	p.R491*	ENST00000358485	NM_001080125.1	491	Cga/Tga	8/9	1	2	FACETS	0.904	0.774	1	0.904	0.774	1	CLONAL	1	TRUE	1	0.55	2		152	189	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932614	49932614	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754083586	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	94	365	0	ENST00000296474.3:c.3257G>A	p.Arg1086Gln	p.R1086Q	ENST00000296474	NM_002447.2	1086	cGa/cAa	14/20	1	2	FACETS	0.944	0.847	1	0.944	0.847	1	CLONAL	1	TRUE	1	0.55	2		365	362	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940468	49940468	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	134	526	0	ENST00000296474.3:c.575G>A	p.Gly192Asp	p.G192D	ENST00000296474	NM_002447.2	192	gGc/gAc	1/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.55	2		526	431	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436857	52436857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	81	320	0	ENST00000460680.1:c.1921G>A	p.Ala641Thr	p.A641T	ENST00000460680	NM_004656.3	641	Gct/Act	15/17	1	2	FACETS	0.938	0.835	1	0.938	0.835	1	CLONAL	1	TRUE	1	0.55	2		320	314	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200768	128200768	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	55	198	0	ENST00000341105.2:c.1037G>T	p.Gly346Val	p.G346V	ENST00000341105	NM_032638.4	346	gGc/gTc	5/6	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.55	2		198	180	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880887	134880887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	86	262	0	ENST00000398015.3:c.1450G>A	p.Ala484Thr	p.A484T	ENST00000398015	NM_004441.4	484	Gcc/Acc	7/16	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.55	2		262	304	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196328	106196328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	125	284	0	ENST00000380013.4:c.4661C>T	p.Thr1554Ile	p.T1554I	ENST00000380013	NM_001127208.2	1554	aCa/aTa	11/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.55	2		284	374	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197190	106197190	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	65	139	0	ENST00000380013.4:c.5523G>T	p.Glu1841Asp	p.E1841D	ENST00000380013	NM_001127208.2	1841	gaG/gaT	11/11	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.55	2		139	207	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524899	187524899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	92	295	1	ENST00000441802.2:c.10781G>A	p.Ser3594Asn	p.S3594N	ENST00000441802	NM_005245.3	3594	aGc/aAc	19/27	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.55	2		296	302	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575474	67575474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	103	198	0	ENST00000274335.5:c.547G>A	p.Ala183Thr	p.A183T	ENST00000274335		183	Gct/Act	4/15	0.168646998979885	3	FACETS	1	0.956	1	0.555	0.5	0.613	INDETERMINATE	1	TRUE	1	0.55	3		198	430	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593343	67593343	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	121	313	0	ENST00000274335.5:c.2089C>T	p.His697Tyr	p.H697Y	ENST00000274335		697	Cat/Tat	15/15	0.168646998979885	3	FACETS	1	0.978	1	0.625	0.568	0.683	INDETERMINATE	1	TRUE	1	0.55	3		313	449	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449546	149449546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376388107	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	75	330	0	ENST00000286301.3:c.1400C>T	p.Thr467Met	p.T467M	ENST00000286301	NM_005211.3	467	aCg/aTg	10/22	1	2	FACETS	0.819	0.723	0.92	0.819	0.723	0.92	CLONAL	1	TRUE	1	0.55	2		330	333	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250724	26250724	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1485980644	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	158	442	0	ENST00000446824.2:c.110A>G	p.Lys37Arg	p.K37R	ENST00000446824	NM_021018.2	37	aAg/aGg	1/1	0.168646998979885	3	FACETS	1	0.983	1	0.627	0.577	0.679	INDETERMINATE	1	TRUE	1	0.55	3		442	584	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166285	32166285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	81	211	0	ENST00000375023.3:c.4669G>A	p.Gly1557Ser	p.G1557S	ENST00000375023	NM_004557.3	1557	Ggc/Agc	26/30	0.168646998979885	3	FACETS	1	0.972	1	0.65	0.579	0.724	INDETERMINATE	1	TRUE	1	0.55	3		211	289	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394349	162394349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137853054	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	95	236	0	ENST00000366898.1:c.719C>T	p.Thr240Met	p.T240M	ENST00000366898	NM_004562.2	240	aCg/aTg	6/12	0.3	2	FACETS	1	0.96	1			1	INDETERMINATE	1	TRUE	NA	0.55	2		236	306	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468150	50468150	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	73	171	0	ENST00000331340.3:c.1385A>G	p.Tyr462Cys	p.Y462C	ENST00000331340	NM_006060.4	462	tAc/tGc	8/8	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.55	2		171	252	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513046	106513046	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	63	164	0	ENST00000359195.3:c.2060G>A	p.Arg687Lys	p.R687K	ENST00000359195	NM_002649.2	687	aGa/aAa	3/11	1	2	FACETS	0.749	0.653	0.851	0.749	0.653	0.851	SUBCLONAL	1	TRUE	1	0.55	2		164	306	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396823	139396823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs942439472	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	56	242	0	ENST00000277541.6:c.5285G>A	p.Arg1762Gln	p.R1762Q	ENST00000277541	NM_017617.3	1762	cGg/cAg	28/34	0.124661773991986	0	FACETS	0.493	0.429	0.559			1	INDETERMINATE	1	TRUE	0	0.55	0		242	186	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333182	70333182	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	83	327	0	ENST00000373644.4:c.1087T>G	p.Ser363Ala	p.S363A	ENST00000373644	NM_030625.2	363	Tct/Gct	2/12	1	2	FACETS	0.92	0.82	1	0.92	0.82	1	CLONAL	1	TRUE	1	0.55	2		327	328	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741573	17741573	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1285231710	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	54	129	1	ENST00000250003.3:c.244C>T	p.Arg82Cys	p.R82C	ENST00000250003	NM_002478.4	82	Cgc/Tgc	1/3	0.3	2	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.55	2		130	140	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200841	67200841	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	69	303	0	ENST00000312629.5:c.829A>C	p.Thr277Pro	p.T277P	ENST00000312629	NM_003952.2	277	Acc/Ccc	10/15	1	2	FACETS	0.922	0.812	1	0.922	0.812	1	CLONAL	1	TRUE	1	0.55	2		303	272	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484049	50484049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	77	226	0	ENST00000394963.4:c.899G>A	p.Arg300His	p.R300H	ENST00000394963	NM_003076.4	300	cGc/cAc	8/13	1	2	FACETS	0.862	0.763	0.966	0.862	0.763	0.966	CLONAL	1	TRUE	1	0.55	2		226	325	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590990	95590990	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772431718	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	59	119	0	ENST00000393063.1:c.919C>T	p.Arg307Cys	p.R307C	ENST00000393063	NM_030621.3	307	Cgt/Tgt	9/28	1	2	FACETS	0.917	0.799	1	0.917	0.799	1	CLONAL	1	TRUE	1	0.55	2		119	234	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641679	23641679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	92	264	0	ENST00000261584.4:c.1796G>A	p.Ser599Asn	p.S599N	ENST00000261584	NM_024675.3	599	aGt/aAt	5/13	1	2	FACETS	0.845	0.756	0.938	0.845	0.756	0.938	CLONAL	1	TRUE	1	0.55	2		264	396	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984704	72984704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	145	543	0	ENST00000268489.5:c.2880G>A	p.Met960Ile	p.M960I	ENST00000268489	NM_006885.3	960	atG/atA	3/10	0.168646998979885	0	FACETS	0.48	0.441	0.521			1	INDETERMINATE	1	TRUE	0	0.55	0		543	494	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533279	29533279	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	92	232	0	ENST00000356175.3:c.1282A>G	p.Lys428Glu	p.K428E	ENST00000356175	NM_000267.3	428	Aag/Gag	12/57	1	2	FACETS	0.847	0.758	0.941	0.847	0.758	0.941	CLONAL	1	TRUE	1	0.55	2		232	395	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448270	56448270	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	48	98	0	ENST00000407977.2:c.375+2T>C		p.X125_splice	ENST00000407977		125			1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.55	2		98	166	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213969	2213969	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	36	102	0	ENST00000398665.3:c.1781G>A	p.Gly594Asp	p.G594D	ENST00000398665	NM_032482.2	594	gGc/gAc	18/28	0.124661773991986	0	FACETS	0.479	0.402	0.561			1	INDETERMINATE	1	TRUE	0	0.55	0		102	123	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222993	5222993	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762510209	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	20	136	0	ENST00000357368.4:c.2810C>T	p.Ala937Val	p.A937V	ENST00000357368	NM_002850.3	937	gCg/gTg	18/38	0.124661773991986	0	FACETS	0.318	0.247	0.398			1	INDETERMINATE	1	TRUE	0	0.55	0		136	103	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172331	7172331	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758151117	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	99	330	0	ENST00000302850.5:c.1238G>A	p.Arg413His	p.R413H	ENST00000302850	NM_000208.2	413	cGt/cAt	5/22	0.124661773991986	0	FACETS	0.421	0.378	0.465			1	INDETERMINATE	1	TRUE	0	0.55	0		330	385	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281250	15281250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184522923	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	42	231	0	ENST00000263388.2:c.5006G>A	p.Arg1669His	p.R1669H	ENST00000263388	NM_000435.2	1669	cGc/cAc	27/33	1	2	FACETS	0.8	0.676	0.933	0.8	0.676	0.933	CLONAL	1	TRUE	1	0.55	2		231	191	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39721126	39721126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771318367	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	95	211	0	ENST00000361337.2:c.629G>A	p.Arg210His	p.R210H	ENST00000361337	NM_003286.2	210	cGc/cAc	9/21	1	2	FACETS	0.924	0.829	1	0.924	0.829	1	CLONAL	1	TRUE	1	0.55	2		211	374	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231788	36231788	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	72	203	0	ENST00000300305.3:c.596G>T	p.Gly199Val	p.G199V	ENST00000300305		199	gGg/gTg	5/8	1	2	FACETS	0.813	0.716	0.916	0.813	0.716	0.916	CLONAL	1	TRUE	1	0.55	2		203	322	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551089	41551089	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	90	486	0	ENST00000263253.7:c.3233C>A	p.Pro1078His	p.P1078H	ENST00000263253	NM_001429.3	1078	cCt/cAt	17/31	1	2	FACETS	0.616	0.548	0.689	0.616	0.548	0.689	SUBCLONAL	1	TRUE	1	0.55	2		486	531	SUCCESS
AR	367	MSKCC	GRCh37	X	66766451	66766451	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	40	79	0	ENST00000374690.3:c.1463A>G	p.Gln488Arg	p.Q488R	ENST00000374690	NM_000044.3	488	cAg/cGg	1/8	1	1	FACETS	0.764	0.67	0.855	1	0.969	1	SUBCLONAL	2	TRUE	0	0.55	1		79	69	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917717	151917717	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	19	80	0	ENST00000262189.6:c.3603del	p.Lys1201AsnfsTer4	p.K1201Nfs*4	ENST00000262189	NM_170606.2	1201	aaA/aa	23/59	1	2	FACETS	0.768	0.594	0.963	0.768	0.594	0.963	CLONAL	1	TRUE	1	0.55	2		80	90	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798220	42798222	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	38	284	0	ENST00000575354.2:c.4178_4180del	p.Lys1393del	p.K1393del	ENST00000575354	NM_015125.3	1392	AAG/-	17/20	0.168646998979885	0	FACETS	0.284	0.236	0.336			1	INDETERMINATE	1	TRUE	0	0.55	0		284	219	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831385	72831386	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGTTGTTGC	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	39	321	0	ENST00000268489.5:c.5195_5196insGCAACAACA	p.Gln1739_Gln1741dup	p.Q1739_Q1741dup	ENST00000268489	NM_006885.3	1739	caa/caGCAACAACAa	9/10	0.168646998979885	0	FACETS	0.204	0.169	0.242			1	INDETERMINATE	1	TRUE	0	0.55	0		321	313	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424734	47424734	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	106	229	0	ENST00000377045.4:c.547del	p.Gln183ArgfsTer109	p.Q183Rfs*109	ENST00000377045	NM_001654.4	181	aCc/ac	6/16	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.55	1		229	222	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116263	209116263	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	135	305	0	ENST00000345146.2:c.13del	p.Ile5SerfsTer7	p.I5Sfs*7	ENST00000345146	NM_005896.2	5	Atc/tc	3/10	1	2	FACETS	0.843	0.77	0.92	0.843	0.77	0.92	CLONAL	1	TRUE	1	0.55	2		305	582	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172203	99172203	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	83	344	0	ENST00000074304.5:c.1769del	p.Cys590LeufsTer21	p.C590Lfs*21	ENST00000074304	NM_001134224.1	590	tGt/tt	17/26	1	2	FACETS	0.94	0.838	1	0.94	0.838	1	CLONAL	1	TRUE	1	0.55	2		344	321	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798164	42798164	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	61	339	0	ENST00000575354.2:c.4122del	p.Thr1375ProfsTer40	p.T1375Pfs*40	ENST00000575354	NM_015125.3	1373	tCc/tc	17/20	0.168646998979885	0	FACETS	0.471	0.412	0.533			1	INDETERMINATE	1	TRUE	0	0.55	0		339	212	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347983	347983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760961378	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	48	275	4	ENST00000262320.3:c.1523del	p.Gly508ValfsTer197	p.G508Vfs*197	ENST00000262320	NM_003502.3	508	gGt/gt	6/11	0.3	1	FACETS	0.536	0.458	0.621	0.536	0.458	0.621	INDETERMINATE	1	TRUE	0	0.55	1		279	236	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306996	65306997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	106	225	4	ENST00000342505.4:c.2580dup	p.Pro861ThrfsTer4	p.P861Tfs*4	ENST00000342505	NM_002227.2	860	-/A	19/25	1	2	FACETS	0.903	0.815	0.995	0.903	0.815	0.995	CLONAL	1	TRUE	1	0.55	2		229	427	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348211	348211	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1458136153	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	46	116	0	ENST00000262320.3:c.1295del	p.Pro432GlnfsTer48	p.P432Qfs*48	ENST00000262320	NM_003502.3	432	cCa/ca	6/11	0.3	1	FACETS	0.962	0.832	1	0.962	0.832	1	INDETERMINATE	1	TRUE	0	0.55	1		116	126	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781141	135781141	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs118203585	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	152	678	2	ENST00000298552.3:c.1824del	p.Phe608LeufsTer21	p.F608Lfs*21	ENST00000298552	NM_001162426.1	608	ttT/tt	15/23	0.124661773991986	0	FACETS	0.419	0.384	0.454			1	INDETERMINATE	1	TRUE	0	0.55	0		680	594	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007824	45007825	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	78	162	0	ENST00000558401.1:c.276dup	p.Thr93HisfsTer2	p.T93Hfs*2	ENST00000558401	NM_004048.2	91	acc/aCcc	2/4	1	2	FACETS	0.86	0.762	0.963	0.86	0.762	0.963	CLONAL	1	TRUE	1	0.55	2		162	330	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	198	611	3	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	0.986	0.916	1	0.986	0.916	1	CLONAL	1	TRUE	1	0.55	2		614	730	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785964	135785964	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs118203506	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	36	139	2	ENST00000298552.3:c.1257del	p.Arg420GlyfsTer20	p.R420Gfs*20	ENST00000298552	NM_001162426.1	419	ccC/cc	12/23	0.124661773991986	0	FACETS	0.446	0.374	0.524			1	INDETERMINATE	1	TRUE	0	0.55	0		141	132	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483185	120483185	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	62	127	0	ENST00000256646.2:c.3176del	p.Asn1059ThrfsTer6	p.N1059Tfs*6	ENST00000256646	NM_024408.3	1059	aAc/ac	19/34	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.55	2		127	224	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202374	138202374	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	25	147	0	ENST00000237289.4:c.2295del	p.Ala766ProfsTer50	p.A766Pfs*50	ENST00000237289	NM_001270507.1	764	gCc/gc	9/9	0.3	3	FACETS	0.513	0.406	0.635			1	INDETERMINATE	1	TRUE	NA	0.55	3		147	226	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781121	161781122	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	rs758718482	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	28	226	0	ENST00000366898.1:c.1283dup	p.Asn428LysfsTer141	p.N428Kfs*141	ENST00000366898	NM_004562.2	428	aat/aaAt	11/12	0.3	2	FACETS	0.256	0.205	0.316			1	INDETERMINATE	1	TRUE	NA	0.55	2		226	397	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245587	41245587	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357522	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	92	338	1	ENST00000357654.3:c.1961del	p.Lys654SerfsTer47	p.K654Sfs*47	ENST00000357654	NM_007294.3	654	aAg/ag	10/23	0.3	1	FACETS	0.567	0.506	0.63	0.567	0.506	0.63	INDETERMINATE	1	TRUE	0	0.55	1		339	428	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934301	39934302	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0004051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	125	201	1	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	0.55	1		202	220	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	56	983	0	ENST00000206249.3:c.1610A>G	p.Tyr537Cys	p.Y537C	ENST00000206249	NM_000125.3	537	tAt/tGt	8/8	0.439667955451005	1	FACETS	0.742	0.641	0.849	0.742	0.641	0.849	SUBCLONAL	1	TRUE	0	0.439667955451005	1		983	268	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112025277	112025277	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	186	530	0	ENST00000368678.4:c.472G>C	p.Asp158His	p.D158H	ENST00000368678		158	Gat/Cat	6/13	0.439667955451005	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.439667955451005	1		530	623	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55238895	55238895	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	88	298	0	ENST00000275493.2:c.1908T>G	p.Cys636Trp	p.C636W	ENST00000275493	NM_005228.3	636	tgT/tgG	16/28	1	2	FACETS	0.825	0.734	0.922	0.825	0.734	0.922	CLONAL	1	TRUE	1	0.439667955451005	2		298	485	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443838	18443838	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	246	344	0	ENST00000266497.5:c.811A>T	p.Ile271Phe	p.I271F	ENST00000266497		271	Atc/Ttc	3/31	0.439667955451005	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.439667955451005	3		344	644	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959063	28959063	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	108	300	0	ENST00000282397.4:c.2075T>G	p.Ile692Ser	p.I692S	ENST00000282397	NM_002019.4	692	aTc/aGc	14/30	0.439667955451005	1	FACETS	0.983	0.89	1	0.983	0.89	1	CLONAL	1	TRUE	0	0.439667955451005	1		300	390	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998898	11998898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	100	237	0	ENST00000353533.5:c.400C>T	p.Arg134Trp	p.R134W	ENST00000353533	NM_003010.3	134	Cgg/Tgg	4/11	0.439667955451005	1	FACETS	0.975	0.879	1	0.975	0.879	1	CLONAL	1	TRUE	0	0.439667955451005	1		237	364	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968871	15968871	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	103	312	0	ENST00000268712.3:c.4879T>G	p.Leu1627Val	p.L1627V	ENST00000268712	NM_006311.3	1627	Ttg/Gtg	33/46	0.439667955451005	1	FACETS	0.914	0.824	1	0.914	0.824	1	CLONAL	1	TRUE	0	0.439667955451005	1		312	400	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216476	108216477	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587782558	NA	P-0004104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	123	293	0	ENST00000278616.4:c.8432dup	p.Ser2812ValfsTer3	p.S2812Vfs*3	ENST00000278616	NM_000051.3	2809	caa/cAaa	58/63	0.439667955451005	1	FACETS	0.953	0.868	1	0.953	0.868	1	CLONAL	1	TRUE	0	0.439667955451005	1		293	458	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0004113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	132	348	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.157789710083213	3	FACETS	0.998	0.906	1	0.998	0.906	1	CLONAL	2	TRUE	1	0.157789710083213	3		348	904	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0004113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	21	625	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.417	0.319	0.531	0.417	0.319	0.531	SUBCLONAL	1	TRUE	1	0.157789710083213	2		625	639	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186775	108186776	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCTAGTAACATATGA	novel	NA	P-0004113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	74	682	0	ENST00000278616.4:c.6136_6151dup	p.Leu2051ProfsTer5	p.L2051Pfs*5	ENST00000278616	NM_000051.3	2045	gcc/gCCCTAGTAACATATGAcc	42/63	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.157789710083213	2		682	800	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952117	178952117	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	115	280	0	ENST00000263967.3:c.3172A>C	p.Ile1058Leu	p.I1058L	ENST00000263967	NM_006218.2	1058	Atc/Ctc	21/21	1	2	FACETS	0.842	0.762	0.924	0.842	0.762	0.924	CLONAL	1	TRUE	1	0.576612787062073	2		280	474	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0004136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	81	175	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.969	0.863	1	0.969	0.863	1	CLONAL	1	TRUE	1	0.576612787062073	2		175	290	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717769	89717770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	135	192	0	ENST00000371953.3:c.800dup	p.Asp268GlyfsTer30	p.D268Gfs*30	ENST00000371953	NM_000314.4	265	cta/ctAa	7/9	1	2	FACETS	0.925	0.861	0.99	1	0.992	1	CLONAL	2	TRUE	1	0.576612787062073	2		192	253	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654642	67654642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	230	484	2	ENST00000264010.4:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000264010	NM_006565.3	377	Cgt/Tgt	6/12	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.576612787062073	2		486	697	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256974	41256974	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs80358146	NA	P-0004136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	137	287	1	ENST00000357654.3:c.213-1G>A		p.X71_splice	ENST00000357654	NM_007294.3	71			NA	2	FACETS	1	0.916	1			1	INDETERMINATE	1	TRUE	NA	0.576612787062073	2		288	475	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0004136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	144	326	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	0.999	0.917	1	0.999	0.917	1	CLONAL	1	TRUE	1	0.576612787062073	2		326	500	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99160393	99160393	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1360678266	NA	P-0004136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	173	403	0	ENST00000074304.5:c.872G>A	p.Arg291Gln	p.R291Q	ENST00000074304	NM_001134224.1	291	cGg/cAg	11/26	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.576612787062073	2		403	543	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617589	158617589	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121912679	NA	P-0004136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	191	474	0	ENST00000263640.3:c.1067G>A	p.Gly356Asp	p.G356D	ENST00000263640	NM_001105.4	356	gGc/gAc	9/11	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.576612787062073	2		474	652	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209110101	209110101	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	218	412	0	ENST00000345146.2:c.462A>G	p.Ile154Met	p.I154M	ENST00000345146	NM_005896.2	154	atA/atG	5/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.576612787062073	2		412	681	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519886	NA	P-0004136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	188	407	0	ENST00000349496.5:c.97T>G	p.Ser33Ala	p.S33A	ENST00000349496	NM_001904.3	33	Tct/Gct	3/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.576612787062073	2		407	597	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807829	1807829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1336255288	NA	P-0004136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	152	413	1	ENST00000260795.2:c.1888G>A	p.Val630Met	p.V630M	ENST00000260795		630	Gtg/Atg	13/17	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.576612787062073	2		414	516	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55603394	55603394	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	212	501	0	ENST00000288135.5:c.2750T>C	p.Phe917Ser	p.F917S	ENST00000288135	NM_000222.2	917	tTc/tCc	20/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.576612787062073	2		501	671	SUCCESS
APC	324	MSKCC	GRCh37	5	112178196	112178196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	195	426	0	ENST00000257430.4:c.6905C>T	p.Ser2302Leu	p.S2302L	ENST00000257430	NM_000038.5	2302	tCa/tTa	16/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.576612787062073	2		426	589	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012310	152012310	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	221	380	1	ENST00000262189.6:c.503C>A	p.Ser168Tyr	p.S168Y	ENST00000262189	NM_170606.2	168	tCt/tAt	4/59	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.576612787062073	2		381	740	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538930	23538930	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	142	485	0	ENST00000380871.4:c.509T>C	p.Ile170Thr	p.I170T	ENST00000380871	NM_006167.3	170	aTa/aCa	2/2	1	2	FACETS	0.817	0.747	0.889	0.817	0.747	0.889	CLONAL	1	TRUE	1	0.576612787062073	2		485	603	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619251	43619251	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	95	256	0	ENST00000355710.3:c.2934G>T	p.Glu978Asp	p.E978D	ENST00000355710	NM_020975.4	978	gaG/gaT	17/20	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.576612787062073	NA		256	354	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533836	533836	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	157	446	0	ENST00000451590.1:c.220A>G	p.Thr74Ala	p.T74A	ENST00000451590	NM_001130442.1	74	Acc/Gcc	3/5	1	2	FACETS	0.983	0.906	1	0.983	0.906	1	CLONAL	1	TRUE	1	0.576612787062073	2		446	554	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456764	32456764	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1565002394	NA	P-0004136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	11	144	0	ENST00000332351.3:c.128T>C	p.Leu43Ser	p.L43S	ENST00000332351	NM_024426.4	43	tTa/tCa	1/10	1	2	FACETS	0.224	0.155	0.31	0.224	0.155	0.31	SUBCLONAL	1	TRUE	1	0.576612787062073	2		144	170	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793388	18793388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	215	408	0	ENST00000266497.5:c.4085G>A	p.Ser1362Asn	p.S1362N	ENST00000266497		1362	aGt/aAt	30/31	1	2	FACETS	0.998	0.931	1	0.998	0.931	1	CLONAL	1	TRUE	1	0.576612787062073	2		408	747	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001981	29001981	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	158	342	0	ENST00000282397.4:c.1184T>C	p.Val395Ala	p.V395A	ENST00000282397	NM_002019.4	395	gTa/gCa	9/30	1	2	FACETS	0.942	0.867	1	0.942	0.867	1	CLONAL	1	TRUE	1	0.576612787062073	2		342	582	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774159	66774159	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	178	446	0	ENST00000307102.5:c.635G>A	p.Ser212Asn	p.S212N	ENST00000307102	NM_002755.3	212	aGc/aAc	6/11	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.576612787062073	2		446	608	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7132201	7132201	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	145	378	0	ENST00000302850.5:c.2810C>T	p.Thr937Met	p.T937M	ENST00000302850	NM_000208.2	937	aCg/aTg	14/22	1	2	FACETS	0.926	0.85	1	0.926	0.85	1	CLONAL	1	TRUE	1	0.576612787062073	2		378	543	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260278	10260278	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	117	317	0	ENST00000340748.4:c.2389T>C	p.Phe797Leu	p.F797L	ENST00000340748		797	Ttc/Ctc	25/40	1	2	FACETS	0.927	0.841	1	0.927	0.841	1	CLONAL	1	TRUE	1	0.576612787062073	2		317	438	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918822	50918822	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	166	583	0	ENST00000440232.2:c.2692C>G	p.Gln898Glu	p.Q898E	ENST00000440232	NM_002691.3	898	Cag/Gag	21/27	1	2	FACETS	0.998	0.922	1	0.998	0.922	1	CLONAL	1	TRUE	1	0.576612787062073	2		583	577	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356405	70356405	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	166	607	1	ENST00000374080.3:c.5300C>A	p.Pro1767His	p.P1767H	ENST00000374080		1767	cCc/cAc	37/45	1	2	FACETS	0.857	0.79	0.926	0.857	0.79	0.926	CLONAL	1	TRUE	1	0.576612787062073	2		608	672	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645357	67645357	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	135	292	0	ENST00000264010.4:c.626del	p.Lys209ArgfsTer13	p.K209Rfs*13	ENST00000264010	NM_006565.3	208	Aaa/aa	3/12	1	2	FACETS	0.925	0.846	1	0.925	0.846	1	CLONAL	1	TRUE	1	0.576612787062073	2		292	506	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882050	36882050	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs780753361	NA	P-0004136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	162	188	0	ENST00000358127.4:c.963del	p.Ala322LeufsTer11	p.A322Lfs*11	ENST00000358127	NM_001280556.1	321	ccC/cc	8/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.576612787062073	2		188	504	SUCCESS
AR	367	MSKCC	GRCh37	X	66766424	66766424	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	43	141	0	ENST00000374690.3:c.1440del	p.Tyr481ThrfsTer29	p.Y481Tfs*29	ENST00000374690	NM_000044.3	479	gCc/gc	1/8	1	2	FACETS	0.915	0.778	1	0.915	0.778	1	CLONAL	1	TRUE	1	0.576612787062073	2		141	163	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481796	40481796	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0004139-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	78	382	0	ENST00000264657.5:c.1110-2A>G		p.X370_splice	ENST00000264657	NM_139276.2	370			1	2	FACETS	0.699	0.613	0.792	0.699	0.613	0.792	SUBCLONAL	1	TRUE	1	0.241808169082486	2		382	923	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332847	153332848	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CACACGA	novel	NA	P-0004139-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	129	250	0	ENST00000281708.4:c.102_108dup	p.Val37SerfsTer24	p.V37Sfs*24	ENST00000281708	NM_033632.3	36	-/TCGTGTG	2/12	0.208037079434195	2	FACETS	0.766	0.696	0.84	0.766	0.696	0.84	SUBCLONAL	2	TRUE	0	0.241808169082486	2		250	696	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0004194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	31	328	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.684	0.555	0.83	0.684	0.555	0.83	SUBCLONAL	1	TRUE	1	0.293305738718108	2		328	309	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0004194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	97	533	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.268801049101747	1	FACETS	0.812	0.724	0.905	0.812	0.724	0.905	CLONAL	1	TRUE	0	0.293305738718108	1		533	695	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004856	16004856	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	102	393	2	ENST00000268712.3:c.2398C>T	p.Gln800Ter	p.Q800*	ENST00000268712	NM_006311.3	800	Cag/Tag	20/46	0.268801049101747	1	FACETS	0.893	0.799	0.992	0.893	0.799	0.992	CLONAL	1	TRUE	0	0.293305738718108	1		395	665	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428510	78428510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754770362	NA	P-0004194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	112	402	0	ENST00000370768.2:c.1289G>A	p.Arg430His	p.R430H	ENST00000370768	NM_003902.3	430	cGt/cAt	14/20	1	2	FACETS	0.975	0.877	1	0.975	0.877	1	CLONAL	1	TRUE	1	0.293305738718108	2		402	783	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938932	178938932	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	36	121	0	ENST00000263967.3:c.2174A>G	p.Asp725Gly	p.D725G	ENST00000263967	NM_006218.2	725	gAt/gGt	14/21	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.293305738718108	2		121	218	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063716	67063717	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0004194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	41	215	0	ENST00000412916.2:c.165+1_165+2dup		p.-55fs	ENST00000412916		55	-/GT		0.293305738718108	1	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	0	0.293305738718108	1		215	229	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032529	12032536	+	frameshift_variant	Frame_Shift_Del	DEL	AAGGAGAT	AAGGAGAT	-	novel	NA	P-0004194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	73	284	0	ENST00000353533.5:c.965_972del	p.Lys322ThrfsTer6	p.K322Tfs*6	ENST00000353533	NM_003010.3	322	aAAGGAGAT/a	9/11	0.268801049101747	1	FACETS	0.961	0.844	1	0.961	0.844	1	CLONAL	1	TRUE	0	0.293305738718108	1		284	442	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0004195-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	90	201	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.144808527737986	4	FACETS	0.897	0.809	0.988	0.897	0.809	0.988	INDETERMINATE	2	TRUE	2	0.67903207741622	4		201	248	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591924	48591924	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs377767348	NA	P-0004195-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	105	356	0	ENST00000342988.3:c.1087T>C	p.Cys363Arg	p.C363R	ENST00000342988	NM_005359.5	363	Tgt/Cgt	9/12	0.57100160082637	1	FACETS	0.973	0.893	1	0.973	0.893	1	CLONAL	1	TRUE	0	0.67903207741622	1		356	210	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413225	139413225	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004195-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	76	393	0	ENST00000277541.6:c.917G>C	p.Cys306Ser	p.C306S	ENST00000277541	NM_017617.3	306	tGc/tCc	6/34	0.67903207741622	3	FACETS	1	0.926	1	0.53	0.47	0.593	CLONAL	1	TRUE	1	0.67903207741622	3		393	283	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465600	99465600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768636512	NA	P-0004195-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	97	239	0	ENST00000268035.6:c.2425G>A	p.Glu809Lys	p.E809K	ENST00000268035	NM_000875.3	809	Gag/Aag	11/21	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.67903207741622	2		239	272	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578410	7578410	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs864622115	NA	P-0004195-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	63	383	0	ENST00000269305.4:c.520A>G	p.Arg174Gly	p.R174G	ENST00000269305	NM_001126112.2	174	Agg/Ggg	5/11	0.67119387648396	1	FACETS	0.839	0.746	0.934	0.839	0.746	0.934	CLONAL	1	TRUE	0	0.67903207741622	1		383	146	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111502	8111503	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004195-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	168	329	0	ENST00000346208.3:c.990dup	p.Asn331GlufsTer21	p.N331Efs*21	ENST00000346208		330	agg/aGgg	5/6	0.182386324906702	5	FACETS	1	0.982	1	0.783	0.728	0.84	INDETERMINATE	2	TRUE	2	0.67903207741622	5		329	425	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0004208-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	176	322	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.225619085363844	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	2	0.26	4		322	753	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850702	63850703	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGAAAAAAATAGAAGGGTATCAGGAATTTTC	novel	NA	P-0004208-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	51	393	0	ENST00000279873.7:c.1483_1513dup	p.Ala505GlufsTer33	p.A505Efs*33	ENST00000279873	NM_032199.2	494	aag/aAGAAAAAAATAGAAGGGTATCAGGAATTTTCag	10/10	1	2	FACETS	0.536	0.454	0.626	0.536	0.454	0.626	SUBCLONAL	1	TRUE	1	0.26	2		393	732	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0004217-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	182	413	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	0.817	0.761	0.874	0.817	0.761	0.874	CLONAL	1	TRUE	1	0.92223358231727	2		413	483	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053221	180053221	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004217-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	275	447	0	ENST00000261937.6:c.1148C>A	p.Ala383Asp	p.A383D	ENST00000261937	NM_182925.4	383	gCc/gAc	9/30	0.92223358231727	3	FACETS	0.93	0.875	0.987	0.465	0.437	0.494	CLONAL	1	TRUE	1	0.92223358231727	3		447	937	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864045	97864046	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	GCTTTCAATGCCAAGACGATTCCAT	novel	NA	P-0004217-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	238	369	0	ENST00000289081.3:c.1596_1620dup	p.Pro541MetfsTer7	p.P541Mfs*7	ENST00000289081	NM_000136.2	540	-/ATGGAATCGTCTTGGCATTGAAAGC	15/15	1	2	FACETS	0.695	0.651	0.739	0.695	0.651	0.739	SUBCLONAL	1	TRUE	1	0.92223358231727	2		369	743	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851663	63851664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004231-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	321	449	0	ENST00000279873.7:c.2442dup	p.Glu815ArgfsTer12	p.E815Rfs*12	ENST00000279873	NM_032199.2	814	tta/ttAa	10/10	0.578808594817652	4	FACETS	0.791	0.747	0.836	0.527	0.498	0.557	SUBCLONAL	2	FALSE	1	0.572858843928261	4		449	1114	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0004232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	175	654	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.495127934916414	1	FACETS	0.935	0.866	1	0.935	0.866	1	CLONAL	1	TRUE	0	0.495127934916414	1		655	569	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0004232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	304	322	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.235398489383804	6	FACETS	0.987	0.934	1	0.987	0.934	1	INDETERMINATE	3	TRUE	3	0.495127934916414	6		322	825	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953730	48953730	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs3092891	NA	P-0004232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	130	531	0	ENST00000267163.4:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000267163	NM_000321.2	445	Cga/Tga	14/27	0.495127934916414	1	FACETS	0.971	0.889	1	0.971	0.889	1	CLONAL	1	TRUE	0	0.495127934916414	1		531	407	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921551	178921551	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	9	638	0	ENST00000263967.3:c.1033A>T	p.Asn345Tyr	p.N345Y	ENST00000263967	NM_006218.2	345	Aat/Tat	5/21	1	2	FACETS	0.114	0.075	0.165	0.114	0.075	0.165	SUBCLONAL	1	TRUE	1	0.495127934916414	2		638	318	SUCCESS
APC	324	MSKCC	GRCh37	5	112170689	112170689	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	88	744	0	ENST00000257430.4:c.1785G>T	p.Leu595Phe	p.L595F	ENST00000257430	NM_000038.5	595	ttG/ttT	15/16	1	2	FACETS	0.948	0.846	1	0.948	0.846	1	CLONAL	1	TRUE	1	0.495127934916414	2		744	375	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575125	64575126	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTA	novel	NA	P-0004232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	76	616	0	ENST00000312049.6:c.679_681dup	p.Tyr227dup	p.Y227dup	ENST00000312049	NM_130799.2	227	-/TAC	4/10	0.495127934916414	3	FACETS	0.887	0.781	0.999	0.443	0.39	0.5	CLONAL	1	TRUE	1	0.495127934916414	3		616	432	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940810	49940811	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0004232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	135	1080	0	ENST00000296474.3:c.231_232dup	p.Leu78ProfsTer9	p.L78Pfs*9	ENST00000296474	NM_002447.2	78	ctg/cCCtg	1/20	1	2	FACETS	0.798	0.727	0.873	0.798	0.727	0.873	SUBCLONAL	1	TRUE	1	0.495127934916414	2		1080	683	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0004251-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	30	265	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.511	0.412	0.625	0.511	0.412	0.625	SUBCLONAL	1	FALSE	1	0.26605911129567	2		265	441	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0004251-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	43	697	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	FALSE	1	0.26605911129567	2		697	320	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004251-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	15	158	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	0.49	0.359	0.648	0.49	0.359	0.648	SUBCLONAL	1	FALSE	1	0.26605911129567	2		158	230	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579409	7579410	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0004251-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	30	118	0	ENST00000269305.4:c.277_278del	p.Leu93ValfsTer55	p.L93Vfs*55	ENST00000269305	NM_001126112.2	93	CTg/g	4/11	1	2	FACETS	1	0.823	1	1	0.823	1	CLONAL	1	FALSE	1	0.26605911129567	2		118	222	SUCCESS
APC	324	MSKCC	GRCh37	5	112173562	112173563	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004251-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	34	247	0	ENST00000257430.4:c.2271_2272insT	p.Lys758Ter	p.K758*	ENST00000257430	NM_000038.5	757	-/T	16/16	1	2	FACETS	1	0.836	1	1	0.836	1	CLONAL	1	FALSE	1	0.26605911129567	2		247	251	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882050	36882050	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs780753361	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	129	188	0	ENST00000358127.4:c.963del	p.Ala322LeufsTer11	p.A322Lfs*11	ENST00000358127	NM_001280556.1	321	ccC/cc	8/10	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.58	2		188	417	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	99	75	1	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	0.575156587589989	2	FACETS	0.779	0.711	0.848			1	SUBCLONAL	2	TRUE	NA	0.58	2		76	219	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	46	110	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.575156587589989	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.58	1		110	104	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735422	204735422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	91	158	0	ENST00000302823.3:c.223C>T	p.Arg75Trp	p.R75W	ENST00000302823	NM_005214.4	75	Cgg/Tgg	2/4	1	2	FACETS	0.971	0.872	1	0.971	0.872	1	CLONAL	1	TRUE	1	0.58	2		158	323	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	129	379	2	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.58	2		381	440	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	80	103	0	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	0.575156587589989	2	FACETS	1	0.95	1			1	CLONAL	1	TRUE	NA	0.58	2		103	248	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	171	246	0	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.58	2		246	568	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121791	2121792	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs137854144	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	78	161	0	ENST00000219476.3:c.1959_1960del	p.Gly654LeufsTer2	p.G654Lfs*2	ENST00000219476	NM_000548.3	651	ccAGag/ccag	19/42	1	2	FACETS	0.697	0.616	0.783	0.697	0.616	0.783	SUBCLONAL	1	TRUE	1	0.58	2		161	386	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030323	180030323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745546499	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	136	292	0	ENST00000261937.6:c.3961C>T	p.Arg1321Trp	p.R1321W	ENST00000261937	NM_182925.4	1321	Cgg/Tgg	30/30	1	2	FACETS	0.727	0.663	0.794	0.727	0.663	0.794	SUBCLONAL	1	TRUE	1	0.58	2		292	645	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285327	212285327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143134749	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	120	182	0	ENST00000342788.4:c.2974C>T	p.Arg992Cys	p.R992C	ENST00000342788	NM_005235.2	992	Cgt/Tgt	25/28	1	2	FACETS	0.934	0.85	1	0.934	0.85	1	CLONAL	1	TRUE	1	0.58	2		182	443	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141426	11141426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	151	218	0	ENST00000358026.2:c.3403C>T	p.Arg1135Trp	p.R1135W	ENST00000358026	NM_001128849.1	1135	Cgg/Tgg	25/36	1	2	FACETS	0.955	0.878	1	0.955	0.878	1	CLONAL	1	TRUE	1	0.58	2		218	545	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138521	11138521	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	208	243	0	ENST00000358026.2:c.3277C>T	p.Arg1093Ter	p.R1093*	ENST00000358026	NM_001128849.1	1093	Cga/Tga	24/36	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.58	2		243	663	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	308	157	7	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	0.575156587589989	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.58	3		164	664	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715979	52715979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786205227	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	152	247	1	ENST00000322088.6:c.544C>T	p.Arg182Trp	p.R182W	ENST00000322088	NM_014225.5	182	Cgg/Tgg	5/15	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.58	2		248	515	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258485	16258485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780910569	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	117	142	0	ENST00000375759.3:c.5750G>A	p.Arg1917His	p.R1917H	ENST00000375759	NM_015001.2	1917	cGc/cAc	11/15	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.58	2		142	399	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325881	65325881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	112	148	0	ENST00000342505.4:c.1241G>A	p.Arg414Gln	p.R414Q	ENST00000342505	NM_002227.2	414	cGg/cAg	9/25	1	2	FACETS	0.966	0.876	1	0.966	0.876	1	CLONAL	1	TRUE	1	0.58	2		148	400	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226553677	226553677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147825810	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	129	213	0	ENST00000366794.5:c.2483C>T	p.Ala828Val	p.A828V	ENST00000366794	NM_001618.3	828	gCg/gTg	18/23	1	2	FACETS	0.935	0.853	1	0.935	0.853	1	CLONAL	1	TRUE	1	0.58	2		213	476	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497847	25497847	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779859478	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	136	299	1	ENST00000264709.3:c.602G>A	p.Arg201His	p.R201H	ENST00000264709	NM_175629.2	201	cGc/cAc	6/23	0.575156587589989	2	FACETS	0.925	0.846	1			1	CLONAL	1	TRUE	NA	0.58	2		300	507	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702211	47702211	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs63750657	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	126	218	0	ENST00000233146.2:c.1807G>T	p.Asp603Tyr	p.D603Y	ENST00000233146	NM_000251.2	603	Gat/Tat	12/16	0.575156587589989	2	FACETS	0.93	0.848	1			1	CLONAL	1	TRUE	NA	0.58	2		218	467	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61710119	61710119	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	118	160	0	ENST00000401558.2:c.2785G>A	p.Val929Ile	p.V929I	ENST00000401558	NM_003400.3	929	Gtt/Att	22/25	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.58	2		160	403	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163278	47163278	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372092336	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	216	318	0	ENST00000409792.3:c.2848C>T	p.Arg950Cys	p.R950C	ENST00000409792	NM_014159.6	950	Cgt/Tgt	3/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.58	2		318	678	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517475	176517475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751304047	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	133	191	0	ENST00000292408.4:c.176G>A	p.Arg59Gln	p.R59Q	ENST00000292408	NM_213647.1	59	cGg/cAg	3/18	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.58	2		191	434	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030232	180030232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371358529	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	194	262	0	ENST00000261937.6:c.4052C>T	p.Pro1351Leu	p.P1351L	ENST00000261937	NM_182925.4	1351	cCg/cTg	30/30	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.58	2		262	607	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552909	106552909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	195	344	1	ENST00000369096.4:c.874C>T	p.Pro292Ser	p.P292S	ENST00000369096	NM_001198.3	292	Ccc/Tcc	5/7	0.100692024055139	0	FACETS	0.351	0.325	0.378			1	INDETERMINATE	1	TRUE	0	0.58	0		345	804	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662652	117662652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	111	201	0	ENST00000368508.3:c.4813G>A	p.Glu1605Lys	p.E1605K	ENST00000368508	NM_002944.2	1605	Gaa/Aaa	29/43	0.100692024055139	0	FACETS	0.396	0.359	0.435			1	INDETERMINATE	1	TRUE	0	0.58	0		201	406	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959117	2959117	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	86	193	0	ENST00000396946.4:c.2399T>A	p.Val800Asp	p.V800D	ENST00000396946	NM_032415.4	800	gTt/gAt	18/25	0.575156587589989	3	FACETS	0.689	0.611	0.773	0.345	0.305	0.387	SUBCLONAL	1	TRUE	1	0.58	3		193	555	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845228	151845228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	144	166	0	ENST00000262189.6:c.13784G>A	p.Arg4595His	p.R4595H	ENST00000262189	NM_170606.2	4595	cGc/cAc	52/59	0.575156587589989	3	FACETS	1	0.98	1	0.608	0.557	0.66	CLONAL	1	TRUE	1	0.58	3		166	527	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737578	145737578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558058260	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	96	177	0	ENST00000428558.2:c.3185G>A	p.Arg1062Gln	p.R1062Q	ENST00000428558	NM_004260.3	1062	cGg/cAg	19/22	1	2	FACETS	0.652	0.583	0.725	0.652	0.583	0.725	SUBCLONAL	1	TRUE	1	0.58	2		177	508	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650071	93650071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1486347243	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	201	241	0	ENST00000375746.1:c.1622C>T	p.Pro541Leu	p.P541L	ENST00000375746	NM_001174167.1	541	cCg/cTg	12/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.58	2		241	613	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446278	70446278	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147119124	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	201	682	0	ENST00000373644.4:c.5218C>T	p.Arg1740Cys	p.R1740C	ENST00000373644	NM_030625.2	1740	Cgc/Tgc	11/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.58	2		682	640	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205534	61205534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140191819	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	135	203	0	ENST00000301761.2:c.319C>T	p.Arg107Cys	p.R107C	ENST00000301761	NM_017841.2	107	Cgc/Tgc	3/4	1	2	FACETS	0.931	0.851	1	0.931	0.851	1	CLONAL	1	TRUE	1	0.58	2		203	500	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025569	1025569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	178	266	0	ENST00000358495.3:c.806G>A	p.Arg269Gln	p.R269Q	ENST00000358495	NM_134424.2	269	cGg/cAg	9/12	1	2	FACETS	0.99	0.917	1	0.99	0.917	1	CLONAL	1	TRUE	1	0.58	2		266	620	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219908	133219908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs969429633	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	134	246	0	ENST00000320574.5:c.4453C>T	p.Arg1485Cys	p.R1485C	ENST00000320574	NM_006231.2	1485	Cgc/Tgc	35/49	1	2	FACETS	0.985	0.902	1	0.985	0.902	1	CLONAL	1	TRUE	1	0.58	2		246	469	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233948	133233948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778212434	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	118	166	0	ENST00000320574.5:c.3446C>T	p.Ala1149Val	p.A1149V	ENST00000320574	NM_006231.2	1149	gCg/gTg	28/49	1	2	FACETS	0.925	0.84	1	0.925	0.84	1	CLONAL	1	TRUE	1	0.58	2		166	440	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563296	21563296	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	169	214	1	ENST00000382592.4:c.623C>T	p.Pro208Leu	p.P208L	ENST00000382592	NM_014572.2	208	cCg/cTg	4/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.58	2		215	486	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66777404	66777404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1334665647	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	85	239	0	ENST00000307102.5:c.770C>T	p.Ala257Val	p.A257V	ENST00000307102	NM_002755.3	257	gCg/gTg	7/11	1	2	FACETS	0.591	0.524	0.662	0.591	0.524	0.662	SUBCLONAL	1	TRUE	1	0.58	2		239	496	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858403	9858403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	93	145	0	ENST00000330684.3:c.2998G>A	p.Val1000Met	p.V1000M	ENST00000330684	NM_001134407.1	1000	Gtg/Atg	13/13	1	2	FACETS	0.943	0.847	1	0.943	0.847	1	CLONAL	1	TRUE	1	0.58	2		145	340	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133239	30133239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750160678	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	346	314	0	ENST00000263025.4:c.259C>T	p.Arg87Trp	p.R87W	ENST00000263025	NM_002746.2	87	Cgg/Tgg	2/9	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.58	2		314	916	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881117	37881117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542027040	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	164	229	0	ENST00000269571.5:c.2446C>T	p.Arg816Cys	p.R816C	ENST00000269571		816	Cgc/Tgc	20/27	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.58	2		229	532	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7128881	7128881	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	35	252	0	ENST00000302850.5:c.2927A>G	p.Tyr976Cys	p.Y976C	ENST00000302850	NM_000208.2	976	tAt/tGt	15/22	1	2	FACETS	0.204	0.166	0.246	0.204	0.166	0.246	SUBCLONAL	1	TRUE	1	0.58	2		252	592	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143000	7143000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369025474	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	116	222	0	ENST00000302850.5:c.2369C>T	p.Thr790Met	p.T790M	ENST00000302850	NM_000208.2	790	aCg/aTg	12/22	1	2	FACETS	0.959	0.871	1	0.959	0.871	1	CLONAL	1	TRUE	1	0.58	2		222	417	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10257072	10257072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	154	214	0	ENST00000340748.4:c.2801G>A	p.Arg934Gln	p.R934Q	ENST00000340748		934	cGa/cAa	27/40	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.58	2		214	485	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271819	15271819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765739997	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	26	59	0	ENST00000263388.2:c.6620G>A	p.Arg2207Gln	p.R2207Q	ENST00000263388	NM_000435.2	2207	cGg/cAg	33/33	1	2	FACETS	0.723	0.582	0.879	0.723	0.582	0.879	SUBCLONAL	1	TRUE	1	0.58	2		59	124	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52705200	52705200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	159	206	0	ENST00000322088.6:c.82C>T	p.Arg28Cys	p.R28C	ENST00000322088	NM_014225.5	28	Cgc/Tgc	2/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.58	2		206	513	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922048	39922048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375650828	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	260	155	0	ENST00000378444.4:c.4124G>A	p.Arg1375Gln	p.R1375Q	ENST00000378444	NM_001123385.1	1375	cGg/cAg	9/15	1	1	FACETS	0.752	0.718	0.787	1	0.995	1	SUBCLONAL	2	TRUE	0	0.58	1		155	423	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928872	44928872	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs755440519	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	218	116	2	ENST00000377967.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000377967	NM_021140.2	658	Cga/Tga	17/29	1	1	FACETS	0.765	0.726	0.802	1	0.994	1	SUBCLONAL	2	TRUE	0	0.58	1		118	349	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429004	47429004	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780392848	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	212	140	0	ENST00000377045.4:c.1367G>A	p.Arg456Gln	p.R456Q	ENST00000377045	NM_001654.4	456	cGa/cAa	13/16	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.58	1		140	388	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223488	53223488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	116	81	0	ENST00000375401.3:c.3871C>T	p.Arg1291Cys	p.R1291C	ENST00000375401	NM_004187.3	1291	Cgc/Tgc	23/26	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.58	1		81	210	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53253966	53253966	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	216	151	0	ENST00000375401.3:c.106C>T	p.Pro36Ser	p.P36S	ENST00000375401	NM_004187.3	36	Ccc/Tcc	1/26	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.58	1		151	379	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130441	29130441	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	150	205	0	ENST00000328354.6:c.269del	p.Pro90LeufsTer20	p.P90Lfs*20	ENST00000328354	NM_007194.3	90	cCt/ct	2/15	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.58	2		205	492	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741811	40741813	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	75	136	0	ENST00000392038.2:c.1159_1161del	p.Lys387del	p.K387del	ENST00000392038	NM_001626.4	387	AAG/-	11/14	1	2	FACETS	0.892	0.79	0.999	0.892	0.79	0.999	CLONAL	1	TRUE	1	0.58	2		136	290	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272337	15272337	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs771517374	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	82	138	0	ENST00000263388.2:c.6102del	p.Gly2035ValfsTer50	p.G2035Vfs*50	ENST00000263388	NM_000435.2	2034	ccC/cc	33/33	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.58	2		138	280	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514998	148515000	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs775039041	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	164	242	2	ENST00000320356.2:c.1209_1211del	p.Glu404del	p.E404del	ENST00000320356	NM_004456.4	403	gaAGAg/gag	10/20	0.575156587589989	3	FACETS	0.857	0.787	0.93	0.429	0.393	0.465	CLONAL	1	TRUE	1	0.58	3		244	851	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426222	49426223	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	112	160	0	ENST00000301067.7:c.12265_12266del	p.Leu4089AlafsTer17	p.L4089Afs*17	ENST00000301067	NM_003482.3	4089	CTg/g	39/54	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.58	2		160	368	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444932	49444933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs767415197	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	27	39	0	ENST00000301067.7:c.2533dup	p.Arg845ProfsTer3	p.R845Pfs*3	ENST00000301067	NM_003482.3	845	cgg/cCgg	10/54	1	2	FACETS	0.782	0.634	0.946	0.782	0.634	0.946	CLONAL	1	TRUE	1	0.58	2		39	119	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156288	106156289	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAC	rs924321610	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	82	201	0	ENST00000380013.4:c.1201_1203dup	p.Pro401dup	p.P401dup	ENST00000380013	NM_001127208.2	401	aca/aCACca	3/11	1	2	FACETS	0.658	0.582	0.737	0.658	0.582	0.737	SUBCLONAL	1	TRUE	1	0.58	2		201	430	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817786	3817790	+	frameshift_variant	Frame_Shift_Del	DEL	TCCTC	TCCTC	-	novel	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	216	330	0	ENST00000262367.5:c.3181_3185del	p.Glu1061ArgfsTer4	p.E1061Rfs*4	ENST00000262367	NM_004380.2	1061	GAGGAa/a	16/31	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.58	2		330	739	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322767	30322768	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	106	152	0	ENST00000322652.5:c.1786dup	p.Thr596AsnfsTer6	p.T596Nfs*6	ENST00000322652	NM_015355.2	594	gaa/gAaa	14/16	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.58	2		152	357	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149818	202149819	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	78	189	0	ENST00000358485.4:c.1264dup	p.Asp422GlyfsTer2	p.D422Gfs*2	ENST00000358485	NM_001080125.1	420	cag/caGg	8/9	1	2	FACETS	0.537	0.473	0.605	0.537	0.473	0.605	SUBCLONAL	1	TRUE	1	0.58	2		189	501	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422080	81422081	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	60	164	0	ENST00000298171.2:c.59dup	p.Gly21ArgfsTer41	p.G21Rfs*41	ENST00000298171	NM_000369.2	19	ctg/ctGg	1/10	1	2	FACETS	0.52	0.449	0.596	0.52	0.449	0.596	SUBCLONAL	1	TRUE	1	0.58	2		164	398	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108788	2108788	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	116	244	0	ENST00000219476.3:c.894del	p.Phe298LeufsTer65	p.F298Lfs*65	ENST00000219476	NM_000548.3	297	Ttt/tt	10/42	1	2	FACETS	0.658	0.594	0.725	0.658	0.594	0.725	SUBCLONAL	1	TRUE	1	0.58	2		244	608	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252856	36252857	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	502	184	0	ENST00000300305.3:c.505dup	p.Arg169LysfsTer44	p.R169Kfs*44	ENST00000300305		169	aga/aAga	4/8	0.392522307230918	4	FACETS	0.997	0.965	1	0.748	0.724	0.771	INDETERMINATE	3	TRUE	0	0.76234504430349	4		184	776	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879810	37879810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	469	156	0	ENST00000269571.5:c.2105C>T	p.Pro702Leu	p.P702L	ENST00000269571		702	cCt/cTt	18/27	0.421824042649348	5	FACETS	1	0.995	1			1	INDETERMINATE	3	TRUE	NA	0.76234504430349	5		156	759	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844210	68844211	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	213	225	0	ENST00000261769.5:c.801dup	p.Lys268Ter	p.K268*	ENST00000261769	NM_004360.3	266	-/T	6/16	0.76234504430349	1	FACETS	0.92	0.87	0.969	0.92	0.87	0.969	CLONAL	1	TRUE	0	0.76234504430349	1		225	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0004268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	72	299	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.201991690624278	2	FACETS	0.907	0.797	1	0.907	0.797	1	CLONAL	2	TRUE	0	0.201991690624278	2		299	393	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162750016	162750016	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	27	315	0	ENST00000367921.3:c.2548C>A	p.Leu850Ile	p.L850I	ENST00000367921	NM_006182.2	850	Ctt/Att	18/18	0.151194255758155	3	FACETS	0.769	0.611	0.948	0.384	0.305	0.474	CLONAL	1	TRUE	1	0.201991690624278	3		315	383	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369290	40369290	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373996796	NA	P-0004268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	35	655	0	ENST00000293328.3:c.1268G>A	p.Arg423Gln	p.R423Q	ENST00000293328	NM_012448.3	423	cGa/cAa	11/19	0.141864023178639	0	FACETS	0.408	0.334	0.493			1	SUBCLONAL	1	TRUE	0	0.201991690624278	0		655	677	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40456579	40456579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1242408805	NA	P-0004268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	54	593	0	ENST00000345506.4:c.1289G>A	p.Arg430Gln	p.R430Q	ENST00000345506	NM_003152.3	430	cGg/cAg	12/20	0.141864023178639	0	FACETS	0.857	0.732	0.993			1	CLONAL	1	TRUE	0	0.201991690624278	0		593	498	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575170	48575170	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0004268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	24	310	0	ENST00000342988.3:c.364A>T	p.Lys122Ter	p.K122*	ENST00000342988	NM_005359.5	122	Aaa/Taa	3/12	0.194784231055249	1	FACETS	0.486	0.38	0.608	0.486	0.38	0.608	SUBCLONAL	1	TRUE	0	0.201991690624278	1		310	440	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099340	27099340	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	AA	novel	NA	P-0004268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	25	366	0	ENST00000324856.7:c.3577delinsAA	p.Asp1193LysfsTer4	p.D1193Kfs*4	ENST00000324856	NM_006015.4	1193	Gat/AAat	14/20	1	2	FACETS	0.611	0.481	0.761	0.611	0.481	0.761	SUBCLONAL	1	TRUE	1	0.201991690624278	2		366	405	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061463	38061463	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	56	275	0	ENST00000250448.2:c.526A>G	p.Ile176Val	p.I176V	ENST00000250448	NM_004496.3	176	Atc/Gtc	2/2	0.320177742154264	1	FACETS	0.627	0.541	0.719	0.627	0.541	0.719	SUBCLONAL	1	TRUE	0	0.474805812866422	1		275	287	SUCCESS
APC	324	MSKCC	GRCh37	5	112174764	112174764	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	124	335	1	ENST00000257430.4:c.3473G>C	p.Arg1158Thr	p.R1158T	ENST00000257430	NM_000038.5	1158	aGa/aCa	16/16	1	2	FACETS	0.962	0.874	1	0.962	0.874	1	CLONAL	1	TRUE	1	0.474805812866422	2		336	543	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866723	37866723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	487	331	0	ENST00000269571.5:c.890C>T	p.Thr297Ile	p.T297I	ENST00000269571		297	aCt/aTt	7/27	0.474805812866422	6	FACETS	0.938	0.904	0.971			1	CLONAL	5	TRUE	NA	0.474805812866422	6		331	853	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130631	29130631	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs376736188	NA	P-0004293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	75	307	0	ENST00000328354.6:c.79C>T	p.Gln27Ter	p.Q27*	ENST00000328354	NM_007194.3	27	Cag/Tag	2/15	1	2	FACETS	0.71	0.624	0.801	0.71	0.624	0.801	SUBCLONAL	1	TRUE	1	0.474805812866422	2		307	445	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856125	68856152	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCAAGTGGGTACCTGAGTTTTATTTTGG	CCAAGTGGGTACCTGAGTTTTATTTTGG	-	novel	NA	P-0004293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	97	337	0	ENST00000261769.5:c.1934_1936+25del		p.X645_splice	ENST00000261769	NM_004360.3	645		12/16	0.474805812866422	1	FACETS	0.992	0.895	1	0.992	0.895	1	CLONAL	1	TRUE	0	0.474805812866422	1		337	314	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164667	36164668	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	110	344	0	ENST00000300305.3:c.1207dup	p.Tyr403LeufsTer197	p.Y403Lfs*197	ENST00000300305		403	tac/tTac	8/8	0.468895524025996	3	FACETS	1	0.93	1	0.519	0.468	0.573	CLONAL	1	TRUE	1	0.474805812866422	3		344	552	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115952	8115953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0004295-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	71	155	0	ENST00000346208.3:c.1299_1300dup	p.His434ProfsTer42	p.H434Pfs*42	ENST00000346208		433	cac/caCCc	6/6	1	2	FACETS	0.865	0.76	0.977	0.865	0.76	0.977	CLONAL	1	TRUE	1	0.46	2		155	357	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587144	212587144	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004295-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	129	323	1	ENST00000342788.4:c.857G>T	p.Gly286Val	p.G286V	ENST00000342788	NM_005235.2	286	gGa/gTa	7/28	1	2	FACETS	0.996	0.907	1	0.996	0.907	1	CLONAL	1	TRUE	1	0.46	2		324	563	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415531	152415531	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004295-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	182	361	0	ENST00000206249.3:c.1381T>G	p.Phe461Val	p.F461V	ENST00000206249	NM_000125.3	461	Ttt/Gtt	7/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.46	2		361	667	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377363	118377363	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0004295-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	67	180	0	ENST00000534358.1:c.10754+2T>C		p.X3585_splice	ENST00000534358	NM_005933.3	3585			0.489758549507568	1	FACETS	0.935	0.823	1	0.935	0.823	1	CLONAL	1	TRUE	0	0.46	1		180	240	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910675	32910675	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs757577670	NA	P-0004295-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	165	558	0	ENST00000380152.3:c.2183A>T	p.Asp728Val	p.D728V	ENST00000380152		728	gAt/gTt	11/27	0.489758549507568	1	FACETS	0.78	0.718	0.844	0.78	0.718	0.844	SUBCLONAL	1	TRUE	0	0.46	1		558	708	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842626	68842627	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004295-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	153	366	0	ENST00000261769.5:c.566dup	p.Tyr190LeufsTer9	p.Y190Lfs*9	ENST00000261769	NM_004360.3	188	gtt/gTtt	5/16	0.489758549507568	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.46	1		366	446	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0004309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	184	338	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.241309867323904	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.331646444454501	3		338	608	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610048	81610048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	57	369	0	ENST00000298171.2:c.1646G>A	p.Cys549Tyr	p.C549Y	ENST00000298171	NM_000369.2	549	tGc/tAc	10/10	1	2	FACETS	0.796	0.684	0.917	0.796	0.684	0.917	CLONAL	1	TRUE	1	0.331646444454501	2		369	432	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873825	151873826	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	74	454	0	ENST00000262189.6:c.8712dup	p.Val2905CysfsTer20	p.V2905Cfs*20	ENST00000262189	NM_170606.2	2904	-/T	38/59	1	2	FACETS	0.934	0.82	1	0.934	0.82	1	CLONAL	1	TRUE	1	0.331646444454501	2		454	478	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0004328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	216	322	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.3	5	FACETS	1	0.966	1	1	0.966	1	CLONAL	4	TRUE	1	0.21	5		322	644	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0004328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	60	572	0	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.260755456470509	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.21	1		572	461	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0004328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	228	415	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.3	5	FACETS	0.947	0.889	1	1	0.987	1	CLONAL	5	TRUE	1	0.21	5		415	603	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510775	120510775	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	121	497	0	ENST00000256646.2:c.1189G>T	p.Gly397Trp	p.G397W	ENST00000256646	NM_024408.3	397	Ggg/Tgg	7/34	0.218302491322202	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.21	3		497	533	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842620	68842620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	82	524	0	ENST00000261769.5:c.556G>A	p.Gly186Ser	p.G186S	ENST00000261769	NM_004360.3	186	Ggc/Agc	5/16	0.3	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.21	1		524	479	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-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	35	88	0	ENST00000487270.1:c.316-31_352del		p.X106_splice	ENST00000487270	NM_133509.3	106		5/11	0.18928771208646	4	FACETS	0.879	0.731	1	1	0.939	1	CLONAL	3	TRUE	2	0.21	4		88	153	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974806	21974807	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	13	165	0	ENST00000304494.5:c.20dup	p.Ser7ArgfsTer8	p.S7Rfs*8	ENST00000304494	NM_000077.4	7	agc/agGc	1/3	0.219619840143199	2	FACETS	0.998	0.718	1	0.499	0.359	0.668	CLONAL	1	TRUE	0	0.21	2		165	124	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0004341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	543	590	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.669778428091848	3	FACETS	0.936	0.909	0.962			1	CLONAL	3	TRUE	NA	0.669778428091848	3		590	771	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858476	57858476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199685332	NA	P-0004341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	210	864	0	ENST00000228682.2:c.214C>T	p.Arg72Trp	p.R72W	ENST00000228682	NM_005269.2	72	Cgg/Tgg	4/12	1	2	FACETS	0.833	0.776	0.892	0.833	0.776	0.892	CLONAL	1	TRUE	1	0.669778428091848	2		864	753	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720857	89720857	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	60	119	0	ENST00000371953.3:c.1008del	p.Ser338LeufsTer6	p.S338Lfs*6	ENST00000371953	NM_000314.4	336	taC/ta	8/9	0.669778428091848	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.669778428091848	1		119	106	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782067	66782068	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	60	384	0	ENST00000307102.5:c.1038dup	p.Ala347ArgfsTer19	p.A347Rfs*19	ENST00000307102	NM_002755.3	345	aac/aaCc	10/11	NA	2	FACETS	0.385	0.332	0.443			1	INDETERMINATE	1	TRUE	NA	0.669778428091848	2		384	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0004346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	57	398	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	0.390491731154421	2	FACETS	0.977	0.868	1	0.977	0.868	1	CLONAL	2	TRUE	0	0.498493676396203	2		398	117	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525048	9525048	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	33	653	0	ENST00000353224.5:c.1837G>A	p.Glu613Lys	p.E613K	ENST00000353224	NM_177990.2	613	Gag/Aag	8/10	0.470466107567145	4	FACETS	0.79	0.647	0.95	0.395	0.323	0.475	CLONAL	1	TRUE	2	0.498493676396203	4		653	251	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268377	142268377	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	42	561	0	ENST00000350721.4:c.3115C>A	p.His1039Asn	p.H1039N	ENST00000350721	NM_001184.3	1039	Cat/Aat	15/47	0.498493676396203	3	FACETS	0.931	0.785	1	0.466	0.392	0.546	CLONAL	1	TRUE	1	0.498493676396203	3		561	226	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84403342	84403342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	59	717	0	ENST00000321945.7:c.143C>T	p.Ser48Phe	p.S48F	ENST00000321945	NM_139076.2	48	tCc/tTc	2/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.498493676396203	NA		717	299	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998706	100998706	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	49	836	0	ENST00000325455.5:c.1096G>C	p.Asp366His	p.D366H	ENST00000325455	NM_001202474.3	366	Gac/Cac	1/8	0.498493676396203	4	FACETS	1	0.926	1	0.571	0.487	0.661	CLONAL	1	TRUE	2	0.498493676396203	4		836	258	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906883	32906883	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	44	414	0	ENST00000380152.3:c.1268T>A	p.Ile423Asn	p.I423N	ENST00000380152		423	aTt/aAt	10/27	0.405068214174554	4	FACETS	1	0.961	1			1	CLONAL	1	TRUE	NA	0.498493676396203	4		414	180	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515177	103515177	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	23	445	0	ENST00000355739.4:c.1678C>T	p.Leu560Phe	p.L560F	ENST00000355739	NM_000123.3	560	Ctt/Ttt	8/15	0.498493676396203	3	FACETS	0.674	0.53	0.838	0.225	0.176	0.28	SUBCLONAL	1	TRUE	0	0.498493676396203	3		445	171	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958249	11958249	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	30	304	0	ENST00000353533.5:c.159C>G	p.Phe53Leu	p.F53L	ENST00000353533	NM_003010.3	53	ttC/ttG	2/11	0.390491731154421	2	FACETS	0.987	0.81	1	0.493	0.405	0.59	CLONAL	1	TRUE	0	0.498493676396203	2		304	122	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619113	37619113	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	41	618	0	ENST00000447079.4:c.789G>C	p.Lys263Asn	p.K263N	ENST00000447079	NM_015083.1	263	aaG/aaC	1/14	0.278287779398245	6	FACETS	1	0.935	1	0.311	0.26	0.367	INDETERMINATE	1	TRUE	2	0.498493676396203	6		618	264	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842402	68842403	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0004346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	102	768	0	ENST00000261769.5:c.464_465dup	p.Trp156ThrfsTer60	p.W156Tfs*60	ENST00000261769	NM_004360.3	155	gac/gACac	4/16	0.475671491588194	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.498493676396203	2		768	194	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	295	226	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	0.823243542340442	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.823243542340442	1		226	416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	156	350	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.823243542340442	1	FACETS	0.974	0.92	1	0.974	0.92	1	CLONAL	1	TRUE	0	0.823243542340442	1		350	229	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736166	204736166	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	238	497	0	ENST00000302823.3:c.529del	p.Tyr177IlefsTer10	p.Y177Ifs*10	ENST00000302823	NM_005214.4	175	Ttt/tt	3/4	0.174689765276104	1	FACETS	0.611	0.575	0.647	0.611	0.575	0.647	INDETERMINATE	1	TRUE	0	0.823243542340442	1		497	557	SUCCESS
ALK	238	MSKCC	GRCh37	2	29430136	29430136	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs74716434	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	31	289	1	ENST00000389048.3:c.3839C>T	p.Ala1280Val	p.A1280V	ENST00000389048	NM_004304.4	1280	gCg/gTg	26/29	1	2	FACETS	0.175	0.141	0.214	0.175	0.141	0.214	SUBCLONAL	1	TRUE	1	0.823243542340442	2		290	430	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166505	118166505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs865949572	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	59	358	0	ENST00000369448.3:c.1015C>T	p.Arg339Cys	p.R339C	ENST00000369448	NM_017709.3	339	Cgt/Tgt	2/2	1	2	FACETS	0.274	0.236	0.316	0.274	0.236	0.316	SUBCLONAL	1	TRUE	1	0.823243542340442	2		358	523	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	175	298	1	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.984	0.917	1	0.984	0.917	1	CLONAL	1	TRUE	1	0.823243542340442	2		299	432	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217207	11217207	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	79	298	0	ENST00000361445.4:c.4469+2T>C		p.X1490_splice	ENST00000361445	NM_004958.3	1490			0.72506372457123	1	FACETS	0.387	0.344	0.432	0.387	0.344	0.432	SUBCLONAL	1	TRUE	0	0.823243542340442	1		298	292	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17380489	17380489	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	283	377	0	ENST00000375499.3:c.26T>C	p.Leu9Ser	p.L9S	ENST00000375499	NM_003000.2	9	tTg/tCg	1/8	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.823243542340442	2		377	615	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797890	45797890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146044717	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	35	461	0	ENST00000450313.1:c.881G>A	p.Arg294His	p.R294H	ENST00000450313	NM_012222.2	294	cGc/cAc	10/16	0.522251013691329	3	FACETS	0.206	0.168	0.249			1	SUBCLONAL	1	TRUE	NA	0.823243542340442	3		461	583	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78435636	78435636	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs867149960	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	271	438	0	ENST00000370768.2:c.184G>T	p.Gly62Ter	p.G62*	ENST00000370768	NM_003902.3	62	Gga/Tga	2/20	1	2	FACETS	0.875	0.825	0.926	0.875	0.825	0.926	CLONAL	1	TRUE	1	0.823243542340442	2		438	752	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99160342	99160342	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	25	287	0	ENST00000074304.5:c.821T>C	p.Val274Ala	p.V274A	ENST00000074304	NM_001134224.1	274	gTg/gCg	11/26	1	2	FACETS	0.182	0.143	0.227	0.182	0.143	0.227	SUBCLONAL	1	TRUE	1	0.823243542340442	2		287	333	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116175	209116175	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1253479303	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	73	398	0	ENST00000345146.2:c.101A>G	p.Tyr34Cys	p.Y34C	ENST00000345146	NM_005896.2	34	tAc/tGc	3/10	0.174689765276104	1	FACETS	0.162	0.141	0.184	0.162	0.141	0.184	INDETERMINATE	1	TRUE	0	0.823243542340442	1		398	646	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713346	30713346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs112465572	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	18	327	0	ENST00000295754.5:c.671G>A	p.Arg224His	p.R224H	ENST00000295754	NM_003242.5	224	cGc/cAc	4/7	0.818518490699036	1	FACETS	0.112	0.084	0.145	0.112	0.084	0.145	SUBCLONAL	1	TRUE	0	0.823243542340442	1		327	229	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070411	37070411	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1553653195	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	171	340	1	ENST00000231790.2:c.1546C>T	p.Gln516Ter	p.Q516*	ENST00000231790	NM_000249.3	516	Cag/Tag	13/19	0.818518490699036	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.823243542340442	1		341	244	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405964	49405964	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	87	448	0	ENST00000418115.1:c.174G>T	p.Trp58Cys	p.W58C	ENST00000418115	NM_001664.2	58	tgG/tgT	3/5	0.818518490699036	1	FACETS	0.289	0.257	0.323	0.289	0.257	0.323	SUBCLONAL	1	TRUE	0	0.823243542340442	1		448	430	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960032	134960032	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779665397	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	59	333	0	ENST00000398015.3:c.2389G>A	p.Ala797Thr	p.A797T	ENST00000398015	NM_004441.4	797	Gcc/Acc	13/16	0.127434229365642	5	FACETS	0.57	0.49	0.657			1	INDETERMINATE	1	TRUE	NA	0.823243542340442	5		333	562	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191379	185191379	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	42	348	0	ENST00000265026.3:c.2260A>C	p.Ser754Arg	p.S754R	ENST00000265026	NM_004721.4	754	Agc/Cgc	11/14	0.823243542340442	4	FACETS	0.229	0.19	0.272	0.076	0.063	0.091	SUBCLONAL	1	TRUE	1	0.823243542340442	4		348	813	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521198	187521198	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	37	578	0	ENST00000441802.2:c.11957A>C	p.Glu3986Ala	p.E3986A	ENST00000441802	NM_005245.3	3986	gAg/gCg	22/27	0.823243542340442	1	FACETS	0.153	0.126	0.183	0.153	0.126	0.183	SUBCLONAL	1	TRUE	0	0.823243542340442	1		578	346	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540721	187540721	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	54	425	0	ENST00000441802.2:c.7019G>A	p.Gly2340Asp	p.G2340D	ENST00000441802	NM_005245.3	2340	gGc/gAc	10/27	0.823243542340442	1	FACETS	0.26	0.223	0.299	0.26	0.223	0.299	SUBCLONAL	1	TRUE	0	0.823243542340442	1		425	297	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876136	35876136	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	263	397	0	ENST00000303115.3:c.928A>T	p.Arg310Trp	p.R310W	ENST00000303115	NM_002185.3	310	Agg/Tgg	8/8	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.823243542340442	2		397	633	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066627	94066627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	314	588	1	ENST00000369303.4:c.1132G>A	p.Glu378Lys	p.E378K	ENST00000369303	NM_004440.3	378	Gaa/Aaa	5/17	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.823243542340442	2		589	633	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413924	139413924	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	153	406	0	ENST00000277541.6:c.836A>G	p.Tyr279Cys	p.Y279C	ENST00000277541	NM_017617.3	279	tAc/tGc	5/34	0.174689765276104	1	FACETS	0.564	0.522	0.606	0.564	0.522	0.606	INDETERMINATE	1	TRUE	0	0.823243542340442	1		406	388	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77060334	77060334	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	28	339	0	ENST00000356341.3:c.837-2A>C		p.X279_splice	ENST00000356341	NM_002576.4	279			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.823243542340442	NA		339	543	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190680	108190680	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1057517302	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	83	310	2	ENST00000278616.4:c.6348-1G>A		p.X2116_splice	ENST00000278616	NM_000051.3	2116			0.174689765276104	1	FACETS	0.226	0.2	0.255	0.226	0.2	0.255	INDETERMINATE	1	TRUE	0	0.823243542340442	1		312	524	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435385	18435385	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	89	445	0	ENST00000266497.5:c.370T>C	p.Cys124Arg	p.C124R	ENST00000266497		124	Tgc/Cgc	1/31	1	2	FACETS	0.357	0.316	0.4	0.357	0.316	0.4	SUBCLONAL	1	TRUE	1	0.823243542340442	2		445	606	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864309	57864309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777242040	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	194	576	0	ENST00000228682.2:c.1786G>A	p.Ala596Thr	p.A596T	ENST00000228682	NM_005269.2	596	Gcc/Acc	12/12	1	2	FACETS	0.866	0.808	0.926	0.866	0.808	0.926	CLONAL	1	TRUE	1	0.823243542340442	2		576	544	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877320	28877320	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	144	213	0	ENST00000282397.4:c.4001C>T	p.Ser1334Phe	p.S1334F	ENST00000282397	NM_002019.4	1334	tCc/tTc	30/30	0.823243542340442	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.823243542340442	1		213	200	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986574	36986574	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437185372	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	21	276	0	ENST00000354822.5:c.1115G>A	p.Gly372Asp	p.G372D	ENST00000354822	NM_001079668.2	372	gGc/gAc	3/3	0.823243542340442	3	FACETS	0.18	0.138	0.229			1	SUBCLONAL	1	TRUE	NA	0.823243542340442	3		276	400	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129325	2129325	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs796053509	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	46	451	0	ENST00000219476.3:c.3180G>A	p.Trp1060Ter	p.W1060*	ENST00000219476	NM_000548.3	1060	tgG/tgA	28/42	0.238239100421965	1	FACETS	0.154	0.13	0.181	0.154	0.13	0.181	INDETERMINATE	1	TRUE	0	0.823243542340442	1		451	426	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857833	9857833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765522252	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	22	512	1	ENST00000330684.3:c.3568C>T	p.His1190Tyr	p.H1190Y	ENST00000330684	NM_001134407.1	1190	Cac/Tac	13/13	0.238239100421965	1	FACETS	0.073	0.056	0.093	0.073	0.056	0.093	INDETERMINATE	1	TRUE	0	0.823243542340442	1		513	430	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821547	72821547	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	118	323	0	ENST00000268489.5:c.10628C>A	p.Ala3543Asp	p.A3543D	ENST00000268489	NM_006885.3	3543	gCt/gAt	10/10	NA	2	FACETS	0.833	0.761	0.908			1	INDETERMINATE	1	TRUE	NA	0.823243542340442	2		323	344	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610421	10610421	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1425671494	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	197	388	1	ENST00000171111.5:c.289A>T	p.Lys97Ter	p.K97*	ENST00000171111	NM_203500.1	97	Aag/Tag	2/6	0.823243542340442	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.823243542340442	1		389	281	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480138	20480138	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	146	426	0	ENST00000346618.3:c.459del	p.Lys154ArgfsTer41	p.K154Rfs*41	ENST00000346618	NM_001949.4	152	aCc/ac	2/7	0.224405096831815	3	FACETS	0.914	0.838	0.992	0.305	0.279	0.331	INDETERMINATE	1	TRUE	0	0.823243542340442	3		426	548	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681016	117681016	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	37	396	0	ENST00000368508.3:c.3604del	p.Asp1202ThrfsTer41	p.D1202Tfs*41	ENST00000368508	NM_002944.2	1202	Gac/ac	23/43	NA	2	FACETS	0.147	0.121	0.177			1	INDETERMINATE	1	TRUE	NA	0.823243542340442	2		396	610	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	44	230	4	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	0.823243542340442	1	FACETS	0.391	0.333	0.452	0.391	0.333	0.452	SUBCLONAL	1	TRUE	0	0.823243542340442	1		234	161	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61729435	61729435	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	45	408	0	ENST00000401558.2:c.312del	p.Lys104AsnfsTer17	p.K104Nfs*17	ENST00000401558	NM_003400.3	104	aaA/aa	5/25	1	2	FACETS	0.162	0.136	0.192	0.162	0.136	0.192	SUBCLONAL	1	TRUE	1	0.823243542340442	2		408	674	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954320	48954321	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	273	325	0	ENST00000267163.4:c.1446dup	p.His483SerfsTer10	p.H483Sfs*10	ENST00000267163	NM_000321.2	481	att/aTtt	16/27	0.823243542340442	1	FACETS	0.931	0.891	0.971	0.931	0.891	0.971	CLONAL	1	TRUE	0	0.823243542340442	1		325	419	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553280	106553281	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs961279924	NA	P-0004382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	71	368	0	ENST00000369096.4:c.1251dup	p.Tyr418LeufsTer6	p.Y418Lfs*6	ENST00000369096	NM_001198.3	415	-/C	5/7	NA	2	FACETS	0.436	0.382	0.493			1	INDETERMINATE	1	TRUE	NA	0.823243542340442	2		368	396	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004438-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	28	245	0				ENST00000310581	NM_198253.2	-/1132			0.169566161845001	3	FACETS	0.95	0.765	1	0.95	0.765	1	CLONAL	2	TRUE	1	0.16	3		245	199	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0004438-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	53	365	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.169566161845001	3	FACETS	1	0.948	1	0.633	0.54	0.736	CLONAL	1	TRUE	1	0.16	3		365	565	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260950	16260950	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004438-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	29	126	0	ENST00000375759.3:c.8215G>A	p.Val2739Met	p.V2739M	ENST00000375759	NM_015001.2	2739	Gtg/Atg	11/15	1	2	FACETS	1	0.828	1	1	0.828	1	CLONAL	1	TRUE	1	0.16	2		126	351	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453119	140453119	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004438-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	55	337	0	ENST00000288602.6:c.1816G>T	p.Gly606Trp	p.G606W	ENST00000288602	NM_004333.4	606	Ggg/Tgg	15/18	0.169566161845001	3	FACETS	1	0.953	1	0.648	0.554	0.751	CLONAL	1	TRUE	1	0.16	3		337	573	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401005	139401005	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1249540119	NA	P-0004438-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	31	370	0	ENST00000277541.6:c.3988C>T	p.Arg1330Cys	p.R1330C	ENST00000277541	NM_017617.3	1330	Cgc/Tgc	24/34	1	2	FACETS	0.783	0.632	0.954	0.783	0.632	0.954	CLONAL	1	TRUE	1	0.16	2		370	495	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652262	36652263	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004438-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	31	252	0	ENST00000244741.5:c.387dup	p.Ser130ValfsTer67	p.S130Vfs*67	ENST00000244741	NM_000389.4	128	-/G	2/3	1	2	FACETS	0.883	0.713	1	0.883	0.713	1	CLONAL	1	TRUE	1	0.16	2		252	439	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182641	38182641	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs387907272	NA	P-0004440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	26	520	0	ENST00000396334.3:c.794T>C	p.Leu265Pro	p.L265P	ENST00000396334	NM_002468.4	265	cTg/cCg	5/5	1	2	FACETS	0.399	0.314	0.497	0.399	0.314	0.497	SUBCLONAL	1	TRUE	1	0.12	2		520	1086	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968305	15968306	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1279	71	527	0	ENST00000268712.3:c.4979dup	p.Thr1661AsnfsTer53	p.T1661Nfs*53	ENST00000268712	NM_006311.3	1660	cca/ccCa	34/46	1	2	FACETS	0.877	0.762	1	0.877	0.762	1	CLONAL	1	TRUE	1	0.12	2		527	1350	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0004472-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	77	327	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.35068891757123	4	FACETS	1	0.942	1	0.546	0.486	0.609	CLONAL	2	TRUE	0	0.379879588920439	4		327	256	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280768	41280768	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004472-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	18	482	0	ENST00000349496.5:c.2281G>C	p.Asp761His	p.D761H	ENST00000349496	NM_001904.3	761	Gac/Cac	15/15	NA	2	FACETS	0.632	0.479	0.809			1	INDETERMINATE	1	TRUE	NA	0.379879588920439	2		482	150	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259173	89259173	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004472-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	17	475	1	ENST00000336596.2:c.317G>A	p.Cys106Tyr	p.C106Y	ENST00000336596	NM_005233.5	106	tGc/tAc	3/17	0.379879588920439	1	FACETS	0.525	0.395	0.677	0.525	0.395	0.677	SUBCLONAL	1	TRUE	0	0.379879588920439	1		476	138	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279194	142279194	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004472-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	18	639	0	ENST00000350721.4:c.1452T>A	p.Asn484Lys	p.N484K	ENST00000350721	NM_001184.3	484	aaT/aaA	6/47	0.379879588920439	2	FACETS	0.571	0.432	0.732	0.285	0.216	0.366	SUBCLONAL	1	TRUE	0	0.379879588920439	2		639	166	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157404	106157404	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs751233117	NA	P-0004472-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	27	548	0	ENST00000380013.4:c.2305C>T	p.Gln769Ter	p.Q769*	ENST00000380013	NM_001127208.2	769	Cag/Tag	3/11	1	2	FACETS	0.737	0.59	0.901	0.737	0.59	0.901	CLONAL	1	TRUE	1	0.379879588920439	2		548	193	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874751	151874751	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004472-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	19	395	0	ENST00000262189.6:c.7787G>T	p.Arg2596Leu	p.R2596L	ENST00000262189	NM_170606.2	2596	cGg/cTg	38/59	0.379879588920439	4	FACETS	0.664	0.505	0.848	0.221	0.168	0.283	SUBCLONAL	1	TRUE	1	0.379879588920439	4		395	208	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103498619	103498619	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0004472-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	26	582	0	ENST00000355739.4:c.3G>A	p.Met1?	p.M1?	ENST00000355739	NM_000123.3	1	atG/atA	1/15	0.257722835968568	2	FACETS	0.815	0.652	0.998	0.407	0.326	0.499	CLONAL	1	TRUE	0	0.379879588920439	2		582	168	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892293	9892293	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004472-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	10	489	0	ENST00000330684.3:c.2197G>T	p.Ala733Ser	p.A733S	ENST00000330684	NM_001134407.1	733	Gca/Tca	11/13	0.379879588920439	1	FACETS	0.422	0.288	0.587	0.422	0.288	0.587	SUBCLONAL	1	TRUE	0	0.379879588920439	1		489	101	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578197	7578197	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004472-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	75	766	0	ENST00000269305.4:c.652G>T	p.Val218Leu	p.V218L	ENST00000269305	NM_001126112.2	218	Gtg/Ttg	6/11	0.275735973279669	4	FACETS	0.913	0.816	1	0.685	0.612	0.759	CLONAL	3	TRUE	0	0.379879588920439	4		766	199	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271779	18271779	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs775964374	NA	P-0004472-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	29	509	0	ENST00000222254.8:c.466G>T	p.Asp156Tyr	p.D156Y	ENST00000222254	NM_005027.3	156	Gac/Tac	4/16	0.133236306305695	5	FACETS	1	0.879	1	0.281	0.227	0.342	INDETERMINATE	1	TRUE	1	0.379879588920439	5		509	213	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910642	50910642	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004472-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	28	893	1	ENST00000440232.2:c.1745C>G	p.Thr582Arg	p.T582R	ENST00000440232	NM_002691.3	582	aCg/aGg	14/27	0.183638053123883	1	FACETS	0.51	0.41	0.624	0.51	0.41	0.624	INDETERMINATE	1	TRUE	0	0.379879588920439	1		894	234	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31379489	31379489	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004472-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	28	612	0	ENST00000328111.2:c.896G>T	p.Arg299Leu	p.R299L	ENST00000328111	NM_006892.3	299	cGa/cTa	8/23	0.379879588920439	6	FACETS	0.917	0.735	1	0.229	0.183	0.281	CLONAL	1	TRUE	2	0.379879588920439	6		612	283	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733343	40733343	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004472-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	10	223	0	ENST00000373198.4:c.3463G>C	p.Val1155Leu	p.V1155L	ENST00000373198	NM_133170.3	1155	Gtg/Ctg	26/32	0.379879588920439	4	FACETS	0.484	0.329	0.678	0.161	0.109	0.226	SUBCLONAL	1	TRUE	1	0.379879588920439	4		223	150	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341493	70341493	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004472-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	35	847	1	ENST00000374080.3:c.928G>T	p.Asp310Tyr	p.D310Y	ENST00000374080		310	Gat/Tat	7/45	0.379879588920439	1	FACETS	0.638	0.526	0.761	0.638	0.526	0.761	SUBCLONAL	1	TRUE	0	0.379879588920439	1		848	234	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394979	394980	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004472-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	27	312	0	ENST00000380956.4:c.376dup	p.Arg126LysfsTer5	p.R126Kfs*5	ENST00000380956	NM_001195286.1	125	-/A	3/9	0.218393810413753	3	FACETS	0.989	0.795	1			1	INDETERMINATE	1	TRUE	NA	0.379879588920439	3		312	171	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	35	245	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.848	0.701	1	1	0.958	1	CLONAL	2	FALSE	1	0.191889642136811	2		245	215	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874261	155874261	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs483352822	NA	P-0004519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	144	496	0	ENST00000368323.3:c.270G>C	p.Met90Ile	p.M90I	ENST00000368323	NM_006912.5	90	atG/atC	5/6	0.16835052589067	3	FACETS	0.844	0.772	0.919	1	0.981	1	CLONAL	3	FALSE	1	0.191889642136811	3		496	650	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023895	27023895	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	13	98	0	ENST00000324856.7:c.1001C>G	p.Ser334Trp	p.S334W	ENST00000324856	NM_006015.4	334	tCg/tGg	1/20	1	2	FACETS	0.975	0.699	1	0.975	0.699	1	CLONAL	1	FALSE	1	0.191889642136811	2		98	139	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086151	16086151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	101	309	0	ENST00000281043.3:c.1327G>A	p.Glu443Lys	p.E443K	ENST00000281043	NM_005378.4	443	Gaa/Aaa	3/3	1	2	FACETS	0.883	0.791	0.981	1	0.985	1	CLONAL	2	FALSE	1	0.191889642136811	2		309	596	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026889	48026889	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1558662873	NA	P-0004519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	106	541	0	ENST00000234420.5:c.1767T>A	p.Tyr589Ter	p.Y589*	ENST00000234420	NM_000179.2	589	taT/taA	4/10	1	2	FACETS	0.979	0.881	1	1	0.988	1	CLONAL	2	FALSE	1	0.191889642136811	2		541	564	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397738	49397738	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	58	734	0	ENST00000418115.1:c.486G>C	p.Lys162Asn	p.K162N	ENST00000418115	NM_001664.2	162	aaG/aaC	5/5	0.191889642136811	1	FACETS	0.678	0.581	0.784	0.678	0.581	0.784	SUBCLONAL	1	FALSE	0	0.191889642136811	1		734	806	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397815	49397815	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	57	535	0	ENST00000418115.1:c.409G>A	p.Glu137Lys	p.E137K	ENST00000418115	NM_001664.2	137	Gag/Aag	5/5	0.191889642136811	1	FACETS	0.855	0.733	0.989	0.855	0.733	0.989	CLONAL	1	FALSE	0	0.191889642136811	1		535	628	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430425	181430425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	55	604	0	ENST00000325404.1:c.277G>A	p.Glu93Lys	p.E93K	ENST00000325404	NM_003106.3	93	Gag/Aag	1/1	1	2	FACETS	0.76	0.649	0.882	0.76	0.649	0.882	SUBCLONAL	1	FALSE	1	0.191889642136811	2		604	754	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218774	66218774	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	40	613	0	ENST00000273854.3:c.2284G>C	p.Asp762His	p.D762H	ENST00000273854	NM_004439.5	762	Gat/Cat	13/18	1	2	FACETS	0.858	0.713	1	0.858	0.713	1	CLONAL	1	FALSE	1	0.191889642136811	2		613	486	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524560	187524560	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0004519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	90	495	0	ENST00000441802.2:c.11120C>G	p.Ser3707Ter	p.S3707*	ENST00000441802	NM_005245.3	3707	tCa/tGa	19/27	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.191889642136811	2		495	694	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167795	56167795	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	77	457	0	ENST00000399503.3:c.1360G>C	p.Glu454Gln	p.E454Q	ENST00000399503	NM_005921.1	454	Gaa/Caa	7/20	1	2	FACETS	1	0.914	1	1	0.984	1	CLONAL	2	FALSE	1	0.191889642136811	2		457	385	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168473	56168473	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765449528	NA	P-0004519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	30	311	0	ENST00000399503.3:c.1429G>A	p.Glu477Lys	p.E477K	ENST00000399503	NM_005921.1	477	Gaa/Aaa	8/20	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	FALSE	1	0.191889642136811	2		311	281	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502230	157502230	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs886039676	NA	P-0004519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	32	321	0	ENST00000346085.5:c.3263C>G	p.Ser1088Ter	p.S1088*	ENST00000346085	NM_020732.3	1088	tCa/tGa	12/20	1	2	FACETS	0.716	0.58	0.869	0.716	0.58	0.869	SUBCLONAL	1	FALSE	1	0.191889642136811	2		321	466	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248205	110248205	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	30	234	0	ENST00000374672.4:c.1267G>A	p.Glu423Lys	p.E423K	ENST00000374672	NM_004235.4	423	Gag/Aag	5/5	0.191889642136811	1	FACETS	0.734	0.592	0.896	0.734	0.592	0.896	SUBCLONAL	1	FALSE	0	0.191889642136811	1		234	385	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492767	50492767	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	151	586	0	ENST00000394963.4:c.1532G>A	p.Gly511Glu	p.G511E	ENST00000394963	NM_003076.4	511	gGa/gAa	13/13	1	2	FACETS	1	0.964	1	1	0.992	1	CLONAL	2	FALSE	1	0.191889642136811	2		586	719	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041512	14041512	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	42	319	0	ENST00000311895.7:c.2059G>C	p.Asp687His	p.D687H	ENST00000311895	NM_005236.2	687	Gat/Cat	11/11	1	2	FACETS	0.872	0.728	1	0.872	0.728	1	CLONAL	1	FALSE	1	0.191889642136811	2		319	502	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884134	37884134	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	65	611	0	ENST00000269571.5:c.3605G>T	p.Gly1202Val	p.G1202V	ENST00000269571		1202	gGa/gTa	27/27	0.138414612395996	4	FACETS	0.927	0.802	1	0.464	0.401	0.532	CLONAL	1	FALSE	2	0.191889642136811	4		611	871	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41199678	41199678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	71	602	0	ENST00000357654.3:c.5449G>A	p.Glu1817Lys	p.E1817K	ENST00000357654	NM_007294.3	1817	Gag/Aag	22/23	0.191889642136811	1	FACETS	0.819	0.713	0.933	0.819	0.713	0.933	CLONAL	1	FALSE	0	0.191889642136811	1		602	817	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912752	32912831	+	frameshift_variant	Frame_Shift_Del	DEL	TTTTGAGACTTCTGATACATTTTTTCAGACTGCAAGTGGGAAAAATATTAGTGTCGCCAAAGAGTCATTTAATAAAATTG	TTTTGAGACTTCTGATACATTTTTTCAGACTGCAAGTGGGAAAAATATTAGTGTCGCCAAAGAGTCATTTAATAAAATTG	-	novel	NA	P-0004519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	46	970	0	ENST00000380152.3:c.4261_4340del	p.Phe1421LysfsTer4	p.F1421Kfs*4	ENST00000380152		1420	gaTTTTGAGACTTCTGATACATTTTTTCAGACTGCAAGTGGGAAAAATATTAGTGTCGCCAAAGAGTCATTTAATAAAATTGta/gata	11/27	0.191889642136811	0	FACETS	0.577	0.485	0.68			1	SUBCLONAL	1	FALSE	0	0.191889642136811	0		970	671	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115953	8115954	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0004519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	73	264	0	ENST00000346208.3:c.1301_1302dup	p.Pro435ThrfsTer41	p.P435Tfs*41	ENST00000346208		433	-/CA	6/6	0.138414612395996	4	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	FALSE	2	0.191889642136811	4		264	399	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061447	38061448	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	52	286	0	ENST00000250448.2:c.541dup	p.Met181AsnfsTer46	p.M181Nfs*46	ENST00000250448	NM_004496.3	181	atg/aAtg	2/2	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	FALSE	1	0.191889642136811	2		286	430	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922793	44922802	+	frameshift_variant	Frame_Shift_Del	DEL	AGCGTCTCTC	AGCGTCTCTC	-	novel	NA	P-0004519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	154	329	0	ENST00000377967.4:c.1657_1666del	p.Val553LeufsTer37	p.V553Lfs*37	ENST00000377967	NM_021140.2	552	AGCGTCTCTCag/ag	16/29	0.191889642136811	0	FACETS	0.942	0.87	1			1	CLONAL	3	FALSE	NA	0.191889642136811	0		329	459	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	358	408	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	0.16087689862599	5	FACETS	0.868	0.826	0.912			1	INDETERMINATE	3	TRUE	NA	0.516850403037453	5		408	944	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775720	9775720	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769029561	NA	P-0004540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	150	350	0	ENST00000377346.4:c.263G>A	p.Arg88His	p.R88H	ENST00000377346	NM_005026.3	88	cGt/cAt	4/24	0.516850403037453	2	FACETS	0.894	0.82	0.972	0.447	0.41	0.486	CLONAL	1	TRUE	0	0.516850403037453	2		350	649	SUCCESS
ATM	472	MSKCC	GRCh37	11	108181012	108181012	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555110484	NA	P-0004540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	178	331	0	ENST00000278616.4:c.5888A>G	p.Asp1963Gly	p.D1963G	ENST00000278616	NM_000051.3	1963	gAt/gGt	39/63	0.4971483859024	2	FACETS	0.957	0.896	1	0.957	0.896	1	CLONAL	2	TRUE	0	0.516850403037453	2		331	360	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420213	49420213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267607237	NA	P-0004544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	314	400	2	ENST00000301067.7:c.15536G>A	p.Arg5179His	p.R5179H	ENST00000301067	NM_003482.3	5179	cGt/cAt	48/54	0.786655065413405	1	FACETS	0.999	0.961	1	0.999	0.961	1	CLONAL	1	TRUE	0	0.815836168961621	1		402	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578266	7578266	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs942158624	NA	P-0004544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	410	491	0	ENST00000269305.4:c.583A>T	p.Ile195Phe	p.I195F	ENST00000269305	NM_001126112.2	195	Atc/Ttc	6/11	0.805380979911749	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.815836168961621	1		491	575	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720737	89720737	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0004544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	25	70	0	ENST00000371953.3:c.888T>A	p.Cys296Ter	p.C296*	ENST00000371953	NM_000314.4	296	tgT/tgA	8/9	1	2	FACETS	0.447	0.357	0.548	0.447	0.357	0.548	SUBCLONAL	1	TRUE	1	0.815836168961621	2		70	137	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693002	89693003	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	186	227	0	ENST00000371953.3:c.491dup	p.Val166SerfsTer14	p.V166Sfs*14	ENST00000371953	NM_000314.4	162	-/A	5/9	1	2	FACETS	0.901	0.839	0.964	0.901	0.839	0.964	CLONAL	1	TRUE	1	0.815836168961621	2		227	506	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589584	67589591	+	protein_altering_variant	In_Frame_Del	DEL	ACATGAAT	ACATGAAT	TC	novel	NA	P-0004544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	648	354	0	ENST00000274335.5:c.1347_1354delinsTC	p.Leu449_Tyr452delinsPheHis	p.L449_Y452delinsFH	ENST00000274335		449	ttACATGAATat/ttTCat	10/15	0.815836168961621	3	FACETS	0.951	0.921	0.981			1	CLONAL	2	TRUE	NA	0.815836168961621	3		354	1176	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166723	32166724	+	missense_variant	Missense_Mutation	DNP	GC	GC	AT	novel	NA	P-0004544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	236	387	0	ENST00000375023.3:c.4514_4515delinsAT	p.Gly1505Asp	p.G1505D	ENST00000375023	NM_004557.3	1505	gGC/gAT	24/30	1	2	FACETS	0.837	0.785	0.89	0.837	0.785	0.89	CLONAL	1	TRUE	1	0.815836168961621	2		387	691	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572931	7572932	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004597-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	174	760	0	ENST00000269305.4:c.1177dup	p.Asp393GlyfsTer78	p.D393Gfs*78	ENST00000269305	NM_001126112.2	393	gac/gGac	11/11	0.316236431496566	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.316236431496566	1		760	645	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89791107	89791107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1290807070	NA	P-0004597-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	38	65	0	ENST00000336032.3:c.494C>T	p.Ala165Val	p.A165V	ENST00000336032	NM_006813.2	165	gCc/gTc	1/2	0.132950914921873	0	FACETS	0.768	0.653	0.888			1	INDETERMINATE	2	TRUE	0	0.316236431496566	0		65	107	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371409680	NA	P-0004597-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	24	661	1	ENST00000269305.4:c.848G>A	p.Arg283His	p.R283H	ENST00000269305	NM_001126112.2	283	cGc/cAc	8/11	0.316236431496566	1	FACETS	0.207	0.161	0.26	0.207	0.161	0.26	SUBCLONAL	1	TRUE	0	0.316236431496566	1		662	617	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955966	55955966	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757722266	NA	P-0004600-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	169	271	0	ENST00000263923.4:c.3196C>T	p.Arg1066Cys	p.R1066C	ENST00000263923	NM_002253.2	1066	Cgc/Tgc	24/30	0.39956249946253	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	2	0.659886080298308	4		271	411	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081519	143081519	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004600-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	209	251	0	ENST00000262992.4:c.1555G>T	p.Glu519Ter	p.E519*	ENST00000262992	NM_001101669.1	519	Gaa/Taa	15/24	0.659886080298308	3	FACETS	0.982	0.924	1	0.655	0.616	0.693	CLONAL	2	TRUE	0	0.659886080298308	3		251	429	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151868429	151868429	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0004600-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	104	188	0	ENST00000262189.6:c.9375-2A>C		p.X3125_splice	ENST00000262189	NM_170606.2	3125			NA	2	FACETS	1	0.907	1			1	INDETERMINATE	1	TRUE	NA	0.659886080298308	2		188	315	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345855	152345855	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004600-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	153	507	2	ENST00000359321.1:c.715A>T	p.Met239Leu	p.M239L	ENST00000359321	NM_005431.1	239	Atg/Ttg	3/3	NA	2	FACETS	0.789	0.725	0.855			1	INDETERMINATE	1	TRUE	NA	0.659886080298308	2		509	588	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492311	56492311	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004600-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	80	317	0	ENST00000267101.3:c.2644A>T	p.Ser882Cys	p.S882C	ENST00000267101	NM_001982.3	882	Agt/Tgt	22/28	0.374524106562326	3	FACETS	0.619	0.546	0.697	0.206	0.182	0.233	INDETERMINATE	1	TRUE	0	0.659886080298308	3		317	521	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197332	26197338	+	protein_altering_variant	In_Frame_Ins	INS	CAGAGCC	CAGAGCC	TGCCGGATCT	novel	NA	P-0004600-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	65	694	1	ENST00000356476.2:c.141_147delinsAGATCCGGCA	p.Ala48_Leu49delinsAspProAla	p.A48_L49delinsDPA	ENST00000356476		47	gtGGCTCTG/gtAGATCCGGCA	1/1	0.503808653622205	6	FACETS	0.457	0.395	0.525	0.114	0.098	0.132	SUBCLONAL	1	TRUE	2	0.659886080298308	6		695	1000	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253747	153253747	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0004692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	101	395	0	ENST00000281708.4:c.985+1G>A		p.X329_splice	ENST00000281708	NM_033632.3	329			0.163984822096527	3	FACETS	0.883	0.793	0.979	0.294	0.264	0.327	INDETERMINATE	1	TRUE	0	0.580827842606629	3		395	508	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5066700	5066700	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	262	597	0	ENST00000381652.3:c.1237C>G	p.Leu413Val	p.L413V	ENST00000381652	NM_004972.3	413	Ctg/Gtg	10/25	0.580827842606629	6	FACETS	1	0.992	1			1	CLONAL	1	TRUE	NA	0.580827842606629	6		597	1322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578552	7578552	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	rs1567554500	NA	P-0004692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	368	273	0	ENST00000269305.4:c.378C>G	p.Tyr126Ter	p.Y126*	ENST00000269305	NM_001126112.2	126	taC/taG	5/11	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	2	TRUE	NA	0.580827842606629	2		273	598	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15364965	15364965	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	87	356	0	ENST00000263377.2:c.2156C>G	p.Thr719Arg	p.T719R	ENST00000263377	NM_058243.2	719	aCa/aGa	11/20	0.34937215321932	2	FACETS	0.39	0.344	0.438	0.195	0.172	0.219	SUBCLONAL	1	TRUE	0	0.580827842606629	2		356	769	SUCCESS
APC	324	MSKCC	GRCh37	5	112175324	112175325	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	186	412	0	ENST00000257430.4:c.4035dup	p.Ser1346IlefsTer8	p.S1346Ifs*8	ENST00000257430	NM_000038.5	1345	gaa/gAaa	16/16	0.580827842606629	2	FACETS	0.928	0.873	0.983	0.928	0.873	0.983	CLONAL	2	TRUE	0	0.580827842606629	2		412	345	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0004702-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	139	180	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	0.344762800892198	1	FACETS	0.881	0.809	0.955	0.881	0.809	0.955	CLONAL	1	TRUE	0	0.535200181578456	1		180	432	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696713	47696713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004702-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	281	276	0	ENST00000347630.2:c.235G>A	p.Glu79Lys	p.E79K	ENST00000347630	NM_001007230.1	79	Gaa/Aaa	5/11	0.209296460253518	2	FACETS	1	0.99	1	0.618	0.583	0.655	INDETERMINATE	1	TRUE	0	0.535200181578456	2		276	849	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115437	115115437	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004702-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	168	442	0	ENST00000257566.3:c.889A>C	p.Asn297His	p.N297H	ENST00000257566	NM_016569.3	297	Aac/Cac	5/8	0.307362970123521	1	FACETS	0.659	0.607	0.712	0.659	0.607	0.712	INDETERMINATE	1	TRUE	0	0.535200181578456	1		442	698	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835751	68835752	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004702-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	255	370	0	ENST00000261769.5:c.343dup	p.Thr115AsnfsTer53	p.T115Nfs*53	ENST00000261769	NM_004360.3	114	-/A	3/16	0.535200181578456	1	FACETS	0.909	0.854	0.965	0.909	0.854	0.965	CLONAL	1	TRUE	0	0.535200181578456	1		370	768	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602390	10602391	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0004708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	87	893	0	ENST00000171111.5:c.1187dup	p.Tyr396Ter	p.Y396*	ENST00000171111	NM_203500.1	396	tac/taAc	3/6	1	2	FACETS	0.89	0.788	0.998	0.89	0.788	0.998	CLONAL	1	TRUE	1	0.29409205217371	2		893	665	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	81	245	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.975	1			1	INDETERMINATE	1	TRUE	NA	0.756112332843649	2		245	170	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0004721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	213	396	1	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	0.177336686961571	4	FACETS	1	0.958	1	1	0.958	1	INDETERMINATE	2	TRUE	2	0.756112332843649	4		397	483	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0004721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	414	689	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	0.364821329868052	4	FACETS	0.925	0.883	0.967	0.925	0.883	0.967	INDETERMINATE	2	TRUE	2	0.756112332843649	4		689	1040	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155454	47155454	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	250	417	4	ENST00000409792.3:c.4627C>T	p.Arg1543Trp	p.R1543W	ENST00000409792	NM_014159.6	1543	Cgg/Tgg	5/21	0.177336686961571	4	FACETS	0.872	0.82	0.924	0.872	0.82	0.924	INDETERMINATE	2	TRUE	2	0.756112332843649	4		421	666	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162824	47162824	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs547630365	NA	P-0004721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	251	331	0	ENST00000409792.3:c.3302G>A	p.Trp1101Ter	p.W1101*	ENST00000409792	NM_014159.6	1101	tGg/tAg	3/21	0.177336686961571	4	FACETS	0.914	0.861	0.967	0.914	0.861	0.967	INDETERMINATE	2	TRUE	2	0.756112332843649	4		331	638	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796882	42796883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761345552	NA	P-0004721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	207	380	1	ENST00000575354.2:c.3347dup	p.Ser1117LysfsTer34	p.S1117Kfs*34	ENST00000575354	NM_015125.3	1114	gcc/gCcc	14/20	NA	2	FACETS	0.861	0.818	0.902			1	INDETERMINATE	2	TRUE	NA	0.756112332843649	2		381	318	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0004757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	118	201	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.171104658175101	8	FACETS	0.988	0.921	1	1	0.991	1	CLONAL	11	TRUE	2	0.171104658175101	8		201	192	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	45	245	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.894	1	1	0.981	1	CLONAL	4	TRUE	1	0.171104658175101	2		245	126	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0004757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	115	198	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.171104658175101	5	FACETS	0.958	0.88	1			1	CLONAL	7	TRUE	NA	0.171104658175101	5		198	252	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0004757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	62	551	0	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	1	2	FACETS	1	0.941	1	1	0.987	1	CLONAL	5	TRUE	1	0.171104658175101	2		551	133	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0004757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	82	75	1	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	0.171104658175101	3	FACETS	0.918	0.828	1	1	0.988	1	CLONAL	6	TRUE	1	0.171104658175101	3		76	189	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753199	57753199	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	50	335	0	ENST00000274289.3:c.817A>G	p.Met273Val	p.M273V	ENST00000274289	NM_006622.3	273	Atg/Gtg	7/14	1	2	FACETS	0.955	0.841	1	1	0.984	1	CLONAL	6	TRUE	1	0.171104658175101	2		335	102	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481823	56481823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1296453299	NA	P-0004757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	59	463	0	ENST00000267101.3:c.751G>A	p.Asp251Asn	p.D251N	ENST00000267101	NM_001982.3	251	Gac/Aac	7/28	1	2	FACETS	0.966	0.861	1	1	0.987	1	CLONAL	6	TRUE	1	0.171104658175101	2		463	119	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040640	47040640	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	51	228	0	ENST00000377604.3:c.1275G>A	p.Trp425Ter	p.W425*	ENST00000377604	NM_001204468.1	425	tgG/tgA	13/24	0.154129968522662	0	FACETS		NA	1			1	NA	10	TRUE	NA	0.171104658175101	0		228	56	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652054	36652055	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	80	524	0	ENST00000244741.5:c.178dup	p.Glu60GlyfsTer3	p.E60Gfs*3	ENST00000244741	NM_000389.4	59	ctg/ctGg	2/3	0.171104658175101	4	FACETS	0.932	0.834	1	1	0.987	1	CLONAL	5	TRUE	2	0.171104658175101	4		524	235	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651995	36651995	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	18	541	0	ENST00000244741.5:c.119del	p.Gly40AlafsTer108	p.G40Afs*108	ENST00000244741	NM_000389.4	39	gcG/gc	2/3	0.171104658175101	4	FACETS	0.765	0.576	0.99	0.383	0.288	0.495	CLONAL	1	TRUE	2	0.171104658175101	4		541	322	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949171	44949172	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	38	234	0	ENST00000377967.4:c.3733dup	p.Thr1245AsnfsTer6	p.T1245Nfs*6	ENST00000377967	NM_021140.2	1244	-/A	25/29	0.154129968522662	0	FACETS	0.939	0.848	1			1	CLONAL	8	TRUE	NA	0.171104658175101	0		234	49	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652125	36652126	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	23	399	0	ENST00000244741.5:c.247_248insT	p.Arg83LeufsTer6	p.R83Lfs*6	ENST00000244741	NM_000389.4	83	cgg/cTgg	2/3	0.171104658175101	4	FACETS	1	0.917	1	0.712	0.558	0.89	CLONAL	1	TRUE	2	0.171104658175101	4		399	221	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	128	250	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.796	0.724	0.872	1	0.987	1	SUBCLONAL	2	TRUE	1	0.28	2		250	574	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142885	30142885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766999851	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	57	230	0	ENST00000389048.3:c.641G>A	p.Arg214His	p.R214H	ENST00000389048	NM_004304.4	214	cGc/cAc	1/29	0.327718258504154	2	FACETS	0.945	0.813	1	0.472	0.406	0.544	CLONAL	1	TRUE	0	0.28	2		230	431	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	117	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.28	2		311	560	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	76	407	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.28	2		407	453	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089706	27089706	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	105	213	0	ENST00000324856.7:c.2666del	p.Gly889AlafsTer2	p.G889Afs*2	ENST00000324856	NM_006015.4	888	Ggg/gg	8/20	1	2	FACETS	0.77	0.693	0.851	1	0.984	1	SUBCLONAL	2	TRUE	1	0.28	2		213	487	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	122	318	1	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	TRUE	1	0.28	2		319	639	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564642	55564642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	90	248	0	ENST00000288135.5:c.530G>A	p.Arg177His	p.R177H	ENST00000288135	NM_000222.2	177	cGc/cAc	3/21	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.28	2		248	636	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223203	5223203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1416280955	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	66	174	0	ENST00000357368.4:c.2600G>A	p.Arg867His	p.R867H	ENST00000357368	NM_002850.3	867	cGc/cAc	18/38	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.28	2		174	364	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297981	15297981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763115768	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	118	343	1	ENST00000263388.2:c.1775G>A	p.Arg592His	p.R592H	ENST00000263388	NM_000435.2	592	cGc/cAc	11/33	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.28	2		344	597	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671655	67671655	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1400980130	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	100	228	0	ENST00000264010.4:c.2070del	p.Glu691SerfsTer30	p.E691Sfs*30	ENST00000264010	NM_006565.3	688	gtA/gt	12/12	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.28	2		228	641	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380283	25380283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913528	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	112	246	0	ENST00000311936.3:c.175G>A	p.Ala59Thr	p.A59T	ENST00000311936	NM_004985.3	59	Gca/Aca	3/5	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.28	2		246	608	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	133	764	2	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.28	2		766	854	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420661	49420661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555185875	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	73	371	0	ENST00000301067.7:c.15088C>T	p.Arg5030Cys	p.R5030C	ENST00000301067	NM_003482.3	5030	Cgt/Tgt	48/54	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.28	2		371	461	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94209523	94209523	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	111	291	0	ENST00000323929.3:c.591del	p.Val198Ter	p.V198*	ENST00000323929	NM_005591.3	197	aaA/aa	7/20	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.28	2		291	742	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491274	2491274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368302066	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	86	241	0	ENST00000355716.4:c.317G>A	p.Arg106His	p.R106H	ENST00000355716	NM_003820.2	106	cGc/cAc	4/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.28	2		241	474	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264445	16264445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1355879966	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	122	293	0	ENST00000375759.3:c.10648G>A	p.Ala3550Thr	p.A3550T	ENST00000375759	NM_015001.2	3550	Gcc/Acc	13/15	1	2	FACETS	0.76	0.69	0.834	1	0.986	1	SUBCLONAL	2	TRUE	1	0.28	2		293	573	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099430	27099430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1227227387	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	103	314	0	ENST00000324856.7:c.3667C>T	p.Arg1223Cys	p.R1223C	ENST00000324856	NM_006015.4	1223	Cgc/Tgc	14/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.28	2		314	641	SUCCESS
FH	2271	MSKCC	GRCh37	1	241669408	241669408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	86	272	0	ENST00000366560.3:c.799C>T	p.Pro267Ser	p.P267S	ENST00000366560	NM_000143.3	267	Cca/Tca	6/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.28	2		272	504	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641544	47641544	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs63750640	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	244	326	0	ENST00000233146.2:c.929T>G	p.Leu310Arg	p.L310R	ENST00000233146	NM_000251.2	310	cTt/cGt	5/16	0.327718258504154	2	FACETS	0.925	0.87	0.98	1	0.992	1	CLONAL	3	TRUE	0	0.28	2		326	628	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661857	227661857	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	66	176	0	ENST00000305123.5:c.1598C>T	p.Thr533Ile	p.T533I	ENST00000305123	NM_005544.2	533	aCc/aTc	1/2	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.28	2		176	377	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165687	185165687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	112	216	2	ENST00000265026.3:c.962C>T	p.Ala321Val	p.A321V	ENST00000265026	NM_004721.4	321	gCg/gTg	5/14	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.28	2		218	625	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138664	55138664	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	88	223	1	ENST00000257290.5:c.1341G>A	p.Trp447Ter	p.W447*	ENST00000257290	NM_006206.4	447	tgG/tgA	9/23	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.28	2		224	540	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197781	66197781	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	76	271	0	ENST00000273854.3:c.2918G>T	p.Trp973Leu	p.W973L	ENST00000273854	NM_004439.5	973	tGg/tTg	17/18	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.28	2		271	524	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592099	67592099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	123	701	2	ENST00000274335.5:c.1915C>T	p.Arg639Ter	p.R639*	ENST00000274335		639	Cga/Tga	14/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.28	2		703	695	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164180	32164180	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	96	208	0	ENST00000375023.3:c.5219G>A	p.Trp1740Ter	p.W1740*	ENST00000375023	NM_004557.3	1740	tGg/tAg	29/30	0.327718258504154	2	FACETS	1	0.979	1	0.708	0.634	0.787	CLONAL	1	TRUE	0	0.28	2		208	484	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157470048	157470048	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	39	145	0	ENST00000346085.5:c.2842G>T	p.Ala948Ser	p.A948S	ENST00000346085	NM_020732.3	948	Gca/Tca	9/20	1	2	FACETS	0.998	0.832	1	0.998	0.832	1	CLONAL	1	TRUE	1	0.28	2		145	279	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106519984	106519984	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	88	203	0	ENST00000359195.3:c.2412G>T	p.Met804Ile	p.M804I	ENST00000359195	NM_002649.2	804	atG/atT	6/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.28	2		203	566	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843375	128843375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773562190	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	88	275	0	ENST00000249373.3:c.482G>A	p.Arg161Gln	p.R161Q	ENST00000249373	NM_005631.4	161	cGg/cAg	2/12	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.28	2		275	547	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841949	151841949	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	85	210	2	ENST00000262189.6:c.14192G>A	p.Ser4731Asn	p.S4731N	ENST00000262189	NM_170606.2	4731	aGc/aAc	55/59	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.28	2		212	520	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135777085	135777085	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1331635112	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	92	215	0	ENST00000298552.3:c.2393C>T	p.Thr798Met	p.T798M	ENST00000298552	NM_001162426.1	798	aCg/aTg	19/23	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.28	2		215	549	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431709	49431709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752428122	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	109	301	0	ENST00000301067.7:c.9430G>A	p.Ala3144Thr	p.A3144T	ENST00000301067	NM_003482.3	3144	Gca/Aca	34/54	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.28	2		301	615	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105240286	105240286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369698909	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	90	270	0	ENST00000349310.3:c.665G>A	p.Arg222His	p.R222H	ENST00000349310	NM_001014432.1	222	cGc/cAc	9/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.28	2		270	558	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2107176	2107176	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	72	264	0	ENST00000219476.3:c.845A>G	p.Asp282Gly	p.D282G	ENST00000219476	NM_000548.3	282	gAc/gGc	9/42	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.28	2		264	431	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828120	3828120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	133	260	0	ENST00000262367.5:c.2005C>T	p.Arg669Trp	p.R669W	ENST00000262367	NM_004380.2	669	Cgg/Tgg	10/31	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.28	2		260	715	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925150	81925150	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	137	365	0	ENST00000359376.3:c.941T>C	p.Met314Thr	p.M314T	ENST00000359376	NM_002661.3	314	aTg/aCg	11/33	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.28	2		365	775	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857933	89857933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780135578	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	88	265	1	ENST00000389301.3:c.1237C>T	p.Arg413Cys	p.R413C	ENST00000389301	NM_000135.2	413	Cgt/Tgt	14/43	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.28	2		266	554	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41251827	41251827	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	146	306	0	ENST00000357654.3:c.512T>C	p.Ile171Thr	p.I171T	ENST00000357654	NM_007294.3	171	aTa/aCa	7/23	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.28	2		306	808	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45423040	45423040	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	103	243	0	ENST00000262160.6:c.88G>A	p.Gly30Arg	p.G30R	ENST00000262160	NM_005901.5	30	Gga/Aga	2/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.28	2		243	556	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799231	42799231	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1251828335	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	20	74	0	ENST00000575354.2:c.4715C>T	p.Ala1572Val	p.A1572V	ENST00000575354	NM_015125.3	1572	gCc/gTc	20/20	1	2	FACETS	0.816	0.628	1	0.816	0.628	1	CLONAL	1	TRUE	1	0.28	2		74	175	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175889	24175889	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1431173741	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	73	271	0	ENST00000263121.7:c.1117A>G	p.Arg373Gly	p.R373G	ENST00000263121	NM_003073.3	373	Agg/Ggg	8/9	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.28	2		271	418	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879892	44879892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	142	130	0	ENST00000377967.4:c.481C>T	p.Pro161Ser	p.P161S	ENST00000377967	NM_021140.2	161	Ccc/Tcc	6/29	1	1	FACETS	0.836	0.772	0.9	1	0.993	1	CLONAL	3	TRUE	0	0.28	1		130	348	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938474	44938474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	158	182	0	ENST00000377967.4:c.3022G>A	p.Ala1008Thr	p.A1008T	ENST00000377967	NM_021140.2	1008	Gca/Aca	20/29	1	1	FACETS	1	0.943	1	1	0.992	1	CLONAL	2	TRUE	0	0.28	1		182	474	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	78	309	0	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.28	2		309	510	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687514	37687514	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	61	144	0	ENST00000447079.4:c.4422del	p.Pro1475LeufsTer24	p.P1475Lfs*24	ENST00000447079	NM_015083.1	1473	cGg/cg	14/14	1	2	FACETS	0.778	0.677	0.886	1	0.973	1	SUBCLONAL	2	TRUE	1	0.28	2		144	280	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919561	96919562	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	89	256	0	ENST00000258439.3:c.701dup	p.Ala235CysfsTer41	p.A235Cfs*41	ENST00000258439	NM_001193304.2	234	cct/ccCt	4/4	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.28	2		256	513	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114799871	114799871	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	154	400	0	ENST00000543371.1:c.539del	p.Pro180ArgfsTer45	p.P180Rfs*45	ENST00000543371	NM_001198531.1	180	Ccg/cg	5/14	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.28	2		400	879	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843237	128843237	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	80	275	0	ENST00000249373.3:c.349del	p.Arg117AlafsTer5	p.R117Afs*5	ENST00000249373	NM_005631.4	115	gCc/gc	2/12	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.28	2		275	474	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186844	142186845	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	84	225	0	ENST00000350721.4:c.6618dup	p.Ser2207IlefsTer15	p.S2207Ifs*15	ENST00000350721	NM_001184.3	2206	-/A	39/47	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.28	2		225	538	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325840	65325840	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	137	270	0	ENST00000342505.4:c.1282G>C	p.Ala428Pro	p.A428P	ENST00000342505	NM_002227.2	428	Gcc/Ccc	9/25	0.361895614067193	1	FACETS	0.343	0.313	0.375	0.343	0.313	0.375	INDETERMINATE	1	TRUE	0	0.75276746886889	1		270	661	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939309	76939309	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	142	402	0	ENST00000373344.5:c.1439C>A	p.Thr480Lys	p.T480K	ENST00000373344	NM_000489.3	480	aCa/aAa	9/35	1	2	FACETS	0.495	0.452	0.541	0.495	0.452	0.541	SUBCLONAL	1	TRUE	1	0.75276746886889	2		402	762	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210320	123210320	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	55	427	0	ENST00000218089.9:c.2672A>G	p.Lys891Arg	p.K891R	ENST00000218089	NM_001042749.1	891	aAg/aGg	26/35	1	2	FACETS	0.195	0.166	0.227	0.195	0.166	0.227	SUBCLONAL	1	TRUE	1	0.75276746886889	2		427	748	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115900	8115901	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	277	284	0	ENST00000346208.3:c.1247dup	p.Thr417AspfsTer90	p.T417Dfs*90	ENST00000346208		416	ctg/cTtg	6/6	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.75276746886889	2		284	696	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0004892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	291	482	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.437613633322629	2		482	1053	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463208	25463208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	161	493	0	ENST00000264709.3:c.2285G>A	p.Gly762Asp	p.G762D	ENST00000264709	NM_175629.2	762	gGc/gAc	19/23	1	2	FACETS	0.779	0.715	0.847	0.779	0.715	0.847	SUBCLONAL	1	TRUE	1	0.437613633322629	2		493	944	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747918	41747918	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	90	416	0	ENST00000226382.2:c.851C>A	p.Pro284Gln	p.P284Q	ENST00000226382	NM_003924.3	284	cCg/cAg	3/3	NA	2	FACETS	0.649	0.576	0.726			1	INDETERMINATE	1	TRUE	NA	0.437613633322629	2		416	634	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540322	187540322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	96	503	0	ENST00000441802.2:c.7418G>A	p.Arg2473Lys	p.R2473K	ENST00000441802	NM_005245.3	2473	aGa/aAa	10/27	0.160076635897101	2	FACETS	0.484	0.43	0.541	0.242	0.215	0.271	INDETERMINATE	1	TRUE	0	0.437613633322629	2		503	907	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879016	151879016	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	257	489	0	ENST00000262189.6:c.5929C>A	p.Gln1977Lys	p.Q1977K	ENST00000262189	NM_170606.2	1977	Caa/Aaa	36/59	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.437613633322629	2		489	1103	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798735	135798735	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	166	364	0	ENST00000298552.3:c.508G>T	p.Gly170Cys	p.G170C	ENST00000298552	NM_001162426.1	170	Ggc/Tgc	6/23	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.437613633322629	2		364	740	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590765	95590765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886037667	NA	P-0004892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	69	524	0	ENST00000393063.1:c.1144G>A	p.Glu382Lys	p.E382K	ENST00000393063	NM_030621.3	382	Gaa/Aaa	9/28	0.255038969655654	1	FACETS	0.265	0.23	0.304	0.265	0.23	0.304	INDETERMINATE	1	TRUE	0	0.437613633322629	1		524	928	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247836	10247836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	267	656	0	ENST00000340748.4:c.4366C>T	p.Arg1456Trp	p.R1456W	ENST00000340748		1456	Cgg/Tgg	36/40	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.437613633322629	2		656	1182	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272230	15272230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763603215	NA	P-0004892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	152	290	0	ENST00000263388.2:c.6209C>T	p.Ala2070Val	p.A2070V	ENST00000263388	NM_000435.2	2070	gCg/gTg	33/33	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.437613633322629	2		290	561	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878994	151878995	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	240	490	0	ENST00000262189.6:c.5950dup	p.Leu1984ProfsTer22	p.L1984Pfs*22	ENST00000262189	NM_170606.2	1984	cta/cCta	36/59	1	2	FACETS	0.996	0.93	1	0.996	0.93	1	CLONAL	1	TRUE	1	0.437613633322629	2		490	1101	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542238	187542244	+	frameshift_variant	Frame_Shift_Del	DEL	ACTTAGT	ACTTAGT	-	novel	NA	P-0004892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	117	587	0	ENST00000441802.2:c.5496_5502del	p.Leu1833TrpfsTer31	p.L1833Wfs*31	ENST00000441802	NM_005245.3	1832	gtACTAAGT/gt	10/27	0.160076635897101	2	FACETS	0.524	0.472	0.58	0.262	0.236	0.29	INDETERMINATE	1	TRUE	0	0.437613633322629	2		587	1020	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506374	120506378	+	frameshift_variant	Frame_Shift_Del	DEL	GGCAA	GGCAA	-	novel	NA	P-0004892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	235	517	0	ENST00000256646.2:c.1734_1738del	p.Cys579ProfsTer9	p.C579Pfs*9	ENST00000256646	NM_024408.3	578	ccTTGCCac/ccac	11/34	1	2	FACETS	0.896	0.835	0.959	0.896	0.835	0.959	CLONAL	1	TRUE	1	0.437613633322629	2		517	1199	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665721	29665721	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0004899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	21	422	0	ENST00000356175.3:c.6757-1G>A		p.X2253_splice	ENST00000356175	NM_000267.3	2253			1	2	FACETS	1	0.79	1	1	0.79	1	CLONAL	1	TRUE	1	0.15	2		422	273	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106509	108106511	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	novel	NA	P-0004899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	22	365	0	ENST00000278616.4:c.444_446del	p.Ile149del	p.I149del	ENST00000278616	NM_000051.3	148	gaCATt/gat	5/63	1	2	FACETS	0.808	0.626	1	0.808	0.626	1	CLONAL	1	TRUE	1	0.15	2		365	363	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033825	49033826	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	26	373	0	ENST00000267163.4:c.1963dup	p.Tyr655LeufsTer13	p.Y655Lfs*13	ENST00000267163	NM_000321.2	654	-/T	20/27	1	2	FACETS	1	0.838	1	1	0.838	1	CLONAL	1	TRUE	1	0.15	2		373	325	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	248	501	1	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	NA	2	FACETS	1	0.953	1			1	INDETERMINATE	1	TRUE	NA	0.817661888457325	2		502	599	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	201	286	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.817661888457325	1	FACETS	0.962	0.915	1	0.962	0.915	1	CLONAL	1	TRUE	0	0.817661888457325	1		286	302	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	152	333	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.871	0.804	0.939	0.871	0.804	0.939	CLONAL	1	TRUE	1	0.817661888457325	2		335	427	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11264688	11264688	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	47	482	0	ENST00000361445.4:c.3874C>A	p.Leu1292Met	p.L1292M	ENST00000361445	NM_004958.3	1292	Ctg/Atg	26/58	NA	2	FACETS	0.189	0.159	0.222			1	INDETERMINATE	1	TRUE	NA	0.817661888457325	2		482	608	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702176	47702176	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	157	332	0	ENST00000233146.2:c.1772C>A	p.Pro591Gln	p.P591Q	ENST00000233146	NM_000251.2	591	cCa/cAa	12/16	0.817661888457325	1	FACETS	0.832	0.78	0.883	0.832	0.78	0.883	CLONAL	1	TRUE	0	0.817661888457325	1		332	273	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933704	49933704	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140736052	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	78	671	1	ENST00000296474.3:c.2573G>A	p.Arg858His	p.R858H	ENST00000296474	NM_002447.2	858	cGc/cAc	10/20	NA	2	FACETS	0.318	0.279	0.359			1	INDETERMINATE	1	TRUE	NA	0.817661888457325	2		672	600	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269074	142269074	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	262	425	0	ENST00000350721.4:c.2876T>C	p.Val959Ala	p.V959A	ENST00000350721	NM_001184.3	959	gTg/gCg	14/47	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.817661888457325	2		425	601	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187560916	187560916	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	287	353	0	ENST00000441802.2:c.3602G>T	p.Arg1201Met	p.R1201M	ENST00000441802	NM_005245.3	1201	aGg/aTg	4/27	0.115286245974383	4	FACETS	0.934	0.884	0.984	0.934	0.884	0.984	INDETERMINATE	2	TRUE	2	0.817661888457325	4		353	683	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032062	26032062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	523	891	1	ENST00000244661.2:c.227C>T	p.Ala76Val	p.A76V	ENST00000244661	NM_003537.3	76	gCc/gTc	1/1	0.157074620155961	4	FACETS	0.86	0.825	0.895	0.86	0.825	0.895	INDETERMINATE	2	TRUE	2	0.817661888457325	4		892	1352	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672116	30672116	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	79	306	0	ENST00000376406.3:c.4844C>T	p.Thr1615Ile	p.T1615I	ENST00000376406	NM_014641.2	1615	aCa/aTa	10/15	0.157074620155961	4	FACETS	0.571	0.502	0.645	0.286	0.251	0.323	INDETERMINATE	1	TRUE	2	0.817661888457325	4		306	615	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673536	30673536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs752227427	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	265	667	0	ENST00000376406.3:c.3424A>G	p.Thr1142Ala	p.T1142A	ENST00000376406	NM_014641.2	1142	Aca/Gca	10/15	0.157074620155961	4	FACETS	1	0.993	1	0.737	0.694	0.782	INDETERMINATE	1	TRUE	2	0.817661888457325	4		667	799	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652015	36652015	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1309823433	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	185	361	0	ENST00000244741.5:c.137G>A	p.Arg46His	p.R46H	ENST00000244741	NM_000389.4	46	cGt/cAt	2/3	0.157074620155961	4	FACETS	0.823	0.766	0.88	0.823	0.766	0.88	INDETERMINATE	2	TRUE	2	0.817661888457325	4		361	500	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519545	137519545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56403507	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	212	365	0	ENST00000367739.4:c.1093G>A	p.Val365Met	p.V365M	ENST00000367739	NM_000416.2	365	Gtg/Atg	7/7	0.157074620155961	4	FACETS	0.91	0.853	0.967	0.91	0.853	0.967	INDETERMINATE	2	TRUE	2	0.817661888457325	4		365	518	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505462	157505462	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	244	410	0	ENST00000346085.5:c.3443A>G	p.Tyr1148Cys	p.Y1148C	ENST00000346085	NM_020732.3	1148	tAc/tGc	13/20	0.157074620155961	4	FACETS	0.871	0.819	0.923	0.871	0.819	0.923	INDETERMINATE	2	TRUE	2	0.817661888457325	4		410	623	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501260	140501260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730880413	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	172	278	0	ENST00000288602.6:c.812G>A	p.Arg271His	p.R271H	ENST00000288602	NM_004333.4	271	cGt/cAt	6/18	0.680305209132487	1	FACETS	0.908	0.857	0.957	0.908	0.857	0.957	CLONAL	1	TRUE	0	0.817661888457325	1		278	274	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864309	117864309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301282588	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	301	493	0	ENST00000297338.2:c.1348C>T	p.Arg450Cys	p.R450C	ENST00000297338	NM_006265.2	450	Cgc/Tgc	11/14	0.157074620155961	4	FACETS	0.882	0.835	0.929	0.882	0.835	0.929	INDETERMINATE	2	TRUE	2	0.817661888457325	4		493	759	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402794	139402794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	106	430	1	ENST00000277541.6:c.3215G>A	p.Gly1072Asp	p.G1072D	ENST00000277541	NM_017617.3	1072	gGc/gAc	20/34	0.782515894132167	1	FACETS	0.487	0.442	0.533	0.487	0.442	0.533	SUBCLONAL	1	TRUE	0	0.817661888457325	1		431	315	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366990	118366990	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	257	472	1	ENST00000534358.1:c.5572C>T	p.Arg1858Ter	p.R1858*	ENST00000534358	NM_005933.3	1858	Cga/Tga	20/36	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.817661888457325	2		473	607	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438641	49438641	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759226682	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	43	434	2	ENST00000301067.7:c.4849C>T	p.Arg1617Trp	p.R1617W	ENST00000301067	NM_003482.3	1617	Cgg/Tgg	19/54	0.115286245974383	4	FACETS	0.351	0.293	0.415	0.175	0.146	0.208	INDETERMINATE	1	TRUE	2	0.817661888457325	4		436	545	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117431	115117431	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	305	470	1	ENST00000257566.3:c.743A>G	p.Tyr248Cys	p.Y248C	ENST00000257566	NM_016569.3	248	tAc/tGc	4/8	0.29573998621455	5	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.817661888457325	5		471	727	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472469	88472469	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	223	536	1	ENST00000360948.2:c.2086G>T	p.Gly696Trp	p.G696W	ENST00000360948	NM_001012338.2	696	Ggg/Tgg	16/19	1	2	FACETS	0.866	0.811	0.922	0.866	0.811	0.922	CLONAL	1	TRUE	1	0.817661888457325	2		537	630	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819655	81819655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	344	621	0	ENST00000359376.3:c.61G>A	p.Ala21Thr	p.A21T	ENST00000359376	NM_002661.3	21	Gcc/Acc	2/33	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.817661888457325	2		621	799	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81891867	81891867	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	214	587	0	ENST00000359376.3:c.338-1G>A		p.X113_splice	ENST00000359376	NM_002661.3	113			0.166077031684873	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.817661888457325	0		587	510	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347470	89347470	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs778780920	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	155	637	0	ENST00000301030.4:c.5480C>A	p.Pro1827His	p.P1827H	ENST00000301030	NM_001256183.1	1827	cCc/cAc	9/13	0.166077031684873	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.817661888457325	0		637	517	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40384055	40384055	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	332	706	0	ENST00000293328.3:c.91C>T	p.Arg31Trp	p.R31W	ENST00000293328	NM_012448.3	31	Cgg/Tgg	2/19	0.131141918856641	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.817661888457325	0		706	783	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208036	5208036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772956659	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	167	505	0	ENST00000357368.4:c.5675C>T	p.Thr1892Met	p.T1892M	ENST00000357368	NM_002850.3	1892	aCg/aTg	37/38	0.131141918856641	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.817661888457325	0		505	445	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245891	5245891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1045893958	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	267	557	1	ENST00000357368.4:c.884G>A	p.Arg295Gln	p.R295Q	ENST00000357368	NM_002850.3	295	cGg/cAg	10/38	0.131141918856641	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.817661888457325	0		558	610	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31025035	31025035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375101983	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	33	394	1	ENST00000375687.4:c.4520C>T	p.Ala1507Val	p.A1507V	ENST00000375687	NM_015338.5	1507	gCg/gTg	13/13	1	2	FACETS	0.157	0.127	0.191	0.157	0.127	0.191	SUBCLONAL	1	TRUE	1	0.817661888457325	2		395	514	SUCCESS
AR	367	MSKCC	GRCh37	X	66931504	66931504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1340026226	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	270	256	1	ENST00000374690.3:c.2146G>A	p.Val716Met	p.V716M	ENST00000374690	NM_000044.3	716	Gtg/Atg	4/8	1	1	FACETS	0.955	0.914	0.994	0.955	0.914	0.994	CLONAL	1	TRUE	0	0.817661888457325	1		257	409	SUCCESS
AR	367	MSKCC	GRCh37	X	66943552	66943552	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137852578	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	386	304	0	ENST00000374690.3:c.2632A>G	p.Thr878Ala	p.T878A	ENST00000374690	NM_000044.3	878	Act/Gct	8/8	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.817661888457325	1		304	458	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	266	299	7	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	0.157074620155961	4	FACETS	0.9	0.85	0.951	0.9	0.85	0.951	INDETERMINATE	2	TRUE	2	0.817661888457325	4		306	657	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	163	361	1	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	1	2	FACETS	0.838	0.775	0.901	0.838	0.775	0.901	CLONAL	1	TRUE	1	0.817661888457325	2		362	476	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030692	48030692	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs267608092	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	24	391	1	ENST00000234420.5:c.3312del	p.Phe1104LeufsTer11	p.F1104Lfs*11	ENST00000234420	NM_000179.2	1102	acT/ac	5/10	0.817661888457325	1	FACETS	0.097	0.076	0.122	0.097	0.076	0.122	SUBCLONAL	1	TRUE	0	0.817661888457325	1		392	358	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261555	142261555	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	165	368	0	ENST00000350721.4:c.3402del	p.Phe1134LeufsTer6	p.F1134Lfs*6	ENST00000350721	NM_001184.3	1134	ttT/tt	17/47	1	2	FACETS	0.668	0.616	0.722	0.668	0.616	0.722	SUBCLONAL	1	TRUE	1	0.817661888457325	2		368	604	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	303	623	6	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	0.131141918856641	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.817661888457325	0		629	865	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	85	139	0	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.66	0.589	0.734	0.66	0.589	0.734	SUBCLONAL	1	TRUE	1	0.817661888457325	2		139	315	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505379	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	240	438	0	ENST00000428830.2:c.675_676del	p.Lys225AsnfsTer19	p.K225Nfs*19	ENST00000428830	NM_001114121.2	223	gAA/g	7/14	1	2	FACETS	0.894	0.839	0.949	0.894	0.839	0.949	CLONAL	1	TRUE	1	0.817661888457325	2		438	657	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664761	138664761	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs797044528	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	37	69	0	ENST00000330315.3:c.804del	p.Gly269AlafsTer2	p.G269Afs*2	ENST00000330315	NM_023067.3	268	ccC/cc	1/1	1	2	FACETS	0.923	0.785	1	0.923	0.785	1	CLONAL	1	TRUE	1	0.817661888457325	2		69	98	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39772564	39772564	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	127	283	0	ENST00000288319.7:c.677del	p.Gly226ValfsTer65	p.G226Vfs*65	ENST00000288319	NM_182918.3	226	gGt/gt	6/10	1	2	FACETS	0.919	0.844	0.996	0.919	0.844	0.996	CLONAL	1	TRUE	1	0.817661888457325	2		283	338	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118365074	118365075	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	215	378	0	ENST00000534358.1:c.5256dup	p.Ala1753SerfsTer32	p.A1753Sfs*32	ENST00000534358	NM_005933.3	1750	-/A	17/36	1	2	FACETS	0.958	0.898	1	0.958	0.898	1	CLONAL	1	TRUE	1	0.817661888457325	2		378	549	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444437	50444437	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	136	236	0	ENST00000331340.3:c.369del	p.Ile124SerfsTer69	p.I124Sfs*69	ENST00000331340	NM_006060.4	123	Ggg/gg	4/8	0.115286245974383	4	FACETS	0.957	0.884	1	0.957	0.884	1	INDETERMINATE	2	TRUE	2	0.817661888457325	4		236	316	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649086	37649086	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	43	431	0	ENST00000447079.4:c.2193del	p.Ile732LeufsTer21	p.I732Lfs*21	ENST00000447079	NM_015083.1	731	Ggg/gg	4/14	0.115286245974383	4	FACETS	0.265	0.221	0.314	0.133	0.11	0.157	INDETERMINATE	1	TRUE	2	0.817661888457325	4		431	721	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134252	11134252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004925-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	152	430	2	ENST00000358026.2:c.2918G>A	p.Arg973Gln	p.R973Q	ENST00000358026	NM_001128849.1	973	cGg/cAg	20/36	0.13599120766691	0	FACETS	0.438	0.401	0.476			1	INDETERMINATE	1	TRUE	0	0.477853373822154	0		432	759	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202857	16202857	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1307834195	NA	P-0004925-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	68	472	2	ENST00000375759.3:c.565C>T	p.Arg189Ter	p.R189*	ENST00000375759	NM_015001.2	189	Cga/Tga	3/15	0.27928123140214	1	FACETS	0.244	0.212	0.28	0.244	0.212	0.28	INDETERMINATE	1	TRUE	0	0.477853373822154	1		474	886	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858186	27858186	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004925-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1326	461	769	0	ENST00000359303.2:c.385C>T	p.Arg129Cys	p.R129C	ENST00000359303	NM_003535.2	129	Cgt/Tgt	1/1	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.477853373822154	2		769	1787	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443694	49443695	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004925-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	323	448	0	ENST00000301067.7:c.3676dup	p.Leu1226ProfsTer24	p.L1226Pfs*24	ENST00000301067	NM_003482.3	1226	ctc/cCtc	11/54	0.471541771431557	3	FACETS	1	0.994	1	0.748	0.707	0.791	CLONAL	1	TRUE	1	0.477853373822154	3		448	1119	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004935-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	100	245	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.27	2		245	568	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004935-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	218	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.871	0.815	0.928	1	0.995	1	CLONAL	3	TRUE	1	0.27	2		311	618	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636758	8636758	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004935-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	69	345	1	ENST00000356435.5:c.151C>A	p.Pro51Thr	p.P51T	ENST00000356435		51	Cca/Aca	2/35	0.299602131346311	2	FACETS	1	0.915	1	0.531	0.464	0.604	CLONAL	1	TRUE	0	0.27	2		346	481	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038909	12038909	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004935-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	92	473	0	ENST00000396373.4:c.1202A>G	p.Tyr401Cys	p.Y401C	ENST00000396373	NM_001987.4	401	tAc/tGc	7/8	1	2	FACETS	0.868	0.771	0.972	0.868	0.771	0.972	CLONAL	1	TRUE	1	0.27	2		473	785	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12043895	12043895	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004935-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	70	503	0	ENST00000396373.4:c.1274A>G	p.Glu425Gly	p.E425G	ENST00000396373	NM_001987.4	425	gAa/gGa	8/8	1	2	FACETS	0.524	0.456	0.599	0.524	0.456	0.599	SUBCLONAL	1	TRUE	1	0.27	2		503	989	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061644	38061645	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0004935-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	35	103	0	ENST00000250448.2:c.343_344dup	p.Met116ProfsTer10	p.M116Pfs*10	ENST00000250448	NM_004496.3	115	gcc/gcGCc	2/2	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.27	2		103	240	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0004937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	268	451	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	0.874053778620953	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.874053778620953	1		451	327	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247304	153247304	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	153	420	0	ENST00000281708.4:c.1498C>A	p.His500Asn	p.H500N	ENST00000281708	NM_033632.3	500	Cat/Aat	10/12	0.874053778620953	1	FACETS	0.696	0.651	0.742	0.696	0.651	0.742	SUBCLONAL	1	TRUE	0	0.874053778620953	1		420	283	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271201	153271202	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	147	369	0	ENST00000281708.4:c.576dup	p.Tyr193IlefsTer63	p.Y193Ifs*63	ENST00000281708	NM_033632.3	192	-/A	3/12	0.874053778620953	1	FACETS	0.471	0.435	0.508	0.471	0.435	0.508	SUBCLONAL	1	TRUE	0	0.874053778620953	1		369	402	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004953-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	97	245	0				ENST00000310581	NM_198253.2	-/1132			0.494926676695711	3	FACETS	0.907	0.811	1	0.453	0.405	0.504	CLONAL	1	TRUE	1	0.524483973796206	3		245	515	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0004953-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	407	403	1	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.494215426441603	4	FACETS	1	0.991	1	0.826	0.794	0.858	CLONAL	3	TRUE	0	0.524483973796206	4		404	716	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196830	123196830	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004953-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	259	346	0	ENST00000218089.9:c.1717C>T	p.Gln573Ter	p.Q573*	ENST00000218089	NM_001042749.1	573	Cag/Tag	18/35	0.335372449595237	2	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.524483973796206	2		346	439	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260464	16260464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004953-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	160	262	0	ENST00000375759.3:c.7729G>A	p.Asp2577Asn	p.D2577N	ENST00000375759	NM_015001.2	2577	Gac/Aac	11/15	0.295212948418557	3	FACETS	0.811	0.75	0.873	0.811	0.75	0.873	INDETERMINATE	2	TRUE	1	0.524483973796206	3		262	475	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106771	27106771	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004953-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	295	444	0	ENST00000324856.7:c.6382C>T	p.Gln2128Ter	p.Q2128*	ENST00000324856	NM_006015.4	2128	Cag/Tag	20/20	0.295212948418557	3	FACETS	0.869	0.821	0.917	0.869	0.821	0.917	INDETERMINATE	2	TRUE	1	0.524483973796206	3		444	817	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812202	43812202	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004953-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	365	627	1	ENST00000372470.3:c.1067C>T	p.Ser356Leu	p.S356L	ENST00000372470	NM_005373.2	356	tCa/tTa	7/12	0.295212948418557	3	FACETS	1	0.994	1	0.703	0.666	0.74	INDETERMINATE	1	TRUE	1	0.524483973796206	3		628	1250	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142927	30142927	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs978946990	NA	P-0004953-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	268	436	0	ENST00000389048.3:c.599G>A	p.Arg200Lys	p.R200K	ENST00000389048	NM_004304.4	200	aGa/aAa	1/29	0.271492402491521	5	FACETS	0.982	0.922	1	0.654	0.615	0.695	INDETERMINATE	2	TRUE	2	0.524483973796206	5		436	930	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12632451	12632451	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004953-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	405	486	1	ENST00000251849.4:c.1216C>A	p.Leu406Met	p.L406M	ENST00000251849	NM_002880.3	406	Ctg/Atg	12/17	0.335372449595237	4	FACETS	1	0.976	1			1	CLONAL	2	TRUE	NA	0.524483973796206	4		487	1136	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436305	52436305	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	novel	NA	P-0004953-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	253	527	0	ENST00000460680.1:c.2189G>C	p.Ter730SerextTer205	p.*730Sext*205	ENST00000460680	NM_004656.3	730	tGa/tCa	17/17	0.494926676695711	3	FACETS	0.752	0.706	0.799	0.752	0.706	0.799	SUBCLONAL	2	TRUE	1	0.524483973796206	3		527	810	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595810	52595810	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004953-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	168	502	0	ENST00000394830.3:c.4105G>C	p.Glu1369Gln	p.E1369Q	ENST00000394830	NM_018313.4	1369	Gag/Cag	26/30	0.494926676695711	3	FACETS	0.79	0.726	0.858	0.395	0.363	0.429	SUBCLONAL	1	TRUE	1	0.524483973796206	3		502	1023	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524459	187524459	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004953-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	249	422	0	ENST00000441802.2:c.11221C>G	p.Leu3741Val	p.L3741V	ENST00000441802	NM_005245.3	3741	Ctg/Gtg	19/27	0.494926676695711	3	FACETS	0.811	0.762	0.861	0.811	0.762	0.861	CLONAL	2	TRUE	1	0.524483973796206	3		422	739	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169228	32169228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1407786575	NA	P-0004953-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	311	448	1	ENST00000375023.3:c.3805G>A	p.Glu1269Lys	p.E1269K	ENST00000375023	NM_004557.3	1269	Gag/Aag	22/30	0.295212948418557	3	FACETS	1	0.994	1	0.707	0.668	0.748	INDETERMINATE	1	TRUE	1	0.524483973796206	3		449	1058	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152373155	152373155	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004953-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1428	212	886	1	ENST00000359321.1:c.10G>A	p.Ala4Thr	p.A4T	ENST00000359321	NM_005431.1	4	Gcc/Acc	1/3	0.174733025337054	5	FACETS	0.881	0.815	0.949			1	INDETERMINATE	1	TRUE	NA	0.524483973796206	5		887	1640	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274882	38274882	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004953-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	179	568	0	ENST00000425967.3:c.1698G>T	p.Met566Ile	p.M566I	ENST00000425967	NM_001174067.1	566	atG/atT	13/19	0.494926676695711	3	FACETS	0.803	0.739	0.869	0.401	0.369	0.435	CLONAL	1	TRUE	1	0.524483973796206	3		568	1073	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710681	114710681	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004953-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	499	821	0	ENST00000543371.1:c.166C>T	p.Gln56Ter	p.Q56*	ENST00000543371	NM_001198531.1	56	Caa/Taa	1/14	0.241676422349992	5	FACETS	1	0.987	1	0.72	0.688	0.752	INDETERMINATE	2	TRUE	2	0.524483973796206	5		821	1574	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121454	108121454	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0004953-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	84	160	0	ENST00000278616.4:c.1262C>G	p.Ser421Ter	p.S421*	ENST00000278616	NM_000051.3	421	tCa/tGa	10/63	0.524538488220672	3	FACETS	1	0.979	1	0.732	0.655	0.813	CLONAL	1	TRUE	1	0.524483973796206	3		160	276	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217308	7217308	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0004953-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	695	770	0	ENST00000380728.2:c.398-1G>C		p.X133_splice	ENST00000380728		133			0.446056109141259	3	FACETS	0.852	0.825	0.878	0.852	0.825	0.878	CLONAL	3	TRUE	0	0.524483973796206	3		770	1309	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678010	58678010	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004953-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	313	389	0	ENST00000305921.3:c.235C>G	p.Leu79Val	p.L79V	ENST00000305921	NM_003620.3	79	Ctc/Gtc	1/6	0.524538488220672	3	FACETS	0.965	0.915	1	0.965	0.915	1	CLONAL	2	TRUE	1	0.524483973796206	3		389	781	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591865	48591865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004953-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	41	626	1	ENST00000342988.3:c.1028C>T	p.Ser343Leu	p.S343L	ENST00000342988	NM_005359.5	343	tCa/tTa	9/12	0.307964065890635	3	FACETS	0.245	0.203	0.291	0.082	0.067	0.097	INDETERMINATE	1	TRUE	0	0.524483973796206	3		627	807	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222997	5222997	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004953-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	205	367	0	ENST00000357368.4:c.2806G>C	p.Glu936Gln	p.E936Q	ENST00000357368	NM_002850.3	936	Gag/Cag	18/38	0.295212948418557	3	FACETS	1	0.991	1	0.73	0.68	0.781	INDETERMINATE	1	TRUE	1	0.524483973796206	3		367	676	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257367	19257367	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004953-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	175	490	0	ENST00000162023.5:c.766C>G	p.Pro256Ala	p.P256A	ENST00000162023		256	Cca/Gca	11/13	0.295212948418557	3	FACETS	1	0.938	1	0.51	0.47	0.551	INDETERMINATE	1	TRUE	1	0.524483973796206	3		490	826	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26911747	26911747	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004953-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	144	534	0	ENST00000381527.3:c.174del	p.Ile59SerfsTer9	p.I59Sfs*9	ENST00000381527	NM_001260.1	58	Ggg/gg	2/13	0.295212948418557	3	FACETS	1	0.942	1	0.519	0.474	0.565	INDETERMINATE	1	TRUE	1	0.524483973796206	3		534	668	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651946	36651947	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004953-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	186	420	0	ENST00000244741.5:c.71dup	p.Val25SerfsTer11	p.V25Sfs*11	ENST00000244741	NM_000389.4	23	ggc/ggCc	2/3	0.295212948418557	3	FACETS	1	0.982	1	0.593	0.549	0.639	INDETERMINATE	1	TRUE	1	0.524483973796206	3		420	755	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0004970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	53	697	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.644	0.547	0.751	0.644	0.547	0.751	SUBCLONAL	1	TRUE	1	0.178720378766732	2		697	921	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220443	1220443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202466	NA	P-0004970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	74	533	0	ENST00000326873.7:c.536C>T	p.Pro179Leu	p.P179L	ENST00000326873	NM_000455.4	179	cCg/cTg	4/10	0.178720378766732	1	FACETS	0.872	0.762	0.991	0.872	0.762	0.991	CLONAL	1	TRUE	0	0.178720378766732	1		533	865	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906436	50906436	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	203	547	1	ENST00000440232.2:c.1097C>A	p.Ala366Asp	p.A366D	ENST00000440232	NM_002691.3	366	gCc/gAc	9/27	0.178720378766732	4	FACETS	0.845	0.783	0.91	0.845	0.783	0.91	CLONAL	3	TRUE	1	0.178720378766732	4		548	1056	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044967	47044967	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	71	271	0	ENST00000377604.3:c.2293C>T	p.Arg765Ter	p.R765*	ENST00000377604	NM_001204468.1	765	Cga/Tga	20/24	1	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.178720378766732	1		271	507	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492898	56492899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0004970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	20	194	0	ENST00000407977.2:c.39_40dup	p.Pro14ArgfsTer5	p.P14Rfs*5	ENST00000407977		14	ccc/cGCcc	2/10	1	2	FACETS	0.713	0.545	0.909	0.713	0.545	0.909	CLONAL	1	TRUE	1	0.178720378766732	2		194	314	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111502	8111503	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	146	329	0	ENST00000346208.3:c.990dup	p.Asn331GlufsTer21	p.N331Efs*21	ENST00000346208		330	agg/aGgg	5/6	0.524401784364449	3	FACETS	0.946	0.865	1	0.473	0.432	0.516	CLONAL	1	TRUE	1	0.524401784364449	3		329	743	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100913	27100913	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	148	251	0	ENST00000324856.7:c.4195C>T	p.Gln1399Ter	p.Q1399*	ENST00000324856	NM_006015.4	1399	Cag/Tag	18/20	0.247060528888489	4	FACETS	0.756	0.694	0.821	0.756	0.694	0.821	INDETERMINATE	2	TRUE	2	0.524401784364449	4		251	569	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799727	72799727	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs767180976	NA	P-0004981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	222	269	0	ENST00000325599.8:c.1442A>G	p.Lys481Arg	p.K481R	ENST00000325599	NM_018130.2	481	aAa/aGa	11/11	0.247060528888489	4	FACETS	0.931	0.871	0.993	0.931	0.871	0.993	INDETERMINATE	2	TRUE	2	0.524401784364449	4		269	693	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023046	27023047	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCAT	novel	NA	P-0004981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	24	32	0	ENST00000324856.7:c.156_157insTGGCA	p.Ala53TrpfsTer50	p.A53Wfs*50	ENST00000324856	NM_006015.4	51	aag/aaGGCATg	1/20	0.247060528888489	4	FACETS	1	0.911	1	0.646	0.516	0.79	INDETERMINATE	1	TRUE	2	0.524401784364449	4		32	108	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652971	29652971	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004982-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	55	413	0	ENST00000356175.3:c.4906G>C	p.Asp1636His	p.D1636H	ENST00000356175	NM_000267.3	1636	Gac/Cac	36/57	0.562183420714266	3	FACETS	0.66	0.567	0.759	0.33	0.283	0.38	SUBCLONAL	1	TRUE	1	0.695922078581066	3		413	323	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115957	8115958	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGTGG	novel	NA	P-0004982-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	145	162	0	ENST00000346208.3:c.1303_1304insGGTGG	p.Pro435ArgfsTer42	p.P435Rfs*42	ENST00000346208		435	ccc/cGGTGGcc	6/6	0.695922078581066	3	FACETS	0.776	0.717	0.836			1	SUBCLONAL	2	TRUE	NA	0.695922078581066	3		162	362	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442077	52442077	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	338	305	0	ENST00000460680.1:c.272G>T	p.Cys91Phe	p.C91F	ENST00000460680	NM_004656.3	91	tGt/tTt	5/17	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	2	TRUE	NA	0.629477060479192	2		305	527	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101558	27101558	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	380	322	0	ENST00000324856.7:c.4840C>T	p.Gln1614Ter	p.Q1614*	ENST00000324856	NM_006015.4	1614	Cag/Tag	18/20	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.629477060479192	2		322	577	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	464323	464323	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1400171944	NA	P-0005000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	69	375	0	ENST00000399788.2:c.870+1G>A		p.X290_splice	ENST00000399788	NM_001042603.1	290			0.629477060479192	5	FACETS	0.496	0.431	0.567	0.165	0.143	0.189	SUBCLONAL	1	TRUE	2	0.629477060479192	5		375	859	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098561	11098562	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCTCGAC	novel	NA	P-0005000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	117	302	0	ENST00000358026.2:c.1083_1089dup	p.Val364ArgfsTer25	p.V364Rfs*25	ENST00000358026	NM_001128849.1	360	ggc/ggCCTCGACc	6/36	0.600138669923035	4	FACETS	0.825	0.745	0.91	0.413	0.372	0.455	CLONAL	1	TRUE	2	0.629477060479192	4		302	734	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	77	245	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.769	0.674	0.87	0.769	0.674	0.87	SUBCLONAL	1	TRUE	1	0.275912050994285	2		245	726	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0005022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	63	365	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.209181401444662	1	FACETS	0.756	0.654	0.865	0.756	0.654	0.865	SUBCLONAL	1	TRUE	0	0.275912050994285	1		365	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0005022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	181	517	2	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.242290531474489	1	FACETS	0.912	0.839	0.988	0.912	0.839	0.988	CLONAL	1	TRUE	0	0.275912050994285	1		519	1240	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260605	10260605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1310	199	599	0	ENST00000340748.4:c.2257G>A	p.Asp753Asn	p.D753N	ENST00000340748		753	Gat/Aat	24/40	1	2	FACETS	0.956	0.883	1	0.956	0.883	1	CLONAL	1	TRUE	1	0.275912050994285	2		599	1509	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206593	108206593	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587782049	NA	P-0005022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	78	483	0	ENST00000278616.4:c.8173G>C	p.Asp2725His	p.D2725H	ENST00000278616	NM_000051.3	2725	Gat/Cat	56/63	0.209181401444662	1	FACETS	0.993	0.875	1	0.993	0.875	1	CLONAL	1	TRUE	0	0.275912050994285	1		483	491	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663770	241663770	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1218102979	NA	P-0005022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	35	275	0	ENST00000366560.3:c.1357C>G	p.Leu453Val	p.L453V	ENST00000366560	NM_000143.3	453	Cta/Gta	9/10	0.154914291371519	3	FACETS	0.802	0.658	0.963	0.401	0.329	0.482	INDETERMINATE	1	TRUE	1	0.275912050994285	3		275	360	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268137	153268137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752114536	NA	P-0005022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	55	525	2	ENST00000281708.4:c.671G>A	p.Arg224Gln	p.R224Q	ENST00000281708	NM_033632.3	224	cGa/cAa	4/12	0.209181401444662	1	FACETS	0.636	0.544	0.737	0.636	0.544	0.737	SUBCLONAL	1	TRUE	0	0.275912050994285	1		527	540	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381550	81381550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	83	460	0	ENST00000222390.5:c.511G>A	p.Asp171Asn	p.D171N	ENST00000222390	NM_000601.4	171	Gac/Aac	5/18	0.209181401444662	1	FACETS	0.923	0.816	1	0.923	0.816	1	CLONAL	1	TRUE	0	0.275912050994285	1		460	562	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332378	70332378	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	134	498	0	ENST00000373644.4:c.283G>C	p.Glu95Gln	p.E95Q	ENST00000373644	NM_030625.2	95	Gag/Cag	2/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.275912050994285	2		498	827	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864237	57864237	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs759589302	NA	P-0005022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1407	240	697	0	ENST00000228682.2:c.1714G>C	p.Glu572Gln	p.E572Q	ENST00000228682	NM_005269.2	572	Gag/Cag	12/12	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.275912050994285	2		697	1647	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533763	41533763	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	218	509	0	ENST00000263253.7:c.1729C>T	p.Gln577Ter	p.Q577*	ENST00000263253	NM_001429.3	577	Cag/Tag	8/31	0.249853354287679	3	FACETS	1	0.991	1	0.747	0.694	0.803	CLONAL	1	TRUE	1	0.275912050994285	3		509	1203	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125094	46125095	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1251963733	NA	P-0005022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	75	306	0	ENST00000334344.6:c.282dup	p.Arg95AlafsTer16	p.R95Afs*16	ENST00000334344	NM_152641.2	94	ttg/ttGg	3/21	1	2	FACETS	0.815	0.714	0.924	0.815	0.714	0.924	CLONAL	1	TRUE	1	0.275912050994285	2		306	667	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123697	46123697	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	139	361	0	ENST00000334344.6:c.79del	p.His27ThrfsTer31	p.H27Tfs*31	ENST00000334344	NM_152641.2	26	ttC/tt	1/21	1	2	FACETS	0.953	0.866	1	0.953	0.866	1	CLONAL	1	TRUE	1	0.275912050994285	2		361	1057	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0005069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	76	227	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.16911397989457	2		227	837	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722905	49722906	+	inframe_insertion,splice_region_variant	In_Frame_Ins	INS	-	-	GGG	novel	NA	P-0005069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	43	198	7	ENST00000449682.2:c.1419_1421dup	p.Pro474dup	p.P474dup	ENST00000449682	NM_020998.3	474	cca/ccCCCa	12/18	0.159676238492796	1	FACETS	1	0.9	1	1	0.973	1	CLONAL	2	TRUE	0	0.16911397989457	1		205	214	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575533	64575533	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	73	822	0	ENST00000312049.6:c.484G>T	p.Val162Phe	p.V162F	ENST00000312049	NM_130799.2	162	Gtt/Ttt	3/10	1	2	FACETS	0.968	0.845	1	0.968	0.845	1	CLONAL	1	TRUE	1	0.16911397989457	2		822	892	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412047	+	splice_donor_variant,intron_variant	Splice_Site	DEL	GTAT	GTAT	AG	novel	NA	P-0005069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	142	476	0	ENST00000397752.3:c.3028+1_3028+4delinsAG		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.16911397989457	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.16911397989457	2		476	709	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165212	47165213	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005088-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	116	519	1	ENST00000409792.3:c.913dup	p.Thr305AsnfsTer4	p.T305Nfs*4	ENST00000409792	NM_014159.6	305	aca/aAca	3/21	0.178082245077224	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	0	0.178082245077224	1		520	988	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443880	52443880	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs916069743	NA	P-0005088-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	64	547	0	ENST00000460680.1:c.15G>A	p.Trp5Ter	p.W5*	ENST00000460680	NM_004656.3	5	tgG/tgA	1/17	0.178082245077224	1	FACETS	0.93	0.805	1	0.93	0.805	1	CLONAL	1	FALSE	0	0.178082245077224	1		547	704	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928870	44928870	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005088-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	67	506	0	ENST00000377967.4:c.1971del	p.Glu657AspfsTer34	p.E657Dfs*34	ENST00000377967	NM_021140.2	657	gAa/ga	17/29	1	2	FACETS	0.643	0.556	0.737	0.643	0.556	0.737	SUBCLONAL	1	FALSE	1	0.178082245077224	2		506	1171	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803350	1803350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	95	389	0	ENST00000260795.2:c.619C>T	p.Arg207Trp	p.R207W	ENST00000260795		207	Cgg/Tgg	5/17	NA	2	FACETS	0.588	0.523	0.658			1	INDETERMINATE	1	TRUE	NA	0.35	2		389	923	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199778	138199778	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	149	354	0	ENST00000237289.4:c.1196A>G	p.Asn399Ser	p.N399S	ENST00000237289	NM_001270507.1	399	aAc/aGc	7/9	1	2	FACETS	0.827	0.754	0.903	0.827	0.754	0.903	CLONAL	1	TRUE	1	0.35	2		354	1030	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845769	151845769	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	52	416	0	ENST00000262189.6:c.13243G>A	p.Gly4415Arg	p.G4415R	ENST00000262189	NM_170606.2	4415	Gga/Aga	52/59	1	2	FACETS	0.456	0.388	0.532	0.456	0.388	0.532	SUBCLONAL	1	TRUE	1	0.35	2		416	651	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715939	52715939	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	166	313	1	ENST00000322088.6:c.504G>T	p.Gln168His	p.Q168H	ENST00000322088	NM_014225.5	168	caG/caT	5/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.35	2		314	894	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937648	44937648	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	103	149	0	ENST00000377967.4:c.2836G>T	p.Glu946Ter	p.E946*	ENST00000377967	NM_021140.2	946	Gaa/Taa	19/29	0.3	2	FACETS	1	0.93	1			1	CLONAL	2	TRUE	NA	0.35	2		149	286	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732740	204732741	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	81	341	0	ENST00000302823.3:c.81dup	p.Leu28SerfsTer32	p.L28Sfs*32	ENST00000302823	NM_005214.4	25	-/T	1/4	1	2	FACETS	0.933	0.825	1	0.933	0.825	1	CLONAL	1	TRUE	1	0.35	2		341	496	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484265	57484361	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGATCAGGTGTGCAAAACCCCTCCCCACCAGAGGACTCTGAGCCCTCTTTCCAAACTACTCCAGACCTTTGCTTTAGATTGGCAATTATTACTGTTT	CGATCAGGTGTGCAAAACCCCTCCCCACCAGAGGACTCTGAGCCCTCTTTCCAAACTACTCCAGACCTTTGCTTTAGATTGGCAATTATTACTGTTT	-	novel	NA	P-0005176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	95	315	0	ENST00000371085.3:c.581_586-42del		p.X194_splice	ENST00000371085	NM_000516.4	194		7/13	0.331752985101526	5	FACETS	0.712	0.634	0.796	0.178	0.158	0.199	INDETERMINATE	1	TRUE	1	0.787134602109948	5		315	739	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579341	7579342	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATGC	novel	NA	P-0005176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	218	425	0	ENST00000269305.4:c.342_345dup	p.Ser116AlafsTer34	p.S116Afs*34	ENST00000269305	NM_001126112.2	115	-/GCAT	4/11	0.781892771522907	1	FACETS	0.991	0.943	1	0.991	0.943	1	CLONAL	1	TRUE	0	0.787134602109948	1		425	339	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0005264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	318	322	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.133993318162859	10	FACETS	0.982	0.929	1			1	CLONAL	8	TRUE	NA	0.133993318162859	10		322	928	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300206	15300206	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	48	668	0	ENST00000263388.2:c.1070G>T	p.Ser357Ile	p.S357I	ENST00000263388	NM_000435.2	357	aGc/aTc	7/33	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.133993318162859	2		668	626	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006890	47006891	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	60	295	0	ENST00000377604.3:c.13dup	p.Arg5LysfsTer7	p.R5Kfs*7	ENST00000377604	NM_001204468.1	4	gaa/gAaa	2/24	1	1	FACETS	0.901	0.782	1	1	0.983	1	CLONAL	3	TRUE	0	0.133993318162859	1		295	309	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0005281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	144	242	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.81	2		242	346	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0005281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	325	576	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.81	2		576	724	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413072	139413072	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	97	455	0	ENST00000277541.6:c.1070T>C	p.Phe357Ser	p.F357S	ENST00000277541	NM_017617.3	357	tTc/tCc	6/34	0.0920657824684421	3	FACETS	0.327	0.291	0.366	0.164	0.145	0.183	INDETERMINATE	1	TRUE	1	0.81	3		455	1028	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791292	42791292	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	267	331	0	ENST00000575354.2:c.352G>T	p.Glu118Ter	p.E118*	ENST00000575354	NM_015125.3	118	Gaa/Taa	3/20	0.844753605979355	1	FACETS	0.978	0.936	1	0.978	0.936	1	CLONAL	1	TRUE	0	0.81	1		331	401	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78425867	78425868	+	splice_donor_variant	Splice_Site	INS	-	-	C	novel	NA	P-0005281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	195	276	0	ENST00000370768.2:c.1576+1dup		p.X526_splice	ENST00000370768	NM_003902.3	526			0.844753605979355	1	FACETS	0.988	0.939	1	0.988	0.939	1	CLONAL	1	TRUE	0	0.81	1		276	290	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005284-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	132	245	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.991	0.915	1	0.991	0.915	1	CLONAL	1	FALSE	1	0.915838248422315	2		245	291	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0005284-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	386	198	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.994	0.975	1	1	0.998	1	CLONAL	2	FALSE	1	0.915838248422315	2		198	424	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412884	49412884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005284-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	371	410	0	ENST00000418115.1:c.139G>A	p.Glu47Lys	p.E47K	ENST00000418115	NM_001664.2	47	Gag/Aag	2/5	1	2	FACETS	0.95	0.906	0.994	0.95	0.906	0.994	CLONAL	1	FALSE	1	0.915838248422315	2		410	853	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652070	36652071	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGG	novel	NA	P-0005284-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	324	290	0	ENST00000244741.5:c.193_195dup	p.Trp65dup	p.W65dup	ENST00000244741	NM_000389.4	65	-/TGG	2/3	0.46394958717938	1	FACETS	0.672	0.642	0.701	0.672	0.642	0.701	INDETERMINATE	1	FALSE	0	0.915838248422315	1		290	571	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993676	90993676	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	325	210	0	ENST00000265433.3:c.247del	p.Met83CysfsTer9	p.M83Cfs*9	ENST00000265433	NM_002485.4	83	Atg/tg	3/16	0.759429745332542	1	FACETS	0.98	0.938	1	0.98	0.938	1	CLONAL	1	TRUE	0	0.759429745332542	1		210	542	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	761	485	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.73289312263876	2	FACETS	0.964	0.941	0.985	0.964	0.941	0.985	CLONAL	2	TRUE	0	0.759429745332542	2		485	1040	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	622	586	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.759429745332542	2	FACETS	1	0.993	1	0.561	0.54	0.581	CLONAL	1	TRUE	0	0.759429745332542	2		586	1461	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	286	286	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.759429745332542	1	FACETS	0.955	0.912	0.998	0.955	0.912	0.998	CLONAL	1	TRUE	0	0.759429745332542	1		286	489	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	547	246	0	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	0.155735819722518	4	FACETS	0.914	0.878	0.951	0.914	0.878	0.951	INDETERMINATE	2	TRUE	2	0.759429745332542	4		246	1386	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913837	32913837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359507	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	601	546	4	ENST00000380152.3:c.5351del	p.Asn1784ThrfsTer7	p.N1784Tfs*7	ENST00000380152		1782	cAa/ca	11/27	1	2	FACETS	0.931	0.895	0.968	0.931	0.895	0.968	CLONAL	1	TRUE	1	0.759429745332542	2		550	1700	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	263	242	2	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	0.759429745332542	1	FACETS	0.912	0.867	0.956	0.912	0.867	0.956	CLONAL	1	TRUE	0	0.759429745332542	1		244	471	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	122	284	0	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	NA	2	FACETS	0.562	0.509	0.617			1	INDETERMINATE	1	TRUE	NA	0.759429745332542	2		284	572	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321245	65321245	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771960711	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	65	390	0	ENST00000342505.4:c.1595G>A	p.Arg532His	p.R532H	ENST00000342505	NM_002227.2	532	cGc/cAc	11/25	NA	2	FACETS	0.229	0.198	0.263			1	INDETERMINATE	1	TRUE	NA	0.759429745332542	2		390	746	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	626	528	3	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	0.16959165192379	3	FACETS	0.77	0.742	0.798	0.77	0.742	0.798	INDETERMINATE	2	TRUE	1	0.759429745332542	3		531	1477	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	240	251	8	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	0.465243077238632	3	FACETS	0.857	0.8	0.915			1	CLONAL	1	TRUE	NA	0.759429745332542	3		259	1018	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661664	227661664	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs761880048	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	156	170	7	ENST00000305123.5:c.1791del	p.His598ThrfsTer38	p.H598Tfs*38	ENST00000305123	NM_005544.2	597	ggG/gg	1/2	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.759429745332542	2		177	365	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246014	41246014	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41286294	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	40	252	1	ENST00000357654.3:c.1534C>T	p.Leu512Phe	p.L512F	ENST00000357654	NM_007294.3	512	Ctt/Ttt	10/23	0.759429745332542	2	FACETS	0.132	0.109	0.157	0.066	0.054	0.079	SUBCLONAL	1	TRUE	0	0.759429745332542	2		253	800	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46733145	46733145	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	270	321	0	ENST00000371975.4:c.906G>C	p.Lys302Asn	p.K302N	ENST00000371975	NM_003579.3	302	aaG/aaC	9/18	0.247984755972547	3	FACETS	0.97	0.911	1			1	INDETERMINATE	1	TRUE	NA	0.759429745332542	3		321	1011	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226551659	226551659	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	88	274	0	ENST00000366794.5:c.2771T>C	p.Val924Ala	p.V924A	ENST00000366794	NM_001618.3	924	gTt/gCt	20/23	1	2	FACETS	0.244	0.215	0.275	0.244	0.215	0.275	SUBCLONAL	1	TRUE	1	0.759429745332542	2		274	950	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082327	16082327	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	267	289	0	ENST00000281043.3:c.141G>T	p.Glu47Asp	p.E47D	ENST00000281043	NM_005378.4	47	gaG/gaT	2/3	0.550673847565799	1	FACETS	0.645	0.609	0.682	0.645	0.609	0.682	SUBCLONAL	1	TRUE	0	0.759429745332542	1		289	676	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965386	25965386	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	64	209	0	ENST00000435504.4:c.3820G>A	p.Ala1274Thr	p.A1274T	ENST00000435504		1274	Gct/Act	13/13	NA	2	FACETS	0.242	0.209	0.278			1	INDETERMINATE	1	TRUE	NA	0.759429745332542	2		209	696	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52677343	52677343	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	348	210	0	ENST00000394830.3:c.916G>A	p.Ala306Thr	p.A306T	ENST00000394830	NM_018313.4	306	Gct/Act	10/30	0.737124205415208	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.759429745332542	1		210	509	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200663	128200663	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	179	221	0	ENST00000341105.2:c.1142A>T	p.Asn381Ile	p.N381I	ENST00000341105	NM_032638.4	381	aAt/aTt	5/6	NA	2	FACETS	0.87	0.807	0.934			1	INDETERMINATE	1	TRUE	NA	0.759429745332542	2		221	542	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217249	66217249	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	39	262	0	ENST00000273854.3:c.2366A>G	p.Lys789Arg	p.K789R	ENST00000273854	NM_004439.5	789	aAg/aGg	14/18	0.759429745332542	1	FACETS	0.173	0.143	0.206	0.173	0.143	0.206	SUBCLONAL	1	TRUE	0	0.759429745332542	1		262	368	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157392	106157392	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	47	212	0	ENST00000380013.4:c.2293A>C	p.Ser765Arg	p.S765R	ENST00000380013	NM_001127208.2	765	Agc/Cgc	3/11	0.759429745332542	1	FACETS	0.161	0.136	0.189	0.161	0.136	0.189	SUBCLONAL	1	TRUE	0	0.759429745332542	1		212	476	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166792	32166792	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	262	207	0	ENST00000375023.3:c.4446G>A	p.Trp1482Ter	p.W1482*	ENST00000375023	NM_004557.3	1482	tgG/tgA	24/30	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.759429745332542	2		207	610	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120569	94120569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	424	472	0	ENST00000369303.4:c.482G>A	p.Gly161Asp	p.G161D	ENST00000369303	NM_004440.3	161	gGt/gAt	3/17	0.288639634093333	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.759429745332542	0		472	1064	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547370	106547370	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	193	195	0	ENST00000369096.4:c.607G>T	p.Asp203Tyr	p.D203Y	ENST00000369096	NM_001198.3	203	Gac/Tac	4/7	NA	2	FACETS	0.684	0.635	0.735			1	INDETERMINATE	1	TRUE	NA	0.759429745332542	2		195	743	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041071	112041071	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs765972374	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	267	451	0	ENST00000368678.4:c.184A>G	p.Thr62Ala	p.T62A	ENST00000368678		62	Acc/Gcc	3/13	NA	2	FACETS	0.531	0.497	0.566			1	INDETERMINATE	1	TRUE	NA	0.759429745332542	2		451	1324	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111553	8111553	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	260	241	0	ENST00000346208.3:c.1039C>A	p.Leu347Ile	p.L347I	ENST00000346208		347	Ctt/Att	5/6	NA	2	FACETS	1	0.942	1			1	INDETERMINATE	1	TRUE	NA	0.759429745332542	2		241	685	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588796	69588796	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	194	307	1	ENST00000168712.1:c.440G>A	p.Gly147Asp	p.G147D	ENST00000168712	NM_002007.2	147	gGc/gAc	2/3	0.249157382356983	1	FACETS	0.457	0.424	0.491	0.457	0.424	0.491	INDETERMINATE	1	TRUE	0	0.759429745332542	1		308	693	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	360046	360046	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	53	307	0	ENST00000262320.3:c.1043T>C	p.Ile348Thr	p.I348T	ENST00000262320	NM_003502.3	348	aTc/aCc	4/11	NA	2	FACETS	0.148	0.126	0.173			1	INDETERMINATE	1	TRUE	NA	0.759429745332542	2		307	940	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15967385	15967385	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	329	195	2	ENST00000268712.3:c.5218C>A	p.Pro1740Thr	p.P1740T	ENST00000268712	NM_006311.3	1740	Cca/Aca	35/46	0.73289312263876	2	FACETS	1	0.994	1	0.642	0.612	0.672	CLONAL	1	TRUE	0	0.759429745332542	2		197	675	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215921	41215921	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507243	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	273	297	1	ENST00000357654.3:c.5122G>A	p.Ala1708Thr	p.A1708T	ENST00000357654	NM_007294.3	1708	Gcg/Acg	17/23	0.759429745332542	2	FACETS	0.877	0.826	0.929	0.438	0.413	0.465	CLONAL	1	TRUE	0	0.759429745332542	2		298	820	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619233	1619233	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	370	256	0	ENST00000344749.5:c.1327G>A	p.Val443Ile	p.V443I	ENST00000344749	NM_001136139.2	443	Gtt/Att	16/19	0.759429745332542	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.759429745332542	1		256	541	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710532	40710532	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	33	187	0	ENST00000373198.4:c.4319T>C	p.Val1440Ala	p.V1440A	ENST00000373198	NM_133170.3	1440	gTg/gCg	31/32	0.618005419291451	1	FACETS	0.101	0.082	0.123	0.101	0.082	0.123	SUBCLONAL	1	TRUE	0	0.759429745332542	1		187	534	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565531	41565531	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	158	232	0	ENST00000263253.7:c.4197T>A	p.Asp1399Glu	p.D1399E	ENST00000263253	NM_001429.3	1399	gaT/gaA	26/31	0.155735819722518	4	FACETS	0.723	0.662	0.788	0.362	0.331	0.394	INDETERMINATE	1	TRUE	2	0.759429745332542	4		232	1012	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222418	53222418	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	75	128	0	ENST00000375401.3:c.4414C>A	p.Pro1472Thr	p.P1472T	ENST00000375401	NM_004187.3	1472	Cca/Aca	26/26	1	1	FACETS	0.35	0.309	0.394	0.35	0.309	0.394	SUBCLONAL	1	TRUE	0	0.759429745332542	1		128	350	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613345	100613345	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	223	167	0	ENST00000308731.7:c.1055del	p.Phe352SerfsTer51	p.F352Sfs*51	ENST00000308731	NM_000061.2	352	tTc/tc	12/19	0.247984755972547	2	FACETS	0.831	0.777	0.886			1	INDETERMINATE	1	TRUE	NA	0.759429745332542	2		167	707	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053347	37053348	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs63751653	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	320	185	0	ENST00000231790.2:c.588dup	p.Gln197ThrfsTer7	p.Q197Tfs*7	ENST00000231790	NM_000249.3	194	-/A	7/19	0.737124205415208	1	FACETS	0.949	0.908	0.989	0.949	0.908	0.989	CLONAL	1	TRUE	0	0.759429745332542	1		185	551	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400934	72400934	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	353	520	3	ENST00000357731.5:c.237del	p.Phe79LeufsTer18	p.F79Lfs*18	ENST00000357731	NM_173808.2	79	ttT/tt	2/7	0.759429745332542	1	FACETS	0.595	0.565	0.626	0.595	0.565	0.626	SUBCLONAL	1	TRUE	0	0.759429745332542	1		523	969	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680292	30680293	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	120	296	0	ENST00000376406.3:c.1426_1427del	p.Lys476AspfsTer2	p.K476Dfs*2	ENST00000376406	NM_014641.2	476	AAg/g	5/15	0.247984755972547	3	FACETS	0.363	0.327	0.402			1	INDETERMINATE	1	TRUE	NA	0.759429745332542	3		296	1201	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974696	21974718	+	protein_altering_variant	In_Frame_Del	DEL	TAACTATTCGGTGCGTTGGGCAG	TAACTATTCGGTGCGTTGGGCAG	CGCAC	novel	NA	P-0005312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	153	208	0	ENST00000304494.5:c.109_131delinsGTGCG	p.Leu37_Tyr44delinsValArg	p.L37_Y44delinsVR	ENST00000304494	NM_000077.4	37	CTGCCCAACGCACCGAATAGTTAc/GTGCGc	1/3	0.752761746890744	1	FACETS	0.814	0.759	0.869	0.814	0.759	0.869	CLONAL	1	TRUE	0	0.759429745332542	1		208	307	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	47	245	0				ENST00000310581	NM_198253.2	-/1132			0.271420817206784	0	FACETS	1	0.893	1			1	CLONAL	2	TRUE	0	0.271420817206784	0		245	122	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0005346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	69	198	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.952	1	1	0.984	1	CLONAL	2	TRUE	1	0.271420817206784	2		198	221	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492608	56492608	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	170	333	0	ENST00000267101.3:c.2758G>C	p.Val920Leu	p.V920L	ENST00000267101	NM_001982.3	920	Gta/Cta	23/28	0.14553038950244	4	FACETS	1	0.956	1	1	0.991	1	INDETERMINATE	3	TRUE	2	0.271420817206784	4		333	509	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005408	150005408	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	147	419	0	ENST00000253339.5:c.817C>G	p.Gln273Glu	p.Q273E	ENST00000253339		273	Caa/Gaa	3/7	0.271420817206784	3	FACETS	0.976	0.894	1			1	CLONAL	2	TRUE	NA	0.271420817206784	3		419	630	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099397	27099397	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	143	347	0	ENST00000324856.7:c.3634C>G	p.Gln1212Glu	p.Q1212E	ENST00000324856	NM_006015.4	1212	Cag/Gag	14/20	0.14553038950244	4	FACETS	0.872	0.8	0.947	1	0.984	1	INDETERMINATE	3	TRUE	2	0.271420817206784	4		347	512	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430359	78430359	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0005346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	177	337	0	ENST00000370768.2:c.809C>G	p.Ser270Ter	p.S270*	ENST00000370768	NM_003902.3	270	tCa/tGa	10/20	0.14553038950244	4	FACETS	0.956	0.886	1	1	0.989	1	INDETERMINATE	3	TRUE	2	0.271420817206784	4		337	578	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715624	30715624	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	126	336	0	ENST00000295754.5:c.1282G>A	p.Glu428Lys	p.E428K	ENST00000295754	NM_003242.5	428	Gaa/Aaa	5/7	0.14553038950244	4	FACETS	1	0.969	1	1	0.969	1	INDETERMINATE	2	TRUE	2	0.271420817206784	4		336	515	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275717	41275717	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	189	322	0	ENST00000349496.5:c.1612C>A	p.Gln538Lys	p.Q538K	ENST00000349496	NM_001904.3	538	Cag/Aag	10/15	0.14553038950244	4	FACETS	0.849	0.788	0.913	1	0.986	1	INDETERMINATE	3	TRUE	2	0.271420817206784	4		322	695	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670652	134670652	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	102	395	0	ENST00000398015.3:c.563C>A	p.Ser188Tyr	p.S188Y	ENST00000398015	NM_004441.4	188	tCt/tAt	3/16	0.271420817206784	1	FACETS	0.839	0.757	0.925	1	0.986	1	CLONAL	2	TRUE	0	0.271420817206784	1		395	387	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526197	189526197	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	230	351	0	ENST00000264731.3:c.461C>G	p.Ser154Cys	p.S154C	ENST00000264731	NM_003722.4	154	tCc/tGc	4/14	0.271420817206784	5	FACETS	1	0.982	1			1	CLONAL	3	TRUE	NA	0.271420817206784	5		351	707	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807335	1807335	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1448843898	NA	P-0005346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	207	423	0	ENST00000260795.2:c.1584G>A	p.Met528Ile	p.M528I	ENST00000260795		528	atG/atA	11/17	1	2	FACETS	0.88	0.822	0.938	1	0.995	1	CLONAL	3	TRUE	1	0.271420817206784	2		423	578	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535364	187535364	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	129	290	0	ENST00000441802.2:c.9210C>G	p.Phe3070Leu	p.F3070L	ENST00000441802	NM_005245.3	3070	ttC/ttG	12/27	0.186162566448159	4	FACETS	0.882	0.805	0.961	1	0.983	1	CLONAL	3	TRUE	2	0.271420817206784	4		290	457	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226031	226031	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	28	56	0	ENST00000264932.6:c.490G>C	p.Glu164Gln	p.E164Q	ENST00000264932	NM_004168.2	164	Gaa/Caa	5/15	0.21660253459392	4	FACETS	1	0.916	1			1	CLONAL	2	TRUE	NA	0.271420817206784	4		56	106	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180536	56180536	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	146	315	0	ENST00000399503.3:c.3865G>C	p.Glu1289Gln	p.E1289Q	ENST00000399503	NM_005921.1	1289	Gaa/Caa	16/20	0.245438766639157	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.271420817206784	4		315	548	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376078	8376078	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	85	232	0	ENST00000356435.5:c.4519G>C	p.Glu1507Gln	p.E1507Q	ENST00000356435		1507	Gag/Cag	28/35	0.271420817206784	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	2	TRUE	0	0.271420817206784	2		232	303	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123260391	123260391	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	155	351	0	ENST00000358487.5:c.1510G>C	p.Asp504His	p.D504H	ENST00000358487	NM_000141.4	504	Gac/Cac	11/18	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	2	TRUE	NA	0.271420817206784	2		351	526	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121609	108121609	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	201	379	0	ENST00000278616.4:c.1417G>C	p.Glu473Gln	p.E473Q	ENST00000278616	NM_000051.3	473	Gaa/Caa	10/63	0.14553038950244	4	FACETS	1	0.985	1	1	0.985	1	INDETERMINATE	2	TRUE	2	0.271420817206784	4		379	770	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431006	49431006	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	138	371	1	ENST00000301067.7:c.10133C>A	p.Ser3378Ter	p.S3378*	ENST00000301067	NM_003482.3	3378	tCa/tAa	34/54	0.14553038950244	4	FACETS	0.966	0.887	1	1	0.987	1	INDETERMINATE	3	TRUE	2	0.271420817206784	4		372	446	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562371	95562371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167159136	NA	P-0005346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	140	265	0	ENST00000393063.1:c.4886C>T	p.Ser1629Leu	p.S1629L	ENST00000393063	NM_030621.3	1629	tCa/tTa	24/28	0.14553038950244	4	FACETS	0.932	0.855	1	1	0.986	1	INDETERMINATE	3	TRUE	2	0.271420817206784	4		265	469	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169561	11169561	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1472952300	NA	P-0005346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	76	296	0	ENST00000358026.2:c.4727C>T	p.Ser1576Phe	p.S1576F	ENST00000358026	NM_001128849.1	1576	tCc/tTc	33/36	1	2	FACETS	1	0.899	1	1	0.984	1	CLONAL	2	TRUE	1	0.271420817206784	2		296	276	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44894174	44894174	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0005346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	228	447	0	ENST00000377967.4:c.565-2A>C		p.X189_splice	ENST00000377967	NM_021140.2	189			0.271420817206784	5	FACETS	1	0.97	1			1	CLONAL	3	TRUE	NA	0.271420817206784	5		447	741	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038519	47038519	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	119	391	0	ENST00000377604.3:c.681C>G	p.Phe227Leu	p.F227L	ENST00000377604	NM_001204468.1	227	ttC/ttG	8/24	0.174716118828415	3	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	1	0.271420817206784	3		391	472	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039429	47039429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	120	358	0	ENST00000377604.3:c.1052C>T	p.Ser351Phe	p.S351F	ENST00000377604	NM_001204468.1	351	tCc/tTc	10/24	0.174716118828415	3	FACETS	0.843	0.768	0.921	1	0.979	1	CLONAL	3	TRUE	1	0.271420817206784	3		358	397	SUCCESS
AR	367	MSKCC	GRCh37	X	66766006	66766006	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	175	423	0	ENST00000374690.3:c.1018G>C	p.Glu340Gln	p.E340Q	ENST00000374690	NM_000044.3	340	Gaa/Caa	1/8	0.174716118828415	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.271420817206784	3		423	616	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918509	44918509	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	341	447	0	ENST00000377967.4:c.995del	p.Asn332IlefsTer27	p.N332Ifs*27	ENST00000377967	NM_021140.2	331	cAa/ca	12/29	0.271420817206784	5	FACETS	0.985	0.936	1			1	CLONAL	4	TRUE	NA	0.271420817206784	5		447	897	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179025	123179025	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	173	364	0	ENST00000218089.9:c.475del	p.Tyr159IlefsTer24	p.Y159Ifs*24	ENST00000218089	NM_001042749.1	158	gaT/ga	8/35	0.174716118828415	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.271420817206784	3		364	617	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652225	36652226	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	163	292	0	ENST00000244741.5:c.349dup	p.Cys117LeufsTer12	p.C117Lfs*12	ENST00000244741	NM_000389.4	116	tct/tcTt	2/3	0.271420817206784	7	FACETS	1	0.972	1			1	CLONAL	3	TRUE	NA	0.271420817206784	7		292	601	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651885	36651886	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	193	243	0	ENST00000244741.5:c.9dup	p.Pro4ThrfsTer32	p.P4Tfs*32	ENST00000244741	NM_000389.4	3	gaa/gAaa	2/3	0.271420817206784	7	FACETS	0.927	0.865	0.99			1	CLONAL	5	TRUE	NA	0.271420817206784	7		243	515	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0005353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	431	563	0	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			NA	2	FACETS	0.958	0.917	0.998			1	INDETERMINATE	2	TRUE	NA	0.473701174353365	2		563	950	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054923	176054923	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	137	484	0	ENST00000367669.3:c.1130C>G	p.Ser377Cys	p.S377C	ENST00000367669	NM_022457.5	377	tCt/tGt	10/20	1	2	FACETS	0.882	0.804	0.963	0.882	0.804	0.963	CLONAL	1	TRUE	1	0.473701174353365	2		484	656	SUCCESS
REL	5966	MSKCC	GRCh37	2	61144116	61144116	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	148	502	0	ENST00000295025.8:c.499C>G	p.Leu167Val	p.L167V	ENST00000295025	NM_002908.2	167	Ctt/Gtt	5/11	0.127173058844074	3	FACETS	0.891	0.814	0.972	0.297	0.271	0.324	INDETERMINATE	1	TRUE	0	0.473701174353365	3		502	867	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645683	12645683	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs397516829	NA	P-0005353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	169	513	0	ENST00000251849.4:c.786T>A	p.Asn262Lys	p.N262K	ENST00000251849	NM_002880.3	262	aaT/aaA	7/17	1	2	FACETS	0.995	0.917	1	0.995	0.917	1	CLONAL	1	TRUE	1	0.473701174353365	2		513	717	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528545	89528545	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0005353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	80	310	0	ENST00000336596.2:c.2847-2A>T		p.X949_splice	ENST00000336596	NM_005233.5	949			1	2	FACETS	0.834	0.738	0.936	0.834	0.738	0.936	CLONAL	1	TRUE	1	0.473701174353365	2		310	405	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430201	181430201	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs750091101	NA	P-0005353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	67	169	0	ENST00000325404.1:c.53C>A	p.Ser18Ter	p.S18*	ENST00000325404	NM_003106.3	18	tCg/tAg	1/1	1	2	FACETS	0.876	0.767	0.992	0.876	0.767	0.992	CLONAL	1	TRUE	1	0.473701174353365	2		169	323	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226087	226087	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	77	225	0	ENST00000264932.6:c.546G>T	p.Lys182Asn	p.K182N	ENST00000264932	NM_004168.2	182	aaG/aaT	5/15	0.473701174353365	3	FACETS	0.942	0.83	1	0.471	0.415	0.53	CLONAL	1	TRUE	1	0.473701174353365	3		225	427	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160566	56160566	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	78	332	0	ENST00000399503.3:c.840G>T	p.Gln280His	p.Q280H	ENST00000399503	NM_005921.1	280	caG/caT	4/20	0.436623003148253	2	FACETS	0.733	0.647	0.826	0.367	0.323	0.413	SUBCLONAL	1	TRUE	0	0.473701174353365	2		332	449	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910686	29910686	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	183	538	0	ENST00000376809.5:c.226A>G	p.Ile76Val	p.I76V	ENST00000376809	NM_002116.7	76	Ata/Gta	2/8	1	2	FACETS	0.946	0.874	1	0.946	0.874	1	CLONAL	1	TRUE	1	0.473701174353365	2		538	817	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180921	32180921	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	117	365	0	ENST00000375023.3:c.2429G>C	p.Cys810Ser	p.C810S	ENST00000375023	NM_004557.3	810	tGt/tCt	15/30	1	2	FACETS	0.868	0.785	0.955	0.868	0.785	0.955	CLONAL	1	TRUE	1	0.473701174353365	2		365	569	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287355	33287355	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	225	497	0	ENST00000374542.5:c.1742C>G	p.Ser581Cys	p.S581C	ENST00000374542	NM_001141970.1	581	tCt/tGt	6/8	0.189765462626628	6	FACETS	0.955	0.889	1			1	INDETERMINATE	2	TRUE	NA	0.473701174353365	6		497	969	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674207	117674207	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	160	597	0	ENST00000368508.3:c.4267G>T	p.Ala1423Ser	p.A1423S	ENST00000368508	NM_002944.2	1423	Gcc/Tcc	26/43	0.18339722254099	0	FACETS	0.509	0.468	0.552			1	INDETERMINATE	1	TRUE	0	0.473701174353365	0		597	698	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201885	152201885	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	75	333	0	ENST00000206249.3:c.739G>T	p.Glu247Ter	p.E247*	ENST00000206249	NM_000125.3	247	Gaa/Taa	3/8	1	2	FACETS	0.665	0.585	0.752	0.665	0.585	0.752	SUBCLONAL	1	TRUE	1	0.473701174353365	2		333	476	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971149	21971149	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786202575	NA	P-0005353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	157	112	0	ENST00000304494.5:c.209C>T	p.Pro70Leu	p.P70L	ENST00000304494	NM_000077.4	70	cCc/cTc	2/3	0.473701174353365	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.473701174353365	3		112	243	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482382	56482382	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	176	571	0	ENST00000267101.3:c.930G>A	p.Met310Ile	p.M310I	ENST00000267101	NM_001982.3	310	atG/atA	8/28	0.105315735114195	4	FACETS	1	0.96	1			1	INDETERMINATE	1	TRUE	NA	0.473701174353365	4		571	1024	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008323	29008323	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760170197	NA	P-0005353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	169	462	0	ENST00000282397.4:c.548G>A	p.Arg183His	p.R183H	ENST00000282397	NM_002019.4	183	cGc/cAc	5/30	0.442346469100544	2	FACETS	0.902	0.831	0.976	0.451	0.415	0.488	CLONAL	1	TRUE	0	0.473701174353365	2		462	791	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610324	81610324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	246	399	0	ENST00000298171.2:c.1922C>T	p.Ser641Leu	p.S641L	ENST00000298171	NM_000369.2	641	tCa/tTa	10/10	0.127173058844074	3	FACETS	0.828	0.776	0.88	0.552	0.517	0.587	INDETERMINATE	2	TRUE	0	0.473701174353365	3		399	776	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979979	7979979	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	93	261	1	ENST00000319144.4:c.1358C>T	p.Ala453Val	p.A453V	ENST00000319144	NM_001139.2	453	gCc/gTc	10/15	NA	2	FACETS	0.796	0.711	0.887			1	INDETERMINATE	1	TRUE	NA	0.473701174353365	2		262	493	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419903	41419903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761607732	NA	P-0005353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	221	541	2	ENST00000373198.4:c.418G>A	p.Gly140Arg	p.G140R	ENST00000373198	NM_133170.3	140	Ggg/Agg	3/32	0.320217905377486	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.473701174353365	1		543	689	SUCCESS
AR	367	MSKCC	GRCh37	X	66765700	66765700	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	348	683	0	ENST00000374690.3:c.712G>T	p.Glu238Ter	p.E238*	ENST00000374690	NM_000044.3	238	Gag/Tag	1/8	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.473701174353365	2		683	1098	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938462	76938462	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1490691498	NA	P-0005353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	97	536	0	ENST00000373344.5:c.2286G>C	p.Lys762Asn	p.K762N	ENST00000373344	NM_000489.3	762	aaG/aaC	9/35	1	2	FACETS	0.568	0.506	0.634	0.568	0.506	0.634	SUBCLONAL	1	TRUE	1	0.473701174353365	2		536	721	SUCCESS
BTK	695	MSKCC	GRCh37	X	100609618	100609618	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	736	878	0	ENST00000308731.7:c.1631G>T	p.Arg544Met	p.R544M	ENST00000308731	NM_000061.2	544	aGg/aTg	16/19	1	2	FACETS	0.903	0.873	0.933	1	0.998	1	CLONAL	2	TRUE	1	0.473701174353365	2		878	1721	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14628912	14629036	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCAAAAGGCGGGGCCGCGCCCCTGGCCGCGAGCACACACCTTCCTCCCCGTAGCGGTCGAAGATCTCGCGCTTGCGCGGGTCGCTGAGCACGTCGTAGGCCTCAGCGATCTCCTTGAACTTCTCC	TCAAAAGGCGGGGCCGCGCCCCTGGCCGCGAGCACACACCTTCCTCCCCGTAGCGGTCGAAGATCTCGCGCTTGCGCGGGTCGCTGAGCACGTCGTAGGCCTCAGCGATCTCCTTGAACTTCTCC	-	novel	NA	P-0005353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	230	372	0	ENST00000254322.2:c.126_211+39del		p.X42_splice	ENST00000254322	NM_006145.1	42		1/3	0.0554351562962192	3	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.473701174353365	3		372	824	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539111	187539125	+	inframe_deletion	In_Frame_Del	DEL	GGTCAAGTTCCTTTA	GGTCAAGTTCCTTTA	-	novel	NA	P-0005353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	158	550	1	ENST00000441802.2:c.8615_8629del	p.Leu2872_His2877delinsTyr	p.L2872_H2877delinsY	ENST00000441802	NM_005245.3	2872	tTAAAGGAACTTGACCat/tat	10/27	0.442346469100544	2	FACETS	1	0.976	1	0.575	0.529	0.622	CLONAL	1	TRUE	0	0.473701174353365	2		551	580	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112571	115112572	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	74	304	0	ENST00000257566.3:c.1168dup	p.Cys390LeufsTer17	p.C390Lfs*17	ENST00000257566	NM_016569.3	390	tgc/tTgc	7/8	0.473701174353365	1	FACETS	0.447	0.391	0.506	0.447	0.391	0.506	SUBCLONAL	1	TRUE	0	0.473701174353365	1		304	534	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	39	245	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.685	0.572	0.809	0.685	0.572	0.809	SUBCLONAL	1	TRUE	1	0.476676239349624	2		245	239	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023696	27023696	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	42	403	0	ENST00000324856.7:c.802C>T	p.Gln268Ter	p.Q268*	ENST00000324856	NM_006015.4	268	Cag/Tag	1/20	1	2	FACETS	0.256	0.213	0.304	0.256	0.213	0.304	SUBCLONAL	1	TRUE	1	0.476676239349624	2		403	689	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151186	202151186	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746684914	NA	P-0005365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	43	433	0	ENST00000358485.4:c.1486G>A	p.Asp496Asn	p.D496N	ENST00000358485	NM_001080125.1	496	Gat/Aat	9/9	1	2	FACETS	0.285	0.238	0.338	0.285	0.238	0.338	SUBCLONAL	1	TRUE	1	0.476676239349624	2		433	632	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637549	52637549	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	49	436	0	ENST00000394830.3:c.2767G>T	p.Glu923Ter	p.E923*	ENST00000394830	NM_018313.4	923	Gaa/Taa	18/30	1	2	FACETS	0.275	0.232	0.323	0.275	0.232	0.323	SUBCLONAL	1	TRUE	1	0.476676239349624	2		436	747	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662953	52662953	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	52	547	1	ENST00000394830.3:c.1400C>T	p.Ser467Leu	p.S467L	ENST00000394830	NM_018313.4	467	tCa/tTa	13/30	1	2	FACETS	0.238	0.202	0.278	0.238	0.202	0.278	SUBCLONAL	1	TRUE	1	0.476676239349624	2		548	917	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138781	37138781	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	117	439	0	ENST00000373509.5:c.214G>A	p.Asp72Asn	p.D72N	ENST00000373509	NM_002648.3	72	Gac/Aac	3/6	0.279696353862484	4	FACETS	1	0.905	1	0.501	0.452	0.553	INDETERMINATE	1	TRUE	2	0.476676239349624	4		439	723	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344035	118344035	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	56	374	0	ENST00000534358.1:c.2161C>T	p.Arg721Ter	p.R721*	ENST00000534358	NM_005933.3	721	Cga/Tga	3/36	1	2	FACETS	0.344	0.294	0.398	0.344	0.294	0.398	SUBCLONAL	1	TRUE	1	0.476676239349624	2		374	684	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492623	56492623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	128	507	1	ENST00000267101.3:c.2773G>A	p.Glu925Lys	p.E925K	ENST00000267101	NM_001982.3	925	Gag/Aag	23/28	0.118137135718443	3	FACETS	0.735	0.665	0.808	0.367	0.332	0.404	INDETERMINATE	1	TRUE	1	0.476676239349624	3		508	905	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347105	89347105	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	44	589	0	ENST00000301030.4:c.5845G>C	p.Glu1949Gln	p.E1949Q	ENST00000301030	NM_001256183.1	1949	Gag/Cag	9/13	1	2	FACETS	0.263	0.219	0.311	0.263	0.219	0.311	SUBCLONAL	1	TRUE	1	0.476676239349624	2		589	703	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179027	123179027	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1569511477	NA	P-0005365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	106	568	0	ENST00000218089.9:c.476A>G	p.Tyr159Cys	p.Y159C	ENST00000218089	NM_001042749.1	159	tAt/tGt	8/35	1	2	FACETS	0.517	0.462	0.574	0.517	0.462	0.574	SUBCLONAL	1	TRUE	1	0.476676239349624	2		568	861	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578545	7578546	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0005365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	37	381	0	ENST00000269305.4:c.384_385insCC	p.Ala129ProfsTer42	p.A129Pfs*42	ENST00000269305	NM_001126112.2	128	-/CC	5/11	1	2	FACETS	0.254	0.208	0.305	0.254	0.208	0.305	SUBCLONAL	1	TRUE	1	0.476676239349624	2		381	612	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032786	30032787	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0005365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	89	508	0	ENST00000338641.4:c.161_162del	p.Leu54ArgfsTer31	p.L54Rfs*31	ENST00000338641	NM_000268.3	54	cTG/c	2/16	1	2	FACETS	0.473	0.419	0.531	0.473	0.419	0.531	SUBCLONAL	1	TRUE	1	0.476676239349624	2		508	789	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	89	458	2	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.785	0.698	0.877	0.785	0.698	0.877	SUBCLONAL	1	TRUE	1	0.428046416703039	2		460	530	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	98	440	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.719	0.642	0.8	0.719	0.642	0.8	SUBCLONAL	1	TRUE	1	0.428046416703039	2		440	637	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	45	104	0	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.428046416703039	2		104	172	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024001	27024002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	51	86	0	ENST00000324856.7:c.1113dup	p.Gln372AlafsTer28	p.Q372Afs*28	ENST00000324856	NM_006015.4	369	-/G	1/20	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.428046416703039	2		86	232	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111579	56111579	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	64	170	0	ENST00000399503.3:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000399503	NM_005921.1	60	cGg/cAg	1/20	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.428046416703039	2		170	259	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012410	152012410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	123	427	0	ENST00000262189.6:c.403G>A	p.Ala135Thr	p.A135T	ENST00000262189	NM_170606.2	135	Gct/Act	4/59	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.428046416703039	2		427	548	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755554	39755554	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	65	584	0	ENST00000288319.7:c.1211del	p.Pro404ArgfsTer25	p.P404Rfs*25	ENST00000288319	NM_182918.3	404	cCg/cg	10/10	1	2	FACETS	0.467	0.404	0.534	0.467	0.404	0.534	SUBCLONAL	1	TRUE	1	0.428046416703039	2		584	651	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	166	720	1	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.974	0.896	1	0.974	0.896	1	CLONAL	1	TRUE	1	0.428046416703039	2		721	796	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211097	55211097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219568637	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	168	619	0	ENST00000275493.2:c.340G>A	p.Glu114Lys	p.E114K	ENST00000275493	NM_005228.3	114	Gaa/Aaa	3/28	1	2	FACETS	0.949	0.873	1	0.949	0.873	1	CLONAL	1	TRUE	1	0.428046416703039	2		619	827	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	295	596	1	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.428046416703039	2		597	1303	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279861	46279866	+	inframe_deletion	In_Frame_Del	DEL	CAGCAA	CAGCAA	-	rs748517056	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	107	538	1	ENST00000371998.3:c.3810_3815del	p.Gln1275_Gln1276del	p.Q1275_Q1276del	ENST00000371998		1263	CAGCAA/-	20/23	1	2	FACETS	0.736	0.661	0.816	0.736	0.661	0.816	SUBCLONAL	1	TRUE	1	0.428046416703039	2		539	679	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	202	604	4	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	0.864	0.8	0.931	0.864	0.8	0.931	CLONAL	1	TRUE	1	0.428046416703039	2		608	1092	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139625	202139626	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	192	688	2	ENST00000358485.4:c.790dup	p.Val264GlyfsTer13	p.V264Gfs*13	ENST00000358485	NM_001080125.1	262	-/G	6/9	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.428046416703039	2		690	881	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933593	39933594	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	174	371	0	ENST00000378444.4:c.1005dup	p.Ser336LeufsTer45	p.S336Lfs*45	ENST00000378444	NM_001123385.1	335	-/C	4/15	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.428046416703039	1		371	447	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993676	90993676	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	134	210	0	ENST00000265433.3:c.247del	p.Met83CysfsTer9	p.M83Cfs*9	ENST00000265433	NM_002485.4	83	Atg/tg	3/16	0.428046416703039	3	FACETS	0.919	0.835	1	0.46	0.417	0.504	CLONAL	1	TRUE	1	0.428046416703039	3		210	827	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497796	120497796	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs367734156	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	168	512	0	ENST00000256646.2:c.2086A>G	p.Thr696Ala	p.T696A	ENST00000256646	NM_024408.3	696	Aca/Gca	13/34	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.428046416703039	2		512	696	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844720	156844720	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1171	329	1058	1	ENST00000524377.1:c.1274C>T	p.Ala425Val	p.A425V	ENST00000524377	NM_002529.3	425	gCc/gTc	11/17	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.428046416703039	2		1059	1500	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176105684	176105684	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	114	372	0	ENST00000367669.3:c.832-1G>A		p.X278_splice	ENST00000367669	NM_022457.5	278			1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.428046416703039	2		372	518	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215633993	215633993	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	59	622	0	ENST00000260947.4:c.1358A>G	p.Asp453Gly	p.D453G	ENST00000260947	NM_000465.2	453	gAt/gGt	5/11	1	2	FACETS	0.308	0.264	0.356	0.308	0.264	0.356	SUBCLONAL	1	TRUE	1	0.428046416703039	2		622	895	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437202	220437202	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	187	976	0	ENST00000243786.2:c.106C>A	p.Leu36Met	p.L36M	ENST00000243786	NM_002191.3	36	Ctg/Atg	1/2	1	2	FACETS	0.779	0.718	0.842	0.779	0.718	0.842	SUBCLONAL	1	TRUE	1	0.428046416703039	2		976	1122	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645694	12645694	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs3730271	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	187	746	0	ENST00000251849.4:c.775T>C	p.Ser259Pro	p.S259P	ENST00000251849	NM_002880.3	259	Tcc/Ccc	7/17	0.428046416703039	2	FACETS	0.982	0.908	1	0.491	0.454	0.53	CLONAL	1	TRUE	0	0.428046416703039	2		746	890	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374326	138374326	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	256	570	2	ENST00000289153.2:c.3118C>A	p.Gln1040Lys	p.Q1040K	ENST00000289153	NM_006219.2	1040	Cag/Aag	22/22	0.428046416703039	2	FACETS	0.878	0.827	0.93	0.878	0.827	0.93	CLONAL	2	TRUE	0	0.428046416703039	2		572	681	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294456	1294456	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	133	322	0	ENST00000310581.5:c.545C>A	p.Thr182Asn	p.T182N	ENST00000310581	NM_198253.2	182	aCt/aAt	2/16	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.428046416703039	2		322	438	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288314	33288314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745927122	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	144	484	0	ENST00000374542.5:c.1094G>A	p.Arg365Gln	p.R365Q	ENST00000374542	NM_001141970.1	365	cGg/cAg	4/8	1	2	FACETS	0.981	0.897	1	0.981	0.897	1	CLONAL	1	TRUE	1	0.428046416703039	2		484	686	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987413	2987413	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	59	494	0	ENST00000396946.4:c.16C>T	p.Pro6Ser	p.P6S	ENST00000396946	NM_032415.4	6	Cca/Tca	3/25	1	2	FACETS	0.494	0.425	0.569	0.494	0.425	0.569	SUBCLONAL	1	TRUE	1	0.428046416703039	2		494	558	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845623	128845623	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs201012381	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	64	516	0	ENST00000249373.3:c.920C>T	p.Thr307Ile	p.T307I	ENST00000249373	NM_005631.4	307	aCc/aTc	4/12	1	2	FACETS	0.47	0.407	0.539	0.47	0.407	0.539	SUBCLONAL	1	TRUE	1	0.428046416703039	2		516	636	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851566	128851566	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	161	675	0	ENST00000249373.3:c.1891G>T	p.Ala631Ser	p.A631S	ENST00000249373	NM_005631.4	631	Gcc/Tcc	11/12	1	2	FACETS	0.912	0.837	0.99	0.912	0.837	0.99	CLONAL	1	TRUE	1	0.428046416703039	2		675	825	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486247	8486247	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139171396	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	157	552	0	ENST00000356435.5:c.2570G>A	p.Arg857His	p.R857H	ENST00000356435		857	cGt/cAt	17/35	0.428046416703039	3	FACETS	0.956	0.875	1	0.478	0.437	0.52	CLONAL	1	TRUE	1	0.428046416703039	3		552	932	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730249	133730249	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	173	615	0	ENST00000318560.5:c.315A>C	p.Lys105Asn	p.K105N	ENST00000318560	NM_005157.4	105	aaA/aaC	3/11	0.428046416703039	3	FACETS	1	0.956	1	0.529	0.486	0.573	CLONAL	1	TRUE	1	0.428046416703039	3		615	928	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998607	100998607	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs778889652	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	221	802	1	ENST00000325455.5:c.1195C>A	p.Arg399Ser	p.R399S	ENST00000325455	NM_001202474.3	399	Cgc/Agc	1/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.428046416703039	2		803	893	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129749	108129749	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs780619951	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	170	484	0	ENST00000278616.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000278616	NM_000051.3	805	Cga/Tga	16/63	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.428046416703039	2		484	743	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120980	115120980	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	106	498	0	ENST00000257566.3:c.26T>C	p.Val9Ala	p.V9A	ENST00000257566	NM_016569.3	9	gTc/gCc	1/8	1	2	FACETS	0.83	0.745	0.918	0.83	0.745	0.918	CLONAL	1	TRUE	1	0.428046416703039	2		498	597	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354353	354353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142097791	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	180	585	1	ENST00000262320.3:c.1205C>T	p.Thr402Met	p.T402M	ENST00000262320	NM_003502.3	402	aCg/aTg	5/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.428046416703039	2		586	774	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128997	30128997	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	238	903	1	ENST00000263025.4:c.769A>G	p.Ile257Val	p.I257V	ENST00000263025	NM_002746.2	257	Att/Gtt	5/9	1	2	FACETS	0.98	0.914	1	0.98	0.914	1	CLONAL	1	TRUE	1	0.428046416703039	2		904	1135	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337296	89337296	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567537413	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	137	524	0	ENST00000301030.4:c.7735C>T	p.Arg2579Cys	p.R2579C	ENST00000301030	NM_001256183.1	2579	Cgc/Tgc	12/13	1	2	FACETS	0.936	0.853	1	0.936	0.853	1	CLONAL	1	TRUE	1	0.428046416703039	2		524	684	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527492	29527492	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	56	551	1	ENST00000356175.3:c.941G>T	p.Arg314Met	p.R314M	ENST00000356175	NM_000267.3	314	aGg/aTg	9/57	1	2	FACETS	0.357	0.305	0.414	0.357	0.305	0.414	SUBCLONAL	1	TRUE	1	0.428046416703039	2		552	733	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217783	2217783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	50	677	1	ENST00000398665.3:c.2557C>T	p.Arg853Cys	p.R853C	ENST00000398665	NM_032482.2	853	Cgc/Tgc	22/28	1	2	FACETS	0.27	0.228	0.317	0.27	0.228	0.317	SUBCLONAL	1	TRUE	1	0.428046416703039	2		678	864	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376280	15376280	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	76	415	0	ENST00000263377.2:c.734A>G	p.Gln245Arg	p.Q245R	ENST00000263377	NM_058243.2	245	cAg/cGg	5/20	1	2	FACETS	0.852	0.75	0.959	0.852	0.75	0.959	CLONAL	1	TRUE	1	0.428046416703039	2		415	417	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188297	10188297	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs869025653	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	160	630	0	ENST00000256474.2:c.444del	p.Phe148LeufsTer11	p.F148Lfs*11	ENST00000256474	NM_000551.3	147	aTt/at	2/3	0.428046416703039	2	FACETS	0.831	0.762	0.903	0.415	0.381	0.452	CLONAL	1	TRUE	0	0.428046416703039	2		630	900	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	360055	360055	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	330	700	2	ENST00000262320.3:c.1034del	p.Pro345HisfsTer69	p.P345Hfs*69	ENST00000262320	NM_003502.3	345	cCa/ca	4/11	1	2	FACETS	0.933	0.886	0.981	1	0.996	1	CLONAL	2	TRUE	1	0.428046416703039	2		702	826	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981861	101981863	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	159	617	1	ENST00000282441.5:c.286_288del	p.Phe96del	p.F96del	ENST00000282441	NM_001130145.2	94	tcCTTc/tcc	1/9	1	2	FACETS	0.948	0.87	1	0.948	0.87	1	CLONAL	1	TRUE	1	0.428046416703039	2		618	784	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248442	59248443	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	123	534	0	ENST00000371222.2:c.300dup	p.Lys101GlnfsTer6	p.K101Qfs*6	ENST00000371222	NM_002228.3	100	-/C	1/1	1	2	FACETS	0.869	0.788	0.955	0.869	0.788	0.955	CLONAL	1	TRUE	1	0.428046416703039	2		534	661	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835781	68835781	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060501215	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	265	570	2	ENST00000261769.5:c.377del	p.Pro126ArgfsTer89	p.P126Rfs*89	ENST00000261769	NM_004360.3	124	cgC/cg	3/16	1	2	FACETS	0.846	0.797	0.895	1	0.994	1	CLONAL	2	TRUE	1	0.428046416703039	2		572	732	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287888	33287889	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCT	novel	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	91	612	0	ENST00000374542.5:c.1362_1364dup	p.Glu457dup	p.E457dup	ENST00000374542	NM_001141970.1	457	gag/gaAGAg	5/8	1	2	FACETS	0.663	0.589	0.742	0.663	0.589	0.742	SUBCLONAL	1	TRUE	1	0.428046416703039	2		612	641	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149799	202149799	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	137	382	0	ENST00000358485.4:c.1245del	p.Phe415LeufsTer26	p.F415Lfs*26	ENST00000358485	NM_001080125.1	414	Ttt/tt	8/9	1	2	FACETS	0.933	0.851	1	0.933	0.851	1	CLONAL	1	TRUE	1	0.428046416703039	2		382	686	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47709925	47709925	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63750084	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	164	611	0	ENST00000233146.2:c.2647del	p.Ile883LeufsTer9	p.I883Lfs*9	ENST00000233146	NM_000251.2	881	gAa/ga	16/16	1	2	FACETS	0.982	0.903	1	0.982	0.903	1	CLONAL	1	TRUE	1	0.428046416703039	2		611	780	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509112	66509113	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	55	409	0	ENST00000273854.3:c.214dup	p.Asp72GlyfsTer17	p.D72Gfs*17	ENST00000273854	NM_004439.5	72	gac/gGac	2/18	1	2	FACETS	0.368	0.314	0.427	0.368	0.314	0.427	SUBCLONAL	1	TRUE	1	0.428046416703039	2		409	699	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912152	29912153	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0005400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	20	68	0	ENST00000376809.5:c.873_874delinsAG	p.Lys292Glu	p.K292E	ENST00000376809	NM_002116.7	291	ccCAag/ccAGag	4/8	0.327198729166808	2	FACETS	1	0.823	1	0.531	0.415	0.661	CLONAL	1	TRUE	0	0.428046416703039	2		68	88	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931463	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622007	NA	P-0005428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	35	282	0	ENST00000374690.3:c.2105T>A	p.Leu702His	p.L702H	ENST00000374690	NM_000044.3	702	cTc/cAc	4/8	0.707397447824401	2	FACETS	0.137	0.112	0.166			1	SUBCLONAL	1	TRUE	NA	0.730237574151529	2		282	698	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114816	108114816	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	132	336	0	ENST00000278616.4:c.633C>A	p.Asp211Glu	p.D211E	ENST00000278616	NM_000051.3	211	gaC/gaA	6/63	1	2	FACETS	0.875	0.802	0.951	0.875	0.802	0.951	CLONAL	1	TRUE	1	0.730237574151529	2		336	413	SUCCESS
AR	367	MSKCC	GRCh37	X	66943551	66943551	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	193	294	0	ENST00000374690.3:c.2631C>G	p.Phe877Leu	p.F877L	ENST00000374690	NM_000044.3	877	ttC/ttG	8/8	0.707397447824401	2	FACETS	0.725	0.673	0.779			1	SUBCLONAL	1	TRUE	NA	0.730237574151529	2		294	729	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592049	67592050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0005428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	203	436	0	ENST00000274335.5:c.1866_1867insGG	p.Thr623GlyfsTer40	p.T623Gfs*40	ENST00000274335		622	aag/aaGGg	14/15	1	2	FACETS	0.837	0.78	0.896	0.837	0.78	0.896	CLONAL	1	TRUE	1	0.730237574151529	2		436	664	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056465	26056466	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0005428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	92	147	0	ENST00000343677.2:c.191_192del	p.Lys64SerfsTer8	p.K64Sfs*8	ENST00000343677	NM_005319.3	64	aAA/a	1/1	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.730237574151529	2		147	221	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0005434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	363	534	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.705554187668967	2		534	1027	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46240659	46240659	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	312	416	0	ENST00000334344.6:c.1519C>T	p.Gln507Ter	p.Q507*	ENST00000334344	NM_152641.2	507	Cag/Tag	12/21	1	2	FACETS	0.929	0.878	0.981	0.929	0.878	0.981	CLONAL	1	FALSE	1	0.705554187668967	2		416	952	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0005434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	202	450	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.705554187668967	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	0	0.705554187668967	1		450	360	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422859	49422859	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371377859	NA	P-0005434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	75	502	0	ENST00000301067.7:c.14236C>T	p.Arg4746Trp	p.R4746W	ENST00000301067	NM_003482.3	4746	Cgg/Tgg	44/54	1	2	FACETS	0.29	0.253	0.329	0.29	0.253	0.329	SUBCLONAL	1	FALSE	1	0.705554187668967	2		502	734	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663421	67663421	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	470	612	0	ENST00000264010.4:c.1822G>T	p.Asp608Tyr	p.D608Y	ENST00000264010	NM_006565.3	608	Gat/Tat	10/12	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.705554187668967	2		612	1322	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125032	46125033	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	374	501	0	ENST00000334344.6:c.220dup	p.Glu74GlyfsTer11	p.E74Gfs*11	ENST00000334344	NM_152641.2	73	-/G	3/21	1	2	FACETS	0.944	0.897	0.992	0.944	0.897	0.992	CLONAL	1	FALSE	1	0.705554187668967	2		501	1123	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111499	8111500	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005469-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	259	569	0	ENST00000346208.3:c.987dup	p.Arg330GlufsTer22	p.R330Efs*22	ENST00000346208		329	agg/aGgg	5/6	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.469209187304022	2		569	1096	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205157	61205157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144867876	NA	P-0005469-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	235	498	1	ENST00000301761.2:c.97C>T	p.Arg33Cys	p.R33C	ENST00000301761	NM_017841.2	33	Cgc/Tgc	2/4	1	2	FACETS	0.92	0.858	0.984	0.92	0.858	0.984	CLONAL	1	TRUE	1	0.469209187304022	2		499	1089	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880984	37880985	+	inframe_insertion	In_Frame_Ins	INS	-	-	TACGTGATGGCT	rs397516977	NA	P-0005483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	237	434	0	ENST00000269571.5:c.2314_2325dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/TACGTGATGGCT	20/27	0.209484604202527	5	FACETS	0.852	0.795	0.912			1	CLONAL	3	TRUE	NA	0.209484604202527	5		434	1163	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0005483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	128	457	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.191887933742693	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.209484604202527	1		457	873	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974696	21974697	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	98	338	0	ENST00000304494.5:c.130_131insC	p.Tyr44SerfsTer76	p.Y44Sfs*76	ENST00000304494	NM_000077.4	44	tac/tCac	1/3	0.191887933742693	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.209484604202527	1		338	638	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0005489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	97	175	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	NA	2	FACETS	0.89	0.802	0.983			1	INDETERMINATE	2	TRUE	NA	0.316704559365531	2		175	344	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0005489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	162	242	0				ENST00000310581	NM_198253.2	-/1132			0.272309681087053	4	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	2	0.316704559365531	4		242	650	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057727	27057727	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	169	683	1	ENST00000324856.7:c.1435C>T	p.Gln479Ter	p.Q479*	ENST00000324856	NM_006015.4	479	Cag/Tag	3/20	1	2	FACETS	0.825	0.757	0.897	0.825	0.757	0.897	CLONAL	1	TRUE	1	0.316704559365531	2		684	1293	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057647	27057647	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	123	482	0	ENST00000324856.7:c.1355C>G	p.Pro452Arg	p.P452R	ENST00000324856	NM_006015.4	452	cCt/cGt	3/20	1	2	FACETS	0.797	0.72	0.879	0.797	0.72	0.879	SUBCLONAL	1	TRUE	1	0.316704559365531	2		482	974	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390197	89390197	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	100	402	0	ENST00000336596.2:c.946G>A	p.Asp316Asn	p.D316N	ENST00000336596	NM_005233.5	316	Gac/Aac	4/17	0.272901691602689	1	FACETS	0.61	0.544	0.68	0.61	0.544	0.68	SUBCLONAL	1	TRUE	0	0.316704559365531	1		402	871	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973826	131973826	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	211	347	0	ENST00000265335.6:c.3529G>C	p.Asp1177His	p.D1177H	ENST00000265335		1177	Gat/Cat	23/25	0.242915258548867	2	FACETS	0.971	0.906	1	0.971	0.906	1	CLONAL	2	TRUE	0	0.316704559365531	2		347	686	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031973	26031973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1209	206	878	1	ENST00000244661.2:c.316G>A	p.Glu106Lys	p.E106K	ENST00000244661	NM_003537.3	106	Gag/Aag	1/1	1	2	FACETS	0.919	0.851	0.991	0.919	0.851	0.991	CLONAL	1	TRUE	1	0.316704559365531	2		879	1415	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904949	101904949	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	101	335	0	ENST00000374994.4:c.937C>G	p.Leu313Val	p.L313V	ENST00000374994	NM_004612.2	313	Ctt/Gtt	5/9	0.316704559365531	2	FACETS	0.915	0.818	1	0.458	0.409	0.509	CLONAL	1	TRUE	0	0.316704559365531	2		335	697	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964207	28964207	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	78	243	0	ENST00000282397.4:c.1695A>T	p.Lys565Asn	p.K565N	ENST00000282397	NM_002019.4	565	aaA/aaT	13/30	NA	2	FACETS	0.947	0.834	1			1	INDETERMINATE	1	TRUE	NA	0.316704559365531	2		243	520	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893373	32893373	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs80358498	NA	P-0005489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	98	356	0	ENST00000380152.3:c.227C>G	p.Ser76Ter	p.S76*	ENST00000380152		76	tCa/tGa	3/27	NA	2	FACETS	0.894	0.798	0.996			1	INDETERMINATE	1	TRUE	NA	0.316704559365531	2		356	692	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375435	15375435	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	109	445	1	ENST00000263377.2:c.992C>A	p.Pro331Gln	p.P331Q	ENST00000263377	NM_058243.2	331	cCa/cAa	6/20	1	2	FACETS	0.784	0.703	0.87	0.784	0.703	0.87	SUBCLONAL	1	TRUE	1	0.316704559365531	2		446	878	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905112	50905112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781132734	NA	P-0005489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	170	614	0	ENST00000440232.2:c.394G>A	p.Asp132Asn	p.D132N	ENST00000440232	NM_002691.3	132	Gat/Aat	4/27	1	2	FACETS	0.947	0.869	1	0.947	0.869	1	CLONAL	1	TRUE	1	0.316704559365531	2		614	1134	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942789	44942790	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0005489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	156	286	0	ENST00000377967.4:c.3369_3370insTA	p.His1124TyrfsTer7	p.H1124Yfs*7	ENST00000377967	NM_021140.2	1123	-/TA	23/29	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.316704559365531	1		286	588	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831438	89831438	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs762804216	NA	P-0005507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	138	675	1	ENST00000389301.3:c.2638C>T	p.Arg880Ter	p.R880*	ENST00000389301	NM_000135.2	880	Cga/Tga	28/43	0.189530862551926	3	FACETS	1	0.973	1	0.586	0.533	0.64	INDETERMINATE	1	TRUE	1	0.372146905533629	3		676	751	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188196	10188196	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0005507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	83	415	0	ENST00000256474.2:c.341-2A>C		p.X114_splice	ENST00000256474	NM_000551.3	114			0.292309958566706	2	FACETS	1	0.974	1	0.67	0.596	0.747	CLONAL	1	TRUE	0	0.372146905533629	2		415	333	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29107927	29107927	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1131691044	NA	P-0005507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	137	682	1	ENST00000328354.6:c.762del	p.Lys255SerfsTer20	p.K255Sfs*20	ENST00000328354	NM_007194.3	254	agG/ag	6/15	1	2	FACETS	0.766	0.696	0.84	0.766	0.696	0.84	SUBCLONAL	1	TRUE	1	0.372146905533629	2		683	961	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643923	52643924	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	108	321	0	ENST00000394830.3:c.1972dup	p.Met658AsnfsTer7	p.M658Nfs*7	ENST00000394830	NM_018313.4	658	atg/aAtg	17/30	0.292309958566706	2	FACETS	0.879	0.799	0.963	0.879	0.799	0.963	CLONAL	2	TRUE	0	0.372146905533629	2		321	330	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953741	48953742	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	384	363	0	ENST00000267163.4:c.1346dup	p.Val450SerfsTer13	p.V450Sfs*13	ENST00000267163	NM_000321.2	448	-/G	14/27	0.438683652225975	4	FACETS	1	0.957	1	1	0.957	1	INDETERMINATE	2	TRUE	2	0.734006968860218	4		363	904	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0005526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	28	175	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.831	1	1	0.957	1	CLONAL	2	FALSE	1	0.136556054118144	2		175	198	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089028	37089028	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	48	556	0	ENST00000231790.2:c.1750G>C	p.Asp584His	p.D584H	ENST00000231790	NM_000249.3	584	Gac/Cac	16/19	0.136609705134637	3	FACETS	0.894	0.761	1	1	0.954	1	CLONAL	3	FALSE	1	0.136556054118144	3		556	280	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098963	47098963	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	40	334	0	ENST00000409792.3:c.6311C>G	p.Ser2104Cys	p.S2104C	ENST00000409792	NM_014159.6	2104	tCt/tGt	15/21	0.136609705134637	3	FACETS	0.851	0.713	1	1	0.938	1	CLONAL	3	FALSE	1	0.136556054118144	3		334	245	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520210	9520210	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	29	610	0	ENST00000353224.5:c.2059C>T	p.Gln687Ter	p.Q687*	ENST00000353224	NM_177990.2	687	Cag/Tag	10/10	1	2	FACETS	0.948	0.765	1	1	0.955	1	CLONAL	2	FALSE	1	0.136556054118144	2		610	224	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933350	39933350	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	41	751	0	ENST00000378444.4:c.1249G>C	p.Asp417His	p.D417H	ENST00000378444	NM_001123385.1	417	Gac/Cac	4/15	0.136609705134637	0	FACETS	0.933	0.781	1			1	CLONAL	2	FALSE	0	0.136556054118144	0		751	278	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502159	157502160	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0005526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	26	436	0	ENST00000346085.5:c.3192_3193insC	p.Asn1065GlnfsTer2	p.N1065Qfs*2	ENST00000346085	NM_020732.3	1064	-/C	12/20	0.136556054118144	5	FACETS	1	0.922	1	0.465	0.368	0.575	CLONAL	1	FALSE	2	0.136556054118144	5		436	329	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152428	56152428	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	C	C	TT	novel	NA	P-0005526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	74	326	0	ENST00000399503.3:c.484delinsTT	p.Arg162LeufsTer2	p.R162Lfs*2	ENST00000399503	NM_005921.1	162	Cgt/TTgt	2/20	0.136556054118144	5	FACETS	1	0.892	1	1	0.892	1	CLONAL	4	FALSE	1	0.136556054118144	5		326	323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0005567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	99	437	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.222119554369303	2		437	798	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934573	NA	P-0005567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	109	460	0	ENST00000269305.4:c.722C>A	p.Ser241Tyr	p.S241Y	ENST00000269305	NM_001126112.2	241	tCc/tAc	7/11	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	FALSE	1	0.222119554369303	2		460	950	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911502	134911502	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	113	377	0	ENST00000398015.3:c.1967G>T	p.Gly656Val	p.G656V	ENST00000398015	NM_004441.4	656	gGg/gTg	11/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.222119554369303	2		377	735	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157041	106157041	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	127	514	2	ENST00000380013.4:c.1942G>T	p.Asp648Tyr	p.D648Y	ENST00000380013	NM_001127208.2	648	Gac/Tac	3/11	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	1	0.222119554369303	2		516	1075	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412539	80412539	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	82	382	1	ENST00000286548.4:c.502G>T	p.Ala168Ser	p.A168S	ENST00000286548	NM_002072.3	168	Gct/Tct	4/7	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	FALSE	1	0.222119554369303	2		383	690	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606748	43606748	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	70	479	0	ENST00000355710.3:c.1357G>T	p.Gly453Trp	p.G453W	ENST00000355710	NM_020975.4	453	Ggg/Tgg	7/20	0.14343954852908	2	FACETS	0.607	0.527	0.693	0.303	0.263	0.347	SUBCLONAL	1	FALSE	0	0.222119554369303	2		479	1039	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514194	69514194	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	94	608	0	ENST00000294312.3:c.487T>G	p.Ser163Ala	p.S163A	ENST00000294312	NM_005117.2	163	Tct/Gct	3/3	1	2	FACETS	0.851	0.755	0.953	0.851	0.755	0.953	CLONAL	1	FALSE	1	0.222119554369303	2		608	995	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244764	46244764	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	48	450	0	ENST00000334344.6:c.2858C>G	p.Ala953Gly	p.A953G	ENST00000334344	NM_152641.2	953	gCt/gGt	15/21	1	2	FACETS	0.508	0.428	0.597	0.508	0.428	0.597	SUBCLONAL	1	FALSE	1	0.222119554369303	2		450	851	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732458	74732458	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1287	77	657	0	ENST00000359995.5:c.451T>C	p.Ser151Pro	p.S151P	ENST00000359995	NM_001195427.1	151	Tcc/Ccc	2/3	1	2	FACETS	0.508	0.444	0.578	0.508	0.444	0.578	SUBCLONAL	1	FALSE	1	0.222119554369303	2		657	1364	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651678	48651678	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	150	550	0	ENST00000376670.3:c.844T>A	p.Cys282Ser	p.C282S	ENST00000376670	NM_002049.3	282	Tgc/Agc	5/6	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.222119554369303	2		550	1220	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201391	133201394	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	GAAG	GAAG	AAAAA	novel	NA	P-0005567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	177	440	1	ENST00000320574.5:c.6750_6753delinsTTTTT	p.Met2252TyrfsTer52	p.M2252Yfs*52	ENST00000320574	NM_006231.2	2250	gtCTTC/gtTTTTT	49/49	1	2	FACETS	0.764	0.703	0.827	1	0.99	1	SUBCLONAL	2	FALSE	1	0.222119554369303	2		441	1043	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183791	10183792	+	stop_gained,inframe_insertion	Nonsense_Mutation	INS	-	-	ATA	novel	NA	P-0005593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	37	319	0	ENST00000256474.2:c.262_263insAAT	p.Val87_Trp88insTer	p.V87_W88ins*	ENST00000256474	NM_000551.3	87	gta/gtATAa	1/3	1	2	FACETS	0.982	0.814	1	0.982	0.814	1	CLONAL	1	TRUE	1	0.27	2		319	279	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067899	30067899	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315498	NA	P-0005598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	337	753	2	ENST00000338641.4:c.1084C>T	p.Gln362Ter	p.Q362*	ENST00000338641	NM_000268.3	362	Cag/Tag	11/16	0.420441284994385	1	FACETS	0.938	0.886	0.991	0.938	0.886	0.991	CLONAL	1	TRUE	0	0.428594512326289	1		755	1317	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46215213	46215214	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	145	329	0	ENST00000334344.6:c.652dup	p.Ser218PhefsTer13	p.S218Ffs*13	ENST00000334344	NM_152641.2	216	-/T	6/21	0.420441284994385	1	FACETS	0.785	0.718	0.855	0.785	0.718	0.855	SUBCLONAL	1	TRUE	0	0.428594512326289	1		329	677	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0005640-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	103	175	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.993	0.902	1	0.993	0.902	1	CLONAL	1	TRUE	1	0.725165546966401	2		175	286	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100976	27100976	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005640-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	268	563	3	ENST00000324856.7:c.4258C>T	p.Gln1420Ter	p.Q1420*	ENST00000324856	NM_006015.4	1420	Cag/Tag	18/20	0.725165546966401	1	FACETS	0.998	0.95	1	0.998	0.95	1	CLONAL	1	TRUE	0	0.725165546966401	1		566	472	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511611	46511611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762595036	NA	P-0005640-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	160	533	0	ENST00000262741.5:c.1166G>A	p.Gly389Glu	p.G389E	ENST00000262741	NM_003629.3	389	gGa/gAa	9/10	NA	2	FACETS	0.761	0.701	0.823			1	INDETERMINATE	1	TRUE	NA	0.725165546966401	2		533	580	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511625	46511625	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005640-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	159	537	0	ENST00000262741.5:c.1152G>C	p.Glu384Asp	p.E384D	ENST00000262741	NM_003629.3	384	gaG/gaC	9/10	NA	2	FACETS	0.756	0.696	0.818			1	INDETERMINATE	1	TRUE	NA	0.725165546966401	2		537	580	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511694	46511694	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005640-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	118	489	0	ENST00000262741.5:c.1083G>C	p.Glu361Asp	p.E361D	ENST00000262741	NM_003629.3	361	gaG/gaC	9/10	NA	2	FACETS	0.741	0.674	0.812			1	INDETERMINATE	1	TRUE	NA	0.725165546966401	2		489	439	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511735	46511735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005640-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	88	403	0	ENST00000262741.5:c.1042G>A	p.Glu348Lys	p.E348K	ENST00000262741	NM_003629.3	348	Gaa/Aaa	9/10	NA	2	FACETS	0.658	0.587	0.732			1	INDETERMINATE	1	TRUE	NA	0.725165546966401	2		403	369	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511744	46511744	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005640-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	77	382	0	ENST00000262741.5:c.1033G>A	p.Glu345Lys	p.E345K	ENST00000262741	NM_003629.3	345	Gag/Aag	9/10	NA	2	FACETS	0.63	0.558	0.707			1	INDETERMINATE	1	TRUE	NA	0.725165546966401	2		382	337	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793362	242793362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137861407	NA	P-0005640-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	300	568	0	ENST00000334409.5:c.715G>A	p.Val239Met	p.V239M	ENST00000334409	NM_005018.2	239	Gtg/Atg	5/5	1	2	FACETS	0.97	0.917	1	0.97	0.917	1	CLONAL	1	TRUE	1	0.725165546966401	2		568	853	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115849	8115850	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACATGTCCTCCCT	novel	NA	P-0005640-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	258	707	0	ENST00000346208.3:c.1196_1208dup	p.Ser404HisfsTer107	p.S404Hfs*107	ENST00000346208		399	cac/cACATGTCCTCCCTac	6/6	1	2	FACETS	0.67	0.627	0.714	0.67	0.627	0.714	SUBCLONAL	1	TRUE	1	0.725165546966401	2		707	1062	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0005664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	96	175	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.25146518182993	2		175	567	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0005664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	132	697	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.165704811357788	3	FACETS	1	0.981	1	0.666	0.604	0.731	CLONAL	1	TRUE	1	0.25146518182993	3		697	887	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130342	11130342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	112	581	1	ENST00000358026.2:c.2581G>A	p.Glu861Lys	p.E861K	ENST00000358026	NM_001128849.1	861	Gag/Aag	18/36	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.25146518182993	2		582	777	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057749	27057749	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1304	207	745	0	ENST00000324856.7:c.1457C>G	p.Ser486Cys	p.S486C	ENST00000324856	NM_006015.4	486	tCc/tGc	3/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.25146518182993	2		745	1511	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057899	27057899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	164	529	0	ENST00000324856.7:c.1607C>T	p.Ser536Phe	p.S536F	ENST00000324856	NM_006015.4	536	tCc/tTc	3/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.25146518182993	2		529	1071	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058072	27058072	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	36	141	0	ENST00000324856.7:c.1780C>T	p.Gln594Ter	p.Q594*	ENST00000324856	NM_006015.4	594	Cag/Tag	3/20	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.25146518182993	2		141	249	SUCCESS
APC	324	MSKCC	GRCh37	5	112179353	112179353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	139	438	0	ENST00000257430.4:c.8062G>A	p.Glu2688Lys	p.E2688K	ENST00000257430	NM_000038.5	2688	Gaa/Aaa	16/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.25146518182993	2		438	869	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157488317	157488317	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	59	226	0	ENST00000346085.5:c.3023C>T	p.Ala1008Val	p.A1008V	ENST00000346085	NM_020732.3	1008	gCa/gTa	10/20	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.25146518182993	2		226	404	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88635831	88635831	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	171	378	0	ENST00000372037.3:c.56C>G	p.Ser19Cys	p.S19C	ENST00000372037	NM_004329.2	19	tCt/tGt	3/13	1	2	FACETS	0.833	0.767	0.902	1	0.991	1	CLONAL	2	TRUE	1	0.25146518182993	2		378	816	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820528	44820528	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0005664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	153	188	0	ENST00000377967.4:c.226-1G>A		p.X76_splice	ENST00000377967	NM_021140.2	76			0.060498999203674	2	FACETS	0.869	0.801	0.938			1	INDETERMINATE	3	TRUE	NA	0.25146518182993	2		188	467	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087378	27087379	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	182	567	0	ENST00000324856.7:c.1956dup	p.Thr653AspfsTer23	p.T653Dfs*23	ENST00000324856	NM_006015.4	651	atg/atGg	5/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.25146518182993	2		567	967	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320936	30320937	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTGCC	novel	NA	P-0005664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	160	552	0	ENST00000322652.5:c.1347_1351dup	p.Pro451LeufsTer7	p.P451Lfs*7	ENST00000322652	NM_015355.2	449	cat/caTTGCCt	12/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.25146518182993	2		552	1170	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776357	76776358	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	199	328	0	ENST00000373344.5:c.7108dup	p.Gln2370ProfsTer7	p.Q2370Pfs*7	ENST00000373344	NM_000489.3	2370	cag/cCag	34/35	0.060498999203674	2	FACETS	1	0.967	1			1	INDETERMINATE	2	TRUE	NA	0.25146518182993	2		328	741	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831263	72831263	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	128	878	2	ENST00000268489.5:c.5318del	p.Asn1773ThrfsTer10	p.N1773Tfs*10	ENST00000268489	NM_006885.3	1773	aAc/ac	9/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.25146518182993	2		880	940	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	52	245	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.21	2		245	422	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127164	22127164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057519911	NA	P-0005690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	13	518	1	ENST00000215832.6:c.964G>A	p.Glu322Lys	p.E322K	ENST00000215832	NM_002745.4	322	Gag/Aag	7/9	1	2	FACETS	0.294	0.209	0.399	0.294	0.209	0.399	SUBCLONAL	1	TRUE	1	0.21	2		519	421	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738181	133738181	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	46	413	0	ENST00000318560.5:c.581C>T	p.Thr194Ile	p.T194I	ENST00000318560	NM_005157.4	194	aCc/aTc	4/11	1	2	FACETS	0.762	0.641	0.896	0.762	0.641	0.896	SUBCLONAL	1	TRUE	1	0.21	2		413	575	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827475	72827475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567512921	NA	P-0005690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	37	857	2	ENST00000268489.5:c.9106C>T	p.Arg3036Trp	p.R3036W	ENST00000268489	NM_006885.3	3036	Cgg/Tgg	9/10	1	2	FACETS	0.607	0.499	0.727	0.607	0.499	0.727	SUBCLONAL	1	TRUE	1	0.21	2		859	581	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245370	153245371	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	13	340	0	ENST00000281708.4:c.1820dup	p.Asp607GlufsTer37	p.D607Efs*37	ENST00000281708	NM_033632.3	607	gat/gaAt	11/12	1	2	FACETS	0.659	0.471	0.887	0.659	0.471	0.887	SUBCLONAL	1	TRUE	1	0.21	2		340	188	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023247	27023259	+	frameshift_variant	Frame_Shift_Del	DEL	CGGAGCCGCCCGG	CGGAGCCGCCCGG	-	novel	NA	P-0005690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	61	290	0	ENST00000324856.7:c.356_368del	p.Glu119AlafsTer109	p.E119Afs*109	ENST00000324856	NM_006015.4	118	aCGGAGCCGCCCGGc/ac	1/20	1	2	FACETS	0.866	0.746	0.996	0.866	0.746	0.996	CLONAL	1	TRUE	1	0.21	2		290	671	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1570	156	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.20987263230639	1	FACETS	0.771	0.703	0.843	0.771	0.703	0.843	SUBCLONAL	1	TRUE	0	0.20987263230639	1		311	1726	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100117	157100119	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs797045268	NA	P-0005720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	10	58	0	ENST00000346085.5:c.1069_1071del	p.Gly357del	p.G357del	ENST00000346085	NM_020732.3	352	GGC/-	1/20	0.204329542304186	1	FACETS	0.651	0.443	0.91	0.651	0.443	0.91	SUBCLONAL	1	TRUE	0	0.20987263230639	1		58	131	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578467	7578468	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCGGGC	novel	NA	P-0005720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2070	219	1022	0	ENST00000269305.4:c.456_462dup	p.Thr155AlafsTer28	p.T155Afs*28	ENST00000269305	NM_001126112.2	154	-/GCCCGGC	5/11	0.20987263230639	1	FACETS	0.816	0.755	0.88	0.816	0.755	0.88	CLONAL	1	TRUE	0	0.20987263230639	1		1022	2289	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958225	54958226	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0005720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1687	200	711	0	ENST00000312783.6:c.381dup	p.Trp128ValfsTer7	p.W128Vfs*7	ENST00000312783	NM_198436.1	127	-/G	6/10	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.20987263230639	2		711	1887	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023559	27023560	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0005801-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	44	485	0	ENST00000324856.7:c.671dup	p.Pro225AlafsTer175	p.P225Afs*175	ENST00000324856	NM_006015.4	222	tac/taCc	1/20	0.232701037256645	1	FACETS	0.206	0.172	0.244	0.206	0.172	0.244	INDETERMINATE	1	TRUE	0	0.453333009677087	1		485	728	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0005801-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	213	575	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.434944159930633	1	FACETS	0.946	0.882	1	0.946	0.882	1	CLONAL	1	TRUE	0	0.453333009677087	1		575	768	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0005801-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	186	503	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.232701037256645	1	FACETS	0.846	0.783	0.911	0.846	0.783	0.911	INDETERMINATE	1	TRUE	0	0.453333009677087	1		503	750	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0005801-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	169	415	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	0.434944159930633	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.453333009677087	1		415	549	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184065	56184065	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005801-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	187	385	0	ENST00000399503.3:c.4270C>T	p.Gln1424Ter	p.Q1424*	ENST00000399503	NM_005921.1	1424	Caa/Taa	19/20	0.434944159930633	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.453333009677087	1		385	558	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562578	95562578	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005801-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	75	439	0	ENST00000393063.1:c.4679C>T	p.Ala1560Val	p.A1560V	ENST00000393063	NM_030621.3	1560	gCg/gTg	24/28	0.26527873593282	1	FACETS	0.441	0.387	0.5	0.441	0.387	0.5	INDETERMINATE	1	TRUE	0	0.453333009677087	1		439	580	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477087	67477087	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005801-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	501	646	0	ENST00000327367.4:c.894C>A	p.Tyr298Ter	p.Y298*	ENST00000327367	NM_005902.3	298	taC/taA	7/9	0.438075546421857	2	FACETS	0.981	0.943	1	0.981	0.943	1	CLONAL	2	TRUE	0	0.453333009677087	2		646	1126	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374929	45374929	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005801-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	238	529	0	ENST00000262160.6:c.914C>T	p.Pro305Leu	p.P305L	ENST00000262160	NM_005901.5	305	cCa/cTa	8/11	0.434944159930633	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.453333009677087	1		529	754	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99472873	99472873	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	226	720	1	ENST00000268035.6:c.2869G>T	p.Val957Phe	p.V957F	ENST00000268035	NM_000875.3	957	Gtc/Ttc	14/21	0.166612782092119	5	FACETS	1	0.965	1	0.704	0.656	0.753	INDETERMINATE	2	TRUE	2	0.321035444188463	5		721	988	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352562	89352562	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	196	715	0	ENST00000301030.4:c.777C>G	p.Asn259Lys	p.N259K	ENST00000301030	NM_001256183.1	259	aaC/aaG	8/13	0.321035444188463	1	FACETS	0.8	0.744	0.857	1	0.992	1	SUBCLONAL	2	TRUE	0	0.321035444188463	1		715	641	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441433	52441447	+	inframe_deletion	In_Frame_Del	DEL	GCCTTGGCCAACTCC	GCCTTGGCCAACTCC	-	novel	NA	P-0005835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	209	639	0	ENST00000460680.1:c.405_419del	p.Glu136_Ala140del	p.E136_A140del	ENST00000460680	NM_004656.3	135	ccGGAGTTGGCCAAGGCc/ccc	6/17	0.321035444188463	2	FACETS	0.988	0.922	1	0.988	0.922	1	CLONAL	2	TRUE	0	0.321035444188463	2		639	659	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851298	63851299	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	145	399	0	ENST00000279873.7:c.2081dup	p.Leu695AlafsTer31	p.L695Afs*31	ENST00000279873	NM_032199.2	692	-/A	10/10	0.321035444188463	12	FACETS	1	0.94	1			1	CLONAL	2	TRUE	NA	0.321035444188463	12		399	1130	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576854	7576868	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TGAAGGGTGAAATAT	TGAAGGGTGAAATAT	A	novel	NA	P-0005835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	189	670	0	ENST00000269305.4:c.978_992delinsT	p.Glu326AspfsTer6	p.E326Dfs*6	ENST00000269305	NM_001126112.2	326	gaATATTTCACCCTTCAg/gaTg	9/11	0.301171504566333	2	FACETS	0.884	0.82	0.949	0.884	0.82	0.949	CLONAL	2	TRUE	0	0.321035444188463	2		670	666	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0005879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	571	672	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.896	0.868	0.923	1	0.998	1	CLONAL	3	TRUE	1	0.46	2		672	924	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162516	47162516	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs554338477	NA	P-0005879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	117	282	0	ENST00000409792.3:c.3610A>G	p.Ile1204Val	p.I1204V	ENST00000409792	NM_014159.6	1204	Att/Gtt	3/21	1	2	FACETS	0.897	0.812	0.987	0.897	0.812	0.987	CLONAL	1	TRUE	1	0.46	2		282	567	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170834766	170834766	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	135	428	0	ENST00000296930.5:c.834G>C	p.Met278Ile	p.M278I	ENST00000296930	NM_002520.6	278	atG/atC	10/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.46	2		428	446	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080375	5080375	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	62	231	0	ENST00000381652.3:c.2278C>G	p.Gln760Glu	p.Q760E	ENST00000381652	NM_004972.3	760	Caa/Gaa	17/25	1	2	FACETS	0.723	0.627	0.825	0.723	0.627	0.825	SUBCLONAL	1	TRUE	1	0.46	2		231	373	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66518915	66518915	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	194	336	0	ENST00000358598.2:c.196C>T	p.Gln66Ter	p.Q66*	ENST00000358598	NM_212471.2	66	Cag/Tag	3/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.46	2		336	660	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444193	49444194	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0005879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	194	603	0	ENST00000301067.7:c.3177dup	p.Lys1060GlufsTer8	p.K1060Efs*8	ENST00000301067	NM_003482.3	1059	-/G	11/54	1	2	FACETS	0.818	0.757	0.882	0.818	0.757	0.882	CLONAL	1	TRUE	1	0.46	2		603	1031	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557246	187557246	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	154	442	0	ENST00000441802.2:c.4116del	p.Val1373LeufsTer4	p.V1373Lfs*4	ENST00000441802	NM_005245.3	1372	ccC/cc	6/27	1	2	FACETS	0.99	0.909	1	0.99	0.909	1	CLONAL	1	TRUE	1	0.46	2		442	676	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0005897-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	129	365	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.224115667788309	3	FACETS	0.986	0.896	1	0.493	0.448	0.541	INDETERMINATE	1	TRUE	1	0.472782516561367	3		365	684	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712537	52712544	+	frameshift_variant	Frame_Shift_Del	DEL	AAGAGCTC	AAGAGCTC	-	novel	NA	P-0005897-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	415	738	0	ENST00000394830.3:c.208_215del	p.Glu70HisfsTer2	p.E70Hfs*2	ENST00000394830	NM_018313.4	70	GAGCTCTTc/c	3/30	0.426996974388382	2	FACETS	0.858	0.82	0.897	0.858	0.82	0.897	CLONAL	2	TRUE	0	0.472782516561367	2		738	1023	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959064	2959064	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005897-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	216	506	0	ENST00000396946.4:c.2452C>T	p.Arg818Trp	p.R818W	ENST00000396946	NM_032415.4	818	Cgg/Tgg	18/25	0.187058957844137	5	FACETS	1	0.979	1	0.381	0.353	0.41	INDETERMINATE	1	TRUE	2	0.472782516561367	5		506	1366	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573874	18573874	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0005897-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	106	454	0	ENST00000266497.5:c.2193-1G>C		p.X731_splice	ENST00000266497		731			1	2	FACETS	0.824	0.741	0.912	0.824	0.741	0.912	CLONAL	1	TRUE	1	0.472782516561367	2		454	544	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636112	28636112	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005897-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	164	616	0	ENST00000241453.7:c.260C>T	p.Ala87Val	p.A87V	ENST00000241453	NM_004119.2	87	gCt/gTt	3/24	0.472782516561367	1	FACETS	0.517	0.474	0.562	0.517	0.474	0.562	SUBCLONAL	1	TRUE	0	0.472782516561367	1		616	1025	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576918	7576919	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005897-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	237	541	0	ENST00000269305.4:c.927dup	p.Asn310GlnfsTer27	p.N310Qfs*27	ENST00000269305	NM_001126112.2	309	-/C	9/11	0.451201318725247	1	FACETS	0.841	0.786	0.898	0.841	0.786	0.898	CLONAL	1	TRUE	0	0.472782516561367	1		541	910	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0005940-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	101	392	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.278767936919968	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.322215159126682	1		392	471	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37863278	37863278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005940-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	1334	455	0	ENST00000269571.5:c.109G>A	p.Ala37Thr	p.A37T	ENST00000269571		37	Gcc/Acc	2/27	0.322215159126682	14	FACETS	0.974	0.959	0.988			1	CLONAL	15	TRUE	NA	0.322215159126682	14		455	1663	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171600	36171600	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0005940-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	42	201	0	ENST00000300305.3:c.965C>G	p.Ser322Ter	p.S322*	ENST00000300305		322	tCa/tGa	7/8	1	2	FACETS	0.706	0.591	0.834	0.706	0.591	0.834	SUBCLONAL	1	TRUE	1	0.322215159126682	2		201	369	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589592	67589593	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTT	novel	NA	P-0005940-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	125	233	0	ENST00000274335.5:c.1356_1357insTTT	p.Tyr452_Asn453insPhe	p.Y452_N453insF	ENST00000274335		452	tat/taTTTt	10/15	0.322215159126682	4	FACETS	0.997	0.914	1			1	CLONAL	3	TRUE	NA	0.322215159126682	4		233	343	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0005944-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	53	625	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	FALSE	1	0.218936783413989	2		625	423	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52692289	52692290	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAGAAGCTGTAGCTACAACTATGGCTTT	novel	NA	P-0005944-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	40	660	0	ENST00000394830.3:c.570_571insAAAGCCATAGTTGTAGCTACAGCTTCTT	p.Glu191LysfsTer10	p.E191Kfs*10	ENST00000394830	NM_018313.4	190	-/AAAGCCATAGTTGTAGCTACAGCTTCTT	6/30	0.218936783413989	1	FACETS	0.755	0.628	0.896	0.755	0.628	0.896	SUBCLONAL	1	FALSE	0	0.218936783413989	1		660	431	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0005968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	13	1035	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.30740598848895	4	FACETS	0.188	0.133	0.255	0.063	0.044	0.085	INDETERMINATE	1	TRUE	1	0.526481207425808	4		1036	402	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0005968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	88	338	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.30740598848895	4	FACETS	0.94	0.855	1	0.94	0.855	1	INDETERMINATE	3	TRUE	1	0.526481207425808	4		338	181	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584560	48584560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	24	528	0	ENST00000342988.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000342988	NM_005359.5	245	Cag/Tag	6/12	1	2	FACETS	0.642	0.509	0.791	0.642	0.509	0.791	SUBCLONAL	1	TRUE	1	0.526481207425808	2		528	142	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871063	12871064	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	137	326	0	ENST00000228872.4:c.291dup	p.Ala98CysfsTer27	p.A98Cfs*27	ENST00000228872	NM_004064.3	97	ggt/ggTt	1/3	0.526481207425808	6	FACETS	0.942	0.867	1			1	CLONAL	3	TRUE	NA	0.526481207425808	6		326	378	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383707	84383707	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1560570492	NA	P-0005968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	12	576	2	ENST00000321945.7:c.1145C>G	p.Ala382Gly	p.A382G	ENST00000321945	NM_139076.2	382	gCa/gGa	9/9	0.187600396475887	3	FACETS	0.276	0.193	0.376	0.092	0.064	0.126	INDETERMINATE	1	TRUE	0	0.526481207425808	3		578	209	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74003504	74003504	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	48	680	0	ENST00000318443.5:c.1575C>A	p.Ser525Arg	p.S525R	ENST00000318443	NM_001024736.1	525	agC/agA	9/10	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.526481207425808	2		680	168	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662321	67662321	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	108	595	0	ENST00000264010.4:c.1567T>G	p.Tyr523Asp	p.Y523D	ENST00000264010	NM_006565.3	523	Tac/Gac	9/12	0.516954665186397	2	FACETS	0.884	0.811	0.958	0.884	0.811	0.958	CLONAL	2	TRUE	0	0.526481207425808	2		595	232	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383703	84383703	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	12	573	2	ENST00000321945.7:c.1149del	p.Met385Ter	p.M385*	ENST00000321945	NM_139076.2	383	tcC/tc	9/9	0.187600396475887	3	FACETS	0.277	0.194	0.378	0.092	0.064	0.126	INDETERMINATE	1	TRUE	0	0.526481207425808	3		575	208	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005972-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	114	449	0	ENST00000206249.3:c.1607T>C	p.Leu536Pro	p.L536P	ENST00000206249	NM_000125.3	536	cTc/cCc	8/8	0.307974221736018	4	FACETS	0.956	0.859	1			1	CLONAL	1	TRUE	NA	0.324905512709966	4		449	973	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225360638	225360638	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005972-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	145	549	0	ENST00000264414.4:c.1753T>G	p.Ser585Ala	p.S585A	ENST00000264414	NM_003590.4	585	Tct/Gct	13/16	1	2	FACETS	0.973	0.888	1	0.973	0.888	1	CLONAL	1	TRUE	1	0.324905512709966	2		549	917	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135777041	135777041	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005972-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	142	563	0	ENST00000298552.3:c.2437G>T	p.Glu813Ter	p.E813*	ENST00000298552	NM_001162426.1	813	Gaa/Taa	19/23	1	2	FACETS	0.979	0.892	1	0.979	0.892	1	CLONAL	1	TRUE	1	0.324905512709966	2		563	893	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578411	7578411	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005972-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	237	412	0	ENST00000269305.4:c.519del	p.Arg174GlyfsTer73	p.R174Gfs*73	ENST00000269305	NM_001126112.2	173	gtG/gt	5/11	0.324905512709966	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.324905512709966	2		412	630	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918078	50918080	+	protein_altering_variant	In_Frame_Ins	INS	TTC	TTC	CTGCTTATCAGT	novel	NA	P-0005972-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	134	664	0	ENST00000440232.2:c.2395_2397delinsCTGCTTATCAGT	p.Phe799delinsLeuLeuIleSer	p.F799delinsLLIS	ENST00000440232	NM_002691.3	799	TTC/CTGCTTATCAGT	20/27	0.31633214060874	3	FACETS	0.808	0.732	0.888			1	CLONAL	1	TRUE	NA	0.324905512709966	3		664	1187	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0005981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	228	378	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.247824590800687	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	0	0.247824590800687	2		378	910	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165663	118165663	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776281952	NA	P-0005981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	117	540	0	ENST00000369448.3:c.173G>A	p.Arg58Gln	p.R58Q	ENST00000369448	NM_017709.3	58	cGg/cAg	2/2	1	2	FACETS	0.786	0.707	0.87	0.786	0.707	0.87	SUBCLONAL	1	TRUE	1	0.247824590800687	2		540	1201	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495306	212495306	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	123	429	0	ENST00000342788.4:c.1960G>T	p.Ala654Ser	p.A654S	ENST00000342788	NM_005235.2	654	Gca/Tca	17/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.247824590800687	2		429	843	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794499	242794499	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	46	419	1	ENST00000334409.5:c.443G>T	p.Arg148Met	p.R148M	ENST00000334409	NM_005018.2	148	aGg/aTg	3/5	1	2	FACETS	0.556	0.467	0.654	0.556	0.467	0.654	SUBCLONAL	1	TRUE	1	0.247824590800687	2		420	668	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543349	65543349	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1218	225	735	0	ENST00000358664.4:c.328C>T	p.Gln110Ter	p.Q110*	ENST00000358664	NM_002382.4	110	Caa/Taa	5/5	0.160258125885117	2	FACETS	1	0.987	1	0.629	0.584	0.676	CLONAL	1	TRUE	0	0.247824590800687	2		735	1443	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222282	2222282	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	171	702	0	ENST00000326181.6:c.566G>C	p.Arg189Pro	p.R189P	ENST00000326181	NM_032271.2	189	cGg/cCg	8/21	0.224134860562793	0	FACETS	0.95	0.872	1			1	CLONAL	1	TRUE	0	0.247824590800687	0		702	1093	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0005981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	164	843	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.234849064322375	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.247824590800687	1		843	1127	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546965	9546965	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	62	317	0	ENST00000353224.5:c.1057G>T	p.Gly353Cys	p.G353C	ENST00000353224	NM_177990.2	353	Ggc/Tgc	5/10	0.22231301374966	3	FACETS	0.701	0.604	0.807	0.351	0.302	0.404	SUBCLONAL	1	TRUE	1	0.247824590800687	3		317	802	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988545	36988546	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1548	1638	760	0	ENST00000354822.5:c.107dup	p.His37AlafsTer9	p.H37Afs*9	ENST00000354822	NM_001079668.2	36	aag/aaAg	2/3	0.247824590800687	11	FACETS	0.975	0.955	0.995			1	CLONAL	9	TRUE	NA	0.247824590800687	11		760	3186	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034417	47034417	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0005981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	139	266	0	ENST00000377604.3:c.503del		p.X168_splice	ENST00000377604	NM_001204468.1	168			1	1	FACETS	0.752	0.687	0.821	1	0.987	1	SUBCLONAL	2	TRUE	0	0.247824590800687	1		266	653	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0005984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	464	654	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.725381982113798	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.725381982113798	1		655	764	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604789	48604789	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	143	465	0	ENST00000342988.3:c.1611C>G	p.Asp537Glu	p.D537E	ENST00000342988	NM_005359.5	537	gaC/gaG	12/12	0.725381982113798	1	FACETS	0.84	0.78	0.901	0.84	0.78	0.901	CLONAL	1	TRUE	0	0.725381982113798	1		465	299	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446235	187446235	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	158	585	1	ENST00000232014.4:c.1453C>T	p.His485Tyr	p.H485Y	ENST00000232014	NM_001130845.1	485	Cat/Tat	6/10	0.365309377169473	1	FACETS	0.332	0.304	0.361	0.332	0.304	0.361	INDETERMINATE	1	TRUE	0	0.725381982113798	1		586	837	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514015	103514015	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	221	555	0	ENST00000355739.4:c.831G>C	p.Glu277Asp	p.E277D	ENST00000355739	NM_000123.3	277	gaG/gaC	7/15	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.725381982113798	2		555	609	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543210	65543210	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876659544	NA	P-0005984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	327	499	0	ENST00000358664.4:c.467G>A	p.Arg156Gln	p.R156Q	ENST00000358664	NM_002382.4	156	cGg/cAg	5/5	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.725381982113798	2		499	857	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17124920	17124920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762370059	NA	P-0005984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	283	454	0	ENST00000285071.4:c.802C>T	p.Arg268Trp	p.R268W	ENST00000285071	NM_144997.5	268	Cgg/Tgg	8/14	0.725381982113798	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.725381982113798	1		454	468	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4090636	4090636	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749615795	NA	P-0005984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	551	651	0	ENST00000262948.5:c.1163G>A	p.Arg388Gln	p.R388Q	ENST00000262948	NM_030662.3	388	cGg/cAg	11/11	0.725381982113798	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.725381982113798	1		651	825	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143079	7143079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138897740	NA	P-0005984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	250	328	0	ENST00000302850.5:c.2290C>T	p.Leu764Phe	p.L764F	ENST00000302850	NM_000208.2	764	Ctt/Ttt	12/22	0.725381982113798	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.725381982113798	1		328	420	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739018	40739018	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	361	581	0	ENST00000373198.4:c.3266A>C	p.Lys1089Thr	p.K1089T	ENST00000373198	NM_133170.3	1089	aAg/aCg	24/32	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.725381982113798	2		581	919	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207802	102207803	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0005984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	354	817	0	ENST00000263464.3:c.1785dup	p.Lys596GlnfsTer18	p.K596Qfs*18	ENST00000263464	NM_001165.4	595	atc/atCc	9/9	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.725381982113798	2		817	952	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575152	48575152	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	357	402	0	ENST00000342988.3:c.346C>T	p.Gln116Ter	p.Q116*	ENST00000342988	NM_005359.5	116	Cag/Tag	3/12	0.408297709666868	2	FACETS	0.845	0.802	0.888	0.845	0.802	0.888	CLONAL	2	TRUE	0	0.408297709666868	2		402	1035	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955033	55955033	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0005991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	213	384	0	ENST00000263923.4:c.3510+2T>C		p.X1170_splice	ENST00000263923	NM_002253.2	1170			0.14426618868596	4	FACETS	0.84	0.781	0.9	0.84	0.781	0.9	INDETERMINATE	2	TRUE	2	0.408297709666868	4		384	875	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216518	108216518	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1214	344	538	0	ENST00000278616.4:c.8467G>A	p.Val2823Ile	p.V2823I	ENST00000278616	NM_000051.3	2823	Gtt/Att	58/63	0.409052008340033	4	FACETS	0.762	0.719	0.805	0.762	0.719	0.805	SUBCLONAL	2	TRUE	2	0.408297709666868	4		538	1558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578267	7578268	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0005991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	314	493	0	ENST00000269305.4:c.580_581dup	p.Ile195LeufsTer53	p.I195Lfs*53	ENST00000269305	NM_001126112.2	194	ctt/ctCTt	6/11	0.278571366602292	3	FACETS	1	0.981	1	0.716	0.678	0.755	CLONAL	2	TRUE	0	0.408297709666868	3		493	862	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	59	697	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.857	0.736	0.99	0.857	0.736	0.99	CLONAL	1	TRUE	1	0.17	2		697	810	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577562	7577563	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGT	novel	NA	P-0006013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	38	375	0	ENST00000269305.4:c.716_718dup	p.Asn239dup	p.N239dup	ENST00000269305	NM_001126112.2	239	agt/aACAgt	7/11	1	2	FACETS	0.726	0.599	0.868	0.726	0.599	0.868	SUBCLONAL	1	TRUE	1	0.17	2		375	616	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	146	697	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.233011217765199	3	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	1	0.2	3		697	783	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs863224683	NA	P-0006066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	82	557	0	ENST00000269305.4:c.388C>G	p.Leu130Val	p.L130V	ENST00000269305	NM_001126112.2	130	Ctc/Gtc	5/11	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.2	2		557	769	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604701	48604701	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	59	612	0	ENST00000342988.3:c.1523G>T	p.Gly508Val	p.G508V	ENST00000342988	NM_005359.5	508	gGc/gTc	12/12	0.177906148566615	1	FACETS	0.862	0.741	0.994	0.862	0.741	0.994	CLONAL	1	TRUE	0	0.2	1		612	616	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18439807	18439807	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	70	437	0	ENST00000266497.5:c.706del	p.Glu236LysfsTer17	p.E236Kfs*17	ENST00000266497		235	gtG/gt	2/31	0.233011217765199	3	FACETS	0.964	0.839	1	0.482	0.419	0.55	CLONAL	1	TRUE	1	0.2	3		437	799	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107135	27107136	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	52	340	0	ENST00000324856.7:c.6747dup	p.Glu2250ArgfsTer28	p.E2250Rfs*28	ENST00000324856	NM_006015.4	2249	tca/tcAa	20/20	0.177906148566615	1	FACETS	0.985	0.84	1	0.985	0.84	1	CLONAL	1	TRUE	0	0.2	1		340	475	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0006090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	567	485	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.641873992592877	2	FACETS	0.938	0.908	0.967	0.938	0.908	0.967	CLONAL	2	TRUE	0	0.651480589966491	2		485	928	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383210	4383210	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2088	128	252	0	ENST00000261254.3:c.4G>A	p.Glu2Lys	p.E2K	ENST00000261254	NM_001759.3	2	Gag/Aag	1/5	0.651480589966491	30	FACETS	0.897	0.809	0.991			1	CLONAL	2	TRUE	NA	0.651480589966491	30		252	2216	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562981	29562981	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs376576925	NA	P-0006090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	1114	486	1	ENST00000356175.3:c.3916C>T	p.Arg1306Ter	p.R1306*	ENST00000356175	NM_000267.3	1306	Cga/Tga	29/57	0.651480589966491	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	4	TRUE	0	0.651480589966491	4		487	1389	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189872	11189872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	251	364	0	ENST00000361445.4:c.5637G>A	p.Met1879Ile	p.M1879I	ENST00000361445	NM_004958.3	1879	atG/atA	40/58	0.651480589966491	2	FACETS	1	0.982	1	0.553	0.52	0.586	CLONAL	1	TRUE	0	0.651480589966491	2		364	697	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401883	139401883	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs753060918	NA	P-0006090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	180	348	0	ENST00000277541.6:c.3517G>T	p.Ala1173Ser	p.A1173S	ENST00000277541	NM_017617.3	1173	Gcc/Tcc	22/34	0.651480589966491	2	FACETS	1	0.949	1	0.514	0.477	0.551	CLONAL	1	TRUE	0	0.651480589966491	2		348	538	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172382	108172382	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs3092907	NA	P-0006090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	187	295	0	ENST00000278616.4:c.5185G>C	p.Val1729Leu	p.V1729L	ENST00000278616	NM_000051.3	1729	Gtt/Ctt	35/63	0.648067183394389	4	FACETS	0.982	0.908	1	0.491	0.454	0.53	CLONAL	1	TRUE	2	0.651480589966491	4		295	965	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989602	15989602	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	215	326	0	ENST00000268712.3:c.3171C>G	p.Ile1057Met	p.I1057M	ENST00000268712	NM_006311.3	1057	atC/atG	23/46	0.641873992592877	2	FACETS	0.952	0.889	1	0.476	0.444	0.509	CLONAL	1	TRUE	0	0.651480589966491	2		326	693	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255704	16255705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	400	247	0	ENST00000375759.3:c.2971dup	p.Ser991PhefsTer31	p.S991Ffs*31	ENST00000375759	NM_015001.2	990	gat/gaTt	11/15	0.324277159123692	3	FACETS	0.901	0.87	0.932			1	INDETERMINATE	3	TRUE	NA	0.651480589966491	3		247	602	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0006174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	320	607	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.815620839072126	1	FACETS	0.887	0.85	0.923	0.887	0.85	0.923	CLONAL	1	TRUE	0	0.815620839072126	1		607	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0006174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	22	464	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.815620839072126	1	FACETS	0.069	0.053	0.087	0.069	0.053	0.087	SUBCLONAL	1	TRUE	0	0.815620839072126	1		464	465	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982019	38982019	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1784	897	318	0	ENST00000357387.3:c.703C>T	p.Leu235Phe	p.L235F	ENST00000357387	NM_152756.3	235	Ctt/Ttt	8/38	0.815620839072126	10	FACETS	1	0.996	1			1	CLONAL	3	TRUE	NA	0.815620839072126	10		318	2681	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81957157	81957157	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202210217	NA	P-0006174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	427	664	2	ENST00000359376.3:c.2375G>A	p.Arg792His	p.R792H	ENST00000359376	NM_002661.3	792	cGt/cAt	22/33	0.209226702958158	1	FACETS	0.556	0.531	0.582	0.556	0.531	0.582	INDETERMINATE	1	TRUE	0	0.815620839072126	1		666	1115	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965167	81965167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17856213	NA	P-0006174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	398	757	2	ENST00000359376.3:c.2647G>A	p.Asp883Asn	p.D883N	ENST00000359376	NM_002661.3	883	Gat/Aat	25/33	0.209226702958158	1	FACETS	0.494	0.47	0.518	0.494	0.47	0.518	INDETERMINATE	1	TRUE	0	0.815620839072126	1		759	1171	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579563	7579564	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATCCATTG	novel	NA	P-0006174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	19	356	1	ENST00000269305.4:c.116_123dup	p.Asp42GlnfsTer5	p.D42Qfs*5	ENST00000269305	NM_001126112.2	41	-/CAATGGAT	4/11	0.815620839072126	1	FACETS	0.08	0.06	0.103	0.08	0.06	0.103	SUBCLONAL	1	TRUE	0	0.815620839072126	1		357	347	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0006189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	246	480	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	0.837	0.783	0.892	0.837	0.783	0.892	CLONAL	1	TRUE	1	0.628994611305764	2		480	935	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29107974	29107974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121908702	NA	P-0006189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	133	631	0	ENST00000328354.6:c.715G>A	p.Glu239Lys	p.E239K	ENST00000328354	NM_007194.3	239	Gag/Aag	6/15	0.628994611305764	1	FACETS	0.828	0.762	0.896	0.828	0.762	0.896	CLONAL	1	TRUE	0	0.628994611305764	1		631	350	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15952173	15952182	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTGCGCCC	CTCTGCGCCC	-	novel	NA	P-0006189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	222	525	0	ENST00000268712.3:c.6513_6522del	p.Arg2171SerfsTer15	p.R2171Sfs*15	ENST00000268712	NM_006311.3	2171	agGGGCGCAGAG/ag	41/46	0.628994611305764	1	FACETS	0.932	0.876	0.989	0.932	0.876	0.989	CLONAL	1	TRUE	0	0.628994611305764	1		525	519	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089741	27089741	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	106	262	0	ENST00000324856.7:c.2697del	p.Ala900ProfsTer19	p.A900Pfs*19	ENST00000324856	NM_006015.4	899	gtC/gt	8/20	1	2	FACETS	0.908	0.822	0.998	0.908	0.822	0.998	CLONAL	1	TRUE	1	0.628994611305764	2		262	371	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244435	46244438	+	frameshift_variant	Frame_Shift_Del	DEL	AGAT	AGAT	-	novel	NA	P-0006189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	161	575	0	ENST00000334344.6:c.2530_2533del	p.Asp844LeufsTer4	p.D844Lfs*4	ENST00000334344	NM_152641.2	843	caAGAT/ca	15/21	0.616083169902745	2	FACETS	1	0.956	1	0.525	0.485	0.565	CLONAL	1	TRUE	0	0.628994611305764	2		575	488	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175802	24175802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	67	487	0	ENST00000263121.7:c.1030G>A	p.Gly344Ser	p.G344S	ENST00000263121	NM_003073.3	344	Ggc/Agc	8/9	0.673688628320241	1	FACETS	0.473	0.415	0.534	0.473	0.415	0.534	SUBCLONAL	1	TRUE	0	0.673688628320241	1		487	279	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165346	47165347	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0006197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	33	359	0	ENST00000409792.3:c.779dup	p.Asn261Ter	p.N261*	ENST00000409792	NM_014159.6	260	tct/tcCt	3/21	0.673688628320241	1	FACETS	0.16	0.13	0.193	0.16	0.13	0.193	SUBCLONAL	1	TRUE	0	0.673688628320241	1		359	407	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441465	52441477	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	ATATCCTTTGCTC	ATATCCTTTGCTC	T	novel	NA	P-0006197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	168	406	0	ENST00000460680.1:c.376-1_387delinsA		p.X126_splice	ENST00000460680	NM_004656.3	126		6/17	0.673688628320241	1	FACETS	0.956	0.893	1	0.956	0.893	1	CLONAL	1	TRUE	0	0.673688628320241	1		406	346	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0006219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	68	348	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.426977902817825	2		348	275	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0006219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	107	487	1	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	0.414793345339022	2	FACETS	0.886	0.807	0.966	0.886	0.807	0.966	CLONAL	2	TRUE	0	0.426977902817825	2		488	283	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178577	56178579	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs750747779	NA	P-0006219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	56	500	0	ENST00000399503.3:c.3560_3562del	p.Glu1187del	p.E1187del	ENST00000399503	NM_005921.1	1184	GAA/-	14/20	1	2	FACETS	0.747	0.643	0.86	0.747	0.643	0.86	SUBCLONAL	1	TRUE	1	0.426977902817825	2		500	351	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794524	42794524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143443453	NA	P-0006219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	165	550	0	ENST00000575354.2:c.1604C>T	p.Ser535Phe	p.S535F	ENST00000575354	NM_015125.3	535	tCt/tTt	10/20	1	2	FACETS	0.838	0.77	0.91	0.838	0.77	0.91	CLONAL	1	TRUE	1	0.426977902817825	2		550	922	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354235	70354235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1174792640	NA	P-0006219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	195	659	0	ENST00000374080.3:c.4646G>A	p.Arg1549His	p.R1549H	ENST00000374080		1549	cGc/cAc	34/45	0.215746997463314	0	FACETS	0.508	0.469	0.547			1	INDETERMINATE	1	TRUE	0	0.426977902817825	0		659	1031	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589583	67589584	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACATGA	novel	NA	P-0006219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	63	332	0	ENST00000274335.5:c.1348_1353dup	p.His450_Glu451dup	p.H450_E451dup	ENST00000274335		450	tta/ttACATGAa	10/15	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.426977902817825	2		332	294	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	184	243	1	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	0.225868100953197	4	FACETS	0.844	0.78	0.91	0.844	0.78	0.91	CLONAL	3	TRUE	1	0.225868100953197	4		244	789	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161907	47161907	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	78	772	1	ENST00000409792.3:c.4219del	p.Arg1407GlyfsTer5	p.R1407Gfs*5	ENST00000409792	NM_014159.6	1407	Agg/gg	3/21	0.225392746175897	3	FACETS	0.783	0.69	0.882	0.783	0.69	0.882	SUBCLONAL	2	TRUE	1	0.225868100953197	3		773	491	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	123	398	1	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	0.225392746175897	3	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	1	0.225868100953197	3		399	581	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793238	42793238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763699553	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	378	372	0	ENST00000575354.2:c.1130C>T	p.Thr377Met	p.T377M	ENST00000575354	NM_015125.3	377	aCg/aTg	7/20	0.225868100953197	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	1	0.225868100953197	4		372	1181	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196213	106196213	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs370735654	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	56	535	0	ENST00000380013.4:c.4546C>T	p.Arg1516Ter	p.R1516*	ENST00000380013	NM_001127208.2	1516	Cga/Tga	11/11	0.225868100953197	3	FACETS	0.942	0.807	1	0.471	0.403	0.545	CLONAL	1	TRUE	1	0.225868100953197	3		535	586	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	54	430	2	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	0.225868100953197	4	FACETS	0.793	0.676	0.922	0.264	0.225	0.308	CLONAL	1	TRUE	1	0.225868100953197	4		432	739	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	119	345	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	0.225392746175897	3	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	1	0.225868100953197	3		345	561	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827964	72827964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768307205	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1286	170	565	0	ENST00000268489.5:c.8617G>A	p.Glu2873Lys	p.E2873K	ENST00000268489	NM_006885.3	2873	Gaa/Aaa	9/10	0.225392746175897	3	FACETS	1	0.974	1	0.575	0.527	0.626	CLONAL	1	TRUE	1	0.225868100953197	3		565	1456	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156747	106156747	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs572712965	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	104	356	0	ENST00000380013.4:c.1648C>T	p.Arg550Ter	p.R550*	ENST00000380013	NM_001127208.2	550	Cga/Tga	3/11	0.225868100953197	3	FACETS	0.885	0.795	0.981	0.885	0.795	0.981	CLONAL	2	TRUE	1	0.225868100953197	3		356	579	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	86	253	1	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	0.225868100953197	4	FACETS	0.784	0.692	0.885	0.261	0.23	0.295	SUBCLONAL	1	TRUE	1	0.225868100953197	4		254	1190	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482926	140482927	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs777474487	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	105	438	1	ENST00000288602.6:c.1208dup	p.Ala404CysfsTer9	p.A404Cfs*9	ENST00000288602	NM_004333.4	403	cct/ccCt	10/18	0.224416505942368	4	FACETS	0.83	0.744	0.92	0.83	0.744	0.92	CLONAL	2	TRUE	2	0.225868100953197	4		439	687	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261497	16261497	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	60	270	1	ENST00000375759.3:c.8762C>T	p.Thr2921Met	p.T2921M	ENST00000375759	NM_015001.2	2921	aCg/aTg	11/15	0.225868100953197	4	FACETS	0.759	0.652	0.876	0.253	0.217	0.292	SUBCLONAL	1	TRUE	1	0.225868100953197	4		271	858	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726951	46726951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141226335	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	83	408	0	ENST00000371975.4:c.785G>A	p.Arg262His	p.R262H	ENST00000371975	NM_003579.3	262	cGt/cAt	8/18	0.225868100953197	4	FACETS	0.867	0.763	0.979	0.289	0.254	0.327	CLONAL	1	TRUE	1	0.225868100953197	4		408	1039	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165791	118165791	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	70	236	0	ENST00000369448.3:c.301A>T	p.Thr101Ser	p.T101S	ENST00000369448	NM_017709.3	101	Aca/Tca	2/2	0.189041914388544	3	FACETS	0.976	0.85	1			1	CLONAL	1	TRUE	NA	0.225868100953197	3		236	707	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497679	120497679	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	53	293	0	ENST00000256646.2:c.2203A>G	p.Thr735Ala	p.T735A	ENST00000256646	NM_024408.3	735	Act/Gct	13/34	0.224416505942368	4	FACETS	1	0.937	1	0.593	0.506	0.688	CLONAL	1	TRUE	2	0.225868100953197	4		293	485	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204515958	204515958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779541672	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	60	397	1	ENST00000367182.3:c.856G>A	p.Asp286Asn	p.D286N	ENST00000367182	NM_001278516.1	286	Gac/Aac	10/11	0.224416505942368	4	FACETS	0.891	0.766	1	0.445	0.383	0.514	CLONAL	1	TRUE	2	0.225868100953197	4		398	731	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243801023	243801023	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	48	243	0	ENST00000263826.5:c.451T>G	p.Leu151Val	p.L151V	ENST00000263826	NM_005465.4	151	Ttg/Gtg	5/13	0.224416505942368	4	FACETS	1	0.89	1	0.533	0.45	0.623	CLONAL	1	TRUE	2	0.225868100953197	4		243	489	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551263	29551263	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	110	364	1	ENST00000389048.3:c.1367A>G	p.Asp456Gly	p.D456G	ENST00000389048	NM_004304.4	456	gAc/gGc	6/29	0.225868100953197	4	FACETS	0.97	0.869	1	0.485	0.434	0.539	CLONAL	1	TRUE	2	0.225868100953197	4		365	1231	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630543	47630543	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1060501993	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	115	244	0	ENST00000233146.2:c.211+2T>C		p.X71_splice	ENST00000233146	NM_000251.2	71			0.225868100953197	4	FACETS	0.965	0.871	1	0.965	0.871	1	CLONAL	2	TRUE	2	0.225868100953197	4		244	647	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113151	209113151	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780642190	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	101	312	0	ENST00000345146.2:c.356G>A	p.Arg119Gln	p.R119Q	ENST00000345146	NM_005896.2	119	cGg/cAg	4/10	0.225392746175897	3	FACETS	0.861	0.771	0.956	0.861	0.771	0.956	CLONAL	2	TRUE	1	0.225868100953197	3		312	578	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659734	227659734	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1022427396	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	62	359	0	ENST00000305123.5:c.3721C>T	p.Arg1241Cys	p.R1241C	ENST00000305123	NM_005544.2	1241	Cgt/Tgt	1/2	0.225392746175897	3	FACETS	0.731	0.63	0.841	0.365	0.315	0.421	SUBCLONAL	1	TRUE	1	0.225868100953197	3		359	836	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582439	119582439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775606264	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	31	254	0	ENST00000316626.5:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000316626		321	cGa/cAa	10/12	0.225392746175897	3	FACETS	0.955	0.774	1	0.477	0.387	0.579	CLONAL	1	TRUE	1	0.225868100953197	3		254	320	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191254	185191254	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	55	211	0	ENST00000265026.3:c.2135A>G	p.Glu712Gly	p.E712G	ENST00000265026	NM_004721.4	712	gAg/gGg	11/14	0.225392746175897	3	FACETS	0.896	0.766	1	0.448	0.383	0.519	CLONAL	1	TRUE	1	0.225868100953197	3		211	605	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271252	1271252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	104	311	0	ENST00000310581.5:c.2450C>T	p.Ala817Val	p.A817V	ENST00000310581	NM_198253.2	817	gCc/gTc	8/16	0.225392746175897	3	FACETS	1	0.972	1	0.626	0.56	0.697	CLONAL	1	TRUE	1	0.225868100953197	3		311	818	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947451	38947451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	75	411	1	ENST00000357387.3:c.4229G>A	p.Arg1410Gln	p.R1410Q	ENST00000357387	NM_152756.3	1410	cGg/cAg	32/38	0.225392746175897	3	FACETS	1	0.909	1	0.523	0.458	0.593	CLONAL	1	TRUE	1	0.225868100953197	3		412	707	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86648996	86648996	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	35	262	0	ENST00000274376.6:c.1276T>C	p.Tyr426His	p.Y426H	ENST00000274376	NM_002890.2	426	Tat/Cat	9/25	0.225392746175897	3	FACETS	0.686	0.561	0.826	0.343	0.28	0.413	SUBCLONAL	1	TRUE	1	0.225868100953197	3		262	503	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672822	86672822	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	83	255	0	ENST00000274376.6:c.2309T>C	p.Leu770Ser	p.L770S	ENST00000274376	NM_002890.2	770	tTa/tCa	17/25	0.225392746175897	3	FACETS	0.794	0.703	0.892	0.794	0.703	0.892	SUBCLONAL	2	TRUE	1	0.225868100953197	3		255	515	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523337	176523337	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	189	386	0	ENST00000292408.4:c.1994T>C	p.Val665Ala	p.V665A	ENST00000292408	NM_213647.1	665	gTg/gCg	15/18	0.225392746175897	3	FACETS	0.968	0.895	1	0.968	0.895	1	CLONAL	2	TRUE	1	0.225868100953197	3		386	962	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398845	398845	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	109	405	0	ENST00000380956.4:c.655A>G	p.Thr219Ala	p.T219A	ENST00000380956	NM_001195286.1	219	Acc/Gcc	6/9	0.225868100953197	4	FACETS	1	0.962	1	0.579	0.519	0.643	CLONAL	1	TRUE	2	0.225868100953197	4		405	1022	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250602	26250602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1378609792	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1686	369	787	0	ENST00000446824.2:c.232G>A	p.Asp78Asn	p.D78N	ENST00000446824	NM_021018.2	78	Gac/Aac	1/1	0.225868100953197	4	FACETS	0.975	0.921	1	0.975	0.921	1	CLONAL	2	TRUE	2	0.225868100953197	4		787	2055	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43738990	43738990	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	66	314	0	ENST00000523873.1:c.7T>C	p.Phe3Leu	p.F3L	ENST00000523873		3	Ttt/Ctt	1/8	0.169929373243681	4	FACETS	0.711	0.616	0.816	0.356	0.308	0.408	SUBCLONAL	1	TRUE	2	0.225868100953197	4		314	1007	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983042	111983042	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1462	111	548	0	ENST00000368678.4:c.1505A>T	p.Lys502Met	p.K502M	ENST00000368678		502	aAg/aTg	13/13	0.169929373243681	4	FACETS	0.766	0.686	0.852	0.383	0.343	0.426	SUBCLONAL	1	TRUE	2	0.225868100953197	4		548	1573	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129285	152129285	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	99	367	0	ENST00000206249.3:c.238T>C	p.Tyr80His	p.Y80H	ENST00000206249	NM_000125.3	80	Tac/Cac	1/8	0.169929373243681	4	FACETS	1	0.918	1	0.518	0.461	0.579	CLONAL	1	TRUE	2	0.225868100953197	4		367	1037	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845624	128845624	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	98	304	0	ENST00000249373.3:c.920+1G>A		p.X307_splice	ENST00000249373	NM_005631.4	307			0.224416505942368	4	FACETS	1	0.945	1	0.549	0.489	0.614	CLONAL	1	TRUE	2	0.225868100953197	4		304	968	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132765	152132765	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	108	265	0	ENST00000262189.6:c.107C>A	p.Pro36His	p.P36H	ENST00000262189	NM_170606.2	36	cCt/cAt	1/59	0.224416505942368	4	FACETS	1	0.98	1	0.706	0.633	0.784	CLONAL	1	TRUE	2	0.225868100953197	4		265	830	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74859009	74859009	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	40	85	0	ENST00000284811.8:c.195A>G	p.Ile65Met	p.I65M	ENST00000284811		65	atA/atG	4/4	0.225868100953197	4	FACETS	1	0.938	1	0.832	0.701	0.973	CLONAL	2	TRUE	1	0.225868100953197	4		85	174	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139408984	139408984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	153	321	1	ENST00000277541.6:c.2185G>A	p.Ala729Thr	p.A729T	ENST00000277541	NM_017617.3	729	Gcc/Acc	13/34	0.224416505942368	4	FACETS	0.96	0.878	1	0.96	0.878	1	CLONAL	2	TRUE	2	0.225868100953197	4		322	865	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498238	498238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	27	178	0	ENST00000399788.2:c.20G>A	p.Gly7Glu	p.G7E	ENST00000399788	NM_001042603.1	7	gGg/gAg	1/28	0.224416505942368	4	FACETS	0.553	0.439	0.684	0.276	0.219	0.342	SUBCLONAL	1	TRUE	2	0.225868100953197	4		178	530	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428701	49428701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761409666	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	68	323	0	ENST00000301067.7:c.10249G>A	p.Ala3417Thr	p.A3417T	ENST00000301067	NM_003482.3	3417	Gca/Aca	35/54	0.225868100953197	5	FACETS	0.905	0.785	1	0.226	0.196	0.259	CLONAL	1	TRUE	1	0.225868100953197	5		323	891	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28674622	28674622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	30	33	0	ENST00000241453.7:c.26G>A	p.Gly9Asp	p.G9D	ENST00000241453	NM_004119.2	9	gGc/gAc	1/24	0.225868100953197	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	2	TRUE	0	0.225868100953197	2		33	110	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041262	29041262	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	40	221	0	ENST00000282397.4:c.166G>A	p.Glu56Lys	p.E56K	ENST00000282397	NM_002019.4	56	Gaa/Aaa	3/30	0.225868100953197	2	FACETS	1	0.845	1	0.507	0.423	0.601	CLONAL	1	TRUE	0	0.225868100953197	2		221	349	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435096	110435096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1035281355	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	129	210	0	ENST00000375856.3:c.3305C>T	p.Thr1102Met	p.T1102M	ENST00000375856	NM_003749.2	1102	aCg/aTg	1/2	0.225868100953197	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.225868100953197	2		210	516	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873814	35873814	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	38	189	0	ENST00000216797.5:c.37A>G	p.Met13Val	p.M13V	ENST00000216797	NM_020529.2	13	Atg/Gtg	1/6	0.169929373243681	4	FACETS	0.579	0.477	0.693	0.289	0.238	0.347	SUBCLONAL	1	TRUE	2	0.225868100953197	4		189	713	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239366	105239366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1340200537	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	189	391	0	ENST00000349310.3:c.1021G>A	p.Glu341Lys	p.E341K	ENST00000349310	NM_001014432.1	341	Gag/Aag	12/15	0.169929373243681	4	FACETS	0.905	0.835	0.977	0.905	0.835	0.977	CLONAL	2	TRUE	2	0.225868100953197	4		391	1134	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358670	67358670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	110	373	0	ENST00000327367.4:c.178G>A	p.Val60Ile	p.V60I	ENST00000327367	NM_005902.3	60	Gtc/Atc	1/9	0.225392746175897	3	FACETS	0.968	0.867	1	0.484	0.433	0.538	CLONAL	1	TRUE	1	0.225868100953197	3		373	1120	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348116	348116	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762212925	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	175	286	0	ENST00000262320.3:c.1390G>A	p.Glu464Lys	p.E464K	ENST00000262320	NM_003502.3	464	Gag/Aag	6/11	0.225868100953197	5	FACETS	1	0.972	1	0.747	0.688	0.808	CLONAL	2	TRUE	2	0.225868100953197	5		286	926	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396464	396464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	219	371	0	ENST00000262320.3:c.562G>A	p.Glu188Lys	p.E188K	ENST00000262320	NM_003502.3	188	Gaa/Aaa	2/11	0.225868100953197	5	FACETS	1	0.942	1	0.678	0.629	0.728	CLONAL	2	TRUE	2	0.225868100953197	5		371	1277	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2132492	2132492	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	89	394	1	ENST00000219476.3:c.3870C>A	p.Ser1290Arg	p.S1290R	ENST00000219476	NM_000548.3	1290	agC/agA	32/42	0.225868100953197	5	FACETS	0.878	0.776	0.988	0.293	0.258	0.33	CLONAL	1	TRUE	2	0.225868100953197	5		395	1202	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352462	89352462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	134	498	2	ENST00000301030.4:c.877G>A	p.Glu293Lys	p.E293K	ENST00000301030	NM_001256183.1	293	Gag/Aag	8/13	0.225392746175897	3	FACETS	1	0.92	1	0.509	0.461	0.56	CLONAL	1	TRUE	1	0.225868100953197	3		500	1298	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024494	16024494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	56	363	0	ENST00000268712.3:c.1724C>T	p.Ala575Val	p.A575V	ENST00000268712	NM_006311.3	575	gCc/gTc	16/46	0.169929373243681	4	FACETS	0.651	0.556	0.755	0.325	0.278	0.378	SUBCLONAL	1	TRUE	2	0.225868100953197	4		363	934	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47679349	47679349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	55	263	1	ENST00000347630.2:c.858G>T	p.Lys286Asn	p.K286N	ENST00000347630	NM_001007230.1	286	aaG/aaT	10/11	0.225868100953197	5	FACETS	1	0.892	1	0.263	0.225	0.306	CLONAL	1	TRUE	1	0.225868100953197	5		264	619	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58700951	58700951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs927779565	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	350	611	0	ENST00000305921.3:c.542G>A	p.Arg181Gln	p.R181Q	ENST00000305921	NM_003620.3	181	cGg/cAg	2/6	0.225868100953197	5	FACETS	0.983	0.93	1	0.737	0.697	0.778	CLONAL	3	TRUE	1	0.225868100953197	5		611	1407	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526442	66526442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	41	265	0	ENST00000358598.2:c.998G>A	p.Arg333His	p.R333H	ENST00000358598	NM_212471.2	333	cGt/cAt	11/11	0.225868100953197	5	FACETS	1	0.879	1	0.267	0.222	0.317	CLONAL	1	TRUE	1	0.225868100953197	5		265	455	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368233	45368233	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	76	410	0	ENST00000262160.6:c.1369G>A	p.Gly457Arg	p.G457R	ENST00000262160	NM_005901.5	457	Gga/Aga	11/11	0.225392746175897	3	FACETS	0.893	0.782	1	0.446	0.391	0.507	CLONAL	1	TRUE	1	0.225868100953197	3		410	839	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218466	5218466	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	79	429	1	ENST00000357368.4:c.4013C>A	p.Pro1338His	p.P1338H	ENST00000357368	NM_002850.3	1338	cCt/cAt	25/38	0.225868100953197	3	FACETS	0.735	0.645	0.833	0.245	0.215	0.278	SUBCLONAL	1	TRUE	0	0.225868100953197	3		430	1059	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951085	17951085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	93	399	2	ENST00000458235.1:c.1208G>A	p.Arg403His	p.R403H	ENST00000458235	NM_000215.3	403	cGc/cAc	9/24	0.225868100953197	4	FACETS	0.858	0.76	0.962	0.286	0.253	0.321	CLONAL	1	TRUE	1	0.225868100953197	4		401	1177	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253876	30253876	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	60	213	0	ENST00000307677.4:c.578A>G	p.Glu193Gly	p.E193G	ENST00000307677	NM_138578.1	193	gAa/gGa	3/3	0.189041914388544	3	FACETS	0.845	0.727	0.973			1	CLONAL	1	TRUE	NA	0.225868100953197	3		213	700	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288269	21288269	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1293	96	537	0	ENST00000354336.3:c.514A>G	p.Met172Val	p.M172V	ENST00000354336	NM_005207.3	172	Atg/Gtg	2/3	0.225868100953197	7	FACETS	0.958	0.85	1	0.239	0.212	0.269	CLONAL	1	TRUE	3	0.225868100953197	7		537	1389	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536193	41536193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	71	336	1	ENST00000263253.7:c.1810C>T	p.Arg604Trp	p.R604W	ENST00000263253	NM_001429.3	604	Cgg/Tgg	9/31	0.225868100953197	7	FACETS	1	0.901	1	0.26	0.226	0.297	CLONAL	1	TRUE	3	0.225868100953197	7		337	945	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222238	53222238	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	74	323	0	ENST00000375401.3:c.4594A>C	p.Thr1532Pro	p.T1532P	ENST00000375401	NM_004187.3	1532	Acc/Ccc	26/26	0.19029376331587	1	FACETS	0.785	0.687	0.892	0.785	0.687	0.892	SUBCLONAL	1	TRUE	0	0.225868100953197	1		323	740	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178635	32178635	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs761063325	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	115	376	2	ENST00000375023.3:c.2759del	p.Pro920LeufsTer12	p.P920Lfs*12	ENST00000375023	NM_004557.3	920	cCt/ct	18/30	0.169929373243681	4	FACETS	1	0.91	1	0.507	0.455	0.562	CLONAL	1	TRUE	2	0.225868100953197	4		378	1231	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719272	190719272	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	29	247	0	ENST00000441310.2:c.1276del	p.Ser426LeufsTer16	p.S426Lfs*16	ENST00000441310	NM_000534.4	425	aTt/at	9/13	0.225392746175897	3	FACETS	0.684	0.548	0.838	0.342	0.274	0.419	SUBCLONAL	1	TRUE	1	0.225868100953197	3		247	418	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871043	12871044	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	102	296	0	ENST00000228872.4:c.275dup	p.Arg93AlafsTer32	p.R93Afs*32	ENST00000228872	NM_004064.3	90	-/C	1/3	0.224416505942368	4	FACETS	1	0.981	1	0.731	0.654	0.814	CLONAL	1	TRUE	2	0.225868100953197	4		296	757	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443611	29443612	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	61	369	2	ENST00000389048.3:c.3605dup	p.Asp1203ArgfsTer82	p.D1203Rfs*82	ENST00000389048	NM_004304.4	1202	gga/ggGa	23/29	0.225868100953197	4	FACETS	0.6	0.516	0.693	0.3	0.258	0.347	SUBCLONAL	1	TRUE	2	0.225868100953197	4		371	1103	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281435	142281435	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	58	347	0	ENST00000350721.4:c.809del	p.Phe270SerfsTer8	p.F270Sfs*8	ENST00000350721	NM_001184.3	270	tTc/tc	4/47	0.225392746175897	3	FACETS	0.929	0.798	1	0.465	0.399	0.537	CLONAL	1	TRUE	1	0.225868100953197	3		347	615	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639588	47639588	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63749897	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	151	317	0	ENST00000233146.2:c.687del	p.Ala230LeufsTer16	p.A230Lfs*16	ENST00000233146	NM_000251.2	227	agA/ag	4/16	0.225868100953197	4	FACETS	0.867	0.792	0.946	0.867	0.792	0.946	CLONAL	2	TRUE	2	0.225868100953197	4		317	945	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340050	116340050	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	35	232	0	ENST00000397752.3:c.917del	p.Lys306ArgfsTer28	p.K306Rfs*28	ENST00000397752	NM_000245.2	304	agA/ag	2/21	0.224416505942368	4	FACETS	0.945	0.775	1	0.473	0.387	0.568	CLONAL	1	TRUE	2	0.225868100953197	4		232	402	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70001016	70001016	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	42	391	0	ENST00000394351.3:c.617del	p.Lys206ArgfsTer6	p.K206Rfs*6	ENST00000394351	NM_000248.3	205	Aaa/aa	6/9	0.225392746175897	3	FACETS	0.585	0.487	0.694	0.292	0.243	0.347	SUBCLONAL	1	TRUE	1	0.225868100953197	3		391	708	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562957	29562958	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	73	426	0	ENST00000356175.3:c.3897dup	p.Leu1300ThrfsTer14	p.L1300Tfs*14	ENST00000356175	NM_000267.3	1298	caa/cAaa	29/57	0.169929373243681	4	FACETS	0.976	0.852	1	0.488	0.426	0.555	CLONAL	1	TRUE	2	0.225868100953197	4		426	812	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89869710	89869710	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	188	423	0	ENST00000389301.3:c.749del	p.Asn250ThrfsTer4	p.N250Tfs*4	ENST00000389301	NM_000135.2	250	aAc/ac	8/43	0.225868100953197	5	FACETS	1	0.978	1			1	CLONAL	2	TRUE	NA	0.225868100953197	5		423	969	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123615	108123616	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs786202474	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	36	221	0	ENST00000278616.4:c.1880dup	p.Gln628ProfsTer7	p.Q628Pfs*7	ENST00000278616	NM_000051.3	625	aat/aaTt	12/63	1	2	FACETS	0.728	0.598	0.873	0.728	0.598	0.873	SUBCLONAL	1	TRUE	1	0.225868100953197	2		221	438	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220432	1220432	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	332	451	0	ENST00000326873.7:c.526del	p.Asp176ThrfsTer111	p.D176Tfs*111	ENST00000326873	NM_000455.4	175	aaG/aa	4/10	0.225868100953197	3	FACETS	1	0.951	1	1	0.951	1	CLONAL	3	TRUE	0	0.225868100953197	3		451	1085	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630494	47630513	+	frameshift_variant	Frame_Shift_Del	DEL	GGGAGGTGTTCAAGACCCAG	GGGAGGTGTTCAAGACCCAG	-	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	164	337	0	ENST00000233146.2:c.167_186del	p.Glu56GlyfsTer19	p.E56Gfs*19	ENST00000233146	NM_000251.2	55	cGGGAGGTGTTCAAGACCCAG/c	1/16	0.225868100953197	4	FACETS	0.873	0.801	0.949	0.873	0.801	0.949	CLONAL	2	TRUE	2	0.225868100953197	4		337	1019	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863319	57863319	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	566	567	2	ENST00000228682.2:c.1418del	p.Gly473AlafsTer40	p.G473Afs*40	ENST00000228682	NM_005269.2	472	Ggg/gg	11/12	0.225868100953197	5	FACETS	0.991	0.951	1	0.991	0.951	1	CLONAL	4	TRUE	1	0.225868100953197	5		569	1692	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072525	5072526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	70	251	0	ENST00000381652.3:c.1680dup	p.Lys561Ter	p.K561*	ENST00000381652	NM_004972.3	559	att/aTtt	13/25	0.212729267191925	2	FACETS	0.801	0.702	0.907	0.801	0.702	0.907	CLONAL	2	TRUE	0	0.225868100953197	2		251	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0006374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	71	417	4	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	0.188678466855098	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.201396872601148	1		421	531	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859704	151859704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1019840408	NA	P-0006374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	50	441	1	ENST00000262189.6:c.10958C>T	p.Pro3653Leu	p.P3653L	ENST00000262189	NM_170606.2	3653	cCt/cTt	43/59	1	2	FACETS	0.798	0.676	0.932	0.798	0.676	0.932	CLONAL	1	TRUE	1	0.201396872601148	2		442	622	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971122	21971123	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	34	297	0	ENST00000304494.5:c.235dup	p.Thr79AsnfsTer41	p.T79Nfs*41	ENST00000304494	NM_000077.4	79	acc/aAcc	2/3	0.188678466855098	1	FACETS	0.853	0.698	1	0.853	0.698	1	CLONAL	1	TRUE	0	0.201396872601148	1		297	356	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380277	+	missense_variant	Missense_Mutation	DNP	TG	TG	GC	novel	NA	P-0006374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	52	428	0	ENST00000311936.3:c.181_182delinsGC	p.Gln61Ala	p.Q61A	ENST00000311936	NM_004985.3	61	CAa/GCa	3/5	0.119648565011822	3	FACETS	0.955	0.813	1	0.478	0.406	0.556	INDETERMINATE	1	TRUE	1	0.201396872601148	3		428	595	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087503	27087503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	245	618	2	ENST00000324856.7:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000324856	NM_006015.4	693	Cga/Tga	5/20	0.60639296740418	1	FACETS	0.708	0.664	0.754	0.708	0.664	0.754	SUBCLONAL	1	TRUE	0	0.60639296740418	1		620	795	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881002	37881003	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCTCCCCA	rs397516982	NA	P-0006376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	436	483	0	ENST00000269571.5:c.2332_2340dup	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	-/GGCTCCCCA	20/27	1	2	FACETS	0.974	0.927	1	0.974	0.927	1	CLONAL	1	TRUE	1	0.60639296740418	2		483	1477	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562734	29562734	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	278	665	1	ENST00000356175.3:c.3814C>T	p.Gln1272Ter	p.Q1272*	ENST00000356175	NM_000267.3	1272	Cag/Tag	28/57	1	2	FACETS	0.978	0.92	1	0.978	0.92	1	CLONAL	1	TRUE	1	0.60639296740418	2		666	938	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023830	27023831	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0006376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	66	594	0	ENST00000324856.7:c.941dup	p.Asp315ArgfsTer85	p.D315Rfs*85	ENST00000324856	NM_006015.4	312	-/G	1/20	0.60639296740418	1	FACETS	0.223	0.193	0.255	0.223	0.193	0.255	SUBCLONAL	1	TRUE	0	0.60639296740418	1		594	681	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508508	29508509	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0006376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	234	734	0	ENST00000356175.3:c.654+2dup		p.X218_splice	ENST00000356175	NM_000267.3	218			1	2	FACETS	0.989	0.926	1	0.989	0.926	1	CLONAL	1	TRUE	1	0.60639296740418	2		734	780	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682418	52682418	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006392-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	176	625	1	ENST00000394830.3:c.755T>G	p.Ile252Arg	p.I252R	ENST00000394830	NM_018313.4	252	aTa/aGa	8/30	0.377564274316048	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.377564274316048	1		626	662	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349582	89349582	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006392-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	88	858	0	ENST00000301030.4:c.3368G>T	p.Ser1123Ile	p.S1123I	ENST00000301030	NM_001256183.1	1123	aGt/aTt	9/13	1	2	FACETS	0.36	0.317	0.405	0.36	0.317	0.405	SUBCLONAL	1	TRUE	1	0.377564274316048	2		858	1296	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228341	53228341	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0006392-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	21	213	0	ENST00000375401.3:c.2062-1G>A		p.X688_splice	ENST00000375401	NM_004187.3	688			1	1	FACETS	0.254	0.195	0.323	0.254	0.195	0.323	SUBCLONAL	1	TRUE	0	0.377564274316048	1		213	355	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191517	10191518	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006392-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	114	479	0	ENST00000256474.2:c.512dup	p.Pro172AlafsTer2	p.P172Afs*2	ENST00000256474	NM_000551.3	170	-/A	3/3	0.377564274316048	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.377564274316048	1		479	478	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28929495	NA	P-0006402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	849	563	1	ENST00000275493.2:c.2155G>A	p.Gly719Ser	p.G719S	ENST00000275493	NM_005228.3	719	Ggc/Agc	18/28	0.416566339433823	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	TRUE	1	0.416566339433823	4		564	1910	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241678	55241678	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517085	NA	P-0006402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	906	592	0	ENST00000275493.2:c.2126A>C	p.Glu709Ala	p.E709A	ENST00000275493	NM_005228.3	709	gAa/gCa	18/28	0.416566339433823	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	1	0.416566339433823	4		592	2003	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435219	110435219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746894027	NA	P-0006402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	487	269	0	ENST00000375856.3:c.3182C>T	p.Ser1061Leu	p.S1061L	ENST00000375856	NM_003749.2	1061	tCg/tTg	1/2	0.257508267887435	6	FACETS	0.976	0.941	1	0.814	0.784	0.843	CLONAL	5	TRUE	0	0.416566339433823	6		269	878	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857932	89857932	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201385829	NA	P-0006402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	180	443	0	ENST00000389301.3:c.1238G>A	p.Arg413His	p.R413H	ENST00000389301	NM_000135.2	413	cGt/cAt	14/43	0.416566339433823	1	FACETS	0.702	0.647	0.759	0.702	0.647	0.759	SUBCLONAL	1	TRUE	0	0.416566339433823	1		443	975	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984475	7984475	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1287	153	605	0	ENST00000319144.4:c.383T>C	p.Val128Ala	p.V128A	ENST00000319144	NM_001139.2	128	gTc/gCc	3/15	1	2	FACETS	0.51	0.465	0.558	0.51	0.465	0.558	SUBCLONAL	1	TRUE	1	0.416566339433823	2		605	1440	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361146	70361146	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	324	564	1	ENST00000374080.3:c.6334C>T	p.Gln2112Ter	p.Q2112*	ENST00000374080		2112	Caa/Taa	43/45	0.416566339433823	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.416566339433823	1		565	1085	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576926	7576927	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0006402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	240	475	0	ENST00000269305.4:c.920-1dup	p.Ala307GlyfsTer30	p.A307Gfs*30	ENST00000269305	NM_001126112.2	307	gca/gGca		1	2	FACETS	0.944	0.88	1	0.944	0.88	1	CLONAL	1	TRUE	1	0.416566339433823	2		475	1221	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577588	7577595	+	frameshift_variant	Frame_Shift_Del	DEL	GGTGGTAC	GGTGGTAC	-	novel	NA	P-0006402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	172	485	0	ENST00000269305.4:c.686_693del	p.Cys229TyrfsTer8	p.C229Yfs*8	ENST00000269305	NM_001126112.2	229	tGTACCACC/t	7/11	1	2	FACETS	0.721	0.662	0.782	0.721	0.662	0.782	SUBCLONAL	1	TRUE	1	0.416566339433823	2		485	1146	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951141	48951141	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	391	528	0	ENST00000267163.4:c.1303G>T	p.Gly435Ter	p.G435*	ENST00000267163	NM_000321.2	435	Gga/Tga	13/27	0.691629288740814	1	FACETS	0.947	0.907	0.986	0.947	0.907	0.986	CLONAL	1	TRUE	0	0.704169422321308	1		528	760	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005580	42005580	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	596	924	0	ENST00000219905.7:c.3316C>T	p.Arg1106Ter	p.R1106*	ENST00000219905	NM_001164273.1	1106	Cga/Tga	9/24	0.666391586136586	1	FACETS	0.801	0.771	0.83	0.801	0.771	0.83	CLONAL	1	TRUE	0	0.704169422321308	1		924	1370	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2111929	2111929	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	566	641	1	ENST00000219476.3:c.1177G>T	p.Glu393Ter	p.E393*	ENST00000219476	NM_000548.3	393	Gag/Tag	12/42	0.704169422321308	1	FACETS	0.829	0.798	0.86	0.829	0.798	0.86	CLONAL	1	TRUE	0	0.704169422321308	1		642	1257	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566476	41566476	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	614	604	0	ENST00000263253.7:c.4353T>A	p.His1451Gln	p.H1451Q	ENST00000263253	NM_001429.3	1451	caT/caA	27/31	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.704169422321308	2		604	1734	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006849	47006849	+	5_prime_UTR_variant	5'UTR	SNP	G	G	A	novel	NA	P-0006408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1519	521	765	0	ENST00000377604.3:c.-32G>A		p.*11*	ENST00000377604	NM_001204468.1	-/852		2/24	NA	2	FACETS	0.725	0.693	0.758			1	INDETERMINATE	1	TRUE	NA	0.704169422321308	2		765	2040	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578463	7578464	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	555	626	0	ENST00000269305.4:c.466_467insT	p.Arg156LeufsTer25	p.R156Lfs*25	ENST00000269305	NM_001126112.2	156	cgc/cTgc	5/11	0.666391586136586	1	FACETS	0.806	0.775	0.837	0.806	0.775	0.837	CLONAL	1	TRUE	0	0.704169422321308	1		626	1267	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900288	101900288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111854391	NA	P-0006430-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	58	763	3	ENST00000374994.4:c.722C>T	p.Ser241Leu	p.S241L	ENST00000374994	NM_004612.2	241	tCg/tTg	4/9	0.295318747326875	5	FACETS	0.649	0.556	0.751			1	SUBCLONAL	1	FALSE	NA	0.330237637083828	5		766	809	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578429	7578430	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0006430-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	120	463	0	ENST00000269305.4:c.499_500dup	p.Gln167HisfsTer4	p.Q167Hfs*4	ENST00000269305	NM_001126112.2	167	cag/caCAg	5/11	0.271984860999305	3	FACETS	0.793	0.719	0.87			1	SUBCLONAL	2	FALSE	NA	0.330237637083828	3		463	534	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087396	27087409	+	frameshift_variant	Frame_Shift_Del	DEL	TGAGTCCTGGAGTG	TGAGTCCTGGAGTG	C	novel	NA	P-0006430-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	190	671	0	ENST00000324856.7:c.1970_1983delinsC	p.Leu657ProfsTer81	p.L657Pfs*81	ENST00000324856	NM_006015.4	657	cTGAGTCCTGGAGTG/cC	5/20	0.255653166284035	4	FACETS	0.845	0.781	0.911	0.845	0.781	0.911	CLONAL	2	FALSE	2	0.330237637083828	4		671	906	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0006448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	341	276	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.47197703997737	2	FACETS	0.896	0.855	0.937	0.896	0.855	0.937	CLONAL	2	TRUE	0	0.557207720834009	2		276	683	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0006448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	172	110	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.288522156662188	3	FACETS	0.949	0.884	1			1	INDETERMINATE	2	TRUE	NA	0.557207720834009	3		110	416	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160588	56160588	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	155	386	1	ENST00000399503.3:c.862C>T	p.Arg288Ter	p.R288*	ENST00000399503	NM_005921.1	288	Cga/Tga	4/20	0.20859115617099	3	FACETS	0.978	0.898	1	0.489	0.449	0.532	INDETERMINATE	1	TRUE	1	0.557207720834009	3		387	727	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467865	66467865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs939351025	NA	P-0006448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	139	407	2	ENST00000273854.3:c.404G>A	p.Arg135Gln	p.R135Q	ENST00000273854	NM_004439.5	135	cGg/cAg	3/18	1	2	FACETS	0.63	0.574	0.689	0.63	0.574	0.689	SUBCLONAL	1	TRUE	1	0.557207720834009	2		409	792	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809497	36809497	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs764022157	NA	P-0006448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	343	405	0	ENST00000373129.3:c.968A>C	p.Asp323Ala	p.D323A	ENST00000373129	NM_032017.1	323	gAc/gCc	10/12	0.472810455086805	2	FACETS	0.853	0.813	0.892	0.853	0.813	0.892	CLONAL	2	TRUE	0	0.557207720834009	2		405	722	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527314	187527314	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	162	330	0	ENST00000441802.2:c.10260A>T	p.Arg3420Ser	p.R3420S	ENST00000441802	NM_005245.3	3420	agA/agT	17/27	0.326241794996377	3	FACETS	1	0.959	1	0.533	0.49	0.578	INDETERMINATE	1	TRUE	1	0.557207720834009	3		330	697	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533685	63533685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1242238043	NA	P-0006448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	490	419	0	ENST00000307078.5:c.1469C>T	p.Ala490Val	p.A490V	ENST00000307078	NM_004655.3	490	gCg/gTg	6/11	0.557207720834009	7	FACETS	0.952	0.91	0.994			1	CLONAL	3	TRUE	NA	0.557207720834009	7		419	1474	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974754	21974766	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGACCCCGGGC	CCCGACCCCGGGC	-	novel	NA	P-0006448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	92	253	0	ENST00000304494.5:c.61_73del	p.Ala21Ter	p.A21*	ENST00000304494	NM_000077.4	21	GCCCGGGGTCGGGta/ta	1/3	0.288522156662188				0.722	0.904				INDETERMINATE	1	TRUE	NA	0.557207720834009	3		253	521	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099102	27099103	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0006448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	386	429	0	ENST00000324856.7:c.3524dup	p.Leu1176IlefsTer17	p.L1176Ifs*17	ENST00000324856	NM_006015.4	1173	atc/atCc	13/20	0.472810455086805	2	FACETS	0.817	0.78	0.854	0.817	0.78	0.854	CLONAL	2	TRUE	0	0.557207720834009	2		429	848	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0006505-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	98	710	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	0.244970233445473	5	FACETS	1	0.96	1	1	0.96	1	CLONAL	3	FALSE	2	0.244970233445473	5		710	324	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833934	44833935	+	stop_gained	Nonsense_Mutation	INS	-	-	AGG	novel	NA	P-0006505-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	88	342	0	ENST00000377967.4:c.359_360insGGA	p.Tyr120delinsTer	p.Y120delins*	ENST00000377967	NM_021140.2	120	tac/tAGGac	4/29	1	1	FACETS	0.97	0.899	1	1	0.991	1	CLONAL	5	FALSE	0	0.244970233445473	1		342	130	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	245	697	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.452342190635898	4	FACETS	0.997	0.935	1	0.997	0.935	1	CLONAL	2	TRUE	2	0.452342190635898	4		697	789	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0006583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	472	437	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	NA	2	FACETS	0.983	0.943	1			1	INDETERMINATE	2	TRUE	NA	0.452342190635898	2		437	1061	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638403	176638403	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	246	361	0	ENST00000439151.2:c.3003C>A	p.Asp1001Glu	p.D1001E	ENST00000439151	NM_022455.4	1001	gaC/gaA	5/23	0.263175956708819	5	FACETS	1	0.972	1	0.71	0.665	0.756	INDETERMINATE	2	TRUE	2	0.452342190635898	5		361	857	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900301	101900301	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	296	427	2	ENST00000374994.4:c.735G>T	p.Glu245Asp	p.E245D	ENST00000374994	NM_004612.2	245	gaG/gaT	4/9	0.452342190635898	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.452342190635898	2		429	627	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196947	108196947	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	243	315	0	ENST00000278616.4:c.6970G>C	p.Ala2324Pro	p.A2324P	ENST00000278616	NM_000051.3	2324	Gca/Cca	47/63	0.452342190635898	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	2	0.452342190635898	4		315	764	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206581	108206581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	303	356	0	ENST00000278616.4:c.8161G>A	p.Asp2721Asn	p.D2721N	ENST00000278616	NM_000051.3	2721	Gac/Aac	56/63	0.452342190635898	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	2	0.452342190635898	4		356	934	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406362	406362	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	274	412	0	ENST00000399788.2:c.4079C>A	p.Thr1360Lys	p.T1360K	ENST00000399788	NM_001042603.1	1360	aCa/aAa	25/28	0.452342190635898	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.452342190635898	4		412	855	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81971431	81971431	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1691	474	602	0	ENST00000359376.3:c.3121G>C	p.Glu1041Gln	p.E1041Q	ENST00000359376	NM_002661.3	1041	Gag/Cag	28/33	0.452342190635898	6	FACETS	0.922	0.878	0.967			1	CLONAL	2	TRUE	NA	0.452342190635898	6		602	2165	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097799	27097800	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	321	340	0	ENST00000324856.7:c.3389dup	p.Gln1131ProfsTer62	p.Q1131Pfs*62	ENST00000324856	NM_006015.4	1130	atc/aTtc	12/20	0.452342190635898	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.452342190635898	3		340	849	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909851	100909851	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	136	258	0	ENST00000325455.5:c.2798del	p.Lys933SerfsTer11	p.K933Sfs*11	ENST00000325455	NM_001202474.3	933	aAg/ag	8/8	0.452342190635898	4	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	2	0.452342190635898	4		258	430	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	58	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.435953032159137	4	FACETS	1	0.906	1	0.531	0.458	0.609	CLONAL	1	TRUE	2	0.486247564957661	4		311	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0006589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	40	654	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA	2	FACETS	0.758	0.636	0.892			1	INDETERMINATE	1	TRUE	NA	0.486247564957661	2		655	217	SUCCESS
APC	324	MSKCC	GRCh37	5	112163696	112163697	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1131691555	NA	P-0006589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	49	441	0	ENST00000257430.4:c.1620dup	p.Gln541ThrfsTer19	p.Q541Tfs*19	ENST00000257430	NM_000038.5	540	tta/ttAa	13/16	0.486247564957661	4	FACETS	0.738	0.626	0.86			1	SUBCLONAL	1	TRUE	NA	0.486247564957661	4		441	406	SUCCESS
APC	324	MSKCC	GRCh37	5	112175541	112175541	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	39	398	0	ENST00000257430.4:c.4251del	p.Ile1418Ter	p.I1418*	ENST00000257430	NM_000038.5	1417	aTt/at	16/16	0.486247564957661	4	FACETS	0.675	0.561	0.802			1	SUBCLONAL	1	TRUE	NA	0.486247564957661	4		398	353	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0006611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	132	373	1	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	0.319161875295281	1	FACETS	0.855	0.778	0.934	0.855	0.778	0.934	CLONAL	1	FALSE	0	0.408896243806543	1		374	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0006611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	296	356	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	NA	2	FACETS	0.988	0.935	1			1	INDETERMINATE	2	FALSE	NA	0.408896243806543	2		356	733	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148516773	148516773	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	47	211	0	ENST00000320356.2:c.914A>G	p.His305Arg	p.H305R	ENST00000320356	NM_004456.4	305	cAt/cGt	9/20	0.327796604036476	4	FACETS	0.491	0.414	0.577	0.246	0.207	0.289	SUBCLONAL	1	FALSE	2	0.408896243806543	4		211	659	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448520	49448520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778462	NA	P-0006611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	120	291	0	ENST00000301067.7:c.191G>A	p.Arg64Gln	p.R64Q	ENST00000301067	NM_003482.3	64	cGg/cAg	3/54	0.319782916183348	3	FACETS	1	0.964	1	0.377	0.341	0.415	CLONAL	1	FALSE	0	0.408896243806543	3		291	625	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105238740	105238740	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	118	367	0	ENST00000349310.3:c.1222T>G	p.Phe408Val	p.F408V	ENST00000349310	NM_001014432.1	408	Ttt/Gtt	13/15	0.325425495426112	3	FACETS	1	0.978	1	0.637	0.576	0.7	CLONAL	1	FALSE	1	0.408896243806543	3		367	546	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0006707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	129	467	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.438981796555179	3	FACETS	0.956	0.876	1	0.956	0.876	1	CLONAL	2	TRUE	1	0.438981796555179	3		468	375	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099422	27099422	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs746809059	NA	P-0006707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	74	705	0	ENST00000324856.7:c.3659T>C	p.Met1220Thr	p.M1220T	ENST00000324856	NM_006015.4	1220	aTg/aCg	14/20	1	2	FACETS	0.714	0.627	0.808	0.714	0.627	0.808	SUBCLONAL	1	TRUE	1	0.438981796555179	2		705	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578510	7578510	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	488	753	0	ENST00000269305.4:c.420del	p.Cys141AlafsTer29	p.C141Afs*29	ENST00000269305	NM_001126112.2	140	acC/ac	5/11	0.420937015265746	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.438981796555179	2		753	935	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911638	114911639	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0006707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	322	706	0	ENST00000543371.1:c.1157_1158dup	p.Arg387GlyfsTer105	p.R387Gfs*105	ENST00000543371	NM_001198531.1	386	cgg/cGGgg	10/14	0.306198776804332	3	FACETS	0.949	0.898	1	0.949	0.898	1	CLONAL	2	TRUE	1	0.438981796555179	3		706	943	SUCCESS
APC	324	MSKCC	GRCh37	5	112174782	112174783	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	54	652	0	ENST00000257430.4:c.3495dup	p.Tyr1166IlefsTer2	p.Y1166Ifs*2	ENST00000257430	NM_000038.5	1164	ata/atAa	16/16	0.438981796555179	3	FACETS	0.86	0.738	0.992	0.43	0.369	0.496	CLONAL	1	TRUE	1	0.438981796555179	3		652	349	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650591	18650591	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs751731010	NA	P-0006709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	46	482	0	ENST00000266497.5:c.2802G>T	p.Gln934His	p.Q934H	ENST00000266497		934	caG/caT	20/31	0.164609089358796	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		482	712	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	115	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.164609089358796	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		311	799	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420289	49420289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768551828	NA	P-0006709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	54	536	0	ENST00000301067.7:c.15460C>T	p.Arg5154Trp	p.R5154W	ENST00000301067	NM_003482.3	5154	Cgg/Tgg	48/54	0.164609089358796	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		536	509	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56871587	56871587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758034157	NA	P-0006709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	51	593	0	ENST00000308159.5:c.1967C>T	p.Pro656Leu	p.P656L	ENST00000308159	NM_014669.4	656	cCg/cTg	18/22	0.164609089358796	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		593	693	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0006709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	114	455	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.322368755869626	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		457	572	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867540	35867541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs869312857	NA	P-0006709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	33	377	0	ENST00000303115.3:c.361dup	p.Ile121AsnfsTer8	p.I121Nfs*8	ENST00000303115	NM_002185.3	118	-/A	3/8	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		377	520	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0006716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	209	348	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.369816861688561	3	FACETS	0.953	0.888	1	0.953	0.888	1	CLONAL	2	TRUE	1	0.369816861688561	3		348	703	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0006716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	219	351	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	0.361685579614448	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.369816861688561	2		351	544	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900209	101900209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	126	655	1	ENST00000374994.4:c.643C>T	p.Arg215Ter	p.R215*	ENST00000374994	NM_004612.2	215	Cga/Tga	4/9	0.361685579614448	2	FACETS	0.884	0.801	0.971	0.442	0.4	0.486	CLONAL	1	TRUE	0	0.369816861688561	2		656	771	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891277	101891277	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	108	604	0	ENST00000374994.4:c.238C>T	p.Arg80Ter	p.R80*	ENST00000374994	NM_004612.2	80	Cga/Tga	2/9	0.361685579614448	2	FACETS	0.786	0.706	0.871	0.393	0.353	0.436	SUBCLONAL	1	TRUE	0	0.369816861688561	2		604	743	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	459813	459813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779410726	NA	P-0006716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	289	553	0	ENST00000399788.2:c.1282C>T	p.Arg428Trp	p.R428W	ENST00000399788	NM_001042603.1	428	Cgg/Tgg	10/28	0.189104500391835	3	FACETS	0.981	0.924	1			1	INDETERMINATE	2	TRUE	NA	0.369816861688561	3		553	944	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581173	48581173	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	266	464	1	ENST00000342988.3:c.477G>T	p.Lys159Asn	p.K159N	ENST00000342988	NM_005359.5	159	aaG/aaT	5/12	0.369816861688561	3	FACETS	0.922	0.872	0.973	0.922	0.872	0.973	CLONAL	3	TRUE	0	0.369816861688561	3		465	616	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579718	7579718	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	223	562	0	ENST00000269305.4:c.78del	p.Pro27LeufsTer17	p.P27Lfs*17	ENST00000269305	NM_001126112.2	26	ctT/ct	3/11	0.361685579614448	2	FACETS	0.918	0.859	0.978	0.918	0.859	0.978	CLONAL	2	TRUE	0	0.369816861688561	2		562	657	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0006726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	55	276	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.749	0.641	0.868	0.749	0.641	0.868	SUBCLONAL	1	TRUE	1	0.245844320934198	2		276	597	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	67	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.752	0.653	0.86	0.752	0.653	0.86	SUBCLONAL	1	TRUE	1	0.245844320934198	2		311	725	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372347	55372347	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868625307	NA	P-0006726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	64	295	2	ENST00000297316.4:c.1037C>T	p.Thr346Met	p.T346M	ENST00000297316	NM_022454.3	346	aCg/aTg	2/2	0.245844320934198	4	FACETS	1	0.923	1	0.548	0.474	0.628	CLONAL	1	TRUE	2	0.245844320934198	4		297	592	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391095	139391095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	45	322	0	ENST00000277541.6:c.7096C>T	p.Gln2366Ter	p.Q2366*	ENST00000277541	NM_017617.3	2366	Cag/Tag	34/34	1	2	FACETS	0.646	0.542	0.76	0.646	0.542	0.76	SUBCLONAL	1	TRUE	1	0.245844320934198	2		322	567	SUCCESS
APC	324	MSKCC	GRCh37	5	112175410	112175411	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0006726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	64	355	1	ENST00000257430.4:c.4120dup	p.Glu1374GlyfsTer12	p.E1374Gfs*12	ENST00000257430	NM_000038.5	1373	-/G	16/16	1	2	FACETS	0.964	0.836	1	0.964	0.836	1	CLONAL	1	TRUE	1	0.245844320934198	2		356	540	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680480	241680480	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0006734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	258	361	0	ENST00000366560.3:c.267+2T>C		p.X89_splice	ENST00000366560	NM_000143.3	89			0.404856122345231	3	FACETS	1	0.992	1	0.716	0.67	0.762	CLONAL	1	TRUE	1	0.427816797997528	3		361	1023	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508954	106508954	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	152	342	0	ENST00000359195.3:c.948C>G	p.Asp316Glu	p.D316E	ENST00000359195	NM_002649.2	316	gaC/gaG	2/11	0.264714880408048	4	FACETS	0.848	0.779	0.92	0.848	0.779	0.92	CLONAL	2	TRUE	2	0.427816797997528	4		342	598	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394757	45394757	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	302	557	0	ENST00000262160.6:c.592C>G	p.His198Asp	p.H198D	ENST00000262160	NM_005901.5	198	Cac/Gac	5/11	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.427816797997528	2		557	984	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306550	41306550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760520624	NA	P-0006734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	88	506	0	ENST00000373198.4:c.1109C>T	p.Thr370Met	p.T370M	ENST00000373198	NM_133170.3	370	aCg/aTg	7/32	0.200429526185955	3	FACETS	0.614	0.543	0.689	0.307	0.271	0.345	INDETERMINATE	1	TRUE	1	0.427816797997528	3		506	814	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107224	27107225	+	frameshift_variant	Frame_Shift_Ins	INS	CT	CT	GTA	novel	NA	P-0006734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	280	345	0	ENST00000324856.7:c.6835_6836delinsGTA	p.Leu2279ValfsTer106	p.L2279Vfs*106	ENST00000324856	NM_006015.4	2279	CTg/GTAg	20/20	0.353534300934963	2	FACETS	0.942	0.89	0.994	0.942	0.89	0.994	CLONAL	2	TRUE	0	0.427816797997528	2		345	695	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850705	63850705	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs201178069	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	86	443	0	ENST00000279873.7:c.1489del	p.Ile497Ter	p.I497*	ENST00000279873	NM_032199.2	495	Aaa/aa	10/10	0.3	3	FACETS	0.965	0.852	1			1	CLONAL	1	TRUE	NA	0.18	3		443	1079	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	96	596	1	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.918	0.815	1	0.918	0.815	1	CLONAL	1	TRUE	1	0.18	2		597	1162	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	50	286	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.64	0.541	0.749	0.64	0.541	0.749	SUBCLONAL	1	TRUE	1	0.18	2		286	868	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	96	333	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.0750021637809374	0	FACETS	0.904	0.809	1			1	INDETERMINATE	2	TRUE	0	0.18	0		335	484	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	61	319	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.859	0.74	0.989	0.859	0.74	0.989	CLONAL	1	TRUE	1	0.18	2		319	789	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	40	320	3	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	0.121254631077498	0	FACETS	0.652	0.541	0.776			1	SUBCLONAL	1	TRUE	0	0.18	0		323	559	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	58	423	2	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.579	0.495	0.671	0.579	0.495	0.671	SUBCLONAL	1	TRUE	1	0.18	2		425	1113	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220389	98220389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370150142	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	53	397	2	ENST00000331920.6:c.3074G>A	p.Arg1025His	p.R1025H	ENST00000331920	NM_000264.3	1025	cGc/cAc	18/24	1	2	FACETS	0.727	0.618	0.847	0.727	0.618	0.847	SUBCLONAL	1	TRUE	1	0.18	2		399	810	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088788	27088788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	48	340	2	ENST00000324856.7:c.2402del	p.Gly801ValfsTer32	p.G801Vfs*32	ENST00000324856	NM_006015.4	799	caG/ca	7/20	1	2	FACETS	0.685	0.577	0.804	0.685	0.577	0.804	SUBCLONAL	1	TRUE	1	0.18	2		342	779	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914070	32914070	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507790	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1473	126	674	1	ENST00000380152.3:c.5583del	p.Val1862Ter	p.V1862*	ENST00000380152		1860	Aaa/aa	11/27	0.3	1	FACETS	0.797	0.718	0.88	0.797	0.718	0.88	SUBCLONAL	1	TRUE	0	0.18	1		675	1599	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023018	27023018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	17	39	0	ENST00000324856.7:c.124G>A	p.Ala42Thr	p.A42T	ENST00000324856	NM_006015.4	42	Gcg/Acg	1/20	1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	1	0.18	2		39	167	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46740345	46740345	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs138693255	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	82	329	0	ENST00000371975.4:c.1825C>T	p.Arg609Ter	p.R609*	ENST00000371975	NM_003579.3	609	Cga/Tga	16/18	0.3	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.18	1		329	765	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165837	118165837	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	58	270	0	ENST00000369448.3:c.347T>A	p.Leu116His	p.L116H	ENST00000369448	NM_017709.3	116	cTt/cAt	2/2	1	2	FACETS	0.804	0.689	0.929	0.804	0.689	0.929	CLONAL	1	TRUE	1	0.18	2		270	802	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403209	213403209	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	56	418	0	ENST00000342788.4:c.46G>A	p.Ala16Thr	p.A16T	ENST00000342788	NM_005235.2	16	Gcg/Acg	1/28	0.0750021637809374	0	FACETS	0.669	0.572	0.775			1	INDETERMINATE	1	TRUE	0	0.18	0		418	763	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623241	52623241	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375764191	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	49	275	0	ENST00000394830.3:c.2810C>T	p.Ala937Val	p.A937V	ENST00000394830	NM_018313.4	937	gCt/gTt	19/30	1	2	FACETS	0.863	0.73	1	0.863	0.73	1	CLONAL	1	TRUE	1	0.18	2		275	631	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911460	134911460	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768101201	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	37	311	0	ENST00000398015.3:c.1925G>A	p.Gly642Asp	p.G642D	ENST00000398015	NM_004441.4	642	gGc/gAc	11/16	0.3	1	FACETS	0.56	0.46	0.672	0.56	0.46	0.672	SUBCLONAL	1	TRUE	0	0.18	1		311	668	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645099	86645099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1305400293	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	66	277	1	ENST00000274376.6:c.1171C>T	p.Arg391Trp	p.R391W	ENST00000274376	NM_002890.2	391	Cgg/Tgg	8/25	0.121254631077498	3	FACETS	0.946	0.819	1	0.473	0.409	0.542	CLONAL	1	TRUE	1	0.18	3		278	845	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170177	32170177	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1483121330	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	50	310	0	ENST00000375023.3:c.3431G>A	p.Gly1144Asp	p.G1144D	ENST00000375023	NM_004557.3	1144	gGc/gAc	21/30	1	2	FACETS	0.863	0.731	1	0.863	0.731	1	CLONAL	1	TRUE	1	0.18	2		310	644	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522274	157522274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567836947	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	67	377	0	ENST00000346085.5:c.4546G>A	p.Val1516Ile	p.V1516I	ENST00000346085	NM_020732.3	1516	Gtc/Atc	18/20	1	2	FACETS	0.854	0.74	0.977	0.854	0.74	0.977	CLONAL	1	TRUE	1	0.18	2		377	872	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525096	157525096	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	54	299	0	ENST00000346085.5:c.4991A>C	p.Asp1664Ala	p.D1664A	ENST00000346085	NM_020732.3	1664	gAt/gCt	19/20	1	2	FACETS	0.756	0.644	0.879	0.756	0.644	0.879	SUBCLONAL	1	TRUE	1	0.18	2		299	794	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239140	98239140	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	44	311	1	ENST00000331920.6:c.1504-1G>T		p.X502_splice	ENST00000331920	NM_000264.3	502			1	2	FACETS	0.684	0.572	0.808	0.684	0.572	0.808	SUBCLONAL	1	TRUE	1	0.18	2		312	715	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133729602	133729602	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	62	367	0	ENST00000318560.5:c.231T>A	p.Asp77Glu	p.D77E	ENST00000318560	NM_005157.4	77	gaT/gaA	2/11	1	2	FACETS	0.842	0.726	0.969	0.842	0.726	0.969	CLONAL	1	TRUE	1	0.18	2		367	818	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332170	70332170	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	64	582	0	ENST00000373644.4:c.75C>A	p.Ser25Arg	p.S25R	ENST00000373644	NM_030625.2	25	agC/agA	2/12	0.3	1	FACETS	0.65	0.561	0.748	0.65	0.561	0.748	SUBCLONAL	1	TRUE	0	0.18	1		582	995	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263382	123263382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148672240	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	56	308	0	ENST00000358487.5:c.1361C>T	p.Thr454Met	p.T454M	ENST00000358487	NM_000141.4	454	aCg/aTg	10/18	0.3	1	FACETS	0.843	0.721	0.976	0.843	0.721	0.976	CLONAL	1	TRUE	0	0.18	1		308	672	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136271	64136271	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	69	328	0	ENST00000334205.4:c.1428+2T>C		p.X476_splice	ENST00000334205	NM_003942.2	476			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.18	2		328	628	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041590	42041590	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1299	126	679	1	ENST00000219905.7:c.5785C>T	p.Gln1929Ter	p.Q1929*	ENST00000219905	NM_001164273.1	1929	Cag/Tag	17/24	0.0750021637809374	0	FACETS	0.806	0.727	0.889			1	INDETERMINATE	1	TRUE	0	0.18	0		680	1425	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66679701	66679701	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	46	406	0	ENST00000307102.5:c.16C>A	p.Pro6Thr	p.P6T	ENST00000307102	NM_002755.3	6	Ccg/Acg	1/11	0.0750021637809374	0	FACETS	0.514	0.431	0.605			1	INDETERMINATE	1	TRUE	0	0.18	0		406	816	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631629	90631629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367982647	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	59	300	1	ENST00000330062.3:c.640G>A	p.Ala214Thr	p.A214T	ENST00000330062	NM_002168.2	214	Gca/Aca	5/11	0.0750021637809374	0	FACETS	0.739	0.635	0.853			1	INDETERMINATE	1	TRUE	0	0.18	0		301	727	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274258	10274258	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	10	119	0	ENST00000330684.3:c.11T>C	p.Val4Ala	p.V4A	ENST00000330684	NM_001134407.1	4	gTg/gCg	2/13	0.121254631077498	0	FACETS	0.566	0.384	0.793			1	SUBCLONAL	1	TRUE	0	0.18	0		119	161	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349011	11349011	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	33	206	1	ENST00000332029.2:c.325C>T	p.Arg109Trp	p.R109W	ENST00000332029	NM_003745.1	109	Cgg/Tgg	2/2	0.121254631077498	0	FACETS	0.638	0.519	0.773			1	SUBCLONAL	1	TRUE	0	0.18	0		207	471	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842472	68842472	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	48	246	0	ENST00000261769.5:c.531+2T>C		p.X177_splice	ENST00000261769	NM_004360.3	177			0.121254631077498	0	FACETS	0.976	0.826	1			1	CLONAL	1	TRUE	0	0.18	0		246	448	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971268	15971268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1215962055	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	58	306	0	ENST00000268712.3:c.4681C>T	p.Arg1561Trp	p.R1561W	ENST00000268712	NM_006311.3	1561	Cgg/Tgg	32/46	1	2	FACETS	0.859	0.737	0.993	0.859	0.737	0.993	CLONAL	1	TRUE	1	0.18	2		306	750	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118616	17118616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112980409	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	63	362	0	ENST00000285071.4:c.1315G>A	p.Val439Met	p.V439M	ENST00000285071	NM_144997.5	439	Gtg/Atg	12/14	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.18	2		362	658	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610604	10610604	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	48	280	0	ENST00000171111.5:c.106A>G	p.Thr36Ala	p.T36A	ENST00000171111	NM_203500.1	36	Act/Gct	2/6	0.121254631077498	0	FACETS	0.724	0.611	0.848			1	SUBCLONAL	1	TRUE	0	0.18	0		280	604	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138563	11138563	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	53	420	0	ENST00000358026.2:c.3319T>C	p.Ser1107Pro	p.S1107P	ENST00000358026	NM_001128849.1	1107	Tcc/Ccc	24/36	0.121254631077498	0	FACETS	0.675	0.575	0.786			1	SUBCLONAL	1	TRUE	0	0.18	0		420	715	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289931	15289931	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	66	421	0	ENST00000263388.2:c.3623A>C	p.Glu1208Ala	p.E1208A	ENST00000263388	NM_000435.2	1208	gAg/gCg	22/33	0.3	1	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	0	0.18	1		421	660	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50916766	50916766	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	63	491	0	ENST00000440232.2:c.2238C>G	p.Ser746Arg	p.S746R	ENST00000440232	NM_002691.3	746	agC/agG	18/27	0.177553985822277	0	FACETS	0.744	0.643	0.855			1	SUBCLONAL	1	TRUE	0	0.18	0		491	771	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918828	50918828	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	79	508	2	ENST00000440232.2:c.2698C>A	p.His900Asn	p.H900N	ENST00000440232	NM_002691.3	900	Cac/Aac	21/27	0.177553985822277	0	FACETS	0.804	0.706	0.91			1	CLONAL	1	TRUE	0	0.18	0		510	895	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651293	45651293	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	77	436	0	ENST00000407780.3:c.732G>T	p.Glu244Asp	p.E244D	ENST00000407780	NM_001283052.1	244	gaG/gaT	5/7	0.121254631077498	0	FACETS	0.939	0.824	1			1	CLONAL	1	TRUE	0	0.18	0		436	747	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755427	39755427	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	60	341	1	ENST00000288319.7:c.1338del	p.Phe446LeufsTer59	p.F446Lfs*59	ENST00000288319	NM_182918.3	446	ttT/tt	10/10	0.121254631077498	0	FACETS	0.616	0.529	0.711			1	SUBCLONAL	1	TRUE	0	0.18	0		342	887	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345768	152345769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs759063323	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	44	420	0	ENST00000359321.1:c.801dup	p.His268ThrfsTer11	p.H268Tfs*11	ENST00000359321	NM_005431.1	267	-/A	3/3	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.18	NA		420	823	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761147	59761147	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	80	351	0	ENST00000259008.2:c.3260del	p.Asn1087IlefsTer21	p.N1087Ifs*21	ENST00000259008	NM_032043.2	1087	aAt/at	20/20	0.0750021637809374	0	FACETS	0.972	0.855	1			1	INDETERMINATE	1	TRUE	0	0.18	0		351	750	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863699	68863702	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	AAGT	AAGT	-	rs587782810	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	19	137	0	ENST00000261769.5:c.2439+5_2439+8del		p.X813_splice	ENST00000261769	NM_004360.3	813		15/16	0.121254631077498	0	FACETS	0.56	0.425	0.719			1	SUBCLONAL	1	TRUE	0	0.18	0		137	309	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711299	114711301	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	79	365	0	ENST00000543371.1:c.318_320del	p.Ile106del	p.I106del	ENST00000543371	NM_001198531.1	105	tTCAtc/ttc	3/14	0.3	2	FACETS	1	0.895	1			1	CLONAL	1	TRUE	NA	0.18	2		365	860	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554356	63554357	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	79	385	0	ENST00000307078.5:c.382_383del	p.Leu128ThrfsTer12	p.L128Tfs*12	ENST00000307078	NM_004655.3	128	TTa/a	2/11	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.18	2		385	875	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411812	63411813	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	48	319	0	ENST00000330258.3:c.1354dup	p.Glu452GlyfsTer8	p.E452Gfs*8	ENST00000330258	NM_152424.3	452	gaa/gGaa	2/2	1	1	FACETS	0.904	0.764	1	0.904	0.764	1	CLONAL	1	TRUE	0	0.18	1		319	537	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796347	42796349	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	86	444	0	ENST00000575354.2:c.3001_3003del	p.Ser1001del	p.S1001del	ENST00000575354	NM_015125.3	999	cCCTcc/ccc	12/20	0.3	3	FACETS	1	0.968	1			1	CLONAL	1	TRUE	NA	0.18	3		444	815	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856624	111856630	+	frameshift_variant	Frame_Shift_Del	DEL	CCGGGCC	CCGGGCC	-	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	32	186	0	ENST00000341259.2:c.685_691del	p.Gly229MetfsTer47	p.G229Mfs*47	ENST00000341259	NM_005475.2	225	cgCCGGGCC/cg	2/8	1	2	FACETS	0.861	0.699	1	0.861	0.699	1	CLONAL	1	TRUE	1	0.18	2		186	413	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438567	49438569	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	56	326	0	ENST00000301067.7:c.4921_4923del	p.Lys1641del	p.K1641del	ENST00000301067	NM_003482.3	1641	AAG/-	19/54	1	2	FACETS	0.724	0.618	0.839	0.724	0.618	0.839	SUBCLONAL	1	TRUE	1	0.18	2		326	860	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736165	204736166	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	85	473	0	ENST00000302823.3:c.529dup	p.Tyr177LeufsTer2	p.Y177Lfs*2	ENST00000302823	NM_005214.4	174	-/T	3/4	1	2	FACETS	0.865	0.762	0.975	0.865	0.762	0.975	CLONAL	1	TRUE	1	0.18	2		473	1092	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262139	10262139	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	74	548	3	ENST00000340748.4:c.2152del	p.Met718CysfsTer59	p.M718Cfs*59	ENST00000340748		718	Atg/tg	23/40	0.121254631077498	0	FACETS	0.697	0.609	0.793			1	SUBCLONAL	1	TRUE	0	0.18	0		551	967	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533938	63533939	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	20	168	0	ENST00000307078.5:c.1214_1215dup	p.Gly406ArgfsTer53	p.G406Rfs*53	ENST00000307078	NM_004655.3	405	-/AG	6/11	0.0750021637809374	0	FACETS	0.519	0.396	0.663			1	INDETERMINATE	1	TRUE	0	0.18	0		168	351	SUCCESS
BLM	641	MSKCC	GRCh37	15	91326110	91326110	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	75	335	0	ENST00000355112.3:c.2618del	p.Lys873ArgfsTer7	p.K873Rfs*7	ENST00000355112	NM_000057.2	872	Aaa/aa	13/22	0.0750021637809374	0	FACETS	0.827	0.724	0.939			1	INDETERMINATE	1	TRUE	0	0.18	0		335	826	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885643	23885643	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1383	110	515	0	ENST00000374561.5:c.275del	p.Pro92LeufsTer34	p.P92Lfs*34	ENST00000374561	NM_002167.4	92	cCt/ct	1/3	1	2	FACETS	0.819	0.733	0.911	0.819	0.733	0.911	CLONAL	1	TRUE	1	0.18	2		515	1493	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97873817	97873817	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	64	372	2	ENST00000289081.3:c.1257del	p.Thr420ArgfsTer27	p.T420Rfs*27	ENST00000289081	NM_000136.2	419	ccC/cc	13/15	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.18	2		374	702	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480325	56480326	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	58	326	0	ENST00000267101.3:c.437dup	p.Val147CysfsTer4	p.V147Cfs*4	ENST00000267101	NM_001982.3	144	-/G	4/28	1	2	FACETS	0.915	0.785	1	0.915	0.785	1	CLONAL	1	TRUE	1	0.18	2		326	704	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245492	153245492	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	57	279	0	ENST00000281708.4:c.1699del	p.Asp567MetfsTer11	p.D567Mfs*11	ENST00000281708	NM_033632.3	567	Gat/at	11/12	1	2	FACETS	0.737	0.631	0.854	0.737	0.631	0.854	SUBCLONAL	1	TRUE	1	0.18	2		279	859	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0006782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	131	576	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.517763942150617	2		576	367	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979987	7979987	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746723399	NA	P-0006782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	54	301	0	ENST00000319144.4:c.1350del	p.Leu451SerfsTer16	p.L451Sfs*16	ENST00000319144	NM_001139.2	450	ggG/gg	10/15	0.517763942150617	3	FACETS	0.87	0.748	1	0.435	0.374	0.501	CLONAL	1	FALSE	1	0.517763942150617	3		301	302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0006782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	337	433	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.517763942150617	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	FALSE	1	0.517763942150617	3		436	662	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937602	76937603	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	53	332	0	ENST00000373344.5:c.3145dup	p.Ile1049AsnfsTer4	p.I1049Nfs*4	ENST00000373344	NM_000489.3	1049	ata/aAta	9/35	0.517763942150617	1	FACETS	0.624	0.538	0.717	0.624	0.538	0.717	SUBCLONAL	1	FALSE	0	0.517763942150617	1		332	243	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953826	131953826	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs368980595	NA	P-0006782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	77	439	0	ENST00000265335.6:c.3229C>T	p.Arg1077Ter	p.R1077*	ENST00000265335		1077	Cga/Tga	21/25	1	2	FACETS	0.847	0.749	0.951	0.847	0.749	0.951	CLONAL	1	FALSE	1	0.517763942150617	2		439	351	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508401	106508401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760958737	NA	P-0006782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	12	155	0	ENST00000359195.3:c.395C>T	p.Pro132Leu	p.P132L	ENST00000359195	NM_002649.2	132	cCg/cTg	2/11	0.517763942150617	3	FACETS	0.449	0.317	0.609	0.224	0.158	0.305	SUBCLONAL	1	FALSE	1	0.517763942150617	3		155	130	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509676	106509676	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139426517	NA	P-0006782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	108	406	0	ENST00000359195.3:c.1670C>T	p.Ala557Val	p.A557V	ENST00000359195	NM_002649.2	557	gCg/gTg	2/11	0.517763942150617	3	FACETS	0.786	0.714	0.861	0.786	0.714	0.861	SUBCLONAL	2	FALSE	1	0.517763942150617	3		406	334	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851979	128851979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777173215	NA	P-0006782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	61	371	0	ENST00000249373.3:c.2051C>T	p.Pro684Leu	p.P684L	ENST00000249373	NM_005631.4	684	cCg/cTg	12/12	0.517763942150617	3	FACETS	0.862	0.748	0.985	0.431	0.374	0.493	CLONAL	1	FALSE	1	0.517763942150617	3		371	344	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514271	69514271	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	66	425	0	ENST00000294312.3:c.410A>G	p.Glu137Gly	p.E137G	ENST00000294312	NM_005117.2	137	gAg/gGg	3/3	0.153541560950512	0	FACETS	0.486	0.427	0.549			1	INDETERMINATE	1	FALSE	0	0.517763942150617	0		425	253	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658370	18658370	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	46	324	0	ENST00000266497.5:c.3175G>A	p.Ala1059Thr	p.A1059T	ENST00000266497		1059	Gca/Aca	22/31	NA	2	FACETS	0.521	0.44	0.609			1	INDETERMINATE	1	FALSE	NA	0.517763942150617	2		324	341	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885947	59885947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs865910081	NA	P-0006782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	49	363	4	ENST00000259008.2:c.799G>A	p.Ala267Thr	p.A267T	ENST00000259008	NM_032043.2	267	Gca/Aca	7/20	0.32139890606871	0	FACETS	0.328	0.28	0.381			1	SUBCLONAL	1	FALSE	0	0.517763942150617	0		367	278	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130266	11130266	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0006782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	48	246	1	ENST00000358026.2:c.2506-1G>T		p.X836_splice	ENST00000358026	NM_001128849.1	836			NA	2	FACETS	0.997	0.855	1			1	INDETERMINATE	1	FALSE	NA	0.517763942150617	2		247	186	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291828	15291828	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376187165	NA	P-0006782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	11	346	3	ENST00000263388.2:c.2938G>A	p.Ala980Thr	p.A980T	ENST00000263388	NM_000435.2	980	Gcc/Acc	18/33	0.252107738227794	0	FACETS	0.132	0.091	0.183			1	INDETERMINATE	1	FALSE	0	0.517763942150617	0		349	155	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923684	39923684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1231642126	NA	P-0006782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	20	410	3	ENST00000378444.4:c.3407G>A	p.Arg1136His	p.R1136H	ENST00000378444	NM_001123385.1	1136	cGc/cAc	7/15	0.517763942150617	1	FACETS	0.335	0.257	0.424	0.335	0.257	0.424	SUBCLONAL	1	FALSE	0	0.517763942150617	1		413	171	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37055897	37055924	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGCTTCAGAATCTCTTTTCTAATAGAG	AAGCTTCAGAATCTCTTTTCTAATAGAG	-	novel	NA	P-0006782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	92	229	0	ENST00000231790.2:c.678-24_681del		p.X226_splice	ENST00000231790	NM_000249.3	226		9/19	1	2	FACETS	0.884	0.804	0.965	1	0.987	1	CLONAL	2	FALSE	1	0.517763942150617	2		229	201	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165945	47165945	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	70	339	0	ENST00000409792.3:c.181del	p.Thr61GlnfsTer50	p.T61Qfs*50	ENST00000409792	NM_014159.6	61	Aca/ca	3/21	1	2	FACETS	0.757	0.664	0.856	0.757	0.664	0.856	SUBCLONAL	1	FALSE	1	0.517763942150617	2		339	357	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920173	76920173	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	47	557	0	ENST00000373344.5:c.3904del	p.Arg1302GlufsTer44	p.R1302Efs*44	ENST00000373344	NM_000489.3	1302	Aga/ga	11/35	0.517763942150617	1	FACETS	0.364	0.307	0.425	0.364	0.307	0.425	SUBCLONAL	1	FALSE	0	0.517763942150617	1		557	370	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0006810-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	336	381	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.503443023440261	5	FACETS	0.886	0.841	0.932	0.886	0.841	0.932	CLONAL	3	TRUE	2	0.503443023440261	5		381	881	SUCCESS
APC	324	MSKCC	GRCh37	5	112174357	112174358	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs876658724	NA	P-0006810-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	196	271	0	ENST00000257430.4:c.3067dup	p.Thr1023AsnfsTer6	p.T1023Nfs*6	ENST00000257430	NM_000038.5	1022	-/A	16/16	NA	2	FACETS	0.899	0.843	0.956			1	INDETERMINATE	2	TRUE	NA	0.503443023440261	2		271	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876658468	NA	P-0006810-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	265	417	0	ENST00000269305.4:c.577C>G	p.His193Asp	p.H193D	ENST00000269305	NM_001126112.2	193	Cat/Gat	6/11	0.502595202728302	2	FACETS	0.859	0.812	0.906	0.859	0.812	0.906	CLONAL	2	TRUE	0	0.503443023440261	2		417	613	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679811	88679811	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006810-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	225	414	0	ENST00000360948.2:c.652A>C	p.Asn218His	p.N218H	ENST00000360948	NM_001012338.2	218	Aac/Cac	7/19	0.455923908578526	3	FACETS	0.917	0.86	0.975	0.917	0.86	0.975	CLONAL	2	TRUE	1	0.503443023440261	3		414	610	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934931	9934931	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006810-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	103	286	0	ENST00000330684.3:c.1359G>C	p.Lys453Asn	p.K453N	ENST00000330684	NM_001134407.1	453	aaG/aaC	6/13	0.503443023440261	8	FACETS	0.956	0.854	1			1	CLONAL	1	TRUE	NA	0.503443023440261	8		286	1074	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	129	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.156301316763434	3	FACETS	0.87	0.79	0.953	1	0.981	1	CLONAL	3	TRUE	1	0.153442530545961	3		311	694	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497847	25497847	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779859478	NA	P-0006834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	75	299	1	ENST00000264709.3:c.602G>A	p.Arg201His	p.R201H	ENST00000264709	NM_175629.2	201	cGc/cAc	6/23	0.156301316763434	3	FACETS	1	0.973	1	0.73	0.639	0.828	CLONAL	1	TRUE	1	0.153442530545961	3		300	721	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100414	157100414	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1438676618	NA	P-0006834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	14	48	0	ENST00000346085.5:c.1351T>C	p.Ser451Pro	p.S451P	ENST00000346085	NM_020732.3	451	Tcg/Ccg	1/20	0.153442530545961	8	FACETS	0.966	0.702	1			1	CLONAL	2	TRUE	NA	0.153442530545961	8		48	138	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444297	49444297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746163543	NA	P-0006834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	96	427	1	ENST00000301067.7:c.3074C>T	p.Ser1025Leu	p.S1025L	ENST00000301067	NM_003482.3	1025	tCg/tTg	11/54	0.153442530545961	7	FACETS	0.768	0.682	0.86	0.384	0.341	0.43	SUBCLONAL	2	TRUE	3	0.153442530545961	7		428	1127	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920458	134920458	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	76	361	0	ENST00000398015.3:c.2273G>A	p.Cys758Tyr	p.C758Y	ENST00000398015	NM_004441.4	758	tGc/tAc	12/16	0.153442530545961	4	FACETS	0.782	0.685	0.886	0.782	0.685	0.886	SUBCLONAL	2	TRUE	2	0.153442530545961	4		361	731	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180641	32180641	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1186558705	NA	P-0006834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	102	312	1	ENST00000375023.3:c.2486G>A	p.Arg829His	p.R829H	ENST00000375023	NM_004557.3	829	cGc/cAc	16/30	NA	2	FACETS	1	0.963	1			1	INDETERMINATE	2	TRUE	NA	0.153442530545961	2		313	571	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553090	106553090	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	161	290	0	ENST00000369096.4:c.1055C>T	p.Pro352Leu	p.P352L	ENST00000369096	NM_001198.3	352	cCt/cTt	5/7	0.153442530545961	6	FACETS	1	0.954	1	0.635	0.582	0.69	CLONAL	3	TRUE	1	0.153442530545961	6		290	864	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139411769	139411769	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752071569	NA	P-0006834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	52	356	0	ENST00000277541.6:c.1510C>T	p.Arg504Cys	p.R504C	ENST00000277541	NM_017617.3	504	Cgc/Tgc	9/34	0.156301316763434	3	FACETS	1	0.937	1	0.598	0.509	0.696	CLONAL	1	TRUE	1	0.153442530545961	3		356	610	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851345	63851345	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	88	214	0	ENST00000279873.7:c.2123A>G	p.Tyr708Cys	p.Y708C	ENST00000279873	NM_032199.2	708	tAc/tGc	10/10	0.153442530545961	13	FACETS	1	0.907	1			1	CLONAL	4	TRUE	NA	0.153442530545961	13		214	517	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023100	33023100	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	61	403	0	ENST00000300177.4:c.209G>C	p.Gly70Ala	p.G70A	ENST00000300177	NM_001191322.1	70	gGg/gCg	2/2	0.156301316763434	3	FACETS	1	0.95	1	0.614	0.529	0.707	CLONAL	1	TRUE	1	0.153442530545961	3		403	697	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972440	81972440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs891516801	NA	P-0006834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	149	543	2	ENST00000359376.3:c.3233G>A	p.Arg1078Gln	p.R1078Q	ENST00000359376	NM_002661.3	1078	cGa/cAa	29/33	0.133375981869285	3	FACETS	0.958	0.874	1	0.958	0.874	1	CLONAL	2	TRUE	1	0.153442530545961	3		545	1091	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39762932	39762932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1401427882	NA	P-0006834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	54	345	0	ENST00000288319.7:c.904C>T	p.Arg302Cys	p.R302C	ENST00000288319	NM_182918.3	302	Cgc/Tgc	9/10	0.156301316763434	3	FACETS	1	0.961	1	0.707	0.604	0.82	CLONAL	1	TRUE	1	0.153442530545961	3		345	536	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440635	56440636	+	stop_gained,frameshift_variant,splice_region_variant	Nonsense_Mutation	INS	-	-	CCAGGCCGGGGGCTCCTTCAGCTCAATCCTCACATGGG	novel	NA	P-0006834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	120	360	0	ENST00000407977.2:c.545_582dup	p.Asp196MetfsTer2	p.D196Mfs*2	ENST00000407977		194	-/CCCATGTGAGGATTGAGCTGAAGGAGCCCCCGGCCTGG		0.156301316763434	3	FACETS	1	0.939	1	0.702	0.634	0.774	CLONAL	2	TRUE	0	0.153442530545961	3		360	800	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576926	7576929	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTA	GCTA	-	novel	NA	P-0006834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	128	323	0	ENST00000269305.4:c.920-3_920del		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	0.156301316763434	3	FACETS	0.878	0.797	0.963			1	CLONAL	3	TRUE	NA	0.153442530545961	3		323	682	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0006905-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	497	292	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.772184336421994	3	FACETS	0.972	0.949	0.994			1	CLONAL	3	TRUE	NA	0.772184336421994	3		292	612	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720711	89720712	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006905-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	80	42	0	ENST00000371953.3:c.867dup	p.Val290SerfsTer8	p.V290Sfs*8	ENST00000371953	NM_000314.4	288	gaa/gAaa	8/9	0.772184336421994	2	FACETS	0.791	0.725	0.855	0.791	0.725	0.855	SUBCLONAL	2	TRUE	0	0.772184336421994	2		42	131	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612209	1612209	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs915880927	NA	P-0006905-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	128	316	0	ENST00000344749.5:c.1810C>T	p.Arg604Ter	p.R604*	ENST00000344749	NM_001136139.2	604	Cga/Tga	18/19	1	2	FACETS	0.568	0.516	0.622	0.568	0.516	0.622	SUBCLONAL	1	TRUE	1	0.772184336421994	2		316	584	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989106	41989107	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006905-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	712	650	1	ENST00000219905.7:c.1901dup	p.Ser635ValfsTer22	p.S635Vfs*22	ENST00000219905	NM_001164273.1	633	gga/ggAa	3/24	0.754554513039188	3	FACETS	0.935	0.906	0.964	0.935	0.906	0.964	CLONAL	2	TRUE	1	0.772184336421994	3		651	1367	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774894	73774895	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006905-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1281	298	473	0	ENST00000254810.4:c.278dup	p.Gln94AlafsTer4	p.Q94Afs*4	ENST00000254810	NM_005324.3	93	ctg/ctTg	3/4	0.707232559291176	5	FACETS	1	0.971	1	0.352	0.33	0.374	CLONAL	1	TRUE	2	0.772184336421994	5		473	1579	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400787	72400795	+	inframe_deletion	In_Frame_Del	DEL	TGTTCTGGG	TGTTCTGGG	-	novel	NA	P-0006905-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	355	545	0	ENST00000357731.5:c.376_384del	p.Pro126_Thr128del	p.P126_T128del	ENST00000357731	NM_173808.2	126	CCCAGAACA/-	2/7	0.772184336421994	3	FACETS	1	0.981	1	0.535	0.507	0.564	CLONAL	1	TRUE	1	0.772184336421994	3		545	1190	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0006912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	342	381	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.212415143673529	5	FACETS	1	0.947	1	0.668	0.631	0.705	INDETERMINATE	2	TRUE	2	0.454935510582872	5		381	1263	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250046	53250047	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs782600511	NA	P-0006912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	272	515	0	ENST00000375401.3:c.202dup	p.Arg68ProfsTer7	p.R68Pfs*7	ENST00000375401	NM_004187.3	68	cga/cCga	2/26	0.338702612434945	1	FACETS	0.687	0.644	0.732	0.687	0.644	0.732	SUBCLONAL	1	TRUE	0	0.454935510582872	1		515	1344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579408	7579430	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGGGCCAGGAGGGGGCTGGTG	CAGGGGCCAGGAGGGGGCTGGTG	-	rs886041861	NA	P-0006912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	163	325	0	ENST00000269305.4:c.257_279del	p.Ala86ValfsTer55	p.A86Vfs*55	ENST00000269305	NM_001126112.2	86	gCACCAGCCCCCTCCTGGCCCCTG/g	4/11	0.454935510582872	1	FACETS	0.816	0.752	0.884	0.816	0.752	0.884	CLONAL	1	TRUE	0	0.454935510582872	1		325	678	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0006920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	378	327	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.289648366166184	4	FACETS	0.922	0.878	0.967			1	CLONAL	3	TRUE	NA	0.383424312231997	4		327	986	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782651	9782651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	83	583	0	ENST00000377346.4:c.2413G>A	p.Gly805Arg	p.G805R	ENST00000377346	NM_005026.3	805	Ggg/Agg	19/24	0.268544570608654	4	FACETS	0.576	0.507	0.651	0.288	0.253	0.326	SUBCLONAL	1	TRUE	2	0.383424312231997	4		583	1039	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467434	66467434	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369606981	NA	P-0006920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	120	362	0	ENST00000273854.3:c.835G>A	p.Glu279Lys	p.E279K	ENST00000273854	NM_004439.5	279	Gaa/Aaa	3/18	0.383424312231997	3	FACETS	0.881	0.795	0.971	0.44	0.397	0.486	CLONAL	1	TRUE	1	0.383424312231997	3		362	847	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591113	67591113	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	139	378	0	ENST00000274335.5:c.1706A>G	p.Asp569Gly	p.D569G	ENST00000274335		569	gAc/gGc	12/15	0.256376545989692	5	FACETS	1	0.961	1	0.369	0.335	0.404	CLONAL	1	TRUE	2	0.383424312231997	5		378	1033	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005380	29005380	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	59	453	0	ENST00000282397.4:c.881G>T	p.Ser294Ile	p.S294I	ENST00000282397	NM_002019.4	294	aGt/aTt	7/30	1	2	FACETS	0.432	0.371	0.498	0.432	0.371	0.498	SUBCLONAL	1	TRUE	1	0.383424312231997	2		453	713	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577521	7577521	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	357	524	0	ENST00000269305.4:c.760A>C	p.Ile254Leu	p.I254L	ENST00000269305	NM_001126112.2	254	Atc/Ctc	7/11	0.319969150574678	3	FACETS	0.84	0.799	0.881	0.84	0.799	0.881	CLONAL	3	TRUE	0	0.383424312231997	3		524	881	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670111	29670111	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	157	491	0	ENST00000356175.3:c.7084A>T	p.Asn2362Tyr	p.N2362Y	ENST00000356175	NM_000267.3	2362	Aac/Tac	47/57	0.319969150574678	3	FACETS	0.858	0.785	0.936	0.286	0.261	0.312	CLONAL	1	TRUE	0	0.383424312231997	3		491	1137	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577500	7577514	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TGGAGTCTTCCAGTG	TGGAGTCTTCCAGTG	-	novel	NA	P-0006920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	341	473	0	ENST00000269305.4:c.767_781del	p.Thr256_Ser260del	p.T256_S260del	ENST00000269305	NM_001126112.2	256	aCACTGGAAGACTCCAgt/agt	7/11	0.319969150574678	3	FACETS	0.864	0.821	0.907	0.864	0.821	0.907	CLONAL	3	TRUE	0	0.383424312231997	3		473	818	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0006934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1494	322	623	6	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	NA	2	FACETS	0.785	0.739	0.833			1	INDETERMINATE	1	TRUE	NA	0.451552052087993	2		629	1816	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519920	NA	P-0006934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	153	272	0	ENST00000397062.3:c.85G>C	p.Asp29His	p.D29H	ENST00000397062	NM_006164.4	29	Gat/Cat	2/5	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.451552052087993	2		272	588	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431241	49431241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	126	422	0	ENST00000301067.7:c.9898G>A	p.Glu3300Lys	p.E3300K	ENST00000301067	NM_003482.3	3300	Gag/Aag	34/54	1	2	FACETS	0.506	0.457	0.558	0.506	0.457	0.558	SUBCLONAL	1	TRUE	1	0.451552052087993	2		422	1102	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432335	49432335	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0006934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	235	475	0	ENST00000301067.7:c.8804C>G	p.Ser2935Ter	p.S2935*	ENST00000301067	NM_003482.3	2935	tCa/tGa	34/54	1	2	FACETS	0.892	0.831	0.955	0.892	0.831	0.955	CLONAL	1	TRUE	1	0.451552052087993	2		475	1167	SUCCESS
ATR	545	MSKCC	GRCh37	3	142257317	142257340	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACAATACCTGTTTTCAATTATGAG	ACAATACCTGTTTTCAATTATGAG	-	novel	NA	P-0006934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	103	295	0	ENST00000350721.4:c.3709_3725+7del		p.X1237_splice	ENST00000350721	NM_001184.3	1237		19/47	1	2	FACETS	0.802	0.719	0.889	0.802	0.719	0.889	CLONAL	1	TRUE	1	0.451552052087993	2		295	569	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792017	42792017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	700	553	0	ENST00000575354.2:c.821G>A	p.Arg274Gln	p.R274Q	ENST00000575354	NM_015125.3	274	cGa/cAa	6/20	0.744541652051009	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.744541652051009	2		553	829	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243050	105243051	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCAGCGGATGATGAAGGTGTTGGGCCGGG	novel	NA	P-0007009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	462	560	0	ENST00000349310.3:c.203_232dup	p.Pro68_Cys77dup	p.P68_C77dup	ENST00000349310	NM_001014432.1	68	ctg/cCCCGGCCCAACACCTTCATCATCCGCTGCCtg	5/15	0.744541652051009	3	FACETS	1	0.995	1	0.663	0.634	0.693	CLONAL	1	TRUE	1	0.744541652051009	3		560	1284	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0007035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	206	348	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.443099310354739	3	FACETS	0.962	0.9	1	0.641	0.6	0.684	CLONAL	2	TRUE	0	0.481279796246741	3		348	552	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958169	2958169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772266095	NA	P-0007035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	173	433	0	ENST00000396946.4:c.2563C>T	p.Arg855Trp	p.R855W	ENST00000396946	NM_032415.4	855	Cgg/Tgg	19/25	0.481279796246741	3	FACETS	0.989	0.91	1	0.494	0.455	0.536	CLONAL	1	TRUE	1	0.481279796246741	3		433	902	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0007035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	357	458	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.481279796246741	2	FACETS	0.943	0.899	0.987	0.943	0.899	0.987	CLONAL	2	TRUE	0	0.481279796246741	2		458	787	SUCCESS
APC	324	MSKCC	GRCh37	5	112175246	112175246	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1057517558	NA	P-0007035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	368	487	0	ENST00000257430.4:c.3956del	p.Pro1319LeufsTer2	p.P1319Lfs*2	ENST00000257430	NM_000038.5	1319	Cct/ct	16/16	0.472998144717219	3	FACETS	0.903	0.865	0.942	0.903	0.865	0.942	CLONAL	3	TRUE	0	0.481279796246741	3		487	700	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772950	135772951	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs118203724	NA	P-0007035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	225	365	1	ENST00000298552.3:c.2672dup	p.Asn891LysfsTer13	p.N891Kfs*13	ENST00000298552	NM_001162426.1	891	aac/aaAc	21/23	0.481279796246741	2	FACETS	0.75	0.703	0.798	0.75	0.703	0.798	SUBCLONAL	2	TRUE	0	0.481279796246741	2		366	623	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639655	47639655	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs864622183	NA	P-0007035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	119	479	1	ENST00000233146.2:c.748G>A	p.Gly250Arg	p.G250R	ENST00000233146	NM_000251.2	250	Gga/Aga	4/16	1	2	FACETS	0.817	0.74	0.899	0.817	0.74	0.899	CLONAL	1	TRUE	1	0.481279796246741	2		480	605	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371782	55371782	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	61	112	0	ENST00000297316.4:c.472G>A	p.Gly158Ser	p.G158S	ENST00000297316	NM_022454.3	158	Ggc/Agc	2/2	1	2	FACETS	0.773	0.682	0.867	1	0.976	1	SUBCLONAL	2	TRUE	1	0.481279796246741	2		112	164	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578177	7578177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	120	582	0	ENST00000269305.4:c.672G>C	p.Glu224Asp	p.E224D	ENST00000269305	NM_001126112.2	224	gaG/gaC	6/11	0.474678178689234	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.474678178689234	1		582	320	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466788	25466788	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	120	535	0	ENST00000264709.3:c.1915C>G	p.Leu639Val	p.L639V	ENST00000264709	NM_175629.2	639	Ctc/Gtc	16/23	0.26782785491541	3	FACETS	1	0.984	1	0.7	0.636	0.766	INDETERMINATE	1	TRUE	1	0.474678178689234	3		535	447	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133883	55133883	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	52	431	0	ENST00000257290.5:c.1096G>C	p.Asp366His	p.D366H	ENST00000257290	NM_006206.4	366	Gat/Cat	7/23	0.26782785491541	3	FACETS	0.886	0.759	1	0.443	0.379	0.512	INDETERMINATE	1	TRUE	1	0.474678178689234	3		431	306	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55225387	55225387	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	97	370	0	ENST00000275493.2:c.1239C>A	p.Asn413Lys	p.N413K	ENST00000275493	NM_005228.3	413	aaC/aaA	11/28	NA	2	FACETS	1	0.961	1			1	INDETERMINATE	1	TRUE	NA	0.474678178689234	2		370	358	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98244444	98244444	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	12	363	0	ENST00000331920.6:c.626T>G	p.Leu209Arg	p.L209R	ENST00000331920	NM_000264.3	209	cTt/cGt	4/24	0.474678178689234	1	FACETS	0.202	0.142	0.276	0.202	0.142	0.276	SUBCLONAL	1	TRUE	0	0.474678178689234	1		363	191	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432859	432859	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	63	518	0	ENST00000399788.2:c.2057C>T	p.Ser686Phe	p.S686F	ENST00000399788	NM_001042603.1	686	tCt/tTt	15/28	0.399692617153971	1	FACETS	0.619	0.539	0.705	0.619	0.539	0.705	SUBCLONAL	1	TRUE	0	0.474678178689234	1		518	327	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23635339	23635339	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	80	463	0	ENST00000261584.4:c.2825G>C	p.Arg942Thr	p.R942T	ENST00000261584	NM_024675.3	942	aGa/aCa	8/13	0.474678178689234	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.474678178689234	1		463	232	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2194543	2194543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	37	716	0	ENST00000398665.3:c.618G>A	p.Met206Ile	p.M206I	ENST00000398665	NM_032482.2	206	atG/atA	7/28	NA	2	FACETS	0.455	0.375	0.543			1	INDETERMINATE	1	TRUE	NA	0.474678178689234	2		716	343	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213568	2213568	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	82	535	0	ENST00000398665.3:c.1588C>G	p.Gln530Glu	p.Q530E	ENST00000398665	NM_032482.2	530	Cag/Gag	17/28	NA	2	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.474678178689234	2		535	298	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228162	53228162	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	93	573	0	ENST00000375401.3:c.2240T>C	p.Leu747Pro	p.L747P	ENST00000375401	NM_004187.3	747	cTg/cCg	15/26	0.34013905315759	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.474678178689234	1		573	277	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117948	70117969	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGGCAAGCTCTGGAGGTAGGA	TGGGCAAGCTCTGGAGGTAGGA	-	novel	NA	P-0007037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	40	303	0	ENST00000245479.2:c.416_431+6del		p.X139_splice	ENST00000245479	NM_000346.3	139		1/3	0.26782785491541	3	FACETS	0.876	0.746	1	0.876	0.746	1	INDETERMINATE	2	TRUE	1	0.474678178689234	3		303	119	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200704	128200705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0007037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	115	508	0	ENST00000341105.2:c.1100dup	p.Asp367GlufsTer17	p.D367Efs*17	ENST00000341105	NM_032638.4	367	gac/gaAc	5/6	0.369733100374298	3	FACETS	1	0.981	1	0.668	0.605	0.733	CLONAL	1	TRUE	1	0.474678178689234	3		508	449	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243034	41243035	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGA	novel	NA	P-0007037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	105	523	0	ENST00000357654.3:c.4108_4111dup	p.Gly1371ValfsTer4	p.G1371Vfs*4	ENST00000357654	NM_007294.3	1371	ggg/gTCTGgg	11/23	0.39823042825389	0	FACETS	0.722	0.654	0.791			1	SUBCLONAL	1	TRUE	0	0.474678178689234	0		523	322	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117942	70117943	+	protein_altering_variant	In_Frame_Ins	INS	AG	AG	CTTGCACA	novel	NA	P-0007037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	42	329	0	ENST00000245479.2:c.410_411delinsCTTGCACA	p.Lys137delinsThrCysThr	p.K137delinsTCT	ENST00000245479	NM_000346.3	137	aAG/aCTTGCACA	1/3	0.26782785491541	3	FACETS	0.883	0.755	1	0.883	0.755	1	INDETERMINATE	2	TRUE	1	0.474678178689234	3		329	124	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0007087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	65	338	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	FALSE	1	0.196601020694051	2		338	568	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	84	218	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.113217126011523	4	FACETS	1	0.962	1	0.614	0.541	0.692	INDETERMINATE	1	FALSE	2	0.196601020694051	4		218	833	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0007087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	72	504	2	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.998	0.871	1	0.998	0.871	1	CLONAL	1	FALSE	1	0.196601020694051	2		506	734	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	118	387	0	ENST00000346208.3:c.1220_1221insA	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcAg	6/6	0.126422888467906	0	FACETS	0.932	0.839	1			1	CLONAL	1	FALSE	0	0.196601020694051	0		387	1035	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2969703	2969703	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777588257	NA	P-0007087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	79	572	0	ENST00000396946.4:c.1576G>A	p.Gly526Arg	p.G526R	ENST00000396946	NM_032415.4	526	Ggg/Agg	12/25	1	2	FACETS	0.861	0.756	0.975	0.861	0.756	0.975	CLONAL	1	FALSE	1	0.196601020694051	2		572	933	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0007087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	35	301	0	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	0.196601020694051	1	FACETS	0.847	0.695	1	0.847	0.695	1	CLONAL	1	FALSE	0	0.196601020694051	1		301	379	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532710	187532710	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1010116749	NA	P-0007087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	57	622	0	ENST00000441802.2:c.9683del	p.Pro3228LeufsTer42	p.P3228Lfs*42	ENST00000441802	NM_005245.3	3228	cCt/ct	14/27	1	2	FACETS	0.923	0.792	1	0.923	0.792	1	CLONAL	1	FALSE	1	0.196601020694051	2		622	628	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45800116	45800116	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	99	594	0	ENST00000450313.1:c.104G>T	p.Gly35Val	p.G35V	ENST00000450313	NM_012222.2	35	gGg/gTg	2/16	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	1	0.196601020694051	2		594	965	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539921	187539921	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	38	482	1	ENST00000441802.2:c.7819T>C	p.Ser2607Pro	p.S2607P	ENST00000441802	NM_005245.3	2607	Tcc/Ccc	10/27	1	2	FACETS	0.666	0.55	0.797	0.666	0.55	0.797	SUBCLONAL	1	FALSE	1	0.196601020694051	2		483	580	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939646	131939646	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	37	498	0	ENST00000265335.6:c.2432A>G	p.Gln811Arg	p.Q811R	ENST00000265335		811	cAa/cGa	15/25	1	2	FACETS	0.77	0.634	0.922	0.77	0.634	0.922	CLONAL	1	FALSE	1	0.196601020694051	2		498	489	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031979	26031979	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1409	131	880	1	ENST00000244661.2:c.310C>A	p.Leu104Ile	p.L104I	ENST00000244661	NM_003537.3	104	Ctc/Atc	1/1	0.196601020694051	7	FACETS	1	0.979	1			1	CLONAL	1	FALSE	NA	0.196601020694051	7		881	1540	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672462	30672462	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148215318	NA	P-0007087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	147	595	4	ENST00000376406.3:c.4498G>A	p.Ala1500Thr	p.A1500T	ENST00000376406	NM_014641.2	1500	Gcc/Acc	10/15	0.136430637577122	3	FACETS	0.901	0.823	0.984	0.601	0.548	0.656	CLONAL	2	FALSE	0	0.196601020694051	3		599	911	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968242	2968242	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	99	596	0	ENST00000396946.4:c.1744C>T	p.Pro582Ser	p.P582S	ENST00000396946	NM_032415.4	582	Ccc/Tcc	13/25	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	FALSE	1	0.196601020694051	2		596	975	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739437	145739437	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1302391250	NA	P-0007087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	75	489	0	ENST00000428558.2:c.1933A>G	p.Thr645Ala	p.T645A	ENST00000428558	NM_004260.3	645	Aca/Gca	12/22	0.0982525080772325	3	FACETS	0.862	0.753	0.98	0.431	0.376	0.49	INDETERMINATE	1	FALSE	1	0.196601020694051	3		489	972	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333957	70333957	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	51	517	0	ENST00000373644.4:c.1862A>G	p.Lys621Arg	p.K621R	ENST00000373644	NM_030625.2	621	aAa/aGa	2/12	0.136430637577122	3	FACETS	0.979	0.832	1	0.326	0.277	0.381	CLONAL	1	FALSE	0	0.196601020694051	3		517	582	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14028136	14028136	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	54	571	0	ENST00000311895.7:c.1190A>G	p.Glu397Gly	p.E397G	ENST00000311895	NM_005236.2	397	gAg/gGg	7/11	0.196601020694051	1	FACETS	0.863	0.737	1	0.863	0.737	1	CLONAL	1	FALSE	0	0.196601020694051	1		571	574	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905143	50905143	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1266	88	660	0	ENST00000440232.2:c.425A>G	p.His142Arg	p.H142R	ENST00000440232	NM_002691.3	142	cAc/cGc	4/27	1	2	FACETS	0.661	0.583	0.745	0.661	0.583	0.745	SUBCLONAL	1	FALSE	1	0.196601020694051	2		660	1354	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205083	123205083	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	76	745	0	ENST00000218089.9:c.2443T>C	p.Tyr815His	p.Y815H	ENST00000218089	NM_001042749.1	815	Tat/Cat	25/35	0.196601020694051	1	FACETS	0.963	0.844	1	0.963	0.844	1	CLONAL	1	FALSE	0	0.196601020694051	1		745	724	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765621	41765621	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	91	647	2	ENST00000301178.4:c.2501del	p.Pro834LeufsTer122	p.P834Lfs*122	ENST00000301178	NM_021913.4	833	Ccc/cc	20/20	1	2	FACETS	0.974	0.864	1	0.974	0.864	1	CLONAL	1	FALSE	1	0.196601020694051	2		649	950	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0007109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	420	433	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.394079902017749	3	FACETS	0.959	0.922	0.996	0.959	0.922	0.996	CLONAL	3	TRUE	0	0.480200552443075	3		436	754	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519925	NA	P-0007109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	138	387	0	ENST00000263967.3:c.1357G>C	p.Glu453Gln	p.E453Q	ENST00000263967	NM_006218.2	453	Gaa/Caa	8/21	0.472860845074824	3	FACETS	0.964	0.879	1	0.482	0.439	0.527	CLONAL	1	TRUE	1	0.480200552443075	3		387	739	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432741	49432741	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1315374796	NA	P-0007109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	79	298	1	ENST00000301067.7:c.8398C>T	p.Gln2800Ter	p.Q2800*	ENST00000301067	NM_003482.3	2800	Cag/Tag	34/54	0.472860845074824	3	FACETS	1	0.931	1	0.537	0.475	0.602	CLONAL	1	TRUE	1	0.480200552443075	3		299	380	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021828	71021828	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0007109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	89	257	0	ENST00000318789.4:c.1531-1G>C		p.X511_splice	ENST00000318789	NM_032682.5	511			0.472860845074824	3	FACETS	0.848	0.754	0.948	0.424	0.377	0.474	CLONAL	1	TRUE	1	0.480200552443075	3		257	542	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468182	50468182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	107	496	1	ENST00000331340.3:c.1417G>A	p.Asp473Asn	p.D473N	ENST00000331340	NM_006060.4	473	Gat/Aat	8/8	1	2	FACETS	0.734	0.66	0.813	0.734	0.66	0.813	SUBCLONAL	1	TRUE	1	0.480200552443075	2		497	607	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458042	120458042	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	138	495	1	ENST00000256646.2:c.7303G>A	p.Asp2435Asn	p.D2435N	ENST00000256646	NM_024408.3	2435	Gac/Aac	34/34	0.404879316270599	3	FACETS	0.93	0.848	1	0.465	0.424	0.509	CLONAL	1	TRUE	1	0.480200552443075	3		496	766	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215617242	215617242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	346	468	0	ENST00000260947.4:c.1606G>A	p.Asp536Asn	p.D536N	ENST00000260947	NM_000465.2	536	Gat/Aat	7/11	0.33876208637296	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.480200552443075	4		468	1009	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197399	26197399	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1754	494	867	0	ENST00000356476.2:c.80G>C	p.Arg27Pro	p.R27P	ENST00000356476		27	cGa/cCa	1/1	0.480200552443075	6	FACETS	0.897	0.855	0.94			1	CLONAL	2	TRUE	NA	0.480200552443075	6		867	2248	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672525	30672525	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	333	654	0	ENST00000376406.3:c.4435G>C	p.Asp1479His	p.D1479H	ENST00000376406	NM_014641.2	1479	Gat/Cat	10/15	0.276009273697307	5	FACETS	0.834	0.79	0.878	0.834	0.79	0.878	INDETERMINATE	3	TRUE	2	0.480200552443075	5		654	954	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741833	145741833	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	303	581	0	ENST00000428558.2:c.670G>C	p.Glu224Gln	p.E224Q	ENST00000428558	NM_004260.3	224	Gag/Cag	5/22	0.404879316270599	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.480200552443075	3		581	727	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12043951	12043951	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	270	443	2	ENST00000396373.4:c.1330G>A	p.Glu444Lys	p.E444K	ENST00000396373	NM_001987.4	444	Gaa/Aaa	8/8	0.276009273697307	5	FACETS	0.942	0.884	1	0.628	0.589	0.668	INDETERMINATE	2	TRUE	2	0.480200552443075	5		445	1027	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346883	73346883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	210	438	0	ENST00000377767.4:c.1334C>T	p.Ser445Leu	p.S445L	ENST00000377767	NM_014953.3	445	tCa/tTa	9/21	0.404879316270599	3	FACETS	0.958	0.889	1	0.479	0.444	0.515	CLONAL	1	TRUE	1	0.480200552443075	3		438	1132	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473630	67473630	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	139	546	0	ENST00000327367.4:c.710A>C	p.Tyr237Ser	p.Y237S	ENST00000327367	NM_005902.3	237	tAc/tCc	6/9	1	2	FACETS	0.878	0.802	0.959	0.878	0.802	0.959	CLONAL	1	TRUE	1	0.480200552443075	2		546	659	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868682	37868682	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	221	529	0	ENST00000269571.5:c.1129C>G	p.Leu377Val	p.L377V	ENST00000269571		377	Ctg/Gtg	9/27	0.480200552443075	3	FACETS	1	0.989	1	0.664	0.619	0.711	CLONAL	1	TRUE	1	0.480200552443075	3		529	859	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138480	11138480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	283	523	0	ENST00000358026.2:c.3236C>T	p.Ser1079Leu	p.S1079L	ENST00000358026	NM_001128849.1	1079	tCg/tTg	24/36	0.480200552443075	1	FACETS	0.828	0.787	0.868	1	0.995	1	CLONAL	2	TRUE	0	0.480200552443075	1		523	541	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798863	42798863	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1256197247	NA	P-0007109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	120	479	0	ENST00000575354.2:c.4435C>G	p.Gln1479Glu	p.Q1479E	ENST00000575354	NM_015125.3	1479	Cag/Gag	19/20	0.404879316270599	3	FACETS	0.942	0.852	1	0.471	0.426	0.518	CLONAL	1	TRUE	1	0.480200552443075	3		479	658	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929104	44929105	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	341	300	0	ENST00000377967.4:c.2205dup	p.Glu736ArgfsTer4	p.E736Rfs*4	ENST00000377967	NM_021140.2	735	gga/ggAa	17/29	0.419021918471609	2	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.480200552443075	2		300	642	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533628	63533628	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	241	686	0	ENST00000307078.5:c.1526del	p.Gln509ArgfsTer180	p.Q509Rfs*180	ENST00000307078	NM_004655.3	509	cAg/cg	6/11	0.480200552443075	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.480200552443075	3		686	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882019	NA	P-0007218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	602	499	0	ENST00000269305.4:c.455dup	p.Pro153AlafsTer28	p.P153Afs*28	ENST00000269305	NM_001126112.2	152	ccg/ccCg	5/11	0.742999524974084	2	FACETS	0.882	0.858	0.905	0.882	0.858	0.905	CLONAL	2	TRUE	0	0.810879704181984	2		499	842	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374935	45374935	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	66	474	0	ENST00000262160.6:c.908C>G	p.Thr303Arg	p.T303R	ENST00000262160	NM_005901.5	303	aCa/aGa	8/11	0.724987231838441	2	FACETS	0.723	0.637	0.814	0.362	0.318	0.407	SUBCLONAL	1	TRUE	0	0.810879704181984	2		474	225	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183742	10183742	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	365	413	3	ENST00000256474.2:c.211C>A	p.Pro71Thr	p.P71T	ENST00000256474	NM_000551.3	71	Ccc/Acc	1/3	0.459947274826106	3	FACETS	0.863	0.825	0.901			1	INDETERMINATE	2	TRUE	NA	0.810879704181984	3		416	733	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672758	86672758	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1204340475	NA	P-0007218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	96	510	0	ENST00000274376.6:c.2245C>T	p.Arg749Ter	p.R749*	ENST00000274376	NM_002890.2	749	Cga/Tga	17/25	0.742999524974084	2	FACETS	0.852	0.793	0.907	0.852	0.793	0.907	CLONAL	2	TRUE	0	0.810879704181984	2		510	139	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274196	10274196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	138	251	1	ENST00000330684.3:c.73G>A	p.Ala25Thr	p.A25T	ENST00000330684	NM_001134407.1	25	Gcg/Acg	2/13	0.810879704181984	4	FACETS	0.93	0.848	1	0.465	0.424	0.508	CLONAL	1	TRUE	2	0.810879704181984	4		252	663	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031687	36031687	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1159129326	NA	P-0007218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1934	290	575	3	ENST00000358208.4:c.1516C>T	p.Pro506Ser	p.P506S	ENST00000358208		506	Cct/Tct	12/12	0.810879704181984	7	FACETS	0.974	0.911	1	0.195	0.182	0.208	CLONAL	1	TRUE	2	0.810879704181984	7		578	2224	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344889	70344889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768834535	NA	P-0007218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	304	700	0	ENST00000374080.3:c.2119G>A	p.Glu707Lys	p.E707K	ENST00000374080		707	Gag/Aag	15/45	0.395510085788371	5	FACETS	1	0.99	1	0.417	0.392	0.442	INDETERMINATE	1	TRUE	2	0.810879704181984	5		700	1329	SUCCESS
APC	324	MSKCC	GRCh37	5	112157591	112157592	+	splice_acceptor_variant	Splice_Site	INS	-	-	GTGCCAGCTCCTGTTGAACATCAGATCTGTCCTGCTGTGTGTGTGGT	novel	NA	P-0007218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	147	440	0	ENST00000257430.4:c.1355_1356insGGTGTGCCAGCTCCTGTTGAACATCAGATCTGTCCTGCTGTGTGTGT		p.X452_splice	ENST00000257430	NM_000038.5	452			0.742999524974084	2	FACETS	0.859	0.792	0.928	0.43	0.396	0.464	CLONAL	1	TRUE	0	0.810879704181984	2		440	422	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903780	114903780	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	160	629	0	ENST00000543371.1:c.785del	p.Pro262HisfsTer23	p.P262Hfs*23	ENST00000543371	NM_001198531.1	262	Cca/ca	7/14	1	2	FACETS	0.771	0.712	0.832	0.771	0.712	0.832	SUBCLONAL	1	TRUE	1	0.810879704181984	2		629	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0007222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	196	654	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.555533076950829	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.615708809984019	1		655	409	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0007222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	89	403	1	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.165404047182456	2	FACETS	0.973	0.873	1	0.487	0.436	0.539	INDETERMINATE	1	TRUE	0	0.615708809984019	2		404	297	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746132	162746132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1374086542	NA	P-0007222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	65	412	1	ENST00000367921.3:c.2255G>A	p.Arg752His	p.R752H	ENST00000367921	NM_006182.2	752	cGc/cAc	16/18	0.261668856138989	3	FACETS	0.669	0.582	0.762	0.223	0.194	0.254	INDETERMINATE	1	TRUE	0	0.615708809984019	3		413	413	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74868211	74868211	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	11	105	0	ENST00000284811.8:c.83A>G	p.Glu28Gly	p.E28G	ENST00000284811		28	gAa/gGa	3/4	0.615745721821845	4	FACETS	0.962	0.68	1	0.321	0.226	0.432	CLONAL	1	TRUE	1	0.615708809984019	4		105	60	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858493	9858493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765257420	NA	P-0007222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	36	469	0	ENST00000330684.3:c.2908C>T	p.Arg970Trp	p.R970W	ENST00000330684	NM_001134407.1	970	Cgg/Tgg	13/13	1	2	FACETS	0.79	0.66	0.93	0.79	0.66	0.93	CLONAL	1	TRUE	1	0.615708809984019	2		469	148	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916143	9916143	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	63	415	0	ENST00000330684.3:c.2146G>T	p.Ala716Ser	p.A716S	ENST00000330684	NM_001134407.1	716	Gcc/Tcc	10/13	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.615708809984019	2		415	188	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042110	14042110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1474828281	NA	P-0007222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	108	432	0	ENST00000311895.7:c.2657G>A	p.Ser886Asn	p.S886N	ENST00000311895	NM_005236.2	886	aGt/aAt	11/11	1	2	FACETS	0.886	0.802	0.974	0.886	0.802	0.974	CLONAL	1	TRUE	1	0.615708809984019	2		432	396	SUCCESS
APC	324	MSKCC	GRCh37	5	112173614	112173615	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0007222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	55	446	0	ENST00000257430.4:c.2323_2324del	p.Asn775TyrfsTer12	p.N775Yfs*12	ENST00000257430	NM_000038.5	775	AAt/t	16/16	0.275098497168771	3	FACETS	1	0.913	1	0.536	0.464	0.612	INDETERMINATE	1	TRUE	1	0.615708809984019	3		446	218	SUCCESS
APC	324	MSKCC	GRCh37	5	112175646	112175647	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0007222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	93	538	0	ENST00000257430.4:c.4356_4357dup	p.Pro1453HisfsTer21	p.P1453Hfs*21	ENST00000257430	NM_000038.5	1452	gta/gtACa	16/16	0.275098497168771	3	FACETS	1	0.952	1	0.553	0.496	0.613	INDETERMINATE	1	TRUE	1	0.615708809984019	3		538	357	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0007230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	289	443	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	1	2	FACETS	0.736	0.694	0.779	0.736	0.694	0.779	SUBCLONAL	1	TRUE	1	0.901351639826402	2		443	871	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544644	65544653	+	frameshift_variant	Frame_Shift_Del	DEL	AAGAGCATTC	AAGAGCATTC	-	novel	NA	P-0007230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	543	399	0	ENST00000358664.4:c.273_282del	p.Gln91HisfsTer76	p.Q91Hfs*76	ENST00000358664	NM_002382.4	91	caGAATGCTCTT/ca	4/5	0.899004073090887	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.901351639826402	1		399	620	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482926	140482927	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs777474487	NA	P-0007311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	32	438	1	ENST00000288602.6:c.1208dup	p.Ala404CysfsTer9	p.A404Cfs*9	ENST00000288602	NM_004333.4	403	cct/ccCt	10/18	0.575442831938352	1	FACETS	0.163	0.132	0.198	0.163	0.132	0.198	SUBCLONAL	1	TRUE	0	0.575442831938352	1		439	486	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0007311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	112	110	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	0.998	0.925	1	1	0.991	1	CLONAL	2	TRUE	1	0.575442831938352	2		110	195	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0007311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	382	433	3	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	0.997	1	CLONAL	2	TRUE	1	0.575442831938352	2		436	651	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029527	14029527	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	22	191	0	ENST00000311895.7:c.1738C>G	p.Leu580Val	p.L580V	ENST00000311895	NM_005236.2	580	Ctt/Gtt	8/11	0.575442831938352	1	FACETS	0.186	0.144	0.235	0.186	0.144	0.235	SUBCLONAL	1	TRUE	0	0.575442831938352	1		191	293	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0007311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	198	415	2	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.575442831938352	2		417	628	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0007311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	118	147	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.936	0.851	1	0.936	0.851	1	CLONAL	1	TRUE	1	0.575442831938352	2		147	438	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245795	5245795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368461283	NA	P-0007311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	29	326	0	ENST00000357368.4:c.980C>T	p.Thr327Met	p.T327M	ENST00000357368	NM_002850.3	327	aCg/aTg	10/38	1	2	FACETS	0.212	0.169	0.26	0.212	0.169	0.26	SUBCLONAL	1	TRUE	1	0.575442831938352	2		326	476	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36824402	36824402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	216	390	2	ENST00000373129.3:c.134C>T	p.Pro45Leu	p.P45L	ENST00000373129	NM_032017.1	45	cCg/cTg	4/12	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.575442831938352	2		392	712	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741822	162741822	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	123	288	0	ENST00000367921.3:c.1513G>T	p.Gly505Cys	p.G505C	ENST00000367921	NM_006182.2	505	Ggt/Tgt	13/18	1	2	FACETS	0.98	0.893	1	0.98	0.893	1	CLONAL	1	TRUE	1	0.575442831938352	2		288	436	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794854	242794854	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1230474759	NA	P-0007311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	26	317	0	ENST00000334409.5:c.355G>A	p.Gly119Ser	p.G119S	ENST00000334409	NM_005018.2	119	Ggc/Agc	2/5	1	2	FACETS	0.209	0.165	0.26	0.209	0.165	0.26	SUBCLONAL	1	TRUE	1	0.575442831938352	2		317	432	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156534	55156534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778597	NA	P-0007311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	226	431	0	ENST00000257290.5:c.2935C>T	p.Arg979Cys	p.R979C	ENST00000257290	NM_006206.4	979	Cgc/Tgc	22/23	0.575442831938352	3	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.575442831938352	3		431	935	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6027082	6027082	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	50	122	0	ENST00000265849.7:c.1314G>T	p.Lys438Asn	p.K438N	ENST00000265849	NM_000535.5	438	aaG/aaT	11/15	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.575442831938352	2		122	161	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570205	87570205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	80	156	0	ENST00000277120.3:c.1945G>A	p.Gly649Ser	p.G649S	ENST00000277120		649	Ggc/Agc	17/19	0.575442831938352	3	FACETS	1	0.956	1	0.577	0.513	0.645	CLONAL	1	TRUE	1	0.575442831938352	3		156	310	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570404	87570404	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	203	496	0	ENST00000277120.3:c.2144G>T	p.Arg715Leu	p.R715L	ENST00000277120		715	cGg/cTg	17/19	0.575442831938352	3	FACETS	1	0.935	1	0.504	0.468	0.542	CLONAL	1	TRUE	1	0.575442831938352	3		496	901	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391506	139391506	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202096917	NA	P-0007311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	203	450	0	ENST00000277541.6:c.6685G>A	p.Val2229Met	p.V2229M	ENST00000277541	NM_017617.3	2229	Gtg/Atg	34/34	0.575442831938352	3	FACETS	1	0.986	1	0.622	0.579	0.667	CLONAL	1	TRUE	1	0.575442831938352	3		450	730	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332759	70332759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775155506	NA	P-0007311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	142	311	0	ENST00000373644.4:c.664C>T	p.Arg222Cys	p.R222C	ENST00000373644	NM_030625.2	222	Cgc/Tgc	2/12	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.575442831938352	2		311	468	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310845	123310845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1474313509	NA	P-0007311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	167	392	1	ENST00000358487.5:c.583G>A	p.Gly195Arg	p.G195R	ENST00000358487	NM_000141.4	195	Ggg/Agg	5/18	1	2	FACETS	0.989	0.913	1	0.989	0.913	1	CLONAL	1	TRUE	1	0.575442831938352	2		393	587	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374583	118374583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1390104203	NA	P-0007311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	25	433	0	ENST00000534358.1:c.7976G>A	p.Arg2659Gln	p.R2659Q	ENST00000534358	NM_005933.3	2659	cGa/cAa	27/36	0.575442831938352	1	FACETS	0.125	0.097	0.156	0.125	0.097	0.156	SUBCLONAL	1	TRUE	0	0.575442831938352	1		433	497	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435979	49435979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	182	413	0	ENST00000301067.7:c.6002G>A	p.Arg2001Gln	p.R2001Q	ENST00000301067	NM_003482.3	2001	cGg/cAg	28/54	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.575442831938352	2		413	610	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914004	32914004	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	273	654	0	ENST00000380152.3:c.5512G>C	p.Glu1838Gln	p.E1838Q	ENST00000380152		1838	Gag/Cag	11/27	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.575442831938352	2		654	919	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980007	7980007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147992320	NA	P-0007311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	161	288	0	ENST00000319144.4:c.1330G>A	p.Val444Ile	p.V444I	ENST00000319144	NM_001139.2	444	Gtt/Att	10/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.575442831938352	2		288	502	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897445	78897445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334868419	NA	P-0007311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	112	427	0	ENST00000306801.3:c.2780G>A	p.Arg927Gln	p.R927Q	ENST00000306801	NM_020761.2	927	cGg/cAg	23/34	1	2	FACETS	0.753	0.68	0.829	0.753	0.68	0.829	SUBCLONAL	1	TRUE	1	0.575442831938352	2		427	517	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125296	7125296	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs777937157	NA	P-0007311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	148	354	0	ENST00000302850.5:c.3256G>A	p.Val1086Met	p.V1086M	ENST00000302850	NM_000208.2	1086	Gtg/Atg	17/22	1	2	FACETS	0.961	0.883	1	0.961	0.883	1	CLONAL	1	TRUE	1	0.575442831938352	2		354	535	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383793	15383793	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768982122	NA	P-0007311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	41	440	1	ENST00000263377.2:c.118G>A	p.Ala40Thr	p.A40T	ENST00000263377	NM_058243.2	40	Gca/Aca	2/20	1	2	FACETS	0.202	0.167	0.24	0.202	0.167	0.24	SUBCLONAL	1	TRUE	1	0.575442831938352	2		441	707	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795412	42795412	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	76	224	0	ENST00000575354.2:c.2492C>T	p.Thr831Met	p.T831M	ENST00000575354	NM_015125.3	831	aCg/aTg	10/20	1	2	FACETS	0.878	0.777	0.983	0.878	0.777	0.983	CLONAL	1	TRUE	1	0.575442831938352	2		224	301	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484814	57484814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	39	417	3	ENST00000371085.3:c.794G>A	p.Arg265His	p.R265H	ENST00000371085	NM_000516.4	265	cGc/cAc	10/13	1	2	FACETS	0.19	0.157	0.227	0.19	0.157	0.227	SUBCLONAL	1	TRUE	1	0.575442831938352	2		420	713	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321345	1321345	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1348679931	NA	P-0007311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	143	406	1	ENST00000400841.2:c.410C>T	p.Thr137Met	p.T137M	ENST00000400841		137	aCg/aTg	4/6	1	1	FACETS	0.569	0.52	0.62	0.569	0.52	0.62	SUBCLONAL	1	TRUE	0	0.575442831938352	1		407	622	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430386	47430386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs979276829	NA	P-0007311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	34	238	0	ENST00000377045.4:c.1661G>A	p.Arg554Gln	p.R554Q	ENST00000377045	NM_001654.4	554	cGg/cAg	15/16	1	1	FACETS	0.244	0.199	0.294	0.244	0.199	0.294	SUBCLONAL	1	TRUE	0	0.575442831938352	1		238	345	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481454	20481455	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	127	270	0	ENST00000346618.3:c.529dup	p.Thr177AsnfsTer4	p.T177Nfs*4	ENST00000346618	NM_001949.4	175	gaa/gAaa	3/7	1	2	FACETS	0.878	0.799	0.959	0.878	0.799	0.959	CLONAL	1	TRUE	1	0.575442831938352	2		270	503	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206647734	206647736	+	missense_variant	Missense_Mutation	TNP	GAG	GAG	TAT	novel	NA	P-0007311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	150	375	0	ENST00000367120.3:c.148_150delinsTAT	p.Glu50Tyr	p.E50Y	ENST00000367120	NM_014002.3	50	GAG/TAT	4/22	1	2	FACETS	0.943	0.866	1	0.943	0.866	1	CLONAL	1	TRUE	1	0.575442831938352	2		375	553	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007318-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	197	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.329274789296579	5	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	3	0.329274789296579	5		311	730	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031973	26031973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007318-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1660	145	865	0	ENST00000244661.2:c.316G>C	p.Glu106Gln	p.E106Q	ENST00000244661	NM_003537.3	106	Gag/Cag	1/1	0.322864781908217	4	FACETS	0.649	0.589	0.712	0.324	0.294	0.356	SUBCLONAL	1	TRUE	2	0.329274789296579	4		865	1805	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936094	49936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007318-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1373	214	776	0	ENST00000296474.3:c.1576G>T	p.Gly526Cys	p.G526C	ENST00000296474	NM_002447.2	526	Ggc/Tgc	4/20	0.329274789296579	3	FACETS	0.954	0.883	1	0.477	0.441	0.514	CLONAL	1	TRUE	1	0.329274789296579	3		776	1587	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120925	115120925	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007318-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	268	427	0	ENST00000257566.3:c.81C>A	p.Asp27Glu	p.D27E	ENST00000257566	NM_016569.3	27	gaC/gaA	1/8	0.329274789296579	5	FACETS	0.869	0.816	0.923	1	0.991	1	CLONAL	3	TRUE	3	0.329274789296579	5		427	933	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544655	65544655	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007318-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	446	546	2	ENST00000358664.4:c.271C>T	p.Gln91Ter	p.Q91*	ENST00000358664	NM_002382.4	91	Cag/Tag	4/5	0.310740242790195	3	FACETS	0.953	0.911	0.994	0.953	0.911	0.994	CLONAL	3	TRUE	0	0.329274789296579	3		548	1104	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40744835	40744835	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007318-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	247	555	0	ENST00000392038.2:c.685A>G	p.Met229Val	p.M229V	ENST00000392038	NM_001626.4	229	Atg/Gtg	8/14	0.140104485961923	4	FACETS	0.865	0.808	0.924	0.865	0.808	0.924	INDETERMINATE	2	TRUE	2	0.329274789296579	4		555	1153	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039625	47039626	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTGCAGATC	novel	NA	P-0007318-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	148	233	0	ENST00000377604.3:c.1084_1092dup	p.Ile362_Gln364dup	p.I362_Q364dup	ENST00000377604	NM_001204468.1	362	-/CTGCAGATC	11/24	0.329274789296579	2	FACETS	1	0.958	1			1	CLONAL	2	TRUE	NA	0.329274789296579	2		233	425	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692920	89692921	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs398123323	NA	P-0007335-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	38	197	0	ENST00000371953.3:c.405dup	p.Cys136MetfsTer44	p.C136Mfs*44	ENST00000371953	NM_000314.4	135	ata/atAa	5/9	1	2	FACETS	0.411	0.339	0.492	0.411	0.339	0.492	SUBCLONAL	1	TRUE	1	0.282248503265284	2		197	655	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249717	110249717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007335-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	115	183	1	ENST00000374672.4:c.958G>A	p.Gly320Ser	p.G320S	ENST00000374672	NM_004235.4	320	Ggt/Agt	3/5	0.282248503265284	3	FACETS	0.882	0.798	0.97	0.882	0.798	0.97	CLONAL	2	TRUE	1	0.282248503265284	3		184	527	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs587781702	NA	P-0007335-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	107	242	0	ENST00000269305.4:c.920-1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.282248503265284	2		242	645	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618689	37618690	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	51	448	0	ENST00000447079.4:c.366dup	p.Leu123ThrfsTer4	p.L123Tfs*4	ENST00000447079	NM_015083.1	122	tta/ttAa	1/14	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		448	917	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0007365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	215	533	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.640627068620732	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.640627068620732	1		533	339	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120612014	120612014	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs782113557	NA	P-0007365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	10	39	1	ENST00000256646.2:c.7G>T	p.Ala3Ser	p.A3S	ENST00000256646	NM_024408.3	3	Gcc/Tcc	1/34	0.209012850765104	2	FACETS	0.363	0.248	0.503	0.182	0.124	0.252	INDETERMINATE	1	TRUE	0	0.640627068620732	2		40	86	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606696	29606696	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769910087	NA	P-0007365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	105	360	0	ENST00000389048.3:c.1184G>A	p.Arg395His	p.R395H	ENST00000389048	NM_004304.4	395	cGt/cAt	5/29	0.209012850765104	2	FACETS	1	0.981	1	0.65	0.593	0.708	INDETERMINATE	1	TRUE	0	0.640627068620732	2		360	252	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920413	114920413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767830105	NA	P-0007365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	241	530	1	ENST00000543371.1:c.1354G>A	p.Gly452Arg	p.G452R	ENST00000543371	NM_001198531.1	452	Ggg/Agg	13/14	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.640627068620732	2		531	524	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801148	1801148	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199968400	NA	P-0007365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	10	309	0	ENST00000260795.2:c.277C>T	p.Arg93Trp	p.R93W	ENST00000260795		93	Cgg/Tgg	2/17	0.640627068620732	1	FACETS	0.112	0.075	0.157	0.112	0.075	0.157	SUBCLONAL	1	TRUE	0	0.640627068620732	1		309	190	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593394	48593394	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	74	294	0	ENST00000342988.3:c.1145A>G	p.His382Arg	p.H382R	ENST00000342988	NM_005359.5	382	cAc/cGc	10/12	0.640627068620732	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.640627068620732	1		294	129	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385182	41385182	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367872006	NA	P-0007365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	59	420	0	ENST00000373198.4:c.779G>A	p.Arg260Gln	p.R260Q	ENST00000373198	NM_133170.3	260	cGg/cAg	6/32	0.233837142779315	4	FACETS	0.518	0.446	0.597	0.173	0.148	0.199	INDETERMINATE	1	TRUE	1	0.640627068620732	4		420	583	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28644740	28644741	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	54	332	1	ENST00000241453.7:c.52dup	p.Ser18PhefsTer24	p.S18Ffs*24	ENST00000241453	NM_004119.2	18	tct/tTct	2/24	0.256044155540753	3	FACETS	0.702	0.603	0.809	0.234	0.201	0.27	INDETERMINATE	1	TRUE	0	0.640627068620732	3		333	317	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0007401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	240	201	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.944	0.89	0.998	1	0.995	1	CLONAL	2	TRUE	1	0.46745262598125	2		201	544	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179441	56179441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	139	343	1	ENST00000399503.3:c.3754G>A	p.Gly1252Arg	p.G1252R	ENST00000399503	NM_005921.1	1252	Gga/Aga	15/20	0.466142629242955	3	FACETS	0.837	0.761	0.916	0.418	0.38	0.458	CLONAL	1	TRUE	1	0.46745262598125	3		344	877	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201879	67201879	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs577172628	NA	P-0007401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	98	273	0	ENST00000312629.5:c.1079C>A	p.Thr360Asn	p.T360N	ENST00000312629	NM_003952.2	360	aCc/aAc	13/15	1	2	FACETS	0.83	0.744	0.922	0.83	0.744	0.922	CLONAL	1	TRUE	1	0.46745262598125	2		273	505	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115700	8115711	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGATTAACAGAC	AGATTAACAGAC	-	novel	NA	P-0007401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	186	412	0	ENST00000346208.3:c.1048-2_1057del		p.X350_splice	ENST00000346208		350		6/6	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.46745262598125	2		412	789	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180546	56180547	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	294	280	0	ENST00000399503.3:c.3876dup	p.Glu1293ArgfsTer16	p.E1293Rfs*16	ENST00000399503	NM_005921.1	1292	aga/agAa	16/20	0.466142629242955	3	FACETS	0.99	0.936	1	0.99	0.936	1	CLONAL	2	TRUE	1	0.46745262598125	3		280	784	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007424-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	59	697	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		697	793	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987105	36987106	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0007424-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	21	232	0	ENST00000354822.5:c.583dup	p.Arg195ProfsTer244	p.R195Pfs*244	ENST00000354822	NM_001079668.2	195	cgg/cCgg	3/3	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		232	313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0007508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	784	455	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.601809245165224	3	FACETS	0.969	0.945	0.993	0.969	0.945	0.993	CLONAL	3	TRUE	0	0.601809245165224	3		457	1166	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0007508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	494	322	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.402596745799682	6	FACETS	0.843	0.807	0.88	0.843	0.807	0.88	CLONAL	3	TRUE	3	0.601809245165224	6		322	1430	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153609	55153609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501520	NA	P-0007508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	143	390	0	ENST00000257290.5:c.2575G>A	p.Val859Met	p.V859M	ENST00000257290	NM_006206.4	859	Gtg/Atg	19/23	1	2	FACETS	0.51	0.465	0.558	0.51	0.465	0.558	SUBCLONAL	1	TRUE	1	0.601809245165224	2		390	931	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300444	11300444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	158	290	0	ENST00000361445.4:c.1702C>T	p.Pro568Ser	p.P568S	ENST00000361445	NM_004958.3	568	Cct/Tct	11/58	0.601809245165224	3	FACETS	0.921	0.845	0.999	0.46	0.422	0.5	CLONAL	1	TRUE	1	0.601809245165224	3		290	742	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001342	29001342	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	218	339	1	ENST00000282397.4:c.1390A>G	p.Ile464Val	p.I464V	ENST00000282397	NM_002019.4	464	Atc/Gtc	10/30	0.580132011396778	3	FACETS	0.928	0.863	0.995	0.464	0.431	0.498	CLONAL	1	TRUE	1	0.601809245165224	3		340	1016	SUCCESS
APC	324	MSKCC	GRCh37	5	112174176	112174177	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0007508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	278	447	0	ENST00000257430.4:c.2886dup	p.Ser963Ter	p.S963*	ENST00000257430	NM_000038.5	962	gat/gaTt	16/16	0.601809245165224	1	FACETS	0.908	0.858	0.959	0.908	0.858	0.959	CLONAL	1	TRUE	0	0.601809245165224	1		447	711	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0007579-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	127	408	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	0.161475879187412	1	FACETS	0.836	0.76	0.916	0.836	0.76	0.916	INDETERMINATE	1	TRUE	0	0.403479680752429	1		408	601	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	276	983	0	ENST00000206249.3:c.1610A>G	p.Tyr537Cys	p.Y537C	ENST00000206249	NM_000125.3	537	tAt/tGt	8/8	0.525748367001818	6	FACETS	1	0.985	1	0.874	0.841	0.905	CLONAL	5	TRUE	0	0.648237478750068	6		983	373	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123107	5123107	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs774539976	NA	P-0007594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	94	311	0	ENST00000381652.3:c.3163A>G	p.Lys1055Glu	p.K1055E	ENST00000381652	NM_004972.3	1055	Aaa/Gaa	23/25	0.594239477366079	2	FACETS	0.815	0.746	0.883	0.815	0.746	0.883	CLONAL	2	TRUE	0	0.648237478750068	2		311	178	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099360	193099360	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	112	288	0	ENST00000367435.3:c.294del	p.Asn99MetfsTer10	p.N99Mfs*10	ENST00000367435	NM_024529.4	98	ctC/ct	3/17	0.648237478750068	6	FACETS	0.961	0.871	1	0.48	0.435	0.527	CLONAL	2	TRUE	2	0.648237478750068	6		288	413	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859689	151859690	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0007594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	106	241	0	ENST00000262189.6:c.10972dup	p.Gln3658ProfsTer30	p.Q3658Pfs*30	ENST00000262189	NM_170606.2	3658	caa/cCaa	43/59	NA	2	FACETS	0.908	0.841	0.975			1	INDETERMINATE	2	TRUE	NA	0.648237478750068	2		241	180	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007607-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	67	697	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.933	0.808	1	0.933	0.808	1	CLONAL	1	TRUE	1	0.13	2		697	1105	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100175	27100176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0007607-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	42	270	0	ENST00000324856.7:c.3977dup	p.Gln1327AlafsTer11	p.Q1327Afs*11	ENST00000324856	NM_006015.4	1324	tac/taCc	16/20	1	2	FACETS	0.822	0.684	0.976	0.822	0.684	0.976	CLONAL	1	TRUE	1	0.13	2		270	786	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436026	56436026	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771831816	NA	P-0007607-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	41	250	0	ENST00000407977.2:c.1111C>T	p.Arg371Ter	p.R371*	ENST00000407977		371	Cga/Tga	9/10	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.13	2		250	579	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143190	24143190	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007607-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1230	83	428	0	ENST00000263121.7:c.422A>G	p.His141Arg	p.H141R	ENST00000263121	NM_003073.3	141	cAc/cGc	4/9	1	2	FACETS	0.973	0.855	1	0.973	0.855	1	CLONAL	1	TRUE	1	0.13	2		428	1313	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	212	480	2	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	0.109745741667261	3	FACETS	1	0.992	1	0.737	0.689	0.785	INDETERMINATE	1	TRUE	1	0.66	3		482	580	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0007675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	278	1035	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.877	0.825	0.93	0.877	0.825	0.93	CLONAL	1	TRUE	1	0.66	2		1036	961	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	109	240	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	0.109745741667261	3	FACETS	0.732	0.659	0.809	0.366	0.329	0.405	INDETERMINATE	1	TRUE	1	0.66	3		240	600	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0007675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	56	193	3	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	0.3	1	FACETS	0.673	0.588	0.762	0.673	0.588	0.762	INDETERMINATE	1	TRUE	0	0.66	1		196	169	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979987	7979987	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746723399	NA	P-0007675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	145	301	0	ENST00000319144.4:c.1350del	p.Leu451SerfsTer16	p.L451Sfs*16	ENST00000319144	NM_001139.2	450	ggG/gg	10/15	1	2	FACETS	0.832	0.764	0.903	0.832	0.764	0.903	CLONAL	1	TRUE	1	0.66	2		301	528	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0007675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	254	333	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.109745741667261	0	FACETS	0.64	0.61	0.669			1	INDETERMINATE	1	TRUE	0	0.66	0		335	409	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0007675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	261	406	4	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	0.243112527728357	3	FACETS	1	0.992	1	0.687	0.646	0.728	INDETERMINATE	1	TRUE	1	0.66	3		410	766	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245024	133245024	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs752846614	NA	P-0007675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	150	412	2	ENST00000320574.5:c.2091del	p.Leu698CysfsTer94	p.L698Cfs*94	ENST00000320574	NM_006231.2	697	ccC/cc	19/49	0.109745741667261	0	FACETS	0.328	0.302	0.355			1	INDETERMINATE	1	TRUE	0	0.66	0		414	471	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435136	110435136	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs780127725	NA	P-0007675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	166	305	0	ENST00000375856.3:c.3265G>C	p.Ala1089Pro	p.A1089P	ENST00000375856	NM_003749.2	1089	Gcc/Ccc	1/2	0.109745741667261	3	FACETS	1	0.989	1	0.716	0.664	0.77	INDETERMINATE	1	TRUE	1	0.66	3		305	467	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022309	31022309	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	199	472	0	ENST00000375687.4:c.1797del	p.Thr600ProfsTer103	p.T600Pfs*103	ENST00000375687	NM_015338.5	598	atC/at	13/13	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.66	2		472	566	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660807	227660808	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs747646240	NA	P-0007675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	133	287	0	ENST00000305123.5:c.2645_2647dup	p.Gln882dup	p.Q882dup	ENST00000305123	NM_005544.2	882	ccc/cAGCcc	1/2	0.109745741667261	3	FACETS	0.907	0.827	0.991	0.453	0.413	0.496	INDETERMINATE	1	TRUE	1	0.66	3		287	591	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630626	158630626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912678	NA	P-0007675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	269	587	0	ENST00000263640.3:c.617G>A	p.Arg206His	p.R206H	ENST00000263640	NM_001105.4	206	cGc/cAc	6/11	0.109745741667261	3	FACETS	1	0.992	1	0.678	0.639	0.719	INDETERMINATE	1	TRUE	1	0.66	3		587	799	SUCCESS
AR	367	MSKCC	GRCh37	X	66765148	66765149	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGC	rs752055010	NA	P-0007675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	26	240	0	ENST00000374690.3:c.170_172dup	p.Leu57dup	p.L57dup	ENST00000374690	NM_000044.3	57	ttg/tTGCtg	1/8	0.3	1	FACETS	0.222	0.176	0.274	0.222	0.176	0.274	INDETERMINATE	1	TRUE	0	0.66	1		240	238	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69229729	69229731	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0007675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	197	355	1	ENST00000462284.1:c.809_811del	p.Glu270del	p.E270del	ENST00000462284	NM_002392.5	269	GAA/-	9/11	0.3	4	FACETS	0.786	0.732	0.842			1	INDETERMINATE	2	TRUE	NA	0.66	4		356	630	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099309	27099310	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	190	385	0	ENST00000324856.7:c.3548dup	p.Asn1183LysfsTer10	p.N1183Kfs*10	ENST00000324856	NM_006015.4	1182	-/A	14/20	0.109745741667261	3	FACETS	1	0.986	1	0.623	0.578	0.668	INDETERMINATE	1	TRUE	1	0.66	3		385	615	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434588	49434589	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0007675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	154	260	0	ENST00000301067.7:c.6964_6965del	p.Lys2322AspfsTer3	p.K2322Dfs*3	ENST00000301067	NM_003482.3	2322	AAg/g	31/54	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.66	2		260	465	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258889	16258889	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	199	828	1	ENST00000375759.3:c.6158del	p.Asn2053ThrfsTer11	p.N2053Tfs*11	ENST00000375759	NM_015001.2	2052	Aaa/aa	11/15	0.109745741667261	3	FACETS	1	0.989	1	0.671	0.625	0.717	INDETERMINATE	1	TRUE	1	0.66	3		829	598	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936811	32936813	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0007675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	198	487	1	ENST00000380152.3:c.7961_7963del	p.Leu2654del	p.L2654del	ENST00000380152		2653	CTT/-	17/27	0.243112527728357	0	FACETS	0.325	0.303	0.349			1	INDETERMINATE	1	TRUE	0	0.66	0		488	627	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023465	31023465	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	214	383	0	ENST00000375687.4:c.2953del	p.Ile985SerfsTer8	p.I985Sfs*8	ENST00000375687	NM_015338.5	984	Aaa/aa	13/13	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.66	2		383	605	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202570	67202570	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	156	448	0	ENST00000312629.5:c.1382del	p.Pro461LeufsTer33	p.P461Lfs*33	ENST00000312629	NM_003952.2	460	gCc/gc	15/15	1	2	FACETS	0.89	0.82	0.962	0.89	0.82	0.962	CLONAL	1	TRUE	1	0.66	2		448	531	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720857	89720862	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTTC	CTTTTC	TT	novel	NA	P-0007675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	308	197	0	ENST00000371953.3:c.1008_1013delinsTT	p.Ser338GlnfsTer5	p.S338Qfs*5	ENST00000371953	NM_000314.4	336	taCTTTTCt/taTTt	8/9	0.718344782052291	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.66	2		197	428	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	73	440	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.737	0.646	0.833	0.737	0.646	0.833	SUBCLONAL	1	TRUE	1	0.438505099868614	2		440	452	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149799	202149799	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	60	382	0	ENST00000358485.4:c.1245del	p.Phe415LeufsTer26	p.F415Lfs*26	ENST00000358485	NM_001080125.1	414	Ttt/tt	8/9	0.198484505324068	3	FACETS	0.49	0.421	0.565	0.245	0.21	0.283	INDETERMINATE	1	TRUE	1	0.438505099868614	3		382	681	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	73	124	0	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.438505099868614	2		124	226	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	138	365	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.438505099868614	2		365	601	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	128	333	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.898	0.826	0.972	1	0.99	1	CLONAL	2	TRUE	1	0.438505099868614	2		335	325	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846336	156846336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781209572	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	140	435	2	ENST00000524377.1:c.1777C>T	p.Arg593Trp	p.R593W	ENST00000524377	NM_002529.3	593	Cgg/Tgg	14/17	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.438505099868614	2		437	571	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149973	202149973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1272714323	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	85	368	2	ENST00000358485.4:c.1414C>T	p.Arg472Ter	p.R472*	ENST00000358485	NM_001080125.1	472	Cga/Tga	8/9	0.198484505324068	3	FACETS	0.705	0.624	0.793	0.353	0.312	0.397	INDETERMINATE	1	TRUE	1	0.438505099868614	3		370	670	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104677	209104677	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	144	393	0	ENST00000345146.2:c.901A>G	p.Lys301Glu	p.K301E	ENST00000345146	NM_005896.2	301	Aag/Gag	8/10	0.198484505324068	3	FACETS	1	0.971	1	0.571	0.522	0.623	INDETERMINATE	1	TRUE	1	0.438505099868614	3		393	701	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370792	225370792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	233	445	0	ENST00000264414.4:c.1087G>A	p.Asp363Asn	p.D363N	ENST00000264414	NM_003590.4	363	Gac/Aac	8/16	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.438505099868614	2		445	821	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794773	242794773	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	32	178	0	ENST00000334409.5:c.436G>T	p.Glu146Ter	p.E146*	ENST00000334409	NM_005018.2	146	Gag/Tag	2/5	1	2	FACETS	0.685	0.56	0.824	0.685	0.56	0.824	SUBCLONAL	1	TRUE	1	0.438505099868614	2		178	213	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180190	38180190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1406387323	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	34	303	0	ENST00000396334.3:c.38C>T	p.Ala13Val	p.A13V	ENST00000396334	NM_002468.4	13	gCc/gTc	1/5	1	2	FACETS	0.439	0.359	0.529	0.439	0.359	0.529	SUBCLONAL	1	TRUE	1	0.438505099868614	2		303	353	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119666150	119666150	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	137	409	2	ENST00000316626.5:c.331C>T	p.Arg111Ter	p.R111*	ENST00000316626		111	Cga/Tga	3/12	1	2	FACETS	0.859	0.783	0.94	0.859	0.783	0.94	CLONAL	1	TRUE	1	0.438505099868614	2		411	727	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202731	128202731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	162	434	0	ENST00000341105.2:c.989G>A	p.Arg330Gln	p.R330Q	ENST00000341105	NM_032638.4	330	cGa/cAa	4/6	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.438505099868614	2		434	655	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808373	1808373	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	27	403	0	ENST00000260795.2:c.2131C>A	p.His711Asn	p.H711N	ENST00000260795		711	Cac/Aac	15/17	1	2	FACETS	0.244	0.193	0.302	0.244	0.193	0.302	SUBCLONAL	1	TRUE	1	0.438505099868614	2		403	505	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332936	153332936	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	65	216	0	ENST00000281708.4:c.20C>A	p.Ser7Tyr	p.S7Y	ENST00000281708	NM_033632.3	7	tCt/tAt	2/12	1	2	FACETS	0.867	0.756	0.985	0.867	0.756	0.985	CLONAL	1	TRUE	1	0.438505099868614	2		216	342	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518309	187518309	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs191917852	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	25	79	0	ENST00000441802.2:c.12385G>A	p.Asp4129Asn	p.D4129N	ENST00000441802	NM_005245.3	4129	Gac/Aac	25/27	1	2	FACETS	0.935	0.748	1	0.935	0.748	1	CLONAL	1	TRUE	1	0.438505099868614	2		79	122	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393357	393357	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	155	326	0	ENST00000380956.4:c.205G>A	p.Ala69Thr	p.A69T	ENST00000380956	NM_001195286.1	69	Gcg/Acg	2/9	0.255492198166878	3	FACETS	0.83	0.765	0.898			1	INDETERMINATE	2	TRUE	NA	0.438505099868614	3		326	519	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181031	32181031	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	136	326	0	ENST00000375023.3:c.2321-2A>G		p.X774_splice	ENST00000375023	NM_004557.3	774			0.438505099868614	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.438505099868614	1		326	448	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286841	33286841	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1473271904	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	103	267	0	ENST00000374542.5:c.2096G>A	p.Cys699Tyr	p.C699Y	ENST00000374542	NM_001141970.1	699	tGc/tAc	7/8	0.438505099868614	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.438505099868614	1		267	326	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020823	112020823	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	457	826	1	ENST00000368678.4:c.748A>G	p.Thr250Ala	p.T250A	ENST00000368678		250	Acc/Gcc	8/13	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.438505099868614	2		827	1588	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005305	150005305	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	190	456	0	ENST00000253339.5:c.920C>T	p.Thr307Ile	p.T307I	ENST00000253339		307	aCt/aTt	3/7	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.438505099868614	2		456	761	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958499	90958499	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	105	297	2	ENST00000265433.3:c.1939A>G	p.Ser647Gly	p.S647G	ENST00000265433	NM_002485.4	647	Agt/Ggt	13/16	1	2	FACETS	0.877	0.788	0.971	0.877	0.788	0.971	CLONAL	1	TRUE	1	0.438505099868614	2		299	546	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376681	8376681	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751203177	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	91	389	0	ENST00000356435.5:c.4432G>A	p.Gly1478Arg	p.G1478R	ENST00000356435		1478	Gga/Aga	27/35	0.215944498902185	4	FACETS	0.828	0.735	0.927	0.414	0.367	0.464	INDETERMINATE	1	TRUE	2	0.438505099868614	4		389	721	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482247	87482247	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	156	507	0	ENST00000277120.3:c.1534G>T	p.Gly512Cys	p.G512C	ENST00000277120		512	Ggt/Tgt	14/19	0.215944498902185	4	FACETS	1	0.982	1	0.627	0.575	0.682	INDETERMINATE	1	TRUE	2	0.438505099868614	4		507	816	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100462	8100462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752779081	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	141	521	0	ENST00000346208.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000346208		146	Gcc/Acc	3/6	1	2	FACETS	0.84	0.766	0.917	0.84	0.766	0.917	CLONAL	1	TRUE	1	0.438505099868614	2		521	766	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615128	43615128	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs794728685	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	64	484	0	ENST00000355710.3:c.2542A>G	p.Met848Val	p.M848V	ENST00000355710	NM_020975.4	848	Atg/Gtg	14/20	1	2	FACETS	0.475	0.411	0.544	0.475	0.411	0.544	SUBCLONAL	1	TRUE	1	0.438505099868614	2		484	615	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245682	46245682	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	186	472	0	ENST00000334344.6:c.3776A>G	p.His1259Arg	p.H1259R	ENST00000334344	NM_152641.2	1259	cAt/cGt	15/21	0.198484505324068	3	FACETS	0.758	0.703	0.815	0.758	0.703	0.815	INDETERMINATE	2	TRUE	1	0.438505099868614	3		472	682	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986668	36986668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	17	14	0	ENST00000354822.5:c.1021G>A	p.Ala341Thr	p.A341T	ENST00000354822	NM_001079668.2	341	Gcc/Acc	3/3	1	2	FACETS	0.834	0.673	0.99	1	0.948	1	CLONAL	3	TRUE	1	0.438505099868614	2		14	31	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560488	95560488	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	18	106	0	ENST00000393063.1:c.5101T>C	p.Tyr1701His	p.Y1701H	ENST00000393063	NM_030621.3	1701	Tac/Cac	25/28	1	2	FACETS	0.495	0.374	0.634	0.495	0.374	0.634	SUBCLONAL	1	TRUE	1	0.438505099868614	2		106	166	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000406	42000406	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	94	552	0	ENST00000219905.7:c.2425G>T	p.Gly809Cys	p.G809C	ENST00000219905	NM_001164273.1	809	Ggt/Tgt	7/24	1	2	FACETS	0.415	0.369	0.466	0.415	0.369	0.466	SUBCLONAL	1	TRUE	1	0.438505099868614	2		552	1032	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857925	9857925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs534440095	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	129	363	0	ENST00000330684.3:c.3476G>A	p.Arg1159His	p.R1159H	ENST00000330684	NM_001134407.1	1159	cGc/cAc	13/13	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.438505099868614	2		363	501	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56871563	56871563	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	111	655	0	ENST00000308159.5:c.1943C>A	p.Pro648His	p.P648H	ENST00000308159	NM_014669.4	648	cCt/cAt	18/22	1	2	FACETS	0.473	0.424	0.525	0.473	0.424	0.525	SUBCLONAL	1	TRUE	1	0.438505099868614	2		655	1071	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	288	471	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	1	0.977	1	1	0.996	1	CLONAL	2	TRUE	1	0.438505099868614	2		471	625	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231506	5231506	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1386910242	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	223	429	2	ENST00000357368.4:c.1970G>A	p.Arg657His	p.R657H	ENST00000357368	NM_002850.3	657	cGc/cAc	14/38	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.438505099868614	2		431	731	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117408	7117408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371841833	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	52	263	0	ENST00000302850.5:c.3808C>T	p.Arg1270Cys	p.R1270C	ENST00000302850	NM_000208.2	1270	Cgc/Tgc	22/22	1	2	FACETS	0.493	0.42	0.573	0.493	0.42	0.573	SUBCLONAL	1	TRUE	1	0.438505099868614	2		263	481	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602707	10602707	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	156	383	0	ENST00000171111.5:c.871C>A	p.Leu291Met	p.L291M	ENST00000171111	NM_203500.1	291	Ctg/Atg	3/6	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.438505099868614	2		383	693	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098557	11098557	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1213473194	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	150	416	1	ENST00000358026.2:c.1075C>T	p.Arg359Trp	p.R359W	ENST00000358026	NM_001128849.1	359	Cgg/Tgg	6/36	1	2	FACETS	0.962	0.881	1	0.962	0.881	1	CLONAL	1	TRUE	1	0.438505099868614	2		417	711	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54963247	54963247	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	126	464	0	ENST00000312783.6:c.7C>T	p.Arg3Ter	p.R3*	ENST00000312783	NM_198436.1	3	Cga/Tga	3/10	1	2	FACETS	0.635	0.574	0.699	0.635	0.574	0.699	SUBCLONAL	1	TRUE	1	0.438505099868614	2		464	905	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159023	24159023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776693680	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	130	376	0	ENST00000263121.7:c.695C>T	p.Thr232Met	p.T232M	ENST00000263121	NM_003073.3	232	aCg/aTg	6/9	1	2	FACETS	0.928	0.844	1	0.928	0.844	1	CLONAL	1	TRUE	1	0.438505099868614	2		376	639	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030658	47030658	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs782679832	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	35	361	2	ENST00000377604.3:c.432+1G>A		p.X144_splice	ENST00000377604	NM_001204468.1	144			0.438505099868614	1	FACETS	0.309	0.253	0.372	0.309	0.253	0.372	SUBCLONAL	1	TRUE	0	0.438505099868614	1		363	403	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205782	108205782	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	116	388	0	ENST00000278616.4:c.8101del	p.Ile2701Ter	p.I2701*	ENST00000278616	NM_000051.3	2699	ccA/cc	55/63	1	2	FACETS	0.834	0.754	0.92	0.834	0.754	0.92	CLONAL	1	TRUE	1	0.438505099868614	2		388	634	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570840	226570841	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	C	novel	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	48	276	0	ENST00000366794.5:c.1055_1056delinsG	p.Lys352SerfsTer29	p.K352Sfs*29	ENST00000366794	NM_001618.3	352	aAA/aG	8/23	1	2	FACETS	0.469	0.396	0.548	0.469	0.396	0.548	SUBCLONAL	1	TRUE	1	0.438505099868614	2		276	467	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683472	182683472	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	118	396	0	ENST00000292782.4:c.73del	p.Thr25GlnfsTer3	p.T25Qfs*3	ENST00000292782	NM_020640.2	25	Aca/ca	2/7	1	2	FACETS	0.779	0.704	0.858	0.779	0.704	0.858	SUBCLONAL	1	TRUE	1	0.438505099868614	2		396	691	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647028	23647028	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1555461597	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	155	436	0	ENST00000261584.4:c.839del	p.Asn280ThrfsTer8	p.N280Tfs*8	ENST00000261584	NM_024675.3	280	aAc/ac	4/13	1	2	FACETS	0.974	0.893	1	0.974	0.893	1	CLONAL	1	TRUE	1	0.438505099868614	2		436	726	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	245	621	1	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	0.198484505324068	3	FACETS	1	0.99	1	0.667	0.624	0.712	INDETERMINATE	1	TRUE	1	0.438505099868614	3		622	1021	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	282	480	6	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.438505099868614	2		486	972	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519505	137519506	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs780346130	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	180	367	2	ENST00000367739.4:c.1132_1133del	p.Ser378PhefsTer6	p.S378Ffs*6	ENST00000367739	NM_000416.2	378	AGt/t	7/7	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.438505099868614	2		369	671	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574678	41574679	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs754418509	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	102	739	1	ENST00000263253.7:c.6970dup	p.His2324ProfsTer55	p.H2324Pfs*55	ENST00000263253	NM_001429.3	2321	-/C	31/31	1	2	FACETS	0.477	0.425	0.531	0.477	0.425	0.531	SUBCLONAL	1	TRUE	1	0.438505099868614	2		740	976	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584583	52584583	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	39	494	0	ENST00000394830.3:c.4430del	p.Pro1477LeufsTer12	p.P1477Lfs*12	ENST00000394830	NM_018313.4	1477	cCt/ct	29/30	1	2	FACETS	0.245	0.202	0.293	0.245	0.202	0.293	SUBCLONAL	1	TRUE	1	0.438505099868614	2		494	725	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885939	111885939	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	565	654	0	ENST00000341259.2:c.1566del	p.Glu523SerfsTer25	p.E523Sfs*25	ENST00000341259	NM_005475.2	521	Ccc/cc	8/8	0.428820120788909	3	FACETS	0.915	0.882	0.947	0.915	0.882	0.947	CLONAL	3	TRUE	0	0.438505099868614	3		654	1145	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	129	197	0	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.438505099868614	2		197	556	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567719	226567719	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	86	431	1	ENST00000366794.5:c.1447del	p.Ala483GlnfsTer3	p.A483Qfs*3	ENST00000366794	NM_001618.3	483	Gca/ca	10/23	1	2	FACETS	0.534	0.472	0.601	0.534	0.472	0.601	SUBCLONAL	1	TRUE	1	0.438505099868614	2		432	734	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100728	8100728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs771019738	NA	P-0007688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	81	304	3	ENST00000346208.3:c.708del	p.Ser237AlafsTer28	p.S237Afs*28	ENST00000346208		234	ttC/tt	3/6	1	2	FACETS	0.886	0.785	0.994	0.886	0.785	0.994	CLONAL	1	TRUE	1	0.438505099868614	2		307	417	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0007698-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	122	365	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	0.50647398394778	2		365	470	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0007698-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	106	625	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.941	0.848	1	0.941	0.848	1	CLONAL	1	TRUE	1	0.50647398394778	2		625	445	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89880997	89880997	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007698-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	315	657	0	ENST00000389301.3:c.214T>A	p.Leu72Met	p.L72M	ENST00000389301	NM_000135.2	72	Ttg/Atg	3/43	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.50647398394778	2		657	1174	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437593	56437593	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007698-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	182	320	0	ENST00000407977.2:c.869G>T	p.Cys290Phe	p.C290F	ENST00000407977		290	tGc/tTc	8/10	0.50647398394778	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.50647398394778	1		320	475	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215357	5215357	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1440179947	NA	P-0007698-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	300	534	0	ENST00000357368.4:c.4261C>T	p.Arg1421Cys	p.R1421C	ENST00000357368	NM_002850.3	1421	Cgc/Tgc	28/38	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.50647398394778	2		534	1110	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641205	12641206	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATAAACAGTTCCAAAAGAGCCTGACCCAATCC	novel	NA	P-0007698-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	168	660	0	ENST00000251849.4:c.1061_1092dup	p.Lys365GlyfsTer21	p.K365Gfs*21	ENST00000251849	NM_002880.3	364	-/GGATTGGGTCAGGCTCTTTTGGAACTGTTTAT	10/17	1	2	FACETS	0.558	0.512	0.607	0.558	0.512	0.607	SUBCLONAL	1	TRUE	1	0.50647398394778	2		660	1188	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0007700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	258	480	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	0.549589678184806	3	FACETS	1	0.99	1	0.643	0.603	0.684	CLONAL	1	TRUE	1	0.549589678184806	3		480	931	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541726	187541726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	186	527	0	ENST00000441802.2:c.6014G>A	p.Gly2005Glu	p.G2005E	ENST00000441802	NM_005245.3	2005	gGg/gAg	10/27	0.549589678184806	3	FACETS	0.995	0.92	1	0.498	0.46	0.537	CLONAL	1	TRUE	1	0.549589678184806	3		527	867	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916937	+	inframe_deletion	In_Frame_Del	DEL	GGCAACCGT	GGCAACCGT	-	novel	NA	P-0007700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	627	801	0	ENST00000263967.3:c.317_325del	p.Gly106_Arg108del	p.G106_R108del	ENST00000263967	NM_006218.2	106	GGCAACCGT/-	2/21	0.527535480975869	4	FACETS	0.862	0.831	0.892	0.862	0.831	0.892	CLONAL	3	TRUE	1	0.549589678184806	4		801	1368	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0007754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	26	328	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.28917972200728	2	FACETS	0.809	0.646	0.993	0.405	0.323	0.497	CLONAL	1	TRUE	0	0.358925038848139	2		328	179	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0007754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	66	322	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.358925038848139	4	FACETS	0.786	0.687	0.891	0.786	0.687	0.891	SUBCLONAL	2	TRUE	2	0.358925038848139	4		322	318	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0007754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	67	466	1	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.27191642596545	2	FACETS	1	0.972	1	0.712	0.626	0.804	CLONAL	1	TRUE	0	0.358925038848139	2		467	262	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339478	81339478	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	50	689	0	ENST00000222390.5:c.1526T>G	p.Val509Gly	p.V509G	ENST00000222390	NM_000601.4	509	gTt/gGt	13/18	0.358925038848139	4	FACETS	0.887	0.754	1	0.443	0.377	0.516	CLONAL	1	TRUE	2	0.358925038848139	4		689	427	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421508	32421508	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1360573634	NA	P-0007754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	49	226	0	ENST00000332351.3:c.1084T>C	p.Phe362Leu	p.F362L	ENST00000332351	NM_024426.4	362	Ttc/Ctc	6/10	0.213755210045889	5	FACETS	0.879	0.751	1	0.586	0.501	0.677	INDETERMINATE	2	TRUE	2	0.358925038848139	5		226	239	SUCCESS
APC	324	MSKCC	GRCh37	5	112175522	112175534	+	frameshift_variant	Frame_Shift_Del	DEL	AGTGGAATGGTAA	AGTGGAATGGTAA	-	novel	NA	P-0007754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	57	340	0	ENST00000257430.4:c.4231_4243del	p.Ser1411ValfsTer4	p.S1411Vfs*4	ENST00000257430	NM_000038.5	1411	AGTGGAATGGTAAgt/gt	16/16	0.27191642596545	2	FACETS	1	0.955	1	0.628	0.544	0.717	CLONAL	1	TRUE	0	0.358925038848139	2		340	253	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044727	47044728	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	75	233	0	ENST00000377604.3:c.2128dup	p.Ser710LysfsTer10	p.S710Kfs*10	ENST00000377604	NM_001204468.1	709	-/A	19/24	1	1	FACETS	0.963	0.864	1	1	0.985	1	CLONAL	2	TRUE	0	0.358925038848139	1		233	178	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266110	41266110	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007773-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	185	491	0	ENST00000349496.5:c.107A>C	p.His36Pro	p.H36P	ENST00000349496	NM_001904.3	36	cAt/cCt	3/15	0.245879219560997	4	FACETS	1	0.93	1	0.502	0.465	0.541	INDETERMINATE	1	TRUE	2	0.923715138147776	4		491	767	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652033	36652033	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007773-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	292	591	1	ENST00000244741.5:c.155A>T	p.Asp52Val	p.D52V	ENST00000244741	NM_000389.4	52	gAc/gTc	2/3	0.878009751467742	3	FACETS	1	0.992	1	0.627	0.593	0.661	CLONAL	1	TRUE	1	0.923715138147776	3		592	737	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716327	52716327	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007773-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	125	491	0	ENST00000322088.6:c.771G>T	p.Trp257Cys	p.W257C	ENST00000322088	NM_014225.5	257	tgG/tgT	6/15	0.636432207182126	4	FACETS	0.701	0.635	0.77			1	SUBCLONAL	1	TRUE	NA	0.923715138147776	4		491	743	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100999	41100999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1371429276	NA	P-0007773-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	106	405	1	ENST00000373198.4:c.1357C>T	p.Arg453Cys	p.R453C	ENST00000373198	NM_133170.3	453	Cgc/Tgc	8/32	0.7371632945016	3	FACETS	0.635	0.572	0.703	0.318	0.286	0.352	SUBCLONAL	1	TRUE	1	0.923715138147776	3		406	528	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577399	64577400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGCTC	novel	NA	P-0007773-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	131	745	0	ENST00000312049.6:c.178_182dup	p.Thr62SerfsTer59	p.T62Sfs*59	ENST00000312049	NM_130799.2	61	ctc/ctGAGCTc	2/10	NA	2	FACETS	0.64	0.585	0.697			1	INDETERMINATE	1	TRUE	NA	0.923715138147776	2		745	443	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593555	48593563	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGGTTAGT	AAGGTTAGT	-	novel	NA	P-0007782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	53	249	0	ENST00000342988.3:c.1306_1308+6del		p.X436_splice	ENST00000342988	NM_005359.5	436		10/12	0.3	1	FACETS	0.753	0.643	0.873	0.753	0.643	0.873	SUBCLONAL	1	TRUE	0	0.26	1		249	471	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027709	152027710	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0007782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	217	582	0	ENST00000262189.6:c.365_366del	p.Ser122CysfsTer9	p.S122Cfs*9	ENST00000262189	NM_170606.2	122	tCT/t	3/59	0.189839759926009	2	FACETS	0.839	0.78	0.9	0.839	0.78	0.9	CLONAL	2	TRUE	0	0.26	2		582	995	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711879	89711882	+	frameshift_variant	Frame_Shift_Del	DEL	TAAC	TAAC	-	novel	NA	P-0007782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	74	341	0	ENST00000371953.3:c.499_502del	p.Thr167PhefsTer15	p.T167Ffs*15	ENST00000371953	NM_000314.4	166	gTAACt/gt	6/9	1	2	FACETS	0.983	0.862	1	0.983	0.862	1	CLONAL	1	TRUE	1	0.26	2		341	579	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593537	48593551	+	inframe_deletion	In_Frame_Del	DEL	TACCCAAGTGCATAT	TACCCAAGTGCATAT	-	novel	NA	P-0007782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	55	294	0	ENST00000342988.3:c.1288_1302del	p.Tyr430_Tyr434del	p.Y430_Y434del	ENST00000342988	NM_005359.5	430	TACCCAAGTGCATAT/-	10/12	0.3	1	FACETS	0.697	0.597	0.807	0.697	0.597	0.807	SUBCLONAL	1	TRUE	0	0.26	1		294	528	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641028	23641028	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	110	433	0	ENST00000261584.4:c.2447del	p.Phe816SerfsTer35	p.F816Sfs*35	ENST00000261584	NM_024675.3	816	tTc/tc	5/13	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.26	2		433	802	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155674	119155687	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTAGGTGGAACGG	CCTAGGTGGAACGG	-	novel	NA	P-0007782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	77	410	0	ENST00000264033.4:c.1432-3_1442del		p.X478_splice	ENST00000264033	NM_005188.3	478		10/16	1	2	FACETS	0.675	0.591	0.765	0.675	0.591	0.765	SUBCLONAL	1	TRUE	1	0.26	2		410	878	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578184	7578187	+	frameshift_variant	Frame_Shift_Del	DEL	GGCT	GGCT	-	novel	NA	P-0007782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	116	498	0	ENST00000269305.4:c.662_665del	p.Glu221GlyfsTer25	p.E221Gfs*25	ENST00000269305	NM_001126112.2	221	gAGCCg/gg	6/11	1	2	FACETS	0.87	0.782	0.962	0.87	0.782	0.962	CLONAL	1	TRUE	1	0.26	2		498	1026	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171704	36171705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0007782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	88	378	0	ENST00000300305.3:c.859_860dup	p.Leu288ThrfsTer24	p.L288Tfs*24	ENST00000300305		287	tac/taTAc	7/8	1	2	FACETS	0.729	0.645	0.82	0.729	0.645	0.82	SUBCLONAL	1	TRUE	1	0.26	2		378	928	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659796	227659797	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0007782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	64	281	0	ENST00000305123.5:c.3658dup	p.Arg1220ProfsTer5	p.R1220Pfs*5	ENST00000305123	NM_005544.2	1220	cgc/cCgc	1/2	1	2	FACETS	0.849	0.735	0.972	0.849	0.735	0.972	CLONAL	1	TRUE	1	0.26	2		281	580	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133748426	133748427	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	CC	novel	NA	P-0007782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	32	213	0	ENST00000318560.5:c.1085+2_1085+3insCC		p.X362_splice	ENST00000318560	NM_005157.4	362			0.3	1	FACETS	0.85	0.693	1	0.85	0.693	1	CLONAL	1	TRUE	0	0.26	1		213	252	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287209	46287209	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	75	277	0	ENST00000334344.6:c.5155del	p.Thr1719LeufsTer2	p.T1719Lfs*2	ENST00000334344	NM_152641.2	1718	ccA/cc	19/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.26	2		277	442	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650794	48650800	+	frameshift_variant	Frame_Shift_Del	DEL	CCACTAC	CCACTAC	-	novel	NA	P-0007782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	151	332	0	ENST00000376670.3:c.664_670del	p.His222TyrfsTer11	p.H222Yfs*11	ENST00000376670	NM_002049.3	221	ggCCACTAC/gg	4/6	0.3	2	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.26	2		332	843	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549497	21549499	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0007782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	14	73	0	ENST00000382592.4:c.2777_2779del	p.Ile926del	p.I926del	ENST00000382592	NM_014572.2	926	aTCAac/aac	8/8	1	2	FACETS	0.855	0.623	1	0.855	0.623	1	CLONAL	1	TRUE	1	0.26	2		73	126	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435669	56435675	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCCTG	CCCCCTG	-	novel	NA	P-0007782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	35	170	0	ENST00000407977.2:c.1462_1468del	p.Gln488SerfsTer12	p.Q488Sfs*12	ENST00000407977		488	CAGGGGGtc/tc	9/10	1	2	FACETS	0.889	0.731	1	0.889	0.731	1	CLONAL	1	TRUE	1	0.26	2		170	303	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482759	67482760	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0007782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	107	443	0	ENST00000327367.4:c.1166_1167dup	p.Thr390Ter	p.T390*	ENST00000327367	NM_005902.3	388	act/acTGt	9/9	1	2	FACETS	0.893	0.8	0.992	0.893	0.8	0.992	CLONAL	1	TRUE	1	0.26	2		443	922	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101740	71101741	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0007782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	114	403	0	ENST00000318789.4:c.457dup	p.Gln153ProfsTer17	p.Q153Pfs*17	ENST00000318789	NM_032682.5	153	cag/cCag	9/21	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.26	2		403	847	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866492	42866494	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	novel	NA	P-0007782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1184	141	608	0	ENST00000398585.3:c.138_140del	p.Ala47del	p.A47del	ENST00000398585	NM_001135099.1	46	ccAGCt/cct	3/14	1	2	FACETS	0.819	0.743	0.898	0.819	0.743	0.898	CLONAL	1	TRUE	1	0.26	2		608	1325	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725180	49725181	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	novel	NA	P-0007782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	35	213	0	ENST00000449682.2:c.242+2_242+3del		p.X81_splice	ENST00000449682	NM_020998.3	81			0.264904039288778	1	FACETS	0.73	0.6	0.875	0.73	0.6	0.875	SUBCLONAL	1	TRUE	0	0.26	1		213	321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577563	7577566	+	protein_altering_variant	In_Frame_Del	DEL	TGTT	TGTT	A	novel	NA	P-0007782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	76	419	0	ENST00000269305.4:c.715_718delinsT	p.Asn239_Ser240delinsCys	p.N239_S240delinsC	ENST00000269305	NM_001126112.2	239	AACAgt/Tgt	7/11	1	2	FACETS	0.832	0.729	0.942	0.832	0.729	0.942	CLONAL	1	TRUE	1	0.26	2		419	703	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850705	63850705	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs201178069	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	145	443	0	ENST00000279873.7:c.1489del	p.Ile497Ter	p.I497*	ENST00000279873	NM_032199.2	495	Aaa/aa	10/10	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.333789756454098	2		443	835	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	73	338	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	0.333789756454098	2		338	361	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	112	402	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.333789756454098	2		402	455	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	57	243	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.867	0.746	0.997	0.867	0.746	0.997	CLONAL	1	TRUE	1	0.333789756454098	2		244	394	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	126	252	0	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	1	FACETS	0.874	0.8	0.949	1	0.989	1	CLONAL	2	TRUE	0	0.333789756454098	1		252	360	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143049	7143049	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777271464	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	48	222	3	ENST00000302850.5:c.2320G>A	p.Val774Met	p.V774M	ENST00000302850	NM_000208.2	774	Gtg/Atg	12/22	1	2	FACETS	0.691	0.585	0.807	0.691	0.585	0.807	SUBCLONAL	1	TRUE	1	0.333789756454098	2		225	416	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	258	335	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.333448360494576	2	FACETS	0.837	0.79	0.884	1	0.991	1	CLONAL	3	TRUE	0	0.333789756454098	2		335	616	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968266	2968266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773909937	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	136	453	0	ENST00000396946.4:c.1720G>A	p.Val574Ile	p.V574I	ENST00000396946	NM_032415.4	574	Gtc/Atc	13/25	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.333789756454098	2		453	686	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775985	9775985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201492009	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	59	179	0	ENST00000377346.4:c.449C>T	p.Ala150Val	p.A150V	ENST00000377346	NM_005026.3	150	gCg/gTg	5/24	1	2	FACETS	0.979	0.847	1	0.979	0.847	1	CLONAL	1	TRUE	1	0.333789756454098	2		179	361	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872018	35872018	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	218	670	1	ENST00000216797.5:c.595G>A	p.Val199Met	p.V199M	ENST00000216797	NM_020529.2	199	Gtg/Atg	4/6	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.333789756454098	2		671	1144	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375016	45375016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226662382	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	86	289	0	ENST00000262160.6:c.827C>T	p.Ser276Leu	p.S276L	ENST00000262160	NM_005901.5	276	tCg/tTg	8/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.333789756454098	2		289	421	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101072	26101072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	153	566	0	ENST00000435504.4:c.20G>A	p.Arg7Lys	p.R7K	ENST00000435504		7	aGg/aAg	1/13	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.333789756454098	2		566	904	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443675	29443675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1034835558	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	86	215	0	ENST00000389048.3:c.3542G>A	p.Arg1181His	p.R1181H	ENST00000389048	NM_004304.4	1181	cGc/cAc	23/29	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.333789756454098	2		215	466	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641689	12641689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759433668	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	111	367	1	ENST00000251849.4:c.952C>T	p.Arg318Trp	p.R318W	ENST00000251849	NM_002880.3	318	Cgg/Tgg	9/17	0.333448360494576	2	FACETS	1	0.966	1	0.58	0.523	0.641	CLONAL	1	TRUE	0	0.333789756454098	2		368	573	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053310	37053310	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs587779022	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	192	390	0	ENST00000231790.2:c.546-1G>A		p.X182_splice	ENST00000231790	NM_000249.3	182			0.333448360494576	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.333789756454098	2		390	475	SUCCESS
APC	324	MSKCC	GRCh37	5	112175025	112175025	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	89	279	0	ENST00000257430.4:c.3734A>C	p.Lys1245Thr	p.K1245T	ENST00000257430	NM_000038.5	1245	aAg/aCg	16/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.333789756454098	2		279	463	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504355	149504355	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	84	303	0	ENST00000261799.4:c.1847A>C	p.Glu616Ala	p.E616A	ENST00000261799	NM_002609.3	616	gAg/gCg	13/23	1	2	FACETS	0.997	0.883	1	0.997	0.883	1	CLONAL	1	TRUE	1	0.333789756454098	2		303	505	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851485	63851485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750226503	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	69	152	0	ENST00000279873.7:c.2263G>A	p.Val755Ile	p.V755I	ENST00000279873	NM_032199.2	755	Gtc/Atc	10/10	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.333789756454098	2		152	353	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856472	111856472	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	85	296	2	ENST00000341259.2:c.523C>T	p.Arg175Trp	p.R175W	ENST00000341259	NM_005475.2	175	Cgg/Tgg	2/8	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.333789756454098	2		298	445	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893578	28893578	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	101	369	0	ENST00000282397.4:c.3268T>G	p.Trp1090Gly	p.W1090G	ENST00000282397	NM_002019.4	1090	Tgg/Ggg	24/30	1	2	FACETS	0.984	0.881	1	0.984	0.881	1	CLONAL	1	TRUE	1	0.333789756454098	2		369	615	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124255	2124255	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs137853995	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	112	357	0	ENST00000219476.3:c.2410T>C	p.Cys804Arg	p.C804R	ENST00000219476	NM_000548.3	804	Tgc/Cgc	22/42	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.333789756454098	2		357	573	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984931	9984931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	173	497	1	ENST00000330684.3:c.1034G>A	p.Gly345Asp	p.G345D	ENST00000330684	NM_001134407.1	345	gGc/gAc	4/13	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.333789756454098	2		498	884	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991497	72991497	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	187	647	0	ENST00000268489.5:c.2548C>A	p.Leu850Ile	p.L850I	ENST00000268489	NM_006885.3	850	Ctc/Atc	2/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.333789756454098	2		647	1054	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346583	89346583	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	94	406	0	ENST00000301030.4:c.6367G>A	p.Ala2123Thr	p.A2123T	ENST00000301030	NM_001256183.1	2123	Gcc/Acc	9/13	1	2	FACETS	0.934	0.833	1	0.934	0.833	1	CLONAL	1	TRUE	1	0.333789756454098	2		406	603	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845237	89845237	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765036744	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	158	452	1	ENST00000389301.3:c.1798C>T	p.Arg600Cys	p.R600C	ENST00000389301	NM_000135.2	600	Cgt/Tgt	20/43	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.333789756454098	2		453	891	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435837	56435837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	68	209	0	ENST00000407977.2:c.1300C>T	p.Pro434Ser	p.P434S	ENST00000407977		434	Ccc/Tcc	9/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.333789756454098	2		209	316	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39570487	39570487	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	114	469	0	ENST00000262039.4:c.683A>T	p.Asp228Val	p.D228V	ENST00000262039	NM_002647.2	228	gAt/gTt	6/25	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.333789756454098	2		469	552	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10259628	10259628	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	133	476	0	ENST00000340748.4:c.2604G>A	p.Trp868Ter	p.W868*	ENST00000340748		868	tgG/tgA	26/40	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.333789756454098	2		476	693	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484426	57484426	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	115	294	0	ENST00000371085.3:c.607C>A	p.Leu203Met	p.L203M	ENST00000371085	NM_000516.4	203	Ctg/Atg	8/13	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.333789756454098	2		294	621	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084145	47084146	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	82	363	0	ENST00000409792.3:c.7143dup	p.Ser2382LeufsTer47	p.S2382Lfs*47	ENST00000409792	NM_014159.6	2381	-/C	17/21	0.333448360494576	2	FACETS	0.873	0.771	0.982	0.436	0.385	0.491	CLONAL	1	TRUE	0	0.333789756454098	2		363	563	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143009	47143010	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	109	564	0	ENST00000409792.3:c.4953dup	p.Thr1652TyrfsTer14	p.T1652Yfs*14	ENST00000409792	NM_014159.6	1651	-/T	8/21	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.333789756454098	2		564	645	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732279	74732279	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	205	617	0	ENST00000359995.5:c.630del	p.Lys211SerfsTer21	p.K211Sfs*21	ENST00000359995	NM_001195427.1	210	ccC/cc	2/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.333789756454098	2		617	1119	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557272	187557273	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1279779959	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	120	407	0	ENST00000441802.2:c.4089dup	p.Thr1364TyrfsTer8	p.T1364Yfs*8	ENST00000441802	NM_005245.3	1363	-/T	6/27	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.333789756454098	2		407	687	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435293	110435295	+	inframe_deletion	In_Frame_Del	DEL	CGG	CGG	-	novel	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	26	59	0	ENST00000375856.3:c.3106_3108del	p.Pro1036del	p.P1036del	ENST00000375856	NM_003749.2	1036	CCG/-	1/2	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.333789756454098	2		59	113	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248461	59248461	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	79	304	0	ENST00000371222.2:c.282del	p.Thr95ProfsTer9	p.T95Pfs*9	ENST00000371222	NM_002228.3	94	ccC/cc	1/1	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.333789756454098	2		304	471	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022666	31022667	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	99	367	0	ENST00000375687.4:c.2156_2157del	p.Glu719GlyfsTer54	p.E719Gfs*54	ENST00000375687	NM_015338.5	717	agGAga/agga	13/13	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.333789756454098	2		367	586	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670328	134670328	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	77	310	3	ENST00000398015.3:c.244del	p.Ala82ProfsTer12	p.A82Pfs*12	ENST00000398015	NM_004441.4	80	cGg/cg	3/16	1	2	FACETS	0.787	0.692	0.89	0.787	0.692	0.89	SUBCLONAL	1	TRUE	1	0.333789756454098	2		313	586	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779452	3779452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	18	482	0	ENST00000262367.5:c.5596C>T	p.Arg1866Cys	p.R1866C	ENST00000262367	NM_004380.2	1866	Cgc/Tgc	31/31	1	2	FACETS	0.382	0.287	0.495	0.382	0.287	0.495	SUBCLONAL	1	TRUE	1	0.284619723879552	2		482	331	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495017	56495017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765277521	NA	P-0007863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	19	366	0	ENST00000267101.3:c.3374G>A	p.Arg1125Gln	p.R1125Q	ENST00000267101	NM_001982.3	1125	cGg/cAg	27/28	1	2	FACETS	0.451	0.342	0.579	0.451	0.342	0.579	SUBCLONAL	1	TRUE	1	0.284619723879552	2		366	296	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673728	37673728	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	90	494	0	ENST00000447079.4:c.2882C>G	p.Pro961Arg	p.P961R	ENST00000447079	NM_015083.1	961	cCt/cGt	10/14	0.284619723879552	15	FACETS	1	0.938	1			1	CLONAL	2	TRUE	NA	0.284619723879552	15		494	829	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244223	5244223	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs199851847	NA	P-0007863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	64	342	0	ENST00000357368.4:c.1259G>T	p.Arg420Leu	p.R420L	ENST00000357368	NM_002850.3	420	cGc/cTc	11/38	0.284619723879552	2	FACETS	1	0.97	1	0.712	0.621	0.809	CLONAL	1	TRUE	0	0.284619723879552	2		342	316	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857074	9857075	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0007863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	40	437	0	ENST00000330684.3:c.4326dup	p.Arg1443GlnfsTer9	p.R1443Qfs*9	ENST00000330684	NM_001134407.1	1442	-/C	13/13	1	2	FACETS	0.752	0.632	0.881	1	0.958	1	SUBCLONAL	2	TRUE	1	0.284619723879552	2		437	187	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0007870-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	28	175	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.402485158561457	4	FACETS	0.748	0.6	0.915	0.374	0.3	0.458	CLONAL	1	TRUE	2	0.402485158561457	4		175	261	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867540	35867541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs869312857	NA	P-0007870-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	56	377	0	ENST00000303115.3:c.361dup	p.Ile121AsnfsTer8	p.I121Nfs*8	ENST00000303115	NM_002185.3	118	-/A	3/8	0.402485158561457	5	FACETS	0.75	0.642	0.868			1	SUBCLONAL	1	TRUE	NA	0.402485158561457	5		377	595	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0007870-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	134	399	0	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	0.323092654024278	2	FACETS	0.806	0.739	0.875	0.806	0.739	0.875	CLONAL	2	TRUE	0	0.402485158561457	2		399	413	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0007870-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	771	381	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.402485158561457	12	FACETS	1	0.991	1			1	CLONAL	8	TRUE	NA	0.402485158561457	12		381	1373	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0007870-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1489	257	668	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.402485158561457	12	FACETS	1	0.977	1			1	CLONAL	2	TRUE	NA	0.402485158561457	12		669	1746	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032474	12032474	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007870-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	92	321	0	ENST00000353533.5:c.910C>T	p.Arg304Ter	p.R304*	ENST00000353533	NM_003010.3	304	Cga/Tga	9/11	0.323092654024278	2	FACETS	1	0.979	1	0.693	0.622	0.767	CLONAL	1	TRUE	0	0.402485158561457	2		321	330	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860281	151860281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007870-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	93	615	0	ENST00000262189.6:c.10381G>A	p.Asp3461Asn	p.D3461N	ENST00000262189	NM_170606.2	3461	Gat/Aat	43/59	0.402485158561457	6	FACETS	0.84	0.745	0.942	0.21	0.186	0.236	CLONAL	1	TRUE	2	0.402485158561457	6		615	993	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0007968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	11	286	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.291	0.2	0.402	0.291	0.2	0.402	SUBCLONAL	1	TRUE	1	0.358909156579592	2		286	211	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528082	29528082	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	24	266	0	ENST00000356175.3:c.1090T>G	p.Phe364Val	p.F364V	ENST00000356175	NM_000267.3	364	Ttc/Gtc	10/57	1	2	FACETS	0.942	0.764	1	1	0.951	1	CLONAL	2	TRUE	1	0.358909156579592	2		266	71	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	40	253	1	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	0.595	0.493	0.708	0.595	0.493	0.708	SUBCLONAL	1	TRUE	1	0.23	2		254	585	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	60	476	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.727	0.625	0.838	0.727	0.625	0.838	SUBCLONAL	1	TRUE	1	0.23	2		476	718	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	60	498	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.988	0.852	1	0.988	0.852	1	CLONAL	1	TRUE	1	0.23	2		498	528	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	66	240	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.813	0.705	0.93	0.813	0.705	0.93	CLONAL	1	TRUE	1	0.23	2		240	706	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	60	301	0	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	1	2	FACETS	0.783	0.674	0.902	0.783	0.674	0.902	CLONAL	1	TRUE	1	0.23	2		301	666	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	73	402	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.683	0.596	0.778	0.683	0.596	0.778	SUBCLONAL	1	TRUE	1	0.23	2		402	929	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	45	309	0	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	0.3	3	FACETS	1	0.887	1			1	CLONAL	1	TRUE	NA	0.23	3		309	409	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007834	45007834	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	84	312	0	ENST00000558401.1:c.285del	p.Asp96MetfsTer7	p.D96Mfs*7	ENST00000558401	NM_004048.2	94	gAa/ga	2/4	1	2	FACETS	0.823	0.726	0.928	0.823	0.726	0.928	CLONAL	1	TRUE	1	0.23	2		312	887	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	54	454	1	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	0.147939292615137	0	FACETS	0.733	0.627	0.85			1	SUBCLONAL	1	TRUE	0	0.23	0		455	493	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331733	8331733	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	31	257	0	ENST00000356435.5:c.5383G>T	p.Gly1795Cys	p.G1795C	ENST00000356435		1795	Ggc/Tgc	33/35	1	2	FACETS	0.526	0.425	0.642	0.526	0.425	0.642	SUBCLONAL	1	TRUE	1	0.23	2		257	512	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199674	138199675	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	66	339	0	ENST00000237289.4:c.1097_1098del	p.Glu366GlyfsTer22	p.E366Gfs*22	ENST00000237289	NM_001270507.1	364	agGAga/agga	7/9	0.3	5	FACETS	0.929	0.805	1			1	CLONAL	1	TRUE	NA	0.23	5		339	831	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4090637	4090637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144383241	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	42	345	1	ENST00000262948.5:c.1162C>T	p.Arg388Trp	p.R388W	ENST00000262948	NM_030662.3	388	Cgg/Tgg	11/11	0.3	1	FACETS	0.657	0.548	0.778	0.657	0.548	0.778	SUBCLONAL	1	TRUE	0	0.23	1		346	492	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425896	49425896	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783685	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	45	444	0	ENST00000301067.7:c.12592C>T	p.Arg4198Ter	p.R4198*	ENST00000301067	NM_003482.3	4198	Cga/Tga	39/54	1	2	FACETS	0.726	0.61	0.855	0.726	0.61	0.855	SUBCLONAL	1	TRUE	1	0.23	2		444	539	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032356	10032356	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763500409	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	19	221	1	ENST00000330684.3:c.467C>T	p.Thr156Met	p.T156M	ENST00000330684	NM_001134407.1	156	aCg/aTg	3/13	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.23	NA		222	311	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2492104	2492104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1359670489	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	61	441	0	ENST00000355716.4:c.502G>A	p.Gly168Arg	p.G168R	ENST00000355716	NM_003820.2	168	Ggg/Agg	5/8	0.3	2	FACETS	0.949	0.819	1			1	CLONAL	1	TRUE	NA	0.23	2		441	559	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254851	16254851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748777153	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	73	409	0	ENST00000375759.3:c.2116C>T	p.Arg706Cys	p.R706C	ENST00000375759	NM_015001.2	706	Cgt/Tgt	11/15	1	2	FACETS	0.814	0.711	0.925	0.814	0.711	0.925	CLONAL	1	TRUE	1	0.23	2		409	780	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36808985	36808985	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	49	454	0	ENST00000373129.3:c.1069A>G	p.Asn357Asp	p.N357D	ENST00000373129	NM_032017.1	357	Aat/Gat	11/12	1	2	FACETS	0.676	0.572	0.791	0.676	0.572	0.791	SUBCLONAL	1	TRUE	1	0.23	2		454	630	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967323	25967323	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	59	379	0	ENST00000435504.4:c.1883C>A	p.Pro628His	p.P628H	ENST00000435504		628	cCc/cAc	13/13	1	2	FACETS	0.687	0.59	0.793	0.687	0.59	0.793	SUBCLONAL	1	TRUE	1	0.23	2		379	747	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090627	71090627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1287988102	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	68	335	0	ENST00000318789.4:c.721G>A	p.Ala241Thr	p.A241T	ENST00000318789	NM_032682.5	241	Gca/Aca	11/21	0.219421242536215	3	FACETS	0.788	0.684	0.9	0.394	0.342	0.45	SUBCLONAL	1	TRUE	1	0.23	3		335	837	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55130043	55130043	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774431464	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	94	430	0	ENST00000257290.5:c.577G>A	p.Val193Ile	p.V193I	ENST00000257290	NM_006206.4	193	Gtc/Atc	4/23	1	2	FACETS	0.977	0.868	1	0.977	0.868	1	CLONAL	1	TRUE	1	0.23	2		430	837	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048785	180048785	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	32	386	0	ENST00000261937.6:c.1777C>A	p.Leu593Ile	p.L593I	ENST00000261937	NM_182925.4	593	Ctc/Atc	13/30	0.3	0	FACETS	0.649	0.528	0.786			1	SUBCLONAL	1	TRUE	0	0.23	0		386	330	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670949	30670949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1259392922	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	53	343	1	ENST00000376406.3:c.5797C>T	p.Arg1933Trp	p.R1933W	ENST00000376406	NM_014641.2	1933	Cgg/Tgg	12/15	0.318356639453506	4	FACETS	0.804	0.684	0.936	0.402	0.342	0.468	CLONAL	1	TRUE	2	0.23	4		344	705	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739374	145739374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776218553	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	65	360	0	ENST00000428558.2:c.1996G>A	p.Gly666Arg	p.G666R	ENST00000428558	NM_004260.3	666	Ggg/Agg	12/22	0.219421242536215	3	FACETS	1	0.959	1	0.638	0.554	0.728	CLONAL	1	TRUE	1	0.23	3		360	494	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451542	70451542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199882600	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	61	417	0	ENST00000373644.4:c.6382G>A	p.Val2128Ile	p.V2128I	ENST00000373644	NM_030625.2	2128	Gtt/Att	12/12	1	2	FACETS	0.578	0.497	0.667	0.578	0.497	0.667	SUBCLONAL	1	TRUE	1	0.23	2		417	917	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376697	118376697	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	58	358	0	ENST00000534358.1:c.10090C>T	p.His3364Tyr	p.H3364Y	ENST00000534358	NM_005933.3	3364	Cac/Tac	27/36	1	2	FACETS	0.936	0.804	1	0.936	0.804	1	CLONAL	1	TRUE	1	0.23	2		358	539	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392858	118392858	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781866935	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	31	341	0	ENST00000534358.1:c.11890G>A	p.Ala3964Thr	p.A3964T	ENST00000534358	NM_005933.3	3964	Gcc/Acc	36/36	1	2	FACETS	0.511	0.412	0.623	0.511	0.412	0.623	SUBCLONAL	1	TRUE	1	0.23	2		341	528	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417042	417042	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs946420332	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	62	347	0	ENST00000399788.2:c.3508G>A	p.Ala1170Thr	p.A1170T	ENST00000399788	NM_001042603.1	1170	Gcc/Acc	23/28	0.3	2	FACETS	0.874	0.755	1			1	CLONAL	1	TRUE	NA	0.23	2		347	617	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432215	49432215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770885860	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	57	368	0	ENST00000301067.7:c.8924G>A	p.Arg2975His	p.R2975H	ENST00000301067	NM_003482.3	2975	cGc/cAc	34/54	1	2	FACETS	0.847	0.727	0.979	0.847	0.727	0.979	CLONAL	1	TRUE	1	0.23	2		368	585	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562747	21562747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747638434	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	12	168	0	ENST00000382592.4:c.1172G>A	p.Arg391His	p.R391H	ENST00000382592	NM_014572.2	391	cGc/cAc	4/8	0.3	2	FACETS	0.621	0.438	0.846			1	SUBCLONAL	1	TRUE	NA	0.23	2		168	168	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138564	2138564	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1473538868	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	46	415	0	ENST00000219476.3:c.5377C>T	p.Arg1793Trp	p.R1793W	ENST00000219476	NM_000548.3	1793	Cgg/Tgg	42/42	0.147939292615137	0	FACETS	0.639	0.538	0.75			1	SUBCLONAL	1	TRUE	0	0.23	0		415	482	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968870	15968870	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	79	333	0	ENST00000268712.3:c.4880T>C	p.Leu1627Ser	p.L1627S	ENST00000268712	NM_006311.3	1627	tTg/tCg	33/46	1	2	FACETS	0.843	0.74	0.953	0.843	0.74	0.953	CLONAL	1	TRUE	1	0.23	2		333	815	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59878762	59878762	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	68	307	0	ENST00000259008.2:c.992T>C	p.Met331Thr	p.M331T	ENST00000259008	NM_032043.2	331	aTg/aCg	8/20	1	2	FACETS	0.906	0.788	1	0.906	0.788	1	CLONAL	1	TRUE	1	0.23	2		307	653	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169468	11169468	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	52	374	0	ENST00000358026.2:c.4634G>A	p.Arg1545His	p.R1545H	ENST00000358026	NM_001128849.1	1545	cGc/cAc	33/36	0.147939292615137	0	FACETS	0.733	0.625	0.851			1	SUBCLONAL	1	TRUE	0	0.23	0		374	475	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012617	36012617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367543238	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	50	286	1	ENST00000358208.4:c.61G>A	p.Ala21Thr	p.A21T	ENST00000358208		21	Gcc/Acc	2/12	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.23	2		287	339	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385182	41385182	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs367872006	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	33	402	0	ENST00000373198.4:c.779G>T	p.Arg260Leu	p.R260L	ENST00000373198	NM_133170.3	260	cGg/cTg	6/32	0.3	1	FACETS	0.487	0.396	0.591	0.487	0.396	0.591	SUBCLONAL	1	TRUE	0	0.23	1		402	521	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556718	41556718	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1425934652	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	35	220	0	ENST00000263253.7:c.3663G>T	p.Gln1221His	p.Q1221H	ENST00000263253	NM_001429.3	1221	caG/caT	20/31	0.104908244202033	0	FACETS	0.579	0.474	0.696			1	INDETERMINATE	1	TRUE	0	0.23	0		220	405	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932804	39932804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774200570	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	70	451	0	ENST00000378444.4:c.1795G>A	p.Gly599Ser	p.G599S	ENST00000378444	NM_001123385.1	599	Ggc/Agc	4/15	1	2	FACETS	0.935	0.815	1	0.935	0.815	1	CLONAL	1	TRUE	1	0.23	2		451	651	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224538	53224538	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556835963	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	55	545	1	ENST00000375401.3:c.3175C>T	p.Arg1059Trp	p.R1059W	ENST00000375401	NM_004187.3	1059	Cgg/Tgg	21/26	1	2	FACETS	0.758	0.648	0.879	0.758	0.648	0.879	SUBCLONAL	1	TRUE	1	0.23	2		546	631	SUCCESS
AR	367	MSKCC	GRCh37	X	66766174	66766174	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	24	208	0	ENST00000374690.3:c.1186G>A	p.Gly396Ser	p.G396S	ENST00000374690	NM_000044.3	396	Ggc/Agc	1/8	1	2	FACETS	0.773	0.607	0.963	0.773	0.607	0.963	CLONAL	1	TRUE	1	0.23	2		208	270	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349689	70349689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs979229015	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	51	378	2	ENST00000374080.3:c.3851G>A	p.Arg1284His	p.R1284H	ENST00000374080		1284	cGc/cAc	27/45	1	2	FACETS	0.697	0.592	0.813	0.697	0.592	0.813	SUBCLONAL	1	TRUE	1	0.23	2		380	636	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211889	123211889	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	84	565	0	ENST00000218089.9:c.2756T>C	p.Leu919Pro	p.L919P	ENST00000218089	NM_001042749.1	919	cTt/cCt	27/35	1	2	FACETS	0.803	0.708	0.905	0.803	0.708	0.905	CLONAL	1	TRUE	1	0.23	2		565	910	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220554	123220554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	93	573	2	ENST00000218089.9:c.3211C>T	p.Arg1071Trp	p.R1071W	ENST00000218089	NM_001042749.1	1071	Cgg/Tgg	30/35	1	2	FACETS	0.664	0.589	0.746	0.664	0.589	0.746	SUBCLONAL	1	TRUE	1	0.23	2		575	1217	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435513	56435513	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	34	338	1	ENST00000407977.2:c.1624del	p.Thr542ProfsTer158	p.T542Pfs*158	ENST00000407977		542	Acc/cc	9/10	1	2	FACETS	0.597	0.487	0.721	0.597	0.487	0.721	SUBCLONAL	1	TRUE	1	0.23	2		339	495	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266583	142266585	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	rs779715723	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	40	305	0	ENST00000350721.4:c.3339_3341del	p.Ile1114del	p.I1114del	ENST00000350721	NM_001184.3	1113	atCATa/ata	16/47	1	2	FACETS	0.604	0.501	0.719	0.604	0.501	0.719	SUBCLONAL	1	TRUE	1	0.23	2		305	576	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101375	27101375	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	52	263	0	ENST00000324856.7:c.4661del	p.Pro1554HisfsTer11	p.P1554Hfs*11	ENST00000324856	NM_006015.4	1553	Ccc/cc	18/20	1	2	FACETS	0.979	0.834	1	0.979	0.834	1	CLONAL	1	TRUE	1	0.23	2		263	462	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193202211	193202211	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	77	398	0	ENST00000367435.3:c.1247del	p.Gly416AlafsTer12	p.G416Afs*12	ENST00000367435	NM_024529.4	415	Ggg/gg	14/17	1	2	FACETS	0.685	0.599	0.777	0.685	0.599	0.777	SUBCLONAL	1	TRUE	1	0.23	2		398	978	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271193	153271193	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0007971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	247	304	0	ENST00000281708.4:c.584+1G>A		p.X195_splice	ENST00000281708	NM_033632.3	195			NA	2	FACETS	1	0.98	1			1	INDETERMINATE	2	TRUE	NA	0.615576880118062	2		304	383	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88677077	88677077	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	161	352	0	ENST00000372037.3:c.862A>G	p.Ile288Val	p.I288V	ENST00000372037	NM_004329.2	288	Ata/Gta	9/13	0.605078227931742	3	FACETS	0.958	0.881	1	0.479	0.44	0.519	CLONAL	1	TRUE	1	0.615576880118062	3		352	714	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576891	7576891	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0007971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	444	418	0	ENST00000269305.4:c.955A>T	p.Lys319Ter	p.K319*	ENST00000269305	NM_001126112.2	319	Aag/Tag	9/11	0.336661882406508	6	FACETS	0.897	0.857	0.938	0.897	0.857	0.938	INDETERMINATE	3	TRUE	3	0.615576880118062	6		418	1196	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578379	7578379	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1567552536	NA	P-0007971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	277	297	0	ENST00000269305.4:c.551del	p.Asp184ValfsTer63	p.D184Vfs*63	ENST00000269305	NM_001126112.2	184	gAt/gt	5/11	0.336661882406508	6	FACETS	1	0.964	1	1	0.964	1	INDETERMINATE	3	TRUE	3	0.615576880118062	6		297	653	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944500	40944501	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0007971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	240	476	0	ENST00000373198.4:c.2001_2002insA	p.Leu668IlefsTer16	p.L668Ifs*16	ENST00000373198	NM_133170.3	667	-/A	12/32	0.336661882406508	6	FACETS	0.762	0.711	0.815	0.508	0.474	0.543	INDETERMINATE	2	TRUE	3	0.615576880118062	6		476	1142	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542062	187542063	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	446	294	0	ENST00000441802.2:c.5677dup	p.Tyr1893LeufsTer15	p.Y1893Lfs*15	ENST00000441802	NM_005245.3	1893	tac/tTac	10/27	0.615576880118062	3	FACETS	0.998	0.967	1	0.998	0.967	1	CLONAL	3	TRUE	0	0.615576880118062	3		294	633	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0007978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	180	330	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	0.328818361442999	2	FACETS	0.959	0.891	1	0.959	0.891	1	CLONAL	2	TRUE	0	0.34171361013218	2		330	549	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120381	94120381	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	271	479	0	ENST00000369303.4:c.670T>C	p.Phe224Leu	p.F224L	ENST00000369303	NM_004440.3	224	Ttt/Ctt	3/17	0.328818361442999	2	FACETS	0.82	0.77	0.871	0.82	0.77	0.871	CLONAL	2	TRUE	0	0.34171361013218	2		479	967	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835933	151835933	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs776004398	NA	P-0007978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	126	353	0	ENST00000262189.6:c.14591G>C	p.Arg4864Thr	p.R4864T	ENST00000262189	NM_170606.2	4864	aGa/aCa	58/59	0.255846283417469	3	FACETS	1	0.968	1	0.577	0.523	0.634	CLONAL	1	TRUE	1	0.34171361013218	3		353	748	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729175	66729175	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121908596	NA	P-0007978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	181	265	0	ENST00000307102.5:c.383G>T	p.Gly128Val	p.G128V	ENST00000307102	NM_002755.3	128	gGc/gTc	3/11	0.225336418751591	4	FACETS	0.997	0.922	1	0.997	0.922	1	CLONAL	2	TRUE	2	0.34171361013218	4		265	713	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124290	2124290	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1203344843	NA	P-0007978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	228	397	0	ENST00000219476.3:c.2445G>T	p.Met815Ile	p.M815I	ENST00000219476	NM_000548.3	815	atG/atT	22/42	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	2	TRUE	NA	0.34171361013218	2		397	616	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216889	7216889	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	289	484	0	ENST00000380728.2:c.632G>C	p.Arg211Thr	p.R211T	ENST00000380728		211	aGa/aCa	7/11	0.328818361442999	2	FACETS	0.972	0.917	1	0.972	0.917	1	CLONAL	2	TRUE	0	0.34171361013218	2		484	870	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222983	1222983	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0007978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	74	174	0	ENST00000326873.7:c.921-1G>A		p.X307_splice	ENST00000326873	NM_000455.4	307			0.34171361013218	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.34171361013218	1		174	277	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600416	10600416	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	215	423	0	ENST00000171111.5:c.1439G>T	p.Gly480Val	p.G480V	ENST00000171111	NM_203500.1	480	gGg/gTg	4/6	0.34171361013218	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.34171361013218	1		423	711	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36024656	36024656	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	235	374	0	ENST00000358208.4:c.645C>G	p.Phe215Leu	p.F215L	ENST00000358208		215	ttC/ttG	6/12	0.271470019458479	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.34171361013218	4		374	868	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741500	39741500	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	158	279	0	ENST00000361337.2:c.1387G>C	p.Glu463Gln	p.E463Q	ENST00000361337	NM_003286.2	463	Gaa/Caa	14/21	0.334535906899819	3	FACETS	1	0.988	1	0.735	0.674	0.797	CLONAL	1	TRUE	1	0.34171361013218	3		279	737	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226617	2226618	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0007978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	130	272	0	ENST00000398665.3:c.4100dup	p.Leu1368ProfsTer170	p.L1368Pfs*170	ENST00000398665	NM_032482.2	1366	cct/ccTt	27/28	0.34171361013218	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.34171361013218	1		272	448	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0007995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	93	440	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.664	0.59	0.744	0.664	0.59	0.744	SUBCLONAL	1	TRUE	1	0.31	2		440	903	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0007995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	177	654	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.3	1	FACETS	0.807	0.743	0.875	0.807	0.743	0.875	CLONAL	1	TRUE	0	0.31	1		655	1195	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0007995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	228	476	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.31	2		476	994	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0007995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	134	402	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.88	0.799	0.966	0.88	0.799	0.966	CLONAL	1	TRUE	1	0.31	2		402	982	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0007995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	98	333	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.887	0.791	0.988	0.887	0.791	0.988	CLONAL	1	TRUE	1	0.31	2		335	713	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	197	592	0	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.31	2		592	1248	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0007995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	19	628	0	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	0.3	1	FACETS	0.119	0.089	0.154	0.119	0.089	0.154	SUBCLONAL	1	TRUE	0	0.31	1		628	870	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0007995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	177	684	8	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	1	2	FACETS	0.931	0.856	1	0.931	0.856	1	CLONAL	1	TRUE	1	0.31	2		692	1227	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0007995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	19	586	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.3	1	FACETS	0.12	0.09	0.155	0.12	0.09	0.155	SUBCLONAL	1	TRUE	0	0.31	1		586	865	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615036	43615036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1345166214	NA	P-0007995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	78	636	0	ENST00000355710.3:c.2450G>A	p.Arg817His	p.R817H	ENST00000355710	NM_020975.4	817	cGc/cAc	14/20	1	2	FACETS	0.475	0.416	0.539	0.475	0.416	0.539	SUBCLONAL	1	TRUE	1	0.31	2		636	1060	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	120	436	1	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	0.140749154937089	0	FACETS	0.636	0.574	0.701			1	INDETERMINATE	1	TRUE	0	0.31	0		437	840	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098591	11098591	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854197	NA	P-0007995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	139	474	1	ENST00000358026.2:c.1109G>A	p.Arg370His	p.R370H	ENST00000358026	NM_001128849.1	370	cGc/cAc	6/36	1	2	FACETS	0.951	0.865	1	0.951	0.865	1	CLONAL	1	TRUE	1	0.31	2		475	943	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310451	65310451	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	157	504	0	ENST00000342505.4:c.2237T>C	p.Val746Ala	p.V746A	ENST00000342505	NM_002227.2	746	gTg/gCg	16/25	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.31	2		504	1012	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917852	29917852	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	139	754	0	ENST00000389048.3:c.816T>G	p.Cys272Trp	p.C272W	ENST00000389048	NM_004304.4	272	tgT/tgG	3/29	1	2	FACETS	0.783	0.711	0.858	0.783	0.711	0.858	SUBCLONAL	1	TRUE	1	0.31	2		754	1146	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590400	67590400	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	103	424	0	ENST00000274335.5:c.1462A>G	p.Asn488Asp	p.N488D	ENST00000274335		488	Aat/Gat	11/15	1	2	FACETS	0.909	0.814	1	0.909	0.814	1	CLONAL	1	TRUE	1	0.31	2		424	731	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434931	49434931	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	79	286	1	ENST00000301067.7:c.6622C>T	p.Gln2208Ter	p.Q2208*	ENST00000301067	NM_003482.3	2208	Cag/Tag	31/54	1	2	FACETS	0.738	0.648	0.833	0.738	0.648	0.833	SUBCLONAL	1	TRUE	1	0.31	2		287	691	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562103	21562103	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1512	205	935	0	ENST00000382592.4:c.1816A>G	p.Met606Val	p.M606V	ENST00000382592	NM_014572.2	606	Atg/Gtg	4/8	1	2	FACETS	0.77	0.712	0.832	0.77	0.712	0.832	SUBCLONAL	1	TRUE	1	0.31	2		935	1717	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225231	53225231	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	189	609	0	ENST00000375401.3:c.2987A>C	p.Lys996Thr	p.K996T	ENST00000375401	NM_004187.3	996	aAg/aCg	20/26	0.242642903377815	2	FACETS	1	0.959	1	0.53	0.489	0.573	CLONAL	1	TRUE	0	0.31	2		609	1151	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637537	52637538	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0007995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	140	626	0	ENST00000394830.3:c.2778_2779del	p.Glu927SerfsTer2	p.E927Sfs*2	ENST00000394830	NM_018313.4	926	agAGaa/agaa	18/30	0.3	1	FACETS	0.791	0.72	0.866	0.791	0.72	0.866	SUBCLONAL	1	TRUE	0	0.31	1		626	965	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37056036	37056037	+	splice_donor_variant	Splice_Site	INS	-	-	T	rs267607791	NA	P-0007995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	114	405	0	ENST00000231790.2:c.790+2dup		p.X264_splice	ENST00000231790	NM_000249.3	264			0.3	1	FACETS	0.858	0.773	0.948	0.858	0.773	0.948	CLONAL	1	TRUE	0	0.31	1		405	724	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660075	227660075	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462380251	NA	P-0007995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	101	391	0	ENST00000305123.5:c.3380del	p.Gly1127AlafsTer12	p.G1127Afs*12	ENST00000305123	NM_005544.2	1127	gGc/gc	1/2	1	2	FACETS	0.885	0.791	0.985	0.885	0.791	0.985	CLONAL	1	TRUE	1	0.31	2		391	736	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112253	115112253	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	29	106	0	ENST00000257566.3:c.1487del	p.Gly496AlafsTer136	p.G496Afs*136	ENST00000257566	NM_016569.3	496	gGc/gc	7/8	1	2	FACETS	0.824	0.665	1	0.824	0.665	1	CLONAL	1	TRUE	1	0.31	2		106	227	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14026116	14026116	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	107	551	0	ENST00000311895.7:c.1081del	p.Met361TrpfsTer15	p.M361Wfs*15	ENST00000311895	NM_005236.2	359	gAa/ga	6/11	1	2	FACETS	0.668	0.597	0.742	0.668	0.597	0.742	SUBCLONAL	1	TRUE	1	0.31	2		551	1034	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155779	106155779	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	95	466	0	ENST00000380013.4:c.685del	p.Thr229HisfsTer21	p.T229Hfs*21	ENST00000380013	NM_001127208.2	227	gAa/ga	3/11	1	2	FACETS	0.714	0.634	0.798	0.714	0.634	0.798	SUBCLONAL	1	TRUE	1	0.31	2		466	859	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0007995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	230	662	3	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.31	2		665	1419	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274568	198274568	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746956131	NA	P-0007995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	139	549	3	ENST00000335508.6:c.830C>T	p.Ala277Val	p.A277V	ENST00000335508	NM_012433.2	277	gCg/gTg	7/25	1	2	FACETS	0.842	0.765	0.923	0.842	0.765	0.923	CLONAL	1	TRUE	1	0.31	2		552	1065	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627839	187627839	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	201	703	3	ENST00000441802.2:c.3143C>A	p.Pro1048His	p.P1048H	ENST00000441802	NM_005245.3	1048	cCt/cAt	2/27	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.31	2		706	1274	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435873	110435873	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	35	129	1	ENST00000375856.3:c.2528C>T	p.Ala843Val	p.A843V	ENST00000375856	NM_003749.2	843	gCc/gTc	1/2	1	2	FACETS	0.862	0.71	1	0.862	0.71	1	CLONAL	1	TRUE	1	0.31	2		130	262	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436576	110436576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	92	345	0	ENST00000375856.3:c.1825G>A	p.Ala609Thr	p.A609T	ENST00000375856	NM_003749.2	609	Gcg/Acg	1/2	1	2	FACETS	0.792	0.704	0.887	0.792	0.704	0.887	SUBCLONAL	1	TRUE	1	0.31	2		345	749	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781465	3781465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	23	176	0	ENST00000262367.5:c.4900G>A	p.Val1634Met	p.V1634M	ENST00000262367	NM_004380.2	1634	Gtg/Atg	30/31	1	2	FACETS	0.376	0.292	0.472	0.376	0.292	0.472	SUBCLONAL	1	TRUE	1	0.31	2		176	395	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508745	38508745	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	121	453	1	ENST00000254066.5:c.793T>C	p.Cys265Arg	p.C265R	ENST00000254066	NM_000964.3	265	Tgc/Cgc	6/9	1	2	FACETS	0.959	0.866	1	0.959	0.866	1	CLONAL	1	TRUE	1	0.31	2		454	814	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271568	15271568	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1273	107	689	0	ENST00000263388.2:c.6871C>G	p.Pro2291Ala	p.P2291A	ENST00000263388	NM_000435.2	2291	Cca/Gca	33/33	1	2	FACETS	0.5	0.447	0.557	0.5	0.447	0.557	SUBCLONAL	1	TRUE	1	0.31	2		689	1380	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271579	15271580	+	missense_variant	Missense_Mutation	DNP	AG	AG	TT	novel	NA	P-0007995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1279	108	680	0	ENST00000263388.2:c.6859_6860delinsAA	p.Leu2287Lys	p.L2287K	ENST00000263388	NM_000435.2	2287	CTg/AAg	33/33	1	2	FACETS	0.502	0.449	0.559	0.502	0.449	0.559	SUBCLONAL	1	TRUE	1	0.31	2		680	1387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0007996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	100	342	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.347585783063926	2	FACETS	0.848	0.778	0.917	1	0.981	1	CLONAL	3	TRUE	0	0.407431943137626	2		342	193	SUCCESS
APC	324	MSKCC	GRCh37	5	112175349	112175353	+	frameshift_variant	Frame_Shift_Del	DEL	AATTT	AATTT	-	novel	NA	P-0007996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	19	266	0	ENST00000257430.4:c.4058_4062del	p.Glu1353ValfsTer20	p.E1353Vfs*20	ENST00000257430	NM_000038.5	1353	gAATTT/g	16/16	1	2	FACETS	0.933	0.72	1	0.933	0.72	1	CLONAL	1	TRUE	1	0.407431943137626	2		266	100	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120003	70120003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	19	50	0	ENST00000245479.2:c.1005G>A	p.Trp335Ter	p.W335*	ENST00000245479	NM_000346.3	335	tgG/tgA	3/3	0.278610886646375	3	FACETS	0.905	0.749	1	1	0.913	1	CLONAL	4	TRUE	0	0.407431943137626	3		50	31	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945263	54945263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	13	300	0	ENST00000312783.6:c.1163C>T	p.Ser388Leu	p.S388L	ENST00000312783	NM_198436.1	388	tCa/tTa	10/10	0.324780118416931	5	FACETS	1	0.857	1	0.445	0.323	0.588	CLONAL	1	TRUE	2	0.407431943137626	5		300	77	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871157	12871158	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0007996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	34	137	0	ENST00000228872.4:c.385dup	p.His129ProfsTer8	p.H129Pfs*8	ENST00000228872	NM_004064.3	128	-/C	1/3	0.407431943137626	4	FACETS	1	0.882	1			1	CLONAL	2	TRUE	NA	0.407431943137626	4		137	110	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	35	253	1	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	0.287	0.234	0.347	0.287	0.234	0.347	SUBCLONAL	1	TRUE	1	0.36	2		254	677	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	104	365	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.217815713597514	3	FACETS	0.756	0.681	0.835	0.756	0.681	0.835	SUBCLONAL	2	TRUE	1	0.36	3		365	451	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	57	338	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.759	0.653	0.874	0.759	0.653	0.874	SUBCLONAL	1	TRUE	1	0.36	2		338	417	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	80	230	4	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.36	2		234	414	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	129	297	0	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	0.217815713597514	3	FACETS	0.805	0.734	0.88	0.805	0.734	0.88	CLONAL	2	TRUE	1	0.36	3		297	525	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	65	263	0	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	1	2	FACETS	0.738	0.641	0.843	0.738	0.641	0.843	SUBCLONAL	1	TRUE	1	0.36	2		263	489	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003784	+	frameshift_variant	Frame_Shift_Del	DEL	CTCT	CTCT	-	novel	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	86	286	0	ENST00000558401.1:c.41_44del	p.Ser14PhefsTer29	p.S14Ffs*29	ENST00000558401	NM_004048.2	13	CTCTct/ct	1/4	1	2	FACETS	0.716	0.634	0.805	0.716	0.634	0.805	SUBCLONAL	1	TRUE	1	0.36	2		286	667	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25368433	25368434	+	intron_variant	Intron	INS	-	-	T	novel	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	105	412	1	ENST00000311936.3:c.451-5589dup		p.*151*	ENST00000311936	NM_004985.3	171/189			1	2	FACETS	0.916	0.822	1	0.916	0.822	1	CLONAL	1	TRUE	1	0.36	2		413	637	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	77	196	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.99	0.873	1	0.99	0.873	1	CLONAL	1	TRUE	1	0.36	2		196	432	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	89	245	1	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	0.217815713597514	3	FACETS	1	0.934	1	0.536	0.476	0.6	CLONAL	1	TRUE	1	0.36	3		246	544	SUCCESS
APC	324	MSKCC	GRCh37	5	112175675	112175676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	67	362	0	ENST00000257430.4:c.4393_4394dup	p.Ser1465ArgfsTer9	p.S1465Rfs*9	ENST00000257430	NM_000038.5	1462	aag/aAGag	16/16	1	2	FACETS	0.741	0.645	0.845	0.741	0.645	0.845	SUBCLONAL	1	TRUE	1	0.36	2		362	502	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499363	89499363	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1317589623	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	70	308	0	ENST00000336596.2:c.2538del	p.Met847TrpfsTer10	p.M847Wfs*10	ENST00000336596	NM_005233.5	845	Ccc/cc	15/17	1	2	FACETS	0.99	0.867	1	0.99	0.867	1	CLONAL	1	TRUE	1	0.36	2		308	393	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198887	67198887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113335412	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	106	324	3	ENST00000312629.5:c.358C>T	p.Arg120Trp	p.R120W	ENST00000312629	NM_003952.2	120	Cgg/Tgg	5/15	1	2	FACETS	0.71	0.636	0.788	0.71	0.636	0.788	SUBCLONAL	1	TRUE	1	0.36	2		327	830	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489534	56489534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775164134	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	78	315	1	ENST00000267101.3:c.1999C>T	p.Arg667Cys	p.R667C	ENST00000267101	NM_001982.3	667	Cgt/Tgt	17/28	1	2	FACETS	0.895	0.789	1	0.895	0.789	1	CLONAL	1	TRUE	1	0.36	2		316	484	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6036958	6036958	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	53	336	1	ENST00000265849.7:c.802del	p.Tyr268ThrfsTer39	p.Y268Tfs*39	ENST00000265849	NM_000535.5	268	Tac/ac	7/15	0.217815713597514	3	FACETS	0.54	0.459	0.628	0.27	0.229	0.314	SUBCLONAL	1	TRUE	1	0.36	3		337	644	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482927	140482927	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	136	397	4	ENST00000288602.6:c.1208del	p.Pro403LeufsTer8	p.P403Lfs*8	ENST00000288602	NM_004333.4	403	cCt/ct	10/18	0.217815713597514	3	FACETS	0.808	0.738	0.88	0.808	0.738	0.88	CLONAL	2	TRUE	1	0.36	3		401	552	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422384	47422384	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	131	410	2	ENST00000377045.4:c.23del	p.Pro8LeufsTer26	p.P8Lfs*26	ENST00000377045	NM_001654.4	6	ggC/gg	2/16	1	2	FACETS	0.935	0.849	1	0.935	0.849	1	CLONAL	1	TRUE	1	0.36	2		412	778	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422892	49422892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751383638	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	93	277	0	ENST00000301067.7:c.14203C>T	p.Arg4735Trp	p.R4735W	ENST00000301067	NM_003482.3	4735	Cgg/Tgg	44/54	1	2	FACETS	0.853	0.759	0.952	0.853	0.759	0.952	CLONAL	1	TRUE	1	0.36	2		277	606	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021190	31021190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369058266	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	104	282	1	ENST00000375687.4:c.1189C>T	p.Arg397Cys	p.R397C	ENST00000375687	NM_015338.5	397	Cgt/Tgt	12/13	1	2	FACETS	0.961	0.863	1	0.961	0.863	1	CLONAL	1	TRUE	1	0.36	2		283	601	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430339	78430339	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	61	377	0	ENST00000370768.2:c.829G>T	p.Gly277Trp	p.G277W	ENST00000370768	NM_003902.3	277	Ggg/Tgg	10/20	1	2	FACETS	0.546	0.47	0.628	0.546	0.47	0.628	SUBCLONAL	1	TRUE	1	0.36	2		377	621	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265047	198265047	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	109	329	0	ENST00000335508.6:c.2830T>G	p.Ser944Ala	p.S944A	ENST00000335508	NM_012433.2	944	Tct/Gct	19/25	0.217815713597514	3	FACETS	1	0.983	1	0.725	0.654	0.799	CLONAL	1	TRUE	1	0.36	3		329	493	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014176	70014176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	119	678	0	ENST00000394351.3:c.1037G>A	p.Gly346Asp	p.G346D	ENST00000394351	NM_000248.3	346	gGc/gAc	9/9	1	2	FACETS	0.702	0.633	0.775	0.702	0.633	0.775	SUBCLONAL	1	TRUE	1	0.36	2		678	942	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910638	29910638	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	71	234	0	ENST00000376809.5:c.178T>G	p.Phe60Val	p.F60V	ENST00000376809	NM_002116.7	60	Ttc/Gtc	2/8	0.343666540612213	3	FACETS	0.782	0.683	0.889	0.391	0.341	0.445	SUBCLONAL	1	TRUE	1	0.36	3		234	595	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680692	30680692	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	56	376	0	ENST00000376406.3:c.1027G>A	p.Val343Ile	p.V343I	ENST00000376406	NM_014641.2	343	Gtt/Att	5/15	0.343666540612213	3	FACETS	0.415	0.354	0.481	0.207	0.177	0.241	SUBCLONAL	1	TRUE	1	0.36	3		376	885	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715413	117715413	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	87	339	0	ENST00000368508.3:c.1076T>C	p.Leu359Pro	p.L359P	ENST00000368508	NM_002944.2	359	cTg/cCg	10/43	1	2	FACETS	0.893	0.793	1	0.893	0.793	1	CLONAL	1	TRUE	1	0.36	2		339	541	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525080	157525080	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	39	342	0	ENST00000346085.5:c.4975A>G	p.Asn1659Asp	p.N1659D	ENST00000346085	NM_020732.3	1659	Aat/Gat	19/20	0.343666540612213	3	FACETS	0.466	0.385	0.556	0.233	0.192	0.278	SUBCLONAL	1	TRUE	1	0.36	3		342	549	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006054	22006054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	159	199	3	ENST00000276925.6:c.349G>A	p.Val117Met	p.V117M	ENST00000276925	NM_004936.3	117	Gtg/Atg	2/2	0.217815713597514	3	FACETS	0.932	0.859	1	0.932	0.859	1	CLONAL	2	TRUE	1	0.36	3		202	559	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336294	80336294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	125	255	0	ENST00000286548.4:c.1025C>T	p.Ala342Val	p.A342V	ENST00000286548	NM_002072.3	342	gCt/gTt	7/7	0.217815713597514	3	FACETS	0.816	0.743	0.893	0.816	0.743	0.893	CLONAL	2	TRUE	1	0.36	3		255	502	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760147	133760147	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376162814	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	61	304	0	ENST00000318560.5:c.2470G>A	p.Val824Met	p.V824M	ENST00000318560	NM_005157.4	824	Gtg/Atg	11/11	0.217815713597514	3	FACETS	0.671	0.579	0.771	0.335	0.289	0.386	SUBCLONAL	1	TRUE	1	0.36	3		304	596	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401405	139401405	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112900950	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	47	119	0	ENST00000277541.6:c.3664G>A	p.Val1222Met	p.V1222M	ENST00000277541	NM_017617.3	1222	Gtg/Atg	23/34	0.217815713597514	3	FACETS	1	0.915	1	0.558	0.474	0.65	CLONAL	1	TRUE	1	0.36	3		119	276	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612156	43612156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs181856591	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	82	267	0	ENST00000355710.3:c.2261C>T	p.Thr754Met	p.T754M	ENST00000355710	NM_020975.4	754	aCg/aTg	12/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.36	2		267	388	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63661937	63661937	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	66	221	0	ENST00000279873.7:c.41G>A	p.Gly14Asp	p.G14D	ENST00000279873	NM_032199.2	14	gGc/gAc	2/10	1	2	FACETS	0.804	0.7	0.916	0.804	0.7	0.916	CLONAL	1	TRUE	1	0.36	2		221	456	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589698	69589698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	27	55	0	ENST00000168712.1:c.155C>T	p.Ala52Val	p.A52V	ENST00000168712	NM_002007.2	52	gCg/gTg	1/3	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.36	2		55	127	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111956081	111956081	+	upstream_gene_variant	5'Flank	SNP	T	T	C	novel	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	31	150	0				ENST00000375549	NM_003002.3	79/98			1	2	FACETS	0.805	0.656	0.971	0.805	0.656	0.971	CLONAL	1	TRUE	1	0.36	2		150	214	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375344	118375344	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	62	255	0	ENST00000534358.1:c.8737A>G	p.Ser2913Gly	p.S2913G	ENST00000534358	NM_005933.3	2913	Agt/Ggt	27/36	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.36	2		255	324	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244133	133244133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759398253	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	130	299	0	ENST00000320574.5:c.2275C>T	p.Arg759Cys	p.R759C	ENST00000320574	NM_006231.2	759	Cgt/Tgt	20/49	1	2	FACETS	0.95	0.863	1	0.95	0.863	1	CLONAL	1	TRUE	1	0.36	2		299	760	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906442	32906442	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	79	458	0	ENST00000380152.3:c.827T>C	p.Val276Ala	p.V276A	ENST00000380152		276	gTa/gCa	10/27	1	2	FACETS	0.763	0.672	0.861	0.763	0.672	0.861	SUBCLONAL	1	TRUE	1	0.36	2		458	575	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40993303	40993303	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	32	376	0	ENST00000267868.3:c.129A>C	p.Glu43Asp	p.E43D	ENST00000267868	NM_002875.4	43	gaA/gaC	3/10	1	2	FACETS	0.347	0.281	0.422	0.347	0.281	0.422	SUBCLONAL	1	TRUE	1	0.36	2		376	512	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456355	99456355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	106	289	0	ENST00000268035.6:c.1672C>T	p.Pro558Ser	p.P558S	ENST00000268035	NM_000875.3	558	Ccc/Tcc	8/21	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.36	2		289	551	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208017	5208017	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	154	360	1	ENST00000357368.4:c.5694G>T	p.Glu1898Asp	p.E1898D	ENST00000357368	NM_002850.3	1898	gaG/gaT	37/38	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.36	2		361	777	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221018	5221018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	72	198	0	ENST00000357368.4:c.3448C>T	p.Pro1150Ser	p.P1150S	ENST00000357368	NM_002850.3	1150	Cct/Tct	20/38	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.36	2		198	370	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272027	15272027	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	55	121	0	ENST00000263388.2:c.6412G>A	p.Ala2138Thr	p.A2138T	ENST00000263388	NM_000435.2	2138	Gca/Aca	33/33	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.36	2		121	204	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308309	15308309	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	115	340	0	ENST00000263388.2:c.197+2T>C		p.X66_splice	ENST00000263388	NM_000435.2	66			1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.36	2		340	629	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355326	15355326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775700444	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	13	39	0	ENST00000263377.2:c.2297C>T	p.Pro766Leu	p.P766L	ENST00000263377	NM_058243.2	766	cCg/cTg	13/20	1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	1	0.36	2		39	58	SUCCESS
AR	367	MSKCC	GRCh37	X	66931405	66931405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	116	521	0	ENST00000374690.3:c.2047C>T	p.Pro683Ser	p.P683S	ENST00000374690	NM_000044.3	683	Cca/Tca	4/8	0.160195433474419	0	FACETS	0.54	0.487	0.596			1	INDETERMINATE	1	TRUE	0	0.36	0		521	764	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727867	78727867	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	42	360	0	ENST00000306801.3:c.716del	p.Asn239ThrfsTer16	p.N239Tfs*16	ENST00000306801	NM_020761.2	238	Aaa/aa	6/34	1	2	FACETS	0.346	0.288	0.411	0.346	0.288	0.411	SUBCLONAL	1	TRUE	1	0.36	2		360	674	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106733	27106734	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	63	316	0	ENST00000324856.7:c.6347_6348del	p.Arg2116ThrfsTer33	p.R2116Tfs*33	ENST00000324856	NM_006015.4	2115	cAG/c	20/20	1	2	FACETS	0.543	0.47	0.624	0.543	0.47	0.624	SUBCLONAL	1	TRUE	1	0.36	2		316	644	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023861	27023861	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1336228861	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	43	101	0	ENST00000324856.7:c.971del	p.Gly324AlafsTer39	p.G324Afs*39	ENST00000324856	NM_006015.4	323	Ggg/gg	1/20	1	2	FACETS	0.944	0.796	1	0.944	0.796	1	CLONAL	1	TRUE	1	0.36	2		101	253	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151290	202151290	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	265	484	0	ENST00000358485.4:c.1596del	p.Lys532AsnfsTer73	p.K532Nfs*73	ENST00000358485	NM_001080125.1	530	agA/ag	9/9	0.217815713597514	3	FACETS	0.764	0.716	0.814	0.764	0.716	0.814	SUBCLONAL	2	TRUE	1	0.36	3		484	1137	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967116	25967116	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	59	206	0	ENST00000435504.4:c.2090del	p.Gly697ValfsTer102	p.G697Vfs*102	ENST00000435504		697	gGt/gt	13/13	0.217815713597514	3	FACETS	0.816	0.703	0.938	0.408	0.351	0.469	CLONAL	1	TRUE	1	0.36	3		206	474	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988309	36988309	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776709	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	34	111	0	ENST00000354822.5:c.344del	p.Gly115AlafsTer10	p.G115Afs*10	ENST00000354822	NM_001079668.2	115	gGc/gc	2/3	1	2	FACETS	0.994	0.821	1	0.994	0.821	1	CLONAL	1	TRUE	1	0.36	2		111	190	SUCCESS
APC	324	MSKCC	GRCh37	5	112174910	112174910	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	52	322	0	ENST00000257430.4:c.3622del	p.Thr1208ProfsTer57	p.T1208Pfs*57	ENST00000257430	NM_000038.5	1207	Aaa/aa	16/16	1	2	FACETS	0.696	0.594	0.808	0.696	0.594	0.808	SUBCLONAL	1	TRUE	1	0.36	2		322	415	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165720	185165720	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	41	240	0	ENST00000265026.3:c.999del	p.Val334LeufsTer14	p.V334Lfs*14	ENST00000265026	NM_004721.4	332	gAa/ga	5/14	1	2	FACETS	0.744	0.623	0.878	0.744	0.623	0.878	SUBCLONAL	1	TRUE	1	0.36	2		240	306	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0008012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	89	175	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.421172596545522	2	FACETS	0.963	0.871	1	0.963	0.871	1	CLONAL	2	TRUE	0	0.427909275230351	2		175	216	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0008012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	145	607	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.306169214723801	2	FACETS	1	0.988	1	0.748	0.688	0.81	CLONAL	1	TRUE	0	0.427909275230351	2		607	453	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645693	12645693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397516827	NA	P-0008012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	110	255	0	ENST00000251849.4:c.776C>T	p.Ser259Phe	p.S259F	ENST00000251849	NM_002880.3	259	tCc/tTc	7/17	NA	2	FACETS	0.957	0.863	1			1	INDETERMINATE	1	TRUE	NA	0.427909275230351	2		255	537	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325179	123325179	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1398842143	NA	P-0008012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	92	297	0	ENST00000358487.5:c.149A>T	p.Tyr50Phe	p.Y50F	ENST00000358487	NM_000141.4	50	tAc/tTc	3/18	0.358011452514515	3	FACETS	0.951	0.847	1	0.475	0.423	0.531	CLONAL	1	TRUE	1	0.427909275230351	3		297	549	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557643	95557643	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	151	345	0	ENST00000393063.1:c.5424G>T	p.Met1808Ile	p.M1808I	ENST00000393063	NM_030621.3	1808	atG/atT	26/28	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.427909275230351	2		345	605	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781222	3781222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	173	307	0	ENST00000262367.5:c.5143G>A	p.Glu1715Lys	p.E1715K	ENST00000262367	NM_004380.2	1715	Gag/Aag	30/31	0.314850066699902	4	FACETS	0.975	0.902	1	0.975	0.902	1	CLONAL	2	TRUE	2	0.427909275230351	4		307	592	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094940	11094940	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	111	447	0	ENST00000358026.2:c.113C>G	p.Ser38Cys	p.S38C	ENST00000358026	NM_001128849.1	38	tCc/tGc	2/36	1	2	FACETS	0.973	0.878	1	0.973	0.878	1	CLONAL	1	TRUE	1	0.427909275230351	2		447	533	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543543	9543543	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	120	401	0	ENST00000353224.5:c.1611C>G	p.His537Gln	p.H537Q	ENST00000353224	NM_177990.2	537	caC/caG	6/10	0.358011452514515	3	FACETS	0.935	0.845	1	0.468	0.422	0.515	CLONAL	1	TRUE	1	0.427909275230351	3		401	728	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040763	47040764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCAG	novel	NA	P-0008012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	126	416	0	ENST00000377604.3:c.1399_1400insCAGG	p.Gly467AlafsTer52	p.G467Afs*52	ENST00000377604	NM_001204468.1	466	-/GCAG	13/24	0.427909275230351	1	FACETS	0.895	0.815	0.979	0.895	0.815	0.979	CLONAL	1	TRUE	0	0.427909275230351	1		416	517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0008032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	404	513	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.115437744850572	5	FACETS	1	0.964	1			1	INDETERMINATE	4	TRUE	NA	0.454466474667481	5		513	744	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391084	89391084	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	115	389	0	ENST00000336596.2:c.1150C>T	p.Pro384Ser	p.P384S	ENST00000336596	NM_005233.5	384	Cct/Tct	5/17	0.454466474667481	3	FACETS	0.809	0.729	0.893	0.404	0.364	0.447	CLONAL	1	TRUE	1	0.454466474667481	3		389	768	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221340	1221340	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0008032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	183	336	0	ENST00000326873.7:c.862+1G>A		p.X288_splice	ENST00000326873	NM_000455.4	288			0.454466474667481	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.454466474667481	2		336	363	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267360	198267360	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs374250186	NA	P-0008032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	129	382	0	ENST00000335508.6:c.1997A>T	p.Lys666Met	p.K666M	ENST00000335508	NM_012433.2	666	aAg/aTg	14/25	0.452464238549551	3	FACETS	0.935	0.849	1	0.468	0.424	0.513	CLONAL	1	TRUE	1	0.454466474667481	3		382	745	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695755	117695755	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	70	271	0	ENST00000369458.3:c.682G>A	p.Glu228Lys	p.E228K	ENST00000369458	NM_024626.3	228	Gaa/Aaa	4/6	0.306527226125266	4	FACETS	1	0.93	1	0.546	0.478	0.619	CLONAL	1	TRUE	2	0.454466474667481	4		271	410	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695827	117695827	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	74	269	0	ENST00000369458.3:c.610G>C	p.Glu204Gln	p.E204Q	ENST00000369458	NM_024626.3	204	Gag/Cag	4/6	0.306527226125266	4	FACETS	0.955	0.838	1	0.477	0.419	0.54	CLONAL	1	TRUE	2	0.454466474667481	4		269	496	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660480	227660480	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	64	184	0	ENST00000305123.5:c.2975T>A	p.Met992Lys	p.M992K	ENST00000305123	NM_005544.2	992	aTg/aAg	1/2	0.452464238549551	3	FACETS	1	0.936	1	0.559	0.488	0.635	CLONAL	1	TRUE	1	0.454466474667481	3		184	309	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127794	47127794	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0008032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	93	246	0	ENST00000409792.3:c.5288C>G	p.Ser1763Ter	p.S1763*	ENST00000409792	NM_014159.6	1763	tCa/tGa	11/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.454466474667481	2		246	301	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665643	86665643	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	83	227	0	ENST00000274376.6:c.1624C>G	p.Gln542Glu	p.Q542E	ENST00000274376	NM_002890.2	542	Cag/Gag	12/25	0.454466474667481	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	0	0.454466474667481	2		227	175	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509893	106509893	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	234	409	0	ENST00000359195.3:c.1887G>T	p.Gln629His	p.Q629H	ENST00000359195	NM_002649.2	629	caG/caT	2/11	0.306527226125266	4	FACETS	0.992	0.929	1	0.992	0.929	1	CLONAL	2	TRUE	2	0.454466474667481	4		409	755	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876925	151876925	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs759152407	NA	P-0008032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	209	274	0	ENST00000262189.6:c.7436G>T	p.Gly2479Val	p.G2479V	ENST00000262189	NM_170606.2	2479	gGa/gTa	37/59	0.454466474667481	5	FACETS	0.883	0.825	0.941	0.883	0.825	0.941	CLONAL	3	TRUE	2	0.454466474667481	5		274	584	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158377	108158377	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	139	352	0	ENST00000278616.4:c.4044G>C	p.Leu1348Phe	p.L1348F	ENST00000278616	NM_000051.3	1348	ttG/ttC	27/63	0.243210406656246	5	FACETS	1	0.975	1	0.772	0.709	0.838	INDETERMINATE	2	TRUE	2	0.454466474667481	5		352	444	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448738	49448738	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	97	415	0	ENST00000301067.7:c.121G>T	p.Val41Phe	p.V41F	ENST00000301067	NM_003482.3	41	Gtc/Ttc	2/54	0.243210406656246	5	FACETS	1	0.933	1	0.354	0.316	0.395	INDETERMINATE	1	TRUE	2	0.454466474667481	5		415	676	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	389	459	0	ENST00000269305.4:c.853G>C	p.Glu285Gln	p.E285Q	ENST00000269305	NM_001126112.2	285	Gag/Cag	8/11	0.115437744850572	5	FACETS	1	0.981	1			1	INDETERMINATE	4	TRUE	NA	0.454466474667481	5		459	695	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611804	1611804	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1343124101	NA	P-0008032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	405	657	0	ENST00000344749.5:c.1858G>C	p.Glu620Gln	p.E620Q	ENST00000344749	NM_001136139.2	620	Gag/Cag	19/19	0.454466474667481	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.454466474667481	2		657	818	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615698	1615698	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145878545	NA	P-0008032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	178	756	1	ENST00000344749.5:c.1573C>T	p.Arg525Trp	p.R525W	ENST00000344749	NM_001136139.2	525	Cgg/Tgg	17/19	0.454466474667481	2	FACETS	1	0.924	1	0.5	0.462	0.54	CLONAL	1	TRUE	0	0.454466474667481	2		757	783	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15273319	15273319	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	325	469	0	ENST00000263388.2:c.5870C>G	p.Ala1957Gly	p.A1957G	ENST00000263388	NM_000435.2	1957	gCc/gGc	32/33	0.454466474667481	2	FACETS	0.982	0.934	1	0.982	0.934	1	CLONAL	2	TRUE	0	0.454466474667481	2		469	728	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574362	41574362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	278	443	0	ENST00000263253.7:c.6647G>A	p.Gly2216Glu	p.G2216E	ENST00000263253	NM_001429.3	2216	gGa/gAa	31/31	0.438242246984071	4	FACETS	1	0.974	1			1	CLONAL	2	TRUE	NA	0.454466474667481	4		443	842	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402526	20402541	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCTGTCGTCGCC	GGCGGCTGTCGTCGCC	-	novel	NA	P-0008032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	124	222	0	ENST00000346618.3:c.64_79del	p.Ala22ProfsTer13	p.A22Pfs*13	ENST00000346618	NM_001949.4	21	ggGGCGGCTGTCGTCGCC/gg	1/7	0.274318026482483	5	FACETS	1	0.98	1	0.831	0.76	0.904	CLONAL	2	TRUE	2	0.454466474667481	5		222	368	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878295	151878295	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	326	363	0	ENST00000262189.6:c.6650del	p.Pro2217LeufsTer22	p.P2217Lfs*22	ENST00000262189	NM_170606.2	2217	cCt/ct	36/59	0.454466474667481	5	FACETS	0.941	0.892	0.99	0.941	0.892	0.99	CLONAL	3	TRUE	2	0.454466474667481	5		363	855	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602324	10602325	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0008032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	239	353	1	ENST00000171111.5:c.1253dup	p.Val420GlyfsTer25	p.V420Gfs*25	ENST00000171111	NM_203500.1	418	gtg/gtTg	3/6	0.454466474667481	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.454466474667481	2		354	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578419	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587781845	NA	P-0008041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	83	246	0	ENST00000269305.4:c.511G>T	p.Glu171Ter	p.E171*	ENST00000269305	NM_001126112.2	171	Gag/Tag	5/11	0.205180580917755	3	FACETS	1	0.917	1	1	0.917	1	INDETERMINATE	2	TRUE	1	0.411628223924	3		246	237	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0008041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	14	442	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.205180580917755	3	FACETS	1	0.855	1	0.631	0.467	0.818	INDETERMINATE	1	TRUE	1	0.411628223924	3		442	65	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0008041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	46	147	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	0.411628223924	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.411628223924	1		147	137	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958438	90958438	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	16	343	0	ENST00000265433.3:c.2000C>G	p.Ser667Cys	p.S667C	ENST00000265433	NM_002485.4	667	tCt/tGt	13/16	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.411628223924	2		343	63	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566538	139566538	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	62	300	0	ENST00000308874.7:c.797C>T	p.Ser266Phe	p.S266F	ENST00000308874		266	tCc/tTc	9/10	0.394578873064187	1	FACETS	0.718	0.624	0.819	0.718	0.624	0.819	SUBCLONAL	1	TRUE	0	0.411628223924	1		300	333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578420	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGTCATGTG	novel	NA	P-0008041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	49	247	0	ENST00000269305.4:c.502_510dup	p.His168_Thr170dup	p.H168_T170dup	ENST00000269305	NM_001126112.2	168	-/CACATGACG	5/11	0.205180580917755	3	FACETS	1	0.928	1	0.574	0.49	0.664	INDETERMINATE	1	TRUE	1	0.411628223924	3		247	250	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	90	245	0				ENST00000310581	NM_198253.2	-/1132			0.239548387534187	1	FACETS	0.718	0.65	0.786	0.718	0.65	0.786	INDETERMINATE	1	TRUE	0	0.745607994557458	1		245	211	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0008060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	186	576	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.978	0.911	1	0.978	0.911	1	CLONAL	1	TRUE	1	0.745607994557458	2		576	510	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791757	42791757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568504941	NA	P-0008060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	287	694	1	ENST00000575354.2:c.643C>T	p.Arg215Trp	p.R215W	ENST00000575354	NM_015125.3	215	Cgg/Tgg	5/20	0.745607994557458	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.745607994557458	1		695	441	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103755	47103758	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	novel	NA	P-0008060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	113	895	0	ENST00000409792.3:c.6188_6191del	p.Arg2063ThrfsTer83	p.R2063Tfs*83	ENST00000409792	NM_014159.6	2063	aGAGAc/ac	14/21	1	2	FACETS	0.38	0.341	0.42	0.38	0.341	0.42	SUBCLONAL	1	TRUE	1	0.745607994557458	2		895	798	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430874	78430877	+	frameshift_variant	Frame_Shift_Del	DEL	CTTC	CTTC	-	novel	NA	P-0008060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	145	520	0	ENST00000370768.2:c.512_515del	p.Gly171AspfsTer20	p.G171Dfs*20	ENST00000370768	NM_003902.3	171	gGAAGa/ga	8/20	0.745607994557458	1	FACETS	0.784	0.728	0.841	0.784	0.728	0.841	SUBCLONAL	1	TRUE	0	0.745607994557458	1		520	311	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432574	78432575	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GATA	novel	NA	P-0008060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	40	481	0	ENST00000370768.2:c.408_409insTATC	p.Ala137TyrfsTer4	p.A137Yfs*4	ENST00000370768	NM_003902.3	136	-/TATC	6/20	0.745607994557458	1	FACETS	0.218	0.182	0.259	0.218	0.182	0.259	SUBCLONAL	1	TRUE	0	0.745607994557458	1		481	308	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0008164-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	71	276	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.287677283893146	1	FACETS	0.89	0.78	1	0.89	0.78	1	CLONAL	1	TRUE	0	0.31	1		276	435	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0008164-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	313	420	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.295992296055669	3	FACETS	0.868	0.821	0.915	0.868	0.821	0.915	CLONAL	3	TRUE	0	0.31	3		420	896	SUCCESS
AR	367	MSKCC	GRCh37	X	66931483	66931483	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008164-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	162	209	0	ENST00000374690.3:c.2125G>T	p.Gly709Ter	p.G709*	ENST00000374690	NM_000044.3	709	Gga/Tga	4/8	0.25366315078194	0	FACETS	0.658	0.607	0.71			1	SUBCLONAL	2	TRUE	NA	0.31	0		209	548	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102097	27102098	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0008164-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	138	414	0	ENST00000324856.7:c.5026dup	p.Leu1676ProfsTer22	p.L1676Pfs*22	ENST00000324856	NM_006015.4	1675	tcc/tCcc	19/20	1	2	FACETS	0.836	0.759	0.917	0.836	0.759	0.917	CLONAL	1	TRUE	1	0.31	2		414	1065	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	96	403	1	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.185739390696383	4	FACETS	1	0.932	1	0.531	0.473	0.593	INDETERMINATE	1	TRUE	2	0.33	4		404	729	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	79	338	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.217548121381611	3	FACETS	0.975	0.859	1	0.488	0.429	0.55	CLONAL	1	TRUE	1	0.33	3		338	572	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	123	476	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.185739390696383	4	FACETS	1	0.983	1	0.706	0.639	0.776	INDETERMINATE	1	TRUE	2	0.33	4		476	702	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	71	621	1	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	0.100428797893363	3	FACETS	0.861	0.752	0.979	0.431	0.376	0.49	INDETERMINATE	1	TRUE	1	0.33	3		622	582	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446278	70446278	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147119124	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	79	682	0	ENST00000373644.4:c.5218C>T	p.Arg1740Cys	p.R1740C	ENST00000373644	NM_030625.2	1740	Cgc/Tgc	11/12	0.3	2	FACETS	1	0.894	1			1	CLONAL	1	TRUE	NA	0.33	2		682	472	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202995	16202995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200777699	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	37	339	0	ENST00000375759.3:c.703C>T	p.Arg235Trp	p.R235W	ENST00000375759	NM_015001.2	235	Cgg/Tgg	3/15	0.217548121381611	4	FACETS	0.842	0.696	1	0.421	0.348	0.503	CLONAL	1	TRUE	2	0.33	4		339	354	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259043	16259043	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	37	405	2	ENST00000375759.3:c.6308G>T	p.Arg2103Met	p.R2103M	ENST00000375759	NM_015001.2	2103	aGg/aTg	11/15	0.217548121381611	4	FACETS	1	0.941	1	0.669	0.556	0.793	CLONAL	1	TRUE	2	0.33	4		407	223	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746102	162746102	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs550210469	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	80	454	0	ENST00000367921.3:c.2225G>A	p.Arg742Gln	p.R742Q	ENST00000367921	NM_006182.2	742	cGg/cAg	16/18	0.185739390696383	4	FACETS	1	0.96	1	0.603	0.531	0.679	INDETERMINATE	1	TRUE	2	0.33	4		454	535	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149071	61149071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772899527	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	80	597	4	ENST00000295025.8:c.1261C>T	p.Arg421Cys	p.R421C	ENST00000295025	NM_002908.2	421	Cgc/Tgc	11/11	0.100428797893363	3	FACETS	0.993	0.875	1	0.496	0.437	0.559	INDETERMINATE	1	TRUE	1	0.33	3		601	569	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368428	225368428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	38	560	0	ENST00000264414.4:c.1318C>T	p.Leu440Phe	p.L440F	ENST00000264414	NM_003590.4	440	Ctt/Ttt	9/16	0.3	4	FACETS	0.515	0.425	0.616			1	SUBCLONAL	1	TRUE	NA	0.33	4		560	595	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098909	47098909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	56	485	1	ENST00000409792.3:c.6365G>A	p.Arg2122Gln	p.R2122Q	ENST00000409792	NM_014159.6	2122	cGg/cAg	15/21	0.185739390696383	4	FACETS	0.981	0.842	1	0.491	0.421	0.567	INDETERMINATE	1	TRUE	2	0.33	4		486	460	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595840	52595840	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	67	610	0	ENST00000394830.3:c.4075C>T	p.Arg1359Cys	p.R1359C	ENST00000394830	NM_018313.4	1359	Cgc/Tgc	26/30	0.3	3	FACETS	1	0.931	1			1	CLONAL	1	TRUE	NA	0.33	3		610	428	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021817	71021817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs797045586	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	54	472	0	ENST00000318789.4:c.1541G>A	p.Arg514His	p.R514H	ENST00000318789	NM_032682.5	514	cGt/cAt	18/21	0.3	7	FACETS	1	0.95	1			1	CLONAL	1	TRUE	NA	0.33	7		472	470	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72866457	72866457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375075276	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	96	547	0	ENST00000325599.8:c.806G>A	p.Arg269His	p.R269H	ENST00000325599	NM_018130.2	269	cGt/cAt	7/11	0.3	3	FACETS	1	0.92	1			1	CLONAL	1	TRUE	NA	0.33	3		547	653	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259603	89259603	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	15	241	0	ENST00000336596.2:c.747A>C	p.Glu249Asp	p.E249D	ENST00000336596	NM_005233.5	249	gaA/gaC	3/17	0.3	3	FACETS	0.407	0.298	0.539			1	SUBCLONAL	1	TRUE	NA	0.33	3		241	260	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612061	189612061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777373892	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	44	378	0	ENST00000264731.3:c.1813C>T	p.Arg605Trp	p.R605W	ENST00000264731	NM_003722.4	605	Cgg/Tgg	14/14	0.185739390696383	4	FACETS	1	0.937	1	0.616	0.519	0.721	INDETERMINATE	1	TRUE	2	0.33	4		378	288	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356208	66356208	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	21	470	0	ENST00000273854.3:c.1289A>G	p.Asp430Gly	p.D430G	ENST00000273854	NM_004439.5	430	gAt/gGt	5/18	1	2	FACETS	0.335	0.257	0.426	0.335	0.257	0.426	SUBCLONAL	1	TRUE	1	0.33	2		470	380	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517730	187517730	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	15	189	0	ENST00000441802.2:c.12964T>C	p.Ser4322Pro	p.S4322P	ENST00000441802	NM_005245.3	4322	Tcc/Ccc	25/27	0.185739390696383	4	FACETS	0.691	0.507	0.91	0.345	0.253	0.455	INDETERMINATE	1	TRUE	2	0.33	4		189	175	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628026	187628026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750746155	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	81	573	0	ENST00000441802.2:c.2956G>A	p.Val986Ile	p.V986I	ENST00000441802	NM_005245.3	986	Gtc/Atc	2/27	0.185739390696383	4	FACETS	1	0.961	1	0.605	0.534	0.68	INDETERMINATE	1	TRUE	2	0.33	4		573	540	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	60	467	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.370518928901407	4	FACETS	1	0.926	1	0.556	0.48	0.638	CLONAL	1	TRUE	2	0.33	4		468	435	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	65	535	1	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.370518928901407	4	FACETS	0.937	0.813	1	0.469	0.406	0.536	CLONAL	1	TRUE	2	0.33	4		536	559	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004721	150004721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1034620976	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	47	480	1	ENST00000253339.5:c.1504C>T	p.Arg502Cys	p.R502C	ENST00000253339		502	Cgt/Tgt	3/7	0.3	2	FACETS	0.764	0.646	0.892			1	SUBCLONAL	1	TRUE	NA	0.33	2		481	373	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946355	2946355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372251654	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	35	521	0	ENST00000396946.4:c.3382G>A	p.Val1128Ile	p.V1128I	ENST00000396946	NM_032415.4	1128	Gta/Ata	25/25	0.3	1	FACETS	0.886	0.733	1	0.886	0.733	1	CLONAL	1	TRUE	0	0.33	1		521	200	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962804	2962804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772900135	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	18	401	2	ENST00000396946.4:c.2104G>A	p.Glu702Lys	p.E702K	ENST00000396946	NM_032415.4	702	Gag/Aag	16/25	0.3	1	FACETS	0.717	0.546	0.915	0.717	0.546	0.915	CLONAL	1	TRUE	0	0.33	1		403	127	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508461	106508461	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762164881	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	11	130	0	ENST00000359195.3:c.455G>A	p.Arg152Gln	p.R152Q	ENST00000359195	NM_002649.2	152	cGg/cAg	2/11	0.267642102074104	4	FACETS	0.806	0.561	1	0.403	0.28	0.553	CLONAL	1	TRUE	2	0.33	4		130	110	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339700	116339700	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	36	395	1	ENST00000397752.3:c.562G>A	p.Val188Ile	p.V188I	ENST00000397752	NM_000245.2	188	Gta/Ata	2/21	0.267642102074104	4	FACETS	0.58	0.477	0.697	0.29	0.238	0.349	SUBCLONAL	1	TRUE	2	0.33	4		396	500	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852274	63852274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1406382655	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	57	318	0	ENST00000279873.7:c.3052G>A	p.Asp1018Asn	p.D1018N	ENST00000279873	NM_032199.2	1018	Gat/Aat	10/10	0.3	11	FACETS	1	0.94	1			1	CLONAL	2	TRUE	NA	0.33	11		318	366	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137761	64137761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	38	504	1	ENST00000334205.4:c.1862C>T	p.Ala621Val	p.A621V	ENST00000334205	NM_003942.2	621	gCg/gTg	15/17	0.217548121381611	4	FACETS	1	0.943	1	0.672	0.56	0.795	CLONAL	1	TRUE	2	0.33	4		505	228	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103408	77103408	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	51	702	0	ENST00000356341.3:c.158G>A	p.Arg53Gln	p.R53Q	ENST00000356341	NM_002576.4	53	cGa/cAa	2/15	0.217548121381611	3	FACETS	0.536	0.455	0.625	0.268	0.227	0.313	SUBCLONAL	1	TRUE	1	0.33	3		702	672	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933406	100933406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150584881	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	93	726	1	ENST00000325455.5:c.1984G>A	p.Val662Ile	p.V662I	ENST00000325455	NM_001202474.3	662	Gtt/Att	4/8	0.217548121381611	3	FACETS	1	0.954	1	0.566	0.504	0.632	CLONAL	1	TRUE	1	0.33	3		727	580	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205332	46205332	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	82	300	0	ENST00000334344.6:c.416C>T	p.Ser139Leu	p.S139L	ENST00000334344	NM_152641.2	139	tCg/tTg	4/21	0.185739390696383	4	FACETS	1	0.975	1	0.708	0.626	0.794	INDETERMINATE	1	TRUE	2	0.33	4		300	467	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420745	49420745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768594066	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	33	336	2	ENST00000301067.7:c.15004C>T	p.Arg5002Trp	p.R5002W	ENST00000301067	NM_003482.3	5002	Cgg/Tgg	48/54	0.185739390696383	4	FACETS	1	0.896	1	0.571	0.468	0.685	INDETERMINATE	1	TRUE	2	0.33	4		338	233	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435048	49435048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369501280	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	16	260	0	ENST00000301067.7:c.6505G>A	p.Ala2169Thr	p.A2169T	ENST00000301067	NM_003482.3	2169	Gcc/Acc	31/54	0.185739390696383	4	FACETS	0.97	0.723	1	0.485	0.361	0.63	INDETERMINATE	1	TRUE	2	0.33	4		260	133	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864528	56864528	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	93	874	0	ENST00000308159.5:c.1016A>G	p.Asn339Ser	p.N339S	ENST00000308159	NM_014669.4	339	aAt/aGt	10/22	0.100428797893363	0	FACETS	0.783	0.699	0.872			1	INDETERMINATE	1	TRUE	0	0.33	0		874	482	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509685	29509685	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	30	333	0	ENST00000356175.3:c.888+2T>C		p.X296_splice	ENST00000356175	NM_000267.3	296			0.217548121381611	3	FACETS	0.582	0.469	0.71	0.291	0.234	0.355	SUBCLONAL	1	TRUE	1	0.33	3		333	364	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250953	10250953	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1434985283	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	31	316	0	ENST00000340748.4:c.3527C>T	p.Ala1176Val	p.A1176V	ENST00000340748		1176	gCg/gTg	32/40	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.33	2		316	175	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098396	11098396	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138097741	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	38	385	0	ENST00000358026.2:c.914C>T	p.Pro305Leu	p.P305L	ENST00000358026	NM_001128849.1	305	cCg/cTg	6/36	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.33	2		385	205	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098423	11098423	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs549254467	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	25	272	0	ENST00000358026.2:c.941C>T	p.Ala314Val	p.A314V	ENST00000358026	NM_001128849.1	314	gCg/gTg	6/36	1	2	FACETS	0.918	0.731	1	0.918	0.731	1	CLONAL	1	TRUE	1	0.33	2		272	165	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626844	14626844	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758885471	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	121	829	1	ENST00000254322.2:c.931C>T	p.Arg311Cys	p.R311C	ENST00000254322	NM_006145.1	311	Cgt/Tgt	3/3	0.3	7	FACETS	0.848	0.766	0.934			1	CLONAL	2	TRUE	NA	0.33	7		830	789	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395665	31395665	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1182001726	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	30	480	0	ENST00000328111.2:c.2518C>T	p.Arg840Ter	p.R840*	ENST00000328111	NM_006892.3	840	Cga/Tga	23/23	1	2	FACETS	0.733	0.594	0.89	0.733	0.594	0.89	SUBCLONAL	1	TRUE	1	0.33	2		480	248	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44970645	44970645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	31	322	0	ENST00000377967.4:c.4195G>A	p.Ala1399Thr	p.A1399T	ENST00000377967	NM_021140.2	1399	Gcc/Acc	29/29	0.3	2	FACETS	0.551	0.446	0.669	0.275	0.223	0.335	SUBCLONAL	1	TRUE	0	0.33	2		322	341	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264985	46264985	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	72	904	0	ENST00000371998.3:c.1860del	p.Lys620AsnfsTer18	p.K620Nfs*18	ENST00000371998		619	Aaa/aa	12/23	1	2	FACETS	0.745	0.651	0.845	0.745	0.651	0.845	SUBCLONAL	1	TRUE	1	0.33	2		904	586	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101401	27101402	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	37	466	0	ENST00000324856.7:c.4689dup	p.Met1564HisfsTer8	p.M1564Hfs*8	ENST00000324856	NM_006015.4	1561	-/C	18/20	0.217548121381611	4	FACETS	0.994	0.823	1	0.497	0.411	0.592	CLONAL	1	TRUE	2	0.33	4		466	300	SUCCESS
APC	324	MSKCC	GRCh37	5	112177716	112177717	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	43	325	0	ENST00000257430.4:c.6430_6431del	p.Leu2144GlyfsTer9	p.L2144Gfs*9	ENST00000257430	NM_000038.5	2142	aTC/a	16/16	0.100428797893363	3	FACETS	0.909	0.763	1	0.455	0.381	0.535	INDETERMINATE	1	TRUE	1	0.33	3		325	334	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903755	114903755	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	78	785	1	ENST00000543371.1:c.763del	p.His255IlefsTer3	p.H255Ifs*3	ENST00000543371	NM_001198531.1	253	atC/at	7/14	1	2	FACETS	0.913	0.804	1	0.913	0.804	1	CLONAL	1	TRUE	1	0.33	2		786	518	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821959	72821960	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs762108866	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	57	248	1	ENST00000268489.5:c.10215dup	p.Gly3406ArgfsTer25	p.G3406Rfs*25	ENST00000268489	NM_006885.3	3405	-/C	10/10	0.100428797893363	0	FACETS	0.592	0.51	0.681			1	INDETERMINATE	1	TRUE	0	0.33	0		249	391	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702382	47702382	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	53	386	0	ENST00000233146.2:c.1978del	p.Asp660IlefsTer25	p.D660Ifs*25	ENST00000233146	NM_000251.2	660	Gat/at	12/16	0.100428797893363	3	FACETS	1	0.878	1	0.514	0.44	0.595	INDETERMINATE	1	TRUE	1	0.33	3		386	364	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	39	470	2	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.33	2		472	216	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154251	2154251	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	39	534	0	ENST00000434045.2:c.677del	p.Gly226AlafsTer30	p.G226Afs*30	ENST00000434045	NM_001127598.1	226	gGc/gc	5/5	1	2	FACETS	0.762	0.642	0.892	1	0.959	1	SUBCLONAL	2	TRUE	1	0.33	2		534	155	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5466787	5466787	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	69	540	0	ENST00000381577.3:c.813del	p.Lys271AsnfsTer44	p.K271Nfs*44	ENST00000381577	NM_014143.3	270	Aaa/aa	6/7	1	2	FACETS	0.886	0.774	1	0.886	0.774	1	CLONAL	1	TRUE	1	0.33	2		540	472	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646084	215646085	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs746325928	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	55	435	0	ENST00000260947.4:c.513dup	p.Asp172ArgfsTer10	p.D172Rfs*10	ENST00000260947	NM_000465.2	171	-/A	4/11	1	2	FACETS	0.697	0.597	0.806	0.697	0.597	0.806	SUBCLONAL	1	TRUE	1	0.33	2		435	478	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646981	23646981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	50	690	0	ENST00000261584.4:c.886del	p.Met296Ter	p.M296*	ENST00000261584	NM_024675.3	296	Atg/tg	4/13	0.3	3	FACETS	0.813	0.691	0.947			1	CLONAL	1	TRUE	NA	0.33	3		690	434	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12043155	12043155	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0008327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	33	388	0	ENST00000353533.5:c.1041-1G>T		p.X347_splice	ENST00000353533	NM_003010.3	347			0.199675503789592	1	FACETS	0.817	0.673	0.975	0.817	0.673	0.975	INDETERMINATE	1	TRUE	0	0.378693993062632	1		388	173	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258889	16258889	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0008327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	144	452	0	ENST00000375759.3:c.6154A>T	p.Lys2052Ter	p.K2052*	ENST00000375759	NM_015001.2	2052	Aaa/Taa	11/15	1	2	FACETS	0.974	0.889	1	0.974	0.889	1	CLONAL	1	TRUE	1	0.378693993062632	2		452	781	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572183	64572183	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	138	433	0	ENST00000312049.6:c.1456G>T	p.Glu486Ter	p.E486*	ENST00000312049	NM_130799.2	486	Gag/Tag	10/10	0.378693993062632	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.378693993062632	1		433	580	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637579	23637579	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	95	448	0	ENST00000261584.4:c.2726T>G	p.Leu909Arg	p.L909R	ENST00000261584	NM_024675.3	909	cTt/cGt	7/13	0.378693993062632	3	FACETS	0.901	0.803	1	0.451	0.401	0.503	CLONAL	1	TRUE	1	0.378693993062632	3		448	662	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973731	15973731	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	100	392	0	ENST00000268712.3:c.4261G>T	p.Glu1421Ter	p.E1421*	ENST00000268712	NM_006311.3	1421	Gaa/Taa	31/46	0.199675503789592	1	FACETS	0.935	0.839	1	0.935	0.839	1	INDETERMINATE	1	TRUE	0	0.378693993062632	1		392	458	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953322	17953322	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	111	294	0	ENST00000458235.1:c.664C>T	p.Arg222Cys	p.R222C	ENST00000458235	NM_000215.3	222	Cgc/Tgc	6/24	1	2	FACETS	0.982	0.885	1	0.982	0.885	1	CLONAL	1	TRUE	1	0.378693993062632	2		294	597	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115941	8115942	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	79	226	0	ENST00000346208.3:c.1290dup	p.Gly431TrpfsTer76	p.G431Wfs*76	ENST00000346208		429	-/T	6/6	1	2	FACETS	0.979	0.865	1	0.979	0.865	1	CLONAL	1	TRUE	1	0.378693993062632	2		226	426	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842659	68842660	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CACCCCCTGTTGGTGTCTTTAC	novel	NA	P-0008369-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	121	520	0	ENST00000261769.5:c.616_617insCCACCCCCTGTTGGTGTCTTTA	p.Ile206ThrfsTer10	p.I206Tfs*10	ENST00000261769	NM_004360.3	199	aca/aCACCCCCTGTTGGTGTCTTTACca	5/16	0.392823671037751	1	FACETS	0.643	0.581	0.708	0.643	0.581	0.708	SUBCLONAL	1	TRUE	0	0.392823671037751	1		520	770	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591135	67591136	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0008444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	106	159	0	ENST00000274335.5:c.1732_1733del	p.Asp578ProfsTer23	p.D578Pfs*23	ENST00000274335		576	acGAga/acga	12/15	0.38954071083514	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.394995921519532	1		159	417	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717727	89717727	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554825226	NA	P-0008444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	160	150	0	ENST00000371953.3:c.752G>T	p.Gly251Val	p.G251V	ENST00000371953	NM_000314.4	251	gGt/gTt	7/9	0.394995921519532	3	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	1	0.394995921519532	3		150	468	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	230	240	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.935	0.877	0.993	1	0.994	1	CLONAL	2	TRUE	1	0.394995921519532	2		240	623	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	167	246	0	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.394995921519532	2		246	734	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0008444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	71	182	0	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	1	2	FACETS	0.687	0.601	0.78	0.687	0.601	0.78	SUBCLONAL	1	TRUE	1	0.394995921519532	2		182	523	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101117	27101117	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	153	269	2	ENST00000324856.7:c.4403del	p.Pro1468LeufsTer13	p.P1468Lfs*13	ENST00000324856	NM_006015.4	1467	Ccc/cc	18/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.394995921519532	2		271	737	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0008444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	70	147	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.985	0.864	1	0.985	0.864	1	CLONAL	1	TRUE	1	0.394995921519532	2		147	360	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796883	42796883	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	115	272	1	ENST00000575354.2:c.3347del	p.Pro1116GlnfsTer45	p.P1116Qfs*45	ENST00000575354	NM_015125.3	1114	gCc/gc	14/20	1	2	FACETS	0.888	0.801	0.979	0.888	0.801	0.979	CLONAL	1	TRUE	1	0.394995921519532	2		273	656	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423632	88423632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1478926904	NA	P-0008444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	95	193	0	ENST00000360948.2:c.2203C>T	p.Arg735Cys	p.R735C	ENST00000360948	NM_001012338.2	735	Cgc/Tgc	18/19	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.394995921519532	2		193	457	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145644	11145644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555785374	NA	P-0008444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	36	150	1	ENST00000358026.2:c.4006C>T	p.Arg1336Cys	p.R1336C	ENST00000358026	NM_001128849.1	1336	Cgc/Tgc	29/36	1	2	FACETS	0.418	0.343	0.502	0.418	0.343	0.502	SUBCLONAL	1	TRUE	1	0.394995921519532	2		151	436	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0008444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	95	192	0	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.976	0.872	1	0.976	0.872	1	CLONAL	1	TRUE	1	0.394995921519532	2		192	493	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257144	19257144	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	52	102	1	ENST00000162023.5:c.819del	p.Thr274ProfsTer?	p.T274Pfs*?	ENST00000162023		273	ccC/cc	12/13	1	2	FACETS	0.957	0.822	1	0.957	0.822	1	CLONAL	1	TRUE	1	0.394995921519532	2		103	275	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275249	41275249	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	59	149	0	ENST00000349496.5:c.1415C>G	p.Thr472Ser	p.T472S	ENST00000349496	NM_001904.3	472	aCc/aGc	9/15	1	2	FACETS	0.743	0.642	0.853	0.743	0.642	0.853	SUBCLONAL	1	TRUE	1	0.394995921519532	2		149	402	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138375045	138375045	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369600257	NA	P-0008444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	113	192	0	ENST00000289153.2:c.3014C>T	p.Ala1005Val	p.A1005V	ENST00000289153	NM_006219.2	1005	gCg/gTg	21/22	1	2	FACETS	0.936	0.845	1	0.936	0.845	1	CLONAL	1	TRUE	1	0.394995921519532	2		192	611	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86668007	86668007	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	96	215	0	ENST00000274376.6:c.1771C>T	p.Arg591Cys	p.R591C	ENST00000274376	NM_002890.2	591	Cgt/Tgt	13/25	1	2	FACETS	0.86	0.768	0.958	0.86	0.768	0.958	CLONAL	1	TRUE	1	0.394995921519532	2		215	565	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072537	5072537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs895187915	NA	P-0008444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	71	154	0	ENST00000381652.3:c.1687G>A	p.Val563Ile	p.V563I	ENST00000381652	NM_004972.3	563	Gta/Ata	13/25	1	2	FACETS	0.801	0.701	0.907	0.801	0.701	0.907	CLONAL	1	TRUE	1	0.394995921519532	2		154	449	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412642	139412642	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	111	179	0	ENST00000277541.6:c.1202C>A	p.Pro401His	p.P401H	ENST00000277541	NM_017617.3	401	cCc/cAc	7/34	1	2	FACETS	0.995	0.897	1	0.995	0.897	1	CLONAL	1	TRUE	1	0.394995921519532	2		179	565	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117336	115117336	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	144	350	0	ENST00000257566.3:c.838G>A	p.Ala280Thr	p.A280T	ENST00000257566	NM_016569.3	280	Gct/Act	4/8	1	2	FACETS	0.919	0.839	1	0.919	0.839	1	CLONAL	1	TRUE	1	0.394995921519532	2		350	793	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828089	72828089	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	201	407	1	ENST00000268489.5:c.8492A>T	p.Asp2831Val	p.D2831V	ENST00000268489	NM_006885.3	2831	gAc/gTc	9/10	1	2	FACETS	0.919	0.851	0.99	0.919	0.851	0.99	CLONAL	1	TRUE	1	0.394995921519532	2		408	1107	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248548	10248548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241729369	NA	P-0008444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	141	210	0	ENST00000340748.4:c.4205G>A	p.Gly1402Asp	p.G1402D	ENST00000340748		1402	gGc/gAc	35/40	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.394995921519532	2		210	691	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288736	15288736	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	12	28	0	ENST00000263388.2:c.4003A>T	p.Ser1335Cys	p.S1335C	ENST00000263388	NM_000435.2	1335	Agc/Tgc	24/33	1	2	FACETS	0.779	0.556	1	0.779	0.556	1	CLONAL	1	TRUE	1	0.394995921519532	2		28	78	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446774	49446775	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0008444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	97	190	0	ENST00000301067.7:c.1035_1036del	p.Cys346SerfsTer17	p.C346Sfs*17	ENST00000301067	NM_003482.3	345	ctCTgt/ctgt	8/54	1	2	FACETS	0.875	0.783	0.974	0.875	0.783	0.974	CLONAL	1	TRUE	1	0.394995921519532	2		190	561	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993013	72993014	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	238	420	0	ENST00000268489.5:c.1031dup	p.Asn344LysfsTer13	p.N344Kfs*13	ENST00000268489	NM_006885.3	344	aac/aaAc	2/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.394995921519532	2		420	1159	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073850	8073851	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTATACAA	novel	NA	P-0008444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	176	415	0	ENST00000377482.5:c.801_808dup	p.His270LeufsTer28	p.H270Lfs*28	ENST00000377482	NM_018948.3	270	cac/cTTGTATACac	4/4	1	2	FACETS	0.839	0.772	0.909	0.839	0.772	0.909	CLONAL	1	TRUE	1	0.394995921519532	2		415	1062	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512377	38512377	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555574293	NA	P-0008444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	54	183	0	ENST00000254066.5:c.1293del	p.Arg432GlyfsTer211	p.R432Gfs*211	ENST00000254066	NM_000964.3	430	Ggg/gg	9/9	1	2	FACETS	0.559	0.478	0.648	0.559	0.478	0.648	SUBCLONAL	1	TRUE	1	0.394995921519532	2		183	489	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466030	69466031	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCGCCA	novel	NA	P-0008444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	89	227	0	ENST00000227507.2:c.868_869insCCCGCCA	p.Val290AlafsTer66	p.V290Afs*66	ENST00000227507	NM_053056.2	290	gtg/gCCCGCCAtg	5/5	1	2	FACETS	0.782	0.695	0.875	0.782	0.695	0.875	SUBCLONAL	1	TRUE	1	0.394995921519532	2		227	576	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0008469-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	103	175	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.325684160821786	2		175	527	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0008469-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1316	274	551	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	0.969	1	CLONAL	1	TRUE	1	0.325684160821786	2		551	1590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579357	7579358	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGTTT	novel	NA	P-0008469-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	223	356	0	ENST00000269305.4:c.329_330insAAACG	p.Leu111AsnfsTer14	p.L111Nfs*14	ENST00000269305	NM_001126112.2	110	cgt/cgAAACGt	4/11	0.291660080806602	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.325684160821786	1		356	1042	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587480	29587489	+	frameshift_variant	Frame_Shift_Del	DEL	TCGTCTACTC	TCGTCTACTC	-	novel	NA	P-0008469-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	257	385	0	ENST00000356175.3:c.4462_4471del	p.Arg1488GlyfsTer62	p.R1488Gfs*62	ENST00000356175	NM_000267.3	1487	caTCGTCTACTC/ca	33/57	0.180371473439395	3	FACETS	0.911	0.854	0.97			1	INDETERMINATE	2	TRUE	NA	0.325684160821786	3		385	1007	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696716	47696716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008472-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	163	336	0	ENST00000347630.2:c.232G>A	p.Glu78Lys	p.E78K	ENST00000347630	NM_001007230.1	78	Gaa/Aaa	5/11	0.25170377147627	1	FACETS	0.758	0.699	0.82	0.758	0.699	0.82	INDETERMINATE	1	TRUE	0	0.522422985535778	1		336	608	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0008472-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	209	452	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.522422985535778	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.522422985535778	1		452	449	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880984	37880985	+	inframe_insertion	In_Frame_Ins	INS	-	-	TACGTGATGGCT	rs397516977	NA	P-0008472-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	717	434	0	ENST00000269571.5:c.2314_2325dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/TACGTGATGGCT	20/27	0.522422985535778	6	FACETS	1	0.99	1			1	CLONAL	4	TRUE	NA	0.522422985535778	6		434	1338	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991559	72991559	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1356851583	NA	P-0008472-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	305	706	0	ENST00000268489.5:c.2486T>C	p.Met829Thr	p.M829T	ENST00000268489	NM_006885.3	829	aTg/aCg	2/10	0.290095929438275	1	FACETS	0.794	0.749	0.841	0.794	0.749	0.841	INDETERMINATE	1	TRUE	0	0.522422985535778	1		706	1086	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81957199	81957199	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008472-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	255	410	0	ENST00000359376.3:c.2417G>T	p.Trp806Leu	p.W806L	ENST00000359376	NM_002661.3	806	tGg/tTg	22/33	0.290095929438275	1	FACETS	1	0.988	1	1	0.988	1	INDETERMINATE	1	TRUE	0	0.522422985535778	1		410	616	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183822	10183823	+	frameshift_variant	Frame_Shift_Ins	INS	CT	CT	GTCG	novel	NA	P-0008479-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	38	144	0	ENST00000256474.2:c.291_292delinsGTCG	p.Tyr98SerfsTer62	p.Y98Sfs*62	ENST00000256474	NM_000551.3	97	ccCTac/ccGTCGac	1/3	1	2	FACETS	1	0.873	1	1	0.969	1	CLONAL	2	TRUE	1	0.19	2		144	190	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0008516-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	312	505	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.433429248392489	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	1	0.433429248392489	4		505	593	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852590	63852591	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0008516-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	37	487	0	ENST00000279873.7:c.3368_3369insA	p.Leu1124AlafsTer37	p.L1124Afs*37	ENST00000279873	NM_032199.2	1123	tcg/tcAg	10/10	1	2	FACETS	0.316	0.26	0.378	0.316	0.26	0.378	SUBCLONAL	1	TRUE	1	0.433429248392489	2		487	541	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578472	7578491	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGGGGTGTGGAATCAAC	GGCGGGGGTGTGGAATCAAC	-	novel	NA	P-0008516-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	265	460	0	ENST00000269305.4:c.439_458del	p.Val147ArgfsTer27	p.V147Rfs*27	ENST00000269305	NM_001126112.2	147	GTTGATTCCACACCCCCGCCc/c	5/11	0.433429248392489	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.433429248392489	1		460	802	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181890	38181890	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	96	366	1	ENST00000396334.3:c.514G>T	p.Glu172Ter	p.E172*	ENST00000396334	NM_002468.4	172	Gag/Tag	3/5	1	2	FACETS	0.724	0.645	0.809	0.724	0.645	0.809	SUBCLONAL	1	TRUE	1	0.356308593149559	2		367	744	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956149	55956149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	101	610	1	ENST00000263923.4:c.3166G>A	p.Asp1056Asn	p.D1056N	ENST00000263923	NM_002253.2	1056	Gat/Aat	23/30	1	2	FACETS	0.811	0.725	0.902	0.811	0.725	0.902	CLONAL	1	TRUE	1	0.356308593149559	2		611	699	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233715	233715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	123	295	0	ENST00000264932.6:c.1019G>A	p.Arg340Lys	p.R340K	ENST00000264932	NM_004168.2	340	aGa/aAa	8/15	1	2	FACETS	0.894	0.809	0.984	0.894	0.809	0.984	CLONAL	1	TRUE	1	0.356308593149559	2		295	772	SUCCESS
APC	324	MSKCC	GRCh37	5	112154992	112154992	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	103	539	0	ENST00000257430.4:c.1263G>T	p.Trp421Cys	p.W421C	ENST00000257430	NM_000038.5	421	tgG/tgT	10/16	1	2	FACETS	0.754	0.674	0.838	0.754	0.674	0.838	SUBCLONAL	1	TRUE	1	0.356308593149559	2		539	767	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056396	180056396	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148616009	NA	P-0008539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	126	367	0	ENST00000261937.6:c.848G>A	p.Arg283His	p.R283H	ENST00000261937	NM_182925.4	283	cGc/cAc	7/30	1	2	FACETS	0.936	0.848	1	0.936	0.848	1	CLONAL	1	TRUE	1	0.356308593149559	2		367	756	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386569	81386569	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	68	509	0	ENST00000222390.5:c.418G>T	p.Val140Leu	p.V140L	ENST00000222390	NM_000601.4	140	Gta/Tta	4/18	1	2	FACETS	0.667	0.581	0.761	0.667	0.581	0.761	SUBCLONAL	1	TRUE	1	0.356308593149559	2		509	572	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8339023	8339023	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	94	429	0	ENST00000356435.5:c.5278G>T	p.Ala1760Ser	p.A1760S	ENST00000356435		1760	Gca/Tca	32/35	0.356308593149559	2	FACETS	1	0.979	1	0.694	0.622	0.77	CLONAL	1	TRUE	0	0.356308593149559	2		429	380	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025941	1025941	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	205	692	0	ENST00000358495.3:c.589G>C	p.Glu197Gln	p.E197Q	ENST00000358495	NM_134424.2	197	Gaa/Caa	8/12	NA	2	FACETS	0.885	0.819	0.954			1	INDETERMINATE	1	TRUE	NA	0.356308593149559	2		692	1300	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865598	57865598	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1348	263	938	0	ENST00000228682.2:c.3075G>C	p.Leu1025Phe	p.L1025F	ENST00000228682	NM_005269.2	1025	ttG/ttC	12/12	1	2	FACETS	0.916	0.856	0.979	0.916	0.856	0.979	CLONAL	1	TRUE	1	0.356308593149559	2		938	1611	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28886201	28886201	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	91	578	0	ENST00000282397.4:c.3421C>A	p.Pro1141Thr	p.P1141T	ENST00000282397	NM_002019.4	1141	Cca/Aca	26/30	1	2	FACETS	0.875	0.778	0.977	0.875	0.778	0.977	CLONAL	1	TRUE	1	0.356308593149559	2		578	584	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205112	123205112	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	90	793	0	ENST00000218089.9:c.2472G>T	p.Glu824Asp	p.E824D	ENST00000218089	NM_001042749.1	824	gaG/gaT	25/35	0.356308593149559	1	FACETS	0.494	0.437	0.554	0.494	0.437	0.554	SUBCLONAL	1	TRUE	0	0.356308593149559	1		793	841	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163619	32163620	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0008539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	75	358	0	ENST00000375023.3:c.5606dup	p.Arg1871SerfsTer45	p.R1871Sfs*45	ENST00000375023	NM_004557.3	1869	ggc/ggGc	30/30	1	2	FACETS	0.799	0.701	0.903	0.799	0.701	0.903	CLONAL	1	TRUE	1	0.356308593149559	2		358	527	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521463	8521463	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	190	444	0	ENST00000356435.5:c.775del	p.Ala259ProfsTer9	p.A259Pfs*9	ENST00000356435		259	Gcc/cc	9/35	0.356308593149559	2	FACETS	0.786	0.73	0.845	0.786	0.73	0.845	SUBCLONAL	2	TRUE	0	0.356308593149559	2		444	678	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0008572-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	43	338	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.883	0.74	1	0.883	0.74	1	CLONAL	1	TRUE	1	0.224432008614405	2		338	434	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200961	108200961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782310	NA	P-0008572-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	27	221	0	ENST00000278616.4:c.7328G>A	p.Arg2443Gln	p.R2443Q	ENST00000278616	NM_000051.3	2443	cGa/cAa	50/63	0.224432008614405	1	FACETS	0.705	0.562	0.868	0.705	0.562	0.868	SUBCLONAL	1	TRUE	0	0.224432008614405	1		221	303	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664729	138664729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008572-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	29	94	0	ENST00000330315.3:c.836G>A	p.Gly279Asp	p.G279D	ENST00000330315	NM_023067.3	279	gGc/gAc	1/1	1	2	FACETS	0.774	0.628	0.936	1	0.944	1	CLONAL	2	TRUE	1	0.224432008614405	2		94	167	SUCCESS
APC	324	MSKCC	GRCh37	5	112176936	112176936	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs34157245	NA	P-0008572-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	67	314	0	ENST00000257430.4:c.5645G>C	p.Arg1882Thr	p.R1882T	ENST00000257430	NM_000038.5	1882	aGa/aCa	16/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.224432008614405	2		314	444	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438712	49438712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008572-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	84	320	2	ENST00000301067.7:c.4778C>T	p.Thr1593Ile	p.T1593I	ENST00000301067	NM_003482.3	1593	aCa/aTa	19/54	1	2	FACETS	0.939	0.829	1	0.939	0.829	1	CLONAL	1	TRUE	1	0.224432008614405	2		322	797	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56801442	56801442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660745	NA	P-0008572-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	67	443	0	ENST00000337432.4:c.946C>T	p.His316Tyr	p.H316Y	ENST00000337432	NM_058216.2	316	Cat/Tat	7/9	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.224432008614405	2		443	586	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661996	29661997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0008572-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	53	310	2	ENST00000356175.3:c.5895dup	p.Gln1966ThrfsTer22	p.Q1966Tfs*22	ENST00000356175	NM_000267.3	1964	gaa/gAaa	39/57	0.193044659213315	1	FACETS	0.991	0.847	1	0.991	0.847	1	CLONAL	1	TRUE	0	0.224432008614405	1		312	423	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867227	68867245	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCTTATGATTCTCTGCT	CGCCTTATGATTCTCTGCT	-	novel	NA	P-0008572-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	127	262	0	ENST00000261769.5:c.2476_2494del	p.Pro826CysfsTer14	p.P826Cfs*14	ENST00000261769	NM_004360.3	825	cCGCCTTATGATTCTCTGCTc/cc	16/16	0.224432008614405	1	FACETS	0.934	0.85	1	1	0.989	1	CLONAL	2	TRUE	0	0.224432008614405	1		262	538	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829809	72829809	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008572-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	362	1065	0	ENST00000268489.5:c.6772del	p.Gln2258ArgfsTer22	p.Q2258Rfs*22	ENST00000268489	NM_006885.3	2258	Cag/ag	9/10	0.224432008614405	1	FACETS	0.953	0.902	1	1	0.996	1	CLONAL	2	TRUE	0	0.224432008614405	1		1065	1502	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0008646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	161	348	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.957	0.878	1	0.957	0.878	1	CLONAL	1	TRUE	1	0.41	2		348	821	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793663	NA	P-0008646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	286	789	0	ENST00000263967.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000263967	NM_006218.2	93	cGg/cAg	2/21	1	2	FACETS	0.948	0.889	1	0.948	0.889	1	CLONAL	1	TRUE	1	0.41	2		789	1472	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874092	151874093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	236	683	0	ENST00000262189.6:c.8445dup	p.Ser2816IlefsTer6	p.S2816Ifs*6	ENST00000262189	NM_170606.2	2815	-/A	38/59	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.41	2		683	1123	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	195	507	0	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	0.924	0.855	0.996	0.924	0.855	0.996	CLONAL	1	TRUE	1	0.41	2		507	1029	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0008646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	250	416	4	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	1	2	FACETS	0.997	0.932	1	0.997	0.932	1	CLONAL	1	TRUE	1	0.41	2		420	1223	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953632	32953633	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359732	NA	P-0008646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	242	163	0	ENST00000380152.3:c.8940dup	p.Glu2981ArgfsTer37	p.E2981Rfs*37	ENST00000380152		2978	tca/tcAa	22/27	1	2	FACETS	0.902	0.841	0.965	0.902	0.841	0.965	CLONAL	1	TRUE	1	0.41	2		163	1309	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0008646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	110	124	0	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	0.945	0.851	1	0.945	0.851	1	CLONAL	1	TRUE	1	0.41	2		124	568	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	163	243	1	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	0.863	0.792	0.938	0.863	0.792	0.938	CLONAL	1	TRUE	1	0.41	2		244	921	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	167	370	0	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.41	2		370	815	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717727	89717727	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554825226	NA	P-0008646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	122	150	0	ENST00000371953.3:c.752G>T	p.Gly251Val	p.G251V	ENST00000371953	NM_000314.4	251	gGt/gTt	7/9	1	2	FACETS	0.957	0.867	1	0.957	0.867	1	CLONAL	1	TRUE	1	0.41	2		150	622	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182050	11182050	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	142	321	0	ENST00000361445.4:c.6796C>T	p.Arg2266Cys	p.R2266C	ENST00000361445	NM_004958.3	2266	Cgc/Tgc	48/58	1	2	FACETS	0.976	0.891	1	0.976	0.891	1	CLONAL	1	TRUE	1	0.41	2		321	710	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070354	37070354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200830026	NA	P-0008646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	167	572	2	ENST00000231790.2:c.1489C>T	p.Arg497Trp	p.R497W	ENST00000231790	NM_000249.3	497	Cgg/Tgg	13/19	1	2	FACETS	0.918	0.844	0.996	0.918	0.844	0.996	CLONAL	1	TRUE	1	0.41	2		574	887	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86681156	86681156	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	177	420	0	ENST00000274376.6:c.2797G>C	p.Val933Leu	p.V933L	ENST00000274376	NM_002890.2	933	Gtg/Ctg	22/25	1	2	FACETS	0.992	0.915	1	0.992	0.915	1	CLONAL	1	TRUE	1	0.41	2		420	870	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69456116	69456116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1239	328	503	2	ENST00000227507.2:c.35C>T	p.Thr12Ile	p.T12I	ENST00000227507	NM_053056.2	12	aCc/aTc	1/5	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.41	2		505	1567	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123901	46123901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	234	345	0	ENST00000334344.6:c.167C>T	p.Thr56Ile	p.T56I	ENST00000334344	NM_152641.2	56	aCt/aTt	2/21	1	2	FACETS	0.952	0.887	1	0.952	0.887	1	CLONAL	1	TRUE	1	0.41	2		345	1199	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40364210	40364210	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0008646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	221	561	0	ENST00000293328.3:c.1474-2A>G		p.X492_splice	ENST00000293328	NM_012448.3	492			0.3	1	FACETS	0.801	0.745	0.859	0.801	0.745	0.859	CLONAL	1	TRUE	0	0.41	1		561	1070	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921157	50921157	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1339	348	637	0	ENST00000440232.2:c.3277G>T	p.Glu1093Ter	p.E1093*	ENST00000440232	NM_002691.3	1093	Gag/Tag	27/27	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.41	2		637	1687	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226124	53226124	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs951268570	NA	P-0008646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	220	420	1	ENST00000375401.3:c.2725C>T	p.Arg909Trp	p.R909W	ENST00000375401	NM_004187.3	909	Cgg/Tgg	19/26	0.3	2	FACETS	0.935	0.869	1			1	CLONAL	1	TRUE	NA	0.41	2		421	1148	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615569	100615569	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs128621193	NA	P-0008646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	195	584	1	ENST00000308731.7:c.763C>T	p.Arg255Ter	p.R255*	ENST00000308731	NM_000061.2	255	Cga/Tga	8/19	0.107062698169328	0	FACETS	0.592	0.548	0.638			1	INDETERMINATE	1	TRUE	0	0.41	0		585	948	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845624	63845627	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	novel	NA	P-0008646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	112	319	2	ENST00000279873.7:c.1366_1369del	p.Glu456MetfsTer22	p.E456Mfs*22	ENST00000279873	NM_032199.2	455	AAAGaa/aa	9/10	1	2	FACETS	0.822	0.74	0.908	0.822	0.74	0.908	CLONAL	1	TRUE	1	0.41	2		321	665	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466039	69466041	+	inframe_deletion	In_Frame_Del	DEL	GTG	GTG	-	novel	NA	P-0008646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	229	447	0	ENST00000227507.2:c.878_880del	p.Val293del	p.V293del	ENST00000227507	NM_053056.2	293	GTG/-	5/5	1	2	FACETS	0.912	0.849	0.978	0.912	0.849	0.978	CLONAL	1	TRUE	1	0.41	2		447	1225	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118391565	118391565	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	67	252	0	ENST00000534358.1:c.11483del	p.Lys3828ArgfsTer31	p.K3828Rfs*31	ENST00000534358	NM_005933.3	3826	ttA/tt	34/36	1	2	FACETS	0.499	0.433	0.57	0.499	0.433	0.57	SUBCLONAL	1	TRUE	1	0.41	2		252	655	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191049	185191049	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	256	451	0	ENST00000265026.3:c.1934del	p.Pro645LeufsTer19	p.P645Lfs*19	ENST00000265026	NM_004721.4	644	Ccc/cc	11/14	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.41	2		451	1211	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534548	140534548	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397507462	NA	P-0008663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	174	483	0	ENST00000288602.6:c.365C>A	p.Ser122Tyr	p.S122Y	ENST00000288602	NM_004333.4	122	tCt/tAt	3/18	0.485649917540132	3	FACETS	1	0.971	1	0.556	0.512	0.601	CLONAL	1	TRUE	1	0.485649917540132	3		483	801	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40771137	40771137	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	232	616	0	ENST00000392038.2:c.38A>G	p.His13Arg	p.H13R	ENST00000392038	NM_001626.4	13	cAc/cGc	2/14	0.485649917540132	3	FACETS	0.915	0.851	0.981			1	CLONAL	1	TRUE	NA	0.485649917540132	3		616	1298	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819960	170819965	+	inframe_deletion	In_Frame_Del	DEL	GATGAA	GATGAA	-	novel	NA	P-0008663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	143	536	0	ENST00000296930.5:c.504_509del	p.Asp168_Glu169del	p.D168_E169del	ENST00000296930	NM_002520.6	168	GATGAA/-	6/11	0.485649917540132	3	FACETS	0.865	0.789	0.945	0.433	0.394	0.473	CLONAL	1	TRUE	1	0.485649917540132	3		536	846	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753011	57753012	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0008663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	132	589	6	ENST00000274289.3:c.1004dup	p.Leu335PhefsTer12	p.L335Ffs*12	ENST00000274289	NM_006622.3	335	ttg/ttTg	7/14	0.485649917540132	3	FACETS	0.857	0.779	0.94	0.429	0.389	0.47	CLONAL	1	TRUE	1	0.485649917540132	3		595	788	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0008671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	26	458	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.749	0.597	0.922	0.749	0.597	0.922	CLONAL	1	TRUE	1	0.324389331461738	2		458	214	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453138	140453139	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTA	rs727502902	NA	P-0008671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	31	356	0	ENST00000288602.6:c.1794_1796dup	p.Thr599dup	p.T599dup	ENST00000288602	NM_004333.4	599	aca/acTACa	15/18	0.324389331461738	1	FACETS	0.895	0.731	1	0.895	0.731	1	CLONAL	1	TRUE	0	0.324389331461738	1		356	179	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412095	63412095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852217	NA	P-0008671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	54	452	3	ENST00000330258.3:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000330258	NM_152424.3	358	Cga/Tga	2/2	0.293718219567122	0	FACETS	0.75	0.655	0.848			1	SUBCLONAL	2	TRUE	NA	0.324389331461738	0		455	150	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874092	151874093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	254	683	0	ENST00000262189.6:c.8445dup	p.Ser2816IlefsTer6	p.S2816Ifs*6	ENST00000262189	NM_170606.2	2815	-/A	38/59	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		683	914	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0008682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	109	398	1	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		399	448	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405902	157405902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1282587061	NA	P-0008682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	51	431	0	ENST00000346085.5:c.2144C>T	p.Pro715Leu	p.P715L	ENST00000346085	NM_020732.3	715	cCg/cTg	6/20	0.0958861895559788	3	FACETS		NA	1			1	NA	NA	TRUE	1	NA	3		431	768	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0008682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	71	201	2	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		203	313	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330610	65330611	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	215	587	0	ENST00000342505.4:c.1035dup	p.Leu346ThrfsTer4	p.L346Tfs*4	ENST00000342505	NM_002227.2	345	-/A	8/25	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		587	866	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390656	139390656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1160184715	NA	P-0008682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	38	715	2	ENST00000277541.6:c.7535C>T	p.Pro2512Leu	p.P2512L	ENST00000277541	NM_017617.3	2512	cCg/cTg	34/34	0.133334819411152	1	FACETS		NA	1			1	NA	NA	TRUE	0	NA	1		717	747	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443799	49443799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs112236653	NA	P-0008682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	224	581	1	ENST00000301067.7:c.3572C>T	p.Pro1191Leu	p.P1191L	ENST00000301067	NM_003482.3	1191	cCg/cTg	11/54	0.0958861895559788	3	FACETS		NA	1			1	NA	NA	TRUE	1	NA	3		582	790	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210735	2210735	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1238067958	NA	P-0008682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	200	646	1	ENST00000398665.3:c.1232G>A	p.Arg411His	p.R411H	ENST00000398665	NM_032482.2	411	cGc/cAc	14/28	0.133334819411152	0	FACETS		NA	1			1	NA	NA	TRUE	0	NA	0		647	724	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574502	41574502	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	127	454	1	ENST00000263253.7:c.6787C>T	p.Arg2263Ter	p.R2263*	ENST00000263253	NM_001429.3	2263	Cga/Tga	31/31	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		455	595	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261065	16261065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs181891870	NA	P-0008682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	62	198	0	ENST00000375759.3:c.8330C>T	p.Ala2777Val	p.A2777V	ENST00000375759	NM_015001.2	2777	gCg/gTg	11/15	0.3	3	FACETS		NA	1			1	NA	NA	TRUE	NA	NA	3		198	296	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65316513	65316513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755406627	NA	P-0008682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	152	374	0	ENST00000342505.4:c.1729C>T	p.Arg577Trp	p.R577W	ENST00000342505	NM_002227.2	577	Cgg/Tgg	12/25	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		374	541	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321195	65321195	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	65	197	0	ENST00000342505.4:c.1645C>T	p.Arg549Ter	p.R549*	ENST00000342505	NM_002227.2	549	Cga/Tga	11/25	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		197	276	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495657	72495657	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	100	319	0	ENST00000477973.2:c.415A>G	p.Thr139Ala	p.T139A	ENST00000477973	NM_012234.5	139	Acc/Gcc	1/4	0.0958861895559788	3	FACETS		NA	1			1	NA	NA	TRUE	1	NA	3		319	447	SUCCESS
APC	324	MSKCC	GRCh37	5	112176693	112176693	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660059	NA	P-0008682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	107	484	2	ENST00000257430.4:c.5402C>T	p.Ala1801Val	p.A1801V	ENST00000257430	NM_000038.5	1801	gCt/gTt	16/16	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		486	671	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951813	2951813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377327574	NA	P-0008682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	139	512	0	ENST00000396946.4:c.3137C>T	p.Ala1046Val	p.A1046V	ENST00000396946	NM_032415.4	1046	gCc/gTc	23/25	0.3	0	FACETS		NA	1			1	NA	NA	TRUE	0	NA	0		512	503	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126729	5126729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774469142	NA	P-0008682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	206	445	1	ENST00000381652.3:c.3337C>T	p.Arg1113Cys	p.R1113C	ENST00000381652	NM_004972.3	1113	Cgc/Tgc	25/25	0.3	2	FACETS		NA	1			1	NA	NA	TRUE	NA	NA	2		446	675	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840613	36840613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756710542	NA	P-0008682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	136	396	1	ENST00000358127.4:c.1120G>A	p.Ala374Thr	p.A374T	ENST00000358127	NM_001280556.1	374	Gct/Act	10/10	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		397	506	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8252001	8252001	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	138	399	0	ENST00000335790.3:c.76G>T	p.Gly26Cys	p.G26C	ENST00000335790	NM_002315.2	26	Ggc/Tgc	2/4	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		399	393	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662396	67662396	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	182	626	0	ENST00000264010.4:c.1642C>A	p.Pro548Thr	p.P548T	ENST00000264010	NM_006565.3	548	Ccc/Acc	9/12	0.133334819411152	1	FACETS		NA	1			1	NA	NA	TRUE	0	NA	1		626	860	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586101	29586101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876658127	NA	P-0008682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	101	371	1	ENST00000356175.3:c.4321C>T	p.Arg1441Trp	p.R1441W	ENST00000356175	NM_000267.3	1441	Cgg/Tgg	32/57	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		372	534	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510573	38510573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	142	522	0	ENST00000254066.5:c.827G>A	p.Arg276Gln	p.R276Q	ENST00000254066	NM_000964.3	276	cGg/cAg	7/9	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		522	684	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740594	58740594	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	269	1047	1	ENST00000305921.3:c.1499C>A	p.Pro500His	p.P500H	ENST00000305921	NM_003620.3	500	cCt/cAt	6/6	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		1048	1128	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755606	39755606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	179	446	1	ENST00000288319.7:c.1159G>A	p.Ala387Thr	p.A387T	ENST00000288319	NM_182918.3	387	Gcc/Acc	10/10	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		447	707	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247580	53247580	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	37	298	0	ENST00000375401.3:c.229G>C	p.Ala77Pro	p.A77P	ENST00000375401	NM_004187.3	77	Gcc/Ccc	3/26	1	1	FACETS		NA	1			1	NA	NA	TRUE	0	NA	1		298	359	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966872	25966873	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0008682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	167	529	3	ENST00000435504.4:c.2333dup	p.Val779SerfsTer25	p.V779Sfs*25	ENST00000435504		778	cca/ccCa	13/13	0.3	2	FACETS		NA	1			1	NA	NA	TRUE	NA	NA	2		532	735	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526212	63526215	+	frameshift_variant	Frame_Shift_Del	DEL	AAGT	AAGT	-	novel	NA	P-0008682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	139	417	0	ENST00000307078.5:c.2411_2414del	p.Tyr804SerfsTer56	p.Y804Sfs*56	ENST00000307078	NM_004655.3	804	tACTTc/tc	11/11	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		417	522	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0008690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	182	352	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.375475427487654	3	FACETS	0.97	0.901	1	0.97	0.901	1	CLONAL	2	TRUE	1	0.414188518131366	3		352	547	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412095	63412095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852217	NA	P-0008690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	513	452	3	ENST00000330258.3:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000330258	NM_152424.3	358	Cga/Tga	2/2	0.326804102103412	2	FACETS	0.935	0.903	0.967			1	CLONAL	3	TRUE	NA	0.414188518131366	2		455	883	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0008690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	52	286	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.337766579957427	1	FACETS	0.644	0.552	0.744	0.644	0.552	0.744	SUBCLONAL	1	TRUE	0	0.414188518131366	1		286	309	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	91	333	0	ENST00000342988.3:c.1610A>T	p.Asp537Val	p.D537V	ENST00000342988	NM_005359.5	537	gAc/gTc	12/12	0.414188518131366	1	FACETS	0.96	0.859	1	0.96	0.859	1	CLONAL	1	TRUE	0	0.414188518131366	1		333	363	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916220	9916220	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1445802934	NA	P-0008690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	81	388	1	ENST00000330684.3:c.2069C>T	p.Thr690Met	p.T690M	ENST00000330684	NM_001134407.1	690	aCg/aTg	10/13	1	2	FACETS	0.998	0.884	1	0.998	0.884	1	CLONAL	1	TRUE	1	0.414188518131366	2		389	392	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884485	151884485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	227	411	1	ENST00000262189.6:c.4870G>A	p.Gly1624Arg	p.G1624R	ENST00000262189	NM_170606.2	1624	Gga/Aga	33/59	0.414188518131366	2	FACETS	0.979	0.92	1	0.979	0.92	1	CLONAL	2	TRUE	0	0.414188518131366	2		412	560	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	495073	495073	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	136	466	0	ENST00000399788.2:c.233A>G	p.Asn78Ser	p.N78S	ENST00000399788	NM_001042603.1	78	aAt/aGt	2/28	0.414188518131366	3	FACETS	0.944	0.858	1			1	CLONAL	1	TRUE	NA	0.414188518131366	3		466	840	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374992	45374992	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	93	359	0	ENST00000262160.6:c.851A>G	p.Gln284Arg	p.Q284R	ENST00000262160	NM_005901.5	284	cAg/cGg	8/11	1	2	FACETS	0.913	0.815	1	0.913	0.815	1	CLONAL	1	TRUE	1	0.414188518131366	2		359	492	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1327707	1327707	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	317	406	0	ENST00000400841.2:c.174C>A	p.Phe58Leu	p.F58L	ENST00000400841		58	ttC/ttA	2/6	0.1891582619482	2	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.414188518131366	2		406	1025	SUCCESS
APC	324	MSKCC	GRCh37	5	112102972	112102973	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	111	414	0	ENST00000257430.4:c.308dup	p.Ser104IlefsTer35	p.S104Ifs*35	ENST00000257430	NM_000038.5	103	gta/gTta	4/16	NA	2	FACETS	0.923	0.832	1			1	INDETERMINATE	1	TRUE	NA	0.414188518131366	2		414	581	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057520000	NA	P-0008752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	513	533	0	ENST00000269305.4:c.452C>A	p.Pro151His	p.P151H	ENST00000269305	NM_001126112.2	151	cCc/cAc	5/11	0.792061477742791	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.794322973571734	1		533	738	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920172	76920173	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	493	564	0	ENST00000373344.5:c.3904dup	p.Arg1302LysfsTer7	p.R1302Kfs*7	ENST00000373344	NM_000489.3	1302	aga/aAga	11/35	1	1	FACETS	0.998	0.966	1	0.998	0.966	1	CLONAL	1	TRUE	0	0.794322973571734	1		564	750	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944808	31944808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	88	738	0	ENST00000340398.3:c.293C>T	p.Ala98Val	p.A98V	ENST00000340398	NM_001013699.2	98	gCg/gTg	1/1	0.794322973571734	1	FACETS	0.15	0.132	0.169	0.15	0.132	0.169	SUBCLONAL	1	TRUE	0	0.794322973571734	1		738	892	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916815	48916815	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	221	467	2	ENST00000267163.4:c.345C>G	p.Phe115Leu	p.F115L	ENST00000267163	NM_000321.2	115	ttC/ttG	3/27	NA	2	FACETS	0.859	0.819	0.897			1	INDETERMINATE	2	TRUE	NA	0.794322973571734	2		469	324	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515342	103515342	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	188	536	0	ENST00000355739.4:c.1843C>A	p.Leu615Met	p.L615M	ENST00000355739	NM_000123.3	615	Ctg/Atg	8/15	0.794322973571734	1	FACETS	0.86	0.81	0.908	0.86	0.81	0.908	CLONAL	1	TRUE	0	0.794322973571734	1		536	332	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	112	245	0				ENST00000310581	NM_198253.2	-/1132			0.722610092958436	2	FACETS	1	0.937	1	0.516	0.471	0.562	CLONAL	1	TRUE	0	0.733141988952215	2		245	296	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0008791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	738	590	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.733141988952215	3	FACETS	1	0.994	1	1	0.998	1	CLONAL	3	TRUE	1	0.733141988952215	3		590	889	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523486	106523486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750632554	NA	P-0008791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	173	237	0	ENST00000359195.3:c.2638G>A	p.Glu880Lys	p.E880K	ENST00000359195	NM_002649.2	880	Gag/Aag	8/11	0.733141988952215	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.733141988952215	2		237	226	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680765	88680765	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	163	381	0	ENST00000360948.2:c.492C>A	p.Cys164Ter	p.C164*	ENST00000360948	NM_001012338.2	164	tgC/tgA	6/19	0.733141988952215	3	FACETS	0.91	0.838	0.984	0.455	0.419	0.492	CLONAL	1	TRUE	1	0.733141988952215	3		381	668	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879904	44879904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs912069418	NA	P-0008791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	333	304	0	ENST00000377967.4:c.493C>T	p.Arg165Ter	p.R165*	ENST00000377967	NM_021140.2	165	Cga/Tga	6/29	0.733141988952215	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.733141988952215	2		304	385	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542475	187542476	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0008791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	463	680	0	ENST00000441802.2:c.5264dup	p.Leu1755PhefsTer4	p.L1755Ffs*4	ENST00000441802	NM_005245.3	1755	ttg/ttTg	10/27	0.728657938340096	3	FACETS	0.916	0.89	0.942	0.916	0.89	0.942	CLONAL	3	TRUE	0	0.733141988952215	3		680	628	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17371306	17371306	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1434	83	696	0	ENST00000375499.3:c.150C>A	p.Asp50Glu	p.D50E	ENST00000375499	NM_003000.2	50	gaC/gaA	2/8	0.204032011593092	5	FACETS	0.543	0.477	0.614	0.181	0.159	0.205	SUBCLONAL	1	TRUE	2	0.288882396610519	5		696	1517	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363342	40363342	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1225852679	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	150	490	0	ENST00000397332.2:c.887A>T	p.Gln296Leu	p.Q296L	ENST00000397332	NM_001033082.2	296	cAg/cTg	3/3	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.288882396610519	2		490	914	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458005	120458005	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs757543412	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	96	454	0	ENST00000256646.2:c.7340G>T	p.Gly2447Val	p.G2447V	ENST00000256646	NM_024408.3	2447	gGt/gTt	34/34	1	2	FACETS	0.684	0.609	0.766	0.684	0.609	0.766	SUBCLONAL	1	TRUE	1	0.288882396610519	2		454	971	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120529637	120529637	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	79	766	1	ENST00000256646.2:c.820G>T	p.Val274Phe	p.V274F	ENST00000256646	NM_024408.3	274	Gtt/Ttt	5/34	1	2	FACETS	0.491	0.43	0.557	0.491	0.43	0.557	SUBCLONAL	1	TRUE	1	0.288882396610519	2		767	1114	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874166	155874166	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs777520196	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1452	190	816	2	ENST00000368323.3:c.365G>T	p.Arg122Leu	p.R122L	ENST00000368323	NM_006912.5	122	cGa/cTa	5/6	0.288882396610519	4	FACETS	1	0.945	1	0.344	0.317	0.373	CLONAL	1	TRUE	1	0.288882396610519	4		818	1642	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445228	29445228	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520019	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	317	638	0	ENST00000389048.3:c.3497T>C	p.Met1166Thr	p.M1166T	ENST00000389048	NM_004304.4	1166	aTg/aCg	22/29	0.288882396610519	3	FACETS	0.889	0.837	0.942	0.889	0.837	0.942	CLONAL	2	TRUE	1	0.288882396610519	3		638	1413	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719492	190719492	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	361	534	0	ENST00000441310.2:c.1494G>T	p.Trp498Cys	p.W498C	ENST00000441310	NM_000534.4	498	tgG/tgT	9/13	0.288882396610519	4	FACETS	0.953	0.904	1	0.953	0.904	1	CLONAL	3	TRUE	1	0.288882396610519	4		534	1127	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198262762	198262762	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	143	753	0	ENST00000335508.6:c.3213G>C	p.Lys1071Asn	p.K1071N	ENST00000335508	NM_012433.2	1071	aaG/aaC	22/25	0.264365940019275	3	FACETS	0.894	0.813	0.98	0.447	0.406	0.49	CLONAL	1	TRUE	1	0.288882396610519	3		753	1267	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646160	215646160	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	96	474	0	ENST00000260947.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000260947	NM_000465.2	146	tgG/tgA	4/11	0.264365940019275	3	FACETS	1	0.908	1	0.51	0.455	0.57	CLONAL	1	TRUE	1	0.288882396610519	3		474	745	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662550	227662550	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	134	440	0	ENST00000305123.5:c.905G>T	p.Arg302Leu	p.R302L	ENST00000305123	NM_005544.2	302	cGa/cTa	1/2	0.264365940019275	3	FACETS	1	0.975	1	0.607	0.551	0.665	CLONAL	1	TRUE	1	0.288882396610519	3		440	875	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663355	227663355	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	141	250	0	ENST00000305123.5:c.100G>T	p.Ala34Ser	p.A34S	ENST00000305123	NM_005544.2	34	Gcg/Tcg	1/2	0.264365940019275	3	FACETS	0.963	0.881	1	0.963	0.881	1	CLONAL	2	TRUE	1	0.288882396610519	3		250	580	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793248	242793250	+	missense_variant	Missense_Mutation	TNP	GTG	GTG	TTT	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	253	599	0	ENST00000334409.5:c.827_829delinsAAA	p.Pro276_Leu277delinsGlnMet	p.P276_L277delinsQM	ENST00000334409	NM_005018.2	276	cCACtg/cAAAtg	5/5	0.264365940019275	3	FACETS	0.804	0.752	0.859	0.804	0.752	0.859	CLONAL	2	TRUE	1	0.288882396610519	3		599	1246	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650274	12650274	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	131	720	0	ENST00000251849.4:c.572G>T	p.Arg191Ile	p.R191I	ENST00000251849	NM_002880.3	191	aGa/aTa	5/17	1	2	FACETS	0.834	0.756	0.918	0.834	0.756	0.918	CLONAL	1	TRUE	1	0.288882396610519	2		720	1087	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437608	52437608	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1458	250	1064	0	ENST00000460680.1:c.1553G>T	p.Arg518Leu	p.R518L	ENST00000460680	NM_004656.3	518	cGg/cTg	13/17	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.288882396610519	2		1064	1708	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72893510	72893510	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	153	664	0	ENST00000325599.8:c.208G>T	p.Gly70Ter	p.G70*	ENST00000325599	NM_018130.2	70	Gga/Tga	2/11	1	2	FACETS	0.96	0.877	1	0.96	0.877	1	CLONAL	1	TRUE	1	0.288882396610519	2		664	1103	SUCCESS
ATR	545	MSKCC	GRCh37	3	142234256	142234256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	108	672	1	ENST00000350721.4:c.4484C>T	p.Ala1495Val	p.A1495V	ENST00000350721	NM_001184.3	1495	gCa/gTa	25/47	0.288882396610519	3	FACETS	0.744	0.666	0.827	0.372	0.333	0.414	SUBCLONAL	1	TRUE	1	0.288882396610519	3		673	1150	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153684	55153684	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1254	87	891	1	ENST00000257290.5:c.2650C>A	p.Leu884Met	p.L884M	ENST00000257290	NM_006206.4	884	Ctg/Atg	19/23	1	2	FACETS	0.449	0.396	0.507	0.449	0.396	0.507	SUBCLONAL	1	TRUE	1	0.288882396610519	2		892	1341	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961746	55961746	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1344205647	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	76	670	0	ENST00000263923.4:c.2815A>G	p.Lys939Glu	p.K939E	ENST00000263923	NM_002253.2	939	Aag/Gag	20/30	1	2	FACETS	0.463	0.405	0.527	0.463	0.405	0.527	SUBCLONAL	1	TRUE	1	0.288882396610519	2		670	1136	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197774	66197774	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	61	677	1	ENST00000273854.3:c.2925G>T	p.Glu975Asp	p.E975D	ENST00000273854	NM_004439.5	975	gaG/gaT	17/18	0.288882396610519	1	FACETS	0.432	0.371	0.498	0.432	0.371	0.498	SUBCLONAL	1	TRUE	0	0.288882396610519	1		678	837	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201839	66201839	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	39	413	0	ENST00000273854.3:c.2663T>A	p.Ile888Asn	p.I888N	ENST00000273854	NM_004439.5	888	aTt/aAt	16/18	0.288882396610519	1	FACETS	0.392	0.324	0.468	0.392	0.324	0.468	SUBCLONAL	1	TRUE	0	0.288882396610519	1		413	589	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539446	187539446	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	75	585	0	ENST00000441802.2:c.8294G>T	p.Ser2765Ile	p.S2765I	ENST00000441802	NM_005245.3	2765	aGt/aTt	10/27	0.205314517424037	0	FACETS	0.455	0.398	0.516			1	SUBCLONAL	1	TRUE	0	0.288882396610519	0		585	812	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627209	86627209	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	103	619	2	ENST00000274376.6:c.584T>A	p.Leu195His	p.L195H	ENST00000274376	NM_002890.2	195	cTc/cAc	2/25	0.288882396610519	1	FACETS	0.878	0.786	0.975	0.878	0.786	0.975	CLONAL	1	TRUE	0	0.288882396610519	1		621	695	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637244	176637244	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	251	604	0	ENST00000439151.2:c.1844G>T	p.Cys615Phe	p.C615F	ENST00000439151	NM_022455.4	615	tGt/tTt	5/23	0.288882396610519	2	FACETS	0.925	0.867	0.985	0.925	0.867	0.985	CLONAL	2	TRUE	0	0.288882396610519	2		604	939	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043968	180043968	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	99	713	0	ENST00000261937.6:c.3028A>G	p.Thr1010Ala	p.T1010A	ENST00000261937	NM_182925.4	1010	Acc/Gcc	22/30	0.288882396610519	2	FACETS	0.554	0.492	0.619	0.277	0.246	0.31	SUBCLONAL	1	TRUE	0	0.288882396610519	2		713	1238	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032155	26032155	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	413	1153	0	ENST00000244661.2:c.134G>T	p.Gly45Val	p.G45V	ENST00000244661	NM_003537.3	45	gGc/gTc	1/1	0.288882396610519	2	FACETS	0.899	0.854	0.944	0.899	0.854	0.944	CLONAL	2	TRUE	0	0.288882396610519	2		1153	1591	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197334	26197334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1563	492	1464	1	ENST00000356476.2:c.145C>A	p.Leu49Met	p.L49M	ENST00000356476		49	Ctg/Atg	1/1	0.288882396610519	2	FACETS	0.829	0.79	0.868	0.829	0.79	0.868	CLONAL	2	TRUE	0	0.288882396610519	2		1465	2055	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680215	30680215	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	423	779	0	ENST00000376406.3:c.1504G>T	p.Asp502Tyr	p.D502Y	ENST00000376406	NM_014641.2	502	Gat/Tat	5/15	0.288882396610519	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.288882396610519	2		779	1452	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729848	41729848	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1662	781	951	0	ENST00000242208.4:c.681C>G	p.Ile227Met	p.I227M	ENST00000242208	NM_002192.2	227	atC/atG	3/3	0.288882396610519	4	FACETS	0.951	0.918	0.985	1	0.997	1	CLONAL	3	TRUE	2	0.288882396610519	4		951	2443	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340097	116340097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35776110	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	67	414	2	ENST00000397752.3:c.959C>T	p.Ala320Val	p.A320V	ENST00000397752	NM_000245.2	320	gCg/gTg	2/21	0.288882396610519	3	FACETS	0.551	0.477	0.631	0.275	0.238	0.316	SUBCLONAL	1	TRUE	1	0.288882396610519	3		416	964	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873458	151873459	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1689	104	739	1	ENST00000262189.6:c.9079_9080delinsTT	p.Gly3027Leu	p.G3027L	ENST00000262189	NM_170606.2	3027	GGa/TTa	38/59	0.278332428262715	4	FACETS	0.518	0.461	0.578			1	SUBCLONAL	1	TRUE	NA	0.288882396610519	4		740	1793	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372052	55372052	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	256	328	1	ENST00000297316.4:c.742G>T	p.Ala248Ser	p.A248S	ENST00000297316	NM_022454.3	248	Gcc/Tcc	2/2	0.288882396610519	4	FACETS	0.914	0.858	0.971	1	0.992	1	CLONAL	3	TRUE	2	0.288882396610519	4		329	833	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868912	117868912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746064262	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	120	645	0	ENST00000297338.2:c.787G>A	p.Asp263Asn	p.D263N	ENST00000297338	NM_006265.2	263	Gat/Aat	7/14	0.288882396610519	4	FACETS	0.964	0.868	1	0.482	0.434	0.533	CLONAL	1	TRUE	2	0.288882396610519	4		645	1111	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971105	21971105	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	88	256	0	ENST00000304494.5:c.253G>C	p.Ala85Pro	p.A85P	ENST00000304494	NM_000077.4	85	Gct/Cct	2/3	0.288882396610519	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.288882396610519	1		256	430	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405143	139405143	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	314	756	0	ENST00000277541.6:c.2702G>T	p.Gly901Val	p.G901V	ENST00000277541	NM_017617.3	901	gGg/gTg	17/34	0.264365940019275	3	FACETS	0.901	0.849	0.955	0.901	0.849	0.955	CLONAL	2	TRUE	1	0.288882396610519	3		756	1380	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409982	139409982	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	193	753	0	ENST00000277541.6:c.1856A>T	p.Gln619Leu	p.Q619L	ENST00000277541	NM_017617.3	619	cAg/cTg	11/34	0.264365940019275	3	FACETS	1	0.986	1	0.642	0.593	0.693	CLONAL	1	TRUE	1	0.288882396610519	3		753	1191	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609942	43609942	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1366	316	1230	1	ENST00000355710.3:c.1894G>T	p.Glu632Ter	p.E632*	ENST00000355710	NM_020975.4	632	Gag/Tag	11/20	0.288882396610519	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.288882396610519	1		1231	1682	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712018	89712018	+	splice_donor_variant	Splice_Site	SNP	T	T	G	rs727504114	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	75	215	0	ENST00000371953.3:c.634+2T>G		p.X212_splice	ENST00000371953	NM_000314.4	212			0.259730356589788	3	FACETS	0.758	0.668	0.854	0.505	0.445	0.569	SUBCLONAL	2	TRUE	0	0.288882396610519	3		215	392	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	532696	532696	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	318	791	0	ENST00000451590.1:c.510G>T	p.Lys170Asn	p.K170N	ENST00000451590	NM_001130442.1	170	aaG/aaT	5/5	0.246854497772866	2	FACETS	0.876	0.826	0.927	0.876	0.826	0.927	CLONAL	2	TRUE	0	0.288882396610519	2		791	1257	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944894	31944894	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	113	380	0	ENST00000340398.3:c.207G>T	p.Arg69Ser	p.R69S	ENST00000340398	NM_001013699.2	69	agG/agT	1/1	0.288882396610519	3	FACETS	1	0.952	1	0.548	0.493	0.606	CLONAL	1	TRUE	1	0.288882396610519	3		380	817	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856190	111856190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	120	428	2	ENST00000341259.2:c.241G>A	p.Asp81Asn	p.D81N	ENST00000341259	NM_005475.2	81	Gac/Aac	2/8	0.288882396610519	3	FACETS	0.916	0.826	1	0.458	0.413	0.506	CLONAL	1	TRUE	1	0.288882396610519	3		430	1038	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28886132	28886132	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	129	713	0	ENST00000282397.4:c.3490C>T	p.Gln1164Ter	p.Q1164*	ENST00000282397	NM_002019.4	1164	Cag/Tag	26/30	1	2	FACETS	0.736	0.666	0.811	0.736	0.666	0.811	SUBCLONAL	1	TRUE	1	0.288882396610519	2		713	1213	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240281	41240281	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	161	521	0	ENST00000379561.5:c.69C>G	p.Cys23Trp	p.C23W	ENST00000379561	NM_002015.3	23	tgC/tgG	1/3	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.288882396610519	2		521	947	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557639	95557639	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	214	756	1	ENST00000393063.1:c.5428G>T	p.Asp1810Tyr	p.D1810Y	ENST00000393063	NM_030621.3	1810	Gat/Tat	26/28	0.288882396610519	3	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.288882396610519	3		757	1293	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476262	88476262	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	144	625	1	ENST00000360948.2:c.1870G>T	p.Asp624Tyr	p.D624Y	ENST00000360948	NM_001012338.2	624	Gac/Tac	15/19	1	2	FACETS	0.87	0.792	0.952	0.87	0.792	0.952	CLONAL	1	TRUE	1	0.288882396610519	2		626	1146	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678470	88678470	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	139	755	0	ENST00000360948.2:c.1066G>T	p.Gly356Ter	p.G356*	ENST00000360948	NM_001012338.2	356	Gga/Tga	9/19	1	2	FACETS	0.759	0.689	0.833	0.759	0.689	0.833	SUBCLONAL	1	TRUE	1	0.288882396610519	2		755	1268	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646393	23646393	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	183	669	0	ENST00000261584.4:c.1474G>T	p.Gly492Trp	p.G492W	ENST00000261584	NM_024675.3	492	Ggg/Tgg	4/13	0.288882396610519	3	FACETS	1	0.971	1			1	CLONAL	1	TRUE	NA	0.288882396610519	3		669	1304	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	260	522	1	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.288882396610519	2	FACETS	0.948	0.89	1	0.948	0.89	1	CLONAL	2	TRUE	0	0.288882396610519	2		523	949	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042354	16042354	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	290	713	0	ENST00000268712.3:c.1320G>T	p.Trp440Cys	p.W440C	ENST00000268712	NM_006311.3	440	tgG/tgT	12/46	0.288882396610519	2	FACETS	0.857	0.805	0.909	0.857	0.805	0.909	CLONAL	2	TRUE	0	0.288882396610519	2		713	1172	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120182	70120184	+	frameshift_variant	Frame_Shift_Del	DEL	CGC	CGC	AG	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	174	404	0	ENST00000245479.2:c.1184_1186delinsAG	p.Thr395LysfsTer8	p.T395Kfs*8	ENST00000245479	NM_000346.3	395	aCGCac/aAGac	3/3	0.200699162658506	4	FACETS	0.924	0.852	1	0.924	0.852	1	CLONAL	2	TRUE	2	0.288882396610519	4		404	840	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610337	10610337	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	356	641	0	ENST00000171111.5:c.373A>T	p.Ile125Phe	p.I125F	ENST00000171111	NM_203500.1	125	Att/Ttt	2/6	0.288882396610519	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.288882396610519	2		641	1133	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741971	40741971	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	602	819	0	ENST00000392038.2:c.1001G>T	p.Trp334Leu	p.W334L	ENST00000392038	NM_001626.4	334	tGg/tTg	11/14	0.259730356589788	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	0	0.288882396610519	3		819	1522	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546860	9546860	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	263	454	0	ENST00000353224.5:c.1162C>A	p.Leu388Met	p.L388M	ENST00000353224	NM_177990.2	388	Ctg/Atg	5/10	0.204032011593092	5	FACETS	1	0.973	1	0.713	0.667	0.76	CLONAL	2	TRUE	2	0.288882396610519	5		454	1220	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561061	9561061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1464884282	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	260	456	0	ENST00000353224.5:c.721G>A	p.Gly241Arg	p.G241R	ENST00000353224	NM_177990.2	241	Ggg/Agg	4/10	0.204032011593092	5	FACETS	1	0.986	1	0.785	0.736	0.837	CLONAL	2	TRUE	2	0.288882396610519	5		456	1095	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561224	9561224	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1259	79	647	0	ENST00000353224.5:c.558G>T	p.Lys186Asn	p.K186N	ENST00000353224	NM_177990.2	186	aaG/aaT	4/10	0.204032011593092	5	FACETS	0.586	0.513	0.665	0.195	0.171	0.222	SUBCLONAL	1	TRUE	2	0.288882396610519	5		647	1338	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877406	40877406	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	243	484	0	ENST00000373198.4:c.2290G>T	p.Val764Leu	p.V764L	ENST00000373198	NM_133170.3	764	Gtg/Ttg	15/32	0.204032011593092	5	FACETS	1	0.966	1	0.703	0.656	0.751	CLONAL	2	TRUE	2	0.288882396610519	5		484	1144	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44520622	44520622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	182	501	0	ENST00000291552.4:c.140C>T	p.Ala47Val	p.A47V	ENST00000291552	NM_006758.2	47	gCc/gTc	3/8	0.278332428262715	4	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.288882396610519	4		501	1178	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145489	24145489	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	64	493	0	ENST00000263121.7:c.508G>T	p.Asp170Tyr	p.D170Y	ENST00000263121	NM_003073.3	170	Gac/Tac	5/9	0.288882396610519	3	FACETS	0.506	0.436	0.581	0.253	0.218	0.291	SUBCLONAL	1	TRUE	1	0.288882396610519	3		493	1003	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857075	9857075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1406	87	707	0	ENST00000330684.3:c.4326del	p.Arg1443GlyfsTer3	p.R1443Gfs*3	ENST00000330684	NM_001134407.1	1442	ccC/cc	13/13	0.288882396610519	3	FACETS	0.462	0.407	0.521			1	SUBCLONAL	1	TRUE	NA	0.288882396610519	3		707	1493	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222015	2222015	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	354	610	0	ENST00000398665.3:c.2848del	p.Ala950ArgfsTer118	p.A950Rfs*118	ENST00000398665	NM_032482.2	949	ttG/tt	24/28	0.288882396610519	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.288882396610519	2		610	1038	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106545	27106546	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1480	285	897	1	ENST00000324856.7:c.6158dup	p.Leu2053PhefsTer46	p.L2053Ffs*46	ENST00000324856	NM_006015.4	2052	-/T	20/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.288882396610519	2		898	1765	SUCCESS
APC	324	MSKCC	GRCh37	5	112102982	112102982	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	247	673	0	ENST00000257430.4:c.317del	p.Arg106LeufsTer19	p.R106Lfs*19	ENST00000257430	NM_000038.5	106	cGt/ct	4/16	NA	2	FACETS	0.808	0.755	0.862			1	INDETERMINATE	2	TRUE	NA	0.288882396610519	2		673	1058	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637724	176637724	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	87	510	0	ENST00000439151.2:c.2324A>G	p.Gln775Arg	p.Q775R	ENST00000439151	NM_022455.4	775	cAa/cGa	5/23	0.342086067435517	4	FACETS	1	0.966	1	0.617	0.548	0.691	CLONAL	1	FALSE	2	0.376738524794452	4		510	515	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637747	176637747	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	94	552	0	ENST00000439151.2:c.2347A>G	p.Lys783Glu	p.K783E	ENST00000439151	NM_022455.4	783	Aaa/Gaa	5/23	0.342086067435517	4	FACETS	1	0.968	1	0.616	0.549	0.686	CLONAL	1	FALSE	2	0.376738524794452	4		552	558	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151847993	151847993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	280	507	1	ENST00000262189.6:c.12766G>A	p.Glu4256Lys	p.E4256K	ENST00000262189	NM_170606.2	4256	Gaa/Aaa	51/59	0.342086067435517	4	FACETS	0.904	0.853	0.955	1	0.993	1	CLONAL	3	FALSE	2	0.376738524794452	4		508	755	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456738	32456738	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	101	271	0	ENST00000332351.3:c.154C>T	p.Arg52Cys	p.R52C	ENST00000332351	NM_024426.4	52	Cgt/Tgt	1/10	0.342086067435517	4	FACETS	1	0.975	1	0.652	0.584	0.724	CLONAL	1	FALSE	2	0.376738524794452	4		271	566	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244664	46244664	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555155026	NA	P-0008833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	326	692	0	ENST00000334344.6:c.2758C>T	p.Gln920Ter	p.Q920*	ENST00000334344	NM_152641.2	920	Cag/Tag	15/21	0.261646806197276	5	FACETS	1	0.97	1			1	CLONAL	3	FALSE	NA	0.376738524794452	5		692	874	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958089	54958089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	159	604	0	ENST00000312783.6:c.518G>A	p.Gly173Glu	p.G173E	ENST00000312783	NM_198436.1	173	gGa/gAa	6/10	0.376738524794452	7	FACETS	1	0.984	1	0.333	0.304	0.363	CLONAL	1	FALSE	3	0.376738524794452	7		604	1230	SUCCESS
AR	367	MSKCC	GRCh37	X	66766326	66766326	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1315489360	NA	P-0008833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	63	185	0	ENST00000374690.3:c.1338G>T	p.Leu446Phe	p.L446F	ENST00000374690	NM_000044.3	446	ttG/ttT	1/8	0.376738524794452	4	FACETS	0.84	0.727	0.963	0.42	0.363	0.482	CLONAL	1	FALSE	2	0.376738524794452	4		185	548	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011150	12011151	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	227	641	0	ENST00000353533.5:c.558dup	p.Lys187Ter	p.K187*	ENST00000353533	NM_003010.3	186	gat/gaTt	5/11	0.336481829358807	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	3	FALSE	0	0.376738524794452	3		641	469	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115840	8115850	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTCCAGACA	CTCTCCAGACA	-	novel	NA	P-0008833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1399	540	740	0	ENST00000346208.3:c.1187_1197del	p.Leu396HisfsTer107	p.L396Hfs*107	ENST00000346208		396	CTCTCCAGACAc/c	6/6	0.376738524794452	5	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	FALSE	3	0.376738524794452	5		740	1939	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0008853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	551	654	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	2	TRUE	NA	0.549649160713943	2		655	983	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0008853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	57	178	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.530315772182636	3	FACETS	0.758	0.653	0.87	0.379	0.326	0.435	SUBCLONAL	1	TRUE	1	0.549649160713943	3		178	349	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146452	185146452	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	139	290	0	ENST00000265026.3:c.83A>T	p.Gln28Leu	p.Q28L	ENST00000265026	NM_004721.4	28	cAa/cTa	2/14	0.549649160713943	3	FACETS	1	0.965	1	0.554	0.506	0.604	CLONAL	1	TRUE	1	0.549649160713943	3		290	582	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435577	18435577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424715687	NA	P-0008853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	97	325	0	ENST00000266497.5:c.562C>T	p.Pro188Ser	p.P188S	ENST00000266497		188	Ccg/Tcg	1/31	0.549649160713943	5	FACETS	0.98	0.875	1	0.327	0.291	0.364	CLONAL	1	TRUE	2	0.549649160713943	5		325	657	SUCCESS
APC	324	MSKCC	GRCh37	5	112173624	112173625	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1554084079	NA	P-0008853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	181	335	0	ENST00000257430.4:c.2336dup	p.Leu779PhefsTer9	p.L779Ffs*9	ENST00000257430	NM_000038.5	778	aat/aaTt	16/16	0.530315772182636	3	FACETS	0.852	0.792	0.912	0.852	0.792	0.912	CLONAL	2	TRUE	1	0.549649160713943	3		335	493	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0008862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	66	697	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.322158033735958	1	FACETS	0.633	0.55	0.723	0.633	0.55	0.723	SUBCLONAL	1	TRUE	0	0.322158033735958	1		697	543	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs863224499	NA	P-0008862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	203	389	1	ENST00000269305.4:c.672+1G>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.286313067795808	1	FACETS	0.813	0.752	0.876	0.813	0.752	0.876	CLONAL	1	TRUE	0	0.322158033735958	1		390	1301	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97933424	97933424	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	61	301	0	ENST00000289081.3:c.458T>A	p.Met153Lys	p.M153K	ENST00000289081	NM_000136.2	153	aTg/aAg	6/15	1	2	FACETS	0.814	0.704	0.934	0.814	0.704	0.934	CLONAL	1	TRUE	1	0.322158033735958	2		301	465	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603040	48603064	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGCAGCAGGCGGCTACTGCACAA	GCAGCAGCAGGCGGCTACTGCACAA	-	rs1568211187	NA	P-0008862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	155	226	0	ENST00000342988.3:c.1343_1367del	p.Gln448LeufsTer20	p.Q448Lfs*20	ENST00000342988	NM_005359.5	447	atGCAGCAGCAGGCGGCTACTGCACAA/at	11/12	0.276722667843396	1	FACETS	0.966	0.885	1	0.966	0.885	1	CLONAL	1	TRUE	0	0.322158033735958	1		226	836	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106712	27106713	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAATGCCGTCCTTTCCCCG	novel	NA	P-0008862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	151	283	2	ENST00000324856.7:c.6326_6344dup	p.Arg2116CysfsTer40	p.R2116Cfs*40	ENST00000324856	NM_006015.4	2108	ccc/ccCAATGCCGTCCTTTCCCCGc	20/20	0.286313067795808	1	FACETS	0.648	0.591	0.708	0.648	0.591	0.708	SUBCLONAL	1	TRUE	0	0.322158033735958	1		285	1214	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467799	50467799	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008930-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	90	498	0	ENST00000331340.3:c.1034G>T	p.Ser345Ile	p.S345I	ENST00000331340	NM_006060.4	345	aGc/aTc	8/8	0.775493039340778	3	FACETS	0.824	0.736	0.916	0.412	0.368	0.458	CLONAL	1	TRUE	1	0.775493039340778	3		498	391	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102131	27102131	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008930-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	156	765	0	ENST00000324856.7:c.5059del	p.Ala1687HisfsTer2	p.A1687Hfs*2	ENST00000324856	NM_006015.4	1686	tGg/tg	19/20	1	2	FACETS	0.927	0.857	0.998	0.927	0.857	0.998	CLONAL	1	TRUE	1	0.775493039340778	2		765	434	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879243	151879244	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008930-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	117	557	0	ENST00000262189.6:c.5701dup	p.Met1901AsnfsTer13	p.M1901Nfs*13	ENST00000262189	NM_170606.2	1901	atg/aAtg	36/59	0.775493039340778	3	FACETS	0.922	0.837	1	0.461	0.418	0.506	CLONAL	1	TRUE	1	0.775493039340778	3		557	454	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	266	245	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.757059675508498	2		245	608	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0009003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	601	411	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.757059675508498	2		411	1516	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468357	89468357	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs867931903	NA	P-0009003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	198	194	0	ENST00000336596.2:c.1891G>A	p.Glu631Lys	p.E631K	ENST00000336596	NM_005233.5	631	Gaa/Aaa	11/17	1	2	FACETS	0.893	0.832	0.955	0.893	0.832	0.955	CLONAL	1	TRUE	1	0.757059675508498	2		194	586	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468526	89468526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	358	295	0	ENST00000336596.2:c.2060G>A	p.Gly687Glu	p.G687E	ENST00000336596	NM_005233.5	687	gGa/gAa	11/17	1	2	FACETS	0.971	0.923	1	0.971	0.923	1	CLONAL	1	TRUE	1	0.757059675508498	2		295	974	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156355	106156355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780355921	NA	P-0009003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	425	328	0	ENST00000380013.4:c.1256C>T	p.Pro419Leu	p.P419L	ENST00000380013	NM_001127208.2	419	cCt/cTt	3/11	1	2	FACETS	0.943	0.899	0.987	0.943	0.899	0.987	CLONAL	1	TRUE	1	0.757059675508498	2		328	1191	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873648	35873648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867618621	NA	P-0009003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	428	360	0	ENST00000303115.3:c.604G>A	p.Glu202Lys	p.E202K	ENST00000303115	NM_002185.3	202	Gag/Aag	5/8	1	2	FACETS	0.953	0.91	0.998	0.953	0.91	0.998	CLONAL	1	TRUE	1	0.757059675508498	2		360	1186	SUCCESS
APC	324	MSKCC	GRCh37	5	112175124	112175124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	272	194	0	ENST00000257430.4:c.3833C>T	p.Ser1278Leu	p.S1278L	ENST00000257430	NM_000038.5	1278	tCa/tTa	16/16	1	2	FACETS	0.974	0.918	1	0.974	0.918	1	CLONAL	1	TRUE	1	0.757059675508498	2		194	738	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439267	149439267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762329575	NA	P-0009003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	446	377	0	ENST00000286301.3:c.2128C>T	p.Arg710Cys	p.R710C	ENST00000286301	NM_005211.3	710	Cgc/Tgc	15/22	1	2	FACETS	0.893	0.852	0.934	0.893	0.852	0.934	CLONAL	1	TRUE	1	0.757059675508498	2		377	1320	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117650567	117650567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	617	606	0	ENST00000368508.3:c.5291G>A	p.Gly1764Glu	p.G1764E	ENST00000368508	NM_002944.2	1764	gGg/gAg	32/43	1	2	FACETS	0.963	0.926	1	0.963	0.926	1	CLONAL	1	TRUE	1	0.757059675508498	2		606	1693	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879358	151879358	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	491	307	0	ENST00000262189.6:c.5587C>T	p.Pro1863Ser	p.P1863S	ENST00000262189	NM_170606.2	1863	Ccc/Tcc	36/59	1	2	FACETS	0.99	0.948	1	0.99	0.948	1	CLONAL	1	TRUE	1	0.757059675508498	2		307	1310	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445208	49445208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	360	261	1	ENST00000301067.7:c.2258C>T	p.Ser753Phe	p.S753F	ENST00000301067	NM_003482.3	753	tCc/tTc	10/54	1	2	FACETS	0.993	0.944	1	0.993	0.944	1	CLONAL	1	TRUE	1	0.757059675508498	2		262	958	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005419	29005419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55687105	NA	P-0009003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	350	290	0	ENST00000282397.4:c.842G>A	p.Arg281Gln	p.R281Q	ENST00000282397	NM_002019.4	281	cGa/cAa	7/30	1	2	FACETS	0.948	0.9	0.997	0.948	0.9	0.997	CLONAL	1	TRUE	1	0.757059675508498	2		290	975	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098601	11098601	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0009003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	392	285	0	ENST00000358026.2:c.1118+1G>T		p.X373_splice	ENST00000358026	NM_001128849.1	373			0.733025948389873	1	FACETS	0.984	0.946	1	0.984	0.946	1	CLONAL	1	TRUE	0	0.757059675508498	1		285	654	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770630	40770630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	384	272	0	ENST00000373198.4:c.2752G>A	p.Gly918Arg	p.G918R	ENST00000373198	NM_133170.3	918	Ggg/Agg	19/32	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.757059675508498	2		272	984	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553007	106553008	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0009003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	478	351	0	ENST00000369096.4:c.973dup	p.Thr325AsnfsTer99	p.T325Nfs*99	ENST00000369096	NM_001198.3	324	-/A	5/7	1	2	FACETS	0.929	0.889	0.97	0.929	0.889	0.97	CLONAL	1	TRUE	1	0.757059675508498	2		351	1359	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412366	139412367	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGCATGCT	novel	NA	P-0009003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	282	267	0	ENST00000277541.6:c.1271_1278dup	p.Gly427SerfsTer207	p.G427Sfs*207	ENST00000277541	NM_017617.3	426	-/AGCATGCG	8/34	0.757059675508498	2	FACETS	0.701	0.659	0.745	0.351	0.329	0.373	SUBCLONAL	1	TRUE	0	0.757059675508498	2		267	1062	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242753	98242756	+	frameshift_variant	Frame_Shift_Del	DEL	ACCA	ACCA	-	novel	NA	P-0009003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	1062	360	0	ENST00000331920.6:c.861_864del	p.Gly288MetfsTer35	p.G288Mfs*35	ENST00000331920	NM_000264.3	287	gtTGGT/gt	6/24	0.757059675508498	2	FACETS	0.979	0.96	0.997	0.979	0.96	0.997	CLONAL	2	TRUE	0	0.757059675508498	2		360	1433	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0009009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	43	697	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.597	0.498	0.708	0.597	0.498	0.708	SUBCLONAL	1	TRUE	1	0.18	2		697	800	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0009009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	61	359	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.775	0.667	0.894	0.775	0.667	0.894	SUBCLONAL	1	TRUE	1	0.18	2		359	874	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469672	NA	P-0009009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	98	284	0	ENST00000374080.3:c.131G>A	p.Gly44Asp	p.G44D	ENST00000374080		44	gGt/gAt	2/45	1	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.18	1		284	676	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743362	162743362	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372362070	NA	P-0009009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	85	379	0	ENST00000367921.3:c.1832G>A	p.Arg611Gln	p.R611Q	ENST00000367921	NM_006182.2	611	cGa/cAa	14/18	1	2	FACETS	0.979	0.863	1	0.979	0.863	1	CLONAL	1	TRUE	1	0.18	2		379	965	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851271	156851271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	57	419	1	ENST00000524377.1:c.2228G>A	p.Gly743Glu	p.G743E	ENST00000524377	NM_002529.3	743	gGa/gAa	17/17	1	2	FACETS	0.857	0.734	0.992	0.857	0.734	0.992	CLONAL	1	TRUE	1	0.18	2		420	739	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143324099	143324099	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	39	263	0	ENST00000262992.4:c.364C>G	p.His122Asp	p.H122D	ENST00000262992	NM_001101669.1	122	Cat/Gat	5/24	1	2	FACETS	0.634	0.524	0.757	0.634	0.524	0.757	SUBCLONAL	1	TRUE	1	0.18	2		263	684	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244097	153244097	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	62	335	1	ENST00000281708.4:c.2060G>T	p.Gly687Val	p.G687V	ENST00000281708	NM_033632.3	687	gGg/gTg	12/12	1	2	FACETS	0.726	0.625	0.836	0.726	0.625	0.836	SUBCLONAL	1	TRUE	1	0.18	2		336	949	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961399	41961399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748756129	NA	P-0009009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1300	118	649	0	ENST00000219905.7:c.307C>T	p.Arg103Cys	p.R103C	ENST00000219905	NM_001164273.1	103	Cgc/Tgc	2/24	1	2	FACETS	0.925	0.831	1	0.925	0.831	1	CLONAL	1	TRUE	1	0.18	2		649	1418	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120345	70120346	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0009009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	96	674	0	ENST00000245479.2:c.1348dup	p.Ser450PhefsTer128	p.S450Ffs*128	ENST00000245479	NM_000346.3	449	-/T	3/3	0.3	2	FACETS	0.836	0.742	0.936			1	CLONAL	1	TRUE	NA	0.18	2		674	1276	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514325	148514325	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	153	533	0	ENST00000320356.2:c.1399A>C	p.Thr467Pro	p.T467P	ENST00000320356	NM_004456.4	467	Aca/Cca	11/20	0.217588832241243	2	FACETS	0.574	0.525	0.625	0.287	0.262	0.313	INDETERMINATE	1	TRUE	0	0.632075497931884	2		533	844	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111458	8111459	+	frameshift_variant	Frame_Shift_Ins	INS	CG	CG	AGT	novel	NA	P-0009026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	559	445	0	ENST00000346208.3:c.944_945delinsAGT	p.Thr315LysfsTer37	p.T315Kfs*37	ENST00000346208		315	aCG/aAGT	5/6	0.119172378400351	3	FACETS	0.833	0.801	0.866	0.833	0.801	0.866	INDETERMINATE	2	TRUE	1	0.632075497931884	3		445	1397	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009089-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	173	245	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.766	0.709	0.825	1	0.99	1	SUBCLONAL	2	TRUE	1	0.401762916138159	2		245	562	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0009089-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	384	373	1	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.401762916138159	2		374	1469	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0009089-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	320	251	0	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	1	2	FACETS	0.874	0.828	0.922	1	0.995	1	CLONAL	2	TRUE	1	0.401762916138159	2		251	911	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258718	115258718	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009089-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	321	289	0	ENST00000369535.4:c.64C>A	p.Gln22Lys	p.Q22K	ENST00000369535	NM_002524.4	22	Cag/Aag	2/7	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.401762916138159	2		289	1082	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667571	29667571	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691073	NA	P-0009089-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	377	449	0	ENST00000356175.3:c.6907C>T	p.Gln2303Ter	p.Q2303*	ENST00000356175	NM_000267.3	2303	Cag/Tag	46/57	1	2	FACETS	0.781	0.741	0.821	1	0.995	1	SUBCLONAL	2	TRUE	1	0.401762916138159	2		449	1202	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339243	70339278	+	inframe_deletion	In_Frame_Del	DEL	TGTAAAACAAGGTTTCAATAACCAGCCTGCTGTCTC	TGTAAAACAAGGTTTCAATAACCAGCCTGCTGTCTC	-	novel	NA	P-0009089-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	460	551	0	ENST00000374080.3:c.122_157del	p.Val41_Ser52del	p.V41_S52del	ENST00000374080		40	aaTGTAAAACAAGGTTTCAATAACCAGCCTGCTGTCTCt/aat	2/45	0.401762916138159	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.401762916138159	1		551	1390	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922235	39922245	+	frameshift_variant	Frame_Shift_Del	DEL	GTGCGCAGCTT	GTGCGCAGCTT	A	novel	NA	P-0009089-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	340	438	0	ENST00000378444.4:c.3927_3937delinsT	p.Ser1310GlnfsTer56	p.S1310Qfs*56	ENST00000378444	NM_001123385.1	1309	ccAAGCTGCGCACca/ccTca	9/15	0.401762916138159	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.401762916138159	1		438	1028	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0009160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	311	328	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.32440932423839	7	FACETS	0.957	0.908	1			1	CLONAL	5	TRUE	NA	0.32440932423839	7		328	726	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111502	8111503	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0009160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1503	433	329	0	ENST00000346208.3:c.990dup	p.Asn331GlufsTer21	p.N331Efs*21	ENST00000346208		330	agg/aGgg	5/6	0.32440932423839	5	FACETS	1	0.968	1			1	CLONAL	2	TRUE	NA	0.32440932423839	5		329	1936	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133805	55133805	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376626935	NA	P-0009160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1241	178	654	1	ENST00000257290.5:c.1018C>T	p.Arg340Trp	p.R340W	ENST00000257290	NM_006206.4	340	Cgg/Tgg	7/23	0.313050694347477	3	FACETS	0.899	0.826	0.975	0.449	0.413	0.488	CLONAL	1	TRUE	1	0.32440932423839	3		655	1419	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0009160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	85	103	0	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	0.32440932423839	7	FACETS	0.779	0.686	0.879			1	SUBCLONAL	1	TRUE	NA	0.32440932423839	7		103	1218	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134448	2134448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45517333	NA	P-0009160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1331	400	609	3	ENST00000219476.3:c.4225C>T	p.Arg1409Trp	p.R1409W	ENST00000219476	NM_000548.3	1409	Cgg/Tgg	34/42	0.287684052999468	4	FACETS	0.943	0.895	0.993	0.943	0.895	0.993	CLONAL	2	TRUE	2	0.32440932423839	4		612	1731	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0009192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	253	403	1	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.222876504359092	3	FACETS	0.769	0.719	0.819			1	INDETERMINATE	2	TRUE	NA	0.380394048877565	3		404	1030	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462351	89462351	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	154	495	0	ENST00000336596.2:c.1823C>A	p.Ala608Asp	p.A608D	ENST00000336596	NM_005233.5	608	gCt/gAt	10/17	0.241672851890725	3	FACETS	0.926	0.846	1	0.463	0.423	0.505	CLONAL	1	TRUE	1	0.380394048877565	3		495	1041	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0009192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	343	337	1	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	0.380394048877565	3	FACETS	0.926	0.881	0.97	0.926	0.881	0.97	CLONAL	3	TRUE	0	0.380394048877565	3		338	773	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245060	46245060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	267	517	1	ENST00000334344.6:c.3154C>T	p.Pro1052Ser	p.P1052S	ENST00000334344	NM_152641.2	1052	Cct/Tct	15/21	0.344902903852274	4	FACETS	0.868	0.814	0.924	0.868	0.814	0.924	CLONAL	2	TRUE	2	0.380394048877565	4		518	1116	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888168	81888168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754914807	NA	P-0009192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	383	719	0	ENST00000359376.3:c.313G>A	p.Val105Ile	p.V105I	ENST00000359376	NM_002661.3	105	Gtc/Atc	3/33	0.335489008581317	3	FACETS	0.96	0.912	1	0.96	0.912	1	CLONAL	2	TRUE	1	0.380394048877565	3		719	1248	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119829	70119830	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0009192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	281	588	0	ENST00000245479.2:c.832_833dup	p.Ser279Ter	p.S279*	ENST00000245479	NM_000346.3	277	-/CT	3/3	0.364910421147921	3	FACETS	0.953	0.897	1	0.953	0.897	1	CLONAL	2	TRUE	1	0.380394048877565	3		588	923	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622262	162622262	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	75	429	0	ENST00000366898.1:c.435del	p.Tyr147MetfsTer30	p.Y147Mfs*30	ENST00000366898	NM_004562.2	145	agC/ag	4/12	0.335489008581317	3	FACETS	0.543	0.475	0.617	0.272	0.237	0.309	SUBCLONAL	1	TRUE	1	0.380394048877565	3		429	864	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120426	70120427	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0009192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	240	863	0	ENST00000245479.2:c.1429dup	p.Tyr477LeufsTer101	p.Y477Lfs*101	ENST00000245479	NM_000346.3	476	-/T	3/3	0.364910421147921	3	FACETS	1	0.985	1	0.6	0.559	0.642	CLONAL	1	TRUE	1	0.380394048877565	3		863	1252	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115952	8115953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0009325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	110	180	0	ENST00000346208.3:c.1300dup	p.His434ProfsTer73	p.H434Pfs*73	ENST00000346208		433	cac/caCc	6/6	0.26639654829463	3	FACETS	0.829	0.747	0.914	0.829	0.747	0.914	CLONAL	2	TRUE	1	0.268961968654296	3		180	560	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371745	45371745	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	53	504	0	ENST00000262160.6:c.1246A>G	p.Met416Val	p.M416V	ENST00000262160	NM_005901.5	416	Atg/Gtg	10/11	1	2	FACETS	0.382	0.325	0.446	0.382	0.325	0.446	SUBCLONAL	1	TRUE	1	0.268961968654296	2		504	1031	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875049	151875056	+	frameshift_variant	Frame_Shift_Del	DEL	GCTCTTGA	GCTCTTGA	-	novel	NA	P-0009325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	108	235	0	ENST00000262189.6:c.7482_7489del	p.Ser2494ArgfsTer28	p.S2494Rfs*28	ENST00000262189	NM_170606.2	2494	agTCAAGAGCgc/aggc	38/59	0.18606215716799	4	FACETS	1	0.981	1	0.711	0.638	0.787	CLONAL	1	TRUE	2	0.268961968654296	4		235	717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0009469-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	270	437	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.314581580200863	2	FACETS	0.806	0.76	0.852	0.806	0.76	0.852	CLONAL	2	TRUE	0	0.468067686372619	2		437	716	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACAACCCCC	rs397517115	NA	P-0009469-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	150	349	0	ENST00000275493.2:c.2311_2319dup	p.Asn771_His773dup	p.N771_H773dup	ENST00000275493	NM_005228.3	771	gac/gACAACCCCCac	20/28	0.320676401382492	4	FACETS	1	0.978	1	0.301	0.275	0.328	CLONAL	1	TRUE	0	0.468067686372619	4		349	781	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015035	27015035	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009469-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	259	489	0	ENST00000335756.4:c.137G>A	p.Gly46Asp	p.G46D	ENST00000335756	NM_001809.3	46	gGt/gAt	2/5	0.314581580200863	2	FACETS	1	0.993	1	0.717	0.674	0.76	CLONAL	1	TRUE	0	0.468067686372619	2		489	772	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	644	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.297756852440406	9	FACETS	1	0.993	1			1	CLONAL	7	TRUE	NA	0.35	9		311	1092	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0009488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	131	509	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.35	2		509	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0009488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	229	533	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.35	2		533	954	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713883	30713883	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143095746	NA	P-0009488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	67	285	0	ENST00000295754.5:c.1208G>A	p.Arg403His	p.R403H	ENST00000295754	NM_003242.5	403	cGt/cAt	4/7	0.262060569586683	1	FACETS	0.599	0.521	0.683	0.599	0.521	0.683	SUBCLONAL	1	TRUE	0	0.35	1		285	527	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394941	394941	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753842732	NA	P-0009488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	146	248	0	ENST00000380956.4:c.337C>T	p.Arg113Trp	p.R113W	ENST00000380956	NM_001195286.1	113	Cgg/Tgg	3/9	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.35	2		248	585	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604797	48604797	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	172	324	0	ENST00000342988.3:c.1619T>A	p.Leu540His	p.L540H	ENST00000342988	NM_005359.5	540	cTt/cAt	12/12	0.249218914802319	0	FACETS	0.604	0.559	0.649			1	SUBCLONAL	2	TRUE	0	0.35	0		324	529	SUCCESS
APC	324	MSKCC	GRCh37	5	112174505	112174505	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	CGTACAAC	novel	NA	P-0009488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	100	297	0	ENST00000257430.4:c.3214delinsCGTACAAC	p.Ser1072ArgfsTer11	p.S1072Rfs*11	ENST00000257430	NM_000038.5	1072	Agt/CGTACAACgt	16/16	0.262060569586683	1	FACETS	0.966	0.867	1	0.966	0.867	1	CLONAL	1	TRUE	0	0.35	1		297	488	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731061	162731061	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009498-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	161	764	0	ENST00000367921.3:c.916T>G	p.Phe306Val	p.F306V	ENST00000367921	NM_006182.2	306	Ttc/Gtc	9/18	1	2	FACETS	0.474	0.433	0.516	0.474	0.433	0.516	SUBCLONAL	1	TRUE	1	0.553796218352364	2		764	1227	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021758	71021758	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009498-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	354	755	0	ENST00000318789.4:c.1600T>A	p.Trp534Arg	p.W534R	ENST00000318789	NM_032682.5	534	Tgg/Agg	18/21	1	2	FACETS	0.974	0.922	1	0.974	0.922	1	CLONAL	1	TRUE	1	0.553796218352364	2		755	1312	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160663	56160663	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs558965285	NA	P-0009498-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	242	548	0	ENST00000399503.3:c.937C>G	p.Arg313Gly	p.R313G	ENST00000399503	NM_005921.1	313	Cgg/Ggg	4/20	1	2	FACETS	0.882	0.824	0.941	0.882	0.824	0.941	CLONAL	1	TRUE	1	0.553796218352364	2		548	991	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624294	89624295	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0009498-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	146	381	0	ENST00000371953.3:c.69dup	p.Asp24ArgfsTer20	p.D24Rfs*20	ENST00000371953	NM_000314.4	23	tta/ttAa	1/9	1	2	FACETS	0.87	0.797	0.946	0.87	0.797	0.946	CLONAL	1	TRUE	1	0.553796218352364	2		381	606	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032537	12032537	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009498-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	202	463	0	ENST00000353533.5:c.974del	p.Pro325LeufsTer4	p.P325Lfs*4	ENST00000353533	NM_003010.3	325	Cct/ct	9/11	0.531728854928512	1	FACETS	0.945	0.883	1	0.945	0.883	1	CLONAL	1	TRUE	0	0.553796218352364	1		463	558	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0009518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	500	783	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.824151726729553	2		783	1119	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466019	69466019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	324	588	0	ENST00000227507.2:c.857C>T	p.Thr286Ile	p.T286I	ENST00000227507	NM_053056.2	286	aCa/aTa	5/5	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.824151726729553	2		588	722	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266112	41266112	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913228	NA	P-0009518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	429	493	0	ENST00000349496.5:c.109T>C	p.Ser37Pro	p.S37P	ENST00000349496	NM_001904.3	37	Tct/Cct	3/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.824151726729553	2		493	1035	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286892	33286892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	318	371	1	ENST00000374542.5:c.2045C>T	p.Ser682Phe	p.S682F	ENST00000374542	NM_001141970.1	682	tCc/tTc	7/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.824151726729553	2		372	716	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692809	89692809	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs781647403	NA	P-0009518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	775	285	0	ENST00000371953.3:c.293T>G	p.Leu98Arg	p.L98R	ENST00000371953	NM_000314.4	98	cTa/cGa	5/9	0.824151726729553	3	FACETS	1	0.998	1	1	0.998	1	CLONAL	3	TRUE	0	0.824151726729553	3		285	827	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566465	41566465	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	610	590	0	ENST00000263253.7:c.4342T>G	p.Phe1448Val	p.F1448V	ENST00000263253	NM_001429.3	1448	Ttc/Gtc	27/31	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.824151726729553	2		590	1413	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591107	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AACC	novel	NA	P-0009518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	390	370	0	ENST00000274335.5:c.1701_1704dup	p.Asp569ThrfsTer34	p.D569Tfs*34	ENST00000274335		567	aaa/aAACCaa	12/15	1	2	FACETS	0.917	0.874	0.961	0.917	0.874	0.961	CLONAL	1	TRUE	1	0.824151726729553	2		370	1032	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0009615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	331	443	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	1	2	FACETS	0.822	0.778	0.867	0.822	0.778	0.867	CLONAL	1	TRUE	1	0.787921061658869	2		443	1022	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443560	49443560	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	320	372	0	ENST00000301067.7:c.3811C>G	p.Leu1271Val	p.L1271V	ENST00000301067	NM_003482.3	1271	Cta/Gta	11/54	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.787921061658869	2		372	796	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716000	52716000	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	401	493	0	ENST00000322088.6:c.565C>G	p.Leu189Val	p.L189V	ENST00000322088	NM_014225.5	189	Ctg/Gtg	5/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.787921061658869	2		493	969	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0009650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	39	276	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.771	0.638	0.918	0.771	0.638	0.918	CLONAL	1	TRUE	1	0.21	2		276	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0009650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	38	455	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.431	0.355	0.517	0.431	0.355	0.517	SUBCLONAL	1	TRUE	1	0.21	2		457	840	SUCCESS
APC	324	MSKCC	GRCh37	5	112174309	112174310	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0009650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	41	438	0	ENST00000257430.4:c.3022dup	p.Ile1008AsnfsTer3	p.I1008Nfs*3	ENST00000257430	NM_000038.5	1006	-/A	16/16	1	2	FACETS	0.904	0.754	1	0.904	0.754	1	CLONAL	1	TRUE	1	0.21	2		438	432	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0009688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	140	480	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	0.326793338802123	5	FACETS	0.948	0.868	1	0.632	0.578	0.688	CLONAL	2	TRUE	2	0.436104381276422	5		480	560	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	443471	443471	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	71	591	0	ENST00000399788.2:c.1426T>C	p.Cys476Arg	p.C476R	ENST00000399788	NM_001042603.1	476	Tgc/Cgc	11/28	0.259497268239821	4	FACETS	0.864	0.755	0.982	0.432	0.377	0.491	INDETERMINATE	1	TRUE	2	0.436104381276422	4		591	541	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161907	47161907	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	44	772	1	ENST00000409792.3:c.4219del	p.Arg1407GlyfsTer5	p.R1407Gfs*5	ENST00000409792	NM_014159.6	1407	Agg/gg	3/21	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.16	2		773	491	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0009706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	11	230	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.828	0.574	1	0.828	0.574	1	CLONAL	1	TRUE	1	0.16	2		230	166	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782177	NA	P-0009706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	56	889	2	ENST00000269305.4:c.644G>T	p.Ser215Ile	p.S215I	ENST00000269305	NM_001126112.2	215	aGt/aTt	6/11	1	2	FACETS	0.974	0.833	1	0.974	0.833	1	CLONAL	1	TRUE	1	0.16	2		891	719	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053022	180053023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750808726	NA	P-0009706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	23	549	2	ENST00000261937.6:c.1267dup	p.Gln423ProfsTer4	p.Q423Pfs*4	ENST00000261937	NM_182925.4	423	cag/cCag	10/30	1	2	FACETS	0.661	0.514	0.831	0.661	0.514	0.831	SUBCLONAL	1	TRUE	1	0.16	2		551	435	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931471	131931471	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753002904	NA	P-0009706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	29	426	0	ENST00000265335.6:c.2176C>T	p.Arg726Cys	p.R726C	ENST00000265335		726	Cgt/Tgt	13/25	1	2	FACETS	0.77	0.617	0.944	0.77	0.617	0.944	CLONAL	1	TRUE	1	0.16	2		426	471	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206667302	206667302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	53	659	2	ENST00000367120.3:c.2095G>T	p.Asp699Tyr	p.D699Y	ENST00000367120	NM_014002.3	699	Gac/Tac	21/22	1	2	FACETS	0.995	0.847	1	0.995	0.847	1	CLONAL	1	TRUE	1	0.16	2		661	666	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144061	55144061	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0009706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	37	618	0	ENST00000257290.5:c.1892-2A>G		p.X631_splice	ENST00000257290	NM_006206.4	631			1	2	FACETS	0.898	0.74	1	0.898	0.74	1	CLONAL	1	TRUE	1	0.16	2		618	515	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457779	149457779	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	26	423	0	ENST00000286301.3:c.625C>T	p.Pro209Ser	p.P209S	ENST00000286301	NM_005211.3	209	Cct/Tct	5/22	1	2	FACETS	0.69	0.545	0.856	0.69	0.545	0.856	SUBCLONAL	1	TRUE	1	0.16	2		423	471	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048207	180048207	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	35	589	0	ENST00000261937.6:c.2066T>C	p.Val689Ala	p.V689A	ENST00000261937	NM_182925.4	689	gTg/gCg	14/30	1	2	FACETS	0.778	0.637	0.938	0.778	0.637	0.938	CLONAL	1	TRUE	1	0.16	2		589	562	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512041	148512041	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	31	543	0	ENST00000320356.2:c.1637A>T	p.Asn546Ile	p.N546I	ENST00000320356	NM_004456.4	546	aAt/aTt	14/20	1	2	FACETS	0.826	0.668	1	0.826	0.668	1	CLONAL	1	TRUE	1	0.16	2		543	469	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344648	118344648	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	34	709	2	ENST00000534358.1:c.2774C>A	p.Ser925Tyr	p.S925Y	ENST00000534358	NM_005933.3	925	tCt/tAt	3/36	1	2	FACETS	0.799	0.652	0.965	0.799	0.652	0.965	CLONAL	1	TRUE	1	0.16	2		711	532	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95595888	95595888	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	47	736	0	ENST00000393063.1:c.655T>G	p.Leu219Val	p.L219V	ENST00000393063	NM_030621.3	219	Ttg/Gtg	7/28	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.16	2		736	504	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961850	41961850	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	51	1077	0	ENST00000219905.7:c.758C>A	p.Pro253Gln	p.P253Q	ENST00000219905	NM_001164273.1	253	cCa/cAa	2/24	1	2	FACETS	0.833	0.707	0.973	0.833	0.707	0.973	CLONAL	1	TRUE	1	0.16	2		1077	765	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347881	347881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	53	1028	1	ENST00000262320.3:c.1625G>A	p.Ser542Asn	p.S542N	ENST00000262320	NM_003502.3	542	aGc/aAc	6/11	1	2	FACETS	0.905	0.77	1	0.905	0.77	1	CLONAL	1	TRUE	1	0.16	2		1029	732	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829529	72829529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	57	1138	0	ENST00000268489.5:c.7052G>A	p.Cys2351Tyr	p.C2351Y	ENST00000268489	NM_006885.3	2351	tGt/tAt	9/10	1	2	FACETS	0.918	0.786	1	0.918	0.786	1	CLONAL	1	TRUE	1	0.16	2		1138	776	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308419	30308419	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	36	744	0	ENST00000262643.3:c.433C>T	p.Arg145Ter	p.R145*	ENST00000262643	NM_001238.2	145	Cga/Tga	6/12	1	2	FACETS	0.765	0.628	0.92	0.765	0.628	0.92	CLONAL	1	TRUE	1	0.16	2		744	588	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910600	50910600	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	46	889	0	ENST00000440232.2:c.1703T>C	p.Leu568Pro	p.L568P	ENST00000440232	NM_002691.3	568	cTg/cCg	14/27	1	2	FACETS	0.811	0.681	0.955	0.811	0.681	0.955	CLONAL	1	TRUE	1	0.16	2		889	709	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719329	52719329	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0009706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	26	593	0	ENST00000322088.6:c.993+2T>C		p.X331_splice	ENST00000322088	NM_014225.5	331			1	2	FACETS	0.754	0.596	0.935	0.754	0.596	0.935	CLONAL	1	TRUE	1	0.16	2		593	431	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222648	53222648	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	51	338	0	ENST00000375401.3:c.4288G>T	p.Asp1430Tyr	p.D1430Y	ENST00000375401	NM_004187.3	1430	Gac/Tac	25/26	1	1	FACETS	0.845	0.721	0.98	1	0.97	1	CLONAL	2	TRUE	0	0.16	1		338	347	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524640	103524640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	45	769	0	ENST00000355739.4:c.2774del	p.Pro925LeufsTer57	p.P925Lfs*57	ENST00000355739	NM_000123.3	924	aCc/ac	13/15	1	2	FACETS	0.909	0.763	1	0.909	0.763	1	CLONAL	1	TRUE	1	0.16	2		769	619	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100302	157100302	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1417035592	NA	P-0009706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	31	474	0	ENST00000346085.5:c.1243del	p.Ala415ProfsTer15	p.A415Pfs*15	ENST00000346085	NM_020732.3	413	tcG/tc	1/20	0.186418343229028	3	FACETS	0.858	0.693	1	0.429	0.346	0.523	CLONAL	1	TRUE	1	0.16	3		474	488	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228329	53228330	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0009706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	33	400	0	ENST00000375401.3:c.2072_2073del	p.Glu691GlyfsTer2	p.E691Gfs*2	ENST00000375401	NM_004187.3	691	gAG/g	15/26	1	1	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	0	0.16	1		400	316	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10271068	10271068	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568238786	NA	P-0009706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	41	718	1	ENST00000340748.4:c.987del	p.Glu331AsnfsTer14	p.E331Nfs*14	ENST00000340748		329	ccC/cc	13/40	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.16	2		719	473	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0009731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	181	618	6	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	1	0.959	1	1	0.993	1	CLONAL	2	TRUE	1	0.161142380787343	2		624	1057	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491645	56491645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	89	310	0	ENST00000267101.3:c.2537G>T	p.Ser846Ile	p.S846I	ENST00000267101	NM_001982.3	846	aGt/aTt	21/28	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.161142380787343	2		310	952	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482437	56482437	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	57	280	0	ENST00000267101.3:c.985A>G	p.Lys329Glu	p.K329E	ENST00000267101	NM_001982.3	329	Aaa/Gaa	8/28	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.161142380787343	2		280	654	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842405	68842406	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0009731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	112	460	0	ENST00000261769.5:c.469dup	p.Val157GlyfsTer11	p.V157Gfs*11	ENST00000261769	NM_004360.3	156	tgg/tGgg	4/16	0.161142380787343	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.161142380787343	1		460	1125	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29662032	29662033	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	C	novel	NA	P-0009731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	93	210	0	ENST00000356175.3:c.5926_5927delinsC	p.Trp1976ArgfsTer15	p.W1976Rfs*15	ENST00000356175	NM_000267.3	1976	TGg/Cg	39/57	1	2	FACETS	1	0.941	1	1	0.987	1	CLONAL	2	TRUE	1	0.161142380787343	2		210	533	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867540	35867541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs869312857	NA	P-0009824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	67	377	0	ENST00000303115.3:c.361dup	p.Ile121AsnfsTer8	p.I121Nfs*8	ENST00000303115	NM_002185.3	118	-/A	3/8	0.249624892717436	7	FACETS	0.69	0.597	0.792			1	SUBCLONAL	1	TRUE	NA	0.249624892717436	7		377	1263	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0009824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	632	654	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.249624892717436	10	FACETS	0.978	0.945	1	0.87	0.84	0.899	CLONAL	8	TRUE	1	0.249624892717436	10		654	1293	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0009824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1445	200	668	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.249624892717436	10	FACETS	0.973	0.899	1	0.216	0.199	0.234	CLONAL	2	TRUE	1	0.249624892717436	10		669	1645	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527847	157527847	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	94	366	0	ENST00000346085.5:c.5572G>C	p.Glu1858Gln	p.E1858Q	ENST00000346085	NM_020732.3	1858	Gag/Cag	20/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.249624892717436	2		366	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138729528	NA	P-0009824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	58	351	0	ENST00000269305.4:c.523C>G	p.Arg175Gly	p.R175G	ENST00000269305	NM_001126112.2	175	Cgc/Ggc	5/11	0.249624892717436	1	FACETS	0.944	0.813	1	0.944	0.813	1	CLONAL	1	TRUE	0	0.249624892717436	1		351	431	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511274	157511274	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	67	403	0	ENST00000346085.5:c.3792G>A	p.Met1264Ile	p.M1264I	ENST00000346085	NM_020732.3	1264	atG/atA	15/20	1	2	FACETS	0.902	0.784	1	0.902	0.784	1	CLONAL	1	TRUE	1	0.249624892717436	2		403	595	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042185	42042185	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0009824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1350	179	971	0	ENST00000219905.7:c.6380C>G	p.Ser2127Ter	p.S2127*	ENST00000219905	NM_001164273.1	2127	tCa/tGa	17/24	1	2	FACETS	0.938	0.862	1	0.938	0.862	1	CLONAL	1	TRUE	1	0.249624892717436	2		971	1529	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611144	100611144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	106	634	0	ENST00000308731.7:c.1462G>A	p.Glu488Lys	p.E488K	ENST00000308731	NM_000061.2	488	Gag/Aag	15/19	0.213447726367651	3	FACETS	0.988	0.884	1	0.494	0.442	0.549	CLONAL	1	TRUE	1	0.249624892717436	3		634	967	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027140	49027141	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0009824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	340	491	0	ENST00000267163.4:c.1709_1710dup	p.Asp571LeufsTer41	p.D571Lfs*41	ENST00000267163	NM_000321.2	569	-/TT	18/27	0.249624892717436	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	1	0.249624892717436	4		491	991	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206942006	206942006	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	30	368	0	ENST00000423557.1:c.512A>T	p.Tyr171Phe	p.Y171F	ENST00000423557	NM_000572.2	171	tAc/tTc	5/5	0.255916318773678	3	FACETS	0.994	0.814	1	0.994	0.814	1	CLONAL	2	FALSE	1	0.255916318773678	3		368	133	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905288	50905288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376236497	NA	P-0009843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	85	731	0	ENST00000440232.2:c.496C>T	p.Arg166Trp	p.R166W	ENST00000440232	NM_002691.3	166	Cgg/Tgg	5/27	0.255916318773678	3	FACETS	0.853	0.758	0.955	0.853	0.758	0.955	CLONAL	2	FALSE	1	0.255916318773678	3		731	439	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627344	37627347	+	frameshift_variant	Frame_Shift_Del	DEL	CCAA	CCAA	-	novel	NA	P-0009843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	73	510	1	ENST00000447079.4:c.1259_1262del	p.Ser420TrpfsTer15	p.S420Wfs*15	ENST00000447079	NM_015083.1	420	tCCAAg/tg	2/14	0.255916318773678	3	FACETS	1	0.934	1	1	0.98	1	CLONAL	3	FALSE	1	0.255916318773678	3		511	201	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061215	38061227	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGCCGTTCTCG	GCAGCCGTTCTCG	-	novel	NA	P-0009843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	241	329	0	ENST00000250448.2:c.762_774del	p.Glu255ThrfsTer62	p.E255Tfs*62	ENST00000250448	NM_004496.3	254	ttCGAGAACGGCTGC/tt	2/2	0.233344501134371	4	FACETS	1	0.985	1	1	0.994	1	CLONAL	4	FALSE	1	0.255916318773678	4		329	528	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650871	37650871	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	43	470	1	ENST00000447079.4:c.2344del	p.Ile782SerfsTer8	p.I782Sfs*8	ENST00000447079	NM_015083.1	781	ttA/tt	5/14	0.255916318773678	3	FACETS	0.992	0.841	1	0.992	0.841	1	CLONAL	2	FALSE	1	0.255916318773678	3		471	191	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934559	9934560	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0009843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	19	455	0	ENST00000330684.3:c.1595dup	p.Ile533AsnfsTer9	p.I533Nfs*9	ENST00000330684	NM_001134407.1	532	gga/ggGa	7/13	0.255916318773678	3	FACETS	0.93	0.72	1	0.93	0.72	1	CLONAL	2	FALSE	1	0.255916318773678	3		455	90	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024001	27024002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0009870-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	26	86	0	ENST00000324856.7:c.1113dup	p.Gln372AlafsTer28	p.Q372Afs*28	ENST00000324856	NM_006015.4	369	-/G	1/20	0.23400710390462	1	FACETS	0.561	0.447	0.69	0.561	0.447	0.69	SUBCLONAL	1	TRUE	0	0.365660256452733	1		86	207	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009870-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	585	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.365660256452733	3	FACETS	0.949	0.914	0.984	1	0.997	1	CLONAL	3	TRUE	1	0.365660256452733	3		311	1329	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0009870-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	275	654	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.365660256452733	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.365660256452733	1		655	1189	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106649	27106649	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009870-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	165	362	0	ENST00000324856.7:c.6260G>A	p.Gly2087Glu	p.G2087E	ENST00000324856	NM_006015.4	2087	gGa/gAa	20/20	0.23400710390462	1	FACETS	0.909	0.836	0.986	0.909	0.836	0.986	CLONAL	1	TRUE	0	0.365660256452733	1		362	811	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971101	21971102	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGCGTCGTGCACGGGTCGGGTGAGAGTGGCGGGGTCGGCGCAGTTGGGCTCCGCGCCGTC	novel	NA	P-0009870-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	17	140	0	ENST00000304494.5:c.256_257insGACGGCGCGGAGCCCAACTGCGCCGACCCCGCCACTCTCACCCGACCCGTGCACGACGCTG	p.Ala86GlyfsTer54	p.A86Gfs*54	ENST00000304494	NM_000077.4	86	gcc/gGACGGCGCGGAGCCCAACTGCGCCGACCCCGCCACTCTCACCCGACCCGTGCACGACGCTGcc	2/3	0.365660256452733	1	FACETS	0.237	0.176	0.309	0.237	0.176	0.309	SUBCLONAL	1	TRUE	0	0.365660256452733	1		140	321	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs79184941	NA	P-0009933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	8	124	0	ENST00000358487.5:c.755C>T	p.Ser252Leu	p.S252L	ENST00000358487	NM_000141.4	252	tCg/tTg	7/18	1	2	FACETS	0.081	0.052	0.119	0.081	0.052	0.119	SUBCLONAL	1	TRUE	1	0.669840181158532	2		124	295	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115883	8115884	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0009933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	322	354	0	ENST00000346208.3:c.1231dup	p.His411ProfsTer96	p.H411Pfs*96	ENST00000346208		410	agc/agCc	6/6	1	2	FACETS	0.98	0.927	1	0.98	0.927	1	CLONAL	1	TRUE	1	0.669840181158532	2		354	981	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0009967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	140	442	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	NA	2	FACETS	0.833	0.757	0.913			1	INDETERMINATE	2	TRUE	NA	0.15	2		442	1120	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057936	27057937	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1415146710	NA	P-0009967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	90	362	0	ENST00000324856.7:c.1650dup	p.Tyr551LeufsTer72	p.Y551Lfs*72	ENST00000324856	NM_006015.4	548	-/C	3/20	0.142715811929755	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.15	1		362	984	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417823	32417823	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	90	345	2	ENST00000332351.3:c.1229T>C	p.Met410Thr	p.M410T	ENST00000332351	NM_024426.4	410	aTg/aCg	7/10	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.15	2		347	1131	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0009971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	95	455	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.318612727550185	1	FACETS	0.781	0.703	0.862	1	0.983	1	SUBCLONAL	2	TRUE	0	0.318612727550185	1		457	321	SUCCESS
APC	324	MSKCC	GRCh37	5	112175235	112175235	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	19	301	0	ENST00000257430.4:c.3944C>A	p.Ser1315Ter	p.S1315*	ENST00000257430	NM_000038.5	1315	tCa/tAa	16/16	1	2	FACETS	0.453	0.344	0.581	0.453	0.344	0.581	SUBCLONAL	1	TRUE	1	0.318612727550185	2		301	263	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920396	114920396	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	113	584	0	ENST00000543371.1:c.1337A>C	p.Lys446Thr	p.K446T	ENST00000543371	NM_001198531.1	446	aAg/aCg	13/14	0.24015663387849	3	FACETS	1	0.91	1	0.669	0.606	0.733	CLONAL	2	TRUE	0	0.318612727550185	3		584	410	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426657	212426657	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	71	434	0	ENST00000342788.4:c.2458C>A	p.Leu820Met	p.L820M	ENST00000342788	NM_005235.2	820	Ctg/Atg	20/28	0.209452265463764	4	FACETS	0.788	0.691	0.89	0.788	0.691	0.89	SUBCLONAL	2	TRUE	2	0.318612727550185	4		434	373	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026118	71026118	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	69	412	0	ENST00000318789.4:c.1504T>A	p.Phe502Ile	p.F502I	ENST00000318789	NM_032682.5	502	Ttc/Atc	17/21	0.219934953324657	3	FACETS	0.77	0.676	0.87	0.77	0.676	0.87	SUBCLONAL	2	TRUE	1	0.318612727550185	3		412	326	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576373	67576373	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	36	254	0	ENST00000274335.5:c.652G>T	p.Glu218Ter	p.E218*	ENST00000274335		218	Gaa/Taa	5/15	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.318612727550185	2		254	195	SUCCESS
APC	324	MSKCC	GRCh37	5	112111340	112111340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1305794169	NA	P-0009971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	41	262	1	ENST00000257430.4:c.437C>T	p.Ala146Val	p.A146V	ENST00000257430	NM_000038.5	146	gCt/gTt	5/16	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.318612727550185	2		263	194	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117680994	117680994	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	42	318	0	ENST00000368508.3:c.3626T>G	p.Leu1209Trp	p.L1209W	ENST00000368508	NM_002944.2	1209	tTg/tGg	23/43	NA	2	FACETS	0.747	0.625	0.881			1	INDETERMINATE	1	TRUE	NA	0.318612727550185	2		318	353	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861143	57861143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772799269	NA	P-0009971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	74	553	0	ENST00000228682.2:c.940C>T	p.Arg314Cys	p.R314C	ENST00000228682	NM_005269.2	314	Cgc/Tgc	9/12	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.318612727550185	2		553	390	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209268	133209268	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs765890291	NA	P-0009971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	99	508	1	ENST00000320574.5:c.6118G>T	p.Ala2040Ser	p.A2040S	ENST00000320574	NM_006231.2	2040	Gcg/Tcg	44/49	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.318612727550185	2		509	415	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457310	67457310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	139	435	0	ENST00000327367.4:c.284C>T	p.Pro95Leu	p.P95L	ENST00000327367	NM_005902.3	95	cCa/cTa	2/9	0.318612727550185	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	0	0.318612727550185	2		435	424	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551071	41551071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	37	613	0	ENST00000263253.7:c.3215C>T	p.Ser1072Phe	p.S1072F	ENST00000263253	NM_001429.3	1072	tCc/tTc	17/31	1	2	FACETS	0.712	0.589	0.85	0.712	0.589	0.85	SUBCLONAL	1	TRUE	1	0.318612727550185	2		613	326	SUCCESS
APC	324	MSKCC	GRCh37	5	112173607	112173607	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	65	407	0	ENST00000257430.4:c.2319del	p.Phe773LeufsTer4	p.F773Lfs*4	ENST00000257430	NM_000038.5	772	acT/ac	16/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.318612727550185	2		407	275	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725043	89725043	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0009971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	31	411	0	ENST00000371953.3:c.1027del		p.X343_splice	ENST00000371953	NM_000314.4	343			0.24015663387849	3	FACETS	0.664	0.537	0.806	0.221	0.179	0.269	SUBCLONAL	1	TRUE	0	0.318612727550185	3		411	340	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089625	27089626	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0009971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	36	479	0	ENST00000324856.7:c.2583dup	p.Ser862LeufsTer10	p.S862Lfs*10	ENST00000324856	NM_006015.4	861	gcc/gCcc	8/20	1	2	FACETS	0.758	0.626	0.906	0.758	0.626	0.906	CLONAL	1	TRUE	1	0.318612727550185	2		479	298	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027998	48027998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757653982	NA	P-0010020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	110	372	0	ENST00000234420.5:c.2876G>A	p.Arg959His	p.R959H	ENST00000234420	NM_000179.2	959	cGc/cAc	4/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.543224891825604	2		372	323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0010020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	210	654	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.473397626555527	1	FACETS	0.888	0.829	0.948	0.888	0.829	0.948	CLONAL	1	TRUE	0	0.543224891825604	1		655	634	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562482	21562483	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGGCG	rs550642106	NA	P-0010020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	10	55	1	ENST00000382592.4:c.1431_1436dup	p.Pro479_Ala480dup	p.P479_A480dup	ENST00000382592	NM_014572.2	479	ccg/ccCGCCCCg	4/8	0.543224891825604	3	FACETS	0.641	0.441	0.885	0.321	0.22	0.443	SUBCLONAL	1	TRUE	1	0.543224891825604	3		56	73	SUCCESS
APC	324	MSKCC	GRCh37	5	112175324	112175324	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1211642532	NA	P-0010020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	39	270	1	ENST00000257430.4:c.4033G>T	p.Glu1345Ter	p.E1345*	ENST00000257430	NM_000038.5	1345	Gaa/Taa	16/16	1	2	FACETS	0.507	0.422	0.601	0.507	0.422	0.601	SUBCLONAL	1	TRUE	1	0.543224891825604	2		271	283	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183272	56183272	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	88	290	0	ENST00000399503.3:c.4182G>T	p.Arg1394Ser	p.R1394S	ENST00000399503	NM_005921.1	1394	agG/agT	18/20	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.543224891825604	2		290	324	SUCCESS
APC	324	MSKCC	GRCh37	5	112174763	112174763	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs587779790	NA	P-0010020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	63	446	0	ENST00000257430.4:c.3472A>T	p.Arg1158Ter	p.R1158*	ENST00000257430	NM_000038.5	1158	Aga/Tga	16/16	1	2	FACETS	0.792	0.69	0.899	0.792	0.69	0.899	SUBCLONAL	1	TRUE	1	0.543224891825604	2		446	293	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509458	106509458	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	33	375	0	ENST00000359195.3:c.1452G>A	p.Met484Ile	p.M484I	ENST00000359195	NM_002649.2	484	atG/atA	2/11	0.270142267767727	2	FACETS	0.247	0.201	0.299	0.123	0.1	0.15	INDETERMINATE	1	TRUE	0	0.543224891825604	2		375	492	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971051	21971051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767642535	NA	P-0010020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	27	199	0	ENST00000304494.5:c.307C>T	p.Arg103Trp	p.R103W	ENST00000304494	NM_000077.4	103	Cgg/Tgg	2/3	0.254391060915881	3	FACETS	0.252	0.2	0.312	0.126	0.1	0.156	INDETERMINATE	1	TRUE	1	0.543224891825604	3		199	501	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445203	49445203	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs549710712	NA	P-0010020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	71	407	0	ENST00000301067.7:c.2263C>T	p.Arg755Trp	p.R755W	ENST00000301067	NM_003482.3	755	Cgg/Tgg	10/54	0.222323224456127	1	FACETS	0.448	0.392	0.508	0.448	0.392	0.508	INDETERMINATE	1	TRUE	0	0.543224891825604	1		407	425	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953781	48953781	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	42	319	0	ENST00000267163.4:c.1384A>G	p.Lys462Glu	p.K462E	ENST00000267163	NM_000321.2	462	Aaa/Gaa	14/27	0.543224891825604	3	FACETS	0.283	0.235	0.336	0.141	0.117	0.168	SUBCLONAL	1	TRUE	1	0.543224891825604	3		319	695	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528200	103528200	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	12	124	1	ENST00000355739.4:c.3508G>T	p.Gly1170Trp	p.G1170W	ENST00000355739	NM_000123.3	1170	Ggg/Tgg	15/15	0.543224891825604	3	FACETS	0.419	0.296	0.569	0.21	0.148	0.285	SUBCLONAL	1	TRUE	1	0.543224891825604	3		125	134	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217310	11217330	+	inframe_deletion	In_Frame_Del	DEL	CCACTCGTGCAGTTTCTCATA	CCACTCGTGCAGTTTCTCATA	-	novel	NA	P-0010020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	123	422	0	ENST00000361445.4:c.4348_4368del	p.Tyr1450_Trp1456del	p.Y1450_W1456del	ENST00000361445	NM_004958.3	1450	TATGAGAAACTGCACGAGTGG/-	30/58	1	2	FACETS	0.814	0.739	0.893	0.814	0.739	0.893	CLONAL	1	TRUE	1	0.543224891825604	2		422	556	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0010070-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	67	465	2	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	1	2	FACETS	0.846	0.733	0.968	0.846	0.733	0.968	CLONAL	1	TRUE	1	0.18	2		467	880	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141679	202141679	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010070-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	70	470	0	ENST00000358485.4:c.967C>A	p.His323Asn	p.H323N	ENST00000358485	NM_001080125.1	323	Cac/Aac	7/9	1	2	FACETS	0.842	0.732	0.961	0.842	0.732	0.961	CLONAL	1	TRUE	1	0.18	2		470	924	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226305	133226305	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010070-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	114	772	5	ENST00000320574.5:c.3753G>A	p.Trp1251Ter	p.W1251*	ENST00000320574	NM_006231.2	1251	tgG/tgA	30/49	1	2	FACETS	0.993	0.892	1	0.993	0.892	1	CLONAL	1	TRUE	1	0.18	2		777	1275	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929426	81929426	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1364308657	NA	P-0010070-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1502	146	903	1	ENST00000359376.3:c.1087G>A	p.Gly363Arg	p.G363R	ENST00000359376	NM_002661.3	363	Ggg/Agg	13/33	1	2	FACETS	0.984	0.895	1	0.984	0.895	1	CLONAL	1	TRUE	1	0.18	2		904	1648	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351431	89351431	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010070-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1440	122	939	0	ENST00000301030.4:c.1519C>A	p.Leu507Met	p.L507M	ENST00000301030	NM_001256183.1	507	Ctg/Atg	9/13	1	2	FACETS	0.868	0.781	0.96	0.868	0.781	0.96	CLONAL	1	TRUE	1	0.18	2		939	1562	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653185	29653185	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555533395	NA	P-0010070-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	65	395	0	ENST00000356175.3:c.5120C>T	p.Ala1707Val	p.A1707V	ENST00000356175	NM_000267.3	1707	gCt/gTt	36/57	1	2	FACETS	0.917	0.793	1	0.917	0.793	1	CLONAL	1	TRUE	1	0.18	2		395	788	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354088	15354088	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010070-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	25	203	0	ENST00000263377.2:c.2792A>G	p.Tyr931Cys	p.Y931C	ENST00000263377	NM_058243.2	931	tAc/tGc	14/20	1	2	FACETS	0.751	0.591	0.934	0.751	0.591	0.934	CLONAL	1	TRUE	1	0.18	2		203	370	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929280	44929280	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010070-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	137	519	0	ENST00000377967.4:c.2380A>C	p.Thr794Pro	p.T794P	ENST00000377967	NM_021140.2	794	Act/Cct	17/29	1	1	FACETS	0.8	0.727	0.876	1	0.988	1	SUBCLONAL	2	TRUE	0	0.18	1		519	866	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412156	63412156	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010070-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	164	664	1	ENST00000330258.3:c.1011G>T	p.Met337Ile	p.M337I	ENST00000330258	NM_152424.3	337	atG/atT	2/2	1	1	FACETS	0.791	0.725	0.86	1	0.989	1	SUBCLONAL	2	TRUE	0	0.18	1		665	1048	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412162	63412162	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010070-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	160	663	0	ENST00000330258.3:c.1005G>T	p.Gln335His	p.Q335H	ENST00000330258	NM_152424.3	335	caG/caT	2/2	1	1	FACETS	0.778	0.712	0.846	1	0.989	1	SUBCLONAL	2	TRUE	0	0.18	1		663	1040	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740727	58740727	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010070-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1659	147	1051	2	ENST00000305921.3:c.1636del	p.Leu546Ter	p.L546*	ENST00000305921	NM_003620.3	544	ggC/gg	6/6	1	2	FACETS	0.904	0.822	0.991	0.904	0.822	0.991	CLONAL	1	TRUE	1	0.18	2		1053	1806	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78811748	78811751	+	frameshift_variant	Frame_Shift_Del	DEL	TCTG	TCTG	-	novel	NA	P-0010070-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	81	581	0	ENST00000306801.3:c.1170_1173del	p.Gln392CysfsTer21	p.Q392Cfs*21	ENST00000306801	NM_020761.2	388	aTCTGt/at	10/34	1	2	FACETS	0.767	0.674	0.868	0.767	0.674	0.868	SUBCLONAL	1	TRUE	1	0.18	2		581	1173	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597361	52597380	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGAAGGAGGTTCAATGACC	GAGAAGGAGGTTCAATGACC	A	novel	NA	P-0010070-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1212	93	834	0	ENST00000394830.3:c.3930_3930+19delinsT		p.X1310_splice	ENST00000394830	NM_018313.4	1310		25/30	1	2	FACETS	0.792	0.702	0.889	0.792	0.702	0.889	SUBCLONAL	1	TRUE	1	0.18	2		834	1305	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0010080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	47	124	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.895	0.76	1	0.895	0.76	1	CLONAL	1	TRUE	1	0.376430819354998	2		124	279	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070577	67070578	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	212	645	1	ENST00000412916.2:c.207dup	p.Pro70SerfsTer13	p.P70Sfs*13	ENST00000412916		67	-/T	3/6	0.376430819354998	1	FACETS	0.947	0.88	1	0.947	0.88	1	CLONAL	1	TRUE	0	0.376430819354998	1		646	966	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56409166	56409166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201811923	NA	P-0010080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	234	739	0	ENST00000348428.3:c.1673G>A	p.Arg558Lys	p.R558K	ENST00000348428	NM_006785.3	558	aGa/aAa	14/17	1	2	FACETS	0.906	0.843	0.971	0.906	0.843	0.971	CLONAL	1	TRUE	1	0.376430819354998	2		739	1372	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624267	89624270	+	frameshift_variant	Frame_Shift_Del	DEL	GGAG	GGAG	-	novel	NA	P-0010080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	59	220	0	ENST00000371953.3:c.41_44del	p.Arg14AsnfsTer9	p.R14Nfs*9	ENST00000371953	NM_000314.4	14	aGGAGa/aa	1/9	1	2	FACETS	0.784	0.677	0.899	0.784	0.677	0.899	SUBCLONAL	1	TRUE	1	0.376430819354998	2		220	400	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0010130-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	126	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.813	0.739	0.89	0.813	0.739	0.89	CLONAL	1	TRUE	1	0.555785185714983	2		311	558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0010130-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	373	485	1	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.535711514578288	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.555785185714983	1		486	960	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954210	48954210	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1354030520	NA	P-0010130-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	64	240	0	ENST00000267163.4:c.1411C>T	p.Gln471Ter	p.Q471*	ENST00000267163	NM_000321.2	471	Caa/Taa	15/27	0.553972884376638	1	FACETS	0.554	0.484	0.629	0.554	0.484	0.629	SUBCLONAL	1	TRUE	0	0.555785185714983	1		240	300	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010130-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	111	399	1	ENST00000263967.3:c.3012G>A	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atA	21/21	0.535711514578288	1	FACETS	0.864	0.785	0.944	0.864	0.785	0.944	CLONAL	1	TRUE	0	0.555785185714983	1		400	334	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145430	58145430	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894340	NA	P-0010130-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	302	351	0	ENST00000257904.6:c.71G>T	p.Arg24Leu	p.R24L	ENST00000257904	NM_000075.3	24	cGt/cTt	2/8	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.555785185714983	2		351	1056	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162747	47162747	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010130-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	73	289	0	ENST00000409792.3:c.3379C>G	p.Gln1127Glu	p.Q1127E	ENST00000409792	NM_014159.6	1127	Caa/Gaa	3/21	0.535711514578288	1	FACETS	0.862	0.767	0.962	0.862	0.767	0.962	CLONAL	1	TRUE	0	0.555785185714983	1		289	220	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72842091	72842091	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010130-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	171	256	0	ENST00000325599.8:c.1157A>G	p.Tyr386Cys	p.Y386C	ENST00000325599	NM_018130.2	386	tAc/tGc	10/11	NA	2	FACETS	0.85	0.784	0.918			1	INDETERMINATE	1	TRUE	NA	0.555785185714983	2		256	724	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168743	32168743	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010130-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	2509	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	0.998	1	1	0.998	1	CLONAL	5	TRUE	0	0.555785185714983	5		553	3191	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469983	157469983	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010130-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	220	303	0	ENST00000346085.5:c.2777A>T	p.Gln926Leu	p.Q926L	ENST00000346085	NM_020732.3	926	cAg/cTg	9/20	0.125285524625805	3	FACETS	1	0.986	1	0.607	0.565	0.649	INDETERMINATE	1	TRUE	1	0.555785185714983	3		303	834	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590642	95590642	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010130-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	251	594	0	ENST00000393063.1:c.1267G>C	p.Glu423Gln	p.E423Q	ENST00000393063	NM_030621.3	423	Gaa/Caa	9/28	1	2	FACETS	0.846	0.791	0.902	0.846	0.791	0.902	CLONAL	1	TRUE	1	0.555785185714983	2		594	1068	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662454	67662454	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010130-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	248	405	0	ENST00000264010.4:c.1700G>C	p.Arg567Pro	p.R567P	ENST00000264010	NM_006565.3	567	cGg/cCg	9/12	0.125285524625805	3	FACETS	0.999	0.933	1	0.499	0.466	0.533	INDETERMINATE	1	TRUE	1	0.555785185714983	3		405	1142	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991365	72991365	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010130-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1403	625	797	1	ENST00000268489.5:c.2680G>T	p.Asp894Tyr	p.D894Y	ENST00000268489	NM_006885.3	894	Gat/Tat	2/10	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.555785185714983	2		798	2028	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511517	38511517	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1416311365	NA	P-0010130-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	236	286	0	ENST00000254066.5:c.1015C>T	p.Arg339Cys	p.R339C	ENST00000254066	NM_000964.3	339	Cgc/Tgc	8/9	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.555785185714983	2		286	797	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2214500	2214500	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010130-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	337	444	0	ENST00000398665.3:c.1828G>T	p.Asp610Tyr	p.D610Y	ENST00000398665	NM_032482.2	610	Gac/Tac	19/28	1	2	FACETS	0.982	0.928	1	0.982	0.928	1	CLONAL	1	TRUE	1	0.555785185714983	2		444	1235	SUCCESS
AR	367	MSKCC	GRCh37	X	66766439	66766439	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010130-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	213	245	0	ENST00000374690.3:c.1451C>A	p.Thr484Asn	p.T484N	ENST00000374690	NM_000044.3	484	aCt/aAt	1/8	0.384136440757541	1	FACETS	0.841	0.786	0.898	0.841	0.786	0.898	CLONAL	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-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	95	409	0	ENST00000373344.5:c.6861G>T	p.Met2287Ile	p.M2287I	ENST00000373344	NM_000489.3	2287	atG/atT	32/35	0.384136440757541	1	FACETS	0.627	0.562	0.695	0.627	0.562	0.695	SUBCLONAL	1	TRUE	0	0.555785185714983	1		409	394	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872017	35872019	+	inframe_deletion	In_Frame_Del	DEL	ACG	ACG	-	novel	NA	P-0010130-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1640	534	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	0.884	0.845	0.924	0.884	0.845	0.924	CLONAL	1	TRUE	1	0.555785185714983	2		741	2174	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030513	47030513	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010130-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1287	496	615	0	ENST00000377604.3:c.292del	p.Arg98GlufsTer36	p.R98Efs*36	ENST00000377604	NM_001204468.1	96	ttC/tt	4/24	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.555785185714983	2		615	1783	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416591	29416591	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010130-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	237	372	0	ENST00000389048.3:c.4362G>C	p.Lys1454Asn	p.K1454N	ENST00000389048	NM_004304.4	1454	aaG/aaC	29/29	1	2	FACETS	0.915	0.855	0.977	0.915	0.855	0.977	CLONAL	1	TRUE	1	0.555785185714983	2		372	932	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500810	8500810	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010130-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	82	335	0	ENST00000356435.5:c.2072C>A	p.Thr691Lys	p.T691K	ENST00000356435		691	aCa/aAa	13/35	0.555785185714983	1	FACETS	0.618	0.549	0.69	0.618	0.549	0.69	SUBCLONAL	1	TRUE	0	0.555785185714983	1		335	345	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56474103	56474103	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010130-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	420	498	0	ENST00000267101.3:c.19C>G	p.Leu7Val	p.L7V	ENST00000267101	NM_001982.3	7	Ctg/Gtg	1/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.555785185714983	2		498	1427	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858369	9858369	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010130-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	124	272	0	ENST00000330684.3:c.3032G>T	p.Arg1011Leu	p.R1011L	ENST00000330684	NM_001134407.1	1011	cGg/cTg	13/13	0.125285524625805	3	FACETS	1	0.962	1	0.555	0.504	0.607	INDETERMINATE	1	TRUE	1	0.555785185714983	3		272	514	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581219	48581219	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010130-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	144	447	1	ENST00000342988.3:c.523G>T	p.Glu175Ter	p.E175*	ENST00000342988	NM_005359.5	175	Gaa/Taa	5/12	0.555785185714983	1	FACETS	0.864	0.795	0.935	0.864	0.795	0.935	CLONAL	1	TRUE	0	0.555785185714983	1		448	433	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209106724	209106725	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010130-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	193	424	0	ENST00000345146.2:c.843_844insT	p.Ala282CysfsTer66	p.A282Cfs*66	ENST00000345146	NM_005896.2	281	-/T	7/10	1	2	FACETS	0.802	0.743	0.863	0.802	0.743	0.863	CLONAL	1	TRUE	1	0.555785185714983	2		424	866	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0010139-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	175	1035	1	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	0.570649353034994	2		1036	594	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0010139-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	247	352	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.443386101698796	4	FACETS	0.931	0.881	0.98			1	CLONAL	3	TRUE	NA	0.570649353034994	4		352	487	SUCCESS
APC	324	MSKCC	GRCh37	5	112175650	112175651	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010139-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	101	689	0	ENST00000257430.4:c.4364dup	p.Asn1455LysfsTer2	p.N1455Kfs*2	ENST00000257430	NM_000038.5	1453	-/A	16/16	0.570649353034994	1	FACETS	0.951	0.864	1	0.951	0.864	1	CLONAL	1	TRUE	0	0.570649353034994	1		689	266	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249510	153249510	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1157879635	NA	P-0010139-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	74	490	0	ENST00000281708.4:c.1268G>T	p.Gly423Val	p.G423V	ENST00000281708	NM_033632.3	423	gGa/gTa	9/12	0.135956932451965	0	FACETS	0.388	0.343	0.435			1	INDETERMINATE	1	TRUE	0	0.570649353034994	0		490	287	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828881	26828881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010139-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	334	516	2	ENST00000381527.3:c.103G>A	p.Val35Ile	p.V35I	ENST00000381527	NM_001260.1	35	Gtc/Atc	1/13	1	2	FACETS	0.951	0.899	1	0.951	0.899	1	CLONAL	1	TRUE	1	0.570649353034994	2		518	1231	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591901	48591901	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010139-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	182	725	0	ENST00000342988.3:c.1064A>G	p.Asp355Gly	p.D355G	ENST00000342988	NM_005359.5	355	gAc/gGc	9/12	0.570649353034994	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.570649353034994	1		725	441	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714657	52714657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010139-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	363	567	0	ENST00000322088.6:c.415G>A	p.Asp139Asn	p.D139N	ENST00000322088	NM_014225.5	139	Gac/Aac	4/15	1	2	FACETS	0.9	0.852	0.949	0.9	0.852	0.949	CLONAL	1	TRUE	1	0.570649353034994	2		567	1414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578283	7578284	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0010139-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	296	575	0	ENST00000269305.4:c.565dup	p.Ala189GlyfsTer20	p.A189Gfs*20	ENST00000269305	NM_001126112.2	189	gcc/gGcc	6/11	0.564751734289693	1	FACETS	0.875	0.827	0.925	0.875	0.827	0.925	CLONAL	1	TRUE	0	0.570649353034994	1		575	847	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	145	596	1	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.886	0.809	0.968	1	0.992	1	CLONAL	3	TRUE	1	0.122668914827043	2		597	889	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	102	338	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.84	0.752	0.933	1	0.989	1	CLONAL	3	TRUE	1	0.122668914827043	2		338	660	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	106	764	2	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	0.87	0.779	0.968	1	0.985	1	CLONAL	2	TRUE	1	0.122668914827043	2		766	993	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	108	621	1	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.973	0.872	1	1	0.987	1	CLONAL	2	TRUE	1	0.122668914827043	2		622	905	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429978	78429978	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	82	483	3	ENST00000370768.2:c.901del	p.Ile301TyrfsTer22	p.I301Yfs*22	ENST00000370768	NM_003902.3	301	Ata/ta	11/20	1	2	FACETS	0.889	0.783	1	1	0.982	1	CLONAL	2	TRUE	1	0.122668914827043	2		486	752	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760967	59760967	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	112	602	4	ENST00000259008.2:c.3440del	p.Asn1147MetfsTer3	p.N1147Mfs*3	ENST00000259008	NM_032043.2	1147	aAt/at	20/20	1	2	FACETS	0.963	0.865	1	1	0.988	1	CLONAL	2	TRUE	1	0.122668914827043	2		606	948	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	54	263	0	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	0.122668914827043	1	FACETS	0.82	0.701	0.95	1	0.97	1	CLONAL	2	TRUE	0	0.122668914827043	1		263	504	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856093	68856093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121964878	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	108	512	0	ENST00000261769.5:c.1901C>T	p.Ala634Val	p.A634V	ENST00000261769	NM_004360.3	634	gCg/gTg	12/16	1	2	FACETS	1	0.969	1	1	0.989	1	CLONAL	2	TRUE	1	0.122668914827043	2		512	729	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106861	27106861	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	78	380	0	ENST00000324856.7:c.6472C>T	p.Arg2158Ter	p.R2158*	ENST00000324856	NM_006015.4	2158	Cga/Tga	20/20	1	2	FACETS	0.851	0.75	0.959	1	0.986	1	CLONAL	3	TRUE	1	0.122668914827043	2		380	498	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120326	94120326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370195460	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	116	693	0	ENST00000369303.4:c.725C>T	p.Ala242Val	p.A242V	ENST00000369303	NM_004440.3	242	gCg/gTg	3/17	0.0891322339450952	0	FACETS	1	0.937	1			1	CLONAL	2	TRUE	0	0.122668914827043	0		693	788	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003784	+	frameshift_variant	Frame_Shift_Del	DEL	CTCT	CTCT	-	novel	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	65	286	0	ENST00000558401.1:c.41_44del	p.Ser14PhefsTer29	p.S14Ffs*29	ENST00000558401	NM_004048.2	13	CTCTct/ct	1/4	0.122668914827043	0	FACETS	0.892	0.775	1			1	CLONAL	2	TRUE	0	0.122668914827043	0		286	521	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430202	181430202	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	20	144	0	ENST00000325404.1:c.59del	p.Gly20AlafsTer26	p.G20Afs*26	ENST00000325404	NM_003106.3	18	tcG/tc	1/1	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.122668914827043	2		144	225	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494309	2494309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780202836	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	67	495	0	ENST00000355716.4:c.700G>A	p.Val234Ile	p.V234I	ENST00000355716	NM_003820.2	234	Gta/Ata	7/8	1	2	FACETS	0.898	0.781	1	1	0.978	1	CLONAL	2	TRUE	1	0.122668914827043	2		495	608	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321324	65321324	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	90	475	1	ENST00000342505.4:c.1516C>A	p.Arg506Ser	p.R506S	ENST00000342505	NM_002227.2	506	Cgc/Agc	11/25	1	2	FACETS	1	0.897	1	1	0.985	1	CLONAL	2	TRUE	1	0.122668914827043	2		476	725	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256439	115256439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774832953	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	86	509	4	ENST00000369535.4:c.272C>T	p.Ala91Val	p.A91V	ENST00000369535	NM_002524.4	91	gCg/gTg	3/7	1	2	FACETS	0.864	0.764	0.972	1	0.982	1	CLONAL	2	TRUE	1	0.122668914827043	2		513	811	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026033	48026033	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1481054050	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	74	527	0	ENST00000234420.5:c.911T>C	p.Val304Ala	p.V304A	ENST00000234420	NM_000179.2	304	gTg/gCg	4/10	1	2	FACETS	0.841	0.736	0.955	1	0.978	1	CLONAL	2	TRUE	1	0.122668914827043	2		527	717	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265030	198265030	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	91	439	0	ENST00000335508.6:c.2847A>T	p.Gln949His	p.Q949H	ENST00000335508	NM_012433.2	949	caA/caT	19/25	1	2	FACETS	0.972	0.863	1	1	0.985	1	CLONAL	2	TRUE	1	0.122668914827043	2		439	763	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947116	178947116	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	85	457	0	ENST00000263967.3:c.2552T>C	p.Val851Ala	p.V851A	ENST00000263967	NM_006218.2	851	gTg/gCg	18/21	1	2	FACETS	1	0.917	1	1	0.985	1	CLONAL	2	TRUE	1	0.122668914827043	2		457	663	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161175	56161175	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	97	470	0	ENST00000399503.3:c.1044C>A	p.Ser348Arg	p.S348R	ENST00000399503	NM_005921.1	348	agC/agA	5/20	1	2	FACETS	0.941	0.838	1	1	0.985	1	CLONAL	2	TRUE	1	0.122668914827043	2		470	840	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522260	157522260	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	82	473	0	ENST00000346085.5:c.4532A>G	p.Gln1511Arg	p.Q1511R	ENST00000346085	NM_020732.3	1511	cAg/cGg	18/20	1	2	FACETS	1	0.927	1	1	0.985	1	CLONAL	2	TRUE	1	0.122668914827043	2		473	625	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625348	69625348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1156753470	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	126	555	0	ENST00000334134.2:c.445G>A	p.Ala149Thr	p.A149T	ENST00000334134	NM_005247.2	149	Gcc/Acc	3/3	1	2	FACETS	1	0.917	1	1	0.992	1	CLONAL	3	TRUE	1	0.122668914827043	2		555	677	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118391600	118391600	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	57	269	0	ENST00000534358.1:c.11513G>T	p.Arg3838Met	p.R3838M	ENST00000534358	NM_005933.3	3838	aGg/aTg	34/36	1	2	FACETS	0.911	0.782	1	1	0.975	1	CLONAL	2	TRUE	1	0.122668914827043	2		269	510	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416834	416834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773306710	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	108	536	0	ENST00000399788.2:c.3716G>A	p.Arg1239Gln	p.R1239Q	ENST00000399788	NM_001042603.1	1239	cGg/cAg	23/28	NA	2	FACETS	1	0.963	1			1	INDETERMINATE	2	TRUE	NA	0.122668914827043	2		536	760	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541651	120541651	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752816549	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	143	700	0	ENST00000229340.5:c.206G>A	p.Arg69His	p.R69H	ENST00000229340	NM_006861.6	69	cGc/cAc	3/6	1	2	FACETS	1	0.971	1	1	0.992	1	CLONAL	2	TRUE	1	0.122668914827043	2		700	1007	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986509	36986509	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	65	535	0	ENST00000354822.5:c.1180A>G	p.Thr394Ala	p.T394A	ENST00000354822	NM_001079668.2	394	Acc/Gcc	3/3	1	2	FACETS	0.873	0.757	0.999	1	0.977	1	CLONAL	2	TRUE	1	0.122668914827043	2		535	607	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129432	30129432	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	120	654	0	ENST00000263025.4:c.596G>A	p.Gly199Asp	p.G199D	ENST00000263025	NM_002746.2	199	gGc/gAc	4/9	1	2	FACETS	1	0.94	1	1	0.989	1	CLONAL	2	TRUE	1	0.122668914827043	2		654	925	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991889	72991889	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	116	764	0	ENST00000268489.5:c.2156A>G	p.Tyr719Cys	p.Y719C	ENST00000268489	NM_006885.3	719	tAc/tGc	2/10	1	2	FACETS	0.982	0.884	1	1	0.988	1	CLONAL	2	TRUE	1	0.122668914827043	2		764	963	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16052769	16052769	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	87	619	0	ENST00000268712.3:c.905A>G	p.Gln302Arg	p.Q302R	ENST00000268712	NM_006311.3	302	cAa/cGa	9/46	1	2	FACETS	0.973	0.861	1	1	0.984	1	CLONAL	2	TRUE	1	0.122668914827043	2		619	729	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508652	38508652	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	110	601	0	ENST00000254066.5:c.700A>G	p.Lys234Glu	p.K234E	ENST00000254066	NM_000964.3	234	Aag/Gag	6/9	1	2	FACETS	1	0.959	1	1	0.989	1	CLONAL	2	TRUE	1	0.122668914827043	2		601	791	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533131	63533131	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	84	493	4	ENST00000307078.5:c.1763C>A	p.Pro588Gln	p.P588Q	ENST00000307078	NM_004655.3	588	cCg/cAg	7/11	1	2	FACETS	1	0.963	1	1	0.987	1	CLONAL	2	TRUE	1	0.122668914827043	2		497	561	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212403	5212403	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs558410776	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	94	541	3	ENST00000357368.4:c.4714C>T	p.Arg1572Trp	p.R1572W	ENST00000357368	NM_002850.3	1572	Cgg/Tgg	31/38	0.122668914827043	3	FACETS	1	0.965	1	0.806	0.717	0.9	CLONAL	2	TRUE	0	0.122668914827043	3		544	673	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988409	36988409	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	13	112	0	ENST00000354822.5:c.244del	p.Ala82ProfsTer19	p.A82Pfs*19	ENST00000354822	NM_001079668.2	82	Gcc/cc	2/3	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.122668914827043	2		112	146	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143052	30143052	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1244823020	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	97	538	0	ENST00000389048.3:c.474del	p.Glu160ArgfsTer26	p.E160Rfs*26	ENST00000389048	NM_004304.4	158	ccC/cc	1/29	0.122668914827043	1	FACETS	1	0.957	1	1	0.988	1	CLONAL	2	TRUE	0	0.122668914827043	1		538	649	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673759	176673759	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	127	438	1	ENST00000439151.2:c.4463del	p.Asn1488MetfsTer15	p.N1488Mfs*15	ENST00000439151	NM_022455.4	1487	Aaa/aa	10/23	1	2	FACETS	1	0.971	1	1	0.991	1	CLONAL	2	TRUE	1	0.122668914827043	2		439	877	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933013	39933013	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	110	281	0	ENST00000378444.4:c.1586del	p.Asn529ThrfsTer60	p.N529Tfs*60	ENST00000378444	NM_001123385.1	529	aAc/ac	4/15	1	1	FACETS	0.905	0.821	0.992	1	0.992	1	CLONAL	5	TRUE	0	0.122668914827043	1		281	372	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217705	7217707	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs757139280	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	161	690	0	ENST00000380728.2:c.220_222del	p.Glu74del	p.E74del	ENST00000380728		74	GAG/-	4/11	1	2	FACETS	1	0.97	1	1	0.992	1	CLONAL	2	TRUE	1	0.122668914827043	2		690	1164	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360589	70360594	+	inframe_deletion	In_Frame_Del	DEL	AGCAGC	AGCAGC	-	rs769857818	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	44	234	0	ENST00000374080.3:c.6162_6167del	p.Gln2075_Gln2076del	p.Q2075_Q2076del	ENST00000374080		2050	gAGCAGCag/gag	42/45	0.122668914827043	0	FACETS	0.983	0.828	1			1	CLONAL	2	TRUE	NA	0.122668914827043	0		234	320	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271233	153271234	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	86	495	0	ENST00000281708.4:c.544dup	p.Ser182PhefsTer74	p.S182Ffs*74	ENST00000281708	NM_033632.3	182	tct/tTct	3/12	1	2	FACETS	0.892	0.788	1	1	0.983	1	CLONAL	2	TRUE	1	0.122668914827043	2		495	786	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	608	697	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.545607981099099	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.571718570117936	3		697	829	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295684	212295684	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	113	480	0	ENST00000342788.4:c.2629G>T	p.Ala877Ser	p.A877S	ENST00000342788	NM_005235.2	877	Gct/Tct	21/28	0.565102905311317	2	FACETS	0.66	0.595	0.728	0.33	0.297	0.364	SUBCLONAL	1	TRUE	0	0.571718570117936	2		480	599	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876425	35876425	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	68	437	0	ENST00000303115.3:c.1217T>G	p.Leu406Arg	p.L406R	ENST00000303115	NM_002185.3	406	cTt/cGt	8/8	0.571718570117936	6	FACETS	0.628	0.545	0.718	0.157	0.136	0.18	SUBCLONAL	1	TRUE	2	0.571718570117936	6		437	812	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340112	116340112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs780802614	NA	P-0010213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	122	396	0	ENST00000397752.3:c.974C>A	p.Pro325His	p.P325H	ENST00000397752	NM_000245.2	325	cCt/cAt	2/21	0.283344858025081	5	FACETS	1	0.981	1	0.444	0.402	0.488	INDETERMINATE	1	TRUE	2	0.571718570117936	5		396	595	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376011	118376011	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	147	645	1	ENST00000534358.1:c.9404C>T	p.Thr3135Ile	p.T3135I	ENST00000534358	NM_005933.3	3135	aCc/aTc	27/36	0.571718570117936	3	FACETS	0.888	0.812	0.967	0.444	0.406	0.484	CLONAL	1	TRUE	1	0.571718570117936	3		646	745	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037492	12037492	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	118	385	0	ENST00000396373.4:c.1123G>T	p.Gly375Ter	p.G375*	ENST00000396373	NM_001987.4	375	Gga/Tga	6/8	0.571718570117936	4	FACETS	0.968	0.875	1	0.242	0.218	0.267	CLONAL	1	TRUE	0	0.571718570117936	4		385	670	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623545	28623545	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	84	426	1	ENST00000241453.7:c.1012C>A	p.Gln338Lys	p.Q338K	ENST00000241453	NM_004119.2	338	Caa/Aaa	8/24	1	2	FACETS	0.744	0.661	0.832	0.744	0.661	0.832	SUBCLONAL	1	TRUE	1	0.571718570117936	2		427	395	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28979946	28979946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764045713	NA	P-0010213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	158	608	2	ENST00000282397.4:c.1522C>T	p.Arg508Cys	p.R508C	ENST00000282397	NM_002019.4	508	Cgc/Tgc	11/30	1	2	FACETS	0.84	0.772	0.91	0.84	0.772	0.91	CLONAL	1	TRUE	1	0.571718570117936	2		610	658	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352598	68352598	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	197	534	0	ENST00000487270.1:c.465A>G	p.Ile155Met	p.I155M	ENST00000487270	NM_133509.3	155	atA/atG	6/11	0.508739480092731	3	FACETS	0.966	0.895	1	0.483	0.447	0.52	CLONAL	1	TRUE	1	0.571718570117936	3		534	917	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645955	67645955	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	67	484	0	ENST00000264010.4:c.883A>C	p.Lys295Gln	p.K295Q	ENST00000264010	NM_006565.3	295	Aag/Cag	4/12	1	2	FACETS	0.373	0.323	0.426	0.373	0.323	0.426	SUBCLONAL	1	TRUE	1	0.571718570117936	2		484	629	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993600	72993600	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	120	629	0	ENST00000268489.5:c.445C>T	p.Gln149Ter	p.Q149*	ENST00000268489	NM_006885.3	149	Cag/Tag	2/10	1	2	FACETS	0.857	0.778	0.939	0.857	0.778	0.939	CLONAL	1	TRUE	1	0.571718570117936	2		629	490	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561237	9561237	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148001479	NA	P-0010213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	96	507	0	ENST00000353224.5:c.545A>G	p.Tyr182Cys	p.Y182C	ENST00000353224	NM_177990.2	182	tAt/tGt	4/10	0.344350683649003	4	FACETS	0.84	0.75	0.937	0.42	0.375	0.469	CLONAL	1	TRUE	2	0.571718570117936	4		507	628	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376659	31376659	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0010213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	76	428	0	ENST00000328111.2:c.655-1G>T		p.X219_splice	ENST00000328111	NM_006892.3	219			0.276493023550627	2	FACETS	0.6	0.528	0.677	0.3	0.264	0.339	INDETERMINATE	1	TRUE	0	0.571718570117936	2		428	443	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740174	162740174	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	305	555	1	ENST00000367921.3:c.1377del	p.Ser460HisfsTer28	p.S460Hfs*28	ENST00000367921	NM_006182.2	459	tCc/tc	12/18	0.277493698192062	4	FACETS	1	0.99	1	1	0.99	1	INDETERMINATE	2	TRUE	2	0.571718570117936	4		556	710	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937163	39937164	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0010213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	117	616	0	ENST00000378444.4:c.19dup	p.Leu7ProfsTer29	p.L7Pfs*29	ENST00000378444	NM_001123385.1	7	ctg/cCtg	2/15	NA	2	FACETS	0.928	0.843	1			1	INDETERMINATE	1	TRUE	NA	0.571718570117936	2		616	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579463	7579463	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	267	423	0	ENST00000269305.4:c.224del	p.Pro75LeufsTer48	p.P75Lfs*48	ENST00000269305	NM_001126112.2	75	cCt/ct	4/11	0.540149116306087	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	0	0.571718570117936	3		423	392	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0010216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	83	480	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	0.265783007962268	2	FACETS	0.561	0.498	0.628	0.281	0.249	0.314	INDETERMINATE	1	TRUE	0	0.716345677388003	2		480	413	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799584	72799584	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	28	589	0	ENST00000325599.8:c.1585T>A	p.Ser529Thr	p.S529T	ENST00000325599	NM_018130.2	529	Tcc/Acc	11/11	0.251218306904089	2	FACETS	1	0.835	1	1	0.835	1	CLONAL	2	TRUE	0	0.253196927579445	2		589	108	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198297	138198297	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	21	551	2	ENST00000237289.4:c.890A>T	p.Glu297Val	p.E297V	ENST00000237289	NM_001270507.1	297	gAg/gTg	6/9	0.182666026410331	3	FACETS	1	0.896	1	0.649	0.505	0.813	CLONAL	1	TRUE	1	0.253196927579445	3		553	144	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526672	106526672	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	19	541	0	ENST00000359195.3:c.2965C>G	p.Pro989Ala	p.P989A	ENST00000359195	NM_002649.2	989	Cct/Gct	10/11	1	2	FACETS	1	0.804	1	1	0.804	1	CLONAL	1	TRUE	1	0.253196927579445	2		541	142	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2125821	2125821	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	35	668	0	ENST00000219476.3:c.2567T>A	p.Leu856His	p.L856H	ENST00000219476	NM_000548.3	856	cTc/cAc	23/42	1	2	FACETS	0.878	0.722	1	0.878	0.722	1	CLONAL	1	TRUE	1	0.253196927579445	2		668	315	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188243	10188244	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0010242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	37	617	0	ENST00000256474.2:c.388dup	p.Val130GlyfsTer2	p.V130Gfs*2	ENST00000256474	NM_000551.3	129	ctg/ctGg	2/3	0.251218306904089	2	FACETS	0.913	0.764	1	0.913	0.764	1	CLONAL	2	TRUE	0	0.253196927579445	2		617	160	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197700	66197700	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010251-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	32	434	0	ENST00000273854.3:c.2999T>A	p.Val1000Glu	p.V1000E	ENST00000273854	NM_004439.5	1000	gTg/gAg	17/18	0.151284248797082	3	FACETS	0.439	0.355	0.533			1	INDETERMINATE	1	TRUE	NA	0.32352864246991	3		434	524	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375921	118375921	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010251-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	108	604	0	ENST00000534358.1:c.9314T>C	p.Ile3105Thr	p.I3105T	ENST00000534358	NM_005933.3	3105	aTc/aCc	27/36	0.165264085070894	5	FACETS	1	0.943	1	0.36	0.322	0.4	INDETERMINATE	1	TRUE	2	0.32352864246991	5		604	919	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32968903	32968905	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	novel	NA	P-0010251-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	113	634	0	ENST00000380152.3:c.9334_9336del	p.Asp3112del	p.D3112del	ENST00000380152		3112	GAC/-	25/27	0.32352864246991	3	FACETS	1	0.922	1	0.514	0.463	0.569	CLONAL	1	TRUE	1	0.32352864246991	3		634	789	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440279	52440280	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0010251-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	305	508	0	ENST00000460680.1:c.772dup	p.Ala258GlyfsTer26	p.A258Gfs*26	ENST00000460680	NM_004656.3	258	gct/gGct	9/17	0.311760186690719	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.32352864246991	2		508	870	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0010268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	269	378	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.911	0.861	0.962	0.911	0.861	0.962	CLONAL	1	TRUE	1	0.901366332320635	2		378	655	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	327	293	0	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.901366332320635	2		293	681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0010268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	544	272	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.874762524594881	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.901366332320635	1		272	652	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541541	187541541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs980333559	NA	P-0010268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	240	361	0	ENST00000441802.2:c.6199G>A	p.Val2067Met	p.V2067M	ENST00000441802	NM_005245.3	2067	Gtg/Atg	10/27	0.458706389015117	1	FACETS	0.348	0.325	0.371	0.348	0.325	0.371	INDETERMINATE	1	TRUE	0	0.901366332320635	1		361	841	SUCCESS
APC	324	MSKCC	GRCh37	5	112170864	112170864	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0010268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	357	332	0	ENST00000257430.4:c.1958+2T>C		p.X653_splice	ENST00000257430	NM_000038.5	653			1	2	FACETS	0.82	0.779	0.861	0.82	0.779	0.861	CLONAL	1	TRUE	1	0.901366332320635	2		332	966	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99460065	99460065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1223585393	NA	P-0010268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	508	332	1	ENST00000268035.6:c.2161G>A	p.Val721Ile	p.V721I	ENST00000268035	NM_000875.3	721	Gtc/Atc	10/21	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.901366332320635	2		333	1126	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794730	42794730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143090600	NA	P-0010268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	101	206	0	ENST00000575354.2:c.1810G>A	p.Glu604Lys	p.E604K	ENST00000575354	NM_015125.3	604	Gaa/Aaa	10/20	0.496913200989957	3	FACETS	0.341	0.304	0.381	0.114	0.101	0.127	INDETERMINATE	1	TRUE	0	0.901366332320635	3		206	952	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731419	47731419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	41	25	0	ENST00000449228.1:c.373G>A	p.Gly125Arg	p.G125R	ENST00000449228	NM_001127240.2	125	Gga/Aga	2/4	0.496913200989957	3	FACETS	1	0.938	1	0.396	0.339	0.456	INDETERMINATE	1	TRUE	0	0.901366332320635	3		25	111	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939921	76939922	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGTCCAACAAAGGCTCTGGGTGACGAATGT	novel	NA	P-0010268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	335	288	0	ENST00000373344.5:c.826_827insACATTCGTCACCCAGAGCCTTTGTTGGACT	p.Asp275_Leu276insTyrIleArgHisProGluProLeuLeuAsp	p.D275_L276insYIRHPEPLLD	ENST00000373344	NM_000489.3	276	ttg/tACATTCGTCACCCAGAGCCTTTGTTGGACTtg	9/35	0.766031260620307	2	FACETS	0.685	0.648	0.723			1	SUBCLONAL	1	TRUE	NA	0.901366332320635	2		288	1085	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534433	187534434	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	165	321	0	ENST00000441802.2:c.9292dup	p.Arg3098LysfsTer24	p.R3098Kfs*24	ENST00000441802	NM_005245.3	3098	agg/aAgg	13/27	0.458706389015117	1	FACETS	0.272	0.25	0.295	0.272	0.25	0.295	INDETERMINATE	1	TRUE	0	0.901366332320635	1		321	739	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638157	176638158	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	155	227	0	ENST00000439151.2:c.2758dup	p.Ser920LysfsTer2	p.S920Kfs*2	ENST00000439151	NM_022455.4	919	-/A	5/23	NA	2	FACETS	0.523	0.48	0.567			1	INDETERMINATE	1	TRUE	NA	0.901366332320635	2		227	658	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	155	454	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	0.983	0.9	1	0.983	0.9	1	CLONAL	1	TRUE	1	0.372423695149215	2		454	847	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	173	604	4	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	0.915	0.842	0.992	0.915	0.842	0.992	CLONAL	1	TRUE	1	0.372423695149215	2		608	1015	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191049	185191049	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	87	451	0	ENST00000265026.3:c.1934del	p.Pro645LeufsTer19	p.P645Lfs*19	ENST00000265026	NM_004721.4	644	Ccc/cc	11/14	1	2	FACETS	0.598	0.529	0.672	0.598	0.529	0.672	SUBCLONAL	1	TRUE	1	0.372423695149215	2		451	781	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	131	379	2	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.994	0.903	1	0.994	0.903	1	CLONAL	1	TRUE	1	0.372423695149215	2		381	708	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	161	406	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	0.372423695149215	2		410	786	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	288	708	11	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	0.993	1	CLONAL	1	TRUE	1	0.372423695149215	2		719	1086	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353819	15353819	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	53	277	1	ENST00000263377.2:c.3061del	p.His1021IlefsTer47	p.H1021Ifs*47	ENST00000263377	NM_058243.2	1021	Cat/at	14/20	0.372423695149215	3	FACETS	0.665	0.567	0.771	0.332	0.283	0.386	SUBCLONAL	1	TRUE	1	0.372423695149215	3		278	508	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	48	423	2	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.302	0.254	0.355	0.302	0.254	0.355	SUBCLONAL	1	TRUE	1	0.372423695149215	2		425	853	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106879	27106879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	110	278	0	ENST00000324856.7:c.6490C>T	p.Arg2164Trp	p.R2164W	ENST00000324856	NM_006015.4	2164	Cgg/Tgg	20/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.372423695149215	2		278	490	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107008	27107008	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	44	259	0	ENST00000324856.7:c.6619C>T	p.Gln2207Ter	p.Q2207*	ENST00000324856	NM_006015.4	2207	Cag/Tag	20/20	1	2	FACETS	0.561	0.471	0.661	0.561	0.471	0.661	SUBCLONAL	1	TRUE	1	0.372423695149215	2		259	421	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71019886	71019886	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	135	316	0	ENST00000318789.4:c.1722+1G>T		p.X574_splice	ENST00000318789	NM_032682.5	574			1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.372423695149215	2		316	708	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026105	71026105	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	120	323	0	ENST00000318789.4:c.1517C>T	p.Ala506Val	p.A506V	ENST00000318789	NM_032682.5	506	gCg/gTg	17/21	1	2	FACETS	0.911	0.824	1	0.911	0.824	1	CLONAL	1	TRUE	1	0.372423695149215	2		323	707	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898826	134898826	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	66	341	0	ENST00000398015.3:c.1882+2T>C		p.X628_splice	ENST00000398015	NM_004441.4	628			1	2	FACETS	0.594	0.515	0.679	0.594	0.515	0.679	SUBCLONAL	1	TRUE	1	0.372423695149215	2		341	597	SUCCESS
ATR	545	MSKCC	GRCh37	3	142255002	142255002	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	41	358	0	ENST00000350721.4:c.3767C>A	p.Pro1256His	p.P1256H	ENST00000350721	NM_001184.3	1256	cCt/cAt	20/47	1	2	FACETS	0.313	0.26	0.373	0.313	0.26	0.373	SUBCLONAL	1	TRUE	1	0.372423695149215	2		358	703	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161350	185161350	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	105	457	0	ENST00000265026.3:c.777G>C	p.Trp259Cys	p.W259C	ENST00000265026	NM_004721.4	259	tgG/tgC	4/14	1	2	FACETS	0.629	0.563	0.7	0.629	0.563	0.7	SUBCLONAL	1	TRUE	1	0.372423695149215	2		457	896	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133571	55133571	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	114	370	1	ENST00000257290.5:c.875C>T	p.Ala292Val	p.A292V	ENST00000257290	NM_006206.4	292	gCc/gTc	6/23	1	2	FACETS	0.918	0.828	1	0.918	0.828	1	CLONAL	1	TRUE	1	0.372423695149215	2		371	667	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589818	55589818	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	86	375	0	ENST00000288135.5:c.1300C>A	p.Pro434Thr	p.P434T	ENST00000288135	NM_000222.2	434	Cca/Aca	8/21	1	2	FACETS	0.648	0.573	0.728	0.648	0.573	0.728	SUBCLONAL	1	TRUE	1	0.372423695149215	2		375	713	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233135	66233135	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	166	441	0	ENST00000273854.3:c.1864G>T	p.Gly622Cys	p.G622C	ENST00000273854	NM_004439.5	622	Ggc/Tgc	10/18	1	2	FACETS	0.904	0.83	0.982	0.904	0.83	0.982	CLONAL	1	TRUE	1	0.372423695149215	2		441	986	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947467	38947467	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	153	389	0	ENST00000357387.3:c.4213C>T	p.Arg1405Ter	p.R1405*	ENST00000357387	NM_152756.3	1405	Cga/Tga	32/38	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.372423695149215	2		389	785	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405225	139405225	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776698364	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	133	354	0	ENST00000277541.6:c.2620G>A	p.Val874Ile	p.V874I	ENST00000277541	NM_017617.3	874	Gtt/Att	17/34	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.372423695149215	2		354	635	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139794896	139794896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	218	608	0	ENST00000247668.2:c.290G>A	p.Arg97His	p.R97H	ENST00000247668	NM_021138.3	97	cGc/cAc	4/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.372423695149215	2		608	988	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685307	89685307	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123317	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	111	275	0	ENST00000371953.3:c.202T>C	p.Tyr68His	p.Y68H	ENST00000371953	NM_000314.4	68	Tac/Cac	3/9	1	2	FACETS	0.927	0.835	1	0.927	0.835	1	CLONAL	1	TRUE	1	0.372423695149215	2		275	643	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	127	315	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.913	0.828	1	0.913	0.828	1	CLONAL	1	TRUE	1	0.372423695149215	2		315	747	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102056856	102056856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	214	483	0	ENST00000282441.5:c.796C>T	p.Arg266Cys	p.R266C	ENST00000282441	NM_001130145.2	266	Cgt/Tgt	4/9	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.372423695149215	2		483	1140	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202251	133202251	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	144	399	0	ENST00000320574.5:c.6637G>A	p.Ala2213Thr	p.A2213T	ENST00000320574	NM_006231.2	2213	Gcc/Acc	47/49	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.372423695149215	2		399	640	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562220	21562220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	357	729	0	ENST00000382592.4:c.1699G>A	p.Gly567Arg	p.G567R	ENST00000382592	NM_014572.2	567	Gga/Aga	4/8	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.372423695149215	2		729	1316	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637597	23637597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1321993373	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	194	439	0	ENST00000261584.4:c.2708C>T	p.Ala903Val	p.A903V	ENST00000261584	NM_024675.3	903	gCt/gTt	7/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.372423695149215	2		439	896	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844112	68844112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854694	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	73	321	0	ENST00000261769.5:c.700G>A	p.Ala234Thr	p.A234T	ENST00000261769	NM_004360.3	234	Gct/Act	6/16	1	2	FACETS	0.637	0.558	0.723	0.637	0.558	0.723	SUBCLONAL	1	TRUE	1	0.372423695149215	2		321	615	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828221	72828221	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	169	801	1	ENST00000268489.5:c.8360C>A	p.Pro2787His	p.P2787H	ENST00000268489	NM_006885.3	2787	cCt/cAt	9/10	1	2	FACETS	0.721	0.661	0.784	0.721	0.661	0.784	SUBCLONAL	1	TRUE	1	0.372423695149215	2		802	1259	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984709	72984709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1490492880	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	241	606	0	ENST00000268489.5:c.2875G>A	p.Asp959Asn	p.D959N	ENST00000268489	NM_006885.3	959	Gac/Aac	3/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.372423695149215	2		606	1197	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	98	253	0	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.372423695149215	2		253	447	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976219	7976219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779729947	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	39	278	0	ENST00000319144.4:c.1976G>A	p.Arg659Gln	p.R659Q	ENST00000319144	NM_001139.2	659	cGg/cAg	15/15	1	2	FACETS	0.479	0.397	0.571	0.479	0.397	0.571	SUBCLONAL	1	TRUE	1	0.372423695149215	2		278	437	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108364	8108364	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	66	222	0	ENST00000585124.1:c.862-2A>G		p.X288_splice	ENST00000585124	NM_004217.3	288			1	2	FACETS	0.815	0.71	0.928	0.815	0.71	0.928	CLONAL	1	TRUE	1	0.372423695149215	2		222	435	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110524	8110524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1322292985	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	95	290	0	ENST00000585124.1:c.368G>A	p.Arg123His	p.R123H	ENST00000585124	NM_004217.3	123	cGc/cAc	5/9	1	2	FACETS	0.878	0.783	0.978	0.878	0.783	0.978	CLONAL	1	TRUE	1	0.372423695149215	2		290	581	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213905	2213905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750798710	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	87	318	0	ENST00000398665.3:c.1717G>A	p.Ala573Thr	p.A573T	ENST00000398665	NM_032482.2	573	Gcc/Acc	18/28	0.372423695149215	3	FACETS	0.964	0.855	1	0.482	0.427	0.54	CLONAL	1	TRUE	1	0.372423695149215	3		318	575	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214604	5214604	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs116515629	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	310	446	0	ENST00000357368.4:c.4462G>A	p.Val1488Ile	p.V1488I	ENST00000357368	NM_002850.3	1488	Gtc/Atc	29/38	0.372423695149215	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.372423695149215	3		446	907	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125394	7125394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748109926	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	223	492	2	ENST00000302850.5:c.3158G>A	p.Arg1053His	p.R1053H	ENST00000302850	NM_000208.2	1053	cGc/cAc	17/22	0.372423695149215	3	FACETS	1	0.989	1	0.664	0.618	0.712	CLONAL	1	TRUE	1	0.372423695149215	3		494	1069	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098501	11098501	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756474511	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	87	258	0	ENST00000358026.2:c.1019C>T	p.Ala340Val	p.A340V	ENST00000358026	NM_001128849.1	340	gCg/gTg	6/36	0.372423695149215	3	FACETS	1	0.972	1	0.65	0.579	0.726	CLONAL	1	TRUE	1	0.372423695149215	3		258	426	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281518	15281518	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1368023123	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	145	361	0	ENST00000263388.2:c.4855C>T	p.Arg1619Cys	p.R1619C	ENST00000263388	NM_000435.2	1619	Cgc/Tgc	26/33	0.372423695149215	3	FACETS	1	0.98	1	0.623	0.569	0.68	CLONAL	1	TRUE	1	0.372423695149215	3		361	741	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383257	42383257	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	218	665	0	ENST00000221972.3:c.277A>G	p.Ile93Val	p.I93V	ENST00000221972	NM_021601.3	93	Atc/Gtc	2/5	0.372423695149215	3	FACETS	1	0.976	1	0.558	0.518	0.6	CLONAL	1	TRUE	1	0.372423695149215	3		665	1244	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798424	42798424	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	162	381	0	ENST00000575354.2:c.4295G>A	p.Cys1432Tyr	p.C1432Y	ENST00000575354	NM_015125.3	1432	tGc/tAc	18/20	0.372423695149215	3	FACETS	1	0.98	1	0.608	0.558	0.661	CLONAL	1	TRUE	1	0.372423695149215	3		381	848	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725076	47725076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs571014601	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	144	512	1	ENST00000449228.1:c.668G>A	p.Arg223Gln	p.R223Q	ENST00000449228	NM_001127240.2	223	cGa/cAa	4/4	0.372423695149215	3	FACETS	1	0.942	1	0.522	0.476	0.57	CLONAL	1	TRUE	1	0.372423695149215	3		513	879	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386351	31386351	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	80	345	0	ENST00000328111.2:c.1576A>G	p.Met526Val	p.M526V	ENST00000328111	NM_006892.3	526	Atg/Gtg	15/23	1	2	FACETS	0.715	0.63	0.806	0.715	0.63	0.806	SUBCLONAL	1	TRUE	1	0.372423695149215	2		345	601	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36024567	36024567	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	127	385	0	ENST00000358208.4:c.556G>A	p.Ala186Thr	p.A186T	ENST00000358208		186	Gcc/Acc	6/12	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.372423695149215	2		385	585	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221706	22221706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	42	95	0	ENST00000215832.6:c.25G>A	p.Ala9Thr	p.A9T	ENST00000215832	NM_002745.4	9	Gcg/Acg	1/9	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.372423695149215	2		95	160	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176338	24176338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	124	438	0	ENST00000263121.7:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000263121	NM_003073.3	377	Cgt/Tgt	9/9	1	2	FACETS	0.988	0.895	1	0.988	0.895	1	CLONAL	1	TRUE	1	0.372423695149215	2		438	674	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067827	30067827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761795291	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	34	229	1	ENST00000338641.4:c.1012C>T	p.Arg338Cys	p.R338C	ENST00000338641	NM_000268.3	338	Cgc/Tgc	11/16	1	2	FACETS	0.467	0.382	0.563	0.467	0.382	0.563	SUBCLONAL	1	TRUE	1	0.372423695149215	2		230	391	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	188	245	1	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.947	0.882	1	1	0.993	1	CLONAL	2	TRUE	1	0.372423695149215	2		246	533	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023904	27023904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1232964733	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	24	85	0	ENST00000324856.7:c.1015del	p.Ala339LeufsTer24	p.A339Lfs*24	ENST00000324856	NM_006015.4	337	tGg/tg	1/20	1	2	FACETS	0.796	0.63	0.983	0.796	0.63	0.983	CLONAL	1	TRUE	1	0.372423695149215	2		85	162	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28624317	28624317	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	237	431	1	ENST00000241453.7:c.657del	p.Val220CysfsTer10	p.V220Cfs*10	ENST00000241453	NM_004119.2	219	aaA/aa	6/24	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.372423695149215	2		432	1049	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263952	104263952	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	49	97	0	ENST00000369902.3:c.47del	p.Pro16ArgfsTer80	p.P16Rfs*80	ENST00000369902	NM_016169.3	15	Ccc/cc	1/12	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.372423695149215	2		97	254	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597588	28597588	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1566063342	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	167	534	4	ENST00000241453.7:c.2317del	p.Arg773GlyfsTer8	p.R773Gfs*8	ENST00000241453	NM_004119.2	773	Agg/gg	19/24	1	2	FACETS	0.801	0.735	0.87	0.801	0.735	0.87	CLONAL	1	TRUE	1	0.372423695149215	2		538	1120	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296358	15296358	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	42	379	1	ENST00000263388.2:c.2084del	p.Pro695ArgfsTer165	p.P695Rfs*165	ENST00000263388	NM_000435.2	695	cCg/cg	13/33	0.372423695149215	3	FACETS	0.374	0.311	0.444	0.187	0.155	0.222	SUBCLONAL	1	TRUE	1	0.372423695149215	3		380	716	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119910	70119910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1297203260	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	112	273	0	ENST00000245479.2:c.916del	p.Val306CysfsTer77	p.V306Cfs*77	ENST00000245479	NM_000346.3	304	ccG/cc	3/3	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.372423695149215	2		273	468	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435283	110435283	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1199629587	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	12	50	0	ENST00000375856.3:c.3118del	p.Glu1040SerfsTer66	p.E1040Sfs*66	ENST00000375856	NM_003749.2	1040	Gag/ag	1/2	1	2	FACETS	0.537	0.38	0.727	0.537	0.38	0.727	SUBCLONAL	1	TRUE	1	0.372423695149215	2		50	120	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372093	55372093	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	36	114	2	ENST00000297316.4:c.788del	p.Pro263ArgfsTer124	p.P263Rfs*124	ENST00000297316	NM_022454.3	261	ggC/gg	2/2	1	2	FACETS	0.925	0.767	1	0.925	0.767	1	CLONAL	1	TRUE	1	0.372423695149215	2		116	209	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053348	37053348	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63751653	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	98	450	0	ENST00000231790.2:c.588del	p.Lys196AsnfsTer6	p.K196Nfs*6	ENST00000231790	NM_000249.3	195	Aaa/aa	7/19	0.372423695149215	2	FACETS	0.598	0.533	0.668	0.299	0.266	0.334	SUBCLONAL	1	TRUE	0	0.372423695149215	2		450	880	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271747	15271747	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs773656789	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	89	426	0	ENST00000263388.2:c.6692del	p.Pro2231GlnfsTer15	p.P2231Qfs*15	ENST00000263388	NM_000435.2	2231	cCa/ca	33/33	0.372423695149215	3	FACETS	0.886	0.786	0.992	0.443	0.393	0.496	CLONAL	1	TRUE	1	0.372423695149215	3		426	640	SUCCESS
APC	324	MSKCC	GRCh37	5	112157627	112157628	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs1554080698	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	149	434	0	ENST00000257430.4:c.1354_1355del	p.Val452SerfsTer7	p.V452Sfs*7	ENST00000257430	NM_000038.5	449	gcTGtg/gctg	11/16	1	2	FACETS	0.978	0.894	1	0.978	0.894	1	CLONAL	1	TRUE	1	0.372423695149215	2		434	818	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012386	152012386	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	128	413	0	ENST00000262189.6:c.427del	p.Ser143ValfsTer3	p.S143Vfs*3	ENST00000262189	NM_170606.2	143	Agt/gt	4/59	1	2	FACETS	0.792	0.717	0.871	0.792	0.717	0.871	SUBCLONAL	1	TRUE	1	0.372423695149215	2		413	868	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	126	416	5	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.372423695149215	2		421	598	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255882	16255883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	109	239	1	ENST00000375759.3:c.3154dup	p.Ile1052AsnfsTer7	p.I1052Nfs*7	ENST00000375759	NM_015001.2	1049	-/A	11/15	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.372423695149215	2		240	557	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40456603	40456605	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1192	66	669	0	ENST00000345506.4:c.1315_1317del	p.Lys439del	p.K439del	ENST00000345506	NM_003152.3	438	gAGAag/gag	12/20	1	2	FACETS	0.282	0.243	0.324	0.282	0.243	0.324	SUBCLONAL	1	TRUE	1	0.372423695149215	2		669	1258	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	114	373	0	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	0.75	0.675	0.83	0.75	0.675	0.83	SUBCLONAL	1	TRUE	1	0.372423695149215	2		373	816	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98003011	98003011	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	132	430	0	ENST00000289081.3:c.265del	p.Ile89PhefsTer2	p.I89Ffs*2	ENST00000289081	NM_000136.2	89	Att/tt	4/15	1	2	FACETS	0.86	0.781	0.944	0.86	0.781	0.944	CLONAL	1	TRUE	1	0.372423695149215	2		430	824	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0010313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	110	440	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.190687955761906	5	FACETS	0.996	0.897	1	0.664	0.598	0.734	CLONAL	2	TRUE	2	0.231725795089563	5		440	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0010313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	147	485	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.188299175797759	3	FACETS	1	0.974	1	0.772	0.708	0.839	CLONAL	2	TRUE	0	0.231725795089563	3		485	611	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356248	66356248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202046693	NA	P-0010313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	35	411	0	ENST00000273854.3:c.1249C>T	p.Arg417Trp	p.R417W	ENST00000273854	NM_004439.5	417	Cgg/Tgg	5/18	0.180131631997085	2	FACETS	0.891	0.732	1	0.446	0.366	0.535	CLONAL	1	TRUE	0	0.231725795089563	2		411	339	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864610	57864610	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	97	913	0	ENST00000228682.2:c.2087C>A	p.Ala696Asp	p.A696D	ENST00000228682	NM_005269.2	696	gCt/gAt	12/12	0.231725795089563	4	FACETS	0.826	0.734	0.925	0.413	0.367	0.463	CLONAL	1	TRUE	2	0.231725795089563	4		913	1248	SUCCESS
AR	367	MSKCC	GRCh37	X	66931256	66931256	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	37	435	0	ENST00000374690.3:c.1898A>C	p.Lys633Thr	p.K633T	ENST00000374690	NM_000044.3	633	aAg/aCg	4/8	1	1	FACETS	0.769	0.635	0.919	0.769	0.635	0.919	CLONAL	1	TRUE	0	0.231725795089563	1		435	367	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0010342-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	179	139	0	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	0.226721805354259	9	FACETS	1	0.965	1	1	0.965	1	CLONAL	5	FALSE	4	0.226721805354259	9		139	533	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0010342-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	174	347	2	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.982	1	1	0.995	1	CLONAL	3	FALSE	1	0.226721805354259	2		349	441	SUCCESS
APC	324	MSKCC	GRCh37	5	112174086	112174086	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs878853432	NA	P-0010342-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	119	394	0	ENST00000257430.4:c.2795C>A	p.Ser932Ter	p.S932*	ENST00000257430	NM_000038.5	932	tCa/tAa	16/16	0.148804393566357	0	FACETS	0.851	0.779	0.925			1	CLONAL	3	FALSE	0	0.226721805354259	0		394	318	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858985	57858985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142957882	NA	P-0010342-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	1058	1068	6	ENST00000228682.2:c.481C>T	p.Arg161Trp	p.R161W	ENST00000228682	NM_005269.2	161	Cgg/Tgg	5/12	0.226721805354259	5	FACETS	0.964	0.94	0.987	1	0.998	1	CLONAL	7	FALSE	1	0.226721805354259	5		1074	1854	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31379464	31379464	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1330365498	NA	P-0010342-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	309	461	1	ENST00000328111.2:c.871A>G	p.Thr291Ala	p.T291A	ENST00000328111	NM_006892.3	291	Acc/Gcc	8/23	0.226721805354259	9	FACETS	1	0.987	1	0.697	0.656	0.74	CLONAL	3	FALSE	4	0.226721805354259	9		462	1402	SUCCESS
APC	324	MSKCC	GRCh37	5	112173661	112173662	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0010342-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	110	327	0	ENST00000257430.4:c.2373_2374del	p.His791GlnfsTer7	p.H791Qfs*7	ENST00000257430	NM_000038.5	790	agACac/agac	16/16	0.148804393566357	0	FACETS	0.767	0.698	0.839			1	SUBCLONAL	3	FALSE	0	0.226721805354259	0		327	326	SUCCESS
APC	324	MSKCC	GRCh37	5	112128198	112128198	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010342-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	159	455	0	ENST00000257430.4:c.704del	p.Leu235TyrfsTer58	p.L235Yfs*58	ENST00000257430	NM_000038.5	234	cTt/ct	7/16	0.148804393566357	0	FACETS	0.739	0.683	0.797			1	SUBCLONAL	3	FALSE	0	0.226721805354259	0		455	489	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0010351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	574	441	1	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	0.868686406436889	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.879948856893955	2		442	643	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382185	152382185	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	407	393	0	ENST00000206249.3:c.1295C>T	p.Ser432Leu	p.S432L	ENST00000206249	NM_000125.3	432	tCa/tTa	6/8	0.475267767349403	1	FACETS	0.712	0.683	0.74	0.712	0.683	0.74	INDETERMINATE	1	TRUE	0	0.879948856893955	1		393	728	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258697	115258697	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	248	274	0	ENST00000369535.4:c.85G>T	p.Val29Leu	p.V29L	ENST00000369535	NM_002524.4	29	Gta/Tta	2/7	1	2	FACETS	0.936	0.882	0.991	0.936	0.882	0.991	CLONAL	1	TRUE	1	0.879948856893955	2		274	602	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982754	90982754	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	439	354	0	ENST00000265433.3:c.734G>C	p.Gly245Ala	p.G245A	ENST00000265433	NM_002485.4	245	gGa/gCa	7/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.879948856893955	2		354	964	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404762	70404762	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1348824746	NA	P-0010351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	24	387	1	ENST00000373644.4:c.2276G>A	p.Gly759Asp	p.G759D	ENST00000373644	NM_030625.2	759	gGc/gAc	4/12	0.879948856893955	1	FACETS	0.064	0.05	0.081	0.064	0.05	0.081	SUBCLONAL	1	TRUE	0	0.879948856893955	1		388	474	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037866	49037866	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs587778860	NA	P-0010351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	612	478	0	ENST00000267163.4:c.2107-1G>C		p.X703_splice	ENST00000267163	NM_000321.2	703			0.868686406436889	2	FACETS	0.957	0.938	0.975	0.957	0.938	0.975	CLONAL	2	TRUE	0	0.879948856893955	2		478	727	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857077	9857077	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	531	513	0	ENST00000330684.3:c.4324C>A	p.Pro1442Thr	p.P1442T	ENST00000330684	NM_001134407.1	1442	Ccc/Acc	13/13	0.879948856893955	1	FACETS	0.987	0.962	1	0.987	0.962	1	CLONAL	1	TRUE	0	0.879948856893955	1		513	685	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273999	10273999	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1405276485	NA	P-0010351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	507	570	0	ENST00000330684.3:c.270G>A	p.Met90Ile	p.M90I	ENST00000330684	NM_001134407.1	90	atG/atA	2/13	0.879948856893955	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.879948856893955	1		570	640	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610540	81610541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	455	495	0	ENST00000298171.2:c.2141dup	p.Asn715GlufsTer4	p.N715Efs*4	ENST00000298171	NM_000369.2	713	cca/ccAa	10/10	0.438159720408242	3	FACETS	1	0.985	1	0.536	0.511	0.561	INDETERMINATE	1	TRUE	1	0.879948856893955	3		495	1390	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0010365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	404	778	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.379423932113976	3	FACETS	0.956	0.909	1	0.956	0.909	1	CLONAL	2	TRUE	1	0.379423932113976	3		778	1325	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0010365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	291	352	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.379423932113976	3	FACETS	0.929	0.875	0.984	0.929	0.875	0.984	CLONAL	2	TRUE	1	0.379423932113976	3		352	982	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0010365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	254	399	0	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	0.379423932113976	2	FACETS	0.999	0.941	1	0.999	0.941	1	CLONAL	2	TRUE	0	0.379423932113976	2		399	670	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735422	204735422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	145	158	0	ENST00000302823.3:c.223C>T	p.Arg75Trp	p.R75W	ENST00000302823	NM_005214.4	75	Cgg/Tgg	2/4	0.368845392973638	3	FACETS	1	0.982	1	0.638	0.583	0.695	CLONAL	1	TRUE	1	0.379423932113976	3		158	713	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183205	56183205	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	105	214	0	ENST00000399503.3:c.4115G>A	p.Gly1372Asp	p.G1372D	ENST00000399503	NM_005921.1	1372	gGt/gAt	18/20	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.379423932113976	2		214	540	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435658	18435658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143896492	NA	P-0010365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	82	256	0	ENST00000266497.5:c.643G>A	p.Gly215Arg	p.G215R	ENST00000266497		215	Gga/Aga	1/31	0.379423932113976	3	FACETS	0.872	0.77	0.981	0.436	0.385	0.491	CLONAL	1	TRUE	1	0.379423932113976	3		256	590	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231459	5231459	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs919758857	NA	P-0010365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	197	482	0	ENST00000357368.4:c.2017G>A	p.Gly673Ser	p.G673S	ENST00000357368	NM_002850.3	673	Ggc/Agc	14/38	0.368845392973638	3	FACETS	0.972	0.898	1	0.486	0.449	0.525	CLONAL	1	TRUE	1	0.379423932113976	3		482	1271	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643768	52643768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	98	494	0	ENST00000394830.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000394830	NM_018313.4	710	Cga/Tga	17/30	0.513156969314445	1	FACETS	0.635	0.57	0.704	0.635	0.57	0.704	SUBCLONAL	1	TRUE	0	0.513156969314445	1		494	447	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613209	52613210	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	33	439	0	ENST00000394830.3:c.3318dup	p.Glu1107ArgfsTer11	p.E1107Rfs*11	ENST00000394830	NM_018313.4	1106	-/A	22/30	0.513156969314445	1	FACETS	0.252	0.205	0.304	0.252	0.205	0.304	SUBCLONAL	1	TRUE	0	0.513156969314445	1		439	380	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447774	187447774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536118071	NA	P-0010376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	115	254	0	ENST00000232014.4:c.419G>A	p.Arg140His	p.R140H	ENST00000232014	NM_001130845.1	140	cGt/cAt	5/10	0.513156969314445	3	FACETS	1	0.94	1	0.526	0.476	0.579	CLONAL	1	TRUE	1	0.513156969314445	3		254	535	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526085	66526085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	156	652	1	ENST00000358598.2:c.916C>T	p.Arg306Trp	p.R306W	ENST00000358598	NM_212471.2	306	Cgg/Tgg	10/11	1	2	FACETS	0.703	0.644	0.765	0.703	0.644	0.765	SUBCLONAL	1	TRUE	1	0.513156969314445	2		653	865	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584643	187584643	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	180	797	0	ENST00000441802.2:c.3390G>T	p.Glu1130Asp	p.E1130D	ENST00000441802	NM_005245.3	1130	gaG/gaT	3/27	0.513156969314445	1	FACETS	0.654	0.604	0.705	0.654	0.604	0.705	SUBCLONAL	1	TRUE	0	0.513156969314445	1		797	798	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721973	176721973	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	98	292	0	ENST00000439151.2:c.7604A>G	p.Gln2535Arg	p.Q2535R	ENST00000439151	NM_022455.4	2535	cAg/cGg	23/23	0.486112899263892	3	FACETS	0.892	0.798	0.991	0.446	0.399	0.496	CLONAL	1	TRUE	1	0.513156969314445	3		292	538	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607553	43607553	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201745826	NA	P-0010376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	38	311	2	ENST00000355710.3:c.1529C>T	p.Ala510Val	p.A510V	ENST00000355710	NM_020975.4	510	gCc/gTc	8/20	1	2	FACETS	0.395	0.327	0.471	0.395	0.327	0.471	SUBCLONAL	1	TRUE	1	0.513156969314445	2		313	375	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144628	119144628	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	73	564	0	ENST00000264033.4:c.641C>T	p.Pro214Leu	p.P214L	ENST00000264033	NM_005188.3	214	cCc/cTc	4/16	1	2	FACETS	0.446	0.39	0.506	0.446	0.39	0.506	SUBCLONAL	1	TRUE	1	0.513156969314445	2		564	638	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183755	10183757	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs5030648	NA	P-0010376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	113	360	0	ENST00000256474.2:c.227_229del	p.Phe76del	p.F76del	ENST00000256474	NM_000551.3	75	aTCTtc/atc	1/3	0.513156969314445	1	FACETS	0.922	0.839	1	0.922	0.839	1	CLONAL	1	TRUE	0	0.513156969314445	1		360	355	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363137	40363138	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	149	436	0	ENST00000397332.2:c.1091dup	p.Ala366GlyfsTer2	p.A366Gfs*2	ENST00000397332	NM_001033082.2	364	gtg/gtTg	3/3	1	2	FACETS	0.857	0.785	0.931	0.857	0.785	0.931	CLONAL	1	TRUE	1	0.513156969314445	2		436	678	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053506	37053507	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	rs63751637	NA	P-0010376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	162	558	0	ENST00000231790.2:c.597_598del	p.Glu199AspfsTer4	p.E199Dfs*4	ENST00000231790	NM_000249.3	198	gGA/g	8/19	0.513156969314445	1	FACETS	0.85	0.785	0.918	0.85	0.785	0.918	CLONAL	1	TRUE	0	0.513156969314445	1		558	552	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0010394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	36	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.983	0.806	1	0.983	0.806	1	CLONAL	1	TRUE	1	0.11	2		311	666	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989581	212989581	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	33	358	2	ENST00000342788.4:c.130C>A	p.Gln44Lys	p.Q44K	ENST00000342788	NM_005235.2	44	Cag/Aag	2/28	1	2	FACETS	0.998	0.811	1	0.998	0.811	1	CLONAL	1	TRUE	1	0.11	2		360	601	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023485	27023486	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0010394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1202	66	762	0	ENST00000324856.7:c.595dup	p.Gln199ProfsTer201	p.Q199Pfs*201	ENST00000324856	NM_006015.4	197	-/C	1/20	1	2	FACETS	0.946	0.818	1	0.946	0.818	1	CLONAL	1	TRUE	1	0.11	2		762	1268	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38064170	38064170	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	61	655	0	ENST00000250448.2:c.8del	p.Gly3GlufsTer3	p.G3Efs*3	ENST00000250448	NM_004496.3	3	gGa/ga	1/2	1	2	FACETS	0.978	0.841	1	0.978	0.841	1	CLONAL	1	TRUE	1	0.11	2		655	1134	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0010428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	8	328	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.6	0.389	0.868	0.6	0.389	0.868	SUBCLONAL	1	TRUE	1	0.283715995718988	2		328	94	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	96	697	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.283715995718988	3	FACETS	0.774	0.692	0.861	0.774	0.692	0.861	SUBCLONAL	2	TRUE	1	0.283715995718988	3		697	499	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023008	27023010	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs587779737	NA	P-0010428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	10	26	0	ENST00000324856.7:c.126_128del	p.Ala45del	p.A45del	ENST00000324856	NM_006015.4	38	gaGGCg/gag	1/20	0.283715995718988	1	FACETS	0.504	0.343	0.704	0.504	0.343	0.704	SUBCLONAL	1	TRUE	0	0.283715995718988	1		26	120	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412110	63412110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852216	NA	P-0010428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1742	306	977	0	ENST00000330258.3:c.1057C>T	p.Arg353Ter	p.R353*	ENST00000330258	NM_152424.3	353	Cga/Tga	2/2	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.283715995718988	2		977	2048	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587777894	NA	P-0010428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	186	642	0	ENST00000361445.4:c.6644C>A	p.Ser2215Tyr	p.S2215Y	ENST00000361445	NM_004958.3	2215	tCt/tAt	47/58	0.250425612759182	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.283715995718988	1		642	1037	SUCCESS
APC	324	MSKCC	GRCh37	5	112175650	112175651	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	142	689	0	ENST00000257430.4:c.4364dup	p.Asn1455LysfsTer2	p.N1455Kfs*2	ENST00000257430	NM_000038.5	1453	-/A	16/16	0.250425612759182	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.283715995718988	1		689	724	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010465-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	214	341	0	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	0.570752150564528	1	FACETS	0.963	0.903	1	0.963	0.903	1	CLONAL	1	TRUE	0	0.58291459692928	1		341	540	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465636	99465636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775915596	NA	P-0010465-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	11	104	0	ENST00000268035.6:c.2461G>A	p.Val821Ile	p.V821I	ENST00000268035	NM_000875.3	821	Gtc/Atc	11/21	0.58291459692928	1	FACETS	0.132	0.091	0.183	0.132	0.091	0.183	SUBCLONAL	1	TRUE	0	0.58291459692928	1		104	203	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280049	18280086	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTGGCGCACCCAGTGCGCGCCCCGGGCCCCGGCCCG	CCCTGGCGCACCCAGTGCGCGCCCCGGGCCCCGGCCCG	-	novel	NA	P-0010465-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	79	77	0	ENST00000222254.8:c.2134_2171del	p.Leu712AlafsTer86	p.L712Afs*86	ENST00000222254	NM_005027.3	711	aCCCTGGCGCACCCAGTGCGCGCCCCGGGCCCCGGCCCG/a	16/16	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.58291459692928	2		77	242	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204513806	204513807	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010465-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	187	207	1	ENST00000367182.3:c.821dup	p.Val275GlyfsTer3	p.V275Gfs*3	ENST00000367182	NM_001278516.1	272	-/A	9/11	0.227541000180519	4	FACETS	0.898	0.843	0.953	0.673	0.632	0.715	INDETERMINATE	3	TRUE	0	0.58291459692928	4		208	377	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0010508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	2792	338	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.623681808475678	16	FACETS	1	0.996	1			1	CLONAL	14	TRUE	NA	0.623681808475678	16		338	3386	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864645	57864645	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1323	845	804	4	ENST00000228682.2:c.2122G>T	p.Glu708Ter	p.E708*	ENST00000228682	NM_005269.2	708	Gaa/Taa	12/12	0.582152437875378	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.623681808475678	4		808	2168	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070596	67070596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	547	411	1	ENST00000412916.2:c.220C>T	p.Gln74Ter	p.Q74*	ENST00000412916		74	Cag/Tag	3/6	0.623681808475678	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.623681808475678	2		412	824	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111475	8111476	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0010508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	185	326	0	ENST00000346208.3:c.962_963insAA	p.Thr322ArgfsTer34	p.T322Rfs*34	ENST00000346208		321	cag/cAAag	5/6	0.589228224328483	3	FACETS	0.961	0.889	1	0.48	0.444	0.518	CLONAL	1	TRUE	1	0.623681808475678	3		326	810	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577271	64577272	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACA	novel	NA	P-0010508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	423	451	0	ENST00000312049.6:c.308_310dup	p.Leu103dup	p.L103dup	ENST00000312049	NM_130799.2	103	tcc/tTGTcc	2/10	NA	2	FACETS	0.91	0.875	0.945			1	INDETERMINATE	2	TRUE	NA	0.623681808475678	2		451	745	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261080	16261121	+	protein_altering_variant	In_Frame_Del	DEL	ACAGTCGGTTCCACCCAGGGTCCATGCCTGTGATCGACGATC	ACAGTCGGTTCCACCCAGGGTCCATGCCTGTGATCGACGATC	TGA	novel	NA	P-0010508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	112	165	0	ENST00000375759.3:c.8345_8386delinsTGA	p.Asn2782_Arg2796delinsMetSer	p.N2782_R2796delinsMS	ENST00000375759	NM_015001.2	2782	aACAGTCGGTTCCACCCAGGGTCCATGCCTGTGATCGACGATCgt/aTGAgt	11/15	0.623681808475678	2	FACETS	1	0.976	1	0.605	0.552	0.659	CLONAL	1	TRUE	0	0.623681808475678	2		165	297	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0010509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	137	201	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.220397607143932	0	FACETS	0.794	0.741	0.847			1	SUBCLONAL	5	FALSE	0	0.220397607143932	0		201	244	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0010509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	71	365	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.913	0.802	1	1	0.981	1	CLONAL	2	FALSE	1	0.220397607143932	2		365	353	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0010509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	70	286	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.957	0.84	1	1	0.981	1	CLONAL	2	FALSE	1	0.220397607143932	2		286	332	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555687605	NA	P-0010509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	43	322	0	ENST00000342988.3:c.1610A>G	p.Asp537Gly	p.D537G	ENST00000342988	NM_005359.5	537	gAc/gGc	12/12	1	2	FACETS	0.735	0.614	0.868	0.735	0.614	0.868	SUBCLONAL	1	FALSE	1	0.220397607143932	2		322	531	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264568	1264568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761308654	NA	P-0010509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	48	440	0	ENST00000310581.5:c.2794G>A	p.Gly932Ser	p.G932S	ENST00000310581	NM_198253.2	932	Ggc/Agc	11/16	0.220397607143932	0	FACETS	0.729	0.622	0.844			1	SUBCLONAL	2	FALSE	0	0.220397607143932	0		440	233	SUCCESS
APC	324	MSKCC	GRCh37	5	112174840	112174840	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0010509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	96	438	0	ENST00000257430.4:c.3549T>A	p.Tyr1183Ter	p.Y1183*	ENST00000257430	NM_000038.5	1183	taT/taA	16/16	1	2	FACETS	1	0.914	1	1	0.987	1	CLONAL	2	FALSE	1	0.220397607143932	2		438	426	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480588	50480588	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	159	429	0	ENST00000394963.4:c.458T>G	p.Phe153Cys	p.F153C	ENST00000394963	NM_003076.4	153	tTt/tGt	4/13	0.205674057982626	4	FACETS	0.9	0.828	0.975	1	0.986	1	CLONAL	3	FALSE	2	0.220397607143932	4		429	652	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117960	70117960	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	86	125	0	ENST00000245479.2:c.428G>A	p.Trp143Ter	p.W143*	ENST00000245479	NM_000346.3	143	tGg/tAg	1/3	0.220397607143932	6	FACETS	0.965	0.869	1			1	CLONAL	5	FALSE	NA	0.220397607143932	6		125	233	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955550	48955550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913304	NA	P-0010518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	383	327	0	ENST00000267163.4:c.1666C>T	p.Arg556Ter	p.R556*	ENST00000267163	NM_000321.2	556	Cga/Tga	17/27	NA	2	FACETS	0.963	0.931	0.995			1	INDETERMINATE	2	TRUE	NA	0.726873068927911	2		327	547	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0010518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	37	124	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.666102861847111	1	FACETS	0.655	0.556	0.757	0.655	0.556	0.757	SUBCLONAL	1	TRUE	0	0.726873068927911	1		124	99	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520006	NA	P-0010518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	768	708	1	ENST00000269305.4:c.821T>C	p.Val274Ala	p.V274A	ENST00000269305	NM_001126112.2	274	gTt/gCt	8/11	0.726873068927911	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.726873068927911	2		709	995	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866376	42866376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777667088	NA	P-0010518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	694	307	3	ENST00000398585.3:c.256G>A	p.Val86Met	p.V86M	ENST00000398585	NM_001135099.1	86	Gtg/Atg	3/14	0.726873068927911	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.726873068927911	3		310	1235	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389254	8389254	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	277	418	1	ENST00000356435.5:c.4364C>A	p.Thr1455Lys	p.T1455K	ENST00000356435		1455	aCa/aAa	26/35	0.678508543998729	4	FACETS	0.927	0.869	0.987	0.463	0.434	0.494	CLONAL	1	TRUE	2	0.726873068927911	4		419	1420	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060643	38060643	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1528	529	599	0	ENST00000250448.2:c.1346C>T	p.Pro449Leu	p.P449L	ENST00000250448	NM_004496.3	449	cCc/cTc	2/2	0.726873068927911	3	FACETS	0.965	0.922	1	0.482	0.461	0.504	CLONAL	1	TRUE	1	0.726873068927911	3		599	2057	SUCCESS
APC	324	MSKCC	GRCh37	5	112176675	112176676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	220	332	0	ENST00000257430.4:c.5390dup	p.Asn1797LysfsTer2	p.N1797Kfs*2	ENST00000257430	NM_000038.5	1795	tca/tcAa	16/16	0.666102861847111	1	FACETS	0.851	0.802	0.9	0.851	0.802	0.9	CLONAL	1	TRUE	0	0.726873068927911	1		332	453	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0010634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	37	175	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.501427040760515	5	FACETS	0.582	0.48	0.697	0.146	0.12	0.175	SUBCLONAL	1	TRUE	1	0.501427040760515	5		175	444	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0010634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	134	110	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	NA	2	FACETS	0.958	0.887	1			1	INDETERMINATE	2	TRUE	NA	0.501427040760515	2		110	279	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0010634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	340	639	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	0.362131597487481	4	FACETS	0.795	0.752	0.84	0.795	0.752	0.84	SUBCLONAL	2	TRUE	2	0.501427040760515	4		639	1280	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782144	NA	P-0010634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	375	461	0	ENST00000269305.4:c.473G>C	p.Arg158Pro	p.R158P	ENST00000269305	NM_001126112.2	158	cGc/cCc	5/11	0.294193176037357	3	FACETS	1	0.992	1	0.781	0.746	0.817	INDETERMINATE	2	TRUE	0	0.501427040760515	3		461	798	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799866	72799866	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	101	364	0	ENST00000325599.8:c.1303G>T	p.Ala435Ser	p.A435S	ENST00000325599	NM_018130.2	435	Gca/Tca	11/11	0.391333628660904	2	FACETS	0.75	0.673	0.832	0.375	0.336	0.416	SUBCLONAL	1	TRUE	0	0.501427040760515	2		364	537	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152105	55152105	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	113	473	0	ENST00000257290.5:c.2537A>T	p.Asp846Val	p.D846V	ENST00000257290	NM_006206.4	846	gAt/gTt	18/23	0.375111284698387	3	FACETS	0.756	0.68	0.835	0.378	0.34	0.418	SUBCLONAL	1	TRUE	1	0.501427040760515	3		473	746	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55270256	55270256	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs771471723	NA	P-0010634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	143	573	0	ENST00000275493.2:c.3209G>C	p.Ser1070Thr	p.S1070T	ENST00000275493	NM_005228.3	1070	aGc/aCc	27/28	0.428227575429124	3	FACETS	0.836	0.762	0.914	0.418	0.381	0.457	CLONAL	1	TRUE	1	0.501427040760515	3		573	853	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118874	115118874	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	115	448	0	ENST00000257566.3:c.467T>A	p.Ile156Lys	p.I156K	ENST00000257566	NM_016569.3	156	aTa/aAa	2/8	1	2	FACETS	0.762	0.688	0.84	0.762	0.688	0.84	SUBCLONAL	1	TRUE	1	0.501427040760515	2		448	602	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033915	49033915	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	280	588	1	ENST00000267163.4:c.2052C>A	p.Phe684Leu	p.F684L	ENST00000267163	NM_000321.2	684	ttC/ttA	20/27	0.391333628660904	2	FACETS	0.818	0.773	0.862	0.818	0.773	0.862	CLONAL	2	TRUE	0	0.501427040760515	2		589	683	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358472	91358472	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	310	632	0	ENST00000355112.3:c.4217A>G	p.Asn1406Ser	p.N1406S	ENST00000355112	NM_000057.2	1406	aAt/aGt	22/22	0.375111284698387	3	FACETS	0.814	0.769	0.86	0.814	0.769	0.86	CLONAL	2	TRUE	1	0.501427040760515	3		632	950	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15960886	15960886	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	200	409	0	ENST00000268712.3:c.6334C>A	p.His2112Asn	p.H2112N	ENST00000268712	NM_006311.3	2112	Cat/Aat	40/46	0.294193176037357	3	FACETS	0.764	0.711	0.818	0.509	0.474	0.546	INDETERMINATE	2	TRUE	0	0.501427040760515	3		409	653	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260213	16260214	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0010634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	35	215	0	ENST00000375759.3:c.7484dup	p.Thr2496TyrfsTer2	p.T2496Yfs*2	ENST00000375759	NM_015001.2	2493	agc/agCc	11/15	0.250046596609004	2	FACETS	0.467	0.384	0.559	0.233	0.192	0.28	INDETERMINATE	1	TRUE	0	0.501427040760515	2		215	299	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0010665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	20	590	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.806	1	1	0.806	1	CLONAL	1	FALSE	1	0.161463090904082	2		590	234	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386537	81386537	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	23	654	0	ENST00000222390.5:c.450G>T	p.Gln150His	p.Q150H	ENST00000222390	NM_000601.4	150	caG/caT	4/18	0.161463090904082	5	FACETS	1	0.89	1	0.417	0.325	0.522	CLONAL	1	FALSE	2	0.161463090904082	5		654	283	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106861	27106861	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	24	380	0	ENST00000324856.7:c.6472C>T	p.Arg2158Ter	p.R2158*	ENST00000324856	NM_006015.4	2158	Cga/Tga	20/20	0.161463090904082	5	FACETS	1	0.924	1	0.733	0.576	0.912	CLONAL	1	FALSE	3	0.161463090904082	5		380	252	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0010665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	17	361	0	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	FALSE	1	0.161463090904082	2		361	157	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265479	152265479	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766779326	NA	P-0010665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	18	452	0	ENST00000206249.3:c.932C>T	p.Thr311Met	p.T311M	ENST00000206249	NM_000125.3	311	aCg/aTg	4/8	0.161463090904082	6	FACETS	0.756	0.572	0.973	0.504	0.381	0.649	CLONAL	2	FALSE	3	0.161463090904082	6		452	195	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12653513	12653513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	22	593	0	ENST00000251849.4:c.256C>T	p.Leu86Phe	p.L86F	ENST00000251849	NM_002880.3	86	Ctc/Ttc	3/17	0.161463090904082	4	FACETS	1	0.902	1	0.668	0.519	0.839	CLONAL	1	FALSE	2	0.161463090904082	4		593	237	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710517	114710517	+	start_lost	Translation_Start_Site	SNP	T	T	G	novel	NA	P-0010665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	84	734	0	ENST00000543371.1:c.2T>G	p.Met1?	p.M1?	ENST00000543371	NM_001198531.1	1	aTg/aGg	1/14	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.161463090904082	2		734	805	SUCCESS
APC	324	MSKCC	GRCh37	5	112173574	112173575	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0010665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	15	456	0	ENST00000257430.4:c.2284dup	p.Ala762GlyfsTer13	p.A762Gfs*13	ENST00000257430	NM_000038.5	761	-/G	16/16	1	2	FACETS	1	0.807	1	1	0.807	1	CLONAL	1	FALSE	1	0.161463090904082	2		456	165	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604762	48604763	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	38	584	0	ENST00000342988.3:c.1586dup	p.Leu529PhefsTer48	p.L529Ffs*48	ENST00000342988	NM_005359.5	528	-/T	12/12	0.153645493113887	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	2	FALSE	0	0.161463090904082	2		584	228	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249017	55249018	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCA	rs1554350381	NA	P-0010675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	127	265	0	ENST00000275493.2:c.2317_2319dup	p.His773dup	p.H773dup	ENST00000275493	NM_005228.3	773	ccc/ccCCAc	20/28	1	2	FACETS	0.997	0.905	1	0.997	0.905	1	CLONAL	1	TRUE	1	0.373407289275149	2		265	682	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36814416	36814416	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	218	495	0	ENST00000373129.3:c.624G>T	p.Arg208Ser	p.R208S	ENST00000373129	NM_032017.1	208	agG/agT	8/12	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.373407289275149	2		495	1117	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0010706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	36	301	0	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	0.678835048426274	3	FACETS	0.234	0.192	0.282	0.117	0.096	0.141	SUBCLONAL	1	TRUE	1	0.769067659558443	3		301	553	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0010706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	39	592	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.769067659558443	3	FACETS	0.208	0.171	0.248	0.104	0.085	0.124	SUBCLONAL	1	TRUE	1	0.769067659558443	3		592	676	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0010706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	676	586	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.553076457120373	4	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.769067659558443	4		586	1389	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0010706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	26	507	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.553076457120373	4	FACETS	0.119	0.093	0.149			1	SUBCLONAL	1	TRUE	NA	0.769067659558443	4		507	1005	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793373	242793373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	32	450	0	ENST00000334409.5:c.704C>T	p.Pro235Leu	p.P235L	ENST00000334409	NM_005018.2	235	cCg/cTg	5/5	0.769067659558443	3	FACETS	0.188	0.152	0.229	0.094	0.076	0.115	SUBCLONAL	1	TRUE	1	0.769067659558443	3		450	614	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740432	58740432	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs775750934	NA	P-0010706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1294	80	827	0	ENST00000305921.3:c.1337C>G	p.Ser446Ter	p.S446*	ENST00000305921	NM_003620.3	446	tCa/tGa	6/6	0.485583691818434	4	FACETS	0.268	0.235	0.304	0.134	0.117	0.152	SUBCLONAL	1	TRUE	2	0.769067659558443	4		827	1374	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23652445	23652445	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	126	575	0	ENST00000261584.4:c.34G>T	p.Glu12Ter	p.E12*	ENST00000261584	NM_024675.3	12	Gag/Tag	1/13	0.236297178107335	6	FACETS	0.865	0.783	0.953			1	INDETERMINATE	1	TRUE	NA	0.769067659558443	6		575	961	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157812	106157812	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	100	340	0	ENST00000380013.4:c.2713G>C	p.Asp905His	p.D905H	ENST00000380013	NM_001127208.2	905	Gat/Cat	3/11	0.769067659558443	3	FACETS	0.511	0.457	0.569	0.256	0.228	0.285	SUBCLONAL	1	TRUE	1	0.769067659558443	3		340	704	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649544	206649544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370426628	NA	P-0010706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	137	282	0	ENST00000367120.3:c.379C>T	p.Arg127Trp	p.R127W	ENST00000367120	NM_014002.3	127	Cgg/Tgg	6/22	0.769067659558443	6	FACETS	0.906	0.823	0.993	0.181	0.164	0.199	CLONAL	1	TRUE	1	0.769067659558443	6		282	998	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243668570	243668570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1443	81	431	0	ENST00000263826.5:c.1421C>T	p.Ser474Phe	p.S474F	ENST00000263826	NM_005465.4	474	tCt/tTt	13/13	0.769067659558443	6	FACETS	0.351	0.307	0.398	0.07	0.061	0.08	SUBCLONAL	1	TRUE	1	0.769067659558443	6		431	1524	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12653541	12653541	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	137	553	0	ENST00000251849.4:c.228G>C	p.Met76Ile	p.M76I	ENST00000251849	NM_002880.3	76	atG/atC	3/17	0.769067659558443	3	FACETS	0.53	0.481	0.581	0.265	0.24	0.291	SUBCLONAL	1	TRUE	1	0.769067659558443	3		553	931	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119545703	119545703	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0010706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	90	292	0	ENST00000316626.5:c.1235-1G>A		p.X412_splice	ENST00000316626		412			0.769067659558443	3	FACETS	0.54	0.48	0.604	0.27	0.24	0.302	SUBCLONAL	1	TRUE	1	0.769067659558443	3		292	600	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181423	185181423	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	163	543	0	ENST00000265026.3:c.1364T>C	p.Ile455Thr	p.I455T	ENST00000265026	NM_004721.4	455	aTt/aCt	8/14	NA	2	FACETS	0.616	0.567	0.667			1	INDETERMINATE	1	TRUE	NA	0.769067659558443	2		543	688	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467708	66467708	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	520	410	0	ENST00000273854.3:c.561T>A	p.Asp187Glu	p.D187E	ENST00000273854	NM_004439.5	187	gaT/gaA	3/18	0.769067659558443	4	FACETS	1	0.969	1	0.674	0.647	0.7	CLONAL	2	TRUE	1	0.769067659558443	4		410	1184	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630744	187630744	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1222	199	742	0	ENST00000441802.2:c.238G>A	p.Glu80Lys	p.E80K	ENST00000441802	NM_005245.3	80	Gaa/Aaa	2/27	0.769067659558443	3	FACETS	0.504	0.466	0.545	0.252	0.233	0.273	SUBCLONAL	1	TRUE	1	0.769067659558443	3		742	1421	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514340	149514340	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	125	607	0	ENST00000261799.4:c.604G>C	p.Asp202His	p.D202H	ENST00000261799	NM_002609.3	202	Gat/Cat	4/23	0.769067659558443	4	FACETS	0.506	0.457	0.558	0.169	0.152	0.186	SUBCLONAL	1	TRUE	1	0.769067659558443	4		607	1136	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858252	27858252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1696	217	1112	1	ENST00000359303.2:c.319G>A	p.Asp107Asn	p.D107N	ENST00000359303	NM_003535.2	107	Gac/Aac	1/1	0.738164839516753	4	FACETS	0.522	0.483	0.562	0.261	0.241	0.281	SUBCLONAL	1	TRUE	2	0.769067659558443	4		1113	1913	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609711	117609711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	144	431	1	ENST00000368508.3:c.6988G>A	p.Glu2330Lys	p.E2330K	ENST00000368508	NM_002944.2	2330	Gaa/Aaa	43/43	0.738164839516753	4	FACETS	0.529	0.481	0.58	0.265	0.24	0.29	SUBCLONAL	1	TRUE	2	0.769067659558443	4		432	1252	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427912	49427912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1313	147	647	0	ENST00000301067.7:c.10678G>A	p.Asp3560Asn	p.D3560N	ENST00000301067	NM_003482.3	3560	Gat/Aat	38/54	0.616060459763905	5	FACETS	0.564	0.513	0.618	0.188	0.171	0.206	SUBCLONAL	1	TRUE	2	0.769067659558443	5		647	1460	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831644	72831644	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	60	799	0	ENST00000268489.5:c.4937C>T	p.Ser1646Phe	p.S1646F	ENST00000268489	NM_006885.3	1646	tCc/tTc	9/10	0.769067659558443	2	FACETS	0.18	0.154	0.208	0.09	0.077	0.104	SUBCLONAL	1	TRUE	0	0.769067659558443	2		799	868	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984813	72984813	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0010706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	136	677	0	ENST00000268489.5:c.2771C>G	p.Ser924Ter	p.S924*	ENST00000268489	NM_006885.3	924	tCa/tGa	3/10	0.769067659558443	2	FACETS	0.507	0.462	0.555	0.254	0.231	0.278	SUBCLONAL	1	TRUE	0	0.769067659558443	2		677	697	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350198	89350198	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	180	1069	0	ENST00000301030.4:c.2752G>C	p.Glu918Gln	p.E918Q	ENST00000301030	NM_001256183.1	918	Gag/Cag	9/13	0.769067659558443	2	FACETS	0.521	0.481	0.563	0.261	0.24	0.282	SUBCLONAL	1	TRUE	0	0.769067659558443	2		1069	898	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45864890	45864890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	131	575	0	ENST00000391945.4:c.1129G>A	p.Glu377Lys	p.E377K	ENST00000391945	NM_000400.3	377	Gaa/Aaa	12/23	0.362689024558275	4	FACETS	0.625	0.567	0.687	0.313	0.283	0.344	INDETERMINATE	1	TRUE	2	0.769067659558443	4		575	964	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343490	70343490	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	58	838	0	ENST00000374080.3:c.1664C>A	p.Ser555Tyr	p.S555Y	ENST00000374080		555	tCt/tAt	12/45	0.26311785381599	3	FACETS	0.199	0.17	0.231	0.066	0.056	0.077	INDETERMINATE	1	TRUE	0	0.769067659558443	3		838	1049	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842455	68842456	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587781290	NA	P-0010706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	295	414	0	ENST00000261769.5:c.521dup	p.Asn174LysfsTer25	p.N174Kfs*25	ENST00000261769	NM_004360.3	172	-/A	4/16	0.769067659558443	2	FACETS	0.971	0.936	1	0.971	0.936	1	CLONAL	2	TRUE	0	0.769067659558443	2		414	395	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210733	5210733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779302415	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	162	355	0	ENST00000357368.4:c.5318C>T	p.Ser1773Leu	p.S1773L	ENST00000357368	NM_002850.3	1773	tCg/tTg	34/38	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.259275695905556	2		355	998	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012441	29012441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55974987	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	91	364	0	ENST00000282397.4:c.430G>A	p.Glu144Lys	p.E144K	ENST00000282397	NM_002019.4	144	Gaa/Aaa	4/30	0.169648957398031	3	FACETS	0.836	0.74	0.938	0.418	0.37	0.469	CLONAL	1	TRUE	1	0.259275695905556	3		364	949	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585494	29585494	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660428	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	114	158	1	ENST00000356175.3:c.4243G>A	p.Glu1415Lys	p.E1415K	ENST00000356175	NM_000267.3	1415	Gaa/Aaa	31/57	0.161990214073899	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.259275695905556	2		159	362	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579408	7579430	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGGGCCAGGAGGGGGCTGGTG	CAGGGGCCAGGAGGGGGCTGGTG	-	rs886041861	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	224	325	0	ENST00000269305.4:c.257_279del	p.Ala86ValfsTer55	p.A86Vfs*55	ENST00000269305	NM_001126112.2	86	gCACCAGCCCCCTCCTGGCCCCTG/g	4/11	0.161990214073899	2	FACETS	0.973	0.907	1	0.973	0.907	1	CLONAL	2	TRUE	0	0.259275695905556	2		325	888	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259786	16259786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	267	298	0	ENST00000375759.3:c.7051C>T	p.Pro2351Ser	p.P2351S	ENST00000375759	NM_015001.2	2351	Cct/Tct	11/15	0.259275695905556	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.259275695905556	4		298	1206	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845416	156845416	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	286	465	1	ENST00000524377.1:c.1459C>T	p.Gln487Ter	p.Q487*	ENST00000524377	NM_002529.3	487	Caa/Taa	12/17	0.259275695905556	3	FACETS	0.92	0.864	0.979	0.92	0.864	0.979	CLONAL	2	TRUE	1	0.259275695905556	3		466	1354	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085921	16085921	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	79	198	0	ENST00000281043.3:c.1097A>C	p.Lys366Thr	p.K366T	ENST00000281043	NM_005378.4	366	aAg/aCg	3/3	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.259275695905556	2		198	528	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917784	29917784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754823963	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	144	330	1	ENST00000389048.3:c.884C>T	p.Ser295Phe	p.S295F	ENST00000389048	NM_004304.4	295	tCc/tTc	3/29	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.259275695905556	2		331	924	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606929	47606929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	144	262	0	ENST00000263735.4:c.679C>T	p.His227Tyr	p.H227Y	ENST00000263735	NM_002354.2	227	Cat/Tat	7/9	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.259275695905556	2		262	930	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145543	61145543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767519747	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	102	287	1	ENST00000295025.8:c.655C>T	p.Arg219Cys	p.R219C	ENST00000295025	NM_002908.2	219	Cgt/Tgt	7/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.259275695905556	2		288	681	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248453	212248453	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371332509	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	106	314	1	ENST00000342788.4:c.3814G>A	p.Gly1272Arg	p.G1272R	ENST00000342788	NM_005235.2	1272	Ggg/Agg	28/28	1	2	FACETS	0.972	0.871	1	0.972	0.871	1	CLONAL	1	TRUE	1	0.259275695905556	2		315	841	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248741	212248741	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	86	225	0	ENST00000342788.4:c.3526A>T	p.Lys1176Ter	p.K1176*	ENST00000342788	NM_005235.2	1176	Aaa/Taa	28/28	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.259275695905556	2		225	660	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632279	215632279	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	162	437	0	ENST00000260947.4:c.1495C>T	p.His499Tyr	p.H499Y	ENST00000260947	NM_000465.2	499	Cac/Tac	6/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.259275695905556	2		437	1190	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008543	70008544	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	65	202	1	ENST00000394351.3:c.830_831delinsTT	p.Ala277Val	p.A277V	ENST00000394351	NM_000248.3	277	gCC/gTT	8/9	0.259275695905556	4	FACETS	0.753	0.652	0.864			1	SUBCLONAL	1	TRUE	NA	0.259275695905556	4		203	838	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021800	71021800	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	82	321	1	ENST00000318789.4:c.1558C>T	p.His520Tyr	p.H520Y	ENST00000318789	NM_032682.5	520	Cac/Tac	18/21	0.138082206345349	3	FACETS	0.821	0.723	0.927			1	INDETERMINATE	1	TRUE	NA	0.259275695905556	3		322	870	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200682	128200682	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	217	366	0	ENST00000341105.2:c.1123C>T	p.Leu375Phe	p.L375F	ENST00000341105	NM_032638.4	375	Ctc/Ttc	5/6	0.259275695905556	2	FACETS	0.953	0.888	1	0.953	0.888	1	CLONAL	2	TRUE	0	0.259275695905556	2		366	878	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138409912	138409912	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	235	353	0	ENST00000289153.2:c.1966C>T	p.Leu656Phe	p.L656F	ENST00000289153	NM_006219.2	656	Ctc/Ttc	13/22	0.259275695905556	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.259275695905556	2		353	889	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189349321	189349321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	213	343	0	ENST00000264731.3:c.17C>T	p.Ser6Leu	p.S6L	ENST00000264731	NM_003722.4	6	tCa/tTa	1/14	0.168308161428978	3	FACETS	0.977	0.908	1	0.651	0.605	0.699	CLONAL	2	TRUE	0	0.259275695905556	3		343	950	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587118	189587118	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761885185	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	235	314	0	ENST00000264731.3:c.1135C>T	p.Arg379Cys	p.R379C	ENST00000264731	NM_003722.4	379	Cgt/Tgt	9/14	0.168308161428978	3	FACETS	1	0.981	1	0.754	0.705	0.805	CLONAL	2	TRUE	0	0.259275695905556	3		314	905	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748257	41748257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	141	410	0	ENST00000226382.2:c.512C>T	p.Ser171Phe	p.S171F	ENST00000226382	NM_003924.3	171	tCc/tTc	3/3	0.259275695905556	3	FACETS	1	0.949	1			1	CLONAL	1	TRUE	NA	0.259275695905556	3		410	1155	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217165	66217165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	167	415	1	ENST00000273854.3:c.2450C>T	p.Ser817Phe	p.S817F	ENST00000273854	NM_004439.5	817	tCt/tTt	14/18	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.259275695905556	2		416	1036	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541697	187541697	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	115	392	0	ENST00000441802.2:c.6043C>T	p.His2015Tyr	p.H2015Y	ENST00000441802	NM_005245.3	2015	Cac/Tac	10/27	1	2	FACETS	0.918	0.826	1	0.918	0.826	1	CLONAL	1	TRUE	1	0.259275695905556	2		392	966	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542722	187542722	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	123	391	0	ENST00000441802.2:c.5018C>T	p.Ser1673Phe	p.S1673F	ENST00000441802	NM_005245.3	1673	tCt/tTt	10/27	1	2	FACETS	0.939	0.848	1	0.939	0.848	1	CLONAL	1	TRUE	1	0.259275695905556	2		391	1010	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226100	226100	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	76	211	1	ENST00000264932.6:c.559C>T	p.His187Tyr	p.H187Y	ENST00000264932	NM_004168.2	187	Cat/Tat	5/15	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.259275695905556	2		212	510	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861010	35861010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	126	290	0	ENST00000303115.3:c.139G>A	p.Glu47Lys	p.E47K	ENST00000303115	NM_002185.3	47	Gaa/Aaa	2/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.259275695905556	2		290	809	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873708	35873708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1394251315	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	105	323	0	ENST00000303115.3:c.664C>T	p.Pro222Ser	p.P222S	ENST00000303115	NM_002185.3	222	Cca/Tca	5/8	1	2	FACETS	0.95	0.85	1	0.95	0.85	1	CLONAL	1	TRUE	1	0.259275695905556	2		323	853	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502728	149502728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	141	323	0	ENST00000261799.4:c.2060G>A	p.Gly687Glu	p.G687E	ENST00000261799	NM_002609.3	687	gGa/gAa	15/23	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.259275695905556	2		323	965	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056405	180056405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	82	218	1	ENST00000261937.6:c.839C>T	p.Pro280Leu	p.P280L	ENST00000261937	NM_182925.4	280	cCc/cTc	7/30	1	2	FACETS	0.973	0.858	1	0.973	0.858	1	CLONAL	1	TRUE	1	0.259275695905556	2		219	650	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673379	30673379	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1327	125	477	0	ENST00000376406.3:c.3581C>T	p.Ser1194Phe	p.S1194F	ENST00000376406	NM_014641.2	1194	tCc/tTc	10/15	0.259275695905556	3	FACETS	0.75	0.676	0.828	0.375	0.338	0.414	SUBCLONAL	1	TRUE	1	0.259275695905556	3		477	1452	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679876	30679876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	81	274	0	ENST00000376406.3:c.1843C>T	p.Leu615Phe	p.L615F	ENST00000376406	NM_014641.2	615	Ctt/Ttt	5/15	0.259275695905556	3	FACETS	0.748	0.658	0.846	0.374	0.329	0.423	SUBCLONAL	1	TRUE	1	0.259275695905556	3		274	943	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680931	30680931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1407	137	515	2	ENST00000376406.3:c.788C>T	p.Pro263Leu	p.P263L	ENST00000376406	NM_014641.2	263	cCt/cTt	5/15	0.259275695905556	3	FACETS	0.773	0.701	0.85	0.387	0.35	0.425	SUBCLONAL	1	TRUE	1	0.259275695905556	3		517	1544	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178632	32178632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	216	423	0	ENST00000375023.3:c.2762G>A	p.Gly921Glu	p.G921E	ENST00000375023	NM_004557.3	921	gGa/gAa	18/30	0.259275695905556	3	FACETS	0.944	0.878	1	0.944	0.878	1	CLONAL	2	TRUE	1	0.259275695905556	3		423	997	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068025	94068025	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	206	516	1	ENST00000369303.4:c.937G>A	p.Glu313Lys	p.E313K	ENST00000369303	NM_004440.3	313	Gaa/Aaa	4/17	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.259275695905556	2		517	1292	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609831	117609831	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	148	447	1	ENST00000368508.3:c.6868G>A	p.Gly2290Ser	p.G2290S	ENST00000368508	NM_002944.2	2290	Ggt/Agt	43/43	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.259275695905556	2		448	1120	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609846	117609846	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1442895655	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	175	465	1	ENST00000368508.3:c.6853G>A	p.Glu2285Lys	p.E2285K	ENST00000368508	NM_002944.2	2285	Gaa/Aaa	43/43	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.259275695905556	2		466	1148	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709099	117709099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	145	376	0	ENST00000368508.3:c.1858C>T	p.Pro620Ser	p.P620S	ENST00000368508	NM_002944.2	620	Cct/Tct	13/43	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.259275695905556	2		376	1066	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710962	117710962	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	75	222	0	ENST00000368508.3:c.1310C>T	p.Pro437Leu	p.P437L	ENST00000368508	NM_002944.2	437	cCt/cTt	12/43	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.259275695905556	2		222	527	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519496	137519496	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	90	258	0	ENST00000367739.4:c.1142C>T	p.Pro381Leu	p.P381L	ENST00000367739	NM_000416.2	381	cCt/cTt	7/7	1	2	FACETS	0.963	0.854	1	0.963	0.854	1	CLONAL	1	TRUE	1	0.259275695905556	2		258	721	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202352	138202352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	89	225	0	ENST00000237289.4:c.2269C>T	p.Pro757Ser	p.P757S	ENST00000237289	NM_001270507.1	757	Ccc/Tcc	9/9	1	2	FACETS	0.966	0.856	1	0.966	0.856	1	CLONAL	1	TRUE	1	0.259275695905556	2		225	711	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510880	157510880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	122	335	0	ENST00000346085.5:c.3655C>T	p.Pro1219Ser	p.P1219S	ENST00000346085	NM_020732.3	1219	Cct/Tct	14/20	1	2	FACETS	0.997	0.9	1	0.997	0.9	1	CLONAL	1	TRUE	1	0.259275695905556	2		335	944	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959226	2959226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	168	306	0	ENST00000396946.4:c.2290G>A	p.Asp764Asn	p.D764N	ENST00000396946	NM_032415.4	764	Gac/Aac	18/25	0.212068191735669	4	FACETS	0.81	0.744	0.879	0.81	0.744	0.879	CLONAL	2	TRUE	2	0.259275695905556	4		306	1007	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026826	6026826	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756127972	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	109	141	0	ENST00000265849.7:c.1570C>T	p.Pro524Ser	p.P524S	ENST00000265849	NM_000535.5	524	Cca/Tca	11/15	0.212068191735669	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.259275695905556	4		141	445	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381466	81381466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	108	464	1	ENST00000222390.5:c.595G>A	p.Glu199Lys	p.E199K	ENST00000222390	NM_000601.4	199	Gaa/Aaa	5/18	0.161990214073899	2	FACETS	0.806	0.722	0.895	0.403	0.361	0.448	CLONAL	1	TRUE	0	0.259275695905556	2		465	1034	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436143	116436143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	109	255	0	ENST00000397752.3:c.4138G>A	p.Asp1380Asn	p.D1380N	ENST00000397752	NM_000245.2	1380	Gac/Aac	21/21	0.161990214073899	2	FACETS	1	0.98	1	0.685	0.616	0.757	CLONAL	1	TRUE	0	0.259275695905556	2		255	614	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875006	151875006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	192	325	0	ENST00000262189.6:c.7532C>T	p.Ser2511Phe	p.S2511F	ENST00000262189	NM_170606.2	2511	tCt/tTt	38/59	NA	2	FACETS	0.94	0.871	1			1	INDETERMINATE	2	TRUE	NA	0.259275695905556	2		325	788	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538897	23538897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1200957711	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	127	403	0	ENST00000380871.4:c.542G>A	p.Arg181Gln	p.R181Q	ENST00000380871	NM_006167.3	181	cGa/cAa	2/2	1	2	FACETS	0.946	0.855	1	0.946	0.855	1	CLONAL	1	TRUE	1	0.259275695905556	2		403	1036	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524937	8524937	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	218	262	0	ENST00000356435.5:c.667T>A	p.Leu223Ile	p.L223I	ENST00000356435		223	Tta/Ata	7/35	0.259275695905556	3	FACETS	1	0.982	1	0.766	0.714	0.819	CLONAL	2	TRUE	0	0.259275695905556	3		262	827	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636799	8636799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	350	375	0	ENST00000356435.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000356435		37	tCt/tTt	2/35	0.259275695905556	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	0	0.259275695905556	3		375	966	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87356825	87356825	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	309	394	1	ENST00000277120.3:c.1178C>T	p.Pro393Leu	p.P393L	ENST00000277120		393	cCt/cTt	10/19	0.259275695905556	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.259275695905556	3		395	1235	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606422	93606423	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	91	325	0	ENST00000375746.1:c.242_243delinsAT	p.Thr81Asn	p.T81N	ENST00000375746	NM_001174167.1	81	aCC/aAT	2/14	0.259275695905556	3	FACETS	0.991	0.879	1	0.496	0.439	0.556	CLONAL	1	TRUE	1	0.259275695905556	3		325	800	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212157	98212157	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	150	365	0	ENST00000331920.6:c.3515C>T	p.Pro1172Leu	p.P1172L	ENST00000331920	NM_000264.3	1172	cCc/cTc	21/24	0.259275695905556	3	FACETS	1	0.97	1	0.57	0.52	0.623	CLONAL	1	TRUE	1	0.259275695905556	3		365	1146	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135804163	135804163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	197	261	1	ENST00000298552.3:c.97C>T	p.Leu33Phe	p.L33F	ENST00000298552	NM_001162426.1	33	Ctc/Ttc	3/23	0.259275695905556	3	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	1	0.259275695905556	3		262	857	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845643	63845643	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	64	130	0	ENST00000279873.7:c.1382C>T	p.Pro461Leu	p.P461L	ENST00000279873	NM_032199.2	461	cCc/cTc	9/10	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.259275695905556	2		130	417	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332943	70332943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	181	515	0	ENST00000373644.4:c.848C>T	p.Ser283Phe	p.S283F	ENST00000373644	NM_030625.2	283	tCt/tTt	2/12	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.259275695905556	2		515	1238	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274696	123274696	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	164	348	0	ENST00000358487.5:c.1222G>A	p.Asp408Asn	p.D408N	ENST00000358487	NM_000141.4	408	Gac/Aac	9/18	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.259275695905556	2		348	1044	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138158	64138158	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747011048	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	123	261	0	ENST00000334205.4:c.2081C>T	p.Ser694Phe	p.S694F	ENST00000334205	NM_003942.2	694	tCt/tTt	16/17	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.259275695905556	2		261	852	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342779	118342780	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	152	344	0	ENST00000534358.1:c.905_906delinsAA	p.Arg302Gln	p.R302Q	ENST00000534358	NM_005933.3	302	cGG/cAA	3/36	0.259275695905556	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.259275695905556	1		344	839	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443814	18443814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	88	283	0	ENST00000266497.5:c.787G>A	p.Asp263Asn	p.D263N	ENST00000266497		263	Gat/Aat	3/31	0.259275695905556	3	FACETS	0.885	0.783	0.995	0.443	0.391	0.498	CLONAL	1	TRUE	1	0.259275695905556	3		283	866	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691101	18691101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1327878312	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	280	274	0	ENST00000266497.5:c.3212C>T	p.Pro1071Leu	p.P1071L	ENST00000266497		1071	cCt/cTt	23/31	0.259275695905556	3	FACETS	0.844	0.794	0.895	1	0.991	1	CLONAL	3	TRUE	1	0.259275695905556	3		274	964	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445376	49445376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	67	240	0	ENST00000301067.7:c.2090C>T	p.Pro697Leu	p.P697L	ENST00000301067	NM_003482.3	697	cCc/cTc	10/54	0.259275695905556	3	FACETS	0.805	0.699	0.921	0.403	0.349	0.461	CLONAL	1	TRUE	1	0.259275695905556	3		240	725	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434077	121434077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	341	416	0	ENST00000257555.6:c.968G>A	p.Gly323Glu	p.G323E	ENST00000257555		323	gGa/gAa	5/10	0.259275695905556	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.259275695905556	3		416	1232	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959133	28959133	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	126	309	0	ENST00000282397.4:c.2005G>A	p.Asp669Asn	p.D669N	ENST00000282397	NM_002019.4	669	Gat/Aat	14/30	0.169648957398031	3	FACETS	1	0.96	1	0.558	0.505	0.615	CLONAL	1	TRUE	1	0.259275695905556	3		309	983	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041073	29041073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	116	293	0	ENST00000282397.4:c.355G>A	p.Glu119Lys	p.E119K	ENST00000282397	NM_002019.4	119	Gaa/Aaa	3/30	0.169648957398031	3	FACETS	1	0.973	1	0.616	0.555	0.68	CLONAL	1	TRUE	1	0.259275695905556	3		293	821	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906999	32906999	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	107	214	0	ENST00000380152.3:c.1384G>A	p.Glu462Lys	p.E462K	ENST00000380152		462	Gaa/Aaa	10/27	0.169648957398031	3	FACETS	0.815	0.733	0.901	0.815	0.733	0.901	CLONAL	2	TRUE	1	0.259275695905556	3		214	572	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907092	32907092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	143	242	0	ENST00000380152.3:c.1477C>T	p.Pro493Ser	p.P493S	ENST00000380152		493	Cca/Tca	10/27	0.169648957398031	3	FACETS	0.895	0.818	0.976	0.895	0.818	0.976	CLONAL	2	TRUE	1	0.259275695905556	3		242	696	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988342	36988342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	50	104	0	ENST00000354822.5:c.311G>A	p.Gly104Glu	p.G104E	ENST00000354822	NM_001079668.2	104	gGg/gAg	2/3	0.259275695905556	3	FACETS	1	0.961	1	0.714	0.61	0.828	CLONAL	1	TRUE	1	0.259275695905556	3		104	305	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610464	81610464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	176	390	0	ENST00000298171.2:c.2062G>A	p.Asp688Asn	p.D688N	ENST00000298171	NM_000369.2	688	Gat/Aat	10/10	0.259275695905556	3	FACETS	1	0.985	1	0.657	0.604	0.712	CLONAL	1	TRUE	1	0.259275695905556	3		390	1168	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989031	41989031	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1431	253	572	1	ENST00000219905.7:c.1823C>T	p.Pro608Leu	p.P608L	ENST00000219905	NM_001164273.1	608	cCa/cTa	3/24	0.169648957398031	3	FACETS	1	0.989	1	0.655	0.61	0.701	CLONAL	1	TRUE	1	0.259275695905556	3		573	1684	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456431	99456431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	138	292	0	ENST00000268035.6:c.1748C>T	p.Ala583Val	p.A583V	ENST00000268035	NM_000875.3	583	gCt/gTt	8/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.259275695905556	2		292	893	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459199	99459199	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	182	498	0	ENST00000268035.6:c.1835C>T	p.Ser612Phe	p.S612F	ENST00000268035	NM_000875.3	612	tCc/tTc	9/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.259275695905556	2		498	1137	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828772	3828772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	190	462	0	ENST00000262367.5:c.1870C>T	p.Arg624Cys	p.R624C	ENST00000262367	NM_004380.2	624	Cgc/Tgc	9/31	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.259275695905556	2		462	1228	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857334	9857334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	106	302	0	ENST00000330684.3:c.4067C>T	p.Ser1356Phe	p.S1356F	ENST00000330684	NM_001134407.1	1356	tCt/tTt	13/13	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.259275695905556	2		302	739	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857391	9857391	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	95	361	0	ENST00000330684.3:c.4010C>T	p.Ser1337Leu	p.S1337L	ENST00000330684	NM_001134407.1	1337	tCg/tTg	13/13	1	2	FACETS	0.874	0.778	0.978	0.874	0.778	0.978	CLONAL	1	TRUE	1	0.259275695905556	2		361	838	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858357	9858359	+	stop_gained	Nonsense_Mutation	TNP	TTC	TTC	ATT	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	48	271	0	ENST00000330684.3:c.3042_3044delinsAAT	p.Trp1014_Lys1015delinsTer	p.W1014_K1015delins*	ENST00000330684	NM_001134407.1	1014	tgGAAg/tgAATg	13/13	1	2	FACETS	0.602	0.508	0.706	0.602	0.508	0.706	SUBCLONAL	1	TRUE	1	0.259275695905556	2		271	615	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892177	9892177	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555488097	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	170	466	0	ENST00000330684.3:c.2313G>A	p.Trp771Ter	p.W771*	ENST00000330684	NM_001134407.1	771	tgG/tgA	11/13	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.259275695905556	2		466	1052	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923482	9923482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	81	320	1	ENST00000330684.3:c.1805G>A	p.Gly602Glu	p.G602E	ENST00000330684	NM_001134407.1	602	gGa/gAa	9/13	1	2	FACETS	0.768	0.675	0.867	0.768	0.675	0.867	SUBCLONAL	1	TRUE	1	0.259275695905556	2		321	814	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274121	10274121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	74	269	0	ENST00000330684.3:c.148G>A	p.Glu50Lys	p.E50K	ENST00000330684	NM_001134407.1	50	Gaa/Aaa	2/13	1	2	FACETS	0.771	0.675	0.876	0.771	0.675	0.876	SUBCLONAL	1	TRUE	1	0.259275695905556	2		269	740	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979527	7979527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064796312	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	275	390	0	ENST00000319144.4:c.1498G>A	p.Asp500Asn	p.D500N	ENST00000319144	NM_001139.2	500	Gat/Aat	11/15	0.161990214073899	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.259275695905556	2		390	1036	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	245	343	0	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	0.161990214073899	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	0	0.259275695905556	2		343	939	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4102403	4102403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457335620	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	180	380	1	ENST00000262948.5:c.499G>A	p.Glu167Lys	p.E167K	ENST00000262948	NM_030662.3	167	Gag/Aag	4/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.259275695905556	2		381	987	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7174602	7174602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	123	322	0	ENST00000302850.5:c.1115G>A	p.Arg372Gln	p.R372Q	ENST00000302850	NM_000208.2	372	cGa/cAa	4/22	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.259275695905556	2		322	900	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290271	15290271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140147764	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	174	474	2	ENST00000263388.2:c.3364G>A	p.Asp1122Asn	p.D1122N	ENST00000263388	NM_000435.2	1122	Gac/Aac	21/33	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.259275695905556	2		476	1219	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946809	17946809	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257320432	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	141	383	0	ENST00000458235.1:c.1838G>A	p.Arg613Gln	p.R613Q	ENST00000458235	NM_000215.3	613	cGa/cAa	14/24	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.259275695905556	2		383	998	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948869	17948869	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	135	334	0	ENST00000458235.1:c.1573G>A	p.Glu525Lys	p.E525K	ENST00000458235	NM_000215.3	525	Gag/Aag	12/24	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.259275695905556	2		334	881	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42790926	42790926	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	155	426	0	ENST00000575354.2:c.71G>A	p.Trp24Ter	p.W24*	ENST00000575354	NM_015125.3	24	tGg/tAg	2/20	1	2	FACETS	0.99	0.904	1	0.99	0.904	1	CLONAL	1	TRUE	1	0.259275695905556	2		426	1208	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794463	42794463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	240	531	0	ENST00000575354.2:c.1543C>T	p.Pro515Ser	p.P515S	ENST00000575354	NM_015125.3	515	Cca/Tca	10/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.259275695905556	2		531	1359	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561555	9561555	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	142	213	0	ENST00000353224.5:c.227C>G	p.Pro76Arg	p.P76R	ENST00000353224	NM_177990.2	76	cCc/cGc	4/10	0.259275695905556	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.259275695905556	2		213	512	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408864	41408864	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	296	396	0	ENST00000373198.4:c.562C>T	p.Pro188Ser	p.P188S	ENST00000373198	NM_133170.3	188	Cca/Tca	4/32	0.259275695905556	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.259275695905556	2		396	1007	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42840334	42840334	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867186402	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	142	380	1	ENST00000398585.3:c.1414G>A	p.Asp472Asn	p.D472N	ENST00000398585	NM_001135099.1	472	Gat/Aat	12/14	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.259275695905556	2		381	1051	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852518	42852518	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766503231	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	172	455	0	ENST00000398585.3:c.568G>A	p.Gly190Arg	p.G190R	ENST00000398585	NM_001135099.1	190	Gga/Aga	6/14	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.259275695905556	2		455	1203	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545901	41545901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1674	457	554	0	ENST00000263253.7:c.2516C>T	p.Thr839Ile	p.T839I	ENST00000263253	NM_001429.3	839	aCc/aTc	14/31	0.259275695905556	5	FACETS	1	0.99	1	0.766	0.728	0.804	CLONAL	2	TRUE	2	0.259275695905556	5		554	2131	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1331479	1331479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	283	308	0	ENST00000400841.2:c.49G>A	p.Gly17Ser	p.G17S	ENST00000400841		17	Ggc/Agc	1/6	0.259275695905556	2	FACETS	1	0.949	1			1	CLONAL	2	TRUE	NA	0.259275695905556	2		308	1081	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349979	70349979	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	293	206	0	ENST00000374080.3:c.3962T>C	p.Met1321Thr	p.M1321T	ENST00000374080		1321	aTg/aCg	28/45	0.259275695905556	2	FACETS	1	0.967	1			1	CLONAL	3	TRUE	NA	0.259275695905556	2		206	732	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76931728	76931728	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	278	234	0	ENST00000373344.5:c.3802G>T	p.Glu1268Ter	p.E1268*	ENST00000373344	NM_000489.3	1268	Gag/Tag	10/35	0.259275695905556	2	FACETS	1	0.986	1			1	CLONAL	3	TRUE	NA	0.259275695905556	2		234	638	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857386	9857387	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0010726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	84	360	0	ENST00000330684.3:c.4014dup	p.Lys1339GlufsTer27	p.K1339Efs*27	ENST00000330684	NM_001134407.1	1338	-/G	13/13	1	2	FACETS	0.786	0.694	0.886	0.786	0.694	0.886	SUBCLONAL	1	TRUE	1	0.259275695905556	2		360	824	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0010812-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	268	365	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.969	0.914	1	0.969	0.914	1	CLONAL	1	TRUE	1	0.798523742532184	2		365	693	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0010812-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	396	452	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.763787557624062	1	FACETS	0.97	0.935	1	0.97	0.935	1	CLONAL	1	TRUE	0	0.798523742532184	1		452	614	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039583	180039583	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs75614493	NA	P-0010812-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	376	864	1	ENST00000261937.6:c.3460G>A	p.Gly1154Arg	p.G1154R	ENST00000261937	NM_182925.4	1154	Gga/Aga	26/30	0.763787557624062	1	FACETS	0.911	0.876	0.946	0.911	0.876	0.946	CLONAL	1	TRUE	0	0.798523742532184	1		865	621	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300155	15300155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768208563	NA	P-0010812-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	360	792	1	ENST00000263388.2:c.1121G>A	p.Arg374Gln	p.R374Q	ENST00000263388	NM_000435.2	374	cGg/cAg	7/33	1	2	FACETS	0.914	0.869	0.96	0.914	0.869	0.96	CLONAL	1	TRUE	1	0.798523742532184	2		793	986	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287446	46287446	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs774801990	NA	P-0010812-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	204	538	0	ENST00000334344.6:c.5305C>T	p.Arg1769Ter	p.R1769*	ENST00000334344	NM_152641.2	1769	Cga/Tga	20/21	1	2	FACETS	0.82	0.765	0.877	0.82	0.765	0.877	CLONAL	1	TRUE	1	0.798523742532184	2		538	623	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251859	212251859	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147514533	NA	P-0010812-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	188	427	0	ENST00000342788.4:c.3200G>A	p.Arg1067Gln	p.R1067Q	ENST00000342788	NM_005235.2	1067	cGa/cAa	27/28	1	2	FACETS	0.925	0.862	0.989	0.925	0.862	0.989	CLONAL	1	TRUE	1	0.798523742532184	2		427	509	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448297	56448298	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1567880599	NA	P-0010812-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	471	503	0	ENST00000407977.2:c.349dup	p.Arg117ProfsTer8	p.R117Pfs*8	ENST00000407977		117	cgc/cCgc	3/10	0.796008691066044	2	FACETS	0.882	0.855	0.908	0.882	0.855	0.908	CLONAL	2	TRUE	0	0.798523742532184	2		503	669	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	47	245	0				ENST00000310581	NM_198253.2	-/1132			0.25594358218952	5	FACETS	0.831	0.705	0.968	0.554	0.47	0.645	CLONAL	2	TRUE	2	0.25594358218952	5		245	306	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019392	42019392	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1152	304	480	1	ENST00000219905.7:c.3445G>A	p.Glu1149Lys	p.E1149K	ENST00000219905	NM_001164273.1	1149	Gag/Aag	10/24	0.25594358218952	3	FACETS	0.92	0.865	0.977	0.92	0.865	0.977	CLONAL	2	TRUE	1	0.25594358218952	3		481	1456	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439142	52439175	+	frameshift_variant	Frame_Shift_Del	DEL	GCATAATTGTGATTGTCTAGAAAGGCCGGCAGCC	GCATAATTGTGATTGTCTAGAAAGGCCGGCAGCC	-	novel	NA	P-0010813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	130	168	0	ENST00000460680.1:c.1067_1100del	p.Arg356ProfsTer63	p.R356Pfs*63	ENST00000460680	NM_004656.3	356	cGGCTGCCGGCCTTTCTAGACAATCACAATTATGCc/cc	11/17	0.25594358218952	2	FACETS	0.841	0.765	0.92	0.841	0.765	0.92	CLONAL	2	TRUE	0	0.25594358218952	2		168	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579441	7579442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0010813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	255	312	0	ENST00000269305.4:c.245dup	p.Ala83GlyfsTer66	p.A83Gfs*66	ENST00000269305	NM_001126112.2	82	ccg/ccCg	4/11	0.25594358218952	4	FACETS	0.976	0.916	1	0.976	0.916	1	CLONAL	3	TRUE	1	0.25594358218952	4		312	855	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521382	187521388	+	frameshift_variant	Frame_Shift_Del	DEL	AGCGAGC	AGCGAGC	-	novel	NA	P-0010813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	102	369	0	ENST00000441802.2:c.11767_11773del	p.Ala3923TrpfsTer3	p.A3923Wfs*3	ENST00000441802	NM_005245.3	3923	GCTCGCTtg/tg	22/27	0.25594358218952	3	FACETS	0.939	0.839	1	0.47	0.419	0.524	CLONAL	1	TRUE	1	0.25594358218952	3		369	957	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584585	187584586	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0010813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	123	384	0	ENST00000441802.2:c.3447_3448delinsTT	p.Met1149_Glu1150delinsIleTer	p.M1149_E1150delinsI*	ENST00000441802	NM_005245.3	1149	atGGaa/atTTaa	3/27	0.25594358218952	3	FACETS	1	0.947	1	0.537	0.484	0.592	CLONAL	1	TRUE	1	0.25594358218952	3		384	1010	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0010826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	34	175	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.237844566265002	3	FACETS	0.804	0.659	0.966	0.804	0.659	0.966	CLONAL	2	TRUE	1	0.15	3		175	303	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	29	245	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.972	0.78	1	0.972	0.78	1	CLONAL	1	TRUE	1	0.15	2		245	398	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021817	71021817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs797045586	NA	P-0010826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	37	472	0	ENST00000318789.4:c.1541G>A	p.Arg514His	p.R514H	ENST00000318789	NM_032682.5	514	cGt/cAt	18/21	1	2	FACETS	0.779	0.641	0.935	0.779	0.641	0.935	CLONAL	1	TRUE	1	0.15	2		472	633	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918276	44918276	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	23	264	0	ENST00000377967.4:c.901C>T	p.Gln301Ter	p.Q301*	ENST00000377967	NM_021140.2	301	Cag/Tag	11/29	1	1	FACETS	0.936	0.731	1	0.936	0.731	1	CLONAL	1	TRUE	0	0.15	1		264	303	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249011	55249012	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAACCCCACACC	novel	NA	P-0010826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	24	576	0	ENST00000275493.2:c.2316_2317insACACCCAACCCC	p.Pro772_His773insThrProAsnPro	p.P772_H773insTPNP	ENST00000275493	NM_005228.3	770	gac/gaCAACCCCACACCc	20/28	1	2	FACETS	0.484	0.378	0.608	0.484	0.378	0.608	SUBCLONAL	1	TRUE	1	0.15	2		576	661	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0010925-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	207	852	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.327227605558425	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.327227605558425	1		852	906	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089539	27089540	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010925-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	137	614	0	ENST00000324856.7:c.2498dup	p.Asn833LysfsTer39	p.N833Kfs*39	ENST00000324856	NM_006015.4	832	ata/atAa	8/20	1	2	FACETS	0.939	0.854	1	0.939	0.854	1	CLONAL	1	TRUE	1	0.327227605558425	2		614	892	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0011029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	572	378	0	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	0.36151587236238	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	0	0.36151587236238	3		378	1219	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55270295	55270295	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1280	391	545	1	ENST00000275493.2:c.3248A>G	p.Asp1083Gly	p.D1083G	ENST00000275493	NM_005228.3	1083	gAc/gGc	27/28	0.316045131192374	4	FACETS	0.881	0.835	0.928	0.881	0.835	0.928	CLONAL	2	TRUE	2	0.36151587236238	4		546	1671	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482871	140482871	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	187	463	0	ENST00000288602.6:c.1264C>G	p.Pro422Ala	p.P422A	ENST00000288602	NM_004333.4	422	Cct/Gct	10/18	0.36151587236238	3	FACETS	1	0.925	1	0.502	0.462	0.543	CLONAL	1	TRUE	1	0.36151587236238	3		463	1217	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778879	76778880	+	stop_gained,inframe_insertion,splice_region_variant	Nonsense_Mutation	INS	-	-	TTA	novel	NA	P-0011029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	237	427	0	ENST00000373344.5:c.6700-1_6700insTAA	p.Lys2233_Asp2234insTer	p.K2233_D2234ins*	ENST00000373344	NM_000489.3	2233	-/TAA		0.36151587236238	2	FACETS	0.787	0.736	0.839	0.787	0.736	0.839	SUBCLONAL	2	TRUE	0	0.36151587236238	2		427	833	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467883	99467883	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	121	361	0	ENST00000268035.6:c.2752del	p.Asp918IlefsTer19	p.D918Ifs*19	ENST00000268035	NM_000875.3	918	Gat/at	13/21	NA	2	FACETS	0.813	0.735	0.896			1	INDETERMINATE	1	TRUE	NA	0.36151587236238	2		361	823	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0011060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	149	391	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.518580777624135	1	FACETS	0.996	0.922	1	0.996	0.922	1	CLONAL	1	TRUE	0	0.565906872784933	1		391	379	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919761	96919761	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1273104139	NA	P-0011060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	106	349	1	ENST00000258439.3:c.502C>T	p.Gln168Ter	p.Q168*	ENST00000258439	NM_001193304.2	168	Cag/Tag	4/4	0.527217066489238	1	FACETS	0.781	0.707	0.857	0.781	0.707	0.857	SUBCLONAL	1	TRUE	0	0.565906872784933	1		350	344	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396916	139396916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761345476	NA	P-0011060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	55	192	0	ENST00000277541.6:c.5192C>T	p.Pro1731Leu	p.P1731L	ENST00000277541	NM_017617.3	1731	cCg/cTg	28/34	0.518580777624135	1	FACETS	0.82	0.715	0.93	0.82	0.715	0.93	CLONAL	1	TRUE	0	0.565906872784933	1		192	170	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206861	102206861	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	233	606	0	ENST00000263464.3:c.1489G>C	p.Asp497His	p.D497H	ENST00000263464	NM_001165.4	497	Gat/Cat	7/9	0.518580777624135	1	FACETS	0.965	0.906	1	0.965	0.906	1	CLONAL	1	TRUE	0	0.565906872784933	1		606	612	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964121	28964121	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	135	417	0	ENST00000282397.4:c.1781C>G	p.Thr594Arg	p.T594R	ENST00000282397	NM_002019.4	594	aCa/aGa	13/30	0.518580777624135	1	FACETS	0.845	0.775	0.916	0.845	0.775	0.916	CLONAL	1	TRUE	0	0.565906872784933	1		417	405	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33430524	33430524	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	152	515	1	ENST00000345365.6:c.616G>A	p.Asp206Asn	p.D206N	ENST00000345365	NM_002878.3	206	Gac/Aac	7/10	0.518580777624135	1	FACETS	0.767	0.707	0.83	0.767	0.707	0.83	SUBCLONAL	1	TRUE	0	0.565906872784933	1		516	502	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271876	15271878	+	frameshift_variant	Frame_Shift_Ins	INS	GGC	GGC	AGAA	novel	NA	P-0011060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	59	248	0	ENST00000263388.2:c.6561_6563delinsTTCT	p.Pro2188SerfsTer54	p.P2188Sfs*54	ENST00000263388	NM_000435.2	2187	ctGCCa/ctTTCTa	33/33	1	2	FACETS	0.993	0.867	1	0.993	0.867	1	CLONAL	1	TRUE	1	0.565906872784933	2		248	210	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101048	27101048	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	75	1014	1	ENST00000324856.7:c.4330G>T	p.Glu1444Ter	p.E1444*	ENST00000324856	NM_006015.4	1444	Gag/Tag	18/20	0.177809965347388	2	FACETS	0.916	0.809	1	0.916	0.809	1	CLONAL	2	TRUE	0	0.231856030811219	2		1015	353	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438603	52438603	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0011076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	41	396	0	ENST00000460680.1:c.1117-1G>A		p.X373_splice	ENST00000460680	NM_004656.3	373			NA	2	FACETS	1	0.92	1			1	INDETERMINATE	2	TRUE	NA	0.231856030811219	2		396	155	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096153	71096153	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	55	357	0	ENST00000318789.4:c.604C>T	p.Gln202Ter	p.Q202*	ENST00000318789	NM_032682.5	202	Caa/Taa	10/21	0.231856030811219	3	FACETS	0.98	0.846	1			1	CLONAL	2	TRUE	NA	0.231856030811219	3		357	270	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120505	70120506	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACAC	novel	NA	P-0011076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	49	573	0	ENST00000245479.2:c.1511_1514dup	p.Gln505HisfsTer74	p.Q505Hfs*74	ENST00000245479	NM_000346.3	503	tac/tACACac	3/3	1	2	FACETS	0.757	0.646	0.878	1	0.964	1	SUBCLONAL	2	TRUE	1	0.231856030811219	2		573	279	SUCCESS
APC	324	MSKCC	GRCh37	5	112175419	112175419	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0011084-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	37	338	0	ENST00000257430.4:c.4128T>A	p.Tyr1376Ter	p.Y1376*	ENST00000257430	NM_000038.5	1376	taT/taA	16/16	0.191840276582679	5	FACETS	0.7	0.576	0.838	0.233	0.192	0.28	SUBCLONAL	1	TRUE	2	0.3	5		338	511	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275239	41275239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011084-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	43	395	1	ENST00000349496.5:c.1405C>T	p.Arg469Cys	p.R469C	ENST00000349496	NM_001904.3	469	Cgt/Tgt	9/15	1	2	FACETS	0.538	0.45	0.636	0.538	0.45	0.636	SUBCLONAL	1	TRUE	1	0.3	2		396	533	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821530	72821530	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773606987	NA	P-0011084-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	63	830	0	ENST00000268489.5:c.10645G>A	p.Glu3549Lys	p.E3549K	ENST00000268489	NM_006885.3	3549	Gag/Aag	10/10	0.27885045871505	0	FACETS	0.317	0.274	0.365			1	SUBCLONAL	1	TRUE	0	0.3	0		830	926	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575116	48575116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011084-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	47	417	0	ENST00000342988.3:c.310C>T	p.Leu104Phe	p.L104F	ENST00000342988	NM_005359.5	104	Ctt/Ttt	3/12	0.3	2	FACETS	0.509	0.429	0.598			1	SUBCLONAL	1	TRUE	NA	0.3	2		417	615	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591129	67591130	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAG	novel	NA	P-0011084-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	33	341	0	ENST00000274335.5:c.1724_1726dup	p.Lys575dup	p.K575dup	ENST00000274335		575	-/AAG	12/15	0.191840276582679	5	FACETS	0.598	0.486	0.725	0.2	0.162	0.242	SUBCLONAL	1	TRUE	2	0.3	5		341	533	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119694	70119694	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011084-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	140	803	0	ENST00000245479.2:c.698del	p.Gly233AlafsTer20	p.G233Afs*20	ENST00000245479	NM_000346.3	232	caG/ca	3/3	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.3	2		803	919	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0011109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	120	276	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.493604579486712	1	FACETS	0.889	0.809	0.971	0.889	0.809	0.971	CLONAL	1	TRUE	0	0.493604579486712	1		276	412	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0011109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	299	402	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.266632820801472	3	FACETS	1	0.983	1	0.72	0.683	0.758	INDETERMINATE	2	TRUE	0	0.493604579486712	3		402	699	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916957	178916957	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200018596	NA	P-0011109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	174	544	0	ENST00000263967.3:c.344G>T	p.Arg115Leu	p.R115L	ENST00000263967	NM_006218.2	115	cGa/cTa	2/21	1	2	FACETS	0.997	0.921	1	0.997	0.921	1	CLONAL	1	TRUE	1	0.493604579486712	2		544	707	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218673	98218673	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368417828	NA	P-0011109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	123	218	2	ENST00000331920.6:c.3191C>T	p.Thr1064Met	p.T1064M	ENST00000331920	NM_000264.3	1064	aCg/aTg	19/24	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.493604579486712	2		220	453	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096570	178096570	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	167	305	0	ENST00000397062.3:c.761T>A	p.Phe254Tyr	p.F254Y	ENST00000397062	NM_006164.4	254	tTc/tAc	5/5	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.493604579486712	2		305	611	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587204	212587204	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs149800322	NA	P-0011109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	238	460	0	ENST00000342788.4:c.797T>C	p.Phe266Ser	p.F266S	ENST00000342788	NM_005235.2	266	tTt/tCt	7/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.493604579486712	2		460	876	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391033	89391033	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1420005671	NA	P-0011109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	173	438	0	ENST00000336596.2:c.1099G>A	p.Gly367Arg	p.G367R	ENST00000336596	NM_005233.5	367	Ggg/Agg	5/17	1	2	FACETS	0.878	0.81	0.95	0.878	0.81	0.95	CLONAL	1	TRUE	1	0.493604579486712	2		438	798	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245316	46245316	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	92	416	0	ENST00000334344.6:c.3410C>A	p.Ser1137Ter	p.S1137*	ENST00000334344	NM_152641.2	1137	tCa/tAa	15/21	0.266632820801472	3	FACETS	0.512	0.454	0.574	0.171	0.151	0.192	INDETERMINATE	1	TRUE	0	0.493604579486712	3		416	908	SUCCESS
APC	324	MSKCC	GRCh37	5	112175440	112175441	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTTAGCAGATGTA	novel	NA	P-0011109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	183	292	0	ENST00000257430.4:c.4150_4162dup	p.Thr1388IlefsTer2	p.T1388Ifs*2	ENST00000257430	NM_000038.5	1383	-/TTTAGCAGATGTA	16/16	0.493604579486712	2	FACETS	1	0.987	1	0.636	0.59	0.683	CLONAL	1	TRUE	0	0.493604579486712	2		292	583	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0011132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	278	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.298327580115864	3	FACETS	0.907	0.851	0.964	0.907	0.851	0.964	CLONAL	2	TRUE	1	0.3	3		311	1175	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584501	189584501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908849	NA	P-0011132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	163	453	1	ENST00000264731.3:c.797G>A	p.Arg266Gln	p.R266Q	ENST00000264731	NM_003722.4	266	cGa/cAa	6/14	1	2	FACETS	0.886	0.812	0.965	0.886	0.812	0.965	CLONAL	1	TRUE	1	0.3	2		454	1226	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397178	397178	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1469969945	NA	P-0011132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1269	173	624	2	ENST00000380956.4:c.563C>T	p.Pro188Leu	p.P188L	ENST00000380956	NM_001195286.1	188	cCg/cTg	5/9	0.298327580115864	3	FACETS	0.92	0.844	0.999	0.46	0.422	0.5	CLONAL	1	TRUE	1	0.3	3		626	1442	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380014	116380014	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1185	204	617	0	ENST00000397752.3:c.1403C>A	p.Ser468Tyr	p.S468Y	ENST00000397752	NM_000245.2	468	tCt/tAt	4/21	1	2	FACETS	0.979	0.906	1	0.979	0.906	1	CLONAL	1	TRUE	1	0.3	2		617	1389	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850223	128850223	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1479888709	NA	P-0011132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	189	539	0	ENST00000249373.3:c.1486A>G	p.Ile496Val	p.I496V	ENST00000249373	NM_005631.4	496	Atc/Gtc	9/12	1	2	FACETS	0.976	0.9	1	0.976	0.9	1	CLONAL	1	TRUE	1	0.3	2		539	1291	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263362	123263362	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs745349225	NA	P-0011132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	181	581	0	ENST00000358487.5:c.1381G>T	p.Ala461Ser	p.A461S	ENST00000358487	NM_000141.4	461	Gca/Tca	10/18	1	2	FACETS	0.961	0.885	1	0.961	0.885	1	CLONAL	1	TRUE	1	0.3	2		581	1255	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245595	46245595	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	283	430	1	ENST00000334344.6:c.3689G>T	p.Cys1230Phe	p.C1230F	ENST00000334344	NM_152641.2	1230	tGt/tTt	15/21	0.298327580115864	3	FACETS	0.902	0.847	0.958	0.902	0.847	0.958	CLONAL	2	TRUE	1	0.3	3		431	1203	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988571	36988571	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1264	223	803	0	ENST00000354822.5:c.82C>A	p.Arg28Ser	p.R28S	ENST00000354822	NM_001079668.2	28	Cgc/Agc	2/3	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.3	2		803	1487	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2202712	2202712	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1194	275	772	1	ENST00000398665.3:c.721A>T	p.Asn241Tyr	p.N241Y	ENST00000398665	NM_032482.2	241	Aat/Tat	9/28	0.3	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.3	1		773	1469	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208009	5208009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746059446	NA	P-0011132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	249	740	1	ENST00000357368.4:c.5702G>A	p.Arg1901Gln	p.R1901Q	ENST00000357368	NM_002850.3	1901	cGg/cAg	37/38	0.3	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.3	1		741	1351	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600510	10600510	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	149	399	0	ENST00000171111.5:c.1345G>T	p.Glu449Ter	p.E449*	ENST00000171111	NM_203500.1	449	Gag/Tag	4/6	0.3	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.3	1		399	746	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11137023	11137023	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0011132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	184	559	1	ENST00000358026.2:c.3215+1G>A		p.X1072_splice	ENST00000358026	NM_001128849.1	1072			0.3	1	FACETS	0.913	0.842	0.988	0.913	0.842	0.988	CLONAL	1	TRUE	0	0.3	1		560	1142	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30311673	30311673	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1324	239	628	0	ENST00000262643.3:c.527A>G	p.Tyr176Cys	p.Y176C	ENST00000262643	NM_001238.2	176	tAt/tGt	7/12	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.3	2		628	1563	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735454	40735455	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0011132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	199	691	0	ENST00000373198.4:c.3418dup	p.Ala1140GlyfsTer35	p.A1140Gfs*35	ENST00000373198	NM_133170.3	1140	gcc/gGcc	25/32	1	2	FACETS	0.943	0.871	1	0.943	0.871	1	CLONAL	1	TRUE	1	0.3	2		691	1407	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221318	1221321	+	frameshift_variant	Frame_Shift_Del	DEL	CCGC	CCGC	GG	novel	NA	P-0011132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	214	594	0	ENST00000326873.7:c.841_844delinsGG	p.Pro281GlyfsTer3	p.P281Gfs*3	ENST00000326873	NM_000455.4	281	CCGCtc/GGtc	6/10	0.3	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.3	1		594	1145	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0011138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	636	327	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.382828347643234	3	FACETS	0.854	0.823	0.885			1	CLONAL	3	TRUE	NA	0.382828347643234	3		327	1545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0011138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	130	378	0	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	0.382828347643234	1	FACETS	0.725	0.658	0.796	0.725	0.658	0.796	SUBCLONAL	1	TRUE	0	0.382828347643234	1		378	757	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843550	156843550	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	146	402	0	ENST00000524377.1:c.976A>T	p.Ser326Cys	p.S326C	ENST00000524377	NM_002529.3	326	Agc/Tgc	8/17	1	2	FACETS	0.629	0.573	0.689	0.629	0.573	0.689	SUBCLONAL	1	TRUE	1	0.382828347643234	2		402	1212	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100553	8100553	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	111	353	0	ENST00000346208.3:c.527C>G	p.Ala176Gly	p.A176G	ENST00000346208		176	gCc/gGc	3/6	1	2	FACETS	0.557	0.5	0.618	0.557	0.5	0.618	SUBCLONAL	1	TRUE	1	0.382828347643234	2		353	1041	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32439164	32439164	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	130	290	0	ENST00000332351.3:c.909C>A	p.Cys303Ter	p.C303*	ENST00000332351	NM_024426.4	303	tgC/tgA	4/10	0.382828347643234	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.382828347643234	1		290	533	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926878	112926878	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	107	320	0	ENST00000351677.2:c.1498C>G	p.Gln500Glu	p.Q500E	ENST00000351677	NM_002834.3	500	Cag/Gag	13/16	0.382828347643234	1	FACETS	0.557	0.5	0.619	0.557	0.5	0.619	SUBCLONAL	1	TRUE	0	0.382828347643234	1		320	811	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954022	32954023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs397507419	NA	P-0011185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	156	407	7	ENST00000380152.3:c.9097dup	p.Thr3033AsnfsTer11	p.T3033Nfs*11	ENST00000380152		3030	aca/acAa	23/27	0.87448920179423	1	FACETS	0.909	0.861	0.954	0.909	0.861	0.954	CLONAL	1	TRUE	0	0.87448920179423	1		414	221	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705517	47705517	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1558521813	NA	P-0011185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	250	472	0	ENST00000233146.2:c.2317A>G	p.Lys773Glu	p.K773E	ENST00000233146	NM_000251.2	773	Aag/Gag	14/16	1	2	FACETS	0.877	0.826	0.929	0.877	0.826	0.929	CLONAL	1	TRUE	1	0.87448920179423	2		472	652	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273096	198273096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	368	457	0	ENST00000335508.6:c.1114C>T	p.Pro372Ser	p.P372S	ENST00000335508	NM_012433.2	372	Cca/Tca	8/25	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.87448920179423	2		457	835	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356427	66356427	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1321339471	NA	P-0011185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	137	251	0	ENST00000273854.3:c.1070C>A	p.Pro357His	p.P357H	ENST00000273854	NM_004439.5	357	cCc/cAc	5/18	0.87448920179423	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.87448920179423	1		251	174	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674171	117674171	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	224	375	0	ENST00000368508.3:c.4303G>A	p.Val1435Ile	p.V1435I	ENST00000368508	NM_002944.2	1435	Gtt/Att	26/43	1	2	FACETS	0.88	0.826	0.935	0.88	0.826	0.935	CLONAL	1	TRUE	1	0.87448920179423	2		375	582	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486251	8486251	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	702	377	0	ENST00000356435.5:c.2566T>G	p.Tyr856Asp	p.Y856D	ENST00000356435		856	Tac/Gac	17/35	0.87448920179423	4	FACETS	0.87	0.845	0.895	0.87	0.845	0.895	CLONAL	3	TRUE	1	0.87448920179423	4		377	1153	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404350	139404350	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	538	451	0	ENST00000277541.6:c.2804C>T	p.Pro935Leu	p.P935L	ENST00000277541	NM_017617.3	935	cCc/cTc	18/34	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.87448920179423	2		451	1226	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717678	89717685	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGACAA	GAAGACAA	-	novel	NA	P-0011185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	77	375	0	ENST00000371953.3:c.704_711del	p.Glu235ValfsTer5	p.E235Vfs*5	ENST00000371953	NM_000314.4	235	GAAGACAAg/g	7/9	0.87448920179423	1	FACETS	0.491	0.439	0.544	0.491	0.439	0.544	SUBCLONAL	1	TRUE	0	0.87448920179423	1		375	202	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1567548223	NA	P-0011185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	573	453	1	ENST00000269305.4:c.797del	p.Gly266AspfsTer79	p.G266Dfs*79	ENST00000269305	NM_001126112.2	266	gGa/ga	8/11	0.87448920179423	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.87448920179423	1		454	721	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443908	49443908	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	510	412	2	ENST00000301067.7:c.3463del	p.Leu1155TrpfsTer9	p.L1155Wfs*9	ENST00000301067	NM_003482.3	1155	Ctg/tg	11/54	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.87448920179423	2		414	1128	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0011270-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	217	280	2	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	0.661259033605513	1	FACETS	0.886	0.832	0.94	0.886	0.832	0.94	CLONAL	1	TRUE	0	0.661259033605513	1		282	496	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441304	149441304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011284-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	140	495	0	ENST00000286301.3:c.1735C>T	p.Arg579Trp	p.R579W	ENST00000286301	NM_005211.3	579	Cgg/Tgg	12/22	1	2	FACETS	0.898	0.818	0.983	0.898	0.818	0.983	CLONAL	1	TRUE	1	0.354549899816094	2		495	879	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579580	7579580	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011284-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	507	450	0	ENST00000269305.4:c.107del	p.Pro36ArgfsTer8	p.P36Rfs*8	ENST00000269305	NM_001126112.2	36	cCg/cg	4/11	0.354549899816094	4	FACETS	0.965	0.929	1			1	CLONAL	4	TRUE	NA	0.354549899816094	4		450	1004	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589586	67589591	+	inframe_deletion	In_Frame_Del	DEL	ATGAAT	ATGAAT	-	novel	NA	P-0011284-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	74	295	0	ENST00000274335.5:c.1351_1356del	p.Glu451_Tyr452del	p.E451_Y452del	ENST00000274335		450	cATGAATat/cat	10/15	0.354549899816094	3	FACETS	0.919	0.806	1	0.459	0.403	0.52	CLONAL	1	TRUE	1	0.354549899816094	3		295	535	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761459	59761460	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs774684620	NA	P-0011284-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	341	406	0	ENST00000259008.2:c.2947dup	p.Ile983AsnfsTer19	p.I983Nfs*19	ENST00000259008	NM_032043.2	983	att/aAtt	20/20	0.354549899816094	3	FACETS	0.945	0.899	0.991	0.945	0.899	0.991	CLONAL	3	TRUE	0	0.354549899816094	3		406	799	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026204	48026204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750440	NA	P-0011284-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	292	525	1	ENST00000234420.5:c.1082G>A	p.Arg361His	p.R361H	ENST00000234420	NM_000179.2	361	cGc/cAc	4/10	0.354549899816094	4	FACETS	0.963	0.905	1	0.963	0.905	1	CLONAL	2	TRUE	2	0.354549899816094	4		526	1159	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030221	180030221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143739828	NA	P-0011284-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	171	541	1	ENST00000261937.6:c.4063G>A	p.Val1355Met	p.V1355M	ENST00000261937	NM_182925.4	1355	Gtg/Atg	30/30	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.354549899816094	2		542	904	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152479	56152479	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011284-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	79	304	0	ENST00000399503.3:c.535del	p.Arg179ValfsTer6	p.R179Vfs*6	ENST00000399503	NM_005921.1	179	Cgt/gt	2/20	0.354549899816094	3	FACETS	0.83	0.73	0.937	0.415	0.365	0.469	CLONAL	1	TRUE	1	0.354549899816094	3		304	632	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0011298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	97	348	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.848	0.754	0.948	0.848	0.754	0.948	CLONAL	1	TRUE	1	0.222384908352643	2		348	1029	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851381	156851381	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	83	410	0	ENST00000524377.1:c.2338C>G	p.Arg780Gly	p.R780G	ENST00000524377	NM_002529.3	780	Cgg/Ggg	17/17	0.203654615212203	3	FACETS	0.934	0.823	1	0.467	0.411	0.527	CLONAL	1	TRUE	1	0.222384908352643	3		410	888	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498082	29498082	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	102	473	0	ENST00000389048.3:c.1924G>T	p.Asp642Tyr	p.D642Y	ENST00000389048	NM_004304.4	642	Gac/Tac	11/29	1	2	FACETS	0.876	0.782	0.977	0.876	0.782	0.977	CLONAL	1	TRUE	1	0.222384908352643	2		473	1047	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94163100	94163100	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1308	133	591	0	ENST00000323929.3:c.2047G>C	p.Gly683Arg	p.G683R	ENST00000323929	NM_005591.3	683	Ggg/Cgg	19/20	1	2	FACETS	0.83	0.751	0.914	0.83	0.751	0.914	CLONAL	1	TRUE	1	0.222384908352643	2		591	1441	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779451	3779451	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	130	547	1	ENST00000262367.5:c.5597G>T	p.Arg1866Leu	p.R1866L	ENST00000262367	NM_004380.2	1866	cGc/cTc	31/31	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.222384908352643	2		548	908	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610298	10610298	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	115	555	1	ENST00000171111.5:c.412G>T	p.Glu138Ter	p.E138*	ENST00000171111	NM_203500.1	138	Gaa/Taa	2/6	0.222384908352643	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.222384908352643	1		556	879	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220492	1220492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	101	445	1	ENST00000326873.7:c.587del	p.Gly196AlafsTer91	p.G196Afs*91	ENST00000326873	NM_000455.4	195	ctG/ct	4/10	0.222384908352643	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.222384908352643	1		446	779	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136170	11136170	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0011298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	94	473	0	ENST00000358026.2:c.3155del	p.Phe1052SerfsTer54	p.F1052Sfs*54	ENST00000358026	NM_001128849.1	1052	Ttc/tc	22/36	0.222384908352643	1	FACETS	0.993	0.883	1	0.993	0.883	1	CLONAL	1	TRUE	0	0.222384908352643	1		473	757	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	TT	novel	NA	P-0011298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	67	232	0	ENST00000304494.5:c.322delinsAA	p.Asp108LysfsTer12	p.D108Kfs*12	ENST00000304494	NM_000077.4	108	Gat/AAat	2/3	0.203021411708812	2	FACETS	1	0.967	1	0.68	0.593	0.774	CLONAL	1	TRUE	0	0.222384908352643	2		232	443	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023007	27023008	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGC	rs587779737	NA	P-0011299-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	18	9	0	ENST00000324856.7:c.126_128dup	p.Ala45dup	p.A45dup	ENST00000324856	NM_006015.4	45	gag/gaGGCg	1/20	1	2	FACETS	1	0.785	1	1	0.939	1	CLONAL	2	TRUE	1	0.338781055215057	2		9	53	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509127	66509127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145126637	NA	P-0011299-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	34	270	0	ENST00000273854.3:c.200G>A	p.Arg67His	p.R67H	ENST00000273854	NM_004439.5	67	cGc/cAc	2/18	1	2	FACETS	0.374	0.305	0.453	0.374	0.305	0.453	SUBCLONAL	1	TRUE	1	0.338781055215057	2		270	536	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519925	NA	P-0011303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	152	387	0	ENST00000263967.3:c.1357G>C	p.Glu453Gln	p.E453Q	ENST00000263967	NM_006218.2	453	Gaa/Caa	8/21	0.39986676236201	3	FACETS	0.758	0.692	0.828	0.379	0.346	0.414	SUBCLONAL	1	TRUE	1	0.39986676236201	3		387	1203	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578499	7578499	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs786203071	NA	P-0011303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	405	408	1	ENST00000269305.4:c.431A>C	p.Gln144Pro	p.Q144P	ENST00000269305	NM_001126112.2	144	cAg/cCg	5/11	0.39986676236201	2	FACETS	0.886	0.844	0.929	0.886	0.844	0.929	CLONAL	2	TRUE	0	0.39986676236201	2		409	1143	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058079	27058079	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	66	95	0	ENST00000324856.7:c.1787G>T	p.Arg596Leu	p.R596L	ENST00000324856	NM_006015.4	596	cGc/cTc	3/20	0.295178269148236	4	FACETS	0.903	0.785	1	0.451	0.392	0.515	CLONAL	1	TRUE	2	0.39986676236201	4		95	512	SUCCESS
INSRR	3645	MSKCC	GRCh37	1	156811503	156811503	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	36	37	0	ENST00000368195.3:c.3481C>A	p.Pro1161Thr	p.P1161T	ENST00000368195	NM_014215.2	1161	Ccc/Acc	20/22	0.387431958112199	5	FACETS	1	0.939	1	0.333	0.276	0.396	CLONAL	1	TRUE	1	0.39986676236201	5		37	216	SUCCESS
ALK	238	MSKCC	GRCh37	2	29541241	29541241	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1239	115	375	0	ENST00000389048.3:c.1576G>T	p.Val526Phe	p.V526F	ENST00000389048	NM_004304.4	526	Gtc/Ttc	8/29	0.39986676236201	3	FACETS	0.51	0.457	0.565	0.255	0.228	0.283	SUBCLONAL	1	TRUE	1	0.39986676236201	3		375	1354	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537945	212537945	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	411	378	0	ENST00000342788.4:c.1660G>T	p.Glu554Ter	p.E554*	ENST00000342788	NM_005235.2	554	Gag/Tag	14/28	0.398829118056119	3	FACETS	0.939	0.894	0.985	0.939	0.894	0.985	CLONAL	2	TRUE	1	0.39986676236201	3		378	1313	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157192782	157192782	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	373	395	0	ENST00000346085.5:c.1772G>T	p.Trp591Leu	p.W591L	ENST00000346085	NM_020732.3	591	tGg/tTg	3/20	0.382693458824667	2	FACETS	0.821	0.78	0.863	0.821	0.78	0.863	CLONAL	2	TRUE	0	0.39986676236201	2		395	1136	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606188	93606188	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	312	245	0	ENST00000375746.1:c.8G>A	p.Ser3Asn	p.S3N	ENST00000375746	NM_001174167.1	3	aGc/aAc	2/14	0.382693458824667	2	FACETS	0.902	0.854	0.951	0.902	0.854	0.951	CLONAL	2	TRUE	0	0.39986676236201	2		245	865	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201002	108201002	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	179	308	0	ENST00000278616.4:c.7369G>C	p.Glu2457Gln	p.E2457Q	ENST00000278616	NM_000051.3	2457	Gag/Cag	50/63	0.398829118056119	3	FACETS	0.978	0.901	1	0.489	0.45	0.53	CLONAL	1	TRUE	1	0.39986676236201	3		308	1098	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248867	133248867	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1310	265	402	1	ENST00000320574.5:c.1728G>T	p.Lys576Asn	p.K576N	ENST00000320574	NM_006231.2	576	aaG/aaT	16/49	0.398829118056119	3	FACETS	1	0.943	1	0.505	0.472	0.539	CLONAL	1	TRUE	1	0.39986676236201	3		403	1575	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610105	28610105	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1703	114	493	0	ENST00000241453.7:c.1385G>A	p.Trp462Ter	p.W462*	ENST00000241453	NM_004119.2	462	tGg/tAg	11/24	0.148168217241184	5	FACETS	0.502	0.45	0.558			1	INDETERMINATE	1	TRUE	NA	0.39986676236201	5		493	1817	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039133	49039133	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs587776786	NA	P-0011303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	224	146	1	ENST00000267163.4:c.2212-1G>A		p.X738_splice	ENST00000267163	NM_000321.2	738			0.39986676236201	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	1	0.39986676236201	3		147	662	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465517	99465517	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1374	243	467	0	ENST00000268035.6:c.2342G>C	p.Arg781Thr	p.R781T	ENST00000268035	NM_000875.3	781	aGa/aCa	11/21	0.398829118056119	3	FACETS	0.902	0.84	0.966	0.451	0.42	0.483	CLONAL	1	TRUE	1	0.39986676236201	3		467	1617	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1206915	1206915	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0011303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	111	161	0	ENST00000326873.7:c.3G>A	p.Met1?	p.M1?	ENST00000326873	NM_000455.4	1	atG/atA	1/10	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.39986676236201	NA		161	624	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144179	11144179	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	309	293	0	ENST00000358026.2:c.3760G>T	p.Glu1254Ter	p.E1254*	ENST00000358026	NM_001128849.1	1254	Gag/Tag	26/36	0.382693458824667	2	FACETS	0.955	0.905	1	0.955	0.905	1	CLONAL	2	TRUE	0	0.39986676236201	2		293	809	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757449	40757449	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1689	243	444	0	ENST00000373198.4:c.2849T>C	p.Leu950Pro	p.L950P	ENST00000373198	NM_133170.3	950	cTg/cCg	20/32	0.357249134858381	4	FACETS	0.881	0.819	0.945	0.294	0.273	0.315	CLONAL	1	TRUE	1	0.39986676236201	4		444	1932	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444986	49444987	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0011303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	96	171	0	ENST00000301067.7:c.2479dup	p.Gln827ProfsTer3	p.Q827Pfs*3	ENST00000301067	NM_003482.3	827	caa/cCaa	10/54	0.398829118056119	3	FACETS	0.76	0.677	0.849	0.38	0.338	0.425	SUBCLONAL	1	TRUE	1	0.39986676236201	3		171	758	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0011331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	651	427	0	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	0.632769725906947	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.632769725906947	3		427	840	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032181	10032181	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	186	365	0	ENST00000330684.3:c.642G>T	p.Lys214Asn	p.K214N	ENST00000330684	NM_001134407.1	214	aaG/aaT	3/13	0.632769725906947	3	FACETS	0.943	0.872	1	0.471	0.436	0.508	CLONAL	1	TRUE	1	0.632769725906947	3		365	821	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015026	27015026	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	470	457	0	ENST00000335756.4:c.128G>T	p.Arg43Leu	p.R43L	ENST00000335756	NM_001809.3	43	cGg/cTg	2/5	0.632769725906947	3	FACETS	0.995	0.955	1	0.995	0.955	1	CLONAL	2	TRUE	1	0.632769725906947	3		457	983	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202786	128202786	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	544	375	1	ENST00000341105.2:c.934G>T	p.Gly312Cys	p.G312C	ENST00000341105	NM_032638.4	312	Ggc/Tgc	4/6	0.632769725906947	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	0	0.632769725906947	3		376	746	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980328	55980328	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	163	434	1	ENST00000263923.4:c.763G>T	p.Gly255Trp	p.G255W	ENST00000263923	NM_002253.2	255	Ggg/Tgg	6/30	0.632769725906947	3	FACETS	0.719	0.66	0.781	0.36	0.33	0.391	SUBCLONAL	1	TRUE	1	0.632769725906947	3		435	943	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118379870	118379870	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	388	352	0	ENST00000534358.1:c.10855G>A	p.Glu3619Lys	p.E3619K	ENST00000534358	NM_005933.3	3619	Gaa/Aaa	29/36	0.632769725906947	3	FACETS	0.954	0.912	0.997	0.954	0.912	0.997	CLONAL	2	TRUE	1	0.632769725906947	3		352	846	SUCCESS
AR	367	MSKCC	GRCh37	X	66766249	66766249	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	78	257	0	ENST00000374690.3:c.1261G>T	p.Gly421Ter	p.G421*	ENST00000374690	NM_000044.3	421	Gga/Tga	1/8	1	2	FACETS	0.839	0.745	0.937	0.839	0.745	0.937	CLONAL	1	TRUE	1	0.632769725906947	2		257	294	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219380	1219381	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0011331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	289	365	0	ENST00000326873.7:c.432_433insT	p.Glu145Ter	p.E145*	ENST00000326873	NM_000455.4	144	-/T	3/10	0.62676141395732	2	FACETS	0.923	0.881	0.964	0.923	0.881	0.964	CLONAL	2	TRUE	0	0.632769725906947	2		365	495	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602687	10602691	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGC	GCAGC	-	novel	NA	P-0011331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	344	385	2	ENST00000171111.5:c.887_891del	p.Arg296GlnfsTer52	p.R296Qfs*52	ENST00000171111	NM_203500.1	296	cGCTGC/c	3/6	0.62676141395732	2	FACETS	0.929	0.891	0.967	0.929	0.891	0.967	CLONAL	2	TRUE	0	0.632769725906947	2		387	585	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	189	326	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	0.822	0.761	0.886	0.822	0.761	0.886	CLONAL	1	TRUE	1	0.52	2		326	884	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	305	501	1	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.52	2		502	1081	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	346	586	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.52	2		586	1289	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205332	46205332	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	192	300	0	ENST00000334344.6:c.416C>T	p.Ser139Leu	p.S139L	ENST00000334344	NM_152641.2	139	tCg/tTg	4/21	1	2	FACETS	0.922	0.854	0.992	0.922	0.854	0.992	CLONAL	1	TRUE	1	0.52	2		300	801	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	342	528	3	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.954	0.901	1	0.954	0.901	1	CLONAL	1	TRUE	1	0.52	2		531	1379	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911535	101911535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113605875	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	264	416	0	ENST00000374994.4:c.1460G>A	p.Arg487Gln	p.R487Q	ENST00000374994	NM_004612.2	487	cGg/cAg	9/9	1	2	FACETS	0.971	0.91	1	0.971	0.91	1	CLONAL	1	TRUE	1	0.52	2		416	1046	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920469	134920469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	249	553	2	ENST00000398015.3:c.2284G>A	p.Asp762Asn	p.D762N	ENST00000398015	NM_004441.4	762	Gac/Aac	12/16	1	2	FACETS	0.967	0.905	1	0.967	0.905	1	CLONAL	1	TRUE	1	0.52	2		555	990	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882049	36882049	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs34810717	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	230	409	0	ENST00000358127.4:c.964G>A	p.Ala322Thr	p.A322T	ENST00000358127	NM_001280556.1	322	Gct/Act	8/10	1	2	FACETS	0.953	0.89	1	0.953	0.89	1	CLONAL	1	TRUE	1	0.52	2		409	928	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	221	392	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.978	0.912	1	0.978	0.912	1	CLONAL	1	TRUE	1	0.52	2		392	869	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	198	354	1	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.829	0.768	0.892	0.829	0.768	0.892	CLONAL	1	TRUE	1	0.52	2		355	919	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042536	37042536	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63751221	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	280	430	0	ENST00000231790.2:c.298C>T	p.Arg100Ter	p.R100*	ENST00000231790	NM_000249.3	100	Cga/Tga	3/19	1	2	FACETS	0.921	0.865	0.979	0.921	0.865	0.979	CLONAL	1	TRUE	1	0.52	2		430	1169	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932018	39932018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367736022	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	280	469	1	ENST00000378444.4:c.2581C>T	p.Arg861Cys	p.R861C	ENST00000378444	NM_001123385.1	861	Cgc/Tgc	4/15	1	2	FACETS	0.996	0.936	1	0.996	0.936	1	CLONAL	1	TRUE	1	0.52	2		470	1081	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003747	45003747	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs1057519877	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	169	370	0	ENST00000558401.1:c.3G>A	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	atG/atA	1/4	1	2	FACETS	0.774	0.712	0.838	0.774	0.712	0.838	SUBCLONAL	1	TRUE	1	0.52	2		370	840	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952073	178952073	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519937	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	208	369	0	ENST00000263967.3:c.3128T>C	p.Met1043Thr	p.M1043T	ENST00000263967	NM_006218.2	1043	aTg/aCg	21/21	1	2	FACETS	0.895	0.831	0.96	0.895	0.831	0.96	CLONAL	1	TRUE	1	0.52	2		369	894	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681757	30681757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779352833	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	284	423	0	ENST00000376406.3:c.340C>T	p.Arg114Cys	p.R114C	ENST00000376406	NM_014641.2	114	Cgt/Tgt	3/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.52	2		423	1047	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873020	136873020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147198552	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	424	721	1	ENST00000241393.3:c.478G>A	p.Val160Ile	p.V160I	ENST00000241393	NM_003467.2	160	Gtc/Atc	2/2	1	2	FACETS	0.992	0.943	1	0.992	0.943	1	CLONAL	1	TRUE	1	0.52	2		722	1644	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521120	187521120	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752997628	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	210	360	0	ENST00000441802.2:c.12035C>T	p.Thr4012Met	p.T4012M	ENST00000441802	NM_005245.3	4012	aCg/aTg	22/27	1	2	FACETS	0.996	0.927	1	0.996	0.927	1	CLONAL	1	TRUE	1	0.52	2		360	811	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132542	11132542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	266	417	0	ENST00000358026.2:c.2758G>A	p.Glu920Lys	p.E920K	ENST00000358026	NM_001128849.1	920	Gag/Aag	19/36	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.52	2		417	1008	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573813	64573813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139936447	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	71	268	0	ENST00000312049.6:c.940C>T	p.Arg314Trp	p.R314W	ENST00000312049	NM_130799.2	314	Cgg/Tgg	7/10	1	2	FACETS	0.438	0.382	0.498	0.438	0.382	0.498	SUBCLONAL	1	TRUE	1	0.52	2		268	624	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777134	9777134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1445282622	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	190	490	0	ENST00000377346.4:c.898C>T	p.Arg300Cys	p.R300C	ENST00000377346	NM_005026.3	300	Cgt/Tgt	7/24	1	2	FACETS	0.657	0.607	0.71	0.657	0.607	0.71	SUBCLONAL	1	TRUE	1	0.52	2		490	1112	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5258030	5258030	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	228	316	0	ENST00000357368.4:c.704G>A	p.Arg235Gln	p.R235Q	ENST00000357368	NM_002850.3	235	cGa/cAa	8/38	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.52	2		316	765	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579344	7579344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	226	341	0	ENST00000269305.4:c.343C>T	p.His115Tyr	p.H115Y	ENST00000269305	NM_001126112.2	115	Cat/Tat	4/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.52	2		341	846	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989087	41989087	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1335	423	778	0	ENST00000219905.7:c.1879C>T	p.Arg627Ter	p.R627*	ENST00000219905	NM_001164273.1	627	Cga/Tga	3/24	1	2	FACETS	0.925	0.879	0.973	0.925	0.879	0.973	CLONAL	1	TRUE	1	0.52	2		778	1758	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856070	151856070	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	369	574	3	ENST00000262189.6:c.11548C>T	p.Arg3850Ter	p.R3850*	ENST00000262189	NM_170606.2	3850	Cga/Tga	44/59	1	2	FACETS	0.962	0.911	1	0.962	0.911	1	CLONAL	1	TRUE	1	0.52	2		577	1475	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117712788	117712788	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	236	403	0	ENST00000369458.3:c.38T>A	p.Ile13Asn	p.I13N	ENST00000369458	NM_024626.3	13	aTt/aAt	2/6	1	2	FACETS	0.954	0.891	1	0.954	0.891	1	CLONAL	1	TRUE	1	0.52	2		403	951	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206647725	206647725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367771392	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	243	355	2	ENST00000367120.3:c.139C>T	p.Arg47Trp	p.R47W	ENST00000367120	NM_014002.3	47	Cgg/Tgg	4/22	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.52	2		357	843	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026846	48026846	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	319	398	0	ENST00000234420.5:c.1724A>G	p.Asp575Gly	p.D575G	ENST00000234420	NM_000179.2	575	gAt/gGt	4/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.52	2		398	1114	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661782	227661782	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs568940466	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	86	242	0	ENST00000305123.5:c.1673A>G	p.Tyr558Cys	p.Y558C	ENST00000305123	NM_005544.2	558	tAc/tGc	1/2	1	2	FACETS	0.67	0.594	0.75	0.67	0.594	0.75	SUBCLONAL	1	TRUE	1	0.52	2		242	494	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182681681	182681681	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	149	374	0	ENST00000292782.4:c.377T>C	p.Met126Thr	p.M126T	ENST00000292782	NM_020640.2	126	aTg/aCg	3/7	1	2	FACETS	0.605	0.552	0.661	0.605	0.552	0.661	SUBCLONAL	1	TRUE	1	0.52	2		374	947	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503816	149503816	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	192	473	0	ENST00000261799.4:c.2020G>T	p.Gly674Ter	p.G674*	ENST00000261799	NM_002609.3	674	Gga/Tga	14/23	1	2	FACETS	0.839	0.777	0.904	0.839	0.777	0.904	CLONAL	1	TRUE	1	0.52	2		473	880	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663640	117663640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1017338335	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	149	290	0	ENST00000368508.3:c.4592C>T	p.Ala1531Val	p.A1531V	ENST00000368508	NM_002944.2	1531	gCt/gTt	28/43	0.3	2	FACETS	0.678	0.62	0.739			1	INDETERMINATE	1	TRUE	NA	0.52	2		290	845	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199856	138199856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748195339	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	163	268	0	ENST00000237289.4:c.1274C>T	p.Pro425Leu	p.P425L	ENST00000237289	NM_001270507.1	425	cCg/cTg	7/9	1	2	FACETS	0.889	0.818	0.963	0.889	0.818	0.963	CLONAL	1	TRUE	1	0.52	2		268	705	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405991	157405991	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554294689	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	305	447	2	ENST00000346085.5:c.2233G>T	p.Gly745Ter	p.G745*	ENST00000346085	NM_020732.3	745	Gga/Tga	6/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.52	2		449	1126	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622221	162622221	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs562500530	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	259	424	0	ENST00000366898.1:c.476C>T	p.Pro159Leu	p.P159L	ENST00000366898	NM_004562.2	159	cCg/cTg	4/12	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.52	2		424	989	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971142	21971142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1563889729	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	52	124	1	ENST00000579755.1:c.259C>T	p.Arg87Cys	p.R87C	ENST00000579755		87	Cgc/Tgc	2/3	1	2	FACETS	0.741	0.636	0.854	0.741	0.636	0.854	SUBCLONAL	1	TRUE	1	0.52	2		125	270	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402738	139402738	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768095251	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	184	304	0	ENST00000277541.6:c.3271G>A	p.Gly1091Ser	p.G1091S	ENST00000277541	NM_017617.3	1091	Ggc/Agc	20/34	1	2	FACETS	0.983	0.91	1	0.983	0.91	1	CLONAL	1	TRUE	1	0.52	2		304	720	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925495	114925495	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	380	689	0	ENST00000543371.1:c.1573C>A	p.Pro525Thr	p.P525T	ENST00000543371	NM_001198531.1	525	Ccc/Acc	14/14	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.52	2		689	1447	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101985004	101985004	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	197	299	0	ENST00000282441.5:c.451C>G	p.Pro151Ala	p.P151A	ENST00000282441	NM_001130145.2	151	Cca/Gca	2/9	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.52	2		299	675	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202261	108202261	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	176	329	0	ENST00000278616.4:c.7606G>T	p.Gly2536Ter	p.G2536*	ENST00000278616	NM_000051.3	2536	Gga/Tga	51/63	1	2	FACETS	0.836	0.771	0.903	0.836	0.771	0.903	CLONAL	1	TRUE	1	0.52	2		329	810	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426650	121426650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139016696	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	229	383	0	ENST00000257555.6:c.341G>A	p.Arg114His	p.R114H	ENST00000257555		114	cGt/cAt	2/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.52	2		383	859	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052626	42052626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1256	433	622	3	ENST00000219905.7:c.7297C>T	p.Arg2433Trp	p.R2433W	ENST00000219905	NM_001164273.1	2433	Cgg/Tgg	20/24	1	2	FACETS	0.986	0.938	1	0.986	0.938	1	CLONAL	1	TRUE	1	0.52	2		625	1689	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	C	novel	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	145	360	0	ENST00000558401.1:c.1A>C	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Ctg	1/4	1	2	FACETS	0.689	0.628	0.751	0.689	0.628	0.751	SUBCLONAL	1	TRUE	1	0.52	2		360	810	SUCCESS
B2M	567	MSKCC	GRCh37	15	45008525	45008525	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs111795848	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	255	412	0	ENST00000558401.1:c.347-2A>G		p.X116_splice	ENST00000558401	NM_004048.2	116			1	2	FACETS	0.892	0.834	0.951	0.892	0.834	0.951	CLONAL	1	TRUE	1	0.52	2		412	1100	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631877	90631877	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755016578	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	200	489	1	ENST00000330062.3:c.476G>A	p.Arg159His	p.R159H	ENST00000330062	NM_002168.2	159	cGc/cAc	4/11	1	2	FACETS	0.753	0.698	0.811	0.753	0.698	0.811	SUBCLONAL	1	TRUE	1	0.52	2		490	1021	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029072	14029072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763619616	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	218	317	0	ENST00000311895.7:c.1283C>T	p.Ala428Val	p.A428V	ENST00000311895	NM_005236.2	428	gCg/gTg	8/11	1	2	FACETS	0.997	0.929	1	0.997	0.929	1	CLONAL	1	TRUE	1	0.52	2		317	841	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873733	37873733	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs199726056	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	243	406	0	ENST00000269571.5:c.1898C>T	p.Ser633Phe	p.S633F	ENST00000269571		633	tCc/tTc	15/27	1	2	FACETS	0.974	0.91	1	0.974	0.91	1	CLONAL	1	TRUE	1	0.52	2		406	960	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41197744	41197744	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	239	618	0	ENST00000357654.3:c.5543A>G	p.Gln1848Arg	p.Q1848R	ENST00000357654	NM_007294.3	1848	cAg/cGg	23/23	1	2	FACETS	0.724	0.675	0.775	0.724	0.675	0.775	SUBCLONAL	1	TRUE	1	0.52	2		618	1269	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78599575	78599575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375687715	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	205	319	0	ENST00000306801.3:c.247C>T	p.Arg83Cys	p.R83C	ENST00000306801	NM_020761.2	83	Cgc/Tgc	2/34	1	2	FACETS	0.914	0.849	0.981	0.914	0.849	0.981	CLONAL	1	TRUE	1	0.52	2		319	863	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217784	2217784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1190279627	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	216	468	1	ENST00000398665.3:c.2558G>A	p.Arg853His	p.R853H	ENST00000398665	NM_032482.2	853	cGc/cAc	22/28	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.52	2		469	791	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100118	11100118	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	69	326	0	ENST00000358026.2:c.1244A>C	p.Gln415Pro	p.Q415P	ENST00000358026	NM_001128849.1	415	cAg/cCg	7/36	1	2	FACETS	0.369	0.321	0.421	0.369	0.321	0.421	SUBCLONAL	1	TRUE	1	0.52	2		326	719	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288819	15288819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1392500489	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	26	109	0	ENST00000263388.2:c.3920C>T	p.Thr1307Met	p.T1307M	ENST00000263388	NM_000435.2	1307	aCg/aTg	24/33	1	2	FACETS	0.503	0.4	0.618	0.503	0.4	0.618	SUBCLONAL	1	TRUE	1	0.52	2		109	199	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945719	17945719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140655992	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	238	427	1	ENST00000458235.1:c.2141C>T	p.Thr714Met	p.T714M	ENST00000458235	NM_000215.3	714	aCg/aTg	16/24	1	2	FACETS	0.926	0.864	0.989	0.926	0.864	0.989	CLONAL	1	TRUE	1	0.52	2		428	989	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258595	19258595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377026490	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	285	493	1	ENST00000162023.5:c.305C>T	p.Pro102Leu	p.P102L	ENST00000162023		102	cCg/cTg	8/13	1	2	FACETS	0.975	0.917	1	0.975	0.917	1	CLONAL	1	TRUE	1	0.52	2		494	1124	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386318	31386318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747146892	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	166	380	2	ENST00000328111.2:c.1543G>A	p.Glu515Lys	p.E515K	ENST00000328111	NM_006892.3	515	Gag/Aag	15/23	1	2	FACETS	0.757	0.696	0.821	0.757	0.696	0.821	SUBCLONAL	1	TRUE	1	0.52	2		382	843	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922001	39922001	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	314	553	0	ENST00000378444.4:c.4171A>G	p.Lys1391Glu	p.K1391E	ENST00000378444	NM_001123385.1	1391	Aag/Gag	9/15	1	2	FACETS	0.945	0.891	1	0.945	0.891	1	CLONAL	1	TRUE	1	0.52	2		553	1278	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223425	53223425	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374468313	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	259	441	1	ENST00000375401.3:c.3934C>T	p.Arg1312Cys	p.R1312C	ENST00000375401	NM_004187.3	1312	Cgc/Tgc	23/26	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.52	2		442	925	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106480	27106481	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0011385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	296	424	0	ENST00000324856.7:c.6092dup	p.Tyr2031Ter	p.Y2031*	ENST00000324856	NM_006015.4	2031	tat/tAat	20/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.52	2		424	1099	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918694	44918694	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	330	373	0	ENST00000377967.4:c.1177C>T	p.Arg393Ter	p.R393*	ENST00000377967	NM_021140.2	393	Cga/Tga	12/29	0.213837330305155	0	FACETS	1	0.961	1			1	CLONAL	3	TRUE	0	0.223589828081938	0		373	755	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964914	25964914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	81	345	1	ENST00000435504.4:c.4292G>A	p.Cys1431Tyr	p.C1431Y	ENST00000435504		1431	tGc/tAc	13/13	1	2	FACETS	0.81	0.713	0.916	0.81	0.713	0.916	CLONAL	1	TRUE	1	0.223589828081938	2		346	894	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268760	41268760	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	440	425	0	ENST00000349496.5:c.998A>T	p.Tyr333Phe	p.Y333F	ENST00000349496	NM_001904.3	333	tAc/tTc	7/15	0.223589828081938	0	FACETS	0.897	0.872	0.921			1	CLONAL	6	TRUE	0	0.223589828081938	0		425	568	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831309	3831309	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0011393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	208	241	0	ENST00000262367.5:c.1574-2A>G		p.X525_splice	ENST00000262367	NM_004380.2	525			1	2	FACETS	1	0.975	1	1	0.995	1	CLONAL	3	TRUE	1	0.223589828081938	2		241	572	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900866	3900867	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTCCTCGTAGAAG	novel	NA	P-0011393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	255	392	0	ENST00000262367.5:c.217_229dup	p.Gly77AlafsTer9	p.G77Afs*9	ENST00000262367	NM_004380.2	77	ggc/gCTTCTACGAGGAGgc	2/31	1	2	FACETS	0.877	0.823	0.932	1	0.996	1	CLONAL	3	TRUE	1	0.223589828081938	2		392	867	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248720	59248721	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCGTTTCCA	novel	NA	P-0011393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	369	424	0	ENST00000371222.2:c.14_22dup	p.Met5_Thr7dup	p.M5_T7dup	ENST00000371222	NM_002228.3	5	acc/aTGGAAACGAcc	1/1	1	2	FACETS	1	0.979	1	1	0.997	1	CLONAL	3	TRUE	1	0.223589828081938	2		424	1045	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188200	10188200	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	70	429	0	ENST00000256474.2:c.343C>A	p.His115Asn	p.H115N	ENST00000256474	NM_000551.3	115	Cac/Aac	2/3	0.242371919300853	1	FACETS	0.711	0.621	0.808	0.711	0.621	0.808	SUBCLONAL	1	TRUE	0	0.32261893930318	1		429	512	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617440	158617440	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	173	722	1	ENST00000263640.3:c.1216G>T	p.Ala406Ser	p.A406S	ENST00000263640	NM_001105.4	406	Gcc/Tcc	9/11	0.163526313490883	3	FACETS	1	0.969	1	0.556	0.51	0.603	INDETERMINATE	1	TRUE	1	0.32261893930318	3		723	1121	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983487	90983488	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0011418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	91	331	0	ENST00000265433.3:c.614_615dup	p.Gly206LeufsTer26	p.G206Lfs*26	ENST00000265433	NM_002485.4	205	-/TT	6/16	1	2	FACETS	0.771	0.684	0.863	0.771	0.684	0.863	SUBCLONAL	1	TRUE	1	0.32261893930318	2		331	732	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098737	47098737	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	113	601	0	ENST00000409792.3:c.6537del	p.Ser2180AlafsTer68	p.S2180Afs*68	ENST00000409792	NM_014159.6	2179	ccC/cc	15/21	0.242371919300853	1	FACETS	0.912	0.822	1	0.912	0.822	1	CLONAL	1	TRUE	0	0.32261893930318	1		601	644	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0011434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	361	536	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.553014579958095	2		536	1117	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575523	64575523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057521111	NA	P-0011434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	231	483	0	ENST00000312049.6:c.494G>A	p.Cys165Tyr	p.C165Y	ENST00000312049	NM_130799.2	165	tGc/tAc	3/10	0.553014579958095	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.553014579958095	1		483	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0011484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	57	366	0	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	1	2	FACETS	0.882	0.756	1	0.882	0.756	1	CLONAL	1	TRUE	1	0.17	2		366	760	SUCCESS
APC	324	MSKCC	GRCh37	5	112175192	112175193	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0011484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	21	158	0	ENST00000257430.4:c.3904dup	p.Leu1302ProfsTer13	p.L1302Pfs*13	ENST00000257430	NM_000038.5	1301	acc/aCcc	16/16	1	2	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	TRUE	1	0.17	2		158	216	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334713	81334713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	263	721	0	ENST00000222390.5:c.2003C>T	p.Pro668Leu	p.P668L	ENST00000222390	NM_000601.4	668	cCa/cTa	17/18	0.508325954396083	3	FACETS	1	0.95	1	0.509	0.476	0.542	CLONAL	1	TRUE	1	0.508298396714884	3		721	1276	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029108	26029108	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	380	504	0	ENST00000435504.4:c.242A>G	p.Tyr81Cys	p.Y81C	ENST00000435504		81	tAt/tGt	4/13	0.508325954396083	3	FACETS	0.904	0.86	0.948	0.904	0.86	0.948	CLONAL	2	TRUE	1	0.508298396714884	3		504	1037	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953759	48953759	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	345	315	0	ENST00000267163.4:c.1362C>A	p.Tyr454Ter	p.Y454*	ENST00000267163	NM_000321.2	454	taC/taA	14/27	0.49660624031724	3	FACETS	0.876	0.837	0.914	0.876	0.837	0.914	CLONAL	3	TRUE	0	0.508298396714884	3		315	648	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923306	9923306	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555492744	NA	P-0011508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	192	527	1	ENST00000330684.3:c.1981C>T	p.Gln661Ter	p.Q661*	ENST00000330684	NM_001134407.1	661	Caa/Taa	9/13	0.492344172110264	2	FACETS	0.988	0.916	1	0.494	0.458	0.531	CLONAL	1	TRUE	0	0.508298396714884	2		528	765	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012112	16012112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	183	527	1	ENST00000268712.3:c.2170G>A	p.Glu724Lys	p.E724K	ENST00000268712	NM_006311.3	724	Gaa/Aaa	19/46	0.492344172110264	2	FACETS	0.873	0.807	0.942	0.436	0.403	0.471	CLONAL	1	TRUE	0	0.508298396714884	2		528	825	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755338	39755338	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	218	593	0	ENST00000288319.7:c.1427G>T	p.Gly476Val	p.G476V	ENST00000288319	NM_182918.3	476	gGc/gTc	10/10	0.508325954396083	3	FACETS	0.938	0.871	1	0.469	0.435	0.504	CLONAL	1	TRUE	1	0.508298396714884	3		593	1147	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579470	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	AG	novel	NA	P-0011508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	303	426	0	ENST00000269305.4:c.217delinsCT	p.Val73LeufsTer76	p.V73Lfs*76	ENST00000269305	NM_001126112.2	73	Gtg/CTtg	4/11	0.492344172110264	2	FACETS	0.916	0.87	0.962	0.916	0.87	0.962	CLONAL	2	TRUE	0	0.508298396714884	2		426	651	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057811	27057811	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1549	96	630	0	ENST00000324856.7:c.1519C>T	p.Gln507Ter	p.Q507*	ENST00000324856	NM_006015.4	507	Caa/Taa	3/20	1	2	FACETS	0.614	0.545	0.689	0.614	0.545	0.689	SUBCLONAL	1	TRUE	1	0.19	2		630	1645	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127709	64127709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	50	300	0	ENST00000334205.4:c.202C>T	p.Arg68Cys	p.R68C	ENST00000334205	NM_003942.2	68	Cgc/Tgc	3/17	1	2	FACETS	0.719	0.609	0.841	0.719	0.609	0.841	SUBCLONAL	1	TRUE	1	0.19	2		300	732	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572350	41572350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	59	370	2	ENST00000263253.7:c.4879C>T	p.Arg1627Trp	p.R1627W	ENST00000263253	NM_001429.3	1627	Cgg/Tgg	30/31	1	2	FACETS	0.635	0.545	0.734	0.635	0.545	0.734	SUBCLONAL	1	TRUE	1	0.19	2		372	978	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685270	89685271	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0011509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	36	120	0	ENST00000371953.3:c.170dup	p.Leu57PhefsTer6	p.L57Ffs*6	ENST00000371953	NM_000314.4	55	-/T	3/9	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.19	2		120	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0011531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	51	276	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.537	0.457	0.624	0.537	0.457	0.624	SUBCLONAL	1	TRUE	1	0.420468415855469	2		276	452	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101267	27101268	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0011531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	57	410	0	ENST00000324856.7:c.4555dup	p.Gln1519ProfsTer13	p.Q1519Pfs*13	ENST00000324856	NM_006015.4	1517	gcc/gCcc	18/20	1	2	FACETS	0.387	0.331	0.448	0.387	0.331	0.448	SUBCLONAL	1	TRUE	1	0.420468415855469	2		410	701	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0011531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	137	520	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	1	2	FACETS	0.704	0.64	0.771	0.704	0.64	0.771	SUBCLONAL	1	TRUE	1	0.420468415855469	2		520	926	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847275	68847277	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0011531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	100	490	0	ENST00000261769.5:c.1199_1201del	p.Asp400del	p.D400del	ENST00000261769	NM_004360.3	399	acTGAt/act	9/16	1	2	FACETS	0.571	0.509	0.637	0.571	0.509	0.637	SUBCLONAL	1	TRUE	1	0.420468415855469	2		490	833	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518457	69518457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	26	109	0	ENST00000294312.3:c.188G>A	p.Arg63His	p.R63H	ENST00000294312	NM_005117.2	63	cGt/cAt	1/3	1	2	FACETS	0.603	0.481	0.742	0.603	0.481	0.742	SUBCLONAL	1	TRUE	1	0.420468415855469	2		109	205	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855958	68855958	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	113	498	1	ENST00000261769.5:c.1766A>T	p.Asn589Ile	p.N589I	ENST00000261769	NM_004360.3	589	aAt/aTt	12/16	1	2	FACETS	0.59	0.53	0.653	0.59	0.53	0.653	SUBCLONAL	1	TRUE	1	0.420468415855469	2		499	911	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937102	39937102	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	210	447	0	ENST00000378444.4:c.81A>T	p.Glu27Asp	p.E27D	ENST00000378444	NM_001123385.1	27	gaA/gaT	2/15	0.263947656073985	3	FACETS	1	0.989	1	0.682	0.634	0.732	CLONAL	1	TRUE	1	0.420468415855469	3		447	886	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630137	100630137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	215	494	0	ENST00000308731.7:c.136C>T	p.Arg46Cys	p.R46C	ENST00000308731	NM_000061.2	46	Cgt/Tgt	2/19	0.263947656073985	3	FACETS	1	0.986	1	0.623	0.579	0.668	CLONAL	1	TRUE	1	0.420468415855469	3		494	994	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0011558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	44	286	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.677	0.571	0.793	0.677	0.571	0.793	SUBCLONAL	1	TRUE	1	0.439029041773334	2		286	296	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0011558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	91	584	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	0.612	0.544	0.685	0.612	0.544	0.685	SUBCLONAL	1	TRUE	1	0.439029041773334	2		584	677	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0011558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	97	576	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	0.658	0.587	0.733	0.658	0.587	0.733	SUBCLONAL	1	TRUE	1	0.439029041773334	2		576	672	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435829	110435855	+	inframe_deletion	In_Frame_Del	DEL	GGCCGGCCCCGAAGGCGCTGGCCGCCT	GGCCGGCCCCGAAGGCGCTGGCCGCCT	-	novel	NA	P-0011558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	17	114	0	ENST00000375856.3:c.2546_2572del	p.Gln849_Gly857del	p.Q849_G857del	ENST00000375856	NM_003749.2	849	cAGGCGGCCAGCGCCTTCGGGGCCGGCCcc/ccc	1/2	1	2	FACETS	0.553	0.416	0.713	0.553	0.416	0.713	SUBCLONAL	1	TRUE	1	0.439029041773334	2		114	140	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0011592-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	100	89	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.225010263017102	3	FACETS	0.967	0.872	1	0.967	0.872	1	CLONAL	3	TRUE	0	0.225010263017102	3		89	341	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570239	87570239	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201105177	NA	P-0011592-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	54	174	1	ENST00000277120.3:c.1979C>T	p.Pro660Leu	p.P660L	ENST00000277120		660	cCg/cTg	17/19	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.225010263017102	2		175	393	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946319	2946319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373819371	NA	P-0011592-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	63	315	0	ENST00000396946.4:c.3418G>A	p.Gly1140Ser	p.G1140S	ENST00000396946	NM_032415.4	1140	Ggc/Agc	25/25	0.225010263017102	3	FACETS	0.698	0.602	0.802			1	SUBCLONAL	1	TRUE	NA	0.225010263017102	3		315	893	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444122	49444122	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011592-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	75	414	1	ENST00000301067.7:c.3249C>A	p.Cys1083Ter	p.C1083*	ENST00000301067	NM_003482.3	1083	tgC/tgA	11/54	0.225010263017102	3	FACETS	0.685	0.599	0.779	0.343	0.299	0.39	SUBCLONAL	1	TRUE	1	0.225010263017102	3		415	1082	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842408	68842409	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0011592-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	242	386	0	ENST00000261769.5:c.471dup	p.Ile158TyrfsTer10	p.I158Yfs*10	ENST00000261769	NM_004360.3	157	gtt/gTtt	4/16	0.225010263017102	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.225010263017102	2		386	1003	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562766	29562778	+	frameshift_variant	Frame_Shift_Del	DEL	TAAAATAATGACA	TAAAATAATGACA	-	novel	NA	P-0011592-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	45	208	0	ENST00000356175.3:c.3847_3859del	p.Lys1283SerfsTer22	p.K1283Sfs*22	ENST00000356175	NM_000267.3	1282	agTAAAATAATGACA/ag	28/57	0.225010263017102	3	FACETS	0.575	0.482	0.679	0.287	0.241	0.34	SUBCLONAL	1	TRUE	1	0.225010263017102	3		208	774	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1558	186	672	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.274547890957492	3	FACETS	0.884	0.813	0.958	0.442	0.406	0.479	CLONAL	1	TRUE	1	0.274547890957492	3		672	1744	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	275	242	0				ENST00000310581	NM_198253.2	-/1132			0.21654595242529	5	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	2	0.274547890957492	5		242	839	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17350491	17350491	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	350	228	0	ENST00000375499.3:c.619C>A	p.Leu207Met	p.L207M	ENST00000375499	NM_003000.2	207	Ctg/Atg	6/8	0.274547890957492	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.274547890957492	3		228	1382	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088766	27088766	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1350	157	263	2	ENST00000324856.7:c.2375C>T	p.Ser792Phe	p.S792F	ENST00000324856	NM_006015.4	792	tCc/tTc	7/20	0.274547890957492	3	FACETS	0.863	0.788	0.942	0.432	0.394	0.471	CLONAL	1	TRUE	1	0.274547890957492	3		265	1507	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241977	72241977	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	251	383	1	ENST00000357731.5:c.413C>T	p.Pro138Leu	p.P138L	ENST00000357731	NM_173808.2	138	cCt/cTt	3/7	0.274547890957492	3	FACETS	1	0.992	1	0.747	0.698	0.799	CLONAL	1	TRUE	1	0.274547890957492	3		384	1391	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462939	120462939	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	312	237	0	ENST00000256646.2:c.5392G>A	p.Asp1798Asn	p.D1798N	ENST00000256646	NM_024408.3	1798	Gac/Aac	30/34	0.274547890957492	3	FACETS	0.996	0.938	1	0.996	0.938	1	CLONAL	2	TRUE	1	0.274547890957492	3		237	1298	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082374	16082374	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	289	271	1	ENST00000281043.3:c.188C>T	p.Pro63Leu	p.P63L	ENST00000281043	NM_005378.4	63	cCc/cTc	2/3	0.16621299015332	3	FACETS	1	0.984	1			1	CLONAL	2	TRUE	NA	0.274547890957492	3		272	1069	SUCCESS
ALK	238	MSKCC	GRCh37	2	29541212	29541213	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1355	483	299	0	ENST00000389048.3:c.1604_1605delinsTT	p.Thr535Ile	p.T535I	ENST00000389048	NM_004304.4	535	aCC/aTT	8/29	0.21654595242529	5	FACETS	0.901	0.859	0.943	0.901	0.859	0.943	CLONAL	3	TRUE	2	0.274547890957492	5		299	1838	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145732	61145732	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1278232982	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	91	174	0	ENST00000295025.8:c.844G>A	p.Asp282Asn	p.D282N	ENST00000295025	NM_002908.2	282	Gat/Aat	7/11	0.21654595242529	5	FACETS	1	0.947	1	0.372	0.33	0.418	CLONAL	1	TRUE	2	0.274547890957492	5		174	838	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622630	158622630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1587	405	462	0	ENST00000263640.3:c.869C>T	p.Ser290Leu	p.S290L	ENST00000263640	NM_001105.4	290	tCg/tTg	8/11	0.274547890957492	4	FACETS	0.944	0.895	0.994	0.944	0.895	0.994	CLONAL	2	TRUE	2	0.274547890957492	4		462	1992	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626461	12626461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs727504827	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	217	226	0	ENST00000251849.4:c.1688G>A	p.Arg563Gln	p.R563Q	ENST00000251849	NM_002880.3	563	cGa/cAa	16/17	0.274547890957492	4	FACETS	0.864	0.802	0.928	0.864	0.802	0.928	CLONAL	2	TRUE	2	0.274547890957492	4		226	1166	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058603	47058603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1483	277	374	1	ENST00000409792.3:c.7675G>A	p.Glu2559Lys	p.E2559K	ENST00000409792	NM_014159.6	2559	Gag/Aag	21/21	0.274547890957492	4	FACETS	1	0.993	1	0.731	0.684	0.779	CLONAL	1	TRUE	2	0.274547890957492	4		375	1760	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405948	49405948	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1698	370	425	0	ENST00000418115.1:c.190G>A	p.Glu64Lys	p.E64K	ENST00000418115	NM_001664.2	64	Gaa/Aaa	3/5	0.274547890957492	4	FACETS	0.831	0.785	0.878	0.831	0.785	0.878	CLONAL	2	TRUE	2	0.274547890957492	4		425	2068	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259262	89259262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770780950	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	217	243	0	ENST00000336596.2:c.406C>T	p.Arg136Ter	p.R136*	ENST00000336596	NM_005233.5	136	Cga/Tga	3/17	0.274547890957492	3	FACETS	0.943	0.878	1	0.943	0.878	1	CLONAL	2	TRUE	1	0.274547890957492	3		243	953	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462356	89462356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	99	231	1	ENST00000336596.2:c.1828C>T	p.His610Tyr	p.H610Y	ENST00000336596	NM_005233.5	610	Cat/Tat	10/17	0.274547890957492	3	FACETS	0.724	0.644	0.809	0.362	0.322	0.405	SUBCLONAL	1	TRUE	1	0.274547890957492	3		232	1133	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499483	89499483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1426641543	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	208	180	0	ENST00000336596.2:c.2653C>T	p.Pro885Ser	p.P885S	ENST00000336596	NM_005233.5	885	Ccc/Tcc	15/17	0.274547890957492	3	FACETS	0.832	0.772	0.895	0.832	0.772	0.895	CLONAL	2	TRUE	1	0.274547890957492	3		180	1035	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920482	134920482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1399	191	332	0	ENST00000398015.3:c.2297C>T	p.Ser766Phe	p.S766F	ENST00000398015	NM_004441.4	766	tCc/tTc	12/16	0.274547890957492	3	FACETS	0.995	0.917	1	0.498	0.458	0.539	CLONAL	1	TRUE	1	0.274547890957492	3		332	1590	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916941	178916941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1527	142	420	1	ENST00000263967.3:c.328G>A	p.Glu110Lys	p.E110K	ENST00000263967	NM_006218.2	110	Gaa/Aaa	2/21	0.274547890957492	3	FACETS	0.705	0.64	0.774	0.352	0.32	0.387	SUBCLONAL	1	TRUE	1	0.274547890957492	3		421	1669	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447106	187447106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	139	248	0	ENST00000232014.4:c.1087C>T	p.Pro363Ser	p.P363S	ENST00000232014	NM_001130845.1	363	Cca/Tca	5/10	0.16621299015332	3	FACETS	1	0.934	1			1	CLONAL	1	TRUE	NA	0.274547890957492	3		248	1114	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589660	67589660	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	150	85	0	ENST00000274335.5:c.1423C>T	p.Gln475Ter	p.Q475*	ENST00000274335		475	Cag/Tag	10/15	0.274547890957492	3	FACETS	1	0.981	1	0.811	0.746	0.878	CLONAL	2	TRUE	0	0.274547890957492	3		85	511	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520471	176520471	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	433	270	0	ENST00000292408.4:c.1316C>T	p.Ser439Phe	p.S439F	ENST00000292408	NM_213647.1	439	tCc/tTc	10/18	0.233002982844497	4	FACETS	0.852	0.811	0.894	0.852	0.811	0.894	CLONAL	3	TRUE	1	0.274547890957492	4		270	1573	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041102	180041103	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	455	325	0	ENST00000261937.6:c.3296_3297delinsTT	p.Ser1099Phe	p.S1099F	ENST00000261937	NM_182925.4	1099	tCC/tTT	24/30	0.233002982844497	4	FACETS	0.86	0.819	0.901	0.86	0.819	0.901	CLONAL	3	TRUE	1	0.274547890957492	4		325	1638	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047194	180047194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	483	367	0	ENST00000261937.6:c.2521C>T	p.Pro841Ser	p.P841S	ENST00000261937	NM_182925.4	841	Ccc/Tcc	17/30	0.233002982844497	4	FACETS	0.941	0.899	0.984	0.941	0.899	0.984	CLONAL	3	TRUE	1	0.274547890957492	4		367	1589	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055886	180055886	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	466	297	0	ENST00000261937.6:c.1099C>T	p.Gln367Ter	p.Q367*	ENST00000261937	NM_182925.4	367	Cag/Tag	8/30	0.233002982844497	4	FACETS	0.909	0.867	0.951	0.909	0.867	0.951	CLONAL	3	TRUE	1	0.274547890957492	4		297	1587	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056631	26056631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779130821	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	41	65	0	ENST00000343677.2:c.26C>T	p.Pro9Leu	p.P9L	ENST00000343677	NM_005319.3	9	cCc/cTc	1/1	0.274547890957492	3	FACETS	0.99	0.827	1	0.495	0.413	0.585	CLONAL	1	TRUE	1	0.274547890957492	3		65	343	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120729	94120729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1801	203	565	0	ENST00000369303.4:c.322G>A	p.Asp108Asn	p.D108N	ENST00000369303	NM_004440.3	108	Gat/Aat	3/17	0.274547890957492	3	FACETS	0.839	0.774	0.907	0.42	0.387	0.454	CLONAL	1	TRUE	1	0.274547890957492	3		565	2004	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609725	117609726	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	287	280	0	ENST00000368508.3:c.6973_6974delinsTT	p.Pro2325Phe	p.P2325F	ENST00000368508	NM_002944.2	2325	CCt/TTt	43/43	NA	2	FACETS	0.878	0.826	0.933			1	INDETERMINATE	2	TRUE	NA	0.274547890957492	2		280	1190	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196865	138196865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	152	302	0	ENST00000237289.4:c.527C>T	p.Ser176Phe	p.S176F	ENST00000237289	NM_001270507.1	176	tCc/tTc	4/9	0.274547890957492	3	FACETS	0.926	0.844	1	0.463	0.422	0.506	CLONAL	1	TRUE	1	0.274547890957492	3		302	1360	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200302	138200302	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	86	143	0	ENST00000237289.4:c.1720C>T	p.Pro574Ser	p.P574S	ENST00000237289	NM_001270507.1	574	Ccc/Tcc	7/9	0.274547890957492	3	FACETS	0.782	0.691	0.88	0.391	0.345	0.44	SUBCLONAL	1	TRUE	1	0.274547890957492	3		143	911	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521986	157521986	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554235614	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	243	263	0	ENST00000346085.5:c.4258C>T	p.Gln1420Ter	p.Q1420*	ENST00000346085	NM_020732.3	1420	Cag/Tag	18/20	0.274547890957492	3	FACETS	0.827	0.772	0.884	0.827	0.772	0.884	CLONAL	2	TRUE	1	0.274547890957492	3		263	1217	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971333	13971333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	256	226	0	ENST00000405192.2:c.596C>T	p.Pro199Leu	p.P199L	ENST00000405192	NM_001163147.1	199	cCt/cTt	8/12	0.274547890957492	4	FACETS	0.896	0.837	0.956	0.896	0.837	0.956	CLONAL	2	TRUE	2	0.274547890957492	4		226	1327	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450319	50450319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	280	280	0	ENST00000331340.3:c.503C>T	p.Ser168Phe	p.S168F	ENST00000331340	NM_006060.4	168	tCc/tTc	5/8	0.274547890957492	4	FACETS	0.887	0.831	0.944	0.887	0.831	0.944	CLONAL	2	TRUE	2	0.274547890957492	4		280	1466	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381541	81381541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1427	321	917	0	ENST00000222390.5:c.520G>A	p.Glu174Lys	p.E174K	ENST00000222390	NM_000601.4	174	Gaa/Aaa	5/18	0.274547890957492	4	FACETS	0.853	0.802	0.904	0.853	0.802	0.904	CLONAL	2	TRUE	2	0.274547890957492	4		917	1748	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545618	106545618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	166	263	0	ENST00000359195.3:c.3095C>T	p.Ser1032Phe	p.S1032F	ENST00000359195	NM_002649.2	1032	tCc/tTc	11/11	0.274547890957492	4	FACETS	1	0.982	1	0.632	0.579	0.688	CLONAL	1	TRUE	2	0.274547890957492	4		263	1219	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750678	128750679	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	269	313	0	ENST00000377970.2:c.215_216delinsTT	p.Pro72Leu	p.P72L	ENST00000377970	NM_002467.4	72	cCC/cTT	2/3	0.274547890957492	3	FACETS	0.88	0.824	0.938	0.88	0.824	0.938	CLONAL	2	TRUE	1	0.274547890957492	3		313	1266	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340407	8340407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201651279	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1341	182	288	0	ENST00000356435.5:c.5189G>A	p.Arg1730Gln	p.R1730Q	ENST00000356435		1730	cGg/cAg	31/35	0.274547890957492	3	FACETS	0.99	0.91	1	0.495	0.455	0.537	CLONAL	1	TRUE	1	0.274547890957492	3		288	1523	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242250	98242251	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	268	220	0	ENST00000331920.6:c.1067_1067+1delinsAA		p.X356_splice	ENST00000331920	NM_000264.3	356		7/24	0.256694204032546	2	FACETS	0.976	0.916	1	0.976	0.916	1	CLONAL	2	TRUE	0	0.274547890957492	2		220	1000	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893662	28893662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	174	174	0	ENST00000282397.4:c.3184C>T	p.Pro1062Ser	p.P1062S	ENST00000282397	NM_002019.4	1062	Cct/Tct	24/30	NA	2	FACETS	0.821	0.757	0.887			1	INDETERMINATE	2	TRUE	NA	0.274547890957492	2		174	772	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012400	29012401	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	223	308	0	ENST00000282397.4:c.470_471delinsTT	p.Pro157Leu	p.P157L	ENST00000282397	NM_002019.4	157	cCC/cTT	4/30	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.274547890957492	2		308	1154	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32899288	32899288	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	97	249	0	ENST00000380152.3:c.392C>T	p.Ser131Phe	p.S131F	ENST00000380152		131	tCc/tTc	4/27	NA	2	FACETS	0.625	0.555	0.699			1	INDETERMINATE	1	TRUE	NA	0.274547890957492	2		249	1131	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438148	110438148	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	109	189	1	ENST00000375856.3:c.253A>T	p.Lys85Ter	p.K85*	ENST00000375856	NM_003749.2	85	Aag/Tag	1/2	0.212669806856225	4	FACETS	1	0.96	1	0.57	0.511	0.632	CLONAL	1	TRUE	2	0.274547890957492	4		190	888	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292743	91292745	+	stop_gained	Nonsense_Mutation	TNP	ATC	ATC	TTT	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	111	249	0	ENST00000355112.3:c.245_247delinsTTT	p.Asn82_Gln83delinsIleTer	p.N82_Q83delinsI*	ENST00000355112	NM_000057.2	82	aATCag/aTTTag	3/22	1	2	FACETS	0.711	0.638	0.79	0.711	0.638	0.79	SUBCLONAL	1	TRUE	1	0.274547890957492	2		249	1137	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213979	2213979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1511	224	426	0	ENST00000326181.6:c.58C>T	p.Pro20Ser	p.P20S	ENST00000326181	NM_032271.2	20	Ccc/Tcc	2/21	0.274547890957492	3	FACETS	1	0.966	1	0.535	0.496	0.575	CLONAL	1	TRUE	1	0.274547890957492	3		426	1735	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070585	67070585	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768598591	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1369	171	279	0	ENST00000412916.2:c.209C>T	p.Pro70Leu	p.P70L	ENST00000412916		70	cCg/cTg	3/6	0.274547890957492	3	FACETS	0.92	0.843	1	0.46	0.421	0.5	CLONAL	1	TRUE	1	0.274547890957492	3		279	1540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577017	7577017	+	splice_donor_variant	Splice_Site	SNP	A	A	T	rs1131691016	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	273	253	0	ENST00000269305.4:c.919+2T>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.274547890957492	3	FACETS	0.943	0.884	1	0.943	0.884	1	CLONAL	2	TRUE	1	0.274547890957492	3		253	1199	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577021	7577021	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1048095040	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	289	256	0	ENST00000269305.4:c.917G>A	p.Arg306Gln	p.R306Q	ENST00000269305	NM_001126112.2	306	cGa/cAa	8/11	0.274547890957492	3	FACETS	0.96	0.902	1	0.96	0.902	1	CLONAL	2	TRUE	1	0.274547890957492	3		256	1247	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548914	29548914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	46	157	0	ENST00000356175.3:c.1688C>T	p.Pro563Leu	p.P563L	ENST00000356175	NM_000267.3	563	cCt/cTt	15/57	0.274547890957492	3	FACETS	0.595	0.5	0.7	0.297	0.25	0.35	SUBCLONAL	1	TRUE	1	0.274547890957492	3		157	641	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39567791	39567791	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs751754985	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	155	132	0	ENST00000262039.4:c.547C>T	p.Arg183Ter	p.R183*	ENST00000262039	NM_002647.2	183	Cga/Tga	5/25	0.274547890957492	3	FACETS	0.923	0.847	1	0.923	0.847	1	CLONAL	2	TRUE	1	0.274547890957492	3		132	696	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214631	5214631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749723623	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1333	107	354	0	ENST00000357368.4:c.4435G>A	p.Val1479Met	p.V1479M	ENST00000357368	NM_002850.3	1479	Gtg/Atg	29/38	1	2	FACETS	0.541	0.484	0.603	0.541	0.484	0.603	SUBCLONAL	1	TRUE	1	0.274547890957492	2		354	1440	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281505	15281505	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774169388	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	154	293	0	ENST00000263388.2:c.4868C>T	p.Pro1623Leu	p.P1623L	ENST00000263388	NM_000435.2	1623	cCg/cTg	26/33	0.274547890957492	3	FACETS	1	0.95	1	0.529	0.482	0.577	CLONAL	1	TRUE	1	0.274547890957492	3		293	1207	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366936	15366936	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1991	163	571	0	ENST00000263377.2:c.1690A>G	p.Lys564Glu	p.K564E	ENST00000263377	NM_058243.2	564	Aaa/Gaa	9/20	0.274547890957492	3	FACETS	0.627	0.572	0.685	0.313	0.286	0.343	SUBCLONAL	1	TRUE	1	0.274547890957492	3		571	2154	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797380	42797380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746056115	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	122	287	0	ENST00000575354.2:c.3742C>T	p.Pro1248Ser	p.P1248S	ENST00000575354	NM_015125.3	1248	Cca/Tca	15/20	1	2	FACETS	0.824	0.744	0.91	0.824	0.744	0.91	CLONAL	1	TRUE	1	0.274547890957492	2		287	1078	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41489069	41489070	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	237	238	0	ENST00000263253.7:c.61_62delinsTT	p.Pro21Leu	p.P21L	ENST00000263253	NM_001429.3	21	CCg/TTg	1/31	0.256694204032546	2	FACETS	0.818	0.764	0.875	0.818	0.764	0.875	CLONAL	2	TRUE	0	0.274547890957492	2		238	1055	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375342	15375343	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGAGGA	novel	NA	P-0012047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1475	103	371	0	ENST00000263377.2:c.1079_1084dup	p.Ile360_Leu361dup	p.I360_L361dup	ENST00000263377	NM_058243.2	360	aag/aTCCTCAag	6/20	0.274547890957492	3	FACETS	0.541	0.482	0.604	0.27	0.241	0.302	SUBCLONAL	1	TRUE	1	0.274547890957492	3		371	1578	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0012064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	264	353	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.280228677721935	5	FACETS	1	0.966	1	1	0.966	1	CLONAL	3	TRUE	2	0.280228677721935	5		353	858	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106898	11106898	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	151	416	1	ENST00000358026.2:c.1603G>T	p.Glu535Ter	p.E535*	ENST00000358026	NM_001128849.1	535	Gag/Tag	10/36	0.260542551937366	2	FACETS	0.799	0.733	0.869	0.799	0.733	0.869	SUBCLONAL	2	TRUE	0	0.280228677721935	2		417	674	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593477	215593477	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	104	362	1	ENST00000260947.4:c.2257G>T	p.Gly753Cys	p.G753C	ENST00000260947	NM_000465.2	753	Ggc/Tgc	11/11	0.280228677721935	3	FACETS	1	0.929	1	0.524	0.469	0.583	CLONAL	1	TRUE	1	0.280228677721935	3		363	807	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281551	15281551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	212	459	2	ENST00000263388.2:c.4822G>A	p.Ala1608Thr	p.A1608T	ENST00000263388	NM_000435.2	1608	Gct/Act	26/33	0.260542551937366	2	FACETS	0.995	0.928	1	0.995	0.928	1	CLONAL	2	TRUE	0	0.280228677721935	2		461	760	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934798	9934798	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs757713617	NA	P-0012064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	173	571	0	ENST00000330684.3:c.1492G>T	p.Gly498Cys	p.G498C	ENST00000330684	NM_001134407.1	498	Ggt/Tgt	6/13	0.280228677721935	3	FACETS	1	0.985	1	0.658	0.605	0.714	CLONAL	1	TRUE	1	0.280228677721935	3		571	1069	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49724702	49724702	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	120	332	0	ENST00000449682.2:c.487C>G	p.Arg163Gly	p.R163G	ENST00000449682	NM_020998.3	163	Cgg/Ggg	5/18	0.259560484910552	2	FACETS	0.85	0.771	0.932	0.85	0.771	0.932	CLONAL	2	TRUE	0	0.280228677721935	2		332	504	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612172	189612172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	119	445	0	ENST00000264731.3:c.1924G>A	p.Val642Met	p.V642M	ENST00000264731	NM_003722.4	642	Gtg/Atg	14/14	0.280228677721935	3	FACETS	0.971	0.875	1	0.486	0.437	0.537	CLONAL	1	TRUE	1	0.280228677721935	3		445	997	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518010	187518010	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	104	325	0	ENST00000441802.2:c.12684G>T	p.Leu4228Phe	p.L4228F	ENST00000441802	NM_005245.3	4228	ttG/ttT	25/27	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.280228677721935	2		325	678	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163848	32163848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1210630301	NA	P-0012064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	87	215	0	ENST00000375023.3:c.5378G>A	p.Arg1793Gln	p.R1793Q	ENST00000375023	NM_004557.3	1793	cGa/cAa	30/30	0.221394660039359	4	FACETS	0.756	0.671	0.846	0.756	0.671	0.846	SUBCLONAL	2	TRUE	2	0.280228677721935	4		215	526	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81399260	81399260	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1390087672	NA	P-0012064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	158	369	1	ENST00000222390.5:c.28C>A	p.Leu10Met	p.L10M	ENST00000222390	NM_000601.4	10	Ctg/Atg	1/18	0.280228677721935	3	FACETS	0.809	0.742	0.878	0.809	0.742	0.878	CLONAL	2	TRUE	1	0.280228677721935	3		370	795	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864336	57864336	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	301	605	0	ENST00000228682.2:c.1813G>T	p.Ala605Ser	p.A605S	ENST00000228682	NM_005269.2	605	Gca/Tca	12/12	0.271552722334711	4	FACETS	1	0.984	1			1	CLONAL	2	TRUE	NA	0.280228677721935	4		605	1224	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610361	10610361	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	195	397	0	ENST00000171111.5:c.349G>T	p.Glu117Ter	p.E117*	ENST00000171111	NM_203500.1	117	Gag/Tag	2/6	0.260542551937366	2	FACETS	0.953	0.885	1	0.953	0.885	1	CLONAL	2	TRUE	0	0.280228677721935	2		397	730	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741860	40741860	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs778561687	NA	P-0012064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	288	366	0	ENST00000392038.2:c.1112G>T	p.Arg371Leu	p.R371L	ENST00000392038	NM_001626.4	371	cGc/cTc	11/14	0.280228677721935	3	FACETS	0.984	0.929	1	0.984	0.929	1	CLONAL	3	TRUE	0	0.280228677721935	3		366	794	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220628	1220629	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0012064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	140	478	0	ENST00000326873.7:c.650dup	p.Ala218GlyfsTer48	p.A218Gfs*48	ENST00000326873	NM_000455.4	216	tcc/tCcc	5/10	0.260542551937366	2	FACETS	0.782	0.714	0.853	0.782	0.714	0.853	SUBCLONAL	2	TRUE	0	0.280228677721935	2		478	639	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	155	697	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	0.259197477797408	2		697	1033	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259563	89259563	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	68	252	0	ENST00000336596.2:c.707A>G	p.Glu236Gly	p.E236G	ENST00000336596	NM_005233.5	236	gAg/gGg	3/17	1	2	FACETS	0.797	0.693	0.91	0.797	0.693	0.91	CLONAL	1	TRUE	1	0.259197477797408	2		252	658	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18439864	18439864	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs751610634	NA	P-0012065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	133	293	0	ENST00000266497.5:c.761+1G>A		p.X254_splice	ENST00000266497		254			1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.259197477797408	2		293	1016	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610285	10610285	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	172	429	0	ENST00000171111.5:c.425C>T	p.Thr142Met	p.T142M	ENST00000171111	NM_203500.1	142	aCg/aTg	2/6	0.259197477797408	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.259197477797408	1		429	1022	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207090	1207091	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	AG	novel	NA	P-0012065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	156	423	0	ENST00000326873.7:c.179_180insGA	p.Tyr60Ter	p.Y60*	ENST00000326873	NM_000455.4	60	tac/tAGac	1/10	0.259197477797408	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.259197477797408	1		423	969	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881002	37881003	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCTCCCCA	rs397516982	NA	P-0012081-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	179	483	0	ENST00000269571.5:c.2332_2340dup	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	-/GGCTCCCCA	20/27	0.209865077593923	2	FACETS	0.795	0.733	0.86	0.795	0.733	0.86	SUBCLONAL	2	TRUE	0	0.239833352350597	2		483	939	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252856	36252857	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012081-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	105	184	0	ENST00000300305.3:c.505dup	p.Arg169LysfsTer44	p.R169Kfs*44	ENST00000300305		169	aga/aAga	4/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.239833352350597	2		184	692	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012081-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	155	437	0	ENST00000269305.4:c.166G>T	p.Glu56Ter	p.E56*	ENST00000269305	NM_001126112.2	56	Gaa/Taa	4/11	0.209865077593923	2	FACETS	0.899	0.825	0.976	0.899	0.825	0.976	CLONAL	2	TRUE	0	0.239833352350597	2		437	719	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155721	56155722	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0012081-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	110	318	0	ENST00000399503.3:c.816_817del	p.Arg273SerfsTer27	p.R273Sfs*27	ENST00000399503	NM_005921.1	271	agAAaa/agaa	3/20	0.22864242773148	2	FACETS	0.757	0.682	0.836	0.757	0.682	0.836	SUBCLONAL	2	TRUE	0	0.239833352350597	2		318	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578213	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	546	686	0	ENST00000269305.4:c.636dup	p.Arg213SerfsTer3	p.R213Sfs*3	ENST00000269305	NM_001126112.2	212	-/T	6/11	0.565516263994213	2	FACETS	0.944	0.911	0.976	0.944	0.911	0.976	CLONAL	2	TRUE	0	0.56781404087494	2		686	1019	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591104	67591115	+	inframe_deletion	In_Frame_Del	DEL	TTAAACCAGACC	TTAAACCAGACC	-	novel	NA	P-0012109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	113	350	0	ENST00000274335.5:c.1700_1711del	p.Lys567_Leu570del	p.K567_L570del	ENST00000274335		566	aTTAAACCAGACCtt/att	12/15	0.56781404087494	3	FACETS	0.7	0.63	0.774	0.35	0.315	0.387	SUBCLONAL	1	TRUE	1	0.56781404087494	3		350	730	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838333	156838333	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	435	622	0	ENST00000524377.1:c.611C>G	p.Ser204Trp	p.S204W	ENST00000524377	NM_002529.3	204	tCg/tGg	6/17	0.343185217567247	5	FACETS	1	0.992	1	0.772	0.737	0.808	CLONAL	2	TRUE	2	0.56781404087494	5		622	1225	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084177	47084177	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	182	386	0	ENST00000409792.3:c.7112T>A	p.Val2371Glu	p.V2371E	ENST00000409792	NM_014159.6	2371	gTg/gAg	17/21	0.56781404087494	5	FACETS	1	0.942	1	0.257	0.236	0.278	CLONAL	1	TRUE	1	0.56781404087494	5		386	1156	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690821	89690821	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0012109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	103	261	0	ENST00000371953.3:c.228T>A	p.Tyr76Ter	p.Y76*	ENST00000371953	NM_000314.4	76	taT/taA	4/9	0.56781404087494	1	FACETS	0.866	0.785	0.949	0.866	0.785	0.949	CLONAL	1	TRUE	0	0.56781404087494	1		261	300	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0012120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	214	494	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.453333064002833	4	FACETS	0.933	0.877	0.991	0.933	0.877	0.991	CLONAL	3	TRUE	1	0.453333064002833	4		494	490	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461563	138461563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558261053	NA	P-0012120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	333	675	1	ENST00000289153.2:c.458G>A	p.Arg153His	p.R153H	ENST00000289153	NM_006219.2	153	cGc/cAc	3/22	0.453333064002833	4	FACETS	0.986	0.939	1	0.986	0.939	1	CLONAL	3	TRUE	1	0.453333064002833	4		676	722	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100703	67100703	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0012120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	158	542	0	ENST00000412916.2:c.399+2T>C		p.X133_splice	ENST00000412916		133			0.453333064002833	2	FACETS	0.996	0.927	1	0.996	0.927	1	CLONAL	2	TRUE	0	0.453333064002833	2		542	350	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226448	41226448	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	119	858	1	ENST00000357654.3:c.4575A>T	p.Gln1525His	p.Q1525H	ENST00000357654	NM_007294.3	1525	caA/caT	14/23	0.420659949275147	3	FACETS	0.925	0.836	1	0.463	0.418	0.51	CLONAL	1	TRUE	1	0.453333064002833	3		859	696	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115730	8115731	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGGC	novel	NA	P-0012120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	145	813	0	ENST00000346208.3:c.1078_1081dup	p.Ile361ArgfsTer11	p.I361Rfs*11	ENST00000346208		359	gaa/gaAGGCa	6/6	0.420659949275147	3	FACETS	0.904	0.825	0.987	0.452	0.412	0.494	CLONAL	1	TRUE	1	0.453333064002833	3		813	868	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117549	4117549	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519910	NA	P-0012122-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	30	396	2	ENST00000262948.5:c.171T>A	p.Phe57Leu	p.F57L	ENST00000262948	NM_030662.3	57	ttT/ttA	2/11	1	2	FACETS	1	0.822	1	1	0.822	1	CLONAL	1	TRUE	1	0.12	2		398	489	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111449	8111450	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012122-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	55	621	0	ENST00000346208.3:c.936dup	p.Ala313SerfsTer39	p.A313Sfs*39	ENST00000346208		312	aga/agAa	5/6	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.12	2		621	839	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	102	245	0				ENST00000310581	NM_198253.2	-/1132			0.183217485685558	1	FACETS	1	0.963	1	1	0.989	1	CLONAL	2	TRUE	0	0.183217485685558	1		245	440	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426893	6426893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519948	NA	P-0012194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	58	464	0	ENST00000356142.4:c.86C>T	p.Pro29Leu	p.P29L	ENST00000356142	NM_018890.3	29	cCt/cTt	2/7	1	2	FACETS	0.948	0.819	1	1	0.977	1	CLONAL	2	TRUE	1	0.183217485685558	2		464	334	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875645	35875645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201449880	NA	P-0012194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	59	419	0	ENST00000303115.3:c.832G>A	p.Asp278Asn	p.D278N	ENST00000303115	NM_002185.3	278	Gat/Aat	7/8	0.183217485685558	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.183217485685558	1		419	458	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633229	12633229	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs368807126	NA	P-0012194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1308	379	501	0	ENST00000251849.4:c.1171A>T	p.Arg391Trp	p.R391W	ENST00000251849	NM_002880.3	391	Agg/Tgg	11/17	0.183217485685558	6	FACETS	1	0.986	1	0.67	0.634	0.707	CLONAL	3	TRUE	1	0.183217485685558	6		501	1687	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390170	89390170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148593404	NA	P-0012194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	147	582	0	ENST00000336596.2:c.919G>A	p.Glu307Lys	p.E307K	ENST00000336596	NM_005233.5	307	Gag/Aag	4/17	1	2	FACETS	0.923	0.843	1	1	0.99	1	CLONAL	2	TRUE	1	0.183217485685558	2		582	869	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372023	55372023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	142	351	0	ENST00000297316.4:c.713C>T	p.Ala238Val	p.A238V	ENST00000297316	NM_022454.3	238	gCc/gTc	2/2	1	2	FACETS	1	0.952	1	1	0.991	1	CLONAL	2	TRUE	1	0.183217485685558	2		351	728	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272140	15272140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	81	187	0	ENST00000263388.2:c.6299C>T	p.Ser2100Leu	p.S2100L	ENST00000263388	NM_000435.2	2100	tCg/tTg	33/33	0.17381868637769	3	FACETS	1	0.937	1	1	0.981	1	CLONAL	3	TRUE	1	0.183217485685558	3		187	299	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916259	9916259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	112	438	0	ENST00000330684.3:c.2030C>T	p.Ser677Phe	p.S677F	ENST00000330684	NM_001134407.1	677	tCc/tTc	10/13	1	2	FACETS	1	0.92	1	1	0.989	1	CLONAL	2	TRUE	1	0.183217485685558	2		438	598	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554350	81554350	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	77	660	0	ENST00000298171.2:c.370G>A	p.Glu124Lys	p.E124K	ENST00000298171	NM_000369.2	124	Gag/Aag	4/10	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.183217485685558	2		660	702	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967209	93967209	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	58	578	0	ENST00000369303.4:c.2143G>A	p.Glu715Lys	p.E715K	ENST00000369303	NM_004440.3	715	Gaa/Aaa	12/17	1	2	FACETS	0.84	0.724	0.964	1	0.973	1	CLONAL	2	TRUE	1	0.183217485685558	2		578	377	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903745	41903746	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0012194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	368	631	2	ENST00000372991.4:c.811dup	p.Arg271ProfsTer53	p.R271Pfs*53	ENST00000372991	NM_001760.3	271	cgg/cCgg	5/5	0.183217485685558	6	FACETS	1	0.986	1	1	0.986	1	CLONAL	4	TRUE	2	0.183217485685558	6		633	1242	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003764	45003764	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0012194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	205	463	0	ENST00000558401.1:c.20T>G	p.Leu7Ter	p.L7*	ENST00000558401	NM_004048.2	7	tTa/tGa	1/4	0.183217485685558	0	FACETS	1	0.977	1			1	CLONAL	2	TRUE	0	0.183217485685558	0		463	815	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263953	16263953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	191	567	1	ENST00000375759.3:c.10322C>T	p.Pro3441Leu	p.P3441L	ENST00000375759	NM_015001.2	3441	cCt/cTt	12/15	1	2	FACETS	0.918	0.847	0.991	1	0.992	1	CLONAL	2	TRUE	1	0.183217485685558	2		568	1136	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086067	16086067	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	168	444	1	ENST00000281043.3:c.1243G>A	p.Glu415Lys	p.E415K	ENST00000281043	NM_005378.4	415	Gag/Aag	3/3	1	2	FACETS	1	0.944	1	1	0.992	1	CLONAL	2	TRUE	1	0.183217485685558	2		445	888	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967324	25967324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334255201	NA	P-0012194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	270	483	0	ENST00000435504.4:c.1882C>T	p.Pro628Ser	p.P628S	ENST00000435504		628	Ccc/Tcc	13/13	1	2	FACETS	0.873	0.818	0.928	1	0.996	1	CLONAL	3	TRUE	1	0.183217485685558	2		483	1126	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096135	178096135	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	110	398	0	ENST00000397062.3:c.1196C>T	p.Ser399Phe	p.S399F	ENST00000397062	NM_006164.4	399	tCt/tTt	5/5	1	2	FACETS	1	0.901	1	1	0.988	1	CLONAL	2	TRUE	1	0.183217485685558	2		398	600	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670234	134670234	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764139128	NA	P-0012194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	104	453	0	ENST00000398015.3:c.145G>A	p.Asp49Asn	p.D49N	ENST00000398015	NM_004441.4	49	Gat/Aat	3/16	1	2	FACETS	0.911	0.817	1	1	0.986	1	CLONAL	2	TRUE	1	0.183217485685558	2		453	623	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	240488	240488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	23	168	0	ENST00000264932.6:c.1448C>T	p.Pro483Leu	p.P483L	ENST00000264932	NM_004168.2	483	cCa/cTa	11/15	0.183217485685558	1	FACETS	1	0.826	1	1	0.95	1	CLONAL	2	TRUE	0	0.183217485685558	1		168	109	SUCCESS
APC	324	MSKCC	GRCh37	5	112178355	112178355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	47	385	0	ENST00000257430.4:c.7064C>T	p.Ser2355Leu	p.S2355L	ENST00000257430	NM_000038.5	2355	tCa/tTa	16/16	0.183217485685558	1	FACETS	0.955	0.813	1	1	0.972	1	CLONAL	2	TRUE	0	0.183217485685558	1		385	244	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486299	8486299	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142009246	NA	P-0012194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	73	289	1	ENST00000356435.5:c.2518C>T	p.Leu840Phe	p.L840F	ENST00000356435		840	Ctt/Ttt	17/35	1	2	FACETS	0.949	0.833	1	1	0.982	1	CLONAL	2	TRUE	1	0.183217485685558	2		290	420	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8497256	8497256	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	23	371	0	ENST00000356435.5:c.2335G>A	p.Asp779Asn	p.D779N	ENST00000356435		779	Gat/Aat	15/35	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.183217485685558	2		371	192	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249341	110249341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1358	272	835	2	ENST00000374672.4:c.1232C>T	p.Ser411Phe	p.S411F	ENST00000374672	NM_004235.4	411	tCc/tTc	4/5	1	2	FACETS	0.911	0.852	0.972	1	0.994	1	CLONAL	2	TRUE	1	0.183217485685558	2		837	1630	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589582	69589582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs934056828	NA	P-0012194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	182	411	0	ENST00000168712.1:c.271G>A	p.Gly91Ser	p.G91S	ENST00000168712	NM_002007.2	91	Ggc/Agc	1/3	1	2	FACETS	0.834	0.771	0.9	1	0.994	1	CLONAL	3	TRUE	1	0.183217485685558	2		411	794	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118379915	118379915	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	104	378	0	ENST00000534358.1:c.10900G>A	p.Glu3634Lys	p.E3634K	ENST00000534358	NM_005933.3	3634	Gaa/Aaa	29/36	1	2	FACETS	0.996	0.894	1	1	0.987	1	CLONAL	2	TRUE	1	0.183217485685558	2		378	570	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422086	81422086	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	101	417	1	ENST00000298171.2:c.62G>A	p.Gly21Glu	p.G21E	ENST00000298171	NM_000369.2	21	gGa/gAa	1/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.183217485685558	2		418	749	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483969	88483969	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	173	480	1	ENST00000360948.2:c.1601A>G	p.Lys534Arg	p.K534R	ENST00000360948	NM_001012338.2	534	aAg/aGg	14/19	1	2	FACETS	1	0.97	1	1	0.993	1	CLONAL	2	TRUE	1	0.183217485685558	2		481	852	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778288	3778288	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	52	277	0	ENST00000262367.5:c.6760C>T	p.Leu2254Phe	p.L2254F	ENST00000262367	NM_004380.2	2254	Ctc/Ttc	31/31	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.183217485685558	2		277	390	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892238	9892238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	212	549	0	ENST00000330684.3:c.2252G>A	p.Gly751Glu	p.G751E	ENST00000330684	NM_001134407.1	751	gGg/gAg	11/13	1	2	FACETS	1	0.982	1	1	0.994	1	CLONAL	2	TRUE	1	0.183217485685558	2		549	985	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41258500	41258500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	56	463	1	ENST00000357654.3:c.185C>T	p.Pro62Leu	p.P62L	ENST00000357654	NM_007294.3	62	cCt/cTt	4/23	1	2	FACETS	1	0.917	1	1	0.979	1	CLONAL	2	TRUE	1	0.183217485685558	2		464	281	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227100	2227100	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	75	176	1	ENST00000398665.3:c.4580C>T	p.Ser1527Phe	p.S1527F	ENST00000398665	NM_032482.2	1527	tCc/tTc	27/28	0.17381868637769	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.183217485685558	3		177	378	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758806	41758806	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	239	721	0	ENST00000301178.4:c.1860A>T	p.Leu620Phe	p.L620F	ENST00000301178	NM_021913.4	620	ttA/ttT	16/20	0.17381868637769	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.183217485685558	3		721	1166	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70350059	70350059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	149	194	1	ENST00000374080.3:c.4042C>T	p.Leu1348Phe	p.L1348F	ENST00000374080		1348	Ctc/Ttc	28/45	1	1	FACETS	0.977	0.904	1	1	0.994	1	CLONAL	4	TRUE	0	0.183217485685558	1		195	378	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870899	12870900	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0012194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	89	318	0	ENST00000228872.4:c.126_127delinsTT	p.Arg43Trp	p.R43W	ENST00000228872	NM_004064.3	42	acCCgg/acTTgg	1/3	0.17381868637769	3	FACETS	0.997	0.886	1	0.997	0.886	1	CLONAL	2	TRUE	1	0.183217485685558	3		318	532	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374360	31374361	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0012194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1192	162	651	0	ENST00000328111.2:c.359_360delinsTT	p.Ser120Phe	p.S120F	ENST00000328111	NM_006892.3	120	tCC/tTT	5/23	0.183217485685558	5	FACETS	0.832	0.762	0.907	0.416	0.381	0.454	CLONAL	2	TRUE	1	0.183217485685558	5		651	1354	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55209987	55209988	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	118	427	0	ENST00000275493.2:c.97_98delinsAA	p.Gly33Asn	p.G33N	ENST00000275493	NM_005228.3	33	GGc/AAc	2/28	1	2	FACETS	0.912	0.824	1	1	0.988	1	CLONAL	2	TRUE	1	0.183217485685558	2		427	706	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0012227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	161	242	0				ENST00000310581	NM_198253.2	-/1132			0.268581775607232	1	FACETS	0.782	0.729	0.834	0.782	0.729	0.834	INDETERMINATE	1	TRUE	0	0.768516295251213	1		242	330	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0012227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	182	576	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.918	0.854	0.984	0.918	0.854	0.984	CLONAL	1	TRUE	1	0.768516295251213	2		576	516	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105920	27105920	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	20	535	1	ENST00000324856.7:c.5531G>A	p.Trp1844Ter	p.W1844*	ENST00000324856	NM_006015.4	1844	tGg/tAg	20/20	0.768516295251213	1	FACETS	0.095	0.072	0.121	0.095	0.072	0.121	SUBCLONAL	1	TRUE	0	0.768516295251213	1		536	338	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775008	73775009	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0012227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	141	394	0	ENST00000254810.4:c.164dup	p.Tyr55Ter	p.Y55*	ENST00000254810	NM_005324.3	55	tat/taAt	3/4	1	2	FACETS	0.696	0.638	0.757	0.696	0.638	0.757	SUBCLONAL	1	TRUE	1	0.768516295251213	2		394	527	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106215	27106215	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	17	396	0	ENST00000324856.7:c.5826del	p.Ile1943LeufsTer13	p.I1943Lfs*13	ENST00000324856	NM_006015.4	1942	ggC/gg	20/20	0.768516295251213	1	FACETS	0.081	0.06	0.106	0.081	0.06	0.106	SUBCLONAL	1	TRUE	0	0.768516295251213	1		396	337	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105830	27105915	+	frameshift_variant	Frame_Shift_Del	DEL	TAAAGATCGTACAGAAGAATGATCCATTTGTGGTGGACTGCTCAGATAAGCTTGGGCGTGTGCAGGAGTTTGACAGTGGCCTGCTG	TAAAGATCGTACAGAAGAATGATCCATTTGTGGTGGACTGCTCAGATAAGCTTGGGCGTGTGCAGGAGTTTGACAGTGGCCTGCTG	CCACTGT	novel	NA	P-0012227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	34	564	0	ENST00000324856.7:c.5441_5526delinsCCACTGT	p.Val1814AlafsTer43	p.V1814Afs*43	ENST00000324856	NM_006015.4	1814	gTAAAGATCGTACAGAAGAATGATCCATTTGTGGTGGACTGCTCAGATAAGCTTGGGCGTGTGCAGGAGTTTGACAGTGGCCTGCTG/gCCACTGT	20/20	0.768516295251213	1	FACETS	0.137	0.112	0.166	0.137	0.112	0.166	SUBCLONAL	1	TRUE	0	0.768516295251213	1		564	397	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727483	66727483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504317	NA	P-0012240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	163	733	0	ENST00000307102.5:c.199G>A	p.Asp67Asn	p.D67N	ENST00000307102	NM_002755.3	67	Gac/Aac	2/11	0.627285454772252	4	FACETS	0.843	0.773	0.916	0.422	0.386	0.458	CLONAL	1	TRUE	2	0.635635189742431	4		733	995	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17355198	17355198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	607	632	0	ENST00000375499.3:c.320G>A	p.Gly107Glu	p.G107E	ENST00000375499	NM_003000.2	107	gGa/gAa	4/8	0.635635189742431	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	1	0.635635189742431	4		632	969	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143324144	143324144	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	352	555	2	ENST00000262992.4:c.319G>C	p.Glu107Gln	p.E107Q	ENST00000262992	NM_001101669.1	107	Gag/Cag	5/24	0.627285454772252	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.635635189742431	4		557	855	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031889	26031889	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	190	850	0	ENST00000244661.2:c.400G>C	p.Glu134Gln	p.E134Q	ENST00000244661	NM_003537.3	134	Gaa/Caa	1/1	0.635635189742431	3	FACETS	0.891	0.825	0.96	0.446	0.412	0.48	CLONAL	1	TRUE	1	0.635635189742431	3		850	884	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557383	29557383	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	303	433	1	ENST00000356175.3:c.3096C>A	p.Cys1032Ter	p.C1032*	ENST00000356175	NM_000267.3	1032	tgC/tgA	23/57	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	2	TRUE	NA	0.635635189742431	2		434	453	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428403	47428403	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1226	269	1289	0	ENST00000377045.4:c.1271A>T	p.Asn424Ile	p.N424I	ENST00000377045	NM_001654.4	424	aAc/aTc	12/16	0.533522850127488	4	FACETS	0.926	0.866	0.988	0.463	0.433	0.494	CLONAL	1	TRUE	2	0.635635189742431	4		1289	1495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578175	7578187	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ACCTCAGGCGGCT	ACCTCAGGCGGCT	-	novel	NA	P-0012240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	448	906	0	ENST00000269305.4:c.662_672+2del		p.X221_splice	ENST00000269305	NM_001126112.2	221		6/11	0.635635189742431	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.635635189742431	2		906	668	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405933	49405933	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	280	954	1	ENST00000418115.1:c.205del	p.Leu69Ter	p.L69*	ENST00000418115	NM_001664.2	69	Ctg/tg	3/5	0.627285454772252	4	FACETS	1	0.968	1	0.524	0.491	0.558	CLONAL	1	TRUE	2	0.635635189742431	4		955	1374	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139078	37139079	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	142	443	2	ENST00000373509.5:c.420dup	p.Glu141ArgfsTer68	p.E141Rfs*68	ENST00000373509	NM_002648.3	140	caa/cAaa	4/6	0.635635189742431	3	FACETS	1	0.955	1	0.532	0.487	0.579	CLONAL	1	TRUE	1	0.635635189742431	3		445	553	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178085	56178085	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	118	420	0	ENST00000399503.3:c.3058C>T	p.Gln1020Ter	p.Q1020*	ENST00000399503	NM_005921.1	1020	Caa/Taa	14/20	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.39	2		420	577	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772198	68772199	+	splice_acceptor_variant	Splice_Site	INS	-	-	G	novel	NA	P-0012243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	186	753	0	ENST00000261769.5:c.49dup		p.X17_splice	ENST00000261769	NM_004360.3	17			0.393521341137916	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.39	1		753	764	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163194	47163194	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012256-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	106	555	0	ENST00000409792.3:c.2932G>T	p.Glu978Ter	p.E978*	ENST00000409792	NM_014159.6	978	Gaa/Taa	3/21	0.0973085450179304	2	FACETS	0.92	0.825	1	1	0.979	1	CLONAL	3	FALSE	0	0.0973085450179304	2		555	789	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52677289	52677289	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0012256-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	152	847	1	ENST00000394830.3:c.970A>T	p.Arg324Ter	p.R324*	ENST00000394830	NM_018313.4	324	Aga/Tga	10/30	0.0973085450179304	2	FACETS	0.918	0.838	1	1	0.985	1	CLONAL	3	FALSE	0	0.0973085450179304	2		848	1134	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750462	41750462	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1194861348	NA	P-0012256-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	51	683	1	ENST00000226382.2:c.166G>A	p.Gly56Ser	p.G56S	ENST00000226382	NM_003924.3	56	Ggc/Agc	1/3	0.0924275404177397	4	FACETS	1	0.951	1			1	CLONAL	1	FALSE	NA	0.0973085450179304	4		684	874	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624297	89624297	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012256-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	42	373	0	ENST00000371953.3:c.71A>T	p.Asp24Val	p.D24V	ENST00000371953	NM_000314.4	24	gAc/gTc	1/9	0.075448133945851	1	FACETS	0.781	0.651	0.924	1	0.958	1	CLONAL	2	FALSE	0	0.0973085450179304	1		373	526	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37882064	37882064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012256-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	43	558	1	ENST00000269571.5:c.2830C>T	p.Pro944Ser	p.P944S	ENST00000269571		944	Ccc/Tcc	23/27	0.0973085450179304	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	FALSE	0	0.0973085450179304	1		559	722	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955527	90955528	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0012256-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	151	664	0	ENST00000265433.3:c.2137dup	p.Ala713GlyfsTer29	p.A713Gfs*29	ENST00000265433	NM_002485.4	713	gct/gGct	14/16	0.0973085450179304	3	FACETS	0.937	0.857	1	1	0.981	1	CLONAL	4	FALSE	0	0.0973085450179304	3		664	868	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183694	10183707	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGCCGGGCGGCC	GAGGCCGGGCGGCC	-	novel	NA	P-0012256-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	87	551	0	ENST00000256474.2:c.164_177del	p.Glu55AlafsTer72	p.E55Afs*72	ENST00000256474	NM_000551.3	55	GAGGCCGGGCGGCCg/g	1/3	0.0973085450179304	2	FACETS	0.93	0.824	1	1	0.975	1	CLONAL	3	FALSE	0	0.0973085450179304	2		551	641	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0012277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	63	250	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.849	0.734	0.973	0.849	0.734	0.973	CLONAL	1	TRUE	1	0.26	2		250	571	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0012277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	51	276	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.155434004295155	2	FACETS	1	0.919	1	0.559	0.477	0.648	INDETERMINATE	1	TRUE	0	0.26	2		276	351	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913250	NA	P-0012277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	85	401	0	ENST00000369535.4:c.34G>T	p.Gly12Cys	p.G12C	ENST00000369535	NM_002524.4	12	Ggt/Tgt	2/7	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.26	2		401	646	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119111	70119111	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	27	137	1	ENST00000245479.2:c.683C>A	p.Ser228Ter	p.S228*	ENST00000245479	NM_000346.3	228	tCg/tAg	2/3	0.165058526038254	3	FACETS	0.798	0.643	0.971	0.798	0.643	0.971	CLONAL	2	TRUE	1	0.26	3		138	147	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051054	180051054	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777308792	NA	P-0012277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	49	356	2	ENST00000261937.6:c.1429C>T	p.Arg477Trp	p.R477W	ENST00000261937	NM_182925.4	477	Cgg/Tgg	11/30	0.3	0	FACETS	0.952	0.811	1			1	CLONAL	1	TRUE	0	0.26	0		358	293	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925183	81925183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	66	571	0	ENST00000359376.3:c.974C>T	p.Ser325Leu	p.S325L	ENST00000359376	NM_002661.3	325	tCg/tTg	11/33	0.3	1	FACETS	0.683	0.592	0.781	0.683	0.592	0.781	SUBCLONAL	1	TRUE	0	0.26	1		571	647	SUCCESS
APC	324	MSKCC	GRCh37	5	112173668	112173669	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1114167564	NA	P-0012277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	52	322	0	ENST00000257430.4:c.2380dup	p.Ser794LysfsTer5	p.S794Kfs*5	ENST00000257430	NM_000038.5	793	caa/cAaa	16/16	1	2	FACETS	0.99	0.845	1	0.99	0.845	1	CLONAL	1	TRUE	1	0.26	2		322	404	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	350	387	0	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	1	0.974	1	1	0.997	1	CLONAL	2	TRUE	1	0.8	2		387	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	138	590	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.606	0.554	0.661	0.606	0.554	0.661	SUBCLONAL	1	TRUE	1	0.8	2		590	569	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460516	149460516	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	31	411	2	ENST00000286301.3:c.121C>T	p.Arg41Ter	p.R41*	ENST00000286301	NM_005211.3	41	Cga/Tga	3/22	1	2	FACETS	0.233	0.188	0.283	0.233	0.188	0.283	SUBCLONAL	1	TRUE	1	0.8	2		413	333	SUCCESS
B2M	567	MSKCC	GRCh37	15	45008529	45008529	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	245	708	0	ENST00000558401.1:c.349C>T	p.Arg117Ter	p.R117*	ENST00000558401	NM_004048.2	117	Cga/Tga	3/4	1	2	FACETS	0.87	0.817	0.924	0.87	0.817	0.924	CLONAL	1	TRUE	1	0.8	2		708	704	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681708	78681708	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767783333	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	149	495	0	ENST00000306801.3:c.416G>A	p.Arg139His	p.R139H	ENST00000306801	NM_020761.2	139	cGc/cAc	4/34	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.8	2		495	368	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342421	70342421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771266719	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	62	733	0	ENST00000374080.3:c.1312C>T	p.Arg438Cys	p.R438C	ENST00000374080		438	Cgc/Tgc	9/45	0.203145792915326	1	FACETS	0.208	0.179	0.238	0.208	0.179	0.238	INDETERMINATE	1	TRUE	0	0.8	1		733	448	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448592	89448592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543425684	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	169	542	0	ENST00000336596.2:c.1556C>T	p.Thr519Met	p.T519M	ENST00000336596	NM_005233.5	519	aCg/aTg	7/17	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.8	2		542	420	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054983	176054983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs991566021	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	278	631	0	ENST00000367669.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000367669	NM_022457.5	357	cGa/cAa	10/20	0.203145792915326	3	FACETS	0.769	0.728	0.81	0.769	0.728	0.81	INDETERMINATE	2	TRUE	1	0.8	3		631	633	SUCCESS
APC	324	MSKCC	GRCh37	5	112175921	112175921	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	74	259	0	ENST00000257430.4:c.4630G>T	p.Glu1544Ter	p.E1544*	ENST00000257430	NM_000038.5	1544	Gaa/Taa	16/16	1	2	FACETS	0.636	0.562	0.713	0.636	0.562	0.713	SUBCLONAL	1	TRUE	1	0.8	2		259	291	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518099	8518099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764400127	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	134	381	0	ENST00000356435.5:c.1292C>T	p.Ser431Leu	p.S431L	ENST00000356435		431	tCg/tTg	10/35	1	2	FACETS	0.971	0.894	1	0.971	0.894	1	CLONAL	1	TRUE	1	0.8	2		381	345	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544702	65544702	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	147	540	0	ENST00000358664.4:c.224G>A	p.Arg75Gln	p.R75Q	ENST00000358664	NM_002382.4	75	cGa/cAa	4/5	0.102917471053861	3	FACETS	0.958	0.88	1	0.479	0.44	0.52	INDETERMINATE	1	TRUE	1	0.8	3		540	537	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111958593	111958593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555186772	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	51	367	0	ENST00000375549.3:c.65G>A	p.Arg22Gln	p.R22Q	ENST00000375549	NM_003002.3	22	cGa/cAa	2/4	1	2	FACETS	0.299	0.255	0.348	0.299	0.255	0.348	SUBCLONAL	1	TRUE	1	0.8	2		367	426	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982356	25982356	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	105	264	0	ENST00000435504.4:c.934C>T	p.Arg312Ter	p.R312*	ENST00000435504		312	Cga/Tga	9/13	1	2	FACETS	0.637	0.575	0.702	0.637	0.575	0.702	SUBCLONAL	1	TRUE	1	0.8	2		264	412	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443345	187443345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	178	417	1	ENST00000232014.4:c.1781G>A	p.Arg594Gln	p.R594Q	ENST00000232014	NM_001130845.1	594	cGa/cAa	8/10	0.3	4	FACETS	0.925	0.862	0.988			1	INDETERMINATE	2	TRUE	NA	0.8	4		418	433	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980345	55980345	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	191	624	0	ENST00000263923.4:c.746G>T	p.Arg249Ile	p.R249I	ENST00000263923	NM_002253.2	249	aGa/aTa	6/30	0.3	1	FACETS	0.596	0.556	0.636	0.596	0.556	0.636	INDETERMINATE	1	TRUE	0	0.8	1		624	481	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720870	89720870	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1554825652	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	166	285	0	ENST00000371953.3:c.1021T>G	p.Phe341Val	p.F341V	ENST00000371953	NM_000314.4	341	Ttt/Gtt	8/9	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.8	2		285	376	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143551	108143551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201780199	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	196	548	0	ENST00000278616.4:c.3256C>T	p.Arg1086Cys	p.R1086C	ENST00000278616	NM_000051.3	1086	Cgc/Tgc	22/63	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.8	2		548	481	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276250	15276250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747223569	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	122	472	0	ENST00000263388.2:c.5744G>A	p.Arg1915His	p.R1915H	ENST00000263388	NM_000435.2	1915	cGc/cAc	31/33	1	2	FACETS	0.933	0.854	1	0.933	0.854	1	CLONAL	1	TRUE	1	0.8	2		472	327	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956220	55956220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190050670	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	159	485	0	ENST00000263923.4:c.3095G>A	p.Arg1032Gln	p.R1032Q	ENST00000263923	NM_002253.2	1032	cGa/cAa	23/30	0.3	1	FACETS	0.607	0.563	0.651	0.607	0.563	0.651	INDETERMINATE	1	TRUE	0	0.8	1		485	393	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171607	36171607	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1569008655	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	119	198	0	ENST00000300305.3:c.958C>T	p.Arg320Ter	p.R320*	ENST00000300305		320	Cga/Tga	7/8	0.3	4	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.8	4		198	369	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210733	5210733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779302415	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	151	355	0	ENST00000357368.4:c.5318C>T	p.Ser1773Leu	p.S1773L	ENST00000357368	NM_002850.3	1773	tCg/tTg	34/38	0.203145792915326	1	FACETS	0.643	0.597	0.691	0.643	0.597	0.691	INDETERMINATE	1	TRUE	0	0.8	1		355	352	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857197	9857197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866121846	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	215	811	2	ENST00000330684.3:c.4204C>T	p.Arg1402Trp	p.R1402W	ENST00000330684	NM_001134407.1	1402	Cgg/Tgg	13/13	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.8	2		813	481	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20483060	20483060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750169257	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	180	457	0	ENST00000346618.3:c.793G>A	p.Glu265Lys	p.E265K	ENST00000346618	NM_001949.4	265	Gag/Aag	4/7	1	2	FACETS	0.928	0.863	0.993	0.928	0.863	0.993	CLONAL	1	TRUE	1	0.8	2		457	485	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683246	88683246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767763451	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	96	381	0	ENST00000372037.3:c.1456C>T	p.Arg486Trp	p.R486W	ENST00000372037	NM_004329.2	486	Cgg/Tgg	12/13	1	2	FACETS	0.696	0.626	0.769	0.696	0.626	0.769	SUBCLONAL	1	TRUE	1	0.8	2		381	345	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	294	1035	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.947	0.896	0.999	0.947	0.896	0.999	CLONAL	1	TRUE	1	0.8	2		1036	776	SUCCESS
APC	324	MSKCC	GRCh37	5	112174802	112174802	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201830995	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	153	355	0	ENST00000257430.4:c.3511C>T	p.Arg1171Cys	p.R1171C	ENST00000257430	NM_000038.5	1171	Cgt/Tgt	16/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.8	2		355	354	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845901	156845901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769486223	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	178	752	0	ENST00000524377.1:c.1531G>A	p.Val511Met	p.V511M	ENST00000524377	NM_002529.3	511	Gtg/Atg	13/17	0.3	1	FACETS	0.668	0.623	0.712	0.668	0.623	0.712	INDETERMINATE	1	TRUE	0	0.8	1		752	400	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520000	106520000	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs759433704	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	105	470	0	ENST00000359195.3:c.2428C>A	p.Pro810Thr	p.P810T	ENST00000359195	NM_002649.2	810	Cca/Aca	6/11	1	2	FACETS	0.616	0.556	0.679	0.616	0.556	0.679	SUBCLONAL	1	TRUE	1	0.8	2		470	426	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432375	49432375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751964761	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	85	551	2	ENST00000301067.7:c.8764C>T	p.Arg2922Trp	p.R2922W	ENST00000301067	NM_003482.3	2922	Cgg/Tgg	34/54	0.3	1	FACETS	0.341	0.303	0.381	0.341	0.303	0.381	INDETERMINATE	1	TRUE	0	0.8	1		553	374	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612073	189612073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142762485	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	25	515	1	ENST00000264731.3:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000264731	NM_003722.4	609	Gaa/Aaa	14/14	1	2	FACETS	0.136	0.107	0.17	0.136	0.107	0.17	SUBCLONAL	1	TRUE	1	0.8	2		516	458	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716344	18716344	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778895247	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	189	432	0	ENST00000266497.5:c.3691G>A	p.Glu1231Lys	p.E1231K	ENST00000266497		1231	Gaa/Aaa	26/31	0.3	3	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.8	3		432	487	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133561	55133561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs958381664	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	176	471	1	ENST00000257290.5:c.865G>A	p.Glu289Lys	p.E289K	ENST00000257290	NM_006206.4	289	Gaa/Aaa	6/23	0.3	1	FACETS	0.662	0.617	0.706	0.662	0.617	0.706	INDETERMINATE	1	TRUE	0	0.8	1		472	399	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50481162	50481162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	191	478	0	ENST00000394963.4:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000394963	NM_003076.4	183	cGa/cAa	5/13	0.102917471053861	3	FACETS	1	0.99	1	0.688	0.642	0.734	INDETERMINATE	1	TRUE	1	0.8	3		478	486	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418997	116418997	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200754673	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	164	301	0	ENST00000397752.3:c.3508C>T	p.Arg1170Ter	p.R1170*	ENST00000397752	NM_000245.2	1170	Cga/Tga	17/21	0.3	4	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.8	4		301	503	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814253	76814253	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	132	685	1	ENST00000373344.5:c.6391C>T	p.Arg2131Ter	p.R2131*	ENST00000373344	NM_000489.3	2131	Cga/Tga	29/35	0.203145792915326	1	FACETS	0.381	0.347	0.416	0.381	0.347	0.416	INDETERMINATE	1	TRUE	0	0.8	1		686	520	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	206	536	1	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.8	2		537	496	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133761036	133761036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1456042173	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	47	637	0	ENST00000318560.5:c.3359C>T	p.Ser1120Leu	p.S1120L	ENST00000318560	NM_005157.4	1120	tCg/tTg	11/11	0.203145792915326	1	FACETS	0.19	0.16	0.222	0.19	0.16	0.222	INDETERMINATE	1	TRUE	0	0.8	1		637	372	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027998	48027998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757653982	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	135	372	0	ENST00000234420.5:c.2876G>A	p.Arg959His	p.R959H	ENST00000234420	NM_000179.2	959	cGc/cAc	4/10	1	2	FACETS	0.739	0.676	0.803	0.739	0.676	0.803	SUBCLONAL	1	TRUE	1	0.8	2		372	457	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921737	111921737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1170116948	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	231	569	1	ENST00000393256.3:c.526G>A	p.Glu176Lys	p.E176K	ENST00000393256	NM_006538.4	176	Gaa/Aaa	4/4	0.394534646384061	4	FACETS	0.931	0.876	0.987	0.931	0.876	0.987	INDETERMINATE	2	TRUE	2	0.8	4		570	558	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805719	43805719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528834914	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	198	546	0	ENST00000372470.3:c.775G>A	p.Glu259Lys	p.E259K	ENST00000372470	NM_005373.2	259	Gaa/Aaa	5/12	0.102917471053861	3	FACETS	0.77	0.722	0.819	0.77	0.722	0.819	INDETERMINATE	2	TRUE	1	0.8	3		546	450	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907683	111907683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146318804	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	269	239	0	ENST00000393256.3:c.457C>T	p.Arg153Trp	p.R153W	ENST00000393256	NM_006538.4	153	Cgg/Tgg	3/4	0.394534646384061	4	FACETS	0.967	0.914	1	0.967	0.914	1	INDETERMINATE	2	TRUE	2	0.8	4		239	626	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922294	100922294	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1315135533	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	326	600	3	ENST00000325455.5:c.2218C>T	p.Arg740Ter	p.R740*	ENST00000325455	NM_001202474.3	740	Cga/Tga	5/8	0.3	4	FACETS	0.997	0.948	1			1	INDETERMINATE	2	TRUE	NA	0.8	4		603	736	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178095	56178095	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374455781	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	211	326	0	ENST00000399503.3:c.3068G>A	p.Arg1023His	p.R1023H	ENST00000399503	NM_005921.1	1023	cGc/cAc	14/20	0.3	5	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.8	5		326	495	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428511	78428511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408536007	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	179	500	1	ENST00000370768.2:c.1288C>T	p.Arg430Cys	p.R430C	ENST00000370768	NM_003902.3	430	Cgt/Tgt	14/20	0.282046453132761	3	FACETS	0.9	0.833	0.97	0.45	0.416	0.485	INDETERMINATE	1	TRUE	1	0.8	3		501	696	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095836	178095836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1328262363	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	224	420	0	ENST00000397062.3:c.1495C>T	p.Arg499Trp	p.R499W	ENST00000397062	NM_006164.4	499	Cgg/Tgg	5/5	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.8	2		420	549	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439281	52439281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143891879	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	125	362	0	ENST00000460680.1:c.961G>A	p.Ala321Thr	p.A321T	ENST00000460680	NM_004656.3	321	Gca/Aca	11/17	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.8	2		362	311	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670615	134670615	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781004053	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	31	748	0	ENST00000398015.3:c.526G>A	p.Ala176Thr	p.A176T	ENST00000398015	NM_004441.4	176	Gct/Act	3/16	1	2	FACETS	0.177	0.143	0.216	0.177	0.143	0.216	SUBCLONAL	1	TRUE	1	0.8	2		748	438	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	167	454	0	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	0.102917471053861	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.8	0		454	384	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951156	48951156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060503078	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	100	448	0	ENST00000267163.4:c.1318G>A	p.Glu440Lys	p.E440K	ENST00000267163	NM_000321.2	440	Gaa/Aaa	13/27	0.102917471053861	3	FACETS	0.814	0.732	0.9	0.407	0.366	0.45	INDETERMINATE	1	TRUE	1	0.8	3		448	430	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953748	48953748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759079385	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	98	331	0	ENST00000267163.4:c.1351C>T	p.Arg451Cys	p.R451C	ENST00000267163	NM_000321.2	451	Cgc/Tgc	14/27	0.102917471053861	3	FACETS	0.997	0.898	1	0.499	0.449	0.55	INDETERMINATE	1	TRUE	1	0.8	3		331	344	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442819	99442819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1365982598	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	31	511	0	ENST00000268035.6:c.1216C>T	p.Arg406Cys	p.R406C	ENST00000268035	NM_000875.3	406	Cgc/Tgc	5/21	1	2	FACETS	0.159	0.128	0.194	0.159	0.128	0.194	SUBCLONAL	1	TRUE	1	0.8	2		511	488	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971393	15971393	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759642635	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	170	462	0	ENST00000268712.3:c.4556C>T	p.Ser1519Leu	p.S1519L	ENST00000268712	NM_006311.3	1519	tCg/tTg	32/46	1	2	FACETS	0.975	0.906	1	0.975	0.906	1	CLONAL	1	TRUE	1	0.8	2		462	436	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543740	29543740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	129	414	1	ENST00000389048.3:c.1423C>T	p.Pro475Ser	p.P475S	ENST00000389048	NM_004304.4	475	Cct/Tct	7/29	0.3	1	FACETS	0.605	0.556	0.654	0.605	0.556	0.654	INDETERMINATE	1	TRUE	0	0.8	1		415	320	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438026	438026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769454180	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	223	462	0	ENST00000399788.2:c.1943G>A	p.Arg648Gln	p.R648Q	ENST00000399788	NM_001042603.1	648	cGa/cAa	14/28	1	2	FACETS	0.943	0.885	1	0.943	0.885	1	CLONAL	1	TRUE	1	0.8	2		462	591	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443758	49443758	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748757592	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	188	685	1	ENST00000301067.7:c.3613G>A	p.Val1205Ile	p.V1205I	ENST00000301067	NM_003482.3	1205	Gtt/Att	11/54	0.3	1	FACETS	0.603	0.562	0.643	0.603	0.562	0.643	INDETERMINATE	1	TRUE	0	0.8	1		686	468	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913023	32913023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376338226	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	317	859	0	ENST00000380152.3:c.4531G>A	p.Glu1511Lys	p.E1511K	ENST00000380152		1511	Gaa/Aaa	11/27	0.203145792915326	1	FACETS	0.619	0.587	0.651	0.619	0.587	0.651	INDETERMINATE	1	TRUE	0	0.8	1		859	768	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142885	30142885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766999851	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	129	230	0	ENST00000389048.3:c.641G>A	p.Arg214His	p.R214H	ENST00000389048	NM_004304.4	214	cGc/cAc	1/29	0.3	1	FACETS	0.741	0.686	0.796	0.741	0.686	0.796	INDETERMINATE	1	TRUE	0	0.8	1		230	261	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940455	29940455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138686378	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	133	408	3	ENST00000389048.3:c.776G>A	p.Arg259His	p.R259H	ENST00000389048	NM_004304.4	259	cGc/cAc	2/29	0.3	1	FACETS	0.536	0.492	0.581	0.536	0.492	0.581	INDETERMINATE	1	TRUE	0	0.8	1		411	372	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645121	86645121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	179	317	1	ENST00000274376.6:c.1193G>A	p.Arg398Gln	p.R398Q	ENST00000274376	NM_002890.2	398	cGa/cAa	8/25	0.3	3	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.8	3		318	446	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649000	86649000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755634472	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	147	361	0	ENST00000274376.6:c.1280G>A	p.Arg427Gln	p.R427Q	ENST00000274376	NM_002890.2	427	cGa/cAa	9/25	0.3	3	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.8	3		361	408	SUCCESS
APC	324	MSKCC	GRCh37	5	112178000	112178000	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768922431	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	215	564	0	ENST00000257430.4:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000257430	NM_000038.5	2237	Cga/Tga	16/16	1	2	FACETS	0.999	0.937	1	0.999	0.937	1	CLONAL	1	TRUE	1	0.8	2		564	538	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729604	41729604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	77	766	1	ENST00000242208.4:c.925C>T	p.Arg309Trp	p.R309W	ENST00000242208	NM_002192.2	309	Cgg/Tgg	3/3	1	2	FACETS	0.353	0.31	0.398	0.353	0.31	0.398	SUBCLONAL	1	TRUE	1	0.8	2		767	546	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	198	452	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.8	2		452	491	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115600	108115600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772821016	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	177	618	0	ENST00000278616.4:c.748C>T	p.Arg250Ter	p.R250*	ENST00000278616	NM_000051.3	250	Cga/Tga	7/63	1	2	FACETS	0.924	0.859	0.99	0.924	0.859	0.99	CLONAL	1	TRUE	1	0.8	2		618	479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577077	7577077	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	172	539	0	ENST00000269305.4:c.861G>T	p.Glu287Asp	p.E287D	ENST00000269305	NM_001126112.2	287	gaG/gaT	8/11	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.8	2		539	426	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169179	119169179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150811339	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	35	503	0	ENST00000264033.4:c.2363G>A	p.Arg788Gln	p.R788Q	ENST00000264033	NM_005188.3	788	cGa/cAa	15/16	1	2	FACETS	0.224	0.183	0.269	0.224	0.183	0.269	SUBCLONAL	1	TRUE	1	0.8	2		503	391	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041074	42041074	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	84	694	2	ENST00000219905.7:c.5452C>T	p.Arg1818Ter	p.R1818*	ENST00000219905	NM_001164273.1	1818	Cga/Tga	16/24	1	2	FACETS	0.299	0.264	0.337	0.299	0.264	0.337	SUBCLONAL	1	TRUE	1	0.8	2		696	702	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131412	202131412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339962485	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	126	481	0	ENST00000358485.4:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000358485	NM_001080125.1	127	cGa/cAa	2/9	1	2	FACETS	0.64	0.583	0.7	0.64	0.583	0.7	SUBCLONAL	1	TRUE	1	0.8	2		481	492	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765694	41765694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61737385	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	117	557	1	ENST00000301178.4:c.2570C>T	p.Ala857Val	p.A857V	ENST00000301178	NM_021913.4	857	gCg/gTg	20/20	1	2	FACETS	0.599	0.543	0.658	0.599	0.543	0.658	SUBCLONAL	1	TRUE	1	0.8	2		558	488	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922293	100922293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149186732	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	46	615	0	ENST00000325455.5:c.2219G>A	p.Arg740Gln	p.R740Q	ENST00000325455	NM_001202474.3	740	cGa/cAa	5/8	0.3	4	FACETS	0.276	0.231	0.325			1	INDETERMINATE	1	TRUE	NA	0.8	4		615	750	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439839	220439839	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761479412	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	220	780	0	ENST00000243786.2:c.692G>A	p.Arg231Gln	p.R231Q	ENST00000243786	NM_002191.3	231	cGa/cAa	2/2	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.8	2		780	539	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517847	187517847	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202133523	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	136	544	1	ENST00000441802.2:c.12847G>A	p.Glu4283Lys	p.E4283K	ENST00000441802	NM_005245.3	4283	Gaa/Aaa	25/27	1	2	FACETS	0.861	0.791	0.932	0.861	0.791	0.932	CLONAL	1	TRUE	1	0.8	2		545	395	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37061907	37061907	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs550914672	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	140	465	0	ENST00000231790.2:c.991G>A	p.Glu331Lys	p.E331K	ENST00000231790	NM_000249.3	331	Gag/Aag	11/19	1	2	FACETS	0.85	0.781	0.92	0.85	0.781	0.92	CLONAL	1	TRUE	1	0.8	2		465	412	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344077	70344077	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	38	881	0	ENST00000374080.3:c.1813C>T	p.Arg605Ter	p.R605*	ENST00000374080		605	Cga/Tga	13/45	0.203145792915326	1	FACETS	0.109	0.089	0.13	0.109	0.089	0.13	INDETERMINATE	1	TRUE	0	0.8	1		881	525	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004247	150004247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	199	632	3	ENST00000253339.5:c.1978C>T	p.Arg660Cys	p.R660C	ENST00000253339		660	Cgt/Tgt	3/7	0.282046453132761	3	FACETS	1	0.992	1	0.747	0.7	0.795	INDETERMINATE	1	TRUE	1	0.8	3		635	466	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844404	156844404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199826686	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	27	912	2	ENST00000524377.1:c.1237G>A	p.Glu413Lys	p.E413K	ENST00000524377	NM_002529.3	413	Gaa/Aaa	10/17	0.3	1	FACETS	0.075	0.059	0.094	0.075	0.059	0.094	INDETERMINATE	1	TRUE	0	0.8	1		914	537	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	208	534	0	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	1	2	FACETS	0.974	0.912	1	0.974	0.912	1	CLONAL	1	TRUE	1	0.8	2		534	534	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3842041	3842041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	241	500	0	ENST00000262367.5:c.1271G>A	p.Arg424Gln	p.R424Q	ENST00000262367	NM_004380.2	424	cGa/cAa	5/31	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.8	2		500	534	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562982	29562982	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1306237220	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	255	686	0	ENST00000356175.3:c.3917G>A	p.Arg1306Gln	p.R1306Q	ENST00000356175	NM_000267.3	1306	cGa/cAa	29/57	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.8	2		686	588	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336625	81336625	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs527951814	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	154	522	0	ENST00000222390.5:c.1597C>T	p.Arg533Ter	p.R533*	ENST00000222390	NM_000601.4	533	Cga/Tga	14/18	1	2	FACETS	0.879	0.812	0.947	0.879	0.812	0.947	CLONAL	1	TRUE	1	0.8	2		522	438	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434090	49434090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779629382	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	20	295	0	ENST00000301067.7:c.7463C>T	p.Ser2488Leu	p.S2488L	ENST00000301067	NM_003482.3	2488	tCg/tTg	31/54	0.3	1	FACETS	0.133	0.101	0.169	0.133	0.101	0.169	INDETERMINATE	1	TRUE	0	0.8	1		295	226	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055755	152055755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1403418496	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	154	504	0	ENST00000262189.6:c.167G>A	p.Arg56Gln	p.R56Q	ENST00000262189	NM_170606.2	56	cGa/cAa	2/59	0.3	3	FACETS	0.963	0.886	1			1	INDETERMINATE	1	TRUE	NA	0.8	3		504	560	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101910054	101910054	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	110	418	0	ENST00000374994.4:c.1374G>A	p.Trp458Ter	p.W458*	ENST00000374994	NM_004612.2	458	tgG/tgA	8/9	1	2	FACETS	0.786	0.713	0.86	0.786	0.713	0.86	SUBCLONAL	1	TRUE	1	0.8	2		418	350	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130163	143130163	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	150	414	0	ENST00000262992.4:c.853G>T	p.Glu285Ter	p.E285*	ENST00000262992	NM_001101669.1	285	Gaa/Taa	11/24	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.8	2		414	368	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687122	176687122	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	208	541	1	ENST00000439151.2:c.5099G>A	p.Arg1700Gln	p.R1700Q	ENST00000439151	NM_022455.4	1700	cGa/cAa	14/23	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.8	2		542	520	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891687	28891687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	137	677	1	ENST00000282397.4:c.3334C>T	p.Arg1112Cys	p.R1112C	ENST00000282397	NM_002019.4	1112	Cgc/Tgc	25/30	0.203145792915326	1	FACETS	0.393	0.359	0.428	0.393	0.359	0.428	INDETERMINATE	1	TRUE	0	0.8	1		678	523	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231757	66231757	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	19	437	0	ENST00000273854.3:c.1943G>T	p.Arg648Ile	p.R648I	ENST00000273854	NM_004439.5	648	aGa/aTa	11/18	0.3	1	FACETS	0.081	0.061	0.104	0.081	0.061	0.104	INDETERMINATE	1	TRUE	0	0.8	1		437	353	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562641	29562641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854562	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	240	651	1	ENST00000356175.3:c.3721C>T	p.Arg1241Ter	p.R1241*	ENST00000356175	NM_000267.3	1241	Cga/Tga	28/57	1	2	FACETS	0.972	0.915	1	0.972	0.915	1	CLONAL	1	TRUE	1	0.8	2		652	617	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542861	187542861	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1340793072	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	169	410	1	ENST00000441802.2:c.4879C>T	p.Arg1627Ter	p.R1627*	ENST00000441802	NM_005245.3	1627	Cga/Tga	10/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.8	2		411	374	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012441	29012441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55974987	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	73	364	0	ENST00000282397.4:c.430G>A	p.Glu144Lys	p.E144K	ENST00000282397	NM_002019.4	144	Gaa/Aaa	4/30	0.203145792915326	1	FACETS	0.264	0.231	0.298	0.264	0.231	0.298	INDETERMINATE	1	TRUE	0	0.8	1		364	415	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94224031	94224031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs116679717	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	138	499	0	ENST00000323929.3:c.121G>A	p.Asp41Asn	p.D41N	ENST00000323929	NM_005591.3	41	Gat/Aat	3/20	1	2	FACETS	0.657	0.601	0.715	0.657	0.601	0.715	SUBCLONAL	1	TRUE	1	0.8	2		499	525	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944562	40944562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868189942	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	101	302	0	ENST00000373198.4:c.1940C>T	p.Ser647Leu	p.S647L	ENST00000373198	NM_133170.3	647	tCg/tTg	12/32	0.3	1	FACETS	0.545	0.494	0.597	0.545	0.494	0.597	INDETERMINATE	1	TRUE	0	0.8	1		302	278	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881467	111881467	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1431222585	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	152	436	1	ENST00000393256.3:c.145G>A	p.Gly49Arg	p.G49R	ENST00000393256	NM_006538.4	49	Gga/Aga	2/4	0.394534646384061	4	FACETS	1	0.979	1	0.595	0.546	0.645	INDETERMINATE	1	TRUE	2	0.8	4		437	575	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405902	157405902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1282587061	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	181	431	0	ENST00000346085.5:c.2144C>T	p.Pro715Leu	p.P715L	ENST00000346085	NM_020732.3	715	cCg/cTg	6/20	0.282046453132761	3	FACETS	1	0.99	1	0.699	0.652	0.747	INDETERMINATE	1	TRUE	1	0.8	3		431	453	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098949	47098949	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	136	329	2	ENST00000409792.3:c.6325C>T	p.Arg2109Ter	p.R2109*	ENST00000409792	NM_014159.6	2109	Cga/Tga	15/21	1	2	FACETS	0.899	0.827	0.973	0.899	0.827	0.973	CLONAL	1	TRUE	1	0.8	2		331	378	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560970	9560970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781706438	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	167	485	0	ENST00000353224.5:c.812C>T	p.Ser271Leu	p.S271L	ENST00000353224	NM_177990.2	271	tCg/tTg	4/10	0.3	2	FACETS	0.949	0.881	1			1	INDETERMINATE	1	TRUE	NA	0.8	2		485	440	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835623	68835623	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35606263	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	224	615	3	ENST00000261769.5:c.214G>A	p.Asp72Asn	p.D72N	ENST00000261769	NM_004360.3	72	Gac/Aac	3/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.8	2		618	529	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028820	47028820	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370571712	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	130	654	0	ENST00000377604.3:c.124C>T	p.Arg42Cys	p.R42C	ENST00000377604	NM_001204468.1	42	Cgt/Tgt	3/24	0.3	2	FACETS	0.779	0.713	0.848			1	INDETERMINATE	1	TRUE	NA	0.8	2		654	417	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168682	32168682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs935064991	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	190	538	2	ENST00000375023.3:c.4241C>T	p.Ala1414Val	p.A1414V	ENST00000375023	NM_004557.3	1414	gCg/gTg	23/30	0.3	1	FACETS	0.722	0.677	0.766	0.722	0.677	0.766	INDETERMINATE	1	TRUE	0	0.8	1		540	395	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457251	89457252	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	126	364	0	ENST00000336596.2:c.1738dup	p.Arg580LysfsTer19	p.R580Kfs*19	ENST00000336596	NM_005233.5	578	gaa/gAaa	9/17	1	2	FACETS	0.908	0.832	0.985	0.908	0.832	0.985	CLONAL	1	TRUE	1	0.8	2		364	347	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953827	131953827	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104895051	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	107	389	1	ENST00000265335.6:c.3230G>A	p.Arg1077Gln	p.R1077Q	ENST00000265335		1077	cGa/cAa	21/25	1	2	FACETS	0.721	0.653	0.792	0.721	0.653	0.792	SUBCLONAL	1	TRUE	1	0.8	2		390	371	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015851	112015851	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	285	757	1	ENST00000368678.4:c.1090C>T	p.Leu364Phe	p.L364F	ENST00000368678		364	Ctt/Ttt	10/13	0.3	4	FACETS	0.893	0.845	0.942			1	INDETERMINATE	2	TRUE	NA	0.8	4		758	718	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650719	67650719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1131691283	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	234	633	0	ENST00000264010.4:c.1024C>T	p.Arg342Cys	p.R342C	ENST00000264010	NM_006565.3	342	Cgt/Tgt	5/12	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.8	2		633	571	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457304	67457304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223765	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	101	482	3	ENST00000327367.4:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000327367	NM_005902.3	93	cGa/cAa	2/9	1	2	FACETS	0.559	0.502	0.618	0.559	0.502	0.618	SUBCLONAL	1	TRUE	1	0.8	2		485	452	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56875705	56875705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs572483425	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	270	769	2	ENST00000308159.5:c.2309C>T	p.Ser770Leu	p.S770L	ENST00000308159	NM_014669.4	770	tCg/tTg	21/22	1	2	FACETS	0.985	0.93	1	0.985	0.93	1	CLONAL	1	TRUE	1	0.8	2		771	685	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428244	47428244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	93	518	3	ENST00000377045.4:c.1204G>A	p.Asp402Asn	p.D402N	ENST00000377045	NM_001654.4	402	Gac/Aac	11/16	0.203145792915326	1	FACETS	0.285	0.254	0.317	0.285	0.254	0.317	INDETERMINATE	1	TRUE	0	0.8	1		521	490	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585494	29585494	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660428	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	89	158	1	ENST00000356175.3:c.4243G>A	p.Glu1415Lys	p.E1415K	ENST00000356175	NM_000267.3	1415	Gaa/Aaa	31/57	1	2	FACETS	0.897	0.808	0.989	0.897	0.808	0.989	CLONAL	1	TRUE	1	0.8	2		159	248	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256832	16256832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs887977680	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	114	392	0	ENST00000375759.3:c.4097G>A	p.Arg1366Gln	p.R1366Q	ENST00000375759	NM_015001.2	1366	cGa/cAa	11/15	0.102917471053861	3	FACETS	0.897	0.813	0.984	0.448	0.406	0.492	INDETERMINATE	1	TRUE	1	0.8	3		392	445	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740098	162740098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781104392	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	126	281	0	ENST00000367921.3:c.1300C>T	p.Arg434Trp	p.R434W	ENST00000367921	NM_006182.2	434	Cgg/Tgg	12/18	0.3	1	FACETS	0.727	0.672	0.782	0.727	0.672	0.782	INDETERMINATE	1	TRUE	0	0.8	1		281	260	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750454	57750454	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	102	587	1	ENST00000274289.3:c.2014C>T	p.Arg672Ter	p.R672*	ENST00000274289	NM_006622.3	672	Cga/Tga	14/14	0.3	5	FACETS	0.728	0.651	0.81			1	INDETERMINATE	1	TRUE	NA	0.8	5		588	771	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291528	10291528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755995375	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	213	578	0	ENST00000340748.4:c.151G>A	p.Glu51Lys	p.E51K	ENST00000340748		51	Gaa/Aaa	3/40	0.203145792915326	1	FACETS	0.619	0.581	0.658	0.619	0.581	0.658	INDETERMINATE	1	TRUE	0	0.8	1		578	516	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987215	2987215	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	79	337	0	ENST00000396946.4:c.214C>T	p.Arg72Ter	p.R72*	ENST00000396946	NM_032415.4	72	Cga/Tga	3/25	1	2	FACETS	0.663	0.589	0.74	0.663	0.589	0.74	SUBCLONAL	1	TRUE	1	0.8	2		337	298	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521544	8521544	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	42	271	0	ENST00000356435.5:c.694C>T	p.Arg232Cys	p.R232C	ENST00000356435		232	Cgc/Tgc	9/35	1	2	FACETS	0.37	0.31	0.435	0.37	0.31	0.435	SUBCLONAL	1	TRUE	1	0.8	2		271	284	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958788	55958788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780764266	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	172	614	1	ENST00000263923.4:c.3065G>A	p.Arg1022Gln	p.R1022Q	ENST00000263923	NM_002253.2	1022	cGa/cAa	22/30	0.3	1	FACETS	0.527	0.488	0.566	0.527	0.488	0.566	INDETERMINATE	1	TRUE	0	0.8	1		615	490	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884866	151884866	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	116	471	0	ENST00000262189.6:c.4727C>A	p.Ser1576Tyr	p.S1576Y	ENST00000262189	NM_170606.2	1576	tCt/tAt	32/59	0.3	3	FACETS	0.855	0.775	0.938			1	INDETERMINATE	1	TRUE	NA	0.8	3		471	475	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793432	18793432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs187869576	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	37	565	0	ENST00000266497.5:c.4129C>T	p.Arg1377Cys	p.R1377C	ENST00000266497		1377	Cgt/Tgt	30/31	0.3	3	FACETS	0.248	0.204	0.297			1	INDETERMINATE	1	TRUE	NA	0.8	3		565	523	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599263	55599263	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	81	405	0	ENST00000288135.5:c.2389A>G	p.Asn797Asp	p.N797D	ENST00000288135	NM_000222.2	797	Aat/Gat	17/21	0.3	1	FACETS	0.402	0.358	0.449	0.402	0.358	0.449	INDETERMINATE	1	TRUE	0	0.8	1		405	302	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99203950	99203950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755469992	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	30	346	1	ENST00000074304.5:c.2813G>A	p.Arg938Gln	p.R938Q	ENST00000074304	NM_001134224.1	938	cGa/cAa	26/26	0.3	2	FACETS	0.212	0.17	0.259			1	INDETERMINATE	1	TRUE	NA	0.8	2		347	354	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136805	55136805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41279521	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	74	436	0	ENST00000257290.5:c.1127G>A	p.Arg376Gln	p.R376Q	ENST00000257290	NM_006206.4	376	cGa/cAa	8/23	0.3	1	FACETS	0.375	0.331	0.421	0.375	0.331	0.421	INDETERMINATE	1	TRUE	0	0.8	1		436	296	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692940	89692940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746152219	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	189	305	1	ENST00000371953.3:c.424C>T	p.Arg142Trp	p.R142W	ENST00000371953	NM_000314.4	142	Cgg/Tgg	5/9	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.8	2		306	451	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123836	46123837	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	153	230	0	ENST00000334344.6:c.109dup	p.Ile37AsnfsTer29	p.I37Nfs*29	ENST00000334344	NM_152641.2	34	-/A	2/21	0.3	3	FACETS	0.922	0.847	0.999			1	INDETERMINATE	1	TRUE	NA	0.8	3		230	581	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307755	11307755	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	263	583	0	ENST00000361445.4:c.1152G>T	p.Lys384Asn	p.K384N	ENST00000361445	NM_004958.3	384	aaG/aaT	8/58	0.102917471053861	3	FACETS	1	0.994	1	0.728	0.688	0.769	INDETERMINATE	1	TRUE	1	0.8	3		583	632	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255695	16255695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567379869	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	126	300	0	ENST00000375759.3:c.2960G>A	p.Arg987His	p.R987H	ENST00000375759	NM_015001.2	987	cGc/cAc	11/15	0.102917471053861	3	FACETS	1	0.985	1	0.674	0.619	0.731	INDETERMINATE	1	TRUE	1	0.8	3		300	327	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257596	16257596	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	125	663	0	ENST00000375759.3:c.4861G>A	p.Glu1621Lys	p.E1621K	ENST00000375759	NM_015001.2	1621	Gaa/Aaa	11/15	0.102917471053861	3	FACETS	0.854	0.777	0.935	0.427	0.388	0.468	INDETERMINATE	1	TRUE	1	0.8	3		663	512	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022943	27022943	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	24	20	0	ENST00000324856.7:c.49C>A	p.Pro17Thr	p.P17T	ENST00000324856	NM_006015.4	17	Ccg/Acg	1/20	0.102917471053861	3	FACETS	0.764	0.628	0.903	0.764	0.628	0.903	INDETERMINATE	2	TRUE	1	0.8	3		20	55	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933176	36933176	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	142	832	2	ENST00000361632.4:c.1941G>T	p.Trp647Cys	p.W647C	ENST00000361632		647	tgG/tgT	14/16	0.102917471053861	3	FACETS	0.826	0.755	0.899	0.413	0.377	0.45	INDETERMINATE	1	TRUE	1	0.8	3		834	602	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521581	46521581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs552393862	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	214	598	0	ENST00000262741.5:c.827G>A	p.Arg276His	p.R276H	ENST00000262741	NM_003629.3	276	cGt/cAt	7/10	0.102917471053861	3	FACETS	1	0.992	1	0.73	0.685	0.776	INDETERMINATE	1	TRUE	1	0.8	3		598	513	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46543230	46543230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	37	612	0	ENST00000262741.5:c.271G>A	p.Asp91Asn	p.D91N	ENST00000262741	NM_003629.3	91	Gat/Aat	3/10	0.102917471053861	3	FACETS	0.196	0.161	0.236	0.098	0.08	0.118	INDETERMINATE	1	TRUE	1	0.8	3		612	660	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313355	65313355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	92	465	0	ENST00000342505.4:c.1759G>A	p.Glu587Lys	p.E587K	ENST00000342505	NM_002227.2	587	Gag/Aag	13/25	0.3	2	FACETS	0.602	0.539	0.669			1	INDETERMINATE	1	TRUE	NA	0.8	2		465	382	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256589	115256589	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	94	392	0	ENST00000369535.4:c.122G>T	p.Arg41Ile	p.R41I	ENST00000369535	NM_002524.4	41	aGa/aTa	3/7	0.282046453132761	3	FACETS	0.741	0.663	0.823	0.37	0.331	0.412	INDETERMINATE	1	TRUE	1	0.8	3		392	444	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458162	120458162	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	77	467	0	ENST00000256646.2:c.7183T>C	p.Ser2395Pro	p.S2395P	ENST00000256646	NM_024408.3	2395	Tca/Cca	34/34	0.282046453132761	3	FACETS	0.587	0.517	0.662	0.294	0.258	0.331	INDETERMINATE	1	TRUE	1	0.8	3		467	459	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550850	150550850	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	280	381	1	ENST00000369026.2:c.806C>A	p.Ser269Tyr	p.S269Y	ENST00000369026	NM_021960.4	269	tCt/tAt	2/3	0.282046453132761	3	FACETS	0.77	0.73	0.812	0.77	0.73	0.812	INDETERMINATE	2	TRUE	1	0.8	3		382	636	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874154	155874154	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	251	613	0	ENST00000368323.3:c.377A>G	p.Asp126Gly	p.D126G	ENST00000368323	NM_006912.5	126	gAt/gGt	5/6	0.282046453132761	3	FACETS	0.83	0.785	0.876	0.83	0.785	0.876	INDETERMINATE	2	TRUE	1	0.8	3		613	529	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874214	155874214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	135	547	1	ENST00000368323.3:c.317G>A	p.Arg106Gln	p.R106Q	ENST00000368323	NM_006912.5	106	cGa/cAa	5/6	0.282046453132761	3	FACETS	1	0.922	1	0.504	0.461	0.548	INDETERMINATE	1	TRUE	1	0.8	3		548	469	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050414	176050414	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148950158	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	33	331	0	ENST00000367669.3:c.1151G>A	p.Arg384Gln	p.R384Q	ENST00000367669	NM_022457.5	384	cGa/cAa	11/20	0.203145792915326	3	FACETS	0.405	0.331	0.488	0.203	0.165	0.244	INDETERMINATE	1	TRUE	1	0.8	3		331	285	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243708810	243708810	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1409078343	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	170	422	0	ENST00000263826.5:c.1251+2T>C		p.X417_splice	ENST00000263826	NM_005465.4	417			0.3	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.8	2		422	376	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800999	243800999	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	143	493	0	ENST00000263826.5:c.475T>G	p.Phe159Val	p.F159V	ENST00000263826	NM_005465.4	159	Ttt/Gtt	5/13	0.3	2	FACETS	0.775	0.713	0.84			1	INDETERMINATE	1	TRUE	NA	0.8	2		493	461	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085656	16085656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201115523	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	256	443	2	ENST00000281043.3:c.832G>A	p.Asp278Asn	p.D278N	ENST00000281043	NM_005378.4	278	Gac/Aac	3/3	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.8	2		445	565	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965778	25965778	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	37	468	0	ENST00000435504.4:c.3428C>A	p.Ser1143Tyr	p.S1143Y	ENST00000435504		1143	tCt/tAt	13/13	1	2	FACETS	0.202	0.166	0.242	0.202	0.166	0.242	SUBCLONAL	1	TRUE	1	0.8	2		468	458	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976426	25976426	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	332	724	1	ENST00000435504.4:c.1119C>A	p.Phe373Leu	p.F373L	ENST00000435504		373	ttC/ttA	11/13	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.8	2		725	782	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015651	27015651	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1392372965	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	186	845	2	ENST00000335756.4:c.238C>T	p.Arg80Cys	p.R80C	ENST00000335756	NM_001809.3	80	Cgt/Tgt	3/5	1	2	FACETS	0.714	0.662	0.768	0.714	0.662	0.768	SUBCLONAL	1	TRUE	1	0.8	2		847	651	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451864	29451864	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	166	676	0	ENST00000389048.3:c.2701A>G	p.Thr901Ala	p.T901A	ENST00000389048	NM_004304.4	901	Acc/Gcc	16/29	0.3	1	FACETS	0.553	0.513	0.594	0.553	0.513	0.594	INDETERMINATE	1	TRUE	0	0.8	1		676	450	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940536	29940536	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	123	552	0	ENST00000389048.3:c.695A>G	p.Asn232Ser	p.N232S	ENST00000389048	NM_004304.4	232	aAc/aGc	2/29	0.3	1	FACETS	0.445	0.405	0.485	0.445	0.405	0.485	INDETERMINATE	1	TRUE	0	0.8	1		552	415	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690230	47690230	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63749947	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	217	516	0	ENST00000233146.2:c.1447G>T	p.Glu483Ter	p.E483*	ENST00000233146	NM_000251.2	483	Gaa/Taa	9/16	1	2	FACETS	0.97	0.91	1	0.97	0.91	1	CLONAL	1	TRUE	1	0.8	2		516	559	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719325	61719325	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	92	320	0	ENST00000401558.2:c.1732G>T	p.Asp578Tyr	p.D578Y	ENST00000401558	NM_003400.3	578	Gat/Tat	16/25	1	2	FACETS	0.617	0.552	0.684	0.617	0.552	0.684	SUBCLONAL	1	TRUE	1	0.8	2		320	373	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719724	61719724	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	167	626	0	ENST00000401558.2:c.1544G>A	p.Arg515Gln	p.R515Q	ENST00000401558	NM_003400.3	515	cGa/cAa	14/25	1	2	FACETS	0.715	0.66	0.771	0.715	0.66	0.771	SUBCLONAL	1	TRUE	1	0.8	2		626	584	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61753593	61753593	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	211	488	1	ENST00000401558.2:c.190G>A	p.Asp64Asn	p.D64N	ENST00000401558	NM_003400.3	64	Gac/Aac	3/25	1	2	FACETS	0.869	0.812	0.927	0.869	0.812	0.927	CLONAL	1	TRUE	1	0.8	2		489	607	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149873	99149873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770541150	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	113	422	0	ENST00000074304.5:c.185G>A	p.Arg62Gln	p.R62Q	ENST00000074304	NM_001134224.1	62	cGa/cAa	5/26	0.3	2	FACETS	0.734	0.666	0.804			1	INDETERMINATE	1	TRUE	NA	0.8	2		422	385	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152295	99152295	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	26	520	1	ENST00000074304.5:c.374G>T	p.Arg125Ile	p.R125I	ENST00000074304	NM_001134224.1	125	aGa/aTa	6/26	0.3	2	FACETS	0.139	0.109	0.173			1	INDETERMINATE	1	TRUE	NA	0.8	2		521	468	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881416	111881416	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200974474	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	264	518	1	ENST00000393256.3:c.94G>A	p.Ala32Thr	p.A32T	ENST00000393256	NM_006538.4	32	Gcc/Acc	2/4	0.394534646384061	4	FACETS	0.969	0.916	1	0.969	0.916	1	INDETERMINATE	2	TRUE	2	0.8	4		519	613	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907698	111907698	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763735035	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	72	640	1	ENST00000393256.3:c.472G>A	p.Glu158Lys	p.E158K	ENST00000393256	NM_006538.4	158	Gag/Aag	3/4	0.394534646384061	4	FACETS	0.501	0.437	0.569	0.25	0.218	0.285	INDETERMINATE	1	TRUE	2	0.8	4		641	647	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096156	178096156	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	244	399	1	ENST00000397062.3:c.1175G>A	p.Gly392Asp	p.G392D	ENST00000397062	NM_006164.4	392	gGt/gAt	5/5	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.8	2		400	582	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719569	190719569	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs560096410	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	34	326	0	ENST00000441310.2:c.1571T>G	p.Leu524Ter	p.L524*	ENST00000441310	NM_000534.4	524	tTa/tGa	9/13	1	2	FACETS	0.246	0.201	0.296	0.246	0.201	0.296	SUBCLONAL	1	TRUE	1	0.8	2		326	346	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257053	198257053	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267599149	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	146	392	0	ENST00000335508.6:c.3889C>T	p.Arg1297Cys	p.R1297C	ENST00000335508	NM_012433.2	1297	Cgt/Tgt	25/25	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.8	2		392	364	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274671	198274671	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	132	497	0	ENST00000335508.6:c.727G>A	p.Glu243Lys	p.E243K	ENST00000335508	NM_012433.2	243	Gag/Aag	7/25	1	2	FACETS	0.733	0.671	0.798	0.733	0.671	0.798	SUBCLONAL	1	TRUE	1	0.8	2		497	450	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137627	202137627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	197	593	1	ENST00000358485.4:c.734G>A	p.Ser245Asn	p.S245N	ENST00000358485	NM_001080125.1	245	aGc/aAc	5/9	1	2	FACETS	0.933	0.871	0.996	0.933	0.871	0.996	CLONAL	1	TRUE	1	0.8	2		594	528	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151289	202151289	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	211	671	0	ENST00000358485.4:c.1589G>T	p.Arg530Ile	p.R530I	ENST00000358485	NM_001080125.1	530	aGa/aTa	9/9	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.8	2		671	517	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735593	204735593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	17	284	0	ENST00000302823.3:c.394G>A	p.Glu132Lys	p.E132K	ENST00000302823	NM_005214.4	132	Gag/Aag	2/4	1	2	FACETS	0.176	0.131	0.23	0.176	0.131	0.23	SUBCLONAL	1	TRUE	1	0.8	2		284	241	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248574	212248574	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	50	625	0	ENST00000342788.4:c.3693G>T	p.Glu1231Asp	p.E1231D	ENST00000342788	NM_005235.2	1231	gaG/gaT	28/28	1	2	FACETS	0.257	0.218	0.3	0.257	0.218	0.3	SUBCLONAL	1	TRUE	1	0.8	2		625	487	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251595	212251595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1044752647	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	113	514	1	ENST00000342788.4:c.3464G>A	p.Arg1155Gln	p.R1155Q	ENST00000342788	NM_005235.2	1155	cGa/cAa	27/28	1	2	FACETS	0.719	0.652	0.788	0.719	0.652	0.788	SUBCLONAL	1	TRUE	1	0.8	2		515	393	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376182	225376182	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	248	666	1	ENST00000264414.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000264414	NM_003590.4	258	Gaa/Taa	6/16	1	2	FACETS	0.872	0.819	0.926	0.872	0.819	0.926	CLONAL	1	TRUE	1	0.8	2		667	711	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662752	227662752	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	176	509	0	ENST00000305123.5:c.703G>A	p.Glu235Lys	p.E235K	ENST00000305123	NM_005544.2	235	Gag/Aag	1/2	1	2	FACETS	0.948	0.882	1	0.948	0.882	1	CLONAL	1	TRUE	1	0.8	2		509	464	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650799	12650799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398525119	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	160	439	1	ENST00000251849.4:c.356C>T	p.Ala119Val	p.A119V	ENST00000251849	NM_002880.3	119	gCg/gTg	4/17	1	2	FACETS	0.962	0.892	1	0.962	0.892	1	CLONAL	1	TRUE	1	0.8	2		440	416	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125724	47125724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	210	510	1	ENST00000409792.3:c.5546C>T	p.Ser1849Leu	p.S1849L	ENST00000409792	NM_014159.6	1849	tCg/tTg	12/21	1	2	FACETS	0.918	0.859	0.978	0.918	0.859	0.978	CLONAL	1	TRUE	1	0.8	2		511	572	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397669	49397669	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	209	509	0	ENST00000418115.1:c.555G>T	p.Lys185Asn	p.K185N	ENST00000418115	NM_001664.2	185	aaG/aaT	5/5	1	2	FACETS	0.95	0.889	1	0.95	0.889	1	CLONAL	1	TRUE	1	0.8	2		509	550	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940714	49940714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	285	708	0	ENST00000296474.3:c.329G>A	p.Gly110Glu	p.G110E	ENST00000296474	NM_002447.2	110	gGa/gAa	1/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.8	2		708	678	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72873637	72873637	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	160	455	0	ENST00000325599.8:c.665A>C	p.Lys222Thr	p.K222T	ENST00000325599	NM_018130.2	222	aAa/aCa	6/11	0.3	4	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.8	4		455	559	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582445	119582445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762651036	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	29	184	0	ENST00000316626.5:c.956G>A	p.Arg319Gln	p.R319Q	ENST00000316626		319	cGa/cAa	10/12	1	2	FACETS	0.28	0.225	0.342	0.28	0.225	0.342	SUBCLONAL	1	TRUE	1	0.8	2		184	259	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884903	134884903	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	128	673	0	ENST00000398015.3:c.1679C>A	p.Ser560Tyr	p.S560Y	ENST00000398015	NM_004441.4	560	tCt/tAt	8/16	1	2	FACETS	0.737	0.674	0.803	0.737	0.674	0.803	SUBCLONAL	1	TRUE	1	0.8	2		673	434	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453531	138453531	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372119491	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	160	544	0	ENST00000289153.2:c.917G>A	p.Arg306Gln	p.R306Q	ENST00000289153	NM_006219.2	306	cGa/cAa	5/22	1	2	FACETS	0.766	0.707	0.827	0.766	0.707	0.827	SUBCLONAL	1	TRUE	1	0.8	2		544	522	SUCCESS
ATR	545	MSKCC	GRCh37	3	142168369	142168369	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	205	430	4	ENST00000350721.4:c.7837C>T	p.Pro2613Ser	p.P2613S	ENST00000350721	NM_001184.3	2613	Ccg/Tcg	47/47	1	2	FACETS	0.974	0.912	1	0.974	0.912	1	CLONAL	1	TRUE	1	0.8	2		434	526	SUCCESS
ATR	545	MSKCC	GRCh37	3	142180803	142180803	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	218	542	0	ENST00000350721.4:c.7171A>G	p.Thr2391Ala	p.T2391A	ENST00000350721	NM_001184.3	2391	Acc/Gcc	42/47	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.8	2		542	525	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226948	142226948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775093063	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	115	315	0	ENST00000350721.4:c.4856C>T	p.Ser1619Phe	p.S1619F	ENST00000350721	NM_001184.3	1619	tCt/tTt	28/47	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.8	2		315	277	SUCCESS
ATR	545	MSKCC	GRCh37	3	142234346	142234346	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	154	316	0	ENST00000350721.4:c.4394C>A	p.Ser1465Tyr	p.S1465Y	ENST00000350721	NM_001184.3	1465	tCt/tAt	25/47	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.8	2		316	349	SUCCESS
ATR	545	MSKCC	GRCh37	3	142257327	142257327	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	121	346	0	ENST00000350721.4:c.3722A>G	p.Asn1241Ser	p.N1241S	ENST00000350721	NM_001184.3	1241	aAc/aGc	19/47	1	2	FACETS	0.82	0.748	0.893	0.82	0.748	0.893	CLONAL	1	TRUE	1	0.8	2		346	369	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278168	142278168	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	125	433	0	ENST00000350721.4:c.1657T>C	p.Ser553Pro	p.S553P	ENST00000350721	NM_001184.3	553	Tct/Cct	7/47	1	2	FACETS	0.691	0.63	0.755	0.691	0.63	0.755	SUBCLONAL	1	TRUE	1	0.8	2		433	452	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916957	178916957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	229	636	0	ENST00000263967.3:c.344G>A	p.Arg115Gln	p.R115Q	ENST00000263967	NM_006218.2	115	cGa/cAa	2/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.8	2		636	566	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936068	178936068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	77	161	0	ENST00000263967.3:c.1610G>A	p.Arg537Gln	p.R537Q	ENST00000263967	NM_006218.2	537	cGa/cAa	10/21	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.8	2		161	179	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951934	178951934	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	71	450	0	ENST00000263967.3:c.2989C>A	p.Leu997Ile	p.L997I	ENST00000263967	NM_006218.2	997	Ctc/Atc	21/21	1	2	FACETS	0.346	0.302	0.393	0.346	0.302	0.393	SUBCLONAL	1	TRUE	1	0.8	2		450	513	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430786	181430786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	183	507	1	ENST00000325404.1:c.638C>T	p.Ser213Leu	p.S213L	ENST00000325404	NM_003106.3	213	tCg/tTg	1/1	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.8	2		508	412	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683508	182683508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	59	339	0	ENST00000292782.4:c.37C>T	p.Arg13Cys	p.R13C	ENST00000292782	NM_020640.2	13	Cgt/Tgt	2/7	1	2	FACETS	0.413	0.357	0.474	0.413	0.357	0.474	SUBCLONAL	1	TRUE	1	0.8	2		339	357	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582038	189582038	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	53	557	0	ENST00000264731.3:c.597G>T	p.Lys199Asn	p.K199N	ENST00000264731	NM_003722.4	199	aaG/aaT	5/14	1	2	FACETS	0.269	0.229	0.312	0.269	0.229	0.312	SUBCLONAL	1	TRUE	1	0.8	2		557	493	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133617	55133617	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1553903298	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	29	414	0	ENST00000257290.5:c.921T>G	p.Ile307Met	p.I307M	ENST00000257290	NM_006206.4	307	atT/atG	6/23	0.3	1	FACETS	0.124	0.099	0.152	0.124	0.099	0.152	INDETERMINATE	1	TRUE	0	0.8	1		414	350	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593663	55593663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	121	423	0	ENST00000288135.5:c.1729C>T	p.Pro577Ser	p.P577S	ENST00000288135	NM_000222.2	577	Cct/Tct	11/21	0.3	1	FACETS	0.565	0.518	0.614	0.565	0.518	0.614	INDETERMINATE	1	TRUE	0	0.8	1		423	321	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602711	55602711	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	21	535	0	ENST00000288135.5:c.2532T>G	p.Cys844Trp	p.C844W	ENST00000288135	NM_000222.2	844	tgT/tgG	18/21	0.3	1	FACETS	0.078	0.059	0.1	0.078	0.059	0.1	INDETERMINATE	1	TRUE	0	0.8	1		535	404	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958809	55958809	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	168	591	0	ENST00000263923.4:c.3044G>A	p.Gly1015Asp	p.G1015D	ENST00000263923	NM_002253.2	1015	gGc/gAc	22/30	0.3	1	FACETS	0.523	0.484	0.562	0.523	0.484	0.562	INDETERMINATE	1	TRUE	0	0.8	1		591	482	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968156	55968156	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	196	580	4	ENST00000263923.4:c.2174G>A	p.Arg725His	p.R725H	ENST00000263923	NM_002253.2	725	cGc/cAc	15/30	0.3	1	FACETS	0.615	0.575	0.656	0.615	0.575	0.656	INDETERMINATE	1	TRUE	0	0.8	1		584	478	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968535	55968535	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	96	460	0	ENST00000263923.4:c.2128G>T	p.Asp710Tyr	p.D710Y	ENST00000263923	NM_002253.2	710	Gac/Tac	14/30	0.3	1	FACETS	0.358	0.321	0.397	0.358	0.321	0.397	INDETERMINATE	1	TRUE	0	0.8	1		460	402	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972907	55972907	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	102	500	0	ENST00000263923.4:c.1483A>C	p.Asn495His	p.N495H	ENST00000263923	NM_002253.2	495	Aat/Cat	11/30	0.3	1	FACETS	0.41	0.37	0.452	0.41	0.37	0.452	INDETERMINATE	1	TRUE	0	0.8	1		500	373	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84388682	84388682	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	108	477	0	ENST00000321945.7:c.606T>G	p.Phe202Leu	p.F202L	ENST00000321945	NM_139076.2	202	ttT/ttG	7/9	1	2	FACETS	0.689	0.623	0.757	0.689	0.623	0.757	SUBCLONAL	1	TRUE	1	0.8	2		477	392	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84403359	84403359	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	206	643	0	ENST00000321945.7:c.126G>T	p.Lys42Asn	p.K42N	ENST00000321945	NM_139076.2	42	aaG/aaT	2/9	1	2	FACETS	0.876	0.818	0.935	0.876	0.818	0.935	CLONAL	1	TRUE	1	0.8	2		643	588	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99812471	99812471	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	145	433	0	ENST00000280892.6:c.198G>T	p.Trp66Cys	p.W66C	ENST00000280892	NM_001130678.1	66	tgG/tgT	3/7	1	2	FACETS	0.851	0.784	0.92	0.851	0.784	0.92	CLONAL	1	TRUE	1	0.8	2		433	426	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155145	106155145	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	236	569	0	ENST00000380013.4:c.46C>T	p.Pro16Ser	p.P16S	ENST00000380013	NM_001127208.2	16	Cca/Tca	3/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.8	2		569	573	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158304	106158304	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	194	561	0	ENST00000380013.4:c.3205A>G	p.Thr1069Ala	p.T1069A	ENST00000380013	NM_001127208.2	1069	Acc/Gcc	3/11	1	2	FACETS	0.869	0.81	0.93	0.869	0.81	0.93	CLONAL	1	TRUE	1	0.8	2		561	558	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193889	106193889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1395976555	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	150	455	1	ENST00000380013.4:c.4351C>T	p.Arg1451Trp	p.R1451W	ENST00000380013	NM_001127208.2	1451	Cgg/Tgg	10/11	1	2	FACETS	0.773	0.712	0.836	0.773	0.712	0.836	SUBCLONAL	1	TRUE	1	0.8	2		456	485	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197281	106197281	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	95	291	0	ENST00000380013.4:c.5614C>A	p.Leu1872Ile	p.L1872I	ENST00000380013	NM_001127208.2	1872	Ctc/Atc	11/11	1	2	FACETS	0.681	0.611	0.753	0.681	0.611	0.753	SUBCLONAL	1	TRUE	1	0.8	2		291	349	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142950045	142950045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	140	450	0	ENST00000262992.4:c.2665G>A	p.Val889Ile	p.V889I	ENST00000262992	NM_001101669.1	889	Gta/Ata	24/24	1	2	FACETS	0.886	0.816	0.958	0.886	0.816	0.958	CLONAL	1	TRUE	1	0.8	2		450	395	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007335	143007335	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	165	389	0	ENST00000262992.4:c.2449A>C	p.Lys817Gln	p.K817Q	ENST00000262992	NM_001101669.1	817	Aaa/Caa	22/24	1	2	FACETS	0.994	0.923	1	0.994	0.923	1	CLONAL	1	TRUE	1	0.8	2		389	415	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143350325	143350325	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	90	222	0	ENST00000262992.4:c.136+1G>A		p.X46_splice	ENST00000262992	NM_001101669.1	46			1	2	FACETS	0.938	0.846	1	0.938	0.846	1	CLONAL	1	TRUE	1	0.8	2		222	240	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517733	187517733	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373442556	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	91	239	1	ENST00000441802.2:c.12961G>A	p.Asp4321Asn	p.D4321N	ENST00000441802	NM_005245.3	4321	Gac/Aac	25/27	1	2	FACETS	0.989	0.895	1	0.989	0.895	1	CLONAL	1	TRUE	1	0.8	2		240	230	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521385	187521385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426195084	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	113	416	0	ENST00000441802.2:c.11770C>T	p.Arg3924Cys	p.R3924C	ENST00000441802	NM_005245.3	3924	Cgc/Tgc	22/27	1	2	FACETS	0.726	0.659	0.796	0.726	0.659	0.796	SUBCLONAL	1	TRUE	1	0.8	2		416	389	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554954	187554954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560351512	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	72	498	0	ENST00000441802.2:c.4207G>A	p.Asp1403Asn	p.D1403N	ENST00000441802	NM_005245.3	1403	Gat/Aat	7/27	1	2	FACETS	0.348	0.304	0.395	0.348	0.304	0.395	SUBCLONAL	1	TRUE	1	0.8	2		498	517	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627734	187627734	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	53	680	0	ENST00000441802.2:c.3248A>C	p.Lys1083Thr	p.K1083T	ENST00000441802	NM_005245.3	1083	aAa/aCa	2/27	1	2	FACETS	0.176	0.149	0.205	0.176	0.149	0.205	SUBCLONAL	1	TRUE	1	0.8	2		680	754	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629400	187629400	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1018407179	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	29	531	2	ENST00000441802.2:c.1582G>A	p.Glu528Lys	p.E528K	ENST00000441802	NM_005245.3	528	Gaa/Aaa	2/27	1	2	FACETS	0.131	0.104	0.161	0.131	0.104	0.161	SUBCLONAL	1	TRUE	1	0.8	2		533	554	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294403	1294403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1322987070	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	77	343	0	ENST00000310581.5:c.598G>A	p.Glu200Lys	p.E200K	ENST00000310581	NM_198253.2	200	Gaa/Aaa	2/16	1	2	FACETS	0.837	0.747	0.931	0.837	0.747	0.931	CLONAL	1	TRUE	1	0.8	2		343	230	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945707	38945707	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	187	495	0	ENST00000357387.3:c.4519A>G	p.Thr1507Ala	p.T1507A	ENST00000357387	NM_152756.3	1507	Aca/Gca	34/38	0.3	3	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.8	3		495	489	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945765	38945765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	155	419	0	ENST00000357387.3:c.4461G>A	p.Met1487Ile	p.M1487I	ENST00000357387	NM_152756.3	1487	atG/atA	34/38	0.3	3	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.8	3		419	404	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958789	38958789	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764805842	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	158	457	2	ENST00000357387.3:c.2323G>A	p.Asp775Asn	p.D775N	ENST00000357387	NM_152756.3	775	Gat/Aat	23/38	0.3	3	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.8	3		459	424	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183210	56183210	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	50	238	0	ENST00000399503.3:c.4120A>C	p.Asn1374His	p.N1374H	ENST00000399503	NM_005921.1	1374	Aat/Cat	18/20	0.3	5	FACETS	0.712	0.606	0.828			1	INDETERMINATE	1	TRUE	NA	0.8	5		238	386	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589546	67589546	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	83	260	0	ENST00000274335.5:c.1309G>C	p.Val437Leu	p.V437L	ENST00000274335		437	Gtc/Ctc	10/15	0.3	5	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.8	5		260	362	SUCCESS
APC	324	MSKCC	GRCh37	5	112128185	112128185	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779805	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	178	537	3	ENST00000257430.4:c.688C>T	p.Arg230Cys	p.R230C	ENST00000257430	NM_000038.5	230	Cgt/Tgt	7/16	1	2	FACETS	0.923	0.859	0.989	0.923	0.859	0.989	CLONAL	1	TRUE	1	0.8	2		540	482	SUCCESS
APC	324	MSKCC	GRCh37	5	112154724	112154724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377665107	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	81	338	1	ENST00000257430.4:c.995G>A	p.Arg332Gln	p.R332Q	ENST00000257430	NM_000038.5	332	cGa/cAa	10/16	1	2	FACETS	0.655	0.583	0.731	0.655	0.583	0.731	SUBCLONAL	1	TRUE	1	0.8	2		339	309	SUCCESS
APC	324	MSKCC	GRCh37	5	112173522	112173522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1158819002	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	162	382	0	ENST00000257430.4:c.2231C>T	p.Ser744Phe	p.S744F	ENST00000257430	NM_000038.5	744	tCt/tTt	16/16	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.8	2		382	402	SUCCESS
APC	324	MSKCC	GRCh37	5	112175764	112175764	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	122	321	0	ENST00000257430.4:c.4473T>G	p.Phe1491Leu	p.F1491L	ENST00000257430	NM_000038.5	1491	ttT/ttG	16/16	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.8	2		321	291	SUCCESS
APC	324	MSKCC	GRCh37	5	112175799	112175799	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	109	298	0	ENST00000257430.4:c.4508C>A	p.Ser1503Ter	p.S1503*	ENST00000257430	NM_000038.5	1503	tCa/tAa	16/16	1	2	FACETS	0.984	0.898	1	0.984	0.898	1	CLONAL	1	TRUE	1	0.8	2		298	277	SUCCESS
APC	324	MSKCC	GRCh37	5	112176890	112176890	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	150	471	0	ENST00000257430.4:c.5599T>G	p.Phe1867Val	p.F1867V	ENST00000257430	NM_000038.5	1867	Ttt/Gtt	16/16	1	2	FACETS	0.933	0.862	1	0.933	0.862	1	CLONAL	1	TRUE	1	0.8	2		471	402	SUCCESS
APC	324	MSKCC	GRCh37	5	112176960	112176960	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	92	410	0	ENST00000257430.4:c.5669C>T	p.Ser1890Leu	p.S1890L	ENST00000257430	NM_000038.5	1890	tCa/tTa	16/16	1	2	FACETS	0.608	0.545	0.675	0.608	0.545	0.675	SUBCLONAL	1	TRUE	1	0.8	2		410	378	SUCCESS
APC	324	MSKCC	GRCh37	5	112177359	112177359	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	95	342	0	ENST00000257430.4:c.6068G>T	p.Arg2023Ile	p.R2023I	ENST00000257430	NM_000038.5	2023	aGa/aTa	16/16	1	2	FACETS	0.764	0.688	0.842	0.764	0.688	0.842	SUBCLONAL	1	TRUE	1	0.8	2		342	311	SUCCESS
APC	324	MSKCC	GRCh37	5	112179816	112179816	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	51	245	0	ENST00000257430.4:c.8525C>A	p.Ser2842Tyr	p.S2842Y	ENST00000257430	NM_000038.5	2842	tCt/tAt	16/16	1	2	FACETS	0.644	0.555	0.739	0.644	0.555	0.739	SUBCLONAL	1	TRUE	1	0.8	2		245	198	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131893077	131893077	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	267	643	1	ENST00000265335.6:c.61G>T	p.Asp21Tyr	p.D21Y	ENST00000265335		21	Gat/Tat	1/25	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.8	2		644	653	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944836	131944836	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	71	232	0	ENST00000265335.6:c.2857A>G	p.Asn953Asp	p.N953D	ENST00000265335		953	Aat/Gat	18/25	1	2	FACETS	0.755	0.669	0.846	0.755	0.669	0.846	SUBCLONAL	1	TRUE	1	0.8	2		232	235	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131951755	131951755	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	129	391	0	ENST00000265335.6:c.3097G>T	p.Glu1033Ter	p.E1033*	ENST00000265335		1033	Gaa/Taa	20/25	1	2	FACETS	0.903	0.829	0.98	0.903	0.829	0.98	CLONAL	1	TRUE	1	0.8	2		391	357	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819954	170819954	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774697729	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	116	448	1	ENST00000296930.5:c.496G>A	p.Asp166Asn	p.D166N	ENST00000296930	NM_002520.6	166	Gat/Aat	6/11	1	2	FACETS	0.613	0.556	0.673	0.613	0.556	0.673	SUBCLONAL	1	TRUE	1	0.8	2		449	473	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562984	176562984	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	153	394	0	ENST00000439151.2:c.880G>T	p.Glu294Ter	p.E294*	ENST00000439151	NM_022455.4	294	Gaa/Taa	2/23	1	2	FACETS	0.902	0.834	0.972	0.902	0.834	0.972	CLONAL	1	TRUE	1	0.8	2		394	424	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637466	176637466	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	120	323	0	ENST00000439151.2:c.2066T>G	p.Phe689Cys	p.F689C	ENST00000439151	NM_022455.4	689	tTt/tGt	5/23	1	2	FACETS	0.796	0.726	0.868	0.796	0.726	0.868	SUBCLONAL	1	TRUE	1	0.8	2		323	377	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720928	176720928	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784209	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	171	473	2	ENST00000439151.2:c.6559C>T	p.Arg2187Ter	p.R2187*	ENST00000439151	NM_022455.4	2187	Cga/Tga	23/23	1	2	FACETS	0.891	0.827	0.956	0.891	0.827	0.956	CLONAL	1	TRUE	1	0.8	2		475	480	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721046	176721046	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	165	391	0	ENST00000439151.2:c.6677T>C	p.Val2226Ala	p.V2226A	ENST00000439151	NM_022455.4	2226	gTa/gCa	23/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.8	2		391	371	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048881	180048881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751002839	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	98	416	1	ENST00000261937.6:c.1681G>A	p.Glu561Lys	p.E561K	ENST00000261937	NM_182925.4	561	Gaa/Aaa	13/30	0.3	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.8	0		417	258	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397142	397142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs999945656	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	22	553	1	ENST00000380956.4:c.527G>A	p.Arg176Gln	p.R176Q	ENST00000380956	NM_001195286.1	176	cGa/cAa	5/9	1	2	FACETS	0.149	0.115	0.188	0.149	0.115	0.188	SUBCLONAL	1	TRUE	1	0.8	2		554	370	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397219	397219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143144957	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	78	511	1	ENST00000380956.4:c.604G>A	p.Gly202Ser	p.G202S	ENST00000380956	NM_001195286.1	202	Ggc/Agc	5/9	1	2	FACETS	0.572	0.506	0.641	0.572	0.506	0.641	SUBCLONAL	1	TRUE	1	0.8	2		512	341	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164810	32164810	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	157	364	0	ENST00000375023.3:c.5092A>G	p.Thr1698Ala	p.T1698A	ENST00000375023	NM_004557.3	1698	Aca/Gca	28/30	0.394534646384061	4	FACETS	0.796	0.736	0.857	0.796	0.736	0.857	INDETERMINATE	2	TRUE	2	0.8	4		364	444	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168933	32168933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs979783685	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	122	709	0	ENST00000375023.3:c.4100C>T	p.Thr1367Met	p.T1367M	ENST00000375023	NM_004557.3	1367	aCg/aTg	22/30	0.3	1	FACETS	0.362	0.329	0.397	0.362	0.329	0.397	INDETERMINATE	1	TRUE	0	0.8	1		709	505	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964502	93964502	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	214	642	0	ENST00000369303.4:c.2395C>A	p.Pro799Thr	p.P799T	ENST00000369303	NM_004440.3	799	Cca/Aca	14/17	0.102917471053861	3	FACETS	1	0.987	1	0.605	0.566	0.645	INDETERMINATE	1	TRUE	1	0.8	3		642	619	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120374	94120374	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	203	777	0	ENST00000369303.4:c.677C>A	p.Ser226Tyr	p.S226Y	ENST00000369303	NM_004440.3	226	tCt/tAt	3/17	0.102917471053861	3	FACETS	0.871	0.809	0.935	0.435	0.404	0.468	INDETERMINATE	1	TRUE	1	0.8	3		777	816	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117630053	117630053	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	106	589	0	ENST00000368508.3:c.6473G>C	p.Gly2158Ala	p.G2158A	ENST00000368508	NM_002944.2	2158	gGt/gCt	41/43	0.3	1	FACETS	0.361	0.326	0.399	0.361	0.326	0.399	INDETERMINATE	1	TRUE	0	0.8	1		589	440	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662676	117662676	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1281612889	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	34	542	0	ENST00000368508.3:c.4789A>G	p.Ile1597Val	p.I1597V	ENST00000368508	NM_002944.2	1597	Atc/Gtc	29/43	0.203145792915326	1	FACETS	0.119	0.097	0.144	0.119	0.097	0.144	INDETERMINATE	1	TRUE	0	0.8	1		542	428	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681075	117681075	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	107	548	0	ENST00000368508.3:c.3545G>T	p.Arg1182Ile	p.R1182I	ENST00000368508	NM_002944.2	1182	aGa/aTa	23/43	0.203145792915326	1	FACETS	0.361	0.326	0.399	0.361	0.326	0.399	INDETERMINATE	1	TRUE	0	0.8	1		548	444	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687371	117687371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748148750	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	182	525	1	ENST00000368508.3:c.2680C>T	p.Arg894Trp	p.R894W	ENST00000368508	NM_002944.2	894	Cgg/Tgg	18/43	0.203145792915326	1	FACETS	0.596	0.556	0.637	0.596	0.556	0.637	INDETERMINATE	1	TRUE	0	0.8	1		526	458	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687431	117687431	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	124	415	0	ENST00000368508.3:c.2620G>T	p.Glu874Ter	p.E874*	ENST00000368508	NM_002944.2	874	Gaa/Taa	18/43	0.203145792915326	1	FACETS	0.52	0.475	0.565	0.52	0.475	0.565	INDETERMINATE	1	TRUE	0	0.8	1		415	358	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710578	117710578	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142303126	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	99	409	0	ENST00000368508.3:c.1694C>T	p.Ser565Leu	p.S565L	ENST00000368508	NM_002944.2	565	tCg/tTg	12/43	0.203145792915326	1	FACETS	0.408	0.367	0.45	0.408	0.367	0.45	INDETERMINATE	1	TRUE	0	0.8	1		409	364	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710903	117710903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	165	507	0	ENST00000368508.3:c.1369G>A	p.Asp457Asn	p.D457N	ENST00000368508	NM_002944.2	457	Gac/Aac	12/43	0.203145792915326	1	FACETS	0.646	0.601	0.692	0.646	0.601	0.692	INDETERMINATE	1	TRUE	0	0.8	1		507	383	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983059	149983059	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	40	635	0	ENST00000253339.5:c.3199A>C	p.Asn1067His	p.N1067H	ENST00000253339		1067	Aat/Cat	7/7	0.282046453132761	3	FACETS	0.261	0.216	0.311	0.131	0.108	0.156	INDETERMINATE	1	TRUE	1	0.8	3		635	536	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001133	150001133	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	204	587	0	ENST00000253339.5:c.2471T>G	p.Phe824Cys	p.F824C	ENST00000253339		824	tTt/tGt	4/7	0.282046453132761	3	FACETS	1	0.991	1	0.689	0.645	0.734	INDETERMINATE	1	TRUE	1	0.8	3		587	518	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001187	150001187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775204857	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	49	671	0	ENST00000253339.5:c.2417G>A	p.Arg806Gln	p.R806Q	ENST00000253339		806	cGa/cAa	4/7	0.282046453132761	3	FACETS	0.294	0.248	0.344	0.147	0.124	0.172	INDETERMINATE	1	TRUE	1	0.8	3		671	584	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201798	152201798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761613029	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	133	343	0	ENST00000206249.3:c.652G>A	p.Asp218Asn	p.D218N	ENST00000206249	NM_000125.3	218	Gac/Aac	3/8	0.282046453132761	3	FACETS	0.911	0.832	0.993	0.455	0.416	0.497	INDETERMINATE	1	TRUE	1	0.8	3		343	511	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099755	157099755	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	38	236	0	ENST00000346085.5:c.692A>C	p.Asn231Thr	p.N231T	ENST00000346085	NM_020732.3	231	aAt/aCt	1/20	0.282046453132761	3	FACETS	0.473	0.393	0.562	0.237	0.196	0.281	INDETERMINATE	1	TRUE	1	0.8	3		236	281	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394444	162394444	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	113	410	0	ENST00000366898.1:c.624T>G	p.Phe208Leu	p.F208L	ENST00000366898	NM_004562.2	208	ttT/ttG	6/12	0.3	1	FACETS	0.603	0.552	0.656	0.603	0.552	0.656	INDETERMINATE	1	TRUE	0	0.8	1		410	281	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394449	162394449	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	107	390	0	ENST00000366898.1:c.619G>A	p.Glu207Lys	p.E207K	ENST00000366898	NM_004562.2	207	Gaa/Aaa	6/12	0.3	1	FACETS	0.603	0.55	0.657	0.603	0.55	0.657	INDETERMINATE	1	TRUE	0	0.8	1		390	266	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974131	2974131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774763617	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	73	525	0	ENST00000396946.4:c.1474C>T	p.Pro492Ser	p.P492S	ENST00000396946	NM_032415.4	492	Ccc/Tcc	10/25	1	2	FACETS	0.591	0.521	0.664	0.591	0.521	0.664	SUBCLONAL	1	TRUE	1	0.8	2		525	309	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979498	2979498	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	26	700	0	ENST00000396946.4:c.749C>A	p.Ser250Tyr	p.S250Y	ENST00000396946	NM_032415.4	250	tCt/tAt	6/25	1	2	FACETS	0.148	0.117	0.184	0.148	0.117	0.184	SUBCLONAL	1	TRUE	1	0.8	2		700	438	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268933	55268933	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	168	540	0	ENST00000275493.2:c.2999C>T	p.Ala1000Val	p.A1000V	ENST00000275493	NM_005228.3	1000	gCc/gTc	25/28	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.8	2		540	418	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509441	106509441	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	159	493	2	ENST00000359195.3:c.1435G>T	p.Glu479Ter	p.E479*	ENST00000359195	NM_002649.2	479	Gaa/Taa	2/11	1	2	FACETS	0.764	0.705	0.825	0.764	0.705	0.825	SUBCLONAL	1	TRUE	1	0.8	2		495	520	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545795	106545795	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	76	363	0	ENST00000359195.3:c.3272T>C	p.Val1091Ala	p.V1091A	ENST00000359195	NM_002649.2	1091	gTt/gCt	11/11	1	2	FACETS	0.559	0.494	0.628	0.559	0.494	0.628	SUBCLONAL	1	TRUE	1	0.8	2		363	340	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398647	116398647	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	137	447	0	ENST00000397752.3:c.2237A>G	p.Glu746Gly	p.E746G	ENST00000397752	NM_000245.2	746	gAa/gGa	9/21	0.3	4	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.8	4		447	484	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411694	116411694	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	193	364	0	ENST00000397752.3:c.2873G>T	p.Arg958Ile	p.R958I	ENST00000397752	NM_000245.2	958	aGa/aTa	13/21	0.3	4	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.8	4		364	627	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846357	128846357	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760560948	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	41	715	0	ENST00000249373.3:c.1193G>A	p.Arg398Gln	p.R398Q	ENST00000249373	NM_005631.4	398	cGa/cAa	6/12	1	2	FACETS	0.24	0.2	0.285	0.24	0.2	0.285	SUBCLONAL	1	TRUE	1	0.8	2		715	427	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506185	148506185	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747933788	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	128	502	0	ENST00000320356.2:c.2173G>A	p.Glu725Lys	p.E725K	ENST00000320356	NM_004456.4	725	Gaa/Aaa	19/20	1	2	FACETS	0.672	0.613	0.734	0.672	0.613	0.734	SUBCLONAL	1	TRUE	1	0.8	2		502	476	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525883	148525883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778968366	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	210	618	0	ENST00000320356.2:c.574G>A	p.Asp192Asn	p.D192N	ENST00000320356	NM_004456.4	192	Gat/Aat	6/20	1	2	FACETS	0.989	0.926	1	0.989	0.926	1	CLONAL	1	TRUE	1	0.8	2		618	531	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880126	151880126	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	36	551	2	ENST00000262189.6:c.5198C>A	p.Ser1733Ter	p.S1733*	ENST00000262189	NM_170606.2	1733	tCg/tAg	35/59	0.3	3	FACETS	0.214	0.175	0.258			1	INDETERMINATE	1	TRUE	NA	0.8	3		553	588	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884835	151884835	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs781008611	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	118	454	1	ENST00000262189.6:c.4758C>A	p.Phe1586Leu	p.F1586L	ENST00000262189	NM_170606.2	1586	ttC/ttA	32/59	0.3	3	FACETS	0.875	0.794	0.959			1	INDETERMINATE	1	TRUE	NA	0.8	3		455	472	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891100	151891100	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	164	366	0	ENST00000262189.6:c.4654A>G	p.Asn1552Asp	p.N1552D	ENST00000262189	NM_170606.2	1552	Aat/Gat	31/59	0.3	3	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.8	3		366	422	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945124	151945124	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	17	193	0	ENST00000262189.6:c.2395A>C	p.Asn799His	p.N799H	ENST00000262189	NM_170606.2	799	Aat/Cat	14/59	0.3	3	FACETS	0.315	0.236	0.408			1	INDETERMINATE	1	TRUE	NA	0.8	3		193	189	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152009026	152009026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369725088	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	105	345	0	ENST00000262189.6:c.596G>A	p.Arg199Gln	p.R199Q	ENST00000262189	NM_170606.2	199	cGa/cAa	5/59	0.3	3	FACETS	1	0.923	1			1	INDETERMINATE	1	TRUE	NA	0.8	3		345	359	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012244	152012244	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748254163	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	327	581	2	ENST00000262189.6:c.569G>A	p.Arg190Gln	p.R190Q	ENST00000262189	NM_170606.2	190	cGa/cAa	4/59	0.3	3	FACETS	0.775	0.737	0.814			1	INDETERMINATE	2	TRUE	NA	0.8	3		583	738	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346094	152346094	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367696886	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	247	828	0	ENST00000359321.1:c.476G>A	p.Arg159His	p.R159H	ENST00000359321	NM_005431.1	159	cGc/cAc	3/3	0.3	1	FACETS	0.623	0.587	0.659	0.623	0.587	0.659	INDETERMINATE	1	TRUE	0	0.8	1		828	595	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864824	117864824	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147956016	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	230	757	1	ENST00000297338.2:c.1285G>A	p.Asp429Asn	p.D429N	ENST00000297338	NM_006265.2	429	Gac/Aac	10/14	0.102917471053861	3	FACETS	1	0.968	1	0.528	0.493	0.563	INDETERMINATE	1	TRUE	1	0.8	3		758	763	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054768	5054768	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	199	480	2	ENST00000381652.3:c.820G>T	p.Glu274Ter	p.E274*	ENST00000381652	NM_004972.3	274	Gaa/Taa	7/25	1	2	FACETS	0.937	0.875	1	0.937	0.875	1	CLONAL	1	TRUE	1	0.8	2		482	531	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471055	8471055	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	59	444	0	ENST00000356435.5:c.3444G>T	p.Lys1148Asn	p.K1148N	ENST00000356435		1148	aaG/aaT	20/35	1	2	FACETS	0.372	0.321	0.428	0.372	0.321	0.428	SUBCLONAL	1	TRUE	1	0.8	2		444	396	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633353	8633353	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	201	579	1	ENST00000356435.5:c.316G>T	p.Glu106Ter	p.E106*	ENST00000356435		106	Gaa/Taa	3/35	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.8	2		580	498	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36846870	36846870	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	123	572	0	ENST00000358127.4:c.1069T>G	p.Ser357Ala	p.S357A	ENST00000358127	NM_001280556.1	357	Tcc/Gcc	9/10	1	2	FACETS	0.94	0.862	1	0.94	0.862	1	CLONAL	1	TRUE	1	0.8	2		572	327	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015151	37015151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	148	513	0	ENST00000358127.4:c.253G>A	p.Gly85Arg	p.G85R	ENST00000358127	NM_001280556.1	85	Gga/Aga	3/10	1	2	FACETS	0.914	0.843	0.985	0.914	0.843	0.985	CLONAL	1	TRUE	1	0.8	2		513	405	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336402	80336402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769315863	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	97	418	0	ENST00000286548.4:c.917G>A	p.Arg306Gln	p.R306Q	ENST00000286548	NM_002072.3	306	cGa/cAa	7/7	1	2	FACETS	0.572	0.513	0.634	0.572	0.513	0.634	SUBCLONAL	1	TRUE	1	0.8	2		418	424	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430633	80430633	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	16	170	0	ENST00000286548.4:c.375G>T	p.Glu125Asp	p.E125D	ENST00000286548	NM_002072.3	125	gaG/gaT	3/7	1	2	FACETS	0.17	0.126	0.223	0.17	0.126	0.223	SUBCLONAL	1	TRUE	1	0.8	2		170	235	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285871	87285871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408094711	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	97	405	0	ENST00000277120.3:c.208G>A	p.Glu70Lys	p.E70K	ENST00000277120		70	Gaa/Aaa	2/19	1	2	FACETS	0.657	0.591	0.727	0.657	0.591	0.727	SUBCLONAL	1	TRUE	1	0.8	2		405	369	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570334	87570334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	191	615	0	ENST00000277120.3:c.2074G>A	p.Asp692Asn	p.D692N	ENST00000277120		692	Gat/Aat	17/19	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.8	2		615	459	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650096	93650096	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	245	544	0	ENST00000375746.1:c.1647C>A	p.Phe549Leu	p.F549L	ENST00000375746	NM_001174167.1	549	ttC/ttA	12/14	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.8	2		544	534	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864002	97864002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369636116	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	137	429	1	ENST00000289081.3:c.1664G>A	p.Arg555Gln	p.R555Q	ENST00000289081	NM_000136.2	555	cGa/cAa	15/15	1	2	FACETS	0.996	0.918	1	0.996	0.918	1	CLONAL	1	TRUE	1	0.8	2		430	344	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904872	101904872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863223832	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	171	429	1	ENST00000374994.4:c.860C>T	p.Ser287Phe	p.S287F	ENST00000374994	NM_004612.2	287	tCc/tTc	5/9	1	2	FACETS	0.976	0.908	1	0.976	0.908	1	CLONAL	1	TRUE	1	0.8	2		430	438	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249753	110249753	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	182	379	0	ENST00000374672.4:c.922G>T	p.Gly308Trp	p.G308W	ENST00000374672	NM_004235.4	308	Ggg/Tgg	3/5	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.8	2		379	439	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249824	110249824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	131	300	0	ENST00000374672.4:c.851C>T	p.Ser284Leu	p.S284L	ENST00000374672	NM_004235.4	284	tCg/tTg	3/5	1	2	FACETS	0.917	0.843	0.994	0.917	0.843	0.994	CLONAL	1	TRUE	1	0.8	2		300	357	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133729465	133729465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	54	346	0	ENST00000318560.5:c.94C>T	p.Pro32Ser	p.P32S	ENST00000318560	NM_005157.4	32	Cca/Tca	2/11	1	2	FACETS	0.359	0.308	0.415	0.359	0.308	0.415	SUBCLONAL	1	TRUE	1	0.8	2		346	376	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755919	133755919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759795929	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	116	502	0	ENST00000318560.5:c.1546C>T	p.Arg516Cys	p.R516C	ENST00000318560	NM_005157.4	516	Cgt/Tgt	10/11	0.203145792915326	1	FACETS	0.519	0.474	0.566	0.519	0.474	0.566	INDETERMINATE	1	TRUE	0	0.8	1		502	335	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796804	135796804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223799508	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	172	491	0	ENST00000298552.3:c.683G>A	p.Arg228Gln	p.R228Q	ENST00000298552	NM_001162426.1	228	cGa/cAa	8/23	0.203145792915326	1	FACETS	0.599	0.557	0.641	0.599	0.557	0.641	INDETERMINATE	1	TRUE	0	0.8	1		491	431	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401080	139401080	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775602958	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	114	514	0	ENST00000277541.6:c.3913G>A	p.Glu1305Lys	p.E1305K	ENST00000277541	NM_017617.3	1305	Gag/Aag	24/34	0.203145792915326	1	FACETS	0.528	0.481	0.576	0.528	0.481	0.576	INDETERMINATE	1	TRUE	0	0.8	1		514	324	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63829495	63829495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	27	379	0	ENST00000279873.7:c.1138G>A	p.Glu380Lys	p.E380K	ENST00000279873	NM_032199.2	380	Gaa/Aaa	8/10	0.3	7	FACETS	0.404	0.321	0.5			1	INDETERMINATE	1	TRUE	NA	0.8	7		379	501	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845627	63845627	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	159	272	0	ENST00000279873.7:c.1366G>T	p.Glu456Ter	p.E456*	ENST00000279873	NM_032199.2	456	Gaa/Taa	9/10	0.3	7	FACETS	1	0.966	1			1	INDETERMINATE	3	TRUE	NA	0.8	7		272	373	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850996	63850996	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	268	389	0	ENST00000279873.7:c.1774G>T	p.Glu592Ter	p.E592*	ENST00000279873	NM_032199.2	592	Gaa/Taa	10/10	0.3	7	FACETS	1	0.988	1			1	INDETERMINATE	3	TRUE	NA	0.8	7		389	584	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332909	70332909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	191	720	2	ENST00000373644.4:c.814G>A	p.Glu272Lys	p.E272K	ENST00000373644	NM_030625.2	272	Gag/Aag	2/12	1	2	FACETS	0.963	0.898	1	0.963	0.898	1	CLONAL	1	TRUE	1	0.8	2		722	496	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446128	70446128	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1349186385	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	109	320	1	ENST00000373644.4:c.5068C>T	p.Arg1690Ter	p.R1690*	ENST00000373644	NM_030625.2	1690	Cga/Tga	11/12	1	2	FACETS	0.943	0.86	1	0.943	0.86	1	CLONAL	1	TRUE	1	0.8	2		321	289	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681299	88681299	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	163	391	0	ENST00000372037.3:c.1189C>G	p.Pro397Ala	p.P397A	ENST00000372037	NM_004329.2	397	Ccc/Gcc	11/13	1	2	FACETS	0.991	0.921	1	0.991	0.921	1	CLONAL	1	TRUE	1	0.8	2		391	411	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8246188	8246188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	118	584	2	ENST00000335790.3:c.446G>A	p.Gly149Asp	p.G149D	ENST00000335790	NM_002315.2	149	gGc/gAc	4/4	0.3	2	FACETS	0.72	0.654	0.787			1	INDETERMINATE	1	TRUE	NA	0.8	2		586	410	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69456245	69456245	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	143	360	0	ENST00000227507.2:c.164C>T	p.Ser55Phe	p.S55F	ENST00000227507	NM_053056.2	55	tCc/tTc	1/5	1	2	FACETS	0.682	0.626	0.741	0.682	0.626	0.741	SUBCLONAL	1	TRUE	1	0.8	2		360	524	SUCCESS
EED	8726	MSKCC	GRCh37	11	85979586	85979586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408450238	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	165	379	1	ENST00000263360.6:c.949G>A	p.Asp317Asn	p.D317N	ENST00000263360	NM_003797.3	317	Gat/Aat	9/12	1	2	FACETS	0.973	0.903	1	0.973	0.903	1	CLONAL	1	TRUE	1	0.8	2		380	424	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192594	94192594	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104895016	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	166	666	2	ENST00000323929.3:c.1480G>A	p.Glu494Lys	p.E494K	ENST00000323929	NM_005591.3	494	Gaa/Aaa	13/20	1	2	FACETS	0.74	0.683	0.798	0.74	0.683	0.798	SUBCLONAL	1	TRUE	1	0.8	2		668	561	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94201000	94201000	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	132	502	1	ENST00000323929.3:c.1077G>T	p.Glu359Asp	p.E359D	ENST00000323929	NM_005591.3	359	gaG/gaT	10/20	1	2	FACETS	0.842	0.772	0.914	0.842	0.772	0.914	CLONAL	1	TRUE	1	0.8	2		503	392	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912717	100912717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1181450031	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	457	710	1	ENST00000325455.5:c.2605C>T	p.Arg869Cys	p.R869C	ENST00000325455	NM_001202474.3	869	Cgt/Tgt	7/8	0.3	4	FACETS	1	0.966	1			1	INDETERMINATE	2	TRUE	NA	0.8	4		711	1020	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999180	100999180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764762671	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	247	632	1	ENST00000325455.5:c.622G>A	p.Ala208Thr	p.A208T	ENST00000325455	NM_001202474.3	208	Gcc/Acc	1/8	0.3	4	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.8	4		633	852	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186796	108186796	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202206540	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	138	486	0	ENST00000278616.4:c.6154G>A	p.Glu2052Lys	p.E2052K	ENST00000278616	NM_000051.3	2052	Gaa/Aaa	42/63	1	2	FACETS	0.682	0.624	0.742	0.682	0.624	0.742	SUBCLONAL	1	TRUE	1	0.8	2		486	506	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344458	118344458	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	71	270	0	ENST00000534358.1:c.2584C>T	p.Arg862Ter	p.R862*	ENST00000534358	NM_005933.3	862	Cga/Tga	3/36	1	2	FACETS	0.648	0.572	0.728	0.648	0.572	0.728	SUBCLONAL	1	TRUE	1	0.8	2		270	274	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344751	118344751	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	225	639	0	ENST00000534358.1:c.2877A>C	p.Lys959Asn	p.K959N	ENST00000534358	NM_005933.3	959	aaA/aaC	3/36	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.8	2		639	555	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390778	118390778	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1555053010	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	106	433	0	ENST00000534358.1:c.11428C>T	p.Arg3810Trp	p.R3810W	ENST00000534358	NM_005933.3	3810	Cgg/Tgg	33/36	1	2	FACETS	0.59	0.532	0.651	0.59	0.532	0.651	SUBCLONAL	1	TRUE	1	0.8	2		433	449	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392634	118392634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555053677	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	120	438	1	ENST00000534358.1:c.11666G>A	p.Arg3889Gln	p.R3889Q	ENST00000534358	NM_005933.3	3889	cGa/cAa	36/36	1	2	FACETS	0.783	0.714	0.855	0.783	0.714	0.855	SUBCLONAL	1	TRUE	1	0.8	2		439	383	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144603	119144603	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1228155346	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	166	445	1	ENST00000264033.4:c.616C>T	p.Arg206Ter	p.R206*	ENST00000264033	NM_005188.3	206	Cga/Tga	4/16	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.8	2		446	401	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416162	416162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	219	707	0	ENST00000399788.2:c.4024G>A	p.Glu1342Lys	p.E1342K	ENST00000399788	NM_001042603.1	1342	Gaa/Aaa	24/28	1	2	FACETS	0.74	0.691	0.79	0.74	0.691	0.79	SUBCLONAL	1	TRUE	1	0.8	2		707	740	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438057	438057	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	236	504	0	ENST00000399788.2:c.1912G>T	p.Glu638Ter	p.E638*	ENST00000399788	NM_001042603.1	638	Gaa/Taa	14/28	1	2	FACETS	0.988	0.929	1	0.988	0.929	1	CLONAL	1	TRUE	1	0.8	2		504	597	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	465663	465663	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	145	646	0	ENST00000399788.2:c.713A>C	p.Lys238Thr	p.K238T	ENST00000399788	NM_001042603.1	238	aAa/aCa	6/28	1	2	FACETS	0.666	0.611	0.724	0.666	0.611	0.724	SUBCLONAL	1	TRUE	1	0.8	2		646	544	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038956	12038956	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	246	378	0	ENST00000396373.4:c.1249T>C	p.Phe417Leu	p.F417L	ENST00000396373	NM_001987.4	417	Ttc/Ctc	7/8	0.3	6	FACETS	0.905	0.853	0.958			1	INDETERMINATE	3	TRUE	NA	0.8	6		378	589	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871797	12871797	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	182	215	2	ENST00000228872.4:c.514G>T	p.Glu172Ter	p.E172*	ENST00000228872	NM_004064.3	172	Gaa/Taa	2/3	0.3	6	FACETS	1	0.983	1			1	INDETERMINATE	2	TRUE	NA	0.8	6		217	503	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650568	18650568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368805708	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	34	442	0	ENST00000266497.5:c.2779C>T	p.Arg927Cys	p.R927C	ENST00000266497		927	Cgt/Tgt	20/31	0.3	3	FACETS	0.248	0.202	0.3			1	INDETERMINATE	1	TRUE	NA	0.8	3		442	479	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793361	18793361	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	168	408	0	ENST00000266497.5:c.4060-2A>C		p.X1354_splice	ENST00000266497		1354			0.3	3	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.8	3		408	397	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244518	46244518	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	155	498	0	ENST00000334344.6:c.2612A>G	p.Gln871Arg	p.Q871R	ENST00000334344	NM_152641.2	871	cAg/cGg	15/21	0.3	3	FACETS	1	0.952	1			1	INDETERMINATE	1	TRUE	NA	0.8	3		498	519	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287500	46287500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457405698	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	16	304	0	ENST00000334344.6:c.5359C>T	p.Arg1787Cys	p.R1787C	ENST00000334344	NM_152641.2	1787	Cgc/Tgc	20/21	0.3	3	FACETS	0.186	0.137	0.245			1	INDETERMINATE	1	TRUE	NA	0.8	3		304	301	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420778	49420778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1427665021	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	145	400	1	ENST00000301067.7:c.14971C>T	p.Arg4991Trp	p.R4991W	ENST00000301067	NM_003482.3	4991	Cgg/Tgg	48/54	0.3	3	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.8	3		401	350	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431669	49431669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	167	552	0	ENST00000301067.7:c.9470G>A	p.Gly3157Glu	p.G3157E	ENST00000301067	NM_003482.3	3157	gGa/gAa	34/54	0.3	1	FACETS	0.634	0.59	0.679	0.634	0.59	0.679	INDETERMINATE	1	TRUE	0	0.8	1		552	395	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438655	49438655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1268188754	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	165	428	1	ENST00000301067.7:c.4835G>A	p.Arg1612His	p.R1612H	ENST00000301067	NM_003482.3	1612	cGc/cAc	19/54	0.3	1	FACETS	0.695	0.648	0.742	0.695	0.648	0.742	INDETERMINATE	1	TRUE	0	0.8	1		429	356	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487641	56487641	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771536549	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	128	496	0	ENST00000267101.3:c.1574G>A	p.Arg525Gln	p.R525Q	ENST00000267101	NM_001982.3	525	cGa/cAa	13/28	0.102917471053861	3	FACETS	0.978	0.893	1	0.489	0.446	0.534	INDETERMINATE	1	TRUE	1	0.8	3		496	458	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858512	57858512	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1364213000	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	251	949	0	ENST00000228682.2:c.250T>C	p.Ser84Pro	p.S84P	ENST00000228682	NM_005269.2	84	Tcc/Ccc	4/12	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.8	NA		949	631	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864193	57864193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746398371	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	188	726	2	ENST00000228682.2:c.1670G>A	p.Arg557His	p.R557H	ENST00000228682	NM_005269.2	557	cGc/cAc	12/12	0.3	1	FACETS	0.535	0.498	0.573	0.535	0.498	0.573	INDETERMINATE	1	TRUE	0	0.8	1		728	527	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233244	69233244	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	283	546	0	ENST00000462284.1:c.1109A>C	p.Lys370Thr	p.K370T	ENST00000462284	NM_002392.5	370	aAa/aCa	11/11	0.282046453132761	4	FACETS	0.96	0.909	1	0.96	0.909	1	INDETERMINATE	2	TRUE	2	0.8	4		546	663	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813333	102813333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs539899150	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	242	543	0	ENST00000307046.8:c.356G>A	p.Arg119His	p.R119H	ENST00000307046	NM_001111285.1	119	cGc/cAc	3/4	0.282046453132761	4	FACETS	0.896	0.843	0.949	0.896	0.843	0.949	INDETERMINATE	2	TRUE	2	0.8	4		543	608	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885459	111885459	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1565991476	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	207	647	0	ENST00000341259.2:c.1237-1G>A		p.X413_splice	ENST00000341259	NM_005475.2	413			0.102917471053861	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.8	0		647	530	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112884111	112884111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	90	359	0	ENST00000351677.2:c.46G>A	p.Ala16Thr	p.A16T	ENST00000351677	NM_002834.3	16	Gca/Aca	2/16	0.102917471053861	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.8	0		359	329	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114234	115114234	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	24	527	0	ENST00000257566.3:c.983G>T	p.Arg328Ile	p.R328I	ENST00000257566	NM_016569.3	328	aGa/aTa	6/8	0.102917471053861	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.8	0		527	429	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115397	115115397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866796237	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	181	594	0	ENST00000257566.3:c.929G>A	p.Arg310Gln	p.R310Q	ENST00000257566	NM_016569.3	310	cGa/cAa	5/8	0.102917471053861	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.8	0		594	448	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120535064	120535064	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	73	783	0	ENST00000229340.5:c.591G>T	p.Lys197Asn	p.K197N	ENST00000229340	NM_006861.6	197	aaG/aaT	6/6	0.102917471053861	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.8	0		783	523	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225525	133225525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762090058	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	337	548	1	ENST00000320574.5:c.4139C>T	p.Ser1380Leu	p.S1380L	ENST00000320574	NM_006231.2	1380	tCg/tTg	32/49	0.102917471053861	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.8	0		549	409	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249419	133249419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756829894	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	90	220	0	ENST00000320574.5:c.1480C>T	p.Arg494Trp	p.R494W	ENST00000320574	NM_006231.2	494	Cgg/Tgg	15/49	0.102917471053861	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.8	0		220	191	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549116	21549116	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	179	586	0	ENST00000382592.4:c.3160C>T	p.Arg1054Ter	p.R1054*	ENST00000382592	NM_014572.2	1054	Cga/Tga	8/8	0.203145792915326	1	FACETS	0.575	0.535	0.615	0.575	0.535	0.615	INDETERMINATE	1	TRUE	0	0.8	1		586	467	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555686	21555686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194403560	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	170	584	1	ENST00000382592.4:c.2584C>T	p.Arg862Trp	p.R862W	ENST00000382592	NM_014572.2	862	Cgg/Tgg	6/8	0.203145792915326	1	FACETS	0.556	0.516	0.596	0.556	0.516	0.596	INDETERMINATE	1	TRUE	0	0.8	1		585	459	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26927898	26927898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	165	382	0	ENST00000381527.3:c.337G>A	p.Ala113Thr	p.A113T	ENST00000381527	NM_001260.1	113	Gct/Act	4/13	0.203145792915326	1	FACETS	0.595	0.552	0.638	0.595	0.552	0.638	INDETERMINATE	1	TRUE	0	0.8	1		382	416	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589787	28589787	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	109	647	0	ENST00000241453.7:c.2593T>C	p.Tyr865His	p.Y865H	ENST00000241453	NM_004119.2	865	Tac/Cac	21/24	0.203145792915326	1	FACETS	0.374	0.338	0.412	0.374	0.338	0.412	INDETERMINATE	1	TRUE	0	0.8	1		647	437	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602341	28602341	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1352217777	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	62	554	0	ENST00000241453.7:c.2027A>G	p.Asn676Ser	p.N676S	ENST00000241453	NM_004119.2	676	aAc/aGc	16/24	0.203145792915326	1	FACETS	0.225	0.194	0.257	0.225	0.194	0.257	INDETERMINATE	1	TRUE	0	0.8	1		554	414	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608456	28608456	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	19	450	0	ENST00000241453.7:c.1686T>G	p.Ile562Met	p.I562M	ENST00000241453	NM_004119.2	562	atT/atG	13/24	0.203145792915326	1	FACETS	0.076	0.057	0.098	0.076	0.057	0.098	INDETERMINATE	1	TRUE	0	0.8	1		450	376	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609707	28609707	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1216208857	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	200	619	0	ENST00000241453.7:c.1522A>C	p.Lys508Gln	p.K508Q	ENST00000241453	NM_004119.2	508	Aaa/Caa	12/24	0.203145792915326	1	FACETS	0.594	0.555	0.633	0.594	0.555	0.633	INDETERMINATE	1	TRUE	0	0.8	1		619	505	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622458	28622458	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	130	443	0	ENST00000241453.7:c.1159C>T	p.Arg387Ter	p.R387*	ENST00000241453	NM_004119.2	387	Cga/Tga	9/24	0.203145792915326	1	FACETS	0.531	0.487	0.576	0.531	0.487	0.576	INDETERMINATE	1	TRUE	0	0.8	1		443	367	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623870	28623870	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	28	385	0	ENST00000241453.7:c.784C>A	p.Leu262Ile	p.L262I	ENST00000241453	NM_004119.2	262	Ctt/Att	7/24	0.203145792915326	1	FACETS	0.126	0.1	0.155	0.126	0.1	0.155	INDETERMINATE	1	TRUE	0	0.8	1		385	334	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28979934	28979934	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	152	498	0	ENST00000282397.4:c.1534A>C	p.Ile512Leu	p.I512L	ENST00000282397	NM_002019.4	512	Ata/Cta	11/30	0.203145792915326	1	FACETS	0.502	0.463	0.542	0.502	0.463	0.542	INDETERMINATE	1	TRUE	0	0.8	1		498	454	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29002009	29002009	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750711298	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	140	435	0	ENST00000282397.4:c.1156C>T	p.Arg386Cys	p.R386C	ENST00000282397	NM_002019.4	386	Cgt/Tgt	9/30	0.203145792915326	1	FACETS	0.524	0.482	0.567	0.524	0.482	0.567	INDETERMINATE	1	TRUE	0	0.8	1		435	401	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041065	29041065	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	114	356	0	ENST00000282397.4:c.363A>C	p.Glu121Asp	p.E121D	ENST00000282397	NM_002019.4	121	gaA/gaC	3/30	0.203145792915326	1	FACETS	0.62	0.567	0.673	0.62	0.567	0.673	INDETERMINATE	1	TRUE	0	0.8	1		356	276	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893435	32893435	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs397507646	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	135	283	0	ENST00000380152.3:c.289G>T	p.Glu97Ter	p.E97*	ENST00000380152		97	Gaa/Taa	3/27	0.203145792915326	1	FACETS	0.559	0.515	0.605	0.559	0.515	0.605	INDETERMINATE	1	TRUE	0	0.8	1		283	362	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906567	32906567	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	101	345	0	ENST00000380152.3:c.952A>C	p.Lys318Gln	p.K318Q	ENST00000380152		318	Aaa/Caa	10/27	0.203145792915326	1	FACETS	0.432	0.389	0.476	0.432	0.389	0.476	INDETERMINATE	1	TRUE	0	0.8	1		345	351	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910726	32910726	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	233	957	0	ENST00000380152.3:c.2234A>C	p.Lys745Thr	p.K745T	ENST00000380152		745	aAa/aCa	11/27	0.203145792915326	1	FACETS	0.452	0.423	0.482	0.452	0.423	0.482	INDETERMINATE	1	TRUE	0	0.8	1		957	773	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911589	32911589	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs780279081	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	87	878	1	ENST00000380152.3:c.3097G>T	p.Asp1033Tyr	p.D1033Y	ENST00000380152		1033	Gat/Tat	11/27	0.203145792915326	1	FACETS	0.199	0.176	0.224	0.199	0.176	0.224	INDETERMINATE	1	TRUE	0	0.8	1		879	655	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914280	32914280	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	295	857	0	ENST00000380152.3:c.5788T>G	p.Leu1930Val	p.L1930V	ENST00000380152		1930	Tta/Gta	11/27	0.203145792915326	1	FACETS	0.591	0.559	0.623	0.591	0.559	0.623	INDETERMINATE	1	TRUE	0	0.8	1		857	749	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915267	32915267	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	121	868	0	ENST00000380152.3:c.6775A>C	p.Asn2259His	p.N2259H	ENST00000380152		2259	Aat/Cat	11/27	0.203145792915326	1	FACETS	0.251	0.227	0.277	0.251	0.227	0.277	INDETERMINATE	1	TRUE	0	0.8	1		868	723	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929156	32929156	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	235	811	0	ENST00000380152.3:c.7166G>T	p.Arg2389Ile	p.R2389I	ENST00000380152		2389	aGa/aTa	14/27	0.203145792915326	1	FACETS	0.599	0.564	0.636	0.599	0.564	0.636	INDETERMINATE	1	TRUE	0	0.8	1		811	588	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939040	48939040	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	21	356	0	ENST00000267163.4:c.872T>C	p.Val291Ala	p.V291A	ENST00000267163	NM_000321.2	291	gTt/gCt	9/27	0.102917471053861	3	FACETS	0.186	0.143	0.237	0.093	0.071	0.119	INDETERMINATE	1	TRUE	1	0.8	3		356	395	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951074	48951074	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	142	319	0	ENST00000267163.4:c.1236A>C	p.Lys412Asn	p.K412N	ENST00000267163	NM_000321.2	412	aaA/aaC	13/27	0.102917471053861	3	FACETS	1	0.986	1	0.664	0.613	0.717	INDETERMINATE	1	TRUE	1	0.8	3		319	374	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349353	73349353	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1026175478	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	206	543	1	ENST00000377767.4:c.983G>A	p.Arg328Gln	p.R328Q	ENST00000377767	NM_014953.3	328	cGa/cAa	6/21	0.102917471053861	3	FACETS	1	0.984	1	0.587	0.548	0.627	INDETERMINATE	1	TRUE	1	0.8	3		544	614	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504507	103504507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758174644	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	220	600	0	ENST00000355739.4:c.128G>A	p.Arg43Gln	p.R43Q	ENST00000355739	NM_000123.3	43	cGg/cAg	2/15	0.102917471053861	3	FACETS	1	0.992	1	0.703	0.659	0.746	INDETERMINATE	1	TRUE	1	0.8	3		600	548	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103508437	103508437	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	19	261	0	ENST00000355739.4:c.503G>T	p.Arg168Ile	p.R168I	ENST00000355739	NM_000123.3	168	aGa/aTa	5/15	0.102917471053861	3	FACETS	0.245	0.186	0.315	0.123	0.093	0.158	INDETERMINATE	1	TRUE	1	0.8	3		261	271	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68301872	68301872	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144348796	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	174	469	1	ENST00000487270.1:c.274G>A	p.Glu92Lys	p.E92K	ENST00000487270	NM_133509.3	92	Gaa/Aaa	4/11	0.102917471053861	3	FACETS	1	0.988	1	0.662	0.615	0.709	INDETERMINATE	1	TRUE	1	0.8	3		470	460	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331814	68331814	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	292	587	0	ENST00000487270.1:c.410C>T	p.Ala137Val	p.A137V	ENST00000487270	NM_133509.3	137	gCt/gTt	5/11	0.102917471053861	3	FACETS	0.823	0.781	0.865	0.823	0.781	0.865	INDETERMINATE	2	TRUE	1	0.8	3		587	621	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95556921	95556921	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	187	429	0	ENST00000393063.1:c.5683C>T	p.Arg1895Ter	p.R1895*	ENST00000393063	NM_030621.3	1895	Cga/Tga	28/28	0.102917471053861	3	FACETS	1	0.991	1	0.726	0.678	0.774	INDETERMINATE	1	TRUE	1	0.8	3		429	451	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572103	95572103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	149	390	1	ENST00000393063.1:c.3005C>T	p.Pro1002Leu	p.P1002L	ENST00000393063	NM_030621.3	1002	cCt/cTt	20/28	0.102917471053861	3	FACETS	1	0.924	1	0.502	0.462	0.544	INDETERMINATE	1	TRUE	1	0.8	3		391	519	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95592924	95592924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755944755	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	20	306	0	ENST00000393063.1:c.896C>T	p.Ser299Leu	p.S299L	ENST00000393063	NM_030621.3	299	tCg/tTg	8/28	0.102917471053861	3	FACETS	0.183	0.14	0.235	0.092	0.07	0.118	INDETERMINATE	1	TRUE	1	0.8	3		306	382	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989110	41989110	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	278	816	1	ENST00000219905.7:c.1902G>T	p.Lys634Asn	p.K634N	ENST00000219905	NM_001164273.1	634	aaG/aaT	3/24	1	2	FACETS	0.922	0.87	0.974	0.922	0.87	0.974	CLONAL	1	TRUE	1	0.8	2		817	754	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040934	42040934	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	279	845	1	ENST00000219905.7:c.5312C>A	p.Ser1771Tyr	p.S1771Y	ENST00000219905	NM_001164273.1	1771	tCt/tAt	16/24	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.8	2		846	697	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040978	42040978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755286142	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	288	865	2	ENST00000219905.7:c.5356C>T	p.Arg1786Trp	p.R1786W	ENST00000219905	NM_001164273.1	1786	Cgg/Tgg	16/24	1	2	FACETS	0.997	0.943	1	0.997	0.943	1	CLONAL	1	TRUE	1	0.8	2		867	722	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66737028	66737028	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	108	492	0	ENST00000307102.5:c.551A>G	p.His184Arg	p.H184R	ENST00000307102	NM_002755.3	184	cAc/cGc	5/11	1	2	FACETS	0.694	0.628	0.763	0.694	0.628	0.763	SUBCLONAL	1	TRUE	1	0.8	2		492	389	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576178	88576178	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368708129	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	141	455	2	ENST00000360948.2:c.1495G>A	p.Asp499Asn	p.D499N	ENST00000360948	NM_001012338.2	499	Gac/Aac	13/19	0.3	1	FACETS	0.624	0.577	0.672	0.624	0.577	0.672	INDETERMINATE	1	TRUE	0	0.8	1		457	339	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726711	88726711	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	100	406	0	ENST00000360948.2:c.333G>T	p.Lys111Asn	p.K111N	ENST00000360948	NM_001012338.2	111	aaG/aaT	4/19	0.3	1	FACETS	0.507	0.459	0.557	0.507	0.459	0.557	INDETERMINATE	1	TRUE	0	0.8	1		406	296	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303846	91303846	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	81	243	0	ENST00000355112.3:c.1243G>T	p.Asp415Tyr	p.D415Y	ENST00000355112	NM_000057.2	415	Gat/Tat	7/22	1	2	FACETS	0.993	0.893	1	0.993	0.893	1	CLONAL	1	TRUE	1	0.8	2		243	204	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3794952	3794952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758668926	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	150	388	0	ENST00000262367.5:c.3925G>A	p.Asp1309Asn	p.D1309N	ENST00000262367	NM_004380.2	1309	Gac/Aac	23/31	0.3	1	FACETS	0.6	0.555	0.646	0.6	0.555	0.646	INDETERMINATE	1	TRUE	0	0.8	1		388	375	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3799657	3799657	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	169	554	0	ENST00000262367.5:c.3807G>T	p.Lys1269Asn	p.K1269N	ENST00000262367	NM_004380.2	1269	aaG/aaT	21/31	0.3	1	FACETS	0.667	0.622	0.713	0.667	0.622	0.713	INDETERMINATE	1	TRUE	0	0.8	1		554	380	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857847	9857847	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	114	704	0	ENST00000330684.3:c.3554A>C	p.Lys1185Thr	p.K1185T	ENST00000330684	NM_001134407.1	1185	aAa/aCa	13/13	1	2	FACETS	0.639	0.579	0.702	0.639	0.579	0.702	SUBCLONAL	1	TRUE	1	0.8	2		704	446	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923379	9923379	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	53	613	1	ENST00000330684.3:c.1908C>A	p.Phe636Leu	p.F636L	ENST00000330684	NM_001134407.1	636	ttC/ttA	9/13	1	2	FACETS	0.311	0.266	0.361	0.311	0.266	0.361	SUBCLONAL	1	TRUE	1	0.8	2		614	426	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934603	9934603	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747838255	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	193	563	1	ENST00000330684.3:c.1552C>T	p.Arg518Cys	p.R518C	ENST00000330684	NM_001134407.1	518	Cgt/Tgt	7/13	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.8	2		564	455	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274007	10274007	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	92	703	1	ENST00000330684.3:c.262G>A	p.Asp88Asn	p.D88N	ENST00000330684	NM_001134407.1	88	Gac/Aac	2/13	1	2	FACETS	0.613	0.549	0.681	0.613	0.549	0.681	SUBCLONAL	1	TRUE	1	0.8	2		704	375	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348918	11348918	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	71	211	0	ENST00000332029.2:c.418A>G	p.Ser140Gly	p.S140G	ENST00000332029	NM_003745.1	140	Agc/Ggc	2/2	1	2	FACETS	0.857	0.762	0.957	0.857	0.762	0.957	CLONAL	1	TRUE	1	0.8	2		211	207	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23640966	23640966	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778587	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	89	311	2	ENST00000261584.4:c.2509G>A	p.Glu837Lys	p.E837K	ENST00000261584	NM_024675.3	837	Gaa/Aaa	5/13	1	2	FACETS	0.654	0.585	0.727	0.654	0.585	0.727	SUBCLONAL	1	TRUE	1	0.8	2		313	340	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646544	23646544	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	118	333	1	ENST00000261584.4:c.1323A>T	p.Lys441Asn	p.K441N	ENST00000261584	NM_024675.3	441	aaA/aaT	4/13	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.8	2		334	289	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129008	30129008	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	202	701	0	ENST00000263025.4:c.758A>C	p.Gln253Pro	p.Q253P	ENST00000263025	NM_002746.2	253	cAg/cCg	5/9	1	2	FACETS	0.868	0.81	0.927	0.868	0.81	0.927	CLONAL	1	TRUE	1	0.8	2		701	582	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827580	72827580	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	264	876	1	ENST00000268489.5:c.9001G>T	p.Glu3001Ter	p.E3001*	ENST00000268489	NM_006885.3	3001	Gaa/Taa	9/10	1	2	FACETS	0.923	0.87	0.977	0.923	0.87	0.977	CLONAL	1	TRUE	1	0.8	2		877	715	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830535	72830535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776901666	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	54	910	0	ENST00000268489.5:c.6046G>A	p.Glu2016Lys	p.E2016K	ENST00000268489	NM_006885.3	2016	Gag/Aag	9/10	1	2	FACETS	0.157	0.133	0.183	0.157	0.133	0.183	SUBCLONAL	1	TRUE	1	0.8	2		910	861	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830640	72830640	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	48	1017	1	ENST00000268489.5:c.5941G>A	p.Glu1981Lys	p.E1981K	ENST00000268489	NM_006885.3	1981	Gaa/Aaa	9/10	1	2	FACETS	0.16	0.135	0.189	0.16	0.135	0.189	SUBCLONAL	1	TRUE	1	0.8	2		1018	748	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830958	72830958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393698686	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	153	920	0	ENST00000268489.5:c.5623G>A	p.Glu1875Lys	p.E1875K	ENST00000268489	NM_006885.3	1875	Gaa/Aaa	9/10	1	2	FACETS	0.56	0.514	0.608	0.56	0.514	0.608	SUBCLONAL	1	TRUE	1	0.8	2		920	683	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832265	72832265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267604632	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	208	761	1	ENST00000268489.5:c.4316G>A	p.Arg1439Gln	p.R1439Q	ENST00000268489	NM_006885.3	1439	cGa/cAa	9/10	1	2	FACETS	0.721	0.672	0.772	0.721	0.672	0.772	SUBCLONAL	1	TRUE	1	0.8	2		762	721	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72833968	72833968	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs529603227	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	180	683	1	ENST00000268489.5:c.3925C>T	p.Arg1309Ter	p.R1309*	ENST00000268489	NM_006885.3	1309	Cga/Tga	8/10	1	2	FACETS	0.663	0.613	0.714	0.663	0.613	0.714	SUBCLONAL	1	TRUE	1	0.8	2		684	679	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991586	72991586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768340392	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	82	862	1	ENST00000268489.5:c.2459G>A	p.Arg820His	p.R820H	ENST00000268489	NM_006885.3	820	cGc/cAc	2/10	1	2	FACETS	0.282	0.248	0.318	0.282	0.248	0.318	SUBCLONAL	1	TRUE	1	0.8	2		863	727	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992667	72992667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2073852	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	301	673	0	ENST00000268489.5:c.1378G>A	p.Glu460Lys	p.E460K	ENST00000268489	NM_006885.3	460	Gaa/Aaa	2/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.8	2		673	640	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348470	89348470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758824643	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	56	923	3	ENST00000301030.4:c.4480C>T	p.Arg1494Trp	p.R1494W	ENST00000301030	NM_001256183.1	1494	Cgg/Tgg	9/13	0.3	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.8	0		926	546	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350504	89350504	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1183047246	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	46	990	0	ENST00000301030.4:c.2446G>A	p.Glu816Lys	p.E816K	ENST00000301030	NM_001256183.1	816	Gaa/Aaa	9/13	0.3	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.8	0		990	615	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351980	89351980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	125	1021	2	ENST00000301030.4:c.970G>A	p.Glu324Lys	p.E324K	ENST00000301030	NM_001256183.1	324	Gaa/Aaa	9/13	0.3	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.8	0		1023	556	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849470	89849470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778045457	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	83	829	2	ENST00000389301.3:c.1511G>A	p.Arg504His	p.R504H	ENST00000389301	NM_000135.2	504	cGc/cAc	16/43	0.3	1	FACETS	0.243	0.215	0.273	0.243	0.215	0.273	INDETERMINATE	1	TRUE	0	0.8	1		831	512	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108548	8108548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	51	454	0	ENST00000585124.1:c.847C>T	p.Arg283Cys	p.R283C	ENST00000585124	NM_004217.3	283	Cgc/Tgc	8/9	1	2	FACETS	0.316	0.269	0.367	0.316	0.269	0.367	SUBCLONAL	1	TRUE	1	0.8	2		454	404	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984764	11984764	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	17	264	0	ENST00000353533.5:c.310G>T	p.Asp104Tyr	p.D104Y	ENST00000353533	NM_003010.3	104	Gac/Tac	3/11	1	2	FACETS	0.159	0.118	0.207	0.159	0.118	0.207	SUBCLONAL	1	TRUE	1	0.8	2		264	267	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032472	12032472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	139	307	0	ENST00000353533.5:c.908G>A	p.Gly303Asp	p.G303D	ENST00000353533	NM_003010.3	303	gGc/gAc	9/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.8	2		307	314	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049728	16049728	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	276	734	0	ENST00000268712.3:c.1044A>C	p.Glu348Asp	p.E348D	ENST00000268712	NM_006311.3	348	gaA/gaC	10/46	1	2	FACETS	0.965	0.911	1	0.965	0.911	1	CLONAL	1	TRUE	1	0.8	2		734	715	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089913	16089913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	178	481	0	ENST00000268712.3:c.197G>A	p.Arg66Gln	p.R66Q	ENST00000268712	NM_006311.3	66	cGa/cAa	3/46	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.8	2		481	437	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663454	29663454	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	41	379	0	ENST00000356175.3:c.6047C>T	p.Ala2016Val	p.A2016V	ENST00000356175	NM_000267.3	2016	gCt/gTt	40/57	1	2	FACETS	0.232	0.193	0.276	0.232	0.193	0.276	SUBCLONAL	1	TRUE	1	0.8	2		379	441	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325897	30325897	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777349343	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	116	452	1	ENST00000322652.5:c.2095G>A	p.Glu699Lys	p.E699K	ENST00000322652	NM_015355.2	699	Gaa/Aaa	16/16	1	2	FACETS	0.613	0.556	0.673	0.613	0.556	0.673	SUBCLONAL	1	TRUE	1	0.8	2		453	473	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650845	37650845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	72	682	0	ENST00000447079.4:c.2317C>T	p.Arg773Cys	p.R773C	ENST00000447079	NM_015083.1	773	Cgt/Tgt	5/14	1	2	FACETS	0.338	0.295	0.383	0.338	0.295	0.383	SUBCLONAL	1	TRUE	1	0.8	2		682	533	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657676	37657676	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	170	492	0	ENST00000447079.4:c.2593A>C	p.Ile865Leu	p.I865L	ENST00000447079	NM_015083.1	865	Att/Ctt	6/14	1	2	FACETS	0.988	0.919	1	0.988	0.919	1	CLONAL	1	TRUE	1	0.8	2		492	430	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681051	37681051	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	174	392	0	ENST00000447079.4:c.3220A>G	p.Thr1074Ala	p.T1074A	ENST00000447079	NM_015083.1	1074	Aca/Gca	12/14	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.8	2		392	388	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359594	40359594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758951069	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	236	778	0	ENST00000293328.3:c.2059C>T	p.Pro687Ser	p.P687S	ENST00000293328	NM_012448.3	687	Ccc/Tcc	16/19	0.3	1	FACETS	0.577	0.543	0.613	0.577	0.543	0.613	INDETERMINATE	1	TRUE	0	0.8	1		778	613	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243774	41243774	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs431825399	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	47	512	0	ENST00000357654.3:c.3774G>T	p.Glu1258Asp	p.E1258D	ENST00000357654	NM_007294.3	1258	gaG/gaT	10/23	0.3	1	FACETS	0.161	0.136	0.189	0.161	0.136	0.189	INDETERMINATE	1	TRUE	0	0.8	1		512	438	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244094	41244094	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80357175	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	168	490	0	ENST00000357654.3:c.3454G>A	p.Asp1152Asn	p.D1152N	ENST00000357654	NM_007294.3	1152	Gac/Aac	10/23	0.3	1	FACETS	0.603	0.56	0.646	0.603	0.56	0.646	INDETERMINATE	1	TRUE	0	0.8	1		490	418	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244213	41244213	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	153	461	0	ENST00000357654.3:c.3335A>C	p.Glu1112Ala	p.E1112A	ENST00000357654	NM_007294.3	1112	gAa/gCa	10/23	0.3	1	FACETS	0.593	0.549	0.638	0.593	0.549	0.638	INDETERMINATE	1	TRUE	0	0.8	1		461	387	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435240	56435240	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	108	189	0	ENST00000407977.2:c.1897T>C	p.Cys633Arg	p.C633R	ENST00000407977		633	Tgc/Cgc	9/10	0.3	5	FACETS	1	0.963	1			1	INDETERMINATE	2	TRUE	NA	0.8	5		189	269	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677911	58677911	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	151	559	0	ENST00000305921.3:c.136T>C	p.Ser46Pro	p.S46P	ENST00000305921	NM_003620.3	46	Tct/Cct	1/6	0.3	2	FACETS	0.689	0.633	0.746			1	INDETERMINATE	1	TRUE	NA	0.8	2		559	548	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734023	58734023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	252	690	2	ENST00000305921.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000305921	NM_003620.3	361	Cgt/Tgt	5/6	0.3	2	FACETS	1	0.962	1			1	INDETERMINATE	1	TRUE	NA	0.8	2		692	614	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740704	58740704	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	257	850	0	ENST00000305921.3:c.1609A>G	p.Thr537Ala	p.T537A	ENST00000305921	NM_003620.3	537	Aca/Gca	6/6	0.3	2	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.8	2		850	622	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740837	58740837	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200809297	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	80	855	2	ENST00000305921.3:c.1742G>A	p.Arg581Gln	p.R581Q	ENST00000305921	NM_003620.3	581	cGa/cAa	6/6	0.3	2	FACETS	0.301	0.264	0.34			1	INDETERMINATE	1	TRUE	NA	0.8	2		857	665	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59861752	59861752	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	149	475	0	ENST00000259008.2:c.1507A>C	p.Lys503Gln	p.K503Q	ENST00000259008	NM_032043.2	503	Aaa/Caa	11/20	0.3	2	FACETS	0.927	0.856	0.999			1	INDETERMINATE	1	TRUE	NA	0.8	2		475	402	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554382	63554382	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	339	528	0	ENST00000307078.5:c.357G>T	p.Gln119His	p.Q119H	ENST00000307078	NM_004655.3	119	caG/caT	2/11	0.394534646384061	4	FACETS	1	0.978	1	1	0.978	1	INDETERMINATE	2	TRUE	2	0.8	4		528	731	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78865623	78865623	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	143	354	2	ENST00000306801.3:c.2087C>A	p.Ser696Tyr	p.S696Y	ENST00000306801	NM_020761.2	696	tCt/tAt	18/34	1	2	FACETS	0.951	0.877	1	0.951	0.877	1	CLONAL	1	TRUE	1	0.8	2		356	376	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756778	756778	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	197	609	0	ENST00000314574.4:c.50G>A	p.Arg17Lys	p.R17K	ENST00000314574	NM_005433.3	17	aGa/aAa	2/12	0.102917471053861	3	FACETS	1	0.989	1	0.648	0.605	0.692	INDETERMINATE	1	TRUE	1	0.8	3		609	532	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39570469	39570469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1380208670	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	63	570	0	ENST00000262039.4:c.665G>A	p.Arg222Gln	p.R222Q	ENST00000262039	NM_002647.2	222	cGa/cAa	6/25	0.102917471053861	3	FACETS	0.402	0.348	0.461	0.201	0.174	0.231	INDETERMINATE	1	TRUE	1	0.8	3		570	548	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395686	45395686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200841904	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	144	464	0	ENST00000262160.6:c.448G>A	p.Glu150Lys	p.E150K	ENST00000262160	NM_005901.5	150	Gaa/Aaa	4/11	0.102917471053861	3	FACETS	0.867	0.795	0.943	0.434	0.397	0.472	INDETERMINATE	1	TRUE	1	0.8	3		464	581	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348487	56348487	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	416	952	0	ENST00000348428.3:c.295A>C	p.Lys99Gln	p.K99Q	ENST00000348428	NM_006785.3	99	Aaa/Caa	2/17	0.102917471053861	3	FACETS	0.786	0.752	0.82	0.786	0.752	0.82	INDETERMINATE	2	TRUE	1	0.8	3		952	926	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56377266	56377266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753977115	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	286	705	1	ENST00000348428.3:c.887G>A	p.Arg296Gln	p.R296Q	ENST00000348428	NM_006785.3	296	cGa/cAa	6/17	0.102917471053861	3	FACETS	1	0.993	1	0.684	0.646	0.722	INDETERMINATE	1	TRUE	1	0.8	3		706	732	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267638	7267638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs896894246	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	26	529	0	ENST00000302850.5:c.370G>A	p.Glu124Lys	p.E124K	ENST00000302850	NM_000208.2	124	Gag/Aag	2/22	0.203145792915326	1	FACETS	0.098	0.077	0.122	0.098	0.077	0.122	INDETERMINATE	1	TRUE	0	0.8	1		529	398	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10259678	10259678	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761717775	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	93	393	0	ENST00000340748.4:c.2554G>A	p.Glu852Lys	p.E852K	ENST00000340748		852	Gag/Aag	26/40	0.203145792915326	1	FACETS	0.429	0.385	0.475	0.429	0.385	0.475	INDETERMINATE	1	TRUE	0	0.8	1		393	325	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291513	10291513	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	149	642	0	ENST00000340748.4:c.166G>T	p.Glu56Ter	p.E56*	ENST00000340748		56	Gaa/Taa	3/40	0.203145792915326	1	FACETS	0.43	0.395	0.466	0.43	0.395	0.466	INDETERMINATE	1	TRUE	0	0.8	1		642	520	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600369	10600369	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs549967865	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	117	696	0	ENST00000171111.5:c.1486G>A	p.Glu496Lys	p.E496K	ENST00000171111	NM_203500.1	496	Gag/Aag	4/6	1	2	FACETS	0.691	0.628	0.757	0.691	0.628	0.757	SUBCLONAL	1	TRUE	1	0.8	2		696	423	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144152	11144152	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	92	414	0	ENST00000358026.2:c.3733G>A	p.Ala1245Thr	p.A1245T	ENST00000358026	NM_001128849.1	1245	Gcc/Acc	26/36	1	2	FACETS	0.653	0.586	0.724	0.653	0.586	0.724	SUBCLONAL	1	TRUE	1	0.8	2		414	352	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276313	15276313	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	72	393	0	ENST00000263388.2:c.5681A>G	p.Asn1894Ser	p.N1894S	ENST00000263388	NM_000435.2	1894	aAc/aGc	31/33	1	2	FACETS	0.614	0.542	0.691	0.614	0.542	0.691	SUBCLONAL	1	TRUE	1	0.8	2		393	293	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748903	41748903	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	107	705	0	ENST00000301178.4:c.1428G>T	p.Lys476Asn	p.K476N	ENST00000301178	NM_021913.4	476	aaG/aaT	11/20	1	2	FACETS	0.618	0.558	0.681	0.618	0.558	0.681	SUBCLONAL	1	TRUE	1	0.8	2		705	433	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520177	9520177	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	155	539	0	ENST00000353224.5:c.2092C>T	p.Pro698Ser	p.P698S	ENST00000353224	NM_177990.2	698	Cca/Tca	10/10	0.3	2	FACETS	0.748	0.689	0.809			1	INDETERMINATE	1	TRUE	NA	0.8	2		539	518	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31372585	31372585	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs545685689	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	109	565	0	ENST00000328111.2:c.226G>A	p.Gly76Arg	p.G76R	ENST00000328111	NM_006892.3	76	Ggg/Agg	4/23	0.102917471053861	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.8	0		565	454	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374312	31374312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs551752168	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	107	583	0	ENST00000328111.2:c.311G>A	p.Arg104Gln	p.R104Q	ENST00000328111	NM_006892.3	104	cGa/cAa	5/23	0.102917471053861	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.8	0		583	432	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31379489	31379489	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	139	519	1	ENST00000328111.2:c.896G>A	p.Arg299Gln	p.R299Q	ENST00000328111	NM_006892.3	299	cGa/cAa	8/23	0.102917471053861	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.8	0		520	417	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394052	31394052	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	141	461	0	ENST00000328111.2:c.2339C>T	p.Ser780Leu	p.S780L	ENST00000328111	NM_006892.3	780	tCg/tTg	22/23	0.102917471053861	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.8	0		461	398	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39713132	39713132	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	25	363	1	ENST00000361337.2:c.538G>T	p.Asp180Tyr	p.D180Y	ENST00000361337	NM_003286.2	180	Gat/Tat	8/21	0.3	3	FACETS	0.209	0.164	0.261			1	INDETERMINATE	1	TRUE	NA	0.8	3		364	418	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728710	39728710	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	112	300	0	ENST00000361337.2:c.990G>T	p.Glu330Asp	p.E330D	ENST00000361337	NM_003286.2	330	gaG/gaT	12/21	0.3	3	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.8	3		300	314	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741523	39741523	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	165	344	0	ENST00000361337.2:c.1410G>T	p.Met470Ile	p.M470I	ENST00000361337	NM_003286.2	470	atG/atT	14/21	0.3	3	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.8	3		344	397	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757463	40757463	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	142	505	0	ENST00000373198.4:c.2835T>G	p.His945Gln	p.H945Q	ENST00000373198	NM_133170.3	945	caT/caG	20/32	0.3	1	FACETS	0.593	0.548	0.64	0.593	0.548	0.64	INDETERMINATE	1	TRUE	0	0.8	1		505	359	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827900	40827900	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	106	576	0	ENST00000373198.4:c.2528C>A	p.Ser843Tyr	p.S843Y	ENST00000373198	NM_133170.3	843	tCt/tAt	17/32	0.3	1	FACETS	0.394	0.355	0.434	0.394	0.355	0.434	INDETERMINATE	1	TRUE	0	0.8	1		576	404	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944432	40944432	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs759518214	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	183	691	3	ENST00000373198.4:c.2070C>A	p.Tyr690Ter	p.Y690*	ENST00000373198	NM_133170.3	690	taC/taA	12/32	0.3	1	FACETS	0.63	0.588	0.672	0.63	0.588	0.672	INDETERMINATE	1	TRUE	0	0.8	1		694	436	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385152	41385152	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751630191	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	104	561	0	ENST00000373198.4:c.809G>A	p.Arg270His	p.R270H	ENST00000373198	NM_133170.3	270	cGc/cAc	6/32	0.3	1	FACETS	0.417	0.377	0.459	0.417	0.377	0.459	INDETERMINATE	1	TRUE	0	0.8	1		561	374	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54948566	54948566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	110	483	0	ENST00000312783.6:c.752G>A	p.Arg251Lys	p.R251K	ENST00000312783	NM_198436.1	251	aGa/aAa	8/10	0.3	2	FACETS	0.65	0.588	0.715			1	INDETERMINATE	1	TRUE	NA	0.8	2		483	423	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39762955	39762955	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	45	472	0	ENST00000288319.7:c.881A>C	p.Gln294Pro	p.Q294P	ENST00000288319	NM_182918.3	294	cAg/cCg	9/10	0.3	3	FACETS	0.462	0.389	0.541			1	INDETERMINATE	1	TRUE	NA	0.8	3		472	341	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817414	39817414	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542019196	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	119	494	0	ENST00000288319.7:c.149G>A	p.Arg50His	p.R50H	ENST00000288319	NM_182918.3	50	cGc/cAc	2/10	0.3	3	FACETS	0.913	0.83	1			1	INDETERMINATE	1	TRUE	NA	0.8	3		494	456	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513331	44513331	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	147	447	1	ENST00000291552.4:c.604C>T	p.Arg202Cys	p.R202C	ENST00000291552	NM_006758.2	202	Cgt/Tgt	8/8	0.394534646384061	4	FACETS	0.875	0.809	0.942	0.875	0.809	0.942	INDETERMINATE	2	TRUE	2	0.8	4		448	378	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162107	22162107	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	126	331	1	ENST00000215832.6:c.148C>T	p.Arg50Ter	p.R50*	ENST00000215832	NM_002745.4	50	Cga/Tga	2/9	1	2	FACETS	0.952	0.874	1	0.952	0.874	1	CLONAL	1	TRUE	1	0.8	2		332	331	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513352	41513352	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	51	626	1	ENST00000263253.7:c.256C>T	p.Arg86Ter	p.R86*	ENST00000263253	NM_001429.3	86	Cga/Tga	2/31	1	2	FACETS	0.197	0.167	0.23	0.197	0.167	0.23	SUBCLONAL	1	TRUE	1	0.8	2		627	647	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41562635	41562635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	175	404	0	ENST00000263253.7:c.3839C>T	p.Ala1280Val	p.A1280V	ENST00000263253	NM_001429.3	1280	gCa/gTa	23/31	1	2	FACETS	0.893	0.829	0.958	0.893	0.829	0.958	CLONAL	1	TRUE	1	0.8	2		404	490	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574391	41574391	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752587236	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	117	549	2	ENST00000263253.7:c.6676C>T	p.Arg2226Trp	p.R2226W	ENST00000263253	NM_001429.3	2226	Cgg/Tgg	31/31	1	2	FACETS	0.622	0.564	0.683	0.622	0.564	0.683	SUBCLONAL	1	TRUE	1	0.8	2		551	470	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574404	41574404	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	102	527	0	ENST00000263253.7:c.6689A>G	p.His2230Arg	p.H2230R	ENST00000263253	NM_001429.3	2230	cAc/cGc	31/31	1	2	FACETS	0.563	0.506	0.623	0.563	0.506	0.623	SUBCLONAL	1	TRUE	1	0.8	2		527	453	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916526	39916526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265777184	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	195	712	2	ENST00000378444.4:c.4477C>T	p.Arg1493Trp	p.R1493W	ENST00000378444	NM_001123385.1	1493	Cgg/Tgg	11/15	0.3	2	FACETS	0.814	0.758	0.871			1	INDETERMINATE	1	TRUE	NA	0.8	2		714	599	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934252	39934252	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775994643	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	219	792	2	ENST00000378444.4:c.347C>T	p.Ser116Leu	p.S116L	ENST00000378444	NM_001123385.1	116	tCg/tTg	4/15	0.3	2	FACETS	0.93	0.871	0.989			1	INDETERMINATE	1	TRUE	NA	0.8	2		794	589	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652362	48652362	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	141	829	0	ENST00000376670.3:c.1033A>G	p.Asn345Asp	p.N345D	ENST00000376670	NM_002049.3	345	Aat/Gat	6/6	0.203145792915326	1	FACETS	0.446	0.409	0.484	0.446	0.409	0.484	INDETERMINATE	1	TRUE	0	0.8	1		829	474	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342639	70342639	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	133	736	1	ENST00000374080.3:c.1400G>T	p.Ser467Ile	p.S467I	ENST00000374080		467	aGt/aTt	10/45	0.203145792915326	1	FACETS	0.454	0.416	0.494	0.454	0.416	0.494	INDETERMINATE	1	TRUE	0	0.8	1		737	439	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912075	76912075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782228142	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	322	780	1	ENST00000373344.5:c.4189G>A	p.Glu1397Lys	p.E1397K	ENST00000373344	NM_000489.3	1397	Gaa/Aaa	13/35	0.203145792915326	1	FACETS	0.756	0.72	0.791	0.756	0.72	0.791	INDETERMINATE	1	TRUE	0	0.8	1		781	639	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937393	76937393	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	49	521	0	ENST00000373344.5:c.3355G>T	p.Glu1119Ter	p.E1119*	ENST00000373344	NM_000489.3	1119	Gaa/Taa	9/35	0.203145792915326	1	FACETS	0.131	0.111	0.154	0.131	0.111	0.154	INDETERMINATE	1	TRUE	0	0.8	1		521	560	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938028	76938028	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143413618	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	136	578	0	ENST00000373344.5:c.2720G>A	p.Arg907Gln	p.R907Q	ENST00000373344	NM_000489.3	907	cGa/cAa	9/35	0.203145792915326	1	FACETS	0.381	0.348	0.416	0.381	0.348	0.416	INDETERMINATE	1	TRUE	0	0.8	1		578	535	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938119	76938119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886044896	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	175	521	1	ENST00000373344.5:c.2629G>A	p.Asp877Asn	p.D877N	ENST00000373344	NM_000489.3	877	Gat/Aat	9/35	0.203145792915326	1	FACETS	0.492	0.457	0.529	0.492	0.457	0.529	INDETERMINATE	1	TRUE	0	0.8	1		522	533	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034532	123034532	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	91	283	0	ENST00000355640.3:c.1289C>A	p.Ser430Ter	p.S430*	ENST00000355640		430	tCa/tAa	6/7	0.203145792915326	1	FACETS	0.442	0.396	0.489	0.442	0.396	0.489	INDETERMINATE	1	TRUE	0	0.8	1		283	309	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123159736	123159736	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1251136516	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	262	743	2	ENST00000218089.9:c.91G>A	p.Glu31Lys	p.E31K	ENST00000218089	NM_001042749.1	31	Gaa/Aaa	4/35	0.203145792915326	1	FACETS	0.688	0.651	0.726	0.688	0.651	0.726	INDETERMINATE	1	TRUE	0	0.8	1		745	571	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197867	123197867	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	122	625	0	ENST00000218089.9:c.1991A>G	p.Lys664Arg	p.K664R	ENST00000218089	NM_001042749.1	664	aAa/aGa	20/35	0.203145792915326	1	FACETS	0.353	0.32	0.387	0.353	0.32	0.387	INDETERMINATE	1	TRUE	0	0.8	1		625	519	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200207	123200207	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	97	528	0	ENST00000218089.9:c.2186T>G	p.Ile729Ser	p.I729S	ENST00000218089	NM_001042749.1	729	aTt/aGt	23/35	0.203145792915326	1	FACETS	0.326	0.291	0.361	0.326	0.291	0.361	INDETERMINATE	1	TRUE	0	0.8	1		528	447	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217306	123217306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768937075	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	110	641	1	ENST00000218089.9:c.2960C>T	p.Pro987Leu	p.P987L	ENST00000218089	NM_001042749.1	987	cCg/cTg	29/35	0.203145792915326	1	FACETS	0.348	0.314	0.384	0.348	0.314	0.384	INDETERMINATE	1	TRUE	0	0.8	1		642	474	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229243	123229243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	146	528	0	ENST00000218089.9:c.3727G>A	p.Glu1243Lys	p.E1243K	ENST00000218089	NM_001042749.1	1243	Gag/Aag	34/35	0.203145792915326	1	FACETS	0.42	0.386	0.456	0.42	0.386	0.456	INDETERMINATE	1	TRUE	0	0.8	1		528	521	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979986	7979987	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs746723399	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	97	374	0	ENST00000319144.4:c.1350dup	p.Leu451AlafsTer27	p.L451Afs*27	ENST00000319144	NM_001139.2	450	-/G	10/15	1	2	FACETS	0.777	0.701	0.856	0.777	0.701	0.856	SUBCLONAL	1	TRUE	1	0.8	2		374	312	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100408	157100409	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGT	novel	NA	P-0012358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	28	86	0	ENST00000346085.5:c.1347_1348insTCG	p.Pro449_Pro450insSer	p.P449_P450insS	ENST00000346085	NM_020732.3	449	ccg/cCGTcg	1/20	0.282046453132761	3	FACETS	0.907	0.741	1	0.454	0.37	0.544	INDETERMINATE	1	TRUE	1	0.8	3		86	108	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582439	119582439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775606264	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	56	254	0	ENST00000316626.5:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000316626		321	cGa/cAa	10/12	1	2	FACETS	0.79	0.678	0.912	0.79	0.678	0.912	CLONAL	1	TRUE	1	0.32	2		254	443	SUCCESS
B2M	567	MSKCC	GRCh37	15	45008529	45008529	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	99	708	0	ENST00000558401.1:c.349C>T	p.Arg117Ter	p.R117*	ENST00000558401	NM_004048.2	117	Cga/Tga	3/4	1	2	FACETS	0.745	0.665	0.831	0.745	0.665	0.831	SUBCLONAL	1	TRUE	1	0.32	2		708	830	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115600	108115600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772821016	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	116	618	0	ENST00000278616.4:c.748C>T	p.Arg250Ter	p.R250*	ENST00000278616	NM_000051.3	250	Cga/Tga	7/63	1	2	FACETS	0.793	0.714	0.877	0.793	0.714	0.877	SUBCLONAL	1	TRUE	1	0.32	2		618	914	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169179	119169179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150811339	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	114	503	0	ENST00000264033.4:c.2363G>A	p.Arg788Gln	p.R788Q	ENST00000264033	NM_005188.3	788	cGa/cAa	15/16	1	2	FACETS	0.965	0.87	1	0.965	0.87	1	CLONAL	1	TRUE	1	0.32	2		503	738	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	127	534	0	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	1	2	FACETS	0.882	0.798	0.97	0.882	0.798	0.97	CLONAL	1	TRUE	1	0.32	2		534	900	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251595	212251595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1044752647	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	117	514	1	ENST00000342788.4:c.3464G>A	p.Arg1155Gln	p.R1155Q	ENST00000342788	NM_005235.2	1155	cGa/cAa	27/28	1	2	FACETS	0.999	0.902	1	0.999	0.902	1	CLONAL	1	TRUE	1	0.32	2		515	732	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	136	265	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.864	0.784	0.947	0.864	0.784	0.947	CLONAL	1	TRUE	1	0.32	2		265	984	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	191	809	0	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	0.32	2		809	1144	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900288	101900288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111854391	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	136	763	3	ENST00000374994.4:c.722C>T	p.Ser241Leu	p.S241L	ENST00000374994	NM_004612.2	241	tCg/tTg	4/9	1	2	FACETS	0.784	0.712	0.861	0.784	0.712	0.861	SUBCLONAL	1	TRUE	1	0.32	2		766	1084	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	80	275	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.899	0.793	1	0.899	0.793	1	CLONAL	1	TRUE	1	0.32	2		275	556	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587777894	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	102	642	0	ENST00000361445.4:c.6644C>A	p.Ser2215Tyr	p.S2215Y	ENST00000361445	NM_004958.3	2215	tCt/tAt	47/58	1	2	FACETS	0.747	0.668	0.832	0.747	0.668	0.832	SUBCLONAL	1	TRUE	1	0.32	2		642	853	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	110	500	1	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.979	0.881	1	0.979	0.881	1	CLONAL	1	TRUE	1	0.32	2		501	702	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967279	38967279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746828213	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	77	514	0	ENST00000357387.3:c.1202G>A	p.Arg401His	p.R401H	ENST00000357387	NM_152756.3	401	cGt/cAt	14/38	1	2	FACETS	0.754	0.662	0.853	0.754	0.662	0.853	SUBCLONAL	1	TRUE	1	0.32	2		514	638	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453486	138453486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451809865	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	62	619	0	ENST00000289153.2:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000289153	NM_006219.2	321	cGa/cAa	5/22	1	2	FACETS	0.427	0.367	0.492	0.427	0.367	0.492	SUBCLONAL	1	TRUE	1	0.32	2		619	908	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089730	27089730	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	88	339	0	ENST00000324856.7:c.2686G>T	p.Glu896Ter	p.E896*	ENST00000324856	NM_006015.4	896	Gaa/Taa	8/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.32	2		339	505	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509723	106509723	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	108	606	2	ENST00000359195.3:c.1717G>T	p.Glu573Ter	p.E573*	ENST00000359195	NM_002649.2	573	Gaa/Taa	2/11	1	2	FACETS	0.839	0.752	0.93	0.839	0.752	0.93	CLONAL	1	TRUE	1	0.32	2		608	805	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63661997	63661997	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	109	495	0	ENST00000279873.7:c.101G>T	p.Arg34Ile	p.R34I	ENST00000279873	NM_032199.2	34	aGa/aTa	2/10	1	2	FACETS	0.871	0.782	0.965	0.871	0.782	0.965	CLONAL	1	TRUE	1	0.32	2		495	782	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907000	32907000	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs56403624	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	64	368	0	ENST00000380152.3:c.1385A>G	p.Glu462Gly	p.E462G	ENST00000380152		462	gAa/gGa	10/27	1	2	FACETS	0.833	0.723	0.952	0.833	0.723	0.952	CLONAL	1	TRUE	1	0.32	2		368	480	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956552	93956552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754119070	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	192	945	0	ENST00000369303.4:c.2684G>A	p.Arg895Gln	p.R895Q	ENST00000369303	NM_004440.3	895	cGa/cAa	15/17	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.32	2		945	1190	SUCCESS
APC	324	MSKCC	GRCh37	5	112175162	112175162	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561588104	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	51	245	0	ENST00000257430.4:c.3871C>T	p.Gln1291Ter	p.Q1291*	ENST00000257430	NM_000038.5	1291	Cag/Tag	16/16	1	2	FACETS	0.906	0.773	1	0.906	0.773	1	CLONAL	1	TRUE	1	0.32	2		245	352	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs770248150	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	95	617	0	ENST00000311936.3:c.351A>C	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaC	4/5	1	2	FACETS	0.928	0.827	1	0.928	0.827	1	CLONAL	1	TRUE	1	0.32	2		617	640	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976476	25976476	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	159	830	0	ENST00000435504.4:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000435504		357	Cga/Tga	11/13	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.32	2		830	969	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322774	30322774	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	24	360	0	ENST00000322652.5:c.1787C>A	p.Thr596Asn	p.T596N	ENST00000322652	NM_015355.2	596	aCc/aAc	14/16	1	2	FACETS	0.346	0.27	0.433	0.346	0.27	0.433	SUBCLONAL	1	TRUE	1	0.32	2		360	434	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932714	49932714	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748943477	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	192	930	2	ENST00000296474.3:c.3157C>T	p.Arg1053Trp	p.R1053W	ENST00000296474	NM_002447.2	1053	Cgg/Tgg	14/20	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.32	2		932	1159	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197563	106197563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745668941	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	138	748	1	ENST00000380013.4:c.5896C>T	p.Arg1966Cys	p.R1966C	ENST00000380013	NM_001127208.2	1966	Cgt/Tgt	11/11	1	2	FACETS	0.906	0.824	0.993	0.906	0.824	0.993	CLONAL	1	TRUE	1	0.32	2		749	952	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681476	30681476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756890775	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	118	615	0	ENST00000376406.3:c.536G>A	p.Arg179His	p.R179H	ENST00000376406	NM_014641.2	179	cGt/cAt	4/15	1	2	FACETS	0.879	0.793	0.97	0.879	0.793	0.97	CLONAL	1	TRUE	1	0.32	2		615	839	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856364	111856364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	24	219	1	ENST00000341259.2:c.415C>T	p.Arg139Cys	p.R139C	ENST00000341259	NM_005475.2	139	Cgc/Tgc	2/8	1	2	FACETS	0.453	0.355	0.566	0.453	0.355	0.566	SUBCLONAL	1	TRUE	1	0.32	2		220	331	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968610	55968610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374980446	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	182	792	0	ENST00000263923.4:c.2053G>A	p.Glu685Lys	p.E685K	ENST00000263923	NM_002253.2	685	Gaa/Aaa	14/30	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.32	2		792	1015	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16040679	16040679	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	122	651	0	ENST00000268712.3:c.1455G>T	p.Glu485Asp	p.E485D	ENST00000268712	NM_006311.3	485	gaG/gaT	14/46	1	2	FACETS	0.96	0.868	1	0.96	0.868	1	CLONAL	1	TRUE	1	0.32	2		651	794	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073667	8073667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749196844	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1291	146	949	1	ENST00000377482.5:c.992G>A	p.Arg331His	p.R331H	ENST00000377482	NM_018948.3	331	cGc/cAc	4/4	1	2	FACETS	0.635	0.577	0.696	0.635	0.577	0.696	SUBCLONAL	1	TRUE	1	0.32	2		950	1437	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983275	149983275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	104	492	1	ENST00000253339.5:c.2983C>T	p.Arg995Cys	p.R995C	ENST00000253339		995	Cgc/Tgc	7/7	1	2	FACETS	0.805	0.721	0.895	0.805	0.721	0.895	CLONAL	1	TRUE	1	0.32	2		493	807	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372343	55372343	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	63	361	0	ENST00000297316.4:c.1033G>A	p.Gly345Ser	p.G345S	ENST00000297316	NM_022454.3	345	Ggc/Agc	2/2	1	2	FACETS	0.712	0.616	0.816	0.712	0.616	0.816	SUBCLONAL	1	TRUE	1	0.32	2		361	553	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118821	61118821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146326268	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	73	408	2	ENST00000295025.8:c.14C>T	p.Ala5Val	p.A5V	ENST00000295025	NM_002908.2	5	gCg/gTg	2/11	1	2	FACETS	0.741	0.648	0.841	0.741	0.648	0.841	SUBCLONAL	1	TRUE	1	0.32	2		410	616	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42002918	42002918	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	147	835	1	ENST00000219905.7:c.2455C>T	p.Arg819Cys	p.R819C	ENST00000219905	NM_001164273.1	819	Cgt/Tgt	8/24	1	2	FACETS	0.91	0.83	0.994	0.91	0.83	0.994	CLONAL	1	TRUE	1	0.32	2		836	1010	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698180	47698180	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63751411	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	64	448	2	ENST00000233146.2:c.1738G>T	p.Glu580Ter	p.E580*	ENST00000233146	NM_000251.2	580	Gaa/Taa	11/16	1	2	FACETS	0.678	0.587	0.776	0.678	0.587	0.776	SUBCLONAL	1	TRUE	1	0.32	2		450	590	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877154	151877154	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs767365126	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	119	527	0	ENST00000262189.6:c.7207C>T	p.Arg2403Ter	p.R2403*	ENST00000262189	NM_170606.2	2403	Cga/Tga	37/59	1	2	FACETS	0.997	0.9	1	0.997	0.9	1	CLONAL	1	TRUE	1	0.32	2		527	746	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6031648	6031648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs116314131	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	120	512	2	ENST00000265849.7:c.944G>A	p.Arg315Gln	p.R315Q	ENST00000265849	NM_000535.5	315	cGa/cAa	9/15	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.32	2		514	719	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554305	81554305	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777252114	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	140	817	1	ENST00000298171.2:c.325C>T	p.Arg109Trp	p.R109W	ENST00000298171	NM_000369.2	109	Cgg/Tgg	4/10	1	2	FACETS	0.954	0.869	1	0.954	0.869	1	CLONAL	1	TRUE	1	0.32	2		818	917	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260146	10260146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751754286	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	138	650	3	ENST00000340748.4:c.2521G>A	p.Glu841Lys	p.E841K	ENST00000340748		841	Gaa/Aaa	25/40	1	2	FACETS	0.979	0.891	1	0.979	0.891	1	CLONAL	1	TRUE	1	0.32	2		653	881	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765576	41765576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763066660	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	130	714	0	ENST00000301178.4:c.2452G>A	p.Glu818Lys	p.E818K	ENST00000301178	NM_021913.4	818	Gaa/Aaa	20/20	1	2	FACETS	0.921	0.835	1	0.921	0.835	1	CLONAL	1	TRUE	1	0.32	2		714	882	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39690066	39690066	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	61	320	0	ENST00000361337.2:c.91C>T	p.Arg31Ter	p.R31*	ENST00000361337	NM_003286.2	31	Cga/Tga	3/21	1	2	FACETS	0.572	0.493	0.659	0.572	0.493	0.659	SUBCLONAL	1	TRUE	1	0.32	2		320	666	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325170	123325170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371358242	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	108	539	0	ENST00000358487.5:c.158C>T	p.Ala53Val	p.A53V	ENST00000358487	NM_000141.4	53	gCg/gTg	3/18	1	2	FACETS	0.915	0.821	1	0.915	0.821	1	CLONAL	1	TRUE	1	0.32	2		539	738	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343913	118343913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264831726	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	114	503	0	ENST00000534358.1:c.2039C>T	p.Ser680Leu	p.S680L	ENST00000534358	NM_005933.3	680	tCg/tTg	3/36	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.32	2		503	680	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727423	66727423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1049040928	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	81	488	3	ENST00000307102.5:c.139C>T	p.Arg47Ter	p.R47*	ENST00000307102	NM_002755.3	47	Cga/Tga	2/11	1	2	FACETS	0.724	0.638	0.817	0.724	0.638	0.817	SUBCLONAL	1	TRUE	1	0.32	2		491	699	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028618	12028618	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	131	623	0	ENST00000353533.5:c.821G>T	p.Arg274Ile	p.R274I	ENST00000353533	NM_003010.3	274	aGa/aTa	8/11	1	2	FACETS	0.947	0.859	1	0.947	0.859	1	CLONAL	1	TRUE	1	0.32	2		623	865	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236086	108236086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782292	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	126	604	1	ENST00000278616.4:c.9022C>T	p.Arg3008Cys	p.R3008C	ENST00000278616	NM_000051.3	3008	Cgt/Tgt	63/63	1	2	FACETS	0.844	0.763	0.929	0.844	0.763	0.929	CLONAL	1	TRUE	1	0.32	2		605	933	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916726	178916726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772110575	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	172	878	2	ENST00000263967.3:c.113G>A	p.Arg38His	p.R38H	ENST00000263967	NM_006218.2	38	cGt/cAt	2/21	1	2	FACETS	0.891	0.818	0.967	0.891	0.818	0.967	CLONAL	1	TRUE	1	0.32	2		880	1207	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953228	81953228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369760877	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	163	874	7	ENST00000359376.3:c.2194C>T	p.Arg732Cys	p.R732C	ENST00000359376	NM_002661.3	732	Cgc/Tgc	20/33	1	2	FACETS	0.919	0.842	0.999	0.919	0.842	0.999	CLONAL	1	TRUE	1	0.32	2		881	1109	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510225	187510225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	141	690	3	ENST00000441802.2:c.13288G>A	p.Asp4430Asn	p.D4430N	ENST00000441802	NM_005245.3	4430	Gac/Aac	27/27	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.32	2		693	843	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285669	46285669	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1368075571	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	117	550	0	ENST00000334344.6:c.5029C>T	p.Arg1677Ter	p.R1677*	ENST00000334344	NM_152641.2	1677	Cga/Tga	17/21	1	2	FACETS	0.877	0.79	0.968	0.877	0.79	0.968	CLONAL	1	TRUE	1	0.32	2		550	834	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	120	709	0	ENST00000320574.5:c.1231G>C	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ctg	13/49	1	2	FACETS	0.999	0.902	1	0.999	0.902	1	CLONAL	1	TRUE	1	0.32	2		709	751	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508059	106508059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142380460	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	72	280	0	ENST00000359195.3:c.53G>A	p.Arg18Gln	p.R18Q	ENST00000359195	NM_002649.2	18	cGa/cAa	2/11	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.32	2		280	416	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363091	40363091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142406322	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	150	632	0	ENST00000397332.2:c.1138C>T	p.Arg380Trp	p.R380W	ENST00000397332	NM_001033082.2	380	Cgg/Tgg	3/3	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.32	2		632	906	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281544	198281544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	167	722	0	ENST00000335508.6:c.587G>A	p.Arg196Gln	p.R196Q	ENST00000335508	NM_012433.2	196	cGa/cAa	6/25	1	2	FACETS	0.952	0.874	1	0.952	0.874	1	CLONAL	1	TRUE	1	0.32	2		722	1096	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665261	117665261	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1158871186	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	91	545	1	ENST00000368508.3:c.4486G>T	p.Asp1496Tyr	p.D1496Y	ENST00000368508	NM_002944.2	1496	Gac/Tac	27/43	1	2	FACETS	0.74	0.656	0.829	0.74	0.656	0.829	SUBCLONAL	1	TRUE	1	0.32	2		546	769	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763428	59763428	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	92	499	0	ENST00000259008.2:c.2674C>A	p.Leu892Ile	p.L892I	ENST00000259008	NM_032043.2	892	Ctt/Att	19/20	1	2	FACETS	0.877	0.779	0.98	0.877	0.779	0.98	CLONAL	1	TRUE	1	0.32	2		499	656	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252940	36252940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	131	522	0	ENST00000300305.3:c.422C>T	p.Ser141Leu	p.S141L	ENST00000300305		141	tCg/tTg	4/8	1	2	FACETS	0.962	0.873	1	0.962	0.873	1	CLONAL	1	TRUE	1	0.32	2		522	851	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163458	108163458	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	129	693	1	ENST00000278616.4:c.4549C>A	p.Leu1517Ile	p.L1517I	ENST00000278616	NM_000051.3	1517	Ctt/Att	30/63	1	2	FACETS	0.879	0.797	0.966	0.879	0.797	0.966	CLONAL	1	TRUE	1	0.32	2		694	917	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181926	38181926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1559484615	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	97	550	1	ENST00000396334.3:c.550G>A	p.Asp184Asn	p.D184N	ENST00000396334	NM_002468.4	184	Gac/Aac	3/5	1	2	FACETS	0.843	0.752	0.94	0.843	0.752	0.94	CLONAL	1	TRUE	1	0.32	2		551	719	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489229	2489229	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	144	784	0	ENST00000355716.4:c.134A>G	p.Asp45Gly	p.D45G	ENST00000355716	NM_003820.2	45	gAc/gGc	2/8	1	2	FACETS	0.933	0.85	1	0.933	0.85	1	CLONAL	1	TRUE	1	0.32	2		784	965	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188180	11188180	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	64	332	0	ENST00000361445.4:c.5914C>T	p.Leu1972Phe	p.L1972F	ENST00000361445	NM_004958.3	1972	Ctc/Ttc	43/58	1	2	FACETS	0.82	0.711	0.937	0.82	0.711	0.937	CLONAL	1	TRUE	1	0.32	2		332	488	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932164	36932164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201556754	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	171	888	4	ENST00000361632.4:c.2305C>T	p.Arg769Cys	p.R769C	ENST00000361632		769	Cgc/Tgc	16/16	1	2	FACETS	0.972	0.893	1	0.972	0.893	1	CLONAL	1	TRUE	1	0.32	2		892	1099	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804370	43804370	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	153	613	1	ENST00000372470.3:c.370G>T	p.Val124Phe	p.V124F	ENST00000372470	NM_005373.2	124	Gtc/Ttc	3/12	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.32	2		614	821	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511630	46511630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773472193	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	130	670	0	ENST00000262741.5:c.1147C>T	p.Arg383Cys	p.R383C	ENST00000262741	NM_003629.3	383	Cgt/Tgt	9/10	1	2	FACETS	0.929	0.842	1	0.929	0.842	1	CLONAL	1	TRUE	1	0.32	2		670	875	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531829	46531829	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs749759127	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	79	645	0	ENST00000262741.5:c.518A>C	p.Asn173Thr	p.N173T	ENST00000262741	NM_003629.3	173	aAt/aCt	5/10	1	2	FACETS	0.77	0.678	0.87	0.77	0.678	0.87	SUBCLONAL	1	TRUE	1	0.32	2		645	641	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733461	85733461	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1228	227	1063	0	ENST00000370580.1:c.551A>C	p.Asn184Thr	p.N184T	ENST00000370580	NM_003921.4	184	aAt/aCt	3/3	1	2	FACETS	0.975	0.906	1	0.975	0.906	1	CLONAL	1	TRUE	1	0.32	2		1063	1455	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736321	85736321	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs764598279	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	166	783	0	ENST00000370580.1:c.326T>C	p.Ile109Thr	p.I109T	ENST00000370580	NM_003921.4	109	aTa/aCa	2/3	1	2	FACETS	0.956	0.877	1	0.956	0.877	1	CLONAL	1	TRUE	1	0.32	2		783	1085	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115251227	115251227	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	160	707	3	ENST00000369535.4:c.499C>T	p.Arg167Ter	p.R167*	ENST00000369535	NM_002524.4	167	Cga/Tga	5/7	1	2	FACETS	0.915	0.838	0.996	0.915	0.838	0.996	CLONAL	1	TRUE	1	0.32	2		710	1093	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551757	150551757	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	24	138	0	ENST00000369026.2:c.250G>T	p.Ala84Ser	p.A84S	ENST00000369026	NM_021960.4	84	Gcc/Tcc	1/3	1	2	FACETS	0.769	0.607	0.954	0.769	0.607	0.954	CLONAL	1	TRUE	1	0.32	2		138	195	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874172	155874172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753425443	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	172	728	1	ENST00000368323.3:c.359G>A	p.Arg120Gln	p.R120Q	ENST00000368323	NM_006912.5	120	cGa/cAa	5/6	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.32	2		729	1064	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725452	162725452	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	131	637	0	ENST00000367921.3:c.566-2A>G		p.X189_splice	ENST00000367921	NM_006182.2	189			1	2	FACETS	0.896	0.812	0.984	0.896	0.812	0.984	CLONAL	1	TRUE	1	0.32	2		637	914	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809195	243809195	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	50	603	0	ENST00000263826.5:c.429G>T	p.Lys143Asn	p.K143N	ENST00000263826	NM_005465.4	143	aaG/aaT	4/13	1	2	FACETS	0.427	0.361	0.499	0.427	0.361	0.499	SUBCLONAL	1	TRUE	1	0.32	2		603	732	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085689	16085689	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	111	617	0	ENST00000281043.3:c.865T>C	p.Ser289Pro	p.S289P	ENST00000281043	NM_005378.4	289	Tcc/Ccc	3/3	1	2	FACETS	0.855	0.769	0.947	0.855	0.769	0.947	CLONAL	1	TRUE	1	0.32	2		617	811	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470522	25470522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	129	614	2	ENST00000264709.3:c.952C>T	p.Arg318Trp	p.R318W	ENST00000264709	NM_175629.2	318	Cgg/Tgg	8/23	1	2	FACETS	0.874	0.791	0.96	0.874	0.791	0.96	CLONAL	1	TRUE	1	0.32	2		616	923	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965940	25965940	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs373514519	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	121	596	0	ENST00000435504.4:c.3266A>G	p.Asn1089Ser	p.N1089S	ENST00000435504		1089	aAc/aGc	13/13	1	2	FACETS	0.878	0.793	0.968	0.878	0.793	0.968	CLONAL	1	TRUE	1	0.32	2		596	861	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451881	29451881	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	152	733	0	ENST00000389048.3:c.2684C>A	p.Ser895Tyr	p.S895Y	ENST00000389048	NM_004304.4	895	tCt/tAt	16/29	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.32	2		733	893	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637243	47637243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	102	463	0	ENST00000233146.2:c.377G>A	p.Gly126Asp	p.G126D	ENST00000233146	NM_000251.2	126	gGc/gAc	3/16	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.32	2		463	634	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033605	48033605	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	38	310	0	ENST00000234420.5:c.3816A>C	p.Glu1272Asp	p.E1272D	ENST00000234420	NM_000179.2	1272	gaA/gaC	9/10	1	2	FACETS	0.637	0.527	0.759	0.637	0.527	0.759	SUBCLONAL	1	TRUE	1	0.32	2		310	373	SUCCESS
REL	5966	MSKCC	GRCh37	2	61128173	61128173	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	61	291	0	ENST00000295025.8:c.349G>T	p.Glu117Ter	p.E117*	ENST00000295025	NM_002908.2	117	Gaa/Taa	4/11	1	2	FACETS	0.784	0.678	0.9	0.784	0.678	0.9	SUBCLONAL	1	TRUE	1	0.32	2		291	486	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61713094	61713094	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1272790060	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	83	391	2	ENST00000401558.2:c.2317G>A	p.Ala773Thr	p.A773T	ENST00000401558	NM_003400.3	773	Gct/Act	20/25	1	2	FACETS	0.957	0.847	1	0.957	0.847	1	CLONAL	1	TRUE	1	0.32	2		393	542	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61753652	61753652	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	70	396	0	ENST00000401558.2:c.131G>T	p.Arg44Ile	p.R44I	ENST00000401558	NM_003400.3	44	aGa/aTa	3/25	1	2	FACETS	0.923	0.807	1	0.923	0.807	1	CLONAL	1	TRUE	1	0.32	2		396	474	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095695	178095695	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	175	752	0	ENST00000397062.3:c.1636A>C	p.Asn546His	p.N546H	ENST00000397062	NM_006164.4	546	Aat/Cat	5/5	1	2	FACETS	0.906	0.833	0.983	0.906	0.833	0.983	CLONAL	1	TRUE	1	0.32	2		752	1207	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190742014	190742014	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	111	544	0	ENST00000441310.2:c.2651T>A	p.Leu884Gln	p.L884Q	ENST00000441310	NM_000534.4	884	cTa/cAa	13/13	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.32	2		544	677	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198262793	198262793	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	137	537	0	ENST00000335508.6:c.3182A>C	p.Glu1061Ala	p.E1061A	ENST00000335508	NM_012433.2	1061	gAg/gCg	22/25	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.32	2		537	810	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137487	202137487	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	137	440	0	ENST00000358485.4:c.715G>T	p.Glu239Ter	p.E239*	ENST00000358485	NM_001080125.1	239	Gaa/Taa	4/9	1	2	FACETS	0.911	0.828	0.998	0.911	0.828	0.998	CLONAL	1	TRUE	1	0.32	2		440	940	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149601	202149601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	147	694	1	ENST00000358485.4:c.1042G>A	p.Val348Ile	p.V348I	ENST00000358485	NM_001080125.1	348	Gta/Ata	8/9	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.32	2		695	893	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576844	212576844	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	109	578	0	ENST00000342788.4:c.1055A>G	p.Asn352Ser	p.N352S	ENST00000342788	NM_005235.2	352	aAc/aGc	9/28	1	2	FACETS	0.941	0.845	1	0.941	0.845	1	CLONAL	1	TRUE	1	0.32	2		578	724	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652753	212652753	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	94	555	0	ENST00000342788.4:c.553G>T	p.Gly185Ter	p.G185*	ENST00000342788	NM_005235.2	185	Gga/Tga	4/28	1	2	FACETS	0.804	0.715	0.898	0.804	0.715	0.898	CLONAL	1	TRUE	1	0.32	2		555	731	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215595211	215595211	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	65	621	1	ENST00000260947.4:c.1925G>T	p.Arg642Ile	p.R642I	ENST00000260947	NM_000465.2	642	aGa/aTa	10/11	1	2	FACETS	0.509	0.44	0.584	0.509	0.44	0.584	SUBCLONAL	1	TRUE	1	0.32	2		622	798	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439864	220439864	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	135	858	0	ENST00000243786.2:c.717G>C	p.Trp239Cys	p.W239C	ENST00000243786	NM_002191.3	239	tgG/tgC	2/2	1	2	FACETS	0.789	0.716	0.867	0.789	0.716	0.867	SUBCLONAL	1	TRUE	1	0.32	2		858	1069	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660327	227660327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	44	296	0	ENST00000305123.5:c.3128C>T	p.Ser1043Phe	p.S1043F	ENST00000305123	NM_005544.2	1043	tCc/tTc	1/2	1	2	FACETS	0.831	0.699	0.975	0.831	0.699	0.975	CLONAL	1	TRUE	1	0.32	2		296	331	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686286	30686286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	139	549	0	ENST00000295754.5:c.142C>T	p.Pro48Ser	p.P48S	ENST00000295754	NM_003242.5	48	Cca/Tca	2/7	1	2	FACETS	0.887	0.807	0.972	0.887	0.807	0.972	CLONAL	1	TRUE	1	0.32	2		549	979	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161694	47161694	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	137	660	0	ENST00000409792.3:c.4432G>T	p.Glu1478Ter	p.E1478*	ENST00000409792	NM_014159.6	1478	Gaa/Taa	3/21	1	2	FACETS	0.991	0.901	1	0.991	0.901	1	CLONAL	1	TRUE	1	0.32	2		660	864	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165106	47165106	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	58	380	0	ENST00000409792.3:c.1020A>C	p.Lys340Asn	p.K340N	ENST00000409792	NM_014159.6	340	aaA/aaC	3/21	1	2	FACETS	0.626	0.538	0.722	0.626	0.538	0.722	SUBCLONAL	1	TRUE	1	0.32	2		380	579	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623223	52623223	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	93	563	0	ENST00000394830.3:c.2828T>C	p.Leu943Ser	p.L943S	ENST00000394830	NM_018313.4	943	tTa/tCa	19/30	1	2	FACETS	0.727	0.645	0.813	0.727	0.645	0.813	SUBCLONAL	1	TRUE	1	0.32	2		563	800	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027140	71027140	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765161575	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	95	510	0	ENST00000318789.4:c.1187C>T	p.Ser396Leu	p.S396L	ENST00000318789	NM_032682.5	396	tCg/tTg	15/21	1	2	FACETS	0.81	0.721	0.905	0.81	0.721	0.905	CLONAL	1	TRUE	1	0.32	2		510	733	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259016	89259016	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	68	255	0	ENST00000336596.2:c.160G>A	p.Glu54Lys	p.E54K	ENST00000336596	NM_005233.5	54	Gag/Aag	3/17	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.32	2		255	360	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259578	89259578	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	77	409	0	ENST00000336596.2:c.722G>T	p.Arg241Met	p.R241M	ENST00000336596	NM_005233.5	241	aGg/aTg	3/17	1	2	FACETS	0.858	0.754	0.969	0.858	0.754	0.969	CLONAL	1	TRUE	1	0.32	2		409	561	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448485	89448485	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	90	509	0	ENST00000336596.2:c.1449T>G	p.Ser483Arg	p.S483R	ENST00000336596	NM_005233.5	483	agT/agG	7/17	1	2	FACETS	0.879	0.781	0.984	0.879	0.781	0.984	CLONAL	1	TRUE	1	0.32	2		509	640	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457220	89457220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	74	430	0	ENST00000336596.2:c.1701C>A	p.Phe567Leu	p.F567L	ENST00000336596	NM_005233.5	567	ttC/ttA	9/17	1	2	FACETS	0.91	0.799	1	0.91	0.799	1	CLONAL	1	TRUE	1	0.32	2		430	508	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138400852	138400852	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1455285725	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	84	739	1	ENST00000289153.2:c.2461C>T	p.Arg821Cys	p.R821C	ENST00000289153	NM_006219.2	821	Cgc/Tgc	17/22	1	2	FACETS	0.531	0.468	0.599	0.531	0.468	0.599	SUBCLONAL	1	TRUE	1	0.32	2		740	989	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417818	138417818	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	144	682	1	ENST00000289153.2:c.1701G>T	p.Glu567Asp	p.E567D	ENST00000289153	NM_006219.2	567	gaG/gaT	11/22	1	2	FACETS	0.954	0.87	1	0.954	0.87	1	CLONAL	1	TRUE	1	0.32	2		683	943	SUCCESS
ATR	545	MSKCC	GRCh37	3	142180893	142180893	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	99	596	0	ENST00000350721.4:c.7081C>A	p.His2361Asn	p.H2361N	ENST00000350721	NM_001184.3	2361	Cat/Aat	42/47	1	2	FACETS	0.982	0.878	1	0.982	0.878	1	CLONAL	1	TRUE	1	0.32	2		596	630	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274755	142274755	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1489808838	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	90	471	1	ENST00000350721.4:c.2305C>A	p.Leu769Ile	p.L769I	ENST00000350721	NM_001184.3	769	Cta/Ata	10/47	1	2	FACETS	0.933	0.829	1	0.933	0.829	1	CLONAL	1	TRUE	1	0.32	2		472	603	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275252	142275252	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	113	585	0	ENST00000350721.4:c.2051C>A	p.Ser684Tyr	p.S684Y	ENST00000350721	NM_001184.3	684	tCt/tAt	9/47	1	2	FACETS	0.891	0.801	0.985	0.891	0.801	0.985	CLONAL	1	TRUE	1	0.32	2		585	793	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184727	185184727	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	143	649	0	ENST00000265026.3:c.1619A>G	p.His540Arg	p.H540R	ENST00000265026	NM_004721.4	540	cAc/cGc	10/14	1	2	FACETS	0.937	0.853	1	0.937	0.853	1	CLONAL	1	TRUE	1	0.32	2		649	954	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526295	189526295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	101	386	4	ENST00000264731.3:c.559G>A	p.Ala187Thr	p.A187T	ENST00000264731	NM_003722.4	187	Gcc/Acc	4/14	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.32	2		390	569	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750542	41750542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	103	598	0	ENST00000226382.2:c.86C>T	p.Ala29Val	p.A29V	ENST00000226382	NM_003924.3	29	gCc/gTc	1/3	1	2	FACETS	0.893	0.799	0.992	0.893	0.799	0.992	CLONAL	1	TRUE	1	0.32	2		598	721	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55130038	55130038	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	133	642	1	ENST00000257290.5:c.572C>T	p.Ala191Val	p.A191V	ENST00000257290	NM_006206.4	191	gCc/gTc	4/23	1	2	FACETS	0.828	0.751	0.909	0.828	0.751	0.909	CLONAL	1	TRUE	1	0.32	2		643	1004	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218771	66218771	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	92	686	0	ENST00000273854.3:c.2287A>G	p.Thr763Ala	p.T763A	ENST00000273854	NM_004439.5	763	Aca/Gca	13/18	1	2	FACETS	0.692	0.614	0.775	0.692	0.614	0.775	SUBCLONAL	1	TRUE	1	0.32	2		686	831	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231761	66231761	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	88	486	0	ENST00000273854.3:c.1939G>T	p.Val647Leu	p.V647L	ENST00000273854	NM_004439.5	647	Gta/Tta	11/18	1	2	FACETS	0.814	0.721	0.912	0.814	0.721	0.912	CLONAL	1	TRUE	1	0.32	2		486	676	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467917	66467917	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	121	657	0	ENST00000273854.3:c.352A>G	p.Ile118Val	p.I118V	ENST00000273854	NM_004439.5	118	Atc/Gtc	3/18	1	2	FACETS	0.975	0.881	1	0.975	0.881	1	CLONAL	1	TRUE	1	0.32	2		657	776	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467948	66467948	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	62	675	0	ENST00000273854.3:c.321G>T	p.Gln107His	p.Q107H	ENST00000273854	NM_004439.5	107	caG/caT	3/18	1	2	FACETS	0.487	0.42	0.561	0.487	0.42	0.561	SUBCLONAL	1	TRUE	1	0.32	2		675	795	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84406219	84406219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370520589	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	96	456	1	ENST00000321945.7:c.7G>A	p.Gly3Arg	p.G3R	ENST00000321945	NM_139076.2	3	Ggg/Agg	1/9	1	2	FACETS	0.926	0.826	1	0.926	0.826	1	CLONAL	1	TRUE	1	0.32	2		457	648	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081579	143081579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	125	619	0	ENST00000262992.4:c.1495G>A	p.Asp499Asn	p.D499N	ENST00000262992	NM_001101669.1	499	Gac/Aac	15/24	1	2	FACETS	0.825	0.746	0.909	0.825	0.746	0.909	CLONAL	1	TRUE	1	0.32	2		619	947	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081594	143081594	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	124	627	0	ENST00000262992.4:c.1480G>T	p.Glu494Ter	p.E494*	ENST00000262992	NM_001101669.1	494	Gag/Tag	15/24	1	2	FACETS	0.826	0.747	0.91	0.826	0.747	0.91	CLONAL	1	TRUE	1	0.32	2		627	938	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249456	153249456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	138	685	1	ENST00000281708.4:c.1322G>A	p.Arg441Gln	p.R441Q	ENST00000281708	NM_033632.3	441	cGg/cAg	9/12	1	2	FACETS	0.951	0.865	1	0.951	0.865	1	CLONAL	1	TRUE	1	0.32	2		686	907	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628622	187628622	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	154	708	0	ENST00000441802.2:c.2360A>C	p.Lys787Thr	p.K787T	ENST00000441802	NM_005245.3	787	aAa/aCa	2/27	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.32	2		708	916	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952460	38952460	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	105	444	0	ENST00000357387.3:c.2965A>G	p.Asn989Asp	p.N989D	ENST00000357387	NM_152756.3	989	Aac/Gac	30/38	1	2	FACETS	0.961	0.862	1	0.961	0.862	1	CLONAL	1	TRUE	1	0.32	2		444	683	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753031	57753031	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs139008001	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	136	639	0	ENST00000274289.3:c.985A>G	p.Ile329Val	p.I329V	ENST00000274289	NM_006622.3	329	Att/Gtt	7/14	1	2	FACETS	0.808	0.733	0.887	0.808	0.733	0.887	CLONAL	1	TRUE	1	0.32	2		639	1052	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86642542	86642542	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	38	325	0	ENST00000274376.6:c.1102+1G>A		p.X368_splice	ENST00000274376	NM_002890.2	368			1	2	FACETS	0.632	0.523	0.753	0.632	0.523	0.753	SUBCLONAL	1	TRUE	1	0.32	2		325	376	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659246	86659246	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	107	688	1	ENST00000274376.6:c.1535G>A	p.Arg512Gln	p.R512Q	ENST00000274376	NM_002890.2	512	cGa/cAa	11/25	1	2	FACETS	0.834	0.748	0.925	0.834	0.748	0.925	CLONAL	1	TRUE	1	0.32	2		689	802	SUCCESS
APC	324	MSKCC	GRCh37	5	112111411	112111411	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	83	482	0	ENST00000257430.4:c.508G>T	p.Asp170Tyr	p.D170Y	ENST00000257430	NM_000038.5	170	Gat/Tat	5/16	1	2	FACETS	0.913	0.807	1	0.913	0.807	1	CLONAL	1	TRUE	1	0.32	2		482	568	SUCCESS
APC	324	MSKCC	GRCh37	5	112173303	112173303	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	95	596	0	ENST00000257430.4:c.2012C>A	p.Ser671Tyr	p.S671Y	ENST00000257430	NM_000038.5	671	tCt/tAt	16/16	1	2	FACETS	0.84	0.748	0.938	0.84	0.748	0.938	CLONAL	1	TRUE	1	0.32	2		596	707	SUCCESS
APC	324	MSKCC	GRCh37	5	112177139	112177139	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	120	598	0	ENST00000257430.4:c.5848A>C	p.Lys1950Gln	p.K1950Q	ENST00000257430	NM_000038.5	1950	Aag/Cag	16/16	1	2	FACETS	0.862	0.778	0.951	0.862	0.778	0.951	CLONAL	1	TRUE	1	0.32	2		598	870	SUCCESS
APC	324	MSKCC	GRCh37	5	112177152	112177152	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	94	546	0	ENST00000257430.4:c.5861T>G	p.Phe1954Cys	p.F1954C	ENST00000257430	NM_000038.5	1954	tTt/tGt	16/16	1	2	FACETS	0.729	0.648	0.815	0.729	0.648	0.815	SUBCLONAL	1	TRUE	1	0.32	2		546	806	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944824	131944824	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	54	297	0	ENST00000265335.6:c.2845G>T	p.Glu949Ter	p.E949*	ENST00000265335		949	Gag/Tag	18/25	1	2	FACETS	0.809	0.693	0.936	0.809	0.693	0.936	CLONAL	1	TRUE	1	0.32	2		297	417	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562826	176562826	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	153	592	1	ENST00000439151.2:c.722G>T	p.Arg241Ile	p.R241I	ENST00000439151	NM_022455.4	241	aGa/aTa	2/23	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.32	2		593	893	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673310	30673310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140843115	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1273	279	1063	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	0.32	2		1064	1552	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181016	32181016	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	111	585	0	ENST00000375023.3:c.2334T>G	p.Asn778Lys	p.N778K	ENST00000375023	NM_004557.3	778	aaT/aaG	15/30	1	2	FACETS	0.873	0.784	0.966	0.873	0.784	0.966	CLONAL	1	TRUE	1	0.32	2		585	795	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32189077	32189077	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	81	540	0	ENST00000375023.3:c.477C>A	p.Phe159Leu	p.F159L	ENST00000375023	NM_004557.3	159	ttC/ttA	4/30	1	2	FACETS	0.728	0.642	0.822	0.728	0.642	0.822	SUBCLONAL	1	TRUE	1	0.32	2		540	695	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015685	112015685	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	176	849	0	ENST00000368678.4:c.1157G>T	p.Arg386Ile	p.R386I	ENST00000368678		386	aGa/aTa	11/13	1	2	FACETS	0.923	0.848	1	0.923	0.848	1	CLONAL	1	TRUE	1	0.32	2		849	1192	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117680985	117680985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771443531	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	99	420	2	ENST00000368508.3:c.3635G>A	p.Arg1212His	p.R1212H	ENST00000368508	NM_002944.2	1212	cGc/cAc	23/43	1	2	FACETS	0.962	0.86	1	0.962	0.86	1	CLONAL	1	TRUE	1	0.32	2		422	643	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681019	117681019	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	137	568	0	ENST00000368508.3:c.3601G>T	p.Gly1201Trp	p.G1201W	ENST00000368508	NM_002944.2	1201	Ggg/Tgg	23/43	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.32	2		568	847	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519451	137519451	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747769538	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	94	390	0	ENST00000367739.4:c.1187C>T	p.Ser396Leu	p.S396L	ENST00000367739	NM_000416.2	396	tCg/tTg	7/7	1	2	FACETS	0.992	0.885	1	0.992	0.885	1	CLONAL	1	TRUE	1	0.32	2		390	592	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519731	137519731	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	42	403	0	ENST00000367739.4:c.907A>G	p.Lys303Glu	p.K303E	ENST00000367739	NM_000416.2	303	Aaa/Gaa	7/7	1	2	FACETS	0.524	0.437	0.62	0.524	0.437	0.62	SUBCLONAL	1	TRUE	1	0.32	2		403	501	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527278	137527278	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146914620	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	116	568	2	ENST00000367739.4:c.368G>A	p.Arg123Gln	p.R123Q	ENST00000367739	NM_000416.2	123	cGa/cAa	3/7	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.32	2		570	710	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005447	150005447	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	142	707	1	ENST00000253339.5:c.778G>T	p.Gly260Cys	p.G260C	ENST00000253339		260	Ggt/Tgt	3/7	1	2	FACETS	0.898	0.818	0.983	0.898	0.818	0.983	CLONAL	1	TRUE	1	0.32	2		708	988	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162475133	162475133	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	103	737	0	ENST00000366898.1:c.608G>T	p.Gly203Val	p.G203V	ENST00000366898	NM_004562.2	203	gGg/gTg	5/12	1	2	FACETS	0.674	0.602	0.751	0.674	0.602	0.751	SUBCLONAL	1	TRUE	1	0.32	2		737	955	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974260	2974260	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	95	522	0	ENST00000396946.4:c.1345C>A	p.Leu449Met	p.L449M	ENST00000396946	NM_032415.4	449	Ctg/Atg	10/25	1	2	FACETS	0.896	0.798	0.999	0.896	0.798	0.999	CLONAL	1	TRUE	1	0.32	2		522	663	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468285	50468285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	69	386	0	ENST00000331340.3:c.1520C>T	p.Ser507Leu	p.S507L	ENST00000331340	NM_006060.4	507	tCg/tTg	8/8	1	2	FACETS	0.808	0.704	0.919	0.808	0.704	0.919	CLONAL	1	TRUE	1	0.32	2		386	534	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224510	55224510	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757265130	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	121	701	0	ENST00000275493.2:c.1192G>A	p.Val398Ile	p.V398I	ENST00000275493	NM_005228.3	398	Gta/Ata	10/28	1	2	FACETS	0.856	0.773	0.944	0.856	0.773	0.944	CLONAL	1	TRUE	1	0.32	2		701	883	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92404108	92404108	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	131	548	2	ENST00000265734.4:c.271G>T	p.Glu91Ter	p.E91*	ENST00000265734	NM_001259.6	91	Gaa/Taa	3/8	1	2	FACETS	0.937	0.85	1	0.937	0.85	1	CLONAL	1	TRUE	1	0.32	2		550	874	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509182	106509182	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	131	689	0	ENST00000359195.3:c.1176A>C	p.Gln392His	p.Q392H	ENST00000359195	NM_002649.2	392	caA/caC	2/11	1	2	FACETS	0.925	0.839	1	0.925	0.839	1	CLONAL	1	TRUE	1	0.32	2		689	885	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340201	116340201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561295443	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	134	604	0	ENST00000397752.3:c.1063G>A	p.Glu355Lys	p.E355K	ENST00000397752	NM_000245.2	355	Gaa/Aaa	2/21	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.32	2		604	833	SUCCESS
MET	4233	MSKCC	GRCh37	7	116417442	116417442	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	84	566	0	ENST00000397752.3:c.3260-1G>A		p.X1087_splice	ENST00000397752	NM_000245.2	1087			1	2	FACETS	0.73	0.645	0.822	0.73	0.645	0.822	SUBCLONAL	1	TRUE	1	0.32	2		566	719	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435812	116435812	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	176	828	0	ENST00000397752.3:c.3902G>T	p.Arg1301Ile	p.R1301I	ENST00000397752	NM_000245.2	1301	aGa/aTa	20/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.32	2		828	1068	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494182	140494182	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	142	674	1	ENST00000288602.6:c.1066C>A	p.Gln356Lys	p.Q356K	ENST00000288602	NM_004333.4	356	Caa/Aaa	8/18	1	2	FACETS	0.954	0.869	1	0.954	0.869	1	CLONAL	1	TRUE	1	0.32	2		675	930	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494188	140494188	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	137	642	0	ENST00000288602.6:c.1060C>T	p.Arg354Ter	p.R354*	ENST00000288602	NM_004333.4	354	Cga/Tga	8/18	1	2	FACETS	0.904	0.822	0.991	0.904	0.822	0.991	CLONAL	1	TRUE	1	0.32	2		642	947	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151164278	151164278	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781512533	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	145	594	0	ENST00000262187.5:c.482G>A	p.Arg161Gln	p.R161Q	ENST00000262187	NM_005614.3	161	cGa/cAa	8/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.32	2		594	791	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859303	151859303	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	113	546	0	ENST00000262189.6:c.11359T>C	p.Ser3787Pro	p.S3787P	ENST00000262189	NM_170606.2	3787	Tct/Cct	43/59	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.32	2		546	660	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874616	151874616	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	109	616	4	ENST00000262189.6:c.7922C>A	p.Ser2641Ter	p.S2641*	ENST00000262189	NM_170606.2	2641	tCa/tAa	38/59	1	2	FACETS	0.88	0.79	0.975	0.88	0.79	0.975	CLONAL	1	TRUE	1	0.32	2		620	774	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101910053	101910053	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	111	544	2	ENST00000374994.4:c.1373G>A	p.Trp458Ter	p.W458*	ENST00000374994	NM_004612.2	458	tGg/tAg	8/9	1	2	FACETS	0.961	0.864	1	0.961	0.864	1	CLONAL	1	TRUE	1	0.32	2		546	722	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797217	135797217	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	123	631	0	ENST00000298552.3:c.652G>T	p.Glu218Ter	p.E218*	ENST00000298552	NM_001162426.1	218	Gaa/Taa	7/23	1	2	FACETS	0.883	0.798	0.972	0.883	0.798	0.972	CLONAL	1	TRUE	1	0.32	2		631	871	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393588	139393588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752928106	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	113	642	0	ENST00000277541.6:c.6058G>A	p.Asp2020Asn	p.D2020N	ENST00000277541	NM_017617.3	2020	Gac/Aac	32/34	1	2	FACETS	0.888	0.799	0.983	0.888	0.799	0.983	CLONAL	1	TRUE	1	0.32	2		642	795	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139408975	139408975	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	91	469	0	ENST00000277541.6:c.2194G>A	p.Asp732Asn	p.D732N	ENST00000277541	NM_017617.3	732	Gac/Aac	13/34	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.32	2		469	558	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409769	139409769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs548000491	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	99	536	3	ENST00000277541.6:c.1987G>A	p.Glu663Lys	p.E663K	ENST00000277541	NM_017617.3	663	Gag/Aag	12/34	1	2	FACETS	0.907	0.811	1	0.907	0.811	1	CLONAL	1	TRUE	1	0.32	2		539	682	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333069	70333069	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	150	765	0	ENST00000373644.4:c.974C>A	p.Ser325Tyr	p.S325Y	ENST00000373644	NM_030625.2	325	tCt/tAt	2/12	1	2	FACETS	0.932	0.851	1	0.932	0.851	1	CLONAL	1	TRUE	1	0.32	2		765	1006	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405821	70405821	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	120	632	0	ENST00000373644.4:c.3335T>C	p.Val1112Ala	p.V1112A	ENST00000373644	NM_030625.2	1112	gTa/gCa	4/12	1	2	FACETS	0.877	0.792	0.968	0.877	0.792	0.968	CLONAL	1	TRUE	1	0.32	2		632	855	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406103	70406103	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	107	515	0	ENST00000373644.4:c.3617T>A	p.Phe1206Tyr	p.F1206Y	ENST00000373644	NM_030625.2	1206	tTt/tAt	4/12	1	2	FACETS	0.938	0.842	1	0.938	0.842	1	CLONAL	1	TRUE	1	0.32	2		515	713	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88672088	88672088	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	39	206	0	ENST00000372037.3:c.622G>T	p.Asp208Tyr	p.D208Y	ENST00000372037	NM_004329.2	208	Gac/Tac	8/13	1	2	FACETS	0.886	0.739	1	0.886	0.739	1	CLONAL	1	TRUE	1	0.32	2		206	275	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692918	89692918	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1114167676	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	78	400	0	ENST00000371953.3:c.402G>T	p.Met134Ile	p.M134I	ENST00000371953	NM_000314.4	134	atG/atT	5/9	1	2	FACETS	0.835	0.734	0.942	0.835	0.734	0.942	CLONAL	1	TRUE	1	0.32	2		400	584	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741411	17741411	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	163	704	0	ENST00000250003.3:c.82G>A	p.Asp28Asn	p.D28N	ENST00000250003	NM_002478.4	28	Gac/Aac	1/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.32	2		704	897	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77043819	77043819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371644543	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	189	765	2	ENST00000356341.3:c.1507G>A	p.Glu503Lys	p.E503K	ENST00000356341	NM_002576.4	503	Gag/Aag	14/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.32	2		767	1080	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047151	77047151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	151	708	1	ENST00000356341.3:c.1393C>T	p.Leu465Phe	p.L465F	ENST00000356341	NM_002576.4	465	Ctc/Ttc	13/15	1	2	FACETS	0.961	0.878	1	0.961	0.878	1	CLONAL	1	TRUE	1	0.32	2		709	982	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201966	102201966	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	144	795	0	ENST00000263464.3:c.1318G>T	p.Glu440Ter	p.E440*	ENST00000263464	NM_001165.4	440	Gaa/Taa	6/9	1	2	FACETS	0.989	0.902	1	0.989	0.902	1	CLONAL	1	TRUE	1	0.32	2		795	910	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160347	108160347	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	63	322	0	ENST00000278616.4:c.4255C>A	p.Leu1419Ile	p.L1419I	ENST00000278616	NM_000051.3	1419	Ctt/Att	29/63	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.32	2		322	384	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342998	118342998	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	112	470	0	ENST00000534358.1:c.1124T>G	p.Leu375Arg	p.L375R	ENST00000534358	NM_005933.3	375	cTc/cGc	3/36	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.32	2		470	658	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343956	118343956	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	121	491	0	ENST00000534358.1:c.2082C>A	p.Ser694Arg	p.S694R	ENST00000534358	NM_005933.3	694	agC/agA	3/36	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.32	2		491	685	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344944	118344944	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	104	485	1	ENST00000534358.1:c.3070G>A	p.Ala1024Thr	p.A1024T	ENST00000534358	NM_005933.3	1024	Gcc/Acc	3/36	1	2	FACETS	0.922	0.826	1	0.922	0.826	1	CLONAL	1	TRUE	1	0.32	2		486	705	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	422312	422312	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	144	802	0	ENST00000399788.2:c.2946G>T	p.Lys982Asn	p.K982N	ENST00000399788	NM_001042603.1	982	aaG/aaT	20/28	1	2	FACETS	0.901	0.821	0.985	0.901	0.821	0.985	CLONAL	1	TRUE	1	0.32	2		802	999	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037430	12037430	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	138	691	0	ENST00000396373.4:c.1061A>G	p.Tyr354Cys	p.Y354C	ENST00000396373	NM_001987.4	354	tAc/tGc	6/8	0.3	3	FACETS	0.926	0.841	1			1	CLONAL	1	TRUE	NA	0.32	3		691	1080	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435088	18435088	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs777959749	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	75	491	0	ENST00000266497.5:c.73C>A	p.Leu25Ile	p.L25I	ENST00000266497		25	Ctc/Atc	1/31	1	2	FACETS	0.721	0.632	0.817	0.721	0.632	0.817	SUBCLONAL	1	TRUE	1	0.32	2		491	650	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46240719	46240719	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	117	537	0	ENST00000334344.6:c.1579T>C	p.Trp527Arg	p.W527R	ENST00000334344	NM_152641.2	527	Tgg/Cgg	12/21	1	2	FACETS	0.947	0.854	1	0.947	0.854	1	CLONAL	1	TRUE	1	0.32	2		537	772	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425016	49425016	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	171	697	0	ENST00000301067.7:c.13472T>G	p.Ile4491Ser	p.I4491S	ENST00000301067	NM_003482.3	4491	aTt/aGt	39/54	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.32	2		697	937	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479274	50479274	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	60	471	0	ENST00000394963.4:c.122G>A	p.Gly41Asp	p.G41D	ENST00000394963	NM_003076.4	41	gGc/gAc	1/13	1	2	FACETS	0.605	0.521	0.696	0.605	0.521	0.696	SUBCLONAL	1	TRUE	1	0.32	2		471	620	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478938	56478938	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs569206705	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	146	730	1	ENST00000267101.3:c.394C>T	p.Arg132Cys	p.R132C	ENST00000267101	NM_001982.3	132	Cgc/Tgc	3/28	1	2	FACETS	0.874	0.797	0.956	0.874	0.797	0.956	CLONAL	1	TRUE	1	0.32	2		731	1044	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490564	56490564	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1282110952	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	110	602	0	ENST00000267101.3:c.2208G>T	p.Lys736Asn	p.K736N	ENST00000267101	NM_001982.3	736	aaG/aaT	19/28	1	2	FACETS	0.84	0.755	0.931	0.84	0.755	0.931	CLONAL	1	TRUE	1	0.32	2		602	818	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432067	121432067	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555212014	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	147	688	1	ENST00000257555.6:c.814C>T	p.Arg272Cys	p.R272C	ENST00000257555		272	Cgc/Tgc	4/10	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.32	2		689	910	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201360	133201360	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs768405124	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	143	702	0	ENST00000320574.5:c.6784G>T	p.Ala2262Ser	p.A2262S	ENST00000320574	NM_006231.2	2262	Gcc/Tcc	49/49	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.32	2		702	853	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967543	26967543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	54	659	0	ENST00000381527.3:c.686C>T	p.Thr229Met	p.T229M	ENST00000381527	NM_001260.1	229	aCg/aTg	7/13	1	2	FACETS	0.429	0.365	0.499	0.429	0.365	0.499	SUBCLONAL	1	TRUE	1	0.32	2		659	787	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28931804	28931804	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	114	628	0	ENST00000282397.4:c.2135G>T	p.Gly712Val	p.G712V	ENST00000282397	NM_002019.4	712	gGa/gTa	15/30	1	2	FACETS	0.845	0.761	0.935	0.845	0.761	0.935	CLONAL	1	TRUE	1	0.32	2		628	843	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005299	29005299	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	109	537	0	ENST00000282397.4:c.962C>A	p.Ser321Tyr	p.S321Y	ENST00000282397	NM_002019.4	321	tCt/tAt	7/30	1	2	FACETS	0.921	0.827	1	0.921	0.827	1	CLONAL	1	TRUE	1	0.32	2		537	740	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906611	32906611	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	37	437	0	ENST00000380152.3:c.996T>G	p.Ile332Met	p.I332M	ENST00000380152		332	atT/atG	10/27	1	2	FACETS	0.469	0.386	0.562	0.469	0.386	0.562	SUBCLONAL	1	TRUE	1	0.32	2		437	493	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906930	32906930	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs80358420	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	52	318	0	ENST00000380152.3:c.1315T>G	p.Phe439Val	p.F439V	ENST00000380152		439	Ttt/Gtt	10/27	1	2	FACETS	0.799	0.682	0.926	0.799	0.682	0.926	CLONAL	1	TRUE	1	0.32	2		318	407	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912209	32912209	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs141196976	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	185	997	0	ENST00000380152.3:c.3717A>C	p.Lys1239Asn	p.K1239N	ENST00000380152		1239	aaA/aaC	11/27	1	2	FACETS	0.94	0.866	1	0.94	0.866	1	CLONAL	1	TRUE	1	0.32	2		997	1230	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954027	32954027	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	93	590	1	ENST00000380152.3:c.9094A>T	p.Lys3032Ter	p.K3032*	ENST00000380152		3032	Aaa/Taa	23/27	1	2	FACETS	0.777	0.691	0.869	0.777	0.691	0.869	SUBCLONAL	1	TRUE	1	0.32	2		591	748	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972643	32972643	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	87	457	0	ENST00000380152.3:c.9993T>G	p.Ile3331Met	p.I3331M	ENST00000380152		3331	atT/atG	27/27	1	2	FACETS	0.838	0.742	0.94	0.838	0.742	0.94	CLONAL	1	TRUE	1	0.32	2		457	649	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972674	32972674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28897761	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	92	554	0	ENST00000380152.3:c.10024G>A	p.Glu3342Lys	p.E3342K	ENST00000380152		3342	Gaa/Aaa	27/27	1	2	FACETS	0.77	0.684	0.862	0.77	0.684	0.862	SUBCLONAL	1	TRUE	1	0.32	2		554	747	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436912	110436912	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	28	209	0	ENST00000375856.3:c.1489T>G	p.Phe497Val	p.F497V	ENST00000375856	NM_003749.2	497	Ttc/Gtc	1/2	1	2	FACETS	0.618	0.495	0.758	0.618	0.495	0.758	SUBCLONAL	1	TRUE	1	0.32	2		209	283	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81557479	81557479	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	92	613	0	ENST00000298171.2:c.459C>A	p.Phe153Leu	p.F153L	ENST00000298171	NM_000369.2	153	ttC/ttA	5/10	1	2	FACETS	0.765	0.679	0.856	0.765	0.679	0.856	SUBCLONAL	1	TRUE	1	0.32	2		613	752	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961238	41961238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	194	1018	0	ENST00000219905.7:c.146C>T	p.Ala49Val	p.A49V	ENST00000219905	NM_001164273.1	49	gCt/gTt	2/24	1	2	FACETS	0.971	0.896	1	0.971	0.896	1	CLONAL	1	TRUE	1	0.32	2		1018	1249	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007686	45007686	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	100	438	0	ENST00000558401.1:c.133T>G	p.Cys45Gly	p.C45G	ENST00000558401	NM_004048.2	45	Tgc/Ggc	2/4	1	2	FACETS	0.839	0.749	0.934	0.839	0.749	0.934	CLONAL	1	TRUE	1	0.32	2		438	745	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007818	45007818	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	118	516	1	ENST00000558401.1:c.265G>T	p.Glu89Ter	p.E89*	ENST00000558401	NM_004048.2	89	Gaa/Taa	2/4	1	2	FACETS	0.897	0.809	0.99	0.897	0.809	0.99	CLONAL	1	TRUE	1	0.32	2		517	822	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354503	91354503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs959925706	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	97	470	0	ENST00000355112.3:c.3943C>T	p.Leu1315Phe	p.L1315F	ENST00000355112	NM_000057.2	1315	Ctc/Ttc	21/22	1	2	FACETS	0.756	0.673	0.844	0.756	0.673	0.844	SUBCLONAL	1	TRUE	1	0.32	2		470	802	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108760	2108760	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	137	736	1	ENST00000219476.3:c.861G>T	p.Glu287Asp	p.E287D	ENST00000219476	NM_000548.3	287	gaG/gaT	10/42	1	2	FACETS	0.979	0.89	1	0.979	0.89	1	CLONAL	1	TRUE	1	0.32	2		737	875	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225549	2225549	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	125	608	1	ENST00000326181.6:c.1552G>A	p.Gly518Ser	p.G518S	ENST00000326181	NM_032271.2	518	Ggc/Agc	17/21	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.32	2		609	752	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788637	3788637	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	125	554	0	ENST00000262367.5:c.4317C>A	p.Phe1439Leu	p.F1439L	ENST00000262367	NM_004380.2	1439	ttC/ttA	26/31	1	2	FACETS	0.903	0.817	0.994	0.903	0.817	0.994	CLONAL	1	TRUE	1	0.32	2		554	865	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808003	3808003	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	131	492	0	ENST00000262367.5:c.3416A>C	p.Lys1139Thr	p.K1139T	ENST00000262367	NM_004380.2	1139	aAg/aCg	18/31	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.32	2		492	714	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819355	3819355	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	83	301	0	ENST00000262367.5:c.2881-1G>A		p.X961_splice	ENST00000262367	NM_004380.2	961			1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.32	2		301	462	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858709	9858709	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	141	672	2	ENST00000330684.3:c.2692C>A	p.Leu898Ile	p.L898I	ENST00000330684	NM_001134407.1	898	Ctc/Atc	13/13	1	2	FACETS	0.975	0.888	1	0.975	0.888	1	CLONAL	1	TRUE	1	0.32	2		674	904	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934633	9934633	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	116	492	0	ENST00000330684.3:c.1522G>A	p.Ala508Thr	p.A508T	ENST00000330684	NM_001134407.1	508	Gca/Aca	7/13	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.32	2		492	675	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641455	23641455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881885	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	88	827	0	ENST00000261584.4:c.2020G>A	p.Asp674Asn	p.D674N	ENST00000261584	NM_024675.3	674	Gac/Aac	5/13	1	2	FACETS	0.511	0.451	0.575	0.511	0.451	0.575	SUBCLONAL	1	TRUE	1	0.32	2		827	1076	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56832410	56832410	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	175	859	0	ENST00000308159.5:c.320A>G	p.Asp107Gly	p.D107G	ENST00000308159	NM_014669.4	107	gAc/gGc	4/22	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.32	2		859	1090	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864551	56864551	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	196	829	0	ENST00000308159.5:c.1039G>A	p.Glu347Lys	p.E347K	ENST00000308159	NM_014669.4	347	Gag/Aag	10/22	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.32	2		829	1224	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116123	67116123	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	130	485	0	ENST00000412916.2:c.407A>G	p.Asp136Gly	p.D136G	ENST00000412916		136	gAt/gGt	5/6	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.32	2		485	748	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655374	67655374	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	141	644	2	ENST00000264010.4:c.1237C>T	p.His413Tyr	p.H413Y	ENST00000264010	NM_006565.3	413	Cat/Tat	7/12	1	2	FACETS	0.98	0.893	1	0.98	0.893	1	CLONAL	1	TRUE	1	0.32	2		646	899	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828045	72828045	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1272	202	1194	0	ENST00000268489.5:c.8536A>G	p.Thr2846Ala	p.T2846A	ENST00000268489	NM_006885.3	2846	Aca/Gca	9/10	1	2	FACETS	0.857	0.792	0.924	0.857	0.792	0.924	CLONAL	1	TRUE	1	0.32	2		1194	1474	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831909	72831909	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1192	235	1062	0	ENST00000268489.5:c.4672A>C	p.Asn1558His	p.N1558H	ENST00000268489	NM_006885.3	1558	Aat/Cat	9/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.32	2		1062	1427	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832394	72832394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774988278	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	211	930	5	ENST00000268489.5:c.4187G>A	p.Arg1396His	p.R1396H	ENST00000268489	NM_006885.3	1396	cGc/cAc	9/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.32	2		935	1168	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217817	7217817	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1194	110	1014	0	ENST00000380728.2:c.194C>G	p.Thr65Ser	p.T65S	ENST00000380728		65	aCc/aGc	3/11	1	2	FACETS	0.527	0.472	0.586	0.527	0.472	0.586	SUBCLONAL	1	TRUE	1	0.32	2		1014	1304	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950304	15950304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763924640	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	164	784	1	ENST00000268712.3:c.6640C>T	p.Arg2214Cys	p.R2214C	ENST00000268712	NM_006311.3	2214	Cgt/Tgt	42/46	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.32	2		785	968	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649073	37649073	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	130	589	0	ENST00000447079.4:c.2178G>C	p.Lys726Asn	p.K726N	ENST00000447079	NM_015083.1	726	aaG/aaC	4/14	1	2	FACETS	0.948	0.86	1	0.948	0.86	1	CLONAL	1	TRUE	1	0.32	2		589	857	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38506046	38506046	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	128	553	0	ENST00000254066.5:c.338G>A	p.Arg113His	p.R113H	ENST00000254066	NM_000964.3	113	cGc/cAc	4/9	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.32	2		553	693	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688750	47688750	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	138	519	1	ENST00000347630.2:c.550T>C	p.Cys184Arg	p.C184R	ENST00000347630	NM_001007230.1	184	Tgc/Cgc	7/11	1	2	FACETS	0.99	0.901	1	0.99	0.901	1	CLONAL	1	TRUE	1	0.32	2		520	871	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696663	47696663	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	159	741	1	ENST00000347630.2:c.285G>T	p.Lys95Asn	p.K95N	ENST00000347630	NM_001007230.1	95	aaG/aaT	5/11	1	2	FACETS	0.915	0.838	0.996	0.915	0.838	0.996	CLONAL	1	TRUE	1	0.32	2		742	1086	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763235	59763235	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	90	609	1	ENST00000259008.2:c.2867C>A	p.Ser956Ter	p.S956*	ENST00000259008	NM_032043.2	956	tCa/tAa	19/20	1	2	FACETS	0.824	0.731	0.922	0.824	0.731	0.922	CLONAL	1	TRUE	1	0.32	2		610	683	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59924493	59924493	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	154	734	0	ENST00000259008.2:c.596T>C	p.Leu199Pro	p.L199P	ENST00000259008	NM_032043.2	199	cTg/cCg	6/20	1	2	FACETS	0.979	0.895	1	0.979	0.895	1	CLONAL	1	TRUE	1	0.32	2		734	983	SUCCESS
YES1	7525	MSKCC	GRCh37	18	732848	732848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755971181	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	146	756	2	ENST00000314574.4:c.1409G>A	p.Arg470Gln	p.R470Q	ENST00000314574	NM_005433.3	470	cGa/cAa	11/12	1	2	FACETS	0.882	0.804	0.964	0.882	0.804	0.964	CLONAL	1	TRUE	1	0.32	2		758	1035	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110155	3110155	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	39	351	0	ENST00000078429.4:c.145G>A	p.Glu49Lys	p.E49K	ENST00000078429	NM_002067.2	49	Gag/Aag	2/7	1	2	FACETS	0.576	0.478	0.686	0.576	0.478	0.686	SUBCLONAL	1	TRUE	1	0.32	2		351	423	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115048	3115048	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769982397	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	100	581	1	ENST00000078429.4:c.583G>A	p.Asp195Asn	p.D195N	ENST00000078429	NM_002067.2	195	Gac/Aac	4/7	1	2	FACETS	0.785	0.701	0.875	0.785	0.701	0.875	SUBCLONAL	1	TRUE	1	0.32	2		582	796	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274217	5274217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	121	651	0	ENST00000357368.4:c.230G>A	p.Arg77His	p.R77H	ENST00000357368	NM_002850.3	77	cGc/cAc	3/38	1	2	FACETS	0.994	0.898	1	0.994	0.898	1	CLONAL	1	TRUE	1	0.32	2		651	761	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246481	10246481	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	101	449	0	ENST00000340748.4:c.4656G>T	p.Glu1552Asp	p.E1552D	ENST00000340748		1552	gaG/gaT	38/40	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.32	2		449	629	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152203	11152203	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	125	567	0	ENST00000358026.2:c.4487A>C	p.Lys1496Thr	p.K1496T	ENST00000358026	NM_001128849.1	1496	aAg/aCg	31/36	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.32	2		567	761	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626848	14626848	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	184	974	0	ENST00000254322.2:c.927G>T	p.Glu309Asp	p.E309D	ENST00000254322	NM_006145.1	309	gaG/gaT	3/3	1	2	FACETS	0.89	0.82	0.964	0.89	0.82	0.964	CLONAL	1	TRUE	1	0.32	2		974	1292	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383651	15383651	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	117	525	0	ENST00000263377.2:c.260T>G	p.Val87Gly	p.V87G	ENST00000263377	NM_058243.2	87	gTg/gGg	2/20	1	2	FACETS	0.983	0.887	1	0.983	0.887	1	CLONAL	1	TRUE	1	0.32	2		525	744	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946842	17946842	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs147408277	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	105	655	0	ENST00000458235.1:c.1805T>C	p.Phe602Ser	p.F602S	ENST00000458235	NM_000215.3	602	tTt/tCt	14/24	1	2	FACETS	0.924	0.829	1	0.924	0.829	1	CLONAL	1	TRUE	1	0.32	2		655	710	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368254	31368254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751741367	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	84	442	2	ENST00000328111.2:c.125G>A	p.Arg42His	p.R42H	ENST00000328111	NM_006892.3	42	cGc/cAc	2/23	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.32	2		444	504	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54959350	54959350	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	82	518	0	ENST00000312783.6:c.350A>C	p.Lys117Thr	p.K117T	ENST00000312783	NM_198436.1	117	aAa/aCa	5/10	1	2	FACETS	0.839	0.74	0.944	0.839	0.74	0.944	CLONAL	1	TRUE	1	0.32	2		518	611	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29090065	29090065	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	23	142	0	ENST00000328354.6:c.1416G>T	p.Lys472Asn	p.K472N	ENST00000328354	NM_007194.3	472	aaG/aaT	13/15	1	2	FACETS	0.681	0.534	0.85	0.681	0.534	0.85	SUBCLONAL	1	TRUE	1	0.32	2		142	211	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29090088	29090088	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	19	96	0	ENST00000328354.6:c.1393A>G	p.Lys465Glu	p.K465E	ENST00000328354	NM_007194.3	465	Aag/Gag	13/15	1	2	FACETS	0.813	0.623	1	0.813	0.623	1	CLONAL	1	TRUE	1	0.32	2		96	146	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1327732	1327732	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	154	743	0	ENST00000400841.2:c.149A>C	p.Lys50Thr	p.K50T	ENST00000400841		50	aAa/aCa	2/6	1	1	FACETS	0.868	0.794	0.946	0.868	0.794	0.946	CLONAL	1	TRUE	0	0.32	1		743	931	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841301	15841301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1195011512	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	142	344	0	ENST00000307771.7:c.1385G>A	p.Arg462Gln	p.R462Q	ENST00000307771	NM_005089.3	462	cGa/cAa	11/11	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.32	1		344	507	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933958	39933958	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	185	437	4	ENST00000378444.4:c.641C>A	p.Ser214Ter	p.S214*	ENST00000378444	NM_001123385.1	214	tCa/tAa	4/15	1	1	FACETS	0.809	0.751	0.869	1	0.992	1	CLONAL	2	TRUE	0	0.32	1		441	600	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424297	47424297	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	125	323	0	ENST00000377045.4:c.302T>G	p.Phe101Cys	p.F101C	ENST00000377045	NM_001654.4	101	tTt/tGt	4/16	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.32	1		323	457	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608930	100608930	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	152	408	0	ENST00000308731.7:c.1678C>A	p.Pro560Thr	p.P560T	ENST00000308731	NM_000061.2	560	Cca/Aca	17/19	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.32	1		408	590	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190082	123190082	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	103	272	0	ENST00000218089.9:c.1301A>G	p.Lys434Arg	p.K434R	ENST00000218089	NM_001042749.1	434	aAa/aGa	14/35	1	1	FACETS	0.759	0.686	0.836	1	0.984	1	SUBCLONAL	2	TRUE	0	0.32	1		272	356	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202447	123202447	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	119	408	0	ENST00000218089.9:c.2299G>T	p.Val767Leu	p.V767L	ENST00000218089	NM_001042749.1	767	Gta/Tta	24/35	1	1	FACETS	0.787	0.717	0.86	1	0.987	1	SUBCLONAL	2	TRUE	0	0.32	1		408	397	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224539	123224539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	206	470	1	ENST00000218089.9:c.3392G>T	p.Arg1131Ile	p.R1131I	ENST00000218089	NM_001042749.1	1131	aGa/aTa	31/35	1	1	FACETS	0.805	0.75	0.861	1	0.992	1	CLONAL	2	TRUE	0	0.32	1		471	672	SUCCESS
APC	324	MSKCC	GRCh37	5	112177434	112177435	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	64	582	2	ENST00000257430.4:c.6149dup	p.Lys2051GlufsTer9	p.K2051Efs*9	ENST00000257430	NM_000038.5	2048	cca/ccAa	16/16	1	2	FACETS	0.5	0.432	0.574	0.5	0.432	0.574	SUBCLONAL	1	TRUE	1	0.32	2		584	800	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	107	590	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.423	0.379	0.471	0.423	0.379	0.471	SUBCLONAL	1	TRUE	1	0.45	2		590	1123	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50481162	50481162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	333	478	0	ENST00000394963.4:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000394963	NM_003076.4	183	cGa/cAa	5/13	1	2	FACETS	0.905	0.859	0.95	1	0.996	1	CLONAL	2	TRUE	1	0.45	2		478	818	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	198	454	0	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	0.45	2		454	832	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	192	452	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.985	0.912	1	0.985	0.912	1	CLONAL	1	TRUE	1	0.45	2		452	866	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041074	42041074	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	318	694	2	ENST00000219905.7:c.5452C>T	p.Arg1818Ter	p.R1818*	ENST00000219905	NM_001164273.1	1818	Cga/Tga	16/24	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.45	2		696	1352	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	39	534	0	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	1	2	FACETS	0.183	0.151	0.219	0.183	0.151	0.219	SUBCLONAL	1	TRUE	1	0.45	2		534	948	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542861	187542861	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1340793072	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	289	410	1	ENST00000441802.2:c.4879C>T	p.Arg1627Ter	p.R1627*	ENST00000441802	NM_005245.3	1627	Cga/Tga	10/27	1	2	FACETS	0.985	0.934	1	1	0.996	1	CLONAL	2	TRUE	1	0.45	2		411	652	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291528	10291528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755995375	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	220	578	0	ENST00000340748.4:c.151G>A	p.Glu51Lys	p.E51K	ENST00000340748		51	Gaa/Aaa	3/40	1	2	FACETS	0.977	0.909	1	0.977	0.909	1	CLONAL	1	TRUE	1	0.45	2		578	1001	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521385	187521385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426195084	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	169	416	0	ENST00000441802.2:c.11770C>T	p.Arg3924Cys	p.R3924C	ENST00000441802	NM_005245.3	3924	Cgc/Tgc	22/27	1	2	FACETS	0.986	0.908	1	0.986	0.908	1	CLONAL	1	TRUE	1	0.45	2		416	762	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089913	16089913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	44	481	0	ENST00000268712.3:c.197G>A	p.Arg66Gln	p.R66Q	ENST00000268712	NM_006311.3	66	cGa/cAa	3/46	1	2	FACETS	0.242	0.202	0.287	0.242	0.202	0.287	SUBCLONAL	1	TRUE	1	0.45	2		481	808	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162107	22162107	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	66	331	1	ENST00000215832.6:c.148C>T	p.Arg50Ter	p.R50*	ENST00000215832	NM_002745.4	50	Cga/Tga	2/9	1	2	FACETS	0.452	0.392	0.517	0.452	0.392	0.517	SUBCLONAL	1	TRUE	1	0.45	2		332	649	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936984	48936984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772678500	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	68	420	0	ENST00000267163.4:c.752G>A	p.Arg251Gln	p.R251Q	ENST00000267163	NM_000321.2	251	cGa/cAa	8/27	1	2	FACETS	0.342	0.297	0.392	0.342	0.297	0.392	SUBCLONAL	1	TRUE	1	0.45	2		420	883	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	167	376	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.45	2		376	708	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137487	202137487	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	90	440	0	ENST00000358485.4:c.715G>T	p.Glu239Ter	p.E239*	ENST00000358485	NM_001080125.1	239	Gaa/Taa	4/9	1	2	FACETS	0.426	0.377	0.478	0.426	0.377	0.478	SUBCLONAL	1	TRUE	1	0.45	2		440	940	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951919	178951919	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	197	413	0	ENST00000263967.3:c.2974C>T	p.Arg992Ter	p.R992*	ENST00000263967	NM_006218.2	992	Cga/Tga	21/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.45	2		413	761	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	189	428	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.98	0.907	1	0.98	0.907	1	CLONAL	1	TRUE	1	0.45	2		428	857	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5078403	5078403	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	34	307	0	ENST00000381652.3:c.2090T>G	p.Leu697Arg	p.L697R	ENST00000381652	NM_004972.3	697	cTt/cGt	16/25	1	2	FACETS	0.225	0.183	0.272	0.225	0.183	0.272	SUBCLONAL	1	TRUE	1	0.45	2		307	672	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875096	151875096	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	53	106	0	ENST00000262189.6:c.7443-1G>T		p.X2481_splice	ENST00000262189	NM_170606.2	2481			1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.45	2		106	190	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7163084	7163084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201034510	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	74	570	0	ENST00000302850.5:c.1988C>T	p.Ala663Val	p.A663V	ENST00000302850	NM_000208.2	663	gCg/gTg	9/22	1	2	FACETS	0.339	0.295	0.386	0.339	0.295	0.386	SUBCLONAL	1	TRUE	1	0.45	2		570	971	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281802	142281802	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	159	409	1	ENST00000350721.4:c.442G>T	p.Glu148Ter	p.E148*	ENST00000350721	NM_001184.3	148	Gaa/Taa	4/47	1	2	FACETS	0.931	0.855	1	0.931	0.855	1	CLONAL	1	TRUE	1	0.45	2		410	759	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254906	16254906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	85	425	1	ENST00000375759.3:c.2171G>A	p.Arg724Gln	p.R724Q	ENST00000375759	NM_015001.2	724	cGa/cAa	11/15	1	2	FACETS	0.464	0.41	0.523	0.464	0.41	0.523	SUBCLONAL	1	TRUE	1	0.45	2		426	814	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642495	117642495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs9489124	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	111	665	0	ENST00000368508.3:c.5704G>A	p.Glu1902Lys	p.E1902K	ENST00000368508	NM_002944.2	1902	Gaa/Aaa	35/43	1	2	FACETS	0.427	0.382	0.474	0.427	0.382	0.474	SUBCLONAL	1	TRUE	1	0.45	2		665	1156	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828383	72828383	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1277890729	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	257	630	1	ENST00000268489.5:c.8198G>A	p.Arg2733His	p.R2733H	ENST00000268489	NM_006885.3	2733	cGt/cAt	9/10	1	2	FACETS	0.998	0.934	1	0.998	0.934	1	CLONAL	1	TRUE	1	0.45	2		631	1144	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345913	70345913	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749801457	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	66	599	3	ENST00000374080.3:c.2450G>A	p.Arg817His	p.R817H	ENST00000374080		817	cGc/cAc	18/45	1	2	FACETS	0.27	0.233	0.31	0.27	0.233	0.31	SUBCLONAL	1	TRUE	1	0.45	2		602	1086	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398917	398917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356308443	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	146	327	0	ENST00000380956.4:c.727G>A	p.Glu243Lys	p.E243K	ENST00000380956	NM_001195286.1	243	Gaa/Aaa	6/9	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.45	2		327	605	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624262	89624263	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587776671	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	71	183	0	ENST00000371953.3:c.40dup	p.Arg14LysfsTer30	p.R14Kfs*30	ENST00000371953	NM_000314.4	12	-/A	1/9	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.45	2		183	314	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856027	151856027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774117324	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1304	80	667	2	ENST00000262189.6:c.11591G>A	p.Arg3864His	p.R3864H	ENST00000262189	NM_170606.2	3864	cGc/cAc	44/59	1	2	FACETS	0.257	0.225	0.292	0.257	0.225	0.292	SUBCLONAL	1	TRUE	1	0.45	2		669	1384	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243237	123243237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55774317	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	298	671	1	ENST00000358487.5:c.2276G>A	p.Arg759Gln	p.R759Q	ENST00000358487	NM_000141.4	759	cGa/cAa	17/18	1	2	FACETS	0.974	0.916	1	0.974	0.916	1	CLONAL	1	TRUE	1	0.45	2		672	1360	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951852	2951852	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770667388	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	57	502	0	ENST00000396946.4:c.3098C>T	p.Ala1033Val	p.A1033V	ENST00000396946	NM_032415.4	1033	gCg/gTg	23/25	1	2	FACETS	0.239	0.204	0.278	0.239	0.204	0.278	SUBCLONAL	1	TRUE	1	0.45	2		502	1059	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827732	72827732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241554729	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	275	687	0	ENST00000268489.5:c.8849G>A	p.Arg2950His	p.R2950H	ENST00000268489	NM_006885.3	2950	cGc/cAc	9/10	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.45	2		687	1195	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245350	53245350	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1556851765	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	144	642	1	ENST00000375401.3:c.687G>T	p.Lys229Asn	p.K229N	ENST00000375401	NM_004187.3	229	aaG/aaT	6/26	1	2	FACETS	0.616	0.561	0.674	0.616	0.561	0.674	SUBCLONAL	1	TRUE	1	0.45	2		643	1039	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310506	65310506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	82	566	1	ENST00000342505.4:c.2182G>A	p.Asp728Asn	p.D728N	ENST00000342505	NM_002227.2	728	Gac/Aac	16/25	1	2	FACETS	0.362	0.318	0.409	0.362	0.318	0.409	SUBCLONAL	1	TRUE	1	0.45	2		567	1007	SUCCESS
FH	2271	MSKCC	GRCh37	1	241661199	241661199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201115573	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	211	490	0	ENST00000366560.3:c.1462G>A	p.Glu488Lys	p.E488K	ENST00000366560	NM_000143.3	488	Gaa/Aaa	10/10	1	2	FACETS	0.972	0.903	1	0.972	0.903	1	CLONAL	1	TRUE	1	0.45	2		490	965	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230405	46230405	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1391481708	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	69	395	0	ENST00000334344.6:c.739C>T	p.Arg247Cys	p.R247C	ENST00000334344	NM_152641.2	247	Cgt/Tgt	7/21	1	2	FACETS	0.543	0.473	0.618	0.543	0.473	0.618	SUBCLONAL	1	TRUE	1	0.45	2		395	565	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102084	27102084	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	281	583	1	ENST00000324856.7:c.5010G>A	p.Trp1670Ter	p.W1670*	ENST00000324856	NM_006015.4	1670	tgG/tgA	19/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.45	2		584	1207	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270084	198270084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777705664	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	87	438	0	ENST00000335508.6:c.1352G>A	p.Arg451Gln	p.R451Q	ENST00000335508	NM_012433.2	451	cGa/cAa	10/25	1	2	FACETS	0.512	0.453	0.576	0.512	0.453	0.576	SUBCLONAL	1	TRUE	1	0.45	2		438	755	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47108598	47108598	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	164	414	3	ENST00000409792.3:c.6071G>A	p.Arg2024Gln	p.R2024Q	ENST00000409792	NM_014159.6	2024	cGa/cAa	13/21	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.45	2		417	724	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956553	93956553	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1035177735	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	555	625	1	ENST00000369303.4:c.2683C>T	p.Arg895Ter	p.R895*	ENST00000369303	NM_004440.3	895	Cga/Tga	15/17	1	2	FACETS	1	0.986	1	1	0.998	1	CLONAL	2	TRUE	1	0.45	2		626	1179	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609382	39609382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1463795009	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	85	423	1	ENST00000262039.4:c.1684G>A	p.Glu562Lys	p.E562K	ENST00000262039	NM_002647.2	562	Gaa/Aaa	15/25	1	2	FACETS	0.42	0.371	0.474	0.42	0.371	0.474	SUBCLONAL	1	TRUE	1	0.45	2		424	899	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845640	72845640	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148354034	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	69	682	1	ENST00000268489.5:c.3700G>A	p.Asp1234Asn	p.D1234N	ENST00000268489	NM_006885.3	1234	Gat/Aat	7/10	1	2	FACETS	0.261	0.226	0.299	0.261	0.226	0.299	SUBCLONAL	1	TRUE	1	0.45	2		683	1176	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20483132	20483132	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	44	455	0	ENST00000346618.3:c.865G>A	p.Glu289Lys	p.E289K	ENST00000346618	NM_001949.4	289	Gag/Aag	4/7	1	2	FACETS	0.224	0.187	0.265	0.224	0.187	0.265	SUBCLONAL	1	TRUE	1	0.45	2		455	873	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575630	55575630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	79	534	0	ENST00000288135.5:c.1156G>A	p.Glu386Lys	p.E386K	ENST00000288135	NM_000222.2	386	Gaa/Aaa	7/21	1	2	FACETS	0.378	0.331	0.428	0.378	0.331	0.428	SUBCLONAL	1	TRUE	1	0.45	2		534	930	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025543	1025543	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	101	499	0	ENST00000358495.3:c.832C>T	p.Arg278Ter	p.R278*	ENST00000358495	NM_134424.2	278	Cga/Tga	9/12	1	2	FACETS	0.52	0.464	0.58	0.52	0.464	0.58	SUBCLONAL	1	TRUE	1	0.45	2		499	863	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907705	76907705	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	309	835	0	ENST00000373344.5:c.4456G>T	p.Asp1486Tyr	p.D1486Y	ENST00000373344	NM_000489.3	1486	Gat/Tat	15/35	1	2	FACETS	0.997	0.938	1	0.997	0.938	1	CLONAL	1	TRUE	1	0.45	2		835	1378	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518262	8518262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	43	413	0	ENST00000356435.5:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000356435		377	Cgc/Tgc	10/35	1	2	FACETS	0.258	0.215	0.306	0.258	0.215	0.306	SUBCLONAL	1	TRUE	1	0.45	2		413	740	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624245	89624245	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554890335	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	30	103	0	ENST00000371953.3:c.19G>T	p.Glu7Ter	p.E7*	ENST00000371953	NM_000314.4	7	Gag/Tag	1/9	1	2	FACETS	0.65	0.528	0.787	0.65	0.528	0.787	SUBCLONAL	1	TRUE	1	0.45	2		103	205	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873237	71873237	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	59	601	0	ENST00000357731.5:c.957G>T	p.Gln319His	p.Q319H	ENST00000357731	NM_173808.2	319	caG/caT	7/7	1	2	FACETS	0.233	0.199	0.27	0.233	0.199	0.27	SUBCLONAL	1	TRUE	1	0.45	2		601	1125	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608897	100608897	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	282	616	0	ENST00000308731.7:c.1711T>C	p.Tyr571His	p.Y571H	ENST00000308731	NM_000061.2	571	Tat/Cat	17/19	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.45	2		616	1190	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245490	16245490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	164	446	0	ENST00000375759.3:c.1465G>A	p.Val489Ile	p.V489I	ENST00000375759	NM_015001.2	489	Gtt/Att	7/15	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.45	2		446	700	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36931974	36931974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372972496	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	92	597	0	ENST00000361632.4:c.2495C>T	p.Ala832Val	p.A832V	ENST00000361632		832	gCg/gTg	16/16	1	2	FACETS	0.362	0.32	0.406	0.362	0.32	0.406	SUBCLONAL	1	TRUE	1	0.45	2		597	1131	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46740305	46740305	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	49	488	0	ENST00000371975.4:c.1785G>T	p.Trp595Cys	p.W595C	ENST00000371975	NM_003579.3	595	tgG/tgT	16/18	1	2	FACETS	0.261	0.22	0.307	0.261	0.22	0.307	SUBCLONAL	1	TRUE	1	0.45	2		488	833	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313333	65313333	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	96	544	2	ENST00000342505.4:c.1781G>T	p.Arg594Ile	p.R594I	ENST00000342505	NM_002227.2	594	aGa/aTa	13/25	1	2	FACETS	0.41	0.364	0.459	0.41	0.364	0.459	SUBCLONAL	1	TRUE	1	0.45	2		546	1041	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699514	117699514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138215115	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	61	283	1	ENST00000369458.3:c.127G>A	p.Ala43Thr	p.A43T	ENST00000369458	NM_024626.3	43	Gcc/Acc	3/6	1	2	FACETS	0.542	0.468	0.622	0.542	0.468	0.622	SUBCLONAL	1	TRUE	1	0.45	2		284	500	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497685	120497685	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1553198236	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	163	353	0	ENST00000256646.2:c.2197A>G	p.Asn733Asp	p.N733D	ENST00000256646	NM_024408.3	733	Aac/Gac	13/34	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.45	2		353	674	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737131	162737131	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866018415	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	125	409	2	ENST00000367921.3:c.1275G>A	p.Trp425Ter	p.W425*	ENST00000367921	NM_006182.2	425	tgG/tgA	11/18	1	2	FACETS	0.817	0.741	0.897	0.817	0.741	0.897	CLONAL	1	TRUE	1	0.45	2		411	680	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027661	48027661	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	47	225	0	ENST00000234420.5:c.2539G>T	p.Glu847Ter	p.E847*	ENST00000234420	NM_000179.2	847	Gaa/Taa	4/10	1	2	FACETS	0.506	0.427	0.592	0.506	0.427	0.592	SUBCLONAL	1	TRUE	1	0.45	2		225	413	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027958	48027958	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1558666905	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	175	443	1	ENST00000234420.5:c.2836G>T	p.Glu946Ter	p.E946*	ENST00000234420	NM_000179.2	946	Gaa/Taa	4/10	1	2	FACETS	0.963	0.888	1	0.963	0.888	1	CLONAL	1	TRUE	1	0.45	2		444	808	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719704	61719704	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	45	470	0	ENST00000401558.2:c.1564A>C	p.Lys522Gln	p.K522Q	ENST00000401558	NM_003400.3	522	Aag/Cag	14/25	1	2	FACETS	0.238	0.199	0.282	0.238	0.199	0.282	SUBCLONAL	1	TRUE	1	0.45	2		470	839	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726957	61726957	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	225	470	0	ENST00000401558.2:c.481G>A	p.Glu161Lys	p.E161K	ENST00000401558	NM_003400.3	161	Gaa/Aaa	7/25	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.45	2		470	924	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128018861	128018861	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	88	607	0	ENST00000285398.2:c.2007A>C	p.Glu669Asp	p.E669D	ENST00000285398	NM_000122.1	669	gaA/gaC	13/15	1	2	FACETS	0.341	0.301	0.384	0.341	0.301	0.384	SUBCLONAL	1	TRUE	1	0.45	2		607	1146	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339002	225339002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	175	560	0	ENST00000264414.4:c.2267G>A	p.Arg756Gln	p.R756Q	ENST00000264414	NM_003590.4	756	cGa/cAa	16/16	1	2	FACETS	0.822	0.757	0.89	0.822	0.757	0.89	CLONAL	1	TRUE	1	0.45	2		560	946	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661672	227661672	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772676919	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	34	361	2	ENST00000305123.5:c.1783C>T	p.Arg595Trp	p.R595W	ENST00000305123	NM_005544.2	595	Cgg/Tgg	1/2	1	2	FACETS	0.229	0.186	0.277	0.229	0.186	0.277	SUBCLONAL	1	TRUE	1	0.45	2		363	660	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089035	37089035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	46	408	1	ENST00000231790.2:c.1757C>T	p.Ala586Val	p.A586V	ENST00000231790	NM_000249.3	586	gCc/gTc	16/19	1	2	FACETS	0.286	0.24	0.336	0.286	0.24	0.336	SUBCLONAL	1	TRUE	1	0.45	2		409	716	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098600	47098600	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs941392264	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	189	483	0	ENST00000409792.3:c.6674T>C	p.Val2225Ala	p.V2225A	ENST00000409792	NM_014159.6	2225	gTg/gCg	15/21	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.45	2		483	830	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161943	47161943	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	156	363	0	ENST00000409792.3:c.4183A>C	p.Lys1395Gln	p.K1395Q	ENST00000409792	NM_014159.6	1395	Aaa/Caa	3/21	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.45	2		363	667	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49724623	49724623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	100	426	0	ENST00000449682.2:c.566C>T	p.Ala189Val	p.A189V	ENST00000449682	NM_020998.3	189	gCt/gTt	5/18	1	2	FACETS	0.682	0.61	0.758	0.682	0.61	0.758	SUBCLONAL	1	TRUE	1	0.45	2		426	652	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89478300	89478300	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	96	328	0	ENST00000336596.2:c.2119T>G	p.Leu707Val	p.L707V	ENST00000336596	NM_005233.5	707	Ttg/Gtg	12/17	1	2	FACETS	0.981	0.879	1	0.981	0.879	1	CLONAL	1	TRUE	1	0.45	2		328	435	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873115	134873115	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	163	416	0	ENST00000398015.3:c.1419G>T	p.Glu473Asp	p.E473D	ENST00000398015	NM_004441.4	473	gaG/gaT	6/16	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.45	2		416	714	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920512	134920512	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	42	424	1	ENST00000398015.3:c.2327C>A	p.Pro776His	p.P776H	ENST00000398015	NM_004441.4	776	cCc/cAc	12/16	1	2	FACETS	0.246	0.204	0.292	0.246	0.204	0.292	SUBCLONAL	1	TRUE	1	0.45	2		425	760	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242849	142242849	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	42	368	0	ENST00000350721.4:c.4138G>T	p.Asp1380Tyr	p.D1380Y	ENST00000350721	NM_001184.3	1380	Gat/Tat	22/47	1	2	FACETS	0.244	0.203	0.29	0.244	0.203	0.29	SUBCLONAL	1	TRUE	1	0.45	2		368	764	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274805	142274805	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	78	386	0	ENST00000350721.4:c.2255A>C	p.Glu752Ala	p.E752A	ENST00000350721	NM_001184.3	752	gAa/gCa	10/47	1	2	FACETS	0.42	0.368	0.475	0.42	0.368	0.475	SUBCLONAL	1	TRUE	1	0.45	2		386	826	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182679036	182679036	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	64	371	0	ENST00000292782.4:c.498G>T	p.Lys166Asn	p.K166N	ENST00000292782	NM_020640.2	166	aaG/aaT	4/7	1	2	FACETS	0.497	0.431	0.57	0.497	0.431	0.57	SUBCLONAL	1	TRUE	1	0.45	2		371	572	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280072	66280072	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	95	470	0	ENST00000273854.3:c.1617A>C	p.Gln539His	p.Q539H	ENST00000273854	NM_004439.5	539	caA/caC	7/18	1	2	FACETS	0.45	0.4	0.504	0.45	0.4	0.504	SUBCLONAL	1	TRUE	1	0.45	2		470	938	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361152	66361152	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	88	481	0	ENST00000273854.3:c.1020G>T	p.Lys340Asn	p.K340N	ENST00000273854	NM_004439.5	340	aaG/aaT	4/18	1	2	FACETS	0.445	0.393	0.5	0.445	0.393	0.5	SUBCLONAL	1	TRUE	1	0.45	2		481	879	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094904	143094904	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	190	553	0	ENST00000262992.4:c.1240C>A	p.Leu414Ile	p.L414I	ENST00000262992	NM_001101669.1	414	Ctc/Atc	14/24	1	2	FACETS	0.889	0.822	0.959	0.889	0.822	0.959	CLONAL	1	TRUE	1	0.45	2		553	950	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159099	143159099	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1332432216	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	141	442	0	ENST00000262992.4:c.754C>T	p.Arg252Ter	p.R252*	ENST00000262992	NM_001101669.1	252	Cga/Tga	10/24	1	2	FACETS	0.889	0.811	0.97	0.889	0.811	0.97	CLONAL	1	TRUE	1	0.45	2		442	705	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509928	187509928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1398903205	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	51	330	1	ENST00000441802.2:c.13585G>A	p.Ala4529Thr	p.A4529T	ENST00000441802	NM_005245.3	4529	Gcg/Acg	27/27	1	2	FACETS	0.34	0.289	0.397	0.34	0.289	0.397	SUBCLONAL	1	TRUE	1	0.45	2		331	666	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541438	187541438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755378789	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	52	499	0	ENST00000441802.2:c.6302G>A	p.Arg2101His	p.R2101H	ENST00000441802	NM_005245.3	2101	cGc/cAc	10/27	1	2	FACETS	0.227	0.192	0.266	0.227	0.192	0.266	SUBCLONAL	1	TRUE	1	0.45	2		499	1017	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542729	187542729	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	50	487	1	ENST00000441802.2:c.5011G>T	p.Glu1671Ter	p.E1671*	ENST00000441802	NM_005245.3	1671	Gaa/Taa	10/27	1	2	FACETS	0.238	0.201	0.279	0.238	0.201	0.279	SUBCLONAL	1	TRUE	1	0.45	2		488	934	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251530	251530	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771111180	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	71	205	0	ENST00000264932.6:c.1741G>A	p.Gly581Arg	p.G581R	ENST00000264932	NM_004168.2	581	Gga/Aga	13/15	1	2	FACETS	0.855	0.751	0.966	0.855	0.751	0.966	CLONAL	1	TRUE	1	0.45	2		205	369	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945794	38945794	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	141	347	0	ENST00000357387.3:c.4432A>C	p.Asn1478His	p.N1478H	ENST00000357387	NM_152756.3	1478	Aat/Cat	34/38	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.45	2		347	584	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177960	56177960	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	262	594	0	ENST00000399503.3:c.2933T>G	p.Leu978Ter	p.L978*	ENST00000399503	NM_005921.1	978	tTa/tGa	14/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.45	2		594	1143	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628427	86628427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	44	257	0	ENST00000274376.6:c.796G>A	p.Glu266Lys	p.E266K	ENST00000274376	NM_002890.2	266	Gaa/Aaa	3/25	1	2	FACETS	0.482	0.404	0.567	0.482	0.404	0.567	SUBCLONAL	1	TRUE	1	0.45	2		257	406	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670680	86670680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	78	315	0	ENST00000274376.6:c.1958G>A	p.Arg653Lys	p.R653K	ENST00000274376	NM_002890.2	653	aGa/aAa	15/25	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.45	2		315	339	SUCCESS
APC	324	MSKCC	GRCh37	5	112175183	112175183	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	23	166	0	ENST00000257430.4:c.3892T>C	p.Ser1298Pro	p.S1298P	ENST00000257430	NM_000038.5	1298	Tct/Cct	16/16	1	2	FACETS	0.3	0.233	0.377	0.3	0.233	0.377	SUBCLONAL	1	TRUE	1	0.45	2		166	341	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694716	176694716	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	210	530	1	ENST00000439151.2:c.5300A>G	p.Tyr1767Cys	p.Y1767C	ENST00000439151	NM_022455.4	1767	tAc/tGc	15/23	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.45	2		531	895	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043465	180043465	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1451816005	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	34	399	0	ENST00000261937.6:c.3121C>T	p.Arg1041Trp	p.R1041W	ENST00000261937	NM_182925.4	1041	Cgg/Tgg	23/30	1	2	FACETS	0.231	0.188	0.28	0.231	0.188	0.28	SUBCLONAL	1	TRUE	1	0.45	2		399	653	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912175	29912175	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs41547331	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	19	128	0	ENST00000376809.5:c.895+1G>A		p.X299_splice	ENST00000376809	NM_002116.7	299			1	2	FACETS	0.444	0.339	0.567	0.444	0.339	0.567	SUBCLONAL	1	TRUE	1	0.45	2		128	190	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43749748	43749748	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	112	611	0	ENST00000523873.1:c.601A>C	p.Thr201Pro	p.T201P	ENST00000523873		201	Acg/Ccg	7/8	1	2	FACETS	0.411	0.368	0.456	0.411	0.368	0.456	SUBCLONAL	1	TRUE	1	0.45	2		611	1212	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609786	117609786	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs141670885	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	208	584	0	ENST00000368508.3:c.6913G>T	p.Glu2305Ter	p.E2305*	ENST00000368508	NM_002944.2	2305	Gaa/Taa	43/43	1	2	FACETS	0.986	0.915	1	0.986	0.915	1	CLONAL	1	TRUE	1	0.45	2		584	938	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647532	117647532	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	189	581	1	ENST00000368508.3:c.5412G>T	p.Lys1804Asn	p.K1804N	ENST00000368508	NM_002944.2	1804	aaG/aaT	33/43	1	2	FACETS	0.904	0.836	0.975	0.904	0.836	0.975	CLONAL	1	TRUE	1	0.45	2		582	929	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686228	117686228	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1489445418	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	85	354	0	ENST00000368508.3:c.3113A>C	p.Glu1038Ala	p.E1038A	ENST00000368508	NM_002944.2	1038	gAa/gCa	20/43	1	2	FACETS	0.512	0.452	0.576	0.512	0.452	0.576	SUBCLONAL	1	TRUE	1	0.45	2		354	738	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117707025	117707025	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	59	284	0	ENST00000368508.3:c.2126-1G>T		p.X709_splice	ENST00000368508	NM_002944.2	709			1	2	FACETS	0.488	0.42	0.562	0.488	0.42	0.562	SUBCLONAL	1	TRUE	1	0.45	2		284	537	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715847	117715847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	150	421	0	ENST00000368508.3:c.911G>A	p.Arg304Lys	p.R304K	ENST00000368508	NM_002944.2	304	aGa/aAa	9/43	1	2	FACETS	0.982	0.9	1	0.982	0.9	1	CLONAL	1	TRUE	1	0.45	2		421	679	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157256631	157256631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1422976996	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	217	460	0	ENST00000346085.5:c.1958C>T	p.Ser653Phe	p.S653F	ENST00000346085	NM_020732.3	653	tCt/tTt	5/20	1	2	FACETS	0.963	0.895	1	0.963	0.895	1	CLONAL	1	TRUE	1	0.45	2		460	1002	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157406006	157406006	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs797045272	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	180	513	2	ENST00000346085.5:c.2248C>T	p.Arg750Ter	p.R750*	ENST00000346085	NM_020732.3	750	Cga/Tga	6/20	1	2	FACETS	0.902	0.832	0.974	0.902	0.832	0.974	CLONAL	1	TRUE	1	0.45	2		515	887	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381567	81381567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370760302	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	192	428	2	ENST00000222390.5:c.494C>T	p.Ser165Leu	p.S165L	ENST00000222390	NM_000601.4	165	tCg/tTg	5/18	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.45	2		430	771	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418859	116418859	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	80	404	0	ENST00000397752.3:c.3370T>G	p.Phe1124Val	p.F1124V	ENST00000397752	NM_000245.2	1124	Ttt/Gtt	17/21	1	2	FACETS	0.435	0.382	0.492	0.435	0.382	0.492	SUBCLONAL	1	TRUE	1	0.45	2		404	817	SUCCESS
MET	4233	MSKCC	GRCh37	7	116422142	116422142	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	59	305	0	ENST00000397752.3:c.3623G>T	p.Arg1208Ile	p.R1208I	ENST00000397752	NM_000245.2	1208	aGa/aTa	18/21	1	2	FACETS	0.438	0.376	0.505	0.438	0.376	0.505	SUBCLONAL	1	TRUE	1	0.45	2		305	599	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850942	128850942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs989582182	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	65	292	0	ENST00000249373.3:c.1789G>A	p.Asp597Asn	p.D597N	ENST00000249373	NM_005631.4	597	Gac/Aac	10/12	1	2	FACETS	0.529	0.459	0.605	0.529	0.459	0.605	SUBCLONAL	1	TRUE	1	0.45	2		292	546	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842334	151842334	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777526116	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	206	485	0	ENST00000262189.6:c.14078G>A	p.Arg4693Gln	p.R4693Q	ENST00000262189	NM_170606.2	4693	cGa/cAa	54/59	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.45	2		485	869	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346115	152346115	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	285	682	1	ENST00000359321.1:c.455C>T	p.Ser152Leu	p.S152L	ENST00000359321	NM_005431.1	152	tCa/tTa	3/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.45	2		683	1159	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485903	8485903	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	49	565	0	ENST00000356435.5:c.2914A>T	p.Ile972Phe	p.I972F	ENST00000356435		972	Att/Ttt	17/35	1	2	FACETS	0.229	0.193	0.268	0.229	0.193	0.268	SUBCLONAL	1	TRUE	1	0.45	2		565	953	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8527354	8527354	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	29	251	0	ENST00000356435.5:c.542-1G>T		p.X181_splice	ENST00000356435		181			1	2	FACETS	0.361	0.29	0.442	0.361	0.29	0.442	SUBCLONAL	1	TRUE	1	0.45	2		251	357	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606578	93606578	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	121	320	1	ENST00000375746.1:c.398A>G	p.Lys133Arg	p.K133R	ENST00000375746	NM_001174167.1	133	aAg/aGg	2/14	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.45	2		321	498	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101909998	101909998	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	154	426	0	ENST00000374994.4:c.1318G>T	p.Glu440Ter	p.E440*	ENST00000374994	NM_004612.2	440	Gaa/Taa	8/9	1	2	FACETS	0.93	0.853	1	0.93	0.853	1	CLONAL	1	TRUE	1	0.45	2		426	736	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406300	70406300	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs750644966	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	195	517	0	ENST00000373644.4:c.3814T>C	p.Ser1272Pro	p.S1272P	ENST00000373644	NM_030625.2	1272	Tcc/Ccc	4/12	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.45	2		517	838	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426835	70426835	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	167	389	0	ENST00000373644.4:c.4495C>A	p.Leu1499Ile	p.L1499I	ENST00000373644	NM_030625.2	1499	Ctt/Att	7/12	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.45	2		389	739	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263935	104263935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775491374	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	167	278	0	ENST00000369902.3:c.26C>T	p.Ala9Val	p.A9V	ENST00000369902	NM_016169.3	9	gCc/gTc	1/12	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.45	2		278	507	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456315	32456315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377072761	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	37	470	1	ENST00000332351.3:c.577G>A	p.Ala193Thr	p.A193T	ENST00000332351	NM_024426.4	193	Gcc/Acc	1/10	1	2	FACETS	0.223	0.183	0.268	0.223	0.183	0.268	SUBCLONAL	1	TRUE	1	0.45	2		471	737	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920785	100920785	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	64	579	0	ENST00000325455.5:c.2363G>T	p.Arg788Leu	p.R788L	ENST00000325455	NM_001202474.3	788	cGg/cTg	6/8	1	2	FACETS	0.282	0.243	0.324	0.282	0.243	0.324	SUBCLONAL	1	TRUE	1	0.45	2		579	1009	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115595	108115595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769166447	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	204	453	0	ENST00000278616.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000278616	NM_000051.3	248	cGa/cAa	7/63	1	2	FACETS	0.991	0.92	1	0.991	0.92	1	CLONAL	1	TRUE	1	0.45	2		453	915	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115681	108115681	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs876660933	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	111	282	0	ENST00000278616.4:c.829G>T	p.Glu277Ter	p.E277*	ENST00000278616	NM_000051.3	277	Gaa/Taa	7/63	1	2	FACETS	0.991	0.895	1	0.991	0.895	1	CLONAL	1	TRUE	1	0.45	2		282	498	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196906	108196906	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381019767	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	89	363	0	ENST00000278616.4:c.6929G>A	p.Ser2310Asn	p.S2310N	ENST00000278616	NM_000051.3	2310	aGt/aAt	47/63	1	2	FACETS	0.517	0.458	0.58	0.517	0.458	0.58	SUBCLONAL	1	TRUE	1	0.45	2		363	765	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344108	118344108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	31	315	0	ENST00000534358.1:c.2234G>A	p.Arg745Gln	p.R745Q	ENST00000534358	NM_005933.3	745	cGa/cAa	3/36	1	2	FACETS	0.241	0.194	0.294	0.241	0.194	0.294	SUBCLONAL	1	TRUE	1	0.45	2		315	572	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503099	125503099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140276570	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	69	457	0	ENST00000428830.2:c.466C>T	p.Arg156Trp	p.R156W	ENST00000428830	NM_001114121.2	156	Cgg/Tgg	6/14	1	2	FACETS	0.399	0.347	0.456	0.399	0.347	0.456	SUBCLONAL	1	TRUE	1	0.45	2		457	768	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409167	4409167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1261984704	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	126	344	1	ENST00000261254.3:c.862G>A	p.Asp288Asn	p.D288N	ENST00000261254	NM_001759.3	288	Gac/Aac	5/5	1	2	FACETS	0.805	0.73	0.883	0.805	0.73	0.883	CLONAL	1	TRUE	1	0.45	2		345	696	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871831	12871831	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs748924503	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	29	231	0	ENST00000228872.4:c.548C>A	p.Ser183Tyr	p.S183Y	ENST00000228872	NM_004064.3	183	tCt/tAt	2/3	1	2	FACETS	0.273	0.219	0.335	0.273	0.219	0.335	SUBCLONAL	1	TRUE	1	0.45	2		231	472	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573931	18573931	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	78	401	0	ENST00000266497.5:c.2249A>C	p.Asn750Thr	p.N750T	ENST00000266497		750	aAt/aCt	15/31	1	2	FACETS	0.446	0.391	0.505	0.446	0.391	0.505	SUBCLONAL	1	TRUE	1	0.45	2		401	778	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425078	49425078	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	103	629	0	ENST00000301067.7:c.13410G>T	p.Lys4470Asn	p.K4470N	ENST00000301067	NM_003482.3	4470	aaG/aaT	39/54	1	2	FACETS	0.441	0.394	0.492	0.441	0.394	0.492	SUBCLONAL	1	TRUE	1	0.45	2		629	1037	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436656	49436656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	162	422	0	ENST00000301067.7:c.5650C>T	p.Pro1884Ser	p.P1884S	ENST00000301067	NM_003482.3	1884	Ccc/Tcc	26/54	1	2	FACETS	0.947	0.871	1	0.947	0.871	1	CLONAL	1	TRUE	1	0.45	2		422	760	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115121002	115121002	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	92	282	0	ENST00000257566.3:c.4A>C	p.Ser2Arg	p.S2R	ENST00000257566	NM_016569.3	2	Agc/Cgc	1/8	1	2	FACETS	0.818	0.729	0.912	0.818	0.729	0.912	CLONAL	1	TRUE	1	0.45	2		282	500	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225538	133225538	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	201	469	0	ENST00000320574.5:c.4126G>T	p.Glu1376Ter	p.E1376*	ENST00000320574	NM_006231.2	1376	Gag/Tag	32/49	1	2	FACETS	0.953	0.884	1	0.953	0.884	1	CLONAL	1	TRUE	1	0.45	2		469	937	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910656	32910656	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	275	725	0	ENST00000380152.3:c.2164A>C	p.Lys722Gln	p.K722Q	ENST00000380152		722	Aaa/Caa	11/27	1	2	FACETS	0.956	0.897	1	0.956	0.897	1	CLONAL	1	TRUE	1	0.45	2		725	1278	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942665	48942665	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	61	414	0	ENST00000267163.4:c.1052T>G	p.Phe351Cys	p.F351C	ENST00000267163	NM_000321.2	351	tTt/tGt	11/27	1	2	FACETS	0.432	0.372	0.497	0.432	0.372	0.497	SUBCLONAL	1	TRUE	1	0.45	2		414	628	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953731	48953731	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs747509282	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	92	294	0	ENST00000267163.4:c.1334G>A	p.Arg445Gln	p.R445Q	ENST00000267163	NM_000321.2	445	cGa/cAa	14/27	1	2	FACETS	0.891	0.795	0.992	0.891	0.795	0.992	CLONAL	1	TRUE	1	0.45	2		294	459	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988537	36988537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	61	630	0	ENST00000354822.5:c.116C>T	p.Thr39Ile	p.T39I	ENST00000354822	NM_001079668.2	39	aCt/aTt	2/3	1	2	FACETS	0.243	0.208	0.281	0.243	0.208	0.281	SUBCLONAL	1	TRUE	1	0.45	2		630	1116	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95596408	95596408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775207591	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	36	375	0	ENST00000393063.1:c.560G>A	p.Arg187Gln	p.R187Q	ENST00000393063	NM_030621.3	187	cGa/cAa	6/28	1	2	FACETS	0.236	0.193	0.285	0.236	0.193	0.285	SUBCLONAL	1	TRUE	1	0.45	2		375	677	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961198	41961198	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	132	759	0	ENST00000219905.7:c.106A>C	p.Thr36Pro	p.T36P	ENST00000219905	NM_001164273.1	36	Act/Cct	2/24	1	2	FACETS	0.462	0.418	0.508	0.462	0.418	0.508	SUBCLONAL	1	TRUE	1	0.45	2		759	1271	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479738	67479738	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	87	536	0	ENST00000327367.4:c.1045G>A	p.Ala349Thr	p.A349T	ENST00000327367	NM_005902.3	349	Gct/Act	8/9	1	2	FACETS	0.421	0.372	0.474	0.421	0.372	0.474	SUBCLONAL	1	TRUE	1	0.45	2		536	919	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669537	88669537	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	244	524	0	ENST00000360948.2:c.1361A>G	p.Asn454Ser	p.N454S	ENST00000360948	NM_001012338.2	454	aAc/aGc	12/19	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.45	2		524	965	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292990	91292990	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	73	390	0	ENST00000355112.3:c.492G>T	p.Glu164Asp	p.E164D	ENST00000355112	NM_000057.2	164	gaG/gaT	3/22	1	2	FACETS	0.487	0.426	0.553	0.487	0.426	0.553	SUBCLONAL	1	TRUE	1	0.45	2		390	666	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396473	396473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	226	563	0	ENST00000262320.3:c.553G>A	p.Ala185Thr	p.A185T	ENST00000262320	NM_003502.3	185	Gcc/Acc	2/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.45	2		563	977	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2221334	2221334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	207	529	4	ENST00000326181.6:c.418G>T	p.Asp140Tyr	p.D140Y	ENST00000326181	NM_032271.2	140	Gac/Tac	6/21	1	2	FACETS	0.961	0.892	1	0.961	0.892	1	CLONAL	1	TRUE	1	0.45	2		533	957	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3824691	3824691	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	153	437	1	ENST00000262367.5:c.2162T>C	p.Met721Thr	p.M721T	ENST00000262367	NM_004380.2	721	aTg/aCg	12/31	1	2	FACETS	0.831	0.761	0.905	0.831	0.761	0.905	CLONAL	1	TRUE	1	0.45	2		438	818	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831302	3831302	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	29	313	0	ENST00000262367.5:c.1579A>C	p.Asn527His	p.N527H	ENST00000262367	NM_004380.2	527	Aat/Cat	7/31	1	2	FACETS	0.227	0.181	0.279	0.227	0.181	0.279	SUBCLONAL	1	TRUE	1	0.45	2		313	569	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032032	10032032	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	236	620	0	ENST00000330684.3:c.791A>G	p.Asn264Ser	p.N264S	ENST00000330684	NM_001134407.1	264	aAc/aGc	3/13	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.45	2		620	1041	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646806	23646806	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1555461474	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	195	584	0	ENST00000261584.4:c.1061C>A	p.Ser354Tyr	p.S354Y	ENST00000261584	NM_024675.3	354	tCt/tAt	4/13	1	2	FACETS	0.864	0.799	0.931	0.864	0.799	0.931	CLONAL	1	TRUE	1	0.45	2		584	1003	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864504	56864504	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	296	723	0	ENST00000308159.5:c.992T>C	p.Leu331Pro	p.L331P	ENST00000308159	NM_014669.4	331	cTg/cCg	10/22	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.45	2		723	1313	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828029	72828029	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1502	98	887	1	ENST00000268489.5:c.8552G>T	p.Gly2851Val	p.G2851V	ENST00000268489	NM_006885.3	2851	gGc/gTc	9/10	1	2	FACETS	0.272	0.241	0.305	0.272	0.241	0.305	SUBCLONAL	1	TRUE	1	0.45	2		888	1600	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828767	72828767	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	260	756	0	ENST00000268489.5:c.7814C>G	p.Ser2605Ter	p.S2605*	ENST00000268489	NM_006885.3	2605	tCa/tGa	9/10	1	2	FACETS	0.881	0.824	0.94	0.881	0.824	0.94	CLONAL	1	TRUE	1	0.45	2		756	1312	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627803	37627803	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	128	588	0	ENST00000447079.4:c.1718T>C	p.Phe573Ser	p.F573S	ENST00000447079	NM_015083.1	573	tTt/tCt	2/14	1	2	FACETS	0.491	0.444	0.541	0.491	0.444	0.541	SUBCLONAL	1	TRUE	1	0.45	2		588	1158	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864776	37864776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs185670819	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	120	309	0	ENST00000269571.5:c.428G>A	p.Arg143Gln	p.R143Q	ENST00000269571		143	cGa/cAa	3/27	1	2	FACETS	0.924	0.838	1	0.924	0.838	1	CLONAL	1	TRUE	1	0.45	2		309	577	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47684637	47684637	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	188	443	0	ENST00000347630.2:c.812A>G	p.Asp271Gly	p.D271G	ENST00000347630	NM_001007230.1	271	gAt/gGt	9/11	1	2	FACETS	0.847	0.782	0.914	0.847	0.782	0.914	CLONAL	1	TRUE	1	0.45	2		443	987	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740750	58740750	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760201595	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	288	719	3	ENST00000305921.3:c.1655G>A	p.Arg552Gln	p.R552Q	ENST00000305921	NM_003620.3	552	cGa/cAa	6/6	1	2	FACETS	0.953	0.895	1	0.953	0.895	1	CLONAL	1	TRUE	1	0.45	2		722	1343	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926523	59926523	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	206	511	1	ENST00000259008.2:c.474G>T	p.Lys158Asn	p.K158N	ENST00000259008	NM_032043.2	158	aaG/aaT	5/20	1	2	FACETS	0.958	0.889	1	0.958	0.889	1	CLONAL	1	TRUE	1	0.45	2		512	956	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533560	63533560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755551294	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	51	571	1	ENST00000307078.5:c.1594G>A	p.Glu532Lys	p.E532K	ENST00000307078	NM_004655.3	532	Gag/Aag	6/11	1	2	FACETS	0.224	0.189	0.262	0.224	0.189	0.262	SUBCLONAL	1	TRUE	1	0.45	2		572	1012	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78617526	78617526	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	156	333	0	ENST00000306801.3:c.266-2A>G		p.X89_splice	ENST00000306801	NM_020761.2	89			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.45	2		333	597	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609349	39609349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201418439	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	48	434	2	ENST00000262039.4:c.1651C>T	p.Arg551Trp	p.R551W	ENST00000262039	NM_002647.2	551	Cgg/Tgg	15/25	1	2	FACETS	0.239	0.201	0.282	0.239	0.201	0.282	SUBCLONAL	1	TRUE	1	0.45	2		436	891	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216658	2216658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758184437	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	71	374	1	ENST00000398665.3:c.2302G>A	p.Ala768Thr	p.A768T	ENST00000398665	NM_032482.2	768	Gca/Aca	20/28	1	2	FACETS	0.504	0.44	0.573	0.504	0.44	0.573	SUBCLONAL	1	TRUE	1	0.45	2		375	626	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626904	14626904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	146	779	0	ENST00000254322.2:c.871C>T	p.Pro291Ser	p.P291S	ENST00000254322	NM_006145.1	291	Cct/Tct	3/3	1	2	FACETS	0.503	0.457	0.55	0.503	0.457	0.55	SUBCLONAL	1	TRUE	1	0.45	2		779	1291	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943395	17943395	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs201643826	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	243	586	0	ENST00000458235.1:c.2613G>T	p.Glu871Asp	p.E871D	ENST00000458235	NM_000215.3	871	gaG/gaT	19/24	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.45	2		586	1079	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946810	17946810	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs149316157	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	47	531	3	ENST00000458235.1:c.1837C>T	p.Arg613Ter	p.R613*	ENST00000458235	NM_000215.3	613	Cga/Tga	14/24	1	2	FACETS	0.242	0.203	0.285	0.242	0.203	0.285	SUBCLONAL	1	TRUE	1	0.45	2		534	862	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387111	31387111	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	198	411	0	ENST00000328111.2:c.1736C>A	p.Ser579Ter	p.S579*	ENST00000328111	NM_006892.3	579	tCa/tAa	16/23	1	2	FACETS	0.97	0.899	1	0.97	0.899	1	CLONAL	1	TRUE	1	0.45	2		411	907	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39726860	39726860	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	142	312	0	ENST00000361337.2:c.858G>T	p.Met286Ile	p.M286I	ENST00000361337	NM_003286.2	286	atG/atT	11/21	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.45	2		312	585	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268417	46268417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	276	715	0	ENST00000371998.3:c.2804C>T	p.Ser935Leu	p.S935L	ENST00000371998		935	tCa/tTa	15/23	1	2	FACETS	0.953	0.894	1	0.953	0.894	1	CLONAL	1	TRUE	1	0.45	2		715	1287	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159110	24159110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779587990	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	122	313	1	ENST00000263121.7:c.782G>A	p.Arg261His	p.R261H	ENST00000263121	NM_003073.3	261	cGc/cAc	6/9	1	2	FACETS	0.855	0.775	0.94	0.855	0.775	0.94	CLONAL	1	TRUE	1	0.45	2		314	634	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091160	29091160	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	120	253	0	ENST00000328354.6:c.1330A>C	p.Lys444Gln	p.K444Q	ENST00000328354	NM_007194.3	444	Aaa/Caa	12/15	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.45	2		253	494	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121319	29121319	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	222	565	0	ENST00000328354.6:c.356A>C	p.Lys119Thr	p.K119T	ENST00000328354	NM_007194.3	119	aAa/aCa	3/15	1	2	FACETS	0.971	0.904	1	0.971	0.904	1	CLONAL	1	TRUE	1	0.45	2		565	1016	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574926	41574926	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	70	429	0	ENST00000263253.7:c.7211C>A	p.Ser2404Ter	p.S2404*	ENST00000263253	NM_001429.3	2404	tCa/tAa	31/31	1	2	FACETS	0.378	0.329	0.431	0.378	0.329	0.431	SUBCLONAL	1	TRUE	1	0.45	2		429	823	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314969	1314969	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	209	512	0	ENST00000400841.2:c.692A>C	p.Lys231Thr	p.K231T	ENST00000400841		231	aAa/aCa	6/6	1	2	FACETS	0.976	0.906	1	0.976	0.906	1	CLONAL	1	TRUE	1	0.45	2		512	952	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429358	47429358	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	199	633	2	ENST00000377045.4:c.1486G>A	p.Gly496Arg	p.G496R	ENST00000377045	NM_001654.4	496	Ggg/Agg	14/16	1	2	FACETS	0.848	0.785	0.913	0.848	0.785	0.913	CLONAL	1	TRUE	1	0.45	2		635	1043	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223505	53223505	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	46	289	0	ENST00000375401.3:c.3854C>A	p.Ala1285Asp	p.A1285D	ENST00000375401	NM_004187.3	1285	gCc/gAc	23/26	1	2	FACETS	0.419	0.353	0.492	0.419	0.353	0.492	SUBCLONAL	1	TRUE	1	0.45	2		289	488	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410075	63410075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201899164	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	47	638	0	ENST00000330258.3:c.3092G>A	p.Gly1031Asp	p.G1031D	ENST00000330258	NM_152424.3	1031	gGc/gAc	2/2	1	2	FACETS	0.222	0.186	0.262	0.222	0.186	0.262	SUBCLONAL	1	TRUE	1	0.45	2		638	940	SUCCESS
AR	367	MSKCC	GRCh37	X	66765047	66765047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1297947716	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	234	638	1	ENST00000374690.3:c.59G>A	p.Arg20Gln	p.R20Q	ENST00000374690	NM_000044.3	20	cGa/cAa	1/8	1	2	FACETS	0.978	0.912	1	0.978	0.912	1	CLONAL	1	TRUE	1	0.45	2		639	1063	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343020	70343020	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	200	532	0	ENST00000374080.3:c.1561C>T	p.Arg521Cys	p.R521C	ENST00000374080		521	Cgt/Tgt	11/45	1	2	FACETS	0.897	0.831	0.965	0.897	0.831	0.965	CLONAL	1	TRUE	1	0.45	2		532	991	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778774	76778774	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	104	663	0	ENST00000373344.5:c.6805G>T	p.Glu2269Ter	p.E2269*	ENST00000373344	NM_000489.3	2269	Gaa/Taa	31/35	1	2	FACETS	0.361	0.322	0.403	0.361	0.322	0.403	SUBCLONAL	1	TRUE	1	0.45	2		663	1279	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778843	76778843	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	224	649	1	ENST00000373344.5:c.6736G>T	p.Glu2246Ter	p.E2246*	ENST00000373344	NM_000489.3	2246	Gaa/Taa	31/35	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.45	2		650	983	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874293	76874293	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	228	527	0	ENST00000373344.5:c.5429T>C	p.Met1810Thr	p.M1810T	ENST00000373344	NM_000489.3	1810	aTg/aCg	21/35	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.45	2		527	938	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891498	76891498	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	203	620	0	ENST00000373344.5:c.4607A>G	p.Lys1536Arg	p.K1536R	ENST00000373344	NM_000489.3	1536	aAg/aGg	16/35	1	2	FACETS	0.889	0.824	0.956	0.889	0.824	0.956	CLONAL	1	TRUE	1	0.45	2		620	1015	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938794	76938794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	230	551	2	ENST00000373344.5:c.1954G>A	p.Asp652Asn	p.D652N	ENST00000373344	NM_000489.3	652	Gat/Aat	9/35	1	2	FACETS	0.998	0.931	1	0.998	0.931	1	CLONAL	1	TRUE	1	0.45	2		553	1024	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215312	123215312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1214610561	NA	P-0012445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	216	602	1	ENST00000218089.9:c.2858G>A	p.Arg953Gln	p.R953Q	ENST00000218089	NM_001042749.1	953	cGa/cAa	28/35	1	2	FACETS	0.939	0.873	1	0.939	0.873	1	CLONAL	1	TRUE	1	0.45	2		603	1022	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0012450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	308	621	2	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.346285090658443	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.346285090658443	2		623	753	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	331	722	0	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	0.346285090658443	2	FACETS	0.956	0.905	1	0.956	0.905	1	CLONAL	2	TRUE	0	0.346285090658443	2		722	1000	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949113	151949120	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTCTTT	TCTTCTTT	-	novel	NA	P-0012450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	123	628	0	ENST00000262189.6:c.1525_1532del	p.Lys509ValfsTer7	p.K509Vfs*7	ENST00000262189	NM_170606.2	509	AAAGAAGAg/g	11/59	NA	2	FACETS	0.926	0.838	1			1	INDETERMINATE	1	TRUE	NA	0.346285090658443	2		628	767	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	499	697	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.174210862214156	5	FACETS	0.9	0.863	0.937			1	INDETERMINATE	3	TRUE	NA	0.572036164361914	5		697	1201	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097624	11097625	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1165714406	NA	P-0012545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	671	946	3	ENST00000358026.2:c.810dup	p.Gly271ArgfsTer16	p.G271Rfs*16	ENST00000358026	NM_001128849.1	268	-/C	5/36	0.572036164361914	2	FACETS	0.91	0.881	0.939	0.91	0.881	0.939	CLONAL	2	TRUE	0	0.572036164361914	2		949	1289	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082339	16082339	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1387579404	NA	P-0012545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	307	692	0	ENST00000281043.3:c.153G>T	p.Lys51Asn	p.K51N	ENST00000281043	NM_005378.4	51	aaG/aaT	2/3	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.572036164361914	2		692	918	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356133	66356133	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	288	629	0	ENST00000273854.3:c.1364G>T	p.Arg455Leu	p.R455L	ENST00000273854	NM_004439.5	455	cGg/cTg	5/18	1	2	FACETS	0.997	0.939	1	0.997	0.939	1	CLONAL	1	TRUE	1	0.572036164361914	2		629	1010	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84388683	84388683	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	196	552	0	ENST00000321945.7:c.605T>G	p.Phe202Cys	p.F202C	ENST00000321945	NM_139076.2	202	tTt/tGt	7/9	1	2	FACETS	0.909	0.844	0.976	0.909	0.844	0.976	CLONAL	1	TRUE	1	0.572036164361914	2		552	754	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524634	106524634	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	239	480	1	ENST00000359195.3:c.2795G>T	p.Cys932Phe	p.C932F	ENST00000359195	NM_002649.2	932	tGt/tTt	9/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.572036164361914	2		481	748	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224163	98224163	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	252	549	2	ENST00000331920.6:c.2678G>T	p.Arg893Leu	p.R893L	ENST00000331920	NM_000264.3	893	cGc/cTc	16/24	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.572036164361914	2		551	860	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332729	70332729	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	223	532	1	ENST00000373644.4:c.634G>A	p.Glu212Lys	p.E212K	ENST00000373644	NM_030625.2	212	Gag/Aag	2/12	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.572036164361914	2		533	771	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934917	9934917	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	281	606	0	ENST00000330684.3:c.1373G>T	p.Gly458Val	p.G458V	ENST00000330684	NM_001134407.1	458	gGg/gTg	6/13	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.572036164361914	2		606	899	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805351	89805351	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	319	662	0	ENST00000389301.3:c.4199G>T	p.Arg1400Leu	p.R1400L	ENST00000389301	NM_000135.2	1400	cGt/cTt	42/43	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.572036164361914	2		662	1085	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222985	1222985	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	313	346	0	ENST00000326873.7:c.922T>G	p.Trp308Gly	p.W308G	ENST00000326873	NM_000455.4	308	Tgg/Ggg	8/10	0.572036164361914	2	FACETS	0.993	0.949	1	0.993	0.949	1	CLONAL	2	TRUE	0	0.572036164361914	2		346	551	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2214594	2214594	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	412	507	0	ENST00000398665.3:c.1922A>T	p.Gln641Leu	p.Q641L	ENST00000398665	NM_032482.2	641	cAg/cTg	19/28	0.572036164361914	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.572036164361914	2		507	707	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600425	10600425	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	748	885	1	ENST00000171111.5:c.1430del	p.Gly477AlafsTer23	p.G477Afs*23	ENST00000171111	NM_203500.1	477	gGc/gc	4/6	0.572036164361914	2	FACETS	0.997	0.969	1	0.997	0.969	1	CLONAL	2	TRUE	0	0.572036164361914	2		886	1311	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501602	149501602	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	184	351	0	ENST00000261799.4:c.2185del	p.His729MetfsTer4	p.H729Mfs*4	ENST00000261799	NM_002609.3	729	Cat/at	16/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.572036164361914	2		351	575	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861837	57861837	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs759838377	NA	P-0012546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1227	448	996	2	ENST00000228682.2:c.1138C>T	p.Arg380Ter	p.R380*	ENST00000228682	NM_005269.2	380	Cga/Tga	10/12	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.512746922440535	2		998	1675	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115965	8115966	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0012546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	91	264	0	ENST00000346208.3:c.1312_1313dup	p.Met438IlefsTer38	p.M438Ifs*38	ENST00000346208		437	-/AT	6/6	1	2	FACETS	0.849	0.758	0.945	0.849	0.758	0.945	CLONAL	1	TRUE	1	0.512746922440535	2		264	418	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0012573-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	39	440	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.115249973139689	4	FACETS	1	0.882	1	0.539	0.448	0.641	INDETERMINATE	1	FALSE	2	0.259443228433962	4		440	351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0012573-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	96	582	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	0.198118131362013	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	2	FALSE	0	0.259443228433962	2		582	353	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217240	11217240	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148486930	NA	P-0012573-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	74	579	1	ENST00000361445.4:c.4438C>T	p.Arg1480Cys	p.R1480C	ENST00000361445	NM_004958.3	1480	Cgc/Tgc	30/58	0.157858869785478	2	FACETS	1	0.948	1	0.577	0.507	0.653	CLONAL	1	FALSE	0	0.259443228433962	2		580	494	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573549	48573549	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0012573-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	51	466	0	ENST00000342988.3:c.133A>T	p.Lys45Ter	p.K45*	ENST00000342988	NM_005359.5	45	Aag/Tag	2/12	0.209735985145798	3	FACETS	1	0.854	1	0.501	0.427	0.583	CLONAL	1	FALSE	1	0.259443228433962	3		466	443	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366650	40366650	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	14	518	0	ENST00000397332.2:c.547A>C	p.Thr183Pro	p.T183P	ENST00000397332	NM_001033082.2	183	Acc/Ccc	2/3	0.456123177481878	6	FACETS	0.665	0.484	0.881	0.222	0.161	0.294	INDETERMINATE	1	FALSE	3	0.827575531223728	6		518	135	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	143	592	0	ENST00000269305.4:c.745del	p.Arg249GlyfsTer96	p.R249Gfs*96	ENST00000269305	NM_001126112.2	249	Agg/gg	7/11	0.737634576330351	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	FALSE	0	0.827575531223728	3		592	161	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224352	55224353	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0012636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	10	518	0	ENST00000275493.2:c.1133+1_1133+2insAG		p.G378fs	ENST00000275493	NM_005228.3	378	ggt/ggGAt		0.827575531223728	5	FACETS	0.381	0.259	0.534	0.127	0.086	0.178	SUBCLONAL	1	FALSE	2	0.827575531223728	5		518	142	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89355022	89355022	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	16	822	0	ENST00000301030.4:c.658C>G	p.Leu220Val	p.L220V	ENST00000301030	NM_001256183.1	220	Ctg/Gtg	7/13	0.773263716965837	4	FACETS	0.257	0.19	0.337	0.064	0.047	0.085	SUBCLONAL	1	FALSE	0	0.827575531223728	4		822	275	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17120391	17120391	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs991762823	NA	P-0012636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	33	535	0	ENST00000285071.4:c.1168G>A	p.Val390Ile	p.V390I	ENST00000285071	NM_144997.5	390	Gta/Ata	10/14	0.737634576330351	3	FACETS	1	0.906	1	0.376	0.314	0.441	CLONAL	1	FALSE	0	0.827575531223728	3		535	100	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939957	76939958	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	96	786	0	ENST00000373344.5:c.790dup	p.Tyr264LeufsTer18	p.Y264Lfs*18	ENST00000373344	NM_000489.3	264	tat/tTat	9/35	0.67641081856776	6	FACETS	1	0.943	1			1	CLONAL	3	FALSE	NA	0.827575531223728	6		786	197	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28931588	NA	P-0012643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	220	462	0	ENST00000349496.5:c.94G>C	p.Asp32His	p.D32H	ENST00000349496	NM_001904.3	32	Gac/Cac	3/15	1	2	FACETS	0.767	0.714	0.821	0.767	0.714	0.821	SUBCLONAL	1	TRUE	1	0.621196972408688	2		462	924	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138599	2138610	+	stop_lost,inframe_deletion	Nonstop_Mutation	DEL	CGAGTTTGTGTG	CGAGTTTGTGTG	-	novel	NA	P-0012643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	320	437	1	ENST00000219476.3:c.5412_5423del	p.Glu1805_Ter1808delextTer15	p.E1805_*1808delext*15	ENST00000219476	NM_000548.3	1805	acCGAGTTTGTGTGa/aca	42/42	0.281117853311091	5	FACETS	1	0.976	1	0.704	0.666	0.742	INDETERMINATE	2	TRUE	2	0.621196972408688	5		438	943	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196950	108196951	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0012643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	271	261	0	ENST00000278616.4:c.6974_6975insCC	p.Asn2326ArgfsTer6	p.N2326Rfs*6	ENST00000278616	NM_000051.3	2325	gcg/gCCcg	47/63	0.563701187597884	2	FACETS	0.823	0.781	0.865	0.823	0.781	0.865	CLONAL	2	TRUE	0	0.621196972408688	2		261	530	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143258	58143258	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	160	441	0	ENST00000257904.6:c.662A>G	p.Asp221Gly	p.D221G	ENST00000257904	NM_000075.3	221	gAc/gGc	6/8	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.63119148099231	2		441	506	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7978914	7978915	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	GAGCTCTCCC	novel	NA	P-0012669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	114	566	0	ENST00000319144.4:c.1643_1652dup	p.Phe553GlufsTer6	p.F553Efs*6	ENST00000319144	NM_001139.2	551	tca/tcGGGAGAGCTCa	12/15	1	2	FACETS	0.74	0.67	0.814	0.74	0.67	0.814	SUBCLONAL	1	TRUE	1	0.63119148099231	2		566	488	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845261	151845261	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	191	619	0	ENST00000262189.6:c.13751G>A	p.Arg4584Gln	p.R4584Q	ENST00000262189	NM_170606.2	4584	cGg/cAg	52/59	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.63119148099231	2		619	583	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0012683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	105	406	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	0.559	0.5	0.621	0.559	0.5	0.621	SUBCLONAL	1	TRUE	1	0.415842101045721	2		406	904	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143035	30143035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	118	506	2	ENST00000389048.3:c.491G>A	p.Gly164Glu	p.G164E	ENST00000389048	NM_004304.4	164	gGg/gAg	1/29	0.403388380113282	3	FACETS	0.601	0.541	0.665	0.3	0.27	0.333	SUBCLONAL	1	TRUE	1	0.415842101045721	3		508	1141	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220303	98220303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	110	316	1	ENST00000331920.6:c.3160G>A	p.Gly1054Arg	p.G1054R	ENST00000331920	NM_000264.3	1054	Ggg/Agg	18/24	1	2	FACETS	0.731	0.657	0.809	0.731	0.657	0.809	SUBCLONAL	1	TRUE	1	0.415842101045721	2		317	724	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037475	12037475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs724159946	NA	P-0012683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	154	318	0	ENST00000396373.4:c.1106G>A	p.Arg369Gln	p.R369Q	ENST00000396373	NM_001987.4	369	cGg/cAg	6/8	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.415842101045721	2		318	694	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883138	37883138	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3049	10073	552	2	ENST00000269571.5:c.3041T>A	p.Met1014Lys	p.M1014K	ENST00000269571		1014	aTg/aAg	25/27	0.415842101045721	37	FACETS	0.986	0.98	0.992			1	CLONAL	31	TRUE	NA	0.415842101045721	37		554	13122	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29083947	29083947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876658872	NA	P-0012683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	35	87	0	ENST00000328354.6:c.1570G>A	p.Glu524Lys	p.E524K	ENST00000328354	NM_007194.3	524	Gaa/Aaa	15/15	1	2	FACETS	0.813	0.672	0.968	0.813	0.672	0.968	CLONAL	1	TRUE	1	0.415842101045721	2		87	207	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545115	41545115	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1286	221	511	0	ENST00000263253.7:c.2315C>A	p.Ser772Ter	p.S772*	ENST00000263253	NM_001429.3	772	tCa/tAa	13/31	1	2	FACETS	0.705	0.654	0.758	0.705	0.654	0.758	SUBCLONAL	1	TRUE	1	0.415842101045721	2		511	1507	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345893	70345893	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	193	202	0	ENST00000374080.3:c.2430G>C	p.Glu810Asp	p.E810D	ENST00000374080		810	gaG/gaC	18/45	0.332350314477154	2	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.415842101045721	2		202	709	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576923	7576955	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAA	AGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAA	-	novel	NA	P-0012683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	263	403	0	ENST00000269305.4:c.920-29_923del		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	0.369327115740009	2	FACETS	0.756	0.71	0.802	0.756	0.71	0.802	SUBCLONAL	2	TRUE	0	0.415842101045721	2		403	837	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119562123	119562124	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0012683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	205	457	0	ENST00000316626.5:c.1212dup	p.Thr405HisfsTer10	p.T405Hfs*10	ENST00000316626		404	-/C	11/12	1	2	FACETS	0.95	0.881	1	0.95	0.881	1	CLONAL	1	TRUE	1	0.415842101045721	2		457	1038	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692979	89692979	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123325	NA	P-0012717-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	287	298	0	ENST00000371953.3:c.463T>C	p.Tyr155His	p.Y155H	ENST00000371953	NM_000314.4	155	Tat/Cat	5/9	0.900426968355235	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.900426968355235	1		298	338	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807361	36807362	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCGCAGGTAGCGCTGCGC	novel	NA	P-0012717-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	190	447	0	ENST00000373129.3:c.1285_1302dup	p.Ala429_Arg434dup	p.A429_R434dup	ENST00000373129	NM_032017.1	429	-/GCGCAGCGCTACCTGCGG	12/12	1	2	FACETS	0.634	0.588	0.681	0.634	0.588	0.681	SUBCLONAL	1	TRUE	1	0.900426968355235	2		447	666	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466019	69466019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	153	588	0	ENST00000227507.2:c.857C>T	p.Thr286Ile	p.T286I	ENST00000227507	NM_053056.2	286	aCa/aTa	5/5	1	2	FACETS	0.807	0.741	0.876	0.807	0.741	0.876	CLONAL	1	TRUE	1	0.57	2		588	665	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	52	1035	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.147	0.125	0.173	0.147	0.125	0.173	SUBCLONAL	1	TRUE	1	0.57	2		1036	1238	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	193	498	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.921	0.855	0.99	0.921	0.855	0.99	CLONAL	1	TRUE	1	0.57	2		498	735	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	245	240	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	0.57	2		240	789	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	52	201	2	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.931	0.804	1	0.931	0.804	1	CLONAL	1	TRUE	1	0.57	2		203	196	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	158	333	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.57	2		335	537	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	187	406	4	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.952	0.883	1	0.952	0.883	1	CLONAL	1	TRUE	1	0.57	2		410	689	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	275	872	2	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	1	2	FACETS	0.996	0.936	1	0.996	0.936	1	CLONAL	1	TRUE	1	0.57	2		874	969	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141498	11141498	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	46	646	2	ENST00000358026.2:c.3480del	p.Leu1161SerfsTer3	p.L1161Sfs*3	ENST00000358026	NM_001128849.1	1159	Ggg/gg	25/36	1	2	FACETS	0.188	0.158	0.222	0.188	0.158	0.222	SUBCLONAL	1	TRUE	1	0.57	2		648	857	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	184	494	0	ENST00000397062.3:c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	NM_006164.4	34	Cga/Gga	2/5	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.57	2		494	516	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	56	423	2	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.177	0.151	0.206	0.177	0.151	0.206	SUBCLONAL	1	TRUE	1	0.57	2		425	1109	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444659	78444659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs908264837	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	158	418	0	ENST00000370768.2:c.30del	p.Ser11LeufsTer43	p.S11Lfs*43	ENST00000370768	NM_003902.3	10	ccC/cc	1/20	1	2	FACETS	0.912	0.839	0.987	0.912	0.839	0.987	CLONAL	1	TRUE	1	0.57	2		418	608	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	57	235	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	1	2	FACETS	0.73	0.632	0.835	0.73	0.632	0.835	SUBCLONAL	1	TRUE	1	0.57	2		235	274	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310208	91310208	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs747341586	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	196	659	2	ENST00000355112.3:c.2268del	p.Asp757ThrfsTer4	p.D757Tfs*4	ENST00000355112	NM_000057.2	754	tcA/tc	10/22	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.57	2		661	657	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163553	32163554	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs777647776	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	73	500	3	ENST00000375023.3:c.5672dup	p.Gly1892ArgfsTer24	p.G1892Rfs*24	ENST00000375023	NM_004557.3	1891	ggc/ggGc	30/30	1	2	FACETS	0.485	0.425	0.55	0.485	0.425	0.55	SUBCLONAL	1	TRUE	1	0.57	2		503	528	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	377	1055	0	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.57	2		1055	1252	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45422959	45422959	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	110	915	2	ENST00000262160.6:c.169C>T	p.Arg57Ter	p.R57*	ENST00000262160	NM_005901.5	57	Cga/Tga	2/11	1	2	FACETS	0.345	0.309	0.383	0.345	0.309	0.383	SUBCLONAL	1	TRUE	1	0.57	2		917	1120	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101117	27101117	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	293	269	2	ENST00000324856.7:c.4403del	p.Pro1468LeufsTer13	p.P1468Lfs*13	ENST00000324856	NM_006015.4	1467	Ccc/cc	18/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.57	2		271	1002	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436128	56436128	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	330	765	1	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	0.57	2		766	1098	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617680	39617680	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	140	561	0	ENST00000262039.4:c.1869del	p.Phe623LeufsTer43	p.F623Lfs*43	ENST00000262039	NM_002647.2	622	Ttt/tt	17/25	1	2	FACETS	0.939	0.86	1	0.939	0.86	1	CLONAL	1	TRUE	1	0.57	2		561	523	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	144	974	0	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	0.496	0.452	0.543	0.496	0.452	0.543	SUBCLONAL	1	TRUE	1	0.57	2		974	1018	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432379	78432379	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	133	378	0	ENST00000370768.2:c.472C>A	p.Gln158Lys	p.Q158K	ENST00000370768	NM_003902.3	158	Cag/Aag	7/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.57	2		378	451	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085999	16085999	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	210	481	0	ENST00000281043.3:c.1175A>G	p.Gln392Arg	p.Q392R	ENST00000281043	NM_005378.4	392	cAg/cGg	3/3	1	2	FACETS	0.972	0.905	1	0.972	0.905	1	CLONAL	1	TRUE	1	0.57	2		481	758	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279557	1279557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	179	513	0	ENST00000310581.5:c.1979C>T	p.Ala660Val	p.A660V	ENST00000310581	NM_198253.2	660	gCa/gTa	5/16	1	2	FACETS	0.926	0.857	0.998	0.926	0.857	0.998	CLONAL	1	TRUE	1	0.57	2		513	678	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176683975	176683975	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	295	858	0	ENST00000439151.2:c.4789A>T	p.Lys1597Ter	p.K1597*	ENST00000439151	NM_022455.4	1597	Aag/Tag	13/23	1	2	FACETS	0.968	0.912	1	0.968	0.912	1	CLONAL	1	TRUE	1	0.57	2		858	1069	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140449215	140449215	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	54	322	0	ENST00000288602.6:c.1864C>T	p.Pro622Ser	p.P622S	ENST00000288602	NM_004333.4	622	Cca/Tca	16/18	1	2	FACETS	0.962	0.834	1	0.962	0.834	1	CLONAL	1	TRUE	1	0.57	2		322	197	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960177	151960177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773970643	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	142	481	1	ENST00000262189.6:c.1223C>T	p.Thr408Met	p.T408M	ENST00000262189	NM_170606.2	408	aCg/aTg	9/59	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.57	2		482	444	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347638	118347638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	149	629	0	ENST00000534358.1:c.3275C>T	p.Thr1092Ile	p.T1092I	ENST00000534358	NM_005933.3	1092	aCc/aTc	4/36	1	2	FACETS	0.557	0.508	0.608	0.557	0.508	0.608	SUBCLONAL	1	TRUE	1	0.57	2		629	939	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133242037	133242037	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	212	381	0	ENST00000320574.5:c.2320-1G>T		p.X774_splice	ENST00000320574	NM_006231.2	774			1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.57	2		381	607	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557797	21557797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	299	732	0	ENST00000382592.4:c.2048G>A	p.Cys683Tyr	p.C683Y	ENST00000382592	NM_014572.2	683	tGc/tAc	5/8	1	2	FACETS	0.964	0.909	1	0.964	0.909	1	CLONAL	1	TRUE	1	0.57	2		732	1088	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782423	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	181	515	0	ENST00000269305.4:c.217G>A	p.Val73Met	p.V73M	ENST00000269305	NM_001126112.2	73	Gtg/Atg	4/11	1	2	FACETS	0.962	0.891	1	0.962	0.891	1	CLONAL	1	TRUE	1	0.57	2		515	660	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435622	56435622	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	124	340	0	ENST00000407977.2:c.1515T>A	p.Phe505Leu	p.F505L	ENST00000407977		505	ttT/ttA	9/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.57	2		340	407	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713366	40713366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	301	632	0	ENST00000373198.4:c.4149G>T	p.Gln1383His	p.Q1383H	ENST00000373198	NM_133170.3	1383	caG/caT	30/32	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.57	2		632	951	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652537	48652537	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs782599587	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	25	388	0	ENST00000376670.3:c.1208C>G	p.Thr403Ser	p.T403S	ENST00000376670	NM_002049.3	403	aCc/aGc	6/6	1	2	FACETS	0.192	0.151	0.24	0.192	0.151	0.24	SUBCLONAL	1	TRUE	1	0.57	2		388	456	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305440	65305440	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	76	590	0	ENST00000342505.4:c.2688del	p.Glu897LysfsTer14	p.E897Kfs*14	ENST00000342505	NM_002227.2	896	ccC/cc	20/25	1	2	FACETS	0.408	0.357	0.462	0.408	0.357	0.462	SUBCLONAL	1	TRUE	1	0.57	2		590	654	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150549852	150549859	+	frameshift_variant,stop_lost	Frame_Shift_Del	DEL	TATCTTAT	TATCTTAT	-	novel	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	175	561	0	ENST00000369026.2:c.1045_1052del	p.Ile349AlafsTer4	p.I349Afs*4	ENST00000369026	NM_021960.4	349	ATAAGATAg/g	3/3	1	2	FACETS	0.953	0.882	1	0.953	0.882	1	CLONAL	1	TRUE	1	0.57	2		561	644	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845628	63845628	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	111	275	0	ENST00000279873.7:c.1370del	p.Asn457MetfsTer22	p.N457Mfs*22	ENST00000279873	NM_032199.2	456	gAa/ga	9/10	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.57	2		275	388	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927422	49927422	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1291	248	1136	1	ENST00000296474.3:c.3882del	p.Phe1294LeufsTer26	p.F1294Lfs*26	ENST00000296474	NM_002447.2	1294	ttT/tt	19/20	1	2	FACETS	0.565	0.527	0.605	0.565	0.527	0.605	SUBCLONAL	1	TRUE	1	0.57	2		1137	1539	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020818	112020819	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1384	491	1031	0	ENST00000368678.4:c.752dup	p.Gln252ThrfsTer7	p.Q252Tfs*7	ENST00000368678		251	cca/ccCa	8/13	1	2	FACETS	0.919	0.877	0.962	0.919	0.877	0.962	CLONAL	1	TRUE	1	0.57	2		1031	1875	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830620	72830620	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1218	422	1166	0	ENST00000268489.5:c.5961del	p.Cys1988AlafsTer9	p.C1988Afs*9	ENST00000268489	NM_006885.3	1987	tcC/tc	9/10	1	2	FACETS	0.903	0.858	0.948	0.903	0.858	0.948	CLONAL	1	TRUE	1	0.57	2		1166	1640	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874316	76874316	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	39	919	0	ENST00000373344.5:c.5406del	p.Lys1802AsnfsTer10	p.K1802Nfs*10	ENST00000373344	NM_000489.3	1802	aaA/aa	21/35	1	2	FACETS	0.178	0.146	0.213	0.178	0.146	0.213	SUBCLONAL	1	TRUE	1	0.57	2		919	770	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242444	55242445	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAAATTCCCGTCGCTATC	rs397517090	NA	P-0012745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	463	344	0	ENST00000275493.2:c.2217_2234dup	p.Ile740_Lys745dup	p.I740_K745dup	ENST00000275493	NM_005228.3	740	-/AAAATTCCCGTCGCTATC	19/28	0.21078070958508	10	FACETS	0.998	0.954	1			1	CLONAL	6	FALSE	NA	0.21078070958508	10		344	1352	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0012754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	93	338	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	0.24	2		338	601	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179386	56179386	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	55	324	0	ENST00000399503.3:c.3702del	p.Lys1234AsnfsTer11	p.K1234Nfs*11	ENST00000399503	NM_005921.1	1233	gcA/gc	15/20	1	2	FACETS	0.692	0.591	0.803	0.692	0.591	0.803	SUBCLONAL	1	TRUE	1	0.24	2		324	662	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152532	56152533	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	34	308	0	ENST00000399503.3:c.589dup	p.Trp197LeufsTer11	p.W197Lfs*11	ENST00000399503	NM_005921.1	196	-/T	2/20	1	2	FACETS	0.607	0.495	0.732	0.607	0.495	0.732	SUBCLONAL	1	TRUE	1	0.24	2		308	467	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012790-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	123	245	0				ENST00000310581	NM_198253.2	-/1132			0.224055542925884	5	FACETS	0.95	0.87	1	0.95	0.87	1	INDETERMINATE	3	TRUE	2	0.418187007048078	5		245	336	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0012790-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	217	618	6	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.327432628821042	3	FACETS	1	0.984	1	0.596	0.554	0.639	CLONAL	1	TRUE	1	0.418187007048078	3		624	1053	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0012790-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	109	517	2	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	0.477	0.427	0.531	0.477	0.427	0.531	SUBCLONAL	1	TRUE	1	0.418187007048078	2		519	1092	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0012790-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	385	678	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	1	0.958	1	1	0.997	1	CLONAL	2	TRUE	1	0.418187007048078	2		678	917	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916728	178916728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012790-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	208	1047	1	ENST00000263967.3:c.115G>A	p.Glu39Lys	p.E39K	ENST00000263967	NM_006218.2	39	Gag/Aag	2/21	0.203653633780919	4	FACETS	1	0.98	1	0.578	0.536	0.623	INDETERMINATE	1	TRUE	2	0.418187007048078	4		1048	1220	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288194	33288194	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs375524506	NA	P-0012790-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	43	500	0	ENST00000374542.5:c.1214C>G	p.Ser405Cys	p.S405C	ENST00000374542	NM_001141970.1	405	tCt/tGt	4/8	1	2	FACETS	0.317	0.265	0.376	0.317	0.265	0.376	SUBCLONAL	1	TRUE	1	0.418187007048078	2		500	648	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850981	63850981	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012790-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	61	577	0	ENST00000279873.7:c.1759G>T	p.Glu587Ter	p.E587*	ENST00000279873	NM_032199.2	587	Gaa/Taa	10/10	1	2	FACETS	0.432	0.372	0.497	0.432	0.372	0.497	SUBCLONAL	1	TRUE	1	0.418187007048078	2		577	676	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198863	67198863	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012790-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	43	604	0	ENST00000312629.5:c.334G>C	p.Asp112His	p.D112H	ENST00000312629	NM_003952.2	112	Gac/Cac	5/15	1	2	FACETS	0.224	0.186	0.265	0.224	0.186	0.265	SUBCLONAL	1	TRUE	1	0.418187007048078	2		604	920	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374271	118374271	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0012790-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	53	862	0	ENST00000534358.1:c.7664C>G	p.Ser2555Ter	p.S2555*	ENST00000534358	NM_005933.3	2555	tCa/tGa	27/36	NA	2	FACETS	0.288	0.245	0.336			1	INDETERMINATE	1	TRUE	NA	0.418187007048078	2		862	880	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448360	49448360	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012790-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	83	846	0	ENST00000301067.7:c.351G>C	p.Gln117His	p.Q117H	ENST00000301067	NM_003482.3	117	caG/caC	3/54	1	2	FACETS	0.383	0.337	0.433	0.383	0.337	0.433	SUBCLONAL	1	TRUE	1	0.418187007048078	2		846	1037	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562625	21562625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1381166851	NA	P-0012790-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	16	103	0	ENST00000382592.4:c.1294G>A	p.Val432Met	p.V432M	ENST00000382592	NM_014572.2	432	Gtg/Atg	4/8	0.203653633780919	4	FACETS	0.478	0.354	0.626	0.239	0.177	0.313	INDETERMINATE	1	TRUE	2	0.418187007048078	4		103	227	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838163	89838163	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012790-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	41	715	0	ENST00000389301.3:c.2074G>T	p.Glu692Ter	p.E692*	ENST00000389301	NM_000135.2	692	Gag/Tag	23/43	0.22186592351116	1	FACETS	0.177	0.147	0.211	0.177	0.147	0.211	INDETERMINATE	1	TRUE	0	0.418187007048078	1		715	875	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121063	3121063	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012790-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	90	804	0	ENST00000078429.4:c.966G>C	p.Lys322Asn	p.K322N	ENST00000078429	NM_002067.2	322	aaG/aaC	7/7	0.16130698102117	2	FACETS	0.464	0.411	0.521	0.232	0.205	0.261	INDETERMINATE	1	TRUE	0	0.418187007048078	2		804	928	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039379	49039379	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012790-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	311	821	1	ENST00000267163.4:c.2366del	p.Pro789LeufsTer21	p.P789Lfs*21	ENST00000267163	NM_000321.2	788	agC/ag	23/27	NA	2	FACETS	0.898	0.851	0.946			1	INDETERMINATE	2	TRUE	NA	0.418187007048078	2		822	828	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105668	27105669	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0012790-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	147	628	0	ENST00000324856.7:c.5282dup	p.Gly1762TrpfsTer11	p.G1762Wfs*11	ENST00000324856	NM_006015.4	1760	gag/gaGg	20/20	1	2	FACETS	0.932	0.852	1	0.932	0.852	1	CLONAL	1	TRUE	1	0.418187007048078	2		628	754	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571448	95571448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373412959	NA	P-0012790-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	25	323	1	ENST00000393063.1:c.3229G>A	p.Asp1077Asn	p.D1077N	ENST00000393063	NM_030621.3	1077	Gat/Aat	21/28	0.283694421626747	2	FACETS	0.305	0.24	0.38	0.153	0.12	0.19	SUBCLONAL	1	TRUE	0	0.418187007048078	2		324	392	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498035	29498035	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012790-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	87	806	0	ENST00000389048.3:c.1971G>C	p.Glu657Asp	p.E657D	ENST00000389048	NM_004304.4	657	gaG/gaC	11/29	0.266016719213989	2	FACETS	0.362	0.319	0.408	0.181	0.159	0.204	SUBCLONAL	1	TRUE	0	0.418187007048078	2		806	1150	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39744994	39744994	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012790-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	62	623	0	ENST00000361337.2:c.1784C>G	p.Ser595Cys	p.S595C	ENST00000361337	NM_003286.2	595	tCc/tGc	17/21	0.418187007048078	3	FACETS	0.39	0.336	0.449	0.195	0.168	0.225	SUBCLONAL	1	TRUE	1	0.418187007048078	3		623	919	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0012807-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	216	175	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.452739295139938	6	FACETS	1	0.973	1	1	0.973	1	CLONAL	4	TRUE	2	0.452739295139938	6		175	432	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772290	68772290	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012807-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	256	678	0	ENST00000261769.5:c.139G>T	p.Glu47Ter	p.E47*	ENST00000261769	NM_004360.3	47	Gag/Tag	2/16	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	2	TRUE	NA	0.452739295139938	2		678	534	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763211	59763211	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012807-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	85	579	0	ENST00000259008.2:c.2891C>G	p.Ser964Cys	p.S964C	ENST00000259008	NM_032043.2	964	tCc/tGc	19/20	0.452739295139938	4	FACETS	0.726	0.642	0.817	0.363	0.321	0.409	SUBCLONAL	1	TRUE	2	0.452739295139938	4		579	751	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248049	59248100	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTCTGAGGCTCCTCCTTCAGGGCCTGCAGCCGCGGGTGCTGCACGGGCAT	CTGTCTGAGGCTCCTCCTTCAGGGCCTGCAGCCGCGGGTGCTGCACGGGCAT	-	novel	NA	P-0012807-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	55	455	0	ENST00000371222.2:c.643_694del	p.Met215CysfsTer29	p.M215Cfs*29	ENST00000371222	NM_002228.3	215	ATGCCCGTGCAGCACCCGCGGCTGCAGGCCCTGAAGGAGGAGCCTCAGACAGtg/tg	1/1	0.113348858137264	6	FACETS	1	0.871	1			1	INDETERMINATE	1	TRUE	NA	0.452739295139938	6		455	455	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252855	36252856	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0012807-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	303	469	0	ENST00000300305.3:c.506dup	p.Gly170ArgfsTer43	p.G170Rfs*43	ENST00000300305		169	aga/agGa	4/8	0.452739295139938	3	FACETS	0.878	0.835	0.921	0.878	0.835	0.921	CLONAL	3	TRUE	0	0.452739295139938	3		469	623	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0012823-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	145	403	1	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.961	0.876	1	0.961	0.876	1	CLONAL	1	TRUE	1	0.32	2		404	943	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0012823-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	124	487	1	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.32	2		488	775	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0012823-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	57	407	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.576	0.494	0.666	0.576	0.494	0.666	SUBCLONAL	1	TRUE	1	0.32	2		407	618	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012823-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	166	562	0	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.32	2		562	806	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743932	41743933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs778012871	NA	P-0012823-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	105	712	1	ENST00000301178.4:c.874dup	p.His292ProfsTer47	p.H292Pfs*47	ENST00000301178	NM_021913.4	289	-/C	7/20	1	2	FACETS	0.621	0.555	0.692	0.621	0.555	0.692	SUBCLONAL	1	TRUE	1	0.32	2		713	1056	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176133025	176133025	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012823-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	120	411	0	ENST00000367669.3:c.568A>G	p.Asn190Asp	p.N190D	ENST00000367669	NM_022457.5	190	Aat/Gat	4/20	1	2	FACETS	0.989	0.894	1	0.989	0.894	1	CLONAL	1	TRUE	1	0.32	2		411	758	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098957	178098957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	127	345	0	ENST00000397062.3:c.88C>T	p.Leu30Phe	p.L30F	ENST00000397062	NM_006164.4	30	Ctt/Ttt	2/5	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.364385974643753	2		345	630	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908179	41908179	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756727994	NA	P-0012826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	192	508	0	ENST00000372991.4:c.343G>A	p.Glu115Lys	p.E115K	ENST00000372991	NM_001760.3	115	Gag/Aag	2/5	0.364385974643753	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.364385974643753	1		508	725	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541663	120541663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	229	692	1	ENST00000229340.5:c.194C>T	p.Ala65Val	p.A65V	ENST00000229340	NM_006861.6	65	gCg/gTg	3/6	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.364385974643753	2		693	1228	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528714	157528715	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	130	451	0	ENST00000346085.5:c.6439dup	p.Arg2147LysfsTer45	p.R2147Kfs*45	ENST00000346085	NM_020732.3	2147	agg/aAgg	20/20	0.364385974643753	1	FACETS	0.95	0.865	1	0.95	0.865	1	CLONAL	1	TRUE	0	0.364385974643753	1		451	614	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941189	36941189	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	317	749	0	ENST00000361632.4:c.150G>C	p.Gln50His	p.Q50H	ENST00000361632		50	caG/caC	3/16	0.226783222279672	1	FACETS	0.792	0.746	0.839	0.792	0.746	0.839	INDETERMINATE	1	TRUE	0	0.446254870159441	1		749	1394	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091812	29091812	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	58	316	0	ENST00000328354.6:c.1145G>C	p.Arg382Thr	p.R382T	ENST00000328354	NM_007194.3	382	aGa/aCa	11/15	0.438185883047126	1	FACETS	0.423	0.364	0.488	0.423	0.364	0.488	SUBCLONAL	1	TRUE	0	0.446254870159441	1		316	477	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650601	48650601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140561920	NA	P-0012831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	290	737	0	ENST00000376670.3:c.571C>T	p.Arg191Cys	p.R191C	ENST00000376670	NM_002049.3	191	Cgt/Tgt	3/6	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.446254870159441	2		737	1279	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754908	57754909	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	163	305	0	ENST00000274289.3:c.281_282insT	p.Cys96MetfsTer10	p.C96Mfs*10	ENST00000274289	NM_006622.3	94	gca/gcTa	2/14	1	2	FACETS	0.907	0.834	0.984	0.907	0.834	0.984	CLONAL	1	TRUE	1	0.446254870159441	2		305	805	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0012848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	95	407	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.959	0.856	1	0.959	0.856	1	CLONAL	1	TRUE	1	0.331706008664186	2		407	597	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	219	480	2	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.331706008664186	2		482	982	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850705	63850705	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs201178069	NA	P-0012848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	159	443	0	ENST00000279873.7:c.1489del	p.Ile497Ter	p.I497*	ENST00000279873	NM_032199.2	495	Aaa/aa	10/10	1	2	FACETS	0.905	0.829	0.986	0.905	0.829	0.986	CLONAL	1	TRUE	1	0.331706008664186	2		443	1059	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675268	176675269	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	240	329	0	ENST00000439151.2:c.4591dup	p.Met1531AsnfsTer4	p.M1531Nfs*4	ENST00000439151	NM_022455.4	1528	-/A	11/23	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.331706008664186	2		329	1252	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs121913468	NA	P-0012848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	205	773	0	ENST00000269571.5:c.2305G>C	p.Asp769His	p.D769H	ENST00000269571		769	Gac/Cac	19/27	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.331706008664186	2		773	1126	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0012848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	274	967	4	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.331706008664186	2		971	1339	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931788	39931788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	107	960	1	ENST00000378444.4:c.2811del	p.Thr938ProfsTer18	p.T938Pfs*18	ENST00000378444	NM_001123385.1	937	ccC/cc	4/15	1	2	FACETS	0.499	0.446	0.556	0.499	0.446	0.556	SUBCLONAL	1	TRUE	1	0.331706008664186	2		961	1293	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711874	89711874	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs786204862	NA	P-0012848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	95	420	0	ENST00000371953.3:c.493-1G>A		p.X165_splice	ENST00000371953	NM_000314.4	165			1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.331706008664186	2		420	552	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591135	67591136	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0012848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	94	159	0	ENST00000274335.5:c.1732_1733del	p.Asp578ProfsTer23	p.D578Pfs*23	ENST00000274335		576	acGAga/acga	12/15	1	2	FACETS	0.911	0.812	1	0.911	0.812	1	CLONAL	1	TRUE	1	0.331706008664186	2		159	622	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434595	110434595	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs555841746	NA	P-0012848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	110	437	0	ENST00000375856.3:c.3806A>C	p.Gln1269Pro	p.Q1269P	ENST00000375856	NM_003749.2	1269	cAg/cCg	1/2	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.331706008664186	2		437	595	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920688	96920688	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369144563	NA	P-0012848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	173	605	3	ENST00000258439.3:c.292G>A	p.Ala98Thr	p.A98T	ENST00000258439	NM_001193304.2	98	Gcc/Acc	3/4	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.331706008664186	2		608	962	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048836	180048836	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	202	800	0	ENST00000261937.6:c.1726C>A	p.Leu576Met	p.L576M	ENST00000261937	NM_182925.4	576	Ctg/Atg	13/30	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.331706008664186	2		800	1040	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431637	6431637	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1554263626	NA	P-0012848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	215	376	0	ENST00000356142.4:c.190T>G	p.Tyr64Asp	p.Y64D	ENST00000356142	NM_018890.3	64	Tat/Gat	3/7	0.331706008664186	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.331706008664186	3		376	660	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841806	151841806	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	68	555	1	ENST00000262189.6:c.14335C>T	p.Arg4779Trp	p.R4779W	ENST00000262189	NM_170606.2	4779	Cgg/Tgg	55/59	0.331706008664186	3	FACETS	0.433	0.375	0.496	0.216	0.187	0.248	SUBCLONAL	1	TRUE	1	0.331706008664186	3		556	1104	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047225	77047225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	65	843	0	ENST00000356341.3:c.1319C>T	p.Ala440Val	p.A440V	ENST00000356341	NM_002576.4	440	gCc/gTc	13/15	1	2	FACETS	0.35	0.302	0.402	0.35	0.302	0.402	SUBCLONAL	1	TRUE	1	0.331706008664186	2		843	1120	SUCCESS
CBL	867	MSKCC	GRCh37	11	119077278	119077278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	210	841	0	ENST00000264033.4:c.151G>A	p.Val51Met	p.V51M	ENST00000264033	NM_005188.3	51	Gtg/Atg	1/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.331706008664186	2		841	1198	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435726	110435726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	81	219	0	ENST00000375856.3:c.2675G>A	p.Arg892His	p.R892H	ENST00000375856	NM_003749.2	892	cGc/cAc	1/2	1	2	FACETS	0.851	0.758	0.948	1	0.983	1	CLONAL	2	TRUE	1	0.331706008664186	2		219	287	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061142	38061142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1384603993	NA	P-0012848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	44	220	0	ENST00000250448.2:c.847G>A	p.Gly283Arg	p.G283R	ENST00000250448	NM_004496.3	283	Ggg/Agg	2/2	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.331706008664186	2		220	192	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5207965	5207965	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	278	973	2	ENST00000357368.4:c.5746C>T	p.Arg1916Ter	p.R1916*	ENST00000357368	NM_002850.3	1916	Cga/Tga	37/38	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.331706008664186	2		975	1456	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296445	15296445	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	245	797	0	ENST00000263388.2:c.1997G>A	p.Cys666Tyr	p.C666Y	ENST00000263388	NM_000435.2	666	tGc/tAc	13/33	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.331706008664186	2		797	1201	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164836	36164836	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	132	625	1	ENST00000300305.3:c.1039A>G	p.Met347Val	p.M347V	ENST00000300305		347	Atg/Gtg	8/8	1	2	FACETS	0.928	0.842	1	0.928	0.842	1	CLONAL	1	TRUE	1	0.331706008664186	2		626	858	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042077	42042077	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1478	275	1232	2	ENST00000219905.7:c.6276del	p.Ala2093ProfsTer9	p.A2093Pfs*9	ENST00000219905	NM_001164273.1	2091	gAa/ga	17/24	1	2	FACETS	0.946	0.885	1	0.946	0.885	1	CLONAL	1	TRUE	1	0.331706008664186	2		1234	1753	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176683984	176683984	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1064793336	NA	P-0012848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1324	253	1074	0	ENST00000439151.2:c.4801del	p.Glu1601LysfsTer41	p.E1601Kfs*41	ENST00000439151	NM_022455.4	1600	Ggg/gg	13/23	1	2	FACETS	0.967	0.902	1	0.967	0.902	1	CLONAL	1	TRUE	1	0.331706008664186	2		1074	1577	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831386	72831388	+	inframe_deletion	In_Frame_Del	DEL	TGC	TGC	-	novel	NA	P-0012848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	93	767	4	ENST00000268489.5:c.5193_5195del	p.Gln1741del	p.Q1741del	ENST00000268489	NM_006885.3	1731	caGCAa/caa	9/10	1	2	FACETS	0.583	0.517	0.653	0.583	0.517	0.653	SUBCLONAL	1	TRUE	1	0.331706008664186	2		771	962	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094387	27094388	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0012848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	133	489	0	ENST00000324856.7:c.3097dup	p.Glu1033GlyfsTer14	p.E1033Gfs*14	ENST00000324856	NM_006015.4	1032	gag/gaGg	11/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.331706008664186	2		489	766	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428239	49428239	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	194	739	0	ENST00000301067.7:c.10461del	p.Ser3488ProfsTer14	p.S3488Pfs*14	ENST00000301067	NM_003482.3	3487	ccC/cc	37/54	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.331706008664186	2		739	962	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257779	198257781	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0012848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	184	779	0	ENST00000335508.6:c.3671_3673del	p.Pro1224del	p.P1224del	ENST00000335508	NM_012433.2	1224	cCTCat/cat	24/25	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.331706008664186	2		779	1097	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0012854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	195	592	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.976	0.905	1	0.976	0.905	1	CLONAL	1	TRUE	1	0.533015442300875	2		592	750	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249002	55249003	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCGTGGA	rs397517109	NA	P-0012854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	331	650	0	ENST00000275493.2:c.2303_2311dup	p.Ser768_Asp770dup	p.S768_D770dup	ENST00000275493	NM_005228.3	768	gcc/gcCAGCGTGGAc	20/28	0.497488671582903	3	FACETS	1	0.994	1			1	CLONAL	1	TRUE	NA	0.533015442300875	3		650	1072	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2588139	2588139	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0012854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	61	145	0	ENST00000342085.4:c.24+2T>G		p.X8_splice	ENST00000342085	NM_002613.4	8			0.353041483884733	3	FACETS	1	0.942	1			1	CLONAL	1	TRUE	NA	0.533015442300875	3		145	253	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088787	27088788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	203	277	0	ENST00000324856.7:c.2402dup	p.Gln802SerfsTer15	p.Q802Sfs*15	ENST00000324856	NM_006015.4	799	cag/caGg	7/20	1	2	FACETS	0.95	0.885	1	1	0.994	1	CLONAL	2	TRUE	1	0.331821741064309	2		277	644	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420661	49420661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555185875	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	80	371	0	ENST00000301067.7:c.15088C>T	p.Arg5030Cys	p.R5030C	ENST00000301067	NM_003482.3	5030	Cgt/Tgt	48/54	0.104549178818446	3	FACETS	1	0.964	1	0.621	0.548	0.697	INDETERMINATE	1	TRUE	1	0.331821741064309	3		371	453	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	184	373	1	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	0.858	0.79	0.929	0.858	0.79	0.929	CLONAL	1	TRUE	1	0.331821741064309	2		374	1293	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	307	623	6	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.331821741064309	2		629	1274	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070577	67070578	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	183	645	1	ENST00000412916.2:c.207dup	p.Pro70SerfsTer13	p.P70Sfs*13	ENST00000412916		67	-/T	3/6	0.331821741064309	1	FACETS	0.891	0.821	0.963	0.891	0.821	0.963	CLONAL	1	TRUE	0	0.331821741064309	1		646	1033	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	80	255	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.104549178818446	3	FACETS	1	0.977	1	0.738	0.653	0.827	INDETERMINATE	1	TRUE	1	0.331821741064309	3		255	381	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	93	359	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.331821741064309	1	FACETS	0.83	0.74	0.926	0.83	0.74	0.926	CLONAL	1	TRUE	0	0.331821741064309	1		359	563	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256768	19256769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1202792889	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	45	335	0	ENST00000162023.5:c.944dup	p.Val316SerfsTer6	p.V316Sfs*6	ENST00000162023		315	cca/ccCa	13/13	0.331821741064309	1	FACETS	0.654	0.551	0.766	0.654	0.551	0.766	SUBCLONAL	1	TRUE	0	0.331821741064309	1		335	346	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057230	180057230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780661773	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	61	534	1	ENST00000261937.6:c.508C>T	p.Arg170Cys	p.R170C	ENST00000261937	NM_182925.4	170	Cgc/Tgc	4/30	0.331821741064309	0	FACETS	0.738	0.64	0.842			1	SUBCLONAL	1	TRUE	0	0.331821741064309	0		535	333	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934126	39934127	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	188	489	0	ENST00000378444.4:c.472dup	p.Ser158LysfsTer28	p.S158Kfs*28	ENST00000378444	NM_001123385.1	158	agt/aAgt	4/15	1	1	FACETS	0.972	0.907	1	1	0.993	1	CLONAL	2	TRUE	0	0.331821741064309	1		489	486	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291083	10291084	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755889652	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	68	637	2	ENST00000340748.4:c.387dup	p.Lys130GlnfsTer19	p.K130Qfs*19	ENST00000340748		129	-/C	4/40	0.331821741064309	1	FACETS	0.523	0.454	0.597	0.523	0.454	0.597	SUBCLONAL	1	TRUE	0	0.331821741064309	1		639	654	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740623	58740624	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs763475304	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1331	262	1334	0	ENST00000305921.3:c.1535dup	p.Asn512LysfsTer16	p.N512Kfs*16	ENST00000305921	NM_003620.3	510	caa/cAaa	6/6	1	2	FACETS	0.991	0.926	1	0.991	0.926	1	CLONAL	1	TRUE	1	0.331821741064309	2		1334	1593	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958479	90958480	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs780235686	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	98	356	0	ENST00000265433.3:c.1958dup	p.Leu654AlafsTer5	p.L654Afs*5	ENST00000265433	NM_002485.4	653	aag/aaAg	13/16	1	2	FACETS	0.998	0.892	1	0.998	0.892	1	CLONAL	1	TRUE	1	0.331821741064309	2		356	592	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512401	38512402	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs745553450	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	53	514	1	ENST00000254066.5:c.1319dup	p.Pro441AlafsTer5	p.P441Afs*5	ENST00000254066	NM_000964.3	438	gcc/gCcc	9/9	1	2	FACETS	0.673	0.574	0.78	0.673	0.574	0.78	SUBCLONAL	1	TRUE	1	0.331821741064309	2		515	475	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154241	2154242	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755455183	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	60	819	3	ENST00000434045.2:c.686dup	p.Glu230ArgfsTer50	p.E230Rfs*50	ENST00000434045	NM_001127598.1	229	cca/ccCa	5/5	0.331821741064309	1	FACETS	0.713	0.616	0.818	0.713	0.616	0.818	SUBCLONAL	1	TRUE	0	0.331821741064309	1		822	423	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390735	139390736	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	75	926	0	ENST00000277541.6:c.7455dup	p.Ser2486LeufsTer21	p.S2486Lfs*21	ENST00000277541	NM_017617.3	2485	-/C	34/34	1	2	FACETS	0.688	0.603	0.78	0.688	0.603	0.78	SUBCLONAL	1	TRUE	1	0.331821741064309	2		926	657	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25368433	25368434	+	intron_variant	Intron	INS	-	-	T	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	165	412	1	ENST00000311936.3:c.451-5589dup		p.*151*	ENST00000311936	NM_004985.3	171/189			0.104549178818446	3	FACETS	1	0.979	1	0.6	0.551	0.652	INDETERMINATE	1	TRUE	1	0.331821741064309	3		413	966	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550472	29550473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs786204255	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	76	359	1	ENST00000356175.3:c.1738dup	p.Tyr580LeufsTer8	p.Y580Lfs*8	ENST00000356175	NM_000267.3	578	ctt/cTtt	16/57	1	2	FACETS	0.824	0.724	0.931	0.824	0.724	0.931	CLONAL	1	TRUE	1	0.331821741064309	2		360	556	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288919	11288919	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	71	518	0	ENST00000361445.4:c.2836T>C	p.Phe946Leu	p.F946L	ENST00000361445	NM_004958.3	946	Ttc/Ctc	19/58	0.331821741064309	1	FACETS	0.694	0.607	0.788	0.694	0.607	0.788	SUBCLONAL	1	TRUE	0	0.331821741064309	1		518	514	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255967	16255967	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	81	326	0	ENST00000375759.3:c.3232T>C	p.Ser1078Pro	p.S1078P	ENST00000375759	NM_015001.2	1078	Tca/Cca	11/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.331821741064309	2		326	361	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303624	65303624	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	129	566	1	ENST00000342505.4:c.3131C>A	p.Pro1044His	p.P1044H	ENST00000342505	NM_002227.2	1044	cCt/cAt	22/25	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.331821741064309	2		567	752	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849113	156849113	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	129	885	0	ENST00000524377.1:c.2005T>G	p.Phe669Val	p.F669V	ENST00000524377	NM_002529.3	669	Ttt/Gtt	15/17	0.331821741064309	3	FACETS	0.988	0.895	1	0.494	0.447	0.543	CLONAL	1	TRUE	1	0.331821741064309	3		885	918	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653255	206653255	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	92	568	0	ENST00000367120.3:c.1226A>G	p.Gln409Arg	p.Q409R	ENST00000367120	NM_014002.3	409	cAg/cGg	11/22	0.331821741064309	3	FACETS	0.882	0.784	0.987	0.441	0.392	0.494	CLONAL	1	TRUE	1	0.331821741064309	3		568	733	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446388	29446388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769322016	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	188	1207	1	ENST00000389048.3:c.3179G>A	p.Arg1060His	p.R1060H	ENST00000389048	NM_004304.4	1060	cGc/cAc	20/29	0.331821741064309	1	FACETS	0.98	0.906	1	0.98	0.906	1	CLONAL	1	TRUE	0	0.331821741064309	1		1208	964	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641544	47641544	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	108	534	0	ENST00000233146.2:c.929T>A	p.Leu310His	p.L310H	ENST00000233146	NM_000251.2	310	cTt/cAt	5/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.331821741064309	2		534	573	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118836	61118836	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs367780559	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	106	410	0	ENST00000295025.8:c.29T>C	p.Ile10Thr	p.I10T	ENST00000295025	NM_002908.2	10	aTa/aCa	2/11	1	2	FACETS	0.794	0.711	0.881	0.794	0.711	0.881	SUBCLONAL	1	TRUE	1	0.331821741064309	2		410	805	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593573	215593573	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554708247	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	105	440	3	ENST00000260947.4:c.2161G>A	p.Ala721Thr	p.A721T	ENST00000260947	NM_000465.2	721	Gca/Aca	11/11	0.331821741064309	1	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	0	0.331821741064309	1		443	518	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125634	47125634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1357325164	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	213	806	0	ENST00000409792.3:c.5636G>A	p.Arg1879His	p.R1879H	ENST00000409792	NM_014159.6	1879	cGc/cAc	12/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.331821741064309	2		806	1136	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405903	49405903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	247	1056	1	ENST00000418115.1:c.235G>A	p.Val79Ile	p.V79I	ENST00000418115	NM_001664.2	79	Gtt/Att	3/5	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.331821741064309	2		1057	1300	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157633	106157633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	163	593	1	ENST00000380013.4:c.2534A>G	p.Lys845Arg	p.K845R	ENST00000380013	NM_001127208.2	845	aAa/aGa	3/11	0.104549178818446	3	FACETS	1	0.987	1	0.699	0.642	0.759	INDETERMINATE	1	TRUE	1	0.331821741064309	3		594	819	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190818	106190818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	161	510	0	ENST00000380013.4:c.4096C>T	p.Arg1366Cys	p.R1366C	ENST00000380013	NM_001127208.2	1366	Cgt/Tgt	9/11	0.104549178818446	3	FACETS	1	0.984	1	0.656	0.602	0.713	INDETERMINATE	1	TRUE	1	0.331821741064309	3		510	862	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876197	35876197	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	91	504	0	ENST00000303115.3:c.989A>G	p.Gln330Arg	p.Q330R	ENST00000303115	NM_002185.3	330	cAg/cGg	8/8	NA	2	FACETS	0.985	0.876	1			1	INDETERMINATE	1	TRUE	NA	0.331821741064309	2		504	557	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950228	38950228	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	102	465	0	ENST00000357387.3:c.3722T>C	p.Val1241Ala	p.V1241A	ENST00000357387	NM_152756.3	1241	gTa/gCa	31/38	0.331821741064309	3	FACETS	1	0.939	1	0.535	0.479	0.595	CLONAL	1	TRUE	1	0.331821741064309	3		465	670	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160640	56160640	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	160	593	0	ENST00000399503.3:c.914A>G	p.Asn305Ser	p.N305S	ENST00000399503	NM_005921.1	305	aAc/aGc	4/20	0.331821741064309	3	FACETS	1	0.98	1	0.611	0.56	0.664	CLONAL	1	TRUE	1	0.331821741064309	3		593	920	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178259	56178259	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	156	636	0	ENST00000399503.3:c.3232A>G	p.Lys1078Glu	p.K1078E	ENST00000399503	NM_005921.1	1078	Aaa/Gaa	14/20	0.331821741064309	3	FACETS	1	0.985	1	0.67	0.614	0.729	CLONAL	1	TRUE	1	0.331821741064309	3		636	818	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750772	57750772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	162	561	0	ENST00000274289.3:c.1832C>T	p.Ala611Val	p.A611V	ENST00000274289	NM_006622.3	611	gCc/gTc	13/14	0.331821741064309	3	FACETS	1	0.984	1	0.653	0.599	0.709	CLONAL	1	TRUE	1	0.331821741064309	3		561	872	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670022	86670022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	64	441	0	ENST00000274376.6:c.1819C>T	p.Pro607Ser	p.P607S	ENST00000274376	NM_002890.2	607	Cca/Tca	14/25	0.331821741064309	3	FACETS	0.623	0.539	0.715	0.311	0.269	0.358	SUBCLONAL	1	TRUE	1	0.331821741064309	3		441	722	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911288	29911288	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs45552635	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	48	142	0	ENST00000376809.5:c.587T>C	p.Leu196Pro	p.L196P	ENST00000376809	NM_002116.7	196	cTg/cCg	3/8	0.328376878552087	3	FACETS	0.823	0.704	0.95	0.548	0.469	0.633	CLONAL	2	TRUE	0	0.331821741064309	3		142	205	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964384	93964384	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	192	966	0	ENST00000369303.4:c.2513G>A	p.Trp838Ter	p.W838*	ENST00000369303	NM_004440.3	838	tGg/tAg	14/17	0.331821741064309	1	FACETS	0.878	0.811	0.948	0.878	0.811	0.948	CLONAL	1	TRUE	0	0.331821741064309	1		966	1099	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997811	149997811	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1481274477	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	153	512	1	ENST00000253339.5:c.2656C>T	p.Arg886Ter	p.R886*	ENST00000253339		886	Cga/Tga	5/7	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.331821741064309	2		513	656	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005146	150005146	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	152	531	0	ENST00000253339.5:c.1079A>G	p.Gln360Arg	p.Q360R	ENST00000253339		360	cAa/cGa	3/7	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.331821741064309	2		531	748	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527410	157527410	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs528688757	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	124	531	0	ENST00000346085.5:c.5135A>G	p.Asp1712Gly	p.D1712G	ENST00000346085	NM_020732.3	1712	gAt/gGt	20/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.331821741064309	2		531	634	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971178	13971178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs904139873	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	135	553	0	ENST00000405192.2:c.751C>T	p.Pro251Ser	p.P251S	ENST00000405192	NM_001163147.1	251	Ccc/Tcc	8/12	0.331821741064309	3	FACETS	1	0.981	1	0.652	0.593	0.713	CLONAL	1	TRUE	1	0.331821741064309	3		553	728	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467672	50467672	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	84	545	0	ENST00000331340.3:c.907A>G	p.Asn303Asp	p.N303D	ENST00000331340	NM_006060.4	303	Aac/Gac	8/8	0.331821741064309	3	FACETS	0.938	0.83	1	0.469	0.415	0.528	CLONAL	1	TRUE	1	0.331821741064309	3		545	629	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55231515	55231515	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs370810719	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	72	359	0	ENST00000275493.2:c.1721G>A	p.Arg574Gln	p.R574Q	ENST00000275493	NM_005228.3	574	cGg/cAg	14/28	0.331821741064309	3	FACETS	1	0.937	1	0.556	0.487	0.63	CLONAL	1	TRUE	1	0.331821741064309	3		359	455	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850344	128850344	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs754958172	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	69	537	0	ENST00000249373.3:c.1607T>C	p.Val536Ala	p.V536A	ENST00000249373	NM_005631.4	536	gTc/gCc	9/12	0.331821741064309	3	FACETS	0.901	0.786	1	0.451	0.393	0.513	CLONAL	1	TRUE	1	0.331821741064309	3		537	538	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860649	151860649	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs201260588	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	371	912	0	ENST00000262189.6:c.10013A>G	p.Asn3338Ser	p.N3338S	ENST00000262189	NM_170606.2	3338	aAc/aGc	43/59	0.331821741064309	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.331821741064309	3		912	1151	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891344	151891344	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	182	403	0	ENST00000262189.6:c.4510G>A	p.Ala1504Thr	p.A1504T	ENST00000262189	NM_170606.2	1504	Gca/Aca	30/59	0.331821741064309	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.331821741064309	3		403	565	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540302	23540302	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	45	302	2	ENST00000380871.4:c.101T>C	p.Ile34Thr	p.I34T	ENST00000380871	NM_006167.3	34	aTc/aCc	1/2	1	2	FACETS	0.979	0.828	1	0.979	0.828	1	CLONAL	1	TRUE	1	0.331821741064309	2		304	277	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209267	98209267	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	131	810	0	ENST00000331920.6:c.4271A>G	p.Asp1424Gly	p.D1424G	ENST00000331920	NM_000264.3	1424	gAt/gGt	23/24	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.331821741064309	2		810	661	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63816974	63816974	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	85	364	0	ENST00000279873.7:c.945A>T	p.Glu315Asp	p.E315D	ENST00000279873	NM_032199.2	315	gaA/gaT	6/10	1	2	FACETS	0.638	0.563	0.718	0.638	0.563	0.718	SUBCLONAL	1	TRUE	1	0.331821741064309	2		364	803	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446138	70446138	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	105	487	0	ENST00000373644.4:c.5078A>G	p.Asn1693Ser	p.N1693S	ENST00000373644	NM_030625.2	1693	aAc/aGc	11/12	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.331821741064309	2		487	564	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188231	108188231	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	77	423	1	ENST00000278616.4:c.6330C>A	p.Asp2110Glu	p.D2110E	ENST00000278616	NM_000051.3	2110	gaC/gaA	43/63	1	2	FACETS	0.8	0.703	0.904	0.8	0.703	0.904	CLONAL	1	TRUE	1	0.331821741064309	2		424	580	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544183	18544183	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	116	531	0	ENST00000266497.5:c.2000T>C	p.Leu667Pro	p.L667P	ENST00000266497		667	cTa/cCa	13/31	0.104549178818446	3	FACETS	1	0.97	1	0.593	0.535	0.654	INDETERMINATE	1	TRUE	1	0.331821741064309	3		531	687	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699294	18699294	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1438011908	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	159	534	0	ENST00000266497.5:c.3395A>G	p.Gln1132Arg	p.Q1132R	ENST00000266497		1132	cAa/cGa	24/31	0.104549178818446	3	FACETS	1	0.985	1	0.664	0.609	0.722	INDETERMINATE	1	TRUE	1	0.331821741064309	3		534	841	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427440	49427440	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	104	687	0	ENST00000301067.7:c.11048A>C	p.Gln3683Pro	p.Q3683P	ENST00000301067	NM_003482.3	3683	cAg/cCg	39/54	0.104549178818446	3	FACETS	1	0.922	1	0.518	0.464	0.575	INDETERMINATE	1	TRUE	1	0.331821741064309	3		687	706	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447056	49447056	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	95	698	0	ENST00000301067.7:c.888A>C	p.Lys296Asn	p.K296N	ENST00000301067	NM_003482.3	296	aaA/aaC	7/54	0.104549178818446	3	FACETS	0.757	0.673	0.847	0.378	0.336	0.424	INDETERMINATE	1	TRUE	1	0.331821741064309	3		698	882	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914669	32914669	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1588	219	1557	2	ENST00000380152.3:c.6177T>A	p.Ser2059Arg	p.S2059R	ENST00000380152		2059	agT/agA	11/27	1	2	FACETS	0.73	0.677	0.787	0.73	0.677	0.787	SUBCLONAL	1	TRUE	1	0.331821741064309	2		1559	1807	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99454633	99454633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	185	695	0	ENST00000268035.6:c.1552A>G	p.Arg518Gly	p.R518G	ENST00000268035	NM_000875.3	518	Agg/Ggg	7/21	0.331821741064309	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.331821741064309	1		695	758	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961036	15961036	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	113	346	0	ENST00000268712.3:c.6184G>T	p.Asp2062Tyr	p.D2062Y	ENST00000268712	NM_006311.3	2062	Gat/Tat	40/46	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.331821741064309	2		346	563	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15967498	15967498	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	157	623	0	ENST00000268712.3:c.5105A>G	p.His1702Arg	p.H1702R	ENST00000268712	NM_006311.3	1702	cAc/cGc	35/46	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.331821741064309	2		623	778	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63545668	63545668	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	53	685	0	ENST00000307078.5:c.926A>G	p.Asp309Gly	p.D309G	ENST00000307078	NM_004655.3	309	gAt/gGt	3/11	1	2	FACETS	0.478	0.407	0.556	0.478	0.407	0.556	SUBCLONAL	1	TRUE	1	0.331821741064309	2		685	668	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78914296	78914296	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	54	470	0	ENST00000306801.3:c.2920A>C	p.Ile974Leu	p.I974L	ENST00000306801	NM_020761.2	974	Atc/Ctc	25/34	1	2	FACETS	0.808	0.692	0.934	0.808	0.692	0.934	CLONAL	1	TRUE	1	0.331821741064309	2		470	403	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575132	48575132	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	126	491	0	ENST00000342988.3:c.326T>C	p.Leu109Pro	p.L109P	ENST00000342988	NM_005359.5	109	cTa/cCa	3/12	1	2	FACETS	0.87	0.787	0.957	0.87	0.787	0.957	CLONAL	1	TRUE	1	0.331821741064309	2		491	873	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390403	56390403	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1400	314	1342	1	ENST00000348428.3:c.1142T>C	p.Val381Ala	p.V381A	ENST00000348428	NM_006785.3	381	gTt/gCt	10/17	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.331821741064309	2		1343	1714	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910276	50910276	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	203	1391	0	ENST00000440232.2:c.1531T>C	p.Tyr511His	p.Y511H	ENST00000440232	NM_002691.3	511	Tac/Cac	13/27	0.331821741064309	1	FACETS	0.948	0.878	1	0.948	0.878	1	CLONAL	1	TRUE	0	0.331821741064309	1		1391	1077	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755579	39755579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779273424	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	125	643	5	ENST00000288319.7:c.1186G>A	p.Ala396Thr	p.A396T	ENST00000288319	NM_182918.3	396	Gcc/Acc	10/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.331821741064309	2		648	565	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656846	45656846	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	38	472	0	ENST00000407780.3:c.310A>G	p.Thr104Ala	p.T104A	ENST00000407780	NM_001283052.1	104	Acc/Gcc	3/7	1	2	FACETS	0.46	0.38	0.55	0.46	0.38	0.55	SUBCLONAL	1	TRUE	1	0.331821741064309	2		472	498	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573882	41573882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758996869	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	140	677	1	ENST00000263253.7:c.6167G>A	p.Arg2056Gln	p.R2056Q	ENST00000263253	NM_001429.3	2056	cGg/cAg	31/31	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.331821741064309	2		678	686	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923844	39923844	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	52	507	0	ENST00000378444.4:c.3247A>G	p.Ser1083Gly	p.S1083G	ENST00000378444	NM_001123385.1	1083	Agt/Ggt	7/15	1	1	FACETS	0.554	0.472	0.643	0.554	0.472	0.643	SUBCLONAL	1	TRUE	0	0.331821741064309	1		507	472	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349909	70349909	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	199	474	0	ENST00000374080.3:c.3892A>G	p.Lys1298Glu	p.K1298E	ENST00000374080		1298	Aag/Gag	28/45	1	1	FACETS	0.944	0.882	1	1	0.994	1	CLONAL	2	TRUE	0	0.331821741064309	1		474	530	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791228	42791229	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	72	403	0	ENST00000575354.2:c.293dup	p.Gly99TrpfsTer6	p.G99Wfs*6	ENST00000575354	NM_015125.3	96	-/C	3/20	0.331821741064309	1	FACETS	0.887	0.779	1	0.887	0.779	1	CLONAL	1	TRUE	0	0.331821741064309	1		403	408	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392144	81392145	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	151	695	0	ENST00000222390.5:c.132dup	p.Ser45IlefsTer28	p.S45Ifs*28	ENST00000222390	NM_000601.4	44	-/A	2/18	0.331821741064309	3	FACETS	1	0.951	1	0.53	0.484	0.578	CLONAL	1	TRUE	1	0.331821741064309	3		695	1001	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874636	35874637	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1384901919	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	108	626	0	ENST00000303115.3:c.799dup	p.Arg267LysfsTer3	p.R267Kfs*3	ENST00000303115	NM_002185.3	264	-/A	6/8	NA	2	FACETS	0.793	0.711	0.88			1	INDETERMINATE	1	TRUE	NA	0.331821741064309	2		626	821	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786070	3786071	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	198	974	0	ENST00000262367.5:c.4694dup	p.Glu1566GlyfsTer8	p.E1566Gfs*8	ENST00000262367	NM_004380.2	1565	aag/aaAg	28/31	0.331821741064309	1	FACETS	0.968	0.896	1	0.968	0.896	1	CLONAL	1	TRUE	0	0.331821741064309	1		974	1028	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791472	42791473	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	171	830	0	ENST00000575354.2:c.455dup	p.Leu153ProfsTer7	p.L153Pfs*7	ENST00000575354	NM_015125.3	151	-/T	4/20	0.331821741064309	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.331821741064309	1		830	834	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060911	38060912	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	83	495	1	ENST00000250448.2:c.1077dup	p.Ile360HisfsTer55	p.I360Hfs*55	ENST00000250448	NM_004496.3	359	-/C	2/2	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.331821741064309	2		496	364	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384650	31384651	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs756395138	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	146	949	4	ENST00000328111.2:c.1359dup	p.Leu454AlafsTer11	p.L454Afs*11	ENST00000328111	NM_006892.3	451	gag/gaGg	13/23	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.331821741064309	2		953	791	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435160	56435161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	44	355	0	ENST00000407977.2:c.1975_1976dup	p.Pro660ValfsTer41	p.P660Vfs*41	ENST00000407977		659	ggt/ggGGt	9/10	1	2	FACETS	0.727	0.611	0.854	0.727	0.611	0.854	SUBCLONAL	1	TRUE	1	0.331821741064309	2		355	365	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156651	106156652	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	150	555	0	ENST00000380013.4:c.1557dup	p.Gly520TrpfsTer2	p.G520Wfs*2	ENST00000380013	NM_001127208.2	518	att/aTtt	3/11	0.104549178818446	3	FACETS	1	0.982	1	0.643	0.588	0.7	INDETERMINATE	1	TRUE	1	0.331821741064309	3		555	820	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360575	118360576	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	204	799	0	ENST00000534358.1:c.4551dup	p.Pro1518ThrfsTer17	p.P1518Tfs*17	ENST00000534358	NM_005933.3	1516	-/A	12/36	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.331821741064309	2		799	1199	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686900	37686901	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs772711685	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	142	719	0	ENST00000447079.4:c.3810dup	p.Gly1271ArgfsTer13	p.G1271Rfs*13	ENST00000447079	NM_015083.1	1268	-/C	14/14	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.331821741064309	2		719	841	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288788	15288789	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	47	209	0	ENST00000263388.2:c.3950dup	p.Gly1318ArgfsTer245	p.G1318Rfs*245	ENST00000263388	NM_000435.2	1317	cca/ccCa	24/33	0.331821741064309	1	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	0	0.331821741064309	1		209	217	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38946580	38946581	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	93	328	0	ENST00000357387.3:c.4388dup	p.His1463GlnfsTer2	p.H1463Qfs*2	ENST00000357387	NM_152756.3	1463	cat/caAt	33/38	NA	2	FACETS	0.963	0.858	1			1	INDETERMINATE	1	TRUE	NA	0.331821741064309	2		328	582	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798768	135798769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	75	390	0	ENST00000298552.3:c.474dup	p.Gly159TrpfsTer59	p.G159Wfs*59	ENST00000298552	NM_001162426.1	158	-/T	6/23	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.331821741064309	2		390	450	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331622	8331623	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	70	982	0	ENST00000356435.5:c.5493dup	p.Glu1832ArgfsTer36	p.E1832Rfs*36	ENST00000356435		1831	-/A	33/35	1	2	FACETS	0.355	0.308	0.406	0.355	0.308	0.406	SUBCLONAL	1	TRUE	1	0.331821741064309	2		982	1189	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161950	47161951	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	110	455	0	ENST00000409792.3:c.4175dup	p.Asn1392LysfsTer6	p.N1392Kfs*6	ENST00000409792	NM_014159.6	1392	aac/aaAc	3/21	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.331821741064309	2		455	614	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0012897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	342	408	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	0.363939807960209	3	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.69577939064327	3		408	1189	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0012897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	335	201	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.401503904858939	5	FACETS	1	0.957	1	0.505	0.479	0.532	INDETERMINATE	2	TRUE	1	0.69577939064327	5		201	974	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	250	556	1	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.36922549011388	3	FACETS	1	0.991	1	0.652	0.612	0.692	INDETERMINATE	1	TRUE	1	0.69577939064327	3		557	743	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49724798	49724798	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs138710044	NA	P-0012897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	14	101	0	ENST00000449682.2:c.469A>C	p.Lys157Gln	p.K157Q	ENST00000449682	NM_020998.3	157	Aag/Cag	4/18	0.335107332705707	1	FACETS	0.271	0.198	0.356	0.271	0.198	0.356	INDETERMINATE	1	TRUE	0	0.69577939064327	1		101	97	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531765	46531765	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	180	695	0	ENST00000262741.5:c.582G>T	p.Glu194Asp	p.E194D	ENST00000262741	NM_003629.3	194	gaG/gaT	5/10	0.36922549011388	3	FACETS	0.539	0.495	0.584	0.269	0.247	0.292	INDETERMINATE	1	TRUE	1	0.69577939064327	3		695	1295	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225561	26225561	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1360	951	1572	1	ENST00000360408.1:c.179A>T	p.Glu60Val	p.E60V	ENST00000360408	NM_003532.2	60	gAg/gTg	1/1	0.377248347804157	4	FACETS	1	0.973	1	1	0.973	1	INDETERMINATE	2	TRUE	2	0.69577939064327	4		1573	2311	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602484	10602485	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0012897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	358	423	0	ENST00000171111.5:c.1093dup	p.Leu365ProfsTer50	p.L365Pfs*50	ENST00000171111	NM_203500.1	365	ctg/cCtg	3/6	0.69577939064327	2	FACETS	0.948	0.912	0.982	0.948	0.912	0.982	CLONAL	2	TRUE	0	0.69577939064327	2		423	543	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012972-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	48	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.908	0.768	1	0.908	0.768	1	CLONAL	1	TRUE	1	0.219370023727181	2		311	482	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023559	27023560	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0012972-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	44	485	0	ENST00000324856.7:c.671dup	p.Pro225AlafsTer175	p.P225Afs*175	ENST00000324856	NM_006015.4	222	tac/taCc	1/20	1	2	FACETS	0.845	0.708	0.995	0.845	0.708	0.995	CLONAL	1	TRUE	1	0.219370023727181	2		485	475	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604768	48604768	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012972-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	68	556	0	ENST00000342988.3:c.1591del	p.Arg531GlyfsTer6	p.R531Gfs*6	ENST00000342988	NM_005359.5	530	caC/ca	12/12	0.219370023727181	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.219370023727181	1		556	473	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641718	23641724	+	protein_altering_variant	In_Frame_Del	DEL	TCATCAT	TCATCAT	C	novel	NA	P-0012972-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	65	538	0	ENST00000261584.4:c.1751_1757delinsG	p.Asp584_Asp586delinsGly	p.D584_D586delinsG	ENST00000261584	NM_024675.3	584	gATGATGAt/gGt	5/13	1	2	FACETS	0.957	0.83	1	0.957	0.83	1	CLONAL	1	TRUE	1	0.219370023727181	2		538	619	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0012977-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	134	333	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.776	0.706	0.849	0.776	0.706	0.849	SUBCLONAL	1	TRUE	1	0.501198737337097	2		335	689	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163377	47163377	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012977-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	235	476	0	ENST00000409792.3:c.2749del	p.Ser917ValfsTer5	p.S917Vfs*5	ENST00000409792	NM_014159.6	917	Agt/gt	3/21	0.501198737337097	1	FACETS	0.88	0.823	0.937	0.88	0.823	0.937	CLONAL	1	TRUE	0	0.501198737337097	1		476	799	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0012977-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1192	342	708	11	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.89	0.84	0.941	0.89	0.84	0.941	CLONAL	1	TRUE	1	0.501198737337097	2		719	1534	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710595	114710597	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs754968616	NA	P-0012977-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1280	374	872	0	ENST00000543371.1:c.85_87del	p.Glu29del	p.E29del	ENST00000543371	NM_001198531.1	27	cAGGag/cag	1/14	1	2	FACETS	0.902	0.854	0.952	0.902	0.854	0.952	CLONAL	1	TRUE	1	0.501198737337097	2		872	1654	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012977-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	221	489	4	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.913	0.85	0.978	0.913	0.85	0.978	CLONAL	1	TRUE	1	0.501198737337097	2		493	966	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223131	5223131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375155482	NA	P-0012977-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	280	586	3	ENST00000357368.4:c.2672C>T	p.Thr891Met	p.T891M	ENST00000357368	NM_002850.3	891	aCg/aTg	18/38	1	2	FACETS	0.957	0.899	1	0.957	0.899	1	CLONAL	1	TRUE	1	0.501198737337097	2		589	1167	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298578	11298578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146049556	NA	P-0012977-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	275	532	1	ENST00000361445.4:c.1883G>A	p.Arg628His	p.R628H	ENST00000361445	NM_004958.3	628	cGc/cAc	12/58	1	2	FACETS	0.998	0.937	1	0.998	0.937	1	CLONAL	1	TRUE	1	0.501198737337097	2		533	1100	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139638	202139638	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012977-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	275	593	0	ENST00000358485.4:c.799A>C	p.Ile267Leu	p.I267L	ENST00000358485	NM_001080125.1	267	Atc/Ctc	6/9	1	2	FACETS	0.778	0.728	0.829	0.778	0.728	0.829	SUBCLONAL	1	TRUE	1	0.501198737337097	2		593	1411	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645475	215645475	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012977-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	334	722	0	ENST00000260947.4:c.1123A>G	p.Thr375Ala	p.T375A	ENST00000260947	NM_000465.2	375	Aca/Gca	4/11	1	2	FACETS	0.904	0.853	0.957	0.904	0.853	0.957	CLONAL	1	TRUE	1	0.501198737337097	2		722	1474	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934240	49934240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012977-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	440	770	2	ENST00000296474.3:c.2267C>T	p.Ala756Val	p.A756V	ENST00000296474	NM_002447.2	756	gCc/gTc	8/20	0.501198737337097	1	FACETS	0.958	0.914	1	0.958	0.914	1	CLONAL	1	TRUE	0	0.501198737337097	1		772	1373	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522433	187522433	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012977-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	326	604	0	ENST00000441802.2:c.11630G>T	p.Ser3877Ile	p.S3877I	ENST00000441802	NM_005245.3	3877	aGc/aTc	21/27	1	2	FACETS	0.983	0.927	1	0.983	0.927	1	CLONAL	1	TRUE	1	0.501198737337097	2		604	1324	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505122	149505122	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1460983846	NA	P-0012977-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1185	363	741	1	ENST00000261799.4:c.1693C>T	p.Arg565Ter	p.R565*	ENST00000261799	NM_002609.3	565	Cga/Tga	12/23	1	2	FACETS	0.936	0.885	0.987	0.936	0.885	0.987	CLONAL	1	TRUE	1	0.501198737337097	2		742	1548	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169952	32169952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151325272	NA	P-0012977-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1453	362	698	0	ENST00000375023.3:c.3656G>A	p.Arg1219Gln	p.R1219Q	ENST00000375023	NM_004557.3	1219	cGg/cAg	21/30	0.501198737337097	3	FACETS	0.995	0.94	1	0.498	0.47	0.526	CLONAL	1	TRUE	1	0.501198737337097	3		698	1815	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508793	106508793	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370152741	NA	P-0012977-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	193	451	0	ENST00000359195.3:c.787G>A	p.Glu263Lys	p.E263K	ENST00000359195	NM_002649.2	263	Gaa/Aaa	2/11	1	2	FACETS	0.865	0.801	0.932	0.865	0.801	0.932	CLONAL	1	TRUE	1	0.501198737337097	2		451	890	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850322	128850322	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012977-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	272	521	0	ENST00000249373.3:c.1585G>T	p.Gly529Cys	p.G529C	ENST00000249373	NM_005631.4	529	Ggc/Tgc	9/12	1	2	FACETS	0.928	0.87	0.987	0.928	0.87	0.987	CLONAL	1	TRUE	1	0.501198737337097	2		521	1170	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741406	17741406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs993043194	NA	P-0012977-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	319	588	2	ENST00000250003.3:c.77C>T	p.Thr26Met	p.T26M	ENST00000250003	NM_002478.4	26	aCg/aTg	1/3	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.501198737337097	2		590	1246	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981709	101981709	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012977-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	96	136	0	ENST00000282441.5:c.130G>A	p.Ala44Thr	p.A44T	ENST00000282441	NM_001130145.2	44	Gcg/Acg	1/9	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.501198737337097	2		136	331	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856005	111856005	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778291950	NA	P-0012977-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	325	682	0	ENST00000341259.2:c.56C>T	p.Pro19Leu	p.P19L	ENST00000341259	NM_005475.2	19	cCg/cTg	2/8	1	2	FACETS	0.988	0.933	1	0.988	0.933	1	CLONAL	1	TRUE	1	0.501198737337097	2		682	1312	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112134	115112134	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012977-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	243	559	1	ENST00000257566.3:c.1606G>A	p.Ala536Thr	p.A536T	ENST00000257566	NM_016569.3	536	Gcc/Acc	7/8	1	2	FACETS	0.873	0.815	0.932	0.873	0.815	0.932	CLONAL	1	TRUE	1	0.501198737337097	2		560	1111	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647581	23647581	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012977-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	311	496	2	ENST00000261584.4:c.286A>T	p.Thr96Ser	p.T96S	ENST00000261584	NM_024675.3	96	Aca/Tca	4/13	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.501198737337097	2		498	1237	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533778	63533778	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368525111	NA	P-0012977-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	239	445	0	ENST00000307078.5:c.1376G>A	p.Arg459His	p.R459H	ENST00000307078	NM_004655.3	459	cGc/cAc	6/11	1	2	FACETS	0.949	0.886	1	0.949	0.886	1	CLONAL	1	TRUE	1	0.501198737337097	2		445	1005	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118954	3118954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012977-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	334	632	1	ENST00000078429.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000078429	NM_002067.2	213	cGg/cAg	5/7	1	2	FACETS	0.989	0.934	1	0.989	0.934	1	CLONAL	1	TRUE	1	0.501198737337097	2		633	1348	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569739	41569739	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012977-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	307	587	1	ENST00000263253.7:c.4730C>A	p.Ser1577Tyr	p.S1577Y	ENST00000263253	NM_001429.3	1577	tCt/tAt	29/31	1	2	FACETS	0.886	0.834	0.94	0.886	0.834	0.94	CLONAL	1	TRUE	1	0.501198737337097	2		588	1383	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053531	37053531	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012977-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	304	658	0	ENST00000231790.2:c.618del	p.Leu207TyrfsTer22	p.L207Yfs*22	ENST00000231790	NM_000249.3	206	acA/ac	8/19	0.501198737337097	1	FACETS	0.892	0.842	0.944	0.892	0.842	0.944	CLONAL	1	TRUE	0	0.501198737337097	1		658	1019	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440912	52440912	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1205668341	NA	P-0012977-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	269	480	1	ENST00000460680.1:c.592del	p.Glu198ArgfsTer33	p.E198Rfs*33	ENST00000460680	NM_004656.3	198	Gag/ag	8/17	0.501198737337097	1	FACETS	0.974	0.917	1	0.974	0.917	1	CLONAL	1	TRUE	0	0.501198737337097	1		481	826	SUCCESS
AR	367	MSKCC	GRCh37	X	66766589	66766590	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012977-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1347	98	736	0	ENST00000374690.3:c.1603dup	p.Tyr535LeufsTer17	p.Y535Lfs*17	ENST00000374690	NM_000044.3	534	cct/ccTt	1/8	1	2	FACETS	0.271	0.24	0.303	0.271	0.24	0.303	SUBCLONAL	1	TRUE	1	0.501198737337097	2		736	1445	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023831	27023831	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1415214478	NA	P-0012977-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	226	435	2	ENST00000324856.7:c.941del	p.Gly314AlafsTer49	p.G314Afs*49	ENST00000324856	NM_006015.4	313	Ggg/gg	1/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.501198737337097	2		437	893	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	27	276	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.237	0.188	0.294	0.237	0.188	0.294	SUBCLONAL	1	TRUE	1	0.348508817559526	2		276	653	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	138	338	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	0.348508817559526	2		338	572	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	281	501	1	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.348508817559526	2		502	1205	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	179	498	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.348508817559526	2		498	819	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445203	49445203	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs549710712	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	39	407	0	ENST00000301067.7:c.2263C>T	p.Arg755Trp	p.R755W	ENST00000301067	NM_003482.3	755	Cgg/Tgg	10/54	1	2	FACETS	0.333	0.275	0.398	0.333	0.275	0.398	SUBCLONAL	1	TRUE	1	0.348508817559526	2		407	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578410	7578410	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs864622115	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	145	383	0	ENST00000269305.4:c.520A>G	p.Arg174Gly	p.R174G	ENST00000269305	NM_001126112.2	174	Agg/Ggg	5/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.348508817559526	2		383	658	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	119	402	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	0.348508817559526	2		402	592	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319442	11319442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769877976	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	262	509	1	ENST00000361445.4:c.25G>A	p.Ala9Thr	p.A9T	ENST00000361445	NM_004958.3	9	Gcc/Acc	2/58	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.348508817559526	2		510	1010	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885833	23885833	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	310	797	1	ENST00000374561.5:c.85G>T	p.Gly29Trp	p.G29W	ENST00000374561	NM_002167.4	29	Ggg/Tgg	1/3	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.348508817559526	2		798	1351	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087437	27087437	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	242	792	1	ENST00000324856.7:c.2011G>T	p.Gly671Ter	p.G671*	ENST00000324856	NM_006015.4	671	Gga/Tga	5/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.348508817559526	2		793	1342	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087447	27087447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	321	769	1	ENST00000324856.7:c.2021G>A	p.Ser674Asn	p.S674N	ENST00000324856	NM_006015.4	674	aGt/aAt	5/20	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.348508817559526	2		770	1397	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106732	27106732	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	258	583	1	ENST00000324856.7:c.6343C>T	p.Gln2115Ter	p.Q2115*	ENST00000324856	NM_006015.4	2115	Cag/Tag	20/20	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.348508817559526	2		584	1032	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932404	36932404	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1293	396	1019	1	ENST00000361632.4:c.2065G>T	p.Gly689Cys	p.G689C	ENST00000361632		689	Ggc/Tgc	16/16	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.348508817559526	2		1020	1689	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305321	65305321	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs780015120	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1210	180	736	0	ENST00000342505.4:c.2807A>G	p.Asn936Ser	p.N936S	ENST00000342505	NM_002227.2	936	aAc/aGc	20/25	1	2	FACETS	0.743	0.683	0.806	0.743	0.683	0.806	SUBCLONAL	1	TRUE	1	0.348508817559526	2		736	1390	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	222	572	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	0.348508817559526	2		572	949	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870382	155870382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	147	590	0	ENST00000368323.3:c.457G>A	p.Ala153Thr	p.A153T	ENST00000368323	NM_006912.5	153	Gcc/Acc	6/6	1	2	FACETS	0.8	0.729	0.874	0.8	0.729	0.874	SUBCLONAL	1	TRUE	1	0.348508817559526	2		590	1055	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838305	156838305	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	149	525	0	ENST00000524377.1:c.583A>G	p.Thr195Ala	p.T195A	ENST00000524377	NM_002529.3	195	Acg/Gcg	6/17	1	2	FACETS	0.997	0.911	1	0.997	0.911	1	CLONAL	1	TRUE	1	0.348508817559526	2		525	858	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841544	156841544	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	192	451	0	ENST00000524377.1:c.847T>C	p.Ser283Pro	p.S283P	ENST00000524377	NM_002529.3	283	Tcc/Ccc	7/17	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.348508817559526	2		451	802	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851274	156851274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751281792	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	174	563	2	ENST00000524377.1:c.2231G>A	p.Arg744His	p.R744H	ENST00000524377	NM_002529.3	744	cGt/cAt	17/17	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.348508817559526	2		565	993	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724626	162724626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879065950	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	201	441	0	ENST00000367921.3:c.398G>A	p.Arg133Gln	p.R133Q	ENST00000367921	NM_006182.2	133	cGg/cAg	5/18	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.348508817559526	2		441	881	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226576420	226576420	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	253	554	0	ENST00000366794.5:c.654A>T	p.Glu218Asp	p.E218D	ENST00000366794	NM_001618.3	218	gaA/gaT	5/23	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.348508817559526	2		554	1019	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966920	25966920	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs756768142	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	241	669	0	ENST00000435504.4:c.2286G>T	p.Gln762His	p.Q762H	ENST00000435504		762	caG/caT	13/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.348508817559526	2		669	1179	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416220	29416220	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1251627719	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	276	632	0	ENST00000389048.3:c.4733C>T	p.Pro1578Leu	p.P1578L	ENST00000389048	NM_004304.4	1578	cCt/cTt	29/29	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.348508817559526	2		632	1233	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178129296	178129296	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	176	493	0	ENST00000397062.3:c.9C>A	p.Asp3Glu	p.D3E	ENST00000397062	NM_006164.4	3	gaC/gaA	1/5	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.348508817559526	2		493	833	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719455	190719455	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1448031799	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	71	392	0	ENST00000441310.2:c.1457G>A	p.Gly486Asp	p.G486D	ENST00000441310	NM_000534.4	486	gGt/gAt	9/13	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.348508817559526	2		392	359	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285218	198285218	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	103	441	0	ENST00000335508.6:c.349G>T	p.Asp117Tyr	p.D117Y	ENST00000335508	NM_012433.2	117	Gat/Tat	4/25	1	2	FACETS	0.857	0.767	0.951	0.857	0.767	0.951	CLONAL	1	TRUE	1	0.348508817559526	2		441	690	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125235	47125235	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	106	654	0	ENST00000409792.3:c.6035T>C	p.Leu2012Pro	p.L2012P	ENST00000409792	NM_014159.6	2012	cTc/cCc	12/21	1	2	FACETS	0.686	0.614	0.762	0.686	0.614	0.762	SUBCLONAL	1	TRUE	1	0.348508817559526	2		654	887	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723561	49723561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	16	23	0	ENST00000449682.2:c.1081C>T	p.Arg361Trp	p.R361W	ENST00000449682	NM_020998.3	361	Cgg/Tgg	9/18	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.348508817559526	2		23	64	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598124	52598124	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	52	576	1	ENST00000394830.3:c.3742G>T	p.Gly1248Ter	p.G1248*	ENST00000394830	NM_018313.4	1248	Gga/Tga	24/30	1	2	FACETS	0.307	0.26	0.359	0.307	0.26	0.359	SUBCLONAL	1	TRUE	1	0.348508817559526	2		577	971	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682379	52682379	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	103	575	0	ENST00000394830.3:c.794C>A	p.Pro265His	p.P265H	ENST00000394830	NM_018313.4	265	cCt/cAt	8/30	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.348508817559526	2		575	580	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70005639	70005639	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763119975	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	120	450	2	ENST00000394351.3:c.668G>A	p.Arg223His	p.R223H	ENST00000394351	NM_000248.3	223	cGc/cAc	7/9	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.348508817559526	2		452	522	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014370	70014370	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1571	236	881	0	ENST00000394351.3:c.1231A>T	p.Ser411Cys	p.S411C	ENST00000394351	NM_000248.3	411	Agc/Tgc	9/9	1	2	FACETS	0.749	0.697	0.805	0.749	0.697	0.805	SUBCLONAL	1	TRUE	1	0.348508817559526	2		881	1807	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037207	71037207	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	162	513	0	ENST00000318789.4:c.1084C>A	p.Leu362Met	p.L362M	ENST00000318789	NM_032682.5	362	Ctg/Atg	14/21	1	2	FACETS	0.964	0.884	1	0.964	0.884	1	CLONAL	1	TRUE	1	0.348508817559526	2		513	964	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204737	128204737	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs35079193	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1296	236	980	1	ENST00000341105.2:c.704C>A	p.Thr235Asn	p.T235N	ENST00000341105	NM_032638.4	235	aCt/aAt	3/6	1	2	FACETS	0.884	0.822	0.948	0.884	0.822	0.948	CLONAL	1	TRUE	1	0.348508817559526	2		981	1532	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851631	134851631	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	218	535	0	ENST00000398015.3:c.1037G>T	p.Arg346Met	p.R346M	ENST00000398015	NM_004441.4	346	aGg/aTg	5/16	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.348508817559526	2		535	903	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960080	134960080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1042786	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	235	517	1	ENST00000398015.3:c.2437G>A	p.Val813Ile	p.V813I	ENST00000398015	NM_004441.4	813	Gtc/Atc	13/16	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.348508817559526	2		518	1052	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664651	138664651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	21	42	0	ENST00000330315.3:c.914C>T	p.Pro305Leu	p.P305L	ENST00000330315	NM_023067.3	305	cCg/cTg	1/1	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.348508817559526	2		42	92	SUCCESS
ATR	545	MSKCC	GRCh37	3	142224120	142224120	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	170	441	0	ENST00000350721.4:c.5057C>A	p.Pro1686His	p.P1686H	ENST00000350721	NM_001184.3	1686	cCt/cAt	29/47	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.348508817559526	2		441	692	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165631	185165631	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	46	486	0	ENST00000265026.3:c.906G>T	p.Lys302Asn	p.K302N	ENST00000265026	NM_004721.4	302	aaG/aaT	5/14	1	2	FACETS	0.315	0.264	0.372	0.315	0.264	0.372	SUBCLONAL	1	TRUE	1	0.348508817559526	2		486	838	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502467	186502467	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs765159897	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	186	644	0	ENST00000323963.5:c.190A>G	p.Ile64Val	p.I64V	ENST00000323963		64	Att/Gtt	3/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.348508817559526	2		644	755	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506946	186506946	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	209	1074	1	ENST00000323963.5:c.1112G>A	p.Gly371Asp	p.G371D	ENST00000323963		371	gGt/gAt	11/11	1	2	FACETS	0.855	0.792	0.922	0.855	0.792	0.922	CLONAL	1	TRUE	1	0.348508817559526	2		1075	1402	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807874	1807874	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	192	631	0	ENST00000260795.2:c.1933C>A	p.Leu645Ile	p.L645I	ENST00000260795		645	Ctc/Atc	13/17	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.348508817559526	2		631	1038	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564613	55564613	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	145	586	0	ENST00000288135.5:c.501G>T	p.Lys167Asn	p.K167N	ENST00000288135	NM_000222.2	167	aaG/aaT	3/21	1	2	FACETS	0.861	0.784	0.94	0.861	0.784	0.94	CLONAL	1	TRUE	1	0.348508817559526	2		586	967	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948780	55948780	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs763426023	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	83	383	0	ENST00000263923.4:c.3685C>T	p.Arg1229Ter	p.R1229*	ENST00000263923	NM_002253.2	1229	Cga/Tga	28/30	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.348508817559526	2		383	367	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55974024	55974024	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	152	353	1	ENST00000263923.4:c.1292C>A	p.Pro431His	p.P431H	ENST00000263923	NM_002253.2	431	cCt/cAt	10/30	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.348508817559526	2		354	751	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535336	66535336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1349494063	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	251	724	2	ENST00000273854.3:c.125C>T	p.Thr42Met	p.T42M	ENST00000273854	NM_004439.5	42	aCg/aTg	1/18	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.348508817559526	2		726	1283	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535429	66535429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	178	364	0	ENST00000273854.3:c.32G>A	p.Arg11His	p.R11H	ENST00000273854	NM_004439.5	11	cGc/cAc	1/18	1	2	FACETS	0.844	0.782	0.908	1	0.992	1	CLONAL	2	TRUE	1	0.348508817559526	2		364	605	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247195	153247195	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	49	577	0	ENST00000281708.4:c.1607C>T	p.Thr536Met	p.T536M	ENST00000281708	NM_033632.3	536	aCg/aTg	10/12	1	2	FACETS	0.308	0.26	0.361	0.308	0.26	0.361	SUBCLONAL	1	TRUE	1	0.348508817559526	2		577	913	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250883	153250883	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	87	552	1	ENST00000281708.4:c.1177C>T	p.Arg393Ter	p.R393*	ENST00000281708	NM_033632.3	393	Cga/Tga	8/12	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.348508817559526	2		553	463	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527264	187527264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754008095	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	190	374	0	ENST00000441802.2:c.10310C>T	p.Ala3437Val	p.A3437V	ENST00000441802	NM_005245.3	3437	gCg/gTg	17/27	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.348508817559526	2		374	808	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539035	187539035	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	306	748	0	ENST00000441802.2:c.8705C>T	p.Ala2902Val	p.A2902V	ENST00000441802	NM_005245.3	2902	gCc/gTc	10/27	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.348508817559526	2		748	1417	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540842	187540842	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	110	558	0	ENST00000441802.2:c.6898A>G	p.Thr2300Ala	p.T2300A	ENST00000441802	NM_005245.3	2300	Acg/Gcg	10/27	1	2	FACETS	0.695	0.624	0.771	0.695	0.624	0.771	SUBCLONAL	1	TRUE	1	0.348508817559526	2		558	908	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630695	187630695	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	195	691	0	ENST00000441802.2:c.287T>C	p.Leu96Pro	p.L96P	ENST00000441802	NM_005245.3	96	cTa/cCa	2/27	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.348508817559526	2		691	1024	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670013	86670013	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1228558466	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	78	398	0	ENST00000274376.6:c.1810C>A	p.His604Asn	p.H604N	ENST00000274376	NM_002890.2	604	Cat/Aat	14/25	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.348508817559526	2		398	375	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939001	131939001	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	13	242	0	ENST00000265335.6:c.2217A>G	p.Ile739Met	p.I739M	ENST00000265335		739	atA/atG	14/25	1	2	FACETS	0.359	0.256	0.484	0.359	0.256	0.484	SUBCLONAL	1	TRUE	1	0.348508817559526	2		242	208	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519670	176519670	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	94	344	0	ENST00000292408.4:c.942G>T	p.Glu314Asp	p.E314D	ENST00000292408	NM_213647.1	314	gaG/gaT	8/18	1	2	FACETS	0.972	0.867	1	0.972	0.867	1	CLONAL	1	TRUE	1	0.348508817559526	2		344	555	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636948	176636948	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	119	378	0	ENST00000439151.2:c.1548A>G	p.Ile516Met	p.I516M	ENST00000439151	NM_022455.4	516	atA/atG	5/23	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.348508817559526	2		378	554	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176671214	176671214	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	121	475	0	ENST00000439151.2:c.4321C>A	p.Leu1441Met	p.L1441M	ENST00000439151	NM_022455.4	1441	Ctg/Atg	9/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.348508817559526	2		475	534	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673718	176673718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754590923	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	180	544	0	ENST00000439151.2:c.4418G>A	p.Arg1473Gln	p.R1473Q	ENST00000439151	NM_022455.4	1473	cGa/cAa	10/23	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.348508817559526	2		544	999	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176715879	176715879	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	338	771	0	ENST00000439151.2:c.6211A>G	p.Lys2071Glu	p.K2071E	ENST00000439151	NM_022455.4	2071	Aaa/Gaa	21/23	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.348508817559526	2		771	1315	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722112	176722112	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	156	370	1	ENST00000439151.2:c.7743G>T	p.Lys2581Asn	p.K2581N	ENST00000439151	NM_022455.4	2581	aaG/aaT	23/23	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.348508817559526	2		371	743	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020964	26020964	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs772494976	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1575	386	1210	1	ENST00000357647.3:c.247C>A	p.Leu83Met	p.L83M	ENST00000357647	NM_003529.2	83	Ctg/Atg	1/1	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.348508817559526	2		1211	1961	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225789	26225789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1919	351	1257	0	ENST00000360408.1:c.407C>T	p.Ala136Val	p.A136V	ENST00000360408	NM_003532.2	136	gCg/gTg	1/1	1	2	FACETS	0.887	0.836	0.94	0.887	0.836	0.94	CLONAL	1	TRUE	1	0.348508817559526	2		1257	2270	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183033	32183033	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	193	560	0	ENST00000375023.3:c.1991A>C	p.Asn664Thr	p.N664T	ENST00000375023	NM_004557.3	664	aAc/aCc	12/30	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.348508817559526	2		560	1054	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793821	89793821	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	96	388	0	ENST00000336032.3:c.890C>A	p.Pro297His	p.P297H	ENST00000336032	NM_006813.2	297	cCt/cAt	2/2	1	2	FACETS	0.945	0.844	1	0.945	0.844	1	CLONAL	1	TRUE	1	0.348508817559526	2		388	583	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956510	93956510	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	198	772	0	ENST00000369303.4:c.2726G>T	p.Arg909Met	p.R909M	ENST00000369303	NM_004440.3	909	aGg/aTg	15/17	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.348508817559526	2		772	903	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967822	93967822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	130	766	0	ENST00000369303.4:c.2105C>T	p.Thr702Ile	p.T702I	ENST00000369303	NM_004440.3	702	aCa/aTa	11/17	1	2	FACETS	0.814	0.738	0.895	0.814	0.738	0.895	CLONAL	1	TRUE	1	0.348508817559526	2		766	916	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552781	106552781	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	235	804	1	ENST00000369096.4:c.746G>T	p.Ser249Ile	p.S249I	ENST00000369096	NM_001198.3	249	aGc/aTc	5/7	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.348508817559526	2		805	1294	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111995815	111995815	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	365	768	0	ENST00000368678.4:c.1283A>G	p.Lys428Arg	p.K428R	ENST00000368678		428	aAg/aGg	12/13	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.348508817559526	2		768	1524	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665285	117665285	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	84	537	0	ENST00000368508.3:c.4462C>A	p.Leu1488Met	p.L1488M	ENST00000368508	NM_002944.2	1488	Ctg/Atg	27/43	1	2	FACETS	0.586	0.517	0.661	0.586	0.517	0.661	SUBCLONAL	1	TRUE	1	0.348508817559526	2		537	822	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677803	117677803	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	75	329	0	ENST00000368508.3:c.4130C>A	p.Pro1377His	p.P1377H	ENST00000368508	NM_002944.2	1377	cCt/cAt	25/43	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.348508817559526	2		329	410	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527547	157527547	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370789207	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	178	358	2	ENST00000346085.5:c.5272G>A	p.Asp1758Asn	p.D1758N	ENST00000346085	NM_020732.3	1758	Gat/Aat	20/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.348508817559526	2		360	794	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468158	50468158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	164	408	0	ENST00000331340.3:c.1393G>A	p.Glu465Lys	p.E465K	ENST00000331340	NM_006060.4	465	Gaa/Aaa	8/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.348508817559526	2		408	707	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508605	106508605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	119	303	0	ENST00000359195.3:c.599C>T	p.Pro200Leu	p.P200L	ENST00000359195	NM_002649.2	200	cCg/cTg	2/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.348508817559526	2		303	562	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523534	106523534	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	156	389	0	ENST00000359195.3:c.2686G>A	p.Val896Met	p.V896M	ENST00000359195	NM_002649.2	896	Gtg/Atg	8/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.348508817559526	2		389	757	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397490	116397490	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1397379383	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	103	466	0	ENST00000397752.3:c.1863-1G>A		p.X621_splice	ENST00000397752	NM_000245.2	621			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.348508817559526	2		466	427	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453123	140453123	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	90	407	0	ENST00000288602.6:c.1812G>T	p.Trp604Cys	p.W604C	ENST00000288602	NM_004333.4	604	tgG/tgT	15/18	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.348508817559526	2		407	483	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846087	151846087	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	172	426	0	ENST00000262189.6:c.12925T>C	p.Phe4309Leu	p.F4309L	ENST00000262189	NM_170606.2	4309	Ttc/Ctc	52/59	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.348508817559526	2		426	859	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877909	151877909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	60	383	0	ENST00000262189.6:c.7036G>T	p.Gly2346Cys	p.G2346C	ENST00000262189	NM_170606.2	2346	Ggc/Tgc	36/59	1	2	FACETS	0.48	0.413	0.554	0.48	0.413	0.554	SUBCLONAL	1	TRUE	1	0.348508817559526	2		383	717	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866512	117866512	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	49	868	0	ENST00000297338.2:c.1133A>G	p.Gln378Arg	p.Q378R	ENST00000297338	NM_006265.2	378	cAg/cGg	9/14	1	2	FACETS	0.318	0.268	0.373	0.318	0.268	0.373	SUBCLONAL	1	TRUE	1	0.348508817559526	2		868	884	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5463089	5463089	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	93	315	0	ENST00000381577.3:c.650A>G	p.Glu217Gly	p.E217G	ENST00000381577	NM_014143.3	217	gAg/gGg	4/7	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.348508817559526	2		315	386	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5465529	5465529	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	103	714	0	ENST00000381577.3:c.713G>T	p.Arg238Met	p.R238M	ENST00000381577	NM_014143.3	238	aGg/aTg	5/7	1	2	FACETS	0.669	0.598	0.745	0.669	0.598	0.745	SUBCLONAL	1	TRUE	1	0.348508817559526	2		714	883	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521456	8521456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	142	553	0	ENST00000356435.5:c.782G>A	p.Gly261Glu	p.G261E	ENST00000356435		261	gGg/gAg	9/35	1	2	FACETS	0.821	0.748	0.899	0.821	0.748	0.899	CLONAL	1	TRUE	1	0.348508817559526	2		553	992	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606223	93606223	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	171	537	0	ENST00000375746.1:c.43T>C	p.Phe15Leu	p.F15L	ENST00000375746	NM_001174167.1	15	Ttc/Ctc	2/14	1	2	FACETS	0.992	0.912	1	0.992	0.912	1	CLONAL	1	TRUE	1	0.348508817559526	2		537	989	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220393	98220393	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	279	576	0	ENST00000331920.6:c.3070C>A	p.Leu1024Ile	p.L1024I	ENST00000331920	NM_000264.3	1024	Ctc/Atc	18/24	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.348508817559526	2		576	1169	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426902	70426902	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	155	449	0	ENST00000373644.4:c.4562T>C	p.Val1521Ala	p.V1521A	ENST00000373644	NM_030625.2	1521	gTg/gCg	7/12	1	2	FACETS	0.861	0.787	0.938	0.861	0.787	0.938	CLONAL	1	TRUE	1	0.348508817559526	2		449	1033	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653802	89653802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	87	393	0	ENST00000371953.3:c.100G>A	p.Ala34Thr	p.A34T	ENST00000371953	NM_000314.4	34	Gct/Act	2/9	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.348508817559526	2		393	338	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692893	89692893	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	71	261	0	ENST00000371953.3:c.377C>A	p.Ala126Asp	p.A126D	ENST00000371953	NM_000314.4	126	gCt/gAt	5/9	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.348508817559526	2		261	344	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410656	32410656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	268	617	3	ENST00000332351.3:c.1502G>A	p.Arg501His	p.R501H	ENST00000332351	NM_024426.4	501	cGc/cAc	10/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.348508817559526	2		620	1136	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32449553	32449553	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770366595	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	245	615	2	ENST00000332351.3:c.821C>T	p.Thr274Ile	p.T274I	ENST00000332351	NM_024426.4	274	aCc/aTc	3/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.348508817559526	2		617	1033	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577269	64577269	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	240	570	0	ENST00000312049.6:c.313C>A	p.Leu105Ile	p.L105I	ENST00000312049	NM_130799.2	105	Ctc/Atc	2/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.348508817559526	2		570	1014	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119659	108119659	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs876660038	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	47	173	0	ENST00000278616.4:c.1066-1G>T		p.X356_splice	ENST00000278616	NM_000051.3	356			1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.348508817559526	2		173	212	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124674	108124674	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	119	527	0	ENST00000278616.4:c.2032A>G	p.Ile678Val	p.I678V	ENST00000278616	NM_000051.3	678	Att/Gtt	13/63	1	2	FACETS	0.959	0.867	1	0.959	0.867	1	CLONAL	1	TRUE	1	0.348508817559526	2		527	712	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344147	118344147	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	147	429	1	ENST00000534358.1:c.2273G>T	p.Arg758Ile	p.R758I	ENST00000534358	NM_005933.3	758	aGa/aTa	3/36	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.348508817559526	2		430	829	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392116	118392116	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	183	366	0	ENST00000534358.1:c.11627A>T	p.Lys3876Met	p.K3876M	ENST00000534358	NM_005933.3	3876	aAg/aTg	35/36	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.348508817559526	2		366	784	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148943	119148943	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	145	501	0	ENST00000264033.4:c.1163A>T	p.Asp388Val	p.D388V	ENST00000264033	NM_005188.3	388	gAt/gTt	8/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.348508817559526	2		501	685	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417101	417101	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	163	414	0	ENST00000399788.2:c.3449C>T	p.Ala1150Val	p.A1150V	ENST00000399788	NM_001042603.1	1150	gCc/gTc	23/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.348508817559526	2		414	770	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1040445	1040445	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	67	632	1	ENST00000358495.3:c.127C>A	p.Leu43Met	p.L43M	ENST00000358495	NM_134424.2	43	Ctg/Atg	3/12	1	2	FACETS	0.32	0.277	0.367	0.32	0.277	0.367	SUBCLONAL	1	TRUE	1	0.348508817559526	2		633	1202	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12043873	12043873	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	140	434	0	ENST00000396373.4:c.1254-2A>G		p.X418_splice	ENST00000396373	NM_001987.4	418			1	2	FACETS	0.95	0.865	1	0.95	0.865	1	CLONAL	1	TRUE	1	0.348508817559526	2		434	846	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426642	49426642	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	129	322	0	ENST00000301067.7:c.11846A>G	p.Gln3949Arg	p.Q3949R	ENST00000301067	NM_003482.3	3949	cAa/cGa	39/54	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.348508817559526	2		322	570	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49449057	49449057	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	247	605	0	ENST00000301067.7:c.49+2T>C		p.X17_splice	ENST00000301067	NM_003482.3	17			1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.348508817559526	2		605	1106	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856530	111856530	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	170	515	0	ENST00000341259.2:c.581A>C	p.Glu194Ala	p.E194A	ENST00000341259	NM_005475.2	194	gAg/gCg	2/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.348508817559526	2		515	855	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28901601	28901601	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	98	616	0	ENST00000282397.4:c.2794A>G	p.Lys932Glu	p.K932E	ENST00000282397	NM_002019.4	932	Aag/Gag	20/30	1	2	FACETS	0.688	0.613	0.767	0.688	0.613	0.767	SUBCLONAL	1	TRUE	1	0.348508817559526	2		616	818	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041123	29041123	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	108	601	0	ENST00000282397.4:c.305C>T	p.Thr102Ile	p.T102I	ENST00000282397	NM_002019.4	102	aCt/aTt	3/30	1	2	FACETS	0.685	0.614	0.76	0.685	0.614	0.76	SUBCLONAL	1	TRUE	1	0.348508817559526	2		601	905	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435409	110435409	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1472585307	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	159	388	0	ENST00000375856.3:c.2992C>T	p.Pro998Ser	p.P998S	ENST00000375856	NM_003749.2	998	Ccc/Tcc	1/2	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.348508817559526	2		388	741	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422074	81422074	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	148	442	0	ENST00000298171.2:c.50G>T	p.Arg17Met	p.R17M	ENST00000298171	NM_000369.2	17	aGg/aTg	1/10	1	2	FACETS	0.984	0.899	1	0.984	0.899	1	CLONAL	1	TRUE	1	0.348508817559526	2		442	863	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609837	81609837	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	127	450	0	ENST00000298171.2:c.1435T>C	p.Ser479Pro	p.S479P	ENST00000298171	NM_000369.2	479	Tct/Cct	10/10	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.348508817559526	2		450	728	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961782	41961782	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1195	72	980	1	ENST00000219905.7:c.690G>T	p.Gln230His	p.Q230H	ENST00000219905	NM_001164273.1	230	caG/caT	2/24	0.348508817559526	1	FACETS	0.269	0.234	0.308	0.269	0.234	0.308	SUBCLONAL	1	TRUE	0	0.348508817559526	1		981	1267	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021464	42021464	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1266	78	1003	1	ENST00000219905.7:c.3760C>A	p.Pro1254Thr	p.P1254T	ENST00000219905	NM_001164273.1	1254	Cca/Aca	11/24	0.348508817559526	1	FACETS	0.275	0.24	0.313	0.275	0.24	0.313	SUBCLONAL	1	TRUE	0	0.348508817559526	1		1004	1344	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040885	42040885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1358068423	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	372	800	0	ENST00000219905.7:c.5263G>A	p.Val1755Met	p.V1755M	ENST00000219905	NM_001164273.1	1755	Gtg/Atg	16/24	0.348508817559526	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.348508817559526	1		800	1297	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003782	45003782	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs752758095	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	98	465	0	ENST00000558401.1:c.38T>C	p.Leu13Pro	p.L13P	ENST00000558401	NM_004048.2	13	cTc/cCc	1/4	0.348508817559526	1	FACETS	0.648	0.578	0.722	0.648	0.578	0.722	SUBCLONAL	1	TRUE	0	0.348508817559526	1		465	717	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73992011	73992011	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	256	730	2	ENST00000318443.5:c.31G>T	p.Gly11Cys	p.G11C	ENST00000318443	NM_001024736.1	11	Ggt/Tgt	2/10	0.348508817559526	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.348508817559526	1		732	1138	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628601	90628601	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	289	820	0	ENST00000330062.3:c.986T>C	p.Leu329Pro	p.L329P	ENST00000330062	NM_002168.2	329	cTg/cCg	8/11	0.348508817559526	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.348508817559526	1		820	1107	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	364669	364669	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	144	463	0	ENST00000262320.3:c.893G>T	p.Arg298Leu	p.R298L	ENST00000262320	NM_003502.3	298	cGg/cTg	3/11	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.348508817559526	2		463	785	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220700	2220700	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1303783514	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	199	543	0	ENST00000326181.6:c.317C>T	p.Thr106Ile	p.T106I	ENST00000326181	NM_032271.2	106	aCa/aTa	5/21	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.348508817559526	2		543	886	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636813	2636813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs547797391	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	280	608	2	ENST00000342085.4:c.1262C>T	p.Ser421Leu	p.S421L	ENST00000342085	NM_002613.4	421	tCg/tTg	11/14	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.348508817559526	2		610	1179	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781359	3781359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	208	570	0	ENST00000262367.5:c.5006C>T	p.Thr1669Ile	p.T1669I	ENST00000262367	NM_004380.2	1669	aCc/aTc	30/31	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.348508817559526	2		570	971	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041717	14041717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	161	552	0	ENST00000311895.7:c.2264C>T	p.Pro755Leu	p.P755L	ENST00000311895	NM_005236.2	755	cCc/cTc	11/11	1	2	FACETS	0.788	0.721	0.858	0.788	0.721	0.858	SUBCLONAL	1	TRUE	1	0.348508817559526	2		552	1173	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831333	72831333	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	302	768	1	ENST00000268489.5:c.5248G>A	p.Ala1750Thr	p.A1750T	ENST00000268489	NM_006885.3	1750	Gct/Act	9/10	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.348508817559526	2		769	1386	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934365	81934365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200919414	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	280	705	1	ENST00000359376.3:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000359376	NM_002661.3	448	Cgg/Tgg	14/33	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.348508817559526	2		706	1180	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89335049	89335049	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	102	344	0	ENST00000301030.4:c.7829A>G	p.Gln2610Arg	p.Q2610R	ENST00000301030	NM_001256183.1	2610	cAg/cGg	13/13	1	2	FACETS	0.905	0.81	1	0.905	0.81	1	CLONAL	1	TRUE	1	0.348508817559526	2		344	647	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108344	8108344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151173438	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	209	451	0	ENST00000585124.1:c.880G>A	p.Ala294Thr	p.A294T	ENST00000585124	NM_004217.3	294	Gct/Act	9/9	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.348508817559526	2		451	928	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16022787	16022787	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	28	489	0	ENST00000268712.3:c.1865C>A	p.Pro622His	p.P622H	ENST00000268712	NM_006311.3	622	cCt/cAt	17/46	1	2	FACETS	0.34	0.271	0.419	0.34	0.271	0.419	SUBCLONAL	1	TRUE	1	0.348508817559526	2		489	472	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049844	16049844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	29	377	1	ENST00000268712.3:c.928C>T	p.Arg310Cys	p.R310C	ENST00000268712	NM_006311.3	310	Cgt/Tgt	10/46	1	2	FACETS	0.376	0.301	0.461	0.376	0.301	0.461	SUBCLONAL	1	TRUE	1	0.348508817559526	2		378	443	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315504	30315504	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	195	606	0	ENST00000322652.5:c.1189A>G	p.Thr397Ala	p.T397A	ENST00000322652	NM_015355.2	397	Act/Gct	10/16	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.348508817559526	2		606	879	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428338	33428338	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	180	512	0	ENST00000345365.6:c.785C>A	p.Pro262His	p.P262H	ENST00000345365	NM_002878.3	262	cCt/cAt	9/10	1	2	FACETS	0.953	0.878	1	0.953	0.878	1	CLONAL	1	TRUE	1	0.348508817559526	2		512	1084	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673809	37673809	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	150	343	0	ENST00000447079.4:c.2963T>C	p.Phe988Ser	p.F988S	ENST00000447079	NM_015083.1	988	tTc/tCc	10/14	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.348508817559526	2		343	675	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696691	47696691	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	228	644	0	ENST00000347630.2:c.257T>C	p.Leu86Pro	p.L86P	ENST00000347630	NM_001007230.1	86	cTt/cCt	5/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.348508817559526	2		644	983	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435681	56435681	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	55	261	0	ENST00000407977.2:c.1456A>G	p.Ser486Gly	p.S486G	ENST00000407977		486	Agc/Ggc	9/10	1	2	FACETS	0.711	0.609	0.821	0.711	0.609	0.821	SUBCLONAL	1	TRUE	1	0.348508817559526	2		261	444	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448325	56448325	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	189	419	0	ENST00000407977.2:c.322A>G	p.Lys108Glu	p.K108E	ENST00000407977		108	Aag/Gag	3/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.348508817559526	2		419	909	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56811479	56811479	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs786201890	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	95	351	1	ENST00000337432.4:c.1027C>T	p.Pro343Ser	p.P343S	ENST00000337432	NM_058216.2	343	Cct/Tct	9/9	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.348508817559526	2		352	505	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774925	73774925	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	175	661	0	ENST00000254810.4:c.248T>C	p.Leu83Pro	p.L83P	ENST00000254810	NM_005324.3	83	cTg/cCg	3/4	1	2	FACETS	0.791	0.727	0.859	0.791	0.727	0.859	SUBCLONAL	1	TRUE	1	0.348508817559526	2		661	1269	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217049	2217049	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	186	498	0	ENST00000398665.3:c.2504C>A	p.Pro835His	p.P835H	ENST00000398665	NM_032482.2	835	cCt/cAt	21/28	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.348508817559526	2		498	805	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215607	5215607	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	121	399	1	ENST00000357368.4:c.4097-1G>T		p.X1366_splice	ENST00000357368	NM_002850.3	1366			1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.348508817559526	2		400	668	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172442	7172442	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	83	305	0	ENST00000302850.5:c.1127A>T	p.Asn376Ile	p.N376I	ENST00000302850	NM_000208.2	376	aAt/aTt	5/22	1	2	FACETS	0.843	0.745	0.947	0.843	0.745	0.947	CLONAL	1	TRUE	1	0.348508817559526	2		305	565	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095027	11095027	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	242	736	1	ENST00000358026.2:c.200A>T	p.Asp67Val	p.D67V	ENST00000358026	NM_001128849.1	67	gAc/gTc	2/36	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.348508817559526	2		737	1263	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095985	11095985	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1366085446	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	243	672	2	ENST00000358026.2:c.259G>A	p.Asp87Asn	p.D87N	ENST00000358026	NM_001128849.1	87	Gac/Aac	3/36	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.348508817559526	2		674	1075	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097215	11097215	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	94	306	0	ENST00000358026.2:c.706C>A	p.Pro236Thr	p.P236T	ENST00000358026	NM_001128849.1	236	Cct/Act	4/36	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.348508817559526	2		306	474	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170810	11170810	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	77	360	1	ENST00000358026.2:c.4954T>A	p.Ser1652Thr	p.S1652T	ENST00000358026	NM_001128849.1	1652	Tcc/Acc	35/36	1	2	FACETS	0.728	0.639	0.823	0.728	0.639	0.823	SUBCLONAL	1	TRUE	1	0.348508817559526	2		361	607	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629051	14629051	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	181	534	1	ENST00000254322.2:c.111G>T	p.Lys37Asn	p.K37N	ENST00000254322	NM_006145.1	37	aaG/aaT	1/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.348508817559526	2		535	877	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291872	15291872	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	138	558	0	ENST00000263388.2:c.2894C>A	p.Pro965His	p.P965H	ENST00000263388	NM_000435.2	965	cCc/cAc	18/33	1	2	FACETS	0.871	0.792	0.954	0.871	0.792	0.954	CLONAL	1	TRUE	1	0.348508817559526	2		558	909	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355210	15355210	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	165	483	0	ENST00000263377.2:c.2413G>A	p.Val805Met	p.V805M	ENST00000263377	NM_058243.2	805	Gtg/Atg	13/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.348508817559526	2		483	810	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273908	18273908	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	262	621	0	ENST00000222254.8:c.1241A>G	p.Asn414Ser	p.N414S	ENST00000222254	NM_005027.3	414	aAt/aGt	10/16	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.348508817559526	2		621	1189	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905974	50905974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746087148	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	295	910	2	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	0.348508817559526	2		912	1295	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714556	52714556	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1489963266	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	241	605	0	ENST00000322088.6:c.314G>A	p.Arg105Gln	p.R105Q	ENST00000322088	NM_014225.5	105	cGg/cAg	4/15	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.348508817559526	2		605	1037	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547031	9547031	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	33	155	0	ENST00000353224.5:c.991G>A	p.Val331Met	p.V331M	ENST00000353224	NM_177990.2	331	Gtg/Atg	5/10	1	2	FACETS	0.992	0.815	1	0.992	0.815	1	CLONAL	1	TRUE	1	0.348508817559526	2		155	191	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264364	46264364	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1452	293	903	0	ENST00000371998.3:c.1411C>A	p.Pro471Thr	p.P471T	ENST00000371998		471	Cct/Act	11/23	1	2	FACETS	0.964	0.904	1	0.964	0.904	1	CLONAL	1	TRUE	1	0.348508817559526	2		903	1745	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527509	41527509	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	55	508	0	ENST00000263253.7:c.1400C>T	p.Ala467Val	p.A467V	ENST00000263253	NM_001429.3	467	gCc/gTc	6/31	1	2	FACETS	0.298	0.254	0.347	0.298	0.254	0.347	SUBCLONAL	1	TRUE	1	0.348508817559526	2		508	1059	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545119	41545119	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	269	707	0	ENST00000263253.7:c.2319G>T	p.Gln773His	p.Q773H	ENST00000263253	NM_001429.3	773	caG/caT	13/31	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.348508817559526	2		707	1280	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573122	41573122	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	166	504	0	ENST00000263253.7:c.5407G>A	p.Val1803Met	p.V1803M	ENST00000263253	NM_001429.3	1803	Gtg/Atg	31/31	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.348508817559526	2		504	916	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922290	39922290	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	206	591	0	ENST00000378444.4:c.3882G>T	p.Lys1294Asn	p.K1294N	ENST00000378444	NM_001123385.1	1294	aaG/aaT	9/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.348508817559526	2		591	1044	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412937	63412937	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201650985	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1246	307	934	2	ENST00000330258.3:c.230G>A	p.Arg77Gln	p.R77Q	ENST00000330258	NM_152424.3	77	cGg/cAg	2/2	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.348508817559526	2		936	1553	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938599	76938599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	33	736	0	ENST00000373344.5:c.2149C>T	p.Pro717Ser	p.P717S	ENST00000373344	NM_000489.3	717	Cca/Tca	9/35	1	2	FACETS	0.303	0.245	0.367	0.303	0.245	0.367	SUBCLONAL	1	TRUE	1	0.348508817559526	2		736	626	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939031	76939031	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs782746892	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	164	755	0	ENST00000373344.5:c.1717G>T	p.Gly573Cys	p.G573C	ENST00000373344	NM_000489.3	573	Ggt/Tgt	9/35	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.348508817559526	2		755	846	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55225357	55225358	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	155	352	0	ENST00000275493.2:c.1214dup	p.Leu405PhefsTer8	p.L405Ffs*8	ENST00000275493	NM_005228.3	403	-/T	11/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.348508817559526	2		352	748	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741839	17741840	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	14	161	0	ENST00000250003.3:c.515dup	p.Gly173TrpfsTer105	p.G173Wfs*105	ENST00000250003	NM_002478.4	170	-/C	1/3	1	2	FACETS	0.294	0.212	0.394	0.294	0.212	0.394	SUBCLONAL	1	TRUE	1	0.348508817559526	2		161	273	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	112	182	0	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	1	2	FACETS	0.774	0.696	0.857	0.774	0.696	0.857	SUBCLONAL	1	TRUE	1	0.348508817559526	2		182	830	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9770516	9770517	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	253	593	1	ENST00000377346.4:c.8dup	p.Gly4TrpfsTer20	p.G4Wfs*20	ENST00000377346	NM_005026.3	1	-/C	3/24	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.348508817559526	2		594	1061	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018150	48018163	+	frameshift_variant	Frame_Shift_Del	DEL	TGATGGAACATTCA	TGATGGAACATTCA	-	novel	NA	P-0012988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	213	574	0	ENST00000234420.5:c.346_359del	p.Asp116ProfsTer15	p.D116Pfs*15	ENST00000234420	NM_000179.2	115	ttTGATGGAACATTCAtc/tttc	2/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.348508817559526	2		574	1059	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0013029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	30	328	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.418	0.338	0.51	0.418	0.338	0.51	SUBCLONAL	1	FALSE	1	0.458110580784821	2		328	313	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0013029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	255	625	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.977	1	1	0.996	1	CLONAL	2	FALSE	1	0.458110580784821	2		625	526	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890149	76890150	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	463	554	0	ENST00000373344.5:c.4744dup	p.Thr1582AsnfsTer19	p.T1582Nfs*19	ENST00000373344	NM_000489.3	1582	aca/aAca	17/35	1	1	FACETS	0.896	0.873	0.918	1	0.998	1	CLONAL	3	FALSE	0	0.458110580784821	1		554	580	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0013029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	1283	843	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.154466478541186	6	FACETS	0.986	0.977	0.994			1	INDETERMINATE	8	FALSE	NA	0.458110580784821	6		843	1361	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958084	54958084	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	31	668	1	ENST00000312783.6:c.523G>A	p.Glu175Lys	p.E175K	ENST00000312783	NM_198436.1	175	Gag/Aag	6/10	0.22660745151545	0	FACETS	0.132	0.106	0.162			1	INDETERMINATE	1	FALSE	0	0.458110580784821	0		669	554	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578283	28578283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138003347	NA	P-0013029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	50	569	3	ENST00000241453.7:c.2888C>T	p.Ser963Leu	p.S963L	ENST00000241453	NM_004119.2	963	tCg/tTg	24/24	0.458110580784821	1	FACETS	0.452	0.385	0.526	0.452	0.385	0.526	SUBCLONAL	1	FALSE	0	0.458110580784821	1		572	372	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164913	106164913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs898441677	NA	P-0013029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	15	385	0	ENST00000380013.4:c.3781C>T	p.Arg1261Cys	p.R1261C	ENST00000380013	NM_001127208.2	1261	Cgc/Tgc	6/11	0.458110580784821	1	FACETS	0.153	0.111	0.203	0.153	0.111	0.203	SUBCLONAL	1	FALSE	0	0.458110580784821	1		385	331	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033352	48033352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750949	NA	P-0013029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	10	569	0	ENST00000234420.5:c.3656C>T	p.Thr1219Ile	p.T1219I	ENST00000234420	NM_000179.2	1219	aCt/aTt	8/10	0.340953373477622	1	FACETS	0.072	0.048	0.103	0.072	0.048	0.103	SUBCLONAL	1	FALSE	0	0.458110580784821	1		569	466	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148659	20148659	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	16	379	0	ENST00000379607.5:c.404G>A	p.Gly135Glu	p.G135E	ENST00000379607	NM_001412.3	135	gGa/gAa	6/7	0.415962702909354	0	FACETS	0.17	0.125	0.223			1	SUBCLONAL	1	FALSE	NA	0.458110580784821	0		379	223	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244077	5244077	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1325	91	1129	0	ENST00000357368.4:c.1405G>A	p.Glu469Lys	p.E469K	ENST00000357368	NM_002850.3	469	Gag/Aag	11/38	1	2	FACETS	0.281	0.248	0.316	0.281	0.248	0.316	SUBCLONAL	1	FALSE	1	0.458110580784821	2		1129	1416	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458114	120458114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	71	827	0	ENST00000256646.2:c.7231G>A	p.Glu2411Lys	p.E2411K	ENST00000256646	NM_024408.3	2411	Gag/Aag	34/34	1	2	FACETS	0.281	0.244	0.321	0.281	0.244	0.321	SUBCLONAL	1	FALSE	1	0.458110580784821	2		827	1102	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830883	156830883	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200815412	NA	P-0013029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	33	543	0	ENST00000524377.1:c.157G>A	p.Asp53Asn	p.D53N	ENST00000524377	NM_002529.3	53	Gat/Aat	1/17	1	2	FACETS	0.258	0.21	0.313	0.258	0.21	0.313	SUBCLONAL	1	FALSE	1	0.458110580784821	2		543	558	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010487	48010487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751838296	NA	P-0013029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	18	372	2	ENST00000234420.5:c.115G>A	p.Gly39Arg	p.G39R	ENST00000234420	NM_000179.2	39	Ggg/Agg	1/10	0.340953373477622	1	FACETS	0.191	0.143	0.248	0.191	0.143	0.248	SUBCLONAL	1	FALSE	0	0.458110580784821	1		374	317	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033618	48033618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	29	363	0	ENST00000234420.5:c.3829G>A	p.Asp1277Asn	p.D1277N	ENST00000234420	NM_000179.2	1277	Gac/Aac	9/10	0.340953373477622	1	FACETS	0.392	0.316	0.478	0.392	0.316	0.478	SUBCLONAL	1	FALSE	0	0.458110580784821	1		363	249	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735572	204735572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553657427	NA	P-0013029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	25	435	0	ENST00000302823.3:c.373G>A	p.Gly125Arg	p.G125R	ENST00000302823	NM_005214.4	125	Gga/Aga	2/4	1	2	FACETS	0.24	0.188	0.299	0.24	0.188	0.299	SUBCLONAL	1	FALSE	1	0.458110580784821	2		435	455	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165375	47165375	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	39	776	0	ENST00000409792.3:c.751G>A	p.Glu251Lys	p.E251K	ENST00000409792	NM_014159.6	251	Gaa/Aaa	3/21	1	2	FACETS	0.226	0.186	0.271	0.226	0.186	0.271	SUBCLONAL	1	FALSE	1	0.458110580784821	2		776	753	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197578	106197578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1265087034	NA	P-0013029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	51	807	2	ENST00000380013.4:c.5911C>T	p.Leu1971Phe	p.L1971F	ENST00000380013	NM_001127208.2	1971	Ctt/Ttt	11/11	0.458110580784821	1	FACETS	0.245	0.207	0.286	0.245	0.207	0.286	SUBCLONAL	1	FALSE	0	0.458110580784821	1		809	702	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176710878	176710878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	43	968	1	ENST00000439151.2:c.6100G>A	p.Val2034Met	p.V2034M	ENST00000439151	NM_022455.4	2034	Gtg/Atg	20/23	0.458110580784821	1	FACETS	0.223	0.186	0.264	0.223	0.186	0.264	SUBCLONAL	1	FALSE	0	0.458110580784821	1		969	650	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045966	26045966	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	663	1403	1	ENST00000540144.1:c.328C>G	p.Leu110Val	p.L110V	ENST00000540144	NM_003531.2	110	Ctg/Gtg	1/1	1	2	FACETS	0.91	0.878	0.943	1	0.998	1	CLONAL	2	FALSE	1	0.458110580784821	2		1404	1590	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157519982	157519982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	48	654	0	ENST00000346085.5:c.4051C>T	p.Pro1351Ser	p.P1351S	ENST00000346085	NM_020732.3	1351	Cct/Tct	17/20	1	2	FACETS	0.256	0.215	0.301	0.256	0.215	0.301	SUBCLONAL	1	FALSE	1	0.458110580784821	2		654	819	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367302	50367302	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	34	496	0	ENST00000331340.3:c.109C>T	p.Leu37Phe	p.L37F	ENST00000331340	NM_006060.4	37	Ctc/Ttc	3/8	1	2	FACETS	0.27	0.22	0.327	0.27	0.22	0.327	SUBCLONAL	1	FALSE	1	0.458110580784821	2		496	549	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333496	70333496	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	57	731	0	ENST00000373644.4:c.1401G>T	p.Gln467His	p.Q467H	ENST00000373644	NM_030625.2	467	caG/caT	2/12	1	2	FACETS	0.369	0.316	0.427	0.369	0.316	0.427	SUBCLONAL	1	FALSE	1	0.458110580784821	2		731	674	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922196	100922196	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	67	1096	0	ENST00000325455.5:c.2316T>A	p.Ser772Arg	p.S772R	ENST00000325455	NM_001202474.3	772	agT/agA	5/8	1	2	FACETS	0.308	0.266	0.353	0.308	0.266	0.353	SUBCLONAL	1	FALSE	1	0.458110580784821	2		1096	951	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224502	108224502	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	29	566	0	ENST00000278616.4:c.8681T>C	p.Phe2894Ser	p.F2894S	ENST00000278616	NM_000051.3	2894	tTt/tCt	60/63	1	2	FACETS	0.223	0.178	0.274	0.223	0.178	0.274	SUBCLONAL	1	FALSE	1	0.458110580784821	2		566	568	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376084	118376084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	54	718	0	ENST00000534358.1:c.9477G>A	p.Met3159Ile	p.M3159I	ENST00000534358	NM_005933.3	3159	atG/atA	27/36	1	2	FACETS	0.323	0.275	0.376	0.323	0.275	0.376	SUBCLONAL	1	FALSE	1	0.458110580784821	2		718	730	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900921	3900921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747862621	NA	P-0013029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	164	1005	0	ENST00000262367.5:c.175C>T	p.Leu59Phe	p.L59F	ENST00000262367	NM_004380.2	59	Ctt/Ttt	2/31	0.340953373477622	1	FACETS	0.524	0.48	0.57	0.524	0.48	0.57	SUBCLONAL	1	FALSE	0	0.458110580784821	1		1005	1053	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341304	89341304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	14	275	0	ENST00000301030.4:c.7631C>T	p.Thr2544Ile	p.T2544I	ENST00000301030	NM_001256183.1	2544	aCc/aTc	11/13	0.446688619636788	0	FACETS	0.159	0.115	0.213			1	SUBCLONAL	1	FALSE	0	0.458110580784821	0		275	208	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836339	89836339	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	42	680	1	ENST00000389301.3:c.2410G>A	p.Gly804Ser	p.G804S	ENST00000389301	NM_000135.2	804	Ggt/Agt	26/43	0.458110580784821	1	FACETS	0.231	0.192	0.274	0.231	0.192	0.274	SUBCLONAL	1	FALSE	0	0.458110580784821	1		681	612	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585419	29585419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199474789	NA	P-0013029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	48	779	0	ENST00000356175.3:c.4168C>T	p.Leu1390Phe	p.L1390F	ENST00000356175	NM_000267.3	1390	Ctc/Ttc	31/57	0.40139976603841	4	FACETS	0.35	0.295	0.411	0.117	0.098	0.137	SUBCLONAL	1	FALSE	1	0.458110580784821	4		779	873	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592353	29592353	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500316	NA	P-0013029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	74	579	0	ENST00000356175.3:c.4768C>T	p.Arg1590Trp	p.R1590W	ENST00000356175	NM_000267.3	1590	Cgg/Tgg	35/57	0.40139976603841	4	FACETS	0.627	0.548	0.712	0.209	0.182	0.238	SUBCLONAL	1	FALSE	1	0.458110580784821	4		579	751	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410180	63410180	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	136	467	0	ENST00000330258.3:c.2987T>C	p.Ile996Thr	p.I996T	ENST00000330258	NM_152424.3	996	aTa/aCa	2/2	1	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	0	0.458110580784821	1		467	425	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860080	57860080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs563340967	NA	P-0013032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1324	188	938	0	ENST00000228682.2:c.820G>A	p.Gly274Ser	p.G274S	ENST00000228682	NM_005269.2	274	Ggc/Agc	8/12	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.21655422756546	2		938	1512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	89	426	0	ENST00000269305.4:c.376T>C	p.Tyr126His	p.Y126H	ENST00000269305	NM_001126112.2	126	Tac/Cac	5/11	0.214672438929006	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.21655422756546	1		426	654	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278062	18278062	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	106	596	0	ENST00000222254.8:c.1682A>C	p.Asn561Thr	p.N561T	ENST00000222254	NM_005027.3	561	aAc/aCc	13/16	1	2	FACETS	0.985	0.881	1	0.985	0.881	1	CLONAL	1	TRUE	1	0.21655422756546	2		596	994	SUCCESS
APC	324	MSKCC	GRCh37	5	112175866	112175867	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCTCCAGTTCAGGAAAATGACAATGGGAATGAAA	novel	NA	P-0013032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	36	374	0	ENST00000257430.4:c.4577_4610dup	p.Glu1538SerfsTer6	p.E1538Sfs*6	ENST00000257430	NM_000038.5	1525	-/CCTCCAGTTCAGGAAAATGACAATGGGAATGAAA	16/16	0.199360311812938	1	FACETS	0.497	0.407	0.597	0.497	0.407	0.597	SUBCLONAL	1	TRUE	0	0.21655422756546	1		374	597	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866452	42866506	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	TTCCGGTTGGTATCCATGGTTTTCATAGTAAGGTCCAATAGCTGGTGGTGACCCC	TTCCGGTTGGTATCCATGGTTTTCATAGTAAGGTCCAATAGCTGGTGGTGACCCC	-	novel	NA	P-0013032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1399	128	904	0	ENST00000398585.3:c.127-1_180del		p.X43_splice	ENST00000398585	NM_001135099.1	43		3/14	1	2	FACETS	0.774	0.699	0.854	0.774	0.699	0.854	SUBCLONAL	1	TRUE	1	0.21655422756546	2		904	1527	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060573	38060573	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1359	164	858	0	ENST00000250448.2:c.1416del	p.Ter473SerfsTer11	p.*473Sfs*11	ENST00000250448	NM_004496.3	472	tcC/tc	2/2	1	2	FACETS	0.995	0.91	1	0.995	0.91	1	CLONAL	1	TRUE	1	0.21655422756546	2		858	1523	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0013043-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	93	494	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.976	0.87	1	0.976	0.87	1	CLONAL	1	TRUE	1	0.351710489483705	2		494	542	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835780	68835781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0013043-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	121	521	0	ENST00000261769.5:c.377dup	p.Pro127AlafsTer41	p.P127Afs*41	ENST00000261769	NM_004360.3	124	cgc/cgCc	3/16	0.351710489483705	1	FACETS	0.87	0.787	0.956	0.87	0.787	0.956	CLONAL	1	TRUE	0	0.351710489483705	1		521	652	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0013056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	17	640	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.273435248190984	1	FACETS	0.147	0.109	0.193	0.147	0.109	0.193	SUBCLONAL	1	TRUE	0	0.273435248190984	1		640	728	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249014	55249015	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCCCCACGTGTG	novel	NA	P-0013056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	210	611	0	ENST00000275493.2:c.2315_2326dup	p.Pro772_Cys775dup	p.P772_C775dup	ENST00000275493	NM_005228.3	772	aac/aaCCCCCACGTGTGc	20/28	0.273435248190984	4	FACETS	1	0.959	1	0.697	0.648	0.749	CLONAL	2	TRUE	1	0.273435248190984	4		611	935	SUCCESS
APC	324	MSKCC	GRCh37	5	112175273	112175273	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123121	NA	P-0013156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	606	406	0	ENST00000257430.4:c.3982C>T	p.Gln1328Ter	p.Q1328*	ENST00000257430	NM_000038.5	1328	Cag/Tag	16/16	0.841652360086457	3	FACETS	0.96	0.942	0.977	0.96	0.942	0.977	CLONAL	3	TRUE	0	0.859846112817311	3		406	700	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870953	12870953	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	262	512	0	ENST00000228872.4:c.180G>C	p.Trp60Cys	p.W60C	ENST00000228872	NM_004064.3	60	tgG/tgC	1/3	0.850115555273807	3	FACETS	0.837	0.785	0.891	0.279	0.261	0.297	CLONAL	1	TRUE	0	0.859846112817311	3		512	1041	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760765	133760765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1477848387	NA	P-0013156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	113	575	0	ENST00000318560.5:c.3088G>A	p.Gly1030Ser	p.G1030S	ENST00000318560	NM_005157.4	1030	Ggc/Agc	11/11	0.50699824426946	3	FACETS	0.334	0.299	0.37	0.111	0.099	0.124	INDETERMINATE	1	TRUE	0	0.859846112817311	3		575	1126	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54959326	54959326	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2143	153	621	0	ENST00000312783.6:c.374A>C	p.Lys125Thr	p.K125T	ENST00000312783	NM_198436.1	125	aAg/aCg	5/10	0.859846112817311	6	FACETS	0.422	0.383	0.462	0.105	0.095	0.116	SUBCLONAL	1	TRUE	2	0.859846112817311	6		621	2296	SUCCESS
AR	367	MSKCC	GRCh37	X	66766408	66766408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	29	70	0	ENST00000374690.3:c.1420G>A	p.Glu474Lys	p.E474K	ENST00000374690	NM_000044.3	474	Gag/Aag	1/8	1	1	FACETS	0.291	0.237	0.351	0.291	0.237	0.351	SUBCLONAL	1	TRUE	0	0.859846112817311	1		70	132	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578226	7578227	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CATCCAAA	novel	NA	P-0013156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	1000	874	0	ENST00000269305.4:c.615_622dup	p.Asp208ValfsTer42	p.D208Vfs*42	ENST00000269305	NM_001126112.2	208	gac/gTTTGGATGac	6/11	0.859846112817311	2	FACETS	0.804	0.787	0.821	0.804	0.787	0.821	CLONAL	2	TRUE	0	0.859846112817311	2		874	1446	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0013345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	327	480	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.543043080624434	2		480	1043	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878144	48878144	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	93	245	0	ENST00000267163.4:c.96C>A	p.Asp32Glu	p.D32E	ENST00000267163	NM_000321.2	32	gaC/gaA	1/27	0.115896200520204	3	FACETS	1	0.936	1	0.532	0.476	0.591	INDETERMINATE	1	TRUE	1	0.543043080624434	3		245	409	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522461	187522461	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	306	790	0	ENST00000441802.2:c.11602G>T	p.Val3868Phe	p.V3868F	ENST00000441802	NM_005245.3	3868	Gtc/Ttc	21/27	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.543043080624434	2		790	898	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151868393	151868393	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	67	643	0	ENST00000262189.6:c.9409C>T	p.Gln3137Ter	p.Q3137*	ENST00000262189	NM_170606.2	3137	Cag/Tag	40/59	0.543043080624434	4	FACETS	0.459	0.398	0.525	0.153	0.132	0.175	SUBCLONAL	1	TRUE	1	0.543043080624434	4		643	830	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	114	365	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.995	0.896	1	0.995	0.896	1	CLONAL	1	TRUE	1	0.290384476021254	2		365	789	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	52	230	0	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	0.290384476021254	2		230	284	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258889	16258889	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	174	828	1	ENST00000375759.3:c.6158del	p.Asn2053ThrfsTer11	p.N2053Tfs*11	ENST00000375759	NM_015001.2	2052	Aaa/aa	11/15	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.290384476021254	2		829	1190	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431874	49431874	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	224	625	1	ENST00000301067.7:c.9265del	p.Val3089TrpfsTer30	p.V3089Wfs*30	ENST00000301067	NM_003482.3	3089	Gtg/tg	34/54	0.263939997513768	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.290384476021254	3		626	816	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592099	67592099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	153	701	2	ENST00000274335.5:c.1915C>T	p.Arg639Ter	p.R639*	ENST00000274335		639	Cga/Tga	14/15	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.290384476021254	2		703	899	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	115	297	0	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.290384476021254	2		297	726	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	102	613	0	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	1	2	FACETS	0.933	0.834	1	0.933	0.834	1	CLONAL	1	TRUE	1	0.290384476021254	2		613	753	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475061	40475063	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	168	1084	0	ENST00000264657.5:c.1847_1849del	p.Glu616del	p.E616del	ENST00000264657	NM_139276.2	616	gAAGga/gga	20/24	1	2	FACETS	0.895	0.82	0.973	0.895	0.82	0.973	CLONAL	1	TRUE	1	0.290384476021254	2		1084	1293	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852118	63852118	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	87	473	0	ENST00000279873.7:c.2901del	p.Lys967AsnfsTer15	p.K967Nfs*15	ENST00000279873	NM_032199.2	966	Aaa/aa	10/10	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.290384476021254	2		473	539	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822585	72822586	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs764626362	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	117	913	2	ENST00000268489.5:c.9589dup	p.Gln3197ProfsTer42	p.Q3197Pfs*42	ENST00000268489	NM_006885.3	3197	cag/cCag	10/10	1	2	FACETS	0.858	0.773	0.949	0.858	0.773	0.949	CLONAL	1	TRUE	1	0.290384476021254	2		915	939	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588981	67588981	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	104	568	0	ENST00000274335.5:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000274335		358	Cga/Tga	8/15	1	2	FACETS	0.91	0.815	1	0.91	0.815	1	CLONAL	1	TRUE	1	0.290384476021254	2		568	787	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157834	106157834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs4145756	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	77	591	0	ENST00000380013.4:c.2735C>T	p.Ala912Val	p.A912V	ENST00000380013	NM_001127208.2	912	gCg/gTg	3/11	1	2	FACETS	0.765	0.672	0.866	0.765	0.672	0.866	SUBCLONAL	1	TRUE	1	0.290384476021254	2		591	693	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434413	140434413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775889922	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	132	736	0	ENST00000288602.6:c.2285C>T	p.Ala762Val	p.A762V	ENST00000288602	NM_004333.4	762	gCg/gTg	18/18	1	2	FACETS	0.941	0.853	1	0.941	0.853	1	CLONAL	1	TRUE	1	0.290384476021254	2		736	966	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38968098	38968098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777143677	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	107	758	0	ENST00000357387.3:c.1007G>A	p.Arg336His	p.R336H	ENST00000357387	NM_152756.3	336	cGt/cAt	12/38	1	2	FACETS	0.905	0.812	1	0.905	0.812	1	CLONAL	1	TRUE	1	0.290384476021254	2		758	814	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741837	17741837	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199584989	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	47	197	1	ENST00000250003.3:c.508G>A	p.Ala170Thr	p.A170T	ENST00000250003	NM_002478.4	170	Gcg/Acg	1/3	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.290384476021254	2		198	288	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884908	134884908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202034365	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	130	799	2	ENST00000398015.3:c.1684G>A	p.Val562Ile	p.V562I	ENST00000398015	NM_004441.4	562	Gtc/Atc	8/16	1	2	FACETS	0.942	0.854	1	0.942	0.854	1	CLONAL	1	TRUE	1	0.290384476021254	2		801	950	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76919038	76919038	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	97	575	1	ENST00000373344.5:c.3953del	p.Asn1318IlefsTer28	p.N1318Ifs*28	ENST00000373344	NM_000489.3	1318	aAt/at	12/35	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.290384476021254	2		576	647	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144708	58144708	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs780052789	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	215	574	1	ENST00000257904.6:c.520G>A	p.Val174Met	p.V174M	ENST00000257904	NM_000075.3	174	Gtg/Atg	4/8	0.263939997513768	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.290384476021254	3		575	819	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163377	47163377	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	110	476	0	ENST00000409792.3:c.2749del	p.Ser917ValfsTer5	p.S917Vfs*5	ENST00000409792	NM_014159.6	917	Agt/gt	3/21	1	2	FACETS	0.847	0.761	0.94	0.847	0.761	0.94	CLONAL	1	TRUE	1	0.290384476021254	2		476	894	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288785	33288785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765273333	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	103	435	0	ENST00000374542.5:c.767G>A	p.Arg256His	p.R256H	ENST00000374542	NM_001141970.1	256	cGc/cAc	3/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.290384476021254	2		435	600	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782390	9782390	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	162	724	0	ENST00000377346.4:c.2323G>T	p.Gly775Cys	p.G775C	ENST00000377346	NM_005026.3	775	Ggc/Tgc	18/24	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.290384476021254	2		724	974	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797118	45797118	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553125609	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	109	732	0	ENST00000450313.1:c.1297G>A	p.Ala433Thr	p.A433T	ENST00000450313	NM_012222.2	433	Gcc/Acc	13/16	1	2	FACETS	0.927	0.832	1	0.927	0.832	1	CLONAL	1	TRUE	1	0.290384476021254	2		732	810	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874184	155874184	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	97	896	0	ENST00000368323.3:c.347A>G	p.Gln116Arg	p.Q116R	ENST00000368323	NM_006912.5	116	cAg/cGg	5/6	1	2	FACETS	0.562	0.5	0.63	0.562	0.5	0.63	SUBCLONAL	1	TRUE	1	0.290384476021254	2		896	1188	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849041	156849041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	124	634	0	ENST00000524377.1:c.1933C>T	p.His645Tyr	p.H645Y	ENST00000524377	NM_002529.3	645	Cat/Tat	15/17	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.290384476021254	2		634	813	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085996	16085996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	127	561	0	ENST00000281043.3:c.1172G>A	p.Arg391His	p.R391H	ENST00000281043	NM_005378.4	391	cGc/cAc	3/3	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.290384476021254	2		561	717	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416659	29416659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	76	529	3	ENST00000389048.3:c.4294C>T	p.Arg1432Trp	p.R1432W	ENST00000389048	NM_004304.4	1432	Cgg/Tgg	29/29	1	2	FACETS	0.945	0.83	1	0.945	0.83	1	CLONAL	1	TRUE	1	0.290384476021254	2		532	554	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030560	48030560	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	126	799	0	ENST00000234420.5:c.3174T>A	p.Asp1058Glu	p.D1058E	ENST00000234420	NM_000179.2	1058	gaT/gaA	5/10	1	2	FACETS	0.846	0.765	0.932	0.846	0.765	0.932	CLONAL	1	TRUE	1	0.290384476021254	2		799	1026	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030670	48030670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750253	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	155	913	3	ENST00000234420.5:c.3284G>A	p.Arg1095His	p.R1095H	ENST00000234420	NM_000179.2	1095	cGc/cAc	5/10	1	2	FACETS	0.969	0.885	1	0.969	0.885	1	CLONAL	1	TRUE	1	0.290384476021254	2		916	1102	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441297	52441297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	121	739	0	ENST00000460680.1:c.473G>A	p.Gly158Asp	p.G158D	ENST00000460680	NM_004656.3	158	gGc/gAc	7/17	1	2	FACETS	0.884	0.797	0.975	0.884	0.797	0.975	CLONAL	1	TRUE	1	0.290384476021254	2		739	943	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430488	181430488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	126	698	0	ENST00000325404.1:c.340C>T	p.Arg114Trp	p.R114W	ENST00000325404	NM_003106.3	114	Cgg/Tgg	1/1	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.290384476021254	2		698	822	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356133	66356133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1349813115	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	110	714	3	ENST00000273854.3:c.1364G>A	p.Arg455Gln	p.R455Q	ENST00000273854	NM_004439.5	455	cGg/cAg	5/18	1	2	FACETS	0.94	0.844	1	0.94	0.844	1	CLONAL	1	TRUE	1	0.290384476021254	2		717	806	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245522	153245522	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	73	607	0	ENST00000281708.4:c.1669G>T	p.Gly557Ter	p.G557*	ENST00000281708	NM_033632.3	557	Gga/Tga	11/12	1	2	FACETS	0.816	0.714	0.926	0.816	0.714	0.926	CLONAL	1	TRUE	1	0.290384476021254	2		607	616	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628340	187628340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536104649	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	72	443	2	ENST00000441802.2:c.2642G>A	p.Arg881His	p.R881H	ENST00000441802	NM_005245.3	881	cGc/cAc	2/27	1	2	FACETS	0.937	0.82	1	0.937	0.82	1	CLONAL	1	TRUE	1	0.290384476021254	2		445	529	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495484	149495484	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	184	1048	0	ENST00000261799.4:c.3163T>C	p.Ser1055Pro	p.S1055P	ENST00000261799	NM_002609.3	1055	Tcc/Ccc	23/23	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.290384476021254	2		1048	1215	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687001	176687001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	122	704	1	ENST00000439151.2:c.4978C>T	p.Arg1660Cys	p.R1660C	ENST00000439151	NM_022455.4	1660	Cgc/Tgc	14/23	1	2	FACETS	0.969	0.876	1	0.969	0.876	1	CLONAL	1	TRUE	1	0.290384476021254	2		705	867	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721397	176721397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1410896719	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	107	741	2	ENST00000439151.2:c.7028C>T	p.Pro2343Leu	p.P2343L	ENST00000439151	NM_022455.4	2343	cCc/cTc	23/23	1	2	FACETS	0.885	0.793	0.982	0.885	0.793	0.982	CLONAL	1	TRUE	1	0.290384476021254	2		743	833	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55231457	55231457	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	144	834	0	ENST00000275493.2:c.1663T>C	p.Cys555Arg	p.C555R	ENST00000275493	NM_005228.3	555	Tgc/Cgc	14/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.290384476021254	2		834	868	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912349	97912349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs182879858	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	129	634	2	ENST00000289081.3:c.542C>T	p.Ala181Val	p.A181V	ENST00000289081	NM_000136.2	181	gCg/gTg	7/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.290384476021254	2		636	778	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750297	133750297	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	152	839	1	ENST00000318560.5:c.1128G>T	p.Leu376Phe	p.L376F	ENST00000318560	NM_005157.4	376	ttG/ttT	7/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.290384476021254	2		840	983	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198471	108198471	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	95	472	0	ENST00000278616.4:c.7075A>G	p.Thr2359Ala	p.T2359A	ENST00000278616	NM_000051.3	2359	Acc/Gcc	48/63	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.290384476021254	2		472	605	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344536	118344536	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	156	866	0	ENST00000534358.1:c.2662T>C	p.Ser888Pro	p.S888P	ENST00000534358	NM_005933.3	888	Tca/Cca	3/36	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.290384476021254	2		866	1045	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375783	118375783	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782800112	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	161	847	2	ENST00000534358.1:c.9176C>T	p.Pro3059Leu	p.P3059L	ENST00000534358	NM_005933.3	3059	cCg/cTg	27/36	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.290384476021254	2		849	1048	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446768	49446768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746039927	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	150	769	0	ENST00000301067.7:c.1042C>T	p.Arg348Cys	p.R348C	ENST00000301067	NM_003482.3	348	Cgc/Tgc	8/54	0.263939997513768	3	FACETS	1	0.927	1	0.509	0.464	0.556	CLONAL	1	TRUE	1	0.290384476021254	3		769	1162	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857515	57857515	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	474	1119	2	ENST00000228682.2:c.41G>A	p.Gly14Asp	p.G14D	ENST00000228682	NM_005269.2	14	gGc/gAc	2/12	0.263939997513768	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.290384476021254	3		1121	1608	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610059	81610059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908872	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	89	684	0	ENST00000298171.2:c.1657G>A	p.Ala553Thr	p.A553T	ENST00000298171	NM_000369.2	553	Gcc/Acc	10/10	1	2	FACETS	0.777	0.688	0.872	0.777	0.688	0.872	SUBCLONAL	1	TRUE	1	0.290384476021254	2		684	789	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582935	95582935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs965350808	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	120	675	3	ENST00000393063.1:c.1607G>A	p.Arg536His	p.R536H	ENST00000393063	NM_030621.3	536	cGt/cAt	11/28	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.290384476021254	2		678	752	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628530	90628530	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	211	865	2	ENST00000330062.3:c.1057C>T	p.Arg353Cys	p.R353C	ENST00000330062	NM_002168.2	353	Cgc/Tgc	8/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.290384476021254	2		867	1135	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304459	91304459	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1314782111	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	102	471	0	ENST00000355112.3:c.1856T>G	p.Phe619Cys	p.F619C	ENST00000355112	NM_000057.2	619	tTc/tGc	7/22	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.290384476021254	2		471	578	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	359996	359996	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324067997	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	184	989	4	ENST00000262320.3:c.1093C>T	p.Arg365Trp	p.R365W	ENST00000262320	NM_003502.3	365	Cgg/Tgg	4/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.290384476021254	2		993	1153	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781216	3781216	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1170699683	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	110	631	1	ENST00000262367.5:c.5149C>T	p.Arg1717Cys	p.R1717C	ENST00000262367	NM_004380.2	1717	Cgc/Tgc	30/31	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.290384476021254	2		632	705	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845230	89845230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374968669	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	189	923	3	ENST00000389301.3:c.1805C>T	p.Ala602Val	p.A602V	ENST00000389301	NM_000135.2	602	gCg/gTg	20/43	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.290384476021254	2		926	1213	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264357	30264357	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	43	322	0	ENST00000322652.5:c.92T>C	p.Val31Ala	p.V31A	ENST00000322652	NM_015355.2	31	gTg/gCg	1/16	1	2	FACETS	0.676	0.566	0.798	0.676	0.566	0.798	SUBCLONAL	1	TRUE	1	0.290384476021254	2		322	438	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526513	66526513	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	107	676	0	ENST00000358598.2:c.1069C>T	p.Arg357Cys	p.R357C	ENST00000358598	NM_212471.2	357	Cgt/Tgt	11/11	1	2	FACETS	0.913	0.819	1	0.913	0.819	1	CLONAL	1	TRUE	1	0.290384476021254	2		676	807	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117478	4117478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	36	413	0	ENST00000262948.5:c.242G>A	p.Gly81Asp	p.G81D	ENST00000262948	NM_030662.3	81	gGc/gAc	2/11	1	2	FACETS	0.477	0.391	0.573	0.477	0.391	0.573	SUBCLONAL	1	TRUE	1	0.290384476021254	2		413	520	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299983	15299983	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1390414547	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	108	555	1	ENST00000263388.2:c.1195G>A	p.Ala399Thr	p.A399T	ENST00000263388	NM_000435.2	399	Gcc/Acc	8/33	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.290384476021254	2		556	664	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917060	50917060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139235742	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	242	1101	3	ENST00000440232.2:c.2312C>T	p.Ala771Val	p.A771V	ENST00000440232	NM_002691.3	771	gCg/gTg	19/27	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.290384476021254	2		1104	1368	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309724	30309724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	260	626	1	ENST00000307677.4:c.298C>T	p.Arg100Trp	p.R100W	ENST00000307677	NM_138578.1	100	Cgg/Tgg	2/3	0.230945308679178	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.290384476021254	3		627	935	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513539	41513539	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753658203	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	128	723	5	ENST00000263253.7:c.443C>T	p.Thr148Met	p.T148M	ENST00000263253	NM_001429.3	148	aCg/aTg	2/31	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.290384476021254	2		728	833	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340958	70340958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1350320350	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	191	896	0	ENST00000374080.3:c.691C>T	p.Arg231Trp	p.R231W	ENST00000374080		231	Cgg/Tgg	5/45	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.290384476021254	2		896	1037	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3824569	3824569	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	97	646	0	ENST00000262367.5:c.2283+1del		p.X761_splice	ENST00000262367	NM_004380.2	761			1	2	FACETS	0.913	0.814	1	0.913	0.814	1	CLONAL	1	TRUE	1	0.290384476021254	2		646	732	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245739	46245739	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	264	714	1	ENST00000334344.6:c.3834del	p.Ser1279AlafsTer16	p.S1279Afs*16	ENST00000334344	NM_152641.2	1278	aCc/ac	15/21	0.263939997513768	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.290384476021254	3		715	936	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729880	30729881	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	46	315	0	ENST00000295754.5:c.1403_1404del	p.Lys468ArgfsTer3	p.K468Rfs*3	ENST00000295754	NM_003242.5	467	gtAAaa/gtaa	6/7	1	2	FACETS	0.788	0.665	0.923	0.788	0.665	0.923	CLONAL	1	TRUE	1	0.290384476021254	2		315	402	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829585	72829585	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	192	1191	1	ENST00000268489.5:c.6996del	p.Lys2332AsnfsTer44	p.K2332Nfs*44	ENST00000268489	NM_006885.3	2332	aaA/aa	9/10	1	2	FACETS	0.987	0.91	1	0.987	0.91	1	CLONAL	1	TRUE	1	0.290384476021254	2		1192	1340	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435201	18435202	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1565550462	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	130	742	0	ENST00000266497.5:c.192dup	p.Val65CysfsTer16	p.V65Cfs*16	ENST00000266497		62	-/T	1/31	0.263939997513768	3	FACETS	1	0.942	1	0.527	0.478	0.58	CLONAL	1	TRUE	1	0.290384476021254	3		742	972	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147771	61147771	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	65	364	0	ENST00000295025.8:c.1086del	p.Glu363AsnfsTer11	p.E363Nfs*11	ENST00000295025	NM_002908.2	361	Aaa/aa	10/11	1	2	FACETS	0.899	0.781	1	0.899	0.781	1	CLONAL	1	TRUE	1	0.290384476021254	2		364	498	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855019	76855019	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	127	913	4	ENST00000373344.5:c.5817del	p.Asp1940IlefsTer15	p.D1940Ifs*15	ENST00000373344	NM_000489.3	1939	aaA/aa	25/35	1	2	FACETS	0.776	0.701	0.855	0.776	0.701	0.855	SUBCLONAL	1	TRUE	1	0.290384476021254	2		917	1127	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413710	138413710	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	125	550	7	ENST00000289153.2:c.1810del	p.Arg604GlyfsTer4	p.R604Gfs*4	ENST00000289153	NM_006219.2	604	Cgg/gg	12/22	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.290384476021254	2		557	715	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	675	817	1	ENST00000269305.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	336	Gag/Tag	10/11	0.522977046430735	3	FACETS	0.934	0.908	0.96	0.934	0.908	0.96	CLONAL	3	TRUE	0	0.589067952793336	3		818	1059	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37059000	37059000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63751448	NA	P-0013402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	100	655	0	ENST00000231790.2:c.794G>A	p.Arg265His	p.R265H	ENST00000231790	NM_000249.3	265	cGt/cAt	10/19	0.200124821573153	2	FACETS	0.575	0.515	0.639	0.288	0.257	0.32	INDETERMINATE	1	TRUE	0	0.589067952793336	2		655	590	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107086	27107087	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0013402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	193	381	0	ENST00000324856.7:c.6700dup	p.Ala2234GlyfsTer44	p.A2234Gfs*44	ENST00000324856	NM_006015.4	2233	cgg/cGgg	20/20	0.300625159688153	3	FACETS	1	0.99	1	0.832	0.785	0.878	INDETERMINATE	2	TRUE	0	0.589067952793336	3		381	340	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0013410-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	1297	443	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	0.740787561717001	3	FACETS	0.975	0.954	0.996			1	CLONAL	2	TRUE	NA	0.862457541600984	3		443	2207	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0013454-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	431	327	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.255549973532704	3	FACETS	0.928	0.884	0.972	0.928	0.884	0.972	CLONAL	3	TRUE	0	0.255549973532704	3		327	1367	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133710889	133710889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866428555	NA	P-0013454-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1369	186	941	1	ENST00000318560.5:c.56C>T	p.Ser19Leu	p.S19L	ENST00000318560	NM_005157.4	19	tCg/tTg	1/11	0.255549973532704	3	FACETS	1	0.956	1	0.528	0.486	0.572	CLONAL	1	TRUE	1	0.255549973532704	3		942	1555	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816265	89816265	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013454-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	117	596	0	ENST00000389301.3:c.3112C>G	p.Leu1038Val	p.L1038V	ENST00000389301	NM_000135.2	1038	Ctc/Gtc	32/43	NA	2	FACETS	0.894	0.805	0.989			1	INDETERMINATE	1	TRUE	NA	0.255549973532704	2		596	1024	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180624	56180625	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013454-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	127	447	0	ENST00000399503.3:c.3955dup	p.Tyr1319LeufsTer6	p.Y1319Lfs*6	ENST00000399503	NM_005921.1	1318	aat/aaTt	16/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.255549973532704	2		447	896	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168751	56168752	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0013454-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	133	569	0	ENST00000399503.3:c.1609_1610del	p.Ser537GlnfsTer3	p.S537Qfs*3	ENST00000399503	NM_005921.1	535	caAGag/caag	9/20	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.255549973532704	2		569	973	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	52	175	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.721	0.615	0.835	0.721	0.615	0.835	SUBCLONAL	1	TRUE	1	0.37	2		175	390	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	304	596	1	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.37	2		597	1146	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	271	226	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.37	2		226	1032	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	181	284	0	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.37	2		284	959	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319341	11319341	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	232	611	0	ENST00000361445.4:c.126G>T	p.Lys42Asn	p.K42N	ENST00000361445	NM_004958.3	42	aaG/aaT	2/58	1	2	FACETS	0.825	0.772	0.879	1	0.993	1	CLONAL	2	TRUE	1	0.37	2		611	760	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16248743	16248743	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	39	405	1	ENST00000375759.3:c.1750-1G>T		p.X584_splice	ENST00000375759	NM_015001.2	584			1	2	FACETS	0.288	0.238	0.345	0.288	0.238	0.345	SUBCLONAL	1	TRUE	1	0.37	2		406	731	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578282	226578282	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	220	633	2	ENST00000366794.5:c.446C>A	p.Pro149Gln	p.P149Q	ENST00000366794	NM_001618.3	149	cCa/cAa	4/23	1	2	FACETS	0.787	0.734	0.84	1	0.993	1	SUBCLONAL	2	TRUE	1	0.37	2		635	756	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61724082	61724082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	59	612	0	ENST00000401558.2:c.820G>A	p.Val274Met	p.V274M	ENST00000401558	NM_003400.3	274	Gtg/Atg	10/25	1	2	FACETS	0.3	0.257	0.347	0.3	0.257	0.347	SUBCLONAL	1	TRUE	1	0.37	2		612	1064	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257146	198257146	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	69	554	0	ENST00000335508.6:c.3796T>A	p.Trp1266Arg	p.W1266R	ENST00000335508	NM_012433.2	1266	Tgg/Agg	25/25	1	2	FACETS	0.401	0.348	0.459	0.401	0.348	0.459	SUBCLONAL	1	TRUE	1	0.37	2		554	930	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735609	204735609	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553657429	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	120	330	0	ENST00000302823.3:c.410C>T	p.Pro137Leu	p.P137L	ENST00000302823	NM_005214.4	137	cCg/cTg	2/4	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.37	2		330	470	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662389	227662389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773817315	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	136	359	1	ENST00000305123.5:c.1066G>A	p.Ala356Thr	p.A356T	ENST00000305123	NM_005544.2	356	Gcc/Acc	1/2	1	2	FACETS	0.849	0.779	0.921	1	0.99	1	CLONAL	2	TRUE	1	0.37	2		360	433	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127716	47127716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	294	514	0	ENST00000409792.3:c.5366G>A	p.Gly1789Asp	p.G1789D	ENST00000409792	NM_014159.6	1789	gGc/gAc	11/21	1	2	FACETS	0.822	0.775	0.87	1	0.995	1	CLONAL	2	TRUE	1	0.37	2		514	967	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504306	186504306	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	146	275	0	ENST00000323963.5:c.643G>A	p.Ala215Thr	p.A215T	ENST00000323963		215	Gcc/Acc	7/11	1	2	FACETS	0.843	0.776	0.913	1	0.99	1	CLONAL	2	TRUE	1	0.37	2		275	468	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	255	554	2	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	0.763	0.716	0.812	1	0.993	1	SUBCLONAL	2	TRUE	1	0.37	2		556	903	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264632	1264632	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	224	779	0	ENST00000310581.5:c.2730A>C	p.Glu910Asp	p.E910D	ENST00000310581	NM_198253.2	910	gaA/gaC	11/16	0.145688391377459	0	FACETS	0.942	0.879	1			1	INDETERMINATE	1	TRUE	0	0.37	0		779	810	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876449	35876449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2229232	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	183	524	0	ENST00000303115.3:c.1241C>T	p.Thr414Met	p.T414M	ENST00000303115	NM_002185.3	414	aCg/aTg	8/8	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.37	2		524	696	SUCCESS
APC	324	MSKCC	GRCh37	5	112175171	112175171	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085373	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	82	239	0	ENST00000257430.4:c.3880C>T	p.Gln1294Ter	p.Q1294*	ENST00000257430	NM_000038.5	1294	Cag/Tag	16/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.37	2		239	336	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	206	416	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	1	2	FACETS	0.819	0.763	0.876	1	0.993	1	CLONAL	2	TRUE	1	0.37	2		416	680	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874710	151874710	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	246	554	0	ENST00000262189.6:c.7828C>T	p.Arg2610Ter	p.R2610*	ENST00000262189	NM_170606.2	2610	Cga/Tga	38/59	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.37	2		554	905	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409425	80409425	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	136	260	0	ENST00000286548.4:c.689T>C	p.Val230Ala	p.V230A	ENST00000286548	NM_002072.3	230	gTa/gCa	5/7	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.37	2		260	495	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606313	93606313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1235073402	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	195	586	1	ENST00000375746.1:c.133C>T	p.Arg45Cys	p.R45C	ENST00000375746	NM_001174167.1	45	Cgc/Tgc	2/14	1	2	FACETS	0.777	0.722	0.834	1	0.991	1	SUBCLONAL	2	TRUE	1	0.37	2		587	678	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1040429	1040429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	242	670	0	ENST00000358495.3:c.143G>A	p.Gly48Asp	p.G48D	ENST00000358495	NM_134424.2	48	gGc/gAc	3/12	NA	2	FACETS	0.764	0.715	0.814			1	INDETERMINATE	2	TRUE	NA	0.37	2		670	856	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202828	133202828	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1368640639	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	47	601	1	ENST00000320574.5:c.6406G>A	p.Gly2136Ser	p.G2136S	ENST00000320574	NM_006231.2	2136	Ggc/Agc	46/49	1	2	FACETS	0.32	0.269	0.376	0.32	0.269	0.376	SUBCLONAL	1	TRUE	1	0.37	2		602	795	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001303	29001303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201407326	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	263	534	0	ENST00000282397.4:c.1429G>A	p.Glu477Lys	p.E477K	ENST00000282397	NM_002019.4	477	Gaa/Aaa	10/30	1	2	FACETS	0.757	0.71	0.805	1	0.993	1	SUBCLONAL	2	TRUE	1	0.37	2		534	939	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007878	45007878	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	224	408	0	ENST00000558401.1:c.325C>T	p.Gln109Ter	p.Q109*	ENST00000558401	NM_004048.2	109	Cag/Tag	2/4	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.37	2		408	810	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130352	2130352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773951533	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	154	554	1	ENST00000219476.3:c.3584C>T	p.Ala1195Val	p.A1195V	ENST00000219476	NM_000548.3	1195	gCg/gTg	30/42	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.37	2		555	596	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135300	2135300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745895675	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	222	653	0	ENST00000219476.3:c.4639G>A	p.Val1547Ile	p.V1547I	ENST00000219476	NM_000548.3	1547	Gtc/Atc	36/42	1	2	FACETS	0.809	0.755	0.863	1	0.993	1	CLONAL	2	TRUE	1	0.37	2		653	742	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858029	9858029	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	260	718	0	ENST00000330684.3:c.3372G>T	p.Lys1124Asn	p.K1124N	ENST00000330684	NM_001134407.1	1124	aaG/aaT	13/13	1	2	FACETS	0.838	0.787	0.889	1	0.994	1	CLONAL	2	TRUE	1	0.37	2		718	839	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660469	67660469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	142	500	0	ENST00000264010.4:c.1369C>T	p.Arg457Ter	p.R457*	ENST00000264010	NM_006565.3	457	Cga/Tga	8/12	1	2	FACETS	0.912	0.831	0.996	0.912	0.831	0.996	CLONAL	1	TRUE	1	0.37	2		500	842	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972439	81972439	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	393	1025	1	ENST00000359376.3:c.3232C>T	p.Arg1078Ter	p.R1078*	ENST00000359376	NM_002661.3	1078	Cga/Tga	29/33	0.291850502747984	0	FACETS	0.998	0.948	1			1	CLONAL	1	TRUE	0	0.37	0		1026	1341	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349604	89349604	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs924589358	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	444	1110	0	ENST00000301030.4:c.3346G>A	p.Ala1116Thr	p.A1116T	ENST00000301030	NM_001256183.1	1116	Gca/Aca	9/13	1	2	FACETS	0.842	0.802	0.881	1	0.996	1	CLONAL	2	TRUE	1	0.37	2		1110	1426	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677273	29677273	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs143474365	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	68	578	0	ENST00000356175.3:c.7331A>G	p.Asp2444Gly	p.D2444G	ENST00000356175	NM_000267.3	2444	gAt/gGt	49/57	1	2	FACETS	0.39	0.338	0.446	0.39	0.338	0.446	SUBCLONAL	1	TRUE	1	0.37	2		578	943	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805453	46805453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	173	896	0	ENST00000290295.7:c.503G>A	p.Ser168Asn	p.S168N	ENST00000290295	NM_006361.5	168	aGt/aAt	1/2	1	2	FACETS	0.767	0.704	0.833	0.767	0.704	0.833	SUBCLONAL	1	TRUE	1	0.37	2		896	1219	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115006	3115006	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1391552100	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	184	617	1	ENST00000078429.4:c.541C>T	p.Arg181Trp	p.R181W	ENST00000078429	NM_002067.2	181	Cgg/Tgg	4/7	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.37	2		618	740	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119286	3119286	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	245	749	0	ENST00000078429.4:c.818T>G	p.Leu273Arg	p.L273R	ENST00000078429	NM_002067.2	273	cTc/cGc	6/7	1	2	FACETS	0.799	0.748	0.85	1	0.993	1	SUBCLONAL	2	TRUE	1	0.37	2		749	829	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955106	17955106	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	186	530	0	ENST00000458235.1:c.121C>A	p.Leu41Ile	p.L41I	ENST00000458235	NM_000215.3	41	Cta/Ata	2/24	1	2	FACETS	0.797	0.739	0.856	1	0.991	1	SUBCLONAL	2	TRUE	1	0.37	2		530	631	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383059	42383059	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	166	543	1	ENST00000221972.3:c.80-1G>T		p.X27_splice	ENST00000221972	NM_021601.3	27			1	2	FACETS	0.782	0.722	0.843	1	0.99	1	SUBCLONAL	2	TRUE	1	0.37	2		544	574	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733279	40733279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201275244	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	127	410	0	ENST00000373198.4:c.3527G>A	p.Arg1176His	p.R1176H	ENST00000373198	NM_133170.3	1176	cGt/cAt	26/32	0.145688391377459	0	FACETS	0.879	0.801	0.96			1	INDETERMINATE	1	TRUE	0	0.37	0		410	492	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224563	123224563	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	380	395	0	ENST00000218089.9:c.3416T>C	p.Met1139Thr	p.M1139T	ENST00000218089	NM_001042749.1	1139	aTg/aCg	31/35	1	1	FACETS	1	0.994	1	1	0.997	1	CLONAL	2	TRUE	0	0.37	1		395	677	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390736	139390736	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	237	761	0	ENST00000277541.6:c.7455del	p.Ser2486ArgfsTer103	p.S2486Rfs*103	ENST00000277541	NM_017617.3	2485	ccC/cc	34/34	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.37	2		761	858	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89811410	89811410	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	44	664	0	ENST00000389301.3:c.3583del	p.Arg1195GlyfsTer52	p.R1195Gfs*52	ENST00000389301	NM_000135.2	1195	Cgg/gg	36/43	1	2	FACETS	0.283	0.236	0.335	0.283	0.236	0.335	SUBCLONAL	1	TRUE	1	0.37	2		664	841	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098688	47098694	+	frameshift_variant	Frame_Shift_Del	DEL	GGTCCAT	GGTCCAT	-	novel	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	269	706	0	ENST00000409792.3:c.6580_6586del	p.Met2194GlnfsTer52	p.M2194Qfs*52	ENST00000409792	NM_014159.6	2194	ATGGACCca/ca	15/21	1	2	FACETS	0.78	0.733	0.828	1	0.994	1	SUBCLONAL	2	TRUE	1	0.37	2		706	932	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155700	106155700	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	184	508	0	ENST00000380013.4:c.605del	p.Asn202ThrfsTer5	p.N202Tfs*5	ENST00000380013	NM_001127208.2	201	Aaa/aa	3/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.37	2		508	859	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646575	23646576	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs786203057	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	137	311	0	ENST00000261584.4:c.1291_1292del	p.His432PhefsTer9	p.H432Ffs*9	ENST00000261584	NM_024675.3	431	AGt/t	4/13	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.37	2		311	539	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117594	70117594	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	179	510	0	ENST00000245479.2:c.66del	p.Ser23AlafsTer38	p.S23Afs*38	ENST00000245479	NM_000346.3	21	gCc/gc	1/3	1	2	FACETS	0.875	0.812	0.939	1	0.992	1	CLONAL	2	TRUE	1	0.37	2		510	553	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	276	775	2	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.37	2		777	1047	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	283	708	11	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.37	2		719	1032	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099639	157099639	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	15	36	0	ENST00000346085.5:c.580del	p.Glu194SerfsTer72	p.E194Sfs*72	ENST00000346085	NM_020732.3	192	atG/at	1/20	1	2	FACETS	0.977	0.727	1	0.977	0.727	1	CLONAL	1	TRUE	1	0.37	2		36	83	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508725	106508725	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	179	478	0	ENST00000359195.3:c.723del	p.Gly242AlafsTer17	p.G242Afs*17	ENST00000359195	NM_002649.2	240	aCc/ac	2/11	0.158095255062422	3	FACETS	1	0.989	1	0.714	0.659	0.771	INDETERMINATE	1	TRUE	1	0.37	3		478	803	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623187	52623187	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	71	680	0	ENST00000394830.3:c.2864del	p.Asn955ThrfsTer53	p.N955Tfs*53	ENST00000394830	NM_018313.4	955	aAc/ac	19/30	1	2	FACETS	0.36	0.313	0.411	0.36	0.313	0.411	SUBCLONAL	1	TRUE	1	0.37	2		680	1067	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	200	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.902	0.835	0.971	0.902	0.835	0.971	CLONAL	1	TRUE	1	0.423478444152931	2		311	1047	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0013499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	332	654	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.423478444152931	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.423478444152931	1		655	1108	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138480	11138480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	243	523	0	ENST00000358026.2:c.3236C>T	p.Ser1079Leu	p.S1079L	ENST00000358026	NM_001128849.1	1079	tCg/tTg	24/36	0.423478444152931	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.423478444152931	1		523	849	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974695	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1554656253	NA	P-0013499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	205	575	0	ENST00000304494.5:c.132C>G	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	taC/taG	1/3	0.423478444152931	1	FACETS	0.96	0.893	1	0.96	0.893	1	CLONAL	1	TRUE	0	0.423478444152931	1		575	795	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966766	44966767	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	355	845	0	ENST00000377967.4:c.3991dup	p.Cys1331LeufsTer2	p.C1331Lfs*2	ENST00000377967	NM_021140.2	1330	-/T	27/29	0.423478444152931	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.423478444152931	1		845	1248	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0013507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	52	328	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.991	0.849	1	0.991	0.849	1	CLONAL	1	TRUE	1	0.355824066320753	2		328	295	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	89	556	1	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.355824066320753	2		557	480	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249348	110249348	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	115	952	0	ENST00000374672.4:c.1225A>C	p.Lys409Gln	p.K409Q	ENST00000374672	NM_004235.4	409	Aag/Cag	4/5	1	2	FACETS	0.866	0.781	0.957	0.866	0.781	0.957	CLONAL	1	TRUE	1	0.355824066320753	2		952	746	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395151	139395151	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	85	678	0	ENST00000277541.6:c.5787G>C	p.Glu1929Asp	p.E1929D	ENST00000277541	NM_017617.3	1929	gaG/gaC	31/34	1	2	FACETS	0.9	0.797	1	0.9	0.797	1	CLONAL	1	TRUE	1	0.355824066320753	2		678	531	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155607	56155608	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0013507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	55	440	0	ENST00000399503.3:c.699_700del	p.Gly234ArgfsTer66	p.G234Rfs*66	ENST00000399503	NM_005921.1	233	ccAGga/ccga	3/20	0.337721656509821	3	FACETS	0.707	0.605	0.818	0.354	0.302	0.409	SUBCLONAL	1	TRUE	1	0.355824066320753	3		440	515	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179388	56179389	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0013507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	158	510	0	ENST00000399503.3:c.3703_3704dup	p.Gln1235HisfsTer11	p.Q1235Hfs*11	ENST00000399503	NM_005921.1	1234	aaa/aaACa	15/20	0.337721656509821	3	FACETS	0.869	0.8	0.94	0.869	0.8	0.94	CLONAL	2	TRUE	1	0.355824066320753	3		510	602	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16055262	16055264	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CTT	CTT	A	novel	NA	P-0013507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	72	495	0	ENST00000268712.3:c.838_840delinsT	p.Lys280TyrfsTer14	p.K280Yfs*14	ENST00000268712	NM_006311.3	280	AAG/T	8/46	1	2	FACETS	0.85	0.745	0.963	0.85	0.745	0.963	CLONAL	1	TRUE	1	0.355824066320753	2		495	476	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0013510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	55	711	0	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	0.732339660960115	16	FACETS	0.782	0.666	0.909			1	CLONAL	1	TRUE	NA	0.732339660960115	16		711	1177	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029445	16029446	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	80	937	4	ENST00000268712.3:c.1584dup	p.Glu529ArgfsTer7	p.E529Rfs*7	ENST00000268712	NM_006311.3	528	-/A	15/46	0.732339660960115	2	FACETS	0.775	0.707	0.842	0.775	0.707	0.842	SUBCLONAL	2	TRUE	0	0.732339660960115	2		941	141	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332899	152332899	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	63	559	0	ENST00000206249.3:c.1205T>A	p.Leu402Gln	p.L402Q	ENST00000206249	NM_000125.3	402	cTa/cAa	5/8	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.732339660960115	2		559	152	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209446	98209446	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	33	510	0	ENST00000331920.6:c.4092C>A	p.Tyr1364Ter	p.Y1364*	ENST00000331920	NM_000264.3	1364	taC/taA	23/24	0.732339660960115	2	FACETS	0.784	0.653	0.924	0.392	0.326	0.462	CLONAL	1	TRUE	0	0.732339660960115	2		510	115	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373923	118373923	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	12	718	0	ENST00000534358.1:c.7316C>G	p.Thr2439Ser	p.T2439S	ENST00000534358	NM_005933.3	2439	aCt/aGt	27/36	0.732339660960115	2	FACETS	0.328	0.232	0.442	0.164	0.116	0.221	SUBCLONAL	1	TRUE	0	0.732339660960115	2		718	100	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109920	115109920	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	26	298	0	ENST00000257566.3:c.1958G>T	p.Ser653Ile	p.S653I	ENST00000257566	NM_016569.3	653	aGc/aTc	8/8	0.732339660960115	3	FACETS	0.96	0.778	1	0.48	0.389	0.58	CLONAL	1	TRUE	1	0.732339660960115	3		298	101	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061347	38061347	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	169	711	0	ENST00000250448.2:c.642G>C	p.Trp214Cys	p.W214C	ENST00000250448	NM_004496.3	214	tgG/tgC	2/2	0.731513453404114	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.732339660960115	3		711	303	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575642	55575643	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0013510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	159	718	0	ENST00000288135.5:c.1169dup	p.Tyr390Ter	p.Y390*	ENST00000288135	NM_000222.2	390	tac/tAac	7/21	0.362464898483876	4	FACETS	0.877	0.821	0.931			1	INDETERMINATE	3	TRUE	NA	0.732339660960115	4		718	286	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060879	38060880	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0013510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	63	546	0	ENST00000250448.2:c.1109_1110del	p.Val370AlafsTer44	p.V370Afs*44	ENST00000250448	NM_004496.3	370	gTG/g	2/2	0.731513453404114	3	FACETS	1	0.935	1	0.552	0.484	0.622	CLONAL	1	TRUE	1	0.732339660960115	3		546	213	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717669	89717673	+	frameshift_variant	Frame_Shift_Del	DEL	ACACG	ACACG	-	novel	NA	P-0013510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	17	661	0	ENST00000371953.3:c.696_700del	p.Arg233GlyfsTer8	p.R233Gfs*8	ENST00000371953	NM_000314.4	232	ACACGa/a	7/9	0.732339660960115	3	FACETS	0.21	0.156	0.274	0.105	0.078	0.137	SUBCLONAL	1	TRUE	1	0.732339660960115	3		661	302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0013577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	477	834	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.739766349036491	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.760426026205773	1		834	759	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	384	536	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	1	2	FACETS	0.878	0.835	0.922	0.878	0.835	0.922	CLONAL	1	TRUE	1	0.760426026205773	2		536	1150	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254252	133254252	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	475	856	0	ENST00000320574.5:c.632T>A	p.Ile211Lys	p.I211K	ENST00000320574	NM_006231.2	211	aTa/aAa	7/49	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.760426026205773	2		856	1171	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029443	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	TTCT	TTCT	-	novel	NA	P-0013577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	569	874	0	ENST00000268712.3:c.1584_1587del	p.Glu529LysfsTer25	p.E529Kfs*25	ENST00000268712	NM_006311.3	528	aaAGAA/aa	15/46	0.739766349036491	1	FACETS	0.979	0.948	1	0.979	0.948	1	CLONAL	1	TRUE	0	0.760426026205773	1		874	947	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591798	48591798	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	256	543	0	ENST00000342988.3:c.961G>T	p.Glu321Ter	p.E321*	ENST00000342988	NM_005359.5	321	Gag/Tag	9/12	0.760426026205773	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.760426026205773	1		543	379	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152182	11152182	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1434396338	NA	P-0013577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	361	650	0	ENST00000358026.2:c.4466A>G	p.Asn1489Ser	p.N1489S	ENST00000358026	NM_001128849.1	1489	aAc/aGc	31/36	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.760426026205773	2		650	930	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938062	76938062	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	109	767	0	ENST00000373344.5:c.2686G>A	p.Asp896Asn	p.D896N	ENST00000373344	NM_000489.3	896	Gat/Aat	9/35	0.211503851969738	1	FACETS	0.172	0.154	0.192	0.172	0.154	0.192	INDETERMINATE	1	TRUE	0	0.760426026205773	1		767	1031	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0013582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	32	710	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	0.198466380326216	2	FACETS	0.224	0.18	0.273	0.112	0.09	0.137	SUBCLONAL	1	TRUE	0	0.247854868148439	2		710	1155	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0013582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	442	637	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.247854868148439	5	FACETS	0.917	0.875	0.96	0.734	0.7	0.768	CLONAL	4	TRUE	0	0.247854868148439	5		637	1334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs967461896	NA	P-0013582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	113	476	0	ENST00000269305.4:c.526T>A	p.Cys176Ser	p.C176S	ENST00000269305	NM_001126112.2	176	Tgc/Agc	5/11	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.247854868148439	2		476	664	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217556	142217557	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1268253442	NA	P-0013582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	112	636	0	ENST00000350721.4:c.5440dup	p.Arg1814LysfsTer8	p.R1814Kfs*8	ENST00000350721	NM_001184.3	1814	aga/aAga	32/47	0.198466380326216	2	FACETS	0.748	0.671	0.83	0.374	0.335	0.415	SUBCLONAL	1	TRUE	0	0.247854868148439	2		636	1208	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	29	168	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.0890089660469238	3	FACETS	1	0.916	1	0.636	0.513	0.774	INDETERMINATE	1	TRUE	1	0.22	3		168	230	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	38	201	2	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	0.0890089660469238	3	FACETS	1	0.936	1	0.646	0.536	0.767	INDETERMINATE	1	TRUE	1	0.22	3		203	297	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	110	407	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.218746336952447	4	FACETS	0.952	0.857	1	0.952	0.857	1	CLONAL	2	TRUE	2	0.22	4		407	641	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	195	708	11	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.3	1	FACETS	0.849	0.786	0.914	1	0.992	1	CLONAL	2	TRUE	0	0.22	1		719	929	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	196	872	2	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	0.218746336952447	3	FACETS	0.789	0.729	0.852	0.526	0.486	0.568	SUBCLONAL	2	TRUE	0	0.22	3		874	1253	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633259	12633259	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559632360	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	265	560	2	ENST00000251849.4:c.1141G>A	p.Asp381Asn	p.D381N	ENST00000251849	NM_002880.3	381	Gac/Aac	11/17	0.218746336952447	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	TRUE	0	0.22	3		562	854	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	161	572	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.0890089660469238	3	FACETS	0.859	0.787	0.933	0.859	0.787	0.933	INDETERMINATE	2	TRUE	1	0.22	3		572	946	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042242	6042242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs114090343	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	155	594	1	ENST00000265849.7:c.379G>A	p.Ala127Thr	p.A127T	ENST00000265849	NM_000535.5	127	Gca/Aca	5/15	0.0890089660469238	0	FACETS	1	0.956	1			1	INDETERMINATE	1	TRUE	0	0.22	0		595	1026	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923086	39923087	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	244	899	1	ENST00000378444.4:c.3621dup	p.Gln1208ThrfsTer8	p.Q1208Tfs*8	ENST00000378444	NM_001123385.1	1207	-/A	8/15	0.3	2	FACETS	0.936	0.874	1			1	CLONAL	2	TRUE	NA	0.22	2		900	1185	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223131	5223131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375155482	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	96	586	3	ENST00000357368.4:c.2672C>T	p.Thr891Met	p.T891M	ENST00000357368	NM_002850.3	891	aCg/aTg	18/38	0.0890089660469238	0	FACETS	0.735	0.658	0.816			1	INDETERMINATE	2	TRUE	0	0.22	0		589	463	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907421	32907421	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359306	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	81	409	6	ENST00000380152.3:c.1813del	p.Ile605TyrfsTer9	p.I605Yfs*9	ENST00000380152		602	ggA/gg	10/27	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.22	2		415	491	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508539	106508539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	18	157	0	ENST00000359195.3:c.533G>A	p.Arg178His	p.R178H	ENST00000359195	NM_002649.2	178	cGt/cAt	2/11	0.0890089660469238	3	FACETS	1	0.812	1	0.544	0.412	0.698	INDETERMINATE	1	TRUE	1	0.22	3		157	167	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190702	11190702	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	109	573	0	ENST00000361445.4:c.5497A>G	p.Thr1833Ala	p.T1833A	ENST00000361445	NM_004958.3	1833	Acc/Gcc	39/58	0.3	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.22	1		573	671	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736523	85736523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	219	850	0	ENST00000370580.1:c.124C>T	p.Arg42Cys	p.R42C	ENST00000370580	NM_003921.4	42	Cgt/Tgt	2/3	0.0890089660469238	3	FACETS	0.891	0.827	0.957	0.891	0.827	0.957	INDETERMINATE	2	TRUE	1	0.22	3		850	1240	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518419	69518419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	10	40	0	ENST00000294312.3:c.226G>A	p.Ala76Thr	p.A76T	ENST00000294312	NM_005117.2	76	Gcg/Acg	1/3	0.0890089660469238	3	FACETS	0.97	0.674	1	0.97	0.674	1	INDETERMINATE	2	TRUE	1	0.22	3		40	52	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416900	416900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377384081	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	111	635	0	ENST00000399788.2:c.3650G>A	p.Arg1217Gln	p.R1217Q	ENST00000399788	NM_001042603.1	1217	cGg/cAg	23/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.22	2		635	800	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18747464	18747464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	70	341	0	ENST00000266497.5:c.3925G>A	p.Val1309Met	p.V1309M	ENST00000266497		1309	Gtg/Atg	28/31	0.3	2	FACETS	0.767	0.671	0.869			1	SUBCLONAL	2	TRUE	NA	0.22	2		341	415	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28908197	28908197	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	182	583	0	ENST00000282397.4:c.2558C>T	p.Pro853Leu	p.P853L	ENST00000282397	NM_002019.4	853	cCt/cTt	18/30	1	2	FACETS	0.873	0.805	0.943	1	0.992	1	CLONAL	2	TRUE	1	0.22	2		583	948	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972778	32972780	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	33	397	0	ENST00000380152.3:c.10131_10133del	p.Glu3377del	p.E3377del	ENST00000380152		3376	tcAGAa/tca	27/27	1	2	FACETS	0.492	0.399	0.597	0.492	0.399	0.597	SUBCLONAL	1	TRUE	1	0.22	2		397	610	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569708	95569708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767166092	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	83	357	2	ENST00000393063.1:c.4025G>A	p.Arg1342His	p.R1342H	ENST00000393063	NM_030621.3	1342	cGc/cAc	22/28	1	2	FACETS	0.81	0.717	0.908	1	0.981	1	CLONAL	2	TRUE	1	0.22	2		359	466	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994658	73994658	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	71	471	1	ENST00000318443.5:c.142C>A	p.Leu48Met	p.L48M	ENST00000318443	NM_001024736.1	48	Ctg/Atg	3/10	1	2	FACETS	0.77	0.675	0.872	1	0.976	1	SUBCLONAL	2	TRUE	1	0.22	2		472	419	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	360031	360031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751638186	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	177	734	0	ENST00000262320.3:c.1058G>A	p.Arg353His	p.R353H	ENST00000262320	NM_003502.3	353	cGc/cAc	4/11	1	2	FACETS	0.863	0.795	0.934	1	0.991	1	CLONAL	2	TRUE	1	0.22	2		734	932	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100489	2100489	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	156	373	0	ENST00000219476.3:c.225+2T>C		p.X75_splice	ENST00000219476	NM_000548.3	75			1	2	FACETS	0.883	0.809	0.96	1	0.99	1	CLONAL	2	TRUE	1	0.22	2		373	803	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858446	89858446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	161	656	0	ENST00000389301.3:c.1114G>A	p.Val372Ile	p.V372I	ENST00000389301	NM_000135.2	372	Gtt/Att	13/43	1	2	FACETS	0.766	0.702	0.832	1	0.989	1	SUBCLONAL	2	TRUE	1	0.22	2		656	956	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657429	29657429	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	155	546	0	ENST00000356175.3:c.5662G>A	p.Val1888Ile	p.V1888I	ENST00000356175	NM_000267.3	1888	Gtc/Atc	38/57	1	2	FACETS	0.823	0.754	0.896	1	0.989	1	CLONAL	2	TRUE	1	0.22	2		546	856	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416262	29416262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	118	672	2	ENST00000389048.3:c.4691C>T	p.Ala1564Val	p.A1564V	ENST00000389048	NM_004304.4	1564	gCc/gTc	29/29	0.0890089660469238	0	FACETS	1	0.963	1			1	INDETERMINATE	1	TRUE	0	0.22	0		674	735	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651277	45651277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	179	759	1	ENST00000407780.3:c.748G>A	p.Gly250Ser	p.G250S	ENST00000407780	NM_001283052.1	250	Ggc/Agc	5/7	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.22	2		760	1103	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72897395	72897395	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1401383230	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	87	627	0	ENST00000325599.8:c.97T>C	p.Phe33Leu	p.F33L	ENST00000325599	NM_018130.2	33	Ttc/Ctc	1/11	0.218746336952447	3	FACETS	0.882	0.779	0.993	0.294	0.259	0.331	CLONAL	1	TRUE	0	0.22	3		627	995	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251949	153251949	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	146	576	0	ENST00000281708.4:c.1057del	p.Ser353ValfsTer24	p.S353Vfs*24	ENST00000281708	NM_033632.3	353	Agt/gt	7/12	0.0890089660469238	3	FACETS	0.814	0.743	0.889	0.814	0.743	0.889	INDETERMINATE	2	TRUE	1	0.22	3		576	905	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592115	67592115	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	156	461	1	ENST00000274335.5:c.1931G>A	p.Gly644Asp	p.G644D	ENST00000274335		644	gGc/gAc	14/15	0.218746336952447	4	FACETS	0.87	0.796	0.948	0.87	0.796	0.948	CLONAL	2	TRUE	2	0.22	4		462	994	SUCCESS
APC	324	MSKCC	GRCh37	5	112175781	112175794	+	frameshift_variant	Frame_Shift_Del	DEL	CAGATGGATTTTCT	CAGATGGATTTTCT	-	novel	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	70	292	0	ENST00000257430.4:c.4490_4503del	p.Pro1497LeufsTer12	p.P1497Lfs*12	ENST00000257430	NM_000038.5	1497	cCAGATGGATTTTCT/c	16/16	0.218746336952447	4	FACETS	0.931	0.815	1	0.931	0.815	1	CLONAL	2	TRUE	2	0.22	4		292	417	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149516579	149516579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465066628	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	135	710	1	ENST00000261799.4:c.32C>T	p.Ala11Val	p.A11V	ENST00000261799	NM_002609.3	11	gCc/gTc	2/23	1	2	FACETS	0.77	0.7	0.843	1	0.987	1	SUBCLONAL	2	TRUE	1	0.22	2		711	797	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129324	152129324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756964962	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	77	475	1	ENST00000206249.3:c.277G>A	p.Gly93Ser	p.G93S	ENST00000206249	NM_000125.3	93	Ggc/Agc	1/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.22	2		476	517	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563519	87563519	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	75	346	0	ENST00000277120.3:c.1907T>C	p.Met636Thr	p.M636T	ENST00000277120		636	aTg/aCg	16/19	1	2	FACETS	0.876	0.772	0.987	1	0.981	1	CLONAL	2	TRUE	1	0.22	2		346	389	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417466	139417466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774966208	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	155	608	1	ENST00000277541.6:c.578G>A	p.Gly193Asp	p.G193D	ENST00000277541	NM_017617.3	193	gGc/gAc	4/34	1	2	FACETS	0.916	0.84	0.996	1	0.991	1	CLONAL	2	TRUE	1	0.22	2		609	769	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202426	123202426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	62	563	1	ENST00000218089.9:c.2278C>T	p.Arg760Cys	p.R760C	ENST00000218089	NM_001042749.1	760	Cgt/Tgt	24/35	0.218746336952447	0	FACETS	0.865	0.749	0.992			1	CLONAL	1	TRUE	0	0.22	0		564	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0013747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	908	485	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.3295846816756	2	FACETS	0.972	0.954	0.989	1	0.999	1	CLONAL	5	TRUE	0	0.3295846816756	2		485	1134	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0013747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	289	576	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.895	0.849	0.942	1	0.996	1	CLONAL	3	TRUE	1	0.3295846816756	2		576	653	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939048	76939048	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0013747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	164	622	0	ENST00000373344.5:c.1700C>G	p.Ser567Ter	p.S567*	ENST00000373344	NM_000489.3	567	tCa/tGa	9/35	0.3295846816756	1	FACETS	0.964	0.886	1	0.964	0.886	1	CLONAL	1	TRUE	0	0.3295846816756	1		622	862	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937501	76937502	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0013747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	150	485	0	ENST00000373344.5:c.3246_3247insC	p.Lys1083GlnfsTer7	p.K1083Qfs*7	ENST00000373344	NM_000489.3	1082	-/C	9/35	0.3295846816756	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.3295846816756	1		485	590	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	127	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.66	0.599	0.725	0.66	0.599	0.725	SUBCLONAL	1	TRUE	1	0.520555961397048	2		311	739	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0013772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	205	485	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.373086243547298	1	FACETS	0.628	0.583	0.675	0.628	0.583	0.675	SUBCLONAL	1	TRUE	0	0.520555961397048	1		485	928	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971292	13971292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772105404	NA	P-0013772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	153	512	1	ENST00000405192.2:c.637C>T	p.Arg213Cys	p.R213C	ENST00000405192	NM_001163147.1	213	Cgc/Tgc	8/12	0.361665689785766	3	FACETS	0.728	0.666	0.794	0.364	0.333	0.397	SUBCLONAL	1	TRUE	1	0.520555961397048	3		513	1017	SUCCESS
APC	324	MSKCC	GRCh37	5	112175761	112175761	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	107	345	0	ENST00000257430.4:c.4473del	p.Phe1491LeufsTer16	p.F1491Lfs*16	ENST00000257430	NM_000038.5	1490	caT/ca	16/16	1	2	FACETS	0.691	0.621	0.765	0.691	0.621	0.765	SUBCLONAL	1	TRUE	1	0.520555961397048	2		345	595	SUCCESS
APC	324	MSKCC	GRCh37	5	112174357	112174358	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs876658724	NA	P-0013772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	104	271	0	ENST00000257430.4:c.3067dup	p.Thr1023AsnfsTer6	p.T1023Nfs*6	ENST00000257430	NM_000038.5	1022	-/A	16/16	1	2	FACETS	0.733	0.659	0.812	0.733	0.659	0.812	SUBCLONAL	1	TRUE	1	0.520555961397048	2		271	545	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343255	118343255	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	277	406	0	ENST00000534358.1:c.1381A>C	p.Lys461Gln	p.K461Q	ENST00000534358	NM_005933.3	461	Aaa/Caa	3/36	0.361665689785766	3	FACETS	1	0.993	1	0.701	0.66	0.744	CLONAL	1	TRUE	1	0.520555961397048	3		406	956	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223235	2223235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773787910	NA	P-0013772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	189	520	0	ENST00000326181.6:c.847C>T	p.Arg283Cys	p.R283C	ENST00000326181	NM_032271.2	283	Cgc/Tgc	10/21	NA	2	FACETS	0.743	0.687	0.802			1	INDETERMINATE	1	TRUE	NA	0.520555961397048	2		520	977	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593413	48593415	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	novel	NA	P-0013772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	142	393	0	ENST00000342988.3:c.1165_1167del	p.Leu389del	p.L389del	ENST00000342988	NM_005359.5	388	caGTTg/cag	10/12	0.408708843088917	1	FACETS	0.667	0.61	0.726	0.667	0.61	0.726	SUBCLONAL	1	TRUE	0	0.520555961397048	1		393	605	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620566	52620566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746373271	NA	P-0013772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	141	459	0	ENST00000394830.3:c.3187C>T	p.Arg1063Trp	p.R1063W	ENST00000394830	NM_018313.4	1063	Cgg/Tgg	21/30	1	2	FACETS	0.613	0.558	0.67	0.613	0.558	0.67	SUBCLONAL	1	TRUE	1	0.520555961397048	2		459	884	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539933	187539933	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	158	466	0	ENST00000441802.2:c.7807G>A	p.Val2603Met	p.V2603M	ENST00000441802	NM_005245.3	2603	Gtg/Atg	10/27	1	2	FACETS	0.73	0.67	0.794	0.73	0.67	0.794	SUBCLONAL	1	TRUE	1	0.520555961397048	2		466	831	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399902	139399902	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	190	571	0	ENST00000277541.6:c.4446C>A	p.Asn1482Lys	p.N1482K	ENST00000277541	NM_017617.3	1482	aaC/aaA	25/34	1	2	FACETS	0.693	0.64	0.748	0.693	0.64	0.748	SUBCLONAL	1	TRUE	1	0.520555961397048	2		571	1053	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	202	778	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.45	2		778	878	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	164	338	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	0.45	2		338	684	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646981	23646981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	183	690	0	ENST00000261584.4:c.886del	p.Met296Ter	p.M296*	ENST00000261584	NM_024675.3	296	Atg/tg	4/13	1	2	FACETS	0.941	0.87	1	0.941	0.87	1	CLONAL	1	TRUE	1	0.45	2		690	864	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	160	252	0	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.45	1		252	496	SUCCESS
APC	324	MSKCC	GRCh37	5	112175675	112175676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	150	362	0	ENST00000257430.4:c.4393_4394dup	p.Ser1465ArgfsTer9	p.S1465Rfs*9	ENST00000257430	NM_000038.5	1462	aag/aAGag	16/16	1	2	FACETS	0.91	0.833	0.99	0.91	0.833	0.99	CLONAL	1	TRUE	1	0.45	2		362	733	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	156	456	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.45	2		456	636	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453398	40453399	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs759027671	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	126	1258	1	ENST00000345506.4:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000345506	NM_003152.3	365	-/C	10/20	1	2	FACETS	0.493	0.445	0.543	0.493	0.445	0.543	SUBCLONAL	1	TRUE	1	0.45	2		1259	1137	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219487	133219487	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	166	804	1	ENST00000320574.5:c.4647del	p.Lys1550AsnfsTer12	p.K1550Nfs*12	ENST00000320574	NM_006231.2	1549	ccC/cc	36/49	1	2	FACETS	0.801	0.736	0.869	0.801	0.736	0.869	CLONAL	1	TRUE	1	0.45	2		805	921	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436713	110436713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	159	602	5	ENST00000375856.3:c.1688C>T	p.Ala563Val	p.A563V	ENST00000375856	NM_003749.2	563	gCg/gTg	1/2	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.45	2		607	683	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564408	86564408	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	55	591	0	ENST00000274376.6:c.144del	p.Tyr49IlefsTer24	p.Y49Ifs*24	ENST00000274376	NM_002890.2	47	gCc/gc	1/25	1	2	FACETS	0.375	0.321	0.436	0.375	0.321	0.436	SUBCLONAL	1	TRUE	1	0.45	2		591	651	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499363	89499363	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1317589623	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	43	308	0	ENST00000336596.2:c.2538del	p.Met847TrpfsTer10	p.M847Wfs*10	ENST00000336596	NM_005233.5	845	Ccc/cc	15/17	1	2	FACETS	0.246	0.205	0.291	0.246	0.205	0.291	SUBCLONAL	1	TRUE	1	0.45	2		308	778	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37056036	37056036	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs267607789	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	102	454	1	ENST00000231790.2:c.790+1G>A		p.X264_splice	ENST00000231790	NM_000249.3	264			1	2	FACETS	0.83	0.745	0.92	0.83	0.745	0.92	CLONAL	1	TRUE	1	0.45	2		455	546	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165282	47165283	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	147	540	2	ENST00000409792.3:c.843dup	p.Glu282ArgfsTer9	p.E282Rfs*9	ENST00000409792	NM_014159.6	281	-/A	3/21	1	2	FACETS	0.981	0.898	1	0.981	0.898	1	CLONAL	1	TRUE	1	0.45	2		542	666	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533939	63533942	+	frameshift_variant	Frame_Shift_Del	DEL	CTCT	CTCT	-	rs771001164	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	57	272	0	ENST00000307078.5:c.1212_1215del	p.Glu405AlafsTer52	p.E405Afs*52	ENST00000307078	NM_004655.3	404	agAGAG/ag	6/11	1	2	FACETS	0.844	0.73	0.968	0.844	0.73	0.968	CLONAL	1	TRUE	1	0.45	2		272	300	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494324	2494324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143033733	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	153	623	1	ENST00000355716.4:c.715G>A	p.Val239Ile	p.V239I	ENST00000355716	NM_003820.2	239	Gtc/Atc	7/8	1	2	FACETS	0.932	0.854	1	0.932	0.854	1	CLONAL	1	TRUE	1	0.45	2		624	730	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741372	17741372	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	169	643	0	ENST00000250003.3:c.43G>C	p.Ala15Pro	p.A15P	ENST00000250003	NM_002478.4	15	Gcc/Ccc	1/3	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.45	2		643	692	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861952	57861952	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777289743	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	204	969	1	ENST00000228682.2:c.1253G>A	p.Arg418Gln	p.R418Q	ENST00000228682	NM_005269.2	418	cGg/cAg	10/12	1	2	FACETS	0.903	0.837	0.971	0.903	0.837	0.971	CLONAL	1	TRUE	1	0.45	2		970	1004	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134526	2134526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1441136255	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	137	677	1	ENST00000219476.3:c.4303G>A	p.Glu1435Lys	p.E1435K	ENST00000219476	NM_000548.3	1435	Gaa/Aaa	34/42	1	2	FACETS	0.881	0.803	0.963	0.881	0.803	0.963	CLONAL	1	TRUE	1	0.45	2		678	691	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828176	3828178	+	inframe_deletion	In_Frame_Del	DEL	TAT	TAT	-	novel	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	103	430	0	ENST00000262367.5:c.1947_1949del	p.Glu649_Tyr650delinsAsp	p.E649_Y650delinsD	ENST00000262367	NM_004380.2	649	gaATAt/gat	10/31	1	2	FACETS	0.849	0.763	0.941	0.849	0.763	0.941	CLONAL	1	TRUE	1	0.45	2		430	539	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63553974	63553975	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	201	763	0	ENST00000307078.5:c.764_765del	p.Leu255GlnfsTer13	p.L255Qfs*13	ENST00000307078	NM_004655.3	255	cTG/c	2/11	1	2	FACETS	0.949	0.88	1	0.949	0.88	1	CLONAL	1	TRUE	1	0.45	2		763	941	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119780	70119781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	75	658	0	ENST00000245479.2:c.788dup	p.Arg264GlnfsTer32	p.R264Qfs*32	ENST00000245479	NM_000346.3	261	gag/gaGg	3/3	1	2	FACETS	0.466	0.408	0.529	0.466	0.408	0.529	SUBCLONAL	1	TRUE	1	0.45	2		658	715	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897406	78897406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754209706	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	138	709	0	ENST00000306801.3:c.2741C>T	p.Ala914Val	p.A914V	ENST00000306801	NM_020761.2	914	gCg/gTg	23/34	1	2	FACETS	0.756	0.688	0.827	0.756	0.688	0.827	SUBCLONAL	1	TRUE	1	0.45	2		709	811	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622415	1622415	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	46	727	2	ENST00000344749.5:c.550-1G>T		p.X184_splice	ENST00000344749	NM_001136139.2	184			1	2	FACETS	0.288	0.242	0.34	0.288	0.242	0.34	SUBCLONAL	1	TRUE	1	0.45	2		729	709	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797321	42797321	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs998901250	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	102	665	0	ENST00000575354.2:c.3683C>T	p.Thr1228Ile	p.T1228I	ENST00000575354	NM_015125.3	1228	aCa/aTa	15/20	1	2	FACETS	0.737	0.66	0.818	0.737	0.66	0.818	SUBCLONAL	1	TRUE	1	0.45	2		665	615	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713742	30713742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504292	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	118	446	0	ENST00000295754.5:c.1067G>A	p.Arg356Gln	p.R356Q	ENST00000295754	NM_003242.5	356	cGg/cAg	4/7	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.45	2		446	488	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090456	37090483	+	frameshift_variant	Frame_Shift_Del	DEL	ATTCCATCCGGAAGCAGTACATATCTGA	ATTCCATCCGGAAGCAGTACATATCTGA	-	novel	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	124	594	0	ENST00000231790.2:c.2051_2078del	p.Tyr684TrpfsTer90	p.Y684Wfs*90	ENST00000231790	NM_000249.3	684	tATTCCATCCGGAAGCAGTACATATCTGAg/tg	18/19	1	2	FACETS	0.849	0.77	0.932	0.849	0.77	0.932	CLONAL	1	TRUE	1	0.45	2		594	649	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163356	47163356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	154	660	0	ENST00000409792.3:c.2770G>A	p.Ala924Thr	p.A924T	ENST00000409792	NM_014159.6	924	Gca/Aca	3/21	1	2	FACETS	0.869	0.796	0.945	0.869	0.796	0.945	CLONAL	1	TRUE	1	0.45	2		660	788	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143033782	143033782	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1273253280	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	182	573	1	ENST00000262992.4:c.2189C>A	p.Pro730His	p.P730H	ENST00000262992	NM_001101669.1	730	cCt/cAt	20/24	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.45	2		574	773	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56171018	56171018	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	121	459	0	ENST00000399503.3:c.1850del	p.Gly617GlufsTer39	p.G617Efs*39	ENST00000399503	NM_005921.1	616	Ggg/gg	10/20	1	2	FACETS	0.939	0.851	1	0.939	0.851	1	CLONAL	1	TRUE	1	0.45	2		459	573	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189357	56189357	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	204	648	2	ENST00000399503.3:c.4390-1G>T		p.X1464_splice	ENST00000399503	NM_005921.1	1464			1	2	FACETS	0.955	0.886	1	0.955	0.886	1	CLONAL	1	TRUE	1	0.45	2		650	949	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056292	26056292	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	147	543	0	ENST00000343677.2:c.365A>T	p.Lys122Met	p.K122M	ENST00000343677	NM_005319.3	122	aAg/aTg	1/1	1	2	FACETS	0.845	0.772	0.921	0.845	0.772	0.921	CLONAL	1	TRUE	1	0.45	2		543	773	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289272	33289272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751031043	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	134	514	0	ENST00000374542.5:c.280C>T	p.Arg94Cys	p.R94C	ENST00000374542	NM_001141970.1	94	Cgt/Tgt	3/8	1	2	FACETS	0.904	0.823	0.988	0.904	0.823	0.988	CLONAL	1	TRUE	1	0.45	2		514	659	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738654	145738654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753536598	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	68	345	0	ENST00000428558.2:c.2410C>T	p.Arg804Trp	p.R804W	ENST00000428558	NM_004260.3	804	Cgg/Tgg	15/22	1	2	FACETS	0.994	0.872	1	0.994	0.872	1	CLONAL	1	TRUE	1	0.45	2		345	304	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900325	101900325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	173	666	1	ENST00000374994.4:c.759G>A	p.Met253Ile	p.M253I	ENST00000374994	NM_004612.2	253	atG/atA	4/9	1	2	FACETS	0.835	0.768	0.904	0.835	0.768	0.904	CLONAL	1	TRUE	1	0.45	2		667	921	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760379	133760379	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	49	604	0	ENST00000318560.5:c.2702C>A	p.Pro901His	p.P901H	ENST00000318560	NM_005157.4	901	cCc/cAc	11/11	1	2	FACETS	0.361	0.305	0.423	0.361	0.305	0.423	SUBCLONAL	1	TRUE	1	0.45	2		604	603	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760982	133760982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780164415	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	234	820	0	ENST00000318560.5:c.3305C>T	p.Ala1102Val	p.A1102V	ENST00000318560	NM_005157.4	1102	gCg/gTg	11/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.45	2		820	971	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395047	139395047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1387329667	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	131	578	0	ENST00000277541.6:c.5891C>T	p.Pro1964Leu	p.P1964L	ENST00000277541	NM_017617.3	1964	cCg/cTg	31/34	1	2	FACETS	0.929	0.845	1	0.929	0.845	1	CLONAL	1	TRUE	1	0.45	2		578	627	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407554	139407554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	190	749	0	ENST00000277541.6:c.2386G>A	p.Ala796Thr	p.A796T	ENST00000277541	NM_017617.3	796	Gcg/Acg	15/34	1	2	FACETS	0.923	0.854	0.995	0.923	0.854	0.995	CLONAL	1	TRUE	1	0.45	2		749	915	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939396	76939396	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	282	472	3	ENST00000373344.5:c.1352C>A	p.Ala451Asp	p.A451D	ENST00000373344	NM_000489.3	451	gCt/gAt	9/35	1	1	FACETS	0.765	0.725	0.805	1	0.994	1	SUBCLONAL	2	TRUE	0	0.45	1		475	635	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	31	245	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.23	2		245	233	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	143	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.198082702617627	2	FACETS	0.807	0.737	0.881	0.807	0.737	0.881	CLONAL	2	TRUE	0	0.23	2		311	770	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0013906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	36	286	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.716	0.589	0.859	0.716	0.589	0.859	SUBCLONAL	1	TRUE	1	0.23	2		286	437	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	64	554	2	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	1	2	FACETS	0.499	0.43	0.574	0.499	0.43	0.574	SUBCLONAL	1	TRUE	1	0.23	2		556	1115	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911535	101911535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113605875	NA	P-0013906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	84	416	0	ENST00000374994.4:c.1460G>A	p.Arg487Gln	p.R487Q	ENST00000374994	NM_004612.2	487	cGg/cAg	9/9	0.298661826483939	1	FACETS	0.855	0.755	0.963	0.855	0.755	0.963	CLONAL	1	TRUE	0	0.23	1		416	756	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123788	11123788	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1064795105	NA	P-0013906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	79	378	2	ENST00000358026.2:c.2438C>T	p.Ser813Leu	p.S813L	ENST00000358026	NM_001128849.1	813	tCa/tTa	16/36	1	2	FACETS	0.831	0.729	0.94	0.831	0.729	0.94	CLONAL	1	TRUE	1	0.23	2		380	827	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123578	108123578	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	41	371	0	ENST00000278616.4:c.1837G>A	p.Val613Met	p.V613M	ENST00000278616	NM_000051.3	613	Gtg/Atg	12/63	1	2	FACETS	1	0.839	1	1	0.839	1	CLONAL	1	TRUE	1	0.23	2		371	355	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354431	354431	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774250998	NA	P-0013906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	97	451	0	ENST00000262320.3:c.1127G>A	p.Arg376Gln	p.R376Q	ENST00000262320	NM_003502.3	376	cGg/cAg	5/11	1	2	FACETS	0.841	0.748	0.94	0.841	0.748	0.94	CLONAL	1	TRUE	1	0.23	2		451	1003	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845883	72845883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756387925	NA	P-0013906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1314	85	737	1	ENST00000268489.5:c.3584G>A	p.Arg1195His	p.R1195H	ENST00000268489	NM_006885.3	1195	cGc/cAc	6/10	1	2	FACETS	0.528	0.465	0.597	0.528	0.465	0.597	SUBCLONAL	1	TRUE	1	0.23	2		738	1399	SUCCESS
APC	324	MSKCC	GRCh37	5	112174214	112174214	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	71	550	0	ENST00000257430.4:c.2926del	p.Arg976GlufsTer4	p.R976Efs*4	ENST00000257430	NM_000038.5	975	Aaa/aa	16/16	1	2	FACETS	0.791	0.689	0.901	0.791	0.689	0.901	CLONAL	1	TRUE	1	0.23	2		550	781	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500948	8500948	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	82	598	0	ENST00000356435.5:c.1934A>G	p.Tyr645Cys	p.Y645C	ENST00000356435		645	tAc/tGc	13/35	1	2	FACETS	0.676	0.594	0.764	0.676	0.594	0.764	SUBCLONAL	1	TRUE	1	0.23	2		598	1055	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0013909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	171	242	0				ENST00000310581	NM_198253.2	-/1132			0.717820318718734	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.717820318718734	3		242	307	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0013909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	283	292	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.717820318718734	2	FACETS	0.971	0.933	1	0.971	0.933	1	CLONAL	2	TRUE	0	0.717820318718734	2		292	406	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919244	48919244	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913296	NA	P-0013909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	293	417	0	ENST00000267163.4:c.409G>T	p.Glu137Ter	p.E137*	ENST00000267163	NM_000321.2	137	Gaa/Taa	4/27	NA	2	FACETS	0.991	0.953	1			1	INDETERMINATE	2	TRUE	NA	0.717820318718734	2		417	412	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46512257	46512257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1239	67	763	1	ENST00000262741.5:c.982G>A	p.Val328Ile	p.V328I	ENST00000262741	NM_003629.3	328	Gtc/Atc	8/10	0.717820318718734	4	FACETS	0.246	0.212	0.282	0.123	0.106	0.141	SUBCLONAL	1	TRUE	2	0.717820318718734	4		764	1306	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584567	48584567	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	136	537	0	ENST00000342988.3:c.740G>A	p.Gly247Glu	p.G247E	ENST00000342988	NM_005359.5	247	gGa/gAa	6/12	0.717820318718734	3	FACETS	0.728	0.663	0.796	0.364	0.331	0.398	SUBCLONAL	1	TRUE	1	0.717820318718734	3		537	707	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589629	67589630	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGATTA	novel	NA	P-0013909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	176	263	0	ENST00000274335.5:c.1393_1398dup	p.Arg465_Leu466dup	p.R465_L466dup	ENST00000274335		465	-/AGATTA	10/15	0.717820318718734	3	FACETS	0.825	0.77	0.88	0.825	0.77	0.88	CLONAL	2	TRUE	1	0.717820318718734	3		263	404	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590411	67590411	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	159	423	0	ENST00000274335.5:c.1477del	p.Ile493TyrfsTer17	p.I493Yfs*17	ENST00000274335		491	atA/at	11/15	0.717820318718734	3	FACETS	0.947	0.871	1	0.473	0.435	0.513	CLONAL	1	TRUE	1	0.717820318718734	3		423	636	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409941	139409942	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0013943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	137	490	0	ENST00000277541.6:c.1896dup	p.Thr633AspfsTer12	p.T633Dfs*12	ENST00000277541	NM_017617.3	632	-/G	11/34	1	2	FACETS	0.922	0.842	1	0.922	0.842	1	CLONAL	1	TRUE	1	0.487134870045973	2		490	610	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964925	55964925	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	440	682	0	ENST00000263923.4:c.2312C>G	p.Thr771Arg	p.T771R	ENST00000263923	NM_002253.2	771	aCg/aGg	16/30	0.487134870045973	3	FACETS	0.95	0.908	0.993			1	CLONAL	2	TRUE	NA	0.487134870045973	3		682	1182	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578463	7578463	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371524413	NA	P-0013943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	155	532	0	ENST00000269305.4:c.467G>C	p.Arg156Pro	p.R156P	ENST00000269305	NM_001126112.2	156	cGc/cCc	5/11	1	2	FACETS	0.982	0.902	1	0.982	0.902	1	CLONAL	1	TRUE	1	0.487134870045973	2		532	648	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797220	135797220	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	207	700	0	ENST00000298552.3:c.649G>T	p.Glu217Ter	p.E217*	ENST00000298552	NM_001162426.1	217	Gaa/Taa	7/23	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.487134870045973	2		700	796	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0013969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	146	328	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.492268381577543	4	FACETS	1	0.983	1	0.423	0.389	0.459	INDETERMINATE	1	TRUE	1	0.851211153287784	4		328	500	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0013969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	547	408	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	0.17921468387556	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.851211153287784	0		408	1347	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333134	70333134	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	59	699	0	ENST00000373644.4:c.1039G>C	p.Glu347Gln	p.E347Q	ENST00000373644	NM_030625.2	347	Gag/Cag	2/12	0.238803564688498	3	FACETS	0.213	0.183	0.247	0.107	0.091	0.124	INDETERMINATE	1	TRUE	1	0.851211153287784	3		699	927	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143510	30143510	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	33	145	0	ENST00000389048.3:c.16C>G	p.Leu6Val	p.L6V	ENST00000389048	NM_004304.4	6	Ctc/Gtc	1/29	0.72938808666563	1	FACETS	0.537	0.453	0.624	0.537	0.453	0.624	SUBCLONAL	1	TRUE	0	0.851211153287784	1		145	83	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433938	149433938	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	44	598	0	ENST00000286301.3:c.2710C>T	p.Gln904Ter	p.Q904*	ENST00000286301	NM_005211.3	904	Cag/Tag	21/22	0.253635329596442	1	FACETS	0.082	0.068	0.097	0.082	0.068	0.097	INDETERMINATE	1	TRUE	0	0.851211153287784	1		598	726	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170064	32170064	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	88	562	0	ENST00000375023.3:c.3544A>C	p.Ser1182Arg	p.S1182R	ENST00000375023	NM_004557.3	1182	Agt/Cgt	21/30	0.238803564688498	3	FACETS	0.286	0.252	0.322	0.143	0.126	0.161	INDETERMINATE	1	TRUE	1	0.851211153287784	3		562	1032	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0013977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	252	437	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.314129556609274	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	FALSE	0	0.314129556609274	2		437	707	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610154	10610154	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	279	637	0	ENST00000171111.5:c.556G>T	p.Gly186Cys	p.G186C	ENST00000171111	NM_203500.1	186	Ggc/Tgc	2/6	0.314129556609274	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	FALSE	0	0.314129556609274	2		637	868	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552222	29552222	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778549	NA	P-0013977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	66	592	0	ENST00000356175.3:c.1955G>A	p.Arg652His	p.R652H	ENST00000356175	NM_000267.3	652	cGt/cAt	17/57	0.313156422521932	3	FACETS	0.526	0.455	0.603	0.175	0.151	0.201	SUBCLONAL	1	FALSE	0	0.314129556609274	3		592	925	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127442	17127442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	158	406	0	ENST00000285071.4:c.412G>A	p.Glu138Lys	p.E138K	ENST00000285071	NM_144997.5	138	Gaa/Aaa	6/14	0.314129556609274	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	FALSE	0	0.314129556609274	2		406	472	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215609851	215609851	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs751710099	NA	P-0013977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	157	579	0	ENST00000260947.4:c.1843C>G	p.Gln615Glu	p.Q615E	ENST00000260947	NM_000465.2	615	Caa/Gaa	9/11	0.252197105130415	4	FACETS	1	0.954	1	0.533	0.487	0.581	CLONAL	1	FALSE	2	0.314129556609274	4		579	1233	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919105	178919105	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	114	314	0	ENST00000263967.3:c.590T>C	p.Ile197Thr	p.I197T	ENST00000263967	NM_006218.2	197	aTa/aCa	4/21	0.238899585882025	4	FACETS	0.761	0.686	0.839	0.761	0.686	0.839	SUBCLONAL	2	FALSE	2	0.314129556609274	4		314	627	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609951	117609951	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	156	591	0	ENST00000368508.3:c.6748G>T	p.Val2250Leu	p.V2250L	ENST00000368508	NM_002944.2	2250	Gtg/Ttg	43/43	0.274610513592635	3	FACETS	1	0.973	1	0.577	0.528	0.629	CLONAL	1	FALSE	1	0.314129556609274	3		591	996	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524667	106524667	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	121	426	2	ENST00000359195.3:c.2828G>T	p.Gly943Val	p.G943V	ENST00000359195	NM_002649.2	943	gGa/gTa	9/11	0.314129556609274	5	FACETS	1	0.976	1	0.314	0.284	0.347	CLONAL	1	FALSE	1	0.314129556609274	5		428	901	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139438480	139438481	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0013977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	386	604	0	ENST00000277541.6:c.135dup	p.Cys46LeufsTer97	p.C46Lfs*97	ENST00000277541	NM_017617.3	45	-/C	2/34	0.313156422521932	3	FACETS	0.916	0.872	0.96	0.916	0.872	0.96	CLONAL	3	FALSE	0	0.314129556609274	3		604	1035	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413058	63413058	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1157159299	NA	P-0013977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	472	547	0	ENST00000330258.3:c.109A>G	p.Thr37Ala	p.T37A	ENST00000330258	NM_152424.3	37	Aca/Gca	2/2	0.294131929318375	2	FACETS	1	0.984	1			1	CLONAL	3	FALSE	NA	0.314129556609274	2		547	960	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	230	365	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.379686458283578	3	FACETS	0.926	0.866	0.988	0.926	0.866	0.988	CLONAL	2	TRUE	1	0.379686458283578	3		365	778	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	305	226	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	0.378914116363469	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.379686458283578	2		226	778	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	154	333	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.918	0.848	0.989	1	0.992	1	CLONAL	2	TRUE	1	0.379686458283578	2		335	442	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100302	157100302	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1417035592	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	88	474	0	ENST00000346085.5:c.1243del	p.Ala415ProfsTer15	p.A415Pfs*15	ENST00000346085	NM_020732.3	413	tcG/tc	1/20	1	2	FACETS	0.931	0.828	1	0.931	0.828	1	CLONAL	1	TRUE	1	0.379686458283578	2		474	498	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	309	246	0	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	0.787	0.743	0.832	1	0.995	1	SUBCLONAL	2	TRUE	1	0.379686458283578	2		246	1034	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	132	625	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	0.379686458283578	2		625	641	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	178	250	1	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.926	0.852	1	0.926	0.852	1	CLONAL	1	TRUE	1	0.379686458283578	2		251	1013	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744048	41744048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376355256	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	149	780	0	ENST00000301178.4:c.983C>T	p.Thr328Met	p.T328M	ENST00000301178	NM_021913.4	328	aCg/aTg	7/20	1	2	FACETS	0.967	0.884	1	0.967	0.884	1	CLONAL	1	TRUE	1	0.379686458283578	2		780	812	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671004	30671005	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	130	688	0	ENST00000376406.3:c.5741dup	p.Ser1915LysfsTer15	p.S1915Kfs*15	ENST00000376406	NM_014641.2	1914	gga/ggGa	12/15	1	2	FACETS	0.905	0.821	0.992	0.905	0.821	0.992	CLONAL	1	TRUE	1	0.379686458283578	2		688	757	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521298	187521299	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	155	989	0	ENST00000441802.2:c.11856dup	p.Gly3953TrpfsTer19	p.G3953Wfs*19	ENST00000441802	NM_005245.3	3952	-/T	22/27	1	2	FACETS	0.728	0.665	0.794	0.728	0.665	0.794	SUBCLONAL	1	TRUE	1	0.379686458283578	2		989	1121	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702265	47702265	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750508	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	236	742	2	ENST00000233146.2:c.1861C>T	p.Arg621Ter	p.R621*	ENST00000233146	NM_000251.2	621	Cga/Tga	12/16	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.379686458283578	2		744	987	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	63	414	2	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	1	2	FACETS	0.357	0.308	0.411	0.357	0.308	0.411	SUBCLONAL	1	TRUE	1	0.379686458283578	2		416	929	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037474	12037474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	105	272	0	ENST00000396373.4:c.1105C>T	p.Arg369Trp	p.R369W	ENST00000396373	NM_001987.4	369	Cgg/Tgg	6/8	1	2	FACETS	0.91	0.817	1	0.91	0.817	1	CLONAL	1	TRUE	1	0.379686458283578	2		272	608	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950625	38950626	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	220	1028	0	ENST00000357387.3:c.3324dup	p.His1109ThrfsTer3	p.H1109Tfs*3	ENST00000357387	NM_152756.3	1108	-/A	31/38	1	2	FACETS	0.86	0.799	0.924	0.86	0.799	0.924	CLONAL	1	TRUE	1	0.379686458283578	2		1028	1347	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	79	472	1	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	0.755	0.665	0.851	0.755	0.665	0.851	SUBCLONAL	1	TRUE	1	0.379686458283578	2		473	551	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100195	27100195	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	110	452	1	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	0.379686458283578	2		453	515	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794441	42794441	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	258	1187	2	ENST00000575354.2:c.1526del	p.Pro509HisfsTer14	p.P509Hfs*14	ENST00000575354	NM_015125.3	507	cgC/cg	10/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.379686458283578	2		1189	1214	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	127	562	0	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	1	2	FACETS	0.816	0.739	0.897	0.816	0.739	0.897	CLONAL	1	TRUE	1	0.379686458283578	2		562	820	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240375	98240375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1293146883	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	136	585	1	ENST00000331920.6:c.1309G>A	p.Val437Ile	p.V437I	ENST00000331920	NM_000264.3	437	Gtc/Atc	9/24	1	2	FACETS	0.924	0.841	1	0.924	0.841	1	CLONAL	1	TRUE	1	0.379686458283578	2		586	775	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097609	27097609	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	83	686	0	ENST00000324856.7:c.3199-1G>A		p.X1067_splice	ENST00000324856	NM_006015.4	1067			1	2	FACETS	0.564	0.497	0.636	0.564	0.497	0.636	SUBCLONAL	1	TRUE	1	0.379686458283578	2		686	775	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366129	15366129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1468704458	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	49	695	0	ENST00000263377.2:c.2026C>T	p.Arg676Trp	p.R676W	ENST00000263377	NM_058243.2	676	Cgg/Tgg	10/20	1	2	FACETS	0.309	0.26	0.362	0.309	0.26	0.362	SUBCLONAL	1	TRUE	1	0.379686458283578	2		695	836	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184622	11184622	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	186	745	1	ENST00000361445.4:c.6595A>G	p.Met2199Val	p.M2199V	ENST00000361445	NM_004958.3	2199	Atg/Gtg	47/58	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.379686458283578	2		746	948	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106978	27106978	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	88	430	2	ENST00000324856.7:c.6589G>T	p.Gly2197Cys	p.G2197C	ENST00000324856	NM_006015.4	2197	Ggc/Tgc	20/20	1	2	FACETS	0.956	0.85	1	0.956	0.85	1	CLONAL	1	TRUE	1	0.379686458283578	2		432	485	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176085815	176085815	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	119	519	0	ENST00000367669.3:c.971G>A	p.Ser324Asn	p.S324N	ENST00000367669	NM_022457.5	324	aGt/aAt	9/20	1	2	FACETS	0.922	0.833	1	0.922	0.833	1	CLONAL	1	TRUE	1	0.379686458283578	2		519	680	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205115	61205115	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	160	712	1	ENST00000301761.2:c.55C>A	p.His19Asn	p.H19N	ENST00000301761	NM_017841.2	19	Cac/Aac	2/4	1	2	FACETS	0.957	0.877	1	0.957	0.877	1	CLONAL	1	TRUE	1	0.379686458283578	2		713	881	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233265	46233265	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	65	594	0	ENST00000334344.6:c.1484T>C	p.Val495Ala	p.V495A	ENST00000334344	NM_152641.2	495	gTa/gCa	11/21	1	2	FACETS	0.445	0.385	0.511	0.445	0.385	0.511	SUBCLONAL	1	TRUE	1	0.379686458283578	2		594	769	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425986	49425986	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	53	891	0	ENST00000301067.7:c.12502A>G	p.Thr4168Ala	p.T4168A	ENST00000301067	NM_003482.3	4168	Aca/Gca	39/54	1	2	FACETS	0.307	0.261	0.358	0.307	0.261	0.358	SUBCLONAL	1	TRUE	1	0.379686458283578	2		891	909	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426973	49426973	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1565778024	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	59	515	3	ENST00000301067.7:c.11515del	p.Gln3839SerfsTer42	p.Q3839Sfs*42	ENST00000301067	NM_003482.3	3839	Cag/ag	39/54	1	2	FACETS	0.612	0.527	0.704	0.612	0.527	0.704	SUBCLONAL	1	TRUE	1	0.379686458283578	2		518	508	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448480	49448480	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	67	676	0	ENST00000301067.7:c.231del	p.His77GlnfsTer53	p.H77Qfs*53	ENST00000301067	NM_003482.3	77	caC/ca	3/54	1	2	FACETS	0.468	0.406	0.535	0.468	0.406	0.535	SUBCLONAL	1	TRUE	1	0.379686458283578	2		676	754	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112939969	112939969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs186919241	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	161	658	0	ENST00000351677.2:c.1621G>A	p.Glu541Lys	p.E541K	ENST00000351677	NM_002834.3	541	Gaa/Aaa	14/16	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.379686458283578	2		658	846	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133236017	133236017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555225676	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	147	649	1	ENST00000320574.5:c.3139G>A	p.Gly1047Arg	p.G1047R	ENST00000320574	NM_006231.2	1047	Ggg/Agg	26/49	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.379686458283578	2		650	758	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878077	48878082	+	inframe_deletion	In_Frame_Del	DEL	CCGCCA	CCGCCA	-	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	45	284	0	ENST00000267163.4:c.34_39del	p.Thr12_Ala13del	p.T12_A13del	ENST00000267163	NM_000321.2	10	gCCGCCAcc/gcc	1/27	1	2	FACETS	0.725	0.612	0.849	0.725	0.612	0.849	SUBCLONAL	1	TRUE	1	0.379686458283578	2		284	327	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422179	81422179	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	109	541	1	ENST00000298171.2:c.155C>A	p.Pro52His	p.P52H	ENST00000298171	NM_000369.2	52	cCc/cAc	1/10	1	2	FACETS	0.954	0.859	1	0.954	0.859	1	CLONAL	1	TRUE	1	0.379686458283578	2		542	602	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351547	89351547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1194186968	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1228	399	1291	0	ENST00000301030.4:c.1403G>A	p.Arg468His	p.R468H	ENST00000301030	NM_001256183.1	468	cGc/cAc	9/13	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.379686458283578	2		1291	1627	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40456579	40456579	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	255	1103	0	ENST00000345506.4:c.1292del	p.Gly431ValfsTer5	p.G431Vfs*5	ENST00000345506	NM_003152.3	430	cGg/cg	12/20	0.379686458283578	1	FACETS	0.829	0.775	0.886	0.829	0.775	0.886	CLONAL	1	TRUE	0	0.379686458283578	1		1103	1312	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243963	5243963	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761695523	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	98	563	2	ENST00000357368.4:c.1519G>A	p.Val507Ile	p.V507I	ENST00000357368	NM_002850.3	507	Gtc/Atc	11/38	1	2	FACETS	0.965	0.864	1	0.965	0.864	1	CLONAL	1	TRUE	1	0.379686458283578	2		565	535	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123674	11123674	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	181	706	0	ENST00000358026.2:c.2324G>A	p.Gly775Asp	p.G775D	ENST00000358026	NM_001128849.1	775	gGc/gAc	16/36	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.379686458283578	2		706	846	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135100	11135100	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555780047	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	131	496	1	ENST00000358026.2:c.3067G>A	p.Glu1023Lys	p.E1023K	ENST00000358026	NM_001128849.1	1023	Gag/Aag	21/36	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.379686458283578	2		497	596	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744384	41744384	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	180	976	1	ENST00000301178.4:c.1004G>C	p.Gly335Ala	p.G335A	ENST00000301178	NM_021913.4	335	gGc/gCc	8/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.379686458283578	2		977	905	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860625	45860625	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	99	1107	0	ENST00000391945.4:c.1382T>G	p.Leu461Arg	p.L461R	ENST00000391945	NM_000400.3	461	cTg/cGg	15/23	1	2	FACETS	0.436	0.388	0.488	0.436	0.388	0.488	SUBCLONAL	1	TRUE	1	0.379686458283578	2		1107	1195	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635626	47635626	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	58	674	0	ENST00000233146.2:c.298G>A	p.Val100Ile	p.V100I	ENST00000233146	NM_000251.2	100	Gtt/Att	2/16	1	2	FACETS	0.339	0.291	0.393	0.339	0.291	0.393	SUBCLONAL	1	TRUE	1	0.379686458283578	2		674	900	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637495	47637496	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	100	489	0	ENST00000233146.2:c.633dup	p.Lys212GlufsTer20	p.K212Efs*20	ENST00000233146	NM_000251.2	210	atg/atGg	3/16	1	2	FACETS	0.956	0.857	1	0.956	0.857	1	CLONAL	1	TRUE	1	0.379686458283578	2		489	551	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158655990	158655990	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	237	1110	0	ENST00000263640.3:c.16A>G	p.Met6Val	p.M6V	ENST00000263640	NM_001105.4	6	Atg/Gtg	3/11	1	2	FACETS	0.89	0.829	0.954	0.89	0.829	0.954	CLONAL	1	TRUE	1	0.379686458283578	2		1110	1402	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514591	44514591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	101	497	0	ENST00000291552.4:c.565C>T	p.Arg189Cys	p.R189C	ENST00000291552	NM_006758.2	189	Cgt/Tgt	7/8	1	2	FACETS	0.854	0.765	0.949	0.854	0.765	0.949	CLONAL	1	TRUE	1	0.379686458283578	2		497	623	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566534	41566535	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	59	764	1	ENST00000263253.7:c.4413dup	p.Asp1472Ter	p.D1472*	ENST00000263253	NM_001429.3	1471	ctt/cTtt	27/31	1	2	FACETS	0.304	0.26	0.352	0.304	0.26	0.352	SUBCLONAL	1	TRUE	1	0.379686458283578	2		765	1023	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433521	138433523	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	104	448	0	ENST00000289153.2:c.1089_1091del	p.Leu364del	p.L364del	ENST00000289153	NM_006219.2	363	ctCCTg/ctg	7/22	1	2	FACETS	0.897	0.804	0.994	0.897	0.804	0.994	CLONAL	1	TRUE	1	0.379686458283578	2		448	611	SUCCESS
ATR	545	MSKCC	GRCh37	3	142232479	142232479	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	111	492	0	ENST00000350721.4:c.4505T>C	p.Val1502Ala	p.V1502A	ENST00000350721	NM_001184.3	1502	gTt/gCt	26/47	1	2	FACETS	0.93	0.837	1	0.93	0.837	1	CLONAL	1	TRUE	1	0.379686458283578	2		492	629	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594094	55594094	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs794726675	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	116	535	4	ENST00000288135.5:c.1879+1G>A		p.X627_splice	ENST00000288135	NM_000222.2	627			1	2	FACETS	0.953	0.861	1	0.953	0.861	1	CLONAL	1	TRUE	1	0.379686458283578	2		539	641	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213842	66213842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	176	838	0	ENST00000273854.3:c.2588G>A	p.Ser863Asn	p.S863N	ENST00000273854	NM_004439.5	863	aGt/aAt	15/18	1	2	FACETS	0.916	0.843	0.992	0.916	0.843	0.992	CLONAL	1	TRUE	1	0.379686458283578	2		838	1012	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236621	236621	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	92	457	0	ENST00000264932.6:c.1339C>T	p.His447Tyr	p.H447Y	ENST00000264932	NM_004168.2	447	Cat/Tat	10/15	1	2	FACETS	0.928	0.828	1	0.928	0.828	1	CLONAL	1	TRUE	1	0.379686458283578	2		457	522	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288177	33288177	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	79	450	0	ENST00000374542.5:c.1231G>T	p.Ala411Ser	p.A411S	ENST00000374542	NM_001141970.1	411	Gcc/Tcc	4/8	1	2	FACETS	0.88	0.776	0.99	0.88	0.776	0.99	CLONAL	1	TRUE	1	0.379686458283578	2		450	473	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200107	138200107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746331032	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	76	351	1	ENST00000237289.4:c.1525G>A	p.Ala509Thr	p.A509T	ENST00000237289	NM_001270507.1	509	Gcc/Acc	7/9	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.379686458283578	2		352	396	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339535	81339535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1192583398	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	363	876	3	ENST00000222390.5:c.1469C>T	p.Thr490Met	p.T490M	ENST00000222390	NM_000601.4	490	aCg/aTg	13/18	0.379686458283578	3	FACETS	0.997	0.946	1	0.997	0.946	1	CLONAL	2	TRUE	1	0.379686458283578	3		879	1141	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92247489	92247489	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	89	752	2	ENST00000265734.4:c.731C>T	p.Pro244Leu	p.P244L	ENST00000265734	NM_001259.6	244	cCt/cTt	7/8	0.379686458283578	3	FACETS	0.472	0.417	0.531	0.236	0.208	0.266	SUBCLONAL	1	TRUE	1	0.379686458283578	3		754	1182	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965798	90965798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554558456	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	56	555	0	ENST00000265433.3:c.1519C>T	p.His507Tyr	p.H507Y	ENST00000265433	NM_002485.4	507	Cat/Tat	11/16	0.379686458283578	3	FACETS	0.475	0.406	0.551	0.237	0.203	0.276	SUBCLONAL	1	TRUE	1	0.379686458283578	3		555	739	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342610	87342610	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	130	582	2	ENST00000277120.3:c.895C>T	p.His299Tyr	p.H299Y	ENST00000277120		299	Cac/Tac	9/19	1	2	FACETS	0.942	0.855	1	0.942	0.855	1	CLONAL	1	TRUE	1	0.379686458283578	2		584	727	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913264	39913265	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	204	953	0	ENST00000378444.4:c.4850dup	p.Leu1617PhefsTer12	p.L1617Ffs*12	ENST00000378444	NM_001123385.1	1617	tta/ttTa	14/15	1	2	FACETS	0.965	0.894	1	0.965	0.894	1	CLONAL	1	TRUE	1	0.379686458283578	2		953	1113	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190405	32190405	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765988217	NA	P-0013981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	140	685	0	ENST00000375023.3:c.334G>A	p.Glu112Lys	p.E112K	ENST00000375023	NM_004557.3	112	Gag/Aag	3/30	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.379686458283578	2		685	721	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013986-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	33	245	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.538	0.438	0.65	0.538	0.438	0.65	SUBCLONAL	1	TRUE	1	0.320328762968417	2		245	383	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106099	27106100	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0013986-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	142	522	0	ENST00000324856.7:c.5715dup	p.Arg1906ThrfsTer8	p.R1906Tfs*8	ENST00000324856	NM_006015.4	1904	gaa/gAaa	20/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.320328762968417	2		522	653	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0013986-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	106	338	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.320328762968417	2		338	644	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087503	27087503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013986-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	134	618	2	ENST00000324856.7:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000324856	NM_006015.4	693	Cga/Tga	5/20	1	2	FACETS	0.795	0.721	0.873	0.795	0.721	0.873	SUBCLONAL	1	TRUE	1	0.320328762968417	2		620	1053	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2221573	2221573	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013986-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	148	808	1	ENST00000326181.6:c.442C>T	p.His148Tyr	p.H148Y	ENST00000326181	NM_032271.2	148	Cac/Tac	7/21	1	2	FACETS	0.889	0.81	0.971	0.889	0.81	0.971	CLONAL	1	TRUE	1	0.320328762968417	2		809	1040	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	143	245	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.469479787415068	2		245	571	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0013991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	231	576	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	0.469479787415068	2		576	916	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555525857	NA	P-0013991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	215	1043	0	ENST00000269305.4:c.596G>A	p.Gly199Glu	p.G199E	ENST00000269305	NM_001126112.2	199	gGa/gAa	6/11	1	2	FACETS	0.692	0.642	0.745	0.692	0.642	0.745	SUBCLONAL	1	TRUE	1	0.469479787415068	2		1043	1323	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236203	108236203	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121434219	NA	P-0013991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	518	797	0	ENST00000278616.4:c.9139C>T	p.Arg3047Ter	p.R3047*	ENST00000278616	NM_000051.3	3047	Cga/Tga	63/63	0.468052271221775	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.469479787415068	2		797	1058	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829039	128829040	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs570242755	NA	P-0013991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	13	86	0	ENST00000249373.3:c.67_69dup	p.Leu23dup	p.L23dup	ENST00000249373	NM_005631.4	23	ggg/ggGCTg	1/12	1	2	FACETS	0.477	0.343	0.638	0.477	0.343	0.638	SUBCLONAL	1	TRUE	1	0.469479787415068	2		86	116	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378643	25378643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730880471	NA	P-0013991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	104	842	1	ENST00000311936.3:c.355G>A	p.Asp119Asn	p.D119N	ENST00000311936	NM_004985.3	119	Gat/Aat	4/5	1	2	FACETS	0.378	0.337	0.422	0.378	0.337	0.422	SUBCLONAL	1	TRUE	1	0.469479787415068	2		843	1172	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107050	27107050	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762698084	NA	P-0013991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	48	574	0	ENST00000324856.7:c.6661C>T	p.Pro2221Ser	p.P2221S	ENST00000324856	NM_006015.4	2221	Cca/Tca	20/20	0.469479787415068	1	FACETS	0.285	0.241	0.334	0.285	0.241	0.334	SUBCLONAL	1	TRUE	0	0.469479787415068	1		574	549	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193172979	193172979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	92	816	1	ENST00000367435.3:c.1027C>T	p.Pro343Ser	p.P343S	ENST00000367435	NM_024529.4	343	Cca/Tca	11/17	1	2	FACETS	0.329	0.291	0.369	0.329	0.291	0.369	SUBCLONAL	1	TRUE	1	0.469479787415068	2		817	1192	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279620	123279620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	55	592	0	ENST00000358487.5:c.812G>A	p.Gly271Glu	p.G271E	ENST00000358487	NM_000141.4	271	gGa/gAa	7/18	1	2	FACETS	0.292	0.249	0.34	0.292	0.249	0.34	SUBCLONAL	1	TRUE	1	0.469479787415068	2		592	802	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457997	69457997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	105	777	0	ENST00000227507.2:c.397C>T	p.Arg133Trp	p.R133W	ENST00000227507	NM_053056.2	133	Cgg/Tgg	2/5	0.468052271221775	2	FACETS	0.413	0.369	0.461	0.207	0.184	0.231	SUBCLONAL	1	TRUE	0	0.469479787415068	2		777	1082	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467886	99467886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	74	717	1	ENST00000268035.6:c.2755C>T	p.Pro919Ser	p.P919S	ENST00000268035	NM_000875.3	919	Cct/Tct	13/21	1	2	FACETS	0.308	0.268	0.35	0.308	0.268	0.35	SUBCLONAL	1	TRUE	1	0.469479787415068	2		718	1025	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853217	68853217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1194	80	913	0	ENST00000261769.5:c.1600G>A	p.Glu534Lys	p.E534K	ENST00000261769	NM_004360.3	534	Gag/Aag	11/16	1	2	FACETS	0.268	0.234	0.303	0.268	0.234	0.303	SUBCLONAL	1	TRUE	1	0.469479787415068	2		913	1274	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797355	42797355	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	116	904	1	ENST00000575354.2:c.3717G>A	p.Trp1239Ter	p.W1239*	ENST00000575354	NM_015125.3	1239	tgG/tgA	15/20	0.469479787415068	1	FACETS	0.406	0.365	0.449	0.406	0.365	0.449	SUBCLONAL	1	TRUE	0	0.469479787415068	1		905	931	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009156	27009156	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	108	438	0	ENST00000335756.4:c.92C>T	p.Pro31Leu	p.P31L	ENST00000335756	NM_001809.3	31	cCc/cTc	1/5	1	2	FACETS	0.737	0.663	0.816	0.737	0.663	0.816	SUBCLONAL	1	TRUE	1	0.469479787415068	2		438	624	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051202	128051202	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	84	772	0	ENST00000285398.2:c.121G>A	p.Ala41Thr	p.A41T	ENST00000285398	NM_000122.1	41	Gcg/Acg	2/15	1	2	FACETS	0.293	0.257	0.331	0.293	0.257	0.331	SUBCLONAL	1	TRUE	1	0.469479787415068	2		772	1223	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268460	198268460	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1162	91	827	0	ENST00000335508.6:c.1568C>T	p.Ala523Val	p.A523V	ENST00000335508	NM_012433.2	523	gCt/gTt	12/25	1	2	FACETS	0.309	0.273	0.348	0.309	0.273	0.348	SUBCLONAL	1	TRUE	1	0.469479787415068	2		827	1253	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386401	31386401	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	63	817	2	ENST00000328111.2:c.1626G>T	p.Trp542Cys	p.W542C	ENST00000328111	NM_006892.3	542	tgG/tgT	15/23	1	2	FACETS	0.256	0.22	0.295	0.256	0.22	0.295	SUBCLONAL	1	TRUE	1	0.469479787415068	2		819	1050	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098675	47098675	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1443135936	NA	P-0013991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1212	103	1001	0	ENST00000409792.3:c.6599C>T	p.Pro2200Leu	p.P2200L	ENST00000409792	NM_014159.6	2200	cCt/cTt	15/21	1	2	FACETS	0.334	0.297	0.373	0.334	0.297	0.373	SUBCLONAL	1	TRUE	1	0.469479787415068	2		1001	1315	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801055	1801055	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs533866031	NA	P-0013991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	67	791	0	ENST00000260795.2:c.184C>T	p.Pro62Ser	p.P62S	ENST00000260795		62	Ccc/Tcc	2/17	1	2	FACETS	0.303	0.262	0.347	0.303	0.262	0.347	SUBCLONAL	1	TRUE	1	0.469479787415068	2		791	942	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541306	187541306	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376279669	NA	P-0013991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	99	874	1	ENST00000441802.2:c.6434C>T	p.Thr2145Ile	p.T2145I	ENST00000441802	NM_005245.3	2145	aCc/aTc	10/27	1	2	FACETS	0.361	0.321	0.404	0.361	0.321	0.404	SUBCLONAL	1	TRUE	1	0.469479787415068	2		875	1169	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945827	38945827	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0013991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	57	398	0	ENST00000357387.3:c.4400-1G>A		p.X1467_splice	ENST00000357387	NM_152756.3	1467			1	2	FACETS	0.434	0.372	0.502	0.434	0.372	0.502	SUBCLONAL	1	TRUE	1	0.469479787415068	2		398	559	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401456	401456	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	33	393	0	ENST00000380956.4:c.778G>A	p.Glu260Lys	p.E260K	ENST00000380956	NM_001195286.1	260	Gaa/Aaa	7/9	1	2	FACETS	0.281	0.228	0.34	0.281	0.228	0.34	SUBCLONAL	1	TRUE	1	0.469479787415068	2		393	501	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527934	157527934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	58	459	0	ENST00000346085.5:c.5659G>A	p.Ala1887Thr	p.A1887T	ENST00000346085	NM_020732.3	1887	Gca/Aca	20/20	1	2	FACETS	0.343	0.294	0.396	0.343	0.294	0.396	SUBCLONAL	1	TRUE	1	0.469479787415068	2		459	721	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325635	87325635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	78	877	1	ENST00000277120.3:c.512C>T	p.Thr171Ile	p.T171I	ENST00000277120		171	aCt/aTt	6/19	1	2	FACETS	0.265	0.232	0.301	0.265	0.232	0.301	SUBCLONAL	1	TRUE	1	0.469479787415068	2		878	1254	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944387	76944387	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1331	73	973	0	ENST00000373344.5:c.518C>T	p.Ala173Val	p.A173V	ENST00000373344	NM_000489.3	173	gCt/gTt	7/35	1	2	FACETS	0.221	0.193	0.253	0.221	0.193	0.253	SUBCLONAL	1	TRUE	1	0.469479787415068	2		973	1404	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0014023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	130	175	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.83122145757539	2		175	297	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0014023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	211	440	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.769	0.718	0.822	0.769	0.718	0.822	SUBCLONAL	1	TRUE	1	0.83122145757539	2		440	660	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	575	240	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.9	0.877	0.922	1	0.998	1	CLONAL	2	TRUE	1	0.83122145757539	2		240	769	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431874	49431874	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	252	625	1	ENST00000301067.7:c.9265del	p.Val3089TrpfsTer30	p.V3089Wfs*30	ENST00000301067	NM_003482.3	3089	Gtg/tg	34/54	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.83122145757539	2		626	584	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0014023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	195	175	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.83122145757539	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.83122145757539	2		175	231	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	148	305	0	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	1	2	FACETS	0.879	0.812	0.948	0.879	0.812	0.948	CLONAL	1	TRUE	1	0.83122145757539	2		305	405	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696716	47696716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	313	336	0	ENST00000347630.2:c.232G>A	p.Glu78Lys	p.E78K	ENST00000347630	NM_001007230.1	78	Gaa/Aaa	5/11	1	2	FACETS	0.931	0.882	0.98	0.931	0.882	0.98	CLONAL	1	TRUE	1	0.83122145757539	2		336	809	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938230	76938230	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	270	667	2	ENST00000373344.5:c.2518del	p.Arg840GlufsTer29	p.R840Efs*29	ENST00000373344	NM_000489.3	840	Aga/ga	9/35	1	2	FACETS	0.774	0.729	0.821	0.774	0.729	0.821	SUBCLONAL	1	TRUE	1	0.83122145757539	2		669	839	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9779983	9779984	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0014023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	39	529	1	ENST00000377346.4:c.1251dup	p.Ile418HisfsTer10	p.I418Hfs*10	ENST00000377346	NM_005026.3	416	tgc/tgCc	10/24	1	2	FACETS	0.122	0.1	0.146	0.122	0.1	0.146	SUBCLONAL	1	TRUE	1	0.83122145757539	2		530	769	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107010	27107010	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	234	333	0	ENST00000324856.7:c.6621del	p.Gln2207HisfsTer24	p.Q2207Hfs*24	ENST00000324856	NM_006015.4	2207	caG/ca	20/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.83122145757539	2		333	563	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432609	78432609	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1233786882	NA	P-0014023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	170	399	0	ENST00000370768.2:c.374G>A	p.Arg125His	p.R125H	ENST00000370768	NM_003902.3	125	cGc/cAc	6/20	1	2	FACETS	0.872	0.809	0.936	0.872	0.809	0.936	CLONAL	1	TRUE	1	0.83122145757539	2		399	469	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468274	120468274	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	171	272	0	ENST00000256646.2:c.4165T>C	p.Cys1389Arg	p.C1389R	ENST00000256646	NM_024408.3	1389	Tgc/Cgc	25/34	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.83122145757539	2		272	402	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653828	89653829	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1554893810	NA	P-0014023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	445	399	0	ENST00000371953.3:c.127dup	p.Glu43GlyfsTer9	p.E43Gfs*9	ENST00000371953	NM_000314.4	42	-/G	2/9	0.83122145757539	2	FACETS	0.988	0.963	1	0.988	0.963	1	CLONAL	2	TRUE	0	0.83122145757539	2		399	542	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466031	69466031	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	294	467	0	ENST00000227507.2:c.869T>G	p.Val290Gly	p.V290G	ENST00000227507	NM_053056.2	290	gTg/gGg	5/5	1	2	FACETS	0.966	0.915	1	0.966	0.915	1	CLONAL	1	TRUE	1	0.83122145757539	2		467	732	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442811	442811	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	56	400	0	ENST00000399788.2:c.1495del	p.Glu499SerfsTer19	p.E499Sfs*19	ENST00000399788	NM_001042603.1	499	Gag/ag	12/28	1	2	FACETS	0.22	0.188	0.255	0.22	0.188	0.255	SUBCLONAL	1	TRUE	1	0.83122145757539	2		400	612	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118831	115118831	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	116	521	0	ENST00000257566.3:c.510G>A	p.Trp170Ter	p.W170*	ENST00000257566	NM_016569.3	170	tgG/tgA	2/8	1	2	FACETS	0.352	0.317	0.389	0.352	0.317	0.389	SUBCLONAL	1	TRUE	1	0.83122145757539	2		521	794	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541730	120541730	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	532	889	0	ENST00000229340.5:c.127G>A	p.Val43Met	p.V43M	ENST00000229340	NM_006861.6	43	Gtg/Atg	3/6	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.83122145757539	2		889	1250	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304375	91304375	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	31	375	0	ENST00000355112.3:c.1772G>T	p.Arg591Leu	p.R591L	ENST00000355112	NM_000057.2	591	cGg/cTg	7/22	1	2	FACETS	0.132	0.106	0.161	0.132	0.106	0.161	SUBCLONAL	1	TRUE	1	0.83122145757539	2		375	566	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347446	91347446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757088548	NA	P-0014023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	309	505	0	ENST00000355112.3:c.3608C>T	p.Ala1203Val	p.A1203V	ENST00000355112	NM_000057.2	1203	gCg/gTg	19/22	1	2	FACETS	0.953	0.903	1	0.953	0.903	1	CLONAL	1	TRUE	1	0.83122145757539	2		505	780	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103442	2103442	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369932305	NA	P-0014023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	193	325	0	ENST00000219476.3:c.325G>A	p.Val109Met	p.V109M	ENST00000219476	NM_000548.3	109	Gtg/Atg	4/42	1	2	FACETS	0.982	0.918	1	0.982	0.918	1	CLONAL	1	TRUE	1	0.83122145757539	2		325	473	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349754	89349755	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	601	1139	0	ENST00000301030.4:c.3195dup	p.His1066ThrfsTer2	p.H1066Tfs*2	ENST00000301030	NM_001256183.1	1065	-/A	9/13	NA	2	FACETS	0.886	0.852	0.921			1	INDETERMINATE	1	TRUE	NA	0.83122145757539	2		1139	1632	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660999	227660999	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	192	447	0	ENST00000305123.5:c.2456del	p.Gly819AspfsTer124	p.G819Dfs*124	ENST00000305123	NM_005544.2	819	gGa/ga	1/2	1	2	FACETS	0.862	0.803	0.922	0.862	0.803	0.922	CLONAL	1	TRUE	1	0.83122145757539	2		447	536	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412377	139412377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	180	346	0	ENST00000277541.6:c.1268G>A	p.Cys423Tyr	p.C423Y	ENST00000277541	NM_017617.3	423	tGc/tAc	8/34	1	2	FACETS	0.906	0.843	0.97	0.906	0.843	0.97	CLONAL	1	TRUE	1	0.83122145757539	2		346	478	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70355039	70355039	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	411	871	1	ENST00000374080.3:c.4961A>T	p.Gln1654Leu	p.Q1654L	ENST00000374080		1654	cAg/cTg	36/45	1	2	FACETS	0.926	0.884	0.969	0.926	0.884	0.969	CLONAL	1	TRUE	1	0.83122145757539	2		872	1068	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577061	7577062	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	88	892	0	ENST00000269305.4:c.876dup	p.Gly293ArgfsTer13	p.G293Rfs*13	ENST00000269305	NM_001126112.2	292	-/A	8/11	0.201320363818859	2	FACETS	1	0.974	1	0.676	0.6	0.756	CLONAL	1	FALSE	0	0.246725825381794	2		892	528	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657668	37657668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	61	617	0	ENST00000447079.4:c.2585G>A	p.Cys862Tyr	p.C862Y	ENST00000447079	NM_015083.1	862	tGt/tAt	6/14	0.189390110483145	4	FACETS	1	0.965	1	0.693	0.599	0.794	CLONAL	1	FALSE	2	0.246725825381794	4		617	445	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222530	2222530	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760394488	NA	P-0014181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	29	1242	1	ENST00000398665.3:c.3362C>T	p.Ser1121Leu	p.S1121L	ENST00000398665	NM_032482.2	1121	tCg/tTg	24/28	NA	2	FACETS	0.407	0.325	0.5			1	INDETERMINATE	1	FALSE	NA	0.246725825381794	2		1243	578	SUCCESS
APC	324	MSKCC	GRCh37	5	112174757	112174757	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	42	315	0	ENST00000257430.4:c.3466G>T	p.Glu1156Ter	p.E1156*	ENST00000257430	NM_000038.5	1156	Gaa/Taa	16/16	0.163541590424855	3	FACETS	0.781	0.657	0.916	0.781	0.657	0.916	CLONAL	2	FALSE	1	0.246725825381794	3		315	245	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0014181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	163	654	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.238632017859181	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	FALSE	1	0.246725825381794	4		654	486	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219676	36219676	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs779867806	NA	P-0014181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	64	861	0	ENST00000222270.7:c.4573G>A	p.Gly1525Arg	p.G1525R	ENST00000222270	NM_014727.1	1525	Gga/Aga	20/37	0.248883108804498	3	FACETS	1	0.898	1	0.521	0.452	0.597	CLONAL	1	FALSE	1	0.246725825381794	3		861	559	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0014246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	73	179	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	0.267124779103722	4	FACETS	1	0.897	1	1	0.897	1	CLONAL	2	TRUE	2	0.36679480528491	4		179	268	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0014246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	168	447	2	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.36679480528491	2	FACETS	0.952	0.883	1	0.952	0.883	1	CLONAL	2	TRUE	0	0.36679480528491	2		449	481	SUCCESS
AR	367	MSKCC	GRCh37	X	66905909	66905909	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	67	173	1	ENST00000374690.3:c.1826G>T	p.Arg609Met	p.R609M	ENST00000374690	NM_000044.3	609	aGg/aTg	3/8	0.282102260766785	2	FACETS	0.923	0.816	1			1	CLONAL	2	TRUE	NA	0.36679480528491	2		174	198	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106657	27106657	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	256	416	0	ENST00000324856.7:c.6268del	p.His2090ThrfsTer45	p.H2090Tfs*45	ENST00000324856	NM_006015.4	2090	Cac/ac	20/20	0.36679480528491	3	FACETS	0.978	0.925	1			1	CLONAL	3	TRUE	NA	0.36679480528491	3		416	563	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89815086	89815086	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs752837228	NA	P-0014246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	164	413	0	ENST00000389301.3:c.3329A>G	p.His1110Arg	p.H1110R	ENST00000389301	NM_000135.2	1110	cAc/cGc	33/43	0.334082529230852	3	FACETS	0.919	0.848	0.992	0.919	0.848	0.992	CLONAL	2	TRUE	1	0.36679480528491	3		413	576	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285837	39285838	+	inframe_insertion	In_Frame_Ins	INS	-	-	TACTGGGAGAGATAAAGGGTTTCTTCGCTTCCTCTT	novel	NA	P-0014246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	52	364	0	ENST00000402219.2:c.286_321dup	p.Lys96_Val107dup	p.K96_V107dup	ENST00000402219	NM_005633.3	96	-/AAGAGGAAGCGAAGAAACCCTTTATCTCTCCCAGTA	3/23	0.267124779103722	4	FACETS	0.974	0.831	1	0.487	0.415	0.565	CLONAL	1	TRUE	2	0.36679480528491	4		364	398	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662922	52662923	+	missense_variant	Missense_Mutation	DNP	CT	CT	GG	novel	NA	P-0014246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	89	321	0	ENST00000394830.3:c.1430_1431delinsCC	p.Gln477Pro	p.Q477P	ENST00000394830	NM_018313.4	477	cAG/cCC	13/30	0.360178905595535	2	FACETS	0.892	0.802	0.985	0.892	0.802	0.985	CLONAL	2	TRUE	0	0.36679480528491	2		321	272	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	226	338	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.673469250290219	4	FACETS	0.904	0.848	0.962	0.904	0.848	0.962	CLONAL	2	TRUE	2	0.673469250290219	4		338	621	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0014273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	506	792	0	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.663136567511186	2	FACETS	0.931	0.901	0.961	0.931	0.901	0.961	CLONAL	2	TRUE	0	0.673469250290219	2		792	807	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509408	149509409	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0014273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	210	601	0	ENST00000261799.4:c.1490dup	p.Gln498AlafsTer34	p.Q498Afs*34	ENST00000261799	NM_002609.3	497	ctg/ctTg	10/23	0.426719921681654	4	FACETS	1	0.969	1	0.538	0.499	0.578	CLONAL	1	TRUE	2	0.673469250290219	4		601	970	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513002	106513002	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	343	374	0	ENST00000359195.3:c.2016C>A	p.Tyr672Ter	p.Y672*	ENST00000359195	NM_002649.2	672	taC/taA	3/11	0.752448510566065	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.752448510566065	3		374	609	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017602	112017602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	271	718	0	ENST00000368678.4:c.911C>T	p.Ser304Phe	p.S304F	ENST00000368678		304	tCc/tTc	9/13	NA	2	FACETS	0.932	0.878	0.987			1	INDETERMINATE	1	TRUE	NA	0.752448510566065	2		718	773	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520072	106520072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	160	409	0	ENST00000359195.3:c.2500C>T	p.His834Tyr	p.H834Y	ENST00000359195	NM_002649.2	834	Cat/Tat	6/11	0.752448510566065	3	FACETS	0.963	0.887	1	0.481	0.443	0.521	CLONAL	1	TRUE	1	0.752448510566065	3		409	608	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101521	27101523	+	frameshift_variant	Frame_Shift_Del	DEL	TAG	TAG	AA	novel	NA	P-0014308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	344	951	1	ENST00000324856.7:c.4803_4805delinsAA	p.Ser1602ThrfsTer10	p.S1602Tfs*10	ENST00000324856	NM_006015.4	1601	ccTAGc/ccAAc	18/20	1	2	FACETS	0.945	0.896	0.994	0.945	0.896	0.994	CLONAL	1	TRUE	1	0.752448510566065	2		952	968	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746014	162746014	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	208	526	0	ENST00000367921.3:c.2137A>G	p.Thr713Ala	p.T713A	ENST00000367921	NM_006182.2	713	Aca/Gca	16/18	0.749399772708486	4	FACETS	0.948	0.88	1	0.316	0.293	0.34	CLONAL	1	TRUE	1	0.752448510566065	4		526	1022	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	430169	430169	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	200	506	0	ENST00000399788.2:c.2533C>T	p.Gln845Ter	p.Q845*	ENST00000399788	NM_001042603.1	845	Caa/Taa	18/28	0.752448510566065	3	FACETS	0.877	0.814	0.942	0.439	0.407	0.471	CLONAL	1	TRUE	1	0.752448510566065	3		506	834	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245553	46245553	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369610372	NA	P-0014308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	392	453	1	ENST00000334344.6:c.3647C>T	p.Thr1216Met	p.T1216M	ENST00000334344	NM_152641.2	1216	aCg/aTg	15/21	0.752448510566065	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.752448510566065	3		454	701	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438234	49438234	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	655	838	0	ENST00000301067.7:c.5035G>T	p.Glu1679Ter	p.E1679*	ENST00000301067	NM_003482.3	1679	Gag/Tag	20/54	0.752448510566065	3	FACETS	0.935	0.905	0.966	0.935	0.905	0.966	CLONAL	2	TRUE	1	0.752448510566065	3		838	1281	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849535	68849535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786202675	NA	P-0014308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	312	820	0	ENST00000261769.5:c.1438G>A	p.Val480Met	p.V480M	ENST00000261769	NM_004360.3	480	Gtg/Atg	10/16	0.749399772708486	4	FACETS	1	0.951	1	0.337	0.317	0.358	CLONAL	1	TRUE	1	0.752448510566065	4		820	1437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579592	7579592	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0014308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	515	648	0	ENST00000269305.4:c.97-2A>T		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.709485261513311	2	FACETS	0.976	0.949	1	0.976	0.949	1	CLONAL	2	TRUE	0	0.752448510566065	2		648	701	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920465	50920465	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	320	702	0	ENST00000440232.2:c.3157C>A	p.Arg1053Ser	p.R1053S	ENST00000440232	NM_002691.3	1053	Cgc/Agc	26/27	1	2	FACETS	0.962	0.911	1	0.962	0.911	1	CLONAL	1	TRUE	1	0.752448510566065	2		702	884	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735398	204735398	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	143	428	0	ENST00000302823.3:c.199A>G	p.Thr67Ala	p.T67A	ENST00000302823	NM_005214.4	67	Act/Gct	2/4	0.752448510566065	3	FACETS	0.978	0.896	1	0.489	0.448	0.531	CLONAL	1	TRUE	1	0.752448510566065	3		428	535	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225362486	225362486	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	362	565	0	ENST00000264414.4:c.1691A>T	p.Tyr564Phe	p.Y564F	ENST00000264414	NM_003590.4	564	tAt/tTt	12/16	0.752448510566065	3	FACETS	0.923	0.883	0.964	0.923	0.883	0.964	CLONAL	2	TRUE	1	0.752448510566065	3		565	717	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225362490	225362491	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	358	585	0	ENST00000264414.4:c.1686dup	p.Phe563IlefsTer6	p.F563Ifs*6	ENST00000264414	NM_003590.4	562	-/A	12/16	0.752448510566065	3	FACETS	0.865	0.825	0.905	0.865	0.825	0.905	CLONAL	2	TRUE	1	0.752448510566065	3		585	757	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526379	31526379	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1310	402	1255	0	ENST00000344624.3:c.661del	p.Ser221ProfsTer5	p.S221Pfs*5	ENST00000344624		221	Tcc/cc	2/33	0.72687659101068	3	FACETS	0.859	0.815	0.904	0.429	0.407	0.452	CLONAL	1	TRUE	1	0.752448510566065	3		1255	1712	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945060	38945060	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	217	659	1	ENST00000357387.3:c.4744C>T	p.Gln1582Ter	p.Q1582*	ENST00000357387	NM_152756.3	1582	Caa/Taa	35/38	0.72687659101068	3	FACETS	0.846	0.787	0.907	0.423	0.393	0.454	CLONAL	1	TRUE	1	0.752448510566065	3		660	938	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852188	128852188	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	729	997	6	ENST00000249373.3:c.2260G>A	p.Ala754Thr	p.A754T	ENST00000249373	NM_005631.4	754	Gcc/Acc	12/12	0.752448510566065	2	FACETS	0.969	0.946	0.991	0.969	0.946	0.991	CLONAL	2	TRUE	0	0.752448510566065	2		1003	1000	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189051	38189051	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	336	866	1	ENST00000317025.8:c.963G>A	p.Trp321Ter	p.W321*	ENST00000317025	NM_023034.1	321	tgG/tgA	5/24	1	2	FACETS	0.924	0.876	0.972	0.924	0.876	0.972	CLONAL	1	TRUE	1	0.752448510566065	2		867	967	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137321044	137321044	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	586	775	0	ENST00000481739.1:c.1001G>C	p.Arg334Pro	p.R334P	ENST00000481739	NM_002957.4	334	cGg/cCg	7/10	0.752448510566065	3	FACETS	0.864	0.833	0.895	0.864	0.833	0.895	CLONAL	2	TRUE	1	0.752448510566065	3		775	1241	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	133	245	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.886	0.806	0.969	0.886	0.806	0.969	CLONAL	1	TRUE	1	0.454450111869052	2		245	661	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39729943	39729943	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	128	665	0	ENST00000361337.2:c.1258A>C	p.Ile420Leu	p.I420L	ENST00000361337	NM_003286.2	420	Atc/Ctc	13/21	1	2	FACETS	0.861	0.782	0.944	0.861	0.782	0.944	CLONAL	1	TRUE	1	0.454450111869052	2		665	654	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858570	27858570	+	start_lost	Translation_Start_Site	SNP	T	T	C	rs766949103	NA	P-0014318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	94	207	0	ENST00000359303.2:c.1A>G	p.Met1?	p.M1?	ENST00000359303	NM_003535.2	1	Atg/Gtg	1/1	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.454450111869052	2		207	384	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684046	29684047	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTCTCTTGGATGAAGAAGTACTTACTGA	novel	NA	P-0014318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	61	765	0	ENST00000356175.3:c.7746_7773dup	p.Pro2592SerfsTer4	p.P2592Sfs*4	ENST00000356175	NM_000267.3	2582	gtt/gTTCTCTTGGATGAAGAAGTACTTACTGAtt	52/57	0.454450111869052	1	FACETS	0.371	0.32	0.427	0.371	0.32	0.427	SUBCLONAL	1	TRUE	0	0.454450111869052	1		765	559	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156735	20156735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	187	401	0	ENST00000379607.5:c.22G>A	p.Gly8Arg	p.G8R	ENST00000379607	NM_001412.3	8	Gga/Aga	2/7	0.298274842223911	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.316375372031206	3		401	656	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346167	89346167	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	116	201	0	ENST00000301030.4:c.6783A>T	p.Glu2261Asp	p.E2261D	ENST00000301030	NM_001256183.1	2261	gaA/gaT	9/13	0.316375372031206	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.316375372031206	2		201	324	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11015670	11015671	+	frameshift_variant	Frame_Shift_Ins	INS	AG	AG	TTTA	novel	NA	P-0014340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	125	626	0	ENST00000327064.4:c.264_265delinsTTTA	p.Glu89LeufsTer37	p.E89Lfs*37	ENST00000327064	NM_199141.1	88	acAGag/acTTTAag	2/16	0.298274842223911	3	FACETS	0.889	0.804	0.98	0.445	0.402	0.49	CLONAL	1	TRUE	1	0.316375372031206	3		626	1029	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11015677	11015693	+	protein_altering_variant	In_Frame_Del	DEL	AGCCGTGTGGGCAAGCA	AGCCGTGTGGGCAAGCA	TCAGT	novel	NA	P-0014340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	118	646	0	ENST00000327064.4:c.271_287delinsTCAGT	p.Arg92_Gln96delinsVal	p.R92_Q96delinsV	ENST00000327064	NM_199141.1	91	AGCCGTGTGGGCAAGCAg/TCAGTg	2/16	0.298274842223911	3	FACETS	0.841	0.757	0.93	0.421	0.378	0.465	CLONAL	1	TRUE	1	0.316375372031206	3		646	1027	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0014389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	258	242	0				ENST00000310581	NM_198253.2	-/1132			0.484743937345261	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.484743937345261	3		242	575	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249002	55249003	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCGTGGA	rs397517109	NA	P-0014389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	595	650	0	ENST00000275493.2:c.2303_2311dup	p.Ser768_Asp770dup	p.S768_D770dup	ENST00000275493	NM_005228.3	768	gcc/gcCAGCGTGGAc	20/28	0.484743937345261	6	FACETS	0.887	0.854	0.92	0.709	0.683	0.736	CLONAL	4	TRUE	1	0.484743937345261	6		650	1363	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226369	2226369	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	218	708	0	ENST00000326181.6:c.1982T>C	p.Val661Ala	p.V661A	ENST00000326181	NM_032271.2	661	gTg/gCg	20/21	1	2	FACETS	0.9	0.837	0.965	0.9	0.837	0.965	CLONAL	1	TRUE	1	0.484743937345261	2		708	999	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772432	56772432	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	153	567	0	ENST00000337432.4:c.286A>T	p.Thr96Ser	p.T96S	ENST00000337432	NM_058216.2	96	Acc/Tcc	2/9	0.290870680932258	4	FACETS	0.893	0.816	0.974	0.446	0.408	0.487	CLONAL	1	TRUE	2	0.484743937345261	4		567	1050	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141035	55141035	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	25	236	0	ENST00000257290.5:c.1681G>C	p.Val561Leu	p.V561L	ENST00000257290	NM_006206.4	561	Gtc/Ctc	12/23	0.373359324146405	3	FACETS	0.275	0.216	0.343	0.137	0.108	0.172	SUBCLONAL	1	TRUE	1	0.484743937345261	3		236	466	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242724	98242724	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1456514392	NA	P-0014389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	241	479	2	ENST00000331920.6:c.893A>G	p.Asn298Ser	p.N298S	ENST00000331920	NM_000264.3	298	aAt/aGt	6/24	0.372595074767405	2	FACETS	1	0.993	1	0.75	0.704	0.796	CLONAL	1	TRUE	0	0.484743937345261	2		481	663	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641544	47641544	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs63750640	NA	P-0014411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	13	326	0	ENST00000233146.2:c.929T>G	p.Leu310Arg	p.L310R	ENST00000233146	NM_000251.2	310	cTt/cGt	5/16	0.466558863861464	4	FACETS	0.493	0.354	0.662	0.247	0.177	0.331	SUBCLONAL	1	TRUE	2	0.583500831756871	4		326	143	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144148	55144148	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519700	NA	P-0014411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	72	616	0	ENST00000257290.5:c.1977C>G	p.Asn659Lys	p.N659K	ENST00000257290	NM_006206.4	659	aaC/aaG	14/23	0.583500831756871	2	FACETS	1	0.946	1	0.556	0.493	0.621	CLONAL	1	TRUE	0	0.583500831756871	2		616	222	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992630	72992630	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1189486286	NA	P-0014411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	15	387	0	ENST00000268489.5:c.1415C>A	p.Ala472Glu	p.A472E	ENST00000268489	NM_006885.3	472	gCg/gAg	2/10	0.521870558280245	4	FACETS	0.316	0.23	0.418	0.158	0.115	0.209	SUBCLONAL	1	TRUE	2	0.583500831756871	4		387	258	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112561	2112561	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	95	739	0	ENST00000219476.3:c.1321T>A	p.Trp441Arg	p.W441R	ENST00000219476	NM_000548.3	441	Tgg/Agg	13/42	0.521870558280245	4	FACETS	1	0.903	1	0.506	0.451	0.563	CLONAL	1	TRUE	2	0.583500831756871	4		739	510	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857678	78857678	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	128	657	0	ENST00000306801.3:c.1748G>C	p.Arg583Thr	p.R583T	ENST00000306801	NM_020761.2	583	aGg/aCg	16/34	0.466558863861464	4	FACETS	1	0.958	1	0.547	0.497	0.6	CLONAL	1	TRUE	2	0.583500831756871	4		657	635	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141111	55141112	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGAGTTTCCAAGAGATGGACTAGTGCTTGAGAT	novel	NA	P-0014411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	48	363	0	ENST00000257290.5:c.1786_1786+1insAGATGGAGTTTCCAAGAGATGGACTAGTGCTTG	p.Leu595_Gly596insGluMetGluPheProArgAspGlyLeuValLeu	p.L595_G596insEMEFPRDGLVL	ENST00000257290	NM_006206.4	586	tgg/tgGGAGTTTCCAAGAGATGGACTAGTGCTTGAGATg	12/23	0.583500831756871	2	FACETS	0.899	0.772	1	0.45	0.386	0.518	CLONAL	1	TRUE	0	0.583500831756871	2		363	183	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	232	352	1	ENST00000304494.5:c.247C>A	p.His83Asn	p.H83N	ENST00000304494	NM_000077.4	83	Cac/Aac	2/3	0.350084044429232	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.388821078117057	2		353	559	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680659	88680659	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	108	603	0	ENST00000360948.2:c.598T>C	p.Phe200Leu	p.F200L	ENST00000360948	NM_001012338.2	200	Ttc/Ctc	6/19	0.308467809953235	3	FACETS	0.823	0.739	0.913	0.412	0.369	0.457	CLONAL	1	TRUE	1	0.388821078117057	3		603	806	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804284	46804284	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	256	829	0	ENST00000290295.7:c.723C>G	p.Ile241Met	p.I241M	ENST00000290295	NM_006361.5	241	atC/atG	2/2	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.388821078117057	2		829	1062	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523271	9523271	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	142	760	0	ENST00000353224.5:c.1966C>G	p.Arg656Gly	p.R656G	ENST00000353224	NM_177990.2	656	Cgg/Ggg	9/10	NA	2	FACETS	0.793	0.722	0.867			1	INDETERMINATE	1	TRUE	NA	0.388821078117057	2		760	921	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648415	30648416	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0014424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	127	671	0	ENST00000295754.5:c.41_42dup	p.Val15SerfsTer23	p.V15Sfs*23	ENST00000295754	NM_003242.5	14	atc/aTCtc	1/7	1	2	FACETS	0.796	0.721	0.875	0.796	0.721	0.875	SUBCLONAL	1	TRUE	1	0.388821078117057	2		671	821	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691813	30691814	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0014424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	203	724	0	ENST00000295754.5:c.316dup	p.Leu106ProfsTer5	p.L106Pfs*5	ENST00000295754	NM_003242.5	105	-/C	3/7	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.388821078117057	2		724	1002	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0014473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	176	175	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.335324350449773	3	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.426562450643846	3		175	836	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596108	43596108	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	279	520	0	ENST00000355710.3:c.275C>G	p.Thr92Ser	p.T92S	ENST00000355710	NM_020975.4	92	aCc/aGc	2/20	0.235441667649658	1	FACETS	0.796	0.747	0.847	0.796	0.747	0.847	INDETERMINATE	1	TRUE	0	0.426562450643846	1		520	1293	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607697	46607697	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	568	583	0	ENST00000263734.3:c.1886C>T	p.Ser629Phe	p.S629F	ENST00000263734	NM_001430.4	629	tCt/tTt	12/16	0.396907205512239	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.426562450643846	3		583	1615	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753336	57753336	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	71	397	0	ENST00000274289.3:c.788T>G	p.Ile263Ser	p.I263S	ENST00000274289	NM_006622.3	263	aTt/aGt	6/14	1	2	FACETS	0.346	0.301	0.395	0.346	0.301	0.395	SUBCLONAL	1	TRUE	1	0.426562450643846	2		397	963	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670138	86670139	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0014473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	124	325	0	ENST00000274376.6:c.1934+2dup		p.X645_splice	ENST00000274376	NM_002890.2	645			1	2	FACETS	0.9	0.816	0.988	0.9	0.816	0.988	CLONAL	1	TRUE	1	0.426562450643846	2		325	646	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411886	116411901	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TTTCTCTCTGTTTTAA	TTTCTCTCTGTTTTAA	-	novel	NA	P-0014473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	644	716	0	ENST00000397752.3:c.2888-17_2888-2del		p.X963_splice	ENST00000397752	NM_000245.2	963			0.426562450643846	2	FACETS	0.966	0.931	1	0.966	0.931	1	CLONAL	2	TRUE	0	0.426562450643846	2		716	1563	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0014479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	69	328	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.825	0.718	0.941	0.825	0.718	0.941	CLONAL	1	FALSE	1	0.235268274516855	2		328	711	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061240	38061240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	101	531	0	ENST00000250448.2:c.749C>T	p.Ser250Phe	p.S250F	ENST00000250448	NM_004496.3	250	tCc/tTc	2/2	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	1	0.235268274516855	2		531	814	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106058	8106058	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	100	453	0	ENST00000346208.3:c.878T>A	p.Met293Lys	p.M293K	ENST00000346208		293	aTg/aAg	4/6	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	FALSE	1	0.235268274516855	2		453	833	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913273	NA	P-0014479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	59	413	0	ENST00000263967.3:c.1624G>C	p.Glu542Gln	p.E542Q	ENST00000263967	NM_006218.2	542	Gaa/Caa	10/21	1	2	FACETS	0.83	0.714	0.957	0.83	0.714	0.957	CLONAL	1	FALSE	1	0.235268274516855	2		413	604	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131142	55131142	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	81	439	1	ENST00000257290.5:c.685G>A	p.Glu229Lys	p.E229K	ENST00000257290	NM_006206.4	229	Gaa/Aaa	5/23	1	2	FACETS	0.897	0.789	1	0.897	0.789	1	CLONAL	1	FALSE	1	0.235268274516855	2		440	768	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420268	49420268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757664799	NA	P-0014479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	104	499	1	ENST00000301067.7:c.15481G>A	p.Glu5161Lys	p.E5161K	ENST00000301067	NM_003482.3	5161	Gag/Aag	48/54	1	2	FACETS	0.923	0.825	1	0.923	0.825	1	CLONAL	1	FALSE	1	0.235268274516855	2		500	958	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622056	43622056	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	58	365	0	ENST00000355710.3:c.3073G>C	p.Asp1025His	p.D1025H	ENST00000355710	NM_020975.4	1025	Gac/Cac	19/20	1	2	FACETS	0.901	0.775	1	0.901	0.775	1	CLONAL	1	FALSE	1	0.235268274516855	2		365	547	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376332	118376332	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	93	512	0	ENST00000534358.1:c.9725C>A	p.Thr3242Asn	p.T3242N	ENST00000534358	NM_005933.3	3242	aCc/aAc	27/36	1	2	FACETS	0.781	0.693	0.876	0.781	0.693	0.876	SUBCLONAL	1	FALSE	1	0.235268274516855	2		512	1012	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610172	28610172	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	77	353	0	ENST00000241453.7:c.1318C>G	p.Gln440Glu	p.Q440E	ENST00000241453	NM_004119.2	440	Caa/Gaa	11/24	1	2	FACETS	0.855	0.749	0.968	0.855	0.749	0.968	CLONAL	1	FALSE	1	0.235268274516855	2		353	766	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28931694	28931694	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	57	340	0	ENST00000282397.4:c.2245C>T	p.Gln749Ter	p.Q749*	ENST00000282397	NM_002019.4	749	Caa/Taa	15/30	1	2	FACETS	0.884	0.759	1	0.884	0.759	1	CLONAL	1	FALSE	1	0.235268274516855	2		340	548	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061226	38061226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	83	478	0	ENST00000250448.2:c.763G>A	p.Glu255Lys	p.E255K	ENST00000250448	NM_004496.3	255	Gag/Aag	2/2	1	2	FACETS	0.973	0.859	1	0.973	0.859	1	CLONAL	1	FALSE	1	0.235268274516855	2		478	725	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210632	2210632	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	75	420	0	ENST00000398665.3:c.1129G>C	p.Glu377Gln	p.E377Q	ENST00000398665	NM_032482.2	377	Gag/Cag	14/28	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	FALSE	1	0.235268274516855	2		420	627	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5258124	5258124	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	75	491	0	ENST00000357368.4:c.610G>C	p.Glu204Gln	p.E204Q	ENST00000357368	NM_002850.3	204	Gaa/Caa	8/38	1	2	FACETS	0.85	0.744	0.964	0.85	0.744	0.964	CLONAL	1	FALSE	1	0.235268274516855	2		491	750	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18956879	18956879	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	87	520	1	ENST00000262803.5:c.322G>T	p.Asp108Tyr	p.D108Y	ENST00000262803	NM_002911.3	108	Gat/Tat	2/24	1	2	FACETS	0.842	0.745	0.947	0.842	0.745	0.947	CLONAL	1	FALSE	1	0.235268274516855	2		521	878	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221618	36221618	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	117	609	0	ENST00000222270.7:c.5287C>G	p.Leu1763Val	p.L1763V	ENST00000222270	NM_014727.1	1763	Ctg/Gtg	26/37	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.235268274516855	2		609	900	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029156	26029156	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	70	420	0	ENST00000435504.4:c.194G>C	p.Arg65Thr	p.R65T	ENST00000435504		65	aGa/aCa	4/13	1	2	FACETS	0.779	0.678	0.888	0.779	0.678	0.888	SUBCLONAL	1	FALSE	1	0.235268274516855	2		420	764	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944455	40944455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	102	544	0	ENST00000373198.4:c.2047G>A	p.Asp683Asn	p.D683N	ENST00000373198	NM_133170.3	683	Gac/Aac	12/32	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	FALSE	1	0.235268274516855	2		544	825	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71050211	71050211	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0014479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	32	263	0	ENST00000318789.4:c.975-1G>A		p.X325_splice	ENST00000318789	NM_032682.5	325			1	2	FACETS	0.566	0.458	0.687	0.566	0.458	0.687	SUBCLONAL	1	FALSE	1	0.235268274516855	2		263	481	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161166	56161166	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0014479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	49	297	0	ENST00000399503.3:c.1036-1G>C		p.X346_splice	ENST00000399503	NM_005921.1	346			1	2	FACETS	0.759	0.642	0.887	0.759	0.642	0.887	SUBCLONAL	1	FALSE	1	0.235268274516855	2		297	549	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170986	56170987	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	33	230	0	ENST00000399503.3:c.1816dup	p.Ser606PhefsTer40	p.S606Ffs*40	ENST00000399503	NM_005921.1	605	aat/aaTt	10/20	1	2	FACETS	0.71	0.579	0.858	0.71	0.579	0.858	SUBCLONAL	1	FALSE	1	0.235268274516855	2		230	395	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933823	39933823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727503826	NA	P-0014479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	82	622	0	ENST00000378444.4:c.776C>T	p.Ser259Leu	p.S259L	ENST00000378444	NM_001123385.1	259	tCg/tTg	4/15	0.193222659089644	1	FACETS	0.726	0.639	0.82	0.726	0.639	0.82	SUBCLONAL	1	FALSE	0	0.235268274516855	1		622	847	SUCCESS
AR	367	MSKCC	GRCh37	X	66765547	66765547	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	120	597	0	ENST00000374690.3:c.559G>C	p.Glu187Gln	p.E187Q	ENST00000374690	NM_000044.3	187	Gag/Cag	1/8	0.193222659089644	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	FALSE	0	0.235268274516855	1		597	882	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443574	29443574	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	265	586	0	ENST00000389048.3:c.3643C>A	p.Pro1215Thr	p.P1215T	ENST00000389048	NM_004304.4	1215	Ccg/Acg	23/29	1	2	FACETS	0.879	0.829	0.93	0.879	0.829	0.93	CLONAL	1	TRUE	1	0.857807742687066	2		586	703	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576888	7576888	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0014483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	182	615	0	ENST00000269305.4:c.958A>T	p.Lys320Ter	p.K320*	ENST00000269305	NM_001126112.2	320	Aag/Tag	9/11	0.843128234535376	1	FACETS	0.973	0.928	1	0.973	0.928	1	CLONAL	1	TRUE	0	0.857807742687066	1		615	249	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090974	77090974	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3711	583	583	1	ENST00000356341.3:c.256C>T	p.His86Tyr	p.H86Y	ENST00000356341	NM_002576.4	86	Cat/Tat	3/15	0.857807742687066	20	FACETS	0.92	0.878	0.963			1	CLONAL	3	TRUE	NA	0.857807742687066	20		584	4294	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794714	120794714	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	224	477	0	ENST00000257552.2:c.643G>C	p.Gly215Arg	p.G215R	ENST00000257552	NM_002442.3	215	Ggc/Cgc	9/15	1	2	FACETS	0.845	0.792	0.899	0.845	0.792	0.899	CLONAL	1	TRUE	1	0.857807742687066	2		477	618	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89807250	89807252	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs397507553	NA	P-0014483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	148	526	1	ENST00000389301.3:c.3788_3790del	p.Phe1263del	p.F1263del	ENST00000389301	NM_000135.2	1263	tTCTcc/tcc	38/43	1	2	FACETS	0.836	0.771	0.901	0.836	0.771	0.901	CLONAL	1	TRUE	1	0.857807742687066	2		527	413	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176504	142176504	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1196005889	NA	P-0014483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	216	427	2	ENST00000350721.4:c.7597C>T	p.Arg2533Ter	p.R2533*	ENST00000350721	NM_001184.3	2533	Cga/Tga	45/47	1	2	FACETS	0.921	0.863	0.979	0.921	0.863	0.979	CLONAL	1	TRUE	1	0.857807742687066	2		429	547	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503816	186503816	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	200	467	1	ENST00000323963.5:c.493G>A	p.Asp165Asn	p.D165N	ENST00000323963		165	Gat/Aat	5/11	1	2	FACETS	0.88	0.822	0.939	0.88	0.822	0.939	CLONAL	1	TRUE	1	0.857807742687066	2		468	530	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152571	56152572	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0014483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	316	337	0	ENST00000399503.3:c.629dup	p.Val211CysfsTer9	p.V211Cfs*9	ENST00000399503	NM_005921.1	209	-/C	2/20	0.842933538163336	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.857807742687066	1		337	396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057520000	NA	P-0014514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	193	533	0	ENST00000269305.4:c.452C>A	p.Pro151His	p.P151H	ENST00000269305	NM_001126112.2	151	cCc/cAc	5/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.272449272286323	2		533	1210	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0014514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	98	454	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.171314754784598	4	FACETS	1	0.947	1	0.552	0.492	0.616	CLONAL	1	TRUE	2	0.272449272286323	4		454	829	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98244261	98244261	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	84	529	0	ENST00000331920.6:c.716C>T	p.Ala239Val	p.A239V	ENST00000331920	NM_000264.3	239	gCg/gTg	5/24	0.214590025579428	5	FACETS	0.716	0.63	0.808	0.239	0.21	0.27	SUBCLONAL	1	TRUE	2	0.272449272286323	5		529	1214	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32189003	32189003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751063545	NA	P-0014514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	124	525	2	ENST00000375023.3:c.551C>T	p.Pro184Leu	p.P184L	ENST00000375023	NM_004557.3	184	cCg/cTg	4/30	NA	2	FACETS	0.973	0.879	1			1	INDETERMINATE	1	TRUE	NA	0.272449272286323	2		527	936	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039414	49039414	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1394	126	571	1	ENST00000267163.4:c.2399C>A	p.Pro800His	p.P800H	ENST00000267163	NM_000321.2	800	cCt/cAt	23/27	0.272449272286323	5	FACETS	0.857	0.773	0.946			1	CLONAL	1	TRUE	NA	0.272449272286323	5		572	1520	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100036	11100036	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	167	625	0	ENST00000358026.2:c.1162C>T	p.Leu388Phe	p.L388F	ENST00000358026	NM_001128849.1	388	Ctt/Ttt	7/36	0.27152316946343	4	FACETS	1	0.978	1	0.397	0.363	0.432	CLONAL	1	TRUE	1	0.272449272286323	4		625	1310	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655233	45655233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771547213	NA	P-0014514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	130	542	2	ENST00000407780.3:c.619C>T	p.Arg207Trp	p.R207W	ENST00000407780	NM_001283052.1	207	Cgg/Tgg	4/7	0.185492740779265	3	FACETS	1	0.917	1	0.507	0.459	0.558	CLONAL	1	TRUE	1	0.272449272286323	3		544	1070	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31493364	31493364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	96	432	1	ENST00000344624.3:c.1792G>A	p.Glu598Lys	p.E598K	ENST00000344624		598	Gag/Aag	10/33	1	2	FACETS	0.768	0.683	0.858	0.768	0.683	0.858	SUBCLONAL	1	TRUE	1	0.272449272286323	2		433	918	SUCCESS
APC	324	MSKCC	GRCh37	5	112175535	112175536	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGGCATTA	novel	NA	P-0014514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	87	334	0	ENST00000257430.4:c.4246_4253dup	p.Ile1418MetfsTer4	p.I1418Mfs*4	ENST00000257430	NM_000038.5	1415	agt/agTGGCATTAt	16/16	0.171314754784598	4	FACETS	1	0.898	1	0.508	0.449	0.571	CLONAL	1	TRUE	2	0.272449272286323	4		334	800	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930152	68930152	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	80	466	0	ENST00000288368.4:c.213G>T	p.Lys71Asn	p.K71N	ENST00000288368	NM_024870.2	71	aaG/aaT	2/40	0.27152316946343	4	FACETS	0.713	0.626	0.807	0.238	0.208	0.269	SUBCLONAL	1	TRUE	1	0.272449272286323	4		466	1048	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828126	3828126	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	49	423	0	ENST00000262367.5:c.1999G>T	p.Glu667Ter	p.E667*	ENST00000262367	NM_004380.2	667	Gaa/Taa	10/31	1	2	FACETS	0.545	0.461	0.639	0.545	0.461	0.639	SUBCLONAL	1	TRUE	1	0.248510116821697	2		423	723	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56839524	56839524	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	49	416	0	ENST00000308159.5:c.469G>C	p.Asp157His	p.D157H	ENST00000308159	NM_014669.4	157	Gac/Cac	5/22	1	2	FACETS	0.542	0.458	0.635	0.542	0.458	0.635	SUBCLONAL	1	TRUE	1	0.248510116821697	2		416	728	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577530	7577533	+	frameshift_variant	Frame_Shift_Ins	INS	TGGG	TGGG	AGGGA	novel	NA	P-0014520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	100	528	0	ENST00000269305.4:c.748_751delinsTCCCT	p.Pro250SerfsTer14	p.P250Sfs*14	ENST00000269305	NM_001126112.2	250	CCCAtc/TCCCTtc	7/11	0.238491266693264	2	FACETS	1	0.896	1	0.502	0.448	0.559	CLONAL	1	TRUE	0	0.248510116821697	2		528	802	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808979	1808979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751115449	NA	P-0014548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	205	372	0	ENST00000260795.2:c.2411C>T	p.Ser804Leu	p.S804L	ENST00000260795		804	tCg/tTg	17/17	1	2	FACETS	0.842	0.783	0.904	0.842	0.783	0.904	CLONAL	1	TRUE	1	0.58864499764157	2		372	827	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374244	138374244	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	248	381	0	ENST00000289153.2:c.3200A>T	p.Asp1067Val	p.D1067V	ENST00000289153	NM_006219.2	1067	gAc/gTc	22/22	0.283065886978894	3	FACETS	1	0.953	1	0.512	0.478	0.546	INDETERMINATE	1	TRUE	1	0.58864499764157	3		381	1066	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913355	NA	P-0014548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	245	327	0	ENST00000288602.6:c.1406G>T	p.Gly469Val	p.G469V	ENST00000288602	NM_004333.4	469	gGa/gTa	11/18	1	2	FACETS	0.969	0.908	1	0.969	0.908	1	CLONAL	1	TRUE	1	0.58864499764157	2		327	859	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528192	103528192	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	331	394	0	ENST00000355739.4:c.3500C>A	p.Ser1167Tyr	p.S1167Y	ENST00000355739	NM_000123.3	1167	tCt/tAt	15/15	0.310667668968549	3	FACETS	1	0.99	1	0.606	0.573	0.64	INDETERMINATE	1	TRUE	1	0.58864499764157	3		394	1201	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160206	22160206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	174	191	0	ENST00000215832.6:c.425C>T	p.Ser142Leu	p.S142L	ENST00000215832	NM_002745.4	142	tCa/tTa	3/9	0.58864499764157	1	FACETS	0.929	0.864	0.995	0.929	0.864	0.995	CLONAL	1	TRUE	0	0.58864499764157	1		191	449	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514199	69514199	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	181	480	0	ENST00000294312.3:c.482C>A	p.Pro161Gln	p.P161Q	ENST00000294312	NM_005117.2	161	cCa/cAa	3/3	0.303656237854411	1	FACETS	0.409	0.377	0.443	0.409	0.377	0.443	INDETERMINATE	1	TRUE	0	0.58864499764157	1		480	1061	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207143	1207144	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	588	754	0	ENST00000326873.7:c.231_232insT	p.Lys78Ter	p.K78*	ENST00000326873	NM_000455.4	77	-/T	1/10	0.58864499764157	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.58864499764157	1		754	1348	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600329	10600329	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	380	479	0	ENST00000171111.5:c.1526G>T	p.Gly509Val	p.G509V	ENST00000171111	NM_203500.1	509	gGg/gTg	4/6	0.58864499764157	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.58864499764157	1		479	821	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505391	25505391	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	243	361	0	ENST00000264709.3:c.367G>T	p.Glu123Ter	p.E123*	ENST00000264709	NM_175629.2	123	Gag/Tag	4/23	1	2	FACETS	0.924	0.864	0.984	0.924	0.864	0.984	CLONAL	1	TRUE	1	0.58864499764157	2		361	894	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484199	8484199	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	304	366	0	ENST00000356435.5:c.3333del	p.Lys1111AsnfsTer13	p.K1111Nfs*13	ENST00000356435		1111	aaG/aa	19/35	0.58864499764157	1	FACETS	0.948	0.898	0.998	0.948	0.898	0.998	CLONAL	1	TRUE	0	0.58864499764157	1		366	769	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0014556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	239	242	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.585479293991306	2		242	742	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171657	36171657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	156	325	0	ENST00000300305.3:c.908C>T	p.Ser303Leu	p.S303L	ENST00000300305		303	tCa/tTa	7/8	1	2	FACETS	0.816	0.75	0.885	0.816	0.75	0.885	CLONAL	1	TRUE	1	0.585479293991306	2		325	653	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0014556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	474	861	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.560505449899022	1	FACETS	0.984	0.943	1	0.984	0.943	1	CLONAL	1	TRUE	0	0.585479293991306	1		861	1164	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435160	56435161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755128667	NA	P-0014556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	219	375	0	ENST00000407977.2:c.1976dup	p.Pro660SerfsTer87	p.P660Sfs*87	ENST00000407977		659	ggt/ggGt	9/10	1	2	FACETS	0.883	0.823	0.945	0.883	0.823	0.945	CLONAL	1	TRUE	1	0.585479293991306	2		375	847	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256527	115256528	+	missense_variant	Missense_Mutation	DNP	CT	CT	TA	novel	NA	P-0014556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	411	511	0	ENST00000369535.4:c.183_184delinsTA	p.Gln61_Glu62delinsHisLys	p.Q61_E62delinsHK	ENST00000369535	NM_002524.4	61	caAGaa/caTAaa	3/7	0.553846689020533	2	FACETS	0.848	0.812	0.883	0.848	0.812	0.883	CLONAL	2	TRUE	0	0.585479293991306	2		511	828	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948260	71948260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	418	859	2	ENST00000298229.2:c.2972G>A	p.Gly991Glu	p.G991E	ENST00000298229	NM_001567.3	991	gGg/gAg	26/28	0.53677384733192	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.585479293991306	1		861	997	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030363	49030363	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	135	187	0	ENST00000267163.4:c.1838C>T	p.Pro613Leu	p.P613L	ENST00000267163	NM_000321.2	613	cCa/cTa	19/27	NA	2	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.585479293991306	2		187	386	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518091	103518091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	154	304	0	ENST00000355739.4:c.2029C>T	p.Pro677Ser	p.P677S	ENST00000355739	NM_000123.3	677	Ccc/Tcc	9/15	0.560505449899022	1	FACETS	0.987	0.915	1	0.987	0.915	1	CLONAL	1	TRUE	0	0.585479293991306	1		304	377	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310221	91310221	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	131	327	0	ENST00000355112.3:c.2275A>G	p.Ile759Val	p.I759V	ENST00000355112	NM_000057.2	759	Atc/Gtc	10/22	1	2	FACETS	0.78	0.71	0.852	0.78	0.71	0.852	SUBCLONAL	1	TRUE	1	0.585479293991306	2		327	574	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991914	72991914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	205	410	0	ENST00000268489.5:c.2131C>T	p.Pro711Ser	p.P711S	ENST00000268489	NM_006885.3	711	Ccc/Tcc	2/10	1	2	FACETS	0.814	0.756	0.874	0.814	0.756	0.874	CLONAL	1	TRUE	1	0.585479293991306	2		410	860	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273919	18273919	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1390325962	NA	P-0014556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	251	461	1	ENST00000222254.8:c.1252G>T	p.Asp418Tyr	p.D418Y	ENST00000222254	NM_005027.3	418	Gac/Tac	10/16	0.53677384733192	1	FACETS	0.885	0.833	0.939	0.885	0.833	0.939	CLONAL	1	TRUE	0	0.585479293991306	1		462	685	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645687	12645687	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397516828	NA	P-0014556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	133	235	0	ENST00000251849.4:c.782C>T	p.Pro261Leu	p.P261L	ENST00000251849	NM_002880.3	261	cCt/cTt	7/17	1	2	FACETS	0.981	0.898	1	0.981	0.898	1	CLONAL	1	TRUE	1	0.585479293991306	2		235	463	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933434	49933434	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	221	556	0	ENST00000296474.3:c.2756C>T	p.Pro919Leu	p.P919L	ENST00000296474	NM_002447.2	919	cCc/cTc	11/20	1	2	FACETS	0.929	0.866	0.993	0.929	0.866	0.993	CLONAL	1	TRUE	1	0.585479293991306	2		556	813	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539213	187539213	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	167	333	0	ENST00000441802.2:c.8527C>T	p.Gln2843Ter	p.Q2843*	ENST00000441802	NM_005245.3	2843	Caa/Taa	10/27	1	2	FACETS	0.975	0.901	1	0.975	0.901	1	CLONAL	1	TRUE	1	0.585479293991306	2		333	585	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875669	35875669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	191	343	0	ENST00000303115.3:c.856C>T	p.Leu286Phe	p.L286F	ENST00000303115	NM_002185.3	286	Ctt/Ttt	7/8	1	2	FACETS	0.929	0.862	0.998	0.929	0.862	0.998	CLONAL	1	TRUE	1	0.585479293991306	2		343	702	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045967	26045968	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs761955716	NA	P-0014556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	160	282	0	ENST00000540144.1:c.331_332del	p.Cys111ArgfsTer5	p.C111Rfs*5	ENST00000540144	NM_003531.2	110	cTG/c	1/1	1	2	FACETS	0.914	0.842	0.988	0.914	0.842	0.988	CLONAL	1	TRUE	1	0.585479293991306	2		282	598	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26046048	26046048	+	stop_lost	Nonstop_Mutation	SNP	A	A	C	novel	NA	P-0014556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	139	184	0	ENST00000540144.1:c.410A>C	p.Ter137SerextTer8	p.*137Sext*8	ENST00000540144	NM_003531.2	137	tAa/tCa	1/1	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.585479293991306	2		184	416	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2966415	2966415	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	306	657	0	ENST00000396946.4:c.1765G>A	p.Glu589Lys	p.E589K	ENST00000396946	NM_032415.4	589	Gaa/Aaa	14/25	1	2	FACETS	0.843	0.794	0.893	0.843	0.794	0.893	CLONAL	1	TRUE	1	0.585479293991306	2		657	1240	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595332	141595332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	317	708	0	ENST00000220592.5:c.101C>T	p.Ser34Phe	p.S34F	ENST00000220592	NM_012154.3	34	tCc/tTc	2/19	1	2	FACETS	0.925	0.873	0.978	0.925	0.873	0.978	CLONAL	1	TRUE	1	0.585479293991306	2		708	1171	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128347951	128347951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777744523	NA	P-0014556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	331	590	0	ENST00000265960.3:c.554C>T	p.Ser185Leu	p.S185L	ENST00000265960	NM_001006617.1	185	tCg/tTg	5/12	0.560505449899022	1	FACETS	0.998	0.949	1	0.998	0.949	1	CLONAL	1	TRUE	0	0.585479293991306	1		590	801	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227856	55227857	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	novel	NA	P-0014564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	34	308	0	ENST00000275493.2:c.1323_1324insGTT	p.Val441dup	p.V441dup	ENST00000275493	NM_005228.3	441	-/GTT	12/28	0.229004810185311	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		308	318	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0014573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	112	328	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.989	0.888	1	0.989	0.888	1	CLONAL	1	TRUE	1	0.21	2		328	1078	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11168340	11168340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774784384	NA	P-0014573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	54	421	0	ENST00000361445.4:c.7532G>A	p.Arg2511Gln	p.R2511Q	ENST00000361445	NM_004958.3	2511	cGg/cAg	57/58	0.3	1	FACETS	0.805	0.687	0.933	0.805	0.687	0.933	CLONAL	1	TRUE	0	0.21	1		421	572	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066924	30066924	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	64	495	0	ENST00000331968.5:c.2207A>G	p.Glu736Gly	p.E736G	ENST00000331968	NM_002742.2	736	gAg/gGg	16/18	1	2	FACETS	0.803	0.694	0.921	0.803	0.694	0.921	CLONAL	1	TRUE	1	0.21	2		495	759	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061517	38061517	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	25	404	0	ENST00000250448.2:c.472G>T	p.Asp158Tyr	p.D158Y	ENST00000250448	NM_004496.3	158	Gac/Tac	2/2	1	2	FACETS	0.568	0.447	0.708	0.568	0.447	0.708	SUBCLONAL	1	TRUE	1	0.21	2		404	419	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845619	68845620	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGGA	novel	NA	P-0014573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	89	609	0	ENST00000261769.5:c.868_871dup	p.Asp291GlyfsTer3	p.D291Gfs*3	ENST00000261769	NM_004360.3	289	gcg/gCGGAcg	7/16	0.3	1	FACETS	0.97	0.86	1	0.97	0.86	1	CLONAL	1	TRUE	0	0.21	1		609	782	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233023	55233023	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	49	535	0	ENST00000275493.2:c.1773C>A	p.Cys591Ter	p.C591*	ENST00000275493	NM_005228.3	591	tgC/tgA	15/28	1	2	FACETS	0.687	0.581	0.805	0.687	0.581	0.805	SUBCLONAL	1	TRUE	1	0.21	2		535	679	SUCCESS
EED	8726	MSKCC	GRCh37	11	85975304	85975304	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	121	371	0	ENST00000263360.6:c.725C>T	p.Ala242Val	p.A242V	ENST00000263360	NM_003797.3	242	gCt/gTt	7/12	1	2	FACETS	0.969	0.88	1	0.969	0.88	1	CLONAL	1	TRUE	1	0.470970872987945	2		371	530	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041826	14041827	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0014625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	196	444	2	ENST00000311895.7:c.2374dup	p.Thr792AsnfsTer23	p.T792Nfs*23	ENST00000311895	NM_005236.2	791	-/A	11/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.470970872987945	2		446	758	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188309	10188309	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs869025655	NA	P-0014625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	168	617	0	ENST00000256474.2:c.452T>C	p.Ile151Thr	p.I151T	ENST00000256474	NM_000551.3	151	aTc/aCc	2/3	0.470970872987945	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.470970872987945	1		617	535	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158186	47158186	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	79	536	0	ENST00000409792.3:c.4513del	p.Ser1505LeufsTer10	p.S1505Lfs*10	ENST00000409792	NM_014159.6	1505	Tct/ct	4/21	0.470970872987945	1	FACETS	0.679	0.6	0.761	0.679	0.6	0.761	SUBCLONAL	1	TRUE	0	0.470970872987945	1		536	378	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637750	52637750	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0014625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	72	417	0	ENST00000394830.3:c.2568-2A>G		p.X856_splice	ENST00000394830	NM_018313.4	856			0.470970872987945	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.470970872987945	1		417	213	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0014645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	116	622	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	0.325843880045902	5	FACETS	0.839	0.754	0.93	0.28	0.251	0.31	CLONAL	1	TRUE	2	0.325843880045902	5		622	1263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578445	7578446	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	221	619	0	ENST00000269305.4:c.484dup	p.Ile162AsnfsTer19	p.I162Nfs*19	ENST00000269305	NM_001126112.2	162	atc/aAtc	5/11	0.276598222219822	2	FACETS	1	0.99	1	0.681	0.634	0.73	CLONAL	1	TRUE	0	0.325843880045902	2		619	996	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291780	15291780	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	204	661	0	ENST00000263388.2:c.2986C>T	p.Gln996Ter	p.Q996*	ENST00000263388	NM_000435.2	996	Cag/Tag	18/33	0.208728211943656	3	FACETS	1	0.986	1	0.637	0.59	0.686	CLONAL	1	TRUE	1	0.325843880045902	3		661	1143	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260600	1260600	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	80	572	0	ENST00000310581.5:c.2959C>G	p.Leu987Val	p.L987V	ENST00000310581	NM_198253.2	987	Ctg/Gtg	12/16	0.325843880045902	3	FACETS	0.573	0.503	0.648	0.286	0.251	0.324	SUBCLONAL	1	TRUE	1	0.325843880045902	3		572	997	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109319929	109319929	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	72	648	0	ENST00000436639.2:c.759G>T	p.Trp253Cys	p.W253C	ENST00000436639	NM_014454.2	253	tgG/tgT	5/10	0.307417730548085	3	FACETS	0.518	0.451	0.59	0.259	0.225	0.295	SUBCLONAL	1	TRUE	1	0.325843880045902	3		648	993	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467718	50467718	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	196	686	0	ENST00000331340.3:c.953C>G	p.Ala318Gly	p.A318G	ENST00000331340	NM_006060.4	318	gCc/gGc	8/8	0.325843880045902	5	FACETS	1	0.989	1	0.467	0.431	0.505	CLONAL	1	TRUE	2	0.325843880045902	5		686	1278	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0014654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	117	175	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.429072293191589	2		175	507	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0014654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	192	327	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.319692845986819	2	FACETS	1	0.927	1	0.501	0.463	0.539	CLONAL	1	TRUE	0	0.429072293191589	2		327	894	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061191	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs879499034	NA	P-0014654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	86	512	1	ENST00000250448.2:c.798C>A	p.Phe266Leu	p.F266L	ENST00000250448	NM_004496.3	266	ttC/ttA	2/2	1	2	FACETS	0.681	0.603	0.763	0.681	0.603	0.763	SUBCLONAL	1	TRUE	1	0.429072293191589	2		513	589	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162397	47162398	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0014654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	137	411	0	ENST00000409792.3:c.3728_3729del	p.Ile1243ThrfsTer32	p.I1243Tfs*32	ENST00000409792	NM_014159.6	1243	aTA/a	3/21	0.190877793826675	3	FACETS	0.785	0.719	0.854	0.785	0.719	0.854	INDETERMINATE	2	TRUE	1	0.429072293191589	3		411	494	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275280	142275280	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	81	811	0	ENST00000350721.4:c.2023T>A	p.Phe675Ile	p.F675I	ENST00000350721	NM_001184.3	675	Ttt/Att	9/47	1	2	FACETS	0.575	0.506	0.648	0.575	0.506	0.648	SUBCLONAL	1	TRUE	1	0.429072293191589	2		811	657	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807509	1807509	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0014654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	83	770	1	ENST00000260795.2:c.1678A>T	p.Lys560Ter	p.K560*	ENST00000260795		560	Aag/Tag	12/17	1	2	FACETS	0.406	0.358	0.459	0.406	0.358	0.459	SUBCLONAL	1	TRUE	1	0.429072293191589	2		771	952	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178148	56178160	+	frameshift_variant	Frame_Shift_Del	DEL	AAACTTTCCCCAG	AAACTTTCCCCAG	GAC	novel	NA	P-0014654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	76	561	1	ENST00000399503.3:c.3121_3133delinsGAC	p.Lys1041AspfsTer38	p.K1041Dfs*38	ENST00000399503	NM_005921.1	1041	AAACTTTCCCCAGtc/GACtc	14/20	1	2	FACETS	0.596	0.523	0.675	0.596	0.523	0.675	SUBCLONAL	1	TRUE	1	0.429072293191589	2		562	594	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933593	39933594	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0014769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	82	371	0	ENST00000378444.4:c.1005dup	p.Ser336LeufsTer45	p.S336Lfs*45	ENST00000378444	NM_001123385.1	335	-/C	4/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.223751404528267	2		371	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0014769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	157	485	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.223751404528267	2		485	1006	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0014769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	97	466	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	0.114597877954337	4	FACETS	1	0.912	1	0.515	0.458	0.576	INDETERMINATE	1	FALSE	2	0.223751404528267	4		466	1031	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	229	365	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.96	0.895	1	0.96	0.895	1	CLONAL	1	FALSE	1	0.469597941176179	2		365	1016	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	162	476	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.888	0.816	0.963	0.888	0.816	0.963	CLONAL	1	FALSE	1	0.469597941176179	2		476	777	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	416	333	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.906	0.866	0.946	1	0.997	1	CLONAL	2	FALSE	1	0.469597941176179	2		335	978	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	398	621	1	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.817	0.779	0.856	1	0.996	1	CLONAL	2	FALSE	1	0.469597941176179	2		622	1037	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	20	359	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.11	0.083	0.141	0.11	0.083	0.141	SUBCLONAL	1	FALSE	1	0.469597941176179	2		359	777	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099906	27099906	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140125151	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	226	556	0	ENST00000324856.7:c.3785G>A	p.Arg1262His	p.R1262H	ENST00000324856	NM_006015.4	1262	cGt/cAt	15/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.469597941176179	2		556	895	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521525	46521525	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	341	594	0	ENST00000262741.5:c.883del	p.Met295Ter	p.M295*	ENST00000262741	NM_003629.3	295	Atg/tg	7/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.469597941176179	2		594	1259	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306942	65306942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776082057	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	160	375	0	ENST00000342505.4:c.2635C>T	p.Arg879Cys	p.R879C	ENST00000342505	NM_002227.2	879	Cgt/Tgt	19/25	1	2	FACETS	0.874	0.802	0.948	0.874	0.802	0.948	CLONAL	1	FALSE	1	0.469597941176179	2		375	780	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115269621	115269622	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	295	878	0	ENST00000438362.2:c.1584_1585del	p.Pro529SerfsTer5	p.P529Sfs*5	ENST00000438362	NM_001242891.1	528	tcTCct/tcct	13/20	1	2	FACETS	0.956	0.899	1	0.956	0.899	1	CLONAL	1	FALSE	1	0.469597941176179	2		878	1314	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724269	112724269	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	302	632	0	ENST00000369452.4:c.153A>C	p.Lys51Asn	p.K51N	ENST00000369452	NM_007373.3	51	aaA/aaC	2/9	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.469597941176179	2		632	1185	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189472	94189473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs757691558	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	195	462	0	ENST00000323929.3:c.1532dup	p.Asn511LysfsTer3	p.N511Kfs*3	ENST00000323929	NM_005591.3	511	aat/aaAt	14/20	1	2	FACETS	0.881	0.815	0.949	0.881	0.815	0.949	CLONAL	1	FALSE	1	0.469597941176179	2		462	943	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644452	18644452	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	216	483	0	ENST00000266497.5:c.2630C>A	p.Pro877His	p.P877H	ENST00000266497		877	cCt/cAt	18/31	1	2	FACETS	0.946	0.88	1	0.946	0.88	1	CLONAL	1	FALSE	1	0.469597941176179	2		483	972	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	255	196	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.905	0.846	0.966	0.905	0.846	0.966	CLONAL	1	FALSE	1	0.469597941176179	2		196	1200	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117323	115117323	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	168	348	0	ENST00000257566.3:c.851A>G	p.Tyr284Cys	p.Y284C	ENST00000257566	NM_016569.3	284	tAc/tGc	4/8	1	2	FACETS	0.926	0.852	1	0.926	0.852	1	CLONAL	1	FALSE	1	0.469597941176179	2		348	773	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519115	103519115	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774078839	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	242	487	0	ENST00000355739.4:c.2453C>T	p.Ala818Val	p.A818V	ENST00000355739	NM_000123.3	818	gCg/gTg	11/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.469597941176179	2		487	968	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40678619	40678619	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761636030	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	205	665	2	ENST00000249776.8:c.361G>A	p.Asp121Asn	p.D121N	ENST00000249776	NM_033286.3	121	Gat/Aat	3/9	1	2	FACETS	0.645	0.596	0.695	0.645	0.596	0.695	SUBCLONAL	1	FALSE	1	0.469597941176179	2		667	1354	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	179	411	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	FALSE	1	0.469597941176179	2		411	754	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293075	91293075	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs367543026	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	226	494	0	ENST00000355112.3:c.582del	p.Phe194LeufsTer11	p.F194Lfs*11	ENST00000355112	NM_000057.2	193	Ttt/tt	3/22	1	2	FACETS	0.972	0.906	1	0.972	0.906	1	CLONAL	1	FALSE	1	0.469597941176179	2		494	990	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127688	2127688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779832805	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	220	585	0	ENST00000219476.3:c.2927G>A	p.Arg976Gln	p.R976Q	ENST00000219476	NM_000548.3	976	cGg/cAg	26/42	1	2	FACETS	0.925	0.861	0.991	0.925	0.861	0.991	CLONAL	1	FALSE	1	0.469597941176179	2		585	1013	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349070	11349070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	154	421	1	ENST00000332029.2:c.266C>T	p.Ala89Val	p.A89V	ENST00000332029	NM_003745.1	89	gCg/gTg	2/2	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.469597941176179	2		422	619	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526531	66526531	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	202	440	0	ENST00000358598.2:c.1087T>G	p.Ser363Ala	p.S363A	ENST00000358598	NM_212471.2	363	Tca/Gca	11/11	1	2	FACETS	0.973	0.903	1	0.973	0.903	1	CLONAL	1	FALSE	1	0.469597941176179	2		440	884	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	134	334	1	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	1	2	FACETS	0.936	0.853	1	0.936	0.853	1	CLONAL	1	FALSE	1	0.469597941176179	2		335	610	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604785	48604785	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	165	493	0	ENST00000342988.3:c.1607T>C	p.Leu536Pro	p.L536P	ENST00000342988	NM_005359.5	536	cTa/cCa	12/12	1	2	FACETS	0.832	0.764	0.902	0.832	0.764	0.902	CLONAL	1	FALSE	1	0.469597941176179	2		493	845	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244196	5244196	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs919253826	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	193	547	2	ENST00000357368.4:c.1286C>T	p.Ala429Val	p.A429V	ENST00000357368	NM_002850.3	429	gCg/gTg	11/38	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	1	0.469597941176179	2		549	805	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267448	7267448	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1412618950	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	225	464	0	ENST00000302850.5:c.560C>T	p.Pro187Leu	p.P187L	ENST00000302850	NM_000208.2	187	cCg/cTg	2/22	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.469597941176179	2		464	899	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097228	11097228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201600949	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	258	618	2	ENST00000358026.2:c.719C>T	p.Pro240Leu	p.P240L	ENST00000358026	NM_001128849.1	240	cCg/cTg	4/36	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.469597941176179	2		620	950	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284889	15284889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	286	747	0	ENST00000263388.2:c.4726G>A	p.Glu1576Lys	p.E1576K	ENST00000263388	NM_000435.2	1576	Gag/Aag	25/33	1	2	FACETS	0.961	0.902	1	0.961	0.902	1	CLONAL	1	FALSE	1	0.469597941176179	2		747	1268	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314680	30314680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141578348	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	158	511	0	ENST00000262643.3:c.1229C>T	p.Ala410Val	p.A410V	ENST00000262643	NM_001238.2	410	gCg/gTg	12/12	1	2	FACETS	0.808	0.741	0.878	0.808	0.741	0.878	CLONAL	1	FALSE	1	0.469597941176179	2		511	833	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	269	765	1	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.891	0.834	0.949	0.891	0.834	0.949	CLONAL	1	FALSE	1	0.469597941176179	2		766	1286	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753385	42753385	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555750642	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	223	682	2	ENST00000222329.4:c.879del	p.Ser295AlafsTer16	p.S295Afs*16	ENST00000222329	NM_006494.2	293	ggG/gg	4/4	1	2	FACETS	0.815	0.758	0.875	0.815	0.758	0.875	CLONAL	1	FALSE	1	0.469597941176179	2		684	1165	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906369	50906369	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	244	649	0	ENST00000440232.2:c.1030T>C	p.Trp344Arg	p.W344R	ENST00000440232	NM_002691.3	344	Tgg/Cgg	9/27	1	2	FACETS	0.931	0.87	0.995	0.931	0.87	0.995	CLONAL	1	FALSE	1	0.469597941176179	2		649	1116	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250095	39250095	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	230	562	0	ENST00000402219.2:c.1474G>T	p.Glu492Ter	p.E492*	ENST00000402219	NM_005633.3	492	Gaa/Taa	10/23	1	2	FACETS	0.941	0.877	1	0.941	0.877	1	CLONAL	1	FALSE	1	0.469597941176179	2		562	1041	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141631	202141631	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	226	526	0	ENST00000358485.4:c.919del	p.Arg307GlyfsTer23	p.R307Gfs*23	ENST00000358485	NM_001080125.1	307	Cgg/gg	7/9	1	2	FACETS	0.857	0.798	0.919	0.857	0.798	0.919	CLONAL	1	FALSE	1	0.469597941176179	2		526	1123	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225362470	225362470	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	118	312	0	ENST00000264414.4:c.1707G>T	p.Lys569Asn	p.K569N	ENST00000264414	NM_003590.4	569	aaG/aaT	12/16	1	2	FACETS	0.882	0.798	0.969	0.882	0.798	0.969	CLONAL	1	FALSE	1	0.469597941176179	2		312	570	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309535	30309535	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	291	649	0	ENST00000307677.4:c.487G>T	p.Val163Leu	p.V163L	ENST00000307677	NM_138578.1	163	Gtg/Ttg	2/3	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	FALSE	1	0.469597941176179	2		649	1236	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030877	36030877	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751005087	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	187	535	0	ENST00000358208.4:c.1156G>A	p.Val386Ile	p.V386I	ENST00000358208		386	Gtc/Atc	10/12	1	2	FACETS	0.943	0.872	1	0.943	0.872	1	CLONAL	1	FALSE	1	0.469597941176179	2		535	845	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899050	40899050	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	144	487	0	ENST00000373198.4:c.2220C>G	p.Cys740Trp	p.C740W	ENST00000373198	NM_133170.3	740	tgC/tgG	14/32	1	2	FACETS	0.811	0.741	0.885	0.811	0.741	0.885	CLONAL	1	FALSE	1	0.469597941176179	2		487	756	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764347	39764347	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	235	584	0	ENST00000288319.7:c.765del	p.Arg256GlyfsTer35	p.R256Gfs*35	ENST00000288319	NM_182918.3	255	ccC/cc	7/10	1	2	FACETS	0.855	0.797	0.915	0.855	0.797	0.915	CLONAL	1	FALSE	1	0.469597941176179	2		584	1171	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682360	52682360	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	144	268	0	ENST00000394830.3:c.813G>T	p.Lys271Asn	p.K271N	ENST00000394830	NM_018313.4	271	aaG/aaT	8/30	1	2	FACETS	0.871	0.796	0.95	0.871	0.796	0.95	CLONAL	1	FALSE	1	0.469597941176179	2		268	704	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665215	138665215	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	354	864	1	ENST00000330315.3:c.350G>A	p.Arg117His	p.R117H	ENST00000330315	NM_023067.3	117	cGc/cAc	1/1	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.469597941176179	2		865	1385	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188303	142188304	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	192	527	0	ENST00000350721.4:c.6427dup	p.Ser2143PhefsTer13	p.S2143Ffs*13	ENST00000350721	NM_001184.3	2143	tca/tTca	38/47	1	2	FACETS	0.889	0.822	0.958	0.889	0.822	0.958	CLONAL	1	FALSE	1	0.469597941176179	2		527	920	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447297	187447297	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	193	571	0	ENST00000232014.4:c.896C>T	p.Ala299Val	p.A299V	ENST00000232014	NM_001130845.1	299	gCc/gTc	5/10	1	2	FACETS	0.938	0.869	1	0.938	0.869	1	CLONAL	1	FALSE	1	0.469597941176179	2		571	876	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521103	187521103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs183364307	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	149	384	0	ENST00000441802.2:c.12052G>A	p.Ala4018Thr	p.A4018T	ENST00000441802	NM_005245.3	4018	Gcc/Acc	22/27	1	2	FACETS	0.873	0.799	0.95	0.873	0.799	0.95	CLONAL	1	FALSE	1	0.469597941176179	2		384	727	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638776	176638776	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	248	612	0	ENST00000439151.2:c.3376G>C	p.Gly1126Arg	p.G1126R	ENST00000439151	NM_022455.4	1126	Gga/Cga	5/23	1	2	FACETS	0.906	0.846	0.967	0.906	0.846	0.967	CLONAL	1	FALSE	1	0.469597941176179	2		612	1166	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911051	29911051	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs199474473	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	250	541	0	ENST00000376809.5:c.350A>G	p.His117Arg	p.H117R	ENST00000376809	NM_002116.7	117	cAc/cGc	3/8	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.469597941176179	2		541	887	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677848	117677848	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	152	389	2	ENST00000368508.3:c.4085C>A	p.Ala1362Glu	p.A1362E	ENST00000368508	NM_002944.2	1362	gCa/gAa	25/43	1	2	FACETS	0.916	0.839	0.995	0.916	0.839	0.995	CLONAL	1	FALSE	1	0.469597941176179	2		391	707	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005002	150005002	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	138	340	0	ENST00000253339.5:c.1223C>T	p.Ser408Phe	p.S408F	ENST00000253339		408	tCt/tTt	3/7	1	2	FACETS	0.866	0.789	0.945	0.866	0.789	0.945	CLONAL	1	FALSE	1	0.469597941176179	2		340	679	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	290	850	4	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	1	2	FACETS	0.878	0.825	0.934	0.878	0.825	0.934	CLONAL	1	FALSE	1	0.469597941176179	2		854	1406	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559350	141559350	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	256	511	0	ENST00000220592.5:c.1451C>T	p.Pro484Leu	p.P484L	ENST00000220592	NM_012154.3	484	cCc/cTc	12/19	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.469597941176179	2		511	1044	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs730881677	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	146	397	0	ENST00000304494.5:c.151-1G>T		p.X51_splice	ENST00000304494	NM_000077.4	51			1	2	FACETS	0.929	0.851	1	0.929	0.851	1	CLONAL	1	FALSE	1	0.469597941176179	2		397	669	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128420047	128420047	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	244	649	4	ENST00000265960.3:c.381del	p.Lys127AsnfsTer20	p.K127Nfs*20	ENST00000265960	NM_001006617.1	127	aaA/aa	4/12	1	2	FACETS	0.848	0.791	0.906	0.848	0.791	0.906	CLONAL	1	FALSE	1	0.469597941176179	2		653	1226	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404341	139404341	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35962301	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	283	692	0	ENST00000277541.6:c.2813G>A	p.Arg938Gln	p.R938Q	ENST00000277541	NM_017617.3	938	cGg/cAg	18/34	1	2	FACETS	0.987	0.927	1	0.987	0.927	1	CLONAL	1	FALSE	1	0.469597941176179	2		692	1221	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045514	47045514	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	232	685	0	ENST00000377604.3:c.2484del	p.Glu829SerfsTer18	p.E829Sfs*18	ENST00000377604	NM_001204468.1	827	atC/at	22/24	1	2	FACETS	0.875	0.815	0.937	0.875	0.815	0.937	CLONAL	1	FALSE	1	0.469597941176179	2		685	1129	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617180	100617180	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	254	606	0	ENST00000308731.7:c.569del	p.Pro190GlnfsTer9	p.P190Qfs*9	ENST00000308731	NM_000061.2	190	cCa/ca	7/19	1	2	FACETS	0.959	0.897	1	0.959	0.897	1	CLONAL	1	FALSE	1	0.469597941176179	2		606	1128	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0014832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1270	297	827	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.286800750936808	2		827	1567	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271746	15271747	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs773656789	NA	P-0014832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	79	782	0	ENST00000263388.2:c.6692dup	p.Ala2233GlyfsTer9	p.A2233Gfs*9	ENST00000263388	NM_000435.2	2231	cca/ccCa	33/33	1	2	FACETS	0.486	0.426	0.551	0.486	0.426	0.551	SUBCLONAL	1	TRUE	1	0.286800750936808	2		782	1134	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851423	63851439	+	frameshift_variant	Frame_Shift_Del	DEL	AGACCCACCATGGCCAA	AGACCCACCATGGCCAA	-	novel	NA	P-0014832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	42	382	0	ENST00000279873.7:c.2203_2219del	p.Thr735HisfsTer2	p.T735Hfs*2	ENST00000279873	NM_032199.2	734	cAGACCCACCATGGCCAA/c	10/10	1	2	FACETS	0.411	0.342	0.488	0.411	0.342	0.488	SUBCLONAL	1	TRUE	1	0.286800750936808	2		382	713	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492882	56492891	+	frameshift_variant	Frame_Shift_Del	DEL	AGCCATCAGC	AGCCATCAGC	-	novel	NA	P-0014832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	111	288	0	ENST00000407977.2:c.48_57del	p.Leu17ProfsTer31	p.L17Pfs*31	ENST00000407977		16	ctGCTGATGGCT/ct	2/10	0.179547150551637	2	FACETS	1	0.982	1	0.721	0.65	0.795	CLONAL	1	TRUE	0	0.286800750936808	2		288	537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578183	7578184	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0014862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	1029	931	0	ENST00000269305.4:c.665dup	p.Pro223AlafsTer2	p.P223Afs*2	ENST00000269305	NM_001126112.2	222	ccg/ccCg	6/11	0.854123294496249	5	FACETS	0.967	0.956	0.978	0.967	0.956	0.978	CLONAL	5	TRUE	0	0.874184673505591	5		931	1125	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434122	12434122	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1170672782	NA	P-0014862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	37	480	0	ENST00000287820.6:c.490C>T	p.Arg164Trp	p.R164W	ENST00000287820	NM_015869.4	164	Cgg/Tgg	4/7	0.736070759229991	4	FACETS	0.755	0.628	0.895	0.378	0.314	0.448	SUBCLONAL	1	TRUE	2	0.874184673505591	4		480	210	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099336	157099362	+	inframe_deletion	In_Frame_Del	DEL	CCACCACCACCACCATGCCCACCACCT	CCACCACCACCACCATGCCCACCACCT	-	rs1225430487	NA	P-0014862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	37	378	0	ENST00000346085.5:c.286_312del	p.His96_His104del	p.H96_H104del	ENST00000346085	NM_020732.3	91	caCCACCACCACCACCATGCCCACCACCTc/cac	1/20	0.82156437794817	6	FACETS	0.525	0.433	0.628	0.175	0.144	0.21	SUBCLONAL	1	TRUE	3	0.874184673505591	6		378	443	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0014883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	9	406	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.200359084822734	4	FACETS	0.253	0.166	0.364	0.084	0.055	0.122	SUBCLONAL	1	TRUE	1	0.200359084822734	4		406	427	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913499	NA	P-0014883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	75	286	1	ENST00000345146.2:c.394C>A	p.Arg132Ser	p.R132S	ENST00000345146	NM_005896.2	132	Cgt/Agt	4/10	1	2	FACETS	0.835	0.739	0.936	1	0.986	1	CLONAL	3	TRUE	1	0.200359084822734	2		287	299	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0014883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	548	485	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.200359084822734	2	FACETS	1	0.987	1	1	0.998	1	CLONAL	4	TRUE	0	0.200359084822734	2		485	1293	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464510	25464510	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	74	777	0	ENST00000264709.3:c.2003A>G	p.Asp668Gly	p.D668G	ENST00000264709	NM_175629.2	668	gAc/gGc	17/23	1	2	FACETS	0.71	0.62	0.808	0.71	0.62	0.808	SUBCLONAL	1	TRUE	1	0.200359084822734	2		777	1040	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872107	76872108	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0014883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	50	262	0	ENST00000373344.5:c.5539dup	p.Tyr1847LeufsTer14	p.Y1847Lfs*14	ENST00000373344	NM_000489.3	1847	tat/tTat	22/35	1	1	FACETS	0.92	0.788	1	1	0.973	1	CLONAL	2	TRUE	0	0.200359084822734	1		262	244	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939163	76939166	+	frameshift_variant	Frame_Shift_Del	DEL	AAAT	AAAT	-	novel	NA	P-0014883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	63	267	0	ENST00000373344.5:c.1582_1585del	p.Ile528LeufsTer33	p.I528Lfs*33	ENST00000373344	NM_000489.3	528	ATTTtt/tt	9/35	1	1	FACETS	1	0.955	1	1	0.983	1	CLONAL	2	TRUE	0	0.200359084822734	1		267	235	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0014948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	175	654	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.231760887511926	1	FACETS	0.643	0.592	0.696	0.643	0.592	0.696	INDETERMINATE	1	TRUE	0	0.43796299734507	1		654	971	SUCCESS
APC	324	MSKCC	GRCh37	5	112157657	112157658	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0014948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	84	399	0	ENST00000257430.4:c.1378dup	p.Glu460GlyfsTer4	p.E460Gfs*4	ENST00000257430	NM_000038.5	459	-/G	11/16	0.43796299734507	1	FACETS	0.504	0.446	0.567	0.504	0.446	0.567	SUBCLONAL	1	TRUE	0	0.43796299734507	1		399	594	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0014971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	86	402	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.159620646760772	4	FACETS	1	0.948	1	0.565	0.499	0.636	CLONAL	1	TRUE	2	0.245449518804121	4		402	772	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0014971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	112	319	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.182589089169339	4	FACETS	0.941	0.848	1	0.627	0.565	0.692	CLONAL	2	TRUE	1	0.245449518804121	4		319	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0014971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	101	748	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.245449518804121	2		748	554	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912134	114912135	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGG	novel	NA	P-0014971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	72	600	0	ENST00000543371.1:c.1205_1207dup	p.Leu402_Ala403insVal	p.L402_A403insV	ENST00000543371	NM_001198531.1	402	ctg/cTGGtg	11/14	0.00716208741407076	3	FACETS	1	0.937	1	0.558	0.488	0.634	INDETERMINATE	1	TRUE	1	0.245449518804121	3		600	590	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468114	50468114	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	108	428	0	ENST00000331340.3:c.1349G>A	p.Arg450His	p.R450H	ENST00000331340	NM_006060.4	450	cGc/cAc	8/8	0.222393269219459	5	FACETS	0.914	0.826	1	0.914	0.826	1	CLONAL	3	TRUE	2	0.245449518804121	5		428	439	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0015022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	44	393	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	0.773	0.648	0.911	0.773	0.648	0.911	CLONAL	1	TRUE	1	0.23	2		393	495	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591139	67591140	+	missense_variant	Missense_Mutation	DNP	GA	GA	CC	novel	NA	P-0015022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	27	346	0	ENST00000274335.5:c.1732_1733delinsCC	p.Asp578Pro	p.D578P	ENST00000274335		578	GAc/CCc	12/15	1	2	FACETS	0.591	0.47	0.73	0.591	0.47	0.73	SUBCLONAL	1	TRUE	1	0.23	2		346	397	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106405	27106406	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCT	novel	NA	P-0015022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	44	565	0	ENST00000324856.7:c.6018_6021dup	p.Leu2008AlafsTer26	p.L2008Afs*26	ENST00000324856	NM_006015.4	2006	ggg/gGGCTgg	20/20	1	2	FACETS	0.575	0.481	0.68	0.575	0.481	0.68	SUBCLONAL	1	TRUE	1	0.23	2		565	665	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624262	89624262	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	80	361	0	ENST00000371953.3:c.36del	p.Asn12LysfsTer12	p.N12Kfs*12	ENST00000371953	NM_000314.4	12	aaC/aa	1/9	1	2	FACETS	0.844	0.747	0.947	1	0.981	1	CLONAL	2	TRUE	1	0.23	2		361	412	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601231	28601231	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs534055748	NA	P-0015022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	45	499	0	ENST00000241453.7:c.2201A>G	p.Asn734Ser	p.N734S	ENST00000241453	NM_004119.2	734	aAt/aGt	17/24	1	2	FACETS	0.595	0.499	0.701	0.595	0.499	0.701	SUBCLONAL	1	TRUE	1	0.23	2		499	658	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0000015-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	56	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.503083733729778	3	FACETS	1	0.898	1	1	0.898	1	CLONAL	2	TRUE	1	0.50481099350364	3		249	136	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0000015-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	61	515	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.50481099350364	1	FACETS	0.941	0.826	1	0.941	0.826	1	CLONAL	1	TRUE	0	0.50481099350364	1		516	192	SUCCESS
ALK	238	MSKCC	GRCh37	2	29450535	29450535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000015-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	47	881	1	ENST00000389048.3:c.2819G>A	p.Gly940Asp	p.G940D	ENST00000389048	NM_004304.4	940	gGc/gAc	17/29	0.50481099350364	2	FACETS	0.766	0.652	0.889	0.383	0.326	0.445	SUBCLONAL	1	TRUE	0	0.50481099350364	2		882	243	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000015-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	45	558	0	ENST00000206249.3:c.1607T>A	p.Leu536His	p.L536H	ENST00000206249	NM_000125.3	536	cTc/cAc	8/8	0.50481099350364	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.50481099350364	1		558	123	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144485	58144485	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000015-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	84	614	0	ENST00000257904.6:c.586G>C	p.Asp196His	p.D196H	ENST00000257904	NM_000075.3	196	Gac/Cac	5/8	0.50481099350364	4	FACETS	1	0.957	1	0.582	0.517	0.652	CLONAL	1	TRUE	2	0.50481099350364	4		614	430	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440637	56440637	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000015-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	79	1148	1	ENST00000407977.2:c.581G>C	p.Trp194Ser	p.W194S	ENST00000407977		194	tGg/tCg	5/10	0.50481099350364	7	FACETS	0.829	0.728	0.938			1	CLONAL	1	TRUE	NA	0.50481099350364	7		1149	854	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0000015-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	75	647	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	0.245786611782919	4	FACETS	0.987	0.868	1	0.329	0.289	0.372	INDETERMINATE	1	TRUE	1	0.50481099350364	4		647	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0000055-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	390	389	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.376127729282209	1	FACETS	0.774	0.737	0.811	1	0.996	1	SUBCLONAL	2	TRUE	0	0.376127729282209	1		390	1088	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256510	115256510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000055-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	195	462	0	ENST00000369535.4:c.201G>A	p.Met67Ile	p.M67I	ENST00000369535	NM_002524.4	67	atG/atA	3/7	0.350388883765222	2	FACETS	1	0.988	1	0.669	0.62	0.719	CLONAL	1	TRUE	0	0.376127729282209	2		462	775	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231242	142231242	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000055-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	46	418	0	ENST00000350721.4:c.4712C>T	p.Ser1571Phe	p.S1571F	ENST00000350721	NM_001184.3	1571	tCt/tTt	27/47	0.167974107518124	5	FACETS	0.482	0.404	0.568	0.161	0.134	0.19	INDETERMINATE	1	TRUE	2	0.376127729282209	5		418	794	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0000055-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	227	538	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	0.167974107518124	5	FACETS	0.812	0.756	0.871	0.542	0.504	0.581	INDETERMINATE	2	TRUE	2	0.376127729282209	5		538	1162	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281521	15281521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000055-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	61	364	0	ENST00000263388.2:c.4852G>A	p.Glu1618Lys	p.E1618K	ENST00000263388	NM_000435.2	1618	Gag/Aag	26/33	1	2	FACETS	0.357	0.307	0.412	0.357	0.307	0.412	SUBCLONAL	1	TRUE	1	0.376127729282209	2		364	908	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589575	67589576	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000055-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	207	257	0	ENST00000274335.5:c.1344dup	p.Leu449IlefsTer3	p.L449Ifs*3	ENST00000274335		446	-/A	10/15	0.332847818380461	4	FACETS	0.798	0.741	0.857	0.798	0.741	0.857	SUBCLONAL	2	TRUE	2	0.376127729282209	4		257	949	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624293	89624293	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs876661244	NA	P-0000104-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	104	161	0	ENST00000371953.3:c.67T>G	p.Leu23Val	p.L23V	ENST00000371953	NM_000314.4	23	Tta/Gta	1/9	1	2	FACETS	0.923	0.83	1	0.923	0.83	1	CLONAL	1	TRUE	1	0.46276363434203	2		161	487	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692887	89692887	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000104-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	79	133	0	ENST00000371953.3:c.371G>C	p.Cys124Ser	p.C124S	ENST00000371953	NM_000314.4	124	tGt/tCt	5/9	1	2	FACETS	0.819	0.724	0.92	0.819	0.724	0.92	CLONAL	1	TRUE	1	0.46276363434203	2		133	417	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061240	38061240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000104-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	257	351	0	ENST00000250448.2:c.749C>T	p.Ser250Phe	p.S250F	ENST00000250448	NM_004496.3	250	tCc/tTc	2/2	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.46276363434203	2		351	854	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845682	68845682	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000104-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	151	397	1	ENST00000261769.5:c.928G>T	p.Glu310Ter	p.E310*	ENST00000261769	NM_004360.3	310	Gag/Tag	7/16	0.46276363434203	1	FACETS	0.987	0.909	1	0.987	0.909	1	CLONAL	1	TRUE	0	0.46276363434203	1		398	508	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344075	118344076	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000104-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	125	262	0	ENST00000534358.1:c.2206dup	p.Arg736LysfsTer7	p.R736Kfs*7	ENST00000534358	NM_005933.3	734	aga/agAa	3/36	1	2	FACETS	0.923	0.839	1	0.923	0.839	1	CLONAL	1	TRUE	1	0.46276363434203	2		262	585	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0000136-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	8	250	2	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.180901761766172	6	FACETS	0.269	0.173	0.395	0.09	0.057	0.132	INDETERMINATE	1	TRUE	3	0.453679736437376	6		252	250	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264010	16264011	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000136-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	205	559	0	ENST00000375759.3:c.10381dup	p.Thr3461AsnfsTer17	p.T3461Nfs*17	ENST00000375759	NM_015001.2	3460	cca/ccAa	12/15	0.165277636507424	4	FACETS	0.936	0.871	1	0.936	0.871	1	INDETERMINATE	2	TRUE	2	0.453679736437376	4		559	702	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115830	8115837	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGGCCG	CCCGGCCG	-	novel	NA	P-0000136-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	381	551	0	ENST00000346208.3:c.1179_1186del	p.Ala394LeufsTer110	p.A394Lfs*110	ENST00000346208		392	aaCCCGGCCGcc/aacc	6/6	0.340298590086211	3	FACETS	0.952	0.906	0.999	0.952	0.906	0.999	CLONAL	2	TRUE	1	0.453679736437376	3		551	1082	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162722894	162722894	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000242-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	89	256	0	ENST00000367921.3:c.92G>T	p.Arg31Leu	p.R31L	ENST00000367921	NM_006182.2	31	cGc/cTc	4/18	0.173141847322382	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	FALSE	2	0.173141847322382	4		256	527	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520006	NA	P-0000242-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	92	466	0	ENST00000269305.4:c.821T>G	p.Val274Gly	p.V274G	ENST00000269305	NM_001126112.2	274	gTt/gGt	8/11	NA	2	FACETS	0.919	0.819	1			1	INDETERMINATE	2	FALSE	NA	0.173141847322382	2		466	578	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252962	36252962	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs74315451	NA	P-0000242-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	43	150	0	ENST00000300305.3:c.400G>C	p.Ala134Pro	p.A134P	ENST00000300305		134	Gct/Cct	4/8	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.173141847322382	2		150	345	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860461	151860462	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000242-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	99	363	0	ENST00000262189.6:c.10200dup	p.Lys3401Ter	p.K3401*	ENST00000262189	NM_170606.2	3400	-/T	43/59	0.173141847322382	3	FACETS	0.886	0.792	0.987	0.886	0.792	0.987	CLONAL	2	FALSE	1	0.173141847322382	3		363	701	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0000247-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	193	315	2	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	0.636030990266093	4	FACETS	0.898	0.83	0.968	0.449	0.415	0.484	CLONAL	1	FALSE	2	0.735954676124388	4		317	1014	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094477	27094477	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000247-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	173	305	0	ENST00000324856.7:c.3185G>A	p.Gly1062Asp	p.G1062D	ENST00000324856	NM_006015.4	1062	gGt/gAt	11/20	0.710711330166276	3	FACETS	0.833	0.768	0.9	0.417	0.384	0.45	CLONAL	1	FALSE	1	0.735954676124388	3		305	772	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670705	86670705	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000247-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	68	189	0	ENST00000274376.6:c.1983A>C	p.Lys661Asn	p.K661N	ENST00000274376	NM_002890.2	661	aaA/aaC	15/25	0.710711330166276	3	FACETS	0.373	0.324	0.426	0.186	0.162	0.213	SUBCLONAL	1	FALSE	1	0.735954676124388	3		189	678	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468094	50468094	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000247-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4533	458	232	0	ENST00000331340.3:c.1329G>C	p.Glu443Asp	p.E443D	ENST00000331340	NM_006060.4	443	gaG/gaC	8/8	0.735954676124388	22	FACETS	1	0.974	1			1	CLONAL	2	FALSE	NA	0.735954676124388	22		232	4991	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468158	50468158	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000247-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5774	648	273	0	ENST00000331340.3:c.1393G>T	p.Glu465Ter	p.E465*	ENST00000331340	NM_006060.4	465	Gaa/Taa	8/8	0.735954676124388	22	FACETS	1	0.992	1			1	CLONAL	2	FALSE	NA	0.735954676124388	22		273	6422	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134423	41134423	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148177044	NA	P-0000247-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1692	206	709	2	ENST00000379561.5:c.1205C>T	p.Thr402Met	p.T402M	ENST00000379561	NM_002015.3	402	aCg/aTg	2/3	0.735954676124388	3	FACETS	0.403	0.372	0.436	0.202	0.186	0.218	SUBCLONAL	1	FALSE	1	0.735954676124388	3		711	1898	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005454	42005454	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000247-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	59	561	3	ENST00000219905.7:c.3190G>T	p.Glu1064Ter	p.E1064*	ENST00000219905	NM_001164273.1	1064	Gag/Tag	9/24	0.635622321511561	3	FACETS	0.205	0.175	0.237	0.068	0.058	0.079	SUBCLONAL	1	FALSE	0	0.735954676124388	3		564	1071	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965221	81965221	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000247-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	281	522	0	ENST00000359376.3:c.2701C>T	p.Gln901Ter	p.Q901*	ENST00000359376	NM_002661.3	901	Cag/Tag	25/33	0.559322889522637	4	FACETS	0.98	0.919	1	0.327	0.306	0.348	CLONAL	1	FALSE	1	0.735954676124388	4		522	1353	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0000276-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	44	509	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	0.3	2		509	280	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281429	142281429	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1406216731	NA	P-0000276-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	47	353	0	ENST00000350721.4:c.815C>T	p.Ser272Leu	p.S272L	ENST00000350721	NM_001184.3	272	tCa/tTa	4/47	0.236707953822675	1	FACETS	0.761	0.644	0.888	0.761	0.644	0.888	SUBCLONAL	1	FALSE	0	0.3	1		353	350	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772210	68772210	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121964875	NA	P-0000276-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	71	779	2	ENST00000261769.5:c.59G>A	p.Trp20Ter	p.W20*	ENST00000261769	NM_004360.3	20	tGg/tAg	2/16	0.3	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	0	0.3	1		781	346	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061187	38061188	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTT	novel	NA	P-0000276-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	44	284	0	ENST00000250448.2:c.799_801dup	p.Lys267dup	p.K267dup	ENST00000250448	NM_004496.3	267	-/AAG	2/2	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	FALSE	1	0.3	2		284	249	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164774	36164775	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0000276-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	42	462	0	ENST00000300305.3:c.1100dup	p.Met368HisfsTer232	p.M368Hfs*232	ENST00000300305		367	ggc/ggGc	8/8	0.13647054780707	4	FACETS	0.989	0.828	1	0.495	0.414	0.584	INDETERMINATE	1	FALSE	2	0.3	4		462	368	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000285-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	220	199	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	0.745463896151672	1	FACETS	0.871	0.823	0.92	0.871	0.823	0.92	CLONAL	1	TRUE	0	0.745463896151672	1		200	425	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11301713	11301713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201601333	NA	P-0000285-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	271	267	0	ENST00000361445.4:c.1438G>A	p.Ala480Thr	p.A480T	ENST00000361445	NM_004958.3	480	Gcc/Acc	10/58	0.745463896151672	1	FACETS	0.948	0.903	0.993	0.948	0.903	0.993	CLONAL	1	TRUE	0	0.745463896151672	1		267	481	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746054	162746054	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000285-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	86	283	0	ENST00000367921.3:c.2177T>C	p.Ile726Thr	p.I726T	ENST00000367921	NM_006182.2	726	aTa/aCa	16/18	0.726370270681034	2	FACETS	0.219	0.193	0.247	0.11	0.096	0.124	SUBCLONAL	1	TRUE	0	0.745463896151672	2		283	1053	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176678845	176678845	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1554198434	NA	P-0000285-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	80	189	0	ENST00000439151.2:c.4756T>C	p.Cys1586Arg	p.C1586R	ENST00000439151	NM_022455.4	1586	Tgt/Cgt	12/23	0.745463896151672	1	FACETS	0.299	0.264	0.336	0.299	0.264	0.336	SUBCLONAL	1	TRUE	0	0.745463896151672	1		189	451	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968259	2968259	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000285-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	402	497	0	ENST00000396946.4:c.1727G>A	p.Arg576His	p.R576H	ENST00000396946	NM_032415.4	576	cGc/cAc	13/25	0.252339274185213	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.745463896151672	0		497	1185	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508064	106508064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000285-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	47	79	0	ENST00000359195.3:c.58C>T	p.Arg20Cys	p.R20C	ENST00000359195	NM_002649.2	20	Cgc/Tgc	2/11	1	2	FACETS	0.378	0.32	0.441	0.378	0.32	0.441	SUBCLONAL	1	TRUE	1	0.745463896151672	2		79	334	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685315	89685315	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1554897280	NA	P-0000285-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	304	281	1	ENST00000371953.3:c.209+1G>A		p.X70_splice	ENST00000371953	NM_000314.4	70			0.745463896151672	1	FACETS	0.94	0.898	0.983	0.94	0.898	0.983	CLONAL	1	TRUE	0	0.745463896151672	1		282	544	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155090	108155090	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1388457632	NA	P-0000285-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	503	375	0	ENST00000278616.4:c.3883C>A	p.Leu1295Ile	p.L1295I	ENST00000278616	NM_000051.3	1295	Ctt/Att	26/63	0.745463896151672	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.745463896151672	1		375	838	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656226	18656226	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000285-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	153	206	0	ENST00000266497.5:c.2905A>G	p.Met969Val	p.M969V	ENST00000266497		969	Atg/Gtg	21/31	0.745463896151672	1	FACETS	0.406	0.373	0.441	0.406	0.373	0.441	SUBCLONAL	1	TRUE	0	0.745463896151672	1		206	634	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219425	133219425	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000285-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	210	482	0	ENST00000320574.5:c.4709G>A	p.Arg1570Gln	p.R1570Q	ENST00000320574	NM_006231.2	1570	cGa/cAa	36/49	0.745463896151672	1	FACETS	0.281	0.26	0.303	0.281	0.26	0.303	SUBCLONAL	1	TRUE	0	0.745463896151672	1		482	1258	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103346	2103346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777459404	NA	P-0000285-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	313	243	0	ENST00000219476.3:c.229G>A	p.Ala77Thr	p.A77T	ENST00000219476	NM_000548.3	77	Gca/Aca	4/42	0.745463896151672	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.745463896151672	1		243	512	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138093	2138093	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000285-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	430	430	0	ENST00000219476.3:c.5113G>A	p.Asp1705Asn	p.D1705N	ENST00000219476	NM_000548.3	1705	Gac/Aac	40/42	0.745463896151672	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.745463896151672	1		430	707	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14028094	14028094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000285-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	269	181	1	ENST00000311895.7:c.1148C>T	p.Ala383Val	p.A383V	ENST00000311895	NM_005236.2	383	gCa/gTa	7/11	0.745463896151672	1	FACETS	0.957	0.911	1	0.957	0.911	1	CLONAL	1	TRUE	0	0.745463896151672	1		182	473	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884289	37884289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000285-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	289	240	0	ENST00000269571.5:c.3760C>T	p.Pro1254Ser	p.P1254S	ENST00000269571		1254	Cca/Tca	27/27	0.745463896151672	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.745463896151672	1		240	472	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36028535	36028535	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000285-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	101	365	0	ENST00000358208.4:c.877A>G	p.Thr293Ala	p.T293A	ENST00000358208		293	Acc/Gcc	8/12	0.745463896151672	1	FACETS	0.203	0.181	0.227	0.203	0.181	0.227	SUBCLONAL	1	TRUE	0	0.745463896151672	1		365	837	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035075	37035075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs63750081	NA	P-0000285-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	695	257	0	ENST00000231790.2:c.37del	p.Glu13ArgfsTer4	p.E13Rfs*4	ENST00000231790	NM_000249.3	13	Gag/ag	1/19	0.745463896151672	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.745463896151672	1		257	971	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289259	33289260	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0000285-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	281	188	0	ENST00000374542.5:c.292_293del	p.Leu98ValfsTer13	p.L98Vfs*13	ENST00000374542	NM_001141970.1	98	CTg/g	3/8	0.745463896151672	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.745463896151672	1		188	461	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572161	64572161	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000285-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	112	134	0	ENST00000312049.6:c.1478del	p.Pro493ArgfsTer66	p.P493Rfs*66	ENST00000312049	NM_130799.2	493	cCg/cg	10/10	0.745463896151672	1	FACETS	0.706	0.646	0.767	0.706	0.646	0.767	SUBCLONAL	1	TRUE	0	0.745463896151672	1		134	267	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307493	118307498	+	inframe_deletion	In_Frame_Del	DEL	CCTCGT	CCTCGT	-	novel	NA	P-0000285-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	149	368	0	ENST00000534358.1:c.267_272del	p.Ser97_Ser98del	p.S97_S98del	ENST00000534358	NM_005933.3	89	gCCTCGTct/gct	1/36	0.745463896151672	1	FACETS	0.255	0.232	0.278	0.255	0.232	0.278	SUBCLONAL	1	TRUE	0	0.745463896151672	1		368	985	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2105476	2105477	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0000285-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	470	318	0	ENST00000219476.3:c.557dup	p.Asn187GlnfsTer2	p.N187Qfs*2	ENST00000219476	NM_000548.3	185	-/T	6/42	0.745463896151672	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.745463896151672	1		318	751	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882019	NA	P-0000285-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	287	246	0	ENST00000269305.4:c.455del	p.Pro152ArgfsTer18	p.P152Rfs*18	ENST00000269305	NM_001126112.2	152	cCg/cg	5/11	0.745463896151672	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.745463896151672	1		246	456	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0000300-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	101	366	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		366	848	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913252	39913253	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs797044647	NA	P-0000300-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	71	737	0	ENST00000378444.4:c.4862dup	p.Gly1622ArgfsTer7	p.G1622Rfs*7	ENST00000378444	NM_001123385.1	1621	cca/ccCa	14/15	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		737	1184	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226564961	226564961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1352340038	NA	P-0000337-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	167	365	0	ENST00000366794.5:c.1789G>A	p.Gly597Ser	p.G597S	ENST00000366794	NM_001618.3	597	Ggt/Agt	13/23	0.376035309611836	3	FACETS	1	0.971	1			1	CLONAL	1	TRUE	NA	0.376035309611836	3		365	942	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371908	55371908	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs750714789	NA	P-0000337-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	38	256	0	ENST00000297316.4:c.598G>T	p.Gly200Cys	p.G200C	ENST00000297316	NM_022454.3	200	Ggc/Tgc	2/2	0.376035309611836	7	FACETS	1	0.88	1			1	CLONAL	1	TRUE	NA	0.376035309611836	7		256	363	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115854	8115855	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0000337-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1787	201	1563	0	ENST00000346208.3:c.1201dup	p.Ser401PhefsTer106	p.S401Ffs*106	ENST00000346208		400	-/T	6/6	0.376035309611836	5	FACETS	0.841	0.776	0.909			1	CLONAL	1	TRUE	NA	0.376035309611836	5		1563	1988	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551866	150551866	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000337-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1430	128	545	0	ENST00000369026.2:c.141G>C	p.Glu47Asp	p.E47D	ENST00000369026	NM_021960.4	47	gaG/gaC	1/3	0.376035309611836	14	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.376035309611836	14		545	1558	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721027	176721027	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000337-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	153	617	0	ENST00000439151.2:c.6658G>A	p.Glu2220Lys	p.E2220K	ENST00000439151	NM_022455.4	2220	Gag/Aag	23/23	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.376035309611836	2		617	648	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000386-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	28	140	0				ENST00000310581	NM_198253.2	-/1132			0.265695273191892	4	FACETS	1	0.93	1	1	0.93	1	INDETERMINATE	2	TRUE	2	0.587246129918985	4		140	61	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833947	44833948	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0000386-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	80	295	0	ENST00000377967.4:c.372_373insTT	p.Asp125LeufsTer56	p.D125Lfs*56	ENST00000377967	NM_021140.2	124	tct/tcTTt	4/29	1	1	FACETS	0.867	0.804	0.925	1	0.988	1	CLONAL	2	TRUE	0	0.587246129918985	1		295	111	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418391	49418391	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000386-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	28	296	0	ENST00000301067.7:c.16022C>A	p.Ser5341Ter	p.S5341*	ENST00000301067	NM_003482.3	5341	tCa/tAa	50/54	0.409225701645536	3	FACETS	0.857	0.694	1	0.428	0.347	0.519	CLONAL	1	TRUE	1	0.587246129918985	3		296	144	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485909	40485909	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000386-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	25	550	0	ENST00000264657.5:c.956G>A	p.Ser319Asn	p.S319N	ENST00000264657	NM_139276.2	319	aGt/aAt	9/24	0.142259569036029	1	FACETS	0.358	0.284	0.441	0.358	0.284	0.441	INDETERMINATE	1	TRUE	0	0.587246129918985	1		550	168	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376455	15376455	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0000386-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	21	461	0	ENST00000263377.2:c.560-1G>T		p.X187_splice	ENST00000263377	NM_058243.2	187			0.563290912760291	4	FACETS	0.597	0.462	0.753	0.199	0.154	0.251	SUBCLONAL	1	TRUE	1	0.587246129918985	4		461	190	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31372595	31372595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749755940	NA	P-0000386-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	26	382	0	ENST00000328111.2:c.236G>A	p.Gly79Glu	p.G79E	ENST00000328111	NM_006892.3	79	gGg/gAg	4/23	0.587246129918985	4	FACETS	0.598	0.476	0.737	0.199	0.158	0.246	SUBCLONAL	1	TRUE	1	0.587246129918985	4		382	235	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107095	27107096	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0000386-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	67	196	0	ENST00000324856.7:c.6711_6712del	p.Leu2238AlafsTer39	p.L2238Afs*39	ENST00000324856	NM_006015.4	2236	CGc/c	20/20	0.247891023114702	3	FACETS	1	0.915	1	1	0.915	1	INDETERMINATE	2	TRUE	1	0.587246129918985	3		196	144	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577035	7577036	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0000412-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	27	369	0	ENST00000269305.4:c.902dup	p.Gly302ArgfsTer4	p.G302Rfs*4	ENST00000269305	NM_001126112.2	301	cca/ccCa	8/11	0.350492199131415	3	FACETS	0.281	0.223	0.347	0.14	0.111	0.174	INDETERMINATE	1	TRUE	1	0.677519488224861	3		369	380	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031970	26031970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000447-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	487	176	0	ENST00000244661.2:c.319G>A	p.Asp107Asn	p.D107N	ENST00000244661	NM_003537.3	107	Gac/Aac	1/1	0.479166717660561	6	FACETS	1	0.968	1			1	CLONAL	4	TRUE	NA	0.479166717660561	6		176	988	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243829	41243829	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000447-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	44	447	0	ENST00000357654.3:c.3719A>T	p.Gln1240Leu	p.Q1240L	ENST00000357654	NM_007294.3	1240	cAg/cTg	10/23	0.440286761079277	2	FACETS	0.294	0.246	0.347	0.147	0.123	0.174	SUBCLONAL	1	TRUE	0	0.479166717660561	2		447	625	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577074	7577075	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0000447-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	336	420	0	ENST00000269305.4:c.863dup	p.Asn288LysfsTer18	p.N288Kfs*18	ENST00000269305	NM_001126112.2	288	aat/aaAt	8/11	0.440286761079277	2	FACETS	0.818	0.777	0.86	0.818	0.777	0.86	CLONAL	2	TRUE	0	0.479166717660561	2		420	857	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0000476-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	30	498	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	0.698553909968268	1	FACETS	0.156	0.125	0.19	0.156	0.125	0.19	SUBCLONAL	1	TRUE	0	0.698553909968268	1		498	359	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231539	5231539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760884281	NA	P-0000490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	129	356	0	ENST00000357368.4:c.1937C>T	p.Thr646Met	p.T646M	ENST00000357368	NM_002850.3	646	aCg/aTg	14/38	0.159081903179654	0	FACETS	0.646	0.588	0.705			1	INDETERMINATE	1	TRUE	0	0.442269727162295	0		356	504	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170948	56170949	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0000490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	91	176	0	ENST00000399503.3:c.1780dup	p.Ala594GlyfsTer52	p.A594Gfs*52	ENST00000399503	NM_005921.1	592	-/G	10/20	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.442269727162295	2		176	411	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115719	8115720	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	201	371	0	ENST00000346208.3:c.1066dup	p.Met356AsnfsTer15	p.M356Nfs*15	ENST00000346208		355	-/A	6/6	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.442269727162295	2		371	841	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262612	16262612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	61	1028	0	ENST00000375759.3:c.9877G>A	p.Val3293Met	p.V3293M	ENST00000375759	NM_015001.2	3293	Gtg/Atg	11/15	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.314866232865974	2		1028	339	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161284202	161284202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748243732	NA	P-0000491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	123	1580	0	ENST00000367975.2:c.7G>A	p.Ala3Thr	p.A3T	ENST00000367975	NM_003001.3	3	Gcg/Acg	1/6	0.300491931799233	3	FACETS	0.85	0.772	0.931	0.85	0.772	0.931	CLONAL	2	TRUE	1	0.314866232865974	3		1580	532	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736302	243736302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	88	395	0	ENST00000263826.5:c.745C>A	p.Arg249Ser	p.R249S	ENST00000263826	NM_005465.4	249	Cgt/Agt	8/13	0.300491931799233	3	FACETS	0.944	0.837	1	0.472	0.418	0.53	CLONAL	1	TRUE	1	0.314866232865974	3		395	685	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443577	29443577	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758172315	NA	P-0000491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	92	786	0	ENST00000389048.3:c.3640C>T	p.Arg1214Cys	p.R1214C	ENST00000389048	NM_004304.4	1214	Cgc/Tgc	23/29	0.314866232865974	3	FACETS	0.912	0.816	1	0.912	0.816	1	CLONAL	2	TRUE	1	0.314866232865974	3		786	371	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498063	29498063	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs116202066	NA	P-0000491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	161	1769	0	ENST00000389048.3:c.1943C>T	p.Thr648Ile	p.T648I	ENST00000389048	NM_004304.4	648	aCa/aTa	11/29	0.314866232865974	3	FACETS	0.861	0.792	0.933	0.861	0.792	0.933	CLONAL	2	TRUE	1	0.314866232865974	3		1769	687	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668617	52668617	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0000491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	144	1447	0	ENST00000394830.3:c.1301+1G>C		p.X434_splice	ENST00000394830	NM_018313.4	434			0.307868387210952	2	FACETS	0.957	0.879	1	0.957	0.879	1	CLONAL	2	TRUE	0	0.314866232865974	2		1447	478	SUCCESS
ATR	545	MSKCC	GRCh37	3	142218528	142218528	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	101	1577	1	ENST00000350721.4:c.5321G>T	p.Arg1774Ile	p.R1774I	ENST00000350721	NM_001184.3	1774	aGa/aTa	31/47	0.300491931799233	3	FACETS	0.985	0.88	1	0.492	0.44	0.548	CLONAL	1	TRUE	1	0.314866232865974	3		1578	754	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155475	106155475	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	129	1066	0	ENST00000380013.4:c.376G>T	p.Gly126Trp	p.G126W	ENST00000380013	NM_001127208.2	126	Ggg/Tgg	3/11	0.314866232865974	2	FACETS	0.951	0.869	1	0.951	0.869	1	CLONAL	2	TRUE	0	0.314866232865974	2		1066	431	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164836	106164836	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	114	985	1	ENST00000380013.4:c.3704G>C	p.Gly1235Ala	p.G1235A	ENST00000380013	NM_001127208.2	1235	gGa/gCa	6/11	0.314866232865974	2	FACETS	0.912	0.828	0.999	0.912	0.828	0.999	CLONAL	2	TRUE	0	0.314866232865974	2		986	397	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527280	187527280	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	123	944	0	ENST00000441802.2:c.10294G>T	p.Asp3432Tyr	p.D3432Y	ENST00000441802	NM_005245.3	3432	Gat/Tat	17/27	0.314866232865974	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.314866232865974	2		944	361	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882060	36882060	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	144	1531	0	ENST00000358127.4:c.953A>T	p.His318Leu	p.H318L	ENST00000358127	NM_001280556.1	318	cAc/cTc	8/10	0.307868387210952	2	FACETS	0.986	0.906	1	0.986	0.906	1	CLONAL	2	TRUE	0	0.314866232865974	2		1531	464	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196900	108196900	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	101	960	0	ENST00000278616.4:c.6923C>G	p.Ala2308Gly	p.A2308G	ENST00000278616	NM_000051.3	2308	gCc/gGc	47/63	0.314866232865974	3	FACETS	0.855	0.769	0.946	0.855	0.769	0.946	CLONAL	2	TRUE	1	0.314866232865974	3		960	434	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417038	417038	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs560791888	NA	P-0000491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	90	1297	0	ENST00000399788.2:c.3512G>T	p.Ser1171Ile	p.S1171I	ENST00000399788	NM_001042603.1	1171	aGt/aTt	23/28	NA	2	FACETS	1	0.943	1			1	INDETERMINATE	1	TRUE	NA	0.314866232865974	2		1297	523	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383345	4383345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	69	1178	1	ENST00000261254.3:c.139G>A	p.Val47Met	p.V47M	ENST00000261254	NM_001759.3	47	Gtg/Atg	1/5	NA	2	FACETS	0.902	0.787	1			1	INDETERMINATE	1	TRUE	NA	0.314866232865974	2		1179	486	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448141	49448141	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	160	1286	0	ENST00000301067.7:c.459G>T	p.Glu153Asp	p.E153D	ENST00000301067	NM_003482.3	153	gaG/gaT	4/54	0.263098082496757	4	FACETS	0.896	0.828	0.966	0.896	0.828	0.966	CLONAL	3	TRUE	1	0.314866232865974	4		1286	497	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781272	3781272	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	106	1110	0	ENST00000262367.5:c.5093A>T	p.Gln1698Leu	p.Q1698L	ENST00000262367	NM_004380.2	1698	cAg/cTg	30/31	0.314866232865974	3	FACETS	0.88	0.793	0.97	0.88	0.793	0.97	CLONAL	2	TRUE	1	0.314866232865974	3		1110	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934574	NA	P-0000491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	168	1624	0	ENST00000269305.4:c.844C>G	p.Arg282Gly	p.R282G	ENST00000269305	NM_001126112.2	282	Cgg/Ggg	8/11	0.307785777386299	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.314866232865974	2		1624	482	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509525	29509525	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0000491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	110	944	1	ENST00000356175.3:c.731-1G>T		p.X244_splice	ENST00000356175	NM_000267.3	244			0.314866232865974	3	FACETS	0.93	0.841	1	0.93	0.841	1	CLONAL	2	TRUE	1	0.314866232865974	3		945	435	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59770850	59770850	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	164	1700	0	ENST00000259008.2:c.2516G>C	p.Trp839Ser	p.W839S	ENST00000259008	NM_032043.2	839	tGg/tCg	18/20	0.314866232865974	3	FACETS	0.792	0.728	0.858	0.792	0.728	0.858	SUBCLONAL	2	TRUE	1	0.314866232865974	3		1700	761	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132399	11132399	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0000491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	150	1587	0	ENST00000358026.2:c.2617-2A>C		p.X873_splice	ENST00000358026	NM_001128849.1	873			0.307785777386299	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.314866232865974	2		1587	431	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024638	31024638	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs191965193	NA	P-0000491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	165	1622	0	ENST00000375687.4:c.4123G>T	p.Gly1375Trp	p.G1375W	ENST00000375687	NM_015338.5	1375	Ggg/Tgg	13/13	0.314866232865974	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.314866232865974	3		1622	576	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225338988	225338989	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0000491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	34	1690	0	ENST00000264414.4:c.2280_2281insA	p.Arg761ThrfsTer34	p.R761Tfs*34	ENST00000264414	NM_003590.4	760	-/A	16/16	0.300491931799233	3	FACETS	0.374	0.305	0.453	0.187	0.152	0.227	SUBCLONAL	1	TRUE	1	0.314866232865974	3		1690	668	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99440129	99440129	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	246	1278	0	ENST00000268035.6:c.1101del	p.Asn368IlefsTer17	p.N368Ifs*17	ENST00000268035	NM_000875.3	366	cGg/cg	4/21	0.297872791921931	3	FACETS	0.995	0.937	1	0.995	0.937	1	CLONAL	3	TRUE	0	0.314866232865974	3		1278	606	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817775	3817776	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0000491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	199	2475	0	ENST00000262367.5:c.3194_3195dup	p.Ser1066ValfsTer34	p.S1066Vfs*34	ENST00000262367	NM_004380.2	1065	-/GT	16/31	0.314866232865974	3	FACETS	0.811	0.752	0.872	0.811	0.752	0.872	CLONAL	2	TRUE	1	0.314866232865974	3		2475	902	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533910	63533910	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	88	828	0	ENST00000307078.5:c.1244del	p.Glu415GlyfsTer43	p.E415Gfs*43	ENST00000307078	NM_004655.3	415	gAg/gg	6/11	0.314866232865974	4	FACETS	1	0.943	1			1	CLONAL	2	TRUE	NA	0.314866232865974	4		828	339	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546737	9546738	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0000491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	88	1020	0	ENST00000353224.5:c.1284_1285delinsAA	p.His429Asn	p.H429N	ENST00000353224	NM_177990.2	428	tcCCat/tcAAat	5/10	0.314866232865974	5	FACETS	0.996	0.888	1	0.664	0.592	0.741	CLONAL	2	TRUE	2	0.314866232865974	5		1020	413	SUCCESS
AR	367	MSKCC	GRCh37	X	66766350	66766351	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGTGGTGGC	rs1555969922	NA	P-0000560-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	50	41	0	ENST00000374690.3:c.1365_1373dup	p.Gly471_Gly473dup	p.G471_G473dup	ENST00000374690	NM_000044.3	471	-/GGTGGTGGC	1/8	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		41	94	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048631	180048631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1391338478	NA	P-0000560-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	50	278	0	ENST00000261937.6:c.1931C>T	p.Ala644Val	p.A644V	ENST00000261937	NM_182925.4	644	gCg/gTg	13/30	0.3	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		278	260	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183091	32183091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000560-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	59	305	0	ENST00000375023.3:c.1933G>A	p.Asp645Asn	p.D645N	ENST00000375023	NM_004557.3	645	Gac/Aac	12/30	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		305	435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0000562-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	16	409	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.823	0.61	1	0.823	0.61	1	CLONAL	1	TRUE	1	0.18	2		411	216	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0000562-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	71	485	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.18	2		485	624	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0000562-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	36	473	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.887	0.729	1	0.887	0.729	1	CLONAL	1	TRUE	1	0.18	2		473	451	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246482	105246482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000562-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	20	437	0	ENST00000349310.3:c.118G>A	p.Glu40Lys	p.E40K	ENST00000349310	NM_001014432.1	40	Gag/Aag	4/15	1	2	FACETS	0.667	0.51	0.852	0.667	0.51	0.852	SUBCLONAL	1	TRUE	1	0.18	2		437	333	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555687605	NA	P-0000562-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	38	437	1	ENST00000342988.3:c.1610A>G	p.Asp537Gly	p.D537G	ENST00000342988	NM_005359.5	537	gAc/gGc	12/12	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.18	2		438	399	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136980	11136980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000562-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	16	326	0	ENST00000358026.2:c.3173C>T	p.Ser1058Phe	p.S1058F	ENST00000358026	NM_001128849.1	1058	tCc/tTc	23/36	1	2	FACETS	0.624	0.461	0.819	0.624	0.461	0.819	SUBCLONAL	1	TRUE	1	0.18	2		326	285	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521298	187521299	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000562-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	56	575	0	ENST00000441802.2:c.11856dup	p.Gly3953TrpfsTer19	p.G3953Wfs*19	ENST00000441802	NM_005245.3	3952	-/T	22/27	1	2	FACETS	0.85	0.727	0.985	0.85	0.727	0.985	CLONAL	1	TRUE	1	0.18	2		575	732	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0000628-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	6424	517	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.674441019666951	24	FACETS	0.982	0.977	0.987			1	CLONAL	23	TRUE	NA	0.674441019666951	24		517	7098	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0000628-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7742	2074	468	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.674441019666951	24	FACETS	1	0.995	1			1	CLONAL	5	TRUE	NA	0.674441019666951	24		468	9816	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0000628-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	457	409	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.674441019666951	2		409	619	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151625	55151625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571523023	NA	P-0000628-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	651	474	0	ENST00000257290.5:c.2411G>A	p.Arg804Gln	p.R804Q	ENST00000257290	NM_006206.4	804	cGa/cAa	17/23	0.66476362942018	2	FACETS	0.98	0.953	1	0.98	0.953	1	CLONAL	2	TRUE	0	0.674441019666951	2		474	985	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143040	47143041	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTCCACT	novel	NA	P-0000628-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	246	378	0	ENST00000409792.3:c.4918-2_4922dup	p.Asn1643AspfsTer25	p.N1643Dfs*25	ENST00000409792	NM_014159.6	1641	act/acAGTGGACt	8/21	NA	2	FACETS	0.812	0.761	0.865			1	INDETERMINATE	1	TRUE	NA	0.674441019666951	2		378	898	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0000687-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	92	110	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.611925518399191	3	FACETS	1	0.942	1	0.538	0.482	0.597	CLONAL	1	TRUE	1	0.611925518399191	3		110	365	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167577	NA	P-0000687-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	224	112	0	ENST00000257430.4:c.4463del	p.Leu1488TyrfsTer19	p.L1488Yfs*19	ENST00000257430	NM_000038.5	1487	acT/ac	16/16	0.611925518399191	3	FACETS	0.984	0.927	1	0.984	0.927	1	CLONAL	2	TRUE	1	0.611925518399191	3		112	486	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627721	187627721	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000687-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	286	244	0	ENST00000441802.2:c.3261G>C	p.Glu1087Asp	p.E1087D	ENST00000441802	NM_005245.3	1087	gaG/gaC	2/27	1	2	FACETS	0.874	0.822	0.927	0.874	0.822	0.927	CLONAL	1	TRUE	1	0.611925518399191	2		244	1070	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509421	106509421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751167601	NA	P-0000687-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	747	229	1	ENST00000359195.3:c.1415G>A	p.Arg472His	p.R472H	ENST00000359195	NM_002649.2	472	cGt/cAt	2/11	0.611925518399191	5	FACETS	0.931	0.9	0.961	0.931	0.9	0.961	CLONAL	3	TRUE	2	0.611925518399191	5		230	1677	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243923	5243923	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778260386	NA	P-0000687-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	116	152	0	ENST00000357368.4:c.1559C>T	p.Thr520Met	p.T520M	ENST00000357368	NM_002850.3	520	aCg/aTg	11/38	0.611925518399191	3	FACETS	0.958	0.867	1	0.479	0.433	0.526	CLONAL	1	TRUE	1	0.611925518399191	3		152	517	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713350	40713350	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000687-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	88	144	0	ENST00000373198.4:c.4165A>T	p.Arg1389Trp	p.R1389W	ENST00000373198	NM_133170.3	1389	Agg/Tgg	30/32	0.611925518399191	6	FACETS	0.735	0.65	0.826	0.184	0.162	0.207	SUBCLONAL	1	TRUE	2	0.611925518399191	6		144	870	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577115	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000687-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	679	247	0	ENST00000269305.4:c.823dup	p.Cys275LeufsTer31	p.C275Lfs*31	ENST00000269305	NM_001126112.2	275	tgt/tTgt	8/11	0.611925518399191	3	FACETS	0.933	0.907	0.958	0.933	0.907	0.958	CLONAL	3	TRUE	0	0.611925518399191	3		247	1036	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0000714-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	70	265	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.246574140622026	3	FACETS	1	0.966	1	0.648	0.569	0.731	CLONAL	1	TRUE	1	0.387543907625328	3		265	333	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350576	15350578	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs747153554	NA	P-0000714-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	44	154	0	ENST00000263377.2:c.3337_3339del	p.Glu1113del	p.E1113del	ENST00000263377	NM_058243.2	1113	GAG/-	16/20	1	2	FACETS	0.694	0.585	0.815	0.694	0.585	0.815	SUBCLONAL	1	TRUE	1	0.387543907625328	2		154	327	SUCCESS
APC	324	MSKCC	GRCh37	5	112164646	112164646	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000714-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	35	135	0	ENST00000257430.4:c.1720G>T	p.Glu574Ter	p.E574*	ENST00000257430	NM_000038.5	574	Gaa/Taa	14/16	1	2	FACETS	0.616	0.507	0.738	0.616	0.507	0.738	SUBCLONAL	1	TRUE	1	0.387543907625328	2		135	293	SUCCESS
YES1	7525	MSKCC	GRCh37	18	742923	742923	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000714-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	81	376	0	ENST00000314574.4:c.1055C>T	p.Ser352Leu	p.S352L	ENST00000314574	NM_005433.3	352	tCa/tTa	8/12	0.166460551390085	2	FACETS	0.831	0.734	0.934	0.416	0.367	0.467	INDETERMINATE	1	TRUE	0	0.387543907625328	2		376	503	SUCCESS
YES1	7525	MSKCC	GRCh37	18	742959	742959	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000714-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	98	453	0	ENST00000314574.4:c.1019C>G	p.Ser340Cys	p.S340C	ENST00000314574	NM_005433.3	340	tCt/tGt	8/12	0.166460551390085	2	FACETS	0.84	0.751	0.935	0.42	0.375	0.468	INDETERMINATE	1	TRUE	0	0.387543907625328	2		453	602	SUCCESS
YES1	7525	MSKCC	GRCh37	18	742978	742978	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000714-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	98	460	1	ENST00000314574.4:c.1000C>G	p.Pro334Ala	p.P334A	ENST00000314574	NM_005433.3	334	Cca/Gca	8/12	0.166460551390085	2	FACETS	0.814	0.728	0.906	0.407	0.364	0.453	INDETERMINATE	1	TRUE	0	0.387543907625328	2		461	621	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743014	743014	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000714-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	109	441	0	ENST00000314574.4:c.964C>G	p.Gln322Glu	p.Q322E	ENST00000314574	NM_005433.3	322	Cag/Gag	8/12	0.166460551390085	2	FACETS	0.894	0.805	0.989	0.447	0.402	0.495	INDETERMINATE	1	TRUE	0	0.387543907625328	2		441	629	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743066	743066	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1318314308	NA	P-0000714-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	123	418	0	ENST00000314574.4:c.912C>G	p.Ile304Met	p.I304M	ENST00000314574	NM_005433.3	304	atC/atG	8/12	0.166460551390085	2	FACETS	0.981	0.889	1	0.491	0.444	0.539	INDETERMINATE	1	TRUE	0	0.387543907625328	2		418	647	SUCCESS
APC	324	MSKCC	GRCh37	5	112175970	112175970	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1114167552	NA	P-0000714-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	22	163	0	ENST00000257430.4:c.4682del	p.Lys1561ArgfsTer4	p.K1561Rfs*4	ENST00000257430	NM_000038.5	1560	gAa/ga	16/16	1	2	FACETS	0.5	0.389	0.628	0.5	0.389	0.628	SUBCLONAL	1	TRUE	1	0.387543907625328	2		163	227	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579706	7579707	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0000714-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	180	427	0	ENST00000269305.4:c.89dup	p.Asn30LysfsTer13	p.N30Kfs*13	ENST00000269305	NM_001126112.2	30	aac/aaAc	3/11	0.216654103798992	2	FACETS	0.875	0.813	0.938	0.875	0.813	0.938	INDETERMINATE	2	TRUE	0	0.387543907625328	2		427	531	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0000724-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	43	189	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.471688837454593	1	FACETS	0.826	0.702	0.958	0.826	0.702	0.958	CLONAL	1	TRUE	0	0.479652637753298	1		189	165	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285314	212285314	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000724-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	18	223	0	ENST00000342788.4:c.2987C>G	p.Pro996Arg	p.P996R	ENST00000342788	NM_005235.2	996	cCc/cGc	25/28	1	2	FACETS	0.343	0.258	0.442	0.343	0.258	0.442	SUBCLONAL	1	TRUE	1	0.479652637753298	2		223	219	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812260	212812260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751175543	NA	P-0000724-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	55	217	0	ENST00000342788.4:c.316C>T	p.Arg106Cys	p.R106C	ENST00000342788	NM_005235.2	106	Cgt/Tgt	3/28	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.479652637753298	2		217	214	SUCCESS
APC	324	MSKCC	GRCh37	5	112173801	112173801	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs79512956	NA	P-0000724-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	59	181	0	ENST00000257430.4:c.2510C>A	p.Ser837Ter	p.S837*	ENST00000257430	NM_000038.5	837	tCa/tAa	16/16	0.471688837454593	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.479652637753298	1		181	145	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578422	7578423	+	inframe_insertion	In_Frame_Ins	INS	-	-	CATGTGCTG	novel	NA	P-0000724-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	32	138	0	ENST00000269305.4:c.499_507dup	p.Gln167_Met169dup	p.Q167_M169dup	ENST00000269305	NM_001126112.2	167	-/CAGCACATG	5/11	0.479652637753298	1	FACETS	0.73	0.602	0.869	0.73	0.602	0.869	SUBCLONAL	1	TRUE	0	0.479652637753298	1		138	139	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012317	152012317	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000768-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	224	593	0	ENST00000262189.6:c.496C>T	p.Gln166Ter	p.Q166*	ENST00000262189	NM_170606.2	166	Caa/Taa	4/59	0.313633197141558	1	FACETS	1	0.984	1	1	0.984	1	INDETERMINATE	1	TRUE	0	0.741056184837756	1		593	352	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568563	41568563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555911574	NA	P-0000768-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	143	385	0	ENST00000263253.7:c.4513G>A	p.Glu1505Lys	p.E1505K	ENST00000263253	NM_001429.3	1505	Gag/Aag	28/31	0.313633197141558	1	FACETS	0.597	0.55	0.645	0.597	0.55	0.645	INDETERMINATE	1	TRUE	0	0.741056184837756	1		385	407	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261554	142261555	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1043355995	NA	P-0000768-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	161	473	0	ENST00000350721.4:c.3402dup	p.Asn1135Ter	p.N1135*	ENST00000350721	NM_001184.3	1134	-/T	17/47	0.741056184837756	3	FACETS	0.838	0.77	0.908	0.419	0.385	0.454	CLONAL	1	TRUE	1	0.741056184837756	3		473	711	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591135	67591151	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GAGAGACCAATACTTGA	GAGAGACCAATACTTGA	-	novel	NA	P-0000768-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	73	195	0	ENST00000274335.5:c.1728_1744del	p.Arg577ValfsTer19	p.R577Vfs*19	ENST00000274335		576	acGAGAGACCAATACTTGAtg/actg	12/15	0.254560231260995	3	FACETS	0.736	0.647	0.83	0.368	0.323	0.415	INDETERMINATE	1	TRUE	1	0.741056184837756	3		195	367	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0000777-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	349	226	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.73124357668512	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.73124357668512	2		226	466	SUCCESS
APC	324	MSKCC	GRCh37	5	112173345	112173345	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000777-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	95	380	0	ENST00000257430.4:c.2054G>A	p.Trp685Ter	p.W685*	ENST00000257430	NM_000038.5	685	tGg/tAg	16/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.73124357668512	2		380	234	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572022	95572022	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000777-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	86	396	0	ENST00000393063.1:c.3086A>G	p.Asn1029Ser	p.N1029S	ENST00000393063	NM_030621.3	1029	aAt/aGt	20/28	NA	2	FACETS	1	0.905	1			1	INDETERMINATE	1	TRUE	NA	0.73124357668512	2		396	234	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000777-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	35	121	0	ENST00000257430.4:c.3919dup	p.Ile1307AsnfsTer8	p.I1307Nfs*8	ENST00000257430	NM_000038.5	1306	gaa/gAaa	16/16	1	2	FACETS	0.785	0.657	0.921	0.785	0.657	0.921	CLONAL	1	TRUE	1	0.73124357668512	2		121	122	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0000786-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	461	509	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	NA	2	FACETS	0.954	0.923	0.985			1	INDETERMINATE	2	TRUE	NA	0.694066115090055	2		509	696	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022913	27022938	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGCCGCCGCCAGCAGCCTGGGCAA	CCCGCCGCCGCCAGCAGCCTGGGCAA	-	rs797045262	NA	P-0000786-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	22	74	0	ENST00000324856.7:c.31_56del	p.Ser11AlafsTer91	p.S11Afs*91	ENST00000324856	NM_006015.4	7	CCCGCCGCCGCCAGCAGCCTGGGCAAc/c	1/20	0.694066115090055	1	FACETS	0.314	0.246	0.39	0.314	0.246	0.39	SUBCLONAL	1	TRUE	0	0.694066115090055	1		74	132	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293592	1293592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1013341756	NA	P-0000786-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	200	335	0	ENST00000310581.5:c.1409G>A	p.Arg470His	p.R470H	ENST00000310581	NM_198253.2	470	cGc/cAc	2/16	1	2	FACETS	0.922	0.859	0.987	0.922	0.859	0.987	CLONAL	1	TRUE	1	0.694066115090055	2		335	625	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142074	108142074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000786-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	335	401	0	ENST00000278616.4:c.3018G>A	p.Met1006Ile	p.M1006I	ENST00000278616	NM_000051.3	1006	atG/atA	20/63	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.694066115090055	2		401	938	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061007	38061022	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCGGGGGCCGGCGC	GCCCGGGGGCCGGCGC	-	novel	NA	P-0000786-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	140	215	0	ENST00000250448.2:c.967_982del	p.Ala323ProfsTer22	p.A323Pfs*22	ENST00000250448	NM_004496.3	323	GCGCCGGCCCCCGGGCcc/cc	2/2	1	2	FACETS	0.834	0.764	0.905	0.834	0.764	0.905	CLONAL	1	TRUE	1	0.694066115090055	2		215	484	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252856	36252857	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0000786-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	254	306	0	ENST00000300305.3:c.505dup	p.Arg169LysfsTer44	p.R169Kfs*44	ENST00000300305		169	aga/aAga	4/8	1	2	FACETS	0.902	0.847	0.959	0.902	0.847	0.959	CLONAL	1	TRUE	1	0.694066115090055	2		306	811	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882019	NA	P-0000804-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	33	574	0	ENST00000269305.4:c.455dup	p.Pro153AlafsTer28	p.P153Afs*28	ENST00000269305	NM_001126112.2	152	ccg/ccCg	5/11	0.176776363025488	2	FACETS	1	0.914	1	0.609	0.498	0.733	CLONAL	1	TRUE	0	0.191504283380257	2		574	283	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0000820-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	244	552	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		552	1195	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252994	36252995	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0000820-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	38	111	0	ENST00000300305.3:c.367dup	p.Asp123GlyfsTer15	p.D123Gfs*15	ENST00000300305		123	gat/gGat	4/8	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		111	610	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589175	67589176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAAA	novel	NA	P-0000835-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	59	390	1	ENST00000274335.5:c.1164_1167dup	p.Tyr390GlufsTer6	p.Y390Efs*6	ENST00000274335		388	ggg/ggGAAAg	9/15	0.223466963093326	5	FACETS	0.907	0.782	1	0.302	0.26	0.347	INDETERMINATE	1	TRUE	2	0.556896145183968	5		391	429	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221313	1221314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs121913321	NA	P-0000873-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	150	441	1	ENST00000326873.7:c.842dup	p.Leu282AlafsTer3	p.L282Afs*3	ENST00000326873	NM_000455.4	279	ggc/ggCc	6/10	0.433157227205093	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.433157227205093	1		442	453	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724562	162724562	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000873-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	148	396	0	ENST00000367921.3:c.334A>C	p.Ile112Leu	p.I112L	ENST00000367921	NM_006182.2	112	Atc/Ctc	5/18	0.433157227205093	5	FACETS	0.974	0.887	1	0.325	0.295	0.355	CLONAL	1	TRUE	2	0.433157227205093	5		396	1158	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716170	243716170	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000873-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	375	541	0	ENST00000263826.5:c.1024G>T	p.Gly342Trp	p.G342W	ENST00000263826	NM_005465.4	342	Ggg/Tgg	10/13	0.255889751192911	6	FACETS	0.971	0.923	1	0.728	0.692	0.765	INDETERMINATE	3	TRUE	2	0.433157227205093	6		541	1109	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266512	198266512	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000873-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	312	344	0	ENST00000335508.6:c.2324G>T	p.Arg775Leu	p.R775L	ENST00000335508	NM_012433.2	775	cGa/cTa	16/25	0.433157227205093	3	FACETS	0.914	0.87	0.958	0.914	0.87	0.958	CLONAL	3	TRUE	0	0.433157227205093	3		344	639	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231754	66231754	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000873-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	71	403	1	ENST00000273854.3:c.1946C>A	p.Thr649Asn	p.T649N	ENST00000273854	NM_004439.5	649	aCt/aAt	11/18	1	2	FACETS	0.591	0.516	0.671	0.591	0.516	0.671	SUBCLONAL	1	TRUE	1	0.433157227205093	2		404	555	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420003	152420003	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs774794965	NA	P-0000873-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	181	349	1	ENST00000206249.3:c.1690G>T	p.Asp564Tyr	p.D564Y	ENST00000206249	NM_000125.3	564	Gac/Tac	8/8	0.164955120192643	2	FACETS	1	0.982	1	0.594	0.55	0.64	INDETERMINATE	1	TRUE	0	0.433157227205093	2		350	703	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923450	9923450	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000873-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	164	431	0	ENST00000330684.3:c.1837T>G	p.Phe613Val	p.F613V	ENST00000330684	NM_001134407.1	613	Ttc/Gtc	9/13	0.433157227205093	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.433157227205093	1		431	563	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584505	39584505	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000873-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	79	228	1	ENST00000262039.4:c.1170G>T	p.Glu390Asp	p.E390D	ENST00000262039	NM_002647.2	390	gaG/gaT	10/25	0.20389302486014	1	FACETS	0.658	0.582	0.74	0.658	0.582	0.74	INDETERMINATE	1	TRUE	0	0.433157227205093	1		229	434	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937556	17937556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000873-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	111	562	0	ENST00000458235.1:c.3371C>T	p.Ser1124Leu	p.S1124L	ENST00000458235	NM_000215.3	1124	tCa/tTa	24/24	NA	2	FACETS	0.81	0.729	0.894			1	INDETERMINATE	1	TRUE	NA	0.433157227205093	2		562	633	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939678	76939678	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000873-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	245	432	2	ENST00000373344.5:c.1070A>C	p.Lys357Thr	p.K357T	ENST00000373344	NM_000489.3	357	aAa/aCa	9/35	0.306310220231572	0	FACETS	0.64	0.605	0.675			1	SUBCLONAL	2	TRUE	NA	0.433157227205093	0		434	501	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918257	44918257	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0000920-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	118	204	0	ENST00000377967.4:c.882T>G	p.Tyr294Ter	p.Y294*	ENST00000377967	NM_021140.2	294	taT/taG	11/29	0.511898111495823	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.526795796215032	1		204	242	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579335	7579336	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0000920-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	72	164	0	ENST00000269305.4:c.350_351dup	p.Thr118GlyfsTer6	p.T118Gfs*6	ENST00000269305	NM_001126112.2	117	-/GG	4/11	0.526795796215032	1	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	0	0.526795796215032	1		164	201	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663687	29663709	+	frameshift_variant	Frame_Shift_Del	DEL	CATGCTTATCTCCAACTCCTACT	CATGCTTATCTCCAACTCCTACT	-	novel	NA	P-0000920-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	48	354	0	ENST00000356175.3:c.6119_6141del	p.Thr2040IlefsTer9	p.T2040Ifs*9	ENST00000356175	NM_000267.3	2040	aCATGCTTATCTCCAACTCCTACT/a	41/57	NA	2	FACETS	0.744	0.634	0.862			1	INDETERMINATE	1	TRUE	NA	0.526795796215032	2		354	245	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0000952-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	1306	285	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.747183913556638	6	FACETS	0.975	0.963	0.987			1	CLONAL	6	TRUE	NA	0.747183913556638	6		285	1490	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0000952-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	277	400	2	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.869	0.819	0.921	0.869	0.819	0.921	CLONAL	1	TRUE	1	0.747183913556638	2		402	853	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087503	27087503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000952-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	419	563	0	ENST00000324856.7:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000324856	NM_006015.4	693	Cga/Tga	5/20	1	2	FACETS	0.946	0.902	0.991	0.946	0.902	0.991	CLONAL	1	TRUE	1	0.747183913556638	2		563	1185	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0000952-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	401	495	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	0.936	0.891	0.981	0.936	0.891	0.981	CLONAL	1	TRUE	1	0.747183913556638	2		495	1147	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554954	187554955	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0000952-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	444	833	0	ENST00000441802.2:c.4206_4207insA	p.Asp1403ArgfsTer16	p.D1403Rfs*16	ENST00000441802	NM_005245.3	1402	-/A	7/27	1	2	FACETS	0.926	0.884	0.969	0.926	0.884	0.969	CLONAL	1	TRUE	1	0.747183913556638	2		833	1283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0001044-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	178	293	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	2	TRUE	NA	0.371953731685891	2		295	427	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202977	16202977	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001044-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	89	208	1	ENST00000375759.3:c.685C>T	p.Arg229Ter	p.R229*	ENST00000375759	NM_015001.2	229	Cga/Tga	3/15	0.371953731685892	3	FACETS	1	0.914	1	0.517	0.459	0.578	CLONAL	1	TRUE	1	0.371953731685891	3		209	549	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217276	11217276	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001044-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	119	341	0	ENST00000361445.4:c.4402G>T	p.Asp1468Tyr	p.D1468Y	ENST00000361445	NM_004958.3	1468	Gac/Tac	30/58	0.371953731685892	3	FACETS	0.839	0.757	0.927	0.42	0.378	0.464	CLONAL	1	TRUE	1	0.371953731685891	3		341	904	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591247	67591247	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0001044-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	152	182	0	ENST00000274335.5:c.1746-1G>A		p.X582_splice	ENST00000274335		582			0.304655908018519	3	FACETS	1	0.948	1	0.69	0.636	0.746	CLONAL	2	TRUE	0	0.371953731685891	3		182	468	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670048	86670048	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0001044-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	320	286	0	ENST00000274376.6:c.1845T>G	p.Tyr615Ter	p.Y615*	ENST00000274376	NM_002890.2	615	taT/taG	14/25	0.304655908018519	3	FACETS	1	0.984	1	0.731	0.692	0.77	CLONAL	2	TRUE	0	0.371953731685891	3		286	931	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920353	134920354	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0001044-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	133	316	0	ENST00000398015.3:c.2169dup	p.Met724TyrfsTer14	p.M724Yfs*14	ENST00000398015	NM_004441.4	723	ggt/ggTt	12/16	1	2	FACETS	0.799	0.725	0.877	0.799	0.725	0.877	SUBCLONAL	1	TRUE	1	0.371953731685891	2		316	895	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435775	56435775	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	ACGTT	novel	NA	P-0001070-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	36	185	0	ENST00000407977.2:c.1362delinsAACGT	p.Ser455ThrfsTer2	p.S455Tfs*2	ENST00000407977		454	cgC/cgAACGT	9/10	0.868867706657413	1	FACETS	0.187	0.154	0.223	0.187	0.154	0.223	SUBCLONAL	1	TRUE	0	0.868867706657413	1		185	251	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0001079-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	189	223	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.954	0.882	1	0.954	0.882	1	CLONAL	1	TRUE	1	0.400025172754992	2		223	990	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736301	243736301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568298910	NA	P-0001079-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	224	362	1	ENST00000263826.5:c.746G>A	p.Arg249His	p.R249H	ENST00000263826	NM_005465.4	249	cGt/cAt	8/13	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.400025172754992	2		363	1101	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111958593	111958593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555186772	NA	P-0001079-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	151	252	0	ENST00000375549.3:c.65G>A	p.Arg22Gln	p.R22Q	ENST00000375549	NM_003002.3	22	cGa/cAa	2/4	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.400025172754992	2		252	726	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28624277	28624277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001079-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1494	106	535	0	ENST00000241453.7:c.697G>A	p.Ala233Thr	p.A233T	ENST00000241453	NM_004119.2	233	Gcc/Acc	6/24	0.184503791204696	3	FACETS	0.397	0.355	0.443	0.199	0.177	0.222	INDETERMINATE	1	TRUE	1	0.400025172754992	3		535	1600	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913143	32913143	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876661062	NA	P-0001079-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	71	243	0	ENST00000380152.3:c.4651C>T	p.Gln1551Ter	p.Q1551*	ENST00000380152		1551	Caa/Taa	11/27	0.400025172754992	3	FACETS	0.441	0.383	0.503	0.22	0.191	0.252	SUBCLONAL	1	TRUE	1	0.400025172754992	3		243	967	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423601	88423601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001079-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	94	397	0	ENST00000360948.2:c.2234G>A	p.Arg745Gln	p.R745Q	ENST00000360948	NM_001012338.2	745	cGg/cAg	18/19	1	2	FACETS	0.551	0.489	0.617	0.551	0.489	0.617	SUBCLONAL	1	TRUE	1	0.400025172754992	2		397	853	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0001079-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	185	283	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.400025172754992	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.400025172754992	1		283	603	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248430	59248431	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0001079-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	104	258	0	ENST00000371222.2:c.312dup	p.Asp105ArgfsTer2	p.D105Rfs*2	ENST00000371222	NM_002228.3	104	-/A	1/1	1	2	FACETS	0.628	0.562	0.698	0.628	0.562	0.698	SUBCLONAL	1	TRUE	1	0.400025172754992	2		258	828	SUCCESS
APC	324	MSKCC	GRCh37	5	112175175	112175175	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001079-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	64	127	0	ENST00000257430.4:c.3885del	p.Ala1296GlnfsTer9	p.A1296Qfs*9	ENST00000257430	NM_000038.5	1295	gAa/ga	16/16	1	2	FACETS	0.78	0.678	0.89	0.78	0.678	0.89	SUBCLONAL	1	TRUE	1	0.400025172754992	2		127	410	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554097	63554098	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0001079-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	355	521	0	ENST00000307078.5:c.641dup	p.Leu215ThrfsTer16	p.L215Tfs*16	ENST00000307078	NM_004655.3	214	gga/ggGa	2/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.400025172754992	2		521	1486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0001104-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	135	389	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.453178683543889	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.453178683543889	1		390	321	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0001104-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	102	265	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.171608511429673	5	FACETS	0.752	0.675	0.832	0.501	0.45	0.555	INDETERMINATE	2	TRUE	2	0.453178683543889	5		265	503	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038912	12038912	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001104-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	146	841	0	ENST00000396373.4:c.1205A>G	p.Tyr402Cys	p.Y402C	ENST00000396373	NM_001987.4	402	tAc/tGc	7/8	0.185619879885463	0	FACETS	0.572	0.524	0.622			1	INDETERMINATE	1	TRUE	0	0.453178683543889	0		841	616	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782654	9782654	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001104-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	146	796	0	ENST00000377346.4:c.2416C>A	p.Leu806Met	p.L806M	ENST00000377346	NM_005026.3	806	Ctg/Atg	19/24	0.279287307296817	1	FACETS	0.85	0.791	0.91	1	0.991	1	CLONAL	2	TRUE	0	0.453178683543889	1		796	293	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917797	29917797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748854412	NA	P-0001104-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	81	873	0	ENST00000389048.3:c.871C>T	p.Arg291Cys	p.R291C	ENST00000389048	NM_004304.4	291	Cgc/Tgc	3/29	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.453178683543889	2		873	299	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808647	1808647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373425119	NA	P-0001104-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	72	765	0	ENST00000260795.2:c.2260G>A	p.Val754Met	p.V754M	ENST00000260795		754	Gtg/Atg	16/17	0.235072263745094	0	FACETS	0.608	0.536	0.683			1	INDETERMINATE	1	TRUE	0	0.453178683543889	0		765	286	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213909	66213909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001104-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	49	879	0	ENST00000273854.3:c.2521C>T	p.Pro841Ser	p.P841S	ENST00000273854	NM_004439.5	841	Cca/Tca	15/18	0.235072263745094	0	FACETS	0.448	0.382	0.519			1	INDETERMINATE	1	TRUE	0	0.453178683543889	0		879	264	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468029	50468029	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001104-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	61	629	0	ENST00000331340.3:c.1264G>A	p.Ala422Thr	p.A422T	ENST00000331340	NM_006060.4	422	Gcg/Acg	8/8	1	2	FACETS	0.891	0.775	1	0.891	0.775	1	CLONAL	1	TRUE	1	0.453178683543889	2		629	302	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504378	8504378	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001104-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	37	726	0	ENST00000356435.5:c.1705T>A	p.Ser569Thr	p.S569T	ENST00000356435		569	Tca/Aca	12/35	0.368045219738678	0	FACETS	0.4	0.333	0.475			1	SUBCLONAL	1	TRUE	0	0.453178683543889	0		726	223	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231337	46231337	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001104-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	38	794	0	ENST00000334344.6:c.1177G>A	p.Glu393Lys	p.E393K	ENST00000334344	NM_152641.2	393	Gaa/Aaa	10/21	0.38607528897574	4	FACETS	0.579	0.479	0.691	0.289	0.239	0.346	SUBCLONAL	1	TRUE	2	0.453178683543889	4		794	421	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432110	121432110	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001104-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	61	818	0	ENST00000257555.6:c.857A>T	p.Tyr286Phe	p.Y286F	ENST00000257555		286	tAc/tTc	4/10	1	2	FACETS	0.65	0.563	0.745	0.65	0.563	0.745	SUBCLONAL	1	TRUE	1	0.453178683543889	2		818	414	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2218120	2218120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001104-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	102	881	0	ENST00000326181.6:c.182C>T	p.Ser61Phe	p.S61F	ENST00000326181	NM_032271.2	61	tCc/tTc	4/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.453178683543889	2		881	356	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857029	9857029	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001104-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	37	957	0	ENST00000330684.3:c.4372C>G	p.Pro1458Ala	p.P1458A	ENST00000330684	NM_001134407.1	1458	Cct/Gct	13/13	1	2	FACETS	0.666	0.553	0.792	0.666	0.553	0.792	SUBCLONAL	1	TRUE	1	0.453178683543889	2		957	245	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439988	56439993	+	frameshift_variant	Frame_Shift_Ins	INS	GGATCC	GGATCC	TCATAATCTG	novel	NA	P-0001104-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	73	748	0	ENST00000407977.2:c.599_604delinsCAGATTATGA	p.Trp200SerfsTer60	p.W200Sfs*60	ENST00000407977		200	tGGATCCta/tCAGATTATGAta	6/10	0.453178683543889	1	FACETS	0.926	0.82	1	0.926	0.82	1	CLONAL	1	TRUE	0	0.453178683543889	1		748	269	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578215	28578216	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0001185-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	224	1014	0	ENST00000241453.7:c.2955_2956del	p.Pro986AlafsTer27	p.P986Afs*27	ENST00000241453	NM_004119.2	985	tcTCcg/tccg	24/24	0.426775570327738	3	FACETS	0.649	0.603	0.697	0.325	0.301	0.349	INDETERMINATE	1	FALSE	1	0.741032936492297	3		1014	1276	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509085	66509085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001185-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	434	849	4	ENST00000273854.3:c.242del	p.Asn81MetfsTer24	p.N81Mfs*24	ENST00000273854	NM_004439.5	81	aAt/at	2/18	0.237816560056385	4	FACETS	1	0.996	1	0.749	0.714	0.784	INDETERMINATE	1	FALSE	2	0.741032936492297	4		853	1362	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0001185-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	439	315	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.519406261452523	3	FACETS	1	0.994	1	0.64	0.61	0.67	CLONAL	1	FALSE	1	0.741032936492297	3		315	1269	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343093	118343093	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs868934108	NA	P-0001185-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	462	602	0	ENST00000534358.1:c.1219C>T	p.Arg407Ter	p.R407*	ENST00000534358	NM_005933.3	407	Cga/Tga	3/36	0.507751992391294	5	FACETS	0.926	0.889	0.963	0.926	0.889	0.963	CLONAL	3	FALSE	2	0.741032936492297	5		602	948	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022913	27022938	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGCCGCCGCCAGCAGCCTGGGCAA	CCCGCCGCCGCCAGCAGCCTGGGCAA	-	rs797045262	NA	P-0001185-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	36	74	0	ENST00000324856.7:c.31_56del	p.Ser11AlafsTer91	p.S11Afs*91	ENST00000324856	NM_006015.4	7	CCCGCCGCCGCCAGCAGCCTGGGCAAc/c	1/20	0.440458520241824	5	FACETS	1	0.854	1	0.344	0.285	0.408	INDETERMINATE	1	FALSE	2	0.741032936492297	5		74	199	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0001185-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	318	404	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	0.514125237533415	2	FACETS	1	0.991	1	0.592	0.562	0.622	CLONAL	1	FALSE	0	0.741032936492297	2		404	725	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716031	243716031	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001185-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	191	788	0	ENST00000263826.5:c.1163G>A	p.Arg388His	p.R388H	ENST00000263826	NM_005465.4	388	cGc/cAc	10/13	0.428439088323294	4	FACETS	0.728	0.672	0.787	0.364	0.336	0.394	INDETERMINATE	1	FALSE	2	0.741032936492297	4		788	1233	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180367	32180367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1382129029	NA	P-0001185-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	231	523	1	ENST00000375023.3:c.2564G>A	p.Arg855His	p.R855H	ENST00000375023	NM_004557.3	855	cGc/cAc	17/30	0.429351430185023	4	FACETS	0.752	0.704	0.801			1	INDETERMINATE	2	FALSE	NA	0.741032936492297	4		524	722	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90990499	90990499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001185-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	495	731	0	ENST00000265433.3:c.533C>T	p.Thr178Ile	p.T178I	ENST00000265433	NM_002485.4	178	aCt/aTt	5/16	0.506559220171163	4	FACETS	0.762	0.728	0.795	0.762	0.728	0.795	SUBCLONAL	2	FALSE	2	0.741032936492297	4		731	1527	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740584	145740584	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs925385244	NA	P-0001185-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	272	537	1	ENST00000428558.2:c.1433A>G	p.His478Arg	p.H478R	ENST00000428558	NM_004260.3	478	cAc/cGc	8/22	0.506559220171163	4	FACETS	1	0.993	1	0.739	0.695	0.783	CLONAL	1	FALSE	2	0.741032936492297	4		538	865	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156624	2156624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747135996	NA	P-0001185-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	364	940	0	ENST00000434045.2:c.298G>A	p.Val100Ile	p.V100I	ENST00000434045	NM_001127598.1	100	Gtc/Atc	3/5	0.486845520265916	3	FACETS	1	0.995	1	0.737	0.702	0.773	CLONAL	1	FALSE	1	0.741032936492297	3		940	913	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244943	46244943	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001185-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	545	875	1	ENST00000334344.6:c.3037C>T	p.Gln1013Ter	p.Q1013*	ENST00000334344	NM_152641.2	1013	Caa/Taa	15/21	0.741032936492297	3	FACETS	1	0.996	1	0.707	0.678	0.736	CLONAL	1	FALSE	1	0.741032936492297	3		876	1426	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004954	16004954	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1249654177	NA	P-0001185-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	530	985	0	ENST00000268712.3:c.2300T>C	p.Leu767Ser	p.L767S	ENST00000268712	NM_006311.3	767	tTa/tCa	20/46	0.531147480068109	4	FACETS	0.825	0.791	0.86	0.413	0.395	0.43	CLONAL	2	FALSE	0	0.741032936492297	4		985	1509	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896573	78896573	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001185-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	743	955	0	ENST00000306801.3:c.2570C>T	p.Thr857Met	p.T857M	ENST00000306801	NM_020761.2	857	aCg/aTg	22/34	0.531147480068109	4	FACETS	1	0.994	1	0.798	0.778	0.818	CLONAL	3	FALSE	0	0.741032936492297	4		955	1094	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356326	70356326	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001185-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	240	552	0	ENST00000374080.3:c.5221C>T	p.Pro1741Ser	p.P1741S	ENST00000374080		1741	Cca/Tca	37/45	0.429351430185023	2	FACETS	0.917	0.861	0.975			1	INDETERMINATE	1	FALSE	NA	0.741032936492297	2		552	706	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001185-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	326	251	0	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	0.440458520241824	5	FACETS	0.918	0.869	0.968	0.612	0.579	0.646	INDETERMINATE	2	FALSE	2	0.741032936492297	5		251	1012	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659240	86659240	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001185-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	541	993	1	ENST00000274376.6:c.1533del	p.Lys511AsnfsTer9	p.K511Nfs*9	ENST00000274376	NM_002890.2	510	gAa/ga	11/25	0.506559220171163	4	FACETS	1	0.996	1	0.733	0.702	0.765	CLONAL	1	FALSE	2	0.741032936492297	4		994	1734	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446283	70446284	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0001185-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1217	458	1142	1	ENST00000373644.4:c.5230dup	p.Arg1744LysfsTer26	p.R1744Kfs*26	ENST00000373644	NM_030625.2	1741	-/A	11/12	0.440458520241824	5	FACETS	0.779	0.742	0.817	0.519	0.495	0.545	INDETERMINATE	2	FALSE	2	0.741032936492297	5		1143	1675	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231185	46231185	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001185-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	436	749	2	ENST00000334344.6:c.1109del	p.Leu370Ter	p.L370*	ENST00000334344	NM_152641.2	369	Ttt/tt	9/21	0.741032936492297	3	FACETS	1	0.986	1	0.541	0.515	0.568	CLONAL	1	FALSE	1	0.741032936492297	3		751	1490	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447772	49447773	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0001185-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	101	151	0	ENST00000301067.7:c.661dup	p.Ala221GlyfsTer13	p.A221Gfs*13	ENST00000301067	NM_003482.3	221	gct/gGct	5/54	0.741032936492297	3	FACETS	0.724	0.649	0.803	0.362	0.324	0.402	SUBCLONAL	1	FALSE	1	0.741032936492297	3		151	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577595	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0001185-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	426	470	1	ENST00000269305.4:c.686_687del	p.Cys229TyrfsTer10	p.C229Yfs*10	ENST00000269305	NM_001126112.2	229	tGT/t	7/11	0.531147480068109	4	FACETS	0.953	0.918	0.987	0.715	0.689	0.741	CLONAL	3	FALSE	0	0.741032936492297	4		471	700	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226423	2226423	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001185-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	170	842	0	ENST00000398665.3:c.3907del	p.Ala1303LeufsTer24	p.A1303Lfs*24	ENST00000398665	NM_032482.2	1301	tcG/tc	27/28	0.500398436261181	3	FACETS	0.71	0.653	0.769	0.355	0.326	0.385	SUBCLONAL	1	FALSE	1	0.741032936492297	3		842	886	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791372	42791373	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0001185-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	157	610	0	ENST00000575354.2:c.436_437del	p.Ser146Ter	p.S146*	ENST00000575354	NM_015125.3	144	acAGag/acag	3/20	0.500398436261181	3	FACETS	0.724	0.664	0.787	0.362	0.332	0.394	SUBCLONAL	1	FALSE	1	0.741032936492297	3		610	802	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175857	24175859	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs875989800	NA	P-0001185-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	271	664	0	ENST00000263121.7:c.1091_1093del	p.Lys364del	p.K364del	ENST00000263121	NM_003073.3	362	gAGAag/gag	8/9	0.500398436261181	3	FACETS	1	0.991	1	0.634	0.597	0.671	CLONAL	1	FALSE	1	0.741032936492297	3		664	791	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572252	41572254	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0001185-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	136	574	0	ENST00000263253.7:c.4785_4787del	p.Phe1596del	p.F1596del	ENST00000263253	NM_001429.3	1594	gTCTtc/gtc	30/31	0.578074834645168	3	FACETS	0.711	0.647	0.777			1	SUBCLONAL	1	FALSE	NA	0.741032936492297	3		574	708	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0001248-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	127	435	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.247101035217462	4	FACETS	1	0.966	1	0.571	0.516	0.628	CLONAL	1	TRUE	2	0.33	4		435	897	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001248-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	88	199	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	0.161981604414826	4	FACETS	0.815	0.726	0.91	0.815	0.726	0.91	INDETERMINATE	2	TRUE	2	0.33	4		200	435	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445041	49445041	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001248-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	52	115	0	ENST00000301067.7:c.2425del	p.Gln809ArgfsTer121	p.Q809Rfs*121	ENST00000301067	NM_003482.3	809	Cag/ag	10/54	0.247101035217462	4	FACETS	0.785	0.674	0.905	0.785	0.674	0.905	CLONAL	2	TRUE	2	0.33	4		115	267	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001248-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	100	251	0	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	0.161981604414826	4	FACETS	1	0.976	1	0.664	0.594	0.738	INDETERMINATE	1	TRUE	2	0.33	4		251	607	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287520	33287520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141395832	NA	P-0001248-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	109	181	1	ENST00000374542.5:c.1577G>A	p.Arg526His	p.R526H	ENST00000374542	NM_001141970.1	526	cGc/cAc	6/8	0.455406402027972	4	FACETS	1	0.97	1	0.608	0.546	0.673	CLONAL	1	TRUE	2	0.33	4		182	723	SUCCESS
AR	367	MSKCC	GRCh37	X	66766350	66766351	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGT	rs746958859	NA	P-0001248-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	38	68	2	ENST00000374690.3:c.1368_1370dup	p.Gly473dup	p.G473dup	ENST00000374690	NM_000044.3	473	-/GGT	1/8	1	2	FACETS	0.768	0.645	0.899	1	0.958	1	SUBCLONAL	2	TRUE	1	0.33	2		70	150	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604533	43604533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs546866208	NA	P-0001248-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	121	369	1	ENST00000355710.3:c.1118C>T	p.Ala373Val	p.A373V	ENST00000355710	NM_020975.4	373	gCg/gTg	6/20	0.303050309369845	4	FACETS	1	0.983	1	0.71	0.642	0.781	CLONAL	1	TRUE	2	0.33	4		370	687	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626153	12626153	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1420280008	NA	P-0001248-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	69	170	0	ENST00000251849.4:c.1807C>A	p.Leu603Met	p.L603M	ENST00000251849	NM_002880.3	603	Ctg/Atg	17/17	0.161981604414826	4	FACETS	1	0.967	1	0.67	0.586	0.76	INDETERMINATE	1	TRUE	2	0.33	4		170	415	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053589	37053589	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs63751615	NA	P-0001248-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	140	340	0	ENST00000231790.2:c.676C>T	p.Arg226Ter	p.R226*	ENST00000231790	NM_000249.3	226	Cga/Tga	8/19	0.161981604414826	4	FACETS	1	0.987	1	0.748	0.682	0.818	INDETERMINATE	1	TRUE	2	0.33	4		340	754	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37092050	37092050	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001248-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	161	451	0	ENST00000231790.2:c.2177C>A	p.Ser726Ter	p.S726*	ENST00000231790	NM_000249.3	726	tCa/tAa	19/19	0.161981604414826	4	FACETS	0.769	0.706	0.835	0.769	0.706	0.835	INDETERMINATE	2	TRUE	2	0.33	4		451	844	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167842	185167842	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001248-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	120	274	0	ENST00000265026.3:c.1165A>G	p.Thr389Ala	p.T389A	ENST00000265026	NM_004721.4	389	Acg/Gcg	6/14	0.247101035217462	4	FACETS	1	0.982	1	0.694	0.627	0.764	CLONAL	1	TRUE	2	0.33	4		274	697	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293661	1293661	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001248-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	57	267	0	ENST00000310581.5:c.1340G>A	p.Arg447His	p.R447H	ENST00000310581	NM_198253.2	447	cGc/cAc	2/16	0.3	3	FACETS	1	0.948	1			1	CLONAL	1	TRUE	NA	0.33	3		267	332	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672297	30672297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001248-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	48	392	0	ENST00000376406.3:c.4663G>A	p.Ala1555Thr	p.A1555T	ENST00000376406	NM_014641.2	1555	Gcc/Acc	10/15	0.3	3	FACETS	0.567	0.478	0.664			1	SUBCLONAL	1	TRUE	NA	0.33	3		392	598	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220320	55220320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001248-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	100	314	0	ENST00000275493.2:c.710C>T	p.Ala237Val	p.A237V	ENST00000275493	NM_005228.3	237	gCt/gTt	6/28	0.247101035217462	4	FACETS	1	0.98	1	0.716	0.641	0.795	CLONAL	1	TRUE	2	0.33	4		314	563	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466019	69466019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001248-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	114	285	0	ENST00000227507.2:c.857C>T	p.Thr286Ile	p.T286I	ENST00000227507	NM_053056.2	286	aCa/aTa	5/5	0.3	5	FACETS	1	0.918	1			1	CLONAL	2	TRUE	NA	0.33	5		285	508	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245270	46245270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001248-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	106	235	0	ENST00000334344.6:c.3364G>A	p.Val1122Ile	p.V1122I	ENST00000334344	NM_152641.2	1122	Gtt/Att	15/21	0.247101035217462	4	FACETS	1	0.97	1	0.61	0.547	0.677	CLONAL	1	TRUE	2	0.33	4		235	700	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222243	2222243	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753021184	NA	P-0001248-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	116	406	1	ENST00000326181.6:c.527C>T	p.Ala176Val	p.A176V	ENST00000326181	NM_032271.2	176	gCg/gTg	8/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.33	2		407	592	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681135	37681135	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001248-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	41	117	0	ENST00000447079.4:c.3304A>T	p.Ile1102Leu	p.I1102L	ENST00000447079	NM_015083.1	1102	Ata/Tta	12/14	0.161981604414826	3	FACETS	1	0.911	1	0.568	0.476	0.668	INDETERMINATE	1	TRUE	1	0.33	3		117	255	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78866552	78866552	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001248-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	34	300	0	ENST00000306801.3:c.2125C>T	p.Arg709Ter	p.R709*	ENST00000306801	NM_020761.2	709	Cga/Tga	19/34	0.161981604414826	3	FACETS	0.383	0.312	0.463	0.191	0.156	0.232	INDETERMINATE	1	TRUE	1	0.33	3		300	627	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214615	5214615	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754694289	NA	P-0001248-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	98	433	0	ENST00000357368.4:c.4451C>T	p.Ser1484Leu	p.S1484L	ENST00000357368	NM_002850.3	1484	tCg/tTg	29/38	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.33	2		433	571	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610612	10610612	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001248-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	99	260	0	ENST00000171111.5:c.98A>G	p.Tyr33Cys	p.Y33C	ENST00000171111	NM_203500.1	33	tAc/tGc	2/6	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.33	2		260	473	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796721	42796721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001248-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	53	211	0	ENST00000575354.2:c.3179G>A	p.Gly1060Asp	p.G1060D	ENST00000575354	NM_015125.3	1060	gGc/gAc	14/20	0.161981604414826	3	FACETS	1	0.934	1	0.581	0.498	0.671	INDETERMINATE	1	TRUE	1	0.33	3		211	322	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395653	31395653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866792483	NA	P-0001248-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	117	353	0	ENST00000328111.2:c.2506G>A	p.Val836Met	p.V836M	ENST00000328111	NM_006892.3	836	Gtg/Atg	23/23	0.161981604414826	4	FACETS	1	0.981	1	0.693	0.626	0.764	INDETERMINATE	1	TRUE	2	0.33	4		353	680	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176357	24176357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001248-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	112	403	1	ENST00000263121.7:c.1148C>T	p.Pro383Leu	p.P383L	ENST00000263121	NM_003073.3	383	cCg/cTg	9/9	0.161981604414826	3	FACETS	1	0.966	1	0.584	0.526	0.645	INDETERMINATE	1	TRUE	1	0.33	3		404	677	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225901	53225901	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001248-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	118	415	0	ENST00000375401.3:c.2948G>A	p.Trp983Ter	p.W983*	ENST00000375401	NM_004187.3	983	tGg/tAg	19/26	1	2	FACETS	0.965	0.871	1	0.965	0.871	1	CLONAL	1	TRUE	1	0.33	2		415	741	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522033	157522033	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001248-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	65	273	0	ENST00000346085.5:c.4308del	p.Gln1437ArgfsTer11	p.Q1437Rfs*11	ENST00000346085	NM_020732.3	1435	ccG/cc	18/20	0.247101035217462	4	FACETS	0.946	0.821	1	0.473	0.41	0.541	CLONAL	1	TRUE	2	0.33	4		273	554	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406317	406318	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0001248-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	96	363	0	ENST00000399788.2:c.4123dup	p.Cys1375LeufsTer2	p.C1375Lfs*2	ENST00000399788	NM_001042603.1	1375	tgt/tTgt	25/28	0.3	2	FACETS	0.726	0.647	0.811			1	SUBCLONAL	1	TRUE	NA	0.33	2		363	801	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007834	45007834	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001248-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	113	162	0	ENST00000558401.1:c.285del	p.Asp96MetfsTer7	p.D96Mfs*7	ENST00000558401	NM_004048.2	94	gAa/ga	2/4	0.161981604414826	4	FACETS	0.771	0.695	0.85	0.771	0.695	0.85	INDETERMINATE	2	TRUE	2	0.33	4		162	591	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238958	5238958	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001248-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	76	329	0	ENST00000357368.4:c.1821del	p.Val608TrpfsTer30	p.V608Wfs*30	ENST00000357368	NM_002850.3	607	ccC/cc	13/38	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.33	2		329	408	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097200	11097205	+	inframe_deletion	In_Frame_Del	DEL	GGCCCT	GGCCCT	-	rs372601826	NA	P-0001248-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	62	236	0	ENST00000358026.2:c.708_713del	p.Gly243_Pro244del	p.G243_P244del	ENST00000358026	NM_001128849.1	231	GGCCCT/-	4/36	1	2	FACETS	0.979	0.849	1	0.979	0.849	1	CLONAL	1	TRUE	1	0.33	2		236	384	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945793	17945793	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001248-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	99	308	1	ENST00000458235.1:c.2067del	p.Trp690GlyfsTer66	p.W690Gfs*66	ENST00000458235	NM_000215.3	689	ccC/cc	16/24	0.161981604414826	3	FACETS	1	0.97	1	0.616	0.552	0.685	INDETERMINATE	1	TRUE	1	0.33	3		309	567	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0001303-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	378	599	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.637857872706033	5	FACETS	0.938	0.891	0.986	0.625	0.594	0.658	CLONAL	2	TRUE	2	0.637857872706033	5		599	1236	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657167	215657167	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001303-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	86	232	0	ENST00000260947.4:c.218A>G	p.Asn73Ser	p.N73S	ENST00000260947	NM_000465.2	73	aAt/aGt	3/11	0.637857872706033	3	FACETS	0.477	0.422	0.537	0.159	0.14	0.179	SUBCLONAL	1	TRUE	0	0.637857872706033	3		232	745	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259311	89259311	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001303-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	116	449	0	ENST00000336596.2:c.455T>C	p.Phe152Ser	p.F152S	ENST00000336596	NM_005233.5	152	tTc/tCc	3/17	0.148052291771802	3	FACETS	0.472	0.424	0.522			1	INDETERMINATE	1	TRUE	NA	0.637857872706033	3		449	1017	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806176	1806176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370064407	NA	P-0001303-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	165	538	0	ENST00000260795.2:c.1195C>T	p.Arg399Cys	p.R399C	ENST00000260795		399	Cgc/Tgc	8/17	0.605124466931772	3	FACETS	0.548	0.502	0.596	0.183	0.167	0.199	SUBCLONAL	1	TRUE	0	0.637857872706033	3		538	1245	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241617	55241617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001303-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	437	332	0	ENST00000275493.2:c.2065G>A	p.Val689Met	p.V689M	ENST00000275493	NM_005228.3	689	Gtg/Atg	18/28	0.637857872706033	5	FACETS	0.995	0.948	1	0.663	0.632	0.694	CLONAL	2	TRUE	2	0.637857872706033	5		332	1348	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144498	11144498	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746219091	NA	P-0001303-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	120	370	0	ENST00000358026.2:c.3830C>T	p.Pro1277Leu	p.P1277L	ENST00000358026	NM_001128849.1	1277	cCg/cTg	27/36	0.637857872706033	2	FACETS	0.518	0.468	0.57	0.259	0.234	0.285	SUBCLONAL	1	TRUE	0	0.637857872706033	2		370	727	SUCCESS
AR	367	MSKCC	GRCh37	X	66863213	66863213	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001303-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1244	224	536	0	ENST00000374690.3:c.1732G>T	p.Gly578Ter	p.G578*	ENST00000374690	NM_000044.3	578	Gga/Tga	2/8	0.637857872706033	4	FACETS	0.784	0.727	0.842	0.261	0.242	0.281	SUBCLONAL	1	TRUE	1	0.637857872706033	4		536	1468	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938397	76938397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001303-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2075	163	754	0	ENST00000373344.5:c.2351C>T	p.Ser784Phe	p.S784F	ENST00000373344	NM_000489.3	784	tCt/tTt	9/35	0.637857872706033	4	FACETS	0.374	0.341	0.409	0.125	0.113	0.137	SUBCLONAL	1	TRUE	1	0.637857872706033	4		754	2238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579577	7579580	+	frameshift_variant	Frame_Shift_Ins	INS	GACG	GACG	ACGAC	novel	NA	P-0001303-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	166	311	0	ENST00000269305.4:c.107_110delinsGTCGT	p.Pro36ArgfsTer7	p.P36Rfs*7	ENST00000269305	NM_001126112.2	36	cCGTCc/cGTCGTc	4/11	0.637857872706033	1	FACETS	0.918	0.855	0.983	0.918	0.855	0.983	CLONAL	1	TRUE	0	0.637857872706033	1		311	386	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963090	38963090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1014232369	NA	P-0001314-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	171	489	2	ENST00000357387.3:c.1454G>A	p.Arg485Gln	p.R485Q	ENST00000357387	NM_152756.3	485	cGa/cAa	17/38	0.592671627746206	5	FACETS	0.856	0.786	0.93	0.285	0.262	0.31	CLONAL	1	TRUE	2	0.592671627746206	5		491	1273	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950625	38950626	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0001314-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1404	253	611	0	ENST00000357387.3:c.3324dup	p.His1109ThrfsTer3	p.H1109Tfs*3	ENST00000357387	NM_152756.3	1108	-/A	31/38	0.592671627746206	5	FACETS	0.973	0.908	1	0.324	0.302	0.347	CLONAL	1	TRUE	2	0.592671627746206	5		611	1657	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0001321-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	85	196	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	1	0.965	1	1	0.987	1	CLONAL	2	TRUE	1	0.171223613693471	2		196	408	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948792	55948792	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs767647176	NA	P-0001321-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	39	340	0	ENST00000263923.4:c.3673C>A	p.Gln1225Lys	p.Q1225K	ENST00000263923	NM_002253.2	1225	Cag/Aag	28/30	0.176042605480892	0	FACETS	0.689	0.57	0.822			1	SUBCLONAL	1	TRUE	0	0.171223613693471	0		340	548	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528105	157528105	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1028186690	NA	P-0001321-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	39	174	0	ENST00000346085.5:c.5830C>T	p.Arg1944Ter	p.R1944*	ENST00000346085	NM_020732.3	1944	Cga/Tga	20/20	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.171223613693471	2		174	430	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508226	106508226	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001321-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	36	546	0	ENST00000359195.3:c.220G>A	p.Val74Met	p.V74M	ENST00000359195	NM_002649.2	74	Gtg/Atg	2/11	0.176042605480892	3	FACETS	0.909	0.752	1			1	CLONAL	2	TRUE	NA	0.171223613693471	3		546	251	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711927	89711928	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554900593	NA	P-0001337-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	131	404	0	ENST00000371953.3:c.548dup	p.Asn184GlufsTer6	p.N184Efs*6	ENST00000371953	NM_000314.4	182	tta/ttAa	6/9	1	2	FACETS	0.968	0.886	1	0.968	0.886	1	CLONAL	1	FALSE	1	0.609302929460637	2		404	444	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517540	176517540	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001381-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	86	388	0	ENST00000292408.4:c.241G>T	p.Gly81Cys	p.G81C	ENST00000292408	NM_213647.1	81	Ggc/Tgc	3/18	0.350518645224112	3	FACETS	1	0.97	1	0.638	0.567	0.713	CLONAL	1	TRUE	1	0.350518645224112	3		388	452	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845223	151845223	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs543734103	NA	P-0001381-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	123	261	0	ENST00000262189.6:c.13789C>T	p.Arg4597Cys	p.R4597C	ENST00000262189	NM_170606.2	4597	Cgc/Tgc	52/59	0.350518645224112	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.350518645224112	4		261	430	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750683	128750683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001381-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	537	509	1	ENST00000377970.2:c.220C>T	p.Pro74Ser	p.P74S	ENST00000377970	NM_002467.4	74	Ccg/Tcg	2/3	0.350518645224112	9	FACETS	1	0.975	1			1	CLONAL	7	TRUE	NA	0.350518645224112	9		510	963	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88679165	88679165	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001381-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	17	113	0	ENST00000372037.3:c.1105C>T	p.Leu369Phe	p.L369F	ENST00000372037	NM_004329.2	369	Ctc/Ttc	10/13	0.350518645224112	2	FACETS	0.698	0.525	0.899	0.349	0.262	0.45	SUBCLONAL	1	TRUE	0	0.350518645224112	2		113	139	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197307	94197307	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001381-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	121	482	0	ENST00000323929.3:c.1197C>G	p.Phe399Leu	p.F399L	ENST00000323929	NM_005591.3	399	ttC/ttG	11/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.350518645224112	2		482	620	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764146326	NA	P-0001381-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	106	505	0	ENST00000269305.4:c.841G>T	p.Asp281Tyr	p.D281Y	ENST00000269305	NM_001126112.2	281	Gac/Tac	8/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.350518645224112	2		505	530	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220717	1220717	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0001381-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	138	400	0	ENST00000326873.7:c.734+1G>A		p.X245_splice	ENST00000326873	NM_000455.4	245			0.350518645224112	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.350518645224112	2		400	379	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546546	9546546	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001381-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	87	328	0	ENST00000353224.5:c.1476C>G	p.Phe492Leu	p.F492L	ENST00000353224	NM_177990.2	492	ttC/ttG	5/10	0.350518645224112	4	FACETS	0.778	0.692	0.868	0.778	0.692	0.868	SUBCLONAL	2	TRUE	2	0.350518645224112	4		328	431	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560947	9560947	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001381-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	178	382	0	ENST00000353224.5:c.835C>A	p.Gln279Lys	p.Q279K	ENST00000353224	NM_177990.2	279	Cag/Aag	4/10	0.350518645224112	4	FACETS	0.929	0.864	0.996	1	0.989	1	CLONAL	3	TRUE	2	0.350518645224112	4		382	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579463	7579464	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0001381-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	42	213	0	ENST00000269305.4:c.223_224insT	p.Pro75LeufsTer74	p.P75Lfs*74	ENST00000269305	NM_001126112.2	75	cct/cTct	4/11	1	2	FACETS	0.974	0.82	1	0.974	0.82	1	CLONAL	1	TRUE	1	0.350518645224112	2		213	246	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572932	7572933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0001460-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	89	323	0	ENST00000269305.4:c.1176dup	p.Asp393ArgfsTer78	p.D393Rfs*78	ENST00000269305	NM_001126112.2	392	-/A	11/11	0.221367450225483	4	FACETS	1	0.918	1			1	CLONAL	1	TRUE	NA	0.221367450225483	4		323	938	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0001460-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	67	229	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.221367450225483	2		229	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001460-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	105	156	0	ENST00000269305.4:c.472C>G	p.Arg158Gly	p.R158G	ENST00000269305	NM_001126112.2	158	Cgc/Ggc	5/11	0.221367450225483	4	FACETS	0.847	0.763	0.935			1	CLONAL	3	TRUE	NA	0.221367450225483	4		156	456	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0001500-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	202	363	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.263485001080266	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	1	0.263485001080266	4		364	574	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0001500-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	80	210	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.937	0.832	1	1	0.984	1	CLONAL	2	TRUE	1	0.263485001080266	2		210	324	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0001500-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	143	591	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	0.263485001080266	4	FACETS	1	0.974	1	0.397	0.361	0.435	CLONAL	1	TRUE	1	0.263485001080266	4		591	1152	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29120965	29120965	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs1555926708	NA	P-0001500-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	217	253	0	ENST00000328354.6:c.592G>C	p.Val198Leu	p.V198L	ENST00000328354	NM_007194.3	198	Gtt/Ctt	4/15	0.263485001080266	4	FACETS	0.977	0.912	1	1	0.992	1	CLONAL	3	TRUE	2	0.263485001080266	4		253	710	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578464	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001500-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	448	347	0	ENST00000269305.4:c.466del	p.Arg156AlafsTer14	p.R156Afs*14	ENST00000269305	NM_001126112.2	156	Cgc/gc	5/11	0.263485001080266	3	FACETS	0.919	0.883	0.954	1	0.997	1	CLONAL	5	TRUE	0	0.263485001080266	3		347	838	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0001500-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	96	634	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.263485001080266	4	FACETS	1	0.968	1	0.411	0.366	0.459	CLONAL	1	TRUE	1	0.263485001080266	4		634	747	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737142	145737142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61755067	NA	P-0001500-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	215	406	0	ENST00000428558.2:c.3424G>A	p.Asp1142Asn	p.D1142N	ENST00000428558	NM_004260.3	1142	Gac/Aac	21/22	0.263485001080266	5	FACETS	0.935	0.871	1	0.935	0.871	1	CLONAL	3	TRUE	2	0.263485001080266	5		406	812	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89881001	89881001	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001500-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	337	409	0	ENST00000389301.3:c.210A>T	p.Lys70Asn	p.K70N	ENST00000389301	NM_000135.2	70	aaA/aaT	3/43	0.263485001080266	6	FACETS	1	0.988	1			1	CLONAL	3	TRUE	NA	0.263485001080266	6		409	1138	SUCCESS
APC	324	MSKCC	GRCh37	5	112175749	112175761	+	frameshift_variant	Frame_Shift_Del	DEL	TACTTTATTACAT	TACTTTATTACAT	-	novel	NA	P-0001500-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	172	245	0	ENST00000257430.4:c.4459_4471del	p.Thr1487LeufsTer16	p.T1487Lfs*16	ENST00000257430	NM_000038.5	1486	gaTACTTTATTACAT/ga	16/16	0.263485001080266	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	1	0.263485001080266	4		245	481	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988224	36988247	+	inframe_deletion	In_Frame_Del	DEL	CCATCCGGGGCCAGAGGCGCTGTT	CCATCCGGGGCCAGAGGCGCTGTT	-	novel	NA	P-0001500-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	38	132	0	ENST00000354822.5:c.406_429del	p.Asn136_Trp143del	p.N136_W143del	ENST00000354822	NM_001079668.2	136	AACAGCGCCTCTGGCCCCGGATGG/-	2/3	0.263485001080266	3	FACETS	0.752	0.627	0.889	0.752	0.627	0.889	SUBCLONAL	2	TRUE	1	0.263485001080266	3		132	217	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122378	17122379	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0001500-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	414	415	0	ENST00000285071.4:c.1016dup	p.Pro340AlafsTer50	p.P340Afs*50	ENST00000285071	NM_144997.5	339	cag/caAg	9/14	0.263485001080266	3	FACETS	0.948	0.911	0.986	1	0.997	1	CLONAL	5	TRUE	0	0.263485001080266	3		415	750	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528707	8528707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs545049137	NA	P-0001500-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	91	347	1	ENST00000356435.5:c.425C>T	p.Thr142Met	p.T142M	ENST00000356435		142	aCg/aTg	4/35	0.230652884385957	3	FACETS	1	0.974	1			1	CLONAL	1	TRUE	NA	0.263485001080266	3		348	585	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584513	48584514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs377767334	NA	P-0001553-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	206	296	0	ENST00000342988.3:c.692dup	p.Ser232GlnfsTer3	p.S232Qfs*3	ENST00000342988	NM_005359.5	229	ctg/ctGg	6/12	0.760969217567869	1	FACETS	0.853	0.805	0.902	0.853	0.805	0.902	CLONAL	1	TRUE	0	0.760969217567869	1		296	393	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667596	29667596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001553-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	217	579	1	ENST00000356175.3:c.6932C>T	p.Ser2311Leu	p.S2311L	ENST00000356175	NM_000267.3	2311	tCa/tTa	46/57	1	2	FACETS	0.444	0.412	0.478	0.444	0.412	0.478	SUBCLONAL	1	TRUE	1	0.760969217567869	2		580	1284	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879665	37879665	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001553-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	129	327	0	ENST00000269571.5:c.2040G>C	p.Gln680His	p.Q680H	ENST00000269571		680	caG/caC	17/27	1	2	FACETS	0.491	0.446	0.539	0.491	0.446	0.539	SUBCLONAL	1	TRUE	1	0.760969217567869	2		327	690	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242480	+	protein_altering_variant	In_Frame_Del	DEL	ATTAAGAGAAGCA	ATTAAGAGAAGCA	C	novel	NA	P-0001553-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	144	556	0	ENST00000275493.2:c.2238_2250delinsC	p.Glu746_Ala750delinsAsp	p.E746_A750delinsD	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCA/gaC	19/28	0.486718765351605	1	FACETS	0.282	0.257	0.308	0.282	0.257	0.308	SUBCLONAL	1	TRUE	0	0.760969217567869	1		556	831	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0001607-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	47	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.959	0.822	1	1	0.974	1	CLONAL	2	TRUE	1	0.280167843736911	2		249	175	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110529	8110529	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001607-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	114	330	0	ENST00000585124.1:c.363G>C	p.Gln121His	p.Q121H	ENST00000585124	NM_004217.3	121	caG/caC	5/9	0.280167843736911	5	FACETS	0.845	0.765	0.928	0.845	0.765	0.928	CLONAL	3	TRUE	2	0.280167843736911	5		330	456	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111506	8111507	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0001607-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	302	475	1	ENST00000346208.3:c.993dup	p.Ala332CysfsTer20	p.A332Cfs*20	ENST00000346208		331	aat/aaTt	5/6	0.280167843736911	12	FACETS	0.935	0.885	0.985			1	CLONAL	7	TRUE	NA	0.280167843736911	12		476	791	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0001631-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	204	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.666899406971896	3	FACETS	0.935	0.88	0.99	0.935	0.88	0.99	CLONAL	2	TRUE	1	0.7297906391478	3		249	408	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519936	NA	P-0001631-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	388	374	0	ENST00000263967.3:c.3127A>T	p.Met1043Leu	p.M1043L	ENST00000263967	NM_006218.2	1043	Atg/Ttg	21/21	0.666899406971896	3	FACETS	0.952	0.912	0.993	0.952	0.912	0.993	CLONAL	2	TRUE	1	0.7297906391478	3		374	762	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845412	151845412	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001631-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	466	343	0	ENST00000262189.6:c.13600C>T	p.Gln4534Ter	p.Q4534*	ENST00000262189	NM_170606.2	4534	Cag/Tag	52/59	0.639909174729371	4	FACETS	0.948	0.908	0.989	0.948	0.908	0.989	CLONAL	2	TRUE	2	0.7297906391478	4		343	1165	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849662	68849663	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0001631-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	447	313	0	ENST00000261769.5:c.1565+1_1565+2dup		p.T522fs	ENST00000261769	NM_004360.3	522	aca/acGTa		0.109840481199842	1	FACETS	1	0.994	1	1	0.994	1	INDETERMINATE	1	TRUE	0	0.7297906391478	1		313	691	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187982	32187982	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001631-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	213	439	0	ENST00000375023.3:c.1239del	p.Gly414AlafsTer24	p.G414Afs*24	ENST00000375023	NM_004557.3	413	acA/ac	7/30	0.683614087203346	4	FACETS	0.786	0.729	0.846	0.393	0.364	0.423	SUBCLONAL	1	TRUE	2	0.7297906391478	4		439	1284	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858332	9858332	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001648-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	66	404	1	ENST00000330684.3:c.3069G>C	p.Gln1023His	p.Q1023H	ENST00000330684	NM_001134407.1	1023	caG/caC	13/13	0.399003057862057	4	FACETS	0.755	0.655	0.863	0.252	0.218	0.288	SUBCLONAL	1	TRUE	1	0.399003057862057	4		405	613	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858599	9858599	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001648-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	88	555	0	ENST00000330684.3:c.2802G>T	p.Met934Ile	p.M934I	ENST00000330684	NM_001134407.1	934	atG/atT	13/13	0.399003057862057	4	FACETS	0.678	0.6	0.762	0.226	0.2	0.254	SUBCLONAL	1	TRUE	1	0.399003057862057	4		555	910	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111499	8111500	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0001648-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	207	582	0	ENST00000346208.3:c.987dup	p.Arg330GlufsTer22	p.R330Efs*22	ENST00000346208		329	agg/aGgg	5/6	0.399003057862057	4	FACETS	0.787	0.731	0.845	0.787	0.731	0.845	SUBCLONAL	2	TRUE	2	0.399003057862057	4		582	922	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249017	55249018	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCA	rs1554350381	NA	P-0001665-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	330	442	1	ENST00000275493.2:c.2317_2319dup	p.His773dup	p.H773dup	ENST00000275493	NM_005228.3	773	ccc/ccCCAc	20/28	0.17182736185974	8	FACETS	0.925	0.875	0.975	1	0.985	1	CLONAL	6	TRUE	3	0.17182736185974	8		443	1049	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0001673-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	90	595	1	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.218883875823937	4	FACETS	1	0.952	1			1	INDETERMINATE	1	TRUE	NA	0.437866624932052	4		596	523	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0001673-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	224	336	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.245615686118532	4	FACETS	1	0.985	1	0.584	0.547	0.621	INDETERMINATE	2	TRUE	0	0.437866624932052	4		336	630	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0001673-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	180	485	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.437866624932052	3	FACETS	0.841	0.779	0.904	0.56	0.519	0.603	CLONAL	2	TRUE	0	0.437866624932052	3		485	596	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2966397	2966397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758980337	NA	P-0001673-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	22	545	2	ENST00000396946.4:c.1783G>A	p.Gly595Arg	p.G595R	ENST00000396946	NM_032415.4	595	Ggg/Agg	14/25	1	2	FACETS	0.286	0.221	0.362	0.286	0.221	0.362	SUBCLONAL	1	TRUE	1	0.437866624932052	2		547	351	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136380	2136380	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001673-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	47	401	0	ENST00000219476.3:c.4849G>C	p.Ala1617Pro	p.A1617P	ENST00000219476	NM_000548.3	1617	Gcc/Ccc	37/42	0.317018712855581	1	FACETS	0.752	0.641	0.871	0.752	0.641	0.871	SUBCLONAL	1	TRUE	0	0.437866624932052	1		401	223	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138140	2138140	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001673-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	53	467	0	ENST00000219476.3:c.5160T>G	p.Asn1720Lys	p.N1720K	ENST00000219476	NM_000548.3	1720	aaT/aaG	40/42	0.317018712855581	1	FACETS	0.75	0.646	0.862	0.75	0.646	0.862	SUBCLONAL	1	TRUE	0	0.437866624932052	1		467	252	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492793	56492793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001673-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	154	542	0	ENST00000407977.2:c.146G>A	p.Arg49Lys	p.R49K	ENST00000407977		49	aGa/aAa	2/10	1	2	FACETS	0.976	0.895	1	0.976	0.895	1	CLONAL	1	TRUE	1	0.437866624932052	2		542	721	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272201	15272202	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0001673-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	21	196	0	ENST00000263388.2:c.6237dup	p.Arg2080AlafsTer15	p.R2080Afs*15	ENST00000263388	NM_000435.2	2079	-/G	33/33	0.317018712855581	1	FACETS	0.531	0.413	0.666	0.531	0.413	0.666	SUBCLONAL	1	TRUE	0	0.437866624932052	1		196	141	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	73	550	3	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.476	0.415	0.541	0.476	0.415	0.541	SUBCLONAL	1	TRUE	1	0.395075151527278	2		553	777	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	80	359	1	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	0.395075151527278	2	FACETS	0.902	0.797	1	0.451	0.398	0.507	CLONAL	1	TRUE	0	0.395075151527278	2		360	449	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	227	596	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.395075151527278	2		596	1018	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	96	183	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.803	0.717	0.895	0.803	0.717	0.895	CLONAL	1	TRUE	1	0.395075151527278	2		183	605	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549263	21549263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780614508	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	247	516	0	ENST00000382592.4:c.3013G>A	p.Val1005Ile	p.V1005I	ENST00000382592	NM_014572.2	1005	Gta/Ata	8/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.395075151527278	2		516	1143	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118934	3118934	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	130	376	1	ENST00000078429.4:c.623del	p.Gly208AlafsTer16	p.G208Afs*16	ENST00000078429	NM_002067.2	206	gtG/gt	5/7	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.395075151527278	2		377	624	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	52	425	0	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	0.395075151527278	3	FACETS	0.331	0.281	0.387	0.166	0.14	0.194	SUBCLONAL	1	TRUE	1	0.395075151527278	3		425	952	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	122	127	0	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	0.985	1	CLONAL	1	TRUE	1	0.395075151527278	2		127	427	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024505	16024505	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	179	597	0	ENST00000268712.3:c.1713del	p.Arg572GlufsTer18	p.R572Efs*18	ENST00000268712	NM_006311.3	571	ggG/gg	16/46	1	2	FACETS	0.843	0.776	0.913	0.843	0.776	0.913	CLONAL	1	TRUE	1	0.395075151527278	2		597	1075	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177584	56177584	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368201444	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	244	440	1	ENST00000399503.3:c.2557C>T	p.Arg853Cys	p.R853C	ENST00000399503	NM_005921.1	853	Cgt/Tgt	14/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.395075151527278	2		441	1104	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310820	123310820	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747502397	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	215	506	0	ENST00000358487.5:c.608G>A	p.Arg203His	p.R203H	ENST00000358487	NM_000141.4	203	cGc/cAc	5/18	1	2	FACETS	0.928	0.861	0.997	0.928	0.861	0.997	CLONAL	1	TRUE	1	0.395075151527278	2		506	1173	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272375	15272375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747559029	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	149	320	1	ENST00000263388.2:c.6064C>T	p.Arg2022Cys	p.R2022C	ENST00000263388	NM_000435.2	2022	Cgc/Tgc	33/33	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.395075151527278	2		321	725	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	261	340	0	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	0.392493258857424	2	FACETS	0.927	0.873	0.981	0.927	0.873	0.981	CLONAL	2	TRUE	0	0.395075151527278	2		340	713	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032794	30032794	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121434259	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	192	394	0	ENST00000338641.4:c.169C>T	p.Arg57Ter	p.R57*	ENST00000338641	NM_000268.3	57	Cga/Tga	2/16	1	2	FACETS	0.965	0.892	1	0.965	0.892	1	CLONAL	1	TRUE	1	0.395075151527278	2		394	1007	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457303	67457303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768713596	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	178	375	3	ENST00000327367.4:c.277C>T	p.Arg93Ter	p.R93*	ENST00000327367	NM_005902.3	93	Cga/Tga	2/9	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.395075151527278	2		378	894	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	109	332	1	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	1	2	FACETS	0.647	0.58	0.718	0.647	0.58	0.718	SUBCLONAL	1	TRUE	1	0.395075151527278	2		333	853	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099312	157099312	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	131	247	0	ENST00000346085.5:c.249G>C	p.Gln83His	p.Q83H	ENST00000346085	NM_020732.3	83	caG/caC	1/20	0.392493258857424	2	FACETS	0.924	0.839	1	0.462	0.419	0.506	CLONAL	1	TRUE	0	0.395075151527278	2		247	718	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255617	16255617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	51	318	0	ENST00000375759.3:c.2882G>A	p.Arg961Lys	p.R961K	ENST00000375759	NM_015001.2	961	aGg/aAg	11/15	1	2	FACETS	0.308	0.261	0.361	0.308	0.261	0.361	SUBCLONAL	1	TRUE	1	0.395075151527278	2		318	837	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814674	43814674	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	94	252	0	ENST00000372470.3:c.1468+1G>A		p.X490_splice	ENST00000372470	NM_005373.2	490			1	2	FACETS	0.845	0.754	0.942	0.845	0.754	0.942	CLONAL	1	TRUE	1	0.395075151527278	2		252	563	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65312353	65312353	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375353661	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	193	377	0	ENST00000342505.4:c.1966G>A	p.Val656Ile	p.V656I	ENST00000342505	NM_002227.2	656	Gtc/Atc	14/25	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.395075151527278	2		377	950	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551491	150551491	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1320297360	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1157	64	401	1	ENST00000369026.2:c.516C>G	p.Asp172Glu	p.D172E	ENST00000369026	NM_021960.4	172	gaC/gaG	1/3	1	2	FACETS	0.265	0.229	0.306	0.265	0.229	0.306	SUBCLONAL	1	TRUE	1	0.395075151527278	2		402	1221	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843653	156843653	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371498291	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	181	435	0	ENST00000524377.1:c.1079C>T	p.Thr360Met	p.T360M	ENST00000524377	NM_002529.3	360	aCg/aTg	8/17	1	2	FACETS	0.905	0.835	0.979	0.905	0.835	0.979	CLONAL	1	TRUE	1	0.395075151527278	2		435	1012	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976484	25976484	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	64	487	0	ENST00000435504.4:c.1061T>C	p.Val354Ala	p.V354A	ENST00000435504		354	gTg/gCg	11/13	1	2	FACETS	0.313	0.27	0.36	0.313	0.27	0.36	SUBCLONAL	1	TRUE	1	0.395075151527278	2		487	1036	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030613	48030613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779617676	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	203	466	0	ENST00000234420.5:c.3227G>A	p.Arg1076His	p.R1076H	ENST00000234420	NM_000179.2	1076	cGc/cAc	5/10	1	2	FACETS	0.927	0.859	0.999	0.927	0.859	0.999	CLONAL	1	TRUE	1	0.395075151527278	2		466	1108	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274611	198274611	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	115	449	0	ENST00000335508.6:c.787G>A	p.Ala263Thr	p.A263T	ENST00000335508	NM_012433.2	263	Gcg/Acg	7/25	1	2	FACETS	0.567	0.51	0.628	0.567	0.51	0.628	SUBCLONAL	1	TRUE	1	0.395075151527278	2		449	1026	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242800930	242800930	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	113	351	0	ENST00000334409.5:c.61C>G	p.Pro21Ala	p.P21A	ENST00000334409	NM_005018.2	21	Cca/Gca	1/5	1	2	FACETS	0.724	0.651	0.801	0.724	0.651	0.801	SUBCLONAL	1	TRUE	1	0.395075151527278	2		351	790	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713660	30713660	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148665451	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	142	254	0	ENST00000295754.5:c.985G>A	p.Ala329Thr	p.A329T	ENST00000295754	NM_003242.5	329	Gcc/Acc	4/7	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.395075151527278	2		254	682	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390222	89390222	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs754818412	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	154	364	0	ENST00000336596.2:c.970+1G>A		p.X324_splice	ENST00000336596	NM_005233.5	324			1	2	FACETS	0.968	0.887	1	0.968	0.887	1	CLONAL	1	TRUE	1	0.395075151527278	2		364	805	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204639	128204639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764747992	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	174	368	0	ENST00000341105.2:c.802G>A	p.Gly268Arg	p.G268R	ENST00000341105	NM_032638.4	268	Gga/Aga	3/6	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.395075151527278	2		368	788	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825440	134825440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	63	412	0	ENST00000398015.3:c.956G>A	p.Cys319Tyr	p.C319Y	ENST00000398015	NM_004441.4	319	tGc/tAc	4/16	1	2	FACETS	0.405	0.349	0.465	0.405	0.349	0.465	SUBCLONAL	1	TRUE	1	0.395075151527278	2		412	788	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374301	138374301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1170276441	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	239	480	0	ENST00000289153.2:c.3143C>T	p.Ala1048Val	p.A1048V	ENST00000289153	NM_006219.2	1048	gCg/gTg	22/22	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.395075151527278	2		480	1052	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665101	138665101	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	85	128	0	ENST00000330315.3:c.464C>T	p.Pro155Leu	p.P155L	ENST00000330315	NM_023067.3	155	cCg/cTg	1/1	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.395075151527278	2		128	314	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430183	181430183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	90	129	1	ENST00000325404.1:c.35C>T	p.Pro12Leu	p.P12L	ENST00000325404	NM_003106.3	12	cCg/cTg	1/1	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.395075151527278	2		130	336	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138645	55138645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1031763557	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	133	304	0	ENST00000257290.5:c.1322C>T	p.Pro441Leu	p.P441L	ENST00000257290	NM_006206.4	441	cCg/cTg	9/23	1	2	FACETS	0.903	0.821	0.989	0.903	0.821	0.989	CLONAL	1	TRUE	1	0.395075151527278	2		304	746	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264670	1264670	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	161	391	0	ENST00000310581.5:c.2692G>A	p.Val898Met	p.V898M	ENST00000310581	NM_198253.2	898	Gtg/Atg	11/16	1	2	FACETS	0.974	0.894	1	0.974	0.894	1	CLONAL	1	TRUE	1	0.395075151527278	2		391	837	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1272305	1272305	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	81	294	0	ENST00000310581.5:c.2377G>T	p.Glu793Ter	p.E793*	ENST00000310581	NM_198253.2	793	Gag/Tag	7/16	1	2	FACETS	0.649	0.572	0.731	0.649	0.572	0.731	SUBCLONAL	1	TRUE	1	0.395075151527278	2		294	632	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294613	1294613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1389956132	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	63	111	0	ENST00000310581.5:c.388G>A	p.Ala130Thr	p.A130T	ENST00000310581	NM_198253.2	130	Gca/Aca	2/16	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.395075151527278	2		111	303	SUCCESS
APC	324	MSKCC	GRCh37	5	112157594	112157594	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	145	389	2	ENST00000257430.4:c.1314G>A	p.Met438Ile	p.M438I	ENST00000257430	NM_000038.5	438	atG/atA	11/16	1	2	FACETS	0.95	0.867	1	0.95	0.867	1	CLONAL	1	TRUE	1	0.395075151527278	2		391	773	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433745	149433745	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537011691	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	303	305	0	ENST00000286301.3:c.2806G>A	p.Gly936Ser	p.G936S	ENST00000286301	NM_005211.3	936	Ggc/Agc	22/22	0.186682784694923	3	FACETS	0.996	0.941	1	0.996	0.941	1	INDETERMINATE	2	TRUE	1	0.395075151527278	3		305	922	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517474	176517474	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	70	310	0	ENST00000292408.4:c.175C>G	p.Arg59Gly	p.R59G	ENST00000292408	NM_213647.1	59	Cgg/Ggg	3/18	1	2	FACETS	0.57	0.497	0.649	0.57	0.497	0.649	SUBCLONAL	1	TRUE	1	0.395075151527278	2		310	622	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419869	152419869	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	56	254	0	ENST00000206249.3:c.1556A>G	p.Asn519Ser	p.N519S	ENST00000206249	NM_000125.3	519	aAc/aGc	8/8	0.392493258857424	2	FACETS	0.503	0.43	0.582	0.251	0.215	0.291	SUBCLONAL	1	TRUE	0	0.395075151527278	2		254	564	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444275	50444275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	120	217	0	ENST00000331340.3:c.205C>T	p.Arg69Cys	p.R69C	ENST00000331340	NM_006060.4	69	Cgt/Tgt	4/8	1	2	FACETS	0.916	0.829	1	0.916	0.829	1	CLONAL	1	TRUE	1	0.395075151527278	2		217	663	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512051	148512051	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	186	299	0	ENST00000320356.2:c.1627A>T	p.Ile543Leu	p.I543L	ENST00000320356	NM_004456.4	543	Ata/Tta	14/20	1	2	FACETS	0.981	0.906	1	0.981	0.906	1	CLONAL	1	TRUE	1	0.395075151527278	2		299	960	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287262	38287262	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs727505373	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	113	450	0	ENST00000425967.3:c.395A>G	p.Tyr132Cys	p.Y132C	ENST00000425967	NM_001174067.1	132	tAt/tGt	4/19	0.395075151527278	2	FACETS	0.666	0.599	0.737	0.333	0.299	0.369	SUBCLONAL	1	TRUE	0	0.395075151527278	2		450	859	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371987	55371987	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	109	224	0	ENST00000297316.4:c.677C>T	p.Pro226Leu	p.P226L	ENST00000297316	NM_022454.3	226	cCg/cTg	2/2	0.395075151527278	2	FACETS	1	0.902	1	0.501	0.451	0.553	CLONAL	1	TRUE	0	0.395075151527278	2		224	551	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80343580	80343580	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	128	239	0	ENST00000286548.4:c.739C>T	p.Arg247Ter	p.R247*	ENST00000286548	NM_002072.3	247	Cga/Tga	6/7	0.395075151527278	3	FACETS	1	0.947	1	0.531	0.482	0.583	CLONAL	1	TRUE	1	0.395075151527278	3		239	730	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908844	101908844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs557200755	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	181	446	0	ENST00000374994.4:c.1208C>T	p.Ala403Val	p.A403V	ENST00000374994	NM_004612.2	403	gCa/gTa	7/9	0.395075151527278	3	FACETS	0.95	0.875	1	0.475	0.437	0.515	CLONAL	1	TRUE	1	0.395075151527278	3		446	1155	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249779	110249779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs551141733	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	113	294	0	ENST00000374672.4:c.896G>A	p.Arg299Gln	p.R299Q	ENST00000374672	NM_004235.4	299	cGg/cAg	3/5	0.395075151527278	3	FACETS	0.98	0.883	1	0.49	0.441	0.542	CLONAL	1	TRUE	1	0.395075151527278	3		294	699	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390617	139390617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567323027	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	167	401	0	ENST00000277541.6:c.7574C>T	p.Pro2525Leu	p.P2525L	ENST00000277541	NM_017617.3	2525	cCg/cTg	34/34	0.395075151527278	3	FACETS	0.955	0.877	1	0.478	0.438	0.519	CLONAL	1	TRUE	1	0.395075151527278	3		401	1060	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399172	139399172	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	96	249	0	ENST00000277541.6:c.4971C>A	p.Ser1657Arg	p.S1657R	ENST00000277541	NM_017617.3	1657	agC/agA	26/34	0.395075151527278	3	FACETS	0.978	0.873	1	0.489	0.436	0.545	CLONAL	1	TRUE	1	0.395075151527278	3		249	595	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851104	63851104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148232588	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	39	304	0	ENST00000279873.7:c.1882G>A	p.Val628Met	p.V628M	ENST00000279873	NM_032199.2	628	Gtg/Atg	10/10	1	2	FACETS	0.272	0.224	0.325	0.272	0.224	0.325	SUBCLONAL	1	TRUE	1	0.395075151527278	2		304	726	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575124	64575124	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	44	264	0	ENST00000312049.6:c.683T>C	p.Met228Thr	p.M228T	ENST00000312049	NM_130799.2	228	aTg/aCg	4/10	1	2	FACETS	0.34	0.284	0.402	0.34	0.284	0.402	SUBCLONAL	1	TRUE	1	0.395075151527278	2		264	655	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466037	69466037	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	136	290	0	ENST00000227507.2:c.875A>G	p.Asp292Gly	p.D292G	ENST00000227507	NM_053056.2	292	gAc/gGc	5/5	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.395075151527278	2		290	581	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518578	69518578	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269709193	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	68	202	0	ENST00000294312.3:c.67C>T	p.Arg23Cys	p.R23C	ENST00000294312	NM_005117.2	23	Cgc/Tgc	1/3	1	2	FACETS	0.925	0.809	1	0.925	0.809	1	CLONAL	1	TRUE	1	0.395075151527278	2		202	372	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77069992	77069992	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	105	394	0	ENST00000356341.3:c.548A>C	p.Asp183Ala	p.D183A	ENST00000356341	NM_002576.4	183	gAt/gCt	6/15	1	2	FACETS	0.544	0.486	0.605	0.544	0.486	0.605	SUBCLONAL	1	TRUE	1	0.395075151527278	2		394	978	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988076	85988076	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	64	368	0	ENST00000263360.6:c.1021G>T	p.Asp341Tyr	p.D341Y	ENST00000263360	NM_003797.3	341	Gat/Tat	10/12	1	2	FACETS	0.419	0.362	0.481	0.419	0.362	0.481	SUBCLONAL	1	TRUE	1	0.395075151527278	2		368	773	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813435	102813435	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	134	340	0	ENST00000307046.8:c.254G>T	p.Arg85Met	p.R85M	ENST00000307046	NM_001111285.1	85	aGg/aTg	3/4	0.395075151527278	2	FACETS	0.897	0.816	0.983	0.449	0.408	0.492	CLONAL	1	TRUE	0	0.395075151527278	2		340	756	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924336	112924336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507536	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	360	363	0	ENST00000351677.2:c.1282G>A	p.Val428Met	p.V428M	ENST00000351677	NM_002834.3	428	Gtg/Atg	11/16	0.395075151527278	2	FACETS	0.968	0.921	1	0.968	0.921	1	CLONAL	2	TRUE	0	0.395075151527278	2		363	941	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110101	115110101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1182949304	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	71	203	0	ENST00000257566.3:c.1777G>A	p.Ala593Thr	p.A593T	ENST00000257566	NM_016569.3	593	Gcc/Acc	8/8	0.395075151527278	2	FACETS	0.985	0.865	1	0.492	0.432	0.557	CLONAL	1	TRUE	0	0.395075151527278	2		203	365	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112554	115112554	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	146	391	0	ENST00000257566.3:c.1186T>C	p.Ser396Pro	p.S396P	ENST00000257566	NM_016569.3	396	Tcc/Ccc	7/8	0.395075151527278	2	FACETS	0.925	0.845	1	0.463	0.422	0.505	CLONAL	1	TRUE	0	0.395075151527278	2		391	799	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249286	133249286	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565971628	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	158	381	0	ENST00000320574.5:c.1613C>T	p.Thr538Ile	p.T538I	ENST00000320574	NM_006231.2	538	aCc/aTc	15/49	0.395075151527278	2	FACETS	0.868	0.796	0.945	0.434	0.398	0.473	CLONAL	1	TRUE	0	0.395075151527278	2		381	921	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436951	110436951	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	33	61	0	ENST00000375856.3:c.1450G>A	p.Gly484Ser	p.G484S	ENST00000375856	NM_003749.2	484	Ggc/Agc	1/2	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.395075151527278	2		61	118	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986991	36986991	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	168	316	0	ENST00000354822.5:c.698C>T	p.Thr233Met	p.T233M	ENST00000354822	NM_001079668.2	233	aCg/aTg	3/3	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.395075151527278	2		316	665	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74000774	74000774	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	210	429	1	ENST00000318443.5:c.1464C>A	p.Cys488Ter	p.C488*	ENST00000318443	NM_001024736.1	488	tgC/tgA	7/10	1	2	FACETS	0.995	0.924	1	0.995	0.924	1	CLONAL	1	TRUE	1	0.395075151527278	2		430	1068	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630791	90630791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1227626398	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	111	240	0	ENST00000330062.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000330062	NM_002168.2	232	gCg/gTg	6/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.395075151527278	2		240	521	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90633818	90633818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371777275	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	168	345	0	ENST00000330062.3:c.266G>A	p.Arg89His	p.R89H	ENST00000330062	NM_002168.2	89	cGt/cAt	3/11	1	2	FACETS	0.91	0.836	0.987	0.91	0.836	0.987	CLONAL	1	TRUE	1	0.395075151527278	2		345	935	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465538	99465538	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	53	413	0	ENST00000268035.6:c.2363C>T	p.Thr788Ile	p.T788I	ENST00000268035	NM_000875.3	788	aCt/aTt	11/21	1	2	FACETS	0.269	0.229	0.314	0.269	0.229	0.314	SUBCLONAL	1	TRUE	1	0.395075151527278	2		413	996	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778194	3778194	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	117	290	1	ENST00000262367.5:c.6854C>A	p.Pro2285His	p.P2285H	ENST00000262367	NM_004380.2	2285	cCc/cAc	31/31	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.395075151527278	2		291	529	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274159	10274159	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	82	323	0	ENST00000330684.3:c.110C>T	p.Ala37Val	p.A37V	ENST00000330684	NM_001134407.1	37	gCg/gTg	2/13	1	2	FACETS	0.642	0.566	0.723	0.642	0.566	0.723	SUBCLONAL	1	TRUE	1	0.395075151527278	2		323	647	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39644793	39644793	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	151	380	0	ENST00000262039.4:c.2522A>G	p.Lys841Arg	p.K841R	ENST00000262039	NM_002647.2	841	aAg/aGg	23/25	1	2	FACETS	0.944	0.863	1	0.944	0.863	1	CLONAL	1	TRUE	1	0.395075151527278	2		380	810	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098534	11098534	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1018881303	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	119	305	2	ENST00000358026.2:c.1052G>A	p.Arg351His	p.R351H	ENST00000358026	NM_001128849.1	351	cGc/cAc	6/36	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.395075151527278	2		307	542	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101932	11101932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	103	327	2	ENST00000358026.2:c.1352G>A	p.Arg451His	p.R451H	ENST00000358026	NM_001128849.1	451	cGc/cAc	8/36	1	2	FACETS	0.815	0.73	0.904	0.815	0.73	0.904	CLONAL	1	TRUE	1	0.395075151527278	2		329	640	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273240	18273240	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	193	361	1	ENST00000222254.8:c.1033C>T	p.Arg345Trp	p.R345W	ENST00000222254	NM_005027.3	345	Cgg/Tgg	9/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.395075151527278	2		362	913	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40742171	40742171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1206035617	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	175	416	3	ENST00000392038.2:c.953C>T	p.Ala318Val	p.A318V	ENST00000392038	NM_001626.4	318	gCg/gTg	10/14	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.395075151527278	2		419	847	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52705276	52705276	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	70	361	0	ENST00000322088.6:c.158C>A	p.Pro53His	p.P53H	ENST00000322088	NM_014225.5	53	cCt/cAt	2/15	1	2	FACETS	0.388	0.337	0.443	0.388	0.337	0.443	SUBCLONAL	1	TRUE	1	0.395075151527278	2		361	914	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714711	52714711	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs780485104	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	136	342	0	ENST00000322088.6:c.469C>T	p.Arg157Ter	p.R157*	ENST00000322088	NM_014225.5	157	Cga/Tga	4/15	1	2	FACETS	0.941	0.856	1	0.941	0.856	1	CLONAL	1	TRUE	1	0.395075151527278	2		342	732	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485397	57485397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	98	247	0	ENST00000371085.3:c.979G>A	p.Glu327Lys	p.E327K	ENST00000371085	NM_000516.4	327	Gag/Aag	12/13	0.392493258857424	2	FACETS	0.601	0.535	0.67	0.3	0.267	0.335	SUBCLONAL	1	TRUE	0	0.395075151527278	2		247	826	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656914	45656914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	148	438	0	ENST00000407780.3:c.242G>A	p.Arg81Gln	p.R81Q	ENST00000407780	NM_001283052.1	81	cGg/cAg	3/7	1	2	FACETS	0.832	0.76	0.908	0.832	0.76	0.908	CLONAL	1	TRUE	1	0.395075151527278	2		438	900	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610608	52610609	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	143	491	0	ENST00000394830.3:c.3564dup	p.Glu1189ArgfsTer6	p.E1189Rfs*6	ENST00000394830	NM_018313.4	1188	-/A	23/30	1	2	FACETS	0.827	0.754	0.904	0.827	0.754	0.904	CLONAL	1	TRUE	1	0.395075151527278	2		491	875	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193762	106193762	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	105	283	0	ENST00000380013.4:c.4227del	p.Lys1409AsnfsTer39	p.K1409Nfs*39	ENST00000380013	NM_001127208.2	1408	ggA/gg	10/11	1	2	FACETS	0.859	0.771	0.952	0.859	0.771	0.952	CLONAL	1	TRUE	1	0.395075151527278	2		283	619	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130120	143130120	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	181	443	1	ENST00000262992.4:c.896del	p.Asn299MetfsTer10	p.N299Mfs*10	ENST00000262992	NM_001101669.1	299	aAt/at	11/24	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.395075151527278	2		444	898	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177011	56177014	+	frameshift_variant	Frame_Shift_Del	DEL	ATAG	ATAG	-	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	98	361	0	ENST00000399503.3:c.2286_2289del	p.Arg763CysfsTer35	p.R763Cfs*35	ENST00000399503	NM_005921.1	761	ATAGat/at	13/20	1	2	FACETS	0.67	0.598	0.747	0.67	0.598	0.747	SUBCLONAL	1	TRUE	1	0.395075151527278	2		361	740	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659182	86659182	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	135	317	0	ENST00000274376.6:c.1475del	p.Asn492IlefsTer6	p.N492Ifs*6	ENST00000274376	NM_002890.2	491	Aaa/aa	11/25	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.395075151527278	2		317	623	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675571	86675571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1561325048	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	130	346	0	ENST00000274376.6:c.2513del	p.Asn838MetfsTer4	p.N838Mfs*4	ENST00000274376	NM_002890.2	836	gAa/ga	19/25	1	2	FACETS	0.846	0.768	0.928	0.846	0.768	0.928	CLONAL	1	TRUE	1	0.395075151527278	2		346	778	SUCCESS
APC	324	MSKCC	GRCh37	5	112177091	112177091	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1131691253	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	186	487	0	ENST00000257430.4:c.5803del	p.Gln1935SerfsTer35	p.Q1935Sfs*35	ENST00000257430	NM_000038.5	1934	Ccc/cc	16/16	1	2	FACETS	0.906	0.836	0.979	0.906	0.836	0.979	CLONAL	1	TRUE	1	0.395075151527278	2		487	1039	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499679	149499679	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	59	295	0	ENST00000261799.4:c.2594del	p.Leu865CysfsTer3	p.L865Cfs*3	ENST00000261799	NM_002609.3	865	tTg/tg	19/23	0.186682784694923	3	FACETS	0.446	0.383	0.515	0.223	0.191	0.258	INDETERMINATE	1	TRUE	1	0.395075151527278	3		295	802	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048756	180048756	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	99	319	0	ENST00000261937.6:c.1806del	p.His602GlnfsTer37	p.H602Qfs*37	ENST00000261937	NM_182925.4	602	caC/ca	13/30	1	2	FACETS	0.748	0.668	0.833	0.748	0.668	0.833	SUBCLONAL	1	TRUE	1	0.395075151527278	2		319	670	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350138	81350139	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	164	451	0	ENST00000222390.5:c.1193dup	p.Asn398LysfsTer37	p.N398Kfs*37	ENST00000222390	NM_000601.4	398	aat/aaAt	10/18	1	2	FACETS	0.904	0.83	0.982	0.904	0.83	0.982	CLONAL	1	TRUE	1	0.395075151527278	2		451	918	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232173	98232175	+	inframe_deletion	In_Frame_Del	DEL	AGC	AGC	-	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	127	316	0	ENST00000331920.6:c.1767_1769del	p.Leu590del	p.L590del	ENST00000331920	NM_000264.3	589	ctGCTc/ctc	13/24	0.395075151527278	3	FACETS	0.829	0.75	0.912	0.414	0.375	0.456	CLONAL	1	TRUE	1	0.395075151527278	3		316	929	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100425	8100425	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	149	457	2	ENST00000346208.3:c.404del	p.Pro135ArgfsTer60	p.P135Rfs*60	ENST00000346208		133	taC/ta	3/6	1	2	FACETS	0.808	0.738	0.882	0.808	0.738	0.882	CLONAL	1	TRUE	1	0.395075151527278	2		459	933	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692825	89692826	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	18	134	0	ENST00000371953.3:c.309_310insA	p.Phe104IlefsTer3	p.F104Ifs*3	ENST00000371953	NM_000314.4	103	-/A	5/9	1	2	FACETS	0.304	0.228	0.393	0.304	0.228	0.393	SUBCLONAL	1	TRUE	1	0.395075151527278	2		134	300	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742463	17742463	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	159	367	0	ENST00000250003.3:c.650del	p.Pro217ArgfsTer33	p.P217Rfs*33	ENST00000250003	NM_002478.4	215	ggC/gg	2/3	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.395075151527278	2		367	780	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274083	10274083	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	168	405	0	ENST00000330684.3:c.186del	p.Leu63CysfsTer5	p.L63Cfs*5	ENST00000330684	NM_001134407.1	62	ggG/gg	2/13	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.395075151527278	2		405	835	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29579996	29579996	+	intron_variant	Intron	DEL	A	A	-	rs1567859802	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	115	366	0	ENST00000356175.3:c.4110+3865del		p.*1370*	ENST00000356175	NM_000267.3	1384/2839			1	2	FACETS	0.841	0.759	0.928	0.841	0.759	0.928	CLONAL	1	TRUE	1	0.395075151527278	2		366	692	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573505	48573506	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	144	339	0	ENST00000342988.3:c.94_95del	p.Ser32Ter	p.S32*	ENST00000342988	NM_005359.5	30	gGA/g	2/12	1	2	FACETS	0.803	0.732	0.877	0.803	0.732	0.877	CLONAL	1	TRUE	1	0.395075151527278	2		339	908	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	29	113	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	0.807	0.653	0.977	0.807	0.653	0.977	CLONAL	1	TRUE	1	0.395075151527278	2		113	182	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262117	10262119	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	154	496	0	ENST00000340748.4:c.2172_2174del	p.Lys725del	p.K725del	ENST00000340748		724	aaGAAa/aaa	23/40	1	2	FACETS	0.751	0.686	0.819	0.751	0.686	0.819	SUBCLONAL	1	TRUE	1	0.395075151527278	2		496	1038	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096027	11096027	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	35	363	1	ENST00000358026.2:c.305del	p.Gly102AlafsTer201	p.G102Afs*201	ENST00000358026	NM_001128849.1	101	Ggg/gg	3/36	1	2	FACETS	0.253	0.207	0.306	0.253	0.207	0.306	SUBCLONAL	1	TRUE	1	0.395075151527278	2		364	699	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0001693-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	25	366	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.766	0.605	0.95	0.766	0.605	0.95	CLONAL	1	TRUE	1	0.239108466347322	2		366	273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0001693-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	27	503	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.225183060019091	1	FACETS	0.97	0.777	1	0.97	0.777	1	CLONAL	1	TRUE	0	0.239108466347322	1		504	205	SUCCESS
APC	324	MSKCC	GRCh37	5	112175198	112175198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001693-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	44	258	0	ENST00000257430.4:c.3907C>T	p.Gln1303Ter	p.Q1303*	ENST00000257430	NM_000038.5	1303	Caa/Taa	16/16	0.239108466347322	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	0	0.239108466347322	2		258	161	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376815	118376815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs942230098	NA	P-0001693-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	24	461	0	ENST00000534358.1:c.10208C>T	p.Pro3403Leu	p.P3403L	ENST00000534358	NM_005933.3	3403	cCg/cTg	27/36	1	2	FACETS	0.956	0.753	1	0.956	0.753	1	CLONAL	1	TRUE	1	0.239108466347322	2		461	210	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913322	28913322	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765475765	NA	P-0001693-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	26	609	0	ENST00000282397.4:c.2471G>A	p.Arg824Gln	p.R824Q	ENST00000282397	NM_002019.4	824	cGg/cAg	17/30	NA	2	FACETS	0.895	0.712	1			1	INDETERMINATE	1	TRUE	NA	0.239108466347322	2		609	243	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156069	119156070	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0001693-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	25	557	0	ENST00000264033.4:c.1739dup	p.Val581CysfsTer4	p.V581Cfs*4	ENST00000264033	NM_005188.3	578	-/C	11/16	1	2	FACETS	0.801	0.633	0.993	0.801	0.633	0.993	CLONAL	1	TRUE	1	0.239108466347322	2		557	261	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78421016	78421016	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0001693-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	29	378	0	ENST00000370768.2:c.1706-2A>C		p.X569_splice	ENST00000370768	NM_003902.3	569			1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.239108466347322	2		378	215	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405225	139405225	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776698364	NA	P-0001693-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	18	371	0	ENST00000277541.6:c.2620G>A	p.Val874Ile	p.V874I	ENST00000277541	NM_017617.3	874	Gtt/Att	17/34	1	2	FACETS	0.814	0.616	1	0.814	0.616	1	CLONAL	1	TRUE	1	0.239108466347322	2		371	185	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477171	67477171	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001693-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	17	384	0	ENST00000327367.4:c.978G>A	p.Trp326Ter	p.W326*	ENST00000327367	NM_005902.3	326	tgG/tgA	7/9	0.239108466347322	2	FACETS	0.694	0.519	0.9	0.347	0.259	0.45	SUBCLONAL	1	TRUE	0	0.239108466347322	2		384	205	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0001730-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	269	419	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.187610385963149	5	FACETS	0.86	0.813	0.907	0.86	0.813	0.907	INDETERMINATE	3	TRUE	2	0.653634774806163	5		420	632	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979563	7979563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1221632429	NA	P-0001730-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	126	537	0	ENST00000319144.4:c.1462C>T	p.Arg488Cys	p.R488C	ENST00000319144	NM_001139.2	488	Cgt/Tgt	11/15	0.653634774806163	3	FACETS	1	0.987	1	0.49	0.449	0.532	CLONAL	1	TRUE	0	0.653634774806163	3		537	348	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688816	47688816	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001730-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	179	460	4	ENST00000347630.2:c.484A>T	p.Ser162Cys	p.S162C	ENST00000347630	NM_001007230.1	162	Agt/Tgt	7/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.653634774806163	2		464	527	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938229	76938230	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0001730-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	211	684	3	ENST00000373344.5:c.2518dup	p.Arg840LysfsTer9	p.R840Kfs*9	ENST00000373344	NM_000489.3	840	aga/aAga	9/35	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.653634774806163	2		687	617	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0001826-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	238	468	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.66745401959964	5	FACETS	1	0.968	1	0.355	0.331	0.381	CLONAL	1	TRUE	2	0.66745401959964	5		468	1339	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0001826-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	412	599	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.66745401959964	5	FACETS	0.995	0.947	1	0.663	0.631	0.695	CLONAL	2	TRUE	2	0.66745401959964	5		599	1242	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884400	151884400	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001826-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1257	259	543	0	ENST00000262189.6:c.4955C>A	p.Ala1652Asp	p.A1652D	ENST00000262189	NM_170606.2	1652	gCc/gAc	33/59	0.66745401959964	5	FACETS	1	0.953	1	0.341	0.319	0.365	CLONAL	1	TRUE	2	0.66745401959964	5		543	1516	SUCCESS
APC	324	MSKCC	GRCh37	5	112174884	112174885	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs864622106	NA	P-0001826-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	421	485	3	ENST00000257430.4:c.3596dup	p.Ser1200GlufsTer8	p.S1200Efs*8	ENST00000257430	NM_000038.5	1198	tca/tcAa	16/16	0.66745401959964	2	FACETS	0.954	0.92	0.987	0.954	0.92	0.987	CLONAL	2	TRUE	0	0.66745401959964	2		488	661	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129753	108129753	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1565399936	NA	P-0001829-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	29	468	0	ENST00000278616.4:c.2417T>G	p.Leu806Trp	p.L806W	ENST00000278616	NM_000051.3	806	tTg/tGg	16/63	1	2	FACETS	0.844	0.683	1	1	0.949	1	CLONAL	2	TRUE	1	0.177092242193589	2		468	194	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237609	16237610	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GATG	novel	NA	P-0001829-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	28	324	0	ENST00000375759.3:c.1058_1061dup	p.Leu355TrpfsTer5	p.L355Wfs*5	ENST00000375759	NM_015001.2	352	-/GATG	5/15	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.177092242193589	2		324	215	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0001830-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	248	285	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.355283064689772	3	FACETS	0.793	0.741	0.846	0.793	0.741	0.846	SUBCLONAL	2	TRUE	1	0.355283064689772	3		285	1037	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0001830-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	344	485	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.355283064689772	3	FACETS	0.913	0.864	0.963	0.913	0.864	0.963	CLONAL	2	TRUE	1	0.355283064689772	3		485	1249	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101625	27101625	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001830-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	107	362	1	ENST00000324856.7:c.4907G>T	p.Arg1636Leu	p.R1636L	ENST00000324856	NM_006015.4	1636	cGg/cTg	18/20	0.355283064689772	4	FACETS	0.636	0.568	0.708	0.318	0.284	0.354	SUBCLONAL	1	TRUE	2	0.355283064689772	4		363	1284	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097272	178097272	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001830-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3117	351	378	0	ENST00000397062.3:c.442C>G	p.Pro148Ala	p.P148A	ENST00000397062	NM_006164.4	148	Ccc/Gcc	4/5	0.355283064689772	15	FACETS	0.943	0.887	1			1	CLONAL	2	TRUE	NA	0.355283064689772	15		378	3468	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963931	2963931	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1286585074	NA	P-0001830-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1266	676	485	1	ENST00000396946.4:c.1876G>T	p.Glu626Ter	p.E626*	ENST00000396946	NM_032415.4	626	Gag/Tag	15/25	0.355283064689772	5	FACETS	1	0.964	1	1	0.964	1	CLONAL	3	TRUE	2	0.355283064689772	5		486	1942	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345926	152345926	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001830-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1623	502	641	3	ENST00000359321.1:c.644G>T	p.Arg215Leu	p.R215L	ENST00000359321	NM_005431.1	215	cGa/cTa	3/3	0.355283064689772	4	FACETS	0.901	0.86	0.943			1	CLONAL	2	TRUE	NA	0.355283064689772	4		644	2125	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325072	123325072	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001830-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	226	533	0	ENST00000358487.5:c.256G>T	p.Val86Leu	p.V86L	ENST00000358487	NM_000141.4	86	Gtg/Ttg	3/18	NA	2	FACETS	0.965	0.897	1			1	INDETERMINATE	1	TRUE	NA	0.355283064689772	2		533	1318	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216533	108216533	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001830-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1365	257	558	0	ENST00000278616.4:c.8482C>T	p.Gln2828Ter	p.Q2828*	ENST00000278616	NM_000051.3	2828	Caa/Taa	58/63	0.355283064689772	3	FACETS	1	0.965	1	0.525	0.49	0.562	CLONAL	1	TRUE	1	0.355283064689772	3		558	1622	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426738	49426738	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001830-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	114	103	0	ENST00000301067.7:c.11750A>G	p.Gln3917Arg	p.Q3917R	ENST00000301067	NM_003482.3	3917	cAg/cGg	39/54	0.322784995707261	4	FACETS	0.973	0.882	1	0.973	0.882	1	CLONAL	2	TRUE	2	0.355283064689772	4		103	447	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609750	81609750	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001830-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1194	324	432	0	ENST00000298171.2:c.1348C>A	p.Arg450Ser	p.R450S	ENST00000298171	NM_000369.2	450	Cgc/Agc	10/10	0.355283064689772	3	FACETS	1	0.993	1	0.707	0.667	0.75	CLONAL	1	TRUE	1	0.355283064689772	3		432	1518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0001830-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	281	377	2	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	0.355283064689772	2	FACETS	0.894	0.842	0.947	0.894	0.842	0.947	CLONAL	2	TRUE	0	0.355283064689772	2		379	885	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219341	1219341	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001830-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	325	355	0	ENST00000326873.7:c.393C>A	p.Tyr131Ter	p.Y131*	ENST00000326873	NM_000455.4	131	taC/taA	3/10	0.306551083689434	2	FACETS	0.951	0.9	1	0.951	0.9	1	CLONAL	2	TRUE	0	0.355283064689772	2		355	962	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527514	41527514	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001830-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	461	386	1	ENST00000263253.7:c.1405G>T	p.Ala469Ser	p.A469S	ENST00000263253	NM_001429.3	469	Gca/Tca	6/31	0.34482527738808	3	FACETS	0.893	0.855	0.931	0.893	0.855	0.931	CLONAL	3	TRUE	0	0.355283064689772	3		387	1141	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332004	81332005	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0001830-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	412	554	0	ENST00000222390.5:c.2079dup	p.Gly694TrpfsTer31	p.G694Wfs*31	ENST00000222390	NM_000601.4	693	-/T	18/18	0.245311080627505	3	FACETS	0.941	0.894	0.988	0.941	0.894	0.988	CLONAL	2	TRUE	1	0.355283064689772	3		554	1452	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001935-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	105	217	1	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	0.40421559113425	4	FACETS	0.794	0.713	0.879			1	INDETERMINATE	1	TRUE	NA	0.770353992233062	4		218	608	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424990	49424990	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001935-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	75	209	0	ENST00000301067.7:c.13498C>G	p.Gln4500Glu	p.Q4500E	ENST00000301067	NM_003482.3	4500	Cag/Gag	39/54	NA	2	FACETS	0.401	0.352	0.453			1	INDETERMINATE	1	TRUE	NA	0.770353992233062	2		209	486	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433758	49433758	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123760	NA	P-0001935-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	104	248	0	ENST00000301067.7:c.7795G>A	p.Gly2599Arg	p.G2599R	ENST00000301067	NM_003482.3	2599	Ggg/Agg	31/54	NA	2	FACETS	0.502	0.451	0.556			1	INDETERMINATE	1	TRUE	NA	0.770353992233062	2		248	538	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795051	42795051	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001935-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	94	302	0	ENST00000575354.2:c.2131A>G	p.Met711Val	p.M711V	ENST00000575354	NM_015125.3	711	Atg/Gtg	10/20	NA	2	FACETS	0.496	0.443	0.552			1	INDETERMINATE	1	TRUE	NA	0.770353992233062	2		302	492	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099063	27099064	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0001935-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	241	250	0	ENST00000324856.7:c.3481_3482dup	p.Pro1162SerfsTer19	p.P1162Sfs*19	ENST00000324856	NM_006015.4	1160	tta/ttAAa	13/20	0.632247273346176	3	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.770353992233062	3		250	656	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032496	12032497	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0001935-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	166	197	0	ENST00000353533.5:c.933_934del	p.Asn311LysfsTer4	p.N311Kfs*4	ENST00000353533	NM_003010.3	311	aAT/a	9/11	0.639492356636935	2	FACETS	0.848	0.802	0.894	0.848	0.802	0.894	CLONAL	2	TRUE	0	0.770353992233062	2		197	254	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0001952-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	198	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.443888959323234	3	FACETS	0.884	0.83	0.938	1	0.991	1	CLONAL	3	TRUE	1	0.443888959323234	3		249	411	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0001952-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	365	285	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.443888959323234	5	FACETS	1	0.977	1	1	0.977	1	CLONAL	4	TRUE	1	0.443888959323234	5		285	666	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419950	152419950	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001952-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	302	273	0	ENST00000206249.3:c.1637C>A	p.Ala546Asp	p.A546D	ENST00000206249	NM_000125.3	546	gCc/gAc	8/8	0.443888959323234	5	FACETS	1	0.962	1	1	0.962	1	CLONAL	3	TRUE	2	0.443888959323234	5		273	742	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645922	67645922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001952-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	368	326	0	ENST00000264010.4:c.850C>T	p.His284Tyr	p.H284Y	ENST00000264010	NM_006565.3	284	Cac/Tac	4/12	0.443888959323234	2	FACETS	0.951	0.915	0.987	1	0.996	1	CLONAL	3	TRUE	0	0.443888959323234	2		326	581	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155725	56155726	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0001952-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	271	262	0	ENST00000399503.3:c.819_820del	p.Arg273SerfsTer27	p.R273Sfs*27	ENST00000399503	NM_005921.1	273	AGa/a	3/20	0.443888959323234	5	FACETS	0.894	0.843	0.947	0.894	0.843	0.947	CLONAL	3	TRUE	2	0.443888959323234	5		262	758	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419914	152419914	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519715	NA	P-0001952-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	151	238	0	ENST00000206249.3:c.1601T>A	p.Val534Glu	p.V534E	ENST00000206249	NM_000125.3	534	gTg/gAg	8/8	0.443888959323234	5	FACETS	0.776	0.711	0.844	0.518	0.474	0.563	SUBCLONAL	2	TRUE	2	0.443888959323234	5		238	730	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913284	39913285	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATCATCTG	novel	NA	P-0001952-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	147	364	0	ENST00000378444.4:c.4823_4830dup	p.Glu1611GlnfsTer10	p.E1611Qfs*10	ENST00000378444	NM_001123385.1	1610	-/CAGATGAT	14/15	0.313733796965835	0	FACETS	0.69	0.633	0.748			1	SUBCLONAL	1	TRUE	0	0.443888959323234	0		364	534	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160539	56160568	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AATAAAAAAAAATGTTGTGAAGTTTCAGAG	AATAAAAAAAAATGTTGTGAAGTTTCAGAG	TTTT	novel	NA	P-0001952-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	216	212	0	ENST00000399503.3:c.835-22_842delinsTTTT		p.X279_splice	ENST00000399503	NM_005921.1	279		4/20	0.443888959323234	5	FACETS	0.848	0.793	0.905	0.848	0.793	0.905	CLONAL	3	TRUE	2	0.443888959323234	5		212	637	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519938	NA	P-0002004-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	246	417	0	ENST00000263967.3:c.1034A>T	p.Asn345Ile	p.N345I	ENST00000263967	NM_006218.2	345	aAt/aTt	5/21	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.39	2		417	536	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0002004-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	379	400	2	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.836	0.799	0.873	1	0.997	1	CLONAL	3	TRUE	1	0.39	2		402	775	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182192	99182192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763716402	NA	P-0002004-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	291	404	0	ENST00000074304.5:c.2257G>A	p.Ala753Thr	p.A753T	ENST00000074304	NM_001134224.1	753	Gcc/Acc	21/26	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.39	2		404	655	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0002004-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	296	489	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.39	2		489	643	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692979	89692979	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123325	NA	P-0002004-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	246	344	0	ENST00000371953.3:c.463T>C	p.Tyr155His	p.Y155H	ENST00000371953	NM_000314.4	155	Tat/Cat	5/9	1	2	FACETS	0.865	0.819	0.911	1	0.996	1	CLONAL	3	TRUE	1	0.39	2		344	486	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136173	11136173	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002004-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	256	424	0	ENST00000358026.2:c.3157C>T	p.Gln1053Ter	p.Q1053*	ENST00000358026	NM_001128849.1	1053	Cag/Tag	22/36	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.39	2		424	546	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592163	67592164	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTAG	novel	NA	P-0002004-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	157	328	0	ENST00000274335.5:c.1984_1985+3dup		p.S660fs	ENST00000274335		660	tct/tcTGTAGt	14/15	1	2	FACETS	0.928	0.858	0.998	1	0.992	1	CLONAL	2	TRUE	1	0.39	2		328	434	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653863	89653895	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAAGGTAAGAATGCTTTGATTTTCTATTTCAAA	TAAGGTAAGAATGCTTTGATTTTCTATTTCAAA	-	novel	NA	P-0002004-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	137	351	0	ENST00000371953.3:c.163_164+31del		p.X55_splice	ENST00000371953	NM_000314.4	55		2/9	1	2	FACETS	0.789	0.724	0.857	1	0.989	1	SUBCLONAL	2	TRUE	1	0.39	2		351	445	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097021	11097033	+	frameshift_variant	Frame_Shift_Del	DEL	CATTTAACCAGAA	CATTTAACCAGAA	-	novel	NA	P-0002004-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	265	520	0	ENST00000358026.2:c.513_525del	p.Phe172SerfsTer127	p.F172Sfs*127	ENST00000358026	NM_001128849.1	171	cCATTTAACCAGAAc/cc	4/36	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.39	2		520	574	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572944	41572944	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002004-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	275	515	0	ENST00000263253.7:c.5230del	p.His1744MetfsTer18	p.H1744Mfs*18	ENST00000263253	NM_001429.3	1743	gtC/gt	31/31	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.39	2		515	598	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255475	16255475	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002006-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	101	269	0	ENST00000375759.3:c.2740G>A	p.Asp914Asn	p.D914N	ENST00000375759	NM_015001.2	914	Gac/Aac	11/15	0.307259866750802	1	FACETS	0.957	0.858	1	0.957	0.858	1	CLONAL	1	TRUE	0	0.311962450471161	1		269	571	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589536	67589536	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0002006-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	27	216	0	ENST00000274335.5:c.1300-1G>T		p.X434_splice	ENST00000274335		434			0.307259866750802	1	FACETS	0.299	0.237	0.37	0.299	0.237	0.37	SUBCLONAL	1	TRUE	0	0.311962450471161	1		216	488	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625263	69625263	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002006-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	60	339	0	ENST00000334134.2:c.530T>C	p.Leu177Pro	p.L177P	ENST00000334134	NM_005247.2	177	cTg/cCg	3/3	1	2	FACETS	0.642	0.553	0.739	0.642	0.553	0.739	SUBCLONAL	1	TRUE	1	0.311962450471161	2		339	599	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050979	49050979	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002006-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	67	183	0	ENST00000267163.4:c.2663G>C	p.Ser888Thr	p.S888T	ENST00000267163	NM_000321.2	888	aGt/aCt	25/27	0.307259866750802	1	FACETS	0.925	0.807	1	0.925	0.807	1	CLONAL	1	TRUE	0	0.311962450471161	1		183	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577599	7577600	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1567550002	NA	P-0002006-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	112	228	0	ENST00000269305.4:c.681dup	p.Asp228Ter	p.D228*	ENST00000269305	NM_001126112.2	227	-/T	7/11	0.244505528601379	2	FACETS	0.818	0.74	0.898	0.818	0.74	0.898	CLONAL	2	TRUE	0	0.311962450471161	2		228	439	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589586	67589591	+	inframe_deletion	In_Frame_Del	DEL	ATGAAT	ATGAAT	-	novel	NA	P-0002022-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	370	695	0	ENST00000274335.5:c.1351_1356del	p.Glu451_Tyr452del	p.E451_Y452del	ENST00000274335		450	cATGAATat/cat	10/15	0.558777751420507	3	FACETS	0.967	0.922	1	0.967	0.922	1	CLONAL	2	TRUE	1	0.558777751420507	3		695	876	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002022-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	184	568	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	0.168967458923365	4	FACETS	0.897	0.834	0.963	0.897	0.834	0.963	INDETERMINATE	2	TRUE	2	0.558777751420507	4		568	572	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221710	55221710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002022-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	30	630	0	ENST00000275493.2:c.754C>T	p.Arg252Cys	p.R252C	ENST00000275493	NM_005228.3	252	Cgc/Tgc	7/28	0.312299075720345	5	FACETS	0.335	0.269	0.41	0.112	0.089	0.137	INDETERMINATE	1	TRUE	2	0.558777751420507	5		630	589	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201685	67201685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536484524	NA	P-0002022-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	158	854	0	ENST00000312629.5:c.986G>A	p.Arg329Gln	p.R329Q	ENST00000312629	NM_003952.2	329	cGg/cAg	12/15	0.313867934975459	3	FACETS	1	0.966	1	0.547	0.503	0.593	INDETERMINATE	1	TRUE	1	0.558777751420507	3		854	661	SUCCESS
ATM	472	MSKCC	GRCh37	11	108127010	108127010	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs2229019	NA	P-0002022-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	410	844	0	ENST00000278616.4:c.2193C>A	p.Tyr731Ter	p.Y731*	ENST00000278616	NM_000051.3	731	taC/taA	14/63	0.331975470476916	3	FACETS	1	0.994	1	0.812	0.779	0.844	INDETERMINATE	2	TRUE	0	0.558777751420507	3		844	771	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721151	176721152	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0002022-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	104	431	0	ENST00000439151.2:c.6782_6783insA	p.Met2261IlefsTer20	p.M2261Ifs*20	ENST00000439151	NM_022455.4	2261	atg/atAg	23/23	1	2	FACETS	0.919	0.829	1	0.919	0.829	1	CLONAL	1	TRUE	1	0.558777751420507	2		431	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0002048-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	173	254	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.536231303700287	3	FACETS	0.821	0.756	0.888	0.41	0.378	0.444	CLONAL	1	TRUE	1	0.657495824390935	3		255	852	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579419	7579420	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs587783062	NA	P-0002048-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	310	341	0	ENST00000269305.4:c.267dup	p.Ser90LeufsTer59	p.S90Lfs*59	ENST00000269305	NM_001126112.2	89	-/C	4/11	0.536231303700287	3	FACETS	0.88	0.835	0.925	0.88	0.835	0.925	CLONAL	2	TRUE	1	0.657495824390935	3		341	712	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0002048-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	225	214	0	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	0.628269484452687	2	FACETS	0.965	0.903	1	0.483	0.451	0.515	CLONAL	1	TRUE	0	0.657495824390935	2		214	709	SUCCESS
APC	324	MSKCC	GRCh37	5	112175324	112175324	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1211642532	NA	P-0002048-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	136	268	0	ENST00000257430.4:c.4033G>T	p.Glu1345Ter	p.E1345*	ENST00000257430	NM_000038.5	1345	Gaa/Taa	16/16	1	2	FACETS	0.827	0.757	0.9	0.827	0.757	0.9	CLONAL	1	TRUE	1	0.657495824390935	2		268	500	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125500	47125500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002048-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	493	405	0	ENST00000409792.3:c.5770C>T	p.Gln1924Ter	p.Q1924*	ENST00000409792	NM_014159.6	1924	Cag/Tag	12/21	0.628269484452687	2	FACETS	0.916	0.884	0.946	0.916	0.884	0.946	CLONAL	2	TRUE	0	0.657495824390935	2		405	819	SUCCESS
APC	324	MSKCC	GRCh37	5	112137081	112137081	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1554076225	NA	P-0002048-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	132	192	0	ENST00000257430.4:c.834+1G>A		p.X278_splice	ENST00000257430	NM_000038.5	278			1	2	FACETS	0.965	0.884	1	0.965	0.884	1	CLONAL	1	TRUE	1	0.657495824390935	2		192	416	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200377	138200377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002048-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	148	234	0	ENST00000237289.4:c.1795G>A	p.Gly599Arg	p.G599R	ENST00000237289	NM_001270507.1	599	Ggg/Agg	7/9	NA	2	FACETS	0.795	0.73	0.863			1	INDETERMINATE	1	TRUE	NA	0.657495824390935	2		234	566	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0002085-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	118	599	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.25966931261705	3	FACETS	1	0.956	1	0.548	0.496	0.604	CLONAL	1	TRUE	1	0.420675081872996	3		599	619	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259502	55259502	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002085-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	116	361	0	ENST00000275493.2:c.2560A>T	p.Thr854Ser	p.T854S	ENST00000275493	NM_005228.3	854	Aca/Tca	21/28	0.25966931261705	3	FACETS	1	0.953	1	0.545	0.493	0.601	CLONAL	1	TRUE	1	0.420675081872996	3		361	612	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030485	49030485	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs483352690	NA	P-0002085-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	23	213	0	ENST00000267163.4:c.1960G>A	p.Val654Met	p.V654M	ENST00000267163	NM_000321.2	654	Gtg/Atg	19/27	0.174201370876308	0	FACETS	0.183	0.142	0.23			1	INDETERMINATE	1	TRUE	0	0.420675081872996	0		213	347	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678619	88678619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148888023	NA	P-0002085-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	15	156	0	ENST00000360948.2:c.917G>A	p.Arg306His	p.R306H	ENST00000360948	NM_001012338.2	306	cGt/cAt	9/19	0.420675081872996	1	FACETS	0.295	0.216	0.389	0.295	0.216	0.389	SUBCLONAL	1	TRUE	0	0.420675081872996	1		156	191	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0002085-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	105	358	0	ENST00000269305.4:c.560-2A>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.29241907743633	1	FACETS	0.857	0.772	0.946	0.857	0.772	0.946	CLONAL	1	TRUE	0	0.420675081872996	1		358	460	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702569	52702569	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002085-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	119	384	0	ENST00000394830.3:c.329del	p.Asn110IlefsTer3	p.N110Ifs*3	ENST00000394830	NM_018313.4	110	aAt/at	4/30	0.420675081872996	1	FACETS	0.773	0.7	0.85	0.773	0.7	0.85	SUBCLONAL	1	TRUE	0	0.420675081872996	1		384	578	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717713	89717714	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002085-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	95	301	0	ENST00000371953.3:c.740dup	p.Leu247PhefsTer6	p.L247Ffs*6	ENST00000371953	NM_000314.4	246	-/T	7/9	0.327271503740387	1	FACETS	0.732	0.655	0.814	0.732	0.655	0.814	SUBCLONAL	1	TRUE	0	0.420675081872996	1		301	487	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115888	8115889	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0002244-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	365	323	0	ENST00000346208.3:c.1236dup	p.Ser413GlnfsTer94	p.S413Qfs*94	ENST00000346208		412	tcc/tCcc	6/6	0.110745895559945	4	FACETS	0.913	0.869	0.957	0.913	0.869	0.957	INDETERMINATE	2	FALSE	2	0.82262222316856	4		323	886	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577497	64577497	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs794728615	NA	P-0002244-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	323	202	0	ENST00000312049.6:c.85C>T	p.Arg29Ter	p.R29*	ENST00000312049	NM_130799.2	29	Cga/Tga	2/10	0.571793967573696	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	0	0.82262222316856	1		202	453	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226330	2226330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778416555	NA	P-0002244-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	605	300	1	ENST00000326181.6:c.1943C>T	p.Ala648Val	p.A648V	ENST00000326181	NM_032271.2	648	gCg/gTg	20/21	0.124158652704825	4	FACETS	1	0.989	1	1	0.989	1	INDETERMINATE	2	FALSE	2	0.82262222316856	4		301	1269	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296182	15296182	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519101	NA	P-0002244-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	296	239	0	ENST00000263388.2:c.2182C>T	p.Arg728Cys	p.R728C	ENST00000263388	NM_000435.2	728	Cgc/Tgc	14/33	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.82262222316856	2		239	690	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115725	8115728	+	frameshift_variant	Frame_Shift_Del	DEL	GAAG	GAAG	-	novel	NA	P-0002244-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	439	346	0	ENST00000346208.3:c.1076_1079del	p.Glu359AlafsTer44	p.E359Afs*44	ENST00000346208		357	aaGAAG/aa	6/6	0.110745895559945	4	FACETS	1	0.967	1	1	0.967	1	INDETERMINATE	2	FALSE	2	0.82262222316856	4		346	963	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0002280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	223	247	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.875	0.817	0.934	0.875	0.817	0.934	CLONAL	1	TRUE	1	0.676258468379146	2		247	754	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	542	436	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.882	0.853	0.91	1	0.998	1	CLONAL	2	TRUE	1	0.676258468379146	2		436	909	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434367	121434367	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	222	421	1	ENST00000257555.6:c.1136del	p.Pro379LeufsTer5	p.P379Lfs*5	ENST00000257555		377	ctC/ct	6/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.676258468379146	2		422	644	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294175	1294175	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	40	269	0	ENST00000310581.5:c.826G>A	p.Ala276Thr	p.A276T	ENST00000310581	NM_198253.2	276	Gcc/Acc	2/16	NA	2	FACETS	0.262	0.217	0.311			1	INDETERMINATE	1	TRUE	NA	0.676258468379146	2		269	452	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057936	27057937	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1415146710	NA	P-0002280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	236	364	0	ENST00000324856.7:c.1650dup	p.Tyr551LeufsTer72	p.Y551Lfs*72	ENST00000324856	NM_006015.4	548	-/C	3/20	1	2	FACETS	0.882	0.826	0.94	0.882	0.826	0.94	CLONAL	1	TRUE	1	0.676258468379146	2		364	791	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0002280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	294	496	0	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	1	2	FACETS	0.894	0.842	0.946	0.894	0.842	0.946	CLONAL	1	TRUE	1	0.676258468379146	2		496	973	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258817	16258817	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs746795233	NA	P-0002280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	264	395	0	ENST00000375759.3:c.6082A>G	p.Met2028Val	p.M2028V	ENST00000375759	NM_015001.2	2028	Atg/Gtg	11/15	1	2	FACETS	0.963	0.906	1	0.963	0.906	1	CLONAL	1	TRUE	1	0.676258468379146	2		395	811	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023390	27023390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	215	271	2	ENST00000324856.7:c.496G>A	p.Ala166Thr	p.A166T	ENST00000324856	NM_006015.4	166	Gcc/Acc	1/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.676258468379146	2		273	556	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99154355	99154355	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	208	365	0	ENST00000074304.5:c.497T>C	p.Ile166Thr	p.I166T	ENST00000074304	NM_001134224.1	166	aTc/aCc	8/26	1	2	FACETS	0.895	0.835	0.958	0.895	0.835	0.958	CLONAL	1	TRUE	1	0.676258468379146	2		365	687	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648416	30648416	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	246	302	0	ENST00000295754.5:c.41T>C	p.Ile14Thr	p.I14T	ENST00000295754	NM_003242.5	14	aTc/aCc	1/7	1	2	FACETS	0.991	0.931	1	0.991	0.931	1	CLONAL	1	TRUE	1	0.676258468379146	2		302	734	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947865	178947865	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	373	530	0	ENST00000263967.3:c.2740G>C	p.Gly914Arg	p.G914R	ENST00000263967	NM_006218.2	914	Gga/Cga	19/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.676258468379146	2		530	1073	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190891	185190891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777869754	NA	P-0002280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	348	552	2	ENST00000265026.3:c.1772G>A	p.Arg591His	p.R591H	ENST00000265026	NM_004721.4	591	cGc/cAc	11/14	1	2	FACETS	0.996	0.945	1	0.996	0.945	1	CLONAL	1	TRUE	1	0.676258468379146	2		554	1033	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876264	35876264	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	264	409	1	ENST00000303115.3:c.1056G>T	p.Glu352Asp	p.E352D	ENST00000303115	NM_002185.3	352	gaG/gaT	8/8	1	2	FACETS	0.982	0.924	1	0.982	0.924	1	CLONAL	1	TRUE	1	0.676258468379146	2		410	795	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98244261	98244261	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	316	607	0	ENST00000331920.6:c.716C>T	p.Ala239Val	p.A239V	ENST00000331920	NM_000264.3	239	gCg/gTg	5/24	1	2	FACETS	0.92	0.869	0.971	0.92	0.869	0.971	CLONAL	1	TRUE	1	0.676258468379146	2		607	1016	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218092	108218092	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1565567541	NA	P-0002280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	225	308	0	ENST00000278616.4:c.8671G>A	p.Gly2891Ser	p.G2891S	ENST00000278616	NM_000051.3	2891	Ggt/Agt	59/63	1	2	FACETS	0.925	0.866	0.987	0.925	0.866	0.987	CLONAL	1	TRUE	1	0.676258468379146	2		308	719	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012380	29012380	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	265	514	0	ENST00000282397.4:c.491A>T	p.Asn164Ile	p.N164I	ENST00000282397	NM_002019.4	164	aAc/aTc	4/30	0.125672906520194	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.676258468379146	0		514	914	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81563048	81563048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760702366	NA	P-0002280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	312	483	0	ENST00000298171.2:c.611C>T	p.Ala204Val	p.A204V	ENST00000298171	NM_000369.2	204	gCt/gTt	7/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.676258468379146	2		483	857	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645384	67645384	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	236	407	0	ENST00000264010.4:c.649G>T	p.Glu217Ter	p.E217*	ENST00000264010	NM_006565.3	217	Gag/Tag	3/12	1	2	FACETS	0.943	0.884	1	0.943	0.884	1	CLONAL	1	TRUE	1	0.676258468379146	2		407	740	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78831603	78831603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	211	420	0	ENST00000306801.3:c.1412G>A	p.Gly471Asp	p.G471D	ENST00000306801	NM_020761.2	471	gGc/gAc	13/34	1	2	FACETS	0.895	0.835	0.957	0.895	0.835	0.957	CLONAL	1	TRUE	1	0.676258468379146	2		420	697	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350217	15350217	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	102	518	0	ENST00000263377.2:c.3562G>T	p.Val1188Phe	p.V1188F	ENST00000263377	NM_058243.2	1188	Gtt/Ttt	17/20	1	2	FACETS	0.313	0.279	0.349	0.313	0.279	0.349	SUBCLONAL	1	TRUE	1	0.676258468379146	2		518	965	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791721	42791721	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	266	419	0	ENST00000575354.2:c.607C>G	p.Pro203Ala	p.P203A	ENST00000575354	NM_015125.3	203	Ccc/Gcc	5/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.676258468379146	2		419	768	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775625	39775625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140222241	NA	P-0002280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	181	277	0	ENST00000288319.7:c.395C>T	p.Thr132Met	p.T132M	ENST00000288319	NM_182918.3	132	aCg/aTg	4/10	1	2	FACETS	0.895	0.83	0.962	0.895	0.83	0.962	CLONAL	1	TRUE	1	0.676258468379146	2		277	598	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343005	70343005	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1569481124	NA	P-0002280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	243	489	0	ENST00000374080.3:c.1546C>T	p.Arg516Cys	p.R516C	ENST00000374080		516	Cgt/Tgt	11/45	1	2	FACETS	0.87	0.815	0.926	0.87	0.815	0.926	CLONAL	1	TRUE	1	0.676258468379146	2		489	826	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611219	100611219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781792640	NA	P-0002280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	234	415	1	ENST00000308731.7:c.1387G>A	p.Val463Ile	p.V463I	ENST00000308731	NM_000061.2	463	Gtc/Atc	15/19	1	2	FACETS	0.982	0.92	1	0.982	0.92	1	CLONAL	1	TRUE	1	0.676258468379146	2		416	705	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456453	29456453	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1558630501	NA	P-0002280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	335	574	0	ENST00000389048.3:c.2465del	p.Gly822ValfsTer9	p.G822Vfs*9	ENST00000389048	NM_004304.4	822	gGt/gt	14/29	1	2	FACETS	0.917	0.868	0.966	0.917	0.868	0.966	CLONAL	1	TRUE	1	0.676258468379146	2		574	1081	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553281	106553281	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	294	427	0	ENST00000369096.4:c.1251del	p.Tyr418ThrfsTer3	p.Y418Tfs*3	ENST00000369096	NM_001198.3	416	Ccc/cc	5/7	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.676258468379146	2		427	824	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1039278	1039281	+	frameshift_variant	Frame_Shift_Del	DEL	ATTA	ATTA	-	novel	NA	P-0002280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	278	603	0	ENST00000358495.3:c.216_219del	p.Asn73TrpfsTer38	p.N73Wfs*38	ENST00000358495	NM_134424.2	72	atTAAT/at	4/12	1	2	FACETS	0.853	0.802	0.905	0.853	0.802	0.905	CLONAL	1	TRUE	1	0.676258468379146	2		603	964	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0002280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	219	650	7	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.802	0.747	0.857	0.802	0.747	0.857	CLONAL	1	TRUE	1	0.676258468379146	2		657	808	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375193	31375194	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0002280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	223	392	0	ENST00000328111.2:c.596dup	p.Met200HisfsTer89	p.M200Hfs*89	ENST00000328111	NM_006892.3	197	cag/caGg	6/23	1	2	FACETS	0.935	0.875	0.998	0.935	0.875	0.998	CLONAL	1	TRUE	1	0.676258468379146	2		392	705	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106696	27106696	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	281	440	1	ENST00000324856.7:c.6310del	p.Ser2104ProfsTer31	p.S2104Pfs*31	ENST00000324856	NM_006015.4	2103	Ttt/tt	20/20	1	2	FACETS	0.956	0.901	1	0.956	0.901	1	CLONAL	1	TRUE	1	0.676258468379146	2		441	869	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0002315-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	263	376	0	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	0.409633435817605	2	FACETS	0.947	0.893	1	0.947	0.893	1	CLONAL	2	TRUE	0	0.409633435817605	2		376	678	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294045	1294045	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1213662764	NA	P-0002315-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	142	474	2	ENST00000310581.5:c.956C>T	p.Thr319Met	p.T319M	ENST00000310581	NM_198253.2	319	aCg/aTg	2/16	0.409633435817605	3	FACETS	0.892	0.813	0.976	0.446	0.406	0.488	CLONAL	1	TRUE	1	0.409633435817605	3		476	936	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433724	149433724	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002315-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	182	450	0	ENST00000286301.3:c.2827G>C	p.Glu943Gln	p.E943Q	ENST00000286301	NM_005211.3	943	Gag/Cag	22/22	0.395520996597594	3	FACETS	0.963	0.887	1	0.321	0.295	0.348	CLONAL	1	TRUE	0	0.409633435817605	3		450	1112	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680745	30680745	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002315-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	110	508	0	ENST00000376406.3:c.974G>C	p.Gly325Ala	p.G325A	ENST00000376406	NM_014641.2	325	gGc/gCc	5/15	0.409633435817605	3	FACETS	0.675	0.606	0.749	0.338	0.303	0.375	SUBCLONAL	1	TRUE	1	0.409633435817605	3		508	958	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416200	416200	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0002315-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	70	532	0	ENST00000399788.2:c.3986C>G	p.Ser1329Ter	p.S1329*	ENST00000399788	NM_001042603.1	1329	tCa/tGa	24/28	NA	2	FACETS	0.551	0.481	0.628			1	INDETERMINATE	1	TRUE	NA	0.409633435817605	2		532	620	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557535	21557535	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002315-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	114	489	0	ENST00000382592.4:c.2310C>G	p.Phe770Leu	p.F770L	ENST00000382592	NM_014572.2	770	ttC/ttG	5/8	0.409633435817605	1	FACETS	0.716	0.646	0.79	0.716	0.646	0.79	SUBCLONAL	1	TRUE	0	0.409633435817605	1		489	618	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56811519	56811519	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0002315-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	53	465	0	ENST00000337432.4:c.1067C>G	p.Ser356Ter	p.S356*	ENST00000337432	NM_058216.2	356	tCa/tGa	9/9	0.409633435817605	2	FACETS	0.57	0.487	0.661	0.285	0.243	0.331	SUBCLONAL	1	TRUE	0	0.409633435817605	2		465	454	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101129	4101129	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs376969315	NA	P-0002315-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	92	291	0	ENST00000262948.5:c.593C>G	p.Ser198Cys	p.S198C	ENST00000262948	NM_030662.3	198	tCc/tGc	6/11	0.35091638646362	2	FACETS	0.889	0.793	0.992	0.445	0.396	0.496	CLONAL	1	TRUE	0	0.409633435817605	2		291	505	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169948	32169949	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0002315-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	144	491	0	ENST00000375023.3:c.3659dup	p.Cys1220TrpfsTer15	p.C1220Wfs*15	ENST00000375023	NM_004557.3	1220	tgc/tgGc	21/30	0.409633435817605	3	FACETS	0.871	0.793	0.952	0.435	0.396	0.476	CLONAL	1	TRUE	1	0.409633435817605	3		491	973	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0002324-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	85	285	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.831	0.737	0.931	1	0.982	1	CLONAL	2	TRUE	1	0.21	2		285	487	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002324-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	106	819	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.21	2		819	745	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240732	53240732	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002324-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	158	536	0	ENST00000375401.3:c.1348G>C	p.Gly450Arg	p.G450R	ENST00000375401	NM_004187.3	450	Ggc/Cgc	10/26	1	2	FACETS	0.763	0.699	0.831	1	0.988	1	SUBCLONAL	2	TRUE	1	0.21	2		536	986	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0002327-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	40	249	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	FALSE	1	0.324124053040776	2		249	208	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0002327-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	67	265	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.98	0.855	1	0.98	0.855	1	CLONAL	1	FALSE	1	0.324124053040776	2		265	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs863224683	NA	P-0002327-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	138	284	0	ENST00000269305.4:c.388C>G	p.Leu130Val	p.L130V	ENST00000269305	NM_001126112.2	130	Ctc/Gtc	5/11	0.324124053040776	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	0	0.324124053040776	1		284	663	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509436	106509436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200175951	NA	P-0002327-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	117	452	1	ENST00000359195.3:c.1430G>A	p.Arg477His	p.R477H	ENST00000359195	NM_002649.2	477	cGt/cAt	2/11	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	FALSE	1	0.324124053040776	2		453	685	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597976	43597976	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774097284	NA	P-0002327-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	217	467	1	ENST00000355710.3:c.524G>A	p.Arg175His	p.R175H	ENST00000355710	NM_020975.4	175	cGc/cAc	3/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.324124053040776	2		468	1097	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377271	118377271	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1555048532	NA	P-0002327-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	119	508	0	ENST00000534358.1:c.10664G>T	p.Gly3555Val	p.G3555V	ENST00000534358	NM_005933.3	3555	gGc/gTc	27/36	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	FALSE	1	0.324124053040776	2		508	728	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207076	1207076	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1131690943	NA	P-0002327-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	166	370	0	ENST00000326873.7:c.164T>C	p.Leu55Pro	p.L55P	ENST00000326873	NM_000455.4	55	cTg/cCg	1/10	0.324124053040776	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	0	0.324124053040776	1		370	822	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659631	88659632	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0002327-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	48	395	0	ENST00000372037.3:c.419dup	p.Val141CysfsTer8	p.V141Cfs*8	ENST00000372037	NM_004329.2	138	-/C	6/13	1	2	FACETS	0.861	0.731	1	0.861	0.731	1	CLONAL	1	FALSE	1	0.324124053040776	2		395	344	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0002387-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	217	250	2	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.538058896878289	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	1	0.538058896878289	4		252	378	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0002387-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	236	491	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	0.520918386733431	4	FACETS	0.78	0.729	0.832	0.52	0.486	0.555	SUBCLONAL	2	TRUE	1	0.538058896878289	4		491	865	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002387-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	288	460	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.538058896878289	1	FACETS	0.795	0.759	0.831	1	0.995	1	SUBCLONAL	2	TRUE	0	0.538058896878289	1		460	492	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0002417-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	518	285	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.984	0.958	1	1	0.998	1	CLONAL	2	TRUE	1	0.757308408911114	2		285	695	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727455	66727455	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs869025608	NA	P-0002417-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	65	428	1	ENST00000307102.5:c.171G>T	p.Lys57Asn	p.K57N	ENST00000307102	NM_002755.3	57	aaG/aaT	2/11	1	2	FACETS	0.161	0.139	0.186	0.161	0.139	0.186	SUBCLONAL	1	TRUE	1	0.757308408911114	2		429	1065	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184750	185184750	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs752255390	NA	P-0002417-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	360	430	0	ENST00000265026.3:c.1642C>T	p.Arg548Trp	p.R548W	ENST00000265026	NM_004721.4	548	Cgg/Tgg	10/14	1	2	FACETS	0.965	0.917	1	0.965	0.917	1	CLONAL	1	TRUE	1	0.757308408911114	2		430	985	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115750	8115750	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs104894164	NA	P-0002417-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	631	619	0	ENST00000346208.3:c.1096C>T	p.Arg366Ter	p.R366*	ENST00000346208		366	Cga/Tga	6/6	0.757308408911114	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.757308408911114	1		619	1009	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435136	18435136	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002417-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	53	432	0	ENST00000266497.5:c.121G>C	p.Asp41His	p.D41H	ENST00000266497		41	Gat/Cat	1/31	1	2	FACETS	0.138	0.117	0.162	0.138	0.117	0.162	SUBCLONAL	1	TRUE	1	0.757308408911114	2		432	1012	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423598	88423598	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002417-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	51	463	0	ENST00000360948.2:c.2237A>C	p.Lys746Thr	p.K746T	ENST00000360948	NM_001012338.2	746	aAg/aCg	18/19	1	2	FACETS	0.139	0.117	0.163	0.139	0.117	0.163	SUBCLONAL	1	TRUE	1	0.757308408911114	2		463	971	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352706	118352707	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATCCC	novel	NA	P-0002417-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	110	351	0	ENST00000534358.1:c.3911_3912insATCCC	p.Ile1305SerfsTer53	p.I1305Sfs*53	ENST00000534358	NM_005933.3	1304	gtc/gtATCCCc	7/36	0.757308408911114	1	FACETS	0.342	0.308	0.377	0.342	0.308	0.377	SUBCLONAL	1	TRUE	0	0.757308408911114	1		351	528	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778157	135778161	+	frameshift_variant	Frame_Shift_Del	DEL	TAACT	TAACT	-	novel	NA	P-0002589-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	70	404	0	ENST00000298552.3:c.2222_2226del	p.Lys741ThrfsTer11	p.K741Tfs*11	ENST00000298552	NM_001162426.1	741	aAGTTA/a	18/23	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		404	379	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781025	135781026	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0002589-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	104	477	1	ENST00000298552.3:c.1939dup	p.Glu647GlyfsTer41	p.E647Gfs*41	ENST00000298552	NM_001162426.1	647	gaa/gGaa	15/23	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		478	480	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152276	99152276	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772559256	NA	P-0002679-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	109	326	0	ENST00000074304.5:c.355G>A	p.Val119Met	p.V119M	ENST00000074304	NM_001134224.1	119	Gtg/Atg	6/26	NA	2	FACETS	0.449	0.404	0.496			1	INDETERMINATE	1	TRUE	NA	0.879395138203484	2		326	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579546	7579547	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	GGGGACAGCATCAA	novel	NA	P-0002679-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	180	218	0	ENST00000269305.4:c.127_140dup	p.Asp48Ter	p.D48*	ENST00000269305	NM_001126112.2	47	ccg/ccTTGATGCTGTCCCCg	4/11	0.607531808985222	1	FACETS	0.816	0.772	0.859	0.816	0.772	0.859	CLONAL	1	TRUE	0	0.879395138203484	1		218	281	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0002680-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	224	344	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	1	2	FACETS	0.998	0.937	1	0.998	0.937	1	CLONAL	1	TRUE	1	0.810209735025212	2		344	554	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860358	151860358	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002680-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	150	360	0	ENST00000262189.6:c.10304G>T	p.Gly3435Val	p.G3435V	ENST00000262189	NM_170606.2	3435	gGt/gTt	43/59	1	2	FACETS	0.715	0.657	0.774	0.715	0.657	0.774	SUBCLONAL	1	TRUE	1	0.810209735025212	2		360	518	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0002700-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	108	285	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.439218430465861	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	2	FALSE	0	0.515936352046298	2		285	209	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778785	9778785	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759798937	NA	P-0002700-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	54	223	0	ENST00000377346.4:c.1054G>A	p.Glu352Lys	p.E352K	ENST00000377346	NM_005026.3	352	Gag/Aag	9/24	0.515936352046298	1	FACETS	0.941	0.82	1	0.941	0.82	1	CLONAL	1	FALSE	0	0.515936352046298	1		223	165	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398843	398843	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002700-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	77	396	0	ENST00000380956.4:c.653G>C	p.Gly218Ala	p.G218A	ENST00000380956	NM_001195286.1	218	gGa/gCa	6/9	NA	2	FACETS	0.883	0.781	0.991			1	INDETERMINATE	1	FALSE	NA	0.515936352046298	2		396	338	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604517	43604517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754116867	NA	P-0002700-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	84	403	0	ENST00000355710.3:c.1102C>T	p.Arg368Cys	p.R368C	ENST00000355710	NM_020975.4	368	Cgc/Tgc	6/20	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	1	0.515936352046298	2		403	308	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348025	348025	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002700-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	66	354	0	ENST00000262320.3:c.1481C>G	p.Pro494Arg	p.P494R	ENST00000262320	NM_003502.3	494	cCg/cGg	6/11	0.149453993173505	0	FACETS	0.595	0.525	0.669			1	INDETERMINATE	1	FALSE	0	0.515936352046298	0		354	208	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856084	68856085	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0002700-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	87	469	0	ENST00000261769.5:c.1893dup	p.His632ThrfsTer31	p.H632Tfs*31	ENST00000261769	NM_004360.3	631	aca/acAa	12/16	0.39346221921609	0	FACETS	0.658	0.592	0.727			1	SUBCLONAL	1	FALSE	0	0.515936352046298	0		469	248	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0002717-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	245	435	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.3	3	FACETS	0.893	0.836	0.953	0.893	0.836	0.953	CLONAL	2	TRUE	1	0.32	3		435	994	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0002717-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	107	313	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.289942358090079	2	FACETS	0.885	0.801	0.972	0.885	0.801	0.972	CLONAL	2	TRUE	0	0.32	2		313	378	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0002717-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	90	571	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.711	0.63	0.798	0.711	0.63	0.798	SUBCLONAL	1	TRUE	1	0.32	2		571	791	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916946	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0002717-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	85	345	0	ENST00000263967.3:c.332_334del	p.Lys111del	p.K111del	ENST00000263967	NM_006218.2	111	AAG/-	2/21	1	2	FACETS	0.922	0.817	1	0.922	0.817	1	CLONAL	1	TRUE	1	0.32	2		345	576	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752960	128752960	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002717-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	171	471	0	ENST00000377970.2:c.1121A>G	p.His374Arg	p.H374R	ENST00000377970	NM_002467.4	374	cAc/cGc	3/3	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.32	2		471	793	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134230	2134230	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs148527903	NA	P-0002717-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	102	473	0	ENST00000219476.3:c.4007C>T	p.Ser1336Leu	p.S1336L	ENST00000219476	NM_000548.3	1336	tCg/tTg	34/42	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.32	2		473	627	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089696	27089697	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0002717-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	84	453	0	ENST00000324856.7:c.2657dup	p.Pro887ThrfsTer49	p.P887Tfs*49	ENST00000324856	NM_006015.4	884	-/C	8/20	1	2	FACETS	0.747	0.659	0.84	0.747	0.659	0.84	SUBCLONAL	1	TRUE	1	0.32	2		453	703	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084150	47084150	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002719-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	136	363	0	ENST00000409792.3:c.7139C>G	p.Pro2380Arg	p.P2380R	ENST00000409792	NM_014159.6	2380	cCc/cGc	17/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.577271417465968	2		363	448	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72893570	72893570	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002719-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	179	453	0	ENST00000325599.8:c.148A>G	p.Thr50Ala	p.T50A	ENST00000325599	NM_018130.2	50	Acc/Gcc	2/11	NA	2	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.577271417465968	2		453	600	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528603	89528603	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002719-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	124	406	0	ENST00000336596.2:c.2903G>T	p.Ser968Ile	p.S968I	ENST00000336596	NM_005233.5	968	aGc/aTc	17/17	NA	2	FACETS	0.868	0.79	0.949			1	INDETERMINATE	1	TRUE	NA	0.577271417465968	2		406	495	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246258	46246258	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002719-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	178	434	0	ENST00000334344.6:c.4352C>T	p.Pro1451Leu	p.P1451L	ENST00000334344	NM_152641.2	1451	cCt/cTt	15/21	0.181969748582772	3	FACETS	1	0.989	1	0.701	0.65	0.753	INDETERMINATE	1	TRUE	1	0.577271417465968	3		434	567	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016273	150016279	+	stop_gained,protein_altering_variant	Nonsense_Mutation	INS	CTTGGTA	CTTGGTA	GAATTCAATT	novel	NA	P-0002719-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	171	603	0	ENST00000253339.5:c.427_433delinsAATTGAATTC	p.Tyr143_Asp145delinsAsnTer	p.Y143_D145delinsN*	ENST00000253339		143	TACCAAGat/AATTGAATTCat	2/7	0.544645337600356	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.577271417465968	1		603	410	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0002751-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	11	282	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.211738512909528	1	FACETS	0.837	0.583	1	0.837	0.583	1	CLONAL	1	TRUE	0	0.211738512909528	1		282	111	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577035	7577036	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0002751-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	12	369	0	ENST00000269305.4:c.902dup	p.Gly302ArgfsTer4	p.G302Rfs*4	ENST00000269305	NM_001126112.2	301	cca/ccCa	8/11	0.1548536701654	1	FACETS	0.956	0.678	1	0.956	0.678	1	CLONAL	1	TRUE	0	0.211738512909528	1		369	106	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0002755-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	229	341	0	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	0.306647628768821	4	FACETS	0.939	0.885	0.992	0.939	0.885	0.992	CLONAL	4	TRUE	0	0.334155635920419	4		341	487	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945140	44945141	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0002755-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	201	470	0	ENST00000377967.4:c.3464_3465insG	p.Asn1156Ter	p.N1156*	ENST00000377967	NM_021140.2	1155	gtt/gtGt	24/29	0.275482221624378	5	FACETS	1	0.956	1			1	CLONAL	2	TRUE	NA	0.334155635920419	5		470	868	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436692	52436692	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0002792-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	24	291	0	ENST00000460680.1:c.1984-2A>G		p.X662_splice	ENST00000460680	NM_004656.3	662			1	2	FACETS	0.192	0.15	0.241	0.192	0.15	0.241	SUBCLONAL	1	FALSE	1	0.590650727152701	2		291	423	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142950062	142950062	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002792-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	21	195	0	ENST00000262992.4:c.2648G>A	p.Gly883Glu	p.G883E	ENST00000262992	NM_001101669.1	883	gGa/gAa	24/24	NA	2	FACETS	0.179	0.137	0.227			1	INDETERMINATE	1	FALSE	NA	0.590650727152701	2		195	398	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038717	47038717	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002792-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	82	79	0	ENST00000377604.3:c.725-1G>A		p.X242_splice	ENST00000377604	NM_001204468.1	242			1	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	0	0.590650727152701	1		79	174	SUCCESS
APC	324	MSKCC	GRCh37	5	112174808	112174817	+	frameshift_variant	Frame_Shift_Del	DEL	GTGGATCAGC	GTGGATCAGC	-	novel	NA	P-0002792-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	117	234	0	ENST00000257430.4:c.3517_3526del	p.Val1173LeufsTer6	p.V1173Lfs*6	ENST00000257430	NM_000038.5	1173	GTGGATCAGCct/ct	16/16	NA	2	FACETS	0.788	0.714	0.865			1	INDETERMINATE	1	FALSE	NA	0.590650727152701	2		234	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578266	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002792-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	146	285	0	ENST00000269305.4:c.583dup	p.Ile195AsnfsTer14	p.I195Nfs*14	ENST00000269305	NM_001126112.2	195	atc/aAtc	6/11	0.566957688312971	1	FACETS	0.783	0.721	0.847	0.783	0.721	0.847	SUBCLONAL	1	FALSE	0	0.590650727152701	1		285	445	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711975	89711975	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1554900635	NA	P-0002825-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	45	297	0	ENST00000371953.3:c.593T>A	p.Met198Lys	p.M198K	ENST00000371953	NM_000314.4	198	aTg/aAg	6/9	0.25515125121704	1	FACETS	0.695	0.586	0.816	0.695	0.586	0.816	SUBCLONAL	1	TRUE	0	0.299087084022797	1		297	368	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982355	25982355	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002825-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	71	342	0	ENST00000435504.4:c.935del	p.Arg312HisfsTer8	p.R312Hfs*8	ENST00000435504		312	cGa/ca	9/13	0.25515125121704	1	FACETS	0.889	0.779	1	0.889	0.779	1	CLONAL	1	TRUE	0	0.299087084022797	1		342	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577499	7577500	+	stop_gained,frameshift_variant,splice_region_variant	Nonsense_Mutation	INS	-	-	TAGG	novel	NA	P-0002825-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	95	318	1	ENST00000269305.4:c.781_782insCCTA	p.Ser261ThrfsTer2	p.S261Tfs*2	ENST00000269305	NM_001126112.2	261	agt/aCCTAgt	7/11	0.25515125121704	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.299087084022797	1		319	504	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0002876-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	200	352	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.342718913133788	5	FACETS	0.961	0.895	1	0.64	0.597	0.685	INDETERMINATE	2	TRUE	2	0.709014249385389	5		352	606	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971133	13971133	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002876-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	73	232	0	ENST00000405192.2:c.796G>T	p.Asp266Tyr	p.D266Y	ENST00000405192	NM_001163147.1	266	Gac/Tac	8/12	0.682230752753572	5	FACETS	0.841	0.738	0.953	0.28	0.245	0.318	CLONAL	1	TRUE	2	0.709014249385389	5		232	505	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509081	106509081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs187257485	NA	P-0002876-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	119	368	0	ENST00000359195.3:c.1075C>T	p.Arg359Cys	p.R359C	ENST00000359195	NM_002649.2	359	Cgc/Tgc	2/11	0.524787742119403	6	FACETS	1	0.97	1	0.395	0.357	0.435	CLONAL	1	TRUE	3	0.709014249385389	6		368	685	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs17849781	NA	P-0002876-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	290	429	0	ENST00000269305.4:c.832C>G	p.Pro278Ala	p.P278A	ENST00000269305	NM_001126112.2	278	Cct/Gct	8/11	0.486675088609065	2	FACETS	0.776	0.74	0.812	0.776	0.74	0.812	SUBCLONAL	2	TRUE	0	0.709014249385389	2		429	527	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0002884-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	73	435	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.934	0.816	1	0.934	0.816	1	CLONAL	1	FALSE	1	0.203624365487283	2		435	768	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0002884-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	32	285	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.78	0.633	0.946	0.78	0.633	0.946	CLONAL	1	FALSE	1	0.203624365487283	2		285	403	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0002884-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	91	473	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	NA	2	FACETS	1	0.949	1			1	INDETERMINATE	1	FALSE	NA	0.203624365487283	2		473	796	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477807	140477807	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs180177038	NA	P-0002884-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	65	407	1	ENST00000288602.6:c.1501G>A	p.Glu501Lys	p.E501K	ENST00000288602	NM_004333.4	501	Gaa/Aaa	12/18	0.146316006802661	3	FACETS	1	0.928	1	0.555	0.481	0.635	CLONAL	1	FALSE	1	0.203624365487283	3		408	634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579468	7579469	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0002884-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	68	257	0	ENST00000269305.4:c.218dup	p.Ala74GlyfsTer75	p.A74Gfs*75	ENST00000269305	NM_001126112.2	73	gtg/gtTg	4/11	1	2	FACETS	0.778	0.68	0.884	1	0.975	1	SUBCLONAL	2	FALSE	1	0.203624365487283	2		257	429	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0002902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	153	366	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	0.434441148824196	2		366	695	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0002902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	118	197	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.434441148824196	2		197	426	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466426	120466426	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	182	471	0	ENST00000256646.2:c.4693T>A	p.Phe1565Ile	p.F1565I	ENST00000256646	NM_024408.3	1565	Ttc/Atc	26/34	1	2	FACETS	0.974	0.9	1	0.974	0.9	1	CLONAL	1	TRUE	1	0.434441148824196	2		471	860	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249542	153249542	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0002902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	105	331	0	ENST00000281708.4:c.1237-1G>A		p.X413_splice	ENST00000281708	NM_033632.3	413			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.434441148824196	2		331	424	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332607	153332607	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	157	564	0	ENST00000281708.4:c.349G>T	p.Glu117Ter	p.E117*	ENST00000281708	NM_033632.3	117	Gag/Tag	2/12	1	2	FACETS	0.991	0.91	1	0.991	0.91	1	CLONAL	1	TRUE	1	0.434441148824196	2		564	729	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369226	118369226	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	141	342	0	ENST00000534358.1:c.5944G>T	p.Asp1982Tyr	p.D1982Y	ENST00000534358	NM_005933.3	1982	Gat/Tat	22/36	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.434441148824196	2		342	578	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134269	2134269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201979616	NA	P-0002902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	158	518	0	ENST00000219476.3:c.4046C>T	p.Ala1349Val	p.A1349V	ENST00000219476	NM_000548.3	1349	gCg/gTg	34/42	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.434441148824196	2		518	692	SUCCESS
APC	324	MSKCC	GRCh37	5	112173273	112173274	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0002902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	110	369	2	ENST00000257430.4:c.1982_1983insA	p.Cys661Ter	p.C661*	ENST00000257430	NM_000038.5	661	tgt/tgAt	16/16	1	2	FACETS	0.921	0.83	1	0.921	0.83	1	CLONAL	1	TRUE	1	0.434441148824196	2		371	550	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123695	46123695	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	112	321	0	ENST00000334344.6:c.77del	p.Phe26SerfsTer32	p.F26Sfs*32	ENST00000334344	NM_152641.2	26	Ttc/tc	1/21	1	2	FACETS	0.908	0.819	1	0.908	0.819	1	CLONAL	1	TRUE	1	0.434441148824196	2		321	568	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2132494	2132494	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	168	517	1	ENST00000219476.3:c.3874del	p.Ser1292ProfsTer33	p.S1292Pfs*33	ENST00000219476	NM_000548.3	1291	gTt/gt	32/42	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.434441148824196	2		518	739	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0002965-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	168	341	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.313670237075291	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.313670237075291	1		341	831	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285225	212285225	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002965-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	198	346	0	ENST00000342788.4:c.3076C>T	p.Gln1026Ter	p.Q1026*	ENST00000342788	NM_005235.2	1026	Cag/Tag	25/28	0.313670237075291	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.313670237075291	1		346	996	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55269458	55269458	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002965-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	224	417	0	ENST00000275493.2:c.3145T>C	p.Cys1049Arg	p.C1049R	ENST00000275493	NM_005228.3	1049	Tgc/Cgc	26/28	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.313670237075291	2		417	1336	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69203009	69203009	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002965-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	211	353	1	ENST00000462284.1:c.36G>T	p.Met12Ile	p.M12I	ENST00000462284	NM_002392.5	12	atG/atT	2/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.313670237075291	2		354	1274	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21553900	21553900	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002965-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	193	457	1	ENST00000382592.4:c.2702T>A	p.Val901Glu	p.V901E	ENST00000382592	NM_014572.2	901	gTg/gAg	7/8	0.313670237075291	1	FACETS	0.993	0.918	1	0.993	0.918	1	CLONAL	1	TRUE	0	0.313670237075291	1		458	1045	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763506	59763506	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002965-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	115	255	0	ENST00000259008.2:c.2596C>T	p.Gln866Ter	p.Q866*	ENST00000259008	NM_032043.2	866	Cag/Tag	19/20	1	2	FACETS	0.873	0.786	0.965	0.873	0.786	0.965	CLONAL	1	TRUE	1	0.313670237075291	2		255	840	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945780	17945781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0002965-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	151	315	0	ENST00000458235.1:c.2079dup	p.Glu694ArgfsTer10	p.E694Rfs*10	ENST00000458235	NM_000215.3	693	-/C	16/24	NA	2	FACETS	0.976	0.892	1			1	INDETERMINATE	1	TRUE	NA	0.313670237075291	2		315	986	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002975-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	98	819	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	0.176334605437725	3	FACETS	1	0.981	1	0.73	0.654	0.81	INDETERMINATE	1	TRUE	1	0.328491338092218	3		819	476	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574690	64574690	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002975-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	50	439	0	ENST00000312049.6:c.785del	p.Lys262SerfsTer19	p.K262Sfs*19	ENST00000312049	NM_130799.2	262	aAg/ag	5/10	0.229344095639253	1	FACETS	0.721	0.614	0.837	0.721	0.614	0.837	SUBCLONAL	1	TRUE	0	0.328491338092218	1		439	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003003-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	281	396	0	ENST00000269305.4:c.96+1G>A		p.X32_splice	ENST00000269305	NM_001126112.2	32			0.750735743166534	1	FACETS	0.904	0.861	0.948	0.904	0.861	0.948	CLONAL	1	TRUE	0	0.750735743166534	1		396	517	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409058	139409058	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003003-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	52	359	0	ENST00000277541.6:c.2111G>T	p.Cys704Phe	p.C704F	ENST00000277541	NM_017617.3	704	tGc/tTc	13/34	0.750735743166534	1	FACETS	0.175	0.149	0.204	0.175	0.149	0.204	SUBCLONAL	1	TRUE	0	0.750735743166534	1		359	495	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193849	106193850	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs777908833	NA	P-0003003-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	111	455	0	ENST00000380013.4:c.4317dup	p.Arg1440ThrfsTer38	p.R1440Tfs*38	ENST00000380013	NM_001127208.2	1437	-/A	10/11	1	2	FACETS	0.331	0.297	0.367	0.331	0.297	0.367	SUBCLONAL	1	TRUE	1	0.750735743166534	2		455	893	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001089	150001090	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	ACGATCAATCAAA	novel	NA	P-0003003-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	345	485	0	ENST00000253339.5:c.2502_2514dup	p.Asp839PhefsTer3	p.D839Ffs*3	ENST00000253339		838	-/TTTGATTGATCGT	4/7	0.750735743166534	1	FACETS	0.853	0.815	0.891	0.853	0.815	0.891	CLONAL	1	TRUE	0	0.750735743166534	1		485	673	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244878	46244878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003019-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	162	762	0	ENST00000334344.6:c.2972C>T	p.Ser991Phe	p.S991F	ENST00000334344	NM_152641.2	991	tCc/tTc	15/21	0.528292545833111	3	FACETS	0.939	0.863	1			1	CLONAL	1	TRUE	NA	0.609090838028397	3		762	739	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245449	46245449	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003019-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	105	435	0	ENST00000334344.6:c.3543T>G	p.Ser1181Arg	p.S1181R	ENST00000334344	NM_152641.2	1181	agT/agG	15/21	0.528292545833111	3	FACETS	0.922	0.83	1			1	CLONAL	1	TRUE	NA	0.609090838028397	3		435	488	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602886	55602887	+	inframe_insertion,splice_region_variant	In_Frame_Ins	INS	-	-	GAAGCA	novel	NA	P-0003019-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	114	461	0	ENST00000288135.5:c.2598_2603dup	p.Ser867_Ser868insArgSer	p.S867_S868insRS	ENST00000288135	NM_000222.2	866	gga/gGAAGCAga		0.293668072679244	6	FACETS	1	0.947	1	0.27	0.243	0.299	INDETERMINATE	1	TRUE	2	0.609090838028397	6		461	769	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	78	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.171008321074198	3	FACETS	1	0.977	1	0.738	0.654	0.826	INDETERMINATE	1	TRUE	1	0.395653042354538	3		249	320	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0003048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	84	597	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.370264574872361	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.395653042354538	1		597	314	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059214	47059214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141852778	NA	P-0003048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	33	326	0	ENST00000409792.3:c.7447G>A	p.Val2483Ile	p.V2483I	ENST00000409792	NM_014159.6	2483	Gtc/Atc	20/21	0.171008321074198	3	FACETS	0.664	0.542	0.8	0.332	0.271	0.4	INDETERMINATE	1	TRUE	1	0.395653042354538	3		326	301	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958219	2958219	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	41	376	0	ENST00000396946.4:c.2513C>T	p.Ala838Val	p.A838V	ENST00000396946	NM_032415.4	838	gCc/gTc	19/25	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.395653042354538	2		376	190	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195276	102195276	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	151	745	1	ENST00000263464.3:c.36T>G	p.Asn12Lys	p.N12K	ENST00000263464	NM_001165.4	12	aaT/aaG	2/9	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.395653042354538	2		746	624	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18276969	18276969	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	12	308	0	ENST00000222254.8:c.1417-1G>A		p.X473_splice	ENST00000222254	NM_005027.3	473			0.235981413729382	0	FACETS	0.154	0.108	0.211			1	INDETERMINATE	1	TRUE	0	0.395653042354538	0		308	238	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100315	27100315	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	104	573	0	ENST00000324856.7:c.4028del	p.Phe1343SerfsTer138	p.F1343Sfs*138	ENST00000324856	NM_006015.4	1343	Ttc/tc	17/20	0.327037239704815	2	FACETS	0.845	0.766	0.926	0.845	0.766	0.926	CLONAL	2	TRUE	0	0.395653042354538	2		573	311	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831196	72831197	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGC	rs570966249	NA	P-0003048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	38	798	0	ENST00000268489.5:c.5382_5384dup	p.Gln1794dup	p.Q1794dup	ENST00000268489	NM_006885.3	1794	cac/caGCAc	9/10	0.267007917442287	0	FACETS	0.337	0.279	0.402			1	SUBCLONAL	1	TRUE	0	0.395653042354538	0		798	344	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198263184	198263184	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0121502-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	175	401	0	ENST00000335508.6:c.3134+1G>A		p.X1045_splice	ENST00000335508	NM_012433.2	1045			1	2	FACETS	0.55	0.507	0.593	0.55	0.507	0.593	SUBCLONAL	1	NA	1	0.916381212636131	2		401	695	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146576	55146576	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs751123873	NA	P-0121502-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	195	482	1	ENST00000257290.5:c.2250G>T	p.Glu750Asp	p.E750D	ENST00000257290	NM_006206.4	750	gaG/gaT	16/23	1	2	FACETS	0.516	0.479	0.556	0.516	0.479	0.556	SUBCLONAL	1	NA	1	0.916381212636131	2		483	824	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170321	119170321	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs768228850	NA	P-0121502-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	448	374	0	ENST00000264033.4:c.2551G>T	p.Ala851Ser	p.A851S	ENST00000264033	NM_005188.3	851	Gcc/Tcc	16/16	0.916381212636131	2	FACETS	1	0.996	1	0.681	0.657	0.704	CLONAL	1	NA	0	0.916381212636131	2		374	718	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727908	41727909	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0121502-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	254	622	0	ENST00000301178.4:c.538dup	p.Leu180ProfsTer30	p.L180Pfs*30	ENST00000301178	NM_021913.4	178	gtc/gtCc	4/20	1	2	FACETS	0.514	0.481	0.548	0.514	0.481	0.548	SUBCLONAL	1	NA	1	0.916381212636131	2		622	1079	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601321	28601321	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121502-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	178	420	0	ENST00000241453.7:c.2111G>T	p.Arg704Ile	p.R704I	ENST00000241453	NM_004119.2	704	aGa/aTa	17/24	0.478227467982678	3	FACETS	0.57	0.525	0.617	0.285	0.262	0.309	INDETERMINATE	1	NA	1	0.916381212636131	3		420	994	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0003070-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	168	331	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.322644295944901	3	FACETS	0.988	0.914	1	0.988	0.914	1	CLONAL	2	TRUE	1	0.372151720748926	3		331	542	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0003070-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	73	314	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.372151720748926	3	FACETS	0.954	0.836	1	0.477	0.418	0.54	CLONAL	1	TRUE	1	0.372151720748926	3		314	488	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17941409	17941409	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003070-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	66	196	0	ENST00000458235.1:c.2999C>A	p.Ser1000Ter	p.S1000*	ENST00000458235	NM_000215.3	1000	tCg/tAg	22/24	0.33005090806065	3	FACETS	0.848	0.745	0.957	0.848	0.745	0.957	CLONAL	2	TRUE	1	0.372151720748926	3		196	248	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577121	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCA	novel	NA	P-0003070-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	202	466	0	ENST00000269305.4:c.815_817dup	p.Val272_Arg273insLeu	p.V272_R273insL	ENST00000269305	NM_001126112.2	273	cgt/cTGCgt	8/11	0.351996698275104	2	FACETS	0.959	0.895	1	0.959	0.895	1	CLONAL	2	TRUE	0	0.372151720748926	2		466	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0003072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	24	460	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	0.181403571741114	2	FACETS	0.16	0.124	0.201	0.08	0.062	0.101	SUBCLONAL	1	TRUE	0	0.272677241187581	2		460	1103	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307160	65307160	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	132	365	0	ENST00000342505.4:c.2528G>T	p.Arg843Ile	p.R843I	ENST00000342505	NM_002227.2	843	aGa/aTa	18/25	0.206146785547624	2	FACETS	1	0.983	1	0.675	0.614	0.74	CLONAL	1	TRUE	0	0.272677241187581	2		365	717	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928225	178928225	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	55	259	0	ENST00000263967.3:c.1411C>G	p.Pro471Ala	p.P471A	ENST00000263967	NM_006218.2	471	Cca/Gca	9/21	0.272677241187581	3	FACETS	1	0.959	1	0.668	0.574	0.77	CLONAL	1	TRUE	1	0.272677241187581	3		259	343	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258986	153258986	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	110	364	0	ENST00000281708.4:c.829C>G	p.Gln277Glu	p.Q277E	ENST00000281708	NM_033632.3	277	Caa/Gaa	5/12	0.181403571741114	2	FACETS	0.93	0.841	1	0.93	0.841	1	CLONAL	2	TRUE	0	0.272677241187581	2		364	434	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223271	2223271	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	166	319	0	ENST00000326181.6:c.883G>T	p.Asp295Tyr	p.D295Y	ENST00000326181	NM_032271.2	295	Gat/Tat	10/21	0.156669947514191	4	FACETS	0.853	0.784	0.926			1	INDETERMINATE	2	TRUE	NA	0.272677241187581	4		319	908	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579565	7579566	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0003072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	102	288	0	ENST00000269305.4:c.121dup	p.Asp41GlyfsTer2	p.D41Gfs*2	ENST00000269305	NM_001126112.2	41	gat/gGat	4/11	0.181403571741114	2	FACETS	1	0.972	1	0.626	0.561	0.694	CLONAL	1	TRUE	0	0.272677241187581	2		288	598	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	76	140	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.848771036416637	2		140	164	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729687	41729687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	226	481	1	ENST00000242208.4:c.842C>T	p.Ala281Val	p.A281V	ENST00000242208	NM_002192.2	281	gCa/gTa	3/3	0.848771036416637	2	FACETS	0.994	0.934	1	0.497	0.467	0.527	CLONAL	1	TRUE	0	0.848771036416637	2		482	536	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371763	118371763	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	171	286	0	ENST00000534358.1:c.6220A>G	p.Ile2074Val	p.I2074V	ENST00000534358	NM_005933.3	2074	Ata/Gta	25/36	0.848771036416637	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.848771036416637	1		286	218	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774995	73774995	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	98	187	0	ENST00000254810.4:c.178G>T	p.Glu60Ter	p.E60*	ENST00000254810	NM_005324.3	60	Gag/Tag	3/4	1	2	FACETS	0.954	0.867	1	0.954	0.867	1	CLONAL	1	TRUE	1	0.848771036416637	2		187	242	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41560094	41560094	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	245	376	2	ENST00000263253.7:c.3766C>T	p.Gln1256Ter	p.Q1256*	ENST00000263253	NM_001429.3	1256	Cag/Tag	22/31	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.848771036416637	2		378	521	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922669	44922670	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	170	307	0	ENST00000377967.4:c.1531dup	p.Arg511LysfsTer15	p.R511Kfs*15	ENST00000377967	NM_021140.2	510	-/A	16/29	0.848771036416637	1	FACETS	0.87	0.822	0.917	0.87	0.822	0.917	CLONAL	1	TRUE	0	0.848771036416637	1		307	265	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346177	89346178	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0003097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	117	160	0	ENST00000301030.4:c.6772dup	p.Ala2258GlyfsTer2	p.A2258Gfs*2	ENST00000301030	NM_001256183.1	2258	gct/gGct	9/13	0.150707274702502	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.848771036416637	0		160	274	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0003118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	328	356	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.420013796913965	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.454771523752809	3		356	542	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0003118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	32	285	0	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	0.454771523752809	2	FACETS	0.667	0.545	0.802	0.333	0.272	0.401	SUBCLONAL	1	TRUE	0	0.454771523752809	2		285	211	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881001	37881002	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGCTCCCC	rs397516981	NA	P-0003118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	334	284	0	ENST00000269571.5:c.2331_2339dup	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	gtg/gtGGGCTCCCCg	20/27	0.414722820642017	4	FACETS	1	0.991	1			1	CLONAL	3	TRUE	NA	0.454771523752809	4		284	626	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168491	56168492	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0003118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	125	284	0	ENST00000399503.3:c.1450_1451del	p.Glu484ThrfsTer8	p.E484Tfs*8	ENST00000399503	NM_005921.1	483	AGa/a	8/20	0.454771523752809	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	0	0.454771523752809	2		284	269	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739033	145739033	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	59	231	0	ENST00000428558.2:c.2122A>G	p.Asn708Asp	p.N708D	ENST00000428558	NM_004260.3	708	Aac/Gac	13/22	0.448756182277483	4	FACETS	0.387	0.331	0.447	0.193	0.165	0.224	SUBCLONAL	1	TRUE	2	0.454771523752809	4		231	976	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521541	8521541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	55	217	0	ENST00000356435.5:c.697C>T	p.Arg233Cys	p.R233C	ENST00000356435		233	Cgt/Tgt	9/35	NA	2	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.454771523752809	2		217	169	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061465	38061465	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	293	227	0	ENST00000250448.2:c.524A>G	p.Tyr175Cys	p.Y175C	ENST00000250448	NM_004496.3	175	tAc/tGc	2/2	0.316277996790698	4	FACETS	1	0.986	1	1	0.995	1	CLONAL	3	TRUE	2	0.454771523752809	4		227	571	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871182	12871182	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1328655695	NA	P-0003118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	131	88	0	ENST00000228872.4:c.410del	p.Pro137ArgfsTer8	p.P137Rfs*8	ENST00000228872	NM_004064.3	137	Ccg/cg	1/3	0.423278549831525	5	FACETS	0.907	0.834	0.983	0.907	0.834	0.983	CLONAL	3	TRUE	2	0.454771523752809	5		88	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0003119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	79	257	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.131433322130819	0	FACETS	0.577	0.507	0.652			1	INDETERMINATE	1	TRUE	0	0.289862762205974	0		257	671	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528588	89528588	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	47	257	0	ENST00000336596.2:c.2888A>T	p.Lys963Met	p.K963M	ENST00000336596	NM_005233.5	963	aAg/aTg	17/17	1	2	FACETS	0.381	0.32	0.448	0.381	0.32	0.448	SUBCLONAL	1	TRUE	1	0.289862762205974	2		257	852	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665210	138665210	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	99	321	0	ENST00000330315.3:c.355G>T	p.Gly119Cys	p.G119C	ENST00000330315	NM_023067.3	119	Ggc/Tgc	1/1	1	2	FACETS	0.654	0.583	0.731	0.654	0.583	0.731	SUBCLONAL	1	TRUE	1	0.289862762205974	2		321	1044	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951894	178951894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369697984	NA	P-0003119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	59	268	0	ENST00000263967.3:c.2949G>A	p.Met983Ile	p.M983I	ENST00000263967	NM_006218.2	983	atG/atA	21/21	0.142775615208735	4	FACETS	0.484	0.415	0.56	0.242	0.207	0.28	INDETERMINATE	1	TRUE	2	0.289862762205974	4		268	1084	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55143565	55143565	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	99	277	0	ENST00000257290.5:c.1797G>T	p.Leu599Phe	p.L599F	ENST00000257290	NM_006206.4	599	ttG/ttT	13/23	1	2	FACETS	0.802	0.715	0.894	0.802	0.715	0.894	CLONAL	1	TRUE	1	0.289862762205974	2		277	852	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155282	55155282	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0003119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	46	206	0	ENST00000257290.5:c.2880+1G>T		p.X960_splice	ENST00000257290	NM_006206.4	960			1	2	FACETS	0.476	0.4	0.56	0.476	0.4	0.56	SUBCLONAL	1	TRUE	1	0.289862762205974	2		206	667	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247271	153247271	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	188	340	0	ENST00000281708.4:c.1531G>T	p.Gly511Cys	p.G511C	ENST00000281708	NM_033632.3	511	Ggc/Tgc	10/12	1	2	FACETS	0.96	0.885	1	0.96	0.885	1	CLONAL	1	TRUE	1	0.289862762205974	2		340	1351	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036016	180036016	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1000190222	NA	P-0003119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	89	341	0	ENST00000261937.6:c.3845A>G	p.Glu1282Gly	p.E1282G	ENST00000261937	NM_182925.4	1282	gAg/gGg	29/30	NA	2	FACETS	0.578	0.511	0.65			1	INDETERMINATE	1	TRUE	NA	0.289862762205974	2		341	1062	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759580	133759580	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	81	317	0	ENST00000318560.5:c.1903G>T	p.Glu635Ter	p.E635*	ENST00000318560	NM_005157.4	635	Gag/Tag	11/11	1	2	FACETS	0.573	0.503	0.648	0.573	0.503	0.648	SUBCLONAL	1	TRUE	1	0.289862762205974	2		317	976	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042160	42042160	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1263	127	519	0	ENST00000219905.7:c.6355G>T	p.Gly2119Ter	p.G2119*	ENST00000219905	NM_001164273.1	2119	Gga/Tga	17/24	0.1847203901522	0	FACETS	0.448	0.404	0.494			1	SUBCLONAL	1	TRUE	0	0.289862762205974	0		519	1390	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72833950	72833950	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	128	343	0	ENST00000268489.5:c.3943T>G	p.Leu1315Val	p.L1315V	ENST00000268489	NM_006885.3	1315	Ttg/Gtg	8/10	0.289862762205974	1	FACETS	0.651	0.588	0.717	0.651	0.588	0.717	SUBCLONAL	1	TRUE	0	0.289862762205974	1		343	1160	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600392	10600392	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	175	354	0	ENST00000171111.5:c.1463A>T	p.Glu488Val	p.E488V	ENST00000171111	NM_203500.1	488	gAg/gTg	4/6	0.289862762205974	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.289862762205974	1		354	897	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436631	8436632	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	80	321	0	ENST00000356435.5:c.4046dup	p.Leu1349PhefsTer5	p.L1349Ffs*5	ENST00000356435		1349	ttg/ttTg	24/35	1	2	FACETS	0.452	0.397	0.513	0.452	0.397	0.513	SUBCLONAL	1	TRUE	1	0.289862762205974	2		321	1220	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0003128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	76	393	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.984	0.886	1			1	INDETERMINATE	1	TRUE	NA	0.913683190891497	2		393	169	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0003128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2294	5578	446	3	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.913683190891497	19	FACETS	0.971	0.962	0.98			1	CLONAL	14	TRUE	NA	0.913683190891497	19		449	7872	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864497	57864497	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs374770255	NA	P-0003128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	18403	499	0	ENST00000228682.2:c.1974G>C	p.Lys658Asn	p.K658N	ENST00000228682	NM_005269.2	658	aaG/aaC	12/12	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.913683190891497	NA		499	18615	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864618	57864618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	22877	551	2	ENST00000228682.2:c.2095G>A	p.Asp699Asn	p.D699N	ENST00000228682	NM_005269.2	699	Gat/Aat	12/12	0.913683190891497	21	FACETS	1	0.999	1			1	CLONAL	21	TRUE	NA	0.913683190891497	21		553	23070	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922122	39922122	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	485	306	0	ENST00000378444.4:c.4050del	p.Tyr1350Ter	p.Y1350*	ENST00000378444	NM_001123385.1	1350	taC/ta	9/15	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.913683190891497	1		306	523	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717704	89717704	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	273	295	0	ENST00000371953.3:c.731del	p.Pro244LeufsTer12	p.P244Lfs*12	ENST00000371953	NM_000314.4	243	ttC/tt	7/9	0.913683190891497	1	FACETS	0.984	0.953	1	0.984	0.953	1	CLONAL	1	TRUE	0	0.913683190891497	1		295	330	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185062	123185063	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTTCAAGGTTA	novel	NA	P-0003128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	503	270	0	ENST00000218089.9:c.1112_1116+6dup		p.R370fs	ENST00000218089	NM_001042749.1	370	cgg/cgGTTCAAGGTTAg	12/35	1	1	FACETS	0.776	0.751	0.8	0.776	0.751	0.8	SUBCLONAL	1	TRUE	0	0.913683190891497	1		270	771	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0003194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	126	273	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.326105661785286	3	FACETS	1	0.953	1	0.543	0.491	0.597	CLONAL	1	TRUE	1	0.326105661785286	3		273	828	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28624284	28624284	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	98	432	0	ENST00000241453.7:c.690G>T	p.Arg230Ser	p.R230S	ENST00000241453	NM_004119.2	230	agG/agT	6/24	NA	2	FACETS	0.998	0.892	1			1	INDETERMINATE	1	TRUE	NA	0.326105661785286	2		432	602	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474494	40474494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	147	426	0	ENST00000264657.5:c.1907C>T	p.Ser636Phe	p.S636F	ENST00000264657	NM_139276.2	636	tCc/tTc	21/24	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.326105661785286	2		426	792	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143983	11143983	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	139	270	1	ENST00000358026.2:c.3564C>A	p.Asp1188Glu	p.D1188E	ENST00000358026	NM_001128849.1	1188	gaC/gaA	26/36	1	2	FACETS	0.782	0.715	0.851	1	0.988	1	SUBCLONAL	2	TRUE	1	0.326105661785286	2		271	545	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130278	11130279	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0003194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	102	325	0	ENST00000358026.2:c.2518dup	p.Ala840GlyfsTer105	p.A840Gfs*105	ENST00000358026	NM_001128849.1	839	-/G	18/36	1	2	FACETS	0.9	0.806	1	0.9	0.806	1	CLONAL	1	TRUE	1	0.326105661785286	2		325	695	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	210	596	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.961	0.898	1	0.961	0.898	1	CLONAL	1	TRUE	1	0.69258176355335	2		596	631	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	176	293	2	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	0.69258176355335	2		295	415	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136799	2136799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137854153	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	353	309	0	ENST00000219476.3:c.4916G>A	p.Arg1639His	p.R1639H	ENST00000219476	NM_000548.3	1639	cGc/cAc	38/42	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.69258176355335	2		309	966	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	75	127	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.853	0.757	0.953	0.853	0.757	0.953	CLONAL	1	TRUE	1	0.69258176355335	2		127	254	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56377265	56377265	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	236	350	2	ENST00000348428.3:c.886C>T	p.Arg296Ter	p.R296*	ENST00000348428	NM_006785.3	296	Cga/Tga	6/17	1	2	FACETS	0.969	0.909	1	0.969	0.909	1	CLONAL	1	TRUE	1	0.69258176355335	2		352	703	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	212	251	0	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.855	0.797	0.914	0.855	0.797	0.914	CLONAL	1	TRUE	1	0.69258176355335	2		251	716	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447772	49447773	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	174	151	0	ENST00000301067.7:c.661dup	p.Ala221GlyfsTer13	p.A221Gfs*13	ENST00000301067	NM_003482.3	221	gct/gGct	5/54	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.69258176355335	2		151	502	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	174	303	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.69258176355335	2		303	477	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	188	249	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.908	0.844	0.974	0.908	0.844	0.974	CLONAL	1	TRUE	1	0.69258176355335	2		249	598	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637555	52637555	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	221	337	0	ENST00000394830.3:c.2761C>T	p.Arg921Ter	p.R921*	ENST00000394830	NM_018313.4	921	Cga/Tga	18/30	1	2	FACETS	0.924	0.863	0.985	0.924	0.863	0.985	CLONAL	1	TRUE	1	0.69258176355335	2		337	691	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256679	19256679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1357520436	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	182	170	1	ENST00000162023.5:c.1034G>A	p.Arg345Gln	p.R345Q	ENST00000162023		345	cGg/cAg	13/13	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.69258176355335	2		171	513	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088788	27088788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	279	241	4	ENST00000324856.7:c.2402del	p.Gly801ValfsTer32	p.G801Vfs*32	ENST00000324856	NM_006015.4	799	caG/ca	7/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.69258176355335	2		245	735	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	115	159	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	1	2	FACETS	0.905	0.823	0.989	0.905	0.823	0.989	CLONAL	1	TRUE	1	0.69258176355335	2		159	367	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107099	27107099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758918502	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	130	139	0	ENST00000324856.7:c.6710C>T	p.Ala2237Val	p.A2237V	ENST00000324856	NM_006015.4	2237	gCg/gTg	20/20	1	2	FACETS	0.95	0.871	1	0.95	0.871	1	CLONAL	1	TRUE	1	0.69258176355335	2		139	395	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666384	206666384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367815847	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	198	215	0	ENST00000367120.3:c.1864C>T	p.Arg622Cys	p.R622C	ENST00000367120	NM_014002.3	622	Cgc/Tgc	19/22	1	2	FACETS	0.915	0.852	0.979	0.915	0.852	0.979	CLONAL	1	TRUE	1	0.69258176355335	2		215	625	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226568861	226568861	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150379323	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	319	281	0	ENST00000366794.5:c.1208G>A	p.Arg403Gln	p.R403Q	ENST00000366794	NM_001618.3	403	cGg/cAg	9/23	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.69258176355335	2		281	905	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497949	25497949	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	304	169	0	ENST00000264709.3:c.500G>A	p.Arg167Gln	p.R167Q	ENST00000264709	NM_175629.2	167	cGg/cAg	6/23	0.69258176355335	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.69258176355335	3		169	534	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635622	47635622	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs763872353	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	265	296	0	ENST00000233146.2:c.294T>A	p.Tyr98Ter	p.Y98*	ENST00000233146	NM_000251.2	98	taT/taA	2/16	0.69258176355335	3	FACETS	1	0.971	1	0.528	0.495	0.561	CLONAL	1	TRUE	1	0.69258176355335	3		296	976	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141631	202141631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs17860424	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	518	258	1	ENST00000358485.4:c.919C>T	p.Arg307Trp	p.R307W	ENST00000358485	NM_001080125.1	307	Cgg/Tgg	7/9	0.69258176355335	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.69258176355335	3		259	956	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439805	220439805	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368930117	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	410	334	0	ENST00000243786.2:c.658C>T	p.Arg220Trp	p.R220W	ENST00000243786	NM_002191.3	220	Cgg/Tgg	2/2	0.69258176355335	3	FACETS	1	0.989	1	0.562	0.535	0.591	CLONAL	1	TRUE	1	0.69258176355335	3		334	1417	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990402	69990402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765051386	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	123	234	0	ENST00000394351.3:c.361G>A	p.Asp121Asn	p.D121N	ENST00000394351	NM_000248.3	121	Gat/Aat	4/9	1	2	FACETS	0.877	0.8	0.956	0.877	0.8	0.956	CLONAL	1	TRUE	1	0.69258176355335	2		234	405	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72842124	72842124	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293451216	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	206	309	1	ENST00000325599.8:c.1124C>T	p.Ala375Val	p.A375V	ENST00000325599	NM_018130.2	375	gCg/gTg	10/11	1	2	FACETS	0.982	0.916	1	0.982	0.916	1	CLONAL	1	TRUE	1	0.69258176355335	2		310	606	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119635000	119635000	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs201787969	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	172	246	0	ENST00000316626.5:c.499C>T	p.Arg167Ter	p.R167*	ENST00000316626		167	Cga/Tga	5/12	1	2	FACETS	0.968	0.898	1	0.968	0.898	1	CLONAL	1	TRUE	1	0.69258176355335	2		246	513	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156639	55156639	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768291477	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	217	228	0	ENST00000257290.5:c.3040G>A	p.Ala1014Thr	p.A1014T	ENST00000257290	NM_006206.4	1014	Gct/Act	22/23	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.69258176355335	2		228	601	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532867	187532867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762890230	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	290	265	1	ENST00000441802.2:c.9526G>A	p.Glu3176Lys	p.E3176K	ENST00000441802	NM_005245.3	3176	Gaa/Aaa	14/27	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.69258176355335	2		266	815	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629103	86629103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753769946	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	180	227	0	ENST00000274376.6:c.848G>A	p.Arg283His	p.R283H	ENST00000274376	NM_002890.2	283	cGt/cAt	4/25	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.69258176355335	2		227	450	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973851	131973851	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747603489	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	203	231	0	ENST00000265335.6:c.3554G>A	p.Arg1185Gln	p.R1185Q	ENST00000265335		1185	cGa/cAa	23/25	1	2	FACETS	0.985	0.919	1	0.985	0.919	1	CLONAL	1	TRUE	1	0.69258176355335	2		231	595	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051024	180051024	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769840412	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	257	252	0	ENST00000261937.6:c.1459C>T	p.Arg487Cys	p.R487C	ENST00000261937	NM_182925.4	487	Cgt/Tgt	11/30	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.69258176355335	2		252	635	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651972	36651972	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373450720	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	224	194	0	ENST00000244741.5:c.94C>T	p.Arg32Cys	p.R32C	ENST00000244741	NM_000389.4	32	Cgc/Tgc	2/3	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.69258176355335	2		194	600	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979281	93979281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	311	431	0	ENST00000369303.4:c.1547G>A	p.Arg516Gln	p.R516Q	ENST00000369303	NM_004440.3	516	cGg/cAg	7/17	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.69258176355335	2		431	750	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001106	150001106	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	227	370	0	ENST00000253339.5:c.2498A>G	p.Asn833Ser	p.N833S	ENST00000253339		833	aAt/aGt	4/7	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.69258176355335	2		370	655	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968260	2968260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	256	250	0	ENST00000396946.4:c.1726C>T	p.Arg576Cys	p.R576C	ENST00000396946	NM_032415.4	576	Cgc/Tgc	13/25	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.69258176355335	2		250	738	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380020	116380020	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	286	319	1	ENST00000397752.3:c.1409C>T	p.Ser470Leu	p.S470L	ENST00000397752	NM_000245.2	470	tCa/tTa	4/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.69258176355335	2		320	774	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843429	128843429	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs115491500	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	189	158	0	ENST00000249373.3:c.536C>T	p.Thr179Met	p.T179M	ENST00000249373	NM_005631.4	179	aCg/aTg	2/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.69258176355335	2		158	477	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845813	151845813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	254	330	0	ENST00000262189.6:c.13199G>A	p.Arg4400Gln	p.R4400Q	ENST00000262189	NM_170606.2	4400	cGg/cAg	52/59	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.69258176355335	2		330	695	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371986	55371986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1339233187	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	22	140	0	ENST00000297316.4:c.676C>T	p.Pro226Ser	p.P226S	ENST00000297316	NM_022454.3	226	Ccg/Tcg	2/2	1	2	FACETS	0.162	0.125	0.206	0.162	0.125	0.206	SUBCLONAL	1	TRUE	1	0.69258176355335	2		140	391	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739068	145739068	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1026729951	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	194	189	0	ENST00000428558.2:c.2087G>A	p.Arg696His	p.R696H	ENST00000428558	NM_004260.3	696	cGt/cAt	13/22	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.69258176355335	2		189	505	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215787	98215787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376844749	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	291	269	0	ENST00000331920.6:c.3422C>T	p.Ala1141Val	p.A1141V	ENST00000331920	NM_000264.3	1141	gCg/gTg	20/24	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.69258176355335	2		269	721	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240362	98240362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767273237	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	241	210	1	ENST00000331920.6:c.1322G>A	p.Arg441His	p.R441H	ENST00000331920	NM_000264.3	441	cGc/cAc	9/24	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.69258176355335	2		211	662	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410064	139410064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1472690723	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	268	247	2	ENST00000277541.6:c.1774C>T	p.Arg592Cys	p.R592C	ENST00000277541	NM_017617.3	592	Cgc/Tgc	11/34	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.69258176355335	2		249	710	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852655	63852655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	272	264	1	ENST00000279873.7:c.3433G>A	p.Ala1145Thr	p.A1145T	ENST00000279873	NM_032199.2	1145	Gct/Act	10/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.69258176355335	2		265	742	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925330	114925330	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368331428	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	379	324	0	ENST00000543371.1:c.1408G>A	p.Val470Ile	p.V470I	ENST00000543371	NM_001198531.1	470	Gtt/Att	14/14	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.69258176355335	2		324	966	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129008	64129008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781669147	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	230	251	1	ENST00000334205.4:c.638C>T	p.Thr213Met	p.T213M	ENST00000334205	NM_003942.2	213	aCg/aTg	6/17	1	2	FACETS	0.926	0.867	0.987	0.926	0.867	0.987	CLONAL	1	TRUE	1	0.69258176355335	2		252	717	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402294	402294	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	307	375	0	ENST00000399788.2:c.4497G>T	p.Lys1499Asn	p.K1499N	ENST00000399788	NM_001042603.1	1499	aaG/aaT	27/28	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.69258176355335	2		375	839	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856065	111856065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778004604	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	183	159	2	ENST00000341259.2:c.116G>A	p.Arg39Gln	p.R39Q	ENST00000341259	NM_005475.2	39	cGg/cAg	2/8	1	2	FACETS	0.93	0.864	0.998	0.93	0.864	0.998	CLONAL	1	TRUE	1	0.69258176355335	2		161	568	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73334690	73334690	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs575285131	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	222	287	0	ENST00000377767.4:c.2770C>T	p.Arg924Ter	p.R924*	ENST00000377767	NM_014953.3	924	Cga/Tga	20/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.69258176355335	2		287	609	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477184	67477184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1320208623	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	173	198	0	ENST00000327367.4:c.991G>A	p.Val331Ile	p.V331I	ENST00000327367	NM_005902.3	331	Gtc/Atc	7/9	1	2	FACETS	0.922	0.854	0.991	0.922	0.854	0.991	CLONAL	1	TRUE	1	0.69258176355335	2		198	542	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500474	99500474	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45475702	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	193	212	0	ENST00000268035.6:c.3907G>A	p.Val1303Ile	p.V1303I	ENST00000268035	NM_000875.3	1303	Gtc/Atc	21/21	1	2	FACETS	0.986	0.919	1	0.986	0.919	1	CLONAL	1	TRUE	1	0.69258176355335	2		212	565	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	359984	359984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	312	350	0	ENST00000262320.3:c.1105C>T	p.Pro369Ser	p.P369S	ENST00000262320	NM_003502.3	369	Cct/Tct	4/11	1	2	FACETS	0.99	0.937	1	0.99	0.937	1	CLONAL	1	TRUE	1	0.69258176355335	2		350	910	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116167	67116167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	294	237	0	ENST00000412916.2:c.451C>T	p.Arg151Cys	p.R151C	ENST00000412916		151	Cgc/Tgc	5/6	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.69258176355335	2		237	842	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984762	72984762	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1224592041	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	362	351	1	ENST00000268489.5:c.2822C>T	p.Ser941Leu	p.S941L	ENST00000268489	NM_006885.3	941	tCg/tTg	3/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.69258176355335	2		352	1007	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138729528	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	132	147	0	ENST00000269305.4:c.523C>T	p.Arg175Cys	p.R175C	ENST00000269305	NM_001126112.2	175	Cgc/Tgc	5/11	1	2	FACETS	0.93	0.852	1	0.93	0.852	1	CLONAL	1	TRUE	1	0.69258176355335	2		147	410	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024477	16024477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1183742719	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	308	245	0	ENST00000268712.3:c.1741C>T	p.Arg581Cys	p.R581C	ENST00000268712	NM_006311.3	581	Cgt/Tgt	16/46	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.69258176355335	2		245	818	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665144	29665144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs562367786	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	46	196	0	ENST00000356175.3:c.6743G>A	p.Arg2248His	p.R2248H	ENST00000356175	NM_000267.3	2248	cGt/cAt	44/57	1	2	FACETS	0.284	0.239	0.334	0.284	0.239	0.334	SUBCLONAL	1	TRUE	1	0.69258176355335	2		196	467	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256956	41256956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357209	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	173	265	0	ENST00000357654.3:c.230C>T	p.Thr77Met	p.T77M	ENST00000357654	NM_007294.3	77	aCg/aTg	5/23	1	2	FACETS	0.929	0.861	0.998	0.929	0.861	0.998	CLONAL	1	TRUE	1	0.69258176355335	2		265	538	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796926	78796926	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	232	231	0	ENST00000306801.3:c.1039T>C	p.Phe347Leu	p.F347L	ENST00000306801	NM_020761.2	347	Ttt/Ctt	9/34	1	2	FACETS	0.923	0.864	0.983	0.923	0.864	0.983	CLONAL	1	TRUE	1	0.69258176355335	2		231	726	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78938101	78938101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1044306323	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	313	289	2	ENST00000306801.3:c.3979G>A	p.Val1327Met	p.V1327M	ENST00000306801	NM_020761.2	1327	Gtg/Atg	34/34	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.69258176355335	2		291	858	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1627375	1627375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368163858	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	311	242	4	ENST00000344749.5:c.349G>A	p.Val117Met	p.V117M	ENST00000344749	NM_001136139.2	117	Gtg/Atg	6/19	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.69258176355335	2		246	854	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246522	10246522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs919486255	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	170	137	0	ENST00000340748.4:c.4615G>A	p.Val1539Met	p.V1539M	ENST00000340748		1539	Gtg/Atg	38/40	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.69258176355335	2		137	446	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284979	15284979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774475688	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	194	187	0	ENST00000263388.2:c.4636C>T	p.Arg1546Cys	p.R1546C	ENST00000263388	NM_000435.2	1546	Cgc/Tgc	25/33	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.69258176355335	2		187	537	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288790	15288790	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	11	41	0	ENST00000263388.2:c.3949C>A	p.Pro1317Thr	p.P1317T	ENST00000263388	NM_000435.2	1317	Cca/Aca	24/33	1	2	FACETS	0.269	0.187	0.37	0.269	0.187	0.37	SUBCLONAL	1	TRUE	1	0.69258176355335	2		41	118	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289746	15289746	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146149484	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	225	166	3	ENST00000263388.2:c.3725G>A	p.Arg1242His	p.R1242H	ENST00000263388	NM_000435.2	1242	cGc/cAc	23/33	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.69258176355335	2		169	550	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312660	30312660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146187350	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	224	294	2	ENST00000262643.3:c.641C>T	p.Ala214Val	p.A214V	ENST00000262643	NM_001238.2	214	gCg/gTg	8/12	0.69258176355335	4	FACETS	0.926	0.861	0.994	0.309	0.287	0.332	CLONAL	1	TRUE	1	0.69258176355335	4		296	1182	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36024670	36024670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	260	270	0	ENST00000358208.4:c.659G>A	p.Arg220His	p.R220H	ENST00000358208		220	cGc/cAc	6/12	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.69258176355335	2		270	750	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264652	46264652	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	311	307	0	ENST00000371998.3:c.1522G>A	p.Ala508Thr	p.A508T	ENST00000371998		508	Gca/Aca	12/23	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.69258176355335	2		307	877	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159109	24159109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1368176286	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	237	201	0	ENST00000263121.7:c.781C>T	p.Arg261Cys	p.R261C	ENST00000263121	NM_003073.3	261	Cgc/Tgc	6/9	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.69258176355335	2		201	648	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410486	63410486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779325879	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	306	138	0	ENST00000330258.3:c.2681G>A	p.Arg894His	p.R894H	ENST00000330258	NM_152424.3	894	cGc/cAc	2/2	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.69258176355335	1		138	440	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799098	42799098	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	522	191	0	ENST00000575354.2:c.4586del	p.Pro1529LeufsTer91	p.P1529Lfs*91	ENST00000575354	NM_015125.3	1528	Ccc/cc	20/20	0.69258176355335	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	1	0.69258176355335	4		191	816	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	54	264	1	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.206	0.175	0.24	0.206	0.175	0.24	SUBCLONAL	1	TRUE	1	0.69258176355335	2		265	756	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760023	133760024	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1368469090	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	249	248	0	ENST00000318560.5:c.2352dup	p.Arg785GlnfsTer7	p.R785Qfs*7	ENST00000318560	NM_005157.4	782	-/C	11/11	1	2	FACETS	0.973	0.914	1	0.973	0.914	1	CLONAL	1	TRUE	1	0.69258176355335	2		248	739	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023096	33023096	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	275	330	1	ENST00000300177.4:c.207del	p.Glu71ArgfsTer13	p.E71Rfs*13	ENST00000300177	NM_001191322.1	69	Ccc/cc	2/2	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.69258176355335	2		331	763	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	345	975	8	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	0.771	0.729	0.813	0.771	0.729	0.813	SUBCLONAL	1	TRUE	1	0.69258176355335	2		983	1293	SUCCESS
ATR	545	MSKCC	GRCh37	3	142255005	142255005	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	73	238	0	ENST00000350721.4:c.3764del	p.Leu1255TyrfsTer7	p.L1255Yfs*7	ENST00000350721	NM_001184.3	1255	tTa/ta	20/47	1	2	FACETS	0.419	0.367	0.475	0.419	0.367	0.475	SUBCLONAL	1	TRUE	1	0.69258176355335	2		238	503	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339744	116339746	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	rs764811491	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	246	284	0	ENST00000397752.3:c.611_613del	p.Ser204del	p.S204del	ENST00000397752	NM_000245.2	202	aaTTCt/aat	2/21	1	2	FACETS	0.936	0.878	0.995	0.936	0.878	0.995	CLONAL	1	TRUE	1	0.69258176355335	2		284	759	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646085	215646085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	193	291	0	ENST00000260947.4:c.513del	p.Asp172MetfsTer40	p.D172Mfs*40	ENST00000260947	NM_000465.2	171	aaA/aa	4/11	0.69258176355335	3	FACETS	0.938	0.869	1	0.469	0.434	0.505	CLONAL	1	TRUE	1	0.69258176355335	3		291	800	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203691	94203691	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	203	301	1	ENST00000323929.3:c.963del	p.Phe321LeufsTer8	p.F321Lfs*8	ENST00000323929	NM_005591.3	321	ttT/tt	9/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.69258176355335	2		302	541	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870820	12870821	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	108	102	0	ENST00000228872.4:c.49dup	p.Asp17GlyfsTer108	p.D17Gfs*108	ENST00000228872	NM_004064.3	16	atg/atGg	1/3	1	2	FACETS	0.969	0.88	1	0.969	0.88	1	CLONAL	1	TRUE	1	0.69258176355335	2		102	322	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265366	152265367	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	200	216	0	ENST00000206249.3:c.823dup	p.Glu275GlyfsTer5	p.E275Gfs*5	ENST00000206249	NM_000125.3	273	-/G	4/8	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.69258176355335	2		216	567	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032388	42032388	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	478	461	0	ENST00000219905.7:c.4575del	p.Lys1525AsnfsTer18	p.K1525Nfs*18	ENST00000219905	NM_001164273.1	1524	gcA/gc	14/24	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.69258176355335	2		461	1284	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0003209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	313	304	3	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	1	2	FACETS	0.968	0.915	1	0.968	0.915	1	CLONAL	1	TRUE	1	0.69258176355335	2		307	934	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0003277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	23	393	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.26	2		393	124	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0003277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	54	442	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	0.3	1	FACETS	0.899	0.77	1	0.899	0.77	1	CLONAL	1	TRUE	0	0.26	1		442	402	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932899	36932899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	68	394	0	ENST00000361632.4:c.1972C>T	p.Leu658Phe	p.L658F	ENST00000361632		658	Ctc/Ttc	15/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.26	2		394	379	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149498324	149498324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747398617	NA	P-0003277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	49	329	0	ENST00000261799.4:c.2890G>A	p.Glu964Lys	p.E964K	ENST00000261799	NM_002609.3	964	Gaa/Aaa	21/23	1	2	FACETS	0.992	0.843	1	0.992	0.843	1	CLONAL	1	TRUE	1	0.26	2		329	380	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519386	137519386	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	77	171	0	ENST00000367739.4:c.1252T>G	p.Cys418Gly	p.C418G	ENST00000367739	NM_000416.2	418	Tgt/Ggt	7/7	0.3	4	FACETS	0.976	0.868	1	1	0.978	1	CLONAL	3	TRUE	2	0.26	4		171	255	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908891	101908891	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs863223827	NA	P-0003277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	50	278	0	ENST00000374994.4:c.1255G>A	p.Gly419Arg	p.G419R	ENST00000374994	NM_004612.2	419	Gga/Aga	7/9	0.3	1	FACETS	0.76	0.653	0.876	1	0.967	1	SUBCLONAL	2	TRUE	0	0.26	1		278	220	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218648	98218649	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0003277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	65	212	0	ENST00000331920.6:c.3215dup	p.Leu1073ProfsTer72	p.L1073Pfs*72	ENST00000331920	NM_000264.3	1072	ggc/ggGc	19/24	0.3	1	FACETS	0.87	0.763	0.983	1	0.979	1	CLONAL	2	TRUE	0	0.26	1		212	250	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394439	162394439	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003283-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	17	251	0	ENST00000366898.1:c.629T>G	p.Phe210Cys	p.F210C	ENST00000366898	NM_004562.2	210	tTt/tGt	6/12	1	2	FACETS	1	0.824	1	1	0.824	1	CLONAL	1	TRUE	1	0.308822933580184	2		251	99	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936807	32936807	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003283-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	24	259	0	ENST00000380152.3:c.7953G>C	p.Arg2651Ser	p.R2651S	ENST00000380152		2651	agG/agC	17/27	0.308822933580184	1	FACETS	1	0.815	1	1	0.815	1	CLONAL	1	TRUE	0	0.308822933580184	1		259	128	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24135858	24135859	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1555876140	NA	P-0003283-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	15	231	0	ENST00000263121.7:c.351dup	p.Thr118HisfsTer52	p.T118Hfs*52	ENST00000263121	NM_003073.3	115	-/C	3/9	0.236041823720172	1	FACETS	0.768	0.568	1	0.768	0.568	1	CLONAL	1	TRUE	0	0.308822933580184	1		231	107	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374628	118374629	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	211	411	0	ENST00000534358.1:c.8023dup	p.Ser2675LysfsTer5	p.S2675Kfs*5	ENST00000534358	NM_005933.3	2674	tta/ttAa	27/36	0.387630249126567	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.387630249126567	1		411	868	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426014	49426014	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	226	357	0	ENST00000301067.7:c.12474del	p.Met4159CysfsTer2	p.M4159Cfs*2	ENST00000301067	NM_003482.3	4158	ccC/cc	39/54	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.387630249126567	2		357	1056	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746002	162746002	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1056323839	NA	P-0003430-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	440	495	1	ENST00000367921.3:c.2125C>T	p.Arg709Ter	p.R709*	ENST00000367921	NM_006182.2	709	Cga/Tga	16/18	0.863256284341888	3	FACETS	0.954	0.92	0.988	0.954	0.92	0.988	CLONAL	2	TRUE	1	0.928823738050823	3		496	727	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808283	99808283	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003430-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	167	330	0	ENST00000280892.6:c.406A>G	p.Thr136Ala	p.T136A	ENST00000280892	NM_001130678.1	136	Aca/Gca	5/7	0.928823738050823	3	FACETS	1	0.976	1	0.373	0.346	0.402	CLONAL	1	TRUE	0	0.928823738050823	3		330	470	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271707	38271707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003430-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3018	1449	475	0	ENST00000425967.3:c.2242C>T	p.His748Tyr	p.H748Y	ENST00000425967	NM_001174067.1	748	Cac/Tac	17/19	0.928823738050823	17	FACETS	0.927	0.903	0.952			1	CLONAL	6	TRUE	NA	0.928823738050823	17		475	4467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587780070	NA	P-0003430-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	287	309	0	ENST00000269305.4:c.535C>A	p.His179Asn	p.H179N	ENST00000269305	NM_001126112.2	179	Cat/Aat	5/11	0.928823738050823	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.928823738050823	2		309	300	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799129	42799129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139613152	NA	P-0003430-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	276	275	0	ENST00000575354.2:c.4613C>T	p.Pro1538Leu	p.P1538L	ENST00000575354	NM_015125.3	1538	cCg/cTg	20/20	0.863256284341888	3	FACETS	0.934	0.891	0.976	0.934	0.891	0.976	CLONAL	2	TRUE	1	0.928823738050823	3		275	466	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095875	29095875	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003430-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	616	592	0	ENST00000328354.6:c.959A>G	p.Lys320Arg	p.K320R	ENST00000328354	NM_007194.3	320	aAa/aGa	9/15	0.885617622069008	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.928823738050823	3		592	962	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440517	49440518	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0003430-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	490	480	0	ENST00000301067.7:c.4292dup	p.Val1432GlyfsTer15	p.V1432Gfs*15	ENST00000301067	NM_003482.3	1431	gag/gaAg	15/54	0.885617622069008	3	FACETS	0.992	0.959	1	0.992	0.959	1	CLONAL	2	TRUE	1	0.928823738050823	3		480	779	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0003536-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	556	366	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.529225432277466	6	FACETS	0.992	0.952	1	0.744	0.714	0.773	CLONAL	3	TRUE	2	0.529225432277466	6		366	1454	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0003536-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	311	498	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	0.526818663900691	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.529225432277466	2		498	582	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0003536-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	311	515	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.526818663900691	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.529225432277466	2		516	552	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012465	29012465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373801409	NA	P-0003536-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	507	255	0	ENST00000282397.4:c.406G>A	p.Val136Ile	p.V136I	ENST00000282397	NM_002019.4	136	Gta/Ata	4/30	0.446445394386848	4	FACETS	0.997	0.967	1			1	CLONAL	4	TRUE	NA	0.529225432277466	4		255	735	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986596	36986596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003536-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	109	128	0	ENST00000354822.5:c.1093G>A	p.Ala365Thr	p.A365T	ENST00000354822	NM_001079668.2	365	Gcc/Acc	3/3	0.517305460678595	3	FACETS	1	0.972	1	0.603	0.545	0.663	CLONAL	1	TRUE	1	0.529225432277466	3		128	432	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007741	45007741	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003536-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	297	231	0	ENST00000558401.1:c.188G>T	p.Gly63Val	p.G63V	ENST00000558401	NM_004048.2	63	gGa/gTa	2/4	0.517305460678595	3	FACETS	0.967	0.916	1	0.967	0.916	1	CLONAL	2	TRUE	1	0.529225432277466	3		231	734	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0003541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	283	408	2	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	1	0.702682045157331	2		410	660	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673752	30673752	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	186	270	0	ENST00000376406.3:c.3208C>G	p.Leu1070Val	p.L1070V	ENST00000376406	NM_014641.2	1070	Ctt/Gtt	10/15	0.132176549747366	5	FACETS	0.996	0.926	1			1	INDETERMINATE	2	FALSE	NA	0.702682045157331	5		270	546	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88678980	88678981	+	stop_gained,inframe_insertion	Nonsense_Mutation	INS	-	-	ATA	novel	NA	P-0003541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	189	145	0	ENST00000372037.3:c.920_921insATA	p.Leu307_Ile308insTer	p.L307_I308ins*	ENST00000372037	NM_004329.2	307	ttg/ttATAg	10/13	NA	2	FACETS	0.971	0.923	1			1	INDETERMINATE	2	FALSE	NA	0.702682045157331	2		145	277	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094479	27094479	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	21	238	0	ENST00000324856.7:c.3187G>T	p.Gly1063Ter	p.G1063*	ENST00000324856	NM_006015.4	1063	Gga/Tga	11/20	1	2	FACETS	1	0.793	1	1	0.793	1	CLONAL	1	TRUE	1	0.14	2		238	291	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99163121	99163121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753463935	NA	P-0003542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	83	388	0	ENST00000074304.5:c.1127G>A	p.Arg376His	p.R376H	ENST00000074304	NM_001134224.1	376	cGc/cAc	13/26	0.195936562703323	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	1	0.14	3		388	565	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968290	134968290	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	39	501	2	ENST00000398015.3:c.2803G>T	p.Ala935Ser	p.A935S	ENST00000398015	NM_004441.4	935	Gct/Tct	15/16	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.14	2		503	505	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038418	180038418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530977029	NA	P-0003542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	26	417	0	ENST00000261937.6:c.3599C>T	p.Ser1200Leu	p.S1200L	ENST00000261937	NM_182925.4	1200	tCg/tTg	27/30	NA	2	FACETS	1	0.812	1			1	INDETERMINATE	1	TRUE	NA	0.14	2		417	362	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398917	398917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356308443	NA	P-0003542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	26	277	0	ENST00000380956.4:c.727G>A	p.Glu243Lys	p.E243K	ENST00000380956	NM_001195286.1	243	Gaa/Aaa	6/9	NA	2	FACETS	1	0.797	1			1	INDETERMINATE	1	TRUE	NA	0.14	2		277	369	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119762	70119763	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0003542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	39	464	0	ENST00000245479.2:c.768dup	p.Arg257AlafsTer39	p.R257Afs*39	ENST00000245479	NM_000346.3	255	gag/gaGg	3/3	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.14	2		464	408	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0003569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	96	599	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.363139852638821	3	FACETS	1	0.979	1	0.707	0.633	0.784	CLONAL	1	TRUE	1	0.363139852638821	3		599	442	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571839	64571840	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	48	770	0	ENST00000312049.6:c.1799dup	p.Ser601ValfsTer78	p.S601Vfs*78	ENST00000312049	NM_130799.2	600	ctg/ctTg	10/10	0.363139852638821	3	FACETS	0.483	0.407	0.566	0.241	0.203	0.283	SUBCLONAL	1	TRUE	1	0.363139852638821	3		770	647	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578496	7578496	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	67	305	0	ENST00000269305.4:c.434T>G	p.Leu145Arg	p.L145R	ENST00000269305	NM_001126112.2	145	cTg/cGg	5/11	0.304929994774394	2	FACETS	0.85	0.75	0.955	0.85	0.75	0.955	CLONAL	2	TRUE	0	0.363139852638821	2		305	217	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251972	153251972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	90	403	0	ENST00000281708.4:c.1034G>A	p.Gly345Asp	p.G345D	ENST00000281708	NM_033632.3	345	gGt/gAt	7/12	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.363139852638821	2		403	495	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677925	58677948	+	inframe_deletion	In_Frame_Del	DEL	TCCGCGGCCGTCGCCGGCCGCCCT	TCCGCGGCCGTCGCCGGCCGCCCT	-	novel	NA	P-0003581-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	74	417	1	ENST00000305921.3:c.153_176del	p.Arg52_Pro59del	p.R52_P59del	ENST00000305921	NM_003620.3	50	ccTCCGCGGCCGTCGCCGGCCGCCCTt/cct	1/6	0.508404912098111	4	FACETS	1	0.957	1	0.596	0.525	0.67	CLONAL	1	TRUE	2	0.584121002116531	4		418	337	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111471	8111472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0003581-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	91	656	0	ENST00000346208.3:c.958dup	p.Cys320LeufsTer32	p.C320Lfs*32	ENST00000346208		319	-/T	5/6	0.514175898914004	4	FACETS	1	0.965	1	0.399	0.356	0.444	CLONAL	1	TRUE	1	0.584121002116531	4		656	412	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115922	8115923	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCG	novel	NA	P-0003581-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	76	465	0	ENST00000346208.3:c.1271_1274dup	p.Ser426AlafsTer82	p.S426Afs*82	ENST00000346208		423	cac/caCCCGc	6/6	0.514175898914004	4	FACETS	1	0.963	1	0.409	0.361	0.459	CLONAL	1	TRUE	1	0.584121002116531	4		465	336	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123722	11123722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1263140481	NA	P-0003586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	266	249	0	ENST00000358026.2:c.2372C>T	p.Ala791Val	p.A791V	ENST00000358026	NM_001128849.1	791	gCg/gTg	16/36	0.718008832036613	2	FACETS	0.912	0.875	0.947	0.912	0.875	0.947	CLONAL	2	FALSE	0	0.769920033502709	2		249	379	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843595	156843595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139875058	NA	P-0003586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	92	386	2	ENST00000524377.1:c.1021G>A	p.Val341Met	p.V341M	ENST00000524377	NM_002529.3	341	Gtg/Atg	8/17	0.769920033502709	5	FACETS	0.573	0.508	0.642	0.191	0.169	0.214	SUBCLONAL	1	FALSE	2	0.769920033502709	5		388	899	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575658	55575658	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	176	282	0	ENST00000288135.5:c.1184C>T	p.Ser395Phe	p.S395F	ENST00000288135	NM_000222.2	395	tCc/tTc	7/21	0.718415502741844	2	FACETS	0.935	0.869	1	0.467	0.434	0.501	CLONAL	1	FALSE	0	0.769920033502709	2		282	489	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514489	149514489	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	274	224	0	ENST00000261799.4:c.455C>A	p.Thr152Lys	p.T152K	ENST00000261799	NM_002609.3	152	aCa/aAa	4/23	0.67750543530847	3	FACETS	1	0.993	1	0.796	0.762	0.828	CLONAL	2	FALSE	0	0.769920033502709	3		224	413	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554353	81554353	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	305	315	0	ENST00000298171.2:c.373C>G	p.Leu125Val	p.L125V	ENST00000298171	NM_000369.2	125	Ctc/Gtc	4/10	0.769920033502709	4	FACETS	0.902	0.855	0.951			1	CLONAL	2	FALSE	NA	0.769920033502709	4		315	777	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239429	105239429	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	68	166	0	ENST00000349310.3:c.958G>T	p.Val320Leu	p.V320L	ENST00000349310	NM_001014432.1	320	Gtg/Ttg	12/15	0.596830003383225	6	FACETS	0.784	0.683	0.894			1	SUBCLONAL	1	FALSE	NA	0.769920033502709	6		166	572	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876593	59876593	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	73	179	0	ENST00000259008.2:c.1208G>T	p.Arg403Leu	p.R403L	ENST00000259008	NM_032043.2	403	cGg/cTg	9/20	0.769920033502709	4	FACETS	0.373	0.325	0.424	0.093	0.081	0.106	SUBCLONAL	1	FALSE	0	0.769920033502709	4		179	901	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602907	10602907	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	227	189	0	ENST00000171111.5:c.671C>T	p.Ser224Phe	p.S224F	ENST00000171111	NM_203500.1	224	tCc/tTc	3/6	0.718008832036613	2	FACETS	0.93	0.89	0.968	0.93	0.89	0.968	CLONAL	2	FALSE	0	0.769920033502709	2		189	317	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579546	7579547	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	240	192	1	ENST00000269305.4:c.140_141insT	p.Asp48GlyfsTer4	p.D48Gfs*4	ENST00000269305	NM_001126112.2	47	ccg/ccTg	4/11	0.718415502741844	2	FACETS	0.956	0.918	0.993	0.956	0.918	0.993	CLONAL	2	FALSE	0	0.769920033502709	2		193	326	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989482	212989483	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0003586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	107	219	3	ENST00000342788.4:c.228_229delinsAA	p.Phe76_Leu77delinsLeuMet	p.F76_L77delinsLM	ENST00000342788	NM_005235.2	76	ttCCtg/ttAAtg	2/28	0.491222677629362	3	FACETS	0.848	0.765	0.935	0.424	0.382	0.468	CLONAL	1	FALSE	1	0.769920033502709	3		222	454	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952518	17952519	+	missense_variant	Missense_Mutation	DNP	CT	CT	TG	novel	NA	P-0003586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	157	171	0	ENST00000458235.1:c.914_915delinsCA	p.Gln305Pro	p.Q305P	ENST00000458235	NM_000215.3	305	cAG/cCA	7/24	0.718008832036613	2	FACETS	1	0.967	1	0.537	0.498	0.576	CLONAL	1	FALSE	0	0.769920033502709	2		171	380	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505463	25505463	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	147	230	0	ENST00000264709.3:c.295C>T	p.Pro99Ser	p.P99S	ENST00000264709	NM_175629.2	99	Ccc/Tcc	4/23	0.521365789430996	4	FACETS	1	0.963	1			1	CLONAL	2	FALSE	NA	0.515833664588032	4		230	403	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046668	180046668	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	130	224	0	ENST00000261937.6:c.2644A>C	p.Lys882Gln	p.K882Q	ENST00000261937	NM_182925.4	882	Aaa/Caa	18/30	0.209032681699157	4	FACETS	1	0.951	1			1	INDETERMINATE	3	FALSE	NA	0.515833664588032	4		224	247	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683192	88683192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199907158	NA	P-0003625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	46	76	0	ENST00000372037.3:c.1402G>A	p.Glu468Lys	p.E468K	ENST00000372037	NM_004329.2	468	Gaa/Aaa	12/13	0.521365789430996	3	FACETS	1	0.953	1	0.656	0.561	0.757	CLONAL	1	FALSE	1	0.515833664588032	3		76	171	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423595	88423595	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	132	231	0	ENST00000360948.2:c.2240T>C	p.Phe747Ser	p.F747S	ENST00000360948	NM_001012338.2	747	tTc/tCc	18/19	0.350436187131171	1	FACETS	0.775	0.721	0.829	1	0.99	1	SUBCLONAL	2	FALSE	0	0.515833664588032	1		231	245	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676208	37676208	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0003625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	112	253	0	ENST00000447079.4:c.2964-1G>C		p.X988_splice	ENST00000447079	NM_015083.1	988			0.488578923888916	4	FACETS	1	0.98	1			1	CLONAL	1	FALSE	NA	0.515833664588032	4		253	490	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061225	38061242	+	inframe_deletion	In_Frame_Del	DEL	TCGAACATGTTGCCGGAG	TCGAACATGTTGCCGGAG	-	novel	NA	P-0003625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	234	171	0	ENST00000250448.2:c.747_764del	p.Asp249_Phe254del	p.D249_F254del	ENST00000250448	NM_004496.3	249	gaCTCCGGCAACATGTTCGAg/gag	2/2	0.515833664588032	8	FACETS	0.946	0.898	0.994			1	CLONAL	6	FALSE	NA	0.515833664588032	8		171	407	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618727	37618728	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	299	268	0	ENST00000447079.4:c.405dup	p.Val136SerfsTer21	p.V136Sfs*21	ENST00000447079	NM_015083.1	135	gaa/gAaa	1/14	0.488578923888916	4	FACETS	0.897	0.858	0.935			1	CLONAL	4	FALSE	NA	0.515833664588032	4		268	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0003665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	125	327	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	1	2	FACETS	0.904	0.822	0.99	0.904	0.822	0.99	CLONAL	1	TRUE	1	0.499220859819515	2		327	554	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	159	436	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.499220859819515	2		436	600	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	194	417	0	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.499220859819515	2		417	661	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0003665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	100	381	1	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.98	0.881	1	0.98	0.881	1	CLONAL	1	TRUE	1	0.499220859819515	2		382	409	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274172	10274173	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1555491538	NA	P-0003665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	95	306	0	ENST00000330684.3:c.96dup	p.Ala33ArgfsTer105	p.A33Rfs*105	ENST00000330684	NM_001134407.1	32	-/C	2/13	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.499220859819515	2		306	379	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958550	175958550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1419838517	NA	P-0003665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	43	493	0	ENST00000367669.3:c.1795C>T	p.Arg599Cys	p.R599C	ENST00000367669	NM_022457.5	599	Cgt/Tgt	16/20	1	2	FACETS	0.244	0.204	0.29	0.244	0.204	0.29	SUBCLONAL	1	TRUE	1	0.499220859819515	2		493	705	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027168	49027168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913305	NA	P-0003665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	168	487	0	ENST00000267163.4:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	579	Cga/Tga	18/27	0.499220859819515	1	FACETS	0.977	0.904	1	0.977	0.904	1	CLONAL	1	TRUE	0	0.499220859819515	1		487	517	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630472	47630472	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63750615	NA	P-0003665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	143	368	0	ENST00000233146.2:c.142G>T	p.Glu48Ter	p.E48*	ENST00000233146	NM_000251.2	48	Gag/Tag	1/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.499220859819515	2		368	519	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026203	48026203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782651	NA	P-0003665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	162	338	1	ENST00000234420.5:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000234420	NM_000179.2	361	Cgc/Tgc	4/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.499220859819515	2		339	603	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587130	189587130	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	138	394	0	ENST00000264731.3:c.1147C>T	p.His383Tyr	p.H383Y	ENST00000264731	NM_003722.4	383	Cat/Tat	9/14	1	2	FACETS	0.917	0.837	1	0.917	0.837	1	CLONAL	1	TRUE	1	0.499220859819515	2		394	603	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539924	187539924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765909046	NA	P-0003665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	177	388	0	ENST00000441802.2:c.7816G>A	p.Gly2606Arg	p.G2606R	ENST00000441802	NM_005245.3	2606	Ggg/Agg	10/27	0.499220859819515	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.499220859819515	1		388	454	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902290	151902290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301632462	NA	P-0003665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	38	116	0	ENST00000262189.6:c.3862C>T	p.Arg1288Trp	p.R1288W	ENST00000262189	NM_170606.2	1288	Cgg/Tgg	25/59	0.499220859819515	3	FACETS	0.919	0.767	1	0.46	0.383	0.543	CLONAL	1	TRUE	1	0.499220859819515	3		116	207	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852251	63852251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137983907	NA	P-0003665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	148	388	2	ENST00000279873.7:c.3029G>A	p.Arg1010Gln	p.R1010Q	ENST00000279873	NM_032199.2	1010	cGg/cAg	10/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.499220859819515	2		390	480	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911639	114911639	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	174	392	0	ENST00000543371.1:c.1157G>A	p.Arg386Gln	p.R386Q	ENST00000543371	NM_001198531.1	386	cGg/cAg	10/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.499220859819515	2		392	596	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201702	67201702	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373702089	NA	P-0003665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	153	424	0	ENST00000312629.5:c.1003G>A	p.Asp335Asn	p.D335N	ENST00000312629	NM_003952.2	335	Gac/Aac	12/15	1	2	FACETS	0.981	0.901	1	0.981	0.901	1	CLONAL	1	TRUE	1	0.499220859819515	2		424	625	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905490	11905490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745855585	NA	P-0003665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	80	208	0	ENST00000396373.4:c.140C>T	p.Ser47Leu	p.S47L	ENST00000396373	NM_001987.4	47	tCg/tTg	2/8	0.499220859819515	1	FACETS	0.891	0.794	0.992	0.891	0.794	0.992	CLONAL	1	TRUE	0	0.499220859819515	1		208	270	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433066	49433066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772742966	NA	P-0003665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	180	443	0	ENST00000301067.7:c.8305G>A	p.Asp2769Asn	p.D2769N	ENST00000301067	NM_003482.3	2769	Gat/Aat	33/54	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.499220859819515	2		443	617	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865573	57865573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	213	618	1	ENST00000228682.2:c.3050G>A	p.Gly1017Asp	p.G1017D	ENST00000228682	NM_005269.2	1017	gGc/gAc	12/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.499220859819515	2		619	797	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341230	341230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756690670	NA	P-0003665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	182	455	0	ENST00000262320.3:c.2254G>A	p.Val752Met	p.V752M	ENST00000262320	NM_003502.3	752	Gtg/Atg	9/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.499220859819515	2		455	561	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944214	81944214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	183	629	0	ENST00000359376.3:c.1823G>A	p.Ser608Asn	p.S608N	ENST00000359376	NM_002661.3	608	aGc/aAc	18/33	0.160057019595652	1	FACETS	0.732	0.677	0.788	0.732	0.677	0.788	INDETERMINATE	1	TRUE	0	0.499220859819515	1		629	752	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120179	70120179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	97	237	0	ENST00000245479.2:c.1181G>A	p.Arg394Gln	p.R394Q	ENST00000245479	NM_000346.3	394	cGa/cAa	3/3	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.499220859819515	2		237	334	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223131	5223131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375155482	NA	P-0003665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	137	455	0	ENST00000357368.4:c.2672C>T	p.Thr891Met	p.T891M	ENST00000357368	NM_002850.3	891	aCg/aTg	18/38	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.499220859819515	2		455	543	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265138	5265138	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	177	453	1	ENST00000357368.4:c.449G>T	p.Arg150Leu	p.R150L	ENST00000357368	NM_002850.3	150	cGg/cTg	5/38	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.499220859819515	2		454	627	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410223	63410223	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	309	251	0	ENST00000330258.3:c.2944A>G	p.Arg982Gly	p.R982G	ENST00000330258	NM_152424.3	982	Agg/Ggg	2/2	0.499220859819515	2	FACETS	0.901	0.866	0.935			1	CLONAL	3	TRUE	NA	0.499220859819515	2		251	458	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637918	176637920	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	novel	NA	P-0003665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	152	332	0	ENST00000439151.2:c.2520_2522del	p.Asn841del	p.N841del	ENST00000439151	NM_022455.4	840	AAC/-	5/23	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.499220859819515	2		332	584	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591122	67591130	+	inframe_deletion	In_Frame_Del	DEL	AGCTGAGAA	AGCTGAGAA	-	novel	NA	P-0003665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	89	249	0	ENST00000274335.5:c.1717_1725del	p.Leu573_Lys575del	p.L573_K575del	ENST00000274335		572	cAGCTGAGAAag/cag	12/15	1	2	FACETS	0.787	0.701	0.878	0.787	0.701	0.878	SUBCLONAL	1	TRUE	1	0.499220859819515	2		249	453	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101751	71101751	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	120	313	0	ENST00000318789.4:c.447del	p.Lys149AsnfsTer57	p.K149Nfs*57	ENST00000318789	NM_032682.5	149	aaA/aa	9/21	1	2	FACETS	0.95	0.862	1	0.95	0.862	1	CLONAL	1	TRUE	1	0.499220859819515	2		313	506	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133208958	133208958	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	126	407	1	ENST00000320574.5:c.6273del	p.Gly2092ValfsTer31	p.G2092Vfs*31	ENST00000320574	NM_006231.2	2091	ccC/cc	45/49	1	2	FACETS	0.848	0.771	0.93	0.848	0.771	0.93	CLONAL	1	TRUE	1	0.499220859819515	2		408	595	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428410	49428411	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1284500089	NA	P-0003665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	138	421	0	ENST00000301067.7:c.10394dup	p.Pro3466ThrfsTer2	p.P3466Tfs*2	ENST00000301067	NM_003482.3	3465	gga/ggGa	36/54	1	2	FACETS	0.852	0.777	0.93	0.852	0.777	0.93	CLONAL	1	TRUE	1	0.499220859819515	2		421	649	SUCCESS
APC	324	MSKCC	GRCh37	5	112157615	112157615	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1334951365	NA	P-0003741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	28	238	0	ENST00000257430.4:c.1335G>T	p.Gln445His	p.Q445H	ENST00000257430	NM_000038.5	445	caG/caT	11/16	0.474918044759288	1	FACETS	0.32	0.257	0.391	0.32	0.257	0.391	SUBCLONAL	1	FALSE	0	0.537585375781345	1		238	238	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061202	38061203	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCGGC	novel	NA	P-0003741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	40	165	0	ENST00000250448.2:c.782_786dup	p.Gln263AlafsTer60	p.Q263Afs*60	ENST00000250448	NM_004496.3	262	-/GCCGC	2/2	0.234997692794014	3	FACETS	1	0.853	1	0.508	0.427	0.595	INDETERMINATE	1	FALSE	1	0.537585375781345	3		165	186	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0003756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	76	397	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.504695310105176	1	FACETS	0.695	0.616	0.777	0.695	0.616	0.777	SUBCLONAL	1	TRUE	0	0.557658779773224	1		397	283	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0003756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	319	435	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.944	0.901	0.987	1	0.996	1	CLONAL	2	TRUE	1	0.557658779773224	2		435	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0003756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	138	604	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.504695310105176	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.557658779773224	1		604	331	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0003756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	130	571	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.267524816352441	1	FACETS	0.749	0.684	0.816	0.749	0.684	0.816	INDETERMINATE	1	TRUE	0	0.557658779773224	1		571	449	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0003756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	43	153	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.423157925429219	2	FACETS	0.511	0.429	0.6	0.255	0.214	0.3	SUBCLONAL	1	TRUE	0	0.557658779773224	2		153	302	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003812-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	52	303	0	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.16	2		303	639	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0003812-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	53	404	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	0.125158330944186	3	FACETS	0.797	0.677	0.928	0.398	0.338	0.464	CLONAL	1	TRUE	1	0.16	3		404	898	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579584	7579585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0003812-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	37	215	0	ENST00000269305.4:c.102dup	p.Pro36AlafsTer7	p.P36Afs*7	ENST00000269305	NM_001126112.2	34	-/C	4/11	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.16	2		215	376	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612980	228612980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571515258	NA	P-0003812-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	23	257	0	ENST00000366696.1:c.47C>T	p.Ala16Val	p.A16V	ENST00000366696	NM_003493.2	16	gCg/gTg	1/1	0.125158330944186	3	FACETS	0.83	0.647	1	0.415	0.323	0.522	CLONAL	1	TRUE	1	0.16	3		257	374	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935535	49935535	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003812-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	30	418	0	ENST00000296474.3:c.1829C>A	p.Thr610Asn	p.T610N	ENST00000296474	NM_002447.2	610	aCt/aAt	5/20	0.3	0	FACETS	0.64	0.515	0.783			1	SUBCLONAL	1	TRUE	0	0.16	0		418	492	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844193	68844193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121964873	NA	P-0003812-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	41	303	2	ENST00000261769.5:c.781G>A	p.Glu261Lys	p.E261K	ENST00000261769	NM_004360.3	261	Gaa/Aaa	6/16	0.125158330944186	1	FACETS	0.932	0.776	1	0.932	0.776	1	CLONAL	1	TRUE	0	0.16	1		305	506	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665732	29665732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003812-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	46	236	0	ENST00000356175.3:c.6767G>A	p.Ser2256Asn	p.S2256N	ENST00000356175	NM_000267.3	2256	aGt/aAt	45/57	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.16	2		236	556	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845959	151845959	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003812-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	37	298	0	ENST00000262189.6:c.13053del	p.Lys4351AsnfsTer5	p.K4351Nfs*5	ENST00000262189	NM_170606.2	4351	aaA/aa	52/59	1	2	FACETS	0.841	0.692	1	0.841	0.692	1	CLONAL	1	TRUE	1	0.16	2		298	550	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506924	186506924	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003812-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	56	369	0	ENST00000323963.5:c.1094del	p.Gly365ValfsTer10	p.G365Vfs*10	ENST00000323963		364	Ggg/gg	11/11	0.223056091029687	4	FACETS	1	0.875	1	0.513	0.438	0.595	CLONAL	1	TRUE	2	0.16	4		369	792	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003866-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	111	249	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	0.529555916795123	2		249	403	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870839	12870840	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0003866-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	131	269	0	ENST00000228872.4:c.67dup	p.His23ProfsTer102	p.H23Pfs*102	ENST00000228872	NM_004064.3	22	-/C	1/3	0.529555916795123	1	FACETS	0.928	0.851	1	0.928	0.851	1	CLONAL	1	TRUE	0	0.529555916795123	1		269	392	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106915	27106915	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	174	143	0	ENST00000324856.7:c.6526C>T	p.Gln2176Ter	p.Q2176*	ENST00000324856	NM_006015.4	2176	Cag/Tag	20/20	0.399418020073973	1	FACETS	0.786	0.739	0.832	0.786	0.739	0.832	INDETERMINATE	1	TRUE	0	0.839574830000291	1		143	306	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0003911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	136	204	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.4986742511149	1	FACETS	0.743	0.691	0.794	0.743	0.691	0.794	INDETERMINATE	1	TRUE	0	0.839574830000291	1		204	253	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652029	36652029	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	142	177	0	ENST00000244741.5:c.151T>G	p.Phe51Val	p.F51V	ENST00000244741	NM_000389.4	51	Ttc/Gtc	2/3	0.430360809129349	1	FACETS	0.656	0.609	0.704	0.656	0.609	0.704	INDETERMINATE	1	TRUE	0	0.839574830000291	1		177	299	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39629525	39629525	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	96	263	0	ENST00000262039.4:c.2219G>T	p.Gly740Val	p.G740V	ENST00000262039	NM_002647.2	740	gGa/gTa	21/25	0.399418020073973	1	FACETS	0.338	0.303	0.374	0.338	0.303	0.374	INDETERMINATE	1	TRUE	0	0.839574830000291	1		263	393	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846179	151846180	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAAATGCTTTGGAAGGCGTTTCTCTC	novel	NA	P-0003911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	111	172	0	ENST00000262189.6:c.12807_12832dup	p.His4278ArgfsTer57	p.H4278Rfs*57	ENST00000262189	NM_170606.2	4278	cat/cGAGAGAAACGCCTTCCAAAGCATTTCat	52/59	1	2	FACETS	0.58	0.524	0.638	0.58	0.524	0.638	SUBCLONAL	1	TRUE	1	0.839574830000291	2		172	456	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	71	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.338200739399029	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	2	0.496941547702226	4		249	187	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0003987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	99	509	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.509490039242538	4	FACETS	0.909	0.821	1	0.909	0.821	1	CLONAL	2	TRUE	2	0.496941547702226	4		509	328	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446247	187446247	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	81	175	0	ENST00000232014.4:c.1441C>T	p.Gln481Ter	p.Q481*	ENST00000232014	NM_001130845.1	481	Cag/Tag	6/10	0.509490039242538	4	FACETS	0.841	0.75	0.937	0.841	0.75	0.937	CLONAL	2	TRUE	2	0.496941547702226	4		175	290	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363243	40363243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	131	212	0	ENST00000397332.2:c.986C>T	p.Ser329Leu	p.S329L	ENST00000397332	NM_001033082.2	329	tCg/tTg	3/3	0.509490039242538	4	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	2	0.496941547702226	4		212	382	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457261	25457261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs992291948	NA	P-0003987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	86	169	0	ENST00000264709.3:c.2626G>A	p.Asp876Asn	p.D876N	ENST00000264709	NM_175629.2	876	Gac/Aac	23/23	0.486067346806628	4	FACETS	0.925	0.829	1			1	CLONAL	2	TRUE	NA	0.496941547702226	4		169	280	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149506	61149506	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	165	251	0	ENST00000295025.8:c.1696G>C	p.Asp566His	p.D566H	ENST00000295025	NM_002908.2	566	Gac/Cac	11/11	0.484338784010811	4	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	2	0.496941547702226	4		251	485	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288537	198288537	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	162	325	0	ENST00000335508.6:c.190G>A	p.Glu64Lys	p.E64K	ENST00000335508	NM_012433.2	64	Gaa/Aaa	2/25	0.509490039242538	4	FACETS	0.996	0.921	1	0.996	0.921	1	CLONAL	2	TRUE	2	0.496941547702226	4		325	490	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979645	55979645	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	95	217	0	ENST00000263923.4:c.802C>T	p.Gln268Ter	p.Q268*	ENST00000263923	NM_002253.2	268	Cag/Tag	7/30	0.338200739399029	4	FACETS	0.872	0.785	0.963	0.872	0.785	0.963	CLONAL	2	TRUE	2	0.496941547702226	4		217	328	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32191635	32191635	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	140	497	0	ENST00000375023.3:c.71G>C	p.Arg24Thr	p.R24T	ENST00000375023	NM_004557.3	24	aGa/aCa	1/30	NA	2	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.496941547702226	2		497	534	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641045	93641045	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0003987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	46	101	0	ENST00000375746.1:c.1392-1G>C		p.X464_splice	ENST00000375746	NM_001174167.1	464			0.338200739399029	4	FACETS	0.871	0.747	1	0.871	0.747	1	CLONAL	2	TRUE	2	0.496941547702226	4		101	159	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412639	139412639	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1037236860	NA	P-0003987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	84	210	0	ENST00000277541.6:c.1205C>T	p.Ser402Leu	p.S402L	ENST00000277541	NM_017617.3	402	tCg/tTg	7/34	0.328624885861345	4	FACETS	0.83	0.741	0.923			1	CLONAL	2	TRUE	NA	0.496941547702226	4		210	305	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117753	108117753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	102	245	0	ENST00000278616.4:c.964G>A	p.Glu322Lys	p.E322K	ENST00000278616	NM_000051.3	322	Gag/Aag	8/63	0.194917610926089	1	FACETS	1	0.984	1	1	0.984	1	INDETERMINATE	1	TRUE	0	0.496941547702226	1		245	219	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443910	18443910	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	103	262	0	ENST00000266497.5:c.883G>T	p.Asp295Tyr	p.D295Y	ENST00000266497		295	Gat/Tat	3/31	0.328624885861345	4	FACETS	0.869	0.785	0.956			1	CLONAL	2	TRUE	NA	0.496941547702226	4		262	357	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934194	48934194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	115	293	0	ENST00000267163.4:c.649C>T	p.Gln217Ter	p.Q217*	ENST00000267163	NM_000321.2	217	Cag/Tag	7/27	NA	2	FACETS	0.784	0.717	0.853			1	INDETERMINATE	2	TRUE	NA	0.496941547702226	2		293	295	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352697	NA	P-0003987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	158	380	0	ENST00000269305.4:c.587G>A	p.Arg196Gln	p.R196Q	ENST00000269305	NM_001126112.2	196	cGa/cAa	6/11	0.4943951776854	2	FACETS	0.978	0.912	1	0.978	0.912	1	CLONAL	2	TRUE	0	0.496941547702226	2		380	325	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688735	47688735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	193	337	0	ENST00000347630.2:c.565G>A	p.Glu189Lys	p.E189K	ENST00000347630	NM_001007230.1	189	Gag/Aag	7/11	0.315728327152758	4	FACETS	0.927	0.869	0.986	1	0.991	1	CLONAL	3	TRUE	2	0.496941547702226	4		337	418	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980877	40980877	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	61	160	0	ENST00000373198.4:c.1609A>G	p.Ser537Gly	p.S537G	ENST00000373198	NM_133170.3	537	Agc/Ggc	10/32	0.486067346806628	4	FACETS	1	0.905	1			1	CLONAL	1	TRUE	NA	0.496941547702226	4		160	349	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466809	57466809	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs200163406	NA	P-0003987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	83	230	0	ENST00000371085.3:c.28G>C	p.Glu10Gln	p.E10Q	ENST00000371085	NM_000516.4	10	Gag/Cag	1/13	0.496941547702226	7	FACETS	1	0.905	1			1	CLONAL	2	TRUE	NA	0.496941547702226	7		230	367	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862100	68862103	+	frameshift_variant	Frame_Shift_Del	DEL	TTTC	TTTC	-	novel	NA	P-0003987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	151	269	0	ENST00000261769.5:c.2190_2193del	p.Leu731GlyfsTer38	p.L731Gfs*38	ENST00000261769	NM_004360.3	730	TTTCtt/tt	14/16	NA	2	FACETS	0.912	0.848	0.978			1	INDETERMINATE	2	TRUE	NA	0.496941547702226	2		269	333	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183246	56183247	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0003987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	236	177	0	ENST00000399503.3:c.4158dup	p.Ala1387CysfsTer33	p.A1387Cfs*33	ENST00000399503	NM_005921.1	1386	att/aTtt	18/20	0.496941547702226	8	FACETS	0.928	0.875	0.98			1	CLONAL	5	TRUE	NA	0.496941547702226	8		177	510	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178029	56178030	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0003987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	125	228	0	ENST00000399503.3:c.3005_3006del	p.Ser1002Ter	p.S1002*	ENST00000399503	NM_005921.1	1001	gTC/g	14/20	0.496941547702226	8	FACETS	0.935	0.848	1			1	CLONAL	2	TRUE	NA	0.496941547702226	8		228	670	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0004006-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	695	526	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.939277813647454	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.939277813647454	2		526	725	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354254	15354254	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004006-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	132	197	0	ENST00000263377.2:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000263377	NM_058243.2	876	Cga/Tga	14/20	1	2	FACETS	0.87	0.802	0.94	0.87	0.802	0.94	CLONAL	1	TRUE	1	0.939277813647454	2		197	323	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923143	48923144	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004006-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	841	283	0	ENST00000267163.4:c.596dup	p.Leu199PhefsTer4	p.L199Ffs*4	ENST00000267163	NM_000321.2	197	-/T	6/27	0.939277813647454	2	FACETS	0.936	0.921	0.949	0.936	0.921	0.949	CLONAL	2	TRUE	0	0.939277813647454	2		283	957	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0004043-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	112	302	0	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.378643639208572	1	FACETS	0.974	0.882	1	0.974	0.882	1	CLONAL	1	TRUE	0	0.408433090042602	1		302	448	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0004043-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16414	1060	571	1	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	0.408433090042602	42	FACETS	0.908	0.876	0.941			1	CLONAL	3	TRUE	NA	0.408433090042602	42		572	17474	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1272311	1272311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141425941	NA	P-0004043-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	76	416	0	ENST00000310581.5:c.2371G>A	p.Val791Ile	p.V791I	ENST00000310581	NM_198253.2	791	Gtc/Atc	7/16	0.25774733455935	5	FACETS	0.655	0.573	0.744	0.218	0.191	0.248	SUBCLONAL	1	TRUE	2	0.408433090042602	5		416	916	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120164	70120164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004043-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	63	271	1	ENST00000245479.2:c.1166C>T	p.Pro389Leu	p.P389L	ENST00000245479	NM_000346.3	389	cCg/cTg	3/3	0.408433090042602	1	FACETS	0.909	0.794	1	0.909	0.794	1	CLONAL	1	TRUE	0	0.408433090042602	1		272	270	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442808	99442809	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004043-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	149	548	0	ENST00000268035.6:c.1211dup	p.Asn404LysfsTer66	p.N404Kfs*66	ENST00000268035	NM_000875.3	402	cta/ctAa	5/21	1	2	FACETS	0.935	0.856	1	0.935	0.856	1	CLONAL	1	TRUE	1	0.408433090042602	2		548	780	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0004087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	110	312	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.852231912359278	3	FACETS	0.883	0.799	0.97	0.441	0.399	0.485	CLONAL	1	TRUE	1	0.852231912359278	3		312	417	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220649	1220649	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	415	269	0	ENST00000326873.7:c.667G>T	p.Glu223Ter	p.E223*	ENST00000326873	NM_000455.4	223	Gag/Tag	5/10	0.777300133020352	2	FACETS	0.919	0.893	0.943	0.919	0.893	0.943	CLONAL	2	TRUE	0	0.852231912359278	2		269	530	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651145	206651145	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	295	216	1	ENST00000367120.3:c.755G>T	p.Arg252Leu	p.R252L	ENST00000367120	NM_014002.3	252	cGg/cTg	8/22	0.385334962663027	6	FACETS	0.856	0.811	0.902	0.856	0.811	0.902	INDETERMINATE	3	TRUE	3	0.852231912359278	6		217	729	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612878	228612878	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	428	433	3	ENST00000366696.1:c.149G>C	p.Arg50Pro	p.R50P	ENST00000366696	NM_003493.2	50	cGc/cCc	1/1	0.385334962663027	6	FACETS	0.85	0.812	0.888	0.85	0.812	0.888	INDETERMINATE	3	TRUE	3	0.852231912359278	6		436	1065	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876585	35876585	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	288	108	0	ENST00000303115.3:c.1377G>T	p.Gln459His	p.Q459H	ENST00000303115	NM_002185.3	459	caG/caT	8/8	0.758068628393276	5	FACETS	0.917	0.88	0.952	0.917	0.88	0.952	CLONAL	4	TRUE	1	0.852231912359278	5		108	420	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673548	30673548	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1177579340	NA	P-0004087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	189	359	0	ENST00000376406.3:c.3412A>T	p.Thr1138Ser	p.T1138S	ENST00000376406	NM_014641.2	1138	Act/Tct	10/15	0.334449948552209	5	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.852231912359278	5		359	781	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978873	13978873	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0004087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	283	150	0	ENST00000405192.2:c.236-2A>G		p.X79_splice	ENST00000405192	NM_001163147.1	79			0.385334962663027	6	FACETS	0.92	0.871	0.969	0.92	0.871	0.969	INDETERMINATE	3	TRUE	3	0.852231912359278	6		150	651	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012425	152012425	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0004087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	152	160	0	ENST00000262189.6:c.390-2A>G		p.X130_splice	ENST00000262189	NM_170606.2	130			0.852231912359278	3	FACETS	0.882	0.81	0.956	0.441	0.405	0.478	CLONAL	1	TRUE	1	0.852231912359278	3		160	577	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972777	32972777	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1555290049	NA	P-0004087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	223	223	0	ENST00000380152.3:c.10127C>G	p.Ser3376Ter	p.S3376*	ENST00000380152		3376	tCa/tGa	27/27	NA	2	FACETS	0.986	0.926	1			1	INDETERMINATE	1	TRUE	NA	0.852231912359278	2		223	531	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041599	42041599	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	673	409	1	ENST00000219905.7:c.5794G>T	p.Gly1932Cys	p.G1932C	ENST00000219905	NM_001164273.1	1932	Ggt/Tgt	17/24	0.852231912359278	3	FACETS	0.926	0.897	0.955	0.926	0.897	0.955	CLONAL	2	TRUE	1	0.852231912359278	3		410	1216	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130286	2130286	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	417	320	0	ENST00000219476.3:c.3518C>A	p.Thr1173Asn	p.T1173N	ENST00000219476	NM_000548.3	1173	aCc/aAc	30/42	NA	2	FACETS	0.93	0.905	0.955			1	INDETERMINATE	2	TRUE	NA	0.852231912359278	2		320	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0004087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	276	171	0	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	0.852231912359278	3	FACETS	0.939	0.894	0.983	0.939	0.894	0.983	CLONAL	2	TRUE	1	0.852231912359278	3		171	492	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265084	10265084	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	207	333	0	ENST00000340748.4:c.1856C>A	p.Thr619Asn	p.T619N	ENST00000340748		619	aCc/aAc	21/40	0.777300133020352	2	FACETS	0.861	0.805	0.918	0.431	0.402	0.459	CLONAL	1	TRUE	0	0.852231912359278	2		333	564	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610312	10610312	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	377	226	1	ENST00000171111.5:c.398T>G	p.Met133Arg	p.M133R	ENST00000171111	NM_203500.1	133	aTg/aGg	2/6	0.777300133020352	2	FACETS	0.905	0.877	0.931	0.905	0.877	0.931	CLONAL	2	TRUE	0	0.852231912359278	2		227	489	SUCCESS
AR	367	MSKCC	GRCh37	X	66905909	66905909	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	293	340	0	ENST00000374690.3:c.1826G>T	p.Arg609Met	p.R609M	ENST00000374690	NM_000044.3	609	aGg/aTg	3/8	NA	2	FACETS	0.955	0.904	1			1	INDETERMINATE	1	TRUE	NA	0.852231912359278	2		340	720	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617180	100617180	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	217	340	0	ENST00000308731.7:c.569C>A	p.Pro190Gln	p.P190Q	ENST00000308731	NM_000061.2	190	cCa/cAa	7/19	0.830511597400021	1	FACETS	0.805	0.763	0.846	0.805	0.763	0.846	CLONAL	1	TRUE	0	0.852231912359278	1		340	363	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167583	24167585	+	frameshift_variant	Frame_Shift_Ins	INS	CAG	CAG	TTAA	novel	NA	P-0004087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	160	104	0	ENST00000263121.7:c.967_969delinsTTAA	p.Gln323LeufsTer38	p.Q323Lfs*38	ENST00000263121	NM_003073.3	323	CAG/TTAA	7/9	NA	2	FACETS	0.89	0.847	0.93			1	INDETERMINATE	2	TRUE	NA	0.852231912359278	2		104	211	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064794618	NA	P-0004112-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	161	246	0	ENST00000269305.4:c.159G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgG/tgA	4/11	NA	2	FACETS	0.967	0.915	1			1	INDETERMINATE	2	TRUE	NA	0.714923374363735	2		246	233	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937602	76937603	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004112-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	287	185	0	ENST00000373344.5:c.3145dup	p.Ile1049AsnfsTer4	p.I1049Nfs*4	ENST00000373344	NM_000489.3	1049	ata/aAta	9/35	0.634072270222245	2	FACETS	1	0.976	1			1	CLONAL	2	TRUE	NA	0.714923374363735	2		185	394	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0004124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	60	435	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.948	0.815	1	0.948	0.815	1	CLONAL	1	TRUE	1	0.15	2		435	844	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219336	1219336	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	49	308	0	ENST00000326873.7:c.388G>T	p.Glu130Ter	p.E130*	ENST00000326873	NM_000455.4	130	Gag/Tag	3/10	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.15	2		308	525	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877106	151877106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	34	285	0	ENST00000262189.6:c.7255C>T	p.Pro2419Ser	p.P2419S	ENST00000262189	NM_170606.2	2419	Cct/Tct	37/59	1	2	FACETS	0.762	0.621	0.921	0.762	0.621	0.921	CLONAL	1	TRUE	1	0.15	2		285	595	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239912	98239912	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	35	232	0	ENST00000331920.6:c.1420G>T	p.Val474Phe	p.V474F	ENST00000331920	NM_000264.3	474	Gtc/Ttc	10/24	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.15	2		232	441	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130334	11130334	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1480398200	NA	P-0004124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	89	440	1	ENST00000358026.2:c.2573C>T	p.Thr858Met	p.T858M	ENST00000358026	NM_001128849.1	858	aCg/aTg	18/36	1	2	FACETS	0.759	0.672	0.851	1	0.979	1	SUBCLONAL	2	TRUE	1	0.15	2		441	782	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306729	41306729	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	34	253	0	ENST00000373198.4:c.930T>A	p.Asn310Lys	p.N310K	ENST00000373198	NM_133170.3	310	aaT/aaA	7/32	1	2	FACETS	0.821	0.67	0.992	0.821	0.67	0.992	CLONAL	1	TRUE	1	0.15	2		253	552	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121325	29121325	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781982	NA	P-0004124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	57	401	0	ENST00000328354.6:c.350G>T	p.Arg117Met	p.R117M	ENST00000328354	NM_007194.3	117	aGg/aTg	3/15	1	2	FACETS	0.812	0.695	0.941	0.812	0.695	0.941	CLONAL	1	TRUE	1	0.15	2		401	936	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599991	10599992	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0004124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	58	353	0	ENST00000171111.5:c.1584_1585del	p.Asp529ProfsTer44	p.D529Pfs*44	ENST00000171111	NM_203500.1	528	caGGac/caac	5/6	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.15	2		353	691	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613209	52613210	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	50	330	0	ENST00000394830.3:c.3318dup	p.Glu1107ArgfsTer11	p.E1107Rfs*11	ENST00000394830	NM_018313.4	1106	-/A	22/30	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.15	2		330	591	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931789	39931790	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0004124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	55	515	0	ENST00000378444.4:c.2809_2810delinsAA	p.Pro937Asn	p.P937N	ENST00000378444	NM_001123385.1	937	CCc/AAc	4/15	1	2	FACETS	0.848	0.723	0.985	0.848	0.723	0.985	CLONAL	1	TRUE	1	0.15	2		515	865	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0004183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	127	285	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.689101212828718	2		285	341	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16046918	16046918	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0004183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	216	448	1	ENST00000268712.3:c.1173+2T>C		p.X391_splice	ENST00000268712	NM_006311.3	391			0.689101212828718	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.689101212828718	1		449	356	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610249	10610250	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGA	novel	NA	P-0004183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	179	579	0	ENST00000171111.5:c.458_460dup	p.Leu153dup	p.L153dup	ENST00000171111	NM_203500.1	153	cac/cTCCac	2/6	1	2	FACETS	0.926	0.859	0.995	0.926	0.859	0.995	CLONAL	1	TRUE	1	0.689101212828718	2		579	561	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0004202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	207	352	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.111247970913209	4	FACETS	1	0.975	1	1	0.975	1	INDETERMINATE	2	FALSE	2	0.20709791570165	4		352	1086	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087911	27087912	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	79	167	0	ENST00000324856.7:c.2200dup	p.Asp734GlyfsTer83	p.D734Gfs*83	ENST00000324856	NM_006015.4	733	tcg/tcGg	6/20	1	2	FACETS	0.932	0.818	1	0.932	0.818	1	CLONAL	1	FALSE	1	0.20709791570165	2		167	819	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0004212-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	257	356	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.677173820398122	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.677173820398122	1		356	465	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24129412	24129413	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGAGGACGAC	novel	NA	P-0004212-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	127	314	0	ENST00000263121.7:c.59_68dup	p.Glu24GlyfsTer50	p.E24Gfs*50	ENST00000263121	NM_003073.3	19	ctg/ctGGAGGACGACg	1/9	0.677472601651905	1	FACETS	0.838	0.772	0.905	0.838	0.772	0.905	CLONAL	1	TRUE	0	0.677173820398122	1		314	296	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979332	93979332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	75	617	0	ENST00000369303.4:c.1496C>T	p.Ser499Leu	p.S499L	ENST00000369303	NM_004440.3	499	tCa/tTa	7/17	1	2	FACETS	0.604	0.529	0.686	0.604	0.529	0.686	SUBCLONAL	1	TRUE	1	0.346660074246249	2		617	716	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983070	149983070	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	62	478	0	ENST00000253339.5:c.3188G>T	p.Gly1063Val	p.G1063V	ENST00000253339		1063	gGa/gTa	7/7	0.34354977582777	3	FACETS	0.67	0.579	0.77	0.335	0.289	0.385	SUBCLONAL	1	TRUE	1	0.346660074246249	3		478	626	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974787	21974787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1563892848	NA	P-0004230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	92	143	0	ENST00000304494.5:c.40G>A	p.Asp14Asn	p.D14N	ENST00000304494	NM_000077.4	14	Gac/Aac	1/3	0.301087676110787	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.346660074246249	1		143	301	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141839	108141839	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	79	335	0	ENST00000278616.4:c.2887A>T	p.Met963Leu	p.M963L	ENST00000278616	NM_000051.3	963	Atg/Ttg	19/63	0.268850332324881	3	FACETS	0.755	0.664	0.854	0.252	0.221	0.285	SUBCLONAL	1	TRUE	0	0.346660074246249	3		335	708	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859574	57859574	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	277	551	0	ENST00000228682.2:c.628C>G	p.Pro210Ala	p.P210A	ENST00000228682	NM_005269.2	210	Ccc/Gcc	7/12	0.214836923151616	4	FACETS	0.903	0.848	0.961	0.903	0.848	0.961	CLONAL	2	TRUE	2	0.346660074246249	4		551	1191	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436876	110436876	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	262	168	0	ENST00000375856.3:c.1525G>C	p.Asp509His	p.D509H	ENST00000375856	NM_003749.2	509	Gac/Cac	1/2	0.346660074246249	3	FACETS	0.878	0.833	0.923	1	0.99	1	CLONAL	4	TRUE	0	0.346660074246249	3		168	505	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984850	72984850	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	137	369	0	ENST00000268489.5:c.2734C>G	p.Pro912Ala	p.P912A	ENST00000268489	NM_006885.3	912	Ccc/Gcc	3/10	0.194704648846742	2	FACETS	0.835	0.759	0.915	0.417	0.379	0.458	INDETERMINATE	1	TRUE	0	0.346660074246249	2		369	947	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993146	72993146	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1198	173	685	0	ENST00000268489.5:c.899A>G	p.His300Arg	p.H300R	ENST00000268489	NM_006885.3	300	cAc/cGc	2/10	0.194704648846742	2	FACETS	0.728	0.668	0.791	0.364	0.334	0.396	INDETERMINATE	1	TRUE	0	0.346660074246249	2		685	1371	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617655	39617655	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0004230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	40	327	0	ENST00000262039.4:c.1840-1G>C		p.X614_splice	ENST00000262039	NM_002647.2	614			0.206827739354965	3	FACETS	0.649	0.54	0.771	0.325	0.27	0.386	INDETERMINATE	1	TRUE	1	0.346660074246249	3		327	417	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051637	30051637	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	292	343	0	ENST00000338641.4:c.571T>G	p.Trp191Gly	p.W191G	ENST00000338641	NM_000268.3	191	Tgg/Ggg	6/16	0.295786345514279	4	FACETS	1	0.984	1	0.82	0.776	0.863	CLONAL	3	TRUE	0	0.346660074246249	4		343	692	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410775	63410775	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	99	521	0	ENST00000330258.3:c.2392C>G	p.Gln798Glu	p.Q798E	ENST00000330258	NM_152424.3	798	Caa/Gaa	2/2	0.346660074246249	1	FACETS	0.593	0.529	0.661	0.593	0.529	0.661	SUBCLONAL	1	TRUE	0	0.346660074246249	1		521	796	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579528	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CAGTGAAC	CAGTGAAC	-	novel	NA	P-0004230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	158	286	0	ENST00000269305.4:c.159_166del	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgGTTCACTGaa/tgaa	4/11	0.268675952644997	2	FACETS	0.808	0.744	0.874	0.808	0.744	0.874	CLONAL	2	TRUE	0	0.346660074246249	2		286	564	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069982	5069983	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	62	426	0	ENST00000381652.3:c.1573dup	p.Thr525AsnfsTer19	p.T525Nfs*19	ENST00000381652	NM_004972.3	524	cca/ccAa	12/25	0.301087676110787	1	FACETS	0.635	0.549	0.727	0.635	0.549	0.727	SUBCLONAL	1	TRUE	0	0.346660074246249	1		426	466	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0004239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	16	315	2	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	1	2	FACETS	0.692	0.511	0.908	0.692	0.511	0.908	SUBCLONAL	1	TRUE	1	0.16	2		317	289	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539018	187539018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374444088	NA	P-0004239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	25	387	0	ENST00000441802.2:c.8722G>A	p.Val2908Ile	p.V2908I	ENST00000441802	NM_005245.3	2908	Gtc/Atc	10/27	1	2	FACETS	0.659	0.518	0.822	0.659	0.518	0.822	SUBCLONAL	1	TRUE	1	0.16	2		387	474	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468089	120468089	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	24	247	0	ENST00000256646.2:c.4350G>T	p.Trp1450Cys	p.W1450C	ENST00000256646	NM_024408.3	1450	tgG/tgT	25/34	1	2	FACETS	0.847	0.664	1	0.847	0.664	1	CLONAL	1	TRUE	1	0.16	2		247	354	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47672695	47672695	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63751693	NA	P-0004239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	29	300	0	ENST00000233146.2:c.1285C>T	p.Gln429Ter	p.Q429*	ENST00000233146	NM_000251.2	429	Cag/Tag	8/16	1	2	FACETS	0.762	0.61	0.934	0.762	0.61	0.934	CLONAL	1	TRUE	1	0.16	2		300	476	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498489	89498489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758657242	NA	P-0004239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	21	241	0	ENST00000336596.2:c.2461G>A	p.Gly821Arg	p.G821R	ENST00000336596	NM_005233.5	821	Gga/Aga	14/17	1	2	FACETS	0.795	0.612	1	0.795	0.612	1	CLONAL	1	TRUE	1	0.16	2		241	330	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156762	106156762	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774158688	NA	P-0004239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	20	222	0	ENST00000380013.4:c.1663C>T	p.Pro555Ser	p.P555S	ENST00000380013	NM_001127208.2	555	Cca/Tca	3/11	1	2	FACETS	0.776	0.594	0.991	0.776	0.594	0.991	CLONAL	1	TRUE	1	0.16	2		222	322	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628568	187628568	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	24	323	0	ENST00000441802.2:c.2414G>A	p.Trp805Ter	p.W805*	ENST00000441802	NM_005245.3	805	tGg/tAg	2/27	1	2	FACETS	0.674	0.528	0.844	0.674	0.528	0.844	SUBCLONAL	1	TRUE	1	0.16	2		323	445	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739591	41739591	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	31	255	0	ENST00000242208.4:c.382G>A	p.Glu128Lys	p.E128K	ENST00000242208	NM_002192.2	128	Gag/Aag	2/3	1	2	FACETS	1	0.824	1	1	0.824	1	CLONAL	1	TRUE	1	0.16	2		255	380	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358940	81358940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	19	289	0	ENST00000222390.5:c.1021C>T	p.Pro341Ser	p.P341S	ENST00000222390	NM_000601.4	341	Cct/Tct	8/18	1	2	FACETS	0.638	0.484	0.821	0.638	0.484	0.821	SUBCLONAL	1	TRUE	1	0.16	2		289	372	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139157	108139157	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	25	269	0	ENST00000278616.4:c.2659G>A	p.Glu887Lys	p.E887K	ENST00000278616	NM_000051.3	887	Gaa/Aaa	18/63	1	2	FACETS	0.797	0.628	0.992	0.797	0.628	0.992	CLONAL	1	TRUE	1	0.16	2		269	392	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244079	46244079	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	24	281	0	ENST00000334344.6:c.2173C>T	p.Gln725Ter	p.Q725*	ENST00000334344	NM_152641.2	725	Cag/Tag	15/21	1	2	FACETS	0.735	0.576	0.92	0.735	0.576	0.92	CLONAL	1	TRUE	1	0.16	2		281	408	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434391	49434391	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	11	129	0	ENST00000301067.7:c.7162C>T	p.Gln2388Ter	p.Q2388*	ENST00000301067	NM_003482.3	2388	Caa/Taa	31/54	1	2	FACETS	0.911	0.631	1	0.911	0.631	1	CLONAL	1	TRUE	1	0.16	2		129	151	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145401	58145401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	17	253	0	ENST00000257904.6:c.100C>T	p.Leu34Phe	p.L34F	ENST00000257904	NM_000075.3	34	Ctc/Ttc	2/8	1	2	FACETS	0.754	0.562	0.981	0.754	0.562	0.981	CLONAL	1	TRUE	1	0.16	2		253	282	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626731	28626731	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142392340	NA	P-0004239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	29	332	0	ENST00000241453.7:c.565G>A	p.Val189Ile	p.V189I	ENST00000241453	NM_004119.2	189	Gtt/Att	5/24	1	2	FACETS	0.871	0.699	1	0.871	0.699	1	CLONAL	1	TRUE	1	0.16	2		332	416	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435219	110435219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746894027	NA	P-0004239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	10	97	0	ENST00000375856.3:c.3182C>T	p.Ser1061Leu	p.S1061L	ENST00000375856	NM_003749.2	1061	tCg/tTg	1/2	1	2	FACETS	0.753	0.511	1	0.753	0.511	1	CLONAL	1	TRUE	1	0.16	2		97	166	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061765	38061765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	24	186	0	ENST00000250448.2:c.224C>T	p.Ala75Val	p.A75V	ENST00000250448	NM_004496.3	75	gCc/gTc	2/2	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.16	2		186	262	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821487	72821487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	57	394	0	ENST00000268489.5:c.10688G>A	p.Arg3563Lys	p.R3563K	ENST00000268489	NM_006885.3	3563	aGa/aAa	10/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.16	2		394	482	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993318	72993318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867647027	NA	P-0004239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	42	440	0	ENST00000268489.5:c.727G>A	p.Asp243Asn	p.D243N	ENST00000268489	NM_006885.3	243	Gat/Aat	2/10	1	2	FACETS	0.833	0.694	0.988	0.833	0.694	0.988	CLONAL	1	TRUE	1	0.16	2		440	630	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453403	40453403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766714643	NA	P-0004239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	35	560	0	ENST00000345506.4:c.1100C>T	p.Pro367Leu	p.P367L	ENST00000345506	NM_003152.3	367	cCc/cTc	10/20	1	2	FACETS	0.665	0.543	0.802	0.665	0.543	0.802	SUBCLONAL	1	TRUE	1	0.16	2		560	658	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5216752	5216752	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	26	275	0	ENST00000357368.4:c.4075G>A	p.Glu1359Lys	p.E1359K	ENST00000357368	NM_002850.3	1359	Gag/Aag	26/38	1	2	FACETS	0.838	0.663	1	0.838	0.663	1	CLONAL	1	TRUE	1	0.16	2		275	388	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271742	15271742	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	14	155	0	ENST00000263388.2:c.6697G>A	p.Ala2233Thr	p.A2233T	ENST00000263388	NM_000435.2	2233	Gcc/Acc	33/33	1	2	FACETS	0.875	0.634	1	0.875	0.634	1	CLONAL	1	TRUE	1	0.16	2		155	200	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31372633	31372633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149520896	NA	P-0004239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	21	295	0	ENST00000328111.2:c.274C>T	p.Arg92Trp	p.R92W	ENST00000328111	NM_006892.3	92	Cgg/Tgg	4/23	1	2	FACETS	0.711	0.547	0.903	0.711	0.547	0.903	CLONAL	1	TRUE	1	0.16	2		295	369	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514606	44514606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	16	161	0	ENST00000291552.4:c.550G>A	p.Glu184Lys	p.E184K	ENST00000291552	NM_006758.2	184	Gag/Aag	7/8	1	2	FACETS	0.678	0.501	0.89	0.678	0.501	0.89	SUBCLONAL	1	TRUE	1	0.16	2		161	295	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504057	123504057	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	20	136	0	ENST00000371139.4:c.233G>A	p.Arg78Gln	p.R78Q	ENST00000371139	NM_001114937.2	78	cGg/cAg	3/4	1	1	FACETS	1	0.802	1	1	0.802	1	CLONAL	1	TRUE	0	0.16	1		136	219	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509959	187509960	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	30	225	0	ENST00000441802.2:c.13553dup	p.Tyr4519LeufsTer30	p.Y4519Lfs*30	ENST00000441802	NM_005245.3	4518	cct/ccCt	27/27	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.16	2		225	295	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557273	187557273	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	30	285	0	ENST00000441802.2:c.4089del	p.Phe1363LeufsTer5	p.F1363Lfs*5	ENST00000441802	NM_005245.3	1363	ttT/tt	6/27	1	2	FACETS	0.887	0.714	1	0.887	0.714	1	CLONAL	1	TRUE	1	0.16	2		285	423	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983286	149983287	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0004239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	18	239	0	ENST00000253339.5:c.2971_2972delinsAA	p.Gly991Lys	p.G991K	ENST00000253339		991	GGa/AAa	7/7	1	2	FACETS	0.666	0.501	0.861	0.666	0.501	0.861	SUBCLONAL	1	TRUE	1	0.16	2		239	338	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409154	139409155	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0004239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	17	178	0	ENST00000277541.6:c.2015-1_2015delinsAA		p.X672_splice	ENST00000277541	NM_017617.3	672		13/34	1	2	FACETS	0.908	0.679	1	0.908	0.679	1	CLONAL	1	TRUE	1	0.16	2		178	234	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749986	162749986	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004246-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	131	493	0	ENST00000367921.3:c.2518C>T	p.Pro840Ser	p.P840S	ENST00000367921	NM_006182.2	840	Ccc/Tcc	18/18	0.244788735189479	5	FACETS	0.918	0.833	1	0.612	0.555	0.671	CLONAL	2	TRUE	2	0.244788735189479	5		493	797	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121909229	NA	P-0004246-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	204	278	0	ENST00000371953.3:c.389G>C	p.Arg130Pro	p.R130P	ENST00000371953	NM_000314.4	130	cGa/cCa	5/9	0.244788735189479	6	FACETS	0.977	0.915	1			1	CLONAL	5	TRUE	NA	0.244788735189479	6		278	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs879253911	NA	P-0004246-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	61	297	0	ENST00000269305.4:c.538G>T	p.Glu180Ter	p.E180*	ENST00000269305	NM_001126112.2	180	Gag/Tag	5/11	0.244788735189479	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	2	TRUE	0	0.244788735189479	2		297	237	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622630	158622630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004246-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	49	711	1	ENST00000263640.3:c.869C>T	p.Ser290Leu	p.S290L	ENST00000263640	NM_001105.4	290	tCg/tTg	8/11	0.244788735189479	4	FACETS	0.534	0.451	0.627	0.267	0.225	0.314	SUBCLONAL	1	TRUE	2	0.244788735189479	4		712	933	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851565	134851565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004246-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	55	312	0	ENST00000398015.3:c.971C>T	p.Ser324Leu	p.S324L	ENST00000398015	NM_004441.4	324	tCa/tTa	5/16	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.244788735189479	2		312	319	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525103	187525103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004246-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	15	187	0	ENST00000441802.2:c.10577C>T	p.Ser3526Leu	p.S3526L	ENST00000441802	NM_005245.3	3526	tCa/tTa	19/27	NA	2	FACETS	0.535	0.392	0.707			1	INDETERMINATE	1	TRUE	NA	0.244788735189479	2		187	229	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541966	187541966	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004246-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	87	395	0	ENST00000441802.2:c.5774A>T	p.Glu1925Val	p.E1925V	ENST00000441802	NM_005245.3	1925	gAg/gTg	10/27	NA	2	FACETS	0.817	0.727	0.912			1	INDETERMINATE	2	TRUE	NA	0.244788735189479	2		395	435	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520065	106520065	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004246-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	92	375	0	ENST00000359195.3:c.2493C>G	p.Ile831Met	p.I831M	ENST00000359195	NM_002649.2	831	atC/atG	6/11	0.244788735189479	4	FACETS	0.811	0.722	0.905	0.811	0.722	0.905	CLONAL	2	TRUE	2	0.244788735189479	4		375	577	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738383	133738383	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004246-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	68	206	0	ENST00000318560.5:c.783G>A	p.Trp261Ter	p.W261*	ENST00000318560	NM_005157.4	261	tgG/tgA	4/11	0.244788735189479	4	FACETS	0.941	0.829	1	0.941	0.829	1	CLONAL	3	TRUE	1	0.244788735189479	4		206	245	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431698	431698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs961046952	NA	P-0004246-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	48	550	0	ENST00000399788.2:c.2311G>A	p.Glu771Lys	p.E771K	ENST00000399788	NM_001042603.1	771	Gag/Aag	17/28	0.227771904687772	4	FACETS	0.603	0.509	0.709	0.302	0.254	0.355	SUBCLONAL	1	TRUE	2	0.244788735189479	4		550	809	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622539	28622539	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004246-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	101	356	0	ENST00000241453.7:c.1078G>T	p.Glu360Ter	p.E360*	ENST00000241453	NM_004119.2	360	Gaa/Taa	9/24	0.244788735189479	1	FACETS	0.905	0.815	0.999	1	0.986	1	CLONAL	2	TRUE	0	0.244788735189479	1		356	400	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355021	73355021	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs755879087	NA	P-0004246-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	32	387	0	ENST00000377767.4:c.349G>C	p.Glu117Gln	p.E117Q	ENST00000377767	NM_014953.3	117	Gag/Cag	2/21	0.217692975404315	2	FACETS	0.541	0.439	0.657	0.271	0.219	0.329	SUBCLONAL	1	TRUE	0	0.244788735189479	2		387	483	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060801	38060801	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004246-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	45	665	0	ENST00000250448.2:c.1188C>A	p.Phe396Leu	p.F396L	ENST00000250448	NM_004496.3	396	ttC/ttA	2/2	0.244788735189479	5	FACETS	0.671	0.562	0.792	0.224	0.187	0.264	SUBCLONAL	1	TRUE	2	0.244788735189479	5		665	749	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835718	68835718	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004246-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	144	602	0	ENST00000261769.5:c.309G>A	p.Trp103Ter	p.W103*	ENST00000261769	NM_004360.3	103	tgG/tgA	3/16	0.244788735189479	1	FACETS	1	0.964	1	1	0.992	1	CLONAL	2	TRUE	0	0.244788735189479	1		602	474	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013741	12013741	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004246-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	92	393	0	ENST00000353533.5:c.683G>C	p.Arg228Thr	p.R228T	ENST00000353533	NM_003010.3	228	aGa/aCa	6/11	0.244788735189479	2	FACETS	0.786	0.702	0.876	0.786	0.702	0.876	SUBCLONAL	2	TRUE	0	0.244788735189479	2		393	478	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681129	37681129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004246-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	51	245	0	ENST00000447079.4:c.3298G>A	p.Asp1100Asn	p.D1100N	ENST00000447079	NM_015083.1	1100	Gat/Aat	12/14	0.244788735189479	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	2	TRUE	0	0.244788735189479	2		245	206	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221036	5221036	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004246-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	15	242	0	ENST00000357368.4:c.3430G>A	p.Asp1144Asn	p.D1144N	ENST00000357368	NM_002850.3	1144	Gac/Aac	20/38	1	2	FACETS	0.492	0.36	0.651	0.492	0.36	0.651	SUBCLONAL	1	TRUE	1	0.244788735189479	2		242	249	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945958	17945958	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004246-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	28	459	0	ENST00000458235.1:c.1981G>A	p.Asp661Asn	p.D661N	ENST00000458235	NM_000215.3	661	Gat/Aat	15/24	0.167790308430535	3	FACETS	0.584	0.466	0.718	0.292	0.233	0.359	SUBCLONAL	1	TRUE	1	0.244788735189479	3		459	440	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411729	63411729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004246-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	81	572	0	ENST00000330258.3:c.1438G>A	p.Glu480Lys	p.E480K	ENST00000330258	NM_152424.3	480	Gag/Aag	2/2	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.244788735189479	2		572	526	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937597	76937597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004246-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	137	587	0	ENST00000373344.5:c.3151G>A	p.Asp1051Asn	p.D1051N	ENST00000373344	NM_000489.3	1051	Gat/Aat	9/35	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.244788735189479	2		587	779	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118710	115118711	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004246-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	173	451	0	ENST00000257566.3:c.630dup	p.Asn211GlnfsTer16	p.N211Qfs*16	ENST00000257566	NM_016569.3	210	-/C	2/8	0.244788735189479	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.244788735189479	4		451	787	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0004328-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	940	599	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.340590307295228	8	FACETS	0.997	0.969	1			1	CLONAL	6	TRUE	NA	0.340590307295228	8		599	1866	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0004328-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	331	717	1	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.340590307295228	2	FACETS	0.851	0.805	0.898	0.851	0.805	0.898	CLONAL	2	TRUE	0	0.340590307295228	2		718	1142	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0004328-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	879	512	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.340590307295228	8	FACETS	1	0.994	1			1	CLONAL	6	TRUE	NA	0.340590307295228	8		512	1631	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510775	120510775	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004328-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	344	686	1	ENST00000256646.2:c.1189G>T	p.Gly397Trp	p.G397W	ENST00000256646	NM_024408.3	397	Ggg/Tgg	7/34	0.260692582797978	3	FACETS	0.889	0.84	0.938	0.889	0.84	0.938	CLONAL	2	TRUE	1	0.340590307295228	3		687	1330	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842620	68842620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004328-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	356	577	0	ENST00000261769.5:c.556G>A	p.Gly186Ser	p.G186S	ENST00000261769	NM_004360.3	186	Ggc/Agc	5/16	0.300048443504981	2	FACETS	0.917	0.869	0.965	0.917	0.869	0.965	CLONAL	2	TRUE	0	0.340590307295228	2		577	1140	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974806	21974807	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004328-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	96	184	0	ENST00000304494.5:c.20dup	p.Ser7ArgfsTer8	p.S7Rfs*8	ENST00000304494	NM_000077.4	7	agc/agGc	1/3	0.340590307295228	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.340590307295228	1		184	324	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0004350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	147	526	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.230417817882305	3	FACETS	1	0.972	1	0.74	0.683	0.797	INDETERMINATE	2	TRUE	0	0.405501944447713	3		526	393	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0004350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	61	442	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.319673118042327	3	FACETS	0.918	0.806	1	0.918	0.806	1	CLONAL	2	TRUE	1	0.405501944447713	3		442	197	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0004350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	43	378	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.334692093807941	1	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	0	0.405501944447713	1		378	161	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922301	178922301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	20	343	0	ENST00000263967.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000263967	NM_006218.2	357	cGa/cAa	6/21	0.260074903439818	4	FACETS	0.825	0.635	1	0.275	0.211	0.348	CLONAL	1	TRUE	1	0.405501944447713	4		343	168	SUCCESS
APC	324	MSKCC	GRCh37	5	112174502	112174502	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876659539	NA	P-0004350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	31	332	0	ENST00000257430.4:c.3211C>T	p.Gln1071Ter	p.Q1071*	ENST00000257430	NM_000038.5	1071	Caa/Taa	16/16	0.319673118042327	3	FACETS	1	0.895	1	0.571	0.467	0.685	CLONAL	1	TRUE	1	0.405501944447713	3		332	161	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435254	49435254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199761931	NA	P-0004350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	65	288	0	ENST00000301067.7:c.6299C>T	p.Pro2100Leu	p.P2100L	ENST00000301067	NM_003482.3	2100	cCg/cTg	31/54	0.319673118042327	3	FACETS	0.82	0.721	0.925	0.82	0.721	0.925	CLONAL	2	TRUE	1	0.405501944447713	3		288	235	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289739	15289739	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	78	342	0	ENST00000263388.2:c.3732G>C	p.Gln1244His	p.Q1244H	ENST00000263388	NM_000435.2	1244	caG/caC	23/33	0.281661330918442	4	FACETS	0.916	0.814	1	0.916	0.814	1	CLONAL	2	TRUE	2	0.405501944447713	4		342	295	SUCCESS
APC	324	MSKCC	GRCh37	5	112175602	112175603	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0004350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	25	545	1	ENST00000257430.4:c.4314_4315dup	p.Pro1439HisfsTer35	p.P1439Hfs*35	ENST00000257430	NM_000038.5	1437	-/AC	16/16	0.319673118042327	3	FACETS	0.656	0.519	0.812	0.328	0.259	0.406	SUBCLONAL	1	TRUE	1	0.405501944447713	3		546	226	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0004407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	132	196	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.382459807702943	3	FACETS	1	0.979	1	0.797	0.733	0.862	CLONAL	2	TRUE	0	0.382459807702943	3		196	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0004407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	63	293	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.203660457974878	2	FACETS	0.781	0.686	0.88	0.781	0.686	0.88	INDETERMINATE	2	TRUE	0	0.382459807702943	2		295	211	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133747537	133747537	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	73	348	0	ENST00000318560.5:c.844G>C	p.Glu282Gln	p.E282Q	ENST00000318560	NM_005157.4	282	Gag/Cag	5/11	0.382746886469733	3	FACETS	0.915	0.802	1	0.457	0.401	0.518	CLONAL	1	TRUE	1	0.382459807702943	3		348	497	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344159	70344159	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199582086	NA	P-0004407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	31	206	0	ENST00000374080.3:c.1895G>A	p.Arg632Gln	p.R632Q	ENST00000374080		632	cGg/cAg	13/45	0.282450052892513	2	FACETS	0.619	0.502	0.749			1	SUBCLONAL	1	TRUE	NA	0.382459807702943	2		206	262	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119650	70119686	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GATTTTCTCGTGCTTGTTCTTTTATTGTCCACAGGGC	GATTTTCTCGTGCTTGTTCTTTTATTGTCCACAGGGC	-	novel	NA	P-0004407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	20	242	0	ENST00000245479.2:c.686-34_688del		p.X229_splice	ENST00000245479	NM_000346.3	229		3/3	0.274368288851971	3	FACETS	0.387	0.296	0.494	0.193	0.148	0.247	SUBCLONAL	1	TRUE	1	0.382459807702943	3		242	322	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120478	70120485	+	frameshift_variant	Frame_Shift_Del	DEL	AGCCCCCA	AGCCCCCA	-	novel	NA	P-0004407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	62	409	0	ENST00000245479.2:c.1480_1487del	p.Ser494AlafsTer81	p.S494Afs*81	ENST00000245479	NM_000346.3	494	AGCCCCCAg/g	3/3	0.274368288851971	3	FACETS	0.746	0.645	0.855	0.373	0.322	0.428	SUBCLONAL	1	TRUE	1	0.382459807702943	3		409	518	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0004426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	67	249	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	0.68	2		249	182	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0004426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	90	204	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.882	0.792	0.976	0.882	0.792	0.976	CLONAL	1	TRUE	1	0.68	2		204	300	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0004426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	74	393	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.878	0.779	0.981	0.878	0.779	0.981	CLONAL	1	TRUE	1	0.68	2		393	248	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860143	151860143	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs747835958	NA	P-0004426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	129	379	0	ENST00000262189.6:c.10519C>T	p.Arg3507Ter	p.R3507*	ENST00000262189	NM_170606.2	3507	Cga/Tga	43/59	1	2	FACETS	0.843	0.77	0.919	0.843	0.77	0.919	CLONAL	1	TRUE	1	0.68	2		379	450	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111959662	111959662	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	125	194	0	ENST00000375549.3:c.241C>T	p.Pro81Ser	p.P81S	ENST00000375549	NM_003002.3	81	Ccg/Tcg	3/4	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.68	2		194	292	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879871	44879871	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	20	305	0	ENST00000377967.4:c.460C>T	p.Gln154Ter	p.Q154*	ENST00000377967	NM_021140.2	154	Cag/Tag	6/29	0.296062374734017	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	NA	0.68	0		305	158	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949751	151949752	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0004426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	142	467	0	ENST00000262189.6:c.1347_1348dup	p.His450ArgfsTer6	p.H450Rfs*6	ENST00000262189	NM_170606.2	450	cac/cGCac	10/59	1	2	FACETS	0.851	0.78	0.923	0.851	0.78	0.923	CLONAL	1	TRUE	1	0.68	2		467	491	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167577	NA	P-0004435-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	55	112	0	ENST00000257430.4:c.4463del	p.Leu1488TyrfsTer19	p.L1488Yfs*19	ENST00000257430	NM_000038.5	1487	acT/ac	16/16	0.286371452196412	1	FACETS	0.693	0.595	0.799	0.693	0.595	0.799	SUBCLONAL	1	TRUE	0	0.353125531372762	1		112	370	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0004435-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	82	1032	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	0.683	0.602	0.77	0.683	0.602	0.77	SUBCLONAL	1	TRUE	1	0.353125531372762	2		1032	680	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856640	111856640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs899111445	NA	P-0004435-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	85	461	0	ENST00000341259.2:c.691G>A	p.Asp231Asn	p.D231N	ENST00000341259	NM_005475.2	231	Gat/Aat	2/8	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.353125531372762	2		461	343	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041747	42041748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004435-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	80	1327	0	ENST00000219905.7:c.5945dup	p.Asn1982LysfsTer23	p.N1982Kfs*23	ENST00000219905	NM_001164273.1	1981	aca/acAa	17/24	1	2	FACETS	0.523	0.46	0.592	0.523	0.46	0.592	SUBCLONAL	1	TRUE	1	0.353125531372762	2		1327	866	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0004451-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	381	435	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.108271048510269	5	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.732406457600504	5		435	900	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427588	49427588	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004451-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	45	165	1	ENST00000301067.7:c.10900C>T	p.Gln3634Ter	p.Q3634*	ENST00000301067	NM_003482.3	3634	Cag/Tag	39/54	0.732406457600504	1	FACETS	0.374	0.318	0.435	0.374	0.318	0.435	SUBCLONAL	1	TRUE	0	0.732406457600504	1		166	208	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492858	56492906	+	frameshift_variant	Frame_Shift_Del	DEL	GCGTCCAAAGCCTGCCTGCAGGGTAGCCATCAGCAGCCAGGGCCAGAGG	GCGTCCAAAGCCTGCCTGCAGGGTAGCCATCAGCAGCCAGGGCCAGAGG	-	novel	NA	P-0004451-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	135	190	0	ENST00000407977.2:c.33_81del	p.Leu12GlnfsTer23	p.L12Qfs*23	ENST00000407977		11	gcCCTCTGGCCCTGGCTGCTGATGGCTACCCTGCAGGCAGGCTTTGGACGC/gc	2/10	1	2	FACETS	0.786	0.719	0.855	0.786	0.719	0.855	SUBCLONAL	1	TRUE	1	0.732406457600504	2		190	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578501	7578502	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004451-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	244	198	0	ENST00000269305.4:c.428dup	p.Gln144AlafsTer5	p.Q144Afs*5	ENST00000269305	NM_001126112.2	143	gtg/gtTg	5/11	0.732406457600504	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.732406457600504	1		198	362	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271819	15271819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765739997	NA	P-0004513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	69	148	1	ENST00000263388.2:c.6620G>A	p.Arg2207Gln	p.R2207Q	ENST00000263388	NM_000435.2	2207	cGg/cAg	33/33	0.483996759178114	4	FACETS	0.884	0.773	1			1	CLONAL	1	TRUE	NA	0.607912704893158	4		149	413	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165644	118165644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs538766512	NA	P-0004513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1601	118	406	0	ENST00000369448.3:c.154G>A	p.Val52Ile	p.V52I	ENST00000369448	NM_017709.3	52	Gtc/Atc	2/2	0.607912704893158	6	FACETS	0.5	0.449	0.555	0.125	0.112	0.139	SUBCLONAL	1	TRUE	2	0.607912704893158	6		406	1719	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660574	227660574	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781090877	NA	P-0004513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	109	296	1	ENST00000305123.5:c.2881G>A	p.Glu961Lys	p.E961K	ENST00000305123	NM_005544.2	961	Gag/Aag	1/2	0.453840428052227	3	FACETS	0.995	0.898	1	0.332	0.299	0.366	CLONAL	1	TRUE	0	0.607912704893158	3		297	470	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467924	50467924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	282	293	1	ENST00000331340.3:c.1159G>A	p.Glu387Lys	p.E387K	ENST00000331340	NM_006060.4	387	Gag/Aag	8/8	0.362839980533149	5	FACETS	1	0.989	1	0.79	0.747	0.835	INDETERMINATE	2	TRUE	2	0.607912704893158	5		294	748	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577093	7577093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882008	NA	P-0004513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	19	539	1	ENST00000269305.4:c.845G>A	p.Arg282Gln	p.R282Q	ENST00000269305	NM_001126112.2	282	cGg/cAg	8/11	1	2	FACETS	0.075	0.056	0.098	0.075	0.056	0.098	SUBCLONAL	1	TRUE	1	0.607912704893158	2		540	830	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202687	108202688	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	409	447	0	ENST00000278616.4:c.7711_7712insA	p.Phe2571TyrfsTer4	p.F2571Yfs*4	ENST00000278616	NM_000051.3	2571	ttt/tAtt	52/63	0.607912704893158	3	FACETS	0.896	0.863	0.928	0.896	0.863	0.928	CLONAL	3	TRUE	0	0.607912704893158	3		447	653	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061224	38061229	+	inframe_deletion	In_Frame_Del	DEL	CTCGAA	CTCGAA	-	novel	NA	P-0004514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	71	326	0	ENST00000250448.2:c.760_765del	p.Phe254_Glu255del	p.F254_E255del	ENST00000250448	NM_004496.3	254	TTCGAG/-	2/2	0.170085266778715	3	FACETS	0.964	0.844	1	0.482	0.422	0.546	INDETERMINATE	1	FALSE	1	0.395721604801373	3		326	446	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259115	16259115	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750173975	NA	P-0004514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	108	254	0	ENST00000375759.3:c.6380C>T	p.Pro2127Leu	p.P2127L	ENST00000375759	NM_015001.2	2127	cCc/cTc	11/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.395721604801373	2		254	482	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5239055	5239055	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	57	342	0	ENST00000357368.4:c.1724C>A	p.Pro575Gln	p.P575Q	ENST00000357368	NM_002850.3	575	cCg/cAg	13/38	1	2	FACETS	0.468	0.401	0.542	0.468	0.401	0.542	SUBCLONAL	1	FALSE	1	0.395721604801373	2		342	615	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667840	37667841	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0004514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	149	378	0	ENST00000447079.4:c.2729_2730dup	p.Glu911ArgfsTer8	p.E911Rfs*8	ENST00000447079	NM_015083.1	909	gga/gGAga	8/14	NA	2	FACETS	0.79	0.721	0.862			1	INDETERMINATE	1	FALSE	NA	0.395721604801373	2		378	953	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618571	37618571	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	101	285	0	ENST00000447079.4:c.248del	p.Phe83SerfsTer9	p.F83Sfs*9	ENST00000447079	NM_015083.1	83	Ttc/tc	1/14	NA	2	FACETS	1	0.9	1			1	INDETERMINATE	1	FALSE	NA	0.395721604801373	2		285	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0004541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	92	409	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.240036651514006	6	FACETS	1	0.962	1	0.786	0.701	0.876	CLONAL	2	TRUE	3	0.240036651514006	6		409	481	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265466	152265466	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	52	285	0	ENST00000206249.3:c.919G>C	p.Ala307Pro	p.A307P	ENST00000206249	NM_000125.3	307	Gcc/Ccc	4/8	0.145851982953106	3	FACETS	1	0.957	1			1	CLONAL	1	TRUE	NA	0.240036651514006	3		285	359	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804267	46804267	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767502912	NA	P-0004541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	96	609	4	ENST00000290295.7:c.740G>A	p.Arg247His	p.R247H	ENST00000290295	NM_006361.5	247	cGc/cAc	2/2	NA	2	FACETS	1	0.957	1			1	INDETERMINATE	1	TRUE	NA	0.240036651514006	2		613	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577134	7577135	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	170	510	0	ENST00000269305.4:c.803dup	p.Asn268LysfsTer4	p.N268Kfs*4	ENST00000269305	NM_001126112.2	268	aac/aaAc	8/11	0.240036651514006	6	FACETS	1	0.96	1	1	0.96	1	CLONAL	3	TRUE	3	0.240036651514006	6		510	658	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0004620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	608	285	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.720822867279592	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.720822867279592	2		285	801	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372518	55372518	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	418	387	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	0.983	1	CLONAL	1	TRUE	1	0.720822867279592	2		387	1097	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372437	55372438	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	505	470	0	ENST00000297316.4:c.1129dup	p.Leu377ProfsTer7	p.L377Pfs*7	ENST00000297316	NM_022454.3	376	ggc/ggCc	2/2	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.720822867279592	2		470	1295	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0004629-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	86	775	0	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	0.395420511504735	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.395420511504735	1		775	275	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569801	67569802	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0004629-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	135	683	0	ENST00000274335.5:c.463_464insTT	p.Ser155PhefsTer23	p.S155Ffs*23	ENST00000274335		154	-/TT	3/15	0.395420511504735	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.395420511504735	1		683	518	SUCCESS
APC	324	MSKCC	GRCh37	5	112175147	112175147	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004629-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	96	618	0	ENST00000257430.4:c.3856del	p.Glu1286LysfsTer2	p.E1286Kfs*2	ENST00000257430	NM_000038.5	1286	Gaa/aa	16/16	0.395420511504735	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.395420511504735	1		618	343	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	28	140	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	0.916	0.754	1	0.916	0.754	1	INDETERMINATE	1	TRUE	0	0.52	1		140	87	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0004638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	223	485	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.3	3	FACETS	0.963	0.904	1			1	INDETERMINATE	2	TRUE	NA	0.52	3		485	561	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0004638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	9	552	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	NA	2	FACETS	0.092	0.06	0.133			1	INDETERMINATE	1	TRUE	NA	0.52	2		552	375	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076745	72076745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	120	637	0	ENST00000357731.5:c.752C>T	p.Pro251Leu	p.P251L	ENST00000357731	NM_173808.2	251	cCg/cTg	5/7	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.52	2		637	410	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247262	153247262	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	53	579	0	ENST00000281708.4:c.1540G>T	p.Val514Phe	p.V514F	ENST00000281708	NM_033632.3	514	Gtt/Ttt	10/12	1	2	FACETS	0.528	0.452	0.611	0.528	0.452	0.611	SUBCLONAL	1	TRUE	1	0.52	2		579	386	SUCCESS
APC	324	MSKCC	GRCh37	5	112175939	112175939	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	164	397	0	ENST00000257430.4:c.4648G>T	p.Glu1550Ter	p.E1550*	ENST00000257430	NM_000038.5	1550	Gag/Tag	16/16	0.3	2	FACETS	0.917	0.856	0.978	0.917	0.856	0.978	INDETERMINATE	2	TRUE	0	0.52	2		397	344	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486302	8486302	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	40	259	0	ENST00000356435.5:c.2515G>A	p.Ala839Thr	p.A839T	ENST00000356435		839	Gct/Act	17/35	0.138634793138203	1	FACETS	0.593	0.498	0.696	0.593	0.498	0.696	INDETERMINATE	1	TRUE	0	0.52	1		259	192	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579406	7579406	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	39	378	0	ENST00000269305.4:c.281C>A	p.Ser94Ter	p.S94*	ENST00000269305	NM_001126112.2	94	tCa/tAa	4/11	0.3	1	FACETS	0.61	0.512	0.716	0.61	0.512	0.716	INDETERMINATE	1	TRUE	0	0.52	1		378	182	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411864	63411864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767572122	NA	P-0004638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	46	713	1	ENST00000330258.3:c.1303G>A	p.Gly435Ser	p.G435S	ENST00000330258	NM_152424.3	435	Ggc/Agc	2/2	0.264664620455825	0	FACETS	0.323	0.274	0.376			1	INDETERMINATE	1	TRUE	0	0.52	0		714	263	SUCCESS
APC	324	MSKCC	GRCh37	5	112173760	112173761	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0004638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	95	411	0	ENST00000257430.4:c.2470_2471dup	p.Tyr825HisfsTer3	p.Y825Hfs*3	ENST00000257430	NM_000038.5	823	-/CC	16/16	0.3	2	FACETS	1	0.959	1	0.564	0.507	0.623	INDETERMINATE	1	TRUE	0	0.52	2		411	324	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0004654-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	212	326	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.559729130942526	2		326	726	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0004654-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	211	396	0	ENST00000346208.3:c.1002_1003dup	p.Asp335GlyfsTer21	p.D335Gfs*21	ENST00000346208		333	-/GG	5/6	1	2	FACETS	0.883	0.821	0.946	0.883	0.821	0.946	CLONAL	1	TRUE	1	0.559729130942526	2		396	854	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0004698-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	135	586	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	0.27103366426527	3	FACETS	0.985	0.9	1	0.985	0.9	1	CLONAL	2	TRUE	1	0.282157227764267	3		586	554	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0004698-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	124	380	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	NA	2	FACETS	0.964	0.878	1			1	INDETERMINATE	2	TRUE	NA	0.282157227764267	2		380	456	SUCCESS
APC	324	MSKCC	GRCh37	5	112175171	112175171	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085373	NA	P-0004698-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	35	319	0	ENST00000257430.4:c.3880C>T	p.Gln1294Ter	p.Q1294*	ENST00000257430	NM_000038.5	1294	Cag/Tag	16/16	0.27103366426527	3	FACETS	0.993	0.818	1	0.497	0.409	0.595	CLONAL	1	TRUE	1	0.282157227764267	3		319	285	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345765	152345766	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004698-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	87	733	0	ENST00000359321.1:c.804_805insG	p.Phe269ValfsTer10	p.F269Vfs*10	ENST00000359321	NM_005431.1	268	-/G	3/3	0.282157227764267	5	FACETS	0.756	0.667	0.852	0.252	0.222	0.284	SUBCLONAL	1	TRUE	2	0.282157227764267	5		733	1161	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0004703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	181	313	2	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.882933605438681	2		315	390	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0004703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	202	428	1	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.882933605438681	2		429	434	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884502	151884502	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0004703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	200	811	0	ENST00000262189.6:c.4853C>G	p.Ser1618Ter	p.S1618*	ENST00000262189	NM_170606.2	1618	tCa/tGa	33/59	1	2	FACETS	0.923	0.863	0.983	0.923	0.863	0.983	CLONAL	1	TRUE	1	0.882933605438681	2		811	491	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427303	49427303	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	246	569	2	ENST00000301067.7:c.11185C>T	p.Gln3729Ter	p.Q3729*	ENST00000301067	NM_003482.3	3729	Cag/Tag	39/54	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.882933605438681	2		571	547	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553402	41553402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	321	648	1	ENST00000263253.7:c.3491G>A	p.Cys1164Tyr	p.C1164Y	ENST00000263253	NM_001429.3	1164	tGt/tAt	18/31	1	2	FACETS	0.961	0.912	1	0.961	0.912	1	CLONAL	1	TRUE	1	0.882933605438681	2		649	757	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41558779	41558779	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	50	862	0	ENST00000263253.7:c.3724G>C	p.Glu1242Gln	p.E1242Q	ENST00000263253	NM_001429.3	1242	Gaa/Caa	21/31	1	2	FACETS	0.13	0.11	0.153	0.13	0.11	0.153	SUBCLONAL	1	TRUE	1	0.882933605438681	2		862	870	SUCCESS
AR	367	MSKCC	GRCh37	X	66941766	66941766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	66	1060	1	ENST00000374690.3:c.2410G>A	p.Glu804Lys	p.E804K	ENST00000374690	NM_000044.3	804	Gaa/Aaa	6/8	1	2	FACETS	0.129	0.111	0.148	0.129	0.111	0.148	SUBCLONAL	1	TRUE	1	0.882933605438681	2		1061	1161	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884794	151884805	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTGTACCTGGCA	TTGTACCTGGCA	-	novel	NA	P-0004703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	133	524	0	ENST00000262189.6:c.4788_4793+6del		p.X1596_splice	ENST00000262189	NM_170606.2	1596		32/59	1	2	FACETS	0.763	0.7	0.827	0.763	0.7	0.827	SUBCLONAL	1	TRUE	1	0.882933605438681	2		524	395	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247277	153247278	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	181	857	1	ENST00000281708.4:c.1524dup	p.Tyr509IlefsTer2	p.Y509Ifs*2	ENST00000281708	NM_033632.3	508	-/A	10/12	1	2	FACETS	0.907	0.846	0.969	0.907	0.846	0.969	CLONAL	1	TRUE	1	0.882933605438681	2		858	452	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433999	49433999	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	218	530	0	ENST00000301067.7:c.7554del	p.Phe2518LeufsTer25	p.F2518Lfs*25	ENST00000301067	NM_003482.3	2518	ttT/tt	31/54	1	2	FACETS	0.876	0.821	0.931	0.876	0.821	0.931	CLONAL	1	TRUE	1	0.882933605438681	2		530	564	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0004718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	1077	595	1	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.808041318862953	7	FACETS	0.939	0.918	0.96			1	CLONAL	5	TRUE	NA	0.808041318862953	7		596	1715	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0004718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	371	599	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.235431114345835	5	FACETS	0.903	0.863	0.943	0.903	0.863	0.943	INDETERMINATE	3	TRUE	2	0.808041318862953	5		599	750	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0004718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	397	572	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	0.77611852878573	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.808041318862953	2		572	479	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354058	15354058	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	27	186	0	ENST00000263377.2:c.2822C>A	p.Pro941His	p.P941H	ENST00000263377	NM_058243.2	941	cCt/cAt	14/20	0.272218090354408	3	FACETS	0.372	0.297	0.458	0.124	0.099	0.153	INDETERMINATE	1	TRUE	0	0.808041318862953	3		186	252	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464364	120464365	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	54	430	0	ENST00000256646.2:c.5281dup	p.Asp1761GlyfsTer2	p.D1761Gfs*2	ENST00000256646	NM_024408.3	1761	gat/gGat	29/34	0.714286982023877	3	FACETS	0.246	0.209	0.286	0.123	0.104	0.143	SUBCLONAL	1	TRUE	1	0.808041318862953	3		430	764	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0004810-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	95	640	1	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.0860946843199419	3	FACETS	1	0.918	1	0.52	0.462	0.582	INDETERMINATE	1	TRUE	1	0.22	3		641	922	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0004810-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	84	341	0	ENST00000269305.4:c.559+1G>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.22	2		341	682	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907428	32907428	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004810-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	88	436	0	ENST00000380152.3:c.1813A>G	p.Ile605Val	p.I605V	ENST00000380152		605	Ata/Gta	10/27	1	2	FACETS	0.809	0.715	0.91	0.809	0.715	0.91	CLONAL	1	TRUE	1	0.22	2		436	989	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321582	30321583	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004810-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	66	354	0	ENST00000322652.5:c.1438dup	p.Tyr480LeufsTer7	p.Y480Lfs*7	ENST00000322652	NM_015355.2	479	-/T		1	2	FACETS	0.936	0.812	1	0.936	0.812	1	CLONAL	1	TRUE	1	0.22	2		354	641	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0004827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	71	307	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.198488474069108	2		307	606	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509826	187509826	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	43	210	1	ENST00000441802.2:c.13687G>T	p.Asp4563Tyr	p.D4563Y	ENST00000441802	NM_005245.3	4563	Gac/Tac	27/27	1	2	FACETS	0.71	0.593	0.84	0.71	0.593	0.84	SUBCLONAL	1	TRUE	1	0.198488474069108	2		211	610	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539387	187539387	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	53	329	0	ENST00000441802.2:c.8353G>A	p.Asp2785Asn	p.D2785N	ENST00000441802	NM_005245.3	2785	Gat/Aat	10/27	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.198488474069108	2		329	499	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273452	38273452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1154	218	551	1	ENST00000425967.3:c.1883C>T	p.Ser628Phe	p.S628F	ENST00000425967	NM_001174067.1	628	tCc/tTc	14/19	0.198488474069108	4	FACETS	0.959	0.89	1	0.64	0.593	0.688	CLONAL	2	TRUE	1	0.198488474069108	4		552	1372	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97887428	97887428	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	185	363	0	ENST00000289081.3:c.936A>G	p.Ile312Met	p.I312M	ENST00000289081	NM_000136.2	312	atA/atG	10/15	0.198488474069108	4	FACETS	1	0.925	1	1	0.925	1	CLONAL	3	TRUE	1	0.198488474069108	4		363	745	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224281	98224281	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1131691700	NA	P-0004827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	43	225	0	ENST00000331920.6:c.2561-1G>A		p.X854_splice	ENST00000331920	NM_000264.3	854			0.198488474069108	4	FACETS	0.809	0.676	0.957	0.27	0.225	0.319	CLONAL	1	TRUE	1	0.198488474069108	4		225	642	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923196	39923196	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	55	203	0	ENST00000378444.4:c.3512C>A	p.Pro1171His	p.P1171H	ENST00000378444	NM_001123385.1	1171	cCt/cAt	8/15	0.153234958045462	0	FACETS	1	0.956	1			1	CLONAL	1	TRUE	NA	0.198488474069108	0		203	342	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196594	106196595	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	82	366	0	ENST00000380013.4:c.4931dup	p.Tyr1645IlefsTer16	p.Y1645Ifs*16	ENST00000380013	NM_001127208.2	1643	tcc/tCcc	11/11	1	2	FACETS	0.752	0.665	0.846	1	0.978	1	SUBCLONAL	2	TRUE	1	0.198488474069108	2		366	549	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0004886-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	80	835	0	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	0.394947467811191	1	FACETS	0.377	0.332	0.426	0.377	0.332	0.426	SUBCLONAL	1	TRUE	0	0.508601004159162	1		835	622	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851303	156851303	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004886-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	54	721	0	ENST00000524377.1:c.2260C>A	p.Pro754Thr	p.P754T	ENST00000524377	NM_002529.3	754	Cca/Aca	17/17	1	2	FACETS	0.38	0.324	0.441	0.38	0.324	0.441	SUBCLONAL	1	TRUE	1	0.508601004159162	2		721	559	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119666135	119666135	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004886-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	67	544	0	ENST00000316626.5:c.346T>G	p.Phe116Val	p.F116V	ENST00000316626		116	Ttc/Gtc	3/12	1	2	FACETS	0.602	0.524	0.684	0.602	0.524	0.684	SUBCLONAL	1	TRUE	1	0.508601004159162	2		544	438	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532930	187532930	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0004886-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	50	352	0	ENST00000441802.2:c.9464-1G>T		p.X3155_splice	ENST00000441802	NM_005245.3	3155			1	2	FACETS	0.509	0.433	0.592	0.509	0.433	0.592	SUBCLONAL	1	TRUE	1	0.508601004159162	2		352	386	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121715	108121715	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004886-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	52	682	0	ENST00000278616.4:c.1523T>G	p.Leu508Arg	p.L508R	ENST00000278616	NM_000051.3	508	cTt/cGt	10/63	0.394947467811191	1	FACETS	0.377	0.321	0.437	0.377	0.321	0.437	SUBCLONAL	1	TRUE	0	0.508601004159162	1		682	405	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380254	25380254	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004886-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	58	652	0	ENST00000311936.3:c.204G>C	p.Arg68Ser	p.R68S	ENST00000311936	NM_004985.3	68	agG/agC	3/5	0.346104625810342	1	FACETS	0.445	0.384	0.512	0.445	0.384	0.512	SUBCLONAL	1	TRUE	0	0.508601004159162	1		652	382	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929507	81929507	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1015688820	NA	P-0004886-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	340	888	0	ENST00000359376.3:c.1168A>G	p.Lys390Glu	p.K390E	ENST00000359376	NM_002661.3	390	Aaa/Gaa	13/33	0.490631044592549	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.508601004159162	1		888	860	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214465	5214465	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004886-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	53	754	0	ENST00000357368.4:c.4521C>G	p.Asn1507Lys	p.N1507K	ENST00000357368	NM_002850.3	1507	aaC/aaG	30/38	0.422066657818809	1	FACETS	0.379	0.324	0.439	0.379	0.324	0.439	SUBCLONAL	1	TRUE	0	0.508601004159162	1		754	410	SUCCESS
APC	324	MSKCC	GRCh37	5	112175273	112175501	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCACCCTAGAACCAAATCCAGCAGACTGCAGGGTTCTAGTTTATCTTCAGAATCAGCCAGGCACAAAGCTGTTGAATTTTCTTCAGGAGCGAAATCTCCCTCCAAAAGTGGTGCTCAGACACCCAAAAGTCCACCTGAACACTATGTTCAGGAGACCCCACTCATGTTTAGCAGATGTACTTCTGTCAGTTCACTTGATAGTTTTGAGAGTCGTTCGATTGCCAGCT	CAGCACCCTAGAACCAAATCCAGCAGACTGCAGGGTTCTAGTTTATCTTCAGAATCAGCCAGGCACAAAGCTGTTGAATTTTCTTCAGGAGCGAAATCTCCCTCCAAAAGTGGTGCTCAGACACCCAAAAGTCCACCTGAACACTATGTTCAGGAGACCCCACTCATGTTTAGCAGATGTACTTCTGTCAGTTCACTTGATAGTTTTGAGAGTCGTTCGATTGCCAGCT	-	novel	NA	P-0004886-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	107	522	0	ENST00000257430.4:c.3983_4211del	p.Gln1328ProfsTer11	p.Q1328Pfs*11	ENST00000257430	NM_000038.5	1328	CAGCACCCTAGAACCAAATCCAGCAGACTGCAGGGTTCTAGTTTATCTTCAGAATCAGCCAGGCACAAAGCTGTTGAATTTTCTTCAGGAGCGAAATCTCCCTCCAAAAGTGGTGCTCAGACACCCAAAAGTCCACCTGAACACTATGTTCAGGAGACCCCACTCATGTTTAGCAGATGTACTTCTGTCAGTTCACTTGATAGTTTTGAGAGTCGTTCGATTGCCAGCTcc/cc	16/16	0.508601004159162	1	FACETS	0.934	0.847	1	0.934	0.847	1	CLONAL	1	TRUE	0	0.508601004159162	1		522	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577028	7577029	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCTCCCTG	novel	NA	P-0004886-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	129	521	0	ENST00000269305.4:c.902_909dup	p.Thr304GlnfsTer44	p.T304Qfs*44	ENST00000269305	NM_001126112.2	303	-/CAGGGAGC	8/11	0.508601004159162	1	FACETS	0.878	0.802	0.956	0.878	0.802	0.956	CLONAL	1	TRUE	0	0.508601004159162	1		521	431	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570416	87570416	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004886-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	83	727	0	ENST00000277120.3:c.2156del	p.Ser719ThrfsTer60	p.S719Tfs*60	ENST00000277120		719	aGc/ac	17/19	0.508601004159162	1	FACETS	0.413	0.364	0.464	0.413	0.364	0.464	SUBCLONAL	1	TRUE	0	0.508601004159162	1		727	590	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545645	106545646	+	missense_variant	Missense_Mutation	DNP	AG	AG	TT	novel	NA	P-0004886-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	38	766	0	ENST00000359195.3:c.3122_3123delinsTT	p.Gln1041Leu	p.Q1041L	ENST00000359195	NM_002649.2	1041	cAG/cTT	11/11	0.508601004159162	2	FACETS	0.352	0.291	0.421	0.176	0.145	0.211	SUBCLONAL	1	TRUE	0	0.508601004159162	2		766	424	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160638	56160638	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	73	676	0	ENST00000399503.3:c.914del	p.Asn305ThrfsTer7	p.N305Tfs*7	ENST00000399503	NM_005921.1	304	acA/ac	4/20	1	2	FACETS	0.625	0.546	0.709	0.625	0.546	0.709	SUBCLONAL	1	FALSE	1	0.370422769693665	2		676	631	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881002	37881003	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCTCCCCA	rs397516982	NA	P-0004908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	130	757	0	ENST00000269571.5:c.2332_2340dup	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	-/GGCTCCCCA	20/27	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	FALSE	1	0.370422769693665	2		757	681	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120880	115120880	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs746244654	NA	P-0004908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	120	678	0	ENST00000257566.3:c.126del	p.Ala43ArgfsTer2	p.A43Rfs*2	ENST00000257566	NM_016569.3	42	ccC/cc	1/8	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.370422769693665	2		678	579	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177598	56177620	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTATTGCAGATGAGGTGGAAA	GGCTATTGCAGATGAGGTGGAAA	-	novel	NA	P-0004908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	126	704	0	ENST00000399503.3:c.2571_2593del	p.Met857IlefsTer39	p.M857Ifs*39	ENST00000399503	NM_005921.1	857	atGGCTATTGCAGATGAGGTGGAAAtt/attt	14/20	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	FALSE	1	0.370422769693665	2		704	679	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	22	366	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.135845826079663	1	FACETS	0.275	0.212	0.347	0.275	0.212	0.347	INDETERMINATE	1	TRUE	0	0.37	1		366	353	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0004924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	67	595	1	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.938	0.819	1	0.938	0.819	1	CLONAL	1	TRUE	1	0.37	2		596	386	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0004924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	112	426	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.37	2		426	425	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433491	138433491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	21	354	0	ENST00000289153.2:c.1121C>T	p.Ser374Leu	p.S374L	ENST00000289153	NM_006219.2	374	tCa/tTa	7/22	1	2	FACETS	0.324	0.249	0.412	0.324	0.249	0.412	SUBCLONAL	1	TRUE	1	0.37	2		354	350	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023108	27023108	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	77	135	2	ENST00000324856.7:c.214G>T	p.Glu72Ter	p.E72*	ENST00000324856	NM_006015.4	72	Gag/Tag	1/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.37	2		137	303	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023126	27023126	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	59	112	0	ENST00000324856.7:c.232G>T	p.Glu78Ter	p.E78*	ENST00000324856	NM_006015.4	78	Gag/Tag	1/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.37	2		112	259	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994400	25994400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778876791	NA	P-0004924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	165	549	0	ENST00000435504.4:c.413C>T	p.Ser138Phe	p.S138F	ENST00000435504		138	tCc/tTc	6/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.37	2		549	776	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027066	71027066	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs893189700	NA	P-0004924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	144	344	0	ENST00000318789.4:c.1261C>A	p.Pro421Thr	p.P421T	ENST00000318789	NM_032682.5	421	Ccc/Acc	15/21	0.3	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.37	1		344	629	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226861	142226861	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	90	420	0	ENST00000350721.4:c.4943C>T	p.Ser1648Phe	p.S1648F	ENST00000350721	NM_001184.3	1648	tCc/tTc	28/47	1	2	FACETS	0.96	0.854	1	0.96	0.854	1	CLONAL	1	TRUE	1	0.37	2		420	507	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55524236	55524236	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1490714621	NA	P-0004924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	198	396	0	ENST00000288135.5:c.55C>T	p.Arg19Cys	p.R19C	ENST00000288135	NM_000222.2	19	Cgc/Tgc	1/21	0.3	2	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.37	2		396	833	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177490	56177490	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	144	449	0	ENST00000399503.3:c.2463G>C	p.Leu821Phe	p.L821F	ENST00000399503	NM_005921.1	821	ttG/ttC	14/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.37	2		449	694	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250561	26250561	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778091229	NA	P-0004924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1533	238	1030	0	ENST00000446824.2:c.273G>A	p.Met91Ile	p.M91I	ENST00000446824	NM_021018.2	91	atG/atA	1/1	1	2	FACETS	0.726	0.675	0.78	0.726	0.675	0.78	SUBCLONAL	1	TRUE	1	0.37	2		1030	1771	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699305	18699305	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1565494747	NA	P-0004924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	69	483	0	ENST00000266497.5:c.3406T>C	p.Tyr1136His	p.Y1136H	ENST00000266497		1136	Tat/Cat	24/31	0.135845826079663	1	FACETS	0.64	0.559	0.727	0.64	0.559	0.727	INDETERMINATE	1	TRUE	0	0.37	1		483	475	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623632	28623632	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	56	360	0	ENST00000241453.7:c.925A>G	p.Met309Val	p.M309V	ENST00000241453	NM_004119.2	309	Atg/Gtg	8/24	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.37	2		360	298	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914776	32914776	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	163	773	0	ENST00000380152.3:c.6284C>T	p.Ser2095Leu	p.S2095L	ENST00000380152		2095	tCa/tTa	11/27	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.37	2		773	824	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556314	29556314	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1282493551	NA	P-0004924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	107	532	0	ENST00000356175.3:c.2681T>C	p.Phe894Ser	p.F894S	ENST00000356175	NM_000267.3	894	tTt/tCt	21/57	1	2	FACETS	0.703	0.63	0.78	0.703	0.63	0.78	SUBCLONAL	1	TRUE	1	0.37	2		532	823	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864656	37864656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs950730453	NA	P-0004924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	68	509	0	ENST00000269571.5:c.308G>A	p.Arg103Gln	p.R103Q	ENST00000269571		103	cGa/cAa	3/27	1	2	FACETS	0.369	0.32	0.423	0.369	0.32	0.423	SUBCLONAL	1	TRUE	1	0.37	2		509	995	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492862	56492862	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	29	206	0	ENST00000407977.2:c.77G>A	p.Gly26Glu	p.G26E	ENST00000407977		26	gGa/gAa	2/10	1	2	FACETS	0.336	0.269	0.412	0.336	0.269	0.412	SUBCLONAL	1	TRUE	1	0.37	2		206	467	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867571	45867571	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	184	380	0	ENST00000391945.4:c.737C>A	p.Ser246Tyr	p.S246Y	ENST00000391945	NM_000400.3	246	tCc/tAc	9/23	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.37	2		380	750	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566522	41566522	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	240	509	0	ENST00000263253.7:c.4399T>C	p.Tyr1467His	p.Y1467H	ENST00000263253	NM_001429.3	1467	Tac/Cac	27/31	1	2	FACETS	0.777	0.727	0.828	1	0.993	1	SUBCLONAL	2	TRUE	1	0.37	2		509	835	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922164	39922164	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	309	593	0	ENST00000378444.4:c.4008C>G	p.Asp1336Glu	p.D1336E	ENST00000378444	NM_001123385.1	1336	gaC/gaG	9/15	0.3	2	FACETS	1	0.992	1			1	CLONAL	1	TRUE	NA	0.37	2		593	1252	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44896926	44896926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	123	505	0	ENST00000377967.4:c.646G>A	p.Glu216Lys	p.E216K	ENST00000377967	NM_021140.2	216	Gaa/Aaa	8/29	0.3	2	FACETS	0.849	0.768	0.935			1	CLONAL	1	TRUE	NA	0.37	2		505	783	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923035	44923035	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	189	472	1	ENST00000377967.4:c.1896G>A	p.Trp632Ter	p.W632*	ENST00000377967	NM_021140.2	632	tgG/tgA	16/29	0.3	2	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.37	2		473	877	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039366	47039366	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	205	563	0	ENST00000377604.3:c.989A>G	p.Asn330Ser	p.N330S	ENST00000377604	NM_001204468.1	330	aAc/aGc	10/24	0.3	2	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.37	2		563	920	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123499615	123499615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	80	444	0	ENST00000371139.4:c.142C>T	p.His48Tyr	p.H48Y	ENST00000371139	NM_001114937.2	48	Cac/Tac	2/4	0.3	2	FACETS	1	0.893	1			1	CLONAL	1	TRUE	NA	0.37	2		444	428	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731425	47731432	+	frameshift_variant	Frame_Shift_Del	DEL	CGGGCCTC	CGGGCCTC	-	novel	NA	P-0004924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	39	69	0	ENST00000449228.1:c.360_367del	p.Arg121AlafsTer126	p.R121Afs*126	ENST00000449228	NM_001127240.2	120	ccGAGGCCCGcg/cccg	2/4	1	2	FACETS	1	0.84	1	1	0.84	1	CLONAL	1	TRUE	1	0.37	2		69	210	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653129	29653130	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	63	320	0	ENST00000356175.3:c.5064_5065insC	p.Asp1689ArgfsTer8	p.D1689Rfs*8	ENST00000356175	NM_000267.3	1688	-/C	36/57	1	2	FACETS	0.694	0.601	0.794	0.694	0.601	0.794	SUBCLONAL	1	TRUE	1	0.37	2		320	491	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385071	31385093	+	frameshift_variant	Frame_Shift_Del	DEL	GAGCTGCTGCTTTGCAGCAACAC	GAGCTGCTGCTTTGCAGCAACAC	-	rs745507181	NA	P-0004924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	66	464	0	ENST00000328111.2:c.1466_1488del	p.Leu489ProfsTer57	p.L489Pfs*57	ENST00000328111	NM_006892.3	486	GAGCTGCTGCTTTGCAGCAACACg/g	14/23	1	2	FACETS	0.401	0.347	0.46	0.401	0.347	0.46	SUBCLONAL	1	TRUE	1	0.37	2		464	889	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650130	206650130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004930-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	120	335	0	ENST00000367120.3:c.650G>A	p.Gly217Asp	p.G217D	ENST00000367120	NM_014002.3	217	gGc/gAc	7/22	0.365062791848459	6	FACETS	0.813	0.733	0.898	0.203	0.183	0.225	INDETERMINATE	1	TRUE	2	0.734080198858136	6		335	992	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907096	101907096	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004930-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	50	346	1	ENST00000374994.4:c.1056A>T	p.Leu352Phe	p.L352F	ENST00000374994	NM_004612.2	352	ttA/ttT	6/9	0.465634294683853	1	FACETS	0.213	0.181	0.248	0.213	0.181	0.248	SUBCLONAL	1	TRUE	0	0.734080198858136	1		347	405	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684052	29684052	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1263740114	NA	P-0004930-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	63	353	0	ENST00000356175.3:c.7750T>G	p.Leu2584Val	p.L2584V	ENST00000356175	NM_000267.3	2584	Ttg/Gtg	52/57	0.328130962214239	2	FACETS	0.352	0.305	0.404	0.176	0.152	0.202	INDETERMINATE	1	TRUE	0	0.734080198858136	2		353	487	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117126	7117126	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1473018725	NA	P-0004930-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	153	448	0	ENST00000302850.5:c.4090A>G	p.Met1364Val	p.M1364V	ENST00000302850	NM_000208.2	1364	Atg/Gtg	22/22	0.560239995309042	1	FACETS	0.379	0.347	0.412	0.379	0.347	0.412	SUBCLONAL	1	TRUE	0	0.734080198858136	1		448	696	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563410	87563411	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0004930-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	75	293	0	ENST00000277120.3:c.1798_1799insGT	p.Asp600GlyfsTer10	p.D600Gfs*10	ENST00000277120		600	gac/gGTac	16/19	0.465634294683853	1	FACETS	0.325	0.286	0.366	0.325	0.286	0.366	SUBCLONAL	1	TRUE	0	0.734080198858136	1		293	398	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266112	+	inframe_deletion	In_Frame_Del	DEL	ACTCTGGAATCCATT	ACTCTGGAATCCATT	-	novel	NA	P-0004930-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	101	376	0	ENST00000349496.5:c.95_109del	p.Asp32_Ser37delinsAla	p.D32_S37delinsA	ENST00000349496	NM_001904.3	32	gACTCTGGAATCCATTct/gct	3/15	1	2	FACETS	0.428	0.383	0.476	0.428	0.383	0.476	SUBCLONAL	1	TRUE	1	0.734080198858136	2		376	643	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0004967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	210	596	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.514958509749647	1	FACETS	0.777	0.723	0.832	0.777	0.723	0.832	SUBCLONAL	1	TRUE	0	0.51578913072784	1		596	778	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149945	99149945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	177	572	1	ENST00000074304.5:c.257C>T	p.Thr86Met	p.T86M	ENST00000074304	NM_001134224.1	86	aCg/aTg	5/26	1	2	FACETS	0.854	0.788	0.922	0.854	0.788	0.922	CLONAL	1	TRUE	1	0.51578913072784	2		573	804	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590403	67590403	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	27	520	0	ENST00000274335.5:c.1465G>T	p.Glu489Ter	p.E489*	ENST00000274335		489	Gaa/Taa	11/15	0.514958509749647	1	FACETS	0.16	0.127	0.198	0.16	0.127	0.198	SUBCLONAL	1	TRUE	0	0.51578913072784	1		520	485	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862749	9862749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150316865	NA	P-0004967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	650	635	1	ENST00000330684.3:c.2554G>A	p.Val852Met	p.V852M	ENST00000330684	NM_001134407.1	852	Gtg/Atg	12/13	NA	2	FACETS	0.922	0.891	0.953			1	INDETERMINATE	2	TRUE	NA	0.51578913072784	2		636	1367	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652320	48652320	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	477	392	2	ENST00000376670.3:c.991G>T	p.Ala331Ser	p.A331S	ENST00000376670	NM_002049.3	331	Gct/Tct	6/6	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.51578913072784	1		394	963	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579344	7579345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	271	585	0	ENST00000269305.4:c.342dup	p.His115AlafsTer34	p.H115Afs*34	ENST00000269305	NM_001126112.2	114	-/G	4/11	0.465760266554376	1	FACETS	0.861	0.809	0.913	0.861	0.809	0.913	CLONAL	1	TRUE	0	0.51578913072784	1		585	906	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0004975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	76	285	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	0.410525123146908	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.409772475926274	1		285	264	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	108	317	0	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	0.410525123146908	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.409772475926274	1		317	322	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888198	112888198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121918453	NA	P-0004975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	91	416	0	ENST00000351677.2:c.214G>A	p.Ala72Thr	p.A72T	ENST00000351677	NM_002834.3	72	Gcc/Acc	3/16	0.410525123146908	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.409772475926274	1		416	266	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	23	491	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	0.266713346895458	1	FACETS	0.636	0.496	0.8	0.636	0.496	0.8	SUBCLONAL	1	TRUE	0	0.17	1		491	389	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927613	131927613	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs786203901	NA	P-0004999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	21	232	0	ENST00000265335.6:c.1680T>G	p.Ser560Arg	p.S560R	ENST00000265335		560	agT/agG	11/25	1	2	FACETS	0.846	0.652	1	0.846	0.652	1	CLONAL	1	TRUE	1	0.17	2		232	292	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864467	162864467	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	38	274	1	ENST00000366898.1:c.46G>T	p.Glu16Ter	p.E16*	ENST00000366898	NM_004562.2	16	Gag/Tag	2/12	1	2	FACETS	1	0.829	1	1	0.829	1	CLONAL	1	TRUE	1	0.17	2		275	446	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763390	59763390	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3786	238	323	0	ENST00000259008.2:c.2712C>A	p.Asp904Glu	p.D904E	ENST00000259008	NM_032043.2	904	gaC/gaA	19/20	0.301071073675417	60	FACETS	1	0.95	1			1	CLONAL	4	TRUE	NA	0.17	60		323	4024	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0005003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	80	265	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.867	0.765	0.975	0.867	0.765	0.975	CLONAL	1	TRUE	1	0.381381910954687	2		265	484	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0005003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	108	288	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.994	0.894	1	0.994	0.894	1	CLONAL	1	TRUE	1	0.381381910954687	2		288	570	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0005003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	105	571	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.381381910954687	2		571	505	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0005003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	42	96	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.381381910954687	2		96	205	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578214	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs864309495	NA	P-0005003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	147	298	0	ENST00000269305.4:c.635_636del	p.Phe212SerfsTer3	p.F212Sfs*3	ENST00000269305	NM_001126112.2	212	tTT/t	6/11	0.36845031106273	1	FACETS	0.948	0.868	1	0.948	0.868	1	CLONAL	1	TRUE	0	0.381381910954687	1		298	658	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368208	45368208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	146	212	0	ENST00000262160.6:c.1394G>A	p.Ser465Asn	p.S465N	ENST00000262160	NM_005901.5	465	aGc/aAc	11/11	0.329952081951774	2	FACETS	1	0.988	1	0.749	0.688	0.812	CLONAL	1	TRUE	0	0.381381910954687	2		212	511	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143044	30143044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	134	277	0	ENST00000389048.3:c.482C>T	p.Ala161Val	p.A161V	ENST00000389048	NM_004304.4	161	gCg/gTg	1/29	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.381381910954687	2		277	627	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014214	70014214	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs150995386	NA	P-0005003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	154	431	0	ENST00000394351.3:c.1075G>C	p.Glu359Gln	p.E359Q	ENST00000394351	NM_000248.3	359	Gag/Cag	9/9	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.381381910954687	2		431	770	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39074223	39074223	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	70	136	0	ENST00000357387.3:c.87T>A	p.Asp29Glu	p.D29E	ENST00000357387	NM_152756.3	29	gaT/gaA	2/38	1	2	FACETS	0.956	0.838	1	0.956	0.838	1	CLONAL	1	TRUE	1	0.381381910954687	2		136	384	SUCCESS
APC	324	MSKCC	GRCh37	5	112173578	112173578	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	86	258	0	ENST00000257430.4:c.2287G>T	p.Glu763Ter	p.E763*	ENST00000257430	NM_000038.5	763	Gaa/Taa	16/16	1	2	FACETS	0.89	0.789	0.996	0.89	0.789	0.996	CLONAL	1	TRUE	1	0.381381910954687	2		258	507	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176684080	176684080	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	38	298	0	ENST00000439151.2:c.4894G>T	p.Gly1632Cys	p.G1632C	ENST00000439151	NM_022455.4	1632	Ggc/Tgc	13/23	1	2	FACETS	0.265	0.218	0.318	0.265	0.218	0.318	SUBCLONAL	1	TRUE	1	0.381381910954687	2		298	752	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720650	89720650	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1257124719	NA	P-0005003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	30	73	0	ENST00000371953.3:c.802-1G>A		p.X268_splice	ENST00000371953	NM_000314.4	268			1	2	FACETS	0.828	0.673	1	0.828	0.673	1	CLONAL	1	TRUE	1	0.381381910954687	2		73	190	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251846	8251846	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	27	229	0	ENST00000335790.3:c.231C>G	p.Asp77Glu	p.D77E	ENST00000335790	NM_002315.2	77	gaC/gaG	2/4	1	2	FACETS	0.29	0.23	0.359	0.29	0.23	0.359	SUBCLONAL	1	TRUE	1	0.381381910954687	2		229	488	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254723	46254723	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	69	263	0	ENST00000334344.6:c.4913C>G	p.Ser1638Cys	p.S1638C	ENST00000334344	NM_152641.2	1638	tCt/tGt	16/21	1	2	FACETS	0.674	0.588	0.767	0.674	0.588	0.767	SUBCLONAL	1	TRUE	1	0.381381910954687	2		263	537	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786715	3786715	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	46	372	0	ENST00000262367.5:c.4496T>A	p.Leu1499Gln	p.L1499Q	ENST00000262367	NM_004380.2	1499	cTg/cAg	27/31	1	2	FACETS	0.302	0.254	0.356	0.302	0.254	0.356	SUBCLONAL	1	TRUE	1	0.381381910954687	2		372	798	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81927367	81927367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781016626	NA	P-0005003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	171	304	0	ENST00000359376.3:c.1040G>A	p.Arg347His	p.R347H	ENST00000359376	NM_002661.3	347	cGc/cAc	12/33	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.381381910954687	2		304	840	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916922	178916927	+	inframe_deletion	In_Frame_Del	DEL	ACCAGT	ACCAGT	-	novel	NA	P-0005003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	145	386	0	ENST00000263967.3:c.310_315del	p.Pro104_Val105del	p.P104_V105del	ENST00000263967	NM_006218.2	103	gaACCAGTa/gaa	2/21	1	2	FACETS	0.935	0.854	1	0.935	0.854	1	CLONAL	1	TRUE	1	0.381381910954687	2		386	813	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554485	63554486	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGG	novel	NA	P-0005003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	177	253	0	ENST00000307078.5:c.251_253dup	p.Ser84dup	p.S84dup	ENST00000307078	NM_004655.3	84	tta/tCCTta	2/11	0.381381910954687	3	FACETS	0.877	0.812	0.944	0.877	0.812	0.944	CLONAL	2	TRUE	1	0.381381910954687	3		253	630	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	194	315	1	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	0.565745893712439	4	FACETS	0.976	0.902	1	0.488	0.451	0.527	CLONAL	1	TRUE	2	0.565745893712439	4		316	1100	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	366	363	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.565745893712439	4	FACETS	1	0.988	1	0.557	0.53	0.584	CLONAL	2	TRUE	0	0.565745893712439	4		364	909	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118934	3118934	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	287	376	1	ENST00000078429.4:c.623del	p.Gly208AlafsTer16	p.G208Afs*16	ENST00000078429	NM_002067.2	206	gtG/gt	5/7	0.565745893712439	2	FACETS	1	0.98	1	0.544	0.513	0.577	CLONAL	1	TRUE	0	0.565745893712439	2		377	932	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	17	336	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.565745893712439	3	FACETS	0.131	0.097	0.171	0.065	0.048	0.086	SUBCLONAL	1	TRUE	1	0.565745893712439	3		336	590	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619834	1619834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761441337	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	589	523	1	ENST00000344749.5:c.1112G>A	p.Arg371Gln	p.R371Q	ENST00000344749	NM_001136139.2	371	cGa/cAa	14/19	0.565745893712439	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.565745893712439	2		524	1035	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247836	10247836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	336	498	3	ENST00000340748.4:c.4366C>T	p.Arg1456Trp	p.R1456W	ENST00000340748		1456	Cgg/Tgg	36/40	0.565745893712439	2	FACETS	1	0.977	1	0.529	0.5	0.558	CLONAL	1	TRUE	0	0.565745893712439	2		501	1123	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736302	243736302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	303	395	0	ENST00000263826.5:c.745C>A	p.Arg249Ser	p.R249S	ENST00000263826	NM_005465.4	249	Cgt/Agt	8/13	0.389063529289572	6	FACETS	1	0.985	1			1	CLONAL	2	TRUE	NA	0.565745893712439	6		395	1017	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	932	435	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.565745893712439	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.565745893712439	3		435	1338	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600393	10600393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	685	481	1	ENST00000171111.5:c.1462G>A	p.Glu488Lys	p.E488K	ENST00000171111	NM_203500.1	488	Gag/Aag	4/6	0.565745893712439	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.565745893712439	2		482	1170	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16235913	16235913	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	192	448	0	ENST00000375759.3:c.979G>T	p.Glu327Ter	p.E327*	ENST00000375759	NM_015001.2	327	Gaa/Taa	4/15	0.366494203804442	4	FACETS	1	0.943	1			1	CLONAL	1	TRUE	NA	0.565745893712439	4		448	1038	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104711	193104711	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	366	381	0	ENST00000367435.3:c.415C>T	p.Arg139Ter	p.R139*	ENST00000367435	NM_024529.4	139	Cga/Tga	5/17	0.518053097165937	4	FACETS	0.936	0.889	0.984	0.624	0.593	0.656	CLONAL	2	TRUE	1	0.565745893712439	4		381	1082	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881543	111881543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	302	364	0	ENST00000393256.3:c.221C>T	p.Ala74Val	p.A74V	ENST00000393256	NM_006538.4	74	gCt/gTt	2/4	0.565745893712439	3	FACETS	1	0.97	1	0.524	0.493	0.556	CLONAL	1	TRUE	1	0.565745893712439	3		364	1307	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723051	49723051	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	29	133	0	ENST00000449682.2:c.1365C>A	p.Asp455Glu	p.D455E	ENST00000449682	NM_020998.3	455	gaC/gaA	11/18	0.565745893712439	2	FACETS	0.336	0.27	0.411	0.168	0.135	0.206	SUBCLONAL	1	TRUE	0	0.565745893712439	2		133	305	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589818	55589818	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	284	443	0	ENST00000288135.5:c.1300C>A	p.Pro434Thr	p.P434T	ENST00000288135	NM_000222.2	434	Cca/Aca	8/21	0.545281334643356	2	FACETS	0.877	0.824	0.931	0.438	0.412	0.466	CLONAL	1	TRUE	0	0.565745893712439	2		443	1145	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138779	37138779	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	167	327	0	ENST00000373509.5:c.212A>G	p.Lys71Arg	p.K71R	ENST00000373509	NM_002648.3	71	aAg/aGg	3/6	1	2	FACETS	0.629	0.578	0.683	0.629	0.578	0.683	SUBCLONAL	1	TRUE	1	0.565745893712439	2		327	938	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552735	106552735	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	329	424	0	ENST00000369096.4:c.700G>T	p.Glu234Ter	p.E234*	ENST00000369096	NM_001198.3	234	Gag/Tag	5/7	NA	2	FACETS	0.981	0.927	1			1	INDETERMINATE	1	TRUE	NA	0.565745893712439	2		424	1185	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968253	2968253	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1298	247	455	0	ENST00000396946.4:c.1733A>G	p.Lys578Arg	p.K578R	ENST00000396946	NM_032415.4	578	aAg/aGg	13/25	0.565745893712439	4	FACETS	0.885	0.825	0.947	0.442	0.412	0.474	CLONAL	1	TRUE	2	0.565745893712439	4		455	1545	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372746	81372746	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	305	328	1	ENST00000222390.5:c.788C>A	p.Pro263His	p.P263H	ENST00000222390	NM_000601.4	263	cCc/cAc	7/18	0.565745893712439	2	FACETS	0.968	0.923	1	0.968	0.923	1	CLONAL	2	TRUE	0	0.565745893712439	2		329	557	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434413	140434413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775889922	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	371	409	0	ENST00000288602.6:c.2285C>T	p.Ala762Val	p.A762V	ENST00000288602	NM_004333.4	762	gCg/gTg	18/18	0.565745893712439	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.565745893712439	2		409	623	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249861	110249861	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1259977843	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	120	180	0	ENST00000374672.4:c.814C>T	p.Arg272Cys	p.R272C	ENST00000374672	NM_004235.4	272	Cgc/Tgc	3/5	0.565745893712439	2	FACETS	0.808	0.733	0.886	0.404	0.366	0.443	CLONAL	1	TRUE	0	0.565745893712439	2		180	525	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333191	70333191	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	157	399	0	ENST00000373644.4:c.1096G>A	p.Gly366Arg	p.G366R	ENST00000373644	NM_030625.2	366	Gga/Aga	2/12	1	2	FACETS	0.967	0.89	1	0.967	0.89	1	CLONAL	1	TRUE	1	0.565745893712439	2		399	574	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658226	18658226	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	512	331	0	ENST00000266497.5:c.3031G>T	p.Ala1011Ser	p.A1011S	ENST00000266497		1011	Gcc/Tcc	22/31	0.565745893712439	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	4	TRUE	0	0.565745893712439	4		331	693	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230438	46230438	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	694	338	0	ENST00000334344.6:c.772G>T	p.Glu258Ter	p.E258*	ENST00000334344	NM_152641.2	258	Gaa/Taa	7/21	0.565745893712439	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	0	0.565745893712439	3		338	1026	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811613	102811613	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	521	366	0	ENST00000307046.8:c.571G>T	p.Gly191Cys	p.G191C	ENST00000307046	NM_001111285.1	191	Ggc/Tgc	4/4	0.565745893712439	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	0	0.565745893712439	3		366	774	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813333	102813333	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	857	367	1	ENST00000307046.8:c.356G>T	p.Arg119Leu	p.R119L	ENST00000307046	NM_001111285.1	119	cGc/cTc	3/4	0.565745893712439	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.565745893712439	3		368	1256	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73991982	73991982	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	311	468	0	ENST00000318443.5:c.2T>C	p.Met1?	p.M1?	ENST00000318443	NM_001024736.1	1	aTg/aCg	2/10	0.343670767421927	3	FACETS	1	0.972	1	0.526	0.495	0.558	CLONAL	1	TRUE	1	0.565745893712439	3		468	1341	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347931	347931	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1805102	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	568	482	0	ENST00000262320.3:c.1575C>G	p.Asp525Glu	p.D525E	ENST00000262320	NM_003502.3	525	gaC/gaG	6/11	0.157725561766472	3	FACETS	1	0.973	1			1	INDETERMINATE	2	TRUE	NA	0.565745893712439	3		482	1272	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222308	2222308	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750329755	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	66	472	0	ENST00000326181.6:c.592G>A	p.Gly198Arg	p.G198R	ENST00000326181	NM_032271.2	198	Ggg/Agg	8/21	0.157725561766472	3	FACETS	0.263	0.227	0.302			1	INDETERMINATE	1	TRUE	NA	0.565745893712439	3		472	1137	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778854	3778854	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	240	384	0	ENST00000262367.5:c.6194G>A	p.Ser2065Asn	p.S2065N	ENST00000262367	NM_004380.2	2065	aGc/aAc	31/31	0.362798525855528	4	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.565745893712439	4		384	1147	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530172	63530172	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1317	486	438	0	ENST00000307078.5:c.2263G>A	p.Gly755Ser	p.G755S	ENST00000307078	NM_004655.3	755	Ggt/Agt	10/11	0.565745893712439	5	FACETS	0.881	0.84	0.922	0.352	0.336	0.369	CLONAL	2	TRUE	0	0.565745893712439	5		438	1803	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125497	7125497	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	60	439	0	ENST00000302850.5:c.3055T>G	p.Ser1019Ala	p.S1019A	ENST00000302850	NM_000208.2	1019	Tct/Gct	17/22	0.565745893712439	2	FACETS	0.2	0.171	0.232	0.1	0.085	0.116	SUBCLONAL	1	TRUE	0	0.565745893712439	2		439	1060	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266769	18266769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778478327	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	243	330	0	ENST00000222254.8:c.80C>T	p.Pro27Leu	p.P27L	ENST00000222254	NM_005027.3	27	cCc/cTc	2/16	0.565745893712439	2	FACETS	1	0.973	1	0.534	0.5	0.569	CLONAL	1	TRUE	0	0.565745893712439	2		330	804	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308117	30308117	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	575	393	0	ENST00000262643.3:c.254G>T	p.Arg85Leu	p.R85L	ENST00000262643	NM_001238.2	85	cGg/cTg	5/12	0.565745893712439	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.565745893712439	2		393	965	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523309	9523309	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	310	385	0	ENST00000353224.5:c.1928A>T	p.Tyr643Phe	p.Y643F	ENST00000353224	NM_177990.2	643	tAc/tTc	9/10	0.43142031084387	4	FACETS	0.977	0.925	1	0.977	0.925	1	CLONAL	2	TRUE	2	0.565745893712439	4		385	878	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845267	42845267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	247	349	0	ENST00000398585.3:c.995C>T	p.Ala332Val	p.A332V	ENST00000398585	NM_001135099.1	332	gCc/gTc	9/14	0.565745893712439	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.565745893712439	1		349	610	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929167	44929167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	319	254	1	ENST00000377967.4:c.2267C>T	p.Ala756Val	p.A756V	ENST00000377967	NM_021140.2	756	gCa/gTa	17/29	1	1	FACETS	0.837	0.804	0.869	1	0.996	1	CLONAL	2	TRUE	0	0.565745893712439	1		255	483	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356792	70356792	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	369	295	0	ENST00000374080.3:c.5464C>A	p.His1822Asn	p.H1822N	ENST00000374080		1822	Cac/Aac	38/45	0.307533982514278	0	FACETS	0.895	0.859	0.931			1	INDETERMINATE	1	TRUE	NA	0.565745893712439	0		295	633	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263730	16263768	+	inframe_deletion	In_Frame_Del	DEL	CCACCCTGCCCGCCCTCCCAGCTCGGTCAGCCCGGCCAG	CCACCCTGCCCGCCCTCCCAGCTCGGTCAGCCCGGCCAG	-	novel	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	218	269	0	ENST00000375759.3:c.10104_10142del	p.Cys3369_Pro3381del	p.C3369_P3381del	ENST00000375759	NM_015001.2	3367	CCACCCTGCCCGCCCTCCCAGCTCGGTCAGCCCGGCCAG/-	12/15	0.270695548542558	4	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.565745893712439	4		269	1096	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73352417	73352418	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs553127065	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	177	343	0	ENST00000377767.4:c.487dup	p.Met163AsnfsTer15	p.M163Nfs*15	ENST00000377767	NM_014953.3	163	atg/aAtg	3/21	1	2	FACETS	0.938	0.868	1	0.938	0.868	1	CLONAL	1	TRUE	1	0.565745893712439	2		343	667	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872461	35872461	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	349	504	1	ENST00000216797.5:c.442del	p.Leu148TyrfsTer16	p.L148Yfs*16	ENST00000216797	NM_020529.2	148	Cta/ta	3/6	1	2	FACETS	0.958	0.906	1	0.958	0.906	1	CLONAL	1	TRUE	1	0.565745893712439	2		505	1288	SUCCESS
APC	324	MSKCC	GRCh37	5	112176179	112176182	+	frameshift_variant	Frame_Shift_Del	DEL	GTTA	GTTA	-	novel	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	87	411	0	ENST00000257430.4:c.4891_4894del	p.Ser1631LeufsTer18	p.S1631Lfs*18	ENST00000257430	NM_000038.5	1630	GTTAgt/gt	16/16	0.565745893712439	1	FACETS	0.447	0.397	0.501	0.447	0.397	0.501	SUBCLONAL	1	TRUE	0	0.565745893712439	1		411	493	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645146	86645149	+	frameshift_variant	Frame_Shift_Del	DEL	CAAT	CAAT	-	novel	NA	P-0005080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	256	286	0	ENST00000274376.6:c.1220_1223del	p.Asn407SerfsTer3	p.N407Sfs*3	ENST00000274376	NM_002890.2	406	aaCAAT/aa	8/25	0.565745893712439	2	FACETS	0.984	0.935	1	0.984	0.935	1	CLONAL	2	TRUE	0	0.565745893712439	2		286	460	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0005109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	173	393	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.843722870586763	2		393	359	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755548	39755548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	189	271	1	ENST00000288319.7:c.1217C>T	p.Ser406Leu	p.S406L	ENST00000288319	NM_182918.3	406	tCa/tTa	10/10	0.103542147834017	4	FACETS	0.926	0.866	0.987	0.926	0.866	0.987	INDETERMINATE	2	TRUE	2	0.843722870586763	4		272	446	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722905	49722906	+	inframe_insertion,splice_region_variant	In_Frame_Ins	INS	-	-	GGG	novel	NA	P-0005109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	10	78	0	ENST00000449682.2:c.1419_1421dup	p.Pro474dup	p.P474dup	ENST00000449682	NM_020998.3	474	cca/ccCCCa	12/18	1	2	FACETS	0.188	0.128	0.263	0.188	0.128	0.263	SUBCLONAL	1	TRUE	1	0.843722870586763	2		78	126	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747879	41747879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	200	262	0	ENST00000226382.2:c.890C>T	p.Ser297Leu	p.S297L	ENST00000226382	NM_003924.3	297	tCg/tTg	3/3	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.843722870586763	2		262	455	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228411	228411	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	169	361	0	ENST00000264932.6:c.733C>T	p.His245Tyr	p.H245Y	ENST00000264932	NM_004168.2	245	Cat/Tat	6/15	NA	2	FACETS	1	0.972	1			1	INDETERMINATE	1	TRUE	NA	0.843722870586763	2		361	371	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117650502	117650502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	229	506	0	ENST00000368508.3:c.5356C>T	p.Leu1786Phe	p.L1786F	ENST00000368508	NM_002944.2	1786	Ctt/Ttt	32/43	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.843722870586763	2		506	536	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662700	117662700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	148	367	0	ENST00000368508.3:c.4765G>A	p.Glu1589Lys	p.E1589K	ENST00000368508	NM_002944.2	1589	Gaa/Aaa	29/43	1	2	FACETS	0.884	0.816	0.953	0.884	0.816	0.953	CLONAL	1	TRUE	1	0.843722870586763	2		367	397	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481403	140481403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913357	NA	P-0005109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	443	277	0	ENST00000288602.6:c.1405G>A	p.Gly469Arg	p.G469R	ENST00000288602	NM_004333.4	469	Gga/Aga	11/18	0.544661170472212	5	FACETS	0.959	0.93	0.988			1	CLONAL	4	TRUE	NA	0.843722870586763	5		277	620	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772092	135772092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	77	104	0	ENST00000298552.3:c.3025G>A	p.Glu1009Lys	p.E1009K	ENST00000298552	NM_001162426.1	1009	Gaa/Aaa	23/23	1	2	FACETS	0.899	0.805	0.996	0.899	0.805	0.996	CLONAL	1	TRUE	1	0.843722870586763	2		104	203	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466936	18466936	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0005109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	171	373	0	ENST00000266497.5:c.1075A>T	p.Lys359Ter	p.K359*	ENST00000266497		359	Aaa/Taa	5/31	1	2	FACETS	0.972	0.905	1	0.972	0.905	1	CLONAL	1	TRUE	1	0.843722870586763	2		373	417	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650664	18650664	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	136	249	0	ENST00000266497.5:c.2875T>C	p.Ser959Pro	p.S959P	ENST00000266497		959	Tcc/Ccc	20/31	1	2	FACETS	0.992	0.916	1	0.992	0.916	1	CLONAL	1	TRUE	1	0.843722870586763	2		249	325	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578548	7578548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	222	256	0	ENST00000269305.4:c.382C>T	p.Pro128Ser	p.P128S	ENST00000269305	NM_001126112.2	128	Cct/Tct	5/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.843722870586763	2		256	504	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561309	9561309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760330867	NA	P-0005109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	236	271	0	ENST00000353224.5:c.473C>T	p.Pro158Leu	p.P158L	ENST00000353224	NM_177990.2	158	cCg/cTg	4/10	0.840862240930391	3	FACETS	0.934	0.885	0.982	0.934	0.885	0.982	CLONAL	2	TRUE	1	0.843722870586763	3		271	426	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730889	40730889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	148	283	0	ENST00000373198.4:c.3646G>A	p.Gly1216Arg	p.G1216R	ENST00000373198	NM_133170.3	1216	Ggg/Agg	27/32	0.840862240930391	3	FACETS	0.961	0.883	1	0.481	0.441	0.521	CLONAL	1	TRUE	1	0.843722870586763	3		283	519	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101025	41101025	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	207	334	0	ENST00000373198.4:c.1331C>T	p.Ser444Phe	p.S444F	ENST00000373198	NM_133170.3	444	tCc/tTc	8/32	NA	2	FACETS	0.767	0.715	0.819			1	INDETERMINATE	1	TRUE	NA	0.843722870586763	2		334	640	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038816	47038816	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	175	130	1	ENST00000377604.3:c.823C>T	p.Pro275Ser	p.P275S	ENST00000377604	NM_001204468.1	275	Ccc/Tcc	9/24	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.843722870586763	1		131	199	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158587	26158598	+	inframe_deletion	In_Frame_Del	DEL	AATTCCTTCGTC	AATTCCTTCGTC	-	novel	NA	P-0005109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	49	187	0	ENST00000289316.2:c.192_203del	p.Ser65_Asn68del	p.S65_N68del	ENST00000289316	NM_138720.2	64	AATTCCTTCGTC/-	1/2	0.843722870586763	4	FACETS	0.311	0.262	0.364	0.104	0.087	0.122	SUBCLONAL	1	TRUE	1	0.843722870586763	4		187	689	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26046036	26046037	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0005109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	257	492	1	ENST00000540144.1:c.398_399delinsAA	p.Gly133Glu	p.G133E	ENST00000540144	NM_003531.2	133	gGG/gAA	1/1	0.843722870586763	4	FACETS	1	0.949	1	0.339	0.317	0.361	CLONAL	1	TRUE	1	0.843722870586763	4		493	1106	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057281	180057281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142252978	NA	P-0005111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	108	284	0	ENST00000261937.6:c.457G>A	p.Ala153Thr	p.A153T	ENST00000261937	NM_182925.4	153	Gcc/Acc	4/30	1	2	FACETS	0.707	0.634	0.783	0.707	0.634	0.783	SUBCLONAL	1	TRUE	1	0.421581549858058	2		284	725	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753205	57753205	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	57	229	0	ENST00000274289.3:c.811T>C	p.Tyr271His	p.Y271H	ENST00000274289	NM_006622.3	271	Tat/Cat	7/14	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.421581549858058	2		229	231	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035245	6035245	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587780062	NA	P-0005111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	136	384	0	ENST00000265849.7:c.823C>T	p.Gln275Ter	p.Q275*	ENST00000265849	NM_000535.5	275	Caa/Taa	8/15	0.421581549858058	1	FACETS	0.898	0.82	0.979	0.898	0.82	0.979	CLONAL	1	TRUE	0	0.421581549858058	1		384	567	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489478	56489478	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	80	349	0	ENST00000267101.3:c.1943T>C	p.Val648Ala	p.V648A	ENST00000267101	NM_001982.3	648	gTg/gCg	17/28	1	2	FACETS	0.749	0.661	0.842	0.749	0.661	0.842	SUBCLONAL	1	TRUE	1	0.421581549858058	2		349	507	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061140	38061141	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCGCTT	rs773567107	NA	P-0005111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	12	34	0	ENST00000250448.2:c.843_848dup	p.Ser282_Gly283dup	p.S282_G283dup	ENST00000250448	NM_004496.3	282	ggg/ggAAGCGGg	2/2	1	2	FACETS	0.518	0.367	0.699	0.518	0.367	0.699	SUBCLONAL	1	TRUE	1	0.421581549858058	2		34	110	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0005194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	104	435	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	0.322974878638071	2		435	589	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849167	76849167	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	100	382	0	ENST00000373344.5:c.6109G>A	p.Val2037Ile	p.V2037I	ENST00000373344	NM_000489.3	2037	Gtc/Atc	26/35	1	2	FACETS	0.901	0.806	1	0.901	0.806	1	CLONAL	1	TRUE	1	0.322974878638071	2		382	687	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222986	1222986	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs864622488	NA	P-0005194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	61	225	0	ENST00000326873.7:c.923G>T	p.Trp308Leu	p.W308L	ENST00000326873	NM_000455.4	308	tGg/tTg	8/10	0.322974878638071	1	FACETS	0.875	0.759	1	0.875	0.759	1	CLONAL	1	TRUE	0	0.322974878638071	1		225	362	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791758	42791758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1380826096	NA	P-0005194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	15	343	0	ENST00000575354.2:c.644G>A	p.Arg215Gln	p.R215Q	ENST00000575354	NM_015125.3	215	cGg/cAg	5/20	1	2	FACETS	0.15	0.109	0.2	0.15	0.109	0.2	SUBCLONAL	1	TRUE	1	0.322974878638071	2		343	620	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741861	162741861	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	194	356	0	ENST00000367921.3:c.1552G>T	p.Val518Leu	p.V518L	ENST00000367921	NM_006182.2	518	Gtg/Ttg	13/18	0.299971326010664	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	1	0.322974878638071	3		356	677	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370845	225370845	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0005194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	67	237	0	ENST00000264414.4:c.1034T>A	p.Leu345Ter	p.L345*	ENST00000264414	NM_003590.4	345	tTa/tAa	8/16	1	2	FACETS	0.847	0.737	0.965	0.847	0.737	0.965	CLONAL	1	TRUE	1	0.322974878638071	2		237	490	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422461	225422461	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	119	345	0	ENST00000264414.4:c.179A>T	p.Asn60Ile	p.N60I	ENST00000264414	NM_003590.4	60	aAt/aTt	2/16	1	2	FACETS	0.983	0.887	1	0.983	0.887	1	CLONAL	1	TRUE	1	0.322974878638071	2		345	750	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915553	131915553	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0005194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	47	186	0	ENST00000265335.6:c.552-1G>T		p.X184_splice	ENST00000265335		184			1	2	FACETS	0.754	0.638	0.881	0.754	0.638	0.881	SUBCLONAL	1	TRUE	1	0.322974878638071	2		186	386	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32189085	32189085	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762851866	NA	P-0005194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	64	295	1	ENST00000375023.3:c.469C>T	p.Arg157Trp	p.R157W	ENST00000375023	NM_004557.3	157	Cgg/Tgg	4/30	1	2	FACETS	0.774	0.671	0.885	0.774	0.671	0.885	SUBCLONAL	1	TRUE	1	0.322974878638071	2		296	512	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120300	94120300	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	66	498	0	ENST00000369303.4:c.751A>T	p.Ser251Cys	p.S251C	ENST00000369303	NM_004440.3	251	Agt/Tgt	3/17	0.103826661711559	0	FACETS	0.419	0.363	0.48			1	INDETERMINATE	1	TRUE	0	0.322974878638071	0		498	660	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435965	116435965	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	101	408	0	ENST00000397752.3:c.3960G>T	p.Trp1320Cys	p.W1320C	ENST00000397752	NM_000245.2	1320	tgG/tgT	21/21	1	2	FACETS	0.943	0.844	1	0.943	0.844	1	CLONAL	1	TRUE	1	0.322974878638071	2		408	663	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448151	49448151	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	96	399	0	ENST00000301067.7:c.449G>T	p.Trp150Leu	p.W150L	ENST00000301067	NM_003482.3	150	tGg/tTg	4/54	1	2	FACETS	0.987	0.881	1	0.987	0.881	1	CLONAL	1	TRUE	1	0.322974878638071	2		399	602	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220634	2220634	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	97	377	0	ENST00000326181.6:c.251G>T	p.Arg84Leu	p.R84L	ENST00000326181	NM_032271.2	84	cGc/cTc	5/21	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.322974878638071	2		377	592	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921598	39921598	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	96	424	0	ENST00000378444.4:c.4222G>T	p.Asp1408Tyr	p.D1408Y	ENST00000378444	NM_001123385.1	1408	Gat/Tat	10/15	1	2	FACETS	0.822	0.733	0.918	0.822	0.733	0.918	CLONAL	1	TRUE	1	0.322974878638071	2		424	723	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932985	39932985	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	88	415	0	ENST00000378444.4:c.1614G>T	p.Gln538His	p.Q538H	ENST00000378444	NM_001123385.1	538	caG/caT	4/15	1	2	FACETS	0.754	0.668	0.846	0.754	0.668	0.846	SUBCLONAL	1	TRUE	1	0.322974878638071	2		415	723	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845619	68845619	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	TA	novel	NA	P-0005194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	135	424	0	ENST00000261769.5:c.865delinsTA	p.Ala289TyrfsTer4	p.A289Yfs*4	ENST00000261769	NM_004360.3	289	Gcg/TAcg	7/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.322974878638071	2		424	751	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577579	7577579	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0121438-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	223	409	0	ENST00000269305.4:c.702C>A	p.Tyr234Ter	p.Y234*	ENST00000269305	NM_001126112.2	234	taC/taA	7/11	0.556514387157732	4	FACETS	0.96	0.916	1	0.96	0.916	1	CLONAL	4	NA	0	0.556514387157732	4		409	325	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225501	2225501	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0121438-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	37	571	0	ENST00000326181.6:c.1504G>A	p.Val502Ile	p.V502I	ENST00000326181	NM_032271.2	502	Gtc/Atc	17/21	0.531580348777869	4	FACETS	0.603	0.499	0.72			1	SUBCLONAL	1	NA	NA	0.556514387157732	4		571	343	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550877	150550881	+	frameshift_variant	Frame_Shift_Del	DEL	TTTGT	TTTGT	-	novel	NA	P-0121438-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	23	299	0	ENST00000369026.2:c.775_779del	p.Thr259LeufsTer16	p.T259Lfs*16	ENST00000369026	NM_021960.4	259	ACAAAc/c	2/3	0.556514387157732	5	FACETS	0.371	0.288	0.466	0.124	0.096	0.156	SUBCLONAL	1	NA	2	0.556514387157732	5		299	409	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150456	157150457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0121438-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	87	473	0	ENST00000346085.5:c.1640dup	p.Gly548ArgfsTer105	p.G548Rfs*105	ENST00000346085	NM_020732.3	546	-/G	2/20	0.515204741009263	5	FACETS	1	0.94	1			1	CLONAL	1	NA	NA	0.556514387157732	5		473	526	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550871	150550871	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0121438-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	23	307	0	ENST00000369026.2:c.785del	p.Gly262AlafsTer4	p.G262Afs*4	ENST00000369026	NM_021960.4	262	gGc/gc	2/3	0.556514387157732	5	FACETS	0.354	0.276	0.446	0.118	0.092	0.149	SUBCLONAL	1	NA	2	0.556514387157732	5		307	428	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435128	110435129	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs772322568	NA	P-0005285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	51	293	0	ENST00000375856.3:c.3272dup	p.Lys1092GlufsTer233	p.K1092Efs*233	ENST00000375856	NM_003749.2	1091	ccg/ccCg	1/2	0.221187986412592	3	FACETS	0.981	0.837	1	0.49	0.418	0.569	CLONAL	1	TRUE	1	0.324913865615783	3		293	372	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0005285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	87	600	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.271103116212127	0	FACETS	0.849	0.755	0.947			1	CLONAL	1	TRUE	0	0.324913865615783	0		600	426	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0005285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	126	485	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.324913865615783	3	FACETS	0.839	0.764	0.919	0.839	0.764	0.919	CLONAL	2	TRUE	1	0.324913865615783	3		485	537	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913837	32913837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359507	NA	P-0005285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	35	743	2	ENST00000380152.3:c.5351del	p.Asn1784ThrfsTer7	p.N1784Tfs*7	ENST00000380152		1782	cAa/ca	11/27	1	2	FACETS	0.311	0.254	0.375	0.311	0.254	0.375	SUBCLONAL	1	TRUE	1	0.324913865615783	2		745	693	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508946	106508946	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	64	354	1	ENST00000359195.3:c.940G>A	p.Ala314Thr	p.A314T	ENST00000359195	NM_002649.2	314	Gcc/Acc	2/11	1	2	FACETS	0.91	0.79	1	0.91	0.79	1	CLONAL	1	TRUE	1	0.324913865615783	2		355	433	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0005285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	57	412	2	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.324913865615783	2		414	347	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086010	16086010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	65	493	0	ENST00000281043.3:c.1186G>A	p.Asp396Asn	p.D396N	ENST00000281043	NM_005378.4	396	Gac/Aac	3/3	1	2	FACETS	0.837	0.727	0.955	0.837	0.727	0.955	CLONAL	1	TRUE	1	0.324913865615783	2		493	478	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535307	66535307	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	60	451	0	ENST00000273854.3:c.154A>G	p.Thr52Ala	p.T52A	ENST00000273854	NM_004439.5	52	Acc/Gcc	1/18	1	2	FACETS	0.824	0.712	0.946	0.824	0.712	0.946	CLONAL	1	TRUE	1	0.324913865615783	2		451	448	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056342	27056343	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0005285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	47	307	0	ENST00000324856.7:c.1338_1339del	p.Gln449AlafsTer173	p.Q449Afs*173	ENST00000324856	NM_006015.4	446	tcTTat/tcat	2/20	1	2	FACETS	0.877	0.743	1	0.877	0.743	1	CLONAL	1	TRUE	1	0.324913865615783	2		307	330	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262576	16262576	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	56	318	0	ENST00000375759.3:c.9841C>A	p.Leu3281Met	p.L3281M	ENST00000375759	NM_015001.2	3281	Ctg/Atg	11/15	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.324913865615783	2		318	316	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082625	16082625	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	13	85	0	ENST00000281043.3:c.439G>A	p.Ala147Thr	p.A147T	ENST00000281043	NM_005378.4	147	Gcc/Acc	2/3	1	2	FACETS	1	0.8	1	1	0.8	1	CLONAL	1	TRUE	1	0.324913865615783	2		85	71	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436886	52436886	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	66	411	0	ENST00000460680.1:c.1892A>T	p.Glu631Val	p.E631V	ENST00000460680	NM_004656.3	631	gAg/gTg	15/17	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.324913865615783	2		411	390	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155653	106155653	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	83	411	0	ENST00000380013.4:c.554A>G	p.Gln185Arg	p.Q185R	ENST00000380013	NM_001127208.2	185	cAg/cGg	3/11	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.324913865615783	2		411	461	SUCCESS
APC	324	MSKCC	GRCh37	5	112170666	112170666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372416031	NA	P-0005285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	79	519	0	ENST00000257430.4:c.1762G>A	p.Val588Ile	p.V588I	ENST00000257430	NM_000038.5	588	Gta/Ata	15/16	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.324913865615783	2		519	446	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738993	145738993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558451720	NA	P-0005285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	48	444	1	ENST00000428558.2:c.2162G>A	p.Arg721Gln	p.R721Q	ENST00000428558	NM_004260.3	721	cGa/cAa	13/22	1	2	FACETS	0.571	0.483	0.669	0.571	0.483	0.669	SUBCLONAL	1	TRUE	1	0.324913865615783	2		445	517	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690847	89690847	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587776667	NA	P-0005285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	67	294	0	ENST00000371953.3:c.253+1G>T		p.X85_splice	ENST00000371953	NM_000314.4	85			1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.324913865615783	2		294	373	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1039231	1039231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144832155	NA	P-0005285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	84	511	0	ENST00000358495.3:c.266C>T	p.Thr89Met	p.T89M	ENST00000358495	NM_134424.2	89	aCg/aTg	4/12	0.324913865615783	3	FACETS	1	0.884	1			1	CLONAL	1	TRUE	NA	0.324913865615783	3		511	601	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427513	49427513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367910969	NA	P-0005285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	166	590	0	ENST00000301067.7:c.10975C>T	p.Pro3659Ser	p.P3659S	ENST00000301067	NM_003482.3	3659	Cct/Tct	39/54	0.324913865615783	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	1	0.324913865615783	3		590	574	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81558873	81558873	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs779806385	NA	P-0005285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	60	458	0	ENST00000298171.2:c.468-2A>G		p.X156_splice	ENST00000298171	NM_000369.2	156			1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.324913865615783	2		458	349	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670754	67670754	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs763918566	NA	P-0005285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	67	425	0	ENST00000264010.4:c.1999C>T	p.Pro667Ser	p.P667S	ENST00000264010	NM_006565.3	667	Cca/Tca	11/12	0.164921332551308	0	FACETS	0.594	0.517	0.676			1	INDETERMINATE	1	TRUE	0	0.324913865615783	0		425	469	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226588	1226588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775978755	NA	P-0005285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	78	503	0	ENST00000326873.7:c.1244G>A	p.Arg415His	p.R415H	ENST00000326873	NM_000455.4	415	cGc/cAc	9/10	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.324913865615783	2		503	450	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969331	44969331	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	80	553	0	ENST00000377967.4:c.4017del	p.Phe1339LeufsTer17	p.F1339Lfs*17	ENST00000377967	NM_021140.2	1338	gTt/gt	28/29	0.271103116212127	0	FACETS	0.764	0.676	0.858			1	SUBCLONAL	1	TRUE	0	0.324913865615783	0		553	435	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106561	27106562	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	67	539	1	ENST00000324856.7:c.6176dup	p.Asn2059LysfsTer40	p.N2059Kfs*40	ENST00000324856	NM_006015.4	2058	gaa/gAaa	20/20	1	2	FACETS	0.754	0.656	0.86	0.754	0.656	0.86	SUBCLONAL	1	TRUE	1	0.324913865615783	2		540	547	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466026	69466028	+	inframe_deletion	In_Frame_Del	DEL	CGA	CGA	-	novel	NA	P-0005285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	89	562	0	ENST00000227507.2:c.866_868del	p.Asp289del	p.D289del	ENST00000227507	NM_053056.2	288	acCGAc/acc	5/5	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.324913865615783	2		562	462	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692981	89692982	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0005285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	75	351	0	ENST00000371953.3:c.468_469dup	p.Glu157GlyfsTer3	p.E157Gfs*3	ENST00000371953	NM_000314.4	155	-/GG	5/9	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.324913865615783	2		351	377	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857549	57857549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	206	593	0	ENST00000228682.2:c.79del	p.Ala27ProfsTer51	p.A27Pfs*51	ENST00000228682	NM_005269.2	25	caG/ca	2/12	0.324913865615783	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.324913865615783	3		593	669	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647028	23647028	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1555461597	NA	P-0005285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	86	547	0	ENST00000261584.4:c.839del	p.Asn280ThrfsTer8	p.N280Tfs*8	ENST00000261584	NM_024675.3	280	aAc/ac	4/13	1	2	FACETS	0.97	0.86	1	0.97	0.86	1	CLONAL	1	TRUE	1	0.324913865615783	2		547	546	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649051	37649051	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	101	587	0	ENST00000447079.4:c.2160del	p.Lys721AsnfsTer32	p.K721Nfs*32	ENST00000447079	NM_015083.1	719	tGg/tg	4/14	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.324913865615783	2		587	535	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100577	157100577	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1289149988	NA	P-0005285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	69	417	0	ENST00000346085.5:c.1518del	p.Gly507AspfsTer16	p.G507Dfs*16	ENST00000346085	NM_020732.3	505	aCc/ac	1/20	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.324913865615783	2		417	372	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107138	27107138	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	62	324	0	ENST00000324856.7:c.6749del	p.Glu2250GlyfsTer17	p.E2250Gfs*17	ENST00000324856	NM_006015.4	2250	gAg/gg	20/20	1	2	FACETS	0.881	0.764	1	0.881	0.764	1	CLONAL	1	TRUE	1	0.324913865615783	2		324	433	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885145	111885145	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs892433462	NA	P-0005285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	83	615	1	ENST00000341259.2:c.1038del	p.Leu347CysfsTer26	p.L347Cfs*26	ENST00000341259	NM_005475.2	345	Ggg/gg	6/8	0.324913865615783	3	FACETS	0.978	0.864	1	0.489	0.432	0.55	CLONAL	1	TRUE	1	0.324913865615783	3		616	607	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505418	25505418	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	56	442	0	ENST00000264709.3:c.340del	p.Ala114ProfsTer48	p.A114Pfs*48	ENST00000264709	NM_175629.2	114	Gcc/cc	4/23	1	2	FACETS	0.944	0.813	1	0.944	0.813	1	CLONAL	1	TRUE	1	0.324913865615783	2		442	365	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567647	226567647	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	34	392	0	ENST00000366794.5:c.1519del	p.Ser507AlafsTer17	p.S507Afs*17	ENST00000366794	NM_001618.3	507	Agc/gc	10/23	0.324913865615783	4	FACETS	0.579	0.472	0.699	0.193	0.157	0.233	SUBCLONAL	1	TRUE	1	0.324913865615783	4		392	479	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099579	157099579	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1562376341	NA	P-0005285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	16	97	0	ENST00000346085.5:c.521del	p.Pro174ArgfsTer6	p.P174Rfs*6	ENST00000346085	NM_020732.3	172	gaC/ga	1/20	1	2	FACETS	0.527	0.391	0.688	0.527	0.391	0.688	SUBCLONAL	1	TRUE	1	0.324913865615783	2		97	187	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0005286-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	30	414	0	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.12	2		414	428	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248998	55248999	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCCAGCG	rs727504263	NA	P-0005286-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	15	337	0	ENST00000275493.2:c.2300_2308dup	p.Ala767_Val769dup	p.A767_V769dup	ENST00000275493	NM_005228.3	767	atg/aTGGCCAGCGtg	20/28	0.153866398928963	3	FACETS	0.621	0.452	0.824	0.31	0.226	0.412	SUBCLONAL	1	TRUE	1	0.12	3		337	427	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240106	41240106	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs34733279	NA	P-0005286-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	10	108	0	ENST00000379561.5:c.244G>A	p.Asp82Asn	p.D82N	ENST00000379561	NM_002015.3	82	Gac/Aac	1/3	0.153866398928963	1	FACETS	0.808	0.552	1	1	0.858	1	CLONAL	2	TRUE	0	0.12	1		108	97	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	148	140	0				ENST00000310581	NM_198253.2	-/1132			0.470623733043664	3	FACETS	0.968	0.897	1	0.968	0.897	1	CLONAL	2	TRUE	1	0.575824493958386	3		140	342	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867571	45867571	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	183	380	0	ENST00000391945.4:c.737C>A	p.Ser246Tyr	p.S246Y	ENST00000391945	NM_000400.3	246	tCc/tAc	9/23	0.217071972578844	1	FACETS	0.685	0.634	0.737	0.685	0.634	0.737	INDETERMINATE	1	TRUE	0	0.575824493958386	1		380	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0005308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	194	283	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.575824493958386	2		283	647	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0005308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	231	582	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	1	2	FACETS	0.671	0.624	0.719	0.671	0.624	0.719	SUBCLONAL	1	TRUE	1	0.575824493958386	2		582	1196	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0005308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	120	431	0	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	1	2	FACETS	0.374	0.336	0.413	0.374	0.336	0.413	SUBCLONAL	1	TRUE	1	0.575824493958386	2		431	1115	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866987936	NA	P-0005308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	12	267	0	ENST00000281708.4:c.1436G>C	p.Arg479Pro	p.R479P	ENST00000281708	NM_033632.3	479	cGa/cCa	10/12	0.417583026654762	1	FACETS	0.05	0.034	0.069	0.05	0.034	0.069	SUBCLONAL	1	TRUE	0	0.575824493958386	1		267	596	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434013	49434013	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	77	136	0	ENST00000301067.7:c.7540C>T	p.Gln2514Ter	p.Q2514*	ENST00000301067	NM_003482.3	2514	Cag/Tag	31/54	1	2	FACETS	0.777	0.688	0.872	0.777	0.688	0.872	SUBCLONAL	1	TRUE	1	0.575824493958386	2		136	344	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682980	241682980	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1463008959	NA	P-0005308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	82	393	0	ENST00000366560.3:c.43G>T	p.Val15Leu	p.V15L	ENST00000366560	NM_000143.3	15	Gtg/Ttg	1/10	1	2	FACETS	0.283	0.248	0.32	0.283	0.248	0.32	SUBCLONAL	1	TRUE	1	0.575824493958386	2		393	1008	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799786	72799786	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	115	344	0	ENST00000325599.8:c.1383C>G	p.Asp461Glu	p.D461E	ENST00000325599	NM_018130.2	461	gaC/gaG	11/11	1	2	FACETS	0.382	0.343	0.424	0.382	0.343	0.424	SUBCLONAL	1	TRUE	1	0.575824493958386	2		344	1045	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921488	178921488	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	280	394	0	ENST00000263967.3:c.970A>G	p.Thr324Ala	p.T324A	ENST00000263967	NM_006218.2	324	Aca/Gca	5/21	1	2	FACETS	0.894	0.84	0.949	0.894	0.84	0.949	CLONAL	1	TRUE	1	0.575824493958386	2		394	1088	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280454	1280454	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0005308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	63	144	0	ENST00000310581.5:c.1770-1G>T		p.X590_splice	ENST00000310581	NM_198253.2	590			0.470623733043664	3	FACETS	0.686	0.595	0.783	0.343	0.297	0.392	SUBCLONAL	1	TRUE	1	0.575824493958386	3		144	411	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188590	32188590	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	201	477	0	ENST00000375023.3:c.865G>C	p.Gly289Arg	p.G289R	ENST00000375023	NM_004557.3	289	Ggc/Cgc	5/30	NA	2	FACETS	0.509	0.47	0.55			1	INDETERMINATE	1	TRUE	NA	0.575824493958386	2		477	1371	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138651	37138651	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	189	293	1	ENST00000373509.5:c.185T>C	p.Leu62Ser	p.L62S	ENST00000373509	NM_002648.3	62	tTg/tCg	2/6	NA	2	FACETS	0.71	0.656	0.765			1	INDETERMINATE	1	TRUE	NA	0.575824493958386	2		294	925	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864304	151864304	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	211	479	0	ENST00000262189.6:c.9677T>C	p.Phe3226Ser	p.F3226S	ENST00000262189	NM_170606.2	3226	tTt/tCt	42/59	1	2	FACETS	0.579	0.536	0.623	0.579	0.536	0.623	SUBCLONAL	1	TRUE	1	0.575824493958386	2		479	1266	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127923122	127923122	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	155	484	0	ENST00000373547.4:c.235A>G	p.Met79Val	p.M79V	ENST00000373547	NM_002721.4	79	Atg/Gtg	3/7	1	2	FACETS	0.424	0.387	0.463	0.424	0.387	0.463	SUBCLONAL	1	TRUE	1	0.575824493958386	2		484	1269	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117782	108117782	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	260	366	0	ENST00000278616.4:c.993G>C	p.Lys331Asn	p.K331N	ENST00000278616	NM_000051.3	331	aaG/aaC	8/63	1	2	FACETS	0.796	0.745	0.848	0.796	0.745	0.848	SUBCLONAL	1	TRUE	1	0.575824493958386	2		366	1135	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141840	108141840	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	127	333	0	ENST00000278616.4:c.2888T>C	p.Met963Thr	p.M963T	ENST00000278616	NM_000051.3	963	aTg/aCg	19/63	1	2	FACETS	0.517	0.468	0.569	0.517	0.468	0.569	SUBCLONAL	1	TRUE	1	0.575824493958386	2		333	853	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047494	49047494	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0005308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	229	234	0	ENST00000267163.4:c.2490-2A>G		p.X830_splice	ENST00000267163	NM_000321.2	830			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.575824493958386	2		234	713	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122881	2122881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749593050	NA	P-0005308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	174	463	0	ENST00000219476.3:c.2252G>A	p.Arg751Gln	p.R751Q	ENST00000219476	NM_000548.3	751	cGa/cAa	21/42	0.301128973243789	1	FACETS	0.454	0.418	0.492	0.454	0.418	0.492	INDETERMINATE	1	TRUE	0	0.575824493958386	1		463	947	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578440	7578440	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0005308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	78	378	0	ENST00000269305.4:c.490A>T	p.Lys164Ter	p.K164*	ENST00000269305	NM_001126112.2	164	Aag/Tag	5/11	1	2	FACETS	0.425	0.373	0.48	0.425	0.373	0.48	SUBCLONAL	1	TRUE	1	0.575824493958386	2		378	638	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291911	15291911	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	166	447	0	ENST00000263388.2:c.2855C>T	p.Pro952Leu	p.P952L	ENST00000263388	NM_000435.2	952	cCc/cTc	18/33	0.217071972578844	1	FACETS	0.454	0.417	0.493	0.454	0.417	0.493	INDETERMINATE	1	TRUE	0	0.575824493958386	1		447	904	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796451	42796451	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0005308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	200	250	0	ENST00000575354.2:c.3009-1G>A		p.X1003_splice	ENST00000575354	NM_015125.3	1003			0.217071972578844	1	FACETS	0.766	0.713	0.82	0.766	0.713	0.82	INDETERMINATE	1	TRUE	0	0.575824493958386	1		250	646	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733220	40733220	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	126	304	0	ENST00000373198.4:c.3586G>C	p.Asp1196His	p.D1196H	ENST00000373198	NM_133170.3	1196	Gat/Cat	26/32	0.166757984283265	5	FACETS	0.745	0.673	0.821	0.248	0.224	0.274	INDETERMINATE	1	TRUE	2	0.575824493958386	5		304	1095	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992156	11992186	+	frameshift_variant	Frame_Shift_Del	DEL	TGACAGCAACACGTTTGAAATGAATGGCAAA	TGACAGCAACACGTTTGAAATGAATGGCAAA	-	novel	NA	P-0005308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	204	361	1	ENST00000396373.4:c.246_276del	p.Ile82MetfsTer6	p.I82Mfs*6	ENST00000396373	NM_001987.4	82	atTGACAGCAACACGTTTGAAATGAATGGCAAA/at	3/8	1	2	FACETS	0.744	0.69	0.8	0.744	0.69	0.8	SUBCLONAL	1	TRUE	1	0.575824493958386	2		362	952	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879910	44879913	+	frameshift_variant	Frame_Shift_Del	DEL	AAGG	AAGG	-	novel	NA	P-0005308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	206	257	0	ENST00000377967.4:c.501_504del	p.Glu168PhefsTer11	p.E168Ffs*11	ENST00000377967	NM_021140.2	167	AAGGaa/aa	6/29	1	1	FACETS	0.685	0.637	0.734	0.685	0.637	0.734	SUBCLONAL	1	TRUE	0	0.575824493958386	1		257	744	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216512	108216515	+	frameshift_variant	Frame_Shift_Del	DEL	ATGG	ATGG	-	novel	NA	P-0005308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	336	470	0	ENST00000278616.4:c.8464_8467del	p.Asp2822PhefsTer34	p.D2822Ffs*34	ENST00000278616	NM_000051.3	2821	ATGGat/at	58/63	1	2	FACETS	0.895	0.846	0.946	0.895	0.846	0.946	CLONAL	1	TRUE	1	0.575824493958386	2		470	1304	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578206	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TATGTCGAAAA	novel	NA	P-0005308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	65	459	0	ENST00000269305.4:c.633_643dup	p.Ser215IlefsTer36	p.S215Ifs*36	ENST00000269305	NM_001126112.2	215	agt/aTTTTCGACATAgt	6/11	1	2	FACETS	0.189	0.163	0.218	0.189	0.163	0.218	SUBCLONAL	1	TRUE	1	0.575824493958386	2		459	1192	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530033	63530041	+	inframe_deletion	In_Frame_Del	DEL	TAATTTCCC	TAATTTCCC	-	novel	NA	P-0005308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	220	306	0	ENST00000307078.5:c.2394_2402del	p.Lys798_Tyr801delinsAsn	p.K798_Y801delinsN	ENST00000307078	NM_004655.3	798	aaGGGAAATTAt/aat	10/11	1	2	FACETS	0.858	0.799	0.918	0.858	0.799	0.918	CLONAL	1	TRUE	1	0.575824493958386	2		306	891	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	62	140	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.620367448231227	2		140	168	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495505	56495505	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	223	363	0	ENST00000267101.3:c.3695G>T	p.Ser1232Ile	p.S1232I	ENST00000267101	NM_001982.3	1232	aGt/aTt	28/28	0.289558415398668	3	FACETS	1	0.988	1	0.628	0.586	0.67	INDETERMINATE	1	TRUE	1	0.620367448231227	3		363	750	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100982	27100983	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0005341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	53	298	0	ENST00000324856.7:c.4268dup	p.Gln1424SerfsTer21	p.Q1424Sfs*21	ENST00000324856	NM_006015.4	1422	tcc/tCcc	18/20	1	2	FACETS	0.273	0.233	0.318	0.273	0.233	0.318	SUBCLONAL	1	TRUE	1	0.620367448231227	2		298	625	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092802	27092802	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	182	365	1	ENST00000324856.7:c.2823del	p.Asn942ThrfsTer26	p.N942Tfs*26	ENST00000324856	NM_006015.4	941	atC/at	9/20	1	2	FACETS	0.868	0.804	0.934	0.868	0.804	0.934	CLONAL	1	TRUE	1	0.620367448231227	2		366	676	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143235862	143235863	+	splice_donor_variant,intron_variant	Splice_Site	DEL	TA	TA	-	novel	NA	P-0005341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	101	196	0	ENST00000262992.4:c.423+2_423+3del		p.X141_splice	ENST00000262992	NM_001101669.1	141			1	2	FACETS	0.79	0.711	0.873	0.79	0.711	0.873	SUBCLONAL	1	TRUE	1	0.620367448231227	2		196	412	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061202	38061203	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCGGT	novel	NA	P-0005348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	167	194	0	ENST00000250448.2:c.786_787insACCGC	p.Gln263ThrfsTer60	p.Q263Tfs*60	ENST00000250448	NM_004496.3	262	-/ACCGC	2/2	0.261588914395855	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.29	3		194	565	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186599	108186599	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876658415	NA	P-0005356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	1281	408	0	ENST00000278616.4:c.6056A>G	p.Tyr2019Cys	p.Y2019C	ENST00000278616	NM_000051.3	2019	tAt/tGt	41/63	0.500102264849151	8	FACETS	0.995	0.98	1			1	CLONAL	8	TRUE	NA	0.500102264849151	8		408	1609	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068405	26068405	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	451	409	3	ENST00000435504.4:c.85A>G	p.Met29Val	p.M29V	ENST00000435504		29	Atg/Gtg	2/13	0.496018457712555	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.500102264849151	4		412	1326	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440468	49440468	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs398123746	NA	P-0005356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	438	450	0	ENST00000301067.7:c.4342T>C	p.Cys1448Arg	p.C1448R	ENST00000301067	NM_003482.3	1448	Tgt/Cgt	15/54	0.500102264849151	6	FACETS	0.963	0.919	1			1	CLONAL	3	TRUE	NA	0.500102264849151	6		450	1213	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551058	41551058	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	523	607	0	ENST00000263253.7:c.3202C>T	p.Gln1068Ter	p.Q1068*	ENST00000263253	NM_001429.3	1068	Cag/Tag	17/31	0.505195950079281	3	FACETS	1	0.984	1			1	CLONAL	2	TRUE	NA	0.500102264849151	3		607	1252	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949128	44949129	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0005356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	630	307	0	ENST00000377967.4:c.3691_3692dup	p.Gly1232LeufsTer34	p.G1232Lfs*34	ENST00000377967	NM_021140.2	1230	gct/gcTAt	25/29	0.505195950079281	2	FACETS	0.883	0.858	0.907			1	CLONAL	3	TRUE	NA	0.500102264849151	2		307	951	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426173	47426174	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATCCAGGT	novel	NA	P-0005356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	403	264	0	ENST00000377045.4:c.694_699+2dup		p.-231fs	ENST00000377045	NM_001654.4	231	-/ATCCAGGT	7/16	0.439173773905045	2	FACETS	1	0.982	1			1	CLONAL	2	TRUE	NA	0.500102264849151	2		264	772	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478853	56478854	+	missense_variant	Missense_Mutation	DNP	CG	CG	AT	novel	NA	P-0005356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	1097	608	1	ENST00000267101.3:c.309_310delinsAT	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	103	cgCGtg/cgATtg	3/28	0.500102264849151	8	FACETS	1	0.987	1			1	CLONAL	5	TRUE	NA	0.500102264849151	8		609	2154	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0005357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	104	196	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.757	0.678	0.842	0.757	0.678	0.842	SUBCLONAL	1	TRUE	1	0.327359773742655	2		196	839	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	41	140	0				ENST00000310581	NM_198253.2	-/1132			0.265598516467909	1	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	0	0.327359773742655	1		140	208	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672135	30672135	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	107	411	0	ENST00000376406.3:c.4825C>G	p.Pro1609Ala	p.P1609A	ENST00000376406	NM_014641.2	1609	Cct/Gct	10/15	0.19712651469269	4	FACETS	0.901	0.807	1	0.451	0.403	0.501	CLONAL	1	TRUE	2	0.327359773742655	4		411	963	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396740	396740	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	151	548	1	ENST00000262320.3:c.286C>T	p.Gln96Ter	p.Q96*	ENST00000262320	NM_003502.3	96	Caa/Taa	2/11	0.327359773742655	1	FACETS	0.93	0.85	1	0.93	0.85	1	CLONAL	1	TRUE	0	0.327359773742655	1		549	830	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655465	67655465	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	146	562	0	ENST00000264010.4:c.1328A>G	p.Asp443Gly	p.D443G	ENST00000264010	NM_006565.3	443	gAc/gGc	7/12	0.214065211368195	1	FACETS	0.716	0.652	0.783	0.716	0.652	0.783	SUBCLONAL	1	TRUE	0	0.327359773742655	1		562	1042	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274251	5274251	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	117	499	0	ENST00000357368.4:c.196T>A	p.Trp66Arg	p.W66R	ENST00000357368	NM_002850.3	66	Tgg/Agg	3/38	0.327359773742655	1	FACETS	0.777	0.701	0.858	0.777	0.701	0.858	SUBCLONAL	1	TRUE	0	0.327359773742655	1		499	769	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627772	37627772	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	38	481	1	ENST00000447079.4:c.1687C>T	p.Gln563Ter	p.Q563*	ENST00000447079	NM_015083.1	563	Caa/Taa	2/14	1	2	FACETS	0.893	0.741	1	0.893	0.741	1	CLONAL	1	TRUE	1	0.28	2		482	304	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618549	37618550	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	38	486	0	ENST00000447079.4:c.226dup	p.Ile76AsnfsTer4	p.I76Nfs*4	ENST00000447079	NM_015083.1	75	-/A	1/14	1	2	FACETS	0.873	0.724	1	0.873	0.724	1	CLONAL	1	TRUE	1	0.28	2		486	311	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876964	151876980	+	frameshift_variant	Frame_Shift_Del	DEL	TAGGGTCCACGCTGATC	TAGGGTCCACGCTGATC	-	novel	NA	P-0005445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	39	487	0	ENST00000262189.6:c.7381_7397del	p.Asp2461SerfsTer3	p.D2461Sfs*3	ENST00000262189	NM_170606.2	2461	GATCAGCGTGGACCCTAt/t	37/59	1	2	FACETS	0.998	0.832	1	0.998	0.832	1	CLONAL	1	TRUE	1	0.28	2		487	279	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0005464-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	94	468	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.261225887768462	5	FACETS	0.796	0.707	0.892	0.265	0.235	0.298	SUBCLONAL	1	TRUE	2	0.356621139489003	5		468	1016	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0005464-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	295	599	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.261225887768462	5	FACETS	1	0.984	1	0.747	0.703	0.792	CLONAL	2	TRUE	2	0.356621139489003	5		599	1133	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0005464-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	398	572	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	0.356621139489003	3	FACETS	0.863	0.823	0.903	0.863	0.823	0.903	CLONAL	3	TRUE	0	0.356621139489003	3		572	1016	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245473	153245473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005464-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	102	442	0	ENST00000281708.4:c.1718G>A	p.Cys573Tyr	p.C573Y	ENST00000281708	NM_033632.3	573	tGc/tAc	11/12	0.356621139489003	3	FACETS	0.926	0.828	1	0.463	0.414	0.515	CLONAL	1	TRUE	1	0.356621139489003	3		442	728	SUCCESS
APC	324	MSKCC	GRCh37	5	112174588	112174589	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005464-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	229	530	0	ENST00000257430.4:c.3297_3298insG	p.Ser1100ValfsTer19	p.S1100Vfs*19	ENST00000257430	NM_000038.5	1099	-/G	16/16	0.273228813528019	2	FACETS	0.795	0.743	0.848	0.795	0.743	0.848	SUBCLONAL	2	TRUE	0	0.356621139489003	2		530	808	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252969	36252977	+	inframe_deletion	In_Frame_Del	DEL	AGTGACCAG	AGTGACCAG	-	novel	NA	P-0005464-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	223	369	0	ENST00000300305.3:c.385_393del	p.Leu129_Thr131del	p.L129_T131del	ENST00000300305		129	CTGGTCACT/-	4/8	0.280581134043713	4	FACETS	1	0.974	1	0.724	0.676	0.774	CLONAL	2	TRUE	1	0.356621139489003	4		369	781	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761459	59761460	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs774684620	NA	P-0005464-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	59	305	0	ENST00000259008.2:c.2947dup	p.Ile983AsnfsTer19	p.I983Nfs*19	ENST00000259008	NM_032043.2	983	att/aAtt	20/20	0.356621139489003	4	FACETS	0.699	0.601	0.806	0.233	0.2	0.269	SUBCLONAL	1	TRUE	1	0.356621139489003	4		305	642	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0005475-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	32	336	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.81	0.656	0.985	0.81	0.656	0.985	CLONAL	1	TRUE	1	0.13	2		336	608	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514780	44514780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769567889	NA	P-0005475-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	39	304	1	ENST00000291552.4:c.467G>A	p.Arg156His	p.R156H	ENST00000291552	NM_006758.2	156	cGt/cAt	6/8	1	2	FACETS	0.939	0.777	1	0.939	0.777	1	CLONAL	1	TRUE	1	0.13	2		305	639	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115916	8115917	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005475-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	39	224	0	ENST00000346208.3:c.1263dup	p.Met422AspfsTer85	p.M422Dfs*85	ENST00000346208		421	ccg/ccGg	6/6	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.13	2		224	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0005483-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	264	319	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.410606911551892	2	FACETS	0.997	0.941	1	0.997	0.941	1	CLONAL	2	TRUE	0	0.410606911551892	2		319	645	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880984	37880985	+	inframe_insertion	In_Frame_Ins	INS	-	-	TACGTGATGGCT	rs397516977	NA	P-0005483-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	703	420	0	ENST00000269571.5:c.2314_2325dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/TACGTGATGGCT	20/27	0.410606911551892	7	FACETS	1	0.97	1	0.805	0.777	0.833	CLONAL	4	TRUE	2	0.410606911551892	7		420	1725	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974696	21974697	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005483-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	246	336	0	ENST00000304494.5:c.130_131insC	p.Tyr44SerfsTer76	p.Y44Sfs*76	ENST00000304494	NM_000077.4	44	tac/tCac	1/3	0.410606911551892	2	FACETS	0.909	0.855	0.964	0.909	0.855	0.964	CLONAL	2	TRUE	0	0.410606911551892	2		336	659	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023962	27023962	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005483-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	12	46	0	ENST00000324856.7:c.1068G>T	p.Arg356Ser	p.R356S	ENST00000324856	NM_006015.4	356	agG/agT	1/20	0.230428381147084	5	FACETS	0.621	0.438	0.845	0.207	0.146	0.282	INDETERMINATE	1	TRUE	2	0.410606911551892	5		46	152	SUCCESS
APC	324	MSKCC	GRCh37	5	112177640	112177640	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005483-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	98	267	0	ENST00000257430.4:c.6349C>T	p.Gln2117Ter	p.Q2117*	ENST00000257430	NM_000038.5	2117	Caa/Taa	16/16	0.410606911551892	3	FACETS	0.983	0.879	1	0.492	0.439	0.547	CLONAL	1	TRUE	1	0.410606911551892	3		267	585	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043414	180043414	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005483-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	72	410	0	ENST00000261937.6:c.3172C>T	p.Leu1058Phe	p.L1058F	ENST00000261937	NM_182925.4	1058	Ctt/Ttt	23/30	0.410606911551892	3	FACETS	0.48	0.418	0.547	0.24	0.209	0.274	SUBCLONAL	1	TRUE	1	0.410606911551892	3		410	881	SUCCESS
ATM	472	MSKCC	GRCh37	11	108213976	108213976	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881322	NA	P-0005483-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	96	316	0	ENST00000278616.4:c.8296G>A	p.Val2766Ile	p.V2766I	ENST00000278616	NM_000051.3	2766	Gtt/Att	57/63	0.410606911551892	5	FACETS	0.913	0.812	1	0.304	0.27	0.34	CLONAL	1	TRUE	2	0.410606911551892	5		316	828	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125525174	125525174	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005483-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	113	376	1	ENST00000428830.2:c.1390G>T	p.Asp464Tyr	p.D464Y	ENST00000428830	NM_001114121.2	464	Gat/Tat	13/14	0.410606911551892	5	FACETS	0.929	0.835	1	0.31	0.278	0.343	CLONAL	1	TRUE	2	0.410606911551892	5		377	957	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207064	1207065	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1131690917	NA	P-0005510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	267	710	0	ENST00000326873.7:c.157dup	p.Asp53GlyfsTer110	p.D53Gfs*110	ENST00000326873	NM_000455.4	51	atg/atGg	1/10	0.222697615125247	1	FACETS	0.796	0.745	0.848	1	0.993	1	SUBCLONAL	2	TRUE	0	0.222697615125247	1		710	1339	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0005510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	89	282	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	0.222697615125247	2		282	659	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041183	29041183	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1272	225	641	0	ENST00000282397.4:c.245G>T	p.Gly82Val	p.G82V	ENST00000282397	NM_002019.4	82	gGa/gTa	3/30	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.222697615125247	2		641	1497	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211752	2211752	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1475	338	938	0	ENST00000398665.3:c.1468T>C	p.Ser490Pro	p.S490P	ENST00000398665	NM_032482.2	490	Tcc/Ccc	16/28	0.222697615125247	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.222697615125247	1		938	1813	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610315	10610315	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	290	704	0	ENST00000171111.5:c.395T>G	p.Val132Gly	p.V132G	ENST00000171111	NM_203500.1	132	gTc/gGc	2/6	0.222697615125247	1	FACETS	0.839	0.788	0.892	1	0.994	1	CLONAL	2	TRUE	0	0.222697615125247	1		704	1379	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961468	54961468	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	135	272	1	ENST00000312783.6:c.164A>T	p.Gln55Leu	p.Q55L	ENST00000312783	NM_198436.1	55	cAg/cTg	4/10	1	2	FACETS	0.806	0.733	0.882	1	0.988	1	CLONAL	2	TRUE	1	0.222697615125247	2		273	752	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795103	242795104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs768249210	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	126	436	0	ENST00000334409.5:c.105dup	p.Thr36HisfsTer70	p.T36Hfs*70	ENST00000334409	NM_005018.2	35	-/C	2/5	1	2	FACETS	0.761	0.692	0.835	0.761	0.692	0.835	SUBCLONAL	1	TRUE	1	0.546108773049129	2		436	606	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	219	265	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.985	0.919	1	0.985	0.919	1	CLONAL	1	TRUE	1	0.546108773049129	2		265	814	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970987	21970987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747621669	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	243	373	0	ENST00000304494.5:c.371G>A	p.Arg124His	p.R124H	ENST00000304494	NM_000077.4	124	cGc/cAc	2/3	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.546108773049129	2		373	742	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991721	72991721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370398587	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	192	302	0	ENST00000268489.5:c.2324C>T	p.Ala775Val	p.A775V	ENST00000268489	NM_006885.3	775	gCg/gTg	2/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.546108773049129	2		302	553	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	301	975	8	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	0.824	0.775	0.875	0.824	0.775	0.875	CLONAL	1	TRUE	1	0.546108773049129	2		983	1337	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	353	428	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.888	0.848	0.928	1	0.996	1	CLONAL	2	TRUE	1	0.546108773049129	2		429	728	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438317	110438322	+	inframe_deletion	In_Frame_Del	DEL	GTTGTT	GTTGTT	-	rs532810290	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	60	95	0	ENST00000375856.3:c.79_84del	p.Asn27_Asn28del	p.N27_N28del	ENST00000375856	NM_003749.2	27	AACAAC/-	1/2	1	2	FACETS	0.955	0.834	1	0.955	0.834	1	CLONAL	1	TRUE	1	0.546108773049129	2		95	230	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794441	42794441	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	241	596	4	ENST00000575354.2:c.1526del	p.Pro509HisfsTer14	p.P509Hfs*14	ENST00000575354	NM_015125.3	507	cgC/cg	10/20	1	2	FACETS	0.981	0.917	1	0.981	0.917	1	CLONAL	1	TRUE	1	0.546108773049129	2		600	900	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554355	81554355	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747687365	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	297	632	0	ENST00000298171.2:c.379del	p.Leu127SerfsTer2	p.L127Sfs*2	ENST00000298171	NM_000369.2	125	ctC/ct	4/10	1	2	FACETS	0.975	0.918	1	0.975	0.918	1	CLONAL	1	TRUE	1	0.546108773049129	2		632	1116	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007619	45007619	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs111482205	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	115	265	0	ENST00000558401.1:c.68-2A>G		p.X23_splice	ENST00000558401	NM_004048.2	23			1	2	FACETS	0.829	0.75	0.911	0.829	0.75	0.911	CLONAL	1	TRUE	1	0.546108773049129	2		265	508	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972893	32972893	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	132	344	1	ENST00000380152.3:c.10248del	p.Lys3416AsnfsTer11	p.K3416Nfs*11	ENST00000380152		3415	Aaa/aa	27/27	1	2	FACETS	0.772	0.703	0.845	0.772	0.703	0.845	SUBCLONAL	1	TRUE	1	0.546108773049129	2		345	626	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038196	128038196	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs150954655	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	249	504	1	ENST00000285398.2:c.1354C>T	p.Arg452Ter	p.R452*	ENST00000285398	NM_000122.1	452	Cga/Tga	9/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.546108773049129	2		505	881	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164832	47164832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1017636782	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	197	423	0	ENST00000409792.3:c.1294C>T	p.Arg432Cys	p.R432C	ENST00000409792	NM_014159.6	432	Cgt/Tgt	3/21	1	2	FACETS	0.952	0.884	1	0.952	0.884	1	CLONAL	1	TRUE	1	0.546108773049129	2		423	758	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458332	120458332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	142	432	0	ENST00000256646.2:c.7013C>T	p.Thr2338Ile	p.T2338I	ENST00000256646	NM_024408.3	2338	aCc/aTc	34/34	1	2	FACETS	0.894	0.818	0.972	0.894	0.818	0.972	CLONAL	1	TRUE	1	0.546108773049129	2		432	582	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468283	120468283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs74522665	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	124	347	0	ENST00000256646.2:c.4156G>A	p.Gly1386Arg	p.G1386R	ENST00000256646	NM_024408.3	1386	Ggg/Agg	25/34	1	2	FACETS	0.905	0.823	0.99	0.905	0.823	0.99	CLONAL	1	TRUE	1	0.546108773049129	2		347	502	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361249	66361249	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1430800927	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	156	381	1	ENST00000273854.3:c.923G>T	p.Gly308Val	p.G308V	ENST00000273854	NM_004439.5	308	gGg/gTg	4/18	1	2	FACETS	0.897	0.824	0.972	0.897	0.824	0.972	CLONAL	1	TRUE	1	0.546108773049129	2		382	637	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535351	66535351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs963468479	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	228	531	2	ENST00000273854.3:c.110G>A	p.Arg37Gln	p.R37Q	ENST00000273854	NM_004439.5	37	cGg/cAg	1/18	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.546108773049129	2		533	820	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678044	117678044	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	180	484	0	ENST00000368508.3:c.3889T>G	p.Tyr1297Asp	p.Y1297D	ENST00000368508	NM_002944.2	1297	Tac/Gac	25/43	1	2	FACETS	0.815	0.752	0.88	0.815	0.752	0.88	CLONAL	1	TRUE	1	0.546108773049129	2		484	809	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145736909	145736909	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776146178	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	189	493	0	ENST00000428558.2:c.3532G>A	p.Gly1178Arg	p.G1178R	ENST00000428558	NM_004260.3	1178	Ggg/Agg	22/22	1	2	FACETS	0.94	0.872	1	0.94	0.872	1	CLONAL	1	TRUE	1	0.546108773049129	2		493	736	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760255	133760255	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	170	439	0	ENST00000318560.5:c.2578G>T	p.Gly860Cys	p.G860C	ENST00000318560	NM_005157.4	860	Ggt/Tgt	11/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.546108773049129	2		439	560	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426084	49426084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1233943512	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	150	466	1	ENST00000301067.7:c.12404C>T	p.Ala4135Val	p.A4135V	ENST00000301067	NM_003482.3	4135	gCt/gTt	39/54	0.546108773049129	2	FACETS	0.928	0.852	1	0.464	0.426	0.504	CLONAL	1	TRUE	0	0.546108773049129	2		467	592	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864196	57864196	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs972690369	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	255	612	3	ENST00000228682.2:c.1673G>A	p.Arg558His	p.R558H	ENST00000228682	NM_005269.2	558	cGc/cAc	12/12	0.546108773049129	2	FACETS	0.895	0.838	0.954	0.448	0.419	0.477	CLONAL	1	TRUE	0	0.546108773049129	2		615	1043	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856335	111856335	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766405916	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	105	98	1	ENST00000341259.2:c.386C>T	p.Pro129Leu	p.P129L	ENST00000341259	NM_005475.2	129	cCg/cTg	2/8	0.546108773049129	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.546108773049129	2		99	187	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563426	21563426	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs377626485	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	280	594	1	ENST00000382592.4:c.493A>G	p.Thr165Ala	p.T165A	ENST00000382592	NM_014572.2	165	Acc/Gcc	4/8	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.546108773049129	2		595	1011	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007686	45007686	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	215	470	0	ENST00000558401.1:c.133T>C	p.Cys45Arg	p.C45R	ENST00000558401	NM_004048.2	45	Tgc/Cgc	2/4	1	2	FACETS	0.966	0.9	1	0.966	0.9	1	CLONAL	1	TRUE	1	0.546108773049129	2		470	815	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478142	99478142	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	343	629	0	ENST00000268035.6:c.3046G>T	p.Gly1016Ter	p.G1016*	ENST00000268035	NM_000875.3	1016	Gga/Tga	16/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.546108773049129	2		629	1219	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829091	72829091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756694889	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	331	714	0	ENST00000268489.5:c.7490C>T	p.Ser2497Leu	p.S2497L	ENST00000268489	NM_006885.3	2497	tCg/tTg	9/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.546108773049129	2		714	1144	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81891937	81891937	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777990663	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	368	784	1	ENST00000359376.3:c.407C>T	p.Ala136Val	p.A136V	ENST00000359376	NM_002661.3	136	gCg/gTg	4/33	1	2	FACETS	0.96	0.909	1	0.96	0.909	1	CLONAL	1	TRUE	1	0.546108773049129	2		785	1404	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302921	15302921	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	131	461	0	ENST00000263388.2:c.529A>G	p.Thr177Ala	p.T177A	ENST00000263388	NM_000435.2	177	Aca/Gca	4/33	1	2	FACETS	0.786	0.716	0.86	0.786	0.716	0.86	SUBCLONAL	1	TRUE	1	0.546108773049129	2		461	610	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349684	15349684	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	73	186	0	ENST00000263377.2:c.3890A>C	p.Gln1297Pro	p.Q1297P	ENST00000263377	NM_058243.2	1297	cAg/cCg	19/20	1	2	FACETS	0.874	0.771	0.982	0.874	0.771	0.982	CLONAL	1	TRUE	1	0.546108773049129	2		186	306	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792885	33792885	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	47	129	0	ENST00000498907.2:c.436del	p.Leu146CysfsTer14	p.L146Cfs*14	ENST00000498907	NM_004364.3	146	Ctg/tg	1/1	1	2	FACETS	0.57	0.483	0.664	0.57	0.483	0.664	SUBCLONAL	1	TRUE	1	0.546108773049129	2		129	302	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532654	63532654	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	124	301	0	ENST00000307078.5:c.1925del	p.Lys642ArgfsTer47	p.K642Rfs*47	ENST00000307078	NM_004655.3	642	aAg/ag	8/11	1	2	FACETS	0.878	0.799	0.962	0.878	0.799	0.962	CLONAL	1	TRUE	1	0.546108773049129	2		301	517	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424113	49424114	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	247	591	3	ENST00000301067.7:c.13948dup	p.Glu4650GlyfsTer12	p.E4650Gfs*12	ENST00000301067	NM_003482.3	4650	gag/gGag	42/54	0.546108773049129	2	FACETS	0.93	0.87	0.991	0.465	0.435	0.496	CLONAL	1	TRUE	0	0.546108773049129	2		594	973	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542110	187542110	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	181	432	0	ENST00000441802.2:c.5630del	p.Pro1877LeufsTer20	p.P1877Lfs*20	ENST00000441802	NM_005245.3	1877	cCt/ct	10/27	1	2	FACETS	0.951	0.88	1	0.951	0.88	1	CLONAL	1	TRUE	1	0.546108773049129	2		432	697	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411530	63411530	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	296	389	0	ENST00000330258.3:c.1637del	p.Leu546CysfsTer16	p.L546Cfs*16	ENST00000330258	NM_152424.3	546	tTg/tg	2/2	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.546108773049129	1		389	630	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567646	226567647	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1159330096	NA	P-0005529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	122	376	0	ENST00000366794.5:c.1519dup	p.Ser507LysfsTer14	p.S507Kfs*14	ENST00000366794	NM_001618.3	507	agc/aAgc	10/23	1	2	FACETS	0.824	0.748	0.904	0.824	0.748	0.904	CLONAL	1	TRUE	1	0.546108773049129	2		376	542	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881001	37881002	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGCTCCCC	rs397516981	NA	P-0005537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	838	284	0	ENST00000269571.5:c.2331_2339dup	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	gtg/gtGGGCTCCCCg	20/27	0.5924522265984	4	FACETS	1	0.994	1	0.796	0.775	0.817	CLONAL	3	TRUE	0	0.602774300515289	4		284	1399	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577569	7577569	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519981	NA	P-0005537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	322	579	0	ENST00000269305.4:c.712T>G	p.Cys238Gly	p.C238G	ENST00000269305	NM_001126112.2	238	Tgt/Ggt	7/11	NA	2	FACETS	0.904	0.863	0.944			1	INDETERMINATE	2	TRUE	NA	0.602774300515289	2		579	591	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675451	30675451	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	137	443	0	ENST00000376406.3:c.2905C>G	p.Pro969Ala	p.P969A	ENST00000376406	NM_014641.2	969	Cct/Gct	8/15	0.602774300515289	6	FACETS	0.916	0.831	1	0.305	0.277	0.335	CLONAL	1	TRUE	3	0.602774300515289	6		443	1095	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188589	32188589	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1201	219	626	3	ENST00000375023.3:c.866G>A	p.Gly289Asp	p.G289D	ENST00000375023	NM_004557.3	289	gGc/gAc	5/30	0.602774300515289	4	FACETS	0.82	0.761	0.882			1	CLONAL	1	TRUE	NA	0.602774300515289	4		629	1420	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	254	898	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	0.35	2		903	1275	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	333	654	0	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.35	2		654	1433	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	191	265	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	0.35	2		265	969	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	232	183	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.35	2		183	585	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251907	153251907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	256	497	4	ENST00000281708.4:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000281708	NM_033632.3	367	Cga/Tga	7/12	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.35	2		501	1181	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263973	104263974	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776579	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	66	172	2	ENST00000369902.3:c.71dup	p.Ala25GlyfsTer23	p.A25Gfs*23	ENST00000369902	NM_016169.3	22	gcc/gCcc	1/12	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.35	2		174	334	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116254	209116254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369048275	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	204	323	0	ENST00000345146.2:c.22G>A	p.Gly8Ser	p.G8S	ENST00000345146	NM_005896.2	8	Ggt/Agt	3/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.35	2		323	1056	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867541	35867541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	172	379	2	ENST00000303115.3:c.361del	p.Ile121Ter	p.I121*	ENST00000303115	NM_002185.3	119	Aaa/aa	3/8	1	2	FACETS	0.911	0.837	0.988	0.911	0.837	0.988	CLONAL	1	TRUE	1	0.35	2		381	1079	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523009	25523009	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	52	506	2	ENST00000264709.3:c.176del	p.Pro59ArgfsTer13	p.P59Rfs*13	ENST00000264709	NM_175629.2	59	cCg/cg	3/23	0.354183285863444	2	FACETS	0.312	0.265	0.365			1	SUBCLONAL	1	TRUE	NA	0.35	2		508	951	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882082	36882082	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	143	461	0	ENST00000358127.4:c.931A>G	p.Thr311Ala	p.T311A	ENST00000358127	NM_001280556.1	311	Acc/Gcc	8/10	1	2	FACETS	0.95	0.866	1	0.95	0.866	1	CLONAL	1	TRUE	1	0.35	2		461	860	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755554	39755554	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	168	383	1	ENST00000288319.7:c.1211del	p.Pro404ArgfsTer25	p.P404Rfs*25	ENST00000288319	NM_182918.3	404	cCg/cg	10/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.35	2		384	865	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543605	9543605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1159424856	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	181	450	1	ENST00000353224.5:c.1549G>A	p.Asp517Asn	p.D517N	ENST00000353224	NM_177990.2	517	Gat/Aat	6/10	1	2	FACETS	0.932	0.858	1	0.932	0.858	1	CLONAL	1	TRUE	1	0.35	2		451	1110	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859859	151859859	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	146	412	2	ENST00000262189.6:c.10803del	p.Lys3604ArgfsTer26	p.K3604Rfs*26	ENST00000262189	NM_170606.2	3601	aaA/aa	43/59	1	2	FACETS	0.946	0.863	1	0.946	0.863	1	CLONAL	1	TRUE	1	0.35	2		414	882	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991721	72991721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370398587	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	183	302	0	ENST00000268489.5:c.2324C>T	p.Ala775Val	p.A775V	ENST00000268489	NM_006885.3	775	gCg/gTg	2/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.35	2		302	740	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11313909	11313909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	173	361	0	ENST00000361445.4:c.827G>A	p.Ser276Asn	p.S276N	ENST00000361445	NM_004958.3	276	aGc/aAc	6/58	0.354183285863444	2	FACETS	1	0.971	1			1	CLONAL	1	TRUE	NA	0.35	2		361	888	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261338	16261338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	134	336	0	ENST00000375759.3:c.8603C>T	p.Ser2868Phe	p.S2868F	ENST00000375759	NM_015001.2	2868	tCc/tTc	11/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.35	2		336	707	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204507392	204507392	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1331	109	526	0	ENST00000367182.3:c.467C>A	p.Pro156His	p.P156H	ENST00000367182	NM_001278516.1	156	cCc/cAc	7/11	1	2	FACETS	0.433	0.387	0.481	0.433	0.387	0.481	SUBCLONAL	1	TRUE	1	0.35	2		526	1440	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143441	30143441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326321652	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	43	143	0	ENST00000389048.3:c.85G>A	p.Ala29Thr	p.A29T	ENST00000389048	NM_004304.4	29	Gcg/Acg	1/29	0.354183285863444	2	FACETS	1	0.935	1			1	CLONAL	1	TRUE	NA	0.35	2		143	203	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437262	220437262	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	199	586	0	ENST00000243786.2:c.166A>G	p.Arg56Gly	p.R56G	ENST00000243786	NM_002191.3	56	Agg/Ggg	1/2	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.35	2		586	1058	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99823069	99823069	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	155	319	0	ENST00000280892.6:c.143T>G	p.Val48Gly	p.V48G	ENST00000280892	NM_001130678.1	48	gTt/gGt	2/7	1	2	FACETS	0.982	0.899	1	0.982	0.899	1	CLONAL	1	TRUE	1	0.35	2		319	902	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627773	187627773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200050180	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	216	466	0	ENST00000441802.2:c.3209G>A	p.Arg1070Gln	p.R1070Q	ENST00000441802	NM_005245.3	1070	cGa/cAa	2/27	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.35	2		466	1150	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86667976	86667976	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	212	473	0	ENST00000274376.6:c.1740A>C	p.Lys580Asn	p.K580N	ENST00000274376	NM_002890.2	580	aaA/aaC	13/25	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.35	2		473	1129	SUCCESS
APC	324	MSKCC	GRCh37	5	112173767	112173767	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	173	365	0	ENST00000257430.4:c.2476T>A	p.Leu826Met	p.L826M	ENST00000257430	NM_000038.5	826	Ttg/Atg	16/16	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.35	2		365	966	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139010	37139010	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	167	434	1	ENST00000373509.5:c.350T>C	p.Val117Ala	p.V117A	ENST00000373509	NM_002648.3	117	gTc/gCc	4/6	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.35	2		435	881	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517873	8517873	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	199	403	0	ENST00000356435.5:c.1518C>A	p.Asp506Glu	p.D506E	ENST00000356435		506	gaC/gaA	10/35	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.35	2		403	1013	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133761015	133761015	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	221	576	0	ENST00000318560.5:c.3338A>G	p.Asp1113Gly	p.D1113G	ENST00000318560	NM_005157.4	1113	gAc/gGc	11/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.35	2		576	1029	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94201025	94201025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780133	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	193	443	2	ENST00000323929.3:c.1052G>A	p.Arg351His	p.R351H	ENST00000323929	NM_005591.3	351	cGt/cAt	10/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.35	2		445	1052	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576213	88576213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	141	378	0	ENST00000360948.2:c.1460G>A	p.Gly487Asp	p.G487D	ENST00000360948	NM_001012338.2	487	gGc/gAc	13/19	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.35	2		378	750	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459927	99459927	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758609703	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	220	452	0	ENST00000268035.6:c.2023G>A	p.Asp675Asn	p.D675N	ENST00000268035	NM_000875.3	675	Gac/Aac	10/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.35	2		452	1074	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116168	67116168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1467426352	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	331	721	1	ENST00000412916.2:c.452G>A	p.Arg151His	p.R151H	ENST00000412916		151	cGc/cAc	5/6	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.35	2		722	1341	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828653	72828653	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777599986	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1267	353	709	0	ENST00000268489.5:c.7928G>A	p.Arg2643His	p.R2643H	ENST00000268489	NM_006885.3	2643	cGt/cAt	9/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.35	2		709	1620	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968309	15968309	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	229	544	0	ENST00000268712.3:c.4976C>A	p.Pro1659His	p.P1659H	ENST00000268712	NM_006311.3	1659	cCt/cAt	34/46	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.35	2		544	1189	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17124854	17124854	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767119281	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	169	402	0	ENST00000285071.4:c.868G>A	p.Ala290Thr	p.A290T	ENST00000285071	NM_144997.5	290	Gct/Act	8/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.35	2		402	805	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56811555	56811555	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1378390389	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	294	444	0	ENST00000337432.4:c.1103G>A	p.Arg368Gln	p.R368Q	ENST00000337432	NM_058216.2	368	cGg/cAg	9/9	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.35	2		444	1273	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736907	736907	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs986350587	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	128	479	0	ENST00000314574.4:c.1192C>T	p.Arg398Trp	p.R398W	ENST00000314574	NM_005433.3	398	Cgg/Tgg	10/12	1	2	FACETS	0.581	0.525	0.64	0.581	0.525	0.64	SUBCLONAL	1	TRUE	1	0.35	2		479	1259	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117225	7117225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374098153	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	82	448	0	ENST00000302850.5:c.3991C>T	p.Arg1331Cys	p.R1331C	ENST00000302850	NM_000208.2	1331	Cgt/Tgt	22/22	1	2	FACETS	0.513	0.451	0.58	0.513	0.451	0.58	SUBCLONAL	1	TRUE	1	0.35	2		448	913	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40743929	40743929	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	201	486	1	ENST00000392038.2:c.778G>T	p.Val260Phe	p.V260F	ENST00000392038	NM_001626.4	260	Gtc/Ttc	9/14	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.35	2		487	924	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775998497	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	115	400	0	ENST00000373198.4:c.3281C>T	p.Pro1094Leu	p.P1094L	ENST00000373198	NM_133170.3	1094	cCg/cTg	24/32	1	2	FACETS	0.904	0.815	0.998	0.904	0.815	0.998	CLONAL	1	TRUE	1	0.35	2		400	727	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24129428	24129428	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	167	413	0	ENST00000263121.7:c.72G>T	p.Glu24Asp	p.E24D	ENST00000263121	NM_003073.3	24	gaG/gaT	1/9	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.35	2		413	688	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572460	41572460	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	208	522	0	ENST00000263253.7:c.4989G>T	p.Gln1663His	p.Q1663H	ENST00000263253	NM_001429.3	1663	caG/caT	30/31	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.35	2		522	1073	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032551	47032551	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1198280152	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	182	541	1	ENST00000377604.3:c.457G>A	p.Gly153Ser	p.G153S	ENST00000377604	NM_001204468.1	153	Ggc/Agc	5/24	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.35	2		542	984	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958479	90958480	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs780235686	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	136	285	0	ENST00000265433.3:c.1958dup	p.Leu654AlafsTer5	p.L654Afs*5	ENST00000265433	NM_002485.4	653	aag/aaAg	13/16	1	2	FACETS	0.935	0.851	1	0.935	0.851	1	CLONAL	1	TRUE	1	0.35	2		285	831	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114271	115114272	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	148	312	0	ENST00000257566.3:c.945dup	p.Gln316ThrfsTer11	p.Q316Tfs*11	ENST00000257566	NM_016569.3	315	-/A	6/8	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.35	2		312	754	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627501	37627501	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	239	528	0	ENST00000447079.4:c.1421del	p.Asn474IlefsTer8	p.N474Ifs*8	ENST00000447079	NM_015083.1	472	gtA/gt	2/14	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.35	2		528	1267	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161939	47161939	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	132	321	3	ENST00000409792.3:c.4187del	p.Asn1396MetfsTer16	p.N1396Mfs*16	ENST00000409792	NM_014159.6	1396	aAt/at	3/21	1	2	FACETS	0.957	0.869	1	0.957	0.869	1	CLONAL	1	TRUE	1	0.35	2		324	788	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221239	1221240	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	231	499	0	ENST00000326873.7:c.762_763insA	p.Phe255IlefsTer11	p.F255Ifs*11	ENST00000326873	NM_000455.4	254	-/A	6/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.35	2		499	1135	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663299	227663301	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs753296153	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	118	296	0	ENST00000305123.5:c.154_156del	p.Lys52del	p.K52del	ENST00000305123	NM_005544.2	52	AAG/-	1/2	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.35	2		296	590	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383118	42383118	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	271	558	5	ENST00000221972.3:c.142del	p.Glu48LysfsTer44	p.E48Kfs*44	ENST00000221972	NM_021601.3	46	ctG/ct	2/5	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.35	2		563	1133	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506173	103506173	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	193	442	0	ENST00000355739.4:c.334del	p.Thr112HisfsTer3	p.T112Hfs*3	ENST00000355739	NM_000123.3	111	Aaa/aa	3/15	1	2	FACETS	0.925	0.854	0.999	0.925	0.854	0.999	CLONAL	1	TRUE	1	0.35	2		442	1192	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101402	27101402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	346	354	0	ENST00000324856.7:c.4689del	p.Met1564Ter	p.M1564*	ENST00000324856	NM_006015.4	1562	Ccc/cc	18/20	0.165582928589825	3	FACETS	0.887	0.844	0.929	1	0.996	1	INDETERMINATE	4	TRUE	1	0.280179435600372	3		354	794	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	191	550	3	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.957	0.894	1	1	0.995	1	CLONAL	3	TRUE	1	0.280179435600372	2		553	475	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	310	654	0	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	1	2	FACETS	0.972	0.922	1	1	0.997	1	CLONAL	3	TRUE	1	0.280179435600372	2		654	759	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	225	247	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.167675057104244	3	FACETS	0.952	0.897	1			1	INDETERMINATE	4	TRUE	NA	0.280179435600372	3		247	481	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99181109	99181109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757028003	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	253	353	0	ENST00000074304.5:c.2050G>A	p.Ala684Thr	p.A684T	ENST00000074304	NM_001134224.1	684	Gcc/Acc	20/26	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	3	TRUE	NA	0.280179435600372	2		353	549	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435160	56435161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755128667	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	162	240	0	ENST00000407977.2:c.1976dup	p.Pro660SerfsTer87	p.P660Sfs*87	ENST00000407977		659	ggt/ggGt	9/10	0.165582928589825	3	FACETS	0.858	0.793	0.925	1	0.985	1	INDETERMINATE	3	TRUE	1	0.280179435600372	3		240	512	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	61	548	1	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	0.280182112390085	1	FACETS	0.7	0.604	0.804	0.7	0.604	0.804	SUBCLONAL	1	TRUE	0	0.280179435600372	1		549	535	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024637	31024637	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	40	418	0	ENST00000375687.4:c.4127del	p.Gly1376ValfsTer74	p.G1376Vfs*74	ENST00000375687	NM_015338.5	1374	gtG/gt	13/13	0.26686507499721	4	FACETS	0.477	0.395	0.568			1	SUBCLONAL	1	TRUE	NA	0.280179435600372	4		418	767	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	198	345	9	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.871	0.813	0.93	1	0.995	1	CLONAL	3	TRUE	1	0.280179435600372	2		354	541	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	124	359	1	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	0.149726103971199	4	FACETS	0.954	0.866	1	0.954	0.866	1	INDETERMINATE	2	TRUE	2	0.280179435600372	4		360	594	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114817	108114817	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786204543	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	263	313	0	ENST00000278616.4:c.640del	p.Ser214ProfsTer16	p.S214Pfs*16	ENST00000278616	NM_000051.3	212	Ttt/tt	6/63	1	2	FACETS	1	0.979	1	1	0.996	1	CLONAL	3	TRUE	1	0.280179435600372	2		313	584	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	29	356	0	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.383	0.306	0.47	0.383	0.306	0.47	SUBCLONAL	1	TRUE	1	0.280179435600372	2		356	541	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223376	2223376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	380	466	0	ENST00000398665.3:c.3492del	p.Val1165CysfsTer8	p.V1165Cfs*8	ENST00000398665	NM_032482.2	1163	Ccc/cc	25/28	1	2	FACETS	1	0.977	1	1	0.997	1	CLONAL	3	TRUE	1	0.280179435600372	2		466	872	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900081	151900081	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	74	259	0	ENST00000262189.6:c.4030del	p.Ile1344Ter	p.I1344*	ENST00000262189	NM_170606.2	1344	Ata/ta	26/59	0.194274563893101	3	FACETS	0.89	0.779	1			1	CLONAL	1	TRUE	NA	0.280179435600372	3		259	677	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692980	89692980	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1060500126	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	246	198	0	ENST00000371953.3:c.464A>G	p.Tyr155Cys	p.Y155C	ENST00000371953	NM_000314.4	155	tAt/tGt	5/9	0.167675057104244	3	FACETS	1	0.977	1			1	INDETERMINATE	4	TRUE	NA	0.280179435600372	3		198	474	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	34	154	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.798	0.654	0.959	0.798	0.654	0.959	CLONAL	1	TRUE	1	0.280179435600372	2		154	304	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422384	47422384	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	33	287	0	ENST00000377045.4:c.23del	p.Pro8LeufsTer26	p.P8Lfs*26	ENST00000377045	NM_001654.4	6	ggC/gg	2/16	0.280182112390085	1	FACETS	0.317	0.257	0.384	0.317	0.257	0.384	SUBCLONAL	1	TRUE	0	0.280179435600372	1		287	640	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806181	1806181	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760502257	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	309	415	1	ENST00000260795.2:c.1206del	p.Lys403ArgfsTer29	p.K403Rfs*29	ENST00000260795		400	agC/ag	8/17	NA	2	FACETS	0.971	0.921	1			1	INDETERMINATE	3	TRUE	NA	0.280179435600372	2		416	757	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424734	47424734	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	241	508	0	ENST00000377045.4:c.547del	p.Gln183ArgfsTer109	p.Q183Rfs*109	ENST00000377045	NM_001654.4	181	aCc/ac	6/16	0.280182112390085	1	FACETS	1	0.959	1	1	0.995	1	CLONAL	2	TRUE	0	0.280179435600372	1		508	719	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	384	600	2	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	0.280182112390085	1	FACETS	0.907	0.866	0.949	1	0.997	1	CLONAL	3	TRUE	0	0.280179435600372	1		602	866	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389203	31389203	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs996239307	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	330	419	0	ENST00000328111.2:c.2116G>A	p.Asp706Asn	p.D706N	ENST00000328111	NM_006892.3	706	Gac/Aac	19/23	NA	2	FACETS	0.895	0.854	0.936			1	INDETERMINATE	4	TRUE	NA	0.280179435600372	2		419	658	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508995	106508995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs62001906	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	166	296	1	ENST00000359195.3:c.989C>T	p.Thr330Met	p.T330M	ENST00000359195	NM_002649.2	330	aCg/aTg	2/11	1	2	FACETS	0.88	0.816	0.945	1	0.994	1	CLONAL	3	TRUE	1	0.280179435600372	2		297	449	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	248	417	0	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	0.194274563893101	3	FACETS	1	0.987	1			1	CLONAL	3	TRUE	NA	0.280179435600372	3		417	582	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174404	11174404	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	34	411	0	ENST00000361445.4:c.7271A>C	p.Asp2424Ala	p.D2424A	ENST00000361445	NM_004958.3	2424	gAc/gCc	53/58	1	2	FACETS	0.368	0.3	0.446	0.368	0.3	0.446	SUBCLONAL	1	TRUE	1	0.280179435600372	2		411	659	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261053	16261053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	284	370	0	ENST00000375759.3:c.8318G>A	p.Cys2773Tyr	p.C2773Y	ENST00000375759	NM_015001.2	2773	tGc/tAc	11/15	0.165582928589825	3	FACETS	0.882	0.835	0.929	1	0.995	1	INDETERMINATE	4	TRUE	1	0.280179435600372	3		370	655	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739809	46739809	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	354	405	0	ENST00000371975.4:c.1611-1G>T		p.X537_splice	ENST00000371975	NM_003579.3	537			0.165582928589825	3	FACETS	0.977	0.933	1	1	0.996	1	INDETERMINATE	4	TRUE	1	0.280179435600372	3		405	737	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743772	46743772	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1185739428	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	387	395	0	ENST00000371975.4:c.2062C>T	p.Arg688Cys	p.R688C	ENST00000371975	NM_003579.3	688	Cgt/Tgt	18/18	0.165582928589825	3	FACETS	0.994	0.951	1	1	0.997	1	INDETERMINATE	4	TRUE	1	0.280179435600372	3		395	792	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506358	120506358	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	164	396	0	ENST00000256646.2:c.1754A>G	p.Gln585Arg	p.Q585R	ENST00000256646	NM_024408.3	585	cAg/cGg	11/34	1	2	FACETS	0.79	0.727	0.856	1	0.99	1	SUBCLONAL	2	TRUE	1	0.280179435600372	2		396	741	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849069	156849069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750168062	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	273	466	0	ENST00000524377.1:c.1961G>A	p.Arg654His	p.R654H	ENST00000524377	NM_002529.3	654	cGc/cAc	15/17	0.280179435600372	5	FACETS	1	0.957	1	0.766	0.721	0.813	CLONAL	3	TRUE	1	0.280179435600372	5		466	903	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193202124	193202124	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	40	287	0	ENST00000367435.3:c.1156T>C	p.Phe386Leu	p.F386L	ENST00000367435	NM_024529.4	386	Ttt/Ctt	14/17	0.280179435600372	5	FACETS	0.625	0.518	0.744	0.156	0.129	0.186	SUBCLONAL	1	TRUE	1	0.280179435600372	5		287	649	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206943190	206943190	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	91	314	0	ENST00000423557.1:c.428A>C	p.Lys143Thr	p.K143T	ENST00000423557	NM_000572.2	143	aAg/aCg	4/5	0.280179435600372	5	FACETS	0.986	0.874	1	0.246	0.218	0.277	CLONAL	1	TRUE	1	0.280179435600372	5		314	936	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470995	25470995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	55	429	0	ENST00000264709.3:c.766C>T	p.Pro256Ser	p.P256S	ENST00000264709	NM_175629.2	256	Ccc/Tcc	7/23	1	2	FACETS	0.473	0.403	0.55	0.473	0.403	0.55	SUBCLONAL	1	TRUE	1	0.280179435600372	2		429	830	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026204	48026204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750440	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	315	388	0	ENST00000234420.5:c.1082G>A	p.Arg361His	p.R361H	ENST00000234420	NM_000179.2	361	cGc/cAc	4/10	1	2	FACETS	1	0.985	1	1	0.997	1	CLONAL	3	TRUE	1	0.280179435600372	2		388	689	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145432	61145432	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	32	289	0	ENST00000295025.8:c.640+2T>C		p.X214_splice	ENST00000295025	NM_002908.2	214			1	2	FACETS	0.487	0.395	0.591	0.487	0.395	0.591	SUBCLONAL	1	TRUE	1	0.280179435600372	2		289	469	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61720166	61720166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1194061733	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	56	329	0	ENST00000401558.2:c.1268G>A	p.Arg423Gln	p.R423Q	ENST00000401558	NM_003400.3	423	cGa/cAa	13/25	1	2	FACETS	0.577	0.493	0.668	0.577	0.493	0.668	SUBCLONAL	1	TRUE	1	0.280179435600372	2		329	693	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99169316	99169316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1320693278	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	279	509	0	ENST00000074304.5:c.1246G>A	p.Ala416Thr	p.A416T	ENST00000074304	NM_001134224.1	416	Gcc/Acc	15/26	NA	2	FACETS	0.968	0.915	1			1	INDETERMINATE	3	TRUE	NA	0.280179435600372	2		509	686	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158636917	158636917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	369	476	2	ENST00000263640.3:c.263G>A	p.Gly88Asp	p.G88D	ENST00000263640	NM_001105.4	88	gGc/gAc	4/11	1	2	FACETS	1	0.989	1	1	0.997	1	CLONAL	3	TRUE	1	0.280179435600372	2		478	793	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718809	190718809	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1433575885	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	28	185	0	ENST00000441310.2:c.966+1G>A		p.X322_splice	ENST00000441310	NM_000534.4	322			1	2	FACETS	0.568	0.454	0.697	0.568	0.454	0.697	SUBCLONAL	1	TRUE	1	0.280179435600372	2		185	352	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662442	227662442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	229	255	0	ENST00000305123.5:c.1013G>A	p.Arg338His	p.R338H	ENST00000305123	NM_005544.2	338	cGc/cAc	1/2	1	2	FACETS	0.877	0.828	0.926	1	0.996	1	CLONAL	4	TRUE	1	0.280179435600372	2		255	466	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067255	37067255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750361	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	43	386	1	ENST00000231790.2:c.1166G>A	p.Arg389Gln	p.R389Q	ENST00000231790	NM_000249.3	389	cGg/cAg	12/19	1	2	FACETS	0.447	0.373	0.53	0.447	0.373	0.53	SUBCLONAL	1	TRUE	1	0.280179435600372	2		387	686	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090477	37090477	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs781780309	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	32	324	0	ENST00000231790.2:c.2072T>A	p.Ile691Lys	p.I691K	ENST00000231790	NM_000249.3	691	aTa/aAa	18/19	1	2	FACETS	0.435	0.352	0.529	0.435	0.352	0.529	SUBCLONAL	1	TRUE	1	0.280179435600372	2		324	525	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182721	38182721	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	377	363	0	ENST00000396334.3:c.874C>A	p.Pro292Thr	p.P292T	ENST00000396334	NM_002468.4	292	Ccc/Acc	5/5	0.165582928589825	3	FACETS	0.911	0.87	0.953	1	0.996	1	INDETERMINATE	4	TRUE	1	0.280179435600372	3		363	842	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226846	142226846	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	237	382	0	ENST00000350721.4:c.4958G>A	p.Arg1653Gln	p.R1653Q	ENST00000350721	NM_001184.3	1653	cGa/cAa	28/47	1	2	FACETS	1	0.943	1	1	0.996	1	CLONAL	3	TRUE	1	0.280179435600372	2		382	563	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225060	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	309	553	1	ENST00000263967.3:c.311C>T	p.Pro104Leu	p.P104L	ENST00000263967	NM_006218.2	104	cCa/cTa	2/21	1	2	FACETS	1	0.949	1	1	0.997	1	CLONAL	3	TRUE	1	0.280179435600372	2		554	735	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161351	185161351	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	47	453	0	ENST00000265026.3:c.778T>C	p.Ser260Pro	p.S260P	ENST00000265026	NM_004721.4	260	Tcc/Ccc	4/14	1	2	FACETS	0.517	0.435	0.607	0.517	0.435	0.607	SUBCLONAL	1	TRUE	1	0.280179435600372	2		453	649	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564477	55564477	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	63	326	0	ENST00000288135.5:c.365G>A	p.Arg122His	p.R122H	ENST00000288135	NM_000222.2	122	cGc/cAc	3/21	0.280182112390085	1	FACETS	0.927	0.805	1	0.927	0.805	1	CLONAL	1	TRUE	0	0.280179435600372	1		326	417	SUCCESS
APC	324	MSKCC	GRCh37	5	112177950	112177950	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	30	342	2	ENST00000257430.4:c.6659A>G	p.Asn2220Ser	p.N2220S	ENST00000257430	NM_000038.5	2220	aAc/aGc	16/16	1	2	FACETS	0.374	0.3	0.458	0.374	0.3	0.458	SUBCLONAL	1	TRUE	1	0.280179435600372	2		344	573	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915666	131915666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	39	390	0	ENST00000265335.6:c.664G>A	p.Glu222Lys	p.E222K	ENST00000265335		222	Gag/Aag	5/25	1	2	FACETS	0.44	0.364	0.525	0.44	0.364	0.525	SUBCLONAL	1	TRUE	1	0.280179435600372	2		390	633	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520328	176520328	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200070761	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	251	379	0	ENST00000292408.4:c.1247G>A	p.Arg416Gln	p.R416Q	ENST00000292408	NM_213647.1	416	cGa/cAa	9/18	1	2	FACETS	1	0.97	1	1	0.996	1	CLONAL	3	TRUE	1	0.280179435600372	2		379	573	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687118	176687118	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	51	462	0	ENST00000439151.2:c.5095T>C	p.Cys1699Arg	p.C1699R	ENST00000439151	NM_022455.4	1699	Tgc/Cgc	14/23	0.280182112390085	3	FACETS	0.499	0.423	0.583			1	SUBCLONAL	1	TRUE	NA	0.280179435600372	3		462	832	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055910	180055910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	32	366	2	ENST00000261937.6:c.1075G>A	p.Ala359Thr	p.A359T	ENST00000261937	NM_182925.4	359	Gca/Aca	8/30	0.280182112390085	1	FACETS	0.409	0.332	0.497	0.409	0.332	0.497	SUBCLONAL	1	TRUE	0	0.280179435600372	1		368	480	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099862	157099862	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1344255932	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	299	360	2	ENST00000346085.5:c.799C>T	p.His267Tyr	p.H267Y	ENST00000346085	NM_020732.3	267	Cac/Tac	1/20	0.243901234122829	3	FACETS	1	0.986	1			1	CLONAL	3	TRUE	NA	0.280179435600372	3		362	725	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843227	128843227	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	211	379	0	ENST00000249373.3:c.334C>A	p.Leu112Ile	p.L112I	ENST00000249373	NM_005631.4	112	Ctc/Atc	2/12	1	2	FACETS	1	0.944	1	1	0.995	1	CLONAL	3	TRUE	1	0.280179435600372	2		379	499	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845147	128845147	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	41	433	2	ENST00000249373.3:c.641G>A	p.Gly214Asp	p.G214D	ENST00000249373	NM_005631.4	214	gGc/gAc	3/12	1	2	FACETS	0.416	0.345	0.495	0.416	0.345	0.495	SUBCLONAL	1	TRUE	1	0.280179435600372	2		435	704	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624519	93624519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	39	341	0	ENST00000375746.1:c.610G>A	p.Ala204Thr	p.A204T	ENST00000375746	NM_001174167.1	204	Gcc/Acc	4/14	1	2	FACETS	0.462	0.382	0.551	0.462	0.382	0.551	SUBCLONAL	1	TRUE	1	0.280179435600372	2		341	603	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135777991	135777991	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	25	306	0	ENST00000298552.3:c.2391+1G>A		p.X797_splice	ENST00000298552	NM_001162426.1	797			1	2	FACETS	0.404	0.317	0.503	0.404	0.317	0.503	SUBCLONAL	1	TRUE	1	0.280179435600372	2		306	442	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396844	139396844	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	267	352	1	ENST00000277541.6:c.5264T>C	p.Leu1755Pro	p.L1755P	ENST00000277541	NM_017617.3	1755	cTg/cCg	28/34	1	2	FACETS	0.968	0.915	1	1	0.996	1	CLONAL	3	TRUE	1	0.280179435600372	2		353	656	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161460	2161460	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	278	473	0	ENST00000434045.2:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000434045	NM_001127598.1	23	Caa/Taa	2/5	0.280179435600372	1	FACETS	0.886	0.839	0.934	1	0.996	1	CLONAL	3	TRUE	0	0.280179435600372	1		473	642	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8246170	8246170	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs770015881	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	33	425	0	ENST00000335790.3:c.464T>C	p.Val155Ala	p.V155A	ENST00000335790	NM_002315.2	155	gTt/gCt	4/4	0.280179435600372	1	FACETS	0.317	0.258	0.385	0.317	0.258	0.385	SUBCLONAL	1	TRUE	0	0.280179435600372	1		425	638	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129139	64129139	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	35	367	0	ENST00000334205.4:c.677T>C	p.Ile226Thr	p.I226T	ENST00000334205	NM_003942.2	226	aTc/aCc	7/17	0.280182112390085	3	FACETS	0.434	0.354	0.523			1	SUBCLONAL	1	TRUE	NA	0.280179435600372	3		367	657	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962586	100962586	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	248	420	0	ENST00000325455.5:c.1811C>A	p.Ala604Asp	p.A604D	ENST00000325455	NM_001202474.3	604	gCt/gAt	3/8	1	2	FACETS	1	0.956	1	1	0.996	1	CLONAL	3	TRUE	1	0.280179435600372	2		420	581	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236204	108236204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1047129530	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	73	384	1	ENST00000278616.4:c.9140G>A	p.Arg3047Gln	p.R3047Q	ENST00000278616	NM_000051.3	3047	cGa/cAa	63/63	1	2	FACETS	0.846	0.74	0.96	0.846	0.74	0.96	CLONAL	1	TRUE	1	0.280179435600372	2		385	616	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	418973	418973	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	38	414	0	ENST00000399788.2:c.3374T>C	p.Met1125Thr	p.M1125T	ENST00000399788	NM_001042603.1	1125	aTg/aCg	22/28	1	2	FACETS	0.4	0.33	0.479	0.4	0.33	0.479	SUBCLONAL	1	TRUE	1	0.280179435600372	2		414	678	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435214	18435214	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	232	383	0	ENST00000266497.5:c.199A>G	p.Thr67Ala	p.T67A	ENST00000266497		67	Act/Gct	1/31	0.280182112390085	1	FACETS	0.983	0.928	1	1	0.996	1	CLONAL	3	TRUE	0	0.280179435600372	1		383	483	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945033	31945033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	37	484	1	ENST00000340398.3:c.68C>T	p.Thr23Met	p.T23M	ENST00000340398	NM_001013699.2	23	aCg/aTg	1/1	0.280182112390085	1	FACETS	0.327	0.269	0.393	0.327	0.269	0.393	SUBCLONAL	1	TRUE	0	0.280179435600372	1		485	694	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557537	21557537	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	38	498	2	ENST00000382592.4:c.2308T>C	p.Phe770Leu	p.F770L	ENST00000382592	NM_014572.2	770	Ttc/Ctc	5/8	NA	2	FACETS	0.383	0.316	0.459			1	INDETERMINATE	1	TRUE	NA	0.280179435600372	2		500	708	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562748	21562748	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1225626637	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	18	194	1	ENST00000382592.4:c.1171C>T	p.Arg391Cys	p.R391C	ENST00000382592	NM_014572.2	391	Cgc/Tgc	4/8	NA	2	FACETS	0.445	0.335	0.575			1	INDETERMINATE	1	TRUE	NA	0.280179435600372	2		195	289	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959402	26959402	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	192	408	0	ENST00000381527.3:c.569T>C	p.Leu190Ser	p.L190S	ENST00000381527	NM_001260.1	190	tTg/tCg	6/13	0.280182112390085	0	FACETS	0.753	0.704	0.801			1	SUBCLONAL	3	TRUE	0	0.280179435600372	0		408	437	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28886236	28886236	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	172	288	0	ENST00000282397.4:c.3387-1G>A		p.X1129_splice	ENST00000282397	NM_002019.4	1129			0.280182112390085	0	FACETS	1	0.953	1			1	CLONAL	2	TRUE	0	0.280179435600372	0		288	429	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590950	95590950	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	259	204	1	ENST00000393063.1:c.959A>C	p.Lys320Thr	p.K320T	ENST00000393063	NM_030621.3	320	aAa/aCa	9/28	1	2	FACETS	1	0.987	1	1	0.996	1	CLONAL	3	TRUE	1	0.280179435600372	2		205	543	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95598915	95598915	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	287	350	0	ENST00000393063.1:c.244T>C	p.Ser82Pro	p.S82P	ENST00000393063	NM_030621.3	82	Tcc/Ccc	4/28	1	2	FACETS	0.962	0.91	1	1	0.996	1	CLONAL	3	TRUE	1	0.280179435600372	2		350	710	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134268	2134268	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	337	456	0	ENST00000219476.3:c.4045G>T	p.Ala1349Ser	p.A1349S	ENST00000219476	NM_000548.3	1349	Gcg/Tcg	34/42	0.165582928589825	3	FACETS	1	0.986	1	1	0.996	1	INDETERMINATE	3	TRUE	1	0.280179435600372	3		456	834	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670755	67670755	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	280	350	0	ENST00000264010.4:c.1999+1G>A		p.X667_splice	ENST00000264010	NM_006565.3	667			1	2	FACETS	0.975	0.923	1	1	0.996	1	CLONAL	3	TRUE	1	0.280179435600372	2		350	683	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821209	72821209	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779473080	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	407	561	1	ENST00000268489.5:c.10966C>T	p.Pro3656Ser	p.P3656S	ENST00000268489	NM_006885.3	3656	Cca/Tca	10/10	1	2	FACETS	1	0.991	1	1	0.997	1	CLONAL	3	TRUE	1	0.280179435600372	2		562	854	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829731	72829731	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs869312913	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	430	598	0	ENST00000268489.5:c.6850C>T	p.Arg2284Ter	p.R2284*	ENST00000268489	NM_006885.3	2284	Cga/Tga	9/10	1	2	FACETS	1	0.993	1	1	0.998	1	CLONAL	3	TRUE	1	0.280179435600372	2		598	887	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993848	72993848	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778500476	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	51	432	0	ENST00000268489.5:c.197C>T	p.Ala66Val	p.A66V	ENST00000268489	NM_006885.3	66	gCg/gTg	2/10	1	2	FACETS	0.633	0.538	0.738	0.633	0.538	0.738	SUBCLONAL	1	TRUE	1	0.280179435600372	2		432	575	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347066	89347066	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	361	540	0	ENST00000301030.4:c.5884C>A	p.Leu1962Met	p.L1962M	ENST00000301030	NM_001256183.1	1962	Ctg/Atg	9/13	NA	2	FACETS	1	0.959	1			1	INDETERMINATE	3	TRUE	NA	0.280179435600372	2		540	853	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8109923	8109923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	107	355	0	ENST00000585124.1:c.572G>A	p.Cys191Tyr	p.C191Y	ENST00000585124	NM_004217.3	191	tGc/tAc	7/9	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.280179435600372	2		355	759	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989690	15989690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	275	451	0	ENST00000268712.3:c.3083G>A	p.Arg1028Gln	p.R1028Q	ENST00000268712	NM_006311.3	1028	cGa/cAa	23/46	1	2	FACETS	0.982	0.929	1	1	0.996	1	CLONAL	3	TRUE	1	0.280179435600372	2		451	666	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17125921	17125921	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769250170	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	141	400	0	ENST00000285071.4:c.673G>A	p.Ala225Thr	p.A225T	ENST00000285071	NM_144997.5	225	Gcc/Acc	7/14	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.280179435600372	2		400	719	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38504571	38504571	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1410890791	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	70	395	0	ENST00000254066.5:c.182T>C	p.Ile61Thr	p.I61T	ENST00000254066	NM_000964.3	61	aTt/aCt	3/9	0.271773460372235	4	FACETS	0.628	0.546	0.718			1	SUBCLONAL	1	TRUE	NA	0.280179435600372	4		395	1018	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821931	59821931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764803896	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	206	359	2	ENST00000259008.2:c.2119C>T	p.Arg707Cys	p.R707C	ENST00000259008	NM_032043.2	707	Cgt/Tgt	15/20	0.280182112390085	1	FACETS	0.869	0.815	0.924	1	0.995	1	CLONAL	3	TRUE	0	0.280179435600372	1		361	485	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63545677	63545677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151247101	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	297	512	1	ENST00000307078.5:c.917C>T	p.Ala306Val	p.A306V	ENST00000307078	NM_004655.3	306	gCg/gTg	3/11	1	2	FACETS	0.914	0.865	0.964	1	0.996	1	CLONAL	3	TRUE	1	0.280179435600372	2		513	773	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681725	78681725	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	303	420	1	ENST00000306801.3:c.433C>T	p.Arg145Ter	p.R145*	ENST00000306801	NM_020761.2	145	Cga/Tga	4/34	1	2	FACETS	1	0.952	1	1	0.997	1	CLONAL	3	TRUE	1	0.280179435600372	2		421	718	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78831689	78831689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755927307	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	279	361	1	ENST00000306801.3:c.1498G>A	p.Ala500Thr	p.A500T	ENST00000306801	NM_020761.2	500	Gca/Aca	13/34	1	2	FACETS	1	0.977	1	1	0.996	1	CLONAL	3	TRUE	1	0.280179435600372	2		362	629	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897330	78897330	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	31	391	1	ENST00000306801.3:c.2665A>G	p.Thr889Ala	p.T889A	ENST00000306801	NM_020761.2	889	Acc/Gcc	23/34	1	2	FACETS	0.383	0.309	0.467	0.383	0.309	0.467	SUBCLONAL	1	TRUE	1	0.280179435600372	2		392	578	SUCCESS
YES1	7525	MSKCC	GRCh37	18	751768	751768	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	177	301	0	ENST00000314574.4:c.308A>G	p.Glu103Gly	p.E103G	ENST00000314574	NM_005433.3	103	gAa/gGa	3/12	1	2	FACETS	0.996	0.928	1	1	0.994	1	CLONAL	3	TRUE	1	0.280179435600372	2		301	423	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222314	2222314	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	49	377	0	ENST00000398665.3:c.3146T>C	p.Ile1049Thr	p.I1049T	ENST00000398665	NM_032482.2	1049	aTc/aCc	24/28	1	2	FACETS	0.51	0.431	0.597	0.51	0.431	0.597	SUBCLONAL	1	TRUE	1	0.280179435600372	2		377	686	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5246056	5246056	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	26	218	0	ENST00000357368.4:c.719T>C	p.Val240Ala	p.V240A	ENST00000357368	NM_002850.3	240	gTc/gCc	10/38	1	2	FACETS	0.458	0.362	0.568	0.458	0.362	0.568	SUBCLONAL	1	TRUE	1	0.280179435600372	2		218	405	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295220	15295220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568357671	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	327	494	0	ENST00000263388.2:c.2452G>A	p.Ala818Thr	p.A818T	ENST00000263388	NM_000435.2	818	Gca/Aca	16/33	1	2	FACETS	1	0.989	1	1	0.997	1	CLONAL	3	TRUE	1	0.280179435600372	2		494	694	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349606	15349606	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	239	313	0	ENST00000263377.2:c.3968A>C	p.Gln1323Pro	p.Q1323P	ENST00000263377	NM_058243.2	1323	cAg/cCg	19/20	1	2	FACETS	0.986	0.928	1	1	0.996	1	CLONAL	3	TRUE	1	0.280179435600372	2		313	577	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278073	18278073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	359	456	1	ENST00000222254.8:c.1693C>T	p.Pro565Ser	p.P565S	ENST00000222254	NM_005027.3	565	Ccg/Tcg	13/16	1	2	FACETS	1	0.967	1	1	0.997	1	CLONAL	3	TRUE	1	0.280179435600372	2		457	838	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731596	47731596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	64	81	1	ENST00000449228.1:c.196G>A	p.Ala66Thr	p.A66T	ENST00000449228	NM_001127240.2	66	Gcc/Acc	2/4	0.194274563893101	3	FACETS	0.911	0.796	1			1	CLONAL	2	TRUE	NA	0.280179435600372	3		82	286	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905324	50905324	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs140707092	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	334	575	1	ENST00000440232.2:c.532G>T	p.Gly178Trp	p.G178W	ENST00000440232	NM_002691.3	178	Ggg/Tgg	5/27	0.280182112390085	1	FACETS	0.957	0.912	1	1	0.997	1	CLONAL	3	TRUE	0	0.280179435600372	1		576	714	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910426	50910426	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368738479	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	39	513	0	ENST00000440232.2:c.1681C>T	p.Arg561Trp	p.R561W	ENST00000440232	NM_002691.3	561	Cgg/Tgg	13/27	0.280182112390085	1	FACETS	0.378	0.313	0.452	0.378	0.313	0.452	SUBCLONAL	1	TRUE	0	0.280179435600372	1		513	633	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714631	52714631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	239	367	1	ENST00000322088.6:c.389C>T	p.Pro130Leu	p.P130L	ENST00000322088	NM_014225.5	130	cCg/cTg	4/15	0.280182112390085	1	FACETS	0.923	0.87	0.975	1	0.996	1	CLONAL	3	TRUE	0	0.280179435600372	1		368	530	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741458	39741458	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1346009286	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	321	418	1	ENST00000361337.2:c.1345C>T	p.Arg449Trp	p.R449W	ENST00000361337	NM_003286.2	449	Cgg/Tgg	14/21	NA	2	FACETS	1	0.972	1			1	INDETERMINATE	3	TRUE	NA	0.280179435600372	2		419	739	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945234	54945234	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	84	284	0	ENST00000312783.6:c.1192T>G	p.Ser398Ala	p.S398A	ENST00000312783	NM_198436.1	398	Tca/Gca	10/10	NA	2	FACETS	1	0.938	1			1	INDETERMINATE	1	TRUE	NA	0.280179435600372	2		284	550	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29120988	29120988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786203483	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	287	390	0	ENST00000328354.6:c.569C>T	p.Ala190Val	p.A190V	ENST00000328354	NM_007194.3	190	gCa/gTa	4/15	1	2	FACETS	0.991	0.938	1	1	0.996	1	CLONAL	3	TRUE	1	0.280179435600372	2		390	689	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223571	53223571	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	149	283	0	ENST00000375401.3:c.3788T>C	p.Val1263Ala	p.V1263A	ENST00000375401	NM_004187.3	1263	gTa/gCa	23/26	0.280182112390085	1	FACETS	0.974	0.906	1	1	0.994	1	CLONAL	3	TRUE	0	0.280179435600372	1		283	313	SUCCESS
AR	367	MSKCC	GRCh37	X	66937326	66937326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137852593	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	139	460	0	ENST00000374690.3:c.2180G>A	p.Arg727His	p.R727H	ENST00000374690	NM_000044.3	727	cGc/cAc	5/8	0.280182112390085	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.280179435600372	1		460	671	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338675	70338675	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	245	423	0	ENST00000374080.3:c.71T>C	p.Val24Ala	p.V24A	ENST00000374080		24	gTt/gCt	1/45	0.280182112390085	1	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	0	0.280179435600372	1		423	654	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429260	78429260	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	72	284	0	ENST00000370768.2:c.1182del	p.Gly395GlufsTer5	p.G395Efs*5	ENST00000370768	NM_003902.3	394	aaA/aa	13/20	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.280179435600372	2		284	474	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759623	133759623	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	261	622	0	ENST00000318560.5:c.1950del	p.Leu651TrpfsTer43	p.L651Wfs*43	ENST00000318560	NM_005157.4	649	aCc/ac	11/11	1	2	FACETS	1	0.971	1	1	0.996	1	CLONAL	3	TRUE	1	0.280179435600372	2		622	596	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774681	73774682	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	56	54	0	ENST00000254810.4:c.405_406del	p.Arg135SerfsTer12	p.R135Sfs*12	ENST00000254810	NM_005324.3	135	agAGct/agct	4/4	1	2	FACETS	1	0.894	1	1	0.979	1	CLONAL	2	TRUE	1	0.280179435600372	2		54	194	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089746	27089755	+	frameshift_variant	Frame_Shift_Del	DEL	TGCATGTTGC	TGCATGTTGC	-	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	133	195	0	ENST00000324856.7:c.2705_2714del	p.His902ProfsTer14	p.H902Pfs*14	ENST00000324856	NM_006015.4	901	aTGCATGTTGCt/at	8/20	0.165582928589825	3	FACETS	0.916	0.84	0.993	1	0.985	1	INDETERMINATE	3	TRUE	1	0.280179435600372	3		195	394	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440431	49440431	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1240601136	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	105	358	0	ENST00000301067.7:c.4379del	p.Pro1460HisfsTer46	p.P1460Hfs*46	ENST00000301067	NM_003482.3	1460	cCa/ca	15/54	0.149726103971199	4	FACETS	1	0.972	1	0.624	0.559	0.693	INDETERMINATE	1	TRUE	2	0.280179435600372	4		358	769	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436227	110436227	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1394911868	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	13	192	0	ENST00000375856.3:c.2174del	p.Gly725AlafsTer102	p.G725Afs*102	ENST00000375856	NM_003749.2	725	gGc/gc	1/2	1	2	FACETS	0.37	0.263	0.5	0.37	0.263	0.5	SUBCLONAL	1	TRUE	1	0.280179435600372	2		192	251	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	296	368	1	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.989	0.937	1	1	0.996	1	CLONAL	3	TRUE	1	0.280179435600372	2		369	712	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134568	2134569	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs397514939	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	47	379	1	ENST00000219476.3:c.4351dup	p.Arg1451ProfsTer73	p.R1451Pfs*73	ENST00000219476	NM_000548.3	1449	tcc/tCcc	34/42	0.165582928589825	3	FACETS	0.529	0.445	0.622	0.265	0.222	0.311	INDETERMINATE	1	TRUE	1	0.280179435600372	3		380	723	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972356	32972356	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	57	284	0	ENST00000380152.3:c.9709del	p.Arg3237GlyfsTer12	p.R3237Gfs*12	ENST00000380152		3236	Aaa/aa	27/27	1	2	FACETS	0.817	0.702	0.943	0.817	0.702	0.943	CLONAL	1	TRUE	1	0.280179435600372	2		284	498	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435986	56435986	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	214	282	0	ENST00000407977.2:c.1151del	p.Gly384AlafsTer35	p.G384Afs*35	ENST00000407977		384	gGc/gc	9/10	0.165582928589825	3	FACETS	0.981	0.923	1	1	0.995	1	INDETERMINATE	4	TRUE	1	0.280179435600372	3		282	444	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061080	38061080	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	12	97	0	ENST00000250448.2:c.909del	p.Ser304AlafsTer17	p.S304Afs*17	ENST00000250448	NM_004496.3	303	ccC/cc	2/2	1	2	FACETS	0.513	0.361	0.698	0.513	0.361	0.698	SUBCLONAL	1	TRUE	1	0.280179435600372	2		97	167	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294530	1294532	+	missense_variant	Missense_Mutation	TNP	CGC	CGC	TGT	novel	NA	P-0005564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	43	191	0	ENST00000310581.5:c.469_471delinsACA	p.Ala157Thr	p.A157T	ENST00000310581	NM_198253.2	157	GCG/ACA	2/16	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.280179435600372	2		191	242	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939673	76939674	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	400	634	0	ENST00000373344.5:c.1074dup	p.Leu359ThrfsTer3	p.L359Tfs*3	ENST00000373344	NM_000489.3	358	-/A	9/35	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.618017595873063	2		634	1252	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0005635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	251	419	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.618017595873063	2		420	695	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0005635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	438	354	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.618017595873063	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.618017595873063	2		354	606	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469958	25469958	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1490273086	NA	P-0005635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	259	471	0	ENST00000264709.3:c.1084C>T	p.Gln362Ter	p.Q362*	ENST00000264709	NM_175629.2	362	Cag/Tag	9/23	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.618017595873063	2		471	827	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1255443	1255443	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763381198	NA	P-0005635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	263	535	2	ENST00000310581.5:c.3116C>T	p.Thr1039Met	p.T1039M	ENST00000310581	NM_198253.2	1039	aCg/aTg	14/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.618017595873063	2		537	810	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729312	41729312	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	398	771	0	ENST00000242208.4:c.1217A>G	p.Asp406Gly	p.D406G	ENST00000242208	NM_002192.2	406	gAt/gGt	3/3	1	2	FACETS	0.956	0.909	1	0.956	0.909	1	CLONAL	1	TRUE	1	0.618017595873063	2		771	1347	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0005715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	143	197	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	0.496866630761358	2	FACETS	0.776	0.718	0.836	0.776	0.718	0.836	SUBCLONAL	2	TRUE	0	0.530967346468192	2		197	347	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100727	8100728	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs771019738	NA	P-0005715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	88	522	0	ENST00000346208.3:c.708dup	p.Ser237GlnfsTer66	p.S237Qfs*66	ENST00000346208		234	ttc/ttCc	3/6	0.530967346468192	4	FACETS	0.508	0.449	0.572	0.169	0.149	0.191	SUBCLONAL	1	TRUE	1	0.530967346468192	4		522	999	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589750	55589750	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	114	624	1	ENST00000288135.5:c.1232C>A	p.Thr411Lys	p.T411K	ENST00000288135	NM_000222.2	411	aCa/aAa	8/21	1	2	FACETS	0.813	0.735	0.895	0.813	0.735	0.895	CLONAL	1	TRUE	1	0.530967346468192	2		625	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577144	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	374	721	0	ENST00000269305.4:c.794T>G	p.Leu265Arg	p.L265R	ENST00000269305	NM_001126112.2	265	cTg/cGg	8/11	0.446035320637377	2	FACETS	0.947	0.906	0.988	0.947	0.906	0.988	CLONAL	2	TRUE	0	0.530967346468192	2		721	744	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869539	102869540	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0005715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	102	565	0	ENST00000307046.8:c.101dup	p.Tyr34Ter	p.Y34*	ENST00000307046	NM_001111285.1	34	tac/taAc	2/4	0.455992066399727	3	FACETS	0.705	0.631	0.783	0.352	0.315	0.392	SUBCLONAL	1	TRUE	1	0.530967346468192	3		565	690	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577151	7577156	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	TACCAC	TACCAC	-	novel	NA	P-0005715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	331	660	0	ENST00000269305.4:c.783-1_787del		p.X261_splice	ENST00000269305	NM_001126112.2	261		8/11	0.446035320637377	2	FACETS	0.962	0.918	1	0.962	0.918	1	CLONAL	2	TRUE	0	0.530967346468192	2		660	648	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207064	1207065	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1131690917	NA	P-0005721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	91	710	0	ENST00000326873.7:c.157dup	p.Asp53GlyfsTer110	p.D53Gfs*110	ENST00000326873	NM_000455.4	51	atg/atGg	1/10	0.3	3	FACETS	1	0.92	1			1	CLONAL	2	TRUE	NA	0.1	3		710	912	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733545	85733545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	82	763	0	ENST00000370580.1:c.467C>T	p.Pro156Leu	p.P156L	ENST00000370580	NM_003921.4	156	cCa/cTa	3/3	1	2	FACETS	0.848	0.746	0.958	1	0.98	1	CLONAL	2	TRUE	1	0.1	2		763	967	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662350	227662350	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	47	386	0	ENST00000305123.5:c.1105C>T	p.Leu369Phe	p.L369F	ENST00000305123	NM_005544.2	369	Ctc/Ttc	1/2	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.1	2		386	771	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244349	46244349	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	43	459	0	ENST00000334344.6:c.2443G>T	p.Val815Phe	p.V815F	ENST00000334344	NM_152641.2	815	Gtt/Ttt	15/21	1	2	FACETS	0.814	0.681	0.962	1	0.962	1	CLONAL	2	TRUE	1	0.1	2		459	528	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223195	2223195	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	57	422	0	ENST00000326181.6:c.807C>G	p.Ile269Met	p.I269M	ENST00000326181	NM_032271.2	269	atC/atG	10/21	0.210332404314982	3	FACETS	1	0.957	1	0.665	0.569	0.771	CLONAL	1	TRUE	1	0.1	3		422	900	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916124	9916124	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376029542	NA	P-0005721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	23	375	0	ENST00000330684.3:c.2165C>T	p.Thr722Met	p.T722M	ENST00000330684	NM_001134407.1	722	aCg/aTg	10/13	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.1	2		375	405	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271527	15271527	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	69	578	0	ENST00000263388.2:c.6912G>T	p.Gln2304His	p.Q2304H	ENST00000263388	NM_000435.2	2304	caG/caT	33/33	0.136060969884247	3	FACETS	0.88	0.765	1	0.88	0.765	1	CLONAL	2	TRUE	1	0.1	3		578	823	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144879	47144879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	94	740	0	ENST00000409792.3:c.4874G>A	p.Arg1625His	p.R1625H	ENST00000409792	NM_014159.6	1625	cGt/cAt	7/21	0.367177891927827	1	FACETS	0.824	0.736	0.918	0.824	0.736	0.918	CLONAL	1	TRUE	0	0.367177891927827	1		740	507	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370788	225370788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760276064	NA	P-0005750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	104	855	5	ENST00000264414.4:c.1091G>A	p.Arg364His	p.R364H	ENST00000264414	NM_003590.4	364	cGt/cAt	8/16	1	2	FACETS	0.882	0.791	0.979	0.882	0.791	0.979	CLONAL	1	TRUE	1	0.367177891927827	2		860	642	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30127996	30127996	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	149	992	0	ENST00000263025.4:c.1133C>G	p.Ala378Gly	p.A378G	ENST00000263025	NM_002746.2	378	gCc/gGc	8/9	1	2	FACETS	0.939	0.858	1	0.939	0.858	1	CLONAL	1	TRUE	1	0.367177891927827	2		992	864	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16041495	16041495	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	140	824	0	ENST00000268712.3:c.1384A>C	p.Ile462Leu	p.I462L	ENST00000268712	NM_006311.3	462	Att/Ctt	13/46	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.367177891927827	2		824	748	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239891	53239891	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	161	504	1	ENST00000375401.3:c.1550A>G	p.Asp517Gly	p.D517G	ENST00000375401	NM_004187.3	517	gAt/gGt	11/26	1	1	FACETS	0.84	0.779	0.903	1	0.991	1	CLONAL	2	TRUE	0	0.367177891927827	1		505	426	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843802	151843802	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	107	653	0	ENST00000262189.6:c.13913del	p.Leu4638TrpfsTer7	p.L4638Wfs*7	ENST00000262189	NM_170606.2	4638	tTg/tg	53/59	1	2	FACETS	0.919	0.826	1	0.919	0.826	1	CLONAL	1	TRUE	1	0.367177891927827	2		653	634	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620440	52620440	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0005750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	102	598	0	ENST00000394830.3:c.3312+1del		p.X1104_splice	ENST00000394830	NM_018313.4	1104			0.367177891927827	1	FACETS	0.907	0.815	1	0.907	0.815	1	CLONAL	1	TRUE	0	0.367177891927827	1		598	500	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183734	10183735	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	103	601	0	ENST00000256474.2:c.204dup	p.Arg69AlafsTer63	p.R69Afs*63	ENST00000256474	NM_000551.3	68	tcg/tcGg	1/3	0.367177891927827	1	FACETS	0.939	0.844	1	0.939	0.844	1	CLONAL	1	TRUE	0	0.367177891927827	1		601	488	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653830	206653830	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	117	752	0	ENST00000367120.3:c.1381G>C	p.Ala461Pro	p.A461P	ENST00000367120	NM_014002.3	461	Gca/Cca	13/22	0.216637554571444	5	FACETS	0.825	0.744	0.912	0.413	0.372	0.456	CLONAL	2	TRUE	1	0.216637554571444	5		752	867	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907202	32907203	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs397507272	NA	P-0005774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	94	493	0	ENST00000380152.3:c.1593dup	p.Glu532ArgfsTer3	p.E532Rfs*3	ENST00000380152		529	-/A	10/27	0.216637554571444	1	FACETS	0.889	0.796	0.988	1	0.985	1	CLONAL	2	TRUE	0	0.216637554571444	1		493	435	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918690	44918690	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	98	234	0	ENST00000377967.4:c.1173del	p.Ala392HisfsTer47	p.A392Hfs*47	ENST00000377967	NM_021140.2	391	gcA/gc	12/29	1	1	FACETS	0.882	0.796	0.97	1	0.99	1	CLONAL	3	TRUE	0	0.216637554571444	1		234	305	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0005778-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	420	285	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	NA	2	FACETS	0.946	0.913	0.977			1	INDETERMINATE	2	TRUE	NA	0.703793266728543	2		285	631	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0005778-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	205	513	1	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.703793266728543	1	FACETS	0.928	0.873	0.982	0.928	0.873	0.982	CLONAL	1	TRUE	0	0.703793266728543	1		514	407	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165791	47165791	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005778-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	22	535	0	ENST00000409792.3:c.335C>A	p.Ser112Ter	p.S112*	ENST00000409792	NM_014159.6	112	tCg/tAg	3/21	0.703793266728543	1	FACETS	0.118	0.091	0.149	0.118	0.091	0.149	SUBCLONAL	1	TRUE	0	0.703793266728543	1		535	344	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998891	11998891	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0005778-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	114	374	1	ENST00000353533.5:c.394-1G>T		p.X132_splice	ENST00000353533	NM_003010.3	132			0.703793266728543	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.703793266728543	1		375	208	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157346	106157352	+	frameshift_variant	Frame_Shift_Del	DEL	AATAAAG	AATAAAG	-	rs1329343855	NA	P-0005778-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	119	461	2	ENST00000380013.4:c.2255_2261del	p.Asn752ArgfsTer59	p.N752Rfs*59	ENST00000380013	NM_001127208.2	749	caAATAAAG/ca	3/11	1	2	FACETS	0.794	0.722	0.868	0.794	0.722	0.868	SUBCLONAL	1	TRUE	1	0.703793266728543	2		463	426	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215313	123215330	+	inframe_deletion	In_Frame_Del	DEL	ACGTTTTGCTTTAACTTT	ACGTTTTGCTTTAACTTT	-	novel	NA	P-0005778-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	373	746	0	ENST00000218089.9:c.2859_2876del	p.Arg954_Phe959del	p.R954_F959del	ENST00000218089	NM_001042749.1	953	cgACGTTTTGCTTTAACTTTt/cgt	28/35	0.171055515391417	6	FACETS	0.93	0.886	0.974			1	INDETERMINATE	3	TRUE	NA	0.703793266728543	6		746	915	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559799	29559799	+	frameshift_variant	Frame_Shift_Ins	INS	T	T	GAAAC	novel	NA	P-0005778-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	150	610	1	ENST00000356175.3:c.3396delinsGAAAC	p.Gly1133LysfsTer63	p.G1133Kfs*63	ENST00000356175	NM_000267.3	1132	cgT/cgGAAAC	26/57	0.703793266728543	1	FACETS	0.763	0.707	0.82	0.763	0.707	0.82	SUBCLONAL	1	TRUE	0	0.703793266728543	1		611	362	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0005855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	299	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.354311548333303	3	FACETS	0.99	0.939	1	0.99	0.939	1	CLONAL	3	TRUE	0	0.337013061780469	3		249	698	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242723	66242723	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	135	731	0	ENST00000273854.3:c.1849C>A	p.Leu617Ile	p.L617I	ENST00000273854	NM_004439.5	617	Cta/Ata	9/18	0.264516347322501	3	FACETS	0.761	0.69	0.836	0.381	0.345	0.418	SUBCLONAL	1	TRUE	1	0.337013061780469	3		731	1230	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828792	72828792	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	341	991	0	ENST00000268489.5:c.7789C>A	p.Pro2597Thr	p.P2597T	ENST00000268489	NM_006885.3	2597	Cca/Aca	9/10	0.352719227602667	3	FACETS	1	0.986	1	0.742	0.702	0.781	CLONAL	2	TRUE	0	0.337013061780469	3		991	1063	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245609	46245609	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	221	625	0	ENST00000334344.6:c.3707del	p.Pro1236HisfsTer7	p.P1236Hfs*7	ENST00000334344	NM_152641.2	1235	Ccc/cc	15/21	NA	2	FACETS	0.752	0.701	0.805			1	INDETERMINATE	2	TRUE	NA	0.337013061780469	2		625	872	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578231	7578232	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAAT	novel	NA	P-0005855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	181	703	1	ENST00000269305.4:c.614_617dup	p.Asp207PhefsTer3	p.D207Ffs*3	ENST00000269305	NM_001126112.2	206	ttg/ttATTTg	6/11	0.354311548333303	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.337013061780469	1		704	669	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180451	38180461	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGACTGCTC	GCCGACTGCTC	-	novel	NA	P-0005855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	141	568	0	ENST00000396334.3:c.300_310del	p.Arg101AlafsTer19	p.R101Afs*19	ENST00000396334	NM_002468.4	100	gGCCGACTGCTC/g	1/5	0.264516347322501	3	FACETS	0.769	0.702	0.838	0.769	0.702	0.838	SUBCLONAL	2	TRUE	1	0.337013061780469	3		568	636	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0005862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	55	536	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			1	2	FACETS	0.767	0.656	0.888	0.767	0.656	0.888	SUBCLONAL	1	TRUE	1	0.254430408749955	2		536	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0005862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	69	254	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	1	2	FACETS	0.873	0.761	0.995	0.873	0.761	0.995	CLONAL	1	TRUE	1	0.254430408749955	2		255	621	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146499	185146499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35266179	NA	P-0005862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	25	426	0	ENST00000265026.3:c.130G>A	p.Glu44Lys	p.E44K	ENST00000265026	NM_004721.4	44	Gag/Aag	2/14	0.206425772354676	3	FACETS	0.535	0.421	0.666	0.178	0.14	0.222	SUBCLONAL	1	TRUE	0	0.254430408749955	3		426	414	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630826	187630826	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0005862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	52	618	1	ENST00000441802.2:c.156T>A	p.Tyr52Ter	p.Y52*	ENST00000441802	NM_005245.3	52	taT/taA	2/27	0.254430408749955	1	FACETS	0.903	0.771	1	0.903	0.771	1	CLONAL	1	TRUE	0	0.254430408749955	1		619	395	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678995	117678995	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	19	384	0	ENST00000368508.3:c.3826A>C	p.Ile1276Leu	p.I1276L	ENST00000368508	NM_002944.2	1276	Att/Ctt	24/43	0.135775302535399	0	FACETS	0.376	0.285	0.483			1	INDETERMINATE	1	TRUE	0	0.254430408749955	0		384	296	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434142	49434142	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057518571	NA	P-0005862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	67	545	0	ENST00000301067.7:c.7411C>T	p.Arg2471Ter	p.R2471*	ENST00000301067	NM_003482.3	2471	Cga/Tga	31/54	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.254430408749955	2		545	493	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553356	41553356	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	43	619	0	ENST00000263253.7:c.3445T>A	p.Phe1149Ile	p.F1149I	ENST00000263253	NM_001429.3	1149	Ttt/Att	18/31	0.184594235600244	3	FACETS	0.818	0.684	0.965	0.409	0.342	0.483	CLONAL	1	TRUE	1	0.254430408749955	3		619	466	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443666	49443667	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0005862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	28	534	0	ENST00000301067.7:c.3704dup	p.Gly1236TrpfsTer14	p.G1236Wfs*14	ENST00000301067	NM_003482.3	1235	ggt/ggGt	11/54	1	2	FACETS	0.46	0.367	0.567	0.46	0.367	0.567	SUBCLONAL	1	TRUE	1	0.254430408749955	2		534	478	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709475	176709476	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGAA	novel	NA	P-0005862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	61	724	0	ENST00000439151.2:c.5906_5909dup	p.Tyr1971Ter	p.Y1971*	ENST00000439151	NM_022455.4	1968	gtg/gTGAAtg	19/23	0.254430408749955	1	FACETS	0.914	0.79	1	0.914	0.79	1	CLONAL	1	TRUE	0	0.254430408749955	1		724	458	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0005883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	148	509	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	0.544674857301855	2		509	497	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692920	89692921	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs398123323	NA	P-0005883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	121	206	0	ENST00000371953.3:c.405dup	p.Cys136MetfsTer44	p.C136Mfs*44	ENST00000371953	NM_000314.4	135	ata/atAa	5/9	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.544674857301855	2		206	427	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692922	89692922	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201044	NA	P-0005883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	124	204	0	ENST00000371953.3:c.406T>C	p.Cys136Arg	p.C136R	ENST00000371953	NM_000314.4	136	Tgt/Cgt	5/9	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.544674857301855	2		204	425	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0005883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	167	273	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	0.544674857301855	2		273	541	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508389	106508389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758375337	NA	P-0005883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	72	139	0	ENST00000359195.3:c.383C>T	p.Thr128Met	p.T128M	ENST00000359195	NM_002649.2	128	aCg/aTg	2/11	0.544674857301855	3	FACETS	1	0.931	1	0.541	0.476	0.609	CLONAL	1	TRUE	1	0.544674857301855	3		139	311	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424970	49424970	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783691	NA	P-0005883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	113	238	0	ENST00000301067.7:c.13518del	p.Ser4507AlafsTer12	p.S4507Afs*12	ENST00000301067	NM_003482.3	4506	ccC/cc	39/54	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.544674857301855	2		238	389	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101112	27101113	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	164	436	0	ENST00000324856.7:c.4395dup	p.Ala1466CysfsTer25	p.A1466Cfs*25	ENST00000324856	NM_006015.4	1465	tct/tcTt	18/20	1	2	FACETS	0.959	0.884	1	0.959	0.884	1	CLONAL	1	TRUE	1	0.544674857301855	2		436	628	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440905	56440906	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	G	novel	NA	P-0005883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	187	474	0	ENST00000407977.2:c.431_432delinsC	p.Asp144AlafsTer14	p.D144Afs*14	ENST00000407977		144	gAT/gC	4/10	1	2	FACETS	0.941	0.871	1	0.941	0.871	1	CLONAL	1	TRUE	1	0.544674857301855	2		474	730	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420288	49420288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886043497	NA	P-0005902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	22	472	1	ENST00000301067.7:c.15461G>A	p.Arg5154Gln	p.R5154Q	ENST00000301067	NM_003482.3	5154	cGg/cAg	48/54	1	2	FACETS	0.16	0.123	0.203	0.16	0.123	0.203	SUBCLONAL	1	FALSE	1	0.645505331855621	2		473	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	80	404	1	ENST00000269305.4:c.481G>T	p.Ala161Ser	p.A161S	ENST00000269305	NM_001126112.2	161	Gcc/Tcc	5/11	1	2	FACETS	0.46	0.405	0.518	0.46	0.405	0.518	SUBCLONAL	1	FALSE	1	0.645505331855621	2		405	539	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687471	37687472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs760014508	NA	P-0005902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	13	244	0	ENST00000447079.4:c.4382dup	p.Thr1463AsnfsTer50	p.T1463Nfs*50	ENST00000447079	NM_015083.1	1459	tgg/tGgg	14/14	1	2	FACETS	0.174	0.123	0.235	0.174	0.123	0.235	SUBCLONAL	1	FALSE	1	0.645505331855621	2		244	232	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519886	NA	P-0005902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	11	381	0	ENST00000349496.5:c.97T>G	p.Ser33Ala	p.S33A	ENST00000349496	NM_001904.3	33	Tct/Gct	3/15	1	2	FACETS	0.103	0.071	0.144	0.103	0.071	0.144	SUBCLONAL	1	FALSE	1	0.645505331855621	2		381	330	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061250	38061250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1459219194	NA	P-0005902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	178	485	0	ENST00000250448.2:c.739C>T	p.His247Tyr	p.H247Y	ENST00000250448	NM_004496.3	247	Cac/Tac	2/2	0.213011299039106	3	FACETS	1	0.99	1	0.724	0.672	0.776	INDETERMINATE	1	FALSE	1	0.645505331855621	3		485	504	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0005905-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	12	250	2	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.633	0.444	0.866	0.633	0.444	0.866	SUBCLONAL	1	TRUE	1	0.14	2		252	271	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0005905-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	22	204	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.3	0	FACETS	1	0.848	1			1	CLONAL	1	TRUE	0	0.14	0		204	241	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806555	1806555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1189213092	NA	P-0005905-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	35	575	0	ENST00000260795.2:c.1271C>T	p.Ser424Phe	p.S424F	ENST00000260795		424	tCc/tTc	9/17	0.3	0	FACETS	0.846	0.698	1			1	CLONAL	2	TRUE	0	0.14	0		575	254	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638375	176638375	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005905-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	24	310	0	ENST00000439151.2:c.2975C>T	p.Ser992Phe	p.S992F	ENST00000439151	NM_022455.4	992	tCt/tTt	5/23	1	2	FACETS	0.888	0.696	1	0.888	0.696	1	CLONAL	1	TRUE	1	0.14	2		310	386	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71019950	71019951	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005905-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	29	215	0	ENST00000318789.4:c.1658dup	p.Ser554PhefsTer4	p.S554Ffs*4	ENST00000318789	NM_032682.5	553	cct/ccCt	19/21	0.0835641815394839	3	FACETS	0.992	0.795	1	0.496	0.397	0.608	INDETERMINATE	1	TRUE	1	0.14	3		215	447	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	130	397	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.375674430921616	2		397	648	SUCCESS
APC	324	MSKCC	GRCh37	5	112175675	112175676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	112	441	0	ENST00000257430.4:c.4393_4394dup	p.Ser1465ArgfsTer9	p.S1465Rfs*9	ENST00000257430	NM_000038.5	1462	aag/aAGag	16/16	1	2	FACETS	0.746	0.671	0.826	0.746	0.671	0.826	SUBCLONAL	1	TRUE	1	0.375674430921616	2		441	799	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778972	9778972	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1214315014	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	76	160	0	ENST00000377346.4:c.1241C>T	p.Ala414Val	p.A414V	ENST00000377346	NM_005026.3	414	gCg/gTg	9/24	0.375674430921616	2	FACETS	0.765	0.672	0.864	0.382	0.336	0.432	SUBCLONAL	1	TRUE	0	0.375674430921616	2		160	529	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216477	108216477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587782558	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	141	396	0	ENST00000278616.4:c.8432del	p.Lys2811SerfsTer46	p.K2811Sfs*46	ENST00000278616	NM_000051.3	2809	cAa/ca	58/63	1	2	FACETS	0.981	0.895	1	0.981	0.895	1	CLONAL	1	TRUE	1	0.375674430921616	2		396	765	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14026115	14026116	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs769120755	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	180	584	0	ENST00000311895.7:c.1081dup	p.Met361AsnfsTer4	p.M361Nfs*4	ENST00000311895	NM_005236.2	359	gaa/gAaa	6/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.375674430921616	2		584	846	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795103	242795104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs768249210	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	93	436	0	ENST00000334409.5:c.105dup	p.Thr36HisfsTer70	p.T36Hfs*70	ENST00000334409	NM_005018.2	35	-/C	2/5	1	2	FACETS	0.654	0.581	0.732	0.654	0.581	0.732	SUBCLONAL	1	TRUE	1	0.375674430921616	2		436	757	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1311	313	898	5	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.375674430921616	2		903	1624	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793211	139793212	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs748531430	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	230	677	1	ENST00000247668.2:c.26dup	p.Gly10TrpfsTer70	p.G10Wfs*70	ENST00000247668	NM_021138.3	7	acc/aCcc	2/11	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.375674430921616	2		678	1203	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	154	356	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.375674430921616	2		356	779	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720712	89720712	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	15	95	0	ENST00000371953.3:c.867del	p.Val290Ter	p.V290*	ENST00000371953	NM_000314.4	288	gAa/ga	8/9	1	2	FACETS	0.799	0.592	1	0.799	0.592	1	CLONAL	1	TRUE	1	0.375674430921616	2		95	100	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117594	70117594	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	231	480	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	0.375674430921616	2		480	854	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120457933	120457933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769520444	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	83	319	2	ENST00000256646.2:c.7412C>T	p.Ala2471Val	p.A2471V	ENST00000256646	NM_024408.3	2471	gCg/gTg	34/34	1	2	FACETS	0.708	0.625	0.797	0.708	0.625	0.797	SUBCLONAL	1	TRUE	1	0.375674430921616	2		321	624	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442044	52442044	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	132	534	0	ENST00000460680.1:c.305A>G	p.Asn102Ser	p.N102S	ENST00000460680	NM_004656.3	102	aAc/aGc	5/17	1	2	FACETS	0.719	0.651	0.789	0.719	0.651	0.789	SUBCLONAL	1	TRUE	1	0.375674430921616	2		534	978	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659191	86659191	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	87	391	0	ENST00000274376.6:c.1480T>C	p.Tyr494His	p.Y494H	ENST00000274376	NM_002890.2	494	Tat/Cat	11/25	1	2	FACETS	0.881	0.782	0.986	0.881	0.782	0.986	CLONAL	1	TRUE	1	0.375674430921616	2		391	526	SUCCESS
APC	324	MSKCC	GRCh37	5	112176903	112176903	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1561601349	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	124	514	0	ENST00000257430.4:c.5612A>T	p.Asp1871Val	p.D1871V	ENST00000257430	NM_000038.5	1871	gAt/gTt	16/16	1	2	FACETS	0.912	0.826	1	0.912	0.826	1	CLONAL	1	TRUE	1	0.375674430921616	2		514	724	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275842	38275842	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	241	603	1	ENST00000425967.3:c.1427G>T	p.Arg476Leu	p.R476L	ENST00000425967	NM_001174067.1	476	cGg/cTg	11/19	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.375674430921616	2		604	1058	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653836	89653836	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	129	454	0	ENST00000371953.3:c.134T>C	p.Val45Ala	p.V45A	ENST00000371953	NM_000314.4	45	gTa/gCa	2/9	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.375674430921616	2		454	610	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298226	123298226	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	79	350	1	ENST00000358487.5:c.628C>T	p.Arg210Ter	p.R210*	ENST00000358487	NM_000141.4	210	Cga/Tga	6/18	1	2	FACETS	0.93	0.822	1	0.93	0.822	1	CLONAL	1	TRUE	1	0.375674430921616	2		351	452	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047314	77047314	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	166	553	0	ENST00000356341.3:c.1230C>A	p.Phe410Leu	p.F410L	ENST00000356341	NM_002576.4	410	ttC/ttA	13/15	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.375674430921616	2		553	868	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374798	118374798	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	148	566	0	ENST00000534358.1:c.8191A>G	p.Thr2731Ala	p.T2731A	ENST00000534358	NM_005933.3	2731	Act/Gct	27/36	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.375674430921616	2		566	784	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402031	402031	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1420917383	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	92	560	0	ENST00000399788.2:c.4760A>G	p.Lys1587Arg	p.K1587R	ENST00000399788	NM_001042603.1	1587	aAg/aGg	27/28	NA	2	FACETS	0.662	0.588	0.741			1	INDETERMINATE	1	TRUE	NA	0.375674430921616	2		560	740	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658254	18658254	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	42	516	0	ENST00000266497.5:c.3059C>A	p.Ala1020Asp	p.A1020D	ENST00000266497		1020	gCt/gAt	22/31	1	2	FACETS	0.289	0.24	0.343	0.289	0.24	0.343	SUBCLONAL	1	TRUE	1	0.375674430921616	2		516	775	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244913	46244913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	169	626	0	ENST00000334344.6:c.3007G>A	p.Val1003Ile	p.V1003I	ENST00000334344	NM_152641.2	1003	Gtc/Atc	15/21	1	2	FACETS	0.928	0.853	1	0.928	0.853	1	CLONAL	1	TRUE	1	0.375674430921616	2		626	969	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214672	133214672	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1397189983	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	67	606	0	ENST00000320574.5:c.5606A>G	p.Asn1869Ser	p.N1869S	ENST00000320574	NM_006231.2	1869	aAc/aGc	41/49	1	2	FACETS	0.34	0.294	0.39	0.34	0.294	0.39	SUBCLONAL	1	TRUE	1	0.375674430921616	2		606	1049	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954040	32954040	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	159	546	0	ENST00000380152.3:c.9107A>G	p.Gln3036Arg	p.Q3036R	ENST00000380152		3036	cAa/cGa	23/27	0.305980689467186	2	FACETS	1	0.987	1	0.692	0.637	0.749	CLONAL	1	TRUE	0	0.375674430921616	2		546	612	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881543	48881543	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1131690907	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	156	457	2	ENST00000267163.4:c.264+1G>A		p.X88_splice	ENST00000267163	NM_000321.2	88			0.305980689467186	2	FACETS	0.761	0.7	0.823	0.761	0.7	0.823	SUBCLONAL	2	TRUE	0	0.375674430921616	2		459	546	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955562	48955562	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	124	467	0	ENST00000267163.4:c.1678T>C	p.Ser560Pro	p.S560P	ENST00000267163	NM_000321.2	560	Tcc/Ccc	17/27	0.305980689467186	2	FACETS	1	0.97	1	0.581	0.528	0.637	CLONAL	1	TRUE	0	0.375674430921616	2		467	568	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5225777	5225777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751437578	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	237	570	3	ENST00000357368.4:c.2455G>A	p.Ala819Thr	p.A819T	ENST00000357368	NM_002850.3	819	Gct/Act	17/38	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.375674430921616	2		573	996	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166396	7166396	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	191	481	0	ENST00000302850.5:c.1630G>T	p.Glu544Ter	p.E544*	ENST00000302850	NM_000208.2	544	Gag/Tag	8/22	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.375674430921616	2		481	892	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145589	11145589	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	101	323	0	ENST00000358026.2:c.3952-1G>T		p.X1318_splice	ENST00000358026	NM_001128849.1	1318			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.375674430921616	2		323	470	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537197	41537197	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	40	594	0	ENST00000263253.7:c.2024T>C	p.Met675Thr	p.M675T	ENST00000263253	NM_001429.3	675	aTg/aCg	10/31	1	2	FACETS	0.293	0.243	0.35	0.293	0.243	0.35	SUBCLONAL	1	TRUE	1	0.375674430921616	2		594	726	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151647	55151647	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs764174646	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	140	457	2	ENST00000257290.5:c.2438del	p.Asn813IlefsTer20	p.N813Ifs*20	ENST00000257290	NM_006206.4	811	tcA/tc	17/23	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.375674430921616	2		459	700	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528057	103528058	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1460687250	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	145	347	0	ENST00000355739.4:c.3370dup	p.Thr1124AsnfsTer26	p.T1124Nfs*26	ENST00000355739	NM_000123.3	1122	cca/ccAa	15/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.375674430921616	2		347	632	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390736	139390736	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	257	604	0	ENST00000277541.6:c.7455del	p.Ser2486ArgfsTer103	p.S2486Rfs*103	ENST00000277541	NM_017617.3	2485	ccC/cc	34/34	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.375674430921616	2		604	1149	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681119	117681120	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs748436511	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	158	566	0	ENST00000368508.3:c.3500dup	p.Leu1167PhefsTer26	p.L1167Ffs*26	ENST00000368508	NM_002944.2	1167	tta/ttTa	23/43	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.375674430921616	2		566	802	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411702	63411703	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	204	356	0	ENST00000330258.3:c.1464dup	p.Leu489AlafsTer19	p.L489Afs*19	ENST00000330258	NM_152424.3	488	-/G	2/2	1	1	FACETS	0.886	0.829	0.943	1	0.994	1	CLONAL	2	TRUE	0	0.375674430921616	1		356	498	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600551	43600551	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	74	614	1	ENST00000355710.3:c.778del	p.Val260Ter	p.V260*	ENST00000355710	NM_020975.4	259	ccG/cc	4/20	1	2	FACETS	0.357	0.312	0.407	0.357	0.312	0.407	SUBCLONAL	1	TRUE	1	0.375674430921616	2		615	1102	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989590	212989591	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	92	492	0	ENST00000342788.4:c.119_120dup	p.Asp41LeufsTer26	p.D41Lfs*26	ENST00000342788	NM_005235.2	40	-/CT	2/28	1	2	FACETS	0.678	0.603	0.759	0.678	0.603	0.759	SUBCLONAL	1	TRUE	1	0.375674430921616	2		492	722	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209298	133209298	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060500809	NA	P-0005987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	206	593	0	ENST00000320574.5:c.6088del	p.Ala2030ProfsTer18	p.A2030Pfs*18	ENST00000320574	NM_006231.2	2030	Gcc/cc	44/49	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.375674430921616	2		593	1004	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0005996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	122	265	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.237362933630334	2	FACETS	1	0.981	1	0.665	0.603	0.729	CLONAL	1	TRUE	0	0.328988296104702	2		265	558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0005996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	146	405	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.328988296104702	2		405	816	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440001	56440001	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0005996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	411	504	1	ENST00000407977.2:c.591T>A	p.Tyr197Ter	p.Y197*	ENST00000407977		197	taT/taA	6/10	0.25722704947131	3	FACETS	1	0.993	1	0.823	0.785	0.863	CLONAL	2	TRUE	0	0.328988296104702	3		505	1178	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88651959	88651960	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0005996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	81	333	0	ENST00000372037.3:c.308_309del	p.Tyr103Ter	p.Y103*	ENST00000372037	NM_004329.2	102	aaATat/aaat	5/13	1	2	FACETS	0.979	0.865	1	0.979	0.865	1	CLONAL	1	TRUE	1	0.328988296104702	2		333	503	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120258	70120259	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1267	192	613	0	ENST00000245479.2:c.1261dup	p.Ser421LysfsTer157	p.S421Kfs*157	ENST00000245479	NM_000346.3	420	-/A	3/3	0.25722704947131	3	FACETS	0.932	0.859	1	0.311	0.286	0.336	CLONAL	1	TRUE	0	0.328988296104702	3		613	1459	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130545	29130545	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	72	536	1	ENST00000328354.6:c.165del	p.Ser56AlafsTer5	p.S56Afs*5	ENST00000328354	NM_007194.3	55	tcC/tc	2/15	1	2	FACETS	0.41	0.357	0.468	0.41	0.357	0.468	SUBCLONAL	1	TRUE	1	0.328988296104702	2		537	1067	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0006026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	277	389	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.83	0.78	0.882	1	0.994	1	CLONAL	2	TRUE	1	0.308840555526104	2		390	1080	SUCCESS
AR	367	MSKCC	GRCh37	X	66766105	66766105	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	63	114	0	ENST00000374690.3:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000374690	NM_000044.3	373	Gga/Aga	1/8	0.232764043513257	0	FACETS	0.829	0.722	0.945			1	CLONAL	1	TRUE	NA	0.308840555526104	0		114	340	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807363	3807364	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0006026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	166	276	0	ENST00000262367.5:c.3623dup	p.Gln1209ThrfsTer25	p.Q1209Tfs*25	ENST00000262367	NM_004380.2	1208	cca/ccCa	19/31	0.308840555526104	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.308840555526104	1		276	798	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730910	40730910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370873414	NA	P-0006026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	119	207	0	ENST00000373198.4:c.3625C>T	p.Arg1209Trp	p.R1209W	ENST00000373198	NM_133170.3	1209	Cgg/Tgg	27/32	0.244372926911136	5	FACETS	0.753	0.68	0.83	0.502	0.453	0.553	SUBCLONAL	2	TRUE	2	0.308840555526104	5		207	749	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570284	95570284	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	59	191	0	ENST00000393063.1:c.3449C>A	p.Ser1150Tyr	p.S1150Y	ENST00000393063	NM_030621.3	1150	tCt/tAt	22/28	1	2	FACETS	0.527	0.453	0.608	0.527	0.453	0.608	SUBCLONAL	1	TRUE	1	0.308840555526104	2		191	725	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781320	3781320	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190311671	NA	P-0006026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	69	383	1	ENST00000262367.5:c.5045G>A	p.Arg1682His	p.R1682H	ENST00000262367	NM_004380.2	1682	cGc/cAc	30/31	0.308840555526104	1	FACETS	0.403	0.35	0.461	0.403	0.35	0.461	SUBCLONAL	1	TRUE	0	0.308840555526104	1		384	937	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743927	40743927	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	57	216	0	ENST00000373198.4:c.3068A>G	p.Asp1023Gly	p.D1023G	ENST00000373198	NM_133170.3	1023	gAc/gGc	23/32	0.244372926911136	5	FACETS	0.562	0.481	0.652	0.187	0.16	0.218	SUBCLONAL	1	TRUE	2	0.308840555526104	5		216	961	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0006046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	247	526	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.324453986362058	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.324453986362058	2		526	710	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	180	435	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.298964350868949	5	FACETS	0.859	0.796	0.924	0.859	0.796	0.924	CLONAL	3	TRUE	2	0.324453986362058	5		435	640	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400905	72400905	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	114	730	2	ENST00000357731.5:c.266C>A	p.Pro89His	p.P89H	ENST00000357731	NM_173808.2	89	cCt/cAt	2/7	0.324453986362058	3	FACETS	0.897	0.807	0.993	0.449	0.403	0.497	CLONAL	1	TRUE	1	0.324453986362058	3		732	910	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25462022	25462022	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	241	492	0	ENST00000264709.3:c.2385G>T	p.Trp795Cys	p.W795C	ENST00000264709	NM_175629.2	795	tgG/tgT	20/23	0.324453986362058	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.324453986362058	3		492	789	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499520	89499520	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	138	291	0	ENST00000336596.2:c.2690G>T	p.Arg897Met	p.R897M	ENST00000336596	NM_005233.5	897	aGg/aTg	15/17	0.298964350868949	5	FACETS	0.937	0.854	1	0.625	0.569	0.682	CLONAL	2	TRUE	2	0.324453986362058	5		291	675	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249460	153249460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	100	452	0	ENST00000281708.4:c.1318G>A	p.Asp440Asn	p.D440N	ENST00000281708	NM_033632.3	440	Gat/Aat	9/12	0.324453986362058	3	FACETS	1	0.977	1	0.667	0.598	0.74	CLONAL	1	TRUE	1	0.324453986362058	3		452	537	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499656	149499656	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	97	559	1	ENST00000261799.4:c.2617G>T	p.Glu873Ter	p.E873*	ENST00000261799	NM_002609.3	873	Gag/Tag	19/23	0.324453986362058	3	FACETS	0.869	0.774	0.97	0.434	0.387	0.485	CLONAL	1	TRUE	1	0.324453986362058	3		560	800	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052917	180052917	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	196	495	0	ENST00000261937.6:c.1373G>T	p.Trp458Leu	p.W458L	ENST00000261937	NM_182925.4	458	tGg/tTg	10/30	0.324453986362058	3	FACETS	0.999	0.928	1	0.999	0.928	1	CLONAL	2	TRUE	1	0.324453986362058	3		495	703	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188861	32188861	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	187	462	0	ENST00000375023.3:c.693T>G	p.Cys231Trp	p.C231W	ENST00000375023	NM_004557.3	231	tgT/tgG	4/30	0.324453986362058	2	FACETS	0.95	0.882	1	0.95	0.882	1	CLONAL	2	TRUE	0	0.324453986362058	2		462	607	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200101	138200101	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	176	267	0	ENST00000237289.4:c.1519A>T	p.Ser507Cys	p.S507C	ENST00000237289	NM_001270507.1	507	Agc/Tgc	7/9	0.324453986362058	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.324453986362058	2		267	510	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140454014	140454014	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs755214031	NA	P-0006046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	122	231	0	ENST00000288602.6:c.1714A>T	p.Ile572Phe	p.I572F	ENST00000288602	NM_004333.4	572	Atc/Ttc	14/18	0.209477174170197	5	FACETS	0.971	0.88	1	0.647	0.587	0.71	CLONAL	2	TRUE	2	0.324453986362058	5		231	576	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500882	8500882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs191877533	NA	P-0006046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	104	439	0	ENST00000356435.5:c.2000C>T	p.Ser667Leu	p.S667L	ENST00000356435		667	tCg/tTg	13/35	0.324453986362058	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.324453986362058	1		439	517	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570239	87570239	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	142	308	0	ENST00000277120.3:c.1979C>G	p.Pro660Arg	p.P660R	ENST00000277120		660	cCg/cGg	17/19	0.209477174170197	5	FACETS	1	0.962	1	0.728	0.666	0.792	CLONAL	2	TRUE	2	0.324453986362058	5		308	596	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911521	101911521	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	188	497	0	ENST00000374994.4:c.1446G>T	p.Arg482Ser	p.R482S	ENST00000374994	NM_004612.2	482	agG/agT	9/9	0.209477174170197	5	FACETS	1	0.984	1	0.809	0.75	0.87	CLONAL	2	TRUE	2	0.324453986362058	5		497	710	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656255	18656255	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	169	527	0	ENST00000266497.5:c.2934G>C	p.Lys978Asn	p.K978N	ENST00000266497		978	aaG/aaC	21/31	0.298964350868949	5	FACETS	1	0.965	1	0.721	0.665	0.78	CLONAL	2	TRUE	2	0.324453986362058	5		527	716	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534359	63534359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886053273	NA	P-0006046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	63	436	0	ENST00000307078.5:c.1162C>T	p.Arg388Cys	p.R388C	ENST00000307078	NM_004655.3	388	Cgc/Tgc	5/11	0.324453986362058	4	FACETS	0.557	0.48	0.641	0.279	0.24	0.321	SUBCLONAL	1	TRUE	2	0.324453986362058	4		436	923	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735521	40735521	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1400066941	NA	P-0006046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	231	456	0	ENST00000373198.4:c.3352A>G	p.Thr1118Ala	p.T1118A	ENST00000373198	NM_133170.3	1118	Acc/Gcc	25/32	0.306182892890812	4	FACETS	0.844	0.79	0.899	0.844	0.79	0.899	CLONAL	3	TRUE	1	0.324453986362058	4		456	745	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979268	40979268	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	71	402	0	ENST00000373198.4:c.1865G>C	p.Ser622Thr	p.S622T	ENST00000373198	NM_133170.3	622	aGt/aCt	11/32	0.306182892890812	4	FACETS	0.896	0.782	1	0.299	0.26	0.34	CLONAL	1	TRUE	1	0.324453986362058	4		402	647	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360689	70360689	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	41	44	0	ENST00000374080.3:c.6249G>T	p.Gln2083His	p.Q2083H	ENST00000374080		2083	caG/caT	42/45	0.324453986362058	2	FACETS	1	0.935	1			1	CLONAL	2	TRUE	NA	0.324453986362058	2		44	108	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45864800	45864801	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	166	648	0	ENST00000391945.4:c.1218dup	p.Val407CysfsTer16	p.V407Cfs*16	ENST00000391945	NM_000400.3	406	-/T	12/23	0.324453986362058	3	FACETS	1	0.981	1	0.611	0.56	0.663	CLONAL	1	TRUE	1	0.324453986362058	3		648	974	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123353328	123353329	+	start_lost	Translation_Start_Site	DNP	CC	CC	AA	novel	NA	P-0006046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	237	484	0	ENST00000358487.5:c.3_4delinsTT	p.MetVal1_?2	p.MV1_?2	ENST00000358487	NM_000141.4	1	atGGtc/atTTtc	2/18	0.324453986362058	4	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	2	0.324453986362058	4		484	955	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	176	460	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.506494210918182	2		460	667	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075122	16075122	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0006051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	113	345	0	ENST00000268712.3:c.430A>T	p.Lys144Ter	p.K144*	ENST00000268712	NM_006311.3	144	Aag/Tag	4/46	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.506494210918182	2		345	439	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842340	68842341	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	153	608	0	ENST00000261769.5:c.403dup	p.Ile135AsnfsTer33	p.I135Nfs*33	ENST00000261769	NM_004360.3	134	gga/ggAa	4/16	0.506494210918182	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.506494210918182	1		608	391	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0006075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	238	596	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.445870461657929	2		596	964	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0006075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	135	223	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.926	0.844	1	0.926	0.844	1	CLONAL	1	TRUE	1	0.445870461657929	2		223	654	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0006075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	295	835	0	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.445870461657929	2		835	1180	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625165	69625165	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369755339	NA	P-0006075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	103	503	0	ENST00000334134.2:c.628C>T	p.Arg210Trp	p.R210W	ENST00000334134	NM_005247.2	210	Cgg/Tgg	3/3	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.445870461657929	2		503	423	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711367	114711368	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0006075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	103	231	0	ENST00000543371.1:c.381+2dup		p.X127_splice	ENST00000543371	NM_001198531.1	127			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.445870461657929	2		231	387	SUCCESS
APC	324	MSKCC	GRCh37	5	112174094	112174095	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs863225332	NA	P-0006093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	312	565	0	ENST00000257430.4:c.2804dup	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	tac/tAac	16/16	0.723094215634973	2	FACETS	0.91	0.874	0.946	0.91	0.874	0.946	CLONAL	2	TRUE	0	0.723094215634973	2		565	474	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119932	70119932	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	405	227	0	ENST00000245479.2:c.934C>T	p.Gln312Ter	p.Q312*	ENST00000245479	NM_000346.3	312	Cag/Tag	3/3	0.689637803988105	4	FACETS	0.981	0.955	1	0.981	0.955	1	CLONAL	4	TRUE	0	0.723094215634973	4		227	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0006093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	792	728	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.689637803988105	4	FACETS	0.947	0.929	0.966	0.947	0.929	0.966	CLONAL	4	TRUE	0	0.723094215634973	4		728	996	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426847	70426847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	536	612	1	ENST00000373644.4:c.4507C>T	p.Arg1503Trp	p.R1503W	ENST00000373644	NM_030625.2	1503	Cgg/Tgg	7/12	0.717552969336063	3	FACETS	0.979	0.955	1	0.979	0.955	1	CLONAL	3	TRUE	0	0.723094215634973	3		613	687	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857017	9857017	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	295	737	2	ENST00000330684.3:c.4384T>A	p.Ser1462Thr	p.S1462T	ENST00000330684	NM_001134407.1	1462	Tct/Act	13/13	0.10512243977372	4	FACETS	0.889	0.84	0.938			1	INDETERMINATE	2	TRUE	NA	0.723094215634973	4		739	791	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41222973	41222973	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	218	1024	0	ENST00000357654.3:c.4958T>C	p.Val1653Ala	p.V1653A	ENST00000357654	NM_007294.3	1653	gTg/gCg	15/23	0.689637803988105	4	FACETS	0.859	0.798	0.923	0.215	0.199	0.231	CLONAL	1	TRUE	0	0.723094215634973	4		1024	1209	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142913	7142913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1283504748	NA	P-0006093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	149	764	0	ENST00000302850.5:c.2456G>A	p.Arg819His	p.R819H	ENST00000302850	NM_000208.2	819	cGc/cAc	12/22	0.330482885420702	3	FACETS	0.651	0.595	0.71	0.217	0.198	0.237	INDETERMINATE	1	TRUE	0	0.723094215634973	3		764	862	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577205	64577205	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	122	910	0	ENST00000312049.6:c.377G>A	p.Trp126Ter	p.W126*	ENST00000312049	NM_130799.2	126	tGg/tAg	2/10	0.314570093847536	1	FACETS	0.88	0.796	0.968	0.88	0.796	0.968	CLONAL	1	TRUE	0	0.314570093847536	1		910	743	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476361	88476361	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	80	493	0	ENST00000360948.2:c.1771C>G	p.Leu591Val	p.L591V	ENST00000360948	NM_001012338.2	591	Ctg/Gtg	15/19	1	2	FACETS	0.674	0.592	0.761	0.674	0.592	0.761	SUBCLONAL	1	TRUE	1	0.314570093847536	2		493	755	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748905	41748905	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	111	739	0	ENST00000301178.4:c.1430A>T	p.Lys477Met	p.K477M	ENST00000301178	NM_021913.4	477	aAg/aTg	11/20	0.314570093847536	1	FACETS	0.769	0.692	0.852	0.769	0.692	0.852	SUBCLONAL	1	TRUE	0	0.314570093847536	1		739	773	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003467	42003468	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0006095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	147	1199	0	ENST00000219905.7:c.3005dup	p.Leu1003ThrfsTer32	p.L1003Tfs*32	ENST00000219905	NM_001164273.1	1002	gca/gCca	8/24	1	2	FACETS	0.88	0.802	0.962	0.88	0.802	0.962	CLONAL	1	TRUE	1	0.314570093847536	2		1199	1062	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809331	243809332	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0006095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	64	528	0	ENST00000263826.5:c.292_293del	p.Trp98AspfsTer22	p.W98Dfs*22	ENST00000263826	NM_005465.4	98	TGg/g	4/13	NA	2	FACETS	0.733	0.635	0.839			1	INDETERMINATE	1	TRUE	NA	0.314570093847536	2		528	555	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466779	25466780	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	ATCA	novel	NA	P-0006095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	145	770	0	ENST00000264709.3:c.1920_1923dup	p.Gly642Ter	p.G642*	ENST00000264709	NM_175629.2	641	-/TGAT	16/23	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.314570093847536	2		770	902	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0006115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	206	315	1	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	0.257727521549094	3	FACETS	0.805	0.75	0.862	0.805	0.75	0.862	INDETERMINATE	2	TRUE	1	0.442556124958623	3		316	706	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0006115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	171	315	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.442556124958623	1	FACETS	0.969	0.895	1	0.969	0.895	1	CLONAL	1	TRUE	0	0.442556124958623	1		315	621	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0006115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	239	377	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.257727521549094	3	FACETS	1	0.989	1	0.649	0.605	0.693	INDETERMINATE	1	TRUE	1	0.442556124958623	3		377	1017	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0006115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	171	383	1	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.442556124958623	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.442556124958623	1		384	540	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716032	243716032	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	68	336	0	ENST00000263826.5:c.1162C>T	p.Arg388Cys	p.R388C	ENST00000263826	NM_005465.4	388	Cgc/Tgc	10/13	1	2	FACETS	0.384	0.333	0.439	0.384	0.333	0.439	SUBCLONAL	1	TRUE	1	0.442556124958623	2		336	801	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190714	11190714	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199646470	NA	P-0006115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	94	352	0	ENST00000361445.4:c.5485A>G	p.Thr1829Ala	p.T1829A	ENST00000361445	NM_004958.3	1829	Acc/Gcc	39/58	0.223113222874398	1	FACETS	0.446	0.396	0.499	0.446	0.396	0.499	INDETERMINATE	1	TRUE	0	0.442556124958623	1		352	742	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17350520	17350520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	127	442	0	ENST00000375499.3:c.590C>T	p.Pro197Leu	p.P197L	ENST00000375499	NM_003000.2	197	cCc/cTc	6/8	0.223113222874398	1	FACETS	0.48	0.434	0.528	0.48	0.434	0.528	INDETERMINATE	1	TRUE	0	0.442556124958623	1		442	931	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094383	27094383	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	36	342	0	ENST00000324856.7:c.3091A>G	p.Thr1031Ala	p.T1031A	ENST00000324856	NM_006015.4	1031	Act/Gct	11/20	0.223113222874398	1	FACETS	0.186	0.152	0.224	0.186	0.152	0.224	INDETERMINATE	1	TRUE	0	0.442556124958623	1		342	681	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096135	178096135	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	96	334	0	ENST00000397062.3:c.1196C>A	p.Ser399Tyr	p.S399Y	ENST00000397062	NM_006164.4	399	tCt/tAt	5/5	1	2	FACETS	0.586	0.522	0.655	0.586	0.522	0.655	SUBCLONAL	1	TRUE	1	0.442556124958623	2		334	740	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735534	204735534	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	77	324	0	ENST00000302823.3:c.335T>C	p.Val112Ala	p.V112A	ENST00000302823	NM_005214.4	112	gTg/gCg	2/4	1	2	FACETS	0.476	0.417	0.539	0.476	0.417	0.539	SUBCLONAL	1	TRUE	1	0.442556124958623	2		324	731	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661662	227661662	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	63	294	0	ENST00000305123.5:c.1793A>G	p.His598Arg	p.H598R	ENST00000305123	NM_005544.2	598	cAc/cGc	1/2	1	2	FACETS	0.51	0.441	0.585	0.51	0.441	0.585	SUBCLONAL	1	TRUE	1	0.442556124958623	2		294	558	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538866	187538866	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1235980656	NA	P-0006115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	230	284	0	ENST00000441802.2:c.8874A>G	p.Ile2958Met	p.I2958M	ENST00000441802	NM_005245.3	2958	atA/atG	10/27	0.378081524733498	2	FACETS	0.826	0.775	0.878	0.826	0.775	0.878	CLONAL	2	TRUE	0	0.442556124958623	2		284	629	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86667956	86667956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1449106680	NA	P-0006115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	236	393	2	ENST00000274376.6:c.1720G>A	p.Ala574Thr	p.A574T	ENST00000274376	NM_002890.2	574	Gca/Aca	13/25	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.442556124958623	2		395	1016	SUCCESS
APC	324	MSKCC	GRCh37	5	112116553	112116553	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	282	423	0	ENST00000257430.4:c.598A>T	p.Met200Leu	p.M200L	ENST00000257430	NM_000038.5	200	Atg/Ttg	6/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.442556124958623	2		423	1147	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056109	26056109	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1220534226	NA	P-0006115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	112	208	0	ENST00000343677.2:c.548A>G	p.Lys183Arg	p.K183R	ENST00000343677	NM_005319.3	183	aAg/aGg	1/1	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.442556124958623	2		208	501	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268059	55268059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	143	466	1	ENST00000275493.2:c.2899G>A	p.Glu967Lys	p.E967K	ENST00000275493	NM_005228.3	967	Gaa/Aaa	24/28	0.257727521549094	3	FACETS	0.616	0.56	0.675	0.308	0.28	0.338	INDETERMINATE	1	TRUE	1	0.442556124958623	3		467	1282	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140508697	140508697	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	141	305	0	ENST00000288602.6:c.603G>T	p.Gln201His	p.Q201H	ENST00000288602	NM_004333.4	201	caG/caT	4/18	0.257727521549094	3	FACETS	0.876	0.798	0.958	0.438	0.399	0.479	INDETERMINATE	1	TRUE	1	0.442556124958623	3		305	888	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345855	152345855	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1257066384	NA	P-0006115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1638	373	596	0	ENST00000359321.1:c.715A>G	p.Met239Val	p.M239V	ENST00000359321	NM_005431.1	239	Atg/Gtg	3/3	0.257727521549094	3	FACETS	1	0.963	1	0.512	0.484	0.541	INDETERMINATE	1	TRUE	1	0.442556124958623	3		596	2011	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248561	8248561	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	109	492	0	ENST00000335790.3:c.326A>T	p.Tyr109Phe	p.Y109F	ENST00000335790	NM_002315.2	109	tAt/tTt	3/4	0.223113222874398	1	FACETS	0.399	0.358	0.443	0.399	0.358	0.443	INDETERMINATE	1	TRUE	0	0.442556124958623	1		492	961	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933219	100933219	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1365	163	704	0	ENST00000325455.5:c.2171G>T	p.Arg724Met	p.R724M	ENST00000325455	NM_001202474.3	724	aGg/aTg	4/8	0.223113222874398	1	FACETS	0.375	0.343	0.409	0.375	0.343	0.409	INDETERMINATE	1	TRUE	0	0.442556124958623	1		704	1528	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813366	102813366	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	97	436	0	ENST00000307046.8:c.323A>G	p.Tyr108Cys	p.Y108C	ENST00000307046	NM_001111285.1	108	tAt/tGt	3/4	0.223113222874398	1	FACETS	0.393	0.35	0.44	0.393	0.35	0.44	INDETERMINATE	1	TRUE	0	0.442556124958623	1		436	868	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28931705	28931705	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	90	390	0	ENST00000282397.4:c.2234A>G	p.Tyr745Cys	p.Y745C	ENST00000282397	NM_002019.4	745	tAc/tGc	15/30	0.191075010582042	0	FACETS	0.29	0.257	0.326			1	INDETERMINATE	1	TRUE	0	0.442556124958623	0		390	781	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434503	110434503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	68	301	0	ENST00000375856.3:c.3898G>A	p.Gly1300Ser	p.G1300S	ENST00000375856	NM_003749.2	1300	Ggc/Agc	1/2	0.191075010582042	0	FACETS	0.384	0.335	0.437			1	INDETERMINATE	1	TRUE	0	0.442556124958623	0		301	446	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133176	30133176	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1414402131	NA	P-0006115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	128	532	2	ENST00000263025.4:c.322C>T	p.Arg108Trp	p.R108W	ENST00000263025	NM_002746.2	108	Cgg/Tgg	2/9	0.223113222874398	1	FACETS	0.447	0.404	0.492	0.447	0.404	0.492	INDETERMINATE	1	TRUE	0	0.442556124958623	1		534	1008	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530141	63530141	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	115	468	0	ENST00000307078.5:c.2294T>C	p.Val765Ala	p.V765A	ENST00000307078	NM_004655.3	765	gTt/gCt	10/11	0.442556124958623	1	FACETS	0.442	0.397	0.489	0.442	0.397	0.489	SUBCLONAL	1	TRUE	0	0.442556124958623	1		468	916	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143987	11143987	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	167	342	0	ENST00000358026.2:c.3568G>A	p.Ala1190Thr	p.A1190T	ENST00000358026	NM_001128849.1	1190	Gcc/Acc	26/36	0.442556124958623	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.442556124958623	1		342	515	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830441	72830441	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	79	415	0	ENST00000268489.5:c.6140del	p.Pro2047LeufsTer54	p.P2047Lfs*54	ENST00000268489	NM_006885.3	2047	cCt/ct	9/10	0.223113222874398	1	FACETS	0.406	0.357	0.459	0.406	0.357	0.459	INDETERMINATE	1	TRUE	0	0.442556124958623	1		415	684	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517815	187517815	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	78	314	0	ENST00000441802.2:c.12879del	p.His4293GlnfsTer56	p.H4293Qfs*56	ENST00000441802	NM_005245.3	4293	caC/ca	25/27	0.378081524733498	2	FACETS	0.504	0.442	0.57	0.252	0.221	0.285	SUBCLONAL	1	TRUE	0	0.442556124958623	2		314	700	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286237	66286238	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	360	480	0	ENST00000273854.3:c.1448dup	p.Asn483LysfsTer21	p.N483Kfs*21	ENST00000273854	NM_004439.5	483	aac/aaAc	6/18	0.378081524733498	2	FACETS	0.763	0.724	0.802	0.763	0.724	0.802	SUBCLONAL	2	TRUE	0	0.442556124958623	2		480	1066	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793677	89793677	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	129	450	0	ENST00000336032.3:c.752del	p.Lys251SerfsTer14	p.K251Sfs*14	ENST00000336032	NM_006813.2	249	gAa/ga	2/2	1	2	FACETS	0.461	0.417	0.508	0.461	0.417	0.508	SUBCLONAL	1	TRUE	1	0.442556124958623	2		450	1264	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222606	157222606	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	190	416	0	ENST00000346085.5:c.1876del	p.Gln626ArgfsTer42	p.Q626Rfs*42	ENST00000346085	NM_020732.3	625	Ccc/cc	4/20	NA	2	FACETS	0.956	0.885	1			1	INDETERMINATE	1	TRUE	NA	0.442556124958623	2		416	898	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110176	8110177	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0006115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	70	376	0	ENST00000585124.1:c.428_429del	p.Tyr143PhefsTer3	p.Y143Ffs*3	ENST00000585124	NM_004217.3	143	tAT/t	6/9	0.442556124958623	1	FACETS	0.369	0.322	0.421	0.369	0.322	0.421	SUBCLONAL	1	TRUE	0	0.442556124958623	1		376	667	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0006148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	31	1096	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.210424988047047	3	FACETS	0.289	0.233	0.354	0.145	0.116	0.177	SUBCLONAL	1	TRUE	1	0.254493255013802	3		1096	949	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519923	29519923	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	44	265	1	ENST00000389048.3:c.1648C>A	p.Leu550Ile	p.L550I	ENST00000389048	NM_004304.4	550	Ctc/Atc	9/29	0.210424988047047	3	FACETS	0.613	0.513	0.724	0.306	0.256	0.362	SUBCLONAL	1	TRUE	1	0.254493255013802	3		266	636	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412453	63412453	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	118	291	0	ENST00000330258.3:c.714A>C	p.Lys238Asn	p.K238N	ENST00000330258	NM_152424.3	238	aaA/aaC	2/2	0.170438257429424	0	FACETS	0.66	0.598	0.724			1	SUBCLONAL	2	TRUE	NA	0.254493255013802	0		291	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579432	7579433	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0006148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	66	287	0	ENST00000269305.4:c.254dup	p.Ala86CysfsTer63	p.A86Cfs*63	ENST00000269305	NM_001126112.2	85	cct/ccCt	4/11	1	2	FACETS	0.681	0.59	0.779	0.681	0.59	0.779	SUBCLONAL	1	TRUE	1	0.254493255013802	2		287	762	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578441	7578442	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	A	novel	NA	P-0006148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	173	312	0	ENST00000269305.4:c.488_489delinsT	p.Tyr163LeufsTer7	p.Y163Lfs*7	ENST00000269305	NM_001126112.2	163	tAC/tT	5/11	1	2	FACETS	0.832	0.767	0.9	1	0.991	1	CLONAL	2	TRUE	1	0.254493255013802	2		312	817	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	125	435	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.975	0.888	1	0.975	0.888	1	CLONAL	1	TRUE	1	0.544666614734061	2		435	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0006183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	249	470	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.338324369188431	0	FACETS	0.621	0.584	0.659			1	SUBCLONAL	1	TRUE	0	0.544666614734061	0		470	670	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517201	NA	P-0006183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	162	273	0	ENST00000263967.3:c.1637A>C	p.Gln546Pro	p.Q546P	ENST00000263967	NM_006218.2	546	cAg/cCg	10/21	0.544666614734061	3	FACETS	0.975	0.906	1	0.975	0.906	1	CLONAL	2	TRUE	1	0.544666614734061	3		273	388	SUCCESS
APC	324	MSKCC	GRCh37	5	112175530	112175530	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	137	446	0	ENST00000257430.4:c.4240del	p.Val1414Ter	p.V1414*	ENST00000257430	NM_000038.5	1413	atG/at	16/16	1	2	FACETS	0.944	0.863	1	0.944	0.863	1	CLONAL	1	TRUE	1	0.544666614734061	2		446	533	SUCCESS
APC	324	MSKCC	GRCh37	5	112173926	112173926	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060503287	NA	P-0006183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	124	409	1	ENST00000257430.4:c.2635C>T	p.Gln879Ter	p.Q879*	ENST00000257430	NM_000038.5	879	Cag/Tag	16/16	1	2	FACETS	0.975	0.888	1	0.975	0.888	1	CLONAL	1	TRUE	1	0.544666614734061	2		410	467	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985385	60985385	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1441924243	NA	P-0006183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	119	775	1	ENST00000333681.4:c.515A>G	p.Asn172Ser	p.N172S	ENST00000333681		172	aAc/aGc	2/3	0.544666614734061	1	FACETS	0.305	0.274	0.337	0.305	0.274	0.337	SUBCLONAL	1	TRUE	0	0.544666614734061	1		776	1044	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170729	11170729	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753578157	NA	P-0006183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	336	686	0	ENST00000358026.2:c.4873G>A	p.Val1625Ile	p.V1625I	ENST00000358026	NM_001128849.1	1625	Gtc/Atc	35/36	1	2	FACETS	0.992	0.937	1	0.992	0.937	1	CLONAL	1	TRUE	1	0.544666614734061	2		686	1244	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623069	52623160	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTTAAAACAAACTTACCAGCTGAATCCTCCCACAGTCTTTCAATACAGACGATATGTGGTTGTAGGTTGGCCTCTGCAGGTTCCACATAGA	ATTTAAAACAAACTTACCAGCTGAATCCTCCCACAGTCTTTCAATACAGACGATATGTGGTTGTAGGTTGGCCTCTGCAGGTTCCACATAGA	-	novel	NA	P-0006183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	109	357	0	ENST00000394830.3:c.2891_2965+17del		p.X964_splice	ENST00000394830	NM_018313.4	964		19/30	0.544666614734061	1	FACETS	0.883	0.802	0.966	0.883	0.802	0.966	CLONAL	1	TRUE	0	0.544666614734061	1		357	330	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023045	31023046	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs750170870	NA	P-0006183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	475	593	0	ENST00000375687.4:c.2535dup	p.Ser846GlnfsTer5	p.S846Qfs*5	ENST00000375687	NM_015338.5	844	acc/aCcc	13/13	0.544666614734061	3	FACETS	0.875	0.837	0.913	0.875	0.837	0.913	CLONAL	2	TRUE	1	0.544666614734061	3		593	1268	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	245	548	1	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.41	2		549	1066	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	100	154	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.41	2		154	437	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	124	196	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.907	0.822	0.996	0.907	0.822	0.996	CLONAL	1	TRUE	1	0.41	2		196	667	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	177	183	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.869	0.807	0.931	1	0.992	1	CLONAL	2	TRUE	1	0.41	2		183	497	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296358	15296358	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	83	543	3	ENST00000263388.2:c.2084del	p.Pro695ArgfsTer165	p.P695Rfs*165	ENST00000263388	NM_000435.2	695	cCg/cg	13/33	1	2	FACETS	0.445	0.392	0.502	0.445	0.392	0.502	SUBCLONAL	1	TRUE	1	0.41	2		546	910	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	38	287	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.467	0.386	0.557	0.467	0.386	0.557	SUBCLONAL	1	TRUE	1	0.41	2		287	397	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178218	56178218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780012235	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	142	434	0	ENST00000399503.3:c.3191G>A	p.Arg1064Lys	p.R1064K	ENST00000399503	NM_005921.1	1064	aGa/aAa	14/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.41	2		434	630	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380277	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913238	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	119	368	0	ENST00000311936.3:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	61	Caa/Aaa	3/5	0.172526837498737	3	FACETS	1	0.941	1	0.528	0.477	0.581	INDETERMINATE	1	TRUE	1	0.41	3		368	663	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101090	26101090	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	74	703	0	ENST00000435504.4:c.2T>C	p.Met1?	p.M1?	ENST00000435504		1	aTg/aCg	1/13	1	2	FACETS	0.415	0.363	0.472	0.415	0.363	0.472	SUBCLONAL	1	TRUE	1	0.41	2		703	869	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867540	35867541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs869312857	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	100	356	0	ENST00000303115.3:c.361dup	p.Ile121AsnfsTer8	p.I121Nfs*8	ENST00000303115	NM_002185.3	118	-/A	3/8	1	2	FACETS	0.825	0.739	0.917	0.825	0.739	0.917	CLONAL	1	TRUE	1	0.41	2		356	591	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890149	76890150	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	245	608	0	ENST00000373344.5:c.4744dup	p.Thr1582AsnfsTer19	p.T1582Nfs*19	ENST00000373344	NM_000489.3	1582	aca/aAca	17/35	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.41	2		608	1137	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268793	98268793	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1554708751	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	85	519	0	ENST00000331920.6:c.290del	p.Asn97ThrfsTer20	p.N97Tfs*20	ENST00000331920	NM_000264.3	97	aAc/ac	2/24	1	2	FACETS	0.396	0.349	0.447	0.396	0.349	0.447	SUBCLONAL	1	TRUE	1	0.41	2		519	1047	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934243	49934243	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1407832113	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	291	736	2	ENST00000296474.3:c.2264del	p.Gly755ValfsTer19	p.G755Vfs*19	ENST00000296474	NM_002447.2	755	gGt/gt	8/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.41	2		738	1302	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46527638	46527638	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	92	486	2	ENST00000262741.5:c.727C>T	p.Arg243Ter	p.R243*	ENST00000262741	NM_003629.3	243	Cga/Tga	6/10	1	2	FACETS	0.484	0.429	0.542	0.484	0.429	0.542	SUBCLONAL	1	TRUE	1	0.41	2		488	928	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510154	120510154	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587595062	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	55	458	1	ENST00000256646.2:c.1355G>A	p.Arg452His	p.R452H	ENST00000256646	NM_024408.3	452	cGt/cAt	8/34	1	2	FACETS	0.409	0.349	0.474	0.409	0.349	0.474	SUBCLONAL	1	TRUE	1	0.41	2		459	656	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156836745	156836745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	99	514	0	ENST00000524377.1:c.403G>A	p.Val135Met	p.V135M	ENST00000524377	NM_002529.3	135	Gtg/Atg	4/17	1	2	FACETS	0.543	0.484	0.606	0.543	0.484	0.606	SUBCLONAL	1	TRUE	1	0.41	2		514	889	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085933	16085933	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	68	325	0	ENST00000281043.3:c.1109T>C	p.Leu370Ser	p.L370S	ENST00000281043	NM_005378.4	370	tTg/tCg	3/3	1	2	FACETS	0.577	0.502	0.658	0.577	0.502	0.658	SUBCLONAL	1	TRUE	1	0.41	2		325	575	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248763	212248763	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	64	230	0	ENST00000342788.4:c.3504G>T	p.Glu1168Asp	p.E1168D	ENST00000342788	NM_005235.2	1168	gaG/gaT	28/28	1	2	FACETS	0.964	0.84	1	0.964	0.84	1	CLONAL	1	TRUE	1	0.41	2		230	324	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935070	49935070	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	136	726	1	ENST00000296474.3:c.1929G>T	p.Glu643Asp	p.E643D	ENST00000296474	NM_002447.2	643	gaG/gaT	6/20	1	2	FACETS	0.501	0.454	0.55	0.501	0.454	0.55	SUBCLONAL	1	TRUE	1	0.41	2		727	1325	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156956	89156956	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	95	404	0	ENST00000336596.2:c.58G>A	p.Gly20Arg	p.G20R	ENST00000336596	NM_005233.5	20	Ggg/Agg	1/17	1	2	FACETS	0.595	0.529	0.665	0.595	0.529	0.665	SUBCLONAL	1	TRUE	1	0.41	2		404	779	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259095	89259095	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	54	391	0	ENST00000336596.2:c.239A>T	p.Asn80Ile	p.N80I	ENST00000336596	NM_005233.5	80	aAt/aTt	3/17	1	2	FACETS	0.534	0.457	0.619	0.534	0.457	0.619	SUBCLONAL	1	TRUE	1	0.41	2		391	493	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961790	55961790	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	150	546	0	ENST00000263923.4:c.2771T>C	p.Leu924Pro	p.L924P	ENST00000263923	NM_002253.2	924	cTg/cCg	20/30	1	2	FACETS	0.97	0.888	1	0.97	0.888	1	CLONAL	1	TRUE	1	0.41	2		546	754	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638701	176638701	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	107	437	0	ENST00000439151.2:c.3301G>A	p.Asp1101Asn	p.D1101N	ENST00000439151	NM_022455.4	1101	Gat/Aat	5/23	1	2	FACETS	0.819	0.736	0.907	0.819	0.736	0.907	CLONAL	1	TRUE	1	0.41	2		437	637	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720964	176720964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	181	489	0	ENST00000439151.2:c.6595C>T	p.Arg2199Cys	p.R2199C	ENST00000439151	NM_022455.4	2199	Cgt/Tgt	23/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.41	2		489	796	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553321	106553321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	100	303	1	ENST00000369096.4:c.1286G>A	p.Ser429Asn	p.S429N	ENST00000369096	NM_001198.3	429	aGc/aAc	5/7	1	2	FACETS	0.966	0.866	1	0.966	0.866	1	CLONAL	1	TRUE	1	0.41	2		304	505	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200477	138200477	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	105	218	0	ENST00000237289.4:c.1895G>C	p.Arg632Thr	p.R632T	ENST00000237289	NM_001270507.1	632	aGa/aCa	7/9	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.41	2		218	497	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891145	101891145	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	40	293	0	ENST00000374994.4:c.106T>C	p.Cys36Arg	p.C36R	ENST00000374994	NM_004612.2	36	Tgt/Cgt	2/9	1	2	FACETS	0.392	0.325	0.466	0.392	0.325	0.466	SUBCLONAL	1	TRUE	1	0.41	2		293	498	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390606	139390606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1052013977	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	281	693	0	ENST00000277541.6:c.7585G>A	p.Val2529Ile	p.V2529I	ENST00000277541	NM_017617.3	2529	Gtc/Atc	34/34	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.41	2		693	1259	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372558	118372558	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs533826575	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	207	403	0	ENST00000534358.1:c.6491C>T	p.Pro2164Leu	p.P2164L	ENST00000534358	NM_005933.3	2164	cCg/cTg	26/36	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.41	2		403	744	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424776	49424776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1249439740	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	242	536	0	ENST00000301067.7:c.13571G>A	p.Arg4524Gln	p.R4524Q	ENST00000301067	NM_003482.3	4524	cGg/cAg	40/54	0.172526837498737	3	FACETS	1	0.986	1	0.598	0.557	0.639	INDETERMINATE	1	TRUE	1	0.41	3		536	1190	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490889	56490889	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	54	449	0	ENST00000267101.3:c.2335C>A	p.Pro779Thr	p.P779T	ENST00000267101	NM_001982.3	779	Cca/Aca	20/28	0.172526837498737	3	FACETS	0.372	0.317	0.433	0.186	0.158	0.217	INDETERMINATE	1	TRUE	1	0.41	3		449	853	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245292	133245292	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	141	479	0	ENST00000320574.5:c.1955C>T	p.Ala652Val	p.A652V	ENST00000320574	NM_006231.2	652	gCt/gTt	18/49	0.172526837498737	3	FACETS	0.937	0.853	1	0.468	0.426	0.512	INDETERMINATE	1	TRUE	1	0.41	3		479	885	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060964	38060964	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35391958	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	88	282	0	ENST00000250448.2:c.1025C>T	p.Ala342Val	p.A342V	ENST00000250448	NM_004496.3	342	gCg/gTg	2/2	1	2	FACETS	0.98	0.873	1	0.98	0.873	1	CLONAL	1	TRUE	1	0.41	2		282	438	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225320	2225320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	115	497	0	ENST00000326181.6:c.1405C>A	p.Leu469Met	p.L469M	ENST00000326181	NM_032271.2	469	Ctg/Atg	16/21	1	2	FACETS	0.634	0.57	0.701	0.634	0.57	0.701	SUBCLONAL	1	TRUE	1	0.41	2		497	885	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274042	10274042	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184494228	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	220	571	3	ENST00000330684.3:c.227G>A	p.Arg76His	p.R76H	ENST00000330684	NM_001134407.1	76	cGc/cAc	2/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.41	2		574	1015	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337248	89337248	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	80	394	0	ENST00000301030.4:c.7783G>T	p.Asp2595Tyr	p.D2595Y	ENST00000301030	NM_001256183.1	2595	Gat/Tat	12/13	1	2	FACETS	0.44	0.387	0.498	0.44	0.387	0.498	SUBCLONAL	1	TRUE	1	0.41	2		394	886	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48586237	48586237	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs878854769	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	90	235	0	ENST00000342988.3:c.906G>A	p.Trp302Ter	p.W302*	ENST00000342988	NM_005359.5	302	tgG/tgA	8/12	1	2	FACETS	0.971	0.866	1	0.971	0.866	1	CLONAL	1	TRUE	1	0.41	2		235	452	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604745	48604745	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	125	433	0	ENST00000342988.3:c.1567T>C	p.Cys523Arg	p.C523R	ENST00000342988	NM_005359.5	523	Tgc/Cgc	12/12	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.41	2		433	606	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248585	10248585	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568220739	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	94	461	1	ENST00000340748.4:c.4168G>A	p.Gly1390Arg	p.G1390R	ENST00000340748		1390	Ggg/Agg	35/40	1	2	FACETS	0.517	0.459	0.579	0.517	0.459	0.579	SUBCLONAL	1	TRUE	1	0.41	2		462	887	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24158992	24158992	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	79	436	0	ENST00000263121.7:c.664C>A	p.Leu222Ile	p.L222I	ENST00000263121	NM_003073.3	222	Ctc/Atc	6/9	1	2	FACETS	0.46	0.404	0.521	0.46	0.404	0.521	SUBCLONAL	1	TRUE	1	0.41	2		436	838	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548294	41548294	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780182045	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	136	431	0	ENST00000263253.7:c.3082G>A	p.Asp1028Asn	p.D1028N	ENST00000263253	NM_001429.3	1028	Gac/Aac	16/31	1	2	FACETS	0.92	0.838	1	0.92	0.838	1	CLONAL	1	TRUE	1	0.41	2		431	721	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911613	39911613	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	89	509	0	ENST00000378444.4:c.5017T>A	p.Leu1673Met	p.L1673M	ENST00000378444	NM_001123385.1	1673	Ttg/Atg	15/15	1	2	FACETS	0.505	0.447	0.567	0.505	0.447	0.567	SUBCLONAL	1	TRUE	1	0.41	2		509	860	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933367	39933367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754579483	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	98	549	0	ENST00000378444.4:c.1232G>A	p.Arg411Gln	p.R411Q	ENST00000378444	NM_001123385.1	411	cGg/cAg	4/15	1	2	FACETS	0.467	0.415	0.522	0.467	0.415	0.522	SUBCLONAL	1	TRUE	1	0.41	2		549	1024	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223742	53223742	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	278	665	0	ENST00000375401.3:c.3617A>G	p.Gln1206Arg	p.Q1206R	ENST00000375401	NM_004187.3	1206	cAg/cGg	23/26	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.41	2		665	1246	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228159	53228159	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	209	464	2	ENST00000375401.3:c.2243G>A	p.Arg748Gln	p.R748Q	ENST00000375401	NM_004187.3	748	cGg/cAg	15/26	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.41	2		466	851	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411737	63411737	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	120	658	0	ENST00000330258.3:c.1430C>A	p.Pro477His	p.P477H	ENST00000330258	NM_152424.3	477	cCt/cAt	2/2	1	2	FACETS	0.554	0.499	0.613	0.554	0.499	0.613	SUBCLONAL	1	TRUE	1	0.41	2		658	1056	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412470	63412470	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1204	120	776	0	ENST00000330258.3:c.697G>A	p.Asp233Asn	p.D233N	ENST00000330258	NM_152424.3	233	Gat/Aat	2/2	1	2	FACETS	0.442	0.398	0.489	0.442	0.398	0.489	SUBCLONAL	1	TRUE	1	0.41	2		776	1324	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480572	123480572	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	62	492	0	ENST00000371139.4:c.80G>A	p.Gly27Asp	p.G27D	ENST00000371139	NM_001114937.2	27	gGc/gAc	1/4	1	2	FACETS	0.308	0.265	0.355	0.308	0.265	0.355	SUBCLONAL	1	TRUE	1	0.41	2		492	983	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352756	118352756	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	53	417	0	ENST00000534358.1:c.3964del	p.Thr1322ProfsTer34	p.T1322Pfs*34	ENST00000534358	NM_005933.3	1321	Aaa/aa	7/36	1	2	FACETS	0.301	0.256	0.351	0.301	0.256	0.351	SUBCLONAL	1	TRUE	1	0.41	2		417	859	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390735	139390736	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	117	610	0	ENST00000277541.6:c.7455dup	p.Ser2486LeufsTer21	p.S2486Lfs*21	ENST00000277541	NM_017617.3	2485	-/C	34/34	1	2	FACETS	0.51	0.458	0.564	0.51	0.458	0.564	SUBCLONAL	1	TRUE	1	0.41	2		610	1120	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360588	70360589	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGCAGC	rs769857818	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	128	421	0	ENST00000374080.3:c.6162_6167dup	p.Gln2075_Gln2076dup	p.Q2075_Q2076dup	ENST00000374080		2075	gag/gAGCAGCag	42/45	1	2	FACETS	0.683	0.618	0.751	0.683	0.618	0.751	SUBCLONAL	1	TRUE	1	0.41	2		421	914	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404809	70404809	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	38	276	1	ENST00000373644.4:c.2328del	p.Lys776AsnfsTer19	p.K776Nfs*19	ENST00000373644	NM_030625.2	775	Aaa/aa	4/12	1	2	FACETS	0.397	0.328	0.474	0.397	0.328	0.474	SUBCLONAL	1	TRUE	1	0.41	2		277	467	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412641	139412641	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	85	498	0	ENST00000277541.6:c.1203del	p.Ser402ArgfsTer229	p.S402Rfs*229	ENST00000277541	NM_017617.3	401	ccC/cc	7/34	1	2	FACETS	0.44	0.388	0.496	0.44	0.388	0.496	SUBCLONAL	1	TRUE	1	0.41	2		498	942	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806180	1806181	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760502257	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	81	511	1	ENST00000260795.2:c.1206dup	p.Lys403GlnfsTer93	p.K403Qfs*93	ENST00000260795		400	agc/agCc	8/17	1	2	FACETS	0.403	0.354	0.456	0.403	0.354	0.456	SUBCLONAL	1	TRUE	1	0.41	2		512	981	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197339	26197343	+	frameshift_variant	Frame_Shift_Del	DEL	ACCGT	ACCGT	-	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1417	120	938	0	ENST00000356476.2:c.136_140del	p.Thr46GlyfsTer27	p.T46Gfs*27	ENST00000356476		46	ACGGTg/g	1/1	1	2	FACETS	0.381	0.342	0.422	0.381	0.342	0.422	SUBCLONAL	1	TRUE	1	0.41	2		938	1537	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262553	16262553	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	45	284	0	ENST00000375759.3:c.9822del	p.Ser3275ValfsTer9	p.S3275Vfs*9	ENST00000375759	NM_015001.2	3273	aCc/ac	11/15	1	2	FACETS	0.431	0.362	0.508	0.431	0.362	0.508	SUBCLONAL	1	TRUE	1	0.41	2		284	509	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223250	2223250	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	96	541	0	ENST00000326181.6:c.863del	p.Lys288ArgfsTer42	p.K288Rfs*42	ENST00000326181	NM_032271.2	288	Aag/ag	10/21	1	2	FACETS	0.482	0.428	0.539	0.482	0.428	0.539	SUBCLONAL	1	TRUE	1	0.41	2		541	972	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245449	46245449	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	163	300	0	ENST00000334344.6:c.3546del	p.Phe1182LeufsTer6	p.F1182Lfs*6	ENST00000334344	NM_152641.2	1181	agT/ag	15/21	0.172526837498737	3	FACETS	0.868	0.801	0.937	0.868	0.801	0.937	INDETERMINATE	2	TRUE	1	0.41	3		300	552	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149634	202149635	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	46	388	0	ENST00000358485.4:c.1077dup	p.Leu360ThrfsTer6	p.L360Tfs*6	ENST00000358485	NM_001080125.1	359	caa/cAaa	8/9	1	2	FACETS	0.42	0.353	0.494	0.42	0.353	0.494	SUBCLONAL	1	TRUE	1	0.41	2		388	534	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199804	108199804	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	51	309	0	ENST00000278616.4:c.7150del	p.Met2384Ter	p.M2384*	ENST00000278616	NM_000051.3	2382	ggA/gg	49/63	1	2	FACETS	0.47	0.4	0.548	0.47	0.4	0.548	SUBCLONAL	1	TRUE	1	0.41	2		309	529	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	131	366	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	0.98	0.891	1			1	INDETERMINATE	1	TRUE	NA	0.417250114089036	2		366	641	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0006213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	200	409	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	0.999	0.925	1	0.999	0.925	1	CLONAL	1	TRUE	1	0.417250114089036	2		409	960	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939140	36939140	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	344	688	1	ENST00000361632.4:c.569G>T	p.Arg190Leu	p.R190L	ENST00000361632		190	cGc/cTc	5/16	0.417250114089036	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.417250114089036	1		689	1296	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710622	114710622	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1375	350	690	2	ENST00000543371.1:c.107C>A	p.Ser36Ter	p.S36*	ENST00000543371	NM_001198531.1	36	tCg/tAg	1/14	1	2	FACETS	0.973	0.918	1	0.973	0.918	1	CLONAL	1	TRUE	1	0.417250114089036	2		692	1725	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557286	29557286	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753082620	NA	P-0006213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	124	367	0	ENST00000356175.3:c.2999G>A	p.Arg1000His	p.R1000H	ENST00000356175	NM_000267.3	1000	cGt/cAt	23/57	1	2	FACETS	0.89	0.806	0.977	0.89	0.806	0.977	CLONAL	1	TRUE	1	0.417250114089036	2		367	668	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239880	53239880	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	371	332	0	ENST00000375401.3:c.1561T>A	p.Tyr521Asn	p.Y521N	ENST00000375401	NM_004187.3	521	Tac/Aac	11/26	1	1	FACETS	0.85	0.811	0.889	1	0.996	1	CLONAL	2	TRUE	0	0.417250114089036	1		332	828	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578247	7578248	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0006213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	253	518	0	ENST00000269305.4:c.601_602del	p.Leu201AlafsTer7	p.L201Afs*7	ENST00000269305	NM_001126112.2	201	TTg/g	6/11	1	2	FACETS	0.956	0.893	1	0.956	0.893	1	CLONAL	1	TRUE	1	0.417250114089036	2		518	1269	SUCCESS
APC	324	MSKCC	GRCh37	5	112174863	112174864	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0006213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	111	329	0	ENST00000257430.4:c.3573_3574del	p.Lys1192ThrfsTer15	p.K1192Tfs*15	ENST00000257430	NM_000038.5	1191	cAG/c	16/16	0.342127637093895	0	FACETS	0.559	0.504	0.616			1	SUBCLONAL	1	TRUE	0	0.417250114089036	0		329	555	SUCCESS
APC	324	MSKCC	GRCh37	5	112175377	112175378	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	61	278	0	ENST00000257430.4:c.4086_4087insT	p.Lys1363Ter	p.K1363*	ENST00000257430	NM_000038.5	1362	-/T	16/16	0.342127637093895	0	FACETS	0.44	0.381	0.504			1	SUBCLONAL	1	TRUE	0	0.417250114089036	0		278	387	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0006282-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	53	196	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.274	0.233	0.319	0.274	0.233	0.319	SUBCLONAL	1	TRUE	1	0.53142988569038	2		196	729	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52676018	52676027	+	frameshift_variant	Frame_Shift_Del	DEL	TTGTAATTGC	TTGTAATTGC	-	novel	NA	P-0006282-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	101	404	0	ENST00000394830.3:c.1030_1039del	p.Ala344TrpfsTer15	p.A344Wfs*15	ENST00000394830	NM_018313.4	344	GCAATTACAAtg/tg	11/30	0.53142988569038	1	FACETS	0.8	0.722	0.881	0.8	0.722	0.881	SUBCLONAL	1	TRUE	0	0.53142988569038	1		404	349	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183858	10183859	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0006282-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	92	161	0	ENST00000256474.2:c.330_331dup	p.Ser111ThrfsTer49	p.S111Tfs*49	ENST00000256474	NM_000551.3	109	-/CA	1/3	0.53142988569038	1	FACETS	0.993	0.897	1	0.993	0.897	1	CLONAL	1	TRUE	0	0.53142988569038	1		161	256	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0006289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	177	265	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	0.504595334199369	2		265	640	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226549740	226549740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	268	243	0	ENST00000366794.5:c.2893G>A	p.Asp965Asn	p.D965N	ENST00000366794	NM_001618.3	965	Gat/Aat	22/23	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.504595334199369	2		243	939	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158207	47158207	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	137	227	0	ENST00000409792.3:c.4492C>T	p.Gln1498Ter	p.Q1498*	ENST00000409792	NM_014159.6	1498	Cag/Tag	4/21	1	2	FACETS	0.89	0.813	0.971	0.89	0.813	0.971	CLONAL	1	TRUE	1	0.504595334199369	2		227	610	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729156	66729156	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876657651	NA	P-0006289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	242	317	0	ENST00000307102.5:c.364A>G	p.Asn122Asp	p.N122D	ENST00000307102	NM_002755.3	122	Aac/Gac	3/11	1	2	FACETS	0.97	0.907	1	0.97	0.907	1	CLONAL	1	TRUE	1	0.504595334199369	2		317	989	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578200	7578222	+	frameshift_variant	Frame_Shift_Del	DEL	CCACACTATGTCGAAAAGTGTTT	CCACACTATGTCGAAAAGTGTTT	-	novel	NA	P-0006289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	248	325	0	ENST00000269305.4:c.627_649del	p.Arg209SerfsTer5	p.R209Sfs*5	ENST00000269305	NM_001126112.2	209	agAAACACTTTTCGACATAGTGTGGtg/agtg	6/11	0.504595334199369	1	FACETS	0.983	0.923	1	0.983	0.923	1	CLONAL	1	TRUE	0	0.504595334199369	1		325	748	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575131	48575132	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0006289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	235	295	1	ENST00000342988.3:c.325_326del	p.Leu109LysfsTer4	p.L109Kfs*4	ENST00000342988	NM_005359.5	109	CTa/a	3/12	0.504595334199369	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.504595334199369	1		296	683	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164156	47164157	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0006289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	103	183	0	ENST00000409792.3:c.1968_1969dup	p.Lys657IlefsTer3	p.K657Ifs*3	ENST00000409792	NM_014159.6	657	aaa/aTAaa	3/21	1	2	FACETS	0.849	0.763	0.939	0.849	0.763	0.939	CLONAL	1	TRUE	1	0.504595334199369	2		183	481	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39593533	39593533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	31	247	0	ENST00000262039.4:c.1298C>T	p.Ser433Phe	p.S433F	ENST00000262039	NM_002647.2	433	tCt/tTt	11/25	0.504595334199369	1	FACETS	0.177	0.143	0.216	0.177	0.143	0.216	SUBCLONAL	1	TRUE	0	0.504595334199369	1		247	519	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0006291-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	216	204	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.713890504492419	3	FACETS	0.964	0.91	1	0.964	0.91	1	CLONAL	2	TRUE	1	0.739795714521483	3		204	415	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0006291-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	149	222	0				ENST00000310581	NM_198253.2	-/1132			0.713890504492419	3	FACETS	1	0.954	1	0.528	0.485	0.572	CLONAL	1	TRUE	1	0.739795714521483	3		222	523	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929545	44929546	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006291-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	451	187	0	ENST00000377967.4:c.2646dup	p.Pro883ThrfsTer23	p.P883Tfs*23	ENST00000377967	NM_021140.2	882	ata/atAa	17/29	0.694254073196429	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.739795714521483	2		187	544	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615035	43615035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142318626	NA	P-0006291-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	163	290	0	ENST00000355710.3:c.2449C>T	p.Arg817Cys	p.R817C	ENST00000355710	NM_020975.4	817	Cgc/Tgc	14/20	0.736142657391903	4	FACETS	0.909	0.835	0.987	0.455	0.417	0.494	CLONAL	1	TRUE	2	0.739795714521483	4		290	843	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175838	24175839	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006291-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	426	358	0	ENST00000263121.7:c.1067dup	p.Thr357AspfsTer4	p.T357Dfs*4	ENST00000263121	NM_003073.3	356	ctg/cTtg	8/9	0.736142657391903	4	FACETS	0.975	0.932	1	0.975	0.932	1	CLONAL	2	TRUE	2	0.739795714521483	4		358	1028	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276860	15276861	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs753725730	NA	P-0006330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	14	665	0	ENST00000263388.2:c.5404dup	p.Ala1802GlyfsTer8	p.A1802Gfs*8	ENST00000263388	NM_000435.2	1802	gct/gGct	30/33	0.385672722621761	3	FACETS	0.522	0.378	0.694	0.261	0.189	0.347	SUBCLONAL	1	TRUE	1	0.385672722621761	3		665	166	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419956	152419956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775806382	NA	P-0006330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	12	629	2	ENST00000206249.3:c.1643G>A	p.Arg548His	p.R548H	ENST00000206249	NM_000125.3	548	cGc/cAc	8/8	0.151827656187548	5	FACETS	0.512	0.36	0.698	0.171	0.12	0.233	INDETERMINATE	1	TRUE	2	0.385672722621761	5		631	192	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	37	366	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.3	3	FACETS		NA	1			1	NA	NA	TRUE	NA	NA	3		366	131	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828353	72828353	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	32	746	0	ENST00000268489.5:c.8228A>G	p.Tyr2743Cys	p.Y2743C	ENST00000268489	NM_006885.3	2743	tAc/tGc	9/10	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		746	182	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101116	27101117	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0006337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	13	540	0	ENST00000324856.7:c.4403dup	p.Gly1469TrpfsTer22	p.G1469Wfs*22	ENST00000324856	NM_006015.4	1466	-/C	18/20	0.207935585458129	1	FACETS		NA	1			1	NA	NA	TRUE	0	NA	1		540	137	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	397	366	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.659009099773292	3	FACETS	0.968	0.927	1	0.968	0.927	1	CLONAL	2	TRUE	1	0.659009099773292	3		366	827	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0006345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	209	324	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	0.560074444982849	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.659009099773292	1		324	421	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0006345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	256	288	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.959	0.901	1	0.959	0.901	1	CLONAL	1	TRUE	1	0.659009099773292	2		288	810	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0006345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	213	492	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.988	0.923	1	0.988	0.923	1	CLONAL	1	TRUE	1	0.659009099773292	2		492	654	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	480	448	0	ENST00000295754.5:c.1583G>T	p.Arg528Leu	p.R528L	ENST00000295754	NM_003242.5	528	cGt/cTt	7/7	0.575399325993506	3	FACETS	0.972	0.944	1	0.972	0.944	1	CLONAL	3	TRUE	0	0.659009099773292	3		448	664	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722431	176722431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	208	547	0	ENST00000439151.2:c.8062C>T	p.His2688Tyr	p.H2688Y	ENST00000439151	NM_022455.4	2688	Cac/Tac	23/23	NA	2	FACETS	0.997	0.931	1			1	INDETERMINATE	1	TRUE	NA	0.659009099773292	2		547	633	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553533	106553533	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	122	255	0	ENST00000369096.4:c.1498G>A	p.Gly500Arg	p.G500R	ENST00000369096	NM_001198.3	500	Ggg/Agg	5/7	NA	2	FACETS	1	0.948	1			1	INDETERMINATE	1	TRUE	NA	0.659009099773292	2		255	352	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076826	72076826	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	204	383	2	ENST00000357731.5:c.671C>T	p.Ala224Val	p.A224V	ENST00000357731	NM_173808.2	224	gCt/gTt	5/7	1	2	FACETS	0.981	0.915	1	0.981	0.915	1	CLONAL	1	TRUE	1	0.659009099773292	2		385	631	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286209	66286209	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	236	541	2	ENST00000273854.3:c.1477G>T	p.Asp493Tyr	p.D493Y	ENST00000273854	NM_004439.5	493	Gat/Tat	6/18	1	2	FACETS	0.958	0.897	1	0.958	0.897	1	CLONAL	1	TRUE	1	0.659009099773292	2		543	748	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488229	56488229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	407	486	0	ENST00000267101.3:c.1748C>T	p.Pro583Leu	p.P583L	ENST00000267101	NM_001982.3	583	cCc/cTc	15/28	0.398360219898511	5	FACETS	1	0.977	1			1	CLONAL	3	TRUE	NA	0.659009099773292	5		486	796	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063331	67063331	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1172602310	NA	P-0006345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	101	295	0	ENST00000412916.2:c.21C>G	p.Asp7Glu	p.D7E	ENST00000412916		7	gaC/gaG	1/6	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.659009099773292	2		295	301	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120472	70120473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0006345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	216	531	0	ENST00000245479.2:c.1477dup	p.His493ProfsTer85	p.H493Pfs*85	ENST00000245479	NM_000346.3	492	acc/aCcc	3/3	1	2	FACETS	0.99	0.925	1	0.99	0.925	1	CLONAL	1	TRUE	1	0.659009099773292	2		531	662	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579472	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	A	novel	NA	P-0006374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	479	886	2	ENST00000269305.4:c.215_216delinsT	p.Pro72LeufsTer51	p.P72Lfs*51	ENST00000269305	NM_001126112.2	72	cCC/cT	4/11	0.593007226926058	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.593007226926058	2		888	772	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859704	151859704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1019840408	NA	P-0006374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	93	378	0	ENST00000262189.6:c.10958C>T	p.Pro3653Leu	p.P3653L	ENST00000262189	NM_170606.2	3653	cCt/cTt	43/59	0.578098047880689	3	FACETS	0.975	0.872	1	0.488	0.436	0.542	CLONAL	1	TRUE	1	0.593007226926058	3		378	417	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971122	21971123	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	333	713	0	ENST00000304494.5:c.235dup	p.Thr79AsnfsTer41	p.T79Nfs*41	ENST00000304494	NM_000077.4	79	acc/aAcc	2/3	0.593007226926058	2	FACETS	0.97	0.928	1	0.97	0.928	1	CLONAL	2	TRUE	0	0.593007226926058	2		713	579	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380277	+	missense_variant	Missense_Mutation	DNP	TG	TG	GC	novel	NA	P-0006374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	895	859	0	ENST00000311936.3:c.181_182delinsGC	p.Gln61Ala	p.Q61A	ENST00000311936	NM_004985.3	61	CAa/GCa	3/5	0.593007226926058	6	FACETS	0.988	0.965	1			1	CLONAL	5	TRUE	NA	0.593007226926058	6		859	1336	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599871	28599872	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	144	570	0	ENST00000253063.3:c.756dup	p.Glu253Ter	p.E253*	ENST00000253063	NM_031459.4	251	-/T	6/10	0.593007226926058	2	FACETS	1	0.942	1	0.516	0.474	0.559	CLONAL	1	TRUE	0	0.593007226926058	2		570	471	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859625	57859625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200097138	NA	P-0006374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1669	228	757	1	ENST00000228682.2:c.679C>T	p.Arg227Cys	p.R227C	ENST00000228682	NM_005269.2	227	Cgt/Tgt	7/12	0.593007226926058	8	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.593007226926058	8		758	1897	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105258971	105258971	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs754031503	NA	P-0006374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	244	908	1	ENST00000349310.3:c.10G>T	p.Val4Leu	p.V4L	ENST00000349310	NM_001014432.1	4	Gtg/Ttg	3/15	0.593007226926058	3	FACETS	1	0.984	1	0.383	0.358	0.409	CLONAL	1	TRUE	0	0.593007226926058	3		909	928	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294969	1294977	+	inframe_deletion	In_Frame_Del	DEL	CCGCCGGGT	CCGCCGGGT	-	novel	NA	P-0006374-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	26	164	0	ENST00000310581.5:c.128_136del	p.Asp43_Ala45del	p.D43_A45del	ENST00000310581	NM_198253.2	43	gACCCGGCGGct/gct	1/16	0.593007226926058	3	FACETS	0.568	0.453	0.699	0.284	0.226	0.35	SUBCLONAL	1	TRUE	1	0.593007226926058	3		164	200	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750945	128750945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	587	663	0	ENST00000377970.2:c.482C>T	p.Ser161Leu	p.S161L	ENST00000377970	NM_002467.4	161	tCa/tTa	2/3	0.546559455343812	3	FACETS	0.898	0.867	0.929	0.898	0.867	0.929	CLONAL	2	TRUE	1	0.797536972742399	3		663	1147	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928509	69928509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs190215588	NA	P-0006380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	410	756	1	ENST00000352241.4:c.329C>T	p.Thr110Met	p.T110M	ENST00000352241	NM_198159.2	110	aCg/aTg	2/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.797536972742399	2		757	975	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864390	57864390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	651	1083	1	ENST00000228682.2:c.1867C>T	p.Arg623Ter	p.R623*	ENST00000228682	NM_005269.2	623	Cga/Tga	12/12	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.797536972742399	2		1084	1499	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914137	32914137	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs80358785	NA	P-0006380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	483	1284	1	ENST00000380152.3:c.5645C>A	p.Ser1882Ter	p.S1882*	ENST00000380152		1882	tCa/tAa	11/27	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.797536972742399	2		1285	1188	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754674	41754674	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	1149	1080	1	ENST00000301178.4:c.1660C>T	p.Gln554Ter	p.Q554*	ENST00000301178	NM_021913.4	554	Cag/Tag	14/20	0.797536972742399	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.797536972742399	3		1081	1994	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266781	18266782	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGTAGTGAGCC	novel	NA	P-0006380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	294	651	0	ENST00000222254.8:c.95_105dup	p.Ala36Ter	p.A36*	ENST00000222254	NM_005027.3	31	ctg/ctGGTAGTGAGCCg	2/16	1	2	FACETS	0.844	0.796	0.892	0.844	0.796	0.892	CLONAL	1	TRUE	1	0.797536972742399	2		651	874	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850704	63850705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	653	1023	3	ENST00000279873.7:c.1489dup	p.Ile497AsnfsTer31	p.I497Nfs*31	ENST00000279873	NM_032199.2	494	-/A	10/10	0.797536972742399	3	FACETS	1	0.997	1	0.476	0.459	0.494	CLONAL	1	TRUE	0	0.797536972742399	3		1026	1603	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0006388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	344	647	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	0.619860751142045	6	FACETS	0.902	0.853	0.953	0.451	0.426	0.477	CLONAL	2	TRUE	2	0.619860751142045	6		647	1378	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712016	89712019	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTA	AGTA	-	novel	NA	P-0006388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	65	145	0	ENST00000371953.3:c.634+3_634+6del		p.X212_splice	ENST00000371953	NM_000314.4	212		6/9	0.619860751142045	2	FACETS	0.953	0.863	1	0.953	0.863	1	CLONAL	2	TRUE	0	0.619860751142045	2		145	110	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794443	42794443	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1670	114	514	1	ENST00000575354.2:c.1523C>A	p.Pro508His	p.P508H	ENST00000575354	NM_015125.3	508	cCc/cAc	10/20	0.3	5	FACETS	0.511	0.458	0.568			1	SUBCLONAL	1	TRUE	NA	0.4	5		515	1784	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15952252	15952253	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGTAGGGCTCCGAAGAGA	novel	NA	P-0006443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	92	471	0	ENST00000268712.3:c.6425_6442dup	p.Val2142_Tyr2147dup	p.V2142_Y2147dup	ENST00000268712	NM_006311.3	2142	gag/gTCTCTTCGGAGCCCTACGag	41/46	1	2	FACETS	0.426	0.377	0.478	0.426	0.377	0.478	SUBCLONAL	1	TRUE	1	0.4	2		471	1080	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0006489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	222	515	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.670133462020737	1	FACETS	0.947	0.893	1	0.947	0.893	1	CLONAL	1	TRUE	0	0.670133462020737	1		516	465	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0006489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	205	262	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	0.670133462020737	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.670133462020737	1		262	380	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693918	47693918	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs746286801	NA	P-0006489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	247	564	0	ENST00000233146.2:c.1632C>G	p.Ile544Met	p.I544M	ENST00000233146	NM_000251.2	544	atC/atG	10/16	1	2	FACETS	0.706	0.66	0.754	0.706	0.66	0.754	SUBCLONAL	1	TRUE	1	0.670133462020737	2		564	1044	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686295	117686295	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	228	408	1	ENST00000368508.3:c.3046C>G	p.Leu1016Val	p.L1016V	ENST00000368508	NM_002944.2	1016	Ctt/Gtt	20/43	0.670133462020737	1	FACETS	0.873	0.822	0.925	0.873	0.822	0.925	CLONAL	1	TRUE	0	0.670133462020737	1		409	518	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692968	89692968	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	227	285	0	ENST00000371953.3:c.452C>A	p.Ala151Asp	p.A151D	ENST00000371953	NM_000314.4	151	gCc/gAc	5/9	0.670133462020737	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.670133462020737	1		285	409	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842405	68842405	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	276	560	0	ENST00000261769.5:c.466T>A	p.Trp156Arg	p.W156R	ENST00000261769	NM_004360.3	156	Tgg/Agg	4/16	0.670133462020737	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.670133462020737	1		560	537	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588859	29588859	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	235	466	0	ENST00000356175.3:c.4645G>T	p.Glu1549Ter	p.E1549*	ENST00000356175	NM_000267.3	1549	Gag/Tag	34/57	0.670133462020737	1	FACETS	0.88	0.829	0.931	0.88	0.829	0.931	CLONAL	1	TRUE	0	0.670133462020737	1		466	530	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160679	56160680	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1169355679	NA	P-0006489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	285	402	0	ENST00000399503.3:c.954dup	p.Leu319ThrfsTer7	p.L319Tfs*7	ENST00000399503	NM_005921.1	318	tta/ttAa	4/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.670133462020737	2		402	844	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287185	33287185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006494-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	378	368	0	ENST00000374542.5:c.1912C>T	p.Gln638Ter	p.Q638*	ENST00000374542	NM_001141970.1	638	Caa/Taa	6/8	0.85261315696269	1	FACETS	0.949	0.917	0.98	0.949	0.917	0.98	CLONAL	1	TRUE	0	0.85261315696269	1		368	536	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593503	215593503	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006494-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	129	510	0	ENST00000260947.4:c.2231A>G	p.Asn744Ser	p.N744S	ENST00000260947	NM_000465.2	744	aAt/aGt	11/11	0.85261315696269	1	FACETS	0.416	0.381	0.453	0.416	0.381	0.453	SUBCLONAL	1	TRUE	0	0.85261315696269	1		510	417	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929048	32929048	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006494-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1605	394	956	0	ENST00000380152.3:c.7058G>T	p.Gly2353Val	p.G2353V	ENST00000380152		2353	gGt/gTt	14/27	1	2	FACETS	0.462	0.438	0.488	0.462	0.438	0.488	SUBCLONAL	1	TRUE	1	0.85261315696269	2		956	1999	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098617	2098617	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1055443730	NA	P-0006494-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	668	611	0	ENST00000219476.3:c.1A>G	p.Met1?	p.M1?	ENST00000219476	NM_000548.3	1	Atg/Gtg	2/42	0.85261315696269	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.85261315696269	1		611	892	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106506	27106507	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0006494-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	425	782	0	ENST00000324856.7:c.6121dup	p.Val2041GlyfsTer58	p.V2041Gfs*58	ENST00000324856	NM_006015.4	2039	-/G	20/20	0.85261315696269	1	FACETS	0.475	0.452	0.497	0.475	0.452	0.497	SUBCLONAL	1	TRUE	0	0.85261315696269	1		782	1205	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923060	44923060	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	46	110	0	ENST00000377967.4:c.1921C>T	p.Gln641Ter	p.Q641*	ENST00000377967	NM_021140.2	641	Cag/Tag	16/29	0.235599862431329	0	FACETS	0.67	0.568	0.78			1	SUBCLONAL	1	TRUE	0	0.350134271356461	0		110	255	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197448	26197448	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	65	708	0	ENST00000356476.2:c.31T>C	p.Ser11Pro	p.S11P	ENST00000356476		11	Tcc/Ccc	1/1	1	2	FACETS	0.519	0.449	0.595	0.519	0.449	0.595	SUBCLONAL	1	TRUE	1	0.350134271356461	2		708	715	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391222	139391222	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0006525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	37	365	0	ENST00000277541.6:c.6969C>G	p.Tyr2323Ter	p.Y2323*	ENST00000277541	NM_017617.3	2323	taC/taG	34/34	0.279167118231122	0	FACETS	0.642	0.534	0.76			1	SUBCLONAL	1	TRUE	0	0.350134271356461	0		365	214	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873720	35873721	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGC	novel	NA	P-0006525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	50	520	0	ENST00000216797.5:c.130_131insGCTC	p.Gln44ArgfsTer43	p.Q44Rfs*43	ENST00000216797	NM_020529.2	44	cag/cGCTCag	1/6	0.350134271356461	1	FACETS	0.552	0.469	0.642	0.552	0.469	0.642	SUBCLONAL	1	TRUE	0	0.350134271356461	1		520	427	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928735	49928735	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759714858	NA	P-0006527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	71	628	0	ENST00000296474.3:c.3539C>T	p.Pro1180Leu	p.P1180L	ENST00000296474	NM_002447.2	1180	cCc/cTc	17/20	1	2	FACETS	0.583	0.507	0.666	0.583	0.507	0.666	SUBCLONAL	1	TRUE	1	0.2	2		628	1218	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711904	89711904	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs786201867	NA	P-0006527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	65	279	0	ENST00000371953.3:c.522T>G	p.Tyr174Ter	p.Y174*	ENST00000371953	NM_000314.4	174	taT/taG	6/9	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.2	2		279	461	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115888	8115889	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0006527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	43	323	0	ENST00000346208.3:c.1236dup	p.Ser413GlnfsTer94	p.S413Qfs*94	ENST00000346208		412	tcc/tCcc	6/6	1	2	FACETS	0.568	0.474	0.673	0.568	0.474	0.673	SUBCLONAL	1	TRUE	1	0.2	2		323	757	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645738	215645738	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	18	394	0	ENST00000260947.4:c.860A>C	p.Glu287Ala	p.E287A	ENST00000260947	NM_000465.2	287	gAg/gCg	4/11	0.147847775628741	1	FACETS	0.781	0.589	1	0.781	0.589	1	CLONAL	1	TRUE	0	0.16	1		394	265	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046053	180046053	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	15	232	0	ENST00000261937.6:c.2818C>A	p.Arg940Ser	p.R940S	ENST00000261937	NM_182925.4	940	Cgc/Agc	20/30	1	2	FACETS	0.856	0.627	1	0.856	0.627	1	CLONAL	1	TRUE	1	0.16	2		232	219	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553561	106553561	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	28	253	0	ENST00000369096.4:c.1526C>A	p.Ala509Asp	p.A509D	ENST00000369096	NM_001198.3	509	gCc/gAc	5/7	1	2	FACETS	0.882	0.704	1	0.882	0.704	1	CLONAL	1	TRUE	1	0.16	2		253	397	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436112	49436112	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	10	101	0	ENST00000301067.7:c.5869G>T	p.Glu1957Ter	p.E1957*	ENST00000301067	NM_003482.3	1957	Gag/Tag	28/54	1	2	FACETS	0.822	0.559	1	0.822	0.559	1	CLONAL	1	TRUE	1	0.16	2		101	152	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220436	133220436	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	55	403	0	ENST00000320574.5:c.4277T>C	p.Val1426Ala	p.V1426A	ENST00000320574	NM_006231.2	1426	gTa/gCa	33/49	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.16	2		403	530	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237688	133237688	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878854857	NA	P-0006540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	62	520	1	ENST00000320574.5:c.2927G>A	p.Arg976His	p.R976H	ENST00000320574	NM_006231.2	976	cGc/cAc	25/49	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.16	2		521	675	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602872	10602872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	95	522	2	ENST00000171111.5:c.706G>A	p.Asp236Asn	p.D236N	ENST00000171111	NM_203500.1	236	Gac/Aac	3/6	1	2	FACETS	0.869	0.774	0.97	1	0.984	1	CLONAL	2	TRUE	1	0.16	2		524	683	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368244	31368244	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	35	424	0	ENST00000328111.2:c.115G>T	p.Glu39Ter	p.E39*	ENST00000328111	NM_006892.3	39	Gag/Tag	2/23	1	2	FACETS	0.766	0.627	0.923	0.766	0.627	0.923	CLONAL	1	TRUE	1	0.16	2		424	571	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092948	29092948	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs201206424	NA	P-0006540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	38	530	0	ENST00000328354.6:c.1036C>G	p.Arg346Gly	p.R346G	ENST00000328354	NM_007194.3	346	Cgt/Ggt	10/15	0.169777162175093	3	FACETS	1	0.852	1	0.517	0.427	0.618	CLONAL	1	TRUE	1	0.16	3		530	496	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63810748	63810749	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0006540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	20	334	0	ENST00000279873.7:c.837dup	p.Val280ArgfsTer7	p.V280Rfs*7	ENST00000279873	NM_032199.2	279	gcc/gCcc	5/10	1	2	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	TRUE	1	0.16	2		334	214	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578473	7578474	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0006540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	47	487	0	ENST00000269305.4:c.456dup	p.Pro153AlafsTer28	p.P153Afs*28	ENST00000269305	NM_001126112.2	152	-/G	5/11	1	2	FACETS	0.94	0.792	1	0.94	0.792	1	CLONAL	1	TRUE	1	0.16	2		487	625	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231723	66231724	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0006540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	17	455	1	ENST00000273854.3:c.1976_1977delinsAA	p.Pro659Gln	p.P659Q	ENST00000273854	NM_004439.5	659	cCC/cAA	11/18	0.3	1	FACETS	0.732	0.547	0.952	0.732	0.547	0.952	CLONAL	1	TRUE	0	0.16	1		456	267	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0006561-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	74	509	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	0.386361363776075	2		509	361	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0006561-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	92	599	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.982	0.876	1	0.982	0.876	1	CLONAL	1	TRUE	1	0.386361363776075	2		599	485	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911542	101911542	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006561-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	87	409	0	ENST00000374994.4:c.1467G>C	p.Lys489Asn	p.K489N	ENST00000374994	NM_004612.2	489	aaG/aaC	9/9	0.386361363776075	1	FACETS	0.966	0.862	1	0.966	0.862	1	CLONAL	1	TRUE	0	0.386361363776075	1		409	376	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099939	27099940	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0006561-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	85	464	0	ENST00000324856.7:c.3821dup	p.Pro1275ThrfsTer12	p.P1275Tfs*12	ENST00000324856	NM_006015.4	1273	atg/atGg	15/20	1	2	FACETS	0.815	0.722	0.914	0.815	0.722	0.914	CLONAL	1	TRUE	1	0.386361363776075	2		464	540	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041669	47041669	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006561-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	93	513	0	ENST00000377604.3:c.1896del	p.Ser633ArgfsTer71	p.S633Rfs*71	ENST00000377604	NM_001204468.1	632	Ccc/cc	17/24	0.324897086134201	1	FACETS	0.676	0.602	0.754	0.676	0.602	0.754	SUBCLONAL	1	TRUE	0	0.386361363776075	1		513	575	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094280	27094280	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0006561-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	26	242	0	ENST00000324856.7:c.2989-1G>A		p.X997_splice	ENST00000324856	NM_006015.4	997			1	2	FACETS	0.418	0.331	0.517	0.418	0.331	0.517	SUBCLONAL	1	TRUE	1	0.386361363776075	2		242	322	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593528	48593528	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006561-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	16	267	0	ENST00000342988.3:c.1279C>G	p.His427Asp	p.H427D	ENST00000342988	NM_005359.5	427	Cat/Gat	10/12	0.287486333152592	1	FACETS	0.209	0.154	0.275	0.209	0.154	0.275	SUBCLONAL	1	TRUE	0	0.386361363776075	1		267	320	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	27	604	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.131	0.103	0.162	0.131	0.103	0.162	SUBCLONAL	1	TRUE	1	0.37	2		604	1118	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	114	574	2	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	1	2	FACETS	0.638	0.573	0.706	0.638	0.573	0.706	SUBCLONAL	1	TRUE	1	0.37	2		576	966	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	13	299	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.127	0.09	0.173	0.127	0.09	0.173	SUBCLONAL	1	TRUE	1	0.37	2		299	553	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	175	378	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.37	2		378	744	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662481	227662481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	48	397	1	ENST00000305123.5:c.974G>A	p.Arg325His	p.R325H	ENST00000305123	NM_005544.2	325	cGt/cAt	1/2	1	2	FACETS	0.4	0.337	0.469	0.4	0.337	0.469	SUBCLONAL	1	TRUE	1	0.37	2		398	649	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612268	189612268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs972760958	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	84	395	0	ENST00000264731.3:c.2020C>T	p.Arg674Cys	p.R674C	ENST00000264731	NM_003722.4	674	Cgc/Tgc	14/14	1	2	FACETS	0.776	0.686	0.872	0.776	0.686	0.872	SUBCLONAL	1	TRUE	1	0.37	2		395	585	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057642	180057642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150416750	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	249	549	0	ENST00000261937.6:c.313G>A	p.Asp105Asn	p.D105N	ENST00000261937	NM_182925.4	105	Gac/Aac	3/30	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.37	2		549	985	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270085	198270085	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	143	594	1	ENST00000335508.6:c.1351C>T	p.Arg451Ter	p.R451*	ENST00000335508	NM_012433.2	451	Cga/Tga	10/25	1	2	FACETS	0.866	0.789	0.946	0.866	0.789	0.946	CLONAL	1	TRUE	1	0.37	2		595	893	SUCCESS
B2M	567	MSKCC	GRCh37	15	45008529	45008529	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	330	458	0	ENST00000558401.1:c.349C>T	p.Arg117Ter	p.R117*	ENST00000558401	NM_004048.2	117	Cga/Tga	3/4	1	2	FACETS	1	0.982	1	1	0.996	1	CLONAL	2	TRUE	1	0.37	2		458	831	SUCCESS
AR	367	MSKCC	GRCh37	X	66765883	66765883	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1213709903	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	306	634	1	ENST00000374690.3:c.895G>A	p.Ala299Thr	p.A299T	ENST00000374690	NM_000044.3	299	Gca/Aca	1/8	1	2	FACETS	0.801	0.756	0.848	1	0.995	1	CLONAL	2	TRUE	1	0.37	2		635	1032	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546931	9546931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs562732119	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	89	446	0	ENST00000353224.5:c.1091C>T	p.Ser364Leu	p.S364L	ENST00000353224	NM_177990.2	364	tCg/tTg	5/10	0.0958005913417619	0	FACETS	0.378	0.334	0.424			1	INDETERMINATE	1	TRUE	0	0.37	0		446	802	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913283	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	48	576	1	ENST00000263967.3:c.3129G>T	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atT	21/21	1	2	FACETS	0.337	0.284	0.396	0.337	0.284	0.396	SUBCLONAL	1	TRUE	1	0.37	2		577	770	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042434	16042434	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1568277803	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	133	610	0	ENST00000268712.3:c.1240C>T	p.Arg414Ter	p.R414*	ENST00000268712	NM_006311.3	414	Cga/Tga	12/46	1	2	FACETS	0.851	0.773	0.933	0.851	0.773	0.933	CLONAL	1	TRUE	1	0.37	2		610	845	SUCCESS
APC	324	MSKCC	GRCh37	5	112177049	112177049	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	232	632	0	ENST00000257430.4:c.5758C>T	p.Arg1920Ter	p.R1920*	ENST00000257430	NM_000038.5	1920	Cga/Tga	16/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.37	2		632	1149	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201874	152201874	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753014570	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	154	446	2	ENST00000206249.3:c.728G>A	p.Arg243His	p.R243H	ENST00000206249	NM_000125.3	243	cGt/cAt	3/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.37	2		448	720	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099338	193099338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	182	480	1	ENST00000367435.3:c.272G>A	p.Arg91Gln	p.R91Q	ENST00000367435	NM_024529.4	91	cGa/cAa	3/17	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.37	2		481	788	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453486	138453486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451809865	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	240	579	2	ENST00000289153.2:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000289153	NM_006219.2	321	cGa/cAa	5/22	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.37	2		581	1038	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604736	48604736	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	184	557	0	ENST00000342988.3:c.1558G>T	p.Glu520Ter	p.E520*	ENST00000342988	NM_005359.5	520	Gaa/Taa	12/12	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.37	2		557	736	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743864	41743864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753706427	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	204	550	0	ENST00000301178.4:c.799G>A	p.Asp267Asn	p.D267N	ENST00000301178	NM_021913.4	267	Gat/Aat	7/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.37	2		550	873	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	248	437	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.37	2		437	992	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938835	178938835	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500029	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	23	26	0	ENST00000263967.3:c.2077C>T	p.Arg693Cys	p.R693C	ENST00000263967	NM_006218.2	693	Cgt/Tgt	14/21	1	2	FACETS	1	0.85	1	1	0.954	1	CLONAL	2	TRUE	1	0.37	2		26	59	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573894	18573894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759658584	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	169	522	0	ENST00000266497.5:c.2212C>T	p.Arg738Cys	p.R738C	ENST00000266497		738	Cgt/Tgt	15/31	0.0958005913417619	0	FACETS	0.814	0.75	0.88			1	INDETERMINATE	1	TRUE	0	0.37	0		522	707	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660639	190660639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772181508	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	155	426	0	ENST00000441310.2:c.277C>T	p.Arg93Cys	p.R93C	ENST00000441310	NM_000534.4	93	Cgt/Tgt	3/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.37	2		426	650	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922973	44922973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	457	752	2	ENST00000377967.4:c.1834C>T	p.Arg612Ter	p.R612*	ENST00000377967	NM_021140.2	612	Cga/Tga	16/29	1	2	FACETS	0.874	0.834	0.915	1	0.997	1	CLONAL	2	TRUE	1	0.37	2		754	1413	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890221	72890221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752101890	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	123	592	2	ENST00000325599.8:c.461G>A	p.Arg154Gln	p.R154Q	ENST00000325599	NM_018130.2	154	cGa/cAa	4/11	1	2	FACETS	0.728	0.658	0.803	0.728	0.658	0.803	SUBCLONAL	1	TRUE	1	0.37	2		594	913	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275290	41275290	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113411271	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	71	448	0	ENST00000349496.5:c.1456C>T	p.Arg486Cys	p.R486C	ENST00000349496	NM_001904.3	486	Cgc/Tgc	9/15	1	2	FACETS	0.533	0.465	0.607	0.533	0.465	0.607	SUBCLONAL	1	TRUE	1	0.37	2		448	720	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591825	48591825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767342	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	202	572	0	ENST00000342988.3:c.988G>A	p.Glu330Lys	p.E330K	ENST00000342988	NM_005359.5	330	Gaa/Aaa	9/12	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.37	2		572	791	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411444	63411444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	259	658	1	ENST00000330258.3:c.1723C>T	p.Arg575Trp	p.R575W	ENST00000330258	NM_152424.3	575	Cgg/Tgg	2/2	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.37	2		659	1067	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418997	116418997	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200754673	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	41	352	0	ENST00000397752.3:c.3508C>T	p.Arg1170Ter	p.R1170*	ENST00000397752	NM_000245.2	1170	Cga/Tga	17/21	1	2	FACETS	0.447	0.372	0.53	0.447	0.372	0.53	SUBCLONAL	1	TRUE	1	0.37	2		352	496	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760819	133760819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769953778	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	202	478	0	ENST00000318560.5:c.3142G>A	p.Glu1048Lys	p.E1048K	ENST00000318560	NM_005157.4	1048	Gag/Aag	11/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.37	2		478	782	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484414	57484414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	357	492	0	ENST00000371085.3:c.595C>T	p.Arg199Cys	p.R199C	ENST00000371085	NM_000516.4	199	Cgc/Tgc	8/13	0.3	4	FACETS	0.877	0.833	0.922			1	CLONAL	3	TRUE	NA	0.37	4		492	1005	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5225773	5225773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1012604149	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	91	527	0	ENST00000357368.4:c.2459G>A	p.Arg820His	p.R820H	ENST00000357368	NM_002850.3	820	cGc/cAc	17/38	1	2	FACETS	0.575	0.51	0.645	0.575	0.51	0.645	SUBCLONAL	1	TRUE	1	0.37	2		527	855	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59770824	59770824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45572934	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	204	589	1	ENST00000259008.2:c.2542C>T	p.Arg848Cys	p.R848C	ENST00000259008	NM_032043.2	848	Cgc/Tgc	18/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.37	2		590	808	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394896	394896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	153	477	1	ENST00000380956.4:c.292C>T	p.Arg98Trp	p.R98W	ENST00000380956	NM_001195286.1	98	Cgg/Tgg	3/9	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.37	2		478	761	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216476	108216477	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587782558	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	211	500	1	ENST00000278616.4:c.8432dup	p.Ser2812ValfsTer3	p.S2812Vfs*3	ENST00000278616	NM_000051.3	2809	caa/cAaa	58/63	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.37	2		501	866	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134142	41134142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144907712	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	122	727	0	ENST00000379561.5:c.1486G>A	p.Val496Ile	p.V496I	ENST00000379561	NM_002015.3	496	Gtc/Atc	2/3	1	2	FACETS	0.544	0.49	0.601	0.544	0.49	0.601	SUBCLONAL	1	TRUE	1	0.37	2		727	1212	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716138	243716138	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	198	634	0	ENST00000263826.5:c.1056G>T	p.Glu352Asp	p.E352D	ENST00000263826	NM_005465.4	352	gaG/gaT	10/13	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.37	2		634	820	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612028	189612028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs900140738	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	48	405	1	ENST00000264731.3:c.1780C>T	p.Arg594Ter	p.R594*	ENST00000264731	NM_003722.4	594	Cga/Tga	14/14	1	2	FACETS	0.402	0.339	0.472	0.402	0.339	0.472	SUBCLONAL	1	TRUE	1	0.37	2		406	645	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733279	40733279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201275244	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	247	389	0	ENST00000373198.4:c.3527G>A	p.Arg1176His	p.R1176H	ENST00000373198	NM_133170.3	1176	cGt/cAt	26/32	0.181860191193325	2	FACETS	0.864	0.81	0.918	0.864	0.81	0.918	INDETERMINATE	2	TRUE	0	0.37	2		389	773	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213873	66213873	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1383933498	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	61	613	1	ENST00000273854.3:c.2557C>T	p.Arg853Ter	p.R853*	ENST00000273854	NM_004439.5	853	Cga/Tga	15/18	0.0958005913417619	0	FACETS	0.259	0.223	0.299			1	INDETERMINATE	1	TRUE	0	0.37	0		614	802	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955481	48955481	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237070816	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	81	600	0	ENST00000267163.4:c.1597G>A	p.Glu533Lys	p.E533K	ENST00000267163	NM_000321.2	533	Gaa/Aaa	17/27	1	2	FACETS	0.459	0.404	0.52	0.459	0.404	0.52	SUBCLONAL	1	TRUE	1	0.37	2		600	953	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366990	118366990	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	83	612	0	ENST00000534358.1:c.5572C>T	p.Arg1858Ter	p.R1858*	ENST00000534358	NM_005933.3	1858	Cga/Tga	20/36	1	2	FACETS	0.485	0.427	0.548	0.485	0.427	0.548	SUBCLONAL	1	TRUE	1	0.37	2		612	925	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	192	285	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.37	2		285	769	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92252390	92252390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373488172	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	194	440	1	ENST00000265734.4:c.658C>T	p.Arg220Cys	p.R220C	ENST00000265734	NM_001259.6	220	Cgt/Tgt	6/8	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.37	2		441	713	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331980	81331980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1383506132	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	203	625	0	ENST00000222390.5:c.2104C>T	p.Arg702Cys	p.R702C	ENST00000222390	NM_000601.4	702	Cgt/Tgt	18/18	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.37	2		625	790	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624840	9624840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1184049921	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	113	534	0	ENST00000353224.5:c.137C>T	p.Thr46Met	p.T46M	ENST00000353224	NM_177990.2	46	aCg/aTg	3/10	0.0958005913417619	0	FACETS	0.474	0.427	0.525			1	INDETERMINATE	1	TRUE	0	0.37	0		534	811	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698180	47698180	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63751411	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	229	506	0	ENST00000233146.2:c.1738G>T	p.Glu580Ter	p.E580*	ENST00000233146	NM_000251.2	580	Gaa/Taa	11/16	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.37	2		506	917	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	51	343	1	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	0.452	0.384	0.527	0.452	0.384	0.527	SUBCLONAL	1	TRUE	1	0.37	2		344	610	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938090	76938090	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	270	589	0	ENST00000373344.5:c.2658G>T	p.Glu886Asp	p.E886D	ENST00000373344	NM_000489.3	886	gaG/gaT	9/35	1	2	FACETS	0.839	0.789	0.89	1	0.994	1	CLONAL	2	TRUE	1	0.37	2		589	870	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715678	30715678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039551	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	228	527	0	ENST00000295754.5:c.1336G>A	p.Asp446Asn	p.D446N	ENST00000295754	NM_003242.5	446	Gat/Aat	5/7	1	2	FACETS	0.753	0.704	0.804	1	0.992	1	SUBCLONAL	2	TRUE	1	0.37	2		527	818	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132927	64132927	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145356210	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	202	523	2	ENST00000334205.4:c.1061G>A	p.Arg354Gln	p.R354Q	ENST00000334205	NM_003942.2	354	cGa/cAa	9/17	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.37	2		525	859	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339175	65339175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180823763	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	188	445	0	ENST00000342505.4:c.361G>A	p.Asp121Asn	p.D121N	ENST00000342505	NM_002227.2	121	Gac/Aac	5/25	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.37	2		445	783	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570260	87570260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777251032	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	120	445	0	ENST00000277120.3:c.2000C>T	p.Ser667Leu	p.S667L	ENST00000277120		667	tCg/tTg	17/19	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.37	2		445	571	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578433	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	197	469	0	ENST00000269305.4:c.497C>A	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	166	tCa/tAa	5/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.37	2		469	816	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073739	8073739	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1361059014	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	659	866	0	ENST00000377482.5:c.920C>T	p.Ser307Leu	p.S307L	ENST00000377482	NM_018948.3	307	tCg/tTg	4/4	1	2	FACETS	0.867	0.838	0.896	1	0.998	1	CLONAL	3	TRUE	1	0.37	2		866	1370	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162904	47162904	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs757432733	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	221	622	0	ENST00000409792.3:c.3222G>T	p.Lys1074Asn	p.K1074N	ENST00000409792	NM_014159.6	1074	aaG/aaT	3/21	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.37	2		622	928	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214404	55214404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770290445	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	119	441	1	ENST00000275493.2:c.530C>T	p.Ser177Leu	p.S177L	ENST00000275493	NM_005228.3	177	tCg/tTg	4/28	1	2	FACETS	0.776	0.7	0.856	0.776	0.7	0.856	SUBCLONAL	1	TRUE	1	0.37	2		442	829	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073588	8073588	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	303	764	0	ENST00000377482.5:c.1071G>T	p.Lys357Asn	p.K357N	ENST00000377482	NM_018948.3	357	aaG/aaT	4/4	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.37	2		764	1352	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781554	9781554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs993552815	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	202	514	0	ENST00000377346.4:c.1864G>A	p.Glu622Lys	p.E622K	ENST00000377346	NM_005026.3	622	Gag/Aag	15/24	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.37	2		514	794	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182154	11182154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	176	636	2	ENST00000361445.4:c.6692C>T	p.Ser2231Leu	p.S2231L	ENST00000361445	NM_004958.3	2231	tCg/tTg	48/58	1	2	FACETS	0.956	0.88	1	0.956	0.88	1	CLONAL	1	TRUE	1	0.37	2		638	995	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11269467	11269467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	57	563	0	ENST00000361445.4:c.3703C>T	p.Arg1235Trp	p.R1235W	ENST00000361445	NM_004958.3	1235	Cgg/Tgg	25/58	1	2	FACETS	0.315	0.269	0.365	0.315	0.269	0.365	SUBCLONAL	1	TRUE	1	0.37	2		563	978	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317015	11317015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759750826	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	41	451	2	ENST00000361445.4:c.479G>A	p.Arg160His	p.R160H	ENST00000361445	NM_004958.3	160	cGc/cAc	4/58	1	2	FACETS	0.28	0.232	0.334	0.28	0.232	0.334	SUBCLONAL	1	TRUE	1	0.37	2		453	791	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245451	16245451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	120	487	0	ENST00000375759.3:c.1426C>T	p.Pro476Ser	p.P476S	ENST00000375759	NM_015001.2	476	Cct/Tct	7/15	1	2	FACETS	0.774	0.699	0.854	0.774	0.699	0.854	SUBCLONAL	1	TRUE	1	0.37	2		487	838	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256750	16256750	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760134992	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	169	516	1	ENST00000375759.3:c.4015C>T	p.Arg1339Cys	p.R1339C	ENST00000375759	NM_015001.2	1339	Cgt/Tgt	11/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.37	2		517	706	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260188	16260188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368603571	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	31	306	1	ENST00000375759.3:c.7453G>A	p.Ala2485Thr	p.A2485T	ENST00000375759	NM_015001.2	2485	Gcc/Acc	11/15	1	2	FACETS	0.331	0.267	0.403	0.331	0.267	0.403	SUBCLONAL	1	TRUE	1	0.37	2		307	507	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261472	16261472	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759105956	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	166	491	0	ENST00000375759.3:c.8737G>A	p.Glu2913Lys	p.E2913K	ENST00000375759	NM_015001.2	2913	Gag/Aag	11/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.37	2		491	694	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799114	45799114	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	245	618	1	ENST00000450313.1:c.319G>T	p.Glu107Ter	p.E107*	ENST00000450313	NM_012222.2	107	Gag/Tag	3/16	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.37	2		619	1043	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531836	46531836	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	199	471	1	ENST00000262741.5:c.511G>T	p.Glu171Ter	p.E171*	ENST00000262741	NM_003629.3	171	Gaa/Taa	5/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.37	2		472	809	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743755	46743755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769015770	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	87	546	0	ENST00000371975.4:c.2045G>A	p.Arg682Gln	p.R682Q	ENST00000371975	NM_003579.3	682	cGa/cAa	18/18	1	2	FACETS	0.549	0.485	0.617	0.549	0.485	0.617	SUBCLONAL	1	TRUE	1	0.37	2		546	857	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248229	59248229	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	15	30	0	ENST00000371222.2:c.514A>T	p.Asn172Tyr	p.N172Y	ENST00000371222	NM_002228.3	172	Aac/Tac	1/1	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.37	2		30	55	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248575	59248575	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	103	556	0	ENST00000371222.2:c.168G>T	p.Lys56Asn	p.K56N	ENST00000371222	NM_002228.3	56	aaG/aaT	1/1	1	2	FACETS	0.608	0.543	0.677	0.608	0.543	0.677	SUBCLONAL	1	TRUE	1	0.37	2		556	916	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248629	59248629	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	231	526	0	ENST00000371222.2:c.114G>T	p.Met38Ile	p.M38I	ENST00000371222	NM_002228.3	38	atG/atT	1/1	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.37	2		526	964	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309764	65309764	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	182	459	1	ENST00000342505.4:c.2386G>T	p.Asp796Tyr	p.D796Y	ENST00000342505	NM_002227.2	796	Gac/Tac	17/25	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.37	2		460	795	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873218	71873218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374884396	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	114	791	3	ENST00000357731.5:c.976G>A	p.Ala326Thr	p.A326T	ENST00000357731	NM_173808.2	326	Gct/Act	7/7	1	2	FACETS	0.616	0.553	0.682	0.616	0.553	0.682	SUBCLONAL	1	TRUE	1	0.37	2		794	1001	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165662	118165662	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768091631	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	231	531	0	ENST00000369448.3:c.172C>T	p.Arg58Trp	p.R58W	ENST00000369448	NM_017709.3	58	Cgg/Tgg	2/2	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.37	2		531	889	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166010	118166010	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767827215	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	199	463	0	ENST00000369448.3:c.520C>T	p.Arg174Trp	p.R174W	ENST00000369448	NM_017709.3	174	Cgg/Tgg	2/2	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.37	2		463	809	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459215	120459215	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1221302379	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	117	525	0	ENST00000256646.2:c.6130C>T	p.Arg2044Cys	p.R2044C	ENST00000256646	NM_024408.3	2044	Cgt/Tgt	34/34	1	2	FACETS	0.843	0.761	0.93	0.843	0.761	0.93	CLONAL	1	TRUE	1	0.37	2		525	750	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462920	120462920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372061331	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	48	425	0	ENST00000256646.2:c.5411C>T	p.Ser1804Leu	p.S1804L	ENST00000256646	NM_024408.3	1804	tCg/tTg	30/34	1	2	FACETS	0.306	0.258	0.36	0.306	0.258	0.36	SUBCLONAL	1	TRUE	1	0.37	2		425	847	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834588	156834588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778566154	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	213	505	1	ENST00000524377.1:c.356G>A	p.Arg119His	p.R119H	ENST00000524377	NM_002529.3	119	cGc/cAc	3/17	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.37	2		506	867	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841520	156841520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	197	502	0	ENST00000524377.1:c.823G>A	p.Glu275Lys	p.E275K	ENST00000524377	NM_002529.3	275	Gag/Aag	7/17	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.37	2		502	853	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844404	156844404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199826686	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1191	109	743	2	ENST00000524377.1:c.1237G>A	p.Glu413Lys	p.E413K	ENST00000524377	NM_002529.3	413	Gaa/Aaa	10/17	1	2	FACETS	0.453	0.405	0.504	0.453	0.405	0.504	SUBCLONAL	1	TRUE	1	0.37	2		745	1300	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740230	162740230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs34869543	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	207	586	0	ENST00000367921.3:c.1432C>T	p.Arg478Cys	p.R478C	ENST00000367921	NM_006182.2	478	Cgc/Tgc	12/18	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.37	2		586	902	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740264	162740264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756149068	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	210	550	1	ENST00000367921.3:c.1466G>A	p.Arg489Gln	p.R489Q	ENST00000367921	NM_006182.2	489	cGa/cAa	12/18	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.37	2		551	848	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193219807	193219807	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	120	356	0	ENST00000367435.3:c.1561T>C	p.Tyr521His	p.Y521H	ENST00000367435	NM_024529.4	521	Tac/Cac	17/17	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.37	2		356	550	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945657	206945657	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1274280163	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	241	640	1	ENST00000423557.1:c.124C>T	p.Arg42Ter	p.R42*	ENST00000423557	NM_000572.2	42	Cga/Tga	1/5	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.37	2		641	1112	SUCCESS
FH	2271	MSKCC	GRCh37	1	241661199	241661199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201115573	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	220	506	0	ENST00000366560.3:c.1462G>A	p.Glu488Lys	p.E488K	ENST00000366560	NM_000143.3	488	Gaa/Aaa	10/10	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.37	2		506	855	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858945	243858945	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	124	586	2	ENST00000263826.5:c.120G>T	p.Glu40Asp	p.E40D	ENST00000263826	NM_005465.4	40	gaG/gaT	2/13	1	2	FACETS	0.842	0.762	0.926	0.842	0.762	0.926	CLONAL	1	TRUE	1	0.37	2		588	796	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690253	47690253	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	134	585	0	ENST00000233146.2:c.1470G>T	p.Lys490Asn	p.K490N	ENST00000233146	NM_000251.2	490	aaG/aaT	9/16	1	2	FACETS	0.815	0.74	0.894	0.815	0.74	0.894	CLONAL	1	TRUE	1	0.37	2		585	889	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033396	48033396	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	227	441	2	ENST00000234420.5:c.3700G>T	p.Glu1234Ter	p.E1234*	ENST00000234420	NM_000179.2	1234	Gaa/Taa	8/10	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.37	2		443	832	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61709651	61709651	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	196	408	0	ENST00000401558.2:c.2836C>A	p.Leu946Ile	p.L946I	ENST00000401558	NM_003400.3	946	Ctt/Att	23/25	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.37	2		408	851	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152649	99152649	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	250	635	0	ENST00000074304.5:c.445C>A	p.His149Asn	p.H149N	ENST00000074304	NM_001134224.1	149	Cat/Aat	7/26	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.37	2		635	982	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190656594	190656594	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768047966	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	196	602	0	ENST00000441310.2:c.59C>T	p.Ser20Leu	p.S20L	ENST00000441310	NM_000534.4	20	tCg/tTg	2/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.37	2		602	946	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719513	190719513	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	183	519	0	ENST00000441310.2:c.1515A>C	p.Lys505Asn	p.K505N	ENST00000441310	NM_000534.4	505	aaA/aaC	9/13	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.37	2		519	770	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266828	198266828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs16865307	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	186	493	1	ENST00000335508.6:c.2104C>T	p.Arg702Trp	p.R702W	ENST00000335508	NM_012433.2	702	Cgg/Tgg	15/25	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.37	2		494	756	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570064	212570064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55671017	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	177	521	0	ENST00000342788.4:c.1177C>T	p.Arg393Trp	p.R393W	ENST00000342788	NM_005235.2	393	Cgg/Tgg	10/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.37	2		521	859	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812263	212812263	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	71	564	0	ENST00000342788.4:c.313A>T	p.Ile105Phe	p.I105F	ENST00000342788	NM_005235.2	105	Att/Ttt	3/28	1	2	FACETS	0.462	0.403	0.527	0.462	0.403	0.527	SUBCLONAL	1	TRUE	1	0.37	2		564	830	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660213	227660213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372681714	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	194	532	1	ENST00000305123.5:c.3242G>A	p.Arg1081His	p.R1081H	ENST00000305123	NM_005544.2	1081	cGc/cAc	1/2	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.37	2		533	814	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650389	12650389	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	179	523	0	ENST00000251849.4:c.457G>T	p.Asp153Tyr	p.D153Y	ENST00000251849	NM_002880.3	153	Gac/Tac	5/17	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.37	2		523	753	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158222	47158222	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	98	396	0	ENST00000409792.3:c.4477G>T	p.Asp1493Tyr	p.D1493Y	ENST00000409792	NM_014159.6	1493	Gat/Tat	4/21	1	2	FACETS	0.722	0.644	0.805	0.722	0.644	0.805	SUBCLONAL	1	TRUE	1	0.37	2		396	734	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162039	47162039	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	220	521	0	ENST00000409792.3:c.4087G>A	p.Asp1363Asn	p.D1363N	ENST00000409792	NM_014159.6	1363	Gac/Aac	3/21	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.37	2		521	865	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162812	47162812	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	147	396	0	ENST00000409792.3:c.3314G>T	p.Arg1105Ile	p.R1105I	ENST00000409792	NM_014159.6	1105	aGa/aTa	3/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.37	2		396	689	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933462	49933462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368644133	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	267	662	1	ENST00000296474.3:c.2728C>T	p.Arg910Trp	p.R910W	ENST00000296474	NM_002447.2	910	Cgg/Tgg	11/20	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.37	2		663	973	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637690	52637690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239654517	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	244	547	0	ENST00000394830.3:c.2626C>T	p.Arg876Cys	p.R876C	ENST00000394830	NM_018313.4	876	Cgt/Tgt	18/30	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.37	2		547	972	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52685797	52685797	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	221	582	0	ENST00000394830.3:c.675G>T	p.Lys225Asn	p.K225N	ENST00000394830	NM_018313.4	225	aaG/aaT	7/30	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.37	2		582	940	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090524	71090524	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs914703084	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	193	634	1	ENST00000318789.4:c.824C>T	p.Ala275Val	p.A275V	ENST00000318789	NM_032682.5	275	gCc/gTc	11/21	1	2	FACETS	0.879	0.812	0.949	0.879	0.812	0.949	CLONAL	1	TRUE	1	0.37	2		635	1187	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259265	89259265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	53	564	0	ENST00000336596.2:c.409G>A	p.Glu137Lys	p.E137K	ENST00000336596	NM_005233.5	137	Gag/Aag	3/17	1	2	FACETS	0.414	0.352	0.482	0.414	0.352	0.482	SUBCLONAL	1	TRUE	1	0.37	2		564	692	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259409	89259409	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	244	778	0	ENST00000336596.2:c.553G>T	p.Asp185Tyr	p.D185Y	ENST00000336596	NM_005233.5	185	Gat/Tat	3/17	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.37	2		778	1031	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259413	89259413	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	79	779	0	ENST00000336596.2:c.557T>C	p.Val186Ala	p.V186A	ENST00000336596	NM_005233.5	186	gTt/gCt	3/17	1	2	FACETS	0.415	0.363	0.47	0.415	0.363	0.47	SUBCLONAL	1	TRUE	1	0.37	2		779	1030	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390995	89390995	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144727411	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	164	637	0	ENST00000336596.2:c.1061G>A	p.Arg354Gln	p.R354Q	ENST00000336596	NM_005233.5	354	cGg/cAg	5/17	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.37	2		637	861	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403560	138403560	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	211	609	3	ENST00000289153.2:c.2222C>T	p.Ala741Val	p.A741V	ENST00000289153	NM_006219.2	741	gCc/gTc	15/22	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.37	2		612	883	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417901	138417901	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	180	400	0	ENST00000289153.2:c.1618G>T	p.Glu540Ter	p.E540*	ENST00000289153	NM_006219.2	540	Gaa/Taa	11/22	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.37	2		400	758	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138423304	138423304	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs902854177	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	170	502	0	ENST00000289153.2:c.1562G>A	p.Ser521Asn	p.S521N	ENST00000289153	NM_006219.2	521	aGt/aAt	10/22	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.37	2		502	756	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231170	142231170	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	263	633	0	ENST00000350721.4:c.4784A>C	p.Lys1595Thr	p.K1595T	ENST00000350721	NM_001184.3	1595	aAa/aCa	27/47	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.37	2		633	1060	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269009	142269009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369913351	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	217	646	0	ENST00000350721.4:c.2941G>A	p.Val981Ile	p.V981I	ENST00000350721	NM_001184.3	981	Gtt/Att	14/47	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.37	2		646	989	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191251	185191251	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	68	341	0	ENST00000265026.3:c.2132C>A	p.Ser711Tyr	p.S711Y	ENST00000265026	NM_004721.4	711	tCt/tAt	11/14	1	2	FACETS	0.649	0.565	0.74	0.649	0.565	0.74	SUBCLONAL	1	TRUE	1	0.37	2		341	566	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191437	185191437	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs374399820	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	114	486	0	ENST00000265026.3:c.2318C>A	p.Ser773Tyr	p.S773Y	ENST00000265026	NM_004721.4	773	tCt/tAt	11/14	1	2	FACETS	0.741	0.666	0.819	0.741	0.666	0.819	SUBCLONAL	1	TRUE	1	0.37	2		486	832	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582042	189582042	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	205	481	0	ENST00000264731.3:c.601C>A	p.Leu201Ile	p.L201I	ENST00000264731	NM_003722.4	201	Ctc/Atc	5/14	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.37	2		481	866	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808377	1808377	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886024	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	62	486	0	ENST00000260795.2:c.2135G>A	p.Arg712His	p.R712H	ENST00000260795		712	cGc/cAc	15/17	0.3	2	FACETS	0.447	0.385	0.514			1	SUBCLONAL	1	TRUE	NA	0.37	2		486	750	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140793	55140793	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	178	390	1	ENST00000257290.5:c.1653+1G>A		p.X551_splice	ENST00000257290	NM_006206.4	551			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.37	NA		391	776	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573323	55573323	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	232	556	2	ENST00000288135.5:c.985G>T	p.Glu329Ter	p.E329*	ENST00000288135	NM_000222.2	329	Gaa/Taa	6/21	0.0958005913417619	0	FACETS	0.854	0.797	0.913			1	INDETERMINATE	1	TRUE	0	0.37	0		558	925	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955615	55955615	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	108	549	0	ENST00000263923.4:c.3330G>T	p.Lys1110Asn	p.K1110N	ENST00000263923	NM_002253.2	1110	aaG/aaT	25/30	0.0958005913417619	0	FACETS	0.417	0.374	0.464			1	INDETERMINATE	1	TRUE	0	0.37	0		549	881	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981166	55981166	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	180	686	0	ENST00000263923.4:c.533C>A	p.Ser178Tyr	p.S178Y	ENST00000263923	NM_002253.2	178	tCc/tAc	5/30	0.0958005913417619	0	FACETS	0.751	0.694	0.811			1	INDETERMINATE	1	TRUE	0	0.37	0		686	816	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197845	66197845	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	39	423	0	ENST00000273854.3:c.2854G>T	p.Val952Leu	p.V952L	ENST00000273854	NM_004439.5	952	Gta/Tta	17/18	0.0958005913417619	0	FACETS	0.255	0.211	0.304			1	INDETERMINATE	1	TRUE	0	0.37	0		423	521	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201816	66201816	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556854839	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	72	446	1	ENST00000273854.3:c.2686C>T	p.Arg896Cys	p.R896C	ENST00000273854	NM_004439.5	896	Cgt/Tgt	16/18	0.0958005913417619	0	FACETS	0.432	0.378	0.491			1	INDETERMINATE	1	TRUE	0	0.37	0		447	567	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231757	66231757	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	105	504	0	ENST00000273854.3:c.1943G>A	p.Arg648Lys	p.R648K	ENST00000273854	NM_004439.5	648	aGa/aAa	11/18	0.0958005913417619	0	FACETS	0.619	0.556	0.685			1	INDETERMINATE	1	TRUE	0	0.37	0		504	578	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286171	66286171	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	109	608	1	ENST00000273854.3:c.1515G>T	p.Lys505Asn	p.K505N	ENST00000273854	NM_004439.5	505	aaG/aaT	6/18	0.0958005913417619	0	FACETS	0.446	0.4	0.494			1	INDETERMINATE	1	TRUE	0	0.37	0		609	833	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99812457	99812457	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	201	537	0	ENST00000280892.6:c.212A>G	p.Asp71Gly	p.D71G	ENST00000280892	NM_001130678.1	71	gAt/gGt	3/7	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.37	2		537	901	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155491	106155491	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	55	629	0	ENST00000380013.4:c.392G>T	p.Arg131Ile	p.R131I	ENST00000380013	NM_001127208.2	131	aGa/aTa	3/11	1	2	FACETS	0.285	0.242	0.331	0.285	0.242	0.331	SUBCLONAL	1	TRUE	1	0.37	2		629	1044	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164897	106164897	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	78	358	0	ENST00000380013.4:c.3765C>A	p.Tyr1255Ter	p.Y1255*	ENST00000380013	NM_001127208.2	1255	taC/taA	6/11	1	2	FACETS	0.688	0.605	0.777	0.688	0.605	0.777	SUBCLONAL	1	TRUE	1	0.37	2		358	613	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180834	106180834	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	163	536	0	ENST00000380013.4:c.3862G>T	p.Gly1288Cys	p.G1288C	ENST00000380013	NM_001127208.2	1288	Ggt/Tgt	7/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.37	2		536	681	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196355	106196355	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	263	643	0	ENST00000380013.4:c.4688C>A	p.Ser1563Tyr	p.S1563Y	ENST00000380013	NM_001127208.2	1563	tCt/tAt	11/11	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.37	2		643	1052	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332586	153332586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768666009	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	96	601	2	ENST00000281708.4:c.370G>A	p.Asp124Asn	p.D124N	ENST00000281708	NM_033632.3	124	Gat/Aat	2/12	1	2	FACETS	0.569	0.506	0.636	0.569	0.506	0.636	SUBCLONAL	1	TRUE	1	0.37	2		603	912	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332946	153332946	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	72	329	0	ENST00000281708.4:c.10G>T	p.Glu4Ter	p.E4*	ENST00000281708	NM_033632.3	4	Gaa/Taa	2/12	1	2	FACETS	0.85	0.745	0.962	0.85	0.745	0.962	CLONAL	1	TRUE	1	0.37	2		329	458	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518306	187518306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs935510544	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	13	151	0	ENST00000441802.2:c.12388G>A	p.Glu4130Lys	p.E4130K	ENST00000441802	NM_005245.3	4130	Gag/Aag	25/27	1	2	FACETS	0.325	0.232	0.439	0.325	0.232	0.439	SUBCLONAL	1	TRUE	1	0.37	2		151	216	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524933	187524933	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749223648	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	79	642	2	ENST00000441802.2:c.10747G>A	p.Asp3583Asn	p.D3583N	ENST00000441802	NM_005245.3	3583	Gac/Aac	19/27	1	2	FACETS	0.417	0.366	0.473	0.417	0.366	0.473	SUBCLONAL	1	TRUE	1	0.37	2		644	1024	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527280	187527280	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554538206	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	201	410	0	ENST00000441802.2:c.10294G>A	p.Asp3432Asn	p.D3432N	ENST00000441802	NM_005245.3	3432	Gat/Aat	17/27	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.37	2		410	828	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532645	187532645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	247	514	0	ENST00000441802.2:c.9748C>A	p.Leu3250Ile	p.L3250I	ENST00000441802	NM_005245.3	3250	Ctt/Att	14/27	1	2	FACETS	0.869	0.816	0.924	1	0.994	1	CLONAL	2	TRUE	1	0.37	2		514	768	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260645	1260645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773537902	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	241	480	1	ENST00000310581.5:c.2914C>T	p.Arg972Cys	p.R972C	ENST00000310581	NM_198253.2	972	Cgc/Tgc	12/16	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.37	2		481	923	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959942	38959942	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	206	623	0	ENST00000357387.3:c.1990G>T	p.Gly664Ter	p.G664*	ENST00000357387	NM_152756.3	664	Gga/Tga	21/38	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.37	2		623	947	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38960001	38960001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	86	494	0	ENST00000357387.3:c.1931G>A	p.Arg644Lys	p.R644K	ENST00000357387	NM_152756.3	644	aGa/aAa	21/38	1	2	FACETS	0.601	0.531	0.676	0.601	0.531	0.676	SUBCLONAL	1	TRUE	1	0.37	2		494	773	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161716	56161716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1416688558	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	70	525	0	ENST00000399503.3:c.1213C>T	p.Arg405Cys	p.R405C	ENST00000399503	NM_005921.1	405	Cgt/Tgt	6/20	1	2	FACETS	0.429	0.373	0.49	0.429	0.373	0.49	SUBCLONAL	1	TRUE	1	0.37	2		525	882	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177587	56177587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371287681	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	214	618	1	ENST00000399503.3:c.2560C>T	p.Arg854Cys	p.R854C	ENST00000399503	NM_005921.1	854	Cgc/Tgc	14/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.37	2		619	927	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178104	56178104	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	142	413	0	ENST00000399503.3:c.3077C>A	p.Ser1026Tyr	p.S1026Y	ENST00000399503	NM_005921.1	1026	tCt/tAt	14/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.37	2		413	555	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750466	57750466	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	216	658	0	ENST00000274289.3:c.2002G>T	p.Glu668Ter	p.E668*	ENST00000274289	NM_006622.3	668	Gaa/Taa	14/14	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.37	2		658	896	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751901	57751901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148954251	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	241	584	0	ENST00000274289.3:c.1336C>T	p.Arg446Trp	p.R446W	ENST00000274289	NM_006622.3	446	Cgg/Tgg	10/14	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.37	2		584	926	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592027	67592027	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	147	480	1	ENST00000274335.5:c.1843G>T	p.Asp615Tyr	p.D615Y	ENST00000274335		615	Gat/Tat	14/15	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.37	2		481	764	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672219	86672219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194205020	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	103	297	0	ENST00000274376.6:c.2021G>A	p.Arg674His	p.R674H	ENST00000274376	NM_002890.2	674	cGc/cAc	16/25	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.37	2		297	416	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672842	86672842	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	131	390	0	ENST00000274376.6:c.2329G>T	p.Glu777Ter	p.E777*	ENST00000274376	NM_002890.2	777	Gaa/Taa	17/25	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.37	2		390	578	SUCCESS
APC	324	MSKCC	GRCh37	5	112111392	112111392	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	65	498	1	ENST00000257430.4:c.489G>T	p.Gln163His	p.Q163H	ENST00000257430	NM_000038.5	163	caG/caT	5/16	1	2	FACETS	0.423	0.366	0.485	0.423	0.366	0.485	SUBCLONAL	1	TRUE	1	0.37	2		499	831	SUCCESS
APC	324	MSKCC	GRCh37	5	112173977	112173977	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	117	452	0	ENST00000257430.4:c.2686G>T	p.Ala896Ser	p.A896S	ENST00000257430	NM_000038.5	896	Gcc/Tcc	16/16	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.37	2		452	597	SUCCESS
APC	324	MSKCC	GRCh37	5	112174119	112174119	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1554084512	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	167	501	0	ENST00000257430.4:c.2828C>A	p.Ser943Ter	p.S943*	ENST00000257430	NM_000038.5	943	tCa/tAa	16/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.37	2		501	769	SUCCESS
APC	324	MSKCC	GRCh37	5	112175780	112175780	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	147	455	0	ENST00000257430.4:c.4489C>T	p.Pro1497Ser	p.P1497S	ENST00000257430	NM_000038.5	1497	Cca/Tca	16/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.37	2		455	640	SUCCESS
APC	324	MSKCC	GRCh37	5	112176008	112176008	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	176	479	0	ENST00000257430.4:c.4717G>T	p.Glu1573Ter	p.E1573*	ENST00000257430	NM_000038.5	1573	Gaa/Taa	16/16	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.37	2		479	693	SUCCESS
APC	324	MSKCC	GRCh37	5	112177839	112177839	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	133	502	0	ENST00000257430.4:c.6548C>A	p.Ser2183Tyr	p.S2183Y	ENST00000257430	NM_000038.5	2183	tCt/tAt	16/16	1	2	FACETS	0.776	0.704	0.851	0.776	0.704	0.851	SUBCLONAL	1	TRUE	1	0.37	2		502	927	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911614	131911614	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs376170006	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	132	481	0	ENST00000265335.6:c.359G>T	p.Arg120Ile	p.R120I	ENST00000265335		120	aGa/aTa	3/25	1	2	FACETS	0.795	0.722	0.873	0.795	0.722	0.873	SUBCLONAL	1	TRUE	1	0.37	2		481	897	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931471	131931471	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753002904	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	160	431	1	ENST00000265335.6:c.2176C>T	p.Arg726Cys	p.R726C	ENST00000265335		726	Cgt/Tgt	13/25	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.37	2		432	610	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149498372	149498372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	214	553	1	ENST00000261799.4:c.2842C>T	p.Arg948Trp	p.R948W	ENST00000261799	NM_002609.3	948	Cgg/Tgg	21/23	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.37	2		554	850	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176671232	176671232	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	222	561	0	ENST00000439151.2:c.4339G>A	p.Glu1447Lys	p.E1447K	ENST00000439151	NM_022455.4	1447	Gaa/Aaa	9/23	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.37	2		561	946	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707616	176707616	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	217	443	1	ENST00000439151.2:c.5673A>T	p.Glu1891Asp	p.E1891D	ENST00000439151	NM_022455.4	1891	gaA/gaT	18/23	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.37	2		444	888	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048238	180048238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324497116	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	56	397	2	ENST00000261937.6:c.2035C>T	p.Arg679Trp	p.R679W	ENST00000261937	NM_182925.4	679	Cgg/Tgg	14/30	1	2	FACETS	0.477	0.408	0.553	0.477	0.408	0.553	SUBCLONAL	1	TRUE	1	0.37	2		399	634	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051042	180051042	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	118	431	0	ENST00000261937.6:c.1441G>T	p.Asp481Tyr	p.D481Y	ENST00000261937	NM_182925.4	481	Gac/Tac	11/30	1	2	FACETS	0.871	0.787	0.961	0.871	0.787	0.961	CLONAL	1	TRUE	1	0.37	2		431	732	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057657	180057657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775457696	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	239	538	0	ENST00000261937.6:c.298G>A	p.Glu100Lys	p.E100K	ENST00000261937	NM_182925.4	100	Gag/Aag	3/30	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.37	2		538	991	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405083	405083	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	219	506	0	ENST00000380956.4:c.1165G>T	p.Glu389Ter	p.E389*	ENST00000380956	NM_001195286.1	389	Gag/Tag	8/9	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.37	2		506	973	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480138	20480138	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1355707187	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	58	586	0	ENST00000346618.3:c.455C>A	p.Thr152Asn	p.T152N	ENST00000346618	NM_001949.4	152	aCc/aAc	2/7	1	2	FACETS	0.344	0.294	0.398	0.344	0.294	0.398	SUBCLONAL	1	TRUE	1	0.37	2		586	912	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481526	20481526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	169	556	0	ENST00000346618.3:c.595G>A	p.Asp199Asn	p.D199N	ENST00000346618	NM_001949.4	199	Gat/Aat	3/7	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.37	2		556	845	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672425	30672425	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	83	585	2	ENST00000376406.3:c.4535C>A	p.Ser1512Tyr	p.S1512Y	ENST00000376406	NM_014641.2	1512	tCt/tAt	10/15	1	2	FACETS	0.49	0.431	0.553	0.49	0.431	0.553	SUBCLONAL	1	TRUE	1	0.37	2		587	916	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181576	32181576	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	228	617	1	ENST00000375023.3:c.2209C>A	p.Pro737Thr	p.P737T	ENST00000375023	NM_004557.3	737	Cca/Aca	14/30	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.37	2		618	985	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965655	93965655	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	212	785	0	ENST00000369303.4:c.2273A>G	p.Asp758Gly	p.D758G	ENST00000369303	NM_004440.3	758	gAc/gGc	13/17	0.3	0	FACETS	0.76	0.706	0.816			1	SUBCLONAL	1	TRUE	0	0.37	0		785	950	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066675	94066675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	239	822	0	ENST00000369303.4:c.1084G>A	p.Asp362Asn	p.D362N	ENST00000369303	NM_004440.3	362	Gat/Aat	5/17	0.3	0	FACETS	0.792	0.739	0.846			1	SUBCLONAL	1	TRUE	0	0.37	0		822	1028	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555357	106555357	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	39	242	0	ENST00000369096.4:c.2474C>A	p.Pro825His	p.P825H	ENST00000369096	NM_001198.3	825	cCt/cAt	7/7	1	2	FACETS	0.584	0.485	0.694	0.584	0.485	0.694	SUBCLONAL	1	TRUE	1	0.37	2		242	361	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609891	117609891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1302341778	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	149	648	1	ENST00000368508.3:c.6808G>A	p.Glu2270Lys	p.E2270K	ENST00000368508	NM_002944.2	2270	Gaa/Aaa	43/43	1	2	FACETS	0.857	0.782	0.935	0.857	0.782	0.935	CLONAL	1	TRUE	1	0.37	2		649	940	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642538	117642538	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	205	793	0	ENST00000368508.3:c.5661G>T	p.Lys1887Asn	p.K1887N	ENST00000368508	NM_002944.2	1887	aaG/aaT	35/43	1	2	FACETS	0.895	0.829	0.964	0.895	0.829	0.964	CLONAL	1	TRUE	1	0.37	2		793	1238	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665330	117665330	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	194	654	0	ENST00000368508.3:c.4417A>G	p.Thr1473Ala	p.T1473A	ENST00000368508	NM_002944.2	1473	Aca/Gca	27/43	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.37	2		654	817	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519320	137519320	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	62	508	0	ENST00000367739.4:c.1318A>G	p.Thr440Ala	p.T440A	ENST00000367739	NM_000416.2	440	Aca/Gca	7/7	1	2	FACETS	0.511	0.441	0.587	0.511	0.441	0.587	SUBCLONAL	1	TRUE	1	0.37	2		508	656	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527407	137527407	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	142	385	0	ENST00000367739.4:c.239T>G	p.Ile80Ser	p.I80S	ENST00000367739	NM_000416.2	80	aTt/aGt	3/7	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.37	2		385	627	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192453	138192453	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	81	461	0	ENST00000237289.4:c.89T>G	p.Phe30Cys	p.F30C	ENST00000237289	NM_001270507.1	30	tTt/tGt	2/9	1	2	FACETS	0.476	0.418	0.538	0.476	0.418	0.538	SUBCLONAL	1	TRUE	1	0.37	2		461	920	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202200	138202200	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3734553	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	178	425	0	ENST00000237289.4:c.2117G>A	p.Arg706Gln	p.R706Q	ENST00000237289	NM_001270507.1	706	cGa/cAa	9/9	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.37	2		425	769	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265569	152265569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	118	447	1	ENST00000206249.3:c.1022C>T	p.Ser341Leu	p.S341L	ENST00000206249	NM_000125.3	341	tCg/tTg	4/8	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.37	2		448	598	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161807901	161807901	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	151	427	1	ENST00000366898.1:c.1092C>A	p.Phe364Leu	p.F364L	ENST00000366898	NM_004562.2	364	ttC/ttA	10/12	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.37	2		428	701	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6031649	6031649	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs200640585	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	223	486	0	ENST00000265849.7:c.943C>T	p.Arg315Ter	p.R315*	ENST00000265849	NM_000535.5	315	Cga/Tga	9/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.37	2		486	968	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946174	13946174	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1176085263	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	146	448	0	ENST00000405192.2:c.922C>T	p.Arg308Trp	p.R308W	ENST00000405192	NM_001163147.1	308	Cgg/Tgg	10/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.37	2		448	619	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739756	41739756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762653354	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	263	850	0	ENST00000242208.4:c.217G>A	p.Asp73Asn	p.D73N	ENST00000242208	NM_002192.2	73	Gat/Aat	2/3	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.37	2		850	1243	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444384	50444384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761574077	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	166	437	1	ENST00000331340.3:c.314C>T	p.Ser105Leu	p.S105L	ENST00000331340	NM_006060.4	105	tCg/tTg	4/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.37	2		438	751	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55270242	55270242	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	183	542	0	ENST00000275493.2:c.3195C>A	p.Phe1065Leu	p.F1065L	ENST00000275493	NM_005228.3	1065	ttC/ttA	27/28	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.37	2		542	790	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92404101	92404101	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	234	463	0	ENST00000265734.4:c.278A>C	p.Lys93Thr	p.K93T	ENST00000265734	NM_001259.6	93	aAa/aCa	3/8	1	2	FACETS	0.84	0.786	0.895	1	0.994	1	CLONAL	2	TRUE	1	0.37	2		463	753	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508514	106508514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1406220505	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	55	182	1	ENST00000359195.3:c.508G>A	p.Asp170Asn	p.D170N	ENST00000359195	NM_002649.2	170	Gac/Aac	2/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.37	2		183	228	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148504761	148504761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397515548	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	87	573	1	ENST00000320356.2:c.2233G>A	p.Glu745Lys	p.E745K	ENST00000320356	NM_004456.4	745	Gaa/Aaa	20/20	1	2	FACETS	0.516	0.455	0.58	0.516	0.455	0.58	SUBCLONAL	1	TRUE	1	0.37	2		574	912	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523708	148523708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520183	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	156	438	1	ENST00000320356.2:c.745G>A	p.Glu249Lys	p.E249K	ENST00000320356	NM_004456.4	249	Gaa/Aaa	8/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.37	2		439	627	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151167676	151167676	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	171	464	0	ENST00000262187.5:c.443C>A	p.Ser148Tyr	p.S148Y	ENST00000262187	NM_005614.3	148	tCt/tAt	7/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.37	2		464	752	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849924	151849924	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	59	547	1	ENST00000262189.6:c.12392G>T	p.Arg4131Ile	p.R4131I	ENST00000262189	NM_170606.2	4131	aGa/aTa	49/59	1	2	FACETS	0.364	0.312	0.42	0.364	0.312	0.42	SUBCLONAL	1	TRUE	1	0.37	2		548	877	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874122	151874122	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	234	586	0	ENST00000262189.6:c.8416C>A	p.Leu2806Ile	p.L2806I	ENST00000262189	NM_170606.2	2806	Ctc/Atc	38/59	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.37	2		586	1039	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879229	151879229	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs763438739	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	55	705	0	ENST00000262189.6:c.5716C>T	p.Arg1906Ter	p.R1906*	ENST00000262189	NM_170606.2	1906	Cga/Tga	36/59	1	2	FACETS	0.297	0.253	0.346	0.297	0.253	0.346	SUBCLONAL	1	TRUE	1	0.37	2		705	1000	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055703	152055703	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	255	625	1	ENST00000262189.6:c.219G>T	p.Glu73Asp	p.E73D	ENST00000262189	NM_170606.2	73	gaG/gaT	2/59	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.37	2		626	1144	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132768	152132768	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	150	329	0	ENST00000262189.6:c.104G>T	p.Arg35Ile	p.R35I	ENST00000262189	NM_170606.2	35	aGa/aTa	1/59	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.37	2		329	581	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152357831	152357831	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	291	718	0	ENST00000359321.1:c.76G>A	p.Glu26Lys	p.E26K	ENST00000359321	NM_005431.1	26	Gaa/Aaa	2/3	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.37	2		718	1203	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287386	38287386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1162148796	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	56	501	1	ENST00000425967.3:c.271C>T	p.Arg91Trp	p.R91W	ENST00000425967	NM_001174067.1	91	Cgg/Tgg	4/19	1	2	FACETS	0.4	0.342	0.464	0.4	0.342	0.464	SUBCLONAL	1	TRUE	1	0.37	2		502	757	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38315038	38315038	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	192	508	0	ENST00000425967.3:c.26G>T	p.Arg9Met	p.R9M	ENST00000425967	NM_001174067.1	9	aGg/aTg	3/19	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.37	2		508	816	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993715	90993715	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	157	347	0	ENST00000265433.3:c.208G>T	p.Asp70Tyr	p.D70Y	ENST00000265433	NM_002485.4	70	Gat/Tat	3/16	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.37	2		347	601	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015094	37015094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	192	528	0	ENST00000358127.4:c.310C>T	p.Arg104Cys	p.R104C	ENST00000358127	NM_001280556.1	104	Cgc/Tgc	3/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.37	2		528	872	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482281	87482281	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	89	629	0	ENST00000277120.3:c.1568A>C	p.Lys523Thr	p.K523T	ENST00000277120		523	aAg/aCg	14/19	1	2	FACETS	0.569	0.504	0.639	0.569	0.504	0.639	SUBCLONAL	1	TRUE	1	0.37	2		629	845	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98011455	98011455	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	184	596	0	ENST00000289081.3:c.119A>G	p.Gln40Arg	p.Q40R	ENST00000289081	NM_000136.2	40	cAg/cGg	2/15	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.37	2		596	805	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224263	98224263	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	146	408	0	ENST00000331920.6:c.2578G>T	p.Asp860Tyr	p.D860Y	ENST00000331920	NM_000264.3	860	Gac/Tac	16/24	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.37	2		408	654	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912029	127912029	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	276	777	0	ENST00000373547.4:c.841G>T	p.Glu281Ter	p.E281*	ENST00000373547	NM_002721.4	281	Gaa/Taa	7/7	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.37	2		777	1148	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781068	135781068	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	286	789	0	ENST00000298552.3:c.1897G>T	p.Gly633Ter	p.G633*	ENST00000298552	NM_001162426.1	633	Gga/Tga	15/23	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.37	2		789	1289	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400310	139400310	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	49	174	0	ENST00000277541.6:c.4038G>T	p.Glu1346Asp	p.E1346D	ENST00000277541	NM_017617.3	1346	gaG/gaT	25/34	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.37	2		174	235	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412302	139412302	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs864622056	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	45	473	1	ENST00000277541.6:c.1343G>A	p.Arg448Gln	p.R448Q	ENST00000277541	NM_017617.3	448	cGa/cAa	8/34	1	2	FACETS	0.275	0.23	0.325	0.275	0.23	0.325	SUBCLONAL	1	TRUE	1	0.37	2		474	886	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100366	8100366	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762524699	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	202	599	0	ENST00000346208.3:c.340C>A	p.Leu114Ile	p.L114I	ENST00000346208		114	Ctc/Atc	3/6	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.37	2		599	970	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852488	63852488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1170860237	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	152	432	1	ENST00000279873.7:c.3266C>T	p.Ser1089Leu	p.S1089L	ENST00000279873	NM_032199.2	1089	tCg/tTg	10/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.37	2		433	660	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852527	63852527	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	169	385	0	ENST00000279873.7:c.3305C>A	p.Ser1102Tyr	p.S1102Y	ENST00000279873	NM_032199.2	1102	tCt/tAt	10/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.37	2		385	710	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406325	70406325	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	64	580	0	ENST00000373644.4:c.3839A>C	p.Lys1280Thr	p.K1280T	ENST00000373644	NM_030625.2	1280	aAa/aCa	4/12	1	2	FACETS	0.421	0.363	0.483	0.421	0.363	0.483	SUBCLONAL	1	TRUE	1	0.37	2		580	822	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450907	70450907	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	70	371	0	ENST00000373644.4:c.5747C>A	p.Pro1916His	p.P1916H	ENST00000373644	NM_030625.2	1916	cCt/cAt	12/12	1	2	FACETS	0.663	0.578	0.754	0.663	0.578	0.754	SUBCLONAL	1	TRUE	1	0.37	2		371	571	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114901057	114901057	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776719680	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	308	727	1	ENST00000543371.1:c.667G>A	p.Asp223Asn	p.D223N	ENST00000543371	NM_001198531.1	223	Gac/Aac	6/14	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.37	2		728	1195	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274691	123274691	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	250	494	1	ENST00000358487.5:c.1227C>A	p.Phe409Leu	p.F409L	ENST00000358487	NM_000141.4	409	ttC/ttA	9/18	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.37	2		495	973	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156731	2156731	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs869320620	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	46	535	0	ENST00000434045.2:c.191C>T	p.Ser64Leu	p.S64L	ENST00000434045	NM_001127598.1	64	tCg/tTg	3/5	1	2	FACETS	0.272	0.228	0.321	0.272	0.228	0.321	SUBCLONAL	1	TRUE	1	0.37	2		535	913	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161506	2161506	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	173	412	0	ENST00000434045.2:c.21A>C	p.Gln7His	p.Q7H	ENST00000434045	NM_001127598.1	7	caA/caC	2/5	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.37	2		412	774	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138828	64138828	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	137	336	0	ENST00000334205.4:c.2195A>C	p.Lys732Thr	p.K732T	ENST00000334205	NM_003942.2	732	aAg/aCg	17/17	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.37	2		336	594	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573823	64573823	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	135	408	0	ENST00000312049.6:c.930G>T	p.Lys310Asn	p.K310N	ENST00000312049	NM_130799.2	310	aaG/aaT	7/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.37	2		408	641	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77048448	77048448	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	110	544	2	ENST00000356341.3:c.1137C>A	p.Phe379Leu	p.F379L	ENST00000356341	NM_002576.4	379	ttC/ttA	12/15	1	2	FACETS	0.74	0.665	0.82	0.74	0.665	0.82	SUBCLONAL	1	TRUE	1	0.37	2		546	803	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77091008	77091008	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	234	519	1	ENST00000356341.3:c.222G>T	p.Glu74Asp	p.E74D	ENST00000356341	NM_002576.4	74	gaG/gaT	3/15	1	2	FACETS	0.765	0.715	0.816	1	0.993	1	SUBCLONAL	2	TRUE	1	0.37	2		520	827	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203791	94203791	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs190142346	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	31	438	0	ENST00000323929.3:c.863G>A	p.Arg288His	p.R288H	ENST00000323929	NM_005591.3	288	cGt/cAt	9/20	1	2	FACETS	0.277	0.223	0.339	0.277	0.223	0.339	SUBCLONAL	1	TRUE	1	0.37	2		438	604	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100619	102100619	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	127	463	0	ENST00000282441.5:c.1463C>A	p.Ser488Tyr	p.S488Y	ENST00000282441	NM_001130145.2	488	tCt/tAt	9/9	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.37	2		463	640	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100657	102100657	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	55	339	0	ENST00000282441.5:c.1501C>A	p.Leu501Ile	p.L501I	ENST00000282441	NM_001130145.2	501	Ctt/Att	9/9	1	2	FACETS	0.665	0.57	0.769	0.665	0.57	0.769	SUBCLONAL	1	TRUE	1	0.37	2		339	447	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195344	102195344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1220112786	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	348	829	1	ENST00000263464.3:c.104C>T	p.Thr35Met	p.T35M	ENST00000263464	NM_001165.4	35	aCg/aTg	2/9	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.37	2		830	1263	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206945	102206945	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	257	608	0	ENST00000263464.3:c.1573T>G	p.Leu525Val	p.L525V	ENST00000263464	NM_001165.4	525	Tta/Gta	7/9	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.37	2		608	1016	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155090	108155090	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	172	481	0	ENST00000278616.4:c.3883C>T	p.Leu1295Phe	p.L1295F	ENST00000278616	NM_000051.3	1295	Ctt/Ttt	26/63	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.37	2		481	686	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158328	108158328	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs1064793805	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	144	418	0	ENST00000278616.4:c.3995T>G	p.Ile1332Ser	p.I1332S	ENST00000278616	NM_000051.3	1332	aTt/aGt	27/63	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.37	2		418	634	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203492	108203492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs138941496	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	150	335	0	ENST00000278616.4:c.7792C>T	p.Arg2598Ter	p.R2598*	ENST00000278616	NM_000051.3	2598	Cga/Tga	53/63	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.37	2		335	644	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118339501	118339501	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	63	445	0	ENST00000534358.1:c.444C>A	p.Phe148Leu	p.F148L	ENST00000534358	NM_005933.3	148	ttC/ttA	2/36	1	2	FACETS	0.494	0.427	0.568	0.494	0.427	0.568	SUBCLONAL	1	TRUE	1	0.37	2		445	689	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375758	118375758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	114	591	1	ENST00000534358.1:c.9151C>T	p.Pro3051Ser	p.P3051S	ENST00000534358	NM_005933.3	3051	Ccc/Tcc	27/36	1	2	FACETS	0.681	0.612	0.754	0.681	0.612	0.754	SUBCLONAL	1	TRUE	1	0.37	2		592	905	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376605	118376605	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	222	499	0	ENST00000534358.1:c.9998C>A	p.Ser3333Tyr	p.S3333Y	ENST00000534358	NM_005933.3	3333	tCt/tAt	27/36	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.37	2		499	908	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148534	119148534	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	226	601	1	ENST00000264033.4:c.1075G>T	p.Asp359Tyr	p.D359Y	ENST00000264033	NM_005188.3	359	Gac/Tac	7/16	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.37	2		602	877	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503175	125503175	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	112	557	0	ENST00000428830.2:c.542G>T	p.Arg181Ile	p.R181I	ENST00000428830	NM_001114121.2	181	aGa/aTa	6/14	1	2	FACETS	0.719	0.646	0.796	0.719	0.646	0.796	SUBCLONAL	1	TRUE	1	0.37	2		557	842	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402109	402109	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	291	740	0	ENST00000399788.2:c.4682G>T	p.Arg1561Ile	p.R1561I	ENST00000399788	NM_001042603.1	1561	aGa/aTa	27/28	0.3	2	FACETS	1	0.992	1			1	CLONAL	1	TRUE	NA	0.37	2		740	1175	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	472145	472145	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	220	531	0	ENST00000399788.2:c.656G>A	p.Arg219Lys	p.R219K	ENST00000399788	NM_001042603.1	219	aGa/aAa	5/28	0.3	2	FACETS	1	0.99	1			1	CLONAL	1	TRUE	NA	0.37	2		531	861	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1034621	1034621	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs577090674	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	110	662	2	ENST00000358495.3:c.538C>T	p.Arg180Cys	p.R180C	ENST00000358495	NM_134424.2	180	Cgc/Tgc	7/12	0.3	2	FACETS	0.483	0.433	0.537			1	SUBCLONAL	1	TRUE	NA	0.37	2		664	1230	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466993	18466993	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs370262872	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	36	539	0	ENST00000266497.5:c.1132C>T	p.Arg378Ter	p.R378*	ENST00000266497		378	Cga/Tga	5/31	0.0958005913417619	0	FACETS	0.178	0.145	0.214			1	INDETERMINATE	1	TRUE	0	0.37	0		539	689	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793439	18793439	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	140	602	0	ENST00000266497.5:c.4136G>T	p.Arg1379Met	p.R1379M	ENST00000266497		1379	aGg/aTg	30/31	0.0958005913417619	0	FACETS	0.559	0.509	0.611			1	INDETERMINATE	1	TRUE	0	0.37	0		602	853	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380289	25380289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	155	533	0	ENST00000311936.3:c.169G>A	p.Asp57Asn	p.D57N	ENST00000311936	NM_004985.3	57	Gac/Aac	3/5	0.0958005913417619	0	FACETS	0.74	0.679	0.804			1	INDETERMINATE	1	TRUE	0	0.37	0		533	713	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245811	46245811	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	240	629	0	ENST00000334344.6:c.3905C>A	p.Ser1302Ter	p.S1302*	ENST00000334344	NM_152641.2	1302	tCa/tAa	15/21	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.37	2		629	948	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416133	49416133	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1422752351	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	194	353	1	ENST00000301067.7:c.16342C>T	p.Arg5448Ter	p.R5448*	ENST00000301067	NM_003482.3	5448	Cga/Tga	52/54	1	2	FACETS	0.798	0.742	0.856	1	0.992	1	SUBCLONAL	2	TRUE	1	0.37	2		354	657	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416466	49416466	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	48	520	0	ENST00000301067.7:c.16245G>T	p.Lys5415Asn	p.K5415N	ENST00000301067	NM_003482.3	5415	aaG/aaT	51/54	1	2	FACETS	0.273	0.229	0.321	0.273	0.229	0.321	SUBCLONAL	1	TRUE	1	0.37	2		520	951	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422861	49422861	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	104	484	0	ENST00000301067.7:c.14234C>A	p.Pro4745His	p.P4745H	ENST00000301067	NM_003482.3	4745	cCt/cAt	44/54	1	2	FACETS	0.783	0.701	0.869	0.783	0.701	0.869	SUBCLONAL	1	TRUE	1	0.37	2		484	718	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427702	49427702	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1481521421	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	211	521	2	ENST00000301067.7:c.10786C>T	p.Arg3596Trp	p.R3596W	ENST00000301067	NM_003482.3	3596	Cgg/Tgg	39/54	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.37	2		523	966	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431493	49431493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1288465936	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	220	508	2	ENST00000301067.7:c.9646G>A	p.Glu3216Lys	p.E3216K	ENST00000301067	NM_003482.3	3216	Gag/Aag	34/54	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.37	2		510	952	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443500	49443500	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1376778182	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	182	389	5	ENST00000301067.7:c.3871C>T	p.Arg1291Trp	p.R1291W	ENST00000301067	NM_003482.3	1291	Cgg/Tgg	11/54	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.37	2		394	732	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445755	49445755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1263886473	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1347	270	965	0	ENST00000301067.7:c.1711C>T	p.Arg571Cys	p.R571C	ENST00000301067	NM_003482.3	571	Cgc/Tgc	10/54	1	2	FACETS	0.903	0.844	0.963	0.903	0.844	0.963	CLONAL	1	TRUE	1	0.37	2		965	1617	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859706	57859706	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	240	618	0	ENST00000228682.2:c.760C>T	p.His254Tyr	p.H254Y	ENST00000228682	NM_005269.2	254	Cac/Tac	7/12	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.37	2		618	1080	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861246	57861246	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745587766	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	247	628	0	ENST00000228682.2:c.1043G>A	p.Arg348Gln	p.R348Q	ENST00000228682	NM_005269.2	348	cGa/cAa	9/12	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.37	2		628	1068	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888313	112888313	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	96	422	0	ENST00000351677.2:c.329A>G	p.Glu110Gly	p.E110G	ENST00000351677	NM_002834.3	110	gAa/gGa	3/16	1	2	FACETS	0.904	0.807	1	0.904	0.807	1	CLONAL	1	TRUE	1	0.37	2		422	574	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120675	115120675	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	218	594	1	ENST00000257566.3:c.331G>T	p.Glu111Ter	p.E111*	ENST00000257566	NM_016569.3	111	Gaa/Taa	1/8	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.37	2		595	987	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249847	133249847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	184	479	1	ENST00000320574.5:c.1376C>T	p.Ser459Phe	p.S459F	ENST00000320574	NM_006231.2	459	tCt/tTt	14/49	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.37	2		480	824	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263897	133263897	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	71	207	0	ENST00000320574.5:c.5C>A	p.Ser2Tyr	p.S2Y	ENST00000320574	NM_006231.2	2	tCt/tAt	1/49	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.37	NA		207	353	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597488	28597488	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs769640419	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	83	456	0	ENST00000241453.7:c.2417C>T	p.Ser806Leu	p.S806L	ENST00000241453	NM_004119.2	806	tCg/tTg	19/24	1	2	FACETS	0.483	0.426	0.546	0.483	0.426	0.546	SUBCLONAL	1	TRUE	1	0.37	2		456	928	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919631	28919631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200840674	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	191	618	0	ENST00000282397.4:c.2306C>T	p.Ala769Val	p.A769V	ENST00000282397	NM_002019.4	769	gCg/gTg	16/30	1	2	FACETS	0.961	0.888	1	0.961	0.888	1	CLONAL	1	TRUE	1	0.37	2		618	1074	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28931772	28931772	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	242	607	1	ENST00000282397.4:c.2167G>T	p.Glu723Ter	p.E723*	ENST00000282397	NM_002019.4	723	Gaa/Taa	15/30	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.37	2		608	946	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008201	29008201	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	66	531	0	ENST00000282397.4:c.670C>T	p.Arg224Ter	p.R224*	ENST00000282397	NM_002019.4	224	Cga/Tga	5/30	1	2	FACETS	0.489	0.423	0.56	0.489	0.423	0.56	SUBCLONAL	1	TRUE	1	0.37	2		531	730	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910849	32910849	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1267	70	833	0	ENST00000380152.3:c.2357C>A	p.Ser786Tyr	p.S786Y	ENST00000380152		786	tCt/tAt	11/27	1	2	FACETS	0.283	0.245	0.324	0.283	0.245	0.324	SUBCLONAL	1	TRUE	1	0.37	2		833	1337	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912067	32912067	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs80358606	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	285	867	0	ENST00000380152.3:c.3575T>G	p.Phe1192Cys	p.F1192C	ENST00000380152		1192	tTt/tGt	11/27	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.37	2		867	1195	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913692	32913692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786202543	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	345	868	1	ENST00000380152.3:c.5200G>A	p.Glu1734Lys	p.E1734K	ENST00000380152		1734	Gaa/Aaa	11/27	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.37	2		869	1271	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32931937	32931937	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	265	585	0	ENST00000380152.3:c.7676C>A	p.Ser2559Tyr	p.S2559Y	ENST00000380152		2559	tCt/tAt	16/27	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.37	2		585	1062	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134594	41134594	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	175	791	2	ENST00000379561.5:c.1034C>A	p.Ser345Tyr	p.S345Y	ENST00000379561	NM_002015.3	345	tCt/tAt	2/3	1	2	FACETS	0.73	0.67	0.792	0.73	0.67	0.792	SUBCLONAL	1	TRUE	1	0.37	2		793	1296	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134687	41134687	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760747458	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	255	703	0	ENST00000379561.5:c.941G>A	p.Arg314His	p.R314H	ENST00000379561	NM_002015.3	314	cGc/cAc	2/3	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.37	2		703	1195	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916801	48916801	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	83	481	1	ENST00000267163.4:c.331G>T	p.Asp111Tyr	p.D111Y	ENST00000267163	NM_000321.2	111	Gat/Tat	3/27	1	2	FACETS	0.599	0.528	0.675	0.599	0.528	0.675	SUBCLONAL	1	TRUE	1	0.37	2		482	749	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337719	73337719	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	119	502	0	ENST00000377767.4:c.1997T>G	p.Phe666Cys	p.F666C	ENST00000377767	NM_014953.3	666	tTt/tGt	16/21	1	2	FACETS	0.813	0.734	0.897	0.813	0.734	0.897	CLONAL	1	TRUE	1	0.37	2		502	791	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347874	73347874	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369590515	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	85	561	0	ENST00000377767.4:c.1187G>A	p.Arg396Gln	p.R396Q	ENST00000377767	NM_014953.3	396	cGg/cAg	8/21	1	2	FACETS	0.49	0.432	0.552	0.49	0.432	0.552	SUBCLONAL	1	TRUE	1	0.37	2		561	938	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434953	110434953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	207	482	0	ENST00000375856.3:c.3448G>A	p.Glu1150Lys	p.E1150K	ENST00000375856	NM_003749.2	1150	Gag/Aag	1/2	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.37	2		482	837	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871728	35871728	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528542318	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	291	696	1	ENST00000216797.5:c.778C>T	p.Arg260Cys	p.R260C	ENST00000216797	NM_020529.2	260	Cgc/Tgc	5/6	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.37	2		697	1178	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060812	38060812	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1329	140	836	0	ENST00000250448.2:c.1177C>A	p.His393Asn	p.H393N	ENST00000250448	NM_004496.3	393	Cac/Aac	2/2	1	2	FACETS	0.515	0.467	0.566	0.515	0.467	0.566	SUBCLONAL	1	TRUE	1	0.37	2		836	1469	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609352	81609352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	216	606	0	ENST00000298171.2:c.950C>T	p.Ala317Val	p.A317V	ENST00000298171	NM_000369.2	317	gCc/gTc	10/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.37	2		606	1040	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560252	95560252	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	68	379	0	ENST00000393063.1:c.5337G>T	p.Lys1779Asn	p.K1779N	ENST00000393063	NM_030621.3	1779	aaG/aaT	25/28	1	2	FACETS	0.53	0.46	0.605	0.53	0.46	0.605	SUBCLONAL	1	TRUE	1	0.37	2		379	694	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569775	95569775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	169	542	0	ENST00000393063.1:c.3958G>A	p.Asp1320Asn	p.D1320N	ENST00000393063	NM_030621.3	1320	Gac/Aac	22/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.37	2		542	719	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023435	33023435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	229	855	2	ENST00000300177.4:c.544G>A	p.Asp182Asn	p.D182N	ENST00000300177	NM_001191322.1	182	Gat/Aat	2/2	1	2	FACETS	0.869	0.807	0.932	0.869	0.807	0.932	CLONAL	1	TRUE	1	0.37	2		857	1425	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41021734	41021734	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1249471221	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	197	498	2	ENST00000267868.3:c.676G>A	p.Ala226Thr	p.A226T	ENST00000267868	NM_002875.4	226	Gcc/Acc	8/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.37	2		500	895	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003283	42003283	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1274	126	885	1	ENST00000219905.7:c.2820G>T	p.Lys940Asn	p.K940N	ENST00000219905	NM_001164273.1	940	aaG/aaT	8/24	1	2	FACETS	0.486	0.439	0.537	0.486	0.439	0.537	SUBCLONAL	1	TRUE	1	0.37	2		886	1400	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040903	42040903	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	294	687	2	ENST00000219905.7:c.5281C>T	p.Arg1761Ter	p.R1761*	ENST00000219905	NM_001164273.1	1761	Cga/Tga	16/24	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.37	2		689	1149	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059447	42059447	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753335816	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	253	736	0	ENST00000219905.7:c.9167C>T	p.Ser3056Leu	p.S3056L	ENST00000219905	NM_001164273.1	3056	tCg/tTg	24/24	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.37	2		736	1141	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457701	67457701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768050588	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	205	460	0	ENST00000327367.4:c.511G>A	p.Glu171Lys	p.E171K	ENST00000327367	NM_005902.3	171	Gag/Aag	3/9	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.37	2		460	831	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690584	88690584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368222977	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	68	434	1	ENST00000360948.2:c.446C>T	p.Thr149Met	p.T149M	ENST00000360948	NM_001012338.2	149	aCg/aTg	5/19	1	2	FACETS	0.48	0.417	0.549	0.48	0.417	0.549	SUBCLONAL	1	TRUE	1	0.37	2		435	765	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292623	91292623	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763065919	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	163	371	0	ENST00000355112.3:c.125C>A	p.Ser42Tyr	p.S42Y	ENST00000355112	NM_000057.2	42	tCt/tAt	3/22	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.37	2		371	641	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292818	91292818	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	223	631	0	ENST00000355112.3:c.320T>C	p.Leu107Ser	p.L107S	ENST00000355112	NM_000057.2	107	tTa/tCa	3/22	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.37	2		631	1037	SUCCESS
BLM	641	MSKCC	GRCh37	15	91298102	91298102	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	261	542	1	ENST00000355112.3:c.1021C>A	p.Leu341Ile	p.L341I	ENST00000355112	NM_000057.2	341	Ctt/Att	5/22	1	2	FACETS	0.791	0.742	0.84	1	0.994	1	SUBCLONAL	2	TRUE	1	0.37	2		543	892	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108831	2108831	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	248	544	0	ENST00000219476.3:c.932C>A	p.Ser311Tyr	p.S311Y	ENST00000219476	NM_000548.3	311	tCt/tAt	10/42	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.37	2		544	939	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126586	2126586	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	182	429	0	ENST00000219476.3:c.2837G>T	p.Ser946Ile	p.S946I	ENST00000219476	NM_000548.3	946	aGt/aTt	25/42	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.37	2		429	726	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781375	3781375	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	174	491	1	ENST00000262367.5:c.4990C>T	p.Arg1664Cys	p.R1664C	ENST00000262367	NM_004380.2	1664	Cgc/Tgc	30/31	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.37	2		492	811	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789666	3789666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	165	633	0	ENST00000262367.5:c.4193C>T	p.Ala1398Val	p.A1398V	ENST00000262367	NM_004380.2	1398	gCt/gTt	25/31	1	2	FACETS	0.784	0.719	0.853	0.784	0.719	0.853	SUBCLONAL	1	TRUE	1	0.37	2		633	1137	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808917	3808917	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	98	521	1	ENST00000262367.5:c.3307C>T	p.Arg1103Ter	p.R1103*	ENST00000262367	NM_004380.2	1103	Cga/Tga	17/31	1	2	FACETS	0.513	0.457	0.574	0.513	0.457	0.574	SUBCLONAL	1	TRUE	1	0.37	2		522	1032	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820617	3820617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	104	437	0	ENST00000262367.5:c.2834C>T	p.Ser945Leu	p.S945L	ENST00000262367	NM_004380.2	945	tCg/tTg	14/31	1	2	FACETS	0.761	0.681	0.845	0.761	0.681	0.845	SUBCLONAL	1	TRUE	1	0.37	2		437	739	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3842041	3842041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	243	584	1	ENST00000262367.5:c.1271G>A	p.Arg424Gln	p.R424Q	ENST00000262367	NM_004380.2	424	cGa/cAa	5/31	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.37	2		585	1004	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857818	9857818	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	82	767	0	ENST00000330684.3:c.3583G>T	p.Asp1195Tyr	p.D1195Y	ENST00000330684	NM_001134407.1	1195	Gac/Tac	13/13	1	2	FACETS	0.378	0.332	0.427	0.378	0.332	0.427	SUBCLONAL	1	TRUE	1	0.37	2		767	1174	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984909	9984909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	111	658	0	ENST00000330684.3:c.1056G>T	p.Glu352Asp	p.E352D	ENST00000330684	NM_001134407.1	352	gaG/gaT	4/13	1	2	FACETS	0.569	0.51	0.631	0.569	0.51	0.631	SUBCLONAL	1	TRUE	1	0.37	2		658	1055	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029408	14029408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368830992	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	166	576	0	ENST00000311895.7:c.1619C>T	p.Ser540Leu	p.S540L	ENST00000311895	NM_005236.2	540	tCg/tTg	8/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.37	2		576	655	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646795	23646795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660876	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	282	754	0	ENST00000261584.4:c.1072C>T	p.Pro358Ser	p.P358S	ENST00000261584	NM_024675.3	358	Ccc/Tcc	4/13	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.37	2		754	1145	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649216	23649216	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	224	568	1	ENST00000261584.4:c.166G>T	p.Asp56Tyr	p.D56Y	ENST00000261584	NM_024675.3	56	Gat/Tat	3/13	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.37	2		569	1015	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830136	72830136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	257	743	0	ENST00000268489.5:c.6445C>T	p.Arg2149Cys	p.R2149C	ENST00000268489	NM_006885.3	2149	Cgc/Tgc	9/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.37	2		743	1283	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993828	72993828	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371922710	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	41	597	1	ENST00000268489.5:c.217G>A	p.Glu73Lys	p.E73K	ENST00000268489	NM_006885.3	73	Gag/Aag	2/10	1	2	FACETS	0.28	0.232	0.333	0.28	0.232	0.333	SUBCLONAL	1	TRUE	1	0.37	2		598	792	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347338	89347338	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1241861780	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	174	805	1	ENST00000301030.4:c.5612C>T	p.Ala1871Val	p.A1871V	ENST00000301030	NM_001256183.1	1871	gCc/gTc	9/13	1	2	FACETS	0.803	0.738	0.871	0.803	0.738	0.871	CLONAL	1	TRUE	1	0.37	2		806	1171	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838216	89838216	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17232973	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	260	437	0	ENST00000389301.3:c.2021C>T	p.Ser674Leu	p.S674L	ENST00000389301	NM_000135.2	674	tCg/tTg	23/43	1	2	FACETS	0.853	0.801	0.905	1	0.994	1	CLONAL	2	TRUE	1	0.37	2		437	824	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845228	89845228	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	234	657	0	ENST00000389301.3:c.1807T>A	p.Phe603Ile	p.F603I	ENST00000389301	NM_000135.2	603	Ttt/Att	20/43	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.37	2		657	1056	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8109897	8109897	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	223	469	0	ENST00000585124.1:c.598G>T	p.Asp200Tyr	p.D200Y	ENST00000585124	NM_004217.3	200	Gac/Tac	7/9	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.37	2		469	884	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998926	11998926	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	45	551	0	ENST00000353533.5:c.428A>C	p.Lys143Thr	p.K143T	ENST00000353533	NM_003010.3	143	aAa/aCa	4/11	1	2	FACETS	0.296	0.248	0.35	0.296	0.248	0.35	SUBCLONAL	1	TRUE	1	0.37	2		551	822	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15978955	15978955	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779823128	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	232	592	2	ENST00000268712.3:c.3563C>T	p.Ser1188Leu	p.S1188L	ENST00000268712	NM_006311.3	1188	tCg/tTg	27/46	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.37	2		594	915	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049815	16049815	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	143	598	1	ENST00000268712.3:c.957G>T	p.Glu319Asp	p.E319D	ENST00000268712	NM_006311.3	319	gaG/gaT	10/46	1	2	FACETS	0.869	0.792	0.949	0.869	0.792	0.949	CLONAL	1	TRUE	1	0.37	2		599	890	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131220	17131220	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	256	562	0	ENST00000285071.4:c.232A>T	p.Lys78Ter	p.K78*	ENST00000285071	NM_144997.5	78	Aag/Tag	4/14	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.37	2		562	1030	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546065	29546065	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1135402815	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	194	546	0	ENST00000356175.3:c.1570G>T	p.Glu524Ter	p.E524*	ENST00000356175	NM_000267.3	524	Gaa/Taa	14/57	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.37	2		546	867	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585374	29585374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555618495	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	34	508	0	ENST00000356175.3:c.4123C>T	p.Arg1375Cys	p.R1375C	ENST00000356175	NM_000267.3	1375	Cgt/Tgt	31/57	1	2	FACETS	0.284	0.231	0.344	0.284	0.231	0.344	SUBCLONAL	1	TRUE	1	0.37	2		508	647	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33430306	33430306	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	119	606	0	ENST00000345365.6:c.705G>T	p.Lys235Asn	p.K235N	ENST00000345365	NM_002878.3	235	aaG/aaT	8/10	1	2	FACETS	0.613	0.552	0.677	0.613	0.552	0.677	SUBCLONAL	1	TRUE	1	0.37	2		606	1050	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873608	37873608	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	213	573	0	ENST00000269571.5:c.1773G>T	p.Lys591Asn	p.K591N	ENST00000269571		591	aaG/aaT	15/27	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.37	2		573	913	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362238	40362238	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	107	753	0	ENST00000293328.3:c.1857C>A	p.Phe619Leu	p.F619L	ENST00000293328	NM_012448.3	619	ttC/ttA	15/19	1	2	FACETS	0.472	0.422	0.526	0.472	0.422	0.526	SUBCLONAL	1	TRUE	1	0.37	2		753	1225	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243673	41243673	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876658340	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	109	657	3	ENST00000357654.3:c.3875C>A	p.Ser1292Tyr	p.S1292Y	ENST00000357654	NM_007294.3	1292	tCt/tAt	10/23	1	2	FACETS	0.636	0.57	0.706	0.636	0.57	0.706	SUBCLONAL	1	TRUE	1	0.37	2		660	926	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780625	56780625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140804406	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	222	538	1	ENST00000337432.4:c.640C>T	p.Arg214Cys	p.R214C	ENST00000337432	NM_058216.2	214	Cgt/Tgt	4/9	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.37	2		539	908	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858253	59858253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778133	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	110	639	2	ENST00000259008.2:c.1742G>A	p.Arg581Gln	p.R581Q	ENST00000259008	NM_032043.2	581	cGa/cAa	12/20	1	2	FACETS	0.535	0.479	0.595	0.535	0.479	0.595	SUBCLONAL	1	TRUE	1	0.37	2		641	1111	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745986	745986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371352602	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	95	467	0	ENST00000314574.4:c.536G>A	p.Arg179Gln	p.R179Q	ENST00000314574	NM_005433.3	179	cGa/cAa	5/12	1	2	FACETS	0.772	0.688	0.862	0.772	0.688	0.862	SUBCLONAL	1	TRUE	1	0.37	2		467	665	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625652	1625652	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs533848977	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	242	543	0	ENST00000344749.5:c.422C>T	p.Ser141Leu	p.S141L	ENST00000344749	NM_001136139.2	141	tCg/tTg	7/19	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.37	2		543	975	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184419	7184419	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	246	529	0	ENST00000302850.5:c.882G>T	p.Lys294Asn	p.K294N	ENST00000302850	NM_000208.2	294	aaG/aaT	3/22	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.37	2		529	1084	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260146	10260146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751754286	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	109	576	1	ENST00000340748.4:c.2521G>A	p.Glu841Lys	p.E841K	ENST00000340748		841	Gaa/Aaa	25/40	1	2	FACETS	0.585	0.524	0.65	0.585	0.524	0.65	SUBCLONAL	1	TRUE	1	0.37	2		577	1007	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10273405	10273405	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200601847	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	187	527	0	ENST00000340748.4:c.898G>A	p.Glu300Lys	p.E300K	ENST00000340748		300	Gaa/Aaa	12/40	1	2	FACETS	0.883	0.814	0.954	0.883	0.814	0.954	CLONAL	1	TRUE	1	0.37	2		527	1145	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597416	10597416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190115073	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	276	593	0	ENST00000171111.5:c.1787G>A	p.Arg596Gln	p.R596Q	ENST00000171111	NM_203500.1	596	cGa/cAa	6/6	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.37	2		593	1092	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278077	15278077	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	211	590	0	ENST00000263388.2:c.5345T>C	p.Val1782Ala	p.V1782A	ENST00000263388	NM_000435.2	1782	gTc/gCc	29/33	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.37	2		590	1002	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299124	15299124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1173660165	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	223	514	0	ENST00000263388.2:c.1414G>A	p.Glu472Lys	p.E472K	ENST00000263388	NM_000435.2	472	Gag/Aag	9/33	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.37	2		514	942	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299856	15299856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1188038977	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	69	536	1	ENST00000263388.2:c.1322G>A	p.Arg441Gln	p.R441Q	ENST00000263388	NM_000435.2	441	cGa/cAa	8/33	1	2	FACETS	0.429	0.373	0.49	0.429	0.373	0.49	SUBCLONAL	1	TRUE	1	0.37	2		537	869	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299883	15299883	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	192	553	0	ENST00000263388.2:c.1295T>C	p.Val432Ala	p.V432A	ENST00000263388	NM_000435.2	432	gTc/gCc	8/33	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.37	2		553	888	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302858	15302858	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375682932	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	72	465	0	ENST00000263388.2:c.592G>A	p.Ala198Thr	p.A198T	ENST00000263388	NM_000435.2	198	Gcg/Acg	4/33	1	2	FACETS	0.527	0.46	0.6	0.527	0.46	0.6	SUBCLONAL	1	TRUE	1	0.37	2		465	738	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349220	15349220	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	163	535	0	ENST00000263377.2:c.4057C>A	p.Leu1353Ile	p.L1353I	ENST00000263377	NM_058243.2	1353	Cta/Ata	20/20	1	2	FACETS	0.914	0.838	0.993	0.914	0.838	0.993	CLONAL	1	TRUE	1	0.37	2		535	964	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948791	17948791	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	225	558	0	ENST00000458235.1:c.1651A>G	p.Thr551Ala	p.T551A	ENST00000458235	NM_000215.3	551	Aca/Gca	12/24	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.37	2		558	995	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792485	33792485	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1568419375	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	34	360	0	ENST00000498907.2:c.836A>G	p.Asp279Gly	p.D279G	ENST00000498907	NM_004364.3	279	gAc/gGc	1/1	1	2	FACETS	0.279	0.227	0.338	0.279	0.227	0.338	SUBCLONAL	1	TRUE	1	0.37	2		360	659	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765576	41765576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763066660	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	205	588	0	ENST00000301178.4:c.2452G>A	p.Glu818Lys	p.E818K	ENST00000301178	NM_021913.4	818	Gaa/Aaa	20/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.37	2		588	945	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794949	42794949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1194868007	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	129	319	0	ENST00000575354.2:c.2029C>T	p.Arg677Trp	p.R677W	ENST00000575354	NM_015125.3	677	Cgg/Tgg	10/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.37	2		319	517	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855871	45855871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370377312	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	213	496	1	ENST00000391945.4:c.1939C>T	p.Arg647Cys	p.R647C	ENST00000391945	NM_000400.3	647	Cgt/Tgt	21/23	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.37	2		497	924	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714742	52714742	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	136	301	0	ENST00000322088.6:c.500G>A	p.Arg167Gln	p.R167Q	ENST00000322088	NM_014225.5	167	cGa/cAa	4/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.37	2		301	609	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546575	9546575	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777430875	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	75	554	0	ENST00000353224.5:c.1447C>T	p.Arg483Trp	p.R483W	ENST00000353224	NM_177990.2	483	Cgg/Tgg	5/10	0.0958005913417619	0	FACETS	0.288	0.251	0.327			1	INDETERMINATE	1	TRUE	0	0.37	0		554	888	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546678	9546678	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	82	499	0	ENST00000353224.5:c.1344C>A	p.Tyr448Ter	p.Y448*	ENST00000353224	NM_177990.2	448	taC/taA	5/10	0.0958005913417619	0	FACETS	0.326	0.287	0.369			1	INDETERMINATE	1	TRUE	0	0.37	0		499	856	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019156	31019156	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	287	620	0	ENST00000375687.4:c.751G>T	p.Asp251Tyr	p.D251Y	ENST00000375687	NM_015338.5	251	Gat/Tat	9/13	0.0958005913417619	0	FACETS	0.829	0.779	0.88			1	INDETERMINATE	1	TRUE	0	0.37	0		620	1179	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31379488	31379488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	75	556	0	ENST00000328111.2:c.895C>T	p.Arg299Ter	p.R299*	ENST00000328111	NM_006892.3	299	Cga/Tga	8/23	0.0958005913417619	0	FACETS	0.283	0.247	0.322			1	INDETERMINATE	1	TRUE	0	0.37	0		556	903	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387102	31387102	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757889243	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	189	486	0	ENST00000328111.2:c.1727G>A	p.Arg576Gln	p.R576Q	ENST00000328111	NM_006892.3	576	cGa/cAa	16/23	0.0958005913417619	0	FACETS	0.776	0.719	0.836			1	INDETERMINATE	1	TRUE	0	0.37	0		486	829	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39706272	39706272	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	135	406	0	ENST00000361337.2:c.330C>A	p.Phe110Leu	p.F110L	ENST00000361337	NM_003286.2	110	ttC/ttA	5/21	0.3	4	FACETS	1	0.938	1			1	CLONAL	1	TRUE	NA	0.37	4		406	960	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400170	41400170	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	280	468	0	ENST00000373198.4:c.589C>T	p.Arg197Ter	p.R197*	ENST00000373198	NM_133170.3	197	Cga/Tga	5/32	0.181860191193325	2	FACETS	0.96	0.906	1	0.96	0.906	1	INDETERMINATE	2	TRUE	0	0.37	2		468	788	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164712	36164712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	44	543	0	ENST00000300305.3:c.1163C>T	p.Ser388Leu	p.S388L	ENST00000300305		388	tCg/tTg	8/8	1	2	FACETS	0.289	0.242	0.343	0.289	0.242	0.343	SUBCLONAL	1	TRUE	1	0.37	2		543	822	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42879912	42879912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	56	146	1	ENST00000398585.3:c.20G>A	p.Gly7Glu	p.G7E	ENST00000398585	NM_001135099.1	7	gGa/gAa	1/14	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.37	2		147	273	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24129431	24129431	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	124	331	0	ENST00000263121.7:c.75C>A	p.Phe25Leu	p.F25L	ENST00000263121	NM_003073.3	25	ttC/ttA	1/9	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.37	2		331	550	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537106	41537106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	231	506	0	ENST00000263253.7:c.1933G>A	p.Glu645Lys	p.E645K	ENST00000263253	NM_001429.3	645	Gaa/Aaa	10/31	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.37	2		506	941	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568574	41568574	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	273	654	0	ENST00000263253.7:c.4524C>A	p.Phe1508Leu	p.F1508L	ENST00000263253	NM_001429.3	1508	ttC/ttA	28/31	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.37	2		654	1112	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572405	41572405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	158	641	0	ENST00000263253.7:c.4934G>A	p.Arg1645Gln	p.R1645Q	ENST00000263253	NM_001429.3	1645	cGa/cAa	30/31	1	2	FACETS	0.865	0.792	0.942	0.865	0.792	0.942	CLONAL	1	TRUE	1	0.37	2		641	987	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932677	39932677	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1255	542	919	0	ENST00000378444.4:c.1922C>A	p.Ser641Tyr	p.S641Y	ENST00000378444	NM_001123385.1	641	tCt/tAt	4/15	1	2	FACETS	0.815	0.781	0.85	1	0.997	1	CLONAL	2	TRUE	1	0.37	2		919	1797	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933587	39933587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	252	614	1	ENST00000378444.4:c.1012C>T	p.Arg338Trp	p.R338W	ENST00000378444	NM_001123385.1	338	Cgg/Tgg	4/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.37	2		615	1211	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941837	44941837	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1253	108	295	0	ENST00000377967.4:c.3161G>T	p.Arg1054Ile	p.R1054I	ENST00000377967	NM_021140.2	1054	aGa/aTa	21/29	1	2	FACETS	0.429	0.383	0.478	0.429	0.383	0.478	SUBCLONAL	1	TRUE	1	0.37	2		295	1361	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969370	44969370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370765411	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	224	740	3	ENST00000377967.4:c.4052G>A	p.Arg1351Gln	p.R1351Q	ENST00000377967	NM_021140.2	1351	cGa/cAa	28/29	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.37	2		743	1111	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006767	47006767	+	5_prime_UTR_variant	5'UTR	SNP	G	G	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	294	594	0	ENST00000377604.3:c.-114G>A		p.*38*	ENST00000377604	NM_001204468.1	-/852		2/24	1	2	FACETS	0.77	0.725	0.816	1	0.994	1	SUBCLONAL	2	TRUE	1	0.37	2		594	1032	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034435	47034435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	380	598	2	ENST00000377604.3:c.520G>A	p.Ala174Thr	p.A174T	ENST00000377604	NM_001204468.1	174	Gcc/Acc	6/24	1	2	FACETS	0.831	0.789	0.874	1	0.996	1	CLONAL	2	TRUE	1	0.37	2		600	1236	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041361	47041361	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782440714	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	367	551	0	ENST00000377604.3:c.1705G>A	p.Val569Ile	p.V569I	ENST00000377604	NM_001204468.1	569	Gtc/Atc	16/24	1	2	FACETS	0.863	0.819	0.908	1	0.996	1	CLONAL	2	TRUE	1	0.37	2		551	1149	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422655	47422655	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1569319031	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	367	695	1	ENST00000377045.4:c.127G>A	p.Asp43Asn	p.D43N	ENST00000377045	NM_001654.4	43	Gac/Aac	3/16	1	2	FACETS	0.799	0.758	0.841	1	0.995	1	SUBCLONAL	2	TRUE	1	0.37	2		696	1241	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422716	47422716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1413219188	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	295	541	0	ENST00000377045.4:c.188G>A	p.Arg63Gln	p.R63Q	ENST00000377045	NM_001654.4	63	cGa/cAa	3/16	1	2	FACETS	0.767	0.723	0.813	1	0.994	1	SUBCLONAL	2	TRUE	1	0.37	2		541	1039	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410948	63410948	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	295	650	2	ENST00000330258.3:c.2219C>A	p.Ser740Tyr	p.S740Y	ENST00000330258	NM_152424.3	740	tCt/tAt	2/2	1	2	FACETS	0.839	0.792	0.888	1	0.995	1	CLONAL	2	TRUE	1	0.37	2		652	950	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412029	63412029	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754922124	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1343	225	1073	2	ENST00000330258.3:c.1138G>A	p.Glu380Lys	p.E380K	ENST00000330258	NM_152424.3	380	Gag/Aag	2/2	1	2	FACETS	0.776	0.72	0.834	0.776	0.72	0.834	SUBCLONAL	1	TRUE	1	0.37	2		1075	1568	SUCCESS
AR	367	MSKCC	GRCh37	X	66765686	66765686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1481518005	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	316	690	2	ENST00000374690.3:c.698C>T	p.Ser233Phe	p.S233F	ENST00000374690	NM_000044.3	233	tCt/tTt	1/8	1	2	FACETS	0.79	0.746	0.835	1	0.995	1	SUBCLONAL	2	TRUE	1	0.37	2		692	1081	SUCCESS
AR	367	MSKCC	GRCh37	X	66766604	66766604	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	265	508	1	ENST00000374690.3:c.1616G>A	p.Arg539His	p.R539H	ENST00000374690	NM_000044.3	539	cGt/cAt	1/8	1	2	FACETS	0.862	0.81	0.914	1	0.994	1	CLONAL	2	TRUE	1	0.37	2		509	831	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346198	70346198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1380	81	758	0	ENST00000374080.3:c.2549G>A	p.Arg850Gln	p.R850Q	ENST00000374080		850	cGg/cAg	19/45	1	2	FACETS	0.3	0.263	0.34	0.3	0.263	0.34	SUBCLONAL	1	TRUE	1	0.37	2		758	1461	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347294	70347294	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	72	539	2	ENST00000374080.3:c.2958G>T	p.Lys986Asn	p.K986N	ENST00000374080		986	aaG/aaT	21/45	1	2	FACETS	0.371	0.323	0.423	0.371	0.323	0.423	SUBCLONAL	1	TRUE	1	0.37	2		541	1049	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814272	76814272	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	256	723	0	ENST00000373344.5:c.6372T>G	p.Ile2124Met	p.I2124M	ENST00000373344	NM_000489.3	2124	atT/atG	29/35	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.37	2		723	1065	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907681	76907681	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1481	444	966	1	ENST00000373344.5:c.4480C>A	p.Gln1494Lys	p.Q1494K	ENST00000373344	NM_000489.3	1494	Caa/Aaa	15/35	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.37	2		967	1925	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937492	76937492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	275	613	0	ENST00000373344.5:c.3256G>A	p.Ala1086Thr	p.A1086T	ENST00000373344	NM_000489.3	1086	Gca/Aca	9/35	1	2	FACETS	0.821	0.773	0.871	1	0.994	1	CLONAL	2	TRUE	1	0.37	2		613	905	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615122	100615122	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	110	574	2	ENST00000308731.7:c.793C>T	p.Pro265Ser	p.P265S	ENST00000308731	NM_000061.2	265	Cct/Tct	9/19	1	2	FACETS	0.477	0.427	0.53	0.477	0.427	0.53	SUBCLONAL	1	TRUE	1	0.37	2		576	1247	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191760	123191760	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1390	117	829	1	ENST00000218089.9:c.1349G>A	p.Arg450Lys	p.R450K	ENST00000218089	NM_001042749.1	450	aGa/aAa	15/35	1	2	FACETS	0.42	0.377	0.465	0.42	0.377	0.465	SUBCLONAL	1	TRUE	1	0.37	2		830	1507	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28980020	28980021	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAA	novel	NA	P-0006684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	160	275	1	ENST00000282397.4:c.1445_1447dup	p.Phe482dup	p.F482dup	ENST00000282397	NM_002019.4	482	tgt/tTTTgt	11/30	1	2	FACETS	0.905	0.836	0.977	0.905	0.836	0.977	CLONAL	1	TRUE	1	0.671933769980173	2		276	526	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0006711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	103	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.453359502829823	3	FACETS	0.988	0.902	1	0.988	0.902	1	CLONAL	2	TRUE	1	0.583187116709848	3		249	231	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0006711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	368	293	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.492194841400139	2	FACETS	0.834	0.796	0.871	0.834	0.796	0.871	CLONAL	2	TRUE	0	0.583187116709848	2		295	757	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0006711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	60	292	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.343010932501941	3	FACETS	1	0.968	1	0.681	0.597	0.77	INDETERMINATE	1	TRUE	1	0.583187116709848	3		292	195	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343789	118343789	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	84	382	0	ENST00000534358.1:c.1915A>G	p.Lys639Glu	p.K639E	ENST00000534358	NM_005933.3	639	Aaa/Gaa	3/36	0.488864520523772	3	FACETS	0.884	0.785	0.989	0.442	0.392	0.495	CLONAL	1	TRUE	1	0.583187116709848	3		382	421	SUCCESS
APC	324	MSKCC	GRCh37	5	112151244	112151245	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0006711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	107	436	0	ENST00000257430.4:c.893_894dup	p.Ser299ThrfsTer7	p.S299Tfs*7	ENST00000257430	NM_000038.5	296	agc/agCAc	9/16	0.343010932501941	3	FACETS	0.913	0.822	1	0.457	0.411	0.505	INDETERMINATE	1	TRUE	1	0.583187116709848	3		436	519	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983930	2983930	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006741-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1223	268	834	3	ENST00000396946.4:c.600C>A	p.Asp200Glu	p.D200E	ENST00000396946	NM_032415.4	200	gaC/gaA	5/25	1	2	FACETS	0.83	0.776	0.886	0.83	0.776	0.886	CLONAL	1	TRUE	1	0.433044449493279	2		837	1491	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445007	49445007	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006741-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	225	610	0	ENST00000301067.7:c.2459A>C	p.Glu820Ala	p.E820A	ENST00000301067	NM_003482.3	820	gAg/gCg	10/54	1	2	FACETS	0.879	0.818	0.943	0.879	0.818	0.943	CLONAL	1	TRUE	1	0.433044449493279	2		610	1182	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576397	7576978	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCGCCACTGCACTCCAGCCTGGGTGACAGAGTGAGACTCTGTCTCCAAAAAAAAAAAAAAAAAAAGCAGGCTAGGCTAAGCTATGATGTTCCTTAGATTAGGTGTATTAAATCCATTTTCAACTTACAATATTTTCAACTTACGACGAGTTTATCAGGAAGTAACACCATCGTAAGTCAAGTAGCATCTGTATCAGGCAAAGTCATAGAACCATTTTCATGCTCTCTTTAACAATTTTCTTTTTGAAAGCTGGTCTGGTCCTTTAAAATATATATTATGGTATAAGTTGGTGTTCTGAAGTTAGTTAGCTACAACCAGGAGCCATTGTCTTTGAGGCATCACTGCCCCCTGATGGCAAATGCCCCAATTGCAGGTAAAACAGTCAAGAAGAAAACGGCATTTTGAGTGTTAGACTGGAAACTTTCCACTTGATAAGAGGTCCCAAGACTTAGTACCTGAAGGGTGAAATATTCTCCATCCAGTGGTTTCTTCTTTGGCTGGGGAGAGGAGCTGGTGTTGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAAAGTGAATCTGAGGCATAACTGCA	CCCGCCACTGCACTCCAGCCTGGGTGACAGAGTGAGACTCTGTCTCCAAAAAAAAAAAAAAAAAAAGCAGGCTAGGCTAAGCTATGATGTTCCTTAGATTAGGTGTATTAAATCCATTTTCAACTTACAATATTTTCAACTTACGACGAGTTTATCAGGAAGTAACACCATCGTAAGTCAAGTAGCATCTGTATCAGGCAAAGTCATAGAACCATTTTCATGCTCTCTTTAACAATTTTCTTTTTGAAAGCTGGTCTGGTCCTTTAAAATATATATTATGGTATAAGTTGGTGTTCTGAAGTTAGTTAGCTACAACCAGGAGCCATTGTCTTTGAGGCATCACTGCCCCCTGATGGCAAATGCCCCAATTGCAGGTAAAACAGTCAAGAAGAAAACGGCATTTTGAGTGTTAGACTGGAAACTTTCCACTTGATAAGAGGTCCCAAGACTTAGTACCTGAAGGGTGAAATATTCTCCATCCAGTGGTTTCTTCTTTGGCTGGGGAGAGGAGCTGGTGTTGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAAAGTGAATCTGAGGCATAACTGCA	-	novel	NA	P-0006741-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	104	5	0	ENST00000269305.4:c.919+41_993+456del		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	0.433044449493279	1	FACETS	1	0.987	1	1	0.993	1	CLONAL	3	TRUE	0	0.433044449493279	1		5	114	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115861	8115862	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGAG	novel	NA	P-0006741-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1279	266	583	0	ENST00000346208.3:c.1208_1211dup	p.His405GlufsTer103	p.H405Efs*103	ENST00000346208		403	ctg/cTGAGtg	6/6	0.164129573461345	5	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.433044449493279	5		583	1545	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351896	89351896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006741-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	192	921	1	ENST00000301030.4:c.1054G>A	p.Asp352Asn	p.D352N	ENST00000301030	NM_001256183.1	352	Gac/Aac	9/13	0.433044449493279	1	FACETS	0.52	0.48	0.562	0.52	0.48	0.562	SUBCLONAL	1	TRUE	0	0.433044449493279	1		922	1336	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319090	62319090	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006741-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1800	303	600	0	ENST00000360203.5:c.1448C>A	p.Ala483Asp	p.A483D	ENST00000360203	NM_001283009.1	483	gCc/gAc	17/35	0.407333921377684	5	FACETS	1	0.979	1	0.366	0.343	0.39	CLONAL	1	TRUE	2	0.433044449493279	5		600	2103	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0006782-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	387	409	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	0.682839789528625	2		411	814	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0006782-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	313	419	1	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	0.682839789528625	2		420	761	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413070	139413072	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0006782-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	43	484	0	ENST00000277541.6:c.1070_1072del	p.Phe357del	p.F357del	ENST00000277541	NM_017617.3	357	tTCTac/tac	6/34	1	2	FACETS	0.155	0.129	0.185	0.155	0.129	0.185	SUBCLONAL	1	TRUE	1	0.682839789528625	2		484	810	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0006782-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	185	467	0	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	0.468	0.431	0.506	0.468	0.431	0.506	SUBCLONAL	1	TRUE	1	0.682839789528625	2		467	1159	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413049	139413049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064795070	NA	P-0006782-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	57	376	0	ENST00000277541.6:c.1093C>T	p.Arg365Cys	p.R365C	ENST00000277541	NM_017617.3	365	Cgc/Tgc	6/34	1	2	FACETS	0.265	0.226	0.306	0.265	0.226	0.306	SUBCLONAL	1	TRUE	1	0.682839789528625	2		376	631	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828383	72828383	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1277890729	NA	P-0006782-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	97	665	0	ENST00000268489.5:c.8198G>A	p.Arg2733His	p.R2733H	ENST00000268489	NM_006885.3	2733	cGt/cAt	9/10	1	2	FACETS	0.258	0.229	0.289	0.258	0.229	0.289	SUBCLONAL	1	TRUE	1	0.682839789528625	2		665	1101	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143993	11143993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568509370	NA	P-0006782-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	180	316	0	ENST00000358026.2:c.3574C>T	p.Arg1192Cys	p.R1192C	ENST00000358026	NM_001128849.1	1192	Cgc/Tgc	26/36	1	2	FACETS	0.991	0.921	1	0.991	0.921	1	CLONAL	1	TRUE	1	0.682839789528625	2		316	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0006782-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	88	260	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	1	2	FACETS	0.606	0.54	0.677	0.606	0.54	0.677	SUBCLONAL	1	TRUE	1	0.682839789528625	2		260	425	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945948	17945948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373027121	NA	P-0006782-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	64	499	0	ENST00000458235.1:c.1991C>T	p.Pro664Leu	p.P664L	ENST00000458235	NM_000215.3	664	cCg/cTg	15/24	1	2	FACETS	0.259	0.223	0.297	0.259	0.223	0.297	SUBCLONAL	1	TRUE	1	0.682839789528625	2		499	725	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509676	106509676	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139426517	NA	P-0006782-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	325	372	0	ENST00000359195.3:c.1670C>T	p.Ala557Val	p.A557V	ENST00000359195	NM_002649.2	557	gCg/gTg	2/11	0.682839789528625	3	FACETS	1	0.99	1	0.594	0.562	0.628	CLONAL	1	TRUE	1	0.682839789528625	3		372	1074	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658370	18658370	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006782-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	339	401	1	ENST00000266497.5:c.3175G>A	p.Ala1059Thr	p.A1059T	ENST00000266497		1059	Gca/Aca	22/31	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.682839789528625	2		402	844	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37055897	37055924	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGCTTCAGAATCTCTTTTCTAATAGAG	AAGCTTCAGAATCTCTTTTCTAATAGAG	-	novel	NA	P-0006782-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	242	296	0	ENST00000231790.2:c.678-24_681del		p.X226_splice	ENST00000231790	NM_000249.3	226		9/19	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.682839789528625	2		296	575	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920173	76920173	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006782-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	562	739	0	ENST00000373344.5:c.3904del	p.Arg1302GlufsTer44	p.R1302Efs*44	ENST00000373344	NM_000489.3	1302	Aga/ga	11/35	0.395006968225154	1	FACETS	0.825	0.794	0.857	0.825	0.794	0.857	INDETERMINATE	1	TRUE	0	0.682839789528625	1		739	1314	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969813	81969813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371326699	NA	P-0006782-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	469	664	1	ENST00000359376.3:c.2882C>T	p.Thr961Met	p.T961M	ENST00000359376	NM_002661.3	961	aCg/aTg	27/33	0.666710548970482	1	FACETS	0.833	0.799	0.868	0.833	0.799	0.868	CLONAL	1	TRUE	0	0.682839789528625	1		665	1086	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15969005	15969005	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200294041	NA	P-0006782-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	59	293	2	ENST00000268712.3:c.4745C>T	p.Ala1582Val	p.A1582V	ENST00000268712	NM_006311.3	1582	gCg/gTg	33/46	1	2	FACETS	0.299	0.257	0.345	0.299	0.257	0.345	SUBCLONAL	1	TRUE	1	0.682839789528625	2		295	577	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748850	41748850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138698106	NA	P-0006782-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	43	601	0	ENST00000301178.4:c.1375G>A	p.Val459Met	p.V459M	ENST00000301178	NM_021913.4	459	Gtg/Atg	11/20	1	2	FACETS	0.147	0.122	0.174	0.147	0.122	0.174	SUBCLONAL	1	TRUE	1	0.682839789528625	2		601	859	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265178	46265178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1202360619	NA	P-0006782-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	499	722	2	ENST00000371998.3:c.2048G>A	p.Arg683Gln	p.R683Q	ENST00000371998		683	cGg/cAg	12/23	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.682839789528625	2		724	1251	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954273	32954273	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359752	NA	P-0006782-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	269	402	0	ENST00000380152.3:c.9253del	p.Thr3085GlnfsTer19	p.T3085Qfs*19	ENST00000380152		3083	Aaa/aa	24/27	1	2	FACETS	0.91	0.856	0.965	0.91	0.856	0.965	CLONAL	1	TRUE	1	0.682839789528625	2		402	866	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0006789-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	509	517	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.500974527970749	5	FACETS	1	0.966	1	0.755	0.725	0.785	CLONAL	3	TRUE	1	0.500974527970749	5		517	1179	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0006789-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	597	582	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.435433317669566	3	FACETS	0.91	0.88	0.94	0.91	0.88	0.94	CLONAL	3	TRUE	0	0.500974527970749	3		582	1092	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242494	55242494	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006789-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	506	474	0	ENST00000275493.2:c.2264C>G	p.Ala755Gly	p.A755G	ENST00000275493	NM_005228.3	755	gCc/gGc	19/28	0.500974527970749	5	FACETS	1	0.987	1	0.797	0.766	0.828	CLONAL	3	TRUE	1	0.500974527970749	5		474	1110	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074100	8074101	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0006789-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1929	340	919	1	ENST00000377482.5:c.557_558dup	p.Thr187LeufsTer61	p.T187Lfs*61	ENST00000377482	NM_018948.3	186	-/CT	4/4	0.311972535114745	4	FACETS	0.898	0.845	0.952			1	CLONAL	1	TRUE	NA	0.500974527970749	4		920	2269	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182641	38182641	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs387907272	NA	P-0006825-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	41	490	2	ENST00000396334.3:c.794T>C	p.Leu265Pro	p.L265P	ENST00000396334	NM_002468.4	265	cTg/cCg	5/5	1	2	FACETS	0.234	0.194	0.279	0.234	0.194	0.279	SUBCLONAL	1	TRUE	1	0.35231144696554	2		492	996	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272207	15272207	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1051094199	NA	P-0006825-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	30	242	0	ENST00000263388.2:c.6232C>T	p.Arg2078Trp	p.R2078W	ENST00000263388	NM_000435.2	2078	Cgg/Tgg	33/33	0.203255368753741	2	FACETS	0.41	0.33	0.501	0.205	0.165	0.251	INDETERMINATE	1	TRUE	0	0.35231144696554	2		242	415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577523	7577524	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006825-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	124	553	0	ENST00000269305.4:c.757dup	p.Thr253AsnfsTer11	p.T253Nfs*11	ENST00000269305	NM_001126112.2	253	acc/aAcc	7/11	1	2	FACETS	0.722	0.652	0.796	0.722	0.652	0.796	SUBCLONAL	1	TRUE	1	0.35231144696554	2		553	975	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0006836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	51	336	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.921	0.782	1	0.921	0.782	1	CLONAL	1	TRUE	1	0.18	2		336	615	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0006836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	127	417	0	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	0.18	2		417	1036	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412958	49412958	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	66	558	0	ENST00000418115.1:c.65T>G	p.Leu22Arg	p.L22R	ENST00000418115	NM_001664.2	22	cTc/cGc	2/5	1	2	FACETS	0.644	0.557	0.739	0.644	0.557	0.739	SUBCLONAL	1	TRUE	1	0.18	2		558	1139	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336625	81336625	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs527951814	NA	P-0006836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	30	420	1	ENST00000222390.5:c.1597C>T	p.Arg533Ter	p.R533*	ENST00000222390	NM_000601.4	533	Cga/Tga	14/18	1	2	FACETS	0.576	0.463	0.705	0.576	0.463	0.705	SUBCLONAL	1	TRUE	1	0.18	2		421	579	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843813	151843813	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	31	336	1	ENST00000262189.6:c.13902G>A	p.Trp4634Ter	p.W4634*	ENST00000262189	NM_170606.2	4634	tgG/tgA	53/59	1	2	FACETS	0.569	0.459	0.695	0.569	0.459	0.695	SUBCLONAL	1	TRUE	1	0.18	2		337	605	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533026	63533027	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCCAC	novel	NA	P-0006836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	120	527	0	ENST00000307078.5:c.1863_1867dup	p.Met623SerfsTer68	p.M623Sfs*68	ENST00000307078	NM_004655.3	623	atg/aGTGGAtg	7/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.18	2		527	1180	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0006843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	169	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.803718033787215	4	FACETS	0.924	0.85	1	0.462	0.425	0.5	CLONAL	1	FALSE	2	0.803718033787215	4		249	821	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0006843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	290	393	0				ENST00000310581	NM_198253.2	-/1132			0.774355787771976	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	FALSE	1	0.803718033787215	3		393	474	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923060	44923060	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	440	110	0	ENST00000377967.4:c.1921C>T	p.Gln641Ter	p.Q641*	ENST00000377967	NM_021140.2	641	Cag/Tag	16/29	0.803718033787215	2	FACETS	1	0.997	1			1	CLONAL	2	FALSE	NA	0.803718033787215	2		110	490	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197427	26197427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1844	350	487	5	ENST00000356476.2:c.52C>T	p.Arg18Cys	p.R18C	ENST00000356476		18	Cgc/Tgc	1/1	0.725641545947931	5	FACETS	0.876	0.825	0.927			1	CLONAL	1	FALSE	NA	0.803718033787215	5		492	2194	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437782	52437782	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0006843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	632	344	0	ENST00000460680.1:c.1379C>G	p.Ser460Ter	p.S460*	ENST00000460680	NM_004656.3	460	tCa/tGa	13/17	0.803718033787215	4	FACETS	0.937	0.903	0.971	0.937	0.903	0.971	CLONAL	2	FALSE	2	0.803718033787215	4		344	1514	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0006843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	354	331	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	0.774355787771976	3	FACETS	0.97	0.919	1	0.485	0.459	0.512	CLONAL	1	FALSE	1	0.803718033787215	3		331	1273	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150022917	150022917	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	361	190	0	ENST00000253339.5:c.346G>C	p.Glu116Gln	p.E116Q	ENST00000253339		116	Gag/Cag	1/7	0.803718033787215	3	FACETS	0.864	0.825	0.902	0.864	0.825	0.902	CLONAL	2	FALSE	1	0.803718033787215	3		190	729	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100871	27100871	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	284	332	1	ENST00000324856.7:c.4153G>T	p.Glu1385Ter	p.E1385*	ENST00000324856	NM_006015.4	1385	Gaa/Taa	18/20	0.801161676643143	3	FACETS	1	0.97	1	0.523	0.492	0.554	CLONAL	1	FALSE	1	0.803718033787215	3		333	947	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101705	27101705	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	233	216	0	ENST00000324856.7:c.4987G>C	p.Asp1663His	p.D1663H	ENST00000324856	NM_006015.4	1663	Gac/Cac	18/20	0.801161676643143	3	FACETS	1	0.951	1	0.51	0.477	0.544	CLONAL	1	FALSE	1	0.803718033787215	3		216	797	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164906	47164906	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1341284759	NA	P-0006843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	186	224	0	ENST00000409792.3:c.1220C>G	p.Ser407Cys	p.S407C	ENST00000409792	NM_014159.6	407	tCt/tGt	3/21	0.803718033787215	4	FACETS	0.852	0.787	0.92	0.426	0.393	0.46	CLONAL	1	FALSE	2	0.803718033787215	4		224	980	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983131	149983131	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1470913808	NA	P-0006843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	277	288	0	ENST00000253339.5:c.3127G>A	p.Asp1043Asn	p.D1043N	ENST00000253339		1043	Gat/Aat	7/7	0.803718033787215	3	FACETS	0.873	0.82	0.928	0.436	0.41	0.464	CLONAL	1	FALSE	1	0.803718033787215	3		288	1107	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983140	149983140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	274	298	0	ENST00000253339.5:c.3118G>A	p.Asp1040Asn	p.D1040N	ENST00000253339		1040	Gat/Aat	7/7	0.803718033787215	3	FACETS	0.88	0.826	0.935	0.44	0.413	0.468	CLONAL	1	FALSE	1	0.803718033787215	3		298	1086	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628510	90628510	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1171	90	283	0	ENST00000330062.3:c.1077G>C	p.Gln359His	p.Q359H	ENST00000330062	NM_002168.2	359	caG/caC	8/11	0.765406431995852	4	FACETS	0.32	0.283	0.361	0.16	0.141	0.181	SUBCLONAL	1	FALSE	2	0.803718033787215	4		283	1261	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484251	57484251	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	152	259	0	ENST00000371085.3:c.565G>A	p.Asp189Asn	p.D189N	ENST00000371085	NM_000516.4	189	Gac/Aac	7/13	0.782285145203363	5	FACETS	0.791	0.722	0.863	0.264	0.24	0.288	SUBCLONAL	1	FALSE	2	0.803718033787215	5		259	1055	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130454	29130454	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs551930027	NA	P-0006843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	243	302	0	ENST00000328354.6:c.256G>C	p.Glu86Gln	p.E86Q	ENST00000328354	NM_007194.3	86	Gag/Cag	2/15	0.803718033787215	4	FACETS	0.915	0.854	0.978	0.458	0.427	0.489	CLONAL	1	FALSE	2	0.803718033787215	4		302	1192	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533795	41533795	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0006843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	224	242	0	ENST00000263253.7:c.1760+1G>A		p.X587_splice	ENST00000263253	NM_001429.3	587			0.803718033787215	4	FACETS	0.94	0.875	1	0.47	0.437	0.504	CLONAL	1	FALSE	2	0.803718033787215	4		242	1070	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087393	27087394	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0006843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	312	353	0	ENST00000324856.7:c.1969_1970del	p.Leu657GlufsTer18	p.L657Efs*18	ENST00000324856	NM_006015.4	656	gCT/g	5/20	0.801161676643143	3	FACETS	0.876	0.826	0.928	0.438	0.413	0.464	CLONAL	1	FALSE	1	0.803718033787215	3		353	1242	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061229	38061230	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0006843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	279	275	0	ENST00000250448.2:c.759dup	p.Phe254ValfsTer39	p.F254Vfs*39	ENST00000250448	NM_004496.3	253	-/G	2/2	0.515810932585903	4	FACETS	1	0.993	1	0.696	0.656	0.738	CLONAL	1	FALSE	2	0.803718033787215	4		275	899	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	174	366	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.246423611064496	2	FACETS	0.892	0.822	0.964	0.892	0.822	0.964	CLONAL	2	TRUE	0	0.246423611064496	2		366	792	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140454014	140454014	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs755214031	NA	P-0006868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	175	231	0	ENST00000288602.6:c.1714A>T	p.Ile572Phe	p.I572F	ENST00000288602	NM_004333.4	572	Atc/Ttc	14/18	0.246423611064496	3	FACETS	0.953	0.879	1	0.953	0.879	1	CLONAL	2	TRUE	1	0.246423611064496	3		231	837	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0006868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	46	393	0				ENST00000310581	NM_198253.2	-/1132			0.211549384051584	3	FACETS	0.926	0.78	1	0.463	0.39	0.543	CLONAL	1	TRUE	1	0.246423611064496	3		393	453	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977953	131977953	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375710541	NA	P-0006868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	182	291	0	ENST00000265335.6:c.3836G>A	p.Arg1279His	p.R1279H	ENST00000265335		1279	cGt/cAt	25/25	0.246423611064496	2	FACETS	0.865	0.799	0.934	0.865	0.799	0.934	CLONAL	2	TRUE	0	0.246423611064496	2		291	854	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482552	56482552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	93	237	0	ENST00000267101.3:c.1009G>A	p.Gly337Arg	p.G337R	ENST00000267101	NM_001982.3	337	Ggg/Agg	9/28	1	2	FACETS	0.958	0.851	1	0.958	0.851	1	CLONAL	1	TRUE	1	0.246423611064496	2		237	788	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004247	150004247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	116	324	0	ENST00000253339.5:c.1978C>T	p.Arg660Cys	p.R660C	ENST00000253339		660	Cgt/Tgt	3/7	1	2	FACETS	0.921	0.829	1	0.921	0.829	1	CLONAL	1	TRUE	1	0.246423611064496	2		324	1022	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999617	100999617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	85	426	1	ENST00000325455.5:c.185G>A	p.Arg62Gln	p.R62Q	ENST00000325455	NM_001202474.3	62	cGg/cAg	1/8	1	2	FACETS	0.694	0.612	0.782	0.694	0.612	0.782	SUBCLONAL	1	TRUE	1	0.246423611064496	2		427	994	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246333	46246333	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	90	246	1	ENST00000334344.6:c.4427C>T	p.Ser1476Phe	p.S1476F	ENST00000334344	NM_152641.2	1476	tCt/tTt	15/21	1	2	FACETS	0.99	0.878	1	0.99	0.878	1	CLONAL	1	TRUE	1	0.246423611064496	2		247	738	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473692	67473692	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	286	254	0	ENST00000327367.4:c.772G>A	p.Asp258Asn	p.D258N	ENST00000327367	NM_005902.3	258	Gat/Aat	6/9	0.223388464631537	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	0	0.246423611064496	3		254	794	SUCCESS
APC	324	MSKCC	GRCh37	5	112175721	112175722	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0006868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	163	204	0	ENST00000257430.4:c.4432_4433del	p.Arg1478GlyfsTer8	p.R1478Gfs*8	ENST00000257430	NM_000038.5	1477	cAG/c	16/16	0.246423611064496	2	FACETS	0.976	0.898	1	0.976	0.898	1	CLONAL	2	TRUE	0	0.246423611064496	2		204	678	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120341	70120342	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0006868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	117	465	0	ENST00000245479.2:c.1344_1345dup	p.Ser449ThrfsTer22	p.S449Tfs*22	ENST00000245479	NM_000346.3	448	tcc/tcCAc	3/3	0.246423611064496	3	FACETS	0.91	0.818	1	0.455	0.409	0.504	CLONAL	1	TRUE	1	0.246423611064496	3		465	1172	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0006901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	167	344	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	1	2	FACETS	0.915	0.841	0.993	0.915	0.841	0.993	CLONAL	1	TRUE	1	0.400479592920514	2		344	911	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913514	NA	P-0006901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	202	315	0	ENST00000288135.5:c.2466T>A	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaA	17/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.400479592920514	2		315	842	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594221	55594221	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913512	NA	P-0006901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	147	354	0	ENST00000288135.5:c.1924A>G	p.Lys642Glu	p.K642E	ENST00000288135	NM_000222.2	642	Aaa/Gaa	13/21	1	2	FACETS	0.89	0.813	0.97	0.89	0.813	0.97	CLONAL	1	TRUE	1	0.400479592920514	2		354	825	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0006910-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	889	552	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.670840476777461	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.669666887528439	3		552	1107	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061463	38061463	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006910-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	236	552	0	ENST00000250448.2:c.526A>G	p.Ile176Val	p.I176V	ENST00000250448	NM_004496.3	176	Atc/Gtc	2/2	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.669666887528439	2		552	659	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859846	151859846	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0006910-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	162	295	1	ENST00000262189.6:c.10816A>T	p.Arg3606Ter	p.R3606*	ENST00000262189	NM_170606.2	3606	Aga/Tga	43/59	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.669666887528439	2		296	457	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120854	115120854	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006910-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	200	363	0	ENST00000257566.3:c.152del	p.Ala51GlyfsTer37	p.A51Gfs*37	ENST00000257566	NM_016569.3	51	gCg/gg	1/8	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.669666887528439	2		363	511	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847253	68847253	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006910-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	278	638	0	ENST00000261769.5:c.1175del	p.Val392GlufsTer5	p.V392Efs*5	ENST00000261769	NM_004360.3	392	gTa/ga	9/16	0.669666887528439	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.669666887528439	1		638	506	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881488	48881489	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0006910-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	115	411	0	ENST00000267163.4:c.219_220dup	p.Ala74GlufsTer4	p.A74Efs*4	ENST00000267163	NM_000321.2	70	-/AG	2/27	0.669666887528439	1	FACETS	0.606	0.551	0.663	0.606	0.551	0.663	SUBCLONAL	1	TRUE	0	0.669666887528439	1		411	377	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031815	10031815	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs397518465	NA	P-0006910-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	205	513	0	ENST00000330684.3:c.1007+1G>A		p.X336_splice	ENST00000330684	NM_001134407.1	336			1	2	FACETS	0.945	0.881	1	0.945	0.881	1	CLONAL	1	TRUE	1	0.669666887528439	2		513	648	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594198	55594198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766264502	NA	P-0006910-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	145	426	0	ENST00000288135.5:c.1901G>A	p.Arg634Gln	p.R634Q	ENST00000288135	NM_000222.2	634	cGg/cAg	13/21	1	2	FACETS	0.715	0.654	0.777	0.715	0.654	0.777	SUBCLONAL	1	TRUE	1	0.669666887528439	2		426	606	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0006926-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	19	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.283725877049456	3	FACETS	0.419	0.317	0.539	0.209	0.158	0.27	SUBCLONAL	1	TRUE	1	0.283725877049456	3		249	365	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006926-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	38	140	0				ENST00000310581	NM_198253.2	-/1132			0.283725877049456	3	FACETS	0.715	0.591	0.853	0.357	0.295	0.427	SUBCLONAL	1	TRUE	1	0.283725877049456	3		140	428	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs121913468	NA	P-0006926-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	339	362	0	ENST00000269571.5:c.2305G>C	p.Asp769His	p.D769H	ENST00000269571		769	Gac/Cac	19/27	0.283725877049456	3	FACETS	0.862	0.817	0.908	1	0.993	1	CLONAL	3	TRUE	1	0.283725877049456	3		362	1055	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0006926-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	65	381	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	0.283725877049456	2	FACETS	0.524	0.453	0.601	0.262	0.226	0.301	SUBCLONAL	1	TRUE	0	0.283725877049456	2		381	875	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458507	120458507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006926-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	29	290	0	ENST00000256646.2:c.6838C>T	p.Pro2280Ser	p.P2280S	ENST00000256646	NM_024408.3	2280	Cct/Tct	34/34	0.189530524512454	4	FACETS	0.456	0.364	0.56	0.228	0.182	0.28	SUBCLONAL	1	TRUE	2	0.283725877049456	4		290	576	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101170	41101170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41279256	NA	P-0006926-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	24	238	0	ENST00000373198.4:c.1186G>A	p.Val396Ile	p.V396I	ENST00000373198	NM_133170.3	396	Gta/Ata	8/32	1	2	FACETS	0.378	0.295	0.473	0.378	0.295	0.473	SUBCLONAL	1	TRUE	1	0.283725877049456	2		238	448	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651901	36651902	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0006926-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	40	293	1	ENST00000244741.5:c.25dup	p.Arg9ProfsTer27	p.R9Pfs*27	ENST00000244741	NM_000389.4	8	gtc/gtCc	2/3	0.283725877049456	2	FACETS	0.432	0.358	0.515	0.216	0.179	0.258	SUBCLONAL	1	TRUE	0	0.283725877049456	2		294	653	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006949-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	215	435	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.355044645021849	3	FACETS	0.956	0.891	1	0.956	0.891	1	CLONAL	2	TRUE	1	0.355044645021849	3		435	746	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0006949-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	170	649	1	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.347997800794924	1	FACETS	0.886	0.815	0.96	0.886	0.815	0.96	CLONAL	1	TRUE	0	0.355044645021849	1		650	889	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974727	21974744	+	inframe_deletion	In_Frame_Del	DEL	CCTCCAGCAGCGCCCGCA	CCTCCAGCAGCGCCCGCA	-	novel	NA	P-0006949-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	78	311	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	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.355044645021849	2		311	433	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730125	41730125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142519810	NA	P-0006949-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1428	80	571	1	ENST00000242208.4:c.404C>T	p.Thr135Met	p.T135M	ENST00000242208	NM_002192.2	135	aCg/aTg	3/3	1	2	FACETS	0.299	0.262	0.339	0.299	0.262	0.339	SUBCLONAL	1	TRUE	1	0.355044645021849	2		572	1508	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129150	64129150	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006949-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	168	454	0	ENST00000334205.4:c.688G>A	p.Glu230Lys	p.E230K	ENST00000334205	NM_003942.2	230	Gag/Aag	7/17	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.355044645021849	2		454	864	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56376693	56376693	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006949-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	238	614	0	ENST00000348428.3:c.733G>T	p.Val245Phe	p.V245F	ENST00000348428	NM_006785.3	245	Gtt/Ttt	5/17	0.347997800794924	1	FACETS	0.958	0.894	1	0.958	0.894	1	CLONAL	1	TRUE	0	0.355044645021849	1		614	1151	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125072	46125106	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTGCTTTAAAACAGTATTACTTGCGGTGAGTAGT	TTTGCTTTAAAACAGTATTACTTGCGGTGAGTAGT	-	novel	NA	P-0006949-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	155	361	1	ENST00000334344.6:c.259_284+9del		p.X87_splice	ENST00000334344	NM_152641.2	87		3/21	0.355044645021849	3	FACETS	1	0.983	1	0.646	0.592	0.702	CLONAL	1	TRUE	1	0.355044645021849	3		362	796	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141468	11141469	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0006949-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	142	449	0	ENST00000358026.2:c.3446dup	p.Tyr1149Ter	p.Y1149*	ENST00000358026	NM_001128849.1	1149	tac/tAac	25/36	0.355044645021849	1	FACETS	0.811	0.74	0.886	0.811	0.74	0.886	CLONAL	1	TRUE	0	0.355044645021849	1		449	811	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176354	24176354	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	277	409	0	ENST00000263121.7:c.1148del	p.Pro383ArgfsTer100	p.P383Rfs*100	ENST00000263121	NM_003073.3	382	gCc/gc	9/9	0.3	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		409	608	SUCCESS
APC	324	MSKCC	GRCh37	5	112174798	112174799	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	86	389	0	ENST00000257430.4:c.3510dup	p.Arg1171ThrfsTer8	p.R1171Tfs*8	ENST00000257430	NM_000038.5	1169	-/A	16/16	0.3	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		389	308	SUCCESS
APC	324	MSKCC	GRCh37	5	112174232	112174232	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	84	464	0	ENST00000257430.4:c.2943del	p.Ser982ArgfsTer23	p.S982Rfs*23	ENST00000257430	NM_000038.5	981	Ccc/cc	16/16	0.3	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		464	379	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066758	77066758	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006992-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	494	646	1	ENST00000356341.3:c.727A>C	p.Lys243Gln	p.K243Q	ENST00000356341	NM_002576.4	243	Aag/Cag	7/15	0.718722150966344	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.718722150966344	1		647	872	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115952	8115953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0006992-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	229	223	0	ENST00000346208.3:c.1300dup	p.His434ProfsTer73	p.H434Pfs*73	ENST00000346208		433	cac/caCc	6/6	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.718722150966344	2		223	627	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0007014-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	372	647	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	0.394675058859893	2	FACETS	0.985	0.938	1	0.985	0.938	1	CLONAL	2	TRUE	0	0.394675058859893	2		647	957	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645652	12645652	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007014-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	92	272	0	ENST00000251849.4:c.817G>T	p.Asp273Tyr	p.D273Y	ENST00000251849	NM_002880.3	273	Gac/Tac	7/17	0.180634166738858	2	FACETS	1	0.964	1	0.589	0.526	0.654	INDETERMINATE	1	TRUE	0	0.394675058859893	2		272	396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0007014-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	173	304	0	ENST00000269305.4:c.376-1G>C		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.394675058859893	1	FACETS	1	0.98	1	1	0.994	1	CLONAL	2	TRUE	0	0.394675058859893	1		304	319	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0007039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	280	363	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.613210419341982	3	FACETS	0.932	0.883	0.982	0.932	0.883	0.982	CLONAL	2	TRUE	1	0.613210419341982	3		364	640	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0007039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	63	336	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.406346046027728	1	FACETS	0.288	0.249	0.33	0.288	0.249	0.33	SUBCLONAL	1	TRUE	0	0.613210419341982	1		336	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	441	549	0	ENST00000269305.4:c.403del	p.Cys135AlafsTer35	p.C135Afs*35	ENST00000269305	NM_001126112.2	135	Tgc/gc	5/11	0.548257923487203	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.613210419341982	1		549	832	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504041	123504041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	68	456	1	ENST00000371139.4:c.217C>T	p.His73Tyr	p.H73Y	ENST00000371139	NM_001114937.2	73	Cat/Tat	3/4	1	2	FACETS	0.476	0.415	0.541	0.476	0.415	0.541	SUBCLONAL	1	TRUE	1	0.613210419341982	2		457	466	SUCCESS
APC	324	MSKCC	GRCh37	5	112175747	112175748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATACTTT	novel	NA	P-0007039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	212	388	0	ENST00000257430.4:c.4459_4465dup	p.Leu1489TyrfsTer27	p.L1489Yfs*27	ENST00000257430	NM_000038.5	1486	gat/gATACTTTat	16/16	0.598137231994782	2	FACETS	1	0.991	1	0.693	0.65	0.736	CLONAL	1	TRUE	0	0.613210419341982	2		388	499	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	131	550	3	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	0.514039794203903	3	FACETS	1	0.938	1	0.519	0.473	0.568	CLONAL	1	TRUE	1	0.522418080596737	3		553	609	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	173	509	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	0.522418080596737	2		509	616	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429978	78429978	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	139	450	3	ENST00000370768.2:c.901del	p.Ile301TyrfsTer22	p.I301Yfs*22	ENST00000370768	NM_003902.3	301	Ata/ta	11/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.522418080596737	2		453	488	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	130	265	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.514039794203903	3	FACETS	0.916	0.833	1	0.458	0.416	0.502	CLONAL	1	TRUE	1	0.522418080596737	3		265	685	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103510737	103510737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146833751	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	119	276	0	ENST00000355739.4:c.641G>A	p.Arg214His	p.R214H	ENST00000355739	NM_000123.3	214	cGc/cAc	6/15	1	2	FACETS	0.871	0.79	0.956	0.871	0.79	0.956	CLONAL	1	TRUE	1	0.522418080596737	2		276	523	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841505	156841505	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145222195	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	216	315	0	ENST00000524377.1:c.808G>A	p.Asp270Asn	p.D270N	ENST00000524377	NM_002529.3	270	Gat/Aat	7/17	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.522418080596737	2		315	683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	223	503	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.961	0.896	1	0.961	0.896	1	CLONAL	1	TRUE	1	0.522418080596737	2		504	888	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	146	524	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.965	0.885	1	0.965	0.885	1	CLONAL	1	TRUE	1	0.522418080596737	2		524	579	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789591	3789591	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	165	253	0	ENST00000262367.5:c.4268del	p.Pro1423LeufsTer36	p.P1423Lfs*36	ENST00000262367	NM_004380.2	1423	cCt/ct	25/31	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.522418080596737	2		253	588	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578215	28578216	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	152	1014	0	ENST00000241453.7:c.2955_2956del	p.Pro986AlafsTer27	p.P986Afs*27	ENST00000241453	NM_004119.2	985	tcTCcg/tccg	24/24	1	2	FACETS	0.813	0.745	0.884	0.813	0.745	0.884	CLONAL	1	TRUE	1	0.522418080596737	2		1014	716	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	128	315	1	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	0.514039794203903	3	FACETS	1	0.974	1	0.592	0.539	0.647	CLONAL	1	TRUE	1	0.522418080596737	3		316	522	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936354	78936354	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	142	325	0	ENST00000306801.3:c.3790del	p.Gln1264ArgfsTer4	p.Q1264Rfs*4	ENST00000306801	NM_020761.2	1262	caC/ca	32/34	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.522418080596737	2		325	514	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	79	188	0	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	0.687	0.607	0.773	0.687	0.607	0.773	SUBCLONAL	1	TRUE	1	0.522418080596737	2		188	440	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	163	263	4	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.522418080596737	2		267	518	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097624	11097625	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1165714406	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	187	415	0	ENST00000358026.2:c.810dup	p.Gly271ArgfsTer16	p.G271Rfs*16	ENST00000358026	NM_001128849.1	268	-/C	5/36	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.522418080596737	2		415	679	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317105	11317105	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1060501909	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	181	360	1	ENST00000361445.4:c.389T>C	p.Ile130Thr	p.I130T	ENST00000361445	NM_004958.3	130	aTt/aCt	4/58	1	2	FACETS	0.972	0.899	1	0.972	0.899	1	CLONAL	1	TRUE	1	0.522418080596737	2		361	713	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713403	30713403	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	32	208	0	ENST00000295754.5:c.728C>A	p.Pro243His	p.P243H	ENST00000295754	NM_003242.5	243	cCc/cAc	4/7	1	2	FACETS	0.247	0.2	0.3	0.247	0.2	0.3	SUBCLONAL	1	TRUE	1	0.522418080596737	2		208	496	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620541	52620541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141958485	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	233	316	0	ENST00000394830.3:c.3212G>A	p.Arg1071His	p.R1071H	ENST00000394830	NM_018313.4	1071	cGc/cAc	21/30	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.522418080596737	2		316	730	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575646	55575646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	189	343	0	ENST00000288135.5:c.1172C>T	p.Thr391Ile	p.T391I	ENST00000288135	NM_000222.2	391	aCa/aTa	7/21	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.522418080596737	2		343	700	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197564	106197564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754215085	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	201	343	1	ENST00000380013.4:c.5897G>A	p.Arg1966His	p.R1966H	ENST00000380013	NM_001127208.2	1966	cGt/cAt	11/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.522418080596737	2		344	741	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131951787	131951787	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	158	243	0	ENST00000265335.6:c.3129G>T	p.Lys1043Asn	p.K1043N	ENST00000265335		1043	aaG/aaT	20/25	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.522418080596737	2		243	588	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979193	93979193	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	178	363	0	ENST00000369303.4:c.1633+2T>C		p.X545_splice	ENST00000369303	NM_004440.3	545			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.522418080596737	2		363	633	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94129026	94129026	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	279	454	0	ENST00000369303.4:c.34A>G	p.Ile12Val	p.I12V	ENST00000369303	NM_004440.3	12	Att/Gtt	1/17	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.522418080596737	2		454	954	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55272947	55272947	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	93	177	0	ENST00000275493.2:c.3272-2A>G		p.X1091_splice	ENST00000275493	NM_005228.3	1091			0.33918453980279	3	FACETS	0.983	0.878	1	0.491	0.439	0.547	CLONAL	1	TRUE	1	0.522418080596737	3		177	457	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738714	145738714	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753386714	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	148	229	2	ENST00000428558.2:c.2350C>T	p.Arg784Trp	p.R784W	ENST00000428558	NM_004260.3	784	Cgg/Tgg	15/22	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.522418080596737	2		231	447	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395186	139395186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	187	344	2	ENST00000277541.6:c.5752G>A	p.Ala1918Thr	p.A1918T	ENST00000277541	NM_017617.3	1918	Gcc/Acc	31/34	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.522418080596737	2		346	594	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111959722	111959722	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	130	167	0	ENST00000375549.3:c.301C>G	p.Leu101Val	p.L101V	ENST00000375549	NM_003002.3	101	Ctt/Gtt	3/4	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.522418080596737	2		167	401	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307462	118307462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782414402	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	94	198	0	ENST00000534358.1:c.235G>A	p.Ala79Thr	p.A79T	ENST00000534358	NM_005933.3	79	Gcc/Acc	1/36	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.522418080596737	2		198	351	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416073	49416073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	277	429	0	ENST00000301067.7:c.16402G>A	p.Gly5468Ser	p.G5468S	ENST00000301067	NM_003482.3	5468	Ggc/Agc	52/54	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.522418080596737	2		429	1005	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885931	111885931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761418716	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	290	428	0	ENST00000341259.2:c.1553G>A	p.Arg518Gln	p.R518Q	ENST00000341259	NM_005475.2	518	cGa/cAa	8/8	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.522418080596737	2		428	910	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907510	32907510	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	145	186	1	ENST00000380152.3:c.1895C>A	p.Ala632Glu	p.A632E	ENST00000380152		632	gCa/gAa	10/27	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.522418080596737	2		187	452	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986997	36986997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	124	260	0	ENST00000354822.5:c.692C>T	p.Thr231Met	p.T231M	ENST00000354822	NM_001079668.2	231	aCg/aTg	3/3	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.522418080596737	2		260	389	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058610	42058610	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	279	578	0	ENST00000219905.7:c.8330A>G	p.Lys2777Arg	p.K2777R	ENST00000219905	NM_001164273.1	2777	aAa/aGa	24/24	1	2	FACETS	0.908	0.853	0.965	0.908	0.853	0.965	CLONAL	1	TRUE	1	0.522418080596737	2		578	1176	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830204	72830204	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	217	475	0	ENST00000268489.5:c.6377C>A	p.Ala2126Glu	p.A2126E	ENST00000268489	NM_006885.3	2126	gCg/gAg	9/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.522418080596737	2		475	700	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831344	72831344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	215	429	0	ENST00000268489.5:c.5237C>T	p.Ala1746Val	p.A1746V	ENST00000268489	NM_006885.3	1746	gCc/gTc	9/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.522418080596737	2		429	725	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961337	15961337	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	189	307	1	ENST00000268712.3:c.6052C>T	p.Arg2018Ter	p.R2018*	ENST00000268712	NM_006311.3	2018	Cga/Tga	39/46	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.522418080596737	2		308	628	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964862	15964862	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	224	364	0	ENST00000268712.3:c.5734A>G	p.Lys1912Glu	p.K1912E	ENST00000268712	NM_006311.3	1912	Aaa/Gaa	37/46	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.522418080596737	2		364	806	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552112	29552112	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1264981771	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	83	186	0	ENST00000356175.3:c.1846-1G>A		p.X616_splice	ENST00000356175	NM_000267.3	616			1	2	FACETS	0.932	0.829	1	0.932	0.829	1	CLONAL	1	TRUE	1	0.522418080596737	2		186	341	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117401	7117401	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	174	290	0	ENST00000302850.5:c.3815G>A	p.Cys1272Tyr	p.C1272Y	ENST00000302850	NM_000208.2	1272	tGc/tAc	22/22	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.522418080596737	2		290	567	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138627	11138627	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	159	205	0	ENST00000358026.2:c.3382+1G>T		p.X1128_splice	ENST00000358026	NM_001128849.1	1128			1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.522418080596737	2		205	479	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272244	15272244	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1168179879	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	13	173	0	ENST00000263388.2:c.6195G>C	p.Arg2065Ser	p.R2065S	ENST00000263388	NM_000435.2	2065	agG/agC	33/33	1	2	FACETS	0.204	0.145	0.276	0.204	0.145	0.276	SUBCLONAL	1	TRUE	1	0.522418080596737	2		173	244	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758265	41758265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	193	331	0	ENST00000301178.4:c.1721G>A	p.Cys574Tyr	p.C574Y	ENST00000301178	NM_021913.4	574	tGc/tAc	15/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.522418080596737	2		331	656	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023957	31023957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139435094	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	93	318	0	ENST00000375687.4:c.3442C>T	p.Arg1148Cys	p.R1148C	ENST00000375687	NM_015338.5	1148	Cgc/Tgc	13/13	1	2	FACETS	0.562	0.501	0.628	0.562	0.501	0.628	SUBCLONAL	1	TRUE	1	0.522418080596737	2		318	633	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375171	31375171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140395707	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	184	368	0	ENST00000328111.2:c.568C>T	p.Arg190Cys	p.R190C	ENST00000328111	NM_006892.3	190	Cgc/Tgc	6/23	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.522418080596737	2		368	675	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655425	45655425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767656796	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	141	252	0	ENST00000407780.3:c.427G>A	p.Val143Ile	p.V143I	ENST00000407780	NM_001283052.1	143	Gtc/Atc	4/7	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.522418080596737	2		252	465	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411486	63411486	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	194	450	0	ENST00000330258.3:c.1681C>A	p.Leu561Ile	p.L561I	ENST00000330258	NM_152424.3	561	Cta/Ata	2/2	0.207627590459753	1	FACETS	0.678	0.629	0.73	0.678	0.629	0.73	INDETERMINATE	1	TRUE	0	0.522418080596737	1		450	809	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859851	151859851	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	109	255	0	ENST00000262189.6:c.10811del	p.Lys3604ArgfsTer26	p.K3604Rfs*26	ENST00000262189	NM_170606.2	3604	aAg/ag	43/59	0.514039794203903	3	FACETS	0.874	0.787	0.966	0.437	0.393	0.483	CLONAL	1	TRUE	1	0.522418080596737	3		255	602	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623186	52623187	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	105	318	0	ENST00000394830.3:c.2864dup	p.Asn955LysfsTer27	p.N955Kfs*27	ENST00000394830	NM_018313.4	955	aac/aaAc	19/30	1	2	FACETS	0.529	0.474	0.588	0.529	0.474	0.588	SUBCLONAL	1	TRUE	1	0.522418080596737	2		318	760	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435198	49435199	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755159728	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	33	122	0	ENST00000301067.7:c.6354dup	p.Ala2119ArgfsTer36	p.A2119Rfs*36	ENST00000301067	NM_003482.3	2118	-/C	31/54	1	2	FACETS	0.672	0.553	0.803	0.672	0.553	0.803	SUBCLONAL	1	TRUE	1	0.522418080596737	2		122	188	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350331	89350332	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	149	559	0	ENST00000301030.4:c.2618_2619del	p.Val873GlyfsTer42	p.V873Gfs*42	ENST00000301030	NM_001256183.1	873	gTG/g	9/13	1	2	FACETS	0.495	0.451	0.541	0.495	0.451	0.541	SUBCLONAL	1	TRUE	1	0.522418080596737	2		559	1153	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154251	2154251	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	104	312	0	ENST00000434045.2:c.677del	p.Gly226AlafsTer30	p.G226Afs*30	ENST00000434045	NM_001127598.1	226	gGc/gc	5/5	1	2	FACETS	0.893	0.804	0.986	0.893	0.804	0.986	CLONAL	1	TRUE	1	0.522418080596737	2		312	446	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347686	118347687	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	151	299	0	ENST00000534358.1:c.3327dup	p.Asn1110GlufsTer2	p.N1110Efs*2	ENST00000534358	NM_005933.3	1108	atg/atGg	4/36	1	2	FACETS	0.962	0.883	1	0.962	0.883	1	CLONAL	1	TRUE	1	0.522418080596737	2		299	601	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434378	49434378	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	175	309	0	ENST00000301067.7:c.7175del	p.Pro2392LeufsTer34	p.P2392Lfs*34	ENST00000301067	NM_003482.3	2392	cCt/ct	31/54	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.522418080596737	2		309	514	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027196	48027196	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs267608083	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	108	259	0	ENST00000234420.5:c.2079del	p.Lys693AsnfsTer43	p.K693Nfs*43	ENST00000234420	NM_000179.2	692	Aaa/aa	4/10	1	2	FACETS	0.709	0.638	0.784	0.709	0.638	0.784	SUBCLONAL	1	TRUE	1	0.522418080596737	2		259	583	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944381	131944382	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs748536322	NA	P-0007055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	160	264	1	ENST00000265335.6:c.2801dup	p.Asn934LysfsTer10	p.N934Kfs*10	ENST00000265335		931	-/A	17/25	1	2	FACETS	0.91	0.837	0.986	0.91	0.837	0.986	CLONAL	1	TRUE	1	0.522418080596737	2		265	673	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856093	68856093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121964878	NA	P-0007129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	109	541	0	ENST00000261769.5:c.1901C>T	p.Ala634Val	p.A634V	ENST00000261769	NM_004360.3	634	gCg/gTg	12/16	0.974845119006813	1	FACETS	0.531	0.488	0.573	0.531	0.488	0.573	SUBCLONAL	1	TRUE	0	0.974845119006813	1		541	216	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542332	187542332	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0007129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	88	339	0	ENST00000441802.2:c.5408C>G	p.Ser1803Ter	p.S1803*	ENST00000441802	NM_005245.3	1803	tCa/tGa	10/27	0.974845119006813	1	FACETS	0.568	0.519	0.616	0.568	0.519	0.616	SUBCLONAL	1	TRUE	0	0.974845119006813	1		339	163	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578484	7578485	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1064793929	NA	P-0007129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	70	508	0	ENST00000269305.4:c.445dup	p.Ser149PhefsTer32	p.S149Ffs*32	ENST00000269305	NM_001126112.2	149	tcc/tTcc	5/11	0.974845119006813	1	FACETS	0.37	0.328	0.413	0.37	0.328	0.413	SUBCLONAL	1	TRUE	0	0.974845119006813	1		508	199	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148507499	148507499	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	17	344	0	ENST00000320356.2:c.1955C>G	p.Ser652Cys	p.S652C	ENST00000320356	NM_004456.4	652	tCt/tGt	17/20	0.908228798548604	1	FACETS	0.077	0.057	0.101	0.077	0.057	0.101	SUBCLONAL	1	TRUE	0	0.974845119006813	1		344	232	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786758	3786758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	72	671	2	ENST00000262367.5:c.4453C>T	p.His1485Tyr	p.H1485Y	ENST00000262367	NM_004380.2	1485	Cat/Tat	27/31	1	2	FACETS	0.496	0.437	0.558	0.496	0.437	0.558	SUBCLONAL	1	TRUE	1	0.974845119006813	2		673	298	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153624	55153624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	73	573	0	ENST00000257290.5:c.2590C>T	p.Pro864Ser	p.P864S	ENST00000257290	NM_006206.4	864	Cct/Tct	19/23	NA	2	FACETS	0.583	0.516	0.653			1	INDETERMINATE	1	TRUE	NA	0.974845119006813	2		573	257	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38966814	38966814	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	64	305	0	ENST00000357387.3:c.1228G>C	p.Glu410Gln	p.E410Q	ENST00000357387	NM_152756.3	410	Gaa/Caa	15/38	1	2	FACETS	0.501	0.438	0.568	0.501	0.438	0.568	SUBCLONAL	1	TRUE	1	0.974845119006813	2		305	262	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180964	32180964	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	60	539	0	ENST00000375023.3:c.2386G>T	p.Gly796Cys	p.G796C	ENST00000375023	NM_004557.3	796	Ggc/Tgc	15/30	1	2	FACETS	0.54	0.471	0.613	0.54	0.471	0.613	SUBCLONAL	1	TRUE	1	0.974845119006813	2		539	228	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905397	11905397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	65	327	2	ENST00000396373.4:c.47C>T	p.Ser16Leu	p.S16L	ENST00000396373	NM_001987.4	16	tCa/tTa	2/8	0.974845119006813	1	FACETS	0.285	0.25	0.322	0.285	0.25	0.322	SUBCLONAL	1	TRUE	0	0.974845119006813	1		329	240	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759403	133759403	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1454190487	NA	P-0007129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	13	704	0	ENST00000318560.5:c.1726G>C	p.Glu576Gln	p.E576Q	ENST00000318560	NM_005157.4	576	Gag/Cag	11/11	1	2	FACETS	0.106	0.075	0.144	0.106	0.075	0.144	SUBCLONAL	1	TRUE	1	0.974845119006813	2		704	251	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952266	17952266	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	19	434	0	ENST00000458235.1:c.1074C>G	p.Phe358Leu	p.F358L	ENST00000458235	NM_000215.3	358	ttC/ttG	8/24	1	2	FACETS	0.136	0.103	0.175	0.136	0.103	0.175	SUBCLONAL	1	TRUE	1	0.974845119006813	2		434	286	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610247	10610247	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	135	595	0	ENST00000171111.5:c.463G>T	p.Val155Phe	p.V155F	ENST00000171111	NM_203500.1	155	Gtc/Ttc	2/6	0.355026387023375	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	FALSE	0	0.372554809883172	1		595	579	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702217	47702217	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs730881777	NA	P-0007131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	122	466	0	ENST00000233146.2:c.1813G>T	p.Val605Phe	p.V605F	ENST00000233146	NM_000251.2	605	Gtt/Ttt	12/16	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	FALSE	1	0.372554809883172	2		466	626	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038124	128038124	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	68	464	0	ENST00000285398.2:c.1426A>C	p.Lys476Gln	p.K476Q	ENST00000285398	NM_000122.1	476	Aaa/Caa	9/15	0.108116280004559	0	FACETS	0.454	0.396	0.518			1	INDETERMINATE	1	FALSE	0	0.372554809883172	0		464	504	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971149	55971149	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs772028072	NA	P-0007131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	73	275	0	ENST00000263923.4:c.1648G>T	p.Gly550Cys	p.G550C	ENST00000263923	NM_002253.2	550	Ggt/Tgt	13/30	0.355026387023375	1	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	FALSE	0	0.372554809883172	1		275	315	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38283700	38283700	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	86	588	0	ENST00000425967.3:c.778A>C	p.Thr260Pro	p.T260P	ENST00000425967	NM_001174067.1	260	Acc/Ccc	7/19	0.355026387023375	1	FACETS	0.639	0.566	0.717	0.639	0.566	0.717	SUBCLONAL	1	FALSE	0	0.372554809883172	1		588	588	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993089	90993089	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	44	195	0	ENST00000265433.3:c.353C>G	p.Ser118Cys	p.S118C	ENST00000265433	NM_002485.4	118	tCt/tGt	4/16	1	2	FACETS	0.671	0.564	0.788	0.671	0.564	0.788	SUBCLONAL	1	FALSE	1	0.372554809883172	2		195	352	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719924	18719924	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	66	472	0	ENST00000266497.5:c.3821A>C	p.His1274Pro	p.H1274P	ENST00000266497		1274	cAc/cCc	27/31	1	2	FACETS	0.651	0.566	0.744	0.651	0.566	0.744	SUBCLONAL	1	FALSE	1	0.372554809883172	2		472	544	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926834	112926834	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	120	534	0	ENST00000351677.2:c.1454A>G	p.Asp485Gly	p.D485G	ENST00000351677	NM_002834.3	485	gAc/gGc	13/16	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.372554809883172	2		534	582	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145667	11145668	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCT	novel	NA	P-0007131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	87	489	0	ENST00000358026.2:c.4031_4034dup	p.Trp1346LeufsTer16	p.W1346Lfs*16	ENST00000358026	NM_001128849.1	1343	-/CCCT	29/36	0.355026387023375	1	FACETS	0.828	0.736	0.925	0.828	0.736	0.925	CLONAL	1	FALSE	0	0.372554809883172	1		489	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578546	7578547	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0007131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	63	357	0	ENST00000269305.4:c.383_384del	p.Pro128ArgfsTer20	p.P128Rfs*20	ENST00000269305	NM_001126112.2	128	cCT/c	5/11	0.33228277704628	1	FACETS	0.688	0.597	0.786	0.688	0.597	0.786	SUBCLONAL	1	FALSE	0	0.372554809883172	1		357	400	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390218	89390222	+	splice_donor_variant,coding_sequence_variant	Splice_Site	ONP	ACCCG	ACCCG	CCCCT	novel	NA	P-0007131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	60	451	0	ENST00000336596.2:c.967_970+1delinsCCCCT		p.X323_splice	ENST00000336596	NM_005233.5	323		4/17	0.33228277704628	1	FACETS	0.484	0.417	0.557	0.484	0.417	0.557	SUBCLONAL	1	FALSE	0	0.372554809883172	1		451	541	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0007278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	93	282	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.167815270381831	3	FACETS	0.833	0.741	0.932	0.833	0.741	0.932	CLONAL	2	TRUE	1	0.167815270381831	3		282	721	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846307	156846307	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs762542314	NA	P-0007278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	61	405	1	ENST00000524377.1:c.1748G>T	p.Arg583Leu	p.R583L	ENST00000524377	NM_002529.3	583	cGc/cTc	14/17	0.139681574511628	4	FACETS	0.803	0.691	0.927	0.402	0.345	0.464	CLONAL	1	TRUE	2	0.167815270381831	4		406	1057	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172127	32172127	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	76	392	0	ENST00000375023.3:c.2905C>A	p.Leu969Ile	p.L969I	ENST00000375023	NM_004557.3	969	Ctc/Atc	19/30	0.167815270381831	3	FACETS	1	0.9	1	0.516	0.451	0.586	CLONAL	1	TRUE	1	0.167815270381831	3		392	951	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224493	108224493	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs748192003	NA	P-0007278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	32	311	0	ENST00000278616.4:c.8672G>A	p.Gly2891Asp	p.G2891D	ENST00000278616	NM_000051.3	2891	gGt/gAt	60/63	1	2	FACETS	0.713	0.577	0.866	0.713	0.577	0.866	SUBCLONAL	1	TRUE	1	0.167815270381831	2		311	535	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220449	1220449	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs886037859	NA	P-0007278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	187	446	0	ENST00000326873.7:c.542A>G	p.Asn181Ser	p.N181S	ENST00000326873	NM_000455.4	181	aAc/aGc	4/10	0.167815270381831	2	FACETS	0.945	0.875	1	1	0.989	1	CLONAL	3	TRUE	0	0.167815270381831	2		446	786	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655437	45655437	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	83	188	0	ENST00000407780.3:c.415A>T	p.Ser139Cys	p.S139C	ENST00000407780	NM_001283052.1	139	Agc/Tgc	4/7	1	2	FACETS	1	0.929	1	1	0.985	1	CLONAL	2	TRUE	1	0.167815270381831	2		188	464	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235833	108235833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1565607453	NA	P-0007278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	38	400	1	ENST00000278616.4:c.8875del	p.Asp2959ThrfsTer4	p.D2959Tfs*4	ENST00000278616	NM_000051.3	2959	Gac/ac	62/63	1	2	FACETS	0.744	0.613	0.89	0.744	0.613	0.89	SUBCLONAL	1	TRUE	1	0.167815270381831	2		401	609	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197275	26197276	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1837	134	951	0	ENST00000356476.2:c.203dup	p.Gln69ProfsTer6	p.Q69Pfs*6	ENST00000356476		68	ttc/ttTc	1/1	0.167815270381831	3	FACETS	0.878	0.794	0.968	0.439	0.397	0.484	CLONAL	1	TRUE	1	0.167815270381831	3		951	1971	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765474	41765474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763936923	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	352	470	2	ENST00000301178.4:c.2350C>T	p.Arg784Trp	p.R784W	ENST00000301178	NM_021913.4	784	Cgg/Tgg	20/20	1	2	FACETS	1	0.982	1	1	0.996	1	CLONAL	2	TRUE	1	0.314756906203688	2		472	1041	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	27	223	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	0.712	0.569	0.874	0.712	0.569	0.874	SUBCLONAL	1	TRUE	1	0.314756906203688	2		223	241	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	61	299	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.314756906203688	2		299	349	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	417	581	1	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	1	2	FACETS	1	0.989	1	1	0.997	1	CLONAL	2	TRUE	1	0.314756906203688	2		582	1191	SUCCESS
BLM	641	MSKCC	GRCh37	15	91290665	91290665	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148545569	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	177	482	2	ENST00000355112.3:c.43C>T	p.Arg15Cys	p.R15C	ENST00000355112	NM_000057.2	15	Cgt/Tgt	2/22	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.314756906203688	2		484	860	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041046	112041046	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762290632	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	653	797	4	ENST00000368678.4:c.209C>T	p.Ser70Leu	p.S70L	ENST00000368678		70	tCg/tTg	3/13	0.111365834396786	0	FACETS	0.77	0.741	0.799			1	INDETERMINATE	2	TRUE	0	0.314756906203688	0		801	1846	SUCCESS
APC	324	MSKCC	GRCh37	5	112177049	112177049	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	294	632	0	ENST00000257430.4:c.5758C>T	p.Arg1920Ter	p.R1920*	ENST00000257430	NM_000038.5	1920	Cga/Tga	16/16	1	2	FACETS	1	0.983	1	1	0.996	1	CLONAL	2	TRUE	1	0.314756906203688	2		632	848	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033396	48033396	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	105	441	2	ENST00000234420.5:c.3700G>T	p.Glu1234Ter	p.E1234*	ENST00000234420	NM_000179.2	1234	Gaa/Taa	8/10	1	2	FACETS	0.929	0.833	1	0.929	0.833	1	CLONAL	1	TRUE	1	0.314756906203688	2		443	718	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857818	9857818	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1191	315	767	0	ENST00000330684.3:c.3583G>T	p.Asp1195Tyr	p.D1195Y	ENST00000330684	NM_001134407.1	1195	Gac/Tac	13/13	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.314756906203688	2		767	1506	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941837	44941837	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	187	295	0	ENST00000377967.4:c.3161G>T	p.Arg1054Ile	p.R1054I	ENST00000377967	NM_021140.2	1054	aGa/aTa	21/29	1	1	FACETS	0.837	0.778	0.898	1	0.992	1	CLONAL	2	TRUE	0	0.314756906203688	1		295	598	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649000	86649000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755634472	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	167	365	0	ENST00000274376.6:c.1280G>A	p.Arg427Gln	p.R427Q	ENST00000274376	NM_002890.2	427	cGa/cAa	9/25	1	2	FACETS	1	0.964	1	1	0.993	1	CLONAL	2	TRUE	1	0.314756906203688	2		365	498	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9770536	9770536	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	258	613	0	ENST00000377346.4:c.23C>A	p.Pro8His	p.P8H	ENST00000377346	NM_005026.3	8	cCc/cAc	3/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.314756906203688	2		613	1409	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182145	11182145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1238905384	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	272	607	0	ENST00000361445.4:c.6701C>T	p.Ser2234Leu	p.S2234L	ENST00000361445	NM_004958.3	2234	tCg/tTg	48/58	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.314756906203688	2		607	1462	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298039	11298039	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779998245	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	199	611	2	ENST00000361445.4:c.2069C>T	p.Ala690Val	p.A690V	ENST00000361445	NM_004958.3	690	gCg/gTg	13/58	1	2	FACETS	0.951	0.879	1	0.951	0.879	1	CLONAL	1	TRUE	1	0.314756906203688	2		613	1330	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255931	16255931	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	118	273	0	ENST00000375759.3:c.3196T>G	p.Cys1066Gly	p.C1066G	ENST00000375759	NM_015001.2	1066	Tgt/Ggt	11/15	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.314756906203688	2		273	673	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258305	16258305	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	250	545	1	ENST00000375759.3:c.5570C>A	p.Ser1857Tyr	p.S1857Y	ENST00000375759	NM_015001.2	1857	tCt/tAt	11/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.314756906203688	2		546	1322	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259967	16259967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	144	553	1	ENST00000375759.3:c.7232C>T	p.Ser2411Leu	p.S2411L	ENST00000375759	NM_015001.2	2411	tCg/tTg	11/15	1	2	FACETS	0.695	0.632	0.762	0.695	0.632	0.762	SUBCLONAL	1	TRUE	1	0.314756906203688	2		554	1316	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935318	36935318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781634406	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1401	312	730	0	ENST00000361632.4:c.1409C>T	p.Ala470Val	p.A470V	ENST00000361632		470	gCg/gTg	10/16	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.314756906203688	2		730	1713	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521488	46521488	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	356	586	0	ENST00000262741.5:c.920A>C	p.Lys307Thr	p.K307T	ENST00000262741	NM_003629.3	307	aAg/aCg	7/10	1	2	FACETS	0.989	0.937	1	1	0.996	1	CLONAL	2	TRUE	1	0.314756906203688	2		586	1144	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531790	46531790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	252	575	0	ENST00000262741.5:c.557C>T	p.Ser186Phe	p.S186F	ENST00000262741	NM_003629.3	186	tCt/tTt	5/10	1	2	FACETS	0.934	0.876	0.994	1	0.995	1	CLONAL	2	TRUE	1	0.314756906203688	2		575	857	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46733272	46733272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs797044888	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	159	477	1	ENST00000371975.4:c.1033G>A	p.Gly345Ser	p.G345S	ENST00000371975	NM_003579.3	345	Ggc/Agc	9/18	1	2	FACETS	0.999	0.915	1	0.999	0.915	1	CLONAL	1	TRUE	1	0.314756906203688	2		478	1011	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46738358	46738358	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	139	461	0	ENST00000371975.4:c.1259A>G	p.Gln420Arg	p.Q420R	ENST00000371975	NM_003579.3	420	cAg/cGg	12/18	1	2	FACETS	0.926	0.842	1	0.926	0.842	1	CLONAL	1	TRUE	1	0.314756906203688	2		461	954	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301893	65301893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	158	312	0	ENST00000342505.4:c.3146C>T	p.Ala1049Val	p.A1049V	ENST00000342505	NM_002227.2	1049	gCt/gTt	23/25	1	2	FACETS	1	0.96	1	1	0.993	1	CLONAL	2	TRUE	1	0.314756906203688	2		312	474	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65304233	65304233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1163790865	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	125	362	2	ENST00000342505.4:c.2882C>T	p.Ser961Leu	p.S961L	ENST00000342505	NM_002227.2	961	tCg/tTg	21/25	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.314756906203688	2		364	784	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65312410	65312410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	264	375	0	ENST00000342505.4:c.1909G>A	p.Glu637Lys	p.E637K	ENST00000342505	NM_002227.2	637	Gag/Aag	14/25	1	2	FACETS	0.997	0.938	1	1	0.995	1	CLONAL	2	TRUE	1	0.314756906203688	2		375	841	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321351	65321351	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	314	421	0	ENST00000342505.4:c.1489A>C	p.Asn497His	p.N497H	ENST00000342505	NM_002227.2	497	Aac/Cac	11/25	1	2	FACETS	1	0.984	1	1	0.996	1	CLONAL	2	TRUE	1	0.314756906203688	2		421	905	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344760	65344760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768706312	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	218	580	2	ENST00000342505.4:c.277C>T	p.Arg93Cys	p.R93C	ENST00000342505	NM_002227.2	93	Cgc/Tgc	4/25	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.314756906203688	2		582	1240	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430001	78430001	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	69	281	0	ENST00000370768.2:c.878G>T	p.Arg293Ile	p.R293I	ENST00000370768	NM_003902.3	293	aGa/aTa	11/20	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.314756906203688	2		281	430	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733470	85733470	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	477	938	0	ENST00000370580.1:c.542G>T	p.Arg181Ile	p.R181I	ENST00000370580	NM_003921.4	181	aGa/aTa	3/3	1	2	FACETS	1	0.991	1	1	0.997	1	CLONAL	2	TRUE	1	0.314756906203688	2		938	1336	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459188	120459188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772005110	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	139	428	0	ENST00000256646.2:c.6157C>T	p.Arg2053Cys	p.R2053C	ENST00000256646	NM_024408.3	2053	Cgc/Tgc	34/34	1	2	FACETS	0.904	0.822	0.99	0.904	0.822	0.99	CLONAL	1	TRUE	1	0.314756906203688	2		428	977	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843535	156843535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369367198	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	441	594	0	ENST00000524377.1:c.961G>A	p.Val321Met	p.V321M	ENST00000524377	NM_002529.3	321	Gtg/Atg	8/17	1	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	1	0.314756906203688	2		594	1204	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204495492	204495492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	113	361	0	ENST00000367182.3:c.83G>A	p.Arg28Gln	p.R28Q	ENST00000367182	NM_001278516.1	28	cGa/cAa	3/11	1	2	FACETS	0.859	0.772	0.95	0.859	0.772	0.95	CLONAL	1	TRUE	1	0.314756906203688	2		361	836	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653437	206653437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782340929	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	129	337	0	ENST00000367120.3:c.1321C>T	p.Arg441Trp	p.R441W	ENST00000367120	NM_014002.3	441	Cgg/Tgg	12/22	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.314756906203688	2		337	744	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206664188	206664188	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	123	285	0	ENST00000367120.3:c.1730A>G	p.Asp577Gly	p.D577G	ENST00000367120	NM_014002.3	577	gAt/gGt	17/22	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.314756906203688	2		285	717	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253371	226253371	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	194	265	0	ENST00000366813.1:c.143C>T	p.Ala48Val	p.A48V	ENST00000366813		48	gCg/gTg	2/3	1	2	FACETS	1	0.95	1	1	0.994	1	CLONAL	2	TRUE	1	0.314756906203688	2		265	601	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253418	226253418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	34	65	0	ENST00000366813.1:c.190C>T	p.Arg64Cys	p.R64C	ENST00000366813		64	Cgc/Tgc	2/3	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.314756906203688	2		65	166	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800973	243800973	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	175	406	0	ENST00000263826.5:c.501G>T	p.Glu167Asp	p.E167D	ENST00000263826	NM_005465.4	167	gaG/gaT	5/13	1	2	FACETS	1	0.93	1	1	0.993	1	CLONAL	2	TRUE	1	0.314756906203688	2		406	554	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243859016	243859016	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs397514606	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	62	244	0	ENST00000263826.5:c.49G>A	p.Glu17Lys	p.E17K	ENST00000263826	NM_005465.4	17	Gaa/Aaa	2/13	1	2	FACETS	0.916	0.803	1	1	0.979	1	CLONAL	2	TRUE	1	0.314756906203688	2		244	215	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086132	16086132	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	142	444	0	ENST00000281043.3:c.1308G>T	p.Glu436Asp	p.E436D	ENST00000281043	NM_005378.4	436	gaG/gaT	3/3	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.314756906203688	2		444	858	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519902	29519902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200364883	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	373	467	0	ENST00000389048.3:c.1669C>T	p.Arg557Cys	p.R557C	ENST00000389048	NM_004304.4	557	Cgt/Tgt	9/29	1	2	FACETS	1	0.991	1	1	0.997	1	CLONAL	2	TRUE	1	0.314756906203688	2		467	1002	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705527	47705527	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	199	490	0	ENST00000233146.2:c.2327C>A	p.Ala776Asp	p.A776D	ENST00000233146	NM_000251.2	776	gCt/gAt	14/16	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.314756906203688	2		490	1008	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027317	48027317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749746725	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	108	466	0	ENST00000234420.5:c.2195G>A	p.Arg732Gln	p.R732Q	ENST00000234420	NM_000179.2	732	cGa/cAa	4/10	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.314756906203688	2		466	632	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028049	48028049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63751113	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	110	462	1	ENST00000234420.5:c.2927G>A	p.Arg976His	p.R976H	ENST00000234420	NM_000179.2	976	cGt/cAt	4/10	1	2	FACETS	0.945	0.849	1	0.945	0.849	1	CLONAL	1	TRUE	1	0.314756906203688	2		463	740	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033343	48033343	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	206	314	0	ENST00000234420.5:c.3647G>A	p.Gly1216Glu	p.G1216E	ENST00000234420	NM_000179.2	1216	gGa/gAa	8/10	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.314756906203688	2		314	565	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61720070	61720070	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	174	293	0	ENST00000401558.2:c.1364A>C	p.Lys455Thr	p.K455T	ENST00000401558	NM_003400.3	455	aAg/aCg	13/25	1	2	FACETS	1	0.965	1	1	0.993	1	CLONAL	2	TRUE	1	0.314756906203688	2		293	518	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726941	61726941	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	132	480	0	ENST00000401558.2:c.497A>C	p.Asn166Thr	p.N166T	ENST00000401558	NM_003400.3	166	aAt/aCt	7/25	1	2	FACETS	0.947	0.859	1	0.947	0.859	1	CLONAL	1	TRUE	1	0.314756906203688	2		480	886	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190708786	190708786	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1223013210	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	117	467	0	ENST00000441310.2:c.679T>C	p.Tyr227His	p.Y227H	ENST00000441310	NM_000534.4	227	Tac/Cac	6/13	1	2	FACETS	0.951	0.857	1	0.951	0.857	1	CLONAL	1	TRUE	1	0.314756906203688	2		467	782	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732526	190732526	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	52	318	0	ENST00000441310.2:c.2344C>A	p.Leu782Ile	p.L782I	ENST00000441310	NM_000534.4	782	Ctt/Att	11/13	1	2	FACETS	0.804	0.686	0.932	0.804	0.686	0.932	CLONAL	1	TRUE	1	0.314756906203688	2		318	411	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273123	198273123	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	353	629	2	ENST00000335508.6:c.1087C>T	p.Pro363Ser	p.P363S	ENST00000335508	NM_012433.2	363	Cca/Tca	8/25	1	2	FACETS	1	0.963	1	1	0.996	1	CLONAL	2	TRUE	1	0.314756906203688	2		631	1100	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131483	202131483	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	237	380	0	ENST00000358485.4:c.451A>C	p.Thr151Pro	p.T151P	ENST00000358485	NM_001080125.1	151	Aca/Cca	2/9	1	2	FACETS	1	0.944	1	1	0.995	1	CLONAL	2	TRUE	1	0.314756906203688	2		380	747	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285315	212285315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	139	384	1	ENST00000342788.4:c.2986C>T	p.Pro996Ser	p.P996S	ENST00000342788	NM_005235.2	996	Ccc/Tcc	25/28	1	2	FACETS	0.946	0.867	1	1	0.991	1	CLONAL	2	TRUE	1	0.314756906203688	2		385	467	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543826	212543826	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775988789	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	150	388	0	ENST00000342788.4:c.1573C>T	p.Arg525Cys	p.R525C	ENST00000342788	NM_005235.2	525	Cgc/Tgc	13/28	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.314756906203688	2		388	879	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578349	212578349	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	72	302	0	ENST00000342788.4:c.908C>A	p.Ser303Tyr	p.S303Y	ENST00000342788	NM_005235.2	303	tCt/tAt	8/28	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.314756906203688	2		302	456	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812205	212812205	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	66	364	0	ENST00000342788.4:c.371G>T	p.Arg124Ile	p.R124I	ENST00000342788	NM_005235.2	124	aGa/aTa	3/28	1	2	FACETS	0.769	0.669	0.879	0.769	0.669	0.879	SUBCLONAL	1	TRUE	1	0.314756906203688	2		364	545	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370695	225370695	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	106	310	0	ENST00000264414.4:c.1184A>C	p.Lys395Thr	p.K395T	ENST00000264414	NM_003590.4	395	aAg/aCg	8/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.314756906203688	2		310	551	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378246	225378246	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	172	324	0	ENST00000264414.4:c.649T>G	p.Phe217Val	p.F217V	ENST00000264414	NM_003590.4	217	Ttt/Gtt	5/16	1	2	FACETS	1	0.971	1	1	0.993	1	CLONAL	2	TRUE	1	0.314756906203688	2		324	500	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378348	225378348	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	79	324	0	ENST00000264414.4:c.547A>C	p.Ile183Leu	p.I183L	ENST00000264414	NM_003590.4	183	Ata/Cta	5/16	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.314756906203688	2		324	475	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225400354	225400354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764765022	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	94	323	1	ENST00000264414.4:c.269G>A	p.Arg90Gln	p.R90Q	ENST00000264414	NM_003590.4	90	cGa/cAa	3/16	1	2	FACETS	0.992	0.884	1	0.992	0.884	1	CLONAL	1	TRUE	1	0.314756906203688	2		324	602	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715646	30715646	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	252	448	0	ENST00000295754.5:c.1304A>T	p.Asn435Ile	p.N435I	ENST00000295754	NM_003242.5	435	aAt/aTt	5/7	1	2	FACETS	1	0.948	1	1	0.995	1	CLONAL	2	TRUE	1	0.314756906203688	2		448	792	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37045898	37045898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	296	497	2	ENST00000231790.2:c.313G>A	p.Ala105Thr	p.A105T	ENST00000231790	NM_000249.3	105	Gcc/Acc	4/19	1	2	FACETS	1	0.975	1	1	0.996	1	CLONAL	2	TRUE	1	0.314756906203688	2		499	891	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37058999	37058999	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs63751194	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	100	335	2	ENST00000231790.2:c.793C>T	p.Arg265Cys	p.R265C	ENST00000231790	NM_000249.3	265	Cgt/Tgt	10/19	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.314756906203688	2		337	626	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268766	41268766	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	120	490	0	ENST00000349496.5:c.1004A>C	p.Lys335Thr	p.K335T	ENST00000349496	NM_001904.3	335	aAa/aCa	7/15	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.314756906203688	2		490	745	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275191	41275191	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770598744	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	127	383	2	ENST00000349496.5:c.1357C>T	p.Arg453Trp	p.R453W	ENST00000349496	NM_001904.3	453	Cgg/Tgg	9/15	1	2	FACETS	0.943	0.854	1	0.943	0.854	1	CLONAL	1	TRUE	1	0.314756906203688	2		385	856	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058676	47058676	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	147	400	0	ENST00000409792.3:c.7602G>T	p.Glu2534Asp	p.E2534D	ENST00000409792	NM_014159.6	2534	gaG/gaT	21/21	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.314756906203688	2		400	899	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103824	47103824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	140	451	0	ENST00000409792.3:c.6122G>A	p.Gly2041Glu	p.G2041E	ENST00000409792	NM_014159.6	2041	gGa/gAa	14/21	1	2	FACETS	0.991	0.902	1	0.991	0.902	1	CLONAL	1	TRUE	1	0.314756906203688	2		451	898	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47108598	47108598	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	177	347	0	ENST00000409792.3:c.6071G>A	p.Arg2024Gln	p.R2024Q	ENST00000409792	NM_014159.6	2024	cGa/cAa	13/21	1	2	FACETS	1	0.968	1	1	0.993	1	CLONAL	2	TRUE	1	0.314756906203688	2		347	524	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158173	47158173	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	164	447	0	ENST00000409792.3:c.4526G>T	p.Arg1509Ile	p.R1509I	ENST00000409792	NM_014159.6	1509	aGa/aTa	4/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.314756906203688	2		447	944	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158224	47158224	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	187	286	0	ENST00000409792.3:c.4475G>A	p.Arg1492Gln	p.R1492Q	ENST00000409792	NM_014159.6	1492	cGa/cAa	4/21	1	2	FACETS	1	0.975	1	1	0.994	1	CLONAL	2	TRUE	1	0.314756906203688	2		286	539	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162161	47162161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147170912	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	104	326	1	ENST00000409792.3:c.3965G>A	p.Arg1322Gln	p.R1322Q	ENST00000409792	NM_014159.6	1322	cGa/cAa	3/21	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.314756906203688	2		327	609	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397670	49397670	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	337	447	0	ENST00000418115.1:c.554A>C	p.Lys185Thr	p.K185T	ENST00000418115	NM_001664.2	185	aAg/aCg	5/5	1	2	FACETS	1	0.973	1	1	0.996	1	CLONAL	2	TRUE	1	0.314756906203688	2		447	1028	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405936	49405936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	546	698	2	ENST00000418115.1:c.202C>T	p.Arg68Cys	p.R68C	ENST00000418115	NM_001664.2	68	Cgc/Tgc	3/5	1	2	FACETS	1	0.991	1	1	0.998	1	CLONAL	2	TRUE	1	0.314756906203688	2		700	1574	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49724717	49724717	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	197	529	0	ENST00000449682.2:c.472T>C	p.Tyr158His	p.Y158H	ENST00000449682	NM_020998.3	158	Tac/Cac	5/18	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.314756906203688	2		529	1161	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932708	49932708	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1646	341	828	0	ENST00000296474.3:c.3163G>T	p.Glu1055Ter	p.E1055*	ENST00000296474	NM_002447.2	1055	Gag/Tag	14/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.314756906203688	2		828	1987	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935523	49935523	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1334	713	910	2	ENST00000296474.3:c.1841G>T	p.Ser614Ile	p.S614I	ENST00000296474	NM_002447.2	614	aGt/aTt	5/20	1	2	FACETS	1	0.993	1	1	0.998	1	CLONAL	2	TRUE	1	0.314756906203688	2		912	2047	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940951	49940951	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1255	295	701	0	ENST00000296474.3:c.92G>A	p.Arg31His	p.R31H	ENST00000296474	NM_002447.2	31	cGc/cAc	1/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.314756906203688	2		701	1550	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643768	52643768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	69	418	0	ENST00000394830.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000394830	NM_018313.4	710	Cga/Tga	17/30	1	2	FACETS	0.771	0.672	0.877	0.771	0.672	0.877	SUBCLONAL	1	TRUE	1	0.314756906203688	2		418	569	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428538	72428538	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	67	260	0	ENST00000477973.2:c.466G>A	p.Ala156Thr	p.A156T	ENST00000477973	NM_012234.5	156	Gca/Aca	2/4	1	2	FACETS	0.963	0.84	1	0.963	0.84	1	CLONAL	1	TRUE	1	0.314756906203688	2		260	442	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72891539	72891539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755870786	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	97	398	0	ENST00000325599.8:c.223C>T	p.Arg75Cys	p.R75C	ENST00000325599	NM_018130.2	75	Cgc/Tgc	3/11	1	2	FACETS	0.872	0.778	0.972	0.872	0.778	0.972	CLONAL	1	TRUE	1	0.314756906203688	2		398	707	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72897461	72897461	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	191	451	0	ENST00000325599.8:c.31G>T	p.Asp11Tyr	p.D11Y	ENST00000325599	NM_018130.2	11	Gat/Tat	1/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.314756906203688	2		451	1067	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391075	89391075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs995238704	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	380	496	0	ENST00000336596.2:c.1141C>T	p.Arg381Cys	p.R381C	ENST00000336596	NM_005233.5	381	Cgc/Tgc	5/17	1	2	FACETS	1	0.989	1	1	0.997	1	CLONAL	2	TRUE	1	0.314756906203688	2		496	1072	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480466	89480466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446890859	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	228	454	0	ENST00000336596.2:c.2303C>T	p.Ser768Leu	p.S768L	ENST00000336596	NM_005233.5	768	tCg/tTg	13/17	1	2	FACETS	0.954	0.892	1	1	0.994	1	CLONAL	2	TRUE	1	0.314756906203688	2		454	759	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498447	89498447	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	46	567	2	ENST00000336596.2:c.2419G>T	p.Val807Leu	p.V807L	ENST00000336596	NM_005233.5	807	Gta/Tta	14/17	1	2	FACETS	0.372	0.312	0.438	0.372	0.312	0.438	SUBCLONAL	1	TRUE	1	0.314756906203688	2		569	786	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499418	89499418	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	303	466	0	ENST00000336596.2:c.2588A>C	p.Lys863Thr	p.K863T	ENST00000336596	NM_005233.5	863	aAa/aCa	15/17	1	2	FACETS	0.976	0.921	1	1	0.996	1	CLONAL	2	TRUE	1	0.314756906203688	2		466	986	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119642254	119642254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757429682	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	81	370	0	ENST00000316626.5:c.443G>A	p.Arg148Gln	p.R148Q	ENST00000316626		148	cGa/cAa	4/12	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.314756906203688	2		370	513	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670847	134670847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	85	241	0	ENST00000398015.3:c.758G>A	p.Cys253Tyr	p.C253Y	ENST00000398015	NM_004441.4	253	tGc/tAc	3/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.314756906203688	2		241	458	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670875	134670875	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	74	199	1	ENST00000398015.3:c.786G>T	p.Glu262Asp	p.E262D	ENST00000398015	NM_004441.4	262	gaG/gaT	3/16	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.314756906203688	2		200	416	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851700	134851700	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	136	445	0	ENST00000398015.3:c.1106G>T	p.Ser369Ile	p.S369I	ENST00000398015	NM_004441.4	369	aGc/aTc	5/16	1	2	FACETS	0.983	0.894	1	0.983	0.894	1	CLONAL	1	TRUE	1	0.314756906203688	2		445	879	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851857	134851857	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	275	433	0	ENST00000398015.3:c.1263G>T	p.Gln421His	p.Q421H	ENST00000398015	NM_004441.4	421	caG/caT	5/16	1	2	FACETS	0.996	0.938	1	1	0.995	1	CLONAL	2	TRUE	1	0.314756906203688	2		433	877	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911602	134911602	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1463657910	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	166	433	0	ENST00000398015.3:c.2067G>T	p.Lys689Asn	p.K689N	ENST00000398015	NM_004441.4	689	aaG/aaT	11/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.314756906203688	2		433	979	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138376545	138376545	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	105	450	1	ENST00000289153.2:c.2929G>T	p.Glu977Ter	p.E977*	ENST00000289153	NM_006219.2	977	Gaa/Taa	20/22	1	2	FACETS	0.973	0.872	1	0.973	0.872	1	CLONAL	1	TRUE	1	0.314756906203688	2		451	686	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453562	138453562	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	115	388	1	ENST00000289153.2:c.886G>T	p.Glu296Ter	p.E296*	ENST00000289153	NM_006219.2	296	Gaa/Taa	5/22	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.314756906203688	2		389	715	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461575	138461575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1225812682	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	175	379	1	ENST00000289153.2:c.446G>A	p.Arg149Gln	p.R149Q	ENST00000289153	NM_006219.2	149	cGa/cAa	3/22	1	2	FACETS	1	0.955	1	1	0.993	1	CLONAL	2	TRUE	1	0.314756906203688	2		380	534	SUCCESS
ATR	545	MSKCC	GRCh37	3	142168368	142168368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1034620994	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	90	368	0	ENST00000350721.4:c.7838C>T	p.Pro2613Leu	p.P2613L	ENST00000350721	NM_001184.3	2613	cCg/cTg	47/47	1	2	FACETS	0.971	0.863	1	0.971	0.863	1	CLONAL	1	TRUE	1	0.314756906203688	2		368	589	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268985	142268985	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs911751877	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	236	521	0	ENST00000350721.4:c.2965C>T	p.Arg989Cys	p.R989C	ENST00000350721	NM_001184.3	989	Cgt/Tgt	14/47	1	2	FACETS	0.958	0.897	1	1	0.994	1	CLONAL	2	TRUE	1	0.314756906203688	2		521	783	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272716	142272716	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	132	522	0	ENST00000350721.4:c.2483T>A	p.Ile828Asn	p.I828N	ENST00000350721	NM_001184.3	828	aTc/aAc	11/47	1	2	FACETS	0.946	0.858	1	0.946	0.858	1	CLONAL	1	TRUE	1	0.314756906203688	2		522	887	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272783	142272783	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	217	364	0	ENST00000350721.4:c.2416C>A	p.Leu806Ile	p.L806I	ENST00000350721	NM_001184.3	806	Ctt/Att	11/47	1	2	FACETS	1	0.982	1	1	0.995	1	CLONAL	2	TRUE	1	0.314756906203688	2		364	611	SUCCESS
ATR	545	MSKCC	GRCh37	3	142286947	142286947	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	144	435	0	ENST00000350721.4:c.109C>A	p.Leu37Met	p.L37M	ENST00000350721	NM_001184.3	37	Ctg/Atg	2/47	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.314756906203688	2		435	712	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937461	178937461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776503460	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	48	250	1	ENST00000263967.3:c.1849C>T	p.Arg617Trp	p.R617W	ENST00000263967	NM_006218.2	617	Cgg/Tgg	12/21	1	2	FACETS	0.908	0.771	1	0.908	0.771	1	CLONAL	1	TRUE	1	0.314756906203688	2		251	336	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952110	178952110	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	93	374	0	ENST00000263967.3:c.3165G>T	p.Met1055Ile	p.M1055I	ENST00000263967	NM_006218.2	1055	atG/atT	21/21	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.314756906203688	2		374	537	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430746	181430746	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	200	514	0	ENST00000325404.1:c.598T>C	p.Tyr200His	p.Y200H	ENST00000325404	NM_003106.3	200	Tac/Cac	1/1	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.314756906203688	2		514	1145	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167740	185167740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	180	644	1	ENST00000265026.3:c.1063G>A	p.Asp355Asn	p.D355N	ENST00000265026	NM_004721.4	355	Gat/Aat	6/14	1	2	FACETS	0.959	0.882	1	0.959	0.882	1	CLONAL	1	TRUE	1	0.314756906203688	2		645	1193	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451337	187451337	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	146	400	0	ENST00000232014.4:c.145G>A	p.Val49Ile	p.V49I	ENST00000232014	NM_001130845.1	49	Gtc/Atc	3/10	1	2	FACETS	0.992	0.905	1	0.992	0.905	1	CLONAL	1	TRUE	1	0.314756906203688	2		400	935	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526268	189526268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	325	404	1	ENST00000264731.3:c.532G>A	p.Asp178Asn	p.D178N	ENST00000264731	NM_003722.4	178	Gac/Aac	4/14	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.314756906203688	2		405	882	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584496	189584496	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	93	536	0	ENST00000264731.3:c.792G>T	p.Leu264Phe	p.L264F	ENST00000264731	NM_003722.4	264	ttG/ttT	6/14	1	2	FACETS	0.878	0.781	0.981	0.878	0.781	0.981	CLONAL	1	TRUE	1	0.314756906203688	2		536	673	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612078	189612078	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs957895088	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	313	460	0	ENST00000264731.3:c.1830C>A	p.Phe610Leu	p.F610L	ENST00000264731	NM_003722.4	610	ttC/ttA	14/14	1	2	FACETS	1	0.964	1	1	0.996	1	CLONAL	2	TRUE	1	0.314756906203688	2		460	969	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161380	55161380	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376544204	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	196	590	0	ENST00000257290.5:c.3211G>A	p.Asp1071Asn	p.D1071N	ENST00000257290	NM_006206.4	1071	Gac/Aac	23/23	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.314756906203688	2		590	1076	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589773	55589773	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752354428	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	328	546	1	ENST00000288135.5:c.1255G>A	p.Asp419Asn	p.D419N	ENST00000288135	NM_000222.2	419	Gac/Aac	8/21	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.314756906203688	2		547	900	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598084	55598084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746503007	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	384	775	2	ENST00000288135.5:c.2281G>A	p.Glu761Lys	p.E761K	ENST00000288135	NM_000222.2	761	Gag/Aag	16/21	1	2	FACETS	1	0.966	1	1	0.997	1	CLONAL	2	TRUE	1	0.314756906203688	2		777	1196	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599334	55599334	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	85	472	0	ENST00000288135.5:c.2460T>G	p.Asp820Glu	p.D820E	ENST00000288135	NM_000222.2	820	gaT/gaG	17/21	1	2	FACETS	0.953	0.844	1	0.953	0.844	1	CLONAL	1	TRUE	1	0.314756906203688	2		472	567	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968607	55968607	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	119	482	0	ENST00000263923.4:c.2056G>T	p.Val686Phe	p.V686F	ENST00000263923	NM_002253.2	686	Gtc/Ttc	14/30	1	2	FACETS	0.806	0.727	0.89	0.806	0.727	0.89	CLONAL	1	TRUE	1	0.314756906203688	2		482	938	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972861	55972861	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	36	336	0	ENST00000263923.4:c.1529A>C	p.Lys510Thr	p.K510T	ENST00000263923	NM_002253.2	510	aAa/aCa	11/30	1	2	FACETS	0.479	0.393	0.575	0.479	0.393	0.575	SUBCLONAL	1	TRUE	1	0.314756906203688	2		336	478	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217207	66217207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	105	490	0	ENST00000273854.3:c.2408C>T	p.Ala803Val	p.A803V	ENST00000273854	NM_004439.5	803	gCc/gTc	14/18	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.314756906203688	2		490	650	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84388627	84388627	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	102	467	0	ENST00000321945.7:c.661T>G	p.Ser221Ala	p.S221A	ENST00000321945	NM_139076.2	221	Tca/Gca	7/9	1	2	FACETS	0.969	0.867	1	0.969	0.867	1	CLONAL	1	TRUE	1	0.314756906203688	2		467	669	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156319	106156319	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	114	280	0	ENST00000380013.4:c.1220C>A	p.Ser407Tyr	p.S407Y	ENST00000380013	NM_001127208.2	407	tCt/tAt	3/11	0.314756906203688	3	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.314756906203688	3		280	682	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143043354	143043354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	80	388	0	ENST00000262992.4:c.2062G>A	p.Asp688Asn	p.D688N	ENST00000262992	NM_001101669.1	688	Gat/Aat	19/24	1	2	FACETS	0.981	0.866	1	0.981	0.866	1	CLONAL	1	TRUE	1	0.314756906203688	2		388	518	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130163	143130163	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	65	344	2	ENST00000262992.4:c.853G>T	p.Glu285Ter	p.E285*	ENST00000262992	NM_001101669.1	285	Gaa/Taa	11/24	1	2	FACETS	0.823	0.715	0.94	0.823	0.715	0.94	CLONAL	1	TRUE	1	0.314756906203688	2		346	502	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159104	143159104	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1405228238	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	208	521	0	ENST00000262992.4:c.749G>A	p.Arg250Gln	p.R250Q	ENST00000262992	NM_001101669.1	250	cGa/cAa	10/24	1	2	FACETS	1	0.943	1	1	0.994	1	CLONAL	2	TRUE	1	0.314756906203688	2		521	653	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247367	153247367	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	66	270	0	ENST00000281708.4:c.1435C>T	p.Arg479Ter	p.R479*	ENST00000281708	NM_033632.3	479	Cga/Tga	10/12	1	2	FACETS	0.924	0.804	1	0.924	0.804	1	CLONAL	1	TRUE	1	0.314756906203688	2		270	454	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268137	153268137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752114536	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	151	452	2	ENST00000281708.4:c.671G>A	p.Arg224Gln	p.R224Q	ENST00000281708	NM_033632.3	224	cGa/cAa	4/12	1	2	FACETS	0.854	0.78	0.933	0.854	0.78	0.933	CLONAL	1	TRUE	1	0.314756906203688	2		454	1123	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516861	187516861	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763565837	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	182	439	1	ENST00000441802.2:c.13120G>A	p.Glu4374Lys	p.E4374K	ENST00000441802	NM_005245.3	4374	Gaa/Aaa	26/27	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.314756906203688	2		440	942	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518054	187518054	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368645432	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	181	431	2	ENST00000441802.2:c.12640G>A	p.Ala4214Thr	p.A4214T	ENST00000441802	NM_005245.3	4214	Gct/Act	25/27	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.314756906203688	2		433	961	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518309	187518309	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs191917852	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	57	104	0	ENST00000441802.2:c.12385G>A	p.Asp4129Asn	p.D4129N	ENST00000441802	NM_005245.3	4129	Gac/Aac	25/27	1	2	FACETS	0.953	0.832	1	1	0.978	1	CLONAL	2	TRUE	1	0.314756906203688	2		104	190	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540874	187540874	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs562612394	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	289	441	0	ENST00000441802.2:c.6866C>T	p.Ala2289Val	p.A2289V	ENST00000441802	NM_005245.3	2289	gCg/gTg	10/27	1	2	FACETS	1	0.966	1	1	0.996	1	CLONAL	2	TRUE	1	0.314756906203688	2		441	888	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541586	187541586	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	157	400	1	ENST00000441802.2:c.6154G>T	p.Glu2052Ter	p.E2052*	ENST00000441802	NM_005245.3	2052	Gaa/Taa	10/27	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.314756906203688	2		401	837	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542053	187542053	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	180	265	0	ENST00000441802.2:c.5687T>C	p.Val1896Ala	p.V1896A	ENST00000441802	NM_005245.3	1896	gTa/gCa	10/27	1	2	FACETS	1	0.984	1	1	0.994	1	CLONAL	2	TRUE	1	0.314756906203688	2		265	478	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187560904	187560904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758878500	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	201	379	0	ENST00000441802.2:c.3614G>A	p.Arg1205Gln	p.R1205Q	ENST00000441802	NM_005245.3	1205	cGa/cAa	4/27	1	2	FACETS	0.959	0.893	1	1	0.993	1	CLONAL	2	TRUE	1	0.314756906203688	2		379	666	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628419	187628419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs180820128	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	96	310	1	ENST00000441802.2:c.2563G>A	p.Gly855Arg	p.G855R	ENST00000441802	NM_005245.3	855	Gga/Aga	2/27	1	2	FACETS	0.887	0.79	0.989	0.887	0.79	0.989	CLONAL	1	TRUE	1	0.314756906203688	2		311	688	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629328	187629328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772458580	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	379	504	0	ENST00000441802.2:c.1654G>A	p.Glu552Lys	p.E552K	ENST00000441802	NM_005245.3	552	Gaa/Aaa	2/27	1	2	FACETS	1	0.987	1	1	0.997	1	CLONAL	2	TRUE	1	0.314756906203688	2		504	1086	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950648	38950648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776074870	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	279	629	2	ENST00000357387.3:c.3302C>T	p.Ser1101Leu	p.S1101L	ENST00000357387	NM_152756.3	1101	tCg/tTg	31/38	1	2	FACETS	1	0.977	1	1	0.996	1	CLONAL	2	TRUE	1	0.314756906203688	2		631	830	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982108	38982108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778526085	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	68	351	1	ENST00000357387.3:c.614G>A	p.Arg205Gln	p.R205Q	ENST00000357387	NM_152756.3	205	cGa/cAa	8/38	1	2	FACETS	0.931	0.812	1	0.931	0.812	1	CLONAL	1	TRUE	1	0.314756906203688	2		352	464	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177875	56177875	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	114	320	1	ENST00000399503.3:c.2848G>T	p.Glu950Ter	p.E950*	ENST00000399503	NM_005921.1	950	Gag/Tag	14/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.314756906203688	2		321	683	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178218	56178218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780012235	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	159	434	0	ENST00000399503.3:c.3191G>A	p.Arg1064Lys	p.R1064K	ENST00000399503	NM_005921.1	1064	aGa/aAa	14/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.314756906203688	2		434	906	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181803	56181803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	119	395	0	ENST00000399503.3:c.4027G>A	p.Glu1343Lys	p.E1343K	ENST00000399503	NM_005921.1	1343	Gaa/Aaa	17/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.314756906203688	2		395	683	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591270	67591270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1289880098	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	230	360	1	ENST00000274335.5:c.1768C>T	p.Arg590Trp	p.R590W	ENST00000274335		590	Cgg/Tgg	13/15	1	2	FACETS	1	0.955	1	1	0.995	1	CLONAL	2	TRUE	1	0.314756906203688	2		361	713	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627262	86627262	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	190	483	0	ENST00000274376.6:c.637C>T	p.Pro213Ser	p.P213S	ENST00000274376	NM_002890.2	213	Cca/Tca	2/25	1	2	FACETS	0.98	0.911	1	1	0.993	1	CLONAL	2	TRUE	1	0.314756906203688	2		483	616	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674323	86674323	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	44	254	0	ENST00000274376.6:c.2455T>G	p.Leu819Val	p.L819V	ENST00000274376	NM_002890.2	819	Tta/Gta	18/25	1	2	FACETS	0.863	0.727	1	0.863	0.727	1	CLONAL	1	TRUE	1	0.314756906203688	2		254	324	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674348	86674348	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	37	219	0	ENST00000274376.6:c.2480C>T	p.Ser827Phe	p.S827F	ENST00000274376	NM_002890.2	827	tCt/tTt	18/25	1	2	FACETS	0.911	0.756	1	0.911	0.756	1	CLONAL	1	TRUE	1	0.314756906203688	2		219	258	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86676361	86676361	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	109	428	0	ENST00000274376.6:c.2639C>A	p.Ser880Tyr	p.S880Y	ENST00000274376	NM_002890.2	880	tCt/tAt	20/25	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.314756906203688	2		428	598	SUCCESS
APC	324	MSKCC	GRCh37	5	112174882	112174882	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	113	379	0	ENST00000257430.4:c.3591C>A	p.Phe1197Leu	p.F1197L	ENST00000257430	NM_000038.5	1197	ttC/ttA	16/16	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.314756906203688	2		379	677	SUCCESS
APC	324	MSKCC	GRCh37	5	112178000	112178000	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768922431	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	51	467	0	ENST00000257430.4:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000257430	NM_000038.5	2237	Cga/Tga	16/16	1	2	FACETS	0.347	0.294	0.406	0.347	0.294	0.406	SUBCLONAL	1	TRUE	1	0.314756906203688	2		467	934	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924421	131924421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146370443	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	81	415	0	ENST00000265335.6:c.1094G>A	p.Arg365Gln	p.R365Q	ENST00000265335		365	cGa/cAa	8/25	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.314756906203688	2		415	485	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500512	149500512	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	195	537	0	ENST00000261799.4:c.2525T>C	p.Ile842Thr	p.I842T	ENST00000261799	NM_002609.3	842	aTc/aCc	18/23	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.314756906203688	2		537	1174	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502666	149502666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749226501	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	334	467	0	ENST00000261799.4:c.2122C>T	p.Arg708Cys	p.R708C	ENST00000261799	NM_002609.3	708	Cgc/Tgc	15/23	1	2	FACETS	1	0.97	1	1	0.996	1	CLONAL	2	TRUE	1	0.314756906203688	2		467	1025	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515354	149515354	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs778982886	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	162	498	0	ENST00000261799.4:c.128T>C	p.Val43Ala	p.V43A	ENST00000261799	NM_002609.3	43	gTc/gCc	3/23	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.314756906203688	2		498	1016	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637150	176637150	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	73	285	0	ENST00000439151.2:c.1750A>C	p.Thr584Pro	p.T584P	ENST00000439151	NM_022455.4	584	Act/Cct	5/23	1	2	FACETS	0.97	0.851	1	0.97	0.851	1	CLONAL	1	TRUE	1	0.314756906203688	2		285	478	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687122	176687122	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	406	507	1	ENST00000439151.2:c.5099G>A	p.Arg1700Gln	p.R1700Q	ENST00000439151	NM_022455.4	1700	cGa/cAa	14/23	1	2	FACETS	1	0.987	1	1	0.997	1	CLONAL	2	TRUE	1	0.314756906203688	2		508	1180	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709535	176709535	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	115	585	3	ENST00000439151.2:c.5962G>T	p.Ala1988Ser	p.A1988S	ENST00000439151	NM_022455.4	1988	Gct/Tct	19/23	1	2	FACETS	0.703	0.632	0.779	0.703	0.632	0.779	SUBCLONAL	1	TRUE	1	0.314756906203688	2		588	1039	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036019	180036019	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	616	652	2	ENST00000261937.6:c.3842C>T	p.Ser1281Leu	p.S1281L	ENST00000261937	NM_182925.4	1281	tCg/tTg	29/30	1	2	FACETS	1	0.995	1	1	0.998	1	CLONAL	2	TRUE	1	0.314756906203688	2		654	1615	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048602	180048602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778453271	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	126	365	1	ENST00000261937.6:c.1960G>A	p.Glu654Lys	p.E654K	ENST00000261937	NM_182925.4	654	Gaa/Aaa	13/30	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.314756906203688	2		366	705	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057245	180057245	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	189	579	0	ENST00000261937.6:c.493C>A	p.Leu165Ile	p.L165I	ENST00000261937	NM_182925.4	165	Ctc/Atc	4/30	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.314756906203688	2		579	1095	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405042	405042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	305	426	0	ENST00000380956.4:c.1124G>A	p.Gly375Asp	p.G375D	ENST00000380956	NM_001195286.1	375	gGc/gAc	8/9	1	2	FACETS	1	0.952	1	1	0.996	1	CLONAL	2	TRUE	1	0.314756906203688	2		426	960	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778042	27778042	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2375	531	1254	3	ENST00000369163.2:c.191G>T	p.Arg64Ile	p.R64I	ENST00000369163	NM_003536.2	64	aGa/aTa	1/1	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.314756906203688	2		1257	2906	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163542	32163542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1187763031	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	201	446	0	ENST00000375023.3:c.5684C>T	p.Ser1895Phe	p.S1895F	ENST00000375023	NM_004557.3	1895	tCt/tTt	30/30	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.314756906203688	2		446	1155	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171944	32171944	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	321	438	0	ENST00000375023.3:c.3088T>G	p.Phe1030Val	p.F1030V	ENST00000375023	NM_004557.3	1030	Ttc/Gtc	19/30	1	2	FACETS	1	0.984	1	1	0.996	1	CLONAL	2	TRUE	1	0.314756906203688	2		438	928	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180645	32180645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	165	578	0	ENST00000375023.3:c.2482C>T	p.Pro828Ser	p.P828S	ENST00000375023	NM_004557.3	828	Ccc/Tcc	16/30	1	2	FACETS	0.764	0.7	0.832	0.764	0.7	0.832	SUBCLONAL	1	TRUE	1	0.314756906203688	2		578	1372	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32189066	32189066	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs777865677	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	201	486	0	ENST00000375023.3:c.488A>G	p.Asn163Ser	p.N163S	ENST00000375023	NM_004557.3	163	aAc/aGc	4/30	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.314756906203688	2		486	1114	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287226	33287226	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	149	407	0	ENST00000374542.5:c.1871A>G	p.Asp624Gly	p.D624G	ENST00000374542	NM_001141970.1	624	gAt/gGt	6/8	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.314756906203688	2		407	863	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140900	37140900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773910971	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	240	536	3	ENST00000373509.5:c.736G>A	p.Glu246Lys	p.E246K	ENST00000373509	NM_002648.3	246	Gaa/Aaa	5/6	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.314756906203688	2		539	1306	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41905072	41905072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1306114338	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	162	403	0	ENST00000372991.4:c.475G>A	p.Asp159Asn	p.D159N	ENST00000372991	NM_001760.3	159	Gat/Aat	3/5	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.314756906203688	2		403	988	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909365	41909365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs116713943	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	152	211	0	ENST00000372991.4:c.23G>A	p.Gly8Asp	p.G8D	ENST00000372991	NM_001760.3	8	gGc/gAc	1/5	1	2	FACETS	0.792	0.727	0.859	1	0.989	1	SUBCLONAL	2	TRUE	1	0.314756906203688	2		211	610	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956553	93956553	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1035177735	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1300	91	796	0	ENST00000369303.4:c.2683C>T	p.Arg895Ter	p.R895*	ENST00000369303	NM_004440.3	895	Cga/Tga	15/17	1	2	FACETS	0.416	0.367	0.468	0.416	0.367	0.468	SUBCLONAL	1	TRUE	1	0.314756906203688	2		796	1391	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956688	93956688	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	190	598	1	ENST00000369303.4:c.2548G>T	p.Glu850Ter	p.E850*	ENST00000369303	NM_004440.3	850	Gaa/Taa	15/17	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.314756906203688	2		599	1169	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964446	93964446	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	189	745	0	ENST00000369303.4:c.2451T>G	p.Ser817Arg	p.S817R	ENST00000369303	NM_004440.3	817	agT/agG	14/17	1	2	FACETS	0.92	0.848	0.994	0.92	0.848	0.994	CLONAL	1	TRUE	1	0.314756906203688	2		745	1306	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979282	93979282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	397	846	3	ENST00000369303.4:c.1546C>T	p.Arg516Trp	p.R516W	ENST00000369303	NM_004440.3	516	Cgg/Tgg	7/17	1	2	FACETS	1	0.988	1	1	0.997	1	CLONAL	2	TRUE	1	0.314756906203688	2		849	1138	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124472	94124472	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	321	699	0	ENST00000369303.4:c.111T>G	p.Asp37Glu	p.D37E	ENST00000369303	NM_004440.3	37	gaT/gaG	2/17	1	2	FACETS	1	0.985	1	1	0.996	1	CLONAL	2	TRUE	1	0.314756906203688	2		699	924	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553461	106553461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446838224	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	76	211	1	ENST00000369096.4:c.1426C>T	p.Arg476Trp	p.R476W	ENST00000369096	NM_001198.3	476	Cgg/Tgg	5/7	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.314756906203688	2		212	470	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983115	111983115	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	607	714	3	ENST00000368678.4:c.1432C>T	p.Arg478Ter	p.R478*	ENST00000368678		478	Cga/Tga	13/13	1	2	FACETS	1	0.991	1	1	0.998	1	CLONAL	2	TRUE	1	0.314756906203688	2		717	1752	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609665	117609665	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371063080	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	66	389	1	ENST00000368508.3:c.7034G>A	p.Gly2345Glu	p.G2345E	ENST00000368508	NM_002944.2	2345	gGg/gAg	43/43	0.111365834396786	0	FACETS	0.59	0.513	0.673			1	INDETERMINATE	1	TRUE	0	0.314756906203688	0		390	487	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677858	117677858	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	99	368	0	ENST00000368508.3:c.4075G>T	p.Glu1359Ter	p.E1359*	ENST00000368508	NM_002944.2	1359	Gag/Tag	25/43	0.111365834396786	0	FACETS	0.847	0.759	0.94			1	INDETERMINATE	1	TRUE	0	0.314756906203688	0		368	509	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678976	117678976	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	64	269	2	ENST00000368508.3:c.3845C>A	p.Pro1282His	p.P1282H	ENST00000368508	NM_002944.2	1282	cCt/cAt	24/43	0.111365834396786	0	FACETS	0.812	0.708	0.924			1	INDETERMINATE	1	TRUE	0	0.314756906203688	0		271	343	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706936	117706936	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	146	545	1	ENST00000368508.3:c.2214G>T	p.Glu738Asp	p.E738D	ENST00000368508	NM_002944.2	738	gaG/gaT	15/43	0.111365834396786	0	FACETS	0.638	0.582	0.698			1	INDETERMINATE	1	TRUE	0	0.314756906203688	0		546	996	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715484	117715484	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	157	313	0	ENST00000368508.3:c.1005A>C	p.Gln335His	p.Q335H	ENST00000368508	NM_002944.2	335	caA/caC	10/43	0.111365834396786	0	FACETS	0.797	0.737	0.857			1	INDETERMINATE	2	TRUE	0	0.314756906203688	0		313	429	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715847	117715847	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	94	399	0	ENST00000368508.3:c.911G>T	p.Arg304Ile	p.R304I	ENST00000368508	NM_002944.2	304	aGa/aTa	9/43	0.111365834396786	0	FACETS	0.613	0.545	0.684			1	INDETERMINATE	1	TRUE	0	0.314756906203688	0		399	668	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138197147	138197147	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1276578378	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	200	294	0	ENST00000237289.4:c.649A>C	p.Ser217Arg	p.S217R	ENST00000237289	NM_001270507.1	217	Agt/Cgt	5/9	1	2	FACETS	1	0.958	1	1	0.994	1	CLONAL	2	TRUE	1	0.314756906203688	2		294	612	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004446	150004446	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	167	483	1	ENST00000253339.5:c.1779T>G	p.Ser593Arg	p.S593R	ENST00000253339		593	agT/agG	3/7	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.314756906203688	2		484	902	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382236	152382236	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	87	393	0	ENST00000206249.3:c.1346A>G	p.Lys449Arg	p.K449R	ENST00000206249	NM_000125.3	449	aAa/aGa	6/8	1	2	FACETS	0.909	0.806	1	0.909	0.806	1	CLONAL	1	TRUE	1	0.314756906203688	2		393	608	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683680	162683680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373593750	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	185	504	1	ENST00000366898.1:c.289C>T	p.Arg97Trp	p.R97W	ENST00000366898	NM_004562.2	97	Cgg/Tgg	3/12	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.314756906203688	2		505	1020	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2949777	2949777	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	174	459	2	ENST00000396946.4:c.3167C>T	p.Ala1056Val	p.A1056V	ENST00000396946	NM_032415.4	1056	gCt/gTt	24/25	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.314756906203688	2		461	1083	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224321	55224321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	150	401	1	ENST00000275493.2:c.1102G>A	p.Asp368Asn	p.D368N	ENST00000275493	NM_005228.3	368	Gat/Aat	9/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.314756906203688	2		402	802	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358931	81358931	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	191	412	0	ENST00000222390.5:c.1030T>G	p.Phe344Val	p.F344V	ENST00000222390	NM_000601.4	344	Ttc/Gtc	8/18	1	2	FACETS	1	0.974	1	1	0.994	1	CLONAL	2	TRUE	1	0.314756906203688	2		412	554	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381451	81381451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	234	501	0	ENST00000222390.5:c.610C>T	p.Pro204Ser	p.P204S	ENST00000222390	NM_000601.4	204	Cct/Tct	5/18	1	2	FACETS	1	0.973	1	1	0.995	1	CLONAL	2	TRUE	1	0.314756906203688	2		501	695	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508783	106508783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	146	502	0	ENST00000359195.3:c.777G>A	p.Met259Ile	p.M259I	ENST00000359195	NM_002649.2	259	atG/atA	2/11	1	2	FACETS	0.93	0.848	1	0.93	0.848	1	CLONAL	1	TRUE	1	0.314756906203688	2		502	997	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522569	106522569	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746783339	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	124	439	0	ENST00000359195.3:c.2546G>A	p.Arg849Gln	p.R849Q	ENST00000359195	NM_002649.2	849	cGa/cAa	7/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.314756906203688	2		439	722	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545616	106545616	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	87	503	1	ENST00000359195.3:c.3093C>A	p.Phe1031Leu	p.F1031L	ENST00000359195	NM_002649.2	1031	ttC/ttA	11/11	1	2	FACETS	0.965	0.856	1	0.965	0.856	1	CLONAL	1	TRUE	1	0.314756906203688	2		504	573	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339605	116339605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56311081	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	94	269	0	ENST00000397752.3:c.467C>T	p.Ser156Leu	p.S156L	ENST00000397752	NM_000245.2	156	tCg/tTg	2/21	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.314756906203688	2		269	560	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411667	116411667	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	33	421	0	ENST00000397752.3:c.2846T>G	p.Leu949Arg	p.L949R	ENST00000397752	NM_000245.2	949	cTt/cGt	13/21	1	2	FACETS	0.328	0.266	0.398	0.328	0.266	0.398	SUBCLONAL	1	TRUE	1	0.314756906203688	2		421	640	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845507	128845507	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	256	593	0	ENST00000249373.3:c.804C>A	p.Phe268Leu	p.F268L	ENST00000249373	NM_005631.4	268	ttC/ttA	4/12	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.314756906203688	2		593	1277	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140507856	140507856	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	71	413	0	ENST00000288602.6:c.615G>T	p.Lys205Asn	p.K205N	ENST00000288602	NM_004333.4	205	aaG/aaT	5/18	1	2	FACETS	0.93	0.814	1	0.93	0.814	1	CLONAL	1	TRUE	1	0.314756906203688	2		413	485	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506448	148506448	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	117	409	0	ENST00000320356.2:c.2064A>C	p.Lys688Asn	p.K688N	ENST00000320356	NM_004456.4	688	aaA/aaC	18/20	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.314756906203688	2		409	681	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148513849	148513849	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	228	445	0	ENST00000320356.2:c.1432G>T	p.Glu478Ter	p.E478*	ENST00000320356	NM_004456.4	478	Gaa/Taa	12/20	1	2	FACETS	1	0.968	1	1	0.995	1	CLONAL	2	TRUE	1	0.314756906203688	2		445	688	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543648	148543648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	143	322	0	ENST00000320356.2:c.160G>A	p.Glu54Lys	p.E54K	ENST00000320356	NM_004456.4	54	Gaa/Aaa	3/20	1	2	FACETS	1	0.966	1	1	0.992	1	CLONAL	2	TRUE	1	0.314756906203688	2		322	417	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188076	151188076	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	463	761	0	ENST00000262187.5:c.77T>G	p.Phe26Cys	p.F26C	ENST00000262187	NM_005614.3	26	tTt/tGt	2/8	1	2	FACETS	1	0.981	1	1	0.997	1	CLONAL	2	TRUE	1	0.314756906203688	2		761	1401	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845300	151845300	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	134	415	1	ENST00000262189.6:c.13712C>A	p.Ser4571Tyr	p.S4571Y	ENST00000262189	NM_170606.2	4571	tCt/tAt	52/59	1	2	FACETS	0.931	0.845	1	0.931	0.845	1	CLONAL	1	TRUE	1	0.314756906203688	2		416	915	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845550	151845550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753793539	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	145	419	0	ENST00000262189.6:c.13462G>A	p.Ala4488Thr	p.A4488T	ENST00000262189	NM_170606.2	4488	Gcc/Acc	52/59	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.314756906203688	2		419	849	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848083	151848083	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	113	278	0	ENST00000262189.6:c.12676G>T	p.Glu4226Ter	p.E4226*	ENST00000262189	NM_170606.2	4226	Gaa/Taa	51/59	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.314756906203688	2		278	585	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864451	151864451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs535118581	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	110	261	0	ENST00000262189.6:c.9530G>A	p.Arg3177His	p.R3177H	ENST00000262189	NM_170606.2	3177	cGt/cAt	42/59	1	2	FACETS	0.872	0.789	0.957	1	0.987	1	CLONAL	2	TRUE	1	0.314756906203688	2		261	401	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878529	151878529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1400133609	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	145	382	1	ENST00000262189.6:c.6416G>A	p.Arg2139Gln	p.R2139Q	ENST00000262189	NM_170606.2	2139	cGa/cAa	36/59	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.314756906203688	2		383	830	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880094	151880094	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	250	527	0	ENST00000262189.6:c.5230G>T	p.Glu1744Ter	p.E1744*	ENST00000262189	NM_170606.2	1744	Gaa/Taa	35/59	1	2	FACETS	0.973	0.913	1	1	0.995	1	CLONAL	2	TRUE	1	0.314756906203688	2		527	816	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880202	151880202	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	180	340	0	ENST00000262189.6:c.5122A>C	p.Lys1708Gln	p.K1708Q	ENST00000262189	NM_170606.2	1708	Aaa/Caa	35/59	1	2	FACETS	1	0.958	1	1	0.993	1	CLONAL	2	TRUE	1	0.314756906203688	2		340	547	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945411	151945411	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	40	215	0	ENST00000262189.6:c.2108A>G	p.His703Arg	p.H703R	ENST00000262189	NM_170606.2	703	cAt/cGt	14/59	1	2	FACETS	0.865	0.722	1	0.865	0.722	1	CLONAL	1	TRUE	1	0.314756906203688	2		215	294	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132713	152132713	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	132	183	0	ENST00000262189.6:c.159G>T	p.Lys53Asn	p.K53N	ENST00000262189	NM_170606.2	53	aaG/aaT	1/59	1	2	FACETS	0.821	0.749	0.895	1	0.988	1	CLONAL	2	TRUE	1	0.314756906203688	2		183	511	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282215	38282215	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	187	266	3	ENST00000425967.3:c.841C>T	p.Arg281Trp	p.R281W	ENST00000425967	NM_001174067.1	281	Cgg/Tgg	8/19	0.314756906203688	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.314756906203688	3		269	611	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371830	55371830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1457048078	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	11	12	0	ENST00000297316.4:c.520G>A	p.Val174Met	p.V174M	ENST00000297316	NM_022454.3	174	Gtg/Atg	2/2	0.314756906203688	3	FACETS	1	0.761	1	1	0.761	1	CLONAL	2	TRUE	1	0.314756906203688	3		12	38	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372205	55372205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs904970570	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	59	127	0	ENST00000297316.4:c.895G>A	p.Ala299Thr	p.A299T	ENST00000297316	NM_022454.3	299	Gcg/Acg	2/2	0.314756906203688	3	FACETS	1	0.954	1	0.623	0.539	0.714	CLONAL	1	TRUE	1	0.314756906203688	3		127	348	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955520	90955520	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	185	408	0	ENST00000265433.3:c.2145G>T	p.Lys715Asn	p.K715N	ENST00000265433	NM_002485.4	715	aaG/aaT	14/16	0.314756906203688	3	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	1	0.314756906203688	3		408	680	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90971067	90971067	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	67	272	0	ENST00000265433.3:c.1010C>A	p.Thr337Asn	p.T337N	ENST00000265433	NM_002485.4	337	aCt/aAt	9/16	0.314756906203688	3	FACETS	0.808	0.702	0.922	0.404	0.351	0.461	CLONAL	1	TRUE	1	0.314756906203688	3		272	610	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90992973	90992973	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	56	251	0	ENST00000265433.3:c.469G>T	p.Val157Phe	p.V157F	ENST00000265433	NM_002485.4	157	Gtt/Ttt	4/16	0.314756906203688	3	FACETS	0.967	0.83	1	0.483	0.415	0.558	CLONAL	1	TRUE	1	0.314756906203688	3		251	426	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738094	145738094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561220929	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1461	267	621	0	ENST00000428558.2:c.2816C>T	p.Ala939Val	p.A939V	ENST00000428558	NM_004260.3	939	gCg/gTg	17/22	0.314756906203688	3	FACETS	1	0.982	1	0.568	0.531	0.607	CLONAL	1	TRUE	1	0.314756906203688	3		621	1728	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741925	145741925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747963862	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	175	409	1	ENST00000428558.2:c.578G>A	p.Arg193Gln	p.R193Q	ENST00000428558	NM_004260.3	193	cGa/cAa	5/22	0.314756906203688	3	FACETS	1	0.966	1	0.547	0.502	0.593	CLONAL	1	TRUE	1	0.314756906203688	3		410	1177	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044449	5044449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371826393	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	108	599	0	ENST00000381652.3:c.397C>T	p.Arg133Trp	p.R133W	ENST00000381652	NM_004972.3	133	Cgg/Tgg	5/25	1	2	FACETS	0.894	0.802	0.991	0.894	0.802	0.991	CLONAL	1	TRUE	1	0.314756906203688	2		599	768	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069154	5069154	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764423560	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	122	378	1	ENST00000381652.3:c.1459C>T	p.Arg487Cys	p.R487C	ENST00000381652	NM_004972.3	487	Cgc/Tgc	11/25	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.314756906203688	2		379	600	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089794	5089794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	218	452	2	ENST00000381652.3:c.2692G>A	p.Glu898Lys	p.E898K	ENST00000381652	NM_004972.3	898	Gaa/Aaa	20/25	1	2	FACETS	0.988	0.923	1	1	0.994	1	CLONAL	2	TRUE	1	0.314756906203688	2		454	701	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126757	5126757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775495966	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	93	430	0	ENST00000381652.3:c.3365G>A	p.Arg1122Gln	p.R1122Q	ENST00000381652	NM_004972.3	1122	cGa/cAa	25/25	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.314756906203688	2		430	525	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317921	8317921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150063446	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	118	483	2	ENST00000356435.5:c.5692C>T	p.Arg1898Cys	p.R1898C	ENST00000356435		1898	Cgt/Tgt	35/35	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.314756906203688	2		485	734	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485933	8485933	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	145	627	0	ENST00000356435.5:c.2884A>G	p.Asn962Asp	p.N962D	ENST00000356435		962	Aac/Gac	17/35	1	2	FACETS	0.848	0.773	0.928	0.848	0.773	0.928	CLONAL	1	TRUE	1	0.314756906203688	2		627	1086	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486268	8486268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs919912664	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	106	386	0	ENST00000356435.5:c.2549T>G	p.Phe850Cys	p.F850C	ENST00000356435		850	tTt/tGt	17/35	1	2	FACETS	0.955	0.857	1	0.955	0.857	1	CLONAL	1	TRUE	1	0.314756906203688	2		386	705	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517931	8517931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	155	530	0	ENST00000356435.5:c.1460C>T	p.Thr487Ile	p.T487I	ENST00000356435		487	aCa/aTa	10/35	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.314756906203688	2		530	951	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518099	8518099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764400127	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	208	315	1	ENST00000356435.5:c.1292C>T	p.Ser431Leu	p.S431L	ENST00000356435		431	tCg/tTg	10/35	1	2	FACETS	1	0.982	1	1	0.995	1	CLONAL	2	TRUE	1	0.314756906203688	2		316	578	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970987	21970987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747621669	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	175	373	0	ENST00000304494.5:c.371G>A	p.Arg124His	p.R124H	ENST00000304494	NM_000077.4	124	cGc/cAc	2/3	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.314756906203688	2		373	983	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994236	21994236	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs370655358	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	149	468	0	ENST00000579755.1:c.95G>T	p.Gly32Val	p.G32V	ENST00000579755		32	gGg/gTg	1/3	1				0.899	1				CLONAL	1	TRUE	1	0.314756906203688	2		468	961	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002672	37002672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	194	500	0	ENST00000358127.4:c.577G>A	p.Asp193Asn	p.D193N	ENST00000358127	NM_001280556.1	193	Gac/Aac	5/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.314756906203688	2		500	1058	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412494	80412494	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	383	600	0	ENST00000286548.4:c.547C>T	p.Arg183Ter	p.R183*	ENST00000286548	NM_002072.3	183	Cga/Tga	4/7	1	2	FACETS	1	0.989	1	1	0.997	1	CLONAL	2	TRUE	1	0.314756906203688	2		600	1074	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325693	87325693	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	119	366	0	ENST00000277120.3:c.570G>T	p.Gln190His	p.Q190H	ENST00000277120		190	caG/caT	6/19	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.314756906203688	2		366	702	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342807	87342807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	112	410	0	ENST00000277120.3:c.1092G>T	p.Lys364Asn	p.K364N	ENST00000277120		364	aaG/aaT	9/19	1	2	FACETS	0.98	0.882	1	0.98	0.882	1	CLONAL	1	TRUE	1	0.314756906203688	2		410	726	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563482	87563482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194954580	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	142	349	1	ENST00000277120.3:c.1870G>A	p.Val624Met	p.V624M	ENST00000277120		624	Gtg/Atg	16/19	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.314756906203688	2		350	800	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93629437	93629437	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs771204624	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	166	383	0	ENST00000375746.1:c.871T>C	p.Ser291Pro	p.S291P	ENST00000375746	NM_001174167.1	291	Tca/Cca	7/14	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.314756906203688	2		383	922	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232137	98232137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1382474804	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	133	416	0	ENST00000331920.6:c.1805G>A	p.Arg602Gln	p.R602Q	ENST00000331920	NM_000264.3	602	cGa/cAa	13/24	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.314756906203688	2		416	833	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249780	110249780	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142583665	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	297	394	2	ENST00000374672.4:c.895C>T	p.Arg299Trp	p.R299W	ENST00000374672	NM_004235.4	299	Cgg/Tgg	3/5	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.314756906203688	2		396	781	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127920534	127920534	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	221	648	0	ENST00000373547.4:c.365T>C	p.Val122Ala	p.V122A	ENST00000373547	NM_002721.4	122	gTc/gCc	4/7	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.314756906203688	2		648	1309	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798770	135798770	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs118203385	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	123	376	0	ENST00000298552.3:c.473T>G	p.Phe158Cys	p.F158C	ENST00000298552	NM_001162426.1	158	tTt/tGt	6/23	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.314756906203688	2		376	770	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100664	8100664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1477514775	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	171	528	0	ENST00000346208.3:c.638C>T	p.Ser213Leu	p.S213L	ENST00000346208		213	tCg/tTg	3/6	1	2	FACETS	0.957	0.879	1	0.957	0.879	1	CLONAL	1	TRUE	1	0.314756906203688	2		528	1135	SUCCESS
RET	5979	MSKCC	GRCh37	10	43598033	43598033	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	162	395	0	ENST00000355710.3:c.581A>G	p.Gln194Arg	p.Q194R	ENST00000355710	NM_020975.4	194	cAg/cGg	3/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.314756906203688	2		395	804	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851087	63851087	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	258	322	0	ENST00000279873.7:c.1865A>G	p.Tyr622Cys	p.Y622C	ENST00000279873	NM_032199.2	622	tAc/tGc	10/10	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.314756906203688	2		322	668	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333850	70333850	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs762232511	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	135	434	0	ENST00000373644.4:c.1755G>T	p.Lys585Asn	p.K585N	ENST00000373644	NM_030625.2	585	aaG/aaT	2/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.314756906203688	2		434	753	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243237	123243237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55774317	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	511	715	0	ENST00000358487.5:c.2276G>A	p.Arg759Gln	p.R759Q	ENST00000358487	NM_000141.4	759	cGa/cAa	17/18	1	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	1	0.314756906203688	2		715	1431	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8246180	8246180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1277982924	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	320	489	0	ENST00000335790.3:c.454G>A	p.Glu152Lys	p.E152K	ENST00000335790	NM_002315.2	152	Gaa/Aaa	4/4	1	2	FACETS	0.981	0.928	1	1	0.996	1	CLONAL	2	TRUE	1	0.314756906203688	2		489	1036	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8246233	8246233	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs201019556	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	149	458	0	ENST00000335790.3:c.401A>G	p.Asn134Ser	p.N134S	ENST00000335790	NM_002315.2	134	aAc/aGc	4/4	1	2	FACETS	0.958	0.875	1	0.958	0.875	1	CLONAL	1	TRUE	1	0.314756906203688	2		458	988	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589546	69589546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	144	229	0	ENST00000168712.1:c.307C>T	p.Arg103Cys	p.R103C	ENST00000168712	NM_002007.2	103	Cgc/Tgc	1/3	1	2	FACETS	0.798	0.731	0.868	1	0.989	1	SUBCLONAL	2	TRUE	1	0.314756906203688	2		229	573	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633620	69633620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	66	51	0	ENST00000334134.2:c.82G>A	p.Asp28Asn	p.D28N	ENST00000334134	NM_005247.2	28	Gat/Aat	1/3	1	2	FACETS	0.879	0.782	0.978	1	0.985	1	CLONAL	3	TRUE	1	0.314756906203688	2		51	159	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076740	102076740	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	537	672	7	ENST00000282441.5:c.919C>T	p.Arg307Ter	p.R307*	ENST00000282441	NM_001130145.2	307	Cga/Tga	5/9	1	2	FACETS	1	0.992	1	1	0.998	1	CLONAL	2	TRUE	1	0.314756906203688	2		679	1514	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195394	102195394	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	176	917	2	ENST00000263464.3:c.154C>T	p.Arg52Cys	p.R52C	ENST00000263464	NM_001165.4	52	Cgt/Tgt	2/9	1	2	FACETS	0.924	0.85	1	0.924	0.85	1	CLONAL	1	TRUE	1	0.314756906203688	2		919	1210	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195949	102195949	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	218	830	0	ENST00000263464.3:c.709A>C	p.Asn237His	p.N237H	ENST00000263464	NM_001165.4	237	Aat/Cat	2/9	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.314756906203688	2		830	1221	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	196	324	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	1	0.972	1	1	0.994	1	CLONAL	2	TRUE	1	0.314756906203688	2		324	576	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342392	118342392	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	182	430	2	ENST00000534358.1:c.518G>A	p.Arg173Gln	p.R173Q	ENST00000534358	NM_005933.3	173	cGa/cAa	3/36	1	2	FACETS	1	0.983	1	1	0.994	1	CLONAL	2	TRUE	1	0.314756906203688	2		432	491	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343121	118343121	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	113	385	1	ENST00000534358.1:c.1247C>A	p.Ala416Asp	p.A416D	ENST00000534358	NM_005933.3	416	gCt/gAt	3/36	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.314756906203688	2		386	694	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343913	118343913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264831726	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	121	375	0	ENST00000534358.1:c.2039C>T	p.Ser680Leu	p.S680L	ENST00000534358	NM_005933.3	680	tCg/tTg	3/36	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.314756906203688	2		375	694	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344941	118344941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	128	376	1	ENST00000534358.1:c.3067G>A	p.Val1023Ile	p.V1023I	ENST00000534358	NM_005933.3	1023	Gtt/Att	3/36	1	2	FACETS	0.966	0.875	1	0.966	0.875	1	CLONAL	1	TRUE	1	0.314756906203688	2		377	842	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352703	118352703	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	187	499	0	ENST00000534358.1:c.3908T>C	p.Leu1303Pro	p.L1303P	ENST00000534358	NM_005933.3	1303	cTg/cCg	7/36	1	2	FACETS	0.959	0.884	1	0.959	0.884	1	CLONAL	1	TRUE	1	0.314756906203688	2		499	1239	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360604	118360604	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	276	487	1	ENST00000534358.1:c.4575+2T>C		p.X1525_splice	ENST00000534358	NM_005933.3	1525			1	2	FACETS	1	0.986	1	1	0.996	1	CLONAL	2	TRUE	1	0.314756906203688	2		488	769	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374747	118374747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	344	502	0	ENST00000534358.1:c.8140C>T	p.Leu2714Phe	p.L2714F	ENST00000534358	NM_005933.3	2714	Ctt/Ttt	27/36	1	2	FACETS	1	0.986	1	1	0.996	1	CLONAL	2	TRUE	1	0.314756906203688	2		502	989	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380777	118380777	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	130	524	0	ENST00000534358.1:c.11015T>G	p.Leu3672Arg	p.L3672R	ENST00000534358	NM_005933.3	3672	cTt/cGt	30/36	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.314756906203688	2		524	783	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118382705	118382705	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555050212	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	135	448	0	ENST00000534358.1:c.11111G>A	p.Arg3704Gln	p.R3704Q	ENST00000534358	NM_005933.3	3704	cGa/cAa	31/36	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.314756906203688	2		448	657	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169085	119169085	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146517083	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	168	450	0	ENST00000264033.4:c.2269G>A	p.Ala757Thr	p.A757T	ENST00000264033	NM_005188.3	757	Gca/Aca	15/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.314756906203688	2		450	990	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419112	419112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778494527	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	79	322	0	ENST00000399788.2:c.3235G>A	p.Asp1079Asn	p.D1079N	ENST00000399788	NM_001042603.1	1079	Gac/Aac	22/28	1	2	FACETS	0.832	0.733	0.939	0.832	0.733	0.939	CLONAL	1	TRUE	1	0.314756906203688	2		322	603	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427300	427300	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	84	287	0	ENST00000399788.2:c.2869G>T	p.Glu957Ter	p.E957*	ENST00000399788	NM_001042603.1	957	Gaa/Taa	19/28	1	2	FACETS	0.781	0.69	0.879	0.781	0.69	0.879	SUBCLONAL	1	TRUE	1	0.314756906203688	2		287	683	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431664	431664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	93	486	1	ENST00000399788.2:c.2345G>A	p.Arg782Gln	p.R782Q	ENST00000399788	NM_001042603.1	782	cGa/cAa	17/28	1	2	FACETS	0.925	0.823	1	0.925	0.823	1	CLONAL	1	TRUE	1	0.314756906203688	2		487	639	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	463244	463244	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs779919288	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	170	498	0	ENST00000399788.2:c.1027G>A	p.Glu343Lys	p.E343K	ENST00000399788	NM_001042603.1	343	Gag/Aag	8/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.314756906203688	2		498	922	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	465599	465599	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	108	431	0	ENST00000399788.2:c.777A>C	p.Glu259Asp	p.E259D	ENST00000399788	NM_001042603.1	259	gaA/gaC	6/28	1	2	FACETS	0.944	0.848	1	0.944	0.848	1	CLONAL	1	TRUE	1	0.314756906203688	2		431	727	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	472245	472245	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	125	336	0	ENST00000399788.2:c.556T>G	p.Leu186Val	p.L186V	ENST00000399788	NM_001042603.1	186	Tta/Gta	5/28	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.314756906203688	2		336	750	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435449	18435449	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	63	359	0	ENST00000266497.5:c.434C>A	p.Ala145Asp	p.A145D	ENST00000266497		145	gCt/gAt	1/31	0.285133655605373	1	FACETS	0.801	0.695	0.915	0.801	0.695	0.915	CLONAL	1	TRUE	0	0.314756906203688	1		359	421	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443902	18443902	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	84	293	0	ENST00000266497.5:c.875T>G	p.Ile292Ser	p.I292S	ENST00000266497		292	aTt/aGt	3/31	0.285133655605373	1	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	0	0.314756906203688	1		293	447	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18477976	18477976	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	137	263	0	ENST00000266497.5:c.1216C>A	p.Leu406Ile	p.L406I	ENST00000266497		406	Ctc/Atc	7/31	0.285133655605373	1	FACETS	0.847	0.777	0.919	1	0.99	1	CLONAL	2	TRUE	0	0.314756906203688	1		263	433	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573890	18573890	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	152	400	0	ENST00000266497.5:c.2208A>C	p.Glu736Asp	p.E736D	ENST00000266497		736	gaA/gaC	15/31	0.285133655605373	1	FACETS	0.795	0.732	0.86	1	0.99	1	SUBCLONAL	2	TRUE	0	0.314756906203688	1		400	512	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380276	+	missense_variant	Missense_Mutation	DNP	TT	TT	GA	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	224	385	0	ENST00000311936.3:c.182_183delinsTC	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAA/cTC	3/5	1	2	FACETS	1	0.973	1	1	0.995	1	CLONAL	2	TRUE	1	0.314756906203688	2		385	664	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230722	46230722	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	68	421	0	ENST00000334344.6:c.971T>G	p.Phe324Cys	p.F324C	ENST00000334344	NM_152641.2	324	tTt/tGt	8/21	1	2	FACETS	0.69	0.6	0.787	0.69	0.6	0.787	SUBCLONAL	1	TRUE	1	0.314756906203688	2		421	626	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233143	46233143	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	217	374	0	ENST00000334344.6:c.1362T>G	p.Ile454Met	p.I454M	ENST00000334344	NM_152641.2	454	atT/atG	11/21	1	2	FACETS	1	0.969	1	1	0.994	1	CLONAL	2	TRUE	1	0.314756906203688	2		374	651	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233223	46233223	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	158	515	0	ENST00000334344.6:c.1442T>G	p.Ile481Ser	p.I481S	ENST00000334344	NM_152641.2	481	aTt/aGt	11/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.314756906203688	2		515	900	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243448	46243448	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	103	533	1	ENST00000334344.6:c.1801C>T	p.Arg601Trp	p.R601W	ENST00000334344	NM_152641.2	601	Cgg/Tgg	14/21	1	2	FACETS	0.922	0.825	1	0.922	0.825	1	CLONAL	1	TRUE	1	0.314756906203688	2		534	710	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416381	49416381	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1436698999	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	252	333	1	ENST00000301067.7:c.16330G>A	p.Glu5444Lys	p.E5444K	ENST00000301067	NM_003482.3	5444	Gaa/Aaa	51/54	1	2	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	1	0.314756906203688	2		334	680	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420076	49420076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	257	611	0	ENST00000301067.7:c.15673C>T	p.Arg5225Cys	p.R5225C	ENST00000301067	NM_003482.3	5225	Cgc/Tgc	48/54	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.314756906203688	2		611	1364	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420253	49420253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758730277	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	211	479	0	ENST00000301067.7:c.15496G>A	p.Ala5166Thr	p.A5166T	ENST00000301067	NM_003482.3	5166	Gct/Act	48/54	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.314756906203688	2		479	1100	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420809	49420809	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	159	366	0	ENST00000301067.7:c.14940G>T	p.Lys4980Asn	p.K4980N	ENST00000301067	NM_003482.3	4980	aaG/aaT	48/54	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.314756906203688	2		366	909	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422859	49422859	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371377859	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	392	420	0	ENST00000301067.7:c.14236C>T	p.Arg4746Trp	p.R4746W	ENST00000301067	NM_003482.3	4746	Cgg/Tgg	44/54	1	2	FACETS	1	0.993	1	1	0.997	1	CLONAL	2	TRUE	1	0.314756906203688	2		420	1024	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446151	49446151	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	91	247	0	ENST00000301067.7:c.1315C>A	p.Pro439Thr	p.P439T	ENST00000301067	NM_003482.3	439	Cca/Aca	10/54	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.314756906203688	2		247	558	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446735	49446735	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372085797	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	161	457	0	ENST00000301067.7:c.1075C>T	p.Arg359Cys	p.R359C	ENST00000301067	NM_003482.3	359	Cgc/Tgc	8/54	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.314756906203688	2		457	1001	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448320	49448320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	193	657	0	ENST00000301067.7:c.391G>A	p.Glu131Lys	p.E131K	ENST00000301067	NM_003482.3	131	Gaa/Aaa	3/54	1	2	FACETS	0.906	0.836	0.98	0.906	0.836	0.98	CLONAL	1	TRUE	1	0.314756906203688	2		657	1353	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484057	50484057	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	191	472	0	ENST00000394963.4:c.907C>T	p.Arg303Ter	p.R303*	ENST00000394963	NM_003076.4	303	Cga/Tga	8/13	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.314756906203688	2		472	1044	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857515	57857515	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs773228040	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1570	385	803	1	ENST00000228682.2:c.41G>T	p.Gly14Val	p.G14V	ENST00000228682	NM_005269.2	14	gGc/gTc	2/12	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.314756906203688	2		804	1955	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861822	57861822	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1792	360	906	1	ENST00000228682.2:c.1123G>T	p.Asp375Tyr	p.D375Y	ENST00000228682	NM_005269.2	375	Gat/Tat	10/12	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.314756906203688	2		907	2152	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233247	69233247	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	139	504	0	ENST00000462284.1:c.1112C>A	p.Thr371Asn	p.T371N	ENST00000462284	NM_002392.5	371	aCt/aAt	11/11	1	2	FACETS	0.947	0.861	1	0.947	0.861	1	CLONAL	1	TRUE	1	0.314756906203688	2		504	933	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811758	102811758	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	103	428	0	ENST00000307046.8:c.426G>T	p.Lys142Asn	p.K142N	ENST00000307046	NM_001111285.1	142	aaG/aaT	4/4	1	2	FACETS	0.904	0.809	1	0.904	0.809	1	CLONAL	1	TRUE	1	0.314756906203688	2		428	724	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891035	112891035	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs755619262	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	119	386	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	0.314756906203688	2		386	654	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926915	112926915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	126	398	0	ENST00000351677.2:c.1535G>A	p.Arg512Gln	p.R512Q	ENST00000351677	NM_002834.3	512	cGa/cAa	13/16	1	2	FACETS	0.981	0.889	1	0.981	0.889	1	CLONAL	1	TRUE	1	0.314756906203688	2		398	816	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437418	121437418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373857078	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	216	300	0	ENST00000257555.6:c.1756G>A	p.Ala586Thr	p.A586T	ENST00000257555		586	Gcc/Acc	9/10	1	2	FACETS	0.854	0.801	0.907	1	0.995	1	CLONAL	3	TRUE	1	0.314756906203688	2		300	536	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215787	133215787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762000608	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1391	298	722	0	ENST00000320574.5:c.5476C>T	p.Arg1826Trp	p.R1826W	ENST00000320574	NM_006231.2	1826	Cgg/Tgg	40/49	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.314756906203688	2		722	1689	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226361	133226361	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs745750549	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	238	693	3	ENST00000320574.5:c.3697C>T	p.Arg1233Ter	p.R1233*	ENST00000320574	NM_006231.2	1233	Cga/Tga	30/49	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.314756906203688	2		696	1377	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589369	28589369	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1048919218	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	357	526	0	ENST00000241453.7:c.2678C>T	p.Pro893Leu	p.P893L	ENST00000241453	NM_004119.2	893	cCg/cTg	22/24	1	2	FACETS	1	0.985	1	1	0.996	1	CLONAL	2	TRUE	1	0.314756906203688	2		526	1040	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28885776	28885776	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	118	507	0	ENST00000282397.4:c.3586G>T	p.Glu1196Ter	p.E1196*	ENST00000282397	NM_002019.4	1196	Gaa/Taa	27/30	1	2	FACETS	0.979	0.883	1	0.979	0.883	1	CLONAL	1	TRUE	1	0.314756906203688	2		507	766	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891687	28891687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	421	650	1	ENST00000282397.4:c.3334C>T	p.Arg1112Cys	p.R1112C	ENST00000282397	NM_002019.4	1112	Cgc/Tgc	25/30	1	2	FACETS	1	0.974	1	1	0.997	1	CLONAL	2	TRUE	1	0.314756906203688	2		651	1296	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959144	28959144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767259336	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	116	509	0	ENST00000282397.4:c.1994G>A	p.Arg665Gln	p.R665Q	ENST00000282397	NM_002019.4	665	cGa/cAa	14/30	1	2	FACETS	0.932	0.84	1	0.932	0.84	1	CLONAL	1	TRUE	1	0.314756906203688	2		509	791	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964202	28964202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374335323	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	188	350	0	ENST00000282397.4:c.1700C>T	p.Pro567Leu	p.P567L	ENST00000282397	NM_002019.4	567	cCg/cTg	13/30	1	2	FACETS	1	0.984	1	1	0.994	1	CLONAL	2	TRUE	1	0.314756906203688	2		350	506	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900705	32900705	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	296	536	0	ENST00000380152.3:c.586A>C	p.Ser196Arg	p.S196R	ENST00000380152		196	Agt/Cgt	7/27	1	2	FACETS	1	0.974	1	1	0.996	1	CLONAL	2	TRUE	1	0.314756906203688	2		536	894	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906570	32906570	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	175	383	0	ENST00000380152.3:c.955A>C	p.Asn319His	p.N319H	ENST00000380152		319	Aat/Cat	10/27	1	2	FACETS	1	0.959	1	1	0.993	1	CLONAL	2	TRUE	1	0.314756906203688	2		383	530	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910414	32910414	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	424	645	2	ENST00000380152.3:c.1922C>A	p.Ser641Tyr	p.S641Y	ENST00000380152		641	tCt/tAt	11/27	1	2	FACETS	1	0.987	1	1	0.997	1	CLONAL	2	TRUE	1	0.314756906203688	2		647	1238	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910695	32910695	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	544	982	1	ENST00000380152.3:c.2203G>A	p.Ala735Thr	p.A735T	ENST00000380152		735	Gct/Act	11/27	1	2	FACETS	1	0.992	1	1	0.998	1	CLONAL	2	TRUE	1	0.314756906203688	2		983	1545	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910770	32910770	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	460	896	0	ENST00000380152.3:c.2278T>G	p.Leu760Val	p.L760V	ENST00000380152		760	Tta/Gta	11/27	1	2	FACETS	1	0.989	1	1	0.997	1	CLONAL	2	TRUE	1	0.314756906203688	2		896	1322	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912749	32912749	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	308	817	0	ENST00000380152.3:c.4257A>C	p.Lys1419Asn	p.K1419N	ENST00000380152		1419	aaA/aaC	11/27	1	2	FACETS	0.98	0.925	1	1	0.996	1	CLONAL	2	TRUE	1	0.314756906203688	2		817	999	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912917	32912917	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	191	859	1	ENST00000380152.3:c.4425G>T	p.Met1475Ile	p.M1475I	ENST00000380152		1475	atG/atT	11/27	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.314756906203688	2		860	1183	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914391	32914391	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	402	938	0	ENST00000380152.3:c.5899A>C	p.Lys1967Gln	p.K1967Q	ENST00000380152		1967	Aag/Cag	11/27	1	2	FACETS	1	0.984	1	1	0.997	1	CLONAL	2	TRUE	1	0.314756906203688	2		938	1189	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945129	32945129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80359104	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	151	591	0	ENST00000380152.3:c.8524C>T	p.Arg2842Cys	p.R2842C	ENST00000380152		2842	Cgc/Tgc	20/27	1	2	FACETS	0.919	0.839	1	0.919	0.839	1	CLONAL	1	TRUE	1	0.314756906203688	2		591	1044	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73333960	73333960	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	69	287	1	ENST00000377767.4:c.2850G>T	p.Lys950Asn	p.K950N	ENST00000377767	NM_014953.3	950	aaG/aaT	21/21	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.314756906203688	2		288	409	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346314	73346314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs575448022	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	158	337	1	ENST00000377767.4:c.1486G>A	p.Glu496Lys	p.E496K	ENST00000377767	NM_014953.3	496	Gaa/Aaa	10/21	1	2	FACETS	1	0.923	1	1	0.992	1	CLONAL	2	TRUE	1	0.314756906203688	2		338	502	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514441	103514441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	98	358	1	ENST00000355739.4:c.942G>A	p.Met314Ile	p.M314I	ENST00000355739	NM_000123.3	314	atG/atA	8/15	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.314756906203688	2		359	569	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986761	36986761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1230966519	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	13	12	0	ENST00000354822.5:c.928G>A	p.Ala310Thr	p.A310T	ENST00000354822	NM_001079668.2	310	Gcc/Acc	3/3	1	2	FACETS	0.826	0.609	1	1	0.898	1	CLONAL	2	TRUE	1	0.314756906203688	2		12	50	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987047	36987047	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	103	318	0	ENST00000354822.5:c.642G>T	p.Lys214Asn	p.K214N	ENST00000354822	NM_001079668.2	214	aaG/aaT	3/3	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.314756906203688	2		318	545	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041375	42041375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764277967	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1417	288	925	1	ENST00000219905.7:c.5570C>T	p.Ser1857Leu	p.S1857L	ENST00000219905	NM_001164273.1	1857	tCg/tTg	17/24	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.314756906203688	2		926	1705	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046767	42046767	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	386	600	0	ENST00000219905.7:c.7139+2T>C		p.X2380_splice	ENST00000219905	NM_001164273.1	2380			1	2	FACETS	1	0.974	1	1	0.997	1	CLONAL	2	TRUE	1	0.314756906203688	2		600	1183	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42057102	42057102	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	604	816	0	ENST00000219905.7:c.7763A>G	p.Asn2588Ser	p.N2588S	ENST00000219905	NM_001164273.1	2588	aAc/aGc	23/24	1	2	FACETS	1	0.991	1	1	0.998	1	CLONAL	2	TRUE	1	0.314756906203688	2		816	1750	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727423	66727423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1049040928	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	186	551	1	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	0.314756906203688	2		552	1162	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727429	66727429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	221	562	4	ENST00000307102.5:c.145C>T	p.Arg49Cys	p.R49C	ENST00000307102	NM_002755.3	49	Cgc/Tgc	2/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.314756906203688	2		566	1189	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482767	67482767	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	406	564	0	ENST00000327367.4:c.1171A>C	p.Ser391Arg	p.S391R	ENST00000327367	NM_005902.3	391	Agt/Cgt	9/9	1	2	FACETS	1	0.985	1	1	0.997	1	CLONAL	2	TRUE	1	0.314756906203688	2		564	1193	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678471	88678471	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	157	598	2	ENST00000360948.2:c.1065G>T	p.Glu355Asp	p.E355D	ENST00000360948	NM_001012338.2	355	gaG/gaT	9/19	1	2	FACETS	0.872	0.797	0.95	0.872	0.797	0.95	CLONAL	1	TRUE	1	0.314756906203688	2		600	1144	SUCCESS
BLM	641	MSKCC	GRCh37	15	91337547	91337547	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	193	273	0	ENST00000355112.3:c.3170A>T	p.Lys1057Ile	p.K1057I	ENST00000355112	NM_000057.2	1057	aAa/aTa	16/22	1	2	FACETS	1	0.985	1	1	0.994	1	CLONAL	2	TRUE	1	0.314756906203688	2		273	513	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358483	91358483	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	114	482	0	ENST00000355112.3:c.4228C>A	p.Leu1410Ile	p.L1410I	ENST00000355112	NM_000057.2	1410	Ctt/Att	22/22	1	2	FACETS	0.683	0.613	0.757	0.683	0.613	0.757	SUBCLONAL	1	TRUE	1	0.314756906203688	2		482	1061	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250799	99250799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	127	351	0	ENST00000268035.6:c.103C>A	p.Pro35Thr	p.P35T	ENST00000268035	NM_000875.3	35	Cca/Aca	2/21	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.314756906203688	2		351	748	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251258	99251258	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	162	487	0	ENST00000268035.6:c.562G>A	p.Glu188Lys	p.E188K	ENST00000268035	NM_000875.3	188	Gag/Aag	2/21	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.314756906203688	2		487	1012	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459939	99459939	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771230491	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	212	543	2	ENST00000268035.6:c.2035G>A	p.Asp679Asn	p.D679N	ENST00000268035	NM_000875.3	679	Gac/Aac	10/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.314756906203688	2		545	1180	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778911	3778911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753688167	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	105	324	0	ENST00000262367.5:c.6137C>T	p.Ala2046Val	p.A2046V	ENST00000262367	NM_004380.2	2046	gCg/gTg	31/31	1	2	FACETS	0.991	0.889	1	0.991	0.889	1	CLONAL	1	TRUE	1	0.314756906203688	2		324	673	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828705	3828705	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	121	406	1	ENST00000262367.5:c.1937G>A	p.Ser646Asn	p.S646N	ENST00000262367	NM_004380.2	646	aGc/aAc	9/31	1	2	FACETS	0.924	0.835	1	0.924	0.835	1	CLONAL	1	TRUE	1	0.314756906203688	2		407	832	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858694	9858694	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	190	599	0	ENST00000330684.3:c.2707A>C	p.Asn903His	p.N903H	ENST00000330684	NM_001134407.1	903	Aac/Cac	13/13	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.314756906203688	2		599	1204	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348996	11348996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750257680	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	106	283	0	ENST00000332029.2:c.340G>A	p.Ala114Thr	p.A114T	ENST00000332029	NM_003745.1	114	Gcc/Acc	2/2	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.314756906203688	2		283	657	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14022025	14022025	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768217559	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	105	430	0	ENST00000311895.7:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000311895	NM_005236.2	242	tGc/tAc	4/11	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.314756906203688	2		430	667	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14031681	14031681	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766395322	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	264	419	2	ENST00000311895.7:c.1870C>T	p.Arg624Trp	p.R624W	ENST00000311895	NM_005236.2	624	Cgg/Tgg	9/11	1	2	FACETS	1	0.985	1	1	0.996	1	CLONAL	2	TRUE	1	0.314756906203688	2		421	741	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23640973	23640973	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	102	389	0	ENST00000261584.4:c.2502T>G	p.His834Gln	p.H834Q	ENST00000261584	NM_024675.3	834	caT/caG	5/13	1	2	FACETS	0.946	0.847	1	0.946	0.847	1	CLONAL	1	TRUE	1	0.314756906203688	2		389	685	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646884	23646884	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	73	393	1	ENST00000261584.4:c.983C>A	p.Ser328Tyr	p.S328Y	ENST00000261584	NM_024675.3	328	tCt/tAt	4/13	1	2	FACETS	0.69	0.603	0.784	0.69	0.603	0.784	SUBCLONAL	1	TRUE	1	0.314756906203688	2		394	672	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133269	30133269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778826879	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1279	715	850	2	ENST00000263025.4:c.229G>A	p.Glu77Lys	p.E77K	ENST00000263025	NM_002746.2	77	Gaa/Aaa	2/9	1	2	FACETS	1	0.994	1	1	0.998	1	CLONAL	2	TRUE	1	0.314756906203688	2		852	1994	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56862974	56862974	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	607	769	1	ENST00000308159.5:c.880C>T	p.Arg294Ter	p.R294*	ENST00000308159	NM_014669.4	294	Cga/Tga	9/22	1	2	FACETS	1	0.994	1	1	0.998	1	CLONAL	2	TRUE	1	0.314756906203688	2		770	1671	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864491	56864491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746856372	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1545	359	911	2	ENST00000308159.5:c.979C>T	p.Arg327Cys	p.R327C	ENST00000308159	NM_014669.4	327	Cgc/Tgc	10/22	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.314756906203688	2		913	1904	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644754	67644754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779609208	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	224	582	1	ENST00000264010.4:c.19G>A	p.Glu7Lys	p.E7K	ENST00000264010	NM_006565.3	7	Gaa/Aaa	3/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.314756906203688	2		583	1322	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645512	67645512	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	54	217	0	ENST00000264010.4:c.777G>T	p.Lys259Asn	p.K259N	ENST00000264010	NM_006565.3	259	aaG/aaT	3/12	1	2	FACETS	0.983	0.844	1	0.983	0.844	1	CLONAL	1	TRUE	1	0.314756906203688	2		217	349	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655380	67655380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	151	511	2	ENST00000264010.4:c.1243C>T	p.Arg415Trp	p.R415W	ENST00000264010	NM_006565.3	415	Cgg/Tgg	7/12	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.314756906203688	2		513	929	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844172	68844172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	206	572	2	ENST00000261769.5:c.760G>A	p.Asp254Asn	p.D254N	ENST00000261769	NM_004360.3	254	Gat/Aat	6/16	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.314756906203688	2		574	1263	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855985	68855985	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780759537	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	229	563	1	ENST00000261769.5:c.1793G>A	p.Arg598Gln	p.R598Q	ENST00000261769	NM_004360.3	598	cGa/cAa	12/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.314756906203688	2		564	1279	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827941	72827941	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1781	364	956	0	ENST00000268489.5:c.8640G>T	p.Met2880Ile	p.M2880I	ENST00000268489	NM_006885.3	2880	atG/atT	9/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.314756906203688	2		956	2145	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829797	72829797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs953863150	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1922	109	956	1	ENST00000268489.5:c.6784G>A	p.Asp2262Asn	p.D2262N	ENST00000268489	NM_006885.3	2262	Gat/Aat	9/10	1	2	FACETS	0.341	0.304	0.38	0.341	0.304	0.38	SUBCLONAL	1	TRUE	1	0.314756906203688	2		957	2031	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845938	72845938	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	521	617	0	ENST00000268489.5:c.3530-1G>A		p.X1177_splice	ENST00000268489	NM_006885.3	1177			1	2	FACETS	1	0.993	1	1	0.998	1	CLONAL	2	TRUE	1	0.314756906203688	2		617	1439	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991599	72991599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1543	413	837	0	ENST00000268489.5:c.2446G>A	p.Ala816Thr	p.A816T	ENST00000268489	NM_006885.3	816	Gcc/Acc	2/10	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.314756906203688	2		837	1956	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993128	72993128	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142256050	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1764	442	951	2	ENST00000268489.5:c.917G>A	p.Arg306Gln	p.R306Q	ENST00000268489	NM_006885.3	306	cGa/cAa	2/10	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.314756906203688	2		953	2206	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993181	72993181	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1986	105	926	0	ENST00000268489.5:c.864A>C	p.Lys288Asn	p.K288N	ENST00000268489	NM_006885.3	288	aaA/aaC	2/10	1	2	FACETS	0.319	0.284	0.357	0.319	0.284	0.357	SUBCLONAL	1	TRUE	1	0.314756906203688	2		926	2091	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81904458	81904458	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	303	619	0	ENST00000359376.3:c.566A>G	p.Glu189Gly	p.E189G	ENST00000359376	NM_002661.3	189	gAa/gGa	7/33	1	2	FACETS	1	0.982	1	1	0.996	1	CLONAL	2	TRUE	1	0.314756906203688	2		619	883	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934326	81934326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745999784	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1449	336	766	0	ENST00000359376.3:c.1303G>A	p.Glu435Lys	p.E435K	ENST00000359376	NM_002661.3	435	Gag/Aag	14/33	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.314756906203688	2		766	1785	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944279	81944279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747373917	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1419	327	829	1	ENST00000359376.3:c.1888C>T	p.Arg630Trp	p.R630W	ENST00000359376	NM_002661.3	630	Cgg/Tgg	18/33	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.314756906203688	2		830	1746	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81960742	81960742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768839912	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	593	901	3	ENST00000359376.3:c.2473G>A	p.Glu825Lys	p.E825K	ENST00000359376	NM_002661.3	825	Gag/Aag	23/33	1	2	FACETS	1	0.994	1	1	0.998	1	CLONAL	2	TRUE	1	0.314756906203688	2		904	1598	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349799	89349799	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1823	354	1027	0	ENST00000301030.4:c.3151G>T	p.Glu1051Ter	p.E1051*	ENST00000301030	NM_001256183.1	1051	Gaa/Taa	9/13	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.314756906203688	2		1027	2177	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805074	89805074	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs74977201	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	253	548	1	ENST00000389301.3:c.4303G>A	p.Ala1435Thr	p.A1435T	ENST00000389301	NM_000135.2	1435	Gcc/Acc	43/43	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.314756906203688	2		549	1246	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976611	7976611	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1445761119	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	228	517	0	ENST00000319144.4:c.1781A>G	p.Asn594Ser	p.N594S	ENST00000319144	NM_001139.2	594	aAc/aGc	14/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.314756906203688	2		517	1349	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028618	12028618	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	148	440	0	ENST00000353533.5:c.821G>T	p.Arg274Ile	p.R274I	ENST00000353533	NM_003010.3	274	aGa/aTa	8/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.314756906203688	2		440	850	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935669	15935669	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	189	446	1	ENST00000268712.3:c.7264C>T	p.Arg2422Ter	p.R2422*	ENST00000268712	NM_006311.3	2422	Cga/Tga	46/46	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.314756906203688	2		447	1120	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942842	15942842	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	400	549	0	ENST00000268712.3:c.6860C>T	p.Ser2287Phe	p.S2287F	ENST00000268712	NM_006311.3	2287	tCc/tTc	44/46	1	2	FACETS	1	0.977	1	1	0.997	1	CLONAL	2	TRUE	1	0.314756906203688	2		549	1219	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964748	15964748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	146	496	0	ENST00000268712.3:c.5848C>T	p.Arg1950Cys	p.R1950C	ENST00000268712	NM_006311.3	1950	Cgt/Tgt	37/46	1	2	FACETS	0.867	0.79	0.948	0.867	0.79	0.948	CLONAL	1	TRUE	1	0.314756906203688	2		496	1070	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965566	15965566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554764533	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	94	326	0	ENST00000268712.3:c.5240G>A	p.Arg1747Gln	p.R1747Q	ENST00000268712	NM_006311.3	1747	cGa/cAa	36/46	1	2	FACETS	0.965	0.86	1	0.965	0.86	1	CLONAL	1	TRUE	1	0.314756906203688	2		326	619	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012192	16012192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	209	409	0	ENST00000268712.3:c.2090C>T	p.Ser697Phe	p.S697F	ENST00000268712	NM_006311.3	697	tCt/tTt	19/46	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	1	0.314756906203688	2		409	553	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049699	16049699	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	157	554	0	ENST00000268712.3:c.1073G>T	p.Arg358Ile	p.R358I	ENST00000268712	NM_006311.3	358	aGa/aTa	10/46	1	2	FACETS	0.952	0.871	1	0.952	0.871	1	CLONAL	1	TRUE	1	0.314756906203688	2		554	1048	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490319	29490319	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500244	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	229	468	1	ENST00000356175.3:c.404G>A	p.Arg135Gln	p.R135Q	ENST00000356175	NM_000267.3	135	cGg/cAg	4/57	1	2	FACETS	0.947	0.886	1	1	0.994	1	CLONAL	2	TRUE	1	0.314756906203688	2		469	768	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687601	29687601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	135	526	0	ENST00000356175.3:c.8194G>A	p.Glu2732Lys	p.E2732K	ENST00000356175	NM_000267.3	2732	Gaa/Aaa	56/57	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.314756906203688	2		526	810	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325737	30325737	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	131	240	0	ENST00000322652.5:c.1935G>T	p.Gln645His	p.Q645H	ENST00000322652	NM_015355.2	645	caG/caT	16/16	1	2	FACETS	1	0.965	1	1	0.991	1	CLONAL	2	TRUE	1	0.314756906203688	2		240	379	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33433413	33433413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80116829	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	168	534	0	ENST00000345365.6:c.568G>A	p.Ala190Thr	p.A190T	ENST00000345365	NM_002878.3	190	Gcc/Acc	6/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.314756906203688	2		534	1018	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687328	37687328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766205887	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	253	516	2	ENST00000447079.4:c.4232C>T	p.Ala1411Val	p.A1411V	ENST00000447079	NM_015083.1	1411	gCg/gTg	14/14	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.314756906203688	2		518	1262	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38506092	38506092	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	457	581	1	ENST00000254066.5:c.384G>T	p.Lys128Asn	p.K128N	ENST00000254066	NM_000964.3	128	aaG/aaT	4/9	1	2	FACETS	1	0.976	1	1	0.997	1	CLONAL	2	TRUE	1	0.314756906203688	2		582	1404	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359740	40359740	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1296	241	739	2	ENST00000293328.3:c.1913G>T	p.Arg638Ile	p.R638I	ENST00000293328	NM_012448.3	638	aGa/aTa	16/19	1	2	FACETS	0.996	0.928	1	0.996	0.928	1	CLONAL	1	TRUE	1	0.314756906203688	2		741	1537	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475047	40475047	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1555563854	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1392	270	715	0	ENST00000264657.5:c.1863C>A	p.Phe621Leu	p.F621L	ENST00000264657	NM_139276.2	621	ttC/ttA	20/24	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.314756906203688	2		715	1662	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696421	47696421	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	235	463	0	ENST00000347630.2:c.402G>T	p.Lys134Asn	p.K134N	ENST00000347630	NM_001007230.1	134	aaG/aaT	6/11	1	2	FACETS	1	0.966	1	1	0.995	1	CLONAL	2	TRUE	1	0.314756906203688	2		463	714	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696745	47696745	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	78	254	0	ENST00000347630.2:c.203G>A	p.Cys68Tyr	p.C68Y	ENST00000347630	NM_001007230.1	68	tGt/tAt	5/11	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.314756906203688	2		254	461	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435927	56435927	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767761157	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	294	401	2	ENST00000407977.2:c.1210C>T	p.Arg404Cys	p.R404C	ENST00000407977		404	Cgc/Tgc	9/10	1	2	FACETS	1	0.982	1	1	0.996	1	CLONAL	2	TRUE	1	0.314756906203688	2		403	857	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59793412	59793412	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852986	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	94	393	0	ENST00000259008.2:c.2392C>T	p.Arg798Ter	p.R798*	ENST00000259008	NM_032043.2	798	Cga/Tga	17/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.314756906203688	2		393	533	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821940	59821940	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	95	351	0	ENST00000259008.2:c.2110T>G	p.Leu704Val	p.L704V	ENST00000259008	NM_032043.2	704	Tta/Gta	15/20	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.314756906203688	2		351	590	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007212	62007212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	149	534	0	ENST00000392795.3:c.470C>T	p.Thr157Met	p.T157M	ENST00000392795	NM_001039933.1	157	aCg/aTg	4/6	1	2	FACETS	0.967	0.883	1	0.967	0.883	1	CLONAL	1	TRUE	1	0.314756906203688	2		534	979	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66521949	66521949	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	131	496	0	ENST00000358598.2:c.604G>T	p.Glu202Ter	p.E202*	ENST00000358598	NM_212471.2	202	Gaa/Taa	7/11	1	2	FACETS	0.999	0.907	1	0.999	0.907	1	CLONAL	1	TRUE	1	0.314756906203688	2		496	833	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936305	78936305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1238	276	674	0	ENST00000306801.3:c.3737C>T	p.Ser1246Leu	p.S1246L	ENST00000306801	NM_020761.2	1246	tCg/tTg	32/34	0.308708104335134	2	FACETS	1	0.985	1	0.579	0.542	0.617	CLONAL	1	TRUE	0	0.314756906203688	2		674	1514	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743013	743013	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	119	491	0	ENST00000314574.4:c.965A>C	p.Gln322Pro	p.Q322P	ENST00000314574	NM_005433.3	322	cAg/cCg	8/12	1	2	FACETS	0.961	0.867	1	0.961	0.867	1	CLONAL	1	TRUE	1	0.314756906203688	2		491	787	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609382	39609382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1463795009	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	295	537	0	ENST00000262039.4:c.1684G>A	p.Glu562Lys	p.E562K	ENST00000262039	NM_002647.2	562	Gaa/Aaa	15/25	1	2	FACETS	0.989	0.932	1	1	0.996	1	CLONAL	2	TRUE	1	0.314756906203688	2		537	948	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617746	39617746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	212	455	1	ENST00000262039.4:c.1930G>A	p.Asp644Asn	p.D644N	ENST00000262039	NM_002647.2	644	Gat/Aat	17/25	1	2	FACETS	1	0.965	1	1	0.994	1	CLONAL	2	TRUE	1	0.314756906203688	2		456	641	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575114	48575114	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	163	490	0	ENST00000342988.3:c.308A>C	p.Asp103Ala	p.D103A	ENST00000342988	NM_005359.5	103	gAt/gCt	3/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.314756906203688	2		490	866	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56377265	56377265	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	394	350	2	ENST00000348428.3:c.886C>T	p.Arg296Ter	p.R296*	ENST00000348428	NM_006785.3	296	Cga/Tga	6/17	1	2	FACETS	0.953	0.905	1	1	0.996	1	CLONAL	2	TRUE	1	0.314756906203688	2		352	1314	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56412976	56412976	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1169	184	763	0	ENST00000348428.3:c.1990C>T	p.Pro664Ser	p.P664S	ENST00000348428	NM_006785.3	664	Ccc/Tcc	16/17	1	2	FACETS	0.864	0.795	0.936	0.864	0.795	0.936	CLONAL	1	TRUE	1	0.314756906203688	2		763	1353	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619834	1619834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761441337	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1399	351	523	1	ENST00000344749.5:c.1112G>A	p.Arg371Gln	p.R371Q	ENST00000344749	NM_001136139.2	371	cGa/cAa	14/19	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.314756906203688	2		524	1750	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2208961	2208961	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	388	479	0	ENST00000398665.3:c.991A>C	p.Asn331His	p.N331H	ENST00000398665	NM_032482.2	331	Aac/Cac	12/28	1	2	FACETS	1	0.979	1	1	0.997	1	CLONAL	2	TRUE	1	0.314756906203688	2		479	1173	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216639	2216639	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	342	416	0	ENST00000398665.3:c.2283G>T	p.Glu761Asp	p.E761D	ENST00000398665	NM_032482.2	761	gaG/gaT	20/28	1	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	1	0.314756906203688	2		416	881	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099307	4099307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758031424	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	232	573	0	ENST00000262948.5:c.811G>A	p.Asp271Asn	p.D271N	ENST00000262948	NM_030662.3	271	Gac/Aac	7/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.314756906203688	2		573	1179	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7152846	7152846	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763692568	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	217	552	0	ENST00000302850.5:c.2122G>A	p.Glu708Lys	p.E708K	ENST00000302850	NM_000208.2	708	Gaa/Aaa	10/22	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.314756906203688	2		552	1164	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10244947	10244947	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	259	637	0	ENST00000340748.4:c.4762A>G	p.Ile1588Val	p.I1588V	ENST00000340748		1588	Att/Gtt	39/40	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.314756906203688	2		637	1398	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247836	10247836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	501	498	3	ENST00000340748.4:c.4366C>T	p.Arg1456Trp	p.R1456W	ENST00000340748		1456	Cgg/Tgg	36/40	1	2	FACETS	1	0.991	1	1	0.997	1	CLONAL	2	TRUE	1	0.314756906203688	2		501	1420	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101937	11101937	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	440	627	0	ENST00000358026.2:c.1357A>G	p.Thr453Ala	p.T453A	ENST00000358026	NM_001128849.1	453	Act/Gct	8/36	1	2	FACETS	1	0.989	1	1	0.997	1	CLONAL	2	TRUE	1	0.314756906203688	2		627	1255	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15365013	15365013	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1453756538	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	193	556	1	ENST00000263377.2:c.2108C>T	p.Ser703Leu	p.S703L	ENST00000263377	NM_058243.2	703	tCg/tTg	11/20	1	2	FACETS	0.962	0.888	1	0.962	0.888	1	CLONAL	1	TRUE	1	0.314756906203688	2		557	1275	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792263	33792263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	263	652	0	ENST00000498907.2:c.1058C>T	p.Ala353Val	p.A353V	ENST00000498907	NM_004364.3	353	gCc/gTc	1/1	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.314756906203688	2		652	1410	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765801	41765801	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	93	224	0	ENST00000301178.4:c.2677G>A	p.Gly893Ser	p.G893S	ENST00000301178	NM_021913.4	893	Ggt/Agt	20/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.314756906203688	2		224	453	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797777	42797777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778206	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	109	504	0	ENST00000575354.2:c.3829C>T	p.Arg1277Cys	p.R1277C	ENST00000575354	NM_015125.3	1277	Cgc/Tgc	16/20	1	2	FACETS	0.731	0.656	0.812	0.731	0.656	0.812	SUBCLONAL	1	TRUE	1	0.314756906203688	2		504	947	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856532	45856532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201165309	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	418	570	1	ENST00000391945.4:c.1726G>A	p.Glu576Lys	p.E576K	ENST00000391945	NM_000400.3	576	Gaa/Aaa	18/23	1	2	FACETS	1	0.981	1	1	0.997	1	CLONAL	2	TRUE	1	0.314756906203688	2		571	1256	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45864886	45864886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200043231	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1349	271	677	2	ENST00000391945.4:c.1133G>A	p.Arg378His	p.R378H	ENST00000391945	NM_000400.3	378	cGc/cAc	12/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.314756906203688	2		679	1620	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520140	9520140	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs766724193	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	180	502	0	ENST00000353224.5:c.2129T>C	p.Val710Ala	p.V710A	ENST00000353224	NM_177990.2	710	gTc/gCc	10/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.314756906203688	2		502	1046	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022317	31022317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778606251	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	193	526	1	ENST00000375687.4:c.1802C>T	p.Thr601Met	p.T601M	ENST00000375687	NM_015338.5	601	aCg/aTg	13/13	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.314756906203688	2		527	1039	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022796	31022796	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146052718	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	264	398	0	ENST00000375687.4:c.2281G>A	p.Ala761Thr	p.A761T	ENST00000375687	NM_015338.5	761	Gcc/Acc	13/13	1	2	FACETS	1	0.98	1	1	0.995	1	CLONAL	2	TRUE	1	0.314756906203688	2		398	768	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023162	31023162	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	462	462	1	ENST00000375687.4:c.2647G>T	p.Glu883Ter	p.E883*	ENST00000375687	NM_015338.5	883	Gaa/Taa	13/13	1	2	FACETS	1	0.985	1	1	0.998	1	CLONAL	3	TRUE	1	0.314756906203688	2		463	933	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395596	31395596	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	187	427	0	ENST00000328111.2:c.2449G>A	p.Asp817Asn	p.D817N	ENST00000328111	NM_006892.3	817	Gac/Aac	23/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.314756906203688	2		427	1006	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39706225	39706225	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	145	401	0	ENST00000361337.2:c.283C>T	p.Arg95Ter	p.R95*	ENST00000361337	NM_003286.2	95	Cga/Tga	5/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.314756906203688	2		401	824	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710547	40710547	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	295	358	0	ENST00000373198.4:c.4304A>G	p.Asn1435Ser	p.N1435S	ENST00000373198	NM_133170.3	1435	aAc/aGc	31/32	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.314756906203688	2		358	796	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710620	40710620	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	138	319	0	ENST00000373198.4:c.4231T>G	p.Cys1411Gly	p.C1411G	ENST00000373198	NM_133170.3	1411	Tgc/Ggc	31/32	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.314756906203688	2		319	736	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743940	40743940	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	143	314	0	ENST00000373198.4:c.3055T>C	p.Tyr1019His	p.Y1019H	ENST00000373198	NM_133170.3	1019	Tac/Cac	23/32	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.314756906203688	2		314	788	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980912	40980912	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	99	325	1	ENST00000373198.4:c.1574C>T	p.Ala525Val	p.A525V	ENST00000373198	NM_133170.3	525	gCt/gTt	10/32	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.314756906203688	2		326	595	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281787	46281787	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1321	264	775	0	ENST00000371998.3:c.4234A>T	p.Met1412Leu	p.M1412L	ENST00000371998		1412	Atg/Ttg	22/23	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.314756906203688	2		775	1585	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945300	54945300	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	61	181	0	ENST00000312783.6:c.1126G>T	p.Glu376Ter	p.E376*	ENST00000312783	NM_198436.1	376	Gaa/Taa	10/10	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.314756906203688	2		181	352	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39762947	39762947	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	228	441	0	ENST00000288319.7:c.889G>T	p.Gly297Ter	p.G297*	ENST00000288319	NM_182918.3	297	Gga/Tga	9/10	1	2	FACETS	1	0.967	1	1	0.995	1	CLONAL	2	TRUE	1	0.314756906203688	2		441	690	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860345	42860345	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1385130606	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	239	591	0	ENST00000398585.3:c.532G>A	p.Gly178Ser	p.G178S	ENST00000398585	NM_001135099.1	178	Ggc/Agc	5/14	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.314756906203688	2		591	1376	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656860	45656860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61737085	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	168	428	0	ENST00000407780.3:c.296G>A	p.Arg99His	p.R99H	ENST00000407780	NM_001283052.1	99	cGc/cAc	3/7	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.314756906203688	2		428	1042	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22142665	22142665	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	66	342	0	ENST00000215832.6:c.737C>T	p.Ser246Phe	p.S246F	ENST00000215832	NM_002745.4	246	tCc/tTc	6/9	1	2	FACETS	0.861	0.749	0.982	0.861	0.749	0.982	CLONAL	1	TRUE	1	0.314756906203688	2		342	487	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22153414	22153414	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	341	420	0	ENST00000215832.6:c.496T>C	p.Cys166Arg	p.C166R	ENST00000215832	NM_002745.4	166	Tgt/Cgt	4/9	1	2	FACETS	1	0.991	1	1	0.997	1	CLONAL	2	TRUE	1	0.314756906203688	2		420	906	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121280	29121280	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs750393263	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	222	607	1	ENST00000328354.6:c.395G>T	p.Arg132Ile	p.R132I	ENST00000328354	NM_007194.3	132	aGa/aTa	3/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.314756906203688	2		608	1190	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30061039	30061039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754093587	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	116	412	0	ENST00000338641.4:c.871C>T	p.Arg291Cys	p.R291C	ENST00000338641	NM_000268.3	291	Cgt/Tgt	9/16	1	2	FACETS	0.902	0.813	0.997	0.902	0.813	0.997	CLONAL	1	TRUE	1	0.314756906203688	2		412	817	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545061	41545061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs544338126	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	157	475	1	ENST00000263253.7:c.2261G>A	p.Arg754His	p.R754H	ENST00000263253	NM_001429.3	754	cGt/cAt	13/31	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.314756906203688	2		476	948	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553191	41553191	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	151	458	0	ENST00000263253.7:c.3280A>C	p.Lys1094Gln	p.K1094Q	ENST00000263253	NM_001429.3	1094	Aag/Cag	18/31	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.314756906203688	2		458	845	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317467	1317467	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	275	729	2	ENST00000400841.2:c.598C>A	p.Pro200Thr	p.P200T	ENST00000400841		200	Cca/Aca	5/6	1	1	FACETS	0.993	0.93	1	0.993	0.93	1	CLONAL	1	TRUE	0	0.314756906203688	1		731	1483	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918987	76918987	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1569536694	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	171	301	0	ENST00000373344.5:c.4004G>T	p.Arg1335Ile	p.R1335I	ENST00000373344	NM_000489.3	1335	aGa/aTa	12/35	1	1	FACETS	0.901	0.835	0.968	1	0.992	1	CLONAL	2	TRUE	0	0.314756906203688	1		301	508	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920233	76920233	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	165	266	0	ENST00000373344.5:c.3844G>A	p.Ala1282Thr	p.A1282T	ENST00000373344	NM_000489.3	1282	Gcc/Acc	11/35	1	1	FACETS	0.812	0.75	0.875	1	0.991	1	CLONAL	2	TRUE	0	0.314756906203688	1		266	544	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939759	76939759	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	296	274	0	ENST00000373344.5:c.989A>C	p.Lys330Thr	p.K330T	ENST00000373344	NM_000489.3	330	aAa/aCa	9/35	1	1	FACETS	0.93	0.894	0.965	1	0.997	1	CLONAL	4	TRUE	0	0.314756906203688	1		274	426	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611255	100611255	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	121	221	0	ENST00000308731.7:c.1351A>C	p.Asn451His	p.N451H	ENST00000308731	NM_000061.2	451	Aat/Cat	15/19	1	1	FACETS	0.81	0.738	0.884	1	0.987	1	CLONAL	2	TRUE	0	0.314756906203688	1		221	400	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611921	100611921	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	169	311	0	ENST00000308731.7:c.1200G>T	p.Lys400Asn	p.K400N	ENST00000308731	NM_000061.2	400	aaG/aaT	14/19	1	1	FACETS	0.92	0.852	0.988	1	0.992	1	CLONAL	2	TRUE	0	0.314756906203688	1		311	492	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630236	100630236	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs128620187	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	347	314	3	ENST00000308731.7:c.37C>T	p.Arg13Ter	p.R13*	ENST00000308731	NM_000061.2	13	Cga/Tga	2/19	1	1	FACETS	0.895	0.861	0.928	1	0.997	1	CLONAL	4	TRUE	0	0.314756906203688	1		317	519	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182863	123182863	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	162	239	0	ENST00000218089.9:c.828A>C	p.Glu276Asp	p.E276D	ENST00000218089	NM_001042749.1	276	gaA/gaC	10/35	1	1	FACETS	0.933	0.863	1	1	0.992	1	CLONAL	2	TRUE	0	0.314756906203688	1		239	465	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200242	123200242	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	311	232	0	ENST00000218089.9:c.2221A>C	p.Ile741Leu	p.I741L	ENST00000218089	NM_001042749.1	741	Atc/Ctc	23/35	1	1	FACETS	0.957	0.922	0.991	1	0.997	1	CLONAL	4	TRUE	0	0.314756906203688	1		232	435	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123499637	123499637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	33	276	1	ENST00000371139.4:c.164G>A	p.Arg55Gln	p.R55Q	ENST00000371139	NM_001114937.2	55	cGa/cAa	2/4	1	1	FACETS	0.411	0.334	0.497	0.411	0.334	0.497	SUBCLONAL	1	TRUE	0	0.314756906203688	1		277	430	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618715	37618716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1408	282	663	0	ENST00000447079.4:c.397dup	p.Ser133LysfsTer24	p.S133Kfs*24	ENST00000447079	NM_015083.1	131	gaa/gAaa	1/14	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.314756906203688	2		663	1690	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286951	33286952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	277	404	0	ENST00000374542.5:c.1985dup	p.Ile663AspfsTer19	p.I663Dfs*19	ENST00000374542	NM_001141970.1	662	aag/aaAg	7/8	1	2	FACETS	0.965	0.908	1	1	0.995	1	CLONAL	2	TRUE	1	0.314756906203688	2		404	912	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	422258	422259	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0007319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	122	485	0	ENST00000399788.2:c.2999dup	p.Ala1001GlyfsTer7	p.A1001Gfs*7	ENST00000399788	NM_001042603.1	1000	aag/aaAg	20/28	1	2	FACETS	0.979	0.885	1	0.979	0.885	1	CLONAL	1	TRUE	1	0.314756906203688	2		485	792	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0007332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	15	397	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.536	0.395	0.704	0.536	0.395	0.704	SUBCLONAL	1	FALSE	1	0.391144621052349	2		397	143	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0007332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	78	1413	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.278864217225918	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	0	0.391144621052349	1		1413	249	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692920	89692921	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs398123323	NA	P-0007335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	81	206	0	ENST00000371953.3:c.405dup	p.Cys136MetfsTer44	p.C136Mfs*44	ENST00000371953	NM_000314.4	135	ata/atAa	5/9	0.3	3	FACETS	1	0.975	1	0.708	0.626	0.796	CLONAL	1	TRUE	1	0.26	3		206	497	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249717	110249717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	111	337	0	ENST00000374672.4:c.958G>A	p.Gly320Ser	p.G320S	ENST00000374672	NM_004235.4	320	Ggt/Agt	3/5	0.3	3	FACETS	0.917	0.828	1	0.917	0.828	1	CLONAL	2	TRUE	1	0.26	3		337	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs587781702	NA	P-0007335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	123	428	0	ENST00000269305.4:c.920-1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.264184508804263	2	FACETS	0.829	0.752	0.909	0.829	0.752	0.909	CLONAL	2	TRUE	0	0.26	2		428	571	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0007360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	60	285	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.962	0.829	1	0.962	0.829	1	CLONAL	1	TRUE	1	0.21	2		285	594	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477854	140477854	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	73	442	0	ENST00000288602.6:c.1454T>G	p.Leu485Trp	p.L485W	ENST00000288602	NM_004333.4	485	tTg/tGg	12/18	1	2	FACETS	0.667	0.581	0.759	0.667	0.581	0.759	SUBCLONAL	1	TRUE	1	0.21	2		442	1043	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350985	89350985	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1711	122	724	0	ENST00000301030.4:c.1965A>C	p.Lys655Asn	p.K655N	ENST00000301030	NM_001256183.1	655	aaA/aaC	9/13	NA	2	FACETS	0.634	0.57	0.702			1	INDETERMINATE	1	TRUE	NA	0.21	2		724	1833	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849290	76849290	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	84	530	0	ENST00000373344.5:c.5986A>G	p.Ser1996Gly	p.S1996G	ENST00000373344	NM_000489.3	1996	Agc/Ggc	26/35	0.256083815168579	1	FACETS	0.554	0.487	0.626	0.554	0.487	0.626	SUBCLONAL	1	TRUE	0	0.21	1		530	1292	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573632	48573633	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	39	232	0	ENST00000342988.3:c.217dup	p.Thr73AsnfsTer31	p.T73Nfs*31	ENST00000342988	NM_005359.5	72	-/A	2/12	1	2	FACETS	0.662	0.548	0.79	0.662	0.548	0.79	SUBCLONAL	1	TRUE	1	0.21	2		232	561	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637632	52637641	+	protein_altering_variant	In_Frame_Del	DEL	GTGGTATAGC	GTGGTATAGC	ATGTTTT	novel	NA	P-0007360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	71	526	0	ENST00000394830.3:c.2675_2684delinsAAAACAT	p.Ser892_Thr895delinsLysAsnIle	p.S892_T895delinsKNI	ENST00000394830	NM_018313.4	892	aGCTATACCACa/aAAAACATa	18/30	1	2	FACETS	0.563	0.489	0.643	0.563	0.489	0.643	SUBCLONAL	1	TRUE	1	0.21	2		526	1202	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0007384-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	455	526	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.446808598920612	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.446808598920612	2		526	1011	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250196	110250196	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867637928	NA	P-0007384-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	53	300	0	ENST00000374672.4:c.479C>T	p.Pro160Leu	p.P160L	ENST00000374672	NM_004235.4	160	cCg/cTg	3/5	0.166627565708442	3	FACETS	0.639	0.546	0.741	0.213	0.182	0.247	INDETERMINATE	1	TRUE	0	0.446808598920612	3		300	454	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059371	42059371	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007384-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	265	780	2	ENST00000219905.7:c.9091A>G	p.Thr3031Ala	p.T3031A	ENST00000219905	NM_001164273.1	3031	Aca/Gca	24/24	1	2	FACETS	0.892	0.835	0.951	0.892	0.835	0.951	CLONAL	1	TRUE	1	0.446808598920612	2		782	1330	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857020	9857020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555481892	NA	P-0007384-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	212	686	1	ENST00000330684.3:c.4381G>A	p.Glu1461Lys	p.E1461K	ENST00000330684	NM_001134407.1	1461	Gaa/Aaa	13/13	0.216592257006652	0	FACETS	0.517	0.48	0.555			1	INDETERMINATE	1	TRUE	0	0.446808598920612	0		687	1016	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432412	49432413	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007384-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	155	599	0	ENST00000301067.7:c.8726dup	p.Ser2910LysfsTer2	p.S2910Kfs*2	ENST00000301067	NM_003482.3	2909	gta/gtTa	34/54	0.359518947937355	1	FACETS	0.694	0.636	0.755	0.694	0.636	0.755	SUBCLONAL	1	TRUE	0	0.446808598920612	1		599	776	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0007385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	135	400	2	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.972	0.884	1	0.972	0.884	1	CLONAL	1	TRUE	1	0.373434717543092	2		402	744	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0007385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	232	591	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.373434717543092	2		591	1103	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0007385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	124	430	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.891	0.807	0.98	0.891	0.807	0.98	CLONAL	1	TRUE	1	0.373434717543092	2		430	745	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603023	48603023	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555687378	NA	P-0007385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	62	305	0	ENST00000342988.3:c.1324C>T	p.Gln442Ter	p.Q442*	ENST00000342988	NM_005359.5	442	Cag/Tag	11/12	0.373434717543092	1	FACETS	0.692	0.601	0.791	0.692	0.601	0.791	SUBCLONAL	1	TRUE	0	0.373434717543092	1		305	390	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101006	27101006	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	143	478	0	ENST00000324856.7:c.4288C>T	p.Gln1430Ter	p.Q1430*	ENST00000324856	NM_006015.4	1430	Cag/Tag	18/20	0.373434717543092	1	FACETS	0.992	0.907	1	0.992	0.907	1	CLONAL	1	TRUE	0	0.373434717543092	1		478	628	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266502	41266502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	118	442	0	ENST00000349496.5:c.299C>T	p.Pro100Leu	p.P100L	ENST00000349496	NM_001904.3	100	cCt/cTt	4/15	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.373434717543092	2		442	625	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160606	56160606	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	114	427	1	ENST00000399503.3:c.880G>C	p.Asp294His	p.D294H	ENST00000399503	NM_005921.1	294	Gat/Cat	4/20	1	2	FACETS	0.915	0.825	1	0.915	0.825	1	CLONAL	1	TRUE	1	0.373434717543092	2		428	667	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777933	3777933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1048314482	NA	P-0007385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	140	825	1	ENST00000262367.5:c.7115C>T	p.Ser2372Leu	p.S2372L	ENST00000262367	NM_004380.2	2372	tCg/tTg	31/31	0.24068591905485	1	FACETS	0.641	0.583	0.702	0.641	0.583	0.702	SUBCLONAL	1	TRUE	0	0.373434717543092	1		826	951	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860808	151860809	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0007385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	110	393	0	ENST00000262189.6:c.9853dup	p.Gln3285ProfsTer41	p.Q3285Pfs*41	ENST00000262189	NM_170606.2	3285	cag/cCag	43/59	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.373434717543092	2		393	502	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	105	366	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.848	0.761	0.94	0.848	0.761	0.94	CLONAL	1	TRUE	1	0.39942130588487	2		366	620	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0007391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	148	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.39942130588487	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.39942130588487	3		249	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0007391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	433	786	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.347640422309067	2	FACETS	0.895	0.854	0.937	0.895	0.854	0.937	CLONAL	2	TRUE	0	0.39942130588487	2		786	1211	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0007391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	242	586	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	1	2	FACETS	0.97	0.905	1	0.97	0.905	1	CLONAL	1	TRUE	1	0.39942130588487	2		586	1249	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795006	42795006	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550975604	NA	P-0007391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	257	368	0	ENST00000575354.2:c.2086C>T	p.Arg696Trp	p.R696W	ENST00000575354	NM_015125.3	696	Cgg/Tgg	10/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.39942130588487	2		368	1101	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377298	118377298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782763989	NA	P-0007391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1230	288	501	0	ENST00000534358.1:c.10691G>A	p.Arg3564Gln	p.R3564Q	ENST00000534358	NM_005933.3	3564	cGg/cAg	27/36	NA	2	FACETS	0.95	0.891	1			1	INDETERMINATE	1	TRUE	NA	0.39942130588487	2		501	1518	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504036	123504036	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	29	243	0	ENST00000371139.4:c.212G>T	p.Gly71Val	p.G71V	ENST00000371139	NM_001114937.2	71	gGg/gTg	3/4	0.39942130588487	2	FACETS	0.316	0.253	0.388			1	SUBCLONAL	1	TRUE	NA	0.39942130588487	2		243	459	SUCCESS
APC	324	MSKCC	GRCh37	5	112175612	112175613	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CACCT	novel	NA	P-0007391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1407	356	589	0	ENST00000257430.4:c.4323_4327dup	p.Pro1443HisfsTer32	p.P1443Hfs*32	ENST00000257430	NM_000038.5	1441	cca/cCACCTca	16/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.39942130588487	2		589	1763	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007425-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	109	140	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.561877797979559	2		140	298	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560476	95560476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007425-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	87	125	0	ENST00000393063.1:c.5113G>A	p.Glu1705Lys	p.E1705K	ENST00000393063	NM_030621.3	1705	Gaa/Aaa	25/28	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.561877797979559	2		125	225	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548888	29548888	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs147594815	NA	P-0007425-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	135	270	0	ENST00000356175.3:c.1662G>T	p.Gln554His	p.Q554H	ENST00000356175	NM_000267.3	554	caG/caT	15/57	0.232134890581292	3	FACETS	0.846	0.778	0.915	0.846	0.778	0.915	INDETERMINATE	2	TRUE	1	0.561877797979559	3		270	364	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627560	37627560	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007425-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	355	554	0	ENST00000447079.4:c.1475T>G	p.Val492Gly	p.V492G	ENST00000447079	NM_015083.1	492	gTt/gGt	2/14	0.232134890581292	3	FACETS	1	0.963	1	1	0.963	1	INDETERMINATE	2	TRUE	1	0.561877797979559	3		554	800	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569728	95569729	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs878855262	NA	P-0007425-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	232	361	0	ENST00000393063.1:c.4004dup	p.Tyr1335Ter	p.Y1335*	ENST00000393063	NM_030621.3	1335	tac/taAc	22/28	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.561877797979559	2		361	577	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0007510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	135	326	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.337093965996252	2		326	780	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891350	101891350	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	115	340	0	ENST00000374994.4:c.311A>T	p.Asp104Val	p.D104V	ENST00000374994	NM_004612.2	104	gAc/gTc	2/9	0.337093965996252	1	FACETS	0.921	0.832	1	0.921	0.832	1	CLONAL	1	TRUE	0	0.337093965996252	1		340	616	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643802	52643803	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAAAA	novel	NA	P-0007510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	116	359	0	ENST00000394830.3:c.2093_2094insTTTTT	p.Thr699PhefsTer2	p.T699Ffs*2	ENST00000394830	NM_018313.4	698	ctg/ctTTTTTg	17/30	0.337093965996252	1	FACETS	0.93	0.841	1	0.93	0.841	1	CLONAL	1	TRUE	0	0.337093965996252	1		359	615	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115982	8115983	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0007539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	14	176	0	ENST00000346208.3:c.1330dup	p.Ter444LeufsTer63	p.*444Lfs*63	ENST00000346208		443	ggt/ggTt	6/6	1	2	FACETS	0.725	0.53	0.956	0.725	0.53	0.956	CLONAL	1	TRUE	1	0.354143903900476	2		176	109	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0007546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	45	485	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.932	0.781	1	0.932	0.781	1	CLONAL	1	TRUE	1	0.14	2		485	690	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143324117	143324117	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	24	353	0	ENST00000262992.4:c.346G>C	p.Asp116His	p.D116H	ENST00000262992	NM_001101669.1	116	Gat/Cat	5/24	1	2	FACETS	0.749	0.586	0.937	0.749	0.586	0.937	CLONAL	1	TRUE	1	0.14	2		353	458	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220563	133220563	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	24	266	1	ENST00000320574.5:c.4150G>T	p.Val1384Leu	p.V1384L	ENST00000320574	NM_006231.2	1384	Gta/Tta	33/49	1	2	FACETS	0.844	0.661	1	0.844	0.661	1	CLONAL	1	TRUE	1	0.14	2		267	406	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196792	123196792	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	41	429	0	ENST00000218089.9:c.1679G>C	p.Arg560Thr	p.R560T	ENST00000218089	NM_001042749.1	560	aGg/aCg	18/35	1	1	FACETS	0.808	0.672	0.961	0.808	0.672	0.961	CLONAL	1	TRUE	0	0.14	1		429	674	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220491	1220492	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0007546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	38	523	0	ENST00000326873.7:c.587dup	p.Val197ArgfsTer69	p.V197Rfs*69	ENST00000326873	NM_000455.4	195	ctg/ctGg	4/10	1	2	FACETS	0.735	0.605	0.88	0.735	0.605	0.88	SUBCLONAL	1	TRUE	1	0.14	2		523	739	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0007601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	230	509	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.48	2		509	956	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050332	128050332	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs34295337	NA	P-0007601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	121	456	0	ENST00000285398.2:c.325C>T	p.Arg109Ter	p.R109*	ENST00000285398	NM_000122.1	109	Cga/Tga	3/15	1	2	FACETS	0.522	0.471	0.577	0.522	0.471	0.577	SUBCLONAL	1	TRUE	1	0.48	2		456	965	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842658	68842659	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	270	643	0	ENST00000261769.5:c.595dup	p.Thr199AsnfsTer10	p.T199Nfs*10	ENST00000261769	NM_004360.3	198	-/A	5/16	0.298494502116503	0	FACETS	0.602	0.566	0.64			1	SUBCLONAL	1	TRUE	0	0.48	0		643	971	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372752	81372752	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768451705	NA	P-0007601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	129	508	0	ENST00000222390.5:c.782G>A	p.Arg261His	p.R261H	ENST00000222390	NM_000601.4	261	cGc/cAc	7/18	0.3	3	FACETS	0.564	0.51	0.621	0.282	0.255	0.311	SUBCLONAL	1	TRUE	1	0.48	3		508	1182	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172487	108172487	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	243	491	0	ENST00000278616.4:c.5290C>G	p.Leu1764Val	p.L1764V	ENST00000278616	NM_000051.3	1764	Cta/Gta	35/63	1	2	FACETS	0.8	0.746	0.855	0.8	0.746	0.855	SUBCLONAL	1	TRUE	1	0.48	2		491	1266	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247911	10247911	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	81	302	0	ENST00000340748.4:c.4291G>T	p.Ala1431Ser	p.A1431S	ENST00000340748		1431	Gcc/Tcc	36/40	1	2	FACETS	0.696	0.615	0.782	0.696	0.615	0.782	SUBCLONAL	1	TRUE	1	0.48	2		302	485	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0007602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	101	250	2	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	0.391457364064154	2		252	508	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	243	435	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.935	0.872	1	0.935	0.872	1	CLONAL	1	TRUE	1	0.391457364064154	2		435	1328	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1330	59	504	2	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	1	2	FACETS	0.217	0.186	0.252	0.217	0.186	0.252	SUBCLONAL	1	TRUE	1	0.391457364064154	2		506	1389	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0007602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	190	491	1	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	1	2	FACETS	0.811	0.748	0.876	0.811	0.748	0.876	CLONAL	1	TRUE	1	0.391457364064154	2		492	1197	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022403	31022425	+	frameshift_variant	Frame_Shift_Del	DEL	CACCACTGCCATAGAGAGGCGGC	CACCACTGCCATAGAGAGGCGGC	-	rs766433101	NA	P-0007602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	99	274	0	ENST00000375687.4:c.1900_1922del	p.Glu635ArgfsTer15	p.E635Rfs*15	ENST00000375687	NM_015338.5	630	CACCACTGCCATAGAGAGGCGGCc/c	13/13	1	2	FACETS	0.775	0.692	0.862	0.775	0.692	0.862	SUBCLONAL	1	TRUE	1	0.391457364064154	2		274	653	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732957	30732957	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504421	NA	P-0007602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	425	402	0	ENST00000295754.5:c.1570G>A	p.Asp524Asn	p.D524N	ENST00000295754	NM_003242.5	524	Gac/Aac	7/7	0.391457364064154	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.391457364064154	2		402	872	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633625	69633625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782733556	NA	P-0007602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	35	72	0	ENST00000334134.2:c.77G>A	p.Arg26Gln	p.R26Q	ENST00000334134	NM_005247.2	26	cGg/cAg	1/3	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.391457364064154	2		72	130	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114905821	114905822	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0007602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1300	327	711	0	ENST00000543371.1:c.842_843del	p.Pro281HisfsTer46	p.P281Hfs*46	ENST00000543371	NM_001198531.1	280	taCCcc/tacc	8/14	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.391457364064154	2		711	1627	SUCCESS
APC	324	MSKCC	GRCh37	5	112176009	112176009	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	187	350	0	ENST00000257430.4:c.4720del	p.Ile1574TyrfsTer2	p.I1574Yfs*2	ENST00000257430	NM_000038.5	1573	gAa/ga	16/16	0.391457364064154	1	FACETS	0.962	0.89	1	0.962	0.89	1	CLONAL	1	TRUE	0	0.391457364064154	1		350	799	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593655	55593656	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACAACTTCCTTATGAACA	novel	NA	P-0007646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	230	275	0	ENST00000288135.5:c.1736_1737insACAACAACTTCCTTATGA	p.Tyr578_Asp579insGluGlnGlnLeuProTyr	p.Y578_D579insEQQLPY	ENST00000288135	NM_000222.2	574	aca/acACAACTTCCTTATGAACAa	11/21	0.450793517707575	3	FACETS	1	0.991	1	0.684	0.638	0.731	CLONAL	1	TRUE	1	0.450793517707575	3		275	914	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0007689-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	87	285	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.241370686394395	3	FACETS	1	0.97	1	0.643	0.57	0.72	CLONAL	1	TRUE	1	0.29020376929814	3		285	534	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874012	151874013	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0007689-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	155	506	0	ENST00000262189.6:c.8525dup	p.Asn2842LysfsTer2	p.N2842Kfs*2	ENST00000262189	NM_170606.2	2842	aat/aaAt	38/59	0.241370686394395	3	FACETS	1	0.984	1	0.657	0.601	0.715	CLONAL	1	TRUE	1	0.29020376929814	3		506	931	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968262	2968262	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007689-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	59	515	0	ENST00000396946.4:c.1724G>T	p.Arg575Ile	p.R575I	ENST00000396946	NM_032415.4	575	aGa/aTa	13/25	0.29020376929814	7	FACETS	0.625	0.535	0.723	0.125	0.107	0.145	SUBCLONAL	1	TRUE	2	0.29020376929814	7		515	1123	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005626	42005626	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007689-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1226	89	765	0	ENST00000219905.7:c.3362A>T	p.Glu1121Val	p.E1121V	ENST00000219905	NM_001164273.1	1121	gAg/gTg	9/24	0.17026734180853	4	FACETS	0.602	0.531	0.678	0.301	0.265	0.339	INDETERMINATE	1	TRUE	2	0.29020376929814	4		765	1315	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779343	3779343	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1369215188	NA	P-0007689-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	43	459	0	ENST00000262367.5:c.5705C>T	p.Thr1902Met	p.T1902M	ENST00000262367	NM_004380.2	1902	aCg/aTg	31/31	0.17026734180853	4	FACETS	0.544	0.454	0.644	0.272	0.227	0.322	INDETERMINATE	1	TRUE	2	0.29020376929814	4		459	703	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578196	7578196	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555525743	NA	P-0007689-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	168	575	0	ENST00000269305.4:c.653T>G	p.Val218Gly	p.V218G	ENST00000269305	NM_001126112.2	218	gTg/gGg	6/11	0.198364692816133	2	FACETS	1	0.989	1	0.737	0.679	0.798	CLONAL	1	TRUE	0	0.29020376929814	2		575	785	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628136	90628137	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007689-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	45	414	0	ENST00000330062.3:c.1182dup	p.Ala395CysfsTer85	p.A395Cfs*85	ENST00000330062	NM_002168.2	394	-/T	10/11	0.17026734180853	4	FACETS	0.544	0.456	0.642	0.272	0.228	0.321	INDETERMINATE	1	TRUE	2	0.29020376929814	4		414	735	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0007753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	59	282	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.181839296445253	4	FACETS	0.859	0.742	0.986	0.573	0.494	0.658	CLONAL	2	TRUE	1	0.203545446370272	4		282	406	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134151	41134151	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1421986524	NA	P-0007753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	47	692	1	ENST00000379561.5:c.1477G>T	p.Gly493Cys	p.G493C	ENST00000379561	NM_002015.3	493	Ggc/Tgc	2/3	1	2	FACETS	0.655	0.551	0.77	0.655	0.551	0.77	SUBCLONAL	1	TRUE	1	0.203545446370272	2		693	705	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573987	7573987	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397516434	NA	P-0007753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	60	513	0	ENST00000269305.4:c.1040C>A	p.Ala347Asp	p.A347D	ENST00000269305	NM_001126112.2	347	gCc/gAc	10/11	0.170760034563523	4	FACETS	1	0.934	1	0.574	0.494	0.661	CLONAL	1	TRUE	2	0.203545446370272	4		513	618	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412008	63412008	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	30	820	3	ENST00000330258.3:c.1159G>T	p.Glu387Ter	p.E387*	ENST00000330258	NM_152424.3	387	Gag/Tag	2/2	1	2	FACETS	0.649	0.523	0.793	0.649	0.523	0.793	SUBCLONAL	1	TRUE	1	0.203545446370272	2		823	454	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665642	86665643	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGATAGTAGTTCAGCACTTTAGTGAAGAA	novel	NA	P-0007753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	10	297	0	ENST00000274376.6:c.1626_1655dup	p.Gln542_Glu551dup	p.Q542_E551dup	ENST00000274376	NM_002890.2	542	-/CAGATAGTAGTTCAGCACTTTAGTGAAGAA	12/25	0.181839296445253	4	FACETS	0.827	0.562	1	0.276	0.187	0.386	CLONAL	1	TRUE	1	0.203545446370272	4		297	143	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218483	1218483	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	63	460	0	ENST00000326873.7:c.358del	p.Glu120LysfsTer9	p.E120Kfs*9	ENST00000326873	NM_000455.4	120	Gaa/aa	2/10	0.181839296445253	4	FACETS	0.756	0.655	0.865	0.504	0.436	0.577	SUBCLONAL	2	TRUE	1	0.203545446370272	4		460	493	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0007814-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	258	419	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.891	0.84	0.942	1	0.996	1	CLONAL	3	FALSE	1	0.298901811215907	2		420	646	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578177	7578177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs267605076	NA	P-0007814-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	645	543	1	ENST00000269305.4:c.672G>T	p.Glu224Asp	p.E224D	ENST00000269305	NM_001126112.2	224	gaG/gaT	6/11	0.298901811215907	2	FACETS	0.969	0.952	0.986	1	0.998	1	CLONAL	6	FALSE	0	0.298901811215907	2		544	742	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909631	76909632	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0007814-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	492	821	0	ENST00000373344.5:c.4273dup	p.Arg1425LysfsTer5	p.R1425Kfs*5	ENST00000373344	NM_000489.3	1425	agg/aAgg	14/35	0.298901811215907	1	FACETS	1	0.995	1	1	0.998	1	CLONAL	2	FALSE	0	0.298901811215907	1		821	1133	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0007842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	63	273	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.310923264292082	4	FACETS	0.513	0.443	0.591	0.257	0.221	0.296	SUBCLONAL	1	TRUE	2	0.360557258953651	4		273	926	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051218	128051218	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	239	386	0	ENST00000285398.2:c.105G>T	p.Gln35His	p.Q35H	ENST00000285398	NM_000122.1	35	caG/caT	2/15	0.341753818167911	3	FACETS	0.978	0.916	1	0.978	0.916	1	CLONAL	2	TRUE	1	0.360557258953651	3		386	800	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498506	89498506	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	208	294	2	ENST00000336596.2:c.2478G>T	p.Trp826Cys	p.W826C	ENST00000336596	NM_005233.5	826	tgG/tgT	14/17	0.360557258953651	6	FACETS	0.891	0.826	0.959			1	CLONAL	2	TRUE	NA	0.360557258953651	6		296	1114	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201792	66201792	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	64	291	0	ENST00000273854.3:c.2710C>T	p.Pro904Ser	p.P904S	ENST00000273854	NM_004439.5	904	Cct/Tct	16/18	1	2	FACETS	0.617	0.535	0.707	0.617	0.535	0.707	SUBCLONAL	1	TRUE	1	0.360557258953651	2		291	575	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874565	35874565	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	476	409	0	ENST00000303115.3:c.721A>T	p.Ile241Phe	p.I241F	ENST00000303115	NM_002185.3	241	Atc/Ttc	6/8	0.328151553862416	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	0	0.360557258953651	3		409	1028	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672882	30672882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	128	550	0	ENST00000376406.3:c.4078G>A	p.Val1360Met	p.V1360M	ENST00000376406	NM_014641.2	1360	Gtg/Atg	10/15	1	2	FACETS	0.667	0.604	0.735	0.667	0.604	0.735	SUBCLONAL	1	TRUE	1	0.360557258953651	2		550	1064	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460511	8460511	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	172	328	0	ENST00000356435.5:c.3775C>G	p.Pro1259Ala	p.P1259A	ENST00000356435		1259	Cca/Gca	22/35	0.360557258953651	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.360557258953651	1		328	624	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974799	21974799	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	54	96	0	ENST00000304494.5:c.28G>T	p.Glu10Ter	p.E10*	ENST00000304494	NM_000077.4	10	Gag/Tag	1/3	0.360557258953651	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.360557258953651	1		96	172	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412378	139412378	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	68	127	0	ENST00000277541.6:c.1267T>G	p.Cys423Gly	p.C423G	ENST00000277541	NM_017617.3	423	Tgc/Ggc	8/34	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	1	TRUE	NA	0.360557258953651	2		127	255	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100349	8100349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	92	379	0	ENST00000346208.3:c.323C>T	p.Thr108Ile	p.T108I	ENST00000346208		108	aCc/aTc	3/6	0.228279009985169	1	FACETS	0.724	0.644	0.808	0.724	0.644	0.808	SUBCLONAL	1	TRUE	0	0.360557258953651	1		379	578	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15975518	15975518	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764561903	NA	P-0007842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	142	338	0	ENST00000268712.3:c.3836G>T	p.Arg1279Met	p.R1279M	ENST00000268712	NM_006311.3	1279	aGg/aTg	29/46	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.360557258953651	2		338	680	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667602	29667602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	225	333	0	ENST00000356175.3:c.6938G>A	p.Gly2313Asp	p.G2313D	ENST00000356175	NM_000267.3	2313	gGt/gAt	46/57	0.223167704416303	3	FACETS	0.762	0.71	0.815	0.762	0.71	0.815	SUBCLONAL	2	TRUE	1	0.360557258953651	3		333	967	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578192	7578193	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	GGCACCACCACACTATGTCGAAAAGTGT	novel	NA	P-0007842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	138	410	1	ENST00000269305.4:c.629_656dup	p.Tyr220HisfsTer5	p.Y220Hfs*5	ENST00000269305	NM_001126112.2	219	ccc/ccACACTTTTCGACATAGTGTGGTGGTGCCc	6/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.360557258953651	2		411	714	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0007852-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	354	504	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	0.648243253315702	2		504	1054	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593660	55593661	+	protein_altering_variant	In_Frame_Ins	INS	CT	CT	ATGATCACAAATGGGAGTGA	novel	NA	P-0007852-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2769	519	484	8	ENST00000288135.5:c.1726_1727delinsATGATCACAAATGGGAGTGA	p.Leu576delinsMetIleThrAsnGlySerAsp	p.L576delinsMITNGSD	ENST00000288135	NM_000222.2	576	CTt/ATGATCACAAATGGGAGTGAt	11/21	0.648243253315702	11	FACETS	0.954	0.909	1			1	CLONAL	2	TRUE	NA	0.648243253315702	11		492	3288	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1307	229	898	5	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.815	0.757	0.875	1	0.992	1	CLONAL	2	TRUE	1	0.182937622673938	2		903	1536	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1491	256	654	0	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	1	2	FACETS	0.801	0.747	0.857	1	0.993	1	CLONAL	2	TRUE	1	0.182937622673938	2		654	1747	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199945	138199945	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	77	168	1	ENST00000237289.4:c.1368del	p.Pro457LeufsTer20	p.P457Lfs*20	ENST00000237289	NM_001270507.1	455	Ggg/gg	7/9	1	2	FACETS	0.857	0.755	0.967	1	0.98	1	CLONAL	2	TRUE	1	0.182937622673938	2		169	491	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	108	539	0	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	0.915	0.818	1	0.915	0.818	1	CLONAL	1	TRUE	1	0.182937622673938	2		539	1291	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	56	336	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.727	0.621	0.843	0.727	0.621	0.843	SUBCLONAL	1	TRUE	1	0.182937622673938	2		336	842	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs786202525	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	95	273	0	ENST00000269305.4:c.532del	p.His178ThrfsTer69	p.H178Tfs*69	ENST00000269305	NM_001126112.2	178	Cac/ac	5/11	1	2	FACETS	0.828	0.738	0.924	1	0.983	1	CLONAL	2	TRUE	1	0.182937622673938	2		273	627	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755554	39755554	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	88	383	1	ENST00000288319.7:c.1211del	p.Pro404ArgfsTer25	p.P404Rfs*25	ENST00000288319	NM_182918.3	404	cCg/cg	10/10	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.182937622673938	2		384	899	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	96	467	0	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	0.967	0.86	1	0.967	0.86	1	CLONAL	1	TRUE	1	0.182937622673938	2		467	1085	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114823	108114823	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747053710	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	56	422	0	ENST00000278616.4:c.640T>C	p.Ser214Pro	p.S214P	ENST00000278616	NM_000051.3	214	Tcc/Ccc	6/63	1	2	FACETS	0.686	0.586	0.795	0.686	0.586	0.795	SUBCLONAL	1	TRUE	1	0.182937622673938	2		422	893	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	125	273	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.182937622673938	2		273	946	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1239	213	538	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	0.802	0.743	0.863	1	0.992	1	CLONAL	2	TRUE	1	0.182937622673938	2		538	1452	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1023835002	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	206	336	0	ENST00000558401.1:c.1A>G	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Gtg	1/4	0.182937622673938	2	FACETS	0.835	0.775	0.897	1	0.986	1	CLONAL	3	TRUE	0	0.182937622673938	2		336	899	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023904	27023904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1232964733	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	18	123	0	ENST00000324856.7:c.1015del	p.Ala339LeufsTer24	p.A339Lfs*24	ENST00000324856	NM_006015.4	337	tGg/tg	1/20	1	2	FACETS	0.769	0.579	0.992	0.769	0.579	0.992	CLONAL	1	TRUE	1	0.182937622673938	2		123	256	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	108	502	1	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.182937622673938	2		503	1135	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953632	32953633	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359732	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1216	128	694	0	ENST00000380152.3:c.8940dup	p.Glu2981ArgfsTer37	p.E2981Rfs*37	ENST00000380152		2978	tca/tcAa	22/27	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.182937622673938	2		694	1344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1213	73	564	3	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	1	2	FACETS	0.621	0.541	0.708	0.621	0.541	0.708	SUBCLONAL	1	TRUE	1	0.182937622673938	2		567	1286	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396908	396908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753659585	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	163	458	1	ENST00000262320.3:c.118G>A	p.Ala40Thr	p.A40T	ENST00000262320	NM_003502.3	40	Gcc/Acc	2/11	1	2	FACETS	0.798	0.731	0.869	1	0.989	1	SUBCLONAL	2	TRUE	1	0.182937622673938	2		459	1116	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007824	45007825	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	44	351	0	ENST00000558401.1:c.276dup	p.Thr93HisfsTer2	p.T93Hfs*2	ENST00000558401	NM_004048.2	91	acc/aCcc	2/4	0.182937622673938	2	FACETS	0.581	0.486	0.687	0.29	0.243	0.344	SUBCLONAL	1	TRUE	0	0.182937622673938	2		351	828	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533838	533838	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	153	450	2	ENST00000451590.1:c.218G>A	p.Arg73His	p.R73H	ENST00000451590	NM_001130442.1	73	cGc/cAc	3/5	1	2	FACETS	0.772	0.705	0.842	1	0.988	1	SUBCLONAL	2	TRUE	1	0.182937622673938	2		452	1084	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061334	38061334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	120	504	0	ENST00000250448.2:c.655C>T	p.Arg219Cys	p.R219C	ENST00000250448	NM_004496.3	219	Cgc/Tgc	2/2	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.182937622673938	2		504	1089	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393357	393357	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	63	305	2	ENST00000380956.4:c.205G>A	p.Ala69Thr	p.A69T	ENST00000380956	NM_001195286.1	69	Gcg/Acg	2/9	1	2	FACETS	0.991	0.856	1	0.991	0.856	1	CLONAL	1	TRUE	1	0.182937622673938	2		307	695	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830754	156830754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	14	59	0	ENST00000524377.1:c.28C>T	p.Leu10Phe	p.L10F	ENST00000524377	NM_002529.3	10	Ctt/Ttt	1/17	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.182937622673938	2		59	105	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543850	212543850	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	83	331	0	ENST00000342788.4:c.1549C>T	p.Pro517Ser	p.P517S	ENST00000342788	NM_005235.2	517	Cca/Tca	13/28	1	2	FACETS	0.998	0.879	1	0.998	0.879	1	CLONAL	1	TRUE	1	0.182937622673938	2		331	909	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370789	225370789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765785569	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	155	528	0	ENST00000264414.4:c.1090C>T	p.Arg364Cys	p.R364C	ENST00000264414	NM_003590.4	364	Cgt/Tgt	8/16	1	2	FACETS	0.789	0.721	0.86	1	0.989	1	SUBCLONAL	2	TRUE	1	0.182937622673938	2		528	1074	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461565	138461565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	162	470	0	ENST00000289153.2:c.456G>A	p.Met152Ile	p.M152I	ENST00000289153	NM_006219.2	152	atG/atA	3/22	1	2	FACETS	0.894	0.819	0.971	1	0.991	1	CLONAL	2	TRUE	1	0.182937622673938	2		470	991	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664838	138664838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773788619	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	18	37	0	ENST00000330315.3:c.727G>A	p.Ala243Thr	p.A243T	ENST00000330315	NM_023067.3	243	Gct/Act	1/1	1	2	FACETS	1	0.769	1	1	0.934	1	CLONAL	2	TRUE	1	0.182937622673938	2		37	98	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509110	66509110	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	123	469	0	ENST00000273854.3:c.217C>A	p.Leu73Met	p.L73M	ENST00000273854	NM_004439.5	73	Ctg/Atg	2/18	1	2	FACETS	0.853	0.772	0.939	1	0.987	1	CLONAL	2	TRUE	1	0.182937622673938	2		469	788	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539978	187539978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1460050406	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	124	365	0	ENST00000441802.2:c.7762G>A	p.Asp2588Asn	p.D2588N	ENST00000441802	NM_005245.3	2588	Gat/Aat	10/27	1	2	FACETS	0.821	0.742	0.903	1	0.987	1	CLONAL	2	TRUE	1	0.182937622673938	2		365	826	SUCCESS
APC	324	MSKCC	GRCh37	5	112102945	112102945	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550945533	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	177	436	1	ENST00000257430.4:c.280C>T	p.Arg94Cys	p.R94C	ENST00000257430	NM_000038.5	94	Cgt/Tgt	4/16	1	2	FACETS	0.869	0.8	0.942	1	0.991	1	CLONAL	2	TRUE	1	0.182937622673938	2		437	1113	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985462	2985462	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	88	457	0	ENST00000396946.4:c.349A>G	p.Thr117Ala	p.T117A	ENST00000396946	NM_032415.4	117	Acc/Gcc	4/25	1	2	FACETS	0.879	0.777	0.99	0.879	0.777	0.99	CLONAL	1	TRUE	1	0.182937622673938	2		457	1094	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534429	140534429	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	43	420	0	ENST00000288602.6:c.484C>T	p.Pro162Ser	p.P162S	ENST00000288602	NM_004333.4	162	Ccc/Tcc	3/18	1	2	FACETS	0.601	0.501	0.712	0.601	0.501	0.712	SUBCLONAL	1	TRUE	1	0.182937622673938	2		420	782	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739881	145739881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764297840	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	149	534	2	ENST00000428558.2:c.1649C>T	p.Ala550Val	p.A550V	ENST00000428558	NM_004260.3	550	gCg/gTg	10/22	1	2	FACETS	0.871	0.795	0.95	1	0.99	1	CLONAL	2	TRUE	1	0.182937622673938	2		536	935	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006005	22006005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	106	449	0	ENST00000276925.6:c.398G>A	p.Arg133His	p.R133H	ENST00000276925	NM_004936.3	133	cGc/cAc	2/2	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.182937622673938	2		449	985	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518485	69518485	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1005963395	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	31	228	1	ENST00000294312.3:c.160G>T	p.Gly54Trp	p.G54W	ENST00000294312	NM_005117.2	54	Ggg/Tgg	1/3	1	2	FACETS	0.751	0.607	0.915	0.751	0.607	0.915	CLONAL	1	TRUE	1	0.182937622673938	2		229	451	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475143	475143	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	141	551	0	ENST00000399788.2:c.494T>C	p.Ile165Thr	p.I165T	ENST00000399788	NM_001042603.1	165	aTt/aCt	4/28	1	2	FACETS	0.792	0.721	0.867	1	0.988	1	SUBCLONAL	2	TRUE	1	0.182937622673938	2		551	973	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524116	18524116	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	51	426	0	ENST00000266497.5:c.1628T>C	p.Ile543Thr	p.I543T	ENST00000266497		543	aTc/aCc	11/31	1	2	FACETS	0.653	0.553	0.763	0.653	0.553	0.763	SUBCLONAL	1	TRUE	1	0.182937622673938	2		426	854	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480076	50480076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	122	409	0	ENST00000394963.4:c.310G>A	p.Ala104Thr	p.A104T	ENST00000394963	NM_003076.4	104	Gcc/Acc	2/13	1	2	FACETS	0.824	0.745	0.908	1	0.987	1	CLONAL	2	TRUE	1	0.182937622673938	2		409	809	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304245	91304245	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs200389141	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	253	580	0	ENST00000355112.3:c.1642C>A	p.Gln548Lys	p.Q548K	ENST00000355112	NM_000057.2	548	Caa/Aaa	7/22	0.182937622673938	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.182937622673938	2		580	1132	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	338210	338210	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1302	113	611	0	ENST00000262320.3:c.2501G>T	p.Gly834Val	p.G834V	ENST00000262320	NM_003502.3	834	gGg/gTg	11/11	1	2	FACETS	0.873	0.783	0.969	0.873	0.783	0.969	CLONAL	1	TRUE	1	0.182937622673938	2		611	1415	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781269	3781269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	173	447	1	ENST00000262367.5:c.5096G>A	p.Gly1699Asp	p.G1699D	ENST00000262367	NM_004380.2	1699	gGc/gAc	30/31	1	2	FACETS	0.987	0.908	1	1	0.992	1	CLONAL	2	TRUE	1	0.182937622673938	2		448	958	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578421	7578421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779000871	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	38	312	0	ENST00000269305.4:c.509C>T	p.Thr170Met	p.T170M	ENST00000269305	NM_001126112.2	170	aCg/aTg	5/11	1	2	FACETS	0.556	0.458	0.666	0.556	0.458	0.666	SUBCLONAL	1	TRUE	1	0.182937622673938	2		312	747	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546105	41546105	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757344870	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	51	219	0	ENST00000263253.7:c.2720C>T	p.Ala907Val	p.A907V	ENST00000263253	NM_001429.3	907	gCt/gTt	14/31	1	2	FACETS	0.886	0.753	1	0.886	0.753	1	CLONAL	1	TRUE	1	0.182937622673938	2		219	629	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932039	39932039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs527732438	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	156	224	0	ENST00000378444.4:c.2560G>A	p.Ala854Thr	p.A854T	ENST00000378444	NM_001123385.1	854	Gcc/Acc	4/15	1	1	FACETS	0.999	0.921	1	1	0.994	1	CLONAL	3	TRUE	0	0.182937622673938	1		224	517	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163554	32163554	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	75	419	2	ENST00000375023.3:c.5672del	p.Gly1891AlafsTer13	p.G1891Afs*13	ENST00000375023	NM_004557.3	1891	gGc/gc	30/30	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.182937622673938	2		421	692	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262680	16262680	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	27	294	2	ENST00000375759.3:c.9950del	p.Pro3317ArgfsTer83	p.P3317Rfs*83	ENST00000375759	NM_015001.2	3315	caC/ca	11/15	1	2	FACETS	0.568	0.451	0.702	0.568	0.451	0.702	SUBCLONAL	1	TRUE	1	0.182937622673938	2		296	520	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619031	37619032	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	86	386	0	ENST00000447079.4:c.711dup	p.Ser238LeufsTer10	p.S238Lfs*10	ENST00000447079	NM_015083.1	236	agc/agCc	1/14	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.182937622673938	2		386	842	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820668	3820668	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	65	367	0	ENST00000262367.5:c.2783del	p.Pro928ArgfsTer70	p.P928Rfs*70	ENST00000262367	NM_004380.2	928	cCg/cg	14/31	1	2	FACETS	0.893	0.773	1	0.893	0.773	1	CLONAL	1	TRUE	1	0.182937622673938	2		367	796	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578463	7578463	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371524413	NA	P-0007891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	95	408	1	ENST00000269305.4:c.467G>C	p.Arg156Pro	p.R156P	ENST00000269305	NM_001126112.2	156	cGc/cCc	5/11	1	2	FACETS	0.738	0.66	0.82	0.738	0.66	0.82	SUBCLONAL	1	TRUE	1	0.565935130678422	2		409	455	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103384	119103384	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1295617809	NA	P-0007891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	60	341	0	ENST00000264033.4:c.422A>G	p.Tyr141Cys	p.Y141C	ENST00000264033	NM_005188.3	141	tAt/tGt	2/16	0.565935130678422	3	FACETS	0.786	0.681	0.899	0.393	0.34	0.45	SUBCLONAL	1	TRUE	1	0.565935130678422	3		341	346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578254	7578254	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551821	NA	P-0007891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	220	527	0	ENST00000269305.4:c.595G>T	p.Gly199Ter	p.G199*	ENST00000269305	NM_001126112.2	199	Gga/Tga	6/11	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.565935130678422	2		527	560	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938373	76938374	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0007891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	131	757	0	ENST00000373344.5:c.2373_2374dup	p.Thr792IlefsTer12	p.T792Ifs*12	ENST00000373344	NM_000489.3	792	act/aTAct	9/35	0.436093006865584	0	FACETS	0.684	0.631	0.737			1	SUBCLONAL	1	TRUE	0	0.565935130678422	0		757	294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0007914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	125	634	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.225426027943583	2	FACETS	0.932	0.864	1	1	0.992	1	CLONAL	5	FALSE	0	0.225426027943583	2		634	238	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913499	NA	P-0007914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	16	453	0	ENST00000345146.2:c.394C>A	p.Arg132Ser	p.R132S	ENST00000345146	NM_005896.2	132	Cgt/Agt	4/10	1	2	FACETS	0.866	0.652	1	1	0.917	1	CLONAL	2	FALSE	1	0.225426027943583	2		453	82	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76919037	76919038	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0007914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	14	545	0	ENST00000373344.5:c.3953dup	p.Asn1318LysfsTer6	p.N1318Kfs*6	ENST00000373344	NM_000489.3	1318	aat/aaAt	12/35	0.225426027943583	0	FACETS	1	0.791	1			1	CLONAL	1	FALSE	0	0.225426027943583	0		545	88	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	201	366	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.396341065658219	3	FACETS	0.808	0.752	0.866	0.808	0.752	0.866	CLONAL	2	TRUE	1	0.447460620191656	3		366	680	SUCCESS
APC	324	MSKCC	GRCh37	5	112174096	112174096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs137854575	NA	P-0007923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	101	852	0	ENST00000257430.4:c.2805C>A	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	taC/taA	16/16	1	2	FACETS	0.847	0.76	0.939	0.847	0.76	0.939	CLONAL	1	TRUE	1	0.447460620191656	2		852	533	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394805	45394805	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	139	563	1	ENST00000262160.6:c.544C>T	p.Arg182Ter	p.R182*	ENST00000262160	NM_005901.5	182	Cga/Tga	5/11	0.375752874280993	2	FACETS	0.849	0.782	0.917	0.849	0.782	0.917	CLONAL	2	TRUE	0	0.447460620191656	2		564	366	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188164	11188164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777893	NA	P-0007923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	71	676	0	ENST00000361445.4:c.5930C>T	p.Thr1977Ile	p.T1977I	ENST00000361445	NM_004958.3	1977	aCa/aTa	43/58	1	2	FACETS	0.778	0.682	0.88	0.778	0.682	0.88	SUBCLONAL	1	TRUE	1	0.447460620191656	2		676	408	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37081782	37081782	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs587778937	NA	P-0007923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	106	704	0	ENST00000231790.2:c.1664T>G	p.Leu555Arg	p.L555R	ENST00000231790	NM_000249.3	555	cTt/cGt	14/19	1	2	FACETS	0.81	0.728	0.896	0.81	0.728	0.896	CLONAL	1	TRUE	1	0.447460620191656	2		704	585	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948135	55948135	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1001071878	NA	P-0007923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	85	961	0	ENST00000263923.4:c.3836C>A	p.Ser1279Tyr	p.S1279Y	ENST00000263923	NM_002253.2	1279	tCt/tAt	29/30	0.447460620191656	1	FACETS	0.563	0.499	0.631	0.563	0.499	0.631	SUBCLONAL	1	TRUE	0	0.447460620191656	1		961	524	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457295	67457295	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	109	866	1	ENST00000327367.4:c.269G>T	p.Arg90Leu	p.R90L	ENST00000327367	NM_005902.3	90	cGc/cTc	2/9	1	2	FACETS	0.804	0.724	0.889	0.804	0.724	0.889	CLONAL	1	TRUE	1	0.447460620191656	2		867	606	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15978899	15978899	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	137	1034	0	ENST00000268712.3:c.3619A>C	p.Lys1207Gln	p.K1207Q	ENST00000268712	NM_006311.3	1207	Aaa/Caa	27/46	0.36505652302839	1	FACETS	0.782	0.714	0.853	0.782	0.714	0.853	SUBCLONAL	1	TRUE	0	0.447460620191656	1		1034	608	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216631	2216631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769937964	NA	P-0007923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	44	730	0	ENST00000398665.3:c.2275C>T	p.Arg759Cys	p.R759C	ENST00000398665	NM_032482.2	759	Cgc/Tgc	20/28	0.39041255435408	3	FACETS	0.447	0.375	0.528	0.224	0.187	0.264	SUBCLONAL	1	TRUE	1	0.447460620191656	3		730	538	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560878	9560878	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	117	1074	0	ENST00000353224.5:c.904A>C	p.Ser302Arg	p.S302R	ENST00000353224	NM_177990.2	302	Agt/Cgt	4/10	0.36166153315524	2	FACETS	0.769	0.694	0.848	0.385	0.347	0.424	SUBCLONAL	1	TRUE	0	0.447460620191656	2		1074	680	SUCCESS
APC	324	MSKCC	GRCh37	5	112175523	112175524	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGGAA	novel	NA	P-0007923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	73	677	0	ENST00000257430.4:c.4236_4240dup	p.Val1414GlufsTer3	p.V1414Efs*3	ENST00000257430	NM_000038.5	1411	agt/agTGGAAt	16/16	1	2	FACETS	0.657	0.575	0.743	0.657	0.575	0.743	SUBCLONAL	1	TRUE	1	0.447460620191656	2		677	497	SUCCESS
APC	324	MSKCC	GRCh37	5	112116500	112116501	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	51	440	0	ENST00000257430.4:c.546dup	p.Asp183ArgfsTer10	p.D183Rfs*10	ENST00000257430	NM_000038.5	182	aca/acAa	6/16	0.345159426577226	1	FACETS	0.47	0.4	0.547	0.47	0.4	0.547	SUBCLONAL	1	TRUE	0	0.390060662166281	1		440	448	SUCCESS
APC	324	MSKCC	GRCh37	5	112175180	112175181	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0007929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	43	250	0	ENST00000257430.4:c.3890_3891dup	p.Ser1298IlefsTer8	p.S1298Ifs*8	ENST00000257430	NM_000038.5	1297	gat/gATat	16/16	0.345159426577226	1	FACETS	0.652	0.549	0.765	0.652	0.549	0.765	SUBCLONAL	1	TRUE	0	0.390060662166281	1		250	272	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578476	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTGCCGGGCGG	GGGTGCCGGGCGG	-	rs876659215	NA	P-0007929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	127	455	1	ENST00000269305.4:c.454_466del	p.Pro152AlafsTer14	p.P152Afs*14	ENST00000269305	NM_001126112.2	152	CCGCCCGGCACCCgc/gc	5/11	0.390060662166281	1	FACETS	0.865	0.786	0.948	0.865	0.786	0.948	CLONAL	1	TRUE	0	0.390060662166281	1		456	606	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0007998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	50	250	2	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.932	0.793	1	0.932	0.793	1	CLONAL	1	TRUE	1	0.294924478653015	2		252	364	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0007998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	148	288	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.998	0.91	1	0.998	0.91	1	CLONAL	1	TRUE	1	0.294924478653015	2		288	1006	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189412	56189412	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	150	356	0	ENST00000399503.3:c.4444C>T	p.Arg1482Ter	p.R1482*	ENST00000399503	NM_005921.1	1482	Cga/Tga	20/20	0.25089316948015	3	FACETS	1	0.972	1	0.576	0.525	0.628	CLONAL	1	TRUE	1	0.294924478653015	3		356	1014	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834552	156834552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540521894	NA	P-0007998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	101	317	0	ENST00000524377.1:c.320C>T	p.Ala107Val	p.A107V	ENST00000524377	NM_002529.3	107	gCg/gTg	3/17	1	2	FACETS	0.886	0.792	0.986	0.886	0.792	0.986	CLONAL	1	TRUE	1	0.294924478653015	2		317	773	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453138	140453139	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTA	rs727502902	NA	P-0007998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	257	248	0	ENST00000288602.6:c.1794_1796dup	p.Thr599dup	p.T599dup	ENST00000288602	NM_004333.4	599	aca/acTACa	15/18	0.294924478653015	4	FACETS	0.932	0.876	0.99	0.932	0.876	0.99	CLONAL	3	TRUE	1	0.294924478653015	4		248	807	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579321	7579322	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs587780067	NA	P-0007998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	191	225	0	ENST00000269305.4:c.365_366del	p.Val122AspfsTer26	p.V122Dfs*26	ENST00000269305	NM_001126112.2	122	gTG/g	4/11	0.294924478653015	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.294924478653015	2		225	608	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467589	66467589	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772693559	NA	P-0007998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	89	329	1	ENST00000273854.3:c.680G>A	p.Arg227His	p.R227H	ENST00000273854	NM_004439.5	227	cGt/cAt	3/18	0.165598794825864	1	FACETS	0.725	0.642	0.813	0.725	0.642	0.813	INDETERMINATE	1	TRUE	0	0.294924478653015	1		330	710	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228339	228339	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	69	144	0	ENST00000264932.6:c.661G>T	p.Ala221Ser	p.A221S	ENST00000264932	NM_004168.2	221	Gcc/Tcc	6/15	0.25089316948015	3	FACETS	1	0.951	1	0.591	0.516	0.672	CLONAL	1	TRUE	1	0.294924478653015	3		144	454	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911177	29911177	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	40	82	0	ENST00000376809.5:c.476C>G	p.Ala159Gly	p.A159G	ENST00000376809	NM_002116.7	159	gCg/gGg	3/8	0.294924478653015	3	FACETS	1	0.951	1	0.701	0.588	0.825	CLONAL	1	TRUE	1	0.294924478653015	3		82	222	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519933	66519933	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	72	241	0	ENST00000358598.2:c.416C>T	p.Ser139Leu	p.S139L	ENST00000358598	NM_212471.2	139	tCa/tTa	4/11	1	2	FACETS	0.802	0.701	0.911	0.802	0.701	0.911	CLONAL	1	TRUE	1	0.294924478653015	2		241	609	SUCCESS
APC	324	MSKCC	GRCh37	5	112174097	112174112	+	frameshift_variant	Frame_Shift_Del	DEL	AATTTCACTAAGTCGG	AATTTCACTAAGTCGG	-	novel	NA	P-0007998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	95	284	0	ENST00000257430.4:c.2808_2823del	p.Asn936LysfsTer14	p.N936Kfs*14	ENST00000257430	NM_000038.5	936	AATTTCACTAAGTCGGaa/aa	16/16	1	2	FACETS	0.966	0.861	1	0.966	0.861	1	CLONAL	1	TRUE	1	0.294924478653015	2		284	667	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599321	55599321	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913507	NA	P-0008001-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	130	342	0	ENST00000288135.5:c.2447A>T	p.Asp816Val	p.D816V	ENST00000288135	NM_000222.2	816	gAc/gTc	17/21	0.296485010648185	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.29	1		342	567	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618952	37618953	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0008001-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	193	336	0	ENST00000447079.4:c.629dup	p.Tyr210Ter	p.Y210*	ENST00000447079	NM_015083.1	210	tac/tAac	1/14	1	2	FACETS	0.848	0.786	0.912	1	0.992	1	CLONAL	2	TRUE	1	0.29	2		336	785	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577599	7577600	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1567550002	NA	P-0008055-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	143	228	0	ENST00000269305.4:c.681dup	p.Asp228Ter	p.D228*	ENST00000269305	NM_001126112.2	227	-/T	7/11	1	2	FACETS	0.861	0.789	0.936	0.861	0.789	0.936	CLONAL	1	TRUE	1	0.585626603424802	2		228	567	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098954	178098954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553488015	NA	P-0008055-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	30	271	0	ENST00000397062.3:c.91G>A	p.Gly31Arg	p.G31R	ENST00000397062	NM_006164.4	31	Gga/Aga	2/5	0.58041555073684	2	FACETS	0.132	0.106	0.162	0.066	0.053	0.081	SUBCLONAL	1	TRUE	0	0.585626603424802	2		271	776	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250867	153250867	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008055-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	155	430	0	ENST00000281708.4:c.1193C>A	p.Ser398Tyr	p.S398Y	ENST00000281708	NM_033632.3	398	tCt/tAt	8/12	0.585626603424802	1	FACETS	0.557	0.511	0.605	0.557	0.511	0.605	SUBCLONAL	1	TRUE	0	0.585626603424802	1		430	672	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953930	131953930	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008055-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	222	306	0	ENST00000265335.6:c.3333G>C	p.Met1111Ile	p.M1111I	ENST00000265335		1111	atG/atC	21/25	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.585626603424802	2		306	749	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986547	36986547	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008055-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	275	322	0	ENST00000354822.5:c.1142A>T	p.Asn381Ile	p.N381I	ENST00000354822	NM_001079668.2	381	aAc/aTc	3/3	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.585626603424802	2		322	923	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31381356	31381356	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008055-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	166	273	0	ENST00000328111.2:c.1081A>G	p.Lys361Glu	p.K361E	ENST00000328111	NM_006892.3	361	Aag/Gag	10/23	1	2	FACETS	0.887	0.818	0.959	0.887	0.818	0.959	CLONAL	1	TRUE	1	0.585626603424802	2		273	639	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968986	15969005	+	frameshift_variant	Frame_Shift_Del	DEL	CTGAAACAGGTAAGCAGCCG	CTGAAACAGGTAAGCAGCCG	-	novel	NA	P-0008055-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	183	301	0	ENST00000268712.3:c.4745_4764del	p.Ala1582GlufsTer28	p.A1582Efs*28	ENST00000268712	NM_006311.3	1582	gCGGCTGCTTACCTGTTTCAG/g	33/46	1	2	FACETS	0.848	0.785	0.914	0.848	0.785	0.914	CLONAL	1	TRUE	1	0.585626603424802	2		301	737	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937314	32937314	+	splice_acceptor_variant	Splice_Site	DEL	A	A	-	rs397507947	NA	P-0008055-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	217	233	0	ENST00000380152.3:c.7977-2del		p.X2659_splice	ENST00000380152		2659			0.585626603424802	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.585626603424802	1		233	516	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668619	52668619	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	60	505	0	ENST00000394830.3:c.1300C>T	p.Arg434Ter	p.R434*	ENST00000394830	NM_018313.4	434	Cga/Tga	12/30	0.268143664925795	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	0	0.268143664925795	1		505	334	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624297	89624297	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs797044910	NA	P-0008061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	72	439	0	ENST00000371953.3:c.71A>G	p.Asp24Gly	p.D24G	ENST00000371953	NM_000314.4	24	gAc/gGc	1/9	0.268143664925795	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	0	0.268143664925795	1		439	376	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246390	53246390	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	100	592	1	ENST00000375401.3:c.592C>T	p.Arg198Ter	p.R198*	ENST00000375401	NM_004187.3	198	Cga/Tga	5/26	0.168887890106111	0	FACETS	1	0.951	1			1	CLONAL	1	FALSE	NA	0.268143664925795	0		593	495	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77051698	77051698	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	41	856	0	ENST00000356341.3:c.1109G>T	p.Cys370Phe	p.C370F	ENST00000356341	NM_002576.4	370	tGc/tTc	11/15	0.199920474029084	1	FACETS	0.461	0.384	0.548	0.461	0.384	0.548	SUBCLONAL	1	FALSE	0	0.268143664925795	1		856	574	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30293200	30293200	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	23	810	0	ENST00000322652.5:c.490T>A	p.Phe164Ile	p.F164I	ENST00000322652	NM_015355.2	164	Ttc/Atc	5/16	0.199920474029084	1	FACETS	0.447	0.349	0.562	0.447	0.349	0.562	SUBCLONAL	1	FALSE	0	0.268143664925795	1		810	332	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226419	2226419	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	88	703	0	ENST00000398665.3:c.3899T>C	p.Leu1300Pro	p.L1300P	ENST00000398665	NM_032482.2	1300	cTg/cCg	27/28	1	2	FACETS	0.744	0.658	0.836	0.744	0.658	0.836	SUBCLONAL	1	FALSE	1	0.268143664925795	2		703	882	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023174	27023174	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	22	209	0	ENST00000324856.7:c.282del	p.Gly95AlafsTer6	p.G95Afs*6	ENST00000324856	NM_006015.4	94	Ccc/cc	1/20	1	2	FACETS	0.615	0.477	0.774	0.615	0.477	0.774	SUBCLONAL	1	FALSE	1	0.268143664925795	2		209	267	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191478	10191479	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0008061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	73	601	0	ENST00000256474.2:c.472dup	p.Leu158ProfsTer16	p.L158Pfs*16	ENST00000256474	NM_000551.3	157	-/C	3/3	0.268143664925795	1	FACETS	0.853	0.747	0.966	0.853	0.747	0.966	CLONAL	1	FALSE	0	0.268143664925795	1		601	553	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164778	47164778	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	66	630	0	ENST00000409792.3:c.1348del	p.Tyr450ThrfsTer34	p.Y450Tfs*34	ENST00000409792	NM_014159.6	450	Tac/ac	3/21	0.268143664925795	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	0	0.268143664925795	1		630	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0008160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	184	283	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.194685717338448	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.244781012309133	2		283	706	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241679	55241681	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	rs397517086	NA	P-0008160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	332	462	0	ENST00000275493.2:c.2127_2129del	p.Glu709_Thr710delinsAsp	p.E709_T710delinsD	ENST00000275493	NM_005228.3	709	gaAACt/gat	18/28	0.244781012309133	5	FACETS	1	0.988	1	0.858	0.812	0.906	CLONAL	3	TRUE	1	0.244781012309133	5		462	1080	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368289	45368290	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCC	novel	NA	P-0008160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	68	410	0	ENST00000262160.6:c.1310_1312dup	p.Trp437_Ile438insArg	p.W437_I438insR	ENST00000262160	NM_005901.5	438	att/aGGAtt	11/11	1	2	FACETS	0.53	0.46	0.607	0.53	0.46	0.607	SUBCLONAL	1	TRUE	1	0.244781012309133	2		410	1048	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0008176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	296	366	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.969	0.912	1	1	0.996	1	CLONAL	3	TRUE	1	0.189850889586524	2		366	1073	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988189	36988189	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0008176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	15	127	0	ENST00000354822.5:c.463+1G>A		p.X155_splice	ENST00000354822	NM_001079668.2	155			1	2	FACETS	1	0.745	1	1	0.745	1	CLONAL	1	TRUE	1	0.189850889586524	2		127	156	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069257	30069257	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0008176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	51	274	0	ENST00000338641.4:c.1123-1G>C		p.X375_splice	ENST00000338641	NM_000268.3	375			0.143664458668877	0	FACETS	0.704	0.602	0.815			1	SUBCLONAL	2	TRUE	0	0.189850889586524	0		274	309	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987148	36987149	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0008176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	23	193	0	ENST00000354822.5:c.539_540dup	p.Lys181AlafsTer48	p.K181Afs*48	ENST00000354822	NM_001079668.2	180	-/GC	3/3	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.189850889586524	2		193	218	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0008185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	15	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.155	0.112	0.206	0.155	0.112	0.206	SUBCLONAL	1	TRUE	1	0.531179495574798	2		249	365	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574678	41574679	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs754418509	NA	P-0008185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1584	96	484	1	ENST00000263253.7:c.6970dup	p.His2324ProfsTer55	p.H2324Pfs*55	ENST00000263253	NM_001429.3	2321	-/C	31/31	1	2	FACETS	0.215	0.19	0.242	0.215	0.19	0.242	SUBCLONAL	1	TRUE	1	0.531179495574798	2		485	1680	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1036354	1036354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1543	95	355	0	ENST00000358495.3:c.424G>A	p.Ala142Thr	p.A142T	ENST00000358495	NM_134424.2	142	Gca/Aca	6/12	1	2	FACETS	0.218	0.193	0.245	0.218	0.193	0.245	SUBCLONAL	1	TRUE	1	0.531179495574798	2		355	1638	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852242	128852242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140172891	NA	P-0008185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	216	228	1	ENST00000249373.3:c.2314C>T	p.Arg772Cys	p.R772C	ENST00000249373	NM_005631.4	772	Cgc/Tgc	12/12	1	2	FACETS	0.841	0.782	0.902	0.841	0.782	0.902	CLONAL	1	TRUE	1	0.531179495574798	2		229	967	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578284	212578284	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	66	384	1	ENST00000342788.4:c.973C>T	p.Pro325Ser	p.P325S	ENST00000342788	NM_005235.2	325	Cct/Tct	8/28	0.531179495574798	1	FACETS	0.251	0.218	0.288	0.251	0.218	0.288	SUBCLONAL	1	TRUE	0	0.531179495574798	1		385	726	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37056036	37056036	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs267607789	NA	P-0008185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	78	174	0	ENST00000231790.2:c.790+1G>A		p.X264_splice	ENST00000231790	NM_000249.3	264			0.531179495574798	1	FACETS	0.321	0.282	0.364	0.321	0.282	0.364	SUBCLONAL	1	TRUE	0	0.531179495574798	1		174	671	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149511562	149511562	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	93	232	0	ENST00000261799.4:c.1223C>A	p.Ser408Tyr	p.S408Y	ENST00000261799	NM_002609.3	408	tCc/tAc	8/23	1	2	FACETS	0.289	0.256	0.325	0.289	0.256	0.325	SUBCLONAL	1	TRUE	1	0.531179495574798	2		232	1210	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858171	27858171	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1567	144	461	0	ENST00000359303.2:c.400G>T	p.Glu134Ter	p.E134*	ENST00000359303	NM_003535.2	134	Gag/Tag	1/1	1	2	FACETS	0.317	0.287	0.348	0.317	0.287	0.348	SUBCLONAL	1	TRUE	1	0.531179495574798	2		461	1711	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424078	49424078	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1471	160	353	0	ENST00000301067.7:c.13984G>T	p.Glu4662Ter	p.E4662*	ENST00000301067	NM_003482.3	4662	Gaa/Taa	42/54	1	2	FACETS	0.369	0.337	0.403	0.369	0.337	0.403	SUBCLONAL	1	TRUE	1	0.531179495574798	2		353	1631	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425741	49425741	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	90	214	0	ENST00000301067.7:c.12747G>C	p.Gln4249His	p.Q4249H	ENST00000301067	NM_003482.3	4249	caG/caC	39/54	1	2	FACETS	0.336	0.297	0.378	0.336	0.297	0.378	SUBCLONAL	1	TRUE	1	0.531179495574798	2		214	1008	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434307	49434307	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1583	87	382	1	ENST00000301067.7:c.7246C>T	p.Gln2416Ter	p.Q2416*	ENST00000301067	NM_003482.3	2416	Cag/Tag	31/54	1	2	FACETS	0.196	0.172	0.222	0.196	0.172	0.222	SUBCLONAL	1	TRUE	1	0.531179495574798	2		383	1670	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438001	49438001	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1239	105	297	0	ENST00000301067.7:c.5170G>T	p.Asp1724Tyr	p.D1724Y	ENST00000301067	NM_003482.3	1724	Gat/Tat	21/54	1	2	FACETS	0.294	0.262	0.328	0.294	0.262	0.328	SUBCLONAL	1	TRUE	1	0.531179495574798	2		297	1344	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819348	3819348	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	90	215	0	ENST00000262367.5:c.2887C>T	p.Gln963Ter	p.Q963*	ENST00000262367	NM_004380.2	963	Cag/Tag	15/31	1	2	FACETS	0.413	0.366	0.464	0.413	0.366	0.464	SUBCLONAL	1	TRUE	1	0.531179495574798	2		215	820	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877465	89877465	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1408	75	313	0	ENST00000389301.3:c.298G>C	p.Asp100His	p.D100H	ENST00000389301	NM_000135.2	100	Gat/Cat	4/43	1	2	FACETS	0.19	0.166	0.217	0.19	0.166	0.217	SUBCLONAL	1	TRUE	1	0.531179495574798	2		313	1483	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2193747	2193747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767206745	NA	P-0008185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1318	78	234	0	ENST00000398665.3:c.553G>A	p.Val185Ile	p.V185I	ENST00000398665	NM_032482.2	185	Gtc/Atc	6/28	1	2	FACETS	0.21	0.184	0.239	0.21	0.184	0.239	SUBCLONAL	1	TRUE	1	0.531179495574798	2		234	1396	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945273	54945273	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	48	170	0	ENST00000312783.6:c.1153G>C	p.Ala385Pro	p.A385P	ENST00000312783	NM_198436.1	385	Gca/Cca	10/10	NA	2	FACETS	0.222	0.187	0.261			1	INDETERMINATE	1	TRUE	NA	0.531179495574798	2		170	814	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413951	139413951	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1592	96	324	0	ENST00000277541.6:c.809del	p.Gly270ValfsTer7	p.G270Vfs*7	ENST00000277541	NM_017617.3	270	gGt/gt	5/34	0.531179495574798	2	FACETS	0.214	0.19	0.241	0.107	0.095	0.121	SUBCLONAL	1	TRUE	0	0.531179495574798	2		324	1688	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	30	509	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.861	0.694	1	0.861	0.694	1	CLONAL	1	TRUE	1	0.173251623997307	2		509	402	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	20	425	0	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.843	0.645	1	0.843	0.645	1	CLONAL	1	TRUE	1	0.173251623997307	2		425	274	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	35	264	0	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	0.902	0.739	1	0.902	0.739	1	CLONAL	1	TRUE	1	0.173251623997307	2		264	448	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	31	356	1	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.758	0.612	0.924	0.758	0.612	0.924	CLONAL	1	TRUE	1	0.173251623997307	2		357	472	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522598	157522598	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554236040	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	48	200	0	ENST00000346085.5:c.4870C>T	p.Arg1624Ter	p.R1624*	ENST00000346085	NM_020732.3	1624	Cga/Tga	18/20	1	2	FACETS	0.759	0.644	0.885	1	0.963	1	SUBCLONAL	2	TRUE	1	0.173251623997307	2		200	365	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432651	49432651	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs727503983	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	48	317	1	ENST00000301067.7:c.8488C>T	p.Arg2830Ter	p.R2830*	ENST00000301067	NM_003482.3	2830	Cga/Tga	34/54	1	2	FACETS	0.757	0.642	0.883	1	0.963	1	SUBCLONAL	2	TRUE	1	0.173251623997307	2		318	366	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177615	56177615	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs563304338	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	28	268	0	ENST00000399503.3:c.2588T>C	p.Val863Ala	p.V863A	ENST00000399503	NM_005921.1	863	gTg/gCg	14/20	1	2	FACETS	0.822	0.657	1	0.822	0.657	1	CLONAL	1	TRUE	1	0.173251623997307	2		268	393	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251907	153251907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	37	497	4	ENST00000281708.4:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000281708	NM_033632.3	367	Cga/Tga	7/12	1	2	FACETS	0.804	0.662	0.964	0.804	0.662	0.964	CLONAL	1	TRUE	1	0.173251623997307	2		501	531	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781157	135781157	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	37	522	0	ENST00000298552.3:c.1808del	p.Pro603ArgfsTer26	p.P603Rfs*26	ENST00000298552	NM_001162426.1	603	cCg/cg	15/23	1	2	FACETS	0.892	0.735	1	0.892	0.735	1	CLONAL	1	TRUE	1	0.173251623997307	2		522	479	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248633	59248634	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	35	319	0	ENST00000371222.2:c.109_110del	p.Ser37HisfsTer69	p.S37Hfs*69	ENST00000371222	NM_002228.3	37	AGc/c	1/1	1	2	FACETS	0.978	0.802	1	0.978	0.802	1	CLONAL	1	TRUE	1	0.173251623997307	2		319	413	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	10	42	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	1	2	FACETS	0.77	0.529	1	1	0.852	1	CLONAL	2	TRUE	1	0.173251623997307	2		42	75	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942751	44942751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763592177	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	35	411	0	ENST00000377967.4:c.3331C>T	p.Arg1111Cys	p.R1111C	ENST00000377967	NM_021140.2	1111	Cgt/Tgt	23/29	0.120894695632288	0	FACETS	0.715	0.586	0.861			1	SUBCLONAL	1	TRUE	0	0.173251623997307	0		411	467	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15374343	15374343	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199679781	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	48	346	0	ENST00000263377.2:c.1229G>A	p.Arg410His	p.R410H	ENST00000263377	NM_058243.2	410	cGt/cAt	7/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.173251623997307	2		346	374	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120529656	120529656	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1553202301	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	26	322	0	ENST00000256646.2:c.801C>A	p.His267Gln	p.H267Q	ENST00000256646	NM_024408.3	267	caC/caA	5/34	1	2	FACETS	0.72	0.569	0.892	0.72	0.569	0.892	SUBCLONAL	1	TRUE	1	0.173251623997307	2		322	417	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568897	212568897	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	30	262	0	ENST00000342788.4:c.1221G>A	p.Trp407Ter	p.W407*	ENST00000342788	NM_005235.2	407	tgG/tgA	11/28	1	2	FACETS	0.866	0.698	1	0.866	0.698	1	CLONAL	1	TRUE	1	0.173251623997307	2		262	400	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924937	49924937	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	23	398	0	ENST00000296474.3:c.4006G>A	p.Val1336Ile	p.V1336I	ENST00000296474	NM_002447.2	1336	Gta/Ata	20/20	0.173251623997307	1	FACETS	0.617	0.48	0.776	0.617	0.48	0.776	SUBCLONAL	1	TRUE	0	0.173251623997307	1		398	393	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549469	187549469	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	30	222	0	ENST00000441802.2:c.4649T>C	p.Val1550Ala	p.V1550A	ENST00000441802	NM_005245.3	1550	gTc/gCc	9/27	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.173251623997307	2		222	319	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38949932	38949932	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	30	271	0	ENST00000357387.3:c.4018A>T	p.Arg1340Ter	p.R1340*	ENST00000357387	NM_152756.3	1340	Aga/Tga	31/38	1	2	FACETS	0.789	0.635	0.964	0.789	0.635	0.964	CLONAL	1	TRUE	1	0.173251623997307	2		271	439	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685262	86685262	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776455532	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	43	229	0	ENST00000274376.6:c.2978G>A	p.Arg993His	p.R993H	ENST00000274376	NM_002890.2	993	cGt/cAt	24/25	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.173251623997307	2		229	373	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552811	106552811	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs779670956	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	45	402	0	ENST00000369096.4:c.776A>G	p.Asn259Ser	p.N259S	ENST00000369096	NM_001198.3	259	aAc/aGc	5/7	1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	1	0.173251623997307	2		402	518	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974166	2974166	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	22	358	1	ENST00000396946.4:c.1439C>T	p.Ser480Leu	p.S480L	ENST00000396946	NM_032415.4	480	tCg/tTg	10/25	1	2	FACETS	0.751	0.582	0.948	0.751	0.582	0.948	CLONAL	1	TRUE	1	0.173251623997307	2		359	338	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231112	98231112	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	16	152	0	ENST00000331920.6:c.2171A>C	p.Glu724Ala	p.E724A	ENST00000331920	NM_000264.3	724	gAg/gCg	14/24	1	2	FACETS	0.821	0.608	1	0.821	0.608	1	CLONAL	1	TRUE	1	0.173251623997307	2		152	225	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139804418	139804418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746259933	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	52	447	1	ENST00000247668.2:c.575G>A	p.Cys192Tyr	p.C192Y	ENST00000247668	NM_021138.3	192	tGc/tAc	6/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.173251623997307	2		448	434	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741541	17741541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773231763	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	10	157	0	ENST00000250003.3:c.212C>T	p.Pro71Leu	p.P71L	ENST00000250003	NM_002478.4	71	cCg/cTg	1/3	1	2	FACETS	0.861	0.586	1	0.861	0.586	1	CLONAL	1	TRUE	1	0.173251623997307	2		157	134	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999042	100999042	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241953281	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	29	297	1	ENST00000325455.5:c.760G>A	p.Ala254Thr	p.A254T	ENST00000325455	NM_001202474.3	254	Gcg/Acg	1/8	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.173251623997307	2		298	245	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198453	108198453	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	24	234	0	ENST00000278616.4:c.7057C>A	p.Pro2353Thr	p.P2353T	ENST00000278616	NM_000051.3	2353	Cct/Act	48/63	1	2	FACETS	0.743	0.582	0.928	0.743	0.582	0.928	CLONAL	1	TRUE	1	0.173251623997307	2		234	373	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864892	57864892	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	42	503	0	ENST00000228682.2:c.2369A>G	p.Tyr790Cys	p.Y790C	ENST00000228682	NM_005269.2	790	tAc/tGc	12/12	1	2	FACETS	0.998	0.833	1	0.998	0.833	1	CLONAL	1	TRUE	1	0.173251623997307	2		503	486	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118715	115118715	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	36	320	0	ENST00000257566.3:c.626T>A	p.Leu209His	p.L209H	ENST00000257566	NM_016569.3	209	cTc/cAc	2/8	1	2	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	TRUE	1	0.173251623997307	2		320	406	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209310	133209310	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	26	328	0	ENST00000320574.5:c.6076A>G	p.Arg2026Gly	p.R2026G	ENST00000320574	NM_006231.2	2026	Agg/Ggg	44/49	1	2	FACETS	0.921	0.73	1	0.921	0.73	1	CLONAL	1	TRUE	1	0.173251623997307	2		328	326	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942686	48942686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767011440	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	32	312	0	ENST00000267163.4:c.1073G>A	p.Arg358Gln	p.R358Q	ENST00000267163	NM_000321.2	358	cGa/cAa	11/27	1	2	FACETS	0.672	0.544	0.816	0.672	0.544	0.816	SUBCLONAL	1	TRUE	1	0.173251623997307	2		312	550	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95577677	95577677	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1060503584	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	41	427	0	ENST00000393063.1:c.2233C>T	p.Arg745Ter	p.R745*	ENST00000393063	NM_030621.3	745	Cga/Tga	15/28	1	2	FACETS	0.881	0.734	1	0.881	0.734	1	CLONAL	1	TRUE	1	0.173251623997307	2		427	537	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943691	9943691	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	28	247	0	ENST00000330684.3:c.1250T>C	p.Val417Ala	p.V417A	ENST00000330684	NM_001134407.1	417	gTc/gCc	5/13	1	2	FACETS	0.937	0.749	1	0.937	0.749	1	CLONAL	1	TRUE	1	0.173251623997307	2		247	345	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40460202	40460202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	75	389	0	ENST00000345506.4:c.1913G>A	p.Arg638His	p.R638H	ENST00000345506	NM_003152.3	638	cGc/cAc	17/20	0.173251623997307	1	FACETS	0.848	0.746	0.958	1	0.98	1	CLONAL	2	TRUE	0	0.173251623997307	1		389	466	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732391	74732391	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	48	517	0	ENST00000359995.5:c.518C>T	p.Ser173Phe	p.S173F	ENST00000359995	NM_001195427.1	173	tCc/tTc	2/3	0.167348412251896	2	FACETS	1	0.927	1	0.585	0.494	0.684	CLONAL	1	TRUE	0	0.173251623997307	2		517	474	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208404	5208404	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	22	277	0	ENST00000357368.4:c.5488-2A>G		p.X1830_splice	ENST00000357368	NM_002850.3	1830			1	2	FACETS	0.944	0.733	1	0.944	0.733	1	CLONAL	1	TRUE	1	0.173251623997307	2		277	269	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221206	5221206	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200191658	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	23	260	0	ENST00000357368.4:c.3260C>T	p.Thr1087Met	p.T1087M	ENST00000357368	NM_002850.3	1087	aCg/aTg	20/38	1	2	FACETS	0.945	0.738	1	0.945	0.738	1	CLONAL	1	TRUE	1	0.173251623997307	2		260	281	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184378	7184378	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	33	298	0	ENST00000302850.5:c.923A>C	p.Asn308Thr	p.N308T	ENST00000302850	NM_000208.2	308	aAc/aCc	3/22	1	2	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	TRUE	1	0.173251623997307	2		298	368	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656873	45656873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	27	287	0	ENST00000407780.3:c.283G>T	p.Asp95Tyr	p.D95Y	ENST00000407780	NM_001283052.1	95	Gac/Tac	3/7	1	2	FACETS	0.903	0.719	1	0.903	0.719	1	CLONAL	1	TRUE	1	0.173251623997307	2		287	345	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855033	76855033	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	56	355	0	ENST00000373344.5:c.5803A>G	p.Lys1935Glu	p.K1935E	ENST00000373344	NM_000489.3	1935	Aaa/Gaa	25/35	0.120894695632288	0	FACETS	1	0.947	1			1	CLONAL	1	TRUE	0	0.173251623997307	0		355	435	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355551	15355552	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	34	442	0	ENST00000263377.2:c.2180dup	p.Lys728GlufsTer91	p.K728Efs*91	ENST00000263377	NM_058243.2	727	aag/aaAg	12/20	1	2	FACETS	0.969	0.792	1	0.969	0.792	1	CLONAL	1	TRUE	1	0.173251623997307	2		442	405	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71019935	71019936	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	27	218	0	ENST00000318789.4:c.1673dup	p.Asn558LysfsTer22	p.N558Kfs*22	ENST00000318789	NM_032682.5	558	aac/aaAc	19/21	1	2	FACETS	0.914	0.728	1	0.914	0.728	1	CLONAL	1	TRUE	1	0.173251623997307	2		218	341	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249750	110249751	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	17	173	0	ENST00000374672.4:c.924dup	p.Arg309AlafsTer14	p.R309Afs*14	ENST00000374672	NM_004235.4	308	-/G	3/5	1	2	FACETS	0.814	0.609	1	0.814	0.609	1	CLONAL	1	TRUE	1	0.173251623997307	2		173	241	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276861	15276861	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	27	201	0	ENST00000263388.2:c.5404del	p.Ala1802LeufsTer23	p.A1802Lfs*23	ENST00000263388	NM_000435.2	1802	Gct/ct	30/33	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.173251623997307	2		201	280	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088659	27088659	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	39	578	1	ENST00000324856.7:c.2272del	p.Gln758ArgfsTer75	p.Q758Rfs*75	ENST00000324856	NM_006015.4	756	aaC/aa	7/20	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.173251623997307	2		579	427	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891126	151891126	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	37	232	0	ENST00000262189.6:c.4628del	p.Pro1543HisfsTer20	p.P1543Hfs*20	ENST00000262189	NM_170606.2	1543	cCa/ca	31/59	1	2	FACETS	1	0.827	1	1	0.827	1	CLONAL	1	TRUE	1	0.173251623997307	2		232	426	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487504	38487504	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748767479	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	47	306	3	ENST00000254066.5:c.38del	p.Gly13AlafsTer29	p.G13Afs*29	ENST00000254066	NM_000964.3	12	Ggg/gg	2/9	1	2	FACETS	0.793	0.672	0.926	1	0.965	1	CLONAL	2	TRUE	1	0.173251623997307	2		309	342	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780216	9780216	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	20	344	1	ENST00000377346.4:c.1389del	p.Asn464ThrfsTer83	p.N464Tfs*83	ENST00000377346	NM_005026.3	462	aaC/aa	11/24	1	2	FACETS	0.647	0.494	0.826	0.647	0.494	0.826	SUBCLONAL	1	TRUE	1	0.173251623997307	2		345	357	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755426	39755427	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0008188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	18	335	0	ENST00000288319.7:c.1338dup	p.Ala447CysfsTer19	p.A447Cfs*19	ENST00000288319	NM_182918.3	446	-/T	10/10	1	2	FACETS	0.658	0.495	0.85	0.658	0.495	0.85	SUBCLONAL	1	TRUE	1	0.173251623997307	2		335	316	SUCCESS
FH	2271	MSKCC	GRCh37	1	241671931	241671931	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	201	452	1	ENST00000366560.3:c.710A>G	p.Gln237Arg	p.Q237R	ENST00000366560	NM_000143.3	237	cAg/cGg	5/10	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		453	665	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619309	37619309	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	125	247	0	ENST00000447079.4:c.985C>T	p.Arg329Ter	p.R329*	ENST00000447079	NM_015083.1	329	Cga/Tga	1/14	0.3	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		247	392	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916517	39916517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	448	351	1	ENST00000378444.4:c.4486G>A	p.Ala1496Thr	p.A1496T	ENST00000378444	NM_001123385.1	1496	Gca/Aca	11/15	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	0	NA	2		352	626	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671654	67671655	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0008235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	202	371	1	ENST00000264010.4:c.2070dup	p.Glu691ArgfsTer5	p.E691Rfs*5	ENST00000264010	NM_006565.3	688	gta/gtAa	12/12	0.3	3	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	3		372	705	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627418	37627418	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	244	479	0	ENST00000447079.4:c.1337del	p.Lys446SerfsTer6	p.K446Sfs*6	ENST00000447079	NM_015083.1	445	Aaa/aa	2/14	0.3	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		479	837	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060571	38060574	+	stop_lost	Nonstop_Mutation	ONP	TAGG	TAGG	AAGA	novel	NA	P-0008235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1267	315	721	0	ENST00000250448.2:c.1415_1418delinsTCTT	p.Ser472_Ter473delinsPheLeu	p.S472_*473delinsFL	ENST00000250448	NM_004496.3	472	tCCTAg/tTCTTg	2/2	0.261035508278159	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		721	1582	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971177	21971177	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913382	NA	P-0008282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	54	108	0	ENST00000304494.5:c.181G>T	p.Glu61Ter	p.E61*	ENST00000304494	NM_000077.4	61	Gag/Tag	2/3	0.329916850363756	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.329916850363756	1		108	208	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578538	7578538	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1131691037	NA	P-0008282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	82	208	1	ENST00000269305.4:c.392A>T	p.Asn131Ile	p.N131I	ENST00000269305	NM_001126112.2	131	aAc/aTc	5/11	0.329916850363756	1	FACETS	0.798	0.706	0.897	0.798	0.706	0.897	SUBCLONAL	1	TRUE	0	0.329916850363756	1		209	520	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411613	116411613	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	188	281	0	ENST00000397752.3:c.2792T>G	p.Phe931Cys	p.F931C	ENST00000397752	NM_000245.2	931	tTc/tGc	13/21	0.300776917577071	3	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	1	0.329916850363756	3		281	663	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411622	116411622	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	177	301	0	ENST00000397752.3:c.2801T>C	p.Leu934Ser	p.L934S	ENST00000397752	NM_000245.2	934	tTg/tCg	13/21	0.300776917577071	3	FACETS	0.907	0.839	0.978	0.907	0.839	0.978	CLONAL	2	TRUE	1	0.329916850363756	3		301	689	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411869	116411989	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTTAACAAGCTCTTTCTTTCTCTCTGTTTTAAGATCTGGGCAGTGAATTAGTTCGCTACGATGCAAGAGTACACACTCCTCATTTGGATAGGCTTGTAAGTGCCCGAAGTGTAAGCCCAA	CTTTAACAAGCTCTTTCTTTCTCTCTGTTTTAAGATCTGGGCAGTGAATTAGTTCGCTACGATGCAAGAGTACACACTCCTCATTTGGATAGGCTTGTAAGTGCCCGAAGTGTAAGCCCAA	-	novel	NA	P-0008282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	57	108	0	ENST00000397752.3:c.2888-32_2976del		p.X963_splice	ENST00000397752	NM_000245.2	963		14/21	0.300776917577071	3	FACETS	0.86	0.747	0.981	0.86	0.747	0.981	CLONAL	2	TRUE	1	0.329916850363756	3		108	234	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593368	67593369	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0008282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	49	223	0	ENST00000274335.5:c.2115dup	p.His706AlafsTer35	p.H706Afs*35	ENST00000274335		705	cag/caGg	15/15	0.189967964850369	3	FACETS	0.485	0.41	0.569	0.243	0.205	0.285	INDETERMINATE	1	TRUE	1	0.329916850363756	3		223	713	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0008303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	76	265	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	0.907	0.804	0.708	0.907	CLONAL	1	TRUE	1	0.418313517713076	2		265	452	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	88	140	0				ENST00000310581	NM_198253.2	-/1132			0.418313517713076	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	0	0.418313517713076	1		140	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs863224499	NA	P-0008303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	195	432	1	ENST00000269305.4:c.672+1G>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.418313517713076	1	FACETS	0.847	0.784	0.911	0.847	0.784	0.911	CLONAL	1	TRUE	0	0.418313517713076	1		433	871	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662326	227662327	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0008303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	86	188	0	ENST00000305123.5:c.1128dup	p.Met377HisfsTer20	p.M377Hfs*20	ENST00000305123	NM_005544.2	376	-/C	1/2	1	2	FACETS	0.783	0.695	0.877	0.783	0.695	0.877	SUBCLONAL	1	TRUE	1	0.418313517713076	2		188	525	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845699	68845700	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0008304-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	232	514	2	ENST00000261769.5:c.946dup	p.Met316AsnfsTer5	p.M316Nfs*5	ENST00000261769	NM_004360.3	315	-/A	7/16	0.3	1	FACETS	0.891	0.834	0.948	1	0.996	1	CLONAL	4	TRUE	0	0.17	1		516	701	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873229	71873229	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	29	798	0	ENST00000357731.5:c.965T>G	p.Ile322Ser	p.I322S	ENST00000357731	NM_173808.2	322	aTt/aGt	7/7	1	2	FACETS	0.285	0.228	0.351	0.285	0.228	0.351	SUBCLONAL	1	TRUE	1	0.351262815623799	2		798	579	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061229	38061230	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0008356-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	56	439	0	ENST00000250448.2:c.759_760insAG	p.Phe254SerfsTer68	p.F254Sfs*68	ENST00000250448	NM_004496.3	253	-/AG	2/2	1	2	FACETS	0.799	0.687	0.921	0.799	0.687	0.921	CLONAL	1	TRUE	1	0.351262815623799	2		439	399	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188078	11188078	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	80	354	0	ENST00000361445.4:c.6016G>T	p.Val2006Phe	p.V2006F	ENST00000361445	NM_004958.3	2006	Gtc/Ttc	43/58	NA	2	FACETS	0.819	0.726	0.918			1	INDETERMINATE	1	TRUE	NA	0.532031687937389	2		354	367	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494650	2494650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762829374	NA	P-0008399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	57	385	0	ENST00000355716.4:c.790G>A	p.Val264Ile	p.V264I	ENST00000355716	NM_003820.2	264	Gtc/Atc	8/8	NA	2	FACETS	0.474	0.407	0.547			1	INDETERMINATE	1	TRUE	NA	0.532031687937389	2		385	452	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937170	39937170	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	204	491	0	ENST00000378444.4:c.13A>G	p.Thr5Ala	p.T5A	ENST00000378444	NM_001123385.1	5	Acc/Gcc	2/15	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.532031687937389	2		491	570	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643325	52643330	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATACCG	ATACCG	-	novel	NA	P-0008399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	110	427	0	ENST00000394830.3:c.2566_2567+4del		p.X856_splice	ENST00000394830	NM_018313.4	856		17/30	0.510544197831055	1	FACETS	0.792	0.718	0.869	0.792	0.718	0.869	SUBCLONAL	1	TRUE	0	0.532031687937389	1		427	383	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183817	10183818	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0008399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	114	265	1	ENST00000256474.2:c.287dup	p.Pro97AlafsTer35	p.P97Afs*35	ENST00000256474	NM_000551.3	96	cag/cAag	1/3	0.510544197831055	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.532031687937389	1		266	306	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0008400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	61	647	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	0.653	0.561	0.753	0.653	0.561	0.753	SUBCLONAL	1	TRUE	1	0.193301787668759	2		647	967	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0008400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	41	331	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.867	0.722	1	0.867	0.722	1	CLONAL	1	TRUE	1	0.193301787668759	2		331	489	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916957	178916957	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	192	465	0	ENST00000263967.3:c.344G>C	p.Arg115Pro	p.R115P	ENST00000263967	NM_006218.2	115	cGa/cCa	2/21	0.383385887966706	3	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.383385887966706	3		465	990	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249013	55249014	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACC	rs397517112	NA	P-0008487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	134	247	0	ENST00000275493.2:c.2312_2314dup	p.Asn771_Pro772insHis	p.N771_P772insH	ENST00000275493	NM_005228.3	771	aac/aACCac	20/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.383385887966706	2		247	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578098	7578176	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CCCCCCTACTGCTCACCTGGAGGGCCACTGACAACCACCCTTAACCCCTCCTCCCAGAGACCCCAGTTGCAAACCAGAC	CCCCCCTACTGCTCACCTGGAGGGCCACTGACAACCACCCTTAACCCCTCCTCCCAGAGACCCCAGTTGCAAACCAGAC	-	novel	NA	P-0008487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	142	168	0	ENST00000269305.4:c.672+1_672+79del		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.251613721118086	1	FACETS	0.998	0.926	1	1	0.992	1	CLONAL	2	TRUE	0	0.383385887966706	1		168	300	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0008568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	71	366	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.126443683806956	3	FACETS	0.838	0.729	0.956	0.419	0.364	0.478	CLONAL	1	TRUE	1	0.17	3		366	1082	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455090	50455090	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	45	260	2	ENST00000331340.3:c.637C>T	p.Arg213Ter	p.R213*	ENST00000331340	NM_006060.4	213	Cga/Tga	6/8	1	2	FACETS	0.682	0.572	0.805	0.682	0.572	0.805	SUBCLONAL	1	TRUE	1	0.17	2		262	776	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604754	48604754	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	76	383	0	ENST00000342988.3:c.1576G>T	p.Glu526Ter	p.E526*	ENST00000342988	NM_005359.5	526	Gaa/Taa	12/12	1	2	FACETS	0.859	0.751	0.976	0.859	0.751	0.976	CLONAL	1	TRUE	1	0.17	2		383	1041	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434090	49434090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779629382	NA	P-0008568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	41	178	0	ENST00000301067.7:c.7463C>T	p.Ser2488Leu	p.S2488L	ENST00000301067	NM_003482.3	2488	tCg/tTg	31/54	0.126443683806956	3	FACETS	1	0.93	1	0.617	0.514	0.731	CLONAL	1	TRUE	1	0.17	3		178	424	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129867	55129867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373126818	NA	P-0008568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	57	426	0	ENST00000257290.5:c.401C>T	p.Thr134Met	p.T134M	ENST00000257290	NM_006206.4	134	aCg/aTg	4/23	0.126443683806956	0	FACETS	0.565	0.483	0.655			1	SUBCLONAL	1	TRUE	0	0.17	0		426	985	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231329	46231329	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0008568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	60	300	0	ENST00000334344.6:c.1169T>G	p.Leu390Ter	p.L390*	ENST00000334344	NM_152641.2	390	tTa/tGa	10/21	0.126443683806956	3	FACETS	0.865	0.744	0.999	0.433	0.372	0.5	CLONAL	1	TRUE	1	0.17	3		300	885	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923281	26923281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1229	74	461	0	ENST00000381527.3:c.277G>A	p.Val93Met	p.V93M	ENST00000381527	NM_001260.1	93	Gtg/Atg	3/13	1	2	FACETS	0.668	0.583	0.761	0.668	0.583	0.761	SUBCLONAL	1	TRUE	1	0.17	2		461	1303	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457713	67457713	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	59	397	0	ENST00000327367.4:c.523A>G	p.Asn175Asp	p.N175D	ENST00000327367	NM_005902.3	175	Aat/Gat	3/9	0.3	3	FACETS	0.786	0.674	0.909			1	CLONAL	1	TRUE	NA	0.17	3		397	958	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604785	48604785	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	62	324	0	ENST00000342988.3:c.1607T>C	p.Leu536Pro	p.L536P	ENST00000342988	NM_005359.5	536	cTa/cCa	12/12	1	2	FACETS	0.783	0.675	0.902	0.783	0.675	0.902	CLONAL	1	TRUE	1	0.17	2		324	931	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117948	70117949	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0008568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	28	157	0	ENST00000245479.2:c.419dup	p.Lys141GlnfsTer111	p.K141Qfs*111	ENST00000245479	NM_000346.3	139	ctg/ctGg	1/3	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.17	2		157	242	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566237	95566238	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1131691195	NA	P-0008568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	76	265	0	ENST00000393063.1:c.4085dup	p.Lys1363GlufsTer13	p.K1363Efs*13	ENST00000393063	NM_030621.3	1362	aag/aaAg	23/28	0.3	2	FACETS	0.853	0.746	0.969			1	CLONAL	1	TRUE	NA	0.17	2		265	1048	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	119	140	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.399018918899742	2		140	514	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934194	48934194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	134	293	0	ENST00000267163.4:c.649C>T	p.Gln217Ter	p.Q217*	ENST00000267163	NM_000321.2	217	Cag/Tag	7/27	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.399018918899742	2		293	626	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652134	36652135	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0008595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	114	261	0	ENST00000244741.5:c.259dup	p.Asp87GlyfsTer2	p.D87Gfs*2	ENST00000244741	NM_000389.4	86	cgg/cGgg	2/3	1	2	FACETS	0.973	0.879	1	0.973	0.879	1	CLONAL	1	TRUE	1	0.399018918899742	2		261	587	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740216	162740216	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775098890	NA	P-0008595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	327	347	1	ENST00000367921.3:c.1418G>A	p.Arg473His	p.R473H	ENST00000367921	NM_006182.2	473	cGc/cAc	12/18	0.315880706300896	3	FACETS	0.996	0.943	1	0.996	0.943	1	CLONAL	2	TRUE	1	0.399018918899742	3		348	987	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857481	68857481	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	89	273	1	ENST00000261769.5:c.2116C>T	p.Gln706Ter	p.Q706*	ENST00000261769	NM_004360.3	706	Caa/Taa	13/16	0.399018918899742	1	FACETS	0.886	0.791	0.987	0.886	0.791	0.987	CLONAL	1	TRUE	0	0.399018918899742	1		274	403	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	222	524	0	ENST00000267101.3:c.273G>A	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atA	3/28	1	2	FACETS	0.919	0.854	0.986	0.919	0.854	0.986	CLONAL	1	TRUE	1	0.399018918899742	2		524	1211	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519851	29519851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762358335	NA	P-0008595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	174	406	3	ENST00000389048.3:c.1720G>A	p.Gly574Arg	p.G574R	ENST00000389048	NM_004304.4	574	Ggg/Agg	9/29	1	2	FACETS	0.938	0.863	1	0.938	0.863	1	CLONAL	1	TRUE	1	0.399018918899742	2		409	930	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491177	120491177	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	89	293	0	ENST00000256646.2:c.2612C>A	p.Thr871Asn	p.T871N	ENST00000256646	NM_024408.3	871	aCc/aAc	17/34	1	2	FACETS	0.705	0.625	0.789	0.705	0.625	0.789	SUBCLONAL	1	TRUE	1	0.399018918899742	2		293	633	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145702	61145702	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	141	323	0	ENST00000295025.8:c.814A>G	p.Ser272Gly	p.S272G	ENST00000295025	NM_002908.2	272	Agt/Ggt	7/11	1	2	FACETS	0.941	0.858	1	0.941	0.858	1	CLONAL	1	TRUE	1	0.399018918899742	2		323	751	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5462911	5462911	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	93	258	0	ENST00000381577.3:c.472G>C	p.Glu158Gln	p.E158Q	ENST00000381577	NM_014143.3	158	Gag/Cag	4/7	NA	2	FACETS	0.793	0.706	0.885			1	INDETERMINATE	1	TRUE	NA	0.399018918899742	2		258	588	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486087	8486087	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	127	420	0	ENST00000356435.5:c.2730G>C	p.Glu910Asp	p.E910D	ENST00000356435		910	gaG/gaC	17/35	0.321236194333316	1	FACETS	0.653	0.592	0.718	0.653	0.592	0.718	SUBCLONAL	1	TRUE	0	0.399018918899742	1		420	780	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445971	49445971	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	213	537	0	ENST00000301067.7:c.1495G>T	p.Glu499Ter	p.E499*	ENST00000301067	NM_003482.3	499	Gag/Tag	10/54	1	2	FACETS	0.821	0.761	0.884	0.821	0.761	0.884	CLONAL	1	TRUE	1	0.399018918899742	2		537	1300	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446079	49446079	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1382	226	686	0	ENST00000301067.7:c.1387G>C	p.Glu463Gln	p.E463Q	ENST00000301067	NM_003482.3	463	Gag/Cag	10/54	1	2	FACETS	0.704	0.654	0.757	0.704	0.654	0.757	SUBCLONAL	1	TRUE	1	0.399018918899742	2		686	1608	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489555	56489555	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	149	411	0	ENST00000267101.3:c.2020A>G	p.Lys674Glu	p.K674E	ENST00000267101	NM_001982.3	674	Aaa/Gaa	17/28	1	2	FACETS	0.903	0.826	0.984	0.903	0.826	0.984	CLONAL	1	TRUE	1	0.399018918899742	2		411	827	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349570	89349570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1611	454	1157	0	ENST00000301030.4:c.3380G>A	p.Arg1127Lys	p.R1127K	ENST00000301030	NM_001256183.1	1127	aGa/aAa	9/13	0.399018918899742	1	FACETS	0.882	0.839	0.926	0.882	0.839	0.926	CLONAL	1	TRUE	0	0.399018918899742	1		1157	2065	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141483	11141483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	126	442	1	ENST00000358026.2:c.3460C>T	p.Leu1154Phe	p.L1154F	ENST00000358026	NM_001128849.1	1154	Ctc/Ttc	25/36	1	2	FACETS	0.718	0.65	0.791	0.718	0.65	0.791	SUBCLONAL	1	TRUE	1	0.399018918899742	2		443	879	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143980	11143980	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	131	262	0	ENST00000358026.2:c.3561G>C	p.Gln1187His	p.Q1187H	ENST00000358026	NM_001128849.1	1187	caG/caC	26/36	1	2	FACETS	0.957	0.87	1	0.957	0.87	1	CLONAL	1	TRUE	1	0.399018918899742	2		262	686	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267938	46267938	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0008595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	269	716	0	ENST00000371998.3:c.2699C>G	p.Ser900Ter	p.S900*	ENST00000371998		900	tCa/tGa	14/23	NA	2	FACETS	0.922	0.863	0.984			1	INDETERMINATE	1	TRUE	NA	0.399018918899742	2		716	1462	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907771	76907771	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1471	254	718	0	ENST00000373344.5:c.4390G>A	p.Glu1464Lys	p.E1464K	ENST00000373344	NM_000489.3	1464	Gaa/Aaa	15/35	0.321236194333316	1	FACETS	0.591	0.551	0.632	0.591	0.551	0.632	SUBCLONAL	1	TRUE	0	0.399018918899742	1		718	1725	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652032	36652057	+	frameshift_variant	Frame_Shift_Del	DEL	GACTTTGTCACCGAGACACCACTGGA	GACTTTGTCACCGAGACACCACTGGA	-	novel	NA	P-0008595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	174	429	0	ENST00000244741.5:c.155_180del	p.Asp52GlyfsTer2	p.D52Gfs*2	ENST00000244741	NM_000389.4	52	GACTTTGTCACCGAGACACCACTGGAg/g	2/3	1	2	FACETS	0.854	0.786	0.926	0.854	0.786	0.926	CLONAL	1	TRUE	1	0.399018918899742	2		429	1021	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542172	187542173	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0008595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	164	428	0	ENST00000441802.2:c.5567dup	p.Leu1857PhefsTer4	p.L1857Ffs*4	ENST00000441802	NM_005245.3	1856	cgt/cgGt	10/27	1	2	FACETS	0.935	0.859	1	0.935	0.859	1	CLONAL	1	TRUE	1	0.399018918899742	2		428	879	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443691	49443702	+	frameshift_variant	Frame_Shift_Del	DEL	AGGAGGGGCTCT	AGGAGGGGCTCT	C	novel	NA	P-0008595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	49	374	0	ENST00000301067.7:c.3669_3680delinsG	p.Glu1224GlyfsTer22	p.E1224Gfs*22	ENST00000301067	NM_003482.3	1223	tcAGAGCCCCTCCTg/tcGg	11/54	1	2	FACETS	0.272	0.229	0.319	0.272	0.229	0.319	SUBCLONAL	1	TRUE	1	0.399018918899742	2		374	904	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0008649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	25	509	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.112	0.087	0.14	0.112	0.087	0.14	SUBCLONAL	1	TRUE	1	0.605748382859675	2		509	739	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	140	140	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.605748382859675	2		140	401	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935705	13935705	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	156	219	0	ENST00000405192.2:c.1151G>A	p.Gly384Glu	p.G384E	ENST00000405192	NM_001163147.1	384	gGa/gAa	12/12	0.605748382859675	3	FACETS	0.983	0.902	1	0.491	0.451	0.533	CLONAL	1	TRUE	1	0.605748382859675	3		219	683	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928025	178928026	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTCTAGTATCTGGAAAAATGGCTTTGAATCTTTGGCCAGTAC	novel	NA	P-0008649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	112	264	0	ENST00000263967.3:c.1307_1348dup	p.Leu436_Pro449dup	p.L436_P449dup	ENST00000263967	NM_006218.2	436	act/aCTCTAGTATCTGGAAAAATGGCTTTGAATCTTTGGCCAGTACct	8/21	1	2	FACETS	0.442	0.397	0.489	0.442	0.397	0.489	SUBCLONAL	1	TRUE	1	0.605748382859675	2		264	837	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008677-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	284	140	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.998	0.944	1	0.998	0.944	1	CLONAL	1	FALSE	1	0.837363974044886	2		140	680	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934190	39934190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146403660	NA	P-0008677-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1231	744	855	3	ENST00000378444.4:c.409G>A	p.Val137Ile	p.V137I	ENST00000378444	NM_001123385.1	137	Gtc/Atc	4/15	1	2	FACETS	0.9	0.869	0.931	0.9	0.869	0.931	CLONAL	1	FALSE	1	0.837363974044886	2		858	1975	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131142	55131142	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008677-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8970	1057	551	1	ENST00000257290.5:c.685G>A	p.Glu229Lys	p.E229K	ENST00000257290	NM_006206.4	229	Gaa/Aaa	5/23	0.837363974044886	13	FACETS	1	0.997	1			1	CLONAL	1	FALSE	NA	0.837363974044886	13		552	10027	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748308	41748308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008677-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	175	340	1	ENST00000226382.2:c.461G>A	p.Arg154His	p.R154H	ENST00000226382	NM_003924.3	154	cGc/cAc	3/3	NA	2	FACETS	0.633	0.585	0.683			1	INDETERMINATE	1	FALSE	NA	0.837363974044886	2		341	660	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576899	7576900	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0008677-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	439	411	1	ENST00000269305.4:c.945_946dup	p.Pro316LeufsTer30	p.P316Lfs*30	ENST00000269305	NM_001126112.2	316	ccc/cTCcc	9/11	0.837363974044886	1	FACETS	0.972	0.941	1	0.972	0.941	1	CLONAL	1	FALSE	0	0.837363974044886	1		412	627	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133835	55133852	+	inframe_deletion	In_Frame_Del	DEL	CTGAAAAACAATCTGACT	CTGAAAAACAATCTGACT	-	novel	NA	P-0008677-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4568	1780	433	0	ENST00000257290.5:c.1052_1069del	p.Lys351_Leu356del	p.K351_L356del	ENST00000257290	NM_006206.4	350	CTGAAAAACAATCTGACT/-	7/23	0.837363974044886	13	FACETS	0.939	0.916	0.961			1	CLONAL	4	FALSE	NA	0.837363974044886	13		433	6348	SUCCESS
APC	324	MSKCC	GRCh37	5	112175675	112175676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	145	441	0	ENST00000257430.4:c.4393_4394dup	p.Ser1465ArgfsTer9	p.S1465Rfs*9	ENST00000257430	NM_000038.5	1462	aag/aAGag	16/16	1	2	FACETS	0.645	0.589	0.704	0.645	0.589	0.704	SUBCLONAL	1	TRUE	1	0.557245663169441	2		441	807	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216477	108216477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587782558	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	287	396	0	ENST00000278616.4:c.8432del	p.Lys2811SerfsTer46	p.K2811Sfs*46	ENST00000278616	NM_000051.3	2809	cAa/ca	58/63	1	2	FACETS	0.776	0.735	0.817	1	0.995	1	SUBCLONAL	2	TRUE	1	0.557245663169441	2		396	664	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	300	359	1	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.91	0.857	0.965	0.91	0.857	0.965	CLONAL	1	TRUE	1	0.557245663169441	2		360	1183	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1154	408	526	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.937	0.891	0.985	0.937	0.891	0.985	CLONAL	1	TRUE	1	0.557245663169441	2		526	1562	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	10	509	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.081	0.054	0.115	0.081	0.054	0.115	SUBCLONAL	1	TRUE	1	0.557245663169441	2		509	444	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	97	265	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.734	0.658	0.815	0.734	0.658	0.815	SUBCLONAL	1	TRUE	1	0.557245663169441	2		265	474	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	152	183	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.87	0.799	0.944	0.87	0.799	0.944	CLONAL	1	TRUE	1	0.557245663169441	2		183	627	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	78	150	1	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	0.239800109560786	3	FACETS	0.923	0.815	1	0.461	0.407	0.518	INDETERMINATE	1	TRUE	1	0.557245663169441	3		151	388	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	110	336	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.731	0.659	0.807	0.731	0.659	0.807	SUBCLONAL	1	TRUE	1	0.557245663169441	2		336	540	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	434	399	10	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	0.88	0.844	0.916	1	0.997	1	CLONAL	2	TRUE	1	0.557245663169441	2		409	885	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2004	638	975	8	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	0.867	0.831	0.903	0.867	0.831	0.903	CLONAL	1	TRUE	1	0.557245663169441	2		983	2642	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1202	417	591	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.924	0.879	0.971	0.924	0.879	0.971	CLONAL	1	TRUE	1	0.557245663169441	2		591	1619	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1742	306	656	1	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	1	2	FACETS	0.536	0.503	0.571	0.536	0.503	0.571	SUBCLONAL	1	TRUE	1	0.557245663169441	2		657	2048	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245447	153245447	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	109	315	1	ENST00000281708.4:c.1744T>C	p.Ser582Pro	p.S582P	ENST00000281708	NM_033632.3	582	Tcg/Ccg	11/12	1	2	FACETS	0.737	0.664	0.813	0.737	0.664	0.813	SUBCLONAL	1	TRUE	1	0.557245663169441	2		316	531	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120232	70120232	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1182	389	551	2	ENST00000245479.2:c.1234C>T	p.Gln412Ter	p.Q412*	ENST00000245479	NM_000346.3	412	Cag/Tag	3/3	1	2	FACETS	0.889	0.843	0.936	0.889	0.843	0.936	CLONAL	1	TRUE	1	0.557245663169441	2		553	1571	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	201	519	3	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	1	2	FACETS	0.702	0.65	0.755	0.702	0.65	0.755	SUBCLONAL	1	TRUE	1	0.557245663169441	2		522	1028	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	18	314	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	1	2	FACETS	0.112	0.084	0.146	0.112	0.084	0.146	SUBCLONAL	1	TRUE	1	0.557245663169441	2		314	577	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	132	135	0	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	0.949	0.867	1	0.949	0.867	1	CLONAL	1	TRUE	1	0.557245663169441	2		135	499	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881489	48881490	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs587778862	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	114	365	0	ENST00000267163.4:c.219_220del	p.Arg73SerfsTer36	p.R73Sfs*36	ENST00000267163	NM_000321.2	71	AGa/a	2/27	1	2	FACETS	0.622	0.561	0.686	0.622	0.561	0.686	SUBCLONAL	1	TRUE	1	0.557245663169441	2		365	658	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	231	417	7	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	1	2	FACETS	0.806	0.752	0.863	0.806	0.752	0.863	CLONAL	1	TRUE	1	0.557245663169441	2		424	1028	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	171	349	2	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	1	2	FACETS	0.717	0.66	0.776	0.717	0.66	0.776	SUBCLONAL	1	TRUE	1	0.557245663169441	2		351	856	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	194	481	8	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.838	0.776	0.901	0.838	0.776	0.901	CLONAL	1	TRUE	1	0.557245663169441	2		489	831	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894228	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	267	376	0	ENST00000451590.1:c.37G>A	p.Gly13Ser	p.G13S	ENST00000451590	NM_001130442.1	13	Ggt/Agt	2/5	1	2	FACETS	0.844	0.791	0.899	0.844	0.791	0.899	CLONAL	1	TRUE	1	0.557245663169441	2		376	1135	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097625	11097625	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1338	503	608	0	ENST00000358026.2:c.810del	p.Met272CysfsTer31	p.M272Cfs*31	ENST00000358026	NM_001128849.1	269	Ccc/cc	5/36	1	2	FACETS	0.981	0.937	1	0.981	0.937	1	CLONAL	1	TRUE	1	0.557245663169441	2		608	1841	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953826	131953826	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs368980595	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	152	394	1	ENST00000265335.6:c.3229C>T	p.Arg1077Ter	p.R1077*	ENST00000265335		1077	Cga/Tga	21/25	1	2	FACETS	0.841	0.771	0.913	0.841	0.771	0.913	CLONAL	1	TRUE	1	0.557245663169441	2		395	649	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271747	15271747	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs773656789	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	263	392	0	ENST00000263388.2:c.6692del	p.Pro2231GlnfsTer15	p.P2231Qfs*15	ENST00000263388	NM_000435.2	2231	cCa/ca	33/33	1	2	FACETS	0.937	0.879	0.997	0.937	0.879	0.997	CLONAL	1	TRUE	1	0.557245663169441	2		392	1007	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653860	89653860	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	89	232	0	ENST00000371953.3:c.158T>C	p.Val53Ala	p.V53A	ENST00000371953	NM_000314.4	53	gTa/gCa	2/9	1	2	FACETS	0.819	0.731	0.912	0.819	0.731	0.912	CLONAL	1	TRUE	1	0.557245663169441	2		232	390	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11175476	11175476	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	111	370	0	ENST00000361445.4:c.7066A>G	p.Ile2356Val	p.I2356V	ENST00000361445	NM_004958.3	2356	Att/Gtt	51/58	1	2	FACETS	0.428	0.384	0.475	0.428	0.384	0.475	SUBCLONAL	1	TRUE	1	0.557245663169441	2		370	931	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436077	51436077	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	147	181	0	ENST00000262662.1:c.37G>T	p.Ala13Ser	p.A13S	ENST00000262662		13	Gct/Tct	3/4	1	2	FACETS	0.758	0.694	0.825	0.758	0.694	0.825	SUBCLONAL	1	TRUE	1	0.557245663169441	2		181	696	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873229	136873229	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756830956	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1431	473	760	1	ENST00000241393.3:c.269C>T	p.Thr90Met	p.T90M	ENST00000241393	NM_003467.2	90	aCg/aTg	2/2	1	2	FACETS	0.892	0.85	0.934	0.892	0.85	0.934	CLONAL	1	TRUE	1	0.557245663169441	2		761	1904	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251859	212251859	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	108	167	0	ENST00000342788.4:c.3200G>T	p.Arg1067Leu	p.R1067L	ENST00000342788	NM_005235.2	1067	cGa/cTa	27/28	1	2	FACETS	0.808	0.728	0.89	0.808	0.728	0.89	CLONAL	1	TRUE	1	0.557245663169441	2		167	480	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498391	89498391	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	97	293	0	ENST00000336596.2:c.2363T>A	p.Ile788Asn	p.I788N	ENST00000336596	NM_005233.5	788	aTc/aAc	14/17	1	2	FACETS	0.931	0.837	1	0.931	0.837	1	CLONAL	1	TRUE	1	0.557245663169441	2		293	374	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478143	138478143	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	88	348	0	ENST00000289153.2:c.43C>A	p.Leu15Ile	p.L15I	ENST00000289153	NM_006219.2	15	Ctt/Att	1/22	1	2	FACETS	0.585	0.519	0.655	0.585	0.519	0.655	SUBCLONAL	1	TRUE	1	0.557245663169441	2		348	540	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921383	178921383	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	158	439	0	ENST00000263967.3:c.865G>A	p.Ala289Thr	p.A289T	ENST00000263967	NM_006218.2	289	Gct/Act	5/21	1	2	FACETS	0.854	0.785	0.926	0.854	0.785	0.926	CLONAL	1	TRUE	1	0.557245663169441	2		439	664	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467370	66467370	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778192399	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	121	203	0	ENST00000273854.3:c.899G>A	p.Gly300Asp	p.G300D	ENST00000273854	NM_004439.5	300	gGc/gAc	3/18	1	2	FACETS	0.876	0.795	0.959	0.876	0.795	0.959	CLONAL	1	TRUE	1	0.557245663169441	2		203	496	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673725	30673725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs78556678	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	284	355	1	ENST00000376406.3:c.3235C>T	p.Arg1079Cys	p.R1079C	ENST00000376406	NM_014641.2	1079	Cgt/Tgt	10/15	0.557245663169441	3	FACETS	0.909	0.852	0.967	0.454	0.426	0.484	CLONAL	1	TRUE	1	0.557245663169441	3		356	1434	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954975	2954975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368119340	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	358	421	0	ENST00000396946.4:c.2735G>A	p.Arg912Gln	p.R912Q	ENST00000396946	NM_032415.4	912	cGg/cAg	21/25	1	2	FACETS	0.992	0.94	1	0.992	0.94	1	CLONAL	1	TRUE	1	0.557245663169441	2		421	1295	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140549958	140549958	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	184	485	0	ENST00000288602.6:c.193T>A	p.Leu65Met	p.L65M	ENST00000288602	NM_004333.4	65	Ttg/Atg	2/18	1	2	FACETS	0.804	0.744	0.867	0.804	0.744	0.867	CLONAL	1	TRUE	1	0.557245663169441	2		485	821	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878230	151878230	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1005934731	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	146	231	0	ENST00000262189.6:c.6715A>G	p.Thr2239Ala	p.T2239A	ENST00000262189	NM_170606.2	2239	Aca/Gca	36/59	1	2	FACETS	0.812	0.744	0.884	0.812	0.744	0.884	CLONAL	1	TRUE	1	0.557245663169441	2		231	645	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965495	90965495	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	137	358	0	ENST00000265433.3:c.1822G>A	p.Val608Ile	p.V608I	ENST00000265433	NM_002485.4	608	Gta/Ata	11/16	1	2	FACETS	0.883	0.807	0.962	0.883	0.807	0.962	CLONAL	1	TRUE	1	0.557245663169441	2		358	557	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965761	90965761	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	113	334	0	ENST00000265433.3:c.1556A>G	p.Asp519Gly	p.D519G	ENST00000265433	NM_002485.4	519	gAc/gGc	11/16	1	2	FACETS	0.774	0.699	0.852	0.774	0.699	0.852	SUBCLONAL	1	TRUE	1	0.557245663169441	2		334	524	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741485	145741485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1200616266	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	320	504	0	ENST00000428558.2:c.1018C>T	p.His340Tyr	p.H340Y	ENST00000428558	NM_004260.3	340	Cac/Tac	5/22	1	2	FACETS	0.963	0.909	1	0.963	0.909	1	CLONAL	1	TRUE	1	0.557245663169441	2		504	1193	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413912	139413912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	322	424	0	ENST00000277541.6:c.848G>A	p.Cys283Tyr	p.C283Y	ENST00000277541	NM_017617.3	283	tGc/tAc	5/34	1	2	FACETS	0.861	0.811	0.911	0.861	0.811	0.911	CLONAL	1	TRUE	1	0.557245663169441	2		424	1343	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102056774	102056774	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	108	370	0	ENST00000282441.5:c.714A>C	p.Gln238His	p.Q238H	ENST00000282441	NM_001130145.2	238	caA/caC	4/9	1	2	FACETS	0.621	0.558	0.687	0.621	0.558	0.687	SUBCLONAL	1	TRUE	1	0.557245663169441	2		370	624	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120888	115120888	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	106	279	0	ENST00000257566.3:c.118T>C	p.Phe40Leu	p.F40L	ENST00000257566	NM_016569.3	40	Ttc/Ctc	1/8	1	2	FACETS	0.739	0.665	0.816	0.739	0.665	0.816	SUBCLONAL	1	TRUE	1	0.557245663169441	2		279	515	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937398	32937398	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs80359044	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	127	331	0	ENST00000380152.3:c.8059G>T	p.Val2687Phe	p.V2687F	ENST00000380152		2687	Gtt/Ttt	18/27	1	2	FACETS	0.807	0.734	0.883	0.807	0.734	0.883	CLONAL	1	TRUE	1	0.557245663169441	2		331	565	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527717	103527717	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769849733	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	153	398	0	ENST00000355739.4:c.3025C>T	p.Arg1009Cys	p.R1009C	ENST00000355739	NM_000123.3	1009	Cgt/Tgt	15/15	1	2	FACETS	0.776	0.711	0.843	0.776	0.711	0.843	SUBCLONAL	1	TRUE	1	0.557245663169441	2		398	708	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610516	81610516	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	216	382	0	ENST00000298171.2:c.2114C>A	p.Ala705Glu	p.A705E	ENST00000298171	NM_000369.2	705	gCa/gAa	10/10	1	2	FACETS	0.913	0.85	0.978	0.913	0.85	0.978	CLONAL	1	TRUE	1	0.557245663169441	2		382	849	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572555	95572555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	87	193	0	ENST00000393063.1:c.2810G>A	p.Arg937His	p.R937H	ENST00000393063	NM_030621.3	937	cGc/cAc	19/28	1	2	FACETS	0.895	0.799	0.995	0.895	0.799	0.995	CLONAL	1	TRUE	1	0.557245663169441	2		193	349	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991141	41991141	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	192	461	0	ENST00000219905.7:c.2092+2T>C		p.X698_splice	ENST00000219905	NM_001164273.1	698			1	2	FACETS	0.896	0.831	0.964	0.896	0.831	0.964	CLONAL	1	TRUE	1	0.557245663169441	2		461	769	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003767	45003767	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	241	348	0	ENST00000558401.1:c.23C>A	p.Ala8Asp	p.A8D	ENST00000558401	NM_004048.2	8	gCt/gAt	1/4	1	2	FACETS	0.842	0.787	0.899	0.842	0.787	0.899	CLONAL	1	TRUE	1	0.557245663169441	2		348	1027	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576184	88576184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770581794	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	214	263	0	ENST00000360948.2:c.1489G>A	p.Gly497Arg	p.G497R	ENST00000360948	NM_001012338.2	497	Ggg/Agg	13/19	1	2	FACETS	0.951	0.885	1	0.951	0.885	1	CLONAL	1	TRUE	1	0.557245663169441	2		263	808	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690595	88690595	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	171	303	1	ENST00000360948.2:c.435G>T	p.Gln145His	p.Q145H	ENST00000360948	NM_001012338.2	145	caG/caT	5/19	1	2	FACETS	0.8	0.737	0.865	0.8	0.737	0.865	SUBCLONAL	1	TRUE	1	0.557245663169441	2		304	767	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90627503	90627503	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	207	279	1	ENST00000330062.3:c.1354C>T	p.Gln452Ter	p.Q452*	ENST00000330062	NM_002168.2	452	Cag/Tag	11/11	1	2	FACETS	0.886	0.823	0.95	0.886	0.823	0.95	CLONAL	1	TRUE	1	0.557245663169441	2		280	839	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136233	2136233	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	204	295	0	ENST00000219476.3:c.4702T>C	p.Ser1568Pro	p.S1568P	ENST00000219476	NM_000548.3	1568	Tcc/Ccc	37/42	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.557245663169441	2		295	723	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663356	67663356	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	337	483	0	ENST00000264010.4:c.1757A>G	p.Glu586Gly	p.E586G	ENST00000264010	NM_006565.3	586	gAa/gGa	10/12	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.557245663169441	2		483	1193	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991706	72991706	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540253425	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	385	318	1	ENST00000268489.5:c.2339C>T	p.Ala780Val	p.A780V	ENST00000268489	NM_006885.3	780	gCg/gTg	2/10	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.557245663169441	2		319	1153	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993545	72993545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1557	513	768	0	ENST00000268489.5:c.500C>T	p.Pro167Leu	p.P167L	ENST00000268489	NM_006885.3	167	cCc/cTc	2/10	1	2	FACETS	0.889	0.849	0.93	0.889	0.849	0.93	CLONAL	1	TRUE	1	0.557245663169441	2		768	2070	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654856	29654856	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1049849034	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	113	205	0	ENST00000356175.3:c.5545C>T	p.Arg1849Trp	p.R1849W	ENST00000356175	NM_000267.3	1849	Cgg/Tgg	37/57	1	2	FACETS	0.843	0.763	0.927	0.843	0.763	0.927	CLONAL	1	TRUE	1	0.557245663169441	2		205	481	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618910	37618910	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	329	458	0	ENST00000447079.4:c.586G>T	p.Asp196Tyr	p.D196Y	ENST00000447079	NM_015083.1	196	Gac/Tac	1/14	1	2	FACETS	0.933	0.881	0.986	0.933	0.881	0.986	CLONAL	1	TRUE	1	0.557245663169441	2		458	1266	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47684670	47684670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376811676	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	167	402	0	ENST00000347630.2:c.779C>T	p.Thr260Met	p.T260M	ENST00000347630	NM_001007230.1	260	aCg/aTg	9/11	1	2	FACETS	0.862	0.795	0.933	0.862	0.795	0.933	CLONAL	1	TRUE	1	0.557245663169441	2		402	695	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532567	63532567	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765845684	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	261	302	0	ENST00000307078.5:c.2012G>A	p.Arg671His	p.R671H	ENST00000307078	NM_004655.3	671	cGc/cAc	8/11	1	2	FACETS	0.952	0.893	1	0.952	0.893	1	CLONAL	1	TRUE	1	0.557245663169441	2		302	984	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593398	48593398	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	101	264	0	ENST00000342988.3:c.1149A>G	p.Ile383Met	p.I383M	ENST00000342988	NM_005359.5	383	atA/atG	10/12	1	2	FACETS	0.813	0.731	0.899	0.813	0.731	0.899	CLONAL	1	TRUE	1	0.557245663169441	2		264	446	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2164203	2164203	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	258	399	0	ENST00000398665.3:c.20T>G	p.Leu7Arg	p.L7R	ENST00000398665	NM_032482.2	7	cTg/cGg	1/28	1	2	FACETS	0.844	0.79	0.9	0.844	0.79	0.9	CLONAL	1	TRUE	1	0.557245663169441	2		399	1097	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7163169	7163169	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	326	415	0	ENST00000302850.5:c.1903T>C	p.Ser635Pro	p.S635P	ENST00000302850	NM_000208.2	635	Tca/Cca	9/22	1	2	FACETS	0.848	0.8	0.898	0.848	0.8	0.898	CLONAL	1	TRUE	1	0.557245663169441	2		415	1379	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919007	50919007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1483458869	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1201	503	545	3	ENST00000440232.2:c.2744C>T	p.Ala915Val	p.A915V	ENST00000440232	NM_002691.3	915	gCg/gTg	22/27	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.557245663169441	2		548	1704	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023460	31023460	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	135	223	0	ENST00000375687.4:c.2945A>G	p.Lys982Arg	p.K982R	ENST00000375687	NM_015338.5	982	aAg/aGg	13/13	0.239800109560786	3	FACETS	0.76	0.691	0.833	0.38	0.345	0.417	INDETERMINATE	1	TRUE	1	0.557245663169441	3		223	815	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22123582	22123582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747124623	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	250	550	0	ENST00000215832.6:c.994G>A	p.Asp332Asn	p.D332N	ENST00000215832	NM_002745.4	332	Gac/Aac	8/9	1	2	FACETS	0.725	0.677	0.775	0.725	0.677	0.775	SUBCLONAL	1	TRUE	1	0.557245663169441	2		550	1237	SUCCESS
AR	367	MSKCC	GRCh37	X	66766229	66766229	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1391852512	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	151	242	0	ENST00000374690.3:c.1241T>C	p.Leu414Pro	p.L414P	ENST00000374690	NM_000044.3	414	cTg/cCg	1/8	0.21050181826867	1	FACETS	0.669	0.615	0.726	0.669	0.615	0.726	INDETERMINATE	1	TRUE	0	0.557245663169441	1		242	584	SUCCESS
AR	367	MSKCC	GRCh37	X	66931357	66931357	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	299	606	1	ENST00000374690.3:c.1999G>T	p.Gly667Cys	p.G667C	ENST00000374690	NM_000044.3	667	Ggc/Tgc	4/8	0.21050181826867	1	FACETS	0.586	0.551	0.622	0.586	0.551	0.622	INDETERMINATE	1	TRUE	0	0.557245663169441	1		607	1321	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910537	29910540	+	frameshift_variant	Frame_Shift_Del	DEL	CCCA	CCCA	-	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	53	102	0	ENST00000376809.5:c.78_81del	p.His27ProfsTer2	p.H27Pfs*2	ENST00000376809	NM_002116.7	26	tCCCAc/tc	2/8	0.557245663169441	3	FACETS	0.728	0.624	0.841	0.364	0.312	0.421	SUBCLONAL	1	TRUE	1	0.557245663169441	3		102	334	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551935	150551946	+	inframe_deletion	In_Frame_Del	DEL	GCCGGCCCCCAA	GCCGGCCCCCAA	-	rs779327179	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	248	359	0	ENST00000369026.2:c.61_72del	p.Leu21_Gly24del	p.L21_G24del	ENST00000369026	NM_021960.4	21	TTGGGGGCCGGC/-	1/3	1	2	FACETS	0.905	0.847	0.965	0.905	0.847	0.965	CLONAL	1	TRUE	1	0.557245663169441	2		359	983	SUCCESS
APC	324	MSKCC	GRCh37	5	112116587	112116587	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	88	260	0	ENST00000257430.4:c.636del	p.Lys212AsnfsTer7	p.K212Nfs*7	ENST00000257430	NM_000038.5	211	gAa/ga	6/16	1	2	FACETS	0.849	0.758	0.945	0.849	0.758	0.945	CLONAL	1	TRUE	1	0.557245663169441	2		260	372	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044511	47044511	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	330	453	0	ENST00000377604.3:c.2012del	p.Asn671IlefsTer33	p.N671Ifs*33	ENST00000377604	NM_001204468.1	670	Aaa/aa	18/24	NA	2	FACETS	0.909	0.858	0.961			1	INDETERMINATE	1	TRUE	NA	0.557245663169441	2		453	1303	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536080	106536080	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1487333791	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	115	212	1	ENST00000369096.4:c.51del	p.Lys18SerfsTer7	p.K18Sfs*7	ENST00000369096	NM_001198.3	16	gCc/gc	2/7	0.239800109560786	3	FACETS	0.874	0.789	0.963	0.437	0.394	0.482	INDETERMINATE	1	TRUE	1	0.557245663169441	3		213	604	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348998	11348998	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	108	189	0	ENST00000332029.2:c.338del	p.Phe113SerfsTer5	p.F113Sfs*5	ENST00000332029	NM_003745.1	113	tTc/tc	2/2	1	2	FACETS	0.775	0.699	0.855	0.775	0.699	0.855	SUBCLONAL	1	TRUE	1	0.557245663169441	2		189	500	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500845	8500845	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1476255325	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	158	317	3	ENST00000356435.5:c.2037del	p.Lys679AsnfsTer9	p.K679Nfs*9	ENST00000356435		679	aaA/aa	13/35	1	2	FACETS	0.782	0.718	0.849	0.782	0.718	0.849	SUBCLONAL	1	TRUE	1	0.557245663169441	2		320	725	SUCCESS
AR	367	MSKCC	GRCh37	X	66766348	66766348	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	42	69	0	ENST00000374690.3:c.1364del	p.Gly455ValfsTer24	p.G455Vfs*24	ENST00000374690	NM_000044.3	454	Ggg/gg	1/8	0.21050181826867	1	FACETS	0.488	0.411	0.571	0.488	0.411	0.571	INDETERMINATE	1	TRUE	0	0.557245663169441	1		69	223	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426606	49426611	+	inframe_deletion	In_Frame_Del	DEL	TGTTGC	TGTTGC	-	rs748029700	NA	P-0008721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1318	356	541	0	ENST00000301067.7:c.11877_11882del	p.Gln3964_Gln3965del	p.Q3964_Q3965del	ENST00000301067	NM_003482.3	3959	caGCAACAa/caa	39/54	1	2	FACETS	0.763	0.721	0.807	0.763	0.721	0.807	SUBCLONAL	1	TRUE	1	0.557245663169441	2		541	1674	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067477	37067477	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008749-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	39	442	0	ENST00000231790.2:c.1388G>A	p.Gly463Glu	p.G463E	ENST00000231790	NM_000249.3	463	gGa/gAa	12/19	1	2	FACETS	0.146	0.12	0.175	0.146	0.12	0.175	SUBCLONAL	1	TRUE	1	0.71727837902371	2		442	745	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030022	36030022	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008749-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1324	197	821	0	ENST00000358208.4:c.1057C>G	p.Leu353Val	p.L353V	ENST00000358208		353	Ctc/Gtc	9/12	1	2	FACETS	0.361	0.333	0.391	0.361	0.333	0.391	SUBCLONAL	1	TRUE	1	0.71727837902371	2		821	1521	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190020	123190021	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008749-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	514	492	0	ENST00000218089.9:c.1240dup	p.Tyr414LeufsTer27	p.Y414Lfs*27	ENST00000218089	NM_001042749.1	413	-/T	14/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.71727837902371	1		492	771	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46740256	46740256	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	84	411	0	ENST00000371975.4:c.1736G>T	p.Gly579Val	p.G579V	ENST00000371975	NM_003579.3	579	gGc/gTc	16/18	0.454714568143349	1	FACETS	0.554	0.491	0.621	0.554	0.491	0.621	SUBCLONAL	1	TRUE	0	0.504874398316303	1		411	449	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659982	227659982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1166934768	NA	P-0008767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	110	476	1	ENST00000305123.5:c.3473G>A	p.Gly1158Glu	p.G1158E	ENST00000305123	NM_005544.2	1158	gGa/gAa	1/2	0.451381875975652	1	FACETS	0.52	0.468	0.574	0.52	0.468	0.574	SUBCLONAL	1	TRUE	0	0.504874398316303	1		477	627	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138383960	138383960	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	154	479	0	ENST00000289153.2:c.2590C>A	p.Gln864Lys	p.Q864K	ENST00000289153	NM_006219.2	864	Cag/Aag	18/22	1	2	FACETS	0.962	0.884	1	0.962	0.884	1	CLONAL	1	TRUE	1	0.504874398316303	2		479	634	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523155	176523155	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	100	428	0	ENST00000292408.4:c.1919T>C	p.Ile640Thr	p.I640T	ENST00000292408	NM_213647.1	640	aTt/aCt	14/18	1	2	FACETS	0.486	0.434	0.542	0.486	0.434	0.542	SUBCLONAL	1	TRUE	1	0.504874398316303	2		428	815	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508793	148508793	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	104	412	0	ENST00000320356.2:c.1871C>G	p.Ser624Cys	p.S624C	ENST00000320356	NM_004456.4	624	tCt/tGt	16/20	1	2	FACETS	0.628	0.563	0.697	0.628	0.563	0.697	SUBCLONAL	1	TRUE	1	0.504874398316303	2		412	656	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336308	80336308	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	82	410	0	ENST00000286548.4:c.1011C>G	p.Ile337Met	p.I337M	ENST00000286548	NM_002072.3	337	atC/atG	7/7	0.249150508370483	1	FACETS	0.356	0.314	0.401	0.356	0.314	0.401	INDETERMINATE	1	TRUE	0	0.504874398316303	1		410	682	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229525	98229525	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	142	573	0	ENST00000331920.6:c.2433C>A	p.Asp811Glu	p.D811E	ENST00000331920	NM_000264.3	811	gaC/gaA	15/24	0.249150508370483	1	FACETS	0.488	0.445	0.534	0.488	0.445	0.534	INDETERMINATE	1	TRUE	0	0.504874398316303	1		573	861	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450080	32450080	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1060501259	NA	P-0008767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	40	371	0	ENST00000332351.3:c.732C>G	p.Phe244Leu	p.F244L	ENST00000332351	NM_024426.4	244	ttC/ttG	2/10	0.472004518284389	1	FACETS	0.212	0.175	0.253	0.212	0.175	0.253	SUBCLONAL	1	TRUE	0	0.504874398316303	1		371	559	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420151	49420151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	77	351	0	ENST00000301067.7:c.15598C>T	p.His5200Tyr	p.H5200Y	ENST00000301067	NM_003482.3	5200	Cat/Tat	48/54	1	2	FACETS	0.441	0.387	0.499	0.441	0.387	0.499	SUBCLONAL	1	TRUE	1	0.504874398316303	2		351	692	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885940	111885940	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1948	165	739	0	ENST00000341259.2:c.1562C>G	p.Pro521Arg	p.P521R	ENST00000341259	NM_005475.2	521	cCc/cGc	8/8	0.450753641048873	4	FACETS	0.466	0.425	0.508	0.155	0.141	0.17	SUBCLONAL	1	TRUE	1	0.504874398316303	4		739	2113	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857662	59857662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	189	489	0	ENST00000259008.2:c.1895C>T	p.Thr632Ile	p.T632I	ENST00000259008	NM_032043.2	632	aCt/aTt	13/20	0.269099173996711	2	FACETS	0.937	0.868	1	0.469	0.434	0.505	INDETERMINATE	1	TRUE	0	0.504874398316303	2		489	799	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15378353	15378353	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	69	326	1	ENST00000263377.2:c.433G>T	p.Asp145Tyr	p.D145Y	ENST00000263377	NM_058243.2	145	Gac/Tac	4/20	0.504874398316303	1	FACETS	0.51	0.446	0.578	0.51	0.446	0.578	SUBCLONAL	1	TRUE	0	0.504874398316303	1		327	401	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40761117	40761118	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGGCAGCGTATGACAAAGGTGTTGGGTCGCGGCCT	novel	NA	P-0008767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	120	459	0	ENST00000392038.2:c.199_234dup	p.Arg67_Leu78dup	p.R67_L78dup	ENST00000392038	NM_001626.4	67	-/AGGCCGCGACCCAACACCTTTGTCATACGCTGCCTG	4/14	0.504874398316303	1	FACETS	0.485	0.439	0.535	0.485	0.439	0.535	SUBCLONAL	1	TRUE	0	0.504874398316303	1		459	732	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918127	50918148	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCCCGGCCCGACGCCCACGA	CCTCCCGGCCCGACGCCCACGA	-	novel	NA	P-0008767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	294	690	0	ENST00000440232.2:c.2446_2467del	p.Ser816AlafsTer65	p.S816Afs*65	ENST00000440232	NM_002691.3	815	tCCTCCCGGCCCGACGCCCACGAc/tc	20/27	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.504874398316303	2		690	1087	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819237	3819237	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	535	973	0	ENST00000262367.5:c.2998G>T	p.Glu1000Ter	p.E1000*	ENST00000262367	NM_004380.2	1000	Gag/Tag	15/31	0.377594783242491	3	FACETS	0.884	0.851	0.918	0.884	0.851	0.918	CLONAL	3	TRUE	0	0.41478718125548	3		973	1174	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657097	45657097	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	22	348	0	ENST00000407780.3:c.59del	p.Thr20IlefsTer10	p.T20Ifs*10	ENST00000407780	NM_001283052.1	20	aCt/at	3/7	1	2	FACETS	0.331	0.257	0.418	0.331	0.257	0.418	SUBCLONAL	1	TRUE	1	0.41478718125548	2		348	320	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576866	7576867	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0008774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	241	822	1	ENST00000269305.4:c.979dup	p.Tyr327LeufsTer10	p.Y327Lfs*10	ENST00000269305	NM_001126112.2	327	tat/tTat	9/11	0.41478718125548	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.41478718125548	1		823	724	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0008782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	127	397	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.933	0.847	1	0.933	0.847	1	CLONAL	1	TRUE	1	0.433540361317955	2		397	628	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0008782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	229	442	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	0.433540361317955	2		442	910	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0008782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	85	295	2	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.769	0.682	0.862	0.769	0.682	0.862	SUBCLONAL	1	TRUE	1	0.433540361317955	2		297	510	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0008782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	262	558	2	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.423655503375637	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.433540361317955	1		560	933	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274897	41274897	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	144	390	0	ENST00000349496.5:c.1147T>C	p.Trp383Arg	p.W383R	ENST00000349496	NM_001904.3	383	Tgg/Cgg	8/15	1	2	FACETS	0.911	0.832	0.994	0.911	0.832	0.994	CLONAL	1	TRUE	1	0.433540361317955	2		390	729	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739866	41739866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	285	619	0	ENST00000242208.4:c.107C>T	p.Pro36Leu	p.P36L	ENST00000242208	NM_002192.2	36	cCg/cTg	2/3	1	2	FACETS	0.936	0.879	0.996	0.936	0.879	0.996	CLONAL	1	TRUE	1	0.433540361317955	2		619	1404	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008941	152008941	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	138	523	0	ENST00000262189.6:c.681A>C	p.Glu227Asp	p.E227D	ENST00000262189	NM_170606.2	227	gaA/gaC	5/59	1	2	FACETS	0.907	0.827	0.991	0.907	0.827	0.991	CLONAL	1	TRUE	1	0.433540361317955	2		523	702	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488244	56488244	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	182	342	1	ENST00000267101.3:c.1763G>T	p.Ser588Ile	p.S588I	ENST00000267101	NM_001982.3	588	aGc/aTc	15/28	1	2	FACETS	0.888	0.82	0.96	0.888	0.82	0.96	CLONAL	1	TRUE	1	0.433540361317955	2		343	945	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69230456	69230456	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	138	372	0	ENST00000462284.1:c.845A>G	p.Tyr282Cys	p.Y282C	ENST00000462284	NM_002392.5	282	tAt/tGt	10/11	1	2	FACETS	0.921	0.84	1	0.921	0.84	1	CLONAL	1	TRUE	1	0.433540361317955	2		372	691	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479845	67479845	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0008782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	185	310	0	ENST00000327367.4:c.1152C>G	p.Tyr384Ter	p.Y384*	ENST00000327367	NM_005902.3	384	taC/taG	8/9	0.305089233005037	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.433540361317955	1		310	628	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151167662	151167665	+	frameshift_variant	Frame_Shift_Del	DEL	TTTC	TTTC	-	novel	NA	P-0008782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	187	431	0	ENST00000262187.5:c.454_457del	p.Glu152IlefsTer11	p.E152Ifs*11	ENST00000262187	NM_005614.3	152	GAAAat/at	7/8	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.433540361317955	2		431	830	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420076	49420076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	33	611	0	ENST00000301067.7:c.15673C>T	p.Arg5225Cys	p.R5225C	ENST00000301067	NM_003482.3	5225	Cgc/Tgc	48/54	0.313571270163535	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	2	TRUE	0	0.313571270163535	2		611	92	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0008819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	28	341	0	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	0.313571270163535	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	2	TRUE	0	0.313571270163535	2		341	81	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0008819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	19	557	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.313571270163535	2	FACETS	0.787	0.612	0.981	0.787	0.612	0.981	CLONAL	2	TRUE	0	0.313571270163535	2		557	77	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074397	8074397	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	20	943	0	ENST00000377482.5:c.262C>T	p.Gln88Ter	p.Q88*	ENST00000377482	NM_018948.3	88	Caa/Taa	4/4	0.313571270163535	3	FACETS	1	0.891	1	0.642	0.497	0.805	CLONAL	1	TRUE	1	0.313571270163535	3		943	115	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0008838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	221	435	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.278324696934698	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.278324696934698	2		435	764	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971116	21971116	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs11552823	NA	P-0008838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	80	210	0	ENST00000304494.5:c.242C>G	p.Pro81Arg	p.P81R	ENST00000304494	NM_000077.4	81	cCc/cGc	2/3	0.278324696934698	2	FACETS	0.933	0.83	1	0.933	0.83	1	CLONAL	2	TRUE	0	0.278324696934698	2		210	308	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869448	102869448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs548821403	NA	P-0008838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	52	344	0	ENST00000307046.8:c.193G>A	p.Val65Met	p.V65M	ENST00000307046	NM_001111285.1	65	Gtg/Atg	2/4	0.238234000844703	3	FACETS	0.91	0.775	1	0.455	0.387	0.528	CLONAL	1	TRUE	1	0.278324696934698	3		344	468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576903	7576904	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0008838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	138	378	0	ENST00000269305.4:c.941_942dup	p.Ser315ProfsTer31	p.S315Pfs*31	ENST00000269305	NM_001126112.2	314	-/CC	9/11	0.278324696934698	2	FACETS	0.98	0.897	1	0.98	0.897	1	CLONAL	2	TRUE	0	0.278324696934698	2		378	506	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0008845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	109	301	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.488	0.44	0.539	0.488	0.44	0.539	SUBCLONAL	1	TRUE	1	0.875034564643358	2		301	510	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0008845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	283	807	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	0.496	0.465	0.528	0.496	0.465	0.528	SUBCLONAL	1	TRUE	1	0.875034564643358	2		807	1304	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1275	232	317	0	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	1	2	FACETS	0.352	0.327	0.378	0.352	0.327	0.378	SUBCLONAL	1	TRUE	1	0.875034564643358	2		317	1507	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15952235	15952235	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	187	513	0	ENST00000268712.3:c.6460C>T	p.Gln2154Ter	p.Q2154*	ENST00000268712	NM_006311.3	2154	Cag/Tag	41/46	1	2	FACETS	0.441	0.407	0.476	0.441	0.407	0.476	SUBCLONAL	1	TRUE	1	0.875034564643358	2		513	970	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206861	36206861	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	112	284	0	ENST00000300305.3:c.651del	p.Ser218AlafsTer19	p.S218Afs*19	ENST00000300305		217	ggG/gg	6/8	1	2	FACETS	0.486	0.438	0.535	0.486	0.438	0.535	SUBCLONAL	1	TRUE	1	0.875034564643358	2		284	527	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252994	36252995	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0008845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	98	290	0	ENST00000300305.3:c.366_367dup	p.Asp123GlyfsTer11	p.D123Gfs*11	ENST00000300305		123	gat/gGGat	4/8	1	2	FACETS	0.45	0.403	0.499	0.45	0.403	0.499	SUBCLONAL	1	TRUE	1	0.875034564643358	2		290	498	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008852-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	116	514	0	ENST00000347630.2:c.399C>A	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttA	6/11	1	2	FACETS	0.727	0.657	0.8	0.727	0.657	0.8	SUBCLONAL	1	TRUE	1	0.560812054410316	2		514	569	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55524244	55524244	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008852-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	161	534	0	ENST00000288135.5:c.63G>T	p.Gln21His	p.Q21H	ENST00000288135	NM_000222.2	21	caG/caT	1/21	0.152224980600437	3	FACETS	0.905	0.84	0.972	0.905	0.84	0.972	INDETERMINATE	2	TRUE	1	0.560812054410316	3		534	406	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374930	45374930	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008852-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	60	508	0	ENST00000262160.6:c.913C>A	p.Pro305Thr	p.P305T	ENST00000262160	NM_005901.5	305	Cca/Aca	8/11	0.560812054410316	1	FACETS	0.356	0.307	0.408	0.356	0.307	0.408	SUBCLONAL	1	TRUE	0	0.560812054410316	1		508	433	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375038	45375041	+	frameshift_variant	Frame_Shift_Del	DEL	AGTA	AGTA	-	novel	NA	P-0008852-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	14	297	0	ENST00000262160.6:c.802_805del	p.Tyr268GlnfsTer9	p.Y268Qfs*9	ENST00000262160	NM_005901.5	268	TACTca/ca	8/11	0.560812054410316	1	FACETS	0.147	0.106	0.197	0.147	0.106	0.197	SUBCLONAL	1	TRUE	0	0.560812054410316	1		297	244	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368311	45368311	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008852-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	26	501	0	ENST00000262160.6:c.1291del	p.Val431Ter	p.V431*	ENST00000262160	NM_005901.5	431	Gta/ta	11/11	0.560812054410316	1	FACETS	0.192	0.152	0.238	0.192	0.152	0.238	SUBCLONAL	1	TRUE	0	0.560812054410316	1		501	348	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416561	49416562	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0008852-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	27	377	0	ENST00000301067.7:c.16149dup	p.Lys5384GlnfsTer75	p.K5384Qfs*75	ENST00000301067	NM_003482.3	5383	-/C	51/54	0.139829199003689	5	FACETS	0.38	0.301	0.469	0.127	0.1	0.157	INDETERMINATE	1	TRUE	2	0.560812054410316	5		377	467	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183735	10183736	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGCGAGCCCTCCCAGGTCATCTTCTGCAAT	novel	NA	P-0008872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	125	367	0	ENST00000256474.2:c.208_237dup	p.Glu70_Arg79dup	p.E70_R79dup	ENST00000256474	NM_000551.3	70	-/CGCGAGCCCTCCCAGGTCATCTTCTGCAAT	1/3	0.282969090275265	2	FACETS	1	0.974	1	0.607	0.55	0.667	CLONAL	1	TRUE	0	0.282969090275265	2		367	728	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0008880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	44	393	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.757	0.633	0.894	0.757	0.633	0.894	SUBCLONAL	1	TRUE	1	0.16	2		393	727	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866444	37866444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	51	641	0	ENST00000269571.5:c.749C>T	p.Ser250Phe	p.S250F	ENST00000269571		250	tCt/tTt	6/27	1	2	FACETS	0.663	0.562	0.776	0.663	0.562	0.776	SUBCLONAL	1	TRUE	1	0.16	2		641	961	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263850	133263850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	31	263	0	ENST00000320574.5:c.52G>A	p.Glu18Lys	p.E18K	ENST00000320574	NM_006231.2	18	Gag/Aag	1/49	1	2	FACETS	0.773	0.625	0.943	0.773	0.625	0.943	CLONAL	1	TRUE	1	0.16	2		263	501	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247367	153247367	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747241612	NA	P-0008880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	23	428	0	ENST00000281708.4:c.1435C>G	p.Arg479Gly	p.R479G	ENST00000281708	NM_033632.3	479	Cga/Gga	10/12	0.0866057684348699	0	FACETS	0.627	0.488	0.788			1	INDETERMINATE	1	TRUE	0	0.16	0		428	385	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843447	3843447	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783461	NA	P-0008880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	74	570	1	ENST00000262367.5:c.1156C>T	p.Arg386Ter	p.R386*	ENST00000262367	NM_004380.2	386	Cga/Tga	4/31	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.16	2		571	843	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860556	45860556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	77	675	2	ENST00000391945.4:c.1451C>T	p.Thr484Met	p.T484M	ENST00000391945	NM_000400.3	484	aCg/aTg	15/23	1	2	FACETS	0.864	0.756	0.981	0.864	0.756	0.981	CLONAL	1	TRUE	1	0.16	2		677	1114	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059176	27059176	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	51	736	0	ENST00000324856.7:c.1813C>T	p.Gln605Ter	p.Q605*	ENST00000324856	NM_006015.4	605	Caa/Taa	4/20	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.16	2		736	593	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917875	29917875	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	41	656	0	ENST00000389048.3:c.793G>A	p.Glu265Lys	p.E265K	ENST00000389048	NM_004304.4	265	Gag/Aag	3/29	1	2	FACETS	0.646	0.537	0.769	0.646	0.537	0.769	SUBCLONAL	1	TRUE	1	0.16	2		656	793	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190656538	190656538	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0008880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	36	612	0	ENST00000441310.2:c.3G>A	p.Met1?	p.M1?	ENST00000441310	NM_000534.4	1	atG/atA	2/13	1	2	FACETS	0.751	0.616	0.903	0.751	0.616	0.903	CLONAL	1	TRUE	1	0.16	2		612	599	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183665	10183665	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs199583685	NA	P-0008880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	90	574	0	ENST00000256474.2:c.134C>G	p.Pro45Arg	p.P45R	ENST00000256474	NM_000551.3	45	cCg/cGg	1/3	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.16	2		574	1007	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125512	47125512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	41	836	0	ENST00000409792.3:c.5758G>A	p.Glu1920Lys	p.E1920K	ENST00000409792	NM_014159.6	1920	Gag/Aag	12/21	1	2	FACETS	0.773	0.642	0.919	0.773	0.642	0.919	CLONAL	1	TRUE	1	0.16	2		836	663	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430398	181430398	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	83	683	0	ENST00000325404.1:c.250G>A	p.Glu84Lys	p.E84K	ENST00000325404	NM_003106.3	84	Gag/Aag	1/1	1	2	FACETS	0.866	0.762	0.979	0.866	0.762	0.979	CLONAL	1	TRUE	1	0.16	2		683	1198	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84390185	84390185	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1060503253	NA	P-0008880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	35	461	0	ENST00000321945.7:c.596G>A	p.Ser199Asn	p.S199N	ENST00000321945	NM_139076.2	199	aGc/aAc	6/9	0.0866057684348699	0	FACETS	0.725	0.593	0.873			1	INDETERMINATE	1	TRUE	0	0.16	0		461	507	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245404	153245404	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	29	692	0	ENST00000281708.4:c.1787C>G	p.Ser596Cys	p.S596C	ENST00000281708	NM_033632.3	596	tCt/tGt	11/12	0.0866057684348699	0	FACETS	0.665	0.533	0.815			1	INDETERMINATE	1	TRUE	0	0.16	0		692	458	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38960510	38960510	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	56	512	0	ENST00000357387.3:c.1841A>G	p.Glu614Gly	p.E614G	ENST00000357387	NM_152756.3	614	gAa/gGa	20/38	1	2	FACETS	0.893	0.768	1	1	0.974	1	CLONAL	2	TRUE	1	0.16	2		512	392	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163813	32163813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	47	363	0	ENST00000375023.3:c.5413G>A	p.Asp1805Asn	p.D1805N	ENST00000375023	NM_004557.3	1805	Gac/Aac	30/30	1	2	FACETS	0.858	0.722	1	0.858	0.722	1	CLONAL	1	TRUE	1	0.16	2		363	685	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510845	157510845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	66	665	0	ENST00000346085.5:c.3620C>T	p.Pro1207Leu	p.P1207L	ENST00000346085	NM_020732.3	1207	cCa/cTa	14/20	1	2	FACETS	0.946	0.819	1	0.946	0.819	1	CLONAL	1	TRUE	1	0.16	2		665	872	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455151	50455151	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	28	363	0	ENST00000331340.3:c.698C>A	p.Pro233Gln	p.P233Q	ENST00000331340	NM_006060.4	233	cCg/cAg	6/8	1	2	FACETS	0.713	0.569	0.878	0.713	0.569	0.878	SUBCLONAL	1	TRUE	1	0.16	2		363	491	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915874	127915874	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	59	909	2	ENST00000373547.4:c.607G>A	p.Asp203Asn	p.D203N	ENST00000373547	NM_002721.4	203	Gat/Aat	6/7	1	2	FACETS	0.986	0.847	1	0.986	0.847	1	CLONAL	1	TRUE	1	0.16	2		911	748	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375239	118375239	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	28	575	0	ENST00000534358.1:c.8632C>G	p.Leu2878Val	p.L2878V	ENST00000534358	NM_005933.3	2878	Ctg/Gtg	27/36	1	2	FACETS	0.756	0.603	0.93	0.756	0.603	0.93	CLONAL	1	TRUE	1	0.16	2		575	463	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491483	18491483	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0008880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	26	533	0	ENST00000266497.5:c.1395+1G>A		p.X465_splice	ENST00000266497		465			1	2	FACETS	0.817	0.646	1	0.817	0.646	1	CLONAL	1	TRUE	1	0.16	2		533	398	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799278	88799278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	59	683	1	ENST00000360948.2:c.107G>A	p.Cys36Tyr	p.C36Y	ENST00000360948	NM_001012338.2	36	tGt/tAt	2/19	1	2	FACETS	0.756	0.649	0.875	0.756	0.649	0.875	SUBCLONAL	1	TRUE	1	0.16	2		684	975	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827870	72827870	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs777143827	NA	P-0008880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	91	953	0	ENST00000268489.5:c.8711A>G	p.Lys2904Arg	p.K2904R	ENST00000268489	NM_006885.3	2904	aAg/aGg	9/10	1	2	FACETS	0.927	0.82	1	0.927	0.82	1	CLONAL	1	TRUE	1	0.16	2		953	1227	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29701088	29701088	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	24	480	0	ENST00000356175.3:c.8372G>A	p.Arg2791Gln	p.R2791Q	ENST00000356175	NM_000267.3	2791	cGa/cAa	57/57	1	2	FACETS	0.649	0.508	0.813	0.649	0.508	0.813	SUBCLONAL	1	TRUE	1	0.16	2		480	462	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584739	48584739	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	44	744	0	ENST00000342988.3:c.817A>T	p.Thr273Ser	p.T273S	ENST00000342988	NM_005359.5	273	Act/Tct	7/12	1	2	FACETS	0.801	0.67	0.946	0.801	0.67	0.946	CLONAL	1	TRUE	1	0.16	2		744	687	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46254148	46254148	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	47	1002	0	ENST00000371998.3:c.280G>A	p.Asp94Asn	p.D94N	ENST00000371998		94	Gat/Aat	5/23	1	2	FACETS	0.69	0.581	0.812	0.69	0.581	0.812	SUBCLONAL	1	TRUE	1	0.16	2		1002	851	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942739	44942739	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760394554	NA	P-0008880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	43	423	0	ENST00000377967.4:c.3319C>T	p.Pro1107Ser	p.P1107S	ENST00000377967	NM_021140.2	1107	Cct/Tct	23/29	1	1	FACETS	0.792	0.666	0.931	1	0.962	1	CLONAL	2	TRUE	0	0.16	1		423	312	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039647	47039647	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556778363	NA	P-0008880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	94	330	2	ENST00000377604.3:c.1099C>T	p.His367Tyr	p.H367Y	ENST00000377604	NM_001204468.1	367	Cac/Tac	11/24	1	1	FACETS	0.858	0.764	0.957	1	0.984	1	CLONAL	2	TRUE	0	0.16	1		332	630	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106497	27106498	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0008880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1300	102	820	0	ENST00000324856.7:c.6109dup	p.Gln2037ProfsTer62	p.Q2037Pfs*62	ENST00000324856	NM_006015.4	2036	-/C	20/20	1	2	FACETS	0.909	0.81	1	0.909	0.81	1	CLONAL	1	TRUE	1	0.16	2		820	1402	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0008919-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	81	435	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.218490559678278	2		435	658	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248528	212248528	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008919-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	126	661	2	ENST00000342788.4:c.3739C>A	p.Leu1247Met	p.L1247M	ENST00000342788	NM_005235.2	1247	Ctg/Atg	28/28	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.218490559678278	2		663	1014	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86669981	86669981	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008919-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	49	266	0	ENST00000274376.6:c.1778T>G	p.Val593Gly	p.V593G	ENST00000274376	NM_002890.2	593	gTc/gGc	14/25	1	2	FACETS	0.908	0.769	1	0.908	0.769	1	CLONAL	1	TRUE	1	0.218490559678278	2		266	494	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118345028	118345028	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008919-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	61	211	0	ENST00000534358.1:c.3154C>T	p.Gln1052Ter	p.Q1052*	ENST00000534358	NM_005933.3	1052	Cag/Tag	3/36	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.218490559678278	2		211	413	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563321	21563321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008919-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	77	615	0	ENST00000382592.4:c.598G>A	p.Gly200Ser	p.G200S	ENST00000382592	NM_014572.2	200	Ggc/Agc	4/8	1	2	FACETS	0.918	0.805	1	0.918	0.805	1	CLONAL	1	TRUE	1	0.218490559678278	2		615	768	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81528521	81528521	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008919-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	98	516	0	ENST00000298171.2:c.200T>A	p.Ile67Asn	p.I67N	ENST00000298171	NM_000369.2	67	aTt/aAt	2/10	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.218490559678278	2		516	861	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81954830	81954830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758623675	NA	P-0008919-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	137	708	0	ENST00000359376.3:c.2263G>A	p.Val755Ile	p.V755I	ENST00000359376	NM_002661.3	755	Gtc/Atc	21/33	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.218490559678278	2		708	1179	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593539	48593539	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008919-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	71	283	0	ENST00000342988.3:c.1290C>A	p.Tyr430Ter	p.Y430*	ENST00000342988	NM_005359.5	430	taC/taA	10/12	0.218490559678278	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.218490559678278	1		283	523	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125076	46125076	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	AG	novel	NA	P-0008919-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	85	417	1	ENST00000334344.6:c.263delinsAG	p.Ala88GlufsTer23	p.A88Efs*23	ENST00000334344	NM_152641.2	88	gCt/gAGt	3/21	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.218490559678278	2		418	712	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0008929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	266	282	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.271175251538658	4	FACETS	0.926	0.874	0.979	1	0.995	1	CLONAL	4	TRUE	2	0.271175251538658	4		282	673	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765474	41765474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763936923	NA	P-0008929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1241	83	470	2	ENST00000301178.4:c.2350C>T	p.Arg784Trp	p.R784W	ENST00000301178	NM_021913.4	784	Cgg/Tgg	20/20	0.271175251538658	3	FACETS	0.525	0.461	0.594	0.263	0.23	0.297	SUBCLONAL	1	TRUE	1	0.271175251538658	3		472	1324	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319367	11319367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	151	356	0	ENST00000361445.4:c.100G>A	p.Glu34Lys	p.E34K	ENST00000361445	NM_004958.3	34	Gag/Aag	2/58	0.271175251538658	3	FACETS	0.962	0.877	1	0.481	0.438	0.526	CLONAL	1	TRUE	1	0.271175251538658	3		356	1314	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838297	156838297	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1668	332	380	0	ENST00000524377.1:c.575G>T	p.Gly192Val	p.G192V	ENST00000524377	NM_002529.3	192	gGt/gTt	6/17	0.271175251538658	7	FACETS	1	0.961	1	0.411	0.386	0.436	CLONAL	2	TRUE	2	0.271175251538658	7		380	2000	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143191873	143191873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	92	531	1	ENST00000262992.4:c.558G>T	p.Met186Ile	p.M186I	ENST00000262992	NM_001101669.1	186	atG/atT	8/24	0.2093754203255	3	FACETS	0.784	0.695	0.879	0.392	0.347	0.44	SUBCLONAL	1	TRUE	1	0.271175251538658	3		532	983	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295346	1295346	+	upstream_gene_variant	5'Flank	SNP	G	G	T	rs1289994362	NA	P-0008929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	408	326	0				ENST00000310581	NM_198253.2	-/1132			0.261265747450113	5	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	2	0.271175251538658	5		326	1257	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873534	151873534	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	230	460	0	ENST00000262189.6:c.9004C>T	p.His3002Tyr	p.H3002Y	ENST00000262189	NM_170606.2	3002	Cac/Tac	38/59	0.271175251538658	4	FACETS	0.977	0.91	1	0.977	0.91	1	CLONAL	2	TRUE	2	0.271175251538658	4		460	1104	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449725	8449725	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	108	368	0	ENST00000356435.5:c.3988G>C	p.Gly1330Arg	p.G1330R	ENST00000356435		1330	Ggt/Cgt	23/35	0.271175251538658	3	FACETS	0.767	0.69	0.848	0.767	0.69	0.848	SUBCLONAL	2	TRUE	1	0.271175251538658	3		368	590	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250439	110250439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	420	405	0	ENST00000374672.4:c.236C>T	p.Ala79Val	p.A79V	ENST00000374672	NM_004235.4	79	gCc/gTc	3/5	0.271175251538658	4	FACETS	0.872	0.829	0.915	1	0.994	1	CLONAL	3	TRUE	2	0.271175251538658	4		405	1506	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787747	135787747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1467020958	NA	P-0008929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	116	440	1	ENST00000298552.3:c.835C>T	p.His279Tyr	p.H279Y	ENST00000298552	NM_001162426.1	279	Cac/Tac	9/23	0.271175251538658	4	FACETS	1	0.961	1	0.569	0.512	0.629	CLONAL	1	TRUE	2	0.271175251538658	4		441	956	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28599040	28599040	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	76	440	0	ENST00000241453.7:c.2248G>T	p.Asp750Tyr	p.D750Y	ENST00000241453	NM_004119.2	750	Gat/Tat	18/24	1	2	FACETS	0.739	0.647	0.837	0.739	0.647	0.837	SUBCLONAL	1	TRUE	1	0.271175251538658	2		440	759	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78820353	78820353	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	828	433	0	ENST00000306801.3:c.1293A>C	p.Glu431Asp	p.E431D	ENST00000306801	NM_020761.2	431	gaA/gaC	11/34	0.271175251538658	5	FACETS	0.972	0.942	1	0.972	0.942	1	CLONAL	5	TRUE	0	0.271175251538658	5		433	1768	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600512	10600512	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	162	313	0	ENST00000171111.5:c.1343A>G	p.Asp448Gly	p.D448G	ENST00000171111	NM_203500.1	448	gAt/gGt	4/6	0.271175251538658	3	FACETS	1	0.96	1	0.54	0.494	0.588	CLONAL	1	TRUE	1	0.271175251538658	3		313	1256	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561484	9561484	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	114	337	2	ENST00000353224.5:c.298C>A	p.Leu100Ile	p.L100I	ENST00000353224	NM_177990.2	100	Cta/Ata	4/10	0.261265747450113	5	FACETS	0.993	0.892	1	0.331	0.297	0.367	CLONAL	1	TRUE	2	0.271175251538658	5		339	1191	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884332	151884365	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATATTCATGGCTTACCAGGGAATTCTTCCTTTAA	ATATTCATGGCTTACCAGGGAATTCTTCCTTTAA	-	novel	NA	P-0008929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	46	253	0	ENST00000262189.6:c.4990_5008+15del		p.X1664_splice	ENST00000262189	NM_170606.2	1664		33/59	0.271175251538658	4	FACETS	0.958	0.808	1	0.479	0.404	0.562	CLONAL	1	TRUE	2	0.271175251538658	4		253	450	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259395	89259396	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	69	679	0	ENST00000336596.2:c.542dup	p.Leu181PhefsTer47	p.L181Ffs*47	ENST00000336596	NM_005233.5	180	tat/taTt	3/17	0.271175251538658	3	FACETS	0.688	0.598	0.786	0.344	0.299	0.393	SUBCLONAL	1	TRUE	1	0.271175251538658	3		679	840	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0008933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	264	515	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.694258123418605	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.726607779466296	1		516	449	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	140	140	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.726607779466296	2		140	298	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0008933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	326	409	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.166185598337114	2	FACETS	1	0.993	1	0.642	0.611	0.673	INDETERMINATE	1	TRUE	0	0.726607779466296	2		409	699	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624272	89624273	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs876661009	NA	P-0008933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	214	155	0	ENST00000371953.3:c.47dup	p.Tyr16Ter	p.Y16*	ENST00000371953	NM_000314.4	16	tat/tAat	1/9	0.726607779466296	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.726607779466296	1		155	330	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0008933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	293	292	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.166185598337114	2	FACETS	0.877	0.839	0.913	0.877	0.839	0.913	INDETERMINATE	2	TRUE	0	0.726607779466296	2		292	460	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390736	139390736	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1210	78	604	0	ENST00000277541.6:c.7455del	p.Ser2486ArgfsTer103	p.S2486Rfs*103	ENST00000277541	NM_017617.3	2485	ccC/cc	34/34	0.128507352650884	4	FACETS	0.678	0.594	0.77	0.339	0.297	0.385	INDETERMINATE	1	TRUE	2	0.217379155592851	4		604	1288	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0008994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	27	509	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.276	0.218	0.343	0.276	0.218	0.343	SUBCLONAL	1	TRUE	1	0.217379155592851	2		509	900	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0008994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	105	381	1	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	0.216465197346687	4	FACETS	1	0.952	1			1	CLONAL	1	TRUE	NA	0.217379155592851	4		382	1054	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203492	108203492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs138941496	NA	P-0008994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	71	335	0	ENST00000278616.4:c.7792C>T	p.Arg2598Ter	p.R2598*	ENST00000278616	NM_000051.3	2598	Cga/Tga	53/63	0.213574072298821	3	FACETS	0.943	0.822	1	0.472	0.411	0.537	CLONAL	1	TRUE	1	0.217379155592851	3		335	768	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579368	7579368	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	65	439	0	ENST00000269305.4:c.319T>G	p.Tyr107Asp	p.Y107D	ENST00000269305	NM_001126112.2	107	Tac/Gac	4/11	1	2	FACETS	0.608	0.526	0.698	0.608	0.526	0.698	SUBCLONAL	1	TRUE	1	0.217379155592851	2		439	983	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155454	47155454	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1173	67	609	0	ENST00000409792.3:c.4627C>T	p.Arg1543Trp	p.R1543W	ENST00000409792	NM_014159.6	1543	Cgg/Tgg	5/21	1	2	FACETS	0.497	0.43	0.57	0.497	0.43	0.57	SUBCLONAL	1	TRUE	1	0.217379155592851	2		609	1240	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248123	59248123	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs370122841	NA	P-0008994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	12	102	0	ENST00000371222.2:c.620C>A	p.Pro207Gln	p.P207Q	ENST00000371222	NM_002228.3	207	cCg/cAg	1/1	0.216465197346687	4	FACETS	0.597	0.42	0.816			1	SUBCLONAL	1	TRUE	NA	0.217379155592851	4		102	225	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104599	209104599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1194	79	666	0	ENST00000345146.2:c.979A>G	p.Thr327Ala	p.T327A	ENST00000345146	NM_005896.2	327	Acc/Gcc	8/10	1	2	FACETS	0.571	0.5	0.648	0.571	0.5	0.648	SUBCLONAL	1	TRUE	1	0.217379155592851	2		666	1273	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391038	139391038	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	60	419	0	ENST00000277541.6:c.7153G>A	p.Val2385Met	p.V2385M	ENST00000277541	NM_017617.3	2385	Gtg/Atg	34/34	0.128507352650884	4	FACETS	0.695	0.597	0.802	0.347	0.298	0.401	INDETERMINATE	1	TRUE	2	0.217379155592851	4		419	967	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118353172	118353172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1178866478	NA	P-0008994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1192	103	558	0	ENST00000534358.1:c.4048C>T	p.Arg1350Cys	p.R1350C	ENST00000534358	NM_005933.3	1350	Cgc/Tgc	8/36	0.213574072298821	3	FACETS	0.811	0.724	0.905	0.406	0.362	0.453	CLONAL	1	TRUE	1	0.217379155592851	3		558	1295	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1039038	1039038	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	139	479	0	ENST00000358495.3:c.295A>G	p.Asn99Asp	p.N99D	ENST00000358495	NM_134424.2	99	Aac/Gac	5/12	0.141028671499924	3	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.217379155592851	3		479	1149	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779169	3779169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759839179	NA	P-0008994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	41	305	0	ENST00000262367.5:c.5879G>A	p.Arg1960Gln	p.R1960Q	ENST00000262367	NM_004380.2	1960	cGg/cAg	31/31	0.213574072298821	3	FACETS	0.705	0.586	0.838	0.353	0.293	0.419	SUBCLONAL	1	TRUE	1	0.217379155592851	3		305	593	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130702	29130702	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779607427	NA	P-0008994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	41	231	0	ENST00000328354.6:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000328354	NM_007194.3	3	cGg/cAg	2/15	1	2	FACETS	0.644	0.535	0.765	0.644	0.535	0.765	SUBCLONAL	1	TRUE	1	0.217379155592851	2		231	586	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41258473	41258474	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	rs397508938	NA	P-0008994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1360	85	644	0	ENST00000357654.3:c.211dup	p.Arg71LysfsTer10	p.R71Kfs*10	ENST00000357654	NM_007294.3	71	agg/aAgg	4/23	0.213574072298821	3	FACETS	0.6	0.528	0.678	0.3	0.264	0.339	SUBCLONAL	1	TRUE	1	0.217379155592851	3		644	1445	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681463	30681463	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1274	113	673	0	ENST00000376406.3:c.549del	p.Lys183AsnfsTer9	p.K183Nfs*9	ENST00000376406	NM_014641.2	183	aaA/aa	4/15	1	2	FACETS	0.75	0.672	0.832	0.75	0.672	0.832	SUBCLONAL	1	TRUE	1	0.217379155592851	2		673	1387	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867224	68867224	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	52	467	0	ENST00000261769.5:c.2474del	p.Pro825ArgfsTer21	p.P825Rfs*21	ENST00000261769	NM_004360.3	824	gCc/gc	16/16	NA	2	FACETS	0.56	0.475	0.654			1	INDETERMINATE	1	TRUE	NA	0.217379155592851	2		467	854	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486049	29486050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0009106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	239	355	0	ENST00000356175.3:c.233dup	p.Asn78LysfsTer29	p.N78Kfs*29	ENST00000356175	NM_000267.3	76	gaa/gAaa	3/57	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.726075291408051	2		355	640	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552152	29552152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199474738	NA	P-0009106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	288	500	0	ENST00000356175.3:c.1885G>A	p.Gly629Arg	p.G629R	ENST00000356175	NM_000267.3	629	Ggg/Agg	17/57	1	2	FACETS	0.981	0.926	1	0.981	0.926	1	CLONAL	1	TRUE	1	0.726075291408051	2		500	809	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0009106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	245	333	1	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	0.99	0.93	1	0.99	0.93	1	CLONAL	1	TRUE	1	0.726075291408051	2		334	682	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593667	55593669	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	rs1060502543	NA	P-0009106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	1455	470	0	ENST00000288135.5:c.1735_1737del	p.Asp579del	p.D579del	ENST00000288135	NM_000222.2	578	tATGat/tat	11/21	0.726075291408051	7	FACETS	1	0.998	1			1	CLONAL	5	TRUE	NA	0.726075291408051	7		470	2059	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244311	5244311	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	729	554	0	ENST00000357368.4:c.1171G>A	p.Gly391Ser	p.G391S	ENST00000357368	NM_002850.3	391	Ggc/Agc	11/38	0.622928973249218	3	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.726075291408051	3		554	1292	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253379	226253379	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	191	273	2	ENST00000366813.1:c.151G>A	p.Glu51Lys	p.E51K	ENST00000366813		51	Gaa/Aaa	2/3	NA	2	FACETS	0.98	0.913	1			1	INDETERMINATE	1	TRUE	NA	0.726075291408051	2		275	537	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163828	47163828	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	285	504	0	ENST00000409792.3:c.2298G>C	p.Met766Ile	p.M766I	ENST00000409792	NM_014159.6	766	atG/atC	3/21	1	2	FACETS	0.953	0.899	1	0.953	0.899	1	CLONAL	1	TRUE	1	0.726075291408051	2		504	824	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495709	72495709	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	344	389	2	ENST00000477973.2:c.363C>A	p.Phe121Leu	p.F121L	ENST00000477973	NM_012234.5	121	ttC/ttA	1/4	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.726075291408051	2		391	896	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164765	32164765	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1480	327	363	0	ENST00000375023.3:c.5137G>C	p.Val1713Leu	p.V1713L	ENST00000375023	NM_004557.3	1713	Gtg/Ctg	28/30	0.726075291408051	5	FACETS	1	0.968	1	0.26	0.245	0.276	CLONAL	1	TRUE	1	0.726075291408051	5		363	1807	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588161	69588161	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	407	760	0	ENST00000168712.1:c.537C>G	p.Ile179Met	p.I179M	ENST00000168712	NM_002007.2	179	atC/atG	3/3	1	2	FACETS	0.956	0.911	1	0.956	0.911	1	CLONAL	1	TRUE	1	0.726075291408051	2		760	1173	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911679	32911679	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876657678	NA	P-0009106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1236	449	935	0	ENST00000380152.3:c.3187C>T	p.Gln1063Ter	p.Q1063*	ENST00000380152		1063	Cag/Tag	11/27	0.503711910270035	3	FACETS	1	0.953	1			1	CLONAL	1	TRUE	NA	0.726075291408051	3		935	1685	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856379	45856379	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	319	515	0	ENST00000391945.4:c.1793C>T	p.Ser598Leu	p.S598L	ENST00000391945	NM_000400.3	598	tCa/tTa	19/23	1	2	FACETS	0.994	0.942	1	0.994	0.942	1	CLONAL	1	TRUE	1	0.726075291408051	2		515	884	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217273	123217273	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	276	456	0	ENST00000218089.9:c.2927A>T	p.Asp976Val	p.D976V	ENST00000218089	NM_001042749.1	976	gAt/gTt	29/35	1	2	FACETS	0.987	0.931	1	0.987	0.931	1	CLONAL	1	TRUE	1	0.726075291408051	2		456	770	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0009146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	22	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.62	0.486	0.771	0.62	0.486	0.771	SUBCLONAL	1	TRUE	1	0.541694711604733	2		249	131	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0009146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	109	503	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.525251917167261	1	FACETS	0.991	0.903	1	0.991	0.903	1	CLONAL	1	TRUE	0	0.541694711604733	1		504	296	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0009146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	77	640	1	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.967	0.858	1	0.967	0.858	1	CLONAL	1	TRUE	1	0.541694711604733	2		641	294	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974696	21974697	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0009146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	85	522	0	ENST00000304494.5:c.130dup	p.Tyr44LeufsTer76	p.Y44Lfs*76	ENST00000304494	NM_000077.4	44	tac/tTac	1/3	0.541694711604733	1	FACETS	0.915	0.822	1	0.915	0.822	1	CLONAL	1	TRUE	0	0.541694711604733	1		522	250	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49423253	49423253	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	74	340	0	ENST00000301067.7:c.14006C>A	p.Ser4669Ter	p.S4669*	ENST00000301067	NM_003482.3	4669	tCa/tAa	43/54	1	2	FACETS	0.926	0.819	1	0.926	0.819	1	CLONAL	1	TRUE	1	0.541694711604733	2		340	295	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396878	396878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773929559	NA	P-0009146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	91	532	0	ENST00000262320.3:c.148G>A	p.Val50Ile	p.V50I	ENST00000262320	NM_003502.3	50	Gtt/Att	2/11	1	2	FACETS	0.974	0.873	1	0.974	0.873	1	CLONAL	1	TRUE	1	0.541694711604733	2		532	345	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579310	7579310	+	splice_donor_variant	Splice_Site	SNP	A	A	C	rs1555526469	NA	P-0009328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	633	219	0	ENST00000269305.4:c.375+2T>G		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.392936045427692	5	FACETS	0.991	0.962	1			1	CLONAL	5	TRUE	NA	0.392936045427692	5		219	1033	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423650	88423650	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	52	221	1	ENST00000360948.2:c.2185C>T	p.His729Tyr	p.H729Y	ENST00000360948	NM_001012338.2	729	Cac/Tac	18/19	1	2	FACETS	0.42	0.357	0.489	0.42	0.357	0.489	SUBCLONAL	1	TRUE	1	0.392936045427692	2		222	630	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874369	76874369	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1243	307	525	1	ENST00000373344.5:c.5353C>T	p.Gln1785Ter	p.Q1785*	ENST00000373344	NM_000489.3	1785	Caa/Taa	21/35	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.392936045427692	2		526	1550	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587454	29587455	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTGACGGCAATGT	novel	NA	P-0009328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	121	309	0	ENST00000356175.3:c.4437_4449dup	p.Leu1484Ter	p.L1484*	ENST00000356175	NM_000267.3	1479	agt/aGTGACGGCAATGTgt	33/57	0.392936045427692	1	FACETS	0.581	0.524	0.641	0.581	0.524	0.641	SUBCLONAL	1	TRUE	0	0.392936045427692	1		309	852	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0009336-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	21	282	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.789	1	1	0.789	1	CLONAL	1	TRUE	1	0.196735040919922	2		282	209	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52661301	52661301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009336-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	33	385	0	ENST00000394830.3:c.1529C>T	p.Ala510Val	p.A510V	ENST00000394830	NM_018313.4	510	gCc/gTc	14/30	0.15519557115778	0	FACETS	1	0.876	1			1	CLONAL	1	TRUE	0	0.196735040919922	0		385	247	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003332	143003332	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009336-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	18	205	0	ENST00000262992.4:c.2494C>A	p.Arg832Ser	p.R832S	ENST00000262992	NM_001101669.1	832	Cgc/Agc	23/24	1	2	FACETS	1	0.781	1	1	0.781	1	CLONAL	1	TRUE	1	0.196735040919922	2		205	177	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2220221	2220221	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009336-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	28	272	0	ENST00000398665.3:c.2806G>T	p.Gly936Cys	p.G936C	ENST00000398665	NM_032482.2	936	Ggc/Tgc	23/28	0.196735040919922	1	FACETS	0.888	0.712	1	0.888	0.712	1	CLONAL	1	TRUE	0	0.196735040919922	1		272	289	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610522	10610522	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009336-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	35	277	1	ENST00000171111.5:c.188C>A	p.Ala63Asp	p.A63D	ENST00000171111	NM_203500.1	63	gCc/gAc	2/6	0.196735040919922	1	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	0	0.196735040919922	1		278	280	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207135	1207136	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0009336-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	41	399	0	ENST00000326873.7:c.225_226dup	p.Ala76GlyfsTer21	p.A76Gfs*21	ENST00000326873	NM_000455.4	75	agg/aGGgg	1/10	0.196735040919922	1	FACETS	0.971	0.81	1	0.971	0.81	1	CLONAL	1	TRUE	0	0.196735040919922	1		399	387	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0009346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1640	337	468	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.845051649217981	5	FACETS	0.915	0.862	0.97	0.305	0.287	0.324	CLONAL	1	TRUE	2	0.845051649217981	5		468	1977	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937070	48937093	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GAACATGAATGTAATATAGATGAG	GAACATGAATGTAATATAGATGAG	-	novel	NA	P-0009346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	253	309	0	ENST00000267163.4:c.839_861+1del		p.EHECNIDEdel	ENST00000267163	NM_000321.2	280	GAACATGAATGTAATATAGATGAG/-	8/27	0.845051649217981	1	FACETS	0.915	0.875	0.954	0.915	0.875	0.954	CLONAL	1	TRUE	0	0.845051649217981	1		309	378	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073546	8073547	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0009346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	674	597	0	ENST00000377482.5:c.1112dup	p.Ser372IlefsTer4	p.S372Ifs*4	ENST00000377482	NM_018948.3	371	gga/ggGa	4/4	0.828641494374313	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.845051649217981	1		597	918	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36421257	36421257	+	5_prime_UTR_variant	5'UTR	DEL	T	T	-	novel	NA	P-0009346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	143	112	0	ENST00000300305.3:c.-61del		p.*21*	ENST00000300305		-/480		1/8	1	2	FACETS	0.973	0.899	1	0.973	0.899	1	CLONAL	1	TRUE	1	0.845051649217981	2		112	348	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242481	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAA	AATTAAGAGAAGCAA	TCC	novel	NA	P-0009346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	734	307	0	ENST00000275493.2:c.2237_2251delinsTCC	p.Glu746_Thr751delinsValPro	p.E746_T751delinsVP	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAAca/gTCCca	19/28	0.845051649217981	5	FACETS	1	0.996	1	0.814	0.787	0.841	CLONAL	2	TRUE	2	0.845051649217981	5		307	1613	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	169	366	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.837	0.774	0.903	0.837	0.774	0.903	CLONAL	1	TRUE	1	0.694681575334506	2		366	581	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0009363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	355	274	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.694681575334506	1	FACETS	0.982	0.939	1	0.982	0.939	1	CLONAL	1	TRUE	0	0.694681575334506	1		274	679	SUCCESS
APC	324	MSKCC	GRCh37	5	112174094	112174095	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs863225332	NA	P-0009363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	177	565	0	ENST00000257430.4:c.2804dup	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	tac/tAac	16/16	1	2	FACETS	0.907	0.841	0.974	0.907	0.841	0.974	CLONAL	1	TRUE	1	0.694681575334506	2		565	562	SUCCESS
APC	324	MSKCC	GRCh37	5	112175760	112175761	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs398123122	NA	P-0009363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	184	220	0	ENST00000257430.4:c.4473dup	p.Ala1492CysfsTer22	p.A1492Cfs*22	ENST00000257430	NM_000038.5	1490	cat/caTt	16/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.694681575334506	2		220	510	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371968	55371968	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	83	125	0	ENST00000297316.4:c.658C>A	p.Pro220Thr	p.P220T	ENST00000297316	NM_022454.3	220	Ccc/Acc	2/2	0.694681575334506	1	FACETS	0.461	0.41	0.515	0.461	0.41	0.515	SUBCLONAL	1	TRUE	0	0.694681575334506	1		125	338	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910882	114910882	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	607	606	1	ENST00000543371.1:c.1001C>A	p.Ser334Ter	p.S334*	ENST00000543371	NM_001198531.1	334	tCa/tAa	9/14	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.694681575334506	2		607	1729	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795422	39795422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140580933	NA	P-0009363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	343	386	0	ENST00000288319.7:c.298G>A	p.Val100Ile	p.V100I	ENST00000288319	NM_182918.3	100	Gtt/Att	3/10	1	2	FACETS	0.843	0.798	0.889	0.843	0.798	0.889	CLONAL	1	TRUE	1	0.694681575334506	2		386	1172	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673703	37673703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	72	431	0	ENST00000447079.4:c.2857G>A	p.Gly953Ser	p.G953S	ENST00000447079	NM_015083.1	953	Ggt/Agt	10/14	0.234780157376167	5	FACETS	0.97	0.856	1			1	CLONAL	3	TRUE	NA	0.234780157376167	5		431	285	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944841	31944842	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0009401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	57	465	0	ENST00000340398.3:c.259_260del	p.Ala87SerfsTer9	p.A87Sfs*9	ENST00000340398	NM_001013699.2	87	GCa/a	1/1	1	2	FACETS	0.975	0.845	1	1	0.978	1	CLONAL	2	TRUE	1	0.234780157376167	2		465	249	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618989	37618990	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0009401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	59	219	0	ENST00000447079.4:c.670dup	p.His224ProfsTer6	p.H224Pfs*6	ENST00000447079	NM_015083.1	222	agc/agCc	1/14	0.234780157376167	5	FACETS	1	0.892	1			1	CLONAL	5	TRUE	NA	0.234780157376167	5		219	135	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0009415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	153	393	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.868	0.801	0.936	0.868	0.801	0.936	CLONAL	1	TRUE	1	0.801443461052843	2		393	440	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653783	89653783	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0009415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	82	340	0	ENST00000371953.3:c.81T>A	p.Tyr27Ter	p.Y27*	ENST00000371953	NM_000314.4	27	taT/taA	2/9	0.801443461052843	1	FACETS	0.304	0.269	0.34	0.304	0.269	0.34	SUBCLONAL	1	TRUE	0	0.801443461052843	1		340	404	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939420	76939420	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	424	307	1	ENST00000373344.5:c.1328C>A	p.Ala443Glu	p.A443E	ENST00000373344	NM_000489.3	443	gCa/gAa	9/35	0.769934731578987	2	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.801443461052843	2		308	1028	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954316	48954316	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	208	261	0	ENST00000267163.4:c.1437del	p.Asp479GlufsTer16	p.D479Efs*16	ENST00000267163	NM_000321.2	479	gaC/ga	16/27	0.517904092493124	1	FACETS	0.585	0.547	0.623	0.585	0.547	0.623	SUBCLONAL	1	TRUE	0	0.801443461052843	1		261	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578533	7578534	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTTGTTGAGGGCAG	novel	NA	P-0009415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	189	393	0	ENST00000269305.4:c.383_396dup	p.Met133LeufsTer42	p.M133Lfs*42	ENST00000269305	NM_001126112.2	132	-/CTGCCCTCAACAAG	5/11	NA	2	FACETS	0.646	0.599	0.695			1	INDETERMINATE	1	TRUE	NA	0.801443461052843	2		393	730	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0009458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	222	293	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	1	0.968	1			1	INDETERMINATE	2	TRUE	NA	0.677487284056798	2		295	322	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058592	72058592	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	802	616	1	ENST00000357731.5:c.848C>A	p.Thr283Asn	p.T283N	ENST00000357731	NM_173808.2	283	aCt/aAt	6/7	0.651990339781479	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.677487284056798	4		617	1919	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120529604	120529604	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	465	343	1	ENST00000256646.2:c.853C>A	p.Arg285Ser	p.R285S	ENST00000256646	NM_024408.3	285	Cgc/Agc	5/34	0.651990339781479	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.677487284056798	4		344	1129	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874285	155874285	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs730881014	NA	P-0009458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	313	253	0	ENST00000368323.3:c.246T>G	p.Phe82Leu	p.F82L	ENST00000368323	NM_006912.5	82	ttT/ttG	5/6	0.651990339781479	4	FACETS	0.962	0.911	1	0.962	0.911	1	CLONAL	2	TRUE	2	0.677487284056798	4		253	806	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176055026	176055026	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs201597739	NA	P-0009458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	232	360	0	ENST00000367669.3:c.1027A>G	p.Thr343Ala	p.T343A	ENST00000367669	NM_022457.5	343	Aca/Gca	10/20	0.651990339781479	4	FACETS	0.913	0.85	0.979	0.457	0.425	0.49	CLONAL	1	TRUE	2	0.677487284056798	4		360	1258	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670859	134670859	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	27	96	0	ENST00000398015.3:c.770C>A	p.Pro257His	p.P257H	ENST00000398015	NM_004441.4	257	cCt/cAt	3/16	0.677487284056798	3	FACETS	0.539	0.432	0.659	0.269	0.216	0.33	SUBCLONAL	1	TRUE	1	0.677487284056798	3		96	198	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367325	50367325	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	70	163	1	ENST00000331340.3:c.132G>T	p.Gln44His	p.Q44H	ENST00000331340	NM_006060.4	44	caG/caT	3/8	0.677487284056798	3	FACETS	0.72	0.631	0.816	0.36	0.315	0.408	SUBCLONAL	1	TRUE	1	0.677487284056798	3		164	384	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133712	41133712	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	834	645	0	ENST00000379561.5:c.1916A>G	p.Gln639Arg	p.Q639R	ENST00000379561	NM_002015.3	639	cAa/cGa	2/3	0.677487284056798	2	FACETS	0.98	0.956	1	0.98	0.956	1	CLONAL	2	TRUE	0	0.677487284056798	2		645	1256	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035052	42035052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	916	664	1	ENST00000219905.7:c.4894G>A	p.Ala1632Thr	p.A1632T	ENST00000219905	NM_001164273.1	1632	Gcc/Acc	15/24	0.677487284056798	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.677487284056798	2		665	1307	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2220180	2220180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	280	414	0	ENST00000398665.3:c.2765C>T	p.Ala922Val	p.A922V	ENST00000398665	NM_032482.2	922	gCc/gTc	23/28	1	2	FACETS	0.977	0.921	1	0.977	0.921	1	CLONAL	1	TRUE	1	0.677487284056798	2		414	846	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937072	48937073	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0009458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	318	308	0	ENST00000267163.4:c.840_841insT	p.His281SerfsTer2	p.H281Sfs*2	ENST00000267163	NM_000321.2	280	-/T	8/27	0.677487284056798	2	FACETS	0.869	0.832	0.906	0.869	0.832	0.906	CLONAL	2	TRUE	0	0.677487284056798	2		308	540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0009467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	304	392	1	ENST00000269305.4:c.560-1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			NA	2	FACETS	0.959	0.91	1			1	INDETERMINATE	2	TRUE	NA	0.439516603494895	2		393	721	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181440	185181440	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	108	396	0	ENST00000265026.3:c.1381G>C	p.Glu461Gln	p.E461Q	ENST00000265026	NM_004721.4	461	Gag/Cag	8/14	0.439858223567094	4	FACETS	0.848	0.761	0.941	0.424	0.38	0.471	CLONAL	1	TRUE	2	0.439516603494895	4		396	834	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0009467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	705	684	1	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.439516603494895	9	FACETS	0.943	0.916	0.971			1	CLONAL	7	TRUE	NA	0.439516603494895	9		685	1233	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295789	212295789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1240072004	NA	P-0009467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	111	416	1	ENST00000342788.4:c.2524C>T	p.Arg842Trp	p.R842W	ENST00000342788	NM_005235.2	842	Cgg/Tgg	21/28	0.403242573043209	3	FACETS	1	0.931	1	0.52	0.469	0.575	CLONAL	1	TRUE	1	0.439516603494895	3		417	592	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082203	16082203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1311546727	NA	P-0009467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	393	422	0	ENST00000281043.3:c.17C>T	p.Thr6Met	p.T6M	ENST00000281043	NM_005378.4	6	aCg/aTg	2/3	0.439858223567094	4	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	2	0.439516603494895	4		422	1268	SUCCESS
ALK	238	MSKCC	GRCh37	2	29497982	29497982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	292	513	1	ENST00000389048.3:c.2024C>T	p.Pro675Leu	p.P675L	ENST00000389048	NM_004304.4	675	cCc/cTc	11/29	0.439858223567094	4	FACETS	0.973	0.917	1	0.973	0.917	1	CLONAL	2	TRUE	2	0.439516603494895	4		514	983	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415594	49415594	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	289	392	0	ENST00000301067.7:c.16583G>T	p.Gly5528Val	p.G5528V	ENST00000301067	NM_003482.3	5528	gGa/gTa	54/54	0.40604258780041	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.439516603494895	4		392	843	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444220	49444220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	433	493	0	ENST00000301067.7:c.3151G>T	p.Val1051Phe	p.V1051F	ENST00000301067	NM_003482.3	1051	Gtt/Ttt	11/54	0.40604258780041	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	2	0.439516603494895	4		493	1417	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444812	49444812	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775553446	NA	P-0009467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	330	348	0	ENST00000301067.7:c.2654C>T	p.Pro885Leu	p.P885L	ENST00000301067	NM_003482.3	885	cCc/cTc	10/54	0.40604258780041	4	FACETS	0.92	0.869	0.971	0.92	0.869	0.971	CLONAL	2	TRUE	2	0.439516603494895	4		348	1175	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240319	5240319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773233463	NA	P-0009467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	400	398	0	ENST00000357368.4:c.1595G>A	p.Arg532Gln	p.R532Q	ENST00000357368	NM_002850.3	532	cGg/cAg	12/38	0.439858223567094	4	FACETS	0.92	0.874	0.967	0.92	0.874	0.967	CLONAL	2	TRUE	2	0.439516603494895	4		398	1424	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170520	11170520	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	190	282	0	ENST00000358026.2:c.4823A>T	p.Glu1608Val	p.E1608V	ENST00000358026	NM_001128849.1	1608	gAg/gTg	34/36	0.439858223567094	4	FACETS	0.857	0.795	0.922	0.857	0.795	0.922	CLONAL	2	TRUE	2	0.439516603494895	4		282	726	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81399272	81399273	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0009467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	233	315	0	ENST00000222390.5:c.15dup	p.Leu6ThrfsTer36	p.L6Tfs*36	ENST00000222390	NM_000601.4	5	-/A	1/18	0.40604258780041	4	FACETS	0.84	0.785	0.898	0.84	0.785	0.898	CLONAL	2	TRUE	2	0.439516603494895	4		315	908	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0009477-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	200	435	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.981	0.913	1	0.981	0.913	1	CLONAL	1	TRUE	1	0.592609079410255	2		435	688	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221313	1221314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs121913321	NA	P-0009477-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	356	441	1	ENST00000326873.7:c.842dup	p.Leu282AlafsTer3	p.L282Afs*3	ENST00000326873	NM_000455.4	279	ggc/ggCc	6/10	0.592609079410255	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.592609079410255	1		442	828	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201813	66201813	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009477-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	167	418	0	ENST00000273854.3:c.2689C>A	p.Leu897Met	p.L897M	ENST00000273854	NM_004439.5	897	Ctg/Atg	16/18	NA	2	FACETS	0.886	0.818	0.957			1	INDETERMINATE	1	TRUE	NA	0.592609079410255	2		418	636	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627259	86627259	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009477-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	201	531	0	ENST00000274376.6:c.634A>T	p.Arg212Trp	p.R212W	ENST00000274376	NM_002890.2	212	Agg/Tgg	2/25	1	2	FACETS	0.933	0.868	1	0.933	0.868	1	CLONAL	1	TRUE	1	0.592609079410255	2		531	727	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508577	106508577	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009477-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	128	173	0	ENST00000359195.3:c.571C>A	p.Arg191Ser	p.R191S	ENST00000359195	NM_002649.2	191	Cgc/Agc	2/11	1	2	FACETS	0.986	0.901	1	0.986	0.901	1	CLONAL	1	TRUE	1	0.592609079410255	2		173	438	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453124	140453124	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009477-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	213	426	0	ENST00000288602.6:c.1811G>T	p.Trp604Leu	p.W604L	ENST00000288602	NM_004333.4	604	tGg/tTg	15/18	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.592609079410255	2		426	656	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597994	43597994	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009477-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	333	567	0	ENST00000355710.3:c.542C>A	p.Pro181His	p.P181H	ENST00000355710	NM_020975.4	181	cCc/cAc	3/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.592609079410255	2		567	1018	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156723	2156723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009477-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	380	596	0	ENST00000434045.2:c.199G>A	p.Val67Met	p.V67M	ENST00000434045	NM_001127598.1	67	Gtg/Atg	3/5	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.592609079410255	2		596	1273	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860084	57860084	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009477-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1205	522	791	0	ENST00000228682.2:c.824G>T	p.Cys275Phe	p.C275F	ENST00000228682	NM_005269.2	275	tGc/tTc	8/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.592609079410255	2		791	1727	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112635	115112635	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009477-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	163	241	0	ENST00000257566.3:c.1105T>A	p.Cys369Ser	p.C369S	ENST00000257566	NM_016569.3	369	Tgt/Agt	7/8	1	2	FACETS	0.972	0.897	1	0.972	0.897	1	CLONAL	1	TRUE	1	0.592609079410255	2		241	566	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857733	9857733	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs770966136	NA	P-0009477-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	315	592	0	ENST00000330684.3:c.3668C>A	p.Thr1223Asn	p.T1223N	ENST00000330684	NM_001134407.1	1223	aCc/aAc	13/13	1	2	FACETS	0.937	0.884	0.991	0.937	0.884	0.991	CLONAL	1	TRUE	1	0.592609079410255	2		592	1135	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123701	11123701	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009477-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	330	482	0	ENST00000358026.2:c.2351G>A	p.Gly784Glu	p.G784E	ENST00000358026	NM_001128849.1	784	gGg/gAg	16/36	0.592609079410255	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.592609079410255	1		482	781	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906317	50906317	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009477-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	335	590	2	ENST00000440232.2:c.978C>A	p.Phe326Leu	p.F326L	ENST00000440232	NM_002691.3	326	ttC/ttA	9/27	0.592609079410255	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.592609079410255	1		592	726	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306557	41306557	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009477-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	242	503	0	ENST00000373198.4:c.1102G>T	p.Gly368Trp	p.G368W	ENST00000373198	NM_133170.3	368	Ggg/Tgg	7/32	1	2	FACETS	0.896	0.838	0.955	0.896	0.838	0.955	CLONAL	1	TRUE	1	0.592609079410255	2		503	912	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934060	39934060	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009477-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	389	340	0	ENST00000378444.4:c.539A>T	p.Asn180Ile	p.N180I	ENST00000378444	NM_001123385.1	180	aAc/aTc	4/15	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.592609079410255	1		340	700	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034476	47034476	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009477-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	447	348	1	ENST00000377604.3:c.561G>A	p.Trp187Ter	p.W187*	ENST00000377604	NM_001204468.1	187	tgG/tgA	6/24	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.592609079410255	1		349	727	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	51	550	3	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.701	0.593	0.819	0.701	0.593	0.819	SUBCLONAL	1	TRUE	1	0.16	2		553	910	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422384	47422384	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	101	287	0	ENST00000377045.4:c.23del	p.Pro8LeufsTer26	p.P8Lfs*26	ENST00000377045	NM_001654.4	6	ggC/gg	2/16	1	1	FACETS	0.781	0.698	0.869	1	0.982	1	SUBCLONAL	2	TRUE	0	0.16	1		287	744	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759623	133759623	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	58	622	0	ENST00000318560.5:c.1950del	p.Leu651TrpfsTer43	p.L651Wfs*43	ENST00000318560	NM_005157.4	649	aCc/ac	11/11	1	2	FACETS	0.703	0.601	0.814	0.703	0.601	0.814	SUBCLONAL	1	TRUE	1	0.16	2		622	1032	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	61	366	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		366	1027	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660269	227660270	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	45	305	0	ENST00000305123.5:c.3185dup	p.Gln1064ThrfsTer17	p.Q1064Tfs*17	ENST00000305123	NM_005544.2	1062	ggc/ggGc	1/2	1	2	FACETS	0.899	0.754	1	0.899	0.754	1	CLONAL	1	TRUE	1	0.16	2		305	626	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434367	121434367	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	120	421	1	ENST00000257555.6:c.1136del	p.Pro379LeufsTer5	p.P379Lfs*5	ENST00000257555		377	ctC/ct	6/10	1	2	FACETS	0.898	0.811	0.99	1	0.988	1	CLONAL	2	TRUE	1	0.16	2		422	835	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429978	78429978	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	68	450	3	ENST00000370768.2:c.901del	p.Ile301TyrfsTer22	p.I301Yfs*22	ENST00000370768	NM_003902.3	301	Ata/ta	11/20	1	2	FACETS	0.757	0.656	0.867	0.757	0.656	0.867	SUBCLONAL	1	TRUE	1	0.16	2		453	1123	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	26	113	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	0.249696553414986	1	FACETS	0.779	0.621	0.956	1	0.937	1	CLONAL	2	TRUE	0	0.16	1		113	192	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088659	27088659	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1194	87	578	1	ENST00000324856.7:c.2272del	p.Gln758ArgfsTer75	p.Q758Rfs*75	ENST00000324856	NM_006015.4	756	aaC/aa	7/20	1	2	FACETS	0.849	0.749	0.957	0.849	0.749	0.957	CLONAL	1	TRUE	1	0.16	2		579	1281	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119932	70119932	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	49	227	0	ENST00000245479.2:c.934C>T	p.Gln312Ter	p.Q312*	ENST00000245479	NM_000346.3	312	Cag/Tag	3/3	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.16	2		227	496	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739881	145739881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764297840	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	79	534	2	ENST00000428558.2:c.1649C>T	p.Ala550Val	p.A550V	ENST00000428558	NM_004260.3	550	gCg/gTg	10/22	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.16	2		536	963	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972893	32972893	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	62	344	1	ENST00000380152.3:c.10248del	p.Lys3416AsnfsTer11	p.K3416Nfs*11	ENST00000380152		3415	Aaa/aa	27/27	1	2	FACETS	0.811	0.698	0.934	0.811	0.698	0.934	CLONAL	1	TRUE	1	0.16	2		345	956	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	22	135	0	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	0.249696553414986	1	FACETS	0.798	0.619	1	0.798	0.619	1	CLONAL	1	TRUE	0	0.16	1		135	317	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11206807	11206807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202187935	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	76	502	1	ENST00000361445.4:c.4612C>T	p.Arg1538Trp	p.R1538W	ENST00000361445	NM_004958.3	1538	Cgg/Tgg	32/58	1	2	FACETS	0.951	0.832	1	0.951	0.832	1	CLONAL	1	TRUE	1	0.16	2		503	999	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202909	16202909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs975826717	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	88	438	1	ENST00000375759.3:c.617G>A	p.Arg206His	p.R206H	ENST00000375759	NM_015001.2	206	cGc/cAc	3/15	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.16	2		439	971	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46738149	46738149	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748839524	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	75	600	0	ENST00000371975.4:c.1181G>A	p.Arg394Gln	p.R394Q	ENST00000371975	NM_003579.3	394	cGg/cAg	11/18	1	2	FACETS	0.779	0.68	0.887	0.779	0.68	0.887	SUBCLONAL	1	TRUE	1	0.16	2		600	1203	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400967	72400967	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1741	125	903	1	ENST00000357731.5:c.204G>T	p.Lys68Asn	p.K68N	ENST00000357731	NM_173808.2	68	aaG/aaT	2/7	1	2	FACETS	0.837	0.754	0.926	0.837	0.754	0.926	CLONAL	1	TRUE	1	0.16	2		904	1866	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142990	30142990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316424431	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	56	495	2	ENST00000389048.3:c.536G>A	p.Arg179His	p.R179H	ENST00000389048	NM_004304.4	179	cGc/cAc	1/29	0.249696553414986	1	FACETS	0.733	0.627	0.851	0.733	0.627	0.851	SUBCLONAL	1	TRUE	0	0.16	1		497	878	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248494	212248494	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	82	609	0	ENST00000342788.4:c.3773A>G	p.Tyr1258Cys	p.Y1258C	ENST00000342788	NM_005235.2	1258	tAc/tGc	28/28	1	2	FACETS	0.831	0.73	0.94	0.831	0.73	0.94	CLONAL	1	TRUE	1	0.16	2		609	1233	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663019	227663019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	54	384	0	ENST00000305123.5:c.436G>A	p.Gly146Arg	p.G146R	ENST00000305123	NM_005544.2	146	Ggg/Agg	1/2	1	2	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	TRUE	1	0.16	2		384	673	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412946	49412946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1405	129	647	2	ENST00000418115.1:c.77G>A	p.Ser26Asn	p.S26N	ENST00000418115	NM_001664.2	26	aGc/aAc	2/5	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.16	2		649	1534	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480471	89480471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	54	414	0	ENST00000336596.2:c.2308G>A	p.Val770Ile	p.V770I	ENST00000336596	NM_005233.5	770	Gtc/Atc	13/17	1	2	FACETS	0.642	0.546	0.748	0.642	0.546	0.748	SUBCLONAL	1	TRUE	1	0.16	2		414	1051	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808304	99808304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	58	355	1	ENST00000280892.6:c.385C>T	p.Arg129Trp	p.R129W	ENST00000280892	NM_001130678.1	129	Cgg/Tgg	5/7	1	2	FACETS	0.989	0.848	1	0.989	0.848	1	CLONAL	1	TRUE	1	0.16	2		356	733	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156223	106156223	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	43	357	0	ENST00000380013.4:c.1124A>G	p.Glu375Gly	p.E375G	ENST00000380013	NM_001127208.2	375	gAa/gGa	3/11	1	2	FACETS	0.66	0.55	0.782	0.66	0.55	0.782	SUBCLONAL	1	TRUE	1	0.16	2		357	815	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755572	57755572	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	34	290	0	ENST00000274289.3:c.215T>C	p.Ile72Thr	p.I72T	ENST00000274289	NM_006622.3	72	aTt/aCt	1/14	1	2	FACETS	0.702	0.573	0.849	0.702	0.573	0.849	SUBCLONAL	1	TRUE	1	0.16	2		290	605	SUCCESS
APC	324	MSKCC	GRCh37	5	112154790	112154790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060503337	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	75	422	0	ENST00000257430.4:c.1061C>T	p.Pro354Leu	p.P354L	ENST00000257430	NM_000038.5	354	cCt/cTt	10/16	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.16	2		422	930	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721517	176721517	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	42	302	0	ENST00000439151.2:c.7148G>A	p.Gly2383Asp	p.G2383D	ENST00000439151	NM_022455.4	2383	gGc/gAc	23/23	NA	2	FACETS	0.715	0.596	0.849			1	INDETERMINATE	1	TRUE	NA	0.16	2		302	734	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225507	26225507	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs761664745	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2112	138	1170	0	ENST00000360408.1:c.125A>G	p.Tyr42Cys	p.Y42C	ENST00000360408	NM_003532.2	42	tAc/tGc	1/1	1	2	FACETS	0.767	0.694	0.844	0.767	0.694	0.844	SUBCLONAL	1	TRUE	1	0.16	2		1170	2250	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169083	32169083	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	78	522	0	ENST00000375023.3:c.3950G>T	p.Arg1317Leu	p.R1317L	ENST00000375023	NM_004557.3	1317	cGg/cTg	22/30	1	2	FACETS	0.962	0.844	1	0.962	0.844	1	CLONAL	1	TRUE	1	0.16	2		522	1013	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005630	150005630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	47	382	1	ENST00000253339.5:c.595G>A	p.Ala199Thr	p.A199T	ENST00000253339		199	Gcc/Acc	3/7	1	2	FACETS	0.708	0.595	0.833	0.708	0.595	0.833	SUBCLONAL	1	TRUE	1	0.16	2		383	830	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2952942	2952942	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	33	347	0	ENST00000396946.4:c.2998G>A	p.Glu1000Lys	p.E1000K	ENST00000396946	NM_032415.4	1000	Gag/Aag	22/25	1	2	FACETS	0.672	0.546	0.815	0.672	0.546	0.815	SUBCLONAL	1	TRUE	1	0.16	2		347	614	SUCCESS
MET	4233	MSKCC	GRCh37	7	116409789	116409789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761243391	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	74	498	0	ENST00000397752.3:c.2674G>A	p.Val892Ile	p.V892I	ENST00000397752	NM_000245.2	892	Gtt/Att	12/21	1	2	FACETS	0.824	0.719	0.938	0.824	0.719	0.938	CLONAL	1	TRUE	1	0.16	2		498	1123	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850308	128850308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	81	523	0	ENST00000249373.3:c.1571C>T	p.Ala524Val	p.A524V	ENST00000249373	NM_005631.4	524	gCc/gTc	9/12	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.16	2		523	994	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874421	151874421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1452053695	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	69	500	0	ENST00000262189.6:c.8117G>A	p.Gly2706Glu	p.G2706E	ENST00000262189	NM_170606.2	2706	gGg/gAg	38/59	1	2	FACETS	0.787	0.683	0.9	0.787	0.683	0.9	SUBCLONAL	1	TRUE	1	0.16	2		500	1096	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117861247	117861247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1501	125	670	0	ENST00000297338.2:c.1642G>A	p.Asp548Asn	p.D548N	ENST00000297338	NM_006265.2	548	Gat/Aat	13/14	1	2	FACETS	0.961	0.866	1	0.961	0.866	1	CLONAL	1	TRUE	1	0.16	2		670	1626	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5467842	5467842	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	73	380	0	ENST00000381577.3:c.853A>G	p.Thr285Ala	p.T285A	ENST00000381577	NM_014143.3	285	Aca/Gca	7/7	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.16	2		380	873	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564744	139564744	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	47	535	0	ENST00000308874.7:c.533C>A	p.Pro178His	p.P178H	ENST00000308874		178	cCc/cAc	7/10	1	2	FACETS	0.717	0.603	0.844	0.717	0.603	0.844	SUBCLONAL	1	TRUE	1	0.16	2		535	819	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274770	123274770	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs773178450	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	62	567	0	ENST00000358487.5:c.1148T>C	p.Ile383Thr	p.I383T	ENST00000358487	NM_000141.4	383	aTa/aCa	9/18	0.249696553414986	1	FACETS	0.657	0.565	0.757	0.657	0.565	0.757	SUBCLONAL	1	TRUE	0	0.16	1		567	1086	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310925	123310925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	68	493	2	ENST00000358487.5:c.503C>T	p.Ala168Val	p.A168V	ENST00000358487	NM_000141.4	168	gCt/gTt	5/18	0.249696553414986	1	FACETS	0.84	0.729	0.961	0.84	0.729	0.961	CLONAL	1	TRUE	0	0.16	1		495	931	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136196	64136196	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398172112	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	58	378	0	ENST00000334205.4:c.1355G>A	p.Arg452His	p.R452H	ENST00000334205	NM_003942.2	452	cGc/cAc	12/17	1	2	FACETS	0.959	0.822	1	0.959	0.822	1	CLONAL	1	TRUE	1	0.16	2		378	756	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633515	69633515	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554981392	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	63	391	0	ENST00000334134.2:c.187C>T	p.Arg63Cys	p.R63C	ENST00000334134	NM_005247.2	63	Cgc/Tgc	1/3	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.16	2		391	604	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201778	102201778	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs768458534	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1772	131	818	0	ENST00000263464.3:c.1130T>G	p.Met377Arg	p.M377R	ENST00000263464	NM_001165.4	377	aTg/aGg	6/9	NA	2	FACETS	0.86	0.777	0.949			1	INDETERMINATE	1	TRUE	NA	0.16	2		818	1903	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343059	118343059	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	38	316	0	ENST00000534358.1:c.1185G>T	p.Gln395His	p.Q395H	ENST00000534358	NM_005933.3	395	caG/caT	3/36	NA	2	FACETS	0.723	0.596	0.865			1	INDETERMINATE	1	TRUE	NA	0.16	2		316	657	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945048	31945048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764152739	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1268	84	704	1	ENST00000340398.3:c.53G>A	p.Arg18His	p.R18H	ENST00000340398	NM_001013699.2	18	cGc/cAc	1/1	1	2	FACETS	0.777	0.683	0.878	0.777	0.683	0.878	SUBCLONAL	1	TRUE	1	0.16	2		705	1352	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865803	57865803	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1575	115	804	0	ENST00000228682.2:c.3280T>C	p.Ser1094Pro	p.S1094P	ENST00000228682	NM_005269.2	1094	Tcc/Ccc	12/12	1	2	FACETS	0.851	0.763	0.944	0.851	0.763	0.944	CLONAL	1	TRUE	1	0.16	2		804	1690	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144503	58144503	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	74	429	0	ENST00000257904.6:c.568A>G	p.Thr190Ala	p.T190A	ENST00000257904	NM_000075.3	190	Aca/Gca	5/8	1	2	FACETS	0.895	0.782	1	0.895	0.782	1	CLONAL	1	TRUE	1	0.16	2		429	1033	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144529	58144529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772079285	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	73	396	0	ENST00000257904.6:c.542G>A	p.Arg181Gln	p.R181Q	ENST00000257904	NM_000075.3	181	cGa/cAa	5/8	1	2	FACETS	0.925	0.807	1	0.925	0.807	1	CLONAL	1	TRUE	1	0.16	2		396	986	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856565	111856565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1386743022	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	60	230	1	ENST00000341259.2:c.616G>A	p.Ala206Thr	p.A206T	ENST00000341259	NM_005475.2	206	Gcc/Acc	2/8	1	2	FACETS	0.789	0.681	0.907	1	0.972	1	CLONAL	2	TRUE	1	0.16	2		231	475	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975639	26975639	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	78	593	0	ENST00000381527.3:c.1147A>G	p.Asn383Asp	p.N383D	ENST00000381527	NM_001260.1	383	Aat/Gat	12/13	NA	2	FACETS	0.842	0.737	0.955			1	INDETERMINATE	1	TRUE	NA	0.16	2		593	1158	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911695	32911695	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1921	126	890	0	ENST00000380152.3:c.3203T>C	p.Val1068Ala	p.V1068A	ENST00000380152		1068	gTa/gCa	11/27	1	2	FACETS	0.769	0.693	0.851	0.769	0.693	0.851	SUBCLONAL	1	TRUE	1	0.16	2		890	2047	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930732	32930732	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	100	313	0	ENST00000380152.3:c.7603T>A	p.Cys2535Ser	p.C2535S	ENST00000380152		2535	Tgt/Agt	15/27	1	2	FACETS	0.822	0.734	0.916	1	0.984	1	CLONAL	2	TRUE	1	0.16	2		313	760	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937540	32937540	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	80	499	1	ENST00000380152.3:c.8201C>A	p.Pro2734His	p.P2734H	ENST00000380152		2734	cCt/cAt	18/27	1	2	FACETS	0.833	0.731	0.944	0.833	0.731	0.944	CLONAL	1	TRUE	1	0.16	2		500	1200	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73340147	73340147	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	77	476	0	ENST00000377767.4:c.1933A>G	p.Thr645Ala	p.T645A	ENST00000377767	NM_014953.3	645	Act/Gct	15/21	1	2	FACETS	0.807	0.706	0.917	0.807	0.706	0.917	CLONAL	1	TRUE	1	0.16	2		476	1192	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436560	110436560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567423781	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	54	329	0	ENST00000375856.3:c.1841C>T	p.Pro614Leu	p.P614L	ENST00000375856	NM_003749.2	614	cCg/cTg	1/2	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.16	2		329	631	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36989325	36989325	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372925758	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	66	460	2	ENST00000354822.5:c.10G>A	p.Gly4Arg	p.G4R	ENST00000354822	NM_001079668.2	4	Gga/Aga	1/3	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.16	2		462	756	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66735652	66735652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	79	562	2	ENST00000307102.5:c.473C>T	p.Ala158Val	p.A158V	ENST00000307102	NM_002755.3	158	gCt/gTt	4/11	1	2	FACETS	0.8	0.701	0.907	0.8	0.701	0.907	CLONAL	1	TRUE	1	0.16	2		564	1235	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312683	91312683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759330541	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1269	92	643	0	ENST00000355112.3:c.2422C>T	p.Arg808Cys	p.R808C	ENST00000355112	NM_000057.2	808	Cgt/Tgt	12/22	1	2	FACETS	0.845	0.748	0.949	0.845	0.748	0.949	CLONAL	1	TRUE	1	0.16	2		643	1361	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106706	2106706	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139060277	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	80	597	0	ENST00000219476.3:c.710C>T	p.Pro237Leu	p.P237L	ENST00000219476	NM_000548.3	237	cCg/cTg	8/42	1	2	FACETS	0.868	0.762	0.983	0.868	0.762	0.983	CLONAL	1	TRUE	1	0.16	2		597	1152	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778131	3778131	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	66	490	0	ENST00000262367.5:c.6917G>T	p.Gly2306Val	p.G2306V	ENST00000262367	NM_004380.2	2306	gGg/gTg	31/31	1	2	FACETS	0.925	0.801	1	0.925	0.801	1	CLONAL	1	TRUE	1	0.16	2		490	892	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779703	3779703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	30	286	1	ENST00000262367.5:c.5345C>T	p.Ala1782Val	p.A1782V	ENST00000262367	NM_004380.2	1782	gCg/gTg	31/31	1	2	FACETS	0.741	0.596	0.906	0.741	0.596	0.906	CLONAL	1	TRUE	1	0.16	2		287	506	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781231	3781231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	67	475	0	ENST00000262367.5:c.5134C>T	p.His1712Tyr	p.H1712Y	ENST00000262367	NM_004380.2	1712	Cac/Tac	30/31	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.16	2		475	796	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347731	89347731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	263	710	0	ENST00000301030.4:c.5219C>T	p.Ala1740Val	p.A1740V	ENST00000301030	NM_001256183.1	1740	gCc/gTc	9/13	1	2	FACETS	1	0.982	1	1	0.995	1	CLONAL	2	TRUE	1	0.16	2		710	1450	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489791	40489791	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	71	544	0	ENST00000264657.5:c.635A>G	p.Gln212Arg	p.Q212R	ENST00000264657	NM_139276.2	212	cAg/cGg	7/24	1	2	FACETS	0.736	0.64	0.84	0.736	0.64	0.84	SUBCLONAL	1	TRUE	1	0.16	2		544	1206	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899236	78899236	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	42	380	0	ENST00000306801.3:c.2875T>C	p.Phe959Leu	p.F959L	ENST00000306801	NM_020761.2	959	Ttc/Ctc	24/34	1	2	FACETS	0.831	0.692	0.985	0.831	0.692	0.985	CLONAL	1	TRUE	1	0.16	2		380	632	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919545	78919545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776174012	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	72	452	0	ENST00000306801.3:c.3104C>T	p.Thr1035Met	p.T1035M	ENST00000306801	NM_020761.2	1035	aCg/aTg	26/34	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.16	2		452	821	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374905	45374905	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	82	570	0	ENST00000262160.6:c.938T>C	p.Leu313Ser	p.L313S	ENST00000262160	NM_005901.5	313	tTa/tCa	8/11	1	2	FACETS	0.844	0.741	0.954	0.844	0.741	0.954	CLONAL	1	TRUE	1	0.16	2		570	1215	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604790	48604790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	87	435	0	ENST00000342988.3:c.1612G>A	p.Glu538Lys	p.E538K	ENST00000342988	NM_005359.5	538	Gaa/Aaa	12/12	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.16	2		435	1012	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349957	15349957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1023216999	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	39	405	1	ENST00000263377.2:c.3695G>A	p.Arg1232Gln	p.R1232Q	ENST00000263377	NM_058243.2	1232	cGg/cAg	18/20	1	2	FACETS	0.723	0.598	0.864	0.723	0.598	0.864	SUBCLONAL	1	TRUE	1	0.16	2		406	674	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271728	18271728	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	69	315	3	ENST00000222254.8:c.416-1G>T		p.X139_splice	ENST00000222254	NM_005027.3	139			1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.16	2		318	740	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796603	42796603	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	42	248	2	ENST00000575354.2:c.3160C>T	p.Gln1054Ter	p.Q1054*	ENST00000575354	NM_015125.3	1054	Cag/Tag	13/20	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.16	2		250	454	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871976	45871976	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	52	410	0	ENST00000391945.4:c.272T>C	p.Leu91Pro	p.L91P	ENST00000391945	NM_000400.3	91	cTc/cCc	5/23	1	2	FACETS	0.735	0.624	0.858	0.735	0.624	0.858	SUBCLONAL	1	TRUE	1	0.16	2		410	884	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918712	50918712	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	59	379	0	ENST00000440232.2:c.2582T>C	p.Val861Ala	p.V861A	ENST00000440232	NM_002691.3	861	gTg/gCg	21/27	1	2	FACETS	0.954	0.819	1	0.954	0.819	1	CLONAL	1	TRUE	1	0.16	2		379	773	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52725428	52725428	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1194775389	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	81	481	0	ENST00000322088.6:c.1595C>T	p.Pro532Leu	p.P532L	ENST00000322088	NM_014225.5	532	cCg/cTg	13/15	1	2	FACETS	0.974	0.856	1	0.974	0.856	1	CLONAL	1	TRUE	1	0.16	2		481	1039	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019387	31019387	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	142	439	0	ENST00000375687.4:c.884T>G	p.Val295Gly	p.V295G	ENST00000375687	NM_015338.5	295	gTg/gGg	10/13	1	2	FACETS	0.842	0.766	0.922	1	0.989	1	CLONAL	2	TRUE	1	0.16	2		439	1054	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031631	36031631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756665933	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	76	589	0	ENST00000358208.4:c.1460C>T	p.Pro487Leu	p.P487L	ENST00000358208		487	cCg/cTg	12/12	1	2	FACETS	0.869	0.76	0.987	0.869	0.76	0.987	CLONAL	1	TRUE	1	0.16	2		589	1093	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710560	40710560	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs188293712	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	45	426	0	ENST00000373198.4:c.4291A>G	p.Thr1431Ala	p.T1431A	ENST00000373198	NM_133170.3	1431	Aca/Gca	31/32	0.249696553414986	1	FACETS	0.664	0.557	0.784	0.664	0.557	0.784	SUBCLONAL	1	TRUE	0	0.16	1		426	779	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513243	44513243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200044775	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	40	306	0	ENST00000291552.4:c.692C>T	p.Ser231Leu	p.S231L	ENST00000291552	NM_006758.2	231	tCg/tTg	8/8	0.108307879880832	0	FACETS	0.659	0.547	0.785			1	SUBCLONAL	1	TRUE	0	0.16	0		306	637	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652269	48652269	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	92	435	0	ENST00000376670.3:c.940A>G	p.Lys314Glu	p.K314E	ENST00000376670	NM_002049.3	314	Aaa/Gaa	6/6	1	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.16	1		435	848	SUCCESS
AR	367	MSKCC	GRCh37	X	66937403	66937403	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886039558	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	114	395	1	ENST00000374690.3:c.2257C>T	p.Arg753Ter	p.R753*	ENST00000374690	NM_000044.3	753	Cga/Tga	5/8	1	1	FACETS	1	0.922	1	1	0.989	1	CLONAL	2	TRUE	0	0.16	1		396	639	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611877	100611877	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	105	436	0	ENST00000308731.7:c.1244T>C	p.Val415Ala	p.V415A	ENST00000308731	NM_000061.2	415	gTa/gCa	14/19	1	1	FACETS	0.786	0.704	0.873	1	0.983	1	SUBCLONAL	2	TRUE	0	0.16	1		436	768	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057893	27057894	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	74	540	0	ENST00000324856.7:c.1605dup	p.Ser536LeufsTer87	p.S536Lfs*87	ENST00000324856	NM_006015.4	534	tac/taCc	3/20	1	2	FACETS	0.761	0.664	0.867	0.761	0.664	0.867	SUBCLONAL	1	TRUE	1	0.16	2		540	1215	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905055	50905055	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	86	725	0	ENST00000440232.2:c.342del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	113	Ggg/gg	4/27	1	2	FACETS	0.941	0.829	1	0.941	0.829	1	CLONAL	1	TRUE	1	0.16	2		725	1143	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1548	125	762	0	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	0.934	0.842	1	0.934	0.842	1	CLONAL	1	TRUE	1	0.16	2		762	1673	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725018	47725019	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs762488821	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	78	588	0	ENST00000449228.1:c.725dup	p.Arg243GlnfsTer7	p.R243Qfs*7	ENST00000449228	NM_001127240.2	242	ggc/ggGc	4/4	1	2	FACETS	0.804	0.704	0.912	0.804	0.704	0.912	CLONAL	1	TRUE	1	0.16	2		588	1213	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336078	73336078	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	145	462	0	ENST00000377767.4:c.2325del	p.Phe775LeufsTer30	p.F775Lfs*30	ENST00000377767	NM_014953.3	775	ttT/tt	17/21	1	2	FACETS	0.789	0.718	0.863	1	0.988	1	SUBCLONAL	2	TRUE	1	0.16	2		462	1149	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444809	49444809	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	67	454	1	ENST00000301067.7:c.2657del	p.Pro886LeufsTer44	p.P886Lfs*44	ENST00000301067	NM_003482.3	886	cCt/ct	10/54	1	2	FACETS	0.883	0.766	1	0.883	0.766	1	CLONAL	1	TRUE	1	0.16	2		455	948	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910346	29910346	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	66	530	0	ENST00000376809.5:c.19del	p.Arg7GlufsTer13	p.R7Efs*13	ENST00000376809	NM_002116.7	6	Ccc/cc	1/8	1	2	FACETS	0.657	0.568	0.754	0.657	0.568	0.754	SUBCLONAL	1	TRUE	1	0.16	2		530	1256	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779211	3779211	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783507	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	23	196	0	ENST00000262367.5:c.5837del	p.Pro1946HisfsTer30	p.P1946Hfs*30	ENST00000262367	NM_004380.2	1946	cCa/ca	31/31	1	2	FACETS	0.812	0.633	1	0.812	0.633	1	CLONAL	1	TRUE	1	0.16	2		196	354	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443789	49443789	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1154	88	597	0	ENST00000301067.7:c.3582del	p.Thr1195HisfsTer17	p.T1195Hfs*17	ENST00000301067	NM_003482.3	1194	ccC/cc	11/54	1	2	FACETS	0.886	0.782	0.997	0.886	0.782	0.997	CLONAL	1	TRUE	1	0.16	2		597	1242	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042176	6042177	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1260	89	639	0	ENST00000265849.7:c.444dup	p.Tyr149LeufsTer23	p.Y149Lfs*23	ENST00000265849	NM_000535.5	148	-/C	5/15	1	2	FACETS	0.825	0.728	0.928	0.825	0.728	0.928	CLONAL	1	TRUE	1	0.16	2		639	1349	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132896	64132896	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	78	694	1	ENST00000334205.4:c.1034del	p.Pro345LeufsTer30	p.P345Lfs*30	ENST00000334205	NM_003942.2	344	Ccc/cc	9/17	1	2	FACETS	0.781	0.684	0.887	0.781	0.684	0.887	SUBCLONAL	1	TRUE	1	0.16	2		695	1248	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173696	108173696	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	80	442	0	ENST00000278616.4:c.5441del	p.Leu1814TrpfsTer14	p.L1814Wfs*14	ENST00000278616	NM_000051.3	1812	gcT/gc	36/63	NA	2	FACETS	0.903	0.793	1			1	INDETERMINATE	1	TRUE	NA	0.16	2		442	1107	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719772	190719773	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	56	372	0	ENST00000441310.2:c.1778dup	p.Asn593LysfsTer3	p.N593Kfs*3	ENST00000441310	NM_000534.4	592	gaa/gAaa	9/13	1	2	FACETS	0.805	0.687	0.933	0.805	0.687	0.933	CLONAL	1	TRUE	1	0.16	2		372	870	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166794	32166795	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	46	394	0	ENST00000375023.3:c.4443_4444del	p.Trp1482AlafsTer39	p.W1482Afs*39	ENST00000375023	NM_004557.3	1481	ctCTgg/ctgg	24/30	1	2	FACETS	0.75	0.63	0.883	0.75	0.63	0.883	SUBCLONAL	1	TRUE	1	0.16	2		394	767	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216109	7216112	+	frameshift_variant	Frame_Shift_Del	DEL	TGGA	TGGA	-	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2050	180	999	0	ENST00000380728.2:c.947_950del	p.Ile316AsnfsTer28	p.I316Nfs*28	ENST00000380728		316	aTCCAa/aa	11/11	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.16	2		999	2230	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482927	140482927	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1287	104	655	3	ENST00000288602.6:c.1208del	p.Pro403LeufsTer8	p.P403Lfs*8	ENST00000288602	NM_004333.4	403	cCt/ct	10/18	1	2	FACETS	0.935	0.834	1	0.935	0.834	1	CLONAL	1	TRUE	1	0.16	2		658	1391	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801138	1801138	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	49	394	0	ENST00000260795.2:c.270del	p.Gln92SerfsTer6	p.Q92Sfs*6	ENST00000260795		89	gtG/gt	2/17	1	2	FACETS	0.798	0.674	0.934	0.798	0.674	0.934	CLONAL	1	TRUE	1	0.16	2		394	768	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913837	32913837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359507	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1989	124	743	2	ENST00000380152.3:c.5351del	p.Asn1784ThrfsTer7	p.N1784Tfs*7	ENST00000380152		1782	cAa/ca	11/27	1	2	FACETS	0.734	0.66	0.812	0.734	0.66	0.812	SUBCLONAL	1	TRUE	1	0.16	2		745	2113	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871043	12871044	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	36	267	0	ENST00000228872.4:c.275dup	p.Arg93AlafsTer32	p.R93Afs*32	ENST00000228872	NM_004064.3	90	-/C	1/3	NA	2	FACETS	0.665	0.545	0.8			1	INDETERMINATE	1	TRUE	NA	0.16	2		267	677	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363132	40363133	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0009484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	83	472	0	ENST00000397332.2:c.1096dup	p.Ala366GlyfsTer2	p.A366Gfs*2	ENST00000397332	NM_001033082.2	366	gct/gGct	3/3	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.16	2		472	1006	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0009614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	132	524	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.248025614626608	2	FACETS	0.969	0.884	1	0.969	0.884	1	CLONAL	2	TRUE	0	0.249047764996767	2		524	547	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971138	21971138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760640852	NA	P-0009614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	65	128	0	ENST00000304494.5:c.220G>A	p.Asp74Asn	p.D74N	ENST00000304494	NM_000077.4	74	Gac/Aac	2/3	0.232192621278743	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	2	TRUE	0	0.249047764996767	2		128	254	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100414	157100414	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1438676618	NA	P-0009614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	10	52	0	ENST00000346085.5:c.1351T>C	p.Ser451Pro	p.S451P	ENST00000346085	NM_020732.3	451	Tcg/Ccg	1/20	0.248025614626608	2	FACETS	0.787	0.538	1	0.394	0.269	0.548	CLONAL	1	TRUE	0	0.249047764996767	2		52	102	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106159	27106159	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	81	226	0	ENST00000324856.7:c.5770G>T	p.Glu1924Ter	p.E1924*	ENST00000324856	NM_006015.4	1924	Gag/Tag	20/20	0.249047764996767	3	FACETS	1	0.966	1	0.632	0.557	0.711	CLONAL	1	TRUE	1	0.249047764996767	3		226	579	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898738	134898738	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	69	501	0	ENST00000398015.3:c.1796C>A	p.Thr599Asn	p.T599N	ENST00000398015	NM_004441.4	599	aCt/aAt	10/16	0.249047764996767	4	FACETS	0.873	0.759	0.996	0.291	0.253	0.332	CLONAL	1	TRUE	1	0.249047764996767	4		501	793	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280144	66280144	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	67	230	0	ENST00000273854.3:c.1545C>A	p.Tyr515Ter	p.Y515*	ENST00000273854	NM_004439.5	515	taC/taA	7/18	1	2	FACETS	0.766	0.67	0.869	1	0.974	1	SUBCLONAL	2	TRUE	1	0.249047764996767	2		230	351	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114901047	114901047	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	125	641	1	ENST00000543371.1:c.657C>A	p.His219Gln	p.H219Q	ENST00000543371	NM_001198531.1	219	caC/caA	6/14	1	2	FACETS	0.872	0.787	0.962	0.872	0.787	0.962	CLONAL	1	TRUE	1	0.249047764996767	2		642	1151	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641473	18641473	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	63	364	0	ENST00000266497.5:c.2472G>C	p.Leu824Phe	p.L824F	ENST00000266497		824	ttG/ttC	17/31	0.249047764996767	2	FACETS	0.829	0.723	0.943	0.829	0.723	0.943	CLONAL	2	TRUE	0	0.249047764996767	2		364	305	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858905	57858905	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	227	645	0	ENST00000228682.2:c.401G>C	p.Gly134Ala	p.G134A	ENST00000228682	NM_005269.2	134	gGa/gCa	5/12	0.249047764996767	3	FACETS	0.912	0.849	0.977	0.912	0.849	0.977	CLONAL	2	TRUE	1	0.249047764996767	3		645	1124	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959346	26959346	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0009614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	45	212	0	ENST00000381527.3:c.515-2A>T		p.X172_splice	ENST00000381527	NM_001260.1	172			0.232192621278743	2	FACETS	0.786	0.666	0.915	0.786	0.666	0.915	CLONAL	2	TRUE	0	0.249047764996767	2		212	230	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134313	41134313	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs146471778	NA	P-0009614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	195	705	0	ENST00000379561.5:c.1315A>G	p.Ile439Val	p.I439V	ENST00000379561	NM_002015.3	439	Ata/Gta	2/3	0.232192621278743	2	FACETS	0.844	0.781	0.909	0.844	0.781	0.909	CLONAL	2	TRUE	0	0.249047764996767	2		705	928	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862891	9862891	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	70	339	0	ENST00000330684.3:c.2412G>C	p.Lys804Asn	p.K804N	ENST00000330684	NM_001134407.1	804	aaG/aaC	12/13	NA	2	FACETS	1	0.907	1			1	INDETERMINATE	1	TRUE	NA	0.249047764996767	2		339	537	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946314	81946314	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	184	495	0	ENST00000359376.3:c.2047A>G	p.Thr683Ala	p.T683A	ENST00000359376	NM_002661.3	683	Acc/Gcc	19/33	0.249047764996767	3	FACETS	0.785	0.724	0.849	0.785	0.724	0.849	SUBCLONAL	2	TRUE	1	0.249047764996767	3		495	1058	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428242	33428242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	118	335	0	ENST00000345365.6:c.881G>A	p.Cys294Tyr	p.C294Y	ENST00000345365	NM_002878.3	294	tGt/tAt	9/10	0.212933707517032	4	FACETS	0.885	0.799	0.974	0.885	0.799	0.974	CLONAL	2	TRUE	2	0.249047764996767	4		335	669	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604743	48604743	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	91	344	0	ENST00000342988.3:c.1565C>G	p.Pro522Arg	p.P522R	ENST00000342988	NM_005359.5	522	cCt/cGt	12/12	0.232192621278743	2	FACETS	1	0.977	1	0.695	0.619	0.775	CLONAL	1	TRUE	0	0.249047764996767	2		344	526	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222166	2222166	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	163	369	0	ENST00000398665.3:c.2998G>T	p.Ala1000Ser	p.A1000S	ENST00000398665	NM_032482.2	1000	Gcc/Tcc	24/28	0.249047764996767	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.249047764996767	2		369	598	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790156	40790156	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	14	143	0	ENST00000373198.4:c.2575C>A	p.Gln859Lys	p.Q859K	ENST00000373198	NM_133170.3	859	Cag/Aag	18/32	1	2	FACETS	0.65	0.471	0.864	0.65	0.471	0.864	SUBCLONAL	1	TRUE	1	0.249047764996767	2		143	173	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41554503	41554503	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	120	307	0	ENST00000263253.7:c.3589A>T	p.Arg1197Trp	p.R1197W	ENST00000263253	NM_001429.3	1197	Agg/Tgg	19/31	0.249047764996767	3	FACETS	0.976	0.885	1	0.976	0.885	1	CLONAL	2	TRUE	1	0.249047764996767	3		307	555	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889095	76889095	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	141	258	0	ENST00000373344.5:c.4915G>T	p.Glu1639Ter	p.E1639*	ENST00000373344	NM_000489.3	1639	Gag/Tag	18/35	0.249047764996767	2	FACETS	0.919	0.852	0.987			1	CLONAL	4	TRUE	NA	0.249047764996767	2		258	308	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790110	40790110	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	29	221	0	ENST00000373198.4:c.2621del	p.Pro874LeufsTer4	p.P874Lfs*4	ENST00000373198	NM_133170.3	874	cCt/ct	18/32	1	2	FACETS	0.679	0.545	0.83	0.679	0.545	0.83	SUBCLONAL	1	TRUE	1	0.249047764996767	2		221	343	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872546	35872547	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0009614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	161	490	1	ENST00000216797.5:c.356dup	p.Ile120AspfsTer9	p.I120Dfs*9	ENST00000216797	NM_020529.2	119	gtg/gtTg	3/6	0.249047764996767	3	FACETS	1	0.985	1	0.681	0.623	0.741	CLONAL	1	TRUE	1	0.249047764996767	3		491	1068	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183097	32183098	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0009614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	265	468	0	ENST00000375023.3:c.1926_1927delinsAA	p.Asp642_Gln643delinsGluLys	p.D642_Q643delinsEK	ENST00000375023	NM_004557.3	642	gaCCag/gaAAag	12/30	0.249047764996767	5	FACETS	0.908	0.854	0.963	0.726	0.683	0.77	CLONAL	4	TRUE	0	0.249047764996767	5		468	805	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141534	11141536	+	missense_variant	Missense_Mutation	TNP	GTG	GTG	TTT	novel	NA	P-0009614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	134	359	1	ENST00000358026.2:c.3511_3513delinsTTT	p.Val1171Phe	p.V1171F	ENST00000358026	NM_001128849.1	1171	GTG/TTT	25/36	0.249047764996767	2	FACETS	0.991	0.905	1	0.991	0.905	1	CLONAL	2	TRUE	0	0.249047764996767	2		360	543	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0009629-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	671	524	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.766602038191258	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.766602038191258	2		524	839	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913499	NA	P-0009629-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	308	582	0	ENST00000345146.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000345146	NM_005896.2	132	Cgt/Ggt	4/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.766602038191258	2		582	778	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589610	67589612	+	inframe_deletion	In_Frame_Del	DEL	AAA	AAA	-	novel	NA	P-0009629-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	103	518	0	ENST00000274335.5:c.1376_1378del	p.Lys459del	p.K459del	ENST00000274335		458	gAAAaa/gaa	10/15	1	2	FACETS	0.306	0.273	0.341	0.306	0.273	0.341	SUBCLONAL	1	TRUE	1	0.766602038191258	2		518	878	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938407	76938407	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009629-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	550	488	2	ENST00000373344.5:c.2341C>T	p.Arg781Ter	p.R781*	ENST00000373344	NM_000489.3	781	Cga/Tga	9/35	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.766602038191258	1		490	738	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170827188	170827188	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009629-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	459	767	2	ENST00000296930.5:c.556G>A	p.Ala186Thr	p.A186T	ENST00000296930	NM_002520.6	186	Gct/Act	7/11	0.766602038191258	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.766602038191258	1		769	683	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413129	139413131	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	novel	NA	P-0009629-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	181	805	0	ENST00000277541.6:c.1011_1013del	p.Asp338del	p.D338del	ENST00000277541	NM_017617.3	337	gaTGAc/gac	6/34	0.766602038191258	1	FACETS	0.393	0.363	0.424	0.393	0.363	0.424	SUBCLONAL	1	TRUE	0	0.766602038191258	1		805	741	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141071	55141072	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0009629-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	80	687	0	ENST00000257290.5:c.1718_1719insGT	p.Ile573MetfsTer22	p.I573Mfs*22	ENST00000257290	NM_006206.4	573	att/aTGtt	12/23	1	2	FACETS	0.221	0.194	0.251	0.221	0.194	0.251	SUBCLONAL	1	TRUE	1	0.766602038191258	2		687	943	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141065	55141066	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0009629-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	81	696	2	ENST00000257290.5:c.1711_1712delinsTT	p.Glu571Leu	p.E571L	ENST00000257290	NM_006206.4	571	GAa/TTa	12/23	1	2	FACETS	0.227	0.199	0.257	0.227	0.199	0.257	SUBCLONAL	1	TRUE	1	0.766602038191258	2		698	931	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009644-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	130	140	0				ENST00000310581	NM_198253.2	-/1132			0.567073033116297	4	FACETS	1	0.977	1			1	CLONAL	2	TRUE	NA	0.86841408914527	4		140	247	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573999	7573999	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009644-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	566	678	0	ENST00000269305.4:c.1028del	p.Glu343GlyfsTer2	p.E343Gfs*2	ENST00000269305	NM_001126112.2	343	gAg/gg	10/11	0.86841408914527	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.86841408914527	2		678	629	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137524641	137524641	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009644-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	242	375	0	ENST00000367739.4:c.728T>G	p.Ile243Arg	p.I243R	ENST00000367739	NM_000416.2	243	aTa/aGa	5/7	1	2	FACETS	0.912	0.858	0.967	0.912	0.858	0.967	CLONAL	1	TRUE	1	0.86841408914527	2		375	611	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652120	36652130	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCCCGGCGA	GGCCCCGGCGA	-	novel	NA	P-0009644-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	840	353	0	ENST00000244741.5:c.246_256del	p.Arg83GlyfsTer2	p.R83Gfs*2	ENST00000244741	NM_000389.4	81	gGGCCCCGGCGA/g	2/3	0.86841408914527	8	FACETS	0.915	0.89	0.941			1	CLONAL	5	TRUE	NA	0.86841408914527	8		353	1524	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266086	41266097	+	inframe_deletion	In_Frame_Del	DEL	AGTCTTACCTGG	AGTCTTACCTGG	-	rs1553630102	NA	P-0009644-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	218	500	0	ENST00000349496.5:c.84_95del	p.Gln28_Asp32delinsHis	p.Q28_D32delinsH	ENST00000349496	NM_001904.3	28	cAGTCTTACCTGGac/cac	3/15	0.741109018699987	4	FACETS	0.927	0.862	0.994	0.463	0.431	0.497	CLONAL	1	TRUE	2	0.86841408914527	4		500	1012	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001539	150001540	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0009644-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	162	323	0	ENST00000253339.5:c.2064dup	p.Glu689ArgfsTer3	p.E689Rfs*3	ENST00000253339		688	-/A	4/7	1	2	FACETS	0.923	0.857	0.991	0.923	0.857	0.991	CLONAL	1	TRUE	1	0.86841408914527	2		323	404	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0009645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	248	435	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.959	0.898	1	0.959	0.898	1	CLONAL	1	TRUE	1	0.568932630386634	2		435	909	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411576	63411576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	425	415	0	ENST00000330258.3:c.1591C>T	p.Arg531Ter	p.R531*	ENST00000330258	NM_152424.3	531	Cga/Tga	2/2	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.568932630386634	1		415	772	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236086	108236086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782292	NA	P-0009645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	598	505	0	ENST00000278616.4:c.9022C>T	p.Arg3008Cys	p.R3008C	ENST00000278616	NM_000051.3	3008	Cgt/Tgt	63/63	0.568234722678487	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.568932630386634	2		505	961	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196045	138196045	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	224	422	0	ENST00000237289.4:c.359T>G	p.Leu120Trp	p.L120W	ENST00000237289	NM_001270507.1	120	tTg/tGg	3/9	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.568932630386634	2		422	742	SUCCESS
APC	324	MSKCC	GRCh37	5	112175817	112175826	+	frameshift_variant	Frame_Shift_Del	DEL	TGAGCCTCGA	TGAGCCTCGA	-	novel	NA	P-0009645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	310	399	0	ENST00000257430.4:c.4532_4541del	p.Leu1511HisfsTer9	p.L1511Hfs*9	ENST00000257430	NM_000038.5	1509	cTGAGCCTCGAt/ct	16/16	NA	2	FACETS	0.847	0.806	0.889			1	INDETERMINATE	2	TRUE	NA	0.568932630386634	2		399	643	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573604	48573605	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0009645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	210	439	0	ENST00000342988.3:c.191dup	p.Asn64LysfsTer6	p.N64Kfs*6	ENST00000342988	NM_005359.5	63	aca/acAa	2/12	0.568932630386634	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.568932630386634	1		439	528	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	128	140	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.91	0.836	0.986			1	INDETERMINATE	1	TRUE	NA	0.832334484355131	2		140	338	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0009649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	287	234	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.776913568815801	2	FACETS	0.953	0.921	0.982	0.953	0.921	0.982	CLONAL	2	TRUE	0	0.832334484355131	2		234	362	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913351	NA	P-0009649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	190	561	1	ENST00000288602.6:c.1397G>A	p.Gly466Glu	p.G466E	ENST00000288602	NM_004333.4	466	gGa/gAa	11/18	0.832334484355131	3	FACETS	0.678	0.626	0.731	0.339	0.313	0.366	SUBCLONAL	1	TRUE	1	0.832334484355131	3		562	954	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322767	30322768	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0009649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	62	424	0	ENST00000322652.5:c.1786dup	p.Thr596AsnfsTer6	p.T596Nfs*6	ENST00000322652	NM_015355.2	594	gaa/gAaa	14/16	0.776913568815801	2	FACETS	0.303	0.262	0.347	0.151	0.131	0.174	SUBCLONAL	1	TRUE	0	0.832334484355131	2		424	492	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871996	35872004	+	inframe_deletion	In_Frame_Del	DEL	CCCAAGGAC	CCCAAGGAC	-	novel	NA	P-0009649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1247	86	1009	1	ENST00000216797.5:c.609_617del	p.Ser204_Gly206del	p.S204_G206del	ENST00000216797	NM_020529.2	203	gtGTCCTTGGGt/gtt	4/6	1	2	FACETS	0.155	0.136	0.175	0.155	0.136	0.175	SUBCLONAL	1	TRUE	1	0.832334484355131	2		1010	1333	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653032	29653037	+	inframe_deletion	In_Frame_Del	DEL	TCTATA	TCTATA	-	rs1135402868	NA	P-0009649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	587	674	1	ENST00000356175.3:c.4973_4978del	p.Ile1658_Tyr1659del	p.I1658_Y1659del	ENST00000356175	NM_000267.3	1656	gTCTATAtc/gtc	36/57	0.776913568815801	2	FACETS	0.873	0.85	0.895	0.873	0.85	0.895	CLONAL	2	TRUE	0	0.832334484355131	2		675	808	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0009654-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	344	397	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.382067493526319	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.503055724814682	1		397	960	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054366	13054366	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs748221094	NA	P-0009654-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1585	517	796	0	ENST00000316448.5:c.976A>G	p.Ile326Val	p.I326V	ENST00000316448	NM_004343.3	326	Atc/Gtc	8/9	1	2	FACETS	0.978	0.934	1	0.978	0.934	1	CLONAL	1	TRUE	1	0.503055724814682	2		796	2102	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910455	32910455	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555282375	NA	P-0009654-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1262	712	819	1	ENST00000380152.3:c.1964del	p.Pro655GlnfsTer5	p.P655Qfs*5	ENST00000380152		655	Cca/ca	11/27	0.503778026584679	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.503055724814682	1		820	1974	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130334	11130334	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1480398200	NA	P-0009728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	77	440	1	ENST00000358026.2:c.2573C>T	p.Thr858Met	p.T858M	ENST00000358026	NM_001128849.1	858	aCg/aTg	18/36	1	2	FACETS	0.421	0.368	0.478	0.421	0.368	0.478	SUBCLONAL	1	TRUE	1	0.33	2		441	1108	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691039	NA	P-0009728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	261	301	2	ENST00000269305.4:c.919+1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			NA	2	FACETS	0.919	0.863	0.976			1	INDETERMINATE	2	TRUE	NA	0.33	2		303	861	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592157	67592158	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTGCT	novel	NA	P-0009728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	159	231	0	ENST00000274335.5:c.1977_1981dup	p.Val661AlafsTer3	p.V661Afs*3	ENST00000274335		658	gcc/gcCTGCTc	14/15	0.165758604502085	2	FACETS	0.753	0.693	0.815	0.753	0.693	0.815	INDETERMINATE	2	TRUE	0	0.33	2		231	640	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061516	38061517	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGC	rs763371315	NA	P-0009819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	41	238	0	ENST00000250448.2:c.470_472dup	p.Gly157dup	p.G157dup	ENST00000250448	NM_004496.3	157	gac/gGCGac	2/2	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.278139562377127	2		238	277	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0009834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	154	509	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.802	0.732	0.875	0.802	0.732	0.875	CLONAL	1	TRUE	1	0.31	2		509	1239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578532	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	160	419	0	ENST00000269305.4:c.398T>A	p.Met133Lys	p.M133K	ENST00000269305	NM_001126112.2	133	aTg/aAg	5/11	0.30244169477744	1	FACETS	0.885	0.811	0.962	0.885	0.811	0.962	CLONAL	1	TRUE	0	0.31	1		419	986	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144147	11144147	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	168	380	0	ENST00000358026.2:c.3728G>C	p.Arg1243Pro	p.R1243P	ENST00000358026	NM_001128849.1	1243	cGg/cCg	26/36	0.30244169477744	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.31	1		380	789	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176566	56176567	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0009834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	155	366	0	ENST00000399503.3:c.2118_2119dup	p.Leu707CysfsTer19	p.L707Cfs*19	ENST00000399503	NM_005921.1	706	ctg/cTGtg	12/20	1	2	FACETS	0.993	0.908	1	0.993	0.908	1	CLONAL	1	TRUE	1	0.31	2		366	1007	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	209	509	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.951	0.886	1	0.951	0.886	1	CLONAL	1	TRUE	1	0.605184825656883	2		509	726	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	94	150	1	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.983	0.885	1	0.983	0.885	1	CLONAL	1	TRUE	1	0.605184825656883	2		151	316	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	315	609	5	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.909	0.858	0.962	0.909	0.858	0.962	CLONAL	1	TRUE	1	0.605184825656883	2		614	1145	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	249	184	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	0.989	0.928	1	0.989	0.928	1	CLONAL	1	TRUE	1	0.605184825656883	2		184	832	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	466	552	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.605184825656883	2		552	1497	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682399	52682400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	342	684	0	ENST00000394830.3:c.773dup	p.Asn258LysfsTer6	p.N258Kfs*6	ENST00000394830	NM_018313.4	258	aat/aaAt	8/30	1	2	FACETS	0.884	0.836	0.934	0.884	0.836	0.934	CLONAL	1	TRUE	1	0.605184825656883	2		684	1278	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	33	91	0	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	1	2	FACETS	0.54	0.443	0.647	0.54	0.443	0.647	SUBCLONAL	1	TRUE	1	0.605184825656883	2		91	202	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438316	110438317	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	rs532810290	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	36	110	2	ENST00000375856.3:c.82_84dup	p.Asn28dup	p.N28dup	ENST00000375856	NM_003749.2	28	-/AAC	1/2	1	2	FACETS	0.522	0.432	0.621	0.522	0.432	0.621	SUBCLONAL	1	TRUE	1	0.605184825656883	2		112	228	SUCCESS
REL	5966	MSKCC	GRCh37	2	61128147	61128147	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1016724251	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	248	353	1	ENST00000295025.8:c.323G>A	p.Arg108Gln	p.R108Q	ENST00000295025	NM_002908.2	108	cGa/cAa	4/11	1	2	FACETS	0.978	0.917	1	0.978	0.917	1	CLONAL	1	TRUE	1	0.605184825656883	2		354	838	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562387	21562387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764960515	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	138	266	0	ENST00000382592.4:c.1532G>A	p.Arg511Gln	p.R511Q	ENST00000382592	NM_014572.2	511	cGg/cAg	4/8	1	2	FACETS	0.831	0.76	0.905	0.831	0.76	0.905	CLONAL	1	TRUE	1	0.605184825656883	2		266	549	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353819	15353819	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	127	392	1	ENST00000263377.2:c.3061del	p.His1021IlefsTer47	p.H1021Ifs*47	ENST00000263377	NM_058243.2	1021	Cat/at	14/20	1	2	FACETS	0.673	0.611	0.737	0.673	0.611	0.737	SUBCLONAL	1	TRUE	1	0.605184825656883	2		393	624	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022592	31022592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs373221034	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	379	518	0	ENST00000375687.4:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000375687	NM_015338.5	693	Cga/Tga	13/13	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.605184825656883	2		518	1194	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1562	560	913	6	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	0.872	0.835	0.91	0.872	0.835	0.91	CLONAL	1	TRUE	1	0.605184825656883	2		919	2122	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347983	347983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760961378	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	320	435	2	ENST00000262320.3:c.1523del	p.Gly508ValfsTer197	p.G508Vfs*197	ENST00000262320	NM_003502.3	508	gGt/gt	6/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.605184825656883	2		437	1006	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646981	23646981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	252	461	3	ENST00000261584.4:c.886del	p.Met296Ter	p.M296*	ENST00000261584	NM_024675.3	296	Atg/tg	4/13	1	2	FACETS	0.717	0.67	0.765	0.717	0.67	0.765	SUBCLONAL	1	TRUE	1	0.605184825656883	2		464	1162	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922695	44922695	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	308	455	0	ENST00000377967.4:c.1556del	p.Arg519HisfsTer29	p.R519Hfs*29	ENST00000377967	NM_021140.2	519	cGa/ca	16/29	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.605184825656883	2		455	1008	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028285	48028285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587779254	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	213	365	1	ENST00000234420.5:c.3163G>A	p.Ala1055Thr	p.A1055T	ENST00000234420	NM_000179.2	1055	Gca/Aca	4/10	1	2	FACETS	0.837	0.779	0.897	0.837	0.779	0.897	CLONAL	1	TRUE	1	0.605184825656883	2		366	841	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114823	108114823	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747053710	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	221	422	0	ENST00000278616.4:c.640T>C	p.Ser214Pro	p.S214P	ENST00000278616	NM_000051.3	214	Tcc/Ccc	6/63	1	2	FACETS	0.843	0.786	0.902	0.843	0.786	0.902	CLONAL	1	TRUE	1	0.605184825656883	2		422	866	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193202236	193202236	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	287	494	0	ENST00000367435.3:c.1268T>C	p.Val423Ala	p.V423A	ENST00000367435	NM_024529.4	423	gTa/gCa	14/17	1	2	FACETS	0.861	0.809	0.913	0.861	0.809	0.913	CLONAL	1	TRUE	1	0.605184825656883	2		494	1102	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226568817	226568817	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	362	539	0	ENST00000366794.5:c.1252A>G	p.Lys418Glu	p.K418E	ENST00000366794	NM_001618.3	418	Aag/Gag	9/23	1	2	FACETS	0.919	0.871	0.968	0.919	0.871	0.968	CLONAL	1	TRUE	1	0.605184825656883	2		539	1302	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086001	16086001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	258	363	0	ENST00000281043.3:c.1177C>T	p.Arg393Cys	p.R393C	ENST00000281043	NM_005378.4	393	Cgc/Tgc	3/3	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.605184825656883	2		363	850	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934774	49934774	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1311	84	599	0	ENST00000296474.3:c.2122A>G	p.Ser708Gly	p.S708G	ENST00000296474	NM_002447.2	708	Agt/Ggt	7/20	1	2	FACETS	0.199	0.175	0.225	0.199	0.175	0.225	SUBCLONAL	1	TRUE	1	0.605184825656883	2		599	1395	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200766	128200766	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	214	374	0	ENST00000341105.2:c.1039A>G	p.Thr347Ala	p.T347A	ENST00000341105	NM_032638.4	347	Acc/Gcc	5/6	1	2	FACETS	0.929	0.866	0.994	0.929	0.866	0.994	CLONAL	1	TRUE	1	0.605184825656883	2		374	761	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183587	185183587	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	318	492	0	ENST00000265026.3:c.1441A>G	p.Asn481Asp	p.N481D	ENST00000265026	NM_004721.4	481	Aat/Gat	9/14	1	2	FACETS	0.984	0.93	1	0.984	0.93	1	CLONAL	1	TRUE	1	0.605184825656883	2		492	1068	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099736	157099736	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	71	110	0	ENST00000346085.5:c.673G>A	p.Ala225Thr	p.A225T	ENST00000346085	NM_020732.3	225	Gcg/Acg	1/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.605184825656883	2		110	205	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624425	140624425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1247014863	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	100	72	0	ENST00000288602.6:c.79G>A	p.Ala27Thr	p.A27T	ENST00000288602	NM_004333.4	27	Gcc/Acc	1/18	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.605184825656883	2		72	234	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215815	98215815	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs878853856	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	238	368	0	ENST00000331920.6:c.3394T>C	p.Ser1132Pro	p.S1132P	ENST00000331920	NM_000264.3	1132	Tcc/Ccc	20/24	1	2	FACETS	0.916	0.857	0.976	0.916	0.857	0.976	CLONAL	1	TRUE	1	0.605184825656883	2		368	859	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760186	133760186	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	210	404	0	ENST00000318560.5:c.2509G>A	p.Gly837Arg	p.G837R	ENST00000318560	NM_005157.4	837	Gga/Aga	11/11	1	2	FACETS	0.94	0.876	1	0.94	0.876	1	CLONAL	1	TRUE	1	0.605184825656883	2		404	738	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779460	3779460	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	266	527	0	ENST00000262367.5:c.5588A>G	p.Gln1863Arg	p.Q1863R	ENST00000262367	NM_004380.2	1863	cAg/cGg	31/31	1	2	FACETS	0.798	0.748	0.849	0.798	0.748	0.849	SUBCLONAL	1	TRUE	1	0.605184825656883	2		527	1102	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844112	68844112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854694	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	260	392	0	ENST00000261769.5:c.700G>A	p.Ala234Thr	p.A234T	ENST00000261769	NM_004360.3	234	Gct/Act	6/16	1	2	FACETS	0.983	0.923	1	0.983	0.923	1	CLONAL	1	TRUE	1	0.605184825656883	2		392	874	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836623	89836623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137913973	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	268	372	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	0.605184825656883	2		372	811	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315373	30315373	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	246	422	0	ENST00000322652.5:c.1058C>A	p.Pro353His	p.P353H	ENST00000322652	NM_015355.2	353	cCt/cAt	10/16	1	2	FACETS	0.869	0.814	0.927	0.869	0.814	0.927	CLONAL	1	TRUE	1	0.605184825656883	2		422	935	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879903	37879903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	279	390	1	ENST00000269571.5:c.2198C>T	p.Thr733Ile	p.T733I	ENST00000269571		733	aCa/aTa	18/27	1	2	FACETS	0.995	0.936	1	0.995	0.936	1	CLONAL	1	TRUE	1	0.605184825656883	2		391	927	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132431	11132431	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	374	576	0	ENST00000358026.2:c.2647G>T	p.Gly883Cys	p.G883C	ENST00000358026	NM_001128849.1	883	Ggt/Tgt	19/36	1	2	FACETS	0.978	0.928	1	0.978	0.928	1	CLONAL	1	TRUE	1	0.605184825656883	2		576	1264	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295210	15295210	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	298	482	3	ENST00000263388.2:c.2462G>A	p.Gly821Asp	p.G821D	ENST00000263388	NM_000435.2	821	gGc/gAc	16/33	1	2	FACETS	0.998	0.941	1	0.998	0.941	1	CLONAL	1	TRUE	1	0.605184825656883	2		485	987	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387962	31387962	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	291	407	0	ENST00000328111.2:c.1763A>G	p.Tyr588Cys	p.Y588C	ENST00000328111	NM_006892.3	588	tAc/tGc	17/23	1	2	FACETS	0.97	0.914	1	0.97	0.914	1	CLONAL	1	TRUE	1	0.605184825656883	2		407	991	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15833853	15833853	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	144	336	2	ENST00000307771.7:c.611G>A	p.Ser204Asn	p.S204N	ENST00000307771	NM_005089.3	204	aGc/aAc	8/11	1	2	FACETS	0.666	0.608	0.726	0.666	0.608	0.726	SUBCLONAL	1	TRUE	1	0.605184825656883	2		338	715	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732892	44732892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	260	426	3	ENST00000377967.4:c.95G>A	p.Gly32Asp	p.G32D	ENST00000377967	NM_021140.2	32	gGc/gAc	1/29	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.605184825656883	2		429	841	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338675	70338675	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	352	595	0	ENST00000374080.3:c.71T>G	p.Val24Gly	p.V24G	ENST00000374080		24	gTt/gGt	1/45	1	2	FACETS	0.957	0.907	1	0.957	0.907	1	CLONAL	1	TRUE	1	0.605184825656883	2		595	1215	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772312	68772341	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGGTGAGGGCGCGCTGCCGGTGTCCCTGG	GAGGTGAGGGCGCGCTGCCGGTGTCCCTGG	-	novel	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	210	350	0	ENST00000261769.5:c.162_163+28del		p.X54_splice	ENST00000261769	NM_004360.3	54		2/16	1	2	FACETS	0.959	0.893	1	0.959	0.893	1	CLONAL	1	TRUE	1	0.605184825656883	2		350	724	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906603	32906603	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359777	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	212	450	0	ENST00000380152.3:c.994del	p.Ile332PhefsTer17	p.I332Ffs*17	ENST00000380152		330	Aaa/aa	10/27	1	2	FACETS	0.807	0.751	0.865	0.807	0.751	0.865	CLONAL	1	TRUE	1	0.605184825656883	2		450	868	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054540	13054543	+	frameshift_variant	Frame_Shift_Del	DEL	AAAT	AAAT	-	novel	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	476	828	0	ENST00000316448.5:c.1067_1070del	p.Gln356ArgfsTer73	p.Q356Rfs*73	ENST00000316448	NM_004343.3	356	cAAATg/cg	9/9	1	2	FACETS	0.967	0.923	1	0.967	0.923	1	CLONAL	1	TRUE	1	0.605184825656883	2		828	1626	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354007	15354008	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	11	51	0	ENST00000263377.2:c.2872dup	p.Leu958ProfsTer135	p.L958Pfs*135	ENST00000263377	NM_058243.2	958	ctg/cCtg	14/20	1	2	FACETS	0.319	0.222	0.438	0.319	0.222	0.438	SUBCLONAL	1	TRUE	1	0.605184825656883	2		51	114	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293075	91293075	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs367543026	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	242	350	1	ENST00000355112.3:c.582del	p.Phe194LeufsTer11	p.F194Lfs*11	ENST00000355112	NM_000057.2	193	Ttt/tt	3/22	1	2	FACETS	0.997	0.934	1	0.997	0.934	1	CLONAL	1	TRUE	1	0.605184825656883	2		351	802	SUCCESS
APC	324	MSKCC	GRCh37	5	112175902	112175903	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906236	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	190	407	0	ENST00000257430.4:c.4612_4613del	p.Glu1538IlefsTer5	p.E1538Ifs*5	ENST00000257430	NM_000038.5	1537	acAGaa/acaa	16/16	1	2	FACETS	0.767	0.71	0.826	0.767	0.71	0.826	SUBCLONAL	1	TRUE	1	0.605184825656883	2		407	819	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991757	72991758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760959844	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	201	342	0	ENST00000268489.5:c.2287dup	p.Glu763GlyfsTer26	p.E763Gfs*26	ENST00000268489	NM_006885.3	763	gag/gGag	2/10	1	2	FACETS	0.933	0.868	1	0.933	0.868	1	CLONAL	1	TRUE	1	0.605184825656883	2		342	712	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211626	46211626	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	260	513	0	ENST00000334344.6:c.595del	p.Ile199SerfsTer16	p.I199Sfs*16	ENST00000334344	NM_152641.2	198	Aaa/aa	5/21	1	2	FACETS	0.889	0.833	0.945	0.889	0.833	0.945	CLONAL	1	TRUE	1	0.605184825656883	2		513	967	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910569	29910570	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	125	159	0	ENST00000376809.5:c.112dup	p.Arg38ProfsTer61	p.R38Pfs*61	ENST00000376809	NM_002116.7	37	tcc/tCcc	2/8	1	2	FACETS	0.943	0.86	1	0.943	0.86	1	CLONAL	1	TRUE	1	0.605184825656883	2		159	438	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794874	42794874	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	128	264	7	ENST00000575354.2:c.1954del	p.Ala652ProfsTer76	p.A652Pfs*76	ENST00000575354	NM_015125.3	652	Gcc/cc	10/20	1	2	FACETS	0.81	0.738	0.886	0.81	0.738	0.886	CLONAL	1	TRUE	1	0.605184825656883	2		271	522	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32189025	32189025	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	198	525	0	ENST00000375023.3:c.529del	p.Gln177ArgfsTer75	p.Q177Rfs*75	ENST00000375023	NM_004557.3	177	Cag/ag	4/30	1	2	FACETS	0.609	0.564	0.657	0.609	0.564	0.657	SUBCLONAL	1	TRUE	1	0.605184825656883	2		525	1074	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0009907-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	125	595	1	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.491521590766416	2		596	471	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061312	38061312	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1329067081	NA	P-0009907-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	179	744	0	ENST00000250448.2:c.677A>G	p.Asp226Gly	p.D226G	ENST00000250448	NM_004496.3	226	gAc/gGc	2/2	1	2	FACETS	0.934	0.862	1	0.934	0.862	1	CLONAL	1	TRUE	1	0.491521590766416	2		744	780	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728678	190728678	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009907-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	135	827	0	ENST00000441310.2:c.2066G>C	p.Arg689Thr	p.R689T	ENST00000441310	NM_000534.4	689	aGa/aCa	10/13	1	2	FACETS	0.959	0.875	1	0.959	0.875	1	CLONAL	1	TRUE	1	0.491521590766416	2		827	573	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178257	56178257	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0009907-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	151	745	0	ENST00000399503.3:c.3230C>G	p.Ser1077Ter	p.S1077*	ENST00000399503	NM_005921.1	1077	tCa/tGa	14/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.491521590766416	2		745	542	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637183	176637183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377471340	NA	P-0009907-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	82	503	0	ENST00000439151.2:c.1783G>A	p.Glu595Lys	p.E595K	ENST00000439151	NM_022455.4	595	Gag/Aag	5/23	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.491521590766416	2		503	328	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289660	33289660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758327720	NA	P-0009907-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	128	426	0	ENST00000374542.5:c.43G>A	p.Glu15Lys	p.E15K	ENST00000374542	NM_001141970.1	15	Gaa/Aaa	2/8	1	2	FACETS	0.961	0.875	1	0.961	0.875	1	CLONAL	1	TRUE	1	0.491521590766416	2		426	542	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244318	46244318	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009907-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	107	499	0	ENST00000334344.6:c.2412A>C	p.Arg804Ser	p.R804S	ENST00000334344	NM_152641.2	804	agA/agC	15/21	1	2	FACETS	0.97	0.875	1	0.97	0.875	1	CLONAL	1	TRUE	1	0.491521590766416	2		499	449	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41818321	41818321	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009907-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	14	30	0	ENST00000373198.4:c.53C>A	p.Pro18Gln	p.P18Q	ENST00000373198	NM_133170.3	18	cCg/cAg	1/32	1	2	FACETS	0.814	0.622	1	1	0.912	1	CLONAL	2	TRUE	1	0.491521590766416	2		30	35	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244322	46244331	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAACATAC	CAGAACATAC	-	novel	NA	P-0009907-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	101	508	0	ENST00000334344.6:c.2419_2428del	p.Asn807HisfsTer12	p.N807Hfs*12	ENST00000334344	NM_152641.2	806	CAGAACATACca/ca	15/21	1	2	FACETS	0.919	0.826	1	0.919	0.826	1	CLONAL	1	TRUE	1	0.491521590766416	2		508	447	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849654	68849655	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0009907-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	103	518	0	ENST00000261769.5:c.1561dup	p.Ile521AsnfsTer16	p.I521Nfs*16	ENST00000261769	NM_004360.3	519	-/A	10/16	0.491521590766416	1	FACETS	0.958	0.867	1	0.958	0.867	1	CLONAL	1	TRUE	0	0.491521590766416	1		518	330	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	187	366	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.271939482102316	2	FACETS	0.953	0.883	1	0.953	0.883	1	CLONAL	2	TRUE	0	0.272411463561632	2		366	720	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143128	30143128	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	94	263	0	ENST00000389048.3:c.398G>T	p.Arg133Leu	p.R133L	ENST00000389048	NM_004304.4	133	cGc/cTc	1/29	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.272411463561632	2		263	628	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953807	55953807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	110	387	1	ENST00000263923.4:c.3629C>A	p.Pro1210His	p.P1210H	ENST00000263923	NM_002253.2	1210	cCc/cAc	27/30	1	2	FACETS	0.971	0.872	1	0.971	0.872	1	CLONAL	1	TRUE	1	0.272411463561632	2		388	832	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206896	162206896	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	93	275	1	ENST00000366898.1:c.779G>T	p.Cys260Phe	p.C260F	ENST00000366898	NM_004562.2	260	tGc/tTc	7/12	0.272411463561632	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	0	0.272411463561632	1		276	579	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154345	2154345	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	165	389	0	ENST00000434045.2:c.583G>T	p.Gly195Cys	p.G195C	ENST00000434045	NM_001127598.1	195	Ggt/Tgt	5/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.272411463561632	2		389	1005	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432139	121432139	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	134	347	0	ENST00000257555.6:c.886G>A	p.Gly296Arg	p.G296R	ENST00000257555		296	Gga/Aga	4/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.272411463561632	2		347	890	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410931	63410931	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	115	456	0	ENST00000330258.3:c.2236C>A	p.Pro746Thr	p.P746T	ENST00000330258	NM_152424.3	746	Cct/Act	2/2	0.271939482102316	2	FACETS	0.877	0.789	0.97	0.438	0.394	0.485	CLONAL	1	TRUE	0	0.272411463561632	2		456	963	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927082	131927083	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0009975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	115	386	0	ENST00000265335.6:c.1620dup	p.Leu541AlafsTer7	p.L541Afs*7	ENST00000265335		540	atg/atGg	10/25	1	2	FACETS	0.852	0.766	0.943	0.852	0.766	0.943	CLONAL	1	TRUE	1	0.272411463561632	2		386	991	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	157	366	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	0.545534358728217	2		366	570	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	233	436	0	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	0.545534358728217	2		436	821	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258001	16258001	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	176	290	0	ENST00000375759.3:c.5266A>G	p.Thr1756Ala	p.T1756A	ENST00000375759	NM_015001.2	1756	Acc/Gcc	11/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.545534358728217	2		290	567	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260371	16260371	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	30	211	0	ENST00000375759.3:c.7636G>C	p.Ala2546Pro	p.A2546P	ENST00000375759	NM_015001.2	2546	Gcc/Ccc	11/15	1	2	FACETS	0.23	0.184	0.281	0.23	0.184	0.281	SUBCLONAL	1	TRUE	1	0.545534358728217	2		211	479	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	359	296	0	ENST00000397062.3:c.92G>A	p.Gly31Glu	p.G31E	ENST00000397062	NM_006164.4	31	gGa/gAa	2/5	0.50876031307865	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.545534358728217	3		296	770	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593575	215593575	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	68	342	0	ENST00000260947.4:c.2159T>C	p.Val720Ala	p.V720A	ENST00000260947	NM_000465.2	720	gTc/gCc	11/11	0.50876031307865	3	FACETS	0.482	0.419	0.551	0.241	0.209	0.276	SUBCLONAL	1	TRUE	1	0.545534358728217	3		342	658	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0009985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	13	223	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	0.50876031307865	3	FACETS	0.157	0.111	0.213	0.078	0.055	0.107	SUBCLONAL	1	TRUE	1	0.545534358728217	3		223	387	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178338	56178338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	97	364	1	ENST00000399503.3:c.3311C>T	p.Ala1104Val	p.A1104V	ENST00000399503	NM_005921.1	1104	gCt/gTt	14/20	1	2	FACETS	0.542	0.484	0.604	0.542	0.484	0.604	SUBCLONAL	1	TRUE	1	0.545534358728217	2		365	656	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394998	394998	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	124	208	1	ENST00000380956.4:c.394G>T	p.Ala132Ser	p.A132S	ENST00000380956	NM_001195286.1	132	Gcc/Tcc	3/9	0.50876031307865	3	FACETS	1	0.963	1	0.556	0.506	0.609	CLONAL	1	TRUE	1	0.545534358728217	3		209	520	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168682	32168682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs935064991	NA	P-0009985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	462	429	2	ENST00000375023.3:c.4241C>T	p.Ala1414Val	p.A1414V	ENST00000375023	NM_004557.3	1414	gCg/gTg	23/30	0.50876031307865	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.545534358728217	3		431	935	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024095	112024095	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	516	480	0	ENST00000368678.4:c.690T>G	p.His230Gln	p.H230Q	ENST00000368678		230	caT/caG	7/13	0.50876031307865	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.545534358728217	3		480	1130	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90992979	90992979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	241	302	0	ENST00000265433.3:c.463G>A	p.Val155Met	p.V155M	ENST00000265433	NM_002485.4	155	Gtg/Atg	4/16	0.50876031307865	3	FACETS	0.908	0.854	0.963	0.908	0.854	0.963	CLONAL	2	TRUE	1	0.545534358728217	3		302	619	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100715	8100715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	151	302	0	ENST00000346208.3:c.689G>A	p.Ser230Asn	p.S230N	ENST00000346208		230	aGc/aAc	3/6	1	2	FACETS	0.945	0.868	1	0.945	0.868	1	CLONAL	1	TRUE	1	0.545534358728217	2		302	586	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604572	43604572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115272158	NA	P-0009985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	228	421	0	ENST00000355710.3:c.1157C>T	p.Ala386Val	p.A386V	ENST00000355710	NM_020975.4	386	gCg/gTg	6/20	0.545534358728217	2	FACETS	1	0.97	1	0.532	0.497	0.568	CLONAL	1	TRUE	0	0.545534358728217	2		421	786	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333939	70333939	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	150	376	0	ENST00000373644.4:c.1844G>A	p.Ser615Asn	p.S615N	ENST00000373644	NM_030625.2	615	aGc/aAc	2/12	0.545534358728217	2	FACETS	0.862	0.79	0.936	0.431	0.395	0.468	CLONAL	1	TRUE	0	0.545534358728217	2		376	638	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720711	89720711	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	39	33	0	ENST00000371953.3:c.862G>T	p.Glu288Ter	p.E288*	ENST00000371953	NM_000314.4	288	Gaa/Taa	8/9	0.545534358728217	2	FACETS	0.917	0.794	1	0.917	0.794	1	CLONAL	2	TRUE	0	0.545534358728217	2		33	78	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445968	49445968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	53	437	0	ENST00000301067.7:c.1498G>A	p.Glu500Lys	p.E500K	ENST00000301067	NM_003482.3	500	Gag/Aag	10/54	1	2	FACETS	0.198	0.168	0.232	0.198	0.168	0.232	SUBCLONAL	1	TRUE	1	0.545534358728217	2		437	980	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347909	347909	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	297	519	3	ENST00000262320.3:c.1597C>T	p.Arg533Ter	p.R533*	ENST00000262320	NM_003502.3	533	Cga/Tga	6/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.545534358728217	2		522	981	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877384	89877384	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	191	312	0	ENST00000389301.3:c.379G>A	p.Ala127Thr	p.A127T	ENST00000389301	NM_000135.2	127	Gct/Act	4/43	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.545534358728217	2		312	626	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215905	41215905	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs80357132	NA	P-0009985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	49	465	0	ENST00000357654.3:c.5138T>C	p.Val1713Ala	p.V1713A	ENST00000357654	NM_007294.3	1713	gTa/gCa	17/23	1	2	FACETS	0.199	0.168	0.234	0.199	0.168	0.234	SUBCLONAL	1	TRUE	1	0.545534358728217	2		465	902	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2199893	2199893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	183	452	0	ENST00000398665.3:c.662G>A	p.Gly221Asp	p.G221D	ENST00000398665	NM_032482.2	221	gGc/gAc	8/28	1	2	FACETS	0.81	0.749	0.874	0.81	0.749	0.874	CLONAL	1	TRUE	1	0.545534358728217	2		452	828	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119235	3119235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529942770	NA	P-0009985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	268	418	1	ENST00000078429.4:c.767G>A	p.Arg256Gln	p.R256Q	ENST00000078429	NM_002067.2	256	cGg/cAg	6/7	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.545534358728217	2		419	791	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050380	13050380	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	61	521	0	ENST00000316448.5:c.332A>G	p.Lys111Arg	p.K111R	ENST00000316448	NM_004343.3	111	aAg/aGg	3/9	1	2	FACETS	0.201	0.172	0.232	0.201	0.172	0.232	SUBCLONAL	1	TRUE	1	0.545534358728217	2		521	1113	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791043	42791043	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	139	237	0	ENST00000575354.2:c.188G>A	p.Ser63Asn	p.S63N	ENST00000575354	NM_015125.3	63	aGc/aAc	2/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.545534358728217	2		237	470	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0009985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	265	600	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.545534358728217	2		600	865	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76764089	76764089	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1557034957	NA	P-0009985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	122	373	0	ENST00000373344.5:c.7219C>T	p.Arg2407Ter	p.R2407*	ENST00000373344	NM_000489.3	2407	Cga/Tga	35/35	1	2	FACETS	0.727	0.659	0.799	0.727	0.659	0.799	SUBCLONAL	1	TRUE	1	0.545534358728217	2		373	615	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873698	151873698	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	93	246	0	ENST00000262189.6:c.8840del	p.Pro2947HisfsTer12	p.P2947Hfs*12	ENST00000262189	NM_170606.2	2947	cCa/ca	38/59	0.50876031307865	3	FACETS	0.882	0.787	0.982	0.441	0.393	0.491	CLONAL	1	TRUE	1	0.545534358728217	3		246	492	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007332	143007332	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	176	327	2	ENST00000262992.4:c.2452del	p.Arg818GlufsTer4	p.R818Efs*4	ENST00000262992	NM_001101669.1	818	Aga/ga	22/24	1	2	FACETS	0.874	0.807	0.944	0.874	0.807	0.944	CLONAL	1	TRUE	1	0.545534358728217	2		329	738	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0009985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	238	609	5	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.98	0.917	1	0.98	0.917	1	CLONAL	1	TRUE	1	0.545534358728217	2		614	890	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436939	49436939	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	230	421	0	ENST00000301067.7:c.5564del	p.Pro1855GlnfsTer21	p.P1855Qfs*21	ENST00000301067	NM_003482.3	1855	cCa/ca	25/54	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.545534358728217	2		421	713	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337684	73337684	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771690280	NA	P-0009985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	181	358	5	ENST00000377767.4:c.2032del	p.Ile678PhefsTer59	p.I678Ffs*59	ENST00000377767	NM_014953.3	678	Att/tt	16/21	1	2	FACETS	0.903	0.835	0.973	0.903	0.835	0.973	CLONAL	1	TRUE	1	0.545534358728217	2		363	735	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027087	71027087	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	122	371	1	ENST00000318789.4:c.1240del	p.Leu414Ter	p.L414*	ENST00000318789	NM_032682.5	414	Ctg/tg	15/21	0.50876031307865	3	FACETS	0.659	0.595	0.726	0.329	0.297	0.363	SUBCLONAL	1	TRUE	1	0.545534358728217	3		372	864	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0009985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	168	276	0	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.545534358728217	2		276	560	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717670	89717671	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0009990-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	90	565	1	ENST00000371953.3:c.696dup	p.Arg233ThrfsTer10	p.R233Tfs*10	ENST00000371953	NM_000314.4	232	aca/acAa	7/9	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.2	2		566	803	SUCCESS
APC	324	MSKCC	GRCh37	5	112175675	112175676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0010007-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	211	441	0	ENST00000257430.4:c.4393_4394dup	p.Ser1465ArgfsTer9	p.S1465Rfs*9	ENST00000257430	NM_000038.5	1462	aag/aAGag	16/16	0.267852088190143	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.355039805198112	1		441	883	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0010007-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	45	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.192520089037485	3	FACETS	0.942	0.795	1	0.471	0.397	0.551	INDETERMINATE	1	TRUE	1	0.355039805198112	3		249	317	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010007-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	48	435	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.0992299837628523	4	FACETS	0.413	0.348	0.485	0.207	0.174	0.243	INDETERMINATE	1	TRUE	2	0.355039805198112	4		435	887	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048631	180048631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1391338478	NA	P-0010007-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	104	278	0	ENST00000261937.6:c.1931C>T	p.Ala644Val	p.A644V	ENST00000261937	NM_182925.4	644	gCg/gTg	13/30	0.203346689915918	3	FACETS	0.855	0.765	0.95	0.427	0.382	0.475	INDETERMINATE	1	TRUE	1	0.355039805198112	3		278	807	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0010007-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	147	485	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.0992299837628523	4	FACETS	1	0.981	1	0.633	0.577	0.69	INDETERMINATE	1	TRUE	2	0.355039805198112	4		485	887	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555687605	NA	P-0010007-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	254	437	1	ENST00000342988.3:c.1610A>G	p.Asp537Gly	p.D537G	ENST00000342988	NM_005359.5	537	gAc/gGc	12/12	0.355039805198112	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.355039805198112	1		438	923	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135691	64135691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151034403	NA	P-0010007-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	215	330	0	ENST00000334205.4:c.1159C>T	p.Arg387Trp	p.R387W	ENST00000334205	NM_003942.2	387	Cgg/Tgg	10/17	0.192520089037485	3	FACETS	1	0.99	1	0.71	0.659	0.761	INDETERMINATE	1	TRUE	1	0.355039805198112	3		330	1005	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119884	70119884	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010007-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	269	400	0	ENST00000245479.2:c.886C>T	p.Gln296Ter	p.Q296*	ENST00000245479	NM_000346.3	296	Cag/Tag	3/3	0.192520089037485	3	FACETS	0.896	0.841	0.952	0.896	0.841	0.952	INDETERMINATE	2	TRUE	1	0.355039805198112	3		400	996	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0010019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	628	604	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.658721346571703	2		604	892	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491645	56491645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	430	486	2	ENST00000267101.3:c.2537G>T	p.Ser846Ile	p.S846I	ENST00000267101	NM_001982.3	846	aGt/aTt	21/28	0.658721346571703	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.658721346571703	4		488	1068	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533180	63533180	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs753824435	NA	P-0010019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	444	413	0	ENST00000307078.5:c.1714G>A	p.Gly572Ser	p.G572S	ENST00000307078	NM_004655.3	572	Ggc/Agc	7/11	0.658721346571703	4	FACETS	1	0.989	1	0.545	0.522	0.569	CLONAL	2	TRUE	0	0.658721346571703	4		413	1025	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900288	101900288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111854391	NA	P-0010019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	247	531	1	ENST00000374994.4:c.722C>T	p.Ser241Leu	p.S241L	ENST00000374994	NM_004612.2	241	tCg/tTg	4/9	0.621693350327565	3	FACETS	0.989	0.925	1	0.495	0.462	0.528	CLONAL	1	TRUE	1	0.658721346571703	3		532	1008	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492732	56492732	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	1186	547	0	ENST00000407977.2:c.207del	p.Phe69LeufsTer7	p.F69Lfs*7	ENST00000407977		69	ttT/tt	2/10	0.658721346571703	4	FACETS	1	0.997	1	1	0.997	1	CLONAL	4	TRUE	0	0.658721346571703	4		547	1423	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052632	42052632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779811318	NA	P-0010019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	695	668	3	ENST00000219905.7:c.7303C>T	p.Arg2435Trp	p.R2435W	ENST00000219905	NM_001164273.1	2435	Cgg/Tgg	20/24	0.658721346571703	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.658721346571703	3		671	1379	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188968	11188968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	216	534	0	ENST00000361445.4:c.5755G>A	p.Val1919Ile	p.V1919I	ENST00000361445	NM_004958.3	1919	Gtc/Atc	41/58	0.621693350327565	3	FACETS	0.893	0.831	0.958	0.447	0.415	0.479	CLONAL	1	TRUE	1	0.658721346571703	3		534	976	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535402	66535402	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	183	268	2	ENST00000273854.3:c.59A>T	p.Asp20Val	p.D20V	ENST00000273854	NM_004439.5	20	gAc/gTc	1/18	0.658721346571703	3	FACETS	1	0.988	1	0.657	0.61	0.705	CLONAL	1	TRUE	1	0.658721346571703	3		270	562	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535430	66535430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	218	167	0	ENST00000273854.3:c.31C>T	p.Arg11Cys	p.R11C	ENST00000273854	NM_004439.5	11	Cgc/Tgc	1/18	0.658721346571703	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.658721346571703	3		167	363	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729775	41729775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1259	263	508	1	ENST00000242208.4:c.754G>A	p.Ala252Thr	p.A252T	ENST00000242208	NM_002192.2	252	Gcc/Acc	3/3	0.589324894655189	5	FACETS	1	0.963	1	0.348	0.325	0.372	CLONAL	1	TRUE	2	0.658721346571703	5		509	1522	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246532	105246532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	167	383	0	ENST00000349310.3:c.68G>A	p.Arg23Gln	p.R23Q	ENST00000349310	NM_001014432.1	23	cGg/cAg	4/15	1	2	FACETS	0.969	0.897	1	0.969	0.897	1	CLONAL	1	TRUE	1	0.658721346571703	2		383	523	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347172	89347173	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0010019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	191	535	1	ENST00000301030.4:c.5777dup	p.Glu1927GlyfsTer23	p.E1927Gfs*23	ENST00000301030	NM_001256183.1	1926	ccg/ccCg	9/13	0.658721346571703	3	FACETS	0.781	0.722	0.842	0.391	0.361	0.421	SUBCLONAL	1	TRUE	1	0.658721346571703	3		536	987	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244905	46244910	+	inframe_deletion	In_Frame_Del	DEL	CTCCTA	CTCCTA	-	novel	NA	P-0010019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	260	462	0	ENST00000334344.6:c.3001_3006del	p.Pro1001_Thr1002del	p.P1001_T1002del	ENST00000334344	NM_152641.2	1000	cCTCCTAct/cct	15/21	0.658721346571703	4	FACETS	0.977	0.914	1	0.489	0.457	0.522	CLONAL	1	TRUE	2	0.658721346571703	4		462	1340	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184372	7184374	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs775724610	NA	P-0010019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	231	474	0	ENST00000302850.5:c.927_929del	p.Asn309del	p.N309del	ENST00000302850	NM_000208.2	309	aaCAAg/aag	3/22	0.658721346571703	3	FACETS	0.936	0.873	1	0.468	0.436	0.501	CLONAL	1	TRUE	1	0.658721346571703	3		474	996	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416952	416953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs771545848	NA	P-0010019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	485	459	3	ENST00000399788.2:c.3597dup	p.Gly1200ArgfsTer7	p.G1200Rfs*7	ENST00000399788	NM_001042603.1	1199	-/A	23/28	0.658721346571703	4	FACETS	0.924	0.884	0.964	0.924	0.884	0.964	CLONAL	2	TRUE	2	0.658721346571703	4		462	1322	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	268	654	0	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.33	2		654	1324	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0010034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	110	293	2	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	0.33	2		295	607	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0010034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	59	234	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.931	0.804	1	0.931	0.804	1	CLONAL	1	TRUE	1	0.33	2		234	384	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0010034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	77	183	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.949	0.835	1	0.949	0.835	1	CLONAL	1	TRUE	1	0.33	2		183	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0010034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	127	356	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.791	0.716	0.871	0.791	0.716	0.871	SUBCLONAL	1	TRUE	1	0.33	2		356	973	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	122	264	1	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	0.3	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.33	1		265	438	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650109	93650109	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	114	412	0	ENST00000375746.1:c.1660G>A	p.Asp554Asn	p.D554N	ENST00000375746	NM_001174167.1	554	Gat/Aat	12/14	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.33	2		412	631	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0010034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	26	355	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.234	0.185	0.292	0.234	0.185	0.292	SUBCLONAL	1	TRUE	1	0.33	2		355	672	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426123	138426123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217537873	NA	P-0010034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	33	361	0	ENST00000289153.2:c.1408G>A	p.Glu470Lys	p.E470K	ENST00000289153	NM_006219.2	470	Gaa/Aaa	9/22	1	2	FACETS	0.332	0.27	0.403	0.332	0.27	0.403	SUBCLONAL	1	TRUE	1	0.33	2		361	602	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424427	49424427	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs577303074	NA	P-0010034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	112	437	1	ENST00000301067.7:c.13796C>T	p.Ala4599Val	p.A4599V	ENST00000301067	NM_003482.3	4599	gCg/gTg	41/54	1	2	FACETS	0.89	0.8	0.984	0.89	0.8	0.984	CLONAL	1	TRUE	1	0.33	2		438	763	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417343	139417343	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150737112	NA	P-0010034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	76	265	0	ENST00000277541.6:c.701G>A	p.Arg234His	p.R234H	ENST00000277541	NM_017617.3	234	cGc/cAc	4/34	0.3	1	FACETS	0.699	0.614	0.791	0.699	0.614	0.791	SUBCLONAL	1	TRUE	0	0.33	1		265	550	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807506	1807506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768385286	NA	P-0010034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	79	600	0	ENST00000260795.2:c.1675G>A	p.Ala559Thr	p.A559T	ENST00000260795		559	Gcc/Acc	12/17	1	2	FACETS	0.638	0.56	0.721	0.638	0.56	0.721	SUBCLONAL	1	TRUE	1	0.33	2		600	751	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961399	41961399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748756129	NA	P-0010034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	163	594	0	ENST00000219905.7:c.307C>T	p.Arg103Cys	p.R103C	ENST00000219905	NM_001164273.1	103	Cgc/Tgc	2/24	0.3	1	FACETS	0.953	0.875	1	0.953	0.875	1	CLONAL	1	TRUE	0	0.33	1		594	866	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780181	9780181	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	104	533	0	ENST00000377346.4:c.1351G>A	p.Glu451Lys	p.E451K	ENST00000377346	NM_005026.3	451	Gag/Aag	11/24	1	2	FACETS	0.7	0.625	0.778	0.7	0.625	0.778	SUBCLONAL	1	TRUE	1	0.33	2		533	901	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272470	11272470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1225763956	NA	P-0010034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	96	304	2	ENST00000361445.4:c.3460C>T	p.Arg1154Trp	p.R1154W	ENST00000361445	NM_004958.3	1154	Cgg/Tgg	23/58	1	2	FACETS	0.912	0.814	1	0.912	0.814	1	CLONAL	1	TRUE	1	0.33	2		306	638	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652308	206652308	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782430885	NA	P-0010034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	137	446	1	ENST00000367120.3:c.1015G>A	p.Val339Met	p.V339M	ENST00000367120	NM_014002.3	339	Gtg/Atg	10/22	1	2	FACETS	0.98	0.892	1	0.98	0.892	1	CLONAL	1	TRUE	1	0.33	2		447	847	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808406	1808406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	62	459	0	ENST00000260795.2:c.2164G>A	p.Asp722Asn	p.D722N	ENST00000260795		722	Gac/Aac	15/17	1	2	FACETS	0.744	0.644	0.853	0.744	0.644	0.853	SUBCLONAL	1	TRUE	1	0.33	2		459	505	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518086	187518086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200185840	NA	P-0010034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	138	470	1	ENST00000441802.2:c.12608G>A	p.Arg4203His	p.R4203H	ENST00000441802	NM_005245.3	4203	cGt/cAt	25/27	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.33	2		471	803	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954933	2954933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755425231	NA	P-0010034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	151	489	1	ENST00000396946.4:c.2777C>T	p.Pro926Leu	p.P926L	ENST00000396946	NM_032415.4	926	cCg/cTg	21/25	1	2	FACETS	0.944	0.863	1	0.944	0.863	1	CLONAL	1	TRUE	1	0.33	2		490	969	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402511	139402511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	122	549	1	ENST00000277541.6:c.3406G>A	p.Gly1136Ser	p.G1136S	ENST00000277541	NM_017617.3	1136	Ggc/Agc	21/34	0.3	1	FACETS	0.815	0.737	0.897	0.815	0.737	0.897	CLONAL	1	TRUE	0	0.33	1		550	758	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420817	49420817	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1289043998	NA	P-0010034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	130	324	0	ENST00000301067.7:c.14932C>T	p.Arg4978Cys	p.R4978C	ENST00000301067	NM_003482.3	4978	Cgc/Tgc	48/54	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.33	2		324	756	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909689	50909689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	141	657	0	ENST00000440232.2:c.1409G>A	p.Arg470His	p.R470H	ENST00000440232	NM_002691.3	470	cGc/cAc	12/27	1	2	FACETS	0.905	0.824	0.991	0.905	0.824	0.991	CLONAL	1	TRUE	1	0.33	2		657	944	SUCCESS
ATR	545	MSKCC	GRCh37	3	142185334	142185334	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	62	247	0	ENST00000350721.4:c.6729del	p.Phe2243LeufsTer8	p.F2243Lfs*8	ENST00000350721	NM_001184.3	2243	ttT/tt	40/47	1	2	FACETS	0.884	0.766	1	0.884	0.766	1	CLONAL	1	TRUE	1	0.33	2		247	425	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955111	17955112	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755706305	NA	P-0010034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	110	458	1	ENST00000458235.1:c.115dup	p.Gln39ProfsTer13	p.Q39Pfs*13	ENST00000458235	NM_000215.3	39	cag/cCag	2/24	1	2	FACETS	0.854	0.767	0.945	0.854	0.767	0.945	CLONAL	1	TRUE	1	0.33	2		459	781	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0010069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	223	595	1	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.947	0.882	1	0.947	0.882	1	CLONAL	1	TRUE	1	0.497917008263645	2		596	946	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519717	NA	P-0010069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	204	354	0	ENST00000206249.3:c.1607T>G	p.Leu536Arg	p.L536R	ENST00000206249	NM_000125.3	536	cTc/cGc	8/8	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.497917008263645	2		354	805	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430758	181430758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	208	357	0	ENST00000325404.1:c.610G>A	p.Ala204Thr	p.A204T	ENST00000325404	NM_003106.3	204	Gcc/Acc	1/1	1	2	FACETS	0.941	0.874	1	0.941	0.874	1	CLONAL	1	TRUE	1	0.497917008263645	2		357	888	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853194	68853194	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	262	496	0	ENST00000261769.5:c.1577G>A	p.Trp526Ter	p.W526*	ENST00000261769	NM_004360.3	526	tGg/tAg	11/16	0.497917008263645	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.497917008263645	1		496	763	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259249	36259250	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0010069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	100	215	0	ENST00000300305.3:c.241dup	p.Val81GlyfsTer57	p.V81Gfs*57	ENST00000300305		81	gtg/gGtg	3/8	1	2	FACETS	0.811	0.728	0.899	0.811	0.728	0.899	CLONAL	1	TRUE	1	0.497917008263645	2		215	495	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235926	133235926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768950975	NA	P-0010075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	113	389	1	ENST00000320574.5:c.3230G>A	p.Arg1077His	p.R1077H	ENST00000320574	NM_006231.2	1077	cGc/cAc	26/49	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.515213762544014	2		390	328	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89335023	89335023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	42	190	0	ENST00000301030.4:c.7855G>A	p.Val2619Met	p.V2619M	ENST00000301030	NM_001256183.1	2619	Gtg/Atg	13/13	NA	2	FACETS	0.863	0.729	1			1	INDETERMINATE	1	TRUE	NA	0.515213762544014	2		190	189	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032514	12032514	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	17	317	0	ENST00000353533.5:c.950T>G	p.Leu317Arg	p.L317R	ENST00000353533	NM_003010.3	317	cTa/cGa	9/11	0.515213762544014	1	FACETS	0.202	0.15	0.262	0.202	0.15	0.262	SUBCLONAL	1	TRUE	0	0.515213762544014	1		317	243	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485403	57485403	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1394557997	NA	P-0010075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	129	392	0	ENST00000371085.3:c.985G>A	p.Gly329Arg	p.G329R	ENST00000371085	NM_000516.4	329	Gga/Aga	12/13	NA	2	FACETS	1	0.952	1			1	INDETERMINATE	1	TRUE	NA	0.515213762544014	2		392	471	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653781	89653782	+	stop_gained,frameshift_variant,splice_region_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0010075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	24	410	0	ENST00000371953.3:c.80dup	p.Tyr27Ter	p.Y27*	ENST00000371953	NM_000314.4	27	tat/tAat		1	2	FACETS	0.336	0.264	0.419	0.336	0.264	0.419	SUBCLONAL	1	TRUE	1	0.515213762544014	2		410	277	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691025	NA	P-0010078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	159	646	0	ENST00000269305.4:c.785G>T	p.Gly262Val	p.G262V	ENST00000269305	NM_001126112.2	262	gGt/gTt	8/11	0.301500044695236	2	FACETS	0.894	0.826	0.965	0.894	0.826	0.965	CLONAL	2	TRUE	0	0.35	2		646	508	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696425	47696425	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519967	NA	P-0010078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	115	582	0	ENST00000347630.2:c.398T>G	p.Phe133Cys	p.F133C	ENST00000347630	NM_001007230.1	133	tTc/tGc	6/11	0.301500044695236	3	FACETS	1	0.97	1	0.595	0.537	0.656	CLONAL	1	TRUE	1	0.35	3		582	649	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257081	198257081	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	54	551	0	ENST00000335508.6:c.3861C>G	p.Ile1287Met	p.I1287M	ENST00000335508	NM_012433.2	1287	atC/atG	25/25	0.222770309229931	3	FACETS	0.619	0.528	0.718	0.309	0.264	0.359	SUBCLONAL	1	TRUE	1	0.35	3		551	586	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021546	31021560	+	inframe_deletion	In_Frame_Del	DEL	GGATCAGGAACCCAA	GGATCAGGAACCCAA	-	novel	NA	P-0010078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	112	390	1	ENST00000375687.4:c.1552_1566del	p.Glu518_Gln522del	p.E518_Q522del	ENST00000375687	NM_015338.5	515	gtGGATCAGGAACCCAAg/gtg	12/13	0.301500044695236	4	FACETS	0.908	0.821	0.998	0.908	0.821	0.998	CLONAL	2	TRUE	2	0.35	4		391	476	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204515962	204515963	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	94	607	0	ENST00000367182.3:c.861dup	p.Lys288Ter	p.K288*	ENST00000367182	NM_001278516.1	287	tct/tcTt	10/11	0.301500044695236	6	FACETS	1	0.929	1	0.212	0.188	0.238	CLONAL	1	TRUE	1	0.35	6		607	861	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0010095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	152	526	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.369771222384444	1	FACETS	0.86	0.788	0.935	0.86	0.788	0.935	CLONAL	1	TRUE	0	0.376597428723062	1		526	762	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927977	178927982	+	inframe_deletion	In_Frame_Del	DEL	CACTGT	CACTGT	-	novel	NA	P-0010095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	37	241	0	ENST00000263967.3:c.1256_1261del	p.His419_Cys420del	p.H419_C420del	ENST00000263967	NM_006218.2	419	CACTGT/-	8/21	0.192814148947951	1	FACETS	0.591	0.489	0.703	0.591	0.489	0.703	INDETERMINATE	1	TRUE	0	0.376597428723062	1		241	270	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035061	42035061	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1245262572	NA	P-0010095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	101	860	0	ENST00000219905.7:c.4903A>G	p.Thr1635Ala	p.T1635A	ENST00000219905	NM_001164273.1	1635	Aca/Gca	15/24	0.235969187143864	1	FACETS	0.424	0.378	0.474	0.424	0.378	0.474	SUBCLONAL	1	TRUE	0	0.376597428723062	1		860	1026	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478632	99478632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1351130675	NA	P-0010095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	50	497	0	ENST00000268035.6:c.3274C>T	p.Arg1092Trp	p.R1092W	ENST00000268035	NM_000875.3	1092	Cgg/Tgg	17/21	0.235969187143864	1	FACETS	0.308	0.26	0.36	0.308	0.26	0.36	SUBCLONAL	1	TRUE	0	0.376597428723062	1		497	700	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063684	67063684	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	204	406	0	ENST00000412916.2:c.133C>T	p.Gln45Ter	p.Q45*	ENST00000412916		45	Cag/Tag	2/6	0.376597428723062	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.376597428723062	1		406	662	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111471	8111472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTCAGACCACCACAACCACACTCTGGAGGAGGAATGCCAATGG	novel	NA	P-0010095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	105	420	0	ENST00000346208.3:c.958_1001dup	p.Asp335ValfsTer35	p.D335Vfs*35	ENST00000346208		319	-/TGTCAGACCACCACAACCACACTCTGGAGGAGGAATGCCAATGG	5/6	0.219398675721162	3	FACETS	0.772	0.691	0.858	0.386	0.345	0.429	INDETERMINATE	1	TRUE	1	0.376597428723062	3		420	858	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010112-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	147	435	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.908	0.832	0.987	0.908	0.832	0.987	CLONAL	1	TRUE	1	0.515648637757495	2		435	628	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0010112-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	130	515	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.515648637757495	1	FACETS	0.821	0.75	0.894	0.821	0.75	0.894	CLONAL	1	TRUE	0	0.515648637757495	1		516	456	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852251	63852251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137983907	NA	P-0010112-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	151	388	2	ENST00000279873.7:c.3029G>A	p.Arg1010Gln	p.R1010Q	ENST00000279873	NM_032199.2	1010	cGg/cAg	10/10	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.515648637757495	2		390	574	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740262	162740262	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs199526949	NA	P-0010112-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	175	508	0	ENST00000367921.3:c.1464A>G	p.Ile488Met	p.I488M	ENST00000367921	NM_006182.2	488	atA/atG	12/18	1	2	FACETS	0.998	0.922	1	0.998	0.922	1	CLONAL	1	TRUE	1	0.515648637757495	2		508	680	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045982	26045982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010112-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	332	1043	1	ENST00000540144.1:c.344C>T	p.Ala115Val	p.A115V	ENST00000540144	NM_003531.2	115	gCt/gTt	1/1	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.515648637757495	2		1044	1241	SUCCESS
BLM	641	MSKCC	GRCh37	15	91306337	91306337	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010112-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	225	547	2	ENST00000355112.3:c.2024C>T	p.Ala675Val	p.A675V	ENST00000355112	NM_000057.2	675	gCg/gTg	8/22	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.515648637757495	2		549	795	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624957	9624957	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs569145578	NA	P-0010112-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	464	463	0	ENST00000353224.5:c.20A>G	p.Lys7Arg	p.K7R	ENST00000353224	NM_177990.2	7	aAa/aGa	3/10	0.515648637757495	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	TRUE	1	0.515648637757495	4		463	900	SUCCESS
APC	324	MSKCC	GRCh37	5	112176036	112176037	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0010112-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	161	462	0	ENST00000257430.4:c.4746_4747dup	p.Met1583ThrfsTer68	p.M1583Tfs*68	ENST00000257430	NM_000038.5	1582	gcc/gcCAc	16/16	0.515648637757495	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.515648637757495	1		462	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0010113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	482	724	0	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	0.50566255720326	2	FACETS	0.762	0.731	0.794	0.762	0.731	0.794	SUBCLONAL	2	TRUE	0	0.555341477632	2		724	1139	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61729395	61729395	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	147	677	0	ENST00000401558.2:c.352A>T	p.Thr118Ser	p.T118S	ENST00000401558	NM_003400.3	118	Act/Tct	5/25	0.296865662909834	4	FACETS	0.981	0.896	1	0.491	0.448	0.535	INDETERMINATE	1	TRUE	2	0.555341477632	4		677	839	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683201	88683201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771452619	NA	P-0010113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	37	307	0	ENST00000372037.3:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000372037	NM_004329.2	471	Cgt/Tgt	12/13	0.555341477632	1	FACETS	0.465	0.387	0.551	0.465	0.387	0.551	SUBCLONAL	1	TRUE	0	0.555341477632	1		307	207	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158431	26158432	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0010113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	189	514	0	ENST00000289316.2:c.36_37dup	p.Lys13ArgfsTer8	p.K13Rfs*8	ENST00000289316	NM_138720.2	12	aag/aAGag	1/2	1	2	FACETS	0.988	0.916	1	0.988	0.916	1	CLONAL	1	TRUE	1	0.555341477632	2		514	689	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3094759	3094760	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCGCGA	novel	NA	P-0010113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	47	305	0	ENST00000078429.4:c.113_118dup	p.Arg38_Glu39dup	p.R38_E39dup	ENST00000078429	NM_002067.2	38	cgg/cgGCGCGAg	1/7	0.251668091385626	1	FACETS	0.248	0.209	0.291	0.248	0.209	0.291	INDETERMINATE	1	TRUE	0	0.555341477632	1		305	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0010114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	130	604	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.546300946771739	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.546300946771739	1		604	336	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631222	176631222	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	155	669	0	ENST00000439151.2:c.1165A>G	p.Arg389Gly	p.R389G	ENST00000439151	NM_022455.4	389	Aga/Gga	4/23	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.546300946771739	2		669	487	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916764	48916765	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	199	553	0	ENST00000267163.4:c.295dup	p.Trp99LeufsTer11	p.W99Lfs*11	ENST00000267163	NM_000321.2	98	-/T	3/27	0.545734840363299	2	FACETS	0.995	0.939	1	0.995	0.939	1	CLONAL	2	TRUE	0	0.546300946771739	2		553	366	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	746	435	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.393108934755385	7	FACETS	1	0.982	1			1	CLONAL	4	TRUE	NA	0.393108934755385	7		435	1837	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0010166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	434	498	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	0.29114260408807	3	FACETS	1	0.974	1	0.686	0.655	0.719	CLONAL	2	TRUE	0	0.393108934755385	3		498	1283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0010166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	301	510	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.278927580716113	2	FACETS	1	0.992	1	0.657	0.618	0.696	CLONAL	1	TRUE	0	0.393108934755385	2		510	1166	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589367	28589367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs577794071	NA	P-0010166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	306	588	2	ENST00000241453.7:c.2680G>A	p.Val894Ile	p.V894I	ENST00000241453	NM_004119.2	894	Gtt/Att	22/24	0.255230707587813	4	FACETS	1	0.994	1	0.747	0.703	0.793	CLONAL	1	TRUE	2	0.393108934755385	4		590	1451	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575109	48575109	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	332	603	0	ENST00000342988.3:c.303G>T	p.Trp101Cys	p.W101C	ENST00000342988	NM_005359.5	101	tgG/tgT	3/12	0.287352928840972	2	FACETS	1	0.994	1	0.707	0.668	0.747	CLONAL	1	TRUE	0	0.393108934755385	2		603	1194	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554043	63554047	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTT	CTCTT	-	novel	NA	P-0010166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	310	558	0	ENST00000307078.5:c.692_696del	p.Glu231GlyfsTer36	p.E231Gfs*36	ENST00000307078	NM_004655.3	231	gAAGAG/g	2/11	0.293465770621646	4	FACETS	0.759	0.714	0.805	0.759	0.714	0.805	SUBCLONAL	2	TRUE	2	0.393108934755385	4		558	1448	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0010219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	375	366	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	TRUE	1	0.642347465204959	2		366	1154	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719259	61719259	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1210452613	NA	P-0010219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1457	471	614	0	ENST00000401558.2:c.1798G>A	p.Val600Ile	p.V600I	ENST00000401558	NM_003400.3	600	Gtt/Att	16/25	0.213675303386643	5	FACETS	1	0.996	1			1	INDETERMINATE	1	TRUE	NA	0.642347465204959	5		614	1928	SUCCESS
APC	324	MSKCC	GRCh37	5	112175162	112175162	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	174	281	0	ENST00000257430.4:c.3871C>G	p.Gln1291Glu	p.Q1291E	ENST00000257430	NM_000038.5	1291	Cag/Gag	16/16	0.642347465204959	1	FACETS	0.965	0.902	1	0.965	0.902	1	CLONAL	1	TRUE	0	0.642347465204959	1		281	381	SUCCESS
APC	324	MSKCC	GRCh37	5	112175221	112175221	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	201	320	0	ENST00000257430.4:c.3930del	p.Ile1311LeufsTer10	p.I1311Lfs*10	ENST00000257430	NM_000038.5	1310	aaG/aa	16/16	0.642347465204959	1	FACETS	0.812	0.759	0.866	0.812	0.759	0.866	CLONAL	1	TRUE	0	0.642347465204959	1		320	523	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720805	89720806	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	106	158	0	ENST00000371953.3:c.959dup	p.Leu320PhefsTer5	p.L320Ffs*5	ENST00000371953	NM_000314.4	319	act/acTt	8/9	0.642347465204959	1	FACETS	0.833	0.759	0.908	0.833	0.759	0.908	CLONAL	1	TRUE	0	0.642347465204959	1		158	269	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230555	46230556	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0010219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	428	590	0	ENST00000334344.6:c.805_806del	p.Leu269IlefsTer10	p.L269Ifs*10	ENST00000334344	NM_152641.2	268	tcTTta/tcta	8/21	1	2	FACETS	0.987	0.941	1	0.987	0.941	1	CLONAL	1	TRUE	1	0.642347465204959	2		590	1350	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153439	108153440	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TT	TT	G	novel	NA	P-0010219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	768	485	0	ENST00000278616.4:c.3579_3580delinsG	p.Leu1194Ter	p.L1194*	ENST00000278616	NM_000051.3	1193	gtTTta/gtGta	25/63	0.638765748129458	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.642347465204959	2		485	1123	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0010264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	97	473	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	NA	2	FACETS	0.923	0.824	1			1	INDETERMINATE	1	TRUE	NA	0.33	2		473	637	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0010264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	44	377	2	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	0.3	1	FACETS	0.607	0.51	0.713	0.607	0.51	0.713	SUBCLONAL	1	TRUE	0	0.33	1		379	367	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497754	120497754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782066959	NA	P-0010264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	60	290	1	ENST00000256646.2:c.2128G>A	p.Glu710Lys	p.E710K	ENST00000256646	NM_024408.3	710	Gag/Aag	13/34	1	2	FACETS	0.909	0.786	1	0.909	0.786	1	CLONAL	1	TRUE	1	0.33	2		291	400	SUCCESS
FIP1L1	81608	MSKCC	GRCh37	4	54280873	54280873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145771023	NA	P-0010264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	44	316	1	ENST00000358575.5:c.862G>A	p.Glu288Lys	p.E288K	ENST00000358575	NM_001134937.1	288	Gaa/Aaa	10/18	1	2	FACETS	0.97	0.818	1	0.97	0.818	1	CLONAL	1	TRUE	1	0.33	2		317	275	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120239	70120239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	81	632	0	ENST00000245479.2:c.1241C>A	p.Ser414Ter	p.S414*	ENST00000245479	NM_000346.3	414	tCg/tAg	3/3	1	2	FACETS	0.904	0.798	1	0.904	0.798	1	CLONAL	1	TRUE	1	0.33	2		632	543	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144096	11144098	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0010264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	114	714	0	ENST00000358026.2:c.3679_3681del	p.Lys1227del	p.K1227del	ENST00000358026	NM_001128849.1	1226	cAGAag/cag	26/36	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.33	2		714	663	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188200	10188200	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	161	453	0	ENST00000256474.2:c.343C>A	p.His115Asn	p.H115N	ENST00000256474	NM_000551.3	115	Cac/Aac	2/3	0.388984180588911	1	FACETS	0.833	0.765	0.905	0.833	0.765	0.905	CLONAL	1	TRUE	0	0.388984180588911	1		453	800	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184613	11184613	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	163	539	0	ENST00000361445.4:c.6604T>C	p.Phe2202Leu	p.F2202L	ENST00000361445	NM_004958.3	2202	Ttc/Ctc	47/58	0.277794855117079	1	FACETS	0.538	0.492	0.586	0.538	0.492	0.586	SUBCLONAL	1	TRUE	0	0.388984180588911	1		539	1255	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255380	16255380	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1272	168	515	1	ENST00000375759.3:c.2645G>T	p.Arg882Leu	p.R882L	ENST00000375759	NM_015001.2	882	cGa/cTa	11/15	0.277794855117079	1	FACETS	0.483	0.442	0.526	0.483	0.442	0.526	SUBCLONAL	1	TRUE	0	0.388984180588911	1		516	1440	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191200	185191200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150518520	NA	P-0010311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	78	153	0	ENST00000265026.3:c.2081C>T	p.Ser694Leu	p.S694L	ENST00000265026	NM_004721.4	694	tCg/tTg	11/14	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.388984180588911	2		153	343	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706917	117706917	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	103	493	2	ENST00000368508.3:c.2233A>T	p.Ile745Phe	p.I745F	ENST00000368508	NM_002944.2	745	Att/Ttt	15/43	1	2	FACETS	0.451	0.403	0.504	0.451	0.403	0.504	SUBCLONAL	1	TRUE	1	0.388984180588911	2		495	1173	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250020	53250020	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs782320705	NA	P-0010311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	350	363	0	ENST00000375401.3:c.228+1G>A		p.X76_splice	ENST00000375401	NM_004187.3	76			1	1	FACETS	0.813	0.773	0.854	1	0.996	1	CLONAL	2	TRUE	0	0.388984180588911	1		363	891	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43749765	43749766	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1699	143	773	0	ENST00000523873.1:c.623dup	p.Asn208LysfsTer12	p.N208Kfs*12	ENST00000523873		206	-/A	7/8	1	2	FACETS	0.399	0.362	0.438	0.399	0.362	0.438	SUBCLONAL	1	TRUE	1	0.388984180588911	2		773	1842	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142947	47142947	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0010311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	138	439	0	ENST00000409792.3:c.5015+1del		p.X1672_splice	ENST00000409792	NM_014159.6	1672			0.388984180588911	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.388984180588911	1		439	501	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0010343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	829	582	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.656868916755	3	FACETS	0.9	0.881	0.92	0.9	0.881	0.92	CLONAL	3	FALSE	0	0.744935617860354	3		582	1131	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144897	47144898	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	GAGTGGCATCTATTATCTGGGAGAAGAGGATC	novel	NA	P-0010343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	146	450	0	ENST00000409792.3:c.4840-16_4855dup	p.Gln1619ArgfsTer7	p.Q1619Rfs*7	ENST00000409792	NM_014159.6	1619	caa/cGATCCTCTTCTCCCAGATAATAGATGCCACTCaa	7/21	0.730738614945296	1	FACETS	0.58	0.534	0.627	0.58	0.534	0.627	SUBCLONAL	1	FALSE	0	0.744935617860354	1		450	424	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604696	48604699	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	GAAA	GAAA	TTGAT	novel	NA	P-0010343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	498	414	0	ENST00000342988.3:c.1518_1521delinsTTGAT	p.Lys507Ter	p.K507*	ENST00000342988	NM_005359.5	506	gtGAAA/gtTTGAT	12/12	0.73385920116169	2	FACETS	0.915	0.886	0.942	0.915	0.886	0.942	CLONAL	2	FALSE	0	0.744935617860354	2		414	731	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0010352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	268	366	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.353551593232614	3	FACETS	1	0.988	1	0.775	0.732	0.818	CLONAL	2	TRUE	0	0.430477179843779	3		366	651	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0010352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	263	274	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.42226592140579	2	FACETS	0.849	0.799	0.899	0.849	0.799	0.899	CLONAL	2	TRUE	0	0.430477179843779	2		274	720	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0010352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	89	292	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.18357011843462	4	FACETS	1	0.972	1	0.644	0.574	0.719	INDETERMINATE	1	TRUE	2	0.430477179843779	4		292	459	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0010352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	153	110	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.18357011843462	4	FACETS	0.798	0.733	0.866	0.798	0.733	0.866	INDETERMINATE	2	TRUE	2	0.430477179843779	4		110	637	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920413	114920413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767830105	NA	P-0010352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	685	793	1	ENST00000543371.1:c.1354G>A	p.Gly452Arg	p.G452R	ENST00000543371	NM_001198531.1	452	Ggg/Agg	13/14	0.42226592140579	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.430477179843779	2		794	1544	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938931	178938931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	225	166	0	ENST00000263967.3:c.2173G>A	p.Asp725Asn	p.D725N	ENST00000263967	NM_006218.2	725	Gat/Aat	14/21	0.430477179843779	6	FACETS	0.902	0.848	0.957			1	CLONAL	4	TRUE	NA	0.430477179843779	6		166	539	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604785	48604786	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGACGA	novel	NA	P-0010352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	152	328	0	ENST00000342988.3:c.1610_1615dup	p.Asp537_Glu538dup	p.D537_E538dup	ENST00000342988	NM_005359.5	537	cta/ctAGACGAa	12/12	0.430477179843779	1	FACETS	0.981	0.902	1	0.981	0.902	1	CLONAL	1	TRUE	0	0.430477179843779	1		328	565	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0010431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	111	352	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.179829252442295	1	FACETS	0.764	0.687	0.845	0.764	0.687	0.845	INDETERMINATE	1	TRUE	0	0.323239664793438	1		352	754	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024008	27024008	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	13	50	0	ENST00000324856.7:c.1114C>T	p.Gln372Ter	p.Q372*	ENST00000324856	NM_006015.4	372	Cag/Tag	1/20	0.323239664793438	1	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	0	0.323239664793438	1		50	51	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100702	67100702	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0010431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	259	555	0	ENST00000412916.2:c.399+1G>T		p.X133_splice	ENST00000412916		133			0.323239664793438	1	FACETS	0.792	0.744	0.842	1	0.994	1	SUBCLONAL	2	TRUE	0	0.323239664793438	1		555	848	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849586	68849586	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	291	580	0	ENST00000261769.5:c.1489del	p.Glu497ArgfsTer25	p.E497Rfs*25	ENST00000261769	NM_004360.3	497	Gag/ag	10/16	0.323239664793438	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.323239664793438	1		580	1034	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0010520-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	90	509	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	0.416057848282614	2		509	388	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188262	10188263	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0010520-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	98	865	0	ENST00000256474.2:c.407_408dup	p.Val137LeufsTer23	p.V137Lfs*23	ENST00000256474	NM_000551.3	135	-/TT	2/3	0.416057848282614	1	FACETS	0.681	0.609	0.757	0.681	0.609	0.757	SUBCLONAL	1	TRUE	0	0.416057848282614	1		865	548	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs786202525	NA	P-0010573-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	148	273	0	ENST00000269305.4:c.532del	p.His178ThrfsTer69	p.H178Tfs*69	ENST00000269305	NM_001126112.2	178	Cac/ac	5/11	0.412839811348623	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.412839811348623	2		273	324	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112602	2112602	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs45517164	NA	P-0010573-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	24	384	0	ENST00000219476.3:c.1361+1G>A		p.X454_splice	ENST00000219476	NM_000548.3	454			1	2	FACETS	0.377	0.296	0.471	0.377	0.296	0.471	SUBCLONAL	1	TRUE	1	0.412839811348623	2		384	308	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902283	50902283	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010573-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	157	884	3	ENST00000440232.2:c.175C>A	p.Gln59Lys	p.Q59K	ENST00000440232	NM_002691.3	59	Cag/Aag	2/27	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.412839811348623	2		887	632	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023849	27023874	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCCCCAGGACGGGGGCGCCGGCAA	GGGCCCCAGGACGGGGGCGCCGGCAA	-	novel	NA	P-0010573-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	244	267	0	ENST00000324856.7:c.961_986del	p.Gln321GlyfsTer70	p.Q321Gfs*70	ENST00000324856	NM_006015.4	319	GGGCCCCAGGACGGGGGCGCCGGCAAg/g	1/20	0.412839811348623	4	FACETS	0.896	0.844	0.95	1	0.992	1	CLONAL	3	TRUE	2	0.412839811348623	4		267	621	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584513	48584514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0010573-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	20	279	0	ENST00000342988.3:c.686_687insTG	p.Ser232AlafsTer10	p.S232Afs*10	ENST00000342988	NM_005359.5	229	ctg/ctTGg	6/12	0.257834499008847	2	FACETS	1	0.843	1	0.551	0.43	0.685	CLONAL	1	TRUE	0	0.412839811348623	2		279	88	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061312	38061312	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1329067081	NA	P-0010638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	204	744	0	ENST00000250448.2:c.677A>G	p.Asp226Gly	p.D226G	ENST00000250448	NM_004496.3	226	gAc/gGc	2/2	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.3572275140885	2		744	1140	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435408	56435408	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	136	520	0	ENST00000407977.2:c.1729C>T	p.Gln577Ter	p.Q577*	ENST00000407977		577	Cag/Tag	9/10	0.323048466003161	3	FACETS	0.901	0.818	0.988	0.451	0.409	0.494	CLONAL	1	TRUE	1	0.3572275140885	3		520	996	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217861	7217862	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0010638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	235	954	0	ENST00000380728.2:c.149_150del	p.Arg50LysfsTer46	p.R50Kfs*46	ENST00000380728		50	aGA/a	3/11	1	2	FACETS	0.972	0.905	1	0.972	0.905	1	CLONAL	1	TRUE	1	0.3572275140885	2		954	1354	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12043192	12043193	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0010638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	174	588	0	ENST00000353533.5:c.1079_1080del	p.Glu360AlafsTer11	p.E360Afs*11	ENST00000353533	NM_003010.3	359	aaAGag/aaag	10/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.3572275140885	2		588	818	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849476	68849477	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	192	683	0	ENST00000261769.5:c.1380dup	p.Pro461ThrfsTer3	p.P461Tfs*3	ENST00000261769	NM_004360.3	460	gta/gtAa	10/16	0.3572275140885	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.3572275140885	1		683	858	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0010673-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	143	251	1	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.358355321394827	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.365155887161374	2		252	372	SUCCESS
APC	324	MSKCC	GRCh37	5	112175358	112175358	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1554085480	NA	P-0010673-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	105	161	0	ENST00000257430.4:c.4067C>G	p.Ser1356Ter	p.S1356*	ENST00000257430	NM_000038.5	1356	tCa/tGa	16/16	0.358355321394827	2	FACETS	0.955	0.868	1	0.955	0.868	1	CLONAL	2	TRUE	0	0.365155887161374	2		161	301	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459777	149459777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1214590308	NA	P-0010673-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	117	186	0	ENST00000286301.3:c.430C>T	p.Arg144Cys	p.R144C	ENST00000286301	NM_005211.3	144	Cgt/Tgt	4/22	0.358355321394827	2	FACETS	0.948	0.865	1	0.948	0.865	1	CLONAL	2	TRUE	0	0.365155887161374	2		186	338	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473792	67473792	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0010673-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	133	152	0	ENST00000327367.4:c.871+1G>T		p.X291_splice	ENST00000327367	NM_005902.3	291			0.365155887161374	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	3	TRUE	0	0.365155887161374	3		152	276	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375029	45375030	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGGTTCTGAGT	novel	NA	P-0010673-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	98	193	0	ENST00000262160.6:c.803_813dup	p.Ala272ThrfsTer10	p.A272Tfs*10	ENST00000262160	NM_005901.5	271	-/ACTCAGAACCT	8/11	0.358355321394827	2	FACETS	0.916	0.828	1	0.916	0.828	1	CLONAL	2	TRUE	0	0.365155887161374	2		193	293	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405943	70405944	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0010673-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	119	409	0	ENST00000373644.4:c.3461dup	p.Ser1155IlefsTer18	p.S1155Ifs*18	ENST00000373644	NM_030625.2	1153	acc/aCcc	4/12	0.365155887161374	3	FACETS	1	0.983	1	0.711	0.644	0.781	CLONAL	1	TRUE	1	0.365155887161374	3		409	542	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249002	55249003	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCGTGGA	rs397517109	NA	P-0010700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	245	449	0	ENST00000275493.2:c.2303_2311dup	p.Ser768_Asp770dup	p.S768_D770dup	ENST00000275493	NM_005228.3	768	gcc/gcCAGCGTGGAc	20/28	0.324441509060384	3	FACETS	1	0.988	1	0.618	0.577	0.66	CLONAL	1	TRUE	1	0.448687807847876	3		449	1082	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416646	29416646	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs544926207	NA	P-0010700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	208	405	0	ENST00000389048.3:c.4307G>A	p.Arg1436His	p.R1436H	ENST00000389048	NM_004304.4	1436	cGc/cAc	29/29	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.448687807847876	2		405	825	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916917	178916917	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	373	937	1	ENST00000263967.3:c.304A>T	p.Ile102Phe	p.I102F	ENST00000263967	NM_006218.2	102	Att/Ttt	2/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.448687807847876	2		938	1524	SUCCESS
APC	324	MSKCC	GRCh37	5	112128166	112128170	+	frameshift_variant	Frame_Shift_Del	DEL	AATCG	AATCG	-	novel	NA	P-0010700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	248	578	0	ENST00000257430.4:c.671_675del	p.Ile224LysfsTer26	p.I224Kfs*26	ENST00000257430	NM_000038.5	223	caAATCGaa/caaa	7/16	0.448687807847876	1	FACETS	0.968	0.907	1	0.968	0.907	1	CLONAL	1	TRUE	0	0.448687807847876	1		578	886	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	66	140	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.615065610134963	NA		140	200	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776520	9776520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	121	676	1	ENST00000377346.4:c.623C>T	p.Ser208Phe	p.S208F	ENST00000377346	NM_005026.3	208	tCc/tTc	6/24	0.615065610134963	1	FACETS	0.688	0.627	0.751	0.688	0.627	0.751	SUBCLONAL	1	FALSE	0	0.615065610134963	1		677	396	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363594	40363594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	312	483	0	ENST00000397332.2:c.635G>A	p.Gly212Asp	p.G212D	ENST00000397332	NM_001033082.2	212	gGt/gAt	3/3	0.615065610134963	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	0	0.615065610134963	1		483	584	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803796	43803796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	116	792	0	ENST00000372470.3:c.106G>A	p.Glu36Lys	p.E36K	ENST00000372470	NM_005373.2	36	Gag/Aag	2/12	0.615065610134963	1	FACETS	0.508	0.46	0.559	0.508	0.46	0.559	SUBCLONAL	1	FALSE	0	0.615065610134963	1		792	514	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512170	120512170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	76	581	3	ENST00000256646.2:c.1072G>A	p.Ala358Thr	p.A358T	ENST00000256646	NM_024408.3	358	Gcc/Acc	6/34	0.465380306680188	1	FACETS	0.292	0.256	0.33	0.292	0.256	0.33	SUBCLONAL	1	FALSE	0	0.615065610134963	1		584	587	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731101	162731101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761991484	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	413	994	2	ENST00000367921.3:c.956C>T	p.Ser319Phe	p.S319F	ENST00000367921	NM_006182.2	319	tCc/tTc	9/18	0.158712665887744	3	FACETS	1	0.994	1	0.653	0.622	0.686	INDETERMINATE	1	FALSE	1	0.615065610134963	3		996	1344	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226566975	226566975	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	48	607	0	ENST00000366794.5:c.1613G>A	p.Gly538Glu	p.G538E	ENST00000366794	NM_001618.3	538	gGa/gAa	12/23	NA	2	FACETS	0.23	0.194	0.27			1	INDETERMINATE	1	FALSE	NA	0.615065610134963	2		607	679	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226595545	226595545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	68	625	0	ENST00000366794.5:c.86C>T	p.Pro29Leu	p.P29L	ENST00000366794	NM_001618.3	29	cCc/cTc	1/23	NA	2	FACETS	0.261	0.226	0.298			1	INDETERMINATE	1	FALSE	NA	0.615065610134963	2		625	848	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612923	228612923	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1201973529	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	208	964	1	ENST00000366696.1:c.104G>A	p.Gly35Asp	p.G35D	ENST00000366696	NM_003493.2	35	gGc/gAc	1/1	NA	2	FACETS	0.898	0.836	0.962			1	INDETERMINATE	1	FALSE	NA	0.615065610134963	2		965	753	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25462083	25462083	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	43	503	0	ENST00000264709.3:c.2324C>T	p.Ser775Phe	p.S775F	ENST00000264709	NM_175629.2	775	tCc/tTc	20/23	NA	2	FACETS	0.24	0.2	0.284			1	INDETERMINATE	1	FALSE	NA	0.615065610134963	2		503	583	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456504	29456504	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	44	952	0	ENST00000389048.3:c.2414T>A	p.Ile805Asn	p.I805N	ENST00000389048	NM_004304.4	805	aTc/aAc	14/29	0.465380306680188	1	FACETS	0.116	0.096	0.137	0.116	0.096	0.137	SUBCLONAL	1	FALSE	0	0.615065610134963	1		952	857	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143452	30143452	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753812499	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	11	127	0	ENST00000389048.3:c.74C>T	p.Thr25Ile	p.T25I	ENST00000389048	NM_004304.4	25	aCc/aTc	1/29	NA	2	FACETS	0.271	0.188	0.373			1	INDETERMINATE	1	FALSE	NA	0.615065610134963	2		127	132	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026348	48026348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	256	535	0	ENST00000234420.5:c.1226G>A	p.Gly409Glu	p.G409E	ENST00000234420	NM_000179.2	409	gGg/gAg	4/10	NA	2	FACETS	0.97	0.911	1			1	INDETERMINATE	1	FALSE	NA	0.615065610134963	2		535	858	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047336	128047336	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	257	650	0	ENST00000285398.2:c.586G>A	p.Glu196Lys	p.E196K	ENST00000285398	NM_000122.1	196	Gaa/Aaa	5/15	0.121554722733827	0	FACETS	0.382	0.358	0.406			1	INDETERMINATE	1	FALSE	0	0.615065610134963	0		650	843	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098966	178098966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	95	398	0	ENST00000397062.3:c.79G>A	p.Asp27Asn	p.D27N	ENST00000397062	NM_006164.4	27	Gat/Aat	2/5	0.131599213590317	4	FACETS	0.55	0.489	0.616	0.275	0.244	0.308	INDETERMINATE	1	FALSE	2	0.615065610134963	4		398	907	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190708732	190708732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1181	89	786	1	ENST00000441310.2:c.625G>A	p.Ala209Thr	p.A209T	ENST00000441310	NM_000534.4	209	Gct/Act	6/13	0.131599213590317	4	FACETS	0.368	0.325	0.414	0.184	0.162	0.207	INDETERMINATE	1	FALSE	2	0.615065610134963	4		787	1270	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728600	190728600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	364	736	0	ENST00000441310.2:c.1988C>T	p.Ala663Val	p.A663V	ENST00000441310	NM_000534.4	663	gCc/gTc	10/13	0.131599213590317	4	FACETS	0.753	0.714	0.793	0.753	0.714	0.793	INDETERMINATE	2	FALSE	2	0.615065610134963	4		736	1269	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	276	419	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.131599213590317	4	FACETS	0.871	0.821	0.923	0.871	0.821	0.923	INDETERMINATE	2	FALSE	2	0.615065610134963	4		420	832	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713142	30713142	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	106	220	0	ENST00000295754.5:c.467G>A	p.Ser156Asn	p.S156N	ENST00000295754	NM_003242.5	156	aGc/aAc	4/7	1	2	FACETS	0.827	0.746	0.91	0.827	0.746	0.91	CLONAL	1	FALSE	1	0.615065610134963	2		220	417	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180334	38180334	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	62	766	0	ENST00000396334.3:c.182C>T	p.Thr61Ile	p.T61I	ENST00000396334	NM_002468.4	61	aCc/aTc	1/5	1	2	FACETS	0.238	0.205	0.274	0.238	0.205	0.274	SUBCLONAL	1	FALSE	1	0.615065610134963	2		766	848	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180439	38180439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1347643055	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	27	462	0	ENST00000396334.3:c.287G>A	p.Gly96Asp	p.G96D	ENST00000396334	NM_002468.4	96	gGc/gAc	1/5	1	2	FACETS	0.163	0.129	0.203	0.163	0.129	0.203	SUBCLONAL	1	FALSE	1	0.615065610134963	2		462	537	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163508	47163508	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs937315949	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	199	442	0	ENST00000409792.3:c.2618C>T	p.Pro873Leu	p.P873L	ENST00000409792	NM_014159.6	873	cCt/cTt	3/21	1	2	FACETS	0.909	0.845	0.975	0.909	0.845	0.975	CLONAL	1	FALSE	1	0.615065610134963	2		442	712	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933277	49933277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	75	936	0	ENST00000296474.3:c.2833G>A	p.Val945Met	p.V945M	ENST00000296474	NM_002447.2	945	Gtg/Atg	12/20	NA	2	FACETS	0.268	0.234	0.304			1	INDETERMINATE	1	FALSE	NA	0.615065610134963	2		936	911	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52675969	52675969	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	309	849	1	ENST00000394830.3:c.1087+1G>A		p.X363_splice	ENST00000394830	NM_018313.4	363			1	2	FACETS	0.917	0.865	0.97	0.917	0.865	0.97	CLONAL	1	FALSE	1	0.615065610134963	2		850	1096	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146617	185146617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	161	424	0	ENST00000265026.3:c.248G>A	p.Ser83Asn	p.S83N	ENST00000265026	NM_004721.4	83	aGc/aAc	2/14	NA	2	FACETS	0.755	0.695	0.818			1	INDETERMINATE	1	FALSE	NA	0.615065610134963	2		424	693	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161366	55161366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775944809	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	48	600	1	ENST00000257290.5:c.3197C>T	p.Thr1066Ile	p.T1066I	ENST00000257290	NM_006206.4	1066	aCc/aTc	23/23	0.615065610134963	1	FACETS	0.181	0.152	0.212	0.181	0.152	0.212	SUBCLONAL	1	FALSE	0	0.615065610134963	1		601	598	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157017	106157017	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	369	815	1	ENST00000380013.4:c.1918C>T	p.Gln640Ter	p.Q640*	ENST00000380013	NM_001127208.2	640	Caa/Taa	3/11	0.615065610134963	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	0	0.615065610134963	1		816	810	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540157	187540157	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	80	808	0	ENST00000441802.2:c.7583C>T	p.Thr2528Ile	p.T2528I	ENST00000441802	NM_005245.3	2528	aCt/aTt	10/27	0.615065610134963	1	FACETS	0.312	0.275	0.352	0.312	0.275	0.352	SUBCLONAL	1	FALSE	0	0.615065610134963	1		808	577	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235267	235267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	118	358	1	ENST00000264932.6:c.1073G>A	p.Gly358Asp	p.G358D	ENST00000264932	NM_004168.2	358	gGc/gAc	9/15	NA	2	FACETS	0.855	0.776	0.936			1	INDETERMINATE	1	FALSE	NA	0.615065610134963	2		359	449	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176919	56176919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1220391568	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	303	564	0	ENST00000399503.3:c.2189G>A	p.Gly730Asp	p.G730D	ENST00000399503	NM_005921.1	730	gGt/gAt	13/20	0.131599213590317	4	FACETS	0.827	0.781	0.874	0.827	0.781	0.874	INDETERMINATE	2	FALSE	2	0.615065610134963	4		564	962	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522681	176522681	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	56	759	0	ENST00000292408.4:c.1778C>T	p.Ala593Val	p.A593V	ENST00000292408	NM_213647.1	593	gCc/gTc	13/18	1	2	FACETS	0.253	0.216	0.294	0.253	0.216	0.294	SUBCLONAL	1	FALSE	1	0.615065610134963	2		759	719	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176715823	176715823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	325	762	1	ENST00000439151.2:c.6155C>T	p.Thr2052Ile	p.T2052I	ENST00000439151	NM_022455.4	2052	aCt/aTt	21/23	1	2	FACETS	0.948	0.896	1	0.948	0.896	1	CLONAL	1	FALSE	1	0.615065610134963	2		763	1115	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722327	176722327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	229	703	0	ENST00000439151.2:c.7958G>A	p.Gly2653Glu	p.G2653E	ENST00000439151	NM_022455.4	2653	gGg/gAg	23/23	1	2	FACETS	0.893	0.834	0.953	0.893	0.834	0.953	CLONAL	1	FALSE	1	0.615065610134963	2		703	834	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036014	180036014	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761503019	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	40	965	0	ENST00000261937.6:c.3847G>A	p.Glu1283Lys	p.E1283K	ENST00000261937	NM_182925.4	1283	Gag/Aag	29/30	0.416155331955945	0	FACETS	0.078	0.064	0.093			1	SUBCLONAL	1	FALSE	0	0.615065610134963	0		965	645	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401742	401742	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	42	536	0	ENST00000380956.4:c.1064C>T	p.Thr355Ile	p.T355I	ENST00000380956	NM_001195286.1	355	aCc/aTc	7/9	NA	2	FACETS	0.259	0.216	0.307			1	INDETERMINATE	1	FALSE	NA	0.615065610134963	2		536	527	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197411	26197411	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2051	233	1213	2	ENST00000356476.2:c.68C>T	p.Thr23Ile	p.T23I	ENST00000356476		23	aCc/aTc	1/1	0.615065610134963	4	FACETS	0.536	0.497	0.576			1	SUBCLONAL	1	FALSE	NA	0.615065610134963	4		1215	2284	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675792	30675792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	527	1189	0	ENST00000376406.3:c.2564G>A	p.Gly855Glu	p.G855E	ENST00000376406	NM_014641.2	855	gGg/gAg	8/15	0.237583073080158	3	FACETS	1	0.995	1	0.661	0.633	0.69	INDETERMINATE	1	FALSE	1	0.615065610134963	3		1189	1695	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287986	33287986	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	368	642	1	ENST00000374542.5:c.1267G>A	p.Ala423Thr	p.A423T	ENST00000374542	NM_001141970.1	423	Gca/Aca	5/8	0.308613324852326	4	FACETS	0.862	0.819	0.906			1	INDETERMINATE	2	FALSE	NA	0.615065610134963	4		643	1121	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117630069	117630069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	69	656	1	ENST00000368508.3:c.6457G>A	p.Glu2153Lys	p.E2153K	ENST00000368508	NM_002944.2	2153	Gag/Aag	41/43	NA	2	FACETS	0.231	0.201	0.265			1	INDETERMINATE	1	FALSE	NA	0.615065610134963	2		657	970	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192576	138192576	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	212	554	0	ENST00000237289.4:c.212G>A	p.Arg71Lys	p.R71K	ENST00000237289	NM_001270507.1	71	aGa/aAa	2/9	1	2	FACETS	0.831	0.773	0.89	0.831	0.773	0.89	CLONAL	1	FALSE	1	0.615065610134963	2		554	830	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005476	150005476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1240662853	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	66	749	0	ENST00000253339.5:c.749C>T	p.Pro250Leu	p.P250L	ENST00000253339		250	cCt/cTt	3/7	1	2	FACETS	0.225	0.194	0.258	0.225	0.194	0.258	SUBCLONAL	1	FALSE	1	0.615065610134963	2		749	954	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467933	50467933	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	25	386	0	ENST00000331340.3:c.1168C>T	p.Pro390Ser	p.P390S	ENST00000331340	NM_006060.4	390	Ccg/Tcg	8/8	1	2	FACETS	0.22	0.173	0.274	0.22	0.173	0.274	SUBCLONAL	1	FALSE	1	0.615065610134963	2		386	370	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339502	81339502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1240	82	894	0	ENST00000222390.5:c.1502C>T	p.Thr501Ile	p.T501I	ENST00000222390	NM_000601.4	501	aCa/aTa	13/18	1	2	FACETS	0.202	0.177	0.229	0.202	0.177	0.229	SUBCLONAL	1	FALSE	1	0.615065610134963	2		894	1322	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374376	81374376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	298	562	0	ENST00000222390.5:c.686G>A	p.Gly229Asp	p.G229D	ENST00000222390	NM_000601.4	229	gGc/gAc	6/18	1	2	FACETS	0.997	0.94	1	0.997	0.94	1	CLONAL	1	FALSE	1	0.615065610134963	2		562	972	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859474	151859474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	75	680	0	ENST00000262189.6:c.11188G>A	p.Gly3730Ser	p.G3730S	ENST00000262189	NM_170606.2	3730	Ggc/Agc	43/59	1	2	FACETS	0.258	0.225	0.293	0.258	0.225	0.293	SUBCLONAL	1	FALSE	1	0.615065610134963	2		680	946	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949023	151949023	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	200	485	1	ENST00000262189.6:c.1621+1G>A		p.X541_splice	ENST00000262189	NM_170606.2	541			1	2	FACETS	0.891	0.828	0.955	0.891	0.828	0.955	CLONAL	1	FALSE	1	0.615065610134963	2		486	730	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271243	38271243	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	151	445	1	ENST00000425967.3:c.2465G>A	p.Gly822Glu	p.G822E	ENST00000425967	NM_001174067.1	822	gGg/gAg	19/19	1	2	FACETS	0.899	0.827	0.974	0.899	0.827	0.974	CLONAL	1	FALSE	1	0.615065610134963	2		446	546	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372427	55372427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	135	781	2	ENST00000297316.4:c.1117C>T	p.Pro373Ser	p.P373S	ENST00000297316	NM_022454.3	373	Cct/Tct	2/2	1	2	FACETS	0.689	0.628	0.753	0.689	0.628	0.753	SUBCLONAL	1	FALSE	1	0.615065610134963	2		783	637	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145736915	145736915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751477241	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	189	592	0	ENST00000428558.2:c.3526G>A	p.Val1176Met	p.V1176M	ENST00000428558	NM_004260.3	1176	Gtg/Atg	22/22	NA	2	FACETS	0.883	0.819	0.949			1	INDETERMINATE	1	FALSE	NA	0.615065610134963	2		592	696	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737160	145737160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	44	531	0	ENST00000428558.2:c.3406G>A	p.Glu1136Lys	p.E1136K	ENST00000428558	NM_004260.3	1136	Gag/Aag	21/22	NA	2	FACETS	0.236	0.197	0.279			1	INDETERMINATE	1	FALSE	NA	0.615065610134963	2		531	606	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741452	145741452	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1429303169	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	338	1018	0	ENST00000428558.2:c.1051G>A	p.Gly351Ser	p.G351S	ENST00000428558	NM_004260.3	351	Ggc/Agc	5/22	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	FALSE	NA	0.615065610134963	2		1018	1006	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376045	8376045	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749675538	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	66	645	1	ENST00000356435.5:c.4552G>A	p.Ala1518Thr	p.A1518T	ENST00000356435		1518	Gcc/Acc	28/35	0.615065610134963	1	FACETS	0.191	0.165	0.219	0.191	0.165	0.219	SUBCLONAL	1	FALSE	0	0.615065610134963	1		646	778	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781440	135781440	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203542	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	377	1207	2	ENST00000298552.3:c.1525C>T	p.Arg509Ter	p.R509*	ENST00000298552	NM_001162426.1	509	Cga/Tga	15/23	0.615065610134963	1	FACETS	0.985	0.94	1	0.985	0.94	1	CLONAL	1	FALSE	0	0.615065610134963	1		1209	862	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412252	139412252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057523819	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	320	388	0	ENST00000277541.6:c.1393G>A	p.Ala465Thr	p.A465T	ENST00000277541	NM_017617.3	465	Gcc/Acc	8/34	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	1	FALSE	NA	0.615065610134963	2		388	695	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450829	70450829	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	33	367	0	ENST00000373644.4:c.5669G>A	p.Gly1890Asp	p.G1890D	ENST00000373644	NM_030625.2	1890	gGt/gAt	12/12	NA	2	FACETS	0.202	0.164	0.245			1	INDETERMINATE	1	FALSE	NA	0.615065610134963	2		367	532	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450915	70450915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1362741370	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	174	364	1	ENST00000373644.4:c.5755G>A	p.Glu1919Lys	p.E1919K	ENST00000373644	NM_030625.2	1919	Gag/Aag	12/12	NA	2	FACETS	1	0.931	1			1	INDETERMINATE	1	FALSE	NA	0.615065610134963	2		365	563	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450988	70450988	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	207	500	0	ENST00000373644.4:c.5828C>T	p.Pro1943Leu	p.P1943L	ENST00000373644	NM_030625.2	1943	cCc/cTc	12/12	NA	2	FACETS	0.939	0.874	1			1	INDETERMINATE	1	FALSE	NA	0.615065610134963	2		500	717	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741677	17741677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	120	447	0	ENST00000250003.3:c.348G>A	p.Met116Ile	p.M116I	ENST00000250003	NM_002478.4	116	atG/atA	1/3	1	2	FACETS	0.956	0.871	1	0.956	0.871	1	CLONAL	1	FALSE	1	0.615065610134963	2		447	408	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201847	67201847	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	74	468	0	ENST00000312629.5:c.1048-1G>A		p.X350_splice	ENST00000312629	NM_003952.2	350			NA	2	FACETS	0.33	0.288	0.375			1	INDETERMINATE	1	FALSE	NA	0.615065610134963	2		468	729	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625206	69625206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	88	646	0	ENST00000334134.2:c.587G>A	p.Ser196Asn	p.S196N	ENST00000334134	NM_005247.2	196	aGt/aAt	3/3	0.479813627931677	0	FACETS	0.28	0.249	0.312			1	SUBCLONAL	1	FALSE	0	0.615065610134963	0		646	394	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192603	94192603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	398	846	2	ENST00000323929.3:c.1471G>A	p.Asp491Asn	p.D491N	ENST00000323929	NM_005591.3	491	Gat/Aat	13/20	NA	2	FACETS	0.961	0.913	1			1	INDETERMINATE	1	FALSE	NA	0.615065610134963	2		848	1347	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118354925	118354925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	255	521	1	ENST00000534358.1:c.4114G>A	p.Glu1372Lys	p.E1372K	ENST00000534358	NM_005933.3	1372	Gag/Aag	9/36	NA	2	FACETS	0.969	0.909	1			1	INDETERMINATE	1	FALSE	NA	0.615065610134963	2		522	856	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242754	46242754	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	38	301	0	ENST00000334344.6:c.1715+1G>A		p.X572_splice	ENST00000334344	NM_152641.2	572			0.476163381684889	3	FACETS	0.246	0.202	0.294			1	SUBCLONAL	1	FALSE	NA	0.615065610134963	3		301	658	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424194	49424194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	144	353	0	ENST00000301067.7:c.13868C>T	p.Pro4623Leu	p.P4623L	ENST00000301067	NM_003482.3	4623	cCc/cTc	42/54	0.476163381684889	3	FACETS	1	0.982	1			1	CLONAL	1	FALSE	NA	0.615065610134963	3		353	488	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424971	49424971	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1166177671	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	218	466	0	ENST00000301067.7:c.13517C>T	p.Pro4506Leu	p.P4506L	ENST00000301067	NM_003482.3	4506	cCc/cTc	39/54	0.476163381684889	3	FACETS	1	0.99	1			1	CLONAL	1	FALSE	NA	0.615065610134963	3		466	697	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445167	49445167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	163	332	0	ENST00000301067.7:c.2299G>A	p.Glu767Lys	p.E767K	ENST00000301067	NM_003482.3	767	Gag/Aag	10/54	0.476163381684889	3	FACETS	1	0.988	1			1	CLONAL	1	FALSE	NA	0.615065610134963	3		332	497	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891010	112891010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	143	298	0	ENST00000351677.2:c.344G>A	p.Gly115Glu	p.G115E	ENST00000351677	NM_002834.3	115	gGa/gAa	4/16	NA	2	FACETS	0.963	0.884	1			1	INDETERMINATE	1	FALSE	NA	0.615065610134963	2		298	483	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557663	21557663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	42	802	0	ENST00000382592.4:c.2182G>A	p.Val728Met	p.V728M	ENST00000382592	NM_014572.2	728	Gtg/Atg	5/8	0.615065610134963	1	FACETS	0.183	0.152	0.217	0.183	0.152	0.217	SUBCLONAL	1	FALSE	0	0.615065610134963	1		802	517	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900709	32900709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876659940	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	155	817	1	ENST00000380152.3:c.590C>T	p.Ser197Phe	p.S197F	ENST00000380152		197	tCt/tTt	7/27	0.615065610134963	1	FACETS	0.348	0.318	0.379	0.348	0.318	0.379	SUBCLONAL	1	FALSE	0	0.615065610134963	1		818	1004	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907143	32907143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	128	510	1	ENST00000380152.3:c.1528G>A	p.Glu510Lys	p.E510K	ENST00000380152		510	Gaa/Aaa	10/27	0.615065610134963	1	FACETS	0.376	0.341	0.413	0.376	0.341	0.413	SUBCLONAL	1	FALSE	0	0.615065610134963	1		511	766	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436141	110436141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1302416889	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	276	698	2	ENST00000375856.3:c.2260G>A	p.Glu754Lys	p.E754K	ENST00000375856	NM_003749.2	754	Gag/Aag	1/2	0.615065610134963	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	0	0.615065610134963	1		700	612	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061012	38061012	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	100	254	0	ENST00000250448.2:c.977C>T	p.Pro326Leu	p.P326L	ENST00000250448	NM_004496.3	326	cCc/cTc	2/2	0.615065610134963	1	FACETS	0.983	0.897	1	0.983	0.897	1	CLONAL	1	FALSE	0	0.615065610134963	1		254	229	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68878150	68878150	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	303	571	0	ENST00000487270.1:c.863G>A	p.Gly288Glu	p.G288E	ENST00000487270	NM_133509.3	288	gGa/gAa	9/11	0.615065610134963	1	FACETS	0.996	0.945	1	0.996	0.945	1	CLONAL	1	FALSE	0	0.615065610134963	1		571	685	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396422	396422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	43	725	1	ENST00000262320.3:c.604C>T	p.Leu202Phe	p.L202F	ENST00000262320	NM_003502.3	202	Ctt/Ttt	2/11	0.121554722733827	0	FACETS	0.07	0.058	0.084			1	INDETERMINATE	1	FALSE	0	0.615065610134963	0		726	766	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777804	3777804	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	263	984	1	ENST00000262367.5:c.7244C>T	p.Pro2415Leu	p.P2415L	ENST00000262367	NM_004380.2	2415	cCc/cTc	31/31	0.121554722733827	0	FACETS	0.375	0.352	0.398			1	INDETERMINATE	1	FALSE	0	0.615065610134963	0		985	879	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843386	3843386	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	132	370	0	ENST00000262367.5:c.1216+1G>A		p.X406_splice	ENST00000262367	NM_004380.2	406			0.121554722733827	0	FACETS	0.311	0.283	0.339			1	INDETERMINATE	1	FALSE	0	0.615065610134963	0		370	532	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772252	68772252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	189	703	1	ENST00000261769.5:c.101C>T	p.Ala34Val	p.A34V	ENST00000261769	NM_004360.3	34	gCc/gTc	2/16	0.465380306680188	1	FACETS	0.631	0.586	0.678	0.631	0.586	0.678	SUBCLONAL	1	FALSE	0	0.615065610134963	1		704	674	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827981	72827981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	301	1268	0	ENST00000268489.5:c.8600C>T	p.Ser2867Phe	p.S2867F	ENST00000268489	NM_006885.3	2867	tCc/tTc	9/10	0.465380306680188	1	FACETS	0.551	0.518	0.584	0.551	0.518	0.584	SUBCLONAL	1	FALSE	0	0.615065610134963	1		1268	1231	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993833	72993833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374747520	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	162	861	0	ENST00000268489.5:c.212C>T	p.Pro71Leu	p.P71L	ENST00000268489	NM_006885.3	71	cCc/cTc	2/10	0.465380306680188	1	FACETS	0.529	0.487	0.574	0.529	0.487	0.574	SUBCLONAL	1	FALSE	0	0.615065610134963	1		861	689	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349906	89349906	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200650209	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	254	1588	1	ENST00000301030.4:c.3044C>T	p.Pro1015Leu	p.P1015L	ENST00000301030	NM_001256183.1	1015	cCc/cTc	9/13	0.589814857235477	1	FACETS	0.544	0.509	0.58	0.544	0.509	0.58	SUBCLONAL	1	FALSE	0	0.615065610134963	1		1589	1052	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350191	89350191	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773527879	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	288	1507	0	ENST00000301030.4:c.2759G>A	p.Arg920Lys	p.R920K	ENST00000301030	NM_001256183.1	920	aGg/aAg	9/13	0.589814857235477	1	FACETS	0.624	0.587	0.661	0.624	0.587	0.661	SUBCLONAL	1	FALSE	0	0.615065610134963	1		1507	1040	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578472	7578472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	76	543	1	ENST00000269305.4:c.458C>T	p.Pro153Leu	p.P153L	ENST00000269305	NM_001126112.2	153	cCc/cTc	5/11	NA	2	FACETS	0.301	0.264	0.342			1	INDETERMINATE	1	FALSE	NA	0.615065610134963	2		544	820	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578511	7578511	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	309	585	0	ENST00000269305.4:c.419C>T	p.Thr140Ile	p.T140I	ENST00000269305	NM_001126112.2	140	aCc/aTc	5/11	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	FALSE	NA	0.615065610134963	2		585	920	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990663	7990663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	181	813	2	ENST00000319144.4:c.98G>A	p.Ser33Asn	p.S33N	ENST00000319144	NM_001139.2	33	aGc/aAc	1/15	1	2	FACETS	0.772	0.714	0.833	0.772	0.714	0.833	SUBCLONAL	1	FALSE	1	0.615065610134963	2		815	762	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585449	29585449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1347152182	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	91	601	1	ENST00000356175.3:c.4198C>T	p.Pro1400Ser	p.P1400S	ENST00000356175	NM_000267.3	1400	Ccg/Tcg	31/57	NA	2	FACETS	0.261	0.231	0.294			1	INDETERMINATE	1	FALSE	NA	0.615065610134963	2		602	1133	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474309	40474309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	323	1044	0	ENST00000264657.5:c.2092G>A	p.Asp698Asn	p.D698N	ENST00000264657	NM_139276.2	698	Gac/Aac	21/24	0.121554722733827	0	FACETS	0.342	0.323	0.362			1	INDETERMINATE	1	FALSE	0	0.615065610134963	0		1044	1181	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226405	41226405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1294	128	1007	0	ENST00000357654.3:c.4618G>A	p.Glu1540Lys	p.E1540K	ENST00000357654	NM_007294.3	1540	Gaa/Aaa	14/23	0.121554722733827	0	FACETS	0.113	0.101	0.125			1	INDETERMINATE	1	FALSE	0	0.615065610134963	0		1007	1422	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246059	41246059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	298	512	1	ENST00000357654.3:c.1489C>T	p.Pro497Ser	p.P497S	ENST00000357654	NM_007294.3	497	Ccc/Tcc	10/23	0.121554722733827	0	FACETS	0.436	0.411	0.46			1	INDETERMINATE	1	FALSE	0	0.615065610134963	0		513	856	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226458	1226458	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	301	733	0	ENST00000326873.7:c.1114G>A	p.Val372Ile	p.V372I	ENST00000326873	NM_000455.4	372	Gtc/Atc	9/10	0.476163381684889	3	FACETS	1	0.993	1			1	CLONAL	1	FALSE	NA	0.615065610134963	3		733	913	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211178	2211178	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	182	597	0	ENST00000398665.3:c.1432G>A	p.Ala478Thr	p.A478T	ENST00000398665	NM_032482.2	478	Gcg/Acg	15/28	0.169934280271336	0	FACETS	0.348	0.322	0.375			1	INDETERMINATE	1	FALSE	0	0.615065610134963	0		597	654	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7120646	7120646	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	193	868	0	ENST00000302850.5:c.3644C>T	p.Thr1215Ile	p.T1215I	ENST00000302850	NM_000208.2	1215	aCt/aTt	20/22	0.540850185207929	1	FACETS	0.617	0.573	0.663	0.617	0.573	0.663	SUBCLONAL	1	FALSE	0	0.615065610134963	1		868	704	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7128957	7128957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	112	410	1	ENST00000302850.5:c.2851C>T	p.Pro951Ser	p.P951S	ENST00000302850	NM_000208.2	951	Ccg/Tcg	15/22	0.540850185207929	1	FACETS	0.533	0.482	0.587	0.533	0.482	0.587	SUBCLONAL	1	FALSE	0	0.615065610134963	1		411	473	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265106	10265106	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	40	804	0	ENST00000340748.4:c.1834G>A	p.Asp612Asn	p.D612N	ENST00000340748		612	Gac/Aac	21/40	NA	2	FACETS	0.163	0.134	0.194			1	INDETERMINATE	1	FALSE	NA	0.615065610134963	2		804	800	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291157	10291157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	346	873	0	ENST00000340748.4:c.314G>A	p.Gly105Glu	p.G105E	ENST00000340748		105	gGa/gAa	4/40	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	FALSE	NA	0.615065610134963	2		873	1086	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597468	10597468	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372588031	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	65	643	1	ENST00000171111.5:c.1735G>A	p.Asp579Asn	p.D579N	ENST00000171111	NM_203500.1	579	Gac/Aac	6/6	NA	2	FACETS	0.261	0.226	0.3			1	INDETERMINATE	1	FALSE	NA	0.615065610134963	2		644	809	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791718	42791718	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1344635105	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	277	499	1	ENST00000575354.2:c.604C>T	p.Arg202Trp	p.R202W	ENST00000575354	NM_015125.3	202	Cgg/Tgg	5/20	NA	2	FACETS	0.796	0.755	0.836			1	INDETERMINATE	2	FALSE	NA	0.615065610134963	2		500	566	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796589	42796589	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1012930800	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	42	298	0	ENST00000575354.2:c.3146G>A	p.Gly1049Asp	p.G1049D	ENST00000575354	NM_015125.3	1049	gGc/gAc	13/20	NA	2	FACETS	0.449	0.377	0.529			1	INDETERMINATE	1	FALSE	NA	0.615065610134963	2		298	304	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799330	42799330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	46	84	0	ENST00000575354.2:c.4814C>T	p.Ala1605Val	p.A1605V	ENST00000575354	NM_015125.3	1605	gCc/gTc	20/20	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.615065610134963	NA		84	91	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29115414	29115414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	67	728	0	ENST00000328354.6:c.652G>A	p.Asp218Asn	p.D218N	ENST00000328354	NM_007194.3	218	Gat/Aat	5/15	NA	2	FACETS	0.233	0.201	0.267			1	INDETERMINATE	1	FALSE	NA	0.615065610134963	2		728	936	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245063	53245063	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	369	1183	1	ENST00000375401.3:c.877G>A	p.Glu293Lys	p.E293K	ENST00000375401	NM_004187.3	293	Gag/Aag	7/26	0.615065610134963	1	FACETS	0.999	0.953	1	0.999	0.953	1	CLONAL	1	FALSE	0	0.615065610134963	1		1184	832	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183819	10183820	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	138	334	0	ENST00000256474.2:c.291dup	p.Tyr98LeufsTer34	p.Y98Lfs*34	ENST00000256474	NM_000551.3	96	-/C	1/3	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	1	0.615065610134963	2		334	432	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027676	48027678	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs587782858	NA	P-0010744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	166	333	0	ENST00000234420.5:c.2561_2563del	p.Lys854del	p.K854del	ENST00000234420	NM_000179.2	852	AAG/-	4/10	NA	2	FACETS	0.935	0.864	1			1	INDETERMINATE	1	FALSE	NA	0.615065610134963	2		333	577	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0010798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	192	363	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.991	0.919	1	0.991	0.919	1	CLONAL	1	TRUE	1	0.524424175262992	2		364	739	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0010798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	137	183	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.865	0.79	0.944	0.865	0.79	0.944	CLONAL	1	TRUE	1	0.524424175262992	2		183	604	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	299	539	0	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.524424175262992	2		539	1132	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	215	303	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	1	2	FACETS	0.98	0.912	1	0.98	0.912	1	CLONAL	1	TRUE	1	0.524424175262992	2		303	837	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	179	199	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.949	0.878	1	0.949	0.878	1	CLONAL	1	TRUE	1	0.524424175262992	2		200	719	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0010798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	59	150	1	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.636	0.55	0.728	0.636	0.55	0.728	SUBCLONAL	1	TRUE	1	0.524424175262992	2		151	354	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0010798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	202	315	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.856	0.794	0.92	0.856	0.794	0.92	CLONAL	1	TRUE	1	0.524424175262992	2		315	900	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0010798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	99	287	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.524424175262992	2		287	344	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271819	15271819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765739997	NA	P-0010798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	189	148	1	ENST00000263388.2:c.6620G>A	p.Arg2207Gln	p.R2207Q	ENST00000263388	NM_000435.2	2207	cGg/cAg	33/33	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.524424175262992	2		149	567	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0010798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	607	571	7	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	0.998	1	CLONAL	2	TRUE	1	0.524424175262992	2		578	1150	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522260	157522260	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	222	367	0	ENST00000346085.5:c.4532A>G	p.Gln1511Arg	p.Q1511R	ENST00000346085	NM_020732.3	1511	cAg/cGg	18/20	1	2	FACETS	0.961	0.896	1	0.961	0.896	1	CLONAL	1	TRUE	1	0.524424175262992	2		367	881	SUCCESS
APC	324	MSKCC	GRCh37	5	112137024	112137024	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	164	273	0	ENST00000257430.4:c.778C>T	p.Gln260Ter	p.Q260*	ENST00000257430	NM_000038.5	260	Cag/Tag	8/16	0.524424175262992	2	FACETS	0.922	0.85	0.998	0.461	0.425	0.499	CLONAL	1	TRUE	0	0.524424175262992	2		273	678	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190792	11190792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1192848906	NA	P-0010798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	179	244	1	ENST00000361445.4:c.5407C>T	p.His1803Tyr	p.H1803Y	ENST00000361445	NM_004958.3	1803	Cac/Tac	39/58	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.524424175262992	2		245	628	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313296	65313296	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs555662015	NA	P-0010798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	307	567	0	ENST00000342505.4:c.1818G>C	p.Lys606Asn	p.K606N	ENST00000342505	NM_002227.2	606	aaG/aaC	13/25	1	2	FACETS	0.934	0.879	0.989	0.934	0.879	0.989	CLONAL	1	TRUE	1	0.524424175262992	2		567	1254	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026794	71026794	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	161	296	0	ENST00000318789.4:c.1428G>T	p.Gln476His	p.Q476H	ENST00000318789	NM_032682.5	476	caG/caT	16/21	1	2	FACETS	0.936	0.861	1	0.936	0.861	1	CLONAL	1	TRUE	1	0.524424175262992	2		296	656	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155467	106155467	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773565437	NA	P-0010798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	255	375	0	ENST00000380013.4:c.368G>A	p.Arg123His	p.R123H	ENST00000380013	NM_001127208.2	123	cGt/cAt	3/11	1	2	FACETS	0.962	0.901	1	0.962	0.901	1	CLONAL	1	TRUE	1	0.524424175262992	2		375	1011	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509648	106509648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	236	409	0	ENST00000359195.3:c.1642C>T	p.Pro548Ser	p.P548S	ENST00000359195	NM_002649.2	548	Ccc/Tcc	2/11	1	2	FACETS	0.989	0.924	1	0.989	0.924	1	CLONAL	1	TRUE	1	0.524424175262992	2		409	910	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397696	116397696	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	174	317	0	ENST00000397752.3:c.1970C>T	p.Pro657Leu	p.P657L	ENST00000397752	NM_000245.2	657	cCt/cTt	8/21	1	2	FACETS	0.986	0.911	1	0.986	0.911	1	CLONAL	1	TRUE	1	0.524424175262992	2		317	673	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371828	55371828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1010687929	NA	P-0010798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	30	14	0	ENST00000297316.4:c.518G>A	p.Arg173His	p.R173H	ENST00000297316	NM_022454.3	173	cGc/cAc	2/2	1	2	FACETS	0.923	0.781	1	1	0.963	1	CLONAL	2	TRUE	1	0.524424175262992	2		14	62	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248573	8248573	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780757257	NA	P-0010798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	288	446	3	ENST00000335790.3:c.314G>A	p.Arg105Gln	p.R105Q	ENST00000335790	NM_002315.2	105	cGg/cAg	3/4	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.524424175262992	2		449	1071	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574678	95574678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	178	343	2	ENST00000393063.1:c.2419G>A	p.Ala807Thr	p.A807T	ENST00000393063	NM_030621.3	807	Gcc/Acc	16/28	1	2	FACETS	0.905	0.836	0.977	0.905	0.836	0.977	CLONAL	1	TRUE	1	0.524424175262992	2		345	750	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353761	40353761	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs547016204	NA	P-0010798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	385	603	0	ENST00000293328.3:c.2359T>C	p.Ser787Pro	p.S787P	ENST00000293328	NM_012448.3	787	Tcg/Ccg	19/19	NA	2	FACETS	1	0.952	1			1	INDETERMINATE	1	TRUE	NA	0.524424175262992	2		603	1462	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120460319	120460319	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1446995271	NA	P-0010798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	145	362	0	ENST00000256646.2:c.5996del	p.Asn1999MetfsTer32	p.N1999Mfs*32	ENST00000256646	NM_024408.3	1999	aAt/at	33/34	1	2	FACETS	0.516	0.47	0.564	0.516	0.47	0.564	SUBCLONAL	1	TRUE	1	0.524424175262992	2		362	1072	SUCCESS
APC	324	MSKCC	GRCh37	5	112164664	112164664	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1060503259	NA	P-0010798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	185	158	0	ENST00000257430.4:c.1742del	p.Lys581ArgfsTer9	p.K581Rfs*9	ENST00000257430	NM_000038.5	580	Aaa/aa	14/16	0.524424175262992	2	FACETS	0.869	0.813	0.925	0.869	0.813	0.925	CLONAL	2	TRUE	0	0.524424175262992	2		158	406	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851941	128851943	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs767361434	NA	P-0010798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	179	390	0	ENST00000249373.3:c.2021_2023del	p.Lys674del	p.K674del	ENST00000249373	NM_005631.4	671	cgGAAg/cgg	12/12	1	2	FACETS	0.754	0.696	0.815	0.754	0.696	0.815	SUBCLONAL	1	TRUE	1	0.524424175262992	2		390	905	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0010800-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	18	250	2	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.813	1	1	0.813	1	CLONAL	1	FALSE	1	0.201615121679158	2		252	164	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63700141	63700141	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010800-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	36	520	0	ENST00000279873.7:c.476A>T	p.Asp159Val	p.D159V	ENST00000279873	NM_032199.2	159	gAc/gTc	3/10	0.171882254866136	3	FACETS	0.959	0.789	1	0.479	0.394	0.575	CLONAL	1	FALSE	1	0.201615121679158	3		520	410	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016666	12016666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010800-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	28	638	0	ENST00000353533.5:c.802C>T	p.Pro268Ser	p.P268S	ENST00000353533	NM_003010.3	268	Cca/Tca	7/11	0.118648973814142	1	FACETS	0.664	0.531	0.816	0.664	0.531	0.816	INDETERMINATE	1	FALSE	0	0.201615121679158	1		638	376	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835590	68835591	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0010800-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	50	836	0	ENST00000261769.5:c.183dup	p.Gly62ArgfsTer32	p.G62Rfs*32	ENST00000261769	NM_004360.3	61	acc/aCcc	3/16	1	2	FACETS	0.881	0.747	1	0.881	0.747	1	CLONAL	1	FALSE	1	0.201615121679158	2		836	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579419	7579420	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs587783062	NA	P-0010816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	732	341	0	ENST00000269305.4:c.267dup	p.Ser90LeufsTer59	p.S90Lfs*59	ENST00000269305	NM_001126112.2	89	-/C	4/11	0.820075529729433	2	FACETS	0.906	0.885	0.926	0.906	0.885	0.926	CLONAL	2	TRUE	0	0.821989117678648	2		341	983	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11308103	11308103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141936187	NA	P-0010816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	563	456	0	ENST00000361445.4:c.889G>A	p.Asp297Asn	p.D297N	ENST00000361445	NM_004958.3	297	Gac/Aac	7/58	0.821989117678648	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.821989117678648	1		456	793	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532860	187532860	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	452	274	0	ENST00000441802.2:c.9533C>G	p.Ser3178Cys	p.S3178C	ENST00000441802	NM_005245.3	3178	tCt/tGt	14/27	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.821989117678648	2		274	1047	SUCCESS
APC	324	MSKCC	GRCh37	5	112170810	112170810	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	620	422	0	ENST00000257430.4:c.1906G>T	p.Gly636Cys	p.G636C	ENST00000257430	NM_000038.5	636	Ggt/Tgt	15/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.821989117678648	2		422	1494	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448089	49448089	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0010816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1227	172	352	0	ENST00000301067.7:c.510+1G>T		p.X170_splice	ENST00000301067	NM_003482.3	170			1	2	FACETS	0.299	0.274	0.325	0.299	0.274	0.325	SUBCLONAL	1	TRUE	1	0.821989117678648	2		352	1399	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554393	63554393	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	488	418	0	ENST00000307078.5:c.346G>C	p.Gly116Arg	p.G116R	ENST00000307078	NM_004655.3	116	Gga/Cga	2/11	0.821989117678648	2	FACETS	0.989	0.949	1	0.495	0.474	0.516	CLONAL	1	TRUE	0	0.821989117678648	2		418	1200	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510728	120510729	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0010816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	576	415	0	ENST00000256646.2:c.1235_1236delinsTT	p.Cys412Phe	p.C412F	ENST00000256646	NM_024408.3	412	tGC/tTT	7/34	1	2	FACETS	0.928	0.891	0.964	0.928	0.891	0.964	CLONAL	1	TRUE	1	0.821989117678648	2		415	1511	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347891	89347891	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	TT	novel	NA	P-0010816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1879	372	528	0	ENST00000301030.4:c.5059delinsAA	p.Glu1687LysfsTer10	p.E1687Kfs*10	ENST00000301030	NM_001256183.1	1687	Gag/AAag	9/13	0.812565150721762	3	FACETS	0.567	0.536	0.6	0.284	0.268	0.3	SUBCLONAL	1	TRUE	1	0.821989117678648	3		528	2251	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280122	142280122	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010860-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	70	639	0	ENST00000350721.4:c.1312C>G	p.Leu438Val	p.L438V	ENST00000350721	NM_001184.3	438	Cta/Gta	5/47	1	2	FACETS	0.773	0.671	0.883	0.773	0.671	0.883	SUBCLONAL	1	TRUE	1	0.17	2		639	1066	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155749	106155749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010860-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	47	469	0	ENST00000380013.4:c.650C>T	p.Ser217Phe	p.S217F	ENST00000380013	NM_001127208.2	217	tCc/tTc	3/11	1	2	FACETS	0.774	0.652	0.91	0.774	0.652	0.91	CLONAL	1	TRUE	1	0.17	2		469	714	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875677	35875677	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010860-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	47	645	0	ENST00000303115.3:c.864G>C	p.Lys288Asn	p.K288N	ENST00000303115	NM_002185.3	288	aaG/aaC	7/8	1	2	FACETS	0.63	0.53	0.741	0.63	0.53	0.741	SUBCLONAL	1	TRUE	1	0.17	2		645	878	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177920	56177920	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010860-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	62	727	0	ENST00000399503.3:c.2893C>T	p.Gln965Ter	p.Q965*	ENST00000399503	NM_005921.1	965	Cag/Tag	14/20	1	2	FACETS	0.707	0.609	0.815	0.707	0.609	0.815	SUBCLONAL	1	TRUE	1	0.17	2		727	1031	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721675	176721675	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010860-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	41	492	0	ENST00000439151.2:c.7306G>C	p.Glu2436Gln	p.E2436Q	ENST00000439151	NM_022455.4	2436	Gaa/Caa	23/23	1	2	FACETS	0.634	0.526	0.754	0.634	0.526	0.754	SUBCLONAL	1	TRUE	1	0.17	2		492	761	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020937	26020937	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010860-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1398	107	1382	0	ENST00000357647.3:c.220G>C	p.Glu74Gln	p.E74Q	ENST00000357647	NM_003529.2	74	Gag/Cag	1/1	1	2	FACETS	0.836	0.747	0.932	0.836	0.747	0.932	CLONAL	1	TRUE	1	0.17	2		1382	1505	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839699	27839699	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010860-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1554	106	1435	0	ENST00000328488.2:c.395G>C	p.Arg132Pro	p.R132P	ENST00000328488	NM_003533.2	132	cGa/cCa	1/1	0.195006635167102	3	FACETS	0.815	0.727	0.909	0.408	0.363	0.455	CLONAL	1	TRUE	1	0.17	3		1435	1660	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652129	36652129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34916193	NA	P-0010860-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	47	462	1	ENST00000244741.5:c.251G>A	p.Arg84Gln	p.R84Q	ENST00000244741	NM_000389.4	84	cGa/cAa	2/3	1	2	FACETS	0.838	0.706	0.984	0.838	0.706	0.984	CLONAL	1	TRUE	1	0.17	2		463	660	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528327	157528327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776894668	NA	P-0010860-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	85	880	2	ENST00000346085.5:c.6052G>A	p.Glu2018Lys	p.E2018K	ENST00000346085	NM_020732.3	2018	Gag/Aag	20/20	1	2	FACETS	0.809	0.713	0.913	0.809	0.713	0.913	CLONAL	1	TRUE	1	0.17	2		882	1236	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974152	2974152	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010860-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	80	770	0	ENST00000396946.4:c.1453G>A	p.Glu485Lys	p.E485K	ENST00000396946	NM_032415.4	485	Gaa/Aaa	10/25	1	2	FACETS	0.89	0.781	1	0.89	0.781	1	CLONAL	1	TRUE	1	0.17	2		770	1058	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186589	108186589	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010860-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	42	524	0	ENST00000278616.4:c.6046G>C	p.Asp2016His	p.D2016H	ENST00000278616	NM_000051.3	2016	Gat/Cat	41/63	1	2	FACETS	0.842	0.702	0.998	0.842	0.702	0.998	CLONAL	1	TRUE	1	0.17	2		524	587	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427557	427557	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs760471868	NA	P-0010860-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	39	533	0	ENST00000399788.2:c.2612C>G	p.Ser871Cys	p.S871C	ENST00000399788	NM_001042603.1	871	tCt/tGt	19/28	1	2	FACETS	0.679	0.561	0.811	0.679	0.561	0.811	SUBCLONAL	1	TRUE	1	0.17	2		533	676	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961377	41961377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010860-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1370	94	1106	3	ENST00000219905.7:c.285G>A	p.Met95Ile	p.M95I	ENST00000219905	NM_001164273.1	95	atG/atA	2/24	1	2	FACETS	0.755	0.669	0.848	0.755	0.669	0.848	SUBCLONAL	1	TRUE	1	0.17	2		1109	1464	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42057177	42057177	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0010860-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1431	129	1047	0	ENST00000219905.7:c.7838C>G	p.Ser2613Ter	p.S2613*	ENST00000219905	NM_001164273.1	2613	tCa/tGa	23/24	1	2	FACETS	0.973	0.879	1	0.973	0.879	1	CLONAL	1	TRUE	1	0.17	2		1047	1560	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496932	29496932	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010860-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	48	519	0	ENST00000356175.3:c.503C>A	p.Ser168Ter	p.S168*	ENST00000356175	NM_000267.3	168	tCa/tAa	5/57	1	2	FACETS	0.856	0.722	1	0.856	0.722	1	CLONAL	1	TRUE	1	0.17	2		519	660	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775238	73775238	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010860-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	55	811	0	ENST00000254810.4:c.18G>T	p.Gln6His	p.Q6H	ENST00000254810	NM_005324.3	6	caG/caT	2/4	1	2	FACETS	0.622	0.53	0.723	0.622	0.53	0.723	SUBCLONAL	1	TRUE	1	0.17	2		811	1040	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2225391	2225391	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010860-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	75	688	0	ENST00000398665.3:c.3601G>C	p.Glu1201Gln	p.E1201Q	ENST00000398665	NM_032482.2	1201	Gag/Cag	26/28	1	2	FACETS	0.956	0.836	1	0.956	0.836	1	CLONAL	1	TRUE	1	0.17	2		688	923	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943403	17943403	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010860-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	77	803	0	ENST00000458235.1:c.2605C>T	p.Gln869Ter	p.Q869*	ENST00000458235	NM_000215.3	869	Cag/Tag	19/24	1	2	FACETS	0.838	0.733	0.951	0.838	0.733	0.951	CLONAL	1	TRUE	1	0.17	2		803	1081	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279766	46279766	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010860-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	96	662	0	ENST00000371998.3:c.3692G>C	p.Arg1231Thr	p.R1231T	ENST00000371998		1231	aGa/aCa	20/23	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.17	2		662	955	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038877	47038877	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010860-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	14	63	0	ENST00000377604.3:c.884C>T	p.Ser295Leu	p.S295L	ENST00000377604	NM_001204468.1	295	tCa/tTa	9/24	1	1	FACETS	0.828	0.607	1	1	0.899	1	CLONAL	2	TRUE	0	0.17	1		63	91	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961361	54961362	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0010860-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	63	408	0	ENST00000312783.6:c.270dup	p.Pro91AlafsTer4	p.P91Afs*4	ENST00000312783	NM_198436.1	90	-/G	4/10	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.17	2		408	634	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0010860-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	123	432	27	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	1	2	FACETS	1	0.945	1	1	0.99	1	CLONAL	2	TRUE	1	0.17	2		459	682	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACT	novel	NA	P-0010891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	124	350	0	ENST00000275493.2:c.2310_2311insTAC	p.Asp770_Asn771insTyr	p.D770_N771insY	ENST00000275493	NM_005228.3	770	gac/gACTac	20/28	0.271945059828801	3	FACETS	1	0.971	1	0.593	0.536	0.653	CLONAL	1	TRUE	1	0.28	3		350	852	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0010917-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	36	250	2	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.665	0.548	0.795	0.665	0.548	0.795	SUBCLONAL	1	TRUE	1	0.33717741964359	2		252	321	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0010917-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	51	183	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.882	0.753	1	0.882	0.753	1	CLONAL	1	TRUE	1	0.33717741964359	2		183	343	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102094434	102094434	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010917-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	140	511	0	ENST00000282441.5:c.1114C>T	p.Gln372Ter	p.Q372*	ENST00000282441	NM_001130145.2	372	Cag/Tag	7/9	0.33717741964359	1	FACETS	0.939	0.857	1	0.939	0.857	1	CLONAL	1	TRUE	0	0.33717741964359	1		511	735	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027167	48027167	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587779225	NA	P-0010917-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	124	630	0	ENST00000234420.5:c.2045C>G	p.Ser682Cys	p.S682C	ENST00000234420	NM_000179.2	682	tCt/tGt	4/10	1	2	FACETS	0.761	0.688	0.839	0.761	0.688	0.839	SUBCLONAL	1	TRUE	1	0.33717741964359	2		630	966	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280666	41280666	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010917-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	176	658	0	ENST00000349496.5:c.2179G>C	p.Asp727His	p.D727H	ENST00000349496	NM_001904.3	727	Gat/Cat	15/15	0.33717741964359	1	FACETS	0.985	0.908	1	0.985	0.908	1	CLONAL	1	TRUE	0	0.33717741964359	1		658	881	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271315	1271315	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010917-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	76	339	0	ENST00000310581.5:c.2387C>G	p.Ser796Cys	p.S796C	ENST00000310581	NM_198253.2	796	tCc/tGc	8/16	1	2	FACETS	0.72	0.632	0.815	0.72	0.632	0.815	SUBCLONAL	1	TRUE	1	0.33717741964359	2		339	626	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89335072	89335072	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0010917-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	94	421	0	ENST00000301030.4:c.7807-1G>C		p.X2603_splice	ENST00000301030	NM_001256183.1	2603			0.33717741964359	1	FACETS	0.748	0.666	0.834	0.748	0.666	0.834	SUBCLONAL	1	TRUE	0	0.33717741964359	1		421	620	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281634	15281634	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010917-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	168	549	4	ENST00000263388.2:c.4739C>T	p.Ser1580Leu	p.S1580L	ENST00000263388	NM_000435.2	1580	tCg/tTg	26/33	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.33717741964359	2		553	892	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849591	68849592	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010917-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	152	682	0	ENST00000261769.5:c.1497dup	p.Gly500TrpfsTer37	p.G500Wfs*37	ENST00000261769	NM_004360.3	498	-/T	10/16	0.33717741964359	1	FACETS	0.896	0.819	0.975	0.896	0.819	0.975	CLONAL	1	TRUE	0	0.33717741964359	1		682	837	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120634	115120635	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACCA	novel	NA	P-0010917-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	191	819	0	ENST00000257566.3:c.368_371dup	p.Ile125GlyfsTer14	p.I125Gfs*14	ENST00000257566	NM_016569.3	124	gtc/gtTGGTc	1/8	1	2	FACETS	0.834	0.769	0.901	0.834	0.769	0.901	CLONAL	1	TRUE	1	0.33717741964359	2		819	1359	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	147	250	2	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.227617932165736	3	FACETS	0.999	0.924	1	1	0.992	1	CLONAL	4	TRUE	1	0.224952280433776	3		252	364	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	68	140	0				ENST00000310581	NM_198253.2	-/1132			0.227617932165736	3	FACETS	0.934	0.83	1	1	0.982	1	CLONAL	4	TRUE	1	0.224952280433776	3		140	180	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204864	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	95	439	0	ENST00000371953.3:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000371953	NM_000314.4	171	Cag/Tag	6/9	1	2	FACETS	0.776	0.693	0.864	1	0.982	1	SUBCLONAL	2	TRUE	1	0.224952280433776	2		439	544	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70441157	70441157	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	rs764225020	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	129	513	1	ENST00000373644.4:c.4832del	p.Asn1611ThrfsTer13	p.N1611Tfs*13	ENST00000373644	NM_030625.2	1609	gAa/ga	9/12	1	2	FACETS	1	0.967	1	1	0.991	1	CLONAL	2	TRUE	1	0.224952280433776	2		514	510	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519925	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	210	482	0	ENST00000263967.3:c.1357G>C	p.Glu453Gln	p.E453Q	ENST00000263967	NM_006218.2	453	Gaa/Caa	8/21	0.227617932165736	3	FACETS	1	0.936	1	1	0.992	1	CLONAL	3	TRUE	1	0.224952280433776	3		482	690	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661866	29661866	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	84	433	0	ENST00000356175.3:c.5760G>C	p.Leu1920Phe	p.L1920F	ENST00000356175	NM_000267.3	1920	ttG/ttC	39/57	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.224952280433776	2		433	507	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	217	796	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	1	2	FACETS	1	0.965	1	1	0.994	1	CLONAL	2	TRUE	1	0.224952280433776	2		796	911	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952138	178952138	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	44	369	0	ENST00000263967.3:c.3193C>T	p.His1065Tyr	p.H1065Y	ENST00000263967	NM_006218.2	1065	Cat/Tat	21/21	0.227617932165736	3	FACETS	0.788	0.661	0.93	0.394	0.33	0.465	CLONAL	1	TRUE	1	0.224952280433776	3		369	552	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264009	16264009	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	154	819	1	ENST00000375759.3:c.10378C>T	p.Pro3460Ser	p.P3460S	ENST00000375759	NM_015001.2	3460	Cca/Tca	12/15	1	2	FACETS	1	0.956	1	1	0.992	1	CLONAL	2	TRUE	1	0.224952280433776	2		820	645	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839850	27839850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	140	1346	3	ENST00000328488.2:c.244G>A	p.Asp82Asn	p.D82N	ENST00000328488	NM_003533.2	82	Gat/Aat	1/1	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.224952280433776	2		1349	859	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056443	26056443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1252419231	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	27	263	0	ENST00000343677.2:c.214G>A	p.Asp72Asn	p.D72N	ENST00000343677	NM_005319.3	72	Gat/Aat	1/1	1	2	FACETS	0.825	0.658	1	0.825	0.658	1	CLONAL	1	TRUE	1	0.224952280433776	2		263	291	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831644	72831644	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	79	1038	0	ENST00000268489.5:c.4937C>T	p.Ser1646Phe	p.S1646F	ENST00000268489	NM_006885.3	1646	tCc/tTc	9/10	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.224952280433776	2		1038	693	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255841	16255841	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	99	366	0	ENST00000375759.3:c.3106G>C	p.Glu1036Gln	p.E1036Q	ENST00000375759	NM_015001.2	1036	Gaa/Caa	11/15	1	2	FACETS	1	0.965	1	1	0.989	1	CLONAL	2	TRUE	1	0.224952280433776	2		366	379	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258869	16258869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	147	672	0	ENST00000375759.3:c.6134G>A	p.Arg2045Lys	p.R2045K	ENST00000375759	NM_015001.2	2045	aGa/aAa	11/15	1	2	FACETS	1	0.97	1	1	0.992	1	CLONAL	2	TRUE	1	0.224952280433776	2		672	583	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259534	16259534	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	54	281	0	ENST00000375759.3:c.6799G>T	p.Glu2267Ter	p.E2267*	ENST00000375759	NM_015001.2	2267	Gag/Tag	11/15	1	2	FACETS	0.953	0.822	1	1	0.976	1	CLONAL	2	TRUE	1	0.224952280433776	2		281	252	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259936	16259936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	141	691	0	ENST00000375759.3:c.7201G>A	p.Asp2401Asn	p.D2401N	ENST00000375759	NM_015001.2	2401	Gac/Aac	11/15	1	2	FACETS	1	0.977	1	1	0.992	1	CLONAL	2	TRUE	1	0.224952280433776	2		691	528	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260623	16260623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	128	509	3	ENST00000375759.3:c.7888G>A	p.Asp2630Asn	p.D2630N	ENST00000375759	NM_015001.2	2630	Gac/Aac	11/15	1	2	FACETS	1	0.972	1	1	0.991	1	CLONAL	2	TRUE	1	0.224952280433776	2		512	491	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262282	16262282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	45	160	0	ENST00000375759.3:c.9547G>A	p.Glu3183Lys	p.E3183K	ENST00000375759	NM_015001.2	3183	Gag/Aag	11/15	1	2	FACETS	0.866	0.742	0.998	1	0.978	1	CLONAL	3	TRUE	1	0.224952280433776	2		160	154	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262375	16262375	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	69	220	0	ENST00000375759.3:c.9640G>A	p.Asp3214Asn	p.D3214N	ENST00000375759	NM_015001.2	3214	Gat/Aat	11/15	1	2	FACETS	0.988	0.875	1	1	0.986	1	CLONAL	3	TRUE	1	0.224952280433776	2		220	207	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46597594	46597594	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	43	677	0	ENST00000262741.5:c.31G>C	p.Asp11His	p.D11H	ENST00000262741	NM_003629.3	11	Gat/Cat	1/10	1	2	FACETS	0.576	0.481	0.682	0.576	0.481	0.682	SUBCLONAL	1	TRUE	1	0.224952280433776	2		677	664	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469044	25469044	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	64	592	0	ENST00000264709.3:c.1414G>C	p.Asp472His	p.D472H	ENST00000264709	NM_175629.2	472	Gat/Cat	11/23	NA	2	FACETS	1	0.866	1			1	INDETERMINATE	1	TRUE	NA	0.224952280433776	2		592	569	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156201	106156201	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	57	439	0	ENST00000380013.4:c.1102G>C	p.Glu368Gln	p.E368Q	ENST00000380013	NM_001127208.2	368	Gaa/Caa	3/11	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.224952280433776	2		439	438	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253817	153253817	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	63	482	1	ENST00000281708.4:c.916C>T	p.Gln306Ter	p.Q306*	ENST00000281708	NM_033632.3	306	Cag/Tag	6/12	1	2	FACETS	0.937	0.81	1	0.937	0.81	1	CLONAL	1	TRUE	1	0.224952280433776	2		483	598	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944358	131944358	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	129	322	0	ENST00000265335.6:c.2770C>A	p.Gln924Lys	p.Q924K	ENST00000265335		924	Caa/Aaa	17/25	1	2	FACETS	1	0.967	1	1	0.991	1	CLONAL	2	TRUE	1	0.224952280433776	2		322	508	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176719054	176719054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	93	630	1	ENST00000439151.2:c.6358G>A	p.Glu2120Lys	p.E2120K	ENST00000439151	NM_022455.4	2120	Gag/Aag	22/23	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.224952280433776	2		631	669	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721189	176721189	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	36	326	0	ENST00000439151.2:c.6820C>T	p.Gln2274Ter	p.Q2274*	ENST00000439151	NM_022455.4	2274	Cag/Tag	23/23	1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	1	0.224952280433776	2		326	320	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480176	20480176	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	134	523	0	ENST00000346618.3:c.493G>C	p.Asp165His	p.D165H	ENST00000346618	NM_001949.4	165	Gat/Cat	2/7	1	2	FACETS	1	0.98	1	1	0.992	1	CLONAL	2	TRUE	1	0.224952280433776	2		523	477	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099823	157099823	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	38	670	0	ENST00000346085.5:c.760C>G	p.Gln254Glu	p.Q254E	ENST00000346085	NM_020732.3	254	Caa/Gaa	1/20	1	2	FACETS	0.78	0.645	0.931	0.78	0.645	0.931	CLONAL	1	TRUE	1	0.224952280433776	2		670	433	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843378	128843378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	105	512	0	ENST00000249373.3:c.485G>A	p.Gly162Asp	p.G162D	ENST00000249373	NM_005631.4	162	gGc/gAc	2/12	1	2	FACETS	1	0.975	1	1	0.99	1	CLONAL	2	TRUE	1	0.224952280433776	2		512	374	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742803	145742803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	24	148	0	ENST00000428558.2:c.208G>A	p.Glu70Lys	p.E70K	ENST00000428558	NM_004260.3	70	Gaa/Aaa	3/22	1	2	FACETS	0.979	0.782	1	1	0.95	1	CLONAL	2	TRUE	1	0.224952280433776	2		148	109	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118370592	118370592	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	72	457	0	ENST00000534358.1:c.6122C>T	p.Ser2041Phe	p.S2041F	ENST00000534358	NM_005933.3	2041	tCc/tTc	24/36	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.224952280433776	2		457	496	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373250	118373250	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	112	689	0	ENST00000534358.1:c.6643C>T	p.Pro2215Ser	p.P2215S	ENST00000534358	NM_005933.3	2215	Cca/Tca	27/36	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.224952280433776	2		689	665	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418667	49418667	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	114	512	0	ENST00000301067.7:c.15847C>G	p.Leu5283Val	p.L5283V	ENST00000301067	NM_003482.3	5283	Ctc/Gtc	49/54	1	2	FACETS	1	0.955	1	1	0.99	1	CLONAL	2	TRUE	1	0.224952280433776	2		512	465	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426643	49426643	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs797045658	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	56	416	0	ENST00000301067.7:c.11845C>T	p.Gln3949Ter	p.Q3949*	ENST00000301067	NM_003482.3	3949	Caa/Taa	39/54	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.224952280433776	2		416	353	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885247	111885247	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	85	923	4	ENST00000341259.2:c.1135C>T	p.Gln379Ter	p.Q379*	ENST00000341259	NM_005475.2	379	Cag/Tag	6/8	1	2	FACETS	0.993	0.877	1	0.993	0.877	1	CLONAL	1	TRUE	1	0.224952280433776	2		927	761	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518152	103518152	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	35	412	0	ENST00000355739.4:c.2090C>T	p.Ser697Phe	p.S697F	ENST00000355739	NM_000123.3	697	tCc/tTc	9/15	1	2	FACETS	0.746	0.612	0.897	0.746	0.612	0.897	SUBCLONAL	1	TRUE	1	0.224952280433776	2		412	417	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610426	81610426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	33	692	0	ENST00000298171.2:c.2024C>T	p.Pro675Leu	p.P675L	ENST00000298171	NM_000369.2	675	cCa/cTa	10/10	1	2	FACETS	0.476	0.386	0.577	0.476	0.386	0.577	SUBCLONAL	1	TRUE	1	0.224952280433776	2		692	617	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467185	99467185	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	106	720	0	ENST00000268035.6:c.2566G>C	p.Glu856Gln	p.E856Q	ENST00000268035	NM_000875.3	856	Gag/Cag	12/21	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.224952280433776	2		720	645	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223363	2223363	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	41	353	0	ENST00000326181.6:c.975G>C	p.Lys325Asn	p.K325N	ENST00000326181	NM_032271.2	325	aaG/aaC	10/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.224952280433776	2		353	245	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805657	89805657	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs761934804	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	175	703	0	ENST00000389301.3:c.4051G>C	p.Glu1351Gln	p.E1351Q	ENST00000389301	NM_000135.2	1351	Gag/Cag	41/43	NA	2	FACETS	0.86	0.796	0.926			1	INDETERMINATE	3	TRUE	NA	0.224952280433776	2		703	603	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576024	29576024	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	59	569	0	ENST00000356175.3:c.3997G>C	p.Glu1333Gln	p.E1333Q	ENST00000356175	NM_000267.3	1333	Gag/Cag	30/57	1	2	FACETS	0.74	0.636	0.854	0.74	0.636	0.854	SUBCLONAL	1	TRUE	1	0.224952280433776	2		569	709	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231355	5231355	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	21	531	0	ENST00000357368.4:c.2121G>C	p.Glu707Asp	p.E707D	ENST00000357368	NM_002850.3	707	gaG/gaC	14/38	0.224952280433776	1	FACETS	0.504	0.388	0.639	0.504	0.388	0.639	SUBCLONAL	1	TRUE	0	0.224952280433776	1		531	329	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152135	11152135	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	48	545	0	ENST00000358026.2:c.4419G>C	p.Lys1473Asn	p.K1473N	ENST00000358026	NM_001128849.1	1473	aaG/aaC	31/36	0.224952280433776	1	FACETS	0.815	0.689	0.952	0.815	0.689	0.952	CLONAL	1	TRUE	0	0.224952280433776	1		545	465	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905524	50905524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1295943468	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	67	855	1	ENST00000440232.2:c.652C>T	p.Arg218Cys	p.R218C	ENST00000440232	NM_002691.3	218	Cgc/Tgc	6/27	0.224952280433776	1	FACETS	0.902	0.784	1	0.902	0.784	1	CLONAL	1	TRUE	0	0.224952280433776	1		856	586	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29115459	29115459	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	44	381	0	ENST00000328354.6:c.607G>A	p.Asp203Asn	p.D203N	ENST00000328354	NM_007194.3	203	Gat/Aat	5/15	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.224952280433776	2		381	335	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513289	41513289	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	129	729	1	ENST00000263253.7:c.193C>T	p.Gln65Ter	p.Q65*	ENST00000263253	NM_001429.3	65	Cag/Tag	2/31	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.224952280433776	2		730	796	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568623	41568623	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	139	535	0	ENST00000263253.7:c.4573G>C	p.Glu1525Gln	p.E1525Q	ENST00000263253	NM_001429.3	1525	Gaa/Caa	28/31	1	2	FACETS	1	0.973	1	1	0.992	1	CLONAL	2	TRUE	1	0.224952280433776	2		535	537	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260485	16260486	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	49	256	0	ENST00000375759.3:c.7756dup	p.Thr2586AsnfsTer10	p.T2586Nfs*10	ENST00000375759	NM_015001.2	2584	gaa/gAaa	11/15	1	2	FACETS	0.778	0.663	0.902	1	0.966	1	CLONAL	2	TRUE	1	0.224952280433776	2		256	280	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010930-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1225	144	819	0	ENST00000346208.3:c.1220_1221insA	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcAg	6/6	1	2	FACETS	0.945	0.86	1	0.945	0.86	1	CLONAL	1	TRUE	1	0.222504558505982	2		819	1369	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0010979-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	249	509	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.951	0.892	1	0.951	0.892	1	CLONAL	1	TRUE	1	0.610192899756639	2		509	858	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522551	176522551	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010979-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	470	643	1	ENST00000292408.4:c.1648G>T	p.Val550Leu	p.V550L	ENST00000292408	NM_213647.1	550	Gtg/Ttg	13/18	0.610192899756639	3	FACETS	0.949	0.91	0.988	0.949	0.91	0.988	CLONAL	2	TRUE	1	0.610192899756639	3		644	1059	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112315	115112316	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0010979-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	39	86	0	ENST00000257566.3:c.1424dup	p.Lys476GlnfsTer216	p.K476Qfs*216	ENST00000257566	NM_016569.3	475	ggc/ggGc	7/8	1	2	FACETS	0.954	0.807	1	0.954	0.807	1	CLONAL	1	TRUE	1	0.610192899756639	2		86	134	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863660	68863661	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCTGCCAAT	novel	NA	P-0010979-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	207	538	1	ENST00000261769.5:c.2403_2412dup	p.Asp805CysfsTer5	p.D805Cfs*5	ENST00000261769	NM_004360.3	800	cgc/cgCCCTGCCAATc	15/16	0.610192899756639	1	FACETS	0.803	0.75	0.857	0.803	0.75	0.857	CLONAL	1	TRUE	0	0.610192899756639	1		539	587	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691892	30691892	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs146497045	NA	P-0010979-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	200	450	0	ENST00000295754.5:c.394A>G	p.Thr132Ala	p.T132A	ENST00000295754	NM_003242.5	132	Act/Gct	3/7	1	2	FACETS	0.945	0.879	1	0.945	0.879	1	CLONAL	1	TRUE	1	0.610192899756639	2		450	694	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677802	47677802	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010979-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	296	671	1	ENST00000347630.2:c.1063T>C	p.Ser355Pro	p.S355P	ENST00000347630	NM_001007230.1	355	Tct/Cct	11/11	0.610192899756639	1	FACETS	0.967	0.917	1	0.967	0.917	1	CLONAL	1	TRUE	0	0.610192899756639	1		672	697	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372090	45372090	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010979-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	313	615	0	ENST00000262160.6:c.1079C>T	p.Pro360Leu	p.P360L	ENST00000262160	NM_005901.5	360	cCc/cTc	9/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.610192899756639	2		615	1007	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224555	123224555	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010979-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	436	1036	0	ENST00000218089.9:c.3408T>A	p.Asp1136Glu	p.D1136E	ENST00000218089	NM_001042749.1	1136	gaT/gaA	31/35	1	2	FACETS	0.97	0.924	1	0.97	0.924	1	CLONAL	1	TRUE	1	0.610192899756639	2		1036	1473	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249964	110250015	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGCTCAGCGACGCCTTCAGCACGAACTTGCCCATCAGCCCGCCACCTGGC	GGCGCTCAGCGACGCCTTCAGCACGAACTTGCCCATCAGCCCGCCACCTGGC	-	novel	NA	P-0010979-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	24	250	0	ENST00000374672.4:c.660_711del	p.Pro221LeufsTer88	p.P221Lfs*88	ENST00000374672	NM_004235.4	220	ccGCCAGGTGGCGGGCTGATGGGCAAGTTCGTGCTGAAGGCGTCGCTGAGCGCC/cc	3/5	0.610192899756639	1	FACETS	0.22	0.172	0.274	0.22	0.172	0.274	SUBCLONAL	1	TRUE	0	0.610192899756639	1		250	249	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552143	29552144	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1555613558	NA	P-0010979-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	315	729	0	ENST00000356175.3:c.1882dup	p.Tyr628LeufsTer6	p.Y628Lfs*6	ENST00000356175	NM_000267.3	626	ctt/cTtt	17/57	0.610192899756639	1	FACETS	0.943	0.895	0.991	0.943	0.895	0.991	CLONAL	1	TRUE	0	0.610192899756639	1		729	761	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458435	120458436	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs771237928	NA	P-0010979-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	160	347	0	ENST00000256646.2:c.6909dup	p.Ile2304HisfsTer9	p.I2304Hfs*9	ENST00000256646	NM_024408.3	2303	-/C	34/34	1	2	FACETS	0.92	0.848	0.994	0.92	0.848	0.994	CLONAL	1	TRUE	1	0.610192899756639	2		347	570	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039233	49039234	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0010979-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	281	675	0	ENST00000267163.4:c.2312_2313del	p.Tyr771CysfsTer23	p.Y771Cfs*23	ENST00000267163	NM_000321.2	771	TAt/t	22/27	0.542051988221209	1	FACETS	0.908	0.858	0.958	0.908	0.858	0.958	CLONAL	1	TRUE	0	0.610192899756639	1		675	705	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0010984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	119	313	2	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.302471340519649	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.35	1		315	483	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205838	108205838	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0010984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	103	298	0	ENST00000278616.4:c.8151+2T>A		p.X2717_splice	ENST00000278616	NM_000051.3	2717			0.233035905634768	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	0	0.35	1		298	481	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913078	32913078	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1671	365	1014	3	ENST00000380152.3:c.4586G>A	p.Gly1529Glu	p.G1529E	ENST00000380152		1529	gGg/gAg	11/27	0.179359826105912	3	FACETS	1	0.99	1	0.602	0.568	0.636	INDETERMINATE	1	TRUE	1	0.35	3		1017	2036	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930898	39930899	+	stop_gained,inframe_insertion	Nonsense_Mutation	INS	-	-	AGCAGCGGGTAGACATAAAATACTGTCCTCTTGTAATCCTTCCATCTATGT	novel	NA	P-0010984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	148	439	0	ENST00000378444.4:c.2998-6_3042dup	p.Ala1014_Tyr1015insThrTer	p.A1014_Y1015insT*	ENST00000378444	NM_001123385.1	1014	-/ACATAGATGGAAGGATTACAAGAGGACAGTATTTTATGTCTACCCGCTGCT	5/15	1	1	FACETS	0.715	0.652	0.781	0.715	0.652	0.781	SUBCLONAL	1	TRUE	0	0.35	1		439	976	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916649	178916667	+	protein_altering_variant	In_Frame_Del	DEL	CATCCACTTGATGCCCCCA	CATCCACTTGATGCCCCCA	GCAT	novel	NA	P-0010984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1394	245	870	0	ENST00000263967.3:c.36_54delinsGCAT	p.Ile13_Pro18delinsHis	p.I13_P18delinsH	ENST00000263967	NM_006218.2	12	ggCATCCACTTGATGCCCCCA/ggGCAT	2/21	1	2	FACETS	0.854	0.796	0.915	0.854	0.796	0.915	CLONAL	1	TRUE	1	0.35	2		870	1639	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0011005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	100	282	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.632	0.564	0.704	0.632	0.564	0.704	SUBCLONAL	1	TRUE	1	0.409177998085657	2		282	774	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041720	47041720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	137	320	0	ENST00000377604.3:c.1945C>T	p.Gln649Ter	p.Q649*	ENST00000377604	NM_001204468.1	649	Caa/Taa	17/24	1	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.409177998085657	1		320	473	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728705	190728705	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	139	481	0	ENST00000441310.2:c.2093A>T	p.Gln698Leu	p.Q698L	ENST00000441310	NM_000534.4	698	cAg/cTg	10/13	1	2	FACETS	0.928	0.846	1	0.928	0.846	1	CLONAL	1	TRUE	1	0.409177998085657	2		481	732	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223003	1223003	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	97	369	0	ENST00000326873.7:c.941del	p.Pro314LeufsTer22	p.P314Lfs*22	ENST00000326873	NM_000455.4	314	Cct/ct	8/10	0.374096085881453	1	FACETS	0.728	0.651	0.809	0.728	0.651	0.809	SUBCLONAL	1	TRUE	0	0.409177998085657	1		369	518	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872951	35872951	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1218	200	1077	0	ENST00000216797.5:c.281T>C	p.Ile94Thr	p.I94T	ENST00000216797	NM_020529.2	94	aTc/aCc	2/6	1	2	FACETS	0.689	0.637	0.744	0.689	0.637	0.744	SUBCLONAL	1	TRUE	1	0.409177998085657	2		1077	1418	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7218349	7218349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868127356	NA	P-0011005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	144	710	0	ENST00000380728.2:c.23C>T	p.Pro8Leu	p.P8L	ENST00000380728		8	cCc/cTc	2/11	1	2	FACETS	0.695	0.633	0.76	0.695	0.633	0.76	SUBCLONAL	1	TRUE	1	0.409177998085657	2		710	1013	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372144	45372144	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	124	606	0	ENST00000262160.6:c.1025G>T	p.Gly342Val	p.G342V	ENST00000262160	NM_005901.5	342	gGt/gTt	9/11	1	2	FACETS	0.615	0.556	0.678	0.615	0.556	0.678	SUBCLONAL	1	TRUE	1	0.409177998085657	2		606	985	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743935	40743935	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	133	479	2	ENST00000373198.4:c.3060G>A	p.Trp1020Ter	p.W1020*	ENST00000373198	NM_133170.3	1020	tgG/tgA	23/32	1	2	FACETS	0.779	0.708	0.855	0.779	0.708	0.855	SUBCLONAL	1	TRUE	1	0.409177998085657	2		481	834	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599926	10599927	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0011005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	185	770	0	ENST00000171111.5:c.1649_1650insA	p.Met550IlefsTer24	p.M550Ifs*24	ENST00000171111	NM_203500.1	550	atg/atAg	5/6	0.374096085881453	1	FACETS	0.737	0.68	0.796	0.737	0.68	0.796	SUBCLONAL	1	TRUE	0	0.409177998085657	1		770	976	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112164	115112164	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	108	584	0	ENST00000257566.3:c.1576del	p.Ala526ProfsTer106	p.A526Pfs*106	ENST00000257566	NM_016569.3	526	Gcc/cc	7/8	1	2	FACETS	0.612	0.549	0.68	0.612	0.549	0.68	SUBCLONAL	1	TRUE	1	0.409177998085657	2		584	862	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0011013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	221	247	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.555708462556288	3	FACETS	1	0.983	1	0.579	0.539	0.62	CLONAL	1	TRUE	1	0.555708462556288	3		247	878	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0011013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	261	368	1	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.955	0.895	1	0.955	0.895	1	CLONAL	1	TRUE	1	0.555708462556288	2		369	984	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0011013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	499	435	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.555708462556288	3	FACETS	0.988	0.949	1	0.988	0.949	1	CLONAL	2	TRUE	1	0.555708462556288	3		435	1161	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638491	176638491	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784096	NA	P-0011013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	269	380	0	ENST00000439151.2:c.3091C>T	p.Arg1031Ter	p.R1031*	ENST00000439151	NM_022455.4	1031	Cga/Tga	5/23	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.555708462556288	2		380	929	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262680	16262680	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	182	294	2	ENST00000375759.3:c.9950del	p.Pro3317ArgfsTer83	p.P3317Rfs*83	ENST00000375759	NM_015001.2	3315	caC/ca	11/15	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.555708462556288	2		296	649	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584514	48584514	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	219	287	0	ENST00000342988.3:c.692del	p.Gly231AlafsTer10	p.G231Afs*10	ENST00000342988	NM_005359.5	229	ctG/ct	6/12	0.555708462556288	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.555708462556288	1		287	548	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1387	377	552	0	ENST00000397062.3:c.246A>T	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaT	2/5	0.555708462556288	3	FACETS	0.983	0.93	1	0.491	0.465	0.519	CLONAL	1	TRUE	1	0.555708462556288	3		552	1764	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119910	70119910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1297203260	NA	P-0011013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	218	432	0	ENST00000245479.2:c.916del	p.Val306CysfsTer77	p.V306Cfs*77	ENST00000245479	NM_000346.3	304	ccG/cc	3/3	0.555708462556288	3	FACETS	0.909	0.845	0.976	0.454	0.422	0.488	CLONAL	1	TRUE	1	0.555708462556288	3		432	1103	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301147	65301147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	267	410	0	ENST00000342505.4:c.3301G>A	p.Val1101Ile	p.V1101I	ENST00000342505	NM_002227.2	1101	Gtc/Atc	24/25	1	2	FACETS	0.911	0.854	0.969	0.911	0.854	0.969	CLONAL	1	TRUE	1	0.555708462556288	2		410	1055	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593563	215593563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782662	NA	P-0011013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	202	371	1	ENST00000260947.4:c.2171C>T	p.Ala724Val	p.A724V	ENST00000260947	NM_000465.2	724	gCg/gTg	11/11	0.555708462556288	3	FACETS	0.853	0.79	0.919	0.427	0.395	0.46	CLONAL	1	TRUE	1	0.555708462556288	3		372	1089	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750536	41750536	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	290	412	1	ENST00000226382.2:c.92C>A	p.Ala31Asp	p.A31D	ENST00000226382	NM_003924.3	31	gCt/gAt	1/3	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.555708462556288	2		413	982	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524964	187524964	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	353	468	0	ENST00000441802.2:c.10716G>C	p.Gln3572His	p.Q3572H	ENST00000441802	NM_005245.3	3572	caG/caC	19/27	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.555708462556288	2		468	1153	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685331	86685331	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	139	180	0	ENST00000274376.6:c.3047G>A	p.Arg1016His	p.R1016H	ENST00000274376	NM_002890.2	1016	cGt/cAt	24/25	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.555708462556288	2		180	479	SUCCESS
APC	324	MSKCC	GRCh37	5	112173323	112173323	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	306	419	0	ENST00000257430.4:c.2032A>G	p.Ser678Gly	p.S678G	ENST00000257430	NM_000038.5	678	Agt/Ggt	16/16	1	2	FACETS	0.991	0.935	1	0.991	0.935	1	CLONAL	1	TRUE	1	0.555708462556288	2		419	1111	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397189	397189	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	345	495	0	ENST00000380956.4:c.574T>C	p.Tyr192His	p.Y192H	ENST00000380956	NM_001195286.1	192	Tac/Cac	5/9	0.555708462556288	3	FACETS	1	0.964	1	0.513	0.485	0.543	CLONAL	1	TRUE	1	0.555708462556288	3		495	1545	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164818	32164818	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	231	301	0	ENST00000375023.3:c.5084A>C	p.Asp1695Ala	p.D1695A	ENST00000375023	NM_004557.3	1695	gAc/gCc	28/30	0.555708462556288	3	FACETS	1	0.98	1	0.561	0.523	0.6	CLONAL	1	TRUE	1	0.555708462556288	3		301	947	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188935	32188935	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1568	126	655	0	ENST00000375023.3:c.619A>G	p.Lys207Glu	p.K207E	ENST00000375023	NM_004557.3	207	Aaa/Gaa	4/30	0.555708462556288	3	FACETS	0.342	0.308	0.378	0.171	0.154	0.189	SUBCLONAL	1	TRUE	1	0.555708462556288	3		655	1694	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508419	106508419	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	21	156	0	ENST00000359195.3:c.413T>C	p.Val138Ala	p.V138A	ENST00000359195	NM_002649.2	138	gTg/gCg	2/11	0.555708462556288	3	FACETS	0.243	0.186	0.309	0.121	0.093	0.155	SUBCLONAL	1	TRUE	1	0.555708462556288	3		156	398	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606233	93606233	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	348	473	0	ENST00000375746.1:c.53G>A	p.Gly18Asp	p.G18D	ENST00000375746	NM_001174167.1	18	gGc/gAc	2/14	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.555708462556288	2		473	1149	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738304	133738304	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	290	381	0	ENST00000318560.5:c.704G>T	p.Trp235Leu	p.W235L	ENST00000318560	NM_005157.4	235	tGg/tTg	4/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.555708462556288	2		381	959	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623560	43623560	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	46	243	0	ENST00000355710.3:c.3188G>A	p.Gly1063Asp	p.G1063D	ENST00000355710	NM_020975.4	1063	gGc/gAc	20/20	0.555708462556288	3	FACETS	0.276	0.231	0.325	0.138	0.115	0.163	SUBCLONAL	1	TRUE	1	0.555708462556288	3		243	767	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042403	42042403	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1569	575	879	4	ENST00000219905.7:c.6598C>T	p.Gln2200Ter	p.Q2200*	ENST00000219905	NM_001164273.1	2200	Cag/Tag	17/24	1	2	FACETS	0.965	0.925	1	0.965	0.925	1	CLONAL	1	TRUE	1	0.555708462556288	2		883	2144	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822319	72822319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1472	426	881	0	ENST00000268489.5:c.9856G>A	p.Ala3286Thr	p.A3286T	ENST00000268489	NM_006885.3	3286	Gca/Aca	10/10	1	2	FACETS	0.808	0.767	0.849	0.808	0.767	0.849	CLONAL	1	TRUE	1	0.555708462556288	2		881	1898	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830204	72830204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752051101	NA	P-0011013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	386	679	5	ENST00000268489.5:c.6377C>T	p.Ala2126Val	p.A2126V	ENST00000268489	NM_006885.3	2126	gCg/gTg	9/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.555708462556288	2		684	1324	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349466	89349466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749473676	NA	P-0011013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1299	568	903	2	ENST00000301030.4:c.3484G>A	p.Asp1162Asn	p.D1162N	ENST00000301030	NM_001256183.1	1162	Gac/Aac	9/13	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.555708462556288	2		905	1867	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572949	41572949	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	322	509	2	ENST00000263253.7:c.5234C>T	p.Ala1745Val	p.A1745V	ENST00000263253	NM_001429.3	1745	gCt/gTt	31/31	1	2	FACETS	0.983	0.928	1	0.983	0.928	1	CLONAL	1	TRUE	1	0.555708462556288	2		511	1179	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589626	67589627	+	inframe_insertion	In_Frame_Ins	INS	-	-	GATAGATTATATGAA	novel	NA	P-0011013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	104	208	0	ENST00000274335.5:c.1392_1406dup	p.Asp464_Glu468dup	p.D464_E468dup	ENST00000274335		464	-/GATAGATTATATGAA	10/15	1	2	FACETS	0.668	0.6	0.74	0.668	0.6	0.74	SUBCLONAL	1	TRUE	1	0.555708462556288	2		208	560	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119768	70119769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0011013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	590	543	0	ENST00000245479.2:c.774dup	p.Pro260AlafsTer36	p.P260Afs*36	ENST00000245479	NM_000346.3	257	cgc/cgCc	3/3	0.555708462556288	3	FACETS	0.939	0.904	0.975	0.939	0.904	0.975	CLONAL	2	TRUE	1	0.555708462556288	3		543	1445	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023827	27023827	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	302	420	0	ENST00000324856.7:c.936del	p.Gly314AlafsTer49	p.G314Afs*49	ENST00000324856	NM_006015.4	311	taC/ta	1/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.555708462556288	2		420	951	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932084	39932085	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1394942244	NA	P-0011013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	53	484	0	ENST00000378444.4:c.2514dup	p.Lys839GlnfsTer5	p.K839Qfs*5	ENST00000378444	NM_001123385.1	838	-/C	4/15	1	2	FACETS	0.182	0.154	0.213	0.182	0.154	0.213	SUBCLONAL	1	TRUE	1	0.555708462556288	2		484	1047	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538811	23538811	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	215	341	0	ENST00000380871.4:c.628del	p.Leu210TrpfsTer76	p.L210Wfs*76	ENST00000380871	NM_006167.3	210	Ctg/tg	2/2	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.555708462556288	2		341	768	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653850	89653850	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0011013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	453	240	0	ENST00000371953.3:c.148del	p.Ile50LeufsTer4	p.I50Lfs*4	ENST00000371953	NM_000314.4	50	Att/tt	2/9	0.555708462556288	3	FACETS	0.972	0.931	1	0.972	0.931	1	CLONAL	2	TRUE	1	0.555708462556288	3		240	1072	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	160	898	5	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.427019149698954	2		903	660	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151647	55151647	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs764174646	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	88	457	2	ENST00000257290.5:c.2438del	p.Asn813IlefsTer20	p.N813Ifs*20	ENST00000257290	NM_006206.4	811	tcA/tc	17/23	1	2	FACETS	0.908	0.808	1	0.908	0.808	1	CLONAL	1	TRUE	1	0.427019149698954	2		459	454	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	35	250	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	0.427019149698954	2		252	147	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087503	27087503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	135	563	0	ENST00000324856.7:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000324856	NM_006015.4	693	Cga/Tga	5/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.427019149698954	2		563	539	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	226	571	7	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.955	0.898	1	1	0.994	1	CLONAL	2	TRUE	1	0.427019149698954	2		578	554	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	103	425	0	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.427019149698954	2		425	367	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027087	71027087	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	99	371	1	ENST00000318789.4:c.1240del	p.Leu414Ter	p.L414*	ENST00000318789	NM_032682.5	414	Ctg/tg	15/21	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.427019149698954	2		372	450	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852527	63852527	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	84	385	0	ENST00000279873.7:c.3305C>A	p.Ser1102Tyr	p.S1102Y	ENST00000279873	NM_032199.2	1102	tCt/tAt	10/10	1	2	FACETS	0.996	0.885	1	0.996	0.885	1	CLONAL	1	TRUE	1	0.427019149698954	2		385	395	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	124	552	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.427019149698954	2	FACETS	1	0.912	1	0.502	0.456	0.551	CLONAL	1	TRUE	0	0.427019149698954	2		552	578	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438316	110438317	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	rs532810290	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	14	110	2	ENST00000375856.3:c.82_84dup	p.Asn28dup	p.N28dup	ENST00000375856	NM_003749.2	28	-/AAC	1/2	1	2	FACETS	0.426	0.309	0.565	0.426	0.309	0.565	SUBCLONAL	1	TRUE	1	0.427019149698954	2		112	154	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353819	15353819	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	58	392	1	ENST00000263377.2:c.3061del	p.His1021IlefsTer47	p.H1021Ifs*47	ENST00000263377	NM_058243.2	1021	Cat/at	14/20	1	2	FACETS	0.785	0.678	0.9	0.785	0.678	0.9	SUBCLONAL	1	TRUE	1	0.427019149698954	2		393	346	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161907	47161907	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	70	487	0	ENST00000409792.3:c.4219del	p.Arg1407GlyfsTer5	p.R1407Gfs*5	ENST00000409792	NM_014159.6	1407	Agg/gg	3/21	0.421207715866109	2	FACETS	0.705	0.616	0.8	0.353	0.308	0.4	SUBCLONAL	1	TRUE	0	0.427019149698954	2		487	465	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	199	453	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.421207715866109	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.427019149698954	2		453	430	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699283	117699283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144508898	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	61	471	1	ENST00000369458.3:c.358G>A	p.Val120Met	p.V120M	ENST00000369458	NM_024626.3	120	Gtg/Atg	3/6	1	2	FACETS	0.638	0.551	0.731	0.638	0.551	0.731	SUBCLONAL	1	TRUE	1	0.427019149698954	2		472	448	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	21	147	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	0.427019149698954	1	FACETS	0.604	0.471	0.755	0.604	0.471	0.755	SUBCLONAL	1	TRUE	0	0.427019149698954	1		147	128	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552144	29552144	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	98	441	1	ENST00000356175.3:c.1882del	p.Tyr628ThrfsTer3	p.Y628Tfs*3	ENST00000356175	NM_000267.3	626	cTt/ct	17/57	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.427019149698954	2		442	426	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs767894241	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	132	565	0	ENST00000358127.4:c.76dup	p.Val26GlyfsTer49	p.V26Gfs*49	ENST00000358127	NM_001280556.1	26	gtt/gGtt	2/10	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.427019149698954	2		565	605	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935606	13935606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326846768	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	74	381	1	ENST00000405192.2:c.1250G>A	p.Arg417His	p.R417H	ENST00000405192	NM_001163147.1	417	cGt/cAt	12/12	1	2	FACETS	0.971	0.856	1	0.971	0.856	1	CLONAL	1	TRUE	1	0.427019149698954	2		382	357	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023079	27023079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	44	131	0	ENST00000324856.7:c.185C>T	p.Ala62Val	p.A62V	ENST00000324856	NM_006015.4	62	gCc/gTc	1/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.427019149698954	2		131	142	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	143	591	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.427019149698954	2		591	634	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	103	540	5	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	1	2	FACETS	0.935	0.84	1	0.935	0.84	1	CLONAL	1	TRUE	1	0.427019149698954	2		545	516	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	152	656	1	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.427019149698954	2		657	621	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934645	9934645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1360906241	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	86	365	1	ENST00000330684.3:c.1510C>T	p.Arg504Trp	p.R504W	ENST00000330684	NM_001134407.1	504	Cgg/Tgg	7/13	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.427019149698954	2		366	397	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11313967	11313967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	141	649	4	ENST00000361445.4:c.769C>T	p.Arg257Trp	p.R257W	ENST00000361445	NM_004958.3	257	Cgg/Tgg	6/58	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.427019149698954	2		653	607	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726655	88726655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772754430	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	89	444	0	ENST00000360948.2:c.389G>A	p.Arg130His	p.R130H	ENST00000360948	NM_001012338.2	130	cGt/cAt	4/19	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.427019149698954	2		444	414	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345768	152345769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs759063323	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	78	393	0	ENST00000359321.1:c.801dup	p.His268ThrfsTer11	p.H268Tfs*11	ENST00000359321	NM_005431.1	267	-/A	3/3	1	2	FACETS	0.812	0.716	0.914	0.812	0.716	0.914	CLONAL	1	TRUE	1	0.427019149698954	2		393	450	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197427	26197427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	61	487	5	ENST00000356476.2:c.52C>T	p.Arg18Cys	p.R18C	ENST00000356476		18	Cgc/Tgc	1/1	0.421207715866109	2	FACETS	0.331	0.284	0.381	0.165	0.142	0.191	SUBCLONAL	1	TRUE	0	0.427019149698954	2		492	864	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562747	21562747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747638434	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	37	136	0	ENST00000382592.4:c.1172G>A	p.Arg391His	p.R391H	ENST00000382592	NM_014572.2	391	cGc/cAc	4/8	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.427019149698954	2		136	152	SUCCESS
APC	324	MSKCC	GRCh37	5	112175952	112175952	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587783031	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	38	238	0	ENST00000257430.4:c.4666del	p.Thr1556LeufsTer9	p.T1556Lfs*9	ENST00000257430	NM_000038.5	1554	gAa/ga	16/16	1	2	FACETS	0.682	0.567	0.809	0.682	0.567	0.809	SUBCLONAL	1	TRUE	1	0.427019149698954	2		238	261	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822586	72822586	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	124	615	5	ENST00000268489.5:c.9589del	p.Gln3197SerfsTer44	p.Q3197Sfs*44	ENST00000268489	NM_006885.3	3197	Cag/ag	10/10	1	2	FACETS	0.9	0.816	0.989	0.9	0.816	0.989	CLONAL	1	TRUE	1	0.427019149698954	2		620	645	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2488167	2488167	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	110	519	0	ENST00000355716.4:c.64A>G	p.Arg22Gly	p.R22G	ENST00000355716	NM_003820.2	22	Agg/Ggg	1/8	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.427019149698954	2		519	492	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107126	27107126	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	61	244	0	ENST00000324856.7:c.6737A>C	p.Glu2246Ala	p.E2246A	ENST00000324856	NM_006015.4	2246	gAg/gCg	20/20	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.427019149698954	2		244	285	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932161	36932161	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	165	699	2	ENST00000361632.4:c.2308T>C	p.Cys770Arg	p.C770R	ENST00000361632		770	Tgt/Cgt	16/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.427019149698954	2		701	644	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193172934	193172934	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	96	391	0	ENST00000367435.3:c.982T>C	p.Ser328Pro	p.S328P	ENST00000367435	NM_024529.4	328	Tct/Cct	11/17	1	2	FACETS	0.91	0.814	1	0.91	0.814	1	CLONAL	1	TRUE	1	0.427019149698954	2		391	494	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663779	241663779	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	48	190	0	ENST00000366560.3:c.1348A>G	p.Asn450Asp	p.N450D	ENST00000366560	NM_000143.3	450	Aat/Gat	9/10	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.427019149698954	2		190	198	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973061	25973061	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	99	534	0	ENST00000435504.4:c.1364C>T	p.Pro455Leu	p.P455L	ENST00000435504		455	cCg/cTg	12/13	1	2	FACETS	0.972	0.872	1	0.972	0.872	1	CLONAL	1	TRUE	1	0.427019149698954	2		534	477	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033679	48033679	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	62	370	0	ENST00000234420.5:c.3890G>A	p.Ser1297Asn	p.S1297N	ENST00000234420	NM_000179.2	1297	aGc/aAc	9/10	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.427019149698954	2		370	290	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61729424	61729424	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	68	384	0	ENST00000401558.2:c.323G>A	p.Gly108Asp	p.G108D	ENST00000401558	NM_003400.3	108	gGc/gAc	5/25	1	2	FACETS	0.854	0.747	0.968	0.854	0.747	0.968	CLONAL	1	TRUE	1	0.427019149698954	2		384	373	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090470	37090470	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs41542214	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	141	324	1	ENST00000231790.2:c.2065C>T	p.Gln689Ter	p.Q689*	ENST00000231790	NM_000249.3	689	Cag/Tag	18/19	0.421207715866109	2	FACETS	0.983	0.909	1	0.983	0.909	1	CLONAL	2	TRUE	0	0.427019149698954	2		325	336	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098610	47098610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778666	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	98	520	0	ENST00000409792.3:c.6664C>T	p.Pro2222Ser	p.P2222S	ENST00000409792	NM_014159.6	2222	Cca/Tca	15/21	0.421207715866109	2	FACETS	0.964	0.864	1	0.482	0.432	0.535	CLONAL	1	TRUE	0	0.427019149698954	2		520	476	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916935	178916935	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	105	583	0	ENST00000263967.3:c.322C>A	p.Arg108Ser	p.R108S	ENST00000263967	NM_006218.2	108	Cgt/Agt	2/21	1	2	FACETS	0.875	0.786	0.969	0.875	0.786	0.969	CLONAL	1	TRUE	1	0.427019149698954	2		583	562	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524402	187524402	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	92	450	0	ENST00000441802.2:c.11278T>C	p.Ser3760Pro	p.S3760P	ENST00000441802	NM_005245.3	3760	Tca/Cca	19/27	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.427019149698954	2		450	431	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294577	1294577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	40	207	1	ENST00000310581.5:c.424C>T	p.Arg142Cys	p.R142C	ENST00000310581	NM_198253.2	142	Cgc/Tgc	2/16	1	2	FACETS	0.918	0.771	1	0.918	0.771	1	CLONAL	1	TRUE	1	0.427019149698954	2		208	204	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160663	56160663	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558965285	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	106	429	1	ENST00000399503.3:c.937C>T	p.Arg313Trp	p.R313W	ENST00000399503	NM_005921.1	313	Cgg/Tgg	4/20	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.427019149698954	2		430	483	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056752	180056752	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368909190	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	104	622	0	ENST00000261937.6:c.760G>A	p.Val254Met	p.V254M	ENST00000261937	NM_182925.4	254	Gtg/Atg	6/30	1	2	FACETS	0.87	0.781	0.963	0.87	0.781	0.963	CLONAL	1	TRUE	1	0.427019149698954	2		622	560	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032224	26032224	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	29	448	0	ENST00000244661.2:c.65C>T	p.Ala22Val	p.A22V	ENST00000244661	NM_003537.3	22	gCt/gTt	1/1	0.421207715866109	2	FACETS	0.306	0.245	0.375	0.153	0.122	0.188	SUBCLONAL	1	TRUE	0	0.427019149698954	2		448	444	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553005	106553005	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs780342019	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	109	490	0	ENST00000369096.4:c.970A>G	p.Ile324Val	p.I324V	ENST00000369096	NM_001198.3	324	Atc/Gtc	5/7	1	2	FACETS	0.991	0.894	1	0.991	0.894	1	CLONAL	1	TRUE	1	0.427019149698954	2		490	515	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469884	157469884	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	97	501	0	ENST00000346085.5:c.2678C>A	p.Ala893Asp	p.A893D	ENST00000346085	NM_020732.3	893	gCt/gAt	9/20	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.427019149698954	2		501	453	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381447	81381447	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	49	511	0	ENST00000222390.5:c.614A>G	p.Gln205Arg	p.Q205R	ENST00000222390	NM_000601.4	205	cAg/cGg	5/18	1	2	FACETS	0.471	0.399	0.55	0.471	0.399	0.55	SUBCLONAL	1	TRUE	1	0.427019149698954	2		511	487	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864329	151864329	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	127	545	0	ENST00000262189.6:c.9652A>G	p.Thr3218Ala	p.T3218A	ENST00000262189	NM_170606.2	3218	Act/Gct	42/59	1	2	FACETS	0.917	0.832	1	0.917	0.832	1	CLONAL	1	TRUE	1	0.427019149698954	2		545	649	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752659	128752659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs977518778	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	25	363	0	ENST00000377970.2:c.820G>A	p.Glu274Lys	p.E274K	ENST00000377970	NM_002467.4	274	Gag/Aag	3/3	1	2	FACETS	0.303	0.238	0.377	0.303	0.238	0.377	SUBCLONAL	1	TRUE	1	0.427019149698954	2		363	387	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850811	63850811	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1322761667	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	112	493	1	ENST00000279873.7:c.1589C>T	p.Ala530Val	p.A530V	ENST00000279873	NM_032199.2	530	gCa/gTa	10/10	1	2	FACETS	0.988	0.892	1	0.988	0.892	1	CLONAL	1	TRUE	1	0.427019149698954	2		494	531	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344182	118344182	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	33	513	0	ENST00000534358.1:c.2308C>A	p.Leu770Ile	p.L770I	ENST00000534358	NM_005933.3	770	Ctc/Atc	3/36	1	2	FACETS	0.288	0.234	0.35	0.288	0.234	0.35	SUBCLONAL	1	TRUE	1	0.427019149698954	2		513	536	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022361	12022361	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	155	705	0	ENST00000396373.4:c.467A>G	p.Asn156Ser	p.N156S	ENST00000396373	NM_001987.4	156	aAc/aGc	5/8	0.11161557152982	3	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.427019149698954	3		705	709	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656215	18656215	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	56	270	0	ENST00000266497.5:c.2894G>C	p.Gly965Ala	p.G965A	ENST00000266497		965	gGa/gCa	21/31	1	2	FACETS	0.933	0.806	1	0.933	0.806	1	CLONAL	1	TRUE	1	0.427019149698954	2		270	281	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244127	46244127	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1300098322	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	89	412	0	ENST00000334344.6:c.2221A>G	p.Ser741Gly	p.S741G	ENST00000334344	NM_152641.2	741	Agt/Ggt	15/21	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.427019149698954	2		412	414	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26970491	26970491	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs201577656	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	57	315	0	ENST00000381527.3:c.860C>T	p.Thr287Met	p.T287M	ENST00000381527	NM_001260.1	287	aCg/aTg	8/13	1	2	FACETS	0.89	0.769	1	0.89	0.769	1	CLONAL	1	TRUE	1	0.427019149698954	2		315	300	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99454670	99454670	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs780247189	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	93	458	0	ENST00000268035.6:c.1589C>T	p.Ala530Val	p.A530V	ENST00000268035	NM_000875.3	530	gCa/gTa	7/21	1	2	FACETS	0.955	0.854	1	0.955	0.854	1	CLONAL	1	TRUE	1	0.427019149698954	2		458	456	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56839504	56839504	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	196	722	0	ENST00000308159.5:c.449C>T	p.Ala150Val	p.A150V	ENST00000308159	NM_014669.4	150	gCa/gTa	5/22	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.427019149698954	2		722	851	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110678	8110678	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs759268563	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	46	476	0	ENST00000585124.1:c.214T>C	p.Phe72Leu	p.F72L	ENST00000585124	NM_004217.3	72	Ttc/Ctc	5/9	1	2	FACETS	0.418	0.352	0.492	0.418	0.352	0.492	SUBCLONAL	1	TRUE	1	0.427019149698954	2		476	515	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961219	15961219	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1326344659	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	55	262	0	ENST00000268712.3:c.6168+2T>C		p.X2056_splice	ENST00000268712	NM_006311.3	2056			1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.427019149698954	2		262	254	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686961	37686961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367703051	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	112	493	2	ENST00000447079.4:c.3865G>A	p.Ala1289Thr	p.A1289T	ENST00000447079	NM_015083.1	1289	Gcc/Acc	14/14	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.427019149698954	2		495	466	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805910	46805910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	115	611	0	ENST00000290295.7:c.46G>A	p.Glu16Lys	p.E16K	ENST00000290295	NM_006361.5	16	Gaa/Aaa	1/2	0.427019149698954	2	FACETS	1	0.967	1	0.574	0.52	0.631	CLONAL	1	TRUE	0	0.427019149698954	2		611	469	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533556	63533556	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147716924	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	121	665	0	ENST00000307078.5:c.1598C>T	p.Ala533Val	p.A533V	ENST00000307078	NM_004655.3	533	gCg/gTg	6/11	0.427019149698954	2	FACETS	1	0.943	1	0.527	0.478	0.578	CLONAL	1	TRUE	0	0.427019149698954	2		665	538	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223404	2223404	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	116	543	0	ENST00000398665.3:c.3515T>C	p.Leu1172Pro	p.L1172P	ENST00000398665	NM_032482.2	1172	cTg/cCg	25/28	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.427019149698954	2		543	491	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226610	2226610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1390114953	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	71	371	0	ENST00000398665.3:c.4090G>A	p.Ala1364Thr	p.A1364T	ENST00000398665	NM_032482.2	1364	Gcc/Acc	27/28	1	2	FACETS	0.926	0.814	1	0.926	0.814	1	CLONAL	1	TRUE	1	0.427019149698954	2		371	359	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136120	11136120	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	143	661	0	ENST00000358026.2:c.3104T>C	p.Leu1035Pro	p.L1035P	ENST00000358026	NM_001128849.1	1035	cTg/cCg	22/36	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.427019149698954	2		661	620	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905752	50905752	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	45	666	0	ENST00000440232.2:c.800A>T	p.Glu267Val	p.E267V	ENST00000440232	NM_002691.3	267	gAg/gTg	7/27	1	2	FACETS	0.362	0.304	0.427	0.362	0.304	0.427	SUBCLONAL	1	TRUE	1	0.427019149698954	2		666	582	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910427	50910427	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750466994	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	122	716	2	ENST00000440232.2:c.1682G>A	p.Arg561Gln	p.R561Q	ENST00000440232	NM_002691.3	561	cGg/cAg	13/27	1	2	FACETS	0.879	0.796	0.966	0.879	0.796	0.966	CLONAL	1	TRUE	1	0.427019149698954	2		718	650	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074207	30074207	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765100922	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	88	658	0	ENST00000338641.4:c.1469C>T	p.Pro490Leu	p.P490L	ENST00000338641	NM_000268.3	490	cCg/cTg	14/16	1	2	FACETS	0.619	0.548	0.694	0.619	0.548	0.694	SUBCLONAL	1	TRUE	1	0.427019149698954	2		658	666	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568502	41568502	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	84	260	0	ENST00000263253.7:c.4453-1G>A		p.X1485_splice	ENST00000263253	NM_001429.3	1485			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.427019149698954	2		260	307	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426305	47426305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	172	385	0	ENST00000377045.4:c.722C>T	p.Thr241Ile	p.T241I	ENST00000377045	NM_001654.4	241	aCt/aTt	8/16	1	1	FACETS	0.861	0.804	0.918	1	0.993	1	CLONAL	2	TRUE	0	0.427019149698954	1		385	368	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650793	37650795	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	92	506	1	ENST00000447079.4:c.2269_2271del	p.Lys757del	p.K757del	ENST00000447079	NM_015083.1	755	ctGAAg/ctg	5/14	1	2	FACETS	0.824	0.734	0.919	0.824	0.734	0.919	CLONAL	1	TRUE	1	0.427019149698954	2		507	523	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90995032	90995032	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	68	345	0	ENST00000265433.3:c.89del	p.Asn30ThrfsTer5	p.N30Tfs*5	ENST00000265433	NM_002485.4	30	aAc/ac	2/16	1	2	FACETS	0.815	0.712	0.924	0.815	0.712	0.924	CLONAL	1	TRUE	1	0.427019149698954	2		345	391	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24134056	24134057	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	115	618	0	ENST00000263121.7:c.214dup	p.Thr72AsnfsTer4	p.T72Nfs*4	ENST00000263121	NM_003073.3	69	-/A	2/9	1	2	FACETS	0.86	0.777	0.948	0.86	0.777	0.948	CLONAL	1	TRUE	1	0.427019149698954	2		618	626	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270726	10270726	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	97	469	0	ENST00000340748.4:c.1009del	p.Met337TrpfsTer8	p.M337Wfs*8	ENST00000340748		337	Atg/tg	14/40	1	2	FACETS	0.981	0.879	1	0.981	0.879	1	CLONAL	1	TRUE	1	0.427019149698954	2		469	463	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716002	52716002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	110	603	0	ENST00000322088.6:c.571del	p.Glu191SerfsTer39	p.E191Sfs*39	ENST00000322088	NM_014225.5	189	ctG/ct	5/15	1	2	FACETS	0.97	0.875	1	0.97	0.875	1	CLONAL	1	TRUE	1	0.427019149698954	2		603	531	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270529	98270530	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs751977093	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	39	287	0	ENST00000331920.6:c.114dup	p.Leu39AlafsTer51	p.L39Afs*51	ENST00000331920	NM_000264.3	38	-/G	1/24	1	2	FACETS	0.774	0.646	0.914	0.774	0.646	0.914	CLONAL	1	TRUE	1	0.427019149698954	2		287	236	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550472	29550473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs786204255	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	33	274	0	ENST00000356175.3:c.1738dup	p.Tyr580LeufsTer8	p.Y580Lfs*8	ENST00000356175	NM_000267.3	578	ctt/cTtt	16/57	1	2	FACETS	0.546	0.446	0.658	0.546	0.446	0.658	SUBCLONAL	1	TRUE	1	0.427019149698954	2		274	283	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447401	49447402	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CA	CA	-	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	104	441	0	ENST00000301067.7:c.696_697del	p.Cys232Ter	p.C232*	ENST00000301067	NM_003482.3	232	tgTGag/tgag	6/54	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.427019149698954	2		441	446	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50482355	50482355	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	104	461	0	ENST00000394963.4:c.711del	p.Phe237LeufsTer5	p.F237Lfs*5	ENST00000394963	NM_003076.4	236	Ttt/tt	6/13	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.427019149698954	2		461	438	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023186	48023189	+	frameshift_variant	Frame_Shift_Del	DEL	AGGA	AGGA	-	novel	NA	P-0011071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	191	891	0	ENST00000234420.5:c.613_616del	p.Glu205LysfsTer5	p.E205Kfs*5	ENST00000234420	NM_000179.2	204	gAGGAa/ga	3/10	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.427019149698954	2		891	886	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256075	16256075	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0011146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	206	302	1	ENST00000375759.3:c.3340A>T	p.Lys1114Ter	p.K1114*	ENST00000375759	NM_015001.2	1114	Aaa/Taa	11/15	0.420227172893637	3	FACETS	1	0.975	1	0.558	0.517	0.6	CLONAL	1	TRUE	1	0.41869197221517	3		303	1067	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274586	198274586	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	459	383	0	ENST00000335508.6:c.812G>A	p.Gly271Asp	p.G271D	ENST00000335508	NM_012433.2	271	gGt/gAt	7/25	0.420227172893637	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.41869197221517	3		383	1130	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285182	212285182	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	257	302	0	ENST00000342788.4:c.3119G>A	p.Arg1040Lys	p.R1040K	ENST00000342788	NM_005235.2	1040	aGa/aAa	25/28	0.420227172893637	3	FACETS	0.953	0.896	1	0.953	0.896	1	CLONAL	2	TRUE	1	0.41869197221517	3		302	779	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715387	117715387	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	329	351	0	ENST00000368508.3:c.1102T>A	p.Leu368Ile	p.L368I	ENST00000368508	NM_002944.2	368	Tta/Ata	10/43	NA	2	FACETS	1	0.962	1			1	INDETERMINATE	2	TRUE	NA	0.41869197221517	2		351	775	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443969	49443969	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	177	292	0	ENST00000301067.7:c.3402G>C	p.Gln1134His	p.Q1134H	ENST00000301067	NM_003482.3	1134	caG/caC	11/54	NA	2	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.41869197221517	2		292	813	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350402	89350402	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2011	706	767	0	ENST00000301030.4:c.2548T>A	p.Phe850Ile	p.F850I	ENST00000301030	NM_001256183.1	850	Ttt/Att	9/13	0.420227172893637	5	FACETS	1	0.97	1	0.404	0.388	0.42	CLONAL	2	TRUE	0	0.41869197221517	5		767	2717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	456	446	0	ENST00000269305.4:c.799C>G	p.Arg267Gly	p.R267G	ENST00000269305	NM_001126112.2	267	Cgg/Ggg	8/11	0.420227172893637	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.41869197221517	2		446	1013	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725011	47725047	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGCCTGCCCCCCGAGTCCCTGACGTCCACCGGGCG	GGGGCCTGCCCCCCGAGTCCCTGACGTCCACCGGGCG	-	novel	NA	P-0011146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	235	509	0	ENST00000449228.1:c.697_733del	p.Arg233SerfsTer45	p.R233Sfs*45	ENST00000449228	NM_001127240.2	233	CGCCCGGTGGACGTCAGGGACTCGGGGGGCAGGCCCCtc/tc	4/4	0.145138571759044	5	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.41869197221517	5		509	1319	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762935	40762936	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0011146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	187	365	0	ENST00000392038.2:c.72dup	p.Arg25ThrfsTer22	p.R25Tfs*22	ENST00000392038	NM_001626.4	24	-/A	3/14	0.412320949163288	4	FACETS	1	0.935	1	0.508	0.468	0.55	CLONAL	1	TRUE	2	0.41869197221517	4		365	1247	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725099	47725100	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGGGCAGGAGTCCCTTACCC	novel	NA	P-0011146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	151	424	0	ENST00000449228.1:c.644_645insGGGTAAGGGACTCCTGCCCT	p.Thr216GlyfsTer20	p.T216Gfs*20	ENST00000449228	NM_001127240.2	215	ctt/ctGGGTAAGGGACTCCTGCCCTt	4/4	0.145138571759044	5	FACETS	0.885	0.807	0.967			1	INDETERMINATE	1	TRUE	NA	0.41869197221517	5		424	1327	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0011187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	382	204	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	NA	2	FACETS	0.915	0.881	0.949			1	INDETERMINATE	2	TRUE	NA	0.693465187561405	2		204	602	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	154	140	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.974	0.899	1	0.974	0.899	1	CLONAL	1	TRUE	1	0.693465187561405	2		140	456	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772950	135772951	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs118203724	NA	P-0011187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	229	737	0	ENST00000298552.3:c.2672dup	p.Asn891LysfsTer13	p.N891Kfs*13	ENST00000298552	NM_001162426.1	891	aac/aaAc	21/23	0.693465187561405	1	FACETS	0.787	0.74	0.835	0.787	0.74	0.835	SUBCLONAL	1	TRUE	0	0.693465187561405	1		737	548	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001348	29001348	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	118	849	0	ENST00000282397.4:c.1384C>A	p.Pro462Thr	p.P462T	ENST00000282397	NM_002019.4	462	Cct/Act	10/30	1	2	FACETS	0.406	0.366	0.449	0.406	0.366	0.449	SUBCLONAL	1	TRUE	1	0.693465187561405	2		849	838	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259047	89259047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	66	522	2	ENST00000336596.2:c.191C>T	p.Pro64Leu	p.P64L	ENST00000336596	NM_005233.5	64	cCc/cTc	3/17	1	2	FACETS	0.289	0.25	0.331	0.289	0.25	0.331	SUBCLONAL	1	TRUE	1	0.693465187561405	2		524	659	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250601	26250601	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	527	1688	0	ENST00000446824.2:c.233A>T	p.Asp78Val	p.D78V	ENST00000446824	NM_021018.2	78	gAc/gTc	1/1	1	2	FACETS	0.942	0.902	0.982	0.942	0.902	0.982	CLONAL	1	TRUE	1	0.693465187561405	2		1688	1614	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	493259	493259	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1231	161	980	0	ENST00000399788.2:c.304G>A	p.Gly102Arg	p.G102R	ENST00000399788	NM_001042603.1	102	Gga/Aga	3/28	0.685795624092801	3	FACETS	0.449	0.411	0.49	0.225	0.205	0.245	SUBCLONAL	1	TRUE	1	0.693465187561405	3		980	1392	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44896898	44896898	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0011187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	512	705	0	ENST00000377967.4:c.620-2A>T		p.X207_splice	ENST00000377967	NM_021140.2	207			1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.693465187561405	1		705	692	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041559	47041559	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0011187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	63	444	0	ENST00000377604.3:c.1786-2A>T		p.X596_splice	ENST00000377604	NM_001204468.1	596			1	1	FACETS	0.246	0.213	0.282	0.246	0.213	0.282	SUBCLONAL	1	TRUE	0	0.693465187561405	1		444	482	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425238	49425257	+	frameshift_variant	Frame_Shift_Del	DEL	TGCTTGATGCTGAGTTGGGA	TGCTTGATGCTGAGTTGGGA	-	novel	NA	P-0011187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	330	934	0	ENST00000301067.7:c.13231_13250del	p.Ser4411GlyfsTer69	p.S4411Gfs*69	ENST00000301067	NM_003482.3	4411	TCCCAACTCAGCATCAAGCAg/g	39/54	0.685795624092801	3	FACETS	1	0.965	1	0.514	0.485	0.543	CLONAL	1	TRUE	1	0.693465187561405	3		934	1247	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0011189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1271	158	468	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.288105183256493	4	FACETS	0.989	0.903	1			1	CLONAL	1	TRUE	NA	0.288105183256493	4		468	1429	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720833	89720836	+	frameshift_variant	Frame_Shift_Del	DEL	AAAT	AAAT	-	rs587782304	NA	P-0011189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	55	199	0	ENST00000371953.3:c.987_990del	p.Asn329LysfsTer14	p.N329Kfs*14	ENST00000371953	NM_000314.4	328	gcAAAT/gc	8/9	0.277157920319668	1	FACETS	0.797	0.684	0.92	0.797	0.684	0.92	CLONAL	1	TRUE	0	0.288105183256493	1		199	410	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0011189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	285	385	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.288105183256493	4	FACETS	1	0.985	1			1	CLONAL	2	TRUE	NA	0.288105183256493	4		385	1121	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604778	48604778	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767383	NA	P-0011189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	162	431	0	ENST00000342988.3:c.1600C>T	p.Gln534Ter	p.Q534*	ENST00000342988	NM_005359.5	534	Cag/Tag	12/12	0.288105183256493	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.288105183256493	1		431	900	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170814959	170814959	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	69	232	0	ENST00000296930.5:c.7G>C	p.Asp3His	p.D3H	ENST00000296930	NM_002520.6	3	Gat/Cat	1/11	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.288105183256493	2		232	440	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707822	176707822	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	123	444	0	ENST00000439151.2:c.5879C>G	p.Thr1960Arg	p.T1960R	ENST00000439151	NM_022455.4	1960	aCa/aGa	18/23	1	2	FACETS	0.916	0.828	1	0.916	0.828	1	CLONAL	1	TRUE	1	0.288105183256493	2		444	932	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039419	47039419	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	160	531	0	ENST00000377604.3:c.1042A>T	p.Ile348Phe	p.I348F	ENST00000377604	NM_001204468.1	348	Atc/Ttc	10/24	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.288105183256493	2		531	1083	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441468	40441469	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCGCT	novel	NA	P-0011189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	152	546	0	ENST00000345506.4:c.44_48dup	p.Gln17CysfsTer69	p.Q17Cfs*69	ENST00000345506	NM_003152.3	13	-/GCGCT	3/20	1	2	FACETS	0.936	0.855	1	0.936	0.855	1	CLONAL	1	TRUE	1	0.288105183256493	2		546	1127	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0011268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	300	282	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.963	0.909	1	1	0.996	1	CLONAL	3	TRUE	1	0.208036660876048	2		282	998	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0011268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	39	393	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.208036660876048	2		393	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0011268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	97	312	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.208036660876048	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.208036660876048	1		312	630	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971194	21971194	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs561034503	NA	P-0011268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	28	110	0	ENST00000304494.5:c.164G>T	p.Gly55Val	p.G55V	ENST00000304494	NM_000077.4	55	gGc/gTc	2/3	1	2	FACETS	0.99	0.794	1	0.99	0.794	1	CLONAL	1	TRUE	1	0.208036660876048	2		110	272	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257453	16257453	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1462210106	NA	P-0011268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	67	437	0	ENST00000375759.3:c.4718C>T	p.Thr1573Ile	p.T1573I	ENST00000375759	NM_015001.2	1573	aCt/aTt	11/15	1	2	FACETS	0.87	0.755	0.995	0.87	0.755	0.995	CLONAL	1	TRUE	1	0.208036660876048	2		437	740	SUCCESS
ALK	238	MSKCC	GRCh37	2	29541192	29541192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372456536	NA	P-0011268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	75	452	2	ENST00000389048.3:c.1625C>T	p.Pro542Leu	p.P542L	ENST00000389048	NM_004304.4	542	cCg/cTg	8/29	1	2	FACETS	0.851	0.745	0.967	0.851	0.745	0.967	CLONAL	1	TRUE	1	0.208036660876048	2		454	847	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89478315	89478315	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	29	264	0	ENST00000336596.2:c.2134C>G	p.Arg712Gly	p.R712G	ENST00000336596	NM_005233.5	712	Cgt/Ggt	12/17	1	2	FACETS	0.706	0.566	0.864	0.706	0.566	0.864	SUBCLONAL	1	TRUE	1	0.208036660876048	2		264	395	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146565	55146565	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	53	349	0	ENST00000257290.5:c.2239G>C	p.Glu747Gln	p.E747Q	ENST00000257290	NM_006206.4	747	Gaa/Caa	16/23	1	2	FACETS	0.744	0.633	0.865	0.744	0.633	0.865	SUBCLONAL	1	TRUE	1	0.208036660876048	2		349	685	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400138	139400138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1434047791	NA	P-0011268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	74	453	0	ENST00000277541.6:c.4210G>A	p.Glu1404Lys	p.E1404K	ENST00000277541	NM_017617.3	1404	Gag/Aag	25/34	1	2	FACETS	0.886	0.774	1	0.886	0.774	1	CLONAL	1	TRUE	1	0.208036660876048	2		453	803	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039893	47039893	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	71	332	0	ENST00000377604.3:c.1236G>T	p.Trp412Cys	p.W412C	ENST00000377604	NM_001204468.1	412	tgG/tgT	12/24	0.208036660876048	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.208036660876048	1		332	520	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224455	123224455	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	109	557	0	ENST00000218089.9:c.3308G>A	p.Trp1103Ter	p.W1103*	ENST00000218089	NM_001042749.1	1103	tGg/tAg	31/35	0.208036660876048	1	FACETS	0.883	0.791	0.981	0.883	0.791	0.981	CLONAL	1	TRUE	0	0.208036660876048	1		557	1063	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974819	21974819	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	17	90	0	ENST00000304494.5:c.8del	p.Pro3ArgfsTer23	p.P3Rfs*23	ENST00000304494	NM_000077.4	3	cCg/cg	1/3	1				0.744	1				CLONAL	1	TRUE	1	0.208036660876048	2		90	165	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499368	89499369	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0011268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	64	372	0	ENST00000336596.2:c.2539dup	p.Met847AsnfsTer26	p.M847Nfs*26	ENST00000336596	NM_005233.5	846	-/A	15/17	1	2	FACETS	0.843	0.729	0.967	0.843	0.729	0.967	CLONAL	1	TRUE	1	0.208036660876048	2		372	730	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579345	7579346	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0011276-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	290	556	0	ENST00000269305.4:c.341dup	p.Leu114PhefsTer35	p.L114Ffs*35	ENST00000269305	NM_001126112.2	114	ttg/ttTg	4/11	0.246639060160727	2	FACETS	0.927	0.871	0.985	0.927	0.871	0.985	CLONAL	2	TRUE	0	0.246639060160727	2		556	1268	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438020	110438020	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1226502838	NA	P-0011276-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	114	265	0	ENST00000375856.3:c.381G>C	p.Glu127Asp	p.E127D	ENST00000375856	NM_003749.2	127	gaG/gaC	1/2	0.240266340259369	4	FACETS	1	0.969	1	0.298	0.268	0.331	CLONAL	1	TRUE	0	0.246639060160727	4		265	966	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	241	786	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.352704011639977	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.380428244202015	2		786	606	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439341	149439341	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	153	836	0	ENST00000286301.3:c.2054C>A	p.Pro685His	p.P685H	ENST00000286301	NM_005211.3	685	cCc/cAc	15/22	0.315833758914436	2	FACETS	1	0.987	1	0.697	0.641	0.755	CLONAL	1	TRUE	0	0.380428244202015	2		836	577	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870231	44870231	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	152	623	3	ENST00000377967.4:c.410G>T	p.Gly137Val	p.G137V	ENST00000377967	NM_021140.2	137	gGt/gTt	5/29	0.267355363852579	2	FACETS	1	0.971	1			1	CLONAL	2	TRUE	NA	0.380428244202015	2		626	366	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	201	995	0	ENST00000269305.4:c.853G>C	p.Glu285Gln	p.E285Q	ENST00000269305	NM_001126112.2	285	Gag/Cag	8/11	0.352704011639977	2	FACETS	1	0.986	1	0.621	0.576	0.667	CLONAL	1	TRUE	0	0.380428244202015	2		995	851	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102078	27102078	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	107	1168	0	ENST00000324856.7:c.5004G>T	p.Glu1668Asp	p.E1668D	ENST00000324856	NM_006015.4	1668	gaG/gaT	19/20	1	2	FACETS	0.7	0.627	0.777	0.7	0.627	0.777	SUBCLONAL	1	TRUE	1	0.380428244202015	2		1168	804	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025945	48025945	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	268	1047	0	ENST00000234420.5:c.823A>G	p.Ser275Gly	p.S275G	ENST00000234420	NM_000179.2	275	Agt/Ggt	4/10	0.3798958209712	2	FACETS	0.902	0.849	0.956	0.902	0.849	0.956	CLONAL	2	TRUE	0	0.380428244202015	2		1047	781	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008571	70008571	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	48	340	0	ENST00000394351.3:c.858G>T	p.Gln286His	p.Q286H	ENST00000394351	NM_000248.3	286	caG/caT	8/9	1	2	FACETS	0.769	0.653	0.896	0.769	0.653	0.896	SUBCLONAL	1	TRUE	1	0.380428244202015	2		340	328	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021779	71021779	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	84	847	0	ENST00000318789.4:c.1579G>A	p.Glu527Lys	p.E527K	ENST00000318789	NM_032682.5	527	Gaa/Aaa	18/21	1	2	FACETS	0.694	0.614	0.781	0.694	0.614	0.781	SUBCLONAL	1	TRUE	1	0.380428244202015	2		847	636	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468399	89468399	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	48	440	0	ENST00000336596.2:c.1933A>G	p.Lys645Glu	p.K645E	ENST00000336596	NM_005233.5	645	Aaa/Gaa	11/17	1	2	FACETS	0.806	0.685	0.938	0.806	0.685	0.938	CLONAL	1	TRUE	1	0.380428244202015	2		440	313	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670744	134670744	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	56	615	1	ENST00000398015.3:c.655G>C	p.Val219Leu	p.V219L	ENST00000398015	NM_004441.4	219	Gtg/Ctg	3/16	1	2	FACETS	0.874	0.752	1	0.874	0.752	1	CLONAL	1	TRUE	1	0.380428244202015	2		616	337	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968233	134968233	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	79	968	1	ENST00000398015.3:c.2746G>T	p.Val916Leu	p.V916L	ENST00000398015	NM_004441.4	916	Gtg/Ttg	15/16	1	2	FACETS	0.658	0.579	0.743	0.658	0.579	0.743	SUBCLONAL	1	TRUE	1	0.380428244202015	2		969	631	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970884	55970884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	185	879	1	ENST00000263923.4:c.1913G>A	p.Gly638Glu	p.G638E	ENST00000263923	NM_002253.2	638	gGa/gAa	13/30	0.32850986016364	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.380428244202015	1		880	667	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197555	106197555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	199	962	0	ENST00000380013.4:c.5888C>T	p.Thr1963Ile	p.T1963I	ENST00000380013	NM_001127208.2	1963	aCt/aTt	11/11	0.292410330746697	3	FACETS	1	0.99	1	0.708	0.657	0.762	CLONAL	1	TRUE	1	0.380428244202015	3		962	879	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143029251	143029251	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	21	505	0	ENST00000262992.4:c.2369C>T	p.Pro790Leu	p.P790L	ENST00000262992	NM_001101669.1	790	cCt/cTt	21/24	0.292410330746697	3	FACETS	0.383	0.295	0.486	0.192	0.147	0.243	SUBCLONAL	1	TRUE	1	0.380428244202015	3		505	343	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143129593	143129593	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	37	630	0	ENST00000262992.4:c.1057A>G	p.Ser353Gly	p.S353G	ENST00000262992	NM_001101669.1	353	Agc/Ggc	12/24	0.292410330746697	3	FACETS	0.621	0.512	0.741	0.31	0.256	0.371	SUBCLONAL	1	TRUE	1	0.380428244202015	3		630	373	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542399	187542399	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	59	738	0	ENST00000441802.2:c.5341A>T	p.Asn1781Tyr	p.N1781Y	ENST00000441802	NM_005245.3	1781	Aac/Tac	10/27	1	2	FACETS	0.755	0.651	0.866	0.755	0.651	0.866	SUBCLONAL	1	TRUE	1	0.380428244202015	2		738	411	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750453	57750453	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	101	936	1	ENST00000274289.3:c.2015G>T	p.Arg672Leu	p.R672L	ENST00000274289	NM_006622.3	672	cGa/cTa	14/14	0.380428244202015	3	FACETS	1	0.941	1	0.536	0.48	0.596	CLONAL	1	TRUE	1	0.380428244202015	3		937	589	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056519	26056519	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs775151245	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	78	282	0	ENST00000343677.2:c.138G>T	p.Lys46Asn	p.K46N	ENST00000343677	NM_005319.3	46	aaG/aaT	1/1	0.380428244202015	4	FACETS	1	0.953	1	0.584	0.514	0.658	CLONAL	1	TRUE	2	0.380428244202015	4		282	485	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225519	26225519	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1460	257	1759	1	ENST00000360408.1:c.137C>A	p.Thr46Asn	p.T46N	ENST00000360408	NM_003532.2	46	aCc/aAc	1/1	0.380428244202015	4	FACETS	1	0.974	1	0.543	0.507	0.581	CLONAL	1	TRUE	2	0.380428244202015	4		1760	1717	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233050	55233050	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	7137	764	2	ENST00000275493.2:c.1800G>T	p.Met600Ile	p.M600I	ENST00000275493	NM_005228.3	600	atG/atT	15/28	0.380428244202015	45	FACETS	0.992	0.988	0.996			1	CLONAL	46	TRUE	NA	0.380428244202015	45		766	7547	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633340	8633340	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	84	1022	0	ENST00000356435.5:c.329C>T	p.Ser110Phe	p.S110F	ENST00000356435		110	tCc/tTc	3/35	0.163911013671385	2	FACETS	0.731	0.646	0.822	0.366	0.323	0.411	INDETERMINATE	1	TRUE	0	0.380428244202015	2		1022	604	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63760000	63760000	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	184	582	0	ENST00000279873.7:c.653G>T	p.Arg218Met	p.R218M	ENST00000279873	NM_032199.2	218	aGg/aTg	4/10	0.295898783959968	4	FACETS	0.999	0.926	1	0.5	0.463	0.538	CLONAL	2	TRUE	0	0.380428244202015	4		582	668	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111958635	111958635	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	117	518	0	ENST00000375549.3:c.107A>T	p.Gln36Leu	p.Q36L	ENST00000375549	NM_003002.3	36	cAg/cTg	2/4	0.380428244202015	3	FACETS	0.787	0.714	0.863	0.525	0.476	0.576	SUBCLONAL	2	TRUE	0	0.380428244202015	3		518	465	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975688	26975688	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	202	1167	2	ENST00000381527.3:c.1196C>A	p.Pro399His	p.P399H	ENST00000381527	NM_001260.1	399	cCc/cAc	12/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.380428244202015	2		1169	883	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436216	110436216	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	87	496	0	ENST00000375856.3:c.2185G>T	p.Ala729Ser	p.A729S	ENST00000375856	NM_003749.2	729	Gcc/Tcc	1/2	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.380428244202015	2		496	369	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95579545	95579545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	28	414	0	ENST00000393063.1:c.1924C>T	p.Pro642Ser	p.P642S	ENST00000393063	NM_030621.3	642	Cca/Tca	13/28	0.163911013671385	2	FACETS	0.549	0.44	0.673	0.275	0.22	0.337	INDETERMINATE	1	TRUE	0	0.380428244202015	2		414	268	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472450	88472450	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	130	826	0	ENST00000360948.2:c.2105G>T	p.Arg702Ile	p.R702I	ENST00000360948	NM_001012338.2	702	aGa/aTa	16/19	0.380428244202015	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.380428244202015	1		826	494	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442735	99442735	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	234	995	0	ENST00000268035.6:c.1132A>G	p.Met378Val	p.M378V	ENST00000268035	NM_000875.3	378	Atg/Gtg	5/21	0.380428244202015	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.380428244202015	1		995	827	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220682	2220682	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	167	1028	2	ENST00000326181.6:c.299G>T	p.Ser100Ile	p.S100I	ENST00000326181	NM_032271.2	100	aGc/aTc	5/21	0.380428244202015	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.380428244202015	1		1030	509	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858247	9858247	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	57	834	0	ENST00000330684.3:c.3154C>G	p.Leu1052Val	p.L1052V	ENST00000330684	NM_001134407.1	1052	Ctt/Gtt	13/13	0.380428244202015	1	FACETS	0.493	0.423	0.569	0.493	0.423	0.569	SUBCLONAL	1	TRUE	0	0.380428244202015	1		834	492	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736898	736898	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1187921871	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	55	940	0	ENST00000314574.4:c.1201A>G	p.Asn401Asp	p.N401D	ENST00000314574	NM_005433.3	401	Aat/Gat	10/12	0.163911013671385	2	FACETS	0.653	0.559	0.754	0.326	0.279	0.377	INDETERMINATE	1	TRUE	0	0.380428244202015	2		940	443	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117327	7117327	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	224	927	1	ENST00000302850.5:c.3889A>T	p.Ser1297Cys	p.S1297C	ENST00000302850	NM_000208.2	1297	Agc/Tgc	22/22	0.3798958209712	2	FACETS	0.936	0.877	0.996	0.936	0.877	0.996	CLONAL	2	TRUE	0	0.380428244202015	2		928	629	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791393	42791393	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	190	874	3	ENST00000575354.2:c.452+1G>T		p.X151_splice	ENST00000575354	NM_015125.3	151			0.3798958209712	2	FACETS	0.837	0.778	0.897	0.837	0.778	0.897	CLONAL	2	TRUE	0	0.380428244202015	2		877	597	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019150	31019150	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	63	976	0	ENST00000375687.4:c.745G>C	p.Glu249Gln	p.E249Q	ENST00000375687	NM_015338.5	249	Gaa/Caa	9/13	0.3798958209712	2	FACETS	0.41	0.354	0.471	0.205	0.177	0.236	SUBCLONAL	1	TRUE	0	0.380428244202015	2		976	808	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386436	31386436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs577581342	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	51	768	1	ENST00000328111.2:c.1661C>T	p.Thr554Met	p.T554M	ENST00000328111	NM_006892.3	554	aCg/aTg	15/23	0.3798958209712	2	FACETS	0.432	0.366	0.504	0.216	0.183	0.252	SUBCLONAL	1	TRUE	0	0.380428244202015	2		769	621	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007791	45007801	+	frameshift_variant	Frame_Shift_Del	DEL	TGGTCTTTCTA	TGGTCTTTCTA	-	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	121	762	0	ENST00000558401.1:c.239_249del	p.Trp80SerfsTer6	p.W80Sfs*6	ENST00000558401	NM_004048.2	80	TGGTCTTTCTAt/t	2/4	0.380428244202015	1	FACETS	0.743	0.672	0.818	0.743	0.672	0.818	SUBCLONAL	1	TRUE	0	0.380428244202015	1		762	693	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248342	212248343	+	frameshift_variant,stop_lost	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	59	645	0	ENST00000342788.4:c.3924_3925del	p.Ter1309SerfsTer7	p.*1309Sfs*7	ENST00000342788	NM_005235.2	1308	gtGTaa/gtaa	28/28	0.277256762865137	3	FACETS	0.677	0.583	0.78	0.339	0.291	0.39	SUBCLONAL	1	TRUE	1	0.380428244202015	3		645	545	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133479	55133479	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	129	821	0	ENST00000257290.5:c.784del	p.Glu262LysfsTer14	p.E262Kfs*14	ENST00000257290	NM_006206.4	261	ctG/ct	6/23	0.32850986016364	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.380428244202015	1		821	497	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858948	57858949	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	107	1439	0	ENST00000228682.2:c.447dup	p.Gly150TrpfsTer9	p.G150Wfs*9	ENST00000228682	NM_005269.2	148	-/T	5/12	0.223586097679401	3	FACETS	0.714	0.639	0.793	0.238	0.213	0.265	INDETERMINATE	1	TRUE	0	0.380428244202015	3		1439	938	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753937	57753938	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0011293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	128	911	0	ENST00000274289.3:c.686_687delinsTT	p.Arg229Ile	p.R229I	ENST00000274289	NM_006622.3	229	aGG/aTT	5/14	0.380428244202015	3	FACETS	1	0.921	1	0.509	0.461	0.559	CLONAL	1	TRUE	1	0.380428244202015	3		911	787	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0011309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	59	377	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	FALSE	1	0.15790997288577	2		377	520	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502690	149502690	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	38	408	0	ENST00000261799.4:c.2098T>G	p.Phe700Val	p.F700V	ENST00000261799	NM_002609.3	700	Ttc/Gtc	15/23	1	2	FACETS	1	0.845	1	1	0.845	1	CLONAL	1	FALSE	1	0.15790997288577	2		408	470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577119	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0011309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	84	459	1	ENST00000269305.4:c.819dup	p.Val274CysfsTer32	p.V274Cfs*32	ENST00000269305	NM_001126112.2	273	-/T	8/11	1	2	FACETS	0.85	0.751	0.955	1	0.981	1	CLONAL	2	FALSE	1	0.15790997288577	2		460	626	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	196	245	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.23410287035933	3	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.470983969922816	3		245	738	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	110	550	3	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.73	0.657	0.807	0.73	0.657	0.807	SUBCLONAL	1	TRUE	1	0.470983969922816	2		553	640	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	307	345	9	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	0.265895005481198	3	FACETS	1	0.981	1	1	0.981	1	INDETERMINATE	2	TRUE	1	0.470983969922816	3		354	753	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	45	154	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.758	0.642	0.884	0.758	0.642	0.884	SUBCLONAL	1	TRUE	1	0.470983969922816	2		154	252	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	147	183	0	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	TRUE	1	0.470983969922816	2		183	450	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	99	127	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.470983969922816	2		127	308	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	138	303	0	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	1	2	FACETS	0.605	0.55	0.663	0.605	0.55	0.663	SUBCLONAL	1	TRUE	1	0.470983969922816	2		303	969	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255266	16255266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776660027	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	131	298	1	ENST00000375759.3:c.2531G>A	p.Arg844Gln	p.R844Q	ENST00000375759	NM_015001.2	844	cGa/cAa	11/15	1	2	FACETS	0.73	0.663	0.801	0.73	0.663	0.801	SUBCLONAL	1	TRUE	1	0.470983969922816	2		299	762	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466800	25466800	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144689354	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	112	371	0	ENST00000264709.3:c.1903C>T	p.Arg635Trp	p.R635W	ENST00000264709	NM_175629.2	635	Cgg/Tgg	16/23	NA	2	FACETS	0.61	0.548	0.675			1	INDETERMINATE	1	TRUE	NA	0.470983969922816	2		371	780	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443576	29443576	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750194005	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	87	322	1	ENST00000389048.3:c.3641G>A	p.Arg1214His	p.R1214H	ENST00000389048	NM_004304.4	1214	cGc/cAc	23/29	0.340114969491941	1	FACETS	0.488	0.432	0.547	0.488	0.432	0.547	SUBCLONAL	1	TRUE	0	0.470983969922816	1		323	579	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99154396	99154396	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764715229	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	120	426	3	ENST00000074304.5:c.538C>T	p.Arg180Trp	p.R180W	ENST00000074304	NM_001134224.1	180	Cgg/Tgg	8/26	1	2	FACETS	0.6	0.542	0.662	0.6	0.542	0.662	SUBCLONAL	1	TRUE	1	0.470983969922816	2		429	849	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047345	128047345	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144491407	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	91	398	1	ENST00000285398.2:c.577G>A	p.Val193Met	p.V193M	ENST00000285398	NM_000122.1	193	Gtg/Atg	5/15	1	2	FACETS	0.578	0.514	0.647	0.578	0.514	0.647	SUBCLONAL	1	TRUE	1	0.470983969922816	2		399	668	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440111	220440111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	187	628	1	ENST00000243786.2:c.964C>T	p.Pro322Ser	p.P322S	ENST00000243786	NM_002191.3	322	Cca/Tca	2/2	1	2	FACETS	0.803	0.741	0.867	0.803	0.741	0.867	CLONAL	1	TRUE	1	0.470983969922816	2		629	989	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275630	41275630	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	76	246	0	ENST00000349496.5:c.1525G>A	p.Ala509Thr	p.A509T	ENST00000349496	NM_001904.3	509	Gct/Act	10/15	1	2	FACETS	0.503	0.441	0.57	0.503	0.441	0.57	SUBCLONAL	1	TRUE	1	0.470983969922816	2		246	641	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944547	38944547	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	71	271	0	ENST00000357387.3:c.4913+1G>A		p.X1638_splice	ENST00000357387	NM_152756.3	1638			1	2	FACETS	0.473	0.412	0.538	0.473	0.412	0.538	SUBCLONAL	1	TRUE	1	0.470983969922816	2		271	638	SUCCESS
APC	324	MSKCC	GRCh37	5	112111381	112111381	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1114167556	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	72	258	1	ENST00000257430.4:c.478G>A	p.Ala160Thr	p.A160T	ENST00000257430	NM_000038.5	160	Gct/Act	5/16	1	2	FACETS	0.502	0.439	0.57	0.502	0.439	0.57	SUBCLONAL	1	TRUE	1	0.470983969922816	2		259	609	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672873	30672873	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1262	230	745	2	ENST00000376406.3:c.4087C>T	p.Pro1363Ser	p.P1363S	ENST00000376406	NM_014641.2	1363	Cct/Tct	10/15	1	2	FACETS	0.655	0.608	0.703	0.655	0.608	0.703	SUBCLONAL	1	TRUE	1	0.470983969922816	2		747	1492	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553146	106553146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	86	257	0	ENST00000369096.4:c.1111C>T	p.Arg371Trp	p.R371W	ENST00000369096	NM_001198.3	371	Cgg/Tgg	5/7	1	2	FACETS	0.698	0.619	0.782	0.698	0.619	0.782	SUBCLONAL	1	TRUE	1	0.470983969922816	2		257	523	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004216	150004216	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs758039363	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	115	323	0	ENST00000253339.5:c.2009G>A	p.Arg670Gln	p.R670Q	ENST00000253339		670	cGg/cAg	3/7	1	2	FACETS	0.638	0.575	0.705	0.638	0.575	0.705	SUBCLONAL	1	TRUE	1	0.470983969922816	2		323	765	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2952993	2952993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369115970	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	83	350	2	ENST00000396946.4:c.2947G>A	p.Val983Met	p.V983M	ENST00000396946	NM_032415.4	983	Gtg/Atg	22/25	1	2	FACETS	0.581	0.513	0.653	0.581	0.513	0.653	SUBCLONAL	1	TRUE	1	0.470983969922816	2		352	607	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852114	128852114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200751953	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	133	496	2	ENST00000249373.3:c.2186C>T	p.Ala729Val	p.A729V	ENST00000249373	NM_005631.4	729	gCg/gTg	12/12	1	2	FACETS	0.749	0.681	0.821	0.749	0.681	0.821	SUBCLONAL	1	TRUE	1	0.470983969922816	2		498	754	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521544	8521544	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	76	211	1	ENST00000356435.5:c.694C>T	p.Arg232Cys	p.R232C	ENST00000356435		232	Cgc/Tgc	9/35	1	2	FACETS	0.647	0.569	0.73	0.647	0.569	0.73	SUBCLONAL	1	TRUE	1	0.470983969922816	2		212	499	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894898	101894898	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776680716	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	126	337	0	ENST00000374994.4:c.451C>T	p.Arg151Cys	p.R151C	ENST00000374994	NM_004612.2	151	Cgc/Tgc	3/9	1	2	FACETS	0.682	0.618	0.75	0.682	0.618	0.75	SUBCLONAL	1	TRUE	1	0.470983969922816	2		337	784	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760559	133760559	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs557879885	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	151	489	3	ENST00000318560.5:c.2882C>T	p.Pro961Leu	p.P961L	ENST00000318560	NM_005157.4	961	cCg/cTg	11/11	1	2	FACETS	0.765	0.7	0.834	0.765	0.7	0.834	SUBCLONAL	1	TRUE	1	0.470983969922816	2		492	838	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910810	114910810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752843698	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	247	663	3	ENST00000543371.1:c.929C>T	p.Pro310Leu	p.P310L	ENST00000543371	NM_001198531.1	310	cCg/cTg	9/14	1	2	FACETS	0.721	0.673	0.772	0.721	0.673	0.772	SUBCLONAL	1	TRUE	1	0.470983969922816	2		666	1454	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216546	108216546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529296539	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	134	347	0	ENST00000278616.4:c.8495G>A	p.Arg2832His	p.R2832H	ENST00000278616	NM_000051.3	2832	cGt/cAt	58/63	1	2	FACETS	0.593	0.538	0.651	0.593	0.538	0.651	SUBCLONAL	1	TRUE	1	0.470983969922816	2		347	960	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342691	118342691	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	73	275	0	ENST00000534358.1:c.817T>A	p.Leu273Ile	p.L273I	ENST00000534358	NM_005933.3	273	Tta/Ata	3/36	1	2	FACETS	0.592	0.518	0.67	0.592	0.518	0.67	SUBCLONAL	1	TRUE	1	0.470983969922816	2		275	524	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037474	12037474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	230	233	0	ENST00000396373.4:c.1105C>T	p.Arg369Trp	p.R369W	ENST00000396373	NM_001987.4	369	Cgg/Tgg	6/8	0.470983969922816	3	FACETS	0.755	0.706	0.806	0.755	0.706	0.806	SUBCLONAL	2	TRUE	1	0.470983969922816	3		233	799	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436599	49436599	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886041405	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	138	465	2	ENST00000301067.7:c.5707C>T	p.Arg1903Ter	p.R1903*	ENST00000301067	NM_003482.3	1903	Cga/Tga	26/54	0.470983969922816	3	FACETS	0.704	0.64	0.772	0.352	0.32	0.386	SUBCLONAL	1	TRUE	1	0.470983969922816	3		467	1028	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111886063	111886063	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770527337	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	408	618	3	ENST00000341259.2:c.1685G>A	p.Arg562Gln	p.R562Q	ENST00000341259	NM_005475.2	562	cGg/cAg	8/8	0.265895005481198	3	FACETS	0.859	0.818	0.901	0.859	0.818	0.901	INDETERMINATE	2	TRUE	1	0.470983969922816	3		621	1246	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519174	103519174	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1218011780	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	71	175	0	ENST00000355739.4:c.2512G>A	p.Val838Met	p.V838M	ENST00000355739	NM_000123.3	838	Gtg/Atg	11/15	1	2	FACETS	0.585	0.512	0.665	0.585	0.512	0.665	SUBCLONAL	1	TRUE	1	0.470983969922816	2		175	515	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435204	110435204	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	93	325	0	ENST00000375856.3:c.3197C>T	p.Thr1066Ile	p.T1066I	ENST00000375856	NM_003749.2	1066	aCc/aTc	1/2	1	2	FACETS	0.654	0.582	0.73	0.654	0.582	0.73	SUBCLONAL	1	TRUE	1	0.470983969922816	2		325	604	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472565	88472565	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371959662	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	88	406	1	ENST00000360948.2:c.1990G>A	p.Ala664Thr	p.A664T	ENST00000360948	NM_001012338.2	664	Gcc/Acc	16/19	1	2	FACETS	0.61	0.541	0.683	0.61	0.541	0.683	SUBCLONAL	1	TRUE	1	0.470983969922816	2		407	613	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348223	348223	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755028316	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	57	259	1	ENST00000262320.3:c.1283C>T	p.Ser428Leu	p.S428L	ENST00000262320	NM_003502.3	428	tCg/tTg	6/11	1	2	FACETS	0.532	0.457	0.613	0.532	0.457	0.613	SUBCLONAL	1	TRUE	1	0.470983969922816	2		260	455	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830285	72830285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750685334	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	112	467	0	ENST00000268489.5:c.6296C>T	p.Pro2099Leu	p.P2099L	ENST00000268489	NM_006885.3	2099	cCg/cTg	9/10	1	2	FACETS	0.646	0.581	0.715	0.646	0.581	0.715	SUBCLONAL	1	TRUE	1	0.470983969922816	2		467	736	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81971386	81971386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774452862	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	130	405	0	ENST00000359376.3:c.3076G>A	p.Ala1026Thr	p.A1026T	ENST00000359376	NM_002661.3	1026	Gca/Aca	28/33	0.277989941343206	0	FACETS	0.359	0.325	0.394			1	INDETERMINATE	1	TRUE	0	0.470983969922816	0		405	814	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346700	89346700	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1189225404	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	147	446	1	ENST00000301030.4:c.6250G>A	p.Ala2084Thr	p.A2084T	ENST00000301030	NM_001256183.1	2084	Gcc/Acc	9/13	1	2	FACETS	0.873	0.799	0.951	0.873	0.799	0.951	CLONAL	1	TRUE	1	0.470983969922816	2		447	715	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350233	89350233	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763544660	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	228	689	2	ENST00000301030.4:c.2717G>A	p.Arg906Gln	p.R906Q	ENST00000301030	NM_001256183.1	906	cGa/cAa	9/13	1	2	FACETS	0.707	0.657	0.758	0.707	0.657	0.758	SUBCLONAL	1	TRUE	1	0.470983969922816	2		691	1370	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351736	89351736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1261106013	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	231	646	1	ENST00000301030.4:c.1214G>A	p.Arg405His	p.R405H	ENST00000301030	NM_001256183.1	405	cGt/cAt	9/13	1	2	FACETS	0.756	0.703	0.81	0.756	0.703	0.81	SUBCLONAL	1	TRUE	1	0.470983969922816	2		647	1298	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89851272	89851272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377637236	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	136	434	0	ENST00000389301.3:c.1460G>A	p.Arg487Gln	p.R487Q	ENST00000389301	NM_000135.2	487	cGg/cAg	15/43	1	2	FACETS	0.684	0.622	0.75	0.684	0.622	0.75	SUBCLONAL	1	TRUE	1	0.470983969922816	2		434	844	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004609	16004609	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	108	357	0	ENST00000268712.3:c.2645C>T	p.Thr882Met	p.T882M	ENST00000268712	NM_006311.3	882	aCg/aTg	20/46	1	2	FACETS	0.617	0.554	0.684	0.617	0.554	0.684	SUBCLONAL	1	TRUE	1	0.470983969922816	2		357	743	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661946	29661946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868094590	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	113	254	0	ENST00000356175.3:c.5840G>A	p.Arg1947Gln	p.R1947Q	ENST00000356175	NM_000267.3	1947	cGa/cAa	39/57	1	2	FACETS	0.672	0.605	0.743	0.672	0.605	0.743	SUBCLONAL	1	TRUE	1	0.470983969922816	2		254	714	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	115	378	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.674	0.607	0.744	0.674	0.607	0.744	SUBCLONAL	1	TRUE	1	0.470983969922816	2		378	725	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883554	37883554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs574436396	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	128	399	0	ENST00000269571.5:c.3166G>A	p.Gly1056Ser	p.G1056S	ENST00000269571		1056	Ggt/Agt	26/27	1	2	FACETS	0.682	0.618	0.749	0.682	0.618	0.749	SUBCLONAL	1	TRUE	1	0.470983969922816	2		399	797	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354428	40354428	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs929910807	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	199	696	0	ENST00000293328.3:c.2167G>A	p.Ala723Thr	p.A723T	ENST00000293328	NM_012448.3	723	Gcc/Acc	18/19	1	2	FACETS	0.714	0.66	0.77	0.714	0.66	0.77	SUBCLONAL	1	TRUE	1	0.470983969922816	2		696	1184	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41247928	41247928	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	155	356	1	ENST00000357654.3:c.605A>G	p.Gln202Arg	p.Q202R	ENST00000357654	NM_007294.3	202	cAa/cGa	9/23	1	2	FACETS	0.738	0.675	0.803	0.738	0.675	0.803	SUBCLONAL	1	TRUE	1	0.470983969922816	2		357	892	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440757	56440757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774211426	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	108	306	1	ENST00000407977.2:c.461C>T	p.Pro154Leu	p.P154L	ENST00000407977		154	cCg/cTg	5/10	1	2	FACETS	0.78	0.702	0.862	0.78	0.702	0.862	SUBCLONAL	1	TRUE	1	0.470983969922816	2		307	588	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007575	62007575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	161	520	1	ENST00000392795.3:c.292G>A	p.Glu98Lys	p.E98K	ENST00000392795	NM_001039933.1	98	Gaa/Aaa	3/6	1	2	FACETS	0.735	0.674	0.799	0.735	0.674	0.799	SUBCLONAL	1	TRUE	1	0.470983969922816	2		521	930	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530048	63530048	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	139	365	1	ENST00000307078.5:c.2387G>A	p.Ser796Asn	p.S796N	ENST00000307078	NM_004655.3	796	aGc/aAc	10/11	1	2	FACETS	0.79	0.72	0.863	0.79	0.72	0.863	SUBCLONAL	1	TRUE	1	0.470983969922816	2		366	747	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265025	5265025	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	113	340	0	ENST00000357368.4:c.562C>T	p.Arg188Ter	p.R188*	ENST00000357368	NM_002850.3	188	Cga/Tga	5/38	1	2	FACETS	0.833	0.752	0.918	0.833	0.752	0.918	CLONAL	1	TRUE	1	0.470983969922816	2		340	576	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299946	15299946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555729077	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	71	344	1	ENST00000263388.2:c.1232C>T	p.Thr411Met	p.T411M	ENST00000263388	NM_000435.2	411	aCg/aTg	8/33	1	2	FACETS	0.572	0.5	0.65	0.572	0.5	0.65	SUBCLONAL	1	TRUE	1	0.470983969922816	2		345	527	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791320	42791320	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754556504	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	86	325	1	ENST00000575354.2:c.380C>T	p.Thr127Met	p.T127M	ENST00000575354	NM_015125.3	127	aCg/aTg	3/20	1	2	FACETS	0.758	0.673	0.848	0.758	0.673	0.848	SUBCLONAL	1	TRUE	1	0.470983969922816	2		326	482	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309466	30309466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752920927	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	180	524	0	ENST00000307677.4:c.556G>A	p.Gly186Ser	p.G186S	ENST00000307677	NM_138578.1	186	Ggc/Agc	2/3	1	2	FACETS	0.688	0.633	0.745	0.688	0.633	0.745	SUBCLONAL	1	TRUE	1	0.470983969922816	2		524	1111	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733337	40733337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746243026	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	42	192	0	ENST00000373198.4:c.3469G>A	p.Asp1157Asn	p.D1157N	ENST00000373198	NM_133170.3	1157	Gat/Aat	26/32	0.277989941343206	0	FACETS	0.289	0.242	0.341			1	INDETERMINATE	1	TRUE	0	0.470983969922816	0		192	326	SUCCESS
AR	367	MSKCC	GRCh37	X	66905930	66905930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754201976	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	113	221	2	ENST00000374690.3:c.1847G>A	p.Arg616His	p.R616H	ENST00000374690	NM_000044.3	616	cGt/cAt	3/8	1	1	FACETS	0.929	0.843	1	0.929	0.843	1	CLONAL	1	TRUE	0	0.470983969922816	1		223	395	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	49	240	0	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	1	2	FACETS	0.572	0.486	0.665	0.572	0.486	0.665	SUBCLONAL	1	TRUE	1	0.470983969922816	2		240	364	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217557	142217557	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1268253442	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	115	300	0	ENST00000350721.4:c.5440del	p.Arg1814GlufsTer10	p.R1814Efs*10	ENST00000350721	NM_001184.3	1814	Aga/ga	32/47	1	2	FACETS	0.664	0.598	0.733	0.664	0.598	0.733	SUBCLONAL	1	TRUE	1	0.470983969922816	2		300	736	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819954	170819959	+	inframe_deletion	In_Frame_Del	DEL	GATGAT	GATGAT	-	novel	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	97	259	0	ENST00000296930.5:c.501_506del	p.Asp167_Asp168del	p.D167_D168del	ENST00000296930	NM_002520.6	166	GATGAT/-	6/11	1	2	FACETS	0.641	0.572	0.714	0.641	0.572	0.714	SUBCLONAL	1	TRUE	1	0.470983969922816	2		259	643	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338696	70338698	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	164	313	0	ENST00000374080.3:c.94_96del	p.Lys32del	p.K32del	ENST00000374080		31	cAGAag/cag	1/45	1	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.470983969922816	1		313	526	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345759	152345760	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs730882049	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	80	283	0	ENST00000359321.1:c.810dup	p.Ile271TyrfsTer8	p.I271Yfs*8	ENST00000359321	NM_005431.1	270	-/T	3/3	1	2	FACETS	0.509	0.447	0.574	0.509	0.447	0.574	SUBCLONAL	1	TRUE	1	0.470983969922816	2		283	668	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693836	47693837	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs63749930	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	211	328	0	ENST00000233146.2:c.1552_1553del	p.Gln518ValfsTer10	p.Q518Vfs*10	ENST00000233146	NM_000251.2	517	gCA/g	10/16	0.325818230157047	2	FACETS	1	0.986	1	0.613	0.571	0.656	CLONAL	1	TRUE	0	0.470983969922816	2		328	731	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0011324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	78	319	1	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.583	0.513	0.658	0.583	0.513	0.658	SUBCLONAL	1	TRUE	1	0.470983969922816	2		320	568	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0011330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	211	600	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.664	0.616	0.715	0.664	0.616	0.715	SUBCLONAL	1	TRUE	1	0.524130230194242	2		600	1212	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0011330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	182	335	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	0.621	0.572	0.672	0.621	0.572	0.672	SUBCLONAL	1	TRUE	1	0.524130230194242	2		335	1119	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023151	27023179	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	-	novel	NA	P-0011330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	120	57	0	ENST00000324856.7:c.267_295del	p.Ser90ProfsTer11	p.S90Pfs*11	ENST00000324856	NM_006015.4	86	gGCGGAGCCGGCAGCGGCGGCGGGCCCGGC/g	1/20	1	2	FACETS	0.851	0.783	0.92	1	0.989	1	CLONAL	2	TRUE	1	0.524130230194242	2		57	269	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188049	151188049	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1526	138	519	0	ENST00000262187.5:c.104A>C	p.Tyr35Ser	p.Y35S	ENST00000262187	NM_005614.3	35	tAc/tCc	2/8	1	2	FACETS	0.316	0.286	0.348	0.316	0.286	0.348	SUBCLONAL	1	TRUE	1	0.524130230194242	2		519	1664	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481621	56481621	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1267	128	529	0	ENST00000267101.3:c.656T>G	p.Phe219Cys	p.F219C	ENST00000267101	NM_001982.3	219	tTt/tGt	6/28	1	2	FACETS	0.35	0.316	0.386	0.35	0.316	0.386	SUBCLONAL	1	TRUE	1	0.524130230194242	2		529	1395	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051127	13051127	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1224218038	NA	P-0011330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1363	275	586	0	ENST00000316448.5:c.563A>G	p.Asn188Ser	p.N188S	ENST00000316448	NM_004343.3	188	aAc/aGc	5/9	1	2	FACETS	0.641	0.599	0.683	0.641	0.599	0.683	SUBCLONAL	1	TRUE	1	0.524130230194242	2		586	1638	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371702	55371703	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0011330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	90	258	0	ENST00000297316.4:c.394dup	p.His132ProfsTer30	p.H132Pfs*30	ENST00000297316	NM_022454.3	131	gac/gaCc	2/2	1	2	FACETS	0.484	0.43	0.543	0.484	0.43	0.543	SUBCLONAL	1	TRUE	1	0.524130230194242	2		258	709	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591104	67591109	+	inframe_deletion	In_Frame_Del	DEL	TTAAAC	TTAAAC	-	novel	NA	P-0011330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	118	249	0	ENST00000274335.5:c.1697_1702del	p.Ile566_Pro568delinsThr	p.I566_P568delinsT	ENST00000274335		566	aTTAAACca/aca	12/15	1	2	FACETS	0.519	0.468	0.574	0.519	0.468	0.574	SUBCLONAL	1	TRUE	1	0.524130230194242	2		249	867	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372446	55372447	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0011330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	191	478	0	ENST00000297316.4:c.1138dup	p.Gln380ProfsTer4	p.Q380Pfs*4	ENST00000297316	NM_022454.3	379	tac/taCc	2/2	1	2	FACETS	0.635	0.587	0.686	0.635	0.587	0.686	SUBCLONAL	1	TRUE	1	0.524130230194242	2		478	1147	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830920	72830920	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0011330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1593	285	792	1	ENST00000268489.5:c.5661del	p.Glu1888LysfsTer26	p.E1888Kfs*26	ENST00000268489	NM_006885.3	1887	aaA/aa	9/10	1	2	FACETS	0.579	0.542	0.617	0.579	0.542	0.617	SUBCLONAL	1	TRUE	1	0.524130230194242	2		793	1878	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624268	89624269	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0011330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	152	197	0	ENST00000371953.3:c.44_45del	p.Arg15IlefsTer28	p.R15Ifs*28	ENST00000371953	NM_000314.4	14	agGAga/agga	1/9	0.323582265071281	2	FACETS	1	0.977	1	0.58	0.534	0.627	CLONAL	1	TRUE	0	0.524130230194242	2		197	500	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0011332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	51	393	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.328715827262809	2		393	220	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720720	89720721	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs786204905	NA	P-0011332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	17	54	0	ENST00000371953.3:c.875dup	p.Asn292LysfsTer6	p.N292Kfs*6	ENST00000371953	NM_000314.4	291	gaa/gAaa	8/9	0.328715827262809	1	FACETS	0.714	0.539	0.918	0.714	0.539	0.918	CLONAL	1	TRUE	0	0.328715827262809	1		54	121	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11181365	11181365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774791298	NA	P-0011332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	99	448	4	ENST00000361445.4:c.6871G>A	p.Val2291Ile	p.V2291I	ENST00000361445	NM_004958.3	2291	Gtc/Atc	49/58	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.328715827262809	2		452	563	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29422366	29422367	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0011332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	70	482	0	ENST00000356175.3:c.39_40del	p.Val14GlnfsTer23	p.V14Qfs*23	ENST00000356175	NM_000267.3	13	gtGGtc/gttc	1/57	0.138254803176981	1	FACETS	0.994	0.872	1	0.994	0.872	1	INDETERMINATE	1	TRUE	0	0.328715827262809	1		482	358	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589555	67589557	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	novel	NA	P-0011332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	85	261	0	ENST00000274335.5:c.1318_1320del	p.Asp440del	p.D440del	ENST00000274335		440	GAT/-	10/15	1	2	FACETS	0.901	0.798	1	0.901	0.798	1	CLONAL	1	TRUE	1	0.328715827262809	2		261	574	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0011348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	72	819	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	0.254680910472948	1	FACETS	0.336	0.293	0.382	0.336	0.293	0.382	INDETERMINATE	1	TRUE	0	0.49	1		819	660	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0011366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	460	197	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	0.6217271009667	3	FACETS	0.925	0.896	0.953	0.925	0.896	0.953	CLONAL	3	TRUE	0	0.668011095742666	3		197	662	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0011366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	426	435	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.428306785426098	3	FACETS	1	0.994	1	0.655	0.625	0.687	CLONAL	1	TRUE	1	0.668011095742666	3		435	1298	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0011366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	30	223	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	0.20387714100823	2	FACETS	0.194	0.156	0.237	0.097	0.078	0.119	INDETERMINATE	1	TRUE	0	0.668011095742666	2		223	463	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398220	25398220	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1255	145	389	1	ENST00000311936.3:c.99T>A	p.Asp33Glu	p.D33E	ENST00000311936	NM_004985.3	33	gaT/gaA	2/5	0.428306785426098	3	FACETS	0.414	0.376	0.453	0.207	0.188	0.227	SUBCLONAL	1	TRUE	1	0.668011095742666	3		390	1400	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920402	114920402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs927089403	NA	P-0011366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1453	220	601	0	ENST00000543371.1:c.1343G>A	p.Arg448Gln	p.R448Q	ENST00000543371	NM_001198531.1	448	cGg/cAg	13/14	1	2	FACETS	0.394	0.365	0.424	0.394	0.365	0.424	SUBCLONAL	1	TRUE	1	0.668011095742666	2		601	1673	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912149	114912149	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1354	350	695	0	ENST00000543371.1:c.1219C>T	p.Arg407Ter	p.R407*	ENST00000543371	NM_001198531.1	407	Cga/Tga	11/14	1	2	FACETS	0.615	0.58	0.65	0.615	0.58	0.65	SUBCLONAL	1	TRUE	1	0.668011095742666	2		695	1704	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771987	135771988	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs2234980	NA	P-0011366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	55	179	0	ENST00000298552.3:c.3127_3129dup	p.Ser1043dup	p.S1043dup	ENST00000298552	NM_001162426.1	1043	-/AGC	23/23	1	2	FACETS	0.392	0.336	0.453	0.392	0.336	0.453	SUBCLONAL	1	TRUE	1	0.668011095742666	2		179	420	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540198	23540198	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758091147	NA	P-0011366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	78	134	0	ENST00000380871.4:c.205G>A	p.Ala69Thr	p.A69T	ENST00000380871	NM_006167.3	69	Gcc/Acc	1/2	0.239825366249138	3	FACETS	0.677	0.597	0.763	0.339	0.298	0.382	INDETERMINATE	1	TRUE	1	0.668011095742666	3		134	460	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119111	70119111	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	74	156	0	ENST00000245479.2:c.683C>A	p.Ser228Ter	p.S228*	ENST00000245479	NM_000346.3	228	tCg/tAg	2/3	0.239825366249138	3	FACETS	0.735	0.647	0.829	0.368	0.323	0.415	INDETERMINATE	1	TRUE	1	0.668011095742666	3		156	402	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954247	17954247	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143586866	NA	P-0011366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1213	169	503	1	ENST00000458235.1:c.362G>A	p.Arg121His	p.R121H	ENST00000458235	NM_000215.3	121	cGc/cAc	4/24	1	2	FACETS	0.366	0.335	0.398	0.366	0.335	0.398	SUBCLONAL	1	TRUE	1	0.668011095742666	2		504	1382	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584779	48584788	+	frameshift_variant	Frame_Shift_Del	DEL	GCCATCTTCA	GCCATCTTCA	-	novel	NA	P-0011366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	152	557	0	ENST00000342988.3:c.859_868del	p.His287ThrfsTer46	p.H287Tfs*46	ENST00000342988	NM_005359.5	286	gGCCATCTTCAg/gg	7/12	0.668011095742666	1	FACETS	0.298	0.272	0.326	0.298	0.272	0.326	SUBCLONAL	1	TRUE	0	0.668011095742666	1		557	1016	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604766	48604766	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs377767377	NA	P-0011366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	243	455	1	ENST00000342988.3:c.1588del	p.His530ThrfsTer7	p.H530Tfs*7	ENST00000342988	NM_005359.5	530	Cac/ac	12/12	0.668011095742666	1	FACETS	0.619	0.58	0.659	0.619	0.58	0.659	SUBCLONAL	1	TRUE	0	0.668011095742666	1		456	783	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120346	70120347	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCTC	novel	NA	P-0011366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1654	400	772	0	ENST00000245479.2:c.1351_1352insCCCT	p.Tyr451SerfsTer128	p.Y451Sfs*128	ENST00000245479	NM_000346.3	450	tcc/tCCTCcc	3/3	0.239825366249138	3	FACETS	0.778	0.737	0.82	0.389	0.368	0.41	INDETERMINATE	1	TRUE	1	0.668011095742666	3		772	2054	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0011374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	261	282	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.432823784892133	3	FACETS	0.906	0.852	0.962	0.906	0.852	0.962	CLONAL	2	TRUE	1	0.435036582118501	3		282	806	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0011374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	174	341	0	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	0.390670951565776	2	FACETS	1	0.988	1	0.677	0.626	0.729	CLONAL	1	TRUE	0	0.435036582118501	2		341	591	SUCCESS
APC	324	MSKCC	GRCh37	5	112173590	112173590	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561575998	NA	P-0011374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	293	374	0	ENST00000257430.4:c.2299C>T	p.Gln767Ter	p.Q767*	ENST00000257430	NM_000038.5	767	Cag/Tag	16/16	0.381910142318612	3	FACETS	0.872	0.828	0.916	0.872	0.828	0.916	CLONAL	3	TRUE	0	0.435036582118501	3		374	627	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852278	128852278	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	96	288	0	ENST00000249373.3:c.2350G>C	p.Asp784His	p.D784H	ENST00000249373	NM_005631.4	784	Gac/Cac	12/12	0.435036582118501	3	FACETS	0.791	0.706	0.883	0.264	0.235	0.295	SUBCLONAL	1	TRUE	0	0.435036582118501	3		288	679	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40761115	40761116	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCAGGCAGCGTATGACAAAGGTGTTGGCG	novel	NA	P-0011429-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	43	458	0	ENST00000392038.2:c.236_237insCGCCAACACCTTTGTCATACGCTGCCTGCA	p.Leu78_Gln79insHisAlaAsnThrPheValIleArgCysLeu	p.L78_Q79insHANTFVIRCL	ENST00000392038	NM_001626.4	79	cag/caCGCCAACACCTTTGTCATACGCTGCCTGCAg	4/14	1	2	FACETS	0.484	0.406	0.569	0.484	0.406	0.569	SUBCLONAL	1	TRUE	1	0.555373824681111	2		458	320	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120457933	120457933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769520444	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	228	319	2	ENST00000256646.2:c.7412C>T	p.Ala2471Val	p.A2471V	ENST00000256646	NM_024408.3	2471	gCg/gTg	34/34	1	2	FACETS	0.94	0.88	1	0.94	0.88	1	CLONAL	1	TRUE	1	0.723285735212916	2		321	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	450	604	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.723285735212916	2		604	1220	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217275	11217275	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	349	632	0	ENST00000361445.4:c.4403A>G	p.Asp1468Gly	p.D1468G	ENST00000361445	NM_004958.3	1468	gAc/gGc	30/58	1	2	FACETS	0.964	0.915	1	0.964	0.915	1	CLONAL	1	TRUE	1	0.723285735212916	2		632	1001	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301163	65301164	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	260	397	0	ENST00000342505.4:c.3284_3285delinsTT	p.Thr1095Ile	p.T1095I	ENST00000342505	NM_002227.2	1095	aCC/aTT	24/25	1	2	FACETS	0.941	0.885	0.998	0.941	0.885	0.998	CLONAL	1	TRUE	1	0.723285735212916	2		397	764	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	244006429	244006429	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	425	600	0	ENST00000263826.5:c.44G>A	p.Arg15Lys	p.R15K	ENST00000263826	NM_005465.4	15	aGg/aAg	1/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.723285735212916	2		600	1104	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068375	26068375	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	168	423	1	ENST00000435504.4:c.115C>T	p.Gln39Ter	p.Q39*	ENST00000435504		39	Cag/Tag	2/13	1	2	FACETS	0.812	0.751	0.876	0.812	0.751	0.876	CLONAL	1	TRUE	1	0.723285735212916	2		424	572	SUCCESS
ALK	238	MSKCC	GRCh37	2	29497997	29497997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	438	717	1	ENST00000389048.3:c.2009C>T	p.Ser670Leu	p.S670L	ENST00000389048	NM_004304.4	670	tCa/tTa	11/29	1	2	FACETS	0.962	0.918	1	0.962	0.918	1	CLONAL	1	TRUE	1	0.723285735212916	2		718	1259	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172168	99172168	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	167	560	1	ENST00000074304.5:c.1734C>A	p.Ser578Arg	p.S578R	ENST00000074304	NM_001134224.1	578	agC/agA	17/26	1	2	FACETS	0.492	0.452	0.534	0.492	0.452	0.534	SUBCLONAL	1	TRUE	1	0.723285735212916	2		561	939	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738254	190738254	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	95	192	0	ENST00000441310.2:c.2506G>A	p.Glu836Lys	p.E836K	ENST00000441310	NM_000534.4	836	Gaa/Aaa	12/13	1	2	FACETS	0.831	0.749	0.917	0.831	0.749	0.917	CLONAL	1	TRUE	1	0.723285735212916	2		192	316	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090440	37090440	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs587778971	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	251	397	0	ENST00000231790.2:c.2035G>T	p.Glu679Ter	p.E679*	ENST00000231790	NM_000249.3	679	Gaa/Taa	18/19	0.723285735212916	1	FACETS	0.98	0.931	1	0.98	0.931	1	CLONAL	1	TRUE	0	0.723285735212916	1		397	452	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146557	185146557	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	555	379	0	ENST00000265026.3:c.188C>T	p.Pro63Leu	p.P63L	ENST00000265026	NM_004721.4	63	cCc/cTc	2/14	0.717838987271684	3	FACETS	0.987	0.952	1	0.987	0.952	1	CLONAL	2	TRUE	1	0.723285735212916	3		379	1059	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184646	185184646	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	411	695	2	ENST00000265026.3:c.1538G>T	p.Gly513Val	p.G513V	ENST00000265026	NM_004721.4	513	gGg/gTg	10/14	0.717838987271684	3	FACETS	1	0.956	1	0.503	0.478	0.529	CLONAL	1	TRUE	1	0.723285735212916	3		697	1538	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971017	55971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	342	530	2	ENST00000263923.4:c.1780C>T	p.His594Tyr	p.H594Y	ENST00000263923	NM_002253.2	594	Cat/Tat	13/30	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.723285735212916	2		532	933	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270177	66270177	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	269	370	0	ENST00000273854.3:c.1705C>T	p.Gln569Ter	p.Q569*	ENST00000273854	NM_004439.5	569	Caa/Taa	8/18	1	2	FACETS	0.934	0.88	0.99	0.934	0.88	0.99	CLONAL	1	TRUE	1	0.723285735212916	2		370	796	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500480	149500480	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778844346	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	340	527	2	ENST00000261799.4:c.2557C>T	p.Arg853Trp	p.R853W	ENST00000261799	NM_002609.3	853	Cgg/Tgg	18/23	1	2	FACETS	0.981	0.931	1	0.981	0.931	1	CLONAL	1	TRUE	1	0.723285735212916	2		529	958	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513223	149513223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	343	567	2	ENST00000261799.4:c.860G>A	p.Gly287Glu	p.G287E	ENST00000261799	NM_002609.3	287	gGg/gAg	6/23	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.723285735212916	2		569	913	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523318	176523318	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	315	510	1	ENST00000292408.4:c.1975G>A	p.Glu659Lys	p.E659K	ENST00000292408	NM_213647.1	659	Gag/Aag	15/18	1	2	FACETS	0.956	0.905	1	0.956	0.905	1	CLONAL	1	TRUE	1	0.723285735212916	2		511	911	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398896	398896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	690	423	0	ENST00000380956.4:c.706G>A	p.Glu236Lys	p.E236K	ENST00000380956	NM_001195286.1	236	Gag/Aag	6/9	0.717838987271684	3	FACETS	0.998	0.967	1	0.998	0.967	1	CLONAL	2	TRUE	1	0.723285735212916	3		423	1301	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163357	32163357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	742	743	2	ENST00000375023.3:c.5869G>A	p.Gly1957Arg	p.G1957R	ENST00000375023	NM_004557.3	1957	Gga/Aga	30/30	0.717838987271684	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.723285735212916	3		745	1383	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187555	32187555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749287849	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	533	370	0	ENST00000375023.3:c.1324G>A	p.Gly442Ser	p.G442S	ENST00000375023	NM_004557.3	442	Ggc/Agc	8/30	0.717838987271684	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.723285735212916	3		370	1003	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436012	116436012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369312680	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	368	591	2	ENST00000397752.3:c.4007G>A	p.Arg1336Gln	p.R1336Q	ENST00000397752	NM_000245.2	1336	cGg/cAg	21/21	0.723285735212916	1	FACETS	0.972	0.932	1	0.972	0.932	1	CLONAL	1	TRUE	0	0.723285735212916	1		593	668	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345990	152345990	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs180805457	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	553	837	0	ENST00000359321.1:c.580A>G	p.Thr194Ala	p.T194A	ENST00000359321	NM_005431.1	194	Acg/Gcg	3/3	0.723285735212916	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.723285735212916	1		837	922	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913384	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	325	176	0	ENST00000304494.5:c.262G>T	p.Glu88Ter	p.E88*	ENST00000304494	NM_000077.4	88	Gag/Tag	2/3	0.715379634315564	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.723285735212916	2		176	414	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413963	139413963	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1743	441	630	0	ENST00000277541.6:c.797G>C	p.Cys266Ser	p.C266S	ENST00000277541	NM_017617.3	266	tGc/tCc	5/34	0.673865852543464	4	FACETS	0.962	0.914	1	0.321	0.304	0.337	CLONAL	1	TRUE	1	0.723285735212916	4		630	2184	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851683	63851683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	234	424	0	ENST00000279873.7:c.2461C>T	p.His821Tyr	p.H821Y	ENST00000279873	NM_032199.2	821	Cat/Tat	10/10	1	2	FACETS	0.967	0.907	1	0.967	0.907	1	CLONAL	1	TRUE	1	0.723285735212916	2		424	669	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119819	108119819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786203815	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	525	410	0	ENST00000278616.4:c.1225C>T	p.Leu409Phe	p.L409F	ENST00000278616	NM_000051.3	409	Ctt/Ttt	9/63	0.723285735212916	2	FACETS	0.967	0.938	0.994	0.967	0.938	0.994	CLONAL	2	TRUE	0	0.723285735212916	2		410	751	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888285	112888285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	262	425	0	ENST00000351677.2:c.301C>T	p.Pro101Ser	p.P101S	ENST00000351677	NM_002834.3	101	Cct/Tct	3/16	1	2	FACETS	0.971	0.914	1	0.971	0.914	1	CLONAL	1	TRUE	1	0.723285735212916	2		425	746	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112025	115112025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446406418	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	222	360	1	ENST00000257566.3:c.1715G>A	p.Gly572Glu	p.G572E	ENST00000257566	NM_016569.3	572	gGg/gAg	7/8	1	2	FACETS	0.998	0.935	1	0.998	0.935	1	CLONAL	1	TRUE	1	0.723285735212916	2		361	615	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120554402	120554402	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	25	109	0	ENST00000229340.5:c.52+1G>A		p.X18_splice	ENST00000229340	NM_006861.6	18			1	2	FACETS	0.325	0.257	0.401	0.325	0.257	0.401	SUBCLONAL	1	TRUE	1	0.723285735212916	2		109	213	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779272	3779272	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	196	375	0	ENST00000262367.5:c.5776C>T	p.Arg1926Trp	p.R1926W	ENST00000262367	NM_004380.2	1926	Cgg/Tgg	31/31	1	2	FACETS	0.928	0.865	0.993	0.928	0.865	0.993	CLONAL	1	TRUE	1	0.723285735212916	2		375	584	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273929	10273929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	396	626	0	ENST00000330684.3:c.340G>A	p.Asp114Asn	p.D114N	ENST00000330684	NM_001134407.1	114	Gat/Aat	2/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.723285735212916	2		626	1022	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337296	89337296	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567537413	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	344	505	1	ENST00000301030.4:c.7735C>T	p.Arg2579Cys	p.R2579C	ENST00000301030	NM_001256183.1	2579	Cgc/Tgc	12/13	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.723285735212916	2		506	923	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813074	89813074	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138112218	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	231	405	0	ENST00000389301.3:c.3431G>A	p.Arg1144Gln	p.R1144Q	ENST00000389301	NM_000135.2	1144	cGg/cAg	35/43	1	2	FACETS	0.948	0.888	1	0.948	0.888	1	CLONAL	1	TRUE	1	0.723285735212916	2		405	674	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577528	7577529	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	284	512	0	ENST00000269305.4:c.752_753delinsAT	p.Ile251Asn	p.I251N	ENST00000269305	NM_001126112.2	251	aTC/aAT	7/11	1	2	FACETS	0.945	0.891	1	0.945	0.891	1	CLONAL	1	TRUE	1	0.723285735212916	2		512	831	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315348	30315349	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	276	327	0	ENST00000322652.5:c.1033_1034delinsTT	p.Pro345Leu	p.P345L	ENST00000322652	NM_015355.2	345	CCa/TTa	10/16	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.723285735212916	2		327	642	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39550367	39550368	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	237	432	0	ENST00000262039.4:c.478_479delinsTT	p.Pro160Phe	p.P160F	ENST00000262039	NM_002647.2	160	CCt/TTt	4/25	1	2	FACETS	0.871	0.816	0.928	0.871	0.816	0.928	CLONAL	1	TRUE	1	0.723285735212916	2		432	752	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238951	5238951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237159914	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	261	508	1	ENST00000357368.4:c.1828C>T	p.Arg610Trp	p.R610W	ENST00000357368	NM_002850.3	610	Cgg/Tgg	13/38	NA	2	FACETS	0.89	0.837	0.944			1	INDETERMINATE	1	TRUE	NA	0.723285735212916	2		509	811	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610330	10610330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	283	470	0	ENST00000171111.5:c.380G>A	p.Gly127Asp	p.G127D	ENST00000171111	NM_203500.1	127	gGt/gAt	2/6	1	2	FACETS	0.977	0.922	1	0.977	0.922	1	CLONAL	1	TRUE	1	0.723285735212916	2		470	801	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560853	9560853	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	355	553	0	ENST00000353224.5:c.929G>A	p.Gly310Glu	p.G310E	ENST00000353224	NM_177990.2	310	gGa/gAa	4/10	1	2	FACETS	0.948	0.9	0.997	0.948	0.9	0.997	CLONAL	1	TRUE	1	0.723285735212916	2		553	1035	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408878	41408878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768757373	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	313	557	2	ENST00000373198.4:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000373198	NM_133170.3	183	cGg/cAg	4/32	0.429168898400744	1	FACETS	0.604	0.572	0.638	0.604	0.572	0.638	INDETERMINATE	1	TRUE	0	0.723285735212916	1		559	914	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755518	39755519	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	270	581	0	ENST00000288319.7:c.1246_1247delinsTT	p.Pro416Leu	p.P416L	ENST00000288319	NM_182918.3	416	CCg/TTg	10/10	1	2	FACETS	0.855	0.804	0.907	0.855	0.804	0.907	CLONAL	1	TRUE	1	0.723285735212916	2		581	873	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006759	47006759	+	5_prime_UTR_variant	5'UTR	SNP	C	C	T	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	342	260	0	ENST00000377604.3:c.-122C>T		p.*41*	ENST00000377604	NM_001204468.1	-/852		2/24	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.723285735212916	1		260	473	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411527	63411527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	524	455	0	ENST00000330258.3:c.1640C>T	p.Ser547Phe	p.S547F	ENST00000330258	NM_152424.3	547	tCc/tTc	2/2	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.723285735212916	1		455	733	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434005	49434005	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	218	420	0	ENST00000301067.7:c.7548del	p.Asn2517IlefsTer26	p.N2517Ifs*26	ENST00000301067	NM_003482.3	2516	ccC/cc	31/54	1	2	FACETS	0.982	0.919	1	0.982	0.919	1	CLONAL	1	TRUE	1	0.723285735212916	2		420	614	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	275	528	3	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.907	0.855	0.961	0.907	0.855	0.961	CLONAL	1	TRUE	1	0.723285735212916	2		531	838	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425456	49425456	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs398123716	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	434	743	1	ENST00000301067.7:c.13032del	p.Lys4345AsnfsTer39	p.K4345Nfs*39	ENST00000301067	NM_003482.3	4344	ccC/cc	39/54	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.723285735212916	2		744	1121	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966873	25966873	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1271466699	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	111	531	5	ENST00000435504.4:c.2333del	p.Pro778GlnfsTer21	p.P778Qfs*21	ENST00000435504		778	cCa/ca	13/13	1	2	FACETS	0.316	0.284	0.351	0.316	0.284	0.351	SUBCLONAL	1	TRUE	1	0.723285735212916	2		536	970	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786734	3786734	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	463	778	0	ENST00000262367.5:c.4477del	p.Ile1493TyrfsTer57	p.I1493Yfs*57	ENST00000262367	NM_004380.2	1493	Ata/ta	27/31	1	2	FACETS	0.941	0.899	0.983	0.941	0.899	0.983	CLONAL	1	TRUE	1	0.723285735212916	2		778	1361	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106029	8106029	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	278	358	0	ENST00000346208.3:c.849del	p.Cys284AlafsTer10	p.C284Afs*10	ENST00000346208		283	ctG/ct	4/6	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.723285735212916	2		358	711	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151246	202151246	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	433	588	0	ENST00000358485.4:c.1550del	p.Asn517ThrfsTer13	p.N517Tfs*13	ENST00000358485	NM_001080125.1	516	Aaa/aa	9/9	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.723285735212916	2		588	1157	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204515939	204515939	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	339	528	2	ENST00000367182.3:c.842del	p.Asn281MetfsTer10	p.N281Mfs*10	ENST00000367182	NM_001278516.1	279	ggA/gg	10/11	1	2	FACETS	0.98	0.929	1	0.98	0.929	1	CLONAL	1	TRUE	1	0.723285735212916	2		530	957	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001455	150001456	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	590	445	0	ENST00000253339.5:c.2148dup	p.Gly717TrpfsTer2	p.G717Wfs*2	ENST00000253339		716	-/T	4/7	0.723285735212916	2	FACETS	0.998	0.972	1	0.998	0.972	1	CLONAL	2	TRUE	0	0.723285735212916	2		445	817	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548269	41548269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	595	404	1	ENST00000263253.7:c.3061del	p.Thr1021LeufsTer3	p.T1021Lfs*3	ENST00000263253	NM_001429.3	1019	ttA/tt	16/31	0.723285735212916	2	FACETS	0.942	0.916	0.968	0.942	0.916	0.968	CLONAL	2	TRUE	0	0.723285735212916	2		405	873	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435128	110435129	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs772322568	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	174	293	0	ENST00000375856.3:c.3272dup	p.Lys1092GlufsTer233	p.K1092Efs*233	ENST00000375856	NM_003749.2	1091	ccg/ccCg	1/2	1	2	FACETS	0.725	0.669	0.782	0.725	0.669	0.782	SUBCLONAL	1	TRUE	1	0.723285735212916	2		293	664	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	404	692	2	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	0.9	0.857	0.944	0.9	0.857	0.944	CLONAL	1	TRUE	1	0.723285735212916	2		694	1241	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293221	91293221	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	153	236	0	ENST00000355112.3:c.726del	p.Ile243LeufsTer6	p.I243Lfs*6	ENST00000355112	NM_000057.2	241	ggC/gg	3/22	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.723285735212916	2		236	420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0011440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	338	450	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.71085270547099	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.71085270547099	1		450	560	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922321	178922321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	142	391	0	ENST00000263967.3:c.1090G>A	p.Gly364Arg	p.G364R	ENST00000263967	NM_006218.2	364	Gga/Aga	6/21	0.346085605302312	3	FACETS	0.526	0.478	0.576	0.175	0.159	0.192	INDETERMINATE	1	TRUE	0	0.71085270547099	3		391	1030	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255694	16255694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376676096	NA	P-0011440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	170	269	1	ENST00000375759.3:c.2959C>T	p.Arg987Cys	p.R987C	ENST00000375759	NM_015001.2	987	Cgc/Tgc	11/15	1	2	FACETS	0.964	0.894	1	0.964	0.894	1	CLONAL	1	TRUE	1	0.71085270547099	2		270	496	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796187	45796187	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs876659420	NA	P-0011440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	430	601	0	ENST00000450313.1:c.1518+1G>T		p.X506_splice	ENST00000450313	NM_012222.2	506			NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.71085270547099	2		601	1125	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468390	120468390	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	186	281	0	ENST00000256646.2:c.4049A>G	p.Lys1350Arg	p.K1350R	ENST00000256646	NM_024408.3	1350	aAa/aGa	25/34	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.71085270547099	2		281	506	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483259	120483259	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	49	383	1	ENST00000256646.2:c.3102C>A	p.Cys1034Ter	p.C1034*	ENST00000256646	NM_024408.3	1034	tgC/tgA	19/34	1	2	FACETS	0.187	0.158	0.22	0.187	0.158	0.22	SUBCLONAL	1	TRUE	1	0.71085270547099	2		384	736	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426749	212426749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1340739738	NA	P-0011440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	136	394	0	ENST00000342788.4:c.2366G>A	p.Ser789Asn	p.S789N	ENST00000342788	NM_005235.2	789	aGc/aAc	20/28	0.346744937172087	1	FACETS	0.419	0.383	0.458	0.419	0.383	0.458	INDETERMINATE	1	TRUE	0	0.71085270547099	1		394	588	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427695	72427695	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	54	382	0	ENST00000477973.2:c.795G>T	p.Lys265Asn	p.K265N	ENST00000477973	NM_012234.5	265	aaG/aaT	4/4	0.71085270547099	1	FACETS	0.309	0.265	0.356	0.309	0.265	0.356	SUBCLONAL	1	TRUE	0	0.71085270547099	1		382	317	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84390206	84390206	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	250	306	0	ENST00000321945.7:c.575G>C	p.Ser192Thr	p.S192T	ENST00000321945	NM_139076.2	192	aGc/aCc	6/9	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.71085270547099	2		306	640	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525618	187525618	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	380	619	1	ENST00000441802.2:c.10461G>T	p.Lys3487Asn	p.K3487N	ENST00000441802	NM_005245.3	3487	aaG/aaT	18/27	1	2	FACETS	0.974	0.926	1	0.974	0.926	1	CLONAL	1	TRUE	1	0.71085270547099	2		620	1098	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527259	187527259	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	236	353	0	ENST00000441802.2:c.10315G>T	p.Val3439Phe	p.V3439F	ENST00000441802	NM_005245.3	3439	Gtc/Ttc	17/27	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.71085270547099	2		353	658	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652062	36652062	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	294	503	1	ENST00000244741.5:c.184G>C	p.Asp62His	p.D62H	ENST00000244741	NM_000389.4	62	Gac/Cac	2/3	0.548516284436701	1	FACETS	0.824	0.782	0.866	0.824	0.782	0.866	CLONAL	1	TRUE	0	0.71085270547099	1		504	647	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211585	98211585	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	224	358	1	ENST00000331920.6:c.3570G>T	p.Leu1190Phe	p.L1190F	ENST00000331920	NM_000264.3	1190	ttG/ttT	22/24	0.71085270547099	1	FACETS	0.965	0.912	1	0.965	0.912	1	CLONAL	1	TRUE	0	0.71085270547099	1		359	421	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417364	139417364	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	272	379	0	ENST00000277541.6:c.680G>T	p.Cys227Phe	p.C227F	ENST00000277541	NM_017617.3	227	tGc/tTc	4/34	0.71085270547099	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.71085270547099	1		379	440	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566528	139566528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	36	496	0	ENST00000308874.7:c.787C>T	p.Gln263Ter	p.Q263*	ENST00000308874		263	Cag/Tag	9/10	0.71085270547099	1	FACETS	0.127	0.104	0.153	0.127	0.104	0.153	SUBCLONAL	1	TRUE	0	0.71085270547099	1		496	513	SUCCESS
EED	8726	MSKCC	GRCh37	11	85961378	85961378	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	49	366	0	ENST00000263360.6:c.155G>C	p.Arg52Pro	p.R52P	ENST00000263360	NM_003797.3	52	cGc/cCc	2/12	0.71085270547099	1	FACETS	0.185	0.157	0.217	0.185	0.157	0.217	SUBCLONAL	1	TRUE	0	0.71085270547099	1		366	480	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436966	110436966	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	18	39	0	ENST00000375856.3:c.1435C>G	p.Gln479Glu	p.Q479E	ENST00000375856	NM_003749.2	479	Cag/Gag	1/2	0.71085270547099	1	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	0	0.71085270547099	1		39	30	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477136	67477136	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	58	501	1	ENST00000327367.4:c.943G>T	p.Val315Phe	p.V315F	ENST00000327367	NM_005902.3	315	Gtc/Ttc	7/9	0.268913129237267	1	FACETS	0.124	0.106	0.144	0.124	0.106	0.144	INDETERMINATE	1	TRUE	0	0.71085270547099	1		502	846	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984891	9984891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	81	633	0	ENST00000330684.3:c.1074C>A	p.His358Gln	p.H358Q	ENST00000330684	NM_001134407.1	358	caC/caA	4/13	NA	2	FACETS	0.199	0.174	0.225			1	INDETERMINATE	1	TRUE	NA	0.71085270547099	2		633	1148	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215376	41215376	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1426821558	NA	P-0011440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	268	463	0	ENST00000357654.3:c.5167A>G	p.Ile1723Val	p.I1723V	ENST00000357654	NM_007294.3	1723	Att/Gtt	18/23	1	2	FACETS	0.876	0.824	0.929	0.876	0.824	0.929	CLONAL	1	TRUE	1	0.71085270547099	2		463	861	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113798	11113798	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	39	433	2	ENST00000358026.2:c.1906G>T	p.Ala636Ser	p.A636S	ENST00000358026	NM_001128849.1	636	Gcc/Tcc	12/36	1	2	FACETS	0.15	0.124	0.18	0.15	0.124	0.18	SUBCLONAL	1	TRUE	1	0.71085270547099	2		435	730	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408894	41408894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1420220673	NA	P-0011440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	47	476	2	ENST00000373198.4:c.532G>A	p.Ala178Thr	p.A178T	ENST00000373198	NM_133170.3	178	Gcc/Acc	4/32	0.374998409709827	1	FACETS	0.107	0.089	0.126	0.107	0.089	0.126	INDETERMINATE	1	TRUE	0	0.71085270547099	1		478	799	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966680	44966680	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1556375815	NA	P-0011440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	484	286	0	ENST00000377967.4:c.3904C>T	p.Gln1302Ter	p.Q1302*	ENST00000377967	NM_021140.2	1302	Caa/Taa	27/29	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.71085270547099	1		286	644	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354972	70354972	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	65	374	0	ENST00000374080.3:c.4894C>A	p.Leu1632Met	p.L1632M	ENST00000374080		1632	Ctg/Atg	36/45	1	1	FACETS	0.197	0.171	0.226	0.197	0.171	0.226	SUBCLONAL	1	TRUE	0	0.71085270547099	1		374	598	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023611	1023612	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0011440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	40	465	0	ENST00000358495.3:c.951_952dup	p.Thr318ArgfsTer5	p.T318Rfs*5	ENST00000358495	NM_134424.2	318	act/aGAct	10/12	0.71085270547099	1	FACETS	0.13	0.108	0.155	0.13	0.108	0.155	SUBCLONAL	1	TRUE	0	0.71085270547099	1		465	557	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852340	63852341	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0011440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	56	361	0	ENST00000279873.7:c.3122_3123dup	p.Gly1042LeufsTer66	p.G1042Lfs*66	ENST00000279873	NM_032199.2	1040	gtc/gTCtc	10/10	0.686795889774121	2	FACETS	0.235	0.201	0.272	0.117	0.1	0.136	SUBCLONAL	1	TRUE	0	0.71085270547099	2		361	671	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922765	44922788	+	inframe_deletion	In_Frame_Del	DEL	GCCACAGCTTGCTCTGACCAGAGT	GCCACAGCTTGCTCTGACCAGAGT	-	novel	NA	P-0011440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	63	297	0	ENST00000377967.4:c.1629_1652del	p.Gln544_Pro551del	p.Q544_P551del	ENST00000377967	NM_021140.2	542	caGCCACAGCTTGCTCTGACCAGAGTg/cag	16/29	1	1	FACETS	0.203	0.175	0.233	0.203	0.175	0.233	SUBCLONAL	1	TRUE	0	0.71085270547099	1		297	563	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096717	178096717	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0011440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	41	249	0	ENST00000397062.3:c.614del	p.Asp205AlafsTer16	p.D205Afs*16	ENST00000397062	NM_006164.4	205	gAc/gc	5/5	NA	2	FACETS	0.198	0.164	0.235			1	INDETERMINATE	1	TRUE	NA	0.71085270547099	2		249	584	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0011448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	193	489	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.791	0.732	0.853	0.791	0.732	0.853	SUBCLONAL	1	TRUE	1	0.523930409069098	2		489	931	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0011448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	356	600	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.523930409069098	2		600	1140	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0011448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	238	449	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	1	2	FACETS	0.93	0.869	0.993	0.93	0.869	0.993	CLONAL	1	TRUE	1	0.523930409069098	2		449	977	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156719	20156719	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	223	616	3	ENST00000379607.5:c.38G>T	p.Arg13Leu	p.R13L	ENST00000379607	NM_001412.3	13	cGc/cTc	2/7	1	2	FACETS	0.845	0.787	0.906	0.845	0.787	0.906	CLONAL	1	TRUE	1	0.523930409069098	2		619	1007	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0011448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	64	144	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	0.812	0.709	0.921	0.812	0.709	0.921	CLONAL	1	TRUE	1	0.523930409069098	2		144	301	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415537	152415537	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519714	NA	P-0011448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	231	544	0	ENST00000206249.3:c.1387T>C	p.Ser463Pro	p.S463P	ENST00000206249	NM_000125.3	463	Tcc/Ccc	7/8	1	2	FACETS	0.86	0.802	0.92	0.86	0.802	0.92	CLONAL	1	TRUE	1	0.523930409069098	2		544	1025	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1485978447	NA	P-0011448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	159	554	0	ENST00000324856.7:c.5164C>T	p.Arg1722Ter	p.R1722*	ENST00000324856	NM_006015.4	1722	Cga/Tga	20/20	1	2	FACETS	0.531	0.486	0.579	0.531	0.486	0.579	SUBCLONAL	1	TRUE	1	0.523930409069098	2		554	1142	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306960	65306960	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	46	523	1	ENST00000342505.4:c.2617C>T	p.Arg873Cys	p.R873C	ENST00000342505	NM_002227.2	873	Cgc/Tgc	19/25	1	2	FACETS	0.16	0.134	0.189	0.16	0.134	0.189	SUBCLONAL	1	TRUE	1	0.523930409069098	2		524	1098	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258060	123258060	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	249	610	0	ENST00000358487.5:c.1621A>C	p.Ile541Leu	p.I541L	ENST00000358487	NM_000141.4	541	Att/Ctt	12/18	1	2	FACETS	0.904	0.845	0.964	0.904	0.845	0.964	CLONAL	1	TRUE	1	0.523930409069098	2		610	1052	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741957	40741957	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	309	614	0	ENST00000392038.2:c.1015G>C	p.Val339Leu	p.V339L	ENST00000392038	NM_001626.4	339	Gtc/Ctc	11/14	1	2	FACETS	0.966	0.91	1	0.966	0.91	1	CLONAL	1	TRUE	1	0.523930409069098	2		614	1221	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692837	89692838	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0011448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	62	106	0	ENST00000371953.3:c.322_323del	p.Leu108Ter	p.L108*	ENST00000371953	NM_000314.4	107	gaTCtt/gatt	5/9	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.523930409069098	2		106	213	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589223	67589225	+	inframe_deletion	In_Frame_Del	DEL	TAA	TAA	-	novel	NA	P-0011448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	140	446	0	ENST00000274335.5:c.1214_1216del	p.Ile405del	p.I405del	ENST00000274335		404	tTAAta/tta	9/15	1	2	FACETS	0.807	0.737	0.881	0.807	0.737	0.881	CLONAL	1	TRUE	1	0.523930409069098	2		446	662	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183752	10183752	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs5030803	NA	P-0011480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	151	294	0	ENST00000256474.2:c.221T>A	p.Val74Asp	p.V74D	ENST00000256474	NM_000551.3	74	gTc/gAc	1/3	0.564919573696498	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.564919573696498	1		294	354	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157256601	157256601	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	311	273	0	ENST00000346085.5:c.1928A>G	p.Asp643Gly	p.D643G	ENST00000346085	NM_020732.3	643	gAc/gGc	5/20	0.564919573696498	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.564919573696498	1		273	731	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942839	44942839	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	430	242	0	ENST00000377967.4:c.3419G>A	p.Gly1140Glu	p.G1140E	ENST00000377967	NM_021140.2	1140	gGg/gAg	23/29	1	1	FACETS	0.759	0.731	0.786	1	0.997	1	SUBCLONAL	2	TRUE	0	0.564919573696498	1		242	720	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595924	52595924	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0011480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	227	518	0	ENST00000394830.3:c.3991del	p.Met1331Ter	p.M1331*	ENST00000394830	NM_018313.4	1331	Atg/tg	26/30	0.564919573696498	1	FACETS	0.602	0.561	0.644	0.602	0.561	0.644	SUBCLONAL	1	TRUE	0	0.564919573696498	1		518	958	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623236	52623237	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCATAA	novel	NA	P-0011480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	53	291	0	ENST00000394830.3:c.2814_2815insTTATGCA	p.Gly939LeufsTer16	p.G939Lfs*16	ENST00000394830	NM_018313.4	938	-/TTATGCA	19/30	0.564919573696498	1	FACETS	0.239	0.204	0.278	0.239	0.204	0.278	SUBCLONAL	1	TRUE	0	0.564919573696498	1		291	563	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0011482-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	113	435	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.108919571364957	3	FACETS	1	0.983	1	0.742	0.668	0.821	INDETERMINATE	1	TRUE	1	0.22	3		435	768	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0011482-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	39	324	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	0.108919571364957	3	FACETS	0.907	0.752	1	0.453	0.376	0.54	INDETERMINATE	1	TRUE	1	0.22	3		324	434	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115594	108115594	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730881336	NA	P-0011482-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	48	539	1	ENST00000278616.4:c.742C>T	p.Arg248Ter	p.R248*	ENST00000278616	NM_000051.3	248	Cga/Tga	7/63	0.108919571364957	3	FACETS	0.759	0.641	0.89	0.38	0.32	0.445	INDETERMINATE	1	TRUE	1	0.22	3		540	638	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686299	30686299	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs767191783	NA	P-0011482-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	49	482	0	ENST00000295754.5:c.155A>C	p.Lys52Thr	p.K52T	ENST00000295754	NM_003242.5	52	aAa/aCa	2/7	0.247520107846809	3	FACETS	0.667	0.564	0.782	0.334	0.282	0.391	SUBCLONAL	1	TRUE	1	0.22	3		482	741	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952054	178952054	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011482-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	33	437	0	ENST00000263967.3:c.3109G>C	p.Glu1037Gln	p.E1037Q	ENST00000263967	NM_006218.2	1037	Gag/Cag	21/21	0.247520107846809	3	FACETS	0.706	0.574	0.854	0.353	0.287	0.427	SUBCLONAL	1	TRUE	1	0.22	3		437	472	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633855	86633855	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011482-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	50	573	0	ENST00000274376.6:c.964A>C	p.Asn322His	p.N322H	ENST00000274376	NM_002890.2	322	Aat/Cat	5/25	0.415657627401206	4	FACETS	0.697	0.589	0.815	0.348	0.294	0.408	SUBCLONAL	1	TRUE	2	0.22	4		573	796	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020667	37020667	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011482-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	18	384	0	ENST00000358127.4:c.178G>C	p.Val60Leu	p.V60L	ENST00000358127	NM_001280556.1	60	Gtc/Ctc	2/10	1	2	FACETS	0.724	0.546	0.933	0.724	0.546	0.933	CLONAL	1	TRUE	1	0.22	2		384	226	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242287	98242287	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758585782	NA	P-0011482-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	33	454	0	ENST00000331920.6:c.1031G>A	p.Gly344Asp	p.G344D	ENST00000331920	NM_000264.3	344	gGt/gAt	7/24	1	2	FACETS	0.865	0.705	1	0.865	0.705	1	CLONAL	1	TRUE	1	0.22	2		454	347	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332543	70332543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011482-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	16	452	0	ENST00000373644.4:c.448G>A	p.Val150Ile	p.V150I	ENST00000373644	NM_030625.2	150	Gta/Ata	2/12	1	2	FACETS	0.566	0.418	0.742	0.566	0.418	0.742	SUBCLONAL	1	TRUE	1	0.22	2		452	257	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645279	67645279	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011482-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	45	498	1	ENST00000264010.4:c.544G>T	p.Glu182Ter	p.E182*	ENST00000264010	NM_006565.3	182	Gaa/Taa	3/12	0.108919571364957	0	FACETS	0.709	0.596	0.833			1	INDETERMINATE	1	TRUE	0	0.22	0		499	450	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864662	37864662	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1348253156	NA	P-0011482-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	98	673	0	ENST00000269571.5:c.314C>T	p.Thr105Ile	p.T105I	ENST00000269571		105	aCc/aTc	3/27	0.247520107846809	3	FACETS	0.852	0.766	0.942	1	0.975	1	CLONAL	3	TRUE	1	0.22	3		673	387	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911526	114911527	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0011482-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	58	674	0	ENST00000543371.1:c.1047_1048dup	p.Ile350ThrfsTer2	p.I350Tfs*2	ENST00000543371	NM_001198531.1	348	-/CA	10/14	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.22	2		674	366	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593649	55593649	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	50	506	0	ENST00000288135.5:c.1715A>G	p.Asp572Gly	p.D572G	ENST00000288135	NM_000222.2	572	gAc/gGc	11/21	0.287405874770296	2	FACETS	1	0.918	1	1	0.918	1	INDETERMINATE	2	TRUE	0	0.662250850226982	2		506	74	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149437136	149437136	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	39	543	1	ENST00000286301.3:c.2152C>T	p.Gln718Ter	p.Q718*	ENST00000286301	NM_005211.3	718	Cag/Tag	16/22	0.38572618483495	1	FACETS	0.78	0.667	0.897	0.78	0.667	0.897	INDETERMINATE	1	TRUE	0	0.662250850226982	1		544	101	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781471	3781471	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	21	186	0	ENST00000262367.5:c.4894T>G	p.Phe1632Val	p.F1632V	ENST00000262367	NM_004380.2	1632	Ttc/Gtc	30/31	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.662250850226982	2		186	52	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57569884	57569885	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0011518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	72	377	0	ENST00000316660.6:c.66dup	p.Val23SerfsTer65	p.V23Sfs*65	ENST00000316660	NM_021127.2	22	gaa/gAaa	2/2	0.662250850226982	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	0	0.662250850226982	2		377	106	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0011529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	163	397	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.685098538085309	1	FACETS	0.966	0.902	1	0.966	0.902	1	CLONAL	1	TRUE	0	0.685098538085309	1		397	324	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913233	32913233	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	384	1139	1	ENST00000380152.3:c.4741G>T	p.Glu1581Ter	p.E1581*	ENST00000380152		1581	Gag/Tag	11/27	0.685098538085309	1	FACETS	0.971	0.93	1	0.971	0.93	1	CLONAL	1	TRUE	0	0.685098538085309	1		1140	759	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869478	102869478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	158	408	1	ENST00000307046.8:c.163G>A	p.Gly55Arg	p.G55R	ENST00000307046	NM_001111285.1	55	Ggg/Agg	2/4	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.685098538085309	2		409	397	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753151	128753151	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	180	443	0	ENST00000377970.2:c.1312C>G	p.Arg438Gly	p.R438G	ENST00000377970	NM_002467.4	438	Cga/Gga	3/3	0.531594963827431	4	FACETS	1	0.978	1	0.385	0.356	0.416	CLONAL	1	TRUE	1	0.685098538085309	4		443	766	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608046	28608046	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	271	846	0	ENST00000241453.7:c.1920G>T	p.Gln640His	p.Q640H	ENST00000241453	NM_004119.2	640	caG/caT	15/24	1	2	FACETS	0.937	0.882	0.994	0.937	0.882	0.994	CLONAL	1	TRUE	1	0.685098538085309	2		846	844	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243523	46243545	+	frameshift_variant	Frame_Shift_Del	DEL	TCTGTTCCTGATGTATCTCCTGC	TCTGTTCCTGATGTATCTCCTGC	-	novel	NA	P-0011529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	53	622	0	ENST00000334344.6:c.1878_1900del	p.Val627PhefsTer72	p.V627Ffs*72	ENST00000334344	NM_152641.2	626	TCTGTTCCTGATGTATCTCCTGCt/t	14/21	1	2	FACETS	0.228	0.194	0.265	0.228	0.194	0.265	SUBCLONAL	1	TRUE	1	0.685098538085309	2		622	679	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0011563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	255	363	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.2698060782523	3	FACETS	1	0.952	1			1	CLONAL	2	TRUE	NA	0.349452933557238	3		364	843	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579357	7579358	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGGAAAC	rs1131691004	NA	P-0011563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	239	466	0	ENST00000269305.4:c.323_329dup	p.Leu111PhefsTer40	p.L111Ffs*40	ENST00000269305	NM_001126112.2	110	cgt/cgGTTTCCGt	4/11	0.341658519368141	2	FACETS	0.864	0.809	0.92	0.864	0.809	0.92	CLONAL	2	TRUE	0	0.349452933557238	2		466	792	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006194	22006194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	68	321	0	ENST00000276925.6:c.209C>T	p.Ala70Val	p.A70V	ENST00000276925	NM_004936.3	70	gCg/gTg	2/2	0.346792309022018	4	FACETS	0.828	0.721	0.945	0.414	0.36	0.473	CLONAL	1	TRUE	2	0.349452933557238	4		321	634	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799759	72799759	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	134	457	0	ENST00000325599.8:c.1410C>G	p.Asp470Glu	p.D470E	ENST00000325599	NM_018130.2	470	gaC/gaG	11/11	0.349452933557238	3	FACETS	1	0.936	1	0.519	0.471	0.569	CLONAL	1	TRUE	1	0.349452933557238	3		457	868	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245452	153245452	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	246	420	0	ENST00000281708.4:c.1739A>G	p.His580Arg	p.H580R	ENST00000281708	NM_033632.3	580	cAc/cGc	11/12	0.319034108818456	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.349452933557238	2		420	676	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574374	95574379	+	inframe_deletion	In_Frame_Del	DEL	CAACTC	CAACTC	-	novel	NA	P-0011563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	66	317	0	ENST00000393063.1:c.2488_2493del	p.Glu830_Leu831del	p.E830_L831del	ENST00000393063	NM_030621.3	830	GAGTTG/-	17/28	0.349452933557238	3	FACETS	0.702	0.609	0.803	0.351	0.304	0.402	SUBCLONAL	1	TRUE	1	0.349452933557238	3		317	632	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249468	153249468	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011603-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	145	473	0	ENST00000281708.4:c.1310G>T	p.Gly437Val	p.G437V	ENST00000281708	NM_033632.3	437	gGa/gTa	9/12	0.356191340892363	1	FACETS	0.723	0.666	0.783	0.723	0.666	0.783	INDETERMINATE	1	TRUE	0	0.618190429638848	1		473	448	SUCCESS
APC	324	MSKCC	GRCh37	5	112175213	112175213	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0011603-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	43	208	0	ENST00000257430.4:c.3922A>T	p.Lys1308Ter	p.K1308*	ENST00000257430	NM_000038.5	1308	Aaa/Taa	16/16	0.356191340892363	1	FACETS	0.373	0.314	0.437	0.373	0.314	0.437	INDETERMINATE	1	TRUE	0	0.618190429638848	1		208	258	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120794	94120794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs570778929	NA	P-0011603-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	459	1142	2	ENST00000369303.4:c.257G>A	p.Arg86Gln	p.R86Q	ENST00000369303	NM_004440.3	86	cGg/cAg	3/17	1	2	FACETS	0.981	0.936	1	0.981	0.936	1	CLONAL	1	TRUE	1	0.618190429638848	2		1144	1513	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210798	2210798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768650995	NA	P-0011603-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	88	408	0	ENST00000398665.3:c.1295C>T	p.Ala432Val	p.A432V	ENST00000398665	NM_032482.2	432	gCa/gTa	14/28	0.327744196205081	1	FACETS	0.419	0.373	0.469	0.419	0.373	0.469	INDETERMINATE	1	TRUE	0	0.618190429638848	1		408	469	SUCCESS
APC	324	MSKCC	GRCh37	5	112103076	112103077	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGAAAGA	novel	NA	P-0011603-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	83	323	0	ENST00000257430.4:c.415_422dup	p.Ser142LysfsTer31	p.S142Kfs*31	ENST00000257430	NM_000038.5	137	-/GAGAAAGA	4/16	0.356191340892363	1	FACETS	0.616	0.55	0.686	0.616	0.55	0.686	INDETERMINATE	1	TRUE	0	0.618190429638848	1		323	301	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	262	140	0				ENST00000310581	NM_198253.2	-/1132			0.438851687253997	6	FACETS	1	0.986	1	1	0.986	1	CLONAL	4	TRUE	2	0.438851687253997	6		140	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0012037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	242	287	0	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	0.368806133327416	2	FACETS	0.901	0.848	0.955	0.901	0.848	0.955	CLONAL	2	TRUE	0	0.438851687253997	2		287	612	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423641	88423641	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	149	237	0	ENST00000360948.2:c.2194C>G	p.Leu732Val	p.L732V	ENST00000360948	NM_001012338.2	732	Ctc/Gtc	18/19	0.413732439502242	4	FACETS	0.757	0.694	0.823	0.757	0.694	0.823	SUBCLONAL	2	TRUE	2	0.438851687253997	4		237	645	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953720	48953734	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTGTTTGTAGCGATA	TTGTTTGTAGCGATA	-	novel	NA	P-0012037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	86	97	0	ENST00000267163.4:c.1333-10_1337del		p.X445_splice	ENST00000267163	NM_000321.2	445		14/27	0.434187583753073	2	FACETS	0.763	0.684	0.843	0.763	0.684	0.843	SUBCLONAL	2	TRUE	0	0.438851687253997	2		97	257	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424436	49424436	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	118	283	0	ENST00000301067.7:c.13787del	p.Gly4596GlufsTer21	p.G4596Efs*21	ENST00000301067	NM_003482.3	4596	gGa/ga	41/54	0.374020981777954	3	FACETS	0.867	0.783	0.957	0.434	0.391	0.479	CLONAL	1	TRUE	1	0.438851687253997	3		283	756	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16005016	16005017	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	219	252	0	ENST00000268712.3:c.2237dup	p.Asn746LysfsTer7	p.N746Kfs*7	ENST00000268712	NM_006311.3	746	aac/aaAc	20/46	0.368806133327416	2	FACETS	0.917	0.861	0.975	0.917	0.861	0.975	CLONAL	2	TRUE	0	0.438851687253997	2		252	544	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166245	32166245	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1454423919	NA	P-0012042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	376	677	0	ENST00000375023.3:c.4709C>T	p.Pro1570Leu	p.P1570L	ENST00000375023	NM_004557.3	1570	cCc/cTc	26/30	1	2	FACETS	0.952	0.906	0.999	0.952	0.906	0.999	CLONAL	1	TRUE	1	0.769862917545866	2		677	1026	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436311	52436311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773230722	NA	P-0012042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	338	534	0	ENST00000460680.1:c.2183G>A	p.Arg728His	p.R728H	ENST00000460680	NM_004656.3	728	cGc/cAc	17/17	NA	2	FACETS	0.918	0.87	0.966			1	INDETERMINATE	1	TRUE	NA	0.769862917545866	2		534	957	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933828	39933829	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	440	714	0	ENST00000378444.4:c.770dup	p.Ser259IlefsTer42	p.S259Ifs*42	ENST00000378444	NM_001123385.1	257	atc/atTc	4/15	1	2	FACETS	0.915	0.874	0.957	0.915	0.874	0.957	CLONAL	1	TRUE	1	0.769862917545866	2		714	1249	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0012078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	90	640	1	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.3	3	FACETS	0.9	0.798	1			1	CLONAL	2	TRUE	NA	0.15	3		641	717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0012078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	74	1413	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	1	2	FACETS	0.979	0.855	1	0.979	0.855	1	CLONAL	1	TRUE	1	0.15	2		1413	1008	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745530	162745530	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	69	1260	2	ENST00000367921.3:c.1945C>T	p.Pro649Ser	p.P649S	ENST00000367921	NM_006182.2	649	Cct/Tct	15/18	1	2	FACETS	0.925	0.803	1	0.925	0.803	1	CLONAL	1	TRUE	1	0.15	2		1262	995	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930320	39930321	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0012078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	79	1516	0	ENST00000378444.4:c.3143dup	p.Ala1049SerfsTer30	p.A1049Sfs*30	ENST00000378444	NM_001123385.1	1048	cca/ccCa	6/15	1	2	FACETS	0.95	0.833	1	0.95	0.833	1	CLONAL	1	TRUE	1	0.15	2		1516	1109	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379426	225379426	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	169	582	1	ENST00000264414.4:c.442C>T	p.Arg148Ter	p.R148*	ENST00000264414	NM_003590.4	148	Cga/Tga	4/16	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.405056859930166	2		583	829	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1224	311	1096	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	0.405056859930166	2		1096	1535	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	95	183	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.836	0.746	0.931	0.836	0.746	0.931	CLONAL	1	TRUE	1	0.405056859930166	2		183	561	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2493197	2493197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762075584	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	240	811	5	ENST00000355716.4:c.637G>A	p.Val213Ile	p.V213I	ENST00000355716	NM_003820.2	213	Gtc/Atc	6/8	1	2	FACETS	0.98	0.914	1	0.98	0.914	1	CLONAL	1	TRUE	1	0.405056859930166	2		816	1209	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199369	11199369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	137	579	1	ENST00000361445.4:c.5122G>A	p.Ala1708Thr	p.A1708T	ENST00000361445	NM_004958.3	1708	Gcc/Acc	36/58	1	2	FACETS	0.968	0.882	1	0.968	0.882	1	CLONAL	1	TRUE	1	0.405056859930166	2		580	699	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303220	11303220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778152958	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	186	672	1	ENST00000361445.4:c.1363G>A	p.Val455Met	p.V455M	ENST00000361445	NM_004958.3	455	Gtg/Atg	9/58	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.405056859930166	2		673	914	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17350493	17350493	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	146	556	0	ENST00000375499.3:c.617A>G	p.Tyr206Cys	p.Y206C	ENST00000375499	NM_003000.2	206	tAt/tGt	6/8	1	2	FACETS	0.781	0.712	0.853	0.781	0.712	0.853	SUBCLONAL	1	TRUE	1	0.405056859930166	2		556	923	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	248	303	0	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.405056859930166	2		303	1163	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363069	40363069	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	182	632	1	ENST00000397332.2:c.1160G>T	p.Arg387Ile	p.R387I	ENST00000397332	NM_001033082.2	387	aGa/aTa	3/3	1	2	FACETS	0.995	0.919	1	0.995	0.919	1	CLONAL	1	TRUE	1	0.405056859930166	2		633	903	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65304164	65304164	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	150	704	0	ENST00000342505.4:c.2951C>T	p.Ala984Val	p.A984V	ENST00000342505	NM_002227.2	984	gCc/gTc	21/25	1	2	FACETS	0.81	0.74	0.884	0.81	0.74	0.884	CLONAL	1	TRUE	1	0.405056859930166	2		704	914	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873245	71873245	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	247	880	0	ENST00000357731.5:c.949A>G	p.Thr317Ala	p.T317A	ENST00000357731	NM_173808.2	317	Aca/Gca	7/7	1	2	FACETS	0.961	0.897	1	0.961	0.897	1	CLONAL	1	TRUE	1	0.405056859930166	2		880	1269	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428507	78428507	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	174	554	1	ENST00000370768.2:c.1292G>T	p.Gly431Val	p.G431V	ENST00000370768	NM_003902.3	431	gGc/gTc	14/20	1	2	FACETS	0.954	0.878	1	0.954	0.878	1	CLONAL	1	TRUE	1	0.405056859930166	2		555	901	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736574	85736574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	196	766	1	ENST00000370580.1:c.73C>T	p.Arg25Cys	p.R25C	ENST00000370580	NM_003921.4	25	Cgt/Tgt	2/3	1	2	FACETS	0.842	0.778	0.908	0.842	0.778	0.908	CLONAL	1	TRUE	1	0.405056859930166	2		767	1150	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115252246	115252246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1456325880	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	219	726	1	ENST00000369535.4:c.394G>A	p.Glu132Lys	p.E132K	ENST00000369535	NM_002524.4	132	Gaa/Aaa	4/7	1	2	FACETS	0.948	0.881	1	0.948	0.881	1	CLONAL	1	TRUE	1	0.405056859930166	2		727	1141	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724625	162724625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757919179	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	146	587	1	ENST00000367921.3:c.397C>T	p.Arg133Trp	p.R133W	ENST00000367921	NM_006182.2	133	Cgg/Tgg	5/18	1	2	FACETS	0.94	0.859	1	0.94	0.859	1	CLONAL	1	TRUE	1	0.405056859930166	2		588	767	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724978	162724978	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	229	812	0	ENST00000367921.3:c.450T>G	p.Ile150Met	p.I150M	ENST00000367921	NM_006182.2	150	atT/atG	6/18	1	2	FACETS	0.95	0.884	1	0.95	0.884	1	CLONAL	1	TRUE	1	0.405056859930166	2		812	1190	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729743	162729743	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	140	517	0	ENST00000367921.3:c.829C>T	p.Arg277Cys	p.R277C	ENST00000367921	NM_006182.2	277	Cgc/Tgc	8/18	1	2	FACETS	0.871	0.793	0.952	0.871	0.793	0.952	CLONAL	1	TRUE	1	0.405056859930166	2		517	794	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612648	228612648	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1346	292	1194	0	ENST00000366696.1:c.379C>A	p.Leu127Met	p.L127M	ENST00000366696	NM_003493.2	127	Ctg/Atg	1/1	1	2	FACETS	0.88	0.826	0.937	0.88	0.826	0.937	CLONAL	1	TRUE	1	0.405056859930166	2		1194	1638	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243708859	243708859	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777060434	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	108	540	0	ENST00000263826.5:c.1204C>T	p.His402Tyr	p.H402Y	ENST00000263826	NM_005465.4	402	Cac/Tac	11/13	1	2	FACETS	0.762	0.684	0.844	0.762	0.684	0.844	SUBCLONAL	1	TRUE	1	0.405056859930166	2		540	700	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716083	243716083	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	106	600	0	ENST00000263826.5:c.1111T>C	p.Ser371Pro	p.S371P	ENST00000263826	NM_005465.4	371	Tca/Cca	10/13	1	2	FACETS	0.666	0.597	0.739	0.666	0.597	0.739	SUBCLONAL	1	TRUE	1	0.405056859930166	2		600	786	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736329	243736329	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	134	567	1	ENST00000263826.5:c.718G>T	p.Glu240Ter	p.E240*	ENST00000263826	NM_005465.4	240	Gag/Tag	8/13	1	2	FACETS	0.826	0.751	0.905	0.826	0.751	0.905	CLONAL	1	TRUE	1	0.405056859930166	2		568	801	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082763	16082763	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	31	95	0	ENST00000281043.3:c.577T>A	p.Phe193Ile	p.F193I	ENST00000281043	NM_005378.4	193	Ttc/Atc	2/3	1	2	FACETS	1	0.831	1	1	0.831	1	CLONAL	1	TRUE	1	0.405056859930166	2		95	151	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519920	29519920	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1172956542	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	135	477	0	ENST00000389048.3:c.1651C>T	p.Arg551Ter	p.R551*	ENST00000389048	NM_004304.4	551	Cga/Tga	9/29	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.405056859930166	2		477	612	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033753	48033753	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1553333707	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	112	505	1	ENST00000234420.5:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000234420	NM_000179.2	1322	Gaa/Taa	9/10	1	2	FACETS	0.78	0.702	0.862	0.78	0.702	0.862	SUBCLONAL	1	TRUE	1	0.405056859930166	2		506	709	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	178	574	2	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	1	2	FACETS	0.868	0.8	0.94	0.868	0.8	0.94	CLONAL	1	TRUE	1	0.405056859930166	2		576	1012	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99136537	99136537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746072331	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	123	634	0	ENST00000074304.5:c.26G>A	p.Arg9His	p.R9H	ENST00000074304	NM_001134224.1	9	cGc/cAc	3/26	1	2	FACETS	0.796	0.72	0.876	0.796	0.72	0.876	SUBCLONAL	1	TRUE	1	0.405056859930166	2		634	763	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172150	99172150	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	178	705	2	ENST00000074304.5:c.1716G>T	p.Lys572Asn	p.K572N	ENST00000074304	NM_001134224.1	572	aaG/aaT	17/26	1	2	FACETS	0.939	0.865	1	0.939	0.865	1	CLONAL	1	TRUE	1	0.405056859930166	2		707	936	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182574	99182574	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	137	466	0	ENST00000074304.5:c.2377C>T	p.Arg793Ter	p.R793*	ENST00000074304	NM_001134224.1	793	Cga/Tga	22/26	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.405056859930166	2		466	624	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268478	198268478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	119	559	0	ENST00000335508.6:c.1550G>A	p.Arg517His	p.R517H	ENST00000335508	NM_012433.2	517	cGt/cAt	12/25	1	2	FACETS	0.766	0.692	0.845	0.766	0.692	0.845	SUBCLONAL	1	TRUE	1	0.405056859930166	2		559	767	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198283258	198283258	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	162	710	1	ENST00000335508.6:c.470G>A	p.Arg157Gln	p.R157Q	ENST00000335508	NM_012433.2	157	cGa/cAa	5/25	1	2	FACETS	0.817	0.749	0.888	0.817	0.749	0.888	CLONAL	1	TRUE	1	0.405056859930166	2		711	979	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149907	202149907	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	153	564	0	ENST00000358485.4:c.1348A>G	p.Arg450Gly	p.R450G	ENST00000358485	NM_001080125.1	450	Aga/Gga	8/9	1	2	FACETS	0.918	0.84	0.999	0.918	0.84	0.999	CLONAL	1	TRUE	1	0.405056859930166	2		564	823	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251860	212251860	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764544368	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	99	336	0	ENST00000342788.4:c.3199C>T	p.Arg1067Ter	p.R1067*	ENST00000342788	NM_005235.2	1067	Cga/Tga	27/28	1	2	FACETS	0.867	0.776	0.963	0.867	0.776	0.963	CLONAL	1	TRUE	1	0.405056859930166	2		336	564	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660195	227660195	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1234342137	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	157	624	0	ENST00000305123.5:c.3260T>C	p.Val1087Ala	p.V1087A	ENST00000305123	NM_005544.2	1087	gTg/gCg	1/2	1	2	FACETS	0.923	0.846	1	0.923	0.846	1	CLONAL	1	TRUE	1	0.405056859930166	2		624	840	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660618	227660618	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	109	436	2	ENST00000305123.5:c.2837T>C	p.Leu946Pro	p.L946P	ENST00000305123	NM_005544.2	946	cTg/cCg	1/2	1	2	FACETS	0.898	0.809	0.993	0.898	0.809	0.993	CLONAL	1	TRUE	1	0.405056859930166	2		438	599	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180433	38180433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	140	537	0	ENST00000396334.3:c.281G>A	p.Arg94His	p.R94H	ENST00000396334	NM_002468.4	94	cGc/cAc	1/5	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.405056859930166	2		537	651	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058713	47058713	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	166	486	0	ENST00000409792.3:c.7565A>C	p.Lys2522Thr	p.K2522T	ENST00000409792	NM_014159.6	2522	aAg/aCg	21/21	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.405056859930166	2		486	817	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125289	47125289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	219	924	0	ENST00000409792.3:c.5981G>A	p.Arg1994Lys	p.R1994K	ENST00000409792	NM_014159.6	1994	aGg/aAg	12/21	1	2	FACETS	0.892	0.829	0.958	0.892	0.829	0.958	CLONAL	1	TRUE	1	0.405056859930166	2		924	1212	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163557	47163557	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767694898	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	83	389	1	ENST00000409792.3:c.2569G>A	p.Gly857Ser	p.G857S	ENST00000409792	NM_014159.6	857	Ggt/Agt	3/21	1	2	FACETS	0.813	0.72	0.913	0.813	0.72	0.913	CLONAL	1	TRUE	1	0.405056859930166	2		390	504	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721989	49721989	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	40	167	0	ENST00000449682.2:c.1870A>G	p.Thr624Ala	p.T624A	ENST00000449682	NM_020998.3	624	Acc/Gcc	16/18	1	2	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	TRUE	1	0.405056859930166	2		167	196	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643357	52643357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	157	638	0	ENST00000394830.3:c.2539G>A	p.Val847Ile	p.V847I	ENST00000394830	NM_018313.4	847	Gta/Ata	17/30	1	2	FACETS	0.897	0.822	0.976	0.897	0.822	0.976	CLONAL	1	TRUE	1	0.405056859930166	2		638	864	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52677301	52677301	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	224	778	1	ENST00000394830.3:c.958C>A	p.Leu320Ile	p.L320I	ENST00000394830	NM_018313.4	320	Ctt/Att	10/30	1	2	FACETS	0.893	0.83	0.959	0.893	0.83	0.959	CLONAL	1	TRUE	1	0.405056859930166	2		779	1238	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027117	71027117	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	156	484	0	ENST00000318789.4:c.1210C>T	p.Pro404Ser	p.P404S	ENST00000318789	NM_032682.5	404	Cct/Tct	15/21	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.405056859930166	2		484	768	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096117	71096117	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	121	471	2	ENST00000318789.4:c.640C>A	p.Leu214Ile	p.L214I	ENST00000318789	NM_032682.5	214	Ctt/Att	10/21	1	2	FACETS	0.89	0.806	0.979	0.89	0.806	0.979	CLONAL	1	TRUE	1	0.405056859930166	2		473	671	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72861918	72861918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs957910250	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	121	521	0	ENST00000325599.8:c.964G>A	p.Val322Met	p.V322M	ENST00000325599	NM_018130.2	322	Gtg/Atg	9/11	1	2	FACETS	0.823	0.744	0.906	0.823	0.744	0.906	CLONAL	1	TRUE	1	0.405056859930166	2		521	726	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391126	89391126	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	137	583	0	ENST00000336596.2:c.1192G>T	p.Asp398Tyr	p.D398Y	ENST00000336596	NM_005233.5	398	Gac/Tac	5/17	1	2	FACETS	0.881	0.802	0.963	0.881	0.802	0.963	CLONAL	1	TRUE	1	0.405056859930166	2		583	768	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462418	89462418	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	92	406	0	ENST00000336596.2:c.1888+2T>C		p.X630_splice	ENST00000336596	NM_005233.5	630			1	2	FACETS	0.854	0.761	0.952	0.854	0.761	0.952	CLONAL	1	TRUE	1	0.405056859930166	2		406	532	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521621	89521621	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	136	498	0	ENST00000336596.2:c.2698A>C	p.Asn900His	p.N900H	ENST00000336596	NM_005233.5	900	Aac/Cac	16/17	1	2	FACETS	0.9	0.819	0.985	0.9	0.819	0.985	CLONAL	1	TRUE	1	0.405056859930166	2		498	746	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851592	134851592	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	159	675	0	ENST00000398015.3:c.998T>C	p.Val333Ala	p.V333A	ENST00000398015	NM_004441.4	333	gTc/gCc	5/16	1	2	FACETS	0.953	0.874	1	0.953	0.874	1	CLONAL	1	TRUE	1	0.405056859930166	2		675	824	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215249	142215249	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745882886	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	193	683	1	ENST00000350721.4:c.5852G>A	p.Arg1951Gln	p.R1951Q	ENST00000350721	NM_001184.3	1951	cGa/cAa	34/47	1	2	FACETS	0.92	0.85	0.992	0.92	0.85	0.992	CLONAL	1	TRUE	1	0.405056859930166	2		684	1036	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269080	142269080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	155	572	1	ENST00000350721.4:c.2870C>T	p.Ala957Val	p.A957V	ENST00000350721	NM_001184.3	957	gCt/gTt	14/47	1	2	FACETS	0.855	0.783	0.931	0.855	0.783	0.931	CLONAL	1	TRUE	1	0.405056859930166	2		573	895	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948101	178948101	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	39	481	0	ENST00000263967.3:c.2873A>G	p.Gln958Arg	p.Q958R	ENST00000263967	NM_006218.2	958	cAg/cGg	20/21	1	2	FACETS	0.249	0.206	0.298	0.249	0.206	0.298	SUBCLONAL	1	TRUE	1	0.405056859930166	2		481	772	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	131	569	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	1	2	FACETS	0.809	0.734	0.887	0.809	0.734	0.887	CLONAL	1	TRUE	1	0.405056859930166	2		569	800	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430396	181430396	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	245	728	0	ENST00000325404.1:c.248C>T	p.Ser83Leu	p.S83L	ENST00000325404	NM_003106.3	83	tCg/tTg	1/1	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.405056859930166	2		728	1068	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430444	181430444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	244	707	0	ENST00000325404.1:c.296C>T	p.Ala99Val	p.A99V	ENST00000325404	NM_003106.3	99	gCg/gTg	1/1	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.405056859930166	2		707	1063	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440303	187440303	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	167	510	0	ENST00000232014.4:c.2064G>T	p.Lys688Asn	p.K688N	ENST00000232014	NM_001130845.1	688	aaG/aaT	10/10	1	2	FACETS	0.991	0.912	1	0.991	0.912	1	CLONAL	1	TRUE	1	0.405056859930166	2		510	832	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444519	187444519	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	149	583	2	ENST00000232014.4:c.1708G>A	p.Gly570Ser	p.G570S	ENST00000232014	NM_001130845.1	570	Ggt/Agt	7/10	1	2	FACETS	0.912	0.834	0.993	0.912	0.834	0.993	CLONAL	1	TRUE	1	0.405056859930166	2		585	807	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447679	187447679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568417048	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	107	425	3	ENST00000232014.4:c.514G>A	p.Ala172Thr	p.A172T	ENST00000232014	NM_001130845.1	172	Gcc/Acc	5/10	1	2	FACETS	0.906	0.815	1	0.906	0.815	1	CLONAL	1	TRUE	1	0.405056859930166	2		428	583	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586473	189586473	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	123	348	0	ENST00000264731.3:c.1097A>G	p.Asp366Gly	p.D366G	ENST00000264731	NM_003722.4	366	gAc/gGc	8/14	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.405056859930166	2		348	605	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136805	55136805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41279521	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	120	485	0	ENST00000257290.5:c.1127G>A	p.Arg376Gln	p.R376Q	ENST00000257290	NM_006206.4	376	cGa/cAa	8/23	1	2	FACETS	0.875	0.792	0.963	0.875	0.792	0.963	CLONAL	1	TRUE	1	0.405056859930166	2		485	677	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968631	55968631	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	179	686	0	ENST00000263923.4:c.2032A>C	p.Thr678Pro	p.T678P	ENST00000263923	NM_002253.2	678	Aca/Cca	14/30	1	2	FACETS	0.837	0.771	0.906	0.837	0.771	0.906	CLONAL	1	TRUE	1	0.405056859930166	2		686	1056	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230740	66230740	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143201043	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	99	478	1	ENST00000273854.3:c.2231C>T	p.Thr744Ile	p.T744I	ENST00000273854	NM_004439.5	744	aCc/aTc	12/18	1	2	FACETS	0.856	0.766	0.951	0.856	0.766	0.951	CLONAL	1	TRUE	1	0.405056859930166	2		479	571	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467698	66467698	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753230187	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	130	587	1	ENST00000273854.3:c.571C>T	p.Arg191Cys	p.R191C	ENST00000273854	NM_004439.5	191	Cgt/Tgt	3/18	1	2	FACETS	0.947	0.86	1	0.947	0.86	1	CLONAL	1	TRUE	1	0.405056859930166	2		588	678	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99806158	99806158	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	47	220	0	ENST00000280892.6:c.514G>A	p.Ala172Thr	p.A172T	ENST00000280892	NM_001130678.1	172	Gct/Act	6/7	1	2	FACETS	0.814	0.691	0.948	0.814	0.691	0.948	CLONAL	1	TRUE	1	0.405056859930166	2		220	285	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99823069	99823069	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	146	545	0	ENST00000280892.6:c.143T>C	p.Val48Ala	p.V48A	ENST00000280892	NM_001130678.1	48	gTt/gCt	2/7	1	2	FACETS	0.906	0.827	0.988	0.906	0.827	0.988	CLONAL	1	TRUE	1	0.405056859930166	2		545	796	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180822	106180822	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	168	523	0	ENST00000380013.4:c.3850T>C	p.Ser1284Pro	p.S1284P	ENST00000380013	NM_001127208.2	1284	Tcc/Ccc	7/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.405056859930166	2		523	781	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	110	210	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.988	0.89	1	0.988	0.89	1	CLONAL	1	TRUE	1	0.405056859930166	2		210	550	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554869	187554869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	188	678	0	ENST00000441802.2:c.4292C>T	p.Ala1431Val	p.A1431V	ENST00000441802	NM_005245.3	1431	gCt/gTt	7/27	1	2	FACETS	0.912	0.842	0.984	0.912	0.842	0.984	CLONAL	1	TRUE	1	0.405056859930166	2		678	1018	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628443	187628443	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	134	553	0	ENST00000441802.2:c.2539A>G	p.Thr847Ala	p.T847A	ENST00000441802	NM_005245.3	847	Aca/Gca	2/27	1	2	FACETS	0.839	0.762	0.919	0.839	0.762	0.919	CLONAL	1	TRUE	1	0.405056859930166	2		553	789	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1255459	1255459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777672180	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	170	532	2	ENST00000310581.5:c.3100C>T	p.Arg1034Cys	p.R1034C	ENST00000310581	NM_198253.2	1034	Cgc/Tgc	14/16	1	2	FACETS	0.981	0.902	1	0.981	0.902	1	CLONAL	1	TRUE	1	0.405056859930166	2		534	856	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876449	35876449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2229232	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	137	510	0	ENST00000303115.3:c.1241C>T	p.Thr414Met	p.T414M	ENST00000303115	NM_002185.3	414	aCg/aTg	8/8	1	2	FACETS	0.985	0.898	1	0.985	0.898	1	CLONAL	1	TRUE	1	0.405056859930166	2		510	687	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950099	38950099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757900166	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	120	490	3	ENST00000357387.3:c.3851C>T	p.Ser1284Leu	p.S1284L	ENST00000357387	NM_152756.3	1284	tCg/tTg	31/38	1	2	FACETS	0.782	0.706	0.861	0.782	0.706	0.861	SUBCLONAL	1	TRUE	1	0.405056859930166	2		493	758	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950411	38950411	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	168	584	0	ENST00000357387.3:c.3539A>C	p.Glu1180Ala	p.E1180A	ENST00000357387	NM_152756.3	1180	gAa/gCa	31/38	1	2	FACETS	0.976	0.898	1	0.976	0.898	1	CLONAL	1	TRUE	1	0.405056859930166	2		584	850	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959902	38959902	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	151	538	0	ENST00000357387.3:c.2030A>G	p.Glu677Gly	p.E677G	ENST00000357387	NM_152756.3	677	gAa/gGa	21/38	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.405056859930166	2		538	739	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160737	56160737	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	182	548	0	ENST00000399503.3:c.1011A>C	p.Lys337Asn	p.K337N	ENST00000399503	NM_005921.1	337	aaA/aaC	4/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.405056859930166	2		548	844	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575550	67575550	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	136	444	0	ENST00000274335.5:c.623C>A	p.Ser208Tyr	p.S208Y	ENST00000274335		208	tCt/tAt	4/15	1	2	FACETS	0.933	0.849	1	0.933	0.849	1	CLONAL	1	TRUE	1	0.405056859930166	2		444	720	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592030	67592030	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	146	442	0	ENST00000274335.5:c.1846T>G	p.Leu616Val	p.L616V	ENST00000274335		616	Ttg/Gtg	14/15	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.405056859930166	2		442	692	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86637113	86637113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	67	239	0	ENST00000274376.6:c.1024G>A	p.Glu342Lys	p.E342K	ENST00000274376	NM_002890.2	342	Gaa/Aaa	6/25	1	2	FACETS	0.835	0.729	0.949	0.835	0.729	0.949	CLONAL	1	TRUE	1	0.405056859930166	2		239	396	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685313	86685313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886060844	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	96	277	0	ENST00000274376.6:c.3029G>A	p.Arg1010Gln	p.R1010Q	ENST00000274376	NM_002890.2	1010	cGa/cAa	24/25	1	2	FACETS	0.992	0.888	1	0.992	0.888	1	CLONAL	1	TRUE	1	0.405056859930166	2		277	478	SUCCESS
APC	324	MSKCC	GRCh37	5	112173365	112173365	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	175	617	0	ENST00000257430.4:c.2074C>A	p.Pro692Thr	p.P692T	ENST00000257430	NM_000038.5	692	Cct/Act	16/16	1	2	FACETS	0.948	0.874	1	0.948	0.874	1	CLONAL	1	TRUE	1	0.405056859930166	2		617	911	SUCCESS
APC	324	MSKCC	GRCh37	5	112179788	112179788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201459013	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	86	348	1	ENST00000257430.4:c.8497C>T	p.Arg2833Cys	p.R2833C	ENST00000257430	NM_000038.5	2833	Cgc/Tgc	16/16	1	2	FACETS	0.788	0.699	0.883	0.788	0.699	0.883	SUBCLONAL	1	TRUE	1	0.405056859930166	2		349	539	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931352	131931352	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	199	667	2	ENST00000265335.6:c.2057G>A	p.Arg686Lys	p.R686K	ENST00000265335		686	aGa/aAa	13/25	1	2	FACETS	0.95	0.88	1	0.95	0.88	1	CLONAL	1	TRUE	1	0.405056859930166	2		669	1034	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456962	149456962	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764483518	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	190	597	2	ENST00000286301.3:c.766C>T	p.Arg256Cys	p.R256C	ENST00000286301	NM_005211.3	256	Cgt/Tgt	6/22	1	2	FACETS	0.965	0.892	1	0.965	0.892	1	CLONAL	1	TRUE	1	0.405056859930166	2		599	972	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709473	176709473	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	195	856	0	ENST00000439151.2:c.5900T>G	p.Phe1967Cys	p.F1967C	ENST00000439151	NM_022455.4	1967	tTt/tGt	19/23	1	2	FACETS	0.875	0.809	0.944	0.875	0.809	0.944	CLONAL	1	TRUE	1	0.405056859930166	2		856	1100	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912165	29912165	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	32	158	0	ENST00000376809.5:c.886C>A	p.Leu296Met	p.L296M	ENST00000376809	NM_002116.7	296	Ctg/Atg	4/8	1	2	FACETS	0.958	0.787	1	0.958	0.787	1	CLONAL	1	TRUE	1	0.405056859930166	2		158	165	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672548	30672548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	294	834	1	ENST00000376406.3:c.4412C>T	p.Ser1471Phe	p.S1471F	ENST00000376406	NM_014641.2	1471	tCt/tTt	10/15	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.405056859930166	2		835	1288	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681477	30681477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28986464	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	173	643	2	ENST00000376406.3:c.535C>T	p.Arg179Cys	p.R179C	ENST00000376406	NM_014641.2	179	Cgt/Tgt	4/15	1	2	FACETS	0.865	0.795	0.937	0.865	0.795	0.937	CLONAL	1	TRUE	1	0.405056859930166	2		645	988	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190396	32190396	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1428476887	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	171	640	0	ENST00000375023.3:c.343C>T	p.Gln115Ter	p.Q115*	ENST00000375023	NM_004557.3	115	Cag/Tag	3/30	1	2	FACETS	0.926	0.852	1	0.926	0.852	1	CLONAL	1	TRUE	1	0.405056859930166	2		640	912	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32191681	32191681	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	224	744	0	ENST00000375023.3:c.25C>A	p.Leu9Met	p.L9M	ENST00000375023	NM_004557.3	9	Ctg/Atg	1/30	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.405056859930166	2		744	1059	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288218	33288218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540123402	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	150	532	0	ENST00000374542.5:c.1190G>A	p.Arg397Gln	p.R397Q	ENST00000374542	NM_001141970.1	397	cGg/cAg	4/8	1	2	FACETS	0.868	0.794	0.946	0.868	0.794	0.946	CLONAL	1	TRUE	1	0.405056859930166	2		532	853	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288764	33288764	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1429735040	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	129	381	2	ENST00000374542.5:c.788G>A	p.Arg263His	p.R263H	ENST00000374542	NM_001141970.1	263	cGc/cAc	3/8	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.405056859930166	2		383	573	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138916	37138916	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	141	511	0	ENST00000373509.5:c.256G>T	p.Val86Leu	p.V86L	ENST00000373509	NM_002648.3	86	Gtg/Ttg	4/6	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.405056859930166	2		511	680	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140870	37140870	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	195	724	1	ENST00000373509.5:c.706G>A	p.Val236Met	p.V236M	ENST00000373509	NM_002648.3	236	Gtg/Atg	5/6	1	2	FACETS	0.939	0.869	1	0.939	0.869	1	CLONAL	1	TRUE	1	0.405056859930166	2		725	1025	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43749815	43749815	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140461341	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	251	775	2	ENST00000523873.1:c.668G>A	p.Arg223His	p.R223H	ENST00000523873		223	cGt/cAt	7/8	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.405056859930166	2		777	1219	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93953254	93953254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1487534212	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	182	806	0	ENST00000369303.4:c.2887G>A	p.Val963Met	p.V963M	ENST00000369303	NM_004440.3	963	Gtg/Atg	17/17	1	2	FACETS	0.934	0.862	1	0.934	0.862	1	CLONAL	1	TRUE	1	0.405056859930166	2		806	962	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967232	93967232	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	131	611	0	ENST00000369303.4:c.2120T>G	p.Val707Gly	p.V707G	ENST00000369303	NM_004440.3	707	gTc/gGc	12/17	1	2	FACETS	0.852	0.774	0.934	0.852	0.774	0.934	CLONAL	1	TRUE	1	0.405056859930166	2		611	759	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967828	93967828	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	222	909	0	ENST00000369303.4:c.2099T>C	p.Val700Ala	p.V700A	ENST00000369303	NM_004440.3	700	gTt/gCt	11/17	1	2	FACETS	0.861	0.8	0.925	0.861	0.8	0.925	CLONAL	1	TRUE	1	0.405056859930166	2		909	1273	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005650	150005650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144805744	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	99	392	0	ENST00000253339.5:c.575C>T	p.Pro192Leu	p.P192L	ENST00000253339		192	cCg/cTg	3/7	1	2	FACETS	0.879	0.787	0.977	0.879	0.787	0.977	CLONAL	1	TRUE	1	0.405056859930166	2		392	556	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522283	157522283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1285642669	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	176	689	0	ENST00000346085.5:c.4555C>T	p.Arg1519Cys	p.R1519C	ENST00000346085	NM_020732.3	1519	Cgt/Tgt	18/20	1	2	FACETS	0.966	0.89	1	0.966	0.89	1	CLONAL	1	TRUE	1	0.405056859930166	2		689	900	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527916	157527916	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	105	410	0	ENST00000346085.5:c.5641C>A	p.Leu1881Ile	p.L1881I	ENST00000346085	NM_020732.3	1881	Ctc/Atc	20/20	1	2	FACETS	0.953	0.857	1	0.953	0.857	1	CLONAL	1	TRUE	1	0.405056859930166	2		410	544	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026467	6026467	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786203379	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	39	151	0	ENST00000265849.7:c.1929G>T	p.Gln643His	p.Q643H	ENST00000265849	NM_000535.5	643	caG/caT	11/15	1	2	FACETS	0.735	0.613	0.869	0.735	0.613	0.869	SUBCLONAL	1	TRUE	1	0.405056859930166	2		151	262	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467747	50467747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	178	655	0	ENST00000331340.3:c.982C>T	p.Arg328Cys	p.R328C	ENST00000331340	NM_006060.4	328	Cgc/Tgc	8/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.405056859930166	2		655	775	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227938	55227938	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	172	623	0	ENST00000275493.2:c.1405T>G	p.Leu469Val	p.L469V	ENST00000275493	NM_005228.3	469	Ttg/Gtg	12/28	1	2	FACETS	0.963	0.886	1	0.963	0.886	1	CLONAL	1	TRUE	1	0.405056859930166	2		623	882	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388086	81388086	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	121	503	0	ENST00000222390.5:c.289C>A	p.Leu97Ile	p.L97I	ENST00000222390	NM_000601.4	97	Ctc/Atc	3/18	1	2	FACETS	0.87	0.787	0.957	0.87	0.787	0.957	CLONAL	1	TRUE	1	0.405056859930166	2		503	687	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509766	106509766	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	144	634	0	ENST00000359195.3:c.1760A>C	p.Lys587Thr	p.K587T	ENST00000359195	NM_002649.2	587	aAa/aCa	2/11	1	2	FACETS	0.817	0.745	0.893	0.817	0.745	0.893	CLONAL	1	TRUE	1	0.405056859930166	2		634	870	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850275	128850275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	197	697	3	ENST00000249373.3:c.1538C>T	p.Pro513Leu	p.P513L	ENST00000249373	NM_005631.4	513	cCg/cTg	9/12	1	2	FACETS	0.947	0.877	1	0.947	0.877	1	CLONAL	1	TRUE	1	0.405056859930166	2		700	1027	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874203	151874203	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	102	494	0	ENST00000262189.6:c.8335C>A	p.Leu2779Ile	p.L2779I	ENST00000262189	NM_170606.2	2779	Ctt/Att	38/59	1	2	FACETS	0.745	0.667	0.828	0.745	0.667	0.828	SUBCLONAL	1	TRUE	1	0.405056859930166	2		494	676	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878956	151878956	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	163	530	0	ENST00000262189.6:c.5989G>T	p.Gly1997Cys	p.G1997C	ENST00000262189	NM_170606.2	1997	Ggc/Tgc	36/59	1	2	FACETS	0.976	0.896	1	0.976	0.896	1	CLONAL	1	TRUE	1	0.405056859930166	2		530	825	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132745	152132745	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1327515855	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	89	466	0	ENST00000262189.6:c.127G>T	p.Asp43Tyr	p.D43Y	ENST00000262189	NM_170606.2	43	Gat/Tat	1/59	1	2	FACETS	0.767	0.681	0.858	0.767	0.681	0.858	SUBCLONAL	1	TRUE	1	0.405056859930166	2		466	573	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955525	90955525	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730881864	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	171	628	1	ENST00000265433.3:c.2140C>T	p.Arg714Ter	p.R714*	ENST00000265433	NM_002485.4	714	Cga/Tga	14/16	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.405056859930166	2		629	816	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737069	145737069	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	117	478	1	ENST00000428558.2:c.3497G>T	p.Gly1166Val	p.G1166V	ENST00000428558	NM_004260.3	1166	gGc/gTc	21/22	1	2	FACETS	0.952	0.86	1	0.952	0.86	1	CLONAL	1	TRUE	1	0.405056859930166	2		479	607	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741937	145741937	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	65	456	0	ENST00000428558.2:c.566G>A	p.Gly189Asp	p.G189D	ENST00000428558	NM_004260.3	189	gGc/gAc	5/22	1	2	FACETS	0.518	0.449	0.594	0.518	0.449	0.594	SUBCLONAL	1	TRUE	1	0.405056859930166	2		456	619	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5462858	5462858	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	87	414	0	ENST00000381577.3:c.419G>T	p.Arg140Ile	p.R140I	ENST00000381577	NM_014143.3	140	aGa/aTa	4/7	1	2	FACETS	0.814	0.722	0.911	0.814	0.722	0.911	CLONAL	1	TRUE	1	0.405056859930166	2		414	528	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504333	8504333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754609275	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	181	557	4	ENST00000356435.5:c.1750C>T	p.Arg584Cys	p.R584C	ENST00000356435		584	Cgt/Tgt	12/35	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.405056859930166	2		561	863	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518081	8518081	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	125	523	0	ENST00000356435.5:c.1310A>G	p.Gln437Arg	p.Q437R	ENST00000356435		437	cAg/cGg	10/35	1	2	FACETS	0.931	0.844	1	0.931	0.844	1	CLONAL	1	TRUE	1	0.405056859930166	2		523	663	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518405	8518405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	58	224	0	ENST00000356435.5:c.986C>T	p.Pro329Leu	p.P329L	ENST00000356435		329	cCt/cTt	10/35	1	2	FACETS	0.955	0.826	1	0.955	0.826	1	CLONAL	1	TRUE	1	0.405056859930166	2		224	300	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528596	8528596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	184	809	2	ENST00000356435.5:c.536G>A	p.Arg179Gln	p.R179Q	ENST00000356435		179	cGa/cAa	4/35	1	2	FACETS	0.824	0.76	0.892	0.824	0.76	0.892	CLONAL	1	TRUE	1	0.405056859930166	2		811	1102	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020754	37020754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	202	720	0	ENST00000358127.4:c.91C>T	p.Arg31Trp	p.R31W	ENST00000358127	NM_001280556.1	31	Cgg/Tgg	2/10	1	2	FACETS	0.98	0.908	1	0.98	0.908	1	CLONAL	1	TRUE	1	0.405056859930166	2		720	1018	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87338539	87338539	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	148	753	0	ENST00000277120.3:c.635A>C	p.Lys212Thr	p.K212T	ENST00000277120		212	aAg/aCg	7/19	1	2	FACETS	0.761	0.695	0.831	0.761	0.695	0.831	SUBCLONAL	1	TRUE	1	0.405056859930166	2		753	960	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93629477	93629477	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	122	471	0	ENST00000375746.1:c.911G>T	p.Arg304Ile	p.R304I	ENST00000375746	NM_001174167.1	304	aGa/aTa	7/14	1	2	FACETS	0.937	0.849	1	0.937	0.849	1	CLONAL	1	TRUE	1	0.405056859930166	2		471	643	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249918	110249918	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	65	261	0	ENST00000374672.4:c.757G>T	p.Gly253Cys	p.G253C	ENST00000374672	NM_004235.4	253	Ggc/Tgc	3/5	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.405056859930166	2		261	307	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133729570	133729570	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138924193	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	246	688	0	ENST00000318560.5:c.199G>A	p.Val67Ile	p.V67I	ENST00000318560	NM_005157.4	67	Gtt/Att	2/11	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.405056859930166	2		688	1200	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391236	139391236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	169	572	0	ENST00000277541.6:c.6955G>A	p.Val2319Met	p.V2319M	ENST00000277541	NM_017617.3	2319	Gtg/Atg	34/34	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.405056859930166	2		572	757	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399387	139399387	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1418474023	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	146	557	0	ENST00000277541.6:c.4756C>T	p.Arg1586Cys	p.R1586C	ENST00000277541	NM_017617.3	1586	Cgc/Tgc	26/34	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.405056859930166	2		557	720	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100420	8100420	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs991194737	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	180	965	2	ENST00000346208.3:c.394G>A	p.Val132Ile	p.V132I	ENST00000346208		132	Gtc/Atc	3/6	1	2	FACETS	0.81	0.746	0.877	0.81	0.746	0.877	CLONAL	1	TRUE	1	0.405056859930166	2		967	1097	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332436	70332436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772124361	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	156	644	0	ENST00000373644.4:c.341G>A	p.Arg114Gln	p.R114Q	ENST00000373644	NM_030625.2	114	cGa/cAa	2/12	1	2	FACETS	0.834	0.763	0.907	0.834	0.763	0.907	CLONAL	1	TRUE	1	0.405056859930166	2		644	924	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426845	70426845	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	123	550	0	ENST00000373644.4:c.4505T>C	p.Val1502Ala	p.V1502A	ENST00000373644	NM_030625.2	1502	gTc/gCc	7/12	1	2	FACETS	0.817	0.74	0.899	0.817	0.74	0.899	CLONAL	1	TRUE	1	0.405056859930166	2		550	743	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	84	299	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.864	0.766	0.968	0.864	0.766	0.968	CLONAL	1	TRUE	1	0.405056859930166	2		299	480	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692940	89692940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746152219	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	104	416	1	ENST00000371953.3:c.424C>T	p.Arg142Trp	p.R142W	ENST00000371953	NM_000314.4	142	Cgg/Tgg	5/9	1	2	FACETS	0.96	0.863	1	0.96	0.863	1	CLONAL	1	TRUE	1	0.405056859930166	2		417	535	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154312	2154312	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	206	999	0	ENST00000434045.2:c.616A>G	p.Arg206Gly	p.R206G	ENST00000434045	NM_001127598.1	206	Agg/Ggg	5/5	1	2	FACETS	0.923	0.856	0.993	0.923	0.856	0.993	CLONAL	1	TRUE	1	0.405056859930166	2		999	1102	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156668	2156668	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	225	836	1	ENST00000434045.2:c.254G>T	p.Ser85Ile	p.S85I	ENST00000434045	NM_001127598.1	85	aGt/aTt	3/5	1	2	FACETS	0.91	0.846	0.976	0.91	0.846	0.976	CLONAL	1	TRUE	1	0.405056859930166	2		837	1221	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94224031	94224031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs116679717	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	133	655	1	ENST00000323929.3:c.121G>A	p.Asp41Asn	p.D41N	ENST00000323929	NM_005591.3	41	Gat/Aat	3/20	0.405056859930166	2	FACETS	0.757	0.687	0.83	0.378	0.343	0.415	SUBCLONAL	1	TRUE	0	0.405056859930166	2		656	868	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912815	100912815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1000609240	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	235	855	0	ENST00000325455.5:c.2507G>A	p.Arg836Gln	p.R836Q	ENST00000325455	NM_001202474.3	836	cGa/cAa	7/8	0.405056859930166	2	FACETS	0.971	0.905	1	0.485	0.452	0.52	CLONAL	1	TRUE	0	0.405056859930166	2		855	1195	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163458	108163458	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	124	668	0	ENST00000278616.4:c.4549C>A	p.Leu1517Ile	p.L1517I	ENST00000278616	NM_000051.3	1517	Ctt/Att	30/63	0.405056859930166	2	FACETS	0.679	0.613	0.748	0.339	0.306	0.374	SUBCLONAL	1	TRUE	0	0.405056859930166	2		668	902	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203565	108203565	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766351395	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	102	383	0	ENST00000278616.4:c.7865C>T	p.Ala2622Val	p.A2622V	ENST00000278616	NM_000051.3	2622	gCa/gTa	53/63	0.405056859930166	2	FACETS	0.989	0.889	1	0.495	0.444	0.548	CLONAL	1	TRUE	0	0.405056859930166	2		383	509	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205756	108205756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531980488	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	118	451	0	ENST00000278616.4:c.8071C>T	p.Arg2691Cys	p.R2691C	ENST00000278616	NM_000051.3	2691	Cgc/Tgc	55/63	0.405056859930166	2	FACETS	0.838	0.757	0.924	0.419	0.378	0.462	CLONAL	1	TRUE	0	0.405056859930166	2		451	695	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343493	118343493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	146	462	0	ENST00000534358.1:c.1619C>A	p.Ser540Tyr	p.S540Y	ENST00000534358	NM_005933.3	540	tCt/tAt	3/36	0.405056859930166	2	FACETS	1	0.926	1	0.507	0.463	0.552	CLONAL	1	TRUE	0	0.405056859930166	2		462	711	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	495134	495134	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	156	499	3	ENST00000399788.2:c.172C>A	p.Gln58Lys	p.Q58K	ENST00000399788	NM_001042603.1	58	Cag/Aag	2/28	NA	2	FACETS	0.877	0.803	0.954			1	INDETERMINATE	1	TRUE	NA	0.405056859930166	2		502	878	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245343	46245343	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	219	651	1	ENST00000334344.6:c.3437C>T	p.Ser1146Leu	p.S1146L	ENST00000334344	NM_152641.2	1146	tCg/tTg	15/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.405056859930166	2		652	1011	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245971	46245971	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	102	513	0	ENST00000334344.6:c.4065A>C	p.Lys1355Asn	p.K1355N	ENST00000334344	NM_152641.2	1355	aaA/aaC	15/21	1	2	FACETS	0.686	0.614	0.763	0.686	0.614	0.763	SUBCLONAL	1	TRUE	1	0.405056859930166	2		513	734	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246216	46246216	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774475353	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	156	689	1	ENST00000334344.6:c.4310C>T	p.Ala1437Val	p.A1437V	ENST00000334344	NM_152641.2	1437	gCg/gTg	15/21	1	2	FACETS	0.842	0.771	0.916	0.842	0.771	0.916	CLONAL	1	TRUE	1	0.405056859930166	2		690	915	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421821	49421821	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	269	884	0	ENST00000301067.7:c.14486A>G	p.Glu4829Gly	p.E4829G	ENST00000301067	NM_003482.3	4829	gAg/gGg	46/54	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.405056859930166	2		884	1328	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431070	49431070	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	176	660	1	ENST00000301067.7:c.10069C>A	p.Leu3357Ile	p.L3357I	ENST00000301067	NM_003482.3	3357	Cta/Ata	34/54	1	2	FACETS	0.901	0.83	0.976	0.901	0.83	0.976	CLONAL	1	TRUE	1	0.405056859930166	2		661	964	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432343	49432343	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	228	732	2	ENST00000301067.7:c.8796G>T	p.Gln2932His	p.Q2932H	ENST00000301067	NM_003482.3	2932	caG/caT	34/54	1	2	FACETS	0.996	0.928	1	0.996	0.928	1	CLONAL	1	TRUE	1	0.405056859930166	2		734	1130	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443607	49443607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	208	704	1	ENST00000301067.7:c.3764G>A	p.Gly1255Asp	p.G1255D	ENST00000301067	NM_003482.3	1255	gGc/gAc	11/54	1	2	FACETS	0.987	0.915	1	0.987	0.915	1	CLONAL	1	TRUE	1	0.405056859930166	2		705	1041	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856617	111856617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1364785726	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	151	316	3	ENST00000341259.2:c.668C>T	p.Ala223Val	p.A223V	ENST00000341259	NM_005475.2	223	gCg/gTg	2/8	1	2	FACETS	0.805	0.742	0.87	1	0.99	1	CLONAL	2	TRUE	1	0.405056859930166	2		319	463	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117425	115117425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	166	618	1	ENST00000257566.3:c.749C>T	p.Pro250Leu	p.P250L	ENST00000257566	NM_016569.3	250	cCc/cTc	4/8	1	2	FACETS	0.994	0.914	1	0.994	0.914	1	CLONAL	1	TRUE	1	0.405056859930166	2		619	825	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219839	133219839	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766511597	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	125	458	0	ENST00000320574.5:c.4522C>T	p.Arg1508Cys	p.R1508C	ENST00000320574	NM_006231.2	1508	Cgc/Tgc	35/49	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.405056859930166	2		458	608	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225553	133225553	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs151278283	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	204	755	2	ENST00000320574.5:c.4111C>T	p.Arg1371Ter	p.R1371*	ENST00000320574	NM_006231.2	1371	Cga/Tga	32/49	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.405056859930166	2		757	958	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225636	133225636	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	116	505	0	ENST00000320574.5:c.4028G>A	p.Gly1343Asp	p.G1343D	ENST00000320574	NM_006231.2	1343	gGc/gAc	32/49	1	2	FACETS	0.903	0.816	0.995	0.903	0.816	0.995	CLONAL	1	TRUE	1	0.405056859930166	2		505	634	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	200	581	1	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.405056859930166	2		582	972	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26978210	26978210	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776727772	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	125	426	0	ENST00000381527.3:c.1387C>T	p.Arg463Trp	p.R463W	ENST00000381527	NM_001260.1	463	Cgg/Tgg	13/13	1	2	FACETS	0.984	0.893	1	0.984	0.893	1	CLONAL	1	TRUE	1	0.405056859930166	2		426	627	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592708	28592708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	153	514	0	ENST00000241453.7:c.2437G>A	p.Ala813Thr	p.A813T	ENST00000241453	NM_004119.2	813	Gcc/Acc	20/24	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.405056859930166	2		514	702	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622478	28622478	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	158	552	0	ENST00000241453.7:c.1139G>T	p.Arg380Ile	p.R380I	ENST00000241453	NM_004119.2	380	aGa/aTa	9/24	1	2	FACETS	0.907	0.832	0.986	0.907	0.832	0.986	CLONAL	1	TRUE	1	0.405056859930166	2		552	860	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28963966	28963966	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	166	680	0	ENST00000282397.4:c.1936G>T	p.Glu646Ter	p.E646*	ENST00000282397	NM_002019.4	646	Gaa/Taa	13/30	1	2	FACETS	0.905	0.831	0.981	0.905	0.831	0.981	CLONAL	1	TRUE	1	0.405056859930166	2		680	906	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911429	32911429	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397507297	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	211	1021	0	ENST00000380152.3:c.2937A>G	p.Ile979Met	p.I979M	ENST00000380152		979	atA/atG	11/27	1	2	FACETS	0.85	0.788	0.915	0.85	0.788	0.915	CLONAL	1	TRUE	1	0.405056859930166	2		1021	1225	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913227	32913227	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1287	298	1059	2	ENST00000380152.3:c.4735G>A	p.Ala1579Thr	p.A1579T	ENST00000380152		1579	Gca/Aca	11/27	1	2	FACETS	0.928	0.872	0.987	0.928	0.872	0.987	CLONAL	1	TRUE	1	0.405056859930166	2		1061	1585	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953497	32953497	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	201	870	2	ENST00000380152.3:c.8798G>T	p.Arg2933Met	p.R2933M	ENST00000380152		2933	aGg/aTg	22/27	1	2	FACETS	0.84	0.777	0.905	0.84	0.777	0.905	CLONAL	1	TRUE	1	0.405056859930166	2		872	1182	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953957	32953957	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	77	454	0	ENST00000380152.3:c.9024T>G	p.Ile3008Met	p.I3008M	ENST00000380152		3008	atT/atG	23/27	1	2	FACETS	0.666	0.585	0.752	0.666	0.585	0.752	SUBCLONAL	1	TRUE	1	0.405056859930166	2		454	571	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134333	41134333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755802918	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1343	306	1093	1	ENST00000379561.5:c.1295G>A	p.Ser432Asn	p.S432N	ENST00000379561	NM_002015.3	432	aGc/aAc	2/3	1	2	FACETS	0.916	0.861	0.973	0.916	0.861	0.973	CLONAL	1	TRUE	1	0.405056859930166	2		1094	1649	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345217	73345217	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	109	658	0	ENST00000377767.4:c.1670+2T>C		p.X557_splice	ENST00000377767	NM_014953.3	557			1	2	FACETS	0.808	0.727	0.894	0.808	0.727	0.894	CLONAL	1	TRUE	1	0.405056859930166	2		658	666	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504506	103504506	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750156480	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	200	651	1	ENST00000355739.4:c.127C>T	p.Arg43Trp	p.R43W	ENST00000355739	NM_000123.3	43	Cgg/Tgg	2/15	1	2	FACETS	0.953	0.883	1	0.953	0.883	1	CLONAL	1	TRUE	1	0.405056859930166	2		652	1036	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436905	110436905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752295410	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	42	188	0	ENST00000375856.3:c.1496C>T	p.Ser499Phe	p.S499F	ENST00000375856	NM_003749.2	499	tCc/tTc	1/2	1	2	FACETS	0.816	0.687	0.958	0.816	0.687	0.958	CLONAL	1	TRUE	1	0.405056859930166	2		188	254	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060922	38060922	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	97	460	0	ENST00000250448.2:c.1067C>A	p.Thr356Asn	p.T356N	ENST00000250448	NM_004496.3	356	aCt/aAt	2/2	1	2	FACETS	0.914	0.818	1	0.914	0.818	1	CLONAL	1	TRUE	1	0.405056859930166	2		460	524	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061651	38061651	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	51	148	0	ENST00000250448.2:c.338T>C	p.Met113Thr	p.M113T	ENST00000250448	NM_004496.3	113	aTg/aCg	2/2	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.405056859930166	2		148	209	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543379	65543379	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs762084527	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	229	735	1	ENST00000358664.4:c.298C>T	p.Arg100Cys	p.R100C	ENST00000358664	NM_002382.4	100	Cgt/Tgt	5/5	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.405056859930166	2		736	1102	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609732	81609732	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs754118014	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	222	812	1	ENST00000298171.2:c.1330T>C	p.Tyr444His	p.Y444H	ENST00000298171	NM_000369.2	444	Tac/Cac	10/10	1	2	FACETS	0.931	0.865	0.998	0.931	0.865	0.998	CLONAL	1	TRUE	1	0.405056859930166	2		813	1178	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95584039	95584039	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	145	507	0	ENST00000393063.1:c.1429A>G	p.Asn477Asp	p.N477D	ENST00000393063	NM_030621.3	477	Aat/Gat	10/28	1	2	FACETS	0.962	0.879	1	0.962	0.879	1	CLONAL	1	TRUE	1	0.405056859930166	2		507	744	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590984	95590984	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1181141404	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	74	310	0	ENST00000393063.1:c.925G>A	p.Val309Ile	p.V309I	ENST00000393063	NM_030621.3	309	Gta/Ata	9/28	1	2	FACETS	0.874	0.769	0.987	0.874	0.769	0.987	CLONAL	1	TRUE	1	0.405056859930166	2		310	418	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023378	33023378	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1472	344	1378	0	ENST00000300177.4:c.487C>T	p.Pro163Ser	p.P163S	ENST00000300177	NM_001191322.1	163	Cca/Tca	2/2	1	2	FACETS	0.935	0.882	0.99	0.935	0.882	0.99	CLONAL	1	TRUE	1	0.405056859930166	2		1378	1816	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042761	42042761	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1234	325	1107	0	ENST00000219905.7:c.6956T>G	p.Ile2319Ser	p.I2319S	ENST00000219905	NM_001164273.1	2319	aTt/aGt	17/24	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.405056859930166	2		1107	1559	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679765	88679765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	206	683	2	ENST00000360948.2:c.698G>A	p.Gly233Asp	p.G233D	ENST00000360948	NM_001012338.2	233	gGc/gAc	7/19	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.405056859930166	2		685	935	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690623	88690623	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	135	474	1	ENST00000360948.2:c.407G>T	p.Ser136Ile	p.S136I	ENST00000360948	NM_001012338.2	136	aGt/aTt	5/19	1	2	FACETS	0.903	0.822	0.988	0.903	0.822	0.988	CLONAL	1	TRUE	1	0.405056859930166	2		475	738	SUCCESS
BLM	641	MSKCC	GRCh37	15	91290665	91290665	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148545569	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	170	482	2	ENST00000355112.3:c.43C>T	p.Arg15Cys	p.R15C	ENST00000355112	NM_000057.2	15	Cgt/Tgt	2/22	1	2	FACETS	0.923	0.849	1	0.923	0.849	1	CLONAL	1	TRUE	1	0.405056859930166	2		484	909	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2105507	2105507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45517113	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	138	394	1	ENST00000219476.3:c.586G>A	p.Ala196Thr	p.A196T	ENST00000219476	NM_000548.3	196	Gca/Aca	6/42	1	2	FACETS	0.971	0.885	1	0.971	0.885	1	CLONAL	1	TRUE	1	0.405056859930166	2		395	702	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131704	2131704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567510707	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	269	949	1	ENST00000219476.3:c.3719G>A	p.Arg1240His	p.R1240H	ENST00000219476	NM_000548.3	1240	cGc/cAc	31/42	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.405056859930166	2		950	1279	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136798	2136798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555438551	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	232	808	1	ENST00000219476.3:c.4915C>T	p.Arg1639Cys	p.R1639C	ENST00000219476	NM_000548.3	1639	Cgc/Tgc	38/42	1	2	FACETS	0.986	0.918	1	0.986	0.918	1	CLONAL	1	TRUE	1	0.405056859930166	2		809	1162	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2137885	2137885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775395648	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	179	636	1	ENST00000219476.3:c.5011G>A	p.Val1671Met	p.V1671M	ENST00000219476	NM_000548.3	1671	Gtg/Atg	39/42	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.405056859930166	2		637	869	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3842042	3842042	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783464	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	181	590	1	ENST00000262367.5:c.1270C>T	p.Arg424Ter	p.R424*	ENST00000262367	NM_004380.2	424	Cga/Tga	5/31	1	2	FACETS	0.909	0.838	0.983	0.909	0.838	0.983	CLONAL	1	TRUE	1	0.405056859930166	2		591	983	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943753	9943753	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	126	475	0	ENST00000330684.3:c.1188C>A	p.Phe396Leu	p.F396L	ENST00000330684	NM_001134407.1	396	ttC/ttA	5/13	1	2	FACETS	0.923	0.837	1	0.923	0.837	1	CLONAL	1	TRUE	1	0.405056859930166	2		475	674	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031970	10031970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	241	892	1	ENST00000330684.3:c.853G>A	p.Asp285Asn	p.D285N	ENST00000330684	NM_001134407.1	285	Gac/Aac	3/13	1	2	FACETS	0.953	0.889	1	0.953	0.889	1	CLONAL	1	TRUE	1	0.405056859930166	2		893	1248	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024709	14024709	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	128	510	0	ENST00000311895.7:c.935C>A	p.Ser312Tyr	p.S312Y	ENST00000311895	NM_005236.2	312	tCt/tAt	5/11	1	2	FACETS	0.881	0.8	0.967	0.881	0.8	0.967	CLONAL	1	TRUE	1	0.405056859930166	2		510	717	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56832416	56832416	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	232	834	0	ENST00000308159.5:c.326C>T	p.Ala109Val	p.A109V	ENST00000308159	NM_014669.4	109	gCc/gTc	4/22	1	2	FACETS	0.932	0.868	0.999	0.932	0.868	0.999	CLONAL	1	TRUE	1	0.405056859930166	2		834	1229	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650653	67650653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	192	607	1	ENST00000264010.4:c.958C>T	p.Arg320Cys	p.R320C	ENST00000264010	NM_006565.3	320	Cgt/Tgt	5/12	1	2	FACETS	0.988	0.913	1	0.988	0.913	1	CLONAL	1	TRUE	1	0.405056859930166	2		608	960	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828579	72828579	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1346	342	1078	0	ENST00000268489.5:c.8002C>T	p.Arg2668Ter	p.R2668*	ENST00000268489	NM_006885.3	2668	Cga/Tga	9/10	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.405056859930166	2		1078	1688	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830135	72830135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1233	301	953	1	ENST00000268489.5:c.6446G>A	p.Arg2149His	p.R2149H	ENST00000268489	NM_006885.3	2149	cGc/cAc	9/10	1	2	FACETS	0.969	0.91	1	0.969	0.91	1	CLONAL	1	TRUE	1	0.405056859930166	2		954	1534	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830945	72830945	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1378	323	1260	0	ENST00000268489.5:c.5636A>C	p.Lys1879Thr	p.K1879T	ENST00000268489	NM_006885.3	1879	aAa/aCa	9/10	1	2	FACETS	0.938	0.883	0.994	0.938	0.883	0.994	CLONAL	1	TRUE	1	0.405056859930166	2		1260	1701	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832175	72832175	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371424734	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	266	924	0	ENST00000268489.5:c.4406C>T	p.Ala1469Val	p.A1469V	ENST00000268489	NM_006885.3	1469	gCc/gTc	9/10	1	2	FACETS	0.976	0.913	1	0.976	0.913	1	CLONAL	1	TRUE	1	0.405056859930166	2		924	1346	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832478	72832478	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs758364697	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	271	971	0	ENST00000268489.5:c.4103A>G	p.Asn1368Ser	p.N1368S	ENST00000268489	NM_006885.3	1368	aAc/aGc	9/10	1	2	FACETS	0.979	0.917	1	0.979	0.917	1	CLONAL	1	TRUE	1	0.405056859930166	2		971	1367	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371722	89371722	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	245	821	0	ENST00000301030.4:c.118C>A	p.Pro40Thr	p.P40T	ENST00000301030	NM_001256183.1	40	Cca/Aca	4/13	NA	2	FACETS	0.895	0.835	0.958			1	INDETERMINATE	1	TRUE	NA	0.405056859930166	2		821	1351	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849415	89849415	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	299	1027	0	ENST00000389301.3:c.1566G>T	p.Lys522Asn	p.K522N	ENST00000389301	NM_000135.2	522	aaG/aaT	16/43	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.405056859930166	2		1027	1426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577589	7577589	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	117	543	0	ENST00000269305.4:c.692C>A	p.Thr231Asn	p.T231N	ENST00000269305	NM_001126112.2	231	aCc/aAc	7/11	1	2	FACETS	0.735	0.663	0.811	0.735	0.663	0.811	SUBCLONAL	1	TRUE	1	0.405056859930166	2		543	786	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965090	15965090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1344029820	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	106	414	0	ENST00000268712.3:c.5506G>A	p.Val1836Met	p.V1836M	ENST00000268712	NM_006311.3	1836	Gtg/Atg	37/46	1	2	FACETS	0.935	0.84	1	0.935	0.84	1	CLONAL	1	TRUE	1	0.405056859930166	2		414	560	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075290	16075290	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1454295299	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	177	563	0	ENST00000268712.3:c.262A>G	p.Ser88Gly	p.S88G	ENST00000268712	NM_006311.3	88	Agt/Ggt	4/46	1	2	FACETS	0.985	0.908	1	0.985	0.908	1	CLONAL	1	TRUE	1	0.405056859930166	2		563	887	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653070	29653070	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	174	623	0	ENST00000356175.3:c.5005A>G	p.Thr1669Ala	p.T1669A	ENST00000356175	NM_000267.3	1669	Acc/Gcc	36/57	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.405056859930166	2		623	856	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667643	29667643	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	173	625	0	ENST00000356175.3:c.6979C>A	p.Leu2327Ile	p.L2327I	ENST00000356175	NM_000267.3	2327	Ctc/Atc	46/57	1	2	FACETS	0.898	0.827	0.973	0.898	0.827	0.973	CLONAL	1	TRUE	1	0.405056859930166	2		625	951	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618501	37618501	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	149	636	0	ENST00000447079.4:c.177A>C	p.Glu59Asp	p.E59D	ENST00000447079	NM_015083.1	59	gaA/gaC	1/14	1	2	FACETS	0.784	0.716	0.856	0.784	0.716	0.856	SUBCLONAL	1	TRUE	1	0.405056859930166	2		636	938	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770041	56770041	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502603	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	173	518	0	ENST00000337432.4:c.37G>A	p.Asp13Asn	p.D13N	ENST00000337432	NM_058216.2	13	Gat/Aat	1/9	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.405056859930166	2		518	752	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780688	56780688	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	124	466	0	ENST00000337432.4:c.703A>C	p.Lys235Gln	p.K235Q	ENST00000337432	NM_058216.2	235	Aag/Cag	4/9	1	2	FACETS	0.88	0.797	0.967	0.88	0.797	0.967	CLONAL	1	TRUE	1	0.405056859930166	2		466	696	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760670	59760670	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	129	594	0	ENST00000259008.2:c.3737C>A	p.Pro1246His	p.P1246H	ENST00000259008	NM_032043.2	1246	cCt/cAt	20/20	1	2	FACETS	0.858	0.779	0.942	0.858	0.779	0.942	CLONAL	1	TRUE	1	0.405056859930166	2		594	742	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554452	63554452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	186	528	2	ENST00000307078.5:c.287G>A	p.Arg96Gln	p.R96Q	ENST00000307078	NM_004655.3	96	cGa/cAa	2/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.405056859930166	2		530	789	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66518898	66518898	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	116	344	0	ENST00000358598.2:c.179A>G	p.Glu60Gly	p.E60G	ENST00000358598	NM_212471.2	60	gAg/gGg	3/11	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.405056859930166	2		344	540	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774949	73774949	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	161	510	0	ENST00000254810.4:c.224T>C	p.Ile75Thr	p.I75T	ENST00000254810	NM_005324.3	75	aTc/aCc	3/4	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.405056859930166	2		510	737	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39535271	39535271	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	125	542	1	ENST00000262039.4:c.15G>T	p.Glu5Asp	p.E5D	ENST00000262039	NM_002647.2	5	gaG/gaT	1/25	1	2	FACETS	0.912	0.827	1	0.912	0.827	1	CLONAL	1	TRUE	1	0.405056859930166	2		543	677	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45423049	45423049	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	191	630	1	ENST00000262160.6:c.79G>T	p.Gly27Ter	p.G27*	ENST00000262160	NM_005901.5	27	Gga/Tga	2/11	1	2	FACETS	0.925	0.855	0.998	0.925	0.855	0.998	CLONAL	1	TRUE	1	0.405056859930166	2		631	1019	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612244	1612244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1325068914	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	237	780	0	ENST00000344749.5:c.1775C>T	p.Ala592Val	p.A592V	ENST00000344749	NM_001136139.2	592	gCc/gTc	18/19	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.405056859930166	2		780	1067	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119007	3119007	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769503200	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	169	695	0	ENST00000078429.4:c.691G>A	p.Ala231Thr	p.A231T	ENST00000078429	NM_002067.2	231	Gcc/Acc	5/7	1	2	FACETS	0.943	0.867	1	0.943	0.867	1	CLONAL	1	TRUE	1	0.405056859930166	2		695	885	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222861	5222861	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1484090676	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	39	325	0	ENST00000357368.4:c.2942C>G	p.Thr981Ser	p.T981S	ENST00000357368	NM_002850.3	981	aCt/aGt	18/38	1	2	FACETS	0.392	0.325	0.468	0.392	0.325	0.468	SUBCLONAL	1	TRUE	1	0.405056859930166	2		325	491	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245949	5245949	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	249	744	1	ENST00000357368.4:c.826G>A	p.Val276Met	p.V276M	ENST00000357368	NM_002850.3	276	Gtg/Atg	10/38	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.405056859930166	2		745	1084	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117159	7117159	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs74495977	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	184	746	1	ENST00000302850.5:c.4057C>T	p.Arg1353Trp	p.R1353W	ENST00000302850	NM_000208.2	1353	Cgg/Tgg	22/22	1	2	FACETS	0.881	0.813	0.952	0.881	0.813	0.952	CLONAL	1	TRUE	1	0.405056859930166	2		747	1031	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265424	10265424	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	142	495	0	ENST00000340748.4:c.1622A>C	p.Asn541Thr	p.N541T	ENST00000340748		541	aAc/aCc	20/40	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.405056859930166	2		495	661	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10283776	10283776	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	298	835	0	ENST00000340748.4:c.710G>T	p.Arg237Ile	p.R237I	ENST00000340748		237	aGa/aTa	8/40	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.405056859930166	2		835	1368	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610075	10610075	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	169	631	1	ENST00000171111.5:c.635G>A	p.Gly212Glu	p.G212E	ENST00000171111	NM_203500.1	212	gGg/gAg	2/6	1	2	FACETS	0.882	0.811	0.957	0.882	0.811	0.957	CLONAL	1	TRUE	1	0.405056859930166	2		632	946	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094831	11094831	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	267	859	0	ENST00000358026.2:c.4T>C	p.Ser2Pro	p.S2P	ENST00000358026	NM_001128849.1	2	Tcc/Ccc	2/36	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.405056859930166	2		859	1280	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121143	11121143	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	213	805	0	ENST00000358026.2:c.2210C>A	p.Ala737Asp	p.A737D	ENST00000358026	NM_001128849.1	737	gCt/gAt	15/36	1	2	FACETS	0.942	0.875	1	0.942	0.875	1	CLONAL	1	TRUE	1	0.405056859930166	2		805	1116	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284936	15284936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs78501403	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	150	538	0	ENST00000263388.2:c.4679G>A	p.Arg1560Gln	p.R1560Q	ENST00000263388	NM_000435.2	1560	cGg/cAg	25/33	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.405056859930166	2		538	717	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303197	15303197	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	154	694	0	ENST00000263388.2:c.331G>A	p.Gly111Ser	p.G111S	ENST00000263388	NM_000435.2	111	Ggc/Agc	3/33	1	2	FACETS	0.882	0.807	0.96	0.882	0.807	0.96	CLONAL	1	TRUE	1	0.405056859930166	2		694	862	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271328	18271328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	236	759	3	ENST00000222254.8:c.370G>A	p.Ala124Thr	p.A124T	ENST00000222254	NM_005027.3	124	Gct/Act	3/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.405056859930166	2		762	1126	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745189	41745189	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	185	756	0	ENST00000301178.4:c.1255C>A	p.Leu419Ile	p.L419I	ENST00000301178	NM_021913.4	419	Ctc/Atc	9/20	1	2	FACETS	0.901	0.831	0.973	0.901	0.831	0.973	CLONAL	1	TRUE	1	0.405056859930166	2		756	1014	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748854	41748854	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	270	860	1	ENST00000301178.4:c.1379C>T	p.Ala460Val	p.A460V	ENST00000301178	NM_021913.4	460	gCc/gTc	11/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.405056859930166	2		861	1297	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758793	41758793	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	266	894	1	ENST00000301178.4:c.1847C>A	p.Pro616His	p.P616H	ENST00000301178	NM_021913.4	616	cCt/cAt	16/20	1	2	FACETS	0.967	0.905	1	0.967	0.905	1	CLONAL	1	TRUE	1	0.405056859930166	2		895	1358	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384628	31384628	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201465442	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	207	786	1	ENST00000328111.2:c.1330G>A	p.Val444Met	p.V444M	ENST00000328111	NM_006892.3	444	Gtg/Atg	13/23	1	2	FACETS	0.886	0.822	0.954	0.886	0.822	0.954	CLONAL	1	TRUE	1	0.405056859930166	2		787	1153	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741540	39741540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	131	350	0	ENST00000361337.2:c.1427C>T	p.Ala476Val	p.A476V	ENST00000361337	NM_003286.2	476	gCt/gTt	14/21	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.405056859930166	2		350	598	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46252808	46252808	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1191	253	901	0	ENST00000371998.3:c.237A>G	p.Ile79Met	p.I79M	ENST00000371998		79	atA/atG	4/23	1	2	FACETS	0.865	0.807	0.925	0.865	0.807	0.925	CLONAL	1	TRUE	1	0.405056859930166	2		901	1444	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256425	46256425	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1200320359	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	304	980	1	ENST00000371998.3:c.653G>A	p.Arg218His	p.R218H	ENST00000371998		218	cGc/cAc	7/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.405056859930166	2		981	1419	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281766	46281766	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	294	912	0	ENST00000371998.3:c.4213A>C	p.Met1405Leu	p.M1405L	ENST00000371998		1405	Atg/Ctg	22/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.405056859930166	2		912	1325	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164703	36164703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	189	752	1	ENST00000300305.3:c.1172C>T	p.Ala391Val	p.A391V	ENST00000300305		391	gCg/gTg	8/8	1	2	FACETS	0.967	0.894	1	0.967	0.894	1	CLONAL	1	TRUE	1	0.405056859930166	2		753	965	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15838356	15838356	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	281	728	0	ENST00000307771.7:c.854C>A	p.Ser285Tyr	p.S285Y	ENST00000307771	NM_005089.3	285	tCt/tAt	10/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.405056859930166	2		728	1183	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934379	39934379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747350059	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	155	497	0	ENST00000378444.4:c.220C>T	p.Arg74Cys	p.R74C	ENST00000378444	NM_001123385.1	74	Cgc/Tgc	4/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.405056859930166	2		497	718	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918695	44918695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746746824	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	134	566	0	ENST00000377967.4:c.1178G>A	p.Arg393Gln	p.R393Q	ENST00000377967	NM_021140.2	393	cGa/cAa	12/29	1	2	FACETS	0.803	0.73	0.88	0.803	0.73	0.88	CLONAL	1	TRUE	1	0.405056859930166	2		566	824	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422686	47422686	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	258	903	2	ENST00000377045.4:c.158G>A	p.Gly53Asp	p.G53D	ENST00000377045	NM_001654.4	53	gGt/gAt	3/16	1	2	FACETS	0.998	0.934	1	0.998	0.934	1	CLONAL	1	TRUE	1	0.405056859930166	2		905	1276	SUCCESS
AR	367	MSKCC	GRCh37	X	66765901	66765901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	207	756	0	ENST00000374690.3:c.913G>A	p.Asp305Asn	p.D305N	ENST00000374690	NM_000044.3	305	Gat/Aat	1/8	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.405056859930166	2		756	968	SUCCESS
AR	367	MSKCC	GRCh37	X	66766561	66766561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	226	892	0	ENST00000374690.3:c.1573G>A	p.Gly525Ser	p.G525S	ENST00000374690	NM_000044.3	525	Ggc/Agc	1/8	1	2	FACETS	0.916	0.852	0.983	0.916	0.852	0.983	CLONAL	1	TRUE	1	0.405056859930166	2		892	1218	SUCCESS
AR	367	MSKCC	GRCh37	X	66931357	66931357	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746143547	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	238	871	3	ENST00000374690.3:c.1999G>A	p.Gly667Ser	p.G667S	ENST00000374690	NM_000044.3	667	Ggc/Agc	4/8	1	2	FACETS	0.92	0.857	0.984	0.92	0.857	0.984	CLONAL	1	TRUE	1	0.405056859930166	2		874	1278	SUCCESS
AR	367	MSKCC	GRCh37	X	66937337	66937337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137852571	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	263	784	0	ENST00000374690.3:c.2191G>A	p.Val731Met	p.V731M	ENST00000374690	NM_000044.3	731	Gtg/Atg	5/8	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.405056859930166	2		784	1278	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829726	76829726	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	204	833	0	ENST00000373344.5:c.6315A>C	p.Glu2105Asp	p.E2105D	ENST00000373344	NM_000489.3	2105	gaA/gaC	28/35	1	2	FACETS	0.942	0.873	1	0.942	0.873	1	CLONAL	1	TRUE	1	0.405056859930166	2		833	1069	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938751	76938751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781821147	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	162	753	1	ENST00000373344.5:c.1997G>A	p.Arg666Gln	p.R666Q	ENST00000373344	NM_000489.3	666	cGa/cAa	9/35	1	2	FACETS	0.819	0.751	0.89	0.819	0.751	0.89	CLONAL	1	TRUE	1	0.405056859930166	2		754	977	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939266	76939266	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	177	740	1	ENST00000373344.5:c.1482G>T	p.Lys494Asn	p.K494N	ENST00000373344	NM_000489.3	494	aaG/aaT	9/35	1	2	FACETS	0.868	0.799	0.94	0.868	0.799	0.94	CLONAL	1	TRUE	1	0.405056859930166	2		741	1007	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195114	123195114	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	196	727	0	ENST00000218089.9:c.1457A>C	p.Asp486Ala	p.D486A	ENST00000218089	NM_001042749.1	486	gAc/gCc	16/35	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.405056859930166	2		727	895	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200065	123200065	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	162	731	0	ENST00000218089.9:c.2137T>G	p.Tyr713Asp	p.Y713D	ENST00000218089	NM_001042749.1	713	Tac/Gac	22/35	1	2	FACETS	0.781	0.716	0.849	0.781	0.716	0.849	SUBCLONAL	1	TRUE	1	0.405056859930166	2		731	1024	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631104	69631104	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	194	875	0	ENST00000334134.2:c.308del	p.Gly103AspfsTer55	p.G103Dfs*55	ENST00000334134	NM_005247.2	103	gGa/ga	2/3	0.405056859930166	2	FACETS	0.857	0.792	0.924	0.428	0.396	0.462	CLONAL	1	TRUE	0	0.405056859930166	2		875	1118	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984600	72984601	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCTG	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1312	325	1029	0	ENST00000268489.5:c.2980_2983dup	p.Leu995ProfsTer53	p.L995Pfs*53	ENST00000268489	NM_006885.3	995	ctc/cCAGCtc	3/10	1	2	FACETS	0.98	0.923	1	0.98	0.923	1	CLONAL	1	TRUE	1	0.405056859930166	2		1029	1637	SUCCESS
APC	324	MSKCC	GRCh37	5	112179496	112179496	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	180	698	0	ENST00000257430.4:c.8206del	p.Thr2736LeufsTer3	p.T2736Lfs*3	ENST00000257430	NM_000038.5	2735	ggA/gg	16/16	1	2	FACETS	0.896	0.826	0.969	0.896	0.826	0.969	CLONAL	1	TRUE	1	0.405056859930166	2		698	992	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805373	46805373	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	321	1074	0	ENST00000290295.7:c.583del	p.Trp195GlyfsTer84	p.W195Gfs*84	ENST00000290295	NM_006361.5	195	Tgg/gg	1/2	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.405056859930166	2		1074	1524	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043349	6043349	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781716	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	68	264	0	ENST00000265849.7:c.325del	p.Glu109LysfsTer3	p.E109Kfs*3	ENST00000265849	NM_000535.5	109	Gaa/aa	4/15	1	2	FACETS	0.863	0.755	0.979	0.863	0.755	0.979	CLONAL	1	TRUE	1	0.405056859930166	2		264	389	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209357	98209358	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	140	680	0	ENST00000331920.6:c.4180_4181insT	p.Arg1394LeufsTer10	p.R1394Lfs*10	ENST00000331920	NM_000264.3	1394	cga/cTga	23/24	1	2	FACETS	0.893	0.814	0.976	0.893	0.814	0.976	CLONAL	1	TRUE	1	0.405056859930166	2		680	774	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0012113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	91	264	0	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	0.405056859930166	2	FACETS	0.67	0.595	0.749	0.335	0.297	0.375	SUBCLONAL	1	TRUE	0	0.405056859930166	2		264	671	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1322	309	898	5	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	0.3	3	FACETS	0.796	0.749	0.846	0.796	0.749	0.846	SUBCLONAL	2	TRUE	1	0.27	3		903	1631	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759623	133759623	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	140	622	0	ENST00000318560.5:c.1950del	p.Leu651TrpfsTer43	p.L651Wfs*43	ENST00000318560	NM_005157.4	649	aCc/ac	11/11	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.27	2		622	992	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	205	366	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.3	3	FACETS	0.923	0.856	0.991	0.923	0.856	0.991	CLONAL	2	TRUE	1	0.27	3		366	934	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	138	524	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.27	2		524	836	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	94	425	0	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.27	2		425	683	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024505	16024505	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	212	597	0	ENST00000268712.3:c.1713del	p.Arg572GlufsTer18	p.R572Efs*18	ENST00000268712	NM_006311.3	571	ggG/gg	16/46	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.27	2		597	1283	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	149	545	1	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.27	2		546	970	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163554	32163554	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	75	419	2	ENST00000375023.3:c.5672del	p.Gly1891AlafsTer13	p.G1891Afs*13	ENST00000375023	NM_004557.3	1891	gGc/gc	30/30	1	2	FACETS	0.746	0.653	0.846	0.746	0.653	0.846	SUBCLONAL	1	TRUE	1	0.27	2		421	745	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436102	49436102	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	17	115	0	ENST00000301067.7:c.5879del	p.Gly1960AlafsTer87	p.G1960Afs*87	ENST00000301067	NM_003482.3	1960	gGc/gc	28/54	0.3	3	FACETS	0.722	0.54	0.936	0.361	0.27	0.468	CLONAL	1	TRUE	1	0.27	3		115	198	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370841	55370841	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759612481	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	61	321	2	ENST00000297316.4:c.143C>T	p.Ala48Val	p.A48V	ENST00000297316	NM_022454.3	48	gCg/gTg	1/2	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.27	2		323	438	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910372	29910372	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs41548119	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	97	631	3	ENST00000376809.5:c.46del	p.Ala16ProfsTer4	p.A16Pfs*4	ENST00000376809	NM_002116.7	14	tcG/tc	1/8	1	2	FACETS	0.762	0.678	0.852	0.762	0.678	0.852	SUBCLONAL	1	TRUE	1	0.27	2		634	943	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843775	151843775	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	232	418	0	ENST00000262189.6:c.13940del	p.Lys4647SerfsTer12	p.K4647Sfs*12	ENST00000262189	NM_170606.2	4647	aAg/ag	53/59	0.293761862344845	3	FACETS	0.931	0.868	0.997	0.931	0.868	0.997	CLONAL	2	TRUE	1	0.27	3		418	1047	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260214	16260214	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	55	273	0	ENST00000375759.3:c.7484del	p.Pro2495LeufsTer4	p.P2495Lfs*4	ENST00000375759	NM_015001.2	2493	agC/ag	11/15	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.27	2		273	394	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116263	209116263	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	108	488	0	ENST00000345146.2:c.13del	p.Ile5SerfsTer7	p.I5Sfs*7	ENST00000345146	NM_005896.2	5	Atc/tc	3/10	1	2	FACETS	0.954	0.855	1	0.954	0.855	1	CLONAL	1	TRUE	1	0.27	2		488	839	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444659	78444659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs908264837	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	108	370	1	ENST00000370768.2:c.30del	p.Ser11LeufsTer43	p.S11Lfs*43	ENST00000370768	NM_003902.3	10	ccC/cc	1/20	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.27	2		371	744	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440741	56440741	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	149	562	0	ENST00000407977.2:c.477G>A	p.Trp159Ter	p.W159*	ENST00000407977		159	tgG/tgA	5/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.27	2		562	888	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971133	21971133	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	58	265	1	ENST00000304494.5:c.225del	p.Ala76ProfsTer70	p.A76Pfs*70	ENST00000304494	NM_000077.4	75	ccC/cc	2/3	1	2	FACETS	0.951	0.818	1	0.951	0.818	1	CLONAL	1	TRUE	1	0.27	2		266	452	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528971	157528972	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	91	311	0	ENST00000346085.5:c.6700_6701del	p.Leu2234GlyfsTer7	p.L2234Gfs*7	ENST00000346085	NM_020732.3	2232	aaCTct/aact	20/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.27	2		311	583	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467573	66467573	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	109	436	0	ENST00000273854.3:c.696del	p.Lys232AsnfsTer36	p.K232Nfs*36	ENST00000273854	NM_004439.5	232	aaA/aa	3/18	1	2	FACETS	0.975	0.875	1	0.975	0.875	1	CLONAL	1	TRUE	1	0.27	2		436	828	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448297	56448298	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1567880599	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	129	480	0	ENST00000407977.2:c.349dup	p.Arg117ProfsTer8	p.R117Pfs*8	ENST00000407977		117	cgc/cCgc	3/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.27	2		480	776	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726423	46726423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	79	319	0	ENST00000371975.4:c.502G>A	p.Val168Ile	p.V168I	ENST00000371975	NM_003579.3	168	Gtc/Atc	7/18	1	2	FACETS	0.961	0.846	1	0.961	0.846	1	CLONAL	1	TRUE	1	0.27	2		319	609	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47602438	47602438	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs587780767	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	147	509	0	ENST00000263735.4:c.491C>T	p.Thr164Ile	p.T164I	ENST00000263735	NM_002354.2	164	aCt/aTt	4/9	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.27	2		509	905	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713598	30713598	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs28934568	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	99	310	0	ENST00000295754.5:c.923T>C	p.Leu308Pro	p.L308P	ENST00000295754	NM_003242.5	308	cTg/cCg	4/7	0.3	2	FACETS	1	0.963	1	0.586	0.524	0.652	CLONAL	1	TRUE	0	0.27	2		310	626	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400021	49400021	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	125	629	0	ENST00000418115.1:c.316T>G	p.Phe106Val	p.F106V	ENST00000418115	NM_001664.2	106	Ttc/Gtc	4/5	0.3	2	FACETS	0.794	0.717	0.876	0.397	0.358	0.438	SUBCLONAL	1	TRUE	0	0.27	2		629	1166	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436342	52436342	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1186981831	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	103	546	2	ENST00000460680.1:c.2152C>T	p.Arg718Trp	p.R718W	ENST00000460680	NM_004656.3	718	Cgg/Tgg	17/17	1	2	FACETS	0.88	0.787	0.979	0.88	0.787	0.979	CLONAL	1	TRUE	1	0.27	2		548	867	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460328	149460328	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	65	317	0	ENST00000286301.3:c.307+2T>C		p.X103_splice	ENST00000286301	NM_005211.3	103			1	2	FACETS	0.926	0.804	1	0.926	0.804	1	CLONAL	1	TRUE	1	0.27	2		317	520	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752812	128752812	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	99	323	0	ENST00000377970.2:c.973G>A	p.Ala325Thr	p.A325T	ENST00000377970	NM_002467.4	325	Gca/Aca	3/3	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.27	2		323	611	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230406	46230406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	171	377	0	ENST00000334344.6:c.740G>A	p.Arg247His	p.R247H	ENST00000334344	NM_152641.2	247	cGt/cAt	7/21	0.3	3	FACETS	0.762	0.701	0.826	0.762	0.701	0.826	SUBCLONAL	2	TRUE	1	0.27	3		377	943	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438060	49438060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	352	533	1	ENST00000301067.7:c.5111G>A	p.Arg1704Gln	p.R1704Q	ENST00000301067	NM_003482.3	1704	cGg/cAg	21/54	0.3	3	FACETS	0.857	0.812	0.903	1	0.993	1	CLONAL	3	TRUE	1	0.27	3		534	1151	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859025	57859025	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1304	308	822	1	ENST00000228682.2:c.521T>C	p.Phe174Ser	p.F174S	ENST00000228682	NM_005269.2	174	tTc/tCc	5/12	0.3	3	FACETS	0.803	0.755	0.853	0.803	0.755	0.853	CLONAL	2	TRUE	1	0.27	3		823	1612	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562783	21562783	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	55	201	0	ENST00000382592.4:c.1136A>G	p.Asp379Gly	p.D379G	ENST00000382592	NM_014572.2	379	gAc/gGc	4/8	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.27	2		201	339	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560460	95560460	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	56	201	0	ENST00000393063.1:c.5129C>T	p.Ala1710Val	p.A1710V	ENST00000393063	NM_030621.3	1710	gCg/gTg	25/28	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.27	2		201	394	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961418	41961418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1372	266	959	2	ENST00000219905.7:c.326G>A	p.Arg109His	p.R109H	ENST00000219905	NM_001164273.1	109	cGt/cAt	2/24	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.27	2		961	1638	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819176	3819176	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	112	632	0	ENST00000262367.5:c.3059A>G	p.Glu1020Gly	p.E1020G	ENST00000262367	NM_004380.2	1020	gAg/gGg	15/31	1	2	FACETS	0.773	0.694	0.858	0.773	0.694	0.858	SUBCLONAL	1	TRUE	1	0.27	2		632	1073	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832693	3832693	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs61754521	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	131	521	0	ENST00000262367.5:c.1565A>G	p.Asn522Ser	p.N522S	ENST00000262367	NM_004380.2	522	aAc/aGc	6/31	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.27	2		521	948	SUCCESS
YES1	7525	MSKCC	GRCh37	18	747947	747947	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766059693	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	146	553	1	ENST00000314574.4:c.443C>T	p.Ala148Val	p.A148V	ENST00000314574	NM_005433.3	148	gCg/gTg	4/12	0.3	3	FACETS	0.958	0.872	1	0.479	0.436	0.525	CLONAL	1	TRUE	1	0.27	3		554	1281	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985571	60985571	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	54	274	0	ENST00000333681.4:c.329G>A	p.Arg110His	p.R110H	ENST00000333681		110	cGc/cAc	2/3	0.3	3	FACETS	0.785	0.671	0.911	0.393	0.335	0.456	CLONAL	1	TRUE	1	0.27	3		274	578	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214637	5214637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757423838	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	338	657	7	ENST00000357368.4:c.4429C>T	p.Arg1477Cys	p.R1477C	ENST00000357368	NM_002850.3	1477	Cgt/Tgt	29/38	0.293761862344845	3	FACETS	0.853	0.808	0.9	1	0.992	1	CLONAL	3	TRUE	1	0.27	3		664	1110	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31020695	31020695	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1208821068	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	89	371	0	ENST00000375687.4:c.992A>G	p.His331Arg	p.H331R	ENST00000375687	NM_015338.5	331	cAt/cGt	11/13	1	2	FACETS	0.872	0.773	0.978	0.872	0.773	0.978	CLONAL	1	TRUE	1	0.27	2		371	756	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39704810	39704810	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	96	224	0	ENST00000361337.2:c.156-1G>A		p.X52_splice	ENST00000361337	NM_003286.2	52			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.27	2		224	570	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914723	39914723	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	231	399	4	ENST00000378444.4:c.4639C>T	p.Arg1547Ter	p.R1547*	ENST00000378444	NM_001123385.1	1547	Cga/Tga	12/15	1	1	FACETS	1	0.965	1	1	0.995	1	CLONAL	2	TRUE	0	0.27	1		403	709	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37061814	37061878	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCAGAATGTGGATGTTAATGTGCACCCCACAAAGCATGAAGTTCACTTCCTGCACGAGGAGAG	CCCCAGAATGTGGATGTTAATGTGCACCCCACAAAGCATGAAGTTCACTTCCTGCACGAGGAGAG	-	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	214	464	1	ENST00000231790.2:c.899_963del	p.Pro300HisfsTer40	p.P300Hfs*40	ENST00000231790	NM_000249.3	300	CCCCAGAATGTGGATGTTAATGTGCACCCCACAAAGCATGAAGTTCACTTCCTGCACGAGGAGAGc/c	11/19	0.3	2	FACETS	0.931	0.867	0.998	0.931	0.867	0.998	CLONAL	2	TRUE	0	0.27	2		465	851	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348561	56348561	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1272	231	816	1	ENST00000348428.3:c.374del	p.Pro125GlnfsTer3	p.P125Qfs*3	ENST00000348428	NM_006785.3	123	agC/ag	2/17	0.3	3	FACETS	1	0.988	1	0.646	0.6	0.694	CLONAL	1	TRUE	1	0.27	3		817	1503	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593635	215593635	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1553612184	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	126	429	0	ENST00000260947.4:c.2099del	p.Gly700AlafsTer14	p.G700Afs*14	ENST00000260947	NM_000465.2	700	gGc/gc	11/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.27	2		429	835	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505370	157505371	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	132	431	0	ENST00000346085.5:c.3356dup	p.Asn1119LysfsTer6	p.N1119Kfs*6	ENST00000346085	NM_020732.3	1117	-/A	13/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.27	2		431	813	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760684	59760685	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	166	546	1	ENST00000259008.2:c.3722dup	p.Asn1241LysfsTer2	p.N1241Kfs*2	ENST00000259008	NM_032043.2	1241	aat/aaAt	20/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.27	2		547	959	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564755	139564755	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	85	470	1	ENST00000308874.7:c.549del	p.Arg184GlyfsTer13	p.R184Gfs*13	ENST00000308874		182	Ccc/cc	7/10	1	2	FACETS	0.807	0.713	0.908	0.807	0.713	0.908	CLONAL	1	TRUE	1	0.27	2		471	780	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797806	42797807	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	131	437	0	ENST00000575354.2:c.3862dup	p.Glu1288GlyfsTer56	p.E1288Gfs*56	ENST00000575354	NM_015125.3	1286	-/G	16/20	0.293761862344845	3	FACETS	1	0.978	1	0.634	0.575	0.696	CLONAL	1	TRUE	1	0.27	3		437	869	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940112	49940112	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760002850	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	204	722	4	ENST00000296474.3:c.931del	p.Ala311ProfsTer27	p.A311Pfs*27	ENST00000296474	NM_002447.2	311	Gcc/cc	1/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.27	2		726	1146	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443512	49443512	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	92	423	0	ENST00000301067.7:c.3859del	p.Glu1287ArgfsTer43	p.E1287Rfs*43	ENST00000301067	NM_003482.3	1287	Gag/ag	11/54	0.3	3	FACETS	0.834	0.74	0.935	0.417	0.37	0.468	CLONAL	1	TRUE	1	0.27	3		423	927	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435274	49435275	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	96	386	0	ENST00000301067.7:c.6278_6279del	p.Ile2093SerfsTer3	p.I2093Sfs*3	ENST00000301067	NM_003482.3	2093	aTA/a	31/54	0.3	3	FACETS	1	0.964	1	0.597	0.532	0.666	CLONAL	1	TRUE	1	0.27	3		386	676	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533939	63533942	+	frameshift_variant	Frame_Shift_Del	DEL	CTCT	CTCT	-	rs771001164	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	46	203	0	ENST00000307078.5:c.1212_1215del	p.Glu405AlafsTer52	p.E405Afs*52	ENST00000307078	NM_004655.3	404	agAGAG/ag	6/11	1	2	FACETS	0.926	0.782	1	0.926	0.782	1	CLONAL	1	TRUE	1	0.27	2		203	368	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521525	46521525	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	219	702	3	ENST00000262741.5:c.883del	p.Met295Ter	p.M295*	ENST00000262741	NM_003629.3	295	Atg/tg	7/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.27	2		705	1317	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38964913	38964913	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	127	360	0	ENST00000357387.3:c.1381A>C	p.Ile461Leu	p.I461L	ENST00000357387	NM_152756.3	461	Atc/Ctc	16/38	1	2	FACETS	0.897	0.816	0.981	0.897	0.816	0.981	CLONAL	1	TRUE	1	0.520634677638857	2		360	544	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842656	68842657	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0012130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	257	716	0	ENST00000261769.5:c.597_598dup	p.Pro200HisfsTer16	p.P200Hfs*16	ENST00000261769	NM_004360.3	198	gac/gACac	5/16	0.520634677638857	1	FACETS	0.958	0.901	1	0.958	0.901	1	CLONAL	1	TRUE	0	0.520634677638857	1		716	762	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764146326	NA	P-0012142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	490	633	0	ENST00000269305.4:c.841G>A	p.Asp281Asn	p.D281N	ENST00000269305	NM_001126112.2	281	Gac/Aac	8/11	0.692044781764108	2	FACETS	0.923	0.896	0.951	0.923	0.896	0.951	CLONAL	2	TRUE	0	0.754768685768392	2		633	703	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354226	70354226	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1423751717	NA	P-0012142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	207	295	1	ENST00000374080.3:c.4637C>T	p.Thr1546Met	p.T1546M	ENST00000374080		1546	aCg/aTg	34/45	0.245841416001621	5	FACETS	1	0.97	1	0.362	0.336	0.39	INDETERMINATE	1	TRUE	2	0.754768685768392	5		296	1076	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099342	157099342	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	151	494	0	ENST00000346085.5:c.279C>A	p.His93Gln	p.H93Q	ENST00000346085	NM_020732.3	93	caC/caA	1/20	0.721399285232748	3	FACETS	0.988	0.908	1			1	CLONAL	1	TRUE	NA	0.754768685768392	3		494	558	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40468897	40468897	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	49	601	0	ENST00000264657.5:c.2167G>A	p.Asp723Asn	p.D723N	ENST00000264657	NM_139276.2	723	Gac/Aac	23/24	0.692044781764108	2	FACETS	0.214	0.181	0.251	0.107	0.09	0.126	SUBCLONAL	1	TRUE	0	0.754768685768392	2		601	606	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054540	42054541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	470	715	2	ENST00000219905.7:c.7731dup	p.Asp2578ArgfsTer45	p.D2578Rfs*45	ENST00000219905	NM_001164273.1	2575	aga/agAa	22/24	0.695384741428141	2	FACETS	0.84	0.812	0.868	0.84	0.812	0.868	CLONAL	2	TRUE	0	0.754768685768392	2		717	741	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0012156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	61	234	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.684125463551548	1	FACETS	0.45	0.392	0.511	0.45	0.392	0.511	SUBCLONAL	1	TRUE	0	0.684125463551548	1		234	261	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776783	NA	P-0012156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	115	348	0	ENST00000267163.4:c.1215+1G>A		p.X405_splice	ENST00000267163	NM_000321.2	405			0.684125463551548	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.684125463551548	1		348	211	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938230	76938230	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	283	504	0	ENST00000373344.5:c.2518del	p.Arg840GlufsTer29	p.R840Efs*29	ENST00000373344	NM_000489.3	840	Aga/ga	9/35	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.684125463551548	1		504	440	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966872	25966873	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0012156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	378	750	0	ENST00000435504.4:c.2333dup	p.Val779SerfsTer25	p.V779Sfs*25	ENST00000435504		778	cca/ccCa	13/13	0.684125463551548	1	FACETS	0.916	0.875	0.956	0.916	0.875	0.956	CLONAL	1	TRUE	0	0.684125463551548	1		750	794	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797286	135797286	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	69	651	0	ENST00000298552.3:c.583T>C	p.Tyr195His	p.Y195H	ENST00000298552	NM_001162426.1	195	Tac/Cac	7/23	0.684125463551548	1	FACETS	0.257	0.224	0.293	0.257	0.224	0.293	SUBCLONAL	1	TRUE	0	0.684125463551548	1		651	516	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256111	123256111	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	472	1148	0	ENST00000358487.5:c.1798T>C	p.Phe600Leu	p.F600L	ENST00000358487	NM_000141.4	600	Ttc/Ctc	13/18	0.684125463551548	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.684125463551548	1		1148	897	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943632	9943632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	335	624	1	ENST00000330684.3:c.1309C>T	p.Arg437Trp	p.R437W	ENST00000330684	NM_001134407.1	437	Cgg/Tgg	5/13	0.684125463551548	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.684125463551548	1		625	616	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579722	7579722	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0012156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	464	904	0	ENST00000269305.4:c.75-1G>A		p.X25_splice	ENST00000269305	NM_001126112.2	25			0.684125463551548	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.684125463551548	1		904	873	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29662010	29662010	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	138	493	0	ENST00000356175.3:c.5906del	p.Pro1969HisfsTer22	p.P1969Hfs*22	ENST00000356175	NM_000267.3	1968	taC/ta	39/57	0.684125463551548	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.684125463551548	1		493	260	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578226	7578226	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1464727668	NA	P-0012176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	257	907	0	ENST00000269305.4:c.623A>T	p.Asp208Val	p.D208V	ENST00000269305	NM_001126112.2	208	gAc/gTc	6/11	0.412042752978869	1	FACETS	0.937	0.878	0.998	0.937	0.878	0.998	CLONAL	1	TRUE	0	0.412042752978869	1		907	1057	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259295	36259296	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	116	269	0	ENST00000300305.3:c.195dup	p.Ala66CysfsTer72	p.A66Cfs*72	ENST00000300305		65	-/T	3/8	0.412042752978869	2	FACETS	0.771	0.702	0.842	0.771	0.702	0.842	SUBCLONAL	2	TRUE	0	0.412042752978869	2		269	365	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0012186-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	77	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.387367263571495	4	FACETS	0.826	0.731	0.926	0.826	0.731	0.926	CLONAL	2	TRUE	2	0.387367263571495	4		249	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0012186-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	169	524	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.337833693009142	2	FACETS	0.955	0.886	1	0.955	0.886	1	CLONAL	2	TRUE	0	0.387367263571495	2		524	457	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123788	11123788	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1064795105	NA	P-0012186-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	146	425	0	ENST00000358026.2:c.2438C>T	p.Ser813Leu	p.S813L	ENST00000358026	NM_001128849.1	813	tCa/tTa	16/36	0.286499674315837	2	FACETS	0.839	0.773	0.908	0.839	0.773	0.908	CLONAL	2	TRUE	0	0.387367263571495	2		425	449	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645381	215645381	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012186-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	117	731	0	ENST00000260947.4:c.1217G>T	p.Arg406Leu	p.R406L	ENST00000260947	NM_000465.2	406	cGa/cTa	4/11	0.386156424728921	3	FACETS	0.887	0.8	0.979	0.443	0.4	0.49	CLONAL	1	TRUE	1	0.387367263571495	3		731	813	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78866524	78866544	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCAGAGGGAGGGAGTTTGAC	CCCAGAGGGAGGGAGTTTGAC	-	novel	NA	P-0012186-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	48	439	0	ENST00000306801.3:c.2102_2122del		p.X701_splice	ENST00000306801	NM_020761.2	701		19/34	0.314987115951135	2	FACETS	0.65	0.551	0.759	0.325	0.275	0.38	SUBCLONAL	1	TRUE	0	0.387367263571495	2		439	381	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206857	36206858	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCTCC	novel	NA	P-0012186-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	180	278	0	ENST00000300305.3:c.650_654dup	p.Leu219GlyfsTer20	p.L219Gfs*20	ENST00000300305		218	-/GGAGC	6/8	0.358185662910008	4	FACETS	0.907	0.844	0.97	0.907	0.844	0.97	CLONAL	3	TRUE	1	0.387367263571495	4		278	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0012214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	21	649	1	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.273534990823591	1	FACETS	0.773	0.601	0.969	0.773	0.601	0.969	CLONAL	1	TRUE	0	0.310271648181247	1		650	148	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117243	7117243	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	27	791	1	ENST00000302850.5:c.3973G>T	p.Glu1325Ter	p.E1325*	ENST00000302850	NM_000208.2	1325	Gag/Tag	22/22	1	2	FACETS	0.737	0.589	0.905	0.737	0.589	0.905	CLONAL	1	TRUE	1	0.310271648181247	2		792	236	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252856	36252856	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	33	404	0	ENST00000300305.3:c.506G>A	p.Arg169Lys	p.R169K	ENST00000300305		169	aGa/aAa	4/8	0.310271648181247	1	FACETS	0.951	0.782	1	0.951	0.782	1	CLONAL	1	TRUE	0	0.310271648181247	1		404	189	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215276	123215276	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	22	840	0	ENST00000218089.9:c.2822C>A	p.Ser941Ter	p.S941*	ENST00000218089	NM_001042749.1	941	tCa/tAa	28/35	0.215028042250252	1	FACETS	0.457	0.355	0.576	0.457	0.355	0.576	SUBCLONAL	1	TRUE	0	0.310271648181247	1		840	262	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001331	150001331	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	48	786	0	ENST00000253339.5:c.2273del	p.Ala758ValfsTer8	p.A758Vfs*8	ENST00000253339		758	gCt/gt	4/7	0.233159203000021	2	FACETS	1	0.954	1	0.664	0.567	0.769	CLONAL	1	TRUE	0	0.310271648181247	2		786	233	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252970	36252971	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	35	418	0	ENST00000300305.3:c.391dup	p.Thr131AsnfsTer7	p.T131Nfs*7	ENST00000300305		131	act/aAct	4/8	0.310271648181247	1	FACETS	1	0.831	1	1	0.831	1	CLONAL	1	TRUE	0	0.310271648181247	1		418	190	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668619	52668619	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012221-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	85	505	0	ENST00000394830.3:c.1300C>T	p.Arg434Ter	p.R434*	ENST00000394830	NM_018313.4	434	Cga/Tga	12/30	0.549004348778851	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.549004348778851	1		505	201	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437696	52437697	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0012221-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	169	1013	2	ENST00000460680.1:c.1464dup	p.Ser489GlnfsTer3	p.S489Qfs*3	ENST00000460680	NM_004656.3	488	-/C	13/17	0.549004348778851	1	FACETS	0.946	0.878	1	0.946	0.878	1	CLONAL	1	TRUE	0	0.549004348778851	1		1015	472	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436405	52436405	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012221-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	32	445	0	ENST00000460680.1:c.2089del	p.Ser697ProfsTer39	p.S697Pfs*39	ENST00000460680	NM_004656.3	697	Tcc/cc	17/17	0.549004348778851	1	FACETS	0.31	0.252	0.374	0.31	0.252	0.374	SUBCLONAL	1	TRUE	0	0.549004348778851	1		445	273	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183787	10183787	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs864622545	NA	P-0012221-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	85	317	0	ENST00000256474.2:c.258del	p.Val87TyrfsTer72	p.V87Yfs*72	ENST00000256474	NM_000551.3	86	Ccc/cc	1/3	0.549004348778851	1	FACETS	0.968	0.871	1	0.968	0.871	1	CLONAL	1	TRUE	0	0.549004348778851	1		317	232	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0012239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	63	786	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	1	2	FACETS	0.676	0.584	0.778	0.676	0.584	0.778	SUBCLONAL	1	TRUE	1	0.22632814510922	2		786	823	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	64	273	0	ENST00000397752.3:c.3028G>A	p.Asp1010Asn	p.D1010N	ENST00000397752	NM_000245.2	1010	Gat/Aat	14/21	NA	2	FACETS	1	0.956	1			1	INDETERMINATE	1	TRUE	NA	0.22632814510922	2		273	453	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157454284	157454284	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554301240	NA	P-0012239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	48	480	0	ENST00000346085.5:c.2494C>T	p.Gln832Ter	p.Q832*	ENST00000346085	NM_020732.3	832	Cag/Tag	8/20	1	2	FACETS	0.53	0.446	0.622	0.53	0.446	0.622	SUBCLONAL	1	TRUE	1	0.22632814510922	2		480	801	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559158	29559159	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	73	478	0	ENST00000356175.3:c.3267dup	p.Gly1090ArgfsTer16	p.G1090Rfs*16	ENST00000356175	NM_000267.3	1089	gaa/gAaa	25/57	1	2	FACETS	0.931	0.814	1	0.931	0.814	1	CLONAL	1	TRUE	1	0.22632814510922	2		478	693	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922294	100922294	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1315135533	NA	P-0012258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	198	726	0	ENST00000325455.5:c.2218C>T	p.Arg740Ter	p.R740*	ENST00000325455	NM_001202474.3	740	Cga/Tga	5/8	0.311872641664074	3	FACETS	1	0.986	1	0.414	0.385	0.445	INDETERMINATE	1	TRUE	0	0.569229856911748	3		726	719	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646831	37646832	+	stop_gained,inframe_insertion	Nonsense_Mutation	INS	-	-	AAACCTGTGAAGAAAGAGAAGGAACAGAGGACACGTCACTGACTT	novel	NA	P-0012258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	99	671	0	ENST00000447079.4:c.1993_1994insGACTTAAACCTGTGAAGAAAGAGAAGGAACAGAGGACACGTCACT	p.His664_Leu665insTer	p.H664_L665ins*	ENST00000447079	NM_015083.1	651	-/AAACCTGTGAAGAAAGAGAAGGAACAGAGGACACGTCACTGACTT	3/14	1	2	FACETS	0.419	0.373	0.467	0.419	0.373	0.467	SUBCLONAL	1	TRUE	1	0.569229856911748	2		671	831	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627916	37627917	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0012258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	314	577	0	ENST00000447079.4:c.1831_1832del	p.Thr611SerfsTer29	p.T611Sfs*29	ENST00000447079	NM_015083.1	611	ACt/t	2/14	1	2	FACETS	0.765	0.727	0.804	1	0.995	1	SUBCLONAL	2	TRUE	1	0.569229856911748	2		577	721	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888121	81888121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762900860	NA	P-0012264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	178	1076	1	ENST00000359376.3:c.266G>A	p.Arg89His	p.R89H	ENST00000359376	NM_002661.3	89	cGc/cAc	3/33	0.478884992456975	1	FACETS	0.811	0.751	0.872	0.811	0.751	0.872	CLONAL	1	TRUE	0	0.527988951247923	1		1077	612	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664915	138664915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs797044527	NA	P-0012264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	38	208	0	ENST00000330315.3:c.650C>T	p.Ser217Phe	p.S217F	ENST00000330315	NM_023067.3	217	tCc/tTc	1/1	0.526878485219378	2	FACETS	0.809	0.677	0.952	0.404	0.338	0.476	CLONAL	1	TRUE	0	0.527988951247923	2		208	178	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551700	150551700	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773052989	NA	P-0012264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	57	252	0	ENST00000369026.2:c.307C>T	p.Arg103Cys	p.R103C	ENST00000369026	NM_021960.4	103	Cgc/Tgc	1/3	0.146771061193207	4	FACETS	1	0.863	1			1	INDETERMINATE	1	TRUE	NA	0.527988951247923	4		252	330	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983031	111983031	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	75	1271	2	ENST00000368678.4:c.1516G>A	p.Glu506Lys	p.E506K	ENST00000368678		506	Gaa/Aaa	13/13	0.13565269289316	3	FACETS	0.31	0.27	0.352	0.103	0.09	0.118	INDETERMINATE	1	TRUE	0	0.527988951247923	3		1273	1160	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762832	40762832	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0012264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	35	641	0	ENST00000392038.2:c.175+1G>C		p.X59_splice	ENST00000392038	NM_001626.4	59			0.18093567022375	2	FACETS	0.277	0.226	0.333	0.138	0.113	0.167	INDETERMINATE	1	TRUE	0	0.527988951247923	2		641	479	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574446	41574446	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1310111885	NA	P-0012264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	50	595	0	ENST00000263253.7:c.6731A>G	p.Gln2244Arg	p.Q2244R	ENST00000263253	NM_001429.3	2244	cAg/cGg	31/31	0.527988951247923	3	FACETS	0.411	0.348	0.48	0.206	0.174	0.24	SUBCLONAL	1	TRUE	1	0.527988951247923	3		595	582	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839812	27839813	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0012264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	84	1886	0	ENST00000328488.2:c.281_282insC	p.Gln94HisfsTer13	p.Q94Hfs*13	ENST00000328488	NM_003533.2	94	cag/caCg	1/1	0.359594360355204	3	FACETS	0.314	0.276	0.355	0.105	0.092	0.119	SUBCLONAL	1	TRUE	0	0.527988951247923	3		1886	1280	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	136	265	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.207092940177766	5	FACETS	1	0.97	1	0.765	0.696	0.837	CLONAL	2	TRUE	2	0.207092940177766	5		265	750	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332337	70332337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761821309	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	168	678	2	ENST00000373644.4:c.242G>A	p.Arg81His	p.R81H	ENST00000373644	NM_030625.2	81	cGc/cAc	2/12	0.207092940177766	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.207092940177766	3		680	744	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979987	7979987	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746723399	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	122	486	0	ENST00000319144.4:c.1350del	p.Leu451SerfsTer16	p.L451Sfs*16	ENST00000319144	NM_001139.2	450	ggG/gg	10/15	0.187340174715713	4	FACETS	0.839	0.761	0.921	1	0.978	1	CLONAL	3	TRUE	2	0.207092940177766	4		486	565	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	109	183	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.187340174715713	4	FACETS	0.971	0.878	1	1	0.983	1	CLONAL	3	TRUE	2	0.207092940177766	4		183	436	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296358	15296358	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	63	543	3	ENST00000263388.2:c.2084del	p.Pro695ArgfsTer165	p.P695Rfs*165	ENST00000263388	NM_000435.2	695	cCg/cg	13/33	0.207092940177766	3	FACETS	1	0.958	1	0.642	0.556	0.735	CLONAL	1	TRUE	1	0.207092940177766	3		546	523	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743932	41743933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs778012871	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	150	865	1	ENST00000301178.4:c.874dup	p.His292ProfsTer47	p.H292Pfs*47	ENST00000301178	NM_021913.4	289	-/C	7/20	0.207092940177766	3	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	TRUE	1	0.207092940177766	3		866	787	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796883	42796883	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	78	760	3	ENST00000575354.2:c.3347del	p.Pro1116GlnfsTer45	p.P1116Qfs*45	ENST00000575354	NM_015125.3	1114	gCc/gc	14/20	0.207092940177766	3	FACETS	1	0.956	1	0.596	0.524	0.674	CLONAL	1	TRUE	1	0.207092940177766	3		763	697	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509085	66509085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	63	849	4	ENST00000273854.3:c.242del	p.Asn81MetfsTer24	p.N81Mfs*24	ENST00000273854	NM_004439.5	81	aAt/at	2/18	0.207092940177766	3	FACETS	1	0.952	1	0.614	0.531	0.703	CLONAL	1	TRUE	1	0.207092940177766	3		853	547	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579419	7579420	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs587783062	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	74	341	0	ENST00000269305.4:c.267dup	p.Ser90LeufsTer59	p.S90Lfs*59	ENST00000269305	NM_001126112.2	89	-/C	4/11	0.187340174715713	4	FACETS	0.783	0.686	0.887	0.783	0.686	0.887	SUBCLONAL	2	TRUE	2	0.207092940177766	4		341	551	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439695	140439695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776664982	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	85	255	0	ENST00000288602.6:c.2044C>T	p.Arg682Trp	p.R682W	ENST00000288602	NM_004333.4	682	Cgg/Tgg	17/18	0.207092940177766	5	FACETS	1	0.951	1	1	0.951	1	CLONAL	3	TRUE	2	0.207092940177766	5		255	321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	195	417	0	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	0.187340174715713	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.207092940177766	4		417	992	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136799	2136799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137854153	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	90	309	0	ENST00000219476.3:c.4916G>A	p.Arg1639His	p.R1639H	ENST00000219476	NM_000548.3	1639	cGc/cAc	38/42	0.122898362386133	3	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.207092940177766	3		309	782	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279861	46279866	+	inframe_deletion	In_Frame_Del	DEL	CAGCAA	CAGCAA	-	rs748517056	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	47	468	1	ENST00000371998.3:c.3810_3815del	p.Gln1275_Gln1276del	p.Q1275_Q1276del	ENST00000371998		1263	CAGCAA/-	20/23	0.187340174715713	4	FACETS	1	0.908	1	0.556	0.469	0.651	CLONAL	1	TRUE	2	0.207092940177766	4		469	493	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381529	81381529	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	102	778	1	ENST00000222390.5:c.532C>T	p.Arg178Ter	p.R178*	ENST00000222390	NM_000601.4	178	Cga/Tga	5/18	0.207092940177766	5	FACETS	1	0.971	1	0.42	0.374	0.468	CLONAL	1	TRUE	2	0.207092940177766	5		779	1025	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144018	11144018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749001381	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	63	561	0	ENST00000358026.2:c.3599G>A	p.Arg1200His	p.R1200H	ENST00000358026	NM_001128849.1	1200	cGt/cAt	26/36	0.207092940177766	3	FACETS	1	0.944	1	0.59	0.51	0.676	CLONAL	1	TRUE	1	0.207092940177766	3		561	569	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939673	76939674	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	91	634	0	ENST00000373344.5:c.1074dup	p.Leu359ThrfsTer3	p.L359Tfs*3	ENST00000373344	NM_000489.3	358	-/A	9/35	0.202888583125263	2	FACETS	0.767	0.682	0.857			1	SUBCLONAL	2	TRUE	NA	0.207092940177766	2		634	573	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250948	10250948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1255153711	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	57	479	0	ENST00000340748.4:c.3532C>T	p.Arg1178Trp	p.R1178W	ENST00000340748		1178	Cgg/Tgg	32/40	0.207092940177766	3	FACETS	1	0.925	1	0.561	0.482	0.648	CLONAL	1	TRUE	1	0.207092940177766	3		479	541	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199945	138199945	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	28	168	1	ENST00000237289.4:c.1368del	p.Pro457LeufsTer20	p.P457Lfs*20	ENST00000237289	NM_001270507.1	455	Ggg/gg	7/9	0.207092940177766	4	FACETS	0.919	0.735	1	0.306	0.245	0.377	CLONAL	1	TRUE	1	0.207092940177766	4		169	355	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512377	38512377	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555574293	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	47	457	1	ENST00000254066.5:c.1293del	p.Arg432GlyfsTer211	p.R432Gfs*211	ENST00000254066	NM_000964.3	430	Ggg/gg	9/9	0.187340174715713	4	FACETS	1	0.918	1	0.57	0.481	0.667	CLONAL	1	TRUE	2	0.207092940177766	4		458	481	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448310	56448310	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567880628	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	104	589	1	ENST00000407977.2:c.337C>T	p.Arg113Ter	p.R113*	ENST00000407977		113	Cga/Tga	3/10	0.187340174715713	4	FACETS	0.964	0.864	1	0.964	0.864	1	CLONAL	2	TRUE	2	0.207092940177766	4		590	629	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073643	8073643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746627277	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	111	1076	3	ENST00000377482.5:c.1016C>T	p.Pro339Leu	p.P339L	ENST00000377482	NM_018948.3	339	cCg/cTg	4/4	0.207092940177766	3	FACETS	1	0.947	1	0.544	0.488	0.604	CLONAL	1	TRUE	1	0.207092940177766	3		1079	1087	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366679	40366679	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs777173419	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	96	443	0	ENST00000397332.2:c.518C>G	p.Ala173Gly	p.A173G	ENST00000397332	NM_001033082.2	173	gCc/gGc	2/3	0.207092940177766	3	FACETS	0.888	0.797	0.983	1	0.977	1	CLONAL	3	TRUE	1	0.207092940177766	3		443	384	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050226	128050226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	148	637	1	ENST00000285398.2:c.431G>A	p.Ser144Asn	p.S144N	ENST00000285398	NM_000122.1	144	aGc/aAc	3/15	0.187340174715713	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.207092940177766	4		638	779	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190708754	190708754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	170	756	0	ENST00000441310.2:c.647C>T	p.Thr216Ile	p.T216I	ENST00000441310	NM_000534.4	216	aCt/aTt	6/13	0.187340174715713	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	2	0.207092940177766	4		756	935	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198262823	198262823	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	54	426	0	ENST00000335508.6:c.3152C>A	p.Ser1051Tyr	p.S1051Y	ENST00000335508	NM_012433.2	1051	tCt/tAt	22/25	0.187340174715713	4	FACETS	1	0.89	1	0.525	0.448	0.61	CLONAL	1	TRUE	2	0.207092940177766	4		426	599	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015194	71015194	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	33	494	0	ENST00000318789.4:c.1736A>G	p.Glu579Gly	p.E579G	ENST00000318789	NM_032682.5	579	gAg/gGg	20/21	0.162881453800097	4	FACETS	0.741	0.603	0.898	0.247	0.201	0.3	SUBCLONAL	1	TRUE	1	0.207092940177766	4		494	519	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644697	134644697	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	40	486	0	ENST00000398015.3:c.98G>A	p.Gly33Asp	p.G33D	ENST00000398015	NM_004441.4	33	gGc/gAc	2/16	0.162881453800097	4	FACETS	0.872	0.724	1	0.291	0.241	0.346	CLONAL	1	TRUE	1	0.207092940177766	4		486	535	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898732	134898732	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	99	779	0	ENST00000398015.3:c.1790C>T	p.Pro597Leu	p.P597L	ENST00000398015	NM_004441.4	597	cCc/cTc	10/16	0.162881453800097	4	FACETS	1	0.98	1	0.488	0.435	0.544	CLONAL	1	TRUE	1	0.207092940177766	4		779	789	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602716	55602716	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	82	724	0	ENST00000288135.5:c.2537A>G	p.Tyr846Cys	p.Y846C	ENST00000288135	NM_000222.2	846	tAc/tGc	18/21	0.207092940177766	3	FACETS	1	0.958	1	0.599	0.527	0.675	CLONAL	1	TRUE	1	0.207092940177766	3		724	730	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251933	153251933	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	212	915	0	ENST00000281708.4:c.1073A>G	p.Gln358Arg	p.Q358R	ENST00000281708	NM_033632.3	358	cAg/cGg	7/12	0.207092940177766	3	FACETS	0.901	0.838	0.965	1	0.989	1	CLONAL	3	TRUE	1	0.207092940177766	3		915	836	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500531	149500531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	143	634	0	ENST00000261799.4:c.2506G>A	p.Glu836Lys	p.E836K	ENST00000261799	NM_002609.3	836	Gaa/Aaa	18/23	0.207092940177766	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.207092940177766	3		634	645	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401745	401745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	47	524	0	ENST00000380956.4:c.1067G>A	p.Cys356Tyr	p.C356Y	ENST00000380956	NM_001195286.1	356	tGc/tAc	7/9	1	2	FACETS	0.921	0.777	1	0.921	0.777	1	CLONAL	1	TRUE	1	0.207092940177766	2		524	493	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910684	29910684	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs41542016	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	71	712	0	ENST00000376809.5:c.224G>A	p.Trp75Ter	p.W75*	ENST00000376809	NM_002116.7	75	tGg/tAg	2/8	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.207092940177766	2		712	673	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687297	117687297	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	151	761	0	ENST00000368508.3:c.2754G>C	p.Leu918Phe	p.L918F	ENST00000368508	NM_002944.2	918	ttG/ttC	18/43	0.207092940177766	4	FACETS	1	0.952	1	0.707	0.647	0.77	CLONAL	2	TRUE	1	0.207092940177766	4		761	830	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004937	150004937	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	260	770	2	ENST00000253339.5:c.1288C>T	p.Gln430Ter	p.Q430*	ENST00000253339		430	Caa/Taa	3/7	0.207092940177766	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	1	0.207092940177766	4		772	874	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739848	41739848	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	188	803	1	ENST00000242208.4:c.125C>T	p.Ala42Val	p.A42V	ENST00000242208	NM_002192.2	42	gCc/gTc	2/3	0.207092940177766	5	FACETS	0.858	0.793	0.925	0.858	0.793	0.925	CLONAL	3	TRUE	2	0.207092940177766	5		804	925	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539063	23539063	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749467152	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	128	608	4	ENST00000380871.4:c.376C>T	p.Arg126Cys	p.R126C	ENST00000380871	NM_006167.3	126	Cgc/Tgc	2/2	0.187340174715713	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.207092940177766	4		612	662	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089702	5089702	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1486560342	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	62	615	1	ENST00000381652.3:c.2600G>A	p.Arg867Gln	p.R867Q	ENST00000381652	NM_004972.3	867	cGg/cAg	20/25	0.187340174715713	4	FACETS	0.876	0.755	1	0.438	0.377	0.504	CLONAL	1	TRUE	2	0.207092940177766	4		616	825	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814869	139814869	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1474752416	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	94	940	1	ENST00000247668.2:c.862G>A	p.Val288Ile	p.V288I	ENST00000247668	NM_021138.3	288	Gtc/Atc	8/11	0.207092940177766	3	FACETS	1	0.96	1	0.587	0.521	0.656	CLONAL	1	TRUE	1	0.207092940177766	3		941	854	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8252049	8252049	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs774615420	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	38	430	0	ENST00000335790.3:c.28G>A	p.Val10Met	p.V10M	ENST00000335790	NM_002315.2	10	Gtg/Atg	2/4	0.207092940177766	3	FACETS	0.993	0.821	1	0.496	0.41	0.592	CLONAL	1	TRUE	1	0.207092940177766	3		430	408	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194110	94194110	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773469981	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	99	775	3	ENST00000323929.3:c.1318G>A	p.Ala440Thr	p.A440T	ENST00000323929	NM_005591.3	440	Gca/Aca	12/20	0.187340174715713	4	FACETS	1	0.961	1	0.587	0.523	0.656	CLONAL	1	TRUE	2	0.207092940177766	4		778	983	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199783	108199783	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	84	357	0	ENST00000278616.4:c.7125T>A	p.Ser2375Arg	p.S2375R	ENST00000278616	NM_000051.3	2375	agT/agA	49/63	0.187340174715713	4	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	2	0.207092940177766	4		357	434	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859598	57859598	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1215799189	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	178	907	2	ENST00000228682.2:c.652C>T	p.Arg218Trp	p.R218W	ENST00000228682	NM_005269.2	218	Cgg/Tgg	7/12	0.187340174715713	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.207092940177766	4		909	892	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248859	133248859	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149296223	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	77	717	1	ENST00000320574.5:c.1736G>A	p.Arg579His	p.R579H	ENST00000320574	NM_006231.2	579	cGc/cAc	16/49	0.187340174715713	4	FACETS	1	0.956	1	0.599	0.525	0.679	CLONAL	1	TRUE	2	0.207092940177766	4		718	749	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660585	67660585	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	223	925	0	ENST00000264010.4:c.1485T>G	p.Phe495Leu	p.F495L	ENST00000264010	NM_006565.3	495	ttT/ttG	8/12	0.187340174715713	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.207092940177766	4		925	1156	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853315	68853315	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	100	562	0	ENST00000261769.5:c.1698A>G	p.Ile566Met	p.I566M	ENST00000261769	NM_004360.3	566	atA/atG	11/16	0.187340174715713	4	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	2	0.207092940177766	4		562	556	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298099	15298099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1243082169	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	65	638	1	ENST00000263388.2:c.1657C>T	p.Pro553Ser	p.P553S	ENST00000263388	NM_000435.2	553	Cca/Tca	11/33	0.207092940177766	3	FACETS	1	0.961	1	0.649	0.563	0.741	CLONAL	1	TRUE	1	0.207092940177766	3		639	534	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376430	15376430	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201736007	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	189	967	2	ENST00000263377.2:c.584C>T	p.Thr195Met	p.T195M	ENST00000263377	NM_058243.2	195	aCg/aTg	5/20	0.207092940177766	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.207092940177766	3		969	908	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257409	19257409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs546609857	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	128	850	1	ENST00000162023.5:c.724G>A	p.Gly242Arg	p.G242R	ENST00000162023		242	Gga/Aga	11/13	0.207092940177766	3	FACETS	0.994	0.903	1	0.994	0.903	1	CLONAL	2	TRUE	1	0.207092940177766	3		851	686	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021497	31021497	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs549287573	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	142	592	1	ENST00000375687.4:c.1496G>A	p.Arg499His	p.R499H	ENST00000375687	NM_015338.5	499	cGt/cAt	12/13	0.187340174715713	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	2	0.207092940177766	4		593	703	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395624	31395624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756972254	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	87	648	1	ENST00000328111.2:c.2477G>A	p.Arg826His	p.R826H	ENST00000328111	NM_006892.3	826	cGc/cAc	23/23	0.187340174715713	4	FACETS	1	0.969	1	0.647	0.572	0.727	CLONAL	1	TRUE	2	0.207092940177766	4		649	784	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259318	36259318	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1569084593	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	37	264	0	ENST00000300305.3:c.173T>C	p.Leu58Pro	p.L58P	ENST00000300305		58	cTg/cCg	3/8	0.207092940177766	2	FACETS	0.76	0.631	0.902	0.76	0.631	0.902	CLONAL	2	TRUE	0	0.207092940177766	2		264	235	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678970	117678970	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	43	397	0	ENST00000368508.3:c.3851del	p.Leu1284Ter	p.L1284*	ENST00000368508	NM_002944.2	1284	tTa/ta	24/43	0.207092940177766	4	FACETS	0.949	0.794	1	0.316	0.264	0.374	CLONAL	1	TRUE	1	0.207092940177766	4		397	528	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954189	48954191	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	114	421	0	ENST00000267163.4:c.1396_1398del	p.Glu466del	p.E466del	ENST00000267163	NM_000321.2	464	GAA/-	15/27	0.187340174715713	4	FACETS	0.86	0.774	0.95	0.86	0.774	0.95	CLONAL	2	TRUE	2	0.207092940177766	4		421	773	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209106756	209106756	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	87	706	0	ENST00000345146.2:c.812del	p.Asn271ThrfsTer20	p.N271Tfs*20	ENST00000345146	NM_005896.2	271	aAc/ac	7/10	0.187340174715713	4	FACETS	1	0.965	1	0.621	0.549	0.698	CLONAL	1	TRUE	2	0.207092940177766	4		706	817	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114733	108114734	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	54	469	0	ENST00000278616.4:c.552_553del	p.Arg184SerfsTer5	p.R184Sfs*5	ENST00000278616	NM_000051.3	184	AGa/a	6/63	0.187340174715713	4	FACETS	1	0.891	1	0.526	0.449	0.611	CLONAL	1	TRUE	2	0.207092940177766	4		469	598	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296203	15296204	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CA	CA	-	novel	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	48	559	0	ENST00000263388.2:c.2160_2161del	p.Cys720Ter	p.C720*	ENST00000263388	NM_000435.2	720	tgTGag/tgag	14/33	0.207092940177766	3	FACETS	1	0.875	1	0.52	0.439	0.608	CLONAL	1	TRUE	1	0.207092940177766	3		559	492	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993014	72993014	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	232	1056	0	ENST00000268489.5:c.1031del	p.Asn344ThrfsTer8	p.N344Tfs*8	ENST00000268489	NM_006885.3	344	aAc/ac	2/10	0.187340174715713	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.207092940177766	4		1056	1250	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245995	5245996	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	96	552	0	ENST00000357368.4:c.779dup	p.Asn261GlnfsTer30	p.N261Qfs*30	ENST00000357368	NM_002850.3	260	ggc/ggGc	10/38	0.207092940177766	3	FACETS	1	0.904	1	1	0.904	1	CLONAL	2	TRUE	1	0.207092940177766	3		552	506	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611771	1611771	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	73	897	0	ENST00000344749.5:c.1891del	p.Gln631ArgfsTer11	p.Q631Rfs*11	ENST00000344749	NM_001136139.2	631	Cag/ag	19/19	0.207092940177766	3	FACETS	0.912	0.796	1	0.456	0.398	0.519	CLONAL	1	TRUE	1	0.207092940177766	3		897	853	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	552	265	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.589061684027811	5	FACETS	0.915	0.888	0.941	0.915	0.888	0.941	CLONAL	4	TRUE	1	0.84168829261052	5		265	811	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073502	8073502	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1052380748	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	1291	733	1	ENST00000377482.5:c.1157G>A	p.Gly386Glu	p.G386E	ENST00000377482	NM_018948.3	386	gGg/gAg	4/4	0.589061684027811	5	FACETS	0.914	0.896	0.931	0.914	0.896	0.931	CLONAL	4	TRUE	1	0.84168829261052	5		734	1899	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261803	16261803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	138	286	1	ENST00000375759.3:c.9068C>T	p.Ala3023Val	p.A3023V	ENST00000375759	NM_015001.2	3023	gCt/gTt	11/15	0.589061684027811	5	FACETS	1	0.983	1	0.329	0.3	0.359	CLONAL	1	TRUE	1	0.84168829261052	5		287	564	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076824	72076824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	232	325	0	ENST00000357731.5:c.673C>T	p.Pro225Ser	p.P225S	ENST00000357731	NM_173808.2	225	Cct/Tct	5/7	0.84168829261052	3	FACETS	0.989	0.925	1			1	CLONAL	1	TRUE	NA	0.84168829261052	3		325	792	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518301	204518301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1405649744	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	563	448	1	ENST00000367182.3:c.964C>T	p.Arg322Cys	p.R322C	ENST00000367182	NM_001278516.1	322	Cgt/Tgt	11/11	0.379760805804632	6	FACETS	0.962	0.926	0.998	0.962	0.926	0.998	INDETERMINATE	3	TRUE	3	0.84168829261052	6		449	1244	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735351	204735351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759766975	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	147	193	0	ENST00000302823.3:c.152G>A	p.Arg51Gln	p.R51Q	ENST00000302823	NM_005214.4	51	cGa/cAa	2/4	0.554045810031893	4	FACETS	0.833	0.77	0.898	0.833	0.77	0.898	CLONAL	2	TRUE	2	0.84168829261052	4		193	386	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285228	212285228	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	433	370	0	ENST00000342788.4:c.3073C>T	p.Pro1025Ser	p.P1025S	ENST00000342788	NM_005235.2	1025	Cct/Tct	25/28	0.554045810031893	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	2	0.84168829261052	4		370	841	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014095	70014095	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	3372	720	2	ENST00000394351.3:c.956C>T	p.Pro319Leu	p.P319L	ENST00000394351	NM_000248.3	319	cCc/cTc	9/9	0.84168829261052	9	FACETS	1	0.998	1			1	CLONAL	9	TRUE	NA	0.84168829261052	9		722	3492	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808632	1808632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	408	664	0	ENST00000260795.2:c.2245G>A	p.Asp749Asn	p.D749N	ENST00000260795		749	Gac/Aac	16/17	0.189739931120769	5	FACETS	1	0.992	1			1	INDETERMINATE	3	TRUE	NA	0.84168829261052	5		664	660	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197421	106197421	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	365	422	0	ENST00000380013.4:c.5754A>T	p.Glu1918Asp	p.E1918D	ENST00000380013	NM_001127208.2	1918	gaA/gaT	11/11	0.47681237052978	3	FACETS	0.874	0.836	0.912	0.874	0.836	0.912	INDETERMINATE	2	TRUE	1	0.84168829261052	3		422	705	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557801	187557801	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	394	392	0	ENST00000441802.2:c.3910C>T	p.Pro1304Ser	p.P1304S	ENST00000441802	NM_005245.3	1304	Ccg/Tcg	5/27	0.47681237052978	3	FACETS	0.873	0.836	0.909	0.873	0.836	0.909	INDETERMINATE	2	TRUE	1	0.84168829261052	3		392	762	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	77	222	0				ENST00000310581	NM_198253.2	-/1132			0.436747247971343	3	FACETS	1	0.963	1	0.591	0.528	0.656	INDETERMINATE	1	TRUE	1	0.84168829261052	3		222	220	SUCCESS
APC	324	MSKCC	GRCh37	5	112177119	112177119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	268	433	0	ENST00000257430.4:c.5828G>A	p.Arg1943Lys	p.R1943K	ENST00000257430	NM_000038.5	1943	aGa/aAa	16/16	1	2	FACETS	0.963	0.91	1	0.963	0.91	1	CLONAL	1	TRUE	1	0.84168829261052	2		433	661	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681787	30681787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	459	390	0	ENST00000376406.3:c.310C>T	p.Pro104Ser	p.P104S	ENST00000376406	NM_014641.2	104	Cct/Tct	3/15	0.519214623795944	6	FACETS	0.938	0.899	0.977	0.938	0.899	0.977	CLONAL	3	TRUE	3	0.84168829261052	6		390	1040	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187944	32187944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	377	431	0	ENST00000375023.3:c.1277G>A	p.Gly426Glu	p.G426E	ENST00000375023	NM_004557.3	426	gGg/gAg	7/30	0.519214623795944	6	FACETS	0.978	0.934	1	0.978	0.934	1	CLONAL	3	TRUE	3	0.84168829261052	6		431	819	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444346	50444346	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	333	301	0	ENST00000331340.3:c.276G>A	p.Met92Ile	p.M92I	ENST00000331340	NM_006060.4	92	atG/atA	4/8	0.379760805804632	6	FACETS	0.92	0.875	0.966	0.92	0.875	0.966	INDETERMINATE	3	TRUE	3	0.84168829261052	6		301	769	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455151	50455151	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446212014	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	224	203	0	ENST00000331340.3:c.698C>T	p.Pro233Leu	p.P233L	ENST00000331340	NM_006060.4	233	cCg/cTg	6/8	0.379760805804632	6	FACETS	0.994	0.937	1	0.994	0.937	1	INDETERMINATE	3	TRUE	3	0.84168829261052	6		203	479	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339799	116339799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	972	466	0	ENST00000397752.3:c.661G>A	p.Glu221Lys	p.E221K	ENST00000397752	NM_000245.2	221	Gaa/Aaa	2/21	0.589061684027811	5	FACETS	0.927	0.907	0.947	0.927	0.907	0.947	CLONAL	4	TRUE	1	0.84168829261052	5		466	1409	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476853	140476853	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	111	340	0	ENST00000288602.6:c.1553G>C	p.Gly518Ala	p.G518A	ENST00000288602	NM_004333.4	518	gGc/gCc	13/18	0.589061684027811	5	FACETS	0.608	0.546	0.675	0.152	0.136	0.169	SUBCLONAL	1	TRUE	1	0.84168829261052	5		340	981	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436600	8436600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs888423638	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	331	342	0	ENST00000356435.5:c.4078G>A	p.Glu1360Lys	p.E1360K	ENST00000356435		1360	Gaa/Aaa	24/35	0.821620926086541	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.84168829261052	2		342	382	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449838	8449838	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	212	227	0	ENST00000356435.5:c.3876-1G>A		p.X1292_splice	ENST00000356435		1292			0.821620926086541	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.84168829261052	2		227	251	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249758	110249758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1307874181	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	492	323	0	ENST00000374672.4:c.917C>T	p.Pro306Leu	p.P306L	ENST00000374672	NM_004235.4	306	cCc/cTc	3/5	0.84168829261052	4	FACETS	1	0.996	1			1	CLONAL	4	TRUE	NA	0.84168829261052	4		323	520	SUCCESS
RET	5979	MSKCC	GRCh37	10	43595997	43595997	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446283609	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	292	390	0	ENST00000355710.3:c.164C>T	p.Ala55Val	p.A55V	ENST00000355710	NM_020975.4	55	gCc/gTc	2/20	0.285543939558228	4	FACETS	0.914	0.875	0.953	0.686	0.656	0.715	INDETERMINATE	3	TRUE	0	0.84168829261052	4		390	466	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998444	100998444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2174	251	433	1	ENST00000325455.5:c.1358C>T	p.Ser453Phe	p.S453F	ENST00000325455	NM_001202474.3	453	tCc/tTc	1/8	0.84168829261052	15	FACETS	0.796	0.74	0.853			1	SUBCLONAL	2	TRUE	NA	0.84168829261052	15		434	2425	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149009	119149009	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	263	245	0	ENST00000264033.4:c.1227+2T>C		p.X409_splice	ENST00000264033	NM_005188.3	409			0.84168829261052	2	FACETS	0.98	0.948	1	0.98	0.948	1	CLONAL	2	TRUE	0	0.84168829261052	2		245	319	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434813	49434813	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	378	441	0	ENST00000301067.7:c.6740C>T	p.Pro2247Leu	p.P2247L	ENST00000301067	NM_003482.3	2247	cCc/cTc	31/54	0.84168829261052	4	FACETS	0.952	0.908	0.996			1	CLONAL	2	TRUE	NA	0.84168829261052	4		441	869	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481662	56481662	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753556193	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	990	503	1	ENST00000267101.3:c.697G>A	p.Gly233Arg	p.G233R	ENST00000267101	NM_001982.3	233	Ggg/Agg	6/28	0.84168829261052	6	FACETS	0.979	0.956	1			1	CLONAL	4	TRUE	NA	0.84168829261052	6		504	1612	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032258	42032258	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	751	609	1	ENST00000219905.7:c.4442C>T	p.Ser1481Phe	p.S1481F	ENST00000219905	NM_001164273.1	1481	tCc/tTc	14/24	0.84168829261052	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.84168829261052	3		610	1202	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857935	9857935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	204	387	0	ENST00000330684.3:c.3466G>A	p.Glu1156Lys	p.E1156K	ENST00000330684	NM_001134407.1	1156	Gaa/Aaa	13/13	0.84168829261052	3	FACETS	1	0.942	1	0.506	0.471	0.542	CLONAL	1	TRUE	1	0.84168829261052	3		387	680	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641767	23641767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786203747	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	126	280	0	ENST00000261584.4:c.1708G>A	p.Glu570Lys	p.E570K	ENST00000261584	NM_024675.3	570	Gag/Aag	5/13	0.84168829261052	3	FACETS	0.8	0.727	0.875	0.4	0.363	0.438	SUBCLONAL	1	TRUE	1	0.84168829261052	3		280	532	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923659	72923659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	578	640	0	ENST00000268489.5:c.3419C>T	p.Thr1140Ile	p.T1140I	ENST00000268489	NM_006885.3	1140	aCc/aTc	4/10	0.759251927079054	4	FACETS	1	0.987	1			1	CLONAL	2	TRUE	NA	0.84168829261052	4		640	1207	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993367	72993368	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	537	655	0	ENST00000268489.5:c.677_678delinsTT	p.Pro226Leu	p.P226L	ENST00000268489	NM_006885.3	226	cCC/cTT	2/10	0.759251927079054	4	FACETS	0.953	0.916	0.99			1	CLONAL	2	TRUE	NA	0.84168829261052	4		655	1233	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685551	29685551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1260740048	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	479	353	1	ENST00000356175.3:c.7961C>T	p.Pro2654Leu	p.P2654L	ENST00000356175	NM_000267.3	2654	cCa/cTa	54/57	0.84168829261052	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.84168829261052	3		354	799	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884198	37884198	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	391	411	0	ENST00000269571.5:c.3669G>A	p.Trp1223Ter	p.W1223*	ENST00000269571		1223	tgG/tgA	27/27	0.84168829261052	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.84168829261052	3		411	632	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098441	11098441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060502062	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	96	339	0	ENST00000358026.2:c.959C>T	p.Pro320Leu	p.P320L	ENST00000358026	NM_001128849.1	320	cCc/cTc	6/36	1	2	FACETS	0.833	0.753	0.915	0.833	0.753	0.915	CLONAL	1	TRUE	1	0.84168829261052	2		339	274	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561235	9561235	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	436	406	0	ENST00000353224.5:c.547T>G	p.Ser183Ala	p.S183A	ENST00000353224	NM_177990.2	183	Tct/Gct	4/10	0.379760805804632	6	FACETS	0.897	0.863	0.931	1	0.994	1	INDETERMINATE	4	TRUE	3	0.84168829261052	6		406	775	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735461	40735461	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	455	498	0	ENST00000373198.4:c.3412C>T	p.Leu1138Phe	p.L1138F	ENST00000373198	NM_133170.3	1138	Ctc/Ttc	25/32	0.379760805804632	6	FACETS	1	0.983	1	1	0.983	1	INDETERMINATE	3	TRUE	3	0.84168829261052	6		498	927	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899066	40899066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199994862	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	474	591	3	ENST00000373198.4:c.2204C>T	p.Pro735Leu	p.P735L	ENST00000373198	NM_133170.3	735	cCg/cTg	14/32	0.379760805804632	6	FACETS	0.979	0.94	1	0.979	0.94	1	INDETERMINATE	3	TRUE	3	0.84168829261052	6		594	1029	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980745	40980745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	307	354	0	ENST00000373198.4:c.1741C>T	p.Arg581Trp	p.R581W	ENST00000373198	NM_133170.3	581	Cgg/Tgg	10/32	0.379760805804632	6	FACETS	0.92	0.873	0.968	0.92	0.873	0.968	INDETERMINATE	3	TRUE	3	0.84168829261052	6		354	709	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100947	41100947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372070542	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	319	335	0	ENST00000373198.4:c.1409G>A	p.Arg470Gln	p.R470Q	ENST00000373198	NM_133170.3	470	cGa/cAa	8/32	0.379760805804632	6	FACETS	1	0.975	1	1	0.975	1	INDETERMINATE	3	TRUE	3	0.84168829261052	6		335	654	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543904	41543904	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	629	524	0	ENST00000263253.7:c.2195C>G	p.Pro732Arg	p.P732R	ENST00000263253	NM_001429.3	732	cCt/cGt	12/31	0.831068687187579	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.84168829261052	4		524	1372	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424260	47424260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	450	263	0	ENST00000377045.4:c.265G>A	p.Glu89Lys	p.E89K	ENST00000377045	NM_001654.4	89	Gag/Aag	4/16	0.441769286970912	2	FACETS	1	0.995	1			1	INDETERMINATE	2	TRUE	NA	0.84168829261052	2		263	507	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410358	63410358	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	503	336	1	ENST00000330258.3:c.2809G>A	p.Glu937Lys	p.E937K	ENST00000330258	NM_152424.3	937	Gaa/Aaa	2/2	0.441769286970912	2	FACETS	1	0.996	1			1	INDETERMINATE	2	TRUE	NA	0.84168829261052	2		337	556	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36819925	36819967	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCCGGGGTAACTGTATGGATGTAGAGACAGGGATCTTACCTC	CCCCGGGGTAACTGTATGGATGTAGAGACAGGGATCTTACCTC	-	novel	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	155	423	0	ENST00000373129.3:c.621_623+40del		p.X207_splice	ENST00000373129	NM_032017.1	207		7/12	0.589061684027811	5	FACETS	0.916	0.838	0.997	0.229	0.209	0.25	CLONAL	1	TRUE	1	0.84168829261052	5		423	910	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625579	1625605	+	inframe_deletion	In_Frame_Del	DEL	GCTGCCGTCTGCCGCTCTCCGCCGGGA	GCTGCCGTCTGCCGCTCTCCGCCGGGA	-	novel	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	191	555	0	ENST00000344749.5:c.469_495del	p.Ser157_Ser165del	p.S157_S165del	ENST00000344749	NM_001136139.2	157	TCCCGGCGGAGAGCGGCAGACGGCAGC/-	7/19	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.84168829261052	2		555	447	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524119	187524121	+	frameshift_variant	Frame_Shift_Del	DEL	GAC	GAC	A	novel	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	172	409	0	ENST00000441802.2:c.11418_11420delinsT	p.Ser3807Ter	p.S3807*	ENST00000441802	NM_005245.3	3806	gtGTCt/gtTt	20/27	0.47681237052978	3	FACETS	0.968	0.895	1	0.484	0.447	0.522	INDETERMINATE	1	TRUE	1	0.84168829261052	3		409	600	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652329	206652330	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782347019	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	373	464	1	ENST00000367120.3:c.1042dup	p.Arg348ProfsTer8	p.R348Pfs*8	ENST00000367120	NM_014002.3	346	gcc/gCcc	10/22	0.379760805804632	6	FACETS	0.881	0.839	0.923	0.881	0.839	0.923	INDETERMINATE	3	TRUE	3	0.84168829261052	6		465	900	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950405	15950412	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCCTGTT	TTCCTGTT	-	novel	NA	P-0012361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	285	372	0	ENST00000268712.3:c.6537-5_6539del		p.X2179_splice	ENST00000268712	NM_006311.3	2179		42/46	0.436747247971343	3	FACETS	0.96	0.916	1	0.96	0.916	1	INDETERMINATE	2	TRUE	1	0.84168829261052	3		372	501	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0012363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	18	524	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.72	0.541	0.932	0.72	0.541	0.932	CLONAL	1	TRUE	1	0.14	2		524	357	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116168	67116168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1467426352	NA	P-0012363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	34	721	1	ENST00000412916.2:c.452G>A	p.Arg151His	p.R151H	ENST00000412916		151	cGc/cAc	5/6	1	2	FACETS	0.812	0.662	0.982	0.812	0.662	0.982	CLONAL	1	TRUE	1	0.14	2		722	598	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0012363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	20	684	1	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	0.654	0.499	0.836	0.654	0.499	0.836	SUBCLONAL	1	TRUE	1	0.14	2		685	437	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481671	56481671	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	40	744	0	ENST00000267101.3:c.706T>C	p.Ser236Pro	p.S236P	ENST00000267101	NM_001982.3	236	Tca/Cca	6/28	1	2	FACETS	0.789	0.654	0.941	0.789	0.654	0.941	CLONAL	1	TRUE	1	0.14	2		744	724	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042136	6042136	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0012363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	45	415	0	ENST00000265849.7:c.485T>G	p.Leu162Ter	p.L162*	ENST00000265849	NM_000535.5	162	tTa/tGa	5/15	0.3	1	FACETS	0.763	0.642	0.895	1	0.96	1	SUBCLONAL	2	TRUE	0	0.14	1		415	392	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46266465	46266465	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	32	1059	0	ENST00000371998.3:c.2450T>G	p.Ile817Arg	p.I817R	ENST00000371998		817	aTa/aGa	13/23	1	2	FACETS	0.736	0.596	0.895	0.736	0.596	0.895	SUBCLONAL	1	TRUE	1	0.14	2		1059	621	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0012410-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	460	366	3	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.564578017559126	3	FACETS	0.945	0.912	0.978	1	0.997	1	CLONAL	3	TRUE	1	0.55	3		369	752	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845182	128845182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012410-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	374	636	9	ENST00000249373.3:c.676G>A	p.Glu226Lys	p.E226K	ENST00000249373	NM_005631.4	226	Gag/Aag	3/12	1	2	FACETS	0.806	0.769	0.843	1	0.996	1	CLONAL	2	TRUE	1	0.55	2		645	844	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954300	48954300	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs1461382798	NA	P-0012410-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	201	237	2	ENST00000267163.4:c.1422-1G>T		p.X474_splice	ENST00000267163	NM_000321.2	474			1	2	FACETS	0.864	0.812	0.916	1	0.994	1	CLONAL	2	TRUE	1	0.55	2		239	423	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936968	48936969	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012410-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	377	490	4	ENST00000267163.4:c.738dup	p.Asn247Ter	p.N247*	ENST00000267163	NM_000321.2	246	att/aTtt	8/27	1	2	FACETS	0.83	0.792	0.868	1	0.996	1	CLONAL	2	TRUE	1	0.55	2		494	826	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	124	140	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.927	0.849	1	0.927	0.849	1	CLONAL	1	TRUE	1	0.773291502142781	2		140	346	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0012434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	241	419	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.952	0.894	1	0.952	0.894	1	CLONAL	1	TRUE	1	0.773291502142781	2		420	655	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795608	42795609	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1555770200	NA	P-0012434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	34	547	0	ENST00000575354.2:c.2694dup	p.Lys899GlnfsTer32	p.K899Qfs*32	ENST00000575354	NM_015125.3	896	-/C	10/20	0.773291502142781	1	FACETS	0.113	0.092	0.137	0.113	0.092	0.137	SUBCLONAL	1	TRUE	0	0.773291502142781	1		547	478	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	95	467	3	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	0.773291502142781	1	FACETS	0.372	0.333	0.413	0.372	0.333	0.413	SUBCLONAL	1	TRUE	0	0.773291502142781	1		470	405	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	258	550	3	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.918	0.863	0.975	0.918	0.863	0.975	CLONAL	1	TRUE	1	0.680241787899558	2		553	826	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	269	417	0	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	0.92	0.865	0.975	0.92	0.865	0.975	CLONAL	1	TRUE	1	0.680241787899558	2		417	860	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	211	436	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	0.680241787899558	2	FACETS	0.778	0.725	0.834	0.389	0.362	0.417	SUBCLONAL	1	TRUE	0	0.680241787899558	2		436	797	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	333	183	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.927	0.89	0.964	1	0.997	1	CLONAL	2	TRUE	1	0.680241787899558	2		183	528	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	466	199	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	0.680241787899558	2	FACETS	0.917	0.886	0.948	0.917	0.886	0.948	CLONAL	2	TRUE	0	0.680241787899558	2		200	747	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	215	381	1	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	0.680241787899558	2	FACETS	0.911	0.85	0.973	0.455	0.425	0.487	CLONAL	1	TRUE	0	0.680241787899558	2		382	694	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103755	47103756	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	379	610	2	ENST00000409792.3:c.6190_6191del	p.Asp2064ProfsTer8	p.D2064Pfs*8	ENST00000409792	NM_014159.6	2064	GAc/c	14/21	1	2	FACETS	0.864	0.82	0.909	0.864	0.82	0.909	CLONAL	1	TRUE	1	0.680241787899558	2		612	1289	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445041	49445041	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	118	115	0	ENST00000301067.7:c.2425del	p.Gln809ArgfsTer121	p.Q809Rfs*121	ENST00000301067	NM_003482.3	809	Cag/ag	10/54	1	2	FACETS	0.834	0.758	0.912	0.834	0.758	0.912	CLONAL	1	TRUE	1	0.680241787899558	2		115	416	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	235	362	2	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	0.825	0.772	0.88	0.825	0.772	0.88	CLONAL	1	TRUE	1	0.680241787899558	2		364	837	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	287	366	3	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	0.945	0.891	1	0.945	0.891	1	CLONAL	1	TRUE	1	0.680241787899558	2		369	893	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	239	363	4	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	1	2	FACETS	0.873	0.817	0.93	0.873	0.817	0.93	CLONAL	1	TRUE	1	0.680241787899558	2		367	805	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845224	128845224	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376509030	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	206	228	3	ENST00000249373.3:c.718G>A	p.Val240Ile	p.V240I	ENST00000249373	NM_005631.4	240	Gtc/Atc	3/12	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.680241787899558	2		231	580	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933593	39933594	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	275	456	0	ENST00000378444.4:c.1005dup	p.Ser336LeufsTer45	p.S336Lfs*45	ENST00000378444	NM_001123385.1	335	-/C	4/15	1	2	FACETS	0.818	0.768	0.868	0.818	0.768	0.868	CLONAL	1	TRUE	1	0.680241787899558	2		456	989	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391799	139391799	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1455334351	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	167	256	0	ENST00000277541.6:c.6392del	p.Gly2131AlafsTer117	p.G2131Afs*117	ENST00000277541	NM_017617.3	2131	gGc/gc	34/34	1	2	FACETS	0.848	0.783	0.915	0.848	0.783	0.915	CLONAL	1	TRUE	1	0.680241787899558	2		256	579	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872138	37872138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375382055	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	319	389	1	ENST00000269571.5:c.1459C>T	p.Arg487Trp	p.R487W	ENST00000269571		487	Cgg/Tgg	12/27	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.680241787899558	2		390	936	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467434	66467434	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369606981	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	199	333	0	ENST00000273854.3:c.835G>A	p.Glu279Lys	p.E279K	ENST00000273854	NM_004439.5	279	Gaa/Aaa	3/18	1	2	FACETS	0.892	0.83	0.955	0.892	0.83	0.955	CLONAL	1	TRUE	1	0.680241787899558	2		333	656	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998627	100998629	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	rs751489196	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	348	494	2	ENST00000325455.5:c.1173_1175del	p.Glu392del	p.E392del	ENST00000325455	NM_001202474.3	391	gaGGAa/gaa	1/8	1	2	FACETS	0.921	0.873	0.97	0.921	0.873	0.97	CLONAL	1	TRUE	1	0.680241787899558	2		496	1111	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241932	72241932	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1391181625	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	947	680	0	ENST00000357731.5:c.458G>C	p.Gly153Ala	p.G153A	ENST00000357731	NM_173808.2	153	gGa/gCa	3/7	0.680241787899558	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.680241787899558	2		680	1350	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37061871	37061871	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63750796	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	288	423	0	ENST00000231790.2:c.955G>T	p.Glu319Ter	p.E319*	ENST00000231790	NM_000249.3	319	Gag/Tag	11/19	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.680241787899558	2		423	847	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37083782	37083782	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	277	505	0	ENST00000231790.2:c.1691T>G	p.Leu564Arg	p.L564R	ENST00000231790	NM_000249.3	564	cTc/cGc	15/19	1	2	FACETS	0.979	0.922	1	0.979	0.922	1	CLONAL	1	TRUE	1	0.680241787899558	2		505	832	SUCCESS
ATR	545	MSKCC	GRCh37	3	142204053	142204053	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	254	442	0	ENST00000350721.4:c.6150G>A	p.Met2050Ile	p.M2050I	ENST00000350721	NM_001184.3	2050	atG/atA	36/47	1	2	FACETS	0.89	0.835	0.946	0.89	0.835	0.946	CLONAL	1	TRUE	1	0.680241787899558	2		442	839	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184179	56184179	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	173	310	3	ENST00000399503.3:c.4384T>A	p.Phe1462Ile	p.F1462I	ENST00000399503	NM_005921.1	1462	Ttt/Att	19/20	1	2	FACETS	0.915	0.847	0.984	0.915	0.847	0.984	CLONAL	1	TRUE	1	0.680241787899558	2		313	556	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26046015	26046015	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	514	614	0	ENST00000540144.1:c.377A>G	p.Gln126Arg	p.Q126R	ENST00000540144	NM_003531.2	126	cAg/cGg	1/1	1	2	FACETS	0.987	0.945	1	0.987	0.945	1	CLONAL	1	TRUE	1	0.680241787899558	2		614	1531	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97869517	97869517	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	280	408	1	ENST00000289081.3:c.1364C>T	p.Ala455Val	p.A455V	ENST00000289081	NM_000136.2	455	gCa/gTa	14/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.680241787899558	2		409	794	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920714	100920714	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	329	631	1	ENST00000325455.5:c.2434C>T	p.Gln812Ter	p.Q812*	ENST00000325455	NM_001202474.3	812	Caa/Taa	6/8	1	2	FACETS	0.916	0.867	0.966	0.916	0.867	0.966	CLONAL	1	TRUE	1	0.680241787899558	2		632	1056	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385279	4385279	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	305	355	0	ENST00000261254.3:c.304G>A	p.Gly102Ser	p.G102S	ENST00000261254	NM_001759.3	102	Ggt/Agt	2/5	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.680241787899558	2		355	827	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433346	49433346	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	125	222	0	ENST00000301067.7:c.8101C>T	p.Arg2701Trp	p.R2701W	ENST00000301067	NM_003482.3	2701	Cgg/Tgg	32/54	1	2	FACETS	0.972	0.889	1	0.972	0.889	1	CLONAL	1	TRUE	1	0.680241787899558	2		222	378	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489583	56489583	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	256	365	1	ENST00000267101.3:c.2048G>T	p.Arg683Leu	p.R683L	ENST00000267101	NM_001982.3	683	cGg/cTg	17/28	1	2	FACETS	0.883	0.829	0.939	0.883	0.829	0.939	CLONAL	1	TRUE	1	0.680241787899558	2		366	852	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562052	21562052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1359079402	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	462	576	2	ENST00000382592.4:c.1867C>T	p.Arg623Trp	p.R623W	ENST00000382592	NM_014572.2	623	Cgg/Tgg	4/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.680241787899558	2		578	1327	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562820	21562820	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1379487930	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	243	297	0	ENST00000382592.4:c.1099G>A	p.Val367Ile	p.V367I	ENST00000382592	NM_014572.2	367	Gtc/Atc	4/8	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.680241787899558	2		297	714	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821604	72821604	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554891628	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	103	94	0	ENST00000268489.5:c.10571G>A	p.Gly3524Asp	p.G3524D	ENST00000268489	NM_006885.3	3524	gGc/gAc	10/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.680241787899558	2		94	261	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984745	72984745	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	386	501	0	ENST00000268489.5:c.2839T>C	p.Cys947Arg	p.C947R	ENST00000268489	NM_006885.3	947	Tgc/Cgc	3/10	1	2	FACETS	0.915	0.87	0.962	0.915	0.87	0.962	CLONAL	1	TRUE	1	0.680241787899558	2		501	1240	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991484	72991484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	605	679	1	ENST00000268489.5:c.2561C>T	p.Pro854Leu	p.P854L	ENST00000268489	NM_006885.3	854	cCc/cTc	2/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.680241787899558	2		680	1624	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991976	72991976	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	405	546	0	ENST00000268489.5:c.2069T>C	p.Met690Thr	p.M690T	ENST00000268489	NM_006885.3	690	aTg/aCg	2/10	1	2	FACETS	0.932	0.887	0.978	0.932	0.887	0.978	CLONAL	1	TRUE	1	0.680241787899558	2		546	1278	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118955	70118955	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	322	408	0	ENST00000245479.2:c.527C>T	p.Pro176Leu	p.P176L	ENST00000245479	NM_000346.3	176	cCg/cTg	2/3	1	2	FACETS	0.961	0.909	1	0.961	0.909	1	CLONAL	1	TRUE	1	0.680241787899558	2		408	985	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2189768	2189768	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479024523	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	402	525	1	ENST00000398665.3:c.238C>T	p.Arg80Cys	p.R80C	ENST00000398665	NM_032482.2	80	Cgt/Tgt	4/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.680241787899558	2		526	1142	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9770523	9770523	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	676	442	0	ENST00000377346.4:c.13del	p.Val5TrpfsTer28	p.V5Wfs*28	ENST00000377346	NM_005026.3	4	Ggg/gg	3/24	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	2	TRUE	NA	0.680241787899558	2		442	927	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909922	100909924	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	novel	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	355	552	0	ENST00000325455.5:c.2725_2727del	p.Met909del	p.M909del	ENST00000325455	NM_001202474.3	909	ATG/-	8/8	1	2	FACETS	0.931	0.883	0.98	0.931	0.883	0.98	CLONAL	1	TRUE	1	0.680241787899558	2		552	1121	SUCCESS
ATR	545	MSKCC	GRCh37	3	142286928	142286929	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	151	384	0	ENST00000350721.4:c.127dup	p.Arg43ProfsTer18	p.R43Pfs*18	ENST00000350721	NM_001184.3	43	cgg/cCgg	2/47	1	2	FACETS	0.812	0.746	0.879	0.812	0.746	0.879	CLONAL	1	TRUE	1	0.680241787899558	2		384	547	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243514	41243516	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	rs397509129	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	345	532	0	ENST00000357654.3:c.4032_4034del	p.Asp1344del	p.D1344del	ENST00000357654	NM_007294.3	1344	gaTGAa/gaa	10/23	1	2	FACETS	0.907	0.859	0.956	0.907	0.859	0.956	CLONAL	1	TRUE	1	0.680241787899558	2		532	1118	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074363	8074363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	711	524	0	ENST00000377482.5:c.296del	p.Pro99GlnfsTer22	p.P99Qfs*22	ENST00000377482	NM_018948.3	99	cCa/ca	4/4	NA	2	FACETS	0.878	0.852	0.903			1	INDETERMINATE	2	TRUE	NA	0.680241787899558	2		524	1191	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850990	63850990	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	212	337	0	ENST00000279873.7:c.1771del	p.Gln591LysfsTer38	p.Q591Kfs*38	ENST00000279873	NM_032199.2	590	Ccc/cc	10/10	1	2	FACETS	0.921	0.859	0.984	0.921	0.859	0.984	CLONAL	1	TRUE	1	0.680241787899558	2		337	677	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307279	118307281	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs1407741917	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	16	22	0	ENST00000534358.1:c.63_65del	p.Gly23del	p.G23del	ENST00000534358	NM_005933.3	18	GGC/-	1/36	1	2	FACETS	0.627	0.474	0.801	0.627	0.474	0.801	SUBCLONAL	1	TRUE	1	0.680241787899558	2		22	75	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40468879	40468879	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	363	434	2	ENST00000264657.5:c.2185del	p.Arg729AlafsTer3	p.R729Afs*3	ENST00000264657	NM_139276.2	729	Cgc/gc	23/24	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.680241787899558	2		436	1058	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0012532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	97	509	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	0.259753870128405	2		509	731	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023007	27023008	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGC	rs587779737	NA	P-0012532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	10	16	0	ENST00000324856.7:c.126_128dup	p.Ala45dup	p.A45dup	ENST00000324856	NM_006015.4	45	gag/gaGGCg	1/20	0.259753870128405	1	FACETS	1	0.839	1	1	0.839	1	CLONAL	1	TRUE	0	0.259753870128405	1		16	48	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309827	65309827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	130	642	0	ENST00000342505.4:c.2323G>A	p.Asp775Asn	p.D775N	ENST00000342505	NM_002227.2	775	Gac/Aac	17/25	0.259753870128405	1	FACETS	0.948	0.859	1	0.948	0.859	1	CLONAL	1	TRUE	0	0.259753870128405	1		642	919	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606132	47606132	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	40	511	0	ENST00000263735.4:c.596C>A	p.Ser199Tyr	p.S199Y	ENST00000263735	NM_002354.2	199	tCt/tAt	6/9	1	2	FACETS	0.417	0.345	0.497	0.417	0.345	0.497	SUBCLONAL	1	TRUE	1	0.259753870128405	2		511	739	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401578	401578	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1050972	NA	P-0012532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	95	498	0	ENST00000380956.4:c.900G>C	p.Gln300His	p.Q300H	ENST00000380956	NM_001195286.1	300	caG/caC	7/9	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.259753870128405	2		498	722	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63661479	63661479	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs766062378	NA	P-0012532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	62	539	0	ENST00000279873.7:c.11A>G	p.Asn4Ser	p.N4S	ENST00000279873	NM_032199.2	4	aAc/aGc	1/10	0.219251912650772	5	FACETS	0.576	0.495	0.664			1	SUBCLONAL	1	TRUE	NA	0.259753870128405	5		539	1152	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145094	58145094	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	82	533	0	ENST00000257904.6:c.250G>C	p.Asp84His	p.D84H	ENST00000257904	NM_000075.3	84	Gac/Cac	3/8	1	2	FACETS	0.776	0.683	0.875	0.776	0.683	0.875	SUBCLONAL	1	TRUE	1	0.259753870128405	2		533	814	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109915	115109915	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	40	235	0	ENST00000257566.3:c.1963C>G	p.Leu655Val	p.L655V	ENST00000257566	NM_016569.3	655	Ctg/Gtg	8/8	1	2	FACETS	0.88	0.733	1	0.88	0.733	1	CLONAL	1	TRUE	1	0.259753870128405	2		235	350	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829549	72829549	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs575480618	NA	P-0012532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1246	126	960	0	ENST00000268489.5:c.7032C>G	p.Ile2344Met	p.I2344M	ENST00000268489	NM_006885.3	2344	atC/atG	9/10	1	2	FACETS	0.707	0.638	0.78	0.707	0.638	0.78	SUBCLONAL	1	TRUE	1	0.259753870128405	2		960	1372	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348135	89348135	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1372	124	1057	1	ENST00000301030.4:c.4815G>T	p.Met1605Ile	p.M1605I	ENST00000301030	NM_001256183.1	1605	atG/atT	9/13	1	2	FACETS	0.638	0.575	0.705	0.638	0.575	0.705	SUBCLONAL	1	TRUE	1	0.259753870128405	2		1058	1496	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348849	89348849	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1567	187	1084	0	ENST00000301030.4:c.4101G>C	p.Lys1367Asn	p.K1367N	ENST00000301030	NM_001256183.1	1367	aaG/aaC	9/13	1	2	FACETS	0.821	0.755	0.89	0.821	0.755	0.89	CLONAL	1	TRUE	1	0.259753870128405	2		1084	1754	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143015	7143015	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145643501	NA	P-0012532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	58	442	0	ENST00000302850.5:c.2354C>T	p.Ser785Leu	p.S785L	ENST00000302850	NM_000208.2	785	tCg/tTg	12/22	1	2	FACETS	0.58	0.497	0.671	0.58	0.497	0.671	SUBCLONAL	1	TRUE	1	0.259753870128405	2		442	770	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577512	7577512	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	134	568	0	ENST00000269305.4:c.769del	p.Leu257TrpfsTer88	p.L257Wfs*88	ENST00000269305	NM_001126112.2	257	Ctg/tg	7/11	0.259753870128405	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.259753870128405	1		568	820	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594221	55594221	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913512	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	2692	354	0	ENST00000288135.5:c.1924A>G	p.Lys642Glu	p.K642E	ENST00000288135	NM_000222.2	642	Aaa/Gaa	13/21	0.487073503697735	23	FACETS	0.987	0.978	0.995			1	CLONAL	22	TRUE	NA	0.487073503697735	23		354	3113	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	131	140	0				ENST00000310581	NM_198253.2	-/1132			0.479446289854363	4	FACETS	0.968	0.887	1	0.968	0.887	1	CLONAL	2	TRUE	2	0.487073503697735	4		140	413	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099953	27099955	+	frameshift_variant	Frame_Shift_Del	DEL	CAC	CAC	TA	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	140	512	0	ENST00000324856.7:c.3832_3834delinsTA	p.His1278TyrfsTer11	p.H1278Yfs*11	ENST00000324856	NM_006015.4	1278	CAC/TA	15/20	0.487699111575531	3	FACETS	1	0.967	1	0.559	0.511	0.61	CLONAL	1	TRUE	1	0.487073503697735	3		512	639	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446310	29446310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138589984	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	96	851	0	ENST00000389048.3:c.3257C>T	p.Ser1086Leu	p.S1086L	ENST00000389048	NM_004304.4	1086	tCg/tTg	20/29	0.234050390180009	4	FACETS	0.47	0.418	0.527	0.235	0.209	0.264	INDETERMINATE	1	TRUE	2	0.487073503697735	4		851	1246	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274698	198274698	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	221	371	0	ENST00000335508.6:c.700G>C	p.Glu234Gln	p.E234Q	ENST00000335508	NM_012433.2	234	Gag/Cag	7/25	0.234050390180009	4	FACETS	0.954	0.892	1	0.954	0.892	1	INDETERMINATE	2	TRUE	2	0.487073503697735	4		371	707	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736116	204736116	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745734610	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	303	602	0	ENST00000302823.3:c.473C>T	p.Pro158Leu	p.P158L	ENST00000302823	NM_005214.4	158	cCa/cTa	3/4	0.234050390180009	4	FACETS	0.976	0.921	1	0.976	0.921	1	INDETERMINATE	2	TRUE	2	0.487073503697735	4		602	948	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578317	212578317	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	235	501	1	ENST00000342788.4:c.940G>A	p.Glu314Lys	p.E314K	ENST00000342788	NM_005235.2	314	Gaa/Aaa	8/28	0.234050390180009	4	FACETS	0.929	0.87	0.99	0.929	0.87	0.99	INDETERMINATE	2	TRUE	2	0.487073503697735	4		502	772	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989619	212989619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	183	336	0	ENST00000342788.4:c.92G>A	p.Gly31Glu	p.G31E	ENST00000342788	NM_005235.2	31	gGa/gAa	2/28	0.234050390180009	4	FACETS	0.931	0.864	1	0.931	0.864	1	INDETERMINATE	2	TRUE	2	0.487073503697735	4		336	600	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026194	71026194	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	272	364	0	ENST00000318789.4:c.1429-1G>C		p.X477_splice	ENST00000318789	NM_032682.5	477			0.487699111575531	3	FACETS	0.967	0.913	1	0.967	0.913	1	CLONAL	2	TRUE	1	0.487073503697735	3		364	718	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457258	89457258	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	232	313	0	ENST00000336596.2:c.1739G>A	p.Arg580Lys	p.R580K	ENST00000336596	NM_005233.5	580	aGa/aAa	9/17	0.487699111575531	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.487073503697735	3		313	560	SUCCESS
ATR	545	MSKCC	GRCh37	3	142238586	142238586	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	181	458	0	ENST00000350721.4:c.4307A>C	p.Asn1436Thr	p.N1436T	ENST00000350721	NM_001184.3	1436	aAc/aCc	24/47	0.487699111575531	3	FACETS	1	0.972	1	0.553	0.511	0.598	CLONAL	1	TRUE	1	0.487073503697735	3		458	835	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584548	189584548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	370	515	0	ENST00000264731.3:c.844G>A	p.Gly282Arg	p.G282R	ENST00000264731	NM_003722.4	282	Gga/Aga	6/14	0.487699111575531	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.487073503697735	3		515	870	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612176	189612176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	305	555	2	ENST00000264731.3:c.1928G>A	p.Arg643Gln	p.R643Q	ENST00000264731	NM_003722.4	643	cGa/cAa	14/14	0.487699111575531	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.487073503697735	3		557	752	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964351	55964351	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4438	267	646	0	ENST00000263923.4:c.2462C>T	p.Pro821Leu	p.P821L	ENST00000263923	NM_002253.2	821	cCt/cTt	17/30	0.487073503697735	23	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.487073503697735	23		646	4705	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156186	106156186	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1338558798	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	230	334	0	ENST00000380013.4:c.1087C>T	p.Pro363Ser	p.P363S	ENST00000380013	NM_001127208.2	363	Cct/Tct	3/11	0.453467074335994	3	FACETS	0.995	0.935	1	0.995	0.935	1	CLONAL	2	TRUE	1	0.487073503697735	3		334	590	SUCCESS
APC	324	MSKCC	GRCh37	5	112179470	112179470	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	462	613	0	ENST00000257430.4:c.8179C>T	p.Gln2727Ter	p.Q2727*	ENST00000257430	NM_000038.5	2727	Cag/Tag	16/16	0.479446289854363	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	2	0.487073503697735	4		613	1194	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672677	30672677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1332	513	825	0	ENST00000376406.3:c.4283C>T	p.Pro1428Leu	p.P1428L	ENST00000376406	NM_014641.2	1428	cCc/cTc	10/15	0.487073503697735	6	FACETS	1	0.991	1	0.563	0.538	0.589	CLONAL	2	TRUE	2	0.487073503697735	6		825	1845	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168991	32168991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1267	167	723	2	ENST00000375023.3:c.4042G>A	p.Glu1348Lys	p.E1348K	ENST00000375023	NM_004557.3	1348	Gaa/Aaa	22/30	0.487073503697735	6	FACETS	0.944	0.865	1	0.236	0.216	0.257	CLONAL	1	TRUE	2	0.487073503697735	6		725	1434	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066618	94066618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	435	892	1	ENST00000369303.4:c.1141C>T	p.Pro381Ser	p.P381S	ENST00000369303	NM_004440.3	381	Ccc/Tcc	5/17	0.244859263732267	5	FACETS	1	0.989	1	0.745	0.709	0.78	INDETERMINATE	2	TRUE	2	0.487073503697735	5		893	1384	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609893	117609893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771217753	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	383	696	1	ENST00000368508.3:c.6806G>A	p.Arg2269Gln	p.R2269Q	ENST00000368508	NM_002944.2	2269	cGa/cAa	43/43	0.244859263732267	5	FACETS	1	0.99	1	0.771	0.733	0.81	INDETERMINATE	2	TRUE	2	0.487073503697735	5		697	1177	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405968	157405968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	318	580	1	ENST00000346085.5:c.2210C>T	p.Pro737Leu	p.P737L	ENST00000346085	NM_020732.3	737	cCc/cTc	6/20	0.244859263732267	5	FACETS	0.838	0.793	0.883	0.838	0.793	0.883	INDETERMINATE	3	TRUE	2	0.487073503697735	5		581	899	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946292	2946292	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747738095	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	113	528	0	ENST00000396946.4:c.3445G>A	p.Val1149Met	p.V1149M	ENST00000396946	NM_032415.4	1149	Gtg/Atg	25/25	0.479446289854363	4	FACETS	0.953	0.858	1	0.477	0.429	0.527	CLONAL	1	TRUE	2	0.487073503697735	4		528	724	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214338	55214339	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	263	473	1	ENST00000275493.2:c.464_465delinsTT	p.Ala155Val	p.A155V	ENST00000275493	NM_005228.3	155	gCC/gTT	4/28	0.479446289854363	4	FACETS	0.942	0.886	1	0.942	0.886	1	CLONAL	2	TRUE	2	0.487073503697735	4		474	852	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340007	116340007	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	219	342	0	ENST00000397752.3:c.869C>T	p.Ser290Phe	p.S290F	ENST00000397752	NM_000245.2	290	tCc/tTc	2/21	0.479446289854363	4	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	2	0.487073503697735	4		342	668	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93607866	93607866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	129	518	0	ENST00000375746.1:c.568G>A	p.Gly190Arg	p.G190R	ENST00000375746	NM_001174167.1	190	Gga/Aga	3/14	0.487073503697735	2	FACETS	1	0.939	1	0.519	0.473	0.567	CLONAL	1	TRUE	0	0.487073503697735	2		518	510	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575542	64575543	+	missense_variant	Missense_Mutation	DNP	AG	AG	GA	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	237	483	0	ENST00000312049.6:c.474_475delinsTC	p.Phe159Leu	p.F159L	ENST00000312049	NM_130799.2	158	gcCTtt/gcTCtt	3/10	0.479446289854363	4	FACETS	0.943	0.884	1	0.943	0.884	1	CLONAL	2	TRUE	2	0.487073503697735	4		483	767	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514329	69514329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	209	337	0	ENST00000294312.3:c.352G>A	p.Glu118Lys	p.E118K	ENST00000294312	NM_005117.2	118	Gaa/Aaa	3/3	0.479446289854363	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.487073503697735	4		337	590	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625189	69625191	+	missense_variant	Missense_Mutation	TNP	GGG	GGG	AGA	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	239	565	1	ENST00000334134.2:c.602_604delinsTCT	p.Pro201_Pro202delinsLeuSer	p.P201_P202delinsLS	ENST00000334134	NM_005247.2	201	cCCCct/cTCTct	3/3	0.479446289854363	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	2	0.487073503697735	4		566	681	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366503	118366503	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	326	521	0	ENST00000534358.1:c.5452G>T	p.Glu1818Ter	p.E1818*	ENST00000534358	NM_005933.3	1818	Gag/Tag	19/36	0.479446289854363	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.487073503697735	4		521	941	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466972	18466972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	197	476	0	ENST00000266497.5:c.1111G>A	p.Glu371Lys	p.E371K	ENST00000266497		371	Gaa/Aaa	5/31	0.487699111575531	4	FACETS	1	0.987	1	0.656	0.608	0.706	CLONAL	1	TRUE	2	0.487073503697735	4		476	917	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650617	18650617	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	235	374	0	ENST00000266497.5:c.2828G>A	p.Trp943Ter	p.W943*	ENST00000266497		943	tGg/tAg	20/31	0.487699111575531	4	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	2	0.487073503697735	4		374	713	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285630	46285630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	330	394	0	ENST00000334344.6:c.4990C>T	p.Pro1664Ser	p.P1664S	ENST00000334344	NM_152641.2	1664	Cca/Tca	17/21	0.487699111575531	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	2	0.487073503697735	4		394	849	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479186	50479186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	280	437	0	ENST00000394963.4:c.34C>T	p.Pro12Ser	p.P12S	ENST00000394963	NM_003076.4	12	Cca/Tca	1/13	0.487699111575531	4	FACETS	0.843	0.797	0.889	1	0.992	1	CLONAL	3	TRUE	2	0.487073503697735	4		437	676	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145022	58145022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs955815089	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	298	473	0	ENST00000257904.6:c.322C>T	p.Pro108Ser	p.P108S	ENST00000257904	NM_000075.3	108	Ccc/Tcc	3/8	0.487699111575531	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.487073503697735	4		473	874	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41999952	41999952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	245	734	0	ENST00000219905.7:c.2215C>T	p.Pro739Ser	p.P739S	ENST00000219905	NM_001164273.1	739	Cca/Tca	6/24	0.487699111575531	3	FACETS	1	0.948	1	0.509	0.475	0.544	CLONAL	1	TRUE	1	0.487073503697735	3		734	1229	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042554	42042554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	255	876	0	ENST00000219905.7:c.6749C>T	p.Pro2250Leu	p.P2250L	ENST00000219905	NM_001164273.1	2250	cCt/cTt	17/24	0.487699111575531	3	FACETS	1	0.983	1	0.571	0.534	0.609	CLONAL	1	TRUE	1	0.487073503697735	3		876	1140	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347803	347803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	145	655	0	ENST00000262320.3:c.1703C>T	p.Pro568Leu	p.P568L	ENST00000262320	NM_003502.3	568	cCa/cTa	6/11	0.305002191084233	5	FACETS	1	0.982	1	0.434	0.396	0.473	CLONAL	1	TRUE	2	0.487073503697735	5		655	792	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778333	3778333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs992349519	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	57	269	0	ENST00000262367.5:c.6715G>A	p.Gly2239Ser	p.G2239S	ENST00000262367	NM_004380.2	2239	Ggc/Agc	31/31	0.305002191084233	5	FACETS	1	0.962	1	0.452	0.39	0.518	CLONAL	1	TRUE	2	0.487073503697735	5		269	299	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858135	9858135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064796981	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	338	711	0	ENST00000330684.3:c.3266C>T	p.Ser1089Leu	p.S1089L	ENST00000330684	NM_001134407.1	1089	tCa/tTa	13/13	0.305002191084233	5	FACETS	1	0.979	1	0.71	0.672	0.749	CLONAL	2	TRUE	2	0.487073503697735	5		711	1127	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992414	72992414	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs62620235	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	613	997	2	ENST00000268489.5:c.1631C>T	p.Ser544Leu	p.S544L	ENST00000268489	NM_006885.3	544	tCg/tTg	2/10	0.305002191084233	5	FACETS	0.928	0.894	0.963	0.928	0.894	0.963	CLONAL	3	TRUE	2	0.487073503697735	5		999	1564	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541577	29541577	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	186	303	0	ENST00000356175.3:c.1501C>T	p.His501Tyr	p.H501Y	ENST00000356175	NM_000267.3	501	Cat/Tat	13/57	0.418183196091266	4	FACETS	0.988	0.918	1	0.988	0.918	1	CLONAL	2	TRUE	2	0.487073503697735	4		303	575	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553513	29553513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1555613784	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	313	439	0	ENST00000356175.3:c.2062G>T	p.Glu688Ter	p.E688*	ENST00000356175	NM_000267.3	688	Gaa/Taa	18/57	0.418183196091266	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.487073503697735	4		439	857	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653266	29653266	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	108	229	0	ENST00000356175.3:c.5201T>A	p.Ile1734Asn	p.I1734N	ENST00000356175	NM_000267.3	1734	aTt/aAt	36/57	0.418183196091266	4	FACETS	0.822	0.744	0.904	0.822	0.744	0.904	CLONAL	2	TRUE	2	0.487073503697735	4		229	401	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58725384	58725384	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1447	242	728	0	ENST00000305921.3:c.958A>G	p.Ile320Val	p.I320V	ENST00000305921	NM_003620.3	320	Att/Gtt	4/6	0.487073503697735	5	FACETS	1	0.946	1	0.339	0.316	0.364	CLONAL	1	TRUE	2	0.487073503697735	5		728	1689	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273549	5273549	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	174	457	2	ENST00000357368.4:c.283C>T	p.Pro95Ser	p.P95S	ENST00000357368	NM_002850.3	95	Ccg/Tcg	4/38	0.479446289854363	4	FACETS	1	0.967	1	0.548	0.504	0.593	CLONAL	1	TRUE	2	0.487073503697735	4		459	970	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7119485	7119485	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	400	595	0	ENST00000302850.5:c.3769C>T	p.Gln1257Ter	p.Q1257*	ENST00000302850	NM_000208.2	1257	Caa/Taa	21/22	0.479446289854363	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.487073503697735	4		595	1157	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730901	40730901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866581671	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	175	340	0	ENST00000373198.4:c.3634G>A	p.Asp1212Asn	p.D1212N	ENST00000373198	NM_133170.3	1212	Gac/Aac	27/32	0.17330962385254	5	FACETS	1	0.985	1			1	INDETERMINATE	2	TRUE	NA	0.487073503697735	5		340	506	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770569	40770569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	234	440	0	ENST00000373198.4:c.2813G>A	p.Gly938Glu	p.G938E	ENST00000373198	NM_133170.3	938	gGg/gAg	19/32	0.17330962385254	5	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.487073503697735	5		440	688	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944527	40944527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371433526	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	210	467	0	ENST00000373198.4:c.1975G>A	p.Asp659Asn	p.D659N	ENST00000373198	NM_133170.3	659	Gat/Aat	12/32	0.17330962385254	5	FACETS	1	0.96	1			1	INDETERMINATE	2	TRUE	NA	0.487073503697735	5		467	716	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933811	39933811	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	194	689	0	ENST00000378444.4:c.788C>T	p.Ser263Leu	p.S263L	ENST00000378444	NM_001123385.1	263	tCa/tTa	4/15	0.234050390180009	4	FACETS	1	0.988	1	0.67	0.62	0.721	INDETERMINATE	1	TRUE	2	0.487073503697735	4		689	884	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732880	44732880	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	176	413	0	ENST00000377967.4:c.83G>T	p.Gly28Val	p.G28V	ENST00000377967	NM_021140.2	28	gGa/gTa	1/29	0.234050390180009	4	FACETS	0.848	0.784	0.913	0.848	0.784	0.913	INDETERMINATE	2	TRUE	2	0.487073503697735	4		413	634	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929059	44929059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	517	754	0	ENST00000377967.4:c.2159C>T	p.Pro720Leu	p.P720L	ENST00000377967	NM_021140.2	720	cCt/cTt	17/29	0.234050390180009	4	FACETS	0.868	0.834	0.903	1	0.996	1	INDETERMINATE	3	TRUE	2	0.487073503697735	4		754	1212	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411719	63411719	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	158	760	0	ENST00000330258.3:c.1448C>T	p.Ser483Leu	p.S483L	ENST00000330258	NM_152424.3	483	tCa/tTa	2/2	0.234050390180009	4	FACETS	0.976	0.893	1	0.488	0.446	0.531	INDETERMINATE	1	TRUE	2	0.487073503697735	4		760	989	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763854	76763855	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	237	753	0	ENST00000373344.5:c.7453_7454delinsAT	p.Gly2485Ile	p.G2485I	ENST00000373344	NM_000489.3	2485	GGa/ATa	35/35	0.234050390180009	4	FACETS	1	0.991	1	0.686	0.64	0.733	INDETERMINATE	1	TRUE	2	0.487073503697735	4		753	1055	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937516	76937516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	97	515	0	ENST00000373344.5:c.3232G>A	p.Glu1078Lys	p.E1078K	ENST00000373344	NM_000489.3	1078	Gag/Aag	9/35	0.234050390180009	4	FACETS	0.671	0.597	0.749	0.335	0.298	0.375	INDETERMINATE	1	TRUE	2	0.487073503697735	4		515	883	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937966	76937966	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	191	528	0	ENST00000373344.5:c.2782G>T	p.Glu928Ter	p.E928*	ENST00000373344	NM_000489.3	928	Gag/Tag	9/35	0.234050390180009	4	FACETS	1	0.99	1	0.741	0.686	0.797	INDETERMINATE	1	TRUE	2	0.487073503697735	4		528	787	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613604	100613604	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	186	526	0	ENST00000308731.7:c.974+1G>A		p.X325_splice	ENST00000308731	NM_000061.2	325			0.234050390180009	4	FACETS	1	0.987	1	0.658	0.608	0.71	INDETERMINATE	1	TRUE	2	0.487073503697735	4		526	863	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220477	123220477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1372684971	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	283	709	1	ENST00000218089.9:c.3134G>A	p.Arg1045Gln	p.R1045Q	ENST00000218089	NM_001042749.1	1045	cGa/cAa	30/35	0.234050390180009	4	FACETS	1	0.993	1	0.738	0.693	0.784	INDETERMINATE	1	TRUE	2	0.487073503697735	4		710	1171	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391170	139391170	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	CCC	novel	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	140	338	0	ENST00000277541.6:c.7021delinsGGG	p.Ser2341GlyfsTer8	p.S2341Gfs*8	ENST00000277541	NM_017617.3	2341	Tcc/GGGcc	34/34	0.487073503697735	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.487073503697735	2		338	255	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661663	227661664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761880048	NA	P-0012550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	135	381	12	ENST00000305123.5:c.1791dup	p.His598AlafsTer13	p.H598Afs*13	ENST00000305123	NM_005544.2	597	-/G	1/2	0.234050390180009	4	FACETS	0.759	0.693	0.827	0.759	0.693	0.827	INDETERMINATE	2	TRUE	2	0.487073503697735	4		393	543	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	73	366	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.725	0.634	0.823	0.725	0.634	0.823	SUBCLONAL	1	TRUE	1	0.327953630010846	2		366	614	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578517	7578517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750600586	NA	P-0012566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	106	625	0	ENST00000269305.4:c.413C>T	p.Ala138Val	p.A138V	ENST00000269305	NM_001126112.2	138	gCc/gTc	5/11	1	2	FACETS	0.902	0.809	1	0.902	0.809	1	CLONAL	1	TRUE	1	0.327953630010846	2		625	717	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372206	55372206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	47	283	1	ENST00000297316.4:c.896C>T	p.Ala299Val	p.A299V	ENST00000297316	NM_022454.3	299	gCg/gTg	2/2	0.327953630010846	3	FACETS	0.967	0.819	1	0.484	0.409	0.565	CLONAL	1	TRUE	1	0.327953630010846	3		284	345	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119781	70119781	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1274036689	NA	P-0012566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	79	778	0	ENST00000245479.2:c.788del	p.Gly263AlafsTer16	p.G263Afs*16	ENST00000245479	NM_000346.3	261	gaG/ga	3/3	1	2	FACETS	0.745	0.655	0.841	0.745	0.655	0.841	SUBCLONAL	1	TRUE	1	0.327953630010846	2		778	647	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265445	152265445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149490424	NA	P-0012566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	85	535	0	ENST00000206249.3:c.898C>T	p.Arg300Cys	p.R300C	ENST00000206249	NM_000125.3	300	Cgc/Tgc	4/8	1	2	FACETS	0.833	0.737	0.936	0.833	0.737	0.936	CLONAL	1	TRUE	1	0.327953630010846	2		535	622	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161807890	161807890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	46	672	0	ENST00000366898.1:c.1103G>A	p.Cys368Tyr	p.C368Y	ENST00000366898	NM_004562.2	368	tGt/tAt	10/12	1	2	FACETS	0.377	0.316	0.444	0.377	0.316	0.444	SUBCLONAL	1	TRUE	1	0.327953630010846	2		672	745	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827826	72827826	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	57	1099	0	ENST00000268489.5:c.8755A>C	p.Ser2919Arg	p.S2919R	ENST00000268489	NM_006885.3	2919	Agc/Cgc	9/10	1	2	FACETS	0.327	0.279	0.379	0.327	0.279	0.379	SUBCLONAL	1	TRUE	1	0.327953630010846	2		1099	1064	SUCCESS
APC	324	MSKCC	GRCh37	5	112173759	112173760	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	61	502	0	ENST00000257430.4:c.2469dup	p.Pro824ThrfsTer20	p.P824Tfs*20	ENST00000257430	NM_000038.5	823	tca/tcAa	16/16	1	2	FACETS	0.686	0.592	0.788	0.686	0.592	0.788	SUBCLONAL	1	TRUE	1	0.327953630010846	2		502	542	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0012568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	362	504	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.687841361500901	2		504	981	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247168	153247168	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1560758208	NA	P-0012568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	297	495	0	ENST00000281708.4:c.1634A>G	p.Tyr545Cys	p.Y545C	ENST00000281708	NM_033632.3	545	tAt/tGt	10/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.687841361500901	2		495	799	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692929	89692929	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1554898159	NA	P-0012568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	182	377	0	ENST00000371953.3:c.413A>G	p.Tyr138Cys	p.Y138C	ENST00000371953	NM_000314.4	138	tAt/tGt	5/9	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.687841361500901	2		377	515	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720673	89720676	+	frameshift_variant	Frame_Shift_Del	DEL	TAAA	TAAA	-	novel	NA	P-0012568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	21	62	0	ENST00000371953.3:c.826_829del	p.Asn276HisfsTer14	p.N276Hfs*14	ENST00000371953	NM_000314.4	275	gTAAAt/gt	8/9	1	2	FACETS	0.664	0.522	0.821	0.664	0.522	0.821	SUBCLONAL	1	TRUE	1	0.687841361500901	2		62	92	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923702	72923703	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0012568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	481	794	0	ENST00000268489.5:c.3375dup	p.Lys1126GlufsTer29	p.K1126Efs*29	ENST00000268489	NM_006885.3	1125	-/G	4/10	1	2	FACETS	0.965	0.922	1	0.965	0.922	1	CLONAL	1	TRUE	1	0.687841361500901	2		794	1450	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087401	27087401	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	446	616	1	ENST00000324856.7:c.1976del	p.Pro659LeufsTer3	p.P659Lfs*3	ENST00000324856	NM_006015.4	659	Cct/ct	5/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.687841361500901	2		617	1235	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589601	67589604	+	protein_altering_variant	In_Frame_Del	DEL	AGTT	AGTT	G	novel	NA	P-0012568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	142	269	0	ENST00000274335.5:c.1364_1367delinsG	p.Gln455_Phe456delinsArg	p.Q455_F456delinsR	ENST00000274335		455	cAGTTt/cGt	10/15	1	2	FACETS	0.943	0.867	1	0.943	0.867	1	CLONAL	1	TRUE	1	0.687841361500901	2		269	438	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	16	356	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	0.068	0.049	0.09	0.068	0.049	0.09	SUBCLONAL	1	TRUE	1	0.785059655004772	2		356	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0012646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	305	293	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.785059655004772	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.785059655004772	1		295	424	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486049	29486050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	167	355	0	ENST00000356175.3:c.233dup	p.Asn78LysfsTer29	p.N78Kfs*29	ENST00000356175	NM_000267.3	76	gaa/gAaa	3/57	1	2	FACETS	0.937	0.869	1	0.937	0.869	1	CLONAL	1	TRUE	1	0.785059655004772	2		355	454	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755602	57755602	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	146	397	0	ENST00000274289.3:c.185A>T	p.His62Leu	p.H62L	ENST00000274289	NM_006622.3	62	cAt/cTt	1/14	1	2	FACETS	0.541	0.494	0.589	0.541	0.494	0.589	SUBCLONAL	1	TRUE	1	0.785059655004772	2		397	688	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845540	151845540	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	128	481	0	ENST00000262189.6:c.13472C>T	p.Ala4491Val	p.A4491V	ENST00000262189	NM_170606.2	4491	gCa/gTa	52/59	0.121703819438298	1	FACETS	0.254	0.23	0.28	0.254	0.23	0.28	INDETERMINATE	1	TRUE	0	0.785059655004772	1		481	779	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90949258	90949258	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs969171734	NA	P-0012646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	200	367	0	ENST00000265433.3:c.2230T>C	p.Phe744Leu	p.F744L	ENST00000265433	NM_002485.4	744	Ttt/Ctt	15/16	1	2	FACETS	0.986	0.921	1	0.986	0.921	1	CLONAL	1	TRUE	1	0.785059655004772	2		367	517	SUCCESS
ATM	472	MSKCC	GRCh37	11	108154963	108154963	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs886039637	NA	P-0012646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	97	217	0	ENST00000278616.4:c.3756T>A	p.Tyr1252Ter	p.Y1252*	ENST00000278616	NM_000051.3	1252	taT/taA	26/63	0.121703819438298	1	FACETS	0.426	0.384	0.471	0.426	0.384	0.471	INDETERMINATE	1	TRUE	0	0.785059655004772	1		217	352	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416729	416729	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	259	467	2	ENST00000399788.2:c.3821C>T	p.Ala1274Val	p.A1274V	ENST00000399788	NM_001042603.1	1274	gCc/gTc	23/28	0.121703819438298	1	FACETS	0.592	0.558	0.627	0.592	0.558	0.627	INDETERMINATE	1	TRUE	0	0.785059655004772	1		469	677	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888156	112888156	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397507505	NA	P-0012646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	179	569	1	ENST00000351677.2:c.172A>G	p.Asn58Asp	p.N58D	ENST00000351677	NM_002834.3	58	Aac/Gac	3/16	1	2	FACETS	0.53	0.488	0.572	0.53	0.488	0.572	SUBCLONAL	1	TRUE	1	0.785059655004772	2		570	861	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541670	120541670	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	434	884	3	ENST00000229340.5:c.187G>A	p.Asp63Asn	p.D63N	ENST00000229340	NM_006861.6	63	Gac/Aac	3/6	1	2	FACETS	0.956	0.913	0.999	0.956	0.913	0.999	CLONAL	1	TRUE	1	0.785059655004772	2		887	1157	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562745	21562745	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778627422	NA	P-0012646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	205	289	0	ENST00000382592.4:c.1174G>A	p.Ala392Thr	p.A392T	ENST00000382592	NM_014572.2	392	Gcg/Acg	4/8	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.785059655004772	2		289	476	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486028	29486028	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0012646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	147	276	0	ENST00000356175.3:c.205A>T	p.Arg69Ter	p.R69*	ENST00000356175	NM_000267.3	69	Aga/Tga	3/57	1	2	FACETS	0.922	0.851	0.995	0.922	0.851	0.995	CLONAL	1	TRUE	1	0.785059655004772	2		276	406	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556484	29556484	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0012646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	103	183	0	ENST00000356175.3:c.2850+1G>C		p.X950_splice	ENST00000356175	NM_000267.3	950			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.785059655004772	2		183	235	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291062	15291062	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371525707	NA	P-0012646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	290	491	0	ENST00000263388.2:c.3148C>T	p.Arg1050Trp	p.R1050W	ENST00000263388	NM_000435.2	1050	Cgg/Tgg	20/33	0.764925844006049	2	FACETS	1	0.99	1	0.587	0.557	0.618	CLONAL	1	TRUE	0	0.785059655004772	2		491	629	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922694	44922694	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397514628	NA	P-0012646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	346	277	1	ENST00000377967.4:c.1555C>T	p.Arg519Ter	p.R519*	ENST00000377967	NM_021140.2	519	Cga/Tga	16/29	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.785059655004772	1		278	439	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645974	215645975	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs587780033	NA	P-0012646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	336	562	0	ENST00000260947.4:c.623dup	p.Lys209GlufsTer5	p.K209Efs*5	ENST00000260947	NM_000465.2	208	aag/aaAg	4/11	1	2	FACETS	0.921	0.874	0.97	0.921	0.874	0.97	CLONAL	1	TRUE	1	0.785059655004772	2		562	929	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0012693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	119	293	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.368495272069959	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.368495272069959	1		295	442	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0012693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	178	363	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.368495272069959	2		364	944	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554327	63554327	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	269	471	0	ENST00000307078.5:c.412T>C	p.Tyr138His	p.Y138H	ENST00000307078	NM_004655.3	138	Tac/Cac	2/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.368495272069959	2		471	1315	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245401	153245401	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	199	303	0	ENST00000281708.4:c.1790G>A	p.Gly597Glu	p.G597E	ENST00000281708	NM_033632.3	597	gGg/gAg	11/12	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.368495272069959	2		303	957	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181840	56181840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768719008	NA	P-0012693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	165	301	1	ENST00000399503.3:c.4064G>A	p.Arg1355His	p.R1355H	ENST00000399503	NM_005921.1	1355	cGt/cAt	17/20	1	2	FACETS	0.976	0.896	1	0.976	0.896	1	CLONAL	1	TRUE	1	0.368495272069959	2		302	918	SUCCESS
APC	324	MSKCC	GRCh37	5	112174182	112174182	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0012693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	175	292	0	ENST00000257430.4:c.2891T>A	p.Leu964Ter	p.L964*	ENST00000257430	NM_000038.5	964	tTa/tAa	16/16	1	2	FACETS	0.928	0.854	1	0.928	0.854	1	CLONAL	1	TRUE	1	0.368495272069959	2		292	1024	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248159	59248174	+	frameshift_variant	Frame_Shift_Del	DEL	AGGCCGGCCGCGCCGT	AGGCCGGCCGCGCCGT	-	novel	NA	P-0012693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	54	46	0	ENST00000371222.2:c.569_584del	p.Tyr190TrpfsTer31	p.Y190Wfs*31	ENST00000371222	NM_002228.3	190	tACGGCGCGGCCGGCCTg/tg	1/1	1	2	FACETS	0.916	0.799	1	1	0.977	1	CLONAL	2	TRUE	1	0.368495272069959	2		46	160	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	338151	338153	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs1204980787	NA	P-0012693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	227	425	0	ENST00000262320.3:c.2558_2560del	p.Lys853del	p.K853del	ENST00000262320	NM_003502.3	853	aAGAtc/atc	11/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.368495272069959	2		425	1181	SUCCESS
APC	324	MSKCC	GRCh37	5	112175769	112175770	+	frameshift_variant	Frame_Shift_Ins	INS	CG	CG	TTAA	novel	NA	P-0012693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	96	180	0	ENST00000257430.4:c.4478_4479delinsTTAA	p.Thr1493IlefsTer15	p.T1493Ifs*15	ENST00000257430	NM_000038.5	1493	aCG/aTTAA	16/16	1	2	FACETS	0.96	0.857	1	0.96	0.857	1	CLONAL	1	TRUE	1	0.368495272069959	2		180	543	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0012747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	291	150	1	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	0.75796669565382	6	FACETS	0.804	0.756	0.853	0.402	0.378	0.427	CLONAL	2	TRUE	2	0.907067508523673	6		151	1123	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0012747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	477	341	0	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	0.278688161088397	2	FACETS	1	0.996	1	0.624	0.601	0.646	INDETERMINATE	1	TRUE	0	0.907067508523673	2		341	843	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578530	7578530	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs267605077	NA	P-0012747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	287	312	0	ENST00000269305.4:c.400T>C	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	Ttt/Ctt	5/11	0.278688161088397	2	FACETS	0.694	0.654	0.735	0.347	0.327	0.368	INDETERMINATE	1	TRUE	0	0.907067508523673	2		312	912	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082397	16082397	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	420	306	0	ENST00000281043.3:c.211A>T	p.Ser71Cys	p.S71C	ENST00000281043	NM_005378.4	71	Agc/Tgc	2/3	0.472834027291127	1	FACETS	0.767	0.739	0.794	0.767	0.739	0.794	INDETERMINATE	1	TRUE	0	0.907067508523673	1		306	660	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845473	128845473	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758800465	NA	P-0012747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	640	442	0	ENST00000249373.3:c.770G>A	p.Arg257Gln	p.R257Q	ENST00000249373	NM_005631.4	257	cGg/cAg	4/12	0.61196781684732	3	FACETS	1	0.997	1	0.684	0.66	0.709	CLONAL	1	TRUE	1	0.907067508523673	3		442	1499	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938414	44938414	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	266	513	0	ENST00000377967.4:c.2962A>C	p.Thr988Pro	p.T988P	ENST00000377967	NM_021140.2	988	Act/Cct	20/29	0.472834027291127	1	FACETS	0.335	0.314	0.356	0.335	0.314	0.356	INDETERMINATE	1	TRUE	0	0.907067508523673	1		513	957	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266038	41266264	+	splice_donor_variant,coding_sequence_variant,intron_variant	In_Frame_Del	DEL	TGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCAT	TGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCAT	-	novel	NA	P-0012747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	87	344	0	ENST00000349496.5:c.37_241+22del		p.M12_D81del	ENST00000349496	NM_001904.3	12		3/15	0.907067508523673	2	FACETS	0.767	0.712	0.819	0.767	0.712	0.819	SUBCLONAL	2	TRUE	0	0.907067508523673	2		344	125	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023196	150023196	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	266	430	0	ENST00000253339.5:c.67del	p.Tyr23IlefsTer32	p.Y23Ifs*32	ENST00000253339		23	Tat/at	1/7	0.384098477776383	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.907067508523673	0		430	629	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0012811-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	85	517	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.279158218217011	3	FACETS	0.96	0.848	1	0.48	0.424	0.54	CLONAL	1	TRUE	1	0.293538384007931	3		517	692	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128028956	128028956	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775316471	NA	P-0012811-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	51	548	0	ENST00000285398.2:c.1901G>A	p.Arg634His	p.R634H	ENST00000285398	NM_000122.1	634	cGt/cAt	12/15	1	2	FACETS	0.465	0.394	0.543	0.465	0.394	0.543	SUBCLONAL	1	TRUE	1	0.293538384007931	2		548	747	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134277	11134277	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012811-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	28	493	0	ENST00000358026.2:c.2943G>T	p.Lys981Asn	p.K981N	ENST00000358026	NM_001128849.1	981	aaG/aaT	20/36	0.113565783462024	0	FACETS	0.271	0.216	0.334			1	INDETERMINATE	1	TRUE	0	0.293538384007931	0		493	497	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170525	11170525	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012811-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	28	417	1	ENST00000358026.2:c.4828G>T	p.Glu1610Ter	p.E1610*	ENST00000358026	NM_001128849.1	1610	Gag/Tag	34/36	0.113565783462024	0	FACETS	0.318	0.254	0.391			1	INDETERMINATE	1	TRUE	0	0.293538384007931	0		418	424	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518257	103518258	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012811-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	51	296	0	ENST00000355739.4:c.2198dup	p.Leu733PhefsTer69	p.L733Ffs*69	ENST00000355739	NM_000123.3	732	aat/aaTt	9/15	0.279158218217011	3	FACETS	0.737	0.626	0.858	0.368	0.313	0.429	SUBCLONAL	1	TRUE	1	0.293538384007931	3		296	541	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881414	37881414	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1131692237	NA	P-0012836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	1110	393	0	ENST00000269571.5:c.2606T>G	p.Leu869Arg	p.L869R	ENST00000269571		869	cTg/cGg	21/27	0.763236544641284	4	FACETS	1	0.983	1			1	CLONAL	3	TRUE	NA	0.775442710627972	4		393	1685	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134184	41134184	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	608	804	0	ENST00000379561.5:c.1444C>G	p.Pro482Ala	p.P482A	ENST00000379561	NM_002015.3	482	Cct/Gct	2/3	1	2	FACETS	0.999	0.961	1	0.999	0.961	1	CLONAL	1	TRUE	1	0.775442710627972	2		804	1570	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863681	68863682	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0012836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	317	348	0	ENST00000261769.5:c.2421_2422dup	p.Gly808ValfsTer9	p.G808Vfs*9	ENST00000261769	NM_004360.3	807	att/atTGt	15/16	0.775442710627972	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.775442710627972	1		348	485	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012877-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	457	366	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.603934720486023	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.603934720486023	3		366	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0012877-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	355	356	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.603934720486023	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.603934720486023	1		356	573	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0012877-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	168	184	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.603934720486023	2		184	424	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856014	45856014	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751084702	NA	P-0012877-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	265	309	1	ENST00000391945.4:c.1892G>A	p.Arg631His	p.R631H	ENST00000391945	NM_000400.3	631	cGc/cAc	20/23	0.603934720486023	3	FACETS	1	0.987	1	0.594	0.557	0.631	CLONAL	1	TRUE	1	0.603934720486023	3		310	962	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0012877-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	344	1010	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.603934720486023	2		1010	965	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61720073	61720073	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012877-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	259	596	0	ENST00000401558.2:c.1361A>G	p.Tyr454Cys	p.Y454C	ENST00000401558	NM_003400.3	454	tAt/tGt	13/25	0.126126372353221	4	FACETS	0.967	0.911	1	0.967	0.911	1	INDETERMINATE	2	TRUE	2	0.603934720486023	4		596	711	SUCCESS
APC	324	MSKCC	GRCh37	5	112175696	112175696	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060503288	NA	P-0012877-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	224	496	0	ENST00000257430.4:c.4405C>T	p.Gln1469Ter	p.Q1469*	ENST00000257430	NM_000038.5	1469	Caa/Taa	16/16	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.603934720486023	2		496	583	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943623	9943623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758815434	NA	P-0012877-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	247	478	0	ENST00000330684.3:c.1318G>A	p.Val440Ile	p.V440I	ENST00000330684	NM_001134407.1	440	Gtc/Atc	5/13	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.603934720486023	2		478	570	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411387	63411387	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012877-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	945	776	0	ENST00000330258.3:c.1780del	p.His594ThrfsTer59	p.H594Tfs*59	ENST00000330258	NM_152424.3	594	Cac/ac	2/2	0.603934720486023	4	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	1	0.603934720486023	4		776	1528	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117687	70117688	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0012877-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	721	769	0	ENST00000245479.2:c.156dup	p.Phe53ValfsTer199	p.F53Vfs*199	ENST00000245479	NM_000346.3	52	acg/acGg	1/3	0.603934720486023	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	1	0.603934720486023	3		769	1349	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0012889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	75	250	2	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.496918269903409	4	FACETS	0.87	0.785	0.954			1	CLONAL	3	TRUE	NA	0.614963300607199	4		252	151	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660269	227660270	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0012889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	46	305	0	ENST00000305123.5:c.3185dup	p.Gln1064ThrfsTer17	p.Q1064Tfs*17	ENST00000305123	NM_005544.2	1062	ggc/ggGc	1/2	0.436266514924308	3	FACETS	0.914	0.778	1	0.457	0.389	0.53	CLONAL	1	TRUE	1	0.614963300607199	3		305	214	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261866	16261866	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	25	236	0	ENST00000375759.3:c.9131G>C	p.Ser3044Thr	p.S3044T	ENST00000375759	NM_015001.2	3044	aGt/aCt	11/15	0.621009998830121	2	FACETS	0.789	0.635	0.959	0.395	0.317	0.48	CLONAL	1	TRUE	0	0.614963300607199	2		236	103	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390716	139390716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751367016	NA	P-0012889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	410	899	0	ENST00000277541.6:c.7475C>T	p.Ser2492Leu	p.S2492L	ENST00000277541	NM_017617.3	2492	tCg/tTg	34/34	0.610748034367629	5	FACETS	1	0.992	1	1	0.992	1	CLONAL	4	TRUE	1	0.614963300607199	5		899	592	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236140	108236140	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	66	630	0	ENST00000278616.4:c.9076C>G	p.Leu3026Val	p.L3026V	ENST00000278616	NM_000051.3	3026	Ctc/Gtc	63/63	0.265769838911839	2	FACETS	0.801	0.703	0.905	0.4	0.351	0.453	INDETERMINATE	1	TRUE	0	0.614963300607199	2		630	268	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500414	99500414	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45526336	NA	P-0012889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	43	721	0	ENST00000268035.6:c.3847G>A	p.Glu1283Lys	p.E1283K	ENST00000268035	NM_000875.3	1283	Gag/Aag	21/21	0.621009998830121	3	FACETS	0.538	0.451	0.633	0.269	0.225	0.317	SUBCLONAL	1	TRUE	1	0.614963300607199	3		721	340	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212488	5212488	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	37	617	0	ENST00000357368.4:c.4629G>C	p.Glu1543Asp	p.E1543D	ENST00000357368	NM_002850.3	1543	gaG/gaC	31/38	1	2	FACETS	0.461	0.382	0.548	0.461	0.382	0.548	SUBCLONAL	1	TRUE	1	0.614963300607199	2		617	261	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067929	30067929	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	94	490	1	ENST00000338641.4:c.1114G>A	p.Glu372Lys	p.E372K	ENST00000338641	NM_000268.3	372	Gaa/Aaa	11/16	0.601637187815672	5	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.614963300607199	5		491	406	SUCCESS
APC	324	MSKCC	GRCh37	5	112157659	112157659	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	120	423	0	ENST00000257430.4:c.1380del	p.Glu461SerfsTer6	p.E461Sfs*6	ENST00000257430	NM_000038.5	460	gAa/ga	11/16	0.621009998830121	3	FACETS	1	0.968	1	0.727	0.672	0.782	CLONAL	2	TRUE	0	0.614963300607199	3		423	234	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111509	8111519	+	frameshift_variant	Frame_Shift_Del	DEL	CCAATGGGGAC	CCAATGGGGAC	-	novel	NA	P-0012889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	78	650	0	ENST00000346208.3:c.997_1007del	p.Asn333CysfsTer15	p.N333Cfs*15	ENST00000346208		332	gCCAATGGGGAC/g	5/6	0.614963300607199	9	FACETS	0.957	0.839	1			1	CLONAL	1	TRUE	NA	0.614963300607199	9		650	836	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858258	27858259	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0012889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	41	1535	0	ENST00000359303.2:c.312_313del	p.Phe105Ter	p.F105*	ENST00000359303	NM_003535.2	104	ctCTtt/cttt	1/1	0.607552618696244	3	FACETS	0.363	0.302	0.431	0.121	0.1	0.144	SUBCLONAL	1	TRUE	0	0.614963300607199	3		1535	480	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	500	654	0	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	1	2	FACETS	0.947	0.908	0.985	0.947	0.908	0.985	CLONAL	1	TRUE	1	0.896767685502334	2		654	1178	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238951	5238951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237159914	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	364	508	1	ENST00000357368.4:c.1828C>T	p.Arg610Trp	p.R610W	ENST00000357368	NM_002850.3	610	Cgg/Tgg	13/38	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.896767685502334	2		509	714	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	259	183	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.76	0.715	0.806	0.76	0.715	0.806	SUBCLONAL	1	TRUE	1	0.896767685502334	2		183	760	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682399	52682400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	415	684	0	ENST00000394830.3:c.773dup	p.Asn258LysfsTer6	p.N258Kfs*6	ENST00000394830	NM_018313.4	258	aat/aaAt	8/30	0.896767685502334	1	FACETS	0.976	0.949	1	0.976	0.949	1	CLONAL	1	TRUE	0	0.896767685502334	1		684	523	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	556	693	0	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	1	2	FACETS	0.981	0.944	1	0.981	0.944	1	CLONAL	1	TRUE	1	0.896767685502334	2		693	1264	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965666	90965666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	271	840	1	ENST00000265433.3:c.1651del	p.Arg551GlyfsTer8	p.R551Gfs*8	ENST00000265433	NM_002485.4	551	Agg/gg	11/16	0.896767685502334	3	FACETS	0.87	0.817	0.925	0.435	0.408	0.463	CLONAL	1	TRUE	1	0.896767685502334	3		841	1006	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	584	575	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	0.896767685502334	3	FACETS	0.939	0.908	0.969	0.939	0.908	0.969	CLONAL	2	TRUE	1	0.896767685502334	3		575	1005	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	231001	231001	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143484394	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	542	744	2	ENST00000264932.6:c.781C>T	p.Arg261Cys	p.R261C	ENST00000264932	NM_004168.2	261	Cgc/Tgc	7/15	0.859913895684317	3	FACETS	1	0.975	1	0.512	0.49	0.534	CLONAL	1	TRUE	1	0.896767685502334	3		746	1710	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	373	346	11	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	0.898	0.873	0.922	1	0.997	1	CLONAL	2	TRUE	1	0.896767685502334	2		357	463	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539951	187539951	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs777631605	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	419	551	0	ENST00000441802.2:c.7789C>T	p.Arg2597Ter	p.R2597*	ENST00000441802	NM_005245.3	2597	Cga/Tga	10/27	0.131374967513714	4	FACETS	0.963	0.922	1	0.963	0.922	1	INDETERMINATE	2	TRUE	2	0.896767685502334	4		551	920	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874637	35874637	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	347	743	8	ENST00000303115.3:c.799del	p.Arg267GlyfsTer28	p.R267Gfs*28	ENST00000303115	NM_002185.3	265	Aaa/aa	6/8	0.859913895684317	3	FACETS	0.875	0.828	0.923	0.438	0.414	0.462	CLONAL	1	TRUE	1	0.896767685502334	3		751	1281	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346338	73346338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	225	647	0	ENST00000377767.4:c.1462G>A	p.Asp488Asn	p.D488N	ENST00000377767	NM_014953.3	488	Gat/Aat	10/21	1	2	FACETS	0.871	0.818	0.925	0.871	0.818	0.925	CLONAL	1	TRUE	1	0.896767685502334	2		647	576	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779129	135779129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	499	739	1	ENST00000298552.3:c.2117G>A	p.Arg706His	p.R706H	ENST00000298552	NM_001162426.1	706	cGt/cAt	17/23	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.896767685502334	2		740	1091	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	439	399	10	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	NA	2	FACETS	0.951	0.911	0.993			1	INDETERMINATE	1	TRUE	NA	0.896767685502334	2		409	1029	SUCCESS
APC	324	MSKCC	GRCh37	5	112173495	112173495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147655929	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	721	649	0	ENST00000257430.4:c.2204C>T	p.Ala735Val	p.A735V	ENST00000257430	NM_000038.5	735	gCg/gTg	16/16	0.896767685502334	3	FACETS	0.979	0.951	1	0.979	0.951	1	CLONAL	2	TRUE	1	0.896767685502334	3		649	1190	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687472	37687472	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	378	469	2	ENST00000447079.4:c.4382del	p.Gly1461AlafsTer38	p.G1461Afs*38	ENST00000447079	NM_015083.1	1459	tGg/tg	14/14	1	2	FACETS	0.995	0.95	1	0.995	0.95	1	CLONAL	1	TRUE	1	0.896767685502334	2		471	847	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969983	161969983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	518	739	1	ENST00000366898.1:c.986del	p.Gly329AlafsTer106	p.G329Afs*106	ENST00000366898	NM_004562.2	329	gGc/gc	9/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.896767685502334	2		740	1121	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636719	176636719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140095431	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	495	682	0	ENST00000439151.2:c.1319G>A	p.Arg440Gln	p.R440Q	ENST00000439151	NM_022455.4	440	cGa/cAa	5/23	0.896767685502334	3	FACETS	1	0.979	1	0.519	0.496	0.542	CLONAL	1	TRUE	1	0.896767685502334	3		682	1541	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563012	21563012	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371362441	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	488	629	0	ENST00000382592.4:c.907G>A	p.Ala303Thr	p.A303T	ENST00000382592	NM_014572.2	303	Gct/Act	4/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.896767685502334	2		629	1037	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777685	9777685	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	344	618	0	ENST00000377346.4:c.1020+1G>A		p.X340_splice	ENST00000377346	NM_005026.3	340			1	2	FACETS	0.876	0.832	0.92	0.876	0.832	0.92	CLONAL	1	TRUE	1	0.896767685502334	2		618	876	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272508	11272508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1481267106	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	317	522	3	ENST00000361445.4:c.3422G>A	p.Arg1141His	p.R1141H	ENST00000361445	NM_004958.3	1141	cGc/cAc	23/58	1	2	FACETS	0.958	0.91	1	0.958	0.91	1	CLONAL	1	TRUE	1	0.896767685502334	2		525	738	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36814357	36814357	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	696	1063	1	ENST00000373129.3:c.683A>G	p.Asp228Gly	p.D228G	ENST00000373129	NM_032017.1	228	gAc/gGc	8/12	1	2	FACETS	0.996	0.963	1	0.996	0.963	1	CLONAL	1	TRUE	1	0.896767685502334	2		1064	1558	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443655	29443655	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	461	701	0	ENST00000389048.3:c.3562C>T	p.Gln1188Ter	p.Q1188*	ENST00000389048	NM_004304.4	1188	Caa/Taa	23/29	1	2	FACETS	0.979	0.939	1	0.979	0.939	1	CLONAL	1	TRUE	1	0.896767685502334	2		701	1050	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437274	220437274	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs980893896	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	719	1202	2	ENST00000243786.2:c.178C>T	p.Arg60Ter	p.R60*	ENST00000243786	NM_002191.3	60	Cga/Tga	1/2	1	2	FACETS	0.985	0.952	1	0.985	0.952	1	CLONAL	1	TRUE	1	0.896767685502334	2		1204	1628	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643497	52643497	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	45	857	0	ENST00000394830.3:c.2399A>G	p.Tyr800Cys	p.Y800C	ENST00000394830	NM_018313.4	800	tAc/tGc	17/30	0.896767685502334	1	FACETS	0.089	0.074	0.105	0.089	0.074	0.105	SUBCLONAL	1	TRUE	0	0.896767685502334	1		857	624	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282733	1282733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	305	534	0	ENST00000310581.5:c.1580G>A	p.Gly527Asp	p.G527D	ENST00000310581	NM_198253.2	527	gGc/gAc	3/16	0.859913895684317	3	FACETS	0.991	0.936	1	0.496	0.468	0.524	CLONAL	1	TRUE	1	0.896767685502334	3		534	994	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861059	35861059	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	286	503	0	ENST00000303115.3:c.188A>G	p.Asp63Gly	p.D63G	ENST00000303115	NM_002185.3	63	gAt/gGt	2/8	0.859913895684317	3	FACETS	0.962	0.906	1	0.481	0.453	0.51	CLONAL	1	TRUE	1	0.896767685502334	3		503	960	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435882	149435882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777247	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	417	659	0	ENST00000286301.3:c.2342C>T	p.Ala781Val	p.A781V	ENST00000286301	NM_005211.3	781	gCg/gTg	18/22	0.896767685502334	3	FACETS	0.983	0.936	1	0.492	0.468	0.516	CLONAL	1	TRUE	1	0.896767685502334	3		659	1370	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721997	176721997	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	402	501	1	ENST00000439151.2:c.7628C>A	p.Pro2543His	p.P2543H	ENST00000439151	NM_022455.4	2543	cCt/cAt	23/23	0.896767685502334	3	FACETS	1	0.971	1	0.514	0.488	0.539	CLONAL	1	TRUE	1	0.896767685502334	3		502	1264	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911132	29911132	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	392	695	1	ENST00000376809.5:c.431G>A	p.Gly144Asp	p.G144D	ENST00000376809	NM_002116.7	144	gGc/gAc	3/8	1	2	FACETS	0.84	0.8	0.88	0.84	0.8	0.88	CLONAL	1	TRUE	1	0.896767685502334	2		696	1041	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345965	152345965	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334975765	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	661	1214	1	ENST00000359321.1:c.605C>T	p.Ala202Val	p.A202V	ENST00000359321	NM_005431.1	202	gCc/gTc	3/3	1	2	FACETS	0.981	0.947	1	0.981	0.947	1	CLONAL	1	TRUE	1	0.896767685502334	2		1215	1502	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786868	135786868	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs118203481	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	510	685	3	ENST00000298552.3:c.1001C>T	p.Ser334Leu	p.S334L	ENST00000298552	NM_001162426.1	334	tCg/tTg	10/23	1	2	FACETS	0.968	0.93	1	0.968	0.93	1	CLONAL	1	TRUE	1	0.896767685502334	2		688	1175	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401023	139401023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149057410	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	568	829	5	ENST00000277541.6:c.3970G>A	p.Val1324Met	p.V1324M	ENST00000277541	NM_017617.3	1324	Gtg/Atg	24/34	1	2	FACETS	0.968	0.931	1	0.968	0.931	1	CLONAL	1	TRUE	1	0.896767685502334	2		834	1309	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258066	123258066	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	516	885	0	ENST00000358487.5:c.1615A>G	p.Lys539Glu	p.K539E	ENST00000358487	NM_000141.4	539	Aag/Gag	12/18	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.896767685502334	2		885	1148	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343580	118343580	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1368855534	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	352	471	2	ENST00000534358.1:c.1706C>T	p.Pro569Leu	p.P569L	ENST00000534358	NM_005933.3	569	cCg/cTg	3/36	1	2	FACETS	0.986	0.94	1	0.986	0.94	1	CLONAL	1	TRUE	1	0.896767685502334	2		473	796	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641562	18641562	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	198	415	0	ENST00000266497.5:c.2561A>G	p.Gln854Arg	p.Q854R	ENST00000266497		854	cAg/cGg	17/31	1	2	FACETS	0.964	0.903	1	0.964	0.903	1	CLONAL	1	TRUE	1	0.896767685502334	2		415	458	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110028	115110028	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200821102	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	409	573	1	ENST00000257566.3:c.1850C>T	p.Ala617Val	p.A617V	ENST00000257566	NM_016569.3	617	gCg/gTg	8/8	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.896767685502334	2		574	836	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245087	133245087	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	259	407	0	ENST00000320574.5:c.2028G>A	p.Met676Ile	p.M676I	ENST00000320574	NM_006231.2	676	atG/atA	19/49	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.896767685502334	2		407	541	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912907	32912907	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	522	1332	0	ENST00000380152.3:c.4415A>C	p.Lys1472Thr	p.K1472T	ENST00000380152		1472	aAg/aCg	11/27	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.896767685502334	2		1332	1156	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32921033	32921033	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs28897743	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	159	495	1	ENST00000380152.3:c.7007G>A	p.Arg2336His	p.R2336H	ENST00000380152		2336	cGc/cAc	13/27	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.896767685502334	2		496	316	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930610	32930610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358973	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	361	562	0	ENST00000380152.3:c.7481G>A	p.Arg2494Gln	p.R2494Q	ENST00000380152		2494	cGa/cAa	15/27	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.896767685502334	2		562	775	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060878	38060878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	419	748	3	ENST00000250448.2:c.1111C>T	p.Pro371Ser	p.P371S	ENST00000250448	NM_004496.3	371	Ccc/Tcc	2/2	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.896767685502334	2		751	899	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341269	341269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371093196	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	549	753	0	ENST00000262320.3:c.2215C>T	p.Arg739Cys	p.R739C	ENST00000262320	NM_003502.3	739	Cgc/Tgc	9/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.896767685502334	2		753	1146	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876648	59876648	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs748001678	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	197	383	0	ENST00000259008.2:c.1153C>A	p.Leu385Met	p.L385M	ENST00000259008	NM_032043.2	385	Ctg/Atg	9/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.896767685502334	2		383	416	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39618751	39618751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752104656	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	195	436	1	ENST00000262039.4:c.1975C>T	p.Arg659Trp	p.R659W	ENST00000262039	NM_002647.2	659	Cgg/Tgg	18/25	1	2	FACETS	0.9	0.842	0.96	0.9	0.842	0.96	CLONAL	1	TRUE	1	0.896767685502334	2		437	483	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650440	48650440	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	718	580	0	ENST00000376670.3:c.410A>C	p.Lys137Thr	p.K137T	ENST00000376670	NM_002049.3	137	aAg/aCg	3/6	1	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.896767685502334	1		580	795	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197732	66197733	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	301	581	0	ENST00000273854.3:c.2966dup	p.Asn989LysfsTer60	p.N989Kfs*60	ENST00000273854	NM_004439.5	989	aat/aaAt	17/18	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.896767685502334	2		581	665	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659788	88659789	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	413	617	0	ENST00000372037.3:c.441dup	p.Asp148Ter	p.D148*	ENST00000372037	NM_004329.2	145	-/T	7/13	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.896767685502334	2		617	855	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989410	7989410	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	563	849	2	ENST00000319144.4:c.276del	p.Asn93ThrfsTer104	p.N93Tfs*104	ENST00000319144	NM_001139.2	92	ccC/cc	2/15	1	2	FACETS	0.973	0.937	1	0.973	0.937	1	CLONAL	1	TRUE	1	0.896767685502334	2		851	1290	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446165	49446166	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs398123715	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	229	485	0	ENST00000301067.7:c.1300dup	p.Leu434ProfsTer12	p.L434Pfs*12	ENST00000301067	NM_003482.3	434	cta/cCta	10/54	1	2	FACETS	0.769	0.721	0.819	0.769	0.721	0.819	SUBCLONAL	1	TRUE	1	0.896767685502334	2		485	664	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438211	49438211	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	638	1010	1	ENST00000301067.7:c.5058del	p.Lys1686AsnfsTer36	p.K1686Nfs*36	ENST00000301067	NM_003482.3	1686	aaA/aa	20/54	1	2	FACETS	0.971	0.936	1	0.971	0.936	1	CLONAL	1	TRUE	1	0.896767685502334	2		1011	1466	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140500161	140500161	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1250	269	1192	0	ENST00000288602.6:c.980+1del		p.X327_splice	ENST00000288602	NM_004333.4	327			1	2	FACETS	0.395	0.369	0.422	0.395	0.369	0.422	SUBCLONAL	1	TRUE	1	0.896767685502334	2		1192	1519	SUCCESS
APC	324	MSKCC	GRCh37	5	112175673	112175673	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	410	654	0	ENST00000257430.4:c.4385del	p.Lys1462ArgfsTer11	p.K1462Rfs*11	ENST00000257430	NM_000038.5	1461	gAa/ga	16/16	0.896767685502334	3	FACETS	0.996	0.948	1	0.498	0.474	0.523	CLONAL	1	TRUE	1	0.896767685502334	3		654	1330	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137729	64137729	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	519	762	0	ENST00000334205.4:c.1834del	p.Ala612ProfsTer44	p.A612Pfs*44	ENST00000334205	NM_003942.2	610	caG/ca	15/17	1	2	FACETS	0.983	0.944	1	0.983	0.944	1	CLONAL	1	TRUE	1	0.896767685502334	2		762	1178	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740375	145740375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35842750	NA	P-0012986-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	79	351	0	ENST00000428558.2:c.1565G>A	p.Arg522His	p.R522H	ENST00000428558	NM_004260.3	522	cGc/cAc	9/22	1	2	FACETS	0.729	0.641	0.823	0.729	0.641	0.823	SUBCLONAL	1	TRUE	1	0.338140561152447	2		351	641	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700238	117700238	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012986-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	105	543	0	ENST00000368508.3:c.2581G>C	p.Val861Leu	p.V861L	ENST00000368508	NM_002944.2	861	Gtt/Ctt	17/43	1	2	FACETS	0.627	0.561	0.698	0.627	0.561	0.698	SUBCLONAL	1	TRUE	1	0.338140561152447	2		543	990	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81991567	81991567	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012986-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	190	926	0	ENST00000359376.3:c.3762A>T	p.Arg1254Ser	p.R1254S	ENST00000359376	NM_002661.3	1254	agA/agT	33/33	0.16245515302026	0	FACETS	0.561	0.517	0.606			1	INDETERMINATE	1	TRUE	0	0.338140561152447	0		926	1327	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938401	76938402	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	TTTTCGTTTCCTTTTTCCTTTATCA	novel	NA	P-0012986-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	225	402	0	ENST00000373344.5:c.2322_2346dup	p.Ser783Ter	p.S783*	ENST00000373344	NM_000489.3	782	-/TGATAAAGGAAAAAGGAAACGAAAA	9/35	0.151189045050279	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.338140561152447	2		402	902	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123025126	123025140	+	inframe_deletion	In_Frame_Del	DEL	TAAACAATATTCATT	TAAACAATATTCATT	-	novel	NA	P-0012986-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	117	256	0	ENST00000355640.3:c.1019_1033del	p.Asn340_Leu344del	p.N340_L344del	ENST00000355640		339	aTAAACAATATTCATTta/ata	4/7	1	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.338140561152447	1		256	511	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0012987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	388	495	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	1	0.61137112493255	2		495	1070	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0012987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	18	510	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.61137112493255	1	FACETS	0.068	0.051	0.089	0.068	0.051	0.089	SUBCLONAL	1	FALSE	0	0.61137112493255	1		510	599	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425644	49425644	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057517992	NA	P-0012987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	185	492	1	ENST00000301067.7:c.12844C>T	p.Arg4282Ter	p.R4282*	ENST00000301067	NM_003482.3	4282	Cga/Tga	39/54	1	2	FACETS	0.946	0.877	1	0.946	0.877	1	CLONAL	1	FALSE	1	0.61137112493255	2		493	640	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004519	150004519	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1480	85	865	0	ENST00000253339.5:c.1706C>G	p.Ser569Cys	p.S569C	ENST00000253339		569	tCt/tGt	3/7	1	2	FACETS	0.178	0.156	0.201	0.178	0.156	0.201	SUBCLONAL	1	FALSE	1	0.61137112493255	2		865	1565	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78931447	78931447	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	215	531	0	ENST00000306801.3:c.3394G>C	p.Glu1132Gln	p.E1132Q	ENST00000306801	NM_020761.2	1132	Gag/Cag	29/34	0.61137112493255	1	FACETS	0.959	0.901	1	0.959	0.901	1	CLONAL	1	FALSE	0	0.61137112493255	1		531	509	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219367	5219367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763007823	NA	P-0012987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	112	574	1	ENST00000357368.4:c.3877G>A	p.Val1293Met	p.V1293M	ENST00000357368	NM_002850.3	1293	Gtg/Atg	23/38	1	2	FACETS	0.45	0.404	0.498	0.45	0.404	0.498	SUBCLONAL	1	FALSE	1	0.61137112493255	2		575	814	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757438	40757438	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	68	587	0	ENST00000373198.4:c.2860G>T	p.Asp954Tyr	p.D954Y	ENST00000373198	NM_133170.3	954	Gat/Tat	20/32	0.61137112493255	3	FACETS	0.262	0.227	0.3	0.131	0.113	0.15	SUBCLONAL	1	FALSE	1	0.61137112493255	3		587	1110	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579327	7579328	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCAA	novel	NA	P-0012987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	217	456	0	ENST00000269305.4:c.359_360insTTGG	p.Lys120AsnfsTer30	p.K120Nfs*30	ENST00000269305	NM_001126112.2	120	aag/aaTTGGg	4/11	0.61137112493255	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	0	0.61137112493255	1		456	464	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0013015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	368	631	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	2	TRUE	NA	0.518121961433612	2		631	680	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958804	55958804	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	150	610	0	ENST00000263923.4:c.3049G>C	p.Glu1017Gln	p.E1017Q	ENST00000263923	NM_002253.2	1017	Gag/Cag	22/30	0.518121961433612	3	FACETS	1	0.925	1	0.506	0.463	0.55	CLONAL	1	TRUE	1	0.518121961433612	3		610	721	SUCCESS
APC	324	MSKCC	GRCh37	5	112090645	112090645	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	99	369	0	ENST00000257430.4:c.58A>T	p.Asn20Tyr	p.N20Y	ENST00000257430	NM_000038.5	20	Aac/Tac	2/16	0.518121961433612	3	FACETS	0.924	0.827	1	0.462	0.413	0.513	CLONAL	1	TRUE	1	0.518121961433612	3		369	521	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484337	50484338	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0013015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	150	550	0	ENST00000394963.4:c.1097_1098insAA	p.Met366IlefsTer36	p.M366Ifs*36	ENST00000394963	NM_003076.4	366	atg/atAAg	9/13	0.518121961433612	3	FACETS	0.952	0.871	1	0.476	0.435	0.518	CLONAL	1	TRUE	1	0.518121961433612	3		550	766	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952139	178952148	+	frameshift_variant	Frame_Shift_Del	DEL	ATGCATTGAA	ATGCATTGAA	TG	novel	NA	P-0013015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	343	303	0	ENST00000263967.3:c.3194_3203delinsTG	p.His1065LeufsTer5	p.H1065Lfs*5	ENST00000263967	NM_006218.2	1065	cATGCATTGAAc/cTGc	21/21	0.518121961433612	5	FACETS	1	0.99	1	0.878	0.844	0.912	CLONAL	4	TRUE	0	0.518121961433612	5		303	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0013046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	230	293	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.52378961925536	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.525852503482383	1		295	573	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0013046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	482	434	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.515682610544265	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.525852503482383	2		434	895	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157920	106157920	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532738858	NA	P-0013046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	255	292	0	ENST00000380013.4:c.2821C>T	p.Pro941Ser	p.P941S	ENST00000380013	NM_001127208.2	941	Cct/Tct	3/11	0.473131644646516	2	FACETS	0.908	0.859	0.957	0.908	0.859	0.957	CLONAL	2	TRUE	0	0.525852503482383	2		292	534	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168484	56168484	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	143	250	0	ENST00000399503.3:c.1440A>T	p.Arg480Ser	p.R480S	ENST00000399503	NM_005921.1	480	agA/agT	8/20	0.52378961925536	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.525852503482383	1		250	400	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152357845	152357845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1371	470	797	1	ENST00000359321.1:c.62G>A	p.Arg21Lys	p.R21K	ENST00000359321	NM_005431.1	21	aGa/aAa	2/3	1	2	FACETS	0.971	0.925	1	0.971	0.925	1	CLONAL	1	TRUE	1	0.525852503482383	2		798	1841	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346334	73346334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	220	430	0	ENST00000377767.4:c.1466C>A	p.Ala489Asp	p.A489D	ENST00000377767	NM_014953.3	489	gCt/gAt	10/21	0.525852503482383	1	FACETS	0.987	0.924	1	0.987	0.924	1	CLONAL	1	TRUE	0	0.525852503482383	1		430	625	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657448	29657448	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555533875	NA	P-0013046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	280	497	0	ENST00000356175.3:c.5681T>C	p.Leu1894Pro	p.L1894P	ENST00000356175	NM_000267.3	1894	cTg/cCg	38/57	0.52378961925536	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.525852503482383	1		497	731	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243571	41243571	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	420	694	0	ENST00000357654.3:c.3977A>G	p.His1326Arg	p.H1326R	ENST00000357654	NM_007294.3	1326	cAt/cGt	10/23	0.525852503482383	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.525852503482383	1		694	1126	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10244973	10244973	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	376	500	0	ENST00000340748.4:c.4736C>G	p.Ala1579Gly	p.A1579G	ENST00000340748		1579	gCc/gGc	39/40	0.525852503482383	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.525852503482383	1		500	906	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965003	25965004	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0013046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	156	538	0	ENST00000435504.4:c.4202dup	p.Tyr1401Ter	p.Y1401*	ENST00000435504		1401	tac/taAc	13/13	0.275315618664078	1	FACETS	0.426	0.389	0.464	0.426	0.389	0.464	INDETERMINATE	1	TRUE	0	0.525852503482383	1		538	1027	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912364	29912364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013050-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	198	460	1	ENST00000376809.5:c.983C>T	p.Ala328Val	p.A328V	ENST00000376809	NM_002116.7	328	gCt/gTt	5/8	1	2	FACETS	0.674	0.626	0.725	0.674	0.626	0.725	SUBCLONAL	1	TRUE	1	0.715203321855032	2		461	821	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609861	117609861	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013050-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	242	757	1	ENST00000368508.3:c.6838G>A	p.Glu2280Lys	p.E2280K	ENST00000368508	NM_002944.2	2280	Gaa/Aaa	43/43	1	2	FACETS	0.575	0.537	0.615	0.575	0.537	0.615	SUBCLONAL	1	TRUE	1	0.715203321855032	2		758	1176	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001394	150001394	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013050-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	240	548	2	ENST00000253339.5:c.2210G>T	p.Arg737Leu	p.R737L	ENST00000253339		737	cGa/cTa	4/7	1	2	FACETS	0.907	0.85	0.965	0.907	0.85	0.965	CLONAL	1	TRUE	1	0.715203321855032	2		550	740	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725111	89725112	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0013050-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	32	95	0	ENST00000371953.3:c.1095_1096insCA	p.Thr366GlnfsTer51	p.T366Qfs*51	ENST00000371953	NM_000314.4	365	gta/gtACa	9/9	0.69887393686215	1	FACETS	0.513	0.426	0.607	0.513	0.426	0.607	SUBCLONAL	1	TRUE	0	0.715203321855032	1		95	112	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	456	435	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.534936281556793	3	FACETS	0.971	0.931	1			1	CLONAL	2	TRUE	NA	0.588012119549803	3		435	1033	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs760043106	NA	P-0013055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	423	718	0	ENST00000269305.4:c.584T>A	p.Ile195Asn	p.I195N	ENST00000269305	NM_001126112.2	195	aTc/aAc	6/11	0.588012119549803	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.588012119549803	1		718	791	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017578	112017578	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	392	1028	0	ENST00000368678.4:c.935C>T	p.Ala312Val	p.A312V	ENST00000368678		312	gCg/gTg	9/13	1	2	FACETS	0.994	0.944	1	0.994	0.944	1	CLONAL	1	TRUE	1	0.588012119549803	2		1028	1342	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	286	615	0	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.588012119549803	2		615	897	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402460	139402460	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	332	781	2	ENST00000277541.6:c.3457C>T	p.Pro1153Ser	p.P1153S	ENST00000277541	NM_017617.3	1153	Ccc/Tcc	21/34	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.588012119549803	2		783	1005	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097635	8097635	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1260955718	NA	P-0013055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	105	355	0	ENST00000346208.3:c.17A>G	p.Asp6Gly	p.D6G	ENST00000346208		6	gAc/gGc	2/6	1	2	FACETS	0.812	0.732	0.895	0.812	0.732	0.895	CLONAL	1	TRUE	1	0.588012119549803	2		355	440	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211574	46211574	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	300	723	0	ENST00000334344.6:c.540C>A	p.Cys180Ter	p.C180*	ENST00000334344	NM_152641.2	180	tgC/tgA	5/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.588012119549803	2		723	1012	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513292	44513292	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1450304522	NA	P-0013055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	333	599	0	ENST00000291552.4:c.643G>A	p.Gly215Ser	p.G215S	ENST00000291552	NM_006758.2	215	Ggt/Agt	8/8	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.588012119549803	2		599	947	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244679	46244680	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCGTAGT	novel	NA	P-0013055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	348	818	0	ENST00000334344.6:c.2775_2781dup	p.Ile928ArgfsTer25	p.I928Rfs*25	ENST00000334344	NM_152641.2	925	agc/aGCGTAGTgc	15/21	1	2	FACETS	0.973	0.921	1	0.973	0.921	1	CLONAL	1	TRUE	1	0.588012119549803	2		818	1217	SUCCESS
APC	324	MSKCC	GRCh37	5	112175940	112175943	+	frameshift_variant	Frame_Shift_Del	DEL	AGAA	AGAA	-	rs863225358	NA	P-0013055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	141	357	0	ENST00000257430.4:c.4652_4655del	p.Lys1551ArgfsTer13	p.K1551Rfs*13	ENST00000257430	NM_000038.5	1550	gAGAAa/ga	16/16	0.588012119549803	1	FACETS	0.954	0.881	1	0.954	0.881	1	CLONAL	1	TRUE	0	0.588012119549803	1		357	355	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0013092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	308	412	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.91063057891746	2		412	663	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412278	139412278	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs864622058	NA	P-0013092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1171	136	698	0	ENST00000277541.6:c.1367G>A	p.Cys456Tyr	p.C456Y	ENST00000277541	NM_017617.3	456	tGc/tAc	8/34	1	2	FACETS	0.229	0.207	0.251	0.229	0.207	0.251	SUBCLONAL	1	TRUE	1	0.91063057891746	2		698	1307	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	122	545	1	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS	0.276	0.248	0.304	0.276	0.248	0.304	SUBCLONAL	1	TRUE	1	0.91063057891746	2		546	972	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577571	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATGTAGTTGTAGTGG	novel	NA	P-0013092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	503	495	0	ENST00000269305.4:c.696_710dup	p.Ile232_Tyr236dup	p.I232_Y236dup	ENST00000269305	NM_001126112.2	232	atg/atCCACTACAACTACATg	7/11	0.91063057891746	2	FACETS	1	0.997	1	0.702	0.679	0.724	CLONAL	1	TRUE	0	0.91063057891746	2		495	787	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0013146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	19	250	2	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.683	0.519	0.877	0.683	0.519	0.877	SUBCLONAL	1	TRUE	1	0.2	2		252	278	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	63	435	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.14654976224396	3	FACETS	1	0.896	1	0.522	0.451	0.599	CLONAL	1	TRUE	1	0.2	3		435	664	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0013146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	86	515	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	0.2	2		516	700	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023830	27023831	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0013146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	66	371	1	ENST00000324856.7:c.941dup	p.Asp315ArgfsTer85	p.D315Rfs*85	ENST00000324856	NM_006015.4	312	-/G	1/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.2	2		372	513	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967831	93967831	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	63	736	0	ENST00000369303.4:c.2096G>C	p.Gly699Ala	p.G699A	ENST00000369303	NM_004440.3	699	gGg/gCg	11/17	1	2	FACETS	0.653	0.563	0.751	0.653	0.563	0.751	SUBCLONAL	1	TRUE	1	0.2	2		736	965	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710593	117710593	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145765584	NA	P-0013146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	33	417	1	ENST00000368508.3:c.1679G>A	p.Arg560His	p.R560H	ENST00000368508	NM_002944.2	560	cGc/cAc	12/43	1	2	FACETS	0.565	0.459	0.685	0.565	0.459	0.685	SUBCLONAL	1	TRUE	1	0.2	2		418	584	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157495252	157495252	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0013146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	33	297	0	ENST00000346085.5:c.3135+1G>T		p.X1045_splice	ENST00000346085	NM_020732.3	1045			1	2	FACETS	0.578	0.47	0.701	0.578	0.47	0.701	SUBCLONAL	1	TRUE	1	0.2	2		297	571	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932920	39932920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	110	473	6	ENST00000378444.4:c.1679C>T	p.Ser560Leu	p.S560L	ENST00000378444	NM_001123385.1	560	tCa/tTa	4/15	NA	2	FACETS	0.908	0.817	1			1	INDETERMINATE	2	TRUE	NA	0.2	2		479	606	SUCCESS
APC	324	MSKCC	GRCh37	5	112175888	112175894	+	frameshift_variant	Frame_Shift_Del	DEL	AATGGGA	AATGGGA	-	novel	NA	P-0013146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	32	302	0	ENST00000257430.4:c.4598_4604del	p.Asn1533MetfsTer30	p.N1533Mfs*30	ENST00000257430	NM_000038.5	1533	AATGGGAat/at	16/16	1	2	FACETS	0.748	0.607	0.907	0.748	0.607	0.907	CLONAL	1	TRUE	1	0.2	2		302	428	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578527	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0013210-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	585	479	0	ENST00000269305.4:c.403dup	p.Cys135LeufsTer14	p.C135Lfs*14	ENST00000269305	NM_001126112.2	135	tgc/tTgc	5/11	0.940402651183018	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.940402651183018	1		479	647	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121004	3121004	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013210-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	397	451	0	ENST00000078429.4:c.907C>G	p.Gln303Glu	p.Q303E	ENST00000078429	NM_002067.2	303	Cag/Gag	7/7	0.940402651183018	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.940402651183018	1		451	420	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426266	49426320	+	frameshift_variant	Frame_Shift_Del	DEL	TTGTGAGTCCCCAGAGAGTGAGGGCTTTACCTCTCCTGGTTCAGTGGCCATTGAC	TTGTGAGTCCCCAGAGAGTGAGGGCTTTACCTCTCCTGGTTCAGTGGCCATTGAC	-	novel	NA	P-0013210-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	225	622	0	ENST00000301067.7:c.12168_12222del	p.Glu4056AspfsTer22	p.E4056Dfs*22	ENST00000301067	NM_003482.3	4056	gaGTCAATGGCCACTGAACCAGGAGAGGTAAAGCCCTCACTCTCTGGGGACTCACAA/ga	39/54	0.459889917831083	1	FACETS	0.291	0.271	0.312	0.291	0.271	0.312	INDETERMINATE	1	TRUE	0	0.940402651183018	1		622	870	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013286-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	315	366	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.368512281384969	4	FACETS	0.96	0.907	1			1	CLONAL	2	TRUE	NA	0.470002528034545	4		366	1026	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0013286-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	215	498	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	0.470002528034545	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.470002528034545	1		498	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576882	7576883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013286-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	174	581	0	ENST00000269305.4:c.963dup	p.Pro322ThrfsTer15	p.P322Tfs*15	ENST00000269305	NM_001126112.2	321	-/A	9/11	0.470002528034545	1	FACETS	0.874	0.808	0.942	0.874	0.808	0.942	CLONAL	1	TRUE	0	0.470002528034545	1		581	648	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468269	50468269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013286-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	49	452	0	ENST00000331340.3:c.1504C>T	p.Arg502Trp	p.R502W	ENST00000331340	NM_006060.4	502	Cgg/Tgg	8/8	0.431364012269957	4	FACETS	0.42	0.355	0.493	0.14	0.118	0.165	SUBCLONAL	1	TRUE	1	0.470002528034545	4		452	729	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73995319	73995320	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0013286-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	12	171	0	ENST00000318443.5:c.628dup	p.Val210GlyfsTer44	p.V210Gfs*44	ENST00000318443	NM_001024736.1	209	cgg/cGgg	4/10	1	2	FACETS	0.258	0.181	0.352	0.258	0.181	0.352	SUBCLONAL	1	TRUE	1	0.470002528034545	2		171	198	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380282	25380282	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013295-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	92	662	0	ENST00000311936.3:c.176C>G	p.Ala59Gly	p.A59G	ENST00000311936	NM_004985.3	59	gCa/gGa	3/5	1	2	FACETS	0.799	0.709	0.896	0.799	0.709	0.896	SUBCLONAL	1	TRUE	1	0.24	2		662	959	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123697	46123697	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013295-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	69	420	0	ENST00000334344.6:c.79del	p.His27ThrfsTer31	p.H27Tfs*31	ENST00000334344	NM_152641.2	26	ttC/tt	1/21	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.24	2		420	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577605	+	inframe_deletion	In_Frame_Del	DEL	ACAGTCAGAGCC	ACAGTCAGAGCC	-	novel	NA	P-0013295-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	60	592	0	ENST00000269305.4:c.676_687del	p.Gly226_Cys229del	p.G226_C229del	ENST00000269305	NM_001126112.2	226	GGCTCTGACTGT/-	7/11	1	2	FACETS	0.712	0.613	0.821	0.712	0.613	0.821	SUBCLONAL	1	TRUE	1	0.24	2		592	702	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986635	36986636	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013295-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	17	109	0	ENST00000354822.5:c.1053dup	p.Gly352ArgfsTer87	p.G352Rfs*87	ENST00000354822	NM_001079668.2	351	-/A	3/3	1	2	FACETS	1	0.829	1	1	0.829	1	CLONAL	1	TRUE	1	0.24	2		109	125	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	83	366	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	0.17727855978472	2		366	851	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934874	NA	P-0013319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	39	634	1	ENST00000269305.4:c.451C>A	p.Pro151Thr	p.P151T	ENST00000269305	NM_001126112.2	151	Ccc/Acc	5/11	1	2	FACETS	0.51	0.421	0.61	0.51	0.421	0.61	SUBCLONAL	1	TRUE	1	0.17727855978472	2		635	862	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117962	70117963	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0013319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	24	245	0	ENST00000245479.2:c.431+1dup		p.R144fs	ENST00000245479	NM_000346.3	144	aga/aGga	1/3	1	2	FACETS	0.831	0.652	1	0.831	0.652	1	CLONAL	1	TRUE	1	0.17727855978472	2		245	326	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427501	49427502	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0013319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	48	762	0	ENST00000301067.7:c.10986_10987delinsTT	p.Met3662_Ala3663delinsIleSer	p.M3662_A3663delinsIS	ENST00000301067	NM_003482.3	3662	atGGca/atTTca	39/54	1	2	FACETS	0.612	0.515	0.719	0.612	0.515	0.719	SUBCLONAL	1	TRUE	1	0.17727855978472	2		762	885	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0013366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	233	485	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.968	0.901	1	0.968	0.901	1	CLONAL	1	TRUE	1	0.381912217756001	2		485	1261	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149465954	149465954	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1202	459	759	0	ENST00000286301.3:c.37A>G	p.Thr13Ala	p.T13A	ENST00000286301	NM_005211.3	13	Aca/Gca	2/22	0.381912217756001	3	FACETS	0.862	0.821	0.903	0.862	0.821	0.903	CLONAL	2	TRUE	1	0.381912217756001	3		759	1661	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871807	12871807	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	45	343	0	ENST00000228872.4:c.524C>A	p.Ser175Ter	p.S175*	ENST00000228872	NM_004064.3	175	tCa/tAa	2/3	1	2	FACETS	0.3	0.251	0.355	0.3	0.251	0.355	SUBCLONAL	1	TRUE	1	0.381912217756001	2		343	785	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443797	18443797	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	67	524	0	ENST00000266497.5:c.770A>G	p.Glu257Gly	p.E257G	ENST00000266497		257	gAa/gGa	3/31	1	2	FACETS	0.346	0.299	0.397	0.346	0.299	0.397	SUBCLONAL	1	TRUE	1	0.381912217756001	2		524	1014	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755585	39755585	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	230	671	0	ENST00000288319.7:c.1180G>A	p.Gly394Arg	p.G394R	ENST00000288319	NM_182918.3	394	Ggg/Agg	10/10	1	2	FACETS	0.877	0.816	0.941	0.877	0.816	0.941	CLONAL	1	TRUE	1	0.381912217756001	2		671	1373	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060912	38060912	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	1285	452	0	ENST00000250448.2:c.1077del	p.Ile360Ter	p.I360*	ENST00000250448	NM_004496.3	359	ccC/cc	2/2	0.381912217756001	9	FACETS	0.988	0.968	1			1	CLONAL	8	TRUE	NA	0.381912217756001	9		452	1990	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396762	139396764	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0013366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	58	514	0	ENST00000277541.6:c.5344_5346del	p.Lys1782del	p.K1782del	ENST00000277541	NM_017617.3	1782	AAG/-	28/34	0.381610630778376	2	FACETS	0.276	0.236	0.32	0.138	0.118	0.16	SUBCLONAL	1	TRUE	0	0.381912217756001	2		514	1101	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961323	41961324	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0013366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1753	369	1017	0	ENST00000219905.7:c.232dup	p.Thr78AsnfsTer4	p.T78Nfs*4	ENST00000219905	NM_001164273.1	77	-/A	2/24	1	2	FACETS	0.911	0.86	0.963	0.911	0.86	0.963	CLONAL	1	TRUE	1	0.381912217756001	2		1017	2122	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089705	27089706	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1286891446	NA	P-0013432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	128	480	0	ENST00000324856.7:c.2666dup	p.Met890HisfsTer46	p.M890Hfs*46	ENST00000324856	NM_006015.4	887	-/G	8/20	1	2	FACETS	0.95	0.865	1	0.95	0.865	1	CLONAL	1	TRUE	1	0.51348641220184	2		480	525	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149436860	149436860	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	104	592	0	ENST00000286301.3:c.2309C>A	p.Ala770Asp	p.A770D	ENST00000286301	NM_005211.3	770	gCt/gAt	17/22	0.389038593088714	3	FACETS	0.653	0.584	0.725	0.326	0.292	0.363	SUBCLONAL	1	TRUE	1	0.51348641220184	3		592	780	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573226	64573226	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	206	706	0	ENST00000312049.6:c.1066G>T	p.Glu356Ter	p.E356*	ENST00000312049	NM_130799.2	356	Gaa/Taa	8/10	0.51348641220184	1	FACETS	0.873	0.814	0.934	0.873	0.814	0.934	CLONAL	1	TRUE	0	0.51348641220184	1		706	683	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155649	56155658	+	frameshift_variant	Frame_Shift_Del	DEL	CCGACGCAGT	CCGACGCAGT	-	novel	NA	P-0013432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	252	417	0	ENST00000399503.3:c.743_752del	p.Arg248LeufsTer12	p.R248Lfs*12	ENST00000399503	NM_005921.1	247	ggCCGACGCAGT/gg	3/20	0.495765040947903	3	FACETS	0.861	0.81	0.914	0.861	0.81	0.914	CLONAL	2	TRUE	1	0.51348641220184	3		417	716	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	181	366	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.915	0.846	0.986	0.915	0.846	0.986	CLONAL	1	TRUE	1	0.542718480419473	2		366	729	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097651	27097652	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0013450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	242	688	0	ENST00000324856.7:c.3242dup	p.Asn1081LysfsTer24	p.N1081Kfs*24	ENST00000324856	NM_006015.4	1080	-/A	12/20	0.542718480419473	1	FACETS	0.949	0.891	1	0.949	0.891	1	CLONAL	1	TRUE	0	0.542718480419473	1		688	685	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379426	225379426	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013498-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	107	582	1	ENST00000264414.4:c.442C>T	p.Arg148Ter	p.R148*	ENST00000264414	NM_003590.4	148	Cga/Tga	4/16	1	2	FACETS	0.785	0.703	0.873	0.785	0.703	0.873	SUBCLONAL	1	TRUE	1	0.267751384930192	2		583	1018	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11276273	11276273	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013498-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	107	629	1	ENST00000361445.4:c.3049G>A	p.Gly1017Arg	p.G1017R	ENST00000361445	NM_004958.3	1017	Gga/Aga	20/58	1	2	FACETS	0.832	0.745	0.924	0.832	0.745	0.924	CLONAL	1	TRUE	1	0.267751384930192	2		630	961	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399790	139399790	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013498-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	81	529	0	ENST00000277541.6:c.4558G>C	p.Asp1520His	p.D1520H	ENST00000277541	NM_017617.3	1520	Gac/Cac	25/34	0.267751384930192	3	FACETS	0.784	0.689	0.886	0.392	0.344	0.443	SUBCLONAL	1	TRUE	1	0.267751384930192	3		529	875	SUCCESS
FH	2271	MSKCC	GRCh37	1	241669354	241669355	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0013498-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	217	635	0	ENST00000366560.3:c.852dup	p.Thr285TyrfsTer2	p.T285Yfs*2	ENST00000366560	NM_000143.3	284	-/T	6/10	0.267751384930192	3	FACETS	0.921	0.856	0.987	0.921	0.856	0.987	CLONAL	2	TRUE	1	0.267751384930192	3		635	998	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230765	53230765	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013498-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	153	413	0	ENST00000375401.3:c.2028del	p.Glu677SerfsTer87	p.E677Sfs*87	ENST00000375401	NM_004187.3	676	gaA/ga	14/26	1	1	FACETS	0.843	0.775	0.914	1	0.99	1	CLONAL	2	TRUE	0	0.267751384930192	1		413	587	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261047	16261048	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0013498-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	95	446	1	ENST00000375759.3:c.8315dup	p.Cys2773ValfsTer8	p.C2773Vfs*8	ENST00000375759	NM_015001.2	2771	aca/acAa	11/15	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.267751384930192	2		447	668	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578281	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	A	rs1215018778	NA	P-0013498-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	374	692	1	ENST00000269305.4:c.568_569delinsT	p.Pro190PhefsTer57	p.P190Ffs*57	ENST00000269305	NM_001126112.2	190	CCt/Tt	6/11	0.217644975527129	3	FACETS	0.988	0.939	1	0.988	0.939	1	CLONAL	3	TRUE	0	0.267751384930192	3		693	1069	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0013513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	293	524	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.471576271735022	4	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	2	0.556316285733376	4		524	807	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0013513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	1018	153	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.556316285733376	17	FACETS	1	0.985	1			1	CLONAL	15	TRUE	NA	0.556316285733376	17		153	1259	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	212	439	0	ENST00000269305.4:c.528C>A	p.Cys176Ter	p.C176*	ENST00000269305	NM_001126112.2	176	tgC/tgA	5/11	0.471576271735022	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	2	0.556316285733376	4		439	545	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637121	176637122	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1299932363	NA	P-0013513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	128	471	0	ENST00000439151.2:c.1727dup	p.Asn576LysfsTer8	p.N576Kfs*8	ENST00000439151	NM_022455.4	574	gga/ggAa	5/23	1	2	FACETS	0.977	0.891	1	0.977	0.891	1	CLONAL	1	TRUE	1	0.556316285733376	2		471	471	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599289	55599289	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs751206924	NA	P-0013513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	253	541	0	ENST00000288135.5:c.2415C>G	p.Ile805Met	p.I805M	ENST00000288135	NM_000222.2	805	atC/atG	17/21	0.471576271735022	4	FACETS	0.942	0.886	1	0.942	0.886	1	CLONAL	2	TRUE	2	0.556316285733376	4		541	751	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675181	176675181	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0013513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	109	455	0	ENST00000439151.2:c.4498-1G>A		p.X1500_splice	ENST00000439151	NM_022455.4	1500			1	2	FACETS	0.879	0.794	0.967	0.879	0.794	0.967	CLONAL	1	TRUE	1	0.556316285733376	2		455	446	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959242	2959242	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	480	429	1	ENST00000396946.4:c.2274C>A	p.Tyr758Ter	p.Y758*	ENST00000396946	NM_032415.4	758	taC/taA	18/25	0.556316285733376	5	FACETS	1	0.97	1	1	0.97	1	CLONAL	4	TRUE	1	0.556316285733376	5		430	788	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715648	18715648	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	201	460	0	ENST00000266497.5:c.3479A>G	p.Glu1160Gly	p.E1160G	ENST00000266497		1160	gAa/gGa	25/31	0.512406711901461	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	2	0.556316285733376	4		460	546	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755688	39755688	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	299	629	0	ENST00000288319.7:c.1077C>A	p.Asn359Lys	p.N359K	ENST00000288319	NM_182918.3	359	aaC/aaA	10/10	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	2	TRUE	NA	0.556316285733376	2		629	531	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435312	56435313	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0013513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	179	379	0	ENST00000407977.2:c.1824dup	p.Arg609AlafsTer4	p.R609Afs*4	ENST00000407977		608	-/G	9/10	0.471576271735022	4	FACETS	0.889	0.825	0.955	0.889	0.825	0.955	CLONAL	2	TRUE	2	0.556316285733376	4		379	563	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860058	151860058	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	106	476	0	ENST00000262189.6:c.10604del	p.Gly3535AspfsTer15	p.G3535Dfs*15	ENST00000262189	NM_170606.2	3535	gGa/ga	43/59	0.556316285733376	5	FACETS	0.943	0.846	1	0.236	0.211	0.262	CLONAL	1	TRUE	1	0.556316285733376	5		476	741	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	258	604	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.33	2		604	1428	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950099	38950099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757900166	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	121	490	3	ENST00000357387.3:c.3851C>T	p.Ser1284Leu	p.S1284L	ENST00000357387	NM_152756.3	1284	tCg/tTg	31/38	1	2	FACETS	0.851	0.768	0.938	0.851	0.768	0.938	CLONAL	1	TRUE	1	0.33	2		493	862	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388086	81388086	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	50	503	0	ENST00000222390.5:c.289C>A	p.Leu97Ile	p.L97I	ENST00000222390	NM_000601.4	97	Ctc/Atc	3/18	1	2	FACETS	0.426	0.361	0.499	0.426	0.361	0.499	SUBCLONAL	1	TRUE	1	0.33	2		503	711	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	179	581	1	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.33	2		582	1029	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890221	72890221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752101890	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	107	592	2	ENST00000325599.8:c.461G>A	p.Arg154Gln	p.R154Q	ENST00000325599	NM_018130.2	154	cGa/cAa	4/11	1	2	FACETS	0.573	0.512	0.637	0.573	0.512	0.637	SUBCLONAL	1	TRUE	1	0.33	2		594	1132	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484414	57484414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	63	492	0	ENST00000371085.3:c.595C>T	p.Arg199Cys	p.R199C	ENST00000371085	NM_000516.4	199	Cgc/Tgc	8/13	1	2	FACETS	0.436	0.376	0.501	0.436	0.376	0.501	SUBCLONAL	1	TRUE	1	0.33	2		492	876	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733279	40733279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201275244	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	107	389	0	ENST00000373198.4:c.3527G>A	p.Arg1176His	p.R1176H	ENST00000373198	NM_133170.3	1176	cGt/cAt	26/32	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.33	2		389	632	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	154	285	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.909	0.831	0.991	0.909	0.831	0.991	CLONAL	1	TRUE	1	0.33	2		285	1027	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	120	343	1	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.33	2		344	693	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188823	32188823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs8192585	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	126	527	2	ENST00000375023.3:c.731C>T	p.Ser244Leu	p.S244L	ENST00000375023	NM_004557.3	244	tCg/tTg	4/30	1	2	FACETS	0.975	0.884	1	0.975	0.884	1	CLONAL	1	TRUE	1	0.33	2		529	783	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104712	193104712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	81	402	0	ENST00000367435.3:c.416G>A	p.Arg139Gln	p.R139Q	ENST00000367435	NM_024529.4	139	cGa/cAa	5/17	1	2	FACETS	0.986	0.871	1	0.986	0.871	1	CLONAL	1	TRUE	1	0.33	2		402	498	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	60	285	0	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	1	2	FACETS	0.785	0.678	0.902	0.785	0.678	0.902	CLONAL	1	TRUE	1	0.33	2		285	463	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	137	455	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.33	2		455	786	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	57	299	1	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	2	FACETS	0.962	0.83	1	0.962	0.83	1	CLONAL	1	TRUE	1	0.33	2		300	359	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504401	8504401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757922864	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	45	383	0	ENST00000356435.5:c.1682G>A	p.Arg561Gln	p.R561Q	ENST00000356435		561	cGa/cAa	12/35	1	2	FACETS	0.489	0.41	0.576	0.489	0.41	0.576	SUBCLONAL	1	TRUE	1	0.33	2		383	558	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	222	642	1	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.33	2		643	1300	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343093	118343093	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs868934108	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	51	602	0	ENST00000534358.1:c.1219C>T	p.Arg407Ter	p.R407*	ENST00000534358	NM_005933.3	407	Cga/Tga	3/36	1	2	FACETS	0.624	0.531	0.727	0.624	0.531	0.727	SUBCLONAL	1	TRUE	1	0.33	2		602	495	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180232	38180232	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	61	548	0	ENST00000396334.3:c.80T>C	p.Val27Ala	p.V27A	ENST00000396334	NM_002468.4	27	gTc/gCc	1/5	1	2	FACETS	0.399	0.343	0.46	0.399	0.343	0.46	SUBCLONAL	1	TRUE	1	0.33	2		548	927	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171607	36171607	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1569008655	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	85	261	0	ENST00000300305.3:c.958C>T	p.Arg320Ter	p.R320*	ENST00000300305		320	Cga/Tga	7/8	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.33	2		261	473	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781467	135781467	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203537	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1306	273	844	3	ENST00000298552.3:c.1498C>T	p.Arg500Ter	p.R500*	ENST00000298552	NM_001162426.1	500	Cga/Tga	15/23	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.33	2		847	1579	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636143	28636143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371663652	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	97	597	0	ENST00000241453.7:c.229G>A	p.Glu77Lys	p.E77K	ENST00000241453	NM_004119.2	77	Gaa/Aaa	3/24	1	2	FACETS	0.561	0.499	0.628	0.561	0.499	0.628	SUBCLONAL	1	TRUE	1	0.33	2		597	1047	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984924	101984924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	99	294	1	ENST00000282441.5:c.371G>A	p.Arg124Gln	p.R124Q	ENST00000282441	NM_001130145.2	124	cGa/cAa	2/9	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.33	2		295	593	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117629975	117629975	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	131	480	0	ENST00000368508.3:c.6551G>T	p.Arg2184Ile	p.R2184I	ENST00000368508	NM_002944.2	2184	aGa/aTa	41/43	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.33	2		480	766	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941657	48941657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1060503077	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	45	384	0	ENST00000267163.4:c.967G>T	p.Glu323Ter	p.E323*	ENST00000267163	NM_000321.2	323	Gaa/Taa	10/27	1	2	FACETS	0.606	0.51	0.712	0.606	0.51	0.712	SUBCLONAL	1	TRUE	1	0.33	2		384	450	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545584	106545584	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142182764	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	74	429	2	ENST00000359195.3:c.3061C>T	p.Arg1021Cys	p.R1021C	ENST00000359195	NM_002649.2	1021	Cgt/Tgt	11/11	1	2	FACETS	0.527	0.46	0.599	0.527	0.46	0.599	SUBCLONAL	1	TRUE	1	0.33	2		431	851	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145543	61145543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767519747	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	74	434	0	ENST00000295025.8:c.655C>T	p.Arg219Cys	p.R219C	ENST00000295025	NM_002908.2	219	Cgt/Tgt	7/11	1	2	FACETS	0.612	0.535	0.695	0.612	0.535	0.695	SUBCLONAL	1	TRUE	1	0.33	2		434	733	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645156	67645156	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	49	558	3	ENST00000264010.4:c.421G>T	p.Glu141Ter	p.E141*	ENST00000264010	NM_006565.3	141	Gaa/Taa	3/12	1	2	FACETS	0.305	0.257	0.358	0.305	0.257	0.358	SUBCLONAL	1	TRUE	1	0.33	2		561	974	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252866	36252866	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs759068561	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	74	436	1	ENST00000300305.3:c.496C>T	p.Arg166Ter	p.R166*	ENST00000300305		166	Cga/Tga	4/8	1	2	FACETS	0.507	0.442	0.576	0.507	0.442	0.576	SUBCLONAL	1	TRUE	1	0.33	2		437	885	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280031	66280031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867811974	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	151	506	1	ENST00000273854.3:c.1658G>A	p.Arg553Gln	p.R553Q	ENST00000273854	NM_004439.5	553	cGa/cAa	7/18	1	2	FACETS	0.882	0.805	0.962	0.882	0.805	0.962	CLONAL	1	TRUE	1	0.33	2		507	1038	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46251038	46251038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1348905384	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	234	729	2	ENST00000371998.3:c.47G>A	p.Arg16Gln	p.R16Q	ENST00000371998		16	cGa/cAa	3/23	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.33	2		731	1412	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679547	86679547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	72	303	0	ENST00000274376.6:c.2708G>A	p.Arg903Gln	p.R903Q	ENST00000274376	NM_002890.2	903	cGa/cAa	21/25	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.33	2		303	428	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118361991	118361991	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1472952558	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	128	464	0	ENST00000534358.1:c.4777C>T	p.Arg1593Cys	p.R1593C	ENST00000534358	NM_005933.3	1593	Cgc/Tgc	14/36	1	2	FACETS	0.988	0.896	1	0.988	0.896	1	CLONAL	1	TRUE	1	0.33	2		464	785	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	148	554	0	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	1	2	FACETS	0.966	0.881	1	0.966	0.881	1	CLONAL	1	TRUE	1	0.33	2		554	929	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178095	56178095	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374455781	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	40	373	0	ENST00000399503.3:c.3068G>A	p.Arg1023His	p.R1023H	ENST00000399503	NM_005921.1	1023	cGc/cAc	14/20	1	2	FACETS	0.372	0.308	0.443	0.372	0.308	0.443	SUBCLONAL	1	TRUE	1	0.33	2		373	652	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487277	56487277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035001455	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	116	425	0	ENST00000267101.3:c.1423C>T	p.Arg475Trp	p.R475W	ENST00000267101	NM_001982.3	475	Cgg/Tgg	12/28	1	2	FACETS	0.884	0.797	0.977	0.884	0.797	0.977	CLONAL	1	TRUE	1	0.33	2		425	795	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719580	61719580	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	42	451	0	ENST00000401558.2:c.1603G>T	p.Asp535Tyr	p.D535Y	ENST00000401558	NM_003400.3	535	Gat/Tat	15/25	1	2	FACETS	0.38	0.316	0.451	0.38	0.316	0.451	SUBCLONAL	1	TRUE	1	0.33	2		451	670	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27093043	27093043	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	155	539	0	ENST00000324856.7:c.2974G>T	p.Glu992Ter	p.E992*	ENST00000324856	NM_006015.4	992	Gaa/Taa	10/20	1	2	FACETS	0.875	0.8	0.954	0.875	0.8	0.954	CLONAL	1	TRUE	1	0.33	2		539	1073	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685209	86685209	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	147	423	1	ENST00000274376.6:c.2926-1G>T		p.X976_splice	ENST00000274376	NM_002890.2	976			1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.33	2		424	858	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528490	29528490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343309278	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	134	597	0	ENST00000356175.3:c.1247G>A	p.Arg416Gln	p.R416Q	ENST00000356175	NM_000267.3	416	cGa/cAa	11/57	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.33	2		597	801	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746018	162746018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	109	520	1	ENST00000367921.3:c.2141G>A	p.Arg714Gln	p.R714Q	ENST00000367921	NM_006182.2	714	cGa/cAa	16/18	1	2	FACETS	0.72	0.646	0.799	0.72	0.646	0.799	SUBCLONAL	1	TRUE	1	0.33	2		521	917	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127911992	127911992	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1401828703	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1396	271	817	1	ENST00000373547.4:c.878G>A	p.Arg293His	p.R293H	ENST00000373547	NM_002721.4	293	cGt/cAt	7/7	1	2	FACETS	0.985	0.921	1	0.985	0.921	1	CLONAL	1	TRUE	1	0.33	2		818	1667	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480110	50480110	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376164103	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	107	386	0	ENST00000394963.4:c.344C>T	p.Ala115Val	p.A115V	ENST00000394963	NM_003076.4	115	gCg/gTg	2/13	1	2	FACETS	0.875	0.785	0.97	0.875	0.785	0.97	CLONAL	1	TRUE	1	0.33	2		386	741	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374403	81374403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372600489	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	164	451	0	ENST00000222390.5:c.659G>A	p.Arg220Gln	p.R220Q	ENST00000222390	NM_000601.4	220	cGa/cAa	6/18	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.33	2		451	837	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649000	86649000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755634472	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	85	365	0	ENST00000274376.6:c.1280G>A	p.Arg427Gln	p.R427Q	ENST00000274376	NM_002890.2	427	cGa/cAa	9/25	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.33	2		365	469	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344036	118344036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	63	441	1	ENST00000534358.1:c.2162G>A	p.Arg721Gln	p.R721Q	ENST00000534358	NM_005933.3	721	cGa/cAa	3/36	1	2	FACETS	0.6	0.519	0.689	0.6	0.519	0.689	SUBCLONAL	1	TRUE	1	0.33	2		442	636	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134988	41134988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	203	875	2	ENST00000379561.5:c.640C>T	p.Arg214Cys	p.R214C	ENST00000379561	NM_002015.3	214	Cgt/Tgt	2/3	1	2	FACETS	0.89	0.823	0.959	0.89	0.823	0.959	CLONAL	1	TRUE	1	0.33	2		877	1383	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494187	140494187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1158980679	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	170	676	1	ENST00000288602.6:c.1061G>A	p.Arg354Gln	p.R354Q	ENST00000288602	NM_004333.4	354	cGa/cAa	8/18	1	2	FACETS	0.9	0.826	0.977	0.9	0.826	0.977	CLONAL	1	TRUE	1	0.33	2		677	1145	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004278	29004278	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	188	506	1	ENST00000282397.4:c.1015C>T	p.Arg339Ter	p.R339*	ENST00000282397	NM_002019.4	339	Cga/Tga	8/30	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.33	2		507	995	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915952	127915952	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs865855853	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1320	101	793	1	ENST00000373547.4:c.529C>T	p.Arg177Ter	p.R177*	ENST00000373547	NM_002721.4	177	Cga/Tga	6/7	1	2	FACETS	0.431	0.383	0.482	0.431	0.383	0.482	SUBCLONAL	1	TRUE	1	0.33	2		794	1421	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405958	70405958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370887665	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	190	630	2	ENST00000373644.4:c.3472C>T	p.Arg1158Trp	p.R1158W	ENST00000373644	NM_030625.2	1158	Cgg/Tgg	4/12	1	2	FACETS	0.961	0.887	1	0.961	0.887	1	CLONAL	1	TRUE	1	0.33	2		632	1198	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951085	17951085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	198	558	0	ENST00000458235.1:c.1208G>A	p.Arg403His	p.R403H	ENST00000458235	NM_000215.3	403	cGc/cAc	9/24	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.33	2		558	1113	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745588	162745588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754868982	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	152	545	1	ENST00000367921.3:c.2003G>A	p.Arg668His	p.R668H	ENST00000367921	NM_006182.2	668	cGc/cAc	15/18	1	2	FACETS	0.859	0.785	0.938	0.859	0.785	0.938	CLONAL	1	TRUE	1	0.33	2		546	1072	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661035	227661035	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	68	409	0	ENST00000305123.5:c.2420C>A	p.Ser807Tyr	p.S807Y	ENST00000305123	NM_005544.2	807	tCt/tAt	1/2	1	2	FACETS	0.585	0.508	0.668	0.585	0.508	0.668	SUBCLONAL	1	TRUE	1	0.33	2		409	705	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955593	55955593	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs373654225	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	208	723	2	ENST00000263923.4:c.3352C>T	p.Arg1118Ter	p.R1118*	ENST00000263923	NM_002253.2	1118	Cga/Tga	25/30	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.33	2		725	1167	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319959	8319959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745582718	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	81	349	0	ENST00000356435.5:c.5542G>A	p.Val1848Ile	p.V1848I	ENST00000356435		1848	Gtt/Att	34/35	1	2	FACETS	0.611	0.537	0.69	0.611	0.537	0.69	SUBCLONAL	1	TRUE	1	0.33	2		349	804	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965761	25965761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377352572	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	53	543	0	ENST00000435504.4:c.3445C>T	p.Arg1149Cys	p.R1149C	ENST00000435504		1149	Cgt/Tgt	13/13	1	2	FACETS	0.363	0.309	0.424	0.363	0.309	0.424	SUBCLONAL	1	TRUE	1	0.33	2		543	884	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265323	152265323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866869178	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	71	462	0	ENST00000206249.3:c.776G>A	p.Arg259Gln	p.R259Q	ENST00000206249	NM_000125.3	259	cGa/cAa	4/8	1	2	FACETS	0.558	0.486	0.636	0.558	0.486	0.636	SUBCLONAL	1	TRUE	1	0.33	2		462	771	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461167	120461167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs983208690	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	43	375	0	ENST00000256646.2:c.5791C>T	p.Arg1931Cys	p.R1931C	ENST00000256646	NM_024408.3	1931	Cgc/Tgc	32/34	1	2	FACETS	0.393	0.328	0.466	0.393	0.328	0.466	SUBCLONAL	1	TRUE	1	0.33	2		375	663	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99454591	99454591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768988732	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	173	647	2	ENST00000268035.6:c.1510C>T	p.Arg504Cys	p.R504C	ENST00000268035	NM_000875.3	504	Cgc/Tgc	7/21	1	2	FACETS	0.858	0.788	0.931	0.858	0.788	0.931	CLONAL	1	TRUE	1	0.33	2		649	1222	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136804	55136804	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	109	432	2	ENST00000257290.5:c.1126C>T	p.Arg376Ter	p.R376*	ENST00000257290	NM_006206.4	376	Cga/Tga	8/23	1	2	FACETS	0.898	0.806	0.994	0.898	0.806	0.994	CLONAL	1	TRUE	1	0.33	2		434	736	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039372	47039372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	76	710	0	ENST00000377604.3:c.995G>A	p.Arg332His	p.R332H	ENST00000377604	NM_001204468.1	332	cGc/cAc	10/24	1	2	FACETS	0.394	0.344	0.448	0.394	0.344	0.448	SUBCLONAL	1	TRUE	1	0.33	2		710	1170	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672759	86672759	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	115	484	1	ENST00000274376.6:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000274376	NM_002890.2	749	cGa/cAa	17/25	1	2	FACETS	0.786	0.707	0.869	0.786	0.707	0.869	SUBCLONAL	1	TRUE	1	0.33	2		485	887	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78866640	78866640	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	52	384	0	ENST00000306801.3:c.2213C>A	p.Ser738Tyr	p.S738Y	ENST00000306801	NM_020761.2	738	tCt/tAt	19/34	1	2	FACETS	0.467	0.397	0.544	0.467	0.397	0.544	SUBCLONAL	1	TRUE	1	0.33	2		384	675	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958788	55958788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780764266	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	202	670	0	ENST00000263923.4:c.3065G>A	p.Arg1022Gln	p.R1022Q	ENST00000263923	NM_002253.2	1022	cGa/cAa	22/30	1	2	FACETS	0.946	0.875	1	0.946	0.875	1	CLONAL	1	TRUE	1	0.33	2		670	1294	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181425	185181425	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1435276633	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	258	615	0	ENST00000265026.3:c.1366C>T	p.Arg456Ter	p.R456*	ENST00000265026	NM_004721.4	456	Cga/Tga	8/14	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.33	2		615	1090	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595622	55595622	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	42	254	0	ENST00000288135.5:c.2112G>T	p.Lys704Asn	p.K704N	ENST00000288135	NM_000222.2	704	aaG/aaT	14/21	1	2	FACETS	0.593	0.496	0.701	0.593	0.496	0.701	SUBCLONAL	1	TRUE	1	0.33	2		254	429	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389107	31389107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749860839	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	95	564	1	ENST00000328111.2:c.2020G>A	p.Glu674Lys	p.E674K	ENST00000328111	NM_006892.3	674	Gaa/Aaa	19/23	1	2	FACETS	0.532	0.472	0.596	0.532	0.472	0.596	SUBCLONAL	1	TRUE	1	0.33	2		565	1082	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663406	67663406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775874494	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	179	548	1	ENST00000264010.4:c.1807C>T	p.Arg603Cys	p.R603C	ENST00000264010	NM_006565.3	603	Cgc/Tgc	10/12	1	2	FACETS	0.91	0.837	0.986	0.91	0.837	0.986	CLONAL	1	TRUE	1	0.33	2		549	1192	SUCCESS
FH	2271	MSKCC	GRCh37	1	241669390	241669390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772190176	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	186	420	2	ENST00000366560.3:c.817G>A	p.Ala273Thr	p.A273T	ENST00000366560	NM_000143.3	273	Gca/Aca	6/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.33	2		422	992	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715350	117715350	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1466068877	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	88	396	0	ENST00000368508.3:c.1139G>T	p.Arg380Ile	p.R380I	ENST00000368508	NM_002944.2	380	aGa/aTa	10/43	1	2	FACETS	0.918	0.815	1	0.918	0.815	1	CLONAL	1	TRUE	1	0.33	2		396	581	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521540	46521540	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	85	673	1	ENST00000262741.5:c.868G>T	p.Glu290Ter	p.E290*	ENST00000262741	NM_003629.3	290	Gaa/Taa	7/10	1	2	FACETS	0.442	0.389	0.499	0.442	0.389	0.499	SUBCLONAL	1	TRUE	1	0.33	2		674	1166	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115252323	115252323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs797045795	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	115	495	0	ENST00000369535.4:c.317C>T	p.Ser106Leu	p.S106L	ENST00000369535	NM_002524.4	106	tCg/tTg	4/7	1	2	FACETS	0.878	0.791	0.97	0.878	0.791	0.97	CLONAL	1	TRUE	1	0.33	2		495	794	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874197	155874197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375724784	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	92	582	0	ENST00000368323.3:c.334C>T	p.Arg112Cys	p.R112C	ENST00000368323	NM_006912.5	112	Cgt/Tgt	5/6	1	2	FACETS	0.476	0.422	0.535	0.476	0.422	0.535	SUBCLONAL	1	TRUE	1	0.33	2		582	1171	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851361	156851361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	146	566	1	ENST00000524377.1:c.2318G>A	p.Ser773Asn	p.S773N	ENST00000524377	NM_002529.3	773	aGc/aAc	17/17	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.33	2		567	857	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956135	175956135	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	163	564	0	ENST00000367669.3:c.2077G>T	p.Glu693Ter	p.E693*	ENST00000367669	NM_022457.5	693	Gaa/Taa	18/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.33	2		564	915	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518428	204518428	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	109	613	0	ENST00000367182.3:c.1091G>T	p.Arg364Ile	p.R364I	ENST00000367182	NM_001278516.1	364	aGa/aTa	11/11	1	2	FACETS	0.52	0.465	0.579	0.52	0.465	0.579	SUBCLONAL	1	TRUE	1	0.33	2		613	1270	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667423	241667423	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913122	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	233	766	3	ENST00000366560.3:c.1027C>T	p.Arg343Ter	p.R343*	ENST00000366560	NM_000143.3	343	Cga/Tga	7/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.33	2		769	1367	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450655	70450655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771857626	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1197	95	675	0	ENST00000373644.4:c.5495C>T	p.Ser1832Leu	p.S1832L	ENST00000373644	NM_030625.2	1832	tCg/tTg	12/12	1	2	FACETS	0.446	0.395	0.5	0.446	0.395	0.5	SUBCLONAL	1	TRUE	1	0.33	2		675	1292	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717613	89717613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	135	429	0	ENST00000371953.3:c.638C>T	p.Pro213Leu	p.P213L	ENST00000371953	NM_000314.4	213	cCt/cTt	7/9	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.33	2		429	714	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104375086	104375086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs36049457	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	86	553	0	ENST00000369902.3:c.1084C>T	p.Arg362Cys	p.R362C	ENST00000369902	NM_016169.3	362	Cgc/Tgc	9/12	1	2	FACETS	0.508	0.448	0.573	0.508	0.448	0.573	SUBCLONAL	1	TRUE	1	0.33	2		553	1025	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202472	67202472	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	96	629	0	ENST00000312629.5:c.1281C>A	p.Phe427Leu	p.F427L	ENST00000312629	NM_003952.2	427	ttC/ttA	15/15	1	2	FACETS	0.5	0.444	0.56	0.5	0.444	0.56	SUBCLONAL	1	TRUE	1	0.33	2		629	1163	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77070063	77070063	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	32	293	0	ENST00000356341.3:c.478-1G>T		p.X160_splice	ENST00000356341	NM_002576.4	160			1	2	FACETS	0.328	0.265	0.399	0.328	0.265	0.399	SUBCLONAL	1	TRUE	1	0.33	2		293	591	SUCCESS
EED	8726	MSKCC	GRCh37	11	85961435	85961435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	68	528	1	ENST00000263360.6:c.212G>A	p.Gly71Glu	p.G71E	ENST00000263360	NM_003797.3	71	gGa/gAa	2/12	1	2	FACETS	0.393	0.341	0.45	0.393	0.341	0.45	SUBCLONAL	1	TRUE	1	0.33	2		529	1048	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199881	108199881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881315	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	40	439	1	ENST00000278616.4:c.7223C>T	p.Ser2408Leu	p.S2408L	ENST00000278616	NM_000051.3	2408	tCg/tTg	49/63	1	2	FACETS	0.317	0.262	0.378	0.317	0.262	0.378	SUBCLONAL	1	TRUE	1	0.33	2		440	765	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149373	119149373	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	49	282	0	ENST00000264033.4:c.1381G>T	p.Glu461Ter	p.E461*	ENST00000264033	NM_005188.3	461	Gaa/Taa	9/16	1	2	FACETS	0.687	0.583	0.802	0.687	0.583	0.802	SUBCLONAL	1	TRUE	1	0.33	2		282	432	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402153	402153	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	212	762	0	ENST00000399788.2:c.4638G>T	p.Lys1546Asn	p.K1546N	ENST00000399788	NM_001042603.1	1546	aaG/aaT	27/28	1	2	FACETS	0.956	0.886	1	0.956	0.886	1	CLONAL	1	TRUE	1	0.33	2		762	1344	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1022573	1022573	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	86	516	0	ENST00000358495.3:c.1241A>C	p.Lys414Thr	p.K414T	ENST00000358495	NM_134424.2	414	aAa/aCa	12/12	1	2	FACETS	0.585	0.516	0.659	0.585	0.516	0.659	SUBCLONAL	1	TRUE	1	0.33	2		516	891	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023634	1023634	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	83	487	1	ENST00000358495.3:c.930G>T	p.Glu310Asp	p.E310D	ENST00000358495	NM_134424.2	310	gaG/gaT	10/12	1	2	FACETS	0.53	0.466	0.598	0.53	0.466	0.598	SUBCLONAL	1	TRUE	1	0.33	2		488	950	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18576934	18576934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765821860	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	114	584	3	ENST00000266497.5:c.2342G>A	p.Arg781His	p.R781H	ENST00000266497		781	cGc/cAc	16/31	1	2	FACETS	0.648	0.582	0.718	0.648	0.582	0.718	SUBCLONAL	1	TRUE	1	0.33	2		587	1067	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699320	18699320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	60	504	0	ENST00000266497.5:c.3421C>A	p.Leu1141Ile	p.L1141I	ENST00000266497		1141	Ctt/Att	24/31	1	2	FACETS	0.393	0.337	0.454	0.393	0.337	0.454	SUBCLONAL	1	TRUE	1	0.33	2		504	925	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800921	18800921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201612275	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	134	532	0	ENST00000266497.5:c.4297G>A	p.Asp1433Asn	p.D1433N	ENST00000266497		1433	Gat/Aat	31/31	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.33	2		532	723	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427368	49427368	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778477	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	54	458	1	ENST00000301067.7:c.11120G>A	p.Arg3707Gln	p.R3707Q	ENST00000301067	NM_003482.3	3707	cGa/cAa	39/54	1	2	FACETS	0.495	0.422	0.575	0.495	0.422	0.575	SUBCLONAL	1	TRUE	1	0.33	2		459	661	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438282	49438282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs192216625	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	64	465	0	ENST00000301067.7:c.4987G>A	p.Glu1663Lys	p.E1663K	ENST00000301067	NM_003482.3	1663	Gaa/Aaa	20/54	1	2	FACETS	0.528	0.457	0.606	0.528	0.457	0.606	SUBCLONAL	1	TRUE	1	0.33	2		465	734	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434071	121434071	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751761766	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	164	572	0	ENST00000257555.6:c.962G>A	p.Arg321His	p.R321H	ENST00000257555		321	cGc/cAc	5/10	1	2	FACETS	0.945	0.866	1	0.945	0.866	1	CLONAL	1	TRUE	1	0.33	2		572	1052	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28971153	28971153	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	85	511	0	ENST00000282397.4:c.1604G>A	p.Cys535Tyr	p.C535Y	ENST00000282397	NM_002019.4	535	tGc/tAc	12/30	1	2	FACETS	0.603	0.532	0.679	0.603	0.532	0.679	SUBCLONAL	1	TRUE	1	0.33	2		511	855	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32920979	32920979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358921	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	88	441	0	ENST00000380152.3:c.6953G>A	p.Arg2318Gln	p.R2318Q	ENST00000380152		2318	cGa/cAa	13/27	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.33	2		441	489	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134955	41134955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1472	117	909	1	ENST00000379561.5:c.673C>T	p.Arg225Cys	p.R225C	ENST00000379561	NM_002015.3	225	Cgt/Tgt	2/3	1	2	FACETS	0.446	0.4	0.495	0.446	0.4	0.495	SUBCLONAL	1	TRUE	1	0.33	2		910	1589	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345270	73345270	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	80	515	0	ENST00000377767.4:c.1619T>C	p.Val540Ala	p.V540A	ENST00000377767	NM_014953.3	540	gTt/gCt	12/21	1	2	FACETS	0.513	0.45	0.58	0.513	0.45	0.58	SUBCLONAL	1	TRUE	1	0.33	2		515	946	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504585	103504585	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747957305	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	84	511	1	ENST00000355739.4:c.206G>A	p.Arg69Gln	p.R69Q	ENST00000355739	NM_000123.3	69	cGa/cAa	2/15	1	2	FACETS	0.455	0.4	0.514	0.455	0.4	0.514	SUBCLONAL	1	TRUE	1	0.33	2		512	1119	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241535	105241535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	83	561	0	ENST00000349310.3:c.445G>A	p.Glu149Lys	p.E149K	ENST00000349310	NM_001014432.1	149	Gag/Aag	7/15	1	2	FACETS	0.494	0.434	0.558	0.494	0.434	0.558	SUBCLONAL	1	TRUE	1	0.33	2		561	1019	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988692	41988692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753241568	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	228	797	1	ENST00000219905.7:c.1484G>A	p.Arg495Gln	p.R495Q	ENST00000219905	NM_001164273.1	495	cGa/cAa	3/24	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.33	2		798	1361	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669573	88669573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	68	493	0	ENST00000360948.2:c.1325C>T	p.Ala442Val	p.A442V	ENST00000360948	NM_001012338.2	442	gCc/gTc	12/19	1	2	FACETS	0.45	0.39	0.515	0.45	0.39	0.515	SUBCLONAL	1	TRUE	1	0.33	2		493	916	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900366	3900366	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1199448193	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	145	538	0	ENST00000262367.5:c.730A>G	p.Thr244Ala	p.T244A	ENST00000262367	NM_004380.2	244	Acg/Gcg	2/31	1	2	FACETS	0.967	0.882	1	0.967	0.882	1	CLONAL	1	TRUE	1	0.33	2		538	909	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858317	9858317	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs796052554	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	113	444	1	ENST00000330684.3:c.3084G>T	p.Gln1028His	p.Q1028H	ENST00000330684	NM_001134407.1	1028	caG/caT	13/13	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.33	2		445	655	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934931	9934931	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	59	432	0	ENST00000330684.3:c.1359G>T	p.Lys453Asn	p.K453N	ENST00000330684	NM_001134407.1	453	aaG/aaT	6/13	1	2	FACETS	0.468	0.402	0.541	0.468	0.402	0.541	SUBCLONAL	1	TRUE	1	0.33	2		432	764	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828024	72828024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200701402	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1771	333	1005	1	ENST00000268489.5:c.8557G>A	p.Ala2853Thr	p.A2853T	ENST00000268489	NM_006885.3	2853	Gca/Aca	9/10	1	2	FACETS	0.959	0.903	1	0.959	0.903	1	CLONAL	1	TRUE	1	0.33	2		1006	2104	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982728	7982728	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	87	346	0	ENST00000319144.4:c.1057C>G	p.Pro353Ala	p.P353A	ENST00000319144	NM_001139.2	353	Ccc/Gcc	8/15	1	2	FACETS	0.93	0.825	1	0.93	0.825	1	CLONAL	1	TRUE	1	0.33	2		346	567	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16021309	16021309	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	192	614	0	ENST00000268712.3:c.1948A>C	p.Ile650Leu	p.I650L	ENST00000268712	NM_006311.3	650	Att/Ctt	18/46	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.33	2		614	1068	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559096	29559096	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	17	97	0	ENST00000356175.3:c.3203T>G	p.Leu1068Trp	p.L1068W	ENST00000356175	NM_000267.3	1068	tTg/tGg	25/57	1	2	FACETS	0.431	0.322	0.56	0.431	0.322	0.56	SUBCLONAL	1	TRUE	1	0.33	2		97	239	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435581	56435581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200166143	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	122	443	0	ENST00000407977.2:c.1556G>A	p.Arg519Gln	p.R519Q	ENST00000407977		519	cGa/cAa	9/10	1	2	FACETS	0.893	0.807	0.984	0.893	0.807	0.984	CLONAL	1	TRUE	1	0.33	2		443	828	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438277	56438277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1449453586	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	102	426	0	ENST00000407977.2:c.716C>T	p.Ala239Val	p.A239V	ENST00000407977		239	gCc/gTc	7/10	1	2	FACETS	0.853	0.763	0.948	0.853	0.763	0.948	CLONAL	1	TRUE	1	0.33	2		426	725	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56787223	56787223	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770637624	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	149	537	2	ENST00000337432.4:c.709C>T	p.Arg237Ter	p.R237*	ENST00000337432	NM_058216.2	237	Cga/Tga	5/9	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.33	2		539	812	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740436	58740436	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs769061997	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1195	222	778	1	ENST00000305921.3:c.1341G>T	p.Glu447Asp	p.E447D	ENST00000305921	NM_003620.3	447	gaG/gaT	6/6	1	2	FACETS	0.95	0.881	1	0.95	0.881	1	CLONAL	1	TRUE	1	0.33	2		779	1417	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821852	59821853	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	72	574	0	ENST00000259008.2:c.2197dup	p.Thr733AsnfsTer4	p.T733Nfs*4	ENST00000259008	NM_032043.2	733	aca/aAca	15/20	1	2	FACETS	0.43	0.375	0.491	0.43	0.375	0.491	SUBCLONAL	1	TRUE	1	0.33	2		574	1014	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609317	39609317	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	75	464	0	ENST00000262039.4:c.1619C>A	p.Ser540Tyr	p.S540Y	ENST00000262039	NM_002647.2	540	tCt/tAt	15/25	1	2	FACETS	0.45	0.393	0.511	0.45	0.393	0.511	SUBCLONAL	1	TRUE	1	0.33	2		464	1011	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56409145	56409145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1308397244	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	102	724	2	ENST00000348428.3:c.1652G>A	p.Arg551Gln	p.R551Q	ENST00000348428	NM_006785.3	551	cGa/cAa	14/17	1	2	FACETS	0.526	0.469	0.587	0.526	0.469	0.587	SUBCLONAL	1	TRUE	1	0.33	2		726	1176	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100016	11100016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749059769	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	354	553	2	ENST00000358026.2:c.1142G>A	p.Arg381Gln	p.R381Q	ENST00000358026	NM_001128849.1	381	cGa/cAa	7/36	1	2	FACETS	0.901	0.854	0.95	1	0.996	1	CLONAL	2	TRUE	1	0.33	2		555	1190	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299898	15299898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	91	588	1	ENST00000263388.2:c.1280G>A	p.Arg427His	p.R427H	ENST00000263388	NM_000435.2	427	cGc/cAc	8/33	1	2	FACETS	0.525	0.465	0.59	0.525	0.465	0.59	SUBCLONAL	1	TRUE	1	0.33	2		589	1050	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355353	15355353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201062276	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	44	211	0	ENST00000263377.2:c.2270C>T	p.Pro757Leu	p.P757L	ENST00000263377	NM_058243.2	757	cCg/cTg	13/20	1	2	FACETS	0.821	0.691	0.963	0.821	0.691	0.963	CLONAL	1	TRUE	1	0.33	2		211	325	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948796	17948796	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201972084	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	208	649	1	ENST00000458235.1:c.1646G>A	p.Arg549Gln	p.R549Q	ENST00000458235	NM_000215.3	549	cGa/cAa	12/24	1	2	FACETS	0.962	0.891	1	0.962	0.891	1	CLONAL	1	TRUE	1	0.33	2		650	1310	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765472	41765472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775504685	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	104	528	1	ENST00000301178.4:c.2348C>T	p.Ser783Leu	p.S783L	ENST00000301178	NM_021913.4	783	tCg/tTg	20/20	1	2	FACETS	0.546	0.488	0.609	0.546	0.488	0.609	SUBCLONAL	1	TRUE	1	0.33	2		529	1154	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52722946	52722946	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	129	506	0	ENST00000322088.6:c.1131C>A	p.Cys377Ter	p.C377*	ENST00000322088	NM_014225.5	377	tgC/tgA	10/15	1	2	FACETS	0.819	0.741	0.9	0.819	0.741	0.9	CLONAL	1	TRUE	1	0.33	2		506	955	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940480	29940480	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	82	550	0	ENST00000389048.3:c.751G>T	p.Asp251Tyr	p.D251Y	ENST00000389048	NM_004304.4	251	Gac/Tac	2/29	1	2	FACETS	0.494	0.434	0.558	0.494	0.434	0.558	SUBCLONAL	1	TRUE	1	0.33	2		550	1006	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693811	47693811	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	103	472	1	ENST00000233146.2:c.1525A>G	p.Lys509Glu	p.K509E	ENST00000233146	NM_000251.2	509	Aaa/Gaa	10/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.33	2		473	571	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921773	111921773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765527733	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	186	574	0	ENST00000393256.3:c.562C>T	p.Arg188Cys	p.R188C	ENST00000393256	NM_006538.4	188	Cgt/Tgt	4/4	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.33	2		574	1068	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136264	202136264	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	144	511	2	ENST00000358485.4:c.508G>T	p.Glu170Ter	p.E170*	ENST00000358485	NM_001080125.1	170	Gaa/Taa	3/9	1	2	FACETS	0.917	0.835	1	0.917	0.835	1	CLONAL	1	TRUE	1	0.33	2		513	952	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378322	225378322	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	49	513	0	ENST00000264414.4:c.573G>T	p.Met191Ile	p.M191I	ENST00000264414	NM_003590.4	191	atG/atT	5/16	1	2	FACETS	0.357	0.302	0.419	0.357	0.302	0.419	SUBCLONAL	1	TRUE	1	0.33	2		513	831	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31381366	31381366	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369336236	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	72	374	0	ENST00000328111.2:c.1091G>A	p.Arg364His	p.R364H	ENST00000328111	NM_006892.3	364	cGt/cAt	10/23	1	2	FACETS	0.595	0.519	0.677	0.595	0.519	0.677	SUBCLONAL	1	TRUE	1	0.33	2		374	733	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36028692	36028692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763438144	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	66	506	1	ENST00000358208.4:c.1034G>A	p.Ser345Asn	p.S345N	ENST00000358208		345	aGc/aAc	8/12	1	2	FACETS	0.483	0.418	0.553	0.483	0.418	0.553	SUBCLONAL	1	TRUE	1	0.33	2		507	829	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513235	44513235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1294151325	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	50	296	0	ENST00000291552.4:c.700C>T	p.Arg234Cys	p.R234C	ENST00000291552	NM_006758.2	234	Cgt/Tgt	8/8	1	2	FACETS	0.505	0.428	0.59	0.505	0.428	0.59	SUBCLONAL	1	TRUE	1	0.33	2		296	600	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553266	41553266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759315982	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	162	556	1	ENST00000263253.7:c.3355G>A	p.Asp1119Asn	p.D1119N	ENST00000263253	NM_001429.3	1119	Gat/Aat	18/31	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.33	2		557	957	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164267	47164267	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	35	433	0	ENST00000409792.3:c.1859G>A	p.Arg620Gln	p.R620Q	ENST00000409792	NM_014159.6	620	cGa/cAa	3/21	1	2	FACETS	0.391	0.319	0.471	0.391	0.319	0.471	SUBCLONAL	1	TRUE	1	0.33	2		433	543	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165275	47165275	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	58	452	0	ENST00000409792.3:c.851C>A	p.Ser284Tyr	p.S284Y	ENST00000409792	NM_014159.6	284	tCc/tAc	3/21	1	2	FACETS	0.537	0.461	0.621	0.537	0.461	0.621	SUBCLONAL	1	TRUE	1	0.33	2		452	654	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933635	49933635	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs781000755	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1251	267	921	0	ENST00000296474.3:c.2642A>C	p.Lys881Thr	p.K881T	ENST00000296474	NM_002447.2	881	aAg/aCg	10/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.33	2		921	1518	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71008475	71008475	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	239	678	0	ENST00000318789.4:c.1957A>G	p.Thr653Ala	p.T653A	ENST00000318789	NM_032682.5	653	Aca/Gca	21/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.33	2		678	1249	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247523	71247523	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	73	351	0	ENST00000318789.4:c.10G>T	p.Glu4Ter	p.E4*	ENST00000318789	NM_032682.5	4	Gaa/Taa	6/21	1	2	FACETS	0.636	0.555	0.722	0.636	0.555	0.722	SUBCLONAL	1	TRUE	1	0.33	2		351	696	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521758	89521758	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	85	374	0	ENST00000336596.2:c.2835G>T	p.Lys945Asn	p.K945N	ENST00000336596	NM_005233.5	945	aaG/aaT	16/17	1	2	FACETS	0.859	0.76	0.964	0.859	0.76	0.964	CLONAL	1	TRUE	1	0.33	2		374	600	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670880	134670880	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	32	192	0	ENST00000398015.3:c.791G>T	p.Ser264Ile	p.S264I	ENST00000398015	NM_004441.4	264	aGc/aTc	3/16	1	2	FACETS	0.574	0.466	0.695	0.574	0.466	0.695	SUBCLONAL	1	TRUE	1	0.33	2		192	338	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880917	134880917	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	86	501	0	ENST00000398015.3:c.1480G>A	p.Asp494Asn	p.D494N	ENST00000398015	NM_004441.4	494	Gat/Aat	7/16	1	2	FACETS	0.535	0.472	0.603	0.535	0.472	0.603	SUBCLONAL	1	TRUE	1	0.33	2		501	974	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176564	142176564	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	78	482	0	ENST00000350721.4:c.7537T>G	p.Phe2513Val	p.F2513V	ENST00000350721	NM_001184.3	2513	Ttt/Gtt	45/47	1	2	FACETS	0.524	0.459	0.594	0.524	0.459	0.594	SUBCLONAL	1	TRUE	1	0.33	2		482	902	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268413	142268413	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	43	405	0	ENST00000350721.4:c.3079G>T	p.Glu1027Ter	p.E1027*	ENST00000350721	NM_001184.3	1027	Gag/Tag	15/47	1	2	FACETS	0.503	0.421	0.595	0.503	0.421	0.595	SUBCLONAL	1	TRUE	1	0.33	2		405	518	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269072	142269072	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	178	472	0	ENST00000350721.4:c.2878C>T	p.Arg960Ter	p.R960*	ENST00000350721	NM_001184.3	960	Cga/Tga	14/47	1	2	FACETS	0.962	0.886	1	0.962	0.886	1	CLONAL	1	TRUE	1	0.33	2		472	1121	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181426	185181426	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1311413742	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	70	608	1	ENST00000265026.3:c.1367G>A	p.Arg456Gln	p.R456Q	ENST00000265026	NM_004721.4	456	cGa/cAa	8/14	1	2	FACETS	0.394	0.342	0.45	0.394	0.342	0.45	SUBCLONAL	1	TRUE	1	0.33	2		609	1078	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184733	185184733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	90	609	0	ENST00000265026.3:c.1625C>T	p.Ser542Phe	p.S542F	ENST00000265026	NM_004721.4	542	tCt/tTt	10/14	1	2	FACETS	0.463	0.409	0.521	0.463	0.409	0.521	SUBCLONAL	1	TRUE	1	0.33	2		609	1178	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140703	55140703	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs974033003	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	67	493	0	ENST00000257290.5:c.1564C>T	p.Arg522Cys	p.R522C	ENST00000257290	NM_006206.4	522	Cgt/Tgt	11/23	1	2	FACETS	0.402	0.348	0.461	0.402	0.348	0.461	SUBCLONAL	1	TRUE	1	0.33	2		493	1010	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161374	55161374	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	69	553	0	ENST00000257290.5:c.3205G>T	p.Asp1069Tyr	p.D1069Y	ENST00000257290	NM_006206.4	1069	Gac/Tac	23/23	1	2	FACETS	0.43	0.373	0.492	0.43	0.373	0.492	SUBCLONAL	1	TRUE	1	0.33	2		553	972	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197747	66197747	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	158	516	0	ENST00000273854.3:c.2952G>T	p.Glu984Asp	p.E984D	ENST00000273854	NM_004439.5	984	gaG/gaT	17/18	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.33	2		516	915	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233097	66233097	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	69	591	0	ENST00000273854.3:c.1902G>T	p.Lys634Asn	p.K634N	ENST00000273854	NM_004439.5	634	aaG/aaT	10/18	1	2	FACETS	0.425	0.369	0.486	0.425	0.369	0.486	SUBCLONAL	1	TRUE	1	0.33	2		591	984	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164733	106164733	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1373336171	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	123	296	0	ENST00000380013.4:c.3601C>T	p.Arg1201Cys	p.R1201C	ENST00000380013	NM_001127208.2	1201	Cgc/Tgc	6/11	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.33	2		296	709	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258980	153258980	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	143	476	0	ENST00000281708.4:c.835G>T	p.Asp279Tyr	p.D279Y	ENST00000281708	NM_033632.3	279	Gac/Tac	5/12	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.33	2		476	798	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629096	187629096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776913986	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	70	504	0	ENST00000441802.2:c.1886C>T	p.Ser629Leu	p.S629L	ENST00000441802	NM_005245.3	629	tCg/tTg	2/27	1	2	FACETS	0.513	0.446	0.585	0.513	0.446	0.585	SUBCLONAL	1	TRUE	1	0.33	2		504	827	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180548	56180548	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	58	417	0	ENST00000399503.3:c.3877G>T	p.Glu1293Ter	p.E1293*	ENST00000399503	NM_005921.1	1293	Gaa/Taa	16/20	1	2	FACETS	0.58	0.498	0.67	0.58	0.498	0.67	SUBCLONAL	1	TRUE	1	0.33	2		417	606	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754304	57754304	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	147	487	3	ENST00000274289.3:c.547C>T	p.Arg183Ter	p.R183*	ENST00000274289	NM_006622.3	183	Cga/Tga	4/14	1	2	FACETS	0.913	0.833	0.997	0.913	0.833	0.997	CLONAL	1	TRUE	1	0.33	2		490	976	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629093	86629093	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	36	371	0	ENST00000274376.6:c.838G>A	p.Asp280Asn	p.D280N	ENST00000274376	NM_002890.2	280	Gat/Aat	4/25	1	2	FACETS	0.425	0.349	0.511	0.425	0.349	0.511	SUBCLONAL	1	TRUE	1	0.33	2		371	513	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502701	149502701	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	157	614	0	ENST00000261799.4:c.2087A>G	p.Asn696Ser	p.N696S	ENST00000261799	NM_002609.3	696	aAc/aGc	15/23	1	2	FACETS	0.87	0.795	0.948	0.87	0.795	0.948	CLONAL	1	TRUE	1	0.33	2		614	1094	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401700	401700	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200311468	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	111	432	4	ENST00000380956.4:c.1022C>T	p.Ala341Val	p.A341V	ENST00000380956	NM_001195286.1	341	gCg/gTg	7/9	1	2	FACETS	0.912	0.82	1	0.912	0.82	1	CLONAL	1	TRUE	1	0.33	2		436	738	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271338	26271339	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1822	130	1212	2	ENST00000305910.3:c.274_275delinsTT	p.Ala92Phe	p.A92F	ENST00000305910	NM_003534.2	92	GCc/TTc	1/1	1	2	FACETS	0.404	0.364	0.446	0.404	0.364	0.446	SUBCLONAL	1	TRUE	1	0.33	2		1214	1952	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287579	33287579	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	148	408	0	ENST00000374542.5:c.1518G>T	p.Lys506Asn	p.K506N	ENST00000374542	NM_001141970.1	506	aaG/aaT	6/8	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.33	2		408	805	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287941	33287941	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756719415	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	63	525	1	ENST00000374542.5:c.1312G>A	p.Glu438Lys	p.E438K	ENST00000374542	NM_001141970.1	438	Gaa/Aaa	5/8	1	2	FACETS	0.423	0.365	0.487	0.423	0.365	0.487	SUBCLONAL	1	TRUE	1	0.33	2		526	902	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117680970	117680970	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	99	297	0	ENST00000368508.3:c.3648+2T>C		p.X1216_splice	ENST00000368508	NM_002944.2	1216			1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.33	2		297	592	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519313	137519313	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	153	515	0	ENST00000367739.4:c.1325G>A	p.Gly442Glu	p.G442E	ENST00000367739	NM_000416.2	442	gGa/gAa	7/7	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.33	2		515	869	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983101	149983101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1165460532	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	81	599	0	ENST00000253339.5:c.3157G>A	p.Glu1053Lys	p.E1053K	ENST00000253339		1053	Gag/Aag	7/7	1	2	FACETS	0.663	0.584	0.749	0.663	0.584	0.749	SUBCLONAL	1	TRUE	1	0.33	2		599	740	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265335	152265335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	61	521	0	ENST00000206249.3:c.788G>A	p.Arg263Lys	p.R263K	ENST00000206249	NM_000125.3	263	aGa/aAa	4/8	1	2	FACETS	0.424	0.365	0.489	0.424	0.365	0.489	SUBCLONAL	1	TRUE	1	0.33	2		521	871	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521884	157521884	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760245781	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	130	441	2	ENST00000346085.5:c.4156C>T	p.Arg1386Cys	p.R1386C	ENST00000346085	NM_020732.3	1386	Cgc/Tgc	18/20	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.33	2		443	761	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979507	2979507	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1198	101	708	0	ENST00000396946.4:c.740G>T	p.Arg247Ile	p.R247I	ENST00000396946	NM_032415.4	247	aGa/aTa	6/25	1	2	FACETS	0.471	0.42	0.527	0.471	0.42	0.527	SUBCLONAL	1	TRUE	1	0.33	2		708	1299	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381520	81381520	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	81	650	1	ENST00000222390.5:c.541C>T	p.Arg181Ter	p.R181*	ENST00000222390	NM_000601.4	181	Cga/Tga	5/18	1	2	FACETS	0.381	0.334	0.431	0.381	0.334	0.431	SUBCLONAL	1	TRUE	1	0.33	2		651	1289	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523560	148523560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	53	386	1	ENST00000320356.2:c.893G>A	p.Arg298His	p.R298H	ENST00000320356	NM_004456.4	298	cGt/cAt	8/20	1	2	FACETS	0.499	0.425	0.58	0.499	0.425	0.58	SUBCLONAL	1	TRUE	1	0.33	2		387	644	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841908	151841908	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	81	568	0	ENST00000262189.6:c.14233G>T	p.Glu4745Ter	p.E4745*	ENST00000262189	NM_170606.2	4745	Gaa/Taa	55/59	1	2	FACETS	0.512	0.45	0.58	0.512	0.45	0.58	SUBCLONAL	1	TRUE	1	0.33	2		568	958	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012382	152012382	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	156	514	0	ENST00000262189.6:c.431C>A	p.Ser144Tyr	p.S144Y	ENST00000262189	NM_170606.2	144	tCc/tAc	4/59	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.33	2		514	827	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345830	152345830	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1364	146	786	2	ENST00000359321.1:c.740C>A	p.Ser247Tyr	p.S247Y	ENST00000359321	NM_005431.1	247	tCt/tAt	3/3	1	2	FACETS	0.586	0.533	0.642	0.586	0.533	0.642	SUBCLONAL	1	TRUE	1	0.33	2		788	1510	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90990534	90990534	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	110	339	0	ENST00000265433.3:c.498T>G	p.Ile166Met	p.I166M	ENST00000265433	NM_002485.4	166	atT/atG	5/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.33	2		339	505	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238329	98238329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1485556285	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	121	448	1	ENST00000331920.6:c.1715C>T	p.Ala572Val	p.A572V	ENST00000331920	NM_000264.3	572	gCg/gTg	12/24	1	2	FACETS	0.829	0.748	0.914	0.829	0.748	0.914	CLONAL	1	TRUE	1	0.33	2		449	885	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98244310	98244310	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1266754583	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	155	492	0	ENST00000331920.6:c.667C>A	p.Leu223Ile	p.L223I	ENST00000331920	NM_000264.3	223	Ctt/Att	5/24	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.33	2		492	928	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250101	110250101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1169388589	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	104	446	0	ENST00000374672.4:c.574G>A	p.Asp192Asn	p.D192N	ENST00000374672	NM_004235.4	192	Gac/Aac	3/5	1	2	FACETS	0.897	0.803	0.995	0.897	0.803	0.995	CLONAL	1	TRUE	1	0.33	2		446	703	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781074	135781074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1307	252	874	1	ENST00000298552.3:c.1891G>A	p.Ala631Thr	p.A631T	ENST00000298552	NM_001162426.1	631	Gca/Aca	15/23	1	2	FACETS	0.98	0.914	1	0.98	0.914	1	CLONAL	1	TRUE	1	0.33	2		875	1559	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781090	135781090	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1243	246	890	0	ENST00000298552.3:c.1875G>T	p.Glu625Asp	p.E625D	ENST00000298552	NM_001162426.1	625	gaG/gaT	15/23	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.33	2		890	1489	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782130	135782130	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	88	573	0	ENST00000298552.3:c.1426G>T	p.Asp476Tyr	p.D476Y	ENST00000298552	NM_001162426.1	476	Gat/Tat	14/23	1	2	FACETS	0.476	0.42	0.536	0.476	0.42	0.536	SUBCLONAL	1	TRUE	1	0.33	2		573	1121	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15822322	15822322	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	215	681	0	ENST00000307771.7:c.399+2T>C		p.X133_splice	ENST00000307771	NM_005089.3	133			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.33	2		681	1247	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224432	53224432	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	203	747	1	ENST00000375401.3:c.3281C>A	p.Ser1094Tyr	p.S1094Y	ENST00000375401	NM_004187.3	1094	tCt/tAt	21/26	1	2	FACETS	0.914	0.845	0.986	0.914	0.845	0.986	CLONAL	1	TRUE	1	0.33	2		748	1346	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228235	53228235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781895754	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1198	199	751	1	ENST00000375401.3:c.2167G>A	p.Asp723Asn	p.D723N	ENST00000375401	NM_004187.3	723	Gac/Aac	15/26	1	2	FACETS	0.863	0.798	0.932	0.863	0.798	0.932	CLONAL	1	TRUE	1	0.33	2		752	1397	SUCCESS
AR	367	MSKCC	GRCh37	X	66765598	66765598	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	89	656	1	ENST00000374690.3:c.610G>A	p.Glu204Lys	p.E204K	ENST00000374690	NM_000044.3	204	Gaa/Aaa	1/8	1	2	FACETS	0.499	0.441	0.561	0.499	0.441	0.561	SUBCLONAL	1	TRUE	1	0.33	2		657	1082	SUCCESS
AR	367	MSKCC	GRCh37	X	66765778	66765778	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1240	131	769	0	ENST00000374690.3:c.790C>T	p.Arg264Trp	p.R264W	ENST00000374690	NM_000044.3	264	Cgg/Tgg	1/8	1	2	FACETS	0.579	0.524	0.638	0.579	0.524	0.638	SUBCLONAL	1	TRUE	1	0.33	2		769	1371	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344096	70344096	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1450	98	878	0	ENST00000374080.3:c.1832A>G	p.His611Arg	p.H611R	ENST00000374080		611	cAc/cGc	13/45	1	2	FACETS	0.384	0.341	0.43	0.384	0.341	0.43	SUBCLONAL	1	TRUE	1	0.33	2		878	1548	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351950	70351950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223696	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1264	103	758	2	ENST00000374080.3:c.4147G>A	p.Ala1383Thr	p.A1383T	ENST00000374080		1383	Gcc/Acc	30/45	1	2	FACETS	0.457	0.407	0.51	0.457	0.407	0.51	SUBCLONAL	1	TRUE	1	0.33	2		760	1367	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845323	76845323	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	63	684	1	ENST00000373344.5:c.6198T>A	p.Asp2066Glu	p.D2066E	ENST00000373344	NM_000489.3	2066	gaT/gaA	27/35	1	2	FACETS	0.461	0.397	0.53	0.461	0.397	0.53	SUBCLONAL	1	TRUE	1	0.33	2		685	829	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872199	76872199	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	43	466	3	ENST00000373344.5:c.5449-1G>T		p.X1817_splice	ENST00000373344	NM_000489.3	1817			1	2	FACETS	0.494	0.413	0.583	0.494	0.413	0.583	SUBCLONAL	1	TRUE	1	0.33	2		469	528	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918870	76918870	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1202	232	796	0	ENST00000373344.5:c.4120+1G>A		p.X1374_splice	ENST00000373344	NM_000489.3	1374			1	2	FACETS	0.981	0.912	1	0.981	0.912	1	CLONAL	1	TRUE	1	0.33	2		796	1434	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617589	100617589	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	77	642	0	ENST00000308731.7:c.480A>C	p.Lys160Asn	p.K160N	ENST00000308731	NM_000061.2	160	aaA/aaC	6/19	1	2	FACETS	0.402	0.351	0.457	0.402	0.351	0.457	SUBCLONAL	1	TRUE	1	0.33	2		642	1161	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211837	123211837	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	129	651	2	ENST00000218089.9:c.2704G>T	p.Glu902Ter	p.E902*	ENST00000218089	NM_001042749.1	902	Gaa/Taa	27/35	1	2	FACETS	0.934	0.847	1	0.934	0.847	1	CLONAL	1	TRUE	1	0.33	2		653	837	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245236	41245237	+	missense_variant	Missense_Mutation	DNP	AA	AA	GG	novel	NA	P-0013537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	71	609	0	ENST00000357654.3:c.2311_2312delinsCC	p.Leu771Pro	p.L771P	ENST00000357654	NM_007294.3	771	TTg/CCg	10/23	1	2	FACETS	0.446	0.388	0.509	0.446	0.388	0.509	SUBCLONAL	1	TRUE	1	0.33	2		609	965	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0013556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	184	196	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.782	0.726	0.84	0.782	0.726	0.84	SUBCLONAL	1	TRUE	1	0.809708609162522	2		196	581	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0013556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	641	485	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.809708609162522	3	FACETS	0.904	0.875	0.934	0.904	0.875	0.934	CLONAL	2	TRUE	1	0.809708609162522	3		485	1230	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0013556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	230	651	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	1	2	FACETS	0.848	0.795	0.902	0.848	0.795	0.902	CLONAL	1	TRUE	1	0.809708609162522	2		651	670	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038902	12038902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159945	NA	P-0013556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	626	900	0	ENST00000396373.4:c.1195C>T	p.Arg399Cys	p.R399C	ENST00000396373	NM_001987.4	399	Cgc/Tgc	7/8	0.809708609162522	3	FACETS	0.916	0.886	0.946	0.916	0.886	0.946	CLONAL	2	TRUE	1	0.809708609162522	3		900	1186	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056244	27056244	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	230	670	1	ENST00000324856.7:c.1240G>T	p.Gly414Ter	p.G414*	ENST00000324856	NM_006015.4	414	Gga/Tga	2/20	1	2	FACETS	0.823	0.771	0.877	0.823	0.771	0.877	CLONAL	1	TRUE	1	0.809708609162522	2		671	690	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998838	100998838	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	360	905	0	ENST00000325455.5:c.964C>T	p.Gln322Ter	p.Q322*	ENST00000325455	NM_001202474.3	322	Cag/Tag	1/8	1	2	FACETS	0.867	0.823	0.911	0.867	0.823	0.911	CLONAL	1	TRUE	1	0.809708609162522	2		905	1026	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590839	95590839	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555374756	NA	P-0013556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	297	709	1	ENST00000393063.1:c.1070C>T	p.Ala357Val	p.A357V	ENST00000393063	NM_030621.3	357	gCa/gTa	9/28	1	2	FACETS	0.964	0.912	1	0.964	0.912	1	CLONAL	1	TRUE	1	0.809708609162522	2		710	761	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	41	435	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.876	1	1	0.971	1	CLONAL	2	TRUE	1	0.234491414124357	2		435	168	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813280	89813280	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437529209	NA	P-0013571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	21	885	2	ENST00000389301.3:c.3367G>A	p.Gly1123Arg	p.G1123R	ENST00000389301	NM_000135.2	1123	Gga/Aga	34/43	0.234491414124357	1	FACETS	0.925	0.717	1	0.925	0.717	1	CLONAL	1	TRUE	0	0.234491414124357	1		887	171	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954049	32954049	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs80359167	NA	P-0013571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	11	739	1	ENST00000380152.3:c.9116C>T	p.Pro3039Leu	p.P3039L	ENST00000380152		3039	cCg/cTg	23/27	1	2	FACETS	0.751	0.522	1	0.751	0.522	1	CLONAL	1	TRUE	1	0.234491414124357	2		740	125	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440720	56440721	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0013571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	17	969	0	ENST00000407977.2:c.497dup	p.Asn167Ter	p.N167*	ENST00000407977		166	ggt/ggGt	5/10	0.234491414124357	1	FACETS	1	0.754	1	1	0.754	1	CLONAL	1	TRUE	0	0.234491414124357	1		969	128	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573573	48573573	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	22	643	1	ENST00000342988.3:c.157G>T	p.Glu53Ter	p.E53*	ENST00000342988	NM_005359.5	53	Gaa/Taa	2/12	1	2	FACETS	0.869	0.685	1	1	0.938	1	CLONAL	2	TRUE	1	0.234491414124357	2		644	108	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599902	10599902	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	10	1076	0	ENST00000171111.5:c.1674del	p.Ile559SerfsTer36	p.I559Sfs*36	ENST00000171111	NM_203500.1	558	ggG/gg	5/6	1	2	FACETS	0.426	0.289	0.6	0.426	0.289	0.6	SUBCLONAL	1	TRUE	1	0.234491414124357	2		1076	200	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1268701	1268701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748503447	NA	P-0013571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	12	806	1	ENST00000310581.5:c.2516C>T	p.Thr839Met	p.T839M	ENST00000310581	NM_198253.2	839	aCg/aTg	9/16	1	2	FACETS	0.758	0.536	1	0.758	0.536	1	CLONAL	1	TRUE	1	0.234491414124357	2		807	135	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685275	86685276	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTGCATGAGAT	novel	NA	P-0013571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	15	530	0	ENST00000274376.6:c.2996_3006dup	p.Val1003MetfsTer25	p.V1003Mfs*25	ENST00000274376	NM_002890.2	997	-/TTGCATGAGAT	24/25	1	2	FACETS	0.847	0.623	1	0.847	0.623	1	CLONAL	1	TRUE	1	0.234491414124357	2		530	151	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0013599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	261	650	7	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.995	0.941	1	0.995	0.941	1	CLONAL	1	TRUE	1	0.885855790290576	2		657	592	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0013599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	335	183	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.922	0.896	0.947	1	0.997	1	CLONAL	2	TRUE	1	0.885855790290576	2		183	410	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141498	11141498	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	258	649	1	ENST00000358026.2:c.3480del	p.Leu1161SerfsTer3	p.L1161Sfs*3	ENST00000358026	NM_001128849.1	1159	Ggg/gg	25/36	1	2	FACETS	0.956	0.903	1	0.956	0.903	1	CLONAL	1	TRUE	1	0.885855790290576	2		650	609	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097084	11097084	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	240	578	0	ENST00000358026.2:c.579del	p.Gln194SerfsTer109	p.Q194Sfs*109	ENST00000358026	NM_001128849.1	192	aGg/ag	4/36	1	2	FACETS	0.994	0.937	1	0.994	0.937	1	CLONAL	1	TRUE	1	0.885855790290576	2		578	545	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560464	95560464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	147	272	0	ENST00000393063.1:c.5125G>A	p.Asp1709Asn	p.D1709N	ENST00000393063	NM_030621.3	1709	Gat/Aat	25/28	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.885855790290576	2		272	325	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668619	52668619	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	297	505	0	ENST00000394830.3:c.1300C>T	p.Arg434Ter	p.R434*	ENST00000394830	NM_018313.4	434	Cga/Tga	12/30	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.885855790290576	2		505	612	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426836	121426836	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1364708195	NA	P-0013599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	209	421	0	ENST00000257555.6:c.526+1G>A		p.X176_splice	ENST00000257555		176			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.885855790290576	2		421	442	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546324	46546324	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	412	664	3	ENST00000262741.5:c.205del	p.Asp69IlefsTer7	p.D69Ifs*7	ENST00000262741	NM_003629.3	69	Gat/at	2/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.885855790290576	2		667	903	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120529603	120529603	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782452794	NA	P-0013599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	71	663	2	ENST00000256646.2:c.854G>A	p.Arg285His	p.R285H	ENST00000256646	NM_024408.3	285	cGc/cAc	5/34	1	2	FACETS	0.188	0.164	0.215	0.188	0.164	0.215	SUBCLONAL	1	TRUE	1	0.885855790290576	2		665	851	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107230	193107230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	56	501	1	ENST00000367435.3:c.439C>T	p.Arg147Cys	p.R147C	ENST00000367435	NM_024529.4	147	Cgc/Tgc	6/17	0.86190473376647	3	FACETS	0.201	0.171	0.233	0.1	0.085	0.117	SUBCLONAL	1	TRUE	1	0.885855790290576	3		502	909	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420416	49420417	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	213	511	0	ENST00000301067.7:c.15332dup	p.Asn5111LysfsTer27	p.N5111Kfs*27	ENST00000301067	NM_003482.3	5111	aat/aaAt	48/54	1	2	FACETS	0.945	0.887	1	0.945	0.887	1	CLONAL	1	TRUE	1	0.885855790290576	2		511	509	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434889	110434889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1021457672	NA	P-0013599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	305	619	2	ENST00000375856.3:c.3512G>A	p.Arg1171His	p.R1171H	ENST00000375856	NM_003749.2	1171	cGc/cAc	1/2	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.885855790290576	2		621	674	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562840	95562840	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	209	490	0	ENST00000393063.1:c.4417del	p.Ser1473GlnfsTer17	p.S1473Qfs*17	ENST00000393063	NM_030621.3	1473	Tca/ca	24/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.885855790290576	2		490	449	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572556	95572556	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1354833117	NA	P-0013599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	185	283	0	ENST00000393063.1:c.2809C>T	p.Arg937Cys	p.R937C	ENST00000393063	NM_030621.3	937	Cgc/Tgc	19/28	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.885855790290576	2		283	360	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67459124	67459125	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1291288543	NA	P-0013599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	342	750	0	ENST00000327367.4:c.545dup	p.Gly183TrpfsTer5	p.G183Wfs*5	ENST00000327367	NM_005902.3	180	-/C	4/9	1	2	FACETS	0.964	0.917	1	0.964	0.917	1	CLONAL	1	TRUE	1	0.885855790290576	2		750	801	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99454645	99454645	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	351	674	0	ENST00000268035.6:c.1564A>G	p.Ser522Gly	p.S522G	ENST00000268035	NM_000875.3	522	Agc/Ggc	7/21	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.885855790290576	2		674	725	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774735	73774736	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0013599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	161	149	0	ENST00000254810.4:c.351_352del	p.Arg117SerfsTer30	p.R117Sfs*30	ENST00000254810	NM_005324.3	117	agAGtc/agtc	4/4	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.885855790290576	2		149	297	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295773	15295773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1248140755	NA	P-0013599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	266	734	3	ENST00000263388.2:c.2354G>A	p.Arg785His	p.R785H	ENST00000263388	NM_000435.2	785	cGc/cAc	15/33	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.885855790290576	2		737	575	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021124	31021124	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748644253	NA	P-0013599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	245	594	1	ENST00000375687.4:c.1123G>A	p.Val375Met	p.V375M	ENST00000375687	NM_015338.5	375	Gtg/Atg	12/13	1	2	FACETS	0.964	0.909	1	0.964	0.909	1	CLONAL	1	TRUE	1	0.885855790290576	2		595	574	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21272469	21272469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	317	812	1	ENST00000354336.3:c.247G>A	p.Ala83Thr	p.A83T	ENST00000354336	NM_005207.3	83	Gcc/Acc	1/3	1	2	FACETS	0.994	0.945	1	0.994	0.945	1	CLONAL	1	TRUE	1	0.885855790290576	2		813	720	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221663	22221663	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs868522804	NA	P-0013599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	157	257	0	ENST00000215832.6:c.68C>A	p.Pro23Gln	p.P23Q	ENST00000215832	NM_002745.4	23	cCg/cAg	1/9	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.885855790290576	2		257	323	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442566	52442566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553646022	NA	P-0013599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	212	440	0	ENST00000460680.1:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000460680	NM_004656.3	60	cGa/cAa	4/17	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.885855790290576	2		440	478	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117650588	117650588	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	507	941	0	ENST00000368508.3:c.5270G>A	p.Gly1757Asp	p.G1757D	ENST00000368508	NM_002944.2	1757	gGc/gAc	32/43	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.885855790290576	2		941	1123	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230923	53230923	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	242	498	0	ENST00000375401.3:c.1870C>T	p.Pro624Ser	p.P624S	ENST00000375401	NM_004187.3	624	Cct/Tct	14/26	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.885855790290576	2		498	484	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937603	76937603	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	289	639	0	ENST00000373344.5:c.3145del	p.Ile1049Ter	p.I1049*	ENST00000373344	NM_000489.3	1049	Ata/ta	9/35	1	2	FACETS	0.859	0.812	0.906	0.859	0.812	0.906	CLONAL	1	TRUE	1	0.885855790290576	2		639	760	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249002	55249003	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCGTGGA	rs397517109	NA	P-0013600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	198	449	0	ENST00000275493.2:c.2303_2311dup	p.Ser768_Asp770dup	p.S768_D770dup	ENST00000275493	NM_005228.3	768	gcc/gcCAGCGTGGAc	20/28	0.298113351253217	4	FACETS	0.937	0.869	1	0.625	0.579	0.672	CLONAL	2	TRUE	1	0.306380805407254	4		449	901	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0013600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	94	295	2	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.249064916550427	2	FACETS	1	0.96	1	0.58	0.517	0.646	CLONAL	1	TRUE	0	0.306380805407254	2		297	529	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622206	1622206	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	189	640	1	ENST00000344749.5:c.669del	p.Ser224GlnfsTer60	p.S224Qfs*60	ENST00000344749	NM_001136139.2	223	ccC/cc	10/19	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.306380805407254	2		641	871	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131895034	131895034	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	111	354	2	ENST00000265335.6:c.188G>T	p.Gly63Val	p.G63V	ENST00000265335		63	gGa/gTa	2/25	0.249064916550427	2	FACETS	0.852	0.772	0.936	0.852	0.772	0.936	CLONAL	2	TRUE	0	0.306380805407254	2		356	425	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0013617-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	117	331	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.29	2		331	794	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0013617-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	162	396	0	ENST00000346208.3:c.1002_1003dup	p.Asp335GlyfsTer21	p.D335Gfs*21	ENST00000346208		333	-/GG	5/6	1	2	FACETS	0.964	0.883	1	0.964	0.883	1	CLONAL	1	TRUE	1	0.29	2		396	1159	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249002	55249003	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCGTGGA	rs397517109	NA	P-0013708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	128	449	0	ENST00000275493.2:c.2303_2311dup	p.Ser768_Asp770dup	p.S768_D770dup	ENST00000275493	NM_005228.3	768	gcc/gcCAGCGTGGAc	20/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.31	2		449	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0013744-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	436	293	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.908276763092115	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.914538168362189	1		295	493	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430839	78430839	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013744-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	124	331	0	ENST00000370768.2:c.550G>A	p.Gly184Arg	p.G184R	ENST00000370768	NM_003902.3	184	Gga/Aga	8/20	0.914538168362189	1	FACETS	0.282	0.256	0.309	0.282	0.256	0.309	SUBCLONAL	1	TRUE	0	0.914538168362189	1		331	522	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622451	28622451	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013744-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	28	330	0	ENST00000241453.7:c.1166C>A	p.Ser389Ter	p.S389*	ENST00000241453	NM_004119.2	389	tCa/tAa	9/24	0.914538168362189	1	FACETS	0.066	0.052	0.082	0.066	0.052	0.082	SUBCLONAL	1	TRUE	0	0.914538168362189	1		330	503	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022276	31022277	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGCCCACTTACCAGATATGCCCCCGGATCATCCCCACCACGGAGTC	novel	NA	P-0013744-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1439	387	485	0	ENST00000375687.4:c.1763_1809dup	p.Cys605ProfsTer114	p.C605Pfs*114	ENST00000375687	NM_015338.5	587	-/CAGCCCACTTACCAGATATGCCCCCGGATCATCCCCACCACGGAGTC	13/13	1	2	FACETS	0.463	0.439	0.489	0.463	0.439	0.489	SUBCLONAL	1	TRUE	1	0.914538168362189	2		485	1826	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929198	44929199	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0013744-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	37	280	0	ENST00000377967.4:c.2298_2299del	p.Ser767Ter	p.S767*	ENST00000377967	NM_021140.2	766	gaTTct/gact	17/29	1	1	FACETS	0.06	0.049	0.073	0.06	0.049	0.073	SUBCLONAL	1	TRUE	0	0.914538168362189	1		280	729	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	375	819	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	0.409203528053668	4	FACETS	1	0.99	1	1	0.99	1	INDETERMINATE	2	TRUE	2	0.760500230347171	4		819	777	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882019	NA	P-0013882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	143	574	0	ENST00000269305.4:c.455dup	p.Pro153AlafsTer28	p.P153Afs*28	ENST00000269305	NM_001126112.2	152	ccg/ccCg	5/11	0.490691782295836	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	0	0.490691782295836	1		574	358	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138103	2138103	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	13	807	1	ENST00000219476.3:c.5123T>A	p.Leu1708Gln	p.L1708Q	ENST00000219476	NM_000548.3	1708	cTg/cAg	40/42	0.490691782295836	0	FACETS	0.12	0.086	0.163			1	SUBCLONAL	1	FALSE	0	0.490691782295836	0		808	224	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0013923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	64	393	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.16	2		393	641	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090086	37090086	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	164	607	0	ENST00000231790.2:c.1975del	p.Arg659AspfsTer2	p.R659Dfs*2	ENST00000231790	NM_000249.3	659	Cga/ga	17/19	0.157958775941598	2	FACETS	0.93	0.853	1	0.93	0.853	1	CLONAL	2	TRUE	0	0.16	2		607	1102	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	43	555	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.66	0.55	0.782	0.66	0.55	0.782	SUBCLONAL	1	TRUE	1	0.16	2		555	815	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952086	178952086	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	38	537	0	ENST00000263967.3:c.3141T>A	p.His1047Gln	p.H1047Q	ENST00000263967	NM_006218.2	1047	caT/caA	21/21	1	2	FACETS	0.539	0.443	0.646	0.539	0.443	0.646	SUBCLONAL	1	TRUE	1	0.16	2		537	882	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678783	52678784	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	121	520	0	ENST00000394830.3:c.835dup	p.Ile279AsnfsTer8	p.I279Nfs*8	ENST00000394830	NM_018313.4	279	ata/aAta	9/30	0.157958775941598	2	FACETS	0.818	0.738	0.902	0.818	0.738	0.902	CLONAL	2	TRUE	0	0.16	2		520	925	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405953	157405954	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1554294674	NA	P-0013923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	53	629	0	ENST00000346085.5:c.2201dup	p.Ser736IlefsTer27	p.S736Ifs*27	ENST00000346085	NM_020732.3	732	ccg/ccGg	6/20	1	2	FACETS	0.689	0.586	0.804	0.689	0.586	0.804	SUBCLONAL	1	TRUE	1	0.16	2		629	961	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041046	112041046	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762290632	NA	P-0013923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1435	82	797	4	ENST00000368678.4:c.209C>T	p.Ser70Leu	p.S70L	ENST00000368678		70	tCg/tTg	3/13	1	2	FACETS	0.676	0.593	0.765	0.676	0.593	0.765	SUBCLONAL	1	TRUE	1	0.16	2		801	1517	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46527624	46527625	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs766789504	NA	P-0013923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1351	100	771	0	ENST00000262741.5:c.740_741del	p.Glu247GlyfsTer3	p.E247Gfs*3	ENST00000262741	NM_003629.3	247	gAG/g	6/10	1	2	FACETS	0.861	0.767	0.963	0.861	0.767	0.963	CLONAL	1	TRUE	1	0.16	2		771	1451	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120460316	120460316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	78	689	1	ENST00000256646.2:c.5999G>A	p.Gly2000Glu	p.G2000E	ENST00000256646	NM_024408.3	2000	gGg/gAg	33/34	1	2	FACETS	0.918	0.804	1	0.918	0.804	1	CLONAL	1	TRUE	1	0.16	2		690	1062	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856077	111856077	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	70	512	0	ENST00000341259.2:c.128G>T	p.Arg43Leu	p.R43L	ENST00000341259	NM_005475.2	43	cGc/cTc	2/8	1	2	FACETS	0.939	0.817	1	0.939	0.817	1	CLONAL	1	TRUE	1	0.16	2		512	932	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792470	33792470	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1196766447	NA	P-0013923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	73	641	0	ENST00000498907.2:c.851A>C	p.Glu284Ala	p.E284A	ENST00000498907	NM_004364.3	284	gAg/gCg	1/1	1	2	FACETS	0.847	0.739	0.965	0.847	0.739	0.965	CLONAL	1	TRUE	1	0.16	2		641	1077	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564569	41564569	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1184	65	624	0	ENST00000263253.7:c.3994del	p.Thr1332ProfsTer4	p.T1332Pfs*4	ENST00000263253	NM_001429.3	1331	Aaa/aa	24/31	1	2	FACETS	0.651	0.562	0.748	0.651	0.562	0.748	SUBCLONAL	1	TRUE	1	0.16	2		624	1249	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713867	30713868	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0013923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	109	600	0	ENST00000295754.5:c.1193_1194del	p.Phe398TrpfsTer14	p.F398Wfs*14	ENST00000295754	NM_003242.5	398	TTt/t	4/7	0.157958775941598	2	FACETS	1	0.976	1	0.658	0.589	0.73	CLONAL	1	TRUE	0	0.16	2		600	1036	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670452	134670452	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	62	505	0	ENST00000398015.3:c.363T>G	p.Ile121Met	p.I121M	ENST00000398015	NM_004441.4	121	atT/atG	3/16	0.157958775941598	2	FACETS	0.931	0.803	1	0.466	0.401	0.536	CLONAL	1	TRUE	0	0.16	2		505	832	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146616	185146616	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	106	501	0	ENST00000265026.3:c.247A>G	p.Ser83Gly	p.S83G	ENST00000265026	NM_004721.4	83	Agc/Ggc	2/14	1	2	FACETS	0.752	0.673	0.836	1	0.982	1	SUBCLONAL	2	TRUE	1	0.16	2		501	881	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591071	67591073	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0013923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	60	408	0	ENST00000274335.5:c.1665_1667del	p.Glu555_Tyr556delinsAsp	p.E555_Y556delinsD	ENST00000274335		555	gAGTat/gat	12/15	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.16	2		408	676	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527970	157527970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1377079397	NA	P-0013923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	33	302	0	ENST00000346085.5:c.5695G>A	p.Glu1899Lys	p.E1899K	ENST00000346085	NM_020732.3	1899	Gaa/Aaa	20/20	1	2	FACETS	0.743	0.604	0.901	0.743	0.604	0.901	CLONAL	1	TRUE	1	0.16	2		302	555	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874341	151874341	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	76	605	0	ENST00000262189.6:c.8197G>T	p.Asp2733Tyr	p.D2733Y	ENST00000262189	NM_170606.2	2733	Gat/Tat	38/59	1	2	FACETS	0.981	0.859	1	0.981	0.859	1	CLONAL	1	TRUE	1	0.16	2		605	968	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0013955-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	107	324	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	FALSE	1	0.56061962703868	2		324	375	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0013955-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	61	313	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	0.818	0.728	0.91	1	0.979	1	CLONAL	2	FALSE	1	0.56061962703868	2		313	133	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578440	7578440	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0013955-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	119	378	0	ENST00000269305.4:c.490A>T	p.Lys164Ter	p.K164*	ENST00000269305	NM_001126112.2	164	Aag/Tag	5/11	0.56061962703868	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	0	0.56061962703868	1		378	260	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11999013	11999013	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0013955-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	97	272	0	ENST00000353533.5:c.513+2T>C		p.X171_splice	ENST00000353533	NM_003010.3	171			0.56061962703868	1	FACETS	0.947	0.858	1	0.947	0.858	1	CLONAL	1	FALSE	0	0.56061962703868	1		272	263	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245447	153245447	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013955-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	279	315	1	ENST00000281708.4:c.1744T>C	p.Ser582Pro	p.S582P	ENST00000281708	NM_033632.3	582	Tcg/Ccg	11/12	0.45262845583408	3	FACETS	1	0.992	1	0.815	0.776	0.855	CLONAL	2	FALSE	0	0.56061962703868	3		316	521	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023217	27023218	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCTA	novel	NA	P-0013955-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	52	189	0	ENST00000324856.7:c.324_328dup	p.Arg110ThrfsTer6	p.R110Tfs*6	ENST00000324856	NM_006015.4	108	ggc/ggCCCTAc	1/20	1	2	FACETS	0.692	0.594	0.798	0.692	0.594	0.798	SUBCLONAL	1	FALSE	1	0.56061962703868	2		189	268	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834548	156834548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763164402	NA	P-0013955-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	157	549	1	ENST00000524377.1:c.316G>A	p.Val106Met	p.V106M	ENST00000524377	NM_002529.3	106	Gtg/Atg	3/17	0.341860393966479	1	FACETS	0.92	0.851	0.991	0.92	0.851	0.991	CLONAL	1	FALSE	0	0.56061962703868	1		550	438	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205726	108205726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064795034	NA	P-0013955-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	87	276	0	ENST00000278616.4:c.8041G>A	p.Val2681Met	p.V2681M	ENST00000278616	NM_000051.3	2681	Gtg/Atg	55/63	1	2	FACETS	0.808	0.72	0.901	0.808	0.72	0.901	CLONAL	1	FALSE	1	0.56061962703868	2		276	384	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862771	9862771	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013955-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	163	448	0	ENST00000330684.3:c.2532G>T	p.Lys844Asn	p.K844N	ENST00000330684	NM_001134407.1	844	aaG/aaT	12/13	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.56061962703868	2		448	514	SUCCESS
APC	324	MSKCC	GRCh37	5	112175164	112175165	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACGAC	novel	NA	P-0013955-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	59	162	0	ENST00000257430.4:c.3876_3880dup	p.Gln1294ArgfsTer13	p.Q1294Rfs*13	ENST00000257430	NM_000038.5	1291	-/ACGAC	16/16	0.56061962703868	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	0	0.56061962703868	1		162	137	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577563	7577563	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1567549584	NA	P-0014061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	62	588	1	ENST00000269305.4:c.718A>G	p.Ser240Gly	p.S240G	ENST00000269305	NM_001126112.2	240	Agt/Ggt	7/11	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.157753209183664	2		589	677	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105709	27105709	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	44	540	1	ENST00000324856.7:c.5320G>T	p.Glu1774Ter	p.E1774*	ENST00000324856	NM_006015.4	1774	Gaa/Taa	20/20	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.157753209183664	2		541	481	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431363	49431386	+	inframe_deletion	In_Frame_Del	DEL	TCCTTCTTCTCATGCTCCAACAGG	TCCTTCTTCTCATGCTCCAACAGG	-	novel	NA	P-0014061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	54	334	0	ENST00000301067.7:c.9753_9776del	p.Asp3251_Lys3258del	p.D3251_K3258del	ENST00000301067	NM_003482.3	3251	gaCCTGTTGGAGCATGAGAAGAAGGAg/gag	34/54	0.157753209183664	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	0	0.157753209183664	2		334	301	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608255	28608255	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	55	749	0	ENST00000241453.7:c.1801C>A	p.Leu601Ile	p.L601I	ENST00000241453	NM_004119.2	601	Ctc/Atc	14/24	1	2	FACETS	0.776	0.662	0.902	0.776	0.662	0.902	CLONAL	1	TRUE	1	0.157753209183664	2		749	898	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001320	29001320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	48	576	0	ENST00000282397.4:c.1412G>T	p.Cys471Phe	p.C471F	ENST00000282397	NM_002019.4	471	tGt/tTt	10/30	1	2	FACETS	0.881	0.743	1	0.881	0.743	1	CLONAL	1	TRUE	1	0.157753209183664	2		576	691	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476242	88476243	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0014061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	52	606	0	ENST00000360948.2:c.1889_1889+1delinsTT		p.X630_splice	ENST00000360948	NM_001012338.2	630		15/19	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.157753209183664	2		606	614	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041474	14041474	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	37	367	2	ENST00000311895.7:c.2021G>T	p.Gly674Val	p.G674V	ENST00000311895	NM_005236.2	674	gGc/gTc	11/11	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.157753209183664	2		369	404	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028622	12028622	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	68	567	0	ENST00000353533.5:c.825A>G	p.Ile275Met	p.I275M	ENST00000353533	NM_003010.3	275	atA/atG	8/11	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.157753209183664	2		567	747	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679336	29679336	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	57	644	1	ENST00000356175.3:c.7456A>T	p.Thr2486Ser	p.T2486S	ENST00000356175	NM_000267.3	2486	Acc/Tcc	50/57	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.157753209183664	2		645	712	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207031	1207031	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	70	460	0	ENST00000326873.7:c.119G>T	p.Arg40Leu	p.R40L	ENST00000326873	NM_000455.4	40	cGc/cTc	1/10	1	2	FACETS	0.847	0.74	0.962	1	0.978	1	CLONAL	2	TRUE	1	0.157753209183664	2		460	524	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946770	17946770	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	75	647	0	ENST00000458235.1:c.1877A>T	p.Gln626Leu	p.Q626L	ENST00000458235	NM_000215.3	626	cAg/cTg	14/24	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.157753209183664	2		647	744	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143164	30143164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779147984	NA	P-0014061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	52	479	0	ENST00000389048.3:c.362G>A	p.Arg121Gln	p.R121Q	ENST00000389048	NM_004304.4	121	cGg/cAg	1/29	1	2	FACETS	0.884	0.755	1	1	0.972	1	CLONAL	2	TRUE	1	0.157753209183664	2		479	373	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273179	198273179	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1242817545	NA	P-0014061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	72	817	0	ENST00000335508.6:c.1031G>T	p.Ser344Ile	p.S344I	ENST00000335508	NM_012433.2	344	aGt/aTt	8/25	1	2	FACETS	0.87	0.758	0.992	0.87	0.758	0.992	CLONAL	1	TRUE	1	0.157753209183664	2		817	1049	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955946	55955946	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	44	635	0	ENST00000263923.4:c.3216G>T	p.Met1072Ile	p.M1072I	ENST00000263923	NM_002253.2	1072	atG/atT	24/30	1	2	FACETS	0.711	0.594	0.84	0.711	0.594	0.84	SUBCLONAL	1	TRUE	1	0.157753209183664	2		635	785	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282703	1282703	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1272053273	NA	P-0014061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	189	530	0	ENST00000310581.5:c.1610G>A	p.Arg537His	p.R537H	ENST00000310581	NM_198253.2	537	cGt/cAt	3/16	0.157753209183664	5	FACETS	0.888	0.822	0.957	0.888	0.822	0.957	CLONAL	4	TRUE	1	0.157753209183664	5		530	834	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294669	1294669	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	17	133	0	ENST00000310581.5:c.332C>T	p.Pro111Leu	p.P111L	ENST00000310581	NM_198253.2	111	cCc/cTc	2/16	0.157753209183664	5	FACETS	1	0.854	1	0.306	0.228	0.397	CLONAL	1	TRUE	1	0.157753209183664	5		133	218	SUCCESS
APC	324	MSKCC	GRCh37	5	112174995	112174995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554085244	NA	P-0014061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	26	385	0	ENST00000257430.4:c.3704C>T	p.Ser1235Phe	p.S1235F	ENST00000257430	NM_000038.5	1235	tCt/tTt	16/16	1	2	FACETS	0.657	0.519	0.815	0.657	0.519	0.815	SUBCLONAL	1	TRUE	1	0.157753209183664	2		385	502	SUCCESS
BTK	695	MSKCC	GRCh37	X	100624986	100624987	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	45	662	0	ENST00000308731.7:c.390_391insA	p.Val131SerfsTer7	p.V131Sfs*7	ENST00000308731	NM_000061.2	130	-/A	5/19	1	2	FACETS	0.666	0.558	0.786	0.666	0.558	0.786	SUBCLONAL	1	TRUE	1	0.157753209183664	2		662	857	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0014095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	38	524	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.106	0.087	0.128	0.106	0.087	0.128	SUBCLONAL	1	TRUE	1	1	2		524	716	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0014095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	25	485	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.112	0.088	0.14	0.112	0.088	0.14	SUBCLONAL	1	TRUE	1	1	2		485	446	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720805	89720808	+	frameshift_variant	Frame_Shift_Del	DEL	CTTT	CTTT	-	rs398123330	NA	P-0014095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	14	184	2	ENST00000371953.3:c.956_959del	p.Thr319LysfsTer24	p.T319Kfs*24	ENST00000371953	NM_000314.4	319	aCTTTa/aa	8/9	0.161895928601389	3	FACETS	0.29	0.21	0.384	0.145	0.105	0.192	INDETERMINATE	1	TRUE	1	1	3		186	145	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249017	55249018	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCA	rs1554350381	NA	P-0014095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	57	442	1	ENST00000275493.2:c.2317_2319dup	p.His773dup	p.H773dup	ENST00000275493	NM_005228.3	773	ccc/ccCCAc	20/28	0.161895928601389	3	FACETS	0.211	0.181	0.245	0.106	0.09	0.123	INDETERMINATE	1	TRUE	1	1	3		443	809	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711874	89711874	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs786204862	NA	P-0014095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	73	416	0	ENST00000371953.3:c.493-1G>A		p.X165_splice	ENST00000371953	NM_000314.4	165			0.161895928601389	3	FACETS	0.607	0.534	0.684	0.303	0.267	0.342	INDETERMINATE	1	TRUE	1	1	3		416	361	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370985	55370985	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	43	352	0	ENST00000297316.4:c.287C>G	p.Ala96Gly	p.A96G	ENST00000297316	NM_022454.3	96	gCc/gGc	1/2	1	2	FACETS	0.141	0.118	0.168	0.141	0.118	0.168	SUBCLONAL	1	TRUE	1	1	2		352	608	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591078	67591089	+	inframe_deletion	In_Frame_Del	DEL	AGAAATTGACAA	AGAAATTGACAA	-	novel	NA	P-0014095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	40	343	0	ENST00000274335.5:c.1672_1683del	p.Glu558_Lys561del	p.E558_K561del	ENST00000274335		557	cgAGAAATTGACAAa/cga	12/15	1	2	FACETS	0.243	0.202	0.288	0.243	0.202	0.288	SUBCLONAL	1	TRUE	1	1	2		343	329	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223604	53223604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	55	474	0	ENST00000375401.3:c.3755G>A	p.Arg1252His	p.R1252H	ENST00000375401	NM_004187.3	1252	cGc/cAc	23/26	1	2	FACETS	0.179	0.153	0.208	0.179	0.153	0.208	SUBCLONAL	1	TRUE	1	1	2		474	613	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588933	67588933	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	AT	novel	NA	P-0014095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	26	318	0	ENST00000274335.5:c.1024delinsAT	p.Glu342IlefsTer4	p.E342Ifs*4	ENST00000274335		342	Gaa/ATaa	8/15	1	2	FACETS	0.157	0.124	0.195	0.157	0.124	0.195	SUBCLONAL	1	TRUE	1	1	2		318	331	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0014116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	43	245	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.271845180489984	2		245	213	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0014116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	32	250	2	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.271845180489984	3	FACETS	1	0.854	1	1	0.854	1	CLONAL	2	TRUE	1	0.271845180489984	3		252	129	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0014116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	47	596	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.271845180489984	2		596	248	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0014116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	18	210	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.597	0.45	0.769	0.597	0.45	0.769	SUBCLONAL	1	TRUE	1	0.271845180489984	2		210	222	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0014116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	47	574	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	1	2	FACETS	0.971	0.822	1	0.971	0.822	1	CLONAL	1	TRUE	1	0.271845180489984	2		574	356	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042266	6042266	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs587781913	NA	P-0014116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	39	455	0	ENST00000265849.7:c.355G>A	p.Asp119Asn	p.D119N	ENST00000265849	NM_000535.5	119	Gat/Aat	5/15	0.143570626726035	3	FACETS	1	0.933	1	0.627	0.523	0.741	INDETERMINATE	1	TRUE	1	0.271845180489984	3		455	260	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577129	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519986	NA	P-0014116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	64	762	1	ENST00000269305.4:c.809T>G	p.Phe270Cys	p.F270C	ENST00000269305	NM_001126112.2	270	tTt/tGt	8/11	0.271845180489984	1	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	0	0.271845180489984	1		763	398	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892310	9892310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	35	333	0	ENST00000330684.3:c.2180C>T	p.Ala727Val	p.A727V	ENST00000330684	NM_001134407.1	727	gCt/gTt	11/13	1	2	FACETS	0.943	0.777	1	0.943	0.777	1	CLONAL	1	TRUE	1	0.271845180489984	2		333	273	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244487	5244487	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	21	164	0	ENST00000357368.4:c.995C>T	p.Pro332Leu	p.P332L	ENST00000357368	NM_002850.3	332	cCc/cTc	11/38	0.205724255960062	2	FACETS	0.835	0.647	1	0.418	0.323	0.526	CLONAL	1	TRUE	0	0.271845180489984	2		164	185	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551061	41551061	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	98	916	0	ENST00000263253.7:c.3205G>A	p.Asp1069Asn	p.D1069N	ENST00000263253	NM_001429.3	1069	Gat/Aat	17/31	0.271845180489984	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.271845180489984	1		916	425	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521763	89521763	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	33	334	0	ENST00000336596.2:c.2840C>G	p.Ser947Cys	p.S947C	ENST00000336596	NM_005233.5	947	tCc/tGc	16/17	0.271845180489984	3	FACETS	1	0.928	1	0.641	0.526	0.769	CLONAL	1	TRUE	1	0.271845180489984	3		334	215	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175217	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0014116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	36	299	0	ENST00000257430.4:c.3929dup	p.Ile1311AspfsTer4	p.I1311Dfs*4	ENST00000257430	NM_000038.5	1309	gaa/gAaa	16/16	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.271845180489984	2		299	210	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0014207-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	118	412	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	0.182737002302678	2	FACETS	1	0.985	1	0.749	0.681	0.821	INDETERMINATE	1	TRUE	0	0.359497567007004	2		412	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0014207-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	345	680	0	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	0.359497567007004	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.359497567007004	1		680	1198	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624936	9624936	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014207-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	56	366	0	ENST00000353224.5:c.41C>A	p.Pro14Gln	p.P14Q	ENST00000353224	NM_177990.2	14	cCg/cAg	3/10	0.359497567007004	1	FACETS	0.456	0.39	0.527	0.456	0.39	0.527	SUBCLONAL	1	TRUE	0	0.359497567007004	1		366	561	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057853	27057853	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014207-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	334	853	3	ENST00000324856.7:c.1561C>T	p.Gln521Ter	p.Q521*	ENST00000324856	NM_006015.4	521	Cag/Tag	3/20	0.359497567007004	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.359497567007004	1		856	1198	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120431	70120431	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014207-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1535	293	1067	2	ENST00000245479.2:c.1437del	p.Ile480SerfsTer43	p.I480Sfs*43	ENST00000245479	NM_000346.3	478	aCc/ac	3/3	0.23510241510923	3	FACETS	1	0.969	1	0.526	0.493	0.56	CLONAL	1	TRUE	1	0.359497567007004	3		1069	1828	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218454	1218454	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014207-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	286	680	0	ENST00000326873.7:c.329T>A	p.Val110Asp	p.V110D	ENST00000326873	NM_000455.4	110	gTc/gAc	2/10	0.359497567007004	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.359497567007004	1		680	1040	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602584	10602584	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014207-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	273	538	0	ENST00000171111.5:c.994G>C	p.Gly332Arg	p.G332R	ENST00000171111	NM_203500.1	332	Ggc/Cgc	3/6	0.359497567007004	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.359497567007004	1		538	880	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620683	52620683	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014207-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	220	294	1	ENST00000394830.3:c.3070G>T	p.Glu1024Ter	p.E1024*	ENST00000394830	NM_018313.4	1024	Gaa/Taa	21/30	0.353179822865562	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.359497567007004	2		295	606	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52621452	52621452	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs1469145695	NA	P-0014207-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	384	584	0	ENST00000394830.3:c.2966-1G>C		p.X989_splice	ENST00000394830	NM_018313.4	989			0.353179822865562	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.359497567007004	2		584	954	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968209	68968209	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014207-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	141	763	0	ENST00000288368.4:c.1238G>C	p.Ser413Thr	p.S413T	ENST00000288368	NM_024870.2	413	aGc/aCc	10/40	1	2	FACETS	0.725	0.659	0.794	0.725	0.659	0.794	SUBCLONAL	1	TRUE	1	0.359497567007004	2		763	1082	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061079	38061080	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGGGTAGA	novel	NA	P-0014207-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	77	215	0	ENST00000250448.2:c.909_910insTCTACCCC	p.Ala305ThrfsTer19	p.A305Tfs*19	ENST00000250448	NM_004496.3	303	-/TCTACCCC	2/2	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.359497567007004	2		215	385	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347117	89347117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184729090	NA	P-0014207-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	115	496	0	ENST00000301030.4:c.5833G>A	p.Glu1945Lys	p.E1945K	ENST00000301030	NM_001256183.1	1945	Gag/Aag	9/13	1	2	FACETS	0.668	0.601	0.739	0.668	0.601	0.739	SUBCLONAL	1	TRUE	1	0.359497567007004	2		496	958	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864466	57864466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367789336	NA	P-0014223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	68	618	2	ENST00000228682.2:c.1943G>A	p.Arg648His	p.R648H	ENST00000228682	NM_005269.2	648	cGt/cAt	12/12	0.21651409827575	3	FACETS	0.71	0.616	0.813	0.355	0.308	0.407	SUBCLONAL	1	TRUE	1	0.22	3		620	966	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249016	55249017	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCCACG	rs397517114	NA	P-0014223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	135	523	0	ENST00000275493.2:c.2315_2320dup	p.His773_Val774insAlaHis	p.H773_V774insAH	ENST00000275493	NM_005228.3	772	ccc/cCCCACGcc	20/28	1	2	FACETS	0.751	0.683	0.823	1	0.986	1	SUBCLONAL	2	TRUE	1	0.22	2		523	817	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259089	153259089	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0014223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	14	198	0	ENST00000281708.4:c.727-1G>C		p.X243_splice	ENST00000281708	NM_033632.3	243			1	2	FACETS	0.493	0.356	0.659	0.493	0.356	0.659	SUBCLONAL	1	TRUE	1	0.22	2		198	258	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0014302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	567	389	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.607819374060793	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.607819374060793	1		390	910	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100358	27100359	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0014302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	484	712	0	ENST00000324856.7:c.4070_4071insCT	p.Gln1357HisfsTer125	p.Q1357Hfs*125	ENST00000324856	NM_006015.4	1357	cag/caCTg	17/20	0.369184310929704	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.607819374060793	1		712	871	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396582	396582	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0014302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	440	665	0	ENST00000262320.3:c.444C>G	p.Tyr148Ter	p.Y148*	ENST00000262320	NM_003502.3	148	taC/taG	2/11	0.591887021930856	2	FACETS	0.854	0.82	0.887	0.854	0.82	0.887	CLONAL	2	TRUE	0	0.607819374060793	2		665	848	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591889	48591889	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	384	512	0	ENST00000342988.3:c.1052A>G	p.Asp351Gly	p.D351G	ENST00000342988	NM_005359.5	351	gAt/gGt	9/12	0.607819374060793	2	FACETS	0.943	0.905	0.98	0.943	0.905	0.98	CLONAL	2	TRUE	0	0.607819374060793	2		512	670	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211749	5211749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759153530	NA	P-0014302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	401	725	0	ENST00000357368.4:c.5086C>T	p.Arg1696Cys	p.R1696C	ENST00000357368	NM_002850.3	1696	Cgc/Tgc	33/38	0.160811184866901	5	FACETS	0.988	0.939	1	0.658	0.626	0.691	INDETERMINATE	2	TRUE	2	0.607819374060793	5		725	1277	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260194	10260194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	524	690	1	ENST00000340748.4:c.2473C>T	p.Leu825Phe	p.L825F	ENST00000340748		825	Ctt/Ttt	25/40	0.160811184866901	5	FACETS	0.86	0.826	0.895	0.86	0.826	0.895	INDETERMINATE	3	TRUE	2	0.607819374060793	5		691	1277	SUCCESS
APC	324	MSKCC	GRCh37	5	112176011	112176011	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	258	416	0	ENST00000257430.4:c.4720A>G	p.Ile1574Val	p.I1574V	ENST00000257430	NM_000038.5	1574	Ata/Gta	16/16	0.197110868354699	4	FACETS	1	0.982	1	1	0.982	1	INDETERMINATE	2	TRUE	2	0.607819374060793	4		416	624	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979230	93979230	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	110	479	0	ENST00000369303.4:c.1598C>G	p.Ala533Gly	p.A533G	ENST00000369303	NM_004440.3	533	gCt/gGt	7/17	1	2	FACETS	0.76	0.687	0.837	0.76	0.687	0.837	SUBCLONAL	1	TRUE	1	0.607819374060793	2		479	476	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	196	437	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.533217239856643	2		437	658	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	158	426	0				ENST00000310581	NM_198253.2	-/1132			0.24017862681302	1	FACETS	0.537	0.493	0.584	0.537	0.493	0.584	INDETERMINATE	1	TRUE	0	0.533217239856643	1		426	809	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547022	9547022	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs58486349	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	163	255	0	ENST00000353224.5:c.1000G>A	p.Asp334Asn	p.D334N	ENST00000353224	NM_177990.2	334	Gat/Aat	5/10	0.180381419843181	2	FACETS	1	0.987	1	0.659	0.61	0.709	INDETERMINATE	1	TRUE	0	0.533217239856643	2		255	464	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579362	7579362	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	382	722	0	ENST00000269305.4:c.325T>A	p.Phe109Ile	p.F109I	ENST00000269305	NM_001126112.2	109	Ttc/Atc	4/11	1	2	FACETS	0.924	0.876	0.974	0.924	0.876	0.974	CLONAL	1	TRUE	1	0.533217239856643	2		722	1550	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395006	139395006	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	224	500	0	ENST00000277541.6:c.5932C>T	p.Gln1978Ter	p.Q1978*	ENST00000277541	NM_017617.3	1978	Cag/Tag	31/34	0.284747879226025	1	FACETS	0.725	0.676	0.775	0.725	0.676	0.775	INDETERMINATE	1	TRUE	0	0.533217239856643	1		500	850	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416773	121416773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779442858	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1686	458	903	3	ENST00000257555.6:c.202C>T	p.Arg68Trp	p.R68W	ENST00000257555		68	Cgg/Tgg	1/10	0.473332243501781	3	FACETS	1	0.963	1	0.507	0.482	0.533	CLONAL	1	TRUE	1	0.533217239856643	3		906	2144	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	582	500	0	ENST00000304494.5:c.143C>T	p.Pro48Leu	p.P48L	ENST00000304494	NM_000077.4	48	cCg/cTg	1/3	0.46660306133796	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.533217239856643	2		500	1038	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391211	139391211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202065858	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	265	747	2	ENST00000277541.6:c.6980G>A	p.Arg2327Gln	p.R2327Q	ENST00000277541	NM_017617.3	2327	cGg/cAg	34/34	0.284747879226025	1	FACETS	0.491	0.459	0.524	0.491	0.459	0.524	INDETERMINATE	1	TRUE	0	0.533217239856643	1		749	1484	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240686	55240686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	483	841	1	ENST00000275493.2:c.1930C>T	p.Pro644Ser	p.P644S	ENST00000275493	NM_005228.3	644	Ccg/Tcg	17/28	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.533217239856643	2		842	1653	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579547	7579547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567557016	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	407	777	2	ENST00000269305.4:c.140del	p.Pro47ArgfsTer76	p.P47Rfs*76	ENST00000269305	NM_001126112.2	47	cCg/cg	4/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.533217239856643	2		779	1474	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426893	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	164	560	1	ENST00000356142.4:c.85_86delinsTT	p.Pro29Phe	p.P29F	ENST00000356142	NM_018890.3	29	CCt/TTt	2/7	1	2	FACETS	0.701	0.643	0.76	0.701	0.643	0.76	SUBCLONAL	1	TRUE	1	0.533217239856643	2		561	878	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041754	29041754	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	151	395	0	ENST00000282397.4:c.65G>A	p.Gly22Glu	p.G22E	ENST00000282397	NM_002019.4	22	gGa/gAa	2/30	0.533217239856643	1	FACETS	0.917	0.846	0.99	0.917	0.846	0.99	CLONAL	1	TRUE	0	0.533217239856643	1		395	453	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031885	26031885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	182	262	0	ENST00000244661.2:c.404G>A	p.Arg135Lys	p.R135K	ENST00000244661	NM_003537.3	135	aGa/aAa	1/1	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.533217239856643	2		262	613	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933211	39933211	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	418	428	0	ENST00000378444.4:c.1388C>T	p.Pro463Leu	p.P463L	ENST00000378444	NM_001123385.1	463	cCc/cTc	4/15	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.533217239856643	1		428	803	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940120	31940120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1525	578	792	0	ENST00000375333.2:c.262G>A	p.Glu88Lys	p.E88K	ENST00000375333	NM_032454.1	88	Gaa/Aaa	2/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.533217239856643	2		792	2103	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087521	27087521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	681	726	0	ENST00000324856.7:c.2095C>T	p.Pro699Ser	p.P699S	ENST00000324856	NM_006015.4	699	Cct/Tct	5/20	0.523640363739195	2	FACETS	0.955	0.925	0.986	0.955	0.925	0.986	CLONAL	2	TRUE	0	0.533217239856643	2		726	1337	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670442	246670443	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1322	395	694	1	ENST00000388985.4:c.77_78delinsTT	p.Pro26Leu	p.P26L	ENST00000388985		26	cCC/cTT	1/12	0.208209340271272	3	FACETS	1	0.985	1	0.546	0.518	0.576	INDETERMINATE	1	TRUE	1	0.533217239856643	3		695	1717	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94224085	94224085	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	158	577	0	ENST00000323929.3:c.67C>T	p.Leu23Phe	p.L23F	ENST00000323929	NM_005591.3	23	Ctt/Ttt	3/20	1	2	FACETS	0.883	0.812	0.957	0.883	0.812	0.957	CLONAL	1	TRUE	1	0.533217239856643	2		577	671	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909881	100909881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1565326353	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	129	429	0	ENST00000325455.5:c.2768G>A	p.Gly923Glu	p.G923E	ENST00000325455	NM_001202474.3	923	gGg/gAg	8/8	1	2	FACETS	0.91	0.829	0.994	0.91	0.829	0.994	CLONAL	1	TRUE	1	0.533217239856643	2		429	532	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160485	108160485	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	117	725	0	ENST00000278616.4:c.4393C>G	p.Leu1465Val	p.L1465V	ENST00000278616	NM_000051.3	1465	Ctt/Gtt	29/63	1	2	FACETS	0.489	0.44	0.54	0.489	0.44	0.54	SUBCLONAL	1	TRUE	1	0.533217239856643	2		725	898	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196857	108196857	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	245	542	1	ENST00000278616.4:c.6880G>A	p.Glu2294Lys	p.E2294K	ENST00000278616	NM_000051.3	2294	Gaa/Aaa	47/63	1	2	FACETS	0.991	0.928	1	0.991	0.928	1	CLONAL	1	TRUE	1	0.533217239856643	2		543	927	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433710	49433710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1371	514	908	2	ENST00000301067.7:c.7843G>A	p.Val2615Ile	p.V2615I	ENST00000301067	NM_003482.3	2615	Gtt/Att	31/54	NA	2	FACETS	1	0.972	1			1	INDETERMINATE	1	TRUE	NA	0.533217239856643	2		910	1885	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924316	112924316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1420362815	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	144	742	3	ENST00000351677.2:c.1262G>A	p.Arg421Gln	p.R421Q	ENST00000351677	NM_002834.3	421	cGg/cAg	11/16	NA	2	FACETS	0.455	0.413	0.498			1	INDETERMINATE	1	TRUE	NA	0.533217239856643	2		745	1188	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012419	29012420	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	228	792	1	ENST00000282397.4:c.451_452delinsAA	p.Gly151Lys	p.G151K	ENST00000282397	NM_002019.4	151	GGa/AAa	4/30	0.533217239856643	1	FACETS	0.75	0.701	0.801	0.75	0.701	0.801	SUBCLONAL	1	TRUE	0	0.533217239856643	1		793	836	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38641681	38641681	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	263	691	0	ENST00000299084.4:c.642del	p.Gln215LysfsTer9	p.Q215Kfs*9	ENST00000299084	NM_152594.2	214	cGg/cg	6/7	0.533217239856643	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.533217239856643	1		691	723	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42053997	42053997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	176	562	1	ENST00000219905.7:c.7459C>T	p.Leu2487Phe	p.L2487F	ENST00000219905	NM_001164273.1	2487	Ctc/Ttc	21/24	0.533217239856643	1	FACETS	0.857	0.794	0.921	0.857	0.794	0.921	CLONAL	1	TRUE	0	0.533217239856643	1		563	565	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748504	43748504	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	365	768	1	ENST00000382044.4:c.2302G>A	p.Glu768Lys	p.E768K	ENST00000382044	NM_001141980.1	768	Gag/Aag	12/28	0.533217239856643	1	FACETS	0.98	0.931	1	0.98	0.931	1	CLONAL	1	TRUE	0	0.533217239856643	1		769	1025	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993512	72993513	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	314	576	2	ENST00000268489.5:c.532_533delinsAA	p.Gly178Lys	p.G178K	ENST00000268489	NM_006885.3	178	GGg/AAg	2/10	0.533217239856643	1	FACETS	0.925	0.875	0.976	0.925	0.875	0.976	CLONAL	1	TRUE	0	0.533217239856643	1		578	934	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81939080	81939080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1368889160	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	368	675	0	ENST00000359376.3:c.1435G>A	p.Gly479Arg	p.G479R	ENST00000359376	NM_002661.3	479	Ggg/Agg	15/33	0.533217239856643	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.533217239856643	1		675	982	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508626	38508626	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	435	781	1	ENST00000254066.5:c.674G>A	p.Trp225Ter	p.W225*	ENST00000254066	NM_000964.3	225	tGg/tAg	6/9	0.533217239856643	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.533217239856643	1		782	1152	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625670	1625670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167586863	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	423	837	1	ENST00000344749.5:c.404C>T	p.Pro135Leu	p.P135L	ENST00000344749	NM_001136139.2	135	cCc/cTc	7/19	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.533217239856643	2		838	1511	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597357	10597357	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1182	379	806	1	ENST00000171111.5:c.1846C>T	p.Gln616Ter	p.Q616*	ENST00000171111	NM_203500.1	616	Cag/Tag	6/6	1	2	FACETS	0.911	0.863	0.96	0.911	0.863	0.96	CLONAL	1	TRUE	1	0.533217239856643	2		807	1561	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763450	41763450	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	431	679	0	ENST00000301178.4:c.2249A>T	p.Tyr750Phe	p.Y750F	ENST00000301178	NM_021913.4	750	tAt/tTt	19/20	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.533217239856643	2		679	1411	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285251	198285251	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	96	522	0	ENST00000335508.6:c.316G>A	p.Glu106Lys	p.E106K	ENST00000335508	NM_012433.2	106	Gag/Aag	4/25	0.284747879226025	1	FACETS	0.318	0.283	0.355	0.318	0.283	0.355	INDETERMINATE	1	TRUE	0	0.533217239856643	1		522	831	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624918	9624918	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	258	511	0	ENST00000353224.5:c.59G>A	p.Arg20Lys	p.R20K	ENST00000353224	NM_177990.2	20	aGg/aAg	3/10	0.180381419843181	2	FACETS	1	0.94	1	0.501	0.47	0.534	INDETERMINATE	1	TRUE	0	0.533217239856643	2		511	965	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023590	31023591	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1210	195	694	1	ENST00000375687.4:c.3075_3076delinsAA	p.Gly1026Arg	p.G1026R	ENST00000375687	NM_015338.5	1025	aaGGga/aaAAga	13/13	0.180381419843181	2	FACETS	0.521	0.48	0.563	0.26	0.24	0.282	INDETERMINATE	1	TRUE	0	0.533217239856643	2		695	1405	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162066	47162066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138005965	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	197	407	2	ENST00000409792.3:c.4060G>A	p.Asp1354Asn	p.D1354N	ENST00000409792	NM_014159.6	1354	Gat/Aat	3/21	NA	2	FACETS	0.879	0.815	0.945			1	INDETERMINATE	1	TRUE	NA	0.533217239856643	2		409	841	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015108	71015108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749121207	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	364	487	0	ENST00000318789.4:c.1822G>A	p.Gly608Arg	p.G608R	ENST00000318789	NM_032682.5	608	Ggg/Agg	20/21	0.242108175857209	4	FACETS	0.841	0.797	0.885			1	INDETERMINATE	2	TRUE	NA	0.533217239856643	4		487	1245	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71161711	71161712	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	224	434	0	ENST00000318789.4:c.257_258delinsAA	p.Arg86Lys	p.R86K	ENST00000318789	NM_032682.5	86	aGG/aAA	7/21	0.242108175857209	4	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.533217239856643	4		434	973	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191080	185191081	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	304	716	2	ENST00000265026.3:c.1961_1962delinsTT	p.Pro654Leu	p.P654L	ENST00000265026	NM_004721.4	654	cCC/cTT	11/14	1	2	FACETS	0.884	0.832	0.937	0.884	0.832	0.937	CLONAL	1	TRUE	1	0.533217239856643	2		718	1290	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801068	1801068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	251	826	0	ENST00000260795.2:c.197G>A	p.Gly66Asp	p.G66D	ENST00000260795		66	gGt/gAt	2/17	0.414354431915952	0	FACETS	0.451	0.422	0.481			1	SUBCLONAL	1	TRUE	0	0.533217239856643	0		826	974	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541651	187541651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	213	374	0	ENST00000441802.2:c.6089G>A	p.Gly2030Glu	p.G2030E	ENST00000441802	NM_005245.3	2030	gGa/gAa	10/27	0.533217239856643	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.533217239856643	1		374	547	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	223612	223612	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	106	389	0	ENST00000264932.6:c.79C>T	p.Gln27Ter	p.Q27*	ENST00000264932	NM_004168.2	27	Caa/Taa	2/15	0.24017862681302	1	FACETS	0.449	0.402	0.497	0.449	0.402	0.497	INDETERMINATE	1	TRUE	0	0.533217239856643	1		389	650	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1268675	1268675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1003575407	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	190	817	0	ENST00000310581.5:c.2542G>A	p.Asp848Asn	p.D848N	ENST00000310581	NM_198253.2	848	Gac/Aac	9/16	0.24017862681302	1	FACETS	0.404	0.373	0.437	0.404	0.373	0.437	INDETERMINATE	1	TRUE	0	0.533217239856643	1		817	1293	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294336	1294336	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	192	554	1	ENST00000310581.5:c.665G>A	p.Arg222Lys	p.R222K	ENST00000310581	NM_198253.2	222	aGg/aAg	2/16	0.24017862681302	1	FACETS	0.535	0.494	0.577	0.535	0.494	0.577	INDETERMINATE	1	TRUE	0	0.533217239856643	1		555	988	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562175	176562175	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	385	717	1	ENST00000439151.2:c.71C>T	p.Ala24Val	p.A24V	ENST00000439151	NM_022455.4	24	gCc/gTc	2/23	0.284747879226025	1	FACETS	0.883	0.839	0.927	0.883	0.839	0.927	INDETERMINATE	1	TRUE	0	0.533217239856643	1		718	1200	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709510	176709511	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAAT	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	170	470	0	ENST00000439151.2:c.5939_5942dup	p.Cys1981Ter	p.C1981*	ENST00000439151	NM_022455.4	1979	-/GAAT	19/23	0.284747879226025	1	FACETS	0.694	0.64	0.749	0.694	0.64	0.749	INDETERMINATE	1	TRUE	0	0.533217239856643	1		470	674	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962888	2962888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1016457945	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1182	391	798	0	ENST00000396946.4:c.2020G>A	p.Asp674Asn	p.D674N	ENST00000396946	NM_032415.4	674	Gac/Aac	16/25	1	2	FACETS	0.932	0.884	0.982	0.932	0.884	0.982	CLONAL	1	TRUE	1	0.533217239856643	2		798	1573	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729407	41729407	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	310	607	1	ENST00000242208.4:c.1122C>A	p.Asn374Lys	p.N374K	ENST00000242208	NM_002192.2	374	aaC/aaA	3/3	1	2	FACETS	0.935	0.881	0.99	0.935	0.881	0.99	CLONAL	1	TRUE	1	0.533217239856643	2		608	1244	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860461	151860461	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	281	751	0	ENST00000262189.6:c.10201A>T	p.Lys3401Ter	p.K3401*	ENST00000262189	NM_170606.2	3401	Aag/Tag	43/59	1	2	FACETS	0.825	0.774	0.878	0.825	0.774	0.878	CLONAL	1	TRUE	1	0.533217239856643	2		751	1277	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400012	139400012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	216	690	0	ENST00000277541.6:c.4336G>T	p.Glu1446Ter	p.E1446*	ENST00000277541	NM_017617.3	1446	Gag/Tag	25/34	0.284747879226025	1	FACETS	0.454	0.421	0.488	0.454	0.421	0.488	INDETERMINATE	1	TRUE	0	0.533217239856643	1		690	1309	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001231	150001231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	73	552	0	ENST00000253339.5:c.2373G>A	p.Met791Ile	p.M791I	ENST00000253339		791	atG/atA	4/7	0.246031300840864	1	FACETS	0.853	0.746	0.968	0.853	0.746	0.968	CLONAL	1	TRUE	0	0.246031300840864	1		552	610	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224578	53224579	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0014310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	65	614	0	ENST00000375401.3:c.3133_3134dup	p.Pro1046ThrfsTer10	p.P1046Tfs*10	ENST00000375401	NM_004187.3	1045	tac/taTAc	21/26	0.246031300840864	1	FACETS	0.61	0.528	0.699	0.61	0.528	0.699	SUBCLONAL	1	TRUE	0	0.246031300840864	1		614	760	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	246	435	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.998	0.935	1	0.998	0.935	1	CLONAL	1	TRUE	1	0.537401443445993	2		435	917	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795608	42795609	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1555770200	NA	P-0014363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	343	547	0	ENST00000575354.2:c.2694dup	p.Lys899GlnfsTer32	p.K899Qfs*32	ENST00000575354	NM_015125.3	896	-/C	10/20	1	2	FACETS	0.944	0.892	0.997	0.944	0.892	0.997	CLONAL	1	TRUE	1	0.537401443445993	2		547	1352	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127724	2127724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397515306	NA	P-0014363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	197	319	1	ENST00000219476.3:c.2963G>A	p.Arg988His	p.R988H	ENST00000219476	NM_000548.3	988	cGc/cAc	26/42	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.537401443445993	2		320	689	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274052	10274052	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs775422876	NA	P-0014363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	324	679	2	ENST00000330684.3:c.217C>A	p.Leu73Met	p.L73M	ENST00000330684	NM_001134407.1	73	Ctg/Atg	2/13	1	2	FACETS	0.993	0.938	1	0.993	0.938	1	CLONAL	1	TRUE	1	0.537401443445993	2		681	1214	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724303	52724303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	227	492	0	ENST00000322088.6:c.1435C>T	p.His479Tyr	p.H479Y	ENST00000322088	NM_014225.5	479	Cat/Tat	12/15	1	2	FACETS	0.876	0.817	0.938	0.876	0.817	0.938	CLONAL	1	TRUE	1	0.537401443445993	2		492	964	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983111	201983111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	69	806	1	ENST00000359651.3:c.960G>T	p.Lys320Asn	p.K320N	ENST00000359651		320	aaG/aaT	7/8	0.268931940551212	3	FACETS	0.426	0.369	0.487	0.213	0.184	0.244	SUBCLONAL	1	TRUE	1	0.34	3		807	1116	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959169	28959169	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0014366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	35	348	0	ENST00000282397.4:c.1970-1G>C		p.X657_splice	ENST00000282397	NM_002019.4	657			1	2	FACETS	0.49	0.402	0.589	0.49	0.402	0.589	SUBCLONAL	1	TRUE	1	0.34	2		348	420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577514	7577515	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGAT	novel	NA	P-0014366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	144	525	0	ENST00000269305.4:c.763_766dup	p.Thr256AsnfsTer9	p.T256Nfs*9	ENST00000269305	NM_001126112.2	256	aca/aATCAca	7/11	0.268931940551212	3	FACETS	1	0.975	1	0.591	0.539	0.645	CLONAL	1	TRUE	1	0.34	3		525	839	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251681	212251681	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	23	382	0	ENST00000342788.4:c.3378G>C	p.Gln1126His	p.Q1126H	ENST00000342788	NM_005235.2	1126	caG/caC	27/28	0.3	1	FACETS	0.252	0.196	0.317	0.252	0.196	0.317	SUBCLONAL	1	TRUE	0	0.34	1		382	446	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665106	182665106	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0014366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	42	469	0	ENST00000292782.4:c.620C>G	p.Ser207Ter	p.S207*	ENST00000292782	NM_020640.2	207	tCa/tGa	6/7	1	2	FACETS	0.377	0.314	0.447	0.377	0.314	0.447	SUBCLONAL	1	TRUE	1	0.34	2		469	656	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411886	116411903	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTCTCTCTGTTTTAAGA	TTTCTCTCTGTTTTAAGA	-	novel	NA	P-0014366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	301	1004	0	ENST00000397752.3:c.2888-16_2889del		p.X963_splice	ENST00000397752	NM_000245.2	963		14/21	0.185072297315216	3	FACETS	0.807	0.76	0.856	0.538	0.506	0.571	INDETERMINATE	2	TRUE	0	0.34	3		1004	1283	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56859013	56859013	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs904265167	NA	P-0014366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	80	627	1	ENST00000519728.1:c.139G>A	p.Glu47Lys	p.E47K	ENST00000519728	NM_002350.3	47	Gaa/Aaa	3/13	0.138176908563996	0	FACETS	0.382	0.336	0.433			1	INDETERMINATE	1	TRUE	0	0.34	0		628	812	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191751	123191751	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	37	511	0	ENST00000218089.9:c.1340T>A	p.Met447Lys	p.M447K	ENST00000218089	NM_001042749.1	447	aTg/aAg	15/35	0.138176908563996	0	FACETS	0.202	0.166	0.243			1	INDETERMINATE	1	TRUE	0	0.34	0		511	710	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0014372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	184	352	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.154173674258789	3	FACETS	0.775	0.715	0.839			1	SUBCLONAL	2	TRUE	NA	0.237232489446306	3		352	1119	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061313	38061313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1204900727	NA	P-0014372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1303	472	660	0	ENST00000250448.2:c.676G>A	p.Asp226Asn	p.D226N	ENST00000250448	NM_004496.3	226	Gac/Aac	2/2	0.208198550639099	4	FACETS	0.925	0.882	0.968	1	0.995	1	CLONAL	3	TRUE	2	0.237232489446306	4		660	1775	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847393	68847393	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	126	452	0	ENST00000261769.5:c.1315del	p.Ala439GlnfsTer16	p.A439Qfs*16	ENST00000261769	NM_004360.3	439	Gca/ca	9/16	0.237232489446306	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.237232489446306	1		452	678	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030223	180030223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200835339	NA	P-0014372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	136	621	0	ENST00000261937.6:c.4061G>A	p.Arg1354His	p.R1354H	ENST00000261937	NM_182925.4	1354	cGc/cAc	30/30	0.154497027813564	3	FACETS	1	0.985	1	0.717	0.652	0.786	CLONAL	1	TRUE	1	0.237232489446306	3		621	894	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0014419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	99	517	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.195711301248534	3	FACETS	0.824	0.736	0.917	0.824	0.736	0.917	CLONAL	2	TRUE	1	0.195711301248534	3		517	674	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579536	7579537	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0014419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	145	801	0	ENST00000269305.4:c.150dup	p.Glu51Ter	p.E51*	ENST00000269305	NM_001126112.2	50	-/T	4/11	0.195711301248534	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.195711301248534	2		801	697	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231661	66231661	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	38	412	0	ENST00000273854.3:c.2039T>A	p.Val680Asp	p.V680D	ENST00000273854	NM_004439.5	680	gTt/gAt	11/18	1	2	FACETS	0.981	0.812	1	0.981	0.812	1	CLONAL	1	TRUE	1	0.195711301248534	2		412	396	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020889	26020889	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	86	352	0	ENST00000357647.3:c.172T>C	p.Ser58Pro	p.S58P	ENST00000357647	NM_003529.2	58	Tcc/Ccc	1/1	0.195711301248534	4	FACETS	0.834	0.742	0.932	0.834	0.742	0.932	CLONAL	3	TRUE	1	0.195711301248534	4		352	420	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109319885	109319885	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	33	624	0	ENST00000436639.2:c.803A>G	p.Tyr268Cys	p.Y268C	ENST00000436639	NM_014454.2	268	tAt/tGt	5/10	0.183073986746674	2	FACETS	0.521	0.423	0.632	0.261	0.211	0.316	SUBCLONAL	1	TRUE	0	0.195711301248534	2		624	647	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729946	41729946	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	64	616	1	ENST00000242208.4:c.583G>T	p.Val195Leu	p.V195L	ENST00000242208	NM_002192.2	195	Gtg/Ttg	3/3	0.195711301248534	3	FACETS	1	0.89	1	0.517	0.447	0.593	CLONAL	1	TRUE	1	0.195711301248534	3		617	695	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922550	56922550	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	35	572	0	ENST00000519728.1:c.1420G>A	p.Asp474Asn	p.D474N	ENST00000519728	NM_002350.3	474	Gac/Aac	13/13	1	2	FACETS	0.596	0.487	0.719	0.596	0.487	0.719	SUBCLONAL	1	TRUE	1	0.195711301248534	2		572	600	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491645	56491645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	247	486	2	ENST00000267101.3:c.2537G>T	p.Ser846Ile	p.S846I	ENST00000267101	NM_001982.3	846	aGt/aTt	21/28	0.376127082432199	3	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.553002808939653	3		488	1004	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0014488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	85	538	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	0.254	0.224	0.288	0.254	0.224	0.288	SUBCLONAL	1	TRUE	1	0.553002808939653	2		538	1208	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0014488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	51	331	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	0.553002808939653	1	FACETS	0.302	0.257	0.351	0.302	0.257	0.351	SUBCLONAL	1	TRUE	0	0.553002808939653	1		331	442	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188064	11188064	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	56	250	0	ENST00000361445.4:c.6030G>C	p.Met2010Ile	p.M2010I	ENST00000361445	NM_004958.3	2010	atG/atC	43/58	NA	2	FACETS	0.387	0.331	0.447			1	INDETERMINATE	1	TRUE	NA	0.553002808939653	2		250	524	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69456209	69456209	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	57	548	0	ENST00000227507.2:c.128C>G	p.Ser43Cys	p.S43C	ENST00000227507	NM_053056.2	43	tCc/tGc	1/5	NA	2	FACETS	0.282	0.242	0.327			1	INDETERMINATE	1	TRUE	NA	0.553002808939653	2		548	730	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	269	489	0	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	0.376127082432199	3	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.553002808939653	3		489	938	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778247	3778247	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	69	464	0	ENST00000262367.5:c.6801G>T	p.Gln2267His	p.Q2267H	ENST00000262367	NM_004380.2	2267	caG/caT	31/31	1	2	FACETS	0.383	0.333	0.437	0.383	0.333	0.437	SUBCLONAL	1	TRUE	1	0.553002808939653	2		464	652	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645885	67645886	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGTTACACGTGTCCACGGCGTTCAAATTTGGATCGTCACATGAAA	novel	NA	P-0014488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	100	487	0	ENST00000264010.4:c.816_860dup	p.Tyr273_Ser287dup	p.Y273_S287dup	ENST00000264010	NM_006565.3	273	-/AGTTACACGTGTCCACGGCGTTCAAATTTGGATCGTCACATGAAA	4/12	0.553002808939653	1	FACETS	0.321	0.286	0.358	0.321	0.286	0.358	SUBCLONAL	1	TRUE	0	0.553002808939653	1		487	816	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853221	68853221	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	241	481	0	ENST00000261769.5:c.1605del	p.Asn536IlefsTer21	p.N536Ifs*21	ENST00000261769	NM_004360.3	535	aTt/at	11/16	0.553002808939653	1	FACETS	0.947	0.89	1	0.947	0.89	1	CLONAL	1	TRUE	0	0.553002808939653	1		481	666	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0014553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	241	245	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.552763628190622	2		245	632	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0014553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	443	327	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.552763628190622	2	FACETS	0.938	0.901	0.975	0.938	0.901	0.975	CLONAL	2	TRUE	0	0.552763628190622	2		327	854	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0014553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	249	186	0	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	0.552763628190622	3	FACETS	0.887	0.843	0.931	0.887	0.843	0.931	CLONAL	3	TRUE	0	0.552763628190622	3		186	432	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727483	66727483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504317	NA	P-0014553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	195	343	0	ENST00000307102.5:c.199G>A	p.Asp67Asn	p.D67N	ENST00000307102	NM_002755.3	67	Gac/Aac	2/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.552763628190622	2		343	663	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907420	32907421	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359306	NA	P-0014553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	371	248	0	ENST00000380152.3:c.1813dup	p.Ile605AsnfsTer11	p.I605Nfs*11	ENST00000380152		602	gga/ggAa	10/27	0.552763628190622	4	FACETS	0.979	0.937	1	0.979	0.937	1	CLONAL	3	TRUE	1	0.552763628190622	4		248	710	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799200	88799200	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0014553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	71	535	2	ENST00000360948.2:c.185C>G	p.Ser62Ter	p.S62*	ENST00000360948	NM_001012338.2	62	tCa/tGa	2/19	1	2	FACETS	0.343	0.299	0.391	0.343	0.299	0.391	SUBCLONAL	1	TRUE	1	0.552763628190622	2		537	749	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141507	11141507	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	236	522	0	ENST00000358026.2:c.3484G>T	p.Gly1162Cys	p.G1162C	ENST00000358026	NM_001128849.1	1162	Ggc/Tgc	25/36	0.552763628190622	3	FACETS	1	0.971	1	0.535	0.499	0.572	CLONAL	1	TRUE	1	0.552763628190622	3		522	1018	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855971	76855971	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	444	257	0	ENST00000373344.5:c.5629C>T	p.Gln1877Ter	p.Q1877*	ENST00000373344	NM_000489.3	1877	Cag/Tag	23/35	0.466673771158163	2	FACETS	0.93	0.904	0.955			1	CLONAL	3	TRUE	NA	0.552763628190622	2		257	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579359	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587780066	NA	P-0014649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1926	181	705	0	ENST00000269305.4:c.328del	p.Arg110ValfsTer13	p.R110Vfs*13	ENST00000269305	NM_001126112.2	110	Cgt/gt	4/11	1	2	FACETS	0.351	0.322	0.381	0.351	0.322	0.381	SUBCLONAL	1	TRUE	1	0.49	2		705	2107	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649665	206649665	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1855	193	751	2	ENST00000367120.3:c.500A>T	p.Asp167Val	p.D167V	ENST00000367120	NM_014002.3	167	gAt/gTt	6/22	1	2	FACETS	0.385	0.354	0.417	0.385	0.354	0.417	SUBCLONAL	1	TRUE	1	0.49	2		753	2048	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016675	12016675	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	66	384	1	ENST00000353533.5:c.811G>A	p.Ala271Thr	p.A271T	ENST00000353533	NM_003010.3	271	Gca/Aca	7/11	1	2	FACETS	0.291	0.251	0.333	0.291	0.251	0.333	SUBCLONAL	1	TRUE	1	0.49	2		385	927	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16056703	16056704	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	106	407	0	ENST00000268712.3:c.738dup	p.Ala247SerfsTer6	p.A247Sfs*6	ENST00000268712	NM_006311.3	246	-/A	7/46	1	2	FACETS	0.393	0.351	0.437	0.393	0.351	0.437	SUBCLONAL	1	TRUE	1	0.49	2		407	1102	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627327	37627327	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2472	577	681	0	ENST00000447079.4:c.1242G>C	p.Lys414Asn	p.K414N	ENST00000447079	NM_015083.1	414	aaG/aaC	2/14	0.3	6	FACETS	0.765	0.731	0.799			1	SUBCLONAL	2	TRUE	NA	0.49	6		681	3049	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593656	55593657	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAACTT	novel	NA	P-0014678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	231	502	0	ENST00000288135.5:c.1724_1729dup	p.Gln575_Leu576dup	p.Q575_L576dup	ENST00000288135	NM_000222.2	575	-/CAACTT	11/21	1	2	FACETS	0.98	0.919	1	1	0.994	1	CLONAL	2	TRUE	1	0.347142363486255	2		502	679	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0014704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	43	640	1	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.249949700711165	4	FACETS	0.882	0.746	1	0.882	0.746	1	CLONAL	2	TRUE	2	0.28963570722912	4		641	217	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971124	21971125	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0014704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	53	500	0	ENST00000304494.5:c.233_234del	p.Leu78HisfsTer41	p.L78Hfs*41	ENST00000304494	NM_000077.4	78	cTC/c	2/3	0.28963570722912	3	FACETS	1	0.911	1	1	0.974	1	CLONAL	3	TRUE	1	0.28963570722912	3		500	133	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680655	88680655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142726068	NA	P-0014704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	23	528	1	ENST00000360948.2:c.602G>A	p.Arg201His	p.R201H	ENST00000360948	NM_001012338.2	201	cGc/cAc	6/19	0.28963570722912	3	FACETS	1	0.9	1			1	CLONAL	1	TRUE	NA	0.28963570722912	3		529	143	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578227	7578230	+	frameshift_variant	Frame_Shift_Del	DEL	CATC	CATC	-	novel	NA	P-0014704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	28	841	2	ENST00000269305.4:c.619_622del	p.Asp207ThrfsTer39	p.D207Tfs*39	ENST00000269305	NM_001126112.2	207	GATGac/ac	6/11	0.28963570722912	1	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	0	0.28963570722912	1		843	145	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439756	220439757	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0014704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	28	763	0	ENST00000243786.2:c.610dup	p.Thr204AsnfsTer7	p.T204Nfs*7	ENST00000243786	NM_002191.3	203	-/A	2/2	0.28963570722912	4	FACETS	0.897	0.727	1	0.897	0.727	1	CLONAL	2	TRUE	2	0.28963570722912	4		763	139	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0014711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	53	285	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.924	0.791	1	0.924	0.791	1	CLONAL	1	TRUE	1	0.315091029167799	2		285	364	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115410	115115411	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0014711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	103	678	0	ENST00000257566.3:c.915dup	p.Thr306HisfsTer21	p.T306Hfs*21	ENST00000257566	NM_016569.3	305	-/C	5/8	0.315091029167799	1	FACETS	0.711	0.636	0.79	0.711	0.636	0.79	SUBCLONAL	1	TRUE	0	0.315091029167799	1		678	775	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844161	68844161	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	107	740	0	ENST00000261769.5:c.749T>A	p.Ile250Asn	p.I250N	ENST00000261769	NM_004360.3	250	aTc/aAc	6/16	0.315091029167799	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.315091029167799	1		740	561	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831304	72831313	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCTGCTGC	CTCCTGCTGC	-	novel	NA	P-0014711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	50	397	0	ENST00000268489.5:c.5268_5277del	p.Gln1757CysfsTer7	p.Q1757Cfs*7	ENST00000268489	NM_006885.3	1756	ctGCAGCAGGAG/ct	9/10	0.315091029167799	1	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	0	0.315091029167799	1		397	262	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984669	11984670	+	splice_region_variant,intron_variant	Splice_Region	DEL	AC	AC	-	novel	NA	P-0014711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	58	399	0	ENST00000353533.5:c.219-3_219-2del		p.X73_splice	ENST00000353533	NM_003010.3	73			0.315091029167799	1	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	0	0.315091029167799	1		399	309	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492851	56492851	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	68	460	0	ENST00000407977.2:c.88C>G	p.Leu30Val	p.L30V	ENST00000407977		30	Ctg/Gtg	2/10	1	2	FACETS	0.848	0.739	0.965	0.848	0.739	0.965	CLONAL	1	TRUE	1	0.315091029167799	2		460	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0014721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	191	621	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	NA	2	FACETS	0.823	0.761	0.887			1	INDETERMINATE	2	TRUE	NA	0.24	2		621	967	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577077	7577077	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs748891343	NA	P-0014721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	164	590	0	ENST00000269305.4:c.861G>C	p.Glu287Asp	p.E287D	ENST00000269305	NM_001126112.2	287	gaG/gaC	8/11	NA	2	FACETS	0.789	0.725	0.856			1	INDETERMINATE	2	TRUE	NA	0.24	2		590	866	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682989	241682989	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199912971	NA	P-0014721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	61	365	0	ENST00000366560.3:c.34C>T	p.Arg12Cys	p.R12C	ENST00000366560	NM_000143.3	12	Cgt/Tgt	1/10	1	2	FACETS	0.799	0.689	0.919	0.799	0.689	0.919	CLONAL	1	TRUE	1	0.24	2		365	636	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524113	18524113	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0014721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	25	226	0	ENST00000266497.5:c.1626-1G>T		p.X542_splice	ENST00000266497		542			1	2	FACETS	0.496	0.39	0.618	0.496	0.39	0.618	SUBCLONAL	1	TRUE	1	0.24	2		226	420	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21643312	21643312	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	43	364	0	ENST00000421138.2:c.215A>T	p.Asp72Val	p.D72V	ENST00000421138		72	gAt/gTt	5/16	1	2	FACETS	0.488	0.407	0.578	0.488	0.407	0.578	SUBCLONAL	1	TRUE	1	0.24	2		364	734	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610414	81610414	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	68	349	0	ENST00000298171.2:c.2012C>A	p.Ser671Tyr	p.S671Y	ENST00000298171	NM_000369.2	671	tCc/tAc	10/10	1	2	FACETS	0.999	0.87	1	0.999	0.87	1	CLONAL	1	TRUE	1	0.24	2		349	567	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559093	29559094	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	19	109	0	ENST00000356175.3:c.3203dup	p.Leu1068PhefsTer21	p.L1068Ffs*21	ENST00000356175	NM_000267.3	1067	gat/gaTt	25/57	1	2	FACETS	0.616	0.468	0.79	0.616	0.468	0.79	SUBCLONAL	1	TRUE	1	0.24	2		109	257	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610454	10610454	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	134	525	0	ENST00000171111.5:c.256C>T	p.Gln86Ter	p.Q86*	ENST00000171111	NM_203500.1	86	Cag/Tag	2/6	0.295948392925993	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.24	1		525	659	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273278	198273278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	54	449	0	ENST00000335508.6:c.932C>T	p.Ala311Val	p.A311V	ENST00000335508	NM_012433.2	311	gCt/gTt	8/25	1	2	FACETS	0.521	0.444	0.607	0.521	0.444	0.607	SUBCLONAL	1	TRUE	1	0.24	2		449	863	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444484	50444484	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	144	243	0	ENST00000331340.3:c.414C>A	p.Ser138Arg	p.S138R	ENST00000331340	NM_006060.4	138	agC/agA	4/8	0.295948392925993	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	TRUE	1	0.24	4		243	450	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509612	106509612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	48	483	0	ENST00000359195.3:c.1606C>T	p.Pro536Ser	p.P536S	ENST00000359195	NM_002649.2	536	Cct/Tct	2/11	1	2	FACETS	0.552	0.465	0.647	0.552	0.465	0.647	SUBCLONAL	1	TRUE	1	0.24	2		483	725	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950518	68950518	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	65	238	0	ENST00000288368.4:c.830G>A	p.Arg277Lys	p.R277K	ENST00000288368	NM_024870.2	277	aGa/aAa	7/40	0.180272917909222	5	FACETS	1	0.958	1	0.425	0.368	0.486	CLONAL	1	TRUE	2	0.24	5		238	578	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739054	145739054	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1182814326	NA	P-0014721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	230	505	1	ENST00000428558.2:c.2101G>A	p.Asp701Asn	p.D701N	ENST00000428558	NM_004260.3	701	Gat/Aat	13/22	0.180272917909222	5	FACETS	0.94	0.878	1	0.94	0.878	1	CLONAL	3	TRUE	2	0.24	5		506	924	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524967	8524967	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	127	299	1	ENST00000356435.5:c.637G>T	p.Ala213Ser	p.A213S	ENST00000356435		213	Gcg/Tcg	7/35	0.295948392925993	2	FACETS	0.935	0.85	1	0.935	0.85	1	CLONAL	2	TRUE	0	0.24	2		300	566	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0014755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	152	301	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.41508952473604	4	FACETS	0.936	0.868	1	0.936	0.868	1	CLONAL	3	TRUE	1	0.41508952473604	4		301	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	273	625	1	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	0.41508952473604	2	FACETS	0.873	0.824	0.924	0.873	0.824	0.924	CLONAL	2	TRUE	0	0.41508952473604	2		626	753	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670327	134670327	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373140258	NA	P-0014755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	203	336	2	ENST00000398015.3:c.238C>T	p.Arg80Trp	p.R80W	ENST00000398015	NM_004441.4	80	Cgg/Tgg	3/16	0.251346878529448	4	FACETS	1	0.986	1			1	CLONAL	2	TRUE	NA	0.41508952473604	4		338	575	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837973	156837973	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1393	135	653	0	ENST00000524377.1:c.506G>A	p.Gly169Glu	p.G169E	ENST00000524377	NM_002529.3	169	gGa/gAa	5/17	0.41508952473604	6	FACETS	0.779	0.705	0.857	0.26	0.235	0.286	SUBCLONAL	1	TRUE	3	0.41508952473604	6		653	1528	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458399	120458399	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	172	452	0	ENST00000256646.2:c.6946G>T	p.Ala2316Ser	p.A2316S	ENST00000256646	NM_024408.3	2316	Gcc/Tcc	34/34	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.41508952473604	2		452	617	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550932	150550932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	93	307	1	ENST00000369026.2:c.724G>A	p.Asp242Asn	p.D242N	ENST00000369026	NM_021960.4	242	Gat/Aat	2/3	0.41508952473604	6	FACETS	0.968	0.86	1	0.323	0.286	0.362	CLONAL	1	TRUE	3	0.41508952473604	6		308	847	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032396	42032396	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	95	432	1	ENST00000219905.7:c.4580C>G	p.Pro1527Arg	p.P1527R	ENST00000219905	NM_001164273.1	1527	cCa/cGa	14/24	0.414714003242243	2	FACETS	0.87	0.777	0.969	0.435	0.388	0.485	CLONAL	1	TRUE	0	0.41508952473604	2		433	526	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678581	88678581	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	93	298	1	ENST00000360948.2:c.955C>A	p.His319Asn	p.H319N	ENST00000360948	NM_001012338.2	319	Cac/Aac	9/19	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.41508952473604	2		299	408	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636803	2636803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	120	629	1	ENST00000342085.4:c.1252G>A	p.Asp418Asn	p.D418N	ENST00000342085	NM_002613.4	418	Gat/Aat	11/14	0.41508952473604	3	FACETS	0.849	0.767	0.937	0.283	0.255	0.313	CLONAL	1	TRUE	0	0.41508952473604	3		630	822	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40456406	40456406	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	152	637	0	ENST00000345506.4:c.1216C>A	p.His406Asn	p.H406N	ENST00000345506	NM_003152.3	406	Cac/Aac	11/20	0.41508952473604	3	FACETS	0.987	0.903	1	0.494	0.451	0.538	CLONAL	1	TRUE	1	0.41508952473604	3		637	896	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626417	12626417	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	260	538	0	ENST00000251849.4:c.1732C>T	p.Pro578Ser	p.P578S	ENST00000251849	NM_002880.3	578	Ccc/Tcc	16/17	0.41508952473604	3	FACETS	0.916	0.86	0.972	0.916	0.86	0.972	CLONAL	2	TRUE	1	0.41508952473604	3		538	826	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875052	151875053	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	146	191	1	ENST00000262189.6:c.7485dup	p.Glu2496ArgfsTer29	p.E2496Rfs*29	ENST00000262189	NM_170606.2	2495	-/A	38/59	0.41508952473604	5	FACETS	0.921	0.85	0.995	0.921	0.85	0.995	CLONAL	3	TRUE	2	0.41508952473604	5		192	413	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0014798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	163	595	1	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.872	0.802	0.944	0.872	0.802	0.944	CLONAL	1	TRUE	1	0.522275525084903	2		596	716	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183240	56183241	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	219	477	0	ENST00000399503.3:c.4151dup	p.Arg1385LysfsTer35	p.R1385Kfs*35	ENST00000399503	NM_005921.1	1384	cta/cTta	18/20	1	2	FACETS	0.928	0.864	0.993	0.928	0.864	0.993	CLONAL	1	TRUE	1	0.522275525084903	2		477	904	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184116	56184116	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	263	490	0	ENST00000399503.3:c.4321G>T	p.Glu1441Ter	p.E1441*	ENST00000399503	NM_005921.1	1441	Gaa/Taa	19/20	1	2	FACETS	0.993	0.932	1	0.993	0.932	1	CLONAL	1	TRUE	1	0.522275525084903	2		490	1014	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0014800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	142	245	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.277163020305645	1	FACETS	0.643	0.587	0.702	0.643	0.587	0.702	INDETERMINATE	1	TRUE	0	0.46987664185763	1		245	719	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196896	108196896	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs56009889	NA	P-0014800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	155	348	0	ENST00000278616.4:c.6919C>G	p.Leu2307Val	p.L2307V	ENST00000278616	NM_000051.3	2307	Ctt/Gtt	47/63	0.107414310321003	3	FACETS	1	0.961	1	0.54	0.495	0.587	INDETERMINATE	1	TRUE	1	0.46987664185763	3		348	754	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89833629	89833629	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1350557471	NA	P-0014800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	145	277	0	ENST00000389301.3:c.2521A>G	p.Ile841Val	p.I841V	ENST00000389301	NM_000135.2	841	Att/Gtt	27/43	1	2	FACETS	0.809	0.739	0.882	0.809	0.739	0.882	CLONAL	1	TRUE	1	0.46987664185763	2		277	763	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576653	7576982	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGTCCTTTAAAATATATATTATGGTATAAGTTGGTGTTCTGAAGTTAGTTAGCTACAACCAGGAGCCATTGTCTTTGAGGCATCACTGCCCCCTGATGGCAAATGCCCCAATTGCAGGTAAAACAGTCAAGAAGAAAACGGCATTTTGAGTGTTAGACTGGAAACTTTCCACTTGATAAGAGGTCCCAAGACTTAGTACCTGAAGGGTGAAATATTCTCCATCCAGTGGTTTCTTCTTTGGCTGGGGAGAGGAGCTGGTGTTGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAAAGTGAATCTGAGGCATAACTGCACCCT	TGGTCCTTTAAAATATATATTATGGTATAAGTTGGTGTTCTGAAGTTAGTTAGCTACAACCAGGAGCCATTGTCTTTGAGGCATCACTGCCCCCTGATGGCAAATGCCCCAATTGCAGGTAAAACAGTCAAGAAGAAAACGGCATTTTGAGTGTTAGACTGGAAACTTTCCACTTGATAAGAGGTCCCAAGACTTAGTACCTGAAGGGTGAAATATTCTCCATCCAGTGGTTTCTTCTTTGGCTGGGGAGAGGAGCTGGTGTTGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAAAGTGAATCTGAGGCATAACTGCACCCT	-	novel	NA	P-0014800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	72	356	0	ENST00000269305.4:c.919+37_993+200del		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	0.46987664185763	1	FACETS	0.368	0.321	0.418	0.368	0.321	0.418	SUBCLONAL	1	TRUE	0	0.46987664185763	1		356	637	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576868	7576886	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTCCATCCAGTGGTTTC	TTCTCCATCCAGTGGTTTC	-	novel	NA	P-0014800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	103	587	0	ENST00000269305.4:c.960_978del	p.Lys320AsnfsTer19	p.K320Nfs*19	ENST00000269305	NM_001126112.2	320	aaGAAACCACTGGATGGAGAA/aa	9/11	0.46987664185763	1	FACETS	0.402	0.359	0.447	0.402	0.359	0.447	SUBCLONAL	1	TRUE	0	0.46987664185763	1		587	835	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519999	NA	P-0014800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	38	530	0	ENST00000269305.4:c.716A>C	p.Asn239Thr	p.N239T	ENST00000269305	NM_001126112.2	239	aAc/aCc	7/11	0.46987664185763	1	FACETS	0.151	0.124	0.181	0.151	0.124	0.181	SUBCLONAL	1	TRUE	0	0.46987664185763	1		530	819	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437521	56437522	+	stop_gained	Nonsense_Mutation	INS	-	-	ACATGCATT	novel	NA	P-0014800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	151	623	0	ENST00000407977.2:c.940_941insAATGCATGT	p.Met313_Phe314insTer	p.M313_F314ins*	ENST00000407977		314	ttc/tAATGCATGTtc	8/10	0.46987664185763	1	FACETS	0.534	0.488	0.583	0.534	0.488	0.583	SUBCLONAL	1	TRUE	0	0.46987664185763	1		623	920	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0014801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	234	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.719	0.669	0.77	0.719	0.669	0.77	SUBCLONAL	1	TRUE	1	0.541732492440776	2		249	1202	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922293	100922293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149186732	NA	P-0014801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	151	274	0	ENST00000325455.5:c.2219G>A	p.Arg740Gln	p.R740Q	ENST00000325455	NM_001202474.3	740	cGa/cAa	5/8	1	2	FACETS	0.644	0.588	0.702	0.644	0.588	0.702	SUBCLONAL	1	TRUE	1	0.541732492440776	2		274	866	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878785	151878785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	183	335	0	ENST00000262189.6:c.6160C>T	p.Gln2054Ter	p.Q2054*	ENST00000262189	NM_170606.2	2054	Cag/Tag	36/59	1	2	FACETS	0.855	0.791	0.922	0.855	0.791	0.922	CLONAL	1	TRUE	1	0.541732492440776	2		335	790	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115718	8115719	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	62	366	0	ENST00000346208.3:c.1065dup	p.Met356TyrfsTer15	p.M356Yfs*15	ENST00000346208		355	act/acTt	6/6	1	2	FACETS	0.247	0.213	0.285	0.247	0.213	0.285	SUBCLONAL	1	TRUE	1	0.541732492440776	2		366	926	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89833629	89833629	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1350557471	NA	P-0014820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	66	277	0	ENST00000389301.3:c.2521A>G	p.Ile841Val	p.I841V	ENST00000389301	NM_000135.2	841	Att/Gtt	27/43	1	2	FACETS	0.943	0.827	1	0.943	0.827	1	CLONAL	1	TRUE	1	0.511109080558822	2		277	274	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	rs786202799	NA	P-0014820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	39	711	1	ENST00000269305.4:c.376-2A>T		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.511109080558822	1	FACETS	0.249	0.206	0.296	0.249	0.206	0.296	SUBCLONAL	1	TRUE	0	0.511109080558822	1		712	457	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38991074	38991074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	163	409	0	ENST00000357387.3:c.560G>A	p.Cys187Tyr	p.C187Y	ENST00000357387	NM_152756.3	187	tGc/tAc	7/38	0.414719322645368	2	FACETS	0.867	0.807	0.927	0.867	0.807	0.927	CLONAL	2	TRUE	0	0.511109080558822	2		409	368	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132814	152132815	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0014820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	123	602	0	ENST00000262189.6:c.57dup	p.Glu20ArgfsTer39	p.E20Rfs*39	ENST00000262189	NM_170606.2	19	-/C	1/59	1	2	FACETS	0.76	0.689	0.835	0.76	0.689	0.835	SUBCLONAL	1	TRUE	1	0.511109080558822	2		602	633	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	206	509	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	1	0.459047091527359	2		509	601	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857311	68857312	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	161	306	0	ENST00000261769.5:c.1947dup	p.Ile650TyrfsTer13	p.I650Yfs*13	ENST00000261769	NM_004360.3	649	tct/tcTt	13/16	0.279369668616621	0	FACETS	0.953	0.885	1			1	CLONAL	1	FALSE	0	0.459047091527359	0		306	398	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206722	36206722	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	198	621	0	ENST00000300305.3:c.790C>T	p.Gln264Ter	p.Q264*	ENST00000300305		264	Cag/Tag	6/8	1	2	FACETS	0.945	0.876	1	0.945	0.876	1	CLONAL	1	FALSE	1	0.459047091527359	2		621	913	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061238	38061239	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGAGTCCGGGTGCAGCGTCCAGTA	novel	NA	P-0014829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	162	634	0	ENST00000250448.2:c.727_750dup	p.Tyr243_Ser250dup	p.Y243_S250dup	ENST00000250448	NM_004496.3	243	-/TACTGGACGCTGCACCCGGACTCC	2/2	0.274398941314545	1	FACETS	0.649	0.596	0.704	0.649	0.596	0.704	INDETERMINATE	1	FALSE	0	0.459047091527359	1		634	838	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117425	115117450	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTGGTATTTGTGCATGGAGTTCAA	GGCTGGTATTTGTGCATGGAGTTCAA	C	novel	NA	P-0014829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	123	349	0	ENST00000257566.3:c.724_749delinsG	p.Leu242AlafsTer6	p.L242Afs*6	ENST00000257566	NM_016569.3	242	TTGAACTCCATGCACAAATACCAGCCc/Gc	4/8	1	2	FACETS	0.848	0.769	0.931	0.848	0.769	0.931	CLONAL	1	FALSE	1	0.459047091527359	2		349	632	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	88	366	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	0.258886662439562	2		366	632	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0014863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	48	292	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.81	0.685	0.946	0.81	0.685	0.946	CLONAL	1	TRUE	1	0.258886662439562	2		292	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0014863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	330	786	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.0935398918501225	3	FACETS	1	0.983	1			1	INDETERMINATE	2	TRUE	NA	0.258886662439562	3		786	1314	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0014863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	62	634	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	0.982	0.849	1	0.982	0.849	1	CLONAL	1	TRUE	1	0.258886662439562	2		634	488	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132465	11132465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	194	807	1	ENST00000358026.2:c.2681C>T	p.Thr894Met	p.T894M	ENST00000358026	NM_001128849.1	894	aCg/aTg	19/36	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.258886662439562	2		808	1374	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711246	114711247	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0014863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	114	546	0	ENST00000543371.1:c.263dup	p.Arg89GlufsTer8	p.R89Efs*8	ENST00000543371	NM_001198531.1	87	-/A	3/14	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.258886662439562	2		546	874	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81979791	81979791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372557475	NA	P-0014863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	85	469	1	ENST00000359376.3:c.3493G>A	p.Val1165Ile	p.V1165I	ENST00000359376	NM_002661.3	1165	Gtt/Att	31/33	1	2	FACETS	0.886	0.783	0.997	0.886	0.783	0.997	CLONAL	1	TRUE	1	0.258886662439562	2		470	741	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	392	761	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.276427120439535	3	FACETS	0.856	0.812	0.9	0.856	0.812	0.9	CLONAL	2	TRUE	1	0.381868290137109	3		761	1429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0014898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	165	354	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.276427120439535	3	FACETS	1	0.934	1	0.51	0.468	0.554	CLONAL	1	TRUE	1	0.381868290137109	3		354	1009	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332875	152332875	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1131692059	NA	P-0014898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	97	387	1	ENST00000206249.3:c.1181G>A	p.Arg394His	p.R394H	ENST00000206249	NM_000125.3	394	cGc/cAc	5/8	1	2	FACETS	0.796	0.711	0.887	0.796	0.711	0.887	SUBCLONAL	1	TRUE	1	0.381868290137109	2		388	638	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493736	56493738	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs781370860	NA	P-0014898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1660	301	669	0	ENST00000267101.3:c.3057_3059del	p.Glu1019del	p.E1019del	ENST00000267101	NM_001982.3	1018	GAG/-	25/28	0.381868290137109	6	FACETS	1	0.993	1			1	CLONAL	1	TRUE	NA	0.381868290137109	6		669	1961	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539886	187539887	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0014898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	195	425	0	ENST00000441802.2:c.7853_7854insAT	p.Leu2619PhefsTer25	p.L2619Ffs*25	ENST00000441802	NM_005245.3	2618	gtt/gtATt	10/27	0.300858810091064	2	FACETS	0.753	0.7	0.808	0.753	0.7	0.808	SUBCLONAL	2	TRUE	0	0.381868290137109	2		425	678	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37034007	37034007	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1466879183	NA	P-0014898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	112	381	0	ENST00000358127.4:c.22C>T	p.Pro8Ser	p.P8S	ENST00000358127	NM_001280556.1	8	Ccg/Tcg	1/10	NA	2	FACETS	0.873	0.786	0.964			1	INDETERMINATE	1	TRUE	NA	0.381868290137109	2		381	672	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	97	509	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.894	0.797	0.996	0.894	0.797	0.996	CLONAL	1	TRUE	1	0.325980422334921	2		509	666	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063312	67063313	+	frameshift_variant,start_lost	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0014929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	69	314	0	ENST00000412916.2:c.3dup	p.Pro2_?1	p.P2_?1	ENST00000412916		1	atg/atGg	1/6	0.325980422334921	1	FACETS	0.916	0.801	1	0.916	0.801	1	CLONAL	1	TRUE	0	0.325980422334921	1		314	387	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847342	68847342	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	200	614	1	ENST00000261769.5:c.1264C>T	p.Gln422Ter	p.Q422*	ENST00000261769	NM_004360.3	422	Caa/Taa	9/16	0.325980422334921	1	FACETS	0.755	0.703	0.809	1	0.991	1	SUBCLONAL	2	TRUE	0	0.325980422334921	1		615	680	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965472	68965472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200682883	NA	P-0014929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	377	617	0	ENST00000288368.4:c.1084C>T	p.Arg362Trp	p.R362W	ENST00000288368	NM_024870.2	362	Cgg/Tgg	9/40	0.325980422334921	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.325980422334921	3		617	1223	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	71	140	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.839	0.747	0.934	1	0.981	1	CLONAL	2	TRUE	1	0.443004055761242	2		140	191	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057747	27057747	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	223	908	1	ENST00000324856.7:c.1455C>A	p.Tyr485Ter	p.Y485*	ENST00000324856	NM_006015.4	485	taC/taA	3/20	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.443004055761242	2		909	691	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691158	18691158	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs756960325	NA	P-0014959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	172	402	0	ENST00000266497.5:c.3269A>G	p.Gln1090Arg	p.Q1090R	ENST00000266497		1090	cAg/cGg	23/31	0.443004055761242	4	FACETS	0.781	0.721	0.844	0.521	0.48	0.563	SUBCLONAL	2	TRUE	1	0.443004055761242	4		402	717	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420314	88420314	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	149	483	0	ENST00000360948.2:c.2372G>T	p.Arg791Leu	p.R791L	ENST00000360948	NM_001012338.2	791	cGg/cTg	19/19	1	2	FACETS	0.761	0.702	0.822	1	0.989	1	SUBCLONAL	2	TRUE	1	0.443004055761242	2		483	442	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225884	2225884	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	131	653	0	ENST00000326181.6:c.1676G>T	p.Gly559Val	p.G559V	ENST00000326181	NM_032271.2	559	gGt/gTt	18/21	1	2	FACETS	0.774	0.71	0.84	1	0.988	1	SUBCLONAL	2	TRUE	1	0.443004055761242	2		653	382	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740632	58740632	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	191	610	0	ENST00000305921.3:c.1537T>A	p.Leu513Met	p.L513M	ENST00000305921	NM_003620.3	513	Ttg/Atg	6/6	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.443004055761242	2		610	781	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143181660	143181661	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0014959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	190	524	0	ENST00000262992.4:c.672_673insAA	p.Pro225AsnfsTer4	p.P225Nfs*4	ENST00000262992	NM_001101669.1	224	-/AA	9/24	0.123703698042655	4	FACETS	1	0.935	1	1	0.935	1	INDETERMINATE	2	TRUE	2	0.443004055761242	4		524	615	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950075	44950075	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	199	280	0	ENST00000377967.4:c.3844A>G	p.Lys1282Glu	p.K1282E	ENST00000377967	NM_021140.2	1282	Aag/Gag	26/29	1	1	FACETS	1	0.983	1	1	0.995	1	CLONAL	2	TRUE	0	0.443004055761242	1		280	320	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0014970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	84	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.914	0.806	1	0.914	0.806	1	CLONAL	1	TRUE	1	0.227273148447962	2		249	809	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532693	187532693	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	83	590	0	ENST00000441802.2:c.9700G>A	p.Glu3234Lys	p.E3234K	ENST00000441802	NM_005245.3	3234	Gaa/Aaa	14/27	1	2	FACETS	0.838	0.738	0.945	0.838	0.738	0.945	CLONAL	1	TRUE	1	0.227273148447962	2		590	872	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187680	11187680	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0014970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	87	552	0	ENST00000361445.4:c.6216+1G>T		p.X2072_splice	ENST00000361445	NM_004958.3	2072			1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.227273148447962	2		552	736	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857525	68857526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0014970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	66	426	0	ENST00000261769.5:c.2161dup	p.Leu721ProfsTer27	p.L721Pfs*27	ENST00000261769	NM_004360.3	720	-/C	13/16	0.227273148447962	1	FACETS	0.903	0.784	1	0.903	0.784	1	CLONAL	1	TRUE	0	0.227273148447962	1		426	570	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554252	29554252	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	35	413	0	ENST00000356175.3:c.2268G>C	p.Gln756His	p.Q756H	ENST00000356175	NM_000267.3	756	caG/caC	19/57	1	2	FACETS	0.545	0.446	0.657	0.545	0.446	0.657	SUBCLONAL	1	TRUE	1	0.227273148447962	2		413	565	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417850	138417850	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	77	685	4	ENST00000289153.2:c.1669C>T	p.Leu557Phe	p.L557F	ENST00000289153	NM_006219.2	557	Ctt/Ttt	11/22	1	2	FACETS	0.814	0.714	0.923	0.814	0.714	0.923	CLONAL	1	TRUE	1	0.227273148447962	2		689	832	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506990	186506990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	57	366	0	ENST00000323963.5:c.1156C>T	p.Arg386Cys	p.R386C	ENST00000323963		386	Cgt/Tgt	11/11	1	2	FACETS	0.912	0.783	1	0.912	0.783	1	CLONAL	1	TRUE	1	0.227273148447962	2		366	550	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047942	180047942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138368337	NA	P-0014970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	67	659	0	ENST00000261937.6:c.2233C>T	p.Arg745Cys	p.R745C	ENST00000261937	NM_182925.4	745	Cgc/Tgc	15/30	1	2	FACETS	0.573	0.496	0.657	0.573	0.496	0.657	SUBCLONAL	1	TRUE	1	0.227273148447962	2		659	1029	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188011	32188011	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	108	769	0	ENST00000375023.3:c.1210G>A	p.Asp404Asn	p.D404N	ENST00000375023	NM_004557.3	404	Gat/Aat	7/30	1	2	FACETS	0.973	0.872	1	0.973	0.872	1	CLONAL	1	TRUE	1	0.227273148447962	2		769	977	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920218	76920218	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	67	537	0	ENST00000373344.5:c.3859G>A	p.Asp1287Asn	p.D1287N	ENST00000373344	NM_000489.3	1287	Gat/Aat	11/35	0.227273148447962	1	FACETS	0.758	0.659	0.867	0.758	0.659	0.867	SUBCLONAL	1	TRUE	0	0.227273148447962	1		537	689	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0015007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	146	265	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	0.385480727944287	2		265	727	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	119	140	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.816	0.736	0.899	0.816	0.736	0.899	CLONAL	1	TRUE	1	0.385480727944287	2		140	757	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161330	55161330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	285	715	0	ENST00000257290.5:c.3161C>T	p.Ser1054Phe	p.S1054F	ENST00000257290	NM_006206.4	1054	tCc/tTc	23/23	0.352272335336419	3	FACETS	0.855	0.805	0.907	0.855	0.805	0.907	CLONAL	2	TRUE	1	0.385480727944287	3		715	1031	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851426	156851426	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	197	1141	0	ENST00000524377.1:c.2383C>A	p.Leu795Met	p.L795M	ENST00000524377	NM_002529.3	795	Ctg/Atg	17/17	1	2	FACETS	0.918	0.849	0.989	0.918	0.849	0.989	CLONAL	1	TRUE	1	0.385480727944287	2		1141	1114	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624273	89624274	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	134	574	0	ENST00000371953.3:c.48dup	p.Gln17SerfsTer27	p.Q17Sfs*27	ENST00000371953	NM_000314.4	16	tat/taTt	1/9	0.385480727944287	1	FACETS	0.966	0.881	1	0.966	0.881	1	CLONAL	1	TRUE	0	0.385480727944287	1		574	581	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416895	416895	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	74	492	0	ENST00000399788.2:c.3655C>T	p.Arg1219Ter	p.R1219*	ENST00000399788	NM_001042603.1	1219	Cga/Tga	23/28	NA	2	FACETS	0.701	0.614	0.793			1	INDETERMINATE	1	TRUE	NA	0.385480727944287	2		492	548	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434057	49434057	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	171	824	0	ENST00000301067.7:c.7496C>T	p.Pro2499Leu	p.P2499L	ENST00000301067	NM_003482.3	2499	cCc/cTc	31/54	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.385480727944287	2		824	826	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184333	7184333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	164	790	0	ENST00000302850.5:c.968C>T	p.Ser323Phe	p.S323F	ENST00000302850	NM_000208.2	323	tCc/tTc	3/22	1	2	FACETS	0.882	0.809	0.958	0.882	0.809	0.958	CLONAL	1	TRUE	1	0.385480727944287	2		790	965	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	162	503	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.779	0.714	0.847	1	0.989	1	SUBCLONAL	2	TRUE	1	0.20750635776768	2		504	1002	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882019	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	65	574	0	ENST00000269305.4:c.455dup	p.Pro153AlafsTer28	p.P153Afs*28	ENST00000269305	NM_001126112.2	152	ccg/ccCg	5/11	1	2	FACETS	0.57	0.492	0.654	0.57	0.492	0.654	SUBCLONAL	1	TRUE	1	0.20750635776768	2		574	1100	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420070	41420070	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	38	329	0	ENST00000373198.4:c.251C>A	p.Ser84Tyr	p.S84Y	ENST00000373198	NM_133170.3	84	tCt/tAt	3/32	1	2	FACETS	0.971	0.804	1	0.971	0.804	1	CLONAL	1	TRUE	1	0.20750635776768	2		329	377	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446247	187446247	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	79	175	0	ENST00000232014.4:c.1441C>T	p.Gln481Ter	p.Q481*	ENST00000232014	NM_001130845.1	481	Cag/Tag	6/10	1	2	FACETS	0.965	0.848	1	0.965	0.848	1	CLONAL	1	TRUE	1	0.20750635776768	2		175	789	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81922859	81922859	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	63	448	0	ENST00000359376.3:c.848C>A	p.Pro283His	p.P283H	ENST00000359376	NM_002661.3	283	cCt/cAt	10/33	1	2	FACETS	0.921	0.796	1	0.921	0.796	1	CLONAL	1	TRUE	1	0.20750635776768	2		448	659	SUCCESS
ATR	545	MSKCC	GRCh37	3	142184028	142184028	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	80	389	0	ENST00000350721.4:c.6952G>A	p.Asp2318Asn	p.D2318N	ENST00000350721	NM_001184.3	2318	Gat/Aat	41/47	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.20750635776768	2		389	645	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682944	241682944	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	62	504	0	ENST00000366560.3:c.79G>T	p.Gly27Cys	p.G27C	ENST00000366560	NM_000143.3	27	Ggc/Tgc	1/10	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.20750635776768	2		504	536	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174901	11174901	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	72	655	1	ENST00000361445.4:c.7133G>T	p.Arg2378Ile	p.R2378I	ENST00000361445	NM_004958.3	2378	aGa/aTa	52/58	1	2	FACETS	0.809	0.705	0.921	0.809	0.705	0.921	CLONAL	1	TRUE	1	0.20750635776768	2		656	858	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17350465	17350465	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	A	novel	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	99	533	0	ENST00000375499.3:c.642+3G>T		p.X214_splice	ENST00000375499	NM_003000.2	214			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.20750635776768	2		533	768	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809851	36809851	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	78	587	0	ENST00000373129.3:c.754G>C	p.Gly252Arg	p.G252R	ENST00000373129	NM_032017.1	252	Ggc/Cgc	9/12	1	2	FACETS	0.936	0.822	1	0.936	0.822	1	CLONAL	1	TRUE	1	0.20750635776768	2		587	803	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873238	71873238	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	44	420	0	ENST00000357731.5:c.956A>T	p.Gln319Leu	p.Q319L	ENST00000357731	NM_173808.2	319	cAg/cTg	7/7	1	2	FACETS	0.732	0.613	0.864	0.732	0.613	0.864	SUBCLONAL	1	TRUE	1	0.20750635776768	2		420	579	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729744	162729744	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	60	592	0	ENST00000367921.3:c.830G>T	p.Arg277Leu	p.R277L	ENST00000367921	NM_006182.2	277	cGc/cTc	8/18	1	2	FACETS	0.74	0.637	0.854	0.74	0.637	0.854	SUBCLONAL	1	TRUE	1	0.20750635776768	2		592	781	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352453	118352453	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	179	416	0	ENST00000534358.1:c.3658T>C	p.Ser1220Pro	p.S1220P	ENST00000534358	NM_005933.3	1220	Tct/Cct	7/36	0.196469682614479	4	FACETS	0.945	0.873	1			1	CLONAL	3	TRUE	NA	0.20750635776768	4		416	735	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425685	49425685	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	36	571	0	ENST00000301067.7:c.12803G>C	p.Gly4268Ala	p.G4268A	ENST00000301067	NM_003482.3	4268	gGa/gCa	39/54	1	2	FACETS	0.596	0.489	0.717	0.596	0.489	0.717	SUBCLONAL	1	TRUE	1	0.20750635776768	2		571	582	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515385	103515385	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	32	301	0	ENST00000355739.4:c.1886A>G	p.Gln629Arg	p.Q629R	ENST00000355739	NM_000123.3	629	cAg/cGg	8/15	1	2	FACETS	0.777	0.631	0.942	0.777	0.631	0.942	CLONAL	1	TRUE	1	0.20750635776768	2		301	397	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000370	42000370	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	151	479	0	ENST00000219905.7:c.2389G>T	p.Gly797Ter	p.G797*	ENST00000219905	NM_001164273.1	797	Gga/Tga	7/24	0.196036151496456	2	FACETS	0.983	0.901	1	0.983	0.901	1	CLONAL	2	TRUE	0	0.20750635776768	2		479	740	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508804	29508804	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1060500274	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	81	394	0	ENST00000356175.3:c.730+1G>T		p.X244_splice	ENST00000356175	NM_000267.3	244			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.20750635776768	2		394	607	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533820	63533820	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868617060	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	75	495	0	ENST00000307078.5:c.1334G>A	p.Arg445Lys	p.R445K	ENST00000307078	NM_004655.3	445	aGg/aAg	6/11	0.0696846874823369	3	FACETS	1	0.972	1	0.702	0.616	0.795	INDETERMINATE	1	TRUE	1	0.20750635776768	3		495	568	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78854237	78854237	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	88	521	0	ENST00000306801.3:c.1532A>G	p.Lys511Arg	p.K511R	ENST00000306801	NM_020761.2	511	aAg/aGg	14/34	0.0696846874823369	3	FACETS	1	0.949	1	0.565	0.499	0.634	INDETERMINATE	1	TRUE	1	0.20750635776768	3		521	829	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600393	10600393	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	128	893	3	ENST00000171111.5:c.1462G>T	p.Glu488Ter	p.E488*	ENST00000171111	NM_203500.1	488	Gag/Tag	4/6	0.20750635776768	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.20750635776768	1		896	980	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954608	17954608	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	92	922	0	ENST00000458235.1:c.286C>T	p.Gln96Ter	p.Q96*	ENST00000458235	NM_000215.3	96	Caa/Taa	3/24	1	2	FACETS	0.889	0.789	0.998	0.889	0.789	0.998	CLONAL	1	TRUE	1	0.20750635776768	2		922	997	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308054	30308054	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs778224499	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	84	516	0	ENST00000262643.3:c.191A>G	p.Asn64Ser	p.N64S	ENST00000262643	NM_001238.2	64	aAt/aGt	5/12	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.20750635776768	2		516	721	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727962	41727962	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	40	462	0	ENST00000301178.4:c.586+1G>T		p.X196_splice	ENST00000301178	NM_021913.4	196			1	2	FACETS	0.827	0.687	0.983	0.827	0.687	0.983	CLONAL	1	TRUE	1	0.20750635776768	2		462	466	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909730	50909730	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	48	879	0	ENST00000440232.2:c.1450G>T	p.Glu484Ter	p.E484*	ENST00000440232	NM_002691.3	484	Gag/Tag	12/27	0.20750635776768	1	FACETS	0.456	0.384	0.535	0.456	0.384	0.535	SUBCLONAL	1	TRUE	0	0.20750635776768	1		879	910	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25990569	25990569	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	87	521	0	ENST00000435504.4:c.658G>T	p.Gly220Ter	p.G220*	ENST00000435504		220	Gga/Tga	8/13	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.20750635776768	2		521	683	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248565	212248565	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	60	489	0	ENST00000342788.4:c.3702del	p.Ala1236ArgfsTer55	p.A1236Rfs*55	ENST00000342788	NM_005235.2	1234	aaG/aa	28/28	1	2	FACETS	0.852	0.733	0.981	0.852	0.733	0.981	CLONAL	1	TRUE	1	0.20750635776768	2		489	679	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546787	9546787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	34	245	0	ENST00000353224.5:c.1235C>T	p.Pro412Leu	p.P412L	ENST00000353224	NM_177990.2	412	cCg/cTg	5/10	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.20750635776768	2		245	259	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757469	40757469	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	80	612	0	ENST00000373198.4:c.2829C>G	p.Tyr943Ter	p.Y943*	ENST00000373198	NM_133170.3	943	taC/taG	20/32	1	2	FACETS	0.972	0.855	1	0.972	0.855	1	CLONAL	1	TRUE	1	0.20750635776768	2		612	793	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877381	40877381	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	73	538	0	ENST00000373198.4:c.2315G>T	p.Gly772Val	p.G772V	ENST00000373198	NM_133170.3	772	gGc/gTc	15/32	1	2	FACETS	0.943	0.824	1	0.943	0.824	1	CLONAL	1	TRUE	1	0.20750635776768	2		538	746	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514533	41514533	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	74	619	1	ENST00000373198.4:c.128A>G	p.Tyr43Cys	p.Y43C	ENST00000373198	NM_133170.3	43	tAt/tGt	2/32	1	2	FACETS	0.849	0.742	0.965	0.849	0.742	0.965	CLONAL	1	TRUE	1	0.20750635776768	2		620	840	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221685	22221685	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1213398032	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	65	301	2	ENST00000215832.6:c.46G>T	p.Gly16Trp	p.G16W	ENST00000215832	NM_002745.4	16	Ggg/Tgg	1/9	0.20750635776768	1	FACETS	0.811	0.708	0.922	1	0.976	1	CLONAL	2	TRUE	0	0.20750635776768	1		303	346	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294258	1294258	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	81	730	0	ENST00000310581.5:c.743G>C	p.Arg248Pro	p.R248P	ENST00000310581	NM_198253.2	248	cGg/cCg	2/16	0.20750635776768	1	FACETS	0.911	0.802	1	0.911	0.802	1	CLONAL	1	TRUE	0	0.20750635776768	1		730	768	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515208	149515208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs141870925	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	91	658	0	ENST00000261799.4:c.274G>T	p.Gly92Trp	p.G92W	ENST00000261799	NM_002609.3	92	Ggg/Tgg	3/23	0.20750635776768	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.20750635776768	1		658	689	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394966	394966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	99	524	0	ENST00000380956.4:c.362C>T	p.Pro121Leu	p.P121L	ENST00000380956	NM_001195286.1	121	cCg/cTg	3/9	0.196036151496456	2	FACETS	1	0.979	1	0.707	0.631	0.787	CLONAL	1	TRUE	0	0.20750635776768	2		524	675	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187989	32187989	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	124	743	1	ENST00000375023.3:c.1232C>A	p.Pro411His	p.P411H	ENST00000375023	NM_004557.3	411	cCc/cAc	7/30	0.196036151496456	2	FACETS	1	0.982	1	0.698	0.631	0.769	CLONAL	1	TRUE	0	0.20750635776768	2		744	856	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519428	137519428	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	28	196	0	ENST00000367739.4:c.1210G>C	p.Glu404Gln	p.E404Q	ENST00000367739	NM_000416.2	404	Gag/Cag	7/7	0.20750635776768	3	FACETS	0.889	0.711	1			1	CLONAL	1	TRUE	NA	0.20750635776768	3		196	335	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469823	157469823	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	116	577	1	ENST00000346085.5:c.2617G>T	p.Gly873Cys	p.G873C	ENST00000346085	NM_020732.3	873	Ggt/Tgt	9/20	0.20750635776768	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.20750635776768	1		578	743	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350060	81350060	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	30	359	0	ENST00000222390.5:c.1271+1G>A		p.X424_splice	ENST00000222390	NM_000601.4	424			1	2	FACETS	0.506	0.406	0.619	0.506	0.406	0.619	SUBCLONAL	1	TRUE	1	0.20750635776768	2		359	572	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69103989	69103989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	49	675	0	ENST00000288368.4:c.4379C>T	p.Pro1460Leu	p.P1460L	ENST00000288368	NM_024870.2	1460	cCa/cTa	36/40	1	2	FACETS	0.495	0.418	0.581	0.495	0.418	0.581	SUBCLONAL	1	TRUE	1	0.20750635776768	2		675	954	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376014	8376014	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	48	372	1	ENST00000356435.5:c.4583C>A	p.Pro1528His	p.P1528H	ENST00000356435		1528	cCt/cAt	28/35	0.20750635776768	1	FACETS	0.899	0.761	1	0.899	0.761	1	CLONAL	1	TRUE	0	0.20750635776768	1		373	461	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465467	8465467	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	47	439	0	ENST00000356435.5:c.3713C>A	p.Ser1238Tyr	p.S1238Y	ENST00000356435		1238	tCt/tAt	21/35	0.20750635776768	1	FACETS	0.785	0.663	0.921	0.785	0.663	0.921	CLONAL	1	TRUE	0	0.20750635776768	1		439	517	SUCCESS
AR	367	MSKCC	GRCh37	X	66765518	66765518	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	78	776	1	ENST00000374690.3:c.530G>A	p.Cys177Tyr	p.C177Y	ENST00000374690	NM_000044.3	177	tGc/tAc	1/8	0.20750635776768	1	FACETS	0.836	0.734	0.946	0.836	0.734	0.946	CLONAL	1	TRUE	0	0.20750635776768	1		777	806	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795103	242795104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs768249210	NA	P-0015030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	71	436	0	ENST00000334409.5:c.105dup	p.Thr36HisfsTer70	p.T36Hfs*70	ENST00000334409	NM_005018.2	35	-/C	2/5	1	2	FACETS	0.712	0.62	0.812	0.712	0.62	0.812	SUBCLONAL	1	TRUE	1	0.226768639065971	2		436	879	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691926	30691926	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	33	507	0	ENST00000295754.5:c.428G>T	p.Cys143Phe	p.C143F	ENST00000295754	NM_003242.5	143	tGc/tTc	3/7	0.226768639065971	1	FACETS	0.755	0.616	0.911	0.755	0.616	0.911	CLONAL	1	TRUE	0	0.226768639065971	1		507	342	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937017	76937017	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	34	502	0	ENST00000373344.5:c.3731C>A	p.Ser1244Tyr	p.S1244Y	ENST00000373344	NM_000489.3	1244	tCt/tAt	9/35	0.226768639065971	3	FACETS	0.933	0.763	1	0.466	0.381	0.561	CLONAL	1	TRUE	1	0.226768639065971	3		502	358	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160679	56160680	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1169355679	NA	P-0015051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	362	402	0	ENST00000399503.3:c.954dup	p.Leu319ThrfsTer7	p.L319Tfs*7	ENST00000399503	NM_005921.1	318	tta/ttAa	4/20	0.234286409215994	8	FACETS	0.988	0.938	1			1	CLONAL	5	TRUE	NA	0.234286409215994	8		402	1065	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0015051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	45	223	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	0.231194686969691	4	FACETS	0.619	0.519	0.731	0.309	0.259	0.366	SUBCLONAL	1	TRUE	2	0.234286409215994	4		223	766	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0015051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	173	548	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.231194686969691	4	FACETS	0.856	0.787	0.928	0.856	0.787	0.928	CLONAL	2	TRUE	2	0.234286409215994	4		548	1065	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070577	67070578	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	118	257	0	ENST00000412916.2:c.207dup	p.Pro70SerfsTer13	p.P70Sfs*13	ENST00000412916		67	-/T	3/6	NA	2	FACETS	0.916	0.829	1			1	INDETERMINATE	2	TRUE	NA	0.234286409215994	2		257	550	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258734	16258735	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	166	546	0	ENST00000375759.3:c.6005dup	p.Asn2002LysfsTer2	p.N2002Kfs*2	ENST00000375759	NM_015001.2	2000	gga/ggAa	11/15	0.234286409215994	7	FACETS	1	0.974	1			1	CLONAL	2	TRUE	NA	0.234286409215994	7		546	984	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111549	8111550	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	182	532	0	ENST00000346208.3:c.1037dup	p.Leu347AlafsTer5	p.L347Afs*5	ENST00000346208		345	-/A	5/6	1	2	FACETS	0.939	0.868	1	1	0.992	1	CLONAL	2	TRUE	1	0.234286409215994	2		532	827	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870966	12870967	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	117	338	0	ENST00000228872.4:c.193_194insG	p.Gln65ArgfsTer60	p.Q65Rfs*60	ENST00000228872	NM_004064.3	65	cag/cGag	1/3	0.234286409215994	6	FACETS	0.897	0.808	0.99			1	CLONAL	2	TRUE	NA	0.234286409215994	6		338	818	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248151	110248151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	187	466	1	ENST00000374672.4:c.1321G>A	p.Asp441Asn	p.D441N	ENST00000374672	NM_004235.4	441	Gat/Aat	5/5	0.17605843412155	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.234286409215994	4		467	869	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0015076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	562	509	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.765549521110994	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.765549521110994	3		509	930	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28934577	NA	P-0015076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	316	490	0	ENST00000269305.4:c.770T>C	p.Leu257Pro	p.L257P	ENST00000269305	NM_001126112.2	257	cTg/cCg	7/11	0.729114367106749	1	FACETS	0.951	0.91	0.991	0.951	0.91	0.991	CLONAL	1	TRUE	0	0.765549521110994	1		490	536	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380346	14380346	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	329	508	1	ENST00000256196.4:c.71G>T	p.Gly24Val	p.G24V	ENST00000256196		24	gGc/gTc	1/6	0.392151312794557	1	FACETS	0.771	0.735	0.808	0.771	0.735	0.808	INDETERMINATE	1	TRUE	0	0.765549521110994	1		509	688	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953526	32953526	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	38	567	1	ENST00000380152.3:c.8827C>T	p.Gln2943Ter	p.Q2943*	ENST00000380152		2943	Cag/Tag	22/27	0.287191941457453	1	FACETS	0.085	0.069	0.102	0.085	0.069	0.102	INDETERMINATE	1	TRUE	0	0.765549521110994	1		568	724	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562779	95562795	+	frameshift_variant	Frame_Shift_Del	DEL	GGCATACTACCTAAGGA	GGCATACTACCTAAGGA	-	novel	NA	P-0015076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	43	314	0	ENST00000393063.1:c.4462_4478del	p.Ser1488IlefsTer6	p.S1488Ifs*6	ENST00000393063	NM_030621.3	1488	TCCTTAGGTAGTATGCCa/a	24/28	1	2	FACETS	0.21	0.175	0.249	0.21	0.175	0.249	SUBCLONAL	1	TRUE	1	0.765549521110994	2		314	535	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821901	59821901	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	124	589	0	ENST00000259008.2:c.2149C>G	p.Leu717Val	p.L717V	ENST00000259008	NM_032043.2	717	Ctg/Gtg	15/20	0.364803154344616	2	FACETS	0.46	0.416	0.505	0.23	0.208	0.253	INDETERMINATE	1	TRUE	0	0.765549521110994	2		589	705	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821921	59821921	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs768393936	NA	P-0015076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	117	489	0	ENST00000259008.2:c.2129C>G	p.Ser710Cys	p.S710C	ENST00000259008	NM_032043.2	710	tCt/tGt	15/20	0.364803154344616	2	FACETS	0.495	0.447	0.545	0.247	0.223	0.273	INDETERMINATE	1	TRUE	0	0.765549521110994	2		489	618	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743894	41743894	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	224	787	0	ENST00000301178.4:c.829G>C	p.Asp277His	p.D277H	ENST00000301178	NM_021913.4	277	Gac/Cac	7/20	1	2	FACETS	0.423	0.392	0.454	0.423	0.392	0.454	SUBCLONAL	1	TRUE	1	0.765549521110994	2		787	1384	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200773	128200774	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTTCTGGCGGC	novel	NA	P-0015076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	333	462	0	ENST00000341105.2:c.1021_1031dup	p.Ala345ProfsTer46	p.A345Pfs*46	ENST00000341105	NM_032638.4	344	aga/agGCCGCCAGAAGa	5/6	0.326409468938126	3	FACETS	1	0.992	1	0.624	0.591	0.657	INDETERMINATE	1	TRUE	1	0.765549521110994	3		462	964	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372470	55372470	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	577	994	0	ENST00000297316.4:c.1160A>G	p.Asn387Ser	p.N387S	ENST00000297316	NM_022454.3	387	aAt/aGt	2/2	NA	2	FACETS	1	0.967	1			1	INDETERMINATE	1	TRUE	NA	0.765549521110994	2		994	1498	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0000043-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	357	80	138	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.499745327197565	3	FACETS	0.916	0.81	1			1	CLONAL	1	TRUE	NA	0.499745327197565	3		138	437	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458129	120458129	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000043-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	658	347	362	0	ENST00000256646.2:c.7216G>T	p.Gly2406Cys	p.G2406C	ENST00000256646	NM_024408.3	2406	Ggt/Tgt	34/34	0.499745327197565	4	FACETS	1	0.972	1	0.691	0.655	0.727	CLONAL	2	TRUE	1	0.499745327197565	4		362	1005	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459060	120459060	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000043-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	772	117	321	0	ENST00000256646.2:c.6285G>T	p.Lys2095Asn	p.K2095N	ENST00000256646	NM_024408.3	2095	aaG/aaT	34/34	0.499745327197565	4	FACETS	0.79	0.712	0.873	0.263	0.237	0.291	SUBCLONAL	1	TRUE	1	0.499745327197565	4		321	889	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743294	162743294	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000043-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	688	131	270	0	ENST00000367921.3:c.1764C>G	p.Phe588Leu	p.F588L	ENST00000367921	NM_006182.2	588	ttC/ttG	14/18	0.332634771562406	3	FACETS	0.8	0.726	0.878			1	SUBCLONAL	1	TRUE	NA	0.499745327197565	3		270	819	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713870	30713870	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1023568316	NA	P-0000043-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	537	136	244	0	ENST00000295754.5:c.1195G>C	p.Gly399Arg	p.G399R	ENST00000295754	NM_003242.5	399	Ggg/Cgg	4/7	0.499745327197565	3	FACETS	1	0.921	1	0.505	0.46	0.552	CLONAL	1	TRUE	1	0.499745327197565	3		244	673	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412983	49412983	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000043-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	689	188	373	0	ENST00000418115.1:c.40G>A	p.Gly14Arg	p.G14R	ENST00000418115	NM_001664.2	14	Gga/Aga	2/5	0.499745327197565	3	FACETS	1	0.965	1	0.536	0.496	0.578	CLONAL	1	TRUE	1	0.499745327197565	3		373	877	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922298	178922298	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000043-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	711	182	293	0	ENST00000263967.3:c.1067T>C	p.Val356Ala	p.V356A	ENST00000263967	NM_006218.2	356	gTt/gCt	6/21	0.499745327197565	3	FACETS	1	0.939	1			1	CLONAL	1	TRUE	NA	0.499745327197565	3		293	893	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128848618	128848618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000043-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	749	145	361	0	ENST00000249373.3:c.1283C>T	p.Ser428Phe	p.S428F	ENST00000249373	NM_005631.4	428	tCc/tTc	7/12	0.499745327197565	4	FACETS	0.973	0.888	1	0.324	0.296	0.355	CLONAL	1	TRUE	1	0.499745327197565	4		361	894	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129358	64129358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1348353894	NA	P-0000043-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	743	188	499	0	ENST00000334205.4:c.790C>T	p.Arg264Trp	p.R264W	ENST00000334205	NM_003942.2	264	Cgg/Tgg	8/17	0.499745327197565	3	FACETS	1	0.933	1	0.337	0.311	0.364	CLONAL	1	TRUE	0	0.499745327197565	3		499	931	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118370572	118370572	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000043-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	387	390	340	0	ENST00000534358.1:c.6102A>C	p.Leu2034Phe	p.L2034F	ENST00000534358	NM_005933.3	2034	ttA/ttC	24/36	0.499745327197565	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.499745327197565	2		340	777	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793366	18793366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000043-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	1148	241	346	0	ENST00000266497.5:c.4063C>T	p.Leu1355Phe	p.L1355F	ENST00000266497		1355	Ctc/Ttc	30/31	0.499745327197565	4	FACETS	1	0.96	1	0.26	0.242	0.279	CLONAL	1	TRUE	0	0.499745327197565	4		346	1389	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479288	50479288	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000043-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	397	120	364	0	ENST00000394963.4:c.136C>G	p.Gln46Glu	p.Q46E	ENST00000394963	NM_003076.4	46	Caa/Gaa	1/13	0.499745327197565	2	FACETS	0.929	0.843	1	0.464	0.421	0.51	CLONAL	1	TRUE	0	0.499745327197565	2		364	517	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239627	105239627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000043-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	801	189	435	0	ENST00000349310.3:c.918G>A	p.Met306Ile	p.M306I	ENST00000349310	NM_001014432.1	306	atG/atA	11/15	0.438664770493146	4	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.499745327197565	4		435	990	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029237	14029237	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000043-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	769	219	373	0	ENST00000311895.7:c.1448G>C	p.Arg483Thr	p.R483T	ENST00000311895	NM_005236.2	483	aGa/aCa	8/11	0.200669838818692	3	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.499745327197565	3		373	988	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221123	5221123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769925793	NA	P-0000043-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	327	119	265	0	ENST00000357368.4:c.3343G>A	p.Ala1115Thr	p.A1115T	ENST00000357368	NM_002850.3	1115	Gcc/Acc	20/38	0.499745327197565	2	FACETS	1	0.95	1	0.534	0.485	0.585	CLONAL	1	TRUE	0	0.499745327197565	2		265	446	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942138	17942138	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000043-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	398	135	377	0	ENST00000458235.1:c.2877C>G	p.Ser959Arg	p.S959R	ENST00000458235	NM_000215.3	959	agC/agG	21/24	0.499745327197565	2	FACETS	1	0.925	1	0.507	0.463	0.553	CLONAL	1	TRUE	0	0.499745327197565	2		377	533	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560921	9560921	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000043-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	375	356	429	0	ENST00000353224.5:c.861G>T	p.Arg287Ser	p.R287S	ENST00000353224	NM_177990.2	287	agG/agT	4/10	0.499745327197565	2	FACETS	0.975	0.93	1	0.975	0.93	1	CLONAL	2	TRUE	0	0.499745327197565	2		429	731	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938964	76938964	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000043-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	1137	359	757	0	ENST00000373344.5:c.1784T>A	p.Leu595His	p.L595H	ENST00000373344	NM_000489.3	595	cTt/cAt	9/35	NA	2	FACETS	0.96	0.909	1			1	INDETERMINATE	1	TRUE	NA	0.499745327197565	2		757	1496	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185005	123185005	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000043-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	811	842	615	1	ENST00000218089.9:c.1052T>A	p.Leu351Gln	p.L351Q	ENST00000218089	NM_001042749.1	351	cTa/cAa	12/35	0.438664770493146	4	FACETS	1	0.984	1			1	CLONAL	3	TRUE	NA	0.499745327197565	4		616	1653	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389292	8389298	+	frameshift_variant	Frame_Shift_Del	DEL	CATTCTC	CATTCTC	-	novel	NA	P-0000043-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	948	159	500	0	ENST00000356435.5:c.4320_4326del	p.Trp1440Ter	p.W1440*	ENST00000356435		1440	tgGAGAATG/tg	26/35	NA	2	FACETS	0.575	0.526	0.626			1	INDETERMINATE	1	TRUE	NA	0.499745327197565	2		500	1107	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525118	187525118	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000043-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	161	64	95	0	ENST00000441802.2:c.10562G>C	p.Gly3521Ala	p.G3521A	ENST00000441802	NM_005245.3	3521	gGa/gCa	19/27	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.499745327197565	2		95	225	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629919	187629919	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000043-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	570	168	433	0	ENST00000441802.2:c.1063G>C	p.Val355Leu	p.V355L	ENST00000441802	NM_005245.3	355	Gtg/Ctg	2/27	1	2	FACETS	0.911	0.839	0.986	0.911	0.839	0.986	CLONAL	1	TRUE	1	0.499745327197565	2		433	738	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279457	1279457	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000043-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	695	115	335	0	ENST00000310581.5:c.2079C>A	p.Phe693Leu	p.F693L	ENST00000310581	NM_198253.2	693	ttC/ttA	5/16	0.438664770493146	4	FACETS	0.852	0.767	0.942			1	CLONAL	1	TRUE	NA	0.499745327197565	4		335	810	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958429	90958429	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000043-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	571	189	345	0	ENST00000265433.3:c.2009G>C	p.Arg670Thr	p.R670T	ENST00000265433	NM_002485.4	670	aGa/aCa	13/16	1	2	FACETS	0.995	0.922	1	0.995	0.922	1	CLONAL	1	TRUE	1	0.499745327197565	2		345	760	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341902	8341902	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000043-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	864	194	465	0	ENST00000356435.5:c.4738G>T	p.Asp1580Tyr	p.D1580Y	ENST00000356435		1580	Gat/Tat	29/35	NA	2	FACETS	0.734	0.678	0.791			1	INDETERMINATE	1	TRUE	NA	0.499745327197565	2		465	1058	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900287	32900287	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000043-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	630	173	291	0	ENST00000380152.3:c.475G>T	p.Val159Leu	p.V159L	ENST00000380152		159	Gtg/Ttg	5/27	0.499745327197565	2	FACETS	0.862	0.795	0.932	0.431	0.397	0.466	CLONAL	1	TRUE	0	0.499745327197565	2		291	803	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789661	3789661	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000043-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	612	210	492	0	ENST00000262367.5:c.4198G>A	p.Glu1400Lys	p.E1400K	ENST00000262367	NM_004380.2	1400	Gag/Aag	25/31	NA	2	FACETS	1	0.948	1			1	INDETERMINATE	1	TRUE	NA	0.499745327197565	2		492	822	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374296	138374296	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1171134914	NA	P-0000086-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	303	451	0	ENST00000289153.2:c.3148A>G	p.Arg1050Gly	p.R1050G	ENST00000289153	NM_006219.2	1050	Agg/Ggg	22/22	0.232522578555301	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.232522578555301	3		451	1318	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145590	11145590	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000086-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	55	190	0	ENST00000358026.2:c.3952C>G	p.Arg1318Gly	p.R1318G	ENST00000358026	NM_001128849.1	1318	Cgc/Ggc	29/36	0.232522578555301	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.232522578555301	1		190	349	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426722	212426722	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000086-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	64	311	0	ENST00000342788.4:c.2393T>G	p.Leu798Arg	p.L798R	ENST00000342788	NM_005235.2	798	cTt/cGt	20/28	1	2	FACETS	0.614	0.531	0.706	0.614	0.531	0.706	SUBCLONAL	1	TRUE	1	0.232522578555301	2		311	896	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141586	202141586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760898260	NA	P-0000105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	182	316	0	ENST00000358485.4:c.874C>T	p.Arg292Trp	p.R292W	ENST00000358485	NM_001080125.1	292	Cgg/Tgg	7/9	0.227766177530609	4	FACETS	0.973	0.898	1	0.973	0.898	1	CLONAL	2	TRUE	2	0.264565082272735	4		316	894	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182734	38182734	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	180	347	0	ENST00000396334.3:c.887C>G	p.Ser296Cys	p.S296C	ENST00000396334	NM_002468.4	296	tCt/tGt	5/5	0.264565082272735	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.264565082272735	3		347	694	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952117	178952117	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	271	201	0	ENST00000263967.3:c.3172A>C	p.Ile1058Leu	p.I1058L	ENST00000263967	NM_006218.2	1058	Atc/Ctc	21/21	0.264565082272735	7	FACETS	0.987	0.929	1	0.987	0.929	1	CLONAL	4	TRUE	3	0.264565082272735	7		201	862	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205814	108205814	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782001	NA	P-0000105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	137	219	0	ENST00000278616.4:c.8129A>G	p.Lys2710Arg	p.K2710R	ENST00000278616	NM_000051.3	2710	aAg/aGg	55/63	0.263741873404025	2	FACETS	0.988	0.904	1	0.988	0.904	1	CLONAL	2	TRUE	0	0.264565082272735	2		219	524	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0000105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	156	361	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.227766177530609	4	FACETS	1	0.921	1	1	0.921	1	CLONAL	2	TRUE	2	0.264565082272735	4		361	743	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577516	7577517	+	missense_variant	Missense_Mutation	DNP	GA	GA	AG	novel	NA	P-0000105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	135	240	0	ENST00000269305.4:c.764_765delinsCT	p.Ile255Thr	p.I255T	ENST00000269305	NM_001126112.2	255	aTC/aCT	7/11	0.264565082272735	3	FACETS	0.858	0.786	0.932	1	0.982	1	CLONAL	3	TRUE	1	0.264565082272735	3		240	449	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0000114-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	137	271	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	NA	2	FACETS	0.989	0.907	1			1	INDETERMINATE	2	TRUE	NA	0.316421397131159	2		271	438	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0000114-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	86	294	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.316421397131159	2		295	440	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776176	135776176	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000114-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	80	326	0	ENST00000298552.3:c.2551C>T	p.Gln851Ter	p.Q851*	ENST00000298552	NM_001162426.1	851	Cag/Tag	20/23	0.223834014725889	0	FACETS	0.944	0.837	1			1	CLONAL	1	TRUE	0	0.316421397131159	0		326	366	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874776	151874779	+	frameshift_variant	Frame_Shift_Del	DEL	GATT	GATT	-	novel	NA	P-0000114-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	33	249	0	ENST00000262189.6:c.7759_7762del	p.Asn2587Ter	p.N2587*	ENST00000262189	NM_170606.2	2587	AATCtg/tg	38/59	1	2	FACETS	0.596	0.486	0.719	0.596	0.486	0.719	SUBCLONAL	1	TRUE	1	0.316421397131159	2		249	350	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598150	55598150	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1379848125	NA	P-0000134-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	220	398	0	ENST00000288135.5:c.2347C>G	p.Leu783Val	p.L783V	ENST00000288135	NM_000222.2	783	Ctc/Gtc	16/21	NA	2	FACETS	0.746	0.697	0.796			1	INDETERMINATE	1	FALSE	NA	0.87384120665756	2		398	675	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913514	NA	P-0000134-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	51	344	0	ENST00000288135.5:c.2466T>A	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaA	17/21	NA	2	FACETS	0.206	0.175	0.24			1	INDETERMINATE	1	FALSE	NA	0.87384120665756	2		344	567	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0000134-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	887	649	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.861403543563603	2	FACETS	0.985	0.969	0.999	0.985	0.969	0.999	CLONAL	2	FALSE	0	0.87384120665756	2		649	1031	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951149	48951149	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000134-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	182	331	0	ENST00000267163.4:c.1312del	p.Cys438ValfsTer19	p.C438Vfs*19	ENST00000267163	NM_000321.2	437	ggT/gg	13/27	0.824013990512289	1	FACETS	0.916	0.872	0.959	0.916	0.872	0.959	CLONAL	1	FALSE	0	0.87384120665756	1		331	256	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0000144-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	76	423	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.221339955612413	1	FACETS	0.551	0.481	0.626	0.551	0.481	0.626	SUBCLONAL	1	TRUE	0	0.230811807213879	1		423	1058	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0000144-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	136	329	2	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.230811807213879	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.230811807213879	1		331	718	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257106	198257106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000144-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	97	259	0	ENST00000335508.6:c.3836C>T	p.Ala1279Val	p.A1279V	ENST00000335508	NM_012433.2	1279	gCt/gTt	25/25	1	2	FACETS	0.872	0.776	0.975	0.872	0.776	0.975	CLONAL	1	TRUE	1	0.230811807213879	2		259	964	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	463397	463397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000144-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	61	205	0	ENST00000399788.2:c.874G>A	p.Asp292Asn	p.D292N	ENST00000399788	NM_001042603.1	292	Gat/Aat	8/28	NA	2	FACETS	0.637	0.548	0.734			1	INDETERMINATE	1	TRUE	NA	0.230811807213879	2		205	830	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842463	68842463	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000144-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	125	222	0	ENST00000261769.5:c.524T>C	p.Leu175Pro	p.L175P	ENST00000261769	NM_004360.3	175	cTg/cCg	4/16	1	2	FACETS	0.955	0.868	1	1	0.989	1	CLONAL	2	TRUE	1	0.230811807213879	2		222	567	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984848	11984848	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0000152-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	79	143	0	ENST00000353533.5:c.393+1G>A		p.X131_splice	ENST00000353533	NM_003010.3	131			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		143	245	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0000180-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	96	153	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.301861181853857	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.28	1		153	408	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447714	187447714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138532510	NA	P-0000180-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	52	122	0	ENST00000232014.4:c.479G>A	p.Arg160His	p.R160H	ENST00000232014	NM_001130845.1	160	cGt/cAt	5/10	0.115134801555631	5	FACETS	1	0.951	1	0.43	0.367	0.499	INDETERMINATE	1	TRUE	2	0.28	5		122	409	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844181	68844181	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000180-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	98	175	0	ENST00000261769.5:c.769G>T	p.Asp257Tyr	p.D257Y	ENST00000261769	NM_004360.3	257	Gac/Tac	6/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.28	2		175	544	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37863308	37863308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1236052395	NA	P-0000180-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	42	275	0	ENST00000269571.5:c.139C>T	p.Arg47Cys	p.R47C	ENST00000269571		47	Cgc/Tgc	2/27	0.295993590660609	3	FACETS	0.431	0.358	0.512			1	SUBCLONAL	1	TRUE	NA	0.28	3		275	794	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0000259-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	40	138	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.837	1	1	0.837	1	CLONAL	1	TRUE	1	0.32	2		138	250	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86667940	86667940	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000259-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	110	267	0	ENST00000274376.6:c.1704G>A	p.Trp568Ter	p.W568*	ENST00000274376	NM_002890.2	568	tgG/tgA	13/25	1	2	FACETS	0.947	0.851	1	0.947	0.851	1	CLONAL	1	TRUE	1	0.32	2		267	726	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060789	38060800	+	inframe_deletion	In_Frame_Del	DEL	GAACGGGTGGTT	GAACGGGTGGTT	-	novel	NA	P-0000259-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	221	766	0	ENST00000250448.2:c.1189_1200del	p.Asn397_Phe400del	p.N397_F400del	ENST00000250448	NM_004496.3	397	AACCACCCGTTC/-	2/2	1	2	FACETS	0.994	0.923	1	0.994	0.923	1	CLONAL	1	TRUE	1	0.32	2		766	1389	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421798	49421798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000309-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1962	956	546	0	ENST00000301067.7:c.14509G>A	p.Gly4837Ser	p.G4837S	ENST00000301067	NM_003482.3	4837	Ggt/Agt	46/54	0.605758802082544	10	FACETS	0.926	0.896	0.955			1	CLONAL	4	TRUE	NA	0.605758802082544	10		546	2918	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956224	175956224	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000334-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	205	256	0	ENST00000367669.3:c.1988C>G	p.Ser663Cys	p.S663C	ENST00000367669	NM_022457.5	663	tCt/tGt	18/20	0.316648516591381	6	FACETS	1	0.987	1	0.43	0.398	0.463	INDETERMINATE	1	TRUE	3	0.637045703098702	6		256	1135	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707916	47707916	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000334-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	149	297	0	ENST00000233146.2:c.2540A>C	p.Lys847Thr	p.K847T	ENST00000233146	NM_000251.2	847	aAa/aCa	15/16	0.316648516591381	6	FACETS	1	0.959	1	0.361	0.33	0.395	INDETERMINATE	1	TRUE	3	0.637045703098702	6		297	981	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165665	185165665	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000334-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	173	261	0	ENST00000265026.3:c.940G>T	p.Ala314Ser	p.A314S	ENST00000265026	NM_004721.4	314	Gct/Tct	5/14	0.637045703098702	5	FACETS	0.95	0.873	1	0.317	0.291	0.344	CLONAL	1	TRUE	2	0.637045703098702	5		261	1118	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431976	49431976	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000334-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	267	399	0	ENST00000301067.7:c.9163C>T	p.Pro3055Ser	p.P3055S	ENST00000301067	NM_003482.3	3055	Cct/Tct	34/54	0.589862035556804	4	FACETS	1	0.961	1			1	CLONAL	1	TRUE	NA	0.637045703098702	4		399	1325	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553356	41553356	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000334-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	296	406	0	ENST00000263253.7:c.3445T>C	p.Phe1149Leu	p.F1149L	ENST00000263253	NM_001429.3	1149	Ttt/Ctt	18/31	0.637045703098702	2	FACETS	1	0.974	1	0.526	0.497	0.556	CLONAL	1	TRUE	0	0.637045703098702	2		406	883	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181269	123181269	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000334-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	526	385	0	ENST00000218089.9:c.733C>G	p.Gln245Glu	p.Q245E	ENST00000218089	NM_001042749.1	245	Caa/Gaa	9/35	NA	2	FACETS	0.923	0.892	0.953			1	INDETERMINATE	2	TRUE	NA	0.637045703098702	2		385	895	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000334-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	286	232	0	ENST00000269305.4:c.395del	p.Lys132ArgfsTer38	p.K132Rfs*38	ENST00000269305	NM_001126112.2	132	aAg/ag	5/11	0.637045703098702	2	FACETS	0.965	0.923	1	0.965	0.923	1	CLONAL	2	TRUE	0	0.637045703098702	2		232	465	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157499	106157499	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000376-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	178	251	0	ENST00000380013.4:c.2400T>A	p.His800Gln	p.H800Q	ENST00000380013	NM_001127208.2	800	caT/caA	3/11	0.566003508467452	1	FACETS	0.625	0.577	0.674	0.625	0.577	0.674	SUBCLONAL	1	TRUE	0	0.566003508467452	1		251	722	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578287	7578287	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000376-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	202	406	0	ENST00000269305.4:c.562del	p.Leu188TrpfsTer59	p.L188Wfs*59	ENST00000269305	NM_001126112.2	188	Ctg/tg	6/11	0.558537949623563	1	FACETS	0.885	0.826	0.946	0.885	0.826	0.946	CLONAL	1	TRUE	0	0.566003508467452	1		406	578	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960190	151960190	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000376-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	110	268	0	ENST00000262189.6:c.1210C>G	p.Leu404Val	p.L404V	ENST00000262189	NM_170606.2	404	Cta/Gta	9/59	0.332297049947755	3	FACETS	0.537	0.481	0.596			1	INDETERMINATE	1	TRUE	NA	0.566003508467452	3		268	929	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699256	18699256	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0000376-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	111	239	0	ENST00000266497.5:c.3358-1G>C		p.X1120_splice	ENST00000266497		1120			0.24483481791415	5	FACETS	0.592	0.53	0.657	0.197	0.176	0.219	INDETERMINATE	1	TRUE	2	0.566003508467452	5		239	1226	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0000381-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	87	138	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.43068623206751	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.43068623206751	1		138	281	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0000381-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	118	266	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.20059321649645	5	FACETS	1	0.982	1	0.465	0.42	0.512	INDETERMINATE	1	TRUE	2	0.43068623206751	5		266	647	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0000381-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	50	78	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.20059321649645	5	FACETS	1	0.963	1	0.488	0.417	0.564	INDETERMINATE	1	TRUE	2	0.43068623206751	5		78	261	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259649	89259649	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000381-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	35	114	0	ENST00000336596.2:c.793G>A	p.Glu265Lys	p.E265K	ENST00000336596	NM_005233.5	265	Gaa/Aaa	3/17	1	2	FACETS	0.86	0.712	1	0.86	0.712	1	CLONAL	1	TRUE	1	0.43068623206751	2		114	189	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945483	151945483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs77325966	NA	P-0000381-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	32	203	0	ENST00000262189.6:c.2036G>A	p.Arg679Lys	p.R679K	ENST00000262189	NM_170606.2	679	aGa/aAa	14/59	0.43068623206751	3	FACETS	0.348	0.282	0.423	0.174	0.141	0.212	SUBCLONAL	1	TRUE	1	0.43068623206751	3		203	519	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960110	151960110	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000381-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	181	374	0	ENST00000262189.6:c.1290G>C	p.Trp430Cys	p.W430C	ENST00000262189	NM_170606.2	430	tgG/tgC	9/59	0.43068623206751	3	FACETS	1	0.928	1	0.503	0.464	0.544	CLONAL	1	TRUE	1	0.43068623206751	3		374	1015	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941691	48941691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000381-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	156	252	0	ENST00000267163.4:c.1001G>A	p.Arg334Lys	p.R334K	ENST00000267163	NM_000321.2	334	aGa/aAa	10/27	0.277322023623974	4	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.43068623206751	4		252	828	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103510731	103510731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000381-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	108	206	0	ENST00000355739.4:c.635C>T	p.Thr212Ile	p.T212I	ENST00000355739	NM_000123.3	212	aCc/aTc	6/15	0.135481987345597	4	FACETS	0.757	0.683	0.834	0.757	0.683	0.834	INDETERMINATE	2	TRUE	2	0.43068623206751	4		206	474	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40742257	40742257	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000381-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	176	522	0	ENST00000392038.2:c.867C>G	p.Ile289Met	p.I289M	ENST00000392038	NM_001626.4	289	atC/atG	10/14	0.13989561306395	0	FACETS	0.658	0.608	0.71			1	INDETERMINATE	1	TRUE	0	0.43068623206751	0		522	707	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723457	52723457	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000381-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	88	344	0	ENST00000322088.6:c.1318G>C	p.Asp440His	p.D440H	ENST00000322088	NM_014225.5	440	Gat/Cat	11/15	NA	2	FACETS	0.777	0.69	0.869			1	INDETERMINATE	1	TRUE	NA	0.43068623206751	2		344	526	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790028	40790028	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000381-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	97	316	0	ENST00000373198.4:c.2703G>C	p.Lys901Asn	p.K901N	ENST00000373198	NM_133170.3	901	aaG/aaC	18/32	0.43068623206751	3	FACETS	1	0.935	1	0.53	0.474	0.59	CLONAL	1	TRUE	1	0.43068623206751	3		316	516	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269114	142269114	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000387-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	275	354	299	1	ENST00000350721.4:c.2836A>G	p.Met946Val	p.M946V	ENST00000350721	NM_001184.3	946	Atg/Gtg	14/47	0.294591636235198	1	FACETS	0.618	0.592	0.644	0.618	0.592	0.644	INDETERMINATE	1	TRUE	0	0.953003677523293	1		300	629	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118345015	118345015	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000387-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	218	238	212	0	ENST00000534358.1:c.3141C>G	p.Asp1047Glu	p.D1047E	ENST00000534358	NM_005933.3	1047	gaC/gaG	3/36	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.953003677523293	2		212	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578518	7578518	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934875	NA	P-0000387-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	22	337	284	1	ENST00000269305.4:c.412G>C	p.Ala138Pro	p.A138P	ENST00000269305	NM_001126112.2	138	Gcc/Ccc	5/11	0.951993713779278	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.953003677523293	1		285	359	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246911	10246911	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000387-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	498	397	360	0	ENST00000340748.4:c.4494G>A	p.Trp1498Ter	p.W1498*	ENST00000340748		1498	tgG/tgA	37/40	1	2	FACETS	0.931	0.89	0.973	0.931	0.89	0.973	CLONAL	1	TRUE	1	0.953003677523293	2		360	895	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936979	48936992	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTCGAACACCCA	ACCTCGAACACCCA	-	novel	NA	P-0000387-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	36	214	402	0	ENST00000267163.4:c.747_760del	p.Pro250AlafsTer16	p.P250Afs*16	ENST00000267163	NM_000321.2	249	tcACCTCGAACACCCAgg/tcgg	8/27	0.951993713779278	1	FACETS	0.94	0.91	0.968	0.94	0.91	0.968	CLONAL	1	TRUE	0	0.953003677523293	1		402	250	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0000395-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	658	260	349	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.212279417568725	4	FACETS	0.95	0.891	1	0.633	0.594	0.673	INDETERMINATE	2	TRUE	1	0.425002820953378	4		349	918	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000395-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	1254	327	661	0	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	0.212279417568725	4	FACETS	1	0.993	1	0.462	0.435	0.49	INDETERMINATE	1	TRUE	1	0.425002820953378	4		661	1581	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391236	89391236	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000395-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	376	52	158	0	ENST00000336596.2:c.1302G>T	p.Gln434His	p.Q434H	ENST00000336596	NM_005233.5	434	caG/caT	5/17	1	2	FACETS	0.572	0.488	0.664	0.572	0.488	0.664	SUBCLONAL	1	TRUE	1	0.425002820953378	2		158	428	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937437	178937437	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000395-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	517	58	254	1	ENST00000263967.3:c.1825C>T	p.Pro609Ser	p.P609S	ENST00000263967	NM_006218.2	609	Cct/Tct	12/21	0.212279417568725	4	FACETS	0.676	0.581	0.78	0.225	0.193	0.26	INDETERMINATE	1	TRUE	1	0.425002820953378	4		255	575	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245455	153245455	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000395-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	820	371	478	0	ENST00000281708.4:c.1736G>T	p.Gly579Val	p.G579V	ENST00000281708	NM_033632.3	579	gGg/gTg	11/12	0.296999530187852	2	FACETS	1	0.995	1	0.733	0.696	0.771	CLONAL	1	TRUE	0	0.425002820953378	2		478	1191	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629504	187629504	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000395-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	682	408	566	0	ENST00000441802.2:c.1478G>T	p.Gly493Val	p.G493V	ENST00000441802	NM_005245.3	493	gGt/gTt	2/27	0.426206855569244	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.425002820953378	1		566	1090	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26021096	26021096	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1376006955	NA	P-0000395-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	492	37	150	0	ENST00000357647.3:c.379C>T	p.Leu127Phe	p.L127F	ENST00000357647	NM_003529.2	127	Ctc/Ttc	1/1	0.426206855569244	4	FACETS	0.469	0.386	0.562	0.156	0.128	0.188	SUBCLONAL	1	TRUE	1	0.425002820953378	4		150	529	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610415	10610415	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000395-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	551	395	521	0	ENST00000171111.5:c.295G>A	p.Val99Met	p.V99M	ENST00000171111	NM_203500.1	99	Gtg/Atg	2/6	0.425002820953378	2	FACETS	0.982	0.938	1	0.982	0.938	1	CLONAL	2	TRUE	0	0.425002820953378	2		521	946	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000471-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	108	254	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.599584228874654	3	FACETS	0.889	0.802	0.981	0.296	0.267	0.327	CLONAL	1	FALSE	0	0.664369221395686	3		254	487	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0000476-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	329	511	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	0.967173278611815	1	FACETS	0.937	0.914	0.958	0.937	0.914	0.958	CLONAL	1	FALSE	0	0.967173278611815	1		511	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578516	7578517	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0000476-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	460	472	2	ENST00000269305.4:c.413_414delinsAA	p.Ala138Glu	p.A138E	ENST00000269305	NM_001126112.2	138	gCC/gAA	5/11	0.594519530588195	4	FACETS	0.798	0.764	0.833			1	SUBCLONAL	2	FALSE	NA	0.967173278611815	4		474	1172	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518427	204518427	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	49	370	0	ENST00000367182.3:c.1090A>G	p.Arg364Gly	p.R364G	ENST00000367182	NM_001278516.1	364	Aga/Gga	11/11	0.10384740025791	5	FACETS	0.583	0.492	0.683	0.146	0.123	0.171	INDETERMINATE	1	TRUE	1	0.285777345805373	5		370	841	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966607	25966607	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	52	277	0	ENST00000435504.4:c.2599A>G	p.Asn867Asp	p.N867D	ENST00000435504		867	Aac/Gac	13/13	NA	2	FACETS	0.86	0.734	0.998			1	INDETERMINATE	1	TRUE	NA	0.285777345805373	2		277	423	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71161773	71161773	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1425273265	NA	P-0000485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	61	354	0	ENST00000318789.4:c.196A>G	p.Arg66Gly	p.R66G	ENST00000318789	NM_032682.5	66	Aga/Gga	7/21	0.24729435865443	2	FACETS	0.735	0.634	0.844	0.367	0.317	0.422	SUBCLONAL	1	TRUE	0	0.285777345805373	2		354	581	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094876	143094876	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	62	316	0	ENST00000262992.4:c.1268T>G	p.Leu423Arg	p.L423R	ENST00000262992	NM_001101669.1	423	cTt/cGt	14/24	1	2	FACETS	0.631	0.544	0.725	0.631	0.544	0.725	SUBCLONAL	1	TRUE	1	0.285777345805373	2		316	688	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339261	116339261	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0000485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	44	456	0	ENST00000397752.3:c.123T>G	p.Tyr41Ter	p.Y41*	ENST00000397752	NM_000245.2	41	taT/taG	2/21	0.10384740025791	5	FACETS	0.56	0.468	0.662	0.14	0.117	0.166	INDETERMINATE	1	TRUE	1	0.285777345805373	5		456	786	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393656	139393656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196509879	NA	P-0000485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	22	193	0	ENST00000277541.6:c.5990C>T	p.Thr1997Met	p.T1997M	ENST00000277541	NM_017617.3	1997	aCg/aTg	32/34	0.285777345805373	4	FACETS	0.561	0.434	0.708	0.187	0.144	0.236	SUBCLONAL	1	TRUE	1	0.285777345805373	4		193	353	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2105444	2105444	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	73	376	0	ENST00000219476.3:c.523G>C	p.Glu175Gln	p.E175Q	ENST00000219476	NM_000548.3	175	Gaa/Caa	6/42	0.285777345805373	1	FACETS	0.872	0.765	0.988	0.872	0.765	0.988	CLONAL	1	TRUE	0	0.285777345805373	1		376	502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0000485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	100	199	0	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	0.285777345805373	1	FACETS	0.996	0.902	1	1	0.988	1	CLONAL	2	TRUE	0	0.285777345805373	1		199	301	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78617549	78617549	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	67	241	3	ENST00000306801.3:c.287A>G	p.Gln96Arg	p.Q96R	ENST00000306801	NM_020761.2	96	cAg/cGg	3/34	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.285777345805373	2		244	451	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795286	42795286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	55	296	0	ENST00000575354.2:c.2366G>A	p.Gly789Glu	p.G789E	ENST00000575354	NM_015125.3	789	gGg/gAg	10/20	0.285777345805373	3	FACETS	1	0.859	1			1	CLONAL	1	TRUE	NA	0.285777345805373	3		296	439	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45854954	45854954	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	27	306	0	ENST00000391945.4:c.2216T>A	p.Leu739His	p.L739H	ENST00000391945	NM_000400.3	739	cTc/cAc	23/23	NA	2	FACETS	0.467	0.371	0.576			1	INDETERMINATE	1	TRUE	NA	0.285777345805373	2		306	405	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921606	39921606	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	74	241	0	ENST00000378444.4:c.4214C>T	p.Ser1405Leu	p.S1405L	ENST00000378444	NM_001123385.1	1405	tCg/tTg	10/15	1	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.285777345805373	1		241	323	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175783	176175784	+	missense_variant	Missense_Mutation	DNP	CT	CT	AC	novel	NA	P-0000485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	53	372	0	ENST00000367669.3:c.331_332delinsGT	p.Arg111Val	p.R111V	ENST00000367669	NM_022457.5	111	AGg/GTg	1/20	0.10384740025791	5	FACETS	0.915	0.78	1	0.229	0.195	0.266	INDETERMINATE	1	TRUE	1	0.285777345805373	5		372	579	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0000511-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	63	179	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.148446666542816	1	FACETS	0.801	0.693	0.918	0.801	0.693	0.918	CLONAL	1	TRUE	0	0.245477805384958	1		179	562	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0000511-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	85	293	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.245477805384958	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.245477805384958	1		293	525	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0000511-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	196	396	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	0.245477805384958	3	FACETS	0.881	0.816	0.95	0.881	0.816	0.95	CLONAL	2	TRUE	1	0.245477805384958	3		396	1017	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433982	49433982	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760263014	NA	P-0000511-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	68	217	0	ENST00000301067.7:c.7571C>T	p.Thr2524Met	p.T2524M	ENST00000301067	NM_003482.3	2524	aCg/aTg	31/54	1	2	FACETS	0.954	0.83	1	0.954	0.83	1	CLONAL	1	TRUE	1	0.245477805384958	2		217	581	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106616	27106616	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000519-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	227	284	0	ENST00000324856.7:c.6227A>T	p.Tyr2076Phe	p.Y2076F	ENST00000324856	NM_006015.4	2076	tAc/tTc	20/20	0.372217799950223	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.440230987368116	1		284	803	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270143	66270143	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000519-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	164	200	0	ENST00000273854.3:c.1739C>G	p.Thr580Arg	p.T580R	ENST00000273854	NM_004439.5	580	aCa/aGa	8/18	1	2	FACETS	0.873	0.802	0.948	0.873	0.802	0.948	CLONAL	1	TRUE	1	0.440230987368116	2		200	853	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741600	17741600	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000519-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	67	124	0	ENST00000250003.3:c.271G>T	p.Gly91Cys	p.G91C	ENST00000250003	NM_002478.4	91	Ggc/Tgc	1/3	1	2	FACETS	0.81	0.707	0.919	0.81	0.707	0.919	CLONAL	1	TRUE	1	0.440230987368116	2		124	376	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741569	17741597	+	frameshift_variant	Frame_Shift_Del	DEL	TGTGCGCGCGCCCAGCGGGCACCACCAGG	TGTGCGCGCGCCCAGCGGGCACCACCAGG	-	novel	NA	P-0000519-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	61	153	0	ENST00000250003.3:c.240_268del	p.Val81GlyfsTer37	p.V81Gfs*37	ENST00000250003	NM_002478.4	80	caTGTGCGCGCGCCCAGCGGGCACCACCAGGcg/cacg	1/3	1	2	FACETS	0.576	0.498	0.661	0.576	0.498	0.661	SUBCLONAL	1	TRUE	1	0.440230987368116	2		153	481	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115956	8115956	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000522-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	167	162	0	ENST00000346208.3:c.1305del	p.Ser436ProfsTer39	p.S436Pfs*39	ENST00000346208		434	caC/ca	6/6	0.61894700798361	4	FACETS	0.765	0.707	0.825	0.765	0.707	0.825	SUBCLONAL	2	TRUE	2	0.61894700798361	4		162	571	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190686	108190686	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0000522-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	307	224	0	ENST00000278616.4:c.6354del	p.Val2119Ter	p.V2119*	ENST00000278616	NM_000051.3	2118	gAa/ga	44/63	0.582673872464626	2	FACETS	0.922	0.881	0.963	0.922	0.881	0.963	CLONAL	2	TRUE	0	0.61894700798361	2		224	538	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0000547-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	960	93	853	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	NA	2	FACETS	0.282	0.25	0.316			1	INDETERMINATE	1	TRUE	NA	0.626951256681815	2		853	1053	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0000547-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	139	89	162	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	0.626951256681815	2		162	228	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416493	29416493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1182539285	NA	P-0000547-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	482	247	573	0	ENST00000389048.3:c.4460C>T	p.Ser1487Leu	p.S1487L	ENST00000389048	NM_004304.4	1487	tCg/tTg	29/29	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.626951256681815	2		573	729	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38946585	38946585	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000547-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	579	42	335	0	ENST00000357387.3:c.4384G>C	p.Ala1462Pro	p.A1462P	ENST00000357387	NM_152756.3	1462	Gcc/Ccc	33/38	0.190833804095354	3	FACETS	0.283	0.236	0.336	0.142	0.118	0.168	INDETERMINATE	1	TRUE	1	0.626951256681815	3		335	621	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061231	38061231	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000547-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	551	305	551	0	ENST00000250448.2:c.758T>A	p.Met253Lys	p.M253K	ENST00000250448	NM_004496.3	253	aTg/aAg	2/2	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.626951256681815	2		551	856	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862076	68862076	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs1385720097	NA	P-0000547-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	201	169	445	0	ENST00000261769.5:c.2165-1G>T		p.X722_splice	ENST00000261769	NM_004360.3	722			0.626951256681815	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.626951256681815	1		445	370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0000552-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	196	172	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.576040612238128	2	FACETS	0.941	0.89	0.992	0.941	0.89	0.992	CLONAL	2	TRUE	0	0.629150352057262	2		172	331	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0000552-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	269	161	4	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	0.629150352057262	2	FACETS	0.999	0.954	1	0.999	0.954	1	CLONAL	2	TRUE	0	0.629150352057262	2		165	428	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0000552-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	336	367	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.629150352057262	2		367	943	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231170	142231170	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000552-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	291	340	0	ENST00000350721.4:c.4784A>T	p.Lys1595Ile	p.K1595I	ENST00000350721	NM_001184.3	1595	aAa/aTa	27/47	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.629150352057262	2		340	921	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459522	50459522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1410124404	NA	P-0000552-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	115	183	0	ENST00000331340.3:c.811G>A	p.Val271Ile	p.V271I	ENST00000331340	NM_006060.4	271	Gtc/Atc	7/8	1	2	FACETS	0.835	0.757	0.915	0.835	0.757	0.915	CLONAL	1	TRUE	1	0.629150352057262	2		183	438	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575103	48575103	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000552-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	35	295	0	ENST00000342988.3:c.297G>T	p.Trp99Cys	p.W99C	ENST00000342988	NM_005359.5	99	tgG/tgT	3/12	0.629150352057262	1	FACETS	0.128	0.104	0.154	0.128	0.104	0.154	SUBCLONAL	1	TRUE	0	0.629150352057262	1		295	597	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0000566-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	26	465	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.887	0.702	1	0.887	0.702	1	CLONAL	1	TRUE	1	0.15	2		465	391	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204737488	204737488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000566-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	65	197	0	ENST00000302823.3:c.625C>T	p.Pro209Ser	p.P209S	ENST00000302823	NM_005214.4	209	Cca/Tca	4/4	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.15	2		197	592	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252866	36252866	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000566-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	56	146	0	ENST00000300305.3:c.496C>G	p.Arg166Gly	p.R166G	ENST00000300305		166	Cga/Gga	4/8	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.15	2		146	723	SUCCESS
AR	367	MSKCC	GRCh37	X	66765166	66765166	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000566-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	24	168	0	ENST00000374690.3:c.178C>A	p.Gln60Lys	p.Q60K	ENST00000374690	NM_000044.3	60	Cag/Aag	1/8	1	2	FACETS	1	0.832	1	1	0.832	1	CLONAL	1	TRUE	1	0.15	2		168	299	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713559	30713559	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0000584-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	191	447	0	ENST00000295754.5:c.884C>G	p.Ser295Ter	p.S295*	ENST00000295754	NM_003242.5	295	tCa/tGa	4/7	1	2	FACETS	0.989	0.926	1	0.989	0.926	1	CLONAL	1	TRUE	1	0.873556312711186	2		447	442	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110251308	110251308	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000584-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	203	639	0	ENST00000374672.4:c.29T>A	p.Met10Lys	p.M10K	ENST00000374672	NM_004235.4	10	aTg/aAg	2/5	1	2	FACETS	0.937	0.877	0.997	0.937	0.877	0.997	CLONAL	1	TRUE	1	0.873556312711186	2		639	496	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321025	30321025	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000584-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	146	446	0	ENST00000322652.5:c.1435G>T	p.Val479Phe	p.V479F	ENST00000322652	NM_015355.2	479	Gtt/Ttt	12/16	0.207385853158768	3	FACETS	1	0.988	1	0.688	0.637	0.74	INDETERMINATE	1	TRUE	1	0.873556312711186	3		446	349	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115873	8115874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0000584-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	318	857	0	ENST00000346208.3:c.1220dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tCcg	6/6	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.873556312711186	2		857	721	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519690	137519690	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000666-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	59	188	0	ENST00000367739.4:c.948A>C	p.Leu316Phe	p.L316F	ENST00000367739	NM_000416.2	316	ttA/ttC	7/7	0.279081412152954	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.833997013435353	0		188	166	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250137	110250137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573230258	NA	P-0000666-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	17	186	0	ENST00000374672.4:c.538C>T	p.Pro180Ser	p.P180S	ENST00000374672	NM_004235.4	180	Cct/Tct	3/5	1	2	FACETS	0.453	0.344	0.577	0.453	0.344	0.577	SUBCLONAL	1	TRUE	1	0.833997013435353	2		186	90	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578464	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000666-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	57	153	0	ENST00000269305.4:c.466del	p.Arg156AlafsTer14	p.R156Afs*14	ENST00000269305	NM_001126112.2	156	Cgc/gc	5/11	0.818717897805275	2	FACETS	0.833	0.759	0.903	0.833	0.759	0.903	CLONAL	2	TRUE	0	0.833997013435353	2		153	82	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0000667-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	622	464	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.680703570071174	4	FACETS	0.909	0.89	0.927	0.909	0.89	0.927	CLONAL	4	FALSE	0	0.812982535055637	4		464	763	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683575	162683575	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000667-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	119	272	0	ENST00000366898.1:c.394C>A	p.Pro132Thr	p.P132T	ENST00000366898	NM_004562.2	132	Cca/Aca	3/12	0.812982535055637	6	FACETS	1	0.918	1	0.204	0.184	0.225	CLONAL	1	FALSE	1	0.812982535055637	6		272	755	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370958	55370958	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs761010069	NA	P-0000667-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	152	159	0	ENST00000297316.4:c.260C>G	p.Ala87Gly	p.A87G	ENST00000297316	NM_022454.3	87	gCg/gGg	1/2	0.812982535055637	6	FACETS	1	0.942	1	0.346	0.316	0.378	CLONAL	1	FALSE	3	0.812982535055637	6		159	945	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431841	49431841	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1179293337	NA	P-0000667-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	122	174	0	ENST00000301067.7:c.9298C>T	p.Pro3100Ser	p.P3100S	ENST00000301067	NM_003482.3	3100	Cct/Tct	34/54	0.812982535055637	6	FACETS	1	0.919	1	0.403	0.368	0.44	CLONAL	2	FALSE	1	0.812982535055637	6		174	391	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863581	68863581	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs753540183	NA	P-0000667-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	131	335	0	ENST00000261769.5:c.2320A>G	p.Arg774Gly	p.R774G	ENST00000261769	NM_004360.3	774	Agg/Ggg	15/16	1	2	FACETS	0.69	0.63	0.752	0.69	0.63	0.752	SUBCLONAL	1	FALSE	1	0.812982535055637	2		335	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0000668-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	65	265	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.143689955170167	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		265	631	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0000704-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	130	162	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.490687963183934	8	FACETS	0.988	0.921	1			1	CLONAL	6	TRUE	NA	0.490687963183934	8		162	221	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719433	190719433	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000704-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	107	221	0	ENST00000441310.2:c.1435G>T	p.Gly479Trp	p.G479W	ENST00000441310	NM_000534.4	479	Ggg/Tgg	9/13	0.491693125263696	4	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	2	0.490687963183934	4		221	318	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681049	30681049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000704-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	118	283	0	ENST00000376406.3:c.670G>A	p.Glu224Lys	p.E224K	ENST00000376406	NM_014641.2	224	Gaa/Aaa	5/15	0.491693125263696	4	FACETS	0.969	0.883	1	0.969	0.883	1	CLONAL	2	TRUE	2	0.490687963183934	4		283	370	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710552	117710552	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000704-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	91	192	0	ENST00000368508.3:c.1720C>G	p.Leu574Val	p.L574V	ENST00000368508	NM_002944.2	574	Ctt/Gtt	12/43	0.490687963183934	15	FACETS	0.997	0.885	1			1	CLONAL	2	TRUE	NA	0.490687963183934	15		192	779	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287437	38287437	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000704-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	101	243	0	ENST00000425967.3:c.220G>C	p.Glu74Gln	p.E74Q	ENST00000425967	NM_001174067.1	74	Gag/Cag	4/19	0.490687963183934	6	FACETS	0.843	0.757	0.933			1	CLONAL	2	TRUE	NA	0.490687963183934	6		243	484	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692790	89692790	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000704-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	108	180	0	ENST00000371953.3:c.274G>C	p.Asp92His	p.D92H	ENST00000371953	NM_000314.4	92	Gac/Cac	5/9	0.486832301405034	2	FACETS	0.925	0.847	1	0.925	0.847	1	CLONAL	2	TRUE	0	0.490687963183934	2		180	238	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426751	49426751	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000704-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	73	154	0	ENST00000301067.7:c.11737C>T	p.Gln3913Ter	p.Q3913*	ENST00000301067	NM_003482.3	3913	Cag/Tag	39/54	0.491693125263696	4	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	2	0.490687963183934	4		154	203	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0000704-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	97	253	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	NA	2	FACETS	0.928	0.846	1			1	INDETERMINATE	2	TRUE	NA	0.490687963183934	2		253	213	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770633	40770633	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000704-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	112	205	1	ENST00000373198.4:c.2749G>A	p.Glu917Lys	p.E917K	ENST00000373198	NM_133170.3	917	Gag/Aag	19/32	0.491693125263696	4	FACETS	0.992	0.902	1	0.992	0.902	1	CLONAL	2	TRUE	2	0.490687963183934	4		206	343	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0000716-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	306	419	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.47194862880165	2	FACETS	0.886	0.849	0.922	1	0.995	1	CLONAL	3	TRUE	0	0.47194862880165	2		421	488	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257251	16257251	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000716-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	147	287	1	ENST00000375759.3:c.4516G>T	p.Gly1506Trp	p.G1506W	ENST00000375759	NM_015001.2	1506	Ggg/Tgg	11/15	NA	2	FACETS	0.752	0.694	0.812			1	INDETERMINATE	2	TRUE	NA	0.47194862880165	2		288	414	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341102	8341102	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs201441177	NA	P-0000716-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	86	409	0	ENST00000356435.5:c.5114T>C	p.Ile1705Thr	p.I1705T	ENST00000356435		1705	aTt/aCt	30/35	0.372788996662735	0	FACETS	0.705	0.632	0.781			1	SUBCLONAL	1	TRUE	0	0.47194862880165	0		409	273	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21968243	21968243	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0000716-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	131	236	0	ENST00000304494.5:c.458-2A>G		p.X153_splice	ENST00000304494	NM_000077.4	153			0.372788996662735	0	FACETS	0.682	0.637	0.725			1	SUBCLONAL	2	TRUE	0	0.47194862880165	0		236	215	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343507	343507	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567261095	NA	P-0000716-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	136	463	1	ENST00000262320.3:c.2167C>T	p.Arg723Ter	p.R723*	ENST00000262320	NM_003502.3	723	Cga/Tga	8/11	0.411500615025228	0	FACETS	0.659	0.615	0.701			1	SUBCLONAL	2	TRUE	0	0.47194862880165	0		464	231	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118365421	118365422	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0000716-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	182	489	0	ENST00000534358.1:c.5307dup	p.Pro1770SerfsTer15	p.P1770Sfs*15	ENST00000534358	NM_005933.3	1768	gtt/gTtt	18/36	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.47194862880165	2		489	596	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508728	148508728	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs267601395	NA	P-0000719-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	305	481	0	ENST00000320356.2:c.1936T>C	p.Tyr646His	p.Y646H	ENST00000320356	NM_004456.4	646	Tac/Cac	16/20	1	2	FACETS	0.964	0.915	1	0.964	0.915	1	CLONAL	1	TRUE	1	0.9	2		481	703	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260215	16260215	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000719-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	218	173	0	ENST00000375759.3:c.7480C>T	p.Pro2494Ser	p.P2494S	ENST00000375759	NM_015001.2	2494	Ccc/Tcc	11/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.9	2		173	453	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045918	180045920	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CTC	CTC	-	rs746341092	NA	P-0000719-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	137	232	0	ENST00000261937.6:c.2851_2853del	p.Glu951del	p.E951del	ENST00000261937	NM_182925.4	951	GAG/-	21/30	1	2	FACETS	0.746	0.685	0.809	0.746	0.685	0.809	SUBCLONAL	1	TRUE	1	0.9	2		232	408	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518079	187518079	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000731-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	113	468	0	ENST00000441802.2:c.12615G>C	p.Met4205Ile	p.M4205I	ENST00000441802	NM_005245.3	4205	atG/atC	25/27	0.530942760750725	4	FACETS	0.859	0.773	0.949	0.429	0.386	0.475	CLONAL	1	TRUE	2	0.530942760750725	4		468	759	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0000731-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	136	208	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.474543380817799	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	0	0.530942760750725	2		208	254	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024509	31024509	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000731-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	94	295	0	ENST00000375687.4:c.3994G>T	p.Val1332Phe	p.V1332F	ENST00000375687	NM_015338.5	1332	Gtt/Ttt	13/13	0.492653971100673	4	FACETS	0.984	0.878	1	0.246	0.219	0.274	CLONAL	1	TRUE	0	0.530942760750725	4		295	551	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937273	76937273	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000731-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	133	607	0	ENST00000373344.5:c.3475G>T	p.Glu1159Ter	p.E1159*	ENST00000373344	NM_000489.3	1159	Gag/Tag	9/35	0.170747362007164	3	FACETS	0.804	0.73	0.881	0.268	0.243	0.294	INDETERMINATE	1	TRUE	0	0.530942760750725	3		607	789	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339747	116339750	+	frameshift_variant	Frame_Shift_Del	DEL	TTCT	TTCT	-	novel	NA	P-0000731-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	115	342	0	ENST00000397752.3:c.610_613del	p.Ser204IlefsTer12	p.S204Ifs*12	ENST00000397752	NM_000245.2	203	tcTTCT/tc	2/21	0.530942760750725	5	FACETS	0.933	0.84	1	0.233	0.21	0.258	CLONAL	1	TRUE	1	0.530942760750725	5		342	834	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411885	116411901	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CTTTCTCTCTGTTTTAA	CTTTCTCTCTGTTTTAA	-	novel	NA	P-0000731-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	165	166	0	ENST00000397752.3:c.2888-18_2888-2del		p.X963_splice	ENST00000397752	NM_000245.2	963			0.530942760750725	5	FACETS	1	0.983	1	0.864	0.808	0.92	CLONAL	3	TRUE	1	0.530942760750725	5		166	323	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0000757-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	559	367	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.897	0.86	0.933	1	0.997	1	CLONAL	2	TRUE	1	0.383684322315675	2		367	1625	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0000757-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	488	464	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.383684322315675	1	FACETS	1	0.996	1	1	0.998	1	CLONAL	2	TRUE	0	0.383684322315675	1		464	834	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743950	46743950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761304456	NA	P-0000757-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	188	222	0	ENST00000371975.4:c.2240G>A	p.Arg747His	p.R747H	ENST00000371975	NM_003579.3	747	cGc/cAc	18/18	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.383684322315675	NA		222	549	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492802	56492802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000757-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	276	279	0	ENST00000407977.2:c.137C>T	p.Ala46Val	p.A46V	ENST00000407977		46	gCt/gTt	2/10	0.383684322315675	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.383684322315675	1		279	1050	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220644	1220644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1167609100	NA	P-0000757-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	170	478	0	ENST00000326873.7:c.662C>T	p.Pro221Leu	p.P221L	ENST00000326873	NM_000455.4	221	cCg/cTg	5/10	0.383684322315675	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.383684322315675	1		478	622	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0000766-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	63	423	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		423	881	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953774	55953774	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000766-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	56	354	1	ENST00000263923.4:c.3662G>A	p.Ser1221Asn	p.S1221N	ENST00000263923	NM_002253.2	1221	aGt/aAt	27/30	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		355	725	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0000785-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	477	318	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.591887780129575	3	FACETS	0.901	0.87	0.931	0.901	0.87	0.931	CLONAL	3	TRUE	0	0.591887780129575	3		318	773	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551522	150551522	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000785-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1669	133	478	0	ENST00000369026.2:c.485C>G	p.Ser162Trp	p.S162W	ENST00000369026	NM_021960.4	162	tCg/tGg	1/3	0.582239278384443	3	FACETS	0.323	0.292	0.356	0.162	0.146	0.178	SUBCLONAL	1	TRUE	1	0.591887780129575	3		478	1802	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715476	117715476	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000785-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	101	199	0	ENST00000368508.3:c.1013A>T	p.Tyr338Phe	p.Y338F	ENST00000368508	NM_002944.2	338	tAt/tTt	10/43	0.329810333358503	1	FACETS	0.468	0.42	0.519	0.468	0.42	0.519	INDETERMINATE	1	TRUE	0	0.591887780129575	1		199	513	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001469	150001469	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs752896748	NA	P-0000785-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	237	308	0	ENST00000253339.5:c.2135G>C	p.Gly712Ala	p.G712A	ENST00000253339		712	gGa/gCa	4/7	0.329810333358503	1	FACETS	0.811	0.761	0.863	0.811	0.761	0.863	INDETERMINATE	1	TRUE	0	0.591887780129575	1		308	695	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220272	55220272	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000785-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	744	295	0	ENST00000275493.2:c.662G>T	p.Gly221Val	p.G221V	ENST00000275493	NM_005228.3	221	gGg/gTg	6/28	0.591887780129575	3	FACETS	0.911	0.886	0.936	0.911	0.886	0.936	CLONAL	3	TRUE	0	0.591887780129575	3		295	1192	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509660	106509660	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000785-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	233	272	1	ENST00000359195.3:c.1654C>A	p.Arg552Ser	p.R552S	ENST00000359195	NM_002649.2	552	Cgc/Agc	2/11	0.572310175955005	4	FACETS	1	0.963	1	0.35	0.326	0.375	CLONAL	1	TRUE	1	0.591887780129575	4		273	1193	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543611	148543611	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000785-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	224	291	0	ENST00000320356.2:c.197A>G	p.Gln66Arg	p.Q66R	ENST00000320356	NM_004456.4	66	cAg/cGg	3/20	0.572310175955005	4	FACETS	0.864	0.803	0.928	0.288	0.267	0.31	CLONAL	1	TRUE	1	0.591887780129575	4		291	1394	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428233	49428233	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs535351117	NA	P-0000785-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	90	218	0	ENST00000301067.7:c.10467G>T	p.Gln3489His	p.Q3489H	ENST00000301067	NM_003482.3	3489	caG/caT	37/54	NA	2	FACETS	0.509	0.452	0.569			1	INDETERMINATE	1	TRUE	NA	0.591887780129575	2		218	598	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515144	103515144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000785-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	141	215	0	ENST00000355739.4:c.1645C>T	p.Leu549Phe	p.L549F	ENST00000355739	NM_000123.3	549	Ctt/Ttt	8/15	0.329810333358503	1	FACETS	0.551	0.503	0.6	0.551	0.503	0.6	INDETERMINATE	1	TRUE	0	0.591887780129575	1		215	609	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610056	81610056	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000785-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	249	226	0	ENST00000298171.2:c.1654C>A	p.Leu552Ile	p.L552I	ENST00000298171	NM_000369.2	552	Ctc/Atc	10/10	0.26775633577023	2	FACETS	1	0.992	1	0.684	0.644	0.724	INDETERMINATE	1	TRUE	0	0.591887780129575	2		226	615	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038595	14038595	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1299031778	NA	P-0000785-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	281	173	0	ENST00000311895.7:c.1920G>C	p.Met640Ile	p.M640I	ENST00000311895	NM_005236.2	640	atG/atC	10/11	0.364732312206424	5	FACETS	1	0.984	1			1	CLONAL	2	TRUE	NA	0.591887780129575	5		173	804	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662454	67662454	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs761621858	NA	P-0000785-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	160	281	0	ENST00000264010.4:c.1700G>T	p.Arg567Leu	p.R567L	ENST00000264010	NM_006565.3	567	cGg/cTg	9/12	0.591887780129575	3	FACETS	0.725	0.665	0.789	0.363	0.332	0.395	SUBCLONAL	1	TRUE	1	0.591887780129575	3		281	966	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912660	NA	P-0000785-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	386	328	0	ENST00000269305.4:c.839G>T	p.Arg280Ile	p.R280I	ENST00000269305	NM_001126112.2	280	aGa/aTa	8/11	0.57782802095609	2	FACETS	0.969	0.93	1	0.969	0.93	1	CLONAL	2	TRUE	0	0.591887780129575	2		328	673	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277939	18277939	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0000785-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	60	160	0	ENST00000222254.8:c.1560-1G>T		p.X520_splice	ENST00000222254	NM_005027.3	520			0.431333909176262	1	FACETS	0.361	0.312	0.414	0.361	0.312	0.414	SUBCLONAL	1	TRUE	0	0.591887780129575	1		160	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0000793-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	155	138	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.305947285589742	3	FACETS	0.974	0.902	1	0.974	0.902	1	CLONAL	3	TRUE	0	0.305947285589742	3		138	400	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403218	213403218	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000793-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	56	375	0	ENST00000342788.4:c.37C>A	p.Leu13Ile	p.L13I	ENST00000342788	NM_005235.2	13	Ctt/Att	1/28	0.271309189165631	4	FACETS	0.761	0.652	0.881	0.254	0.217	0.294	SUBCLONAL	1	TRUE	1	0.305947285589742	4		375	628	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197837	66197837	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000793-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	133	292	0	ENST00000273854.3:c.2862T>G	p.Asn954Lys	p.N954K	ENST00000273854	NM_004439.5	954	aaT/aaG	17/18	0.297926137671155	2	FACETS	0.981	0.898	1	0.981	0.898	1	CLONAL	2	TRUE	0	0.305947285589742	2		292	443	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428240	33428240	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs752910287	NA	P-0000793-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	54	320	0	ENST00000345365.6:c.883C>G	p.Leu295Val	p.L295V	ENST00000345365	NM_002878.3	295	Ctg/Gtg	9/10	0.305947285589742	7	FACETS	0.945	0.806	1			1	CLONAL	1	TRUE	NA	0.305947285589742	7		320	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0000855-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	168	328	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.285526542279438	3	FACETS	1	0.977	1			1	CLONAL	3	TRUE	NA	0.285526542279438	3		328	401	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92300792	92300792	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000855-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	34	239	0	ENST00000265734.4:c.595C>G	p.Pro199Ala	p.P199A	ENST00000265734	NM_001259.6	199	Ccc/Gcc	5/8	0.285526542279438	3	FACETS	0.889	0.729	1	0.445	0.364	0.535	CLONAL	1	TRUE	1	0.285526542279438	3		239	306	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953201	17953201	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000855-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	19	386	0	ENST00000458235.1:c.785T>G	p.Leu262Arg	p.L262R	ENST00000458235	NM_000215.3	262	cTt/cGt	6/24	0.285526542279438	3	FACETS	0.738	0.562	0.943	0.369	0.281	0.472	CLONAL	1	TRUE	1	0.285526542279438	3		386	206	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849170	76849170	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0000855-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	192	418	1	ENST00000373344.5:c.6106A>T	p.Lys2036Ter	p.K2036*	ENST00000373344	NM_000489.3	2036	Aaa/Taa	26/35	0.225267783775808	2	FACETS	0.95	0.888	1			1	CLONAL	3	TRUE	NA	0.285526542279438	2		419	472	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0000875-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	65	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.558	0.482	0.64	0.558	0.482	0.64	SUBCLONAL	1	TRUE	1	0.27	2		326	863	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0000875-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	104	655	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	0.781	0.698	0.87	0.781	0.698	0.87	SUBCLONAL	1	TRUE	1	0.27	2		655	986	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0000875-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	109	570	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	1	2	FACETS	0.805	0.721	0.894	0.805	0.721	0.894	CLONAL	1	TRUE	1	0.27	2		570	1003	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725046	162725046	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000875-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	47	274	0	ENST00000367921.3:c.518C>A	p.Ser173Tyr	p.S173Y	ENST00000367921	NM_006182.2	173	tCc/tAc	6/18	1	2	FACETS	0.626	0.528	0.735	0.626	0.528	0.735	SUBCLONAL	1	TRUE	1	0.27	2		274	556	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101768	71101768	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000875-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	37	312	0	ENST00000318789.4:c.430C>G	p.Gln144Glu	p.Q144E	ENST00000318789	NM_032682.5	144	Caa/Gaa	9/21	1	2	FACETS	0.389	0.319	0.467	0.389	0.319	0.467	SUBCLONAL	1	TRUE	1	0.27	2		312	705	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157411	106157411	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000875-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	44	180	0	ENST00000380013.4:c.2312G>C	p.Arg771Thr	p.R771T	ENST00000380013	NM_001127208.2	771	aGa/aCa	3/11	0.0693177544335364	3	FACETS	0.723	0.606	0.852	0.361	0.303	0.426	INDETERMINATE	1	TRUE	1	0.27	3		180	512	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534443	187534443	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs764300308	NA	P-0000875-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	42	236	0	ENST00000441802.2:c.9283C>G	p.Leu3095Val	p.L3095V	ENST00000441802	NM_005245.3	3095	Ctt/Gtt	13/27	0.3	1	FACETS	0.384	0.32	0.456	0.384	0.32	0.456	SUBCLONAL	1	TRUE	0	0.27	1		236	700	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115931	8115931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000875-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	53	162	0	ENST00000346208.3:c.1277C>T	p.Ser426Phe	p.S426F	ENST00000346208		426	tCc/tTc	6/6	NA	2	FACETS	0.603	0.513	0.701			1	INDETERMINATE	1	TRUE	NA	0.27	2		162	651	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192065	108192065	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1317619286	NA	P-0000875-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	22	225	0	ENST00000278616.4:c.6490G>C	p.Glu2164Gln	p.E2164Q	ENST00000278616	NM_000051.3	2164	Gag/Cag	45/63	1	2	FACETS	0.309	0.239	0.392	0.309	0.239	0.392	SUBCLONAL	1	TRUE	1	0.27	2		225	527	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432741	49432741	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1315374796	NA	P-0000875-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	17	115	0	ENST00000301067.7:c.8398C>T	p.Gln2800Ter	p.Q2800*	ENST00000301067	NM_003482.3	2800	Cag/Tag	34/54	1	2	FACETS	0.516	0.385	0.671	0.516	0.385	0.671	SUBCLONAL	1	TRUE	1	0.27	2		115	244	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432068	121432068	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137853238	NA	P-0000875-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	108	339	0	ENST00000257555.6:c.815G>A	p.Arg272His	p.R272H	ENST00000257555		272	cGc/cAc	4/10	NA	2	FACETS	0.723	0.647	0.804			1	INDETERMINATE	1	TRUE	NA	0.27	2		339	1106	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209274	133209274	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs181570274	NA	P-0000875-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	115	358	0	ENST00000320574.5:c.6112G>A	p.Glu2038Lys	p.E2038K	ENST00000320574	NM_006231.2	2038	Gag/Aag	44/49	NA	2	FACETS	0.825	0.741	0.913			1	INDETERMINATE	1	TRUE	NA	0.27	2		358	1033	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881440	37881440	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000875-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	52	175	0	ENST00000269571.5:c.2632C>T	p.His878Tyr	p.H878Y	ENST00000269571		878	Cat/Tat	21/27	1	2	FACETS	0.883	0.754	1	0.883	0.754	1	CLONAL	1	TRUE	1	0.27	2		175	436	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40761067	40761067	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000875-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	60	179	0	ENST00000392038.2:c.285G>C	p.Glu95Asp	p.E95D	ENST00000392038	NM_001626.4	95	gaG/gaC	4/14	1	2	FACETS	0.765	0.659	0.88	0.765	0.659	0.88	SUBCLONAL	1	TRUE	1	0.27	2		179	581	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222640	53222640	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000875-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	40	146	0	ENST00000375401.3:c.4296G>C	p.Glu1432Asp	p.E1432D	ENST00000375401	NM_004187.3	1432	gaG/gaC	25/26	0.293632212599396	0	FACETS	0.41	0.34	0.487			1	SUBCLONAL	1	TRUE	NA	0.27	0		146	528	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356777	70356777	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000875-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	61	329	0	ENST00000374080.3:c.5449C>T	p.Pro1817Ser	p.P1817S	ENST00000374080		1817	Cct/Tct	38/45	0.293632212599396	0	FACETS	0.38	0.327	0.438			1	SUBCLONAL	1	TRUE	NA	0.27	0		329	868	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777666	9777666	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28730670	NA	P-0000893-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	132	70	277	0	ENST00000377346.4:c.1002C>A	p.Asn334Lys	p.N334K	ENST00000377346	NM_005026.3	334	aaC/aaA	8/24	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.529639113929082	2		277	202	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725458	117725458	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000893-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	151	11	402	0	ENST00000368508.3:c.423C>A	p.Ser141Arg	p.S141R	ENST00000368508	NM_002944.2	141	agC/agA	5/43	0.410868061092934	0	FACETS	0.121	0.083	0.167			1	SUBCLONAL	1	TRUE	0	0.529639113929082	0		402	162	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971023	21971023	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000893-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	106	41	229	0	ENST00000304494.5:c.335G>C	p.Arg112Pro	p.R112P	ENST00000304494	NM_000077.4	112	cGt/cCt	2/3	0.529639113929082	1	FACETS	0.774	0.657	0.899	0.774	0.657	0.899	SUBCLONAL	1	TRUE	0	0.529639113929082	1		229	147	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115764	8115764	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000893-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	150	12	551	0	ENST00000346208.3:c.1110C>A	p.Ser370Arg	p.S370R	ENST00000346208		370	agC/agA	6/6	NA	2	FACETS	0.28	0.197	0.381			1	INDETERMINATE	1	TRUE	NA	0.529639113929082	2		551	162	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729094	66729099	+	inframe_deletion	In_Frame_Del	DEL	TGGAGA	TGGAGA	-	novel	NA	P-0000893-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	127	47	381	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	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.529639113929082	2		381	174	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0000940-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	138	573	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.417828421322677	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.417828421322677	1		574	485	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0000940-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	178	212	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.417828421322677	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.417828421322677	2		212	402	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0000940-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	120	367	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.962	0.871	1	0.962	0.871	1	CLONAL	1	TRUE	1	0.417828421322677	2		367	597	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0000940-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	115	330	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.417828421322677	2		330	474	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105848	27105848	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs747495829	NA	P-0000940-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	107	268	0	ENST00000324856.7:c.5459A>G	p.Asn1820Ser	p.N1820S	ENST00000324856	NM_006015.4	1820	aAt/aGt	20/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.417828421322677	2		268	452	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805693	43805693	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000940-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	31	329	0	ENST00000372470.3:c.749A>T	p.Asn250Ile	p.N250I	ENST00000372470	NM_005373.2	250	aAc/aTc	5/12	1	2	FACETS	0.275	0.222	0.336	0.275	0.222	0.336	SUBCLONAL	1	TRUE	1	0.417828421322677	2		329	539	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491082	120491082	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000940-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	109	240	0	ENST00000256646.2:c.2707T>G	p.Phe903Val	p.F903V	ENST00000256646	NM_024408.3	903	Ttc/Gtc	17/34	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.417828421322677	2		240	457	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917793	29917793	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149145987	NA	P-0000940-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	108	418	0	ENST00000389048.3:c.875G>A	p.Arg292His	p.R292H	ENST00000389048	NM_004304.4	292	cGc/cAc	3/29	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.417828421322677	2		418	502	SUCCESS
APC	324	MSKCC	GRCh37	5	112175780	112175780	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000940-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	82	237	0	ENST00000257430.4:c.4490del	p.Pro1497GlnfsTer10	p.P1497Qfs*10	ENST00000257430	NM_000038.5	1497	Cca/ca	16/16	1	2	FACETS	0.986	0.875	1	0.986	0.875	1	CLONAL	1	TRUE	1	0.417828421322677	2		237	398	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0000956-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	108	358	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.651595512395846	7	FACETS	1	0.926	1			1	CLONAL	1	FALSE	NA	0.651595512395846	7		358	838	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201099	108201099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759728261	NA	P-0000956-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	43	262	0	ENST00000278616.4:c.7466C>T	p.Ser2489Phe	p.S2489F	ENST00000278616	NM_000051.3	2489	tCc/tTc	50/63	0.633903130233211	3	FACETS	0.462	0.387	0.544	0.231	0.193	0.272	SUBCLONAL	1	FALSE	1	0.651595512395846	3		262	379	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920467	134920467	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000956-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	79	456	0	ENST00000398015.3:c.2282C>T	p.Ser761Phe	p.S761F	ENST00000398015	NM_004441.4	761	tCc/tTc	12/16	0.57120660490122	3	FACETS	0.64	0.565	0.721	0.32	0.282	0.361	SUBCLONAL	1	FALSE	1	0.651595512395846	3		456	502	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455075	50455075	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000956-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	143	300	0	ENST00000331340.3:c.622C>T	p.Arg208Ter	p.R208*	ENST00000331340	NM_006060.4	208	Cga/Tga	6/8	0.651595512395846	6	FACETS	1	0.987	1	0.498	0.455	0.543	CLONAL	1	FALSE	3	0.651595512395846	6		300	676	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200963	108200963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000956-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	115	269	0	ENST00000278616.4:c.7330G>A	p.Glu2444Lys	p.E2444K	ENST00000278616	NM_000051.3	2444	Gag/Aag	50/63	0.633903130233211	3	FACETS	1	0.979	1	0.639	0.582	0.699	CLONAL	1	FALSE	1	0.651595512395846	3		269	366	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877181	151877181	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000966-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	186	52	339	0	ENST00000262189.6:c.7180C>T	p.Gln2394Ter	p.Q2394*	ENST00000262189	NM_170606.2	2394	Cag/Tag	37/59	0.324492536748946	3	FACETS	1	0.929	1	0.566	0.487	0.651	CLONAL	1	TRUE	1	0.478369649679456	3		339	238	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022613	31022619	+	frameshift_variant	Frame_Shift_Del	DEL	TATCCTC	TATCCTC	-	novel	NA	P-0000966-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	214	60	832	0	ENST00000375687.4:c.2100_2106del	p.Tyr700Ter	p.Y700*	ENST00000375687	NM_015338.5	700	TATCCTCta/ta	13/13	1	2	FACETS	0.916	0.796	1	0.916	0.796	1	CLONAL	1	TRUE	1	0.478369649679456	2		832	274	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0000997-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	217	553	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.308927954248507	3	FACETS	0.875	0.816	0.935	0.875	0.816	0.935	CLONAL	2	TRUE	1	0.378790779014649	3		553	779	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0000997-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	370	504	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.0746231227293015	4	FACETS	1	0.978	1			1	INDETERMINATE	3	TRUE	NA	0.378790779014649	4		505	862	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0000997-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	231	599	0	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	0.378790779014649	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.378790779014649	1		599	752	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000997-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	216	512	1	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	0.30854273868972	2	FACETS	0.839	0.783	0.895	0.839	0.783	0.895	CLONAL	2	TRUE	0	0.378790779014649	2		513	680	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094251	193094251	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000997-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	160	614	1	ENST00000367435.3:c.141G>T	p.Lys47Asn	p.K47N	ENST00000367435	NM_024529.4	47	aaG/aaT	2/17	0.375903548579244	3	FACETS	0.858	0.785	0.935	0.429	0.392	0.468	CLONAL	1	TRUE	1	0.378790779014649	3		615	1171	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570814	226570814	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000997-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	164	372	0	ENST00000366794.5:c.1082C>A	p.Thr361Asn	p.T361N	ENST00000366794	NM_001618.3	361	aCc/aAc	8/23	0.375903548579244	3	FACETS	0.795	0.728	0.865	0.397	0.364	0.433	SUBCLONAL	1	TRUE	1	0.378790779014649	3		372	1296	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736238	243736238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000997-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	68	417	1	ENST00000263826.5:c.809G>A	p.Arg270His	p.R270H	ENST00000263826	NM_005465.4	270	cGt/cAt	8/13	0.375903548579244	3	FACETS	0.598	0.52	0.683	0.299	0.26	0.342	SUBCLONAL	1	TRUE	1	0.378790779014649	3		418	714	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497950	25497950	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000997-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	100	281	0	ENST00000264709.3:c.499C>T	p.Arg167Trp	p.R167W	ENST00000264709	NM_175629.2	167	Cgg/Tgg	6/23	0.158310203190053	1	FACETS	0.674	0.603	0.749	0.674	0.603	0.749	INDETERMINATE	1	TRUE	0	0.378790779014649	1		281	635	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958863	38958863	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000997-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	240	596	0	ENST00000357387.3:c.2249G>A	p.Trp750Ter	p.W750*	ENST00000357387	NM_152756.3	750	tGg/tAg	23/38	0.285755285917499	4	FACETS	0.886	0.828	0.946	0.886	0.828	0.946	CLONAL	2	TRUE	2	0.378790779014649	4		596	986	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371005	55371005	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000997-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	115	331	0	ENST00000297316.4:c.307G>T	p.Gly103Cys	p.G103C	ENST00000297316	NM_022454.3	103	Ggc/Tgc	1/2	0.218197893096543	3	FACETS	0.963	0.868	1	0.481	0.434	0.532	INDETERMINATE	1	TRUE	1	0.378790779014649	3		331	750	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203549	108203549	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000997-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	95	426	0	ENST00000278616.4:c.7849G>A	p.Val2617Ile	p.V2617I	ENST00000278616	NM_000051.3	2617	Gtc/Atc	53/63	0.286618250547597	3	FACETS	0.846	0.754	0.945	0.282	0.251	0.315	CLONAL	1	TRUE	0	0.378790779014649	3		426	705	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610687	81610687	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767693393	NA	P-0000997-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	101	513	0	ENST00000298171.2:c.2285C>T	p.Thr762Met	p.T762M	ENST00000298171	NM_000369.2	762	aCg/aTg	10/10	0.218197893096543	3	FACETS	0.877	0.784	0.976	0.439	0.392	0.488	INDETERMINATE	1	TRUE	1	0.378790779014649	3		513	723	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853886	59853886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759142191	NA	P-0000997-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	111	673	0	ENST00000259008.2:c.1973G>A	p.Arg658Gln	p.R658Q	ENST00000259008	NM_032043.2	658	cGg/cAg	14/20	0.378790779014649	1	FACETS	0.669	0.602	0.74	0.669	0.602	0.74	SUBCLONAL	1	TRUE	0	0.378790779014649	1		673	710	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231335	5231335	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769069932	NA	P-0000997-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	91	383	1	ENST00000357368.4:c.2141G>A	p.Arg714His	p.R714H	ENST00000357368	NM_002850.3	714	cGc/cAc	14/38	0.201307246259525	3	FACETS	0.696	0.617	0.78	0.232	0.205	0.26	INDETERMINATE	1	TRUE	0	0.378790779014649	3		384	821	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17949084	17949084	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000997-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	206	555	0	ENST00000458235.1:c.1557C>G	p.Asp519Glu	p.D519E	ENST00000458235	NM_000215.3	519	gaC/gaG	11/24	0.211830603813204	4	FACETS	0.755	0.7	0.812	0.378	0.35	0.406	INDETERMINATE	2	TRUE	0	0.378790779014649	4		555	993	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664693	138664693	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000997-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	12	23	0	ENST00000330315.3:c.872A>G	p.His291Arg	p.H291R	ENST00000330315	NM_023067.3	291	cAc/cGc	1/1	0.285755285917499	4	FACETS	0.982	0.699	1	0.491	0.349	0.66	CLONAL	1	TRUE	2	0.378790779014649	4		23	89	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0001016-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	457	349	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.728092209941583	3	FACETS		NA	1	1	0.998	1	NA	4	TRUE	0	0.728092209941583	3		349	483	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161364	55161364	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001016-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	125	367	0	ENST00000257290.5:c.3195G>C	p.Glu1065Asp	p.E1065D	ENST00000257290	NM_006206.4	1065	gaG/gaC	23/23	0.39480827633609	6	FACETS	0.774	0.699	0.853	0.258	0.233	0.285	INDETERMINATE	1	TRUE	3	0.728092209941583	6		367	1090	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557642	95557642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001016-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	1451	526	1	ENST00000393063.1:c.5425G>A	p.Gly1809Arg	p.G1809R	ENST00000393063	NM_030621.3	1809	Ggg/Agg	26/28	0.728092209941583	4	FACETS		NA	1			1	NA	5	TRUE	NA	0.728092209941583	4		527	1513	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0001053-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	204	599	0	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	0.505353248741189	1	FACETS	0.859	0.8	0.92	0.859	0.8	0.92	CLONAL	1	TRUE	0	0.505353248741189	1		599	702	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0001053-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	121	469	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.652	0.589	0.717	0.652	0.589	0.717	SUBCLONAL	1	TRUE	1	0.505353248741189	2		469	735	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919281	48919281	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001053-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	190	595	0	ENST00000267163.4:c.446C>A	p.Ser149Ter	p.S149*	ENST00000267163	NM_000321.2	149	tCa/tAa	4/27	0.463234352317303	1	FACETS	0.809	0.75	0.869	0.809	0.75	0.869	CLONAL	1	TRUE	0	0.505353248741189	1		595	695	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473606	67473606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1232187684	NA	P-0001053-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	181	530	0	ENST00000327367.4:c.686C>T	p.Pro229Leu	p.P229L	ENST00000327367	NM_005902.3	229	cCg/cTg	6/9	1	2	FACETS	0.821	0.757	0.886	0.821	0.757	0.886	CLONAL	1	TRUE	1	0.505353248741189	2		530	873	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876659675	NA	P-0001053-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	294	383	1	ENST00000269305.4:c.764T>A	p.Ile255Asn	p.I255N	ENST00000269305	NM_001126112.2	255	aTc/aAc	7/11	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	2	TRUE	NA	0.505353248741189	2		384	547	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184095	123184095	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001053-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	277	386	0	ENST00000218089.9:c.953T>G	p.Met318Arg	p.M318R	ENST00000218089	NM_001042749.1	318	aTg/aGg	11/35	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.505353248741189	1		386	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0001063-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	315	419	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.42771686760251	2	FACETS	0.981	0.931	1	0.981	0.931	1	CLONAL	2	TRUE	0	0.42771686760251	2		421	751	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974792	21974792	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs141798398	NA	P-0001063-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	305	153	1	ENST00000304494.5:c.35C>A	p.Ser12Ter	p.S12*	ENST00000304494	NM_000077.4	12	tCg/tAg	1/3	0.42771686760251	3	FACETS	0.896	0.859	0.933	1	0.993	1	CLONAL	4	TRUE	0	0.42771686760251	3		154	483	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239897	98239899	+	inframe_deletion	In_Frame_Del	DEL	GTG	GTG	-	novel	NA	P-0001063-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	234	257	0	ENST00000331920.6:c.1433_1435del	p.Ala478_Leu479delinsVal	p.A478_L479delinsV	ENST00000331920	NM_000264.3	478	gCACtg/gtg	10/24	0.42231938569812	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.42771686760251	2		257	483	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0001077-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	234	138	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.487555682704164	4	FACETS	0.992	0.937	1	0.992	0.937	1	CLONAL	3	TRUE	1	0.487555682704164	4		138	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0001077-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	302	655	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.440634401723683	2	FACETS	0.899	0.853	0.945	0.899	0.853	0.945	CLONAL	2	TRUE	0	0.487555682704164	2		655	689	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606652	29606652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764207516	NA	P-0001077-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	195	575	0	ENST00000389048.3:c.1228G>A	p.Gly410Arg	p.G410R	ENST00000389048	NM_004304.4	410	Gga/Aga	5/29	1	2	FACETS	0.951	0.882	1	0.951	0.882	1	CLONAL	1	TRUE	1	0.487555682704164	2		575	841	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566790	212566790	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001077-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	102	586	0	ENST00000342788.4:c.1391G>C	p.Ser464Thr	p.S464T	ENST00000342788	NM_005235.2	464	aGc/aCc	12/28	0.440634401723683	2	FACETS	0.534	0.478	0.595	0.267	0.239	0.298	SUBCLONAL	1	TRUE	0	0.487555682704164	2		586	783	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562850	21562850	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1418882962	NA	P-0001077-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	308	375	0	ENST00000382592.4:c.1069G>A	p.Val357Met	p.V357M	ENST00000382592	NM_014572.2	357	Gtg/Atg	4/8	0.229911402287864	6	FACETS	0.896	0.851	0.942			1	INDETERMINATE	4	TRUE	NA	0.487555682704164	6		375	696	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980892	40980892	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001077-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	248	388	0	ENST00000373198.4:c.1594A>C	p.Ser532Arg	p.S532R	ENST00000373198	NM_133170.3	532	Agt/Cgt	10/32	0.255855898756814	4	FACETS	0.864	0.809	0.92	0.864	0.809	0.92	INDETERMINATE	2	TRUE	2	0.487555682704164	4		388	876	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858936	89858936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1392468988	NA	P-0001096-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	205	188	0	ENST00000389301.3:c.1026G>A	p.Met342Ile	p.M342I	ENST00000389301	NM_000135.2	342	atG/atA	12/43	0.554516555424655	4	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.845611023527353	4		188	777	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976475	25976476	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0001096-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	436	600	3	ENST00000435504.4:c.1069_1070del	p.Arg357ThrfsTer4	p.R357Tfs*4	ENST00000435504		357	CGa/a	11/13	0.845611023527353	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.845611023527353	1		603	568	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033341	48033365	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGGAAGAGGTACTGCAACATTTGAT	AGGAAGAGGTACTGCAACATTTGAT	-	novel	NA	P-0001096-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4333	285	374	0	ENST00000234420.5:c.3647-2_3669del		p.X1216_splice	ENST00000234420	NM_000179.2	1216		8/10	0.845611023527353	11	FACETS	0.701	0.655	0.75			1	SUBCLONAL	1	TRUE	NA	0.845611023527353	11		374	4618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578181	7578181	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138983188	NA	P-0001153-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	142	379	0	ENST00000269305.4:c.668C>T	p.Pro223Leu	p.P223L	ENST00000269305	NM_001126112.2	223	cCt/cTt	6/11	1	2	FACETS	0.807	0.736	0.881	1	0.988	1	CLONAL	2	TRUE	1	0.225833496213104	2		379	779	SUCCESS
APC	324	MSKCC	GRCh37	5	112173968	112173968	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs199740875	NA	P-0001153-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	54	158	0	ENST00000257430.4:c.2677G>T	p.Glu893Ter	p.E893*	ENST00000257430	NM_000038.5	893	Gaa/Taa	16/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.225833496213104	2		158	384	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001153-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	118	396	0	ENST00000347630.2:c.397T>C	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	Ttc/Ctc	6/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.225833496213104	2		396	963	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980849	40980849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs548511212	NA	P-0001153-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	60	267	0	ENST00000373198.4:c.1637G>A	p.Arg546Gln	p.R546Q	ENST00000373198	NM_133170.3	546	cGg/cAg	10/32	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.225833496213104	2		267	435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540652	NA	P-0001168-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	360	475	0	ENST00000269305.4:c.743G>C	p.Arg248Pro	p.R248P	ENST00000269305	NM_001126112.2	248	cGg/cCg	7/11	0.715154472149137	2	FACETS	0.93	0.898	0.962	0.93	0.898	0.962	CLONAL	2	FALSE	0	0.748386642672098	2		475	517	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936338	78936338	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1212387005	NA	P-0001168-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1188	188	640	1	ENST00000306801.3:c.3770C>T	p.Thr1257Met	p.T1257M	ENST00000306801	NM_020761.2	1257	aCg/aTg	32/34	0.748386642672098	3	FACETS	0.502	0.462	0.543	0.167	0.154	0.181	SUBCLONAL	1	FALSE	0	0.748386642672098	3		641	1376	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717720	89717721	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0001168-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	615	439	0	ENST00000371953.3:c.746_747insCT	p.Gly251ValfsTer6	p.G251Vfs*6	ENST00000371953	NM_000314.4	249	gtg/gTCtg	7/9	0.748386642672098	2	FACETS	0.949	0.924	0.973	0.949	0.924	0.973	CLONAL	2	FALSE	0	0.748386642672098	2		439	866	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288876	33288876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	104	361	0	ENST00000374542.5:c.676G>A	p.Ala226Thr	p.A226T	ENST00000374542	NM_001141970.1	226	Gca/Aca	3/8	0.245943418010652	3	FACETS	0.822	0.74	0.909	0.822	0.74	0.909	CLONAL	2	FALSE	1	0.3	3		361	485	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673374	30673374	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001195-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	50	650	0	ENST00000376406.3:c.3586G>A	p.Val1196Ile	p.V1196I	ENST00000376406	NM_014641.2	1196	Gtc/Atc	10/15	0.30390136300332	3	FACETS	1	0.89	1	0.525	0.448	0.609	CLONAL	1	TRUE	1	0.386331947413451	3		650	294	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88678940	88678940	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001195-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	49	489	0	ENST00000372037.3:c.880G>C	p.Ala294Pro	p.A294P	ENST00000372037	NM_004329.2	294	Gca/Cca	10/13	0.386331947413451	1	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	0	0.386331947413451	1		489	204	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339471	339485	+	inframe_deletion	In_Frame_Del	DEL	TGAACTGGCCCAGGG	TGAACTGGCCCAGGG	-	novel	NA	P-0001195-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	24	806	0	ENST00000262320.3:c.2417_2431del	p.Thr806_Phe810del	p.T806_F810del	ENST00000262320	NM_003502.3	806	aCCCTGGGCCAGTTCAag/aag	10/11	0.386331947413451	0	FACETS	0.557	0.442	0.685			1	SUBCLONAL	1	TRUE	0	0.386331947413451	0		806	137	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158551	26158551	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001204-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	57	214	0	ENST00000289316.2:c.154G>C	p.Asp52His	p.D52H	ENST00000289316	NM_138720.2	52	Gac/Cac	1/2	0.3	5	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	5		214	777	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001204-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1609	95	654	0	ENST00000347630.2:c.399C>A	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttA	6/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		654	1704	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921577	39921577	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001236-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	140	584	0	ENST00000378444.4:c.4243G>T	p.Glu1415Ter	p.E1415*	ENST00000378444	NM_001123385.1	1415	Gag/Tag	10/15	NA	2	FACETS	0.901	0.83	0.974			1	INDETERMINATE	2	TRUE	NA	0.400474560180333	2		584	388	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921577	39921577	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001236-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	338	584	0	ENST00000378444.4:c.4243G>T	p.Glu1415Ter	p.E1415*	ENST00000378444	NM_001123385.1	1415	Gag/Tag	10/15	0.4520264107538	3	FACETS	1	0.965	1	0.514	0.485	0.543	CLONAL	1	TRUE	1	0.635790867242856	3		584	1363	SUCCESS
CBL	867	MSKCC	GRCh37	11	119168155	119168155	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001236-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	53	672	0	ENST00000264033.4:c.2215T>C	p.Ser739Pro	p.S739P	ENST00000264033	NM_005188.3	739	Tcc/Ccc	14/16	0.635790867242856	2	FACETS	0.202	0.172	0.236	0.101	0.086	0.118	SUBCLONAL	1	TRUE	0	0.635790867242856	2		672	824	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001242-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	114	241	0	ENST00000269305.4:c.736del	p.Met246Ter	p.M246*	ENST00000269305	NM_001126112.2	246	Atg/tg	7/11	0.29143527270528	1	FACETS	0.842	0.764	0.922	1	0.987	1	CLONAL	2	TRUE	0	0.29143527270528	1		241	397	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447406	187447406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1460631604	NA	P-0001259-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	65	239	0	ENST00000232014.4:c.787G>A	p.Glu263Lys	p.E263K	ENST00000232014	NM_001130845.1	263	Gaa/Aaa	5/10	1	2	FACETS	0.812	0.705	0.929	0.812	0.705	0.929	CLONAL	1	FALSE	1	0.278286793323563	2		239	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578538	7578538	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001262-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	52	237	0	ENST00000269305.4:c.392A>G	p.Asn131Ser	p.N131S	ENST00000269305	NM_001126112.2	131	aAc/aGc	5/11	0.314887658126868	1	FACETS	0.656	0.56	0.762	0.656	0.56	0.762	SUBCLONAL	1	FALSE	0	0.314887658126868	1		237	424	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0001343-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	2568	408	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.784599124723626	13	FACETS	1	0.997	1	0.858	0.847	0.868	CLONAL	10	TRUE	1	0.784599124723626	13		408	3380	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11204778	11204778	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001343-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	140	415	1	ENST00000361445.4:c.4799A>G	p.Glu1600Gly	p.E1600G	ENST00000361445	NM_004958.3	1600	gAg/gGg	34/58	0.234689181214747	4	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.784599124723626	4		416	486	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435311	56435311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759694077	NA	P-0001343-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	86	205	1	ENST00000407977.2:c.1826G>A	p.Arg609Gln	p.R609Q	ENST00000407977		609	cGg/cAg	9/10	0.784599124723626	3	FACETS	0.895	0.799	0.996	0.448	0.399	0.498	CLONAL	1	TRUE	1	0.784599124723626	3		206	341	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834552	156834552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540521894	NA	P-0001345-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	101	458	0	ENST00000524377.1:c.320C>T	p.Ala107Val	p.A107V	ENST00000524377	NM_002529.3	107	gCg/gTg	3/17	1	2	FACETS	0.883	0.791	0.98	1	0.985	1	CLONAL	2	TRUE	1	0.2	2		458	572	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157927	106157927	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001345-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	90	222	0	ENST00000380013.4:c.2828A>G	p.Gln943Arg	p.Q943R	ENST00000380013	NM_001127208.2	943	cAg/cGg	3/11	1	2	FACETS	0.987	0.88	1	1	0.986	1	CLONAL	2	TRUE	1	0.2	2		222	456	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0001366-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	410	266	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.597350068314182	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	1	0.597350068314182	4		266	707	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979987	7979987	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746723399	NA	P-0001366-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	56	240	2	ENST00000319144.4:c.1350del	p.Leu451SerfsTer16	p.L451Sfs*16	ENST00000319144	NM_001139.2	450	ggG/gg	10/15	0.597350068314182	2	FACETS	0.826	0.716	0.943	0.413	0.358	0.472	CLONAL	1	TRUE	0	0.597350068314182	2		242	227	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976488	25976488	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001366-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	526	634	1	ENST00000435504.4:c.1057C>T	p.Gln353Ter	p.Q353*	ENST00000435504		353	Cag/Tag	11/13	0.597350068314182	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.597350068314182	2		635	799	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0001402-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	21	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.16843516440681	5	FACETS	0.335	0.257	0.427	0.112	0.085	0.143	SUBCLONAL	1	TRUE	2	0.27	5		326	652	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	190	456	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.945	0.883	1			1	INDETERMINATE	1	FALSE	NA	0.870698392441927	2		456	462	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	322	212	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.98	0.931	1	0.98	0.931	1	CLONAL	1	FALSE	1	0.870698392441927	2		213	755	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	14	246	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.053	0.037	0.071	0.053	0.037	0.071	SUBCLONAL	1	FALSE	1	0.870698392441927	2		246	611	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805236	43805236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	89	394	1	ENST00000372470.3:c.686G>A	p.Arg229Lys	p.R229K	ENST00000372470	NM_005373.2	229	aGa/aAa	4/12	0.860519553554528	1	FACETS	0.253	0.225	0.283	0.253	0.225	0.283	SUBCLONAL	1	FALSE	0	0.870698392441927	1		395	456	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794464	242794464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	185	446	0	ENST00000334409.5:c.478C>T	p.Pro160Ser	p.P160S	ENST00000334409	NM_005018.2	160	Ccc/Tcc	3/5	1	2	FACETS	0.516	0.477	0.557	0.516	0.477	0.557	SUBCLONAL	1	FALSE	1	0.870698392441927	2		446	823	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139486	47139486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	261	647	0	ENST00000409792.3:c.5101G>A	p.Gly1701Arg	p.G1701R	ENST00000409792	NM_014159.6	1701	Gga/Aga	9/21	1	2	FACETS	0.479	0.448	0.511	0.479	0.448	0.511	SUBCLONAL	1	FALSE	1	0.870698392441927	2		647	1251	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119562168	119562168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	543	666	0	ENST00000316626.5:c.1168C>T	p.Leu390Phe	p.L390F	ENST00000316626		390	Ctt/Ttt	11/12	1	2	FACETS	0.952	0.915	0.99	0.952	0.915	0.99	CLONAL	1	FALSE	1	0.870698392441927	2		666	1310	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638735	176638735	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs901175981	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	176	478	0	ENST00000439151.2:c.3335G>A	p.Ser1112Asn	p.S1112N	ENST00000439151	NM_022455.4	1112	aGc/aAc	5/23	1	2	FACETS	0.487	0.449	0.527	0.487	0.449	0.527	SUBCLONAL	1	FALSE	1	0.870698392441927	2		478	830	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555054	106555054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	163	307	0	ENST00000369096.4:c.2171C>T	p.Thr724Ile	p.T724I	ENST00000369096	NM_001198.3	724	aCc/aTc	7/7	1	2	FACETS	0.475	0.436	0.515	0.475	0.436	0.515	SUBCLONAL	1	FALSE	1	0.870698392441927	2		307	789	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412040	116412040	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	64	302	0	ENST00000397752.3:c.3025G>T	p.Glu1009Ter	p.E1009*	ENST00000397752	NM_000245.2	1009	Gaa/Taa	14/21	1	2	FACETS	0.281	0.243	0.321	0.281	0.243	0.321	SUBCLONAL	1	FALSE	1	0.870698392441927	2		302	524	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456885	32456885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	160	181	0	ENST00000332351.3:c.7G>A	p.Asp3Asn	p.D3N	ENST00000332351	NM_024426.4	3	Gac/Aac	1/10	1	2	FACETS	0.972	0.904	1	0.972	0.904	1	CLONAL	1	FALSE	1	0.870698392441927	2		181	378	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577197	64577197	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	286	537	0	ENST00000312049.6:c.385C>T	p.Leu129Phe	p.L129F	ENST00000312049	NM_130799.2	129	Ctc/Ttc	2/10	1	2	FACETS	0.564	0.53	0.599	0.564	0.53	0.599	SUBCLONAL	1	FALSE	1	0.870698392441927	2		537	1164	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514089	69514089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	367	548	0	ENST00000294312.3:c.592G>A	p.Asp198Asn	p.D198N	ENST00000294312	NM_005117.2	198	Gac/Aac	3/3	1	2	FACETS	0.938	0.893	0.983	0.938	0.893	0.983	CLONAL	1	FALSE	1	0.870698392441927	2		548	899	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436031	49436031	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	240	225	0	ENST00000301067.7:c.5950C>T	p.Pro1984Ser	p.P1984S	ENST00000301067	NM_003482.3	1984	Ccc/Tcc	28/54	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.870698392441927	2		225	526	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444956	49444956	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	49	217	0	ENST00000301067.7:c.2510C>T	p.Ser837Phe	p.S837F	ENST00000301067	NM_003482.3	837	tCt/tTt	10/54	1	2	FACETS	0.259	0.22	0.303	0.259	0.22	0.303	SUBCLONAL	1	FALSE	1	0.870698392441927	2		217	434	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039467	49039467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	232	489	0	ENST00000267163.4:c.2452G>A	p.Gly818Ser	p.G818S	ENST00000267163	NM_000321.2	818	Ggt/Agt	23/27	1	2	FACETS	0.492	0.458	0.527	0.492	0.458	0.527	SUBCLONAL	1	FALSE	1	0.870698392441927	2		489	1083	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129197	2129197	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397515302	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	99	460	0	ENST00000219476.3:c.3131G>A	p.Arg1044Lys	p.R1044K	ENST00000219476	NM_000548.3	1044	aGg/aAg	27/42	NA	2	FACETS	0.276	0.246	0.308			1	INDETERMINATE	1	FALSE	NA	0.870698392441927	2		460	824	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632765	23632765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	190	437	0	ENST00000261584.4:c.3031G>A	p.Glu1011Lys	p.E1011K	ENST00000261584	NM_024675.3	1011	Gag/Aag	10/13	1	2	FACETS	0.52	0.481	0.56	0.52	0.481	0.56	SUBCLONAL	1	FALSE	1	0.870698392441927	2		437	839	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67132613	67132613	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	410	535	0	ENST00000412916.2:c.496G>A	p.Ala166Thr	p.A166T	ENST00000412916		166	Gca/Aca	6/6	1	2	FACETS	0.879	0.838	0.919	0.879	0.838	0.919	CLONAL	1	FALSE	1	0.870698392441927	2		535	1072	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868289	37868289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	310	401	0	ENST00000269571.5:c.1010C>T	p.Pro337Leu	p.P337L	ENST00000269571		337	cCc/cTc	8/27	1	2	FACETS	0.858	0.812	0.904	0.858	0.812	0.904	CLONAL	1	FALSE	1	0.870698392441927	2		401	830	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730795	40730795	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	330	430	0	ENST00000373198.4:c.3740C>T	p.Ser1247Phe	p.S1247F	ENST00000373198	NM_133170.3	1247	tCc/tTc	27/32	1	2	FACETS	0.986	0.937	1	0.986	0.937	1	CLONAL	1	FALSE	1	0.870698392441927	2		430	769	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564477	41564477	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	372	424	1	ENST00000263253.7:c.3899C>T	p.Thr1300Ile	p.T1300I	ENST00000263253	NM_001429.3	1300	aCc/aTc	24/31	0.198651343107326	1	FACETS	0.61	0.582	0.638	0.61	0.582	0.638	INDETERMINATE	1	FALSE	0	0.870698392441927	1		425	791	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222169	53222169	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	159	339	0	ENST00000375401.3:c.4663C>T	p.Pro1555Ser	p.P1555S	ENST00000375401	NM_004187.3	1555	Ccg/Tcg	26/26	0.870698392441927	1	FACETS	0.504	0.467	0.542	0.504	0.467	0.542	SUBCLONAL	1	FALSE	0	0.870698392441927	1		339	409	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439690	51439691	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	469	354	0	ENST00000262662.1:c.256_257del	p.Leu86ThrfsTer9	p.L86Tfs*9	ENST00000262662		85	acTTta/acta	4/4	0.860519553554528	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	0	0.870698392441927	1		354	601	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794730	42794731	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs35068781	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	390	406	0	ENST00000575354.2:c.1813dup	p.Ser605LysfsTer85	p.S605Kfs*85	ENST00000575354	NM_015125.3	604	gaa/gAaa	10/20	0.870698392441927	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	0	0.870698392441927	1		406	503	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845941	151845941	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	107	373	0	ENST00000262189.6:c.13071G>A	p.Trp4357Ter	p.W4357*	ENST00000262189	NM_170606.2	4357	tgG/tgA	52/59	1	2	FACETS	0.257	0.23	0.286	0.257	0.23	0.286	SUBCLONAL	1	FALSE	1	0.870698392441927	2		373	957	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551747	150551747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	29	130	0	ENST00000369026.2:c.260C>T	p.Pro87Leu	p.P87L	ENST00000369026	NM_021960.4	87	cCc/cTc	1/3	1	2	FACETS	0.189	0.151	0.231	0.189	0.151	0.231	SUBCLONAL	1	FALSE	1	0.870698392441927	2		130	353	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176132955	176132955	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	58	407	0	ENST00000367669.3:c.638G>A	p.Ser213Asn	p.S213N	ENST00000367669	NM_022457.5	213	aGc/aAc	4/20	1	2	FACETS	0.14	0.12	0.163	0.14	0.12	0.163	SUBCLONAL	1	FALSE	1	0.870698392441927	2		407	951	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009159	27009159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	195	199	0	ENST00000335756.4:c.95C>T	p.Ser32Phe	p.S32F	ENST00000335756	NM_001809.3	32	tCc/tTc	1/5	1	2	FACETS	0.995	0.932	1	0.995	0.932	1	CLONAL	1	FALSE	1	0.870698392441927	2		199	450	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659940	227659940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs553359474	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1206	93	503	0	ENST00000305123.5:c.3515G>A	p.Gly1172Asp	p.G1172D	ENST00000305123	NM_005544.2	1172	gGt/gAt	1/2	1	2	FACETS	0.164	0.145	0.185	0.164	0.145	0.185	SUBCLONAL	1	FALSE	1	0.870698392441927	2		503	1299	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446264	187446264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761505079	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	61	390	0	ENST00000232014.4:c.1424G>A	p.Cys475Tyr	p.C475Y	ENST00000232014	NM_001130845.1	475	tGc/tAc	6/10	1	2	FACETS	0.153	0.131	0.177	0.153	0.131	0.177	SUBCLONAL	1	FALSE	1	0.870698392441927	2		390	915	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549722	187549722	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	59	437	0	ENST00000441802.2:c.4519C>T	p.Leu1507Phe	p.L1507F	ENST00000441802	NM_005245.3	1507	Ctt/Ttt	8/27	0.870698392441927	1	FACETS	0.151	0.13	0.174	0.151	0.13	0.174	SUBCLONAL	1	FALSE	0	0.870698392441927	1		437	507	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287626	33287626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	25	236	1	ENST00000374542.5:c.1471G>A	p.Asp491Asn	p.D491N	ENST00000374542	NM_001141970.1	491	Gat/Aat	6/8	1	2	FACETS	0.126	0.099	0.158	0.126	0.099	0.158	SUBCLONAL	1	FALSE	1	0.870698392441927	2		237	455	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015577	112015577	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	151	575	0	ENST00000368678.4:c.1264+1G>A		p.X422_splice	ENST00000368678		422			1	2	FACETS	0.259	0.236	0.283	0.259	0.236	0.283	SUBCLONAL	1	FALSE	1	0.870698392441927	2		575	1340	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112029197	112029197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1199978400	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	555	718	1	ENST00000368678.4:c.371C>T	p.Ser124Phe	p.S124F	ENST00000368678		124	tCc/tTc	5/13	1	2	FACETS	0.945	0.908	0.982	0.945	0.908	0.982	CLONAL	1	FALSE	1	0.870698392441927	2		719	1349	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412040	116412040	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	40	302	0	ENST00000397752.3:c.3025G>A	p.Glu1009Lys	p.E1009K	ENST00000397752	NM_000245.2	1009	Gaa/Aaa	14/21	1	2	FACETS	0.175	0.145	0.209	0.175	0.145	0.209	SUBCLONAL	1	FALSE	1	0.870698392441927	2		302	524	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212145	98212145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	78	572	0	ENST00000331920.6:c.3527C>T	p.Ser1176Phe	p.S1176F	ENST00000331920	NM_000264.3	1176	tCt/tTt	21/24	NA	2	FACETS	0.138	0.12	0.157			1	INDETERMINATE	1	FALSE	NA	0.870698392441927	2		572	1298	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104377129	104377129	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	104	539	0	ENST00000369902.3:c.1240G>T	p.Glu414Ter	p.E414*	ENST00000369902	NM_016169.3	414	Gaa/Taa	10/12	0.12147287390485	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.870698392441927	0		539	1010	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160468	108160468	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	77	379	0	ENST00000278616.4:c.4376G>A	p.Gly1459Glu	p.G1459E	ENST00000278616	NM_000051.3	1459	gGa/gAa	29/63	1	2	FACETS	0.145	0.126	0.165	0.145	0.126	0.165	SUBCLONAL	1	FALSE	1	0.870698392441927	2		379	1221	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178702	108178702	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	45	240	0	ENST00000278616.4:c.5753G>A	p.Arg1918Lys	p.R1918K	ENST00000278616	NM_000051.3	1918	aGa/aAa	38/63	1	2	FACETS	0.205	0.172	0.242	0.205	0.172	0.242	SUBCLONAL	1	FALSE	1	0.870698392441927	2		240	504	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348792	118348792	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1330	171	624	0	ENST00000534358.1:c.3445G>A	p.Gly1149Arg	p.G1149R	ENST00000534358	NM_005933.3	1149	Gga/Aga	5/36	1	2	FACETS	0.262	0.24	0.285	0.262	0.24	0.285	SUBCLONAL	1	FALSE	1	0.870698392441927	2		624	1501	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434654	49434654	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757251259	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	111	391	0	ENST00000301067.7:c.6899G>A	p.Gly2300Glu	p.G2300E	ENST00000301067	NM_003482.3	2300	gGg/gAg	31/54	1	2	FACETS	0.342	0.307	0.379	0.342	0.307	0.379	SUBCLONAL	1	FALSE	1	0.870698392441927	2		391	745	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233982	133233982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	88	427	1	ENST00000320574.5:c.3412G>A	p.Gly1138Arg	p.G1138R	ENST00000320574	NM_006231.2	1138	Gga/Aga	28/49	0.12147287390485	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.870698392441927	0		428	803	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240267	41240267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	184	307	0	ENST00000379561.5:c.83C>T	p.Pro28Leu	p.P28L	ENST00000379561	NM_002015.3	28	cCc/cTc	1/3	1	2	FACETS	0.572	0.529	0.616	0.572	0.529	0.616	SUBCLONAL	1	FALSE	1	0.870698392441927	2		307	739	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059135	42059135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	156	680	0	ENST00000219905.7:c.8855C>T	p.Ser2952Phe	p.S2952F	ENST00000219905	NM_001164273.1	2952	tCt/tTt	24/24	0.12147287390485	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.870698392441927	0		680	1215	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059270	42059270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1454972852	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	256	664	0	ENST00000219905.7:c.8990C>T	p.Ala2997Val	p.A2997V	ENST00000219905	NM_001164273.1	2997	gCt/gTt	24/24	0.12147287390485	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.870698392441927	0		664	1195	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56870544	56870544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	517	698	0	ENST00000308159.5:c.1814C>T	p.Thr605Ile	p.T605I	ENST00000308159	NM_014669.4	605	aCa/aTa	17/22	1	2	FACETS	0.916	0.879	0.954	0.916	0.879	0.954	CLONAL	1	FALSE	1	0.870698392441927	2		698	1296	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828281	72828281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1313	159	707	0	ENST00000268489.5:c.8300G>A	p.Gly2767Glu	p.G2767E	ENST00000268489	NM_006885.3	2767	gGa/gAa	9/10	1	2	FACETS	0.248	0.226	0.271	0.248	0.226	0.271	SUBCLONAL	1	FALSE	1	0.870698392441927	2		707	1472	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131319	17131319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	121	505	1	ENST00000285071.4:c.133G>A	p.Ala45Thr	p.A45T	ENST00000285071	NM_144997.5	45	Gcg/Acg	4/14	1	2	FACETS	0.27	0.243	0.298	0.27	0.243	0.298	SUBCLONAL	1	FALSE	1	0.870698392441927	2		506	1031	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256249	41256249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	51	356	0	ENST00000357654.3:c.331G>A	p.Glu111Lys	p.E111K	ENST00000357654	NM_007294.3	111	Gaa/Aaa	6/23	1	2	FACETS	0.148	0.125	0.173	0.148	0.125	0.173	SUBCLONAL	1	FALSE	1	0.870698392441927	2		356	792	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119695	70119695	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1195	79	505	1	ENST00000245479.2:c.697G>A	p.Gly233Ser	p.G233S	ENST00000245479	NM_000346.3	233	Ggc/Agc	3/3	1	2	FACETS	0.142	0.124	0.162	0.142	0.124	0.162	SUBCLONAL	1	FALSE	1	0.870698392441927	2		506	1274	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905277	50905277	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	88	691	0	ENST00000440232.2:c.485G>C	p.Gly162Ala	p.G162A	ENST00000440232	NM_002691.3	162	gGt/gCt	5/27	0.870698392441927	1	FACETS	0.152	0.134	0.171	0.152	0.134	0.171	SUBCLONAL	1	FALSE	0	0.870698392441927	1		691	750	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264775	46264775	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1282	81	717	1	ENST00000371998.3:c.1645G>A	p.Asp549Asn	p.D549N	ENST00000371998		549	Gat/Aat	12/23	1	2	FACETS	0.137	0.119	0.155	0.137	0.119	0.155	SUBCLONAL	1	FALSE	1	0.870698392441927	2		718	1363	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46275920	46275920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	177	736	2	ENST00000371998.3:c.3356G>A	p.Gly1119Glu	p.G1119E	ENST00000371998		1119	gGg/gAg	18/23	1	2	FACETS	0.297	0.273	0.323	0.297	0.273	0.323	SUBCLONAL	1	FALSE	1	0.870698392441927	2		738	1367	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175857	24175859	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs875989800	NA	P-0001420-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	350	509	0	ENST00000263121.7:c.1091_1093del	p.Lys364del	p.K364del	ENST00000263121	NM_003073.3	362	gAGAag/gag	8/9	0.198651343107326	1	FACETS	0.478	0.454	0.502	0.478	0.454	0.502	INDETERMINATE	1	FALSE	0	0.870698392441927	1		509	950	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0121574-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	137	553	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.983	0.896	1	0.983	0.896	1	CLONAL	1	NA	1	0.42	2		553	664	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001433-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	256	516	0	ENST00000425967.3:c.1731C>G	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaG	13/19	1	2	FACETS	0.954	0.894	1	0.954	0.894	1	CLONAL	1	TRUE	1	0.584142117343283	2		516	919	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527461	29527461	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786203950	NA	P-0001433-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	523	381	0	ENST00000356175.3:c.910C>T	p.Arg304Ter	p.R304*	ENST00000356175	NM_000267.3	304	Cga/Tga	9/57	0.584142117343283	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.584142117343283	2		381	802	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951169	48951169	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001439-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	207	186	0	ENST00000267163.4:c.1331A>G	p.Gln444Arg	p.Q444R	ENST00000267163	NM_000321.2	444	cAg/cGg	13/27	NA	2	FACETS	0.963	0.922	1			1	INDETERMINATE	2	TRUE	NA	0.787779698208383	2		186	273	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650397	48650397	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001439-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	136	678	0	ENST00000376670.3:c.367G>T	p.Asp123Tyr	p.D123Y	ENST00000376670	NM_002049.3	123	Gat/Tat	3/6	0.709054657190661	5	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.787779698208383	5		678	623	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109656	115109658	+	inframe_deletion	In_Frame_Del	DEL	GCG	GCG	-	novel	NA	P-0001439-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	153	415	0	ENST00000257566.3:c.2220_2222del	p.Ser740_Ala741delinsArg	p.S740_A741delinsR	ENST00000257566	NM_016569.3	740	agCGCg/agg	8/8	0.533621006550382	3	FACETS	0.937	0.875	0.998	0.937	0.875	0.998	CLONAL	2	TRUE	1	0.787779698208383	3		415	289	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183872	10183872	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs730882032	NA	P-0001522-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	74	198	0	ENST00000256474.2:c.340+1G>A		p.X114_splice	ENST00000256474	NM_000551.3	114			0.289576474751693	3	FACETS	0.913	0.808	1			1	CLONAL	2	TRUE	NA	0.347256766729899	3		198	274	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139519	47139519	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001522-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	154	492	0	ENST00000409792.3:c.5068G>C	p.Gly1690Arg	p.G1690R	ENST00000409792	NM_014159.6	1690	Gga/Cga	9/21	0.258968948170211	2	FACETS	0.8	0.737	0.867	0.8	0.737	0.867	SUBCLONAL	2	TRUE	0	0.347256766729899	2		492	554	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442077	52442077	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001522-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	103	290	0	ENST00000460680.1:c.272G>T	p.Cys91Phe	p.C91F	ENST00000460680	NM_004656.3	91	tGt/tTt	5/17	0.258968948170211	2	FACETS	1	0.976	1	0.646	0.581	0.714	CLONAL	1	TRUE	0	0.347256766729899	2		290	459	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374245	138374245	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001522-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	256	399	0	ENST00000289153.2:c.3199G>C	p.Asp1067His	p.D1067H	ENST00000289153	NM_006219.2	1067	Gac/Cac	22/22	0.347256766729899	3	FACETS	0.875	0.825	0.926	0.875	0.825	0.926	CLONAL	3	TRUE	0	0.347256766729899	3		399	659	SUCCESS
ATR	545	MSKCC	GRCh37	3	142254009	142254009	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001522-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	36	265	0	ENST00000350721.4:c.3858G>T	p.Gln1286His	p.Q1286H	ENST00000350721	NM_001184.3	1286	caG/caT	21/47	0.347256766729899	3	FACETS	0.393	0.322	0.473	0.131	0.107	0.158	SUBCLONAL	1	TRUE	0	0.347256766729899	3		265	619	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276755	15276755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138265894	NA	P-0001522-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	95	423	1	ENST00000263388.2:c.5510G>A	p.Arg1837His	p.R1837H	ENST00000263388	NM_000435.2	1837	cGt/cAt	30/33	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.347256766729899	2		424	490	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0001529-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	971	60	408	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		408	1031	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798129	45798129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501346	NA	P-0001529-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	634	55	344	0	ENST00000450313.1:c.722G>A	p.Arg241Gln	p.R241Q	ENST00000450313	NM_012222.2	241	cGg/cAg	9/16	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		344	689	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900615	3900615	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001529-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	640	40	303	0	ENST00000262367.5:c.481C>A	p.Leu161Met	p.L161M	ENST00000262367	NM_004380.2	161	Ctg/Atg	2/31	0.3	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		303	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0001529-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	764	17	416	0	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		416	781	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266713	198266713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776846119	NA	P-0001532-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	463	291	1	ENST00000335508.6:c.2219G>A	p.Gly740Glu	p.G740E	ENST00000335508	NM_012433.2	740	gGa/gAa	15/25	1	2	FACETS	0.975	0.933	1	0.975	0.933	1	CLONAL	1	TRUE	1	0.793370013862729	2		292	1197	SUCCESS
ATM	472	MSKCC	GRCh37	11	108137962	108137962	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001532-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	496	339	0	ENST00000278616.4:c.2531G>T	p.Gly844Val	p.G844V	ENST00000278616	NM_000051.3	844	gGa/gTa	17/63	1	2	FACETS	0.996	0.954	1	0.996	0.954	1	CLONAL	1	TRUE	1	0.793370013862729	2		339	1256	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508353	106508353	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001540-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	40	163	0	ENST00000359195.3:c.347T>G	p.Val116Gly	p.V116G	ENST00000359195	NM_002649.2	116	gTg/gGg	2/11	0.335057308428586	3	FACETS	1	0.875	1	0.528	0.441	0.623	CLONAL	1	TRUE	1	0.335057308428586	3		163	264	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32918791	32918791	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs886040935	NA	P-0001540-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	80	403	0	ENST00000380152.3:c.6937+1G>A		p.X2313_splice	ENST00000380152		2313			NA	2	FACETS	0.551	0.484	0.624			1	INDETERMINATE	1	TRUE	NA	0.335057308428586	2		403	866	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577578	7577578	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001544-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	125	461	0	ENST00000269305.4:c.703A>G	p.Asn235Asp	p.N235D	ENST00000269305	NM_001126112.2	235	Aac/Gac	7/11	0.424220688546586	0	FACETS		NA	1			1	NA	2	TRUE	0	0.567755516897716	0		461	184	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0001548-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	573	408	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.435028332938472	6	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	3	0.576926325037763	6		408	1251	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0001548-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	370	551	0	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	NA	2	FACETS	0.912	0.873	0.951			1	INDETERMINATE	2	TRUE	NA	0.576926325037763	2		551	703	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0001551-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	46	677	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	1	2	FACETS	0.283	0.237	0.334	0.283	0.237	0.334	SUBCLONAL	1	TRUE	1	0.34	2		677	955	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0001570-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	255	2142	0	ENST00000269305.4:c.559+1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.428320472636671	2	FACETS	0.874	0.831	0.917	1	0.993	1	CLONAL	3	FALSE	0	0.428320472636671	2		2142	454	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423601	88423601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001570-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	242	2691	3	ENST00000360948.2:c.2234G>A	p.Arg745Gln	p.R745Q	ENST00000360948	NM_001012338.2	745	cGg/cAg	18/19	0.356153328282566	4	FACETS	0.905	0.858	0.951	0.905	0.858	0.951	CLONAL	4	FALSE	0	0.428320472636671	4		2694	446	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251805	212251805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001570-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	84	2178	1	ENST00000342788.4:c.3254C>T	p.Thr1085Ile	p.T1085I	ENST00000342788	NM_005235.2	1085	aCt/aTt	27/28	0.260534175175106	5	FACETS	0.902	0.803	1	0.602	0.535	0.671	CLONAL	2	FALSE	2	0.428320472636671	5		2179	357	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245984	5245984	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001570-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	247	2537	0	ENST00000357368.4:c.791T>C	p.Ile264Thr	p.I264T	ENST00000357368	NM_002850.3	264	aTc/aCc	10/38	0.428320472636671	1	FACETS	0.818	0.772	0.864	1	0.994	1	CLONAL	2	FALSE	0	0.428320472636671	1		2537	554	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0001575-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	484	328	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA	2	FACETS	0.998	0.965	1			1	INDETERMINATE	2	TRUE	NA	0.653853367665254	2		328	742	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806119	1806119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931614	NA	P-0001598-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	539	473	2	ENST00000260795.2:c.1138G>A	p.Gly380Arg	p.G380R	ENST00000260795		380	Ggg/Agg	8/17	0.661193401983599	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	1	0.661193401983599	3		475	970	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807335	1807335	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001598-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	420	410	0	ENST00000260795.2:c.1584G>C	p.Met528Ile	p.M528I	ENST00000260795		528	atG/atC	11/17	0.661193401983599	3	FACETS	0.939	0.899	0.979	0.939	0.899	0.979	CLONAL	2	TRUE	1	0.661193401983599	3		410	900	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022015	5022015	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001598-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	428	405	1	ENST00000381652.3:c.28G>C	p.Glu10Gln	p.E10Q	ENST00000381652	NM_004972.3	10	Gaa/Caa	3/25	0.563272861776911	3	FACETS	1	0.976	1			1	CLONAL	2	TRUE	NA	0.661193401983599	3		406	841	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0001598-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	186	332	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.661193401983599	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.661193401983599	1		332	343	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263310	123263310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001598-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	229	400	0	ENST00000358487.5:c.1433G>A	p.Arg478Lys	p.R478K	ENST00000358487	NM_000141.4	478	aGa/aAa	10/18	0.661193401983599	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.661193401983599	1		400	434	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345776	152345776	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0001598-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	277	522	0	ENST00000359321.1:c.794T>G	p.Leu265Ter	p.L265*	ENST00000359321	NM_005431.1	265	tTa/tGa	3/3	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.661193401983599	2		522	807	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350198	89350198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001598-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	390	710	0	ENST00000301030.4:c.2752G>A	p.Glu918Lys	p.E918K	ENST00000301030	NM_001256183.1	918	Gag/Aag	9/13	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.661193401983599	2		710	1076	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0001614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	11	154	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.473	0.327	0.653	0.473	0.327	0.653	SUBCLONAL	1	FALSE	1	0.251673284587197	2		154	185	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0001614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	17	266	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.443	0.33	0.577	0.443	0.33	0.577	SUBCLONAL	1	FALSE	1	0.251673284587197	2		266	305	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435160	56435161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755128667	NA	P-0001614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	26	261	0	ENST00000407977.2:c.1976dup	p.Pro660SerfsTer87	p.P660Sfs*87	ENST00000407977		659	ggt/ggGt	9/10	0.152835619809862	3	FACETS	0.797	0.632	0.984	0.398	0.316	0.492	CLONAL	1	FALSE	1	0.251673284587197	3		261	292	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101402	27101402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	34	357	1	ENST00000324856.7:c.4689del	p.Met1564Ter	p.M1564*	ENST00000324856	NM_006015.4	1562	Ccc/cc	18/20	0.185725662998885	5	FACETS	1	0.892	1	0.377	0.309	0.454	CLONAL	1	FALSE	2	0.251673284587197	5		358	329	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161907	47161907	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	63	499	1	ENST00000409792.3:c.4219del	p.Arg1407GlyfsTer5	p.R1407Gfs*5	ENST00000409792	NM_014159.6	1407	Agg/gg	3/21	0.185725662998885	5	FACETS	0.833	0.723	0.951	0.555	0.482	0.634	CLONAL	2	FALSE	2	0.251673284587197	5		500	414	SUCCESS
APC	324	MSKCC	GRCh37	5	112177787	112177787	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764527706	NA	P-0001614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	33	368	0	ENST00000257430.4:c.6496C>T	p.Arg2166Ter	p.R2166*	ENST00000257430	NM_000038.5	2166	Cga/Tga	16/16	0.251673284587197	5	FACETS	0.976	0.796	1	0.325	0.265	0.393	CLONAL	1	FALSE	2	0.251673284587197	5		368	370	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182169	99182169	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	20	423	0	ENST00000074304.5:c.2234A>C	p.Lys745Thr	p.K745T	ENST00000074304	NM_001134224.1	745	aAa/aCa	21/26	1	2	FACETS	0.651	0.499	0.829	0.651	0.499	0.829	SUBCLONAL	1	FALSE	1	0.251673284587197	2		423	244	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37061805	37061805	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63750736	NA	P-0001614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	23	468	0	ENST00000231790.2:c.889G>T	p.Glu297Ter	p.E297*	ENST00000231790	NM_000249.3	297	Gaa/Taa	11/19	0.185725662998885	5	FACETS	0.95	0.742	1	0.317	0.247	0.397	CLONAL	1	FALSE	2	0.251673284587197	5		468	265	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911607	134911607	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	15	349	0	ENST00000398015.3:c.2072G>T	p.Arg691Leu	p.R691L	ENST00000398015	NM_004441.4	691	cGg/cTg	11/16	1	2	FACETS	0.599	0.439	0.79	0.599	0.439	0.79	SUBCLONAL	1	FALSE	1	0.251673284587197	2		349	199	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927019	131927019	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140333740	NA	P-0001614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	44	475	0	ENST00000265335.6:c.1556G>A	p.Arg519His	p.R519H	ENST00000265335		519	cGt/cAt	10/25	0.251673284587197	5	FACETS	1	0.937	1	0.415	0.348	0.488	CLONAL	1	FALSE	2	0.251673284587197	5		475	387	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683942	117683942	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	25	515	0	ENST00000368508.3:c.3205T>C	p.Trp1069Arg	p.W1069R	ENST00000368508	NM_002944.2	1069	Tgg/Cgg	21/43	0.228176385349603	0	FACETS	0.527	0.416	0.654			1	SUBCLONAL	1	FALSE	0	0.251673284587197	0		515	282	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878176	151878176	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	25	345	0	ENST00000262189.6:c.6769C>T	p.Arg2257Ter	p.R2257*	ENST00000262189	NM_170606.2	2257	Cga/Tga	36/59	0.152835619809862	3	FACETS	0.738	0.583	0.917	0.369	0.291	0.459	CLONAL	1	FALSE	1	0.251673284587197	3		345	303	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393576	139393576	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774262180	NA	P-0001614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	35	384	0	ENST00000277541.6:c.6070G>A	p.Val2024Ile	p.V2024I	ENST00000277541	NM_017617.3	2024	Gta/Ata	32/34	0.152835619809862	3	FACETS	1	0.883	1	0.549	0.452	0.658	CLONAL	1	FALSE	1	0.251673284587197	3		384	285	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402690	139402690	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs41309764	NA	P-0001614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	38	372	0	ENST00000277541.6:c.3319C>T	p.Arg1107Ter	p.R1107*	ENST00000277541	NM_017617.3	1107	Cga/Tga	20/34	0.152835619809862	3	FACETS	1	0.934	1	0.637	0.529	0.755	CLONAL	1	FALSE	1	0.251673284587197	3		372	267	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533877	533877	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730880460	NA	P-0001614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	30	468	0	ENST00000451590.1:c.179G>A	p.Gly60Asp	p.G60D	ENST00000451590	NM_001130442.1	60	gGc/gAc	3/5	0.145488884004273	0	FACETS	0.549	0.443	0.669			1	INDETERMINATE	1	FALSE	0	0.251673284587197	0		468	325	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490834	56490834	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759458720	NA	P-0001614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	28	343	0	ENST00000267101.3:c.2280G>A	p.Met760Ile	p.M760I	ENST00000267101	NM_001982.3	760	atG/atA	20/28	0.185725662998885	5	FACETS	1	0.908	1	0.415	0.333	0.508	CLONAL	1	FALSE	2	0.251673284587197	5		343	246	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679253	88679253	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	17	423	0	ENST00000360948.2:c.784A>T	p.Asn262Tyr	p.N262Y	ENST00000360948	NM_001012338.2	262	Aat/Tat	8/19	0.228814470837326	0	FACETS	0.518	0.388	0.672			1	SUBCLONAL	1	FALSE	0	0.251673284587197	0		423	195	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267704	7267704	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	25	345	0	ENST00000302850.5:c.304C>A	p.Leu102Met	p.L102M	ENST00000302850	NM_000208.2	102	Ctg/Atg	2/22	1	2	FACETS	0.717	0.566	0.89	0.717	0.566	0.89	SUBCLONAL	1	FALSE	1	0.251673284587197	2		345	277	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298740	15298740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	42	447	0	ENST00000263388.2:c.1558G>A	p.Ala520Thr	p.A520T	ENST00000263388	NM_000435.2	520	Gcc/Acc	10/33	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	FALSE	1	0.251673284587197	2		447	300	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256680	19256680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	29	333	0	ENST00000162023.5:c.1033C>T	p.Arg345Trp	p.R345W	ENST00000162023		345	Cgg/Tgg	13/13	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.251673284587197	NA		333	285	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045676	47045676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	17	355	0	ENST00000377604.3:c.2557C>T	p.Arg853Trp	p.R853W	ENST00000377604	NM_001204468.1	853	Cgg/Tgg	23/24	0.21588428450135	1	FACETS	0.562	0.421	0.73	0.562	0.421	0.73	SUBCLONAL	1	FALSE	0	0.251673284587197	1		355	210	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648383	30648383	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1281085856	NA	P-0001614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	23	270	0	ENST00000295754.5:c.12del	p.Leu5CysfsTer32	p.L5Cfs*32	ENST00000295754	NM_003242.5	3	cGg/cg	1/7	0.185725662998885	5	FACETS	0.705	0.55	0.886	0.235	0.183	0.296	SUBCLONAL	1	FALSE	2	0.251673284587197	5		270	357	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37038183	37038184	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs63750469	NA	P-0001614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	37	440	0	ENST00000231790.2:c.190_191del	p.Asn64TrpfsTer14	p.N64Wfs*14	ENST00000231790	NM_000249.3	64	AAt/t	2/19	0.185725662998885	5	FACETS	0.851	0.701	1	0.284	0.233	0.34	CLONAL	1	FALSE	2	0.251673284587197	5		440	476	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165213	47165213	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	37	365	1	ENST00000409792.3:c.913del	p.Thr305GlnfsTer35	p.T305Qfs*35	ENST00000409792	NM_014159.6	305	Aca/ca	3/21	0.185725662998885	5	FACETS	1	0.886	1	0.366	0.302	0.437	CLONAL	1	FALSE	2	0.251673284587197	5		366	369	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511094	148511094	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	33	328	0	ENST00000320356.2:c.1808del	p.Asn603MetfsTer72	p.N603Mfs*72	ENST00000320356	NM_004456.4	603	aAt/at	15/20	0.152835619809862	3	FACETS	0.884	0.721	1	0.442	0.36	0.533	CLONAL	1	FALSE	1	0.251673284587197	3		328	334	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413073	139413075	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0001614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	34	449	0	ENST00000277541.6:c.1067_1069del	p.Ser356del	p.S356del	ENST00000277541	NM_017617.3	356	tCCTtc/ttc	6/34	0.152835619809862	3	FACETS	0.954	0.781	1	0.477	0.39	0.573	CLONAL	1	FALSE	1	0.251673284587197	3		449	319	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160451	108160451	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	36	435	0	ENST00000278616.4:c.4363del	p.Ser1455ValfsTer3	p.S1455Vfs*3	ENST00000278616	NM_000051.3	1453	atA/at	29/63	0.152835619809862	3	FACETS	0.928	0.765	1	0.464	0.382	0.556	CLONAL	1	FALSE	1	0.251673284587197	3		435	347	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245574	46245576	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs1565623935	NA	P-0001614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	28	373	0	ENST00000334344.6:c.3670_3672del	p.Pro1224del	p.P1224del	ENST00000334344	NM_152641.2	1223	tCTCct/tct	15/21	0.185725662998885	5	FACETS	1	0.862	1	0.366	0.293	0.449	CLONAL	1	FALSE	2	0.251673284587197	5		373	279	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220672	1220674	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0001614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	24	487	0	ENST00000326873.7:c.692_694del	p.Phe231del	p.F231del	ENST00000326873	NM_000455.4	230	acCTTc/acc	5/10	1	2	FACETS	0.568	0.445	0.709	0.568	0.445	0.709	SUBCLONAL	1	FALSE	1	0.251673284587197	2		487	336	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350213	15350213	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368540009	NA	P-0001614-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	17	521	0	ENST00000263377.2:c.3566C>T	p.Ala1189Val	p.A1189V	ENST00000263377	NM_058243.2	1189	gCg/gTg	17/20	1	2	FACETS	0.512	0.382	0.666	0.512	0.382	0.666	SUBCLONAL	1	FALSE	1	0.251673284587197	2		521	264	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0001629-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	385	475	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.520535314922517	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.549547759803236	2		475	674	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0001629-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	163	600	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	0.917	0.845	0.992	0.917	0.845	0.992	CLONAL	1	TRUE	1	0.549547759803236	2		600	647	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188164	11188164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777893	NA	P-0001629-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	150	509	0	ENST00000361445.4:c.5930C>T	p.Thr1977Ile	p.T1977I	ENST00000361445	NM_004958.3	1977	aCa/aTa	43/58	NA	2	FACETS	0.841	0.771	0.914			1	INDETERMINATE	1	TRUE	NA	0.549547759803236	2		509	649	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001629-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	195	507	0	ENST00000206249.3:c.1607T>C	p.Leu536Pro	p.L536P	ENST00000206249	NM_000125.3	536	cTc/cCc	8/8	0.113547445885607	4	FACETS	0.759	0.705	0.815	0.759	0.705	0.815	INDETERMINATE	2	TRUE	2	0.549547759803236	4		507	724	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900884	3900884	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001629-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	261	655	0	ENST00000262367.5:c.212C>T	p.Ser71Leu	p.S71L	ENST00000262367	NM_004380.2	71	tCg/tTg	2/31	1	2	FACETS	0.973	0.913	1	0.973	0.913	1	CLONAL	1	TRUE	1	0.549547759803236	2		655	976	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0001631-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	172	138	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.474167573897035	1	FACETS	0.77	0.716	0.824	0.77	0.716	0.824	SUBCLONAL	1	TRUE	0	0.685005726495744	1		138	429	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519936	NA	P-0001631-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	323	460	1	ENST00000263967.3:c.3127A>T	p.Met1043Leu	p.M1043L	ENST00000263967	NM_006218.2	1043	Atg/Ttg	21/21	0.474167573897035	1	FACETS	0.883	0.84	0.926	0.883	0.84	0.926	CLONAL	1	TRUE	0	0.685005726495744	1		461	702	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845412	151845412	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001631-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	286	517	0	ENST00000262189.6:c.13600C>T	p.Gln4534Ter	p.Q4534*	ENST00000262189	NM_170606.2	4534	Cag/Tag	52/59	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.685005726495744	2		517	821	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849662	68849663	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0001631-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	197	393	0	ENST00000261769.5:c.1565+1_1565+2dup		p.T522fs	ENST00000261769	NM_004360.3	522	aca/acGTa		0.685005726495744	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.685005726495744	1		393	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0001637-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	40	329	2	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.331425859207238	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.331425859207238	1		331	149	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851747	134851747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001637-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	32	1132	0	ENST00000398015.3:c.1153G>A	p.Gly385Ser	p.G385S	ENST00000398015	NM_004441.4	385	Ggc/Agc	5/16	0.243972470238663	2	FACETS	1	0.858	1	0.528	0.432	0.633	CLONAL	1	TRUE	0	0.331425859207238	2		1132	183	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676271	29676271	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0001637-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	54	892	0	ENST00000356175.3:c.7258+2T>A		p.X2420_splice	ENST00000356175	NM_000267.3	2420			0.273994646996449	3	FACETS	0.798	0.689	0.915	0.798	0.689	0.915	CLONAL	2	TRUE	1	0.331425859207238	3		892	238	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023964	31023964	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773823004	NA	P-0001637-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	22	1361	0	ENST00000375687.4:c.3449G>A	p.Gly1150Glu	p.G1150E	ENST00000375687	NM_015338.5	1150	gGa/gAa	13/13	0.273994646996449	3	FACETS	0.656	0.51	0.824	0.328	0.255	0.412	SUBCLONAL	1	TRUE	1	0.331425859207238	3		1361	236	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012563	36012563	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001637-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	10	866	0	ENST00000358208.4:c.7A>T	p.Ser3Cys	p.S3C	ENST00000358208		3	Agc/Tgc	2/12	0.273994646996449	3	FACETS	0.591	0.403	0.825	0.296	0.201	0.413	SUBCLONAL	1	TRUE	1	0.331425859207238	3		866	119	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591103	67591117	+	inframe_deletion	In_Frame_Del	DEL	ATTAAACCAGACCTT	ATTAAACCAGACCTT	-	novel	NA	P-0001637-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	44	924	0	ENST00000274335.5:c.1698_1712del	p.Lys567_Ile571del	p.K567_I571del	ENST00000274335		566	ATTAAACCAGACCTT/-	12/15	0.20192418965335	3	FACETS	0.85	0.723	0.987	0.567	0.482	0.658	CLONAL	2	TRUE	0	0.331425859207238	3		924	182	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0001646-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	23	553	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.232663583718044	5	FACETS	0.355	0.275	0.448	0.118	0.091	0.15	SUBCLONAL	1	TRUE	2	0.232663583718044	5		553	751	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	198	553	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.264952998885414	3	FACETS	1	0.98	1	0.575	0.533	0.618	INDETERMINATE	1	TRUE	1	0.53	3		553	822	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	119	308	1	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	0.264952998885414	3	FACETS	0.916	0.829	1	0.458	0.414	0.504	INDETERMINATE	1	TRUE	1	0.53	3		309	620	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	85	291	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.618	0.548	0.693	0.618	0.548	0.693	SUBCLONAL	1	TRUE	1	0.53	2		291	519	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256769	19256769	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	38	264	0	ENST00000162023.5:c.944del	p.Pro315GlnfsTer?	p.P315Qfs*?	ENST00000162023		315	cCa/ca	13/13	0.301456061771193	1	FACETS	0.549	0.459	0.647	0.549	0.459	0.647	INDETERMINATE	1	TRUE	0	0.53	1		264	192	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057814	27057814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770551517	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	133	781	0	ENST00000324856.7:c.1522C>T	p.Pro508Ser	p.P508S	ENST00000324856	NM_006015.4	508	Cca/Tca	3/20	0.227306512797679	0	FACETS	0.29	0.263	0.318			1	INDETERMINATE	1	TRUE	0	0.53	0		781	814	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818383	43818383	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	103	566	0	ENST00000372470.3:c.1848C>A	p.Cys616Ter	p.C616*	ENST00000372470	NM_005373.2	616	tgC/tgA	12/12	NA	2	FACETS	0.613	0.549	0.68			1	INDETERMINATE	1	TRUE	NA	0.53	2		566	634	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251578	212251578	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	135	412	0	ENST00000342788.4:c.3481G>T	p.Glu1161Ter	p.E1161*	ENST00000342788	NM_005235.2	1161	Gaa/Taa	27/28	1	2	FACETS	0.692	0.63	0.758	0.692	0.63	0.758	SUBCLONAL	1	TRUE	1	0.53	2		412	736	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119545684	119545684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141519181	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	105	404	0	ENST00000316626.5:c.1253G>A	p.Arg418His	p.R418H	ENST00000316626		418	cGt/cAt	12/12	1	2	FACETS	0.577	0.517	0.64	0.577	0.517	0.64	SUBCLONAL	1	TRUE	1	0.53	2		404	687	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213843	66213843	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	147	802	0	ENST00000273854.3:c.2587A>T	p.Ser863Cys	p.S863C	ENST00000273854	NM_004439.5	863	Agt/Tgt	15/18	1	2	FACETS	0.628	0.573	0.685	0.628	0.573	0.685	SUBCLONAL	1	TRUE	1	0.53	2		802	884	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099312	157099312	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	58	237	0	ENST00000346085.5:c.249G>C	p.Gln83His	p.Q83H	ENST00000346085	NM_020732.3	83	caG/caC	1/20	1	2	FACETS	0.487	0.42	0.561	0.487	0.42	0.561	SUBCLONAL	1	TRUE	1	0.53	2		237	449	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249145	55249145	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1278942267	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	155	572	0	ENST00000275493.2:c.2443C>T	p.Leu815Phe	p.L815F	ENST00000275493	NM_005228.3	815	Ctc/Ttc	20/28	0.264952998885414	3	FACETS	1	0.979	1	0.595	0.546	0.645	INDETERMINATE	1	TRUE	1	0.53	3		572	622	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371903	116371903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs544274181	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	238	423	0	ENST00000397752.3:c.1382G>A	p.Arg461His	p.R461H	ENST00000397752	NM_000245.2	461	cGc/cAc	3/21	0.264952998885414	3	FACETS	1	0.99	1	0.653	0.611	0.696	INDETERMINATE	1	TRUE	1	0.53	3		423	870	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845391	151845391	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	163	485	1	ENST00000262189.6:c.13621C>T	p.Arg4541Ter	p.R4541*	ENST00000262189	NM_170606.2	4541	Cga/Tga	52/59	NA	2	FACETS	0.861	0.793	0.933			1	INDETERMINATE	1	TRUE	NA	0.53	2		486	714	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737591	145737591	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375297971	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	99	544	0	ENST00000428558.2:c.3172C>T	p.Arg1058Cys	p.R1058C	ENST00000428558	NM_004260.3	1058	Cgt/Tgt	19/22	0.259135126085348	1	FACETS	0.798	0.72	0.88	0.798	0.72	0.88	INDETERMINATE	1	TRUE	0	0.53	1		544	344	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98241289	98241289	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	109	592	0	ENST00000331920.6:c.1208A>G	p.Tyr403Cys	p.Y403C	ENST00000331920	NM_000264.3	403	tAt/tGt	8/24	0.17279503356991	0	FACETS	0.305	0.274	0.338			1	INDETERMINATE	1	TRUE	0	0.53	0		592	633	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101910055	101910055	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	126	433	0	ENST00000374994.4:c.1375C>T	p.Gln459Ter	p.Q459*	ENST00000374994	NM_004612.2	459	Cag/Tag	8/9	NA	2	FACETS	0.65	0.589	0.715			1	INDETERMINATE	1	TRUE	NA	0.53	2		433	731	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589720	69589720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	10	30	0	ENST00000168712.1:c.133C>T	p.Arg45Cys	p.R45C	ENST00000168712	NM_002007.2	45	Cgc/Tgc	1/3	0.301456061771193	0	FACETS	0.394	0.275	0.533			1	INDETERMINATE	1	TRUE	0	0.53	0		30	45	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871787	12871787	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	174	303	0	ENST00000228872.4:c.504C>A	p.Asn168Lys	p.N168K	ENST00000228872	NM_004064.3	168	aaC/aaA	2/3	0.301456061771193	6	FACETS	1	0.988	1	0.474	0.436	0.514	INDETERMINATE	1	TRUE	3	0.53	6		303	951	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944982	31944982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	68	348	0	ENST00000340398.3:c.119G>A	p.Arg40His	p.R40H	ENST00000340398	NM_001013699.2	40	cGc/cAc	1/1	1	2	FACETS	0.554	0.483	0.63	0.554	0.483	0.63	SUBCLONAL	1	TRUE	1	0.53	2		348	463	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041554	14041554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772728961	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	98	485	1	ENST00000311895.7:c.2101C>T	p.Arg701Cys	p.R701C	ENST00000311895	NM_005236.2	701	Cgt/Tgt	11/11	0.161239315515101	0	FACETS	0.249	0.222	0.278			1	INDETERMINATE	1	TRUE	0	0.53	0		486	698	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428326	33428326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779808083	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	93	493	0	ENST00000345365.6:c.797G>A	p.Arg266His	p.R266H	ENST00000345365	NM_002878.3	266	cGc/cAc	9/10	0.161239315515101	0	FACETS	0.286	0.255	0.32			1	INDETERMINATE	1	TRUE	0	0.53	0		493	576	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7128960	7128960	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139944962	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	60	380	0	ENST00000302850.5:c.2848G>A	p.Val950Ile	p.V950I	ENST00000302850	NM_000208.2	950	Gtc/Atc	15/22	0.301456061771193	0	FACETS	0.307	0.265	0.351			1	INDETERMINATE	1	TRUE	0	0.53	0		380	347	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145710	11145710	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	77	543	0	ENST00000358026.2:c.4072A>G	p.Thr1358Ala	p.T1358A	ENST00000358026	NM_001128849.1	1358	Acc/Gcc	29/36	0.301456061771193	0	FACETS	0.409	0.362	0.459			1	INDETERMINATE	1	TRUE	0	0.53	0		543	334	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349660	15349660	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1347307625	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	18	327	0	ENST00000263377.2:c.3914C>T	p.Ala1305Val	p.A1305V	ENST00000263377	NM_058243.2	1305	gCt/gTt	19/20	0.301456061771193	1	FACETS	0.185	0.139	0.239	0.185	0.139	0.239	INDETERMINATE	1	TRUE	0	0.53	1		327	270	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794047	42794047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1391719010	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	65	469	1	ENST00000575354.2:c.1408C>T	p.Arg470Trp	p.R470W	ENST00000575354	NM_015125.3	470	Cgg/Tgg	9/20	0.301456061771193	1	FACETS	0.447	0.389	0.51	0.447	0.389	0.51	INDETERMINATE	1	TRUE	0	0.53	1		470	403	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860886	45860886	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	28	595	1	ENST00000391945.4:c.1307+2T>C		p.X436_splice	ENST00000391945	NM_000400.3	436			0.301456061771193	1	FACETS	0.25	0.2	0.307	0.25	0.2	0.307	INDETERMINATE	1	TRUE	0	0.53	1		596	311	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657072	45657072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	50	369	0	ENST00000407780.3:c.84G>A	p.Met28Ile	p.M28I	ENST00000407780	NM_001283052.1	28	atG/atA	3/7	0.301456061771193	1	FACETS	0.431	0.367	0.5	0.431	0.367	0.5	INDETERMINATE	1	TRUE	0	0.53	1		369	322	SUCCESS
AR	367	MSKCC	GRCh37	X	66766211	66766211	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	87	186	0	ENST00000374690.3:c.1223A>T	p.Tyr408Phe	p.Y408F	ENST00000374690	NM_000044.3	408	tAt/tTt	1/8	0.265459035124272	0	FACETS	0.724	0.654	0.796			1	INDETERMINATE	1	TRUE	NA	0.53	0		186	213	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584510	52584511	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	95	549	0	ENST00000394830.3:c.4502_4503del	p.Glu1501GlyfsTer7	p.E1501Gfs*7	ENST00000394830	NM_018313.4	1501	gAG/g	29/30	0.301456061771193	1	FACETS	0.398	0.354	0.444	0.398	0.354	0.444	INDETERMINATE	1	TRUE	0	0.53	1		549	662	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959898	38959898	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	166	594	0	ENST00000357387.3:c.2034del	p.Lys678AsnfsTer14	p.K678Nfs*14	ENST00000357387	NM_152756.3	678	aaA/aa	21/38	1	2	FACETS	0.698	0.641	0.757	0.698	0.641	0.757	SUBCLONAL	1	TRUE	1	0.53	2		594	898	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405826	70405827	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	119	639	0	ENST00000373644.4:c.3345dup	p.Tyr1116IlefsTer19	p.Y1116Ifs*19	ENST00000373644	NM_030625.2	1114	caa/cAaa	4/12	0.301456061771193	1	FACETS	0.474	0.428	0.522	0.474	0.428	0.522	INDETERMINATE	1	TRUE	0	0.53	1		639	697	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	25	236	0	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	0.476	0.378	0.588	0.476	0.378	0.588	SUBCLONAL	1	TRUE	1	0.53	2		236	198	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870898	12870898	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	143	394	0	ENST00000228872.4:c.127del	p.Arg43GlyfsTer28	p.R43Gfs*28	ENST00000228872	NM_004064.3	42	aCc/ac	1/3	0.301456061771193	6	FACETS	1	0.984	1	0.45	0.41	0.491	INDETERMINATE	1	TRUE	3	0.53	6		394	824	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431198	49431199	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	74	509	0	ENST00000301067.7:c.9940dup	p.Ser3314PhefsTer109	p.S3314Ffs*109	ENST00000301067	NM_003482.3	3314	tcc/tTcc	34/54	1	2	FACETS	0.668	0.587	0.754	0.668	0.587	0.754	SUBCLONAL	1	TRUE	1	0.53	2		509	418	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519134	103519135	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	152	514	0	ENST00000355739.4:c.2478dup	p.Asn827Ter	p.N827*	ENST00000355739	NM_000123.3	824	-/T	11/15	1	2	FACETS	0.632	0.578	0.689	0.632	0.578	0.689	SUBCLONAL	1	TRUE	1	0.53	2		514	907	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270725	10270726	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	66	701	0	ENST00000340748.4:c.1009dup	p.Met337AsnfsTer28	p.M337Nfs*28	ENST00000340748		337	atg/aAtg	14/40	0.301456061771193	0	FACETS	0.264	0.23	0.301			1	INDETERMINATE	1	TRUE	0	0.53	0		701	443	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24135859	24135859	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	32	445	0	ENST00000263121.7:c.351del	p.Thr118ProfsTer25	p.T118Pfs*25	ENST00000263121	NM_003073.3	116	Ccc/cc	3/9	0.17279503356991	0	FACETS	0.135	0.109	0.164			1	INDETERMINATE	1	TRUE	0	0.53	0		445	420	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139613	202139614	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0001649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	121	519	0	ENST00000358485.4:c.775dup	p.Glu259GlyfsTer18	p.E259Gfs*18	ENST00000358485	NM_001080125.1	258	-/G	6/9	1	2	FACETS	0.627	0.567	0.691	0.627	0.567	0.691	SUBCLONAL	1	TRUE	1	0.53	2		519	728	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396835	139396835	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373841359	NA	P-0001684-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	28	364	3	ENST00000277541.6:c.5273G>A	p.Arg1758His	p.R1758H	ENST00000277541	NM_017617.3	1758	cGc/cAc	28/34	0.294616350454374	3	FACETS	1	0.897	1	0.589	0.476	0.713	CLONAL	1	TRUE	1	0.37396379199324	3		367	151	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	64	228	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.55	0.477	0.629	0.55	0.477	0.629	SUBCLONAL	1	TRUE	1	0.459102990520032	2		228	507	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	59	154	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.661	0.571	0.758	0.661	0.571	0.758	SUBCLONAL	1	TRUE	1	0.459102990520032	2		154	389	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	179	345	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.459102990520032	2		345	652	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	111	738	12	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.459102990520032	2		750	481	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523009	25523009	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	40	393	1	ENST00000264709.3:c.176del	p.Pro59ArgfsTer13	p.P59Rfs*13	ENST00000264709	NM_175629.2	59	cCg/cg	3/23	0.459102990520032	2	FACETS	0.289	0.24	0.345	0.145	0.12	0.173	SUBCLONAL	1	TRUE	0	0.459102990520032	2		394	602	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	63	276	0	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.643	0.558	0.735	0.643	0.558	0.735	SUBCLONAL	1	TRUE	1	0.459102990520032	2		276	427	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	142	179	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.918	0.838	1	0.918	0.838	1	CLONAL	1	TRUE	1	0.459102990520032	2		179	674	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396746	139396746	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	69	178	0	ENST00000277541.6:c.5362G>A	p.Gly1788Ser	p.G1788S	ENST00000277541	NM_017617.3	1788	Ggc/Agc	28/34	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.459102990520032	2		178	272	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	155	372	1	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.459102990520032	2		373	583	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710578	40710578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs943054949	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	167	309	0	ENST00000373198.4:c.4273G>A	p.Val1425Met	p.V1425M	ENST00000373198	NM_133170.3	1425	Gtg/Atg	31/32	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.459102990520032	2		309	652	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	29	294	0	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.221	0.176	0.272	0.221	0.176	0.272	SUBCLONAL	1	TRUE	1	0.459102990520032	2		294	572	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	266	399	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.459102990520032	2		399	1086	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244091	153244091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	265	443	1	ENST00000281708.4:c.2066G>A	p.Arg689Gln	p.R689Q	ENST00000281708	NM_033632.3	689	cGg/cAg	12/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.459102990520032	2		444	1084	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261155	16261155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1032279699	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	55	181	0	ENST00000375759.3:c.8420G>A	p.Arg2807His	p.R2807H	ENST00000375759	NM_015001.2	2807	cGt/cAt	11/15	1	2	FACETS	0.812	0.7	0.933	0.812	0.7	0.933	CLONAL	1	TRUE	1	0.459102990520032	2		181	295	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743773	46743773	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs111408489	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	169	368	0	ENST00000371975.4:c.2063G>A	p.Arg688His	p.R688H	ENST00000371975	NM_003579.3	688	cGt/cAt	18/18	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.459102990520032	2		368	692	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691954	30691954	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs750421240	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	146	201	0	ENST00000295754.5:c.454+2T>C		p.X152_splice	ENST00000295754	NM_003242.5	152			1	2	FACETS	0.9	0.823	0.98	0.9	0.823	0.98	CLONAL	1	TRUE	1	0.459102990520032	2		201	707	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713721	30713721	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	79	252	0	ENST00000295754.5:c.1046A>T	p.Lys349Met	p.K349M	ENST00000295754	NM_003242.5	349	aAg/aTg	4/7	1	2	FACETS	0.602	0.53	0.679	0.602	0.53	0.679	SUBCLONAL	1	TRUE	1	0.459102990520032	2		252	572	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732996	30732996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893809	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	201	332	0	ENST00000295754.5:c.1609C>T	p.Arg537Cys	p.R537C	ENST00000295754	NM_003242.5	537	Cgc/Tgc	7/7	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.459102990520032	2		332	779	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200744	128200744	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906631	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	133	363	0	ENST00000341105.2:c.1061C>T	p.Thr354Met	p.T354M	ENST00000341105	NM_032638.4	354	aCg/aTg	5/6	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.459102990520032	2		363	528	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198307	185198307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374643532	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	140	266	1	ENST00000265026.3:c.2789G>A	p.Arg930His	p.R930H	ENST00000265026	NM_004721.4	930	cGt/cAt	13/14	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.459102990520032	2		267	598	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443313	187443313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1466914215	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	147	266	0	ENST00000232014.4:c.1813G>A	p.Glu605Lys	p.E605K	ENST00000232014	NM_001130845.1	605	Gaa/Aaa	8/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.459102990520032	2		266	604	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964925	55964925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149745504	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	167	410	0	ENST00000263923.4:c.2312C>T	p.Thr771Met	p.T771M	ENST00000263923	NM_002253.2	771	aCg/aTg	16/30	1	2	FACETS	0.801	0.736	0.869	0.801	0.736	0.869	CLONAL	1	TRUE	1	0.459102990520032	2		410	908	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630299	187630299	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	121	396	0	ENST00000441802.2:c.683G>C	p.Gly228Ala	p.G228A	ENST00000441802	NM_005245.3	228	gGc/gCc	2/27	1	2	FACETS	0.63	0.569	0.694	0.63	0.569	0.694	SUBCLONAL	1	TRUE	1	0.459102990520032	2		396	837	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86667971	86667971	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770599456	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	214	434	0	ENST00000274376.6:c.1735C>T	p.Arg579Trp	p.R579W	ENST00000274376	NM_002890.2	579	Cgg/Tgg	13/25	1	2	FACETS	0.927	0.861	0.995	0.927	0.861	0.995	CLONAL	1	TRUE	1	0.459102990520032	2		434	1006	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056232	26056232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1231531360	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	564	477	0	ENST00000343677.2:c.425C>T	p.Ala142Val	p.A142V	ENST00000343677	NM_005319.3	142	gCt/gTt	1/1	0.459102990520032	3	FACETS	0.861	0.83	0.893			1	CLONAL	3	TRUE	NA	0.459102990520032	3		477	1169	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710594	117710594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768790336	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	197	358	0	ENST00000368508.3:c.1678C>T	p.Arg560Cys	p.R560C	ENST00000368508	NM_002944.2	560	Cgc/Tgc	12/43	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.459102990520032	2		358	805	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332923	152332923	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	130	334	0	ENST00000206249.3:c.1229T>C	p.Leu410Ser	p.L410S	ENST00000206249	NM_000125.3	410	tTg/tCg	5/8	1	2	FACETS	0.852	0.774	0.933	0.852	0.774	0.933	CLONAL	1	TRUE	1	0.459102990520032	2		334	665	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987337	2987337	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	111	400	0	ENST00000396946.4:c.92A>G	p.His31Arg	p.H31R	ENST00000396946	NM_032415.4	31	cAc/cGc	3/25	1	2	FACETS	0.577	0.518	0.639	0.577	0.518	0.639	SUBCLONAL	1	TRUE	1	0.459102990520032	2		400	838	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860742	151860742	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	106	339	0	ENST00000262189.6:c.9920T>C	p.Val3307Ala	p.V3307A	ENST00000262189	NM_170606.2	3307	gTg/gCg	43/59	1	2	FACETS	0.559	0.501	0.621	0.559	0.501	0.621	SUBCLONAL	1	TRUE	1	0.459102990520032	2		339	826	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739599	145739599	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766726409	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	121	285	0	ENST00000428558.2:c.1852C>T	p.Arg618Trp	p.R618W	ENST00000428558	NM_004260.3	618	Cgg/Tgg	11/22	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.459102990520032	2		285	467	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457418	5457418	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs759740264	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	24	148	0	ENST00000381577.3:c.392A>G	p.Asn131Ser	p.N131S	ENST00000381577	NM_014143.3	131	aAt/aGt	3/7	1	2	FACETS	0.235	0.184	0.295	0.235	0.184	0.295	SUBCLONAL	1	TRUE	1	0.459102990520032	2		148	444	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231290	98231290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767947110	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	87	353	0	ENST00000331920.6:c.1993C>T	p.Arg665Cys	p.R665C	ENST00000331920	NM_000264.3	665	Cgc/Tgc	14/24	1	2	FACETS	0.584	0.517	0.655	0.584	0.517	0.655	SUBCLONAL	1	TRUE	1	0.459102990520032	2		353	649	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894922	101894922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	243	505	0	ENST00000374994.4:c.475C>T	p.Pro159Ser	p.P159S	ENST00000374994	NM_004612.2	159	Cca/Tca	3/9	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.459102990520032	2		505	1057	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401302	139401302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80340744	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	125	289	0	ENST00000277541.6:c.3767C>T	p.Pro1256Leu	p.P1256L	ENST00000277541	NM_017617.3	1256	cCg/cTg	23/34	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.459102990520032	2		289	487	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309821	104309821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34406289	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	160	321	0	ENST00000369902.3:c.412G>A	p.Ala138Thr	p.A138T	ENST00000369902	NM_016169.3	138	Gca/Aca	3/12	1	2	FACETS	0.98	0.901	1	0.98	0.901	1	CLONAL	1	TRUE	1	0.459102990520032	2		321	711	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447841	49447841	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748834953	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	113	260	0	ENST00000301067.7:c.593C>T	p.Ala198Val	p.A198V	ENST00000301067	NM_003482.3	198	gCg/gTg	5/54	1	2	FACETS	0.82	0.74	0.905	0.82	0.74	0.905	CLONAL	1	TRUE	1	0.459102990520032	2		260	600	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202870	133202870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	43	312	0	ENST00000320574.5:c.6364G>A	p.Val2122Met	p.V2122M	ENST00000320574	NM_006231.2	2122	Gtg/Atg	46/49	NA	2	FACETS	0.403	0.337	0.476			1	INDETERMINATE	1	TRUE	NA	0.459102990520032	2		312	465	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900353	3900353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374499169	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	95	412	0	ENST00000262367.5:c.743C>T	p.Pro248Leu	p.P248L	ENST00000262367	NM_004380.2	248	cCg/cTg	2/31	1	2	FACETS	0.55	0.489	0.614	0.55	0.489	0.614	SUBCLONAL	1	TRUE	1	0.459102990520032	2		412	753	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979640	7979640	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774958790	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	39	285	0	ENST00000319144.4:c.1385G>A	p.Gly462Asp	p.G462D	ENST00000319144	NM_001139.2	462	gGc/gAc	11/15	1	2	FACETS	0.332	0.275	0.396	0.332	0.275	0.396	SUBCLONAL	1	TRUE	1	0.459102990520032	2		285	512	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968211	15968211	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1436156803	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	110	458	0	ENST00000268712.3:c.5074C>A	p.Pro1692Thr	p.P1692T	ENST00000268712	NM_006311.3	1692	Ccg/Acg	34/46	1	2	FACETS	0.5	0.448	0.555	0.5	0.448	0.555	SUBCLONAL	1	TRUE	1	0.459102990520032	2		458	958	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627865	37627865	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	206	478	0	ENST00000447079.4:c.1780G>A	p.Ala594Thr	p.A594T	ENST00000447079	NM_015083.1	594	Gct/Act	2/14	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.459102990520032	2		478	881	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508290	38508290	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	120	337	0	ENST00000254066.5:c.598C>A	p.Pro200Thr	p.P200T	ENST00000254066	NM_000964.3	200	Cct/Act	5/9	1	2	FACETS	0.826	0.747	0.908	0.826	0.747	0.908	CLONAL	1	TRUE	1	0.459102990520032	2		337	633	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677757	47677757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772401624	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	196	304	0	ENST00000347630.2:c.1108C>T	p.Arg370Cys	p.R370C	ENST00000347630	NM_001007230.1	370	Cgc/Tgc	11/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.459102990520032	2		304	823	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118918	70118918	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	53	463	0	ENST00000245479.2:c.490C>T	p.Gln164Ter	p.Q164*	ENST00000245479	NM_000346.3	164	Cag/Tag	2/3	1	2	FACETS	0.316	0.269	0.368	0.316	0.269	0.368	SUBCLONAL	1	TRUE	1	0.459102990520032	2		463	730	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119104	70119104	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	28	185	0	ENST00000245479.2:c.676G>T	p.Glu226Ter	p.E226*	ENST00000245479	NM_000346.3	226	Gag/Tag	2/3	1	2	FACETS	0.457	0.366	0.559	0.457	0.366	0.559	SUBCLONAL	1	TRUE	1	0.459102990520032	2		185	267	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39629506	39629506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1431988901	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	270	331	0	ENST00000262039.4:c.2200G>A	p.Val734Met	p.V734M	ENST00000262039	NM_002647.2	734	Gtg/Atg	21/25	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.459102990520032	2		331	1062	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395736	45395736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	81	348	0	ENST00000262160.6:c.398G>A	p.Arg133His	p.R133H	ENST00000262160	NM_005901.5	133	cGc/cAc	4/11	1	2	FACETS	0.392	0.344	0.443	0.392	0.344	0.443	SUBCLONAL	1	TRUE	1	0.459102990520032	2		348	901	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118948	3118948	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587777022	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	90	347	0	ENST00000078429.4:c.632C>T	p.Ser211Leu	p.S211L	ENST00000078429	NM_002067.2	211	tCg/tTg	5/7	1	2	FACETS	0.899	0.802	1	0.899	0.802	1	CLONAL	1	TRUE	1	0.459102990520032	2		347	436	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298764	15298764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	123	285	0	ENST00000263388.2:c.1534G>A	p.Ala512Thr	p.A512T	ENST00000263388	NM_000435.2	512	Gcc/Acc	10/33	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.459102990520032	2		285	516	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795597	42795597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142397024	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	139	390	0	ENST00000575354.2:c.2677C>T	p.Pro893Ser	p.P893S	ENST00000575354	NM_015125.3	893	Ccc/Tcc	10/20	1	2	FACETS	0.969	0.885	1	0.969	0.885	1	CLONAL	1	TRUE	1	0.459102990520032	2		390	625	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145550	24145550	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	135	323	0	ENST00000263121.7:c.569G>A	p.Arg190Gln	p.R190Q	ENST00000263121	NM_003073.3	190	cGg/cAg	5/9	1	2	FACETS	0.979	0.893	1	0.979	0.893	1	CLONAL	1	TRUE	1	0.459102990520032	2		323	601	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032822	30032822	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	100	382	0	ENST00000338641.4:c.197A>G	p.Tyr66Cys	p.Y66C	ENST00000338641	NM_000268.3	66	tAc/tGc	2/16	1	2	FACETS	0.513	0.458	0.572	0.513	0.458	0.572	SUBCLONAL	1	TRUE	1	0.459102990520032	2		382	849	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197725	123197725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749851312	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	146	232	0	ENST00000218089.9:c.1849C>T	p.Arg617Trp	p.R617W	ENST00000218089	NM_001042749.1	617	Cgg/Tgg	20/35	1	1	FACETS	0.904	0.83	0.981	0.904	0.83	0.981	CLONAL	1	TRUE	0	0.459102990520032	1		232	542	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	71	426	2	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	0.459102990520032	2	FACETS	0.502	0.438	0.571	0.251	0.219	0.286	SUBCLONAL	1	TRUE	0	0.459102990520032	2		428	616	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149728	202149728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	114	479	0	ENST00000358485.4:c.1173del	p.Ile392SerfsTer4	p.I392Sfs*4	ENST00000358485	NM_001080125.1	390	gCc/gc	8/9	1	2	FACETS	0.629	0.566	0.695	0.629	0.566	0.695	SUBCLONAL	1	TRUE	1	0.459102990520032	2		479	790	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22008941	22008943	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	75	375	0	ENST00000276925.6:c.10_12del	p.Glu4del	p.E4del	ENST00000276925	NM_004936.3	4	GAG/-	1/2	1	2	FACETS	0.508	0.445	0.576	0.508	0.445	0.576	SUBCLONAL	1	TRUE	1	0.459102990520032	2		375	643	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438175	56438176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0001685-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	201	407	0	ENST00000407977.2:c.816_817dup	p.Ala273ValfsTer147	p.A273Vfs*147	ENST00000407977		273	gcc/gTGcc	7/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.459102990520032	2		407	831	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152093	55152093	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121908585	NA	P-0001692-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	121	484	2	ENST00000257290.5:c.2525A>T	p.Asp842Val	p.D842V	ENST00000257290	NM_006206.4	842	gAc/gTc	18/23	0.230676749768865	3	FACETS	1	0.944	1			1	CLONAL	2	TRUE	NA	0.270948185112345	3		486	481	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048221	180048221	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001692-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	47	422	0	ENST00000261937.6:c.2052G>C	p.Leu684Phe	p.L684F	ENST00000261937	NM_182925.4	684	ttG/ttC	14/30	0.270948185112345	1	FACETS	0.842	0.713	0.984	0.842	0.713	0.984	CLONAL	1	TRUE	0	0.270948185112345	1		422	356	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0001702-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	143	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.778	0.709	0.851	0.778	0.709	0.851	SUBCLONAL	1	TRUE	1	0.399108664340567	2		326	921	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0001702-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	116	266	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.766	0.69	0.846	0.766	0.69	0.846	SUBCLONAL	1	TRUE	1	0.399108664340567	2		266	759	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0001702-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	177	583	1	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.917	0.845	0.993	0.917	0.845	0.993	CLONAL	1	TRUE	1	0.399108664340567	2		584	967	SUCCESS
APC	324	MSKCC	GRCh37	5	112116486	112116486	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0001702-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	115	441	0	ENST00000257430.4:c.532-1G>T		p.X178_splice	ENST00000257430	NM_000038.5	178			1	2	FACETS	0.778	0.701	0.859	0.778	0.701	0.859	SUBCLONAL	1	TRUE	1	0.399108664340567	2		441	741	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119795	70119804	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCTATCGA	CCCCTATCGA	-	novel	NA	P-0001702-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	118	714	0	ENST00000245479.2:c.798_807del	p.Pro267SerfsTer9	p.P267Sfs*9	ENST00000245479	NM_000346.3	266	cCCCCTATCGAc/cc	3/3	1	2	FACETS	0.692	0.624	0.765	0.692	0.624	0.765	SUBCLONAL	1	TRUE	1	0.399108664340567	2		714	854	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0001725-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	354	655	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.704216592711097	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.704216592711097	2		655	482	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742840	17742840	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001725-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	152	491	0	ENST00000250003.3:c.748G>A	p.Asp250Asn	p.D250N	ENST00000250003	NM_002478.4	250	Gac/Aac	3/3	0.548969252074893	2	FACETS	1	0.958	1	0.526	0.487	0.567	CLONAL	1	TRUE	0	0.704216592711097	2		491	410	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100597	102100597	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001725-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	91	491	0	ENST00000282441.5:c.1441G>C	p.Asp481His	p.D481H	ENST00000282441	NM_001130145.2	481	Gac/Cac	9/9	0.548969252074893	2	FACETS	0.594	0.53	0.662	0.297	0.265	0.331	SUBCLONAL	1	TRUE	0	0.704216592711097	2		491	435	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309590	30309590	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001725-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	160	601	0	ENST00000307677.4:c.432C>G	p.Phe144Leu	p.F144L	ENST00000307677	NM_138578.1	144	ttC/ttG	2/3	0.561403618037756	4	FACETS	0.951	0.873	1	0.476	0.436	0.517	CLONAL	1	TRUE	2	0.704216592711097	4		601	814	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190086	123190086	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0001725-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	268	494	1	ENST00000218089.9:c.1304+1G>T		p.X435_splice	ENST00000218089	NM_001042749.1	435			0.546139476841694	3	FACETS	1	0.968	1			1	CLONAL	2	TRUE	NA	0.704216592711097	3		495	502	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0001732-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	101	408	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.556653226853046	4	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	2	0.563894184651691	4		408	272	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0001732-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	10	162	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.563894184651691	2	FACETS	0.381	0.261	0.53	0.191	0.13	0.265	SUBCLONAL	1	TRUE	0	0.563894184651691	2		162	93	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913283	NA	P-0001732-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	96	570	0	ENST00000263967.3:c.3129G>T	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atT	21/21	0.563894184651691	2	FACETS	0.91	0.834	0.987	0.91	0.834	0.987	CLONAL	2	TRUE	0	0.563894184651691	2		570	187	SUCCESS
APC	324	MSKCC	GRCh37	5	112175175	112175175	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001732-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	42	319	0	ENST00000257430.4:c.3885del	p.Ala1296GlnfsTer9	p.A1296Qfs*9	ENST00000257430	NM_000038.5	1295	gAa/ga	16/16	1	2	FACETS	0.987	0.839	1	0.987	0.839	1	CLONAL	1	TRUE	1	0.563894184651691	2		319	151	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776116	9776116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569586715	NA	P-0001732-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	96	392	0	ENST00000377346.4:c.580G>A	p.Val194Ile	p.V194I	ENST00000377346	NM_005026.3	194	Gtt/Att	5/24	1	2	FACETS	0.984	0.885	1	0.984	0.885	1	CLONAL	1	TRUE	1	0.563894184651691	2		392	346	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120002	70120002	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001732-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	169	99	0	ENST00000245479.2:c.1004G>A	p.Trp335Ter	p.W335*	ENST00000245479	NM_000346.3	335	tGg/tAg	3/3	0.563894184651691	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.563894184651691	3		99	220	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0001741-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	224	408	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.512074607363619	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.511802629702941	1		408	469	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101286	27101286	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1238182894	NA	P-0001741-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	161	567	0	ENST00000324856.7:c.4568A>G	p.Tyr1523Cys	p.Y1523C	ENST00000324856	NM_006015.4	1523	tAt/tGt	18/20	0.445933372168873	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.511802629702941	1		567	395	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690261	47690261	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001741-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	74	605	0	ENST00000233146.2:c.1478A>C	p.Gln493Pro	p.Q493P	ENST00000233146	NM_000251.2	493	cAg/cCg	9/16	0.356025783285834	1	FACETS	0.518	0.456	0.585	0.518	0.456	0.585	SUBCLONAL	1	TRUE	0	0.511802629702941	1		605	415	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202810	128202810	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001741-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	95	543	0	ENST00000341105.2:c.910C>A	p.Pro304Thr	p.P304T	ENST00000341105	NM_032638.4	304	Cct/Act	4/6	0.179848581666425	1	FACETS	0.778	0.699	0.861	0.778	0.699	0.861	INDETERMINATE	1	TRUE	0	0.511802629702941	1		543	355	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390546	139390546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200893930	NA	P-0001741-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	55	643	0	ENST00000277541.6:c.7645C>T	p.Arg2549Cys	p.R2549C	ENST00000277541	NM_017617.3	2549	Cgc/Tgc	34/34	0.356025783285834	1	FACETS	0.495	0.426	0.57	0.495	0.426	0.57	SUBCLONAL	1	TRUE	0	0.511802629702941	1		643	323	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121438927	121438927	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001741-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	110	738	0	ENST00000257555.6:c.1828C>G	p.Leu610Val	p.L610V	ENST00000257555		610	Ctg/Gtg	10/10	NA	2	FACETS	1	0.917	1			1	INDETERMINATE	1	TRUE	NA	0.511802629702941	2		738	424	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191129	2191129	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001741-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	143	674	0	ENST00000398665.3:c.383A>T	p.Tyr128Phe	p.Y128F	ENST00000398665	NM_032482.2	128	tAc/tTc	5/28	0.512074607363619	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.511802629702941	1		674	286	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602314	10602314	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001741-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	127	550	0	ENST00000171111.5:c.1264G>T	p.Asp422Tyr	p.D422Y	ENST00000171111	NM_203500.1	422	Gat/Tat	3/6	0.512074607363619	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.511802629702941	1		550	272	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579585	7579585	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001741-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	111	413	0	ENST00000269305.4:c.102del	p.Leu35CysfsTer9	p.L35Cfs*9	ENST00000269305	NM_001126112.2	34	ccC/cc	4/11	0.445933372168873	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.511802629702941	1		413	252	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096913	11096914	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0001741-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	109	712	0	ENST00000358026.2:c.404_405del	p.Pro135ArgfsTer23	p.P135Rfs*23	ENST00000358026	NM_001128849.1	135	cCA/c	4/36	0.512074607363619	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.511802629702941	1		712	258	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807822	3807823	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0001741-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	67	505	0	ENST00000262367.5:c.3596_3597delinsTT	p.Cys1199Phe	p.C1199F	ENST00000262367	NM_004380.2	1199	tGC/tTT	18/31	0.396832910446115	1	FACETS	0.444	0.387	0.505	0.444	0.387	0.505	SUBCLONAL	1	TRUE	0	0.511802629702941	1		505	439	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249358	153249358	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0001760-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	58	290	0	ENST00000281708.4:c.1418+2T>G		p.X473_splice	ENST00000281708	NM_033632.3	473			0.412306779131576	5	FACETS	1	0.959	1			1	CLONAL	1	FALSE	NA	0.556212819403794	5		290	295	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045881	180045881	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001760-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	10	347	0	ENST00000261937.6:c.2890G>T	p.Val964Leu	p.V964L	ENST00000261937	NM_182925.4	964	Gtg/Ttg	21/30	0.477361674934003	1	FACETS	0.26	0.177	0.361	0.26	0.177	0.361	SUBCLONAL	1	FALSE	0	0.556212819403794	1		347	100	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038526	47038526	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001760-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	28	439	0	ENST00000377604.3:c.688C>G	p.Arg230Gly	p.R230G	ENST00000377604	NM_001204468.1	230	Cga/Gga	8/24	0.29178235657791	2	FACETS	0.491	0.395	0.599	0.246	0.197	0.3	INDETERMINATE	1	FALSE	0	0.556212819403794	2		439	205	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577587	7577587	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001760-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	42	252	0	ENST00000269305.4:c.694del	p.Ile232SerfsTer15	p.I232Sfs*15	ENST00000269305	NM_001126112.2	232	Atc/tc	7/11	0.562204537924327	3	FACETS	0.718	0.603	0.843	0.359	0.301	0.422	SUBCLONAL	1	FALSE	1	0.556212819403794	3		252	269	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976458	25976458	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001779-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	157	597	0	ENST00000435504.4:c.1087G>A	p.Glu363Lys	p.E363K	ENST00000435504		363	Gag/Aag	11/13	1	2	FACETS	0.833	0.769	0.9	0.833	0.769	0.9	CLONAL	1	TRUE	1	0.743326341548042	2		597	507	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295795	212295795	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369248674	NA	P-0001780-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	204	633	1	ENST00000342788.4:c.2518G>A	p.Val840Ile	p.V840I	ENST00000342788	NM_005235.2	840	Gtt/Att	21/28	0.451283202013117	3	FACETS	1	0.973	1	0.365	0.339	0.392	CLONAL	1	TRUE	0	0.534741971202698	3		634	883	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168699	56168699	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001780-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	630	657	1	ENST00000399503.3:c.1553C>G	p.Ala518Gly	p.A518G	ENST00000399503	NM_005921.1	518	gCa/gGa	9/20	0.5347918279834	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.534741971202698	3		658	1492	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715754	18715754	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001780-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	556	597	0	ENST00000266497.5:c.3585A>T	p.Glu1195Asp	p.E1195D	ENST00000266497		1195	gaA/gaT	25/31	0.358739321580237	3	FACETS	0.96	0.923	0.998			1	CLONAL	2	TRUE	NA	0.534741971202698	3		597	1372	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202301	133202301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001780-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	142	541	0	ENST00000320574.5:c.6587C>T	p.Ser2196Phe	p.S2196F	ENST00000320574	NM_006231.2	2196	tCc/tTc	47/49	0.5347918279834	3	FACETS	1	0.975	1	0.587	0.538	0.639	CLONAL	1	TRUE	1	0.534741971202698	3		541	573	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874353	76874353	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001780-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	262	742	0	ENST00000373344.5:c.5369C>G	p.Ala1790Gly	p.A1790G	ENST00000373344	NM_000489.3	1790	gCa/gGa	21/35	1	2	FACETS	0.918	0.861	0.978	0.918	0.861	0.978	CLONAL	1	TRUE	1	0.534741971202698	2		742	1067	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970980	55971013	+	frameshift_variant	Frame_Shift_Del	DEL	AAGTTCTTGCAAACAGGTGTGGGCAACTCTCCCA	AAGTTCTTGCAAACAGGTGTGGGCAACTCTCCCA	-	novel	NA	P-0001780-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	68	706	0	ENST00000263923.4:c.1784_1817del	p.Val595GlyfsTer7	p.V595Gfs*7	ENST00000263923	NM_002253.2	595	gTGGGAGAGTTGCCCACACCTGTTTGCAAGAACTTg/gg	13/30	1	2	FACETS	0.381	0.331	0.435	0.381	0.331	0.435	SUBCLONAL	1	TRUE	1	0.534741971202698	2		706	668	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397223	397223	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001811-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	73	432	0	ENST00000380956.4:c.608A>G	p.His203Arg	p.H203R	ENST00000380956	NM_001195286.1	203	cAc/cGc	5/9	1	2	FACETS	0.682	0.595	0.776	0.682	0.595	0.776	SUBCLONAL	1	TRUE	1	0.25	2		432	856	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514145	69514145	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001811-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	60	620	0	ENST00000294312.3:c.536T>A	p.Leu179His	p.L179H	ENST00000294312	NM_005117.2	179	cTc/cAc	3/3	1	2	FACETS	0.513	0.441	0.593	0.513	0.441	0.593	SUBCLONAL	1	TRUE	1	0.25	2		620	935	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247186	153247186	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001813-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	595	201	352	0	ENST00000281708.4:c.1616G>T	p.Gly539Val	p.G539V	ENST00000281708	NM_033632.3	539	gGg/gTg	10/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.430623883525457	2		352	796	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325695	87325695	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001813-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	383	115	359	0	ENST00000277120.3:c.572T>C	p.Ile191Thr	p.I191T	ENST00000277120		191	aTa/aCa	6/19	0.430623883525457	1	FACETS	0.842	0.762	0.925	0.842	0.762	0.925	CLONAL	1	TRUE	0	0.430623883525457	1		359	498	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363799	118363799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001813-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	392	110	390	0	ENST00000534358.1:c.5032G>A	p.Glu1678Lys	p.E1678K	ENST00000534358	NM_005933.3	1678	Gag/Aag	16/36	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.430623883525457	2		390	502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs878854073	NA	P-0001813-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	156	70	271	0	ENST00000269305.4:c.673-1G>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.430623883525457	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.430623883525457	1		271	226	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628638	187628638	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001813-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	554	151	472	0	ENST00000441802.2:c.2344del	p.Arg782ValfsTer9	p.R782Vfs*9	ENST00000441802	NM_005245.3	782	Cgt/gt	2/27	1	2	FACETS	0.995	0.912	1	0.995	0.912	1	CLONAL	1	TRUE	1	0.430623883525457	2		472	705	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412039	116412050	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGAAGGTATATT	AGAAGGTATATT	-	novel	NA	P-0001813-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	231	139	231	0	ENST00000397752.3:c.3024_3028+7del		p.X1008_splice	ENST00000397752	NM_000245.2	1008		14/21	0.430623883525457	2	FACETS	0.872	0.804	0.942	0.872	0.804	0.942	CLONAL	2	TRUE	0	0.430623883525457	2		231	370	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548938	29548938	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660135	NA	P-0001813-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	173	31	158	0	ENST00000356175.3:c.1714del	p.Glu572ArgfsTer14	p.E572Rfs*14	ENST00000356175	NM_000267.3	571	tGg/tg	15/57	0.430623883525457	1	FACETS	0.554	0.451	0.668	0.554	0.451	0.668	SUBCLONAL	1	TRUE	0	0.430623883525457	1		158	204	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247186	153247186	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001813-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	278	352	0	ENST00000281708.4:c.1616G>T	p.Gly539Val	p.G539V	ENST00000281708	NM_033632.3	539	gGg/gTg	10/12	1	2	FACETS	0.948	0.893	1	0.948	0.893	1	CLONAL	1	TRUE	1	0.675534447949386	2		352	868	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363799	118363799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001813-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	305	390	0	ENST00000534358.1:c.5032G>A	p.Glu1678Lys	p.E1678K	ENST00000534358	NM_005933.3	1678	Gag/Aag	16/36	1	2	FACETS	0.936	0.884	0.989	0.936	0.884	0.989	CLONAL	1	TRUE	1	0.675534447949386	2		390	965	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs878854073	NA	P-0001813-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	213	271	0	ENST00000269305.4:c.673-1G>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.668861344449492	1	FACETS	0.757	0.709	0.805	0.757	0.709	0.805	SUBCLONAL	1	TRUE	0	0.675534447949386	1		271	552	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628638	187628638	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001813-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	352	472	0	ENST00000441802.2:c.2344del	p.Arg782ValfsTer9	p.R782Vfs*9	ENST00000441802	NM_005245.3	782	Cgt/gt	2/27	1	2	FACETS	0.888	0.842	0.936	0.888	0.842	0.936	CLONAL	1	TRUE	1	0.675534447949386	2		472	1173	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412039	116412050	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGAAGGTATATT	AGAAGGTATATT	-	novel	NA	P-0001813-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	335	231	0	ENST00000397752.3:c.3024_3028+7del		p.X1008_splice	ENST00000397752	NM_000245.2	1008		14/21	0.631750923954848	3	FACETS	1	0.991	1	0.756	0.724	0.788	CLONAL	2	TRUE	0	0.675534447949386	3		231	585	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548938	29548938	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660135	NA	P-0001813-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	26	158	0	ENST00000356175.3:c.1714del	p.Glu572ArgfsTer14	p.E572Rfs*14	ENST00000356175	NM_000267.3	571	tGg/tg	15/57	0.675534447949386	1	FACETS	0.392	0.315	0.478	0.392	0.315	0.478	SUBCLONAL	1	TRUE	0	0.675534447949386	1		158	130	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279516	1279516	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773813809	NA	P-0001813-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	231	339	0	ENST00000310581.5:c.2020G>A	p.Gly674Ser	p.G674S	ENST00000310581	NM_198253.2	674	Ggc/Agc	5/16	0.460274887317601	3	FACETS	0.776	0.723	0.831			1	SUBCLONAL	1	TRUE	NA	0.675534447949386	3		339	1179	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176132111	176132111	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001835-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	97	606	0	ENST00000367669.3:c.656G>T	p.Trp219Leu	p.W219L	ENST00000367669	NM_022457.5	219	tGg/tTg	5/20	1	2	FACETS	0.534	0.478	0.594	0.534	0.478	0.594	SUBCLONAL	1	TRUE	1	0.721969451748565	2		606	503	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47087991	47087991	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001835-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	111	469	0	ENST00000409792.3:c.7084C>T	p.Gln2362Ter	p.Q2362*	ENST00000409792	NM_014159.6	2362	Cag/Tag	16/21	0.721969451748565	1	FACETS	0.467	0.422	0.513	0.467	0.422	0.513	SUBCLONAL	1	TRUE	0	0.721969451748565	1		469	421	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637186	176637186	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001835-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	120	504	0	ENST00000439151.2:c.1786G>A	p.Gly596Ser	p.G596S	ENST00000439151	NM_022455.4	596	Ggt/Agt	5/23	1	2	FACETS	0.662	0.601	0.726	0.662	0.601	0.726	SUBCLONAL	1	TRUE	1	0.721969451748565	2		504	502	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797314	135797314	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001835-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	24	441	0	ENST00000298552.3:c.555C>A	p.Tyr185Ter	p.Y185*	ENST00000298552	NM_001162426.1	185	taC/taA	7/23	0.721969451748565	1	FACETS	0.15	0.118	0.188	0.15	0.118	0.188	SUBCLONAL	1	TRUE	0	0.721969451748565	1		441	283	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78865554	78865554	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001835-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	66	592	0	ENST00000306801.3:c.2018A>C	p.Gln673Pro	p.Q673P	ENST00000306801	NM_020761.2	673	cAg/cCg	18/34	1	2	FACETS	0.456	0.397	0.519	0.456	0.397	0.519	SUBCLONAL	1	TRUE	1	0.721969451748565	2		592	401	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582075	52582093	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	GTGATTAAACATTTTCTAG	GTGATTAAACATTTTCTAG	-	novel	NA	P-0001835-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	431	44	1	ENST00000394830.3:c.4735_*4del		p.*1579*	ENST00000394830	NM_018313.4	1579		30/30	0.721969451748565	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.721969451748565	1		45	684	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038213	30038213	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001835-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	136	732	0	ENST00000338641.4:c.389del	p.Lys130ArgfsTer44	p.K130Rfs*44	ENST00000338641	NM_000268.3	129	gAa/ga	4/16	0.721969451748565	1	FACETS	0.498	0.456	0.542	0.498	0.456	0.542	SUBCLONAL	1	TRUE	0	0.721969451748565	1		732	483	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097703	27097703	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001850-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	178	292	0	ENST00000324856.7:c.3292C>T	p.Gln1098Ter	p.Q1098*	ENST00000324856	NM_006015.4	1098	Cag/Tag	12/20	0.267185121566669	3	FACETS	1	0.982	1	0.797	0.737	0.858	CLONAL	2	TRUE	0	0.267185121566669	3		292	632	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0001856-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1505	237	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.650219732866834	7	FACETS	1	0.974	1			1	CLONAL	1	TRUE	NA	0.650219732866834	7		326	1742	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599321	55599321	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913507	NA	P-0001856-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	34	294	0	ENST00000288135.5:c.2447A>T	p.Asp816Val	p.D816V	ENST00000288135	NM_000222.2	816	gAc/gTc	17/21	1	2	FACETS	0.197	0.161	0.239	0.197	0.161	0.239	SUBCLONAL	1	TRUE	1	0.650219732866834	2		294	530	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0001864-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	235	620	2	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.905	0.848	0.964	0.905	0.848	0.964	CLONAL	1	TRUE	1	0.688444489280789	2		622	754	SUCCESS
APC	324	MSKCC	GRCh37	5	112175118	112175118	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1060503299	NA	P-0001864-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	177	407	0	ENST00000257430.4:c.3827C>A	p.Ser1276Ter	p.S1276*	ENST00000257430	NM_000038.5	1276	tCa/tAa	16/16	1	2	FACETS	0.93	0.862	0.999	0.93	0.862	0.999	CLONAL	1	TRUE	1	0.688444489280789	2		407	553	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945387	151945387	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001864-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	41	259	0	ENST00000262189.6:c.2132C>G	p.Pro711Arg	p.P711R	ENST00000262189	NM_170606.2	711	cCt/cGt	14/59	0.380399437315342	5	FACETS	0.404	0.335	0.48	0.135	0.111	0.16	INDETERMINATE	1	TRUE	2	0.688444489280789	5		259	600	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118339530	118339530	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001864-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	126	631	0	ENST00000534358.1:c.473G>C	p.Arg158Thr	p.R158T	ENST00000534358	NM_005933.3	158	aGa/aCa	2/36	0.688444489280789	2	FACETS	0.45	0.407	0.495	0.225	0.203	0.248	SUBCLONAL	1	TRUE	0	0.688444489280789	2		631	814	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480341	56480341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001864-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	642	575	0	ENST00000267101.3:c.448G>A	p.Glu150Lys	p.E150K	ENST00000267101	NM_001982.3	150	Gag/Aag	4/28	0.46719645320384	4	FACETS	1	0.996	1	0.832	0.804	0.859	CLONAL	2	TRUE	1	0.688444489280789	4		575	1262	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26978097	26978097	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001864-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	1619	651	2	ENST00000381527.3:c.1274C>G	p.Ser425Cys	p.S425C	ENST00000381527	NM_001260.1	425	tCc/tGc	13/13	0.688444489280789	6	FACETS	1	0.997	1	1	0.997	1	CLONAL	5	TRUE	1	0.688444489280789	6		653	2119	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647556	23647556	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001864-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	316	605	0	ENST00000261584.4:c.311C>G	p.Pro104Arg	p.P104R	ENST00000261584	NM_024675.3	104	cCt/cGt	4/13	NA	2	FACETS	0.768	0.724	0.812			1	INDETERMINATE	1	TRUE	NA	0.688444489280789	2		605	1196	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976555	7976555	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001864-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	626	553	0	ENST00000319144.4:c.1837G>T	p.Glu613Ter	p.E613*	ENST00000319144	NM_001139.2	613	Gag/Tag	14/15	0.688444489280789	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.688444489280789	2		553	844	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044997	47044997	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001864-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	138	261	0	ENST00000377604.3:c.2323A>G	p.Ile775Val	p.I775V	ENST00000377604	NM_001204468.1	775	Atc/Gtc	20/24	1	1	FACETS	0.64	0.588	0.693	0.64	0.588	0.693	SUBCLONAL	1	TRUE	0	0.688444489280789	1		261	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577497	7577509	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ACCTGGAGTCTTC	ACCTGGAGTCTTC	-	novel	NA	P-0001864-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	269	408	0	ENST00000269305.4:c.772_782+2del		p.X258_splice	ENST00000269305	NM_001126112.2	258		7/11	0.688444489280789	2	FACETS	0.977	0.936	1	0.977	0.936	1	CLONAL	2	TRUE	0	0.688444489280789	2		408	400	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398280	25398281	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0001864-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	582	580	0	ENST00000311936.3:c.38_39delinsTT	p.Gly13Val	p.G13V	ENST00000311936	NM_004985.3	13	gGC/gTT	2/5	0.688444489280789	3	FACETS	0.999	0.964	1	0.999	0.964	1	CLONAL	2	TRUE	1	0.688444489280789	3		580	1138	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696432	47696432	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519968	NA	P-0001884-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	175	507	0	ENST00000347630.2:c.391T>G	p.Trp131Gly	p.W131G	ENST00000347630	NM_001007230.1	131	Tgg/Ggg	6/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.32	2		507	879	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17371315	17371315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060503762	NA	P-0001884-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	167	495	0	ENST00000375499.3:c.141G>A	p.Trp47Ter	p.W47*	ENST00000375499	NM_003000.2	47	tgG/tgA	2/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.32	2		495	858	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243859016	243859016	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs397514606	NA	P-0001884-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	126	313	0	ENST00000263826.5:c.49G>A	p.Glu17Lys	p.E17K	ENST00000263826	NM_005465.4	17	Gaa/Aaa	2/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.32	2		313	650	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163373	47163373	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0001884-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	121	454	0	ENST00000409792.3:c.2753C>G	p.Ser918Ter	p.S918*	ENST00000409792	NM_014159.6	918	tCa/tGa	3/21	1	2	FACETS	0.902	0.815	0.995	0.902	0.815	0.995	CLONAL	1	TRUE	1	0.32	2		454	838	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339499	81339499	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1562873352	NA	P-0001884-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	183	646	0	ENST00000222390.5:c.1505G>C	p.Arg502Pro	p.R502P	ENST00000222390	NM_000601.4	502	cGa/cCa	13/18	0.302555357110961	3	FACETS	1	0.945	1	0.517	0.475	0.56	CLONAL	1	TRUE	1	0.32	3		646	1284	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796909	42796909	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001884-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	107	457	0	ENST00000575354.2:c.3367G>C	p.Ala1123Pro	p.A1123P	ENST00000575354	NM_015125.3	1123	Gcc/Ccc	14/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.32	2		457	589	SUCCESS
AR	367	MSKCC	GRCh37	X	66943591	66943591	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001884-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	2434	330	0	ENST00000374690.3:c.2671G>T	p.Asp891Tyr	p.D891Y	ENST00000374690	NM_000044.3	891	Gac/Tac	8/8	0.302555357110961	13	FACETS	0.976	0.968	0.983			1	CLONAL	16	TRUE	NA	0.32	13		330	2689	SUCCESS
APC	324	MSKCC	GRCh37	5	112175806	112175806	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001884-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	127	357	0	ENST00000257430.4:c.4516del	p.Leu1506Ter	p.L1506*	ENST00000257430	NM_000038.5	1505	agC/ag	16/16	0.302555357110961	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.32	1		357	507	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749952	162749952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001888-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	344	318	0	ENST00000367921.3:c.2484G>A	p.Met828Ile	p.M828I	ENST00000367921	NM_006182.2	828	atG/atA	18/18	NA	2	FACETS	0.965	0.924	1			1	INDETERMINATE	2	TRUE	NA	0.592001026552558	2		318	602	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0001888-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	223	175	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	2	TRUE	NA	0.592001026552558	2		175	348	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0001888-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	275	273	0	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	0.570564215983999	2	FACETS	0.825	0.783	0.867	0.825	0.783	0.867	CLONAL	2	TRUE	0	0.592001026552558	2		273	563	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692841	89692843	+	stop_gained	Nonsense_Mutation	TNP	GAC	GAC	TAA	novel	NA	P-0001888-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	61	99	0	ENST00000371953.3:c.325_327delinsTAA	p.Asp109Ter	p.D109*	ENST00000371953	NM_000314.4	109	GAC/TAA	5/9	NA	2	FACETS	0.873	0.781	0.965			1	INDETERMINATE	2	TRUE	NA	0.592001026552558	2		99	118	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0001889-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	632	403	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.855823855951789	2		403	1430	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578507	7578507	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519977	NA	P-0001889-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	303	319	1	ENST00000269305.4:c.423C>G	p.Cys141Trp	p.C141W	ENST00000269305	NM_001126112.2	141	tgC/tgG	5/11	0.855823855951789	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.855823855951789	1		320	403	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115871	8115872	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0001889-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	488	359	0	ENST00000346208.3:c.1219_1220del	p.Ser407AlafsTer99	p.S407Afs*99	ENST00000346208		406	aTC/a	6/6	1	2	FACETS	0.92	0.882	0.959	0.92	0.882	0.959	CLONAL	1	TRUE	1	0.855823855951789	2		359	1239	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0001894-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	280	351	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.316691790153318	5	FACETS	0.98	0.923	1	0.735	0.692	0.779	CLONAL	3	FALSE	1	0.316691790153318	5		351	887	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183656	10183656	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001894-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	236	372	0	ENST00000256474.2:c.125A>T	p.Glu42Val	p.E42V	ENST00000256474	NM_000551.3	42	gAg/gTg	1/3	0.316329834289696	3	FACETS	1	0.991	1	0.718	0.669	0.769	CLONAL	1	FALSE	1	0.316691790153318	3		372	1202	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0001911-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	842	437	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.513545495839213	5	FACETS	1	0.993	1			1	CLONAL	5	TRUE	NA	0.513545495839213	5		437	1121	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145661	61145661	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001911-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	59	388	0	ENST00000295025.8:c.773C>T	p.Thr258Ile	p.T258I	ENST00000295025	NM_002908.2	258	aCa/aTa	7/11	1	2	FACETS	0.261	0.223	0.301	0.261	0.223	0.301	SUBCLONAL	1	TRUE	1	0.513545495839213	2		388	882	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157184	106157184	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001911-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	57	398	1	ENST00000380013.4:c.2085G>T	p.Met695Ile	p.M695I	ENST00000380013	NM_001127208.2	695	atG/atT	3/11	0.513545495839213	1	FACETS	0.28	0.24	0.323	0.28	0.24	0.323	SUBCLONAL	1	TRUE	0	0.513545495839213	1		399	590	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265398	152265398	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001911-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	112	328	0	ENST00000206249.3:c.851G>A	p.Gly284Glu	p.G284E	ENST00000206249	NM_000125.3	284	gGa/gAa	4/8	0.513545495839213	1	FACETS	0.685	0.62	0.754	0.685	0.62	0.754	SUBCLONAL	1	TRUE	0	0.513545495839213	1		328	473	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576258	88576258	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001911-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	30	217	0	ENST00000360948.2:c.1415G>T	p.Ser472Ile	p.S472I	ENST00000360948	NM_001012338.2	472	aGt/aTt	13/19	0.474005067099976	1	FACETS	0.325	0.263	0.395	0.325	0.263	0.395	SUBCLONAL	1	TRUE	0	0.513545495839213	1		217	267	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650770	67650770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1363179074	NA	P-0001911-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	68	332	0	ENST00000264010.4:c.1075G>A	p.Ala359Thr	p.A359T	ENST00000264010	NM_006565.3	359	Gcc/Acc	5/12	0.513545495839213	1	FACETS	0.411	0.358	0.468	0.411	0.358	0.468	SUBCLONAL	1	TRUE	0	0.513545495839213	1		332	479	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234442	41234442	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001911-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	321	521	0	ENST00000357654.3:c.4336G>T	p.Glu1446Ter	p.E1446*	ENST00000357654	NM_007294.3	1446	Gaa/Taa	12/23	0.513545495839213	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.513545495839213	1		521	724	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790172	40790172	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001911-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	16	218	0	ENST00000373198.4:c.2559C>G	p.Ser853Arg	p.S853R	ENST00000373198	NM_133170.3	853	agC/agG	18/32	0.513545495839213	1	FACETS	0.2	0.148	0.263	0.2	0.148	0.263	SUBCLONAL	1	TRUE	0	0.513545495839213	1		218	231	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574019	41574019	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001911-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	56	334	0	ENST00000263253.7:c.6304G>T	p.Gly2102Trp	p.G2102W	ENST00000263253	NM_001429.3	2102	Ggg/Tgg	31/31	0.310162239236063	1	FACETS	0.497	0.428	0.572	0.497	0.428	0.572	SUBCLONAL	1	TRUE	0	0.513545495839213	1		334	326	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922955	39922955	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001911-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	174	568	0	ENST00000378444.4:c.3753C>A	p.Asn1251Lys	p.N1251K	ENST00000378444	NM_001123385.1	1251	aaC/aaA	8/15	0.380850810205369	1	FACETS	0.787	0.727	0.848	0.787	0.727	0.848	SUBCLONAL	1	TRUE	0	0.513545495839213	1		568	640	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360586	70360586	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001911-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	66	343	0	ENST00000374080.3:c.6146C>G	p.Pro2049Arg	p.P2049R	ENST00000374080		2049	cCt/cGt	42/45	0.380850810205369	1	FACETS	0.456	0.397	0.519	0.456	0.397	0.519	SUBCLONAL	1	TRUE	0	0.513545495839213	1		343	419	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148516708	148516708	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001930-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	119	205	0	ENST00000320356.2:c.979C>T	p.Pro327Ser	p.P327S	ENST00000320356	NM_004456.4	327	Cca/Tca	9/20	0.436490826582184	4	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.52	4		205	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578226	7578226	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1464727668	NA	P-0001931-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	109	333	0	ENST00000269305.4:c.623A>T	p.Asp208Val	p.D208V	ENST00000269305	NM_001126112.2	208	gAc/gTc	6/11	1	2	FACETS	0.784	0.706	0.866	1	0.984	1	SUBCLONAL	2	TRUE	1	0.24487721595868	2		333	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0001945-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	82	264	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.686566313140002	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.696746849402315	1		264	146	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0001945-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	18	392	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.696746849402315	1	FACETS	0.14	0.105	0.181	0.14	0.105	0.181	SUBCLONAL	1	TRUE	0	0.696746849402315	1		392	241	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725042	89725042	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0001945-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	116	234	0	ENST00000371953.3:c.1027-2A>T		p.X343_splice	ENST00000371953	NM_000314.4	343			NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.696746849402315	2		234	268	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521174	187521174	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1471762687	NA	P-0001945-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	14	308	0	ENST00000441802.2:c.11981G>C	p.Arg3994Thr	p.R3994T	ENST00000441802	NM_005245.3	3994	aGa/aCa	22/27	NA	2	FACETS	0.188	0.135	0.251			1	INDETERMINATE	1	TRUE	NA	0.696746849402315	2		308	214	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038384	180038384	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001945-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	73	260	0	ENST00000261937.6:c.3633G>T	p.Gln1211His	p.Q1211H	ENST00000261937	NM_182925.4	1211	caG/caT	27/30	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.696746849402315	2		260	198	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720726	89720726	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs878853944	NA	P-0001945-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	15	52	0	ENST00000371953.3:c.877G>T	p.Gly293Ter	p.G293*	ENST00000371953	NM_000314.4	293	Gga/Tga	8/9	NA	2	FACETS	0.545	0.406	0.705			1	INDETERMINATE	1	TRUE	NA	0.696746849402315	2		52	79	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0001945-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	152	303	0	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	0.686566313140002	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.696746849402315	1		303	246	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029499	16029499	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001945-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	14	262	0	ENST00000268712.3:c.1531G>C	p.Glu511Gln	p.E511Q	ENST00000268712	NM_006311.3	511	Gaa/Caa	15/46	0.686566313140002	1	FACETS	0.125	0.09	0.167	0.125	0.09	0.167	SUBCLONAL	1	TRUE	0	0.696746849402315	1		262	210	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228040	53228040	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001945-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	106	300	0	ENST00000375401.3:c.2274del	p.Met759CysfsTer5	p.M759Cfs*5	ENST00000375401	NM_004187.3	758	gcC/gc	16/26	0.689151296069629	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.696746849402315	1		300	170	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128036912	128036912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001965-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	271	578	0	ENST00000285398.2:c.1567G>A	p.Val523Met	p.V523M	ENST00000285398	NM_000122.1	523	Gtg/Atg	10/15	0.484364889158804	4	FACETS	0.876	0.826	0.927	0.876	0.826	0.927	CLONAL	2	TRUE	2	0.698564522937039	4		578	752	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859879	151859879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001965-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	122	532	0	ENST00000262189.6:c.10783G>A	p.Asp3595Asn	p.D3595N	ENST00000262189	NM_170606.2	3595	Gat/Aat	43/59	1	2	FACETS	0.91	0.83	0.991	0.91	0.83	0.991	CLONAL	1	TRUE	1	0.698564522937039	2		532	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577525	+	inframe_deletion	In_Frame_Del	DEL	AGTGTGATGATGGTG	AGTGTGATGATGGTG	-	novel	NA	P-0001965-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	212	460	0	ENST00000269305.4:c.756_770del	p.Thr253_Leu257del	p.T253_L257del	ENST00000269305	NM_001126112.2	252	ctCACCATCATCACACTg/ctg	7/11	0.694920528986007	2	FACETS	0.963	0.918	1	0.963	0.918	1	CLONAL	2	TRUE	0	0.698564522937039	2		460	315	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30733033	30733033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001973-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	57	362	0	ENST00000295754.5:c.1646G>A	p.Gly549Glu	p.G549E	ENST00000295754	NM_003242.5	549	gGg/gAg	7/7	1	2	FACETS	0.252	0.216	0.292	0.252	0.216	0.292	SUBCLONAL	1	TRUE	1	0.799099753154253	2		362	565	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114257	115114257	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001973-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	102	362	0	ENST00000257566.3:c.960G>T	p.Gln320His	p.Q320H	ENST00000257566	NM_016569.3	320	caG/caT	6/8	1	2	FACETS	0.429	0.384	0.476	0.429	0.384	0.476	SUBCLONAL	1	TRUE	1	0.799099753154253	2		362	595	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140879	37140879	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001992-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	211	306	0	ENST00000373509.5:c.715G>C	p.Asp239His	p.D239H	ENST00000373509	NM_002648.3	239	Gat/Cat	5/6	0.305001598857437	1	FACETS	0.686	0.645	0.728	0.686	0.645	0.728	INDETERMINATE	1	TRUE	0	0.786814510613463	1		306	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579410	7579410	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567556123	NA	P-0001992-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	167	283	0	ENST00000269305.4:c.277del	p.Leu93CysfsTer30	p.L93Cfs*30	ENST00000269305	NM_001126112.2	93	Ctg/tg	4/11	0.785906100169317	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.786814510613463	1		283	253	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191477	10191477	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002005-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	50	331	0	ENST00000256474.2:c.470del	p.Thr157IlefsTer2	p.T157Ifs*2	ENST00000256474	NM_000551.3	157	aCt/at	3/3	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.27	2		331	254	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722375	176722375	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002023-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	83	861	3	ENST00000439151.2:c.8006A>G	p.Gln2669Arg	p.Q2669R	ENST00000439151	NM_022455.4	2669	cAa/cGa	23/23	1	2	FACETS	0.62	0.547	0.697	0.62	0.547	0.697	SUBCLONAL	1	TRUE	1	0.454877714128055	2		864	589	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115853	8115854	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0002023-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	144	871	0	ENST00000346208.3:c.1200dup	p.Ser401ValfsTer106	p.S401Vfs*106	ENST00000346208		400	atg/atGg	6/6	0.292854800281837	3	FACETS	0.811	0.745	0.879	0.811	0.745	0.879	CLONAL	2	TRUE	1	0.454877714128055	3		871	479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0002025-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	161	573	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.55753127853843	2		574	415	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0002025-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	288	536	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	NA	2	FACETS	0.98	0.934	1			1	INDETERMINATE	2	TRUE	NA	0.55753127853843	2		536	527	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519893	NA	P-0002025-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	240	648	0	ENST00000267101.3:c.310G>T	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ttg	3/28	0.358917341982049	3	FACETS	1	0.988	1	0.777	0.736	0.819	CLONAL	2	TRUE	0	0.55753127853843	3		648	472	SUCCESS
APC	324	MSKCC	GRCh37	5	112175621	112175621	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002025-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	117	625	0	ENST00000257430.4:c.4330C>T	p.Gln1444Ter	p.Q1444*	ENST00000257430	NM_000038.5	1444	Caa/Taa	16/16	1	2	FACETS	0.978	0.889	1	0.978	0.889	1	CLONAL	1	TRUE	1	0.55753127853843	2		625	429	SUCCESS
APC	324	MSKCC	GRCh37	5	112174043	112174043	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002025-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	40	425	0	ENST00000257430.4:c.2752del	p.Glu918ArgfsTer37	p.E918Rfs*37	ENST00000257430	NM_000038.5	918	Gag/ag	16/16	1	2	FACETS	0.446	0.371	0.528	0.446	0.371	0.528	SUBCLONAL	1	TRUE	1	0.55753127853843	2		425	322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0002066-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	184	366	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.526373605796727	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.576118015961967	1		366	404	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843613	156843613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561243137	NA	P-0002066-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	127	572	0	ENST00000524377.1:c.1039C>T	p.Arg347Cys	p.R347C	ENST00000524377	NM_002529.3	347	Cgc/Tgc	8/17	0.508047323249139	3	FACETS	0.839	0.761	0.92	0.28	0.253	0.307	CLONAL	1	TRUE	0	0.576118015961967	3		572	677	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052882	180052882	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002066-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	67	447	0	ENST00000261937.6:c.1408G>T	p.Ala470Ser	p.A470S	ENST00000261937	NM_182925.4	470	Gcc/Tcc	10/30	NA	2	FACETS	0.437	0.38	0.499			1	INDETERMINATE	1	TRUE	NA	0.576118015961967	2		447	532	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928060	178928086	+	inframe_deletion	In_Frame_Del	DEL	GCCAGTACCTCATGGATTAGAAGATTT	GCCAGTACCTCATGGATTAGAAGATTT	-	novel	NA	P-0002084-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	61	211	0	ENST00000263967.3:c.1340_1366del	p.Pro447_Leu455del	p.P447_L455del	ENST00000263967	NM_006218.2	446	tgGCCAGTACCTCATGGATTAGAAGATTTg/tgg	8/21	0.62177156877935	3	FACETS	1	0.954	1	0.601	0.526	0.679	CLONAL	1	TRUE	1	0.629866189378321	3		211	212	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944447	40944447	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	37	567	0	ENST00000373198.4:c.2055G>C	p.Lys685Asn	p.K685N	ENST00000373198	NM_133170.3	685	aaG/aaC	12/32	1	2	FACETS	0.411	0.341	0.489	0.411	0.341	0.489	SUBCLONAL	1	TRUE	1	0.72005071862518	2		567	250	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260330	16260330	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749588150	NA	P-0002105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	59	299	0	ENST00000375759.3:c.7595G>A	p.Ser2532Asn	p.S2532N	ENST00000375759	NM_015001.2	2532	aGc/aAc	11/15	0.313105196065729	3	FACETS	0.832	0.722	0.948			1	INDETERMINATE	1	TRUE	NA	0.72005071862518	3		299	268	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248635	59248635	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1172545314	NA	P-0002105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	68	526	0	ENST00000371222.2:c.108G>C	p.Gln36His	p.Q36H	ENST00000371222	NM_002228.3	36	caG/caC	1/1	0.270933133914293	1	FACETS	0.332	0.29	0.377	0.332	0.29	0.377	INDETERMINATE	1	TRUE	0	0.72005071862518	1		526	364	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143065	30143065	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	128	515	0	ENST00000389048.3:c.461G>T	p.Cys154Phe	p.C154F	ENST00000389048	NM_004304.4	154	tGc/tTc	1/29	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.72005071862518	NA		515	294	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131498	202131498	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	62	289	0	ENST00000358485.4:c.466C>G	p.Gln156Glu	p.Q156E	ENST00000358485	NM_001080125.1	156	Caa/Gaa	2/9	0.381135609023192	3	FACETS	0.825	0.719	0.938	0.412	0.359	0.469	INDETERMINATE	1	TRUE	1	0.72005071862518	3		289	284	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259477	89259477	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	49	547	0	ENST00000336596.2:c.621G>C	p.Lys207Asn	p.K207N	ENST00000336596	NM_005233.5	207	aaG/aaC	3/17	0.479513390883055	1	FACETS	0.358	0.306	0.415	0.358	0.306	0.415	SUBCLONAL	1	TRUE	0	0.72005071862518	1		547	243	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670895	134670895	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	22	144	0	ENST00000398015.3:c.805+1G>A		p.X269_splice	ENST00000398015	NM_004441.4	269			0.4184840435911	3	FACETS	0.444	0.346	0.557	0.222	0.173	0.279	INDETERMINATE	1	TRUE	1	0.72005071862518	3		144	187	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430245	181430245	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1360786606	NA	P-0002105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	132	266	0	ENST00000325404.1:c.97A>C	p.Asn33His	p.N33H	ENST00000325404	NM_003106.3	33	Aac/Cac	1/1	0.479303858034476	4	FACETS	0.869	0.798	0.941	0.869	0.798	0.941	CLONAL	2	TRUE	2	0.72005071862518	4		266	363	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146592	185146592	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	227	393	0	ENST00000265026.3:c.223G>A	p.Asp75Asn	p.D75N	ENST00000265026	NM_004721.4	75	Gat/Aat	2/14	0.479303858034476	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.72005071862518	4		393	468	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561788	55561788	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	67	486	0	ENST00000288135.5:c.178G>A	p.Asp60Asn	p.D60N	ENST00000288135	NM_000222.2	60	Gat/Aat	2/21	1	2	FACETS	0.608	0.533	0.688	0.608	0.533	0.688	SUBCLONAL	1	TRUE	1	0.72005071862518	2		486	306	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356170	66356170	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	87	460	0	ENST00000273854.3:c.1327G>T	p.Ala443Ser	p.A443S	ENST00000273854	NM_004439.5	443	Gca/Tca	5/18	1	2	FACETS	0.933	0.838	1	0.933	0.838	1	CLONAL	1	TRUE	1	0.72005071862518	2		460	259	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541097	187541097	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	95	353	0	ENST00000441802.2:c.6643T>C	p.Phe2215Leu	p.F2215L	ENST00000441802	NM_005245.3	2215	Ttc/Ctc	10/27	0.72005071862518	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.72005071862518	1		353	159	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233612	233612	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	68	270	0	ENST00000264932.6:c.916C>G	p.Leu306Val	p.L306V	ENST00000264932	NM_004168.2	306	Ctc/Gtc	8/15	0.405099113783643	4	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.72005071862518	4		270	255	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665681	86665681	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	69	554	0	ENST00000274376.6:c.1662C>G	p.Ile554Met	p.I554M	ENST00000274376	NM_002890.2	554	atC/atG	12/25	0.72005071862518	1	FACETS	0.505	0.445	0.567	0.505	0.445	0.567	SUBCLONAL	1	TRUE	0	0.72005071862518	1		554	243	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220249	55220249	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	68	532	0	ENST00000275493.2:c.639C>G	p.Ile213Met	p.I213M	ENST00000275493	NM_005228.3	213	atC/atG	6/28	NA	2	FACETS	0.617	0.541	0.698			1	INDETERMINATE	1	TRUE	NA	0.72005071862518	2		532	306	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346620	81346620	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	102	469	0	ENST00000222390.5:c.1333G>C	p.Asp445His	p.D445H	ENST00000222390	NM_000601.4	445	Gat/Cat	11/18	0.313105196065729	3	FACETS	0.922	0.83	1			1	INDETERMINATE	1	TRUE	NA	0.72005071862518	3		469	418	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372711	81372711	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	94	535	0	ENST00000222390.5:c.823G>C	p.Asp275His	p.D275H	ENST00000222390	NM_000601.4	275	Gac/Cac	7/18	0.313105196065729	3	FACETS	0.922	0.827	1			1	INDETERMINATE	1	TRUE	NA	0.72005071862518	3		535	385	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275875	38275875	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	240	342	0	ENST00000425967.3:c.1394G>A	p.Ser465Asn	p.S465N	ENST00000425967	NM_001174067.1	465	aGt/aAt	11/19	0.697728704417155	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.72005071862518	2		342	294	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341851	8341851	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866497340	NA	P-0002105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	103	592	0	ENST00000356435.5:c.4789C>T	p.Gln1597Ter	p.Q1597*	ENST00000356435		1597	Caa/Taa	29/35	0.72005071862518	1	FACETS	0.776	0.708	0.844	0.776	0.708	0.844	SUBCLONAL	1	TRUE	0	0.72005071862518	1		592	236	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518104	8518104	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	39	501	0	ENST00000356435.5:c.1287G>T	p.Leu429Phe	p.L429F	ENST00000356435		429	ttG/ttT	10/35	0.72005071862518	1	FACETS	0.35	0.293	0.412	0.35	0.293	0.412	SUBCLONAL	1	TRUE	0	0.72005071862518	1		501	198	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133747569	133747569	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	37	413	0	ENST00000318560.5:c.876G>C	p.Glu292Asp	p.E292D	ENST00000318560	NM_005157.4	292	gaG/gaC	5/11	0.697260167208049	2	FACETS	0.395	0.327	0.47	0.198	0.163	0.235	SUBCLONAL	1	TRUE	0	0.72005071862518	2		413	260	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233256	46233256	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	16	497	0	ENST00000334344.6:c.1475A>G	p.Gln492Arg	p.Q492R	ENST00000334344	NM_152641.2	492	cAg/cGg	11/21	NA	2	FACETS	0.155	0.114	0.204			1	INDETERMINATE	1	TRUE	NA	0.72005071862518	2		497	286	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212597	133212597	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	41	354	0	ENST00000320574.5:c.5692G>T	p.Glu1898Ter	p.E1898*	ENST00000320574	NM_006231.2	1898	Gag/Tag	42/49	0.214536941452673	1	FACETS	0.249	0.208	0.294	0.249	0.208	0.294	INDETERMINATE	1	TRUE	0	0.72005071862518	1		354	293	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959028	28959028	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	159	575	0	ENST00000282397.4:c.2110G>C	p.Glu704Gln	p.E704Q	ENST00000282397	NM_002019.4	704	Gag/Cag	14/30	0.72005071862518	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.72005071862518	1		575	244	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68301861	68301861	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	140	547	0	ENST00000487270.1:c.263C>T	p.Ser88Phe	p.S88F	ENST00000487270	NM_133509.3	88	tCt/tTt	4/11	0.526586241063647	3	FACETS	1	0.983	1	0.631	0.58	0.683	CLONAL	1	TRUE	1	0.72005071862518	3		547	419	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562623	95562623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	170	511	0	ENST00000393063.1:c.4634C>T	p.Ser1545Phe	p.S1545F	ENST00000393063	NM_030621.3	1545	tCt/tTt	24/28	0.526586241063647	3	FACETS	0.873	0.814	0.931	0.873	0.814	0.931	CLONAL	2	TRUE	1	0.72005071862518	3		511	368	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828091	3828091	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	127	559	0	ENST00000262367.5:c.2034C>G	p.Ile678Met	p.I678M	ENST00000262367	NM_004380.2	678	atC/atG	10/31	0.228263209531995	2	FACETS	1	0.976	1	0.578	0.532	0.625	INDETERMINATE	1	TRUE	0	0.72005071862518	2		559	305	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916254	9916254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415214536	NA	P-0002105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	83	469	0	ENST00000330684.3:c.2035C>T	p.Pro679Ser	p.P679S	ENST00000330684	NM_001134407.1	679	Cct/Tct	10/13	0.619257239177265	1	FACETS	0.659	0.592	0.728	0.659	0.592	0.728	SUBCLONAL	1	TRUE	0	0.72005071862518	1		469	224	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004961	16004961	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	46	616	0	ENST00000268712.3:c.2293C>G	p.Pro765Ala	p.P765A	ENST00000268712	NM_006311.3	765	Ccc/Gcc	20/46	0.697728704417155	2	FACETS	0.359	0.303	0.42	0.179	0.151	0.21	SUBCLONAL	1	TRUE	0	0.72005071862518	2		616	356	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243906	41243906	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs398122675	NA	P-0002105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	52	509	0	ENST00000357654.3:c.3642G>C	p.Glu1214Asp	p.E1214D	ENST00000357654	NM_007294.3	1214	gaG/gaC	10/23	0.381135609023192	3	FACETS	0.564	0.483	0.653	0.282	0.241	0.327	INDETERMINATE	1	TRUE	1	0.72005071862518	3		509	348	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602369	10602369	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	241	495	0	ENST00000171111.5:c.1209G>T	p.Trp403Cys	p.W403C	ENST00000171111	NM_203500.1	403	tgG/tgT	3/6	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	2	TRUE	NA	0.72005071862518	2		495	321	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796475	42796475	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1050497856	NA	P-0002105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	217	396	0	ENST00000575354.2:c.3032G>C	p.Gly1011Ala	p.G1011A	ENST00000575354	NM_015125.3	1011	gGc/gCc	13/20	0.72005071862518	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.72005071862518	2		396	301	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076862	41076862	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs750249800	NA	P-0002105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	27	508	1	ENST00000373198.4:c.1558G>A	p.Glu520Lys	p.E520K	ENST00000373198	NM_133170.3	520	Gag/Aag	9/32	1	2	FACETS	0.299	0.238	0.367	0.299	0.238	0.367	SUBCLONAL	1	TRUE	1	0.72005071862518	2		509	251	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485763	57485763	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	147	384	0	ENST00000371085.3:c.1064G>T	p.Gly355Val	p.G355V	ENST00000371085	NM_000516.4	355	gGg/gTg	13/13	0.670311617959947	3	FACETS	0.814	0.755	0.875			1	CLONAL	2	TRUE	NA	0.72005071862518	3		384	341	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464450	25464450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369713081	NA	P-0002115-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	459	39	412	5	ENST00000264709.3:c.2063G>A	p.Arg688His	p.R688H	ENST00000264709	NM_175629.2	688	cGc/cAc	17/23	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		417	498	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765541	41765541	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1266211650	NA	P-0002115-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	620	74	538	0	ENST00000301178.4:c.2417C>G	p.Thr806Arg	p.T806R	ENST00000301178	NM_021913.4	806	aCa/aGa	20/20	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		538	694	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0002132-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	131	138	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.453784972777045	2		138	481	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0002157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	283	437	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.360311584371354	2	FACETS	0.827	0.78	0.874	0.827	0.78	0.874	CLONAL	2	TRUE	0	0.42407617881057	2		437	807	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148875	119148876	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0002157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	87	244	0	ENST00000264033.4:c.1096-1_1096delinsAA		p.X366_splice	ENST00000264033	NM_005188.3	366		8/16	0.329631601335307	2	FACETS	1	0.981	1	0.746	0.669	0.826	CLONAL	1	TRUE	0	0.42407617881057	2		244	275	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0002157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	123	443	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.3781112500007	1	FACETS	0.864	0.785	0.947	0.864	0.785	0.947	CLONAL	1	TRUE	0	0.42407617881057	1		443	529	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803898	43803898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	138	310	0	ENST00000372470.3:c.208C>T	p.Pro70Ser	p.P70S	ENST00000372470	NM_005373.2	70	Ccg/Tcg	2/12	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.42407617881057	2		310	544	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660639	190660639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772181508	NA	P-0002157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	77	320	0	ENST00000441310.2:c.277C>T	p.Arg93Cys	p.R93C	ENST00000441310	NM_000534.4	93	Cgt/Tgt	3/13	1	2	FACETS	0.696	0.612	0.785	0.696	0.612	0.785	SUBCLONAL	1	TRUE	1	0.42407617881057	2		320	522	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288996	212288996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	76	525	0	ENST00000342788.4:c.2750G>A	p.Gly917Glu	p.G917E	ENST00000342788	NM_005235.2	917	gGa/gAa	23/28	1	2	FACETS	0.615	0.54	0.695	0.615	0.54	0.695	SUBCLONAL	1	TRUE	1	0.42407617881057	2		525	583	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287331	33287331	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	127	418	0	ENST00000374542.5:c.1766C>T	p.Ser589Phe	p.S589F	ENST00000374542	NM_001141970.1	589	tCc/tTc	6/8	1	2	FACETS	0.742	0.672	0.816	0.742	0.672	0.816	SUBCLONAL	1	TRUE	1	0.42407617881057	2		418	807	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344102	118344102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	183	359	0	ENST00000534358.1:c.2228C>T	p.Pro743Leu	p.P743L	ENST00000534358	NM_005933.3	743	cCt/cTt	3/36	0.329631601335307	2	FACETS	0.798	0.741	0.855	0.798	0.741	0.855	SUBCLONAL	2	TRUE	0	0.42407617881057	2		359	541	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118361911	118361911	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	159	341	0	ENST00000534358.1:c.4697G>A	p.Gly1566Glu	p.G1566E	ENST00000534358	NM_005933.3	1566	gGa/gAa	14/36	0.329631601335307	2	FACETS	1	0.989	1	0.737	0.68	0.795	CLONAL	1	TRUE	0	0.42407617881057	2		341	509	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118391528	118391528	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	168	290	0	ENST00000534358.1:c.11441G>A	p.Ser3814Asn	p.S3814N	ENST00000534358	NM_005933.3	3814	aGc/aAc	34/36	0.329631601335307	2	FACETS	1	0.989	1	0.723	0.669	0.779	CLONAL	1	TRUE	0	0.42407617881057	2		290	548	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434545	121434545	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1343874863	NA	P-0002157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	119	426	0	ENST00000257555.6:c.1309G>A	p.Gly437Ser	p.G437S	ENST00000257555		437	Ggc/Agc	6/10	1	2	FACETS	0.792	0.715	0.872	0.792	0.715	0.872	SUBCLONAL	1	TRUE	1	0.42407617881057	2		426	709	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005320	29005320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	75	505	0	ENST00000282397.4:c.941G>T	p.Arg314Met	p.R314M	ENST00000282397	NM_002019.4	314	aGg/aTg	7/30	0.305135047860956	3	FACETS	0.834	0.732	0.943	0.417	0.366	0.472	CLONAL	1	TRUE	1	0.42407617881057	3		505	514	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047495	49047495	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs587778838	NA	P-0002157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	52	390	0	ENST00000267163.4:c.2490-1G>A		p.X830_splice	ENST00000267163	NM_000321.2	830			0.42430314198523	1	FACETS	0.615	0.527	0.711	0.615	0.527	0.711	SUBCLONAL	1	TRUE	0	0.42407617881057	1		390	314	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730918	40730918	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	133	251	0	ENST00000373198.4:c.3617C>T	p.Pro1206Leu	p.P1206L	ENST00000373198	NM_133170.3	1206	cCc/cTc	27/32	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.42407617881057	2		251	511	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573868	41573868	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	133	468	0	ENST00000263253.7:c.6153A>C	p.Leu2051Phe	p.L2051F	ENST00000263253	NM_001429.3	2051	ttA/ttC	31/31	1	2	FACETS	0.74	0.672	0.811	0.74	0.672	0.811	SUBCLONAL	1	TRUE	1	0.42407617881057	2		468	848	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939505	76939505	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	135	501	1	ENST00000373344.5:c.1243T>C	p.Ser415Pro	p.S415P	ENST00000373344	NM_000489.3	415	Tcc/Ccc	9/35	0.42430314198523	1	FACETS	0.99	0.905	1	0.99	0.905	1	CLONAL	1	TRUE	0	0.42407617881057	1		502	507	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406663	70406667	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAA	AAAAA	-	novel	NA	P-0002157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	109	458	1	ENST00000373644.4:c.4177_4181del	p.Lys1393PhefsTer2	p.K1393Ffs*2	ENST00000373644	NM_030625.2	1393	AAAAAt/t	4/12	0.413613061629714	1	FACETS	0.797	0.719	0.879	0.797	0.719	0.879	SUBCLONAL	1	TRUE	0	0.42407617881057	1		459	508	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573873	41573875	+	missense_variant	Missense_Mutation	TNP	ACC	ACC	CCT	novel	NA	P-0002157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	132	466	0	ENST00000263253.7:c.6158_6160delinsCCT	p.Asn2053_Leu2054delinsThrPhe	p.N2053_L2054delinsTF	ENST00000263253	NM_001429.3	2053	aACCtt/aCCTtt	31/31	1	2	FACETS	0.726	0.659	0.797	0.726	0.659	0.797	SUBCLONAL	1	TRUE	1	0.42407617881057	2		466	857	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656268	18656269	+	missense_variant	Missense_Mutation	DNP	TC	TC	CA	novel	NA	P-0002157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	70	480	1	ENST00000266497.5:c.2947_2948delinsCA	p.Ser983His	p.S983H	ENST00000266497		983	TCt/CAt	21/31	0.3781112500007	1	FACETS	0.458	0.399	0.521	0.458	0.399	0.521	SUBCLONAL	1	TRUE	0	0.42407617881057	1		481	568	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029464	14029465	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0002157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	142	330	0	ENST00000311895.7:c.1675_1676delinsAA	p.Gly559Asn	p.G559N	ENST00000311895	NM_005236.2	559	GGt/AAt	8/11	0.3781112500007	1	FACETS	0.934	0.855	1	0.934	0.855	1	CLONAL	1	TRUE	0	0.42407617881057	1		330	565	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105694	27105695	+	stop_gained	Nonsense_Mutation	DNP	CT	CT	TA	novel	NA	P-0002157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	41	365	0	ENST00000324856.7:c.5305_5306delinsTA	p.Leu1769Ter	p.L1769*	ENST00000324856	NM_006015.4	1769	CTa/TAa	20/20	1	2	FACETS	0.382	0.318	0.454	0.382	0.318	0.454	SUBCLONAL	1	TRUE	1	0.42407617881057	2		365	506	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0002162-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	110	162	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.536531402284595	5	FACETS	1	0.932	1	0.349	0.313	0.386	CLONAL	1	TRUE	2	0.536531402284595	5		162	707	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278901	1278901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772441504	NA	P-0002162-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	77	263	3	ENST00000310581.5:c.2141C>T	p.Thr714Met	p.T714M	ENST00000310581	NM_198253.2	714	aCg/aTg	6/16	0.208215040898924	5	FACETS	0.607	0.531	0.688	0.202	0.177	0.23	INDETERMINATE	1	TRUE	2	0.536531402284595	5		266	854	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149029	61149029	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002162-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	296	469	0	ENST00000295025.8:c.1219C>A	p.Leu407Met	p.L407M	ENST00000295025	NM_002908.2	407	Ctg/Atg	11/11	0.536531402284595	3	FACETS	0.992	0.933	1	0.496	0.466	0.527	CLONAL	1	TRUE	1	0.536531402284595	3		469	1410	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149662	61149662	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002162-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	65	118	0	ENST00000295025.8:c.1852C>G	p.Gln618Glu	p.Q618E	ENST00000295025	NM_002908.2	618	Caa/Gaa	11/11	0.536531402284595	3	FACETS	0.837	0.73	0.953	0.419	0.365	0.477	CLONAL	1	TRUE	1	0.536531402284595	3		118	367	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670548	30670548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560973662	NA	P-0002162-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	532	448	1	ENST00000376406.3:c.5972G>A	p.Arg1991Gln	p.R1991Q	ENST00000376406	NM_014641.2	1991	cGg/cAg	13/15	0.532141732039614	2	FACETS	0.921	0.887	0.955	0.921	0.887	0.955	CLONAL	2	TRUE	0	0.536531402284595	2		449	1077	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729202	66729202	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002162-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	194	304	1	ENST00000307102.5:c.410G>T	p.Gly137Val	p.G137V	ENST00000307102	NM_002755.3	137	gGc/gTc	3/11	0.536531402284595	6	FACETS	1	0.975	1	0.283	0.261	0.306	CLONAL	1	TRUE	2	0.536531402284595	6		305	1326	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219413	1219413	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0002162-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	266	261	0	ENST00000326873.7:c.464+1G>C		p.X155_splice	ENST00000326873	NM_000455.4	155			NA	2	FACETS	0.946	0.898	0.995			1	INDETERMINATE	2	TRUE	NA	0.536531402284595	2		261	524	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742762	39742762	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002162-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	477	429	0	ENST00000361337.2:c.1605C>G	p.Ile535Met	p.I535M	ENST00000361337	NM_003286.2	535	atC/atG	15/21	0.536531402284595	3	FACETS	0.952	0.912	0.992	0.952	0.912	0.992	CLONAL	2	TRUE	1	0.536531402284595	3		429	1185	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710579	40710579	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002162-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	164	341	0	ENST00000373198.4:c.4272C>A	p.Asp1424Glu	p.D1424E	ENST00000373198	NM_133170.3	1424	gaC/gaA	31/32	0.536531402284595	3	FACETS	0.867	0.796	0.941	0.434	0.398	0.471	CLONAL	1	TRUE	1	0.536531402284595	3		341	894	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175951	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1392778905	NA	P-0002164-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	209	324	0	ENST00000257430.4:c.4660G>T	p.Glu1554Ter	p.E1554*	ENST00000257430	NM_000038.5	1554	Gaa/Taa	16/16	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.652285631979806	2		324	485	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0002164-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	190	349	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.652285631979806	2		349	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782177	NA	P-0002164-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	343	558	0	ENST00000269305.4:c.644G>A	p.Ser215Asn	p.S215N	ENST00000269305	NM_001126112.2	215	aGt/aAt	6/11	0.652285631979806	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.652285631979806	1		558	583	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170914	99170914	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1227700629	NA	P-0002164-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	284	486	0	ENST00000074304.5:c.1543C>T	p.Arg515Ter	p.R515*	ENST00000074304	NM_001134224.1	515	Cga/Tga	16/26	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.652285631979806	2		486	862	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152491	56152491	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561183082	NA	P-0002164-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	228	348	0	ENST00000399503.3:c.547C>T	p.Arg183Ter	p.R183*	ENST00000399503	NM_005921.1	183	Cga/Tga	2/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.652285631979806	2		348	648	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696676	176696676	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002164-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	335	535	0	ENST00000439151.2:c.5377G>A	p.Glu1793Lys	p.E1793K	ENST00000439151	NM_022455.4	1793	Gag/Aag	16/23	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.652285631979806	2		535	861	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636951	176636952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002164-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	208	441	0	ENST00000439151.2:c.1554dup	p.Glu519Ter	p.E519*	ENST00000439151	NM_022455.4	517	-/T	5/23	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.652285631979806	2		441	638	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002166-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	51	456	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.172905751800096	2		456	501	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0002166-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	29	531	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.536	0.429	0.659	0.536	0.429	0.659	SUBCLONAL	1	TRUE	1	0.172905751800096	2		531	626	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0002166-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	118	162	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.172905751800096	3	FACETS	0.934	0.85	1			1	CLONAL	4	TRUE	NA	0.172905751800096	3		162	397	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0002166-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	88	531	0	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.172905751800096	2		531	882	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972916	25972916	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002166-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	39	623	0	ENST00000435504.4:c.1509G>C	p.Lys503Asn	p.K503N	ENST00000435504		503	aaG/aaC	12/13	1	2	FACETS	0.464	0.382	0.555	0.464	0.382	0.555	SUBCLONAL	1	TRUE	1	0.172905751800096	2		623	973	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3827617	3827617	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002166-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	233	742	1	ENST00000262367.5:c.2155C>T	p.Gln719Ter	p.Q719*	ENST00000262367	NM_004380.2	719	Caa/Taa	11/31	0.172905751800096	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.172905751800096	2		743	1240	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565532	41565532	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002166-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	90	617	0	ENST00000263253.7:c.4198A>T	p.Ser1400Cys	p.S1400C	ENST00000263253	NM_001429.3	1400	Agt/Tgt	26/31	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.172905751800096	2		617	1015	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-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	79	419	0	ENST00000377967.4:c.565-7_566del		p.X189_splice	ENST00000377967	NM_021140.2	189		7/29	1	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.172905751800096	1		419	616	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039356	47039358	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0002166-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	121	377	0	ENST00000377604.3:c.985_987del	p.Ser329del	p.S329del	ENST00000377604	NM_001204468.1	327	TCC/-	10/24	1	1	FACETS	0.949	0.858	1	1	0.989	1	CLONAL	2	TRUE	0	0.172905751800096	1		377	674	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123199759	123199760	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0002166-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	85	341	0	ENST00000218089.9:c.2059_2060insCA	p.Val687AlafsTer6	p.V687Afs*6	ENST00000218089	NM_001042749.1	687	gta/gCAta	21/35	1	1	FACETS	0.864	0.765	0.968	1	0.982	1	CLONAL	2	TRUE	0	0.172905751800096	1		341	520	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450300	50450300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002170-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	265	380	1	ENST00000331340.3:c.484C>T	p.Arg162Trp	p.R162W	ENST00000331340	NM_006060.4	162	Cgg/Tgg	5/8	0.539207273085409	3	FACETS	1	0.956	1	0.513	0.48	0.547	CLONAL	1	TRUE	1	0.54366967504352	3		381	1209	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590858	95590858	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002170-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	290	476	0	ENST00000393063.1:c.1051T>C	p.Phe351Leu	p.F351L	ENST00000393063	NM_030621.3	351	Ttc/Ctc	9/28	1	2	FACETS	0.98	0.922	1	0.98	0.922	1	CLONAL	1	TRUE	1	0.54366967504352	2		476	1089	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265151	10265151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002170-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	351	316	0	ENST00000340748.4:c.1789G>A	p.Ala597Thr	p.A597T	ENST00000340748		597	Gcc/Acc	21/40	0.259765348840081	3	FACETS	0.888	0.844	0.932	0.888	0.844	0.932	INDETERMINATE	2	TRUE	1	0.54366967504352	3		316	925	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755612	39755612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776452839	NA	P-0002170-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	292	419	0	ENST00000288319.7:c.1153C>T	p.Arg385Cys	p.R385C	ENST00000288319	NM_182918.3	385	Cgc/Tgc	10/10	1	2	FACETS	0.927	0.872	0.983	0.927	0.872	0.983	CLONAL	1	TRUE	1	0.54366967504352	2		419	1159	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900253	32900258	+	inframe_deletion	In_Frame_Del	DEL	ATGTAC	ATGTAC	-	novel	NA	P-0002170-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	180	423	0	ENST00000380152.3:c.442_447del	p.Cys148_Thr149del	p.C148_T149del	ENST00000380152		147	caATGTACa/caa	5/27	1	2	FACETS	0.905	0.836	0.975	0.905	0.836	0.975	CLONAL	1	TRUE	1	0.54366967504352	2		423	732	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755554	39755554	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002170-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	278	379	0	ENST00000288319.7:c.1211del	p.Pro404ArgfsTer25	p.P404Rfs*25	ENST00000288319	NM_182918.3	404	cCg/cg	10/10	1	2	FACETS	0.968	0.909	1	0.968	0.909	1	CLONAL	1	TRUE	1	0.54366967504352	2		379	1057	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157093	106157093	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002187-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	359	484	0	ENST00000380013.4:c.1994C>A	p.Thr665Lys	p.T665K	ENST00000380013	NM_001127208.2	665	aCa/aAa	3/11	0.397718529604737	3	FACETS	0.996	0.945	1	0.996	0.945	1	CLONAL	2	TRUE	1	0.397718529604737	3		484	1087	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520000	106520000	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs759433704	NA	P-0002187-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	165	390	0	ENST00000359195.3:c.2428C>A	p.Pro810Thr	p.P810T	ENST00000359195	NM_002649.2	810	Cca/Aca	6/11	0.104032698192334	5	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.397718529604737	5		390	1005	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80646059	80646059	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002187-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	50	161	0	ENST00000286548.4:c.93G>C	p.Arg31Ser	p.R31S	ENST00000286548	NM_002072.3	31	agG/agC	1/7	1	2	FACETS	0.967	0.827	1	0.967	0.827	1	CLONAL	1	TRUE	1	0.397718529604737	2		161	260	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782153	135782153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002187-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	195	506	0	ENST00000298552.3:c.1403C>T	p.Ser468Phe	p.S468F	ENST00000298552	NM_001162426.1	468	tCt/tTt	14/23	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.397718529604737	2		506	926	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396341	139396341	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002187-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	133	372	0	ENST00000277541.6:c.5497G>A	p.Asp1833Asn	p.D1833N	ENST00000277541	NM_017617.3	1833	Gac/Aac	30/34	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.397718529604737	2		372	643	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155200	108155200	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002187-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	243	355	0	ENST00000278616.4:c.3993G>T	p.Gln1331His	p.Q1331H	ENST00000278616	NM_000051.3	1331	caG/caT	26/63	0.395732500184487	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	0	0.397718529604737	2		355	606	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924327	112924327	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002187-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	240	423	0	ENST00000351677.2:c.1273G>T	p.Asp425Tyr	p.D425Y	ENST00000351677	NM_002834.3	425	Gac/Tac	11/16	0.104032698192334	5	FACETS	1	0.968	1			1	INDETERMINATE	2	TRUE	NA	0.397718529604737	5		423	911	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249269	133249269	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002187-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	302	393	1	ENST00000320574.5:c.1630G>T	p.Val544Leu	p.V544L	ENST00000320574	NM_006231.2	544	Gtg/Ttg	15/49	0.164876153101217	4	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.397718529604737	4		394	873	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160415	108160415	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002187-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	326	438	1	ENST00000278616.4:c.4323del	p.Tyr1442IlefsTer9	p.Y1442Ifs*9	ENST00000278616	NM_000051.3	1441	atA/at	29/63	0.395732500184487	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.397718529604737	2		439	755	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117717359	117717359	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002190-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	168	348	0	ENST00000368508.3:c.848C>G	p.Ser283Cys	p.S283C	ENST00000368508	NM_002944.2	283	tCt/tGt	8/43	NA	2	FACETS	1	0.955	1			1	INDETERMINATE	1	TRUE	NA	0.289483229581431	2		348	1094	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132512	11132512	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002190-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	56	374	0	ENST00000358026.2:c.2728A>G	p.Thr910Ala	p.T910A	ENST00000358026	NM_001128849.1	910	Acg/Gcg	19/36	0.258825828673812	1	FACETS	0.505	0.432	0.585	0.505	0.432	0.585	SUBCLONAL	1	TRUE	0	0.289483229581431	1		374	655	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954378	48954378	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0002195-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	501	399	0	ENST00000267163.4:c.1498+1G>C		p.X500_splice	ENST00000267163	NM_000321.2	500			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		399	570	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0002199-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	112	358	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.3	5	FACETS	0.917	0.829	1			1	CLONAL	2	TRUE	NA	0.44	5		358	461	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0002199-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	66	408	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.140848582499953	3	FACETS	0.718	0.624	0.819	0.359	0.312	0.41	INDETERMINATE	1	TRUE	1	0.44	3		408	510	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0002199-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	73	431	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.237208459056126	3	FACETS	0.904	0.793	1	0.452	0.396	0.511	INDETERMINATE	1	TRUE	1	0.44	3		431	448	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491645	56491645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002199-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	87	311	0	ENST00000267101.3:c.2537G>T	p.Ser846Ile	p.S846I	ENST00000267101	NM_001982.3	846	aGt/aTt	21/28	0.3	5	FACETS	0.816	0.727	0.911			1	CLONAL	2	TRUE	NA	0.44	5		311	402	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0002199-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	17	324	0	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	0.3	3	FACETS	0.236	0.175	0.308			1	SUBCLONAL	1	TRUE	NA	0.44	3		324	400	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398243	25398243	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs794727277	NA	P-0002199-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	96	398	0	ENST00000311936.3:c.76A>T	p.Asn26Tyr	p.N26Y	ENST00000311936	NM_004985.3	26	Aat/Tat	2/5	0.140848582499953	3	FACETS	1	0.904	1	0.506	0.452	0.563	INDETERMINATE	1	TRUE	1	0.44	3		398	526	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440904	56440904	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1458799446	NA	P-0002199-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	85	317	1	ENST00000407977.2:c.433C>T	p.Arg145Ter	p.R145*	ENST00000407977		145	Cga/Tga	4/10	0.3	4	FACETS	0.846	0.754	0.941			1	CLONAL	2	TRUE	NA	0.44	4		318	329	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549389	187549389	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002203-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	49	492	0	ENST00000441802.2:c.4729del	p.Val1577LeufsTer8	p.V1577Lfs*8	ENST00000441802	NM_005245.3	1577	Gtt/tt	9/27	1	2	FACETS	0.674	0.569	0.789	0.674	0.569	0.789	SUBCLONAL	1	TRUE	1	0.209588104600895	2		492	694	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0002205-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	116	138	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.373917971742514	2	FACETS	0.837	0.77	0.905	1	0.982	1	CLONAL	3	TRUE	0	0.373917971742514	2		138	247	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702235	47702235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369385048	NA	P-0002205-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	117	441	0	ENST00000233146.2:c.1831G>A	p.Val611Met	p.V611M	ENST00000233146	NM_000251.2	611	Gtg/Atg	12/16	0.155723547792687	3	FACETS	0.915	0.832	1	0.915	0.832	1	INDETERMINATE	2	TRUE	1	0.373917971742514	3		441	406	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099041	27099042	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0002205-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	229	352	0	ENST00000324856.7:c.3457_3458del	p.Ser1153HisfsTer39	p.S1153Hfs*39	ENST00000324856	NM_006015.4	1153	TCc/c	13/20	0.373917971742514	2	FACETS	0.974	0.923	1	1	0.994	1	CLONAL	3	TRUE	0	0.373917971742514	2		352	419	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287185	33287185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002233-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	359	420	0	ENST00000374542.5:c.1912C>T	p.Gln638Ter	p.Q638*	ENST00000374542	NM_001141970.1	638	Caa/Taa	6/8	0.702332591147323	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.702332591147323	1		420	630	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526239	189526239	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002233-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	468	329	0	ENST00000264731.3:c.503A>G	p.Asn168Ser	p.N168S	ENST00000264731	NM_003722.4	168	aAc/aGc	4/14	0.702332591147323	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.702332591147323	1		329	847	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0002252-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	79	366	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.816462076069969	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.816462076069969	1		366	101	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023627	27023627	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002252-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	163	247	0	ENST00000324856.7:c.733G>T	p.Ala245Ser	p.A245S	ENST00000324856	NM_006015.4	245	Gcg/Tcg	1/20	0.407758694586115	5	FACETS	0.778	0.718	0.84	0.519	0.478	0.56	INDETERMINATE	2	TRUE	2	0.816462076069969	5		247	571	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335061	65335061	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002252-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	131	503	0	ENST00000342505.4:c.580G>T	p.Val194Phe	p.V194F	ENST00000342505	NM_002227.2	194	Gtc/Ttc	6/25	0.407758694586115	5	FACETS	1	0.941	1	0.686	0.63	0.742	INDETERMINATE	2	TRUE	2	0.816462076069969	5		503	347	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012855	176012855	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002252-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	113	564	0	ENST00000367669.3:c.1521G>T	p.Lys507Asn	p.K507N	ENST00000367669	NM_022457.5	507	aaG/aaT	13/20	0.715913428284183	4	FACETS	0.942	0.863	1	0.942	0.863	1	CLONAL	2	TRUE	2	0.816462076069969	4		564	267	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185195144	185195144	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002252-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	141	596	0	ENST00000265026.3:c.2461G>A	p.Gly821Arg	p.G821R	ENST00000265026	NM_004721.4	821	Ggg/Agg	12/14	0.777136880070668	4	FACETS	0.917	0.848	0.988	0.917	0.848	0.988	CLONAL	2	TRUE	2	0.816462076069969	4		596	342	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201650	66201650	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002252-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	84	520	0	ENST00000273854.3:c.2852G>T	p.Arg951Ile	p.R951I	ENST00000273854	NM_004439.5	951	aGa/aTa	16/18	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.816462076069969	2		520	203	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196330	106196330	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002252-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	130	540	2	ENST00000380013.4:c.4663G>C	p.Glu1555Gln	p.E1555Q	ENST00000380013	NM_001127208.2	1555	Gag/Cag	11/11	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.816462076069969	2		542	307	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673653	30673653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002252-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	193	564	0	ENST00000376406.3:c.3307C>T	p.Pro1103Ser	p.P1103S	ENST00000376406	NM_014641.2	1103	Cca/Tca	10/15	0.777136880070668	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.816462076069969	4		564	395	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845612	63845612	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002252-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	88	395	0	ENST00000279873.7:c.1351A>T	p.Ser451Cys	p.S451C	ENST00000279873	NM_032199.2	451	Agc/Tgc	9/10	0.816462076069969	2	FACETS	0.989	0.931	1	0.989	0.931	1	CLONAL	2	TRUE	0	0.816462076069969	2		395	109	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409114	4409114	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002252-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	128	465	0	ENST00000261254.3:c.809A>T	p.Lys270Met	p.K270M	ENST00000261254	NM_001759.3	270	aAg/aTg	5/5	0.816462076069969	7	FACETS	0.913	0.832	0.998			1	CLONAL	2	TRUE	NA	0.816462076069969	7		465	522	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916143	9916143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762659685	NA	P-0002252-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	55	513	0	ENST00000330684.3:c.2146G>A	p.Ala716Thr	p.A716T	ENST00000330684	NM_001134407.1	716	Gcc/Acc	10/13	0.407758694586115	5	FACETS	1	0.939	1	0.387	0.334	0.444	INDETERMINATE	1	TRUE	2	0.816462076069969	5		513	258	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222113	2222113	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002252-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	471	537	0	ENST00000398665.3:c.2945G>T	p.Ser982Ile	p.S982I	ENST00000398665	NM_032482.2	982	aGc/aTc	24/28	0.816462076069969	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.816462076069969	3		537	526	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164892	36164892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757999827	NA	P-0002252-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	123	287	0	ENST00000300305.3:c.983C>T	p.Thr328Ile	p.T328I	ENST00000300305		328	aCa/aTa	8/8	0.816462076069969	3	FACETS	0.903	0.822	0.987	0.451	0.411	0.494	CLONAL	1	TRUE	1	0.816462076069969	3		287	470	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396887	139396887	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002252-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	660	297	0	ENST00000277541.6:c.5221del	p.Ala1741ArgfsTer57	p.A1741Rfs*57	ENST00000277541	NM_017617.3	1741	Gcg/cg	28/34	0.816462076069969	5	FACETS	1	0.99	1	1	0.99	1	CLONAL	5	TRUE	0	0.816462076069969	5		297	716	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433560	49433560	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002252-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	378	573	0	ENST00000301067.7:c.7993del	p.Gln2665ArgfsTer26	p.Q2665Rfs*26	ENST00000301067	NM_003482.3	2665	Cag/ag	31/54	0.816462076069969	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	1	0.816462076069969	4		573	549	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0002257-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	336	172	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	2	TRUE	NA	0.868466413651461	2		172	353	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106543582	106543582	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002257-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	80	435	0	ENST00000369096.4:c.384G>C	p.Lys128Asn	p.K128N	ENST00000369096	NM_001198.3	128	aaG/aaC	3/7	NA	2	FACETS	0.305	0.268	0.344			1	INDETERMINATE	1	TRUE	NA	0.868466413651461	2		435	604	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979562	2979562	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002260-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	84	530	0	ENST00000396946.4:c.685A>T	p.Ile229Phe	p.I229F	ENST00000396946	NM_032415.4	229	Atc/Ttc	6/25	0.528812642125623	3	FACETS	0.392	0.345	0.443	0.196	0.172	0.222	SUBCLONAL	1	TRUE	1	0.528812642125623	3		530	1024	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934589	9934628	+	frameshift_variant	Frame_Shift_Del	DEL	CACCACTTCAGAACGTTCCTCATTGATGGTGAGCGAGCCA	CACCACTTCAGAACGTTCCTCATTGATGGTGAGCGAGCCA	-	novel	NA	P-0002269-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	159	506	0	ENST00000330684.3:c.1527_1566del	p.Gly510ThrfsTer28	p.G510Tfs*28	ENST00000330684	NM_001134407.1	509	gtTGGCTCGCTCACCATCAATGAGGAACGTTCTGAAGTGGTG/gt	7/13	0.916679890485175	2	FACETS	0.768	0.711	0.827	0.384	0.355	0.414	SUBCLONAL	1	TRUE	0	0.923806700772565	2		506	448	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560500	65560500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs387906651	NA	P-0002276-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	116	386	376	0	ENST00000358664.4:c.97C>T	p.Arg33Ter	p.R33*	ENST00000358664	NM_002382.4	33	Cga/Tga	3/5	0.850785413359982	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.850785413359982	1		376	502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0002285-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	133	609	0	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	0.653849652492839	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.681015886165466	2		609	170	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245454	16245454	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002285-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	42	531	0	ENST00000375759.3:c.1429C>T	p.Gln477Ter	p.Q477*	ENST00000375759	NM_015001.2	477	Cag/Tag	7/15	0.488430712693614	3	FACETS	0.704	0.592	0.825			1	SUBCLONAL	1	TRUE	NA	0.681015886165466	3		531	235	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566118	95566118	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002285-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	57	279	0	ENST00000393063.1:c.4205T>A	p.Met1402Lys	p.M1402K	ENST00000393063	NM_030621.3	1402	aTg/aAg	23/28	0.254514830014156	2	FACETS	0.951	0.832	1	0.476	0.416	0.538	INDETERMINATE	1	TRUE	0	0.681015886165466	2		279	176	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95579529	95579529	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002285-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	44	379	0	ENST00000393063.1:c.1940C>G	p.Thr647Ser	p.T647S	ENST00000393063	NM_030621.3	647	aCt/aGt	13/28	0.254514830014156	2	FACETS	0.891	0.763	1	0.446	0.381	0.514	INDETERMINATE	1	TRUE	0	0.681015886165466	2		379	145	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428164	47428164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145056294	NA	P-0002285-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	35	674	0	ENST00000377045.4:c.1124G>A	p.Arg375Gln	p.R375Q	ENST00000377045	NM_001654.4	375	cGg/cAg	11/16	NA	2	FACETS	0.69	0.574	0.815			1	INDETERMINATE	1	TRUE	NA	0.681015886165466	2		674	149	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270594	98270594	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002285-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	11	39	0	ENST00000331920.6:c.50del	p.Gly17AlafsTer63	p.G17Afs*63	ENST00000331920	NM_000264.3	17	gGc/gc	1/24	NA	2	FACETS	1	0.798	1			1	INDETERMINATE	1	TRUE	NA	0.681015886165466	2		39	29	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025924	48025924	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1553412217	NA	P-0002295-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	213	442	0	ENST00000234420.5:c.802G>C	p.Asp268His	p.D268H	ENST00000234420	NM_000179.2	268	Gac/Cac	4/10	1	2	FACETS	0.947	0.883	1	0.947	0.883	1	CLONAL	1	TRUE	1	0.61105294377002	2		442	736	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161957	47161957	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0002295-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	580	428	0	ENST00000409792.3:c.4169C>G	p.Ser1390Ter	p.S1390*	ENST00000409792	NM_014159.6	1390	tCa/tGa	3/21	0.61105294377002	2	FACETS	0.978	0.947	1	0.978	0.947	1	CLONAL	2	TRUE	0	0.61105294377002	2		428	971	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162683	47162683	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141227139	NA	P-0002295-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	629	451	2	ENST00000409792.3:c.3443C>T	p.Ser1148Phe	p.S1148F	ENST00000409792	NM_014159.6	1148	tCc/tTc	3/21	0.61105294377002	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.61105294377002	2		453	1010	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163476	47163476	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002295-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	422	374	0	ENST00000409792.3:c.2650C>T	p.Gln884Ter	p.Q884*	ENST00000409792	NM_014159.6	884	Cag/Tag	3/21	0.61105294377002	2	FACETS	0.95	0.914	0.986	0.95	0.914	0.986	CLONAL	2	TRUE	0	0.61105294377002	2		374	727	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500933	8500933	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002314-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	100	395	0	ENST00000356435.5:c.1949C>A	p.Thr650Asn	p.T650N	ENST00000356435		650	aCt/aAt	13/35	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		395	1176	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435287	18435287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002314-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	95	405	0	ENST00000266497.5:c.272C>T	p.Ser91Phe	p.S91F	ENST00000266497		91	tCt/tTt	1/31	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		405	1195	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578470	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGGG	novel	NA	P-0002317-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	419	374	0	ENST00000269305.4:c.457_460dup	p.Gly154AlafsTer28	p.G154Afs*28	ENST00000269305	NM_001126112.2	154	ggc/gCCCGgc	5/11	0.7736209142949	1	FACETS	0.981	0.946	1	0.981	0.946	1	CLONAL	1	TRUE	0	0.7736209142949	1		374	677	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0002338-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	80	409	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.162055652535529	7	FACETS	0.98	0.866	1	0.735	0.649	0.826	CLONAL	3	FALSE	3	0.162055652535529	7		409	472	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976872	55976872	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs551579207	NA	P-0002338-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	67	599	0	ENST00000263923.4:c.1040G>C	p.Arg347Pro	p.R347P	ENST00000263923	NM_002253.2	347	cGt/cCt	8/30	0.136199178484057	4	FACETS	0.799	0.695	0.913	0.799	0.695	0.913	CLONAL	2	FALSE	2	0.162055652535529	4		599	601	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149982897	149982897	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002338-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	90	527	0	ENST00000253339.5:c.3361G>C	p.Glu1121Gln	p.E1121Q	ENST00000253339		1121	Gag/Cag	7/7	0.162055652535529	6	FACETS	0.913	0.812	1			1	CLONAL	3	FALSE	NA	0.162055652535529	6		527	537	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650937	37650937	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002338-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	29	505	0	ENST00000447079.4:c.2409G>C	p.Lys803Asn	p.K803N	ENST00000447079	NM_015083.1	803	aaG/aaC	5/14	0.162055652535529	3	FACETS	0.955	0.767	1	0.478	0.383	0.585	CLONAL	1	FALSE	1	0.162055652535529	3		505	405	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593532	48593532	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002338-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	31	351	0	ENST00000342988.3:c.1283A>T	p.Lys428Met	p.K428M	ENST00000342988	NM_005359.5	428	aAg/aTg	10/12	0.161142658590646	3	FACETS	1	0.894	1	0.581	0.47	0.706	CLONAL	1	FALSE	1	0.162055652535529	3		351	356	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020190	123020190	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002338-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	75	639	0	ENST00000355640.3:c.678T>A	p.Asn226Lys	p.N226K	ENST00000355640		226	aaT/aaA	2/7	0.162055652535529	3	FACETS	0.898	0.788	1	0.898	0.788	1	CLONAL	2	FALSE	1	0.162055652535529	3		639	557	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200219	123200219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002338-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	55	657	0	ENST00000218089.9:c.2198C>T	p.Ala733Val	p.A733V	ENST00000218089	NM_001042749.1	733	gCa/gTa	23/35	0.162055652535529	3	FACETS	0.996	0.85	1	0.498	0.425	0.578	CLONAL	1	FALSE	1	0.162055652535529	3		657	737	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0002357-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	38	431	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.582	0.48	0.697	0.582	0.48	0.697	SUBCLONAL	1	TRUE	1	0.17	2		431	768	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0002357-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	59	386	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	1	2	FACETS	0.985	0.846	1	0.985	0.846	1	CLONAL	1	TRUE	1	0.17	2		386	705	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952030	178952030	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002357-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	57	433	0	ENST00000263967.3:c.3085G>C	p.Asp1029His	p.D1029H	ENST00000263967	NM_006218.2	1029	Gat/Cat	21/21	1	2	FACETS	0.875	0.75	1	0.875	0.75	1	CLONAL	1	TRUE	1	0.17	2		433	766	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577041	7577041	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002357-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	78	509	0	ENST00000269305.4:c.897del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	299	ctG/ct	8/11	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.17	2		509	858	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670847	134670847	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002375-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	209	244	0	ENST00000398015.3:c.758G>T	p.Cys253Phe	p.C253F	ENST00000398015	NM_004441.4	253	tGc/tTc	3/16	0.61633219411341	4	FACETS	0.935	0.883	0.988	1	0.992	1	CLONAL	3	TRUE	2	0.612921030470768	4		244	392	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456348	32456348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002375-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	114	587	0	ENST00000332351.3:c.544C>T	p.Pro182Ser	p.P182S	ENST00000332351	NM_024426.4	182	Cct/Tct	1/10	0.61633219411341	3	FACETS	0.77	0.695	0.85	0.385	0.347	0.425	SUBCLONAL	1	TRUE	1	0.612921030470768	3		587	631	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456366	32456366	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002375-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	109	551	0	ENST00000332351.3:c.526C>G	p.Arg176Gly	p.R176G	ENST00000332351	NM_024426.4	176	Cgc/Ggc	1/10	0.61633219411341	3	FACETS	0.764	0.688	0.845	0.382	0.344	0.423	SUBCLONAL	1	TRUE	1	0.612921030470768	3		551	608	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435035	110435035	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002375-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	97	204	0	ENST00000375856.3:c.3366G>C	p.Gln1122His	p.Q1122H	ENST00000375856	NM_003749.2	1122	caG/caC	1/2	0.612921030470768	10	FACETS	1	0.905	1			1	CLONAL	1	TRUE	NA	0.612921030470768	10		204	1072	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347972	347972	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002375-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	144	669	0	ENST00000262320.3:c.1534G>T	p.Gly512Trp	p.G512W	ENST00000262320	NM_003502.3	512	Ggg/Tgg	6/11	0.255444964629893	4	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.612921030470768	4		669	584	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456679	32456680	+	missense_variant	Missense_Mutation	DNP	GG	GG	TA	novel	NA	P-0002375-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	45	148	0	ENST00000332351.3:c.212_213delinsTA	p.Ser71Leu	p.S71L	ENST00000332351	NM_024426.4	71	tCC/tTA	1/10	0.61633219411341	3	FACETS	0.892	0.758	1	0.446	0.379	0.519	CLONAL	1	TRUE	1	0.612921030470768	3		148	215	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456322	32456323	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0002375-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	106	625	0	ENST00000332351.3:c.569_570delinsTT	p.Ser190Phe	p.S190F	ENST00000332351	NM_024426.4	190	tCC/tTT	1/10	0.61633219411341	3	FACETS	0.711	0.638	0.787	0.355	0.319	0.394	SUBCLONAL	1	TRUE	1	0.612921030470768	3		625	636	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846067	68846067	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002376-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	747	206	848	0	ENST00000261769.5:c.1038A>T	p.Gln346His	p.Q346H	ENST00000261769	NM_004360.3	346	caA/caT	8/16	0.728746334320364	4	FACETS	1	0.944	1	0.34	0.315	0.366	CLONAL	1	TRUE	1	0.735426120046845	4		848	953	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0002411-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	167	138	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.702661810712743	3	FACETS	0.972	0.896	1	0.486	0.448	0.525	CLONAL	1	TRUE	1	0.702661810712743	3		138	661	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0002411-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	241	465	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.702661810712743	2		465	659	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098957	178098957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002411-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	645	373	0	ENST00000397062.3:c.88C>T	p.Leu30Phe	p.L30F	ENST00000397062	NM_006164.4	30	Ctt/Ttt	2/5	0.702661810712743	2	FACETS	0.884	0.858	0.91	0.884	0.858	0.91	CLONAL	2	TRUE	0	0.702661810712743	2		373	1038	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0002411-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	246	311	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	0.676718535364924	2	FACETS	0.939	0.881	0.997	0.469	0.44	0.499	CLONAL	1	TRUE	0	0.702661810712743	2		311	746	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344790	65344790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770735783	NA	P-0002411-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	232	368	0	ENST00000342505.4:c.247G>A	p.Glu83Lys	p.E83K	ENST00000342505	NM_002227.2	83	Gag/Aag	4/25	0.676718535364924	2	FACETS	0.89	0.833	0.948	0.445	0.416	0.474	CLONAL	1	TRUE	0	0.702661810712743	2		368	742	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71161761	71161761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002411-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	304	432	0	ENST00000318789.4:c.208C>T	p.Leu70Phe	p.L70F	ENST00000318789	NM_032682.5	70	Ctt/Ttt	7/21	0.652241911743985	3	FACETS	0.901	0.848	0.955	0.45	0.424	0.478	CLONAL	1	TRUE	1	0.702661810712743	3		432	1298	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936070	178936070	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002411-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	132	164	0	ENST00000263967.3:c.1612G>T	p.Asp538Tyr	p.D538Y	ENST00000263967	NM_006218.2	538	Gat/Tat	10/21	0.702661810712743	3	FACETS	1	0.943	1	0.521	0.476	0.568	CLONAL	1	TRUE	1	0.702661810712743	3		164	487	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443346	187443346	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002411-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	179	374	0	ENST00000232014.4:c.1780C>G	p.Arg594Gly	p.R594G	ENST00000232014	NM_001130845.1	594	Cga/Gga	8/10	0.702661810712743	3	FACETS	0.587	0.54	0.637	0.294	0.27	0.319	SUBCLONAL	1	TRUE	1	0.702661810712743	3		374	1172	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447739	187447739	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002411-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	226	282	0	ENST00000232014.4:c.454C>G	p.Gln152Glu	p.Q152E	ENST00000232014	NM_001130845.1	152	Caa/Gaa	5/10	0.702661810712743	3	FACETS	0.982	0.916	1	0.491	0.458	0.525	CLONAL	1	TRUE	1	0.702661810712743	3		282	885	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673619	30673619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002411-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	355	528	0	ENST00000376406.3:c.3341G>A	p.Arg1114Lys	p.R1114K	ENST00000376406	NM_014641.2	1114	aGa/aAa	10/15	1	2	FACETS	0.951	0.902	1	0.951	0.902	1	CLONAL	1	TRUE	1	0.702661810712743	2		528	1063	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675523	30675523	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002411-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	390	611	0	ENST00000376406.3:c.2833G>T	p.Asp945Tyr	p.D945Y	ENST00000376406	NM_014641.2	945	Gat/Tat	8/15	1	2	FACETS	0.99	0.942	1	0.99	0.942	1	CLONAL	1	TRUE	1	0.702661810712743	2		611	1121	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675808	30675808	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002411-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	475	703	0	ENST00000376406.3:c.2548G>A	p.Glu850Lys	p.E850K	ENST00000376406	NM_014641.2	850	Gaa/Aaa	8/15	1	2	FACETS	0.959	0.916	1	0.959	0.916	1	CLONAL	1	TRUE	1	0.702661810712743	2		703	1410	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675823	30675823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002411-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	462	698	1	ENST00000376406.3:c.2533G>A	p.Asp845Asn	p.D845N	ENST00000376406	NM_014641.2	845	Gat/Aat	8/15	1	2	FACETS	0.97	0.927	1	0.97	0.927	1	CLONAL	1	TRUE	1	0.702661810712743	2		699	1355	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675877	30675877	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002411-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	442	685	0	ENST00000376406.3:c.2479G>C	p.Glu827Gln	p.E827Q	ENST00000376406	NM_014641.2	827	Gag/Cag	8/15	1	2	FACETS	0.937	0.894	0.981	0.937	0.894	0.981	CLONAL	1	TRUE	1	0.702661810712743	2		685	1342	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983893	2983893	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002411-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1446	371	520	0	ENST00000396946.4:c.637G>A	p.Glu213Lys	p.E213K	ENST00000396946	NM_032415.4	213	Gag/Aag	5/25	0.649170159001566	4	FACETS	0.99	0.936	1	0.33	0.312	0.349	CLONAL	1	TRUE	1	0.702661810712743	4		520	1817	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420788	49420788	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002411-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	278	382	0	ENST00000301067.7:c.14961G>A	p.Trp4987Ter	p.W4987*	ENST00000301067	NM_003482.3	4987	tgG/tgA	48/54	1	2	FACETS	0.976	0.92	1	0.976	0.92	1	CLONAL	1	TRUE	1	0.702661810712743	2		382	811	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434376	49434376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002411-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	201	237	0	ENST00000301067.7:c.7177G>A	p.Glu2393Lys	p.E2393K	ENST00000301067	NM_003482.3	2393	Gag/Aag	31/54	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.702661810712743	2		237	556	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448765	49448765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002411-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	246	367	0	ENST00000301067.7:c.94G>A	p.Asp32Asn	p.D32N	ENST00000301067	NM_003482.3	32	Gac/Aac	2/54	1	2	FACETS	0.833	0.78	0.886	0.833	0.78	0.886	CLONAL	1	TRUE	1	0.702661810712743	2		367	841	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65569036	65569036	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002411-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	268	363	0	ENST00000358664.4:c.22G>A	p.Glu8Lys	p.E8K	ENST00000358664	NM_002382.4	8	Gag/Aag	1/5	1	2	FACETS	0.871	0.819	0.924	0.871	0.819	0.924	CLONAL	1	TRUE	1	0.702661810712743	2		363	876	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041521	14041521	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002411-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	241	291	0	ENST00000311895.7:c.2068G>A	p.Glu690Lys	p.E690K	ENST00000311895	NM_005236.2	690	Gaa/Aaa	11/11	0.652241911743985	3	FACETS	0.885	0.827	0.946	0.443	0.413	0.473	CLONAL	1	TRUE	1	0.702661810712743	3		291	1047	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0002412-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	298	423	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.413355518304967	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	FALSE	1	0.419318824251823	3		423	784	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207021	1207021	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913324	NA	P-0002412-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	142	233	0	ENST00000326873.7:c.109C>T	p.Gln37Ter	p.Q37*	ENST00000326873	NM_000455.4	37	Cag/Tag	1/10	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.419318824251823	NA		233	375	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662082	227662082	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002412-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	104	320	0	ENST00000305123.5:c.1373G>C	p.Gly458Ala	p.G458A	ENST00000305123	NM_005544.2	458	gGt/gCt	1/2	0.413355518304967	3	FACETS	1	0.965	1	0.584	0.525	0.646	CLONAL	1	FALSE	1	0.419318824251823	3		320	514	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955556	55955556	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002412-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	228	497	0	ENST00000263923.4:c.3389A>T	p.Tyr1130Phe	p.Y1130F	ENST00000263923	NM_002253.2	1130	tAt/tTt	25/30	0.189459704640043	3	FACETS	0.924	0.865	0.984	0.924	0.865	0.984	INDETERMINATE	2	FALSE	1	0.419318824251823	3		497	712	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945066	31945066	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002412-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	128	222	0	ENST00000340398.3:c.35C>A	p.Thr12Asn	p.T12N	ENST00000340398	NM_001013699.2	12	aCc/aAc	1/1	0.413355518304967	3	FACETS	0.952	0.871	1	0.952	0.871	1	CLONAL	2	FALSE	1	0.419318824251823	3		222	388	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602823	10602823	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002412-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	195	295	0	ENST00000171111.5:c.755G>T	p.Trp252Leu	p.W252L	ENST00000171111	NM_203500.1	252	tGg/tTg	3/6	0.419318824251823	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	FALSE	0	0.419318824251823	2		295	464	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0002423-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	103	280	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.235292869541041	2	FACETS	0.983	0.888	1	0.983	0.888	1	CLONAL	2	FALSE	0	0.289354310249804	2		280	362	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952120	76952120	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002423-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	172	240	2	ENST00000373344.5:c.315A>C	p.Glu105Asp	p.E105D	ENST00000373344	NM_000489.3	105	gaA/gaC	5/35	0.289354310249804	2	FACETS	1	0.964	1			1	CLONAL	3	FALSE	NA	0.289354310249804	2		242	378	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023093	150023094	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002423-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	123	485	0	ENST00000253339.5:c.169dup	p.Met57AsnfsTer20	p.M57Nfs*20	ENST00000253339		57	atg/aAtg	1/7	0.254640419565927	2	FACETS	0.92	0.838	1	0.92	0.838	1	CLONAL	2	FALSE	0	0.289354310249804	2		485	462	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249014	55249015	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGT	novel	NA	P-0002423-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	634	310	1	ENST00000275493.2:c.2313_2314insGTC	p.Asn771_Pro772insVal	p.N771_P772insV	ENST00000275493	NM_005228.3	771	aac/aaCGTc	20/28	0.289354310249804	14	FACETS	1	0.987	1			1	CLONAL	11	FALSE	NA	0.289354310249804	14		311	1058	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0002424-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	447	293	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.778614982064415	1	FACETS	0.986	0.952	1	0.986	0.952	1	CLONAL	1	TRUE	0	0.778614982064415	1		293	711	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0002429-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	237	443	1	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	1	0.409140123185727	2		444	502	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913492	NA	P-0002429-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	408	393	0	ENST00000286548.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000286548	NM_002072.3	209	cAa/cTa	5/7	0.32905990579478	4	FACETS	0.905	0.873	0.936	1	0.997	1	CLONAL	5	TRUE	1	0.409140123185727	4		393	621	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502657	149502657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002429-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	111	424	0	ENST00000261799.4:c.2131C>T	p.Pro711Ser	p.P711S	ENST00000261799	NM_002609.3	711	Ccc/Tcc	15/23	0.179904819983191	5	FACETS	1	0.971	1	0.404	0.363	0.447	INDETERMINATE	1	TRUE	2	0.409140123185727	5		424	723	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332902	152332902	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002429-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	232	478	0	ENST00000206249.3:c.1208T>G	p.Leu403Arg	p.L403R	ENST00000206249	NM_000125.3	403	cTg/cGg	5/8	0.388690008802277	1	FACETS	0.958	0.904	1	1	0.995	1	CLONAL	2	TRUE	0	0.409140123185727	1		478	471	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0002441-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	119	408	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	0.222781949151364	2		408	879	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0002441-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	62	282	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.222781949151364	1	FACETS	0.926	0.801	1	0.926	0.801	1	CLONAL	1	TRUE	0	0.222781949151364	1		282	534	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670486	134670486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002441-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	90	401	0	ENST00000398015.3:c.397C>T	p.Pro133Ser	p.P133S	ENST00000398015	NM_004441.4	133	Ccc/Tcc	3/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.222781949151364	2		401	653	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0002442-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	170	138	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.441860361195446	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.463584911552164	2		138	340	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042434	16042434	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1568277803	NA	P-0002442-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	197	462	1	ENST00000268712.3:c.1240C>T	p.Arg414Ter	p.R414*	ENST00000268712	NM_006311.3	414	Cga/Tga	12/46	0.441860361195446	2	FACETS	0.932	0.873	0.992	0.932	0.873	0.992	CLONAL	2	TRUE	0	0.463584911552164	2		463	456	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245393	153245393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002442-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	189	408	0	ENST00000281708.4:c.1798G>A	p.Asp600Asn	p.D600N	ENST00000281708	NM_033632.3	600	Gat/Aat	11/12	0.42601978031809	3	FACETS	0.951	0.886	1	0.951	0.886	1	CLONAL	2	TRUE	1	0.463584911552164	3		408	528	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615035	43615035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142318626	NA	P-0002442-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	105	458	0	ENST00000355710.3:c.2449C>T	p.Arg817Cys	p.R817C	ENST00000355710	NM_020975.4	817	Cgc/Tgc	14/20	0.42601978031809	3	FACETS	1	0.932	1	0.523	0.47	0.579	CLONAL	1	TRUE	1	0.463584911552164	3		458	533	SUCCESS
APC	324	MSKCC	GRCh37	5	112175186	112175187	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	T	novel	NA	P-0002442-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	197	222	0	ENST00000257430.4:c.3895_3896delinsT	p.Ala1299LeufsTer6	p.A1299Lfs*6	ENST00000257430	NM_000038.5	1299	GCt/Tt	16/16	0.463584911552164	4	FACETS	0.878	0.829	0.928	0.878	0.829	0.928	CLONAL	4	TRUE	0	0.463584911552164	4		222	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0002451-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	179	2142	0	ENST00000269305.4:c.559+1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.469477907151892	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.469477907151892	1		2142	444	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248998	55248999	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCCAGCG	rs727504263	NA	P-0002451-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	202	229	0	ENST00000275493.2:c.2300_2308dup	p.Ala767_Val769dup	p.A767_V769dup	ENST00000275493	NM_005228.3	767	atg/aTGGCCAGCGtg	20/28	1	2	FACETS	0.989	0.918	1	0.989	0.918	1	CLONAL	1	TRUE	1	0.469477907151892	2		229	870	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132522	11132522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778175819	NA	P-0002451-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	42	287	0	ENST00000358026.2:c.2738C>T	p.Pro913Leu	p.P913L	ENST00000358026	NM_001128849.1	913	cCg/cTg	19/36	0.469477907151892	1	FACETS	0.167	0.138	0.198	0.167	0.138	0.198	SUBCLONAL	1	TRUE	0	0.469477907151892	1		287	822	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0002599-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	65	531	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	TRUE	1	0.546701390800455	2		531	202	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0002599-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	86	464	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.546701390800455	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.546701390800455	1		464	213	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735635	204735635	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002599-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	69	147	0	ENST00000302823.3:c.436G>T	p.Gly146Ter	p.G146*	ENST00000302823	NM_005214.4	146	Gga/Tga	2/4	1	2	FACETS	0.953	0.839	1	0.953	0.839	1	CLONAL	1	TRUE	1	0.546701390800455	2		147	265	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55229225	55229225	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs371114444	NA	P-0002599-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	65	207	0	ENST00000275493.2:c.1532C>A	p.Ser511Tyr	p.S511Y	ENST00000275493	NM_005228.3	511	tCc/tAc	13/28	0.202686320139084	3	FACETS	1	0.965	1	0.644	0.566	0.727	INDETERMINATE	1	TRUE	1	0.546701390800455	3		207	235	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332909	70332909	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002599-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	95	443	0	ENST00000373644.4:c.814G>C	p.Glu272Gln	p.E272Q	ENST00000373644	NM_030625.2	272	Gag/Cag	2/12	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.546701390800455	2		443	307	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333266	70333266	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002599-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	79	391	0	ENST00000373644.4:c.1171G>A	p.Glu391Lys	p.E391K	ENST00000373644	NM_030625.2	391	Gag/Aag	2/12	1	2	FACETS	0.99	0.88	1	0.99	0.88	1	CLONAL	1	TRUE	1	0.546701390800455	2		391	292	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488282	56488282	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002599-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	131	327	0	ENST00000267101.3:c.1801T>A	p.Tyr601Asn	p.Y601N	ENST00000267101	NM_001982.3	601	Tac/Aac	15/28	0.546701390800455	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.546701390800455	1		327	301	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973093	25973093	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002599-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	107	371	0	ENST00000435504.4:c.1332del	p.Glu445LysfsTer77	p.E445Kfs*77	ENST00000435504		444	aaA/aa	12/13	0.546701390800455	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.546701390800455	1		371	276	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205083	123205084	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0002599-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	132	232	0	ENST00000218089.9:c.2444dup	p.Tyr815Ter	p.Y815*	ENST00000218089	NM_001042749.1	815	tat/tAat	25/35	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.546701390800455	1		232	247	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534259	534259	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121917757	NA	P-0002603-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	474	136	337	0	ENST00000451590.1:c.64C>A	p.Gln22Lys	p.Q22K	ENST00000451590	NM_001130442.1	22	Cag/Aag	2/5	1	2	FACETS	0.929	0.848	1	0.929	0.848	1	CLONAL	1	TRUE	1	0.48	2		337	610	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0002617-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	99	475	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.299796034899661	5	FACETS	1	0.906	1	0.505	0.453	0.56	CLONAL	2	TRUE	1	0.299796034899661	5		475	474	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681416	88681416	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002617-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	31	232	0	ENST00000372037.3:c.1306A>T	p.Ile436Phe	p.I436F	ENST00000372037	NM_004329.2	436	Atc/Ttc	11/13	0.209714385877548	5	FACETS	1	0.825	1	0.671	0.55	0.803	CLONAL	2	TRUE	2	0.299796034899661	5		232	149	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217399	7217399	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs746318470	NA	P-0002617-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	74	575	0	ENST00000380728.2:c.397G>T	p.Gly133Trp	p.G133W	ENST00000380728		133	Ggg/Tgg	5/11	0.214233681207082	3	FACETS	1	0.905	1			1	CLONAL	2	TRUE	NA	0.299796034899661	3		575	277	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871001	12871001	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002627-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	482	263	0	ENST00000228872.4:c.228G>A	p.Trp76Ter	p.W76*	ENST00000228872	NM_004064.3	76	tgG/tgA	1/3	0.632980712450879	6	FACETS	0.925	0.883	0.968	0.462	0.441	0.484	CLONAL	2	TRUE	2	0.800877619506327	6		263	1693	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4090691	4090693	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0002627-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	156	323	0	ENST00000262948.5:c.1106_1108del	p.Ile369del	p.I369del	ENST00000262948	NM_030662.3	369	aTCAag/aag	11/11	1	2	FACETS	0.294	0.268	0.321	0.294	0.268	0.321	SUBCLONAL	1	TRUE	1	0.800877619506327	2		323	1324	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0002646-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	184	421	1	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.468330164717149	1	FACETS	0.992	0.921	1	0.992	0.921	1	CLONAL	1	TRUE	0	0.478436651671627	1		422	590	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188584	11188584	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1356294807	NA	P-0002646-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	100	496	0	ENST00000361445.4:c.5837T>C	p.Ile1946Thr	p.I1946T	ENST00000361445	NM_004958.3	1946	aTt/aCt	42/58	0.188120288980998	1	FACETS	0.353	0.315	0.394	0.353	0.315	0.394	INDETERMINATE	1	TRUE	0	0.478436651671627	1		496	901	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440140	49440140	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002646-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	81	469	0	ENST00000301067.7:c.4486A>G	p.Thr1496Ala	p.T1496A	ENST00000301067	NM_003482.3	1496	Aca/Gca	16/54	0.188120288980998	1	FACETS	0.317	0.278	0.358	0.317	0.278	0.358	INDETERMINATE	1	TRUE	0	0.478436651671627	1		469	813	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102874134	102874134	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002646-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	82	558	0	ENST00000307046.8:c.26C>A	p.Thr9Asn	p.T9N	ENST00000307046	NM_001111285.1	9	aCc/aAc	1/4	0.188120288980998	1	FACETS	0.267	0.235	0.303	0.267	0.235	0.303	INDETERMINATE	1	TRUE	0	0.478436651671627	1		558	975	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953486	32953486	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002646-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	88	433	1	ENST00000380152.3:c.8787G>T	p.Leu2929Phe	p.L2929F	ENST00000380152		2929	ttG/ttT	22/27	0.478436651671627	1	FACETS	0.457	0.405	0.512	0.457	0.405	0.512	SUBCLONAL	1	TRUE	0	0.478436651671627	1		434	613	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514563	41514563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002646-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	83	440	0	ENST00000373198.4:c.98C>T	p.Ser33Phe	p.S33F	ENST00000373198	NM_133170.3	33	tCc/tTc	2/32	0.257020688701557	2	FACETS	0.464	0.409	0.523	0.232	0.204	0.262	INDETERMINATE	1	TRUE	0	0.478436651671627	2		440	748	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	rs786202799	NA	P-0002655-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	407	176	0	ENST00000269305.4:c.376-2A>T		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.919037035245137	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.919037035245137	2		176	427	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0002655-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	677	361	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	NA	2	FACETS	0.993	0.978	1			1	INDETERMINATE	2	TRUE	NA	0.919037035245137	2		361	742	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247409	71247409	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002655-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	391	246	0	ENST00000318789.4:c.124C>G	p.Pro42Ala	p.P42A	ENST00000318789	NM_032682.5	42	Ccg/Gcg	6/21	0.907271771164775	2	FACETS	0.983	0.963	1	0.983	0.963	1	CLONAL	2	TRUE	0	0.919037035245137	2		246	433	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404795	404795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375955542	NA	P-0002655-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2539	335	345	0	ENST00000399788.2:c.4399C>T	p.Arg1467Trp	p.R1467W	ENST00000399788	NM_001042603.1	1467	Cgg/Tgg	26/28	0.919037035245137	8	FACETS	0.953	0.896	1			1	CLONAL	1	TRUE	NA	0.919037035245137	8		345	2874	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390784	139390793	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCAGCGAC	TGGCAGCGAC	-	novel	NA	P-0002655-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	790	281	0	ENST00000277541.6:c.7398_7407del	p.Ser2467ProfsTer7	p.S2467Pfs*7	ENST00000277541	NM_017617.3	2466	acGTCGCTGCCA/ac	34/34	0.919037035245137	3	FACETS	0.991	0.979	1	0.991	0.979	1	CLONAL	3	TRUE	0	0.919037035245137	3		281	844	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0002688-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	25	408	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.19632517558367	9	FACETS	0.363	0.284	0.455	0.073	0.056	0.091	SUBCLONAL	1	TRUE	4	0.19632517558367	9		408	1183	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6414401	6414401	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002688-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	18	51	0	ENST00000356142.4:c.35G>T	p.Gly12Val	p.G12V	ENST00000356142	NM_018890.3	12	gGa/gTa	1/7	0.19632517558367	5	FACETS	1	0.823	1	0.371	0.28	0.479	CLONAL	1	TRUE	2	0.19632517558367	5		51	213	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537228	80537228	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	371	299	0	ENST00000286548.4:c.170A>T	p.Lys57Met	p.K57M	ENST00000286548	NM_002072.3	57	aAg/aTg	2/7	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		299	794	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0002708-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	32	570	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	NA	2	FACETS	0.878	0.739	1			1	INDETERMINATE	2	TRUE	NA	0.455420292856622	2		570	80	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0002708-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	393	464	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	0.455420292856622	21	FACETS	1	0.987	1			1	CLONAL	19	TRUE	NA	0.455420292856622	21		464	474	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52709255	52709255	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002708-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	13	474	0	ENST00000322088.6:c.209C>T	p.Ala70Val	p.A70V	ENST00000322088	NM_014225.5	70	gCa/gTa	3/15	1	2	FACETS	0.641	0.464	0.851	0.641	0.464	0.851	SUBCLONAL	1	TRUE	1	0.455420292856622	2		474	89	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723503	52723503	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002708-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	19	441	1	ENST00000322088.6:c.1363+1G>A		p.X455_splice	ENST00000322088	NM_014225.5	455			1	2	FACETS	0.927	0.718	1	0.927	0.718	1	CLONAL	1	TRUE	1	0.455420292856622	2		442	90	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0002757-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	1315	573	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.678710340990984	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.677991801283701	2		574	1897	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632269	215632270	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0002757-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	137	480	0	ENST00000260947.4:c.1504_1505delinsAA	p.Ala502Asn	p.A502N	ENST00000260947	NM_000465.2	502	GCc/AAc	6/11	0.365429625178904	1	FACETS	0.195	0.177	0.215	0.195	0.177	0.215	INDETERMINATE	1	TRUE	0	0.677991801283701	1		480	1369	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430936	181430936	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002757-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	194	428	0	ENST00000325404.1:c.788C>A	p.Ala263Glu	p.A263E	ENST00000325404	NM_003106.3	263	gCg/gAg	1/1	0.663502153133425	2	FACETS	0.398	0.367	0.43	0.199	0.183	0.215	SUBCLONAL	1	TRUE	0	0.677991801283701	2		428	1439	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514857	103514857	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002757-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	185	292	0	ENST00000355739.4:c.1358C>G	p.Ser453Cys	p.S453C	ENST00000355739	NM_000123.3	453	tCt/tGt	8/15	0.479557661069685	3	FACETS	0.554	0.51	0.6	0.185	0.17	0.2	SUBCLONAL	1	TRUE	0	0.677991801283701	3		292	1319	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513300	44513300	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002757-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	848	311	0	ENST00000291552.4:c.635G>C	p.Gly212Ala	p.G212A	ENST00000291552	NM_006758.2	212	gGc/gCc	8/8	1	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	1	0.677991801283701	2		311	1765	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0002775-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	73	138	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.280658261736126	3	FACETS	1	0.943	1	0.73	0.65	0.813	CLONAL	2	TRUE	0	0.38387049519854	3		138	207	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257434	16257434	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002775-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	23	401	0	ENST00000375759.3:c.4699G>A	p.Glu1567Lys	p.E1567K	ENST00000375759	NM_015001.2	1567	Gag/Aag	11/15	1	2	FACETS	0.275	0.214	0.346	0.275	0.214	0.346	SUBCLONAL	1	TRUE	1	0.38387049519854	2		401	436	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096481	178096481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002775-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	37	313	0	ENST00000397062.3:c.850G>A	p.Glu284Lys	p.E284K	ENST00000397062	NM_006164.4	284	Gaa/Aaa	5/5	0.382361777442359	1	FACETS	0.361	0.297	0.432	0.361	0.297	0.432	SUBCLONAL	1	TRUE	0	0.38387049519854	1		313	432	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609825	117609825	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1291536074	NA	P-0002775-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	117	479	0	ENST00000368508.3:c.6874C>G	p.Leu2292Val	p.L2292V	ENST00000368508	NM_002944.2	2292	Cta/Gta	43/43	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.38387049519854	2		479	512	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373293	118373293	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0002775-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	66	479	0	ENST00000534358.1:c.6686C>G	p.Ser2229Ter	p.S2229*	ENST00000534358	NM_005933.3	2229	tCa/tGa	27/36	1	2	FACETS	0.654	0.568	0.746	0.654	0.568	0.746	SUBCLONAL	1	TRUE	1	0.38387049519854	2		479	526	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346365	73346365	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002775-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	23	368	0	ENST00000377767.4:c.1435G>C	p.Asp479His	p.D479H	ENST00000377767	NM_014953.3	479	Gac/Cac	10/21	0.319026283206404	3	FACETS	0.354	0.276	0.446	0.177	0.138	0.223	SUBCLONAL	1	TRUE	1	0.38387049519854	3		368	403	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65569036	65569036	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs752477890	NA	P-0002775-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	32	427	0	ENST00000358664.4:c.22G>T	p.Glu8Ter	p.E8*	ENST00000358664	NM_002382.4	8	Gag/Tag	1/5	0.290443421054262	3	FACETS	0.471	0.382	0.571	0.235	0.191	0.286	SUBCLONAL	1	TRUE	1	0.38387049519854	3		427	422	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038202	30038202	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002775-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	104	480	0	ENST00000338641.4:c.375G>C	p.Gln125His	p.Q125H	ENST00000338641	NM_000268.3	125	caG/caC	4/16	0.375093208434258	1	FACETS	0.905	0.814	1	0.905	0.814	1	CLONAL	1	TRUE	0	0.38387049519854	1		480	484	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050664	30050664	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002775-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	31	460	0	ENST00000338641.4:c.466A>C	p.Ser156Arg	p.S156R	ENST00000338641	NM_000268.3	156	Agt/Cgt	5/16	0.375093208434258	1	FACETS	0.337	0.273	0.41	0.337	0.273	0.41	SUBCLONAL	1	TRUE	0	0.38387049519854	1		460	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0002783-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	301	437	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.468051285944908	3	FACETS	0.951	0.907	0.995	0.951	0.907	0.995	CLONAL	3	TRUE	0	0.479013720755509	3		437	546	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0002783-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	133	392	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.461197263107223	2	FACETS	1	0.976	1	0.595	0.544	0.647	CLONAL	1	TRUE	0	0.479013720755509	2		392	467	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0002783-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	1640	318	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.479013720755509	18	FACETS	1	0.996	1	0.967	0.954	0.979	CLONAL	16	TRUE	1	0.479013720755509	18		318	2013	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0002783-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1320	1006	407	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.479013720755509	18	FACETS	0.97	0.942	0.997	0.513	0.498	0.528	CLONAL	9	TRUE	1	0.479013720755509	18		407	2326	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851006	63851006	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002783-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	71	310	0	ENST00000279873.7:c.1784T>A	p.Phe595Tyr	p.F595Y	ENST00000279873	NM_032199.2	595	tTc/tAc	10/10	0.479013720755509	3	FACETS	0.933	0.818	1	0.466	0.409	0.528	CLONAL	1	TRUE	1	0.479013720755509	3		310	394	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99452113	99452113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002783-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	70	337	0	ENST00000268035.6:c.1447G>A	p.Gly483Arg	p.G483R	ENST00000268035	NM_000875.3	483	Ggg/Agg	6/21	0.343942183316093	4	FACETS	0.859	0.751	0.976	0.43	0.375	0.488	CLONAL	1	TRUE	2	0.479013720755509	4		337	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0002809-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	19	399	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		399	743	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0002855-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	80	138	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.312231742789009	1	FACETS	0.908	0.802	1	0.908	0.802	1	CLONAL	1	FALSE	0	0.312231742789009	1		138	476	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0002855-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	349	536	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	NA	2	FACETS	0.977	0.931	1			1	INDETERMINATE	3	FALSE	NA	0.312231742789009	2		536	763	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0002855-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	93	219	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.312231742789009	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	0	0.312231742789009	1		219	439	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520027	106520027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370034420	NA	P-0002855-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	50	383	0	ENST00000359195.3:c.2455G>A	p.Asp819Asn	p.D819N	ENST00000359195	NM_002649.2	819	Gat/Aat	6/11	1	2	FACETS	0.416	0.352	0.487	0.416	0.352	0.487	SUBCLONAL	1	FALSE	1	0.312231742789009	2		383	770	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191068	2191068	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757313197	NA	P-0002855-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	58	383	0	ENST00000398665.3:c.322C>T	p.Arg108Cys	p.R108C	ENST00000398665	NM_032482.2	108	Cgc/Tgc	5/28	0.207291440805725	2	FACETS	0.371	0.318	0.43	0.186	0.159	0.215	SUBCLONAL	1	FALSE	0	0.312231742789009	2		383	1001	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913315	NA	P-0002865-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	212	312	0	ENST00000326873.7:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000326873	NM_000455.4	194	Gac/Tac	4/10	0.871016203126651	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.888584696049215	2		312	237	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467412	66467412	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs750247121	NA	P-0002865-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	85	294	0	ENST00000273854.3:c.857T>A	p.Ile286Asn	p.I286N	ENST00000273854	NM_004439.5	286	aTc/aAc	3/18	0.504285280672689	2	FACETS	0.471	0.419	0.527	0.236	0.209	0.264	INDETERMINATE	1	TRUE	0	0.888584696049215	2		294	406	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737817	145737817	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368982201	NA	P-0002865-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	53	220	1	ENST00000428558.2:c.3013C>T	p.Arg1005Trp	p.R1005W	ENST00000428558	NM_004260.3	1005	Cgg/Tgg	18/22	0.442401643923188	1	FACETS	0.311	0.269	0.357	0.311	0.269	0.357	INDETERMINATE	1	TRUE	0	0.888584696049215	1		221	213	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947603	48947603	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0002865-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	230	353	0	ENST00000267163.4:c.1190C>G	p.Ser397Ter	p.S397*	ENST00000267163	NM_000321.2	397	tCa/tGa	12/27	0.804856329048662	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.888584696049215	1		353	283	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504481	103504481	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs373207563	NA	P-0002865-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	108	285	0	ENST00000355739.4:c.102G>T	p.Trp34Cys	p.W34C	ENST00000355739	NM_000123.3	34	tgG/tgT	2/15	0.507550190270477	1	FACETS	0.383	0.347	0.42	0.383	0.347	0.42	INDETERMINATE	1	TRUE	0	0.888584696049215	1		285	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577563	7577563	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002865-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	164	264	0	ENST00000269305.4:c.718A>T	p.Ser240Cys	p.S240C	ENST00000269305	NM_001126112.2	240	Agt/Tgt	7/11	0.888584696049215	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.888584696049215	1		264	201	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602314	10602314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002865-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	266	408	0	ENST00000171111.5:c.1264G>A	p.Asp422Asn	p.D422N	ENST00000171111	NM_203500.1	422	Gat/Aat	3/6	0.886638923815772	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.888584696049215	2		408	292	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0002898-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	250	396	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	0.963	1	CLONAL	1	TRUE	1	0.76148177561415	2		396	638	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591857	48591857	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002898-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	253	458	0	ENST00000342988.3:c.1020G>C	p.Lys340Asn	p.K340N	ENST00000342988	NM_005359.5	340	aaG/aaC	9/12	0.76148177561415	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.76148177561415	1		458	376	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969468	44969471	+	frameshift_variant	Frame_Shift_Del	DEL	ATGC	ATGC	-	novel	NA	P-0002898-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	265	272	0	ENST00000377967.4:c.4151_4154del	p.Met1384LysfsTer8	p.M1384Kfs*8	ENST00000377967	NM_021140.2	1384	ATGCaa/aa	28/29	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.76148177561415	1		272	362	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849801	156849801	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754452975	NA	P-0002898-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	313	267	0	ENST00000524377.1:c.2057G>A	p.Arg686His	p.R686H	ENST00000524377	NM_002529.3	686	cGc/cAc	16/17	0.736890360728267	3	FACETS	0.967	0.922	1	0.967	0.922	1	CLONAL	2	TRUE	1	0.76148177561415	3		267	587	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229572	5229572	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1027605608	NA	P-0002898-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	32	69	0	ENST00000357368.4:c.2279A>T	p.Tyr760Phe	p.Y760F	ENST00000357368	NM_002850.3	760	tAc/tTc	15/38	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.76148177561415	2		69	78	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39721124	39721125	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0002898-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	220	393	0	ENST00000361337.2:c.629_630del	p.Arg210LeufsTer3	p.R210Lfs*3	ENST00000361337	NM_003286.2	209	gaGCgc/gagc	9/21	1	2	FACETS	0.955	0.895	1	0.955	0.895	1	CLONAL	1	TRUE	1	0.76148177561415	2		393	605	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0002954-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	107	423	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA	2	FACETS	0.856	0.771	0.945			1	INDETERMINATE	2	FALSE	NA	0.243723844271203	2		423	513	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775978	9775978	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002954-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	46	403	0	ENST00000377346.4:c.442G>T	p.Glu148Ter	p.E148*	ENST00000377346	NM_005026.3	148	Gag/Tag	5/24	NA	2	FACETS	0.914	0.771	1			1	INDETERMINATE	1	FALSE	NA	0.243723844271203	2		403	413	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361105	66361105	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0002954-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	74	457	0	ENST00000273854.3:c.1066+1G>T		p.X356_splice	ENST00000273854	NM_004439.5	356			0.243723844271203	3	FACETS	0.809	0.711	0.913	0.809	0.711	0.913	CLONAL	2	FALSE	1	0.243723844271203	3		457	421	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521421	8521421	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002954-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	108	516	0	ENST00000356435.5:c.817G>T	p.Ala273Ser	p.A273S	ENST00000356435		273	Gca/Tca	9/35	0.243723844271203	1	FACETS	0.929	0.84	1	1	0.988	1	CLONAL	2	FALSE	0	0.243723844271203	1		516	419	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325645	87325645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002954-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	59	552	1	ENST00000277120.3:c.522G>T	p.Leu174Phe	p.L174F	ENST00000277120		174	ttG/ttT	6/19	0.243723844271203	3	FACETS	1	0.901	1	0.528	0.455	0.608	CLONAL	1	FALSE	1	0.243723844271203	3		553	514	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106054	8106054	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002954-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	47	352	0	ENST00000346208.3:c.874A>G	p.Lys292Glu	p.K292E	ENST00000346208		292	Aaa/Gaa	4/6	0.243723844271203	3	FACETS	0.981	0.829	1	0.491	0.414	0.574	CLONAL	1	FALSE	1	0.243723844271203	3		352	441	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236229	108236229	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002954-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	98	360	0	ENST00000278616.4:c.9165G>A	p.Trp3055Ter	p.W3055*	ENST00000278616	NM_000051.3	3055	tgG/tgA	63/63	0.243723844271203	3	FACETS	0.852	0.767	0.94	0.852	0.767	0.94	CLONAL	3	FALSE	0	0.243723844271203	3		360	353	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245972	46245972	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002954-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	93	415	0	ENST00000334344.6:c.4066C>A	p.Pro1356Thr	p.P1356T	ENST00000334344	NM_152641.2	1356	Ccg/Acg	15/21	0.243723844271203	5	FACETS	1	0.943	1	0.725	0.647	0.807	CLONAL	2	FALSE	2	0.243723844271203	5		415	479	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868298	37868298	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002954-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	65	309	0	ENST00000269571.5:c.1019G>C	p.Arg340Pro	p.R340P	ENST00000269571		340	cGa/cCa	8/27	0.243723844271203	3	FACETS	1	0.961	1	0.648	0.563	0.739	CLONAL	1	FALSE	1	0.243723844271203	3		309	462	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39537606	39537606	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002954-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	31	431	0	ENST00000262039.4:c.140C>A	p.Ser47Ter	p.S47*	ENST00000262039	NM_002647.2	47	tCa/tAa	2/25	1	2	FACETS	0.656	0.53	0.797	0.656	0.53	0.797	SUBCLONAL	1	FALSE	1	0.243723844271203	2		431	388	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610509	10610509	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002954-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	117	483	0	ENST00000171111.5:c.201G>T	p.Met67Ile	p.M67I	ENST00000171111	NM_203500.1	67	atG/atT	2/6	0.243723844271203	2	FACETS	0.925	0.838	1	0.925	0.838	1	CLONAL	2	FALSE	0	0.243723844271203	2		483	519	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0002955-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	333	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.396097616705644	4	FACETS	0.87	0.829	0.912	1	0.994	1	CLONAL	3	TRUE	2	0.561952420712025	4		326	709	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120496232	120496232	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002955-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	248	594	0	ENST00000256646.2:c.2299C>T	p.Gln767Ter	p.Q767*	ENST00000256646	NM_024408.3	767	Cag/Tag	14/34	0.498602990271031	3	FACETS	0.909	0.856	0.962	0.909	0.856	0.962	CLONAL	2	TRUE	1	0.561952420712025	3		594	622	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218052	108218052	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002955-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	132	344	0	ENST00000278616.4:c.8631G>T	p.Leu2877Phe	p.L2877F	ENST00000278616	NM_000051.3	2877	ttG/ttT	59/63	0.505670860351633	3	FACETS	1	0.972	1	0.58	0.529	0.633	CLONAL	1	TRUE	1	0.561952420712025	3		344	519	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938823	76938823	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002955-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	82	576	0	ENST00000373344.5:c.1925A>C	p.Asn642Thr	p.N642T	ENST00000373344	NM_000489.3	642	aAt/aCt	9/35	NA	2	FACETS	0.519	0.458	0.584			1	INDETERMINATE	1	TRUE	NA	0.561952420712025	2		576	562	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094296	193094297	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0002955-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	341	467	0	ENST00000367435.3:c.187_188del	p.Leu63ThrfsTer2	p.L63Tfs*2	ENST00000367435	NM_024529.4	62	ttTCta/ttta	2/17	0.512194671941314	5	FACETS	1	0.979	1	0.785	0.749	0.822	CLONAL	3	TRUE	1	0.561952420712025	5		467	712	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851531	128851531	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002955-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	251	533	0	ENST00000249373.3:c.1858del	p.Gln620SerfsTer156	p.Q620Sfs*156	ENST00000249373	NM_005631.4	619	gCc/gc	11/12	0.55365968757226	2	FACETS	0.965	0.916	1	0.965	0.916	1	CLONAL	2	TRUE	0	0.561952420712025	2		533	463	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220599	1220612	+	frameshift_variant	Frame_Shift_Del	DEL	CGGACGACACCTGC	CGGACGACACCTGC	-	novel	NA	P-0002955-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	214	450	0	ENST00000326873.7:c.622_635del	p.Asp208GlnfsTer53	p.D208Qfs*53	ENST00000326873	NM_000455.4	206	gCGGACGACACCTGC/g	5/10	0.561952420712025	3	FACETS	0.854	0.807	0.899			1	CLONAL	3	TRUE	NA	0.561952420712025	3		450	381	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143466	108143466	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002955-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	203	502	0	ENST00000278616.4:c.3171A>T	p.Lys1057Asn	p.K1057N	ENST00000278616	NM_000051.3	1057	aaA/aaT	22/63	0.505670860351633	3	FACETS	0.819	0.765	0.874	0.819	0.765	0.874	CLONAL	2	TRUE	1	0.561952420712025	3		502	565	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0002956-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	313	408	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.414952861469245	2	FACETS	0.838	0.794	0.883	0.838	0.794	0.883	CLONAL	2	TRUE	0	0.461579496640548	2		408	809	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520017	NA	P-0002956-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	379	508	1	ENST00000326873.7:c.647C>T	p.Ser216Phe	p.S216F	ENST00000326873	NM_000455.4	216	tCc/tTc	5/10	0.461579496640548	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.461579496640548	2		509	721	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788651	3788651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002956-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	107	391	0	ENST00000262367.5:c.4303G>A	p.Asp1435Asn	p.D1435N	ENST00000262367	NM_004380.2	1435	Gat/Aat	26/31	0.461579496640548	1	FACETS	0.531	0.477	0.589	0.531	0.477	0.589	SUBCLONAL	1	TRUE	0	0.461579496640548	1		391	671	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045784	143045784	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002956-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	273	427	0	ENST00000262992.4:c.1850G>T	p.Cys617Phe	p.C617F	ENST00000262992	NM_001101669.1	617	tGt/tTt	17/24	0.461579496640548	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.461579496640548	1		427	622	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287220	38287220	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002956-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	474	493	0	ENST00000425967.3:c.437A>T	p.Tyr146Phe	p.Y146F	ENST00000425967	NM_001174067.1	146	tAc/tTc	4/19	0.433732907527019	3	FACETS	0.949	0.913	0.984	0.949	0.913	0.984	CLONAL	3	TRUE	0	0.461579496640548	3		493	888	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158420	108158420	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002956-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	204	316	0	ENST00000278616.4:c.4087A>T	p.Thr1363Ser	p.T1363S	ENST00000278616	NM_000051.3	1363	Act/Tct	27/63	0.461579496640548	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.461579496640548	1		316	520	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457264	67457264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750707381	NA	P-0002956-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	253	339	0	ENST00000327367.4:c.238C>T	p.Arg80Trp	p.R80W	ENST00000327367	NM_005902.3	80	Cgg/Tgg	2/9	0.461579496640548	2	FACETS	0.968	0.915	1	0.968	0.915	1	CLONAL	2	TRUE	0	0.461579496640548	2		339	566	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143985	11143985	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002956-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	297	417	0	ENST00000358026.2:c.3566G>T	p.Arg1189Leu	p.R1189L	ENST00000358026	NM_001128849.1	1189	cGa/cTa	26/36	0.461579496640548	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.461579496640548	2		417	570	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17940951	17940951	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002956-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	32	409	0	ENST00000458235.1:c.3173A>G	p.Gln1058Arg	p.Q1058R	ENST00000458235	NM_000215.3	1058	cAg/cGg	23/24	0.461579496640548	2	FACETS	0.288	0.233	0.35	0.144	0.116	0.175	SUBCLONAL	1	TRUE	0	0.461579496640548	2		409	481	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770610	40770610	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002956-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	205	385	0	ENST00000373198.4:c.2772C>A	p.Asp924Glu	p.D924E	ENST00000373198	NM_133170.3	924	gaC/gaA	19/32	0.461579496640548	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.461579496640548	1		385	547	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222235	53222235	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002956-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	114	418	0	ENST00000375401.3:c.4597A>G	p.Thr1533Ala	p.T1533A	ENST00000375401	NM_004187.3	1533	Act/Gct	26/26	0.461579496640548	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.461579496640548	1		418	369	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030464	49030465	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTTCA	novel	NA	P-0002956-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	206	338	0	ENST00000267163.4:c.1940_1944dup	p.Leu649PhefsTer11	p.L649Ffs*11	ENST00000267163	NM_000321.2	647	ctt/cTTTCAtt	19/27	0.461579496640548	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.461579496640548	1		338	632	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374988	45374989	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0002956-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	238	403	0	ENST00000262160.6:c.854_855delinsTT	p.Arg285Ile	p.R285I	ENST00000262160	NM_005901.5	285	aGG/aTT	8/11	0.461579496640548	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.461579496640548	1		403	623	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157454272	157454272	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002974-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	345	203	0	ENST00000346085.5:c.2482A>T	p.Ile828Phe	p.I828F	ENST00000346085	NM_020732.3	828	Atc/Ttc	8/20	0.711051830189731	1	FACETS	0.997	0.953	1	0.997	0.953	1	CLONAL	1	TRUE	0	0.71	1		203	629	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578192	7578193	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	A	novel	NA	P-0002979-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	185	578	1	ENST00000269305.4:c.656_657delinsT	p.Pro219LeufsTer28	p.P219Lfs*28	ENST00000269305	NM_001126112.2	219	cCC/cT	6/11	0.390887563020226	2	FACETS	0.954	0.89	1	0.954	0.89	1	CLONAL	2	TRUE	0	0.426230928215441	2		579	455	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2113016	2113020	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTC	CTGTC	-	novel	NA	P-0002979-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	502	471	2	ENST00000219476.3:c.1407_1411del	p.Ser470CysfsTer10	p.S470Cfs*10	ENST00000219476	NM_000548.3	469	CTGTCc/c	14/42	0.426230928215441	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	0	0.426230928215441	3		473	926	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039224	49039234	+	frameshift_variant	Frame_Shift_Del	DEL	ATTTTGCAGTA	ATTTTGCAGTA	-	novel	NA	P-0002979-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	45	505	0	ENST00000267163.4:c.2302_2312del	p.Ile768CysfsTer23	p.I768Cfs*23	ENST00000267163	NM_000321.2	768	ATTTTGCAGTAt/t	22/27	0.370281535307535	2	FACETS	0.806	0.682	0.94	0.403	0.341	0.47	CLONAL	1	TRUE	0	0.426230928215441	2		505	262	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796886	45796886	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002993-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	88	363	0	ENST00000450313.1:c.1444C>A	p.His482Asn	p.H482N	ENST00000450313	NM_012222.2	482	Cac/Aac	14/16	0.264020676725213	1	FACETS	0.628	0.563	0.696	0.628	0.563	0.696	INDETERMINATE	1	TRUE	0	0.637943748377296	1		363	299	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033427	48033427	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0002993-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	61	364	0	ENST00000234420.5:c.3731T>A	p.Leu1244Ter	p.L1244*	ENST00000234420	NM_000179.2	1244	tTa/tAa	8/10	0.637943748377296	3	FACETS	0.762	0.662	0.87	0.381	0.331	0.435	SUBCLONAL	1	TRUE	1	0.637943748377296	3		364	331	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919203	178919203	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002993-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	84	310	0	ENST00000263967.3:c.688C>T	p.Arg230Ter	p.R230*	ENST00000263967	NM_006218.2	230	Cga/Tga	4/21	0.637943748377296	2	FACETS	0.872	0.779	0.97	0.436	0.389	0.485	CLONAL	1	TRUE	0	0.637943748377296	2		310	302	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18576973	18576973	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs1445321034	NA	P-0002993-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	140	294	0	ENST00000266497.5:c.2381G>A	p.Trp794Ter	p.W794*	ENST00000266497		794	tGg/tAg	16/31	0.637943748377296	6	FACETS	1	0.972	1			1	CLONAL	2	TRUE	NA	0.637943748377296	6		294	441	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003002-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	258	548	0	ENST00000346208.3:c.1220_1221insA	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcAg	6/6	0.173047322395738	6	FACETS	0.977	0.919	1	0.977	0.919	1	INDETERMINATE	3	TRUE	3	0.435509432697611	6		548	756	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015010	37015010	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762649232	NA	P-0003002-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	62	457	0	ENST00000358127.4:c.394G>A	p.Val132Ile	p.V132I	ENST00000358127	NM_001280556.1	132	Gtc/Atc	3/10	0.429060210454146	3	FACETS	0.651	0.562	0.746	0.325	0.281	0.373	SUBCLONAL	1	TRUE	1	0.435509432697611	3		457	533	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	33	138	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.291199285350836	4	FACETS	0.85	0.706	1	0.85	0.706	1	CLONAL	2	TRUE	2	0.450287901062403	4		138	125	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578520	7578520	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	37	230	0	ENST00000269305.4:c.410T>A	p.Leu137Gln	p.L137Q	ENST00000269305	NM_001126112.2	137	cTg/cAg	5/11	0.450287901062403	1	FACETS	0.916	0.769	1	0.916	0.769	1	CLONAL	1	TRUE	0	0.450287901062403	1		230	139	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0003045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	230	408	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	0.831732475054412	2		408	514	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263973	104263974	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776579	NA	P-0003045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	52	197	3	ENST00000369902.3:c.71dup	p.Ala25GlyfsTer23	p.A25Gfs*23	ENST00000369902	NM_016169.3	22	gcc/gCcc	1/12	0.831732475054412	2	FACETS	0.561	0.483	0.644	0.28	0.241	0.322	SUBCLONAL	1	TRUE	0	0.831732475054412	2		200	223	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278222	15278222	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	183	360	0	ENST00000263388.2:c.5200G>A	p.Val1734Ile	p.V1734I	ENST00000263388	NM_000435.2	1734	Gta/Ata	29/33	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.831732475054412	2		360	429	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	138	176	0	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.959	0.885	1	0.959	0.885	1	CLONAL	1	TRUE	1	0.831732475054412	2		176	346	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692911	89692911	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	286	269	0	ENST00000371953.3:c.395G>C	p.Gly132Ala	p.G132A	ENST00000371953	NM_000314.4	132	gGt/gCt	5/9	0.831732475054412	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.831732475054412	2		269	312	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555928	226555928	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766364807	NA	P-0003045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	211	313	0	ENST00000366794.5:c.2249C>T	p.Pro750Leu	p.P750L	ENST00000366794	NM_001618.3	750	cCg/cTg	16/23	0.818922238526505	3	FACETS	1	0.965	1	0.527	0.491	0.563	CLONAL	1	TRUE	1	0.831732475054412	3		313	682	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694599	176694599	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	227	442	0	ENST00000439151.2:c.5183C>A	p.Ala1728Asp	p.A1728D	ENST00000439151	NM_022455.4	1728	gCt/gAt	15/23	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.831732475054412	2		442	490	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176719049	176719049	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	229	348	0	ENST00000439151.2:c.6353A>T	p.Glu2118Val	p.E2118V	ENST00000439151	NM_022455.4	2118	gAa/gTa	22/23	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.831732475054412	2		348	480	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420190	49420190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775954885	NA	P-0003045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	218	440	2	ENST00000301067.7:c.15559G>A	p.Ala5187Thr	p.A5187T	ENST00000301067	NM_003482.3	5187	Gcc/Acc	48/54	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.831732475054412	2		442	485	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557639	95557639	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	181	492	0	ENST00000393063.1:c.5428G>T	p.Asp1810Tyr	p.D1810Y	ENST00000393063	NM_030621.3	1810	Gat/Tat	26/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.831732475054412	2		492	406	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562290	95562290	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1431986661	NA	P-0003045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	217	504	0	ENST00000393063.1:c.4967A>G	p.Asp1656Gly	p.D1656G	ENST00000393063	NM_030621.3	1656	gAt/gGt	24/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.831732475054412	2		504	481	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644869	67644869	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753730952	NA	P-0003045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	186	355	0	ENST00000264010.4:c.134C>T	p.Thr45Met	p.T45M	ENST00000264010	NM_006565.3	45	aCg/aTg	3/12	0.831732475054412	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.831732475054412	1		355	215	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761255	59761255	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	255	566	0	ENST00000259008.2:c.3152A>G	p.Asp1051Gly	p.D1051G	ENST00000259008	NM_032043.2	1051	gAt/gGt	20/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.831732475054412	2		566	581	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899255	78899255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1211315034	NA	P-0003045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	152	267	0	ENST00000306801.3:c.2894G>A	p.Arg965His	p.R965H	ENST00000306801	NM_020761.2	965	cGc/cAc	24/34	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.831732475054412	2		267	343	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411444	63411444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	231	584	0	ENST00000330258.3:c.1723C>T	p.Arg575Trp	p.R575W	ENST00000330258	NM_152424.3	575	Cgg/Tgg	2/2	0.188369230450915	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.831732475054412	0		584	477	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030591	48030591	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	228	448	0	ENST00000234420.5:c.3209del	p.Gly1070ValfsTer9	p.G1070Vfs*9	ENST00000234420	NM_000179.2	1069	Ggg/gg	5/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.831732475054412	2		448	494	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0003045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	89	176	2	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.831732475054412	2		178	209	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280077	18280077	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	15	43	0	ENST00000222254.8:c.2163del	p.Gly722AlafsTer152	p.G722Afs*152	ENST00000222254	NM_005027.3	720	ggC/gg	16/16	1	2	FACETS	0.633	0.477	0.807	0.633	0.477	0.807	SUBCLONAL	1	TRUE	1	0.831732475054412	2		43	57	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0003045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	186	398	15	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.831732475054412	2		413	434	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946416	2946418	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs770299746	NA	P-0003045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	218	548	0	ENST00000396946.4:c.3319_3321del	p.Glu1107del	p.E1107del	ENST00000396946	NM_032415.4	1107	GAG/-	25/25	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.831732475054412	2		548	499	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023769	27023769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	163	384	1	ENST00000324856.7:c.879del	p.Thr294ProfsTer69	p.T294Pfs*69	ENST00000324856	NM_006015.4	292	aCc/ac	1/20	1	2	FACETS	0.951	0.883	1	0.951	0.883	1	CLONAL	1	TRUE	1	0.831732475054412	2		385	412	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911417	32911419	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs80359363	NA	P-0003045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	280	808	0	ENST00000380152.3:c.2927_2929del	p.Ser976del	p.S976del	ENST00000380152		975	atCTCc/atc	11/27	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.831732475054412	2		808	619	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374939	118374939	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0003045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	232	448	1	ENST00000534358.1:c.8336del	p.Asn2779MetfsTer11	p.N2779Mfs*11	ENST00000534358	NM_005933.3	2778	Aaa/aa	27/36	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.831732475054412	2		449	533	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0003046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	85	553	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.925	1	1	0.986	1	CLONAL	2	FALSE	1	0.205716547158107	2		553	393	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245976	5245976	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	160	469	0	ENST00000357368.4:c.799G>A	p.Val267Met	p.V267M	ENST00000357368	NM_002850.3	267	Gtg/Atg	10/38	0.0858269707599364	3	FACETS	0.961	0.885	1	1	0.988	1	INDETERMINATE	3	FALSE	1	0.205716547158107	3		469	595	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574035	7574035	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs867389695	NA	P-0003046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	191	477	0	ENST00000269305.4:c.994-2A>G		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.205716547158107	1	FACETS	1	0.96	1	1	0.995	1	CLONAL	3	FALSE	0	0.205716547158107	1		477	533	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651171	206651171	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	103	265	0	ENST00000367120.3:c.781T>A	p.Tyr261Asn	p.Y261N	ENST00000367120	NM_014002.3	261	Tac/Aac	8/22	1	2	FACETS	1	0.974	1	1	0.989	1	CLONAL	2	FALSE	1	0.205716547158107	2		265	404	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25468901	25468901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	120	410	2	ENST00000264709.3:c.1462C>T	p.Arg488Trp	p.R488W	ENST00000264709	NM_175629.2	488	Cgg/Tgg	12/23	0.205716547158107	1	FACETS	0.819	0.741	0.901	1	0.987	1	CLONAL	2	FALSE	0	0.205716547158107	1		412	639	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681314	88681314	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	75	287	2	ENST00000372037.3:c.1204G>T	p.Val402Leu	p.V402L	ENST00000372037	NM_004329.2	402	Gtg/Ttg	11/13	0.205716547158107	1	FACETS	0.847	0.747	0.954	1	0.98	1	CLONAL	2	FALSE	0	0.205716547158107	1		289	386	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573563	48573564	+	stop_gained	Nonsense_Mutation	DNP	GA	GA	TT	novel	NA	P-0003046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	61	401	0	ENST00000342988.3:c.147_148delinsTT	p.Glu49_Lys50delinsAspTer	p.E49_K50delinsD*	ENST00000342988	NM_005359.5	49	gaGAaa/gaTTaa	2/12	0.205716547158107	0	FACETS	0.985	0.861	1			1	CLONAL	2	FALSE	0	0.205716547158107	0		401	239	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136980	11136980	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	147	381	0	ENST00000358026.2:c.3173C>G	p.Ser1058Cys	p.S1058C	ENST00000358026	NM_001128849.1	1058	tCc/tGc	23/36	0.0858269707599364	3	FACETS	0.837	0.766	0.91	1	0.981	1	INDETERMINATE	3	FALSE	1	0.205716547158107	3		381	628	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027815	48027815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	347	471	0	ENST00000234420.5:c.2693C>T	p.Pro898Leu	p.P898L	ENST00000234420	NM_000179.2	898	cCt/cTt	4/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.811742929766533	2		471	840	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212252696	212252696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	166	309	0	ENST00000342788.4:c.3157C>T	p.Pro1053Ser	p.P1053S	ENST00000342788	NM_005235.2	1053	Cct/Tct	26/28	1	2	FACETS	0.909	0.843	0.976	0.909	0.843	0.976	CLONAL	1	TRUE	1	0.811742929766533	2		309	450	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956205	55956205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148668147	NA	P-0003047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	388	538	1	ENST00000263923.4:c.3110C>T	p.Ser1037Leu	p.S1037L	ENST00000263923	NM_002253.2	1037	tCg/tTg	23/30	1	2	FACETS	0.936	0.892	0.981	0.936	0.892	0.981	CLONAL	1	TRUE	1	0.811742929766533	2		539	1021	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540188	187540188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	430	698	0	ENST00000441802.2:c.7552G>A	p.Asp2518Asn	p.D2518N	ENST00000441802	NM_005245.3	2518	Gat/Aat	10/27	1	2	FACETS	0.922	0.88	0.964	0.922	0.88	0.964	CLONAL	1	TRUE	1	0.811742929766533	2		698	1149	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584768	187584768	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	244	296	0	ENST00000441802.2:c.3266-1G>A		p.X1089_splice	ENST00000441802	NM_005245.3	1089			1	2	FACETS	0.999	0.94	1	0.999	0.94	1	CLONAL	1	TRUE	1	0.811742929766533	2		296	602	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519408	176519408	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0003047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	411	507	0	ENST00000292408.4:c.814A>T	p.Lys272Ter	p.K272*	ENST00000292408	NM_213647.1	272	Aag/Tag	7/18	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.811742929766533	2		507	996	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231433	98231433	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	110	124	0	ENST00000331920.6:c.1850C>T	p.Pro617Leu	p.P617L	ENST00000331920	NM_000264.3	617	cCc/cTc	14/24	1	2	FACETS	0.951	0.868	1	0.951	0.868	1	CLONAL	1	TRUE	1	0.811742929766533	2		124	285	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608053	28608053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	447	664	0	ENST00000241453.7:c.1913C>T	p.Ser638Leu	p.S638L	ENST00000241453	NM_004119.2	638	tCa/tTa	15/24	1	2	FACETS	0.982	0.939	1	0.982	0.939	1	CLONAL	1	TRUE	1	0.811742929766533	2		664	1122	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954188	48954188	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	325	448	1	ENST00000267163.4:c.1390-1G>A		p.X464_splice	ENST00000267163	NM_000321.2	464			1	2	FACETS	0.977	0.927	1	0.977	0.927	1	CLONAL	1	TRUE	1	0.811742929766533	2		449	820	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954299	48954299	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs1395304450	NA	P-0003047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	224	414	0	ENST00000267163.4:c.1422-2A>T		p.X474_splice	ENST00000267163	NM_000321.2	474			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.811742929766533	2		414	538	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831298	3831298	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	224	319	0	ENST00000262367.5:c.1583C>T	p.Pro528Leu	p.P528L	ENST00000262367	NM_004380.2	528	cCa/cTa	7/31	1	2	FACETS	0.973	0.914	1	0.973	0.914	1	CLONAL	1	TRUE	1	0.811742929766533	2		319	567	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577579	7577579	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	296	361	2	ENST00000269305.4:c.702C>A	p.Tyr234Ter	p.Y234*	ENST00000269305	NM_001126112.2	234	taC/taA	7/11	1	2	FACETS	0.948	0.897	1	0.948	0.897	1	CLONAL	1	TRUE	1	0.811742929766533	2		363	769	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578202	7578202	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520004	NA	P-0003047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	566	554	0	ENST00000269305.4:c.647T>G	p.Val216Gly	p.V216G	ENST00000269305	NM_001126112.2	216	gTg/gGg	6/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.811742929766533	2		554	1302	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422406	47422407	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0003047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	436	338	1	ENST00000377045.4:c.40_41delinsTT	p.Pro14Leu	p.P14L	ENST00000377045	NM_001654.4	14	CCa/TTa	2/16	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.811742929766533	1		339	549	SUCCESS
AR	367	MSKCC	GRCh37	X	66931285	66931285	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	533	374	2	ENST00000374690.3:c.1927G>A	p.Glu643Lys	p.E643K	ENST00000374690	NM_000044.3	643	Gaa/Aaa	4/8	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.811742929766533	1		376	663	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725198	49725198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759497617	NA	P-0003049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	11	136	2	ENST00000449682.2:c.227C>T	p.Pro76Leu	p.P76L	ENST00000449682	NM_020998.3	76	cCc/cTc	2/18	0.292770022783612	2	FACETS	0.45	0.311	0.621	0.225	0.155	0.311	SUBCLONAL	1	TRUE	0	0.292770022783612	2		138	167	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848043	151848043	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	24	375	0	ENST00000262189.6:c.12716G>A	p.Ser4239Asn	p.S4239N	ENST00000262189	NM_170606.2	4239	aGt/aAt	51/59	0.292770022783612	3	FACETS	0.764	0.601	0.951	0.382	0.3	0.476	CLONAL	1	TRUE	1	0.292770022783612	3		375	246	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577073	7577073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	296	504	0	ENST00000269305.4:c.865C>T	p.Leu289Phe	p.L289F	ENST00000269305	NM_001126112.2	289	Ctc/Ttc	8/11	0.292770022783612	4	FACETS	0.957	0.907	1	1	0.992	1	CLONAL	4	TRUE	1	0.292770022783612	4		504	683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576826	7576867	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTGATAAGAGGTCCCAAGACTTAGTACCTGAAGGGTGAAATA	TTGATAAGAGGTCCCAAGACTTAGTACCTGAAGGGTGAAATA	-	novel	NA	P-0003049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	104	283	0	ENST00000269305.4:c.979_993+27del		p.X327_splice	ENST00000269305	NM_001126112.2	327		9/11	0.292770022783612	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	3	TRUE	1	0.292770022783612	4		283	270	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0003053-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	129	609	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.400933495725648	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.400933495725648	1		609	460	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0003054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	138	435	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.452906484702736	3	FACETS	0.995	0.907	1	0.498	0.453	0.544	CLONAL	1	TRUE	1	0.452906484702736	3		435	751	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0003054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	100	119	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.452906484702736	4	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	2	0.452906484702736	4		119	284	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607188	189607188	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	194	619	2	ENST00000264731.3:c.1567C>T	p.Gln523Ter	p.Q523*	ENST00000264731	NM_003722.4	523	Cag/Tag	12/14	0.452906484702736	5	FACETS	1	0.969	1	0.365	0.336	0.394	CLONAL	1	TRUE	2	0.452906484702736	5		621	1315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0003054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	290	470	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.452906484702736	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.452906484702736	2		470	619	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46512240	46512240	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	159	577	0	ENST00000262741.5:c.999G>C	p.Lys333Asn	p.K333N	ENST00000262741	NM_003629.3	333	aaG/aaC	8/10	0.409871800910421	3	FACETS	0.941	0.863	1	0.471	0.431	0.512	CLONAL	1	TRUE	1	0.452906484702736	3		577	915	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288534	198288534	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	194	566	0	ENST00000335508.6:c.193G>A	p.Asp65Asn	p.D65N	ENST00000335508	NM_012433.2	65	Gat/Aat	2/25	0.452906484702736	2	FACETS	1	0.945	1	0.512	0.474	0.551	CLONAL	1	TRUE	0	0.452906484702736	2		566	837	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52685820	52685820	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	138	446	0	ENST00000394830.3:c.652C>A	p.Pro218Thr	p.P218T	ENST00000394830	NM_018313.4	218	Cca/Aca	7/30	0.452906484702736	3	FACETS	0.83	0.754	0.908	0.415	0.377	0.454	CLONAL	1	TRUE	1	0.452906484702736	3		446	901	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456436	89456436	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	139	499	0	ENST00000336596.2:c.1612G>A	p.Glu538Lys	p.E538K	ENST00000336596	NM_005233.5	538	Gaa/Aaa	8/17	0.452906484702736	3	FACETS	0.998	0.91	1	0.499	0.455	0.546	CLONAL	1	TRUE	1	0.452906484702736	3		499	754	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281328	142281328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	105	369	0	ENST00000350721.4:c.916G>A	p.Glu306Lys	p.E306K	ENST00000350721	NM_001184.3	306	Gaa/Aaa	4/47	0.452906484702736	4	FACETS	0.812	0.727	0.902	0.406	0.363	0.451	CLONAL	1	TRUE	2	0.452906484702736	4		369	830	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226001	226001	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1560987595	NA	P-0003054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	45	85	0	ENST00000264932.6:c.460G>A	p.Glu154Lys	p.E154K	ENST00000264932	NM_004168.2	154	Gaa/Aaa	5/15	NA	2	FACETS	1	0.95	1			1	INDETERMINATE	1	TRUE	NA	0.452906484702736	2		85	156	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250784	26250784	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	235	788	0	ENST00000446824.2:c.50C>T	p.Pro17Leu	p.P17L	ENST00000446824	NM_021018.2	17	cCg/cTg	1/1	0.452906484702736	3	FACETS	1	0.975	1	0.365	0.34	0.391	CLONAL	1	TRUE	0	0.452906484702736	3		788	1163	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148507499	148507499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	135	348	0	ENST00000320356.2:c.1955C>T	p.Ser652Phe	p.S652F	ENST00000320356	NM_004456.4	652	tCt/tTt	17/20	0.452906484702736	1	FACETS	0.985	0.902	1	0.985	0.902	1	CLONAL	1	TRUE	0	0.452906484702736	1		348	468	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650044	93650044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	162	473	0	ENST00000375746.1:c.1595G>A	p.Gly532Glu	p.G532E	ENST00000375746	NM_001174167.1	532	gGa/gAa	12/14	0.395094339890511	3	FACETS	0.944	0.866	1			1	CLONAL	1	TRUE	NA	0.452906484702736	3		473	929	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685287	89685287	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs398123316	NA	P-0003054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	172	249	0	ENST00000371953.3:c.182A>G	p.His61Arg	p.H61R	ENST00000371953	NM_000314.4	61	cAt/cGt	3/9	0.452906484702736	4	FACETS	0.896	0.828	0.966	0.896	0.828	0.966	CLONAL	2	TRUE	2	0.452906484702736	4		249	616	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135954	64135954	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	125	413	0	ENST00000334205.4:c.1215C>G	p.Phe405Leu	p.F405L	ENST00000334205	NM_003942.2	405	ttC/ttG	11/17	0.409871800910421	3	FACETS	0.959	0.869	1	0.479	0.434	0.527	CLONAL	1	TRUE	1	0.452906484702736	3		413	706	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967503	26967503	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0003054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	126	337	0	ENST00000381527.3:c.647-1G>C		p.X216_splice	ENST00000381527	NM_001260.1	216			0.452906484702736	4	FACETS	0.975	0.883	1	0.325	0.294	0.358	CLONAL	1	TRUE	1	0.452906484702736	4		337	829	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602317	28602317	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs757518348	NA	P-0003054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	158	469	0	ENST00000241453.7:c.2051C>T	p.Ser684Leu	p.S684L	ENST00000241453	NM_004119.2	684	tCa/tTa	16/24	0.452906484702736	4	FACETS	1	0.932	1	0.34	0.311	0.37	CLONAL	1	TRUE	1	0.452906484702736	4		469	994	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041519	42041519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	224	867	0	ENST00000219905.7:c.5714C>T	p.Ser1905Phe	p.S1905F	ENST00000219905	NM_001164273.1	1905	tCt/tTt	17/24	0.452906484702736	3	FACETS	0.943	0.876	1	0.471	0.438	0.506	CLONAL	1	TRUE	1	0.452906484702736	3		867	1287	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100482	2100482	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	112	380	0	ENST00000219476.3:c.220G>T	p.Glu74Ter	p.E74*	ENST00000219476	NM_000548.3	74	Gaa/Taa	3/42	0.452906484702736	6	FACETS	0.885	0.794	0.982			1	CLONAL	1	TRUE	NA	0.452906484702736	6		380	1065	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126525	2126525	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	182	524	0	ENST00000219476.3:c.2776G>C	p.Asp926His	p.D926H	ENST00000219476	NM_000548.3	926	Gac/Cac	25/42	0.452906484702736	6	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.452906484702736	6		524	1359	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029051	14029051	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1567247685	NA	P-0003054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	54	292	0	ENST00000311895.7:c.1262G>C	p.Arg421Thr	p.R421T	ENST00000311895	NM_005236.2	421	aGa/aCa	8/11	0.452906484702736	6	FACETS	0.449	0.382	0.523			1	SUBCLONAL	1	TRUE	NA	0.452906484702736	6		292	1012	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845583	72845583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769603301	NA	P-0003054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	259	734	0	ENST00000268489.5:c.3757C>T	p.Arg1253Cys	p.R1253C	ENST00000268489	NM_006885.3	1253	Cgc/Tgc	7/10	0.452906484702736	2	FACETS	1	0.984	1	0.574	0.538	0.611	CLONAL	1	TRUE	0	0.452906484702736	2		734	996	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349067	89349067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	277	842	0	ENST00000301030.4:c.3883G>A	p.Asp1295Asn	p.D1295N	ENST00000301030	NM_001256183.1	1295	Gac/Aac	9/13	0.452906484702736	2	FACETS	1	0.981	1	0.551	0.518	0.586	CLONAL	1	TRUE	0	0.452906484702736	2		842	1109	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682381	37682381	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	114	418	0	ENST00000447079.4:c.3572C>T	p.Ser1191Leu	p.S1191L	ENST00000447079	NM_015083.1	1191	tCa/tTa	13/14	0.452906484702736	3	FACETS	0.768	0.691	0.849	0.384	0.345	0.425	SUBCLONAL	1	TRUE	1	0.452906484702736	3		418	804	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884145	37884145	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	134	476	0	ENST00000269571.5:c.3616C>A	p.Gln1206Lys	p.Q1206K	ENST00000269571		1206	Cag/Aag	27/27	0.452906484702736	3	FACETS	0.765	0.694	0.839	0.382	0.347	0.42	SUBCLONAL	1	TRUE	1	0.452906484702736	3		476	949	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098380	11098380	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	130	499	0	ENST00000358026.2:c.898C>T	p.Gln300Ter	p.Q300*	ENST00000358026	NM_001128849.1	300	Cag/Tag	6/36	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.452906484702736	2		499	570	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952349	17952349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201387977	NA	P-0003054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	99	361	0	ENST00000458235.1:c.991G>A	p.Glu331Lys	p.E331K	ENST00000458235	NM_000215.3	331	Gag/Aag	8/24	1	2	FACETS	0.839	0.752	0.931	0.839	0.752	0.931	CLONAL	1	TRUE	1	0.452906484702736	2		361	521	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958078	54958078	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	183	456	0	ENST00000312783.6:c.529C>T	p.Gln177Ter	p.Q177*	ENST00000312783	NM_198436.1	177	Cag/Tag	6/10	0.452906484702736	4	FACETS	1	0.978	1	0.578	0.533	0.625	CLONAL	1	TRUE	2	0.452906484702736	4		456	1016	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15821874	15821874	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	153	762	0	ENST00000307771.7:c.267G>C	p.Lys89Asn	p.K89N	ENST00000307771	NM_005089.3	89	aaG/aaC	4/11	0.452906484702736	3	FACETS	0.701	0.64	0.765	0.351	0.32	0.383	SUBCLONAL	1	TRUE	1	0.452906484702736	3		762	1182	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339566	70339566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	163	687	0	ENST00000374080.3:c.235G>A	p.Glu79Lys	p.E79K	ENST00000374080		79	Gag/Aag	3/45	0.452906484702736	3	FACETS	0.77	0.705	0.837	0.385	0.352	0.419	SUBCLONAL	1	TRUE	1	0.452906484702736	3		687	1147	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566418	139566418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374930413	NA	P-0003055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	44	300	0	ENST00000308874.7:c.677C>T	p.Ser226Leu	p.S226L	ENST00000308874		226	tCg/tTg	9/10	0.214179698829103	1	FACETS	0.42	0.352	0.496	0.42	0.352	0.496	SUBCLONAL	1	TRUE	0	0.316641161043018	1		300	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0003055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	115	606	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.316641161043018	2		606	603	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941657	48941657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1060503077	NA	P-0003055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	232	716	0	ENST00000267163.4:c.967G>T	p.Glu323Ter	p.E323*	ENST00000267163	NM_000321.2	323	Gaa/Taa	10/27	NA	2	FACETS	0.85	0.794	0.907			1	INDETERMINATE	2	TRUE	NA	0.316641161043018	2		716	862	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332857	153332857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	48	804	0	ENST00000281708.4:c.99G>A	p.Met33Ile	p.M33I	ENST00000281708	NM_033632.3	33	atG/atA	2/12	0.162382907536325	2	FACETS	0.345	0.29	0.405	0.172	0.145	0.203	INDETERMINATE	1	TRUE	0	0.316641161043018	2		804	880	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878937	117878937	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	206	1199	0	ENST00000297338.2:c.32G>C	p.Arg11Thr	p.R11T	ENST00000297338	NM_006265.2	11	aGa/aCa	2/14	0.157326977214349	3	FACETS	1	0.971	1	0.548	0.507	0.59	INDETERMINATE	1	TRUE	1	0.316641161043018	3		1199	1376	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229487	98229487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	88	1000	0	ENST00000331920.6:c.2471G>A	p.Arg824Lys	p.R824K	ENST00000331920	NM_000264.3	824	aGg/aAg	15/24	0.214179698829103	1	FACETS	0.465	0.411	0.523	0.465	0.411	0.523	SUBCLONAL	1	TRUE	0	0.316641161043018	1		1000	1006	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333845	70333845	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	58	830	0	ENST00000373644.4:c.1750G>C	p.Glu584Gln	p.E584Q	ENST00000373644	NM_030625.2	584	Gaa/Caa	2/12	0.214179698829103	1	FACETS	0.372	0.318	0.43	0.372	0.318	0.43	SUBCLONAL	1	TRUE	0	0.316641161043018	1		830	830	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741558	17741558	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	44	371	0	ENST00000250003.3:c.229G>A	p.Glu77Lys	p.E77K	ENST00000250003	NM_002478.4	77	Gag/Aag	1/3	0.11780428923567	5	FACETS	0.988	0.83	1	0.247	0.207	0.291	INDETERMINATE	1	TRUE	1	0.316641161043018	5		371	415	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911658	32911658	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1422	298	1427	1	ENST00000380152.3:c.3166C>G	p.Gln1056Glu	p.Q1056E	ENST00000380152		1056	Caa/Gaa	11/27	0.316641161043018	3	FACETS	1	0.99	1	0.423	0.396	0.45	CLONAL	1	TRUE	0	0.316641161043018	3		1428	1720	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873835	35873835	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs923187160	NA	P-0003055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	56	414	0	ENST00000216797.5:c.16G>A	p.Glu6Lys	p.E6K	ENST00000216797	NM_020529.2	6	Gag/Aag	1/6	0.316641161043018	3	FACETS	0.859	0.737	0.992			1	CLONAL	1	TRUE	NA	0.316641161043018	3		414	477	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663362	67663362	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	51	754	0	ENST00000264010.4:c.1763G>C	p.Gly588Ala	p.G588A	ENST00000264010	NM_006565.3	588	gGa/gCa	10/12	NA	2	FACETS	0.506	0.429	0.59			1	INDETERMINATE	1	TRUE	NA	0.316641161043018	2		754	637	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490348	29490348	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786203460	NA	P-0003055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	91	844	0	ENST00000356175.3:c.433C>G	p.Leu145Val	p.L145V	ENST00000356175	NM_000267.3	145	Ctc/Gtc	4/57	1	2	FACETS	0.58	0.514	0.651	0.58	0.514	0.651	SUBCLONAL	1	TRUE	1	0.316641161043018	2		844	991	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730799	40730799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	61	616	0	ENST00000373198.4:c.3736G>A	p.Glu1246Lys	p.E1246K	ENST00000373198	NM_133170.3	1246	Gaa/Aaa	27/32	0.316641161043018	3	FACETS	0.546	0.469	0.629	0.273	0.234	0.315	SUBCLONAL	1	TRUE	1	0.316641161043018	3		616	818	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346550	81346550	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs148293411	NA	P-0003060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	328	209	0	ENST00000222390.5:c.1403G>A	p.Arg468His	p.R468H	ENST00000222390	NM_000601.4	468	cGt/cAt	11/18	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		209	815	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647022	23647022	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	364	226	0	ENST00000261584.4:c.845G>C	p.Arg282Thr	p.R282T	ENST00000261584	NM_024675.3	282	aGa/aCa	4/13	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		226	809	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0003063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	271	328	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.458348212250793	2	FACETS	0.875	0.826	0.924	0.875	0.826	0.924	CLONAL	2	TRUE	0	0.458348212250793	2		328	676	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048116	180048116	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs753297291	NA	P-0003063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	114	344	0	ENST00000261937.6:c.2157G>C	p.Glu719Asp	p.E719D	ENST00000261937	NM_182925.4	719	gaG/gaC	14/30	0.458348212250793	2	FACETS	0.946	0.855	1	0.473	0.427	0.521	CLONAL	1	TRUE	0	0.458348212250793	2		344	526	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548222	41548222	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	130	284	0	ENST00000263253.7:c.3010G>C	p.Asp1004His	p.D1004H	ENST00000263253	NM_001429.3	1004	Gac/Cac	16/31	0.459820923574741	3	FACETS	0.933	0.847	1	0.311	0.282	0.342	CLONAL	1	TRUE	0	0.458348212250793	3		284	747	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	23	456	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.858	1			1	INDETERMINATE	1	TRUE	NA	0.855630964264463	2		456	51	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631839	90631839	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519906	NA	P-0003065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	105	263	0	ENST00000330062.3:c.514A>T	p.Arg172Trp	p.R172W	ENST00000330062	NM_002168.2	172	Agg/Tgg	4/11	1	2	FACETS	0.906	0.825	0.988	0.906	0.825	0.988	CLONAL	1	TRUE	1	0.855630964264463	2		263	271	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413214	139413214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	57	417	1	ENST00000277541.6:c.928G>A	p.Gly310Arg	p.G310R	ENST00000277541	NM_017617.3	310	Ggg/Agg	6/34	0.265269875846045	4	FACETS	0.7	0.604	0.805	0.35	0.302	0.403	INDETERMINATE	1	TRUE	2	0.855630964264463	4		418	353	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562291	95562291	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	141	403	0	ENST00000393063.1:c.4966G>T	p.Asp1656Tyr	p.D1656Y	ENST00000393063	NM_030621.3	1656	Gat/Tat	24/28	1	2	FACETS	0.896	0.826	0.966	0.896	0.826	0.966	CLONAL	1	TRUE	1	0.855630964264463	2		403	368	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796765	42796772	+	frameshift_variant	Frame_Shift_Del	DEL	GTGCCCAG	GTGCCCAG	-	novel	NA	P-0003065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	127	288	0	ENST00000575354.2:c.3223_3230del	p.Val1075SerfsTer73	p.V1075Sfs*73	ENST00000575354	NM_015125.3	1075	GTGCCCAGt/t	14/20	0.655683192292936	1	FACETS	0.88	0.825	0.933	0.88	0.825	0.933	CLONAL	1	TRUE	0	0.855630964264463	1		288	193	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0003096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	89	318	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.979	0.867	1	0.979	0.867	1	CLONAL	1	TRUE	1	0.220313066341989	2		318	825	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0003096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	87	225	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.220313066341989	2		225	685	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809247	243809247	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	83	365	0	ENST00000263826.5:c.377A>T	p.Asp126Val	p.D126V	ENST00000263826	NM_005465.4	126	gAt/gTt	4/13	0.200334897076799	4	FACETS	0.841	0.74	0.95	0.28	0.246	0.317	CLONAL	1	TRUE	1	0.220313066341989	4		365	1093	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20488473	20488473	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1185761411	NA	P-0003096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	172	287	0	ENST00000346618.3:c.1129T>G	p.Ser377Ala	p.S377A	ENST00000346618	NM_001949.4	377	Tcc/Gcc	6/7	0.220313066341989	3	FACETS	0.974	0.896	1	0.974	0.896	1	CLONAL	2	TRUE	1	0.220313066341989	3		287	890	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570204	87570204	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	19	121	0	ENST00000277120.3:c.1944C>G	p.His648Gln	p.H648Q	ENST00000277120		648	caC/caG	17/19	0.220313066341989	1	FACETS	0.571	0.433	0.732	0.571	0.433	0.732	SUBCLONAL	1	TRUE	0	0.220313066341989	1		121	269	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520246	9520246	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	64	209	0	ENST00000353224.5:c.2023G>T	p.Gly675Ter	p.G675*	ENST00000353224	NM_177990.2	675	Gga/Tga	10/10	1	2	FACETS	0.834	0.721	0.956	0.834	0.721	0.956	CLONAL	1	TRUE	1	0.220313066341989	2		209	697	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412891	63412891	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	73	345	0	ENST00000330258.3:c.276G>T	p.Lys92Asn	p.K92N	ENST00000330258	NM_152424.3	92	aaG/aaT	2/2	0.220313066341989	1	FACETS	0.652	0.568	0.742	0.652	0.568	0.742	SUBCLONAL	1	TRUE	0	0.220313066341989	1		345	905	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431912	49431913	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCGAT	novel	NA	P-0003126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	142	211	0	ENST00000301067.7:c.9222_9226dup	p.Ala3076AspfsTer45	p.A3076Dfs*45	ENST00000301067	NM_003482.3	3076	gct/gATCGGct	34/54	1	2	FACETS	0.913	0.833	0.996	1	0.99	1	CLONAL	2	TRUE	1	0.21	2		211	741	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38942407	38942407	+	stop_lost	Nonstop_Mutation	SNP	C	C	A	novel	NA	P-0003138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	194	266	0	ENST00000357387.3:c.5126G>T	p.Ter1709LeuextTer29	p.*1709Lext*29	ENST00000357387	NM_152756.3	1709	tGa/tTa	38/38	1	2	FACETS	0.69	0.641	0.739	0.69	0.641	0.739	SUBCLONAL	1	TRUE	1	0.880596106507586	2		266	639	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725055	89725055	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0003141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	64	145	0	ENST00000371953.3:c.1038C>G	p.Tyr346Ter	p.Y346*	ENST00000371953	NM_000314.4	346	taC/taG	9/9	1	2	FACETS	0.988	0.87	1	1	0.985	1	CLONAL	3	FALSE	1	0.208530186918965	2		145	207	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134479	30134479	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	36	137	0	ENST00000263025.4:c.52G>C	p.Glu18Gln	p.E18Q	ENST00000263025	NM_002746.2	18	Gag/Cag	1/9	1	2	FACETS	0.951	0.783	1	0.951	0.783	1	CLONAL	1	FALSE	1	0.208530186918965	2		137	363	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178638	56178707	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAGTTCCTCAGCTGCAGGTTGAAAATGGAGAAGATATCATCATTATTCAACAGGATGTAAGTATAGATTC	TAGTTCCTCAGCTGCAGGTTGAAAATGGAGAAGATATCATCATTATTCAACAGGATGTAAGTATAGATTC	-	novel	NA	P-0003141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	26	98	0	ENST00000399503.3:c.3612_3666+15del		p.X1204_splice	ENST00000399503	NM_005921.1	1204		14/20	0.200517522428241	3	FACETS	1	0.879	1	0.578	0.46	0.713	CLONAL	1	FALSE	1	0.208530186918965	3		98	238	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112438	115112438	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1423724888	NA	P-0003150-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	62	157	0	ENST00000257566.3:c.1302C>G	p.Asp434Glu	p.D434E	ENST00000257566	NM_016569.3	434	gaC/gaG	7/8	1	2	FACETS	0.879	0.768	0.997	0.879	0.768	0.997	CLONAL	1	TRUE	1	0.561805290909708	2		157	251	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226164	2226164	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	115	379	0	ENST00000326181.6:c.1861T>G	p.Tyr621Asp	p.Y621D	ENST00000326181	NM_032271.2	621	Tac/Gac	19/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		379	359	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153252021	153252021	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0003171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	150	313	0	ENST00000281708.4:c.986-1G>C		p.X329_splice	ENST00000281708	NM_033632.3	329			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		313	430	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	21	423	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.505	0.388	0.643	0.505	0.388	0.643	SUBCLONAL	1	FALSE	1	0.156817447034236	2		423	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913343	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	151	363	0	ENST00000269305.4:c.817C>G	p.Arg273Gly	p.R273G	ENST00000269305	NM_001126112.2	273	Cgt/Ggt	8/11	0.156817447034236	2	FACETS	0.902	0.824	0.985	0.902	0.824	0.985	CLONAL	2	FALSE	0	0.156817447034236	2		363	1067	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076755	72076755	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	60	433	0	ENST00000357731.5:c.742G>T	p.Ala248Ser	p.A248S	ENST00000357731	NM_173808.2	248	Gca/Tca	5/7	1	2	FACETS	0.756	0.649	0.873	0.756	0.649	0.873	SUBCLONAL	1	FALSE	1	0.156817447034236	2		433	1012	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086130	16086130	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	97	239	0	ENST00000281043.3:c.1306G>T	p.Glu436Ter	p.E436*	ENST00000281043	NM_005378.4	436	Gag/Tag	3/3	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	FALSE	NA	0.156817447034236	2		239	885	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99154325	99154325	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	38	207	0	ENST00000074304.5:c.468-1G>A		p.X156_splice	ENST00000074304	NM_001134224.1	156			1	2	FACETS	0.753	0.621	0.901	0.753	0.621	0.901	CLONAL	1	FALSE	1	0.156817447034236	2		207	644	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568839	212568839	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	36	344	0	ENST00000342788.4:c.1279G>C	p.Val427Leu	p.V427L	ENST00000342788	NM_005235.2	427	Gta/Cta	11/28	0.156817447034236	3	FACETS	0.905	0.743	1	0.453	0.371	0.544	CLONAL	1	FALSE	1	0.156817447034236	3		344	547	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370713	225370713	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	42	300	0	ENST00000264414.4:c.1166C>A	p.Ser389Ter	p.S389*	ENST00000264414	NM_003590.4	389	tCa/tAa	8/16	0.156817447034236	1	FACETS	0.845	0.705	1	0.845	0.705	1	CLONAL	1	FALSE	0	0.156817447034236	1		300	584	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161891	47161891	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	136	418	0	ENST00000409792.3:c.4235A>T	p.Glu1412Val	p.E1412V	ENST00000409792	NM_014159.6	1412	gAg/gTg	3/21	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.156817447034236	NA		418	864	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861055	35861055	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	94	254	0	ENST00000303115.3:c.184C>A	p.Pro62Thr	p.P62T	ENST00000303115	NM_002185.3	62	Cca/Aca	2/8	0.125719391309448	4	FACETS	0.93	0.827	1	0.93	0.827	1	CLONAL	2	FALSE	2	0.156817447034236	4		254	746	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111450	56111450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	26	106	0	ENST00000399503.3:c.50C>T	p.Ala17Val	p.A17V	ENST00000399503	NM_005921.1	17	gCc/gTc	1/20	0.125719391309448	4	FACETS	0.966	0.765	1	0.483	0.382	0.599	CLONAL	1	FALSE	2	0.156817447034236	4		106	397	SUCCESS
APC	324	MSKCC	GRCh37	5	112154810	112154810	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	112	305	0	ENST00000257430.4:c.1081C>A	p.His361Asn	p.H361N	ENST00000257430	NM_000038.5	361	Cat/Aat	10/16	1	2	FACETS	0.859	0.773	0.951	1	0.986	1	CLONAL	2	FALSE	1	0.156817447034236	2		305	831	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971286	13971286	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	146	279	0	ENST00000405192.2:c.643A>G	p.Met215Val	p.M215V	ENST00000405192	NM_001163147.1	215	Atg/Gtg	8/12	1	2	FACETS	1	0.946	1	1	0.991	1	CLONAL	2	FALSE	1	0.156817447034236	2		279	887	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221802	55221802	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	309	398	0	ENST00000275493.2:c.846G>T	p.Glu282Asp	p.E282D	ENST00000275493	NM_005228.3	282	gaG/gaT	7/28	1	2	FACETS	1	0.972	1	1	0.996	1	CLONAL	3	FALSE	1	0.156817447034236	2		398	1249	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499831	8499831	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	40	243	0	ENST00000356435.5:c.2138G>T	p.Gly713Val	p.G713V	ENST00000356435		713	gGt/gTt	14/35	1	2	FACETS	0.892	0.74	1	0.892	0.74	1	CLONAL	1	FALSE	1	0.156817447034236	2		243	572	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970966	21970966	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	64	212	0	ENST00000304494.5:c.392G>C	p.Arg131Pro	p.R131P	ENST00000304494	NM_000077.4	131	cGc/cCc	2/3	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	1	0.156817447034236	2		212	619	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971195	21971195	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	17	78	0	ENST00000304494.5:c.163G>T	p.Gly55Cys	p.G55C	ENST00000304494	NM_000077.4	55	Ggc/Tgc	2/3	1				0.721	1				CLONAL	1	FALSE	1	0.156817447034236	2		78	225	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77043870	77043870	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	111	425	0	ENST00000356341.3:c.1456A>G	p.Asn486Asp	p.N486D	ENST00000356341	NM_002576.4	486	Aac/Gac	14/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.156817447034236	2		425	1172	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999042	100999042	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	114	289	0	ENST00000325455.5:c.760G>T	p.Ala254Ser	p.A254S	ENST00000325455	NM_001202474.3	254	Gcg/Tcg	1/8	1	2	FACETS	0.838	0.754	0.928	1	0.986	1	CLONAL	2	FALSE	1	0.156817447034236	2		289	867	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076656	102076656	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	56	187	0	ENST00000282441.5:c.835G>C	p.Val279Leu	p.V279L	ENST00000282441	NM_001130145.2	279	Gtg/Ctg	5/9	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	FALSE	1	0.156817447034236	2		187	707	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431772	49431772	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	104	213	0	ENST00000301067.7:c.9367G>T	p.Glu3123Ter	p.E3123*	ENST00000301067	NM_003482.3	3123	Gag/Tag	34/54	0.156817447034236	3	FACETS	0.911	0.816	1	0.911	0.816	1	CLONAL	2	FALSE	1	0.156817447034236	3		213	785	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486597	56486597	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	99	317	0	ENST00000267101.3:c.1176G>T	p.Glu392Asp	p.E392D	ENST00000267101	NM_001982.3	392	gaG/gaT	10/28	0.156817447034236	3	FACETS	1	0.98	1	0.737	0.657	0.822	CLONAL	1	FALSE	1	0.156817447034236	3		317	924	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861789	57861789	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs562388922	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1227	153	470	0	ENST00000228682.2:c.1090T>C	p.Cys364Arg	p.C364R	ENST00000228682	NM_005269.2	364	Tgt/Cgt	10/12	0.156817447034236	3	FACETS	0.762	0.695	0.833	0.762	0.695	0.833	SUBCLONAL	2	FALSE	1	0.156817447034236	3		470	1380	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864714	57864714	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	154	442	0	ENST00000228682.2:c.2191G>T	p.Gly731Ter	p.G731*	ENST00000228682	NM_005269.2	731	Gga/Tga	12/12	0.156817447034236	3	FACETS	0.908	0.829	0.991	0.908	0.829	0.991	CLONAL	2	FALSE	1	0.156817447034236	3		442	1166	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947611	48947611	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs535576919	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	28	225	0	ENST00000267163.4:c.1198C>G	p.Leu400Val	p.L400V	ENST00000267163	NM_000321.2	400	Ctg/Gtg	12/27	1	2	FACETS	0.817	0.652	1	0.817	0.652	1	CLONAL	1	FALSE	1	0.156817447034236	2		225	437	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514842	103514842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	49	198	0	ENST00000355739.4:c.1343C>T	p.Ser448Leu	p.S448L	ENST00000355739	NM_000123.3	448	tCa/tTa	8/15	1	2	FACETS	0.961	0.813	1	0.961	0.813	1	CLONAL	1	FALSE	1	0.156817447034236	2		198	650	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867335	68867335	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	185	310	0	ENST00000261769.5:c.2582A>G	p.Tyr861Cys	p.Y861C	ENST00000261769	NM_004360.3	861	tAc/tGc	16/16	0.156817447034236	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	FALSE	1	0.156817447034236	3		310	1070	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89815072	89815072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868782409	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	238	336	1	ENST00000389301.3:c.3343G>A	p.Glu1115Lys	p.E1115K	ENST00000389301	NM_000135.2	1115	Gag/Aag	33/43	0.156817447034236	2	FACETS	0.933	0.87	0.997	1	0.991	1	CLONAL	3	FALSE	0	0.156817447034236	2		337	1085	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774795	73774795	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	76	301	0	ENST00000254810.4:c.292G>T	p.Glu98Ter	p.E98*	ENST00000254810	NM_005324.3	98	Gaa/Taa	4/4	0.156817447034236	3	FACETS	0.832	0.727	0.946			1	CLONAL	1	FALSE	NA	0.156817447034236	3		301	1256	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39623751	39623751	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	45	375	0	ENST00000262039.4:c.2158G>T	p.Glu720Ter	p.E720*	ENST00000262039	NM_002647.2	720	Gag/Tag	20/25	1	2	FACETS	0.907	0.761	1	0.907	0.761	1	CLONAL	1	FALSE	1	0.156817447034236	2		375	633	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932044	39932044	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	61	174	0	ENST00000378444.4:c.2555T>C	p.Phe852Ser	p.F852S	ENST00000378444	NM_001123385.1	852	tTc/tCc	4/15	0.156817447034236	0	FACETS	0.719	0.622	0.825			1	SUBCLONAL	2	FALSE	NA	0.156817447034236	0		174	456	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934026	39934026	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	62	212	0	ENST00000378444.4:c.573G>C	p.Trp191Cys	p.W191C	ENST00000378444	NM_001123385.1	191	tgG/tgC	4/15	0.156817447034236	0	FACETS	1	0.958	1			1	CLONAL	1	FALSE	NA	0.156817447034236	0		212	516	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230856	53230856	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	116	199	0	ENST00000375401.3:c.1937A>T	p.Glu646Val	p.E646V	ENST00000375401	NM_004187.3	646	gAg/gTg	14/26	1	1	FACETS	0.837	0.757	0.92	1	0.99	1	CLONAL	3	FALSE	0	0.156817447034236	1		199	543	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410401	63410401	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	130	189	0	ENST00000330258.3:c.2766G>T	p.Gln922His	p.Q922H	ENST00000330258	NM_152424.3	922	caG/caT	2/2	1	1	FACETS	0.853	0.776	0.933	1	0.992	1	CLONAL	3	FALSE	0	0.156817447034236	1		189	597	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184047	123184047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	43	162	0	ENST00000218089.9:c.905C>T	p.Ala302Val	p.A302V	ENST00000218089	NM_001042749.1	302	gCt/gTt	11/35	1	1	FACETS	0.773	0.649	0.909	1	0.96	1	CLONAL	2	FALSE	0	0.156817447034236	1		162	327	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870798	12870798	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	51	86	0	ENST00000228872.4:c.27del	p.Ser10AlafsTer32	p.S10Afs*32	ENST00000228872	NM_004064.3	9	Ggg/gg	1/3	1	2	FACETS	0.901	0.769	1	1	0.972	1	CLONAL	2	FALSE	1	0.156817447034236	2		86	361	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476295	88476295	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	79	329	0	ENST00000360948.2:c.1837del	p.Leu613SerfsTer8	p.L613Sfs*8	ENST00000360948	NM_001012338.2	613	Ctc/tc	15/19	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.156817447034236	2		329	779	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	36	162	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.892	0.747	1	0.892	0.747	1	CLONAL	1	TRUE	1	0.572309431143629	2		162	141	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912359	97912359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554302947	NA	P-0003223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	69	271	0	ENST00000289081.3:c.532G>A	p.Glu178Lys	p.E178K	ENST00000289081	NM_000136.2	178	Gag/Aag	7/15	1	2	FACETS	0.826	0.726	0.931	0.826	0.726	0.931	CLONAL	1	TRUE	1	0.572309431143629	2		271	292	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857481	68857481	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	85	336	0	ENST00000261769.5:c.2116C>T	p.Gln706Ter	p.Q706*	ENST00000261769	NM_004360.3	706	Caa/Taa	13/16	0.572309431143629	1	FACETS	0.959	0.864	1	0.959	0.864	1	CLONAL	1	TRUE	0	0.572309431143629	1		336	221	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0003224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	87	266	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	0.34646440036536	2		266	455	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	85	254	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.34646440036536	2		254	416	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023307	27023307	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0003224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	11	61	0	ENST00000324856.7:c.413C>G	p.Ser138Ter	p.S138*	ENST00000324856	NM_006015.4	138	tCa/tGa	1/20	0.34646440036536	1	FACETS	0.75	0.527	1	0.75	0.527	1	CLONAL	1	TRUE	0	0.34646440036536	1		61	70	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263850	133263850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	20	74	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	0.34646440036536	NA		74	138	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0003224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	141	451	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.34646440036536	2		451	631	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962631	38962631	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	93	364	0	ENST00000357387.3:c.1624G>C	p.Glu542Gln	p.E542Q	ENST00000357387	NM_152756.3	542	Gag/Cag	18/38	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.34646440036536	2		364	488	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168741	56168741	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775802110	NA	P-0003224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	128	285	0	ENST00000399503.3:c.1595G>A	p.Arg532Gln	p.R532Q	ENST00000399503	NM_005921.1	532	cGa/cAa	9/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.34646440036536	2		285	665	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131951767	131951767	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	73	279	0	ENST00000265335.6:c.3109G>C	p.Glu1037Gln	p.E1037Q	ENST00000265335		1037	Gaa/Caa	20/25	1	2	FACETS	0.994	0.873	1	0.994	0.873	1	CLONAL	1	TRUE	1	0.34646440036536	2		279	424	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478625	99478625	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	115	323	0	ENST00000268035.6:c.3267T>A	p.Ser1089Arg	p.S1089R	ENST00000268035	NM_000875.3	1089	agT/agA	17/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.34646440036536	2		323	559	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867192	68867192	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	82	208	0	ENST00000261769.5:c.2440-1G>A		p.X814_splice	ENST00000261769	NM_004360.3	814			0.34646440036536	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.34646440036536	1		208	294	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554307	29554307	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	102	241	0	ENST00000356175.3:c.2323G>A	p.Glu775Lys	p.E775K	ENST00000356175	NM_000267.3	775	Gag/Aag	19/57	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.34646440036536	2		241	566	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303651	30303651	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776712074	NA	P-0003224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	112	258	0	ENST00000262643.3:c.79C>T	p.Arg27Cys	p.R27C	ENST00000262643	NM_001238.2	27	Cgc/Tgc	3/12	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.34646440036536	2		258	512	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388695	31388695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	108	312	0	ENST00000328111.2:c.1960C>T	p.Leu654Phe	p.L654F	ENST00000328111	NM_006892.3	654	Ctc/Ttc	18/23	0.34646440036536	3	FACETS	1	0.943	1	0.536	0.482	0.594	CLONAL	1	TRUE	1	0.34646440036536	3		312	682	SUCCESS
AR	367	MSKCC	GRCh37	X	66766213	66766213	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs939465023	NA	P-0003224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	57	180	0	ENST00000374690.3:c.1225G>A	p.Gly409Arg	p.G409R	ENST00000374690	NM_000044.3	409	Ggg/Agg	1/8	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.34646440036536	2		180	321	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111524	8111525	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0003224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	98	295	0	ENST00000346208.3:c.1011dup	p.Cys338LeufsTer14	p.C338Lfs*14	ENST00000346208		337	gtc/gtCc	5/6	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.34646440036536	2		295	536	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0003247-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	166	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.296334467879368	1	FACETS	0.976	0.898	1	0.976	0.898	1	CLONAL	1	TRUE	0	0.36	1		326	775	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457168	25457168	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003247-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	85	309	0	ENST00000264709.3:c.2719G>T	p.Glu907Ter	p.E907*	ENST00000264709	NM_175629.2	907	Gag/Tag	23/23	0.1976520503774	1	FACETS	0.738	0.654	0.827	0.738	0.654	0.827	INDETERMINATE	1	TRUE	0	0.36	1		309	525	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984019	2984019	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003247-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	89	406	0	ENST00000396946.4:c.511G>T	p.Val171Leu	p.V171L	ENST00000396946	NM_032415.4	171	Gtg/Ttg	5/25	1	2	FACETS	0.697	0.618	0.782	0.697	0.618	0.782	SUBCLONAL	1	TRUE	1	0.36	2		406	709	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355224	81355224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745555932	NA	P-0003247-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	79	313	0	ENST00000222390.5:c.1150G>A	p.Asp384Asn	p.D384N	ENST00000222390	NM_000601.4	384	Gat/Aat	9/18	1	2	FACETS	0.657	0.578	0.742	0.657	0.578	0.742	SUBCLONAL	1	TRUE	1	0.36	2		313	668	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904946	101904947	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0003247-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	98	319	1	ENST00000374994.4:c.934_935delinsTT	p.Gly312Phe	p.G312F	ENST00000374994	NM_004612.2	312	GGt/TTt	5/9	0.296334467879368	1	FACETS	0.737	0.658	0.82	0.737	0.658	0.82	SUBCLONAL	1	TRUE	0	0.36	1		320	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577518	7577518	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519995	NA	P-0003247-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	36	255	0	ENST00000269305.4:c.763A>T	p.Ile255Phe	p.I255F	ENST00000269305	NM_001126112.2	255	Atc/Ttc	7/11	0.296334467879368	1	FACETS	0.522	0.431	0.624	0.522	0.431	0.624	SUBCLONAL	1	TRUE	0	0.36	1		255	314	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131408	17131408	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003247-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	47	247	0	ENST00000285071.4:c.44G>T	p.Gly15Val	p.G15V	ENST00000285071	NM_144997.5	15	gGc/gTc	4/14	0.296334467879368	1	FACETS	0.746	0.633	0.869	0.746	0.633	0.869	SUBCLONAL	1	TRUE	0	0.36	1		247	287	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019534	123019534	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003247-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	72	395	0	ENST00000355640.3:c.22G>A	p.Gly8Arg	p.G8R	ENST00000355640		8	Gga/Aga	2/7	0.269314586739023	1	FACETS	0.552	0.483	0.627	0.552	0.483	0.627	SUBCLONAL	1	TRUE	0	0.36	1		395	594	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0003286-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	228	293	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.546356003263994	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.591182426487943	1		293	513	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003286-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	75	162	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.972	0.863	1	0.972	0.863	1	CLONAL	1	TRUE	1	0.591182426487943	2		162	261	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571837	64571837	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003286-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	350	610	0	ENST00000312049.6:c.1802C>A	p.Ser601Tyr	p.S601Y	ENST00000312049	NM_130799.2	601	tCt/tAt	10/10	NA	2	FACETS	0.982	0.93	1			1	INDETERMINATE	1	TRUE	NA	0.591182426487943	2		610	1206	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047178	77047178	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003286-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3584	277	457	0	ENST00000356341.3:c.1366G>A	p.Glu456Lys	p.E456K	ENST00000356341	NM_002576.4	456	Gaa/Aaa	13/15	0.591182426487943	10	FACETS	0.817	0.762	0.874			1	CLONAL	1	TRUE	NA	0.591182426487943	10		457	3861	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070871	30070871	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs74315503	NA	P-0003286-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	222	367	0	ENST00000338641.4:c.1387G>T	p.Glu463Ter	p.E463*	ENST00000338641	NM_000268.3	463	Gag/Tag	13/16	0.546356003263994	1	FACETS	0.974	0.915	1	0.974	0.915	1	CLONAL	1	TRUE	0	0.591182426487943	1		367	543	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	98	271	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	0.750935116156672	2		271	218	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	459	573	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.750935116156672	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.750935116156672	2		574	575	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	29	203	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.205	0.164	0.251	0.205	0.164	0.251	SUBCLONAL	1	TRUE	1	0.750935116156672	2		203	377	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900239	101900239	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564161544	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	24	279	0	ENST00000374994.4:c.673C>T	p.Arg225Trp	p.R225W	ENST00000374994	NM_004612.2	225	Cgg/Tgg	4/9	0.15276832446733	3	FACETS	0.238	0.186	0.297	0.119	0.093	0.149	INDETERMINATE	1	TRUE	1	0.750935116156672	3		279	370	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36824337	36824337	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	216	301	0	ENST00000373129.3:c.198+1G>A		p.X66_splice	ENST00000373129	NM_032017.1	66			1	2	FACETS	0.999	0.936	1	0.999	0.936	1	CLONAL	1	TRUE	1	0.750935116156672	2		301	576	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204499828	204499828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	67	188	0	ENST00000367182.3:c.170G>A	p.Gly57Asp	p.G57D	ENST00000367182	NM_001278516.1	57	gGt/gAt	4/11	1	2	FACETS	0.879	0.777	0.985	0.879	0.777	0.985	CLONAL	1	TRUE	1	0.750935116156672	2		188	203	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662023	227662023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776903727	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	31	199	0	ENST00000305123.5:c.1432G>A	p.Ala478Thr	p.A478T	ENST00000305123	NM_005544.2	478	Gcc/Acc	1/2	0.732569435745957	1	FACETS	0.143	0.116	0.174	0.143	0.116	0.174	SUBCLONAL	1	TRUE	0	0.750935116156672	1		199	360	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940030	49940030	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	257	400	0	ENST00000296474.3:c.1013G>A	p.Ser338Asn	p.S338N	ENST00000296474	NM_002447.2	338	aGc/aAc	1/20	1	2	FACETS	0.871	0.818	0.924	0.871	0.818	0.924	CLONAL	1	TRUE	1	0.750935116156672	2		400	786	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021824	71021824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	90	218	0	ENST00000318789.4:c.1534G>A	p.Ala512Thr	p.A512T	ENST00000318789	NM_032682.5	512	Gca/Aca	18/21	1	2	FACETS	0.922	0.83	1	0.922	0.83	1	CLONAL	1	TRUE	1	0.750935116156672	2		218	260	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851843	134851843	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1305200941	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	67	254	0	ENST00000398015.3:c.1249C>T	p.Pro417Ser	p.P417S	ENST00000398015	NM_004441.4	417	Ccc/Tcc	5/16	0.586301530233999	3	FACETS	0.391	0.34	0.447			1	SUBCLONAL	1	TRUE	NA	0.750935116156672	3		254	627	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960114	134960114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	122	232	0	ENST00000398015.3:c.2471C>T	p.Pro824Leu	p.P824L	ENST00000398015	NM_004441.4	824	cCc/cTc	13/16	0.210157485767021	1	FACETS	0.681	0.625	0.738	0.681	0.625	0.738	INDETERMINATE	1	TRUE	0	0.750935116156672	1		232	298	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968291	134968291	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	180	307	0	ENST00000398015.3:c.2804C>T	p.Ala935Val	p.A935V	ENST00000398015	NM_004441.4	935	gCt/gTt	15/16	0.210157485767021	1	FACETS	0.563	0.523	0.604	0.563	0.523	0.604	INDETERMINATE	1	TRUE	0	0.750935116156672	1		307	532	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275272	142275272	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	120	289	0	ENST00000350721.4:c.2031C>G	p.Ile677Met	p.I677M	ENST00000350721	NM_001184.3	677	atC/atG	9/47	0.210157485767021	1	FACETS	0.672	0.616	0.729	0.672	0.616	0.729	INDETERMINATE	1	TRUE	0	0.750935116156672	1		289	297	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181384	185181384	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253585116	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	100	279	0	ENST00000265026.3:c.1325G>A	p.Ser442Asn	p.S442N	ENST00000265026	NM_004721.4	442	aGt/aAt	8/14	0.210157485767021	1	FACETS	0.566	0.512	0.621	0.566	0.512	0.621	INDETERMINATE	1	TRUE	0	0.750935116156672	1		279	294	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803616	1803616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779284979	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	107	149	1	ENST00000260795.2:c.794C>T	p.Ala265Val	p.A265V	ENST00000260795		265	gCg/gTg	6/17	1	2	FACETS	0.528	0.475	0.583	0.528	0.475	0.583	SUBCLONAL	1	TRUE	1	0.750935116156672	2		150	540	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968673	55968673	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs755067067	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	17	186	0	ENST00000263923.4:c.1990C>T	p.Arg664Cys	p.R664C	ENST00000263923	NM_002253.2	664	Cgt/Tgt	14/30	1	2	FACETS	0.158	0.117	0.206	0.158	0.117	0.206	SUBCLONAL	1	TRUE	1	0.750935116156672	2		186	287	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549883	187549883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs186220887	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	10	192	0	ENST00000441802.2:c.4358G>A	p.Arg1453His	p.R1453H	ENST00000441802	NM_005245.3	1453	cGt/cAt	8/27	0.750935116156672	1	FACETS	0.112	0.075	0.157	0.112	0.075	0.157	SUBCLONAL	1	TRUE	0	0.750935116156672	1		192	149	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260597	1260597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	207	237	0	ENST00000310581.5:c.2962G>A	p.Asp988Asn	p.D988N	ENST00000310581	NM_198253.2	988	Gat/Aat	12/16	0.750935116156672	3	FACETS	0.982	0.914	1	0.491	0.457	0.527	CLONAL	1	TRUE	1	0.750935116156672	3		237	772	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293917	1293917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	202	216	0	ENST00000310581.5:c.1084G>A	p.Glu362Lys	p.E362K	ENST00000310581	NM_198253.2	362	Gag/Aag	2/16	0.750935116156672	3	FACETS	1	0.986	1	0.612	0.57	0.654	CLONAL	1	TRUE	1	0.750935116156672	3		216	605	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524295	176524295	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	43	220	0	ENST00000292408.4:c.2156A>G	p.Tyr719Cys	p.Y719C	ENST00000292408	NM_213647.1	719	tAc/tGc	17/18	0.750935116156672	1	FACETS	0.184	0.154	0.218	0.184	0.154	0.218	SUBCLONAL	1	TRUE	0	0.750935116156672	1		220	388	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176618958	176618958	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	11	312	0	ENST00000439151.2:c.1001G>A	p.Arg334His	p.R334H	ENST00000439151	NM_022455.4	334	cGc/cAc	3/23	0.750935116156672	1	FACETS	0.086	0.059	0.119	0.086	0.059	0.119	SUBCLONAL	1	TRUE	0	0.750935116156672	1		312	213	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708981	117708981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	117	283	0	ENST00000368508.3:c.1976C>T	p.Pro659Leu	p.P659L	ENST00000368508	NM_002944.2	659	cCc/cTc	13/43	0.214920663547397	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.750935116156672	0		283	319	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715882	117715882	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	122	240	0	ENST00000368508.3:c.876G>A	p.Trp292Ter	p.W292*	ENST00000368508	NM_002944.2	292	tgG/tgA	9/43	0.214920663547397	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.750935116156672	0		240	310	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527697	157527697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745372243	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	56	216	0	ENST00000346085.5:c.5422C>T	p.Arg1808Cys	p.R1808C	ENST00000346085	NM_020732.3	1808	Cgt/Tgt	20/20	0.121480093591953	4	FACETS	0.481	0.412	0.556	0.24	0.206	0.278	INDETERMINATE	1	TRUE	2	0.750935116156672	4		216	543	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971352	13971352	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	101	184	0	ENST00000405192.2:c.577C>T	p.Pro193Ser	p.P193S	ENST00000405192	NM_001163147.1	193	Ccc/Tcc	8/12	0.750935116156672	3	FACETS	0.794	0.713	0.879			1	SUBCLONAL	1	TRUE	NA	0.750935116156672	3		184	466	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455073	50455073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	130	193	1	ENST00000331340.3:c.620G>A	p.Gly207Asp	p.G207D	ENST00000331340	NM_006060.4	207	gGc/gAc	6/8	0.750935116156672	3	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.750935116156672	3		194	375	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92462489	92462489	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	271	276	0	ENST00000265734.4:c.149G>A	p.Gly50Asp	p.G50D	ENST00000265734	NM_001259.6	50	gGc/gAc	2/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.750935116156672	2		276	683	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850343	128850343	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1367686794	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	217	201	1	ENST00000249373.3:c.1606G>A	p.Val536Ile	p.V536I	ENST00000249373	NM_005631.4	536	Gtc/Atc	9/12	1	2	FACETS	0.991	0.929	1	0.991	0.929	1	CLONAL	1	TRUE	1	0.750935116156672	2		202	583	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864281	117864281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	107	362	1	ENST00000297338.2:c.1376G>A	p.Ser459Asn	p.S459N	ENST00000297338	NM_006265.2	459	aGc/aAc	11/14	0.750935116156672	5	FACETS	0.895	0.804	0.992	0.224	0.201	0.248	CLONAL	1	TRUE	1	0.750935116156672	5		363	677	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739596	145739596	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773620376	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	191	204	0	ENST00000428558.2:c.1855C>T	p.Pro619Ser	p.P619S	ENST00000428558	NM_004260.3	619	Ccc/Tcc	11/22	0.750935116156672	5	FACETS	1	0.975	1	0.281	0.26	0.304	CLONAL	1	TRUE	1	0.750935116156672	5		204	961	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090805	5090805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	108	268	0	ENST00000381652.3:c.2953G>A	p.Glu985Lys	p.E985K	ENST00000381652	NM_004972.3	985	Gag/Aag	22/25	NA	2	FACETS	1	0.944	1			1	INDETERMINATE	1	TRUE	NA	0.750935116156672	2		268	275	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317273	87317273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	130	279	0	ENST00000277120.3:c.298G>A	p.Asp100Asn	p.D100N	ENST00000277120		100	Gat/Aat	4/19	0.15276832446733	3	FACETS	1	0.988	1	0.749	0.689	0.809	INDETERMINATE	1	TRUE	1	0.750935116156672	3		279	318	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772715	135772715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	147	336	0	ENST00000298552.3:c.2831C>T	p.Ala944Val	p.A944V	ENST00000298552	NM_001162426.1	944	gCa/gTa	22/23	0.15276832446733	3	FACETS	1	0.989	1	0.736	0.68	0.792	INDETERMINATE	1	TRUE	1	0.750935116156672	3		336	366	SUCCESS
EED	8726	MSKCC	GRCh37	11	85963244	85963244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	83	198	0	ENST00000263360.6:c.322G>A	p.Gly108Arg	p.G108R	ENST00000263360	NM_003797.3	108	Gga/Aga	3/12	1	2	FACETS	0.895	0.802	0.991	0.895	0.802	0.991	CLONAL	1	TRUE	1	0.750935116156672	2		198	247	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360878	118360878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	98	218	0	ENST00000534358.1:c.4610G>A	p.Gly1537Glu	p.G1537E	ENST00000534358	NM_005933.3	1537	gGa/gAa	13/36	NA	2	FACETS	0.909	0.823	0.999			1	INDETERMINATE	1	TRUE	NA	0.750935116156672	2		218	287	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375167	118375167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	106	282	0	ENST00000534358.1:c.8560G>A	p.Asp2854Asn	p.D2854N	ENST00000534358	NM_005933.3	2854	Gac/Aac	27/36	NA	2	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.750935116156672	2		282	249	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133234555	133234555	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs757323968	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	19	167	0	ENST00000320574.5:c.3277G>A	p.Ala1093Thr	p.A1093T	ENST00000320574	NM_006231.2	1093	Gcc/Acc	27/49	1	2	FACETS	0.178	0.134	0.228	0.178	0.134	0.228	SUBCLONAL	1	TRUE	1	0.750935116156672	2		167	285	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678383	88678383	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	139	354	0	ENST00000360948.2:c.1153G>A	p.Gly385Ser	p.G385S	ENST00000360948	NM_001012338.2	385	Ggc/Agc	9/19	0.15276832446733	3	FACETS	1	0.955	1	0.532	0.487	0.577	INDETERMINATE	1	TRUE	1	0.750935116156672	3		354	479	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358399	91358399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	57	299	0	ENST00000355112.3:c.4144G>A	p.Ala1382Thr	p.A1382T	ENST00000355112	NM_000057.2	1382	Gcc/Acc	22/22	0.15276832446733	3	FACETS	0.765	0.662	0.875	0.382	0.331	0.438	INDETERMINATE	1	TRUE	1	0.750935116156672	3		299	273	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442820	99442820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148662051	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	20	216	0	ENST00000268035.6:c.1217G>A	p.Arg406His	p.R406H	ENST00000268035	NM_000875.3	406	cGc/cAc	5/21	0.15276832446733	3	FACETS	0.233	0.177	0.297	0.116	0.088	0.149	INDETERMINATE	1	TRUE	1	0.750935116156672	3		216	315	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100447	2100447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397515045	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	156	271	0	ENST00000219476.3:c.185G>A	p.Gly62Glu	p.G62E	ENST00000219476	NM_000548.3	62	gGg/gAg	3/42	1	2	FACETS	0.973	0.9	1	0.973	0.9	1	CLONAL	1	TRUE	1	0.750935116156672	2		271	427	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138319	2138319	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373365980	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	73	294	2	ENST00000219476.3:c.5252G>A	p.Arg1751His	p.R1751H	ENST00000219476	NM_000548.3	1751	cGc/cAc	41/42	1	2	FACETS	0.328	0.287	0.372	0.328	0.287	0.372	SUBCLONAL	1	TRUE	1	0.750935116156672	2		296	593	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348785	11348785	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	111	107	0	ENST00000332029.2:c.551C>T	p.Ala184Val	p.A184V	ENST00000332029	NM_003745.1	184	gCc/gTc	2/2	1	2	FACETS	0.995	0.908	1	0.995	0.908	1	CLONAL	1	TRUE	1	0.750935116156672	2		107	297	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041738	14041738	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	154	268	0	ENST00000311895.7:c.2285A>G	p.Asp762Gly	p.D762G	ENST00000311895	NM_005236.2	762	gAc/gGc	11/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.750935116156672	2		268	370	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647091	23647091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	103	290	1	ENST00000261584.4:c.776G>A	p.Ser259Asn	p.S259N	ENST00000261584	NM_024675.3	259	aGt/aAt	4/13	1	2	FACETS	0.998	0.907	1	0.998	0.907	1	CLONAL	1	TRUE	1	0.750935116156672	2		291	275	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56870603	56870603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	119	346	0	ENST00000308159.5:c.1873G>A	p.Ala625Thr	p.A625T	ENST00000308159	NM_014669.4	625	Gca/Aca	17/22	1	2	FACETS	0.911	0.832	0.992	0.911	0.832	0.992	CLONAL	1	TRUE	1	0.750935116156672	2		346	348	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15976785	15976785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	125	403	0	ENST00000268712.3:c.3769G>A	p.Gly1257Arg	p.G1257R	ENST00000268712	NM_006311.3	1257	Ggg/Agg	28/46	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.750935116156672	2		403	292	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17117087	17117087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764899882	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	31	295	0	ENST00000285071.4:c.1622C>T	p.Ala541Val	p.A541V	ENST00000285071	NM_144997.5	541	gCg/gTg	14/14	1	2	FACETS	0.139	0.112	0.17	0.139	0.112	0.17	SUBCLONAL	1	TRUE	1	0.750935116156672	2		295	595	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359678	40359678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1188688435	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	168	426	0	ENST00000293328.3:c.1975C>T	p.Arg659Cys	p.R659C	ENST00000293328	NM_012448.3	659	Cgc/Tgc	16/19	0.469554269922744	1	FACETS	0.711	0.662	0.761	0.711	0.662	0.761	SUBCLONAL	1	TRUE	0	0.750935116156672	1		426	393	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805535	46805535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1405620801	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	274	484	0	ENST00000290295.7:c.421G>A	p.Ala141Thr	p.A141T	ENST00000290295	NM_006361.5	141	Gcc/Acc	1/2	0.469554269922744	1	FACETS	0.678	0.641	0.716	0.678	0.641	0.716	SUBCLONAL	1	TRUE	0	0.750935116156672	1		484	672	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740619	58740619	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1476011414	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	129	398	0	ENST00000305921.3:c.1524G>A	p.Met508Ile	p.M508I	ENST00000305921	NM_003620.3	508	atG/atA	6/6	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.750935116156672	2		398	335	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278099	15278099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139983430	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	44	339	0	ENST00000263388.2:c.5323G>A	p.Ala1775Thr	p.A1775T	ENST00000263388	NM_000435.2	1775	Gca/Aca	29/33	0.15276832446733	3	FACETS	0.213	0.178	0.252	0.106	0.089	0.126	INDETERMINATE	1	TRUE	1	0.750935116156672	3		339	757	SUCCESS
AXL	558	MSKCC	GRCh37	19	41759510	41759510	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	210	274	0	ENST00000301178.4:c.1933C>G	p.Pro645Ala	p.P645A	ENST00000301178	NM_021913.4	645	Ccc/Gcc	17/20	0.15276832446733	3	FACETS	0.774	0.726	0.822	0.774	0.726	0.822	INDETERMINATE	2	TRUE	1	0.750935116156672	3		274	497	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796290	42796290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	297	287	0	ENST00000575354.2:c.2939C>T	p.Pro980Leu	p.P980L	ENST00000575354	NM_015125.3	980	cCc/cTc	12/20	0.15276832446733	3	FACETS	1	0.993	1	0.686	0.649	0.724	INDETERMINATE	1	TRUE	1	0.750935116156672	3		287	793	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902741	50902741	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	228	383	0	ENST00000440232.2:c.316G>A	p.Gly106Ser	p.G106S	ENST00000440232	NM_002691.3	106	Ggc/Agc	3/27	0.15276832446733	3	FACETS	1	0.992	1	0.7	0.657	0.743	INDETERMINATE	1	TRUE	1	0.750935116156672	3		383	597	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905772	50905772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854557	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	57	342	1	ENST00000440232.2:c.820G>A	p.Ala274Thr	p.A274T	ENST00000440232	NM_002691.3	274	Gcc/Acc	7/27	0.15276832446733	3	FACETS	0.238	0.203	0.276	0.119	0.101	0.138	INDETERMINATE	1	TRUE	1	0.750935116156672	3		343	878	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912874	50912874	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	317	386	1	ENST00000440232.2:c.2105G>A	p.Gly702Asp	p.G702D	ENST00000440232	NM_002691.3	702	gGc/gAc	17/27	0.15276832446733	3	FACETS	1	0.994	1	0.728	0.69	0.766	INDETERMINATE	1	TRUE	1	0.750935116156672	3		387	798	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264634	46264634	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	118	271	0	ENST00000371998.3:c.1505-1G>A		p.X502_splice	ENST00000371998		502			0.5461935865438	1	FACETS	0.55	0.501	0.6	0.55	0.501	0.6	SUBCLONAL	1	TRUE	0	0.750935116156672	1		271	357	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485014	57485014	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	97	220	0	ENST00000371085.3:c.848G>A	p.Arg283His	p.R283H	ENST00000371085	NM_000516.4	283	cGc/cAc	11/13	NA	2	FACETS	0.51	0.456	0.566			1	INDETERMINATE	1	TRUE	NA	0.750935116156672	2		220	507	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755389	39755389	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	111	260	0	ENST00000288319.7:c.1376G>A	p.Gly459Asp	p.G459D	ENST00000288319	NM_182918.3	459	gGt/gAt	10/10	1	2	FACETS	0.904	0.823	0.988	0.904	0.823	0.988	CLONAL	1	TRUE	1	0.750935116156672	2		260	327	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30090768	30090768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293851600	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	240	329	0	ENST00000338641.4:c.1765G>A	p.Val589Met	p.V589M	ENST00000338641	NM_000268.3	589	Gtg/Atg	16/16	1	2	FACETS	0.925	0.868	0.983	0.925	0.868	0.983	CLONAL	1	TRUE	1	0.750935116156672	2		329	691	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019696	123019696	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147946593	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	18	139	0	ENST00000355640.3:c.184C>T	p.Arg62Trp	p.R62W	ENST00000355640		62	Cgg/Tgg	2/7	0.2939738318328	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	NA	0.750935116156672	0		139	138	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937914	76937914	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	131	153	0	ENST00000373344.5:c.2834del	p.Lys945ArgfsTer25	p.K945Rfs*25	ENST00000373344	NM_000489.3	945	aAg/ag	9/35	0.2939738318328	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	NA	0.750935116156672	0		153	169	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0003303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	30	423	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.681	0.547	0.834	0.681	0.547	0.834	SUBCLONAL	1	TRUE	1	0.14	2		423	629	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0003303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	42	649	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	1	2	FACETS	0.819	0.682	0.971	0.819	0.682	0.971	CLONAL	1	TRUE	1	0.14	2		649	733	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612975	228612975	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	36	470	0	ENST00000366696.1:c.52C>A	p.Arg18Ser	p.R18S	ENST00000366696	NM_003493.2	18	Cgc/Agc	1/1	0.3	2	FACETS	1	0.851	1			1	CLONAL	1	TRUE	NA	0.14	2		470	494	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972870	25972870	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	32	474	0	ENST00000435504.4:c.1555G>C	p.Glu519Gln	p.E519Q	ENST00000435504		519	Gaa/Caa	12/13	1	2	FACETS	0.805	0.652	0.978	0.805	0.652	0.978	CLONAL	1	TRUE	1	0.14	2		474	568	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036987	180036987	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	43	516	0	ENST00000261937.6:c.3725G>C	p.Arg1242Thr	p.R1242T	ENST00000261937	NM_182925.4	1242	aGa/aCa	28/30	1	2	FACETS	1	0.839	1	1	0.839	1	CLONAL	1	TRUE	1	0.14	2		516	612	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453179	140453179	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913340	NA	P-0003303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	27	280	0	ENST00000288602.6:c.1756G>A	p.Glu586Lys	p.E586K	ENST00000288602	NM_004333.4	586	Gaa/Aaa	15/18	1	2	FACETS	0.938	0.746	1	0.938	0.746	1	CLONAL	1	TRUE	1	0.14	2		280	411	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112395	115112395	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	17	190	0	ENST00000257566.3:c.1345C>A	p.Leu449Met	p.L449M	ENST00000257566	NM_016569.3	449	Ctg/Atg	7/8	1	2	FACETS	1	0.762	1	1	0.762	1	CLONAL	1	TRUE	1	0.14	2		190	238	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0003317-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	1929	318	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.317997869265062	24	FACETS	0.982	0.968	0.995			1	CLONAL	22	TRUE	NA	0.317997869265062	24		318	2527	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0003317-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	217	552	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.308573566566722	2	FACETS	0.953	0.89	1	0.953	0.89	1	CLONAL	2	TRUE	0	0.317997869265062	2		552	716	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300489	11300489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1350423605	NA	P-0003317-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	76	455	0	ENST00000361445.4:c.1657C>T	p.Arg553Cys	p.R553C	ENST00000361445	NM_004958.3	553	Cgc/Tgc	11/58	0.305460794267301	3	FACETS	0.916	0.804	1	0.458	0.402	0.518	CLONAL	1	TRUE	1	0.317997869265062	3		455	605	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225628	225628	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876660259	NA	P-0003317-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	27	217	0	ENST00000264932.6:c.407A>T	p.Gln136Leu	p.Q136L	ENST00000264932	NM_004168.2	136	cAg/cTg	4/15	0.317997869265062	5	FACETS	0.621	0.494	0.766	0.207	0.164	0.256	SUBCLONAL	1	TRUE	2	0.317997869265062	5		217	404	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983495	90983495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003317-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	105	284	0	ENST00000265433.3:c.608C>T	p.Pro203Leu	p.P203L	ENST00000265433	NM_002485.4	203	cCa/cTa	6/16	0.308891913585916	4	FACETS	1	0.976	1	0.65	0.582	0.721	CLONAL	1	TRUE	2	0.317997869265062	4		284	670	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004673	16004673	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003317-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	110	603	0	ENST00000268712.3:c.2581G>C	p.Val861Leu	p.V861L	ENST00000268712	NM_006311.3	861	Gtg/Ctg	20/46	0.308573566566722	2	FACETS	0.987	0.888	1	0.493	0.444	0.546	CLONAL	1	TRUE	0	0.317997869265062	2		603	701	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039841	47039847	+	frameshift_variant	Frame_Shift_Del	DEL	GTCGCAT	GTCGCAT	-	novel	NA	P-0003317-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	152	540	1	ENST00000377604.3:c.1184_1190del	p.Ser395ThrfsTer88	p.S395Tfs*88	ENST00000377604	NM_001204468.1	395	aGTCGCATc/ac	12/24	0.159994733610767	2	FACETS	0.753	0.691	0.817	0.753	0.691	0.817	INDETERMINATE	2	TRUE	0	0.317997869265062	2		541	635	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162134	47162134	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003323-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	16	254	0	ENST00000409792.3:c.3992T>C	p.Leu1331Pro	p.L1331P	ENST00000409792	NM_014159.6	1331	cTa/cCa	3/21	0.207864760432396	1	FACETS	0.38	0.282	0.494	0.38	0.282	0.494	INDETERMINATE	1	TRUE	0	0.438662377398131	1		254	150	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878227	151878227	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	271	200	0	ENST00000262189.6:c.6718A>G	p.Arg2240Gly	p.R2240G	ENST00000262189	NM_170606.2	2240	Aga/Gga	36/59	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.94717642350494	2		200	569	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021665	31021665	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	39	131	0	ENST00000375687.4:c.1664T>G	p.Val555Gly	p.V555G	ENST00000375687	NM_015338.5	555	gTt/gGt	12/13	0.3	3	FACETS	0.656	0.543	0.782	0.328	0.271	0.391	SUBCLONAL	1	TRUE	1	0.24	3		131	555	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574023	7574024	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0003365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	133	314	0	ENST00000269305.4:c.1003dup	p.Arg335ProfsTer2	p.R335Pfs*2	ENST00000269305	NM_001126112.2	335	cgt/cCgt	10/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.24	2		314	905	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0003367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	102	225	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.285144226751538	3	FACETS	1	0.973	1	0.632	0.566	0.701	CLONAL	1	FALSE	1	0.3	3		225	619	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003375-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	62	162	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.524318044330765	1	FACETS	0.899	0.791	1	0.899	0.791	1	CLONAL	1	TRUE	0	0.524318044330765	1		162	194	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003375-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	135	248	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.22742804876426	1	FACETS	0.636	0.58	0.695	0.636	0.58	0.695	INDETERMINATE	1	TRUE	0	0.524318044330765	1		248	597	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182557	99182557	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003375-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	129	277	0	ENST00000074304.5:c.2360A>G	p.Gln787Arg	p.Q787R	ENST00000074304	NM_001134224.1	787	cAg/cGg	22/26	0.167587572829409	1	FACETS	0.782	0.714	0.853	0.782	0.714	0.853	INDETERMINATE	1	TRUE	0	0.524318044330765	1		277	464	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223439	53223439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1322675151	NA	P-0003375-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	198	416	1	ENST00000375401.3:c.3920G>A	p.Arg1307Gln	p.R1307Q	ENST00000375401	NM_004187.3	1307	cGg/cAg	23/26	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.524318044330765	2		417	680	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913499	NA	P-0003428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	155	229	0	ENST00000345146.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000345146	NM_005896.2	132	Cgt/Ggt	4/10	0.190197314134445	1	FACETS	0.983	0.915	1	1	0.994	1	CLONAL	4	TRUE	0	0.21	1		229	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786201059	NA	P-0003428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	413	392	1	ENST00000269305.4:c.856G>C	p.Glu286Gln	p.E286Q	ENST00000269305	NM_001126112.2	286	Gaa/Caa	8/11	0.3	3	FACETS	0.986	0.962	1			1	CLONAL	9	TRUE	NA	0.21	3		393	490	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937833	76937836	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0003428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	236	446	0	ENST00000373344.5:c.2912_2915del	p.Lys971ThrfsTer31	p.K971Tfs*31	ENST00000373344	NM_000489.3	971	aAAGAc/ac	9/35	0.121269591710922	0	FACETS	0.81	0.763	0.858			1	INDETERMINATE	4	TRUE	0	0.21	0		446	548	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294078	1294078	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	12	208	0	ENST00000310581.5:c.923del	p.Pro308HisfsTer43	p.P308Hfs*43	ENST00000310581	NM_198253.2	308	cCa/ca	2/16	1	2	FACETS	0.49	0.344	0.67	0.49	0.344	0.67	SUBCLONAL	1	TRUE	1	0.21	2		208	233	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003429-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	22	456	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.977	0.784	1	1	0.948	1	CLONAL	2	TRUE	1	0.335921698623644	2		456	67	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0003429-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	27	531	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.335921698623644	1	FACETS	0.643	0.515	0.787	0.643	0.515	0.787	SUBCLONAL	1	TRUE	0	0.335921698623644	1		531	208	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512376	149512376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746410632	NA	P-0003429-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	47	512	1	ENST00000261799.4:c.1064G>A	p.Arg355His	p.R355H	ENST00000261799	NM_002609.3	355	cGc/cAc	7/23	1	2	FACETS	0.864	0.732	1	0.864	0.732	1	CLONAL	1	TRUE	1	0.335921698623644	2		513	324	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416600	49416600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003429-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	39	400	0	ENST00000301067.7:c.16111G>A	p.Glu5371Lys	p.E5371K	ENST00000301067	NM_003482.3	5371	Gag/Aag	51/54	1	2	FACETS	0.803	0.669	0.952	0.803	0.669	0.952	CLONAL	1	TRUE	1	0.335921698623644	2		400	289	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796085	78796085	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003429-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	53	451	1	ENST00000306801.3:c.975G>C	p.Trp325Cys	p.W325C	ENST00000306801	NM_020761.2	325	tgG/tgC	8/34	1	2	FACETS	0.879	0.753	1	0.879	0.753	1	CLONAL	1	TRUE	1	0.335921698623644	2		452	359	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796958	78796958	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003429-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	53	570	1	ENST00000306801.3:c.1071G>A	p.Met357Ile	p.M357I	ENST00000306801	NM_020761.2	357	atG/atA	9/34	1	2	FACETS	0.83	0.711	0.961	0.83	0.711	0.961	CLONAL	1	TRUE	1	0.335921698623644	2		571	380	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678783	52678784	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0003429-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	61	537	0	ENST00000394830.3:c.835dup	p.Ile279AsnfsTer8	p.I279Nfs*8	ENST00000394830	NM_018313.4	279	ata/aAta	9/30	0.335921698623644	1	FACETS	0.846	0.734	0.967	0.846	0.734	0.967	CLONAL	1	TRUE	0	0.335921698623644	1		537	357	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0003447-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	47	212	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.881	1	1	0.98	1	CLONAL	3	FALSE	1	0.149146784066673	2		213	203	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0003447-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	104	573	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.149146784066673	5	FACETS	1	0.937	1			1	CLONAL	6	FALSE	NA	0.149146784066673	5		574	274	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0003447-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	109	419	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.149146784066673	5	FACETS	1	0.95	1			1	CLONAL	6	FALSE	NA	0.149146784066673	5		421	281	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584475	187584475	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1163622953	NA	P-0003447-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	23	290	0	ENST00000441802.2:c.3558C>A	p.Phe1186Leu	p.F1186L	ENST00000441802	NM_005245.3	1186	ttC/ttA	3/27	0.149146784066673	0	FACETS	0.951	0.75	1			1	CLONAL	2	FALSE	0	0.149146784066673	0		290	138	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814253	76814253	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003447-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	64	258	0	ENST00000373344.5:c.6391C>T	p.Arg2131Ter	p.R2131*	ENST00000373344	NM_000489.3	2131	Cga/Tga	29/35	0.149146784066673	0	FACETS	0.955	0.881	1			1	CLONAL	9	FALSE	NA	0.149146784066673	0		258	85	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434455	121434455	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003451-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	163	521	0	ENST00000257555.6:c.1219T>A	p.Ser407Thr	p.S407T	ENST00000257555		407	Tca/Aca	6/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.362782799042477	2		521	773	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0003457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	209	261	0	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	NA	2	FACETS	1	0.946	1			1	INDETERMINATE	1	TRUE	NA	0.784974870122163	2		261	527	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0003474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	134	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	1	0.931	1			1	INDETERMINATE	1	TRUE	NA	0.421638512572439	2		326	620	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	78	138	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	0.421638512572439	2		138	354	SUCCESS
APC	324	MSKCC	GRCh37	5	112173975	112173975	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	105	192	0	ENST00000257430.4:c.2684C>A	p.Ser895Ter	p.S895*	ENST00000257430	NM_000038.5	895	tCa/tAa	16/16	1	2	FACETS	0.969	0.872	1	0.969	0.872	1	CLONAL	1	TRUE	1	0.421638512572439	2		192	514	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393168	393168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	117	198	0	ENST00000380956.4:c.16G>A	p.Gly6Ser	p.G6S	ENST00000380956	NM_001195286.1	6	Ggc/Agc	2/9	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.421638512572439	2		198	393	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371710	45371710	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0003474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	128	313	0	ENST00000262160.6:c.1280+1G>T		p.X427_splice	ENST00000262160	NM_005901.5	427			0.236632934102661	0	FACETS	0.773	0.706	0.843			1	INDETERMINATE	1	TRUE	0	0.421638512572439	0		313	454	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354597	70354597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767396596	NA	P-0003474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	160	399	0	ENST00000374080.3:c.4762G>A	p.Val1588Met	p.V1588M	ENST00000374080		1588	Gtg/Atg	35/45	0.306143616865751	1	FACETS	0.693	0.636	0.753	0.693	0.636	0.753	SUBCLONAL	1	TRUE	0	0.421638512572439	1		399	864	SUCCESS
APC	324	MSKCC	GRCh37	5	112175636	112175636	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0003474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	209	375	0	ENST00000257430.4:c.4346del	p.Lys1449SerfsTer24	p.K1449Sfs*24	ENST00000257430	NM_000038.5	1449	Aag/ag	16/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.421638512572439	2		375	946	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	37	162	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.765898981162151	4	FACETS	0.934	0.78	1	0.311	0.26	0.368	CLONAL	1	TRUE	1	0.786128128604748	4		162	180	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566418	139566418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374930413	NA	P-0003485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	59	300	0	ENST00000308874.7:c.677C>T	p.Ser226Leu	p.S226L	ENST00000308874		226	tCg/tTg	9/10	0.786128128604748	4	FACETS	0.9	0.78	1	0.45	0.39	0.514	CLONAL	1	TRUE	2	0.786128128604748	4		300	298	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347974	347974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140190126	NA	P-0003485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	69	475	0	ENST00000262320.3:c.1532C>T	p.Ser511Leu	p.S511L	ENST00000262320	NM_003502.3	511	tCg/tTg	6/11	0.723663054988394	3	FACETS	0.843	0.741	0.951	0.422	0.37	0.476	CLONAL	1	TRUE	1	0.786128128604748	3		475	290	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343697	118343697	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	58	358	0	ENST00000534358.1:c.1823G>A	p.Arg608Gln	p.R608Q	ENST00000534358	NM_005933.3	608	cGa/cAa	3/36	1	2	FACETS	0.727	0.634	0.825	0.727	0.634	0.825	SUBCLONAL	1	TRUE	1	0.786128128604748	2		358	203	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910744	29910744	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0003485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	77	443	1	ENST00000376809.5:c.284C>G	p.Ser95Ter	p.S95*	ENST00000376809	NM_002116.7	95	tCa/tGa	2/8	1	2	FACETS	0.975	0.873	1	0.975	0.873	1	CLONAL	1	TRUE	1	0.786128128604748	2		444	201	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089640	27089640	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	98	474	1	ENST00000324856.7:c.2596C>T	p.Arg866Trp	p.R866W	ENST00000324856	NM_006015.4	866	Cgg/Tgg	8/20	1	2	FACETS	0.934	0.846	1	0.934	0.846	1	CLONAL	1	TRUE	1	0.786128128604748	2		475	267	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248372	212248372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	71	377	0	ENST00000342788.4:c.3895C>T	p.Pro1299Ser	p.P1299S	ENST00000342788	NM_005235.2	1299	Cca/Tca	28/28	0.778484233620876	2	FACETS	1	0.909	1	0.51	0.455	0.566	CLONAL	1	TRUE	0	0.786128128604748	2		377	177	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447111	187447111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	95	336	0	ENST00000232014.4:c.1082C>T	p.Ser361Phe	p.S361F	ENST00000232014	NM_001130845.1	361	tCc/tTc	5/10	0.765898981162151	4	FACETS	1	0.956	1	0.375	0.336	0.415	CLONAL	1	TRUE	1	0.786128128604748	4		336	384	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500844	149500844	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	85	419	0	ENST00000261799.4:c.2386C>G	p.Pro796Ala	p.P796A	ENST00000261799	NM_002609.3	796	Cca/Gca	17/23	0.786128128604748	3	FACETS	1	0.895	1	0.5	0.447	0.556	CLONAL	1	TRUE	1	0.786128128604748	3		419	301	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271297	26271297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	92	961	0	ENST00000305910.3:c.316G>A	p.Glu106Lys	p.E106K	ENST00000305910	NM_003534.2	106	Gag/Aag	1/1	1	2	FACETS	0.857	0.773	0.945	0.857	0.773	0.945	CLONAL	1	TRUE	1	0.786128128604748	2		961	273	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915961	127915961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	103	703	1	ENST00000373547.4:c.520G>A	p.Asp174Asn	p.D174N	ENST00000373547	NM_002721.4	174	Gat/Aat	6/7	0.786128128604748	4	FACETS	0.947	0.852	1	0.474	0.426	0.524	CLONAL	1	TRUE	2	0.786128128604748	4		704	494	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41962024	41962024	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0003485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	99	779	0	ENST00000219905.7:c.932C>G	p.Ser311Ter	p.S311*	ENST00000219905	NM_001164273.1	311	tCa/tGa	2/24	0.196039058903872	5	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.786128128604748	5		779	466	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052693	42052693	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	114	648	0	ENST00000219905.7:c.7364C>T	p.Ser2455Phe	p.S2455F	ENST00000219905	NM_001164273.1	2455	tCt/tTt	20/24	0.196039058903872	5	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.786128128604748	5		648	490	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348032	348032	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372115709	NA	P-0003485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	78	369	0	ENST00000262320.3:c.1474C>T	p.Arg492Cys	p.R492C	ENST00000262320	NM_003502.3	492	Cgc/Tgc	6/11	0.723663054988394	3	FACETS	0.987	0.878	1	0.494	0.439	0.551	CLONAL	1	TRUE	1	0.786128128604748	3		369	280	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348188	348188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1266269685	NA	P-0003485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	58	218	0	ENST00000262320.3:c.1318C>T	p.Pro440Ser	p.P440S	ENST00000262320	NM_003502.3	440	Ccc/Tcc	6/11	0.723663054988394	3	FACETS	0.918	0.799	1	0.459	0.399	0.522	CLONAL	1	TRUE	1	0.786128128604748	3		218	224	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051645	13051645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375135016	NA	P-0003485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	118	809	2	ENST00000316448.5:c.904G>A	p.Asp302Asn	p.D302N	ENST00000316448	NM_004343.3	302	Gat/Aat	7/9	0.786128128604748	3	FACETS	1	0.936	1	0.518	0.471	0.566	CLONAL	1	TRUE	1	0.786128128604748	3		811	404	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911589	39911589	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768919602	NA	P-0003485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	88	518	0	ENST00000378444.4:c.5041C>T	p.Arg1681Cys	p.R1681C	ENST00000378444	NM_001123385.1	1681	Cgc/Tgc	15/15	0.352315657243335	3	FACETS	0.894	0.799	0.993	0.298	0.266	0.331	INDETERMINATE	1	TRUE	0	0.786128128604748	3		518	349	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874369	76874369	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	82	651	0	ENST00000373344.5:c.5353C>G	p.Gln1785Glu	p.Q1785E	ENST00000373344	NM_000489.3	1785	Caa/Gaa	21/35	0.352315657243335	3	FACETS	0.959	0.855	1	0.32	0.285	0.357	INDETERMINATE	1	TRUE	0	0.786128128604748	3		651	303	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0003502-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	133	351	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.3	4	FACETS	1	0.976	1	0.795	0.726	0.866	CLONAL	2	TRUE	1	0.28140622755399	4		351	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782329	NA	P-0003502-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	61	162	0	ENST00000269305.4:c.746G>C	p.Arg249Thr	p.R249T	ENST00000269305	NM_001126112.2	249	aGg/aCg	7/11	0.196259569401208	3	FACETS	0.778	0.675	0.887	0.518	0.45	0.591	SUBCLONAL	2	TRUE	0	0.28140622755399	3		162	318	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972563	25972563	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0003502-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	36	201	0	ENST00000435504.4:c.1860+2T>C		p.X620_splice	ENST00000435504		620			0.186546663879455	2	FACETS	0.792	0.653	0.947	0.396	0.326	0.474	CLONAL	1	TRUE	0	0.28140622755399	2		201	323	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161270	185161270	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003502-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	29	299	0	ENST00000265026.3:c.697A>G	p.Met233Val	p.M233V	ENST00000265026	NM_004721.4	233	Atg/Gtg	4/14	0.290921604103909	3	FACETS	0.534	0.428	0.655	0.267	0.214	0.328	SUBCLONAL	1	TRUE	1	0.28140622755399	3		299	440	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762416	41762416	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1046496875	NA	P-0003502-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	40	309	0	ENST00000301178.4:c.2096A>G	p.Asn699Ser	p.N699S	ENST00000301178	NM_021913.4	699	aAt/aGt	18/20	1	2	FACETS	0.654	0.543	0.776	0.654	0.543	0.776	SUBCLONAL	1	TRUE	1	0.28140622755399	2		309	435	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0003508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	39	326	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		326	873	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649052	37649052	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	489	403	1	ENST00000447079.4:c.2157G>A	p.Trp719Ter	p.W719*	ENST00000447079	NM_015083.1	719	tgG/tgA	4/14	0.3	9	FACETS	1	0.991	1			1	INDETERMINATE	4	TRUE	NA	0.8	9		404	1056	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249083	55249083	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	86	468	0	ENST00000275493.2:c.2381C>A	p.Pro794His	p.P794H	ENST00000275493	NM_005228.3	794	cCc/cAc	20/28	NA	2	FACETS	0.922	0.822	1			1	INDETERMINATE	1	FALSE	NA	0.519469539026651	2		468	359	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574002	7574002	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs375338359	NA	P-0003528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	400	425	0	ENST00000269305.4:c.1025G>C	p.Arg342Pro	p.R342P	ENST00000269305	NM_001126112.2	342	cGa/cCa	10/11	0.3	3	FACETS	0.987	0.943	1			1	CLONAL	3	TRUE	NA	0.34	3		425	930	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546036	29546037	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs267606600	NA	P-0003528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	192	311	1	ENST00000356175.3:c.1541_1542del	p.Gln514ArgfsTer43	p.Q514Rfs*43	ENST00000356175	NM_000267.3	514	cAG/c	14/57	0.289325063373083	2	FACETS	0.962	0.895	1	0.962	0.895	1	CLONAL	2	TRUE	0	0.34	2		312	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520006	NA	P-0003538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	256	488	0	ENST00000269305.4:c.821T>C	p.Val274Ala	p.V274A	ENST00000269305	NM_001126112.2	274	gTt/gCt	8/11	0.717519918155334	1	FACETS	0.927	0.881	0.974	0.927	0.881	0.974	CLONAL	1	TRUE	0	0.74	1		488	470	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932083	36932083	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	239	546	0	ENST00000361632.4:c.2386C>T	p.Pro796Ser	p.P796S	ENST00000361632		796	Ccc/Tcc	16/16	0.717519918155334	3	FACETS	0.885	0.827	0.945	0.442	0.413	0.473	CLONAL	1	TRUE	1	0.74	3		546	1000	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024488	16024488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568152376	NA	P-0003538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	232	393	2	ENST00000268712.3:c.1730G>A	p.Ser577Asn	p.S577N	ENST00000268712	NM_006311.3	577	aGt/aAt	16/46	1	2	FACETS	0.987	0.927	1	0.987	0.927	1	CLONAL	1	TRUE	1	0.74	2		395	635	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391887	139391887	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003543-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	94	392	0	ENST00000277541.6:c.6304C>T	p.Gln2102Ter	p.Q2102*	ENST00000277541	NM_017617.3	2102	Cag/Tag	34/34	0.2605038723453	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.2605038723453	1		392	424	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371796	118371796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003543-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	52	376	0	ENST00000534358.1:c.6253G>A	p.Asp2085Asn	p.D2085N	ENST00000534358	NM_005933.3	2085	Gat/Aat	25/36	0.2605038723453	1	FACETS	0.802	0.684	0.931	0.802	0.684	0.931	CLONAL	1	TRUE	0	0.2605038723453	1		376	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574022	7574023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CG	novel	NA	P-0003543-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	83	406	0	ENST00000269305.4:c.1003_1004dup	p.Glu336ValfsTer10	p.E336Vfs*10	ENST00000269305	NM_001126112.2	335	cgt/cgCGt	10/11	0.253995323839049	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.2605038723453	1		406	385	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183797	10183797	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs5030807	NA	P-0003583-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	52	109	0	ENST00000256474.2:c.266T>A	p.Leu89His	p.L89H	ENST00000256474	NM_000551.3	89	cTc/cAc	1/3	0.173918510619184	2	FACETS	0.949	0.81	1	0.474	0.405	0.551	CLONAL	1	TRUE	0	0.25854460274033	2		109	424	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0003609-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	86	553	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.306470469651417	4	FACETS	0.899	0.8	1	0.899	0.8	1	CLONAL	2	TRUE	2	0.306470469651417	4		553	408	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0003609-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	32	491	0				ENST00000310581	NM_198253.2	-/1132			0.158206320875173	5	FACETS	1	0.923	1	0.819	0.678	0.972	INDETERMINATE	2	TRUE	2	0.306470469651417	5		491	124	SUCCESS
APC	324	MSKCC	GRCh37	5	112179765	112179765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003609-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	80	261	0	ENST00000257430.4:c.8474C>T	p.Ser2825Phe	p.S2825F	ENST00000257430	NM_000038.5	2825	tCc/tTc	16/16	0.158206320875173	5	FACETS	0.97	0.859	1	0.646	0.572	0.725	INDETERMINATE	2	TRUE	2	0.306470469651417	5		261	393	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025569	1025569	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003609-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	33	365	0	ENST00000358495.3:c.806G>T	p.Arg269Leu	p.R269L	ENST00000358495	NM_134424.2	269	cGg/cTg	9/12	0.158206320875173	5	FACETS	0.738	0.601	0.892	0.246	0.2	0.298	INDETERMINATE	1	TRUE	2	0.306470469651417	5		365	426	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781255	3781255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003609-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	82	284	0	ENST00000262367.5:c.5110G>T	p.Val1704Phe	p.V1704F	ENST00000262367	NM_004380.2	1704	Gtc/Ttc	30/31	0.143066175036128	4	FACETS	1	0.893	1	1	0.893	1	INDETERMINATE	2	TRUE	2	0.306470469651417	4		284	348	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117529	4117529	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003609-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	21	81	0	ENST00000262948.5:c.191T>A	p.Val64Asp	p.V64D	ENST00000262948	NM_030662.3	64	gTc/gAc	2/11	0.306470469651417	3	FACETS	1	0.845	1	1	0.845	1	CLONAL	2	TRUE	1	0.306470469651417	3		81	73	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0003628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	208	553	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	0.473295413190105	2		553	804	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0003628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	152	293	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.473295413190105	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.473295413190105	1		293	467	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271321	26271321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	298	955	0	ENST00000305910.3:c.292G>A	p.Glu98Lys	p.E98K	ENST00000305910	NM_003534.2	98	Gag/Aag	1/1	1	2	FACETS	0.981	0.922	1	0.981	0.922	1	CLONAL	1	TRUE	1	0.473295413190105	2		955	1284	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849852	156849852	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	108	427	0	ENST00000524377.1:c.2108A>C	p.Lys703Thr	p.K703T	ENST00000524377	NM_002529.3	703	aAg/aCg	16/17	0.461928526947765	3	FACETS	0.548	0.491	0.609	0.274	0.245	0.305	SUBCLONAL	1	TRUE	1	0.473295413190105	3		427	1030	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99169377	99169377	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	175	330	0	ENST00000074304.5:c.1307C>G	p.Ala436Gly	p.A436G	ENST00000074304	NM_001134224.1	436	gCc/gGc	15/26	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.473295413190105	2		330	662	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165333	47165333	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	183	435	0	ENST00000409792.3:c.793G>T	p.Glu265Ter	p.E265*	ENST00000409792	NM_014159.6	265	Gaa/Taa	3/21	0.473295413190105	1	FACETS	0.842	0.78	0.907	0.842	0.78	0.907	CLONAL	1	TRUE	0	0.473295413190105	1		435	701	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448483	89448483	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	155	393	0	ENST00000336596.2:c.1447A>C	p.Ser483Arg	p.S483R	ENST00000336596	NM_005233.5	483	Agt/Cgt	7/17	NA	2	FACETS	0.862	0.79	0.937			1	INDETERMINATE	1	TRUE	NA	0.473295413190105	2		393	760	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189349368	189349368	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0003628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	387	357	0	ENST00000264731.3:c.62+2T>G		p.X21_splice	ENST00000264731	NM_003722.4	21			0.461928526947765	3	FACETS	0.834	0.798	0.871	1	0.994	1	CLONAL	3	TRUE	1	0.473295413190105	3		357	808	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042175	6042175	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	190	398	0	ENST00000265849.7:c.446A>G	p.Tyr149Cys	p.Y149C	ENST00000265849	NM_000535.5	149	tAc/tGc	5/15	0.461928526947765	3	FACETS	1	0.966	1	0.538	0.498	0.581	CLONAL	1	TRUE	1	0.473295413190105	3		398	922	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779804	135779804	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	96	363	0	ENST00000298552.3:c.2035T>G	p.Phe679Val	p.F679V	ENST00000298552	NM_001162426.1	679	Ttt/Gtt	16/23	1	2	FACETS	0.512	0.456	0.572	0.512	0.456	0.572	SUBCLONAL	1	TRUE	1	0.473295413190105	2		363	792	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405480	70405480	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	251	498	0	ENST00000373644.4:c.2994A>C	p.Lys998Asn	p.K998N	ENST00000373644	NM_030625.2	998	aaA/aaC	4/12	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.473295413190105	2		498	996	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446194	70446194	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0003628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	94	444	0	ENST00000373644.4:c.5134A>T	p.Lys1712Ter	p.K1712*	ENST00000373644	NM_030625.2	1712	Aag/Tag	11/12	1	2	FACETS	0.463	0.412	0.519	0.463	0.412	0.519	SUBCLONAL	1	TRUE	1	0.473295413190105	2		444	857	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246701	41246701	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	220	468	0	ENST00000357654.3:c.847T>G	p.Leu283Val	p.L283V	ENST00000357654	NM_007294.3	283	Tta/Gta	10/23	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.473295413190105	2		468	908	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0003630-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	72	282	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.309395220642828	2	FACETS	1	0.962	1	1	0.984	1	CLONAL	3	FALSE	0	0.309796653716828	2		282	136	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	82	315	0	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	1	2	FACETS	0.862	0.768	0.96	0.862	0.768	0.96	CLONAL	1	TRUE	1	0.619925360000085	2		315	307	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155582	56155583	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAATCAC	novel	NA	P-0003641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	74	229	0	ENST00000399503.3:c.675_681dup	p.Leu228GlufsTer6	p.L228Efs*6	ENST00000399503	NM_005921.1	225	atg/atGAATCACg	3/20	1	2	FACETS	0.841	0.744	0.942	0.841	0.744	0.942	CLONAL	1	TRUE	1	0.619925360000085	2		229	284	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179388	56179389	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	T	novel	NA	P-0003641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	88	282	0	ENST00000399503.3:c.3701_3702delinsT	p.Lys1234IlefsTer11	p.K1234Ifs*11	ENST00000399503	NM_005921.1	1234	aAA/aT	15/20	1	2	FACETS	0.887	0.794	0.985	0.887	0.794	0.985	CLONAL	1	TRUE	1	0.619925360000085	2		282	320	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0003712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	272	408	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.3	3	FACETS	1	0.946	1	1	0.993	1	CLONAL	3	TRUE	1	0.22	3		408	909	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409128	139409128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	94	279	0	ENST00000277541.6:c.2041G>A	p.Glu681Lys	p.E681K	ENST00000277541	NM_017617.3	681	Gag/Aag	13/34	1	2	FACETS	0.856	0.765	0.953	1	0.984	1	CLONAL	2	TRUE	1	0.22	2		279	499	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029336	14029336	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	82	395	0	ENST00000311895.7:c.1547G>T	p.Arg516Leu	p.R516L	ENST00000311895	NM_005236.2	516	cGa/cTa	8/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.22	2		395	624	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038877	47038877	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0003712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	16	129	0	ENST00000377604.3:c.884C>G	p.Ser295Ter	p.S295*	ENST00000377604	NM_001204468.1	295	tCa/tGa	9/24	0.246190678070069	1	FACETS	0.804	0.598	1	0.804	0.598	1	CLONAL	1	TRUE	0	0.22	1		129	161	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0003717-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	99	349	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.473608077194328	1	FACETS	0.799	0.72	0.882	0.799	0.72	0.882	SUBCLONAL	1	TRUE	0	0.510072866645123	1		349	362	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266245	41266245	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0003717-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	220	280	0	ENST00000349496.5:c.241+1G>T		p.X81_splice	ENST00000349496	NM_001904.3	81			NA	2	FACETS	0.926	0.872	0.98			1	INDETERMINATE	2	TRUE	NA	0.510072866645123	2		280	466	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602973	55602973	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774405431	NA	P-0003717-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	83	290	1	ENST00000288135.5:c.2683G>A	p.Ala895Thr	p.A895T	ENST00000288135	NM_000222.2	895	Gca/Aca	19/21	1	2	FACETS	0.8	0.71	0.895	0.8	0.71	0.895	SUBCLONAL	1	TRUE	1	0.510072866645123	2		291	407	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473615	67473615	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003717-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	124	398	0	ENST00000327367.4:c.695G>A	p.Trp232Ter	p.W232*	ENST00000327367	NM_005902.3	232	tGg/tAg	6/9	0.473608077194328	1	FACETS	0.888	0.81	0.968	0.888	0.81	0.968	CLONAL	1	TRUE	0	0.510072866645123	1		398	408	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266002	41266029	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	In_Frame_Del	DEL	GTTTCGTATTTATAGCTGATTTGATGGA	GTTTCGTATTTATAGCTGATTTGATGGA	-	novel	NA	P-0003717-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	208	268	2	ENST00000349496.5:c.14-12_29del		p.A5_E9del	ENST00000349496	NM_001904.3	5		3/15	NA	2	FACETS	0.925	0.869	0.98			1	INDETERMINATE	2	TRUE	NA	0.510072866645123	2		270	441	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0003720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	133	266	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.405664790279747	3	FACETS	0.986	0.904	1	0.986	0.904	1	CLONAL	2	TRUE	1	0.405664790279747	3		266	400	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0003720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	171	293	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.23854009578864	3	FACETS	0.942	0.88	1			1	INDETERMINATE	3	TRUE	NA	0.405664790279747	3		293	359	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793663	NA	P-0003720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	284	697	0	ENST00000263967.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000263967	NM_006218.2	93	cGg/cAg	2/21	0.405664790279747	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.405664790279747	3		697	781	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	64	208	0	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	0.405664790279747	3	FACETS	0.874	0.76	0.998	0.437	0.38	0.499	CLONAL	1	TRUE	1	0.405664790279747	3		208	434	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231728	66231728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	75	313	0	ENST00000273854.3:c.1972G>A	p.Asp658Asn	p.D658N	ENST00000273854	NM_004439.5	658	Gat/Aat	11/18	0.269007703908683	3	FACETS	1	0.971	1	0.668	0.59	0.75	CLONAL	1	TRUE	1	0.405664790279747	3		313	333	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245399	153245399	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	206	329	0	ENST00000281708.4:c.1792A>C	p.Asn598His	p.N598H	ENST00000281708	NM_033632.3	598	Aat/Cat	11/12	0.269007703908683	3	FACETS	0.963	0.906	1	1	0.992	1	CLONAL	3	TRUE	1	0.405664790279747	3		329	423	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86686657	86686657	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	91	391	0	ENST00000274376.6:c.3101A>C	p.Gln1034Pro	p.Q1034P	ENST00000274376	NM_002890.2	1034	cAa/cCa	25/25	0.405664790279747	3	FACETS	0.996	0.886	1	0.498	0.443	0.556	CLONAL	1	TRUE	1	0.405664790279747	3		391	542	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962834	2962834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778151	NA	P-0003720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	53	119	0	ENST00000396946.4:c.2074G>A	p.Val692Met	p.V692M	ENST00000396946	NM_032415.4	692	Gtg/Atg	16/25	0.405664790279747	6	FACETS	1	0.912	1			1	CLONAL	1	TRUE	NA	0.405664790279747	6		119	432	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22008835	22008835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	108	262	1	ENST00000276925.6:c.118C>T	p.Pro40Ser	p.P40S	ENST00000276925	NM_004936.3	40	Ccc/Tcc	1/2	0.329928081381596	4	FACETS	0.762	0.687	0.841	0.762	0.687	0.841	SUBCLONAL	2	TRUE	2	0.405664790279747	4		263	491	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852434	42852434	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781089181	NA	P-0003720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	102	221	0	ENST00000398585.3:c.652G>A	p.Gly218Arg	p.G218R	ENST00000398585	NM_001135099.1	218	Ggg/Agg	6/14	NA	2	FACETS	1	0.962	1			1	INDETERMINATE	1	TRUE	NA	0.405664790279747	2		221	439	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	138	208	0	ENST00000257430.4:c.3964del	p.Glu1322LysfsTer93	p.E1322Kfs*93	ENST00000257430	NM_000038.5	1322	Gaa/aa	16/16	0.405664790279747	3	FACETS	0.943	0.865	1	0.943	0.865	1	CLONAL	2	TRUE	1	0.405664790279747	3		208	434	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120210	70120228	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCCACTACAGCGAGCAG	CAGCCACTACAGCGAGCAG	-	novel	NA	P-0003720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	108	201	1	ENST00000245479.2:c.1216_1234del	p.His406SerfsTer58	p.H406Sfs*58	ENST00000245479	NM_000346.3	404	ccCAGCCACTACAGCGAGCAG/cc	3/3	0.329928081381596	4	FACETS	0.785	0.708	0.865	0.785	0.708	0.865	SUBCLONAL	2	TRUE	2	0.405664790279747	4		202	477	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183825	10183825	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	52	252	0	ENST00000256474.2:c.294C>A	p.Tyr98Ter	p.Y98*	ENST00000256474	NM_000551.3	98	taC/taA	1/3	0.315941955230616	1	FACETS	0.886	0.758	1	0.886	0.758	1	CLONAL	1	TRUE	0	0.315941955230616	1		252	313	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246658	46246658	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0003721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	84	130	0	ENST00000334344.6:c.4752T>G	p.Tyr1584Ter	p.Y1584*	ENST00000334344	NM_152641.2	1584	taT/taG	15/21	0.266978741788488	2	FACETS	0.883	0.789	0.982	0.883	0.789	0.982	CLONAL	2	TRUE	0	0.315941955230616	2		130	301	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561090	9561090	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	89	260	0	ENST00000353224.5:c.692C>A	p.Ser231Ter	p.S231*	ENST00000353224	NM_177990.2	231	tCa/tAa	4/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.315941955230616	2		260	466	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420130	49420130	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003737-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	247	387	4	ENST00000301067.7:c.15619C>A	p.Pro5207Thr	p.P5207T	ENST00000301067	NM_003482.3	5207	Ccc/Acc	48/54	0.604996154795025	4	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	2	0.620954599402693	4		391	639	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435370	110435370	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003737-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	72	114	0	ENST00000375856.3:c.3031T>G	p.Ser1011Ala	p.S1011A	ENST00000375856	NM_003749.2	1011	Tcc/Gcc	1/2	0.529486525081632	5	FACETS	1	0.895	1			1	CLONAL	2	TRUE	NA	0.620954599402693	5		114	222	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339439	339439	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0003737-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	29	523	0	ENST00000262320.3:c.2462+1G>T		p.X821_splice	ENST00000262320	NM_003502.3	821			0.61817196173997	2	FACETS	0.226	0.181	0.277	0.113	0.09	0.139	SUBCLONAL	1	TRUE	0	0.620954599402693	2		523	413	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100551	102100571	+	inframe_deletion	In_Frame_Del	DEL	AGAAGGAGAGGAGCTGATGCC	AGAAGGAGAGGAGCTGATGCC	-	novel	NA	P-0003737-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	274	421	0	ENST00000282441.5:c.1396_1416del	p.Glu466_Pro472del	p.E466_P472del	ENST00000282441	NM_001130145.2	465	atAGAAGGAGAGGAGCTGATGCCa/ata	9/9	0.604996154795025	4	FACETS	0.977	0.922	1	0.977	0.922	1	CLONAL	2	TRUE	2	0.620954599402693	4		421	732	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097737	27097737	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003737-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	295	495	0	ENST00000324856.7:c.3329del	p.Gly1110GlufsTer51	p.G1110Efs*51	ENST00000324856	NM_006015.4	1109	cGg/cg	12/20	0.620954599402693	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.620954599402693	2		495	469	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0003740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	267	536	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.216076391696807	6	FACETS	1	0.984	1	1	0.984	1	INDETERMINATE	3	TRUE	3	0.671716546990969	6		536	567	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719412	190719412	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0003740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	141	206	0	ENST00000441310.2:c.1414A>T	p.Lys472Ter	p.K472*	ENST00000441310	NM_000534.4	472	Aaa/Taa	9/13	0.228446635303196	5	FACETS	1	0.957	1	0.706	0.65	0.763	INDETERMINATE	2	TRUE	2	0.671716546990969	5		206	398	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418274	139418274	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	56	266	0	ENST00000277541.6:c.298A>T	p.Thr100Ser	p.T100S	ENST00000277541	NM_017617.3	100	Aca/Tca	3/34	0.653172169655576	3	FACETS	0.485	0.416	0.56	0.162	0.138	0.187	SUBCLONAL	1	TRUE	0	0.671716546990969	3		266	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577062	7577070	+	frameshift_variant	Frame_Shift_Del	DEL	TTTCTTGCG	TTTCTTGCG	C	novel	NA	P-0003740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	252	287	0	ENST00000269305.4:c.868_876delinsG	p.Arg290GlyfsTer13	p.R290Gfs*13	ENST00000269305	NM_001126112.2	290	CGCAAGAAA/G	8/11	0.66927757678974	2	FACETS	0.998	0.954	1	0.998	0.954	1	CLONAL	2	TRUE	0	0.671716546990969	2		287	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	rs786202799	NA	P-0003764-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	261	176	0	ENST00000269305.4:c.376-2A>T		p.X126_splice	ENST00000269305	NM_001126112.2	126			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		176	286	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855999	45856016	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCACCTTGAGAATGCGG	CTCACCTTGAGAATGCGG	-	novel	NA	P-0003764-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	82	339	0	ENST00000391945.4:c.1890_1902+5del		p.X630_splice	ENST00000391945	NM_000400.3	630		20/23	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		339	307	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0003784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	208	475	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	NA	2	FACETS	0.986	0.931	1			1	INDETERMINATE	2	TRUE	NA	0.56429714583759	2		475	374	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480579	120480579	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	156	388	0	ENST00000256646.2:c.3238C>T	p.Gln1080Ter	p.Q1080*	ENST00000256646	NM_024408.3	1080	Cag/Tag	20/34	1	2	FACETS	0.867	0.796	0.939	0.867	0.796	0.939	CLONAL	1	TRUE	1	0.56429714583759	2		388	638	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450265	50450265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	116	376	0	ENST00000331340.3:c.449G>A	p.Cys150Tyr	p.C150Y	ENST00000331340	NM_006060.4	150	tGc/tAc	5/8	1	2	FACETS	0.947	0.86	1	0.947	0.86	1	CLONAL	1	TRUE	1	0.56429714583759	2		376	434	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248153	98248153	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	124	245	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	0.56429714583759	2		245	378	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645412	67645412	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	139	277	0	ENST00000264010.4:c.677A>G	p.Tyr226Cys	p.Y226C	ENST00000264010	NM_006565.3	226	tAc/tGc	3/12	0.56429714583759	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.56429714583759	1		277	344	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016550	12016550	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	155	354	0	ENST00000353533.5:c.686A>T	p.Asp229Val	p.D229V	ENST00000353533	NM_003010.3	229	gAt/gTt	7/11	0.554892280443764	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.56429714583759	1		354	344	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119113	70119113	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	76	152	0	ENST00000245479.2:c.685G>A	p.Gly229Arg	p.G229R	ENST00000245479	NM_000346.3	229	Ggg/Agg	2/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.56429714583759	2		152	206	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546556	9546556	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	135	339	0	ENST00000353224.5:c.1466A>G	p.Glu489Gly	p.E489G	ENST00000353224	NM_177990.2	489	gAa/gGa	5/10	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.56429714583759	2		339	448	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112120	115112123	+	frameshift_variant	Frame_Shift_Del	DEL	ACCC	ACCC	-	novel	NA	P-0003784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	206	408	0	ENST00000257566.3:c.1617_1620del	p.Met539IlefsTer92	p.M539Ifs*92	ENST00000257566	NM_016569.3	539	atGGGT/at	7/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.56429714583759	2		408	604	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876382	35876382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1283489708	NA	P-0003798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	15	267	0	ENST00000303115.3:c.1174G>A	p.Glu392Lys	p.E392K	ENST00000303115	NM_002185.3	392	Gag/Aag	8/8	0.381225245733986	3	FACETS	0.478	0.35	0.631	0.239	0.175	0.316	SUBCLONAL	1	TRUE	1	0.381225245733986	3		267	196	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755594	39755594	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	16	304	0	ENST00000288319.7:c.1171G>C	p.Asp391His	p.D391H	ENST00000288319	NM_182918.3	391	Gac/Cac	10/10	0.25295392641582	5	FACETS	0.524	0.387	0.686	0.175	0.129	0.229	SUBCLONAL	1	TRUE	2	0.381225245733986	5		304	252	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075609	8075609	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1404100307	NA	P-0003798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	20	445	0	ENST00000377482.5:c.71G>A	p.Arg24Gln	p.R24Q	ENST00000377482	NM_018948.3	24	cGa/cAa	2/4	0.14849577869098	3	FACETS	0.343	0.262	0.439	0.114	0.087	0.147	INDETERMINATE	1	TRUE	0	0.381225245733986	3		445	364	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090533	71090533	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	13	288	0	ENST00000318789.4:c.815A>T	p.Asn272Ile	p.N272I	ENST00000318789	NM_032682.5	272	aAc/aTc	11/21	0.225710543534381	3	FACETS	0.374	0.267	0.505	0.187	0.133	0.253	INDETERMINATE	1	TRUE	1	0.381225245733986	3		288	217	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272131	38272131	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1427855487	NA	P-0003798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	17	298	0	ENST00000425967.3:c.2087A>G	p.Lys696Arg	p.K696R	ENST00000425967	NM_001174067.1	696	aAg/aGg	16/19	0.381225245733986	4	FACETS	0.47	0.351	0.612	0.235	0.175	0.306	SUBCLONAL	1	TRUE	2	0.381225245733986	4		298	262	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871252	35871252	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	127	455	2	ENST00000216797.5:c.921C>G	p.Asp307Glu	p.D307E	ENST00000216797	NM_020529.2	307	gaC/gaG	6/6	0.324739118977324	3	FACETS	1	0.98	1	0.649	0.59	0.711	CLONAL	1	TRUE	1	0.381225245733986	3		457	611	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118378305	118378306	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0003798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	23	257	0	ENST00000534358.1:c.10816_10817delinsTT	p.Glu3606Leu	p.E3606L	ENST00000534358	NM_005933.3	3606	GAg/TTg	28/36	1	2	FACETS	0.461	0.36	0.577	0.461	0.36	0.577	SUBCLONAL	1	TRUE	1	0.381225245733986	2		257	262	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678777	52678777	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	52	234	0	ENST00000394830.3:c.842A>G	p.Tyr281Cys	p.Y281C	ENST00000394830	NM_018313.4	281	tAt/tGt	9/30	1	2	FACETS	0.844	0.718	0.983	0.844	0.718	0.983	CLONAL	1	FALSE	1	0.191963925459844	2		234	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578494	7578494	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs786203064	NA	P-0003799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	85	200	0	ENST00000269305.4:c.436T>G	p.Trp146Gly	p.W146G	ENST00000269305	NM_001126112.2	146	Tgg/Ggg	5/11	1	2	FACETS	1	0.934	1	1	0.986	1	CLONAL	2	FALSE	1	0.191963925459844	2		200	413	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578184	7578184	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567551073	NA	P-0003818-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	177	321	0	ENST00000269305.4:c.665del	p.Pro222ArgfsTer25	p.P222Rfs*25	ENST00000269305	NM_001126112.2	222	cCg/cg	6/11	0.34647131196541	2	FACETS	0.97	0.903	1	0.97	0.903	1	CLONAL	2	TRUE	0	0.403911880129458	2		321	452	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166192	118166192	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1337416217	NA	P-0003821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	54	209	0	ENST00000369448.3:c.702G>C	p.Lys234Asn	p.K234N	ENST00000369448	NM_017709.3	234	aaG/aaC	2/2	1	2	FACETS	0.74	0.632	0.859	0.74	0.632	0.859	SUBCLONAL	1	TRUE	1	0.252509251630294	2		209	578	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646003	215646003	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553622597	NA	P-0003821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	56	258	0	ENST00000260947.4:c.595T>C	p.Ser199Pro	p.S199P	ENST00000260947	NM_000465.2	199	Tct/Cct	4/11	1	2	FACETS	0.781	0.669	0.903	0.781	0.669	0.903	CLONAL	1	TRUE	1	0.252509251630294	2		258	568	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921567	178921567	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553821144	NA	P-0003821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	50	167	0	ENST00000263967.3:c.1049A>G	p.Asp350Gly	p.D350G	ENST00000263967	NM_006218.2	350	gAc/gGc	5/21	0.145996119633347	3	FACETS	1	0.946	1	0.628	0.535	0.73	INDETERMINATE	1	TRUE	1	0.252509251630294	3		167	355	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181363	185181363	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	124	254	0	ENST00000265026.3:c.1304A>C	p.Lys435Thr	p.K435T	ENST00000265026	NM_004721.4	435	aAa/aCa	8/14	0.145996119633347	3	FACETS	0.872	0.791	0.958	0.872	0.791	0.958	INDETERMINATE	2	TRUE	1	0.252509251630294	3		254	634	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536192	106536192	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	49	157	0	ENST00000369096.4:c.159G>T	p.Glu53Asp	p.E53D	ENST00000369096	NM_001198.3	53	gaG/gaT	2/7	1	2	FACETS	0.681	0.576	0.796	0.681	0.576	0.796	SUBCLONAL	1	TRUE	1	0.252509251630294	2		157	570	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525532	137525532	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0003821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	49	253	0	ENST00000367739.4:c.483T>A	p.Tyr161Ter	p.Y161*	ENST00000367739	NM_000416.2	161	taT/taA	4/7	1	2	FACETS	0.686	0.58	0.802	0.686	0.58	0.802	SUBCLONAL	1	TRUE	1	0.252509251630294	2		253	566	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012370	152012370	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	53	226	0	ENST00000262189.6:c.443G>C	p.Gly148Ala	p.G148A	ENST00000262189	NM_170606.2	148	gGa/gCa	4/59	0.252509251630294	1	FACETS	0.708	0.604	0.822	0.708	0.604	0.822	SUBCLONAL	1	TRUE	0	0.252509251630294	1		226	518	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752770	128752770	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	43	151	0	ENST00000377970.2:c.931G>T	p.Val311Phe	p.V311F	ENST00000377970	NM_002467.4	311	Gtc/Ttc	3/3	0.252509251630294	3	FACETS	0.717	0.599	0.847	0.358	0.299	0.424	SUBCLONAL	1	TRUE	1	0.252509251630294	3		151	535	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563512	87563512	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	25	148	1	ENST00000277120.3:c.1900G>T	p.Glu634Ter	p.E634*	ENST00000277120		634	Gag/Tag	16/19	0.252509251630294	1	FACETS	0.453	0.357	0.564	0.453	0.357	0.564	SUBCLONAL	1	TRUE	0	0.252509251630294	1		149	382	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237701	133237701	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	200	241	1	ENST00000320574.5:c.2914G>C	p.Glu972Gln	p.E972Q	ENST00000320574	NM_006231.2	972	Gag/Cag	25/49	1	2	FACETS	1	0.976	1	1	0.994	1	CLONAL	2	TRUE	1	0.252509251630294	2		242	713	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578206	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs886039484	NA	P-0003821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	64	239	0	ENST00000269305.4:c.643A>G	p.Ser215Gly	p.S215G	ENST00000269305	NM_001126112.2	215	Agt/Ggt	6/11	0.252509251630294	1	FACETS	0.776	0.672	0.888	0.776	0.672	0.888	SUBCLONAL	1	TRUE	0	0.252509251630294	1		239	571	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024194	31024194	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	48	253	0	ENST00000375687.4:c.3679G>T	p.Glu1227Ter	p.E1227*	ENST00000375687	NM_015338.5	1227	Gaa/Taa	13/13	0.252509251630294	1	FACETS	0.656	0.555	0.768	0.656	0.555	0.768	SUBCLONAL	1	TRUE	0	0.252509251630294	1		253	506	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676218	29676219	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0003821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	52	209	0	ENST00000356175.3:c.7208_7209del	p.Arg2403LysfsTer3	p.R2403Kfs*3	ENST00000356175	NM_000267.3	2403	AGa/a	48/57	0.252509251630294	1	FACETS	0.871	0.744	1	0.871	0.744	1	CLONAL	1	TRUE	0	0.252509251630294	1		209	413	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856116	68856117	+	missense_variant	Missense_Mutation	DNP	TA	TA	CC	novel	NA	P-0003821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	29	202	0	ENST00000261769.5:c.1924_1925delinsCC	p.Tyr642Pro	p.Y642P	ENST00000261769	NM_004360.3	642	TAc/CCc	12/16	0.226125843261499	1	FACETS	0.403	0.323	0.495	0.403	0.323	0.495	SUBCLONAL	1	TRUE	0	0.252509251630294	1		202	498	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443686	29443686	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	164	316	0	ENST00000389048.3:c.3531G>T	p.Gln1177His	p.Q1177H	ENST00000389048	NM_004304.4	1177	caG/caT	23/29	1	2	FACETS	1	0.957	1	1	0.993	1	CLONAL	2	TRUE	1	0.4	2		316	394	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202639	67202639	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	novel	NA	P-0003845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	120	258	0	ENST00000312629.5:c.1448A>G	p.Ter483TrpextTer6	p.*483Wext*6	ENST00000312629	NM_003952.2	483	tAg/tGg	15/15	1	2	FACETS	1	0.952	1	1	0.991	1	CLONAL	2	TRUE	1	0.4	2		258	285	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0003854-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	110	282	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.36890414479849	2	FACETS	0.934	0.855	1	0.934	0.855	1	CLONAL	2	TRUE	0	0.452939380841359	2		282	260	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220649	1220649	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003854-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	209	357	2	ENST00000326873.7:c.667G>T	p.Glu223Ter	p.E223*	ENST00000326873	NM_000455.4	223	Gag/Tag	5/10	0.452939380841359	2	FACETS	0.916	0.858	0.973	0.916	0.858	0.973	CLONAL	2	TRUE	0	0.452939380841359	2		359	504	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587162	212587162	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003854-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	135	404	0	ENST00000342788.4:c.839A>G	p.Asn280Ser	p.N280S	ENST00000342788	NM_005235.2	280	aAt/aGt	7/28	0.296999221775115	4	FACETS	1	0.915	1	0.504	0.457	0.552	CLONAL	1	TRUE	2	0.452939380841359	4		404	860	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938938	178938938	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003854-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	17	133	0	ENST00000263967.3:c.2180C>T	p.Thr727Ile	p.T727I	ENST00000263967	NM_006218.2	727	aCa/aTa	14/21	0.342579395430852	4	FACETS	0.413	0.308	0.538			1	SUBCLONAL	1	TRUE	NA	0.452939380841359	4		133	264	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146743	185146743	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003854-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	288	304	0	ENST00000265026.3:c.374G>T	p.Ser125Ile	p.S125I	ENST00000265026	NM_004721.4	125	aGt/aTt	2/14	0.444914106262967	3	FACETS	1	0.983	1			1	CLONAL	3	TRUE	NA	0.452939380841359	3		304	491	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532615	187532615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003854-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	123	394	0	ENST00000441802.2:c.9778G>A	p.Glu3260Lys	p.E3260K	ENST00000441802	NM_005245.3	3260	Gaa/Aaa	14/27	1	2	FACETS	0.965	0.876	1	0.965	0.876	1	CLONAL	1	TRUE	1	0.452939380841359	2		394	563	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66679750	66679750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003854-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	172	433	1	ENST00000307102.5:c.65G>T	p.Gly22Val	p.G22V	ENST00000307102	NM_002755.3	22	gGg/gTg	1/11	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.452939380841359	2		434	514	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911128	40911128	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0003854-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	257	561	0	ENST00000373198.4:c.2176+1G>T		p.X726_splice	ENST00000373198	NM_133170.3	726			0.24987876631032	5	FACETS	0.853	0.798	0.909	0.569	0.532	0.606	INDETERMINATE	2	TRUE	2	0.452939380841359	5		561	1117	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480167	20480167	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003854-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	63	423	0	ENST00000346618.3:c.484C>T	p.Arg162Ter	p.R162*	ENST00000346618	NM_001949.4	162	Cga/Tga	2/7	0.430841604012467	4	FACETS	0.621	0.537	0.713	0.207	0.179	0.238	SUBCLONAL	1	TRUE	1	0.452939380841359	4		423	651	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372347	55372347	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868625307	NA	P-0003854-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	30	264	0	ENST00000297316.4:c.1037C>T	p.Thr346Met	p.T346M	ENST00000297316	NM_022454.3	346	aCg/aTg	2/2	0.280518228155549	5	FACETS	0.664	0.536	0.809	0.221	0.178	0.27	SUBCLONAL	1	TRUE	2	0.452939380841359	5		264	335	SUCCESS
AR	367	MSKCC	GRCh37	X	66942794	66942794	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003854-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1255	71	585	0	ENST00000374690.3:c.2575C>T	p.Gln859Ter	p.Q859*	ENST00000374690	NM_000044.3	859	Cag/Tag	7/8	0.452939380841359	5	FACETS	0.397	0.345	0.454			1	SUBCLONAL	1	TRUE	NA	0.452939380841359	5		585	1326	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0003863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	74	212	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.593587707793207	1	FACETS	0.868	0.775	0.963	0.868	0.775	0.963	CLONAL	1	TRUE	0	0.606395241968412	1		212	196	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566418	139566418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374930413	NA	P-0003863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	23	300	0	ENST00000308874.7:c.677C>T	p.Ser226Leu	p.S226L	ENST00000308874		226	tCg/tTg	9/10	0.606395241968412	3	FACETS	0.278	0.216	0.349	0.139	0.108	0.175	SUBCLONAL	1	TRUE	1	0.606395241968412	3		300	356	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637900	39637900	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	168	302	0	ENST00000262039.4:c.2317C>G	p.Leu773Val	p.L773V	ENST00000262039	NM_002647.2	773	Ctt/Gtt	22/25	NA	2	FACETS	1	0.95	1			1	INDETERMINATE	1	TRUE	NA	0.606395241968412	2		302	536	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845722	151845722	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	158	326	0	ENST00000262189.6:c.13290G>C	p.Leu4430Phe	p.L4430F	ENST00000262189	NM_170606.2	4430	ttG/ttC	52/59	0.606395241968412	3	FACETS	0.897	0.823	0.974	0.449	0.411	0.487	CLONAL	1	TRUE	1	0.606395241968412	3		326	757	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244682	46244682	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	198	316	0	ENST00000334344.6:c.2776G>C	p.Val926Leu	p.V926L	ENST00000334344	NM_152641.2	926	Gta/Cta	15/21	1	2	FACETS	0.86	0.799	0.924	0.86	0.799	0.924	CLONAL	1	TRUE	1	0.606395241968412	2		316	759	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578440	7578440	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs879254249	NA	P-0003863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	113	196	0	ENST00000269305.4:c.490A>G	p.Lys164Glu	p.K164E	ENST00000269305	NM_001126112.2	164	Aag/Gag	5/11	0.593587707793207	1	FACETS	0.944	0.864	1	0.944	0.864	1	CLONAL	1	TRUE	0	0.606395241968412	1		196	275	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632358	1632358	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	163	272	0	ENST00000344749.5:c.192G>C	p.Gln64His	p.Q64H	ENST00000344749	NM_001136139.2	64	caG/caC	4/19	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.606395241968412	2		272	537	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249013	55249014	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACCACC	novel	NA	P-0003863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	1193	235	0	ENST00000275493.2:c.2314_2315insACCACC	p.Asn771_Pro772insHisHis	p.N771_P772insHH	ENST00000275493	NM_005228.3	771	aac/aACCACCac	20/28	0.606395241968412	11	FACETS	1	0.995	1			1	CLONAL	9	TRUE	NA	0.606395241968412	11		235	1572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0003873-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	415	282	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	NA	2	FACETS	0.936	0.907	0.963			1	INDETERMINATE	2	TRUE	NA	0.793321000858309	2		282	559	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401400	139401400	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003873-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	157	156	0	ENST00000277541.6:c.3669C>A	p.Asp1223Glu	p.D1223E	ENST00000277541	NM_017617.3	1223	gaC/gaA	23/34	0.219377426994028	3	FACETS	1	0.989	1	0.703	0.652	0.755	INDETERMINATE	1	TRUE	1	0.793321000858309	3		156	393	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	315	215	0	ENST00000397752.3:c.3028G>C	p.Asp1010His	p.D1010H	ENST00000397752	NM_000245.2	1010	Gat/Cat	14/21	0.363656975857299	5	FACETS	0.984	0.936	1	0.984	0.936	1	CLONAL	4	TRUE	1	0.363656975857299	5		215	680	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411709	116411709	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	84	268	0	ENST00000397752.3:c.2887+1G>A		p.X963_splice	ENST00000397752	NM_000245.2	963			0.363656975857299	5	FACETS	0.881	0.778	0.993	0.22	0.194	0.249	CLONAL	1	TRUE	1	0.363656975857299	5		268	810	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579310	7579310	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1555526469	NA	P-0003879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	231	230	0	ENST00000269305.4:c.375+2T>C		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.363656975857299	3	FACETS	0.91	0.856	0.964	0.91	0.856	0.964	CLONAL	3	TRUE	0	0.363656975857299	3		230	550	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955109	17955109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140784576	NA	P-0003879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	98	312	0	ENST00000458235.1:c.118C>T	p.Arg40Cys	p.R40C	ENST00000458235	NM_000215.3	40	Cgc/Tgc	2/24	0.344083801399971	3	FACETS	1	0.899	1	0.503	0.449	0.56	CLONAL	1	TRUE	1	0.363656975857299	3		312	633	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231106	53231106	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556842168	NA	P-0003879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	158	465	1	ENST00000375401.3:c.1796G>A	p.Arg599His	p.R599H	ENST00000375401	NM_004187.3	599	cGt/cAt	13/26	0.223991903951457	1	FACETS	0.897	0.822	0.974	0.897	0.822	0.974	CLONAL	1	TRUE	0	0.363656975857299	1		466	793	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155312	106155316	+	frameshift_variant	Frame_Shift_Del	DEL	TAGTC	TAGTC	-	novel	NA	P-0003879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	323	339	0	ENST00000380013.4:c.213_217del	p.Asn71LysfsTer5	p.N71Kfs*5	ENST00000380013	NM_001127208.2	71	aaTAGTCgt/aagt	3/11	0.363656975857299	5	FACETS	1	0.991	1	0.832	0.786	0.879	CLONAL	2	TRUE	2	0.363656975857299	5		339	1100	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0003899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	504	152	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.534093636064781	2	FACETS	0.984	0.948	1	0.984	0.948	1	CLONAL	2	TRUE	0	0.535374667793738	2		152	957	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069476	30069476	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	93	71	0	ENST00000338641.4:c.1340+1G>A		p.X447_splice	ENST00000338641	NM_000268.3	447			0.508123916452525	1	FACETS	0.922	0.831	1	0.922	0.831	1	CLONAL	1	TRUE	0	0.535374667793738	1		71	276	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0003903-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	469	266	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.780057501270508	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.780057501270508	3		266	805	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003903-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	456	396	0	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.780057501270508	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.780057501270508	2		396	567	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641212	93641212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200320837	NA	P-0003903-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	466	349	2	ENST00000375746.1:c.1558C>T	p.Arg520Cys	p.R520C	ENST00000375746	NM_001174167.1	520	Cgt/Tgt	11/14	0.780057501270508	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.780057501270508	3		351	814	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575422	64575422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003903-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1237	287	507	0	ENST00000312049.6:c.595C>T	p.His199Tyr	p.H199Y	ENST00000312049	NM_130799.2	199	Cac/Tac	3/10	0.780057501270508	5	FACETS	1	0.967	1			1	CLONAL	1	TRUE	NA	0.780057501270508	5		507	1524	SUCCESS
APC	324	MSKCC	GRCh37	5	112175720	112175720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003903-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	220	333	1	ENST00000257430.4:c.4429C>T	p.Gln1477Ter	p.Q1477*	ENST00000257430	NM_000038.5	1477	Cag/Tag	16/16	0.427563954633728	6	FACETS	0.804	0.749	0.861	0.536	0.499	0.574	INDETERMINATE	2	TRUE	3	0.780057501270508	6		334	898	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196062	67196062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003903-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2061	248	438	0	ENST00000312629.5:c.46G>A	p.Glu16Lys	p.E16K	ENST00000312629	NM_003952.2	16	Gag/Aag	1/15	0.780057501270508	10	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.780057501270508	10		438	2309	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332836	65332836	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003903-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	187	388	0	ENST00000342505.4:c.703C>G	p.Leu235Val	p.L235V	ENST00000342505	NM_002227.2	235	Ctc/Gtc	7/25	0.780057501270508	2	FACETS	0.864	0.804	0.926	0.432	0.402	0.463	CLONAL	1	TRUE	0	0.780057501270508	2		388	555	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120508147	120508147	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003903-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1670	163	474	0	ENST00000256646.2:c.1610C>G	p.Ser537Cys	p.S537C	ENST00000256646	NM_024408.3	537	tCc/tGc	10/34	0.780057501270508	6	FACETS	0.584	0.533	0.637			1	SUBCLONAL	1	TRUE	NA	0.780057501270508	6		474	1833	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52649421	52649421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1169377404	NA	P-0003903-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	165	470	1	ENST00000394830.3:c.1870G>A	p.Glu624Lys	p.E624K	ENST00000394830	NM_018313.4	624	Gag/Aag	16/30	0.780057501270508	3	FACETS	0.57	0.523	0.62	0.285	0.261	0.31	SUBCLONAL	1	TRUE	1	0.780057501270508	3		471	1031	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178106	142178106	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003903-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	186	357	0	ENST00000350721.4:c.7312G>C	p.Glu2438Gln	p.E2438Q	ENST00000350721	NM_001184.3	2438	Gag/Cag	43/47	0.780057501270508	3	FACETS	0.923	0.855	0.993	0.462	0.427	0.497	CLONAL	1	TRUE	1	0.780057501270508	3		357	718	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504396	186504396	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003903-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	53	469	0	ENST00000323963.5:c.733G>C	p.Glu245Gln	p.E245Q	ENST00000323963		245	Gaa/Caa	7/11	0.780057501270508	3	FACETS	0.209	0.177	0.244	0.105	0.088	0.122	SUBCLONAL	1	TRUE	1	0.780057501270508	3		469	903	SUCCESS
APC	324	MSKCC	GRCh37	5	112178100	112178100	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003903-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	252	485	0	ENST00000257430.4:c.6809C>G	p.Ser2270Cys	p.S2270C	ENST00000257430	NM_000038.5	2270	tCt/tGt	16/16	0.427563954633728	6	FACETS	1	0.991	1	0.46	0.43	0.492	INDETERMINATE	1	TRUE	3	0.780057501270508	6		485	1198	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287286	33287286	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003903-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	155	464	0	ENST00000374542.5:c.1811G>C	p.Gly604Ala	p.G604A	ENST00000374542	NM_001141970.1	604	gGa/gCa	6/8	0.780057501270508	3	FACETS	0.583	0.534	0.635	0.292	0.267	0.318	SUBCLONAL	1	TRUE	1	0.780057501270508	3		464	947	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523561	106523561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003903-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	119	363	0	ENST00000359195.3:c.2713G>A	p.Glu905Lys	p.E905K	ENST00000359195	NM_002649.2	905	Gaa/Aaa	8/11	0.780057501270508	3	FACETS	0.518	0.468	0.572	0.259	0.234	0.286	SUBCLONAL	1	TRUE	1	0.780057501270508	3		363	818	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961477	41961477	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003903-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	216	737	0	ENST00000219905.7:c.385C>G	p.Pro129Ala	p.P129A	ENST00000219905	NM_001164273.1	129	Cct/Gct	2/24	1	2	FACETS	0.554	0.515	0.595	0.554	0.515	0.595	SUBCLONAL	1	TRUE	1	0.780057501270508	2		737	999	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358387	91358387	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1555425417	NA	P-0003903-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	356	513	1	ENST00000355112.3:c.4132G>T	p.Gly1378Ter	p.G1378*	ENST00000355112	NM_000057.2	1378	Gga/Tga	22/22	0.780057501270508	3	FACETS	1	0.988	1	0.568	0.539	0.598	CLONAL	1	TRUE	1	0.780057501270508	3		514	1116	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974947	15974947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759882620	NA	P-0003903-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	141	450	0	ENST00000268712.3:c.3928G>A	p.Asp1310Asn	p.D1310N	ENST00000268712	NM_006311.3	1310	Gat/Aat	30/46	0.780057501270508	2	FACETS	0.558	0.51	0.608	0.279	0.255	0.304	SUBCLONAL	1	TRUE	0	0.780057501270508	2		450	648	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974970	15974970	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003903-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	115	386	0	ENST00000268712.3:c.3905G>C	p.Arg1302Thr	p.R1302T	ENST00000268712	NM_006311.3	1302	aGa/aCa	30/46	0.780057501270508	2	FACETS	0.549	0.496	0.604	0.275	0.248	0.302	SUBCLONAL	1	TRUE	0	0.780057501270508	2		386	537	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483067	29483067	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003903-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	166	450	0	ENST00000356175.3:c.127C>G	p.Leu43Val	p.L43V	ENST00000356175	NM_000267.3	43	Cta/Gta	2/57	0.466705329346213	4	FACETS	0.784	0.72	0.851			1	INDETERMINATE	1	TRUE	NA	0.780057501270508	4		450	966	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884296	37884296	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0003903-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	56	291	0	ENST00000269571.5:c.3767G>C	p.Ter1256SerextTer10	p.*1256Sext*10	ENST00000269571		1256	tGa/tCa	27/27	0.745492416275378	4	FACETS	0.351	0.3	0.407	0.175	0.15	0.204	SUBCLONAL	1	TRUE	2	0.780057501270508	4		291	729	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10274007	10274007	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003903-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	114	422	0	ENST00000340748.4:c.873A>T	p.Lys291Asn	p.K291N	ENST00000340748		291	aaA/aaT	11/40	0.780057501270508	2	FACETS	0.407	0.367	0.45	0.204	0.183	0.225	SUBCLONAL	1	TRUE	0	0.780057501270508	2		422	718	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17949154	17949154	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1428081698	NA	P-0003903-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	73	544	1	ENST00000458235.1:c.1487C>T	p.Thr496Ile	p.T496I	ENST00000458235	NM_000215.3	496	aCa/aTa	11/24	0.780057501270508	2	FACETS	0.22	0.192	0.251	0.11	0.096	0.126	SUBCLONAL	1	TRUE	0	0.780057501270508	2		545	851	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793228	33793228	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003903-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	127	142	1	ENST00000498907.2:c.93C>A	p.Phe31Leu	p.F31L	ENST00000498907	NM_004364.3	31	ttC/ttA	1/1	0.780057501270508	3	FACETS	1	0.979	1	0.613	0.562	0.666	CLONAL	1	TRUE	1	0.780057501270508	3		143	369	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608277	100608277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003903-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	207	668	0	ENST00000308731.7:c.1813G>A	p.Glu605Lys	p.E605K	ENST00000308731	NM_000061.2	605	Gag/Aag	18/19	0.638187329491667	3	FACETS	0.533	0.493	0.574			1	SUBCLONAL	1	TRUE	NA	0.780057501270508	3		668	1385	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060942	38060943	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003903-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	52	281	0	ENST00000250448.2:c.1046dup	p.Leu349PhefsTer66	p.L349Ffs*66	ENST00000250448	NM_004496.3	349	ttg/ttTg	2/2	0.642765998880728	3	FACETS	0.288	0.244	0.335	0.144	0.122	0.168	SUBCLONAL	1	TRUE	1	0.780057501270508	3		281	644	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0003926-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	102	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.352137783693603	2		326	464	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562482	21562483	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGGCG	rs550642106	NA	P-0003944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	11	58	0	ENST00000382592.4:c.1431_1436dup	p.Pro479_Ala480dup	p.P479_A480dup	ENST00000382592	NM_014572.2	479	ccg/ccCGCCCCg	4/8	0.597635042452196	1	FACETS	0.568	0.405	0.756	0.568	0.405	0.756	SUBCLONAL	1	TRUE	0	0.592559295740218	1		58	46	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095703	178095703	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1258	529	703	1	ENST00000397062.3:c.1628A>G	p.Lys543Arg	p.K543R	ENST00000397062	NM_006164.4	543	aAa/aGa	5/5	0.2655351562533	3	FACETS	1	0.995	1	0.648	0.62	0.676	INDETERMINATE	1	TRUE	1	0.592559295740218	3		704	1787	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911485	134911485	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	155	391	0	ENST00000398015.3:c.1950C>G	p.Ile650Met	p.I650M	ENST00000398015	NM_004441.4	650	atC/atG	11/16	0.597635042452196	1	FACETS	0.793	0.733	0.856	0.793	0.733	0.856	SUBCLONAL	1	TRUE	0	0.592559295740218	1		391	464	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358640	67358640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223751	NA	P-0003944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	418	513	0	ENST00000327367.4:c.148G>A	p.Glu50Lys	p.E50K	ENST00000327367	NM_005902.3	50	Gag/Aag	1/9	0.27057370519289	0	FACETS	0.659	0.631	0.687			1	INDETERMINATE	1	TRUE	0	0.592559295740218	0		513	872	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119711	17119711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199889477	NA	P-0003944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	177	422	0	ENST00000285071.4:c.1283C>T	p.Pro428Leu	p.P428L	ENST00000285071	NM_144997.5	428	cCc/cTc	11/14	0.597635042452196	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.592559295740218	1		422	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003972-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	468	543	0	ENST00000269305.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	336	Gag/Tag	10/11	0.707578416131182	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.707578416131182	2		543	649	SUCCESS
ATR	545	MSKCC	GRCh37	3	142253946	142253946	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003972-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	238	309	0	ENST00000350721.4:c.3921G>C	p.Leu1307Phe	p.L1307F	ENST00000350721	NM_001184.3	1307	ttG/ttC	21/47	0.470931636300106	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.707578416131182	1		309	331	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056270	26056270	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs766767455	NA	P-0003972-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	258	384	0	ENST00000343677.2:c.387G>C	p.Lys129Asn	p.K129N	ENST00000343677	NM_005319.3	129	aaG/aaC	1/1	0.409645955899095	4	FACETS	0.936	0.882	0.991	0.936	0.882	0.991	INDETERMINATE	2	TRUE	2	0.707578416131182	4		384	665	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158660	26158660	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003972-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	40	22	0	ENST00000289316.2:c.263C>G	p.Ser88Trp	p.S88W	ENST00000289316	NM_138720.2	88	tCg/tGg	1/2	0.409645955899095	4	FACETS	0.961	0.845	1	1	0.968	1	INDETERMINATE	3	TRUE	2	0.707578416131182	4		22	67	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839943	27839943	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003972-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	396	1054	2	ENST00000328488.2:c.151G>T	p.Glu51Ter	p.E51*	ENST00000328488	NM_003533.2	51	Gag/Tag	1/1	0.409645955899095	4	FACETS	0.806	0.767	0.845	0.806	0.767	0.845	INDETERMINATE	2	TRUE	2	0.707578416131182	4		1056	1186	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309759	104309759	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003972-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	237	558	0	ENST00000369902.3:c.350G>T	p.Gly117Val	p.G117V	ENST00000369902	NM_016169.3	117	gGc/gTc	3/12	0.216820195751188	2	FACETS	1	0.992	1	0.67	0.632	0.708	INDETERMINATE	1	TRUE	0	0.707578416131182	2		558	500	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374881	118374881	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	45	254	0	ENST00000534358.1:c.8274T>G	p.Ile2758Met	p.I2758M	ENST00000534358	NM_005933.3	2758	atT/atG	27/36	0.29459366310996	4	FACETS	1	0.942	1			1	CLONAL	2	TRUE	NA	0.29459366310996	4		254	162	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0004066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	72	318	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.236236022444365	3	FACETS	1	0.959	1	0.618	0.541	0.702	CLONAL	1	FALSE	1	0.236236022444365	3		318	551	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241677	55241677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504256	NA	P-0004066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	113	321	0	ENST00000275493.2:c.2125G>A	p.Glu709Lys	p.E709K	ENST00000275493	NM_005228.3	709	Gaa/Aaa	18/28	0.236236022444365	3	FACETS	0.829	0.748	0.915	0.829	0.748	0.915	CLONAL	2	FALSE	1	0.236236022444365	3		321	645	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	39	738	12	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.725	0.605	0.858	0.725	0.605	0.858	SUBCLONAL	1	TRUE	1	0.405910579069938	2		750	265	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867541	35867541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	72	216	1	ENST00000303115.3:c.361del	p.Ile121Ter	p.I121*	ENST00000303115	NM_002185.3	119	Aaa/aa	3/8	1	2	FACETS	0.921	0.809	1	0.921	0.809	1	CLONAL	1	TRUE	1	0.405910579069938	2		217	385	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	96	367	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.903	0.807	1	0.903	0.807	1	CLONAL	1	TRUE	1	0.405910579069938	2		367	524	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	49	176	0	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.669	0.568	0.778	0.669	0.568	0.778	SUBCLONAL	1	TRUE	1	0.405910579069938	2		176	361	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	17	276	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	NA	2	FACETS	0.144	0.107	0.189			1	INDETERMINATE	1	TRUE	NA	0.405910579069938	2		276	581	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490980	56490980	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs931676601	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	72	206	0	ENST00000267101.3:c.2426A>G	p.Gln809Arg	p.Q809R	ENST00000267101	NM_001982.3	809	cAg/cGg	20/28	1	2	FACETS	0.831	0.729	0.94	0.831	0.729	0.94	CLONAL	1	TRUE	1	0.405910579069938	2		206	427	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	63	277	0	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	1	2	FACETS	0.57	0.493	0.653	0.57	0.493	0.653	SUBCLONAL	1	TRUE	1	0.405910579069938	2		277	545	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	63	445	0	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	1	2	FACETS	0.56	0.485	0.642	0.56	0.485	0.642	SUBCLONAL	1	TRUE	1	0.405910579069938	2		445	554	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	21	90	0	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.52	0.402	0.656	0.52	0.402	0.656	SUBCLONAL	1	TRUE	1	0.405910579069938	2		90	199	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	84	378	0	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.834	0.739	0.936	0.834	0.739	0.936	CLONAL	1	TRUE	1	0.405910579069938	2		378	496	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791356	42791356	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760049446	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	36	220	0	ENST00000575354.2:c.416G>A	p.Arg139Gln	p.R139Q	ENST00000575354	NM_015125.3	139	cGg/cAg	3/20	1	2	FACETS	0.383	0.315	0.46	0.383	0.315	0.46	SUBCLONAL	1	TRUE	1	0.405910579069938	2		220	463	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968322	2968323	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs762770988	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	63	149	1	ENST00000396946.4:c.1663dup	p.Arg555ProfsTer38	p.R555Pfs*38	ENST00000396946	NM_032415.4	555	cgg/cCgg	13/25	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.405910579069938	2		150	303	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	52	308	1	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	1	2	FACETS	0.956	0.821	1	0.956	0.821	1	CLONAL	1	TRUE	1	0.405910579069938	2		309	268	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739581	145739581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375100228	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	83	193	0	ENST00000428558.2:c.1870G>A	p.Val624Ile	p.V624I	ENST00000428558	NM_004260.3	624	Gtc/Atc	11/22	0.405910579069938	3	FACETS	0.984	0.871	1	0.492	0.435	0.552	CLONAL	1	TRUE	1	0.405910579069938	3		193	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	12	143	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	1	2	FACETS	0.176	0.123	0.242	0.176	0.123	0.242	SUBCLONAL	1	TRUE	1	0.405910579069938	2		143	336	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007824	45007825	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	58	230	0	ENST00000558401.1:c.276dup	p.Thr93HisfsTer2	p.T93Hfs*2	ENST00000558401	NM_004048.2	91	acc/aCcc	2/4	1	2	FACETS	0.663	0.571	0.763	0.663	0.571	0.763	SUBCLONAL	1	TRUE	1	0.405910579069938	2		230	431	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11210203	11210203	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	40	326	0	ENST00000361445.4:c.4550C>T	p.Ala1517Val	p.A1517V	ENST00000361445	NM_004958.3	1517	gCt/gTt	31/58	1	2	FACETS	0.281	0.233	0.335	0.281	0.233	0.335	SUBCLONAL	1	TRUE	1	0.405910579069938	2		326	701	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47601139	47601139	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	89	178	0	ENST00000263735.4:c.377G>A	p.Arg126Lys	p.R126K	ENST00000263735	NM_002354.2	126	aGa/aAa	3/9	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.405910579069938	2		178	425	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936564	49936564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199940178	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	118	474	1	ENST00000296474.3:c.1363C>T	p.Arg455Cys	p.R455C	ENST00000296474	NM_002447.2	455	Cgc/Tgc	2/20	1	2	FACETS	0.724	0.653	0.799	0.724	0.653	0.799	SUBCLONAL	1	TRUE	1	0.405910579069938	2		475	803	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247411	71247411	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756099573	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	73	146	0	ENST00000318789.4:c.122C>T	p.Thr41Met	p.T41M	ENST00000318789	NM_032682.5	41	aCg/aTg	6/21	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.405910579069938	2		146	340	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215250	142215250	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs758234545	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	111	353	1	ENST00000350721.4:c.5851C>T	p.Arg1951Ter	p.R1951*	ENST00000350721	NM_001184.3	1951	Cga/Tga	34/47	1	2	FACETS	0.825	0.743	0.912	0.825	0.743	0.912	CLONAL	1	TRUE	1	0.405910579069938	2		354	663	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178095	56178095	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374455781	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	71	218	0	ENST00000399503.3:c.3068G>A	p.Arg1023His	p.R1023H	ENST00000399503	NM_005921.1	1023	cGc/cAc	14/20	1	2	FACETS	0.909	0.797	1	0.909	0.797	1	CLONAL	1	TRUE	1	0.405910579069938	2		218	385	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858432	27858432	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	85	219	0	ENST00000359303.2:c.139G>C	p.Val47Leu	p.V47L	ENST00000359303	NM_003535.2	47	Gtg/Ctg	1/1	0.39417986029905	2	FACETS	1	0.938	1	0.54	0.48	0.603	CLONAL	1	TRUE	0	0.405910579069938	2		219	388	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829192	128829192	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	57	112	0	ENST00000249373.3:c.200C>T	p.Ala67Val	p.A67V	ENST00000249373	NM_005631.4	67	gCt/gTt	1/12	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.405910579069938	2		112	261	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274929	38274929	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749758370	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	111	330	0	ENST00000425967.3:c.1651G>A	p.Ala551Thr	p.A551T	ENST00000425967	NM_001174067.1	551	Gca/Aca	13/19	0.405910579069938	3	FACETS	0.869	0.781	0.962	0.435	0.39	0.481	CLONAL	1	TRUE	1	0.405910579069938	3		330	757	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572189	64572189	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	82	262	0	ENST00000312049.6:c.1450C>T	p.Arg484Trp	p.R484W	ENST00000312049	NM_130799.2	484	Cgg/Tgg	10/10	1	2	FACETS	0.835	0.739	0.937	0.835	0.739	0.937	CLONAL	1	TRUE	1	0.405910579069938	2		262	484	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200476	67200476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777468878	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	99	225	0	ENST00000312629.5:c.670G>A	p.Ala224Thr	p.A224T	ENST00000312629	NM_003952.2	224	Gcc/Acc	8/15	1	2	FACETS	0.974	0.873	1	0.974	0.873	1	CLONAL	1	TRUE	1	0.405910579069938	2		225	501	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373403	118373403	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	116	269	0	ENST00000534358.1:c.6796T>G	p.Ser2266Ala	p.S2266A	ENST00000534358	NM_005933.3	2266	Tct/Gct	27/36	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.405910579069938	2		269	510	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691128	18691128	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	68	254	0	ENST00000266497.5:c.3239A>G	p.Tyr1080Cys	p.Y1080C	ENST00000266497		1080	tAc/tGc	23/31	1	2	FACETS	0.745	0.65	0.846	0.745	0.65	0.846	SUBCLONAL	1	TRUE	1	0.405910579069938	2		254	450	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679727	88679727	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	73	224	0	ENST00000360948.2:c.736A>G	p.Thr246Ala	p.T246A	ENST00000360948	NM_001012338.2	246	Act/Gct	7/19	1	2	FACETS	0.66	0.578	0.748	0.66	0.578	0.748	SUBCLONAL	1	TRUE	1	0.405910579069938	2		224	545	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467182	99467182	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	69	300	0	ENST00000268035.6:c.2563C>A	p.Pro855Thr	p.P855T	ENST00000268035	NM_000875.3	855	Cct/Act	12/21	1	2	FACETS	0.564	0.491	0.642	0.564	0.491	0.642	SUBCLONAL	1	TRUE	1	0.405910579069938	2		300	603	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2218149	2218149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757105676	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	36	430	0	ENST00000326181.6:c.211C>T	p.Arg71Trp	p.R71W	ENST00000326181	NM_032271.2	71	Cgg/Tgg	4/21	1	2	FACETS	0.266	0.217	0.32	0.266	0.217	0.32	SUBCLONAL	1	TRUE	1	0.405910579069938	2		430	668	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641097	23641097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	44	242	0	ENST00000261584.4:c.2378G>A	p.Gly793Asp	p.G793D	ENST00000261584	NM_024675.3	793	gGc/gAc	5/13	1	2	FACETS	0.39	0.326	0.46	0.39	0.326	0.46	SUBCLONAL	1	TRUE	1	0.405910579069938	2		242	556	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822267	72822267	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	150	429	0	ENST00000268489.5:c.9908T>G	p.Leu3303Arg	p.L3303R	ENST00000268489	NM_006885.3	3303	cTc/cGc	10/10	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.405910579069938	NA		429	767	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984616	72984616	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142600441	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	118	414	2	ENST00000268489.5:c.2968C>T	p.Arg990Cys	p.R990C	ENST00000268489	NM_006885.3	990	Cgc/Tgc	3/10	0.201957234028544	0	FACETS	0.446	0.402	0.492			1	INDETERMINATE	1	TRUE	0	0.405910579069938	0		416	775	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985596	60985596	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761696930	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	31	88	0	ENST00000333681.4:c.304G>A	p.Asp102Asn	p.D102N	ENST00000333681		102	Gac/Aac	2/3	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.405910579069938	2		88	143	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4097323	4097323	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151133017	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	81	244	0	ENST00000262948.5:c.938G>A	p.Arg313Gln	p.R313Q	ENST00000262948	NM_030662.3	313	cGg/cAg	8/11	1	2	FACETS	0.706	0.623	0.795	0.706	0.623	0.795	SUBCLONAL	1	TRUE	1	0.405910579069938	2		244	565	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251552	10251552	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375976847	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	107	272	0	ENST00000340748.4:c.3380C>T	p.Pro1127Leu	p.P1127L	ENST00000340748		1127	cCg/cTg	31/40	1	2	FACETS	0.953	0.858	1	0.953	0.858	1	CLONAL	1	TRUE	1	0.405910579069938	2		272	553	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905512	50905512	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1200514497	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	112	345	0	ENST00000440232.2:c.640G>A	p.Val214Met	p.V214M	ENST00000440232	NM_002691.3	214	Gtg/Atg	6/27	NA	2	FACETS	1	0.92	1			1	INDETERMINATE	1	TRUE	NA	0.405910579069938	2		345	540	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253807	30253807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1447088802	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	113	219	0	ENST00000307677.4:c.647C>T	p.Thr216Met	p.T216M	ENST00000307677	NM_138578.1	216	aCg/aTg	3/3	0.405910579069938	3	FACETS	1	0.923	1	0.514	0.463	0.567	CLONAL	1	TRUE	1	0.405910579069938	3		219	652	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845376	42845376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537370123	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	68	199	0	ENST00000398585.3:c.886G>A	p.Gly296Ser	p.G296S	ENST00000398585	NM_001135099.1	296	Ggc/Agc	9/14	1	2	FACETS	0.677	0.59	0.77	0.677	0.59	0.77	SUBCLONAL	1	TRUE	1	0.405910579069938	2		199	495	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656849	45656849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199766847	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	111	191	0	ENST00000407780.3:c.307G>A	p.Val103Ile	p.V103I	ENST00000407780	NM_001283052.1	103	Gtc/Atc	3/7	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.405910579069938	2		191	489	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933883	39933883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	68	278	1	ENST00000378444.4:c.716C>T	p.Thr239Ile	p.T239I	ENST00000378444	NM_001123385.1	239	aCc/aTc	4/15	0.201957234028544	0	FACETS	0.384	0.334	0.437			1	INDETERMINATE	1	TRUE	0	0.405910579069938	0		279	519	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76931785	76931785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	66	370	0	ENST00000373344.5:c.3745G>A	p.Ala1249Thr	p.A1249T	ENST00000373344	NM_000489.3	1249	Gcc/Acc	10/35	0.201957234028544	0	FACETS	0.318	0.276	0.364			1	INDETERMINATE	1	TRUE	0	0.405910579069938	0		370	607	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468185	120468185	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	22	153	1	ENST00000256646.2:c.4254del	p.Ser1419AlafsTer8	p.S1419Afs*8	ENST00000256646	NM_024408.3	1418	ccC/cc	25/34	1	2	FACETS	0.289	0.223	0.365	0.289	0.223	0.365	SUBCLONAL	1	TRUE	1	0.405910579069938	2		154	375	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675170	30675172	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs1472156046	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	78	323	0	ENST00000376406.3:c.3073_3075del	p.Lys1025del	p.K1025del	ENST00000376406	NM_014641.2	1025	AAG/-	9/15	0.39417986029905	2	FACETS	0.582	0.512	0.658	0.291	0.256	0.329	SUBCLONAL	1	TRUE	0	0.405910579069938	2		323	660	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347456	91347456	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	40	280	0	ENST00000355112.3:c.3621del	p.Val1208CysfsTer71	p.V1208Cfs*71	ENST00000355112	NM_000057.2	1206	gcA/gc	19/22	1	2	FACETS	0.349	0.289	0.415	0.349	0.289	0.415	SUBCLONAL	1	TRUE	1	0.405910579069938	2		280	565	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830902	72830903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	126	579	0	ENST00000268489.5:c.5677_5678dup	p.Asp1894GlyfsTer21	p.D1894Gfs*21	ENST00000268489	NM_006885.3	1893	agg/agAGg	9/10	0.201957234028544	0	FACETS	0.443	0.401	0.487			1	INDETERMINATE	1	TRUE	0	0.405910579069938	0		579	833	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178503	56178503	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	53	290	0	ENST00000399503.3:c.3479del	p.Lys1160ArgfsTer12	p.K1160Rfs*12	ENST00000399503	NM_005921.1	1159	gAa/ga	14/20	1	2	FACETS	0.484	0.413	0.563	0.484	0.413	0.563	SUBCLONAL	1	TRUE	1	0.405910579069938	2		290	539	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492828	56492829	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	108	231	0	ENST00000407977.2:c.110_111del	p.Glu37ValfsTer2	p.E37Vfs*2	ENST00000407977		37	gAG/g	2/10	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.405910579069938	2		231	517	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699401	47699404	+	frameshift_variant	Frame_Shift_Del	DEL	CACA	CACA	-	novel	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	56	263	0	ENST00000347630.2:c.104_107del	p.Met35ArgfsTer30	p.M35Rfs*30	ENST00000347630	NM_001007230.1	35	aTGTGg/ag	4/11	1	2	FACETS	0.657	0.564	0.758	0.657	0.564	0.758	SUBCLONAL	1	TRUE	1	0.405910579069938	2		263	420	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142051	108142051	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	53	280	0	ENST00000278616.4:c.2999del	p.Asn1000ThrfsTer2	p.N1000Tfs*2	ENST00000278616	NM_000051.3	999	Aaa/aa	20/63	1	2	FACETS	0.472	0.402	0.549	0.472	0.402	0.549	SUBCLONAL	1	TRUE	1	0.405910579069938	2		280	553	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262326	46262326	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	130	467	0	ENST00000371998.3:c.915del	p.Phe305LeufsTer3	p.F305Lfs*3	ENST00000371998		304	Ttt/tt	9/23	NA	2	FACETS	0.701	0.635	0.77			1	INDETERMINATE	1	TRUE	NA	0.405910579069938	2		467	914	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0004090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	336	328	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.744620233652903	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.744620233652903	1		328	547	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972840	32972840	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	852	213	0	ENST00000380152.3:c.10190C>T	p.Ser3397Phe	p.S3397F	ENST00000380152		3397	tCc/tTc	27/27	0.744620233652903	4	FACETS	1	0.988	1			1	CLONAL	3	TRUE	NA	0.744620233652903	4		213	1305	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0004096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	41	138	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	FALSE	1	0.222109056950728	2		138	256	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026368	48026368	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	38	195	0	ENST00000234420.5:c.1246A>G	p.Ile416Val	p.I416V	ENST00000234420	NM_000179.2	416	Att/Gtt	4/10	1	2	FACETS	0.915	0.758	1	0.915	0.758	1	CLONAL	1	FALSE	1	0.222109056950728	2		195	374	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259123	89259123	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	32	207	0	ENST00000336596.2:c.267G>T	p.Arg89Ser	p.R89S	ENST00000336596	NM_005233.5	89	agG/agT	3/17	1	2	FACETS	1	0.826	1	1	0.826	1	CLONAL	1	FALSE	1	0.222109056950728	2		207	284	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999443	100999443	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11571144	NA	P-0004096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	42	396	0	ENST00000325455.5:c.359C>T	p.Ala120Val	p.A120V	ENST00000325455	NM_001202474.3	120	gCg/gTg	1/8	0.222109056950728	0	FACETS	0.76	0.636	0.898			1	SUBCLONAL	1	FALSE	0	0.222109056950728	0		396	387	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822124	72822124	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	23	309	0	ENST00000268489.5:c.10051G>C	p.Ala3351Pro	p.A3351P	ENST00000268489	NM_006885.3	3351	Gcc/Ccc	10/10	0.222109056950728	0	FACETS	0.434	0.338	0.546			1	SUBCLONAL	1	FALSE	0	0.222109056950728	0		309	371	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380276	+	missense_variant	Missense_Mutation	DNP	TT	TT	CG	novel	NA	P-0004096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	37	241	0	ENST00000311936.3:c.182_183delinsCG	p.Gln61Pro	p.Q61P	ENST00000311936	NM_004985.3	61	cAA/cCG	3/5	0.169578585189193	3	FACETS	1	0.855	1	0.52	0.429	0.621	CLONAL	1	FALSE	1	0.222109056950728	3		241	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0004130-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	221	607	1	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.630984667252027	2	FACETS	0.794	0.75	0.837	0.794	0.75	0.837	SUBCLONAL	2	FALSE	0	0.677637458142972	2		608	411	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199967	128199967	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004130-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	21	300	0	ENST00000341105.2:c.1338C>G	p.Phe446Leu	p.F446L	ENST00000341105	NM_032638.4	446	ttC/ttG	6/6	0.467988917236781	4	FACETS	0.297	0.228	0.377	0.149	0.114	0.189	SUBCLONAL	1	FALSE	2	0.677637458142972	4		300	350	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549308	187549308	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004130-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	192	366	0	ENST00000441802.2:c.4810G>A	p.Gly1604Arg	p.G1604R	ENST00000441802	NM_005245.3	1604	Gga/Aga	9/27	0.610322958366748	2	FACETS	0.964	0.914	1	0.964	0.914	1	CLONAL	2	FALSE	0	0.677637458142972	2		366	294	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78519437	78519437	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004130-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	61	168	0	ENST00000306801.3:c.8C>A	p.Ser3Tyr	p.S3Y	ENST00000306801	NM_020761.2	3	tCc/tAc	1/34	0.423296100391618	5	FACETS	0.782	0.684	0.887	0.522	0.456	0.591	SUBCLONAL	2	FALSE	2	0.677637458142972	5		168	232	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208290	5208290	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004130-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	252	597	0	ENST00000357368.4:c.5600A>C	p.Lys1867Thr	p.K1867T	ENST00000357368	NM_002850.3	1867	aAg/aCg	36/38	0.630984667252027	2	FACETS	0.885	0.843	0.927	0.885	0.843	0.927	CLONAL	2	FALSE	0	0.677637458142972	2		597	420	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997826	149997826	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004130-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	238	486	1	ENST00000253339.5:c.2641del	p.Asp881IlefsTer11	p.D881Ifs*11	ENST00000253339		881	Gat/at	5/7	0.610322958366748	2	FACETS	0.832	0.79	0.874	0.832	0.79	0.874	CLONAL	2	FALSE	0	0.677637458142972	2		487	422	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176085759	176085759	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0004130-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	188	359	0	ENST00000367669.3:c.1026+1del		p.X342_splice	ENST00000367669	NM_022457.5	342			NA	2	FACETS	0.811	0.764	0.858			1	INDETERMINATE	2	FALSE	NA	0.677637458142972	2		359	342	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120526	94120536	+	frameshift_variant	Frame_Shift_Del	DEL	TCCAATCTCTC	TCCAATCTCTC	-	novel	NA	P-0004130-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	295	879	0	ENST00000369303.4:c.515_525del	p.Arg172ThrfsTer35	p.R172Tfs*35	ENST00000369303	NM_004440.3	172	aGAGAGATTGGA/a	3/17	0.439823146712841	5	FACETS	1	0.963	1	0.684	0.646	0.722	CLONAL	2	FALSE	2	0.677637458142972	5		879	856	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0004133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	467	535	0	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	0.289797978420822	4	FACETS	0.879	0.841	0.916	0.879	0.841	0.916	CLONAL	4	TRUE	0	0.29957889647306	4		535	1153	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358586	67358587	+	missense_variant	Missense_Mutation	DNP	GA	GA	CG	novel	NA	P-0004133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	99	467	0	ENST00000327367.4:c.94_95delinsCG	p.Glu32Arg	p.E32R	ENST00000327367	NM_005902.3	32	GAg/CGg	1/9	0.267673038429275	3	FACETS	0.851	0.759	0.95	0.425	0.379	0.475	CLONAL	1	TRUE	1	0.29957889647306	3		467	893	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183724	10183724	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	43	357	0	ENST00000256474.2:c.193T>A	p.Ser65Thr	p.S65T	ENST00000256474	NM_000551.3	65	Tcg/Acg	1/3	0.592800852241569	1	FACETS	0.266	0.223	0.314	0.266	0.223	0.314	SUBCLONAL	1	TRUE	0	0.637322316663636	1		357	345	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307256	118307256	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	13	37	1	ENST00000534358.1:c.29C>T	p.Pro10Leu	p.P10L	ENST00000534358	NM_005933.3	10	cCc/cTc	1/36	0.584497581009878	1	FACETS	0.591	0.437	0.764	0.591	0.437	0.764	SUBCLONAL	1	TRUE	0	0.637322316663636	1		38	47	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28908189	28908189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368881360	NA	P-0004141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	111	427	0	ENST00000282397.4:c.2566C>T	p.Arg856Trp	p.R856W	ENST00000282397	NM_002019.4	856	Cgg/Tgg	18/30	1	2	FACETS	0.359	0.322	0.398	0.359	0.322	0.398	SUBCLONAL	1	TRUE	1	0.637322316663636	2		427	971	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575560	64575560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	82	288	0	ENST00000312049.6:c.457del	p.Asp153ThrfsTer32	p.D153Tfs*32	ENST00000312049	NM_130799.2	153	Gac/ac	3/10	0.584497581009878	1	FACETS	0.426	0.377	0.477	0.426	0.377	0.477	SUBCLONAL	1	TRUE	0	0.637322316663636	1		288	412	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692863	89692868	+	inframe_deletion	In_Frame_Del	DEL	ACAATC	ACAATC	-	novel	NA	P-0004141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	64	94	0	ENST00000371953.3:c.348_353del	p.Asn117_His118del	p.N117_H118del	ENST00000371953	NM_000314.4	116	gACAATCat/gat	5/9	0.584497581009878	1	FACETS	0.716	0.632	0.804	0.716	0.632	0.804	SUBCLONAL	1	TRUE	0	0.637322316663636	1		94	191	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4388076	4388076	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	74	277	0	ENST00000261254.3:c.562T>A	p.Cys188Ser	p.C188S	ENST00000261254	NM_001759.3	188	Tgt/Agt	3/5	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.665524302853665	2		277	178	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273506	5273506	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	78	728	0	ENST00000357368.4:c.326C>G	p.Ala109Gly	p.A109G	ENST00000357368	NM_002850.3	109	gCc/gGc	4/38	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.665524302853665	2		728	204	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579529	7579529	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658483	NA	P-0004223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	41	320	0	ENST00000269305.4:c.158G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tGg/tAg	4/11	0.495049142220253	1	FACETS	0.998	0.852	1	0.998	0.852	1	CLONAL	1	TRUE	0	0.510243668047253	1		320	120	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098478	47098478	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	25	349	0	ENST00000409792.3:c.6796C>T	p.Gln2266Ter	p.Q2266*	ENST00000409792	NM_014159.6	2266	Cag/Tag	15/21	0.510243668047253	1	FACETS	0.579	0.463	0.708	0.579	0.463	0.708	SUBCLONAL	1	TRUE	0	0.510243668047253	1		349	126	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166449	32166449	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	48	522	0	ENST00000375023.3:c.4594G>A	p.Glu1532Lys	p.E1532K	ENST00000375023	NM_004557.3	1532	Gag/Aag	25/30	0.361183021601514	2	FACETS	1	0.947	1	0.611	0.527	0.7	CLONAL	1	TRUE	0	0.510243668047253	2		522	154	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572588	64572588	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	38	233	0	ENST00000312049.6:c.1268G>A	p.Trp423Ter	p.W423*	ENST00000312049	NM_130799.2	423	tGg/tAg	9/10	0.510243668047253	1	FACETS	0.965	0.818	1	0.965	0.818	1	CLONAL	1	TRUE	0	0.510243668047253	1		233	115	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144609	119144609	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	42	416	0	ENST00000264033.4:c.622G>T	p.Ala208Ser	p.A208S	ENST00000264033	NM_005188.3	208	Gct/Tct	4/16	0.510243668047253	1	FACETS	0.818	0.695	0.948	0.818	0.695	0.948	CLONAL	1	TRUE	0	0.510243668047253	1		416	150	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440097	49440097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	40	399	0	ENST00000301067.7:c.4529G>A	p.Cys1510Tyr	p.C1510Y	ENST00000301067	NM_003482.3	1510	tGt/tAt	16/54	1	2	FACETS	0.945	0.797	1	0.945	0.797	1	CLONAL	1	TRUE	1	0.510243668047253	2		399	166	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136342	2136342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	28	393	0	ENST00000219476.3:c.4811G>A	p.Gly1604Asp	p.G1604D	ENST00000219476	NM_000548.3	1604	gGc/gAc	37/42	0.296923539943386	0	FACETS	0.538	0.44	0.643			1	INDETERMINATE	1	TRUE	0	0.510243668047253	0		393	100	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573666	48573666	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0004223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	18	160	0	ENST00000342988.3:c.249+1G>A		p.X83_splice	ENST00000342988	NM_005359.5	83			0.39553849450443	1	FACETS	0.665	0.512	0.837	0.665	0.512	0.837	SUBCLONAL	1	TRUE	0	0.510243668047253	1		160	79	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288192	33288193	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0004223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	34	266	0	ENST00000374542.5:c.1215_1216del	p.Ala406ArgfsTer11	p.A406Rfs*11	ENST00000374542	NM_001141970.1	405	tcTGca/tcca	4/8	0.361183021601514	2	FACETS	1	0.846	1	0.509	0.423	0.601	CLONAL	1	TRUE	0	0.510243668047253	2		266	131	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851663	63851664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004231-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	82	449	0	ENST00000279873.7:c.2442dup	p.Glu815ArgfsTer12	p.E815Rfs*12	ENST00000279873	NM_032199.2	814	tta/ttAa	10/10	0.331036964925025	3	FACETS	0.66	0.581	0.744	0.33	0.29	0.372	SUBCLONAL	1	TRUE	1	0.413779248839709	3		449	725	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0004270-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	134	212	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.928	0.857	1	1	0.991	1	CLONAL	2	TRUE	1	0.455380733919251	2		213	317	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0004270-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	185	573	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.259761991414047	3	FACETS	0.814	0.755	0.874	0.814	0.755	0.874	INDETERMINATE	2	TRUE	1	0.455380733919251	3		574	613	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890142	76890145	+	frameshift_variant	Frame_Shift_Del	DEL	TTTC	TTTC	-	novel	NA	P-0004270-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	239	242	0	ENST00000373344.5:c.4749_4752del	p.Lys1583AsnfsTer22	p.K1583Nfs*22	ENST00000373344	NM_000489.3	1583	aaGAAA/aa	17/35	1	1	FACETS	1	0.993	1	1	0.996	1	CLONAL	2	TRUE	0	0.455380733919251	1		242	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691003	NA	P-0004270-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	211	256	0	ENST00000269305.4:c.96+1G>T		p.X32_splice	ENST00000269305	NM_001126112.2	32			0.259761991414047	3	FACETS	0.927	0.874	0.98	1	0.992	1	INDETERMINATE	3	TRUE	1	0.455380733919251	3		256	409	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0004272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	253	381	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.657555555618091	3	FACETS	0.976	0.923	1	0.976	0.923	1	CLONAL	2	TRUE	1	0.657555555618091	3		381	524	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0004272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	41	491	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.877	1			1	INDETERMINATE	1	TRUE	NA	0.657555555618091	2		491	121	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436296	110436297	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGG	rs34412495	NA	P-0004272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	18	69	1	ENST00000375856.3:c.2102_2104dup	p.Ala701dup	p.A701dup	ENST00000375856	NM_003749.2	701	gtg/gCCGtg	1/2	0.657555555618091	4	FACETS	0.726	0.553	0.926	0.363	0.276	0.463	CLONAL	1	TRUE	2	0.657555555618091	4		70	125	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418935	116418935	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	93	321	0	ENST00000397752.3:c.3446G>T	p.Ser1149Ile	p.S1149I	ENST00000397752	NM_000245.2	1149	aGt/aTt	17/21	0.657555555618091	3	FACETS	0.85	0.76	0.946	0.425	0.38	0.473	CLONAL	1	TRUE	1	0.657555555618091	3		321	442	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336403	80336403	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	55	195	0	ENST00000286548.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000286548	NM_002072.3	306	Cga/Tga	7/7	1	2	FACETS	0.824	0.715	0.939	0.824	0.715	0.939	CLONAL	1	TRUE	1	0.657555555618091	2		195	203	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801074	135801074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	108	321	0	ENST00000298552.3:c.263C>T	p.Ser88Phe	p.S88F	ENST00000298552	NM_001162426.1	88	tCc/tTc	5/23	0.657555555618091	3	FACETS	0.866	0.781	0.956			1	CLONAL	1	TRUE	NA	0.657555555618091	3		321	504	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413137	139413137	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	157	404	0	ENST00000277541.6:c.1005C>G	p.Asn335Lys	p.N335K	ENST00000277541	NM_017617.3	335	aaC/aaG	6/34	0.153765261477176	5	FACETS	0.789	0.726	0.854			1	INDETERMINATE	2	TRUE	NA	0.657555555618091	5		404	601	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033967	49033967	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	224	304	0	ENST00000267163.4:c.2104C>A	p.Gln702Lys	p.Q702K	ENST00000267163	NM_000321.2	702	Caa/Aaa	20/27	0.245116980185764	3	FACETS	0.929	0.887	0.969			1	INDETERMINATE	3	TRUE	NA	0.657555555618091	3		304	325	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533770	63533770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502156	NA	P-0004272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	147	234	0	ENST00000307078.5:c.1384C>T	p.Pro462Ser	p.P462S	ENST00000307078	NM_004655.3	462	Ccc/Tcc	6/11	0.596106056658313	4	FACETS	0.908	0.838	0.98	0.908	0.838	0.98	CLONAL	2	TRUE	2	0.657555555618091	4		234	408	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30956897	30956897	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	285	482	0	ENST00000375687.4:c.223C>T	p.Pro75Ser	p.P75S	ENST00000375687	NM_015338.5	75	Cct/Tct	4/13	0.636576240423997	4	FACETS	0.897	0.847	0.948	0.897	0.847	0.948	CLONAL	2	TRUE	2	0.657555555618091	4		482	801	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578284	7578310	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCAGACCTAAGAGCAATCAGTGAGGAA	CCAGACCTAAGAGCAATCAGTGAGGAA	-	novel	NA	P-0004272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	211	371	0	ENST00000269305.4:c.560-21_565del		p.X187_splice	ENST00000269305	NM_001126112.2	187		6/11	0.657555555618091	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.657555555618091	2		371	303	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423414	116423414	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004294-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	925	703	2	ENST00000397752.3:c.3689A>C	p.Tyr1230Ser	p.Y1230S	ENST00000397752	NM_000245.2	1230	tAt/tCt	19/21	0.340594139058543	11	FACETS	0.945	0.92	0.969			1	CLONAL	9	FALSE	NA	0.340594139058543	11		705	1618	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475147	475147	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0004294-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	220	695	0	ENST00000399788.2:c.490A>T	p.Arg164Ter	p.R164*	ENST00000399788	NM_001042603.1	164	Aga/Tga	4/28	0.195193238471138	3	FACETS	0.905	0.849	0.961	1	0.991	1	INDETERMINATE	3	FALSE	1	0.340594139058543	3		695	557	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298695	15298695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004294-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	67	618	0	ENST00000263388.2:c.1603G>A	p.Glu535Lys	p.E535K	ENST00000263388	NM_000435.2	535	Gag/Aag	10/33	0.346864564212209	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	0	0.340594139058543	1		618	234	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105728	27105728	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004294-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	127	471	1	ENST00000324856.7:c.5340del	p.Val1781Ter	p.V1781*	ENST00000324856	NM_006015.4	1780	gAa/ga	20/20	0.15553133431221	3	FACETS	0.978	0.893	1			1	INDETERMINATE	2	FALSE	NA	0.340594139058543	3		472	446	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0004298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	333	212	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.985	0.937	1	0.985	0.937	1	CLONAL	1	TRUE	1	0.880124441101655	2		213	768	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0004298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	379	266	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	0.880124441101655	2		266	861	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890108	76890108	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	487	404	1	ENST00000373344.5:c.4786A>G	p.Met1596Val	p.M1596V	ENST00000373344	NM_000489.3	1596	Atg/Gtg	17/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.880124441101655	1		405	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577019	+	stop_gained,frameshift_variant,splice_region_variant	Nonsense_Mutation	INS	-	-	CTCGCTTAGTGCTCCCTGGGGGCAG	novel	NA	P-0004298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	304	426	0	ENST00000269305.4:c.895_919dup	p.Leu308AlafsTer6	p.L308Afs*6	ENST00000269305	NM_001126112.2	307	gca/gCTGCCCCCAGGGAGCACTAAGCGAGca		0.880124441101655	2	FACETS	1	0.982	1	0.534	0.507	0.561	CLONAL	1	TRUE	0	0.880124441101655	2		426	647	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911560	101911561	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	310	457	0	ENST00000374994.4:c.1486dup	p.Ser496LysfsTer28	p.S496Kfs*28	ENST00000374994	NM_004612.2	495	-/A	9/9	0.199261707689903	1	FACETS	0.522	0.495	0.55	0.522	0.495	0.55	INDETERMINATE	1	TRUE	0	0.880124441101655	1		457	755	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0004319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	275	138	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.0725312744493189	3	FACETS	0.968	0.934	1			1	INDETERMINATE	10	FALSE	NA	0.173436427704505	3		138	356	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0004319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	275	212	1	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	0.997	1	CLONAL	4	FALSE	1	0.173436427704505	2		213	721	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531052	187531052	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	166	329	0	ENST00000441802.2:c.9971A>T	p.Asn3324Ile	p.N3324I	ENST00000441802	NM_005245.3	3324	aAt/aTt	15/27	0.173436427704505	1	FACETS	0.876	0.808	0.947	1	0.993	1	CLONAL	3	FALSE	0	0.173436427704505	1		329	665	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855033	76855034	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	325	368	0	ENST00000373344.5:c.5802dup	p.Lys1935GlufsTer7	p.K1935Efs*7	ENST00000373344	NM_000489.3	1934	-/G	25/35	0.173436427704505	1	FACETS	0.88	0.833	0.928	1	0.997	1	CLONAL	4	FALSE	0	0.173436427704505	1		368	972	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0004337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	113	579	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.324377832587843	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		579	314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574002	7574002	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs375338359	NA	P-0004351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	192	425	0	ENST00000269305.4:c.1025G>C	p.Arg342Pro	p.R342P	ENST00000269305	NM_001126112.2	342	cGa/cCa	10/11	0.236358296438116	3	FACETS	0.861	0.794	0.931	0.861	0.794	0.931	CLONAL	2	TRUE	1	0.18	3		425	1350	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144726	58144726	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	153	241	0	ENST00000257904.6:c.502C>G	p.Gln168Glu	p.Q168E	ENST00000257904	NM_000075.3	168	Cag/Gag	4/8	0.236358296438116	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.18	3		241	845	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578517	7578517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750600586	NA	P-0004360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	69	162	0	ENST00000269305.4:c.413C>T	p.Ala138Val	p.A138V	ENST00000269305	NM_001126112.2	138	gCc/gTc	5/11	0.450405527372424	2	FACETS	0.911	0.829	0.991	1	0.979	1	CLONAL	3	TRUE	0	0.446799274670214	2		162	113	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480074	120480074	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	14	127	0	ENST00000256646.2:c.3353A>T	p.His1118Leu	p.H1118L	ENST00000256646	NM_024408.3	1118	cAc/cTc	21/34	0.316783110587156	4	FACETS	0.708	0.516	0.937	0.236	0.172	0.313	CLONAL	1	TRUE	1	0.446799274670214	4		127	128	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803183	1803183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764712450	NA	P-0004360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	41	235	2	ENST00000260795.2:c.535G>A	p.Ala179Thr	p.A179T	ENST00000260795		179	Gct/Act	4/17	0.31678060512305	3	FACETS	0.936	0.799	1			1	CLONAL	2	TRUE	NA	0.446799274670214	3		237	120	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771923	135771923	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753388676	NA	P-0004384-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	37	301	2	ENST00000298552.3:c.3194C>T	p.Thr1065Met	p.T1065M	ENST00000298552	NM_001162426.1	1065	aCg/aTg	23/23	0.25781905349675	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.824533150122863	0		303	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578393	7578393	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876660821	NA	P-0004384-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	236	270	0	ENST00000269305.4:c.537T>A	p.His179Gln	p.H179Q	ENST00000269305	NM_001126112.2	179	caT/caA	5/11	0.819137915482399	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	0	0.824533150122863	1		270	305	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0004399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	416	138	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.552047289880272	3	FACETS	0.991	0.956	1	0.991	0.956	1	CLONAL	3	TRUE	0	0.552047289880272	3		138	647	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0004399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	964	408	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.526798767045105	4	FACETS	1	0.997	1	1	0.998	1	CLONAL	3	TRUE	2	0.552047289880272	4		408	1566	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876476	35876476	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	217	234	0	ENST00000303115.3:c.1268C>G	p.Ser423Cys	p.S423C	ENST00000303115	NM_002185.3	423	tCt/tGt	8/8	0.552047289880272	4	FACETS	1	0.947	1	0.341	0.317	0.367	CLONAL	1	TRUE	1	0.552047289880272	4		234	1192	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435139	18435139	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	184	263	0	ENST00000266497.5:c.124C>G	p.Gln42Glu	p.Q42E	ENST00000266497		42	Cag/Gag	1/31	0.526798767045105	4	FACETS	0.846	0.779	0.916	0.423	0.389	0.458	CLONAL	1	TRUE	2	0.552047289880272	4		263	1223	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0004402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	58	367	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.200480610590901	5	FACETS	1	0.942	1			1	CLONAL	1	TRUE	NA	0.325461423709078	5		367	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0004402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	140	293	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.314718174606489	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.325461423709078	2		293	397	SUCCESS
APC	324	MSKCC	GRCh37	5	112175162	112175162	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561588104	NA	P-0004402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	120	195	0	ENST00000257430.4:c.3871C>T	p.Gln1291Ter	p.Q1291*	ENST00000257430	NM_000038.5	1291	Cag/Tag	16/16	0.325461423709078	4	FACETS	0.94	0.866	1	0.94	0.866	1	CLONAL	4	TRUE	0	0.325461423709078	4		195	260	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843578	156843578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758490619	NA	P-0004402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	165	569	1	ENST00000524377.1:c.1004C>T	p.Pro335Leu	p.P335L	ENST00000524377	NM_002529.3	335	cCg/cTg	8/17	0.229159773395855	5	FACETS	1	0.98	1	0.792	0.73	0.856	CLONAL	2	TRUE	2	0.325461423709078	5		570	635	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591251	67591251	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	87	244	2	ENST00000274335.5:c.1749G>A	p.Trp583Ter	p.W583*	ENST00000274335		583	tgG/tgA	13/15	0.156487520943403	4	FACETS	0.891	0.8	0.986			1	INDETERMINATE	3	TRUE	NA	0.325461423709078	4		246	265	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961884	15961884	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs970987519	NA	P-0004402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	150	379	0	ENST00000268712.3:c.5911G>A	p.Asp1971Asn	p.D1971N	ENST00000268712	NM_006311.3	1971	Gat/Aat	38/46	0.314718174606489	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.325461423709078	2		379	434	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736486	85736486	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	556	1284	1	ENST00000370580.1:c.161A>G	p.Glu54Gly	p.E54G	ENST00000370580	NM_003921.4	54	gAa/gGa	2/3	0.916687647391624	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.916687647391624	1		1285	651	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777875	3777875	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	413	854	0	ENST00000262367.5:c.7173G>T	p.Met2391Ile	p.M2391I	ENST00000262367	NM_004380.2	2391	atG/atT	31/31	1	2	FACETS	0.955	0.913	0.997	0.955	0.913	0.997	CLONAL	1	TRUE	1	0.916687647391624	2		854	944	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941725	48941732	+	frameshift_variant	Frame_Shift_Del	DEL	TGATTCTA	TGATTCTA	-	novel	NA	P-0004427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	275	516	0	ENST00000267163.4:c.1036_1043del	p.Asp346ArgfsTer4	p.D346Rfs*4	ENST00000267163	NM_000321.2	345	acTGATTCTAta/acta	10/27	0.916687647391624	1	FACETS	0.964	0.933	0.993	0.964	0.933	0.993	CLONAL	1	TRUE	0	0.916687647391624	1		516	337	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	114	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.165716964123432	1	FACETS	1	0.943	1	1	0.989	1	CLONAL	2	TRUE	0	0.165716964123432	1		326	593	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs864622237	NA	P-0004460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	63	205	0	ENST00000269305.4:c.700T>A	p.Tyr234Asn	p.Y234N	ENST00000269305	NM_001126112.2	234	Tac/Aac	7/11	1	2	FACETS	0.895	0.776	1	1	0.977	1	CLONAL	2	TRUE	1	0.165716964123432	2		205	425	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672497	30672497	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs200629873	NA	P-0004460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	44	329	0	ENST00000376406.3:c.4463C>G	p.Thr1488Arg	p.T1488R	ENST00000376406	NM_014641.2	1488	aCa/aGa	10/15	1	2	FACETS	0.745	0.623	0.88	0.745	0.623	0.88	SUBCLONAL	1	TRUE	1	0.165716964123432	2		329	713	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110251306	110251306	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	22	235	0	ENST00000374672.4:c.31G>T	p.Ala11Ser	p.A11S	ENST00000374672	NM_004235.4	11	Gct/Tct	2/5	1	2	FACETS	0.684	0.53	0.864	0.684	0.53	0.864	SUBCLONAL	1	TRUE	1	0.165716964123432	2		235	388	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122617	108122617	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1060501694	NA	P-0004460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	37	381	0	ENST00000278616.4:c.1661C>A	p.Thr554Lys	p.T554K	ENST00000278616	NM_000051.3	554	aCg/aAg	11/63	0.165716964123432	3	FACETS	0.831	0.684	0.996	0.415	0.342	0.498	CLONAL	1	TRUE	1	0.165716964123432	3		381	582	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045904	47045904	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	105	472	0	ENST00000377604.3:c.2699G>T	p.Gly900Val	p.G900V	ENST00000377604	NM_001204468.1	900	gGt/gTt	24/24	0.125128414915819	4	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.165716964123432	4		472	999	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916843	48916843	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	87	205	0	ENST00000267163.4:c.373del	p.Glu125LysfsTer11	p.E125Kfs*11	ENST00000267163	NM_000321.2	125	Gaa/aa	3/27	0.165716964123432	3	FACETS	0.984	0.878	1	1	0.979	1	CLONAL	3	TRUE	1	0.165716964123432	3		205	385	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057969	27057969	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	86	256	0	ENST00000324856.7:c.1678del	p.Tyr560ThrfsTer59	p.Y560Tfs*59	ENST00000324856	NM_006015.4	559	ccT/cc	3/20	0.141518030894484	2	FACETS	0.942	0.835	1	0.942	0.835	1	CLONAL	2	TRUE	0	0.165716964123432	2		256	551	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027634	48027636	+	inframe_deletion	In_Frame_Del	DEL	CCA	CCA	-	novel	NA	P-0004460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	17	171	0	ENST00000234420.5:c.2512_2514del	p.Pro838del	p.P838del	ENST00000234420	NM_000179.2	838	CCA/-	4/10	1	2	FACETS	0.912	0.682	1	0.912	0.682	1	CLONAL	1	TRUE	1	0.165716964123432	2		171	225	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0004466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	44	162	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.932	1	1	0.976	1	CLONAL	2	TRUE	1	0.241605848886097	2		162	156	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803171	1803171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1161547820	NA	P-0004466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	44	283	0	ENST00000260795.2:c.523C>T	p.Arg175Cys	p.R175C	ENST00000260795		175	Cgc/Tgc	4/17	1	2	FACETS	0.759	0.642	0.886	1	0.961	1	SUBCLONAL	2	TRUE	1	0.241605848886097	2		283	240	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425601	49425601	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0004466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	22	279	0	ENST00000301067.7:c.12887T>A	p.Leu4296Ter	p.L4296*	ENST00000301067	NM_003482.3	4296	tTa/tAa	39/54	1	2	FACETS	0.717	0.557	0.902	0.717	0.557	0.902	CLONAL	1	TRUE	1	0.241605848886097	2		279	254	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060989	38060990	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0004466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	18	120	0	ENST00000250448.2:c.999_1000del	p.Gln333HisfsTer81	p.Q333Hfs*81	ENST00000250448	NM_004496.3	333	caGAct/cact	2/2	1	2	FACETS	1	0.806	1	1	0.806	1	CLONAL	1	TRUE	1	0.241605848886097	2		120	139	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	46	543	0	ENST00000269305.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	336	Gag/Tag	10/11	0.46899580423062	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.46899580423062	1		543	116	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852534	63852534	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	20	206	1	ENST00000279873.7:c.3312G>C	p.Gln1104His	p.Q1104H	ENST00000279873	NM_032199.2	1104	caG/caC	10/10	0.46899580423062	8	FACETS	1	0.829	1			1	CLONAL	1	TRUE	NA	0.46899580423062	8		207	187	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124249	2124249	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	16	310	0	ENST00000219476.3:c.2404A>C	p.Ser802Arg	p.S802R	ENST00000219476	NM_000548.3	802	Agc/Cgc	22/42	0.154719645807475	3	FACETS	0.842	0.632	1	0.281	0.21	0.362	INDETERMINATE	1	TRUE	0	0.46899580423062	3		310	100	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857811	9857811	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	14	295	0	ENST00000330684.3:c.3590G>T	p.Gly1197Val	p.G1197V	ENST00000330684	NM_001134407.1	1197	gGt/gTt	13/13	0.154719645807475	3	FACETS	0.752	0.551	0.989	0.251	0.183	0.33	INDETERMINATE	1	TRUE	0	0.46899580423062	3		295	98	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983153	7983153	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	29	365	0	ENST00000319144.4:c.861C>G	p.Phe287Leu	p.F287L	ENST00000319144	NM_001139.2	287	ttC/ttG	7/15	0.46899580423062	1	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	0	0.46899580423062	1		365	86	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206884	36206884	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	14	109	0	ENST00000300305.3:c.628C>G	p.Leu210Val	p.L210V	ENST00000300305		210	Cta/Gta	6/8	0.1590256104862	5	FACETS	1	0.784	1			1	INDETERMINATE	1	TRUE	NA	0.46899580423062	5		109	94	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941887	44941887	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0004483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	36	362	0	ENST00000377967.4:c.3209+2T>G		p.X1070_splice	ENST00000377967	NM_021140.2	1070			0.333853764546313	0	FACETS	0.709	0.597	0.828			1	SUBCLONAL	1	TRUE	0	0.46899580423062	0		362	115	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720939	119720966	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGAATCACAAAGTTTGGCTTGATATA	CCTGAATCACAAAGTTTGGCTTGATATA	-	novel	NA	P-0004483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	53	317	0	ENST00000316626.5:c.209_236del	p.Val70GlufsTer23	p.V70Efs*23	ENST00000316626		70	gTATATCAAGCCAAACTTTGTGATTCAGGa/ga	2/12	0.325027010748237	5	FACETS	0.837	0.722	0.96	0.558	0.481	0.64	CLONAL	2	TRUE	2	0.46899580423062	5		317	230	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737133	162737144	+	inframe_deletion	In_Frame_Del	DEL	AGAAAATGCTGG	AGAAAATGCTGG	-	novel	NA	P-0004483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	17	202	0	ENST00000367921.3:c.1281_1292del	p.Met428_Lys431del	p.M428_K431del	ENST00000367921	NM_006182.2	426	cAGAAAATGCTGGag/cag	11/18	0.401428251167484	4	FACETS	0.705	0.53	0.91	0.235	0.176	0.304	CLONAL	1	TRUE	1	0.46899580423062	4		202	151	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934342	39934343	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0004483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	23	321	0	ENST00000378444.4:c.256_257delinsTT	p.Gly86Leu	p.G86L	ENST00000378444	NM_001123385.1	86	GGa/TTa	4/15	0.333853764546313	0	FACETS	0.744	0.6	0.899			1	SUBCLONAL	1	TRUE	0	0.46899580423062	0		321	70	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599333	55599333	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	405	358	0	ENST00000288135.5:c.2459A>C	p.Asp820Ala	p.D820A	ENST00000288135	NM_000222.2	820	gAt/gCt	17/21	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.820368261254374	2		358	916	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560493	65560493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	401	377	1	ENST00000358664.4:c.104G>T	p.Arg35Leu	p.R35L	ENST00000358664	NM_002382.4	35	cGt/cTt	3/5	0.820368261254374	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.820368261254374	1		378	555	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593583	55593604	+	protein_altering_variant	In_Frame_Del	DEL	AACCCATGTATGAAGTACAGTG	AACCCATGTATGAAGTACAGTG	TTCT	novel	NA	P-0004509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	297	426	0	ENST00000288135.5:c.1649_1670delinsTTCT	p.Lys550_Trp557delinsIleLeu	p.K550_W557delinsIL	ENST00000288135	NM_000222.2	550	aAACCCATGTATGAAGTACAGTGg/aTTCTg	11/21	NA	2	FACETS	0.861	0.814	0.909			1	INDETERMINATE	1	TRUE	NA	0.820368261254374	2		426	841	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	100	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.93	0.832	1	0.93	0.832	1	CLONAL	1	TRUE	1	0.367790901092919	2		326	585	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0004511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	61	138	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	TRUE	1	0.367790901092919	2		138	300	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0004511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	148	620	2	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.367790901092919	2		622	736	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208010	5208010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	104	415	1	ENST00000357368.4:c.5701C>T	p.Arg1901Trp	p.R1901W	ENST00000357368	NM_002850.3	1901	Cgg/Tgg	37/38	1	2	FACETS	0.941	0.844	1	0.941	0.844	1	CLONAL	1	TRUE	1	0.367790901092919	2		416	601	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244138	153244138	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	145	398	0	ENST00000281708.4:c.2019G>A	p.Trp673Ter	p.W673*	ENST00000281708	NM_033632.3	673	tgG/tgA	12/12	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.367790901092919	2		398	708	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244290	153244290	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	88	254	0	ENST00000281708.4:c.1867C>T	p.His623Tyr	p.H623Y	ENST00000281708	NM_033632.3	623	Cat/Tat	12/12	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.367790901092919	2		254	450	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473635	67473635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906853	NA	P-0004511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	141	352	0	ENST00000327367.4:c.715G>A	p.Glu239Lys	p.E239K	ENST00000327367	NM_005902.3	239	Gag/Aag	6/9	0.258590929658948	2	FACETS	1	0.988	1	0.746	0.683	0.81	CLONAL	1	TRUE	0	0.367790901092919	2		352	514	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473647	67473647	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886039137	NA	P-0004511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	32	346	0	ENST00000327367.4:c.727C>T	p.Arg243Cys	p.R243C	ENST00000327367	NM_005902.3	243	Cgc/Tgc	6/9	0.258590929658948	2	FACETS	0.337	0.272	0.409	0.168	0.136	0.205	SUBCLONAL	1	TRUE	0	0.367790901092919	2		346	517	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374935	45374935	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	192	360	1	ENST00000262160.6:c.908C>G	p.Thr303Arg	p.T303R	ENST00000262160	NM_005901.5	303	aCa/aGa	8/11	0.258590929658948	2	FACETS	0.899	0.836	0.962	0.899	0.836	0.962	CLONAL	2	TRUE	0	0.367790901092919	2		361	581	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411936	63411936	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	144	572	0	ENST00000330258.3:c.1231G>T	p.Glu411Ter	p.E411*	ENST00000330258	NM_152424.3	411	Gaa/Taa	2/2	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.367790901092919	2		572	740	SUCCESS
APC	324	MSKCC	GRCh37	5	112170816	112170816	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	113	385	0	ENST00000257430.4:c.1912del	p.Ile638TyrfsTer8	p.I638Yfs*8	ENST00000257430	NM_000038.5	638	Ata/ta	15/16	1	2	FACETS	0.993	0.895	1	0.993	0.895	1	CLONAL	1	TRUE	1	0.367790901092919	2		385	619	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358693	67358693	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	31	259	1	ENST00000327367.4:c.204del	p.Arg69GlyfsTer47	p.R69Gfs*47	ENST00000327367	NM_005902.3	67	atC/at	1/9	0.258590929658948	2	FACETS	0.419	0.339	0.51	0.21	0.169	0.255	SUBCLONAL	1	TRUE	0	0.367790901092919	2		260	402	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422497	225422497	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	670	385	0	ENST00000264414.4:c.143A>G	p.Asn48Ser	p.N48S	ENST00000264414	NM_003590.4	48	aAt/aGt	2/16	0.7799497568316	2	FACETS	0.972	0.949	0.994	0.972	0.949	0.994	CLONAL	2	TRUE	0	0.7799497568316	2		385	884	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713826	30713826	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	240	254	0	ENST00000295754.5:c.1151A>C	p.Asn384Thr	p.N384T	ENST00000295754	NM_003242.5	384	aAt/aCt	4/7	0.7799497568316	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.7799497568316	1		254	373	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628022	187628022	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	336	413	0	ENST00000441802.2:c.2960A>T	p.Gln987Leu	p.Q987L	ENST00000441802	NM_005245.3	987	cAg/cTg	2/27	0.7799497568316	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.7799497568316	1		413	515	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876230	35876230	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	493	308	1	ENST00000303115.3:c.1022G>T	p.Gly341Val	p.G341V	ENST00000303115	NM_002185.3	341	gGa/gTa	8/8	0.690759239830669	3	FACETS	0.969	0.933	1	0.969	0.933	1	CLONAL	2	TRUE	1	0.7799497568316	3		309	907	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793902	89793902	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs578015348	NA	P-0004517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	129	178	0	ENST00000336032.3:c.971A>G	p.Lys324Arg	p.K324R	ENST00000336032	NM_006813.2	324	aAa/aGa	2/2	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.7799497568316	2		178	320	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971003	21971003	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	237	293	1	ENST00000304494.5:c.355G>T	p.Glu119Ter	p.E119*	ENST00000304494	NM_000077.4	119	Gag/Tag	2/3	0.7799497568316	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.7799497568316	1		294	360	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396454	139396454	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	337	347	0	ENST00000277541.6:c.5471G>T	p.Arg1824Leu	p.R1824L	ENST00000277541	NM_017617.3	1824	cGg/cTg	29/34	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.7799497568316	2		347	825	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88672140	88672140	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	256	308	0	ENST00000372037.3:c.674T>G	p.Leu225Trp	p.L225W	ENST00000372037	NM_004329.2	225	tTg/tGg	8/13	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.7799497568316	2		308	618	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309744	104309744	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	336	417	0	ENST00000369902.3:c.335G>A	p.Gly112Glu	p.G112E	ENST00000369902	NM_016169.3	112	gGa/gAa	3/12	1	2	FACETS	0.967	0.918	1	0.967	0.918	1	CLONAL	1	TRUE	1	0.7799497568316	2		417	891	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999053	100999053	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	292	470	0	ENST00000325455.5:c.749G>T	p.Gly250Val	p.G250V	ENST00000325455	NM_001202474.3	250	gGa/gTa	1/8	0.7799497568316	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.7799497568316	1		470	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0004517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	252	300	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.7799497568316	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.7799497568316	1		300	368	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650809	37650809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	337	394	0	ENST00000447079.4:c.2281G>A	p.Asp761Asn	p.D761N	ENST00000447079	NM_015083.1	761	Gac/Aac	5/14	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.7799497568316	2		394	864	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372109	45372109	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	380	387	0	ENST00000262160.6:c.1060G>C	p.Ala354Pro	p.A354P	ENST00000262160	NM_005901.5	354	Gca/Cca	9/11	0.333105296849088	1	FACETS	0.755	0.722	0.789	0.755	0.722	0.789	INDETERMINATE	1	TRUE	0	0.7799497568316	1		387	787	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023569	27023570	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	T	novel	NA	P-0004517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	309	333	0	ENST00000324856.7:c.675_676delinsT	p.Ala226ProfsTer6	p.A226Pfs*6	ENST00000324856	NM_006015.4	225	ccCGcc/ccTcc	1/20	0.7799497568316	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.7799497568316	1		333	439	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259521	55259521	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004523-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	122	325	0	ENST00000275493.2:c.2579A>T	p.Lys860Ile	p.K860I	ENST00000275493	NM_005228.3	860	aAa/aTa	21/28	NA	2	FACETS	0.766	0.692	0.843			1	INDETERMINATE	1	TRUE	NA	0.414988010161855	2		325	768	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061886	38061886	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004523-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	189	360	0	ENST00000250448.2:c.103A>T	p.Asn35Tyr	p.N35Y	ENST00000250448	NM_004496.3	35	Aac/Tac	2/2	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.414988010161855	2		360	897	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846059	68846060	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGGTTCAAGCTGCTGACCTTCAAGGTGAGGGGTTAAGCACAACAGC	novel	NA	P-0004523-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	75	369	0	ENST00000261769.5:c.1031_1076dup	p.Thr360GlyfsTer5	p.T360Gfs*5	ENST00000261769	NM_004360.3	344	gtg/gTGGTTCAAGCTGCTGACCTTCAAGGTGAGGGGTTAAGCACAACAGCtg	8/16	0.414988010161855	1	FACETS	0.398	0.349	0.452	0.398	0.349	0.452	SUBCLONAL	1	TRUE	0	0.414988010161855	1		369	719	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0004530-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	74	328	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.918	0.801	1	0.918	0.801	1	CLONAL	1	TRUE	1	0.15	2		328	1075	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804283	43804283	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	92	466	0	ENST00000372470.3:c.283T>G	p.Phe95Val	p.F95V	ENST00000372470	NM_005373.2	95	Ttt/Gtt	3/12	1	2	FACETS	0.304	0.27	0.34	0.304	0.27	0.34	SUBCLONAL	1	TRUE	1	0.867617282360633	2		466	698	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104569	193104569	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	585	450	0	ENST00000367435.3:c.356A>C	p.Gln119Pro	p.Q119P	ENST00000367435	NM_024529.4	119	cAg/cCg	4/17	0.868125511608054	4	FACETS	0.972	0.936	1	0.648	0.624	0.672	CLONAL	2	TRUE	1	0.867617282360633	4		450	1296	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406568	70406568	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0004550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	355	555	1	ENST00000373644.4:c.4082C>G	p.Ser1361Ter	p.S1361*	ENST00000373644	NM_030625.2	1361	tCa/tGa	4/12	0.868125511608054	3	FACETS	0.984	0.932	1			1	CLONAL	1	TRUE	NA	0.867617282360633	3		556	1193	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912290	29912789	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCCCACCATCCCCATCGTGGGCATCATTGCTGGCCTGGTTCTCCTTGGAGCTGTGATCACTGGAGCTGTGGTCGCTGCCGTGATGTGGAGGAGGAAGAGCTCAGGTGGAGAAGGGGTGAAGGGTGGGGTCTGAGATTTCTTGTCTCACTGAGGGTTCCAAGCCCCAGCTAGAAATGTGCCCTGTCTCATTACTGGGAAGCACCGTCCACAATCATGGGCCTACCCAGTCTGGGCCCTGTGTGCCAGCACTTACTCTTTTGTAAAGCACCTGTTAAAATGAAGGACAGATTTATCACCTTGATTACGGCGGTGATGGGACCTGATCCCAGCAGTCACAAGTCACAGGGGAAGGTCCCTGAGGACAGACCTCAGGAGGGCTATTGGTCCAGGACCCACACCTGCTTTCTTCATGTTTCCTGATCCCGCCCTGGGTCTGCAGTCACACATTTCTGGAAACTTCTCTGGGGTCCAAGACTAGGAGGTTCCTCTAGGACCTTAAG	GCCCACCATCCCCATCGTGGGCATCATTGCTGGCCTGGTTCTCCTTGGAGCTGTGATCACTGGAGCTGTGGTCGCTGCCGTGATGTGGAGGAGGAAGAGCTCAGGTGGAGAAGGGGTGAAGGGTGGGGTCTGAGATTTCTTGTCTCACTGAGGGTTCCAAGCCCCAGCTAGAAATGTGCCCTGTCTCATTACTGGGAAGCACCGTCCACAATCATGGGCCTACCCAGTCTGGGCCCTGTGTGCCAGCACTTACTCTTTTGTAAAGCACCTGTTAAAATGAAGGACAGATTTATCACCTTGATTACGGCGGTGATGGGACCTGATCCCAGCAGTCACAAGTCACAGGGGAAGGTCCCTGAGGACAGACCTCAGGAGGGCTATTGGTCCAGGACCCACACCTGCTTTCTTCATGTTTCCTGATCCCGCCCTGGGTCTGCAGTCACACATTTCTGGAAACTTCTCTGGGGTCCAAGACTAGGAGGTTCCTCTAGGACCTTAAG	-	novel	NA	P-0004550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	193	253	0	ENST00000376809.5:c.913_1013-43del		p.X305_splice	ENST00000376809	NM_002116.7	305		5/8	0.165241586754748	3	FACETS	1	0.992	1	0.74	0.693	0.787	INDETERMINATE	1	TRUE	1	0.867617282360633	3		253	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0004556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	60	408	0	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	1	2	FACETS	0.733	0.629	0.846	0.733	0.629	0.846	SUBCLONAL	1	TRUE	1	0.18	2		408	910	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867614	78867614	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	95	506	0	ENST00000306801.3:c.2350A>G	p.Ile784Val	p.I784V	ENST00000306801	NM_020761.2	784	Atc/Gtc	20/34	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.18	2		506	936	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190311	32190311	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	37	193	0	ENST00000375023.3:c.428del	p.Cys143SerfsTer109	p.C143Sfs*109	ENST00000375023	NM_004557.3	143	tGc/tc	3/30	1	2	FACETS	0.939	0.774	1	0.939	0.774	1	CLONAL	1	TRUE	1	0.18	2		193	438	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0004558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	289	266	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.559385928673662	3	FACETS	0.993	0.941	1	0.993	0.941	1	CLONAL	2	TRUE	1	0.559385928673662	3		266	666	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0004558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	235	853	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.559385928673662	2		853	800	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306996	65306997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	128	342	6	ENST00000342505.4:c.2580dup	p.Pro861ThrfsTer4	p.P861Tfs*4	ENST00000342505	NM_002227.2	860	-/A	19/25	0.559385928673662	1	FACETS	0.717	0.654	0.782	0.717	0.654	0.782	SUBCLONAL	1	TRUE	0	0.559385928673662	1		348	460	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176719062	176719062	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	183	323	1	ENST00000439151.2:c.6366T>A	p.Phe2122Leu	p.F2122L	ENST00000439151	NM_022455.4	2122	ttT/ttA	22/23	NA	2	FACETS	1	0.949	1			1	INDETERMINATE	1	TRUE	NA	0.559385928673662	2		324	636	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780071	NA	P-0004564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	267	342	0	ENST00000269305.4:c.580C>T	p.Leu194Phe	p.L194F	ENST00000269305	NM_001126112.2	194	Ctt/Ttt	6/11	0.480652666122398	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.480652666122398	1		342	838	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050354	176050354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	75	335	0	ENST00000367669.3:c.1211C>T	p.Ser404Leu	p.S404L	ENST00000367669	NM_022457.5	404	tCa/tTa	11/20	0.191246936875901	1	FACETS	0.577	0.508	0.65	0.577	0.508	0.65	INDETERMINATE	1	TRUE	0	0.480652666122398	1		335	411	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005677	42005677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	157	218	0	ENST00000219905.7:c.3413G>A	p.Arg1138Lys	p.R1138K	ENST00000219905	NM_001164273.1	1138	aGa/aAa	9/24	0.480652666122398	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.480652666122398	1		218	481	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0004566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	10	138	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.116	0.078	0.164	0.116	0.078	0.164	SUBCLONAL	1	TRUE	1	0.622879687870975	2		138	276	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0004566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	121	266	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.747	0.678	0.819	0.747	0.678	0.819	SUBCLONAL	1	TRUE	1	0.622879687870975	2		266	520	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0004566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	303	536	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.622879687870975	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.622879687870975	2		536	473	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170027	32170027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746443332	NA	P-0004566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	255	516	1	ENST00000375023.3:c.3581C>T	p.Pro1194Leu	p.P1194L	ENST00000375023	NM_004557.3	1194	cCg/cTg	21/30	1	2	FACETS	0.97	0.911	1	0.97	0.911	1	CLONAL	1	TRUE	1	0.622879687870975	2		517	844	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670619	30670619	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	223	492	0	ENST00000376406.3:c.5901A>C	p.Glu1967Asp	p.E1967D	ENST00000376406	NM_014641.2	1967	gaA/gaC	13/15	1	2	FACETS	0.866	0.808	0.925	0.866	0.808	0.925	CLONAL	1	TRUE	1	0.622879687870975	2		492	827	SUCCESS
APC	324	MSKCC	GRCh37	5	112175694	112175706	+	frameshift_variant	Frame_Shift_Del	DEL	AGCAAGCTGCAGT	AGCAAGCTGCAGT	-	novel	NA	P-0004566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	342	449	1	ENST00000257430.4:c.4404_4416del	p.Gln1469MetfsTer34	p.Q1469Mfs*34	ENST00000257430	NM_000038.5	1468	aAGCAAGCTGCAGTa/aa	16/16	0.622879687870975	2	FACETS	0.947	0.907	0.986	0.947	0.907	0.986	CLONAL	2	TRUE	0	0.622879687870975	2		450	580	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925316	114925317	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs745872748	NA	P-0004566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	503	322	10	ENST00000543371.1:c.1403dup	p.Cys469ValfsTer8	p.C469Vfs*8	ENST00000543371	NM_001198531.1	465	aga/agAa	14/14	0.622879687870975	2	FACETS	0.822	0.791	0.852	0.822	0.791	0.852	CLONAL	2	TRUE	0	0.622879687870975	2		332	983	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	116	248	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.597864465615352	1	FACETS	0.447	0.404	0.493	0.447	0.404	0.493	SUBCLONAL	1	TRUE	0	0.597864465615352	1		248	608	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0004611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	252	244	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.597864465615352	1	FACETS	0.949	0.894	1	0.949	0.894	1	CLONAL	1	TRUE	0	0.597864465615352	1		244	623	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524834	187524834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771664786	NA	P-0004611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	282	294	0	ENST00000441802.2:c.10846G>A	p.Val3616Ile	p.V3616I	ENST00000441802	NM_005245.3	3616	Gta/Ata	19/27	1	2	FACETS	0.975	0.917	1	0.975	0.917	1	CLONAL	1	TRUE	1	0.597864465615352	2		294	968	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196774	123196774	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	215	427	0	ENST00000218089.9:c.1661A>C	p.Lys554Thr	p.K554T	ENST00000218089	NM_001042749.1	554	aAg/aCg	18/35	0.453070366852944	1	FACETS	0.435	0.404	0.468	0.435	0.404	0.468	SUBCLONAL	1	TRUE	0	0.597864465615352	1		427	1158	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0004631-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	80	175	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.300606063582295	1	FACETS	0.887	0.784	0.997	0.887	0.784	0.997	CLONAL	1	TRUE	0	0.327289699624602	1		175	461	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646021	215646021	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004631-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	91	265	0	ENST00000260947.4:c.577G>C	p.Glu193Gln	p.E193Q	ENST00000260947	NM_000465.2	193	Gag/Cag	4/11	1	2	FACETS	0.714	0.633	0.8	0.714	0.633	0.8	SUBCLONAL	1	TRUE	1	0.327289699624602	2		265	779	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168719	56168719	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004631-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	111	214	0	ENST00000399503.3:c.1573C>T	p.Gln525Ter	p.Q525*	ENST00000399503	NM_005921.1	525	Cag/Tag	9/20	1	2	FACETS	0.89	0.8	0.985	0.89	0.8	0.985	CLONAL	1	TRUE	1	0.327289699624602	2		214	762	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738811	145738811	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004631-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	20	124	0	ENST00000428558.2:c.2254G>C	p.Glu752Gln	p.E752Q	ENST00000428558	NM_004260.3	752	Gaa/Caa	14/22	0.327289699624602	3	FACETS	0.412	0.315	0.527	0.206	0.157	0.264	SUBCLONAL	1	TRUE	1	0.327289699624602	3		124	345	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416623	121416623	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004631-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	57	219	0	ENST00000257555.6:c.52G>C	p.Glu18Gln	p.E18Q	ENST00000257555		18	Gag/Cag	1/10	0.327289699624602	1	FACETS	0.891	0.769	1	0.891	0.769	1	CLONAL	1	TRUE	0	0.327289699624602	1		219	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0004637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	38	231	0	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	0.389507779451127	3	FACETS	0.5	0.413	0.596	0.25	0.206	0.298	SUBCLONAL	1	TRUE	1	0.48	3		231	393	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	260	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.370690645556651	2		326	1096	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0004647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	45	573	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.233762653142565	1	FACETS	0.478	0.402	0.561	0.478	0.402	0.561	SUBCLONAL	1	TRUE	0	0.370690645556651	1		574	414	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156968	89156968	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	45	229	0	ENST00000336596.2:c.70C>A	p.Pro24Thr	p.P24T	ENST00000336596	NM_005233.5	24	Ccg/Acg	1/17	1	2	FACETS	0.397	0.333	0.468	0.397	0.333	0.468	SUBCLONAL	1	TRUE	1	0.370690645556651	2		229	612	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0004647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	100	315	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	0.370690645556651	3	FACETS	0.84	0.751	0.936			1	CLONAL	1	TRUE	NA	0.370690645556651	3		315	761	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400033	49400033	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	84	322	0	ENST00000418115.1:c.304G>A	p.Glu102Lys	p.E102K	ENST00000418115	NM_001664.2	102	Gaa/Aaa	4/5	1	2	FACETS	0.696	0.615	0.783	0.696	0.615	0.783	SUBCLONAL	1	TRUE	1	0.370690645556651	2		322	651	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593424	67593424	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764019194	NA	P-0004647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	42	144	0	ENST00000274335.5:c.2170C>T	p.Arg724Ter	p.R724*	ENST00000274335		724	Cga/Tga	15/15	0.370690645556651	3	FACETS	0.67	0.56	0.791			1	SUBCLONAL	1	TRUE	NA	0.370690645556651	3		144	401	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864388	162864388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368134308	NA	P-0004647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	77	230	0	ENST00000366898.1:c.125G>A	p.Arg42His	p.R42H	ENST00000366898	NM_004562.2	42	cGt/cAt	2/12	NA	2	FACETS	0.721	0.634	0.815			1	INDETERMINATE	1	TRUE	NA	0.370690645556651	2		230	576	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729613	41729613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs564878978	NA	P-0004647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	63	330	0	ENST00000242208.4:c.916C>T	p.Arg306Cys	p.R306C	ENST00000242208	NM_002192.2	306	Cgc/Tgc	3/3	1	2	FACETS	0.422	0.364	0.485	0.422	0.364	0.485	SUBCLONAL	1	TRUE	1	0.370690645556651	2		330	805	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333555	70333555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150689919	NA	P-0004647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	48	285	0	ENST00000373644.4:c.1460C>T	p.Ser487Leu	p.S487L	ENST00000373644	NM_030625.2	487	tCa/tTa	2/12	NA	2	FACETS	0.574	0.486	0.671			1	INDETERMINATE	1	TRUE	NA	0.370690645556651	2		285	451	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439984	56439985	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	172	228	0	ENST00000407977.2:c.607dup	p.Met203AsnfsTer56	p.M203Nfs*56	ENST00000407977		203	atg/aAtg	6/10	0.336136584852629	2	FACETS	0.81	0.749	0.872	0.81	0.749	0.872	CLONAL	2	TRUE	0	0.370690645556651	2		228	573	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0004689-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	79	266	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.883	0.775	0.999	0.883	0.775	0.999	CLONAL	1	TRUE	1	0.21	2		266	852	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0004689-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1184	101	328	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.749	0.667	0.836	0.749	0.667	0.836	SUBCLONAL	1	TRUE	1	0.21	2		328	1285	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0004689-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	46	140	2	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	1	FACETS	0.973	0.821	1	0.973	0.821	1	CLONAL	1	TRUE	0	0.21	1		142	403	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004689-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	71	411	0	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS	0.701	0.61	0.8	0.701	0.61	0.8	SUBCLONAL	1	TRUE	1	0.21	2		411	964	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443757	52443757	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1208026193	NA	P-0004689-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	90	243	1	ENST00000460680.1:c.40C>T	p.Leu14Phe	p.L14F	ENST00000460680	NM_004656.3	14	Ctc/Ttc	2/17	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.21	2		244	667	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733279	40733279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201275244	NA	P-0004689-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	93	342	1	ENST00000373198.4:c.3527G>A	p.Arg1176His	p.R1176H	ENST00000373198	NM_133170.3	1176	cGt/cAt	26/32	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.21	2		343	803	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0004736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	73	368	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	1	0.909	1	1	0.983	1	CLONAL	2	FALSE	1	0.161474896378878	2		368	434	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591085	67591085	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519839	NA	P-0004736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	72	388	0	ENST00000274335.5:c.1678G>T	p.Asp560Tyr	p.D560Y	ENST00000274335		560	Gac/Tac	12/15	0.161474896378878	3	FACETS	0.914	0.8	1	0.914	0.8	1	CLONAL	2	FALSE	1	0.161474896378878	3		388	527	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057991	27057992	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0004736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	28	345	0	ENST00000324856.7:c.1700_1701dup	p.Pro568SerfsTer52	p.P568Sfs*52	ENST00000324856	NM_006015.4	567	cag/cAGag	3/20	0.12464857217858	0	FACETS	1	0.878	1			1	CLONAL	1	FALSE	0	0.161474896378878	0		345	256	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105693	27105694	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0004736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	31	489	0	ENST00000324856.7:c.5305_5306del	p.Leu1769ArgfsTer3	p.L1769Rfs*3	ENST00000324856	NM_006015.4	1768	ctTCta/ctta	20/20	0.12464857217858	0	FACETS	0.701	0.567	0.854			1	SUBCLONAL	1	FALSE	0	0.161474896378878	0		489	459	SUCCESS
APC	324	MSKCC	GRCh37	5	112170777	112170780	+	frameshift_variant	Frame_Shift_Del	DEL	CAGA	CAGA	-	rs878853420	NA	P-0004736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	48	557	0	ENST00000257430.4:c.1875_1878del	p.Asn627LeufsTer2	p.N627Lfs*2	ENST00000257430	NM_000038.5	625	CAGAca/ca	15/16	0.161474896378878	3	FACETS	0.906	0.765	1	0.453	0.382	0.532	CLONAL	1	FALSE	1	0.161474896378878	3		557	709	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0004744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	41	553	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.666	0.553	0.793	0.666	0.553	0.793	SUBCLONAL	1	TRUE	1	0.13	2		553	947	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578525	7578525	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	35	432	0	ENST00000269305.4:c.405C>A	p.Cys135Ter	p.C135*	ENST00000269305	NM_001126112.2	135	tgC/tgA	5/11	1	2	FACETS	0.58	0.473	0.701	0.58	0.473	0.701	SUBCLONAL	1	TRUE	1	0.13	2		432	928	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719268	190719268	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	224	296	1	ENST00000441310.2:c.1270G>T	p.Glu424Ter	p.E424*	ENST00000441310	NM_000534.4	424	Gaa/Taa	9/13	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.6774268807411	2		297	636	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190937	185190937	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	382	631	0	ENST00000265026.3:c.1818G>C	p.Leu606Phe	p.L606F	ENST00000265026	NM_004721.4	606	ttG/ttC	11/14	1	2	FACETS	0.8	0.759	0.843	0.8	0.759	0.843	SUBCLONAL	1	TRUE	1	0.6774268807411	2		631	1409	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160601	56160601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	276	389	0	ENST00000399503.3:c.875C>T	p.Ser292Leu	p.S292L	ENST00000399503	NM_005921.1	292	tCa/tTa	4/20	1	2	FACETS	0.876	0.824	0.929	0.876	0.824	0.929	CLONAL	1	TRUE	1	0.6774268807411	2		389	930	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421519	32421519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	280	377	0	ENST00000332351.3:c.1073C>T	p.Thr358Met	p.T358M	ENST00000332351	NM_024426.4	358	aCg/aTg	6/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.6774268807411	2		377	807	SUCCESS
ATM	472	MSKCC	GRCh37	11	108138048	108138048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	363	407	0	ENST00000278616.4:c.2617G>A	p.Gly873Arg	p.G873R	ENST00000278616	NM_000051.3	873	Gga/Aga	17/63	0.6774268807411	1	FACETS	0.976	0.933	1	0.976	0.933	1	CLONAL	1	TRUE	0	0.6774268807411	1		407	726	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995373	15995373	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0004753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	64	374	0	ENST00000268712.3:c.2821-1G>T		p.X941_splice	ENST00000268712	NM_006311.3	941			0.6774268807411	1	FACETS	0.201	0.174	0.231	0.201	0.174	0.231	SUBCLONAL	1	TRUE	0	0.6774268807411	1		374	622	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919262	48919301	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGTTGATAATGCTATGTCAAGACTGTTGAAGAAGTATG	AAAGTTGATAATGCTATGTCAAGACTGTTGAAGAAGTATG	-	novel	NA	P-0004753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	244	328	0	ENST00000267163.4:c.428_467del	p.Lys143MetfsTer19	p.K143Mfs*19	ENST00000267163	NM_000321.2	143	AAAGTTGATAATGCTATGTCAAGACTGTTGAAGAAGTATGat/at	4/27	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.6774268807411	2		328	486	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061575	38061576	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0004753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	195	218	0	ENST00000250448.2:c.412_413dup	p.Met138IlefsTer2	p.M138Ifs*2	ENST00000250448	NM_004496.3	138	atg/atATg	2/2	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.6774268807411	2		218	534	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120780	115120787	+	frameshift_variant	Frame_Shift_Del	DEL	TGCCGGTC	TGCCGGTC	-	novel	NA	P-0004753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	302	441	0	ENST00000257566.3:c.219_226del	p.Glu73AspfsTer35	p.E73Dfs*35	ENST00000257566	NM_016569.3	73	gaGACCGGCAtc/gatc	1/8	1	2	FACETS	0.99	0.935	1	0.99	0.935	1	CLONAL	1	TRUE	1	0.6774268807411	2		441	901	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579590	7579591	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0004753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	277	328	0	ENST00000269305.4:c.97-2_97-1dup	p.Leu35ProfsTer10	p.L35Pfs*10	ENST00000269305	NM_001126112.2	32	-/AG		0.6774268807411	1	FACETS	0.942	0.894	0.991	0.942	0.894	0.991	CLONAL	1	TRUE	0	0.6774268807411	1		328	574	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151932964	151932971	+	frameshift_variant	Frame_Shift_Del	DEL	CCGACAGT	CCGACAGT	-	novel	NA	P-0004753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	187	8	0	ENST00000262189.6:c.2700_2707del	p.Leu901AlafsTer30	p.L901Afs*30	ENST00000262189	NM_170606.2	900	ggACTGTCGGgg/gggg	16/59	0.6774268807411	3	FACETS		NA	1	1	0.995	1	NA	4	TRUE	1	0.6774268807411	3		8	208	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0004811-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	399	437	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	NA	2	FACETS	0.964	0.924	1			1	INDETERMINATE	2	TRUE	NA	0.541261204650809	2		437	765	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0004811-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	213	388	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.541261204650809	2		388	657	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0004834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	327	464	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.354781101094678	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	0	0.392747616455118	3		464	651	SUCCESS
APC	324	MSKCC	GRCh37	5	112175174	112175174	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	120	205	0	ENST00000257430.4:c.3883G>T	p.Glu1295Ter	p.E1295*	ENST00000257430	NM_000038.5	1295	Gaa/Taa	16/16	0.247167504889589	3	FACETS	1	0.951	1	0.706	0.645	0.769	CLONAL	2	TRUE	0	0.392747616455118	3		205	345	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057235	180057235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148392893	NA	P-0004834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	42	335	0	ENST00000261937.6:c.503C>T	p.Thr168Met	p.T168M	ENST00000261937	NM_182925.4	168	aCg/aTg	4/30	0.247167504889589	3	FACETS	0.711	0.595	0.839	0.237	0.198	0.28	SUBCLONAL	1	TRUE	0	0.392747616455118	3		335	360	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858185	27858185	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	86	599	1	ENST00000359303.2:c.386G>A	p.Arg129His	p.R129H	ENST00000359303	NM_003535.2	129	cGt/cAt	1/1	0.392747616455118	4	FACETS	0.606	0.535	0.683	0.202	0.178	0.228	SUBCLONAL	1	TRUE	1	0.392747616455118	4		600	1006	SUCCESS
APC	324	MSKCC	GRCh37	5	112170752	112170753	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0004834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	89	452	0	ENST00000257430.4:c.1848_1849del	p.Leu616PhefsTer17	p.L616Ffs*17	ENST00000257430	NM_000038.5	616	ttGGtt/tttt	15/16	0.247167504889589	3	FACETS	0.711	0.63	0.797	0.237	0.21	0.266	SUBCLONAL	1	TRUE	0	0.392747616455118	3		452	763	SUCCESS
APC	324	MSKCC	GRCh37	5	112170745	112170746	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	89	442	0	ENST00000257430.4:c.1842dup	p.Phe615IlefsTer19	p.F615Ifs*19	ENST00000257430	NM_000038.5	614	gca/gcAa	15/16	0.247167504889589	3	FACETS	0.718	0.636	0.806	0.239	0.212	0.269	SUBCLONAL	1	TRUE	0	0.392747616455118	3		442	755	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397489	116397489	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1370688649	NA	P-0004878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	100	337	0	ENST00000397752.3:c.1863-2A>G		p.X621_splice	ENST00000397752	NM_000245.2	621			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		337	1265	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78420999	78420999	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	59	210	1	ENST00000370768.2:c.1721C>T	p.Pro574Leu	p.P574L	ENST00000370768	NM_003902.3	574	cCa/cTa	18/20	0.170011300781171	3	FACETS	0.607	0.522	0.699	0.303	0.261	0.35	INDETERMINATE	1	TRUE	1	0.38	3		211	609	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604747	48604747	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	36	296	0	ENST00000342988.3:c.1569C>G	p.Cys523Trp	p.C523W	ENST00000342988	NM_005359.5	523	tgC/tgG	12/12	1	2	FACETS	0.303	0.248	0.365	0.303	0.248	0.365	SUBCLONAL	1	TRUE	1	0.38	2		296	625	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212043	5212043	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs575673773	NA	P-0004882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	66	470	0	ENST00000357368.4:c.4988C>G	p.Ala1663Gly	p.A1663G	ENST00000357368	NM_002850.3	1663	gCc/gGc	32/38	1	2	FACETS	0.512	0.444	0.585	0.512	0.444	0.585	SUBCLONAL	1	TRUE	1	0.38	2		470	679	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911151	40911151	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	58	344	0	ENST00000373198.4:c.2154C>A	p.Asn718Lys	p.N718K	ENST00000373198	NM_133170.3	718	aaC/aaA	13/32	1	2	FACETS	0.416	0.356	0.481	0.416	0.356	0.481	SUBCLONAL	1	TRUE	1	0.38	2		344	734	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0004923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	169	437	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.21750133845067	1	FACETS	0.812	0.746	0.882	0.812	0.746	0.882	CLONAL	1	FALSE	0	0.329409477667901	1		437	1055	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0004923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	114	225	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.329409477667901	2		225	612	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941830	44941831	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	132	486	0	ENST00000377967.4:c.3160dup	p.Arg1054LysfsTer5	p.R1054Kfs*5	ENST00000377967	NM_021140.2	1052	gaa/gAaa	21/29	0.329409477667901	1	FACETS	0.624	0.566	0.687	0.624	0.566	0.687	SUBCLONAL	1	FALSE	0	0.329409477667901	1		486	1072	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332456	70332456	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	106	424	0	ENST00000373644.4:c.361G>T	p.Val121Phe	p.V121F	ENST00000373644	NM_030625.2	121	Gtc/Ttc	2/12	0.152162270673171	0	FACETS	0.484	0.433	0.538			1	INDETERMINATE	1	FALSE	0	0.329409477667901	0		424	891	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288836	33288836	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	96	194	0	ENST00000374542.5:c.716T>C	p.Leu239Pro	p.L239P	ENST00000374542	NM_001141970.1	239	cTa/cCa	3/8	0.675734513506861	1	FACETS	0.975	0.892	1	0.975	0.892	1	CLONAL	1	TRUE	0	0.680138723044874	1		194	191	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928108	+	inframe_deletion	In_Frame_Del	DEL	GAAGATTTGCTGAACCCTATTGGTGTTACT	GAAGATTTGCTGAACCCTATTGGTGTTACT	-	novel	NA	P-0004991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	94	276	0	ENST00000263967.3:c.1358_1387del	p.Glu453_Thr462del	p.E453_T462del	ENST00000263967	NM_006218.2	453	GAAGATTTGCTGAACCCTATTGGTGTTACT/-	8/21	1	2	FACETS	0.753	0.676	0.834	0.753	0.676	0.834	SUBCLONAL	1	TRUE	1	0.680138723044874	2		276	367	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663443	29663444	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	130	324	1	ENST00000356175.3:c.6037dup	p.Thr2013AsnfsTer26	p.T2013Nfs*26	ENST00000356175	NM_000267.3	2012	-/A	40/57	0.680138723044874	1	FACETS	0.952	0.881	1	0.952	0.881	1	CLONAL	1	TRUE	0	0.680138723044874	1		325	265	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224608	108224609	+	splice_donor_variant	Splice_Site	INS	-	-	T	rs1565579654	NA	P-0005004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	105	238	0	ENST00000278616.4:c.8786+2dup		p.X2929_splice	ENST00000278616	NM_000051.3	2929			1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.767520100858385	2		238	253	SUCCESS
ATM	472	MSKCC	GRCh37	11	108127039	108127040	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	127	262	0	ENST00000278616.4:c.2223dup	p.Lys742Ter	p.K742*	ENST00000278616	NM_000051.3	741	tat/taTt	14/63	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.767520100858385	2		262	288	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073667	8073667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749196844	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	285	674	0	ENST00000377482.5:c.992G>A	p.Arg331His	p.R331H	ENST00000377482	NM_018948.3	331	cGc/cAc	4/4	1	2	FACETS	0.641	0.602	0.682	0.641	0.602	0.682	SUBCLONAL	1	TRUE	1	0.65	2		674	1367	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11297917	11297917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1331182647	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	342	427	0	ENST00000361445.4:c.2191C>T	p.Arg731Cys	p.R731C	ENST00000361445	NM_004958.3	731	Cgc/Tgc	13/58	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.65	2		427	933	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11314010	11314010	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	224	586	0	ENST00000361445.4:c.726G>T	p.Glu242Asp	p.E242D	ENST00000361445	NM_004958.3	242	gaG/gaT	6/58	1	2	FACETS	0.685	0.638	0.734	0.685	0.638	0.734	SUBCLONAL	1	TRUE	1	0.65	2		586	1006	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17371319	17371319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772551056	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	163	546	1	ENST00000375499.3:c.137G>A	p.Arg46Gln	p.R46Q	ENST00000375499	NM_003000.2	46	cGa/cAa	2/8	1	2	FACETS	0.542	0.497	0.588	0.542	0.497	0.588	SUBCLONAL	1	TRUE	1	0.65	2		547	926	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097814	27097814	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	127	365	0	ENST00000324856.7:c.3403C>T	p.Pro1135Ser	p.P1135S	ENST00000324856	NM_006015.4	1135	Cct/Tct	12/20	1	2	FACETS	0.634	0.576	0.695	0.634	0.576	0.695	SUBCLONAL	1	TRUE	1	0.65	2		365	616	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363634	40363634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	184	278	0	ENST00000397332.2:c.595G>A	p.Glu199Lys	p.E199K	ENST00000397332	NM_001033082.2	199	Gaa/Aaa	3/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.65	2		278	499	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46527650	46527650	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1287980956	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	370	555	0	ENST00000262741.5:c.715G>T	p.Glu239Ter	p.E239*	ENST00000262741	NM_003629.3	239	Gaa/Taa	6/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.65	2		555	1040	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46736348	46736348	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	155	486	0	ENST00000371975.4:c.1060A>G	p.Lys354Glu	p.K354E	ENST00000371975	NM_003579.3	354	Aag/Gag	10/18	1	2	FACETS	0.486	0.444	0.53	0.486	0.444	0.53	SUBCLONAL	1	TRUE	1	0.65	2		486	981	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330618	65330618	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs958983466	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	148	384	0	ENST00000342505.4:c.1028G>A	p.Arg343Gln	p.R343Q	ENST00000342505	NM_002227.2	343	cGg/cAg	8/25	1	2	FACETS	0.574	0.524	0.625	0.574	0.524	0.625	SUBCLONAL	1	TRUE	1	0.65	2		384	794	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332628	65332628	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748142963	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	303	506	0	ENST00000342505.4:c.911C>T	p.Ser304Leu	p.S304L	ENST00000342505	NM_002227.2	304	tCg/tTg	7/25	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.65	2		506	865	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400888	72400888	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs200216525	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	187	703	0	ENST00000357731.5:c.283A>G	p.Thr95Ala	p.T95A	ENST00000357731	NM_173808.2	95	Aca/Gca	2/7	1	2	FACETS	0.528	0.487	0.571	0.528	0.487	0.571	SUBCLONAL	1	TRUE	1	0.65	2		703	1090	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414953	78414953	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	49	374	2	ENST00000370768.2:c.1813C>T	p.Pro605Ser	p.P605S	ENST00000370768	NM_003902.3	605	Cca/Tca	19/20	1	2	FACETS	0.251	0.212	0.294	0.251	0.212	0.294	SUBCLONAL	1	TRUE	1	0.65	2		376	600	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749901	162749901	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	29	361	0	ENST00000367921.3:c.2434-1G>T		p.X812_splice	ENST00000367921	NM_006182.2	812			1	2	FACETS	0.158	0.126	0.194	0.158	0.126	0.194	SUBCLONAL	1	TRUE	1	0.65	2		361	566	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094337	193094337	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	29	308	0	ENST00000367435.3:c.227G>A	p.Arg76Gln	p.R76Q	ENST00000367435	NM_024529.4	76	cGa/cAa	2/17	1	2	FACETS	0.155	0.124	0.191	0.155	0.124	0.191	SUBCLONAL	1	TRUE	1	0.65	2		308	576	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976476	25976476	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	327	571	1	ENST00000435504.4:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000435504		357	Cga/Tga	11/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.65	2		572	960	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982356	25982356	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	232	372	0	ENST00000435504.4:c.934C>T	p.Arg312Ter	p.R312*	ENST00000435504		312	Cga/Tga	9/13	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.65	2		372	644	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068387	26068387	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	233	449	4	ENST00000435504.4:c.103C>A	p.Leu35Ile	p.L35I	ENST00000435504		35	Ctt/Att	2/13	1	2	FACETS	0.924	0.865	0.985	0.924	0.865	0.985	CLONAL	1	TRUE	1	0.65	2		453	776	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754800	29754800	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1424913232	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	202	521	2	ENST00000389048.3:c.1135C>T	p.Pro379Ser	p.P379S	ENST00000389048	NM_004304.4	379	Ccc/Tcc	4/29	1	2	FACETS	0.634	0.588	0.682	0.634	0.588	0.682	SUBCLONAL	1	TRUE	1	0.65	2		523	980	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703539	47703539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1203462814	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	323	586	1	ENST00000233146.2:c.2039G>A	p.Arg680Gln	p.R680Q	ENST00000233146	NM_000251.2	680	cGa/cAa	13/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.65	2		587	939	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023086	48023086	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	436	654	5	ENST00000234420.5:c.511G>T	p.Glu171Ter	p.E171*	ENST00000234420	NM_000179.2	171	Gaa/Taa	3/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.65	2		659	1272	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027115	48027115	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1333555322	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	63	554	0	ENST00000234420.5:c.1993G>T	p.Glu665Ter	p.E665*	ENST00000234420	NM_000179.2	665	Gag/Tag	4/10	1	2	FACETS	0.216	0.186	0.249	0.216	0.186	0.249	SUBCLONAL	1	TRUE	1	0.65	2		554	898	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118941	61118941	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1456684871	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	282	433	1	ENST00000295025.8:c.134G>A	p.Arg45Gln	p.R45Q	ENST00000295025	NM_002908.2	45	cGa/cAa	2/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.65	2		434	846	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149129	61149129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144119768	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	62	481	0	ENST00000295025.8:c.1319C>T	p.Ser440Leu	p.S440L	ENST00000295025	NM_002908.2	440	tCg/tTg	11/11	1	2	FACETS	0.193	0.166	0.223	0.193	0.166	0.223	SUBCLONAL	1	TRUE	1	0.65	2		481	989	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61706027	61706027	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	199	602	0	ENST00000401558.2:c.3144G>T	p.Glu1048Asp	p.E1048D	ENST00000401558	NM_003400.3	1048	gaG/gaT	25/25	1	2	FACETS	0.584	0.541	0.629	0.584	0.541	0.629	SUBCLONAL	1	TRUE	1	0.65	2		602	1048	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726927	61726927	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	57	488	1	ENST00000401558.2:c.511C>A	p.Leu171Ile	p.L171I	ENST00000401558	NM_003400.3	171	Ctt/Att	7/25	1	2	FACETS	0.188	0.16	0.218	0.188	0.16	0.218	SUBCLONAL	1	TRUE	1	0.65	2		489	935	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189322	99189322	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759626940	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	114	399	0	ENST00000074304.5:c.2578C>T	p.Arg860Trp	p.R860W	ENST00000074304	NM_001134224.1	860	Cgg/Tgg	24/26	1	2	FACETS	0.404	0.363	0.447	0.404	0.363	0.447	SUBCLONAL	1	TRUE	1	0.65	2		399	868	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872498	136872498	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs104893624	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	408	713	2	ENST00000241393.3:c.1000C>T	p.Arg334Ter	p.R334*	ENST00000241393	NM_003467.2	334	Cga/Tga	2/2	1	2	FACETS	0.958	0.912	1	0.958	0.912	1	CLONAL	1	TRUE	1	0.65	2		715	1310	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149803	202149803	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	128	411	0	ENST00000358485.4:c.1244T>G	p.Phe415Cys	p.F415C	ENST00000358485	NM_001080125.1	415	tTt/tGt	8/9	1	2	FACETS	0.529	0.48	0.581	0.529	0.48	0.581	SUBCLONAL	1	TRUE	1	0.65	2		411	744	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209101857	209101857	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	140	459	0	ENST00000345146.2:c.1191C>A	p.Phe397Leu	p.F397L	ENST00000345146	NM_005896.2	397	ttC/ttA	10/10	1	2	FACETS	0.472	0.43	0.517	0.472	0.43	0.517	SUBCLONAL	1	TRUE	1	0.65	2		459	912	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251841	212251841	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	165	327	1	ENST00000342788.4:c.3218C>A	p.Ala1073Asp	p.A1073D	ENST00000342788	NM_005235.2	1073	gCt/gAt	27/28	1	2	FACETS	0.942	0.871	1	0.942	0.871	1	CLONAL	1	TRUE	1	0.65	2		328	539	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342954	225342954	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	168	549	1	ENST00000264414.4:c.2138C>A	p.Ser713Tyr	p.S713Y	ENST00000264414	NM_003590.4	713	tCt/tAt	15/16	1	2	FACETS	0.511	0.469	0.555	0.511	0.469	0.555	SUBCLONAL	1	TRUE	1	0.65	2		550	1011	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662581	227662581	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1397135584	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	173	317	0	ENST00000305123.5:c.874C>T	p.Pro292Ser	p.P292S	ENST00000305123	NM_005544.2	292	Ccc/Tcc	1/2	1	2	FACETS	0.88	0.814	0.948	0.88	0.814	0.948	CLONAL	1	TRUE	1	0.65	2		317	605	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641904	12641904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752713997	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	105	311	0	ENST00000251849.4:c.845G>A	p.Arg282Gln	p.R282Q	ENST00000251849	NM_002880.3	282	cGa/cAa	8/17	1	2	FACETS	0.466	0.418	0.517	0.466	0.418	0.517	SUBCLONAL	1	TRUE	1	0.65	2		311	693	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715686	30715686	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	104	515	0	ENST00000295754.5:c.1344C>A	p.Tyr448Ter	p.Y448*	ENST00000295754	NM_003242.5	448	taC/taA	5/7	1	2	FACETS	0.356	0.318	0.396	0.356	0.318	0.396	SUBCLONAL	1	TRUE	1	0.65	2		515	899	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165881	47165881	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	180	540	0	ENST00000409792.3:c.245A>C	p.Lys82Thr	p.K82T	ENST00000409792	NM_014159.6	82	aAa/aCa	3/21	1	2	FACETS	0.546	0.503	0.591	0.546	0.503	0.591	SUBCLONAL	1	TRUE	1	0.65	2		540	1014	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405936	49405936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	506	601	2	ENST00000418115.1:c.202C>T	p.Arg68Cys	p.R68C	ENST00000418115	NM_001664.2	68	Cgc/Tgc	3/5	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.65	2		603	1281	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582141	52582141	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1164015194	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	342	523	0	ENST00000394830.3:c.4687C>T	p.Arg1563Ter	p.R1563*	ENST00000394830	NM_018313.4	1563	Cga/Tga	30/30	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.65	2		523	1042	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021785	71021785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs112795301	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	120	449	0	ENST00000318789.4:c.1573C>T	p.Arg525Ter	p.R525*	ENST00000318789	NM_032682.5	525	Cga/Tga	18/21	1	2	FACETS	0.495	0.447	0.545	0.495	0.447	0.545	SUBCLONAL	1	TRUE	1	0.65	2		449	746	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498521	89498521	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	119	491	1	ENST00000336596.2:c.2493G>T	p.Gln831His	p.Q831H	ENST00000336596	NM_005233.5	831	caG/caT	14/17	1	2	FACETS	0.519	0.469	0.572	0.519	0.469	0.572	SUBCLONAL	1	TRUE	1	0.65	2		492	705	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873008	134873008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201012406	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	129	434	1	ENST00000398015.3:c.1312C>T	p.Pro438Ser	p.P438S	ENST00000398015	NM_004441.4	438	Ccc/Tcc	6/16	1	2	FACETS	0.496	0.45	0.545	0.496	0.45	0.545	SUBCLONAL	1	TRUE	1	0.65	2		435	800	SUCCESS
ATR	545	MSKCC	GRCh37	3	142168393	142168393	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	45	421	0	ENST00000350721.4:c.7813A>G	p.Thr2605Ala	p.T2605A	ENST00000350721	NM_001184.3	2605	Act/Gct	47/47	1	2	FACETS	0.178	0.149	0.21	0.178	0.149	0.21	SUBCLONAL	1	TRUE	1	0.65	2		421	779	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176561	142176561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	256	432	0	ENST00000350721.4:c.7540C>T	p.Arg2514Cys	p.R2514C	ENST00000350721	NM_001184.3	2514	Cgc/Tgc	45/47	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.65	2		432	737	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274880	142274880	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs372610600	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	158	516	0	ENST00000350721.4:c.2180C>A	p.Ser727Tyr	p.S727Y	ENST00000350721	NM_001184.3	727	tCt/tAt	10/47	1	2	FACETS	0.495	0.453	0.539	0.495	0.453	0.539	SUBCLONAL	1	TRUE	1	0.65	2		516	982	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921529	178921529	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	143	372	0	ENST00000263967.3:c.1011A>C	p.Lys337Asn	p.K337N	ENST00000263967	NM_006218.2	337	aaA/aaC	5/21	1	2	FACETS	0.588	0.537	0.642	0.588	0.537	0.642	SUBCLONAL	1	TRUE	1	0.65	2		372	748	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502222	186502222	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	249	665	1	ENST00000323963.5:c.31G>T	p.Glu11Ter	p.E11*	ENST00000323963		11	Gaa/Taa	2/11	1	2	FACETS	0.548	0.511	0.587	0.548	0.511	0.587	SUBCLONAL	1	TRUE	1	0.65	2		666	1397	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573436	55573436	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	67	307	2	ENST00000288135.5:c.1098G>T	p.Glu366Asp	p.E366D	ENST00000288135	NM_000222.2	366	gaG/gaT	6/21	0.0817351260368112	0	FACETS	0.131	0.114	0.15			1	INDETERMINATE	1	TRUE	0	0.65	0		309	549	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973911	55973911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs941528100	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	157	297	1	ENST00000263923.4:c.1405G>A	p.Glu469Lys	p.E469K	ENST00000263923	NM_002253.2	469	Gag/Aag	10/30	0.0817351260368112	0	FACETS	0.358	0.331	0.387			1	INDETERMINATE	1	TRUE	0	0.65	0		298	472	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467631	66467631	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	97	337	0	ENST00000273854.3:c.638C>G	p.Ala213Gly	p.A213G	ENST00000273854	NM_004439.5	213	gCt/gGt	3/18	1	2	FACETS	0.499	0.446	0.556	0.499	0.446	0.556	SUBCLONAL	1	TRUE	1	0.65	2		337	598	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003205	143003205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751420268	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	96	470	0	ENST00000262992.4:c.2621G>A	p.Arg874Gln	p.R874Q	ENST00000262992	NM_001101669.1	874	cGa/cAa	23/24	1	2	FACETS	0.308	0.274	0.345	0.308	0.274	0.345	SUBCLONAL	1	TRUE	1	0.65	2		470	959	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524510	187524510	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	122	494	0	ENST00000441802.2:c.11170G>T	p.Glu3724Ter	p.E3724*	ENST00000441802	NM_005245.3	3724	Gaa/Taa	19/27	1	2	FACETS	0.473	0.428	0.522	0.473	0.428	0.522	SUBCLONAL	1	TRUE	1	0.65	2		494	793	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524525	187524525	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35670235	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	126	509	0	ENST00000441802.2:c.11155G>A	p.Val3719Met	p.V3719M	ENST00000441802	NM_005245.3	3719	Gtg/Atg	19/27	1	2	FACETS	0.457	0.414	0.503	0.457	0.414	0.503	SUBCLONAL	1	TRUE	1	0.65	2		509	848	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541232	187541232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377169844	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	284	499	1	ENST00000441802.2:c.6508G>A	p.Val2170Ile	p.V2170I	ENST00000441802	NM_005245.3	2170	Gtt/Att	10/27	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.65	2		500	847	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557367	187557367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746932852	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	82	368	0	ENST00000441802.2:c.3995G>A	p.Arg1332His	p.R1332H	ENST00000441802	NM_005245.3	1332	cGc/cAc	6/27	1	2	FACETS	0.422	0.372	0.475	0.422	0.372	0.475	SUBCLONAL	1	TRUE	1	0.65	2		368	598	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282633	1282633	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554041306	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	192	552	1	ENST00000310581.5:c.1680C>A	p.Phe560Leu	p.F560L	ENST00000310581	NM_198253.2	560	ttC/ttA	3/16	1	2	FACETS	0.525	0.484	0.567	0.525	0.484	0.567	SUBCLONAL	1	TRUE	1	0.65	2		553	1126	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177810	56177810	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	90	443	0	ENST00000399503.3:c.2783C>A	p.Ser928Tyr	p.S928Y	ENST00000399503	NM_005921.1	928	tCt/tAt	14/20	1	2	FACETS	0.363	0.322	0.407	0.363	0.322	0.407	SUBCLONAL	1	TRUE	1	0.65	2		443	763	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752383	57752383	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	128	357	0	ENST00000274289.3:c.1190A>C	p.Lys397Thr	p.K397T	ENST00000274289	NM_006622.3	397	aAg/aCg	9/14	1	2	FACETS	0.567	0.514	0.622	0.567	0.514	0.622	SUBCLONAL	1	TRUE	1	0.65	2		357	695	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645121	86645121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	80	407	0	ENST00000274376.6:c.1193G>A	p.Arg398Gln	p.R398Q	ENST00000274376	NM_002890.2	398	cGa/cAa	8/25	1	2	FACETS	0.367	0.323	0.415	0.367	0.323	0.415	SUBCLONAL	1	TRUE	1	0.65	2		407	670	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685313	86685313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886060844	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	102	325	0	ENST00000274376.6:c.3029G>A	p.Arg1010Gln	p.R1010Q	ENST00000274376	NM_002890.2	1010	cGa/cAa	24/25	1	2	FACETS	0.532	0.477	0.59	0.532	0.477	0.59	SUBCLONAL	1	TRUE	1	0.65	2		325	590	SUCCESS
APC	324	MSKCC	GRCh37	5	112175457	112175457	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	121	396	0	ENST00000257430.4:c.4166C>A	p.Ser1389Tyr	p.S1389Y	ENST00000257430	NM_000038.5	1389	tCt/tAt	16/16	1	2	FACETS	0.546	0.494	0.601	0.546	0.494	0.601	SUBCLONAL	1	TRUE	1	0.65	2		396	682	SUCCESS
APC	324	MSKCC	GRCh37	5	112176873	112176873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	149	506	0	ENST00000257430.4:c.5582C>A	p.Ser1861Tyr	p.S1861Y	ENST00000257430	NM_000038.5	1861	tCt/tAt	16/16	1	2	FACETS	0.534	0.488	0.583	0.534	0.488	0.583	SUBCLONAL	1	TRUE	1	0.65	2		506	858	SUCCESS
APC	324	MSKCC	GRCh37	5	112177653	112177653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	221	345	1	ENST00000257430.4:c.6362C>T	p.Ala2121Val	p.A2121V	ENST00000257430	NM_000038.5	2121	gCt/gTt	16/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.65	2		346	628	SUCCESS
APC	324	MSKCC	GRCh37	5	112177901	112177901	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs752654519	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	171	464	0	ENST00000257430.4:c.6610C>T	p.Arg2204Ter	p.R2204*	ENST00000257430	NM_000038.5	2204	Cga/Tga	16/16	1	2	FACETS	0.69	0.635	0.746	0.69	0.635	0.746	SUBCLONAL	1	TRUE	1	0.65	2		464	763	SUCCESS
APC	324	MSKCC	GRCh37	5	112178314	112178314	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	88	389	0	ENST00000257430.4:c.7023A>T	p.Lys2341Asn	p.K2341N	ENST00000257430	NM_000038.5	2341	aaA/aaT	16/16	1	2	FACETS	0.371	0.329	0.417	0.371	0.329	0.417	SUBCLONAL	1	TRUE	1	0.65	2		389	729	SUCCESS
APC	324	MSKCC	GRCh37	5	112179765	112179765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	107	261	0	ENST00000257430.4:c.8474C>T	p.Ser2825Phe	p.S2825F	ENST00000257430	NM_000038.5	2825	tCc/tTc	16/16	1	2	FACETS	0.435	0.39	0.483	0.435	0.39	0.483	SUBCLONAL	1	TRUE	1	0.65	2		261	757	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944981	131944981	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554099388	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	83	313	0	ENST00000265335.6:c.2929G>T	p.Glu977Ter	p.E977*	ENST00000265335		977	Gaa/Taa	19/25	1	2	FACETS	0.397	0.35	0.447	0.397	0.35	0.447	SUBCLONAL	1	TRUE	1	0.65	2		313	643	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457758	149457758	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs758322216	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	326	448	1	ENST00000286301.3:c.646C>T	p.Arg216Ter	p.R216*	ENST00000286301	NM_005211.3	216	Cga/Tga	5/22	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.65	2		449	876	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500491	149500491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770930584	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	69	492	0	ENST00000261799.4:c.2546G>A	p.Arg849Gln	p.R849Q	ENST00000261799	NM_002609.3	849	cGa/cAa	18/23	1	2	FACETS	0.191	0.165	0.219	0.191	0.165	0.219	SUBCLONAL	1	TRUE	1	0.65	2		492	1111	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637141	176637141	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	54	394	1	ENST00000439151.2:c.1741G>T	p.Glu581Ter	p.E581*	ENST00000439151	NM_022455.4	581	Gaa/Taa	5/23	1	2	FACETS	0.246	0.209	0.286	0.246	0.209	0.286	SUBCLONAL	1	TRUE	1	0.65	2		395	676	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176719061	176719061	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	66	578	0	ENST00000439151.2:c.6365T>G	p.Phe2122Cys	p.F2122C	ENST00000439151	NM_022455.4	2122	tTt/tGt	22/23	1	2	FACETS	0.181	0.156	0.208	0.181	0.156	0.208	SUBCLONAL	1	TRUE	1	0.65	2		578	1122	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056274	180056274	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770915197	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	368	566	0	ENST00000261937.6:c.970G>A	p.Glu324Lys	p.E324K	ENST00000261937	NM_182925.4	324	Gag/Aag	7/30	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.65	2		566	1000	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673724	30673724	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61733207	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	212	575	0	ENST00000376406.3:c.3236G>A	p.Arg1079His	p.R1079H	ENST00000376406	NM_014641.2	1079	cGt/cAt	10/15	1	2	FACETS	0.627	0.582	0.673	0.627	0.582	0.673	SUBCLONAL	1	TRUE	1	0.65	2		575	1041	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679722	30679722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381054079	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	190	558	1	ENST00000376406.3:c.1997C>T	p.Ala666Val	p.A666V	ENST00000376406	NM_014641.2	666	gCc/gTc	5/15	1	2	FACETS	0.578	0.534	0.624	0.578	0.534	0.624	SUBCLONAL	1	TRUE	1	0.65	2		559	1011	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681733	30681733	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs137893469	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	327	533	0	ENST00000376406.3:c.364C>A	p.Leu122Ile	p.L122I	ENST00000376406	NM_014641.2	122	Ctc/Atc	3/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.65	2		533	983	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171613	32171613	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	360	482	0	ENST00000375023.3:c.3165C>A	p.Cys1055Ter	p.C1055*	ENST00000375023	NM_004557.3	1055	tgC/tgA	20/30	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.65	2		482	1007	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288180	33288180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772037578	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	100	340	0	ENST00000374542.5:c.1228G>A	p.Glu410Lys	p.E410K	ENST00000374542	NM_001141970.1	410	Gaa/Aaa	4/8	1	2	FACETS	0.496	0.444	0.552	0.496	0.444	0.552	SUBCLONAL	1	TRUE	1	0.65	2		340	620	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140891	37140891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	219	474	1	ENST00000373509.5:c.727G>A	p.Glu243Lys	p.E243K	ENST00000373509	NM_002648.3	243	Gag/Aag	5/6	1	2	FACETS	0.646	0.601	0.693	0.646	0.601	0.693	SUBCLONAL	1	TRUE	1	0.65	2		475	1043	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748479	43748479	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45533131	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	183	569	1	ENST00000523873.1:c.433C>T	p.Arg145Ter	p.R145*	ENST00000523873		145	Cga/Tga	6/8	1	2	FACETS	0.428	0.394	0.464	0.428	0.394	0.464	SUBCLONAL	1	TRUE	1	0.65	2		570	1316	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793712	89793712	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	271	437	0	ENST00000336032.3:c.781A>C	p.Asn261His	p.N261H	ENST00000336032	NM_006813.2	261	Aat/Cat	2/2	1	2	FACETS	0.971	0.913	1	0.971	0.913	1	CLONAL	1	TRUE	1	0.65	2		437	859	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553383	106553383	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	85	269	0	ENST00000369096.4:c.1348C>A	p.Leu450Ile	p.L450I	ENST00000369096	NM_001198.3	450	Ctc/Atc	5/7	1	2	FACETS	0.521	0.462	0.584	0.521	0.462	0.584	SUBCLONAL	1	TRUE	1	0.65	2		269	502	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020867	112020867	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	135	617	0	ENST00000368678.4:c.704C>A	p.Ala235Asp	p.A235D	ENST00000368678		235	gCt/gAt	8/13	1	2	FACETS	0.352	0.319	0.387	0.352	0.319	0.387	SUBCLONAL	1	TRUE	1	0.65	2		617	1180	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024121	112024121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	81	722	0	ENST00000368678.4:c.664G>A	p.Glu222Lys	p.E222K	ENST00000368678		222	Gaa/Aaa	7/13	1	2	FACETS	0.205	0.179	0.232	0.205	0.179	0.232	SUBCLONAL	1	TRUE	1	0.65	2		722	1217	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117639416	117639416	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	264	486	0	ENST00000368508.3:c.5941-1G>A		p.X1981_splice	ENST00000368508	NM_002944.2	1981			1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.65	2		486	805	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662582	117662582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	245	468	0	ENST00000368508.3:c.4883G>A	p.Gly1628Glu	p.G1628E	ENST00000368508	NM_002944.2	1628	gGa/gAa	29/43	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.65	2		468	700	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683849	117683849	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	154	449	0	ENST00000368508.3:c.3298G>T	p.Asp1100Tyr	p.D1100Y	ENST00000368508	NM_002944.2	1100	Gac/Tac	21/43	1	2	FACETS	0.585	0.536	0.637	0.585	0.536	0.637	SUBCLONAL	1	TRUE	1	0.65	2		449	810	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117746788	117746788	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	283	544	0	ENST00000368508.3:c.32T>A	p.Leu11His	p.L11H	ENST00000368508	NM_002944.2	11	cTt/cAt	1/43	1	2	FACETS	0.924	0.87	0.98	0.924	0.87	0.98	CLONAL	1	TRUE	1	0.65	2		544	942	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192545	138192545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs970781981	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	142	421	1	ENST00000237289.4:c.181C>T	p.Arg61Trp	p.R61W	ENST00000237289	NM_001270507.1	61	Cgg/Tgg	2/9	1	2	FACETS	0.527	0.48	0.576	0.527	0.48	0.576	SUBCLONAL	1	TRUE	1	0.65	2		422	829	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023160	150023160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	309	534	0	ENST00000253339.5:c.103C>T	p.Arg35Trp	p.R35W	ENST00000253339		35	Cgg/Tgg	1/7	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.65	2		534	939	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023166	150023166	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	151	549	0	ENST00000253339.5:c.97G>T	p.Glu33Ter	p.E33*	ENST00000253339		33	Gaa/Taa	1/7	1	2	FACETS	0.491	0.448	0.535	0.491	0.448	0.535	SUBCLONAL	1	TRUE	1	0.65	2		549	947	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265535	152265535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571716552	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	197	387	0	ENST00000206249.3:c.988G>A	p.Glu330Lys	p.E330K	ENST00000206249	NM_000125.3	330	Gag/Aag	4/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.65	2		387	563	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332849	152332849	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	155	520	1	ENST00000206249.3:c.1155G>T	p.Glu385Asp	p.E385D	ENST00000206249	NM_000125.3	385	gaG/gaT	5/8	1	2	FACETS	0.556	0.509	0.605	0.556	0.509	0.605	SUBCLONAL	1	TRUE	1	0.65	2		521	858	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92252390	92252390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373488172	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	106	350	0	ENST00000265734.4:c.658C>T	p.Arg220Cys	p.R220C	ENST00000265734	NM_001259.6	220	Cgt/Tgt	6/8	1	2	FACETS	0.565	0.508	0.626	0.565	0.508	0.626	SUBCLONAL	1	TRUE	1	0.65	2		350	577	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494187	140494187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1158980679	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	132	579	0	ENST00000288602.6:c.1061G>A	p.Arg354Gln	p.R354Q	ENST00000288602	NM_004333.4	354	cGa/cAa	8/18	1	2	FACETS	0.396	0.359	0.435	0.396	0.359	0.435	SUBCLONAL	1	TRUE	1	0.65	2		579	1026	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151164255	151164255	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	131	306	0	ENST00000262187.5:c.505A>C	p.Lys169Gln	p.K169Q	ENST00000262187	NM_005614.3	169	Aaa/Caa	8/8	1	2	FACETS	0.6	0.545	0.657	0.6	0.545	0.657	SUBCLONAL	1	TRUE	1	0.65	2		306	672	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873888	151873888	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	306	545	0	ENST00000262189.6:c.8650C>T	p.Arg2884Ter	p.R2884*	ENST00000262189	NM_170606.2	2884	Cga/Tga	38/59	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.65	2		545	942	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879673	151879673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	65	116	0	ENST00000262189.6:c.5272C>T	p.Arg1758Cys	p.R1758C	ENST00000262189	NM_170606.2	1758	Cgt/Tgt	36/59	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.65	2		116	196	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90995011	90995011	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	135	385	0	ENST00000265433.3:c.110A>C	p.Asn37Thr	p.N37T	ENST00000265433	NM_002485.4	37	aAt/aCt	2/16	1	2	FACETS	0.464	0.421	0.508	0.464	0.421	0.508	SUBCLONAL	1	TRUE	1	0.65	2		385	896	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465513	8465513	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	107	558	1	ENST00000356435.5:c.3667C>A	p.Gln1223Lys	p.Q1223K	ENST00000356435		1223	Caa/Aaa	21/35	1	2	FACETS	0.402	0.36	0.446	0.402	0.36	0.446	SUBCLONAL	1	TRUE	1	0.65	2		559	820	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518315	8518315	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	203	289	0	ENST00000356435.5:c.1076A>C	p.Lys359Thr	p.K359T	ENST00000356435		359	aAa/aCa	10/35	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.65	2		289	520	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636754	8636754	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	40	451	0	ENST00000356435.5:c.155G>T	p.Arg52Ile	p.R52I	ENST00000356435		52	aGa/aTa	2/35	1	2	FACETS	0.166	0.137	0.199	0.166	0.137	0.199	SUBCLONAL	1	TRUE	1	0.65	2		451	740	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570325	87570325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	175	566	0	ENST00000277120.3:c.2065G>A	p.Val689Met	p.V689M	ENST00000277120		689	Gtg/Atg	17/19	1	2	FACETS	0.493	0.453	0.535	0.493	0.453	0.535	SUBCLONAL	1	TRUE	1	0.65	2		566	1092	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771933	135771933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs118203745	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	247	395	0	ENST00000298552.3:c.3184C>T	p.Arg1062Trp	p.R1062W	ENST00000298552	NM_001162426.1	1062	Cgg/Tgg	23/23	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.65	2		395	668	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772842	135772842	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	139	593	0	ENST00000298552.3:c.2781G>T	p.Lys927Asn	p.K927N	ENST00000298552	NM_001162426.1	927	aaG/aaT	21/23	1	2	FACETS	0.395	0.359	0.433	0.395	0.359	0.433	SUBCLONAL	1	TRUE	1	0.65	2		593	1083	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395204	139395204	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375978224	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	218	488	0	ENST00000277541.6:c.5734G>A	p.Asp1912Asn	p.D1912N	ENST00000277541	NM_017617.3	1912	Gac/Aac	31/34	1	2	FACETS	0.632	0.587	0.678	0.632	0.587	0.678	SUBCLONAL	1	TRUE	1	0.65	2		488	1062	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139438548	139438548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	111	438	0	ENST00000277541.6:c.68G>A	p.Arg23Gln	p.R23Q	ENST00000277541	NM_017617.3	23	cGa/cAa	2/34	1	2	FACETS	0.338	0.303	0.375	0.338	0.303	0.375	SUBCLONAL	1	TRUE	1	0.65	2		438	1011	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332258	70332258	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	384	788	0	ENST00000373644.4:c.163G>T	p.Glu55Ter	p.E55*	ENST00000373644	NM_030625.2	55	Gaa/Taa	2/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.65	2		788	1108	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332424	70332424	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	230	466	0	ENST00000373644.4:c.329C>A	p.Ser110Tyr	p.S110Y	ENST00000373644	NM_030625.2	110	tCt/tAt	2/12	1	2	FACETS	0.904	0.845	0.964	0.904	0.845	0.964	CLONAL	1	TRUE	1	0.65	2		466	783	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405969	70405969	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	174	676	1	ENST00000373644.4:c.3483G>T	p.Lys1161Asn	p.K1161N	ENST00000373644	NM_030625.2	1161	aaG/aaT	4/12	1	2	FACETS	0.495	0.455	0.537	0.495	0.455	0.537	SUBCLONAL	1	TRUE	1	0.65	2		677	1082	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70442623	70442623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867702783	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	311	536	0	ENST00000373644.4:c.4945C>T	p.Arg1649Trp	p.R1649W	ENST00000373644	NM_030625.2	1649	Cgg/Tgg	10/12	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.65	2		536	910	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451131	70451131	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	167	500	1	ENST00000373644.4:c.5971G>T	p.Asp1991Tyr	p.D1991Y	ENST00000373644	NM_030625.2	1991	Gat/Tat	12/12	1	2	FACETS	0.528	0.485	0.573	0.528	0.485	0.573	SUBCLONAL	1	TRUE	1	0.65	2		501	973	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243232	123243232	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	88	741	2	ENST00000358487.5:c.2281C>A	p.Leu761Ile	p.L761I	ENST00000358487	NM_000141.4	761	Ctc/Atc	17/18	1	2	FACETS	0.229	0.202	0.258	0.229	0.202	0.258	SUBCLONAL	1	TRUE	1	0.65	2		743	1181	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247514	123247514	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	91	385	0	ENST00000358487.5:c.1977G>T	p.Lys659Asn	p.K659N	ENST00000358487	NM_000141.4	659	aaG/aaT	14/18	1	2	FACETS	0.36	0.319	0.404	0.36	0.319	0.404	SUBCLONAL	1	TRUE	1	0.65	2		385	777	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	183	640	0	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	1	2	FACETS	0.519	0.479	0.562	0.519	0.479	0.562	SUBCLONAL	1	TRUE	1	0.65	2		640	1084	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258036	123258036	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519045	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	68	614	0	ENST00000358487.5:c.1645A>C	p.Asn549His	p.N549H	ENST00000358487	NM_000141.4	549	Aat/Cat	12/18	1	2	FACETS	0.19	0.165	0.218	0.19	0.165	0.218	SUBCLONAL	1	TRUE	1	0.65	2		614	1099	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533535	533535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	190	544	0	ENST00000451590.1:c.368G>A	p.Arg123His	p.R123H	ENST00000451590	NM_001130442.1	123	cGc/cAc	4/5	1	2	FACETS	0.555	0.512	0.599	0.555	0.512	0.599	SUBCLONAL	1	TRUE	1	0.65	2		544	1054	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102098284	102098284	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	62	543	1	ENST00000282441.5:c.1248C>A	p.Phe416Leu	p.F416L	ENST00000282441	NM_001130145.2	416	ttC/ttA	8/9	1	2	FACETS	0.181	0.156	0.209	0.181	0.156	0.209	SUBCLONAL	1	TRUE	1	0.65	2		544	1053	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206828	102206828	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1329812731	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	176	772	0	ENST00000263464.3:c.1456A>G	p.Thr486Ala	p.T486A	ENST00000263464	NM_001165.4	486	Aca/Gca	7/9	1	2	FACETS	0.402	0.369	0.436	0.402	0.369	0.436	SUBCLONAL	1	TRUE	1	0.65	2		772	1348	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098533	108098533	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs55861249	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	101	283	0	ENST00000278616.4:c.103C>T	p.Arg35Ter	p.R35*	ENST00000278616	NM_000051.3	35	Cga/Tga	3/63	1	2	FACETS	0.5	0.448	0.556	0.5	0.448	0.556	SUBCLONAL	1	TRUE	1	0.65	2		283	621	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115594	108115594	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730881336	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	308	519	0	ENST00000278616.4:c.742C>T	p.Arg248Ter	p.R248*	ENST00000278616	NM_000051.3	248	Cga/Tga	7/63	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.65	2		519	824	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115600	108115600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772821016	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	262	520	2	ENST00000278616.4:c.748C>T	p.Arg250Ter	p.R250*	ENST00000278616	NM_000051.3	250	Cga/Tga	7/63	1	2	FACETS	0.97	0.912	1	0.97	0.912	1	CLONAL	1	TRUE	1	0.65	2		522	831	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180999	108180999	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	130	413	0	ENST00000278616.4:c.5875G>T	p.Glu1959Ter	p.E1959*	ENST00000278616	NM_000051.3	1959	Gaa/Taa	39/63	1	2	FACETS	0.533	0.483	0.584	0.533	0.483	0.584	SUBCLONAL	1	TRUE	1	0.65	2		413	751	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216568	108216568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs767845728	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	151	487	0	ENST00000278616.4:c.8517C>A	p.Phe2839Leu	p.F2839L	ENST00000278616	NM_000051.3	2839	ttC/ttA	58/63	1	2	FACETS	0.565	0.516	0.615	0.565	0.516	0.615	SUBCLONAL	1	TRUE	1	0.65	2		487	823	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342413	118342413	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	49	494	0	ENST00000534358.1:c.539G>T	p.Arg180Ile	p.R180I	ENST00000534358	NM_005933.3	180	aGa/aTa	3/36	1	2	FACETS	0.172	0.145	0.202	0.172	0.145	0.202	SUBCLONAL	1	TRUE	1	0.65	2		494	878	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374237	118374237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	48	536	0	ENST00000534358.1:c.7630G>A	p.Glu2544Lys	p.E2544K	ENST00000534358	NM_005933.3	2544	Gaa/Aaa	27/36	1	2	FACETS	0.176	0.148	0.207	0.176	0.148	0.207	SUBCLONAL	1	TRUE	1	0.65	2		536	838	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	461474	461474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770858476	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	357	448	0	ENST00000399788.2:c.1046G>A	p.Arg349Gln	p.R349Q	ENST00000399788	NM_001042603.1	349	cGa/cAa	9/28	0.3	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.65	2		448	954	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385236	4385236	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	50	514	0	ENST00000261254.3:c.261C>A	p.Phe87Leu	p.F87L	ENST00000261254	NM_001759.3	87	ttC/ttA	2/5	0.3	2	FACETS	0.166	0.14	0.195			1	INDETERMINATE	1	TRUE	NA	0.65	2		514	928	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466962	18466962	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	303	525	1	ENST00000266497.5:c.1101G>T	p.Gln367His	p.Q367H	ENST00000266497		367	caG/caT	5/31	1	2	FACETS	0.996	0.941	1	0.996	0.941	1	CLONAL	1	TRUE	1	0.65	2		526	936	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245445	46245445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1390936994	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	76	368	0	ENST00000334344.6:c.3539C>T	p.Thr1180Met	p.T1180M	ENST00000334344	NM_152641.2	1180	aCg/aTg	15/21	1	2	FACETS	0.353	0.309	0.4	0.353	0.309	0.4	SUBCLONAL	1	TRUE	1	0.65	2		368	663	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285642	46285642	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	124	475	0	ENST00000334344.6:c.5002C>A	p.Leu1668Ile	p.L1668I	ENST00000334344	NM_152641.2	1668	Ctt/Att	17/21	1	2	FACETS	0.436	0.394	0.48	0.436	0.394	0.48	SUBCLONAL	1	TRUE	1	0.65	2		475	876	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418718	49418718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760369709	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	211	303	1	ENST00000301067.7:c.15796C>T	p.Arg5266Cys	p.R5266C	ENST00000301067	NM_003482.3	5266	Cgc/Tgc	49/54	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.65	2		304	587	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432650	49432650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1271513534	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1209	88	623	0	ENST00000301067.7:c.8489G>A	p.Arg2830Gln	p.R2830Q	ENST00000301067	NM_003482.3	2830	cGa/cAa	34/54	1	2	FACETS	0.209	0.184	0.236	0.209	0.184	0.236	SUBCLONAL	1	TRUE	1	0.65	2		623	1297	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445026	49445026	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	99	293	0	ENST00000301067.7:c.2440C>G	p.His814Asp	p.H814D	ENST00000301067	NM_003482.3	814	Cac/Gac	10/54	1	2	FACETS	0.537	0.481	0.597	0.537	0.481	0.597	SUBCLONAL	1	TRUE	1	0.65	2		293	567	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446409	49446409	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	311	433	0	ENST00000301067.7:c.1196G>A	p.Gly399Glu	p.G399E	ENST00000301067	NM_003482.3	399	gGg/gAg	9/54	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.65	2		433	865	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447372	49447372	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	216	496	1	ENST00000301067.7:c.726C>A	p.Phe242Leu	p.F242L	ENST00000301067	NM_003482.3	242	ttC/ttA	6/54	1	2	FACETS	0.603	0.56	0.648	0.603	0.56	0.648	SUBCLONAL	1	TRUE	1	0.65	2		497	1102	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492748	50492748	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	138	483	1	ENST00000394963.4:c.1513G>T	p.Glu505Ter	p.E505*	ENST00000394963	NM_003076.4	505	Gaa/Taa	13/13	1	2	FACETS	0.456	0.414	0.5	0.456	0.414	0.5	SUBCLONAL	1	TRUE	1	0.65	2		484	931	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	203	539	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	1	2	FACETS	0.62	0.574	0.667	0.62	0.574	0.667	SUBCLONAL	1	TRUE	1	0.65	2		539	1008	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	380	540	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.65	2		540	970	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589298	28589298	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	275	469	2	ENST00000241453.7:c.2749G>T	p.Glu917Ter	p.E917*	ENST00000241453	NM_004119.2	917	Gaa/Taa	22/24	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.65	2		471	801	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623592	28623592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	96	404	2	ENST00000241453.7:c.965G>T	p.Arg322Ile	p.R322I	ENST00000241453	NM_004119.2	322	aGa/aTa	8/24	1	2	FACETS	0.407	0.362	0.454	0.407	0.362	0.454	SUBCLONAL	1	TRUE	1	0.65	2		406	726	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004278	29004278	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	260	499	1	ENST00000282397.4:c.1015C>T	p.Arg339Ter	p.R339*	ENST00000282397	NM_002019.4	339	Cga/Tga	8/30	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.65	2		500	797	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041180	29041180	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	60	527	0	ENST00000282397.4:c.248G>T	p.Arg83Ile	p.R83I	ENST00000282397	NM_002019.4	83	aGa/aTa	3/30	1	2	FACETS	0.196	0.168	0.227	0.196	0.168	0.227	SUBCLONAL	1	TRUE	1	0.65	2		527	940	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907322	32907322	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	260	445	0	ENST00000380152.3:c.1707G>T	p.Gln569His	p.Q569H	ENST00000380152		569	caG/caT	10/27	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.65	2		445	763	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912314	32912314	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	374	744	1	ENST00000380152.3:c.3822G>T	p.Lys1274Asn	p.K1274N	ENST00000380152		1274	aaG/aaT	11/27	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.65	2		745	1133	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914142	32914142	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	426	818	0	ENST00000380152.3:c.5650A>C	p.Ile1884Leu	p.I1884L	ENST00000380152		1884	Att/Ctt	11/27	1	2	FACETS	0.982	0.936	1	0.982	0.936	1	CLONAL	1	TRUE	1	0.65	2		818	1335	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914478	32914478	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358833	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	195	817	0	ENST00000380152.3:c.5986G>A	p.Ala1996Thr	p.A1996T	ENST00000380152		1996	Gca/Aca	11/27	1	2	FACETS	0.478	0.441	0.516	0.478	0.441	0.516	SUBCLONAL	1	TRUE	1	0.65	2		817	1256	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32920972	32920972	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	70	402	0	ENST00000380152.3:c.6946A>C	p.Lys2316Gln	p.K2316Q	ENST00000380152		2316	Aaa/Caa	13/27	1	2	FACETS	0.335	0.292	0.382	0.335	0.292	0.382	SUBCLONAL	1	TRUE	1	0.65	2		402	642	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103510743	103510743	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	139	406	0	ENST00000355739.4:c.647G>T	p.Arg216Ile	p.R216I	ENST00000355739	NM_000123.3	216	aGa/aTa	6/15	1	2	FACETS	0.559	0.509	0.611	0.559	0.509	0.611	SUBCLONAL	1	TRUE	1	0.65	2		406	765	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524594	103524594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	262	462	2	ENST00000355739.4:c.2725C>T	p.Pro909Ser	p.P909S	ENST00000355739	NM_000123.3	909	Cct/Tct	13/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.65	2		464	790	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557615	95557615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	140	516	1	ENST00000393063.1:c.5452G>A	p.Ala1818Thr	p.A1818T	ENST00000393063	NM_030621.3	1818	Gcc/Acc	26/28	1	2	FACETS	0.488	0.444	0.535	0.488	0.444	0.535	SUBCLONAL	1	TRUE	1	0.65	2		517	882	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95573964	95573964	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	72	450	1	ENST00000393063.1:c.2785G>T	p.Asp929Tyr	p.D929Y	ENST00000393063	NM_030621.3	929	Gat/Tat	18/28	1	2	FACETS	0.231	0.201	0.264	0.231	0.201	0.264	SUBCLONAL	1	TRUE	1	0.65	2		451	957	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574324	95574324	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	114	458	0	ENST00000393063.1:c.2543G>T	p.Arg848Ile	p.R848I	ENST00000393063	NM_030621.3	848	aGa/aTa	17/28	1	2	FACETS	0.468	0.421	0.517	0.468	0.421	0.517	SUBCLONAL	1	TRUE	1	0.65	2		458	750	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961330	41961330	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	432	716	0	ENST00000219905.7:c.238G>A	p.Asp80Asn	p.D80N	ENST00000219905	NM_001164273.1	80	Gat/Aat	2/24	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.65	2		716	1197	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003060	42003060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756706031	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	78	773	1	ENST00000219905.7:c.2597G>A	p.Arg866Gln	p.R866Q	ENST00000219905	NM_001164273.1	866	cGa/cAa	8/24	1	2	FACETS	0.194	0.17	0.221	0.194	0.17	0.221	SUBCLONAL	1	TRUE	1	0.65	2		774	1236	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690568	88690568	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	126	385	0	ENST00000360948.2:c.462A>C	p.Glu154Asp	p.E154D	ENST00000360948	NM_001012338.2	154	gaA/gaC	5/19	1	2	FACETS	0.586	0.531	0.643	0.586	0.531	0.643	SUBCLONAL	1	TRUE	1	0.65	2		385	662	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304460	91304460	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	53	334	0	ENST00000355112.3:c.1857C>A	p.Phe619Leu	p.F619L	ENST00000355112	NM_000057.2	619	ttC/ttA	7/22	1	2	FACETS	0.263	0.224	0.306	0.263	0.224	0.306	SUBCLONAL	1	TRUE	1	0.65	2		334	620	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467206	99467206	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	140	522	0	ENST00000268035.6:c.2587C>A	p.Leu863Ile	p.L863I	ENST00000268035	NM_000875.3	863	Cta/Ata	12/21	1	2	FACETS	0.441	0.401	0.484	0.441	0.401	0.484	SUBCLONAL	1	TRUE	1	0.65	2		522	976	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339599	339599	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138816818	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	176	429	1	ENST00000262320.3:c.2303C>T	p.Ser768Leu	p.S768L	ENST00000262320	NM_003502.3	768	tCg/tTg	10/11	1	2	FACETS	0.558	0.513	0.604	0.558	0.513	0.604	SUBCLONAL	1	TRUE	1	0.65	2		430	971	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828772	3828772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	154	566	1	ENST00000262367.5:c.1870C>T	p.Arg624Cys	p.R624C	ENST00000262367	NM_004380.2	624	Cgc/Tgc	9/31	1	2	FACETS	0.385	0.351	0.421	0.385	0.351	0.421	SUBCLONAL	1	TRUE	1	0.65	2		567	1230	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858394	9858394	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1555482781	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	215	447	0	ENST00000330684.3:c.3007G>T	p.Glu1003Ter	p.E1003*	ENST00000330684	NM_001134407.1	1003	Gaa/Taa	13/13	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.65	2		447	655	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14031641	14031641	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	274	511	1	ENST00000311895.7:c.1830C>A	p.Tyr610Ter	p.Y610*	ENST00000311895	NM_005236.2	610	taC/taA	9/11	1	2	FACETS	0.919	0.865	0.975	0.919	0.865	0.975	CLONAL	1	TRUE	1	0.65	2		512	917	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632792	23632792	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	109	339	0	ENST00000261584.4:c.3004G>T	p.Glu1002Ter	p.E1002*	ENST00000261584	NM_024675.3	1002	Gaa/Taa	10/13	1	2	FACETS	0.565	0.508	0.624	0.565	0.508	0.624	SUBCLONAL	1	TRUE	1	0.65	2		339	594	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828552	72828552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	558	758	2	ENST00000268489.5:c.8029G>A	p.Glu2677Lys	p.E2677K	ENST00000268489	NM_006885.3	2677	Gag/Aag	9/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.65	2		760	1604	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347725	89347725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759287339	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	531	663	1	ENST00000301030.4:c.5225C>T	p.Ser1742Leu	p.S1742L	ENST00000301030	NM_001256183.1	1742	tCg/tTg	9/13	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.65	2		664	1447	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351986	89351986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1407933251	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1460	332	762	3	ENST00000301030.4:c.964G>A	p.Glu322Lys	p.E322K	ENST00000301030	NM_001256183.1	322	Gag/Aag	9/13	1	2	FACETS	0.57	0.537	0.604	0.57	0.537	0.604	SUBCLONAL	1	TRUE	1	0.65	2		765	1792	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371736	89371736	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	385	496	0	ENST00000301030.4:c.104C>A	p.Ser35Tyr	p.S35Y	ENST00000301030	NM_001256183.1	35	tCt/tAt	4/13	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.65	2		496	1159	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877132	89877132	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	125	489	0	ENST00000389301.3:c.505G>T	p.Glu169Ter	p.E169*	ENST00000389301	NM_000135.2	169	Gaa/Taa	5/43	1	2	FACETS	0.384	0.347	0.424	0.384	0.347	0.424	SUBCLONAL	1	TRUE	1	0.65	2		489	1001	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577077	7577077	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	35	474	0	ENST00000269305.4:c.861G>T	p.Glu287Asp	p.E287D	ENST00000269305	NM_001126112.2	287	gaG/gaT	8/11	1	2	FACETS	0.102	0.083	0.124	0.102	0.083	0.124	SUBCLONAL	1	TRUE	1	0.65	2		474	1052	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1262	26	464	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.062	0.048	0.078	0.062	0.048	0.078	SUBCLONAL	1	TRUE	1	0.65	2		464	1288	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118374	17118374	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200660337	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	159	467	3	ENST00000285071.4:c.1463C>T	p.Ala488Val	p.A488V	ENST00000285071	NM_144997.5	488	gCg/gTg	13/14	1	2	FACETS	0.458	0.419	0.499	0.458	0.419	0.499	SUBCLONAL	1	TRUE	1	0.65	2		470	1068	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552222	29552222	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778549	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	104	488	1	ENST00000356175.3:c.1955G>A	p.Arg652His	p.R652H	ENST00000356175	NM_000267.3	652	cGt/cAt	17/57	1	2	FACETS	0.378	0.338	0.421	0.378	0.338	0.421	SUBCLONAL	1	TRUE	1	0.65	2		489	846	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556313	29556313	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	160	534	0	ENST00000356175.3:c.2680T>G	p.Phe894Val	p.F894V	ENST00000356175	NM_000267.3	894	Ttt/Gtt	21/57	1	2	FACETS	0.513	0.47	0.558	0.513	0.47	0.558	SUBCLONAL	1	TRUE	1	0.65	2		534	960	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	313	406	1	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.65	2		407	826	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325752	30325752	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	71	278	0	ENST00000322652.5:c.1950G>T	p.Lys650Asn	p.K650N	ENST00000322652	NM_015355.2	650	aaG/aaT	16/16	1	2	FACETS	0.379	0.33	0.431	0.379	0.33	0.431	SUBCLONAL	1	TRUE	1	0.65	2		278	577	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325849	30325849	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	115	446	0	ENST00000322652.5:c.2047G>T	p.Glu683Ter	p.E683*	ENST00000322652	NM_015355.2	683	Gaa/Taa	16/16	1	2	FACETS	0.426	0.384	0.471	0.426	0.384	0.471	SUBCLONAL	1	TRUE	1	0.65	2		446	830	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627201	37627201	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	150	454	0	ENST00000447079.4:c.1116G>T	p.Lys372Asn	p.K372N	ENST00000447079	NM_015083.1	372	aaG/aaT	2/14	1	2	FACETS	0.542	0.496	0.591	0.542	0.496	0.591	SUBCLONAL	1	TRUE	1	0.65	2		454	851	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244368	41244368	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	145	588	0	ENST00000357654.3:c.3180A>C	p.Glu1060Asp	p.E1060D	ENST00000357654	NM_007294.3	1060	gaA/gaC	10/23	1	2	FACETS	0.481	0.439	0.526	0.481	0.439	0.526	SUBCLONAL	1	TRUE	1	0.65	2		588	927	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245759	41245759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55650082	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	139	474	0	ENST00000357654.3:c.1789G>A	p.Glu597Lys	p.E597K	ENST00000357654	NM_007294.3	597	Gaa/Aaa	10/23	1	2	FACETS	0.546	0.497	0.597	0.546	0.497	0.597	SUBCLONAL	1	TRUE	1	0.65	2		474	783	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47700110	47700110	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	136	383	0	ENST00000347630.2:c.63T>G	p.Ser21Arg	p.S21R	ENST00000347630	NM_001007230.1	21	agT/agG	3/11	1	2	FACETS	0.591	0.538	0.646	0.591	0.538	0.646	SUBCLONAL	1	TRUE	1	0.65	2		383	708	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440734	56440734	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	305	442	0	ENST00000407977.2:c.484G>C	p.Val162Leu	p.V162L	ENST00000407977		162	Gtg/Ctg	5/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.65	2		442	837	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677944	58677944	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	160	419	2	ENST00000305921.3:c.169G>A	p.Ala57Thr	p.A57T	ENST00000305921	NM_003620.3	57	Gcc/Acc	1/6	1	2	FACETS	0.58	0.532	0.63	0.58	0.532	0.63	SUBCLONAL	1	TRUE	1	0.65	2		421	849	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63531801	63531801	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200460573	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	196	541	1	ENST00000307078.5:c.2180C>T	p.Ser727Leu	p.S727L	ENST00000307078	NM_004655.3	727	tCg/tTg	9/11	1	2	FACETS	0.578	0.534	0.623	0.578	0.534	0.623	SUBCLONAL	1	TRUE	1	0.65	2		542	1044	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63537656	63537656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201387209	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	187	562	0	ENST00000307078.5:c.976C>T	p.Arg326Cys	p.R326C	ENST00000307078	NM_004655.3	326	Cgt/Tgt	4/11	1	2	FACETS	0.588	0.543	0.635	0.588	0.543	0.635	SUBCLONAL	1	TRUE	1	0.65	2		562	978	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604790	48604790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	91	433	1	ENST00000342988.3:c.1612G>A	p.Glu538Lys	p.E538K	ENST00000342988	NM_005359.5	538	Gaa/Aaa	12/12	1	2	FACETS	0.399	0.354	0.447	0.399	0.354	0.447	SUBCLONAL	1	TRUE	1	0.65	2		434	701	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211615	5211615	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	132	393	0	ENST00000357368.4:c.5220C>A	p.Phe1740Leu	p.F1740L	ENST00000357368	NM_002850.3	1740	ttC/ttA	33/38	1	2	FACETS	0.53	0.481	0.581	0.53	0.481	0.581	SUBCLONAL	1	TRUE	1	0.65	2		393	767	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117249	7117249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	150	529	0	ENST00000302850.5:c.3967G>A	p.Asp1323Asn	p.D1323N	ENST00000302850	NM_000208.2	1323	Gac/Aac	22/22	1	2	FACETS	0.414	0.377	0.452	0.414	0.377	0.452	SUBCLONAL	1	TRUE	1	0.65	2		529	1116	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7174602	7174602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	462	490	0	ENST00000302850.5:c.1115G>A	p.Arg372Gln	p.R372Q	ENST00000302850	NM_000208.2	372	cGa/cAa	4/22	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.65	2		490	1149	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10267124	10267124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751093624	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	66	546	1	ENST00000340748.4:c.1294G>A	p.Glu432Lys	p.E432K	ENST00000340748		432	Gaa/Aaa	17/40	1	2	FACETS	0.196	0.169	0.225	0.196	0.169	0.225	SUBCLONAL	1	TRUE	1	0.65	2		547	1037	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11114047	11114047	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	244	631	1	ENST00000358026.2:c.1975G>T	p.Glu659Ter	p.E659*	ENST00000358026	NM_001128849.1	659	Gaa/Taa	13/36	1	2	FACETS	0.557	0.519	0.596	0.557	0.519	0.596	SUBCLONAL	1	TRUE	1	0.65	2		632	1348	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144820	11144820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747286271	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	220	513	0	ENST00000358026.2:c.3895G>A	p.Asp1299Asn	p.D1299N	ENST00000358026	NM_001128849.1	1299	Gac/Aac	28/36	1	2	FACETS	0.582	0.541	0.625	0.582	0.541	0.625	SUBCLONAL	1	TRUE	1	0.65	2		513	1163	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145689	11145689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318154109	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	443	569	1	ENST00000358026.2:c.4051G>A	p.Asp1351Asn	p.D1351N	ENST00000358026	NM_001128849.1	1351	Gac/Aac	29/36	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.65	2		570	1235	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951059	17951059	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	387	541	0	ENST00000458235.1:c.1234C>A	p.Leu412Ile	p.L412I	ENST00000458235	NM_000215.3	412	Ctc/Atc	9/24	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.65	2		541	1060	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856532	45856532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201165309	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	197	560	0	ENST00000391945.4:c.1726G>A	p.Glu576Lys	p.E576K	ENST00000391945	NM_000400.3	576	Gaa/Aaa	18/23	1	2	FACETS	0.549	0.507	0.592	0.549	0.507	0.592	SUBCLONAL	1	TRUE	1	0.65	2		560	1105	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538331	9538331	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	316	566	0	ENST00000353224.5:c.1667T>C	p.Leu556Pro	p.L556P	ENST00000353224	NM_177990.2	556	cTc/cCc	7/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.65	2		566	918	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023666	31023666	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768333722	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	143	595	0	ENST00000375687.4:c.3151C>T	p.Arg1051Cys	p.R1051C	ENST00000375687	NM_015338.5	1051	Cgt/Tgt	13/13	1	2	FACETS	0.412	0.374	0.451	0.412	0.374	0.451	SUBCLONAL	1	TRUE	1	0.65	2		595	1069	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024664	31024664	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	389	547	0	ENST00000375687.4:c.4149G>T	p.Glu1383Asp	p.E1383D	ENST00000375687	NM_015338.5	1383	gaG/gaT	13/13	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.65	2		547	990	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388711	31388711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	279	426	1	ENST00000328111.2:c.1976C>T	p.Pro659Leu	p.P659L	ENST00000328111	NM_006892.3	659	cCa/cTa	18/23	1	2	FACETS	0.996	0.938	1	0.996	0.938	1	CLONAL	1	TRUE	1	0.65	2		427	862	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39709856	39709856	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	98	344	1	ENST00000361337.2:c.483G>T	p.Lys161Asn	p.K161N	ENST00000361337	NM_003286.2	161	aaG/aaT	7/21	1	2	FACETS	0.45	0.402	0.502	0.45	0.402	0.502	SUBCLONAL	1	TRUE	1	0.65	2		345	670	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39713142	39713142	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	123	511	0	ENST00000361337.2:c.548A>C	p.Lys183Thr	p.K183T	ENST00000361337	NM_003286.2	183	aAa/aCa	8/21	1	2	FACETS	0.4	0.361	0.441	0.4	0.361	0.441	SUBCLONAL	1	TRUE	1	0.65	2		511	946	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728718	39728718	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	96	326	0	ENST00000361337.2:c.998A>C	p.Lys333Thr	p.K333T	ENST00000361337	NM_003286.2	333	aAa/aCa	12/21	1	2	FACETS	0.465	0.415	0.519	0.465	0.415	0.519	SUBCLONAL	1	TRUE	1	0.65	2		326	635	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420103	41420103	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	61	271	0	ENST00000373198.4:c.218C>A	p.Ser73Tyr	p.S73Y	ENST00000373198	NM_133170.3	73	tCt/tAt	3/32	1	2	FACETS	0.467	0.404	0.535	0.467	0.404	0.535	SUBCLONAL	1	TRUE	1	0.65	2		271	402	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262324	46262324	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	407	764	0	ENST00000371998.3:c.908G>T	p.Arg303Ile	p.R303I	ENST00000371998		303	aGa/aTa	9/23	1	2	FACETS	0.999	0.951	1	0.999	0.951	1	CLONAL	1	TRUE	1	0.65	2		764	1253	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29090089	29090089	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764396738	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	41	85	0	ENST00000328354.6:c.1392G>T	p.Lys464Asn	p.K464N	ENST00000328354	NM_007194.3	464	aaG/aaT	13/15	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.65	2		85	123	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537100	41537100	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	294	435	1	ENST00000263253.7:c.1927G>T	p.Glu643Ter	p.E643*	ENST00000263253	NM_001429.3	643	Gaa/Taa	10/31	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.65	2		436	876	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732861	44732861	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	198	201	0	ENST00000377967.4:c.64G>T	p.Glu22Ter	p.E22*	ENST00000377967	NM_021140.2	22	Gaa/Taa	1/29	1	1	FACETS	0.78	0.729	0.833	0.78	0.729	0.833	SUBCLONAL	1	TRUE	0	0.65	1		201	527	SUCCESS
AR	367	MSKCC	GRCh37	X	66765887	66765887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	37	315	0	ENST00000374690.3:c.899G>A	p.Gly300Asp	p.G300D	ENST00000374690	NM_000044.3	300	gGc/gAc	1/8	1	1	FACETS	0.131	0.107	0.157	0.131	0.107	0.157	SUBCLONAL	1	TRUE	0	0.65	1		315	587	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347744	70347744	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs771092011	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	180	292	2	ENST00000374080.3:c.2983G>A	p.Asp995Asn	p.D995N	ENST00000374080		995	Gac/Aac	22/45	1	1	FACETS	0.672	0.624	0.722	0.672	0.624	0.722	SUBCLONAL	1	TRUE	0	0.65	1		294	556	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776304	76776304	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs122445100	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	378	356	0	ENST00000373344.5:c.7162G>T	p.Glu2388Ter	p.E2388*	ENST00000373344	NM_000489.3	2388	Gaa/Taa	34/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.65	1		356	593	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937317	76937317	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	28	213	0	ENST00000373344.5:c.3431G>T	p.Arg1144Ile	p.R1144I	ENST00000373344	NM_000489.3	1144	aGa/aTa	9/35	1	1	FACETS	0.173	0.138	0.212	0.173	0.138	0.212	SUBCLONAL	1	TRUE	0	0.65	1		213	337	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937587	76937587	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	275	234	0	ENST00000373344.5:c.3161C>A	p.Ser1054Tyr	p.S1054Y	ENST00000373344	NM_000489.3	1054	tCt/tAt	9/35	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.65	1		234	409	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939761	76939761	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	192	342	0	ENST00000373344.5:c.987G>T	p.Lys329Asn	p.K329N	ENST00000373344	NM_000489.3	329	aaG/aaT	9/35	1	1	FACETS	0.71	0.661	0.759	0.71	0.661	0.759	SUBCLONAL	1	TRUE	0	0.65	1		342	562	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164853	123164853	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761786663	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	49	363	0	ENST00000218089.9:c.166G>A	p.Gly56Ser	p.G56S	ENST00000218089	NM_001042749.1	56	Ggt/Agt	5/35	1	1	FACETS	0.151	0.127	0.177	0.151	0.127	0.177	SUBCLONAL	1	TRUE	0	0.65	1		363	675	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6045566	6045567	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	45	241	0	ENST00000265849.7:c.119dup	p.Glu41GlyfsTer13	p.E41Gfs*13	ENST00000265849	NM_000535.5	40	aag/aaAg	2/15	1	2	FACETS	0.233	0.196	0.275	0.233	0.196	0.275	SUBCLONAL	1	TRUE	1	0.65	2		241	593	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426876	49426876	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	327	502	1	ENST00000301067.7:c.11612del	p.Ala3871GlufsTer10	p.A3871Efs*10	ENST00000301067	NM_003482.3	3871	gCa/ga	39/54	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.65	2		503	917	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416504	49416504	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	350	475	0	ENST00000301067.7:c.16207del	p.Arg5403AlafsTer15	p.R5403Afs*15	ENST00000301067	NM_003482.3	5403	Cgc/gc	51/54	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.65	2		475	888	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0005064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	338	359	0	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	0.805142858402089	2	FACETS	0.831	0.801	0.86	0.831	0.801	0.86	CLONAL	2	TRUE	0	0.851118424983396	2		359	478	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591247	67591247	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0005064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	191	371	0	ENST00000274335.5:c.1746-1G>A		p.X582_splice	ENST00000274335		582			0.851118424983396	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.851118424983396	1		371	244	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71019901	71019901	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	101	408	0	ENST00000318789.4:c.1708A>T	p.Asn570Tyr	p.N570Y	ENST00000318789	NM_032682.5	570	Aat/Tat	19/21	0.20705121042408	1	FACETS	0.293	0.263	0.325	0.293	0.263	0.325	INDETERMINATE	1	TRUE	0	0.851118424983396	1		408	465	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63829510	63829510	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	104	320	0	ENST00000279873.7:c.1153C>A	p.Pro385Thr	p.P385T	ENST00000279873	NM_032199.2	385	Cct/Act	8/10	1	2	FACETS	0.542	0.488	0.599	0.542	0.488	0.599	SUBCLONAL	1	TRUE	1	0.851118424983396	2		320	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578281	7578281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	456	421	0	ENST00000269305.4:c.568C>T	p.Pro190Ser	p.P190S	ENST00000269305	NM_001126112.2	190	Cct/Tct	6/11	0.805142858402089	2	FACETS	0.972	0.949	0.994	0.972	0.949	0.994	CLONAL	2	TRUE	0	0.851118424983396	2		421	551	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11204767	11204767	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	355	483	0	ENST00000361445.4:c.4810C>T	p.Gln1604Ter	p.Q1604*	ENST00000361445	NM_004958.3	1604	Cag/Tag	34/58	1	2	FACETS	0.964	0.917	1	0.964	0.917	1	CLONAL	1	TRUE	1	0.820200593482498	2		483	898	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294214	11294214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	204	375	0	ENST00000361445.4:c.2317G>A	p.Glu773Lys	p.E773K	ENST00000361445	NM_004958.3	773	Gag/Aag	14/58	1	2	FACETS	0.983	0.92	1	0.983	0.92	1	CLONAL	1	TRUE	1	0.820200593482498	2		375	506	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101084	27101084	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	407	630	0	ENST00000324856.7:c.4366C>T	p.Pro1456Ser	p.P1456S	ENST00000324856	NM_006015.4	1456	Cca/Tca	18/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.820200593482498	2		630	979	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102073	27102073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	352	624	0	ENST00000324856.7:c.4999C>T	p.Pro1667Ser	p.P1667S	ENST00000324856	NM_006015.4	1667	Ccg/Tcg	19/20	1	2	FACETS	0.978	0.93	1	0.978	0.93	1	CLONAL	1	TRUE	1	0.820200593482498	2		624	878	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65300262	65300262	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	199	259	0	ENST00000342505.4:c.3448G>A	p.Glu1150Lys	p.E1150K	ENST00000342505	NM_002227.2	1150	Gaa/Aaa	25/25	1	2	FACETS	0.974	0.911	1	0.974	0.911	1	CLONAL	1	TRUE	1	0.820200593482498	2		259	498	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330507	65330507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	327	393	0	ENST00000342505.4:c.1139C>T	p.Ser380Phe	p.S380F	ENST00000342505	NM_002227.2	380	tCt/tTt	8/25	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.820200593482498	2		393	725	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204495546	204495546	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1365149083	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	449	447	0	ENST00000367182.3:c.137T>C	p.Met46Thr	p.M46T	ENST00000367182	NM_001278516.1	46	aTg/aCg	3/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.820200593482498	2		447	1068	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994344	25994344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	307	528	0	ENST00000435504.4:c.469C>T	p.Pro157Ser	p.P157S	ENST00000435504		157	Cca/Tca	6/13	NA	2	FACETS	0.937	0.887	0.987			1	INDETERMINATE	1	TRUE	NA	0.820200593482498	2		528	799	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116179	209116179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555882127	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	287	446	3	ENST00000345146.2:c.97C>T	p.Pro33Ser	p.P33S	ENST00000345146	NM_005896.2	33	Ccc/Tcc	3/10	1	2	FACETS	0.929	0.878	0.981	0.929	0.878	0.981	CLONAL	1	TRUE	1	0.820200593482498	2		449	753	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794956	242794956	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773964049	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	361	605	0	ENST00000334409.5:c.253G>A	p.Asp85Asn	p.D85N	ENST00000334409	NM_005018.2	85	Gac/Aac	2/5	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.820200593482498	2		605	872	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163410	47163410	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs940126759	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	280	358	0	ENST00000409792.3:c.2716C>T	p.Pro906Ser	p.P906S	ENST00000409792	NM_014159.6	906	Cca/Tca	3/21	1	2	FACETS	0.973	0.919	1	0.973	0.919	1	CLONAL	1	TRUE	1	0.820200593482498	2		358	702	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259262	89259262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770780950	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	262	496	1	ENST00000336596.2:c.406C>T	p.Arg136Ter	p.R136*	ENST00000336596	NM_005233.5	136	Cga/Tga	3/17	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.820200593482498	2		497	602	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499354	89499354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	248	443	0	ENST00000336596.2:c.2524C>T	p.Arg842Ter	p.R842*	ENST00000336596	NM_005233.5	842	Cga/Tga	15/17	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.820200593482498	2		443	587	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948183	55948183	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	291	467	0	ENST00000263923.4:c.3788T>C	p.Val1263Ala	p.V1263A	ENST00000263923	NM_002253.2	1263	gTt/gCt	29/30	0.820200593482498	1	FACETS	0.985	0.946	1	0.985	0.946	1	CLONAL	1	TRUE	0	0.820200593482498	1		467	425	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968069	55968069	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	198	351	0	ENST00000263923.4:c.2261T>G	p.Ile754Arg	p.I754R	ENST00000263923	NM_002253.2	754	aTa/aGa	15/30	0.820200593482498	1	FACETS	0.985	0.938	1	0.985	0.938	1	CLONAL	1	TRUE	0	0.820200593482498	1		351	289	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201799	66201799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	209	418	0	ENST00000273854.3:c.2703G>A	p.Met901Ile	p.M901I	ENST00000273854	NM_004439.5	901	atG/atA	16/18	0.820200593482498	1	FACETS	0.951	0.905	0.996	0.951	0.905	0.996	CLONAL	1	TRUE	0	0.820200593482498	1		418	316	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156859	106156859	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	324	457	0	ENST00000380013.4:c.1760C>T	p.Pro587Leu	p.P587L	ENST00000380013	NM_001127208.2	587	cCa/cTa	3/11	0.806063441118221	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.820200593482498	1		457	463	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86676391	86676392	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	247	378	0	ENST00000274376.6:c.2669_2670delinsTT	p.Thr890Ile	p.T890I	ENST00000274376	NM_002890.2	890	aCC/aTT	20/25	0.820200593482498	1	FACETS	0.918	0.876	0.959	0.918	0.876	0.959	CLONAL	1	TRUE	0	0.820200593482498	1		378	387	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393165	393165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	256	429	0	ENST00000380956.4:c.13G>A	p.Gly5Ser	p.G5S	ENST00000380956	NM_001195286.1	5	Ggc/Agc	2/9	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.820200593482498	2		429	583	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032215	26032215	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs984289609	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	228	519	0	ENST00000244661.2:c.74C>T	p.Ala25Val	p.A25V	ENST00000244661	NM_003537.3	25	gCt/gTt	1/1	1	2	FACETS	0.806	0.754	0.858	0.806	0.754	0.858	CLONAL	1	TRUE	1	0.820200593482498	2		519	690	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056490	26056490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138831824	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	143	169	0	ENST00000343677.2:c.167G>A	p.Gly56Glu	p.G56E	ENST00000343677	NM_005319.3	56	gGa/gAa	1/1	1	2	FACETS	0.958	0.885	1	0.958	0.885	1	CLONAL	1	TRUE	1	0.820200593482498	2		169	364	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680127	30680127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1172894988	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	343	518	1	ENST00000376406.3:c.1592C>T	p.Pro531Leu	p.P531L	ENST00000376406	NM_014641.2	531	cCa/cTa	5/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.820200593482498	2		519	815	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286913	33286913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	153	189	0	ENST00000374542.5:c.2024C>T	p.Ser675Phe	p.S675F	ENST00000374542	NM_001141970.1	675	tCc/tTc	7/8	1	2	FACETS	0.99	0.917	1	0.99	0.917	1	CLONAL	1	TRUE	1	0.820200593482498	2		189	377	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066579	94066579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	418	830	0	ENST00000369303.4:c.1180G>A	p.Gly394Arg	p.G394R	ENST00000369303	NM_004440.3	394	Gga/Aga	5/17	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.820200593482498	2		830	1000	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704520	117704520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	270	461	0	ENST00000368508.3:c.2456C>T	p.Ser819Phe	p.S819F	ENST00000368508	NM_002944.2	819	tCc/tTc	16/43	NA	2	FACETS	0.97	0.916	1			1	INDETERMINATE	1	TRUE	NA	0.820200593482498	2		461	679	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959036	2959036	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	275	434	0	ENST00000396946.4:c.2480T>C	p.Leu827Pro	p.L827P	ENST00000396946	NM_032415.4	827	cTg/cCg	18/25	1	2	FACETS	0.938	0.886	0.991	0.938	0.886	0.991	CLONAL	1	TRUE	1	0.820200593482498	2		434	715	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55219001	55219001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	285	510	0	ENST00000275493.2:c.574C>T	p.Pro192Ser	p.P192S	ENST00000275493	NM_005228.3	192	Cca/Tca	5/28	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.820200593482498	2		510	690	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224472	55224472	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	373	582	0	ENST00000275493.2:c.1154C>T	p.Pro385Leu	p.P385L	ENST00000275493	NM_005228.3	385	cCt/cTt	10/28	1	2	FACETS	0.978	0.932	1	0.978	0.932	1	CLONAL	1	TRUE	1	0.820200593482498	2		582	930	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242502	55242502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	218	376	0	ENST00000275493.2:c.2272G>A	p.Glu758Lys	p.E758K	ENST00000275493	NM_005228.3	758	Gaa/Aaa	19/28	1	2	FACETS	0.907	0.85	0.965	0.907	0.85	0.965	CLONAL	1	TRUE	1	0.820200593482498	2		376	586	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508562	106508562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415434072	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	165	212	0	ENST00000359195.3:c.556G>A	p.Ala186Thr	p.A186T	ENST00000359195	NM_002649.2	186	Gcg/Acg	2/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.820200593482498	2		212	383	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371721	116371721	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	231	341	1	ENST00000397752.3:c.1201-1G>A		p.X401_splice	ENST00000397752	NM_000245.2	401			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.820200593482498	2		342	525	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873984	151873984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	334	473	0	ENST00000262189.6:c.8554C>T	p.Pro2852Ser	p.P2852S	ENST00000262189	NM_170606.2	2852	Cct/Tct	38/59	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.820200593482498	2		473	773	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879469	151879469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	324	533	1	ENST00000262189.6:c.5476C>T	p.His1826Tyr	p.H1826Y	ENST00000262189	NM_170606.2	1826	Cat/Tat	36/59	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.820200593482498	2		534	741	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868495	117868495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	292	567	0	ENST00000297338.2:c.847C>T	p.Pro283Ser	p.P283S	ENST00000297338	NM_006265.2	283	Ccc/Tcc	8/14	1	2	FACETS	0.914	0.864	0.965	0.914	0.864	0.965	CLONAL	1	TRUE	1	0.820200593482498	2		567	779	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341925	8341925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	307	431	0	ENST00000356435.5:c.4715G>A	p.Arg1572Lys	p.R1572K	ENST00000356435		1572	aGa/aAa	29/35	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.820200593482498	2		431	639	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760169	133760169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768153649	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	266	402	1	ENST00000318560.5:c.2492C>T	p.Pro831Leu	p.P831L	ENST00000318560	NM_005157.4	831	cCc/cTc	11/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.820200593482498	2		403	603	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413088	139413088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	366	592	0	ENST00000277541.6:c.1054G>A	p.Asp352Asn	p.D352N	ENST00000277541	NM_017617.3	352	Gac/Aac	6/34	1	2	FACETS	0.989	0.942	1	0.989	0.942	1	CLONAL	1	TRUE	1	0.820200593482498	2		592	902	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820295	139820295	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	516	753	0	ENST00000247668.2:c.1448C>T	p.Ser483Phe	p.S483F	ENST00000247668	NM_021138.3	483	tCc/tTc	11/11	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.820200593482498	2		753	1093	SUCCESS
RET	5979	MSKCC	GRCh37	10	43602002	43602002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754859905	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	264	464	2	ENST00000355710.3:c.1046C>T	p.Ala349Val	p.A349V	ENST00000355710	NM_020975.4	349	gCg/gTg	5/20	NA	2	FACETS	0.954	0.9	1			1	INDETERMINATE	1	TRUE	NA	0.820200593482498	2		466	675	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615593	43615593	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	335	480	1	ENST00000355710.3:c.2672C>T	p.Ser891Leu	p.S891L	ENST00000355710	NM_020975.4	891	tCg/tTg	15/20	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.820200593482498	NA		481	814	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851362	63851362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1485685267	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	197	281	0	ENST00000279873.7:c.2140C>T	p.Pro714Ser	p.P714S	ENST00000279873	NM_032199.2	714	Ccc/Tcc	10/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.820200593482498	2		281	451	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94179033	94179033	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750926542	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	355	521	0	ENST00000323929.3:c.1810C>T	p.Arg604Cys	p.R604C	ENST00000323929	NM_005591.3	604	Cgt/Tgt	16/20	1	2	FACETS	0.947	0.901	0.994	0.947	0.901	0.994	CLONAL	1	TRUE	1	0.820200593482498	2		521	914	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514039	125514040	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	290	654	0	ENST00000428830.2:c.977_978delinsTT	p.Ser326Phe	p.S326F	ENST00000428830	NM_001114121.2	326	tCC/tTT	10/14	NA	2	FACETS	0.911	0.861	0.962			1	INDETERMINATE	1	TRUE	NA	0.820200593482498	2		654	776	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404762	404762	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	376	514	0	ENST00000399788.2:c.4432G>A	p.Asp1478Asn	p.D1478N	ENST00000399788	NM_001042603.1	1478	Gac/Aac	26/28	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.820200593482498	2		514	825	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385378	4385378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	237	268	1	ENST00000261254.3:c.403G>A	p.Glu135Lys	p.E135K	ENST00000261254	NM_001759.3	135	Gag/Aag	2/5	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.820200593482498	2		269	551	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420377	49420377	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1322243072	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	391	533	0	ENST00000301067.7:c.15372G>A	p.Met5124Ile	p.M5124I	ENST00000301067	NM_003482.3	5124	atG/atA	48/54	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.820200593482498	2		533	882	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444082	49444082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	217	249	1	ENST00000301067.7:c.3289C>T	p.Pro1097Ser	p.P1097S	ENST00000301067	NM_003482.3	1097	Cca/Tca	11/54	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.820200593482498	2		250	441	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416876	121416876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	249	457	0	ENST00000257555.6:c.305C>T	p.Ala102Val	p.A102V	ENST00000257555		102	gCc/gTc	1/10	1	2	FACETS	0.971	0.915	1	0.971	0.915	1	CLONAL	1	TRUE	1	0.820200593482498	2		457	625	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26974677	26974677	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	252	422	0	ENST00000381527.3:c.1021C>T	p.Pro341Ser	p.P341S	ENST00000381527	NM_001260.1	341	Cct/Tct	10/13	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.820200593482498	2		422	614	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601274	28601274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	325	530	0	ENST00000241453.7:c.2158G>A	p.Glu720Lys	p.E720K	ENST00000241453	NM_004119.2	720	Gaa/Aaa	17/24	1	2	FACETS	0.908	0.861	0.956	0.908	0.861	0.956	CLONAL	1	TRUE	1	0.820200593482498	2		530	873	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28644650	28644650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1394449672	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	295	474	0	ENST00000241453.7:c.143G>A	p.Gly48Glu	p.G48E	ENST00000241453	NM_004119.2	48	gGg/gAg	2/24	1	2	FACETS	0.943	0.892	0.994	0.943	0.892	0.994	CLONAL	1	TRUE	1	0.820200593482498	2		474	763	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609655	81609655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	225	659	0	ENST00000298171.2:c.1253G>A	p.Arg418Lys	p.R418K	ENST00000298171	NM_000369.2	418	aGa/aAa	10/10	1	2	FACETS	0.6	0.559	0.642	0.6	0.559	0.642	SUBCLONAL	1	TRUE	1	0.820200593482498	2		659	915	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95584014	95584015	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	218	307	0	ENST00000393063.1:c.1453_1454delinsAA	p.Gly485Lys	p.G485K	ENST00000393063	NM_030621.3	485	GGg/AAg	10/28	1	2	FACETS	0.963	0.903	1	0.963	0.903	1	CLONAL	1	TRUE	1	0.820200593482498	2		307	552	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799140	88799140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	258	458	0	ENST00000360948.2:c.245C>T	p.Ser82Phe	p.S82F	ENST00000360948	NM_001012338.2	82	tCc/tTc	2/19	0.806063441118221	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.820200593482498	1		458	366	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820605	3820605	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147083140	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	214	211	0	ENST00000262367.5:c.2846C>T	p.Pro949Leu	p.P949L	ENST00000262367	NM_004380.2	949	cCg/cTg	14/31	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.820200593482498	2		211	498	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900926	3900926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	446	655	0	ENST00000262367.5:c.170G>A	p.Gly57Glu	p.G57E	ENST00000262367	NM_004380.2	57	gGg/gAg	2/31	1	2	FACETS	0.979	0.936	1	0.979	0.936	1	CLONAL	1	TRUE	1	0.820200593482498	2		655	1111	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273997	10273997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	338	629	0	ENST00000330684.3:c.272C>T	p.Ser91Phe	p.S91F	ENST00000330684	NM_001134407.1	91	tCc/tTc	2/13	1	2	FACETS	0.986	0.937	1	0.986	0.937	1	CLONAL	1	TRUE	1	0.820200593482498	2		629	836	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56867144	56867144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs908131101	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	391	686	0	ENST00000308159.5:c.1363G>A	p.Val455Met	p.V455M	ENST00000308159	NM_014669.4	455	Gtg/Atg	13/22	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.820200593482498	2		686	946	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81904539	81904539	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs201294738	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	460	634	0	ENST00000359376.3:c.647C>T	p.Ser216Leu	p.S216L	ENST00000359376	NM_002661.3	216	tCg/tTg	7/33	0.113016096662656	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.820200593482498	0		634	1077	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	435	602	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	1	2	FACETS	0.999	0.955	1	0.999	0.955	1	CLONAL	1	TRUE	1	0.820200593482498	2		602	1062	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579415	7579415	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	225	284	0	ENST00000269305.4:c.272G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tGg/tAg	4/11	1	2	FACETS	0.999	0.939	1	0.999	0.939	1	CLONAL	1	TRUE	1	0.820200593482498	2		284	549	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17116985	17116985	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763604691	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	340	484	0	ENST00000285071.4:c.1724C>T	p.Ser575Leu	p.S575L	ENST00000285071	NM_144997.5	575	tCg/tTg	14/14	1	2	FACETS	0.971	0.922	1	0.971	0.922	1	CLONAL	1	TRUE	1	0.820200593482498	2		484	854	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554636	63554636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	91	129	0	ENST00000307078.5:c.103C>T	p.Pro35Ser	p.P35S	ENST00000307078	NM_004655.3	35	Ccg/Tcg	2/11	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.820200593482498	2		129	215	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050364	13050364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	501	815	2	ENST00000316448.5:c.316G>A	p.Gly106Arg	p.G106R	ENST00000316448	NM_004343.3	106	Ggg/Agg	3/9	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.820200593482498	2		817	1176	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271796	15271796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	117	172	0	ENST00000263388.2:c.6643C>T	p.Pro2215Ser	p.P2215S	ENST00000263388	NM_000435.2	2215	Cca/Tca	33/33	1	2	FACETS	0.926	0.847	1	0.926	0.847	1	CLONAL	1	TRUE	1	0.820200593482498	2		172	308	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260222	19260222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	292	478	0	ENST00000162023.5:c.71G>A	p.Arg24Gln	p.R24Q	ENST00000162023		24	cGg/cAg	7/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.820200593482498	2		478	681	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314670	30314671	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	276	469	0	ENST00000262643.3:c.1219_1220delinsTT	p.Pro407Leu	p.P407L	ENST00000262643	NM_001238.2	407	CCg/TTg	12/12	1	2	FACETS	0.881	0.831	0.932	0.881	0.831	0.932	CLONAL	1	TRUE	1	0.820200593482498	2		469	764	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906384	50906384	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	362	673	4	ENST00000440232.2:c.1045C>T	p.Pro349Ser	p.P349S	ENST00000440232	NM_002691.3	349	Ccc/Tcc	9/27	NA	2	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.820200593482498	2		677	855	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742640	39742640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	333	439	0	ENST00000361337.2:c.1483G>A	p.Glu495Lys	p.E495K	ENST00000361337	NM_003286.2	495	Gaa/Aaa	15/21	1	2	FACETS	0.996	0.947	1	0.996	0.947	1	CLONAL	1	TRUE	1	0.820200593482498	2		439	815	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730916	40730916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765075213	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	205	214	0	ENST00000373198.4:c.3619C>T	p.Arg1207Cys	p.R1207C	ENST00000373198	NM_133170.3	1207	Cgt/Tgt	27/32	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.820200593482498	2		214	457	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979350	40979350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747923769	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	228	334	0	ENST00000373198.4:c.1783G>A	p.Asp595Asn	p.D595N	ENST00000373198	NM_133170.3	595	Gac/Aac	11/32	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.820200593482498	2		334	550	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866378	42866378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	216	291	0	ENST00000398585.3:c.254C>T	p.Pro85Leu	p.P85L	ENST00000398585	NM_001135099.1	85	cCc/cTc	3/14	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.820200593482498	2		291	459	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22142665	22142665	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	198	358	0	ENST00000215832.6:c.737C>T	p.Ser246Phe	p.S246F	ENST00000215832	NM_002745.4	246	tCc/tTc	6/9	1	2	FACETS	0.853	0.796	0.912	0.853	0.796	0.912	CLONAL	1	TRUE	1	0.820200593482498	2		358	566	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932980	39932980	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238996683	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	275	551	0	ENST00000378444.4:c.1619G>A	p.Arg540Gln	p.R540Q	ENST00000378444	NM_001123385.1	540	cGg/cAg	4/15	NA	2	FACETS	0.765	0.72	0.811			1	INDETERMINATE	1	TRUE	NA	0.820200593482498	2		551	877	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412688	63412688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	338	603	1	ENST00000330258.3:c.479C>T	p.Pro160Leu	p.P160L	ENST00000330258	NM_152424.3	160	cCc/cTc	2/2	0.142364289996183	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.820200593482498	0		604	833	SUCCESS
AR	367	MSKCC	GRCh37	X	66905852	66905852	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	278	528	0	ENST00000374690.3:c.1769G>A	p.Gly590Glu	p.G590E	ENST00000374690	NM_000044.3	590	gGg/gAg	3/8	0.142364289996183	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.820200593482498	0		528	699	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339657	70339657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	367	807	0	ENST00000374080.3:c.326C>T	p.Ser109Phe	p.S109F	ENST00000374080		109	tCc/tTc	3/45	0.142364289996183	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.820200593482498	0		807	940	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341448	70341448	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	334	509	0	ENST00000374080.3:c.883C>T	p.Arg295Cys	p.R295C	ENST00000374080		295	Cgc/Tgc	7/45	0.142364289996183	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.820200593482498	0		509	741	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343507	70343507	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	291	745	0	ENST00000374080.3:c.1681C>T	p.Pro561Ser	p.P561S	ENST00000374080		561	Ccc/Tcc	12/45	0.142364289996183	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.820200593482498	0		745	799	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346257	70346257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	361	669	0	ENST00000374080.3:c.2608G>A	p.Val870Met	p.V870M	ENST00000374080		870	Gtg/Atg	19/45	0.142364289996183	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.820200593482498	0		669	868	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938821	76938821	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	318	528	0	ENST00000373344.5:c.1927G>T	p.Glu643Ter	p.E643*	ENST00000373344	NM_000489.3	643	Gaa/Taa	9/35	0.142364289996183	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.820200593482498	0		528	756	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181208	123181208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	287	597	0	ENST00000218089.9:c.672G>A	p.Met224Ile	p.M224I	ENST00000218089	NM_001042749.1	224	atG/atA	9/35	0.142364289996183	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.820200593482498	0		597	859	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195668	123195668	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	325	601	0	ENST00000218089.9:c.1582A>G	p.Thr528Ala	p.T528A	ENST00000218089	NM_001042749.1	528	Acc/Gcc	17/35	0.142364289996183	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.820200593482498	0		601	813	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199674	138199675	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	297	452	0	ENST00000237289.4:c.1097_1098del	p.Glu366GlyfsTer22	p.E366Gfs*22	ENST00000237289	NM_001270507.1	364	agGAga/agga	7/9	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.820200593482498	2		452	718	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808952	1808953	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	234	405	0	ENST00000260795.2:c.2384_2385delinsTT	p.Pro795Leu	p.P795L	ENST00000260795		795	cCC/cTT	17/17	0.806063441118221	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.820200593482498	1		405	300	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541071	187541073	+	frameshift_variant	Frame_Shift_Del	DEL	AGG	AGG	GA	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	250	405	0	ENST00000441802.2:c.6667_6669delinsTC	p.Pro2223SerfsTer17	p.P2223Sfs*17	ENST00000441802	NM_005245.3	2223	CCT/TC	10/27	0.806063441118221	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.820200593482498	1		405	341	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663588	117663590	+	missense_variant	Missense_Mutation	TNP	CTC	CTC	TTT	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	221	449	0	ENST00000368508.3:c.4642_4644delinsAAA	p.Glu1548Lys	p.E1548K	ENST00000368508	NM_002944.2	1548	GAG/AAA	28/43	NA	2	FACETS	0.862	0.807	0.918			1	INDETERMINATE	1	TRUE	NA	0.820200593482498	2		449	625	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983275	149983275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	59	368	0	ENST00000253339.5:c.2983C>T	p.Arg995Cys	p.R995C	ENST00000253339		995	Cgc/Tgc	7/7	1	2	FACETS	0.213	0.183	0.246	0.213	0.183	0.246	SUBCLONAL	1	TRUE	1	0.820200593482498	2		368	676	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864243	117864243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	47	741	0	ENST00000297338.2:c.1414C>T	p.Pro472Ser	p.P472S	ENST00000297338	NM_006265.2	472	Cca/Tca	11/14	1	2	FACETS	0.13	0.109	0.153	0.13	0.109	0.153	SUBCLONAL	1	TRUE	1	0.820200593482498	2		741	883	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912014	127912014	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773765410	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	417	857	0	ENST00000373547.4:c.856C>T	p.Arg286Trp	p.R286W	ENST00000373547	NM_002721.4	286	Cgg/Tgg	7/7	1	2	FACETS	0.994	0.95	1	0.994	0.95	1	CLONAL	1	TRUE	1	0.820200593482498	2		857	1023	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852224	63852224	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	53	539	0	ENST00000279873.7:c.3002T>A	p.Met1001Lys	p.M1001K	ENST00000279873	NM_032199.2	1001	aTg/aAg	10/10	1	2	FACETS	0.15	0.127	0.175	0.15	0.127	0.175	SUBCLONAL	1	TRUE	1	0.820200593482498	2		539	860	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170533	108170533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	49	535	0	ENST00000278616.4:c.5098C>T	p.Leu1700Phe	p.L1700F	ENST00000278616	NM_000051.3	1700	Ctt/Ttt	34/63	NA	2	FACETS	0.148	0.124	0.174			1	INDETERMINATE	1	TRUE	NA	0.820200593482498	2		535	809	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480001	50480001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	342	539	0	ENST00000394963.4:c.235C>T	p.Pro79Ser	p.P79S	ENST00000394963	NM_003076.4	79	Cct/Tct	2/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.820200593482498	2		539	819	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027168	49027168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913305	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	293	493	0	ENST00000267163.4:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	579	Cga/Tga	18/27	1	2	FACETS	0.871	0.823	0.92	0.871	0.823	0.92	CLONAL	1	TRUE	1	0.820200593482498	2		493	820	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076902	41076902	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	53	514	0	ENST00000373198.4:c.1518G>A	p.Trp506Ter	p.W506*	ENST00000373198	NM_133170.3	506	tgG/tgA	9/32	1	2	FACETS	0.168	0.143	0.196	0.168	0.143	0.196	SUBCLONAL	1	TRUE	1	0.820200593482498	2		514	768	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513598	41513600	+	missense_variant	Missense_Mutation	TNP	GGG	GGG	AGA	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	319	630	0	ENST00000263253.7:c.502_504delinsAGA	p.Gly168Arg	p.G168R	ENST00000263253	NM_001429.3	168	GGG/AGA	2/31	1	2	FACETS	0.927	0.879	0.976	0.927	0.879	0.976	CLONAL	1	TRUE	1	0.820200593482498	2		630	839	SUCCESS
AR	367	MSKCC	GRCh37	X	66766555	66766555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	50	669	0	ENST00000374690.3:c.1567G>A	p.Glu523Lys	p.E523K	ENST00000374690	NM_000044.3	523	Gaa/Aaa	1/8	0.142364289996183	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.820200593482498	0		669	860	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11204767	11204767	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	621	483	0	ENST00000361445.4:c.4810C>T	p.Gln1604Ter	p.Q1604*	ENST00000361445	NM_004958.3	1604	Cag/Tag	34/58	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.968297239439603	2		483	1276	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294214	11294214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	483	375	0	ENST00000361445.4:c.2317G>A	p.Glu773Lys	p.E773K	ENST00000361445	NM_004958.3	773	Gag/Aag	14/58	1	2	FACETS	0.978	0.94	1	0.978	0.94	1	CLONAL	1	TRUE	1	0.968297239439603	2		375	1020	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101084	27101084	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	562	630	0	ENST00000324856.7:c.4366C>T	p.Pro1456Ser	p.P1456S	ENST00000324856	NM_006015.4	1456	Cca/Tca	18/20	1	2	FACETS	0.93	0.895	0.965	0.93	0.895	0.965	CLONAL	1	TRUE	1	0.968297239439603	2		630	1248	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102073	27102073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	700	624	0	ENST00000324856.7:c.4999C>T	p.Pro1667Ser	p.P1667S	ENST00000324856	NM_006015.4	1667	Ccg/Tcg	19/20	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.968297239439603	2		624	1329	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65300262	65300262	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	291	259	0	ENST00000342505.4:c.3448G>A	p.Glu1150Lys	p.E1150K	ENST00000342505	NM_002227.2	1150	Gaa/Aaa	25/25	1	2	FACETS	0.965	0.916	1	0.965	0.916	1	CLONAL	1	TRUE	1	0.968297239439603	2		259	623	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330507	65330507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	399	393	0	ENST00000342505.4:c.1139C>T	p.Ser380Phe	p.S380F	ENST00000342505	NM_002227.2	380	tCt/tTt	8/25	1	2	FACETS	0.952	0.91	0.993	0.952	0.91	0.993	CLONAL	1	TRUE	1	0.968297239439603	2		393	866	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204495546	204495546	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1365149083	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	378	447	0	ENST00000367182.3:c.137T>C	p.Met46Thr	p.M46T	ENST00000367182	NM_001278516.1	46	aTg/aCg	3/11	1	2	FACETS	0.941	0.898	0.983	0.941	0.898	0.983	CLONAL	1	TRUE	1	0.968297239439603	2		447	830	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994344	25994344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	576	528	0	ENST00000435504.4:c.469C>T	p.Pro157Ser	p.P157S	ENST00000435504		157	Cca/Tca	6/13	1	2	FACETS	0.978	0.943	1	0.978	0.943	1	CLONAL	1	TRUE	1	0.968297239439603	2		528	1216	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116179	209116179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555882127	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	540	446	3	ENST00000345146.2:c.97C>T	p.Pro33Ser	p.P33S	ENST00000345146	NM_005896.2	33	Ccc/Tcc	3/10	1	2	FACETS	0.972	0.935	1	0.972	0.935	1	CLONAL	1	TRUE	1	0.968297239439603	2		449	1148	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794956	242794956	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773964049	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	628	605	0	ENST00000334409.5:c.253G>A	p.Asp85Asn	p.D85N	ENST00000334409	NM_005018.2	85	Gac/Aac	2/5	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.968297239439603	2		605	1205	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163410	47163410	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs940126759	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	400	358	0	ENST00000409792.3:c.2716C>T	p.Pro906Ser	p.P906S	ENST00000409792	NM_014159.6	906	Cca/Tca	3/21	1	2	FACETS	0.997	0.954	1	0.997	0.954	1	CLONAL	1	TRUE	1	0.968297239439603	2		358	829	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259262	89259262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770780950	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	287	496	1	ENST00000336596.2:c.406C>T	p.Arg136Ter	p.R136*	ENST00000336596	NM_005233.5	136	Cga/Tga	3/17	1	2	FACETS	0.796	0.752	0.84	0.796	0.752	0.84	SUBCLONAL	1	TRUE	1	0.968297239439603	2		497	745	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499354	89499354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	342	443	0	ENST00000336596.2:c.2524C>T	p.Arg842Ter	p.R842*	ENST00000336596	NM_005233.5	842	Cga/Tga	15/17	1	2	FACETS	0.961	0.916	1	0.961	0.916	1	CLONAL	1	TRUE	1	0.968297239439603	2		443	735	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808952	1808952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	405	350	0	ENST00000260795.2:c.2384C>T	p.Pro795Leu	p.P795L	ENST00000260795		795	cCc/cTc	17/17	0.968297239439603	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.968297239439603	1		350	425	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948183	55948183	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	431	467	0	ENST00000263923.4:c.3788T>C	p.Val1263Ala	p.V1263A	ENST00000263923	NM_002253.2	1263	gTt/gCt	29/30	0.968297239439603	1	FACETS	0.998	0.983	1	0.998	0.983	1	CLONAL	1	TRUE	0	0.968297239439603	1		467	460	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968069	55968069	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	341	351	0	ENST00000263923.4:c.2261T>G	p.Ile754Arg	p.I754R	ENST00000263923	NM_002253.2	754	aTa/aGa	15/30	0.968297239439603	1	FACETS	0.995	0.977	1	0.995	0.977	1	CLONAL	1	TRUE	0	0.968297239439603	1		351	365	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201799	66201799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	439	418	0	ENST00000273854.3:c.2703G>A	p.Met901Ile	p.M901I	ENST00000273854	NM_004439.5	901	atG/atA	16/18	0.968297239439603	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.968297239439603	1		418	454	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156859	106156859	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	515	457	0	ENST00000380013.4:c.1760C>T	p.Pro587Leu	p.P587L	ENST00000380013	NM_001127208.2	587	cCa/cTa	3/11	0.968297239439603	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.968297239439603	1		457	523	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541073	187541073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	369	351	0	ENST00000441802.2:c.6667C>T	p.Pro2223Ser	p.P2223S	ENST00000441802	NM_005245.3	2223	Cct/Tct	10/27	0.968297239439603	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.968297239439603	1		351	386	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86676391	86676392	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	330	378	0	ENST00000274376.6:c.2669_2670delinsTT	p.Thr890Ile	p.T890I	ENST00000274376	NM_002890.2	890	aCC/aTT	20/25	0.968297239439603	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.968297239439603	1		378	347	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393165	393165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	314	429	0	ENST00000380956.4:c.13G>A	p.Gly5Ser	p.G5S	ENST00000380956	NM_001195286.1	5	Ggc/Agc	2/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.968297239439603	NA		429	595	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032215	26032215	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs984289609	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	365	519	0	ENST00000244661.2:c.74C>T	p.Ala25Val	p.A25V	ENST00000244661	NM_003537.3	25	gCt/gTt	1/1	0.303675833776588	1	FACETS	0.471	0.449	0.494	0.471	0.449	0.494	INDETERMINATE	1	TRUE	0	0.968297239439603	1		519	825	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056490	26056490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138831824	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	188	169	0	ENST00000343677.2:c.167G>A	p.Gly56Glu	p.G56E	ENST00000343677	NM_005319.3	56	gGa/gAa	1/1	0.303675833776588	1	FACETS	0.487	0.456	0.519	0.487	0.456	0.519	INDETERMINATE	1	TRUE	0	0.968297239439603	1		169	411	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680127	30680127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1172894988	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	478	518	1	ENST00000376406.3:c.1592C>T	p.Pro531Leu	p.P531L	ENST00000376406	NM_014641.2	531	cCa/cTa	5/15	1	2	FACETS	0.876	0.84	0.912	0.876	0.84	0.912	CLONAL	1	TRUE	1	0.968297239439603	2		519	1127	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286913	33286913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	439	189	0	ENST00000374542.5:c.2024C>T	p.Ser675Phe	p.S675F	ENST00000374542	NM_001141970.1	675	tCc/tTc	7/8	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.968297239439603	2		189	898	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066579	94066579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	630	830	0	ENST00000369303.4:c.1180G>A	p.Gly394Arg	p.G394R	ENST00000369303	NM_004440.3	394	Gga/Aga	5/17	1	2	FACETS	0.899	0.867	0.932	0.899	0.867	0.932	CLONAL	1	TRUE	1	0.968297239439603	2		830	1447	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663590	117663590	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	374	472	0	ENST00000368508.3:c.4642G>A	p.Glu1548Lys	p.E1548K	ENST00000368508	NM_002944.2	1548	Gag/Aag	28/43	1	2	FACETS	0.891	0.85	0.933	0.891	0.85	0.933	CLONAL	1	TRUE	1	0.968297239439603	2		472	867	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704520	117704520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	452	461	0	ENST00000368508.3:c.2456C>T	p.Ser819Phe	p.S819F	ENST00000368508	NM_002944.2	819	tCc/tTc	16/43	1	2	FACETS	0.99	0.95	1	0.99	0.95	1	CLONAL	1	TRUE	1	0.968297239439603	2		461	943	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959036	2959036	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	481	434	0	ENST00000396946.4:c.2480T>C	p.Leu827Pro	p.L827P	ENST00000396946	NM_032415.4	827	cTg/cCg	18/25	1	2	FACETS	0.97	0.932	1	0.97	0.932	1	CLONAL	1	TRUE	1	0.968297239439603	2		434	1024	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55219001	55219001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	434	510	0	ENST00000275493.2:c.574C>T	p.Pro192Ser	p.P192S	ENST00000275493	NM_005228.3	192	Cca/Tca	5/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.968297239439603	2		510	881	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224472	55224472	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	497	582	0	ENST00000275493.2:c.1154C>T	p.Pro385Leu	p.P385L	ENST00000275493	NM_005228.3	385	cCt/cTt	10/28	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.968297239439603	2		582	1024	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242502	55242502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	361	376	0	ENST00000275493.2:c.2272G>A	p.Glu758Lys	p.E758K	ENST00000275493	NM_005228.3	758	Gaa/Aaa	19/28	1	2	FACETS	0.954	0.91	0.997	0.954	0.91	0.997	CLONAL	1	TRUE	1	0.968297239439603	2		376	782	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508562	106508562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415434072	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	258	212	0	ENST00000359195.3:c.556G>A	p.Ala186Thr	p.A186T	ENST00000359195	NM_002649.2	186	Gcg/Acg	2/11	1	2	FACETS	0.987	0.934	1	0.987	0.934	1	CLONAL	1	TRUE	1	0.968297239439603	2		212	540	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371721	116371721	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	287	341	1	ENST00000397752.3:c.1201-1G>A		p.X401_splice	ENST00000397752	NM_000245.2	401			1	2	FACETS	0.965	0.916	1	0.965	0.916	1	CLONAL	1	TRUE	1	0.968297239439603	2		342	614	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873984	151873984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	460	473	0	ENST00000262189.6:c.8554C>T	p.Pro2852Ser	p.P2852S	ENST00000262189	NM_170606.2	2852	Cct/Tct	38/59	1	2	FACETS	0.987	0.947	1	0.987	0.947	1	CLONAL	1	TRUE	1	0.968297239439603	2		473	963	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879469	151879469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	521	533	1	ENST00000262189.6:c.5476C>T	p.His1826Tyr	p.H1826Y	ENST00000262189	NM_170606.2	1826	Cat/Tat	36/59	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.968297239439603	2		534	1040	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868495	117868495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	420	567	0	ENST00000297338.2:c.847C>T	p.Pro283Ser	p.P283S	ENST00000297338	NM_006265.2	283	Ccc/Tcc	8/14	1	2	FACETS	0.995	0.953	1	0.995	0.953	1	CLONAL	1	TRUE	1	0.968297239439603	2		567	872	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341925	8341925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	399	431	0	ENST00000356435.5:c.4715G>A	p.Arg1572Lys	p.R1572K	ENST00000356435		1572	aGa/aAa	29/35	1	2	FACETS	0.972	0.93	1	0.972	0.93	1	CLONAL	1	TRUE	1	0.968297239439603	2		431	848	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912014	127912015	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	632	736	0	ENST00000373547.4:c.855_856delinsTT	p.Arg286Trp	p.R286W	ENST00000373547	NM_002721.4	285	ttCCgg/ttTTgg	7/7	1	2	FACETS	0.93	0.898	0.963	0.93	0.898	0.963	CLONAL	1	TRUE	1	0.968297239439603	2		736	1403	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760169	133760169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768153649	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	486	402	1	ENST00000318560.5:c.2492C>T	p.Pro831Leu	p.P831L	ENST00000318560	NM_005157.4	831	cCc/cTc	11/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.968297239439603	2		403	989	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413088	139413088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	597	592	0	ENST00000277541.6:c.1054G>A	p.Asp352Asn	p.D352N	ENST00000277541	NM_017617.3	352	Gac/Aac	6/34	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.968297239439603	2		592	1227	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820295	139820295	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	693	753	0	ENST00000247668.2:c.1448C>T	p.Ser483Phe	p.S483F	ENST00000247668	NM_021138.3	483	tCc/tTc	11/11	1	2	FACETS	0.981	0.949	1	0.981	0.949	1	CLONAL	1	TRUE	1	0.968297239439603	2		753	1459	SUCCESS
RET	5979	MSKCC	GRCh37	10	43602002	43602002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754859905	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	426	464	2	ENST00000355710.3:c.1046C>T	p.Ala349Val	p.A349V	ENST00000355710	NM_020975.4	349	gCg/gTg	5/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.968297239439603	2		466	872	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615593	43615593	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	421	480	1	ENST00000355710.3:c.2672C>T	p.Ser891Leu	p.S891L	ENST00000355710	NM_020975.4	891	tCg/tTg	15/20	1	2	FACETS	0.926	0.886	0.966	0.926	0.886	0.966	CLONAL	1	TRUE	1	0.968297239439603	2		481	939	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851362	63851362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1485685267	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	270	281	0	ENST00000279873.7:c.2140C>T	p.Pro714Ser	p.P714S	ENST00000279873	NM_032199.2	714	Ccc/Tcc	10/10	1	2	FACETS	0.928	0.878	0.978	0.928	0.878	0.978	CLONAL	1	TRUE	1	0.968297239439603	2		281	601	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94179033	94179033	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750926542	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	419	521	0	ENST00000323929.3:c.1810C>T	p.Arg604Cys	p.R604C	ENST00000323929	NM_005591.3	604	Cgt/Tgt	16/20	1	2	FACETS	0.956	0.916	0.997	0.956	0.916	0.997	CLONAL	1	TRUE	1	0.968297239439603	2		521	905	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514039	125514040	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	503	654	0	ENST00000428830.2:c.977_978delinsTT	p.Ser326Phe	p.S326F	ENST00000428830	NM_001114121.2	326	tCC/tTT	10/14	NA	2	FACETS	0.944	0.907	0.981			1	INDETERMINATE	1	TRUE	NA	0.968297239439603	2		654	1101	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404762	404762	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	475	514	0	ENST00000399788.2:c.4432G>A	p.Asp1478Asn	p.D1478N	ENST00000399788	NM_001042603.1	1478	Gac/Aac	26/28	NA	2	FACETS	0.976	0.937	1			1	INDETERMINATE	1	TRUE	NA	0.968297239439603	2		514	1005	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385378	4385378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	318	268	1	ENST00000261254.3:c.403G>A	p.Glu135Lys	p.E135K	ENST00000261254	NM_001759.3	135	Gag/Aag	2/5	NA	2	FACETS	0.86	0.816	0.904			1	INDETERMINATE	1	TRUE	NA	0.968297239439603	2		269	764	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420377	49420377	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1322243072	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	543	533	0	ENST00000301067.7:c.15372G>A	p.Met5124Ile	p.M5124I	ENST00000301067	NM_003482.3	5124	atG/atA	48/54	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.968297239439603	2		533	1111	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444082	49444082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	474	249	1	ENST00000301067.7:c.3289C>T	p.Pro1097Ser	p.P1097S	ENST00000301067	NM_003482.3	1097	Cca/Tca	11/54	1	2	FACETS	0.924	0.887	0.962	0.924	0.887	0.962	CLONAL	1	TRUE	1	0.968297239439603	2		250	1059	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480000	50480001	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	505	447	1	ENST00000394963.4:c.234_235delinsTT	p.Pro79Ser	p.P79S	ENST00000394963	NM_003076.4	78	ccCCct/ccTTct	2/13	1	2	FACETS	0.952	0.915	0.989	0.952	0.915	0.989	CLONAL	1	TRUE	1	0.968297239439603	2		448	1096	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416876	121416876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	495	457	0	ENST00000257555.6:c.305C>T	p.Ala102Val	p.A102V	ENST00000257555		102	gCc/gTc	1/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.968297239439603	2		457	973	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26974677	26974677	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	365	422	0	ENST00000381527.3:c.1021C>T	p.Pro341Ser	p.P341S	ENST00000381527	NM_001260.1	341	Cct/Tct	10/13	1	2	FACETS	0.901	0.859	0.943	0.901	0.859	0.943	CLONAL	1	TRUE	1	0.968297239439603	2		422	837	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601274	28601274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	457	530	0	ENST00000241453.7:c.2158G>A	p.Glu720Lys	p.E720K	ENST00000241453	NM_004119.2	720	Gaa/Aaa	17/24	1	2	FACETS	0.956	0.917	0.996	0.956	0.917	0.996	CLONAL	1	TRUE	1	0.968297239439603	2		530	987	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28644650	28644650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1394449672	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	391	474	0	ENST00000241453.7:c.143G>A	p.Gly48Glu	p.G48E	ENST00000241453	NM_004119.2	48	gGg/gAg	2/24	1	2	FACETS	0.947	0.905	0.989	0.947	0.905	0.989	CLONAL	1	TRUE	1	0.968297239439603	2		474	853	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027167	49027168	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	435	502	2	ENST00000267163.4:c.1734_1735delinsTT	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	578	gaCCga/gaTTga	18/27	1	2	FACETS	0.893	0.855	0.932	0.893	0.855	0.932	CLONAL	1	TRUE	1	0.968297239439603	2		504	1006	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609655	81609655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	668	659	0	ENST00000298171.2:c.1253G>A	p.Arg418Lys	p.R418K	ENST00000298171	NM_000369.2	418	aGa/aAa	10/10	1	2	FACETS	0.99	0.957	1	0.99	0.957	1	CLONAL	1	TRUE	1	0.968297239439603	2		659	1394	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95584014	95584015	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	368	307	0	ENST00000393063.1:c.1453_1454delinsAA	p.Gly485Lys	p.G485K	ENST00000393063	NM_030621.3	485	GGg/AAg	10/28	1	2	FACETS	0.949	0.906	0.992	0.949	0.906	0.992	CLONAL	1	TRUE	1	0.968297239439603	2		307	801	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799140	88799140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	506	458	0	ENST00000360948.2:c.245C>T	p.Ser82Phe	p.S82F	ENST00000360948	NM_001012338.2	82	tCc/tTc	2/19	0.968297239439603	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.968297239439603	1		458	530	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820605	3820605	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147083140	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	312	211	0	ENST00000262367.5:c.2846C>T	p.Pro949Leu	p.P949L	ENST00000262367	NM_004380.2	949	cCg/cTg	14/31	1	2	FACETS	0.965	0.917	1	0.965	0.917	1	CLONAL	1	TRUE	1	0.968297239439603	2		211	668	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900926	3900926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	593	655	0	ENST00000262367.5:c.170G>A	p.Gly57Glu	p.G57E	ENST00000262367	NM_004380.2	57	gGg/gAg	2/31	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.968297239439603	2		655	1211	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273997	10273997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	584	629	0	ENST00000330684.3:c.272C>T	p.Ser91Phe	p.S91F	ENST00000330684	NM_001134407.1	91	tCc/tTc	2/13	1	2	FACETS	0.969	0.934	1	0.969	0.934	1	CLONAL	1	TRUE	1	0.968297239439603	2		629	1245	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56867144	56867144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs908131101	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	655	686	0	ENST00000308159.5:c.1363G>A	p.Val455Met	p.V455M	ENST00000308159	NM_014669.4	455	Gtg/Atg	13/22	0.303675833776588	1	FACETS	0.508	0.491	0.525	0.508	0.491	0.525	INDETERMINATE	1	TRUE	0	0.968297239439603	1		686	1374	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81904539	81904539	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs201294738	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	480	634	0	ENST00000359376.3:c.647C>T	p.Ser216Leu	p.S216L	ENST00000359376	NM_002661.3	216	tCg/tTg	7/33	0.303675833776588	1	FACETS	0.51	0.49	0.53	0.51	0.49	0.53	INDETERMINATE	1	TRUE	0	0.968297239439603	1		634	1003	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	567	602	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.968297239439603	2		602	1142	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579415	7579415	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	457	284	0	ENST00000269305.4:c.272G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tGg/tAg	4/11	1	2	FACETS	0.962	0.923	1	0.962	0.923	1	CLONAL	1	TRUE	1	0.968297239439603	2		284	981	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17116985	17116985	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763604691	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	478	484	0	ENST00000285071.4:c.1724C>T	p.Ser575Leu	p.S575L	ENST00000285071	NM_144997.5	575	tCg/tTg	14/14	1	2	FACETS	0.95	0.912	0.988	0.95	0.912	0.988	CLONAL	1	TRUE	1	0.968297239439603	2		484	1039	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554636	63554636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	320	129	0	ENST00000307078.5:c.103C>T	p.Pro35Ser	p.P35S	ENST00000307078	NM_004655.3	35	Ccg/Tcg	2/11	1	2	FACETS	0.992	0.945	1	0.992	0.945	1	CLONAL	1	TRUE	1	0.968297239439603	2		129	666	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050364	13050364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	700	815	2	ENST00000316448.5:c.316G>A	p.Gly106Arg	p.G106R	ENST00000316448	NM_004343.3	106	Ggg/Agg	3/9	1	2	FACETS	0.97	0.938	1	0.97	0.938	1	CLONAL	1	TRUE	1	0.968297239439603	2		817	1491	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271796	15271796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	345	172	0	ENST00000263388.2:c.6643C>T	p.Pro2215Ser	p.P2215S	ENST00000263388	NM_000435.2	2215	Cca/Tca	33/33	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.968297239439603	2		172	703	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260222	19260222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	473	478	0	ENST00000162023.5:c.71G>A	p.Arg24Gln	p.R24Q	ENST00000162023		24	cGg/cAg	7/13	1	2	FACETS	0.992	0.953	1	0.992	0.953	1	CLONAL	1	TRUE	1	0.968297239439603	2		478	985	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314670	30314671	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	358	469	0	ENST00000262643.3:c.1219_1220delinsTT	p.Pro407Leu	p.P407L	ENST00000262643	NM_001238.2	407	CCg/TTg	12/12	1	2	FACETS	0.916	0.873	0.959	0.916	0.873	0.959	CLONAL	1	TRUE	1	0.968297239439603	2		469	807	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906384	50906384	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	639	673	4	ENST00000440232.2:c.1045C>T	p.Pro349Ser	p.P349S	ENST00000440232	NM_002691.3	349	Ccc/Tcc	9/27	1	2	FACETS	0.994	0.96	1	0.994	0.96	1	CLONAL	1	TRUE	1	0.968297239439603	2		677	1328	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52705281	52705281	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	466	423	0	ENST00000322088.6:c.163C>A	p.Leu55Ile	p.L55I	ENST00000322088	NM_014225.5	55	Ctt/Att	2/15	1	2	FACETS	0.99	0.951	1	0.99	0.951	1	CLONAL	1	TRUE	1	0.968297239439603	2		423	972	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742640	39742640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	328	439	0	ENST00000361337.2:c.1483G>A	p.Glu495Lys	p.E495K	ENST00000361337	NM_003286.2	495	Gaa/Aaa	15/21	1	2	FACETS	0.953	0.907	0.999	0.953	0.907	0.999	CLONAL	1	TRUE	1	0.968297239439603	2		439	711	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730916	40730916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765075213	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	322	214	0	ENST00000373198.4:c.3619C>T	p.Arg1207Cys	p.R1207C	ENST00000373198	NM_133170.3	1207	Cgt/Tgt	27/32	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.968297239439603	2		214	663	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979350	40979350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747923769	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	347	334	0	ENST00000373198.4:c.1783G>A	p.Asp595Asn	p.D595N	ENST00000373198	NM_133170.3	595	Gac/Aac	11/32	1	2	FACETS	0.956	0.911	1	0.956	0.911	1	CLONAL	1	TRUE	1	0.968297239439603	2		334	750	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866378	42866378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	476	291	0	ENST00000398585.3:c.254C>T	p.Pro85Leu	p.P85L	ENST00000398585	NM_001135099.1	85	cCc/cTc	3/14	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.968297239439603	2		291	953	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22142665	22142665	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	268	358	0	ENST00000215832.6:c.737C>T	p.Ser246Phe	p.S246F	ENST00000215832	NM_002745.4	246	tCc/tTc	6/9	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.968297239439603	2		358	550	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513598	41513598	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	512	456	0	ENST00000263253.7:c.502G>A	p.Gly168Arg	p.G168R	ENST00000263253	NM_001429.3	168	Ggg/Agg	2/31	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.968297239439603	2		456	1040	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932980	39932980	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238996683	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	560	551	0	ENST00000378444.4:c.1619G>A	p.Arg540Gln	p.R540Q	ENST00000378444	NM_001123385.1	540	cGg/cAg	4/15	NA	2	FACETS	0.948	0.913	0.983			1	INDETERMINATE	1	TRUE	NA	0.968297239439603	2		551	1220	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412688	63412688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	493	603	1	ENST00000330258.3:c.479C>T	p.Pro160Leu	p.P160L	ENST00000330258	NM_152424.3	160	cCc/cTc	2/2	NA	2	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.968297239439603	2		604	1009	SUCCESS
AR	367	MSKCC	GRCh37	X	66905852	66905852	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	409	528	0	ENST00000374690.3:c.1769G>A	p.Gly590Glu	p.G590E	ENST00000374690	NM_000044.3	590	gGg/gAg	3/8	NA	2	FACETS	0.965	0.924	1			1	INDETERMINATE	1	TRUE	NA	0.968297239439603	2		528	875	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339657	70339657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	655	807	0	ENST00000374080.3:c.326C>T	p.Ser109Phe	p.S109F	ENST00000374080		109	tCc/tTc	3/45	NA	2	FACETS	0.981	0.948	1			1	INDETERMINATE	1	TRUE	NA	0.968297239439603	2		807	1379	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341448	70341448	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	683	509	0	ENST00000374080.3:c.883C>T	p.Arg295Cys	p.R295C	ENST00000374080		295	Cgc/Tgc	7/45	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.968297239439603	2		509	1316	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343507	70343507	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	559	745	0	ENST00000374080.3:c.1681C>T	p.Pro561Ser	p.P561S	ENST00000374080		561	Ccc/Tcc	12/45	NA	2	FACETS	0.887	0.853	0.921			1	INDETERMINATE	1	TRUE	NA	0.968297239439603	2		745	1302	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346257	70346257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	571	669	0	ENST00000374080.3:c.2608G>A	p.Val870Met	p.V870M	ENST00000374080		870	Gtg/Atg	19/45	NA	2	FACETS	0.921	0.887	0.956			1	INDETERMINATE	1	TRUE	NA	0.968297239439603	2		669	1280	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938821	76938821	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	474	528	0	ENST00000373344.5:c.1927G>T	p.Glu643Ter	p.E643*	ENST00000373344	NM_000489.3	643	Gaa/Taa	9/35	NA	2	FACETS	0.972	0.934	1			1	INDETERMINATE	1	TRUE	NA	0.968297239439603	2		528	1007	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181208	123181208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	373	597	0	ENST00000218089.9:c.672G>A	p.Met224Ile	p.M224I	ENST00000218089	NM_001042749.1	224	atG/atA	9/35	NA	2	FACETS	0.861	0.82	0.902			1	INDETERMINATE	1	TRUE	NA	0.968297239439603	2		597	895	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195668	123195668	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	477	601	0	ENST00000218089.9:c.1582A>G	p.Thr528Ala	p.T528A	ENST00000218089	NM_001042749.1	528	Acc/Gcc	17/35	NA	2	FACETS	0.991	0.952	1			1	INDETERMINATE	1	TRUE	NA	0.968297239439603	2		601	994	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541069	187541069	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	357	347	0	ENST00000441802.2:c.6671del	p.Phe2224SerfsTer16	p.F2224Sfs*16	ENST00000441802	NM_005245.3	2224	tTc/tc	10/27	0.968297239439603	1	FACETS	0.985	0.967	1	0.985	0.967	1	CLONAL	1	TRUE	0	0.968297239439603	1		347	386	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199674	138199675	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0005127-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	434	452	0	ENST00000237289.4:c.1097_1098del	p.Glu366GlyfsTer22	p.E366Gfs*22	ENST00000237289	NM_001270507.1	364	agGAga/agga	7/9	1	2	FACETS	0.903	0.864	0.942	0.903	0.864	0.942	CLONAL	1	TRUE	1	0.968297239439603	2		452	993	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484194	120484194	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	141	364	0	ENST00000256646.2:c.2936T>A	p.Phe979Tyr	p.F979Y	ENST00000256646	NM_024408.3	979	tTt/tAt	18/34	0.413543176769466	3	FACETS	0.788	0.717	0.863	0.394	0.358	0.432	SUBCLONAL	1	TRUE	1	0.413349886631641	3		364	1045	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188234	10188235	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	344	381	0	ENST00000256474.2:c.378dup	p.Gly127TrpfsTer5	p.G127Wfs*5	ENST00000256474	NM_000551.3	126	gat/gaTt	2/3	0.411740179186447	2	FACETS	0.93	0.883	0.977	0.93	0.883	0.977	CLONAL	2	TRUE	0	0.413349886631641	2		381	895	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439148	52439149	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0005226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	146	189	0	ENST00000460680.1:c.1093_1094del	p.Asn365LeufsTer32	p.N365Lfs*32	ENST00000460680	NM_004656.3	365	AAt/t	11/17	0.411740179186447	2	FACETS	0.952	0.88	1	0.952	0.88	1	CLONAL	2	TRUE	0	0.413349886631641	2		189	371	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	172	351	2	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.96	0.885	1	0.96	0.885	1	CLONAL	1	TRUE	1	0.469217104166874	2		353	764	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639588	47639588	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63749897	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	142	331	1	ENST00000233146.2:c.687del	p.Ala230LeufsTer16	p.A230Lfs*16	ENST00000233146	NM_000251.2	227	agA/ag	4/16	1	2	FACETS	0.937	0.856	1	0.937	0.856	1	CLONAL	1	TRUE	1	0.469217104166874	2		332	646	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	309	573	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.469217104166874	2		574	1260	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	250	616	0	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	1	2	FACETS	0.768	0.717	0.821	0.768	0.717	0.821	SUBCLONAL	1	TRUE	1	0.469217104166874	2		616	1387	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	176	553	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.994	0.917	1	0.994	0.917	1	CLONAL	1	TRUE	1	0.469217104166874	2		553	755	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	173	371	1	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.812	0.748	0.879	0.812	0.748	0.879	CLONAL	1	TRUE	1	0.469217104166874	2		372	908	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	217	738	12	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.929	0.864	0.996	0.929	0.864	0.996	CLONAL	1	TRUE	1	0.469217104166874	2		750	996	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296358	15296358	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	230	585	2	ENST00000263388.2:c.2084del	p.Pro695ArgfsTer165	p.P695Rfs*165	ENST00000263388	NM_000435.2	695	cCg/cg	13/33	1	2	FACETS	0.933	0.869	0.998	0.933	0.869	0.998	CLONAL	1	TRUE	1	0.469217104166874	2		587	1051	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418947	116418947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	227	248	1	ENST00000397752.3:c.3458C>T	p.Pro1153Leu	p.P1153L	ENST00000397752	NM_000245.2	1153	cCg/cTg	17/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.469217104166874	2		249	813	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965666	90965666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	78	283	1	ENST00000265433.3:c.1651del	p.Arg551GlyfsTer8	p.R551Gfs*8	ENST00000265433	NM_002485.4	551	Agg/gg	11/16	1	2	FACETS	0.641	0.564	0.722	0.641	0.564	0.722	SUBCLONAL	1	TRUE	1	0.469217104166874	2		284	519	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039583	180039583	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs75614493	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	269	568	0	ENST00000261937.6:c.3460G>A	p.Gly1154Arg	p.G1154R	ENST00000261937	NM_182925.4	1154	Gga/Aga	26/30	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.469217104166874	2		568	1079	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	324	291	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.939	0.893	0.986	1	0.996	1	CLONAL	2	TRUE	1	0.469217104166874	2		292	735	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867541	35867541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	106	216	1	ENST00000303115.3:c.361del	p.Ile121Ter	p.I121*	ENST00000303115	NM_002185.3	119	Aaa/aa	3/8	1	2	FACETS	0.823	0.74	0.91	0.823	0.74	0.91	CLONAL	1	TRUE	1	0.469217104166874	2		217	549	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592108	67592108	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1419325070	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	161	203	0	ENST00000274335.5:c.1924C>T	p.Arg642Ter	p.R642*	ENST00000274335		642	Cga/Tga	14/15	1	2	FACETS	0.993	0.913	1	0.993	0.913	1	CLONAL	1	TRUE	1	0.469217104166874	2		203	691	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	298	501	0	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	1	2	FACETS	0.977	0.919	1	0.977	0.919	1	CLONAL	1	TRUE	1	0.469217104166874	2		501	1300	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	143	250	0	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	1	2	FACETS	0.991	0.907	1	0.991	0.907	1	CLONAL	1	TRUE	1	0.469217104166874	2		250	615	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578215	28578216	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	232	399	1	ENST00000241453.7:c.2955_2956del	p.Pro986AlafsTer27	p.P986Afs*27	ENST00000241453	NM_004119.2	985	tcTCcg/tccg	24/24	1	2	FACETS	0.999	0.932	1	0.999	0.932	1	CLONAL	1	TRUE	1	0.469217104166874	2		400	990	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523009	25523009	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	135	393	1	ENST00000264709.3:c.176del	p.Pro59ArgfsTer13	p.P59Rfs*13	ENST00000264709	NM_175629.2	59	cCg/cg	3/23	1	2	FACETS	0.519	0.471	0.57	0.519	0.471	0.57	SUBCLONAL	1	TRUE	1	0.469217104166874	2		394	1108	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	223	276	0	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.996	0.928	1	0.996	0.928	1	CLONAL	1	TRUE	1	0.469217104166874	2		276	954	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215595164	215595164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3738888	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	110	350	0	ENST00000260947.4:c.1972C>T	p.Arg658Cys	p.R658C	ENST00000260947	NM_000465.2	658	Cgc/Tgc	10/11	1	2	FACETS	0.678	0.609	0.75	0.678	0.609	0.75	SUBCLONAL	1	TRUE	1	0.469217104166874	2		350	692	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	95	217	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.529	0.47	0.591	0.529	0.47	0.591	SUBCLONAL	1	TRUE	1	0.469217104166874	2		217	766	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962929	2962929	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	359	588	0	ENST00000396946.4:c.1979G>T	p.Arg660Leu	p.R660L	ENST00000396946	NM_032415.4	660	cGg/cTg	16/25	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.469217104166874	2		588	1332	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952138	178952138	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	25	251	0	ENST00000263967.3:c.3193C>T	p.His1065Tyr	p.H1065Y	ENST00000263967	NM_006218.2	1065	Cat/Tat	21/21	1	2	FACETS	0.218	0.171	0.273	0.218	0.171	0.273	SUBCLONAL	1	TRUE	1	0.469217104166874	2		251	488	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	175	288	2	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	NA	2	FACETS	1	0.925	1			1	INDETERMINATE	1	TRUE	NA	0.469217104166874	2		290	744	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	257	505	2	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	0.969	0.907	1	0.969	0.907	1	CLONAL	1	TRUE	1	0.469217104166874	2		507	1130	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260214	16260214	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	36	342	0	ENST00000375759.3:c.7484del	p.Pro2495LeufsTer4	p.P2495Lfs*4	ENST00000375759	NM_015001.2	2493	agC/ag	11/15	1	2	FACETS	0.214	0.175	0.258	0.214	0.175	0.258	SUBCLONAL	1	TRUE	1	0.469217104166874	2		342	718	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	186	563	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.959	0.887	1	0.959	0.887	1	CLONAL	1	TRUE	1	0.469217104166874	2		568	827	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	178	390	7	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.931	0.859	1	0.931	0.859	1	CLONAL	1	TRUE	1	0.469217104166874	2		397	815	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622138	1622138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370087169	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	288	439	2	ENST00000344749.5:c.737C>T	p.Pro246Leu	p.P246L	ENST00000344749	NM_001136139.2	246	cCg/cTg	10/19	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.469217104166874	2		441	1078	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523486	106523486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750632554	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	171	259	0	ENST00000359195.3:c.2638G>A	p.Glu880Lys	p.E880K	ENST00000359195	NM_002649.2	880	Gag/Aag	8/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.469217104166874	2		259	672	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355326	15355326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775700444	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	168	307	0	ENST00000263377.2:c.2297C>T	p.Pro766Leu	p.P766L	ENST00000263377	NM_058243.2	766	cCg/cTg	13/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.469217104166874	2		307	683	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214696	5214696	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369756620	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	278	459	0	ENST00000357368.4:c.4370G>A	p.Cys1457Tyr	p.C1457Y	ENST00000357368	NM_002850.3	1457	tGt/tAt	29/38	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.469217104166874	2		459	1049	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372254	55372254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1358462345	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	79	451	1	ENST00000297316.4:c.944C>T	p.Pro315Leu	p.P315L	ENST00000297316	NM_022454.3	315	cCg/cTg	2/2	1	2	FACETS	0.31	0.271	0.351	0.31	0.271	0.351	SUBCLONAL	1	TRUE	1	0.469217104166874	2		452	1087	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439919	56439919	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	299	429	0	ENST00000407977.2:c.673del	p.Arg225AlafsTer194	p.R225Afs*194	ENST00000407977		225	Cgc/gc	6/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.469217104166874	2		429	1077	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822586	72822586	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	202	327	4	ENST00000268489.5:c.9589del	p.Gln3197SerfsTer44	p.Q3197Sfs*44	ENST00000268489	NM_006885.3	3197	Cag/ag	10/10	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.469217104166874	2		331	860	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	203	553	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.881	0.817	0.948	0.881	0.817	0.948	CLONAL	1	TRUE	1	0.469217104166874	2		557	982	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074240	8074240	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs34409716	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	209	402	1	ENST00000377482.5:c.419del	p.Phe140SerfsTer35	p.F140Sfs*35	ENST00000377482	NM_018948.3	140	tTc/tc	4/4	1	2	FACETS	0.999	0.928	1	0.999	0.928	1	CLONAL	1	TRUE	1	0.469217104166874	2		403	892	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321264	65321264	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	156	431	0	ENST00000342505.4:c.1576C>A	p.Leu526Ile	p.L526I	ENST00000342505	NM_002227.2	526	Ctc/Atc	11/25	1	2	FACETS	0.671	0.614	0.731	0.671	0.614	0.731	SUBCLONAL	1	TRUE	1	0.469217104166874	2		431	991	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695947	117695947	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	222	421	0	ENST00000369458.3:c.490G>T	p.Glu164Ter	p.E164*	ENST00000369458	NM_024626.3	164	Gag/Tag	4/6	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.469217104166874	2		421	931	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176104185	176104185	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs761037413	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	131	330	0	ENST00000367669.3:c.929G>T	p.Ser310Ile	p.S310I	ENST00000367669	NM_022457.5	310	aGc/aTc	8/20	1	2	FACETS	0.997	0.909	1	0.997	0.909	1	CLONAL	1	TRUE	1	0.469217104166874	2		330	560	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570819	226570820	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	206	395	0	ENST00000366794.5:c.1076dup	p.Glu360ArgfsTer29	p.E360Rfs*29	ENST00000366794	NM_001618.3	359	cca/ccCa	8/23	1	2	FACETS	0.938	0.871	1	0.938	0.871	1	CLONAL	1	TRUE	1	0.469217104166874	2		395	936	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927413	245927413	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs529041742	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	235	438	0	ENST00000388985.4:c.1115A>G	p.Gln372Arg	p.Q372R	ENST00000388985		372	cAa/cGa	11/12	1	2	FACETS	0.983	0.917	1	0.983	0.917	1	CLONAL	1	TRUE	1	0.469217104166874	2		438	1019	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097779	8097779	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	291	556	0	ENST00000346208.3:c.161A>G	p.Asp54Gly	p.D54G	ENST00000346208		54	gAc/gGc	2/6	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.469217104166874	2		556	1186	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100451	8100452	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	298	545	1	ENST00000346208.3:c.431dup	p.His145ProfsTer158	p.H145Pfs*158	ENST00000346208		142	tcg/tcGg	3/6	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.469217104166874	2		546	1177	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405565	70405565	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	174	391	0	ENST00000373644.4:c.3079A>G	p.Thr1027Ala	p.T1027A	ENST00000373644	NM_030625.2	1027	Act/Gct	4/12	1	2	FACETS	0.982	0.906	1	0.982	0.906	1	CLONAL	1	TRUE	1	0.469217104166874	2		391	755	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939260	71939260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	286	433	0	ENST00000298229.2:c.209G>A	p.Arg70His	p.R70H	ENST00000298229	NM_001567.3	70	cGc/cAc	2/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.469217104166874	2		433	1084	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999794	100999794	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1196735070	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	206	409	0	ENST00000325455.5:c.8A>C	p.Glu3Ala	p.E3A	ENST00000325455	NM_001202474.3	3	gAg/gCg	1/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.469217104166874	2		409	798	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480010	50480010	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	248	439	1	ENST00000394963.4:c.249del	p.Asn84ThrfsTer79	p.N84Tfs*79	ENST00000394963	NM_003076.4	82	Ggg/gg	2/13	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.469217104166874	2		440	1052	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241994	105241994	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	67	386	1	ENST00000349310.3:c.430C>A	p.Arg144Ser	p.R144S	ENST00000349310	NM_001014432.1	144	Cgc/Agc	6/15	1	2	FACETS	0.301	0.26	0.345	0.301	0.26	0.345	SUBCLONAL	1	TRUE	1	0.469217104166874	2		387	950	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643525	38643525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779966392	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	237	444	0	ENST00000299084.4:c.995G>A	p.Arg332His	p.R332H	ENST00000299084	NM_152594.2	332	cGt/cAt	7/7	1	2	FACETS	0.991	0.925	1	0.991	0.925	1	CLONAL	1	TRUE	1	0.469217104166874	2		444	1019	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712851	43712851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750560493	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	346	537	0	ENST00000382044.4:c.4333G>A	p.Val1445Met	p.V1445M	ENST00000382044	NM_001141980.1	1445	Gtg/Atg	21/28	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.469217104166874	2		537	1248	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396234	396234	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	322	456	0	ENST00000262320.3:c.792del	p.Gly265GlufsTer149	p.G265Efs*149	ENST00000262320	NM_003502.3	264	ccC/cc	2/11	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.469217104166874	2		456	1117	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226561	1226561	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748202003	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	308	544	2	ENST00000326873.7:c.1217C>T	p.Ala406Val	p.A406V	ENST00000326873	NM_000455.4	406	gCg/gTg	9/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.469217104166874	2		546	1212	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249233	10249233	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	132	393	2	ENST00000340748.4:c.3949G>A	p.Ala1317Thr	p.A1317T	ENST00000340748		1317	Gcc/Acc	34/40	1	2	FACETS	0.6	0.544	0.659	0.6	0.544	0.659	SUBCLONAL	1	TRUE	1	0.469217104166874	2		395	938	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10259582	10259582	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	58	497	1	ENST00000340748.4:c.2650C>T	p.Pro884Ser	p.P884S	ENST00000340748		884	Cca/Tca	26/40	1	2	FACETS	0.227	0.194	0.264	0.227	0.194	0.264	SUBCLONAL	1	TRUE	1	0.469217104166874	2		498	1088	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281361	15281362	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	231	493	0	ENST00000263388.2:c.4894dup	p.Glu1632GlyfsTer47	p.E1632Gfs*47	ENST00000263388	NM_000435.2	1632	gag/gGag	27/33	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.469217104166874	2		493	903	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950351	17950351	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	278	506	0	ENST00000458235.1:c.1376A>G	p.Asp459Gly	p.D459G	ENST00000458235	NM_000215.3	459	gAt/gGt	10/24	1	2	FACETS	0.992	0.931	1	0.992	0.931	1	CLONAL	1	TRUE	1	0.469217104166874	2		506	1195	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36208928	36208928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	42	40	0	ENST00000222270.7:c.8C>T	p.Ala3Val	p.A3V	ENST00000222270	NM_014727.1	3	gCg/gTg	1/37	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.469217104166874	2		40	147	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795105	42795105	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	194	567	0	ENST00000575354.2:c.2185T>C	p.Tyr729His	p.Y729H	ENST00000575354	NM_015125.3	729	Tat/Cat	10/20	1	2	FACETS	0.658	0.607	0.711	0.658	0.607	0.711	SUBCLONAL	1	TRUE	1	0.469217104166874	2		567	1257	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912075	50912077	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs398122386	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	320	627	1	ENST00000440232.2:c.1812_1814del	p.Ser605del	p.S605del	ENST00000440232	NM_002691.3	603	ttCTCc/ttc	15/27	1	2	FACETS	0.989	0.932	1	0.989	0.932	1	CLONAL	1	TRUE	1	0.469217104166874	2		628	1379	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250209	39250209	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	211	570	0	ENST00000402219.2:c.1360G>T	p.Gly454Ter	p.G454*	ENST00000402219	NM_005633.3	454	Gga/Tga	10/23	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.469217104166874	2		570	885	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513298	44513298	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761520409	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	405	538	0	ENST00000291552.4:c.637G>A	p.Gly213Ser	p.G213S	ENST00000291552	NM_006758.2	213	Ggt/Agt	8/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.469217104166874	2		538	1566	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916730	178916730	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	53	320	0	ENST00000263967.3:c.117G>T	p.Glu39Asp	p.E39D	ENST00000263967	NM_006218.2	39	gaG/gaT	2/21	1	2	FACETS	0.377	0.321	0.438	0.377	0.321	0.438	SUBCLONAL	1	TRUE	1	0.469217104166874	2		320	600	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630855	187630855	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560660262	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	256	450	0	ENST00000441802.2:c.127G>A	p.Val43Met	p.V43M	ENST00000441802	NM_005245.3	43	Gtg/Atg	2/27	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.469217104166874	2		450	1017	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522697	67522697	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	114	223	0	ENST00000274335.5:c.196del	p.Arg66GlyfsTer9	p.R66Gfs*9	ENST00000274335		65	gAa/ga	1/15	1	2	FACETS	0.871	0.787	0.959	0.871	0.787	0.959	CLONAL	1	TRUE	1	0.469217104166874	2		223	558	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41905129	41905129	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	365	255	0	ENST00000372991.4:c.418T>C	p.Trp140Arg	p.W140R	ENST00000372991	NM_001760.3	140	Tgg/Cgg	3/5	0.469217104166874	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.469217104166874	2		255	743	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874826	151874826	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142788583	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	132	230	1	ENST00000262189.6:c.7712G>A	p.Arg2571Gln	p.R2571Q	ENST00000262189	NM_170606.2	2571	cGg/cAg	38/59	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.469217104166874	2		231	522	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372065	55372065	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	409	468	1	ENST00000297316.4:c.755G>A	p.Ser252Asn	p.S252N	ENST00000297316	NM_022454.3	252	aGc/aAc	2/2	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.469217104166874	2		469	1178	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740554	145740554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	275	477	0	ENST00000428558.2:c.1463C>T	p.Ala488Val	p.A488V	ENST00000428558	NM_004260.3	488	gCa/gTa	8/22	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.469217104166874	2		477	1165	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781380	135781380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751125011	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	252	408	1	ENST00000298552.3:c.1585G>A	p.Ala529Thr	p.A529T	ENST00000298552	NM_001162426.1	529	Gcc/Acc	15/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.469217104166874	2		409	1006	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293682	137293682	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568762857	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	269	551	1	ENST00000481739.1:c.233C>T	p.Ser78Leu	p.S78L	ENST00000481739	NM_002957.4	78	tCg/tTg	2/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.469217104166874	2		552	1064	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403372	139403372	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375260339	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	264	469	0	ENST00000277541.6:c.3121G>A	p.Gly1041Ser	p.G1041S	ENST00000277541	NM_017617.3	1041	Ggc/Agc	19/34	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.469217104166874	2		469	1026	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922945	39922945	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	249	195	0	ENST00000378444.4:c.3763G>T	p.Glu1255Ter	p.E1255*	ENST00000378444	NM_001123385.1	1255	Gag/Tag	8/15	1	1	FACETS	0.804	0.761	0.848	1	0.994	1	CLONAL	2	TRUE	0	0.469217104166874	1		195	505	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	258	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.296053247229422	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.307097364246979	3		326	862	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0005307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	84	138	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.919	0.813	1	0.919	0.813	1	CLONAL	1	TRUE	1	0.307097364246979	2		138	595	SUCCESS
APC	324	MSKCC	GRCh37	5	112174490	112174493	+	frameshift_variant	Frame_Shift_Del	DEL	CAAT	CAAT	-	rs587779353	NA	P-0005307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	127	548	0	ENST00000257430.4:c.3202_3205del	p.Ser1068GlyfsTer57	p.S1068Gfs*57	ENST00000257430	NM_000038.5	1067	CAATca/ca	16/16	1	2	FACETS	0.906	0.82	0.997	0.906	0.82	0.997	CLONAL	1	TRUE	1	0.307097364246979	2		548	913	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270593	98270595	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	rs756897237	NA	P-0005307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	12	30	0	ENST00000331920.6:c.49_51del	p.Gly17del	p.G17del	ENST00000331920	NM_000264.3	17	GGC/-	1/24	1	2	FACETS	0.62	0.439	0.84	0.62	0.439	0.84	SUBCLONAL	1	TRUE	1	0.307097364246979	2		30	126	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593504	48593504	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	155	473	0	ENST00000342988.3:c.1255G>T	p.Gly419Trp	p.G419W	ENST00000342988	NM_005359.5	419	Ggg/Tgg	10/12	0.307097364246979	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.307097364246979	1		473	638	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729271	41729271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749989847	NA	P-0005307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1567	236	956	1	ENST00000242208.4:c.1258G>A	p.Val420Met	p.V420M	ENST00000242208	NM_002192.2	420	Gtg/Atg	3/3	0.296053247229422	3	FACETS	0.983	0.914	1	0.492	0.457	0.528	CLONAL	1	TRUE	1	0.307097364246979	3		957	1803	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339223	70339223	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2177	199	860	0	ENST00000374080.3:c.100G>T	p.Asp34Tyr	p.D34Y	ENST00000374080		34	Gat/Tat	2/45	0.307097364246979	3	FACETS	0.629	0.58	0.681	0.315	0.29	0.341	SUBCLONAL	1	TRUE	1	0.307097364246979	3		860	2376	SUCCESS
APC	324	MSKCC	GRCh37	5	112175760	112175761	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs398123122	NA	P-0005307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	92	420	0	ENST00000257430.4:c.4473dup	p.Ala1492CysfsTer22	p.A1492Cfs*22	ENST00000257430	NM_000038.5	1490	cat/caTt	16/16	1	2	FACETS	0.834	0.741	0.934	0.834	0.741	0.934	CLONAL	1	TRUE	1	0.307097364246979	2		420	718	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579399	7579401	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs878854068	NA	P-0005307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	48	489	0	ENST00000269305.4:c.286_288del	p.Ser96del	p.S96del	ENST00000269305	NM_001126112.2	96	TCT/-	4/11	1	2	FACETS	0.348	0.293	0.409	0.348	0.293	0.409	SUBCLONAL	1	TRUE	1	0.307097364246979	2		489	898	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476791	140476791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	269	2008	1	ENST00000288602.6:c.1615C>T	p.His539Tyr	p.H539Y	ENST00000288602	NM_004333.4	539	Cac/Tac	13/18	1	2	FACETS	0.886	0.83	0.944	0.886	0.83	0.944	CLONAL	1	TRUE	1	0.470440496928804	2		2009	1291	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0005372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	238	551	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	0.470440496928804	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.470440496928804	1		551	686	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0005372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	48	651	3				ENST00000310581	NM_198253.2	-/1132			0.470440496928804	1	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	0	0.470440496928804	1		654	148	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	152	1618	0	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	0.415154670160569	1	FACETS	0.897	0.825	0.971	0.897	0.825	0.971	CLONAL	1	TRUE	0	0.470440496928804	1		1618	551	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188515	11188515	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1399999266	NA	P-0005372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	206	1824	1	ENST00000361445.4:c.5906C>A	p.Pro1969His	p.P1969H	ENST00000361445	NM_004958.3	1969	cCc/cAc	42/58	0.319552475430283	1	FACETS	0.864	0.804	0.926	0.864	0.804	0.926	CLONAL	1	TRUE	0	0.470440496928804	1		1825	775	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794982	242794982	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	66	2265	0	ENST00000334409.5:c.227C>G	p.Thr76Arg	p.T76R	ENST00000334409	NM_005018.2	76	aCg/aGg	2/5	NA	2	FACETS	0.302	0.261	0.347			1	INDETERMINATE	1	TRUE	NA	0.470440496928804	2		2265	928	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52663040	52663040	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	132	975	0	ENST00000394830.3:c.1313A>G	p.Lys438Arg	p.K438R	ENST00000394830	NM_018313.4	438	aAg/aGg	13/30	1	2	FACETS	0.788	0.717	0.863	0.788	0.717	0.863	SUBCLONAL	1	TRUE	1	0.470440496928804	2		975	712	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561758	55561758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200950545	NA	P-0005372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	187	1396	0	ENST00000288135.5:c.148G>A	p.Val50Met	p.V50M	ENST00000288135	NM_000222.2	50	Gtg/Atg	2/21	0.240039354214611	1	FACETS	0.721	0.667	0.777	0.721	0.667	0.777	INDETERMINATE	1	TRUE	0	0.470440496928804	1		1396	843	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593383	55593383	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0005372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	244	1553	0	ENST00000288135.5:c.1541-1G>A		p.X514_splice	ENST00000288135	NM_000222.2	514			0.240039354214611	1	FACETS	0.839	0.784	0.894	0.839	0.784	0.894	INDETERMINATE	1	TRUE	0	0.470440496928804	1		1553	946	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541786	187541786	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	365	2010	0	ENST00000441802.2:c.5954C>T	p.Ser1985Phe	p.S1985F	ENST00000441802	NM_005245.3	1985	tCt/tTt	10/27	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.470440496928804	2		2010	1201	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163342	32163342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	297	2273	3	ENST00000375023.3:c.5884G>A	p.Ala1962Thr	p.A1962T	ENST00000375023	NM_004557.3	1962	Gcc/Acc	30/30	0.14004514748776	3	FACETS	1	0.992	1	0.655	0.616	0.695	INDETERMINATE	1	TRUE	1	0.470440496928804	3		2276	1191	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658334	117658334	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs573549832	NA	P-0005372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1378	182	2541	0	ENST00000368508.3:c.5248+1G>A		p.X1750_splice	ENST00000368508	NM_002944.2	1750			1	2	FACETS	0.496	0.456	0.538	0.496	0.456	0.538	SUBCLONAL	1	TRUE	1	0.470440496928804	2		2541	1560	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211407	98211407	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	206	1769	0	ENST00000331920.6:c.3748C>G	p.Pro1250Ala	p.P1250A	ENST00000331920	NM_000264.3	1250	Cct/Gct	22/24	0.319552475430283	1	FACETS	0.924	0.86	0.989	0.924	0.86	0.989	CLONAL	1	TRUE	0	0.470440496928804	1		1769	725	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405958	70405958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370887665	NA	P-0005372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	146	2185	3	ENST00000373644.4:c.3472C>T	p.Arg1158Trp	p.R1158W	ENST00000373644	NM_030625.2	1158	Cgg/Tgg	4/12	0.470440496928804	1	FACETS	0.464	0.423	0.507	0.464	0.423	0.507	SUBCLONAL	1	TRUE	0	0.470440496928804	1		2188	1023	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112365	115112365	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	41	771	1	ENST00000257566.3:c.1375C>A	p.Arg459Ser	p.R459S	ENST00000257566	NM_016569.3	459	Cgc/Agc	7/8	0.14004514748776	3	FACETS	0.558	0.465	0.66	0.279	0.232	0.33	INDETERMINATE	1	TRUE	1	0.470440496928804	3		772	386	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459321	99459321	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	146	1841	1	ENST00000268035.6:c.1957C>T	p.Gln653Ter	p.Q653*	ENST00000268035	NM_000875.3	653	Cag/Tag	9/21	0.378738808725566	1	FACETS	0.527	0.481	0.576	0.527	0.481	0.576	SUBCLONAL	1	TRUE	0	0.470440496928804	1		1842	900	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788632	3788632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756756076	NA	P-0005372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	133	2026	0	ENST00000262367.5:c.4322G>A	p.Arg1441Gln	p.R1441Q	ENST00000262367	NM_004380.2	1441	cGg/cAg	26/31	0.470440496928804	1	FACETS	0.495	0.449	0.544	0.495	0.449	0.544	SUBCLONAL	1	TRUE	0	0.470440496928804	1		2026	873	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900578	3900578	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	218	1747	0	ENST00000262367.5:c.518C>T	p.Pro173Leu	p.P173L	ENST00000262367	NM_004380.2	173	cCt/cTt	2/31	0.470440496928804	1	FACETS	0.918	0.856	0.981	0.918	0.856	0.981	CLONAL	1	TRUE	0	0.470440496928804	1		1747	772	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14031641	14031641	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0005372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	94	1782	0	ENST00000311895.7:c.1830C>G	p.Tyr610Ter	p.Y610*	ENST00000311895	NM_005236.2	610	taC/taG	9/11	0.470440496928804	1	FACETS	0.341	0.303	0.383	0.341	0.303	0.383	SUBCLONAL	1	TRUE	0	0.470440496928804	1		1782	895	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81960742	81960742	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	134	2315	0	ENST00000359376.3:c.2473G>C	p.Glu825Gln	p.E825Q	ENST00000359376	NM_002661.3	825	Gag/Cag	23/33	0.463487718189741	0	FACETS	0.303	0.274	0.333			1	SUBCLONAL	1	TRUE	0	0.470440496928804	0		2315	996	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682506	37682506	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	289	2001	2	ENST00000447079.4:c.3697G>T	p.Asp1233Tyr	p.D1233Y	ENST00000447079	NM_015083.1	1233	Gac/Tac	13/14	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.470440496928804	2		2003	1018	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37863258	37863258	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	273	1803	1	ENST00000269571.5:c.89A>G	p.Asp30Gly	p.D30G	ENST00000269571		30	gAc/gGc	2/27	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.470440496928804	2		1804	947	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699354	47699354	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	149	1928	0	ENST00000347630.2:c.154A>G	p.Ile52Val	p.I52V	ENST00000347630	NM_001007230.1	52	Att/Gtt	4/11	1	2	FACETS	0.502	0.458	0.55	0.502	0.458	0.55	SUBCLONAL	1	TRUE	1	0.470440496928804	2		1928	1261	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051258	13051258	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0005372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	353	2260	1	ENST00000316448.5:c.694A>T	p.Lys232Ter	p.K232*	ENST00000316448	NM_004343.3	232	Aag/Tag	5/9	0.470440496928804	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.470440496928804	1		2261	1095	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537104	41537104	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	238	1861	0	ENST00000263253.7:c.1931T>C	p.Leu644Pro	p.L644P	ENST00000263253	NM_001429.3	644	cTa/cCa	10/31	0.470440496928804	1	FACETS	0.913	0.854	0.973	0.913	0.854	0.973	CLONAL	1	TRUE	0	0.470440496928804	1		1861	848	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15809122	15809122	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	328	1122	1	ENST00000307771.7:c.107G>A	p.Arg36Gln	p.R36Q	ENST00000307771	NM_005089.3	36	cGa/cAa	2/11	1	1	FACETS	0.804	0.767	0.842	1	0.996	1	CLONAL	2	TRUE	0	0.470440496928804	1		1123	663	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870204	44870204	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0005372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	333	995	0	ENST00000377967.4:c.385-2A>G		p.X129_splice	ENST00000377967	NM_021140.2	129			1	1	FACETS	0.774	0.738	0.811	1	0.995	1	SUBCLONAL	2	TRUE	0	0.470440496928804	1		995	699	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913666	32913716	+	inframe_deletion	In_Frame_Del	DEL	CTGAAAATGACAAAAATCATCTCTCCGAAAAACAAGATACTTATTTAAGTA	CTGAAAATGACAAAAATCATCTCTCCGAAAAACAAGATACTTATTTAAGTA	-	novel	NA	P-0005372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1499	288	2757	3	ENST00000380152.3:c.5174_5224del	p.Ala1725_Asn1742delinsAsp	p.A1725_N1742delinsD	ENST00000380152		1725	gCTGAAAATGACAAAAATCATCTCTCCGAAAAACAAGATACTTATTTAAGTAac/gac	11/27	0.19659497239682	2	FACETS	0.685	0.642	0.73	0.343	0.321	0.365	INDETERMINATE	1	TRUE	0	0.470440496928804	2		2760	1787	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252973	36253000	+	frameshift_variant	Frame_Shift_Del	DEL	ACCAGAGTGCCATCTGGAACATCCCCTA	ACCAGAGTGCCATCTGGAACATCCCCTA	-	novel	NA	P-0005372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	134	1464	0	ENST00000300305.3:c.362_389del	p.Leu121ProfsTer3	p.L121Pfs*3	ENST00000300305		121	cTAGGGGATGTTCCAGATGGCACTCTGGTc/cc	4/8	1	2	FACETS	0.605	0.549	0.664	0.605	0.549	0.664	SUBCLONAL	1	TRUE	1	0.470440496928804	2		1464	941	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045868	47045876	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CACAGGCCC	CACAGGCCC	-	novel	NA	P-0005372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	175	842	0	ENST00000377604.3:c.2668-5_2671del		p.X890_splice	ENST00000377604	NM_001204468.1	890		24/24	1	1	FACETS	0.818	0.766	0.869	1	0.992	1	CLONAL	2	TRUE	0	0.470440496928804	1		842	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0005475-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	395	364	1	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	0.121197390949261	3	FACETS	0.986	0.944	1	1	0.996	1	INDETERMINATE	3	TRUE	1	0.4	3		365	801	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933307	49933307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749037053	NA	P-0005475-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	244	437	0	ENST00000296474.3:c.2803G>A	p.Val935Ile	p.V935I	ENST00000296474	NM_002447.2	935	Gta/Ata	12/20	0.161071201360853	4	FACETS	1	0.96	1	1	0.994	1	INDETERMINATE	3	TRUE	2	0.4	4		437	557	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514780	44514780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769567889	NA	P-0005475-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	333	304	1	ENST00000291552.4:c.467G>A	p.Arg156His	p.R156H	ENST00000291552	NM_006758.2	156	cGt/cAt	6/8	0.229381935355651	0	FACETS	0.803	0.767	0.839			1	INDETERMINATE	2	TRUE	0	0.4	0		305	622	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115916	8115917	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005475-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	113	224	0	ENST00000346208.3:c.1263dup	p.Met422AspfsTer85	p.M422Dfs*85	ENST00000346208		421	ccg/ccGg	6/6	0.285119823927342	0	FACETS	0.61	0.558	0.663			1	SUBCLONAL	2	TRUE	0	0.4	0		224	278	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0005562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	374	381	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.3381091307313	5	FACETS	0.845	0.802	0.89			1	CLONAL	3	TRUE	NA	0.3381091307313	5		381	1315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578247	7578247	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	368	445	0	ENST00000269305.4:c.602del	p.Leu201CysfsTer46	p.L201Cfs*46	ENST00000269305	NM_001126112.2	201	tTg/tg	6/11	0.337754035259193	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.3381091307313	2		445	984	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40743879	40743879	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	114	326	0	ENST00000392038.2:c.828C>G	p.Ile276Met	p.I276M	ENST00000392038	NM_001626.4	276	atC/atG	9/14	0.3381091307313	5	FACETS	0.878	0.789	0.974	0.293	0.263	0.325	CLONAL	1	TRUE	2	0.3381091307313	5		326	1157	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339987	70339987	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	402	241	0	ENST00000374080.3:c.520A>G	p.Lys174Glu	p.K174E	ENST00000374080		174	Aag/Gag	4/45	0.324254114112898	2	FACETS	1	0.988	1			1	CLONAL	3	TRUE	NA	0.3381091307313	2		241	737	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	179	456	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.976	0.906	1	0.976	0.906	1	CLONAL	1	TRUE	1	0.701652895787543	2		456	523	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28929495	NA	P-0005701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10003	2255	557	3	ENST00000275493.2:c.2155G>T	p.Gly719Cys	p.G719C	ENST00000275493	NM_005228.3	719	Ggc/Tgc	18/28	0.701652895787543	26	FACETS	0.988	0.965	1			1	CLONAL	5	TRUE	NA	0.701652895787543	26		560	12258	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888199	112888199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918454	NA	P-0005701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	32	614	1	ENST00000351677.2:c.215C>T	p.Ala72Val	p.A72V	ENST00000351677	NM_002834.3	72	gCc/gTc	3/16	1	2	FACETS	0.102	0.082	0.125	0.102	0.082	0.125	SUBCLONAL	1	TRUE	1	0.701652895787543	2		615	890	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690805	89690805	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	174	262	0	ENST00000371953.3:c.212G>A	p.Cys71Tyr	p.C71Y	ENST00000371953	NM_000314.4	71	tGt/tAt	4/9	0.701652895787543	1	FACETS	0.97	0.91	1	0.97	0.91	1	CLONAL	1	TRUE	0	0.701652895787543	1		262	332	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459737	149459737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148673905	NA	P-0005701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	312	590	1	ENST00000286301.3:c.470C>T	p.Ser157Leu	p.S157L	ENST00000286301	NM_005211.3	157	tCg/tTg	4/22	NA	2	FACETS	0.903	0.853	0.954			1	INDETERMINATE	1	TRUE	NA	0.701652895787543	2		591	985	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	315	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.552166225517304	5	FACETS	0.917	0.87	0.964	0.917	0.87	0.964	CLONAL	3	TRUE	2	0.556484627502952	5		326	755	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723067	52723067	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770861676	NA	P-0005741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	363	412	0	ENST00000322088.6:c.1252C>T	p.Arg418Trp	p.R418W	ENST00000322088	NM_014225.5	418	Cgg/Tgg	10/15	NA	2	FACETS	0.95	0.909	0.99			1	INDETERMINATE	2	TRUE	NA	0.556484627502952	2		412	687	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0005741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	429	369	2	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.465475081316377	3	FACETS	0.844	0.812	0.877	0.844	0.812	0.877	CLONAL	3	TRUE	0	0.556484627502952	3		371	778	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845890	156845890	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750477154	NA	P-0005741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1624	420	834	0	ENST00000524377.1:c.1520G>A	p.Arg507His	p.R507H	ENST00000524377	NM_002529.3	507	cGc/cAc	13/17	0.556484627502952	3	FACETS	0.944	0.896	0.993	0.472	0.448	0.497	CLONAL	1	TRUE	1	0.556484627502952	3		834	2044	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416618	49416618	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	180	383	0	ENST00000301067.7:c.16093C>T	p.Gln5365Ter	p.Q5365*	ENST00000301067	NM_003482.3	5365	Cag/Tag	51/54	0.556484627502952	2	FACETS	1	0.93	1	0.502	0.465	0.541	CLONAL	1	TRUE	0	0.556484627502952	2		383	644	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713364	30713364	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150116445	NA	P-0005812-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	223	538	1	ENST00000295754.5:c.689C>T	p.Thr230Met	p.T230M	ENST00000295754	NM_003242.5	230	aCg/aTg	4/7	0.185579140375661	4	FACETS	0.962	0.903	1	1	0.992	1	INDETERMINATE	3	TRUE	2	0.374743168919839	4		539	567	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0005813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	435	264	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.64411783248553	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.64411783248553	1		264	778	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0005813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	276	409	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	1	2	FACETS	0.929	0.874	0.986	0.929	0.874	0.986	CLONAL	1	TRUE	1	0.64411783248553	2		409	922	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445190	49445216	+	inframe_deletion	In_Frame_Del	DEL	GGCTCCTCAGGCCGGGGGGACAGGTGC	GGCTCCTCAGGCCGGGGGGACAGGTGC	-	rs587778449	NA	P-0005813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	81	390	1	ENST00000301067.7:c.2250_2276del	p.Arg755_Pro763del	p.R755_P763del	ENST00000301067	NM_003482.3	750	ccGCACCTGTCCCCCCGGCCTGAGGAGCCa/cca	10/54	NA	2	FACETS	0.328	0.289	0.371			1	INDETERMINATE	1	TRUE	NA	0.64411783248553	2		391	766	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039377	49039378	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCCTTACAAGTTTCCTAGTTC	novel	NA	P-0005813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	308	685	0	ENST00000267163.4:c.2363_2384dup	p.Arg798GlnfsTer4	p.R798Qfs*4	ENST00000267163	NM_000321.2	788	agc/aGCCCTTACAAGTTTCCTAGTTCgc	23/27	0.64411783248553	1	FACETS	0.765	0.723	0.806	0.765	0.723	0.806	SUBCLONAL	1	TRUE	0	0.64411783248553	1		685	848	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	27	456	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.916	0.742	1			1	INDETERMINATE	2	TRUE	NA	0.243544520226465	2		456	121	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0005848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	49	423	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.243544520226465	2		423	346	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333850	70333850	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs762232511	NA	P-0005848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	41	528	2	ENST00000373644.4:c.1755G>T	p.Lys585Asn	p.K585N	ENST00000373644	NM_030625.2	585	aaG/aaT	2/12	0.243544520226465	3	FACETS	0.895	0.753	1	0.895	0.753	1	CLONAL	2	TRUE	1	0.243544520226465	3		530	211	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650633	18650633	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	59	516	0	ENST00000266497.5:c.2844G>T	p.Leu948Phe	p.L948F	ENST00000266497		948	ttG/ttT	20/31	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.243544520226465	2		516	369	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27093012	27093012	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	51	746	0	ENST00000324856.7:c.2943G>A	p.Met981Ile	p.M981I	ENST00000324856	NM_006015.4	981	atG/atA	10/20	0.152108144341637	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.243544520226465	1		746	292	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097721	27097721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	42	671	0	ENST00000324856.7:c.3310G>A	p.Glu1104Lys	p.E1104K	ENST00000324856	NM_006015.4	1104	Gaa/Aaa	12/20	0.152108144341637	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.243544520226465	1		671	257	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466851	25466851	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	19	480	0	ENST00000264709.3:c.1852G>A	p.Asp618Asn	p.D618N	ENST00000264709	NM_175629.2	618	Gac/Aac	16/23	0.152108144341637	1	FACETS	1	0.778	1	1	0.778	1	CLONAL	1	TRUE	0	0.243544520226465	1		480	135	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99181106	99181106	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	19	481	0	ENST00000074304.5:c.2047A>T	p.Thr683Ser	p.T683S	ENST00000074304	NM_001134224.1	683	Acc/Tcc	20/26	1	2	FACETS	0.975	0.746	1	0.975	0.746	1	CLONAL	1	TRUE	1	0.243544520226465	2		481	160	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939884	49939884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	32	793	1	ENST00000296474.3:c.1159G>A	p.Glu387Lys	p.E387K	ENST00000296474	NM_002447.2	387	Gaa/Aaa	1/20	0.225955021883908	0	FACETS	1	0.822	1			1	CLONAL	1	TRUE	0	0.243544520226465	0		794	198	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280109	66280109	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	59	471	0	ENST00000273854.3:c.1580C>A	p.Ala527Glu	p.A527E	ENST00000273854	NM_004439.5	527	gCa/gAa	7/18	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.243544520226465	2		471	365	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258956	153258956	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	72	572	0	ENST00000281708.4:c.859G>C	p.Glu287Gln	p.E287Q	ENST00000281708	NM_033632.3	287	Gag/Cag	5/12	1	2	FACETS	0.799	0.702	0.902	1	0.978	1	CLONAL	2	TRUE	1	0.243544520226465	2		572	370	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36653556	36653556	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	34	559	0	ENST00000244741.5:c.474C>G	p.Ile158Met	p.I158M	ENST00000244741	NM_000389.4	158	atC/atG	3/3	0.152108144341637	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.243544520226465	1		559	164	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140870	37140870	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	22	657	0	ENST00000373509.5:c.706G>T	p.Val236Leu	p.V236L	ENST00000373509	NM_002648.3	236	Gtg/Ttg	5/6	0.152108144341637	1	FACETS	0.763	0.594	0.957	0.763	0.594	0.957	CLONAL	1	TRUE	0	0.243544520226465	1		657	208	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949166	151949166	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	59	442	0	ENST00000262189.6:c.1479C>A	p.His493Gln	p.H493Q	ENST00000262189	NM_170606.2	493	caC/caA	11/59	1	2	FACETS	0.776	0.673	0.888	1	0.972	1	SUBCLONAL	2	TRUE	1	0.243544520226465	2		442	312	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248124	98248124	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	24	493	0	ENST00000331920.6:c.427A>T	p.Thr143Ser	p.T143S	ENST00000331920	NM_000264.3	143	Act/Tct	3/24	1	2	FACETS	0.943	0.743	1	0.943	0.743	1	CLONAL	1	TRUE	1	0.243544520226465	2		493	209	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59886090	59886090	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	40	422	0	ENST00000259008.2:c.656G>T	p.Cys219Phe	p.C219F	ENST00000259008	NM_032043.2	219	tGt/tTt	7/20	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.243544520226465	2		422	307	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221975	1221975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568710381	NA	P-0005848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	25	623	0	ENST00000326873.7:c.890G>A	p.Arg297Lys	p.R297K	ENST00000326873	NM_000455.4	297	aGg/aAg	7/10	0.243544520226465	0	FACETS	1	0.867	1			1	CLONAL	1	TRUE	0	0.243544520226465	0		623	139	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247345	153247346	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	70	443	0	ENST00000281708.4:c.1456dup	p.Trp486LeufsTer4	p.W486Lfs*4	ENST00000281708	NM_033632.3	486	tgg/tTgg	10/12	1	2	FACETS	0.861	0.756	0.972	1	0.979	1	CLONAL	2	TRUE	1	0.243544520226465	2		443	334	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0005873-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	136	367	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.39	2		367	630	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550900	150550900	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005873-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	84	188	0	ENST00000369026.2:c.756T>A	p.His252Gln	p.H252Q	ENST00000369026	NM_021960.4	252	caT/caA	2/3	0.206531220386295	3	FACETS	1	0.921	1	0.525	0.465	0.589	INDETERMINATE	1	TRUE	1	0.39	3		188	490	SUCCESS
APC	324	MSKCC	GRCh37	5	112176926	112176926	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587779799	NA	P-0005873-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	140	382	0	ENST00000257430.4:c.5635G>T	p.Ala1879Ser	p.A1879S	ENST00000257430	NM_000038.5	1879	Gct/Tct	16/16	0.206531220386295	3	FACETS	1	0.971	1	0.574	0.523	0.627	INDETERMINATE	1	TRUE	1	0.39	3		382	747	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453185	140453185	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005873-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	99	226	0	ENST00000288602.6:c.1750C>T	p.Leu584Phe	p.L584F	ENST00000288602	NM_004333.4	584	Ctt/Ttt	15/18	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.39	2		226	505	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359975	87359975	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005873-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	135	330	0	ENST00000277120.3:c.1283G>T	p.Arg428Leu	p.R428L	ENST00000277120		428	cGg/cTg	11/19	1	2	FACETS	0.931	0.847	1	0.931	0.847	1	CLONAL	1	TRUE	1	0.39	2		330	744	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039687	47039688	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTTTGCCAAG	novel	NA	P-0005873-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	146	606	0	ENST00000377604.3:c.1141_1150dup	p.Gly384ValfsTer6	p.G384Vfs*6	ENST00000377604	NM_001204468.1	380	gag/gaGTTTGCCAAGg	11/24	1	2	FACETS	0.865	0.789	0.944	0.865	0.789	0.944	CLONAL	1	TRUE	1	0.39	2		606	866	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019605	42019606	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0005989-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	715	755	0	ENST00000219905.7:c.3657+2dup		p.X1219_splice	ENST00000219905	NM_001164273.1	1219			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		755	1437	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575521	64575521	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1565648511	NA	P-0006018-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	411	810	2	ENST00000312049.6:c.496C>T	p.Gln166Ter	p.Q166*	ENST00000312049	NM_130799.2	166	Cag/Tag	3/10	0.659505574764848	1	FACETS	0.983	0.941	1	0.983	0.941	1	CLONAL	1	TRUE	0	0.659505574764848	1		812	850	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286531	33286532	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006018-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	103	448	0	ENST00000374542.5:c.2211dup	p.Asp738ArgfsTer3	p.D738Rfs*3	ENST00000374542	NM_001141970.1	737	-/A	8/8	0.659505574764848	1	FACETS	0.865	0.789	0.942	0.865	0.789	0.942	CLONAL	1	TRUE	0	0.659505574764848	1		448	242	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860143	151860143	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs747835958	NA	P-0006060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	101	380	4	ENST00000262189.6:c.10519C>T	p.Arg3507Ter	p.R3507*	ENST00000262189	NM_170606.2	3507	Cga/Tga	43/59	0.314091033680112	3	FACETS	0.863	0.772	0.959	0.431	0.386	0.48	CLONAL	1	TRUE	1	0.440148516234218	3		384	649	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0006060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	485	423	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.312716305536696	4	FACETS	0.908	0.871	0.946	1	0.996	1	CLONAL	3	TRUE	2	0.440148516234218	4		423	1165	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0006060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	250	421	1	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.440148516234218	NA		422	569	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11210189	11210189	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	96	430	0	ENST00000361445.4:c.4564G>A	p.Gly1522Ser	p.G1522S	ENST00000361445	NM_004958.3	1522	Ggt/Agt	31/58	0.312716305536696	4	FACETS	0.635	0.564	0.71	0.317	0.282	0.355	SUBCLONAL	1	TRUE	2	0.440148516234218	4		430	990	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46527726	46527726	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	110	295	1	ENST00000262741.5:c.639G>T	p.Arg213Ser	p.R213S	ENST00000262741	NM_003629.3	213	agG/agT	6/10	0.314091033680112	3	FACETS	0.885	0.796	0.979	0.443	0.398	0.49	CLONAL	1	TRUE	1	0.440148516234218	3		296	689	SUCCESS
REL	5966	MSKCC	GRCh37	2	61144075	61144075	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	122	574	0	ENST00000295025.8:c.458A>T	p.Gln153Leu	p.Q153L	ENST00000295025	NM_002908.2	153	cAa/cTa	5/11	1	2	FACETS	0.684	0.618	0.754	0.684	0.618	0.754	SUBCLONAL	1	TRUE	1	0.440148516234218	2		574	810	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524584	187524584	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs892630031	NA	P-0006060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	112	436	0	ENST00000441802.2:c.11096A>G	p.Glu3699Gly	p.E3699G	ENST00000441802	NM_005245.3	3699	gAg/gGg	19/27	0.339267836167083	2	FACETS	0.701	0.631	0.775	0.35	0.315	0.388	SUBCLONAL	1	TRUE	0	0.440148516234218	2		436	726	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531125	187531125	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	97	434	2	ENST00000441802.2:c.9898G>T	p.Glu3300Ter	p.E3300*	ENST00000441802	NM_005245.3	3300	Gag/Tag	15/27	0.339267836167083	2	FACETS	0.735	0.656	0.818	0.367	0.328	0.409	SUBCLONAL	1	TRUE	0	0.440148516234218	2		436	600	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224620	224620	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	45	164	0	ENST00000264932.6:c.296A>G	p.His99Arg	p.H99R	ENST00000264932	NM_004168.2	99	cAc/cGc	3/15	0.440148516234218	6	FACETS	0.671	0.563	0.79	0.112	0.093	0.132	SUBCLONAL	1	TRUE	0	0.440148516234218	6		164	573	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876457	35876457	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	110	382	0	ENST00000303115.3:c.1249C>G	p.Pro417Ala	p.P417A	ENST00000303115	NM_002185.3	417	Cct/Gct	8/8	0.440148516234218	6	FACETS	0.813	0.728	0.903	0.163	0.145	0.181	CLONAL	1	TRUE	1	0.440148516234218	6		382	1156	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624481	140624481	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs774925605	NA	P-0006060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	43	145	0	ENST00000288602.6:c.23G>T	p.Gly8Val	p.G8V	ENST00000288602	NM_004333.4	8	gGt/gTt	1/18	0.314091033680112	3	FACETS	0.861	0.725	1	0.43	0.362	0.505	CLONAL	1	TRUE	1	0.440148516234218	3		145	277	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138116	64138116	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	89	342	0	ENST00000334205.4:c.2039G>T	p.Arg680Leu	p.R680L	ENST00000334205	NM_003942.2	680	cGc/cTc	16/17	0.314091033680112	3	FACETS	0.772	0.685	0.865	0.386	0.342	0.433	SUBCLONAL	1	TRUE	1	0.440148516234218	3		342	639	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577430	64577430	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	248	505	0	ENST00000312049.6:c.152A>T	p.Asn51Ile	p.N51I	ENST00000312049	NM_130799.2	51	aAc/aTc	2/10	0.314091033680112	3	FACETS	0.787	0.737	0.837	0.787	0.737	0.837	SUBCLONAL	2	TRUE	1	0.440148516234218	3		505	874	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109974	115109974	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	102	409	1	ENST00000257566.3:c.1904G>T	p.Arg635Leu	p.R635L	ENST00000257566	NM_016569.3	635	cGc/cTc	8/8	0.312716305536696	4	FACETS	0.832	0.744	0.926	0.416	0.372	0.463	CLONAL	1	TRUE	2	0.440148516234218	4		410	802	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544748	65544748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	164	311	0	ENST00000358664.4:c.178C>T	p.Arg60Trp	p.R60W	ENST00000358664	NM_002382.4	60	Cgg/Tgg	4/5	0.34309512255662	3	FACETS	1	0.988	1	0.718	0.662	0.776	CLONAL	1	TRUE	1	0.440148516234218	3		311	633	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028571	42028571	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	404	801	0	ENST00000219905.7:c.4109G>C	p.Gly1370Ala	p.G1370A	ENST00000219905	NM_001164273.1	1370	gGc/gCc	13/24	0.402322618205654	2	FACETS	0.859	0.819	0.899	0.859	0.819	0.899	CLONAL	2	TRUE	0	0.440148516234218	2		801	1069	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420309	88420309	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	256	263	0	ENST00000360948.2:c.2377C>G	p.Arg793Gly	p.R793G	ENST00000360948	NM_001012338.2	793	Cga/Gga	19/19	0.402322618205654	2	FACETS	0.906	0.854	0.958	0.906	0.854	0.958	CLONAL	2	TRUE	0	0.440148516234218	2		263	642	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678416	88678416	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	818	689	0	ENST00000360948.2:c.1120G>T	p.Gly374Cys	p.G374C	ENST00000360948	NM_001012338.2	374	Ggc/Tgc	9/19	0.440148516234218	4	FACETS	0.977	0.951	1	0.977	0.951	1	CLONAL	4	TRUE	0	0.440148516234218	4		689	1370	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984842	11984842	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	217	344	0	ENST00000353533.5:c.388G>T	p.Val130Phe	p.V130F	ENST00000353533	NM_003010.3	130	Gtt/Ttt	3/11	0.288361617901473	3	FACETS	1	0.981	1	0.743	0.697	0.789	CLONAL	2	TRUE	0	0.440148516234218	3		344	540	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291118	10291118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs149362098	NA	P-0006060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	279	444	0	ENST00000340748.4:c.353G>T	p.Arg118Leu	p.R118L	ENST00000340748		118	cGt/cTt	4/40	0.339267836167083	2	FACETS	0.854	0.807	0.903	0.854	0.807	0.903	CLONAL	2	TRUE	0	0.440148516234218	2		444	742	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260177	19260177	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	274	447	0	ENST00000162023.5:c.116G>C	p.Cys39Ser	p.C39S	ENST00000162023		39	tGt/tCt	7/13	0.440148516234218	3	FACETS	0.902	0.849	0.956	0.902	0.849	0.956	CLONAL	2	TRUE	1	0.440148516234218	3		447	842	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019880	123019880	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	108	449	0	ENST00000355640.3:c.368G>T	p.Ser123Ile	p.S123I	ENST00000355640		123	aGc/aTc	2/7	0.34309512255662	3	FACETS	0.785	0.704	0.87	0.392	0.352	0.435	SUBCLONAL	1	TRUE	1	0.440148516234218	3		449	763	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164048	47164049	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0006060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	76	461	0	ENST00000409792.3:c.2077dup	p.Ala693GlyfsTer7	p.A693Gfs*7	ENST00000409792	NM_014159.6	693	gct/gGct	3/21	0.339267836167083	2	FACETS	0.508	0.445	0.575	0.254	0.222	0.288	SUBCLONAL	1	TRUE	0	0.440148516234218	2		461	680	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509959	106509959	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	208	477	0	ENST00000359195.3:c.1954del	p.Glu652ArgfsTer16	p.E652Rfs*16	ENST00000359195	NM_002649.2	651	ttG/tt	2/11	0.314091033680112	3	FACETS	1	0.985	1	0.615	0.571	0.66	CLONAL	1	TRUE	1	0.440148516234218	3		477	938	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578365	212578365	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	126	333	0	ENST00000342788.4:c.892del	p.Val298TrpfsTer2	p.V298Wfs*2	ENST00000342788	NM_005235.2	298	Gtg/tg	8/28	0.34309512255662	3	FACETS	1	0.984	1	0.693	0.631	0.758	CLONAL	1	TRUE	1	0.440148516234218	3		333	504	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864689	57864690	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0006060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	272	661	0	ENST00000228682.2:c.2166_2167delinsTT	p.Met722_Asp723delinsIleTyr	p.M722_D723delinsIY	ENST00000228682	NM_005269.2	722	atGGac/atTTac	12/12	0.312716305536696	4	FACETS	1	0.993	1	0.74	0.694	0.787	CLONAL	1	TRUE	2	0.440148516234218	4		661	1203	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37056029	37056029	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553645342	NA	P-0006086-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	65	453	0	ENST00000231790.2:c.784A>G	p.Ile262Val	p.I262V	ENST00000231790	NM_000249.3	262	Atc/Gtc	9/19	0.201133493422376	3	FACETS	0.92	0.797	1	0.46	0.398	0.528	CLONAL	1	TRUE	1	0.201133493422376	3		453	773	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115975	8115976	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0006086-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	33	188	0	ENST00000346208.3:c.1323dup	p.Met442HisfsTer65	p.M442Hfs*65	ENST00000346208		441	gcc/gCcc	6/6	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.201133493422376	2		188	268	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434259	49434262	+	frameshift_variant	Frame_Shift_Del	DEL	CAGA	CAGA	-	rs1555192210	NA	P-0006098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	548	1037	0	ENST00000301067.7:c.7291_7294del	p.Ser2431LeufsTer53	p.S2431Lfs*53	ENST00000301067	NM_003482.3	2431	TCTGct/ct	31/54	0.861825532853477	2	FACETS	0.934	0.897	0.971	0.467	0.448	0.486	CLONAL	1	TRUE	0	0.861825532853477	2		1037	1362	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589557	67589598	+	inframe_deletion	In_Frame_Del	DEL	TAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACAC	TAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACAC	-	novel	NA	P-0006098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	159	433	0	ENST00000274335.5:c.1321_1362del	p.Asn441_Thr454del	p.N441_T454del	ENST00000274335		440	gaTAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACACt/gat	10/15	1	2	FACETS	0.782	0.723	0.842	0.782	0.723	0.842	SUBCLONAL	1	TRUE	1	0.861825532853477	2		433	472	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027928	48027928	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	548	582	0	ENST00000234420.5:c.2806G>T	p.Asp936Tyr	p.D936Y	ENST00000234420	NM_000179.2	936	Gat/Tat	4/10	0.861825532853477	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.861825532853477	2		582	633	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139818342	139818342	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs972932325	NA	P-0006098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	399	768	0	ENST00000247668.2:c.1177C>T	p.Arg393Cys	p.R393C	ENST00000247668	NM_021138.3	393	Cgt/Tgt	10/11	1	2	FACETS	0.889	0.848	0.931	0.889	0.848	0.931	CLONAL	1	TRUE	1	0.861825532853477	2		768	1041	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827801	72827801	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	219	903	1	ENST00000268489.5:c.8780G>T	p.Ser2927Ile	p.S2927I	ENST00000268489	NM_006885.3	2927	aGt/aTt	9/10	0.861825532853477	1	FACETS	0.366	0.341	0.391	0.366	0.341	0.391	SUBCLONAL	1	TRUE	0	0.861825532853477	1		904	791	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131313	17131313	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs369115472	NA	P-0006098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	382	682	0	ENST00000285071.4:c.139G>C	p.Glu47Gln	p.E47Q	ENST00000285071	NM_144997.5	47	Gaa/Caa	4/14	1	2	FACETS	0.995	0.949	1	0.995	0.949	1	CLONAL	1	TRUE	1	0.861825532853477	2		682	891	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872485	35872645	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGAGCTCAGGATCACAGCCAGCTCCCAGAAGTGCCTCAGCAATTTCTGGCTGGTTGGTGATCACAGCCAAGTGGAGTGGAGTCTACGAATGCAAGAGAGACCAGAGAAAGTAAGCCATGGACCAAACCCACACCCCGAGTTCCCCTCAACCCGTGTCTCCT	GGAGCTCAGGATCACAGCCAGCTCCCAGAAGTGCCTCAGCAATTTCTGGCTGGTTGGTGATCACAGCCAAGTGGAGTGGAGTCTACGAATGCAAGAGAGACCAGAGAAAGTAAGCCATGGACCAAACCCACACCCCGAGTTCCCCTCAACCCGTGTCTCCT	-	novel	NA	P-0006098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	307	944	0	ENST00000216797.5:c.337-79_418del		p.X113_splice	ENST00000216797	NM_020529.2	113		3/6	0.852745016422828	1	FACETS	0.762	0.728	0.796	0.762	0.728	0.796	SUBCLONAL	1	TRUE	0	0.861825532853477	1		944	532	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427965	49427966	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0006098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	331	596	0	ENST00000301067.7:c.10624_10625del	p.Leu3542ValfsTer13	p.L3542Vfs*13	ENST00000301067	NM_003482.3	3542	CTg/g	38/54	0.861825532853477	2	FACETS	0.916	0.869	0.962	0.458	0.434	0.481	CLONAL	1	TRUE	0	0.861825532853477	2		596	839	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0006118-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	360	536	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			NA	2	FACETS	1	0.978	1			1	INDETERMINATE	2	TRUE	NA	0.511973683781843	2		536	679	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683246	88683246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767763451	NA	P-0006118-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	94	334	0	ENST00000372037.3:c.1456C>T	p.Arg486Trp	p.R486W	ENST00000372037	NM_004329.2	486	Cgg/Tgg	12/13	1	2	FACETS	0.944	0.846	1	0.944	0.846	1	CLONAL	1	TRUE	1	0.511973683781843	2		334	389	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0006118-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	196	117	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	NA	2	FACETS	1	0.959	1			1	INDETERMINATE	2	TRUE	NA	0.511973683781843	2		117	374	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490356	56490356	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006118-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	151	532	0	ENST00000267101.3:c.2125C>G	p.Leu709Val	p.L709V	ENST00000267101	NM_001982.3	709	Cta/Gta	18/28	0.469366178375304	4	FACETS	0.866	0.791	0.945	0.433	0.395	0.473	CLONAL	1	TRUE	2	0.511973683781843	4		532	1030	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349482	73349482	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006118-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	82	401	0	ENST00000377767.4:c.854G>C	p.Arg285Thr	p.R285T	ENST00000377767	NM_014953.3	285	aGa/aCa	6/21	0.511973683781843	3	FACETS	0.843	0.746	0.947	0.281	0.248	0.316	CLONAL	1	TRUE	0	0.511973683781843	3		401	477	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256236	41256236	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006118-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	46	459	0	ENST00000357654.3:c.344C>G	p.Pro115Arg	p.P115R	ENST00000357654	NM_007294.3	115	cCt/cGt	6/23	0.478684293196051	3	FACETS	0.278	0.233	0.328			1	SUBCLONAL	1	TRUE	NA	0.511973683781843	3		459	811	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575106	48575106	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006118-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	125	494	0	ENST00000342988.3:c.300G>T	p.Arg100Ser	p.R100S	ENST00000342988	NM_005359.5	100	agG/agT	3/12	0.511973683781843	1	FACETS	0.869	0.793	0.948	0.869	0.793	0.948	CLONAL	1	TRUE	0	0.511973683781843	1		494	418	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619127	1619127	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006118-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	117	430	0	ENST00000344749.5:c.1433C>G	p.Pro478Arg	p.P478R	ENST00000344749	NM_001136139.2	478	cCt/cGt	16/19	0.511973683781843	3	FACETS	1	0.951	1	0.54	0.488	0.593	CLONAL	1	TRUE	1	0.511973683781843	3		430	532	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953275	17953301	+	inframe_deletion	In_Frame_Del	DEL	CTTGGCCATGAGCGAGTGCCGGTCTGC	CTTGGCCATGAGCGAGTGCCGGTCTGC	-	novel	NA	P-0006118-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	104	438	0	ENST00000458235.1:c.685_711del	p.Ala229_Lys237del	p.A229_K237del	ENST00000458235	NM_000215.3	229	GCAGACCGGCACTCGCTCATGGCCAAG/-	6/24	0.511973683781843	3	FACETS	0.842	0.756	0.933	0.421	0.378	0.467	CLONAL	1	TRUE	1	0.511973683781843	3		438	606	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912563	32912564	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006118-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	550	713	0	ENST00000380152.3:c.4074dup	p.Thr1359TyrfsTer2	p.T1359Yfs*2	ENST00000380152		1357	-/T	11/27	0.0778433697827925	3	FACETS	1	0.976	1			1	INDETERMINATE	3	TRUE	NA	0.511973683781843	3		713	891	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0006166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	24	162	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	0.334421969219652	2		162	96	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	55	621	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.334421969219652	1	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	0	0.334421969219652	1		621	261	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0006166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	10	78	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.586	0.4	0.816	0.586	0.4	0.816	SUBCLONAL	1	TRUE	1	0.334421969219652	2		78	102	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0006166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	35	417	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	0.334421969219652	1	FACETS	0.876	0.725	1	0.876	0.725	1	CLONAL	1	TRUE	0	0.334421969219652	1		417	199	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045016	47045016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556782040	NA	P-0006166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	50	357	0	ENST00000377604.3:c.2342C>T	p.Ser781Leu	p.S781L	ENST00000377604	NM_001204468.1	781	tCa/tTa	20/24	0.334421969219652	1	FACETS	0.64	0.545	0.745	0.64	0.545	0.745	SUBCLONAL	1	TRUE	0	0.334421969219652	1		357	389	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226568850	226568850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	33	339	0	ENST00000366794.5:c.1219G>A	p.Glu407Lys	p.E407K	ENST00000366794	NM_001618.3	407	Gaa/Aaa	9/23	0.334421969219652	3	FACETS	0.704	0.575	0.85	0.352	0.287	0.425	SUBCLONAL	1	TRUE	1	0.334421969219652	3		339	327	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881573	111881573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	37	277	0	ENST00000393256.3:c.251G>A	p.Arg84Lys	p.R84K	ENST00000393256	NM_006538.4	84	aGa/aAa	2/4	0.300945988490072	5	FACETS	0.992	0.82	1			1	CLONAL	1	TRUE	NA	0.334421969219652	5		277	335	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433775	149433775	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	24	261	0	ENST00000286301.3:c.2776C>G	p.Leu926Val	p.L926V	ENST00000286301	NM_005211.3	926	Ctg/Gtg	22/22	1	2	FACETS	0.632	0.498	0.786	0.632	0.498	0.786	SUBCLONAL	1	TRUE	1	0.334421969219652	2		261	227	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858327	27858327	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	67	623	0	ENST00000359303.2:c.244G>A	p.Asp82Asn	p.D82N	ENST00000359303	NM_003535.2	82	Gac/Aac	1/1	0.283490150471418	3	FACETS	1	0.93	1	0.55	0.48	0.626	CLONAL	1	TRUE	1	0.334421969219652	3		623	425	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6048643	6048643	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs375507981	NA	P-0006166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	77	276	0	ENST00000265849.7:c.8G>C	p.Arg3Pro	p.R3P	ENST00000265849	NM_000535.5	3	cGa/cCa	1/15	0.283490150471418	3	FACETS	1	0.914	1	0.524	0.461	0.591	CLONAL	1	TRUE	1	0.334421969219652	3		276	513	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3799638	3799638	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1190687085	NA	P-0006166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	51	297	0	ENST00000262367.5:c.3826G>C	p.Asp1276His	p.D1276H	ENST00000262367	NM_004380.2	1276	Gac/Cac	21/31	0.283490150471418	3	FACETS	0.886	0.763	1	0.886	0.763	1	CLONAL	2	TRUE	1	0.334421969219652	3		297	201	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231773	36231773	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	38	269	0	ENST00000300305.3:c.611G>C	p.Arg204Pro	p.R204P	ENST00000300305		204	cGa/cCa	5/8	1	2	FACETS	0.864	0.719	1	0.864	0.719	1	CLONAL	1	TRUE	1	0.334421969219652	2		269	263	SUCCESS
AR	367	MSKCC	GRCh37	X	66766051	66766051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	80	351	1	ENST00000374690.3:c.1063G>A	p.Glu355Lys	p.E355K	ENST00000374690	NM_000044.3	355	Gag/Aag	1/8	0.334421969219652	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.334421969219652	1		352	324	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630140	100630140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	17	391	0	ENST00000308731.7:c.133G>A	p.Glu45Lys	p.E45K	ENST00000308731	NM_000061.2	45	Gaa/Aaa	2/19	0.334421969219652	1	FACETS	0.481	0.361	0.623	0.481	0.361	0.623	SUBCLONAL	1	TRUE	0	0.334421969219652	1		391	176	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087446	27087446	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	190	541	0	ENST00000324856.7:c.2020A>G	p.Ser674Gly	p.S674G	ENST00000324856	NM_006015.4	674	Agt/Ggt	5/20	0.456110402542481	4	FACETS	0.845	0.779	0.913			1	CLONAL	1	TRUE	NA	0.520602223892789	4		541	1314	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431618	6431618	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	73	190	0	ENST00000356142.4:c.171T>A	p.Asp57Glu	p.D57E	ENST00000356142	NM_018890.3	57	gaT/gaA	3/7	0.497990099038119	5	FACETS	0.823	0.72	0.934	0.274	0.24	0.312	CLONAL	1	TRUE	2	0.520602223892789	5		190	607	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431634	6431634	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	80	173	0	ENST00000356142.4:c.187G>A	p.Asp63Asn	p.D63N	ENST00000356142	NM_018890.3	63	Gat/Aat	3/7	0.497990099038119	5	FACETS	0.909	0.801	1	0.303	0.267	0.342	CLONAL	1	TRUE	2	0.520602223892789	5		173	602	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372193	55372193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753081636	NA	P-0006226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	77	214	0	ENST00000297316.4:c.883G>A	p.Val295Met	p.V295M	ENST00000297316	NM_022454.3	295	Gtg/Atg	2/2	0.483968917184412	4	FACETS	0.847	0.745	0.956	0.424	0.372	0.478	CLONAL	1	TRUE	2	0.520602223892789	4		214	531	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273883	10273883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	155	447	0	ENST00000330684.3:c.386G>A	p.Gly129Glu	p.G129E	ENST00000330684	NM_001134407.1	129	gGg/gAg	2/13	0.520602223892789	4	FACETS	0.831	0.759	0.906	0.415	0.379	0.453	CLONAL	1	TRUE	2	0.520602223892789	4		447	1090	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872198	76872198	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	32	187	0	ENST00000373344.5:c.5449A>G	p.Arg1817Gly	p.R1817G	ENST00000373344	NM_000489.3	1817	Agg/Ggg	22/35	0.456110402542481	2	FACETS	0.283	0.229	0.344			1	SUBCLONAL	1	TRUE	NA	0.520602223892789	2		187	434	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95577700	95577700	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	217	579	0	ENST00000393063.1:c.2210del	p.Pro737GlnfsTer21	p.P737Qfs*21	ENST00000393063	NM_030621.3	737	cCa/ca	15/28	0.483968917184412	4	FACETS	0.928	0.861	0.998	0.464	0.43	0.499	CLONAL	1	TRUE	2	0.520602223892789	4		579	1366	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902698	50902699	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0006226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1297	226	585	0	ENST00000440232.2:c.275_276del	p.Glu92AlafsTer10	p.E92Afs*10	ENST00000440232	NM_002691.3	91	acAGag/acag	3/27	0.483968917184412	4	FACETS	0.867	0.805	0.931	0.433	0.402	0.466	CLONAL	1	TRUE	2	0.520602223892789	4		585	1523	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910684	32910685	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0006226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1293	237	768	0	ENST00000380152.3:c.2192_2193del	p.Glu731GlyfsTer19	p.E731Gfs*19	ENST00000380152		731	gAA/g	11/27	0.237704021233691	4	FACETS	0.905	0.842	0.97			1	INDETERMINATE	1	TRUE	NA	0.520602223892789	4		768	1530	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855943	68855953	+	frameshift_variant	Frame_Shift_Del	DEL	TCCTGTCTGAT	TCCTGTCTGAT	-	novel	NA	P-0006226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	338	403	0	ENST00000261769.5:c.1751_1761del	p.Ile584SerfsTer3	p.I584Sfs*3	ENST00000261769	NM_004360.3	584	aTCCTGTCTGAT/a	12/16	0.480819091564921	2	FACETS	0.963	0.919	1	0.963	0.919	1	CLONAL	2	TRUE	0	0.520602223892789	2		403	674	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	112	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.97	0.876	1	0.97	0.876	1	CLONAL	1	TRUE	1	0.445725965913258	2		326	518	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0006230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	80	336	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.6	0.529	0.677	0.6	0.529	0.677	SUBCLONAL	1	TRUE	1	0.445725965913258	2		337	598	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99175929	99175929	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	83	417	1	ENST00000074304.5:c.1841G>A	p.Cys614Tyr	p.C614Y	ENST00000074304	NM_001134224.1	614	tGc/tAc	18/26	0.206372611964602	2	FACETS	0.459	0.405	0.518	0.23	0.202	0.259	INDETERMINATE	1	TRUE	0	0.445725965913258	2		418	811	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968551	55968551	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	82	434	0	ENST00000263923.4:c.2112T>A	p.Asn704Lys	p.N704K	ENST00000263923	NM_002253.2	704	aaT/aaA	14/30	0.445725965913258	1	FACETS	0.482	0.425	0.543	0.482	0.425	0.543	SUBCLONAL	1	TRUE	0	0.445725965913258	1		434	593	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578293	7578977	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGAGCAATCAGTGAGGAATCAGAGGCCTGGGGACCCTGGGCAACCAGCCCTGTCGTCTCTCCAGCCCCAGCTGCTCACCATCGCTATCTGAGCAGCGCTCATGGTGGGGGCAGCGCCTCACAACCTCCGTCATGTGCTGTGACTGCTTGTAGATGGCCATGGCGCGGACGCGGGTGCCGGGCGGGGGTGTGGAATCAACCCACAGCTGCACAGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAAGCAACTGGAAGACGGCAGCAAAGAAACAAACATGCGTAAGCACCTCCTGCAACCCACTAGCGAGCTAGAGAGAGTTGGCGTCTACACCTCAGGAGCTTTTCTTTTTTTTTTTTTTTTTTGAGATAGGGTCTTGCTCTGTCACTCAGGCTGGAGCACAGTGGTGTGATCACAGCTCACTGCAGCCTCCATCTCCTGGCCTCAAGTGATCTTCCCACCTCAGCCTCCTAAGTGGCTGGGACTATAGGTGTGCACCACCATGCCTGGCTAATTTTTTGTATTTTTTTGTAGAGACGAGGTTTCATCATGTTACCCAGGCTGGTCTTGAACTCCTGGGCTCAGGTGATCTGCCTGCCTTGGCCTCTTTGAG	AGAGCAATCAGTGAGGAATCAGAGGCCTGGGGACCCTGGGCAACCAGCCCTGTCGTCTCTCCAGCCCCAGCTGCTCACCATCGCTATCTGAGCAGCGCTCATGGTGGGGGCAGCGCCTCACAACCTCCGTCATGTGCTGTGACTGCTTGTAGATGGCCATGGCGCGGACGCGGGTGCCGGGCGGGGGTGTGGAATCAACCCACAGCTGCACAGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAAGCAACTGGAAGACGGCAGCAAAGAAACAAACATGCGTAAGCACCTCCTGCAACCCACTAGCGAGCTAGAGAGAGTTGGCGTCTACACCTCAGGAGCTTTTCTTTTTTTTTTTTTTTTTTGAGATAGGGTCTTGCTCTGTCACTCAGGCTGGAGCACAGTGGTGTGATCACAGCTCACTGCAGCCTCCATCTCCTGGCCTCAAGTGATCTTCCCACCTCAGCCTCCTAAGTGGCTGGGACTATAGGTGTGCACCACCATGCCTGGCTAATTTTTTGTATTTTTTTGTAGAGACGAGGTTTCATCATGTTACCCAGGCTGGTCTTGAACTCCTGGGCTCAGGTGATCTGCCTGCCTTGGCCTCTTTGAG	-	novel	NA	P-0006230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	138	383	0	ENST00000269305.4:c.375+335_560-4del		p.X125_splice	ENST00000269305	NM_001126112.2	125		5/11	0.178572498108913	1	FACETS	0.767	0.701	0.837	0.767	0.701	0.837	INDETERMINATE	1	TRUE	0	0.445725965913258	1		383	627	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411206	63411207	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	198	515	0	ENST00000330258.3:c.1960dup	p.Tyr654LeufsTer53	p.Y654Lfs*53	ENST00000330258	NM_152424.3	654	tat/tTat	2/2	0.43383872280102	1	FACETS	0.8	0.742	0.86	0.8	0.742	0.86	SUBCLONAL	1	TRUE	0	0.445725965913258	1		515	863	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534479	187534479	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	21	243	1	ENST00000441802.2:c.9247del	p.Thr3083ProfsTer33	p.T3083Pfs*33	ENST00000441802	NM_005245.3	3083	Acc/cc	13/27	0.445725965913258	1	FACETS	0.214	0.164	0.272	0.214	0.164	0.272	SUBCLONAL	1	TRUE	0	0.445725965913258	1		244	342	SUCCESS
APC	324	MSKCC	GRCh37	5	112175607	112175608	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCCTCCA	novel	NA	P-0006230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	174	476	0	ENST00000257430.4:c.4319_4320insTCCATCC	p.Pro1442SerfsTer15	p.P1442Sfs*15	ENST00000257430	NM_000038.5	1439	cct/ccTCCTCCAt	16/16	1	2	FACETS	0.94	0.866	1	0.94	0.866	1	CLONAL	1	TRUE	1	0.445725965913258	2		476	831	SUCCESS
ATM	472	MSKCC	GRCh37	11	108213958	108213959	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs775899653	NA	P-0006265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	60	295	0	ENST00000278616.4:c.8283_8284del	p.Gln2762AlafsTer6	p.Q2762Afs*6	ENST00000278616	NM_000051.3	2760	CTc/c	57/63	1	2	FACETS	0.818	0.705	0.94	0.818	0.705	0.94	CLONAL	1	TRUE	1	0.291158920026897	2		295	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0006265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	114	487	0	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.281114196194939	1	FACETS	0.746	0.671	0.825	0.746	0.671	0.825	SUBCLONAL	1	TRUE	0	0.291158920026897	1		487	897	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444932	49444933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs767415197	NA	P-0006265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	22	159	0	ENST00000301067.7:c.2533dup	p.Arg845ProfsTer3	p.R845Pfs*3	ENST00000301067	NM_003482.3	845	cgg/cCgg	10/54	1	2	FACETS	0.451	0.349	0.569	0.451	0.349	0.569	SUBCLONAL	1	TRUE	1	0.291158920026897	2		159	335	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786748	3786748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	106	506	0	ENST00000262367.5:c.4463C>T	p.Pro1488Leu	p.P1488L	ENST00000262367	NM_004380.2	1488	cCa/cTa	27/31	0.291158920026897	3	FACETS	0.772	0.69	0.859	0.386	0.345	0.43	SUBCLONAL	1	TRUE	1	0.291158920026897	3		506	1081	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023676	27023676	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	45	345	0	ENST00000324856.7:c.782C>G	p.Ser261Trp	p.S261W	ENST00000324856	NM_006015.4	261	tCg/tGg	1/20	0.281114196194939	1	FACETS	0.367	0.308	0.434	0.367	0.308	0.434	SUBCLONAL	1	TRUE	0	0.291158920026897	1		345	719	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46715730	46715730	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	140	510	0	ENST00000371975.4:c.149C>A	p.Pro50His	p.P50H	ENST00000371975	NM_003579.3	50	cCt/cAt	3/18	0.281114196194939	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.291158920026897	1		510	786	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098962	178098962	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	91	242	0	ENST00000397062.3:c.83T>C	p.Ile28Thr	p.I28T	ENST00000397062	NM_006164.4	28	aTa/aCa	2/5	0.161283467281939	3	FACETS	0.808	0.721	0.9	0.808	0.721	0.9	INDETERMINATE	2	TRUE	1	0.291158920026897	3		242	443	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778051	27778051	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769595845	NA	P-0006265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1365	262	884	0	ENST00000369163.2:c.200C>T	p.Pro67Leu	p.P67L	ENST00000369163	NM_003536.2	67	cCt/cTt	1/1	0.198571179677385	2	FACETS	1	0.978	1	0.553	0.516	0.591	CLONAL	1	TRUE	0	0.291158920026897	2		884	1627	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910349	29910349	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	121	403	1	ENST00000376809.5:c.19C>T	p.Arg7Ter	p.R7*	ENST00000376809	NM_002116.7	7	Cga/Tga	1/8	0.281114196194939	1	FACETS	0.981	0.887	1	0.981	0.887	1	CLONAL	1	TRUE	0	0.291158920026897	1		404	724	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670985	30670985	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	103	381	0	ENST00000376406.3:c.5761G>A	p.Ala1921Thr	p.A1921T	ENST00000376406	NM_014641.2	1921	Gca/Aca	12/15	0.281114196194939	1	FACETS	0.849	0.76	0.943	0.849	0.76	0.943	CLONAL	1	TRUE	0	0.291158920026897	1		381	712	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596008	43596008	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	152	390	0	ENST00000355710.3:c.175G>T	p.Ala59Ser	p.A59S	ENST00000355710	NM_020975.4	59	Gcc/Tcc	2/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.291158920026897	2		390	838	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136054	64136054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	49	253	0	ENST00000334205.4:c.1315G>A	p.Val439Ile	p.V439I	ENST00000334205	NM_003942.2	439	Gtc/Atc	11/17	1	2	FACETS	0.629	0.533	0.735	0.629	0.533	0.735	SUBCLONAL	1	TRUE	1	0.291158920026897	2		253	535	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633677	69633677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	16	60	0	ENST00000334134.2:c.25C>T	p.Leu9Phe	p.L9F	ENST00000334134	NM_005247.2	9	Ctc/Ttc	1/3	1	2	FACETS	0.964	0.721	1	0.964	0.721	1	CLONAL	1	TRUE	1	0.291158920026897	2		60	114	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1042172	1042172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356534157	NA	P-0006265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	58	465	0	ENST00000358495.3:c.53C>T	p.Ala18Val	p.A18V	ENST00000358495	NM_134424.2	18	gCt/gTt	2/12	NA	2	FACETS	0.402	0.344	0.466			1	INDETERMINATE	1	TRUE	NA	0.291158920026897	2		465	991	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435887	49435887	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	56	445	0	ENST00000301067.7:c.6094A>G	p.Lys2032Glu	p.K2032E	ENST00000301067	NM_003482.3	2032	Aag/Gag	28/54	1	2	FACETS	0.416	0.355	0.483	0.416	0.355	0.483	SUBCLONAL	1	TRUE	1	0.291158920026897	2		445	925	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435136	110435136	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs780127725	NA	P-0006265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	57	271	1	ENST00000375856.3:c.3265G>C	p.Ala1089Pro	p.A1089P	ENST00000375856	NM_003749.2	1089	Gcc/Ccc	1/2	0.281114196194939	1	FACETS	0.592	0.508	0.684	0.592	0.508	0.684	SUBCLONAL	1	TRUE	0	0.291158920026897	1		272	565	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610314	81610314	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	27	337	0	ENST00000298171.2:c.1912G>A	p.Ala638Thr	p.A638T	ENST00000298171	NM_000369.2	638	Gcc/Acc	10/10	0.291158920026897	1	FACETS	0.322	0.255	0.398	0.322	0.255	0.398	SUBCLONAL	1	TRUE	0	0.291158920026897	1		337	492	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337232	89337232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1354874973	NA	P-0006265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	48	325	0	ENST00000301030.4:c.7799G>A	p.Arg2600His	p.R2600H	ENST00000301030	NM_001256183.1	2600	cGc/cAc	12/13	1	2	FACETS	0.503	0.424	0.589	0.503	0.424	0.589	SUBCLONAL	1	TRUE	1	0.291158920026897	2		325	656	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118345	17118345	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	57	423	0	ENST00000285071.4:c.1492G>T	p.Asp498Tyr	p.D498Y	ENST00000285071	NM_144997.5	498	Gat/Tat	13/14	0.281114196194939	1	FACETS	0.421	0.36	0.488	0.421	0.36	0.488	SUBCLONAL	1	TRUE	0	0.291158920026897	1		423	794	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681124	37681124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	43	307	0	ENST00000447079.4:c.3293C>T	p.Ala1098Val	p.A1098V	ENST00000447079	NM_015083.1	1098	gCt/gTt	12/14	1	2	FACETS	0.571	0.478	0.675	0.571	0.478	0.675	SUBCLONAL	1	TRUE	1	0.291158920026897	2		307	517	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166214	118166214	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	60	346	0	ENST00000369448.3:c.728del	p.Gly243AspfsTer24	p.G243Dfs*24	ENST00000369448	NM_017709.3	242	Ggg/gg	2/2	0.281114196194939	1	FACETS	0.576	0.496	0.664	0.576	0.496	0.664	SUBCLONAL	1	TRUE	0	0.291158920026897	1		346	611	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330629	65330630	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	62	291	0	ENST00000342505.4:c.1016dup	p.Asn339LysfsTer2	p.N339Kfs*2	ENST00000342505	NM_002227.2	339	aat/aaAt	8/25	0.281114196194939	1	FACETS	0.65	0.561	0.746	0.65	0.561	0.746	SUBCLONAL	1	TRUE	0	0.291158920026897	1		291	560	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444378	49444378	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	40	331	1	ENST00000301067.7:c.2993del	p.Pro998LeufsTer2	p.P998Lfs*2	ENST00000301067	NM_003482.3	998	cCt/ct	11/54	1	2	FACETS	0.399	0.331	0.476	0.399	0.331	0.476	SUBCLONAL	1	TRUE	1	0.291158920026897	2		332	688	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97934431	97934432	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	A	novel	NA	P-0006265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	33	271	0	ENST00000289081.3:c.346-3dup		p.X116_splice	ENST00000289081	NM_000136.2	116			1	2	FACETS	0.429	0.349	0.52	0.429	0.349	0.52	SUBCLONAL	1	TRUE	1	0.291158920026897	2		271	528	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344955	118344955	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	79	327	0	ENST00000534358.1:c.3086del	p.Lys1029ArgfsTer65	p.K1029Rfs*65	ENST00000534358	NM_005933.3	1027	ctA/ct	3/36	1	2	FACETS	0.981	0.865	1	0.981	0.865	1	CLONAL	1	TRUE	1	0.291158920026897	2		327	553	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233090	69233090	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746910913	NA	P-0006265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	81	361	0	ENST00000462284.1:c.961del	p.Leu321PhefsTer52	p.L321Ffs*52	ENST00000462284	NM_002392.5	319	Ccc/cc	11/11	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.291158920026897	2		361	556	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817720	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	221	481	0	ENST00000262367.5:c.3250dup	p.Ile1084AsnfsTer3	p.I1084Nfs*3	ENST00000262367	NM_004380.2	1084	atc/aAtc		0.291158920026897	3	FACETS	0.946	0.881	1	0.946	0.881	1	CLONAL	2	TRUE	1	0.291158920026897	3		481	919	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005310	29005311	+	missense_variant	Missense_Mutation	DNP	TG	TG	AT	novel	NA	P-0006265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	71	352	0	ENST00000282397.4:c.950_951delinsAT	p.Pro317His	p.P317H	ENST00000282397	NM_002019.4	317	cCA/cAT	7/30	0.291158920026897	1	FACETS	0.811	0.709	0.92	0.811	0.709	0.92	CLONAL	1	TRUE	0	0.291158920026897	1		352	514	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287185	33287185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006494-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	373	420	0	ENST00000374542.5:c.1912C>T	p.Gln638Ter	p.Q638*	ENST00000374542	NM_001141970.1	638	Caa/Taa	6/8	NA	2	FACETS	0.95	0.916	0.984			1	INDETERMINATE	2	TRUE	NA	0.692144872676315	2		420	567	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098617	2098617	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1055443730	NA	P-0006494-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	374	403	0	ENST00000219476.3:c.1A>G	p.Met1?	p.M1?	ENST00000219476	NM_000548.3	1	Atg/Gtg	2/42	0.692144872676315	2	FACETS	0.982	0.948	1	0.982	0.948	1	CLONAL	2	TRUE	0	0.692144872676315	2		403	550	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206647673	206647673	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0006541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	121	212	0	ENST00000367120.3:c.88-1G>A		p.X30_splice	ENST00000367120	NM_014002.3	30			0.361195876709919	3	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.730582076798157	3		212	358	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725042	89725042	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0006541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	775	234	0	ENST00000371953.3:c.1027-2A>T		p.X343_splice	ENST00000371953	NM_000314.4	343			0.747437141990456	3	FACETS	1	0.998	1	1	0.998	1	CLONAL	3	TRUE	0	0.730582076798157	3		234	838	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0006541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	276	183	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.730582076798157	6	FACETS	0.889	0.84	0.939	0.889	0.84	0.939	CLONAL	3	TRUE	3	0.730582076798157	6		183	697	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419837	41419837	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs267605939	NA	P-0006541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	107	285	0	ENST00000373198.4:c.484C>T	p.Gln162Ter	p.Q162*	ENST00000373198	NM_133170.3	162	Cag/Tag	3/32	NA	2	FACETS	0.738	0.667	0.812			1	INDETERMINATE	1	TRUE	NA	0.730582076798157	2		285	397	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476791	140476791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	402	2008	1	ENST00000288602.6:c.1615C>T	p.His539Tyr	p.H539Y	ENST00000288602	NM_004333.4	539	Cac/Tac	13/18	0.730582076798157	6	FACETS	0.905	0.863	0.946	0.905	0.863	0.946	CLONAL	3	TRUE	3	0.730582076798157	6		2009	998	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187419	32187419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	102	328	0	ENST00000375023.3:c.1460G>A	p.Gly487Glu	p.G487E	ENST00000375023	NM_004557.3	487	gGa/gAa	8/30	0.636428459454344	5	FACETS	0.856	0.766	0.951			1	CLONAL	1	TRUE	NA	0.730582076798157	5		328	684	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439664	220439664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs992068119	NA	P-0006541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	761	729	0	ENST00000243786.2:c.517C>T	p.Pro173Ser	p.P173S	ENST00000243786	NM_002191.3	173	Ccc/Tcc	2/2	0.622834296386615	5	FACETS	0.958	0.934	0.982			1	CLONAL	4	TRUE	NA	0.730582076798157	5		729	1139	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164307	47164307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	229	264	0	ENST00000409792.3:c.1819C>T	p.Pro607Ser	p.P607S	ENST00000409792	NM_014159.6	607	Cct/Tct	3/21	0.453117312815237	4	FACETS	0.999	0.94	1			1	CLONAL	2	TRUE	NA	0.730582076798157	4		264	543	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102904	71102904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	97	159	0	ENST00000318789.4:c.303G>A	p.Met101Ile	p.M101I	ENST00000318789	NM_032682.5	101	atG/atA	8/21	0.65857273757628	3	FACETS	0.778	0.707	0.85			1	SUBCLONAL	2	TRUE	NA	0.730582076798157	3		159	233	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911572	134911572	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	110	229	0	ENST00000398015.3:c.2037C>A	p.Asn679Lys	p.N679K	ENST00000398015	NM_004441.4	679	aaC/aaA	11/16	0.269431585526373	2	FACETS	0.764	0.692	0.839	0.382	0.346	0.42	INDETERMINATE	1	TRUE	0	0.730582076798157	2		229	394	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554861	187554861	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	227	342	0	ENST00000441802.2:c.4300G>A	p.Gly1434Arg	p.G1434R	ENST00000441802	NM_005245.3	1434	Gga/Aga	7/27	0.747437141990456	3	FACETS	1	0.975	1	0.543	0.507	0.58	CLONAL	1	TRUE	1	0.730582076798157	3		342	781	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680877	30680877	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2720	521	623	0	ENST00000376406.3:c.842G>T	p.Gly281Val	p.G281V	ENST00000376406	NM_014641.2	281	gGg/gTg	5/15	0.730582076798157	12	FACETS	1	0.97	1	0.256	0.244	0.269	CLONAL	2	TRUE	4	0.730582076798157	12		623	3241	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2949769	2949769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376446854	NA	P-0006541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	100	280	0	ENST00000396946.4:c.3175G>A	p.Gly1059Ser	p.G1059S	ENST00000396946	NM_032415.4	1059	Ggc/Agc	24/25	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.730582076798157	2		280	236	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241632	55241632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	102	279	1	ENST00000275493.2:c.2080C>T	p.Pro694Ser	p.P694S	ENST00000275493	NM_005228.3	694	Ccc/Tcc	18/28	NA	2	FACETS	0.834	0.754	0.916			1	INDETERMINATE	1	TRUE	NA	0.730582076798157	2		280	335	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346575	81346575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	599	373	0	ENST00000222390.5:c.1378C>T	p.Pro460Ser	p.P460S	ENST00000222390	NM_000601.4	460	Cct/Tct	11/18	0.747437141990456	4	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.730582076798157	4		373	1308	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477794	140477794	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	210	247	0	ENST00000288602.6:c.1514T>A	p.Leu505His	p.L505H	ENST00000288602	NM_004333.4	505	cTc/cAc	12/18	0.730582076798157	6	FACETS	0.809	0.753	0.868	0.54	0.502	0.579	CLONAL	2	TRUE	3	0.730582076798157	6		247	874	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915939	127915939	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	396	704	2	ENST00000373547.4:c.542G>A	p.Arg181Gln	p.R181Q	ENST00000373547	NM_002721.4	181	cGg/cAg	6/7	0.671737349902196	3	FACETS	0.811	0.774	0.847	0.811	0.774	0.847	CLONAL	2	TRUE	1	0.730582076798157	3		706	913	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137832	64137832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753090599	NA	P-0006541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	548	480	0	ENST00000334205.4:c.1933G>A	p.Glu645Lys	p.E645K	ENST00000334205	NM_003942.2	645	Gag/Aag	15/17	0.747437141990456	4	FACETS	0.958	0.927	0.989	0.958	0.927	0.989	CLONAL	3	TRUE	1	0.730582076798157	4		480	903	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200425	67200425	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	235	208	0	ENST00000312629.5:c.619C>T	p.His207Tyr	p.H207Y	ENST00000312629	NM_003952.2	207	Cac/Tac	8/15	0.747437141990456	4	FACETS	1	0.982	1	0.733	0.692	0.775	CLONAL	2	TRUE	1	0.730582076798157	4		208	506	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514302	69514302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1255340343	NA	P-0006541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	100	327	1	ENST00000294312.3:c.379C>T	p.Arg127Cys	p.R127C	ENST00000294312	NM_005117.2	127	Cgc/Tgc	3/3	0.734250141579754	1	FACETS	0.57	0.515	0.626	0.57	0.515	0.626	SUBCLONAL	1	TRUE	0	0.730582076798157	1		328	305	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119809	108119809	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	257	298	0	ENST00000278616.4:c.1215T>G	p.Asn405Lys	p.N405K	ENST00000278616	NM_000051.3	405	aaT/aaG	9/63	0.747437141990456	3	FACETS	1	0.989	1	0.612	0.575	0.65	CLONAL	1	TRUE	1	0.730582076798157	3		298	785	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444024	49444024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	193	288	0	ENST00000301067.7:c.3347C>T	p.Ser1116Phe	p.S1116F	ENST00000301067	NM_003482.3	1116	tCt/tTt	11/54	0.747437141990456	5	FACETS	0.85	0.79	0.912	0.567	0.527	0.608	CLONAL	2	TRUE	2	0.730582076798157	5		288	651	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859436	57859436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	422	689	1	ENST00000228682.2:c.581C>T	p.Pro194Leu	p.P194L	ENST00000228682	NM_005269.2	194	cCc/cTc	6/12	0.730582076798157	8	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.730582076798157	8		690	1515	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554305	81554305	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777252114	NA	P-0006541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	470	485	0	ENST00000298171.2:c.325C>T	p.Arg109Trp	p.R109W	ENST00000298171	NM_000369.2	109	Cgg/Tgg	4/10	0.747437141990456	6	FACETS	0.984	0.943	1	0.984	0.943	1	CLONAL	3	TRUE	3	0.730582076798157	6		485	1073	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349080	11349080	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	78	112	0	ENST00000332029.2:c.256G>T	p.Val86Leu	p.V86L	ENST00000332029	NM_003745.1	86	Gtg/Ttg	2/2	0.747437141990456	3	FACETS	1	0.961	1	0.59	0.526	0.657	CLONAL	1	TRUE	1	0.730582076798157	3		112	247	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863648	68863648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782549	NA	P-0006541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	164	317	0	ENST00000261769.5:c.2387G>A	p.Arg796Gln	p.R796Q	ENST00000261769	NM_004360.3	796	cGg/cAg	15/16	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.730582076798157	2		317	365	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288726	15288726	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	26	74	0	ENST00000263388.2:c.4013G>C	p.Ser1338Thr	p.S1338T	ENST00000263388	NM_000435.2	1338	aGc/aCc	24/33	0.747437141990456	3	FACETS	1	0.938	1	0.704	0.579	0.835	CLONAL	1	TRUE	1	0.730582076798157	3		74	69	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538302	9538302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	238	365	0	ENST00000353224.5:c.1696C>T	p.His566Tyr	p.H566Y	ENST00000353224	NM_177990.2	566	Cac/Tac	7/10	0.65857273757628	3	FACETS	0.803	0.756	0.85			1	CLONAL	2	TRUE	NA	0.730582076798157	3		365	554	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714436	40714436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1228688924	NA	P-0006541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	124	201	0	ENST00000373198.4:c.3961G>A	p.Glu1321Lys	p.E1321K	ENST00000373198	NM_133170.3	1321	Gag/Aag	29/32	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.730582076798157	2		201	279	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727065	40727065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866502487	NA	P-0006541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	119	251	0	ENST00000373198.4:c.3899C>T	p.Ala1300Val	p.A1300V	ENST00000373198	NM_133170.3	1300	gCc/gTc	28/32	NA	2	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.730582076798157	2		251	293	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159743	20159743	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	522	278	1	ENST00000379607.5:c.16G>T	p.Gly6Cys	p.G6C	ENST00000379607	NM_001412.3	6	Ggt/Tgt	1/7	0.730582076798157	4	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.730582076798157	4		279	1015	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032155	26032155	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006541-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4007	438	852	0	ENST00000244661.2:c.134G>A	p.Gly45Asp	p.G45D	ENST00000244661	NM_003537.3	45	gGc/gAc	1/1	0.730582076798157	12	FACETS	1	0.992	1	0.179	0.169	0.19	CLONAL	1	TRUE	5	0.730582076798157	12		852	4445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0006568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	283	293	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.520133730846971	1	FACETS	0.975	0.922	1	0.975	0.922	1	CLONAL	1	FALSE	0	0.58347260885973	1		293	705	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914091	32914094	+	frameshift_variant	Frame_Shift_Del	DEL	ACAG	ACAG	-	rs397507356	NA	P-0006568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	222	1284	0	ENST00000380152.3:c.5603_5606del	p.Asp1868ValfsTer5	p.D1868Vfs*5	ENST00000380152		1867	ACAGac/ac	11/27	0.520133730846971	1	FACETS	0.951	0.892	1	0.951	0.892	1	CLONAL	1	FALSE	0	0.58347260885973	1		1284	567	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189912	66189912	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	95	606	0	ENST00000273854.3:c.3034C>T	p.Leu1012Phe	p.L1012F	ENST00000273854	NM_004439.5	1012	Ctt/Ttt	18/18	0.32270757457789	1	FACETS	0.73	0.657	0.805	0.73	0.657	0.805	INDETERMINATE	1	FALSE	0	0.58347260885973	1		606	316	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856020	151856020	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	134	770	0	ENST00000262189.6:c.11598G>C	p.Lys3866Asn	p.K3866N	ENST00000262189	NM_170606.2	3866	aaG/aaC	44/59	1	2	FACETS	0.852	0.778	0.929	0.852	0.778	0.929	CLONAL	1	FALSE	1	0.58347260885973	2		770	539	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114265	115114266	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0006568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	114	575	2	ENST00000257566.3:c.950_951dup	p.Thr318SerfsTer6	p.T318Sfs*6	ENST00000257566	NM_016569.3	317	-/TC	6/8	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.58347260885973	2		577	365	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660709	227660709	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1486830625	NA	P-0006570-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	229	626	0	ENST00000305123.5:c.2746C>T	p.His916Tyr	p.H916Y	ENST00000305123	NM_005544.2	916	Cac/Tac	1/2	1	2	FACETS	0.837	0.779	0.898	0.837	0.779	0.898	CLONAL	1	TRUE	1	0.439338611644713	2		626	1245	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72881603	72881603	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006570-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	212	535	0	ENST00000325599.8:c.516G>T	p.Lys172Asn	p.K172N	ENST00000325599	NM_018130.2	172	aaG/aaT	5/11	1	2	FACETS	0.985	0.915	1	0.985	0.915	1	CLONAL	1	TRUE	1	0.439338611644713	2		535	980	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786090	3786090	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006570-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1343	402	876	0	ENST00000262367.5:c.4675G>T	p.Glu1559Ter	p.E1559*	ENST00000262367	NM_004380.2	1559	Gaa/Taa	28/31	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.439338611644713	2		876	1745	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936316	78936316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006570-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	356	946	0	ENST00000306801.3:c.3748C>T	p.Leu1250Phe	p.L1250F	ENST00000306801	NM_020761.2	1250	Ctt/Ttt	32/34	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.439338611644713	2		946	1524	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051610	30051610	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs74315495	NA	P-0006570-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	228	547	1	ENST00000338641.4:c.544G>T	p.Glu182Ter	p.E182*	ENST00000338641	NM_000268.3	182	Gaa/Taa	6/16	0.439338611644713	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.439338611644713	1		548	803	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0006720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	33	293	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.475	0.385	0.577	0.475	0.385	0.577	SUBCLONAL	1	TRUE	1	0.14	2		293	993	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881001	37881002	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGCTCCCC	rs397516981	NA	P-0006720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	30	386	1	ENST00000269571.5:c.2331_2339dup	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	gtg/gtGGGCTCCCCg	20/27	1	2	FACETS	0.41	0.328	0.503	0.41	0.328	0.503	SUBCLONAL	1	TRUE	1	0.14	2		387	1046	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188196	10188217	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGGTCACCTTTGGCTCTTCAGA	AGGTCACCTTTGGCTCTTCAGA	-	novel	NA	P-0006762-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	43	431	0	ENST00000256474.2:c.341-2_360del		p.X114_splice	ENST00000256474	NM_000551.3	114		2/3	0.581728053547239	1	FACETS	0.845	0.725	0.971	0.845	0.725	0.971	CLONAL	1	TRUE	0	0.581728053547239	1		431	124	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781079	135781079	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs118203594	NA	P-0006762-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	46	941	0	ENST00000298552.3:c.1886del	p.Lys629ArgfsTer24	p.K629Rfs*24	ENST00000298552	NM_001162426.1	629	aAg/ag	15/23	1	2	FACETS	0.879	0.751	1	0.879	0.751	1	CLONAL	1	TRUE	1	0.581728053547239	2		941	180	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647545	117647545	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006762-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	39	837	0	ENST00000368508.3:c.5399A>T	p.Asn1800Ile	p.N1800I	ENST00000368508	NM_002944.2	1800	aAt/aTt	33/43	NA	2	FACETS	1	0.895	1			1	INDETERMINATE	1	TRUE	NA	0.581728053547239	2		837	125	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005364	42005386	+	frameshift_variant	Frame_Shift_Del	DEL	AAACCTATCCACACAATCATAAG	AAACCTATCCACACAATCATAAG	-	novel	NA	P-0006762-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	42	792	0	ENST00000219905.7:c.3100_3122del	p.Lys1034GlufsTer9	p.K1034Efs*9	ENST00000219905	NM_001164273.1	1034	AAACCTATCCACACAATCATAAGg/g	9/24	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.581728053547239	2		792	140	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180351	38180351	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs750337749	NA	P-0006779-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	85	500	0	ENST00000396334.3:c.199A>G	p.Met67Val	p.M67V	ENST00000396334	NM_002468.4	67	Atg/Gtg	1/5	1	2	FACETS	0.269	0.237	0.304	0.269	0.237	0.304	SUBCLONAL	1	TRUE	1	0.529449744193915	2		500	1193	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017552	112017552	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006779-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	264	527	0	ENST00000368678.4:c.961G>C	p.Asp321His	p.D321H	ENST00000368678		321	Gac/Cac	9/13	0.214984158801833	1	FACETS	0.7	0.657	0.745	0.7	0.657	0.745	INDETERMINATE	1	TRUE	0	0.529449744193915	1		527	1047	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186815	108186815	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0006779-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	283	333	0	ENST00000278616.4:c.6173C>G	p.Ser2058Ter	p.S2058*	ENST00000278616	NM_000051.3	2058	tCa/tGa	42/63	0.248827251346703	3	FACETS	0.886	0.837	0.936	0.886	0.837	0.936	INDETERMINATE	2	TRUE	1	0.529449744193915	3		333	763	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645157	67645157	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006779-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	74	364	0	ENST00000264010.4:c.422A>G	p.Glu141Gly	p.E141G	ENST00000264010	NM_006565.3	141	gAa/gGa	3/12	0.288152183990935	1	FACETS	0.351	0.308	0.398	0.351	0.308	0.398	INDETERMINATE	1	TRUE	0	0.529449744193915	1		364	585	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221243	1221243	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1057520606	NA	P-0006793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	595	631	0	ENST00000326873.7:c.766G>T	p.Glu256Ter	p.E256*	ENST00000326873	NM_000455.4	256	Gaa/Taa	6/10	0.517632520931769	2	FACETS	0.99	0.956	1	0.99	0.956	1	CLONAL	2	TRUE	0	0.517632520931769	2		631	1161	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0006793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	564	693	1	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.41437378570349	3	FACETS	0.931	0.894	0.967			1	CLONAL	2	TRUE	NA	0.517632520931769	3		694	1474	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0006793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	278	470	0	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	0.517632520931769	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.517632520931769	1		470	692	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870952	12870952	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	171	342	0	ENST00000228872.4:c.179G>A	p.Trp60Ter	p.W60*	ENST00000228872	NM_004064.3	60	tGg/tAg	1/3	0.34551971263809	3	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.517632520931769	3		342	652	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518020	187518020	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755404071	NA	P-0006793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	218	404	0	ENST00000441802.2:c.12674C>T	p.Thr4225Met	p.T4225M	ENST00000441802	NM_005245.3	4225	aCg/aTg	25/27	0.505328318274274	1	FACETS	0.997	0.933	1	0.997	0.933	1	CLONAL	1	TRUE	0	0.517632520931769	1		404	626	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101327	27101327	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	493	574	0	ENST00000324856.7:c.4609C>T	p.Gln1537Ter	p.Q1537*	ENST00000324856	NM_006015.4	1537	Cag/Tag	18/20	0.399090879106521	3	FACETS	0.988	0.948	1	0.988	0.948	1	CLONAL	2	TRUE	1	0.517632520931769	3		574	1213	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630396	47630396	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs200632093	NA	P-0006793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	594	579	0	ENST00000233146.2:c.66C>G	p.Phe22Leu	p.F22L	ENST00000233146	NM_000251.2	22	ttC/ttG	1/16	0.517632520931769	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.517632520931769	3		579	1351	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728779	190728779	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	347	337	0	ENST00000441310.2:c.2167G>T	p.Glu723Ter	p.E723*	ENST00000441310	NM_000534.4	723	Gaa/Taa	10/13	0.500644081112963	3	FACETS	0.899	0.853	0.945	0.899	0.853	0.945	CLONAL	2	TRUE	1	0.517632520931769	3		337	939	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295792	212295792	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	411	488	0	ENST00000342788.4:c.2521C>T	p.His841Tyr	p.H841Y	ENST00000342788	NM_005235.2	841	Cat/Tat	21/28	0.500644081112963	3	FACETS	1	0.995	1	0.743	0.707	0.78	CLONAL	1	TRUE	1	0.517632520931769	3		488	1345	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646195	215646195	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	277	271	0	ENST00000260947.4:c.403G>T	p.Asp135Tyr	p.D135Y	ENST00000260947	NM_000465.2	135	Gat/Tat	4/11	0.500644081112963	3	FACETS	0.92	0.869	0.972	0.92	0.869	0.972	CLONAL	2	TRUE	1	0.517632520931769	3		271	732	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440045	220440045	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1336	367	814	0	ENST00000243786.2:c.898C>A	p.Pro300Thr	p.P300T	ENST00000243786	NM_002191.3	300	Cca/Aca	2/2	0.500644081112963	3	FACETS	1	0.974	1	0.524	0.495	0.553	CLONAL	1	TRUE	1	0.517632520931769	3		814	1703	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390065	89390065	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0006793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	202	167	0	ENST00000336596.2:c.815-1G>T		p.X272_splice	ENST00000336596	NM_005233.5	272			0.515169400695482	2	FACETS	0.893	0.838	0.948	0.893	0.838	0.948	CLONAL	2	TRUE	0	0.517632520931769	2		167	437	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390221	89390221	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs531563474	NA	P-0006793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	254	240	0	ENST00000336596.2:c.970C>G	p.Arg324Gly	p.R324G	ENST00000336596	NM_005233.5	324	Cga/Gga	4/17	0.515169400695482	2	FACETS	0.935	0.885	0.985	0.935	0.885	0.985	CLONAL	2	TRUE	0	0.517632520931769	2		240	525	SUCCESS
ATR	545	MSKCC	GRCh37	3	142204114	142204114	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	166	422	0	ENST00000350721.4:c.6089C>A	p.Ala2030Glu	p.A2030E	ENST00000350721	NM_001184.3	2030	gCg/gAg	36/47	0.517632520931769	3	FACETS	0.848	0.779	0.921	0.424	0.389	0.461	CLONAL	1	TRUE	1	0.517632520931769	3		422	952	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609749	117609749	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	404	441	0	ENST00000368508.3:c.6950A>G	p.Gln2317Arg	p.Q2317R	ENST00000368508	NM_002944.2	2317	cAa/cGa	43/43	0.515169400695482	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.517632520931769	2		441	764	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026817	6026817	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	148	367	0	ENST00000265849.7:c.1579A>T	p.Arg527Trp	p.R527W	ENST00000265849	NM_000535.5	527	Agg/Tgg	11/15	0.500644081112963	3	FACETS	0.968	0.885	1	0.484	0.442	0.527	CLONAL	1	TRUE	1	0.517632520931769	3		367	744	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339742	116339742	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	144	278	0	ENST00000397752.3:c.604A>G	p.Asn202Asp	p.N202D	ENST00000397752	NM_000245.2	202	Aat/Gat	2/21	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.517632520931769	2		278	526	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	463372	463372	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	336	369	0	ENST00000399788.2:c.899G>T	p.Gly300Val	p.G300V	ENST00000399788	NM_001042603.1	300	gGt/gTt	8/28	0.34551971263809	3	FACETS	0.868	0.823	0.914			1	CLONAL	2	TRUE	NA	0.517632520931769	3		369	941	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420870	49420870	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370465399	NA	P-0006793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	430	393	0	ENST00000301067.7:c.14879G>A	p.Arg4960Gln	p.R4960Q	ENST00000301067	NM_003482.3	4960	cGa/cAa	48/54	0.517632520931769	3	FACETS	0.959	0.917	1	0.959	0.917	1	CLONAL	2	TRUE	1	0.517632520931769	3		393	1090	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919668	28919668	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	415	424	0	ENST00000282397.4:c.2269C>A	p.Leu757Met	p.L757M	ENST00000282397	NM_002019.4	757	Ctg/Atg	16/30	0.515169400695482	2	FACETS	0.973	0.933	1	0.973	0.933	1	CLONAL	2	TRUE	0	0.517632520931769	2		424	824	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910950	32910950	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	410	409	0	ENST00000380152.3:c.2458G>T	p.Asp820Tyr	p.D820Y	ENST00000380152		820	Gat/Tat	11/27	0.515169400695482	2	FACETS	0.964	0.923	1	0.964	0.923	1	CLONAL	2	TRUE	0	0.517632520931769	2		409	822	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023262	33023262	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	281	625	0	ENST00000300177.4:c.371C>A	p.Ser124Tyr	p.S124Y	ENST00000300177	NM_001191322.1	124	tCt/tAt	2/2	1	2	FACETS	0.957	0.899	1	0.957	0.899	1	CLONAL	1	TRUE	1	0.517632520931769	2		625	1135	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647734	2647734	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	440	446	0	ENST00000342085.4:c.1637G>C	p.Arg546Pro	p.R546P	ENST00000342085	NM_002613.4	546	cGa/cCa	14/14	0.517632520931769	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.517632520931769	2		446	733	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604707	48604707	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	202	403	0	ENST00000342988.3:c.1529G>C	p.Gly510Ala	p.G510A	ENST00000342988	NM_005359.5	510	gGa/gCa	12/12	0.505328318274274	1	FACETS	0.982	0.916	1	0.982	0.916	1	CLONAL	1	TRUE	0	0.517632520931769	1		403	589	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219979	5219979	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	483	614	0	ENST00000357368.4:c.3736G>T	p.Val1246Leu	p.V1246L	ENST00000357368	NM_002850.3	1246	Gtg/Ttg	22/38	0.517632520931769	2	FACETS	0.975	0.938	1	0.975	0.938	1	CLONAL	2	TRUE	0	0.517632520931769	2		614	957	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713421	40713421	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	419	519	1	ENST00000373198.4:c.4094C>A	p.Thr1365Lys	p.T1365K	ENST00000373198	NM_133170.3	1365	aCg/aAg	30/32	0.250582745736889	5	FACETS	1	0.977	1	0.695	0.661	0.729	INDETERMINATE	2	TRUE	2	0.517632520931769	5		520	1380	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195724	123195724	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	190	543	0	ENST00000218089.9:c.1638G>T	p.Arg546Ser	p.R546S	ENST00000218089	NM_001042749.1	546	agG/agT	17/35	NA	2	FACETS	0.755	0.698	0.815			1	INDETERMINATE	1	TRUE	NA	0.517632520931769	2		543	972	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831437	89831437	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	242	602	0	ENST00000389301.3:c.2639G>T	p.Arg880Leu	p.R880L	ENST00000389301	NM_000135.2	880	cGa/cTa	28/43	0.517632520931769	2	FACETS	0.959	0.897	1	0.48	0.448	0.512	CLONAL	1	TRUE	0	0.517632520931769	2		602	975	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054635	13054635	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs971167629	NA	P-0006793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	228	430	1	ENST00000316448.5:c.1162G>T	p.Asp388Tyr	p.D388Y	ENST00000316448	NM_004343.3	388	Gat/Tat	9/9	0.517632520931769	2	FACETS	1	0.963	1	0.522	0.488	0.558	CLONAL	1	TRUE	0	0.517632520931769	2		431	843	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62305356	62305356	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	508	615	1	ENST00000360203.5:c.829G>T	p.Asp277Tyr	p.D277Y	ENST00000360203	NM_001283009.1	277	Gac/Tac	10/35	0.250582745736889	5	FACETS	1	0.993	1	0.783	0.75	0.817	INDETERMINATE	2	TRUE	2	0.517632520931769	5		616	1484	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033167	69033167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	383	407	0	ENST00000288368.4:c.3607G>A	p.Glu1203Lys	p.E1203K	ENST00000288368	NM_024870.2	1203	Gaa/Aaa	30/40	0.457212300718287	4	FACETS	0.921	0.875	0.968	0.921	0.875	0.968	CLONAL	2	TRUE	2	0.517632520931769	4		407	1219	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104579	69104579	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	487	529	0	ENST00000288368.4:c.4423C>A	p.Pro1475Thr	p.P1475T	ENST00000288368	NM_024870.2	1475	Cct/Act	37/40	0.457212300718287	4	FACETS	0.915	0.874	0.956	0.915	0.874	0.956	CLONAL	2	TRUE	2	0.517632520931769	4		529	1561	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70971021	70971021	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1627	226	622	0	ENST00000276594.2:c.1240T>G	p.Tyr414Asp	p.Y414D	ENST00000276594	NM_024504.3	414	Tac/Gac	6/8	0.457212300718287	4	FACETS	0.715	0.663	0.769	0.358	0.331	0.385	SUBCLONAL	1	TRUE	2	0.517632520931769	4		622	1853	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925316	114925317	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs745872748	NA	P-0006861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	543	322	10	ENST00000543371.1:c.1403dup	p.Cys469ValfsTer8	p.C469Vfs*8	ENST00000543371	NM_001198531.1	465	aga/agAa	14/14	0.49558023065692	3	FACETS	1	0.994	1	0.752	0.725	0.778	CLONAL	2	TRUE	0	0.617924089701981	3		332	1020	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0006861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	127	442	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.967	0.884	1	0.967	0.884	1	CLONAL	1	TRUE	1	0.617924089701981	2		442	425	SUCCESS
APC	324	MSKCC	GRCh37	5	112170862	112170862	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1060503318	NA	P-0006861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	85	278	0	ENST00000257430.4:c.1958G>A	p.Arg653Lys	p.R653K	ENST00000257430	NM_000038.5	653	aGg/aAg	15/16	1	2	FACETS	0.768	0.685	0.857	0.768	0.685	0.857	SUBCLONAL	1	TRUE	1	0.617924089701981	2		278	358	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197716	123197716	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	141	342	2	ENST00000218089.9:c.1840C>T	p.Arg614Ter	p.R614*	ENST00000218089	NM_001042749.1	614	Cga/Tga	20/35	0.525987817179565	4	FACETS	0.803	0.731	0.879	0.402	0.365	0.44	CLONAL	1	TRUE	2	0.617924089701981	4		344	919	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554725	63554726	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0006861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	135	133	0	ENST00000307078.5:c.13_14del	p.Met5ValfsTer14	p.M5Vfs*14	ENST00000307078	NM_004655.3	5	ATg/g	2/11	1	2	FACETS	0.881	0.806	0.959	0.881	0.806	0.959	CLONAL	1	TRUE	1	0.617924089701981	2		133	496	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233793	133233794	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1555225149	NA	P-0006861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	346	354	0	ENST00000320574.5:c.3510dup	p.Leu1171ThrfsTer6	p.L1171Tfs*6	ENST00000320574	NM_006231.2	1170	-/A	29/49	1	2	FACETS	0.933	0.883	0.984	0.933	0.883	0.984	CLONAL	1	TRUE	1	0.617924089701981	2		354	1200	SUCCESS
APC	324	MSKCC	GRCh37	5	112175363	112175366	+	stop_gained	Nonsense_Mutation	ONP	GCGA	GCGA	TCGT	novel	NA	P-0006861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	80	188	0	ENST00000257430.4:c.4072_4075delinsTCGT	p.Ala1358_Lys1359delinsSerTer	p.A1358_K1359delinsS*	ENST00000257430	NM_000038.5	1358	GCGAaa/TCGTaa	16/16	1	2	FACETS	0.729	0.647	0.817	0.729	0.647	0.817	SUBCLONAL	1	TRUE	1	0.617924089701981	2		188	355	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286240	66286240	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006925-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	208	415	0	ENST00000273854.3:c.1446A>C	p.Lys482Asn	p.K482N	ENST00000273854	NM_004439.5	482	aaA/aaC	6/18	1	2	FACETS	0.861	0.798	0.926	0.861	0.798	0.926	CLONAL	1	TRUE	1	0.438244973180019	2		415	1103	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254705	46254706	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0006925-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	232	472	0	ENST00000334344.6:c.4896dup	p.Met1633HisfsTer8	p.M1633Hfs*8	ENST00000334344	NM_152641.2	1632	ttc/ttCc	16/21	NA	2	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.438244973180019	2		472	953	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436412	52436412	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006925-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	111	389	0	ENST00000460680.1:c.2082del	p.Asn695ThrfsTer41	p.N695Tfs*41	ENST00000460680	NM_004656.3	694	caG/ca	17/17	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.438244973180019	2		389	457	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637163	176637163	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	65	292	0	ENST00000439151.2:c.1763A>C	p.Asp588Ala	p.D588A	ENST00000439151	NM_022455.4	588	gAc/gCc	5/23	NA	2	FACETS	0.861	0.746	0.985			1	INDETERMINATE	1	TRUE	NA	0.255997170623688	2		292	590	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673744	176673744	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784118	NA	P-0007056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	57	481	1	ENST00000439151.2:c.4444C>T	p.Gln1482Ter	p.Q1482*	ENST00000439151	NM_022455.4	1482	Cag/Tag	10/23	NA	2	FACETS	0.444	0.379	0.515			1	INDETERMINATE	1	TRUE	NA	0.255997170623688	2		482	1003	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0007423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	18	138	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.299577110944614	4	FACETS	0.972	0.754	1			1	CLONAL	2	TRUE	NA	0.39	4		138	66	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115704	8115705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1564405153	NA	P-0007423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	63	376	0	ENST00000346208.3:c.1052dup	p.Asn351LysfsTer20	p.N351Kfs*20	ENST00000346208		350	-/A	6/6	0.304837425403244	4	FACETS	1	0.937	1	1	0.937	1	CLONAL	3	TRUE	1	0.39	4		376	139	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112399	115112400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0007423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	21	194	0	ENST00000257566.3:c.1340dup	p.Gly448ArgfsTer244	p.G448Rfs*244	ENST00000257566	NM_016569.3	447	cgc/cgGc	7/8	1	2	FACETS	0.945	0.758	1	1	0.946	1	CLONAL	2	TRUE	1	0.39	2		194	57	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063703	67063704	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0007423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	18	236	0	ENST00000412916.2:c.152_153del	p.Gly51AlafsTer31	p.G51Afs*31	ENST00000412916		51	gGC/g	2/6	0.240837880644026	1	FACETS	1	0.848	1	1	0.947	1	CLONAL	2	TRUE	0	0.39	1		236	35	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177371	56177402	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGTAATGAATGTTTTTTTCTTTCAGGTATAA	TGGTAATGAATGTTTTTTTCTTTCAGGTATAA	CCTGAAAGAAAAAAACATTCATT	novel	NA	P-0007423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	38	237	0	ENST00000399503.3:c.2370-26_2375delinsCCTGAAAGAAAAAAACATTCATT		p.X790_splice	ENST00000399503	NM_005921.1	790		14/20	0.304837425403244	6	FACETS	1	0.901	1	0.81	0.689	0.938	CLONAL	3	TRUE	2	0.39	6		237	107	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0007564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	186	266	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.653302735398502	2		266	564	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	277	254	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.653302735398502	3	FACETS	0.942	0.893	0.992	0.942	0.893	0.992	CLONAL	2	TRUE	1	0.653302735398502	3		254	597	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184101	56184101	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	363	441	0	ENST00000399503.3:c.4306G>A	p.Gly1436Ser	p.G1436S	ENST00000399503	NM_005921.1	1436	Ggc/Agc	19/20	0.653302735398502	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.653302735398502	3		441	713	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160703	56160704	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0007564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	202	455	0	ENST00000399503.3:c.980dup	p.Leu328ProfsTer10	p.L328Pfs*10	ENST00000399503	NM_005921.1	326	tct/tcTt	4/20	0.653302735398502	3	FACETS	0.996	0.925	1	0.498	0.462	0.535	CLONAL	1	TRUE	1	0.653302735398502	3		455	824	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0007575-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	228	305	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.537411678957104	2	FACETS	0.928	0.877	0.979	0.928	0.877	0.979	CLONAL	2	TRUE	0	0.555634234119146	2		305	442	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149604	202149604	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007575-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	194	338	0	ENST00000358485.4:c.1045G>C	p.Glu349Gln	p.E349Q	ENST00000358485	NM_001080125.1	349	Gag/Cag	8/9	0.555634234119146	4	FACETS	1	0.98	1	0.386	0.357	0.417	CLONAL	1	TRUE	1	0.555634234119146	4		338	937	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86676366	86676366	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007575-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	338	355	0	ENST00000274376.6:c.2644C>T	p.Gln882Ter	p.Q882*	ENST00000274376	NM_002890.2	882	Cag/Tag	20/25	0.537411678957104	2	FACETS	0.975	0.932	1	0.975	0.932	1	CLONAL	2	TRUE	0	0.555634234119146	2		355	624	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197402	94197402	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007575-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	64	341	0	ENST00000323929.3:c.1102G>T	p.Asp368Tyr	p.D368Y	ENST00000323929	NM_005591.3	368	Gac/Tac	11/20	0.537318218014027	3	FACETS	0.459	0.397	0.526	0.229	0.198	0.263	SUBCLONAL	1	TRUE	1	0.555634234119146	3		341	642	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136988	11136988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007575-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	147	409	0	ENST00000358026.2:c.3181G>A	p.Glu1061Lys	p.E1061K	ENST00000358026	NM_001128849.1	1061	Gag/Aag	23/36	0.535207433030269	4	FACETS	0.865	0.789	0.944	0.432	0.394	0.472	CLONAL	1	TRUE	2	0.555634234119146	4		409	952	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260603	16260609	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGGAT	GCCGGAT	-	novel	NA	P-0007575-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	128	352	0	ENST00000375759.3:c.7871_7877del	p.Arg2624LeufsTer12	p.R2624Lfs*12	ENST00000375759	NM_015001.2	2623	aGCCGGATg/ag	11/15	0.555634234119146	3	FACETS	0.867	0.787	0.951	0.434	0.393	0.476	CLONAL	1	TRUE	1	0.555634234119146	3		352	679	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	163	408	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.412195070080602	2		408	775	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204864	NA	P-0007628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	448	321	1	ENST00000371953.3:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000371953	NM_000314.4	171	Cag/Tag	6/9	0.406566604278092	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	0	0.412195070080602	3		322	833	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17124931	17124931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372304384	NA	P-0007628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	99	238	0	ENST00000285071.4:c.791C>T	p.Ala264Val	p.A264V	ENST00000285071	NM_144997.5	264	gCg/gTg	8/14	1	2	FACETS	0.972	0.872	1	0.972	0.872	1	CLONAL	1	TRUE	1	0.412195070080602	2		238	494	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30090772	30090772	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	156	413	1	ENST00000338641.4:c.1769C>A	p.Ala590Asp	p.A590D	ENST00000338641	NM_000268.3	590	gCc/gAc	16/16	1	2	FACETS	0.964	0.884	1	0.964	0.884	1	CLONAL	1	TRUE	1	0.412195070080602	2		414	785	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591109	67591110	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGACCTTAT	novel	NA	P-0007628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	203	315	0	ENST00000274335.5:c.1704_1713dup	p.Gln572ArgfsTer33	p.Q572Rfs*33	ENST00000274335		568	cca/cCAGACCTTATca	12/15	0.403374259550891	3	FACETS	0.755	0.701	0.81	0.755	0.701	0.81	SUBCLONAL	2	TRUE	1	0.412195070080602	3		315	787	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118864	70118867	+	frameshift_variant	Frame_Shift_Del	DEL	CTGA	CTGA	-	novel	NA	P-0007628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	147	331	0	ENST00000245479.2:c.436_439del	p.Leu146ThrfsTer36	p.L146Tfs*36	ENST00000245479	NM_000346.3	146	CTGAac/ac	2/3	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.412195070080602	2		331	673	SUCCESS
APC	324	MSKCC	GRCh37	5	112170822	112170822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1114167575	NA	P-0007772-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	10	661	1	ENST00000257430.4:c.1918C>T	p.Arg640Trp	p.R640W	ENST00000257430	NM_000038.5	640	Cgg/Tgg	15/16	1	2	FACETS	0.439	0.297	0.617	0.439	0.297	0.617	SUBCLONAL	1	FALSE	1	0.247613249764742	2		662	184	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606245	93606245	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140421546	NA	P-0007772-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	10	663	1	ENST00000375746.1:c.65G>A	p.Arg22Gln	p.R22Q	ENST00000375746	NM_001174167.1	22	cGg/cAg	2/14	1	2	FACETS	0.454	0.307	0.637	0.454	0.307	0.637	SUBCLONAL	1	FALSE	1	0.247613249764742	2		664	178	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121438954	121438954	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1316999782	NA	P-0007772-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	10	743	0	ENST00000257555.6:c.1855G>A	p.Glu619Lys	p.E619K	ENST00000257555		619	Gag/Aag	10/10	0.152196174984139	0	FACETS	0.305	0.207	0.43			1	SUBCLONAL	1	FALSE	0	0.247613249764742	0		743	199	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	112	456	0				ENST00000310581	NM_198253.2	-/1132			0.203505354740811	4	FACETS	0.905	0.818	0.996	1	0.981	1	CLONAL	3	TRUE	2	0.203505354740811	4		456	488	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180528	56180528	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs371578161	NA	P-0007981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	163	336	0	ENST00000399503.3:c.3857A>T	p.Glu1286Val	p.E1286V	ENST00000399503	NM_005921.1	1286	gAa/gTa	16/20	0.203505354740811	4	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	2	0.203505354740811	4		336	948	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423413	116423413	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913247	NA	P-0007981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	414	402	0	ENST00000397752.3:c.3688T>C	p.Tyr1230His	p.Y1230H	ENST00000397752	NM_000245.2	1230	Tat/Cat	19/21	0.203505354740811	6	FACETS	1	0.974	1	1	0.974	1	CLONAL	4	TRUE	2	0.203505354740811	6		402	1381	SUCCESS
EED	8726	MSKCC	GRCh37	11	85963229	85963229	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	186	363	0	ENST00000263360.6:c.307T>A	p.Trp103Arg	p.W103R	ENST00000263360	NM_003797.3	103	Tgg/Agg	3/12	0.192454140243283	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.203505354740811	2		363	813	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723100	49723101	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0007981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	80	203	0	ENST00000449682.2:c.1314_1315dup	p.Asp439GlyfsTer88	p.D439Gfs*88	ENST00000449682	NM_020998.3	439	gat/gGGat	11/18	0.203505354740811	3	FACETS	0.757	0.667	0.853	0.757	0.667	0.853	SUBCLONAL	2	TRUE	1	0.203505354740811	3		203	572	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0007999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	86	225	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.825	0.73	0.926	0.825	0.73	0.926	CLONAL	1	TRUE	1	0.32135653870777	2		225	649	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156968	89156968	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	179	229	0	ENST00000336596.2:c.70C>A	p.Pro24Thr	p.P24T	ENST00000336596	NM_005233.5	24	Ccg/Acg	1/17	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.32135653870777	2		229	837	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999711	100999711	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	234	587	0	ENST00000325455.5:c.91C>A	p.Pro31Thr	p.P31T	ENST00000325455	NM_001202474.3	31	Cca/Aca	1/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.32135653870777	2		587	1305	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0007999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	176	433	2	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.32135653870777	2		435	1087	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829889	72829889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1179466504	NA	P-0007999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1217	263	698	3	ENST00000268489.5:c.6692C>T	p.Pro2231Leu	p.P2231L	ENST00000268489	NM_006885.3	2231	cCg/cTg	9/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.32135653870777	2		701	1480	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670066	29670066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	176	507	0	ENST00000356175.3:c.7039G>A	p.Glu2347Lys	p.E2347K	ENST00000356175	NM_000267.3	2347	Gag/Aag	47/57	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.32135653870777	2		507	963	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920463	50920463	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	127	413	0	ENST00000440232.2:c.3155C>G	p.Ser1052Trp	p.S1052W	ENST00000440232	NM_002691.3	1052	tCg/tGg	26/27	0.278577819553318	3	FACETS	0.986	0.893	1	0.329	0.297	0.362	CLONAL	1	TRUE	0	0.32135653870777	3		413	930	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356741	70356741	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1372	81	560	0	ENST00000374080.3:c.5413G>T	p.Gly1805Cys	p.G1805C	ENST00000374080		1805	Ggc/Tgc	38/45	1	2	FACETS	0.347	0.304	0.393	0.347	0.304	0.393	SUBCLONAL	1	TRUE	1	0.32135653870777	2		560	1453	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916937	+	inframe_deletion	In_Frame_Del	DEL	GGCAACCGT	GGCAACCGT	-	novel	NA	P-0007999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	163	696	0	ENST00000263967.3:c.317_325del	p.Gly106_Arg108del	p.G106_R108del	ENST00000263967	NM_006218.2	106	GGCAACCGT/-	2/21	1	2	FACETS	0.878	0.804	0.955	0.878	0.804	0.955	CLONAL	1	TRUE	1	0.32135653870777	2		696	1156	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435160	56435161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755128667	NA	P-0007999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	78	261	0	ENST00000407977.2:c.1976dup	p.Pro660SerfsTer87	p.P660Sfs*87	ENST00000407977		659	ggt/ggGt	9/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.32135653870777	2		261	384	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835700	68835700	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	221	485	0	ENST00000261769.5:c.293del	p.Phe98SerfsTer19	p.F98Sfs*19	ENST00000261769	NM_004360.3	97	caT/ca	3/16	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.32135653870777	2		485	1353	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0008002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	247	162	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.283113636070348	6	FACETS	0.98	0.924	1			1	CLONAL	5	TRUE	NA	0.283113636070348	6		162	558	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99154374	99154374	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	74	363	1	ENST00000074304.5:c.516G>T	p.Gln172His	p.Q172H	ENST00000074304	NM_001134224.1	172	caG/caT	8/26	1	2	FACETS	0.581	0.508	0.661	0.581	0.508	0.661	SUBCLONAL	1	TRUE	1	0.283113636070348	2		364	899	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748240	41748240	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	84	432	0	ENST00000226382.2:c.529G>A	p.Asp177Asn	p.D177N	ENST00000226382	NM_003924.3	177	Gac/Aac	3/3	1	2	FACETS	0.659	0.58	0.743	0.659	0.58	0.743	SUBCLONAL	1	TRUE	1	0.283113636070348	2		432	901	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129887	55129887	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	145	488	0	ENST00000257290.5:c.421G>C	p.Glu141Gln	p.E141Q	ENST00000257290	NM_006206.4	141	Gag/Cag	4/23	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.283113636070348	2		488	974	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530453	187530453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	64	309	0	ENST00000441802.2:c.10090G>A	p.Gly3364Arg	p.G3364R	ENST00000441802	NM_005245.3	3364	Gga/Aga	16/27	1	2	FACETS	0.624	0.539	0.715	0.624	0.539	0.715	SUBCLONAL	1	TRUE	1	0.283113636070348	2		309	725	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849867	151849867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	54	300	1	ENST00000262189.6:c.12449G>A	p.Gly4150Glu	p.G4150E	ENST00000262189	NM_170606.2	4150	gGa/gAa	49/59	0.240001019553322	2	FACETS	0.503	0.429	0.585	0.252	0.214	0.293	SUBCLONAL	1	TRUE	0	0.283113636070348	2		301	758	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38283765	38283765	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0008002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	47	305	0	ENST00000425967.3:c.715-2A>C		p.X239_splice	ENST00000425967	NM_001174067.1	239			1	2	FACETS	0.543	0.458	0.638	0.543	0.458	0.638	SUBCLONAL	1	TRUE	1	0.283113636070348	2		305	611	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405851	70405851	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	216	471	0	ENST00000373644.4:c.3365C>A	p.Thr1122Lys	p.T1122K	ENST00000373644	NM_030625.2	1122	aCa/aAa	4/12	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.283113636070348	2		471	1110	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195866	102195866	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	189	649	2	ENST00000263464.3:c.626G>T	p.Gly209Val	p.G209V	ENST00000263464	NM_001165.4	209	gGt/gTt	2/9	0.240001019553322	2	FACETS	1	0.978	1	0.577	0.532	0.624	CLONAL	1	TRUE	0	0.283113636070348	2		651	1157	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375222	118375222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	69	372	1	ENST00000534358.1:c.8615C>T	p.Ser2872Leu	p.S2872L	ENST00000534358	NM_005933.3	2872	tCa/tTa	27/36	0.240001019553322	2	FACETS	0.67	0.582	0.764	0.335	0.291	0.382	SUBCLONAL	1	TRUE	0	0.283113636070348	2		373	728	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566158	95566158	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	45	292	0	ENST00000393063.1:c.4165C>G	p.Gln1389Glu	p.Q1389E	ENST00000393063	NM_030621.3	1389	Caa/Gaa	23/28	0.283113636070348	1	FACETS	0.475	0.399	0.56	0.475	0.399	0.56	SUBCLONAL	1	TRUE	0	0.283113636070348	1		292	574	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000025	42000025	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1223	192	647	0	ENST00000219905.7:c.2288G>A	p.Trp763Ter	p.W763*	ENST00000219905	NM_001164273.1	763	tGg/tAg	6/24	1	2	FACETS	0.959	0.884	1	0.959	0.884	1	CLONAL	1	TRUE	1	0.283113636070348	2		647	1415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578531	7578531	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	112	318	0	ENST00000269305.4:c.399G>T	p.Met133Ile	p.M133I	ENST00000269305	NM_001126112.2	133	atG/atT	5/11	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.283113636070348	2		318	772	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733038	74733038	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	202	444	0	ENST00000359995.5:c.205G>C	p.Glu69Gln	p.E69Q	ENST00000359995	NM_001195427.1	69	Gag/Cag	1/3	0.279957825940678	3	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.283113636070348	3		444	1087	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2208953	2208953	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	104	463	0	ENST00000398665.3:c.983G>T	p.Ser328Ile	p.S328I	ENST00000398665	NM_032482.2	328	aGt/aTt	12/28	0.283113636070348	1	FACETS	0.629	0.562	0.7	0.629	0.562	0.7	SUBCLONAL	1	TRUE	0	0.283113636070348	1		463	1003	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578527	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0008002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	109	319	0	ENST00000269305.4:c.403dup	p.Cys135LeufsTer14	p.C135Lfs*14	ENST00000269305	NM_001126112.2	135	tgc/tTgc	5/11	1	2	FACETS	0.994	0.892	1	0.994	0.892	1	CLONAL	1	TRUE	1	0.283113636070348	2		319	775	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971180	21971180	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	27	74	0	ENST00000304494.5:c.178del	p.Ala60ArgfsTer86	p.A60Rfs*86	ENST00000304494	NM_000077.4	60	Gcg/cg	2/3	0.283113636070348	1	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	0	0.283113636070348	1		74	138	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	85	302	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	1	2	FACETS	0.715	0.631	0.805	0.715	0.631	0.805	SUBCLONAL	1	TRUE	1	0.283113636070348	2		302	840	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643328	52643328	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0008053-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	35	560	0	ENST00000394830.3:c.2567+1G>C		p.X856_splice	ENST00000394830	NM_018313.4	856			1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		560	470	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191582	10191583	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0008053-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	53	642	0	ENST00000256474.2:c.578dup	p.Asn193LysfsTer63	p.N193Kfs*63	ENST00000256474	NM_000551.3	192	cca/ccAa	3/3	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		642	848	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165229	47165229	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008053-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	45	579	0	ENST00000409792.3:c.897del	p.Leu300Ter	p.L300*	ENST00000409792	NM_014159.6	299	agT/ag	3/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		579	640	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0008126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	335	442	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.939	0.888	0.993	0.939	0.888	0.993	CLONAL	1	TRUE	1	0.548575822761965	2		442	1300	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123615	108123616	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs786202474	NA	P-0008126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	126	369	0	ENST00000278616.4:c.1880dup	p.Gln628ProfsTer7	p.Q628Pfs*7	ENST00000278616	NM_000051.3	625	aat/aaTt	12/63	0.269924127075263	1	FACETS	0.342	0.309	0.376	0.342	0.309	0.376	INDETERMINATE	1	TRUE	0	0.548575822761965	1		369	976	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205735	108205735	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555127102	NA	P-0008126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	342	427	0	ENST00000278616.4:c.8050C>T	p.Gln2684Ter	p.Q2684*	ENST00000278616	NM_000051.3	2684	Cag/Tag	55/63	0.269924127075263	1	FACETS	0.815	0.772	0.859	0.815	0.772	0.859	INDETERMINATE	1	TRUE	0	0.548575822761965	1		427	1110	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680751	88680751	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	316	398	0	ENST00000360948.2:c.506G>T	p.Arg169Leu	p.R169L	ENST00000360948	NM_001012338.2	169	cGc/cTc	6/19	0.548575822761965	1	FACETS	0.985	0.933	1	0.985	0.933	1	CLONAL	1	TRUE	0	0.548575822761965	1		398	849	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207081	1207081	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs137854584	NA	P-0008126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	327	406	1	ENST00000326873.7:c.169G>T	p.Glu57Ter	p.E57*	ENST00000326873	NM_000455.4	57	Gaa/Taa	1/10	0.548575822761965	1	FACETS	0.903	0.855	0.952	0.903	0.855	0.952	CLONAL	1	TRUE	0	0.548575822761965	1		407	958	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0008169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	83	246	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.332574241687388	6	FACETS	0.947	0.839	1	0.473	0.419	0.531	CLONAL	2	TRUE	2	0.332574241687388	6		246	439	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0008169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	139	621	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.288672425460853	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.332574241687388	2		623	385	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248371	212248371	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	45	426	0	ENST00000342788.4:c.3896C>T	p.Pro1299Leu	p.P1299L	ENST00000342788	NM_005235.2	1299	cCa/cTa	28/28	0.332574241687388	3	FACETS	0.759	0.639	0.891	0.379	0.319	0.446	SUBCLONAL	1	TRUE	1	0.332574241687388	3		426	416	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032034	26032034	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	74	951	0	ENST00000244661.2:c.255C>G	p.Phe85Leu	p.F85L	ENST00000244661	NM_003537.3	85	ttC/ttG	1/1	0.220540827915752	3	FACETS	0.855	0.749	0.969	0.428	0.374	0.485	CLONAL	1	TRUE	1	0.332574241687388	3		951	607	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626871	14626871	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	91	790	0	ENST00000254322.2:c.904C>T	p.Leu302Phe	p.L302F	ENST00000254322	NM_006145.1	302	Ctc/Ttc	3/3	0.303245992990095	3	FACETS	1	0.943	1			1	CLONAL	1	TRUE	NA	0.332574241687388	3		790	583	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914859	32914860	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359577	NA	P-0008169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	72	894	1	ENST00000380152.3:c.6373dup	p.Thr2125AsnfsTer4	p.T2125Nfs*4	ENST00000380152		2123	gaa/gAaa	11/27	0.332574241687388	1	FACETS	0.597	0.521	0.678	0.597	0.521	0.678	SUBCLONAL	1	TRUE	0	0.332574241687388	1		895	605	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434623	99434624	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0008169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	37	308	2	ENST00000268035.6:c.710_711delinsTT	p.Gly237Val	p.G237V	ENST00000268035	NM_000875.3	237	gGC/gTT	3/21	0.288672425460853	2	FACETS	0.89	0.738	1	0.445	0.369	0.529	CLONAL	1	TRUE	0	0.332574241687388	2		310	250	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610694	52610694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753432959	NA	P-0008207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	501	498	0	ENST00000394830.3:c.3479G>A	p.Arg1160Gln	p.R1160Q	ENST00000394830	NM_018313.4	1160	cGa/cAa	23/30	0.605619392631244	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.605800637726044	2		498	774	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438345	110438345	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	15	58	0	ENST00000375856.3:c.56A>C	p.Asn19Thr	p.N19T	ENST00000375856	NM_003749.2	19	aAc/aCc	1/2	1	2	FACETS	0.786	0.591	1	0.786	0.591	1	CLONAL	1	TRUE	1	0.605800637726044	2		58	63	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347924	347924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756071423	NA	P-0008207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	329	662	0	ENST00000262320.3:c.1582G>A	p.Gly528Ser	p.G528S	ENST00000262320	NM_003502.3	528	Ggc/Agc	6/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.605800637726044	2		662	1048	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591118	67591129	+	inframe_deletion	In_Frame_Del	DEL	ATCCAGCTGAGA	ATCCAGCTGAGA	-	novel	NA	P-0008207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	138	376	0	ENST00000274335.5:c.1712_1723del	p.Ile571_Arg574del	p.I571_R574del	ENST00000274335		571	ATCCAGCTGAGA/-	12/15	1	2	FACETS	0.732	0.669	0.799	0.732	0.669	0.799	SUBCLONAL	1	TRUE	1	0.605800637726044	2		376	622	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998514	100998515	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0008207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	242	513	0	ENST00000325455.5:c.1287dup	p.Thr430AspfsTer144	p.T430Dfs*144	ENST00000325455	NM_001202474.3	429	-/G	1/8	0.570144076731631	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.605800637726044	1		513	545	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249009	55249010	+	inframe_insertion	In_Frame_Ins	INS	-	-	GACAACCCC	novel	NA	P-0008207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	346	428	0	ENST00000275493.2:c.2308_2316dup	p.Asp770_Pro772dup	p.D770_P772dup	ENST00000275493	NM_005228.3	770	-/GACAACCCC	20/28	0.605800637726044	3	FACETS	0.761	0.722	0.8	0.761	0.722	0.8	SUBCLONAL	2	TRUE	1	0.605800637726044	3		428	978	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	146	266	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.937	0.855	1	0.937	0.855	1	CLONAL	1	TRUE	1	0.366745237593421	2		266	850	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	258	367	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.349261588542907	2	FACETS	0.898	0.845	0.953	0.898	0.845	0.953	CLONAL	2	TRUE	0	0.366745237593421	2		367	783	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	73	179	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.801	0.702	0.907	0.801	0.702	0.907	CLONAL	1	TRUE	1	0.366745237593421	2		179	497	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	106	176	0	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.902	0.81	0.999	0.902	0.81	0.999	CLONAL	1	TRUE	1	0.366745237593421	2		176	641	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074217	8074217	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372669618	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1436	258	1172	4	ENST00000377482.5:c.442C>T	p.Arg148Trp	p.R148W	ENST00000377482	NM_018948.3	148	Cgg/Tgg	4/4	1	2	FACETS	0.831	0.775	0.888	0.831	0.775	0.888	CLONAL	1	TRUE	1	0.366745237593421	2		1176	1694	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881363	111881363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	309	561	2	ENST00000393256.3:c.41G>A	p.Arg14Gln	p.R14Q	ENST00000393256	NM_006538.4	14	cGa/cAa	2/4	NA	2	FACETS	0.854	0.806	0.902			1	INDETERMINATE	2	TRUE	NA	0.366745237593421	2		563	987	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158627002	158627002	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	247	944	0	ENST00000263640.3:c.668G>T	p.Trp223Leu	p.W223L	ENST00000263640	NM_001105.4	223	tGg/tTg	7/11	0.349261588542907	2	FACETS	0.957	0.892	1	0.478	0.446	0.512	CLONAL	1	TRUE	0	0.366745237593421	2		944	1408	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042536	37042536	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63751221	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	324	658	0	ENST00000231790.2:c.298C>T	p.Arg100Ter	p.R100*	ENST00000231790	NM_000249.3	100	Cga/Tga	3/19	0.349261588542907	2	FACETS	0.89	0.842	0.938	0.89	0.842	0.938	CLONAL	2	TRUE	0	0.366745237593421	2		658	993	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196838	106196838	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	124	527	0	ENST00000380013.4:c.5171A>G	p.Tyr1724Cys	p.Y1724C	ENST00000380013	NM_001127208.2	1724	tAt/tGt	11/11	1	2	FACETS	0.785	0.71	0.865	0.785	0.71	0.865	SUBCLONAL	1	TRUE	1	0.366745237593421	2		527	861	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081567	143081567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	167	597	0	ENST00000262992.4:c.1507G>A	p.Val503Met	p.V503M	ENST00000262992	NM_001101669.1	503	Gtg/Atg	15/24	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.366745237593421	2		597	910	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519219	187519219	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	55	556	1	ENST00000441802.2:c.12164C>A	p.Pro4055Gln	p.P4055Q	ENST00000441802	NM_005245.3	4055	cCg/cAg	23/27	1	2	FACETS	0.365	0.311	0.425	0.365	0.311	0.425	SUBCLONAL	1	TRUE	1	0.366745237593421	2		557	821	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629103	86629103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753769946	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	107	475	0	ENST00000274376.6:c.848G>A	p.Arg283His	p.R283H	ENST00000274376	NM_002890.2	283	cGt/cAt	4/25	1	2	FACETS	0.763	0.684	0.846	0.763	0.684	0.846	SUBCLONAL	1	TRUE	1	0.366745237593421	2		475	765	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	126	330	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.949	0.86	1	0.949	0.86	1	CLONAL	1	TRUE	1	0.366745237593421	2		330	724	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431646	6431646	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	112	377	0	ENST00000356142.4:c.199T>A	p.Leu67Ile	p.L67I	ENST00000356142	NM_018890.3	67	Tta/Ata	3/7	0.350167937017654	3	FACETS	1	0.955	1	0.552	0.497	0.61	CLONAL	1	TRUE	1	0.366745237593421	3		377	655	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860143	151860143	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs747835958	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	140	380	4	ENST00000262189.6:c.10519C>T	p.Arg3507Ter	p.R3507*	ENST00000262189	NM_170606.2	3507	Cga/Tga	43/59	0.350167937017654	3	FACETS	1	0.925	1	0.509	0.463	0.557	CLONAL	1	TRUE	1	0.366745237593421	3		384	888	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209340	98209340	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	150	516	1	ENST00000331920.6:c.4198G>T	p.Gly1400Cys	p.G1400C	ENST00000331920	NM_000264.3	1400	Ggc/Tgc	23/24	0.366745237593421	3	FACETS	1	0.966	1	0.554	0.507	0.605	CLONAL	1	TRUE	1	0.366745237593421	3		517	873	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238357	98238357	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146616780	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	203	512	1	ENST00000331920.6:c.1687G>A	p.Ala563Thr	p.A563T	ENST00000331920	NM_000264.3	563	Gcg/Acg	12/24	0.366745237593421	3	FACETS	0.942	0.877	1	0.942	0.877	1	CLONAL	2	TRUE	1	0.366745237593421	3		513	695	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395218	139395218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs970443298	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	130	523	1	ENST00000277541.6:c.5720C>T	p.Pro1907Leu	p.P1907L	ENST00000277541	NM_017617.3	1907	cCg/cTg	31/34	0.366745237593421	3	FACETS	1	0.966	1	0.566	0.514	0.621	CLONAL	1	TRUE	1	0.366745237593421	3		524	741	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396823	139396823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs942439472	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	119	386	1	ENST00000277541.6:c.5285G>A	p.Arg1762Gln	p.R1762Q	ENST00000277541	NM_017617.3	1762	cGg/cAg	28/34	0.366745237593421	3	FACETS	1	0.985	1	0.741	0.672	0.814	CLONAL	1	TRUE	1	0.366745237593421	3		387	518	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399156	139399156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769050541	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	83	403	0	ENST00000277541.6:c.4987C>T	p.Arg1663Trp	p.R1663W	ENST00000277541	NM_017617.3	1663	Cgg/Tgg	26/34	0.366745237593421	3	FACETS	1	0.947	1	0.561	0.497	0.63	CLONAL	1	TRUE	1	0.366745237593421	3		403	477	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405696	139405696	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	62	583	0	ENST00000277541.6:c.2495C>A	p.Pro832Gln	p.P832Q	ENST00000277541	NM_017617.3	832	cCg/cAg	16/34	0.366745237593421	3	FACETS	0.512	0.441	0.589	0.256	0.22	0.295	SUBCLONAL	1	TRUE	1	0.366745237593421	3		583	782	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115685	108115685	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	102	383	0	ENST00000278616.4:c.833T>A	p.Val278Asp	p.V278D	ENST00000278616	NM_000051.3	278	gTc/gAc	7/63	1	2	FACETS	0.924	0.828	1	0.924	0.828	1	CLONAL	1	TRUE	1	0.366745237593421	2		383	602	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392801	118392801	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	137	542	0	ENST00000534358.1:c.11833T>C	p.Tyr3945His	p.Y3945H	ENST00000534358	NM_005933.3	3945	Tac/Cac	36/36	1	2	FACETS	0.896	0.815	0.981	0.896	0.815	0.981	CLONAL	1	TRUE	1	0.366745237593421	2		542	834	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56474086	56474086	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	38	492	0	ENST00000267101.3:c.2T>C	p.Met1?	p.M1?	ENST00000267101	NM_001982.3	1	aTg/aCg	1/28	0.349261588542907	2	FACETS	0.342	0.282	0.409	0.171	0.141	0.205	SUBCLONAL	1	TRUE	0	0.366745237593421	2		492	606	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487277	56487277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035001455	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	174	327	0	ENST00000267101.3:c.1423C>T	p.Arg475Trp	p.R475W	ENST00000267101	NM_001982.3	475	Cgg/Tgg	12/28	0.349261588542907	2	FACETS	0.861	0.798	0.926	0.861	0.798	0.926	CLONAL	2	TRUE	0	0.366745237593421	2		327	551	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110073	115110073	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	70	297	0	ENST00000257566.3:c.1805C>A	p.Pro602His	p.P602H	ENST00000257566	NM_016569.3	602	cCt/cAt	8/8	0.365912389203417	2	FACETS	1	0.891	1	0.509	0.446	0.576	CLONAL	1	TRUE	0	0.366745237593421	2		297	375	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906954	32906954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555281846	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	63	260	0	ENST00000380152.3:c.1339C>T	p.Pro447Ser	p.P447S	ENST00000380152		447	Cca/Tca	10/27	0.287897011614612	4	FACETS	0.707	0.611	0.812	0.354	0.305	0.406	SUBCLONAL	1	TRUE	2	0.366745237593421	4		260	664	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937368	32937368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555286958	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	125	394	1	ENST00000380152.3:c.8029G>A	p.Glu2677Lys	p.E2677K	ENST00000380152		2677	Gaa/Aaa	18/27	0.287897011614612	4	FACETS	1	0.935	1	0.522	0.472	0.574	CLONAL	1	TRUE	2	0.366745237593421	4		395	893	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434595	110434595	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs555841746	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	67	301	0	ENST00000375856.3:c.3806A>C	p.Gln1269Pro	p.Q1269P	ENST00000375856	NM_003749.2	1269	cAg/cCg	1/2	0.290623769962112	4	FACETS	0.908	0.79	1			1	CLONAL	1	TRUE	NA	0.366745237593421	4		301	550	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041041	42041041	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1246	242	1037	0	ENST00000219905.7:c.5419C>T	p.Gln1807Ter	p.Q1807*	ENST00000219905	NM_001164273.1	1807	Cag/Tag	16/24	0.366745237593421	2	FACETS	0.887	0.826	0.95	0.443	0.413	0.475	CLONAL	1	TRUE	0	0.366745237593421	2		1037	1488	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003812	45003812	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	262	419	0	ENST00000558401.1:c.67+1G>A		p.X23_splice	ENST00000558401	NM_004048.2	23			0.366745237593421	2	FACETS	0.857	0.805	0.909	0.857	0.805	0.909	CLONAL	2	TRUE	0	0.366745237593421	2		419	834	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727490	88727490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1222179640	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	254	446	2	ENST00000360948.2:c.289G>A	p.Val97Met	p.V97M	ENST00000360948	NM_001012338.2	97	Gtg/Atg	3/19	0.366745237593421	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.366745237593421	2		448	680	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3842097	3842097	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	109	349	0	ENST00000262367.5:c.1217-2A>G		p.X406_splice	ENST00000262367	NM_004380.2	406			1	2	FACETS	0.96	0.864	1	0.96	0.864	1	CLONAL	1	TRUE	1	0.366745237593421	2		349	619	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346436	89346436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369545274	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	193	924	3	ENST00000301030.4:c.6514G>A	p.Gly2172Arg	p.G2172R	ENST00000301030	NM_001256183.1	2172	Ggg/Agg	9/13	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.366745237593421	2		927	1042	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41219713	41219713	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs730881495	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	66	436	0	ENST00000357654.3:c.4987-1G>T		p.X1663_splice	ENST00000357654	NM_007294.3	1663			1	2	FACETS	0.521	0.452	0.596	0.521	0.452	0.596	SUBCLONAL	1	TRUE	1	0.366745237593421	2		436	691	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677977	58677977	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	69	343	0	ENST00000305921.3:c.202C>A	p.Pro68Thr	p.P68T	ENST00000305921	NM_003620.3	68	Cca/Aca	1/6	1	2	FACETS	0.851	0.744	0.967	0.851	0.744	0.967	CLONAL	1	TRUE	1	0.366745237593421	2		343	442	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985514	60985514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	140	542	4	ENST00000333681.4:c.386G>A	p.Arg129His	p.R129H	ENST00000333681		129	cGc/cAc	2/3	1	2	FACETS	0.864	0.786	0.945	0.864	0.786	0.945	CLONAL	1	TRUE	1	0.366745237593421	2		546	884	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098446	11098446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502089	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	80	385	1	ENST00000358026.2:c.964G>A	p.Ala322Thr	p.A322T	ENST00000358026	NM_001128849.1	322	Gcc/Acc	6/36	1	2	FACETS	0.976	0.863	1	0.976	0.863	1	CLONAL	1	TRUE	1	0.366745237593421	2		386	447	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302975	15302975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755339807	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	62	262	0	ENST00000263388.2:c.475G>A	p.Val159Met	p.V159M	ENST00000263388	NM_000435.2	159	Gtg/Atg	4/33	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.366745237593421	2		262	314	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955130	17955130	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs565783591	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	122	410	0	ENST00000458235.1:c.97C>T	p.Arg33Trp	p.R33W	ENST00000458235	NM_000215.3	33	Cgg/Tgg	2/24	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.366745237593421	2		410	547	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929472	44929472	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	271	469	2	ENST00000377967.4:c.2572G>T	p.Gly858Trp	p.G858W	ENST00000377967	NM_021140.2	858	Ggg/Tgg	17/29	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.366745237593421	1		471	824	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412110	63412110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852216	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	231	1181	1	ENST00000330258.3:c.1057C>T	p.Arg353Ter	p.R353*	ENST00000330258	NM_152424.3	353	Cga/Tga	2/2	1	1	FACETS	0.799	0.749	0.849	1	0.993	1	SUBCLONAL	2	TRUE	0	0.366745237593421	1		1182	644	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	109	457	1	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.963	0.867	1	0.963	0.867	1	CLONAL	1	TRUE	1	0.366745237593421	2		458	617	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647028	23647028	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1555461597	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	133	565	0	ENST00000261584.4:c.839del	p.Asn280ThrfsTer8	p.N280Tfs*8	ENST00000261584	NM_024675.3	280	aAc/ac	4/13	1	2	FACETS	0.784	0.711	0.861	0.784	0.711	0.861	SUBCLONAL	1	TRUE	1	0.366745237593421	2		565	925	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	74	549	0	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	0.349261588542907	2	FACETS	0.692	0.606	0.784	0.346	0.303	0.392	SUBCLONAL	1	TRUE	0	0.366745237593421	2		549	583	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	180	648	2	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	0.828	0.762	0.897	0.828	0.762	0.897	CLONAL	1	TRUE	1	0.366745237593421	2		650	1185	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023903	27023904	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	24	185	0	ENST00000324856.7:c.1015dup	p.Ala339GlyfsTer61	p.A339Gfs*61	ENST00000324856	NM_006015.4	337	tgg/tGgg	1/20	1	2	FACETS	0.476	0.374	0.593	0.476	0.374	0.593	SUBCLONAL	1	TRUE	1	0.366745237593421	2		185	275	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846307	156846308	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	130	615	2	ENST00000524377.1:c.1753dup	p.Leu585ProfsTer6	p.L585Pfs*6	ENST00000524377	NM_002529.3	583	cgc/cgCc	14/17	1	2	FACETS	0.872	0.791	0.957	0.872	0.791	0.957	CLONAL	1	TRUE	1	0.366745237593421	2		617	813	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238958	5238958	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	61	380	0	ENST00000357368.4:c.1821del	p.Val608TrpfsTer30	p.V608Wfs*30	ENST00000357368	NM_002850.3	607	ccC/cc	13/38	1	2	FACETS	0.798	0.69	0.914	0.798	0.69	0.914	CLONAL	1	TRUE	1	0.366745237593421	2		380	417	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903745	41903746	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	128	623	1	ENST00000372991.4:c.811dup	p.Arg271ProfsTer53	p.R271Pfs*53	ENST00000372991	NM_001760.3	271	cgg/cCgg	5/5	0.290623769962112	4	FACETS	0.833	0.753	0.918			1	CLONAL	1	TRUE	NA	0.366745237593421	4		624	1145	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923086	39923087	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	189	459	0	ENST00000378444.4:c.3621dup	p.Gln1208ThrfsTer8	p.Q1208Tfs*8	ENST00000378444	NM_001123385.1	1207	-/A	8/15	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.366745237593421	1		459	585	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161939	47161939	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	93	411	0	ENST00000409792.3:c.4187del	p.Asn1396MetfsTer16	p.N1396Mfs*16	ENST00000409792	NM_014159.6	1396	aAt/at	3/21	0.324591030902163	2	FACETS	0.741	0.66	0.829	0.371	0.33	0.415	SUBCLONAL	1	TRUE	0	0.366745237593421	2		411	684	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907283	32907283	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	135	448	0	ENST00000380152.3:c.1670del	p.Leu557Ter	p.L557*	ENST00000380152		556	aaT/aa	10/27	0.287897011614612	4	FACETS	0.924	0.838	1	0.462	0.419	0.507	CLONAL	1	TRUE	2	0.366745237593421	4		448	1089	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215361	41215361	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs34570933	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	145	625	0	ENST00000357654.3:c.5182del	p.Met1728CysfsTer2	p.M1728Cfs*2	ENST00000357654	NM_007294.3	1728	Atg/tg	18/23	1	2	FACETS	0.816	0.744	0.892	0.816	0.744	0.892	CLONAL	1	TRUE	1	0.366745237593421	2		625	969	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740623	58740624	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs763475304	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1367	241	1033	2	ENST00000305921.3:c.1535dup	p.Asn512LysfsTer16	p.N512Kfs*16	ENST00000305921	NM_003620.3	510	caa/cAaa	6/6	1	2	FACETS	0.817	0.761	0.876	0.817	0.761	0.876	CLONAL	1	TRUE	1	0.366745237593421	2		1035	1608	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099468	157099470	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	rs1429292576	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	118	502	0	ENST00000346085.5:c.413_415del	p.Asn138del	p.N138del	ENST00000346085	NM_020732.3	135	tcCAAc/tcc	1/20	0.366745237593421	3	FACETS	0.862	0.777	0.952	0.431	0.388	0.476	CLONAL	1	TRUE	1	0.366745237593421	3		502	883	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796882	42796883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761345552	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	124	727	0	ENST00000575354.2:c.3347dup	p.Ser1117LysfsTer34	p.S1117Kfs*34	ENST00000575354	NM_015125.3	1114	gcc/gCcc	14/20	1	2	FACETS	0.852	0.771	0.937	0.852	0.771	0.937	CLONAL	1	TRUE	1	0.366745237593421	2		727	794	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156320	106156321	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1296522926	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	108	380	0	ENST00000380013.4:c.1226dup	p.Pro410SerfsTer33	p.P410Sfs*33	ENST00000380013	NM_001127208.2	407	-/C	3/11	1	2	FACETS	0.883	0.794	0.978	0.883	0.794	0.978	CLONAL	1	TRUE	1	0.366745237593421	2		380	667	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033792	48033795	+	splice_donor_variant,intron_variant	Splice_Site	DEL	TAAC	TAAC	-	rs267608132	NA	P-0008226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	91	367	0	ENST00000234420.5:c.4001+12_4001+15del		p.X1334_splice	ENST00000234420	NM_000179.2	1334			0.366745237593421	2	FACETS	0.8	0.712	0.895	0.4	0.356	0.448	SUBCLONAL	1	TRUE	0	0.366745237593421	2		367	620	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435395	56435396	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGGC	novel	NA	P-0008232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	23	266	0	ENST00000407977.2:c.1737_1741dup	p.Pro581ArgfsTer121	p.P581Rfs*121	ENST00000407977		581	cct/cGCCTCct	9/10	0.3	4	FACETS	0.66	0.514	0.828			1	SUBCLONAL	1	TRUE	NA	0.27	4		266	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579391	7579392	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAGGGACAGAAGATGA	novel	NA	P-0008373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	236	347	0	ENST00000269305.4:c.280_295dup	p.Ser99PhefsTer55	p.S99Ffs*55	ENST00000269305	NM_001126112.2	99	tcc/tTCATCTTCTGTCCCTTcc	4/11	0.441025704872318	3	FACETS	0.847	0.795	0.901	0.565	0.53	0.601	CLONAL	2	FALSE	0	0.514304720982991	3		347	681	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436009	110436009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767024195	NA	P-0008552-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	163	199	0	ENST00000375856.3:c.2392G>A	p.Val798Ile	p.V798I	ENST00000375856	NM_003749.2	798	Gtt/Att	1/2	0.898633377392954	2	FACETS	1	0.978	1	0.554	0.517	0.59	CLONAL	1	TRUE	0	0.908473955450252	2		199	324	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs28934577	NA	P-0008552-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	403	257	0	ENST00000269305.4:c.770T>G	p.Leu257Arg	p.L257R	ENST00000269305	NM_001126112.2	257	cTg/cGg	7/11	0.908204367132877	3	FACETS	0.927	0.891	0.962	0.927	0.891	0.962	CLONAL	2	TRUE	1	0.908473955450252	3		257	696	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576885	7576885	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0008552-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	244	392	0	ENST00000269305.4:c.961A>T	p.Lys321Ter	p.K321*	ENST00000269305	NM_001126112.2	321	Aaa/Taa	9/11	0.908204367132877	3	FACETS	0.96	0.899	1	0.48	0.449	0.511	CLONAL	1	TRUE	1	0.908473955450252	3		392	814	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460504	8460504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148300682	NA	P-0008552-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	160	322	0	ENST00000356435.5:c.3782C>T	p.Thr1261Met	p.T1261M	ENST00000356435		1261	aCg/aTg	22/35	0.908473955450252	3	FACETS	0.84	0.773	0.908	0.42	0.386	0.454	CLONAL	1	TRUE	1	0.908473955450252	3		322	610	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025543	1025543	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008552-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	299	364	0	ENST00000358495.3:c.832C>T	p.Arg278Ter	p.R278*	ENST00000358495	NM_134424.2	278	Cga/Tga	9/12	0.81872757558855	4	FACETS	0.969	0.912	1			1	CLONAL	1	TRUE	NA	0.908473955450252	4		364	1296	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65568283	65568283	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008552-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	271	248	0	ENST00000358664.4:c.44A>G	p.Gln15Arg	p.Q15R	ENST00000358664	NM_002382.4	15	cAa/cGa	2/5	0.752974738495716	4	FACETS	0.808	0.762	0.854	0.808	0.762	0.854	CLONAL	2	TRUE	2	0.908473955450252	4		248	705	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110085	8110085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199630207	NA	P-0008552-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	128	188	0	ENST00000585124.1:c.520G>A	p.Glu174Lys	p.E174K	ENST00000585124	NM_004217.3	174	Gag/Aag	6/9	0.908204367132877	3	FACETS	0.99	0.905	1	0.495	0.452	0.539	CLONAL	1	TRUE	1	0.908473955450252	3		188	414	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	99	456	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		456	196	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0008563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	253	504	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.267091084321742	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.267091084321742	3		505	950	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937996	76938021	+	frameshift_variant	Frame_Shift_Del	DEL	TGGAAGCACTTGCTTGCTGCTTCTTA	TGGAAGCACTTGCTTGCTGCTTCTTA	-	novel	NA	P-0008563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	136	214	0	ENST00000373344.5:c.2727_2752del	p.Lys910Ter	p.K910*	ENST00000373344	NM_000489.3	909	ccTAAGAAGCAGCAAGCAAGTGCTTCCAct/ccct	9/35	0.237291391699892	2	FACETS	1	0.974	1			1	CLONAL	2	TRUE	NA	0.267091084321742	2		214	442	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138294	2138311	+	inframe_deletion	In_Frame_Del	DEL	CGGCTCCGCCACATCAAG	CGGCTCCGCCACATCAAG	-	rs137854218	NA	P-0008563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	160	349	0	ENST00000219476.3:c.5238_5255del	p.His1746_Arg1751del	p.H1746_R1751del	ENST00000219476	NM_000548.3	1743	CGGCTCCGCCACATCAAG/-	41/42	0.267091084321742	3	FACETS	1	0.981	1	0.625	0.572	0.68	CLONAL	1	TRUE	1	0.267091084321742	3		349	1087	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191488	10191488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs5030818	NA	P-0008566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	114	273	0	ENST00000256474.2:c.481C>T	p.Arg161Ter	p.R161*	ENST00000256474	NM_000551.3	161	Cga/Tga	3/3	0.37618977520707	1	FACETS	0.932	0.843	1	0.932	0.843	1	CLONAL	1	TRUE	0	0.37618977520707	1		273	528	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668750	52668750	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	113	401	0	ENST00000394830.3:c.1169del	p.Tyr390LeufsTer14	p.Y390Lfs*14	ENST00000394830	NM_018313.4	390	tAt/tt	12/30	0.37618977520707	1	FACETS	0.812	0.732	0.895	0.812	0.732	0.895	CLONAL	1	TRUE	0	0.37618977520707	1		401	601	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	435	456	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		456	775	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0008571-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	129	259	0	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.21	2		259	1038	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111982979	111982979	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008571-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2202	178	428	1	ENST00000368678.4:c.1568C>T	p.Ala523Val	p.A523V	ENST00000368678		523	gCg/gTg	13/13	1	2	FACETS	0.712	0.653	0.775	0.712	0.653	0.775	SUBCLONAL	1	TRUE	1	0.21	2		429	2380	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008573-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	53	456	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.892	0.766	1	0.892	0.766	1	CLONAL	1	TRUE	1	0.40844078249629	2		456	291	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0008573-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	102	553	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	0.40844078249629	2		553	439	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587780070	NA	P-0008573-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	77	176	0	ENST00000269305.4:c.535C>G	p.His179Asp	p.H179D	ENST00000269305	NM_001126112.2	179	Cat/Gat	5/11	0.214358143056284	2	FACETS	0.782	0.697	0.871	0.782	0.697	0.871	INDETERMINATE	2	TRUE	0	0.40844078249629	2		176	241	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069354	30069354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315501	NA	P-0008573-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	94	280	0	ENST00000338641.4:c.1219C>T	p.Gln407Ter	p.Q407*	ENST00000338641	NM_000268.3	407	Cag/Tag	12/16	0.390500194923241	1	FACETS	0.898	0.804	0.996	0.898	0.804	0.996	CLONAL	1	TRUE	0	0.40844078249629	1		280	408	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0008577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	22	138	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.211791004548586	4	FACETS	0.723	0.56	0.913	0.362	0.28	0.457	CLONAL	1	FALSE	2	0.211791004548586	4		138	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0008577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	157	328	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA	2	FACETS	0.966	0.887	1			1	INDETERMINATE	2	FALSE	NA	0.211791004548586	2		328	767	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0008577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	1718	318	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.211791004548586	30	FACETS	0.985	0.971	0.999			1	CLONAL	29	FALSE	NA	0.211791004548586	30		318	2251	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044892	47044892	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	109	381	0	ENST00000377604.3:c.2218G>T	p.Glu740Ter	p.E740*	ENST00000377604	NM_001204468.1	740	Gag/Tag	20/24	1	2	FACETS	0.931	0.839	1	1	0.987	1	CLONAL	2	FALSE	1	0.211791004548586	2		381	553	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149860	202149860	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0008577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	53	303	0	ENST00000358485.4:c.1301C>G	p.Ser434Ter	p.S434*	ENST00000358485	NM_001080125.1	434	tCa/tGa	8/9	0.211791004548586	3	FACETS	0.956	0.815	1	0.478	0.407	0.556	CLONAL	1	FALSE	1	0.211791004548586	3		303	579	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912286	29912286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	59	336	0	ENST00000376809.5:c.905C>T	p.Ser302Phe	p.S302F	ENST00000376809	NM_002116.7	302	tCc/tTc	5/8	0.211791004548586	3	FACETS	0.941	0.809	1	0.47	0.404	0.543	CLONAL	1	FALSE	1	0.211791004548586	3		336	655	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982021	93982021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867625037	NA	P-0008577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	44	390	0	ENST00000369303.4:c.1444G>A	p.Glu482Lys	p.E482K	ENST00000369303	NM_004440.3	482	Gag/Aag	6/17	0.172225415444569	1	FACETS	0.488	0.408	0.577	0.488	0.408	0.577	SUBCLONAL	1	FALSE	0	0.211791004548586	1		390	762	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515262	103515262	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	66	309	0	ENST00000355739.4:c.1763G>T	p.Ser588Ile	p.S588I	ENST00000355739	NM_000123.3	588	aGc/aTc	8/15	0.143247867597842	3	FACETS	1	0.928	1	0.368	0.319	0.421	CLONAL	1	FALSE	0	0.211791004548586	3		309	624	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207027	1207027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876658779	NA	P-0008577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	50	264	0	ENST00000326873.7:c.115C>T	p.Arg39Cys	p.R39C	ENST00000326873	NM_000455.4	39	Cgc/Tgc	1/10	NA	2	FACETS	1	0.941	1			1	INDETERMINATE	1	FALSE	NA	0.211791004548586	2		264	387	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259173	36259173	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	72	420	1	ENST00000300305.3:c.318G>A	p.Trp106Ter	p.W106*	ENST00000300305		106	tgG/tgA	3/8	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	FALSE	1	0.211791004548586	2		421	641	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0008579-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	62	385	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.654	0.564	0.753	0.654	0.564	0.753	SUBCLONAL	1	FALSE	1	0.238480579672087	2		385	795	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0008579-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	86	194	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	NA	2	FACETS	1	0.968	1			1	INDETERMINATE	1	FALSE	NA	0.238480579672087	2		194	570	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727453	66727453	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397516790	NA	P-0008579-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	41	317	0	ENST00000307102.5:c.169A>G	p.Lys57Glu	p.K57E	ENST00000307102	NM_002755.3	57	Aag/Gag	2/11	0.238480579672087	6	FACETS	0.798	0.664	0.949			1	CLONAL	1	FALSE	NA	0.238480579672087	6		317	636	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273974	10273974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773569899	NA	P-0008579-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	37	425	0	ENST00000330684.3:c.295G>A	p.Val99Met	p.V99M	ENST00000330684	NM_001134407.1	99	Gtg/Atg	2/13	0.171336239918305	1	FACETS	0.559	0.46	0.669	0.559	0.46	0.669	SUBCLONAL	1	FALSE	0	0.238480579672087	1		425	489	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028612	12028612	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008579-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	48	312	0	ENST00000353533.5:c.815C>T	p.Pro272Leu	p.P272L	ENST00000353533	NM_003010.3	272	cCt/cTt	8/11	0.237944698279621	3	FACETS	0.694	0.586	0.814	0.347	0.293	0.407	SUBCLONAL	1	FALSE	1	0.238480579672087	3		312	649	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577595	+	inframe_deletion	In_Frame_Del	DEL	AGTGGATGGTGGTAC	AGTGGATGGTGGTAC	-	novel	NA	P-0008579-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	25	242	0	ENST00000269305.4:c.686_700del	p.Cys229_His233del	p.C229_H233del	ENST00000269305	NM_001126112.2	229	tGTACCACCATCCACTac/tac	7/11	0.237944698279621	3	FACETS	0.489	0.384	0.61	0.244	0.192	0.305	SUBCLONAL	1	FALSE	1	0.238480579672087	3		242	480	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061190	38061190	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008592-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	59	241	0	ENST00000250448.2:c.799A>C	p.Lys267Gln	p.K267Q	ENST00000250448	NM_004496.3	267	Aag/Cag	2/2	1	2	FACETS	0.985	0.849	1	0.985	0.849	1	CLONAL	1	TRUE	1	0.262812871532764	2		241	456	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839743	42839743	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs936556491	NA	P-0008592-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	157	441	0	ENST00000398585.3:c.1496G>A	p.Gly499Asp	p.G499D	ENST00000398585	NM_001135099.1	499	gGt/gAt	13/14	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.262812871532764	2		441	1002	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793127	42793127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767142293	NA	P-0008597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	355	478	0	ENST00000575354.2:c.1019G>A	p.Arg340Gln	p.R340Q	ENST00000575354	NM_015125.3	340	cGg/cAg	7/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.599015868372196	2		478	1076	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0008598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	118	491	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.877	0.791	0.967	0.877	0.791	0.967	CLONAL	1	TRUE	1	0.344677009917457	2		491	781	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578266	7578266	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs942158624	NA	P-0008598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	170	466	1	ENST00000269305.4:c.583A>T	p.Ile195Phe	p.I195F	ENST00000269305	NM_001126112.2	195	Atc/Ttc	6/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.344677009917457	2		467	891	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717778	89717778	+	splice_donor_variant	Splice_Site	SNP	T	T	A	rs1114167665	NA	P-0008598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	52	125	0	ENST00000371953.3:c.801+2T>A		p.X267_splice	ENST00000371953	NM_000314.4	267			0.344677009917457	1	FACETS	0.939	0.806	1	0.939	0.806	1	CLONAL	1	TRUE	0	0.344677009917457	1		125	266	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164475	36164475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1442794209	NA	P-0008598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	74	225	2	ENST00000300305.3:c.1400C>T	p.Ala467Val	p.A467V	ENST00000300305		467	gCg/gTg	8/8	1	2	FACETS	0.946	0.831	1	0.946	0.831	1	CLONAL	1	TRUE	1	0.344677009917457	2		227	454	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0008599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	79	333	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.158784924427022	3	FACETS	1	0.971	1	0.69	0.605	0.782	CLONAL	1	TRUE	1	0.12	3		333	1011	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0008599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	26	207	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	1	2	FACETS	0.792	0.626	0.984	0.792	0.626	0.984	CLONAL	1	TRUE	1	0.12	2		207	547	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501595	149501595	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	32	192	0	ENST00000261799.4:c.2192C>A	p.Ser731Tyr	p.S731Y	ENST00000261799	NM_002609.3	731	tCc/tAc	16/23	1	2	FACETS	0.879	0.711	1	0.879	0.711	1	CLONAL	1	TRUE	1	0.12	2		192	607	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0008600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	243	399	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.615745401440267	2		399	759	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0008600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	258	542	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.954	0.896	1	0.954	0.896	1	CLONAL	1	TRUE	1	0.615745401440267	2		542	878	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022403	31022425	+	frameshift_variant	Frame_Shift_Del	DEL	CACCACTGCCATAGAGAGGCGGC	CACCACTGCCATAGAGAGGCGGC	-	rs766433101	NA	P-0008600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	92	186	0	ENST00000375687.4:c.1900_1922del	p.Glu635ArgfsTer15	p.E635Rfs*15	ENST00000375687	NM_015338.5	630	CACCACTGCCATAGAGAGGCGGCc/c	13/13	0.604188030627345	3	FACETS	0.737	0.657	0.823	0.369	0.328	0.412	SUBCLONAL	1	TRUE	1	0.615745401440267	3		186	530	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508741	29508741	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567826110	NA	P-0008600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	247	544	1	ENST00000356175.3:c.668G>A	p.Trp223Ter	p.W223*	ENST00000356175	NM_000267.3	223	tGg/tAg	7/57	0.615745401440267	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.615745401440267	1		545	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578181	7578181	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	470	539	0	ENST00000269305.4:c.668del	p.Pro223LeufsTer24	p.P223Lfs*24	ENST00000269305	NM_001126112.2	223	cCt/ct	6/11	0.615745401440267	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.615745401440267	1		539	971	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0008601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	419	464	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.383782046519904	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.383782046519904	1		464	1463	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0008601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	323	318	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.383782046519904	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.383782046519904	1		318	980	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210075	55210075	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	241	596	0	ENST00000275493.2:c.185T>G	p.Leu62Arg	p.L62R	ENST00000275493	NM_005228.3	62	cTt/cGt	2/28	0.383782046519904	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.383782046519904	1		596	904	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0008659-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	212	381	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.743625495842173	2		381	531	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458194	120458194	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745586179	NA	P-0008659-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	342	356	0	ENST00000256646.2:c.7151C>T	p.Pro2384Leu	p.P2384L	ENST00000256646	NM_024408.3	2384	cCc/cTc	34/34	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.743625495842173	2		356	766	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808603	1808603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008659-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	434	607	0	ENST00000260795.2:c.2216C>T	p.Pro739Leu	p.P739L	ENST00000260795		739	cCc/cTc	16/17	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.743625495842173	2		607	1045	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149450021	149450021	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs775029262	NA	P-0008659-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	194	254	0	ENST00000286301.3:c.1196G>A	p.Arg399Gln	p.R399Q	ENST00000286301	NM_005211.3	399	cGa/cAa	8/22	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.743625495842173	2		254	440	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652107	36652107	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008659-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	299	344	0	ENST00000244741.5:c.229T>A	p.Tyr77Asn	p.Y77N	ENST00000244741	NM_000389.4	77	Tac/Aac	2/3	0.543577039773892	4	FACETS	1	0.994	1	0.478	0.451	0.506	CLONAL	1	TRUE	1	0.743625495842173	4		344	977	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437716	49437716	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008659-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	462	624	0	ENST00000301067.7:c.5254A>G	p.Lys1752Glu	p.K1752E	ENST00000301067	NM_003482.3	1752	Aag/Gag	22/54	1	2	FACETS	0.992	0.949	1	0.992	0.949	1	CLONAL	1	TRUE	1	0.743625495842173	2		624	1252	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947540	48947540	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0008659-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	253	304	1	ENST00000267163.4:c.1128-1G>C		p.X376_splice	ENST00000267163	NM_000321.2	376			0.650665298177149	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.743625495842173	1		305	300	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473779	67473779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906850	NA	P-0008659-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	252	325	1	ENST00000327367.4:c.859C>T	p.Arg287Trp	p.R287W	ENST00000327367	NM_005902.3	287	Cgg/Tgg	6/9	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.743625495842173	2		326	657	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277874	41277875	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGC	novel	NA	P-0008659-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	217	439	0	ENST00000349496.5:c.1839_1841dup	p.Ala615dup	p.A615dup	ENST00000349496	NM_001904.3	615	gta/gtAGCa	12/15	1	2	FACETS	0.994	0.931	1	0.994	0.931	1	CLONAL	1	TRUE	1	0.743625495842173	2		439	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0008692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	73	229	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.221215553253195	2		229	445	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527397	157527398	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0008692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	194	376	0	ENST00000346085.5:c.5127dup	p.Ala1710SerfsTer3	p.A1710Sfs*3	ENST00000346085	NM_020732.3	1708	caa/cAaa	20/20	0.215809497719154	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.221215553253195	2		376	826	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384651	31384651	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	138	605	0	ENST00000328111.2:c.1359del	p.Leu454SerfsTer136	p.L454Sfs*136	ENST00000328111	NM_006892.3	451	gaG/ga	13/23	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.221215553253195	2		605	1173	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120479	70120480	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0008692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	102	436	0	ENST00000245479.2:c.1486dup	p.Gln496ProfsTer82	p.Q496Pfs*82	ENST00000245479	NM_000346.3	494	agc/agCc	3/3	1	2	FACETS	0.942	0.841	1	0.942	0.841	1	CLONAL	1	TRUE	1	0.221215553253195	2		436	979	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0008877-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	260	356	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.83218385898663	1	FACETS	0.96	0.92	0.999	0.96	0.92	0.999	CLONAL	1	TRUE	0	0.83218385898663	1		356	380	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942685	48942685	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913301	NA	P-0008877-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	446	460	0	ENST00000267163.4:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000267163	NM_000321.2	358	Cga/Tga	11/27	0.83218385898663	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.83218385898663	1		460	598	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442534	52442534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753629908	NA	P-0008877-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	159	334	0	ENST00000460680.1:c.211G>A	p.Val71Met	p.V71M	ENST00000460680	NM_004656.3	71	Gtg/Atg	4/17	1	2	FACETS	0.532	0.489	0.577	0.532	0.489	0.577	SUBCLONAL	1	TRUE	1	0.83218385898663	2		334	718	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260635	1260635	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008877-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	31	454	0	ENST00000310581.5:c.2924T>C	p.Phe975Ser	p.F975S	ENST00000310581	NM_198253.2	975	tTt/tCt	12/16	0.350390131259591	1	FACETS	0.1	0.081	0.122	0.1	0.081	0.122	INDETERMINATE	1	TRUE	0	0.83218385898663	1		454	434	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0008935-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	49	465	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	0.261803112257291	3	FACETS	0.641	0.543	0.749	0.321	0.271	0.375	SUBCLONAL	1	TRUE	1	0.378582928825108	3		465	480	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115251172	115251172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008935-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	87	510	0	ENST00000369535.4:c.554C>T	p.Pro185Leu	p.P185L	ENST00000369535	NM_002524.4	185	cCa/cTa	5/7	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.378582928825108	2		510	316	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945793	38945793	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008935-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	18	342	0	ENST00000357387.3:c.4433A>G	p.Asn1478Ser	p.N1478S	ENST00000357387	NM_152756.3	1478	aAt/aGt	34/38	0.374358648601868	4	FACETS	0.424	0.319	0.549	0.141	0.106	0.183	SUBCLONAL	1	TRUE	1	0.378582928825108	4		342	309	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394431	162394431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008935-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	42	436	0	ENST00000366898.1:c.637G>A	p.Gly213Arg	p.G213R	ENST00000366898	NM_004562.2	213	Gga/Aga	6/12	0.112954883655742	5	FACETS	1	0.947	1	0.333	0.28	0.392	INDETERMINATE	1	TRUE	1	0.378582928825108	5		436	261	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335053	81335053	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008935-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	38	313	0	ENST00000222390.5:c.1774G>T	p.Asp592Tyr	p.D592Y	ENST00000222390	NM_000601.4	592	Gat/Tat	16/18	0.112954883655742	5	FACETS	0.779	0.651	0.919	0.39	0.325	0.46	INDETERMINATE	2	TRUE	1	0.378582928825108	5		313	202	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437037	110437037	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008935-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	22	30	0	ENST00000375856.3:c.1364G>T	p.Gly455Val	p.G455V	ENST00000375856	NM_003749.2	455	gGc/gTc	1/2	0.237178296340479	2	FACETS	1	0.862	1	0.564	0.445	0.697	CLONAL	1	TRUE	0	0.378582928825108	2		30	103	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943776	9943776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1277595711	NA	P-0008935-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	54	254	1	ENST00000330684.3:c.1165G>A	p.Val389Met	p.V389M	ENST00000330684	NM_001134407.1	389	Gtg/Atg	5/13	1	2	FACETS	0.645	0.552	0.747	0.645	0.552	0.747	SUBCLONAL	1	TRUE	1	0.378582928825108	2		255	442	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89839741	89839741	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008935-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	83	525	0	ENST00000389301.3:c.1952G>T	p.Gly651Val	p.G651V	ENST00000389301	NM_000135.2	651	gGa/gTa	22/43	0.112954883655742	5	FACETS	0.885	0.78	0.997	0.221	0.195	0.25	INDETERMINATE	1	TRUE	1	0.378582928825108	5		525	777	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7126606	7126606	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008935-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	115	358	0	ENST00000302850.5:c.3002G>T	p.Ser1001Ile	p.S1001I	ENST00000302850	NM_000208.2	1001	aGt/aTt	16/22	0.220044368061943	2	FACETS	1	0.92	1	0.511	0.461	0.563	INDETERMINATE	1	TRUE	0	0.378582928825108	2		358	595	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57470699	57470699	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008935-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	103	325	0	ENST00000371085.3:c.172A>G	p.Lys58Glu	p.K58E	ENST00000371085	NM_000516.4	58	Aag/Gag	2/13	0.261803112257291	3	FACETS	0.83	0.748	0.914	0.83	0.748	0.914	CLONAL	2	TRUE	1	0.378582928825108	3		325	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	AA	novel	NA	P-0008935-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	146	492	0	ENST00000269305.4:c.880delinsTT	p.Glu294LeufsTer12	p.E294Lfs*12	ENST00000269305	NM_001126112.2	294	Gag/TTag	8/11	0.220044368061943	2	FACETS	0.978	0.893	1	0.489	0.446	0.533	INDETERMINATE	1	TRUE	0	0.378582928825108	2		492	789	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	57	456	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.881	0.759	1	0.881	0.759	1	CLONAL	1	TRUE	1	0.324195957786818	2		456	399	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423474	116423474	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913245	NA	P-0008943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	336	429	0	ENST00000397752.3:c.3749T>C	p.Met1250Thr	p.M1250T	ENST00000397752	NM_000245.2	1250	aTg/aCg	19/21	0.321279340935155	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.324195957786818	3		429	1139	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722347	176722347	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	148	374	1	ENST00000439151.2:c.7978C>A	p.Gln2660Lys	p.Q2660K	ENST00000439151	NM_022455.4	2660	Cag/Aag	23/23	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.324195957786818	2		375	891	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885930	111885930	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs138410505	NA	P-0008943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1303	86	567	1	ENST00000341259.2:c.1552C>T	p.Arg518Ter	p.R518*	ENST00000341259	NM_005475.2	518	Cga/Tga	8/8	0.321279340935155	3	FACETS	0.444	0.391	0.501	0.222	0.195	0.251	SUBCLONAL	1	TRUE	1	0.324195957786818	3		568	1389	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099931	27099932	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0008943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	118	381	0	ENST00000324856.7:c.3810_3811insAG	p.Val1271ArgfsTer19	p.V1271Rfs*19	ENST00000324856	NM_006015.4	1270	-/AG	15/20	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.324195957786818	2		381	726	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009254-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	48	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	0.705	0.983	0.837	0.705	0.983	CLONAL	1	TRUE	1	0.12	2		326	956	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0009254-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	26	138	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.73	0.576	0.907	0.73	0.576	0.907	CLONAL	1	TRUE	1	0.12	2		138	594	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0009254-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	24	106	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.12	2		106	342	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39623707	39623707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009254-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	51	320	0	ENST00000262039.4:c.2114G>A	p.Arg705Lys	p.R705K	ENST00000262039	NM_002647.2	705	aGa/aAa	20/25	1	2	FACETS	0.94	0.797	1	0.94	0.797	1	CLONAL	1	TRUE	1	0.12	2		320	904	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950033	44950034	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0009254-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	41	242	0	ENST00000377967.4:c.3803dup	p.Pro1269ThrfsTer22	p.P1269Tfs*22	ENST00000377967	NM_021140.2	1268	gta/gTta	26/29	1	1	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	TRUE	0	0.12	1		242	631	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0009406-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	358	167	266	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.345374158534268	3	FACETS	0.821	0.759	0.884	0.821	0.759	0.884	CLONAL	2	TRUE	1	0.480672802672375	3		266	525	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181413	185181413	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009406-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	583	94	369	0	ENST00000265026.3:c.1354G>C	p.Glu452Gln	p.E452Q	ENST00000265026	NM_004721.4	452	Gaa/Caa	8/14	0.345374158534268	3	FACETS	0.717	0.638	0.8	0.358	0.319	0.4	SUBCLONAL	1	TRUE	1	0.480672802672375	3		369	677	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181440	185181440	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009406-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	494	82	300	0	ENST00000265026.3:c.1381G>C	p.Glu461Gln	p.E461Q	ENST00000265026	NM_004721.4	461	Gag/Cag	8/14	0.345374158534268	3	FACETS	0.735	0.649	0.827	0.367	0.324	0.414	SUBCLONAL	1	TRUE	1	0.480672802672375	3		300	576	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874919	151874919	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009406-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	423	193	413	0	ENST00000262189.6:c.7619A>T	p.His2540Leu	p.H2540L	ENST00000262189	NM_170606.2	2540	cAt/cTt	38/59	0.315458292130896	2	FACETS	1	0.988	1	0.652	0.606	0.699	CLONAL	1	TRUE	0	0.480672802672375	2		413	616	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405802	70405802	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009406-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	334	80	284	0	ENST00000373644.4:c.3316A>G	p.Ser1106Gly	p.S1106G	ENST00000373644	NM_030625.2	1106	Agc/Ggc	4/12	1	2	FACETS	0.804	0.711	0.902	0.804	0.711	0.902	CLONAL	1	TRUE	1	0.480672802672375	2		284	414	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102056760	102056760	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009406-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	284	101	396	0	ENST00000282441.5:c.700G>C	p.Asp234His	p.D234H	ENST00000282441	NM_001130145.2	234	Gat/Cat	4/9	0.386873856104517	1	FACETS	0.829	0.747	0.915	0.829	0.747	0.915	CLONAL	1	TRUE	0	0.480672802672375	1		396	385	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188181	108188181	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009406-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	477	111	353	0	ENST00000278616.4:c.6280G>A	p.Glu2094Lys	p.E2094K	ENST00000278616	NM_000051.3	2094	Gaa/Aaa	43/63	0.386873856104517	1	FACETS	0.597	0.538	0.659	0.597	0.538	0.659	SUBCLONAL	1	TRUE	0	0.480672802672375	1		353	588	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188190	108188190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009406-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	454	105	347	0	ENST00000278616.4:c.6289G>A	p.Glu2097Lys	p.E2097K	ENST00000278616	NM_000051.3	2097	Gaa/Aaa	43/63	0.386873856104517	1	FACETS	0.594	0.533	0.657	0.594	0.533	0.657	SUBCLONAL	1	TRUE	0	0.480672802672375	1		347	559	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923137	48923137	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009406-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	371	83	368	0	ENST00000267163.4:c.585G>A	p.Trp195Ter	p.W195*	ENST00000267163	NM_000321.2	195	tgG/tgA	6/27	0.33712029757371	2	FACETS	0.761	0.674	0.853	0.38	0.337	0.427	SUBCLONAL	1	TRUE	0	0.480672802672375	2		368	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0009406-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	519	152	591	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.480672802672375	1	FACETS	0.716	0.657	0.778	0.716	0.657	0.778	SUBCLONAL	1	TRUE	0	0.480672802672375	1		591	671	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874913	151874913	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009406-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	417	193	404	0	ENST00000262189.6:c.7625del	p.Ser2542TyrfsTer20	p.S2542Yfs*20	ENST00000262189	NM_170606.2	2542	tCa/ta	38/59	0.315458292130896	2	FACETS	1	0.988	1	0.658	0.612	0.705	CLONAL	1	TRUE	0	0.480672802672375	2		404	610	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0009638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	29	392	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.279	0.223	0.344	0.279	0.223	0.344	SUBCLONAL	1	TRUE	1	0.203722100101934	2		392	1019	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643778	52643778	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	63	421	0	ENST00000394830.3:c.2118G>T	p.Met706Ile	p.M706I	ENST00000394830	NM_018313.4	706	atG/atT	17/30	1	2	FACETS	0.719	0.62	0.827	0.719	0.62	0.827	SUBCLONAL	1	TRUE	1	0.203722100101934	2		421	860	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974095	2974095	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	62	313	0	ENST00000396946.4:c.1510G>T	p.Gly504Cys	p.G504C	ENST00000396946	NM_032415.4	504	Ggc/Tgc	10/25	0.1857605695984	3	FACETS	0.955	0.824	1	0.478	0.412	0.549	CLONAL	1	TRUE	1	0.203722100101934	3		313	702	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979403	2979403	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	84	502	0	ENST00000396946.4:c.844G>T	p.Glu282Ter	p.E282*	ENST00000396946	NM_032415.4	282	Gag/Tag	6/25	0.1857605695984	3	FACETS	0.775	0.682	0.875	0.388	0.341	0.438	SUBCLONAL	1	TRUE	1	0.203722100101934	3		502	1172	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374362	81374362	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	69	416	0	ENST00000222390.5:c.700C>A	p.Arg234Ser	p.R234S	ENST00000222390	NM_000601.4	234	Cgc/Agc	6/18	0.203722100101934	1	FACETS	0.637	0.553	0.728	0.637	0.553	0.728	SUBCLONAL	1	TRUE	0	0.203722100101934	1		416	955	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861236	57861236	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200802561	NA	P-0009638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1509	133	837	1	ENST00000228682.2:c.1033G>A	p.Ala345Thr	p.A345T	ENST00000228682	NM_005269.2	345	Gcc/Acc	9/12	1	2	FACETS	0.795	0.719	0.876	0.795	0.719	0.876	SUBCLONAL	1	TRUE	1	0.203722100101934	2		838	1642	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347908	347908	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1561	142	969	2	ENST00000262320.3:c.1598G>T	p.Arg533Leu	p.R533L	ENST00000262320	NM_003502.3	533	cGa/cTa	6/11	1	2	FACETS	0.819	0.743	0.899	0.819	0.743	0.899	CLONAL	1	TRUE	1	0.203722100101934	2		971	1703	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969955	81969955	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	127	697	2	ENST00000359376.3:c.3024G>T	p.Gln1008His	p.Q1008H	ENST00000359376	NM_002661.3	1008	caG/caT	27/33	1	2	FACETS	0.963	0.87	1	0.963	0.87	1	CLONAL	1	TRUE	1	0.203722100101934	2		699	1295	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0009638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	125	622	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.113471176616016	1	FACETS	1	0.981	1	1	0.981	1	INDETERMINATE	1	TRUE	0	0.203722100101934	1		622	812	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246463	41246463	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	87	567	0	ENST00000357654.3:c.1085A>G	p.Glu362Gly	p.E362G	ENST00000357654	NM_007294.3	362	gAg/gGg	10/23	0.202372695822745	1	FACETS	0.687	0.607	0.774	0.687	0.607	0.774	SUBCLONAL	1	TRUE	0	0.203722100101934	1		567	1116	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220382	1220382	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	90	501	0	ENST00000326873.7:c.475C>T	p.Gln159Ter	p.Q159*	ENST00000326873	NM_000455.4	159	Cag/Tag	4/10	0.203722100101934	1	FACETS	0.893	0.791	1	0.893	0.791	1	CLONAL	1	TRUE	0	0.203722100101934	1		501	889	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138515	11138515	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0009638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	109	491	0	ENST00000358026.2:c.3271A>T	p.Lys1091Ter	p.K1091*	ENST00000358026	NM_001128849.1	1091	Aaa/Taa	24/36	0.203722100101934	1	FACETS	0.929	0.833	1	0.929	0.833	1	CLONAL	1	TRUE	0	0.203722100101934	1		491	1034	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412460	63412460	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	153	449	0	ENST00000330258.3:c.707G>C	p.Gly236Ala	p.G236A	ENST00000330258	NM_152424.3	236	gGg/gCg	2/2	1	1	FACETS	0.766	0.7	0.834	1	0.988	1	SUBCLONAL	2	TRUE	0	0.203722100101934	1		449	881	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971083	21971084	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0009638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	31	162	0	ENST00000304494.5:c.274dup	p.Asp92GlyfsTer28	p.D92Gfs*28	ENST00000304494	NM_000077.4	92	gac/gGac	2/3	0.203722100101934	1	FACETS	0.673	0.544	0.819	0.673	0.544	0.819	SUBCLONAL	1	TRUE	0	0.203722100101934	1		162	406	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738765	145738765	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	rs758541711	NA	P-0009638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	80	362	0	ENST00000428558.2:c.2299del	p.Val767TrpfsTer76	p.V767Wfs*76	ENST00000428558	NM_004260.3	767	Gtg/tg	15/22	1	2	FACETS	0.928	0.816	1	0.928	0.816	1	CLONAL	1	TRUE	1	0.203722100101934	2		362	846	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600352	10600355	+	frameshift_variant	Frame_Shift_Del	DEL	TGTG	TGTG	-	novel	NA	P-0009638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	129	569	0	ENST00000171111.5:c.1500_1503del	p.Ile500MetfsTer3	p.I500Mfs*3	ENST00000171111	NM_203500.1	500	atCACA/at	4/6	0.203722100101934	1	FACETS	0.959	0.867	1	0.959	0.867	1	CLONAL	1	TRUE	0	0.203722100101934	1		569	1186	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55974052	55974052	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	37	231	0	ENST00000263923.4:c.1264del	p.Gln422ArgfsTer7	p.Q422Rfs*7	ENST00000263923	NM_002253.2	422	Cag/ag	10/30	1	2	FACETS	0.688	0.566	0.824	0.688	0.566	0.824	SUBCLONAL	1	TRUE	1	0.203722100101934	2		231	528	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	114	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.685	0.615	0.76	0.685	0.615	0.76	SUBCLONAL	1	FALSE	1	0.3	2		326	1109	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0009848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	93	579	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	NA	2	FACETS	0.613	0.543	0.687			1	INDETERMINATE	1	FALSE	NA	0.3	2		579	1012	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0009850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	202	583	1	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.622139378262957	2		584	645	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0009850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	115	219	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.622139378262957	2		219	354	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14017064	14017064	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	110	388	0	ENST00000405192.2:c.223C>G	p.Gln75Glu	p.Q75E	ENST00000405192	NM_001163147.1	75	Cag/Gag	5/12	0.622139378262957	4	FACETS	0.855	0.769	0.946	0.285	0.256	0.316	CLONAL	1	TRUE	1	0.622139378262957	4		388	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577567	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1567549651	NA	P-0009850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	307	402	1	ENST00000269305.4:c.714dup	p.Asn239Ter	p.N239*	ENST00000269305	NM_001126112.2	238	-/T	7/11	0.611288441994444	2	FACETS	0.867	0.827	0.907	0.867	0.827	0.907	CLONAL	2	TRUE	0	0.622139378262957	2		403	569	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880957	134880957	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770406411	NA	P-0009850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	173	364	2	ENST00000398015.3:c.1520G>A	p.Arg507His	p.R507H	ENST00000398015	NM_004441.4	507	cGt/cAt	7/16	0.361874459016924	3	FACETS	0.981	0.905	1	0.491	0.452	0.53	INDETERMINATE	1	TRUE	1	0.622139378262957	3		366	743	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117718	115117718	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	160	473	0	ENST00000257566.3:c.717G>C	p.Gln239His	p.Q239H	ENST00000257566	NM_016569.3	239	caG/caC	3/8	1	2	FACETS	0.83	0.764	0.898	0.83	0.764	0.898	CLONAL	1	TRUE	1	0.622139378262957	2		473	620	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117765	115117765	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	181	505	1	ENST00000257566.3:c.670C>A	p.Pro224Thr	p.P224T	ENST00000257566	NM_016569.3	224	Cca/Aca	3/8	1	2	FACETS	0.845	0.782	0.909	0.845	0.782	0.909	CLONAL	1	TRUE	1	0.622139378262957	2		506	689	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31390225	31390225	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	640	415	0	ENST00000328111.2:c.2180C>G	p.Ser727Cys	p.S727C	ENST00000328111	NM_006892.3	727	tCt/tGt	20/23	0.622139378262957	6	FACETS	1	0.984	1	1	0.984	1	CLONAL	4	TRUE	2	0.622139378262957	6		415	1128	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913343	NA	P-0009868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	571	605	1	ENST00000269305.4:c.817C>A	p.Arg273Ser	p.R273S	ENST00000269305	NM_001126112.2	273	Cgt/Agt	8/11	0.497436082855564	2	FACETS	0.995	0.961	1	0.995	0.961	1	CLONAL	2	TRUE	0	0.534946847583495	2		606	1073	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153691	55153691	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	507	504	0	ENST00000257290.5:c.2657G>T	p.Trp886Leu	p.W886L	ENST00000257290	NM_006206.4	886	tGg/tTg	19/23	0.502669681333836	4	FACETS	0.984	0.942	1	0.984	0.942	1	CLONAL	2	TRUE	2	0.534946847583495	4		504	1479	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188208	108188208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	65	341	0	ENST00000278616.4:c.6307G>A	p.Ala2103Thr	p.A2103T	ENST00000278616	NM_000051.3	2103	Gca/Aca	43/63	0.286829151639177	5	FACETS	0.345	0.298	0.397	0.115	0.099	0.133	INDETERMINATE	1	TRUE	2	0.534946847583495	5		341	1268	SUCCESS
APC	324	MSKCC	GRCh37	5	112175597	112175598	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0009868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	555	481	0	ENST00000257430.4:c.4307dup	p.Ser1436ArgfsTer2	p.S1436Rfs*2	ENST00000257430	NM_000038.5	1436	agt/aGgt	16/16	0.527876778220487	2	FACETS	0.886	0.853	0.919	0.886	0.853	0.919	CLONAL	2	TRUE	0	0.534946847583495	2		481	1171	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741585	17741585	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	20	37	1	ENST00000250003.3:c.256G>A	p.Gly86Arg	p.G86R	ENST00000250003	NM_002478.4	86	Ggg/Agg	1/3	1	2	FACETS	0.973	0.76	1	1	0.94	1	CLONAL	2	TRUE	1	0.225797515931246	2		38	91	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576889	7576890	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0009906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	128	426	0	ENST00000269305.4:c.956dup	p.Lys320GlufsTer17	p.K320Efs*17	ENST00000269305	NM_001126112.2	319	aag/aaAg	9/11	0.225797515931246	2	FACETS	0.9	0.818	0.986	0.9	0.818	0.986	CLONAL	2	TRUE	0	0.225797515931246	2		426	630	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522275	157522275	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	142	455	0	ENST00000346085.5:c.4547del	p.Val1516AlafsTer63	p.V1516Afs*63	ENST00000346085	NM_020732.3	1516	gTc/gc	18/20	0.225797515931246	2	FACETS	0.922	0.842	1	0.922	0.842	1	CLONAL	2	TRUE	0	0.225797515931246	2		455	682	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595893	52595906	+	frameshift_variant	Frame_Shift_Del	DEL	ATCTCACTGCTGAA	ATCTCACTGCTGAA	-	novel	NA	P-0009906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	89	554	0	ENST00000394830.3:c.4009_4022del	p.Phe1337GlufsTer5	p.F1337Efs*5	ENST00000394830	NM_018313.4	1337	TTCAGCAGTGAGATg/g	26/30	0.225797515931246	1	FACETS	0.886	0.785	0.995	0.886	0.785	0.995	CLONAL	1	TRUE	0	0.225797515931246	1		554	789	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577329	64577330	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs386134253	NA	P-0010084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	55	532	1	ENST00000312049.6:c.252dup	p.Ile85TyrfsTer32	p.I85Yfs*32	ENST00000312049	NM_130799.2	84	-/T	2/10	0.24007115978874	5	FACETS	1	0.942	1			1	INDETERMINATE	3	TRUE	NA	0.728330492270919	5		533	97	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540935	187540935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	12	255	0	ENST00000441802.2:c.6805G>A	p.Val2269Met	p.V2269M	ENST00000441802	NM_005245.3	2269	Gtg/Atg	10/27	NA	2	FACETS	0.54	0.388	0.717			1	INDETERMINATE	1	TRUE	NA	0.728330492270919	2		255	61	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879277	151879277	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs956673837	NA	P-0010084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	36	383	0	ENST00000262189.6:c.5668C>T	p.Arg1890Ter	p.R1890*	ENST00000262189	NM_170606.2	1890	Cga/Tga	36/59	0.388068208576215	3	FACETS	0.992	0.858	1	0.992	0.858	1	INDETERMINATE	2	TRUE	1	0.728330492270919	3		383	68	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094426	27094427	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	73	352	0	ENST00000324856.7:c.3135dup	p.Arg1046Ter	p.R1046*	ENST00000324856	NM_006015.4	1045	ggt/ggTt	11/20	0.385516100942122	6	FACETS	0.938	0.84	1	0.938	0.84	1	INDETERMINATE	3	TRUE	3	0.728330492270919	6		352	175	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0010202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	72	231	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.328310447273562	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.328310447273562	1		231	293	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495741	72495741	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	166	461	0	ENST00000477973.2:c.331G>T	p.Glu111Ter	p.E111*	ENST00000477973	NM_012234.5	111	Gaa/Taa	1/4	0.328310447273562	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.328310447273562	1		461	833	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916929	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1434	483	1072	3	ENST00000263967.3:c.316G>T	p.Gly106Cys	p.G106C	ENST00000263967	NM_006218.2	106	Ggc/Tgc	2/21	0.294316953694668	3	FACETS	0.893	0.852	0.936	0.893	0.852	0.936	CLONAL	2	TRUE	1	0.328310447273562	3		1075	1917	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191035	185191035	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	241	466	0	ENST00000265026.3:c.1916A>C	p.Gln639Pro	p.Q639P	ENST00000265026	NM_004721.4	639	cAg/cCg	11/14	0.294316953694668	3	FACETS	0.905	0.846	0.966	0.905	0.846	0.966	CLONAL	2	TRUE	1	0.328310447273562	3		466	944	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187989	32187989	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	195	495	0	ENST00000375023.3:c.1232C>G	p.Pro411Arg	p.P411R	ENST00000375023	NM_004557.3	411	cCc/cGc	7/30	0.173622190520349	2	FACETS	1	0.988	1	0.675	0.625	0.727	INDETERMINATE	1	TRUE	0	0.328310447273562	2		495	880	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066608	94066608	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	322	987	0	ENST00000369303.4:c.1151G>T	p.Ser384Ile	p.S384I	ENST00000369303	NM_004440.3	384	aGt/aTt	5/17	0.328310447273562	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.328310447273562	1		987	1333	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988048	85988048	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	167	418	0	ENST00000263360.6:c.993G>A	p.Trp331Ter	p.W331*	ENST00000263360	NM_003797.3	331	tgG/tgA	10/12	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.328310447273562	2		418	766	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816138	89816138	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	99	501	0	ENST00000389301.3:c.3239G>T	p.Arg1080Leu	p.R1080L	ENST00000389301	NM_000135.2	1080	cGg/cTg	32/43	0.328310447273562	1	FACETS	0.717	0.64	0.799	0.717	0.64	0.799	SUBCLONAL	1	TRUE	0	0.328310447273562	1		501	703	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39550394	39550394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	114	380	1	ENST00000262039.4:c.505G>A	p.Glu169Lys	p.E169K	ENST00000262039	NM_002647.2	169	Gaa/Aaa	4/25	0.328310447273562	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.328310447273562	1		381	535	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313152	30313152	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1511	260	971	1	ENST00000262643.3:c.846G>T	p.Leu282Phe	p.L282F	ENST00000262643	NM_001238.2	282	ttG/ttT	10/12	0.328310447273562	3	FACETS	1	0.961	1	0.521	0.486	0.557	CLONAL	1	TRUE	1	0.328310447273562	3		972	1771	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775252	73775252	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	172	738	0	ENST00000254810.4:c.4del	p.Ala2ProfsTer35	p.A2Pfs*35	ENST00000254810	NM_005324.3	2	Gcc/cc	2/4	1	2	FACETS	0.928	0.853	1	0.928	0.853	1	CLONAL	1	TRUE	1	0.328310447273562	2		738	1129	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0010203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	340	367	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.765	0.73	0.8	1	0.996	1	SUBCLONAL	2	FALSE	1	0.657757928038007	2		367	676	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0010203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	257	349	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.61336742129847	1	FACETS	0.942	0.89	0.993	0.942	0.89	0.993	CLONAL	1	FALSE	0	0.657757928038007	1		349	557	SUCCESS
APC	324	MSKCC	GRCh37	5	112174096	112174096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs137854575	NA	P-0010203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	159	347	0	ENST00000257430.4:c.2805C>A	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	taC/taA	16/16	1	2	FACETS	0.847	0.78	0.915	0.847	0.78	0.915	CLONAL	1	FALSE	1	0.657757928038007	2		347	571	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	138	311	1	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	1	2	FACETS	0.912	0.836	0.99	0.912	0.836	0.99	CLONAL	1	FALSE	1	0.657757928038007	2		312	460	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467901	66467901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762375181	NA	P-0010203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	212	451	0	ENST00000273854.3:c.368C>T	p.Ala123Val	p.A123V	ENST00000273854	NM_004439.5	123	gCt/gTt	3/18	0.248889296039496	1	FACETS	0.705	0.658	0.752	0.705	0.658	0.752	INDETERMINATE	1	FALSE	0	0.657757928038007	1		451	614	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119889	70119889	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	187	332	0	ENST00000245479.2:c.891C>A	p.Tyr297Ter	p.Y297*	ENST00000245479	NM_000346.3	297	taC/taA	3/3	1	2	FACETS	0.916	0.85	0.983	0.916	0.85	0.983	CLONAL	1	FALSE	1	0.657757928038007	2		332	621	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573597	48573598	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	49	336	0	ENST00000342988.3:c.182dup	p.Thr62AsnfsTer8	p.T62Nfs*8	ENST00000342988	NM_005359.5	61	ata/aTta	2/12	0.657757928038007	1	FACETS	0.254	0.215	0.296	0.254	0.215	0.296	SUBCLONAL	1	FALSE	0	0.657757928038007	1		336	394	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925621	114925622	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCC	novel	NA	P-0010203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1451	377	973	0	ENST00000543371.1:c.1701_1704dup	p.Ser569ProfsTer41	p.S569Pfs*41	ENST00000543371	NM_001198531.1	567	gcc/gCCCCcc	14/14	1	2	FACETS	0.627	0.593	0.662	0.627	0.593	0.662	SUBCLONAL	1	FALSE	1	0.657757928038007	2		973	1828	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0010255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	182	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.355915059257774	2		326	952	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0010255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	119	437	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.355915059257774	1	FACETS	0.822	0.743	0.905	0.822	0.743	0.905	CLONAL	1	FALSE	0	0.355915059257774	1		437	669	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713856	30713856	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	133	419	0	ENST00000295754.5:c.1181G>T	p.Cys394Phe	p.C394F	ENST00000295754	NM_003242.5	394	tGc/tTc	4/7	0.284666134015213	1	FACETS	0.892	0.811	0.976	0.892	0.811	0.976	CLONAL	1	FALSE	0	0.355915059257774	1		419	689	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73343037	73343037	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	111	284	0	ENST00000377767.4:c.1769A>T	p.Tyr590Phe	p.Y590F	ENST00000377767	NM_014953.3	590	tAt/tTt	14/21	0.284666134015213	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	FALSE	0	0.355915059257774	1		284	506	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240340	5240340	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	84	447	1	ENST00000357368.4:c.1574C>T	p.Pro525Leu	p.P525L	ENST00000357368	NM_002850.3	525	cCg/cTg	12/38	0.178820038958033	0	FACETS	0.555	0.491	0.623			1	INDETERMINATE	1	FALSE	0	0.355915059257774	0		448	548	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44894225	44894226	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	202	587	0	ENST00000377967.4:c.615dup	p.Glu206Ter	p.E206*	ENST00000377967	NM_021140.2	205	gct/gcTt	7/29	0.355915059257774	1	FACETS	0.988	0.917	1	0.988	0.917	1	CLONAL	1	FALSE	0	0.355915059257774	1		587	944	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0010260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	78	352	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.316493764001357	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.316493764001357	1		352	325	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267360	198267360	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs374250186	NA	P-0010260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	97	470	0	ENST00000335508.6:c.1997A>C	p.Lys666Thr	p.K666T	ENST00000335508	NM_012433.2	666	aAg/aCg	14/25	1	2	FACETS	0.903	0.805	1	0.903	0.805	1	CLONAL	1	TRUE	1	0.316493764001357	2		470	679	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713425	30713425	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	39	239	0	ENST00000295754.5:c.753del	p.Gly253ValfsTer11	p.G253Vfs*11	ENST00000295754	NM_003242.5	250	gtG/gt	4/7	0.316493764001357	1	FACETS	0.774	0.645	0.916	0.774	0.645	0.916	CLONAL	1	TRUE	0	0.316493764001357	1		239	268	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0010361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	75	138	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.274498268806922	2	FACETS	0.873	0.772	0.979	0.873	0.772	0.979	CLONAL	2	TRUE	0	0.276345254236728	2		138	311	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0010361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	255	266	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.276345254236728	5	FACETS	0.923	0.869	0.978	0.923	0.869	0.978	CLONAL	4	TRUE	1	0.276345254236728	5		266	707	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113243	209113243	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs758622511	NA	P-0010361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	182	454	0	ENST00000345146.2:c.264G>T	p.Leu88Phe	p.L88F	ENST00000345146	NM_005896.2	88	ttG/ttT	4/10	0.257367273853633	3	FACETS	0.845	0.78	0.913	0.845	0.78	0.913	CLONAL	2	TRUE	1	0.276345254236728	3		454	887	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843365	128843365	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748690872	NA	P-0010361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	72	323	0	ENST00000249373.3:c.472G>A	p.Glu158Lys	p.E158K	ENST00000249373	NM_005631.4	158	Gag/Aag	2/12	0.257367273853633	3	FACETS	0.88	0.769	1	0.44	0.384	0.5	CLONAL	1	TRUE	1	0.276345254236728	3		323	674	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641067	93641067	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	208	258	0	ENST00000375746.1:c.1413C>G	p.Ile471Met	p.I471M	ENST00000375746	NM_001174167.1	471	atC/atG	11/14	0.276345254236728	6	FACETS	0.982	0.918	1			1	CLONAL	4	TRUE	NA	0.276345254236728	6		258	595	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741220	40741220	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	199	443	0	ENST00000392038.2:c.1213G>C	p.Glu405Gln	p.E405Q	ENST00000392038	NM_001626.4	405	Gag/Cag	12/14	NA	2	FACETS	1	0.963	1			1	INDETERMINATE	2	TRUE	NA	0.276345254236728	2		443	683	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873679	151873680	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTTGACACATGATTGGATGGGGATC	novel	NA	P-0010361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	42	160	0	ENST00000262189.6:c.8858_8859insGATCCCCATCCAATCATGTGTCAAG	p.Ser2953ArgfsTer23	p.S2953Rfs*23	ENST00000262189	NM_170606.2	2953	agt/agGATCCCCATCCAATCATGTGTCAAGt	38/59	0.257367273853633	3	FACETS	0.925	0.774	1	0.463	0.387	0.546	CLONAL	1	TRUE	1	0.276345254236728	3		160	374	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091371	193091373	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0010361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	130	365	0	ENST00000367435.3:c.46_48del	p.Lys16del	p.K16del	ENST00000367435	NM_024529.4	14	cAGAag/cag	1/17	0.257367273853633	3	FACETS	0.825	0.75	0.903	0.825	0.75	0.903	CLONAL	2	TRUE	1	0.276345254236728	3		365	649	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016608	12016609	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	T	novel	NA	P-0010361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	120	359	0	ENST00000353533.5:c.744_745delinsT	p.Gly249AlafsTer27	p.G249Afs*27	ENST00000353533	NM_003010.3	248	ttCGgc/ttTgc	7/11	0.274498268806922	2	FACETS	0.8	0.725	0.878	0.8	0.725	0.878	SUBCLONAL	2	TRUE	0	0.276345254236728	2		359	543	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146697	185146697	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010381-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	297	319	0	ENST00000265026.3:c.328A>G	p.Thr110Ala	p.T110A	ENST00000265026	NM_004721.4	110	Aca/Gca	2/14	0.321352509236677	2	FACETS	0.988	0.933	1	0.988	0.933	1	CLONAL	2	TRUE	0	0.32628019249453	2		319	921	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165083	47165085	+	frameshift_variant	Frame_Shift_Del	DEL	TCC	TCC	AA	novel	NA	P-0010381-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	116	492	0	ENST00000409792.3:c.1041_1043delinsTT	p.Lys347AsnfsTer2	p.K347Nfs*2	ENST00000409792	NM_014159.6	347	aaGGAa/aaTTa	3/21	0.32628019249453	1	FACETS	0.708	0.638	0.783	0.708	0.638	0.783	SUBCLONAL	1	TRUE	0	0.32628019249453	1		492	840	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	52	297	1	ENST00000269305.4:c.166G>T	p.Glu56Ter	p.E56*	ENST00000269305	NM_001126112.2	56	Gaa/Taa	4/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.22	2		298	344	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142990	47142990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	26	489	2	ENST00000409792.3:c.4973C>T	p.Ser1658Leu	p.S1658L	ENST00000409792	NM_014159.6	1658	tCa/tTa	8/21	1	2	FACETS	0.725	0.575	0.897	0.725	0.575	0.897	SUBCLONAL	1	TRUE	1	0.22	2		491	326	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158275	106158275	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0010555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	16	346	0	ENST00000380013.4:c.3176C>G	p.Ser1059Ter	p.S1059*	ENST00000380013	NM_001127208.2	1059	tCa/tGa	3/11	0.198021001003442	1	FACETS	0.412	0.304	0.542	0.412	0.304	0.542	SUBCLONAL	1	TRUE	0	0.22	1		346	314	SUCCESS
APC	324	MSKCC	GRCh37	5	112173615	112173615	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1356979249	NA	P-0010555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	23	290	0	ENST00000257430.4:c.2324A>G	p.Asn775Ser	p.N775S	ENST00000257430	NM_000038.5	775	aAt/aGt	16/16	1	2	FACETS	0.798	0.624	0.999	0.798	0.624	0.999	CLONAL	1	TRUE	1	0.22	2		290	262	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61725838	61725838	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	135	339	0	ENST00000401558.2:c.729G>T	p.Glu243Asp	p.E243D	ENST00000401558	NM_003400.3	243	gaG/gaT	9/25	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.365352151486142	2		339	619	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647500	117647500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	237	686	1	ENST00000368508.3:c.5444G>A	p.Cys1815Tyr	p.C1815Y	ENST00000368508	NM_002944.2	1815	tGc/tAc	33/43	0.365352151486142	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.365352151486142	1		687	941	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023282	27023282	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	83	233	0	ENST00000324856.7:c.388del	p.Asp130MetfsTer102	p.D130Mfs*102	ENST00000324856	NM_006015.4	130	Gat/at	1/20	0.316916222386749	1	FACETS	0.975	0.866	1	0.975	0.866	1	CLONAL	1	TRUE	0	0.365352151486142	1		233	381	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073791	8073792	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0010574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	327	1003	0	ENST00000377482.5:c.866_867dup	p.Pro290TyrfsTer6	p.P290Yfs*6	ENST00000377482	NM_018948.3	289	-/TA	4/4	0.316916222386749	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.365352151486142	1		1003	1359	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0010612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	492	264	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.541716335772417	2	FACETS	0.993	0.957	1	0.993	0.957	1	CLONAL	2	TRUE	0	0.541447959077287	2		264	915	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484596	57484596	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913494	NA	P-0010612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	171	224	0	ENST00000371085.3:c.680A>T	p.Gln227Leu	p.Q227L	ENST00000371085	NM_000516.4	227	cAg/cTg	9/13	0.541716335772417	3	FACETS	0.907	0.835	0.982	0.453	0.417	0.491	CLONAL	1	TRUE	1	0.541447959077287	3		224	885	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602446	10602446	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	582	421	0	ENST00000171111.5:c.1132G>T	p.Gly378Cys	p.G378C	ENST00000171111	NM_203500.1	378	Ggc/Tgc	3/6	0.541716335772417	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.541447959077287	2		421	1016	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293689	1293689	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	218	250	0	ENST00000310581.5:c.1312C>A	p.Pro438Thr	p.P438T	ENST00000310581	NM_198253.2	438	Ccc/Acc	2/16	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.541447959077287	2		250	654	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861093	35861093	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0010612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	130	287	0	ENST00000303115.3:c.221+1G>T		p.X74_splice	ENST00000303115	NM_002185.3	74			1	2	FACETS	0.79	0.719	0.864	0.79	0.719	0.864	SUBCLONAL	1	TRUE	1	0.541447959077287	2		287	608	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876155	35876155	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	247	399	0	ENST00000303115.3:c.947C>A	p.Ala316Asp	p.A316D	ENST00000303115	NM_002185.3	316	gCt/gAt	8/8	1	2	FACETS	0.917	0.858	0.978	0.917	0.858	0.978	CLONAL	1	TRUE	1	0.541447959077287	2		399	995	SUCCESS
APC	324	MSKCC	GRCh37	5	112090652	112090652	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	278	312	0	ENST00000257430.4:c.65A>G	p.Asn22Ser	p.N22S	ENST00000257430	NM_000038.5	22	aAt/aGt	2/16	1	2	FACETS	0.973	0.915	1	0.973	0.915	1	CLONAL	1	TRUE	1	0.541447959077287	2		312	1055	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923356	131923356	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	192	216	0	ENST00000265335.6:c.859A>G	p.Ser287Gly	p.S287G	ENST00000265335		287	Agt/Ggt	6/25	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.541447959077287	2		216	628	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845624	128845624	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs747256384	NA	P-0010612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	456	264	0	ENST00000249373.3:c.920+1G>T		p.X307_splice	ENST00000249373	NM_005631.4	307			0.541716335772417	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.541447959077287	3		264	924	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151933011	151933011	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	229	104	0	ENST00000262189.6:c.2660G>T	p.Gly887Val	p.G887V	ENST00000262189	NM_170606.2	887	gGg/gTg	16/59	0.541716335772417	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.541447959077287	3		104	495	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375976	8375976	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	332	437	1	ENST00000356435.5:c.4621T>A	p.Cys1541Ser	p.C1541S	ENST00000356435		1541	Tgt/Agt	28/35	0.541716335772417	1	FACETS	0.977	0.927	1	0.977	0.927	1	CLONAL	1	TRUE	0	0.541447959077287	1		438	915	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912675	100912675	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0010612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1202	601	450	0	ENST00000325455.5:c.2646+1G>A		p.X882_splice	ENST00000325455	NM_001202474.3	882			0.541716335772417	3	FACETS	0.782	0.751	0.814			1	SUBCLONAL	2	TRUE	NA	0.541447959077287	3		450	1803	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912834	100912834	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0010612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	634	412	0	ENST00000325455.5:c.2489-1G>A		p.X830_splice	ENST00000325455	NM_001202474.3	830			0.541716335772417	3	FACETS	0.852	0.82	0.885			1	CLONAL	2	TRUE	NA	0.541447959077287	3		412	1746	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141808	108141808	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	601	335	0	ENST00000278616.4:c.2856G>T	p.Lys952Asn	p.K952N	ENST00000278616	NM_000051.3	952	aaG/aaT	19/63	0.541716335772417	3	FACETS	1	0.981	1			1	CLONAL	2	TRUE	NA	0.541447959077287	3		335	1373	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428063	49428063	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	308	207	0	ENST00000301067.7:c.10527G>T	p.Gln3509His	p.Q3509H	ENST00000301067	NM_003482.3	3509	caG/caT	38/54	0.541716335772417	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.541447959077287	3		207	696	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440131	49440131	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	650	399	0	ENST00000301067.7:c.4495G>T	p.Gly1499Trp	p.G1499W	ENST00000301067	NM_003482.3	1499	Ggg/Tgg	16/54	0.541716335772417	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.541447959077287	3		399	1448	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924309	112924309	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1306943402	NA	P-0010612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	269	420	1	ENST00000351677.2:c.1255C>T	p.His419Tyr	p.H419Y	ENST00000351677	NM_002834.3	419	Cac/Tac	11/16	0.513927595311989	3	FACETS	0.86	0.805	0.917	0.43	0.402	0.459	CLONAL	1	TRUE	1	0.541447959077287	3		421	1468	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574713	95574713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	399	411	0	ENST00000393063.1:c.2384C>T	p.Pro795Leu	p.P795L	ENST00000393063	NM_030621.3	795	cCt/cTt	16/28	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.541447959077287	2		411	1336	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56875705	56875705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs572483425	NA	P-0010612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	422	568	0	ENST00000308159.5:c.2309C>T	p.Ser770Leu	p.S770L	ENST00000308159	NM_014669.4	770	tCg/tTg	21/22	0.541447959077287	2	FACETS	1	0.975	1	0.519	0.493	0.545	CLONAL	1	TRUE	0	0.541447959077287	2		568	1503	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944246	81944246	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	798	587	0	ENST00000359376.3:c.1855G>T	p.Glu619Ter	p.E619*	ENST00000359376	NM_002661.3	619	Gag/Tag	18/33	0.541447959077287	2	FACETS	0.977	0.948	1	0.977	0.948	1	CLONAL	2	TRUE	0	0.541447959077287	2		587	1509	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138626	11138626	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	455	248	0	ENST00000358026.2:c.3382G>T	p.Gly1128Ter	p.G1128*	ENST00000358026	NM_001128849.1	1128	Gga/Tga	24/36	0.541716335772417	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.541447959077287	2		248	826	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944505	40944505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	307	401	0	ENST00000373198.4:c.1997C>T	p.Ala666Val	p.A666V	ENST00000373198	NM_133170.3	666	gCt/gTt	12/32	0.251215574062343	3	FACETS	0.985	0.926	1	0.328	0.308	0.349	INDETERMINATE	1	TRUE	0	0.541447959077287	3		401	1463	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941975	44941975	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	365	297	0	ENST00000377967.4:c.3225G>T	p.Arg1075Ser	p.R1075S	ENST00000377967	NM_021140.2	1075	agG/agT	22/29	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.541447959077287	1		297	673	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76764086	76764086	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	294	198	0	ENST00000373344.5:c.7222A>G	p.Ile2408Val	p.I2408V	ENST00000373344	NM_000489.3	2408	Ata/Gta	35/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.541447959077287	1		198	573	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295744	212295745	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	601	373	0	ENST00000342788.4:c.2568dup	p.Val857CysfsTer16	p.V857Cfs*16	ENST00000342788	NM_005235.2	856	-/T	21/28	0.541716335772417	3	FACETS	0.956	0.92	0.992	0.956	0.92	0.992	CLONAL	2	TRUE	1	0.541447959077287	3		373	1476	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426884	49426885	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0010612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	479	341	0	ENST00000301067.7:c.11603_11604delinsTT	p.Gly3868Val	p.G3868V	ENST00000301067	NM_003482.3	3868	gGG/gTT	39/54	0.541716335772417	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.541447959077287	3		341	1116	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0010643-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	23	266	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		266	618	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	177	445	0	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	1	2	FACETS	0.975	0.899	1	0.975	0.899	1	CLONAL	1	TRUE	1	0.416352489762424	2		445	872	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881414	37881414	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1131692237	NA	P-0010655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	371	405	0	ENST00000269571.5:c.2606T>G	p.Leu869Arg	p.L869R	ENST00000269571		869	cTg/cGg	21/27	0.416352489762424	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.416352489762424	3		405	956	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238378	98238378	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1318405179	NA	P-0010655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	144	458	0	ENST00000331920.6:c.1666G>A	p.Val556Ile	p.V556I	ENST00000331920	NM_000264.3	556	Gtc/Atc	12/24	1	2	FACETS	0.824	0.752	0.9	0.824	0.752	0.9	CLONAL	1	TRUE	1	0.416352489762424	2		458	839	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835650	68835650	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	251	689	0	ENST00000261769.5:c.242del	p.Gly81ValfsTer2	p.G81Vfs*2	ENST00000261769	NM_004360.3	81	Ggt/gt	3/16	0.416352489762424	1	FACETS	0.95	0.889	1	0.95	0.889	1	CLONAL	1	TRUE	0	0.416352489762424	1		689	1005	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112434	115112435	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	170	346	0	ENST00000257566.3:c.1305dup	p.Arg436ThrfsTer3	p.R436Tfs*3	ENST00000257566	NM_016569.3	435	-/A	7/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.416352489762424	2		346	694	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0010680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	386	536	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.433331174609741	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	2	0.485313334445832	4		536	958	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0010680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	184	345	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.274850589314819	4	FACETS	0.762	0.705	0.821	0.762	0.705	0.821	INDETERMINATE	2	TRUE	2	0.485313334445832	4		345	739	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0010680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1265	879	680	1	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	0.485313334445832	5	FACETS	0.973	0.943	1	0.973	0.943	1	CLONAL	3	TRUE	2	0.485313334445832	5		681	2144	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574678	41574679	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs754418509	NA	P-0010680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	621	788	0	ENST00000263253.7:c.6970dup	p.His2324ProfsTer55	p.H2324Pfs*55	ENST00000263253	NM_001429.3	2321	-/C	31/31	0.243890919838587	3	FACETS	0.853	0.824	0.882	0.853	0.824	0.882	INDETERMINATE	3	TRUE	0	0.485313334445832	3		788	1243	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	178	279	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	0.335058324752433	4	FACETS	0.947	0.878	1	0.947	0.878	1	CLONAL	2	TRUE	2	0.485313334445832	4		279	575	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129749	108129749	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs780619951	NA	P-0010680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	394	370	0	ENST00000278616.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000278616	NM_000051.3	805	Cga/Tga	16/63	0.419017859759619	3	FACETS	0.862	0.826	0.899	0.862	0.826	0.899	CLONAL	3	TRUE	0	0.485313334445832	3		370	780	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953076	2953076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	252	322	0	ENST00000396946.4:c.2864G>A	p.Gly955Asp	p.G955D	ENST00000396946	NM_032415.4	955	gGc/gAc	22/25	NA	2	FACETS	0.991	0.938	1			1	INDETERMINATE	2	TRUE	NA	0.485313334445832	2		322	524	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248648	212248648	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	86	456	0	ENST00000342788.4:c.3619C>G	p.Leu1207Val	p.L1207V	ENST00000342788	NM_005235.2	1207	Ctg/Gtg	28/28	0.124134099796373	4	FACETS	0.506	0.446	0.57	0.253	0.223	0.285	INDETERMINATE	1	TRUE	2	0.485313334445832	4		456	1040	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190946	185190946	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1560132601	NA	P-0010680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1416	308	869	0	ENST00000265026.3:c.1827G>C	p.Gln609His	p.Q609H	ENST00000265026	NM_004721.4	609	caG/caC	11/14	0.485313334445832	5	FACETS	1	0.991	1	0.424	0.398	0.451	CLONAL	1	TRUE	2	0.485313334445832	5		869	1724	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521306	187521306	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	322	646	1	ENST00000441802.2:c.11849T>A	p.Val3950Glu	p.V3950E	ENST00000441802	NM_005245.3	3950	gTg/gAg	22/27	0.124134099796373	4	FACETS	0.907	0.858	0.958	0.907	0.858	0.958	INDETERMINATE	2	TRUE	2	0.485313334445832	4		647	1086	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751931	57751931	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55768901	NA	P-0010680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1264	527	689	0	ENST00000274289.3:c.1306G>A	p.Glu436Lys	p.E436K	ENST00000274289	NM_006622.3	436	Gaa/Aaa	10/14	0.274850589314819	4	FACETS	0.901	0.862	0.94	0.901	0.862	0.94	INDETERMINATE	2	TRUE	2	0.485313334445832	4		689	1791	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858552	57858552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143548857	NA	P-0010680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	276	765	1	ENST00000228682.2:c.290C>T	p.Thr97Met	p.T97M	ENST00000228682	NM_005269.2	97	aCg/aTg	4/12	0.433331174609741	4	FACETS	1	0.98	1	0.555	0.52	0.592	CLONAL	1	TRUE	2	0.485313334445832	4		766	1521	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46266423	46266423	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	282	703	0	ENST00000371998.3:c.2408T>A	p.Ile803Asn	p.I803N	ENST00000371998		803	aTt/aAt	13/23	NA	2	FACETS	0.856	0.803	0.911			1	INDETERMINATE	1	TRUE	NA	0.485313334445832	2		703	1357	SUCCESS
APC	324	MSKCC	GRCh37	5	112175645	112175645	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	294	532	0	ENST00000257430.4:c.4354del	p.Val1452TyrfsTer21	p.V1452Yfs*21	ENST00000257430	NM_000038.5	1452	Gta/ta	16/16	0.274850589314819	4	FACETS	0.824	0.776	0.873	0.824	0.776	0.873	INDETERMINATE	2	TRUE	2	0.485313334445832	4		532	1092	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0010681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1523	140	152	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.16	2		152	1663	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0010681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1246	88	433	2	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	1	2	FACETS	0.825	0.728	0.929	0.825	0.728	0.929	CLONAL	1	TRUE	1	0.16	2		435	1334	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138521	11138521	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1340	75	596	1	ENST00000358026.2:c.3277C>T	p.Arg1093Ter	p.R1093*	ENST00000358026	NM_001128849.1	1093	Cga/Tga	24/36	1	2	FACETS	0.663	0.578	0.754	0.663	0.578	0.754	SUBCLONAL	1	TRUE	1	0.16	2		597	1415	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307983	11307983	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1262	84	508	0	ENST00000361445.4:c.1009A>T	p.Ser337Cys	p.S337C	ENST00000361445	NM_004958.3	337	Agc/Tgc	7/58	1	2	FACETS	0.78	0.686	0.881	0.78	0.686	0.881	SUBCLONAL	1	TRUE	1	0.16	2		508	1346	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646166	215646166	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	37	256	0	ENST00000260947.4:c.432A>C	p.Lys144Asn	p.K144N	ENST00000260947	NM_000465.2	144	aaA/aaC	4/11	1	2	FACETS	0.724	0.595	0.868	0.724	0.595	0.868	SUBCLONAL	1	TRUE	1	0.16	2		256	639	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43745244	43745244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2518	243	867	2	ENST00000523873.1:c.157C>T	p.His53Tyr	p.H53Y	ENST00000523873		53	Cat/Tat	3/8	0.3	3	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.16	3		869	2761	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937095	76937095	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	563	800	0	ENST00000373344.5:c.3653A>T	p.Glu1218Val	p.E1218V	ENST00000373344	NM_000489.3	1218	gAg/gTg	9/35	1	2	FACETS	0.942	0.907	0.978	0.942	0.907	0.978	CLONAL	1	TRUE	1	0.941666602564129	2		800	1269	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131178	55131179	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGGT	novel	NA	P-0010753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	236	639	0	ENST00000257290.5:c.722_725dup	p.Val243GlyfsTer3	p.V243Gfs*3	ENST00000257290	NM_006206.4	241	gag/gAGGTag	5/23	1	2	FACETS	0.426	0.397	0.456	0.426	0.397	0.456	SUBCLONAL	1	TRUE	1	0.941666602564129	2		639	1177	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131150	55131151	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTG	novel	NA	P-0010753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	180	644	0	ENST00000257290.5:c.696_698dup	p.Val233dup	p.V233dup	ENST00000257290	NM_006206.4	233	-/GTG	5/23	1	2	FACETS	0.314	0.289	0.341	0.314	0.289	0.341	SUBCLONAL	1	TRUE	1	0.941666602564129	2		644	1216	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	113	353	0	ENST00000397062.3:c.92G>A	p.Gly31Glu	p.G31E	ENST00000397062	NM_006164.4	31	gGa/gAa	2/5	0.470553322303949	3	FACETS	0.792	0.714	0.873	0.396	0.357	0.437	SUBCLONAL	1	TRUE	1	0.633819341520012	3		353	593	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578485	7578485	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1064793929	NA	P-0010817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	164	396	0	ENST00000269305.4:c.445del	p.Ser149ProfsTer21	p.S149Pfs*21	ENST00000269305	NM_001126112.2	149	Tcc/cc	5/11	0.470553322303949	3	FACETS	0.851	0.782	0.922	0.425	0.391	0.461	CLONAL	1	TRUE	1	0.633819341520012	3		396	801	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595930	52595930	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs367999949	NA	P-0010817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	354	594	0	ENST00000394830.3:c.3985A>G	p.Ile1329Val	p.I1329V	ENST00000394830	NM_018313.4	1329	Atc/Gtc	26/30	0.464462005438553	2	FACETS	0.766	0.731	0.801	0.766	0.731	0.801	SUBCLONAL	2	TRUE	0	0.633819341520012	2		594	729	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280031	66280031	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	104	435	0	ENST00000273854.3:c.1658G>T	p.Arg553Leu	p.R553L	ENST00000273854	NM_004439.5	553	cGa/cTa	7/18	0.47255736938453	3	FACETS	0.607	0.544	0.674	0.303	0.272	0.337	SUBCLONAL	1	TRUE	1	0.633819341520012	3		435	712	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412325	139412325	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	491	434	0	ENST00000277541.6:c.1320T>G	p.Cys440Trp	p.C440W	ENST00000277541	NM_017617.3	440	tgT/tgG	8/34	0.633819341520012	3	FACETS	1	0.995	1	0.809	0.78	0.837	CLONAL	2	TRUE	0	0.633819341520012	3		434	841	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923260	26923260	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	323	563	0	ENST00000381527.3:c.256C>G	p.Leu86Val	p.L86V	ENST00000381527	NM_001260.1	86	Ctg/Gtg	3/13	0.464462005438553	2	FACETS	1	0.994	1	0.687	0.653	0.721	CLONAL	1	TRUE	0	0.633819341520012	2		563	742	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426812	49426813	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCGT	novel	NA	P-0010817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	210	333	0	ENST00000301067.7:c.11675_11676insACGA	p.Pro3893ArgfsTer120	p.P3893Rfs*120	ENST00000301067	NM_003482.3	3892	cag/caACGAg	39/54	0.417687193162651	4	FACETS	0.761	0.71	0.814	0.761	0.71	0.814	SUBCLONAL	2	TRUE	2	0.633819341520012	4		333	711	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425773	49425774	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0010817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	243	410	1	ENST00000301067.7:c.12714_12715del	p.Gln4239AspfsTer94	p.Q4239Dfs*94	ENST00000301067	NM_003482.3	4238	cgCCag/cgag	39/54	0.417687193162651	4	FACETS	0.897	0.843	0.953	0.897	0.843	0.953	CLONAL	2	TRUE	2	0.633819341520012	4		411	698	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579316	7579317	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	257	350	0	ENST00000269305.4:c.370dup	p.Cys124LeufsTer25	p.C124Lfs*25	ENST00000269305	NM_001126112.2	124	tgc/tTgc	4/11	0.470553322303949	3	FACETS	0.846	0.798	0.895	0.846	0.798	0.895	CLONAL	2	TRUE	1	0.633819341520012	3		350	631	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947540	48947540	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0010836-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	57	334	0	ENST00000267163.4:c.1128-1G>A		p.X376_splice	ENST00000267163	NM_000321.2	376			0.266294707731473	1	FACETS	0.937	0.807	1	0.937	0.807	1	CLONAL	1	TRUE	0	0.266294707731473	1		334	396	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23635400	23635400	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010836-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	124	494	0	ENST00000261584.4:c.2764A>C	p.Ile922Leu	p.I922L	ENST00000261584	NM_024675.3	922	Ata/Cta	8/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.266294707731473	2		494	815	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411882	116411896	+	splice_region_variant,intron_variant	Splice_Region	DEL	TTTCTTTCTCTCTGT	TTTCTTTCTCTCTGT	-	novel	NA	P-0010836-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	226	758	0	ENST00000397752.3:c.2888-18_2888-4del		p.X963_splice	ENST00000397752	NM_000245.2	963			0.22958606448648	2	FACETS	0.769	0.715	0.824	0.769	0.715	0.824	SUBCLONAL	2	TRUE	0	0.266294707731473	2		758	1104	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0011012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	9	423	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.392664682803801	5	FACETS	0.155	0.102	0.223	0.052	0.034	0.075	INDETERMINATE	1	TRUE	2	0.922686719299528	5		423	300	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0011012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	17	368	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.392664682803801	5	FACETS	0.293	0.218	0.382	0.098	0.072	0.128	INDETERMINATE	1	TRUE	2	0.922686719299528	5		368	300	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739678	41739678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	36	952	0	ENST00000242208.4:c.295G>A	p.Gly99Arg	p.G99R	ENST00000242208	NM_002192.2	99	Ggg/Agg	2/3	NA	2	FACETS	0.129	0.105	0.155			1	INDETERMINATE	1	TRUE	NA	0.922686719299528	2		952	605	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113343	209113344	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0011012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	15	408	0	ENST00000345146.2:c.163dup	p.Gln55ProfsTer14	p.Q55Pfs*14	ENST00000345146	NM_005896.2	55	caa/cCaa	4/10	0.396774295471963	6	FACETS	0.482	0.353	0.635	0.161	0.117	0.212	INDETERMINATE	1	TRUE	3	0.922686719299528	6		408	192	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0011217-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	508	358	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.733367241198919	3	FACETS	0.818	0.786	0.851			1	CLONAL	2	TRUE	NA	0.733367241198919	3		358	1157	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023559	27023560	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0011217-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	177	449	0	ENST00000324856.7:c.671dup	p.Pro225AlafsTer175	p.P225Afs*175	ENST00000324856	NM_006015.4	222	tac/taCc	1/20	1	2	FACETS	0.53	0.489	0.574	0.53	0.489	0.574	SUBCLONAL	1	TRUE	1	0.733367241198919	2		449	910	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477837	140477851	+	inframe_deletion	In_Frame_Del	DEL	TAGGTGCTGTCACAT	TAGGTGCTGTCACAT	-	novel	NA	P-0011217-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	319	487	0	ENST00000288602.6:c.1457_1471del	p.Asn486_Pro490del	p.N486_P490del	ENST00000288602	NM_004333.4	486	aATGTGACAGCACCTAca/aca	12/18	1	2	FACETS	0.7	0.661	0.741	0.7	0.661	0.741	SUBCLONAL	1	TRUE	1	0.733367241198919	2		487	1242	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702260	47702260	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs63749982	NA	P-0011217-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	271	429	0	ENST00000233146.2:c.1856A>G	p.Tyr619Cys	p.Y619C	ENST00000233146	NM_000251.2	619	tAt/tGt	12/16	1	2	FACETS	0.616	0.577	0.656	0.616	0.577	0.656	SUBCLONAL	1	TRUE	1	0.733367241198919	2		429	1200	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449808	8449808	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779920240	NA	P-0011217-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	181	359	0	ENST00000356435.5:c.3905G>A	p.Ser1302Asn	p.S1302N	ENST00000356435		1302	aGc/aAc	23/35	0.490321410160447	2	FACETS	0.593	0.548	0.641	0.297	0.274	0.321	SUBCLONAL	1	TRUE	0	0.733367241198919	2		359	832	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741637	17741637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011217-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	34	183	0	ENST00000250003.3:c.308G>A	p.Arg103His	p.R103H	ENST00000250003	NM_002478.4	103	cGc/cAc	1/3	1	2	FACETS	0.217	0.177	0.262	0.217	0.177	0.262	SUBCLONAL	1	TRUE	1	0.733367241198919	2		183	428	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138885	64138885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1382584499	NA	P-0011217-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	78	367	0	ENST00000334205.4:c.2252C>T	p.Pro751Leu	p.P751L	ENST00000334205	NM_003942.2	751	cCg/cTg	17/17	1	2	FACETS	0.346	0.304	0.391	0.346	0.304	0.391	SUBCLONAL	1	TRUE	1	0.733367241198919	2		367	615	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499701	18499701	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011217-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	94	361	0	ENST00000266497.5:c.1556C>A	p.Pro519His	p.P519H	ENST00000266497		519	cCc/cAc	10/31	1	2	FACETS	0.315	0.28	0.353	0.315	0.28	0.353	SUBCLONAL	1	TRUE	1	0.733367241198919	2		361	813	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446697	49446697	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0011217-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	37	242	0	ENST00000301067.7:c.1112+1G>A		p.X371_splice	ENST00000301067	NM_003482.3	371			1	2	FACETS	0.161	0.132	0.193	0.161	0.132	0.193	SUBCLONAL	1	TRUE	1	0.733367241198919	2		242	628	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974798	15974798	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011217-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	242	415	0	ENST00000268712.3:c.4077T>G	p.Ile1359Met	p.I1359M	ENST00000268712	NM_006311.3	1359	atT/atG	30/46	1	2	FACETS	0.641	0.598	0.684	0.641	0.598	0.684	SUBCLONAL	1	TRUE	1	0.733367241198919	2		415	1030	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0011358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	131	491	0				ENST00000310581	NM_198253.2	-/1132			0.243430434026702	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.320267647926867	1		491	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0011358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	161	329	2	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.293189409395277	1	FACETS	0.899	0.825	0.977	0.899	0.825	0.977	CLONAL	1	TRUE	0	0.320267647926867	1		331	939	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0011358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	98	311	0	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	1	2	FACETS	0.688	0.613	0.768	0.688	0.613	0.768	SUBCLONAL	1	TRUE	1	0.320267647926867	2		311	890	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0011358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	175	286	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.320267647926867	2		286	744	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023954	27023954	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	26	61	0	ENST00000324856.7:c.1060C>T	p.Gln354Ter	p.Q354*	ENST00000324856	NM_006015.4	354	Caa/Taa	1/20	1	2	FACETS	0.748	0.596	0.921	0.748	0.596	0.921	CLONAL	1	TRUE	1	0.320267647926867	2		61	217	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218348	133218348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1171272614	NA	P-0011358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	128	364	0	ENST00000320574.5:c.5263G>A	p.Gly1755Arg	p.G1755R	ENST00000320574	NM_006231.2	1755	Ggg/Agg	39/49	1	2	FACETS	0.875	0.792	0.962	0.875	0.792	0.962	CLONAL	1	TRUE	1	0.320267647926867	2		364	914	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0011383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	711	328	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	2	TRUE	NA	0.799103477975047	2		328	844	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0011383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	202	491	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.783	0.742	0.822			1	INDETERMINATE	2	TRUE	NA	0.799103477975047	2		491	323	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0011383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	4189	395	0	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.799103477975047	15	FACETS	1	0.999	1			1	CLONAL	13	TRUE	NA	0.799103477975047	15		395	4837	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321351	1321351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763354527	NA	P-0011383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	371	426	0	ENST00000400841.2:c.404C>T	p.Thr135Met	p.T135M	ENST00000400841		135	aCg/aTg	4/6	0.426305401842815	6	FACETS	1	0.992	1	0.597	0.567	0.626	INDETERMINATE	2	TRUE	2	0.799103477975047	6		426	1011	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120326	94120326	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	418	487	2	ENST00000369303.4:c.725C>A	p.Ala242Glu	p.A242E	ENST00000369303	NM_004440.3	242	gCg/gAg	3/17	1	2	FACETS	0.948	0.905	0.992	0.948	0.905	0.992	CLONAL	1	TRUE	1	0.799103477975047	2		489	1103	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222346	53222346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	208	526	1	ENST00000375401.3:c.4486G>A	p.Glu1496Lys	p.E1496K	ENST00000375401	NM_004187.3	1496	Gaa/Aaa	26/26	0.358990932694736	5	FACETS	0.948	0.879	1			1	INDETERMINATE	1	TRUE	NA	0.799103477975047	5		527	1207	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756766	756767	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0011383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	201	411	0	ENST00000314574.4:c.61dup	p.Thr21AsnfsTer33	p.T21Nfs*33	ENST00000314574	NM_005433.3	21	act/aAct	2/12	0.422891547791423	1	FACETS	0.46	0.428	0.492	0.46	0.428	0.492	INDETERMINATE	1	TRUE	0	0.799103477975047	1		411	657	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0011391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	101	212	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.971	0.867	1	0.971	0.867	1	CLONAL	1	TRUE	1	0.24977760162588	2		212	833	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043377	180043377	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771345898	NA	P-0011391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	158	403	1	ENST00000261937.6:c.3209G>A	p.Arg1070His	p.R1070H	ENST00000261937	NM_182925.4	1070	cGc/cAc	23/30	0.239684458341506	1	FACETS	0.873	0.798	0.952	0.873	0.798	0.952	CLONAL	1	TRUE	0	0.24977760162588	1		404	1268	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0011391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	129	367	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.897	0.812	0.988	0.897	0.812	0.988	CLONAL	1	TRUE	1	0.24977760162588	2		367	1151	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099098	27099098	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	120	282	0	ENST00000324856.7:c.3514C>T	p.Gln1172Ter	p.Q1172*	ENST00000324856	NM_006015.4	1172	Cag/Tag	13/20	0.228809229073263	1	FACETS	0.84	0.757	0.928	0.84	0.757	0.928	CLONAL	1	TRUE	0	0.24977760162588	1		282	1001	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459858	149459858	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs566891025	NA	P-0011391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	85	326	1	ENST00000286301.3:c.349G>A	p.Val117Met	p.V117M	ENST00000286301	NM_005211.3	117	Gtg/Atg	4/22	0.214378488317868	2	FACETS	0.723	0.637	0.814	0.361	0.318	0.407	SUBCLONAL	1	TRUE	0	0.24977760162588	2		327	942	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604784	48604790	+	frameshift_variant	Frame_Shift_Del	DEL	CTAGACG	CTAGACG	-	novel	NA	P-0011391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	130	279	0	ENST00000342988.3:c.1606_1612del	p.Leu536LysfsTer14	p.L536Kfs*14	ENST00000342988	NM_005359.5	536	CTAGACGaa/aa	12/12	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.24977760162588	2		279	984	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624279	89624280	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0011391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	85	198	0	ENST00000371953.3:c.55dup	p.Asp19GlyfsTer25	p.D19Gfs*25	ENST00000371953	NM_000314.4	18	gag/gaGg	1/9	1	2	FACETS	0.989	0.875	1	0.989	0.875	1	CLONAL	1	TRUE	1	0.24977760162588	2		198	688	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578515	7578515	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1212996409	NA	P-0011403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	749	381	0	ENST00000269305.4:c.415A>T	p.Lys139Ter	p.K139*	ENST00000269305	NM_001126112.2	139	Aag/Tag	5/11	0.959656072641689	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.959656072641689	1		381	781	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679087	117679087	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	514	330	0	ENST00000368508.3:c.3734C>A	p.Ser1245Ter	p.S1245*	ENST00000368508	NM_002944.2	1245	tCa/tAa	24/43	1	2	FACETS	0.94	0.904	0.977	0.94	0.904	0.977	CLONAL	1	TRUE	1	0.959656072641689	2		330	1139	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729700	41729700	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	1028	697	1	ENST00000242208.4:c.829G>T	p.Gly277Cys	p.G277C	ENST00000242208	NM_002192.2	277	Ggt/Tgt	3/3	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.959656072641689	2		698	2069	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512084	148512084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	638	351	0	ENST00000320356.2:c.1594C>T	p.Arg532Trp	p.R532W	ENST00000320356	NM_004456.4	532	Cgg/Tgg	14/20	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.959656072641689	2		351	1234	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033823	49033823	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0011403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	586	399	0	ENST00000267163.4:c.1961-1G>T		p.X654_splice	ENST00000267163	NM_000321.2	654			0.959656072641689	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.959656072641689	1		399	626	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272849	18272849	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs767402281	NA	P-0011403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2135	307	474	0	ENST00000222254.8:c.889G>C	p.Val297Leu	p.V297L	ENST00000222254	NM_005027.3	297	Gtt/Ctt	7/16	0.873469039274037	3	FACETS	0.388	0.363	0.413	0.194	0.181	0.207	SUBCLONAL	1	TRUE	1	0.959656072641689	3		474	2442	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0011439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	1241	491	0				ENST00000310581	NM_198253.2	-/1132			0.487710067379422	6	FACETS	1	0.991	1			1	CLONAL	4	TRUE	NA	0.785412074595454	6		491	1988	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0011439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	225	543	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.457	0.425	0.49	0.457	0.425	0.49	SUBCLONAL	1	TRUE	1	0.785412074595454	2		543	1254	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0011439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	508	531	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.384169381491052	1	FACETS	1	0.995	1	1	0.995	1	INDETERMINATE	1	TRUE	0	0.785412074595454	1		531	711	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874092	151874093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0011439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1296	1033	934	0	ENST00000262189.6:c.8445dup	p.Ser2816IlefsTer6	p.S2816Ifs*6	ENST00000262189	NM_170606.2	2815	-/A	38/59	0.424917417732087	3	FACETS	0.786	0.765	0.809	0.786	0.765	0.809	INDETERMINATE	2	TRUE	1	0.785412074595454	3		934	2329	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265579	198265579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	297	767	1	ENST00000335508.6:c.2578G>A	p.Glu860Lys	p.E860K	ENST00000335508	NM_012433.2	860	Gaa/Aaa	18/25	0.384169381491052	1	FACETS	0.344	0.323	0.365	0.344	0.323	0.365	INDETERMINATE	1	TRUE	0	0.785412074595454	1		768	1336	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440431	49440431	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1240601136	NA	P-0011439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	230	557	1	ENST00000301067.7:c.4379del	p.Pro1460HisfsTer46	p.P1460Hfs*46	ENST00000301067	NM_003482.3	1460	cCa/ca	15/54	0.384169381491052	1	FACETS	0.378	0.353	0.405	0.378	0.353	0.405	INDETERMINATE	1	TRUE	0	0.785412074595454	1		558	940	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737627	145737627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771349728	NA	P-0011439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	562	721	3	ENST00000428558.2:c.3136G>A	p.Glu1046Lys	p.E1046K	ENST00000428558	NM_004260.3	1046	Gag/Aag	19/22	0.424917417732087	3	FACETS	1	0.993	1	0.578	0.554	0.603	INDETERMINATE	1	TRUE	1	0.785412074595454	3		724	1723	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438067	49438067	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886043414	NA	P-0011439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	567	616	4	ENST00000301067.7:c.5104C>T	p.Arg1702Ter	p.R1702*	ENST00000301067	NM_003482.3	1702	Cga/Tga	21/54	0.384169381491052	1	FACETS	0.714	0.688	0.74	0.714	0.688	0.74	INDETERMINATE	1	TRUE	0	0.785412074595454	1		620	1228	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874923	151874923	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	530	668	0	ENST00000262189.6:c.7615C>T	p.Gln2539Ter	p.Q2539*	ENST00000262189	NM_170606.2	2539	Cag/Tag	38/59	0.424917417732087	3	FACETS	1	0.991	1	0.56	0.536	0.585	INDETERMINATE	1	TRUE	1	0.785412074595454	3		668	1677	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097641	27097641	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	584	709	0	ENST00000324856.7:c.3230C>A	p.Ala1077Glu	p.A1077E	ENST00000324856	NM_006015.4	1077	gCa/gAa	12/20	0.384169381491052	1	FACETS	0.735	0.708	0.761	0.735	0.708	0.761	INDETERMINATE	1	TRUE	0	0.785412074595454	1		709	1229	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265492	198265492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	292	723	3	ENST00000335508.6:c.2665G>A	p.Glu889Lys	p.E889K	ENST00000335508	NM_012433.2	889	Gaa/Aaa	18/25	0.384169381491052	1	FACETS	0.351	0.329	0.373	0.351	0.329	0.373	INDETERMINATE	1	TRUE	0	0.785412074595454	1		726	1287	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148544368	148544368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	485	618	0	ENST00000320356.2:c.23C>T	p.Ser8Phe	p.S8F	ENST00000320356	NM_004456.4	8	tCt/tTt	2/20	0.424917417732087	3	FACETS	1	0.989	1	0.554	0.529	0.579	INDETERMINATE	1	TRUE	1	0.785412074595454	3		618	1552	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873492	151873492	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1415	632	914	0	ENST00000262189.6:c.9046C>G	p.Gln3016Glu	p.Q3016E	ENST00000262189	NM_170606.2	3016	Caa/Gaa	38/59	0.424917417732087	3	FACETS	1	0.991	1	0.547	0.526	0.569	INDETERMINATE	1	TRUE	1	0.785412074595454	3		914	2047	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876929	151876929	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	416	534	0	ENST00000262189.6:c.7432C>T	p.His2478Tyr	p.H2478Y	ENST00000262189	NM_170606.2	2478	Cat/Tat	37/59	0.424917417732087	3	FACETS	1	0.988	1	0.556	0.529	0.583	INDETERMINATE	1	TRUE	1	0.785412074595454	3		534	1327	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409501	80409501	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	96	471	0	ENST00000286548.4:c.613G>A	p.Asp205Asn	p.D205N	ENST00000286548	NM_002072.3	205	Gat/Aat	5/7	0.741324695581337	2	FACETS	0.26	0.231	0.291	0.13	0.115	0.146	SUBCLONAL	1	TRUE	0	0.785412074595454	2		471	939	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100754	8100754	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	412	511	1	ENST00000346208.3:c.728C>A	p.Ser243Tyr	p.S243Y	ENST00000346208		243	tCc/tAc	3/6	0.384169381491052	1	FACETS	0.757	0.725	0.789	0.757	0.725	0.789	INDETERMINATE	1	TRUE	0	0.785412074595454	1		512	842	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46215230	46215230	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	195	531	0	ENST00000334344.6:c.665G>A	p.Gly222Glu	p.G222E	ENST00000334344	NM_152641.2	222	gGa/gAa	6/21	0.384169381491052	1	FACETS	0.338	0.313	0.365	0.338	0.313	0.365	INDETERMINATE	1	TRUE	0	0.785412074595454	1		531	891	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218838	133218838	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	633	732	1	ENST00000320574.5:c.5098G>A	p.Asp1700Asn	p.D1700N	ENST00000320574	NM_006231.2	1700	Gat/Aat	38/49	0.384169381491052	1	FACETS	0.783	0.757	0.809	0.783	0.757	0.809	INDETERMINATE	1	TRUE	0	0.785412074595454	1		733	1250	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843534	3843534	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121434625	NA	P-0011439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	452	522	1	ENST00000262367.5:c.1069C>T	p.Gln357Ter	p.Q357*	ENST00000262367	NM_004380.2	357	Cag/Tag	4/31	1	2	FACETS	0.949	0.907	0.991	0.949	0.907	0.991	CLONAL	1	TRUE	1	0.785412074595454	2		523	1213	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900440	3900440	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	596	795	0	ENST00000262367.5:c.656G>T	p.Gly219Val	p.G219V	ENST00000262367	NM_004380.2	219	gGa/gTa	2/31	1	2	FACETS	0.958	0.921	0.995	0.958	0.921	0.995	CLONAL	1	TRUE	1	0.785412074595454	2		795	1584	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804357	46804357	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749518336	NA	P-0011439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1443	359	856	4	ENST00000290295.7:c.650G>A	p.Arg217His	p.R217H	ENST00000290295	NM_006361.5	217	cGc/cAc	2/2	1	2	FACETS	0.507	0.479	0.536	0.507	0.479	0.536	SUBCLONAL	1	TRUE	1	0.785412074595454	2		860	1802	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164627	36164627	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	240	526	0	ENST00000300305.3:c.1248C>G	p.Phe416Leu	p.F416L	ENST00000300305		416	ttC/ttG	8/8	0.384169381491052	1	FACETS	0.407	0.381	0.435	0.407	0.381	0.435	INDETERMINATE	1	TRUE	0	0.785412074595454	1		526	911	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573187	64573196	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCTACTTC	TGGCTACTTC	-	novel	NA	P-0011439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	507	796	3	ENST00000312049.6:c.1096_1105del	p.Glu366MetfsTer8	p.E366Mfs*8	ENST00000312049	NM_130799.2	366	GAAGTAGCCAat/at	8/10	0.767525375840879	1	FACETS	0.838	0.807	0.868	0.838	0.807	0.868	CLONAL	1	TRUE	0	0.785412074595454	1		799	936	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0011545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	152	553	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.43125516541983	4	FACETS	0.936	0.862	1	0.936	0.862	1	CLONAL	2	TRUE	2	0.478550335875547	4		553	502	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279368	38279368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	261	546	2	ENST00000425967.3:c.1121C>T	p.Ala374Val	p.A374V	ENST00000425967	NM_001174067.1	374	gCg/gTg	9/19	0.223873019380471	5	FACETS	1	0.973	1	0.709	0.666	0.753	INDETERMINATE	2	TRUE	2	0.478550335875547	5		548	881	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92244566	92244566	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	29	299	0	ENST00000265734.4:c.869C>G	p.Ser290Cys	p.S290C	ENST00000265734	NM_001259.6	290	tCt/tGt	8/8	0.43125516541983	4	FACETS	0.33	0.264	0.405	0.165	0.132	0.203	SUBCLONAL	1	TRUE	2	0.478550335875547	4		299	543	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467792	99467792	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	106	419	0	ENST00000268035.6:c.2661G>C	p.Lys887Asn	p.K887N	ENST00000268035	NM_000875.3	887	aaG/aaC	13/21	0.262712060983594	5	FACETS	1	0.924	1	0.346	0.31	0.384	INDETERMINATE	1	TRUE	2	0.478550335875547	5		419	734	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41199719	41199719	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs80357149	NA	P-0011545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	415	501	1	ENST00000357654.3:c.5408G>T	p.Gly1803Val	p.G1803V	ENST00000357654	NM_007294.3	1803	gGt/gTt	22/23	0.478550335875547	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	0	0.478550335875547	3		502	711	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578196	7578197	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCACCACACTAT	novel	NA	P-0011545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	286	562	0	ENST00000269305.4:c.641_652dup	p.Val217_Val218insAspSerValVal	p.V217_V218insDSVV	ENST00000269305	NM_001126112.2	218	gtg/gATAGTGTGGTGGtg	6/11	0.478550335875547	2	FACETS	0.845	0.8	0.891	0.845	0.8	0.891	CLONAL	2	TRUE	0	0.478550335875547	2		562	707	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0012119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	67	491	0				ENST00000310581	NM_198253.2	-/1132			0.143091966355557	3	FACETS	0.915	0.8	1	0.915	0.8	1	CLONAL	2	TRUE	1	0.226472378406732	3		491	360	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0012119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	122	621	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.170108100146056	2	FACETS	0.797	0.721	0.876	0.797	0.721	0.876	SUBCLONAL	2	TRUE	0	0.226472378406732	2		623	676	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0012119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	1147	152	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.226472378406732	11	FACETS	1	0.994	1			1	CLONAL	12	TRUE	NA	0.226472378406732	11		152	1651	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871202	35871202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200772681	NA	P-0012119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	37	469	0	ENST00000303115.3:c.424G>A	p.Gly142Arg	p.G142R	ENST00000303115	NM_002185.3	142	Gga/Aga	4/8	0.143091966355557	3	FACETS	0.66	0.543	0.791	0.33	0.271	0.396	SUBCLONAL	1	TRUE	1	0.226472378406732	3		469	551	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242662	46242662	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	65	447	1	ENST00000334344.6:c.1624C>T	p.Arg542Ter	p.R542*	ENST00000334344	NM_152641.2	542	Cga/Tga	13/21	0.174100288417805	2	FACETS	1	0.969	1	0.707	0.615	0.805	CLONAL	1	TRUE	0	0.226472378406732	2		448	406	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553249	106553249	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1415765117	NA	P-0012119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	100	624	0	ENST00000369096.4:c.1214C>T	p.Ser405Leu	p.S405L	ENST00000369096	NM_001198.3	405	tCg/tTg	5/7	0.143091966355557	3	FACETS	0.861	0.771	0.956	0.861	0.771	0.956	CLONAL	2	TRUE	1	0.226472378406732	3		624	571	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344593	118344593	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064797056	NA	P-0012119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	89	1261	0	ENST00000534358.1:c.2719C>T	p.Pro907Ser	p.P907S	ENST00000534358	NM_005933.3	907	Cct/Tct	3/36	1	2	FACETS	0.95	0.842	1	0.95	0.842	1	CLONAL	1	TRUE	1	0.226472378406732	2		1261	827	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540164	187540164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1401234994	NA	P-0012119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	46	872	0	ENST00000441802.2:c.7576C>T	p.His2526Tyr	p.H2526Y	ENST00000441802	NM_005245.3	2526	Cac/Tac	10/27	1	2	FACETS	0.715	0.602	0.841	0.715	0.602	0.841	SUBCLONAL	1	TRUE	1	0.226472378406732	2		872	568	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181543	32181543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	39	662	0	ENST00000375023.3:c.2242C>T	p.Pro748Ser	p.P748S	ENST00000375023	NM_004557.3	748	Cct/Tct	14/30	0.143091966355557	3	FACETS	0.743	0.615	0.886	0.372	0.307	0.443	SUBCLONAL	1	TRUE	1	0.226472378406732	3		662	516	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704646	117704646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	78	538	0	ENST00000368508.3:c.2330G>A	p.Gly777Glu	p.G777E	ENST00000368508	NM_002944.2	777	gGa/gAa	16/43	0.143091966355557	3	FACETS	1	0.974	1	0.709	0.624	0.8	CLONAL	1	TRUE	1	0.226472378406732	3		538	541	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486082	8486082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	83	811	1	ENST00000356435.5:c.2735C>T	p.Ser912Phe	p.S912F	ENST00000356435		912	tCc/tTc	17/35	0.170108100146056	2	FACETS	1	0.942	1	0.555	0.49	0.625	CLONAL	1	TRUE	0	0.226472378406732	2		812	660	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104353479	104353479	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0012119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	25	445	0	ENST00000369902.3:c.683+1G>A		p.X228_splice	ENST00000369902	NM_016169.3	228			1	2	FACETS	0.617	0.486	0.767	0.617	0.486	0.767	SUBCLONAL	1	TRUE	1	0.226472378406732	2		445	358	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205188	61205188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	64	687	0	ENST00000301761.2:c.128C>T	p.Ser43Phe	p.S43F	ENST00000301761	NM_017841.2	43	tCc/tTc	2/4	1	2	FACETS	0.866	0.749	0.992	0.866	0.749	0.992	CLONAL	1	TRUE	1	0.226472378406732	2		687	653	SUCCESS
ATM	472	MSKCC	GRCh37	11	108128209	108128209	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	47	501	0	ENST00000278616.4:c.2252C>T	p.Ser751Phe	p.S751F	ENST00000278616	NM_000051.3	751	tCt/tTt	15/63	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.226472378406732	2		501	394	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923494	9923494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	93	577	0	ENST00000330684.3:c.1793C>T	p.Ser598Phe	p.S598F	ENST00000330684	NM_001134407.1	598	tCt/tTt	9/13	0.197986433925049	2	FACETS	0.861	0.769	0.958	0.861	0.769	0.958	CLONAL	2	TRUE	0	0.226472378406732	2		577	477	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727132	40727132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	87	719	0	ENST00000373198.4:c.3832G>A	p.Asp1278Asn	p.D1278N	ENST00000373198	NM_133170.3	1278	Gac/Aac	28/32	0.151581566015098	4	FACETS	0.788	0.698	0.883	0.788	0.698	0.883	SUBCLONAL	2	TRUE	2	0.226472378406732	4		719	598	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0012132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	101	179	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.384806215377432	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	0	0.384806215377432	1		179	306	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934112	48934151	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	GAATCTCTAACTTTCTTTAAAAATGTACATTTTTTTTTCA	GAATCTCTAACTTTCTTTAAAAATGTACATTTTTTTTTCA	-	novel	NA	P-0012132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	17	165	0	ENST00000267163.4:c.608-40_608-1del		p.X203_splice	ENST00000267163	NM_000321.2	203			0.384806215377432	1	FACETS	0.294	0.219	0.382	0.294	0.219	0.382	SUBCLONAL	1	FALSE	0	0.384806215377432	1		165	243	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0012167-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	66	443	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.15	2		443	819	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779042	135779042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012167-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	51	334	0	ENST00000298552.3:c.2204C>T	p.Ala735Val	p.A735V	ENST00000298552	NM_001162426.1	735	gCc/gTc	17/23	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.15	2		334	666	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012205-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	171	456	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.941	0.87	1	0.941	0.87	1	CLONAL	1	TRUE	1	0.641302358313938	2		456	567	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0012205-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	218	266	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.874	0.815	0.934	0.874	0.815	0.934	CLONAL	1	TRUE	1	0.641302358313938	2		266	778	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806092	1806092	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913484	NA	P-0012205-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	419	654	3	ENST00000260795.2:c.1111A>T	p.Ser371Cys	p.S371C	ENST00000260795		371	Agt/Tgt	8/17	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.641302358313938	2		657	1211	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0012205-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	238	345	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.641302358313938	2		345	733	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764146326	NA	P-0012205-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	387	639	1	ENST00000269305.4:c.841G>T	p.Asp281Tyr	p.D281Y	ENST00000269305	NM_001126112.2	281	Gac/Tac	8/11	1	2	FACETS	0.916	0.87	0.963	0.916	0.87	0.963	CLONAL	1	TRUE	1	0.641302358313938	2		640	1317	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652225	36652226	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012205-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	247	397	0	ENST00000244741.5:c.349dup	p.Cys117LeufsTer12	p.C117Lfs*12	ENST00000244741	NM_000389.4	116	tct/tcTt	2/3	1	2	FACETS	0.956	0.896	1	0.956	0.896	1	CLONAL	1	TRUE	1	0.641302358313938	2		397	806	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105736	27105736	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012205-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	263	439	0	ENST00000324856.7:c.5347G>T	p.Glu1783Ter	p.E1783*	ENST00000324856	NM_006015.4	1783	Gaa/Taa	20/20	1	2	FACETS	0.981	0.922	1	0.981	0.922	1	CLONAL	1	TRUE	1	0.641302358313938	2		439	836	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106621	27106621	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs869312956	NA	P-0012205-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	326	508	2	ENST00000324856.7:c.6232G>A	p.Glu2078Lys	p.E2078K	ENST00000324856	NM_006015.4	2078	Gag/Aag	20/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.641302358313938	2		510	971	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817820	3817820	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0012205-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	438	804	4	ENST00000262367.5:c.3151A>T	p.Lys1051Ter	p.K1051*	ENST00000262367	NM_004380.2	1051	Aag/Tag	16/31	1	2	FACETS	0.884	0.841	0.927	0.884	0.841	0.927	CLONAL	1	TRUE	1	0.641302358313938	2		808	1546	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349958	89349958	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs747806088	NA	P-0012205-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	610	1147	0	ENST00000301030.4:c.2992G>C	p.Glu998Gln	p.E998Q	ENST00000301030	NM_001256183.1	998	Gag/Cag	9/13	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.641302358313938	2		1147	1771	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918259	44918259	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0012205-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	212	170	0	ENST00000377967.4:c.884C>G	p.Ser295Ter	p.S295*	ENST00000377967	NM_021140.2	295	tCa/tGa	11/29	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.641302358313938	1		170	343	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024217	112024217	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	26	740	0	ENST00000368678.4:c.568C>A	p.Arg190Ser	p.R190S	ENST00000368678		190	Cgt/Agt	7/13	0.111535064366241	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		740	338	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568668	41568668	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0012391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	40	323	0	ENST00000263253.7:c.4617+1G>A		p.X1539_splice	ENST00000263253	NM_001429.3	1539			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		323	695	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872132	35872441	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TATGGAACAAGTAGTCTTATCTTCTGAATTTTAAGAACCCACAGTCTGGGTTCTGAAAGAACTTTATAAAGGCATCCAATAGGCACTTTGCACACATATTTTCTCAACCTTCCAAATGTTAGGAGTTTAAGCTCTTGCCTGGACTCCTTAAGTTGGCCCACCTGCCCCTTCTCCACGTCACCTGCCCTCCGAGGGGGTGGGGCAGGGCAGGGAGGCAGACATACCATTGTAGTTGGTAGCCTTCAGGATGGAGTGGAGGTGCGGGGTGGTGCAGGACTGAGTCAGGACTCCCACGCTGGCCAGGCAGCCC	TATGGAACAAGTAGTCTTATCTTCTGAATTTTAAGAACCCACAGTCTGGGTTCTGAAAGAACTTTATAAAGGCATCCAATAGGCACTTTGCACACATATTTTCTCAACCTTCCAAATGTTAGGAGTTTAAGCTCTTGCCTGGACTCCTTAAGTTGGCCCACCTGCCCCTTCTCCACGTCACCTGCCCTCCGAGGGGGTGGGGCAGGGCAGGGAGGCAGACATACCATTGTAGTTGGTAGCCTTCAGGATGGAGTGGAGGTGCGGGGTGGTGCAGGACTGAGTCAGGACTCCCACGCTGGCCAGGCAGCCC	-	novel	NA	P-0012391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	243	273	1	ENST00000216797.5:c.462_548-67del		p.X154_splice	ENST00000216797	NM_020529.2	154		3/6	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		274	731	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0012394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	737	423	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.536153937919295	3	FACETS	1	0.996	1	0.737	0.718	0.756	CLONAL	2	TRUE	0	0.843902585721385	3		423	1123	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597431	10597431	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	970	694	0	ENST00000171111.5:c.1772G>T	p.Trp591Leu	p.W591L	ENST00000171111	NM_203500.1	591	tGg/tTg	6/6	0.843902585721385	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.843902585721385	2		694	1143	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221243	1221243	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1057520606	NA	P-0012394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	2086	631	0	ENST00000326873.7:c.766G>T	p.Glu256Ter	p.E256*	ENST00000326873	NM_000455.4	256	Gaa/Taa	6/10	0.527740366908588	5	FACETS	0.982	0.974	0.989			1	CLONAL	5	TRUE	NA	0.843902585721385	5		631	2282	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900321	3900321	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs750216784	NA	P-0012394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	458	640	1	ENST00000262367.5:c.775G>T	p.Ala259Ser	p.A259S	ENST00000262367	NM_004380.2	259	Gca/Tca	2/31	1	2	FACETS	0.976	0.935	1	0.976	0.935	1	CLONAL	1	TRUE	1	0.843902585721385	2		641	1112	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830820	156830820	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	210	301	0	ENST00000524377.1:c.94G>T	p.Gly32Cys	p.G32C	ENST00000524377	NM_002529.3	32	Ggc/Tgc	1/17	0.843902585721385	3	FACETS	0.941	0.877	1	0.471	0.438	0.504	CLONAL	1	TRUE	1	0.843902585721385	3		301	752	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845364	156845364	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1386	509	796	1	ENST00000524377.1:c.1407G>T	p.Met469Ile	p.M469I	ENST00000524377	NM_002529.3	469	atG/atT	12/17	0.843902585721385	3	FACETS	0.905	0.865	0.946	0.453	0.432	0.473	CLONAL	1	TRUE	1	0.843902585721385	3		797	1895	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521768	89521768	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	257	274	0	ENST00000336596.2:c.2845G>C	p.Asp949His	p.D949H	ENST00000336596	NM_005233.5	949	Gat/Cat	16/17	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.843902585721385	2		274	530	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156541	55156541	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	421	579	0	ENST00000257290.5:c.2942G>T	p.Arg981Leu	p.R981L	ENST00000257290	NM_006206.4	981	cGt/cTt	22/23	1	2	FACETS	0.993	0.949	1	0.993	0.949	1	CLONAL	1	TRUE	1	0.843902585721385	2		579	1005	SUCCESS
APC	324	MSKCC	GRCh37	5	112162894	112162894	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	443	626	1	ENST00000257430.4:c.1498T>A	p.Tyr500Asn	p.Y500N	ENST00000257430	NM_000038.5	500	Tat/Aat	12/16	1	2	FACETS	0.967	0.925	1	0.967	0.925	1	CLONAL	1	TRUE	1	0.843902585721385	2		627	1086	SUCCESS
APC	324	MSKCC	GRCh37	5	112179175	112179175	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554088722	NA	P-0012394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	281	396	1	ENST00000257430.4:c.7884G>T	p.Gln2628His	p.Q2628H	ENST00000257430	NM_000038.5	2628	caG/caT	16/16	1	2	FACETS	0.906	0.856	0.957	0.906	0.856	0.957	CLONAL	1	TRUE	1	0.843902585721385	2		397	735	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876964	151876964	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199592124	NA	P-0012394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	408	555	0	ENST00000262189.6:c.7397A>G	p.Tyr2466Cys	p.Y2466C	ENST00000262189	NM_170606.2	2466	tAt/tGt	37/59	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.843902585721385	2		555	956	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742906	17742906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	214	308	0	ENST00000250003.3:c.814G>A	p.Ala272Thr	p.A272T	ENST00000250003	NM_002478.4	272	Gcg/Acg	3/3	1	2	FACETS	0.968	0.908	1	0.968	0.908	1	CLONAL	1	TRUE	1	0.843902585721385	2		308	524	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425763	49425763	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	686	507	0	ENST00000301067.7:c.12725C>G	p.Pro4242Arg	p.P4242R	ENST00000301067	NM_003482.3	4242	cCc/cGc	39/54	0.536153937919295	3	FACETS	1	0.996	1	0.763	0.743	0.783	CLONAL	2	TRUE	0	0.843902585721385	3		507	1010	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846059	68846059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	541	757	0	ENST00000261769.5:c.1030G>A	p.Val344Met	p.V344M	ENST00000261769	NM_004360.3	344	Gtg/Atg	8/16	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.843902585721385	2		757	1183	SUCCESS
AR	367	MSKCC	GRCh37	X	66765403	66765403	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	412	621	1	ENST00000374690.3:c.415G>T	p.Val139Leu	p.V139L	ENST00000374690	NM_000044.3	139	Gtg/Ttg	1/8	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.843902585721385	2		622	921	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855006	76855006	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	650	892	0	ENST00000373344.5:c.5830del	p.Ser1944ValfsTer11	p.S1944Vfs*11	ENST00000373344	NM_000489.3	1944	Agt/gt	25/35	1	2	FACETS	0.922	0.888	0.956	0.922	0.888	0.956	CLONAL	1	TRUE	1	0.843902585721385	2		892	1671	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098421	11098422	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	T	novel	NA	P-0012394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	841	521	0	ENST00000358026.2:c.939_940delinsT	p.Ala314ArgfsTer12	p.A314Rfs*12	ENST00000358026	NM_001128849.1	313	ccCGcg/ccTcg	6/36	0.843902585721385	2	FACETS	0.96	0.942	0.977	0.96	0.942	0.977	CLONAL	2	TRUE	0	0.843902585721385	2		521	1038	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653808	89653808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012422-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	92	523	0	ENST00000371953.3:c.106G>A	p.Gly36Arg	p.G36R	ENST00000371953	NM_000314.4	36	Gga/Aga	2/9	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	FALSE	1	0.230704742152969	2		523	797	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953037	2953037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012422-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	82	593	1	ENST00000396946.4:c.2903C>T	p.Ala968Val	p.A968V	ENST00000396946	NM_032415.4	968	gCc/gTc	22/25	1	2	FACETS	0.895	0.789	1	0.895	0.789	1	CLONAL	1	FALSE	1	0.230704742152969	2		594	794	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692991	89692991	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786202688	NA	P-0012422-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	80	357	0	ENST00000371953.3:c.475A>G	p.Arg159Gly	p.R159G	ENST00000371953	NM_000314.4	159	Agg/Ggg	5/9	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.230704742152969	2		357	588	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913514	NA	P-0012564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	452	559	0	ENST00000288135.5:c.2466T>G	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaG	17/21	0.396900372592983	2	FACETS	1	0.997	1	0.75	0.722	0.777	INDETERMINATE	1	TRUE	0	0.782016467102465	2		559	771	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208338	5208338	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	460	955	0	ENST00000357368.4:c.5552A>G	p.Lys1851Arg	p.K1851R	ENST00000357368	NM_002850.3	1851	aAg/aGg	36/38	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.782016467102465	2		955	1117	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593635	55593664	+	inframe_deletion	In_Frame_Del	DEL	TTATGTTTACATAGACCCAACACAACTTCC	TTATGTTTACATAGACCCAACACAACTTCC	-	novel	NA	P-0012564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	29	835	0	ENST00000288135.5:c.1706_1735del	p.Val569_Tyr578del	p.V569_Y578del	ENST00000288135	NM_000222.2	567	aaTTATGTTTACATAGACCCAACACAACTTCCt/aat	11/21	0.396900372592983	2	FACETS	0.068	0.054	0.084	0.034	0.027	0.042	INDETERMINATE	1	TRUE	0	0.782016467102465	2		835	1089	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65569047	65569047	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	434	947	0	ENST00000358664.4:c.11del	p.Asn4ThrfsTer61	p.N4Tfs*61	ENST00000358664	NM_002382.4	4	aAc/ac	1/5	0.782016467102465	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.782016467102465	1		947	652	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0012703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	151	423	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.519	0.473	0.566	0.519	0.473	0.566	SUBCLONAL	1	TRUE	1	0.520922273652009	2		423	1118	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0012703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	74	265	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.509	0.446	0.577	0.509	0.446	0.577	SUBCLONAL	1	TRUE	1	0.520922273652009	2		265	558	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143034	47143034	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1256	175	580	0	ENST00000409792.3:c.4929C>G	p.Asn1643Lys	p.N1643K	ENST00000409792	NM_014159.6	1643	aaC/aaG	8/21	1	2	FACETS	0.47	0.431	0.51	0.47	0.431	0.51	SUBCLONAL	1	TRUE	1	0.520922273652009	2		580	1431	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289641	33289641	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	120	475	0	ENST00000374542.5:c.62A>G	p.Gln21Arg	p.Q21R	ENST00000374542	NM_001141970.1	21	cAg/cGg	2/8	1	2	FACETS	0.51	0.46	0.563	0.51	0.46	0.563	SUBCLONAL	1	TRUE	1	0.520922273652009	2		475	903	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224604	108224604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555142909	NA	P-0012703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	110	446	0	ENST00000278616.4:c.8783G>A	p.Arg2928Lys	p.R2928K	ENST00000278616	NM_000051.3	2928	aGa/aAa	60/63	1	2	FACETS	0.433	0.388	0.481	0.433	0.388	0.481	SUBCLONAL	1	TRUE	1	0.520922273652009	2		446	975	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023844	27023845	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0012703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	88	424	0	ENST00000324856.7:c.951dup	p.Gly318TrpfsTer82	p.G318Wfs*82	ENST00000324856	NM_006015.4	317	agt/agTt	1/20	1	2	FACETS	0.543	0.482	0.609	0.543	0.482	0.609	SUBCLONAL	1	TRUE	1	0.520922273652009	2		424	622	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0012788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	277	351	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.265838672696491	5	FACETS	1	0.986	1	0.777	0.728	0.826	CLONAL	2	TRUE	2	0.265838672696491	5		351	1251	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579722	7579722	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0012788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	89	606	0	ENST00000269305.4:c.75-1G>T		p.X25_splice	ENST00000269305	NM_001126112.2	25			1	2	FACETS	0.651	0.575	0.732	0.651	0.575	0.732	SUBCLONAL	1	TRUE	1	0.265838672696491	2		606	1029	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612283	1612283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759261756	NA	P-0012788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	99	874	0	ENST00000344749.5:c.1736C>T	p.Ser579Leu	p.S579L	ENST00000344749	NM_001136139.2	579	tCg/tTg	18/19	1	2	FACETS	0.63	0.56	0.704	0.63	0.56	0.704	SUBCLONAL	1	TRUE	1	0.265838672696491	2		874	1183	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0012869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	482	553	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.632686417383415	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.632686417383415	3		553	969	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0012869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	525	622	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.632686417383415	2		622	804	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0012869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	482	548	2				ENST00000310581	NM_198253.2	-/1132			0.605807431258358	5	FACETS	0.985	0.952	1	0.985	0.952	1	CLONAL	4	TRUE	1	0.632686417383415	5		550	754	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176719045	176719045	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784190	NA	P-0012869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	299	661	2	ENST00000439151.2:c.6349C>T	p.Arg2117Ter	p.R2117*	ENST00000439151	NM_022455.4	2117	Cga/Tga	22/23	0.632686417383415	1	FACETS	0.99	0.94	1	0.99	0.94	1	CLONAL	1	TRUE	0	0.632686417383415	1		663	653	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053221	180053221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	260	765	2	ENST00000261937.6:c.1148C>T	p.Ala383Val	p.A383V	ENST00000261937	NM_182925.4	383	gCc/gTc	9/30	0.632686417383415	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.632686417383415	1		767	534	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197366	94197366	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766182900	NA	P-0012869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	444	614	0	ENST00000323929.3:c.1138C>T	p.Arg380Cys	p.R380C	ENST00000323929	NM_005591.3	380	Cgc/Tgc	11/20	0.632686417383415	2	FACETS	0.994	0.959	1	0.994	0.959	1	CLONAL	2	TRUE	0	0.632686417383415	2		614	706	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0012933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	108	553	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.959	0.864	1	0.959	0.864	1	CLONAL	1	TRUE	1	0.437509303790859	2		553	515	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0012933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	197	175	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.437509303790859	1	FACETS	0.968	0.899	1	0.968	0.899	1	CLONAL	1	TRUE	0	0.437509303790859	1		175	727	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0012933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	45	117	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	1	2	FACETS	0.823	0.697	0.959	0.823	0.697	0.959	CLONAL	1	TRUE	1	0.437509303790859	2		117	250	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0012933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	48	179	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.958	0.818	1	0.958	0.818	1	CLONAL	1	TRUE	1	0.437509303790859	2		179	229	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553257	106553257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	208	441	1	ENST00000369096.4:c.1222G>A	p.Ala408Thr	p.A408T	ENST00000369096	NM_001198.3	408	Gct/Act	5/7	1	2	FACETS	0.981	0.911	1	0.981	0.911	1	CLONAL	1	TRUE	1	0.437509303790859	2		442	969	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471048	8471048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	91	329	0	ENST00000356435.5:c.3451C>T	p.Arg1151Cys	p.R1151C	ENST00000356435		1151	Cgc/Tgc	20/35	1	2	FACETS	0.754	0.671	0.842	0.754	0.671	0.842	SUBCLONAL	1	TRUE	1	0.437509303790859	2		329	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0012978-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	98	419	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.209938773323799	2		421	737	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437623	52437623	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0012978-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	102	1303	0	ENST00000460680.1:c.1538C>G	p.Ser513Ter	p.S513*	ENST00000460680	NM_004656.3	513	tCa/tGa	13/17	1	2	FACETS	0.999	0.892	1	0.999	0.892	1	CLONAL	1	FALSE	1	0.209938773323799	2		1303	973	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287315	46287315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1565642121	NA	P-0012978-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	51	551	0	ENST00000334344.6:c.5260C>T	p.Arg1754Ter	p.R1754*	ENST00000334344	NM_152641.2	1754	Cga/Tga	19/21	1	2	FACETS	0.945	0.804	1	0.945	0.804	1	CLONAL	1	FALSE	1	0.209938773323799	2		551	514	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532590	187532590	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0012978-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	58	717	0	ENST00000441802.2:c.9803C>G	p.Ser3268Ter	p.S3268*	ENST00000441802	NM_005245.3	3268	tCa/tGa	14/27	0.188522682442105	1	FACETS	0.875	0.752	1	0.875	0.752	1	CLONAL	1	FALSE	0	0.209938773323799	1		717	565	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427369	49427369	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1565779294	NA	P-0012978-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	47	617	0	ENST00000301067.7:c.11119C>T	p.Arg3707Ter	p.R3707*	ENST00000301067	NM_003482.3	3707	Cga/Tga	39/54	1	2	FACETS	0.963	0.813	1	0.963	0.813	1	CLONAL	1	FALSE	1	0.209938773323799	2		617	465	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805620	46805620	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012978-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	112	1352	0	ENST00000290295.7:c.336G>C	p.Glu112Asp	p.E112D	ENST00000290295	NM_006361.5	112	gaG/gaC	1/2	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.209938773323799	2		1352	892	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149751	202149751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012978-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	58	880	1	ENST00000358485.4:c.1192C>T	p.Gln398Ter	p.Q398*	ENST00000358485	NM_001080125.1	398	Cag/Tag	8/9	1	2	FACETS	0.741	0.635	0.856	0.741	0.635	0.856	SUBCLONAL	1	FALSE	1	0.209938773323799	2		881	746	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199825	138199825	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012978-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	76	678	0	ENST00000237289.4:c.1243C>G	p.Gln415Glu	p.Q415E	ENST00000237289	NM_001270507.1	415	Caa/Gaa	7/9	0.152602004286867	2	FACETS	1	0.947	1	0.573	0.502	0.648	CLONAL	1	FALSE	0	0.209938773323799	2		678	632	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0013014-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	33	185	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.284498121779366	2	FACETS	1	0.834	1	0.511	0.417	0.615	CLONAL	1	TRUE	0	0.23	2		185	281	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913283	NA	P-0013014-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	72	570	0	ENST00000263967.3:c.3129G>T	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atT	21/21	1	2	FACETS	0.975	0.852	1	0.975	0.852	1	CLONAL	1	TRUE	1	0.23	2		570	642	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711875	89711875	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587782603	NA	P-0013014-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	166	342	0	ENST00000371953.3:c.493G>A	p.Gly165Arg	p.G165R	ENST00000371953	NM_000314.4	165	Gga/Aga	6/9	0.284498121779366	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.23	2		342	601	SUCCESS
APC	324	MSKCC	GRCh37	5	112173928	112173928	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs763546422	NA	P-0013014-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	79	353	0	ENST00000257430.4:c.2637G>C	p.Gln879His	p.Q879H	ENST00000257430	NM_000038.5	879	caG/caC	16/16	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.23	2		353	555	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39537648	39537648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013014-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	105	516	1	ENST00000262039.4:c.182G>A	p.Cys61Tyr	p.C61Y	ENST00000262039	NM_002647.2	61	tGt/tAt	2/25	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.23	2		517	804	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339328	70339328	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0013014-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	112	433	0	ENST00000374080.3:c.204+1G>T		p.X68_splice	ENST00000374080		68			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.23	2		433	757	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591117	67591118	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0013014-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	33	313	0	ENST00000274335.5:c.1711_1712del	p.Ile571ProfsTer30	p.I571Pfs*30	ENST00000274335		570	ctTAtc/cttc	12/15	1	2	FACETS	0.516	0.419	0.626	0.516	0.419	0.626	SUBCLONAL	1	TRUE	1	0.23	2		313	556	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102119	27102120	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCTCT	novel	NA	P-0013014-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	115	724	0	ENST00000324856.7:c.5045_5046insTCTCT	p.Glu1683LeufsTer2	p.E1683Lfs*2	ENST00000324856	NM_006015.4	1682	gca/gcTCTCTa	19/20	1	2	FACETS	0.937	0.842	1	0.937	0.842	1	CLONAL	1	TRUE	1	0.23	2		724	1067	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591153	67591154	+	splice_donor_variant	Splice_Site	DEL	GT	GT	C	novel	NA	P-0013014-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	75	309	0	ENST00000274335.5:c.1745+1_1745+2delinsC		p.X582_splice	ENST00000274335		582			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.23	2		309	557	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152093	55152093	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121908585	NA	P-0013017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	422	484	2	ENST00000257290.5:c.2525A>T	p.Asp842Val	p.D842V	ENST00000257290	NM_006206.4	842	gAc/gTc	18/23	0.854747407267337	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.854747407267337	1		486	542	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627410	37627410	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1250327068	NA	P-0013017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	462	727	0	ENST00000447079.4:c.1325T>G	p.Leu442Trp	p.L442W	ENST00000447079	NM_015083.1	442	tTg/tGg	2/14	1	2	FACETS	0.986	0.945	1	0.986	0.945	1	CLONAL	1	TRUE	1	0.854747407267337	2		727	1096	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913517	NA	P-0013024-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	19	765	0	ENST00000288135.5:c.1676T>A	p.Val559Asp	p.V559D	ENST00000288135	NM_000222.2	559	gTt/gAt	11/21	0.212859801411551	4	FACETS	0.237	0.179	0.306	0.079	0.059	0.102	SUBCLONAL	1	TRUE	1	0.294663800922867	4		765	705	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211458	46211475	+	inframe_deletion	In_Frame_Del	DEL	CTGCGTCAAAGTTATGGG	CTGCGTCAAAGTTATGGG	-	novel	NA	P-0013039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	29	286	0	ENST00000334344.6:c.427_444del	p.Arg143_Leu148del	p.R143_L148del	ENST00000334344	NM_152641.2	142	CTGCGTCAAAGTTATGGG/-	5/21	1	2	FACETS	0.183	0.146	0.226	0.183	0.146	0.226	SUBCLONAL	1	TRUE	1	0.598942537346463	2		286	528	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593662	55593664	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0013039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	223	436	0	ENST00000288135.5:c.1729_1731del	p.Pro577del	p.P577del	ENST00000288135	NM_000222.2	576	ctTCCt/ctt	11/21	1	2	FACETS	0.965	0.901	1	0.965	0.901	1	CLONAL	1	TRUE	1	0.598942537346463	2		436	772	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	31	154	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.552	0.448	0.668	0.552	0.448	0.668	SUBCLONAL	1	TRUE	1	0.422501522348165	2		154	266	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	69	217	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.422501522348165	2		217	319	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	128	367	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	0.422501522348165	2		367	573	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	28	162	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.597	0.48	0.729	0.597	0.48	0.729	SUBCLONAL	1	TRUE	1	0.422501522348165	2		162	222	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412110	63412110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852216	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1248	360	1181	1	ENST00000330258.3:c.1057C>T	p.Arg353Ter	p.R353*	ENST00000330258	NM_152424.3	353	Cga/Tga	2/2	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.422501522348165	2		1182	1608	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	113	378	0	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.901	0.813	0.993	0.901	0.813	0.993	CLONAL	1	TRUE	1	0.422501522348165	2		378	594	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	140	419	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.422501522348165	2		419	607	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489535	56489535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1403278713	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	212	395	1	ENST00000267101.3:c.2000G>A	p.Arg667His	p.R667H	ENST00000267101	NM_001982.3	667	cGt/cAt	17/28	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.422501522348165	2		396	775	SUCCESS
APC	324	MSKCC	GRCh37	5	112175675	112175676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	119	418	0	ENST00000257430.4:c.4393_4394dup	p.Ser1465ArgfsTer9	p.S1465Rfs*9	ENST00000257430	NM_000038.5	1462	aag/aAGag	16/16	1	2	FACETS	0.815	0.737	0.898	0.815	0.737	0.898	CLONAL	1	TRUE	1	0.422501522348165	2		418	691	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	115	374	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.422501522348165	2		374	520	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	145	451	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.422501522348165	2		451	640	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	109	333	0	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.422501522348165	2		333	479	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129329	152129329	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	155	497	1	ENST00000206249.3:c.287del	p.Gly96ValfsTer13	p.G96Vfs*13	ENST00000206249	NM_000125.3	94	ctG/ct	1/8	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.422501522348165	2		498	709	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480483	57480483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	29	290	1	ENST00000371085.3:c.478C>T	p.Arg160Cys	p.R160C	ENST00000371085	NM_000516.4	160	Cgt/Tgt	6/13	1	2	FACETS	0.288	0.231	0.354	0.288	0.231	0.354	SUBCLONAL	1	TRUE	1	0.422501522348165	2		291	476	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249542	153249542	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	84	237	0	ENST00000281708.4:c.1237-1G>A		p.X413_splice	ENST00000281708	NM_033632.3	413			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.422501522348165	2		237	333	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81960742	81960742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768839912	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	306	915	1	ENST00000359376.3:c.2473G>A	p.Glu825Lys	p.E825K	ENST00000359376	NM_002661.3	825	Gag/Aag	23/33	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.422501522348165	2		916	1299	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439936	56439936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377765604	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	85	434	3	ENST00000407977.2:c.656G>A	p.Arg219His	p.R219H	ENST00000407977		219	cGc/cAc	6/10	1	2	FACETS	0.541	0.478	0.609	0.541	0.478	0.609	SUBCLONAL	1	TRUE	1	0.422501522348165	2		437	744	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	181	411	0	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	0.18416692816425	2	FACETS	1	0.987	1	0.647	0.599	0.697	INDETERMINATE	1	TRUE	0	0.422501522348165	2		411	662	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392858	118392858	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781866935	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	144	433	0	ENST00000534358.1:c.11890G>A	p.Ala3964Thr	p.A3964T	ENST00000534358	NM_005933.3	3964	Gcc/Acc	36/36	1	2	FACETS	0.906	0.828	0.989	0.906	0.828	0.989	CLONAL	1	TRUE	1	0.422501522348165	2		433	752	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857238	78857238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866939416	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	187	542	0	ENST00000306801.3:c.1604C>T	p.Thr535Met	p.T535M	ENST00000306801	NM_020761.2	535	aCg/aTg	15/34	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.422501522348165	2		542	865	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041266	47041266	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	274	874	2	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	0.422501522348165	2		876	1113	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094449	27094449	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	92	348	0	ENST00000324856.7:c.3157C>T	p.Arg1053Cys	p.R1053C	ENST00000324856	NM_006015.4	1053	Cgc/Tgc	11/20	1	2	FACETS	0.923	0.823	1	0.923	0.823	1	CLONAL	1	TRUE	1	0.422501522348165	2		348	472	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870301	155870301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764151643	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	117	671	2	ENST00000368323.3:c.538C>T	p.Arg180Trp	p.R180W	ENST00000368323	NM_006912.5	180	Cgg/Tgg	6/6	1	2	FACETS	0.5	0.449	0.553	0.5	0.449	0.553	SUBCLONAL	1	TRUE	1	0.422501522348165	2		673	1108	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497824	25497824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	85	540	0	ENST00000264709.3:c.625C>T	p.Arg209Cys	p.R209C	ENST00000264709	NM_175629.2	209	Cgc/Tgc	6/23	1	2	FACETS	0.566	0.5	0.637	0.566	0.5	0.637	SUBCLONAL	1	TRUE	1	0.422501522348165	2		540	711	SUCCESS
ALK	238	MSKCC	GRCh37	2	29541235	29541235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758494304	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	173	416	2	ENST00000389048.3:c.1582G>A	p.Ala528Thr	p.A528T	ENST00000389048	NM_004304.4	528	Gct/Act	8/29	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.422501522348165	2		418	777	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917799	29917799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	101	545	1	ENST00000389048.3:c.869G>T	p.Trp290Leu	p.W290L	ENST00000389048	NM_004304.4	290	tGg/tTg	3/29	1	2	FACETS	0.543	0.484	0.605	0.543	0.484	0.605	SUBCLONAL	1	TRUE	1	0.422501522348165	2		546	881	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143117	30143117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757382067	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	82	575	3	ENST00000389048.3:c.409C>T	p.Arg137Cys	p.R137C	ENST00000389048	NM_004304.4	137	Cgt/Tgt	1/29	1	2	FACETS	0.481	0.423	0.543	0.481	0.423	0.543	SUBCLONAL	1	TRUE	1	0.422501522348165	2		578	807	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99163066	99163066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769868588	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	140	355	1	ENST00000074304.5:c.1072G>A	p.Val358Ile	p.V358I	ENST00000074304	NM_001134224.1	358	Gtc/Atc	13/26	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.422501522348165	2		356	558	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127445	55127445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1560466833	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	83	582	0	ENST00000257290.5:c.233G>A	p.Ser78Asn	p.S78N	ENST00000257290	NM_006206.4	78	aGc/aAc	3/23	1	2	FACETS	0.452	0.398	0.51	0.452	0.398	0.51	SUBCLONAL	1	TRUE	1	0.422501522348165	2		582	870	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540380	187540380	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202097333	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	112	300	0	ENST00000441802.2:c.7360C>T	p.Arg2454Trp	p.R2454W	ENST00000441802	NM_005245.3	2454	Cgg/Tgg	10/27	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.422501522348165	2		300	447	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944548	38944548	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs925027853	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	93	411	0	ENST00000357387.3:c.4913C>T	p.Thr1638Ile	p.T1638I	ENST00000357387	NM_152756.3	1638	aCa/aTa	36/38	1	2	FACETS	0.775	0.691	0.865	0.775	0.691	0.865	SUBCLONAL	1	TRUE	1	0.422501522348165	2		411	568	SUCCESS
APC	324	MSKCC	GRCh37	5	112173374	112173374	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	150	500	0	ENST00000257430.4:c.2083C>T	p.Gln695Ter	p.Q695*	ENST00000257430	NM_000038.5	695	Cag/Tag	16/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.422501522348165	2		500	659	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514414	149514414	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759684681	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	173	565	0	ENST00000261799.4:c.530G>A	p.Arg177His	p.R177H	ENST00000261799	NM_002609.3	177	cGt/cAt	4/23	1	2	FACETS	0.965	0.889	1	0.965	0.889	1	CLONAL	1	TRUE	1	0.422501522348165	2		565	849	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398863	398863	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1321465734	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	114	587	1	ENST00000380956.4:c.673C>A	p.Pro225Thr	p.P225T	ENST00000380956	NM_001195286.1	225	Cca/Aca	6/9	0.422501522348165	2	FACETS	0.559	0.502	0.619	0.279	0.251	0.31	SUBCLONAL	1	TRUE	0	0.422501522348165	2		588	966	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045799	26045799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1384	384	1376	1	ENST00000540144.1:c.161G>A	p.Arg54His	p.R54H	ENST00000540144	NM_003531.2	54	cGc/cAc	1/1	0.422501522348165	2	FACETS	1	0.967	1	0.514	0.487	0.542	CLONAL	1	TRUE	0	0.422501522348165	2		1377	1768	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14026264	14026264	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	97	257	0	ENST00000405192.2:c.180A>C	p.Glu60Asp	p.E60D	ENST00000405192	NM_001163147.1	60	gaA/gaC	4/12	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.422501522348165	2		257	425	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444483	50444483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	35	88	0	ENST00000331340.3:c.413G>A	p.Ser138Asn	p.S138N	ENST00000331340	NM_006060.4	138	aGc/aAc	4/8	1	2	FACETS	0.91	0.755	1	0.91	0.755	1	CLONAL	1	TRUE	1	0.422501522348165	2		88	182	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242454	55242454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778250	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	86	421	0	ENST00000275493.2:c.2224G>A	p.Val742Ile	p.V742I	ENST00000275493	NM_005228.3	742	Gtc/Atc	19/28	1	2	FACETS	0.783	0.694	0.877	0.783	0.694	0.877	SUBCLONAL	1	TRUE	1	0.422501522348165	2		421	520	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395479	116395479	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	138	386	0	ENST00000397752.3:c.1772G>C	p.Arg591Pro	p.R591P	ENST00000397752	NM_000245.2	591	cGg/cCg	6/21	1	2	FACETS	0.99	0.903	1	0.99	0.903	1	CLONAL	1	TRUE	1	0.422501522348165	2		386	660	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738814	145738814	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750304658	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	135	305	3	ENST00000428558.2:c.2251C>T	p.Arg751Trp	p.R751W	ENST00000428558	NM_004260.3	751	Cgg/Tgg	14/22	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.422501522348165	2		308	505	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900964	114900964	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1353	409	1194	0	ENST00000543371.1:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000543371	NM_001198531.1	192	Cag/Tag	6/14	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.422501522348165	2		1194	1762	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218066	108218066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1252051440	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	62	254	0	ENST00000278616.4:c.8645C>T	p.Ser2882Leu	p.S2882L	ENST00000278616	NM_000051.3	2882	tCa/tTa	59/63	1	2	FACETS	0.692	0.6	0.792	0.692	0.6	0.792	SUBCLONAL	1	TRUE	1	0.422501522348165	2		254	424	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352595	118352595	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	193	529	0	ENST00000534358.1:c.3800T>C	p.Val1267Ala	p.V1267A	ENST00000534358	NM_005933.3	1267	gTc/gCc	7/36	1	2	FACETS	0.947	0.876	1	0.947	0.876	1	CLONAL	1	TRUE	1	0.422501522348165	2		529	965	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945025	31945025	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1267	134	934	0	ENST00000340398.3:c.76G>A	p.Ala26Thr	p.A26T	ENST00000340398	NM_001013699.2	26	Gcc/Acc	1/1	1	2	FACETS	0.453	0.41	0.498	0.453	0.41	0.498	SUBCLONAL	1	TRUE	1	0.422501522348165	2		934	1401	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230569	46230569	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	161	593	0	ENST00000334344.6:c.818C>A	p.Pro273His	p.P273H	ENST00000334344	NM_152641.2	273	cCt/cAt	8/21	1	2	FACETS	0.912	0.837	0.99	0.912	0.837	0.99	CLONAL	1	TRUE	1	0.422501522348165	2		593	836	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518146	103518146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	41	295	0	ENST00000355739.4:c.2084C>T	p.Ala695Val	p.A695V	ENST00000355739	NM_000123.3	695	gCt/gTt	9/15	1	2	FACETS	0.398	0.331	0.472	0.398	0.331	0.472	SUBCLONAL	1	TRUE	1	0.422501522348165	2		295	488	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220634	2220634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375735405	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	354	815	1	ENST00000326181.6:c.251G>A	p.Arg84His	p.R84H	ENST00000326181	NM_032271.2	84	cGc/cAc	5/21	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.422501522348165	2		816	1412	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533740	63533740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	81	425	0	ENST00000307078.5:c.1414C>T	p.His472Tyr	p.H472Y	ENST00000307078	NM_004655.3	472	Cac/Tac	6/11	1	2	FACETS	0.596	0.525	0.672	0.596	0.525	0.672	SUBCLONAL	1	TRUE	1	0.422501522348165	2		425	643	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248620	10248620	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757243017	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	168	403	0	ENST00000340748.4:c.4133G>A	p.Arg1378Gln	p.R1378Q	ENST00000340748		1378	cGg/cAg	35/40	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.422501522348165	2		403	640	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719286	52719286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775654171	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	224	537	1	ENST00000322088.6:c.952C>T	p.Arg318Trp	p.R318W	ENST00000322088	NM_014225.5	318	Cgg/Tgg	8/15	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.422501522348165	2		538	897	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411416	63411416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773828754	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	239	731	0	ENST00000330258.3:c.1751G>A	p.Arg584His	p.R584H	ENST00000330258	NM_152424.3	584	cGt/cAt	2/2	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.422501522348165	2		731	1095	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411575	63411575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs904761868	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	274	1035	2	ENST00000330258.3:c.1592G>A	p.Arg531Gln	p.R531Q	ENST00000330258	NM_152424.3	531	cGa/cAa	2/2	1	2	FACETS	0.918	0.86	0.978	0.918	0.86	0.978	CLONAL	1	TRUE	1	0.422501522348165	2		1037	1413	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918952	76918952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1299	101	872	1	ENST00000373344.5:c.4039G>A	p.Val1347Met	p.V1347M	ENST00000373344	NM_000489.3	1347	Gtg/Atg	12/35	1	2	FACETS	0.342	0.304	0.382	0.342	0.304	0.382	SUBCLONAL	1	TRUE	1	0.422501522348165	2		873	1400	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940002	76940002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	106	638	0	ENST00000373344.5:c.746G>A	p.Gly249Asp	p.G249D	ENST00000373344	NM_000489.3	249	gGt/gAt	9/35	1	2	FACETS	0.509	0.455	0.566	0.509	0.455	0.566	SUBCLONAL	1	TRUE	1	0.422501522348165	2		638	986	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952115	76952115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782431661	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	189	658	1	ENST00000373344.5:c.320C>T	p.Ala107Val	p.A107V	ENST00000373344	NM_000489.3	107	gCg/gTg	5/35	1	2	FACETS	0.975	0.901	1	0.975	0.901	1	CLONAL	1	TRUE	1	0.422501522348165	2		659	918	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792110	42792112	+	inframe_deletion	In_Frame_Del	DEL	CTG	CTG	-	novel	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	73	254	0	ENST00000575354.2:c.921_923del	p.Ala308del	p.A308del	ENST00000575354	NM_015125.3	305	aCTGct/act	6/20	1	2	FACETS	0.934	0.822	1	0.934	0.822	1	CLONAL	1	TRUE	1	0.422501522348165	2		254	370	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47710024	47710027	+	frameshift_variant	Frame_Shift_Del	DEL	AAGT	AAGT	-	novel	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	85	352	0	ENST00000233146.2:c.2743_2746del	p.Val915Ter	p.V915*	ENST00000233146	NM_000251.2	914	gAAGTa/ga	16/16	1	2	FACETS	0.813	0.721	0.911	0.813	0.721	0.911	CLONAL	1	TRUE	1	0.422501522348165	2		352	495	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81973536	81973538	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	124	787	0	ENST00000359376.3:c.3355_3357del	p.Lys1119del	p.K1119del	ENST00000359376	NM_002661.3	1118	gAGAag/gag	30/33	1	2	FACETS	0.557	0.503	0.615	0.557	0.503	0.615	SUBCLONAL	1	TRUE	1	0.422501522348165	2		787	1053	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653780	89653781	+	splice_acceptor_variant	Splice_Site	DEL	AG	AG	-	rs1554893747	NA	P-0013082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	33	281	0	ENST00000371953.3:c.80-1_80del		p.X27_splice	ENST00000371953	NM_000314.4	27			1	2	FACETS	0.421	0.343	0.509	0.421	0.343	0.509	SUBCLONAL	1	TRUE	1	0.422501522348165	2		281	371	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913517	NA	P-0013114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	364	765	0	ENST00000288135.5:c.1676T>A	p.Val559Asp	p.V559D	ENST00000288135	NM_000222.2	559	gTt/gAt	11/21	1	2	FACETS	0.943	0.896	0.99	0.943	0.896	0.99	CLONAL	1	TRUE	1	0.761612473968189	2		765	1014	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913514	NA	P-0013114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	283	559	0	ENST00000288135.5:c.2466T>G	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaG	17/21	1	2	FACETS	0.903	0.852	0.955	0.903	0.852	0.955	CLONAL	1	TRUE	1	0.761612473968189	2		559	823	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870896	12870896	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	467	494	0	ENST00000228872.4:c.124del	p.Thr42ProfsTer29	p.T42Pfs*29	ENST00000228872	NM_004064.3	41	ttA/tt	1/3	0.74364593036748	2	FACETS	0.949	0.921	0.976	0.949	0.921	0.976	CLONAL	2	TRUE	0	0.761612473968189	2		494	646	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0013219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	367	282	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.495311833255048	2	FACETS	0.946	0.903	0.989	0.946	0.903	0.989	CLONAL	2	TRUE	0	0.501227268077499	2		282	774	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609721	28609721	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	238	903	0	ENST00000241453.7:c.1508T>G	p.Met503Arg	p.M503R	ENST00000241453	NM_004119.2	503	aTg/aGg	12/24	0.500284597670754	1	FACETS	0.927	0.868	0.987	0.927	0.868	0.987	CLONAL	1	TRUE	0	0.501227268077499	1		903	768	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624289	89624290	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GACTT	novel	NA	P-0013219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	293	405	0	ENST00000371953.3:c.64_68dup	p.Asp24ThrfsTer2	p.D24Tfs*2	ENST00000371953	NM_000314.4	21	-/GACTT	1/9	0.495311833255048	2	FACETS	0.955	0.907	1	0.955	0.907	1	CLONAL	2	TRUE	0	0.501227268077499	2		405	612	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	60	228	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.984	0.852	1	0.984	0.852	1	CLONAL	1	TRUE	1	0.32	2		228	381	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	40	154	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.912	0.762	1	0.912	0.762	1	CLONAL	1	TRUE	1	0.32	2		154	274	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718106	117718106	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs774163740	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	130	740	0	ENST00000368508.3:c.751T>C	p.Tyr251His	p.Y251H	ENST00000368508	NM_002944.2	251	Tac/Cac	7/43	0.0958552485006182	0	FACETS	0.617	0.559	0.678			1	INDETERMINATE	1	TRUE	0	0.32	0		740	896	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796883	42796883	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	203	885	2	ENST00000575354.2:c.3347del	p.Pro1116GlnfsTer45	p.P1116Qfs*45	ENST00000575354	NM_015125.3	1114	gCc/gc	14/20	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.32	2		887	1235	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	221	648	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.296628409040779	2	FACETS	0.888	0.829	0.948	0.888	0.829	0.948	CLONAL	2	TRUE	0	0.32	2		648	778	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204842	128204842	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs768767517	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	184	929	4	ENST00000341105.2:c.599del	p.Gly200ValfsTer18	p.G200Vfs*18	ENST00000341105	NM_032638.4	200	gGt/gt	3/6	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.32	2		933	1069	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	200	1214	6	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.915	0.846	0.987	0.915	0.846	0.987	CLONAL	1	TRUE	1	0.32	2		1220	1366	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	126	680	5	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	1	2	FACETS	0.952	0.862	1	0.952	0.862	1	CLONAL	1	TRUE	1	0.32	2		685	827	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	94	557	0	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	0.952	0.849	1	0.952	0.849	1	CLONAL	1	TRUE	1	0.32	2		557	617	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	247	351	2	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.944	1	1	0.995	1	CLONAL	2	TRUE	1	0.32	2		353	767	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785963	135785964	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs118203506	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	101	617	0	ENST00000298552.3:c.1257dup	p.Arg420GlnfsTer22	p.R420Qfs*22	ENST00000298552	NM_001162426.1	419	-/C	12/23	1	2	FACETS	0.8	0.715	0.891	0.8	0.715	0.891	SUBCLONAL	1	TRUE	1	0.32	2		617	789	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567647	226567647	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	131	659	5	ENST00000366794.5:c.1519del	p.Ser507AlafsTer17	p.S507Afs*17	ENST00000366794	NM_001618.3	507	Agc/gc	10/23	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.32	2		664	805	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835781	68835781	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060501215	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	151	733	0	ENST00000261769.5:c.377del	p.Pro126ArgfsTer89	p.P126Rfs*89	ENST00000261769	NM_004360.3	124	cgC/cg	3/16	1	2	FACETS	0.863	0.787	0.942	0.863	0.787	0.942	CLONAL	1	TRUE	1	0.32	2		733	1094	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	103	857	3	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	0.595	0.531	0.663	0.595	0.531	0.663	SUBCLONAL	1	TRUE	1	0.32	2		860	1082	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460476	149460476	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	114	756	0	ENST00000286301.3:c.161del	p.Pro54HisfsTer58	p.P54Hfs*58	ENST00000286301	NM_005211.3	54	cCa/ca	3/22	1	2	FACETS	0.804	0.723	0.89	0.804	0.723	0.89	CLONAL	1	TRUE	1	0.32	2		756	886	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639588	47639588	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63749897	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	129	331	1	ENST00000233146.2:c.687del	p.Ala230LeufsTer16	p.A230Lfs*16	ENST00000233146	NM_000251.2	227	agA/ag	4/16	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.32	2		332	784	SUCCESS
ATM	472	MSKCC	GRCh37	11	108213958	108213959	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs775899653	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	91	295	0	ENST00000278616.4:c.8283_8284del	p.Gln2762AlafsTer6	p.Q2762Afs*6	ENST00000278616	NM_000051.3	2760	CTc/c	57/63	1	2	FACETS	0.885	0.786	0.989	0.885	0.786	0.989	CLONAL	1	TRUE	1	0.32	2		295	643	SUCCESS
APC	324	MSKCC	GRCh37	5	112177864	112177864	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs775076289	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	51	477	0	ENST00000257430.4:c.6579del	p.Val2194PhefsTer5	p.V2194Ffs*5	ENST00000257430	NM_000038.5	2191	ggA/gg	16/16	1	2	FACETS	0.474	0.402	0.554	0.474	0.402	0.554	SUBCLONAL	1	TRUE	1	0.32	2		477	672	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401637	401637	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	61	602	0	ENST00000380956.4:c.963del	p.Asp322ThrfsTer62	p.D322Tfs*62	ENST00000380956	NM_001195286.1	320	gCc/gc	7/9	1	2	FACETS	0.53	0.456	0.61	0.53	0.456	0.61	SUBCLONAL	1	TRUE	1	0.32	2		602	720	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765753	41765753	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761731744	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	117	521	2	ENST00000301178.4:c.2629G>A	p.Ala877Thr	p.A877T	ENST00000301178	NM_021913.4	877	Gct/Act	20/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.32	2		523	562	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101417	27101417	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	54	808	0	ENST00000324856.7:c.4703del	p.Pro1568LeufsTer44	p.P1568Lfs*44	ENST00000324856	NM_006015.4	1567	Ccc/cc	18/20	1	2	FACETS	0.374	0.318	0.436	0.374	0.318	0.436	SUBCLONAL	1	TRUE	1	0.32	2		808	902	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431722	49431722	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555190550	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	183	868	0	ENST00000301067.7:c.9417del	p.Lys3140ArgfsTer2	p.K3140Rfs*2	ENST00000301067	NM_003482.3	3139	ccC/cc	34/54	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.32	2		868	1073	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65311293	65311293	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	123	903	1	ENST00000342505.4:c.2018del	p.Gly673ValfsTer30	p.G673Vfs*30	ENST00000342505	NM_002227.2	673	gGt/gt	15/25	1	2	FACETS	0.741	0.669	0.818	0.741	0.669	0.818	SUBCLONAL	1	TRUE	1	0.32	2		904	1037	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255563	16255563	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	75	622	1	ENST00000375759.3:c.2828A>G	p.Lys943Arg	p.K943R	ENST00000375759	NM_015001.2	943	aAg/aGg	11/15	1	2	FACETS	0.5	0.437	0.569	0.5	0.437	0.569	SUBCLONAL	1	TRUE	1	0.32	2		623	937	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106390	27106390	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	51	478	0	ENST00000324856.7:c.6001A>G	p.Met2001Val	p.M2001V	ENST00000324856	NM_006015.4	2001	Atg/Gtg	20/20	1	2	FACETS	0.484	0.41	0.564	0.484	0.41	0.564	SUBCLONAL	1	TRUE	1	0.32	2		478	659	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248633	59248633	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	64	857	1	ENST00000371222.2:c.110G>T	p.Ser37Ile	p.S37I	ENST00000371222	NM_002228.3	37	aGc/aTc	1/1	1	2	FACETS	0.355	0.306	0.408	0.355	0.306	0.408	SUBCLONAL	1	TRUE	1	0.32	2		858	1128	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226564924	226564924	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	124	803	0	ENST00000366794.5:c.1826A>G	p.Asp609Gly	p.D609G	ENST00000366794	NM_001618.3	609	gAt/gGt	13/23	1	2	FACETS	0.814	0.736	0.897	0.814	0.736	0.897	CLONAL	1	TRUE	1	0.32	2		803	952	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010391	48010391	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1064795094	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	83	618	0	ENST00000234420.5:c.19C>A	p.Leu7Met	p.L7M	ENST00000234420	NM_000179.2	7	Ctg/Atg	1/10	1	2	FACETS	0.642	0.566	0.724	0.642	0.566	0.724	SUBCLONAL	1	TRUE	1	0.32	2		618	808	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172172	99172172	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	106	798	0	ENST00000074304.5:c.1738G>T	p.Ala580Ser	p.A580S	ENST00000074304	NM_001134224.1	580	Gcc/Tcc	17/26	1	2	FACETS	0.672	0.601	0.747	0.672	0.601	0.747	SUBCLONAL	1	TRUE	1	0.32	2		798	986	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794898	242794898	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138016578	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	90	778	1	ENST00000334409.5:c.311G>A	p.Arg104His	p.R104H	ENST00000334409	NM_005018.2	104	cGt/cAt	2/5	1	2	FACETS	0.561	0.496	0.63	0.561	0.496	0.63	SUBCLONAL	1	TRUE	1	0.32	2		779	1003	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691910	30691910	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	35	484	0	ENST00000295754.5:c.412T>C	p.Cys138Arg	p.C138R	ENST00000295754	NM_003242.5	138	Tgt/Cgt	3/7	0.296628409040779	2	FACETS	0.331	0.271	0.4	0.166	0.135	0.2	SUBCLONAL	1	TRUE	0	0.32	2		484	660	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557947	187557947	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	134	728	2	ENST00000441802.2:c.3764C>A	p.Pro1255His	p.P1255H	ENST00000441802	NM_005245.3	1255	cCt/cAt	5/27	1	2	FACETS	0.855	0.776	0.939	0.855	0.776	0.939	CLONAL	1	TRUE	1	0.32	2		730	979	SUCCESS
APC	324	MSKCC	GRCh37	5	112178714	112178714	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1246562800	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	111	749	0	ENST00000257430.4:c.7423A>G	p.Thr2475Ala	p.T2475A	ENST00000257430	NM_000038.5	2475	Act/Gct	16/16	1	2	FACETS	0.849	0.763	0.94	0.849	0.763	0.94	CLONAL	1	TRUE	1	0.32	2		749	817	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176662867	176662867	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	55	521	0	ENST00000439151.2:c.3842T>C	p.Leu1281Pro	p.L1281P	ENST00000439151	NM_022455.4	1281	cTt/cCt	6/23	1	2	FACETS	0.467	0.399	0.542	0.467	0.399	0.542	SUBCLONAL	1	TRUE	1	0.32	2		521	736	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910368	29910368	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	132	853	0	ENST00000376809.5:c.38T>G	p.Leu13Arg	p.L13R	ENST00000376809	NM_002116.7	13	cTc/cGc	1/8	1	2	FACETS	0.877	0.795	0.963	0.877	0.795	0.963	CLONAL	1	TRUE	1	0.32	2		853	941	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288785	33288785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765273333	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	108	394	0	ENST00000374542.5:c.767G>A	p.Arg256His	p.R256H	ENST00000374542	NM_001141970.1	256	cGc/cAc	3/8	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.32	2		394	637	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199898	138199898	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755138189	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	32	340	1	ENST00000237289.4:c.1316G>A	p.Arg439Gln	p.R439Q	ENST00000237289	NM_001270507.1	439	cGg/cAg	7/9	1	2	FACETS	0.449	0.364	0.546	0.449	0.364	0.546	SUBCLONAL	1	TRUE	1	0.32	2		341	445	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738633	145738633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	50	257	0	ENST00000428558.2:c.2431C>T	p.Pro811Ser	p.P811S	ENST00000428558	NM_004260.3	811	Cct/Tct	15/22	1	2	FACETS	0.775	0.66	0.902	0.775	0.66	0.902	CLONAL	1	TRUE	1	0.32	2		257	403	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624598	93624598	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	149	717	0	ENST00000375746.1:c.689A>G	p.Glu230Gly	p.E230G	ENST00000375746	NM_001174167.1	230	gAg/gGg	4/14	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.32	2		717	928	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759832	133759832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145494071	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	102	417	0	ENST00000318560.5:c.2155G>A	p.Ala719Thr	p.A719T	ENST00000318560	NM_005157.4	719	Gcc/Acc	11/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.32	2		417	512	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154426	2154426	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	143	917	0	ENST00000434045.2:c.502A>G	p.Lys168Glu	p.K168E	ENST00000434045	NM_001127598.1	168	Aag/Gag	5/5	1	2	FACETS	0.873	0.795	0.955	0.873	0.795	0.955	CLONAL	1	TRUE	1	0.32	2		917	1024	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196146	108196146	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	43	617	0	ENST00000278616.4:c.6682A>C	p.Thr2228Pro	p.T2228P	ENST00000278616	NM_000051.3	2228	Aca/Cca	46/63	1	2	FACETS	0.349	0.291	0.413	0.349	0.291	0.413	SUBCLONAL	1	TRUE	1	0.32	2		617	771	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244815	46244815	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1270	67	1050	1	ENST00000334344.6:c.2909C>A	p.Pro970Gln	p.P970Q	ENST00000334344	NM_152641.2	970	cCa/cAa	15/21	1	2	FACETS	0.313	0.271	0.36	0.313	0.271	0.36	SUBCLONAL	1	TRUE	1	0.32	2		1051	1337	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003794	45003794	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196771735	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	74	669	1	ENST00000558401.1:c.50G>A	p.Gly17Asp	p.G17D	ENST00000558401	NM_004048.2	17	gGc/gAc	1/4	1	2	FACETS	0.574	0.501	0.652	0.574	0.501	0.652	SUBCLONAL	1	TRUE	1	0.32	2		670	806	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858538	9858538	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	46	849	1	ENST00000330684.3:c.2863A>G	p.Ile955Val	p.I955V	ENST00000330684	NM_001134407.1	955	Att/Gtt	13/13	1	2	FACETS	0.315	0.264	0.371	0.315	0.264	0.371	SUBCLONAL	1	TRUE	1	0.32	2		850	914	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849487	68849487	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	148	881	0	ENST00000261769.5:c.1390G>A	p.Val464Ile	p.V464I	ENST00000261769	NM_004360.3	464	Gtc/Atc	10/16	1	2	FACETS	0.866	0.79	0.946	0.866	0.79	0.946	CLONAL	1	TRUE	1	0.32	2		881	1068	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862207	68862207	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	95	505	0	ENST00000261769.5:c.2295G>T	p.Gln765His	p.Q765H	ENST00000261769	NM_004360.3	765	caG/caT	14/16	1	2	FACETS	0.925	0.824	1	0.925	0.824	1	CLONAL	1	TRUE	1	0.32	2		505	642	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81957133	81957133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1476399695	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	325	994	3	ENST00000359376.3:c.2351G>A	p.Arg784Gln	p.R784Q	ENST00000359376	NM_002661.3	784	cGa/cAa	22/33	1	2	FACETS	0.758	0.715	0.803	1	0.994	1	SUBCLONAL	2	TRUE	1	0.32	2		997	1339	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935665	15935665	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	121	592	0	ENST00000268712.3:c.7268A>C	p.Glu2423Ala	p.E2423A	ENST00000268712	NM_006311.3	2423	gAg/gCg	46/46	1	2	FACETS	0.899	0.812	0.991	0.899	0.812	0.991	CLONAL	1	TRUE	1	0.32	2		592	841	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118585	17118585	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	70	718	0	ENST00000285071.4:c.1346T>C	p.Leu449Pro	p.L449P	ENST00000285071	NM_144997.5	449	cTc/cCc	12/14	1	2	FACETS	0.388	0.336	0.443	0.388	0.336	0.443	SUBCLONAL	1	TRUE	1	0.32	2		718	1129	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220129	5220129	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	58	445	0	ENST00000357368.4:c.3586C>A	p.Leu1196Met	p.L1196M	ENST00000357368	NM_002850.3	1196	Ctg/Atg	22/38	1	2	FACETS	0.602	0.517	0.695	0.602	0.517	0.695	SUBCLONAL	1	TRUE	1	0.32	2		445	602	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602847	10602847	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	94	706	0	ENST00000171111.5:c.731A>G	p.Glu244Gly	p.E244G	ENST00000171111	NM_203500.1	244	gAg/gGg	3/6	1	2	FACETS	0.604	0.536	0.676	0.604	0.536	0.676	SUBCLONAL	1	TRUE	1	0.32	2		706	973	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42384771	42384771	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1312	77	1134	0	ENST00000221972.3:c.533C>T	p.Ala178Val	p.A178V	ENST00000221972	NM_021601.3	178	gCc/gTc	4/5	1	2	FACETS	0.346	0.303	0.394	0.346	0.303	0.394	SUBCLONAL	1	TRUE	1	0.32	2		1134	1389	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917041	50917041	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759190487	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1231	229	1144	2	ENST00000440232.2:c.2293G>A	p.Val765Met	p.V765M	ENST00000440232	NM_002691.3	765	Gtg/Atg	19/27	1	2	FACETS	0.98	0.911	1	0.98	0.911	1	CLONAL	1	TRUE	1	0.32	2		1146	1460	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024687	31024687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	139	956	1	ENST00000375687.4:c.4172G>A	p.Ser1391Asn	p.S1391N	ENST00000375687	NM_015338.5	1391	aGt/aAt	13/13	1	2	FACETS	0.821	0.746	0.9	0.821	0.746	0.9	CLONAL	1	TRUE	1	0.32	2		957	1058	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354981	70354981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	172	1044	0	ENST00000374080.3:c.4903G>A	p.Val1635Ile	p.V1635I	ENST00000374080		1635	Gtt/Att	36/45	0.0958552485006182	0	FACETS	0.554	0.508	0.602			1	INDETERMINATE	1	TRUE	0	0.32	0		1044	1320	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196990	123196990	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	57	829	0	ENST00000218089.9:c.1756A>G	p.Thr586Ala	p.T586A	ENST00000218089	NM_001042749.1	586	Act/Gct	19/35	0.0958552485006182	0	FACETS	0.292	0.249	0.338			1	INDETERMINATE	1	TRUE	0	0.32	0		829	830	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645737	215645738	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs786201868	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	127	715	0	ENST00000260947.4:c.860_861del	p.Glu287ValfsTer5	p.E287Vfs*5	ENST00000260947	NM_000465.2	287	gAG/g	4/11	1	2	FACETS	0.944	0.855	1	0.944	0.855	1	CLONAL	1	TRUE	1	0.32	2		715	841	SUCCESS
APC	324	MSKCC	GRCh37	5	112179036	112179036	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	46	495	0	ENST00000257430.4:c.7749del	p.Ala2584GlnfsTer9	p.A2584Qfs*9	ENST00000257430	NM_000038.5	2582	gAa/ga	16/16	1	2	FACETS	0.432	0.363	0.508	0.432	0.363	0.508	SUBCLONAL	1	TRUE	1	0.32	2		495	666	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926603	59926603	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	74	525	0	ENST00000259008.2:c.394del	p.Thr132ProfsTer25	p.T132Pfs*25	ENST00000259008	NM_032043.2	132	Acc/cc	5/20	1	2	FACETS	0.776	0.68	0.88	0.776	0.68	0.88	SUBCLONAL	1	TRUE	1	0.32	2		525	596	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675433	30675433	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	137	709	0	ENST00000376406.3:c.2923del	p.Asp975ThrfsTer23	p.D975Tfs*23	ENST00000376406	NM_014641.2	975	Gac/ac	8/15	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.32	2		709	816	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138382756	138382756	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	51	654	2	ENST00000289153.2:c.2788del	p.Thr930LeufsTer62	p.T930Lfs*62	ENST00000289153	NM_006219.2	930	Act/ct	19/22	1	2	FACETS	0.383	0.324	0.448	0.383	0.324	0.448	SUBCLONAL	1	TRUE	1	0.32	2		656	832	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620679	52620679	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	64	451	0	ENST00000394830.3:c.3074del	p.Asn1025ThrfsTer109	p.N1025Tfs*109	ENST00000394830	NM_018313.4	1025	aAc/ac	21/30	1	2	FACETS	0.645	0.558	0.739	0.645	0.558	0.739	SUBCLONAL	1	TRUE	1	0.32	2		451	620	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434982	49434983	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	77	419	0	ENST00000301067.7:c.6570dup	p.Thr2191HisfsTer11	p.T2191Hfs*11	ENST00000301067	NM_003482.3	2190	-/C	31/54	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.32	2		419	478	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619216	1619216	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	207	949	0	ENST00000344749.5:c.1344del	p.Glu449ArgfsTer37	p.E449Rfs*37	ENST00000344749	NM_001136139.2	448	ccC/cc	16/19	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.32	2		949	1255	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649561	48649561	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	197	1201	0	ENST00000376670.3:c.49del	p.Gln17SerfsTer120	p.Q17Sfs*120	ENST00000376670	NM_002049.3	15	ctC/ct	2/6	0.0958552485006182	0	FACETS	0.668	0.617	0.721			1	INDETERMINATE	1	TRUE	0	0.32	0		1201	1253	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249243	10249243	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	168	600	0	ENST00000340748.4:c.3939del	p.Ile1314SerfsTer28	p.I1314Sfs*28	ENST00000340748		1313	gcC/gc	34/40	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.32	2		600	833	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480586	123480587	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	35	564	0	ENST00000371139.4:c.97dup	p.Asp33GlyfsTer35	p.D33Gfs*35	ENST00000371139	NM_001114937.2	32	agg/aGgg	1/4	0.0958552485006182	0	FACETS	0.223	0.182	0.269			1	INDETERMINATE	1	TRUE	0	0.32	0		564	668	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29083899	29083900	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	32	209	0	ENST00000328354.6:c.1617_1618del	p.Ala540CysfsTer9	p.A540Cfs*9	ENST00000328354	NM_007194.3	539	tgTGct/tgct	15/15	1	2	FACETS	0.66	0.537	0.798	0.66	0.537	0.798	SUBCLONAL	1	TRUE	1	0.32	2		209	303	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925318	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	220	982	0	ENST00000543371.1:c.1402_1403del	p.Lys468ValfsTer8	p.K468Vfs*8	ENST00000543371	NM_001198531.1	465	agAAaa/agaa	14/14	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.32	2		982	1156	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233239	69233240	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0013227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	137	744	0	ENST00000462284.1:c.1111dup	p.Thr371AsnfsTer5	p.T371Nfs*5	ENST00000462284	NM_002392.5	368	-/A	11/11	1	2	FACETS	0.883	0.802	0.968	0.883	0.802	0.968	CLONAL	1	TRUE	1	0.32	2		744	970	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0013337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	48	225	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.759	0.64	0.891	0.759	0.64	0.891	SUBCLONAL	1	TRUE	1	0.17	2		225	744	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0013337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	26	404	0	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	1	2	FACETS	0.569	0.449	0.706	0.569	0.449	0.706	SUBCLONAL	1	TRUE	1	0.17	2		404	538	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508805	106508805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762805000	NA	P-0013337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	84	480	1	ENST00000359195.3:c.799G>A	p.Glu267Lys	p.E267K	ENST00000359195	NM_002649.2	267	Gaa/Aaa	2/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.17	2		481	841	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	66	614	4	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	1	2	FACETS	0.746	0.645	0.856	0.746	0.645	0.856	SUBCLONAL	1	TRUE	1	0.17	2		618	1041	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195488	102195488	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1310	71	946	0	ENST00000263464.3:c.248C>G	p.Thr83Ser	p.T83S	ENST00000263464	NM_001165.4	83	aCt/aGt	2/9	1	2	FACETS	0.605	0.526	0.691	0.605	0.526	0.691	SUBCLONAL	1	TRUE	1	0.17	2		946	1381	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392718	118392718	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	68	599	0	ENST00000534358.1:c.11750A>G	p.Tyr3917Cys	p.Y3917C	ENST00000534358	NM_005933.3	3917	tAt/tGt	36/36	1	2	FACETS	0.906	0.786	1	0.906	0.786	1	CLONAL	1	TRUE	1	0.17	2		599	883	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490853	56490853	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	80	573	0	ENST00000267101.3:c.2299G>A	p.Asp767Asn	p.D767N	ENST00000267101	NM_001982.3	767	Gac/Aac	20/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.17	2		573	702	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	34	456	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.636	0.522	0.763			1	INDETERMINATE	1	TRUE	NA	0.406439021015555	2		456	263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057519990	NA	P-0013349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	181	727	1	ENST00000269305.4:c.796G>T	p.Gly266Ter	p.G266*	ENST00000269305	NM_001126112.2	266	Gga/Tga	8/11	0.274857403006477	4	FACETS	0.807	0.746	0.871	0.807	0.746	0.871	CLONAL	2	TRUE	2	0.406439021015555	4		728	776	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577578	7577578	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	156	461	0	ENST00000269305.4:c.703A>G	p.Asn235Asp	p.N235D	ENST00000269305	NM_001126112.2	235	Aac/Gac	7/11	0.274857403006477	4	FACETS	0.827	0.759	0.896	0.827	0.759	0.896	CLONAL	2	TRUE	2	0.406439021015555	4		461	653	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359084	81359084	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747693036	NA	P-0013349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	138	577	1	ENST00000222390.5:c.877A>G	p.Met293Val	p.M293V	ENST00000222390	NM_000601.4	293	Atg/Gtg	8/18	0.193056114566913	4	FACETS	0.87	0.795	0.947	0.87	0.795	0.947	INDETERMINATE	2	TRUE	2	0.406439021015555	4		578	549	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636208	28636208	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	rs1293973888	NA	P-0013349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	48	477	0	ENST00000241453.7:c.166-2A>T		p.X56_splice	ENST00000241453	NM_004119.2	56			1	2	FACETS	0.576	0.488	0.673	0.576	0.488	0.673	SUBCLONAL	1	TRUE	1	0.406439021015555	2		477	410	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941170	36941170	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	102	1069	2	ENST00000361632.4:c.169C>A	p.Pro57Thr	p.P57T	ENST00000361632		57	Ccg/Acg	3/16	0.313841941191372	3	FACETS	0.717	0.641	0.799	0.359	0.32	0.4	SUBCLONAL	1	TRUE	1	0.406439021015555	3		1071	842	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843619	156843619	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	365	891	1	ENST00000524377.1:c.1045A>T	p.Asn349Tyr	p.N349Y	ENST00000524377	NM_002529.3	349	Aac/Tac	8/17	0.406439021015555	3	FACETS	0.94	0.898	0.983	0.94	0.898	0.983	CLONAL	3	TRUE	0	0.406439021015555	3		892	766	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566703	212566703	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	94	403	4	ENST00000342788.4:c.1478C>A	p.Ala493Asp	p.A493D	ENST00000342788	NM_005235.2	493	gCt/gAt	12/28	0.313841941191372	3	FACETS	0.754	0.676	0.835	0.754	0.676	0.835	SUBCLONAL	2	TRUE	1	0.406439021015555	3		407	369	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226783	142226783	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479079956	NA	P-0013349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	46	347	0	ENST00000350721.4:c.5021G>A	p.Gly1674Glu	p.G1674E	ENST00000350721	NM_001184.3	1674	gGa/gAa	28/47	0.313841941191372	3	FACETS	0.746	0.63	0.873	0.373	0.315	0.437	SUBCLONAL	1	TRUE	1	0.406439021015555	3		347	365	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467368	66467368	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	107	426	0	ENST00000273854.3:c.901A>T	p.Thr301Ser	p.T301S	ENST00000273854	NM_004439.5	301	Acc/Tcc	3/18	0.192906836729928	2	FACETS	1	0.976	1	0.631	0.57	0.695	INDETERMINATE	1	TRUE	0	0.406439021015555	2		426	417	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193880	106193880	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	147	692	0	ENST00000380013.4:c.4342A>T	p.Ser1448Cys	p.S1448C	ENST00000380013	NM_001127208.2	1448	Agt/Tgt	10/11	0.320617397946953	3	FACETS	1	0.985	1	0.673	0.616	0.732	CLONAL	1	TRUE	1	0.406439021015555	3		692	647	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177806	56177806	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs781412824	NA	P-0013349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	54	548	0	ENST00000399503.3:c.2779A>G	p.Ile927Val	p.I927V	ENST00000399503	NM_005921.1	927	Att/Gtt	14/20	1	2	FACETS	0.597	0.511	0.691	0.597	0.511	0.691	SUBCLONAL	1	TRUE	1	0.406439021015555	2		548	445	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149450067	149450067	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0013349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	53	724	1	ENST00000286301.3:c.1150A>T	p.Arg384Ter	p.R384*	ENST00000286301	NM_005211.3	384	Aga/Tga	8/22	1	2	FACETS	0.585	0.499	0.678	0.585	0.499	0.678	SUBCLONAL	1	TRUE	1	0.406439021015555	2		725	446	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052985	180052985	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	69	658	0	ENST00000261937.6:c.1305C>A	p.Tyr435Ter	p.Y435*	ENST00000261937	NM_182925.4	435	taC/taA	10/30	1	2	FACETS	0.729	0.636	0.828	0.729	0.636	0.828	SUBCLONAL	1	TRUE	1	0.406439021015555	2		658	466	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166215	32166215	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	251	632	0	ENST00000375023.3:c.4739T>A	p.Leu1580Gln	p.L1580Q	ENST00000375023	NM_004557.3	1580	cTg/cAg	26/30	0.406439021015555	3	FACETS	1	0.987	1	0.772	0.727	0.817	CLONAL	2	TRUE	0	0.406439021015555	3		632	642	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287578	33287578	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	59	496	0	ENST00000374542.5:c.1519A>G	p.Asn507Asp	p.N507D	ENST00000374542	NM_001141970.1	507	Aac/Gac	6/8	0.406439021015555	3	FACETS	0.622	0.535	0.716	0.207	0.178	0.239	SUBCLONAL	1	TRUE	0	0.406439021015555	3		496	562	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508334	106508334	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	61	221	0	ENST00000359195.3:c.328T>A	p.Tyr110Asn	p.Y110N	ENST00000359195	NM_002649.2	110	Tac/Aac	2/11	0.193056114566913	4	FACETS	0.851	0.743	0.966	0.851	0.743	0.966	INDETERMINATE	2	TRUE	2	0.406439021015555	4		221	248	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873594	151873594	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	139	583	0	ENST00000262189.6:c.8944G>T	p.Val2982Phe	p.V2982F	ENST00000262189	NM_170606.2	2982	Gtt/Ttt	38/59	0.295627835661277	3	FACETS	1	0.986	1	0.705	0.644	0.768	CLONAL	1	TRUE	1	0.406439021015555	3		583	584	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879625	151879625	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	31	185	0	ENST00000262189.6:c.5320G>C	p.Glu1774Gln	p.E1774Q	ENST00000262189	NM_170606.2	1774	Gaa/Caa	36/59	0.295627835661277	3	FACETS	0.816	0.664	0.985	0.408	0.332	0.493	CLONAL	1	TRUE	1	0.406439021015555	3		185	225	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63700033	63700033	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	50	380	1	ENST00000279873.7:c.368G>T	p.Gly123Val	p.G123V	ENST00000279873	NM_032199.2	123	gGc/gTc	3/10	0.193056114566913	4	FACETS	0.718	0.61	0.837	0.359	0.305	0.419	INDETERMINATE	1	TRUE	2	0.406439021015555	4		381	482	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998208	100998208	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1297421643	NA	P-0013349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	71	637	1	ENST00000325455.5:c.1594G>T	p.Glu532Ter	p.E532*	ENST00000325455	NM_001202474.3	532	Gag/Tag	1/8	0.295627835661277	3	FACETS	0.943	0.826	1	0.471	0.413	0.534	CLONAL	1	TRUE	1	0.406439021015555	3		638	446	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	472209	472209	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	174	698	0	ENST00000399788.2:c.592A>T	p.Ser198Cys	p.S198C	ENST00000399788	NM_001042603.1	198	Agc/Tgc	5/28	0.193056114566913	4	FACETS	0.793	0.732	0.857	0.793	0.732	0.857	INDETERMINATE	2	TRUE	2	0.406439021015555	4		698	759	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422616	49422616	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	151	617	1	ENST00000301067.7:c.14377G>T	p.Ala4793Ser	p.A4793S	ENST00000301067	NM_003482.3	4793	Gcc/Tcc	45/54	0.274857403006477	4	FACETS	0.755	0.692	0.821	0.755	0.692	0.821	SUBCLONAL	2	TRUE	2	0.406439021015555	4		618	692	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426634	121426634	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0013349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	122	557	1	ENST00000257555.6:c.327-2A>T		p.X109_splice	ENST00000257555		109			0.274857403006477	4	FACETS	0.785	0.712	0.86	0.785	0.712	0.86	SUBCLONAL	2	TRUE	2	0.406439021015555	4		558	538	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514674	103514674	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	54	425	0	ENST00000355739.4:c.1175A>C	p.Lys392Thr	p.K392T	ENST00000355739	NM_000123.3	392	aAg/aCg	8/15	0.313841941191372	3	FACETS	0.72	0.616	0.833	0.36	0.308	0.417	SUBCLONAL	1	TRUE	1	0.406439021015555	3		425	444	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435876	110435876	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	35	162	0	ENST00000375856.3:c.2525A>T	p.Gln842Leu	p.Q842L	ENST00000375856	NM_003749.2	842	cAg/cTg	1/2	0.313841941191372	3	FACETS	1	0.934	1	0.64	0.531	0.757	CLONAL	1	TRUE	1	0.406439021015555	3		162	162	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871223	35871223	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0013349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	53	839	0	ENST00000216797.5:c.950T>G	p.Leu317Ter	p.L317*	ENST00000216797	NM_020529.2	317	tTa/tGa	6/6	1	2	FACETS	0.349	0.296	0.406	0.349	0.296	0.406	SUBCLONAL	1	TRUE	1	0.406439021015555	2		839	748	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560409	95560409	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1262583273	NA	P-0013349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	49	412	0	ENST00000393063.1:c.5180A>C	p.His1727Pro	p.H1727P	ENST00000393063	NM_030621.3	1727	cAc/cCc	25/28	1	2	FACETS	0.737	0.627	0.857	0.737	0.627	0.857	SUBCLONAL	1	TRUE	1	0.406439021015555	2		412	327	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678524	88678524	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	211	488	0	ENST00000360948.2:c.1012A>G	p.Asn338Asp	p.N338D	ENST00000360948	NM_001012338.2	338	Aat/Gat	9/19	0.168675514235305	6	FACETS	0.968	0.909	1			1	INDETERMINATE	4	TRUE	NA	0.406439021015555	6		488	486	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485751	40485751	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1427784630	NA	P-0013349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	195	898	0	ENST00000264657.5:c.989C>G	p.Pro330Arg	p.P330R	ENST00000264657	NM_139276.2	330	cCc/cGc	10/24	0.193056114566913	4	FACETS	0.808	0.749	0.869	0.808	0.749	0.869	INDETERMINATE	2	TRUE	2	0.406439021015555	4		898	835	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7120740	7120740	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	78	766	0	ENST00000302850.5:c.3550A>T	p.Ile1184Phe	p.I1184F	ENST00000302850	NM_000208.2	1184	Atc/Ttc	20/22	0.295627835661277	3	FACETS	0.664	0.583	0.75	0.332	0.291	0.375	SUBCLONAL	1	TRUE	1	0.406439021015555	3		766	696	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288888	15288888	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	73	291	0	ENST00000263388.2:c.3851C>A	p.Pro1284Gln	p.P1284Q	ENST00000263388	NM_000435.2	1284	cCg/cAg	24/33	0.295627835661277	3	FACETS	1	0.974	1	0.711	0.627	0.799	CLONAL	1	TRUE	1	0.406439021015555	3		291	304	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410846	63410846	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	158	442	0	ENST00000330258.3:c.2321T>A	p.Val774Glu	p.V774E	ENST00000330258	NM_152424.3	774	gTa/gAa	2/2	0.23739938770381	2	FACETS	0.836	0.773	0.901			1	INDETERMINATE	2	TRUE	NA	0.406439021015555	2		442	465	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345516	70345516	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	246	469	0	ENST00000374080.3:c.2375A>T	p.Gln792Leu	p.Q792L	ENST00000374080		792	cAg/cTg	17/45	0.23739938770381	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.406439021015555	2		469	504	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858334	27858335	+	stop_gained	Nonsense_Mutation	DNP	GA	GA	TC	novel	NA	P-0013349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	279	1352	0	ENST00000359303.2:c.236_237inv	p.Phe79Ter	p.F79*	ENST00000359303	NM_003535.2	79	tTC/tGA	1/1	0.406439021015555	3	FACETS	0.994	0.937	1	0.663	0.624	0.702	CLONAL	2	TRUE	0	0.406439021015555	3		1352	831	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165665	108165665	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	202	549	0	ENST00000278616.4:c.4791del	p.Leu1598SerfsTer3	p.L1598Sfs*3	ENST00000278616	NM_000051.3	1596	caT/ca	32/63	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		549	301	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118716	115118717	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	331	622	0	ENST00000257566.3:c.624dup	p.Leu209ThrfsTer18	p.L209Tfs*18	ENST00000257566	NM_016569.3	208	-/A	2/8	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		622	934	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844244	68844244	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs943875725	NA	P-0013539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	64	372	0	ENST00000261769.5:c.832G>C	p.Gly278Arg	p.G278R	ENST00000261769	NM_004360.3	278	Gga/Cga	6/16	0.226932052052369	1	FACETS	0.931	0.807	1	0.931	0.807	1	CLONAL	1	TRUE	0	0.226932052052369	1		372	537	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0013550-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	44	138	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.192319697666961	2	FACETS	0.79	0.668	0.922	0.395	0.334	0.461	INDETERMINATE	1	FALSE	0	0.468232541728663	2		138	238	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0013550-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	55	561	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	0.192319697666961	2	FACETS	0.457	0.391	0.529	0.229	0.195	0.265	INDETERMINATE	1	FALSE	0	0.468232541728663	2		561	514	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0013567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	137	423	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.508331066499489	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	1	0.508331066499489	3		423	328	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803899	43803899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61754776	NA	P-0013567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	111	383	0	ENST00000372470.3:c.209C>T	p.Pro70Leu	p.P70L	ENST00000372470	NM_005373.2	70	cCg/cTg	2/12	0.508331066499489	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.508331066499489	2		383	207	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602584	10602584	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1208201314	NA	P-0013567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	155	474	1	ENST00000171111.5:c.994G>T	p.Gly332Cys	p.G332C	ENST00000171111	NM_203500.1	332	Ggc/Tgc	3/6	0.508331066499489	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.508331066499489	2		475	268	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221303	1221307	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGA	GGCGA	-	novel	NA	P-0013567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	161	628	0	ENST00000326873.7:c.826_830del	p.Gly276LeufsTer7	p.G276Lfs*7	ENST00000326873	NM_000455.4	276	GGCGAc/c	6/10	0.508331066499489	2	FACETS	0.999	0.934	1	0.999	0.934	1	CLONAL	2	TRUE	0	0.508331066499489	2		628	317	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368482	225368482	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	160	460	0	ENST00000264414.4:c.1264A>T	p.Met422Leu	p.M422L	ENST00000264414	NM_003590.4	422	Atg/Ttg	9/16	0.508331066499489	3	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	1	0.508331066499489	3		460	387	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576823	67576823	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	46	189	0	ENST00000274335.5:c.905A>T	p.Gln302Leu	p.Q302L	ENST00000274335		302	cAg/cTg	6/15	0.508331066499489	3	FACETS	0.752	0.645	0.864	0.752	0.645	0.864	SUBCLONAL	2	TRUE	1	0.508331066499489	3		189	151	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032198	26032199	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0013567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	111	723	0	ENST00000244661.2:c.90_91del	p.Pro31GlyfsTer67	p.P31Gfs*67	ENST00000244661	NM_003537.3	30	gcGCcg/gccg	1/1	0.490563582291509	2	FACETS	0.772	0.705	0.84	0.772	0.705	0.84	SUBCLONAL	2	TRUE	0	0.508331066499489	2		723	283	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350155	81350155	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs758567520	NA	P-0013567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	107	407	0	ENST00000222390.5:c.1177C>G	p.Arg393Gly	p.R393G	ENST00000222390	NM_000601.4	393	Cgt/Ggt	10/18	0.508331066499489	4	FACETS	0.887	0.803	0.973	0.887	0.803	0.973	CLONAL	2	TRUE	2	0.508331066499489	4		407	358	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000084	30000085	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	108	559	0	ENST00000338641.4:c.98dup	p.Met33IlefsTer16	p.M33Ifs*16	ENST00000338641	NM_000268.3	33	atg/aTtg	1/16	1	2	FACETS	0.936	0.838	1	0.936	0.838	1	CLONAL	1	TRUE	1	0.203510973970826	2		559	1134	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0013759-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	161	351	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.308509115213665	3	FACETS	1	0.983	1	0.64	0.587	0.696	CLONAL	1	TRUE	1	0.338219205025798	3		351	869	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593667	55593669	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	rs1060502543	NA	P-0013776-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	283	600	0	ENST00000288135.5:c.1735_1737del	p.Asp579del	p.D579del	ENST00000288135	NM_000222.2	578	tATGat/tat	11/21	1	2	FACETS	0.88	0.83	0.931	0.88	0.83	0.931	CLONAL	1	TRUE	1	0.763927045113407	2		600	842	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524178	18524178	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013776-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	396	617	0	ENST00000266497.5:c.1690G>A	p.Gly564Arg	p.G564R	ENST00000266497		564	Ggg/Agg	11/31	1	2	FACETS	0.709	0.673	0.745	0.709	0.673	0.745	SUBCLONAL	1	TRUE	1	0.763927045113407	2		617	1463	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979330	40979330	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013776-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	317	493	0	ENST00000373198.4:c.1803T>G	p.Asn601Lys	p.N601K	ENST00000373198	NM_133170.3	601	aaT/aaG	11/32	1	2	FACETS	0.946	0.896	0.997	0.946	0.896	0.997	CLONAL	1	TRUE	1	0.763927045113407	2		493	877	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426123	138426123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217537873	NA	P-0013858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	308	550	0	ENST00000289153.2:c.1408G>A	p.Glu470Lys	p.E470K	ENST00000289153	NM_006219.2	470	Gaa/Aaa	9/22	1	2	FACETS	0.982	0.931	1	0.982	0.931	1	CLONAL	1	TRUE	1	0.811269972512614	2		550	773	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443865	18443865	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	316	618	0	ENST00000266497.5:c.838T>C	p.Tyr280His	p.Y280H	ENST00000266497		280	Tat/Cat	3/31	1	2	FACETS	0.961	0.911	1	0.961	0.911	1	CLONAL	1	TRUE	1	0.811269972512614	2		618	811	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440203	220440203	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0013858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	358	1109	0	ENST00000243786.2:c.1056T>G	p.Tyr352Ter	p.Y352*	ENST00000243786	NM_002191.3	352	taT/taG	2/2	1	2	FACETS	0.649	0.615	0.685	0.649	0.615	0.685	SUBCLONAL	1	TRUE	1	0.811269972512614	2		1109	1359	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030224	180030224	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761089407	NA	P-0013858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	772	735	2	ENST00000261937.6:c.4060C>T	p.Arg1354Cys	p.R1354C	ENST00000261937	NM_182925.4	1354	Cgc/Tgc	30/30	0.811269972512614	3	FACETS	0.981	0.953	1	0.981	0.953	1	CLONAL	2	TRUE	1	0.811269972512614	3		737	1364	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720737	89720737	+	frameshift_variant	Frame_Shift_Ins	INS	T	T	GGG	novel	NA	P-0013858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	15	120	0	ENST00000371953.3:c.888delinsGGG	p.Cys296TrpfsTer12	p.C296Wfs*12	ENST00000371953	NM_000314.4	296	tgT/tgGGG	8/9	1	2	FACETS	0.324	0.239	0.424	0.324	0.239	0.424	SUBCLONAL	1	TRUE	1	0.811269972512614	2		120	114	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0013871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	29	138	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		138	731	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0013873-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	135	138	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.248128586895905	3	FACETS	0.924	0.848	1	0.924	0.848	1	INDETERMINATE	2	TRUE	1	0.441747872514333	3		138	404	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0013873-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	189	491	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.794	0.739	0.85	1	0.992	1	SUBCLONAL	2	TRUE	1	0.441747872514333	2		491	539	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0013873-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	291	531	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.124803657522973	4	FACETS	0.911	0.863	0.96			1	INDETERMINATE	3	TRUE	NA	0.441747872514333	4		531	695	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797221	135797222	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs118203417	NA	P-0013873-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	243	559	0	ENST00000298552.3:c.647_648del	p.Phe216Ter	p.F216*	ENST00000298552	NM_001162426.1	216	tTT/t	7/23	0.441747872514333	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.441747872514333	1		559	808	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397781	139397781	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013873-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	88	291	0	ENST00000277541.6:c.5020T>C	p.Ser1674Pro	p.S1674P	ENST00000277541	NM_017617.3	1674	Tcc/Ccc	27/34	0.441747872514333	1	FACETS	0.739	0.658	0.824	0.739	0.658	0.824	SUBCLONAL	1	TRUE	0	0.441747872514333	1		291	420	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245033	46245033	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs139789595	NA	P-0013927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	196	817	0	ENST00000334344.6:c.3127C>T	p.Gln1043Ter	p.Q1043*	ENST00000334344	NM_152641.2	1043	Caa/Taa	15/21	0.251093553557913	5	FACETS	1	0.96	1	0.704	0.651	0.758	CLONAL	2	TRUE	2	0.251093553557913	5		817	1018	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067050	143067050	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1188846860	NA	P-0013927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	90	774	0	ENST00000262992.4:c.1663A>C	p.Asn555His	p.N555H	ENST00000262992	NM_001101669.1	555	Aac/Cac	16/24	0.220748222872389	4	FACETS	0.837	0.741	0.941	0.419	0.37	0.471	CLONAL	1	TRUE	2	0.251093553557913	4		774	1071	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0013939-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1266	200	640	0	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	1	2	FACETS	0.95	0.878	1	0.95	0.878	1	CLONAL	1	TRUE	1	0.287195319365991	2		640	1466	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0013939-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	88	364	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.893	0.792	1	0.893	0.792	1	CLONAL	1	TRUE	1	0.287195319365991	2		364	686	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0013939-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	218	481	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.240872753679449	2	FACETS	0.841	0.783	0.9	0.841	0.783	0.9	CLONAL	2	TRUE	0	0.287195319365991	2		482	903	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692835	89692835	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs57374291	NA	P-0013939-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	51	171	0	ENST00000371953.3:c.319G>T	p.Asp107Tyr	p.D107Y	ENST00000371953	NM_000314.4	107	Gat/Tat	5/9	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.287195319365991	2		171	262	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371799	55371820	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCCGCGCTGGGCCCCGAG	GGCGGCCGCGCTGGGCCCCGAG	-	novel	NA	P-0013939-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	49	109	0	ENST00000297316.4:c.499_520del	p.Leu167TrpfsTer213	p.L167Wfs*213	ENST00000297316	NM_022454.3	163	caGGCGGCCGCGCTGGGCCCCGAG/ca	2/2	1	2	FACETS	0.845	0.725	0.973	1	0.971	1	CLONAL	2	TRUE	1	0.287195319365991	2		109	202	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720877	89720877	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0013942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	25	295	1	ENST00000371953.3:c.1026+2T>A		p.X342_splice	ENST00000371953	NM_000314.4	342			1	2	FACETS	0.942	0.742	1	0.942	0.742	1	CLONAL	1	TRUE	1	0.15	2		296	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579403	7579403	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	61	703	0	ENST00000269305.4:c.284C>G	p.Ser95Cys	p.S95C	ENST00000269305	NM_001126112.2	95	tCt/tGt	4/11	1	2	FACETS	0.905	0.778	1	0.905	0.778	1	CLONAL	1	TRUE	1	0.15	2		703	899	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557630	95557630	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	203	422	0	ENST00000393063.1:c.5437G>C	p.Glu1813Gln	p.E1813Q	ENST00000393063	NM_030621.3	1813	Gag/Cag	26/28	0.491418834411013	4	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	2	0.814679551261134	4		422	450	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262168	16262168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	67	75	0	ENST00000375759.3:c.9433G>A	p.Ala3145Thr	p.A3145T	ENST00000375759	NM_015001.2	3145	Gct/Act	11/15	0.714242760227668	4	FACETS	0.904	0.805	1	0.904	0.805	1	CLONAL	2	TRUE	2	0.814679551261134	4		75	165	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608307	43608307	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	184	307	0	ENST00000355710.3:c.1655C>A	p.Thr552Asn	p.T552N	ENST00000355710	NM_020975.4	552	aCc/aAc	9/20	0.380709736501626	5	FACETS	0.907	0.851	0.963	0.907	0.851	0.963	INDETERMINATE	3	TRUE	2	0.814679551261134	5		307	369	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333837	70333837	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	143	380	0	ENST00000373644.4:c.1742C>G	p.Pro581Arg	p.P581R	ENST00000373644	NM_030625.2	581	cCg/cGg	2/12	0.321040957827395	6	FACETS	0.918	0.842	0.996	0.612	0.561	0.664	INDETERMINATE	2	TRUE	3	0.814679551261134	6		380	503	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685270	89685270	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	97	130	0	ENST00000371953.3:c.165G>T	p.Arg55Ser	p.R55S	ENST00000371953	NM_000314.4	55	agG/agT	3/9	0.321040957827395	6	FACETS	1	0.951	1	1	0.951	1	INDETERMINATE	3	TRUE	3	0.814679551261134	6		130	197	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122736	108122736	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	112	232	0	ENST00000278616.4:c.1780G>T	p.Glu594Ter	p.E594*	ENST00000278616	NM_000051.3	594	Gaa/Taa	11/63	0.380709736501626	5	FACETS	0.982	0.896	1	0.655	0.597	0.714	INDETERMINATE	2	TRUE	2	0.814679551261134	5		232	311	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491378	18491378	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	105	243	0	ENST00000266497.5:c.1291A>G	p.Ile431Val	p.I431V	ENST00000266497		431	Att/Gtt	8/31	0.295489884676991	5	FACETS	0.994	0.904	1			1	INDETERMINATE	2	TRUE	NA	0.814679551261134	5		243	288	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590968	95590968	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	149	191	0	ENST00000393063.1:c.941del	p.Gly314AspfsTer8	p.G314Dfs*8	ENST00000393063	NM_030621.3	314	gGa/ga	9/28	0.491418834411013	4	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	2	0.814679551261134	4		191	314	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831704	72831704	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	324	485	0	ENST00000268489.5:c.4877C>G	p.Ala1626Gly	p.A1626G	ENST00000268489	NM_006885.3	1626	gCa/gGa	9/10	0.79528008498304	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.814679551261134	2		485	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0013954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	173	240	0	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.814679551261134	2	FACETS	0.974	0.933	1	0.974	0.933	1	CLONAL	2	TRUE	0	0.814679551261134	2		240	218	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575666	48575667	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TC	TC	-	rs377767328	NA	P-0013954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	193	288	0	ENST00000342988.3:c.430_431del	p.Ser144ArgfsTer7	p.S144Rfs*7	ENST00000342988	NM_005359.5	142	gaTCtc/gatc	4/12	NA	2	FACETS	0.955	0.915	0.993			1	INDETERMINATE	2	TRUE	NA	0.814679551261134	2		288	248	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115070	3115070	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	150	337	0	ENST00000078429.4:c.605G>T	p.Arg202Leu	p.R202L	ENST00000078429	NM_002067.2	202	cGg/cTg	4/7	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.814679551261134	2		337	313	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741844	40741844	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	103	307	0	ENST00000392038.2:c.1128G>T	p.Glu376Asp	p.E376D	ENST00000392038	NM_001626.4	376	gaG/gaT	11/14	0.643335131900976	3	FACETS	1	0.943	1	0.53	0.479	0.582	CLONAL	1	TRUE	1	0.814679551261134	3		307	336	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99169358	99169358	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	168	328	0	ENST00000074304.5:c.1288G>T	p.Glu430Ter	p.E430*	ENST00000074304	NM_001134224.1	430	Gag/Tag	15/26	0.380709736501626	5	FACETS	1	0.974	1	0.733	0.681	0.785	INDETERMINATE	2	TRUE	2	0.814679551261134	5		328	417	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561075	9561075	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	231	253	0	ENST00000353224.5:c.707C>A	p.Pro236His	p.P236H	ENST00000353224	NM_177990.2	236	cCt/cAt	4/10	0.665099918063261	5	FACETS	1	0.952	1	1	0.952	1	CLONAL	3	TRUE	2	0.814679551261134	5		253	418	SUCCESS
APC	324	MSKCC	GRCh37	5	112111324	112111324	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs879254087	NA	P-0013954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	119	135	0	ENST00000257430.4:c.423-2A>T		p.X141_splice	ENST00000257430	NM_000038.5	141			0.814679551261134	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.814679551261134	2		135	142	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520182	176520182	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0013954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	180	335	0	ENST00000292408.4:c.1101T>A	p.Tyr367Ter	p.Y367*	ENST00000292408	NM_213647.1	367	taT/taA	9/18	0.321040957827395	6	FACETS	1	0.984	1	0.802	0.746	0.859	INDETERMINATE	2	TRUE	3	0.814679551261134	6		335	483	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045786	26045786	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	493	768	1	ENST00000540144.1:c.148C>A	p.Arg50Ser	p.R50S	ENST00000540144	NM_003531.2	50	Cgc/Agc	1/1	0.794094669334171	3	FACETS	0.993	0.972	1	0.993	0.972	1	CLONAL	3	TRUE	0	0.814679551261134	3		769	572	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729554	41729554	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	322	577	0	ENST00000242208.4:c.975G>T	p.Gln325His	p.Q325H	ENST00000242208	NM_002192.2	325	caG/caT	3/3	0.814679551261134	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.814679551261134	2		577	393	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250436	110250436	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	126	300	1	ENST00000374672.4:c.239G>T	p.Gly80Val	p.G80V	ENST00000374672	NM_004235.4	80	gGt/gTt	3/5	0.422166152840096	5	FACETS	1	0.929	1	0.676	0.62	0.733	INDETERMINATE	2	TRUE	2	0.814679551261134	5		301	339	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934293	39934294	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0013954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	203	544	1	ENST00000378444.4:c.305_306delinsTT	p.Arg102Leu	p.R102L	ENST00000378444	NM_001123385.1	102	cGG/cTT	4/15	0.643335131900976	3	FACETS	1	0.987	1	0.618	0.577	0.66	CLONAL	1	TRUE	1	0.814679551261134	3		545	567	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424656	47424656	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	216	549	2	ENST00000377045.4:c.464A>T	p.Tyr155Phe	p.Y155F	ENST00000377045	NM_001654.4	155	tAc/tTc	6/16	NA	2	FACETS	0.955	0.896	1			1	INDETERMINATE	1	TRUE	NA	0.814679551261134	2		551	555	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356306	70356306	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	181	426	0	ENST00000374080.3:c.5201C>A	p.Pro1734His	p.P1734H	ENST00000374080		1734	cCc/cAc	37/45	0.2907239769957	5	FACETS	0.914	0.849	0.981	0.609	0.566	0.654	INDETERMINATE	2	TRUE	2	0.814679551261134	5		426	540	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938940	76938940	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	234	494	1	ENST00000373344.5:c.1808C>A	p.Ala603Asp	p.A603D	ENST00000373344	NM_000489.3	603	gCt/gAt	9/35	0.2907239769957	5	FACETS	1	0.976	1	0.716	0.673	0.76	INDETERMINATE	2	TRUE	2	0.814679551261134	5		495	594	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980435	7980435	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760428119	NA	P-0013971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	174	739	0	ENST00000319144.4:c.1148C>T	p.Thr383Met	p.T383M	ENST00000319144	NM_001139.2	383	aCg/aTg	9/15	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.440770689949065	2		739	758	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092780	27092780	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	182	843	0	ENST00000324856.7:c.2802del	p.Asn935IlefsTer6	p.N935Ifs*6	ENST00000324856	NM_006015.4	934	aTt/at	9/20	0.440770689949065	1	FACETS	0.918	0.85	0.989	0.918	0.85	0.989	CLONAL	1	TRUE	0	0.440770689949065	1		843	701	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902197	151902197	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	140	464	0	ENST00000262189.6:c.3955G>A	p.Asp1319Asn	p.D1319N	ENST00000262189	NM_170606.2	1319	Gat/Aat	25/59	NA	2	FACETS	1	0.954	1			1	INDETERMINATE	1	TRUE	NA	0.440770689949065	2		464	596	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0013976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	122	138	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.778343999136332	6	FACETS	1	0.958	1	0.432	0.394	0.471	CLONAL	2	TRUE	1	0.778343999136332	6		138	371	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0013976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	87	531	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.935	0.842	1	0.935	0.842	1	CLONAL	1	TRUE	1	0.778343999136332	2		531	239	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0013976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	496	627	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	0.778343999136332	5	FACETS	0.921	0.892	0.949	0.921	0.892	0.949	CLONAL	4	TRUE	1	0.778343999136332	5		627	750	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36934763	36934763	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs757913112	NA	P-0013976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	177	1151	0	ENST00000361632.4:c.1570G>C	p.Glu524Gln	p.E524Q	ENST00000361632		524	Gaa/Caa	11/16	NA	2	FACETS	0.944	0.877	1			1	INDETERMINATE	1	TRUE	NA	0.778343999136332	2		1151	482	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487212	56487212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144549266	NA	P-0013976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	48	466	1	ENST00000267101.3:c.1358G>A	p.Arg453His	p.R453H	ENST00000267101	NM_001982.3	453	cGt/cAt	12/28	0.190535249731863	4	FACETS	0.667	0.566	0.776	0.333	0.283	0.388	INDETERMINATE	1	TRUE	2	0.778343999136332	4		467	329	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28931763	28931763	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	95	881	0	ENST00000282397.4:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000282397	NM_002019.4	726	Gaa/Aaa	15/30	0.629985853611149	1	FACETS	0.475	0.427	0.524	0.475	0.427	0.524	SUBCLONAL	1	TRUE	0	0.778343999136332	1		881	314	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827828	72827828	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0013976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	152	1210	0	ENST00000268489.5:c.8753C>G	p.Ser2918Ter	p.S2918*	ENST00000268489	NM_006885.3	2918	tCa/tGa	9/10	0.411091534398284	1	FACETS	0.623	0.577	0.67	0.623	0.577	0.67	INDETERMINATE	1	TRUE	0	0.778343999136332	1		1210	383	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89839718	89839718	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	135	911	1	ENST00000389301.3:c.1975G>A	p.Glu659Lys	p.E659K	ENST00000389301	NM_000135.2	659	Gag/Aag	22/43	1	2	FACETS	0.876	0.804	0.949	0.876	0.804	0.949	CLONAL	1	TRUE	1	0.778343999136332	2		912	396	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268411	142268411	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	67	464	0	ENST00000350721.4:c.3081G>C	p.Glu1027Asp	p.E1027D	ENST00000350721	NM_001184.3	1027	gaG/gaC	15/47	0.506245726847068	4	FACETS	0.853	0.745	0.968			1	CLONAL	1	TRUE	NA	0.778343999136332	4		464	359	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636654	176636654	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	48	674	0	ENST00000439151.2:c.1254G>C	p.Leu418Phe	p.L418F	ENST00000439151	NM_022455.4	418	ttG/ttC	5/23	0.115529048748031	5	FACETS	0.602	0.51	0.704			1	INDETERMINATE	1	TRUE	NA	0.778343999136332	5		674	444	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638614	176638614	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784098	NA	P-0013976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	56	809	0	ENST00000439151.2:c.3214C>T	p.Arg1072Ter	p.R1072*	ENST00000439151	NM_022455.4	1072	Cga/Tga	5/23	0.115529048748031	5	FACETS	0.658	0.564	0.76			1	INDETERMINATE	1	TRUE	NA	0.778343999136332	5		809	474	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0014016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	10	162	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.248048353158305	1	FACETS	0.196	0.132	0.277	0.196	0.132	0.277	SUBCLONAL	1	TRUE	0	0.248048353158305	1		162	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578529	7578531	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	novel	NA	P-0014016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	159	421	0	ENST00000269305.4:c.399_401del	p.Met133_Phe134delinsIle	p.M133_F134delinsI	ENST00000269305	NM_001126112.2	133	atGTTt/att	5/11	0.248048353158305	2	FACETS	0.983	0.904	1	0.983	0.904	1	CLONAL	2	TRUE	0	0.248048353158305	2		421	652	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528705	8528705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370111525	NA	P-0014016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	78	530	1	ENST00000356435.5:c.427G>A	p.Ala143Thr	p.A143T	ENST00000356435		143	Gcc/Acc	4/35	0.0738206581313721	3	FACETS	0.923	0.81	1	0.461	0.405	0.522	INDETERMINATE	1	TRUE	1	0.248048353158305	3		531	766	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0014032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	139	541	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.653	0.594	0.714	0.653	0.594	0.714	SUBCLONAL	1	TRUE	1	0.52522860836303	2		541	811	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481403	140481403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913357	NA	P-0014032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	163	540	0	ENST00000288602.6:c.1405G>A	p.Gly469Arg	p.G469R	ENST00000288602	NM_004333.4	469	Gga/Aga	11/18	1	2	FACETS	0.863	0.794	0.935	0.863	0.794	0.935	CLONAL	1	TRUE	1	0.52522860836303	2		540	719	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206609	108206609	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	251	615	0	ENST00000278616.4:c.8189A>T	p.Gln2730Leu	p.Q2730L	ENST00000278616	NM_000051.3	2730	cAg/cTg	56/63	0.483424574466071	1	FACETS	0.961	0.904	1	0.961	0.904	1	CLONAL	1	TRUE	0	0.52522860836303	1		615	733	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398262	25398262	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913538	NA	P-0014036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	393	388	0	ENST00000311936.3:c.57G>C	p.Leu19Phe	p.L19F	ENST00000311936	NM_004985.3	19	ttG/ttC	2/5	1	2	FACETS	0.948	0.903	0.994	0.948	0.903	0.994	CLONAL	1	TRUE	1	0.758449580401516	2		388	1093	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76919014	76919014	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0014036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	482	447	0	ENST00000373344.5:c.3977C>G	p.Ser1326Ter	p.S1326*	ENST00000373344	NM_000489.3	1326	tCa/tGa	12/35	0.758449580401516	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.758449580401516	1		447	765	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577305	64577307	+	frameshift_variant	Frame_Shift_Ins	INS	AGC	AGC	GCTT	novel	NA	P-0014036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	500	426	0	ENST00000312049.6:c.275_277delinsAAGC	p.Arg92GlnfsTer25	p.R92Qfs*25	ENST00000312049	NM_130799.2	92	cGCTtc/cAAGCtc	2/10	0.758449580401516	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.758449580401516	1		426	788	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345545	70345545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014038-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	28	467	0	ENST00000374080.3:c.2404G>A	p.Gly802Arg	p.G802R	ENST00000374080		802	Gga/Aga	17/45	0.198833194546037	2	FACETS	1	0.911	1			1	CLONAL	1	FALSE	NA	0.198833194546037	2		467	224	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0014094-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	153	579	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		579	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0014096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	70	437	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.0873802716821759	3	FACETS	0.743	0.647	0.847			1	INDETERMINATE	1	TRUE	NA	0.308998548916233	3		437	704	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856658	111856658	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	33	360	0	ENST00000341259.2:c.709C>A	p.Leu237Met	p.L237M	ENST00000341259	NM_005475.2	237	Ctg/Atg	2/8	1	2	FACETS	0.526	0.428	0.636	0.526	0.428	0.636	SUBCLONAL	1	TRUE	1	0.308998548916233	2		360	406	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242279	98242279	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1060502279	NA	P-0014096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	50	565	1	ENST00000331920.6:c.1039G>T	p.Val347Phe	p.V347F	ENST00000331920	NM_000264.3	347	Gtc/Ttc	7/24	1	2	FACETS	0.548	0.464	0.64	0.548	0.464	0.64	SUBCLONAL	1	TRUE	1	0.308998548916233	2		566	591	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410498	139410520	+	frameshift_variant	Frame_Shift_Del	DEL	GTGCTGGCACACTCGTCCACATC	GTGCTGGCACACTCGTCCACATC	-	novel	NA	P-0014096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	46	795	0	ENST00000277541.6:c.1582_1604del	p.Asp528ProfsTer34	p.D528Pfs*34	ENST00000277541	NM_017617.3	528	GATGTGGACGAGTGTGCCAGCACc/c	10/34	1	2	FACETS	0.428	0.36	0.505	0.428	0.36	0.505	SUBCLONAL	1	TRUE	1	0.308998548916233	2		795	695	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951122	48951128	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	GAAATTT	GAAATTT	TGTATAGGATACATCTTTAAA	novel	NA	P-0014096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	43	488	0	ENST00000267163.4:c.1284_1290delinsTGTATAGGATACATCTTTAAA	p.Glu428AspfsTer3	p.E428Dfs*3	ENST00000267163	NM_000321.2	428	gaGAAATTT/gaTGTATAGGATACATCTTTAAA	13/27	1	2	FACETS	0.368	0.307	0.436	0.368	0.307	0.436	SUBCLONAL	1	TRUE	1	0.308998548916233	2		488	756	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	398	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.335443334245305	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	FALSE	1	0.547881731974893	3		326	799	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828553	72828553	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs771903702	NA	P-0014146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	238	1327	0	ENST00000268489.5:c.8028C>G	p.His2676Gln	p.H2676Q	ENST00000268489	NM_006885.3	2676	caC/caG	9/10	0.325939739717652	0	FACETS	0.504	0.472	0.537			1	INDETERMINATE	1	FALSE	0	0.547881731974893	0		1327	779	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	70	456	0				ENST00000310581	NM_198253.2	-/1132			0.155683591442328	3	FACETS	0.984	0.862	1	0.492	0.431	0.558	INDETERMINATE	1	TRUE	1	0.411370508854071	3		456	417	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476307	88476307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772244244	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	127	645	1	ENST00000360948.2:c.1825G>A	p.Asp609Asn	p.D609N	ENST00000360948	NM_001012338.2	609	Gat/Aat	15/19	0.411370508854071	3	FACETS	1	0.948	1	0.533	0.484	0.585	CLONAL	1	TRUE	1	0.411370508854071	3		646	698	SUCCESS
APC	324	MSKCC	GRCh37	5	112173803	112173803	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	37	254	0	ENST00000257430.4:c.2512A>T	p.Arg838Ter	p.R838*	ENST00000257430	NM_000038.5	838	Aga/Tga	16/16	0.301306868260665	1	FACETS	0.674	0.561	0.798	0.674	0.561	0.798	SUBCLONAL	1	TRUE	0	0.411370508854071	1		254	212	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944419	40944419	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	94	481	0	ENST00000373198.4:c.2083C>T	p.Leu695Phe	p.L695F	ENST00000373198	NM_133170.3	695	Ctc/Ttc	12/32	1	2	FACETS	0.853	0.761	0.95	0.853	0.761	0.95	CLONAL	1	TRUE	1	0.411370508854071	2		481	536	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131142	55131142	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	50	425	0	ENST00000257290.5:c.685G>A	p.Glu229Lys	p.E229K	ENST00000257290	NM_006206.4	229	Gaa/Aaa	5/23	1	2	FACETS	0.493	0.418	0.575	0.493	0.418	0.575	SUBCLONAL	1	TRUE	1	0.411370508854071	2		425	493	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868132	56868132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	59	433	1	ENST00000308159.5:c.1630C>T	p.Pro544Ser	p.P544S	ENST00000308159	NM_014669.4	544	Cca/Tca	14/22	NA	2	FACETS	0.583	0.502	0.671			1	INDETERMINATE	1	TRUE	NA	0.411370508854071	2		434	492	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584548	189584548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	39	428	1	ENST00000264731.3:c.844G>A	p.Gly282Arg	p.G282R	ENST00000264731	NM_003722.4	282	Gga/Aga	6/14	1	2	FACETS	0.401	0.332	0.478	0.401	0.332	0.478	SUBCLONAL	1	TRUE	1	0.411370508854071	2		429	473	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955863	55955863	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868047715	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	70	397	1	ENST00000263923.4:c.3299C>T	p.Ser1100Phe	p.S1100F	ENST00000263923	NM_002253.2	1100	tCc/tTc	24/30	1	2	FACETS	0.857	0.751	0.971	0.857	0.751	0.971	CLONAL	1	TRUE	1	0.411370508854071	2		398	397	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148875	119148876	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	47	244	0	ENST00000264033.4:c.1096-1_1096delinsAA		p.X366_splice	ENST00000264033	NM_005188.3	366		8/16	0.411370508854071	1	FACETS	0.779	0.664	0.903	0.779	0.664	0.903	CLONAL	1	TRUE	0	0.411370508854071	1		244	233	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020155	123020155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778612322	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	145	657	2	ENST00000355640.3:c.643C>T	p.Arg215Cys	p.R215C	ENST00000355640		215	Cgt/Tgt	2/7	1	2	FACETS	0.898	0.82	0.98	0.898	0.82	0.98	CLONAL	1	TRUE	1	0.411370508854071	2		659	785	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101517	27101517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	124	724	0	ENST00000324856.7:c.4799C>T	p.Ser1600Phe	p.S1600F	ENST00000324856	NM_006015.4	1600	tCt/tTt	18/20	0.155683591442328	3	FACETS	0.862	0.78	0.949	0.431	0.39	0.475	INDETERMINATE	1	TRUE	1	0.411370508854071	3		724	843	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468327	120468327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	157	464	0	ENST00000256646.2:c.4112C>T	p.Pro1371Leu	p.P1371L	ENST00000256646	NM_024408.3	1371	cCc/cTc	25/34	0.155683591442328	3	FACETS	0.8	0.737	0.866	0.8	0.737	0.866	INDETERMINATE	2	TRUE	1	0.411370508854071	3		464	575	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656233	18656233	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	38	392	1	ENST00000266497.5:c.2912C>T	p.Pro971Leu	p.P971L	ENST00000266497		971	cCt/cTt	21/31	1	2	FACETS	0.455	0.376	0.543	0.455	0.376	0.543	SUBCLONAL	1	TRUE	1	0.411370508854071	2		393	406	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103520573	103520573	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	25	289	0	ENST00000355739.4:c.2644C>T	p.Pro882Ser	p.P882S	ENST00000355739	NM_000123.3	882	Cct/Tct	12/15	1	2	FACETS	0.338	0.266	0.42	0.338	0.266	0.42	SUBCLONAL	1	TRUE	1	0.411370508854071	2		289	360	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465634	99465634	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	78	342	0	ENST00000268035.6:c.2459T>A	p.Phe820Tyr	p.F820Y	ENST00000268035	NM_000875.3	820	tTc/tAc	11/21	0.411370508854071	3	FACETS	0.878	0.773	0.99	0.439	0.386	0.495	CLONAL	1	TRUE	1	0.411370508854071	3		342	521	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99486228	99486228	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	237	536	0	ENST00000268035.6:c.3534G>T	p.Trp1178Cys	p.W1178C	ENST00000268035	NM_000875.3	1178	tgG/tgT	19/21	0.411370508854071	3	FACETS	0.977	0.916	1	0.977	0.916	1	CLONAL	2	TRUE	1	0.411370508854071	3		536	711	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953199	81953199	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	95	305	0	ENST00000359376.3:c.2165A>C	p.Lys722Thr	p.K722T	ENST00000359376	NM_002661.3	722	aAg/aCg	20/33	0.411370508854071	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.411370508854071	1		305	289	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347747	89347747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	95	403	0	ENST00000301030.4:c.5203C>T	p.Leu1735Phe	p.L1735F	ENST00000301030	NM_001256183.1	1735	Ctc/Ttc	9/13	0.411370508854071	1	FACETS	0.973	0.873	1	0.973	0.873	1	CLONAL	1	TRUE	0	0.411370508854071	1		403	377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577106	+	missense_variant	Missense_Mutation	DNP	GG	GG	AC	novel	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	140	668	3	ENST00000269305.4:c.832_833delinsGT	p.Pro278Val	p.P278V	ENST00000269305	NM_001126112.2	278	CCt/GTt	8/11	1	2	FACETS	0.914	0.833	0.998	0.914	0.833	0.998	CLONAL	1	TRUE	1	0.411370508854071	2		671	745	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559101	29559101	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202023	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	79	146	0	ENST00000356175.3:c.3208C>T	p.Gln1070Ter	p.Q1070*	ENST00000356175	NM_000267.3	1070	Cag/Tag	25/57	0.411370508854071	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.411370508854071	1		146	206	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585490	29585490	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	77	256	0	ENST00000356175.3:c.4239A>T	p.Arg1413Ser	p.R1413S	ENST00000356175	NM_000267.3	1413	agA/agT	31/57	0.411370508854071	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.411370508854071	1		256	242	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78931513	78931513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750857501	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	102	423	0	ENST00000306801.3:c.3460C>T	p.Arg1154Cys	p.R1154C	ENST00000306801	NM_020761.2	1154	Cgt/Tgt	29/34	0.155683591442328	3	FACETS	1	0.962	1	0.575	0.516	0.637	INDETERMINATE	1	TRUE	1	0.411370508854071	3		423	520	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271882	18271882	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	132	667	0	ENST00000222254.8:c.485T>C	p.Val162Ala	p.V162A	ENST00000222254	NM_005027.3	162	gTg/gCg	5/16	1	2	FACETS	0.905	0.823	0.991	0.905	0.823	0.991	CLONAL	1	TRUE	1	0.411370508854071	2		667	709	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519831	29519831	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1460645072	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	47	595	1	ENST00000389048.3:c.1740G>A	p.Met580Ile	p.M580I	ENST00000389048	NM_004304.4	580	atG/atA	9/29	1	2	FACETS	0.386	0.325	0.453	0.386	0.325	0.453	SUBCLONAL	1	TRUE	1	0.411370508854071	2		596	592	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46583371	46583372	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	49	456	1	ENST00000263734.3:c.299_300delinsTT	p.Ala100Val	p.A100V	ENST00000263734	NM_001430.4	100	gCC/gTT	3/16	1	2	FACETS	0.422	0.357	0.494	0.422	0.357	0.494	SUBCLONAL	1	TRUE	1	0.411370508854071	2		457	564	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306631	41306631	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	112	627	0	ENST00000373198.4:c.1028C>T	p.Pro343Leu	p.P343L	ENST00000373198	NM_133170.3	343	cCc/cTc	7/32	1	2	FACETS	0.905	0.816	0.998	0.905	0.816	0.998	CLONAL	1	TRUE	1	0.411370508854071	2		627	602	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755556	39755557	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	96	344	0	ENST00000288319.7:c.1208_1209delinsTT	p.Pro403Leu	p.P403L	ENST00000288319	NM_182918.3	403	cCC/cTT	10/10	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.411370508854071	2		344	416	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755756	39755756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	25	387	3	ENST00000288319.7:c.1009G>A	p.Gly337Arg	p.G337R	ENST00000288319	NM_182918.3	337	Ggg/Agg	10/10	1	2	FACETS	0.331	0.261	0.412	0.331	0.261	0.412	SUBCLONAL	1	TRUE	1	0.411370508854071	2		390	367	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566468	41566468	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	58	415	0	ENST00000263253.7:c.4345C>T	p.His1449Tyr	p.H1449Y	ENST00000263253	NM_001429.3	1449	Cat/Tat	27/31	1	2	FACETS	0.522	0.449	0.602	0.522	0.449	0.602	SUBCLONAL	1	TRUE	1	0.411370508854071	2		415	540	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152548	56152548	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	90	282	0	ENST00000399503.3:c.604T>G	p.Leu202Val	p.L202V	ENST00000399503	NM_005921.1	202	Ttg/Gtg	2/20	0.155683591442328	3	FACETS	1	0.969	1	0.621	0.554	0.691	INDETERMINATE	1	TRUE	1	0.411370508854071	3		282	425	SUCCESS
APC	324	MSKCC	GRCh37	5	112154991	112154992	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	62	514	1	ENST00000257430.4:c.1262_1263delinsAA	p.Trp421Ter	p.W421*	ENST00000257430	NM_000038.5	421	tGG/tAA	10/16	0.155683591442328	3	FACETS	0.563	0.486	0.647	0.282	0.243	0.324	INDETERMINATE	1	TRUE	1	0.411370508854071	3		515	645	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497272	149497272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201061735	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	85	670	0	ENST00000261799.4:c.3046G>A	p.Glu1016Lys	p.E1016K	ENST00000261799	NM_002609.3	1016	Gag/Aag	22/23	1	2	FACETS	0.568	0.501	0.639	0.568	0.501	0.639	SUBCLONAL	1	TRUE	1	0.411370508854071	2		670	728	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520411	176520411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1342829829	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	152	645	0	ENST00000292408.4:c.1256C>T	p.Ser419Phe	p.S419F	ENST00000292408	NM_213647.1	419	tCc/tTc	10/18	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.411370508854071	2		645	705	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190843	32190843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	114	754	0	ENST00000375023.3:c.94C>T	p.Pro32Ser	p.P32S	ENST00000375023	NM_004557.3	32	Cca/Tca	2/30	1	2	FACETS	0.717	0.646	0.793	0.717	0.646	0.793	SUBCLONAL	1	TRUE	1	0.411370508854071	2		754	773	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066550	94066550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	58	325	0	ENST00000369303.4:c.1209G>A	p.Met403Ile	p.M403I	ENST00000369303	NM_004440.3	403	atG/atA	5/17	1	2	FACETS	0.707	0.609	0.812	0.707	0.609	0.812	SUBCLONAL	1	TRUE	1	0.411370508854071	2		325	399	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946076	13946076	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	72	364	0	ENST00000405192.2:c.1020T>G	p.Phe340Leu	p.F340L	ENST00000405192	NM_001163147.1	340	ttT/ttG	10/12	1	2	FACETS	0.846	0.742	0.956	0.846	0.742	0.956	CLONAL	1	TRUE	1	0.411370508854071	2		364	414	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492909	8492909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	57	409	2	ENST00000356435.5:c.2420G>A	p.Gly807Glu	p.G807E	ENST00000356435		807	gGa/gAa	16/35	0.159543492041953	0	FACETS	0.335	0.287	0.387			1	INDETERMINATE	1	TRUE	0	0.411370508854071	0		411	487	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815563	139815563	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	240	520	0	ENST00000247668.2:c.1034T>C	p.Met345Thr	p.M345T	ENST00000247668	NM_021138.3	345	aTg/aCg	9/11	0.411370508854071	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.411370508854071	3		520	688	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932903	39932903	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	80	403	0	ENST00000378444.4:c.1696C>A	p.Arg566Ser	p.R566S	ENST00000378444	NM_001123385.1	566	Cgc/Agc	4/15	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.411370508854071	2		403	386	SUCCESS
AR	367	MSKCC	GRCh37	X	66863171	66863171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	47	489	0	ENST00000374690.3:c.1690G>A	p.Gly564Arg	p.G564R	ENST00000374690	NM_000044.3	564	Gga/Aga	2/8	1	2	FACETS	0.449	0.379	0.526	0.449	0.379	0.526	SUBCLONAL	1	TRUE	1	0.411370508854071	2		489	509	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854897	76854897	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	51	596	0	ENST00000373344.5:c.5939C>T	p.Ser1980Phe	p.S1980F	ENST00000373344	NM_000489.3	1980	tCt/tTt	25/35	1	2	FACETS	0.53	0.451	0.616	0.53	0.451	0.616	SUBCLONAL	1	TRUE	1	0.411370508854071	2		596	468	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889101	76889101	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	96	425	0	ENST00000373344.5:c.4909G>A	p.Glu1637Lys	p.E1637K	ENST00000373344	NM_000489.3	1637	Gaa/Aaa	18/35	1	2	FACETS	0.919	0.822	1	0.919	0.822	1	CLONAL	1	TRUE	1	0.411370508854071	2		425	508	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99154369	99154369	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	37	441	0	ENST00000074304.5:c.511T>C	p.Trp171Arg	p.W171R	ENST00000074304	NM_001134224.1	171	Tgg/Cgg	8/26	1	2	FACETS	0.318	0.261	0.381	0.318	0.261	0.381	SUBCLONAL	1	TRUE	1	0.411370508854071	2		441	566	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252808	10252808	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	102	543	0	ENST00000340748.4:c.3157T>A	p.Phe1053Ile	p.F1053I	ENST00000340748		1053	Ttc/Atc	29/40	1	2	FACETS	0.808	0.724	0.897	0.808	0.724	0.897	CLONAL	1	TRUE	1	0.411370508854071	2		543	614	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11018750	11018750	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773989666	NA	P-0014227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	75	741	2	ENST00000327064.4:c.382C>T	p.Arg128Trp	p.R128W	ENST00000327064	NM_199141.1	128	Cgg/Tgg	3/16	1	2	FACETS	0.413	0.361	0.469	0.413	0.361	0.469	SUBCLONAL	1	TRUE	1	0.411370508854071	2		743	883	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	208	456	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.846	0.79	0.903	0.846	0.79	0.903	CLONAL	1	TRUE	1	0.811907525936501	2		456	606	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0014229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	322	152	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	0.811907525936501	2		152	750	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955550	48955550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913304	NA	P-0014229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	156	271	2	ENST00000267163.4:c.1666C>T	p.Arg556Ter	p.R556*	ENST00000267163	NM_000321.2	556	Cga/Tga	17/27	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.811907525936501	2		273	360	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037966	49037966	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	149	308	0	ENST00000267163.4:c.2206C>T	p.Gln736Ter	p.Q736*	ENST00000267163	NM_000321.2	736	Cag/Tag	21/27	1	2	FACETS	0.961	0.889	1	0.961	0.889	1	CLONAL	1	TRUE	1	0.811907525936501	2		308	382	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041612	14041612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	207	317	1	ENST00000311895.7:c.2159C>T	p.Pro720Leu	p.P720L	ENST00000311895	NM_005236.2	720	cCa/cTa	11/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.811907525936501	2		318	481	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557639	95557639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775912475	NA	P-0014229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	304	565	0	ENST00000393063.1:c.5428G>A	p.Asp1810Asn	p.D1810N	ENST00000393063	NM_030621.3	1810	Gat/Aat	26/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.811907525936501	2		565	697	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561090	9561090	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	112	259	0	ENST00000353224.5:c.692C>T	p.Ser231Leu	p.S231L	ENST00000353224	NM_177990.2	231	tCa/tTa	4/10	0.780137326255885	3	FACETS	1	0.93	1	0.514	0.467	0.564	CLONAL	1	TRUE	1	0.811907525936501	3		259	377	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876163	35876163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	192	460	0	ENST00000303115.3:c.955G>A	p.Glu319Lys	p.E319K	ENST00000303115	NM_002185.3	319	Gaa/Aaa	8/8	1	2	FACETS	0.938	0.876	1	0.938	0.876	1	CLONAL	1	TRUE	1	0.811907525936501	2		460	504	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501586	149501586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772861468	NA	P-0014229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	200	328	0	ENST00000261799.4:c.2201G>A	p.Gly734Glu	p.G734E	ENST00000261799	NM_002609.3	734	gGg/gAg	16/23	1	2	FACETS	0.97	0.907	1	0.97	0.907	1	CLONAL	1	TRUE	1	0.811907525936501	2		328	508	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932280	36932280	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	305	540	0	ENST00000361632.4:c.2189A>C	p.Gln730Pro	p.Q730P	ENST00000361632		730	cAg/cCg	16/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.811907525936501	2		540	746	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982309	201982309	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0014229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	303	615	0	ENST00000359651.3:c.689-1G>A		p.X230_splice	ENST00000359651		230			0.780137326255885	3	FACETS	0.886	0.834	0.938	0.443	0.417	0.469	CLONAL	1	TRUE	1	0.811907525936501	3		615	1185	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856216	111856217	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0014229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	195	254	3	ENST00000341259.2:c.267_268delinsTT	p.Arg90Trp	p.R90W	ENST00000341259	NM_005475.2	89	taCCgg/taTTgg	2/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.811907525936501	2		257	410	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120785249	120785249	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	246	500	0	ENST00000257552.2:c.859G>A	p.Gly287Ser	p.G287S	ENST00000257552	NM_002442.3	287	Ggc/Agc	12/15	1	2	FACETS	0.864	0.812	0.918	0.864	0.812	0.918	CLONAL	1	TRUE	1	0.811907525936501	2		500	701	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964224	28964224	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	99	168	0	ENST00000282397.4:c.1678C>T	p.His560Tyr	p.H560Y	ENST00000282397	NM_002019.4	560	Cat/Tat	13/30	1	2	FACETS	0.893	0.81	0.979	0.893	0.81	0.979	CLONAL	1	TRUE	1	0.811907525936501	2		168	273	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041665	29041665	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	164	313	0	ENST00000282397.4:c.154C>T	p.Gln52Ter	p.Q52*	ENST00000282397	NM_002019.4	52	Caa/Taa	2/30	1	2	FACETS	0.924	0.857	0.993	0.924	0.857	0.993	CLONAL	1	TRUE	1	0.811907525936501	2		313	437	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95597871	95597871	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	187	401	0	ENST00000393063.1:c.413G>A	p.Trp138Ter	p.W138*	ENST00000393063	NM_030621.3	138	tGg/tAg	5/28	1	2	FACETS	0.948	0.884	1	0.948	0.884	1	CLONAL	1	TRUE	1	0.811907525936501	2		401	486	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304239	91304239	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	175	373	0	ENST00000355112.3:c.1636G>A	p.Glu546Lys	p.E546K	ENST00000355112	NM_000057.2	546	Gaa/Aaa	7/22	1	2	FACETS	0.978	0.91	1	0.978	0.91	1	CLONAL	1	TRUE	1	0.811907525936501	2		373	441	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857476	9857476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145602289	NA	P-0014229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	165	415	0	ENST00000330684.3:c.3925C>T	p.Arg1309Trp	p.R1309W	ENST00000330684	NM_001134407.1	1309	Cgg/Tgg	13/13	1	2	FACETS	0.928	0.861	0.996	0.928	0.861	0.996	CLONAL	1	TRUE	1	0.811907525936501	2		415	438	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559809	29559809	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1341314304	NA	P-0014229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	170	289	0	ENST00000356175.3:c.3406C>T	p.Arg1136Trp	p.R1136W	ENST00000356175	NM_000267.3	1136	Cgg/Tgg	26/57	1	2	FACETS	0.967	0.899	1	0.967	0.899	1	CLONAL	1	TRUE	1	0.811907525936501	2		289	433	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873615	37873615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	348	643	1	ENST00000269571.5:c.1780C>T	p.Pro594Ser	p.P594S	ENST00000269571		594	Ccc/Tcc	15/27	1	2	FACETS	0.972	0.924	1	0.972	0.924	1	CLONAL	1	TRUE	1	0.811907525936501	2		644	882	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436154	56436154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	267	493	0	ENST00000407977.2:c.983C>T	p.Pro328Leu	p.P328L	ENST00000407977		328	cCc/cTc	9/10	1	2	FACETS	0.966	0.911	1	0.966	0.911	1	CLONAL	1	TRUE	1	0.811907525936501	2		493	681	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7293826	7293826	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	12	13	0	ENST00000302850.5:c.77C>T	p.Ala26Val	p.A26V	ENST00000302850	NM_000208.2	26	gCg/gTg	1/22	1	2	FACETS	0.896	0.664	1	0.896	0.664	1	CLONAL	1	TRUE	1	0.811907525936501	2		13	33	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291119	10291119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745455817	NA	P-0014229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	394	666	0	ENST00000340748.4:c.352C>T	p.Arg118Cys	p.R118C	ENST00000340748		118	Cgt/Tgt	4/40	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.811907525936501	2		666	948	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144132	11144132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	355	690	1	ENST00000358026.2:c.3713C>T	p.Ser1238Phe	p.S1238F	ENST00000358026	NM_001128849.1	1238	tCc/tTc	26/36	1	2	FACETS	0.985	0.937	1	0.985	0.937	1	CLONAL	1	TRUE	1	0.811907525936501	2		691	888	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378288	225378288	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	160	285	0	ENST00000264414.4:c.607G>A	p.Glu203Lys	p.E203K	ENST00000264414	NM_003590.4	203	Gaa/Aaa	5/16	1	2	FACETS	0.983	0.912	1	0.983	0.912	1	CLONAL	1	TRUE	1	0.811907525936501	2		285	401	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755422	39755422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1460346267	NA	P-0014229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	239	530	0	ENST00000288319.7:c.1343C>T	p.Ala448Val	p.A448V	ENST00000288319	NM_182918.3	448	gCc/gTc	10/10	0.811907525936501	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.811907525936501	1		530	337	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41279558	41279558	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748653573	NA	P-0014229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	183	360	1	ENST00000349496.5:c.2128C>T	p.Arg710Cys	p.R710C	ENST00000349496	NM_001904.3	710	Cgc/Tgc	14/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.811907525936501	2		361	434	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455643	189455643	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs151051217	NA	P-0014229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	166	402	0	ENST00000264731.3:c.177G>A	p.Trp59Ter	p.W59*	ENST00000264731	NM_003722.4	59	tgG/tgA	2/14	1	2	FACETS	0.995	0.925	1	0.995	0.925	1	CLONAL	1	TRUE	1	0.811907525936501	2		402	411	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155354	106155354	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0014229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	362	363	0	ENST00000380013.4:c.255T>A	p.Tyr85Ter	p.Y85*	ENST00000380013	NM_001127208.2	85	taT/taA	3/11	0.811907525936501	2	FACETS	0.993	0.965	1	0.993	0.965	1	CLONAL	2	TRUE	0	0.811907525936501	2		363	449	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153252021	153252021	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0014229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	239	295	0	ENST00000281708.4:c.986-1G>A		p.X329_splice	ENST00000281708	NM_033632.3	329			0.811907525936501	2	FACETS	0.994	0.96	1	0.994	0.96	1	CLONAL	2	TRUE	0	0.811907525936501	2		295	296	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140813	37140813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1176016480	NA	P-0014229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	230	410	0	ENST00000373509.5:c.649C>T	p.Arg217Cys	p.R217C	ENST00000373509	NM_002648.3	217	Cgc/Tgc	5/6	1	2	FACETS	0.984	0.924	1	0.984	0.924	1	CLONAL	1	TRUE	1	0.811907525936501	2		410	576	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553594	106553594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs960785645	NA	P-0014229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	169	267	0	ENST00000369096.4:c.1559G>A	p.Gly520Glu	p.G520E	ENST00000369096	NM_001198.3	520	gGa/gAa	5/7	0.811907525936501	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.811907525936501	1		267	247	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938337	76938337	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	219	415	0	ENST00000373344.5:c.2411C>T	p.Ser804Phe	p.S804F	ENST00000373344	NM_000489.3	804	tCt/tTt	9/35	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.811907525936501	2		415	514	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128748867	128748867	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	160	295	0	ENST00000377970.2:c.28C>T	p.Gln10Ter	p.Q10*	ENST00000377970	NM_002467.4	10	Cag/Tag	1/3	1	2	FACETS	0.952	0.883	1	0.952	0.883	1	CLONAL	1	TRUE	1	0.811907525936501	2		295	414	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942216	71942216	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	233	466	0	ENST00000298229.2:c.1480G>A	p.Asp494Asn	p.D494N	ENST00000298229	NM_001567.3	494	Gat/Aat	12/28	1	2	FACETS	0.905	0.85	0.962	0.905	0.85	0.962	CLONAL	1	TRUE	1	0.811907525936501	2		466	634	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0014242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	681	491	0				ENST00000310581	NM_198253.2	-/1132			0.688500532599875	4	FACETS	0.903	0.877	0.93	0.903	0.877	0.93	CLONAL	3	TRUE	1	0.7871359867364	4		491	1141	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612073	189612073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142762485	NA	P-0014242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	301	458	0	ENST00000264731.3:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000264731	NM_003722.4	609	Gaa/Aaa	14/14	1	2	FACETS	0.926	0.876	0.977	0.926	0.876	0.977	CLONAL	1	TRUE	1	0.7871359867364	2		458	826	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258580	16258580	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749892338	NA	P-0014242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	257	392	1	ENST00000375759.3:c.5845C>T	p.Arg1949Trp	p.R1949W	ENST00000375759	NM_015001.2	1949	Cgg/Tgg	11/15	1	2	FACETS	0.94	0.885	0.995	0.94	0.885	0.995	CLONAL	1	TRUE	1	0.7871359867364	2		393	695	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873660	35873660	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs201559094	NA	P-0014242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	151	307	1	ENST00000303115.3:c.616C>T	p.Arg206Ter	p.R206*	ENST00000303115	NM_002185.3	206	Cga/Tga	5/8	0.688500532599875	4	FACETS	0.935	0.857	1	0.312	0.285	0.339	CLONAL	1	TRUE	1	0.7871359867364	4		308	733	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0014242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	1738	319	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.7871359867364	8	FACETS	0.989	0.976	1			1	CLONAL	7	TRUE	NA	0.7871359867364	8		319	2145	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575658	55575658	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	267	347	1	ENST00000288135.5:c.1184C>T	p.Ser395Phe	p.S395F	ENST00000288135	NM_000222.2	395	tCc/tTc	7/21	1	2	FACETS	0.993	0.937	1	0.993	0.937	1	CLONAL	1	TRUE	1	0.7871359867364	2		348	683	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561520	9561520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	306	420	0	ENST00000353224.5:c.262G>A	p.Asp88Asn	p.D88N	ENST00000353224	NM_177990.2	88	Gat/Aat	4/10	1	2	FACETS	0.994	0.942	1	0.994	0.942	1	CLONAL	1	TRUE	1	0.7871359867364	2		420	782	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7132201	7132201	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	208	551	0	ENST00000302850.5:c.2810C>T	p.Thr937Met	p.T937M	ENST00000302850	NM_000208.2	937	aCg/aTg	14/22	1	2	FACETS	0.469	0.435	0.505	0.469	0.435	0.505	SUBCLONAL	1	TRUE	1	0.7871359867364	2		551	1127	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381514	81381514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	203	293	0	ENST00000222390.5:c.547G>A	p.Glu183Lys	p.E183K	ENST00000222390	NM_000601.4	183	Gaa/Aaa	5/18	1	2	FACETS	0.885	0.826	0.945	0.885	0.826	0.945	CLONAL	1	TRUE	1	0.7871359867364	2		293	583	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599234	28599234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763645640	NA	P-0014242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	451	614	1	ENST00000253063.3:c.680C>T	p.Ala227Val	p.A227V	ENST00000253063	NM_031459.4	227	gCc/gTc	5/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.7871359867364	2		615	1072	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458800	120458800	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2181	562	523	0	ENST00000256646.2:c.6545C>T	p.Pro2182Leu	p.P2182L	ENST00000256646	NM_024408.3	2182	cCt/cTt	34/34	0.7871359867364	8	FACETS	0.875	0.836	0.915			1	CLONAL	2	TRUE	NA	0.7871359867364	8		523	2743	SUCCESS
FH	2271	MSKCC	GRCh37	1	241661202	241661202	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	51	473	0	ENST00000366560.3:c.1459A>C	p.Ile487Leu	p.I487L	ENST00000366560	NM_000143.3	487	Atc/Ctc	10/10	1	2	FACETS	0.152	0.129	0.179	0.152	0.129	0.179	SUBCLONAL	1	TRUE	1	0.7871359867364	2		473	850	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601977	43601977	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	406	667	0	ENST00000355710.3:c.1021C>T	p.Gln341Ter	p.Q341*	ENST00000355710	NM_020975.4	341	Cag/Tag	5/20	1	2	FACETS	0.938	0.894	0.982	0.938	0.894	0.982	CLONAL	1	TRUE	1	0.7871359867364	2		667	1100	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405212	70405212	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	262	409	0	ENST00000373644.4:c.2726C>T	p.Ser909Phe	p.S909F	ENST00000373644	NM_030625.2	909	tCc/tTc	4/12	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.7871359867364	2		409	623	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027169	49027169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751560923	NA	P-0014242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	93	368	0	ENST00000267163.4:c.1736G>A	p.Arg579Gln	p.R579Q	ENST00000267163	NM_000321.2	579	cGa/cAa	18/27	NA	2	FACETS	0.553	0.495	0.615			1	INDETERMINATE	1	TRUE	NA	0.7871359867364	2		368	427	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527940	103527940	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	242	301	1	ENST00000355739.4:c.3248C>A	p.Thr1083Lys	p.T1083K	ENST00000355739	NM_000123.3	1083	aCa/aAa	15/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.7871359867364	2		302	588	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290228	15290228	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	425	665	1	ENST00000263388.2:c.3407C>T	p.Ser1136Leu	p.S1136L	ENST00000263388	NM_000435.2	1136	tCa/tTa	21/33	1	2	FACETS	0.928	0.885	0.971	0.928	0.885	0.971	CLONAL	1	TRUE	1	0.7871359867364	2		666	1164	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637479	47637479	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	210	323	0	ENST00000233146.2:c.613G>A	p.Glu205Lys	p.E205K	ENST00000233146	NM_000251.2	205	Gag/Aag	3/16	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.7871359867364	2		323	531	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273135	198273135	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	299	482	0	ENST00000335508.6:c.1075C>T	p.Pro359Ser	p.P359S	ENST00000335508	NM_012433.2	359	Cca/Tca	8/25	1	2	FACETS	0.907	0.857	0.957	0.907	0.857	0.957	CLONAL	1	TRUE	1	0.7871359867364	2		482	838	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113155	209113155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371567806	NA	P-0014242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	189	295	0	ENST00000345146.2:c.352C>T	p.Pro118Ser	p.P118S	ENST00000345146	NM_005896.2	118	Ccc/Tcc	4/10	1	2	FACETS	0.924	0.861	0.988	0.924	0.861	0.988	CLONAL	1	TRUE	1	0.7871359867364	2		295	520	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385068	31385068	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	276	374	0	ENST00000328111.2:c.1453C>T	p.Arg485Ter	p.R485*	ENST00000328111	NM_006892.3	485	Cga/Tga	14/23	1	2	FACETS	0.923	0.87	0.976	0.923	0.87	0.976	CLONAL	1	TRUE	1	0.7871359867364	2		374	760	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485864	57485864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	191	283	0	ENST00000371085.3:c.1165C>T	p.Arg389Cys	p.R389C	ENST00000371085	NM_000516.4	389	Cgt/Tgt	13/13	1	2	FACETS	0.897	0.836	0.96	0.897	0.836	0.96	CLONAL	1	TRUE	1	0.7871359867364	2		283	541	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032752	30032752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	452	266	0	ENST00000338641.4:c.127G>A	p.Gly43Arg	p.G43R	ENST00000338641	NM_000268.3	43	Ggg/Agg	2/16	0.779385571712439	3	FACETS	0.956	0.92	0.992	0.956	0.92	0.992	CLONAL	2	TRUE	1	0.7871359867364	3		266	837	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702657	52702657	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	119	257	0	ENST00000394830.3:c.241C>T	p.Gln81Ter	p.Q81*	ENST00000394830	NM_018313.4	81	Caa/Taa	4/30	0.786290838037553	1	FACETS	0.97	0.905	1	0.97	0.905	1	CLONAL	1	TRUE	0	0.7871359867364	1		257	189	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259571	89259571	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	191	256	0	ENST00000336596.2:c.715C>T	p.Pro239Ser	p.P239S	ENST00000336596	NM_005233.5	239	Cct/Tct	3/17	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.7871359867364	2		256	452	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851633	134851633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	243	323	3	ENST00000398015.3:c.1039G>A	p.Glu347Lys	p.E347K	ENST00000398015	NM_004441.4	347	Gag/Aag	5/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.7871359867364	2		326	600	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169988252	169988252	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1361108822	NA	P-0014242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	116	369	0	ENST00000295797.4:c.494G>A	p.Gly165Glu	p.G165E	ENST00000295797	NM_002740.5	165	gGa/gAa	6/18	1	2	FACETS	0.445	0.401	0.49	0.445	0.401	0.49	SUBCLONAL	1	TRUE	1	0.7871359867364	2		369	663	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280395	1280395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747940807	NA	P-0014242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	327	475	1	ENST00000310581.5:c.1828C>T	p.Arg610Trp	p.R610W	ENST00000310581	NM_198253.2	610	Cgg/Tgg	4/16	0.688500532599875	4	FACETS	1	0.979	1	0.359	0.339	0.38	CLONAL	1	TRUE	1	0.7871359867364	4		476	1378	SUCCESS
APC	324	MSKCC	GRCh37	5	112177943	112177943	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	233	314	1	ENST00000257430.4:c.6652C>T	p.Gln2218Ter	p.Q2218*	ENST00000257430	NM_000038.5	2218	Caa/Taa	16/16	0.7871359867364	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.7871359867364	1		315	349	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120359	94120359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778087526	NA	P-0014242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	140	200	0	ENST00000369303.4:c.692G>A	p.Arg231Gln	p.R231Q	ENST00000369303	NM_004440.3	231	cGa/cAa	3/17	0.7871359867364	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.7871359867364	1		200	207	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101417	27101417	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	110	808	0	ENST00000324856.7:c.4703del	p.Pro1568LeufsTer44	p.P1568Lfs*44	ENST00000324856	NM_006015.4	1567	Ccc/cc	18/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.28	2		808	684	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	142	738	12	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.815	0.746	0.888	1	0.989	1	CLONAL	2	TRUE	1	0.28	2		750	622	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	111	563	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.933	1	1	0.989	1	CLONAL	2	TRUE	1	0.28	2		568	383	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	83	385	0	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.28	1		385	348	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308382	15308383	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs749829137	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	114	1232	1	ENST00000263388.2:c.125dup	p.Cys43LeufsTer32	p.C43Lfs*32	ENST00000263388	NM_000435.2	42	cct/ccCt	2/33	1	2	FACETS	0.726	0.652	0.804	0.726	0.652	0.804	SUBCLONAL	1	TRUE	1	0.28	2		1233	1122	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1223	159	1363	1	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	1	2	FACETS	0.822	0.751	0.896	0.822	0.751	0.896	CLONAL	1	TRUE	1	0.28	2		1364	1382	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	128	966	4	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	0.985	0.892	1	0.985	0.892	1	CLONAL	1	TRUE	1	0.28	2		970	928	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217783	2217783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	125	1052	0	ENST00000398665.3:c.2557C>T	p.Arg853Cys	p.R853C	ENST00000398665	NM_032482.2	853	Cgc/Tgc	22/28	1	2	FACETS	0.888	0.803	0.979	0.888	0.803	0.979	CLONAL	1	TRUE	1	0.28	2		1052	1005	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691807	30691807	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	54	729	0	ENST00000295754.5:c.312del	p.Lys105SerfsTer19	p.K105Sfs*19	ENST00000295754	NM_003242.5	103	gaC/ga	3/7	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.28	2		729	374	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225507	26225507	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs761664745	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	57	374	0	ENST00000360408.1:c.125A>G	p.Tyr42Cys	p.Y42C	ENST00000360408	NM_003532.2	42	tAc/tGc	1/1	0.131249516587539	3	FACETS	1	0.954	1	0.634	0.546	0.729	INDETERMINATE	1	TRUE	1	0.28	3		374	366	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420067	152420067	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141662120	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	25	468	0	ENST00000206249.3:c.1754C>T	p.Thr585Met	p.T585M	ENST00000206249	NM_000125.3	585	aCg/aTg	8/8	0.131249516587539	3	FACETS	0.562	0.443	0.7	0.281	0.221	0.35	INDETERMINATE	1	TRUE	1	0.28	3		468	362	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128016909	128016909	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs944132286	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	86	692	1	ENST00000285398.2:c.2180A>T	p.Glu727Val	p.E727V	ENST00000285398	NM_000122.1	727	gAg/gTg	14/15	1	2	FACETS	0.831	0.735	0.934	0.831	0.735	0.934	CLONAL	1	TRUE	1	0.28	2		693	739	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681120	117681120	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs748436511	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	32	536	0	ENST00000368508.3:c.3500del	p.Leu1167Ter	p.L1167*	ENST00000368508	NM_002944.2	1167	tTa/ta	23/43	0.131249516587539	3	FACETS	0.991	0.808	1	0.495	0.404	0.598	INDETERMINATE	1	TRUE	1	0.28	3		536	263	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258556	16258556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	75	627	0	ENST00000375759.3:c.5821G>A	p.Ala1941Thr	p.A1941T	ENST00000375759	NM_015001.2	1941	Gct/Act	11/15	1	2	FACETS	0.767	0.672	0.87	0.767	0.672	0.87	SUBCLONAL	1	TRUE	1	0.28	2		627	698	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101501	27101501	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1463725053	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	111	1233	0	ENST00000324856.7:c.4783A>G	p.Met1595Val	p.M1595V	ENST00000324856	NM_006015.4	1595	Atg/Gtg	18/20	1	2	FACETS	0.764	0.685	0.847	0.764	0.685	0.847	SUBCLONAL	1	TRUE	1	0.28	2		1233	1038	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45805891	45805891	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	102	810	0	ENST00000450313.1:c.36G>T	p.Trp12Cys	p.W12C	ENST00000450313	NM_012222.2	12	tgG/tgT	1/16	1	2	FACETS	0.846	0.756	0.942	0.846	0.756	0.942	CLONAL	1	TRUE	1	0.28	2		810	861	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305457	65305457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	34	453	1	ENST00000342505.4:c.2671C>T	p.Leu891Phe	p.L891F	ENST00000342505	NM_002227.2	891	Ctc/Ttc	20/25	1	2	FACETS	0.678	0.555	0.817	0.678	0.555	0.817	SUBCLONAL	1	TRUE	1	0.28	2		454	358	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166443	118166443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868489427	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	33	314	0	ENST00000369448.3:c.953C>T	p.Thr318Ile	p.T318I	ENST00000369448	NM_017709.3	318	aCc/aTc	2/2	1	2	FACETS	0.719	0.587	0.867	0.719	0.587	0.867	SUBCLONAL	1	TRUE	1	0.28	2		314	328	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120469220	120469220	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	69	652	0	ENST00000256646.2:c.3907A>G	p.Thr1303Ala	p.T1303A	ENST00000256646	NM_024408.3	1303	Acc/Gcc	24/34	1	2	FACETS	0.842	0.734	0.959	0.842	0.734	0.959	CLONAL	1	TRUE	1	0.28	2		652	585	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958564	175958564	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	16	647	0	ENST00000367669.3:c.1781T>C	p.Val594Ala	p.V594A	ENST00000367669	NM_022457.5	594	gTa/gCa	16/20	1	2	FACETS	0.407	0.3	0.534	0.407	0.3	0.534	SUBCLONAL	1	TRUE	1	0.28	2		647	281	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104375090	104375090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554854578	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	74	721	1	ENST00000369902.3:c.1088C>T	p.Thr363Met	p.T363M	ENST00000369902	NM_016169.3	363	aCg/aTg	9/12	1	2	FACETS	0.744	0.651	0.845	0.744	0.651	0.845	SUBCLONAL	1	TRUE	1	0.28	2		722	710	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942053	71942053	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	112	1183	1	ENST00000298229.2:c.1322del	p.Asn441ThrfsTer2	p.N441Tfs*2	ENST00000298229	NM_001567.3	439	ccA/cc	12/28	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.28	2		1184	769	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948259	71948259	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	161	1763	0	ENST00000298229.2:c.2974del	p.Val992SerfsTer139	p.V992Sfs*139	ENST00000298229	NM_001567.3	991	Ggg/gg	26/28	1	2	FACETS	0.891	0.815	0.971	0.891	0.815	0.971	CLONAL	1	TRUE	1	0.28	2		1763	1291	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944943	31944943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	84	583	0	ENST00000340398.3:c.158G>A	p.Arg53His	p.R53H	ENST00000340398	NM_001013699.2	53	cGt/cAt	1/1	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.28	2		583	591	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448408	49448408	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs797045661	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	98	798	3	ENST00000301067.7:c.303del	p.Ser102AlafsTer28	p.S102Afs*28	ENST00000301067	NM_003482.3	101	ggG/gg	3/54	1	2	FACETS	0.983	0.877	1	0.983	0.877	1	CLONAL	1	TRUE	1	0.28	2		801	712	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49449100	49449100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451360303	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	81	612	2	ENST00000301067.7:c.8G>A	p.Ser3Asn	p.S3N	ENST00000301067	NM_003482.3	3	aGc/aAc	1/54	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.28	2		614	559	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481648	56481648	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs774589520	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	120	880	0	ENST00000267101.3:c.683A>G	p.His228Arg	p.H228R	ENST00000267101	NM_001982.3	228	cAt/cGt	6/28	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.28	2		880	855	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144864	58144864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778185	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	47	531	2	ENST00000257904.6:c.364C>T	p.Arg122Cys	p.R122C	ENST00000257904	NM_000075.3	122	Cgc/Tgc	4/8	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.28	2		533	324	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794732	120794732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1276733276	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	102	851	1	ENST00000257552.2:c.625G>A	p.Ala209Thr	p.A209T	ENST00000257552	NM_002442.3	209	Gcc/Acc	9/15	1	2	FACETS	0.777	0.694	0.865	0.777	0.694	0.865	SUBCLONAL	1	TRUE	1	0.28	2		852	938	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209345	133209345	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	99	881	0	ENST00000320574.5:c.6041G>T	p.Gly2014Val	p.G2014V	ENST00000320574	NM_006231.2	2014	gGg/gTg	44/49	1	2	FACETS	0.861	0.768	0.96	0.861	0.768	0.96	CLONAL	1	TRUE	1	0.28	2		881	821	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28880897	28880897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372046832	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	48	435	0	ENST00000282397.4:c.3733G>A	p.Asp1245Asn	p.D1245N	ENST00000282397	NM_002019.4	1245	Gac/Aac	29/30	1	2	FACETS	0.801	0.678	0.936	0.801	0.678	0.936	CLONAL	1	TRUE	1	0.28	2		435	428	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134954	41134954	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	22	334	0	ENST00000379561.5:c.674G>A	p.Arg225His	p.R225H	ENST00000379561	NM_002015.3	225	cGt/cAt	2/3	1	2	FACETS	1	0.783	1	1	0.783	1	CLONAL	1	TRUE	1	0.28	2		334	157	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955484	48955484	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	14	395	0	ENST00000267163.4:c.1600A>C	p.Ser534Arg	p.S534R	ENST00000267163	NM_000321.2	534	Agt/Cgt	17/27	1	2	FACETS	0.549	0.398	0.731	0.549	0.398	0.731	SUBCLONAL	1	TRUE	1	0.28	2		395	182	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524654	103524654	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	54	538	0	ENST00000355739.4:c.2785A>G	p.Asn929Asp	p.N929D	ENST00000355739	NM_000123.3	929	Aac/Gac	13/15	1	2	FACETS	0.879	0.752	1	0.879	0.752	1	CLONAL	1	TRUE	1	0.28	2		538	439	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435652	110435652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753831518	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	162	1287	4	ENST00000375856.3:c.2749G>A	p.Gly917Ser	p.G917S	ENST00000375856	NM_003749.2	917	Ggc/Agc	1/2	1	2	FACETS	0.928	0.849	1	0.928	0.849	1	CLONAL	1	TRUE	1	0.28	2		1291	1247	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437412	110437412	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	69	862	0	ENST00000375856.3:c.989A>G	p.Asn330Ser	p.N330S	ENST00000375856	NM_003749.2	330	aAc/aGc	1/2	1	2	FACETS	0.593	0.515	0.677	0.593	0.515	0.677	SUBCLONAL	1	TRUE	1	0.28	2		862	831	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194831	30194831	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368595371	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	41	774	1	ENST00000331968.5:c.314G>A	p.Arg105His	p.R105H	ENST00000331968	NM_002742.2	105	cGc/cAc	2/18	1	2	FACETS	0.745	0.622	0.882	0.745	0.622	0.882	SUBCLONAL	1	TRUE	1	0.28	2		775	393	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670391	88670391	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	13	430	0	ENST00000360948.2:c.1293+2T>C		p.X431_splice	ENST00000360948	NM_001012338.2	431			1	2	FACETS	0.366	0.26	0.494	0.366	0.26	0.494	SUBCLONAL	1	TRUE	1	0.28	2		430	254	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465390	99465390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145300307	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	49	495	0	ENST00000268035.6:c.2215C>T	p.Arg739Trp	p.R739W	ENST00000268035	NM_000875.3	739	Cgg/Tgg	11/21	1	2	FACETS	0.943	0.802	1	0.943	0.802	1	CLONAL	1	TRUE	1	0.28	2		495	371	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354308	354308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757610038	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	44	720	0	ENST00000262320.3:c.1250G>A	p.Arg417His	p.R417H	ENST00000262320	NM_003502.3	417	cGc/cAc	5/11	1	2	FACETS	0.371	0.31	0.439	0.371	0.31	0.439	SUBCLONAL	1	TRUE	1	0.28	2		720	848	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67132641	67132641	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	39	721	0	ENST00000412916.2:c.524G>A	p.Gly175Asp	p.G175D	ENST00000412916		175	gGt/gAt	6/6	1	2	FACETS	0.829	0.689	0.984	0.829	0.689	0.984	CLONAL	1	TRUE	1	0.28	2		721	336	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349156	89349156	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	100	1436	1	ENST00000301030.4:c.3794C>T	p.Ser1265Phe	p.S1265F	ENST00000301030	NM_001256183.1	1265	tCc/tTc	9/13	1	2	FACETS	0.742	0.661	0.828	0.742	0.661	0.828	SUBCLONAL	1	TRUE	1	0.28	2		1437	963	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437578	56437578	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs746762909	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	104	893	0	ENST00000407977.2:c.884A>G	p.His295Arg	p.H295R	ENST00000407977		295	cAt/cGt	8/10	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.28	2		893	720	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492772	56492773	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	72	728	0	ENST00000407977.2:c.166dup	p.Asp56GlyfsTer19	p.D56Gfs*19	ENST00000407977		56	gac/gGac	2/10	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.28	2		728	480	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533914	63533914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751229839	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	68	410	0	ENST00000307078.5:c.1240C>T	p.Arg414Trp	p.R414W	ENST00000307078	NM_004655.3	414	Cgg/Tgg	6/11	1	2	FACETS	0.945	0.824	1	0.945	0.824	1	CLONAL	1	TRUE	1	0.28	2		410	514	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615812	1615812	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771807324	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	32	552	1	ENST00000344749.5:c.1459C>T	p.Arg487Ter	p.R487*	ENST00000344749	NM_001136139.2	487	Cga/Tga	17/19	1	2	FACETS	0.373	0.302	0.454	0.373	0.302	0.454	SUBCLONAL	1	TRUE	1	0.28	2		553	613	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226751	2226751	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs575524083	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	150	1256	6	ENST00000398665.3:c.4231G>A	p.Ala1411Thr	p.A1411T	ENST00000398665	NM_032482.2	1411	Gcc/Acc	27/28	1	2	FACETS	0.91	0.829	0.994	0.91	0.829	0.994	CLONAL	1	TRUE	1	0.28	2		1262	1178	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221081	5221081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199805837	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	58	690	0	ENST00000357368.4:c.3385G>A	p.Ala1129Thr	p.A1129T	ENST00000357368	NM_002850.3	1129	Gcc/Acc	20/38	1	2	FACETS	0.685	0.588	0.79	0.685	0.588	0.79	SUBCLONAL	1	TRUE	1	0.28	2		690	605	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262175	10262175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1254979538	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	67	829	1	ENST00000340748.4:c.2116G>A	p.Asp706Asn	p.D706N	ENST00000340748		706	Gat/Aat	23/40	1	2	FACETS	0.893	0.777	1	0.893	0.777	1	CLONAL	1	TRUE	1	0.28	2		830	536	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129671	11129671	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1282230193	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	86	900	1	ENST00000358026.2:c.2477C>T	p.Ala826Val	p.A826V	ENST00000358026	NM_001128849.1	826	gCc/gTc	17/36	1	2	FACETS	0.898	0.795	1	0.898	0.795	1	CLONAL	1	TRUE	1	0.28	2		901	684	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18964077	18964077	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	52	595	0	ENST00000262803.5:c.1078del	p.Asp360MetfsTer46	p.D360Mfs*46	ENST00000262803	NM_002911.3	358	caG/ca	8/24	1	2	FACETS	0.699	0.596	0.813	0.699	0.596	0.813	SUBCLONAL	1	TRUE	1	0.28	2		595	531	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910381	50910381	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	118	1059	0	ENST00000440232.2:c.1636C>A	p.Leu546Met	p.L546M	ENST00000440232	NM_002691.3	546	Ctg/Atg	13/27	1	2	FACETS	0.847	0.763	0.936	0.847	0.763	0.936	CLONAL	1	TRUE	1	0.28	2		1059	995	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910394	50910394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	116	1053	1	ENST00000440232.2:c.1649G>A	p.Gly550Asp	p.G550D	ENST00000440232	NM_002691.3	550	gGc/gAc	13/27	1	2	FACETS	0.836	0.752	0.925	0.836	0.752	0.925	CLONAL	1	TRUE	1	0.28	2		1054	991	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966526	25966526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	45	665	0	ENST00000435504.4:c.2680G>A	p.Ala894Thr	p.A894T	ENST00000435504		894	Gcc/Acc	13/13	1	2	FACETS	0.726	0.61	0.853	0.726	0.61	0.853	SUBCLONAL	1	TRUE	1	0.28	2		665	443	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991737	25991737	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	36	327	0	ENST00000435504.4:c.505G>A	p.Ala169Thr	p.A169T	ENST00000435504		169	Gcg/Acg	7/13	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.28	2		327	247	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703590	47703590	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750398	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	44	688	0	ENST00000233146.2:c.2090G>A	p.Cys697Tyr	p.C697Y	ENST00000233146	NM_000251.2	697	tGt/tAt	13/16	1	2	FACETS	0.888	0.747	1	0.888	0.747	1	CLONAL	1	TRUE	1	0.28	2		688	354	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182601	99182601	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	57	409	0	ENST00000074304.5:c.2404G>T	p.Gly802Cys	p.G802C	ENST00000074304	NM_001134224.1	802	Ggc/Tgc	22/26	1	2	FACETS	0.981	0.844	1	0.981	0.844	1	CLONAL	1	TRUE	1	0.28	2		409	415	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989623	212989623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	22	276	0	ENST00000342788.4:c.88G>A	p.Ala30Thr	p.A30T	ENST00000342788	NM_005235.2	30	Gca/Aca	2/28	1	2	FACETS	0.728	0.566	0.913	0.728	0.566	0.913	CLONAL	1	TRUE	1	0.28	2		276	216	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661852	227661852	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	115	1244	0	ENST00000305123.5:c.1603A>G	p.Thr535Ala	p.T535A	ENST00000305123	NM_005544.2	535	Acc/Gcc	1/2	1	2	FACETS	0.878	0.79	0.971	0.878	0.79	0.971	CLONAL	1	TRUE	1	0.28	2		1244	936	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175871	24175871	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	82	625	2	ENST00000263121.7:c.1099G>A	p.Asp367Asn	p.D367N	ENST00000263121	NM_003073.3	367	Gac/Aac	8/9	0.131249516587539	0	FACETS	0.716	0.632	0.806			1	INDETERMINATE	1	TRUE	0	0.28	0		627	589	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37038114	37038114	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	18	116	0	ENST00000231790.2:c.121G>A	p.Asp41Asn	p.D41N	ENST00000231790	NM_000249.3	41	Gat/Aat	2/19	1	2	FACETS	0.905	0.7	1	1	0.931	1	CLONAL	2	TRUE	1	0.28	2		116	71	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928978	49928978	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs200454353	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	74	860	0	ENST00000296474.3:c.3388C>T	p.Arg1130Ter	p.R1130*	ENST00000296474	NM_002447.2	1130	Cga/Tga	16/20	1	2	FACETS	0.67	0.586	0.761	0.67	0.586	0.761	SUBCLONAL	1	TRUE	1	0.28	2		860	789	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940586	49940586	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	31	793	0	ENST00000296474.3:c.457A>G	p.Thr153Ala	p.T153A	ENST00000296474	NM_002447.2	153	Aca/Gca	1/20	1	2	FACETS	0.362	0.292	0.442	0.362	0.292	0.442	SUBCLONAL	1	TRUE	1	0.28	2		793	612	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678753	52678753	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs780700287	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	47	509	0	ENST00000394830.3:c.866A>G	p.His289Arg	p.H289R	ENST00000394830	NM_018313.4	289	cAt/cGt	9/30	1	2	FACETS	0.779	0.658	0.912	0.779	0.658	0.912	CLONAL	1	TRUE	1	0.28	2		509	431	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987043	69987043	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	71	846	0	ENST00000394351.3:c.104A>G	p.Tyr35Cys	p.Y35C	ENST00000394351	NM_000248.3	35	tAc/tGc	2/9	1	2	FACETS	0.795	0.694	0.904	0.795	0.694	0.904	CLONAL	1	TRUE	1	0.28	2		846	638	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977886	134977886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	34	603	0	ENST00000398015.3:c.2879G>A	p.Gly960Asp	p.G960D	ENST00000398015	NM_004441.4	960	gGc/gAc	16/16	1	2	FACETS	0.807	0.661	0.969	0.807	0.661	0.969	CLONAL	1	TRUE	1	0.28	2		603	301	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928065	178928065	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	40	639	0	ENST00000263967.3:c.1343T>C	p.Val448Ala	p.V448A	ENST00000263967	NM_006218.2	448	gTa/gCa	8/21	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.28	2		639	253	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191118	185191118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs564401067	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	65	617	1	ENST00000265026.3:c.1999G>A	p.Ala667Thr	p.A667T	ENST00000265026	NM_004721.4	667	Gcc/Acc	11/14	1	2	FACETS	0.886	0.769	1	0.886	0.769	1	CLONAL	1	TRUE	1	0.28	2		618	524	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604280	189604280	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	82	688	0	ENST00000264731.3:c.1447A>G	p.Asn483Asp	p.N483D	ENST00000264731	NM_003722.4	483	Aac/Gac	11/14	1	2	FACETS	0.957	0.845	1	0.957	0.845	1	CLONAL	1	TRUE	1	0.28	2		688	612	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79974842	79974842	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1418423507	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	36	558	0	ENST00000265081.6:c.1270G>A	p.Val424Ile	p.V424I	ENST00000265081	NM_002439.4	424	Gta/Ata	8/24	1	2	FACETS	0.464	0.381	0.558	0.464	0.381	0.558	SUBCLONAL	1	TRUE	1	0.28	2		558	554	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911141	29911141	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	33	638	0	ENST00000376809.5:c.440A>G	p.Tyr147Cys	p.Y147C	ENST00000376809	NM_002116.7	147	tAc/tGc	3/8	0.131249516587539	3	FACETS	0.587	0.477	0.71	0.293	0.238	0.355	INDETERMINATE	1	TRUE	1	0.28	3		638	458	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730120	41730120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	28	373	0	ENST00000242208.4:c.409C>T	p.His137Tyr	p.H137Y	ENST00000242208	NM_002192.2	137	Cac/Tac	3/3	1	2	FACETS	0.637	0.51	0.781	0.637	0.51	0.781	SUBCLONAL	1	TRUE	1	0.28	2		373	314	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367272	50367272	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	58	503	0	ENST00000331340.3:c.79G>T	p.Gly27Cys	p.G27C	ENST00000331340	NM_006060.4	27	Ggc/Tgc	3/8	1	2	FACETS	0.76	0.653	0.876	0.76	0.653	0.876	SUBCLONAL	1	TRUE	1	0.28	2		503	545	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455067	50455067	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	42	347	0	ENST00000331340.3:c.614A>T	p.Tyr205Phe	p.Y205F	ENST00000331340	NM_006060.4	205	tAt/tTt	6/8	1	2	FACETS	1	0.839	1	1	0.839	1	CLONAL	1	TRUE	1	0.28	2		347	300	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214332	55214332	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	82	742	0	ENST00000275493.2:c.458A>G	p.Asn153Ser	p.N153S	ENST00000275493	NM_005228.3	153	aAc/aGc	4/28	1	2	FACETS	0.73	0.643	0.824	0.73	0.643	0.824	SUBCLONAL	1	TRUE	1	0.28	2		742	802	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506217	148506217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	52	721	0	ENST00000320356.2:c.2141G>A	p.Gly714Asp	p.G714D	ENST00000320356	NM_004456.4	714	gGt/gAt	19/20	1	2	FACETS	0.91	0.777	1	0.91	0.777	1	CLONAL	1	TRUE	1	0.28	2		721	408	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992721	68992721	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs764112302	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	43	816	2	ENST00000288368.4:c.1693del	p.Ser565ArgfsTer10	p.S565Rfs*10	ENST00000288368	NM_024870.2	562	cgT/cg	16/40	1	2	FACETS	0.853	0.716	1	0.853	0.716	1	CLONAL	1	TRUE	1	0.28	2		818	360	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002849	69002849	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	30	350	0	ENST00000288368.4:c.2149C>T	p.Gln717Ter	p.Q717*	ENST00000288368	NM_024870.2	717	Cag/Tag	20/40	1	2	FACETS	0.983	0.797	1	0.983	0.797	1	CLONAL	1	TRUE	1	0.28	2		350	218	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737081	145737081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747815189	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	60	707	2	ENST00000428558.2:c.3485G>A	p.Arg1162His	p.R1162H	ENST00000428558	NM_004260.3	1162	cGc/cAc	21/22	1	2	FACETS	0.821	0.708	0.944	0.821	0.708	0.944	CLONAL	1	TRUE	1	0.28	2		709	522	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436642	8436642	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs373554730	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	27	575	0	ENST00000356435.5:c.4036A>G	p.Ile1346Val	p.I1346V	ENST00000356435		1346	Att/Gtt	24/35	1	2	FACETS	0.817	0.653	1	0.817	0.653	1	CLONAL	1	TRUE	1	0.28	2		575	236	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974782	21974782	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs138677674	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	26	271	1	ENST00000304494.5:c.45G>A	p.Trp15Ter	p.W15*	ENST00000304494	NM_000077.4	15	tgG/tgA	1/3	1	2	FACETS	0.889	0.708	1	0.889	0.708	1	CLONAL	1	TRUE	1	0.28	2		272	209	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180358	27180358	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	53	442	0	ENST00000380036.4:c.1022A>T	p.Glu341Val	p.E341V	ENST00000380036	NM_000459.3	341	gAg/gTg	7/23	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.28	2		442	325	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27190602	27190602	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1193419868	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	70	918	0	ENST00000380036.4:c.1403A>G	p.Glu468Gly	p.E468G	ENST00000380036	NM_000459.3	468	gAg/gGg	10/23	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.28	2		918	487	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912259	97912259	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	50	640	1	ENST00000289081.3:c.632C>A	p.Pro211His	p.P211H	ENST00000289081	NM_000136.2	211	cCt/cAt	7/15	1	2	FACETS	0.749	0.636	0.873	0.749	0.636	0.873	SUBCLONAL	1	TRUE	1	0.28	2		641	477	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250227	110250227	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	79	857	0	ENST00000374672.4:c.448T>C	p.Phe150Leu	p.F150L	ENST00000374672	NM_004235.4	150	Ttc/Ctc	3/5	1	2	FACETS	0.891	0.784	1	0.891	0.784	1	CLONAL	1	TRUE	1	0.28	2		857	633	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137321028	137321028	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	109	1084	2	ENST00000481739.1:c.985G>A	p.Gly329Arg	p.G329R	ENST00000481739	NM_002957.4	329	Ggg/Agg	7/10	1	2	FACETS	0.758	0.679	0.842	0.758	0.679	0.842	SUBCLONAL	1	TRUE	1	0.28	2		1086	1027	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841027	15841027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1420213041	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	81	509	0	ENST00000307771.7:c.1111G>A	p.Asp371Asn	p.D371N	ENST00000307771	NM_005089.3	371	Gac/Aac	11/11	1	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.28	1		509	422	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933617	39933617	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	73	275	0	ENST00000378444.4:c.982del	p.Asp328ThrfsTer50	p.D328Tfs*50	ENST00000378444	NM_001123385.1	328	Gac/ac	4/15	1	1	FACETS	1	0.894	1	1	0.984	1	CLONAL	2	TRUE	0	0.28	1		275	223	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937657	44937657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	30	287	0	ENST00000377967.4:c.2845C>T	p.Arg949Cys	p.R949C	ENST00000377967	NM_021140.2	949	Cgt/Tgt	19/29	1	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.28	1		287	124	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243965	53243965	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	123	588	0	ENST00000375401.3:c.1028A>G	p.Asp343Gly	p.D343G	ENST00000375401	NM_004187.3	343	gAt/gGt	8/26	1	1	FACETS	0.769	0.7	0.842	1	0.986	1	SUBCLONAL	2	TRUE	0	0.28	1		588	491	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360576	70360576	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	163	570	0	ENST00000374080.3:c.6136G>A	p.Ala2046Thr	p.A2046T	ENST00000374080		2046	Gcc/Acc	42/45	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.28	1		570	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0014275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	308	328	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.435513063615503	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.435513063615503	1		328	1008	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	172	408	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.882	0.811	0.955	0.882	0.811	0.955	CLONAL	1	TRUE	1	0.435513063615503	2		408	896	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0014275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	294	403	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.967	0.909	1	0.967	0.909	1	CLONAL	1	TRUE	1	0.435513063615503	2		403	1396	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591933	48591933	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	GT	novel	NA	P-0014275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	143	352	0	ENST00000342988.3:c.1096delinsGT	p.Gln366ValfsTer12	p.Q366Vfs*12	ENST00000342988	NM_005359.5	366	Caa/GTaa	9/12	0.435513063615503	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.435513063615503	1		352	505	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0014311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	177	648	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.439394587709122	2		648	763	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441253	52441253	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	152	595	0	ENST00000460680.1:c.517T>C	p.Tyr173His	p.Y173H	ENST00000460680	NM_004656.3	173	Tat/Cat	7/17	0.439394587709122	1	FACETS	0.989	0.909	1	0.989	0.909	1	CLONAL	1	TRUE	0	0.439394587709122	1		595	546	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630136	100630136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555980871	NA	P-0014311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	130	515	1	ENST00000308731.7:c.137G>A	p.Arg46His	p.R46H	ENST00000308731	NM_000061.2	46	cGt/cAt	2/19	1	2	FACETS	0.954	0.868	1	0.954	0.868	1	CLONAL	1	TRUE	1	0.439394587709122	2		516	620	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	78	138	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.404	0.353	0.458	0.404	0.353	0.458	SUBCLONAL	1	TRUE	1	0.339405299534912	2		138	1139	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971000	21971000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	210	544	0	ENST00000304494.5:c.358G>T	p.Glu120Ter	p.E120*	ENST00000304494	NM_000077.4	120	Gag/Tag	2/3	0.339405299534912	1	FACETS	0.979	0.908	1	0.979	0.908	1	CLONAL	1	TRUE	0	0.339405299534912	1		544	1050	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743931	46743931	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	49	408	0	ENST00000371975.4:c.2221G>T	p.Glu741Ter	p.E741*	ENST00000371975	NM_003579.3	741	Gag/Tag	18/18	1	2	FACETS	0.319	0.269	0.374	0.319	0.269	0.374	SUBCLONAL	1	TRUE	1	0.339405299534912	2		408	906	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576853	7576853	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs11575996	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	231	473	0	ENST00000269305.4:c.993G>T	p.Gln331His	p.Q331H	ENST00000269305	NM_001126112.2	331	caG/caT	9/11	0.339405299534912	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.339405299534912	1		473	1092	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120795	115120795	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	63	386	1	ENST00000257566.3:c.211del	p.Ala71ArgfsTer17	p.A71Rfs*17	ENST00000257566	NM_016569.3	71	Gcg/cg	1/8	1	2	FACETS	0.456	0.393	0.524	0.456	0.393	0.524	SUBCLONAL	1	TRUE	1	0.339405299534912	2		387	814	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074091	8074091	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	69	302	0	ENST00000377482.5:c.568G>T	p.Asp190Tyr	p.D190Y	ENST00000377482	NM_018948.3	190	Gat/Tat	4/4	1	2	FACETS	0.61	0.531	0.695	0.61	0.531	0.695	SUBCLONAL	1	TRUE	1	0.339405299534912	2		302	667	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303199	11303199	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	136	540	2	ENST00000361445.4:c.1384G>T	p.Ala462Ser	p.A462S	ENST00000361445	NM_004958.3	462	Gcc/Tcc	9/58	1	2	FACETS	0.716	0.65	0.786	0.716	0.65	0.786	SUBCLONAL	1	TRUE	1	0.339405299534912	2		542	1119	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430784	78430784	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	138	431	0	ENST00000370768.2:c.605G>T	p.Gly202Val	p.G202V	ENST00000370768	NM_003902.3	202	gGa/gTa	8/20	1	2	FACETS	0.727	0.66	0.797	0.727	0.66	0.797	SUBCLONAL	1	TRUE	1	0.339405299534912	2		431	1119	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115277140	115277140	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238807388	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	109	359	0	ENST00000438362.2:c.643G>A	p.Gly215Ser	p.G215S	ENST00000438362	NM_001242891.1	215	Ggt/Agt	7/20	1	2	FACETS	0.673	0.604	0.747	0.673	0.604	0.747	SUBCLONAL	1	TRUE	1	0.339405299534912	2		359	954	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117712729	117712729	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	139	488	0	ENST00000369458.3:c.97G>T	p.Gly33Trp	p.G33W	ENST00000369458	NM_024626.3	33	Ggg/Tgg	2/6	1	2	FACETS	0.756	0.687	0.828	0.756	0.687	0.828	SUBCLONAL	1	TRUE	1	0.339405299534912	2		488	1084	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981833	201981833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	180	618	0	ENST00000359651.3:c.545del	p.Gly182AlafsTer72	p.G182Afs*72	ENST00000359651		182	Ggc/gc	4/8	1	2	FACETS	0.808	0.743	0.876	0.808	0.743	0.876	CLONAL	1	TRUE	1	0.339405299534912	2		618	1313	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612642	228612642	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	143	492	2	ENST00000366696.1:c.385C>A	p.Arg129Ser	p.R129S	ENST00000366696	NM_003493.2	129	Cgc/Agc	1/1	1	2	FACETS	0.784	0.713	0.858	0.784	0.713	0.858	SUBCLONAL	1	TRUE	1	0.339405299534912	2		494	1075	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725073	89725073	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	62	188	0	ENST00000371953.3:c.1056G>T	p.Glu352Asp	p.E352D	ENST00000371953	NM_000314.4	352	gaG/gaT	9/9	0.339405299534912	1	FACETS	0.68	0.589	0.779	0.68	0.589	0.779	SUBCLONAL	1	TRUE	0	0.339405299534912	1		188	446	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575400	64575400	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	77	520	0	ENST00000312049.6:c.617G>C	p.Arg206Pro	p.R206P	ENST00000312049	NM_130799.2	206	cGc/cCc	3/10	1	2	FACETS	0.398	0.348	0.452	0.398	0.348	0.452	SUBCLONAL	1	TRUE	1	0.339405299534912	2		520	1141	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944508	71944508	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	80	636	0	ENST00000298229.2:c.2064G>T	p.Trp688Cys	p.W688C	ENST00000298229	NM_001567.3	688	tgG/tgT	18/28	1	2	FACETS	0.387	0.339	0.439	0.387	0.339	0.439	SUBCLONAL	1	TRUE	1	0.339405299534912	2		636	1218	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175479	108175479	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	88	410	1	ENST00000278616.4:c.5574G>C	p.Trp1858Cys	p.W1858C	ENST00000278616	NM_000051.3	1858	tgG/tgC	37/63	1	2	FACETS	0.625	0.553	0.702	0.625	0.553	0.702	SUBCLONAL	1	TRUE	1	0.339405299534912	2		411	830	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342648	118342648	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs781870146	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	83	313	0	ENST00000534358.1:c.774G>T	p.Arg258Ser	p.R258S	ENST00000534358	NM_005933.3	258	agG/agT	3/36	1	2	FACETS	0.652	0.575	0.735	0.652	0.575	0.735	SUBCLONAL	1	TRUE	1	0.339405299534912	2		313	750	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435295	18435295	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	131	361	0	ENST00000266497.5:c.280C>A	p.Arg94Ser	p.R94S	ENST00000266497		94	Cgt/Agt	1/31	0.26708580873892	1	FACETS	0.72	0.653	0.791	0.72	0.653	0.791	SUBCLONAL	1	TRUE	0	0.339405299534912	1		361	890	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420432	49420432	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	136	494	1	ENST00000301067.7:c.15317G>T	p.Arg5106Leu	p.R5106L	ENST00000301067	NM_003482.3	5106	cGc/cTc	48/54	1	2	FACETS	0.737	0.669	0.809	0.737	0.669	0.809	SUBCLONAL	1	TRUE	1	0.339405299534912	2		495	1087	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446479	49446479	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	45	353	0	ENST00000301067.7:c.1126G>T	p.Glu376Ter	p.E376*	ENST00000301067	NM_003482.3	376	Gag/Tag	9/54	1	2	FACETS	0.347	0.291	0.41	0.347	0.291	0.41	SUBCLONAL	1	TRUE	1	0.339405299534912	2		353	764	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109980	115109980	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1231	198	820	1	ENST00000257566.3:c.1898C>A	p.Thr633Asn	p.T633N	ENST00000257566	NM_016569.3	633	aCc/aAc	8/8	1	2	FACETS	0.816	0.754	0.882	0.816	0.754	0.882	CLONAL	1	TRUE	1	0.339405299534912	2		821	1429	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219159	133219159	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	172	635	0	ENST00000320574.5:c.4885G>C	p.Ala1629Pro	p.A1629P	ENST00000320574	NM_006231.2	1629	Gcc/Ccc	37/49	1	2	FACETS	0.789	0.724	0.857	0.789	0.724	0.857	SUBCLONAL	1	TRUE	1	0.339405299534912	2		635	1284	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912475	32912475	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	58	384	0	ENST00000380152.3:c.3983G>T	p.Ser1328Ile	p.S1328I	ENST00000380152		1328	aGt/aTt	11/27	1	2	FACETS	0.388	0.332	0.449	0.388	0.332	0.449	SUBCLONAL	1	TRUE	1	0.339405299534912	2		384	881	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434614	110434614	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781421239	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	89	612	0	ENST00000375856.3:c.3787G>A	p.Gly1263Arg	p.G1263R	ENST00000375856	NM_003749.2	1263	Ggg/Agg	1/2	NA	2	FACETS	0.472	0.417	0.531			1	INDETERMINATE	1	TRUE	NA	0.339405299534912	2		612	1112	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420291	88420291	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	123	445	0	ENST00000360948.2:c.2395G>T	p.Val799Leu	p.V799L	ENST00000360948	NM_001012338.2	799	Gtg/Ttg	19/19	1	2	FACETS	0.715	0.646	0.789	0.715	0.646	0.789	SUBCLONAL	1	TRUE	1	0.339405299534912	2		445	1013	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339441	339441	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1201	66	523	0	ENST00000262320.3:c.2461A>T	p.Arg821Ter	p.R821*	ENST00000262320	NM_003502.3	821	Aga/Tga	10/11	1	2	FACETS	0.307	0.265	0.353	0.307	0.265	0.353	SUBCLONAL	1	TRUE	1	0.339405299534912	2		523	1267	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817818	3817818	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1397	80	642	0	ENST00000262367.5:c.3153G>C	p.Lys1051Asn	p.K1051N	ENST00000262367	NM_004380.2	1051	aaG/aaC	16/31	1	2	FACETS	0.319	0.279	0.362	0.319	0.279	0.362	SUBCLONAL	1	TRUE	1	0.339405299534912	2		642	1477	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3824597	3824597	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	61	393	0	ENST00000262367.5:c.2256G>C	p.Gln752His	p.Q752H	ENST00000262367	NM_004380.2	752	caG/caC	12/31	1	2	FACETS	0.382	0.329	0.441	0.382	0.329	0.441	SUBCLONAL	1	TRUE	1	0.339405299534912	2		393	940	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858241	9858241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	53	339	0	ENST00000330684.3:c.3160G>A	p.Glu1054Lys	p.E1054K	ENST00000330684	NM_001134407.1	1054	Gaa/Aaa	13/13	1	2	FACETS	0.373	0.317	0.434	0.373	0.317	0.434	SUBCLONAL	1	TRUE	1	0.339405299534912	2		339	838	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670670	67670670	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	139	591	0	ENST00000264010.4:c.1915C>A	p.Gln639Lys	p.Q639K	ENST00000264010	NM_006565.3	639	Cag/Aag	11/12	1	2	FACETS	0.655	0.595	0.719	0.655	0.595	0.719	SUBCLONAL	1	TRUE	1	0.339405299534912	2		591	1250	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57567433	57567433	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	66	474	0	ENST00000316660.6:c.24G>T	p.Lys8Asn	p.K8N	ENST00000316660	NM_021127.2	8	aaG/aaT	1/2	0.26708580873892	1	FACETS	0.338	0.292	0.388	0.338	0.292	0.388	SUBCLONAL	1	TRUE	0	0.339405299534912	1		474	956	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2164229	2164229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	67	544	0	ENST00000398665.3:c.46G>A	p.Glu16Lys	p.E16K	ENST00000398665	NM_032482.2	16	Gag/Aag	1/28	0.339405299534912	1	FACETS	0.308	0.266	0.353	0.308	0.266	0.353	SUBCLONAL	1	TRUE	0	0.339405299534912	1		544	1065	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218503	5218503	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1195	169	681	1	ENST00000357368.4:c.3976A>T	p.Asn1326Tyr	p.N1326Y	ENST00000357368	NM_002850.3	1326	Aac/Tac	25/38	0.339405299534912	1	FACETS	0.606	0.556	0.659	0.606	0.556	0.659	SUBCLONAL	1	TRUE	0	0.339405299534912	1		682	1364	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221015	5221015	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	150	390	0	ENST00000357368.4:c.3451G>A	p.Val1151Ile	p.V1151I	ENST00000357368	NM_002850.3	1151	Gtc/Atc	20/38	0.339405299534912	1	FACETS	0.874	0.799	0.952	0.874	0.799	0.952	CLONAL	1	TRUE	0	0.339405299534912	1		390	840	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211243	36211243	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1759	366	988	0	ENST00000222270.7:c.994C>A	p.His332Asn	p.H332N	ENST00000222270	NM_014727.1	332	Cat/Aat	3/37	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.339405299534912	2		988	2125	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221331	36221331	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1486	115	690	0	ENST00000222270.7:c.5165G>T	p.Gly1722Val	p.G1722V	ENST00000222270	NM_014727.1	1722	gGg/gTg	24/37	1	2	FACETS	0.423	0.379	0.47	0.423	0.379	0.47	SUBCLONAL	1	TRUE	1	0.339405299534912	2		690	1601	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426687	212426687	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	141	570	0	ENST00000342788.4:c.2428G>C	p.Glu810Gln	p.E810Q	ENST00000342788	NM_005235.2	810	Gag/Cag	20/28	1	2	FACETS	0.747	0.679	0.819	0.747	0.679	0.819	SUBCLONAL	1	TRUE	1	0.339405299534912	2		570	1112	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215595149	215595149	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	113	420	0	ENST00000260947.4:c.1987A>C	p.Asn663His	p.N663H	ENST00000260947	NM_000465.2	663	Aac/Cac	10/11	1	2	FACETS	0.683	0.613	0.757	0.683	0.613	0.757	SUBCLONAL	1	TRUE	1	0.339405299534912	2		420	975	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660316	227660316	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	35	305	0	ENST00000305123.5:c.3139C>A	p.Pro1047Thr	p.P1047T	ENST00000305123	NM_005544.2	1047	Cct/Act	1/2	1	2	FACETS	0.331	0.27	0.399	0.331	0.27	0.399	SUBCLONAL	1	TRUE	1	0.339405299534912	2		305	623	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520152	9520152	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	47	350	0	ENST00000353224.5:c.2117C>A	p.Pro706Gln	p.P706Q	ENST00000353224	NM_177990.2	706	cCg/cAg	10/10	0.339405299534912	1	FACETS	0.328	0.276	0.386	0.328	0.276	0.386	SUBCLONAL	1	TRUE	0	0.339405299534912	1		350	701	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264944	46264944	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	123	432	2	ENST00000371998.3:c.1814G>T	p.Gly605Val	p.G605V	ENST00000371998		605	gGg/gTg	12/23	1	2	FACETS	0.746	0.673	0.822	0.746	0.673	0.822	SUBCLONAL	1	TRUE	1	0.339405299534912	2		434	972	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52676041	52676041	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	139	491	0	ENST00000394830.3:c.1016G>T	p.Gly339Val	p.G339V	ENST00000394830	NM_018313.4	339	gGa/gTa	11/30	1	2	FACETS	0.666	0.605	0.731	0.666	0.605	0.731	SUBCLONAL	1	TRUE	1	0.339405299534912	2		491	1229	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851784	134851784	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	149	565	0	ENST00000398015.3:c.1190G>C	p.Trp397Ser	p.W397S	ENST00000398015	NM_004441.4	397	tGg/tCg	5/16	1	2	FACETS	0.76	0.692	0.83	0.76	0.692	0.83	SUBCLONAL	1	TRUE	1	0.339405299534912	2		565	1156	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977879	134977879	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	125	464	0	ENST00000398015.3:c.2872T>A	p.Leu958Met	p.L958M	ENST00000398015	NM_004441.4	958	Ttg/Atg	16/16	1	2	FACETS	0.732	0.662	0.807	0.732	0.662	0.807	SUBCLONAL	1	TRUE	1	0.339405299534912	2		464	1006	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612083	189612083	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	137	500	0	ENST00000264731.3:c.1835C>A	p.Ser612Tyr	p.S612Y	ENST00000264731	NM_003722.4	612	tCc/tAc	14/14	1	2	FACETS	0.697	0.633	0.765	0.697	0.633	0.765	SUBCLONAL	1	TRUE	1	0.339405299534912	2		500	1158	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808913	1808913	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	63	632	0	ENST00000260795.2:c.2345C>G	p.Ser782Cys	p.S782C	ENST00000260795		782	tCc/tGc	17/17	1	2	FACETS	0.309	0.266	0.356	0.309	0.266	0.356	SUBCLONAL	1	TRUE	1	0.339405299534912	2		632	1203	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920179	1920179	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	84	707	1	ENST00000382891.5:c.1239G>C	p.Glu413Asp	p.E413D	ENST00000382891	NM_133335.3	413	gaG/gaC	5/22	1	2	FACETS	0.376	0.331	0.425	0.376	0.331	0.425	SUBCLONAL	1	TRUE	1	0.339405299534912	2		708	1316	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129917	55129917	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	123	581	2	ENST00000257290.5:c.451C>A	p.Arg151Ser	p.R151S	ENST00000257290	NM_006206.4	151	Cgc/Agc	4/23	1	2	FACETS	0.635	0.572	0.701	0.635	0.572	0.701	SUBCLONAL	1	TRUE	1	0.339405299534912	2		583	1142	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129957	55129957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	120	661	1	ENST00000257290.5:c.491G>A	p.Ser164Asn	p.S164N	ENST00000257290	NM_006206.4	164	aGt/aAt	4/23	1	2	FACETS	0.635	0.572	0.702	0.635	0.572	0.702	SUBCLONAL	1	TRUE	1	0.339405299534912	2		662	1113	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55960973	55960973	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	52	321	0	ENST00000263923.4:c.2967G>T	p.Glu989Asp	p.E989D	ENST00000263923	NM_002253.2	989	gaG/gaT	21/30	1	2	FACETS	0.429	0.364	0.5	0.429	0.364	0.5	SUBCLONAL	1	TRUE	1	0.339405299534912	2		321	715	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99802246	99802246	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	34	221	0	ENST00000280892.6:c.647G>T	p.Gly216Val	p.G216V	ENST00000280892	NM_001130678.1	216	gGt/gTt	7/7	1	2	FACETS	0.406	0.331	0.491	0.406	0.331	0.491	SUBCLONAL	1	TRUE	1	0.339405299534912	2		221	493	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067094	143067094	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	119	443	0	ENST00000262992.4:c.1619A>T	p.Asp540Val	p.D540V	ENST00000262992	NM_001101669.1	540	gAc/gTc	16/24	1	2	FACETS	0.761	0.686	0.841	0.761	0.686	0.841	SUBCLONAL	1	TRUE	1	0.339405299534912	2		443	921	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540001	187540001	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	56	343	0	ENST00000441802.2:c.7739G>C	p.Cys2580Ser	p.C2580S	ENST00000441802	NM_005245.3	2580	tGc/tCc	10/27	0.339405299534912	1	FACETS	0.384	0.328	0.445	0.384	0.328	0.445	SUBCLONAL	1	TRUE	0	0.339405299534912	1		343	714	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501449	149501449	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs750066915	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	126	582	0	ENST00000261799.4:c.2338C>A	p.Pro780Thr	p.P780T	ENST00000261799	NM_002609.3	780	Ccc/Acc	16/23	1	2	FACETS	0.659	0.595	0.726	0.659	0.595	0.726	SUBCLONAL	1	TRUE	1	0.339405299534912	2		582	1127	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805656	32805656	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1214	92	652	0	ENST00000374899.4:c.355C>G	p.Leu119Val	p.L119V	ENST00000374899	NM_018833.2	119	Ctg/Gtg	2/12	1	2	FACETS	0.415	0.367	0.467	0.415	0.367	0.467	SUBCLONAL	1	TRUE	1	0.339405299534912	2		652	1306	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099233	157099233	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	62	476	0	ENST00000346085.5:c.170C>G	p.Ser57Trp	p.S57W	ENST00000346085	NM_020732.3	57	tCg/tGg	1/20	1	2	FACETS	0.355	0.305	0.409	0.355	0.305	0.409	SUBCLONAL	1	TRUE	1	0.339405299534912	2		476	1030	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431634	6431634	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	115	390	1	ENST00000356142.4:c.187G>T	p.Asp63Tyr	p.D63Y	ENST00000356142	NM_018890.3	63	Gat/Tat	3/7	1	2	FACETS	0.758	0.682	0.838	0.758	0.682	0.838	SUBCLONAL	1	TRUE	1	0.339405299534912	2		391	894	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729265	41729265	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	94	352	0	ENST00000242208.4:c.1264del	p.Glu422SerfsTer26	p.E422Sfs*26	ENST00000242208	NM_002192.2	422	Gag/ag	3/3	1	2	FACETS	0.685	0.609	0.766	0.685	0.609	0.766	SUBCLONAL	1	TRUE	1	0.339405299534912	2		352	809	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729332	41729332	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	107	468	0	ENST00000242208.4:c.1197G>T	p.Met399Ile	p.M399I	ENST00000242208	NM_002192.2	399	atG/atT	3/3	1	2	FACETS	0.624	0.558	0.693	0.624	0.558	0.693	SUBCLONAL	1	TRUE	1	0.339405299534912	2		468	1011	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392055	81392055	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	105	368	0	ENST00000222390.5:c.222T>A	p.Cys74Ter	p.C74*	ENST00000222390	NM_000601.4	74	tgT/tgA	2/18	1	2	FACETS	0.664	0.594	0.738	0.664	0.594	0.738	SUBCLONAL	1	TRUE	1	0.339405299534912	2		368	932	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434571	140434571	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	21	134	0	ENST00000288602.6:c.2128-1G>C		p.X710_splice	ENST00000288602	NM_004333.4	710			1	2	FACETS	0.334	0.256	0.424	0.334	0.256	0.424	SUBCLONAL	1	TRUE	1	0.339405299534912	2		134	371	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089819	5089819	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	105	373	0	ENST00000381652.3:c.2717A>G	p.Gln906Arg	p.Q906R	ENST00000381652	NM_004972.3	906	cAg/cGg	20/25	0.339405299534912	1	FACETS	0.584	0.522	0.649	0.584	0.522	0.649	SUBCLONAL	1	TRUE	0	0.339405299534912	1		373	880	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504371	8504371	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	201	504	0	ENST00000356435.5:c.1712G>T	p.Arg571Met	p.R571M	ENST00000356435		571	aGg/aTg	12/35	0.339405299534912	1	FACETS	0.897	0.831	0.966	0.897	0.831	0.966	CLONAL	1	TRUE	0	0.339405299534912	1		504	1096	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246458	53246458	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	133	505	0	ENST00000375401.3:c.524A>T	p.Gln175Leu	p.Q175L	ENST00000375401	NM_004187.3	175	cAg/cTg	5/26	0.339405299534912	1	FACETS	0.73	0.662	0.8	0.73	0.662	0.8	SUBCLONAL	1	TRUE	0	0.339405299534912	1		505	892	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333719	70333719	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	73	441	0	ENST00000373644.4:c.1624G>C	p.Asp542His	p.D542H	ENST00000373644	NM_030625.2	542	Gac/Cac	2/12	NA	2	FACETS	0.402	0.35	0.458			1	INDETERMINATE	1	TRUE	NA	0.339405299534912	2		441	1070	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975602	26975602	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	26	210	0	ENST00000381527.3:c.1111-1G>T		p.X371_splice	ENST00000381527	NM_001260.1	371			1	2	FACETS	0.311	0.246	0.387	0.311	0.246	0.387	SUBCLONAL	1	TRUE	1	0.339405299534912	2		210	492	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907118	32907118	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	73	399	0	ENST00000380152.3:c.1503C>G	p.Ile501Met	p.I501M	ENST00000380152		501	atC/atG	10/27	1	2	FACETS	0.47	0.41	0.535	0.47	0.41	0.535	SUBCLONAL	1	TRUE	1	0.339405299534912	2		399	916	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945213	32945213	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782010	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	58	458	0	ENST00000380152.3:c.8608C>T	p.Gln2870Ter	p.Q2870*	ENST00000380152		2870	Cag/Tag	20/27	1	2	FACETS	0.322	0.275	0.373	0.322	0.275	0.373	SUBCLONAL	1	TRUE	1	0.339405299534912	2		458	1061	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954267	32954267	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs879255472	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	52	428	2	ENST00000380152.3:c.9241G>T	p.Val3081Phe	p.V3081F	ENST00000380152		3081	Gtt/Ttt	24/27	1	2	FACETS	0.324	0.275	0.378	0.324	0.275	0.378	SUBCLONAL	1	TRUE	1	0.339405299534912	2		430	946	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244684	41244684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1391	84	668	1	ENST00000357654.3:c.2864C>T	p.Ser955Leu	p.S955L	ENST00000357654	NM_007294.3	955	tCa/tTa	10/23	0.188927176939744	2	FACETS	0.336	0.295	0.38	0.168	0.147	0.19	INDETERMINATE	1	TRUE	0	0.339405299534912	2		669	1475	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375543	15375543	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1312	205	828	0	ENST00000263377.2:c.884C>G	p.Thr295Ser	p.T295S	ENST00000263377	NM_058243.2	295	aCc/aGc	6/20	0.339405299534912	1	FACETS	0.661	0.611	0.713	0.661	0.611	0.713	SUBCLONAL	1	TRUE	0	0.339405299534912	1		828	1517	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259527	89259527	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs754158548	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	46	405	0	ENST00000336596.2:c.671T>C	p.Val224Ala	p.V224A	ENST00000336596	NM_005233.5	224	gTg/gCg	3/17	1	2	FACETS	0.306	0.257	0.361	0.306	0.257	0.361	SUBCLONAL	1	TRUE	1	0.339405299534912	2		405	885	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159157	143159157	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	44	279	2	ENST00000262992.4:c.696G>T	p.Lys232Asn	p.K232N	ENST00000262992	NM_001101669.1	232	aaG/aaT	10/24	1	2	FACETS	0.398	0.333	0.471	0.398	0.333	0.471	SUBCLONAL	1	TRUE	1	0.339405299534912	2		281	651	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622231	162622231	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	63	376	0	ENST00000366898.1:c.466A>G	p.Arg156Gly	p.R156G	ENST00000366898	NM_004562.2	156	Aga/Gga	4/12	1	2	FACETS	0.425	0.366	0.489	0.425	0.366	0.489	SUBCLONAL	1	TRUE	1	0.339405299534912	2		376	874	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0014397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	331	491	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.929	0.882	0.976	0.929	0.882	0.976	CLONAL	1	TRUE	1	0.848459053980058	2		491	840	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0014397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	309	464	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.263195403519519	3	FACETS	1	0.994	1	0.678	0.643	0.714	INDETERMINATE	1	TRUE	1	0.848459053980058	3		464	765	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0014397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	301	821	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.263195403519519	3	FACETS	1	0.994	1	0.727	0.69	0.765	INDETERMINATE	1	TRUE	1	0.848459053980058	3		821	695	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798153	42798153	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	177	885	0	ENST00000575354.2:c.4108del	p.Val1370CysfsTer45	p.V1370Cfs*45	ENST00000575354	NM_015125.3	1369	gaG/ga	17/20	0.439245255902542	1	FACETS	0.327	0.302	0.353	0.327	0.302	0.353	INDETERMINATE	1	TRUE	0	0.848459053980058	1		885	734	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593657	55593679	+	protein_altering_variant	In_Frame_Del	DEL	CAACTTCCTTATGATCACAAATG	CAACTTCCTTATGATCACAAATG	TT	novel	NA	P-0014399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	291	499	2	ENST00000288135.5:c.1723_1745delinsTT	p.Gln575_Trp582delinsLeu	p.Q575_W582delinsL	ENST00000288135	NM_000222.2	575	CAACTTCCTTATGATCACAAATGg/TTg	11/21	0.90605710245453	1	FACETS	0.885	0.852	0.916	0.885	0.852	0.916	CLONAL	1	TRUE	0	0.90605710245453	1		501	397	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778122	135778123	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0014399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	438	497	0	ENST00000298552.3:c.2260dup	p.Leu754ProfsTer7	p.L754Pfs*7	ENST00000298552	NM_001162426.1	754	ctg/cCtg	18/23	0.90605710245453	1	FACETS	0.928	0.902	0.953	0.928	0.902	0.953	CLONAL	1	TRUE	0	0.90605710245453	1		497	570	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553478	29553478	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781807	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	436	488	4	ENST00000356175.3:c.2033del	p.Pro678ArgfsTer10	p.P678Rfs*10	ENST00000356175	NM_000267.3	676	aCc/ac	18/57	0.379715401588231	2	FACETS	0.853	0.814	0.892	0.853	0.814	0.892	CLONAL	2	TRUE	0	0.42797479344813	2		492	1195	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	433	567	3	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	0.379715401588231	2	FACETS	1	0.996	1	0.736	0.702	0.772	CLONAL	1	TRUE	0	0.42797479344813	2		570	1374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576910	7576910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	529	557	0	ENST00000269305.4:c.936del	p.Ser313AlafsTer32	p.S313Afs*32	ENST00000269305	NM_001126112.2	312	acC/ac	9/11	0.379715401588231	2	FACETS	0.983	0.945	1	0.983	0.945	1	CLONAL	2	TRUE	0	0.42797479344813	2		557	1257	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434940	49434940	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	208	425	0	ENST00000301067.7:c.6613del	p.Ala2205ProfsTer59	p.A2205Pfs*59	ENST00000301067	NM_003482.3	2205	Gcc/cc	31/54	1	2	FACETS	0.869	0.806	0.935	0.869	0.806	0.935	CLONAL	1	TRUE	1	0.42797479344813	2		425	1118	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597792	43597793	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CG	CG	AC	novel	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	148	478	0	ENST00000355710.3:c.340_341delinsAC	p.Arg114Thr	p.R114T	ENST00000355710	NM_020975.4	114	CGc/ACc	3/20	1	2	FACETS	0.695	0.634	0.759	0.695	0.634	0.759	SUBCLONAL	1	TRUE	1	0.42797479344813	2		478	995	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151824	108151824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200765255	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	180	394	0	ENST00000278616.4:c.3505G>A	p.Glu1169Lys	p.E1169K	ENST00000278616	NM_000051.3	1169	Gaa/Aaa	24/63	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.42797479344813	2		394	800	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103510703	103510703	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	152	364	0	ENST00000355739.4:c.607G>T	p.Glu203Ter	p.E203*	ENST00000355739	NM_000123.3	203	Gaa/Taa	6/15	1	2	FACETS	0.913	0.836	0.993	0.913	0.836	0.993	CLONAL	1	TRUE	1	0.42797479344813	2		364	778	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871748	35871748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	230	387	2	ENST00000216797.5:c.758C>T	p.Pro253Leu	p.P253L	ENST00000216797	NM_020529.2	253	cCc/cTc	5/6	1	2	FACETS	0.934	0.87	1	0.934	0.87	1	CLONAL	1	TRUE	1	0.42797479344813	2		389	1151	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678404	88678404	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	225	645	1	ENST00000360948.2:c.1132C>A	p.Leu378Ile	p.L378I	ENST00000360948	NM_001012338.2	378	Ctc/Atc	9/19	1	2	FACETS	0.782	0.726	0.839	0.782	0.726	0.839	SUBCLONAL	1	TRUE	1	0.42797479344813	2		646	1345	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680792	88680792	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	189	450	1	ENST00000360948.2:c.465G>T	p.Leu155Phe	p.L155F	ENST00000360948	NM_001012338.2	155	ttG/ttT	6/19	1	2	FACETS	0.912	0.843	0.984	0.912	0.843	0.984	CLONAL	1	TRUE	1	0.42797479344813	2		451	968	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858026	9858026	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1177482891	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	151	426	0	ENST00000330684.3:c.3375G>C	p.Glu1125Asp	p.E1125D	ENST00000330684	NM_001134407.1	1125	gaG/gaC	13/13	1	2	FACETS	0.753	0.688	0.821	0.753	0.688	0.821	SUBCLONAL	1	TRUE	1	0.42797479344813	2		426	937	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273958	10273958	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	285	676	1	ENST00000330684.3:c.311C>A	p.Thr104Lys	p.T104K	ENST00000330684	NM_001134407.1	104	aCg/aAg	2/13	1	2	FACETS	0.943	0.884	1	0.943	0.884	1	CLONAL	1	TRUE	1	0.42797479344813	2		677	1413	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650677	67650677	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	213	474	0	ENST00000264010.4:c.982G>T	p.Asp328Tyr	p.D328Y	ENST00000264010	NM_006565.3	328	Gac/Tac	5/12	1	2	FACETS	0.88	0.817	0.946	0.88	0.817	0.946	CLONAL	1	TRUE	1	0.42797479344813	2		474	1131	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831582	72831582	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	264	599	0	ENST00000268489.5:c.4999A>G	p.Asn1667Asp	p.N1667D	ENST00000268489	NM_006885.3	1667	Aat/Gat	9/10	1	2	FACETS	0.996	0.932	1	0.996	0.932	1	CLONAL	1	TRUE	1	0.42797479344813	2		599	1239	SUCCESS
YES1	7525	MSKCC	GRCh37	18	732914	732914	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1384930568	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	228	591	2	ENST00000314574.4:c.1343G>A	p.Arg448Gln	p.R448Q	ENST00000314574	NM_005433.3	448	cGg/cAg	11/12	1	2	FACETS	0.907	0.844	0.972	0.907	0.844	0.972	CLONAL	1	TRUE	1	0.42797479344813	2		593	1175	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210417	2210417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	257	489	0	ENST00000398665.3:c.1024C>T	p.Arg342Trp	p.R342W	ENST00000398665	NM_032482.2	342	Cgg/Tgg	13/28	0.42797479344813	1	FACETS	0.997	0.935	1	0.997	0.935	1	CLONAL	1	TRUE	0	0.42797479344813	1		489	947	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123682	11123682	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	269	491	0	ENST00000358026.2:c.2332G>A	p.Ala778Thr	p.A778T	ENST00000358026	NM_001128849.1	778	Gcc/Acc	16/36	0.42797479344813	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.42797479344813	1		491	963	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054605	13054607	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs573652087	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	214	358	1	ENST00000316448.5:c.1142_1144del	p.Glu381del	p.E381del	ENST00000316448	NM_004343.3	378	GAG/-	9/9	0.42797479344813	1	FACETS	0.946	0.881	1	0.946	0.881	1	CLONAL	1	TRUE	0	0.42797479344813	1		359	831	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068368	26068369	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	141	364	0	ENST00000435504.4:c.121_122del	p.Glu41ArgfsTer26	p.E41Rfs*26	ENST00000435504		41	GAa/a	2/13	1	2	FACETS	0.91	0.83	0.993	0.91	0.83	0.993	CLONAL	1	TRUE	1	0.42797479344813	2		364	724	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026911	48026912	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587780670	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	117	259	0	ENST00000234420.5:c.1794dup	p.Gly599ArgfsTer8	p.G599Rfs*8	ENST00000234420	NM_000179.2	597	gaa/gAaa	4/10	1	2	FACETS	0.873	0.789	0.962	0.873	0.789	0.962	CLONAL	1	TRUE	1	0.42797479344813	2		259	626	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128028968	128028971	+	frameshift_variant	Frame_Shift_Del	DEL	CCAT	CCAT	AAA	novel	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	211	506	1	ENST00000285398.2:c.1886_1889delinsTTT	p.His629LeufsTer12	p.H629Lfs*12	ENST00000285398	NM_000122.1	629	cATGGt/cTTTt	12/15	1	2	FACETS	0.892	0.827	0.958	0.892	0.827	0.958	CLONAL	1	TRUE	1	0.42797479344813	2		507	1106	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728500	190728500	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs139932286	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	141	416	2	ENST00000441310.2:c.1888C>T	p.Arg630Ter	p.R630*	ENST00000441310	NM_000534.4	630	Cga/Tga	10/13	1	2	FACETS	0.935	0.853	1	0.935	0.853	1	CLONAL	1	TRUE	1	0.42797479344813	2		418	705	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225360560	225360561	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	73	171	0	ENST00000264414.4:c.1830dup	p.Tyr611IlefsTer4	p.Y611Ifs*4	ENST00000264414	NM_003590.4	610	-/A	13/16	1	2	FACETS	0.956	0.841	1	0.956	0.841	1	CLONAL	1	TRUE	1	0.42797479344813	2		171	357	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37038115	37038115	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs63751094	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	101	195	0	ENST00000231790.2:c.122A>G	p.Asp41Gly	p.D41G	ENST00000231790	NM_000249.3	41	gAt/gGt	2/19	0.416614285551315	1	FACETS	0.971	0.875	1	0.971	0.875	1	CLONAL	1	TRUE	0	0.42797479344813	1		195	382	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851724	134851724	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	256	390	0	ENST00000398015.3:c.1130T>A	p.Val377Glu	p.V377E	ENST00000398015	NM_004441.4	377	gTg/gAg	5/16	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.42797479344813	2		390	980	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964328	55964328	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	155	401	0	ENST00000263923.4:c.2485T>G	p.Phe829Val	p.F829V	ENST00000263923	NM_002253.2	829	Ttc/Gtc	17/30	NA	2	FACETS	0.956	0.876	1			1	INDETERMINATE	1	TRUE	NA	0.42797479344813	2		401	758	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226092	226092	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	185	414	1	ENST00000264932.6:c.551G>T	p.Gly184Val	p.G184V	ENST00000264932	NM_004168.2	184	gGg/gTg	5/15	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.42797479344813	2		415	853	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753151	57753152	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	149	237	0	ENST00000274289.3:c.864_865del	p.Tyr289Ter	p.Y289*	ENST00000274289	NM_006622.3	288	acTTat/acat	7/14	0.42797479344813	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.42797479344813	1		237	506	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670703	86670703	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	91	206	0	ENST00000274376.6:c.1984del	p.Thr662GlnfsTer16	p.T662Qfs*16	ENST00000274376	NM_002890.2	661	Aaa/aa	15/25	0.42797479344813	1	FACETS	0.986	0.884	1	0.986	0.884	1	CLONAL	1	TRUE	0	0.42797479344813	1		206	339	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271243	26271243	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	174	353	0	ENST00000305910.3:c.370G>T	p.Asp124Tyr	p.D124Y	ENST00000305910	NM_003534.2	124	Gac/Tac	1/1	NA	2	FACETS	0.898	0.827	0.973			1	INDETERMINATE	1	TRUE	NA	0.42797479344813	2		353	905	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663622	117663622	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752499456	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	146	447	0	ENST00000368508.3:c.4610C>T	p.Ser1537Leu	p.S1537L	ENST00000368508	NM_002944.2	1537	tCa/tTa	28/43	0.42797479344813	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.42797479344813	1		447	527	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526608	106526608	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	154	336	0	ENST00000359195.3:c.2901C>A	p.His967Gln	p.H967Q	ENST00000359195	NM_002649.2	967	caC/caA	10/11	1	2	FACETS	0.971	0.89	1	0.971	0.89	1	CLONAL	1	TRUE	1	0.42797479344813	2		336	741	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002822	69002822	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	177	230	0	ENST00000288368.4:c.2122G>T	p.Ala708Ser	p.A708S	ENST00000288368	NM_024870.2	708	Gct/Tct	20/40	0.379859087968678	3	FACETS	0.93	0.863	0.999	0.93	0.863	0.999	CLONAL	2	TRUE	1	0.42797479344813	3		230	540	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517944	8517944	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	135	317	1	ENST00000356435.5:c.1447G>T	p.Val483Leu	p.V483L	ENST00000356435		483	Gtg/Ttg	10/35	0.42797479344813	1	FACETS	0.856	0.782	0.934	0.856	0.782	0.934	CLONAL	1	TRUE	0	0.42797479344813	1		318	579	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185544	27185545	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1262	228	563	0	ENST00000380036.4:c.1250dup	p.Asp418Ter	p.D418*	ENST00000380036	NM_000459.3	415	ctc/ctCc	9/23	0.313209972174913	3	FACETS	0.868	0.807	0.932	0.434	0.403	0.466	CLONAL	1	TRUE	1	0.42797479344813	3		563	1490	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137321073	137321073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768721235	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	203	385	0	ENST00000481739.1:c.1030G>A	p.Ala344Thr	p.A344T	ENST00000481739	NM_002957.4	344	Gcc/Acc	7/10	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.42797479344813	2		385	943	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855036	76855036	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	121	385	0	ENST00000373344.5:c.5800G>T	p.Gly1934Trp	p.G1934W	ENST00000373344	NM_000489.3	1934	Ggg/Tgg	25/35	1	2	FACETS	0.915	0.829	1	0.915	0.829	1	CLONAL	1	TRUE	1	0.42797479344813	2		385	618	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920253	76920253	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	143	331	0	ENST00000373344.5:c.3824T>C	p.Met1275Thr	p.M1275T	ENST00000373344	NM_000489.3	1275	aTg/aCg	11/35	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.42797479344813	2		331	601	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952081	76952081	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	121	385	1	ENST00000373344.5:c.354G>A	p.Met118Ile	p.M118I	ENST00000373344	NM_000489.3	118	atG/atA	5/35	1	2	FACETS	0.818	0.74	0.9	0.818	0.74	0.9	CLONAL	1	TRUE	1	0.42797479344813	2		386	691	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224766	123224766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	181	514	0	ENST00000218089.9:c.3530G>A	p.Arg1177Lys	p.R1177K	ENST00000218089	NM_001042749.1	1177	aGa/aAa	32/35	1	2	FACETS	0.784	0.722	0.848	0.784	0.722	0.848	SUBCLONAL	1	TRUE	1	0.42797479344813	2		514	1079	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0014459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	27	394	0	ENST00000311936.3:c.34_35delinsCT	p.Gly12Leu	p.G12L	ENST00000311936	NM_004985.3	12	GGt/CTt	2/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		394	678	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012922	176012922	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	163	443	0	ENST00000367669.3:c.1454T>G	p.Leu485Arg	p.L485R	ENST00000367669	NM_022457.5	485	cTg/cGg	13/20	0.178712605793095	3	FACETS	1	0.988	1	0.734	0.673	0.797	CLONAL	1	TRUE	1	0.27	3		443	934	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528119	29528122	+	frameshift_variant	Frame_Shift_Del	DEL	TGAT	TGAT	-	novel	NA	P-0014508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	249	463	0	ENST00000356175.3:c.1130_1133del	p.Ile377ThrfsTer9	p.I377Tfs*9	ENST00000356175	NM_000267.3	376	aTGATt/at	10/57	0.208532318432471	3	FACETS	1	0.989	1	0.824	0.772	0.877	CLONAL	2	TRUE	0	0.27	3		463	847	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971345	13971345	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	68	336	0	ENST00000405192.2:c.584A>G	p.Asn195Ser	p.N195S	ENST00000405192	NM_001163147.1	195	aAc/aGc	8/12	0.201847354930746	4	FACETS	0.81	0.703	0.925	0.405	0.351	0.463	CLONAL	1	TRUE	2	0.27	4		336	790	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	901	408	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.547143153745012	5	FACETS	0.902	0.88	0.924			1	CLONAL	4	TRUE	NA	0.69861755912252	5		408	1464	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0014544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	367	655	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.664778502851573	1	FACETS	0.791	0.754	0.829	0.791	0.754	0.829	SUBCLONAL	1	TRUE	0	0.69861755912252	1		655	864	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309784	104309784	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1355	558	548	0	ENST00000369902.3:c.375G>C	p.Lys125Asn	p.K125N	ENST00000369902	NM_016169.3	125	aaG/aaC	3/12	0.615391657266779	5	FACETS	0.855	0.819	0.892			1	CLONAL	2	TRUE	NA	0.69861755912252	5		548	1913	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215595214	215595214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752870879	NA	P-0014544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	181	339	0	ENST00000260947.4:c.1922G>A	p.Arg641Gln	p.R641Q	ENST00000260947	NM_000465.2	641	cGa/cAa	10/11	0.621900423047271	3	FACETS	0.992	0.918	1	0.496	0.459	0.534	CLONAL	1	TRUE	1	0.69861755912252	3		339	705	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739698	46740201	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCTCCAAGGGACTCTGCTTTCTTGGGTCTTTTTAAAAAAATTTTTATTTTTAATTTTTTTTCCCCCTAATCATTGAAGCTTTATTTTCTTGGGTCTCGAATCCCCCTTCAGGTACTTATACGTCCGCCTGGATGGCACGATGTCCATTAAGAAGCGAGCCAAGGTTGTAGAACGCTTCAATAGTCCATCGGTAAATGCACATCCCCGTCCCCACACCACCAATGCAGTATCATCAGAATTAAGGAATGATAGAGAAGCTATAAGGGGTTACCTTGATTTTTTTTTTTTTTAATTCCCCTAGTGGATATAGTAGGATTTGTCTGGTTGGTGATGGCTGGGCTGGAAACTGACTGTGTGTGTTGGGATTGGCTGGCTGGTGAGCAGATAAACTGGTGGTTTTCACAATTGGTACTGAGTAGTATAGAGGCATGAGGGAGGAGCTGGTTGGGCTGAGCAGGATCCCAGTTTAGGCTATAAGAGGTTCCTTTTCTCCTGTTTCTTCT	CTCTCCAAGGGACTCTGCTTTCTTGGGTCTTTTTAAAAAAATTTTTATTTTTAATTTTTTTTCCCCCTAATCATTGAAGCTTTATTTTCTTGGGTCTCGAATCCCCCTTCAGGTACTTATACGTCCGCCTGGATGGCACGATGTCCATTAAGAAGCGAGCCAAGGTTGTAGAACGCTTCAATAGTCCATCGGTAAATGCACATCCCCGTCCCCACACCACCAATGCAGTATCATCAGAATTAAGGAATGATAGAGAAGCTATAAGGGGTTACCTTGATTTTTTTTTTTTTTAATTCCCCTAGTGGATATAGTAGGATTTGTCTGGTTGGTGATGGCTGGGCTGGAAACTGACTGTGTGTGTTGGGATTGGCTGGCTGGTGAGCAGATAAACTGGTGGTTTTCACAATTGGTACTGAGTAGTATAGAGGCATGAGGGAGGAGCTGGTTGGGCTGAGCAGGATCCCAGTTTAGGCTATAAGAGGTTCCTTTTCTCCTGTTTCTTCT	-	novel	NA	P-0014544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	70	42	0	ENST00000371975.4:c.1611-110_1690-7del		p.X537_splice	ENST00000371975	NM_003579.3	537		15/18	0.615391657266779	5	FACETS	0.844	0.755	0.935			1	CLONAL	3	TRUE	NA	0.69861755912252	5		42	162	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451183	70451183	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	569	489	0	ENST00000373644.4:c.6023G>T	p.Gly2008Val	p.G2008V	ENST00000373644	NM_030625.2	2008	gGg/gTg	12/12	0.615391657266779	5	FACETS	0.978	0.939	1			1	CLONAL	2	TRUE	NA	0.69861755912252	5		489	1705	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129017	30129017	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	308	560	0	ENST00000263025.4:c.749A>G	p.Tyr250Cys	p.Y250C	ENST00000263025	NM_002746.2	250	tAc/tGc	5/9	0.526414200479418	3	FACETS	0.914	0.86	0.969			1	CLONAL	1	TRUE	NA	0.69861755912252	3		560	1302	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89806450	89806450	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	302	563	0	ENST00000389301.3:c.3886G>C	p.Glu1296Gln	p.E1296Q	ENST00000389301	NM_000135.2	1296	Gag/Cag	39/43	0.612242506131144	2	FACETS	0.843	0.795	0.892	0.421	0.397	0.446	CLONAL	1	TRUE	0	0.69861755912252	2		563	1026	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41276110	41276110	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs778775133	NA	P-0014544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1185	256	394	0	ENST00000357654.3:c.4G>T	p.Asp2Tyr	p.D2Y	ENST00000357654	NM_007294.3	2	Gat/Tat	2/23	0.603360784638638	4	FACETS	0.864	0.807	0.923	0.432	0.403	0.462	CLONAL	1	TRUE	2	0.69861755912252	4		394	1441	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919480	78919480	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	292	573	0	ENST00000306801.3:c.3039G>C	p.Leu1013Phe	p.L1013F	ENST00000306801	NM_020761.2	1013	ttG/ttC	26/34	0.598650312677099	3	FACETS	0.822	0.772	0.873	0.411	0.386	0.437	CLONAL	1	TRUE	1	0.69861755912252	3		573	1373	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736142	204736142	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	205	313	0	ENST00000302823.3:c.499C>A	p.Leu167Ile	p.L167I	ENST00000302823	NM_005214.4	167	Ctt/Att	3/4	0.621900423047271	3	FACETS	0.994	0.924	1	0.497	0.462	0.533	CLONAL	1	TRUE	1	0.69861755912252	3		313	797	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383257	31383257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	252	491	0	ENST00000328111.2:c.1169C>T	p.Ser390Phe	p.S390F	ENST00000328111	NM_006892.3	390	tCt/tTt	11/23	0.598650312677099	3	FACETS	0.817	0.764	0.872	0.409	0.382	0.436	CLONAL	1	TRUE	1	0.69861755912252	3		491	1191	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264656	46264656	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	107	196	0	ENST00000371998.3:c.1526C>G	p.Ser509Cys	p.S509C	ENST00000371998		509	tCt/tGt	12/23	0.598650312677099	3	FACETS	0.822	0.74	0.907	0.411	0.37	0.454	CLONAL	1	TRUE	1	0.69861755912252	3		196	503	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265142	46265142	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	161	249	0	ENST00000371998.3:c.2012C>G	p.Ser671Cys	p.S671C	ENST00000371998		671	tCc/tGc	12/23	0.598650312677099	3	FACETS	0.919	0.845	0.995	0.459	0.422	0.498	CLONAL	1	TRUE	1	0.69861755912252	3		249	677	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374909	149374909	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	581	577	0	ENST00000360632.3:c.185C>G	p.Ser62Trp	p.S62W	ENST00000360632	NM_015472.4	62	tCg/tGg	2/7	0.599643755798403	4	FACETS	0.913	0.877	0.948	0.608	0.585	0.632	CLONAL	2	TRUE	1	0.69861755912252	4		577	1548	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155234	185155234	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0014544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	139	246	0	ENST00000265026.3:c.476-1G>C		p.X159_splice	ENST00000265026	NM_004721.4	159			0.599643755798403	4	FACETS	0.922	0.841	1	0.307	0.28	0.336	CLONAL	1	TRUE	1	0.69861755912252	4		246	733	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198315	185198315	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	400	411	1	ENST00000265026.3:c.2797G>A	p.Glu933Lys	p.E933K	ENST00000265026	NM_004721.4	933	Gag/Aag	13/14	0.599643755798403	4	FACETS	0.89	0.848	0.932	0.593	0.565	0.622	CLONAL	2	TRUE	1	0.69861755912252	4		412	1093	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539454	187539454	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	380	318	0	ENST00000441802.2:c.8286G>T	p.Leu2762Phe	p.L2762F	ENST00000441802	NM_005245.3	2762	ttG/ttT	10/27	0.612242506131144	2	FACETS	0.866	0.833	0.899	0.866	0.833	0.899	CLONAL	2	TRUE	0	0.69861755912252	2		318	628	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064721	80064721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	214	416	0	ENST00000265081.6:c.2152G>A	p.Glu718Lys	p.E718K	ENST00000265081	NM_002439.4	718	Gaa/Aaa	15/24	0.600191064379942	2	FACETS	0.84	0.784	0.898	0.42	0.392	0.449	CLONAL	1	TRUE	0	0.69861755912252	2		416	729	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37141772	37141772	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	279	541	0	ENST00000373509.5:c.847G>C	p.Glu283Gln	p.E283Q	ENST00000373509	NM_002648.3	283	Gaa/Caa	6/6	0.598650312677099	3	FACETS	0.864	0.811	0.919	0.432	0.405	0.46	CLONAL	1	TRUE	1	0.69861755912252	3		541	1247	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080560	5080560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	122	253	0	ENST00000381652.3:c.2311C>T	p.Gln771Ter	p.Q771*	ENST00000381652	NM_004972.3	771	Cag/Tag	18/25	0.598650312677099	3	FACETS	0.758	0.687	0.832	0.379	0.343	0.416	SUBCLONAL	1	TRUE	1	0.69861755912252	3		253	622	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641218	93641218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	170	327	0	ENST00000375746.1:c.1564G>A	p.Asp522Asn	p.D522N	ENST00000375746	NM_001174167.1	522	Gat/Aat	11/14	1	2	FACETS	0.829	0.766	0.894	0.829	0.766	0.894	CLONAL	1	TRUE	1	0.69861755912252	2		327	587	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222966	53222966	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0014544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	391	740	0	ENST00000375401.3:c.4106C>G	p.Ser1369Ter	p.S1369*	ENST00000375401	NM_004187.3	1369	tCa/tGa	24/26	0.680512593270738	1	FACETS	0.809	0.773	0.846	0.809	0.773	0.846	CLONAL	1	TRUE	0	0.69861755912252	1		740	900	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430668	80430668	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	117	536	0	ENST00000286548.4:c.340C>T	p.Arg114Ter	p.R114*	ENST00000286548	NM_002072.3	114	Cga/Tga	3/7	1	2	FACETS	0.9	0.81	0.995	0.9	0.81	0.995	CLONAL	1	TRUE	1	0.269443206999474	2		536	965	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72891539	72891539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755870786	NA	P-0014569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	85	408	1	ENST00000325599.8:c.223C>T	p.Arg75Cys	p.R75C	ENST00000325599	NM_018130.2	75	Cgc/Tgc	3/11	0.269443206999474	4	FACETS	0.808	0.713	0.911	0.404	0.356	0.456	CLONAL	1	TRUE	2	0.269443206999474	4		409	991	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434325	49434325	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1698	260	901	0	ENST00000301067.7:c.7228C>T	p.Arg2410Ter	p.R2410*	ENST00000301067	NM_003482.3	2410	Cga/Tga	31/54	0.243183361055552	4	FACETS	1	0.988	1	0.626	0.583	0.669	CLONAL	1	TRUE	2	0.269443206999474	4		901	1958	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46736381	46736381	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs559500678	NA	P-0014569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	139	461	0	ENST00000371975.4:c.1093C>T	p.Arg365Ter	p.R365*	ENST00000371975	NM_003579.3	365	Cga/Tga	10/18	0.265587886672524	2	FACETS	1	0.964	1	0.558	0.507	0.611	CLONAL	1	TRUE	0	0.269443206999474	2		461	925	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456255	32456255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1594	170	717	0	ENST00000332351.3:c.637C>T	p.Arg213Cys	p.R213C	ENST00000332351	NM_024426.4	213	Cgc/Tgc	1/10	0.269443206999474	4	FACETS	0.908	0.832	0.989	0.454	0.416	0.495	CLONAL	1	TRUE	2	0.269443206999474	4		717	1764	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158594953	158594953	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs750457181	NA	P-0014569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	92	393	0	ENST00000263640.3:c.1394C>T	p.Pro465Leu	p.P465L	ENST00000263640	NM_001105.4	465	cCg/cTg	10/11	0.266812621410533	2	FACETS	0.872	0.774	0.977	0.436	0.387	0.489	CLONAL	1	TRUE	0	0.269443206999474	2		393	783	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46276052	46276052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139321788	NA	P-0014569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1266	112	599	2	ENST00000371998.3:c.3488G>A	p.Arg1163Gln	p.R1163Q	ENST00000371998		1163	cGg/cAg	18/23	0.269443206999474	3	FACETS	0.685	0.613	0.76	0.342	0.306	0.38	SUBCLONAL	1	TRUE	1	0.269443206999474	3		601	1378	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397767	49397767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1649	183	656	0	ENST00000418115.1:c.457G>A	p.Ala153Thr	p.A153T	ENST00000418115	NM_001664.2	153	Gct/Act	5/5	0.269443206999474	4	FACETS	0.941	0.865	1	0.471	0.432	0.511	CLONAL	1	TRUE	2	0.269443206999474	4		656	1832	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521724	89521725	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0014569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	108	418	0	ENST00000336596.2:c.2804_2805del	p.Val935GlyfsTer6	p.V935Gfs*6	ENST00000336596	NM_005233.5	934	gGT/g	16/17	0.269443206999474	4	FACETS	0.969	0.868	1	0.485	0.434	0.539	CLONAL	1	TRUE	2	0.269443206999474	4		418	1050	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798210	32798210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768337366	NA	P-0014569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1298	189	668	0	ENST00000374899.4:c.1469C>T	p.Thr490Met	p.T490M	ENST00000374899	NM_018833.2	490	aCg/aTg	9/12	0.269443206999474	4	FACETS	1	0.981	1	0.599	0.552	0.648	CLONAL	1	TRUE	2	0.269443206999474	4		668	1487	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042129	6042129	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	45	266	0	ENST00000265849.7:c.492del	p.Thr165HisfsTer36	p.T165Hfs*36	ENST00000265849	NM_000535.5	164	tcC/tc	5/15	0.269443206999474	3	FACETS	0.624	0.524	0.736	0.312	0.262	0.368	SUBCLONAL	1	TRUE	1	0.269443206999474	3		266	607	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864648	68864648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	41	171	0	ENST00000288368.4:c.19G>A	p.Gly7Arg	p.G7R	ENST00000288368	NM_024870.2	7	Gga/Aga	1/40	0.269443206999474	5	FACETS	0.822	0.684	0.975	0.274	0.228	0.325	CLONAL	1	TRUE	2	0.269443206999474	5		171	520	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939412	76939412	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	65	611	0	ENST00000373344.5:c.1336G>T	p.Gly446Ter	p.G446*	ENST00000373344	NM_000489.3	446	Gga/Tga	9/35	0.265587886672524	2	FACETS	0.398	0.344	0.458	0.199	0.172	0.229	SUBCLONAL	1	TRUE	0	0.269443206999474	2		611	1211	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0014723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	475	349	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.575980639372067	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.616707208074282	1		349	1064	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9928063	9928063	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	90	304	0	ENST00000330684.3:c.1676T>A	p.Val559Glu	p.V559E	ENST00000330684	NM_001134407.1	559	gTg/gAg	8/13	0.558942424032123	3	FACETS	0.615	0.546	0.688	0.307	0.273	0.344	SUBCLONAL	1	TRUE	1	0.616707208074282	3		304	621	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813908	50813908	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	226	477	0	ENST00000398568.2:c.1462A>G	p.Ile488Val	p.I488V	ENST00000398568	NM_001042412.1	488	Atc/Gtc	8/18	0.558942424032123	3	FACETS	0.742	0.689	0.796	0.371	0.344	0.398	SUBCLONAL	1	TRUE	1	0.616707208074282	3		477	1293	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959159	2959159	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	276	508	0	ENST00000396946.4:c.2357G>T	p.Ser786Ile	p.S786I	ENST00000396946	NM_032415.4	786	aGc/aTc	18/25	0.616707208074282	1	FACETS	0.521	0.489	0.554	0.521	0.489	0.554	SUBCLONAL	1	TRUE	0	0.616707208074282	1		508	1188	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137323819	137323819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1588	479	538	0	ENST00000481739.1:c.1112G>A	p.Arg371His	p.R371H	ENST00000481739	NM_002957.4	371	cGc/cAc	8/10	0.511742532641033	4	FACETS	1	0.993	1	0.304	0.289	0.319	CLONAL	1	TRUE	0	0.616707208074282	4		538	2067	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939038	76939038	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	81	367	0	ENST00000373344.5:c.1710C>G	p.Asn570Lys	p.N570K	ENST00000373344	NM_000489.3	570	aaC/aaG	9/35	0.445063330422448	3	FACETS	0.96	0.852	1	0.48	0.426	0.537	CLONAL	1	TRUE	1	0.616707208074282	3		367	358	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195690	123195690	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	102	529	0	ENST00000218089.9:c.1604G>C	p.Cys535Ser	p.C535S	ENST00000218089	NM_001042749.1	535	tGt/tCt	17/35	0.445063330422448	3	FACETS	0.641	0.574	0.713	0.321	0.287	0.357	SUBCLONAL	1	TRUE	1	0.616707208074282	3		529	675	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0014730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	141	138	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.310299290201702	3	FACETS	1	0.926	1	0.51	0.464	0.559	CLONAL	1	TRUE	1	0.310299290201702	3		138	1029	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106074	8106075	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0014730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	128	435	0	ENST00000346208.3:c.897_898dup	p.Leu300ProfsTer56	p.L300Pfs*56	ENST00000346208		298	-/CC	4/6	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.310299290201702	2		435	788	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118851	115118851	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	105	347	0	ENST00000257566.3:c.490A>G	p.Lys164Glu	p.K164E	ENST00000257566	NM_016569.3	164	Aaa/Gaa	2/8	0.284464448542109	3	FACETS	1	0.939	1	0.533	0.478	0.592	CLONAL	1	TRUE	1	0.310299290201702	3		347	733	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178474	56178475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0014730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	111	252	0	ENST00000399503.3:c.3449dup	p.Ser1151ValfsTer9	p.S1151Vfs*9	ENST00000399503	NM_005921.1	1149	-/A	14/20	0.310299290201702	3	FACETS	0.864	0.781	0.952	0.864	0.781	0.952	CLONAL	2	TRUE	1	0.310299290201702	3		252	478	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184120	56184120	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	122	351	0	ENST00000399503.3:c.4325T>G	p.Met1442Arg	p.M1442R	ENST00000399503	NM_005921.1	1442	aTg/aGg	19/20	0.310299290201702	3	FACETS	1	0.97	1	0.59	0.533	0.65	CLONAL	1	TRUE	1	0.310299290201702	3		351	770	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0014781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	170	543	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	0.440875120310682	2		543	744	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863636	68863637	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0014781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	303	634	0	ENST00000261769.5:c.2376dup	p.Ser793GlufsTer14	p.S793Efs*14	ENST00000261769	NM_004360.3	792	atg/atGg	15/16	0.440875120310682	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.440875120310682	1		634	951	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068294	16068295	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0014781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	14	45	0	ENST00000268712.3:c.616_617del	p.Gln206ThrfsTer4	p.Q206Tfs*4	ENST00000268712	NM_006311.3	206	CAa/a	5/46	0.421314544095645	1	FACETS	0.786	0.583	1	0.786	0.583	1	CLONAL	1	TRUE	0	0.440875120310682	1		45	63	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211580	98211580	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762040036	NA	P-0014781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	169	550	1	ENST00000331920.6:c.3575G>A	p.Arg1192His	p.R1192H	ENST00000331920	NM_000264.3	1192	cGc/cAc	22/24	1	2	FACETS	0.94	0.865	1	0.94	0.865	1	CLONAL	1	TRUE	1	0.440875120310682	2		551	816	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930252	39930252	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	204	575	1	ENST00000378444.4:c.3212T>C	p.Ile1071Thr	p.I1071T	ENST00000378444	NM_001123385.1	1071	aTt/aCt	6/15	1	2	FACETS	0.902	0.836	0.97	0.902	0.836	0.97	CLONAL	1	TRUE	1	0.440875120310682	2		576	1026	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37865628	37865628	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1227559137	NA	P-0014782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	476	724	0	ENST00000269571.5:c.497C>T	p.Thr166Met	p.T166M	ENST00000269571		166	aCg/aTg	4/27	0.824663573619043	3	FACETS	1	0.971	1	0.511	0.488	0.535	CLONAL	1	TRUE	1	0.834419695737386	3		724	1582	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0014804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	307	609	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	1	2	FACETS	1	0.991	1	1	0.996	1	CLONAL	2	TRUE	1	0.215597505195667	2		609	1141	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432139	121432139	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	99	582	1	ENST00000257555.6:c.886G>A	p.Gly296Arg	p.G296R	ENST00000257555		296	Gga/Aga	4/10	1	2	FACETS	0.832	0.741	0.929	0.832	0.741	0.929	CLONAL	1	TRUE	1	0.215597505195667	2		583	1104	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692877	89692878	+	missense_variant	Missense_Mutation	DNP	GC	GC	AG	novel	NA	P-0014804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	74	299	2	ENST00000371953.3:c.361_362delinsAG	p.Ala121Arg	p.A121R	ENST00000371953	NM_000314.4	121	GCa/AGa	5/9	0.164064216748748	2	FACETS	1	0.954	1	0.597	0.523	0.676	CLONAL	1	TRUE	0	0.215597505195667	2		301	575	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14021885	14021885	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	46	309	0	ENST00000311895.7:c.585G>T	p.Arg195Ser	p.R195S	ENST00000311895	NM_005236.2	195	agG/agT	4/11	1	2	FACETS	0.57	0.479	0.672	0.57	0.479	0.672	SUBCLONAL	1	TRUE	1	0.215597505195667	2		309	748	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663431	29663431	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	102	494	0	ENST00000356175.3:c.6024G>C	p.Glu2008Asp	p.E2008D	ENST00000356175	NM_000267.3	2008	gaG/gaC	40/57	1	2	FACETS	0.837	0.746	0.933	0.837	0.746	0.933	CLONAL	1	TRUE	1	0.215597505195667	2		494	1131	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219400	5219400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	115	705	1	ENST00000357368.4:c.3844G>A	p.Gly1282Arg	p.G1282R	ENST00000357368	NM_002850.3	1282	Ggg/Agg	23/38	0.147776359716903	0	FACETS	0.725	0.651	0.804			1	SUBCLONAL	1	TRUE	0	0.215597505195667	0		706	1154	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416789	29416789	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0014804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	34	227	0	ENST00000389048.3:c.4165-1G>A		p.X1389_splice	ENST00000389048	NM_004304.4	1389			0.215597505195667	2	FACETS	0.712	0.581	0.859	0.356	0.29	0.43	SUBCLONAL	1	TRUE	0	0.215597505195667	2		227	443	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266208	41266208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	42	343	1	ENST00000349496.5:c.205G>A	p.Gly69Arg	p.G69R	ENST00000349496	NM_001904.3	69	Gga/Aga	3/15	1	2	FACETS	0.53	0.441	0.629	0.53	0.441	0.629	SUBCLONAL	1	TRUE	1	0.215597505195667	2		344	735	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53254031	53254031	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	22	608	1	ENST00000375401.3:c.41G>T	p.Cys14Phe	p.C14F	ENST00000375401	NM_004187.3	14	tGc/tTc	1/26	0.526834610874034	2	FACETS	0.168	0.13	0.213	0.084	0.065	0.107	SUBCLONAL	1	TRUE	0	0.602060541138666	2		609	435	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937689	76937689	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	171	409	0	ENST00000373344.5:c.3059del	p.Pro1020LeufsTer13	p.P1020Lfs*13	ENST00000373344	NM_000489.3	1020	cCt/ct	9/35	0.526834610874034	2	FACETS	0.983	0.925	1	0.983	0.925	1	CLONAL	2	TRUE	0	0.602060541138666	2		409	289	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911534	101911536	+	missense_variant	Missense_Mutation	TNP	CGG	CGG	TGT	novel	NA	P-0014873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	111	594	2	ENST00000374994.4:c.1459_1461delinsTGT	p.Arg487Cys	p.R487C	ENST00000374994	NM_004612.2	487	CGG/TGT	9/9	0.221736512193422	3	FACETS	1	0.967	1	0.575	0.521	0.632	INDETERMINATE	1	TRUE	1	0.602060541138666	3		596	417	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440906	52440906	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	226	613	0	ENST00000460680.1:c.598G>C	p.Glu200Gln	p.E200Q	ENST00000460680	NM_004656.3	200	Gag/Cag	8/17	0.569970967614961	4	FACETS	0.851	0.796	0.907	0.567	0.53	0.605	CLONAL	2	TRUE	1	0.575823623384592	4		613	727	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193202134	193202134	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	41	273	0	ENST00000367435.3:c.1166C>T	p.Ser389Leu	p.S389L	ENST00000367435	NM_024529.4	389	tCa/tTa	14/17	1	2	FACETS	0.993	0.826	1	0.993	0.826	1	CLONAL	1	TRUE	1	0.13	2		273	635	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951171	48951171	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587778846	NA	P-0014906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	44	432	1	ENST00000267163.4:c.1332+1G>T		p.X444_splice	ENST00000267163	NM_000321.2	444			1	2	FACETS	0.938	0.784	1	0.938	0.784	1	CLONAL	1	TRUE	1	0.13	2		433	722	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447079	187447079	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs759914346	NA	P-0014906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	80	790	0	ENST00000232014.4:c.1114G>T	p.Ala372Ser	p.A372S	ENST00000232014	NM_001130845.1	372	Gcc/Tcc	5/10	1	2	FACETS	0.996	0.873	1	0.996	0.873	1	CLONAL	1	TRUE	1	0.13	2		790	1236	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	423	548	2				ENST00000310581	NM_198253.2	-/1132			0.693837106430838	5	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	2	0.693837106430838	5		550	796	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11297958	11297958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs566273004	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	171	652	0	ENST00000361445.4:c.2150G>A	p.Arg717Gln	p.R717Q	ENST00000361445	NM_004958.3	717	cGa/cAa	13/58	0.587617587460057	4	FACETS	1	0.963	1	0.537	0.495	0.581	CLONAL	1	TRUE	2	0.693837106430838	4		652	777	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873250	71873250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747740530	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	99	478	0	ENST00000357731.5:c.944C>T	p.Pro315Leu	p.P315L	ENST00000357731	NM_173808.2	315	cCa/cTa	7/7	0.587617587460057	4	FACETS	0.828	0.741	0.92	0.414	0.37	0.46	CLONAL	1	TRUE	2	0.693837106430838	4		478	584	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275395	115275395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267597936	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	91	567	2	ENST00000438362.2:c.1018C>T	p.Pro340Ser	p.P340S	ENST00000438362	NM_001242891.1	340	Cct/Tct	10/20	0.587617587460057	4	FACETS	0.838	0.746	0.936	0.419	0.373	0.468	CLONAL	1	TRUE	2	0.693837106430838	4		569	530	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165603	118165603	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148397151	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	90	409	0	ENST00000369448.3:c.113G>A	p.Arg38Gln	p.R38Q	ENST00000369448	NM_017709.3	38	cGa/cAa	2/2	0.587617587460057	4	FACETS	0.828	0.736	0.924	0.414	0.368	0.462	CLONAL	1	TRUE	2	0.693837106430838	4		409	531	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166202	118166202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	206	479	0	ENST00000369448.3:c.712G>A	p.Glu238Lys	p.E238K	ENST00000369448	NM_017709.3	238	Gaa/Aaa	2/2	0.587617587460057	4	FACETS	0.866	0.809	0.924	0.866	0.809	0.924	CLONAL	2	TRUE	2	0.693837106430838	4		479	581	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844401	156844401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	478	924	0	ENST00000524377.1:c.1234G>A	p.Asp412Asn	p.D412N	ENST00000524377	NM_002529.3	412	Gac/Aac	10/17	0.587617587460057	4	FACETS	0.992	0.951	1	0.992	0.951	1	CLONAL	2	TRUE	2	0.693837106430838	4		924	1176	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982370	201982371	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	175	896	3	ENST00000359651.3:c.749_750delinsTT	p.Pro250Leu	p.P250L	ENST00000359651		250	cCC/cTT	6/8	0.587617587460057	4	FACETS	0.824	0.758	0.893	0.412	0.379	0.447	CLONAL	1	TRUE	2	0.693837106430838	4		899	1037	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204513703	204513703	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	84	367	0	ENST00000367182.3:c.713T>C	p.Leu238Ser	p.L238S	ENST00000367182	NM_001278516.1	238	tTg/tCg	9/11	0.587617587460057	4	FACETS	0.998	0.886	1	0.499	0.443	0.558	CLONAL	1	TRUE	2	0.693837106430838	4		367	411	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667404	241667404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	277	651	0	ENST00000366560.3:c.1046C>T	p.Pro349Leu	p.P349L	ENST00000366560	NM_000143.3	349	cCt/cTt	7/10	0.587617587460057	4	FACETS	0.91	0.859	0.962	0.91	0.859	0.962	CLONAL	2	TRUE	2	0.693837106430838	4		651	743	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692872	89692872	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	69	344	0	ENST00000371953.3:c.356T>C	p.Val119Ala	p.V119A	ENST00000371953	NM_000314.4	119	gTt/gCt	5/9	0.587617587460057	4	FACETS	1	0.939	1	0.556	0.488	0.628	CLONAL	1	TRUE	2	0.693837106430838	4		344	303	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298154	123298154	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	114	643	1	ENST00000358487.5:c.700G>T	p.Glu234Ter	p.E234*	ENST00000358487	NM_000141.4	234	Gag/Tag	6/18	0.587617587460057	4	FACETS	0.806	0.726	0.889	0.403	0.363	0.445	CLONAL	1	TRUE	2	0.693837106430838	4		644	691	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135677	64135677	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	224	830	1	ENST00000334205.4:c.1145C>T	p.Pro382Leu	p.P382L	ENST00000334205	NM_003942.2	382	cCt/cTt	10/17	0.670397233110722	3	FACETS	1	0.958	1	0.518	0.483	0.554	CLONAL	1	TRUE	1	0.693837106430838	3		831	839	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137722	64137722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	182	910	2	ENST00000334205.4:c.1823C>T	p.Pro608Leu	p.P608L	ENST00000334205	NM_003942.2	608	cCc/cTc	15/17	0.670397233110722	3	FACETS	0.916	0.847	0.988	0.458	0.423	0.494	CLONAL	1	TRUE	1	0.693837106430838	3		912	771	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	82	479	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	0.670397233110722	3	FACETS	0.677	0.599	0.76	0.339	0.299	0.38	SUBCLONAL	1	TRUE	1	0.693837106430838	3		479	470	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118355603	118355604	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	96	637	1	ENST00000534358.1:c.4245_4246delinsAA	p.Trp1415_Glu1416delinsTer	p.W1415_E1416delins*	ENST00000534358	NM_005933.3	1415	tgGGag/tgAAag	10/36	NA	2	FACETS	0.769	0.691	0.85			1	INDETERMINATE	1	TRUE	NA	0.693837106430838	2		638	360	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404956	404956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773583219	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	102	482	0	ENST00000399788.2:c.4238C>T	p.Ser1413Phe	p.S1413F	ENST00000399788	NM_001042603.1	1413	tCt/tTt	26/28	0.693837106430838	3	FACETS	0.894	0.804	0.988	0.447	0.402	0.494	CLONAL	1	TRUE	1	0.693837106430838	3		482	443	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398050	4398050	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	159	667	0	ENST00000261254.3:c.614G>A	p.Gly205Glu	p.G205E	ENST00000261254	NM_001759.3	205	gGa/gAa	4/5	0.693837106430838	3	FACETS	0.969	0.892	1	0.485	0.446	0.525	CLONAL	1	TRUE	1	0.693837106430838	3		667	637	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552630	18552630	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200787716	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	76	527	0	ENST00000266497.5:c.2041C>T	p.Arg681Cys	p.R681C	ENST00000266497		681	Cgc/Tgc	14/31	0.278690350620177	3	FACETS	0.751	0.662	0.845			1	INDETERMINATE	1	TRUE	NA	0.693837106430838	3		527	393	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245103	46245103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1004162984	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	157	535	0	ENST00000334344.6:c.3197C>T	p.Pro1066Leu	p.P1066L	ENST00000334344	NM_152641.2	1066	cCg/cTg	15/21	0.680297926790261	3	FACETS	1	0.954	1	0.526	0.484	0.57	CLONAL	1	TRUE	1	0.693837106430838	3		535	579	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246102	46246102	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	119	518	0	ENST00000334344.6:c.4196T>A	p.Leu1399Ter	p.L1399*	ENST00000334344	NM_152641.2	1399	tTa/tAa	15/21	0.680297926790261	3	FACETS	1	0.974	1	0.595	0.542	0.65	CLONAL	1	TRUE	1	0.693837106430838	3		518	388	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431409	49431409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1258009682	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	240	613	0	ENST00000301067.7:c.9730G>A	p.Glu3244Lys	p.E3244K	ENST00000301067	NM_003482.3	3244	Gag/Aag	34/54	0.680297926790261	3	FACETS	0.843	0.794	0.891	0.843	0.794	0.891	CLONAL	2	TRUE	1	0.693837106430838	3		613	553	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864636	57864636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	195	772	1	ENST00000228682.2:c.2113G>A	p.Glu705Lys	p.E705K	ENST00000228682	NM_005269.2	705	Gaa/Aaa	12/12	0.587617587460057	4	FACETS	1	0.967	1	0.537	0.498	0.579	CLONAL	1	TRUE	2	0.693837106430838	4		773	886	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811643	102811643	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	171	771	2	ENST00000307046.8:c.541G>A	p.Glu181Lys	p.E181K	ENST00000307046	NM_001111285.1	181	Gag/Aag	4/4	0.670397233110722	3	FACETS	0.951	0.878	1	0.476	0.439	0.514	CLONAL	1	TRUE	1	0.693837106430838	3		773	698	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005411	29005412	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	42	475	0	ENST00000282397.4:c.849_850delinsTT	p.Gln284Ter	p.Q284*	ENST00000282397	NM_002019.4	283	gaCCaa/gaTTaa	7/30	0.58442924619513	5	FACETS	0.547	0.456	0.647	0.182	0.152	0.216	SUBCLONAL	1	TRUE	2	0.693837106430838	5		475	452	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953482	32953483	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	218	498	1	ENST00000380152.3:c.8783_8784delinsTT	p.Ala2928Val	p.A2928V	ENST00000380152		2928	gCC/gTT	22/27	0.58442924619513	5	FACETS	0.9	0.847	0.953	0.9	0.847	0.953	CLONAL	3	TRUE	2	0.693837106430838	5		499	475	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353922	68353922	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	163	435	1	ENST00000487270.1:c.756+1G>A		p.X252_splice	ENST00000487270	NM_133509.3	252			0.587617587460057	4	FACETS	0.802	0.742	0.864	0.802	0.742	0.864	CLONAL	2	TRUE	2	0.693837106430838	4		436	496	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108820	2108821	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	528	796	1	ENST00000219476.3:c.921_922delinsTT	p.Arg308Trp	p.R308W	ENST00000219476	NM_000548.3	307	caCCgg/caTTgg	10/42	0.693837106430838	5	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	2	0.693837106430838	5		797	1012	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2113046	2113046	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	174	779	0	ENST00000219476.3:c.1435T>C	p.Phe479Leu	p.F479L	ENST00000219476	NM_000548.3	479	Ttc/Ctc	14/42	0.693837106430838	5	FACETS	0.969	0.891	1	0.323	0.297	0.351	CLONAL	1	TRUE	2	0.693837106430838	5		779	1056	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225558	2225558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	182	803	1	ENST00000326181.6:c.1561C>T	p.His521Tyr	p.H521Y	ENST00000326181	NM_032271.2	521	Cac/Tac	17/21	0.693837106430838	5	FACETS	0.965	0.89	1	0.322	0.296	0.349	CLONAL	1	TRUE	2	0.693837106430838	5		804	1109	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658569	3658569	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	295	749	0	ENST00000294008.3:c.397C>T	p.Pro133Ser	p.P133S	ENST00000294008	NM_032444.2	133	Ccg/Tcg	2/15	0.693837106430838	5	FACETS	0.877	0.827	0.929	0.585	0.551	0.619	CLONAL	2	TRUE	2	0.693837106430838	5		749	989	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857436	9857436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	229	538	0	ENST00000330684.3:c.3965G>A	p.Gly1322Glu	p.G1322E	ENST00000330684	NM_001134407.1	1322	gGa/gAa	13/13	0.693837106430838	5	FACETS	0.919	0.86	0.979	0.613	0.573	0.653	CLONAL	2	TRUE	2	0.693837106430838	5		538	733	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858016	9858016	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	232	653	0	ENST00000330684.3:c.3385C>T	p.His1129Tyr	p.H1129Y	ENST00000330684	NM_001134407.1	1129	Cac/Tac	13/13	0.693837106430838	5	FACETS	0.886	0.829	0.945	0.591	0.553	0.63	CLONAL	2	TRUE	2	0.693837106430838	5		653	770	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858066	9858066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	142	657	0	ENST00000330684.3:c.3335C>T	p.Ser1112Phe	p.S1112F	ENST00000330684	NM_001134407.1	1112	tCc/tTc	13/13	0.693837106430838	5	FACETS	1	0.948	1	0.352	0.32	0.384	CLONAL	1	TRUE	2	0.693837106430838	5		657	792	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031901	10031901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756447522	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	432	623	1	ENST00000330684.3:c.922G>A	p.Glu308Lys	p.E308K	ENST00000330684	NM_001134407.1	308	Gag/Aag	3/13	0.693837106430838	5	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	2	0.693837106430838	5		624	778	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032408	10032408	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	137	308	0	ENST00000330684.3:c.415G>A	p.Asp139Asn	p.D139N	ENST00000330684	NM_001134407.1	139	Gat/Aat	3/13	0.693837106430838	5	FACETS	1	0.95	1	0.696	0.64	0.753	CLONAL	2	TRUE	2	0.693837106430838	5		308	386	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857530	68857530	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	88	394	0	ENST00000261769.5:c.2164+1G>A		p.X722_splice	ENST00000261769	NM_004360.3	722			0.670397233110722	3	FACETS	0.854	0.762	0.952	0.427	0.381	0.476	CLONAL	1	TRUE	1	0.693837106430838	3		394	400	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984754	72984754	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	154	665	0	ENST00000268489.5:c.2830C>G	p.Leu944Val	p.L944V	ENST00000268489	NM_006885.3	944	Ctc/Gtc	3/10	0.670397233110722	3	FACETS	0.936	0.859	1	0.468	0.429	0.508	CLONAL	1	TRUE	1	0.693837106430838	3		665	639	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993629	72993630	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	141	588	1	ENST00000268489.5:c.415_416delinsAA	p.Gly139Asn	p.G139N	ENST00000268489	NM_006885.3	139	GGc/AAc	2/10	0.670397233110722	3	FACETS	1	0.957	1	0.535	0.49	0.581	CLONAL	1	TRUE	1	0.693837106430838	3		589	512	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805956	89805956	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	149	568	0	ENST00000389301.3:c.3940A>G	p.Arg1314Gly	p.R1314G	ENST00000389301	NM_000135.2	1314	Agg/Ggg	40/43	0.578567895976996	4	FACETS	1	0.944	1			1	CLONAL	1	TRUE	NA	0.693837106430838	4		568	700	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519985	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	180	782	0	ENST00000269305.4:c.857A>T	p.Glu286Val	p.E286V	ENST00000269305	NM_001126112.2	286	gAa/gTa	8/11	0.587617587460057	4	FACETS	0.931	0.858	1	0.465	0.429	0.503	CLONAL	1	TRUE	2	0.693837106430838	4		782	944	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950408	15950408	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	83	554	0	ENST00000268712.3:c.6537-1G>A		p.X2179_splice	ENST00000268712	NM_006311.3	2179			0.587617587460057	4	FACETS	0.725	0.641	0.815	0.362	0.32	0.408	SUBCLONAL	1	TRUE	2	0.693837106430838	4		554	559	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15952196	15952196	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1014515209	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	154	652	0	ENST00000268712.3:c.6499C>T	p.Leu2167Phe	p.L2167F	ENST00000268712	NM_006311.3	2167	Ctc/Ttc	41/46	0.587617587460057	4	FACETS	1	0.946	1	0.521	0.477	0.566	CLONAL	1	TRUE	2	0.693837106430838	4		652	722	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118401	17118401	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	144	690	0	ENST00000285071.4:c.1436G>A	p.Gly479Asp	p.G479D	ENST00000285071	NM_144997.5	479	gGc/gAc	13/14	0.587617587460057	4	FACETS	0.92	0.84	1	0.46	0.42	0.502	CLONAL	1	TRUE	2	0.693837106430838	4		690	764	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670136	29670136	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	97	492	1	ENST00000356175.3:c.7109T>C	p.Val2370Ala	p.V2370A	ENST00000356175	NM_000267.3	2370	gTt/gCt	47/57	0.587617587460057	4	FACETS	0.875	0.783	0.973	0.438	0.391	0.487	CLONAL	1	TRUE	2	0.693837106430838	4		493	541	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683478	29683478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	125	432	0	ENST00000356175.3:c.7553G>A	p.Gly2518Glu	p.G2518E	ENST00000356175	NM_000267.3	2518	gGa/gAa	51/57	0.587617587460057	4	FACETS	0.852	0.78	0.926	0.852	0.78	0.926	CLONAL	2	TRUE	2	0.693837106430838	4		432	358	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40468852	40468852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	148	654	0	ENST00000264657.5:c.2212G>A	p.Gly738Arg	p.G738R	ENST00000264657	NM_139276.2	738	Gga/Aga	23/24	0.587617587460057	4	FACETS	0.893	0.816	0.974	0.447	0.408	0.487	CLONAL	1	TRUE	2	0.693837106430838	4		654	809	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534462	63534462	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	177	662	0	ENST00000307078.5:c.1060-1G>A		p.X354_splice	ENST00000307078	NM_004655.3	354			0.664353536077522	5	FACETS	0.963	0.886	1	0.321	0.295	0.348	CLONAL	1	TRUE	2	0.693837106430838	5		662	1081	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56412913	56412913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	153	425	1	ENST00000348428.3:c.1927C>T	p.Pro643Ser	p.P643S	ENST00000348428	NM_006785.3	643	Cca/Tca	16/17	0.587617587460057	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.693837106430838	4		426	342	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101275	4101275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1262143092	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	350	662	1	ENST00000262948.5:c.532C>T	p.Leu178Phe	p.L178F	ENST00000262948	NM_030662.3	178	Ctc/Ttc	5/11	0.65273442974382	4	FACETS	1	0.971	1	0.685	0.652	0.719	CLONAL	2	TRUE	1	0.693837106430838	4		663	831	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143092	7143093	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	115	656	0	ENST00000302850.5:c.2276_2277delinsAA	p.Arg759Gln	p.R759Q	ENST00000302850	NM_000208.2	759	cGG/cAA	12/22	0.65273442974382	4	FACETS	0.779	0.702	0.86	0.26	0.234	0.287	SUBCLONAL	1	TRUE	1	0.693837106430838	4		656	721	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7174684	7174684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1188187072	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	362	712	1	ENST00000302850.5:c.1033G>A	p.Glu345Lys	p.E345K	ENST00000302850	NM_000208.2	345	Gag/Aag	4/22	0.65273442974382	4	FACETS	1	0.982	1	0.706	0.672	0.739	CLONAL	2	TRUE	1	0.693837106430838	4		713	835	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950418	17950418	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	195	778	0	ENST00000458235.1:c.1309A>G	p.Thr437Ala	p.T437A	ENST00000458235	NM_000215.3	437	Acc/Gcc	10/24	0.65273442974382	4	FACETS	1	0.965	1	0.356	0.33	0.384	CLONAL	1	TRUE	1	0.693837106430838	4		778	891	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744416	41744416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	371	833	0	ENST00000301178.4:c.1036G>A	p.Gly346Arg	p.G346R	ENST00000301178	NM_021913.4	346	Ggg/Agg	8/20	0.65273442974382	4	FACETS	1	0.983	1	0.708	0.675	0.741	CLONAL	2	TRUE	1	0.693837106430838	4		833	853	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051268	128051268	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	131	680	0	ENST00000285398.2:c.55T>C	p.Tyr19His	p.Y19H	ENST00000285398	NM_000122.1	19	Tat/Cat	2/15	0.587617587460057	4	FACETS	0.966	0.879	1	0.483	0.439	0.529	CLONAL	1	TRUE	2	0.693837106430838	4		680	662	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158594119	158594119	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	184	538	1	ENST00000263640.3:c.1454G>A	p.Arg485Lys	p.R485K	ENST00000263640	NM_001105.4	485	aGa/aAa	11/11	0.587617587460057	4	FACETS	0.812	0.755	0.871	0.812	0.755	0.871	CLONAL	2	TRUE	2	0.693837106430838	4		539	553	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209106823	209106824	+	missense_variant	Missense_Mutation	DNP	TA	TA	AG	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	130	706	0	ENST00000345146.2:c.744_745delinsCT	p.Arg249Trp	p.R249W	ENST00000345146	NM_005896.2	248	caTAgg/caCTgg	7/10	0.587617587460057	4	FACETS	0.835	0.758	0.916	0.418	0.379	0.458	CLONAL	1	TRUE	2	0.693837106430838	4		706	760	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530082	212530082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	99	341	1	ENST00000342788.4:c.1837G>A	p.Glu613Lys	p.E613K	ENST00000342788	NM_005235.2	613	Gag/Aag	15/28	0.587617587460057	4	FACETS	1	0.96	1	0.569	0.511	0.629	CLONAL	1	TRUE	2	0.693837106430838	4		342	425	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546835	9546835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	67	416	0	ENST00000353224.5:c.1187C>T	p.Ser396Phe	p.S396F	ENST00000353224	NM_177990.2	396	tCc/tTc	5/10	0.587617587460057	4	FACETS	0.814	0.71	0.925	0.407	0.355	0.463	CLONAL	1	TRUE	2	0.693837106430838	4		416	402	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739064	40739064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780908301	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	133	631	3	ENST00000373198.4:c.3220G>A	p.Val1074Ile	p.V1074I	ENST00000373198	NM_133170.3	1074	Gtt/Att	24/32	0.587617587460057	4	FACETS	0.831	0.756	0.911	0.416	0.378	0.456	CLONAL	1	TRUE	2	0.693837106430838	4		634	781	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739117	40739117	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	249	619	0	ENST00000373198.4:c.3167A>C	p.His1056Pro	p.H1056P	ENST00000373198	NM_133170.3	1056	cAt/cCt	24/32	0.587617587460057	4	FACETS	0.948	0.893	1	0.948	0.893	1	CLONAL	2	TRUE	2	0.693837106430838	4		619	641	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790158	40790158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781621750	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	120	550	0	ENST00000373198.4:c.2573C>T	p.Ser858Phe	p.S858F	ENST00000373198	NM_133170.3	858	tCc/tTc	18/32	0.587617587460057	4	FACETS	0.948	0.858	1	0.474	0.429	0.521	CLONAL	1	TRUE	2	0.693837106430838	4		550	618	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400175	41400175	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	159	680	0	ENST00000373198.4:c.584T>A	p.Phe195Tyr	p.F195Y	ENST00000373198	NM_133170.3	195	tTt/tAt	5/32	0.587617587460057	4	FACETS	1	0.956	1	0.53	0.487	0.575	CLONAL	1	TRUE	2	0.693837106430838	4		680	732	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46255817	46255817	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	100	569	0	ENST00000371998.3:c.429A>T	p.Gln143His	p.Q143H	ENST00000371998		143	caA/caT	6/23	0.587617587460057	4	FACETS	0.842	0.754	0.935	0.421	0.377	0.468	CLONAL	1	TRUE	2	0.693837106430838	4		569	580	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945308	54945308	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	193	312	0	ENST00000312783.6:c.1118T>C	p.Met373Thr	p.M373T	ENST00000312783	NM_198436.1	373	aTg/aCg	10/10	0.587617587460057	4	FACETS	0.908	0.856	0.959	1	0.992	1	CLONAL	3	TRUE	2	0.693837106430838	4		312	346	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755401	39755401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	165	737	1	ENST00000288319.7:c.1364C>T	p.Ser455Leu	p.S455L	ENST00000288319	NM_182918.3	455	tCa/tTa	10/10	0.587617587460057	4	FACETS	1	0.969	1	0.552	0.508	0.598	CLONAL	1	TRUE	2	0.693837106430838	4		738	730	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000004	30000004	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	186	366	0	ENST00000338641.4:c.17C>T	p.Ala6Val	p.A6V	ENST00000338641	NM_000268.3	6	gCt/gTt	1/16	0.664353536077522	5	FACETS	1	0.965	1	0.705	0.657	0.755	CLONAL	2	TRUE	2	0.693837106430838	5		366	517	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712531	52712531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	208	751	1	ENST00000394830.3:c.221G>A	p.Arg74Lys	p.R74K	ENST00000394830	NM_018313.4	74	aGg/aAg	3/30	0.65273442974382	4	FACETS	1	0.98	1	0.383	0.356	0.411	CLONAL	1	TRUE	1	0.693837106430838	4		752	884	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89478288	89478288	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	65	535	1	ENST00000336596.2:c.2107G>A	p.Glu703Lys	p.E703K	ENST00000336596	NM_005233.5	703	Gag/Aag	12/17	0.65273442974382	4	FACETS	0.698	0.606	0.796	0.233	0.202	0.266	SUBCLONAL	1	TRUE	1	0.693837106430838	4		536	455	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149238699	149238699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	347	864	0	ENST00000360632.3:c.1096G>A	p.Gly366Arg	p.G366R	ENST00000360632	NM_015472.4	366	Gga/Aga	7/7	0.65273442974382	4	FACETS	0.982	0.933	1	0.654	0.622	0.687	CLONAL	2	TRUE	1	0.693837106430838	4		864	863	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612073	189612073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142762485	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	593	458	0	ENST00000264731.3:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000264731	NM_003722.4	609	Gaa/Aaa	14/14	0.581894351456596	4	FACETS	0.981	0.959	1	1	0.998	1	CLONAL	4	TRUE	2	0.693837106430838	4		458	738	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913517	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	335	558	0	ENST00000288135.5:c.1676T>C	p.Val559Ala	p.V559A	ENST00000288135	NM_000222.2	559	gTt/gCt	11/21	0.693837106430838	3	FACETS	0.953	0.92	0.984	0.953	0.92	0.984	CLONAL	3	TRUE	0	0.693837106430838	3		558	455	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593630	55593630	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519705	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	380	581	0	ENST00000288135.5:c.1696A>G	p.Asn566Asp	p.N566D	ENST00000288135	NM_000222.2	566	Aac/Gac	11/21	0.693837106430838	3	FACETS	0.962	0.932	0.992	0.962	0.932	0.992	CLONAL	3	TRUE	0	0.693837106430838	3		581	511	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627774	187627774	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1183516785	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	159	648	0	ENST00000441802.2:c.3208C>T	p.Arg1070Ter	p.R1070*	ENST00000441802	NM_005245.3	1070	Cga/Tga	2/27	0.693837106430838	4	FACETS	0.957	0.878	1	0.239	0.219	0.26	CLONAL	1	TRUE	0	0.693837106430838	4		648	811	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963117	38963117	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	108	302	0	ENST00000357387.3:c.1427T>G	p.Leu476Ter	p.L476*	ENST00000357387	NM_152756.3	476	tTa/tGa	17/38	0.693837106430838	5	FACETS	0.838	0.759	0.92	0.559	0.506	0.614	CLONAL	2	TRUE	2	0.693837106430838	5		302	379	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178155	56178155	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	412	546	0	ENST00000399503.3:c.3128C>T	p.Ser1043Phe	p.S1043F	ENST00000399503	NM_005921.1	1043	tCc/tTc	14/20	0.693837106430838	5	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	2	0.693837106430838	5		546	769	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522616	67522619	+	frameshift_variant	Frame_Shift_Del	DEL	TAGC	TAGC	AGT	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	178	503	2	ENST00000274335.5:c.113_116delinsAGT	p.Val38GlufsTer19	p.V38Efs*19	ENST00000274335		38	gTAGCt/gAGTt	1/15	0.693837106430838	5	FACETS	0.753	0.696	0.812	0.502	0.464	0.542	SUBCLONAL	2	TRUE	2	0.693837106430838	5		505	695	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940120	31940120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	180	779	0	ENST00000375333.2:c.262G>A	p.Glu88Lys	p.E88K	ENST00000375333	NM_032454.1	88	Gaa/Aaa	2/8	0.693837106430838	5	FACETS	0.968	0.891	1	0.323	0.297	0.35	CLONAL	1	TRUE	2	0.693837106430838	5		779	1094	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	214	790	0	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	0.693837106430838	5	FACETS	1	0.98	1	0.381	0.353	0.409	CLONAL	1	TRUE	2	0.693837106430838	5		790	1102	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821451	32821452	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	150	755	2	ENST00000354258.4:c.142_143delinsTT	p.Pro48Phe	p.P48F	ENST00000354258	NM_000593.5	48	CCc/TTc	1/11	0.693837106430838	5	FACETS	0.931	0.85	1	0.31	0.283	0.339	CLONAL	1	TRUE	2	0.693837106430838	5		757	948	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015634	112015634	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	159	572	0	ENST00000368678.4:c.1208T>G	p.Ile403Ser	p.I403S	ENST00000368678		403	aTt/aGt	11/13	0.670397233110722	3	FACETS	1	0.978	1	0.58	0.535	0.627	CLONAL	1	TRUE	1	0.693837106430838	3		572	532	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729275	41729275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	180	438	0	ENST00000242208.4:c.1254G>A	p.Met418Ile	p.M418I	ENST00000242208	NM_002192.2	418	atG/atA	3/3	0.693837106430838	6	FACETS	0.903	0.836	0.973	0.602	0.557	0.649	CLONAL	2	TRUE	3	0.693837106430838	6		438	686	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240819	55240819	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	131	895	1	ENST00000275493.2:c.2061+2T>A		p.X687_splice	ENST00000275493	NM_005228.3	687			0.693837106430838	6	FACETS	0.719	0.651	0.791	0.24	0.216	0.264	SUBCLONAL	1	TRUE	3	0.693837106430838	6		896	1254	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509849	106509849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426277818	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	306	682	0	ENST00000359195.3:c.1843G>A	p.Glu615Lys	p.E615K	ENST00000359195	NM_002649.2	615	Gaa/Aaa	2/11	0.693837106430838	7	FACETS	0.985	0.928	1	0.493	0.464	0.522	CLONAL	2	TRUE	3	0.693837106430838	7		682	1224	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520027	106520027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370034420	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	125	383	0	ENST00000359195.3:c.2455G>A	p.Asp819Asn	p.D819N	ENST00000359195	NM_002649.2	819	Gat/Aat	6/11	0.693837106430838	7	FACETS	0.761	0.691	0.836	0.381	0.345	0.418	SUBCLONAL	2	TRUE	3	0.693837106430838	7		383	647	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340015	116340015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	349	418	0	ENST00000397752.3:c.877G>A	p.Glu293Lys	p.E293K	ENST00000397752	NM_000245.2	293	Gaa/Aaa	2/21	0.693837106430838	7	FACETS	1	0.964	1	1	0.964	1	CLONAL	4	TRUE	3	0.693837106430838	7		418	681	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411586	116411586	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	162	461	0	ENST00000397752.3:c.2765A>T	p.Lys922Ile	p.K922I	ENST00000397752	NM_000245.2	922	aAa/aTa	13/21	0.693837106430838	7	FACETS	1	0.923	1	0.501	0.461	0.542	CLONAL	2	TRUE	3	0.693837106430838	7		461	637	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508728	148508728	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs267601395	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	465	481	0	ENST00000320356.2:c.1936T>C	p.Tyr646His	p.Y646H	ENST00000320356	NM_004456.4	646	Tac/Cac	16/20	0.693837106430838	7	FACETS	0.933	0.896	0.971	0.933	0.896	0.971	CLONAL	4	TRUE	3	0.693837106430838	7		481	982	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864598	56864598	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	126	858	0	ENST00000519728.1:c.561T>A	p.Ser187Arg	p.S187R	ENST00000519728	NM_002350.3	187	agT/agA	7/13	0.410967086052194	4	FACETS	0.809	0.733	0.889	0.405	0.366	0.445	INDETERMINATE	1	TRUE	2	0.693837106430838	4		858	760	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56912075	56912075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	233	773	1	ENST00000519728.1:c.1303G>A	p.Glu435Lys	p.E435K	ENST00000519728	NM_002350.3	435	Gaa/Aaa	12/13	0.410967086052194	4	FACETS	0.849	0.796	0.903	0.849	0.796	0.903	INDETERMINATE	2	TRUE	2	0.693837106430838	4		774	670	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956771	68956771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774302685	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	145	758	4	ENST00000288368.4:c.889C>T	p.Arg297Cys	p.R297C	ENST00000288368	NM_024870.2	297	Cgt/Tgt	8/40	0.410967086052194	4	FACETS	0.859	0.784	0.938	0.43	0.392	0.469	INDETERMINATE	1	TRUE	2	0.693837106430838	4		762	824	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989671	68989671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	275	729	2	ENST00000288368.4:c.1609G>T	p.Val537Phe	p.V537F	ENST00000288368	NM_024870.2	537	Gtt/Ttt	15/40	0.410967086052194	4	FACETS	1	0.986	1	1	0.986	1	INDETERMINATE	2	TRUE	2	0.693837106430838	4		731	601	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069599	69069599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	109	704	1	ENST00000288368.4:c.4274C>T	p.Ser1425Phe	p.S1425F	ENST00000288368	NM_024870.2	1425	tCt/tTt	35/40	0.410967086052194	4	FACETS	0.935	0.842	1	0.468	0.421	0.517	INDETERMINATE	1	TRUE	2	0.693837106430838	4		705	569	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341168	8341168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	80	613	0	ENST00000356435.5:c.5048C>T	p.Ser1683Phe	p.S1683F	ENST00000356435		1683	tCc/tTc	30/35	1	2	FACETS	0.776	0.691	0.866	0.776	0.691	0.866	SUBCLONAL	1	TRUE	1	0.693837106430838	2		613	297	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484270	8484270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867884876	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	124	611	0	ENST00000356435.5:c.3262C>T	p.Arg1088Cys	p.R1088C	ENST00000356435		1088	Cgt/Tgt	19/35	1	2	FACETS	0.896	0.818	0.976	0.896	0.818	0.976	CLONAL	1	TRUE	1	0.693837106430838	2		611	399	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499727	8499727	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	140	616	0	ENST00000356435.5:c.2242C>T	p.Gln748Ter	p.Q748*	ENST00000356435		748	Cag/Tag	14/35	1	2	FACETS	0.97	0.892	1	0.97	0.892	1	CLONAL	1	TRUE	1	0.693837106430838	2		616	416	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518111	8518111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	88	469	2	ENST00000356435.5:c.1280G>A	p.Arg427Gln	p.R427Q	ENST00000356435		427	cGa/cAa	10/35	1	2	FACETS	0.869	0.779	0.962	0.869	0.779	0.962	CLONAL	1	TRUE	1	0.693837106430838	2		471	292	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563545	87563545	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	98	564	0	ENST00000277120.3:c.1933C>T	p.Leu645Phe	p.L645F	ENST00000277120		645	Ctc/Ttc	16/19	1	2	FACETS	0.848	0.765	0.935	0.848	0.765	0.935	CLONAL	1	TRUE	1	0.693837106430838	2		564	333	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212173	98212173	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1131690985	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	116	589	0	ENST00000331920.6:c.3499G>A	p.Gly1167Arg	p.G1167R	ENST00000331920	NM_000264.3	1167	Ggg/Agg	21/24	1	2	FACETS	0.779	0.708	0.854	0.779	0.708	0.854	SUBCLONAL	1	TRUE	1	0.693837106430838	2		589	429	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613605	100613605	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	130	315	1	ENST00000308731.7:c.974G>A	p.Gly325Glu	p.G325E	ENST00000308731	NM_000061.2	325	gGg/gAg	11/19	0.578567895976996	2	FACETS	1	0.97	1			1	CLONAL	1	TRUE	NA	0.693837106430838	2		316	336	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858020	152858020	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	100	181	0	ENST00000406277.2:c.595C>T	p.Gln199Ter	p.Q199*	ENST00000406277	NM_152274.4	199	Cag/Tag	6/7	0.578567895976996	2	FACETS	1	0.951	1			1	CLONAL	2	TRUE	NA	0.693837106430838	2		181	141	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	106	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.75	0.677	0.825	0.75	0.677	0.825	SUBCLONAL	1	TRUE	1	0.705289662626134	2		326	401	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144149	11144149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	293	643	1	ENST00000358026.2:c.3730C>T	p.Arg1244Cys	p.R1244C	ENST00000358026	NM_001128849.1	1244	Cgc/Tgc	26/36	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.705289662626134	2		644	820	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	164	456	0				ENST00000310581	NM_198253.2	-/1132			0.137327023774977	4	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.839573853786248	4		456	508	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0014966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	719	553	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.803822221019803	4	FACETS	0.961	0.945	0.975	0.961	0.945	0.975	CLONAL	4	TRUE	0	0.839573853786248	4		553	820	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771562	112771562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1247102305	NA	P-0014966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	362	448	0	ENST00000369452.4:c.1735C>T	p.Arg579Cys	p.R579C	ENST00000369452	NM_007373.3	579	Cgt/Tgt	9/9	0.804402063237667	2	FACETS	0.933	0.905	0.96	0.933	0.905	0.96	CLONAL	2	TRUE	0	0.839573853786248	2		448	462	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135385	30135385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	34	414	2	ENST00000331968.5:c.433C>T	p.Arg145Cys	p.R145C	ENST00000331968	NM_002742.2	145	Cgt/Tgt	3/18	0.804402063237667	2	FACETS	0.146	0.119	0.177	0.073	0.059	0.089	SUBCLONAL	1	TRUE	0	0.839573853786248	2		416	554	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226494	1226494	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752015385	NA	P-0014966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	276	734	2	ENST00000326873.7:c.1150C>T	p.Arg384Trp	p.R384W	ENST00000326873	NM_000455.4	384	Cgg/Tgg	9/10	0.780337959169467	3	FACETS	1	0.974	1	0.53	0.499	0.562	CLONAL	1	TRUE	1	0.839573853786248	3		736	880	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807582	1807582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145183329	NA	P-0014966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	196	720	1	ENST00000260795.2:c.1751C>T	p.Pro584Leu	p.P584L	ENST00000260795		584	cCg/cTg	12/17	1	2	FACETS	0.949	0.887	1	0.949	0.887	1	CLONAL	1	TRUE	1	0.839573853786248	2		721	492	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961796	55961796	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	179	449	0	ENST00000263923.4:c.2765G>A	p.Gly922Glu	p.G922E	ENST00000263923	NM_002253.2	922	gGa/gAa	20/30	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.839573853786248	2		449	413	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	213	456	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.989	0.924	1	0.989	0.924	1	CLONAL	1	TRUE	1	0.699594137780604	2		456	616	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294042	1294042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	516	739	0	ENST00000310581.5:c.959C>T	p.Pro320Leu	p.P320L	ENST00000310581	NM_198253.2	320	cCt/cTt	2/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.699594137780604	2		739	1414	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811603	102811603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	258	461	0	ENST00000307046.8:c.581G>A	p.Gly194Glu	p.G194E	ENST00000307046	NM_001111285.1	194	gGa/gAa	4/4	1	2	FACETS	0.972	0.914	1	0.972	0.914	1	CLONAL	1	TRUE	1	0.699594137780604	2		461	759	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073739	8073740	+	missense_variant	Missense_Mutation	DNP	GA	GA	AG	novel	NA	P-0014969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	129	260	1	ENST00000377482.5:c.919_920delinsCT	p.Ser307Leu	p.S307L	ENST00000377482	NM_018948.3	307	TCg/CTg	4/4	0.386426147763408	1	FACETS	0.563	0.514	0.613	0.563	0.514	0.613	INDETERMINATE	1	TRUE	0	0.699594137780604	1		261	426	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607612	43607612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	338	604	0	ENST00000355710.3:c.1588G>A	p.Glu530Lys	p.E530K	ENST00000355710	NM_020975.4	530	Gag/Aag	8/20	1	2	FACETS	0.906	0.858	0.955	0.906	0.858	0.955	CLONAL	1	TRUE	1	0.699594137780604	2		604	1066	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195362	102195362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	232	392	0	ENST00000263464.3:c.122C>T	p.Ala41Val	p.A41V	ENST00000263464	NM_001165.4	41	gCt/gTt	2/9	1	2	FACETS	0.882	0.825	0.94	0.882	0.825	0.94	CLONAL	1	TRUE	1	0.699594137780604	2		392	752	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526545	66526545	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	232	390	0	ENST00000358598.2:c.1101A>T	p.Lys367Asn	p.K367N	ENST00000358598	NM_212471.2	367	aaA/aaT	11/11	1	2	FACETS	0.862	0.807	0.919	0.862	0.807	0.919	CLONAL	1	TRUE	1	0.699594137780604	2		390	769	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735558	204735558	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	192	424	1	ENST00000302823.3:c.359G>A	p.Arg120Lys	p.R120K	ENST00000302823	NM_005214.4	120	aGg/aAg	2/4	1	2	FACETS	0.744	0.69	0.799	0.744	0.69	0.799	SUBCLONAL	1	TRUE	1	0.699594137780604	2		425	738	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645759	215645759	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0014969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	243	450	1	ENST00000260947.4:c.839T>A	p.Leu280Ter	p.L280*	ENST00000260947	NM_000465.2	280	tTa/tAa	4/11	1	2	FACETS	0.965	0.906	1	0.965	0.906	1	CLONAL	1	TRUE	1	0.699594137780604	2		451	720	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057311	30057312	+	missense_variant	Missense_Mutation	DNP	TC	TC	CT	novel	NA	P-0014969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	246	361	0	ENST00000338641.4:c.793_794delinsCT	p.Ser265Leu	p.S265L	ENST00000338641	NM_000268.3	265	TCg/CTg	8/16	1	2	FACETS	0.936	0.879	0.995	0.936	0.879	0.995	CLONAL	1	TRUE	1	0.699594137780604	2		361	751	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069424	30069424	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	283	456	0	ENST00000338641.4:c.1289T>G	p.Val430Gly	p.V430G	ENST00000338641	NM_000268.3	430	gTg/gGg	12/16	1	2	FACETS	0.961	0.906	1	0.961	0.906	1	CLONAL	1	TRUE	1	0.699594137780604	2		456	842	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39074463	39074463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113585934	NA	P-0014969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	269	381	0	ENST00000357387.3:c.17G>A	p.Arg6His	p.R6H	ENST00000357387	NM_152756.3	6	cGc/cAc	1/38	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.699594137780604	2		381	714	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981339	68981339	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	122	370	0	ENST00000288368.4:c.1411C>T	p.Pro471Ser	p.P471S	ENST00000288368	NM_024870.2	471	Cca/Tca	12/40	1	2	FACETS	0.63	0.571	0.691	0.63	0.571	0.691	SUBCLONAL	1	TRUE	1	0.699594137780604	2		370	554	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0014997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	299	138	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.272148483525883	3	FACETS	0.984	0.931	1	0.984	0.931	1	CLONAL	3	TRUE	0	0.290405343021158	3		138	799	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	176	266	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.261566784196644	4	FACETS	0.953	0.879	1	0.953	0.879	1	CLONAL	2	TRUE	2	0.290405343021158	4		266	821	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803416	1803416	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368831528	NA	P-0014997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	123	836	1	ENST00000260795.2:c.685G>A	p.Val229Ile	p.V229I	ENST00000260795		229	Gtc/Atc	5/17	1	2	FACETS	0.963	0.87	1	0.963	0.87	1	CLONAL	1	TRUE	1	0.290405343021158	2		837	880	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843796	151843796	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	172	411	0	ENST00000262189.6:c.13919C>G	p.Pro4640Arg	p.P4640R	ENST00000262189	NM_170606.2	4640	cCt/cGt	53/59	0.261566784196644	4	FACETS	0.977	0.901	1	0.977	0.901	1	CLONAL	2	TRUE	2	0.290405343021158	4		411	782	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	249	248	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	0.594	0.556	0.633	0.594	0.556	0.633	SUBCLONAL	1	TRUE	1	0.928382139124098	2		248	903	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914003	32914003	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	433	508	0	ENST00000380152.3:c.5511T>G	p.Phe1837Leu	p.F1837L	ENST00000380152		1837	ttT/ttG	11/27	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.928382139124098	2		508	882	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61713008	61713008	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	441	473	0	ENST00000401558.2:c.2403del	p.Ser802ValfsTer5	p.S802Vfs*5	ENST00000401558	NM_003400.3	801	ctT/ct	20/25	1	2	FACETS	0.95	0.91	0.99	0.95	0.91	0.99	CLONAL	1	TRUE	1	0.928382139124098	2		473	1000	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729099	66729104	+	inframe_deletion	In_Frame_Del	DEL	ATCAAA	ATCAAA	-	novel	NA	P-0015010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	245	674	0	ENST00000307102.5:c.307_312del	p.Ile103_Lys104del	p.I103_K104del	ENST00000307102	NM_002755.3	103	ATCAAA/-	3/11	0.37474068457649	3	FACETS	1	0.987	1	0.613	0.572	0.654	CLONAL	1	TRUE	1	0.441967353630196	3		674	1105	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100796	8100796	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1398302384	NA	P-0015010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	101	673	0	ENST00000346208.3:c.770C>T	p.Ser257Phe	p.S257F	ENST00000346208		257	tCc/tTc	3/6	1	2	FACETS	0.598	0.534	0.666	0.598	0.534	0.666	SUBCLONAL	1	TRUE	1	0.441967353630196	2		673	764	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0015035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	463	621	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.69406047521245	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.693920990880954	2		623	582	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429757	78429757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755419864	NA	P-0015035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	160	298	1	ENST00000370768.2:c.1031G>A	p.Arg344Gln	p.R344Q	ENST00000370768	NM_003902.3	344	cGa/cAa	12/20	0.69406047521245	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	1	0.693920990880954	3		299	304	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023212	27023224	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGGGCCCTAGG	CGCGGGCCCTAGG	-	novel	NA	P-0015035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	89	375	0	ENST00000324856.7:c.319_331del	p.Ala107ProfsTer3	p.A107Pfs*3	ENST00000324856	NM_006015.4	106	aaCGCGGGCCCTAGG/aa	1/20	0.166572093828252	3	FACETS	0.909	0.812	1	0.303	0.27	0.337	INDETERMINATE	1	TRUE	0	0.693920990880954	3		375	380	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656213	18656213	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0015035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	157	385	0	ENST00000266497.5:c.2894-2A>G		p.X965_splice	ENST00000266497		965			0.69406047521245	3	FACETS	0.907	0.845	0.97	0.907	0.845	0.97	CLONAL	2	TRUE	1	0.693920990880954	3		385	336	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434165	12434165	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	57	538	1	ENST00000287820.6:c.533T>G	p.Leu178Arg	p.L178R	ENST00000287820	NM_015869.4	178	cTt/cGt	4/7	0.562625095184442	1	FACETS	0.277	0.238	0.319	0.277	0.238	0.319	SUBCLONAL	1	TRUE	0	0.693920990880954	1		539	387	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394445	162394445	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs938983242	NA	P-0015035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	106	371	0	ENST00000366898.1:c.623T>G	p.Phe208Cys	p.F208C	ENST00000366898	NM_004562.2	208	tTt/tGt	6/12	0.69406047521245	3	FACETS	1	0.917	1	0.508	0.459	0.559	CLONAL	1	TRUE	1	0.693920990880954	3		371	405	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759385	133759385	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	90	731	0	ENST00000318560.5:c.1708C>T	p.Pro570Ser	p.P570S	ENST00000318560	NM_005157.4	570	Cca/Tca	11/11	0.486773123650114	3	FACETS	0.489	0.434	0.548	0.245	0.217	0.274	SUBCLONAL	1	TRUE	1	0.693920990880954	3		731	714	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0000004-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	244	711	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.370774561946513	10	FACETS	1	0.975	1			1	CLONAL	7	FALSE	NA	0.370774561946513	10		712	446	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265908	16265908	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000004-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	73	1071	0	ENST00000375759.3:c.10981A>T	p.Ile3661Phe	p.I3661F	ENST00000375759	NM_015001.2	3661	Att/Ttt	15/15	0.260594372922569	4	FACETS	1	0.945	1	0.38	0.333	0.431	CLONAL	1	FALSE	1	0.370774561946513	4		1071	473	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945083	151945083	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000004-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	11	193	0	ENST00000262189.6:c.2436G>A	p.Met812Ile	p.M812I	ENST00000262189	NM_170606.2	812	atG/atA	14/59	0.140578337012625	6	FACETS	1	0.751	1			1	INDETERMINATE	1	FALSE	NA	0.370774561946513	6		193	95	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578518	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGGCAGGTCTTGGC	CAGGGCAGGTCTTGGC	-	novel	NA	P-0000004-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	58	600	0	ENST00000269305.4:c.412_427del	p.Ala138CysfsTer27	p.A138Cfs*27	ENST00000269305	NM_001126112.2	138	GCCAAGACCTGCCCTGtg/tg	5/11	0.357004239880574	2	FACETS	1	0.944	1	0.586	0.508	0.669	CLONAL	1	FALSE	0	0.370774561946513	2		600	267	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339012	225339012	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000039-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	98	784	0	ENST00000264414.4:c.2257T>C	p.Tyr753His	p.Y753H	ENST00000264414	NM_003590.4	753	Tat/Cat	16/16	0.303632004640264	4	FACETS	0.564	0.503	0.629	0.282	0.251	0.315	INDETERMINATE	1	TRUE	2	0.78	4		784	793	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750275	133750275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000039-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	27	610	0	ENST00000318560.5:c.1106G>A	p.Cys369Tyr	p.C369Y	ENST00000318560	NM_005157.4	369	tGc/tAc	7/11	0.303632004640264	1	FACETS	0.189	0.15	0.232	0.189	0.15	0.232	INDETERMINATE	1	TRUE	0	0.78	1		610	224	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0000057-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	132	62	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.147797715155338	3	FACETS	1	0.963	1	0.55	0.502	0.6	INDETERMINATE	1	TRUE	1	0.598067478343072	3		62	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0000057-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	261	511	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.562179339960114	1	FACETS	0.87	0.82	0.921	0.87	0.82	0.921	CLONAL	1	TRUE	0	0.598067478343072	1		512	703	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593578	215593578	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000057-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	217	302	0	ENST00000260947.4:c.2156C>G	p.Thr719Arg	p.T719R	ENST00000260947	NM_000465.2	719	aCa/aGa	11/11	1	2	FACETS	0.942	0.879	1	0.942	0.879	1	CLONAL	1	TRUE	1	0.598067478343072	2		302	770	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198238	185198238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000057-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	262	282	0	ENST00000265026.3:c.2720C>T	p.Ser907Phe	p.S907F	ENST00000265026	NM_004721.4	907	tCt/tTt	13/14	0.147797715155338	3	FACETS	0.787	0.741	0.834	0.787	0.741	0.834	INDETERMINATE	2	TRUE	1	0.598067478343072	3		282	723	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172007	32172007	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000057-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	164	287	0	ENST00000375023.3:c.3025G>C	p.Glu1009Gln	p.E1009Q	ENST00000375023	NM_004557.3	1009	Gag/Cag	19/30	NA	2	FACETS	0.954	0.88	1			1	INDETERMINATE	1	TRUE	NA	0.598067478343072	2		287	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0000058-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	348	357	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.642830189298703	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.642830189298703	2		357	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0000062-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	581	378	0	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	0.559145669615648	2		378	846	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523605	148523605	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778304	NA	P-0000062-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	54	354	0	ENST00000320356.2:c.848C>T	p.Thr283Met	p.T283M	ENST00000320356	NM_004456.4	283	aCg/aTg	8/20	1	2	FACETS	0.187	0.159	0.218	0.187	0.159	0.218	SUBCLONAL	1	TRUE	1	0.559145669615648	2		354	1034	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222656	69222656	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000062-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1485	328	435	0	ENST00000462284.1:c.629A>T	p.Glu210Val	p.E210V	ENST00000462284	NM_002392.5	210	gAg/gTg	8/11	0.333817323154689	3	FACETS	0.828	0.78	0.878	0.414	0.39	0.439	INDETERMINATE	1	TRUE	1	0.559145669615648	3		435	1813	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99486153	99486153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000062-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	69	318	0	ENST00000268035.6:c.3459T>G	p.Asp1153Glu	p.D1153E	ENST00000268035	NM_000875.3	1153	gaT/gaG	19/21	NA	2	FACETS	0.248	0.215	0.284			1	INDETERMINATE	1	TRUE	NA	0.559145669615648	2		318	996	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602303	10602303	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs754011905	NA	P-0000062-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	422	409	0	ENST00000171111.5:c.1275C>G	p.Ile425Met	p.I425M	ENST00000171111	NM_203500.1	425	atC/atG	3/6	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.559145669615648	2		409	1229	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223386	53223386	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000062-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	151	266	0	ENST00000375401.3:c.3973C>G	p.Pro1325Ala	p.P1325A	ENST00000375401	NM_004187.3	1325	Cct/Gct	23/26	1	1	FACETS	0.585	0.536	0.636	0.585	0.536	0.636	SUBCLONAL	1	TRUE	0	0.559145669615648	1		266	665	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0000119-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	250	315	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.556346768666973	4	FACETS	1	0.963	1			1	CLONAL	2	TRUE	NA	0.567640673735546	4		315	669	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535352	66535352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368790458	NA	P-0000119-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	146	442	0	ENST00000273854.3:c.109C>T	p.Arg37Trp	p.R37W	ENST00000273854	NM_004439.5	37	Cgg/Tgg	1/18	0.216139886709114	5	FACETS	1	0.975	1	0.759	0.7	0.82	INDETERMINATE	2	TRUE	2	0.567640673735546	5		442	418	SUCCESS
APC	324	MSKCC	GRCh37	5	112174580	112174580	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000119-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	214	357	0	ENST00000257430.4:c.3289G>T	p.Glu1097Ter	p.E1097*	ENST00000257430	NM_000038.5	1097	Gaa/Taa	16/16	0.52743171978796	4	FACETS	0.928	0.867	0.99	0.928	0.867	0.99	CLONAL	2	TRUE	2	0.567640673735546	4		357	637	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877909	151877909	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000119-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	149	226	0	ENST00000262189.6:c.7036G>C	p.Gly2346Arg	p.G2346R	ENST00000262189	NM_170606.2	2346	Ggc/Cgc	36/59	0.480343165444999	4	FACETS	0.953	0.879	1	0.953	0.879	1	CLONAL	2	TRUE	2	0.567640673735546	4		226	432	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121438948	121438948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146855738	NA	P-0000119-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	38	477	2	ENST00000257555.6:c.1849G>A	p.Val617Ile	p.V617I	ENST00000257555		617	Gtc/Atc	10/10	0.567640673735546	2	FACETS	0.285	0.236	0.341	0.143	0.118	0.171	SUBCLONAL	1	TRUE	0	0.567640673735546	2		479	469	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575078	48575078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000119-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	275	359	0	ENST00000342988.3:c.272C>T	p.Pro91Leu	p.P91L	ENST00000342988	NM_005359.5	91	cCt/cTt	3/12	0.548972779505161	2	FACETS	0.957	0.911	1	0.957	0.911	1	CLONAL	2	TRUE	0	0.567640673735546	2		359	506	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195164	123195164	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000119-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	287	435	0	ENST00000218089.9:c.1507C>G	p.Leu503Val	p.L503V	ENST00000218089	NM_001042749.1	503	Ctg/Gtg	16/35	0.567640673735546	5	FACETS	1	0.993	1			1	CLONAL	1	TRUE	NA	0.567640673735546	5		435	1256	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916947	178916952	+	inframe_deletion	In_Frame_Del	DEL	ATCCTC	ATCCTC	-	novel	NA	P-0000119-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	142	286	0	ENST00000263967.3:c.335_340del	p.Ile112_Leu113del	p.I112_L113del	ENST00000263967	NM_006218.2	112	ATCCTC/-	2/21	0.480343165444999	4	FACETS	0.775	0.711	0.842	0.775	0.711	0.842	SUBCLONAL	2	TRUE	2	0.567640673735546	4		286	506	SUCCESS
APC	324	MSKCC	GRCh37	5	112175603	112175604	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	T	novel	NA	P-0000119-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	210	379	0	ENST00000257430.4:c.4312_4313delinsT	p.Thr1438TyrfsTer35	p.T1438Yfs*35	ENST00000257430	NM_000038.5	1438	ACa/Ta	16/16	0.52743171978796	4	FACETS	0.833	0.777	0.891	0.833	0.777	0.891	CLONAL	2	TRUE	2	0.567640673735546	4		379	696	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000120-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	8	336	0	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	0.136057280999169	4	FACETS	0.152	0.097	0.224	0.076	0.048	0.112	INDETERMINATE	1	TRUE	2	0.497161388972492	4		336	316	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087944	27087944	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0000120-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	87	293	0	ENST00000324856.7:c.2231C>G	p.Ser744Ter	p.S744*	ENST00000324856	NM_006015.4	744	tCa/tGa	6/20	0.283354328774704	4	FACETS	0.829	0.742	0.921	0.829	0.742	0.921	INDETERMINATE	2	TRUE	2	0.497161388972492	4		293	316	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991610	25991610	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0000120-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	12	228	0	ENST00000435504.4:c.631+1G>C		p.X211_splice	ENST00000435504		211			0.497161388972492	1	FACETS	0.188	0.132	0.257	0.188	0.132	0.257	SUBCLONAL	1	TRUE	0	0.497161388972492	1		228	193	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046310	180046310	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000120-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	10	284	0	ENST00000261937.6:c.2704C>A	p.His902Asn	p.H902N	ENST00000261937	NM_182925.4	902	Cac/Aac	19/30	1	2	FACETS	0.229	0.155	0.321	0.229	0.155	0.321	SUBCLONAL	1	TRUE	1	0.497161388972492	2		284	176	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686863	37686863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000120-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	157	311	0	ENST00000447079.4:c.3767C>T	p.Pro1256Leu	p.P1256L	ENST00000447079	NM_015083.1	1256	cCt/cTt	14/14	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.497161388972492	2		311	476	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866328	42866328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150389990	NA	P-0000120-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	87	197	0	ENST00000398585.3:c.304G>A	p.Val102Ile	p.V102I	ENST00000398585	NM_001135099.1	102	Gtc/Atc	3/14	0.251669968840998	4	FACETS	1	0.959	1	1	0.959	1	INDETERMINATE	2	TRUE	2	0.497161388972492	4		197	233	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0000126-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	231	179	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.481197731443678	3	FACETS	0.886	0.831	0.943	0.886	0.831	0.943	CLONAL	2	TRUE	1	0.481197731443678	3		179	672	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0000126-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	239	86	1	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.481197731443678	3	FACETS	1	0.952	1	1	0.994	1	CLONAL	3	TRUE	1	0.481197731443678	3		87	410	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692922	89692922	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201044	NA	P-0000126-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	251	156	0	ENST00000371953.3:c.406T>C	p.Cys136Arg	p.C136R	ENST00000371953	NM_000314.4	136	Tgt/Cgt	5/9	0.481197731443678	2	FACETS	0.935	0.883	0.987	0.935	0.883	0.987	CLONAL	2	TRUE	0	0.481197731443678	2		156	558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0000126-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	171	124	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	0.481197731443678	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.481197731443678	2		124	339	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859842	151859842	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000126-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	238	167	0	ENST00000262189.6:c.10820del	p.Thr3607LysfsTer23	p.T3607Kfs*23	ENST00000262189	NM_170606.2	3607	aCa/aa	43/59	0.2691111979541	5	FACETS	1	0.989	1	0.829	0.778	0.881	INDETERMINATE	2	TRUE	2	0.481197731443678	5		167	685	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0000129-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	454	157	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.580190713246903	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.585955208153749	2		157	769	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0000154-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	535	376	2	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.643947707686003	4	FACETS	0.985	0.946	1	0.985	0.946	1	CLONAL	2	TRUE	2	0.643947707686003	4		378	1386	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913499	NA	P-0000154-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	379	269	0	ENST00000345146.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000345146	NM_005896.2	132	Cgt/Ggt	4/10	0.547565270836261	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.643947707686003	4		269	908	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55225421	55225421	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs558565565	NA	P-0000154-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	98	247	0	ENST00000275493.2:c.1273A>C	p.Ile425Leu	p.I425L	ENST00000275493	NM_005228.3	425	Atc/Ctc	11/28	0.612776745640182	4	FACETS	0.622	0.555	0.694	0.311	0.277	0.347	SUBCLONAL	1	TRUE	2	0.643947707686003	4		247	804	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0000167-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	42	129	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.359000923372515	1	FACETS	0.905	0.765	1	0.905	0.765	1	CLONAL	1	TRUE	0	0.386203454576027	1		129	194	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0000167-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	77	190	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	0.359000923372515	1	FACETS	0.904	0.799	1	0.904	0.799	1	CLONAL	1	TRUE	0	0.386203454576027	1		190	356	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849521	68849521	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000167-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	194	456	0	ENST00000261769.5:c.1424del	p.Val475GlyfsTer6	p.V475Gfs*6	ENST00000261769	NM_004360.3	475	gTg/gg	10/16	0.386203454576027	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.386203454576027	1		456	669	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261208	16261208	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779552895	NA	P-0000167-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	64	136	0	ENST00000375759.3:c.8473G>A	p.Glu2825Lys	p.E2825K	ENST00000375759	NM_015001.2	2825	Gaa/Aaa	11/15	NA	2	FACETS	0.969	0.844	1			1	INDETERMINATE	1	TRUE	NA	0.386203454576027	2		136	342	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551777	150551777	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000167-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	41	80	0	ENST00000369026.2:c.230C>T	p.Ala77Val	p.A77V	ENST00000369026	NM_021960.4	77	gCg/gTg	1/3	0.386203454576027	3	FACETS	0.889	0.744	1	0.444	0.372	0.524	CLONAL	1	TRUE	1	0.386203454576027	3		80	285	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143134	30143134	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000167-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	108	395	0	ENST00000389048.3:c.392C>T	p.Ser131Phe	p.S131F	ENST00000389048	NM_004304.4	131	tCc/tTc	1/29	NA	2	FACETS	0.85	0.764	0.941			1	INDETERMINATE	1	TRUE	NA	0.386203454576027	2		395	658	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000167-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	67	310	0	ENST00000397062.3:c.92G>A	p.Gly31Glu	p.G31E	ENST00000397062	NM_006164.4	31	gGa/gAa	2/5	1	2	FACETS	0.369	0.319	0.423	0.369	0.319	0.423	SUBCLONAL	1	TRUE	1	0.386203454576027	2		310	941	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163020	47163020	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000167-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	52	379	0	ENST00000409792.3:c.3106G>A	p.Glu1036Lys	p.E1036K	ENST00000409792	NM_014159.6	1036	Gaa/Aaa	3/21	1	2	FACETS	0.32	0.271	0.373	0.32	0.271	0.373	SUBCLONAL	1	TRUE	1	0.386203454576027	2		379	842	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163634	47163634	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0000167-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	62	235	0	ENST00000409792.3:c.2492C>G	p.Ser831Ter	p.S831*	ENST00000409792	NM_014159.6	831	tCa/tGa	3/21	1	2	FACETS	0.491	0.424	0.564	0.491	0.424	0.564	SUBCLONAL	1	TRUE	1	0.386203454576027	2		235	654	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71064734	71064734	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000167-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	49	214	0	ENST00000318789.4:c.940G>C	p.Glu314Gln	p.E314Q	ENST00000318789	NM_032682.5	314	Gaa/Caa	12/21	1	2	FACETS	0.407	0.344	0.477	0.407	0.344	0.477	SUBCLONAL	1	TRUE	1	0.386203454576027	2		214	623	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138431061	138431061	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000167-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	100	308	0	ENST00000289153.2:c.1388C>T	p.Ser463Phe	p.S463F	ENST00000289153	NM_006219.2	463	tCt/tTt	8/22	1	2	FACETS	0.661	0.59	0.737	0.661	0.59	0.737	SUBCLONAL	1	TRUE	1	0.386203454576027	2		308	783	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048764	180048764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000167-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	30	545	0	ENST00000261937.6:c.1798G>A	p.Asp600Asn	p.D600N	ENST00000261937	NM_182925.4	600	Gat/Aat	13/30	1	2	FACETS	0.262	0.21	0.32	0.262	0.21	0.32	SUBCLONAL	1	TRUE	1	0.386203454576027	2		545	594	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852161	128852161	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000167-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	132	477	2	ENST00000249373.3:c.2233C>T	p.Gln745Ter	p.Q745*	ENST00000249373	NM_005631.4	745	Cag/Tag	12/12	1	2	FACETS	0.843	0.765	0.924	0.843	0.765	0.924	CLONAL	1	TRUE	1	0.386203454576027	2		479	811	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199841	108199841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000167-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	41	219	0	ENST00000278616.4:c.7183G>A	p.Asp2395Asn	p.D2395N	ENST00000278616	NM_000051.3	2395	Gat/Aat	49/63	1	2	FACETS	0.378	0.315	0.45	0.378	0.315	0.45	SUBCLONAL	1	TRUE	1	0.386203454576027	2		219	561	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420901	49420901	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000167-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	108	285	0	ENST00000301067.7:c.14848C>G	p.Leu4950Val	p.L4950V	ENST00000301067	NM_003482.3	4950	Ctg/Gtg	48/54	0.386203454576027	3	FACETS	0.853	0.766	0.946			1	CLONAL	1	TRUE	NA	0.386203454576027	3		285	782	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432504	49432504	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000167-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	170	364	0	ENST00000301067.7:c.8635G>C	p.Glu2879Gln	p.E2879Q	ENST00000301067	NM_003482.3	2879	Gag/Cag	34/54	0.386203454576027	3	FACETS	1	0.963	1			1	CLONAL	1	TRUE	NA	0.386203454576027	3		364	972	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913332	28913332	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000167-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	140	490	0	ENST00000282397.4:c.2461G>T	p.Glu821Ter	p.E821*	ENST00000282397	NM_002019.4	821	Gag/Tag	17/30	0.25794851783385	1	FACETS	0.683	0.622	0.748	0.683	0.622	0.748	SUBCLONAL	1	TRUE	0	0.386203454576027	1		490	856	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972634	32972634	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000167-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	138	285	0	ENST00000380152.3:c.9984C>G	p.Phe3328Leu	p.F3328L	ENST00000380152		3328	ttC/ttG	27/27	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.386203454576027	2		285	672	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437379	110437379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000167-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	27	82	0	ENST00000375856.3:c.1022G>A	p.Arg341His	p.R341H	ENST00000375856	NM_003749.2	341	cGc/cAc	1/2	1	2	FACETS	0.689	0.552	0.843	0.689	0.552	0.843	SUBCLONAL	1	TRUE	1	0.386203454576027	2		82	203	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2645847	2645847	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1378928701	NA	P-0000167-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	131	281	0	ENST00000342085.4:c.1397G>A	p.Arg466Gln	p.R466Q	ENST00000342085	NM_002613.4	466	cGg/cAg	12/14	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.386203454576027	2		281	669	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641161	23641161	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000167-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	36	317	0	ENST00000261584.4:c.2314G>A	p.Asp772Asn	p.D772N	ENST00000261584	NM_024675.3	772	Gat/Aat	5/13	1	2	FACETS	0.301	0.246	0.362	0.301	0.246	0.362	SUBCLONAL	1	TRUE	1	0.386203454576027	2		317	620	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118870	70118870	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs886041242	NA	P-0000167-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	136	372	0	ENST00000245479.2:c.442G>T	p.Glu148Ter	p.E148*	ENST00000245479	NM_000346.3	148	Gag/Tag	2/3	0.386203454576027	1	FACETS	0.971	0.887	1	0.971	0.887	1	CLONAL	1	TRUE	0	0.386203454576027	1		372	585	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0000167-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	76	349	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.370266848563711	1	FACETS	0.55	0.483	0.623	0.55	0.483	0.623	SUBCLONAL	1	TRUE	0	0.386203454576027	1		349	577	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604750	48604750	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000167-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	40	301	0	ENST00000342988.3:c.1572G>C	p.Trp524Cys	p.W524C	ENST00000342988	NM_005359.5	524	tgG/tgC	12/12	0.370266848563711	1	FACETS	0.285	0.236	0.339	0.285	0.236	0.339	SUBCLONAL	1	TRUE	0	0.386203454576027	1		301	587	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922906	39922906	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs140897453	NA	P-0000167-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	226	555	0	ENST00000378444.4:c.3802A>G	p.Arg1268Gly	p.R1268G	ENST00000378444	NM_001123385.1	1268	Aga/Gga	8/15	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.386203454576027	2		555	984	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261468	16261468	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000167-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	94	214	0	ENST00000375759.3:c.8733del	p.Lys2911AsnfsTer19	p.K2911Nfs*19	ENST00000375759	NM_015001.2	2911	aaG/aa	11/15	NA	2	FACETS	0.882	0.787	0.983			1	INDETERMINATE	1	TRUE	NA	0.386203454576027	2		214	552	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920469	134920469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000178-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	146	427	1	ENST00000398015.3:c.2284G>A	p.Asp762Asn	p.D762N	ENST00000398015	NM_004441.4	762	Gac/Aac	12/16	0.155179423746424	5	FACETS	1	0.965	1	0.372	0.339	0.408	INDETERMINATE	1	TRUE	2	0.281366210697203	5		428	1321	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187537	32187537	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000178-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	74	181	0	ENST00000375023.3:c.1342C>G	p.His448Asp	p.H448D	ENST00000375023	NM_004557.3	448	Cat/Gat	8/30	0.281366210697203	7	FACETS	1	0.955	1	0.302	0.264	0.344	CLONAL	1	TRUE	3	0.281366210697203	7		181	741	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372206	55372206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000178-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	70	191	0	ENST00000297316.4:c.896C>T	p.Ala299Val	p.A299V	ENST00000297316	NM_022454.3	299	gCg/gTg	2/2	0.233448667107208	3	FACETS	1	0.962	1	0.425	0.372	0.482	CLONAL	1	TRUE	0	0.281366210697203	3		191	445	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435802	110435802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000178-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	19	76	0	ENST00000375856.3:c.2599C>T	p.Pro867Ser	p.P867S	ENST00000375856	NM_003749.2	867	Cct/Tct	1/2	0.281366210697203	5	FACETS	1	0.786	1			1	CLONAL	1	TRUE	NA	0.281366210697203	5		76	186	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0000178-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	308	265	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.233448667107208	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.281366210697203	3		265	753	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419834	41419834	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0000178-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	112	303	0	ENST00000373198.4:c.486+1G>C		p.X162_splice	ENST00000373198	NM_133170.3	162			0.281366210697203	4	FACETS	0.891	0.799	0.989	0.297	0.266	0.33	CLONAL	1	TRUE	1	0.281366210697203	4		303	1145	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0000186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	305	378	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.43874685100068	2		378	1239	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917820	29917820	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	244	468	1	ENST00000389048.3:c.848T>C	p.Leu283Pro	p.L283P	ENST00000389048	NM_004304.4	283	cTc/cCc	3/29	NA	2	FACETS	0.804	0.75	0.861			1	INDETERMINATE	1	TRUE	NA	0.43874685100068	2		469	1383	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371786	116371786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	354	454	0	ENST00000397752.3:c.1265C>T	p.Thr422Ile	p.T422I	ENST00000397752	NM_000245.2	422	aCa/aTa	3/21	0.17190806970138	2	FACETS	0.77	0.731	0.81	0.77	0.731	0.81	INDETERMINATE	2	TRUE	0	0.43874685100068	2		454	1048	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851033	63851033	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202205668	NA	P-0000186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	194	270	0	ENST00000279873.7:c.1811C>T	p.Pro604Leu	p.P604L	ENST00000279873	NM_032199.2	604	cCg/cTg	10/10	1	2	FACETS	0.915	0.846	0.985	0.915	0.846	0.985	CLONAL	1	TRUE	1	0.43874685100068	2		270	967	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106908	27106910	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-	novel	NA	P-0000186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	286	280	0	ENST00000324856.7:c.6519_6521del	p.Asn2173_Leu2174delinsLys	p.N2173_L2174delinsK	ENST00000324856	NM_006015.4	2173	aaCCTg/aag	20/20	0.17190806970138	2	FACETS	1	0.991	1	0.645	0.607	0.684	INDETERMINATE	1	TRUE	0	0.43874685100068	2		280	1011	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1360	359	425	0	ENST00000269305.4:c.833del	p.Pro278LeufsTer67	p.P278Lfs*67	ENST00000269305	NM_001126112.2	278	cCt/ct	8/11	NA	2	FACETS	0.952	0.9	1			1	INDETERMINATE	1	TRUE	NA	0.43874685100068	2		425	1719	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0000195-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	99	399	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		399	185	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653796	89653798	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs1554893765	NA	P-0000201-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	369	455	1	ENST00000371953.3:c.97_99del	p.Ile33del	p.I33del	ENST00000371953	NM_000314.4	32	ATT/-	2/9	0.7209226431414	1	FACETS	0.852	0.814	0.891	0.852	0.814	0.891	CLONAL	1	TRUE	0	0.7209226431414	1		456	768	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226576371	226576371	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000201-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2416	489	644	1	ENST00000366794.5:c.703G>C	p.Glu235Gln	p.E235Q	ENST00000366794	NM_001618.3	235	Gaa/Caa	5/23	0.713668463089335	5	FACETS	0.972	0.925	1	0.243	0.231	0.255	CLONAL	1	TRUE	1	0.7209226431414	5		645	2905	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641421	47641421	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0000201-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	419	526	0	ENST00000233146.2:c.806C>G	p.Ser269Ter	p.S269*	ENST00000233146	NM_000251.2	269	tCa/tGa	5/16	1	2	FACETS	0.961	0.917	1	0.961	0.917	1	CLONAL	1	TRUE	1	0.7209226431414	2		526	1209	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672267	86672267	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000201-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	305	358	0	ENST00000274376.6:c.2069T>G	p.Phe690Cys	p.F690C	ENST00000274376	NM_002890.2	690	tTt/tGt	16/25	1	2	FACETS	0.896	0.847	0.947	0.896	0.847	0.947	CLONAL	1	TRUE	1	0.7209226431414	2		358	944	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419909	152419909	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000201-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	234	232	0	ENST00000206249.3:c.1596C>G	p.Asn532Lys	p.N532K	ENST00000206249	NM_000125.3	532	aaC/aaG	8/8	0.7209226431414	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.7209226431414	1		232	382	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012253	152012253	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1563831738	NA	P-0000201-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	1031	631	0	ENST00000262189.6:c.560C>G	p.Ser187Ter	p.S187*	ENST00000262189	NM_170606.2	187	tCa/tGa	4/59	0.7209226431414	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.7209226431414	2		631	1406	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487568	56487568	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000201-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	305	455	0	ENST00000267101.3:c.1501G>A	p.Asp501Asn	p.D501N	ENST00000267101	NM_001982.3	501	Gac/Aac	13/28	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.7209226431414	2		455	841	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112079	115112079	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000201-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	346	390	1	ENST00000257566.3:c.1661C>G	p.Ser554Trp	p.S554W	ENST00000257566	NM_016569.3	554	tCg/tGg	7/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.7209226431414	2		391	914	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118709	115118709	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs756408358	NA	P-0000201-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	643	446	4	ENST00000257566.3:c.632A>C	p.Asn211Thr	p.N211T	ENST00000257566	NM_016569.3	211	aAc/aCc	2/8	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.7209226431414	2		450	1544	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845585	68845585	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1555515596	NA	P-0000201-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	435	322	4	ENST00000261769.5:c.833-2A>G		p.X278_splice	ENST00000261769	NM_004360.3	278			0.7209226431414	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.7209226431414	2		326	601	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120810	115120810	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000201-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	328	381	3	ENST00000257566.3:c.196del	p.Asp66IlefsTer22	p.D66Ifs*22	ENST00000257566	NM_016569.3	66	Gat/at	1/8	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.7209226431414	2		384	838	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148526886	148526886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000210-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	26	507	0	ENST00000320356.2:c.418G>A	p.Asp140Asn	p.D140N	ENST00000320356	NM_004456.4	140	Gat/Aat	5/20	0.278203174170224	4	FACETS	0.63	0.499	0.78	0.315	0.249	0.39	SUBCLONAL	1	TRUE	2	0.283341451739113	4		507	374	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573533	41573533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000210-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	98	599	0	ENST00000263253.7:c.5818C>T	p.Arg1940Cys	p.R1940C	ENST00000263253	NM_001429.3	1940	Cgc/Tgc	31/31	0.278203174170224	4	FACETS	0.936	0.834	1	0.468	0.417	0.523	CLONAL	1	TRUE	2	0.283341451739113	4		599	948	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0000216-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	165	62	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.471108174992112	3	FACETS	0.9	0.833	0.968	0.9	0.833	0.968	CLONAL	2	TRUE	1	0.468488246789046	3		62	483	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804950	43804950	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000216-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	285	432	0	ENST00000372470.3:c.400G>T	p.Ala134Ser	p.A134S	ENST00000372470	NM_005373.2	134	Gct/Tct	4/12	0.468488246789046	2	FACETS	1	0.991	1	0.63	0.593	0.668	CLONAL	1	TRUE	0	0.468488246789046	2		432	965	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527303	187527303	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774392890	NA	P-0000216-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	215	516	0	ENST00000441802.2:c.10271C>T	p.Thr3424Met	p.T3424M	ENST00000441802	NM_005245.3	3424	aCg/aTg	17/27	1	2	FACETS	0.947	0.881	1	0.947	0.881	1	CLONAL	1	TRUE	1	0.468488246789046	2		516	969	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751180	57751180	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000216-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1505	227	519	0	ENST00000274289.3:c.1687G>C	p.Glu563Gln	p.E563Q	ENST00000274289	NM_006622.3	563	Gag/Cag	12/14	0.471108174992112	4	FACETS	0.822	0.763	0.883	0.411	0.381	0.442	CLONAL	1	TRUE	2	0.468488246789046	4		519	1732	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247514	123247514	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000216-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	350	656	0	ENST00000358487.5:c.1977G>C	p.Lys659Asn	p.K659N	ENST00000358487	NM_000141.4	659	aaG/aaC	14/18	0.465579723496485	2	FACETS	1	0.986	1	0.557	0.527	0.588	CLONAL	1	TRUE	0	0.468488246789046	2		656	1341	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913476	NA	P-0000216-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	656	624	0	ENST00000358487.5:c.1647T>G	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaG	12/18	0.465579723496485	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.468488246789046	2		624	1381	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911530	32911530	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0000216-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	184	415	0	ENST00000380152.3:c.3038C>G	p.Ser1013Ter	p.S1013*	ENST00000380152		1013	tCa/tGa	11/27	0.471108174992112	3	FACETS	0.922	0.85	0.996	0.461	0.425	0.498	CLONAL	1	TRUE	1	0.468488246789046	3		415	1052	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591886	48591886	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000216-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	288	694	0	ENST00000342988.3:c.1049T>G	p.Val350Gly	p.V350G	ENST00000342988	NM_005359.5	350	gTt/gGt	9/12	0.395606928772932	1	FACETS	0.919	0.866	0.975	0.919	0.866	0.975	CLONAL	1	TRUE	0	0.468488246789046	1		694	1024	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0000217-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	73	62	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.603752523916934	3	FACETS	0.894	0.801	0.99	0.894	0.801	0.99	CLONAL	2	TRUE	1	0.603752523916934	3		62	176	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428467	72428467	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000217-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	153	631	0	ENST00000477973.2:c.537G>C	p.Glu179Asp	p.E179D	ENST00000477973	NM_012234.5	179	gaG/gaC	2/4	0.603752523916934	3	FACETS	0.943	0.864	1	0.471	0.432	0.512	CLONAL	1	TRUE	1	0.603752523916934	3		631	700	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152009032	152009032	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0000217-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	173	203	0	ENST00000262189.6:c.591-1G>A		p.X197_splice	ENST00000262189	NM_170606.2	197			0.603752523916934	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.603752523916934	3		203	327	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055756	152055756	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1283285486	NA	P-0000217-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	99	363	0	ENST00000262189.6:c.166C>T	p.Arg56Ter	p.R56*	ENST00000262189	NM_170606.2	56	Cga/Tga	2/59	0.603752523916934	3	FACETS	1	0.955	1	0.554	0.499	0.613	CLONAL	1	TRUE	1	0.603752523916934	3		363	385	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562293	21562293	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000217-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	97	492	0	ENST00000382592.4:c.1626G>C	p.Gln542His	p.Q542H	ENST00000382592	NM_014572.2	542	caG/caC	4/8	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.603752523916934	2		492	274	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584436	39584436	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000217-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	80	322	0	ENST00000262039.4:c.1101A>T	p.Leu367Phe	p.L367F	ENST00000262039	NM_002647.2	367	ttA/ttT	10/25	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.603752523916934	2		322	264	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817469	39817469	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000217-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	103	382	0	ENST00000288319.7:c.94G>C	p.Glu32Gln	p.E32Q	ENST00000288319	NM_182918.3	32	Gag/Cag	2/10	0.603752523916934	3	FACETS	1	0.969	1	0.592	0.534	0.652	CLONAL	1	TRUE	1	0.603752523916934	3		382	375	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288090	21288090	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000217-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	99	321	0	ENST00000354336.3:c.335C>G	p.Ser112Cys	p.S112C	ENST00000354336	NM_005207.3	112	tCt/tGt	2/3	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.603752523916934	2		321	321	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918276	44918276	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000217-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	104	194	0	ENST00000377967.4:c.901C>T	p.Gln301Ter	p.Q301*	ENST00000377967	NM_021140.2	301	Cag/Tag	11/29	0.226724659464369	0	FACETS	0.785	0.726	0.842			1	INDETERMINATE	1	TRUE	NA	0.603752523916934	0		194	174	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922731	44922731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000217-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	138	257	0	ENST00000377967.4:c.1592C>T	p.Ser531Leu	p.S531L	ENST00000377967	NM_021140.2	531	tCa/tTa	16/29	0.226724659464369	0	FACETS		NA	1			1	INDETERMINATE	2	TRUE	NA	0.603752523916934	0		257	205	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181326	123181326	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000217-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	112	160	0	ENST00000218089.9:c.790C>A	p.Leu264Ile	p.L264I	ENST00000218089	NM_001042749.1	264	Cta/Ata	9/35	0.226724659464369	0	FACETS	0.84	0.783	0.896			1	INDETERMINATE	1	TRUE	NA	0.603752523916934	0		160	175	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140487379	140487379	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000217-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	253	401	0	ENST00000288602.6:c.1146G>C	p.Leu382Phe	p.L382F	ENST00000288602	NM_004333.4	382	ttG/ttC	9/18	0.603752523916934	3	FACETS	0.99	0.936	1	0.99	0.936	1	CLONAL	2	TRUE	1	0.603752523916934	3		401	551	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333723	70333723	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000217-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	110	429	0	ENST00000373644.4:c.1628G>C	p.Arg543Thr	p.R543T	ENST00000373644	NM_030625.2	543	aGa/aCa	2/12	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.603752523916934	2		429	340	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007747	45007747	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000217-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	102	248	0	ENST00000558401.1:c.194G>T	p.Arg65Ile	p.R65I	ENST00000558401	NM_004048.2	65	aGa/aTa	2/4	1	2	FACETS	0.952	0.86	1	0.952	0.86	1	CLONAL	1	TRUE	1	0.603752523916934	2		248	355	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553236	41553236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000217-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	72	402	0	ENST00000263253.7:c.3325G>A	p.Gly1109Arg	p.G1109R	ENST00000263253	NM_001429.3	1109	Gga/Aga	18/31	1	2	FACETS	0.745	0.656	0.839	0.745	0.656	0.839	SUBCLONAL	1	TRUE	1	0.603752523916934	2		402	320	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556707	41556707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000217-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	57	254	0	ENST00000263253.7:c.3652G>A	p.Asp1218Asn	p.D1218N	ENST00000263253	NM_001429.3	1218	Gac/Aac	20/31	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.603752523916934	2		254	180	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566451	41566451	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000217-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	98	391	0	ENST00000263253.7:c.4328G>C	p.Gly1443Ala	p.G1443A	ENST00000263253	NM_001429.3	1443	gGa/gCa	27/31	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.603752523916934	2		391	303	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568584	41568584	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000217-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	84	301	0	ENST00000263253.7:c.4534G>T	p.Val1512Phe	p.V1512F	ENST00000263253	NM_001429.3	1512	Gtt/Ttt	28/31	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.603752523916934	2		301	267	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0000219-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	91	525	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	1	2	FACETS	0.53	0.469	0.595	0.53	0.469	0.595	SUBCLONAL	1	TRUE	1	0.35	2		525	981	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481433	140481433	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000219-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	116	584	2	ENST00000288602.6:c.1375G>T	p.Val459Leu	p.V459L	ENST00000288602	NM_004333.4	459	Gtg/Ttg	11/18	1	2	FACETS	0.641	0.577	0.71	0.641	0.577	0.71	SUBCLONAL	1	TRUE	1	0.35	2		586	1034	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591892	48591892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767345	NA	P-0000219-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	80	675	0	ENST00000342988.3:c.1055G>A	p.Gly352Glu	p.G352E	ENST00000342988	NM_005359.5	352	gGa/gAa	9/12	1	2	FACETS	0.446	0.391	0.505	0.446	0.391	0.505	SUBCLONAL	1	TRUE	1	0.35	2		675	1025	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226187	53226187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376775932	NA	P-0000219-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	79	653	1	ENST00000375401.3:c.2662C>T	p.Arg888Cys	p.R888C	ENST00000375401	NM_004187.3	888	Cgt/Tgt	19/26	1	2	FACETS	0.434	0.38	0.492	0.434	0.38	0.492	SUBCLONAL	1	TRUE	1	0.35	2		654	1041	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0000225-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	28	95	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	NA	2	FACETS	0.38	0.303	0.469			1	INDETERMINATE	1	TRUE	NA	0.279849874077754	2		95	526	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629920	187629920	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000225-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1707	114	433	0	ENST00000441802.2:c.1062C>A	p.His354Gln	p.H354Q	ENST00000441802	NM_005245.3	354	caC/caA	2/27	0.279849874077754	1	FACETS	0.385	0.345	0.428	0.385	0.345	0.428	SUBCLONAL	1	TRUE	0	0.279849874077754	1		433	1821	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69458666	69458666	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000225-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1837	313	461	0	ENST00000227507.2:c.481A>G	p.Ile161Val	p.I161V	ENST00000227507	NM_053056.2	161	Att/Gtt	3/5	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.279849874077754	2		461	2150	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0000225-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1287	386	425	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.279849874077754	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.279849874077754	1		425	1673	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215339	5215339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs114545401	NA	P-0000225-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1334	139	400	0	ENST00000357368.4:c.4279G>A	p.Ala1427Thr	p.A1427T	ENST00000357368	NM_002850.3	1427	Gcc/Acc	28/38	0.279849874077754	1	FACETS	0.58	0.526	0.637	0.58	0.526	0.637	SUBCLONAL	1	TRUE	0	0.279849874077754	1		400	1473	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970991	21970991	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000225-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1154	213	357	0	ENST00000304494.5:c.367del	p.His123IlefsTer23	p.H123Ifs*23	ENST00000304494	NM_000077.4	123	Cat/at	2/3	NA				0.975	1				INDETERMINATE	1	TRUE	NA	0.279849874077754	2		357	1367	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974719	21974724	+	inframe_deletion	In_Frame_Del	DEL	CGCCCC	CGCCCC	-	novel	NA	P-0000225-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1223	263	300	0	ENST00000304494.5:c.103_108del	p.Gly35_Ala36del	p.G35_A36del	ENST00000304494	NM_000077.4	35	GGGGCG/-	1/3	NA				0.989	1				INDETERMINATE	1	TRUE	NA	0.279849874077754	2		300	1486	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0000235-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	400	62	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.57	6	FACETS	0.938	0.903	0.972			1	CLONAL	5	TRUE	NA	0.568862772544053	6		62	641	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65348993	65348993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000235-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	122	161	0	ENST00000342505.4:c.172G>A	p.Glu58Lys	p.E58K	ENST00000342505	NM_002227.2	58	Gag/Aag	3/25	1	2	FACETS	0.907	0.825	0.992	0.907	0.825	0.992	CLONAL	1	TRUE	1	0.568862772544053	2		161	473	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230874	66230874	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000235-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	283	233	0	ENST00000273854.3:c.2097A>C	p.Lys699Asn	p.K699N	ENST00000273854	NM_004439.5	699	aaA/aaC	12/18	1	2	FACETS	0.976	0.919	1	0.976	0.919	1	CLONAL	1	TRUE	1	0.568862772544053	2		233	1019	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540157	187540157	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000235-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	322	300	0	ENST00000441802.2:c.7583C>G	p.Thr2528Ser	p.T2528S	ENST00000441802	NM_005245.3	2528	aCt/aGt	10/27	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.568862772544053	2		300	1080	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039516	180039516	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000235-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	178	389	0	ENST00000261937.6:c.3527G>T	p.Arg1176Met	p.R1176M	ENST00000261937	NM_182925.4	1176	aGg/aTg	26/30	0.2	1	FACETS	0.816	0.757	0.876	0.816	0.757	0.876	INDETERMINATE	1	TRUE	0	0.568862772544053	1		389	549	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513012	106513012	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000235-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	175	116	0	ENST00000359195.3:c.2026G>T	p.Ala676Ser	p.A676S	ENST00000359195	NM_002649.2	676	Gcc/Tcc	3/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.568862772544053	2		116	590	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432042	49432042	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000235-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	257	549	0	ENST00000301067.7:c.9097A>T	p.Thr3033Ser	p.T3033S	ENST00000301067	NM_003482.3	3033	Acc/Tcc	34/54	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.568862772544053	2		549	836	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579582	7579583	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	G	novel	NA	P-0000235-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	95	221	0	ENST00000269305.4:c.104_105delinsC	p.Leu35SerfsTer9	p.L35Sfs*9	ENST00000269305	NM_001126112.2	35	tTG/tC	4/11	0.57	1	FACETS	0.93	0.842	1	0.93	0.842	1	CLONAL	1	TRUE	0	0.568862772544053	1		221	257	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719273	61719273	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000253-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	442	432	1	ENST00000401558.2:c.1784G>A	p.Cys595Tyr	p.C595Y	ENST00000401558	NM_003400.3	595	tGc/tAc	16/25	1	2	FACETS	0.966	0.925	1	1	0.998	1	CLONAL	5	TRUE	1	0.191141333453259	2		433	958	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726735	41726735	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000260-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	264	40	272	0	ENST00000301178.4:c.280G>A	p.Asp94Asn	p.D94N	ENST00000301178	NM_021913.4	94	Gat/Aat	2/20	0.186233738524328	1	FACETS	0.58	0.484	0.686	0.58	0.484	0.686	INDETERMINATE	1	TRUE	0	0.37	1		272	304	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593603	55593603	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913235	NA	P-0000306-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	228	303	0	ENST00000288135.5:c.1669T>C	p.Trp557Arg	p.W557R	ENST00000288135	NM_000222.2	557	Tgg/Cgg	11/21	0.635345274280241	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.635345274280241	3		303	395	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266778	198266779	+	missense_variant	Missense_Mutation	DNP	AG	AG	TA	novel	NA	P-0000313-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	71	42	374	0	ENST00000335508.6:c.2153_2154delinsTA	p.Pro718Leu	p.P718L	ENST00000335508	NM_012433.2	718	cCT/cTA	15/25	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	FALSE	1	0.700411274006724	2		374	113	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285585	46285585	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000316-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	310	619	0	ENST00000334344.6:c.4945G>T	p.Val1649Phe	p.V1649F	ENST00000334344	NM_152641.2	1649	Gtt/Ttt	17/21	1	2	FACETS	0.923	0.871	0.977	0.923	0.871	0.977	CLONAL	1	TRUE	1	0.595810284630443	2		619	1127	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057520005	NA	P-0000316-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	400	934	0	ENST00000269305.4:c.820G>C	p.Val274Leu	p.V274L	ENST00000269305	NM_001126112.2	274	Gtt/Ctt	8/11	0.595810284630443	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.595810284630443	1		934	766	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221785	55221786	+	missense_variant	Missense_Mutation	DNP	AT	AT	GA	novel	NA	P-0000316-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	691	763	0	ENST00000275493.2:c.829_830delinsGA	p.Met277Glu	p.M277E	ENST00000275493	NM_005228.3	277	ATg/GAg	7/28	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.595810284630443	2		763	1075	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101254	27101254	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000323-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	216	379	0	ENST00000324856.7:c.4536G>T	p.Gln1512His	p.Q1512H	ENST00000324856	NM_006015.4	1512	caG/caT	18/20	0.196112601029872	5	FACETS	0.806	0.75	0.863			1	INDETERMINATE	2	TRUE	NA	0.585184528205981	5		379	860	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265352	152265352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142712646	NA	P-0000323-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	40	207	0	ENST00000206249.3:c.805C>T	p.Arg269Cys	p.R269C	ENST00000206249	NM_000125.3	269	Cgc/Tgc	4/8	0.27441452436146	6	FACETS	0.407	0.337	0.485	0.102	0.084	0.122	INDETERMINATE	1	TRUE	2	0.585184528205981	6		207	729	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976828	2976828	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000323-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	191	424	0	ENST00000396946.4:c.1184A>T	p.Gln395Leu	p.Q395L	ENST00000396946	NM_032415.4	395	cAg/cTg	9/25	0.341264178949776	6	FACETS	1	0.966	1	0.361	0.332	0.39	INDETERMINATE	1	TRUE	3	0.585184528205981	6		424	1309	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037877	49037877	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000323-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	162	647	0	ENST00000267163.4:c.2117G>A	p.Cys706Tyr	p.C706Y	ENST00000267163	NM_000321.2	706	tGt/tAt	21/27	0.585184528205981	1	FACETS	0.944	0.876	1	0.944	0.876	1	CLONAL	1	TRUE	0	0.585184528205981	1		647	415	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726685	88726685	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000323-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	162	475	0	ENST00000360948.2:c.359C>A	p.Pro120His	p.P120H	ENST00000360948	NM_001012338.2	120	cCc/cAc	4/19	1	2	FACETS	0.769	0.707	0.833	0.769	0.707	0.833	SUBCLONAL	1	TRUE	1	0.585184528205981	2		475	720	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786706	3786706	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000323-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1256	241	622	0	ENST00000262367.5:c.4505G>T	p.Trp1502Leu	p.W1502L	ENST00000262367	NM_004380.2	1502	tGg/tTg	27/31	0.424350189978987	5	FACETS	1	0.955	1	0.344	0.32	0.369	CLONAL	1	TRUE	2	0.585184528205981	5		622	1497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519985	NA	P-0000323-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	487	439	0	ENST00000269305.4:c.857A>G	p.Glu286Gly	p.E286G	ENST00000269305	NM_001126112.2	286	gAa/gGa	8/11	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	2	TRUE	NA	0.585184528205981	2		439	812	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39535320	39535320	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0000323-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	320	326	0	ENST00000262039.4:c.64A>T	p.Lys22Ter	p.K22*	ENST00000262039	NM_002647.2	22	Aag/Tag	1/25	0.585184528205981	4	FACETS	0.994	0.942	1	0.994	0.942	1	CLONAL	2	TRUE	2	0.585184528205981	4		326	872	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602767	10602767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000323-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	482	280	2	ENST00000171111.5:c.811G>A	p.Val271Met	p.V271M	ENST00000171111	NM_203500.1	271	Gtg/Atg	3/6	0.585184528205981	4	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.585184528205981	4		282	1108	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814318	76814318	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0000323-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	422	554	0	ENST00000373344.5:c.6327-1G>T		p.X2109_splice	ENST00000373344	NM_000489.3	2109			0.585184528205981	4	FACETS	1	0.99	1			1	CLONAL	2	TRUE	NA	0.585184528205981	4		554	1023	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618777	37618792	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGCGTTCGAATGAG	AAAGCGTTCGAATGAG	-	novel	NA	P-0000323-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	168	436	0	ENST00000447079.4:c.453_468del	p.Lys152ArgfsTer10	p.K152Rfs*10	ENST00000447079	NM_015083.1	151	tcAAAGCGTTCGAATGAG/tc	1/14	0.585184528205981	3	FACETS	0.808	0.742	0.876	0.404	0.371	0.438	CLONAL	1	TRUE	1	0.585184528205981	3		436	919	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39746871	39746871	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000323-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	84	274	0	ENST00000361337.2:c.1885del	p.Leu629PhefsTer16	p.L629Ffs*16	ENST00000361337	NM_003286.2	629	Ctt/tt	18/21	0.341264178949776	6	FACETS	1	0.933	1	0.359	0.318	0.404	INDETERMINATE	1	TRUE	3	0.585184528205981	6		274	578	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129429	64129430	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0000323-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	255	352	0	ENST00000334205.4:c.861_862delinsCT	p.Gly288Trp	p.G288W	ENST00000334205	NM_003942.2	287	gcGGgg/gcCTgg	8/17	0.27441452436146	6	FACETS	0.905	0.847	0.964	0.453	0.423	0.482	INDETERMINATE	2	TRUE	2	0.585184528205981	6		352	1045	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163297	32163297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1239036035	NA	P-0000325-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	442	130	864	3	ENST00000375023.3:c.5929G>A	p.Glu1977Lys	p.E1977K	ENST00000375023	NM_004557.3	1977	Gag/Aag	30/30	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.430929336851839	2		867	572	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432651	49432651	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs727503983	NA	P-0000325-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	159	50	370	0	ENST00000301067.7:c.8488C>T	p.Arg2830Ter	p.R2830*	ENST00000301067	NM_003482.3	2830	Cga/Tga	34/54	0.190381224014242	1	FACETS	0.871	0.748	1	0.871	0.748	1	INDETERMINATE	1	TRUE	0	0.430929336851839	1		370	209	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602475	10602475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000325-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	113	139	454	0	ENST00000171111.5:c.1103G>A	p.Cys368Tyr	p.C368Y	ENST00000171111	NM_203500.1	368	tGc/tAc	3/6	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.430929336851839	NA		454	252	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0000341-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	166	271	0	ENST00000269305.4:c.559+1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		271	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0000343-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	25	415	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.256432209003781	1	FACETS	0.36	0.283	0.449	0.36	0.283	0.449	SUBCLONAL	1	FALSE	0	0.256432209003781	1		415	472	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0000343-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	28	269	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.256432209003781	1	FACETS	0.501	0.4	0.616	0.501	0.4	0.616	SUBCLONAL	1	FALSE	0	0.256432209003781	1		269	380	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000343-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	54	526	0	ENST00000263967.3:c.3012G>A	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atA	21/21	1	2	FACETS	0.738	0.63	0.856	0.738	0.63	0.856	SUBCLONAL	1	FALSE	1	0.256432209003781	2		526	571	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577564	7577564	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000343-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	12	301	0	ENST00000269305.4:c.717C>A	p.Asn239Lys	p.N239K	ENST00000269305	NM_001126112.2	239	aaC/aaA	7/11	0.256432209003781	1	FACETS	0.289	0.203	0.396	0.289	0.203	0.396	SUBCLONAL	1	FALSE	0	0.256432209003781	1		301	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0000348-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	305	467	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.432961157928561	2	FACETS	0.996	0.945	1	0.996	0.945	1	CLONAL	2	TRUE	0	0.432961157928561	2		467	707	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242470	+	missense_variant	Missense_Mutation	DNP	TT	TT	CC	rs397517096	NA	P-0000348-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	1932	296	0	ENST00000275493.2:c.2239_2240delinsCC	p.Leu747Pro	p.L747P	ENST00000275493	NM_005228.3	747	TTa/CCa	19/28	0.432961157928561	19	FACETS	0.979	0.967	0.991			1	CLONAL	18	TRUE	NA	0.432961157928561	19		296	2370	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030314	180030314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777755208	NA	P-0000348-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	317	551	2	ENST00000261937.6:c.3970C>T	p.Arg1324Trp	p.R1324W	ENST00000261937	NM_182925.4	1324	Cgg/Tgg	30/30	0.374409575635545	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	2	0.432961157928561	4		553	1038	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0000360-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	198	311	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.34107506248679	1	FACETS	0.822	0.766	0.88	0.822	0.766	0.88	INDETERMINATE	1	TRUE	0	0.568835572340892	1		311	606	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553245	106553245	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771869527	NA	P-0000366-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	55	297	0	ENST00000369096.4:c.1210C>T	p.Pro404Ser	p.P404S	ENST00000369096	NM_001198.3	404	Ccc/Tcc	5/7	0.235104069957544	3	FACETS	0.182	0.155	0.212	0.091	0.077	0.106	INDETERMINATE	1	TRUE	1	0.891951975283295	3		297	979	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097007	11097007	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000366-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	52	463	0	ENST00000358026.2:c.498C>A	p.Asn166Lys	p.N166K	ENST00000358026	NM_001128849.1	166	aaC/aaA	4/36	0.269708486629674	1	FACETS	0.066	0.055	0.077	0.066	0.055	0.077	INDETERMINATE	1	TRUE	0	0.891951975283295	1		463	982	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579437	7579437	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000366-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	246	177	0	ENST00000269305.4:c.250del	p.Ala84ProfsTer39	p.A84Pfs*39	ENST00000269305	NM_001126112.2	84	Gcc/cc	4/11	0.891951975283295	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.891951975283295	1		177	298	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394390	162394390	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000379-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	243	340	0	ENST00000366898.1:c.678G>T	p.Leu226Phe	p.L226F	ENST00000366898	NM_004562.2	226	ttG/ttT	6/12	1	2	FACETS	0.94	0.886	0.994	1	0.996	1	CLONAL	3	TRUE	1	0.308903142855074	2		340	558	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0000390-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	82	201	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.367385129032736	10	FACETS	0.978	0.889	1	0.978	0.889	1	CLONAL	7	FALSE	3	0.367385129032736	10		201	161	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0000390-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	22	323	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.367385129032736	5	FACETS	0.815	0.641	1	0.543	0.427	0.673	CLONAL	2	FALSE	2	0.367385129032736	5		323	114	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934573	NA	P-0000390-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	42	320	0	ENST00000269305.4:c.722C>A	p.Ser241Tyr	p.S241Y	ENST00000269305	NM_001126112.2	241	tCc/tAc	7/11	0.367385129032736	5	FACETS	1	0.873	1	1	0.873	1	CLONAL	3	FALSE	2	0.367385129032736	5		320	116	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851286	156851286	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745776726	NA	P-0000391-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	44	662	0	ENST00000524377.1:c.2243G>A	p.Arg748Gln	p.R748Q	ENST00000524377	NM_002529.3	748	cGg/cAg	17/17	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		662	481	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446900	18446900	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000394-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	272	501	0	ENST00000266497.5:c.985C>A	p.Pro329Thr	p.P329T	ENST00000266497		329	Ccc/Acc	4/31	1	2	FACETS	0.967	0.906	1	1	0.996	1	CLONAL	3	TRUE	1	0.147529924809018	2		501	1271	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41558721	41558753	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTTAGTACAATAAATAAAGAACAATTTTCCAA	CCTTAGTACAATAAATAAAGAACAATTTTCCAA	-	novel	NA	P-0000394-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	69	623	0	ENST00000263253.7:c.3672-6_3698del		p.X1224_splice	ENST00000263253	NM_001429.3	1224		21/31	NA	2	FACETS	0.883	0.767	1			1	INDETERMINATE	1	TRUE	NA	0.147529924809018	2		623	1059	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721202	61721202	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000403-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	28	346	0	ENST00000401558.2:c.1072T>C	p.Ser358Pro	p.S358P	ENST00000401558	NM_003400.3	358	Tct/Cct	12/25	0.66843950796108	2	FACETS	0.412	0.333	0.499	0.206	0.166	0.25	SUBCLONAL	1	TRUE	0	0.866690842405827	2		346	157	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023008	27023010	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs587779737	NA	P-0000403-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	12	13	0	ENST00000324856.7:c.126_128del	p.Ala45del	p.A45del	ENST00000324856	NM_006015.4	38	gaGGCg/gag	1/20	0.426948629995038	2	FACETS	0.138	0.096	0.188	0.069	0.048	0.094	INDETERMINATE	1	TRUE	0	0.866690842405827	2		13	201	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578439	7578439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000403-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	257	264	0	ENST00000269305.4:c.491del	p.Lys164SerfsTer6	p.K164Sfs*6	ENST00000269305	NM_001126112.2	164	aAg/ag	5/11	NA	2	FACETS	0.985	0.956	1			1	INDETERMINATE	2	TRUE	NA	0.866690842405827	2		264	301	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0000429-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	44	542	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.628357631742558	12	FACETS	0.857	0.717	1			1	CLONAL	1	FALSE	NA	0.628357631742558	12		542	677	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485993	8485993	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000429-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	14	307	0	ENST00000356435.5:c.2824C>A	p.Pro942Thr	p.P942T	ENST00000356435		942	Cct/Act	17/35	0.628357631742558	2	FACETS	0.495	0.363	0.65	0.248	0.181	0.325	SUBCLONAL	1	FALSE	0	0.628357631742558	2		307	90	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0000431-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	26	100	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.277893990627677	1	FACETS	1	0.842	1	1	0.842	1	CLONAL	1	TRUE	0	0.277893990627677	1		100	152	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000466-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	47	927	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.168515865010625	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		927	516	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060986	38060986	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000466-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	24	331	0	ENST00000250448.2:c.1003C>A	p.Leu335Met	p.L335M	ENST00000250448	NM_004496.3	335	Ctg/Atg	2/2	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		331	282	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028657	12028657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000466-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	70	495	1	ENST00000353533.5:c.860G>A	p.Arg287His	p.R287H	ENST00000353533	NM_003010.3	287	cGc/cAc	8/11	0.127771375524107	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		496	827	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164704	36164710	+	frameshift_variant	Frame_Shift_Del	DEL	CTTGCGA	CTTGCGA	-	novel	NA	P-0000466-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	64	653	0	ENST00000300305.3:c.1165_1171del	p.Ser389ArgfsTer203	p.S389Rfs*203	ENST00000300305		389	TCGCAAGcg/cg	8/8	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		653	605	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372127	55372127	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000472-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	170	106	0	ENST00000297316.4:c.817C>T	p.Arg273Ter	p.R273*	ENST00000297316	NM_022454.3	273	Cga/Tga	2/2	0.888982208881412	6	FACETS	1	0.986	1	0.335	0.309	0.363	CLONAL	1	TRUE	2	0.888982208881412	6		106	792	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000472-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	582	279	0	ENST00000269305.4:c.470T>G	p.Val157Gly	p.V157G	ENST00000269305	NM_001126112.2	157	gTc/gGc	5/11	NA	2	FACETS	1	0.997	1			1	INDETERMINATE	2	TRUE	NA	0.888982208881412	2		279	614	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0000499-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	265	237	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.853653270806097	2	FACETS	1	0.984	1	0.547	0.518	0.577	CLONAL	1	TRUE	0	0.853653270806097	2		237	567	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577554	+	frameshift_variant	Frame_Shift_Del	DEL	TGCCGCCCAT	TGCCGCCCAT	-	novel	NA	P-0000499-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	140	222	0	ENST00000269305.4:c.727_736del	p.Met243Ter	p.M243*	ENST00000269305	NM_001126112.2	243	ATGGGCGGCAtg/tg	7/11	0.853653270806097	1	FACETS	0.995	0.942	1	0.995	0.942	1	CLONAL	1	TRUE	0	0.853653270806097	1		222	189	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696449	47696449	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000505-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	52	239	0	ENST00000347630.2:c.374T>G	p.Phe125Cys	p.F125C	ENST00000347630	NM_001007230.1	125	tTt/tGt	6/11	1	2	FACETS	0.494	0.419	0.577	0.494	0.419	0.577	SUBCLONAL	1	TRUE	1	0.22	2		239	956	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225400279	225400279	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000505-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	62	177	0	ENST00000264414.4:c.344C>G	p.Ala115Gly	p.A115G	ENST00000264414	NM_003590.4	115	gCt/gGt	3/16	1	2	FACETS	0.611	0.526	0.704	0.611	0.526	0.704	SUBCLONAL	1	TRUE	1	0.22	2		177	922	SUCCESS
ATR	545	MSKCC	GRCh37	3	142177822	142177822	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000505-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	42	142	0	ENST00000350721.4:c.7481A>C	p.Asp2494Ala	p.D2494A	ENST00000350721	NM_001184.3	2494	gAt/gCt	44/47	1	2	FACETS	0.583	0.486	0.691	0.583	0.486	0.691	SUBCLONAL	1	TRUE	1	0.22	2		142	655	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627337	37627340	+	frameshift_variant	Frame_Shift_Del	DEL	AAGG	AAGG	-	novel	NA	P-0000505-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	103	158	0	ENST00000447079.4:c.1253_1256del	p.Lys418SerfsTer17	p.K418Sfs*17	ENST00000447079	NM_015083.1	418	AAGGag/ag	2/14	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.22	2		158	759	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0000512-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	126	445	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		445	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0000513-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	119	593	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.334405750460146	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.334405750460146	1		593	440	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845196	151845196	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs968112164	NA	P-0000513-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	113	422	0	ENST00000262189.6:c.13816G>C	p.Asp4606His	p.D4606H	ENST00000262189	NM_170606.2	4606	Gat/Cat	52/59	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.334405750460146	2		422	488	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006442	12006442	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000513-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	109	589	1	ENST00000396373.4:c.410G>T	p.Gly137Val	p.G137V	ENST00000396373	NM_001987.4	137	gGa/gTa	4/8	0.334405750460146	6	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.334405750460146	6		590	765	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636168	28636168	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000513-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	43	393	0	ENST00000241453.7:c.204A>C	p.Arg68Ser	p.R68S	ENST00000241453	NM_004119.2	68	agA/agC	3/24	0.269270299744329	0	FACETS	0.344	0.288	0.407			1	SUBCLONAL	1	TRUE	0	0.334405750460146	0		393	497	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953916	32953916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000513-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	141	392	0	ENST00000380152.3:c.8983G>A	p.Asp2995Asn	p.D2995N	ENST00000380152		2995	Gat/Aat	23/27	0.159551783436372	2	FACETS	1	0.987	1	0.724	0.663	0.789	INDETERMINATE	1	TRUE	0	0.334405750460146	2		392	582	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73343051	73343051	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0000513-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	51	252	0	ENST00000377767.4:c.1756-1G>T		p.X586_splice	ENST00000377767	NM_014953.3	586			0.159551783436372	2	FACETS	0.782	0.667	0.908	0.391	0.333	0.454	INDETERMINATE	1	TRUE	0	0.334405750460146	2		252	390	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298691	15298691	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0000513-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	18	342	0	ENST00000263388.2:c.1606+1G>C		p.X536_splice	ENST00000263388	NM_000435.2	536			0.334405750460146	1	FACETS	0.316	0.237	0.408	0.316	0.237	0.408	SUBCLONAL	1	TRUE	0	0.334405750460146	1		342	284	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs17849781	NA	P-0000532-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	310	367	0	ENST00000269305.4:c.832C>A	p.Pro278Thr	p.P278T	ENST00000269305	NM_001126112.2	278	Cct/Act	8/11	0.46026555094901	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.478552038827816	2		367	610	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727087	243727087	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000532-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	216	294	0	ENST00000263826.5:c.883G>C	p.Glu295Gln	p.E295Q	ENST00000263826	NM_005465.4	295	Gaa/Caa	9/13	0.478552038827816	5	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.478552038827816	5		294	1181	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972825	25972825	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000532-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	426	325	0	ENST00000435504.4:c.1600G>A	p.Glu534Lys	p.E534K	ENST00000435504		534	Gaa/Aaa	12/13	0.478552038827816	3	FACETS	0.983	0.946	1	0.983	0.946	1	CLONAL	3	TRUE	0	0.478552038827816	3		325	748	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518560	204518560	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0000532-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	123	190	0	ENST00000367182.3:c.1223C>G	p.Ser408Ter	p.S408*	ENST00000367182	NM_001278516.1	408	tCa/tGa	11/11	0.478552038827816	7	FACETS	1	0.913	1			1	CLONAL	1	TRUE	NA	0.478552038827816	7		190	1115	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660388	227660388	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000532-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	80	120	0	ENST00000305123.5:c.3067G>T	p.Glu1023Ter	p.E1023*	ENST00000305123	NM_005544.2	1023	Gag/Tag	1/2	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.478552038827816	2		120	326	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017578	112017578	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000532-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	150	426	0	ENST00000368678.4:c.935C>T	p.Ala312Val	p.A312V	ENST00000368678		312	gCg/gTg	9/13	0.44736330667509	3	FACETS	0.838	0.766	0.914	0.419	0.383	0.457	CLONAL	1	TRUE	1	0.478552038827816	3		426	927	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217909	2217909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1230117726	NA	P-0000532-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	111	239	0	ENST00000398665.3:c.2683G>A	p.Glu895Lys	p.E895K	ENST00000398665	NM_032482.2	895	Gag/Aag	22/28	0.44736330667509	3	FACETS	1	0.952	1	0.544	0.491	0.6	CLONAL	1	TRUE	1	0.478552038827816	3		239	528	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395649	31395649	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000532-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	237	253	0	ENST00000328111.2:c.2502G>A	p.Trp834Ter	p.W834*	ENST00000328111	NM_006892.3	834	tgG/tgA	23/23	0.406410800121908	4	FACETS	0.97	0.909	1	0.97	0.909	1	CLONAL	2	TRUE	2	0.478552038827816	4		253	755	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99192904	99192907	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTG	AGTG	-	rs779160550	NA	P-0000532-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1512	105	228	0	ENST00000268035.6:c.94+3_94+6del		p.X32_splice	ENST00000268035	NM_000875.3	32		1/21	0.478552038827816	11	FACETS	0.856	0.763	0.955			1	CLONAL	1	TRUE	NA	0.478552038827816	11		228	1617	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0000543-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	185	428	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.507017762436966	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	0	0.522303437200804	1		428	469	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457242	25457242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147001633	NA	P-0000543-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	10	252	2	ENST00000264709.3:c.2645G>A	p.Arg882His	p.R882H	ENST00000264709	NM_175629.2	882	cGc/cAc	23/23	1	2	FACETS	0.109	0.073	0.155	0.109	0.073	0.155	SUBCLONAL	1	FALSE	1	0.522303437200804	2		254	350	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770132	56770132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766958594	NA	P-0000543-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	83	403	0	ENST00000337432.4:c.128C>T	p.Pro43Leu	p.P43L	ENST00000337432	NM_058216.2	43	cCc/cTc	1/9	0.221073064141124	2	FACETS	0.46	0.406	0.518	0.23	0.203	0.259	INDETERMINATE	1	FALSE	0	0.522303437200804	2		403	691	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0000553-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	152	415	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.602439349965552	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.602439349965552	1		415	350	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0000553-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	55	445	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.383723355611739	4	FACETS	0.369	0.314	0.428			1	SUBCLONAL	1	TRUE	NA	0.602439349965552	4		446	794	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0000553-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	24	329	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.383723355611739	4	FACETS	0.16	0.125	0.202			1	SUBCLONAL	1	TRUE	NA	0.602439349965552	4		329	796	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161298269	161298269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000553-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	49	363	0	ENST00000367975.2:c.161C>T	p.Pro54Leu	p.P54L	ENST00000367975	NM_003001.3	54	cCc/cTc	3/6	0.36047144243225	3	FACETS	0.341	0.289	0.4	0.114	0.096	0.134	INDETERMINATE	1	TRUE	0	0.602439349965552	3		363	620	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402023	402023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000553-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	235	554	0	ENST00000399788.2:c.4768G>A	p.Asp1590Asn	p.D1590N	ENST00000399788	NM_001042603.1	1590	Gac/Aac	27/28	0.335688993282662	3	FACETS	0.966	0.901	1			1	INDETERMINATE	1	TRUE	NA	0.602439349965552	3		554	1051	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10277309	10277309	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000553-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	61	570	0	ENST00000340748.4:c.808G>T	p.Val270Leu	p.V270L	ENST00000340748		270	Gtg/Ttg	10/40	0.473208985394428	1	FACETS	0.354	0.306	0.405	0.354	0.306	0.405	SUBCLONAL	1	TRUE	0	0.602439349965552	1		570	400	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456527	189456527	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000555-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	113	195	0	ENST00000264731.3:c.288C>G	p.Ile96Met	p.I96M	ENST00000264731	NM_003722.4	96	atC/atG	3/14	1	2	FACETS	0.459	0.413	0.506	0.459	0.413	0.506	SUBCLONAL	1	TRUE	1	0.810677959314819	2		195	608	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039225	49039225	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000555-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	466	298	0	ENST00000267163.4:c.2306del	p.Leu769CysfsTer41	p.L769Cfs*41	ENST00000267163	NM_000321.2	768	aTt/at	22/27	0.810677959314819	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.810677959314819	1		298	673	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050679	30050679	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000581-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	612	352	0	ENST00000338641.4:c.481G>T	p.Gly161Ter	p.G161*	ENST00000338641	NM_000268.3	161	Gga/Tga	5/16	0.905716948231711	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.905716948231711	1		352	739	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575447	64575466	+	frameshift_variant	Frame_Shift_Del	DEL	CCCATTGGGCCCAAACACTA	CCCATTGGGCCCAAACACTA	-	novel	NA	P-0000581-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	247	360	0	ENST00000312049.6:c.551_570del	p.Val184GlyfsTer5	p.V184Gfs*5	ENST00000312049	NM_130799.2	184	gTAGTGTTTGGGCCCAATGGG/g	3/10	0.905716948231711	1	FACETS	0.656	0.622	0.689	0.656	0.622	0.689	SUBCLONAL	1	TRUE	0	0.905716948231711	1		360	455	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115956	8115956	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000595-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	109	144	0	ENST00000346208.3:c.1305del	p.Ser436ProfsTer39	p.S436Pfs*39	ENST00000346208		434	caC/ca	6/6	0.1707039933697	5	FACETS	0.768	0.694	0.846	0.512	0.462	0.564	INDETERMINATE	2	TRUE	2	0.576249375337647	5		144	459	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0000599-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	240	311	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	0.506473920093294	2		311	881	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0000599-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	102	129	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	0.506473920093294	2		129	372	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69788764	69788764	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000599-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	174	266	0	ENST00000352241.4:c.16G>C	p.Gly6Arg	p.G6R	ENST00000352241	NM_198159.2	6	Ggg/Cgg	1/10	0.506473920093294	1	FACETS	0.97	0.899	1	0.97	0.899	1	CLONAL	1	TRUE	0	0.506473920093294	1		266	529	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468490	89468490	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000600-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	116	235	0	ENST00000336596.2:c.2024G>T	p.Gly675Val	p.G675V	ENST00000336596	NM_005233.5	675	gGa/gTa	11/17	0.338300248158378	4	FACETS	0.944	0.85	1	0.472	0.425	0.522	CLONAL	1	FALSE	2	0.338300248158378	4		235	972	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462780	69462780	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs759570740	NA	P-0000600-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	257	325	0	ENST00000227507.2:c.593A>G	p.Asn198Ser	p.N198S	ENST00000227507	NM_053056.2	198	aAt/aGt	4/5	0.220734528287446	5	FACETS	0.993	0.933	1	0.993	0.933	1	CLONAL	3	FALSE	2	0.338300248158378	5		325	769	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0000627-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	135	271	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.253343755705283	2	FACETS	0.998	0.919	1	1	0.988	1	CLONAL	3	TRUE	0	0.253343755705283	2		271	356	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088729	27088729	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000627-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	121	411	0	ENST00000324856.7:c.2338C>T	p.Gln780Ter	p.Q780*	ENST00000324856	NM_006015.4	780	Cag/Tag	7/20	NA	2	FACETS	0.787	0.713	0.864			1	INDETERMINATE	2	TRUE	NA	0.253343755705283	2		411	607	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498012	29498012	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000627-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	175	698	0	ENST00000389048.3:c.1994A>C	p.Lys665Thr	p.K665T	ENST00000389048	NM_004304.4	665	aAa/aCa	11/29	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.253343755705283	2		698	1071	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670486	134670486	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000627-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	131	434	0	ENST00000398015.3:c.397C>A	p.Pro133Thr	p.P133T	ENST00000398015	NM_004441.4	133	Ccc/Acc	3/16	0.189499695847155	2	FACETS	0.78	0.709	0.854	0.78	0.709	0.854	SUBCLONAL	2	TRUE	0	0.253343755705283	2		434	663	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612175	189612175	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1560311554	NA	P-0000627-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	81	476	0	ENST00000264731.3:c.1927C>T	p.Arg643Ter	p.R643*	ENST00000264731	NM_003722.4	643	Cga/Tga	14/14	0.214459891738457	4	FACETS	0.812	0.714	0.918	0.406	0.357	0.459	CLONAL	1	TRUE	2	0.253343755705283	4		476	987	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633797	86633797	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000627-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	165	236	0	ENST00000274376.6:c.906A>T	p.Leu302Phe	p.L302F	ENST00000274376	NM_002890.2	302	ttA/ttT	5/25	0.253343755705283	3	FACETS	0.931	0.856	1	0.931	0.856	1	CLONAL	2	TRUE	1	0.253343755705283	3		236	788	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675424	30675424	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000627-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	148	454	0	ENST00000376406.3:c.2932G>T	p.Gly978Ter	p.G978*	ENST00000376406	NM_014641.2	978	Gga/Tga	8/15	0.198825858410781	5	FACETS	1	0.917	1	0.668	0.611	0.729	CLONAL	2	TRUE	2	0.253343755705283	5		454	804	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499654	8499654	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1434452721	NA	P-0000627-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	204	276	0	ENST00000356435.5:c.2315A>T	p.Asp772Val	p.D772V	ENST00000356435		772	gAt/gTt	14/35	0.253343755705283	4	FACETS	0.981	0.913	1	0.981	0.913	1	CLONAL	3	TRUE	1	0.253343755705283	4		276	686	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431898	49431898	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000627-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	74	304	0	ENST00000301067.7:c.9241G>T	p.Glu3081Ter	p.E3081*	ENST00000301067	NM_003482.3	3081	Gaa/Taa	34/54	0.253343755705283	3	FACETS	1	0.968	1	0.665	0.583	0.752	CLONAL	1	TRUE	1	0.253343755705283	3		304	495	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434196	121434196	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000627-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	87	395	0	ENST00000257555.6:c.1087C>A	p.Leu363Met	p.L363M	ENST00000257555		363	Ctg/Atg	5/10	0.253343755705283	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.253343755705283	1		395	528	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967506	26967506	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000627-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	113	353	0	ENST00000381527.3:c.649A>G	p.Ile217Val	p.I217V	ENST00000381527	NM_001260.1	217	Att/Gtt	7/13	0.253343755705283	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.253343755705283	1		353	645	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134418	2134418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45466399	NA	P-0000627-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	238	613	2	ENST00000219476.3:c.4195G>A	p.Gly1399Arg	p.G1399R	ENST00000219476	NM_000548.3	1399	Ggg/Agg	34/42	0.241794047789466	3	FACETS	0.963	0.899	1			1	CLONAL	2	TRUE	NA	0.253343755705283	3		615	1099	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89825100	89825100	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000627-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	63	294	0	ENST00000389301.3:c.2866C>T	p.Gln956Ter	p.Q956*	ENST00000389301	NM_000135.2	956	Cag/Tag	30/43	0.159656395496713	1	FACETS	0.877	0.76	1	0.877	0.76	1	CLONAL	1	TRUE	0	0.253343755705283	1		294	495	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587385	29587385	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0000627-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	100	344	0	ENST00000356175.3:c.4368-2A>T		p.X1456_splice	ENST00000356175	NM_000267.3	1456			0.253343755705283	3	FACETS	0.842	0.751	0.94	0.421	0.375	0.47	CLONAL	1	TRUE	1	0.253343755705283	3		344	1056	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714705	52714705	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000627-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	78	364	0	ENST00000322088.6:c.463T>A	p.Tyr155Asn	p.Y155N	ENST00000322088	NM_014225.5	155	Tac/Aac	4/15	0.253343755705283	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.253343755705283	1		364	398	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613371	100613371	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000627-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	83	414	0	ENST00000308731.7:c.1029G>T	p.Gln343His	p.Q343H	ENST00000308731	NM_000061.2	343	caG/caT	12/19	0.253343755705283	0	FACETS	0.871	0.77	0.978			1	CLONAL	1	TRUE	0	0.253343755705283	0		414	562	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615556	100615556	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000627-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	97	687	0	ENST00000308731.7:c.776G>T	p.Gly259Val	p.G259V	ENST00000308731	NM_000061.2	259	gGg/gTg	8/19	0.253343755705283	0	FACETS	0.677	0.603	0.756			1	SUBCLONAL	1	TRUE	0	0.253343755705283	0		687	845	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229223	123229223	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000627-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	122	495	0	ENST00000218089.9:c.3707C>T	p.Pro1236Leu	p.P1236L	ENST00000218089	NM_001042749.1	1236	cCa/cTa	34/35	0.160916779820561	1	FACETS	0.742	0.669	0.819	0.742	0.669	0.819	SUBCLONAL	1	TRUE	0	0.253343755705283	1		495	1134	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206647728	206647728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000627-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	118	284	0	ENST00000367120.3:c.145del	p.Arg49AlafsTer5	p.R49Afs*5	ENST00000367120	NM_014002.3	48	Ccc/cc	4/22	0.253343755705283	5	FACETS	1	0.912	1	0.505	0.456	0.556	CLONAL	2	TRUE	1	0.253343755705283	5		284	637	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900060	151900060	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000627-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	389	548	5	ENST00000262189.6:c.4051del	p.Arg1351GlyfsTer23	p.R1351Gfs*23	ENST00000262189	NM_170606.2	1351	Agg/gg	26/59	0.253343755705283	3	FACETS	0.875	0.831	0.92			1	CLONAL	3	TRUE	NA	0.253343755705283	3		553	1318	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665152	29665158	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	AGCAAGG	AGCAAGG	-	novel	NA	P-0000627-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	84	207	0	ENST00000356175.3:c.6751_6756+1del		p.X2251_splice	ENST00000356175	NM_000267.3	2251		44/57	0.253343755705283	3	FACETS	1	0.965	1	0.622	0.549	0.699	CLONAL	1	TRUE	1	0.253343755705283	3		207	601	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750377	133750377	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000629-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	461	448	567	0	ENST00000318560.5:c.1208T>C	p.Ile403Thr	p.I403T	ENST00000318560	NM_005157.4	403	aTc/aCc	7/11	0.420017314879406	3	FACETS	0.867	0.832	0.902	0.867	0.832	0.902	INDETERMINATE	2	FALSE	1	0.794440239271377	3		567	909	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42840334	42840334	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867186402	NA	P-0000633-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	44	386	0	ENST00000398585.3:c.1414G>A	p.Asp472Asn	p.D472N	ENST00000398585	NM_001135099.1	472	Gat/Aat	12/14	0.14523930448459	6	FACETS	1	0.913	1	0.286	0.239	0.338	CLONAL	1	FALSE	2	0.14523930448459	6		386	683	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057302	30057302	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315496	NA	P-0000633-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	162	412	0	ENST00000338641.4:c.784C>T	p.Arg262Ter	p.R262*	ENST00000338641	NM_000268.3	262	Cga/Tga	8/16	0.14523930448459	0	FACETS	1	0.949	1			1	CLONAL	4	FALSE	0	0.14523930448459	0		412	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579440	7579440	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs867725248	NA	P-0000633-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	150	310	0	ENST00000269305.4:c.247del	p.Ala83ArgfsTer40	p.A83Rfs*40	ENST00000269305	NM_001126112.2	83	Gcg/cg	4/11	0.14523930448459	3	FACETS	1	0.97	1	1	0.994	1	CLONAL	8	FALSE	0	0.14523930448459	3		310	261	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0000636-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	134	322	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.41446084103939	5	FACETS	1	0.966	1	0.739	0.676	0.804	CLONAL	2	TRUE	2	0.41446084103939	5		322	473	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442023	52442023	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1553645939	NA	P-0000636-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	118	243	0	ENST00000460680.1:c.326G>T	p.Gly109Val	p.G109V	ENST00000460680	NM_004656.3	109	gGa/gTa	5/17	0.412599836803712	2	FACETS	0.924	0.846	1	0.924	0.846	1	CLONAL	2	TRUE	0	0.41446084103939	2		243	308	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975399	13975399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs186330943	NA	P-0000636-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	79	206	0	ENST00000405192.2:c.488G>A	p.Arg163Gln	p.R163Q	ENST00000405192	NM_001163147.1	163	cGg/cAg	7/12	0.41446084103939	5	FACETS	0.896	0.794	1	0.597	0.529	0.669	CLONAL	2	TRUE	2	0.41446084103939	5		206	345	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281190	15281190	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000636-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	50	544	0	ENST00000263388.2:c.5066G>C	p.Gly1689Ala	p.G1689A	ENST00000263388	NM_000435.2	1689	gGt/gCt	27/33	0.347227964838762	4	FACETS	0.634	0.538	0.74			1	SUBCLONAL	1	TRUE	NA	0.41446084103939	4		544	538	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412289	139412289	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000641-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	102	401	0	ENST00000277541.6:c.1356C>A	p.Asp452Glu	p.D452E	ENST00000277541	NM_017617.3	452	gaC/gaA	8/34	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.391871817452576	2		401	501	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243668558	243668558	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751275167	NA	P-0000643-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	531	50	240	0	ENST00000263826.5:c.1433G>A	p.Arg478Gln	p.R478Q	ENST00000263826	NM_005465.4	478	cGa/cAa	13/13	0.218010946840312	3	FACETS	0.691	0.585	0.806	0.345	0.292	0.403	SUBCLONAL	1	TRUE	1	0.28472973876397	3		240	581	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0000661-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	75	14	62	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.482465027934982	4	FACETS	0.985	0.722	1	0.492	0.361	0.646	CLONAL	1	TRUE	2	0.469612099020372	4		62	89	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0000661-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	296	10	467	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.251899678900487	4	FACETS	0.205	0.138	0.289	0.102	0.069	0.145	INDETERMINATE	1	TRUE	2	0.469612099020372	4		467	306	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246436	105246436	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000661-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	159	116	388	0	ENST00000349310.3:c.164T>A	p.Phe55Tyr	p.F55Y	ENST00000349310	NM_001014432.1	55	tTc/tAc	4/15	0.251899678900487	4	FACETS	0.88	0.807	0.954	1	0.983	1	INDETERMINATE	3	TRUE	2	0.469612099020372	4		388	275	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458750	120458751	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0000661-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	101	19	144	0	ENST00000256646.2:c.6594_6595del	p.Leu2199IlefsTer4	p.L2199Ifs*4	ENST00000256646	NM_024408.3	2198	gcACta/gcta	34/34	0.364834714853425	3	FACETS	0.833	0.64	1	0.416	0.32	0.527	CLONAL	1	TRUE	1	0.469612099020372	3		144	120	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651282	52651282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000676-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	195	214	0	ENST00000394830.3:c.1814C>T	p.Ser605Phe	p.S605F	ENST00000394830	NM_018313.4	605	tCc/tTc	15/30	0.33422597306516	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	FALSE	0	0.33422597306516	2		214	527	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651430	52651430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000676-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	240	357	0	ENST00000394830.3:c.1666C>T	p.Pro556Ser	p.P556S	ENST00000394830	NM_018313.4	556	Cct/Tct	15/30	0.33422597306516	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	FALSE	0	0.33422597306516	2		357	642	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272163	142272163	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000676-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	283	223	0	ENST00000350721.4:c.2711C>G	p.Ser904Cys	p.S904C	ENST00000350721	NM_001184.3	904	tCt/tGt	13/47	0.33422597306516	3	FACETS	1	0.987	1			1	CLONAL	3	FALSE	NA	0.33422597306516	3		223	588	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486037	8486037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000676-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	149	258	0	ENST00000356435.5:c.2780C>T	p.Ser927Leu	p.S927L	ENST00000356435		927	tCa/tTa	17/35	0.33422597306516	2	FACETS	0.841	0.773	0.912	0.841	0.773	0.912	CLONAL	2	FALSE	0	0.33422597306516	2		258	530	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633620	69633620	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000676-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	16	17	0	ENST00000334134.2:c.82G>C	p.Asp28His	p.D28H	ENST00000334134	NM_005247.2	28	Gat/Cat	1/3	0.33422597306516	5	FACETS	1	0.852	1	0.785	0.598	0.994	CLONAL	2	FALSE	2	0.33422597306516	5		17	61	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342841	118342841	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000676-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	101	168	0	ENST00000534358.1:c.967G>C	p.Glu323Gln	p.E323Q	ENST00000534358	NM_005933.3	323	Gaa/Caa	3/36	0.33422597306516	5	FACETS	0.906	0.813	1	0.604	0.542	0.669	CLONAL	2	FALSE	2	0.33422597306516	5		168	501	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434409	121434409	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000676-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	98	254	0	ENST00000257555.6:c.1173G>C	p.Gln391His	p.Q391H	ENST00000257555		391	caG/caC	6/10	0.33422597306516	5	FACETS	1	0.958	1	0.384	0.342	0.429	CLONAL	1	FALSE	2	0.33422597306516	5		254	764	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577567	7577567	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920789	NA	P-0000676-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	118	124	0	ENST00000269305.4:c.714T>G	p.Cys238Trp	p.C238W	ENST00000269305	NM_001126112.2	238	tgT/tgG	7/11	0.24094057350859	3	FACETS	1	0.93	1	0.683	0.622	0.747	CLONAL	2	FALSE	0	0.33422597306516	3		124	402	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602923	10602923	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370923924	NA	P-0000676-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	160	179	0	ENST00000171111.5:c.655G>A	p.Glu219Lys	p.E219K	ENST00000171111	NM_203500.1	219	Gag/Aag	3/6	0.281820548091193	3	FACETS	1	0.978	1	0.766	0.708	0.826	CLONAL	2	FALSE	0	0.33422597306516	3		179	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0000684-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1243	339	445	0	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.186396581992475	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.186396581992475	2		445	1582	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082280	16082280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1218586780	NA	P-0000684-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1778	170	548	0	ENST00000281043.3:c.94G>A	p.Glu32Lys	p.E32K	ENST00000281043	NM_005378.4	32	Gaa/Aaa	2/3	0.113045720382783	3	FACETS	1	0.934	1	0.512	0.468	0.558	CLONAL	1	TRUE	1	0.186396581992475	3		548	1948	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086007	16086007	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000684-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	86	236	0	ENST00000281043.3:c.1183A>G	p.Asn395Asp	p.N395D	ENST00000281043	NM_005378.4	395	Aac/Gac	3/3	0.113045720382783	3	FACETS	1	0.939	1	0.55	0.485	0.619	CLONAL	1	TRUE	1	0.186396581992475	3		236	917	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898819	134898819	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000684-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	152	258	0	ENST00000398015.3:c.1877G>T	p.Gly626Val	p.G626V	ENST00000398015	NM_004441.4	626	gGa/gTa	10/16	0.186396581992475	6	FACETS	0.947	0.864	1	0.474	0.432	0.517	CLONAL	2	TRUE	2	0.186396581992475	6		258	1182	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659245	86659245	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554048066	NA	P-0000684-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	114	258	0	ENST00000274376.6:c.1534C>T	p.Arg512Ter	p.R512*	ENST00000274376	NM_002890.2	512	Cga/Tga	11/25	0.179339401141664	2	FACETS	0.932	0.841	1	0.932	0.841	1	CLONAL	2	TRUE	0	0.186396581992475	2		258	656	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117632202	117632202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139881304	NA	P-0000684-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	47	165	0	ENST00000368508.3:c.6214C>T	p.Arg2072Trp	p.R2072W	ENST00000368508	NM_002944.2	2072	Cgg/Tgg	39/43	0.0585639195406473	4	FACETS	1	0.931	1	0.598	0.505	0.701	INDETERMINATE	1	TRUE	2	0.186396581992475	4		165	500	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005068	150005068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000684-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	125	193	0	ENST00000253339.5:c.1157C>T	p.Pro386Leu	p.P386L	ENST00000253339		386	cCt/cTt	3/7	0.0585639195406473	4	FACETS	1	0.948	1	1	0.948	1	INDETERMINATE	2	TRUE	2	0.186396581992475	4		193	744	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246147	46246147	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000684-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	99	251	0	ENST00000334344.6:c.4241G>C	p.Arg1414Thr	p.R1414T	ENST00000334344	NM_152641.2	1414	aGa/aCa	15/21	0.186396581992475	5	FACETS	1	0.907	1	1	0.907	1	CLONAL	2	TRUE	3	0.186396581992475	5		251	669	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39600669	39600669	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000684-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	59	407	0	ENST00000262039.4:c.1484G>A	p.Trp495Ter	p.W495*	ENST00000262039	NM_002647.2	495	tGg/tAg	13/25	NA	2	FACETS	0.798	0.685	0.922			1	INDETERMINATE	1	TRUE	NA	0.186396581992475	2		407	793	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303605	30303605	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000684-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	214	264	0	ENST00000262643.3:c.33G>T	p.Lys11Asn	p.K11N	ENST00000262643	NM_001238.2	11	aaG/aaT	3/12	0.0585639195406473	4	FACETS	1	0.978	1	1	0.978	1	INDETERMINATE	2	TRUE	2	0.186396581992475	4		264	1205	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308383	15308383	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000684-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1536	314	465	0	ENST00000263388.2:c.125del	p.Pro42LeufsTer194	p.P42Lfs*194	ENST00000263388	NM_000435.2	42	cCt/ct	2/33	0.0585639195406473	4	FACETS	1	0.978	1	1	0.978	1	INDETERMINATE	2	TRUE	2	0.186396581992475	4		465	1850	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40998459	40998459	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000693-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	211	444	2	ENST00000267868.3:c.310A>G	p.Thr104Ala	p.T104A	ENST00000267868	NM_002875.4	104	Act/Gct	4/10	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.732875871974759	2		446	573	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230523	46230523	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0000708-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	123	228	0	ENST00000334344.6:c.773-1G>C		p.X258_splice	ENST00000334344	NM_152641.2	258			0.802025745747997	9	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.802025745747997	9		228	940	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230543	46230543	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000708-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	135	239	0	ENST00000334344.6:c.792G>T	p.Trp264Cys	p.W264C	ENST00000334344	NM_152641.2	264	tgG/tgT	8/21	0.802025745747997	9	FACETS	1	0.976	1			1	CLONAL	1	TRUE	NA	0.802025745747997	9		239	1044	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113172	209113172	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000722-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	44	414	0	ENST00000345146.2:c.335T>C	p.Ile112Thr	p.I112T	ENST00000345146	NM_005896.2	112	aTt/aCt	4/10	0.209873142156776	3	FACETS	0.773	0.648	0.913	0.387	0.324	0.457	CLONAL	1	TRUE	1	0.209873142156776	3		414	599	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293174	212293174	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000733-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	17	312	0	ENST00000342788.4:c.2678A>G	p.His893Arg	p.H893R	ENST00000342788	NM_005235.2	893	cAt/cGt	22/28	1	2	FACETS	0.355	0.265	0.461	0.355	0.265	0.461	SUBCLONAL	1	TRUE	1	0.404247418849221	2		312	237	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0000740-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	10	415	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.570292526518234	2	FACETS	0.078	0.052	0.111	0.039	0.026	0.056	SUBCLONAL	1	TRUE	0	0.570292526518234	2		415	450	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390656	139390656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1160184715	NA	P-0000740-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	173	284	0	ENST00000277541.6:c.7535C>T	p.Pro2512Leu	p.P2512L	ENST00000277541	NM_017617.3	2512	cCg/cTg	34/34	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.570292526518234	2		284	448	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624300	89624300	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786204912	NA	P-0000740-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	17	105	0	ENST00000371953.3:c.74T>C	p.Leu25Ser	p.L25S	ENST00000371953	NM_000314.4	25	tTg/tCg	1/9	0.560783471902168	2	FACETS	0.206	0.154	0.269	0.103	0.077	0.135	SUBCLONAL	1	TRUE	0	0.570292526518234	2		105	289	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426601	49426601	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000740-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	285	351	0	ENST00000301067.7:c.11887C>T	p.Gln3963Ter	p.Q3963*	ENST00000301067	NM_003482.3	3963	Cag/Tag	39/54	0.433608136160947	4	FACETS	0.974	0.919	1	0.974	0.919	1	CLONAL	2	TRUE	2	0.570292526518234	4		351	806	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs967461896	NA	P-0000740-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	10	152	0	ENST00000269305.4:c.526T>C	p.Cys176Arg	p.C176R	ENST00000269305	NM_001126112.2	176	Tgc/Cgc	5/11	0.570292526518234	2	FACETS	0.187	0.126	0.262	0.093	0.063	0.131	SUBCLONAL	1	TRUE	0	0.570292526518234	2		152	188	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0000742-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	94	181	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.464456588175372	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.464456588175372	1		181	268	SUCCESS
APC	324	MSKCC	GRCh37	5	112175235	112175235	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000742-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	142	147	0	ENST00000257430.4:c.3944C>A	p.Ser1315Ter	p.S1315*	ENST00000257430	NM_000038.5	1315	tCa/tAa	16/16	0.424591899746967	2	FACETS	0.869	0.802	0.936	0.869	0.802	0.936	CLONAL	2	TRUE	0	0.464456588175372	2		147	352	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951838	2951838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199916182	NA	P-0000742-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	238	341	0	ENST00000396946.4:c.3112G>A	p.Ala1038Thr	p.A1038T	ENST00000396946	NM_032415.4	1038	Gcc/Acc	23/25	NA	2	FACETS	0.765	0.718	0.813			1	INDETERMINATE	2	TRUE	NA	0.464456588175372	2		341	670	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17743002	17743002	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000742-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	39	276	0	ENST00000250003.3:c.910G>A	p.Ala304Thr	p.A304T	ENST00000250003	NM_002478.4	304	Gcc/Acc	3/3	1	2	FACETS	0.498	0.414	0.592	0.498	0.414	0.592	SUBCLONAL	1	TRUE	1	0.464456588175372	2		276	337	SUCCESS
AR	367	MSKCC	GRCh37	X	66905872	66905872	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137852569	NA	P-0000742-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	131	225	0	ENST00000374690.3:c.1789G>A	p.Ala597Thr	p.A597T	ENST00000374690	NM_000044.3	597	Gcc/Acc	3/8	1	1	FACETS	0.747	0.68	0.816	0.747	0.68	0.816	SUBCLONAL	1	TRUE	0	0.464456588175372	1		225	580	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0000765-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	185	520	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.759	0.707	0.812	1	0.991	1	SUBCLONAL	2	TRUE	1	0.49220627502483	2		520	495	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467167	25467167	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000765-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	124	250	0	ENST00000264709.3:c.1708G>T	p.Gly570Trp	p.G570W	ENST00000264709	NM_175629.2	570	Ggg/Tgg	15/23	1	2	FACETS	0.845	0.767	0.927	0.845	0.767	0.927	CLONAL	1	TRUE	1	0.49220627502483	2		250	596	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149863	202149863	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000765-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	128	217	0	ENST00000358485.4:c.1304A>T	p.Glu435Val	p.E435V	ENST00000358485	NM_001080125.1	435	gAg/gTg	8/9	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.49220627502483	2		217	513	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803464	1803464	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000765-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	80	214	0	ENST00000260795.2:c.733G>C	p.Val245Leu	p.V245L	ENST00000260795		245	Gtg/Ctg	5/17	1	2	FACETS	0.637	0.562	0.717	0.637	0.562	0.717	SUBCLONAL	1	TRUE	1	0.49220627502483	2		214	510	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201843	66201843	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000765-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	87	144	0	ENST00000273854.3:c.2659G>C	p.Val887Leu	p.V887L	ENST00000273854	NM_004439.5	887	Gtg/Ctg	16/18	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.49220627502483	2		144	330	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589642	67589642	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000765-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	59	97	0	ENST00000274335.5:c.1405G>T	p.Glu469Ter	p.E469*	ENST00000274335		469	Gaa/Taa	10/15	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.49220627502483	2		97	217	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287818	33287818	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000765-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	192	308	0	ENST00000374542.5:c.1435G>C	p.Glu479Gln	p.E479Q	ENST00000374542	NM_001141970.1	479	Gag/Cag	5/8	1	2	FACETS	0.916	0.848	0.986	0.916	0.848	0.986	CLONAL	1	TRUE	1	0.49220627502483	2		308	852	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161990392	161990392	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000765-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	102	229	0	ENST00000366898.1:c.928G>T	p.Glu310Ter	p.E310*	ENST00000366898	NM_004562.2	310	Gag/Tag	8/12	0.461205201869468	1	FACETS	0.88	0.795	0.969	0.88	0.795	0.969	CLONAL	1	TRUE	0	0.49220627502483	1		229	355	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495077	56495077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746015375	NA	P-0000765-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	150	250	0	ENST00000267101.3:c.3434C>T	p.Pro1145Leu	p.P1145L	ENST00000267101	NM_001982.3	1145	cCa/cTa	27/28	1	2	FACETS	0.867	0.794	0.943	0.867	0.794	0.943	CLONAL	1	TRUE	1	0.49220627502483	2		250	703	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888210	112888210	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121918464	NA	P-0000765-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	126	252	0	ENST00000351677.2:c.226G>C	p.Glu76Gln	p.E76Q	ENST00000351677	NM_002834.3	76	Gag/Cag	3/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.49220627502483	2		252	450	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118863	115118863	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000765-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	124	229	0	ENST00000257566.3:c.478G>T	p.Asp160Tyr	p.D160Y	ENST00000257566	NM_016569.3	160	Gac/Tac	2/8	1	2	FACETS	0.933	0.848	1	0.933	0.848	1	CLONAL	1	TRUE	1	0.49220627502483	2		229	540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0000765-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	85	145	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.461205201869468	1	FACETS	0.862	0.771	0.958	0.862	0.771	0.958	CLONAL	1	TRUE	0	0.49220627502483	1		145	302	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735503	40735503	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000765-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	128	221	0	ENST00000373198.4:c.3370G>T	p.Glu1124Ter	p.E1124*	ENST00000373198	NM_133170.3	1124	Gag/Tag	25/32	NA	2	FACETS	0.895	0.814	0.98			1	INDETERMINATE	1	TRUE	NA	0.49220627502483	2		221	581	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778738	76778738	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000765-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	108	404	0	ENST00000373344.5:c.6841G>T	p.Glu2281Ter	p.E2281*	ENST00000373344	NM_000489.3	2281	Gag/Tag	31/35	0.49220627502483	0	FACETS	0.771	0.702	0.841			1	SUBCLONAL	1	TRUE	0	0.49220627502483	0		404	289	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106048	27106056	+	inframe_deletion	In_Frame_Del	DEL	GGTACACCA	GGTACACCA	-	novel	NA	P-0000765-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	49	113	0	ENST00000324856.7:c.5661_5669del	p.Pro1889_Thr1891del	p.P1889_T1891del	ENST00000324856	NM_006015.4	1887	GGTACACCA/-	20/20	1	2	FACETS	0.535	0.455	0.623	0.535	0.455	0.623	SUBCLONAL	1	TRUE	1	0.49220627502483	2		113	372	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0000774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	77	62	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.754745128625017	3	FACETS	0.789	0.698	0.886	0.395	0.349	0.443	SUBCLONAL	1	TRUE	1	0.754745128625017	3		62	356	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0000774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	192	320	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.705549816749614	4	FACETS	1	0.965	1	0.535	0.496	0.576	CLONAL	1	TRUE	2	0.754745128625017	4		320	834	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0000774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	188	525	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.705549816749614	4	FACETS	1	0.978	1	0.569	0.527	0.613	CLONAL	1	TRUE	2	0.754745128625017	4		525	768	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259289	16259289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	14	88	0	ENST00000375759.3:c.6554C>T	p.Ser2185Phe	p.S2185F	ENST00000375759	NM_015001.2	2185	tCt/tTt	11/15	NA	2	FACETS	0.16	0.115	0.214			1	INDETERMINATE	1	TRUE	NA	0.754745128625017	2		88	232	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405991	70405991	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	237	341	0	ENST00000373644.4:c.3505C>T	p.Gln1169Ter	p.Q1169*	ENST00000373644	NM_030625.2	1169	Caa/Taa	4/12	0.754745128625017	3	FACETS	0.995	0.931	1	0.498	0.465	0.531	CLONAL	1	TRUE	1	0.754745128625017	3		341	869	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220400	1220400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	51	316	0	ENST00000326873.7:c.493G>A	p.Glu165Lys	p.E165K	ENST00000326873	NM_000455.4	165	Gag/Aag	4/10	NA	2	FACETS	0.183	0.155	0.214			1	INDETERMINATE	1	TRUE	NA	0.754745128625017	2		316	738	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349191	15349191	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1442837351	NA	P-0000774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	194	288	0	ENST00000263377.2:c.4086C>G	p.Phe1362Leu	p.F1362L	ENST00000263377	NM_058243.2	1362	ttC/ttG	20/20	NA	2	FACETS	0.874	0.814	0.936			1	INDETERMINATE	1	TRUE	NA	0.754745128625017	2		288	588	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944447	40944447	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	220	324	0	ENST00000373198.4:c.2055G>C	p.Lys685Asn	p.K685N	ENST00000373198	NM_133170.3	685	aaG/aaC	12/32	0.734459419803314	2	FACETS	0.917	0.858	0.977	0.458	0.429	0.489	CLONAL	1	TRUE	0	0.754745128625017	2		324	636	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17371325	17371330	+	inframe_deletion	In_Frame_Del	DEL	ATGGCA	ATGGCA	-	novel	NA	P-0000774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	49	378	0	ENST00000375499.3:c.126_131del	p.Ala43_Ile44del	p.A43_I44del	ENST00000375499	NM_003000.2	42	ttTGCCATc/ttc	2/8	NA	2	FACETS	0.154	0.13	0.181			1	INDETERMINATE	1	TRUE	NA	0.754745128625017	2		378	843	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171716	36171720	+	frameshift_variant	Frame_Shift_Del	DEL	CTGAT	CTGAT	-	novel	NA	P-0000774-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	254	169	0	ENST00000300305.3:c.845_849del	p.Asp282ValfsTer316	p.D282Vfs*316	ENST00000300305		282	gATCAG/g	7/8	0.754745128625017	4	FACETS	1	0.993	1	0.737	0.692	0.783	CLONAL	1	TRUE	2	0.754745128625017	4		169	801	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0000776-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	248	181	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.492294329599366	2	FACETS	0.986	0.934	1	0.986	0.934	1	CLONAL	2	TRUE	0	0.533099687934681	2		181	472	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567309	226567309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000776-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	354	274	0	ENST00000366794.5:c.1577C>T	p.Thr526Ile	p.T526I	ENST00000366794	NM_001618.3	526	aCt/aTt	11/23	0.533099687934681	3	FACETS	0.893	0.848	0.938	0.893	0.848	0.938	CLONAL	2	TRUE	1	0.533099687934681	3		274	942	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0000783-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	474	362	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.436695823423288	3	FACETS	0.941	0.905	0.977			1	INDETERMINATE	2	TRUE	NA	0.73082364367582	3		362	941	SUCCESS
APC	324	MSKCC	GRCh37	5	112177930	112177930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35540155	NA	P-0000783-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	164	318	0	ENST00000257430.4:c.6639G>A	p.Met2213Ile	p.M2213I	ENST00000257430	NM_000038.5	2213	atG/atA	16/16	NA	2	FACETS	1	0.963	1			1	INDETERMINATE	1	TRUE	NA	0.73082364367582	2		318	424	SUCCESS
EED	8726	MSKCC	GRCh37	11	85977219	85977219	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000783-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	210	292	0	ENST00000263360.6:c.821T>C	p.Ile274Thr	p.I274T	ENST00000263360	NM_003797.3	274	aTt/aCt	8/12	1	2	FACETS	0.956	0.894	1	0.956	0.894	1	CLONAL	1	TRUE	1	0.73082364367582	2		292	601	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117888	70117888	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs886043537	NA	P-0000783-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	68	223	0	ENST00000245479.2:c.356C>A	p.Ala119Glu	p.A119E	ENST00000245479	NM_000346.3	119	gCg/gAg	1/3	0.620761753561413	3	FACETS	1	0.965	1	0.623	0.551	0.697	CLONAL	1	TRUE	1	0.73082364367582	3		223	204	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914954	32914955	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs80359596	NA	P-0000783-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	160	310	0	ENST00000380152.3:c.6468_6469del	p.Gln2157IlefsTer18	p.Q2157Ifs*18	ENST00000380152		2154	taTCtc/tatc	11/27	NA	2	FACETS	0.888	0.821	0.957			1	INDETERMINATE	1	TRUE	NA	0.73082364367582	2		310	493	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86686665	86686665	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000795-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	88	309	0	ENST00000274376.6:c.3109C>G	p.Gln1037Glu	p.Q1037E	ENST00000274376	NM_002890.2	1037	Caa/Gaa	25/25	0.197068671522286	4	FACETS	0.76	0.671	0.856	0.38	0.335	0.428	SUBCLONAL	1	TRUE	2	0.244451239286438	4		309	1179	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243560	46243560	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs779708870	NA	P-0000795-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	156	233	0	ENST00000334344.6:c.1912+1G>A		p.X638_splice	ENST00000334344	NM_152641.2	638			0.244451239286438	7	FACETS	1	0.927	1			1	CLONAL	2	TRUE	NA	0.244451239286438	7		233	1013	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725097	47725097	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000795-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	120	477	0	ENST00000449228.1:c.647C>T	p.Thr216Ile	p.T216I	ENST00000449228	NM_001127240.2	216	aCc/aTc	4/4	0.244451239286438	3	FACETS	1	0.929	1	0.519	0.467	0.573	CLONAL	1	TRUE	1	0.244451239286438	3		477	1062	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22153384	22153384	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000795-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	99	425	0	ENST00000215832.6:c.526C>A	p.Pro176Thr	p.P176T	ENST00000215832	NM_002745.4	176	Cca/Aca	4/9	0.244451239286438	3	FACETS	0.741	0.66	0.829			1	SUBCLONAL	1	TRUE	NA	0.244451239286438	3		425	1226	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0000797-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	47	405	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.154973390580094	2	FACETS	0.514	0.433	0.603	0.257	0.216	0.302	INDETERMINATE	1	FALSE	0	0.3	2		405	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0000811-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	86	293	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	0.951	0.858	1			1	INDETERMINATE	2	TRUE	NA	0.422750150165395	2		294	214	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0000814-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	100	415	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.39136517632307	5	FACETS	1	0.932	1	0.35	0.314	0.388	INDETERMINATE	1	FALSE	2	0.942346608539194	5		415	488	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405953	49405953	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000814-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	68	391	0	ENST00000418115.1:c.185G>T	p.Gly62Val	p.G62V	ENST00000418115	NM_001664.2	62	gGg/gTg	3/5	0.339083084308298	5	FACETS	0.603	0.524	0.687	0.201	0.174	0.229	INDETERMINATE	1	FALSE	2	0.942346608539194	5		391	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0000829-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	136	271	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.258347487009696	2	FACETS	0.79	0.72	0.864	0.79	0.72	0.864	SUBCLONAL	2	TRUE	0	0.258347487009696	2		271	666	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190717379	190717379	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0000829-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	193	282	0	ENST00000441310.2:c.700-2A>G		p.X234_splice	ENST00000441310	NM_000534.4	234			0.203137198873137	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	2	0.258347487009696	4		282	877	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595873	52595873	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000829-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	396	466	0	ENST00000394830.3:c.4042C>T	p.Gln1348Ter	p.Q1348*	ENST00000394830	NM_018313.4	1348	Caa/Taa	26/30	0.258347487009696	2	FACETS	0.985	0.935	1	0.985	0.935	1	CLONAL	2	TRUE	0	0.258347487009696	2		466	1556	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515169	148515169	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000829-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1547	239	378	0	ENST00000320356.2:c.1040G>A	p.Arg347Gln	p.R347Q	ENST00000320356	NM_004456.4	347	cGg/cAg	10/20	0.258347487009696	6	FACETS	0.786	0.731	0.843	0.393	0.365	0.422	SUBCLONAL	2	TRUE	2	0.258347487009696	6		378	1786	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495119	56495119	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000829-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1325	327	474	0	ENST00000267101.3:c.3476A>T	p.Tyr1159Phe	p.Y1159F	ENST00000267101	NM_001982.3	1159	tAt/tTt	27/28	0.258347487009696	4	FACETS	0.964	0.908	1	0.964	0.908	1	CLONAL	2	TRUE	2	0.258347487009696	4		474	1652	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321626	30321626	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000829-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	345	300	0	ENST00000322652.5:c.1481G>T	p.Cys494Phe	p.C494F	ENST00000322652	NM_015355.2	494	tGt/tTt	13/16	0.258347487009696	5	FACETS	1	0.967	1	1	0.967	1	CLONAL	3	TRUE	2	0.258347487009696	5		300	1201	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0000839-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	289	711	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.354679136667809	2	FACETS	0.955	0.903	1	0.955	0.903	1	CLONAL	2	TRUE	0	0.415116077226069	2		712	729	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0000839-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	99	357	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.715	0.639	0.796	0.715	0.639	0.796	SUBCLONAL	1	TRUE	1	0.415116077226069	2		357	667	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174395	11174395	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1085307113	NA	P-0000839-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	150	313	0	ENST00000361445.4:c.7280T>A	p.Leu2427Gln	p.L2427Q	ENST00000361445	NM_004958.3	2427	cTg/cAg	53/58	1	2	FACETS	0.937	0.858	1	0.937	0.858	1	CLONAL	1	TRUE	1	0.415116077226069	2		313	771	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106827	27106829	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	novel	NA	P-0000846-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	73	236	0	ENST00000324856.7:c.6440_6442del	p.Leu2147del	p.L2147del	ENST00000324856	NM_006015.4	2146	aaGTTg/aag	20/20	0.401689789061792	1	FACETS	0.894	0.788	1	0.894	0.788	1	CLONAL	1	TRUE	0	0.401689789061792	1		236	325	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0000858-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	82	542	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		542	493	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0000864-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	209	711	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.273924847222848	2	FACETS	1	0.976	1	1	0.995	1	CLONAL	4	FALSE	0	0.273924847222848	2		712	361	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161716	56161716	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000864-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	376	268	0	ENST00000399503.3:c.1213del	p.Arg405ValfsTer31	p.R405Vfs*31	ENST00000399503	NM_005921.1	405	Cgt/gt	6/20	0.273924847222848	8	FACETS	0.94	0.896	0.984	0.94	0.896	0.984	CLONAL	6	FALSE	2	0.273924847222848	8		268	887	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167804	56167805	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0000864-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	186	214	0	ENST00000399503.3:c.1370_1371del	p.Thr457SerfsTer3	p.T457Sfs*3	ENST00000399503	NM_005921.1	457	ACa/a	7/20	0.273924847222848	8	FACETS	0.953	0.881	1	0.477	0.44	0.514	CLONAL	3	FALSE	2	0.273924847222848	8		214	865	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0000867-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	66	425	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	0.257704289766095	4	FACETS	1	0.91	1	0.53	0.46	0.605	CLONAL	1	TRUE	2	0.32	4		425	514	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374244	138374244	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000867-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	193	683	0	ENST00000289153.2:c.3200A>T	p.Asp1067Val	p.D1067V	ENST00000289153	NM_006219.2	1067	gAc/gTc	22/22	0.273455096075759	4	FACETS	0.938	0.873	1	0.938	0.873	1	CLONAL	3	TRUE	1	0.32	4		683	566	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724379	117724379	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs2243380	NA	P-0000867-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	27	470	0	ENST00000368508.3:c.500G>T	p.Arg167Leu	p.R167L	ENST00000368508	NM_002944.2	167	cGa/cTa	6/43	0.161096184746417	3	FACETS	0.536	0.427	0.662			1	INDETERMINATE	1	TRUE	NA	0.32	3		470	365	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	441055	441055	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778756065	NA	P-0000867-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	83	489	0	ENST00000399788.2:c.1703G>A	p.Arg568His	p.R568H	ENST00000399788	NM_001042603.1	568	cGt/cAt	13/28	NA	2	FACETS	1	0.922	1			1	INDETERMINATE	1	TRUE	NA	0.32	2		489	493	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022652	12022652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200525003	NA	P-0000867-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	27	358	0	ENST00000396373.4:c.758C>T	p.Pro253Leu	p.P253L	ENST00000396373	NM_001987.4	253	cCg/cTg	5/8	0.3	8	FACETS	0.776	0.622	0.951	0.388	0.311	0.476	CLONAL	2	TRUE	4	0.32	8		358	213	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662370	67662370	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000867-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	17	710	0	ENST00000264010.4:c.1616A>T	p.Asp539Val	p.D539V	ENST00000264010	NM_006565.3	539	gAc/gTc	9/12	1	2	FACETS	0.402	0.3	0.524	0.402	0.3	0.524	SUBCLONAL	1	TRUE	1	0.32	2		710	264	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0000874-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	239	278	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.877	0.825	0.931	0.877	0.825	0.931	CLONAL	1	TRUE	1	0.878647950422323	2		278	620	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0000874-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	282	411	0	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	0.878647950422323	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.878647950422323	1		411	329	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207162	1207162	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs137853076	NA	P-0000876-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	15	283	0	ENST00000326873.7:c.250A>T	p.Lys84Ter	p.K84*	ENST00000326873	NM_000455.4	84	Aag/Tag	1/10	0.174333580306437	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		283	88	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0000898-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	17	375	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.423333483402044	4	FACETS	0.368	0.275	0.478	0.184	0.137	0.239	SUBCLONAL	1	TRUE	2	0.667345632009057	4		375	231	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974732	21974732	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000898-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	21	494	0	ENST00000304494.5:c.95T>A	p.Leu32Gln	p.L32Q	ENST00000304494	NM_000077.4	32	cTg/cAg	1/3	0.385672507540961	3	FACETS	0.724	0.565	0.902	0.362	0.282	0.451	INDETERMINATE	1	TRUE	1	0.667345632009057	3		494	116	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658326	18658326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560894742	NA	P-0000898-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	14	364	0	ENST00000266497.5:c.3131C>T	p.Ser1044Leu	p.S1044L	ENST00000266497		1044	tCg/tTg	22/31	0.21121927219339	5	FACETS	0.451	0.327	0.601	0.15	0.109	0.201	INDETERMINATE	1	TRUE	2	0.667345632009057	5		364	186	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827909	40827909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778174338	NA	P-0000898-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	11	377	0	ENST00000373198.4:c.2519C>T	p.Ser840Phe	p.S840F	ENST00000373198	NM_133170.3	840	tCt/tTt	17/32	0.271553510887452	5	FACETS	0.5	0.347	0.688	0.167	0.115	0.23	INDETERMINATE	1	TRUE	2	0.667345632009057	5		377	132	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0000901-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	264	330	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.442865986022951	3	FACETS	0.753	0.707	0.801	0.753	0.707	0.801	SUBCLONAL	2	TRUE	1	0.455871966816422	3		332	944	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0000901-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	171	221	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.455871966816422	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.455871966816422	1		221	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0000901-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	137	134	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.311245646705204	2	FACETS	0.866	0.798	0.935	0.866	0.798	0.935	CLONAL	2	TRUE	0	0.455871966816422	2		134	347	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259310	16259310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000901-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	14	126	0	ENST00000375759.3:c.6575C>T	p.Ala2192Val	p.A2192V	ENST00000375759	NM_015001.2	2192	gCa/gTa	11/15	NA	2	FACETS	0.219	0.158	0.294			1	INDETERMINATE	1	TRUE	NA	0.455871966816422	2		126	280	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456492	29456492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000901-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1257	170	401	0	ENST00000389048.3:c.2426G>A	p.Arg809Lys	p.R809K	ENST00000389048	NM_004304.4	809	aGa/aAa	14/29	0.455871966816422	3	FACETS	0.642	0.588	0.698	0.321	0.294	0.349	SUBCLONAL	1	TRUE	1	0.455871966816422	3		401	1427	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89176410	89176410	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000901-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	56	156	0	ENST00000336596.2:c.140A>T	p.Tyr47Phe	p.Y47F	ENST00000336596	NM_005233.5	47	tAt/tTt	2/17	0.455871966816422	1	FACETS	0.477	0.409	0.549	0.477	0.409	0.549	SUBCLONAL	1	TRUE	0	0.455871966816422	1		156	398	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534285	534285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894226	NA	P-0000910-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	170	587	0	ENST00000451590.1:c.38G>T	p.Gly13Val	p.G13V	ENST00000451590	NM_001130442.1	13	gGt/gTt	2/5	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.801889396807601	2		587	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0000911-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	598	415	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.420111402865284	4	FACETS	0.993	0.968	1	1	0.998	1	CLONAL	4	TRUE	2	0.589456711600207	4		415	812	SUCCESS
APC	324	MSKCC	GRCh37	5	112175328	112175328	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0000911-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	235	179	0	ENST00000257430.4:c.4037C>G	p.Ser1346Ter	p.S1346*	ENST00000257430	NM_000038.5	1346	tCa/tGa	16/16	0.589456711600207	2	FACETS	0.975	0.925	1	0.975	0.925	1	CLONAL	2	TRUE	0	0.589456711600207	2		179	409	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720649	89720649	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs587782455	NA	P-0000911-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	39	60	0	ENST00000371953.3:c.802-2A>T		p.X268_splice	ENST00000371953	NM_000314.4	268			0.589456711600207	2	FACETS	1	0.897	1	0.538	0.456	0.624	CLONAL	1	TRUE	0	0.589456711600207	2		60	123	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293172	212293172	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000911-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	87	310	0	ENST00000342788.4:c.2680T>A	p.Tyr894Asn	p.Y894N	ENST00000342788	NM_005235.2	894	Tac/Aac	22/28	0.525245479720915	4	FACETS	0.692	0.613	0.777	0.231	0.204	0.259	SUBCLONAL	1	TRUE	1	0.589456711600207	4		310	678	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0000922-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	238	375	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.2247557773473	3	FACETS	0.96	0.895	1	0.96	0.895	1	CLONAL	2	TRUE	1	0.2247557773473	3		375	1227	SUCCESS
APC	324	MSKCC	GRCh37	5	112175921	112175921	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000922-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	81	192	0	ENST00000257430.4:c.4630G>T	p.Glu1544Ter	p.E1544*	ENST00000257430	NM_000038.5	1544	Gaa/Taa	16/16	0.175961066882557	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.2247557773473	1		192	539	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266410	55266410	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000922-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	94	392	0	ENST00000275493.2:c.2702G>A	p.Gly901Glu	p.G901E	ENST00000275493	NM_005228.3	901	gGg/gAg	23/28	0.2247557773473	3	FACETS	0.958	0.851	1	0.479	0.425	0.537	CLONAL	1	TRUE	1	0.2247557773473	3		392	971	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45423120	45423120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000922-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	86	215	0	ENST00000262160.6:c.8C>T	p.Ser3Phe	p.S3F	ENST00000262160	NM_005901.5	3	tCc/tTc	2/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.2247557773473	2		215	647	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0000929-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	6680	525	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.841113598093972	38	FACETS	0.997	0.994	1			1	CLONAL	37	TRUE	NA	0.841113598093972	38		525	6950	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579330	7579330	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000929-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	255	426	0	ENST00000269305.4:c.357del	p.Lys120SerfsTer3	p.K120Sfs*3	ENST00000269305	NM_001126112.2	119	gcC/gc	4/11	0.827280165615824	2	FACETS	0.936	0.902	0.967	0.936	0.902	0.967	CLONAL	2	TRUE	0	0.841113598093972	2		426	324	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878187	48878187	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0000929-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	116	101	0	ENST00000267163.4:c.137+2T>A		p.X46_splice	ENST00000267163	NM_000321.2	46			NA	2	FACETS	0.999	0.953	1			1	INDETERMINATE	2	TRUE	NA	0.841113598093972	2		101	138	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581157	48581157	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1555685624	NA	P-0000970-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	14	264	0	ENST00000342988.3:c.461C>G	p.Ser154Ter	p.S154*	ENST00000342988	NM_005359.5	154	tCa/tGa	5/12	0.778788806379065	1	FACETS	0.11	0.079	0.147	0.11	0.079	0.147	SUBCLONAL	1	TRUE	0	0.78	1		264	199	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0000973-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	96	415	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.47605326866607	2	FACETS	0.858	0.779	0.939	0.858	0.779	0.939	CLONAL	2	TRUE	0	0.47605326866607	2		415	235	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852362	63852362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000973-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	29	409	0	ENST00000279873.7:c.3140C>T	p.Ser1047Phe	p.S1047F	ENST00000279873	NM_032199.2	1047	tCt/tTt	10/10	0.47605326866607	5	FACETS	0.852	0.687	1	0.213	0.171	0.26	CLONAL	1	TRUE	1	0.47605326866607	5		409	245	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641750	23641750	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000973-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	11	520	0	ENST00000261584.4:c.1725G>C	p.Trp575Cys	p.W575C	ENST00000261584	NM_024675.3	575	tgG/tgC	5/13	0.47605326866607	3	FACETS	0.267	0.184	0.37	0.134	0.092	0.185	SUBCLONAL	1	TRUE	1	0.47605326866607	3		520	214	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562800	176562800	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000973-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	15	353	0	ENST00000439151.2:c.696G>C	p.Gln232His	p.Q232H	ENST00000439151	NM_022455.4	232	caG/caC	2/23	0.170566096505822	5	FACETS	0.454	0.332	0.6	0.113	0.083	0.15	INDETERMINATE	1	TRUE	1	0.47605326866607	5		353	238	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250998	10250998	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000973-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	14	219	0	ENST00000340748.4:c.3482C>G	p.Ser1161Cys	p.S1161C	ENST00000340748		1161	tCt/tGt	32/40	0.47605326866607	1	FACETS	0.39	0.284	0.515	0.39	0.284	0.515	SUBCLONAL	1	TRUE	0	0.47605326866607	1		219	115	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0000979-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	122	330	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.251422055577707	10	FACETS	0.95	0.858	1			1	CLONAL	2	TRUE	NA	0.251422055577707	10		332	1024	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0000979-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	106	408	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.251422055577707	2	FACETS	0.913	0.829	0.999	1	0.982	1	CLONAL	3	TRUE	0	0.251422055577707	2		408	308	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627164	86627164	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0000979-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	29	221	0	ENST00000274376.6:c.540-1G>A		p.X180_splice	ENST00000274376	NM_002890.2	180			1	2	FACETS	0.867	0.699	1	0.867	0.699	1	CLONAL	1	TRUE	1	0.251422055577707	2		221	266	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829243	128829243	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000979-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	35	223	0	ENST00000249373.3:c.251C>T	p.Pro84Leu	p.P84L	ENST00000249373	NM_005631.4	84	cCc/cTc	1/12	1	2	FACETS	0.746	0.613	0.896	0.746	0.613	0.896	SUBCLONAL	1	TRUE	1	0.251422055577707	2		223	373	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12043910	12043910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772935596	NA	P-0000979-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	132	326	0	ENST00000396373.4:c.1289G>A	p.Arg430Gln	p.R430Q	ENST00000396373	NM_001987.4	430	cGa/cAa	8/8	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	2	TRUE	NA	0.251422055577707	2		326	477	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272000	15272000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000979-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	50	72	0	ENST00000263388.2:c.6439G>A	p.Gly2147Ser	p.G2147S	ENST00000263388	NM_000435.2	2147	Ggt/Agt	33/33	0.22480731455496	4	FACETS	1	0.905	1			1	CLONAL	3	TRUE	NA	0.251422055577707	4		72	157	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914091	32914094	+	frameshift_variant	Frame_Shift_Del	DEL	ACAG	ACAG	-	rs397507356	NA	P-0000979-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	60	194	0	ENST00000380152.3:c.5603_5606del	p.Asp1868ValfsTer5	p.D1868Vfs*5	ENST00000380152		1867	ACAGac/ac	11/27	0.251422055577707	4	FACETS	1	0.933	1	0.559	0.486	0.637	CLONAL	2	TRUE	0	0.251422055577707	4		194	267	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0000989-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	110	520	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.403443479218751	2		520	487	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520088	106520088	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000989-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	34	273	0	ENST00000359195.3:c.2516G>T	p.Arg839Leu	p.R839L	ENST00000359195	NM_002649.2	839	cGc/cTc	6/11	1	2	FACETS	0.763	0.628	0.912	0.763	0.628	0.912	CLONAL	1	TRUE	1	0.403443479218751	2		273	221	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319844	8319844	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs778246855	NA	P-0000989-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	81	591	0	ENST00000356435.5:c.5657T>C	p.Met1886Thr	p.M1886T	ENST00000356435		1886	aTg/aCg	34/35	0.403443479218751	1	FACETS	0.848	0.752	0.95	0.848	0.752	0.95	CLONAL	1	TRUE	0	0.403443479218751	1		591	378	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133242014	133242014	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500855	NA	P-0000989-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	70	351	1	ENST00000320574.5:c.2342C>T	p.Ala781Val	p.A781V	ENST00000320574	NM_006231.2	781	gCg/gTg	21/49	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.403443479218751	2		352	330	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220715	1220715	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000989-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	75	398	0	ENST00000326873.7:c.733C>T	p.Leu245Phe	p.L245F	ENST00000326873	NM_000455.4	245	Ctc/Ttc	5/10	0.33730695372319	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.403443479218751	1		398	282	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602572	10602572	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000989-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	51	405	0	ENST00000171111.5:c.1006C>T	p.Arg336Ter	p.R336*	ENST00000171111	NM_203500.1	336	Cga/Tga	3/6	0.403443479218751	1	FACETS	0.824	0.707	0.949	0.824	0.707	0.949	CLONAL	1	TRUE	0	0.403443479218751	1		405	245	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129700	11129700	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0000989-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	66	444	0	ENST00000358026.2:c.2505+1G>T		p.X835_splice	ENST00000358026	NM_001128849.1	835			0.403443479218751	1	FACETS	0.978	0.858	1	0.978	0.858	1	CLONAL	1	TRUE	0	0.403443479218751	1		444	267	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795353	39795353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs187337793	NA	P-0000989-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	72	562	0	ENST00000288319.7:c.367C>T	p.Arg123Cys	p.R123C	ENST00000288319	NM_182918.3	123	Cgc/Tgc	3/10	1	2	FACETS	0.929	0.817	1	0.929	0.817	1	CLONAL	1	TRUE	1	0.403443479218751	2		562	384	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0001001-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	178	282	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.42634234234175	2		283	341	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285455	38285455	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001001-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	270	491	0	ENST00000425967.3:c.698G>C	p.Arg233Thr	p.R233T	ENST00000425967	NM_001174067.1	233	aGa/aCa	6/19	0.216008817523295	4	FACETS	1	0.963	1	1	0.994	1	INDETERMINATE	3	TRUE	2	0.42634234234175	4		491	590	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471086	8471086	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0001001-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	59	302	0	ENST00000356435.5:c.3414-1G>C		p.X1138_splice	ENST00000356435		1138			0.415848341103509	1	FACETS	0.857	0.745	0.976	0.857	0.745	0.976	CLONAL	1	TRUE	0	0.42634234234175	1		302	254	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202684	108202684	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1555124587	NA	P-0001001-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	110	294	1	ENST00000278616.4:c.7708G>T	p.Glu2570Ter	p.E2570*	ENST00000278616	NM_000051.3	2570	Gaa/Taa	52/63	0.42634234234175	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.42634234234175	1		295	282	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0001001-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	365	508	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	0.407108366294286	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	4	TRUE	0	0.42634234234175	4		508	605	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001001-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	231	242	0	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	0.407108366294286	4	FACETS	1	0.953	1	1	0.953	1	CLONAL	4	TRUE	0	0.42634234234175	4		242	385	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592251	29592251	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs797044942	NA	P-0001001-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	143	397	0	ENST00000356175.3:c.4666C>T	p.Gln1556Ter	p.Q1556*	ENST00000356175	NM_000267.3	1556	Cag/Tag	35/57	0.42634234234175	2	FACETS	0.932	0.861	1	0.932	0.861	1	CLONAL	2	TRUE	0	0.42634234234175	2		397	360	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572220	64572238	+	frameshift_variant	Frame_Shift_Del	DEL	CTCGCCCCACGGCTCCTCG	CTCGCCCCACGGCTCCTCG	-	novel	NA	P-0001001-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	16	103	0	ENST00000312049.6:c.1401_1419del	p.Glu468LysfsTer85	p.E468Kfs*85	ENST00000312049	NM_130799.2	467	gcCGAGGAGCCGTGGGGCGAG/gc	10/10	0.182175611697021	5	FACETS	1	0.86	1			1	INDETERMINATE	1	TRUE	NA	0.42634234234175	5		103	99	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167709	185167709	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001010-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	76	617	2	ENST00000265026.3:c.1032G>A	p.Trp344Ter	p.W344*	ENST00000265026	NM_004721.4	344	tgG/tgA	6/14	0.305613139056433	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.305613139056433	1		619	329	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001017-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	9	336	0	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	0.64311442528177	2	FACETS	0.066	0.043	0.095	0.033	0.021	0.048	SUBCLONAL	1	TRUE	0	0.670860359784241	2		336	407	SUCCESS
APC	324	MSKCC	GRCh37	5	112170679	112170679	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0001017-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	88	292	0	ENST00000257430.4:c.1775T>A	p.Leu592Ter	p.L592*	ENST00000257430	NM_000038.5	592	tTa/tAa	15/16	0.392022088205318	1	FACETS	0.524	0.468	0.582	0.524	0.468	0.582	INDETERMINATE	1	TRUE	0	0.670860359784241	1		292	333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs864622237	NA	P-0001017-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	352	247	0	ENST00000269305.4:c.700T>C	p.Tyr234His	p.Y234H	ENST00000269305	NM_001126112.2	234	Tac/Cac	7/11	NA	2	FACETS	0.801	0.766	0.836			1	INDETERMINATE	2	TRUE	NA	0.670860359784241	2		247	655	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056588	26056590	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs751086925	NA	P-0001017-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	135	153	0	ENST00000343677.2:c.67_69del	p.Lys23del	p.K23del	ENST00000343677	NM_005319.3	23	AAG/-	1/1	0.342338591911483	4	FACETS	0.857	0.779	0.938	0.214	0.194	0.235	INDETERMINATE	1	TRUE	0	0.670860359784241	4		153	785	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635167	87635167	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001029-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	351	316	0	ENST00000277120.3:c.2219G>T	p.Ser740Ile	p.S740I	ENST00000277120		740	aGc/aTc	18/19	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.786226015915335	2		316	885	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683594	29683594	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001029-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	183	197	0	ENST00000356175.3:c.7669G>T	p.Glu2557Ter	p.E2557*	ENST00000356175	NM_000267.3	2557	Gaa/Taa	51/57	0.673184593893705	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.786226015915335	1		197	256	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285609	38285609	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs762665767	NA	P-0001051-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	216	197	262	0	ENST00000425967.3:c.544G>A	p.Val182Ile	p.V182I	ENST00000425967	NM_001174067.1	182	Gta/Ata	6/19	0.145796171516992	4	FACETS	1	0.965	1	1	0.965	1	INDETERMINATE	2	TRUE	2	0.847100249386559	4		262	413	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121076	11121076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1131691371	NA	P-0001051-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	316	143	466	0	ENST00000358026.2:c.2143G>A	p.Asp715Asn	p.D715N	ENST00000358026	NM_001128849.1	715	Gat/Aat	15/36	0.161686643920022	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.847100249386559	0		466	459	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468112	120468112	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001051-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	232	162	362	0	ENST00000256646.2:c.4327del	p.Cys1443AlafsTer110	p.C1443Afs*110	ENST00000256646	NM_024408.3	1443	Tgc/gc	25/34	1	2	FACETS	0.971	0.902	1	0.971	0.902	1	CLONAL	1	TRUE	1	0.847100249386559	2		362	394	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0001054-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	184	330	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.756370800133476	1	FACETS	0.734	0.687	0.782	0.734	0.687	0.782	SUBCLONAL	1	TRUE	0	0.756370800133476	1		332	412	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0001054-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	107	140	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.720451216773923	3	FACETS	0.833	0.763	0.904	0.833	0.763	0.904	CLONAL	2	TRUE	1	0.756370800133476	3		140	234	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458011	120458011	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001054-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	26	246	0	ENST00000256646.2:c.7334C>G	p.Pro2445Arg	p.P2445R	ENST00000256646	NM_024408.3	2445	cCt/cGt	34/34	0.756370800133476	3	FACETS	0.467	0.372	0.574	0.233	0.186	0.287	SUBCLONAL	1	TRUE	1	0.756370800133476	3		246	203	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606696	29606696	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769910087	NA	P-0001054-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	34	333	1	ENST00000389048.3:c.1184G>A	p.Arg395His	p.R395H	ENST00000389048	NM_004304.4	395	cGt/cAt	5/29	0.702447696792978	1	FACETS	0.299	0.246	0.357	0.299	0.246	0.357	SUBCLONAL	1	TRUE	0	0.756370800133476	1		334	187	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912655	NA	P-0001054-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	161	238	0	ENST00000269305.4:c.725G>C	p.Cys242Ser	p.C242S	ENST00000269305	NM_001126112.2	242	tGc/tCc	7/11	0.654295955010418	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.756370800133476	2		238	211	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591891	48591891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912581	NA	P-0001054-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	135	407	0	ENST00000342988.3:c.1054G>A	p.Gly352Arg	p.G352R	ENST00000342988	NM_005359.5	352	Gga/Aga	9/12	0.62617074144821	1	FACETS	0.937	0.873	0.999	0.937	0.873	0.999	CLONAL	1	TRUE	0	0.756370800133476	1		407	237	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260328	10260328	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148987580	NA	P-0001054-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	85	222	0	ENST00000340748.4:c.2339C>T	p.Thr780Met	p.T780M	ENST00000340748		780	aCg/aTg	25/40	0.72672342014232	2	FACETS	1	0.979	1	0.657	0.597	0.717	CLONAL	1	TRUE	0	0.756370800133476	2		222	171	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920227	76920227	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001054-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	48	690	0	ENST00000373344.5:c.3850C>A	p.Leu1284Ile	p.L1284I	ENST00000373344	NM_000489.3	1284	Ctt/Att	11/35	0.551854599957215	1	FACETS	0.322	0.274	0.374	0.322	0.274	0.374	SUBCLONAL	1	TRUE	0	0.756370800133476	1		690	245	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610525	215610529	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCC	CAGCC	-	novel	NA	P-0001054-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	34	430	0	ENST00000260947.4:c.1727_1731del	p.Gly576ValfsTer10	p.G576Vfs*10	ENST00000260947	NM_000465.2	576	gGGCTG/g	8/11	0.540838191636448	1	FACETS	0.24	0.197	0.287	0.24	0.197	0.287	SUBCLONAL	1	TRUE	0	0.756370800133476	1		430	233	SUCCESS
APC	324	MSKCC	GRCh37	5	112175765	112175774	+	frameshift_variant	Frame_Shift_Del	DEL	GCCACGGAAA	GCCACGGAAA	-	novel	NA	P-0001054-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	56	244	0	ENST00000257430.4:c.4475_4484del	p.Ala1492ValfsTer12	p.A1492Vfs*12	ENST00000257430	NM_000038.5	1492	GCCACGGAAAgt/gt	16/16	0.756370800133476	1	FACETS	0.731	0.645	0.817	0.731	0.645	0.817	SUBCLONAL	1	TRUE	0	0.756370800133476	1		244	126	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501242	140501242	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001054-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	64	287	0	ENST00000288602.6:c.830del	p.Pro277HisfsTer2	p.P277Hfs*2	ENST00000288602	NM_004333.4	277	cCa/ca	6/18	0.756370800133476	5	FACETS	0.657	0.569	0.752	0.219	0.189	0.251	SUBCLONAL	1	TRUE	2	0.756370800133476	5		287	550	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0001061-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	110	221	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.551501947865585	4	FACETS	1	0.958	1	0.724	0.66	0.789	CLONAL	2	FALSE	1	0.551501947865585	4		221	285	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838389	156838389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1357016517	NA	P-0001061-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	43	319	0	ENST00000524377.1:c.667G>A	p.Glu223Lys	p.E223K	ENST00000524377	NM_002529.3	223	Gag/Aag	6/17	0.32119249406451	6	FACETS	0.77	0.651	0.899			1	INDETERMINATE	2	FALSE	NA	0.551501947865585	6		319	213	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001061-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	52	290	0	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	0.24540986339951	6	FACETS	0.958	0.826	1	0.319	0.275	0.366	INDETERMINATE	2	FALSE	0	0.551501947865585	6		290	207	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347756	347756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769767245	NA	P-0001061-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	40	482	0	ENST00000262320.3:c.1750G>A	p.Ala584Thr	p.A584T	ENST00000262320	NM_003502.3	584	Gct/Act	6/11	0.39903648847183	5	FACETS	1	0.944	1	0.437	0.367	0.514	CLONAL	1	FALSE	2	0.551501947865585	5		482	202	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546919	9546919	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0001061-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	13	333	0	ENST00000353224.5:c.1103C>G	p.Ser368Ter	p.S368*	ENST00000353224	NM_177990.2	368	tCa/tGa	5/10	0.436266361168973	4	FACETS	0.446	0.319	0.6	0.223	0.159	0.3	SUBCLONAL	1	FALSE	2	0.551501947865585	4		333	164	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	189	181	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.953	0.886	1	0.953	0.886	1	CLONAL	1	TRUE	1	0.703589806077128	2		181	564	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515036	103515036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775996769	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	207	282	2	ENST00000355739.4:c.1537G>A	p.Ala513Thr	p.A513T	ENST00000355739	NM_000123.3	513	Gca/Aca	8/15	1	2	FACETS	0.943	0.88	1	0.943	0.88	1	CLONAL	1	TRUE	1	0.703589806077128	2		284	624	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	65	343	2	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.293	0.253	0.335	0.293	0.253	0.335	SUBCLONAL	1	TRUE	1	0.703589806077128	2		345	631	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	175	302	1	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.817	0.756	0.88	0.817	0.756	0.88	CLONAL	1	TRUE	1	0.703589806077128	2		303	609	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680489	241680489	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200007371	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	289	432	0	ENST00000366560.3:c.260G>A	p.Arg87His	p.R87H	ENST00000366560	NM_000143.3	87	cGc/cAc	2/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.703589806077128	2		432	798	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638491	176638491	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784096	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	204	378	0	ENST00000439151.2:c.3091C>T	p.Arg1031Ter	p.R1031*	ENST00000439151	NM_022455.4	1031	Cga/Tga	5/23	NA	2	FACETS	0.983	0.918	1			1	INDETERMINATE	1	TRUE	NA	0.703589806077128	2		378	590	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131402	17131402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398124537	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	223	368	3	ENST00000285071.4:c.50G>A	p.Arg17His	p.R17H	ENST00000285071	NM_144997.5	17	cGc/cAc	4/14	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.703589806077128	2		371	590	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339154	65339154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	244	389	0	ENST00000342505.4:c.382C>T	p.Arg128Cys	p.R128C	ENST00000342505	NM_002227.2	128	Cgt/Tgt	5/25	1	2	FACETS	0.98	0.92	1	0.98	0.92	1	CLONAL	1	TRUE	1	0.703589806077128	2		389	708	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724541	162724541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759709680	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	276	420	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	0.703589806077128	2		420	735	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268512	142268512	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	163	247	0	ENST00000350721.4:c.2980A>G	p.Thr994Ala	p.T994A	ENST00000350721	NM_001184.3	994	Aca/Gca	15/47	1	2	FACETS	0.948	0.877	1	0.948	0.877	1	CLONAL	1	TRUE	1	0.703589806077128	2		247	489	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553257	106553257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	280	416	0	ENST00000369096.4:c.1222G>A	p.Ala408Thr	p.A408T	ENST00000369096	NM_001198.3	408	Gct/Act	5/7	0.703081037941821	1	FACETS	0.975	0.928	1	0.975	0.928	1	CLONAL	1	TRUE	0	0.703589806077128	1		416	529	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012289	152012289	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	304	454	0	ENST00000262189.6:c.524A>C	p.Asp175Ala	p.D175A	ENST00000262189	NM_170606.2	175	gAc/gCc	4/59	1	2	FACETS	0.873	0.824	0.923	0.873	0.824	0.923	CLONAL	1	TRUE	1	0.703589806077128	2		454	990	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752963	128752963	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	296	377	0	ENST00000377970.2:c.1124A>C	p.Asn375Thr	p.N375T	ENST00000377970	NM_002467.4	375	aAc/aCc	3/3	1	2	FACETS	0.969	0.916	1	0.969	0.916	1	CLONAL	1	TRUE	1	0.703589806077128	2		377	868	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417422	139417422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745817995	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	217	374	0	ENST00000277541.6:c.622G>A	p.Ala208Thr	p.A208T	ENST00000277541	NM_017617.3	208	Gcc/Acc	4/34	1	2	FACETS	0.949	0.887	1	0.949	0.887	1	CLONAL	1	TRUE	1	0.703589806077128	2		374	650	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600615	43600615	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	289	380	0	ENST00000355710.3:c.841G>A	p.Ala281Thr	p.A281T	ENST00000355710	NM_020975.4	281	Gcc/Acc	4/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.703589806077128	2		380	745	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333143	70333143	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767493807	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	231	492	0	ENST00000373644.4:c.1048G>A	p.Glu350Lys	p.E350K	ENST00000373644	NM_030625.2	350	Gaa/Aaa	2/12	NA	2	FACETS	0.995	0.933	1			1	INDETERMINATE	1	TRUE	NA	0.703589806077128	2		492	660	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123353286	123353286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs984992964	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	281	481	0	ENST00000358487.5:c.46G>A	p.Ala16Thr	p.A16T	ENST00000358487	NM_000141.4	16	Gca/Aca	2/18	NA	2	FACETS	1	0.961	1			1	INDETERMINATE	1	TRUE	NA	0.703589806077128	2		481	781	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741868	17741868	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1466899825	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	44	59	0	ENST00000250003.3:c.539C>T	p.Ala180Val	p.A180V	ENST00000250003	NM_002478.4	180	gCg/gTg	1/3	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.703589806077128	2		59	123	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186775	108186775	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	260	391	0	ENST00000278616.4:c.6133G>A	p.Ala2045Thr	p.A2045T	ENST00000278616	NM_000051.3	2045	Gcc/Acc	42/63	0.703589806077128	1	FACETS	0.952	0.904	1	0.952	0.904	1	CLONAL	1	TRUE	0	0.703589806077128	1		391	503	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144521	58144521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	258	304	0	ENST00000257904.6:c.550G>A	p.Glu184Lys	p.E184K	ENST00000257904	NM_000075.3	184	Gaa/Aaa	5/8	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.703589806077128	2		304	728	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233576	69233576	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	199	222	0	ENST00000462284.1:c.1441T>C	p.Cys481Arg	p.C481R	ENST00000462284	NM_002392.5	481	Tgc/Cgc	11/11	1	2	FACETS	0.985	0.919	1	0.985	0.919	1	CLONAL	1	TRUE	1	0.703589806077128	2		222	574	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435459	110435459	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	199	235	0	ENST00000375856.3:c.2942T>A	p.Leu981His	p.L981H	ENST00000375856	NM_003749.2	981	cTc/cAc	1/2	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.703589806077128	2		235	549	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061472	38061472	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	257	281	0	ENST00000250448.2:c.517T>C	p.Tyr173His	p.Y173H	ENST00000250448	NM_004496.3	173	Tac/Cac	2/2	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.703589806077128	2		281	689	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442813	99442813	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs764403253	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	210	391	0	ENST00000268035.6:c.1210A>C	p.Asn404His	p.N404H	ENST00000268035	NM_000875.3	404	Aac/Cac	5/21	1	2	FACETS	0.882	0.823	0.942	0.882	0.823	0.942	CLONAL	1	TRUE	1	0.703589806077128	2		391	677	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846129	68846129	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	234	367	0	ENST00000261769.5:c.1100A>G	p.Asp367Gly	p.D367G	ENST00000261769	NM_004360.3	367	gAc/gGc	8/16	1	2	FACETS	0.889	0.833	0.947	0.889	0.833	0.947	CLONAL	1	TRUE	1	0.703589806077128	2		367	748	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245027	41245027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1800709	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	290	441	0	ENST00000357654.3:c.2521C>T	p.Arg841Trp	p.R841W	ENST00000357654	NM_007294.3	841	Cgg/Tgg	10/23	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.703589806077128	2		441	817	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696432	47696432	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519968	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	243	461	1	ENST00000347630.2:c.391T>G	p.Trp131Gly	p.W131G	ENST00000347630	NM_001007230.1	131	Tgg/Ggg	6/11	1	2	FACETS	0.854	0.8	0.909	0.854	0.8	0.909	CLONAL	1	TRUE	1	0.703589806077128	2		462	809	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238941	5238941	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs913402227	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	130	234	0	ENST00000357368.4:c.1838C>T	p.Thr613Met	p.T613M	ENST00000357368	NM_002850.3	613	aCg/aTg	13/38	1	2	FACETS	0.91	0.833	0.989	0.91	0.833	0.989	CLONAL	1	TRUE	1	0.703589806077128	2		234	406	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39657709	39657709	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	182	234	0	ENST00000361337.2:c.2T>C	p.Met1?	p.M1?	ENST00000361337	NM_003286.2	1	aTg/aCg	1/21	1	2	FACETS	0.917	0.852	0.984	0.917	0.852	0.984	CLONAL	1	TRUE	1	0.703589806077128	2		234	564	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42840450	42840450	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	157	241	1	ENST00000398585.3:c.1298T>C	p.Val433Ala	p.V433A	ENST00000398585	NM_001135099.1	433	gTg/gCg	12/14	1	2	FACETS	0.867	0.799	0.936	0.867	0.799	0.936	CLONAL	1	TRUE	1	0.703589806077128	2		242	515	SUCCESS
AR	367	MSKCC	GRCh37	X	66937395	66937395	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	325	267	0	ENST00000374690.3:c.2249T>C	p.Met750Thr	p.M750T	ENST00000374690	NM_000044.3	750	aTg/aCg	5/8	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.703589806077128	1		267	465	SUCCESS
AR	367	MSKCC	GRCh37	X	66943543	66943543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852581	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	350	261	0	ENST00000374690.3:c.2623C>T	p.His875Tyr	p.H875Y	ENST00000374690	NM_000044.3	875	Cat/Tat	8/8	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.703589806077128	1		261	484	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306976	65306976	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	226	455	0	ENST00000342505.4:c.2601del	p.Thr868HisfsTer8	p.T868Hfs*8	ENST00000342505	NM_002227.2	867	ccC/cc	19/25	1	2	FACETS	0.773	0.722	0.826	0.773	0.722	0.826	SUBCLONAL	1	TRUE	1	0.703589806077128	2		455	831	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330611	65330611	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	268	450	0	ENST00000342505.4:c.1035del	p.Lys345AsnfsTer32	p.K345Nfs*32	ENST00000342505	NM_002227.2	345	aaA/aa	8/25	1	2	FACETS	0.89	0.837	0.944	0.89	0.837	0.944	CLONAL	1	TRUE	1	0.703589806077128	2		450	856	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497245	149497245	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	66	393	0	ENST00000261799.4:c.3073del	p.Leu1025CysfsTer20	p.L1025Cfs*20	ENST00000261799	NM_002609.3	1025	Ctg/tg	22/23	1	2	FACETS	0.27	0.234	0.31	0.27	0.234	0.31	SUBCLONAL	1	TRUE	1	0.703589806077128	2		393	694	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796883	42796883	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	252	473	1	ENST00000575354.2:c.3347del	p.Pro1116GlnfsTer45	p.P1116Qfs*45	ENST00000575354	NM_015125.3	1114	gCc/gc	14/20	1	2	FACETS	0.91	0.855	0.967	0.91	0.855	0.967	CLONAL	1	TRUE	1	0.703589806077128	2		474	787	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164805	36164805	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	266	426	1	ENST00000300305.3:c.1070del	p.Pro357ArgfsTer237	p.P357Rfs*237	ENST00000300305		357	cCg/cg	8/8	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.703589806077128	2		427	741	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465274	120465274	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs752668646	NA	P-0001080-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	182	283	0	ENST00000256646.2:c.4987C>G	p.Leu1663Val	p.L1663V	ENST00000256646	NM_024408.3	1663	Ctt/Gtt	27/34	0.287309206038899	5	FACETS	1	0.969	1	0.717	0.666	0.769	INDETERMINATE	2	TRUE	2	0.598075365967251	5		283	537	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460441	8460441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001080-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	185	300	0	ENST00000356435.5:c.3845G>A	p.Cys1282Tyr	p.C1282Y	ENST00000356435		1282	tGc/tAc	22/35	0.518444533177556	2	FACETS	1	0.992	1	0.745	0.697	0.794	CLONAL	1	TRUE	0	0.598075365967251	2		300	415	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521487	8521487	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758577045	NA	P-0001080-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	218	357	0	ENST00000356435.5:c.751G>A	p.Gly251Arg	p.G251R	ENST00000356435		251	Gga/Aga	9/35	0.518444533177556	2	FACETS	1	0.991	1	0.675	0.633	0.717	CLONAL	1	TRUE	0	0.598075365967251	2		357	540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578419	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587781845	NA	P-0001080-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	109	227	0	ENST00000269305.4:c.511G>T	p.Glu171Ter	p.E171*	ENST00000269305	NM_001126112.2	171	Gag/Tag	5/11	0.598075365967251	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.598075365967251	1		227	189	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562720	29562720	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0001080-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	297	540	0	ENST00000356175.3:c.3800T>A	p.Leu1267Ter	p.L1267*	ENST00000356175	NM_000267.3	1267	tTg/tAg	28/57	0.598075365967251	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.598075365967251	1		540	563	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756634	756634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1387077624	NA	P-0001080-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	288	633	0	ENST00000314574.4:c.194C>T	p.Ser65Phe	p.S65F	ENST00000314574	NM_005433.3	65	tCc/tTc	2/12	0.598075365967251	4	FACETS	0.9	0.849	0.952	0.9	0.849	0.952	CLONAL	2	TRUE	2	0.598075365967251	4		633	855	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881458	48881483	+	frameshift_variant	Frame_Shift_Del	DEL	ATGTCAGAAATTAAAGATACCAGATC	ATGTCAGAAATTAAAGATACCAGATC	-	novel	NA	P-0001080-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	112	341	0	ENST00000267163.4:c.188_213del	p.Lys63ArgfsTer38	p.K63Rfs*38	ENST00000267163	NM_000321.2	60	ttATGTCAGAAATTAAAGATACCAGATCat/ttat	2/27	NA	2	FACETS	0.697	0.63	0.769			1	INDETERMINATE	1	TRUE	NA	0.598075365967251	2		341	537	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0001097-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	230	322	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.219809299539659	5	FACETS	0.932	0.869	0.997			1	CLONAL	3	TRUE	NA	0.219809299539659	5		322	995	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0001105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	218	230	0	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	0.332441546995297	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.332441546995297	2		230	578	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0001105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	185	265	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	0.256751128024401	5	FACETS	1	0.977	1	0.756	0.7	0.815	CLONAL	2	TRUE	2	0.332441546995297	5		265	735	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922364	178922364	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	254	269	0	ENST00000263967.3:c.1133G>T	p.Cys378Phe	p.C378F	ENST00000263967	NM_006218.2	378	tGt/tTt	6/21	0.256751128024401	5	FACETS	1	0.989	1	0.83	0.778	0.883	CLONAL	2	TRUE	2	0.332441546995297	5		269	920	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358987	81358987	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1263	110	458	0	ENST00000222390.5:c.974C>A	p.Pro325Gln	p.P325Q	ENST00000222390	NM_000601.4	325	cCa/cAa	8/18	0.332441546995297	5	FACETS	0.722	0.647	0.803	0.241	0.215	0.268	SUBCLONAL	1	TRUE	2	0.332441546995297	5		458	1373	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566439	41566439	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	205	355	0	ENST00000263253.7:c.4316C>G	p.Pro1439Arg	p.P1439R	ENST00000263253	NM_001429.3	1439	cCa/cGa	27/31	0.150067344578358	5	FACETS	0.963	0.893	1	0.642	0.595	0.69	INDETERMINATE	2	TRUE	2	0.332441546995297	5		355	960	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092734	27092734	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	271	353	0	ENST00000324856.7:c.2756del	p.Asn919IlefsTer5	p.N919Ifs*5	ENST00000324856	NM_006015.4	919	Aat/at	9/20	0.256751128024401	5	FACETS	1	0.989	1	0.819	0.77	0.87	CLONAL	2	TRUE	2	0.332441546995297	5		353	994	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729871	47729871	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001105-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	208	354	0	ENST00000449228.1:c.518del	p.Gly173AlafsTer56	p.G173Afs*56	ENST00000449228	NM_001127240.2	173	gGc/gc	3/4	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.332441546995297	2		354	1080	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0001107-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	66	330	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.278739321468131	5	FACETS	0.924	0.808	1	0.616	0.539	0.699	CLONAL	2	TRUE	2	0.32475371152359	5		332	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0001107-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	392	675	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.32475371152359	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	1	0.32475371152359	4		676	921	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944998	31944998	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748979871	NA	P-0001107-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	149	241	0	ENST00000340398.3:c.103G>A	p.Gly35Arg	p.G35R	ENST00000340398	NM_001013699.2	35	Ggg/Agg	1/1	0.278739321468131	5	FACETS	0.813	0.743	0.886	0.542	0.495	0.591	CLONAL	2	TRUE	2	0.32475371152359	5		241	839	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033934	49033934	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001107-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	95	313	1	ENST00000267163.4:c.2071G>T	p.Glu691Ter	p.E691*	ENST00000267163	NM_000321.2	691	Gag/Tag	20/27	0.244978574904737	5	FACETS	0.906	0.816	1	0.906	0.816	1	CLONAL	3	TRUE	2	0.32475371152359	5		314	320	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473723	67473723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223740	NA	P-0001107-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	71	338	0	ENST00000327367.4:c.803G>A	p.Arg268His	p.R268H	ENST00000327367	NM_005902.3	268	cGc/cAc	6/9	0.32475371152359	5	FACETS	0.729	0.635	0.831	0.243	0.211	0.277	SUBCLONAL	1	TRUE	2	0.32475371152359	5		338	892	SUCCESS
APC	324	MSKCC	GRCh37	5	112174758	112174761	+	frameshift_variant	Frame_Shift_Del	DEL	AAGA	AAGA	-	rs1554085029	NA	P-0001107-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	44	277	0	ENST00000257430.4:c.3467_3470del	p.Glu1156GlyfsTer8	p.E1156Gfs*8	ENST00000257430	NM_000038.5	1156	gAAGAg/gg	16/16	0.244978574904737	5	FACETS	0.895	0.758	1	0.597	0.505	0.696	CLONAL	2	TRUE	2	0.32475371152359	5		277	225	SUCCESS
APC	324	MSKCC	GRCh37	5	112175524	112175524	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001107-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	68	300	0	ENST00000257430.4:c.4233del	p.Ser1411ArgfsTer4	p.S1411Rfs*4	ENST00000257430	NM_000038.5	1411	agT/ag	16/16	0.244978574904737	5	FACETS	0.924	0.809	1	0.616	0.539	0.698	CLONAL	2	TRUE	2	0.32475371152359	5		300	337	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0001123-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	302	201	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.422336055925293	5	FACETS	0.951	0.9	1	0.951	0.9	1	CLONAL	3	TRUE	2	0.422336055925293	5		201	819	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0001123-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	80	597	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.275567945658728	1	FACETS	0.542	0.478	0.611	0.542	0.478	0.611	SUBCLONAL	1	TRUE	0	0.422336055925293	1		597	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0001123-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	73	403	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	0.275567945658728	1	FACETS	0.903	0.797	1	0.903	0.797	1	CLONAL	1	TRUE	0	0.422336055925293	1		403	302	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450634	70450634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747878740	NA	P-0001126-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	140	709	0	ENST00000373644.4:c.5474C>T	p.Ser1825Leu	p.S1825L	ENST00000373644	NM_030625.2	1825	tCa/tTa	12/12	NA	2	FACETS	1	0.92	1			1	INDETERMINATE	1	TRUE	NA	0.405517572161206	2		709	685	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439756	52439795	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAAGAGGTCCCAAACCCCCCAGTACCTGTGTGGTTGCCCT	CAAGAGGTCCCAAACCCCCCAGTACCTGTGTGGTTGCCCT	-	novel	NA	P-0001126-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	26	575	0	ENST00000460680.1:c.917_931+25del		p.X306_splice	ENST00000460680	NM_004656.3	306		10/17	0.229358114024431	4	FACETS	0.454	0.359	0.563			1	INDETERMINATE	1	TRUE	NA	0.405517572161206	4		575	397	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912660	NA	P-0001127-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	279	353	0	ENST00000269305.4:c.839G>T	p.Arg280Ile	p.R280I	ENST00000269305	NM_001126112.2	280	aGa/aTa	8/11	0.3702228654514	2	FACETS	0.814	0.77	0.86	0.814	0.77	0.86	CLONAL	2	TRUE	0	0.49500491588484	2		353	692	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521708	89521708	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0001127-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	74	285	0	ENST00000336596.2:c.2785A>T	p.Lys929Ter	p.K929*	ENST00000336596	NM_005233.5	929	Aag/Tag	16/17	1	2	FACETS	0.742	0.653	0.837	0.742	0.653	0.837	SUBCLONAL	1	TRUE	1	0.49500491588484	2		285	403	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600377	10600377	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001127-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	241	460	0	ENST00000171111.5:c.1478A>C	p.Glu493Ala	p.E493A	ENST00000171111	NM_203500.1	493	gAg/gCg	4/6	0.49500491588484	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.49500491588484	1		460	696	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40367069	40367069	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1391870973	NA	P-0001150-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	397	653	0	ENST00000397332.2:c.128A>G	p.Tyr43Cys	p.Y43C	ENST00000397332	NM_001033082.2	43	tAt/tGt	2/3	1	2	FACETS	0.969	0.922	1	0.969	0.922	1	CLONAL	1	TRUE	1	0.724817474957304	2		653	1131	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645889	215645889	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587780035	NA	P-0001150-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1281	394	853	1	ENST00000260947.4:c.709C>T	p.Gln237Ter	p.Q237*	ENST00000260947	NM_000465.2	237	Caa/Taa	4/11	0.389389238842439	3	FACETS	0.884	0.838	0.931			1	INDETERMINATE	1	TRUE	NA	0.724817474957304	3		854	1675	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69788753	69788753	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001150-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	441	369	0	ENST00000352241.4:c.5A>C	p.Gln2Pro	p.Q2P	ENST00000352241	NM_198159.2	2	cAg/cCg	1/10	0.724817474957304	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.724817474957304	2		369	605	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005365	150005365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs918439730	NA	P-0001150-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	343	550	2	ENST00000253339.5:c.860G>A	p.Arg287Gln	p.R287Q	ENST00000253339		287	cGa/cAa	3/7	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.724817474957304	2		552	925	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913351	NA	P-0001150-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	575	405	0	ENST00000288602.6:c.1397G>T	p.Gly466Val	p.G466V	ENST00000288602	NM_004333.4	466	gGa/gTa	11/18	0.724817474957304	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.724817474957304	3		405	1063	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001150-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	193	340	0	ENST00000269305.4:c.481G>T	p.Ala161Ser	p.A161S	ENST00000269305	NM_001126112.2	161	Gcc/Tcc	5/11	0.724817474957304	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.724817474957304	1		340	302	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17129563	17129563	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001150-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	350	595	0	ENST00000285071.4:c.323G>T	p.Ser108Ile	p.S108I	ENST00000285071	NM_144997.5	108	aGc/aTc	5/14	0.724817474957304	1	FACETS	0.976	0.934	1	0.976	0.934	1	CLONAL	1	TRUE	0	0.724817474957304	1		595	631	SUCCESS
APC	324	MSKCC	GRCh37	5	112173669	112173670	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0001150-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	219	342	0	ENST00000257430.4:c.2379_2380del	p.Tyr796TrpfsTer2	p.Y796Wfs*2	ENST00000257430	NM_000038.5	793	cAA/c	16/16	1	2	FACETS	0.914	0.855	0.975	0.914	0.855	0.975	CLONAL	1	TRUE	1	0.724817474957304	2		342	661	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175755	+	frameshift_variant	Frame_Shift_Del	DEL	TTTA	TTTA	-	novel	NA	P-0001150-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	163	280	0	ENST00000257430.4:c.4463_4466del	p.Leu1488TyrfsTer18	p.L1488Yfs*18	ENST00000257430	NM_000038.5	1487	acTTTA/ac	16/16	1	2	FACETS	0.813	0.751	0.878	0.813	0.751	0.878	CLONAL	1	TRUE	1	0.724817474957304	2		280	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0001151-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	204	593	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.256557730756467	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.256557730756467	1		593	997	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459250	120459250	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001151-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	42	182	0	ENST00000256646.2:c.6095A>G	p.His2032Arg	p.H2032R	ENST00000256646	NM_024408.3	2032	cAt/cGt	34/34	1	2	FACETS	0.793	0.663	0.937	0.793	0.663	0.937	CLONAL	1	TRUE	1	0.256557730756467	2		182	413	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748290	41748290	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001151-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	85	572	1	ENST00000226382.2:c.479C>T	p.Ala160Val	p.A160V	ENST00000226382	NM_003924.3	160	gCg/gTg	3/3	0.256557730756467	1	FACETS	0.664	0.586	0.748	0.664	0.586	0.748	SUBCLONAL	1	TRUE	0	0.256557730756467	1		573	870	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201874	152201874	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753014570	NA	P-0001151-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	72	370	0	ENST00000206249.3:c.728G>A	p.Arg243His	p.R243H	ENST00000206249	NM_000125.3	243	cGt/cAt	3/8	0.153702897364396	2	FACETS	0.652	0.568	0.742	0.326	0.284	0.371	INDETERMINATE	1	TRUE	0	0.256557730756467	2		370	861	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683540	29683540	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001151-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	137	299	2	ENST00000356175.3:c.7615G>T	p.Glu2539Ter	p.E2539*	ENST00000356175	NM_000267.3	2539	Gaa/Taa	51/57	NA	2	FACETS	0.925	0.845	1			1	INDETERMINATE	2	TRUE	NA	0.256557730756467	2		301	577	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492689	56492689	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001151-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	446	499	0	ENST00000407977.2:c.250C>T	p.Gln84Ter	p.Q84*	ENST00000407977		84	Cag/Tag	2/10	0.256557730756467	2	FACETS	0.959	0.916	1	1	0.996	1	CLONAL	3	TRUE	0	0.256557730756467	2		499	1209	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057520007	NA	P-0001152-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	175	518	0	ENST00000269305.4:c.614A>C	p.Tyr205Ser	p.Y205S	ENST00000269305	NM_001126112.2	205	tAt/tCt	6/11	0.647135882997178	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.647135882997178	1		518	291	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120241	70120241	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001152-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	135	511	0	ENST00000245479.2:c.1246del	p.Gln416AsnfsTer54	p.Q416Nfs*54	ENST00000245479	NM_000346.3	415	Ccc/cc	3/3	1	2	FACETS	0.841	0.769	0.916	0.841	0.769	0.916	CLONAL	1	TRUE	1	0.647135882997178	2		511	496	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0001166-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	244	711	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.215006237558268	5	FACETS	1	0.954	1	0.806	0.763	0.848	INDETERMINATE	4	TRUE	0	0.432349641527242	5		712	462	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17350515	17350515	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001166-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	134	617	2	ENST00000375499.3:c.595T>G	p.Tyr199Asp	p.Y199D	ENST00000375499	NM_003000.2	199	Tac/Gac	6/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.432349641527242	2		619	527	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96930957	96930957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001166-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	48	531	0	ENST00000258439.3:c.163C>T	p.His55Tyr	p.H55Y	ENST00000258439	NM_001193304.2	55	Cac/Tac	2/4	1	2	FACETS	0.499	0.422	0.583	0.499	0.422	0.583	SUBCLONAL	1	TRUE	1	0.432349641527242	2		531	445	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524215	18524215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769408892	NA	P-0001166-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	44	874	1	ENST00000266497.5:c.1727C>T	p.Ala576Val	p.A576V	ENST00000266497		576	gCg/gTg	11/31	0.432349641527242	1	FACETS	0.232	0.194	0.274	0.232	0.194	0.274	SUBCLONAL	1	TRUE	0	0.432349641527242	1		875	688	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249348	110249348	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001169-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	314	612	0	ENST00000374672.4:c.1225A>C	p.Lys409Gln	p.K409Q	ENST00000374672	NM_004235.4	409	Aag/Cag	4/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		612	809	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223958	2223958	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001169-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	83	564	0	ENST00000326181.6:c.1172C>A	p.Thr391Asn	p.T391N	ENST00000326181	NM_032271.2	391	aCc/aAc	13/21	0.0954149807560514	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		564	294	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089935	16089935	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001175-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	42	379	0	ENST00000268712.3:c.175C>T	p.Gln59Ter	p.Q59*	ENST00000268712	NM_006311.3	59	Caa/Taa	3/46	0.246819741943352	0	FACETS	0.769	0.658	0.884			1	SUBCLONAL	2	TRUE	0	0.311095604097912	0		379	121	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0001182-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	92	293	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.401914553571297	1	FACETS	0.924	0.841	1	1	0.987	1	CLONAL	2	TRUE	0	0.401914553571297	1		294	198	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0001194-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	187	293	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.515050711276719	2	FACETS	0.979	0.919	1	0.979	0.919	1	CLONAL	2	TRUE	0	0.515050711276719	2		294	371	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0001194-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	156	357	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.515050711276719	2		357	469	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970971	21970971	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001194-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	144	370	0	ENST00000304494.5:c.387C>A	p.Tyr129Ter	p.Y129*	ENST00000304494	NM_000077.4	129	taC/taA	2/3	0.515050711276719	3	FACETS	1	0.981	1	0.624	0.572	0.679	CLONAL	1	TRUE	1	0.515050711276719	3		370	563	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576801	212576801	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001194-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	217	452	0	ENST00000342788.4:c.1098G>T	p.Leu366Phe	p.L366F	ENST00000342788	NM_005235.2	366	ttG/ttT	9/28	NA	2	FACETS	0.9	0.847	0.954			1	INDETERMINATE	2	TRUE	NA	0.515050711276719	2		452	468	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481857	56481857	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519817	NA	P-0001194-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	328	575	0	ENST00000267101.3:c.785C>A	p.Pro262His	p.P262H	ENST00000267101	NM_001982.3	262	cCt/cAt	7/28	0.515050711276719	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.515050711276719	3		575	748	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152055	11152055	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs878854224	NA	P-0001194-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	76	296	0	ENST00000358026.2:c.4339C>T	p.Arg1447Ter	p.R1447*	ENST00000358026	NM_001128849.1	1447	Cga/Tga	31/36	0.110886591825825	0	FACETS	0.492	0.436	0.551			1	INDETERMINATE	1	TRUE	0	0.515050711276719	0		296	291	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170453	11170453	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555795884	NA	P-0001194-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	101	376	0	ENST00000358026.2:c.4756C>T	p.Gln1586Ter	p.Q1586*	ENST00000358026	NM_001128849.1	1586	Cag/Tag	34/36	0.110886591825825	0	FACETS	0.58	0.524	0.638			1	INDETERMINATE	1	TRUE	0	0.515050711276719	0		376	328	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022476	31022476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200756074	NA	P-0001194-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	49	246	0	ENST00000375687.4:c.1961C>T	p.Ala654Val	p.A654V	ENST00000375687	NM_015338.5	654	gCc/gTc	13/13	1	2	FACETS	0.951	0.817	1	0.951	0.817	1	CLONAL	1	TRUE	1	0.515050711276719	2		246	200	SUCCESS
AR	367	MSKCC	GRCh37	X	66931346	66931346	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0001194-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	159	329	1	ENST00000374690.3:c.1988C>G	p.Ser663Ter	p.S663*	ENST00000374690	NM_000044.3	663	tCa/tGa	4/8	0.49978735813728	0	FACETS		NA	1			1	NA	2	TRUE	NA	0.515050711276719	0		330	273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573944	7573944	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555524354	NA	P-0001216-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	44	574	1	ENST00000269305.4:c.1083del	p.Ser362AlafsTer8	p.S362Afs*8	ENST00000269305	NM_001126112.2	361	ggG/gg	10/11	0.29148378335553	1	FACETS	0.481	0.403	0.568	0.481	0.403	0.568	SUBCLONAL	1	TRUE	0	0.29148378335553	1		575	536	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087503	27087503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001216-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	94	497	1	ENST00000324856.7:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000324856	NM_006015.4	693	Cga/Tga	5/20	0.29148378335553	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.29148378335553	1		498	476	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420213	49420213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267607237	NA	P-0001216-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	50	477	0	ENST00000301067.7:c.15536G>A	p.Arg5179His	p.R5179H	ENST00000301067	NM_003482.3	5179	cGt/cAt	48/54	1	2	FACETS	0.631	0.535	0.736	0.631	0.535	0.736	SUBCLONAL	1	TRUE	1	0.29148378335553	2		477	544	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552152	29552152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199474738	NA	P-0001216-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	114	558	0	ENST00000356175.3:c.1885G>A	p.Gly629Arg	p.G629R	ENST00000356175	NM_000267.3	629	Ggg/Agg	17/57	0.29148378335553	1	FACETS	0.987	0.89	1	0.987	0.89	1	CLONAL	1	TRUE	0	0.29148378335553	1		558	677	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222373	2222373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001216-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	74	358	0	ENST00000398665.3:c.3205G>A	p.Ala1069Thr	p.A1069T	ENST00000398665	NM_032482.2	1069	Gcc/Acc	24/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.29148378335553	2		358	377	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541324	187541324	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001216-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	169	669	0	ENST00000441802.2:c.6416del	p.Lys2139SerfsTer8	p.K2139Sfs*8	ENST00000441802	NM_005245.3	2139	aAg/ag	10/27	0.217414920196321	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.29148378335553	1		669	812	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752800	57752800	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001216-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	95	495	4	ENST00000274289.3:c.1128del	p.Asp377ThrfsTer26	p.D377Tfs*26	ENST00000274289	NM_006622.3	376	aaA/aa	8/14	0.242165228469431	4	FACETS	0.814	0.723	0.912	0.407	0.361	0.456	CLONAL	1	TRUE	2	0.29148378335553	4		499	1034	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434005	49434005	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001216-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	27	331	0	ENST00000301067.7:c.7548del	p.Asn2517IlefsTer26	p.N2517Ifs*26	ENST00000301067	NM_003482.3	2516	ccC/cc	31/54	1	2	FACETS	0.51	0.406	0.63	0.51	0.406	0.63	SUBCLONAL	1	TRUE	1	0.29148378335553	2		331	363	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319454	11319454	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001224-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	306	54	446	0	ENST00000361445.4:c.13G>T	p.Gly5Ter	p.G5*	ENST00000361445	NM_004958.3	5	Gga/Tga	2/58	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.609224187433301	NA		446	360	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101469	27101469	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001224-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	191	154	521	0	ENST00000324856.7:c.4751A>T	p.Gln1584Leu	p.Q1584L	ENST00000324856	NM_006015.4	1584	cAg/cTg	18/20	0.609224187433301	3	FACETS	0.956	0.888	1	0.956	0.888	1	CLONAL	2	TRUE	1	0.609224187433301	3		521	345	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696790	176696790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001224-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	222	175	345	0	ENST00000439151.2:c.5491G>A	p.Asp1831Asn	p.D1831N	ENST00000439151	NM_022455.4	1831	Gat/Aat	16/23	0.491535817370575	3	FACETS	0.944	0.881	1	0.944	0.881	1	CLONAL	2	TRUE	1	0.609224187433301	3		345	397	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671529	30671529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763745278	NA	P-0001224-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	443	81	611	0	ENST00000376406.3:c.5431C>T	p.Arg1811Cys	p.R1811C	ENST00000376406	NM_014641.2	1811	Cgc/Tgc	10/15	0.480700357072387	5	FACETS	0.971	0.858	1			1	CLONAL	1	TRUE	NA	0.609224187433301	5		611	524	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673631	30673631	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001224-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	412	160	620	0	ENST00000376406.3:c.3329G>T	p.Arg1110Leu	p.R1110L	ENST00000376406	NM_014641.2	1110	cGg/cTg	10/15	0.480700357072387	5	FACETS	0.879	0.81	0.95			1	CLONAL	2	TRUE	NA	0.609224187433301	5		620	572	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528865	157528865	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001224-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	200	206	415	0	ENST00000346085.5:c.6590G>T	p.Arg2197Met	p.R2197M	ENST00000346085	NM_020732.3	2197	aGg/aTg	20/20	0.609224187433301	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.609224187433301	3		415	406	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978832	13978832	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001224-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	585	322	486	2	ENST00000405192.2:c.275C>T	p.Pro92Leu	p.P92L	ENST00000405192	NM_001163147.1	92	cCc/cTc	6/12	0.609224187433301	4	FACETS	0.938	0.888	0.988	0.469	0.444	0.494	CLONAL	2	TRUE	0	0.609224187433301	4		488	907	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340409	8340409	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001224-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	176	114	536	0	ENST00000356435.5:c.5187G>T	p.Trp1729Cys	p.W1729C	ENST00000356435		1729	tgG/tgT	31/35	0.578643126695785	1	FACETS	0.897	0.821	0.976	0.897	0.821	0.976	CLONAL	1	TRUE	0	0.609224187433301	1		536	290	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517931	8517931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001224-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	223	145	578	0	ENST00000356435.5:c.1460C>T	p.Thr487Ile	p.T487I	ENST00000356435		487	aCa/aTa	10/35	0.578643126695785	1	FACETS	0.899	0.831	0.969	0.899	0.831	0.969	CLONAL	1	TRUE	0	0.609224187433301	1		578	368	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100272	8100272	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001224-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	281	120	446	0	ENST00000346208.3:c.246C>A	p.Ser82Arg	p.S82R	ENST00000346208		82	agC/agA	3/6	0.609224187433301	5	FACETS	0.94	0.857	1	0.627	0.571	0.685	CLONAL	2	TRUE	2	0.609224187433301	5		446	401	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26911735	26911735	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001224-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	215	429	431	0	ENST00000381527.3:c.160A>G	p.Ile54Val	p.I54V	ENST00000381527	NM_001260.1	54	Ata/Gta	2/13	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.609224187433301	2		431	644	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626691	28626691	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001224-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	155	211	460	0	ENST00000241453.7:c.605A>T	p.Gln202Leu	p.Q202L	ENST00000241453	NM_004119.2	202	cAg/cTg	5/24	0.601044554947146	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.609224187433301	1		460	366	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68290264	68290264	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001224-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	520	140	484	0	ENST00000487270.1:c.4G>T	p.Gly2Cys	p.G2C	ENST00000487270	NM_133509.3	2	Ggt/Tgt	2/11	0.329061474571918	4	FACETS	1	0.967	1	0.56	0.511	0.611	INDETERMINATE	1	TRUE	2	0.609224187433301	4		484	660	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609863	81609863	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001224-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	258	66	522	0	ENST00000298171.2:c.1461C>A	p.Asp487Glu	p.D487E	ENST00000298171	NM_000369.2	487	gaC/gaA	10/10	0.329061474571918	4	FACETS	1	0.922	1	0.538	0.47	0.61	INDETERMINATE	1	TRUE	2	0.609224187433301	4		522	324	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900791	3900791	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001224-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	124	113	369	1	ENST00000262367.5:c.305A>G	p.Gln102Arg	p.Q102R	ENST00000262367	NM_004380.2	102	cAg/cGg	2/31	0.333969221590985	4	FACETS	0.84	0.772	0.907			1	INDETERMINATE	3	TRUE	NA	0.609224187433301	4		370	237	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428333	33428333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001224-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	313	72	578	0	ENST00000345365.6:c.790C>T	p.Leu264Phe	p.L264F	ENST00000345365	NM_002878.3	264	Ctc/Ttc	9/10	0.223342394292708	5	FACETS	1	0.953	1			1	INDETERMINATE	1	TRUE	NA	0.609224187433301	5		578	385	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780611	56780611	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001224-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	388	222	559	0	ENST00000337432.4:c.626A>G	p.Tyr209Cys	p.Y209C	ENST00000337432	NM_058216.2	209	tAt/tGt	4/9	0.322352223986316	4	FACETS	0.961	0.901	1	0.961	0.901	1	INDETERMINATE	2	TRUE	2	0.609224187433301	4		559	610	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57569902	57569902	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001224-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	261	366	391	0	ENST00000316660.6:c.82C>T	p.Gln28Ter	p.Q28*	ENST00000316660	NM_021127.2	28	Caa/Taa	2/2	0.486359381140476	3	FACETS	0.833	0.8	0.867	0.833	0.8	0.867	CLONAL	3	TRUE	0	0.609224187433301	3		391	627	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683677	162683677	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001224-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	293	35	515	0	ENST00000366898.1:c.292del	p.Glu98SerfsTer5	p.E98Sfs*5	ENST00000366898	NM_004562.2	98	Gag/ag	3/12	0.609224187433301	3	FACETS	0.457	0.375	0.548	0.229	0.187	0.274	SUBCLONAL	1	TRUE	1	0.609224187433301	3		515	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001224-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	82	131	503	0	ENST00000269305.4:c.166del	p.Glu56LysfsTer67	p.E56Kfs*67	ENST00000269305	NM_001126112.2	56	Gaa/aa	4/11	NA	2	FACETS	1	0.943	1			1	INDETERMINATE	2	TRUE	NA	0.609224187433301	2		503	213	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266104	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0001224-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	409	195	472	1	ENST00000349496.5:c.100_101delinsTT	p.Gly34Leu	p.G34L	ENST00000349496	NM_001904.3	34	GGa/TTa	3/15	0.209080604179102	4	FACETS	0.853	0.794	0.913	0.853	0.794	0.913	INDETERMINATE	2	TRUE	2	0.609224187433301	4		473	604	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085823	16085824	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	T	novel	NA	P-0001224-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	183	83	489	0	ENST00000281043.3:c.999_1000delinsT	p.Ala334ProfsTer17	p.A334Pfs*17	ENST00000281043	NM_005378.4	333	gcCGcc/gcTcc	3/3	0.322352223986316	4	FACETS	0.824	0.737	0.915	0.824	0.737	0.915	INDETERMINATE	2	TRUE	2	0.609224187433301	4		489	266	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188207	10188207	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001232-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	177	333	1	ENST00000256474.2:c.350G>T	p.Trp117Leu	p.W117L	ENST00000256474	NM_000551.3	117	tGg/tTg	2/3	0.426022096926461	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.426022096926461	1		334	585	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741998	40741998	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs374756725	NA	P-0001232-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	142	400	0	ENST00000392038.2:c.974A>G	p.Asn325Ser	p.N325S	ENST00000392038	NM_001626.4	325	aAt/aGt	11/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.426022096926461	2		400	542	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436617	52436617	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0001232-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	31	232	0	ENST00000460680.1:c.2056+1del		p.X686_splice	ENST00000460680	NM_004656.3	686			0.426022096926461	1	FACETS	0.346	0.28	0.42	0.346	0.28	0.42	SUBCLONAL	1	TRUE	0	0.426022096926461	1		232	331	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52663010	52663013	+	frameshift_variant	Frame_Shift_Del	DEL	AAAT	AAAT	-	novel	NA	P-0001232-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	32	336	0	ENST00000394830.3:c.1340_1343del	p.His447ArgfsTer5	p.H447Rfs*5	ENST00000394830	NM_018313.4	447	cATTTg/cg	13/30	0.426022096926461	1	FACETS	0.327	0.266	0.397	0.327	0.266	0.397	SUBCLONAL	1	TRUE	0	0.426022096926461	1		336	361	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001241-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	246	186	0	ENST00000397752.3:c.3028G>T	p.Asp1010Tyr	p.D1010Y	ENST00000397752	NM_000245.2	1010	Gat/Tat	14/21	0.581270976671829	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.581270976671829	3		186	319	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105817	27105817	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001241-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	35	226	0	ENST00000324856.7:c.5428G>C	p.Asp1810His	p.D1810H	ENST00000324856	NM_006015.4	1810	Gac/Cac	20/20	0.22000199173866	4	FACETS	0.952	0.788	1	0.317	0.262	0.378	INDETERMINATE	1	TRUE	1	0.581270976671829	4		226	200	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39744041	39744041	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001241-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	38	251	0	ENST00000361337.2:c.1669A>C	p.Asn557His	p.N557H	ENST00000361337	NM_003286.2	557	Aac/Cac	16/21	0.469083652412228	3	FACETS	0.654	0.544	0.775	0.327	0.272	0.388	SUBCLONAL	1	TRUE	1	0.581270976671829	3		251	258	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916531	39916531	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001241-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	73	499	0	ENST00000378444.4:c.4472A>G	p.Asn1491Ser	p.N1491S	ENST00000378444	NM_001123385.1	1491	aAt/aGt	11/15	0.519626171253765	1	FACETS	0.66	0.584	0.74	0.66	0.584	0.74	SUBCLONAL	1	TRUE	0	0.581270976671829	1		499	270	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0001247-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	104	293	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.617426921949272	2	FACETS	0.946	0.878	1	0.946	0.878	1	CLONAL	2	FALSE	0	0.674792970042662	2		294	163	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521633	89521633	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001247-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	332	380	0	ENST00000336596.2:c.2710G>T	p.Asp904Tyr	p.D904Y	ENST00000336596	NM_005233.5	904	Gac/Tac	16/17	0.674792970042662	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	FALSE	2	0.674792970042662	4		380	802	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430851	181430851	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001247-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	140	625	0	ENST00000325404.1:c.703A>T	p.Met235Leu	p.M235L	ENST00000325404	NM_003106.3	235	Atg/Ttg	1/1	0.674792970042662	6	FACETS	0.963	0.876	1	0.193	0.175	0.211	CLONAL	1	FALSE	1	0.674792970042662	6		625	1012	SUCCESS
APC	324	MSKCC	GRCh37	5	112176089	112176089	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001247-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	241	349	0	ENST00000257430.4:c.4798A>G	p.Lys1600Glu	p.K1600E	ENST00000257430	NM_000038.5	1600	Aaa/Gaa	16/16	0.674792970042662	4	FACETS	0.962	0.905	1	0.962	0.905	1	CLONAL	2	FALSE	2	0.674792970042662	4		349	622	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595542	55595542	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001265-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	93	389	0	ENST00000288135.5:c.2032C>A	p.Leu678Ile	p.L678I	ENST00000288135	NM_000222.2	678	Ctt/Att	14/21	0.451973083237277	1	FACETS	0.339	0.303	0.377	0.339	0.303	0.377	INDETERMINATE	1	TRUE	0	0.784739040698189	1		389	425	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977981	131977981	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001265-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	382	190	0	ENST00000265335.6:c.3864G>T	p.Arg1288Ser	p.R1288S	ENST00000265335		1288	agG/agT	25/25	0.750058953834308	3	FACETS	0.945	0.919	0.971	0.945	0.919	0.971	CLONAL	3	TRUE	0	0.784739040698189	3		190	478	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577043	7577044	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0001265-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	245	385	0	ENST00000269305.4:c.894_895del	p.Glu298AspfsTer7	p.E298Dfs*7	ENST00000269305	NM_001126112.2	298	gaGCtg/gatg	8/11	0.784739040698189	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.784739040698189	1		385	379	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250206	110250206	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001268-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	268	207	0	ENST00000374672.4:c.469G>T	p.Gly157Trp	p.G157W	ENST00000374672	NM_004235.4	157	Ggg/Tgg	3/5	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	2	TRUE	NA	0.591268374179486	2		207	419	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038902	12038902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159945	NA	P-0001268-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	529	342	0	ENST00000396373.4:c.1195C>T	p.Arg399Cys	p.R399C	ENST00000396373	NM_001987.4	399	Cgc/Tgc	7/8	0.591268374179486	7	FACETS	0.892	0.857	0.927			1	CLONAL	4	TRUE	NA	0.591268374179486	7		342	1243	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577129	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519986	NA	P-0001268-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	360	380	0	ENST00000269305.4:c.809T>C	p.Phe270Ser	p.F270S	ENST00000269305	NM_001126112.2	270	tTt/tCt	8/11	0.591268374179486	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.591268374179486	2		380	605	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300105	15300105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001268-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	142	357	0	ENST00000263388.2:c.1171G>A	p.Asp391Asn	p.D391N	ENST00000263388	NM_000435.2	391	Gat/Aat	7/33	0.58613798108825	4	FACETS	0.932	0.85	1			1	CLONAL	1	TRUE	NA	0.591268374179486	4		357	820	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001272-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	347	425	0	ENST00000269305.4:c.833del	p.Pro278LeufsTer67	p.P278Lfs*67	ENST00000269305	NM_001126112.2	278	cCt/ct	8/11	0.228808828894754	4	FACETS	0.952	0.906	0.998			1	CLONAL	4	FALSE	NA	0.293312690284465	4		425	804	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215921	41215921	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001272-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	219	434	0	ENST00000357654.3:c.5122G>C	p.Ala1708Pro	p.A1708P	ENST00000357654	NM_007294.3	1708	Gcg/Ccg	17/23	0.293312690284465	1	FACETS	0.915	0.855	0.977	1	0.994	1	CLONAL	2	FALSE	0	0.293312690284465	1		434	696	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795469	42795469	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001273-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	165	308	0	ENST00000575354.2:c.2549C>A	p.Ala850Glu	p.A850E	ENST00000575354	NM_015125.3	850	gCa/gAa	10/20	0.105753080858915	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.848018821818206	0		308	437	SUCCESS
APC	324	MSKCC	GRCh37	5	112128161	112128161	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001275-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	240	321	0	ENST00000257430.4:c.664C>T	p.Gln222Ter	p.Q222*	ENST00000257430	NM_000038.5	222	Cag/Tag	7/16	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.491114960217853	2		321	682	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0001285-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	29	331	0	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.239858930106424	3	FACETS	0.224	0.179	0.274	0.112	0.089	0.137	INDETERMINATE	1	TRUE	1	0.89	3		331	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0001305-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	119	604	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.248848864740503	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.248848864740503	2		604	452	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226556019	226556019	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001305-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	97	242	0	ENST00000366794.5:c.2158G>T	p.Val720Leu	p.V720L	ENST00000366794	NM_001618.3	720	Gtg/Ttg	16/23	0.1979795862936	3	FACETS	1	0.937	1	1	0.937	1	CLONAL	3	TRUE	0	0.248848864740503	3		242	279	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920381	134920381	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001305-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	85	531	0	ENST00000398015.3:c.2196G>A	p.Met732Ile	p.M732I	ENST00000398015	NM_004441.4	732	atG/atA	12/16	NA	2	FACETS	0.89	0.792	0.993			1	INDETERMINATE	2	TRUE	NA	0.248848864740503	2		531	384	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259174	36259174	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001305-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	153	539	0	ENST00000300305.3:c.317G>T	p.Trp106Leu	p.W106L	ENST00000300305		106	tGg/tTg	3/8	1	2	FACETS	0.815	0.747	0.887	1	0.989	1	CLONAL	2	TRUE	1	0.248848864740503	2		539	754	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428427	47428427	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001305-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	29	792	0	ENST00000377045.4:c.1295C>G	p.Ser432Cys	p.S432C	ENST00000377045	NM_001654.4	432	tCt/tGt	12/16	0.248848864740503	0	FACETS	0.41	0.329	0.503			1	SUBCLONAL	1	TRUE	0	0.248848864740503	0		792	427	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339327	70339327	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001305-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	30	386	0	ENST00000374080.3:c.204G>T	p.Lys68Asn	p.K68N	ENST00000374080		68	aaG/aaT	2/45	0.248848864740503	0	FACETS	0.382	0.307	0.467			1	SUBCLONAL	1	TRUE	0	0.248848864740503	0		386	474	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0001322-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1521	100	542	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.617	0.549	0.69	0.617	0.549	0.69	SUBCLONAL	1	TRUE	1	0.2	2		542	1621	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0001322-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	64	322	0	ENST00000262160.6:c.1391C>G	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tGa	11/11	1	2	FACETS	0.745	0.644	0.856	0.745	0.644	0.856	SUBCLONAL	1	TRUE	1	0.2	2		322	859	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087458	27087458	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001322-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1270	73	541	0	ENST00000324856.7:c.2032C>T	p.Gln678Ter	p.Q678*	ENST00000324856	NM_006015.4	678	Cag/Tag	5/20	1	2	FACETS	0.544	0.473	0.62	0.544	0.473	0.62	SUBCLONAL	1	TRUE	1	0.2	2		541	1343	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457303	67457303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768713596	NA	P-0001322-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	108	448	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	0.2	2		449	1076	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0001328-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	993	201	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.650093142910883	10	FACETS	0.992	0.972	1	0.992	0.972	1	CLONAL	8	TRUE	2	0.650093142910883	10		201	1386	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0001328-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1296	295	320	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.650093142910883	10	FACETS	1	0.959	1	0.257	0.241	0.273	CLONAL	2	TRUE	2	0.650093142910883	10		320	1591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579369	7579369	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555526581	NA	P-0001328-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	216	303	0	ENST00000269305.4:c.318C>G	p.Ser106Arg	p.S106R	ENST00000269305	NM_001126112.2	106	agC/agG	4/11	0.650093142910883	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.650093142910883	2		303	326	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241677	55241677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504256	NA	P-0001328-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	1373	383	0	ENST00000275493.2:c.2125G>A	p.Glu709Lys	p.E709K	ENST00000275493	NM_005228.3	709	Gaa/Aaa	18/28	0.650093142910883	10	FACETS	1	0.983	1	1	0.983	1	CLONAL	8	TRUE	2	0.650093142910883	10		383	1900	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156602	55156602	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001328-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	42	311	0	ENST00000257290.5:c.3003G>T	p.Lys1001Asn	p.K1001N	ENST00000257290	NM_006206.4	1001	aaG/aaT	22/23	0.617134036961308	3	FACETS	0.307	0.256	0.364	0.153	0.128	0.182	SUBCLONAL	1	TRUE	1	0.650093142910883	3		311	558	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55086984	55086984	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs759582787	NA	P-0001328-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1273	96	302	0	ENST00000275493.2:c.14G>C	p.Gly5Ala	p.G5A	ENST00000275493	NM_005228.3	5	gGg/gCg	1/28	0.650093142910883	10	FACETS	0.777	0.689	0.87	0.097	0.086	0.109	SUBCLONAL	1	TRUE	2	0.650093142910883	10		302	1369	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692890	89692890	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001328-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	194	162	0	ENST00000371953.3:c.374A>C	p.Lys125Thr	p.K125T	ENST00000371953	NM_000314.4	125	aAa/aCa	5/9	0.650093142910883	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.650093142910883	2		162	280	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563434	21563434	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001328-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	114	613	0	ENST00000382592.4:c.485T>A	p.Leu162His	p.L162H	ENST00000382592	NM_014572.2	162	cTc/cAc	4/8	0.508393037463497	4	FACETS	0.568	0.511	0.63			1	SUBCLONAL	1	TRUE	NA	0.650093142910883	4		613	1018	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347191	70347191	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001332-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	217	201	1	ENST00000374080.3:c.2855G>A	p.Cys952Tyr	p.C952Y	ENST00000374080		952	tGt/tAt	21/45	1	1	FACETS	0.94	0.888	0.993	1	0.996	1	CLONAL	6	TRUE	0	0.17	1		202	414	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372320	55372320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001332-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	83	227	0	ENST00000297316.4:c.1010C>T	p.Pro337Leu	p.P337L	ENST00000297316	NM_022454.3	337	cCg/cTg	2/2	0.3	1	FACETS	0.858	0.764	0.958	1	0.987	1	CLONAL	3	TRUE	0	0.17	1		227	347	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0001338-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	148	402	1	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.224836730826146	3	FACETS	1	0.963	1	0.547	0.5	0.596	INDETERMINATE	1	TRUE	1	0.448399604299372	3		403	739	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0001338-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	230	505	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.433783266947338	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.448399604299372	1		505	643	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0001338-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	2285	311	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.448399604299372	14	FACETS	1	0.998	1			1	CLONAL	14	TRUE	NA	0.448399604299372	14		311	2595	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0001346-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	220	330	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.945	0.882	1	0.945	0.882	1	CLONAL	1	TRUE	1	0.584937468916787	2		332	796	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578496	7578496	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782197	NA	P-0001346-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	199	302	1	ENST00000269305.4:c.434T>C	p.Leu145Pro	p.L145P	ENST00000269305	NM_001126112.2	145	cTg/cCg	5/11	0.584937468916787	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.584937468916787	1		303	445	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143984	11143984	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs267607070	NA	P-0001346-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	157	198	0	ENST00000358026.2:c.3565C>T	p.Arg1189Ter	p.R1189*	ENST00000358026	NM_001128849.1	1189	Cga/Tga	26/36	0.241985374484135	1	FACETS	0.754	0.695	0.814	0.754	0.695	0.814	INDETERMINATE	1	TRUE	0	0.584937468916787	1		198	504	SUCCESS
APC	324	MSKCC	GRCh37	5	112175908	112175917	+	frameshift_variant	Frame_Shift_Del	DEL	AGAGCAGCCT	AGAGCAGCCT	-	novel	NA	P-0001346-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	164	174	0	ENST00000257430.4:c.4618_4627del	p.Glu1540LysfsTer22	p.E1540Kfs*22	ENST00000257430	NM_000038.5	1539	tcAGAGCAGCCT/tc	16/16	0.584937468916787	2	FACETS	1	0.989	1	0.696	0.646	0.746	CLONAL	1	TRUE	0	0.584937468916787	2		174	403	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0001400-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	223	366	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.130910877502567	4	FACETS	0.939	0.88	0.999	0.939	0.88	0.999	INDETERMINATE	2	TRUE	2	0.642369343295112	4		366	607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0001400-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	223	393	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.642369343295112	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	TRUE	0	0.642369343295112	3		393	301	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934172	39934172	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1446473852	NA	P-0001400-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	150	1159	0	ENST00000378444.4:c.427A>G	p.Asn143Asp	p.N143D	ENST00000378444	NM_001123385.1	143	Aat/Gat	4/15	0.386908352113479	1	FACETS	0.656	0.604	0.71	0.656	0.604	0.71	SUBCLONAL	1	TRUE	0	0.642369343295112	1		1159	483	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813049	76813049	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001400-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	381	1106	0	ENST00000373344.5:c.6572A>G	p.Asp2191Gly	p.D2191G	ENST00000373344	NM_000489.3	2191	gAt/gGt	30/35	0.386908352113479	1	FACETS	0.871	0.831	0.912	0.871	0.831	0.912	CLONAL	1	TRUE	0	0.642369343295112	1		1106	924	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589584	67589589	+	inframe_deletion	In_Frame_Del	DEL	ACATGA	ACATGA	-	novel	NA	P-0001400-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	203	311	0	ENST00000274335.5:c.1348_1353del	p.His450_Glu451del	p.H450_E451del	ENST00000274335		449	ttACATGAa/tta	10/15	0.350847953182983	5	FACETS	0.955	0.89	1	0.636	0.593	0.681	INDETERMINATE	2	TRUE	2	0.642369343295112	5		311	650	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0001402-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	37	330	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.3	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		332	868	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0001402-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	57	445	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		446	921	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189835	66189835	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs55784741	NA	P-0001403-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	252	697	2	ENST00000273854.3:c.3111G>T	p.Leu1037Phe	p.L1037F	ENST00000273854	NM_004439.5	1037	ttG/ttT	18/18	0.279868177829772	3	FACETS	0.809	0.757	0.863	0.809	0.757	0.863	CLONAL	2	TRUE	1	0.31865767085836	3		699	1133	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289662	33289662	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001403-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	71	439	0	ENST00000374542.5:c.41A>C	p.Asp14Ala	p.D14A	ENST00000374542	NM_001141970.1	14	gAc/gCc	2/8	0.31865767085836	3	FACETS	0.806	0.703	0.917	0.403	0.351	0.459	CLONAL	1	TRUE	1	0.31865767085836	3		439	641	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151750	108151750	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0001403-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	209	417	0	ENST00000278616.4:c.3431T>A	p.Leu1144Ter	p.L1144*	ENST00000278616	NM_000051.3	1144	tTg/tAg	24/63	0.31865767085836	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.31865767085836	2		417	624	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762846821	NA	P-0001437-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	14	197	0	ENST00000269305.4:c.461G>A	p.Gly154Asp	p.G154D	ENST00000269305	NM_001126112.2	154	gGc/gAc	5/11	0.217133609259291	0	FACETS	0.188	0.135	0.252			1	SUBCLONAL	1	TRUE	0	0.288604721884629	0		197	367	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574010	7574010	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001438-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	31	411	0	ENST00000269305.4:c.1017del	p.Met340CysfsTer5	p.M340Cfs*5	ENST00000269305	NM_001126112.2	339	gaG/ga	10/11	1	2	FACETS	0.432	0.348	0.527	0.432	0.348	0.527	SUBCLONAL	1	FALSE	1	0.233166346433329	2		411	616	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0001442-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	93	201	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.74959873912272	3	FACETS	0.824	0.737	0.915	0.412	0.368	0.458	CLONAL	1	TRUE	1	0.74959873912272	3		201	414	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0001442-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	219	342	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.871	0.814	0.929	0.871	0.814	0.929	CLONAL	1	TRUE	1	0.74959873912272	2		342	671	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0001442-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	203	335	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	0.109557625401692	4	FACETS	0.911	0.852	0.971	0.911	0.852	0.971	INDETERMINATE	2	TRUE	2	0.74959873912272	4		335	520	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242511	55242511	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913418	NA	P-0001442-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	114	273	0	ENST00000275493.2:c.2281G>T	p.Asp761Tyr	p.D761Y	ENST00000275493	NM_005228.3	761	Gat/Tat	19/28	0.74959873912272	3	FACETS	0.915	0.829	1	0.458	0.414	0.503	CLONAL	1	TRUE	1	0.74959873912272	3		273	457	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931463	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622007	NA	P-0001446-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2019	371	255	0	ENST00000374690.3:c.2105T>A	p.Leu702His	p.L702H	ENST00000374690	NM_000044.3	702	cTc/cAc	4/8	0.807560330678246	6	FACETS	1	0.949	1			1	CLONAL	1	TRUE	NA	0.807560330678246	6		255	2390	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176700715	176700715	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001446-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	219	281	0	ENST00000439151.2:c.5552A>G	p.Gln1851Arg	p.Q1851R	ENST00000439151	NM_022455.4	1851	cAa/cGa	17/23	0.519061465594584	1	FACETS	0.596	0.559	0.633	0.596	0.559	0.633	SUBCLONAL	1	TRUE	0	0.807560330678246	1		281	543	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978862	13978862	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001446-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	94	325	0	ENST00000405192.2:c.245A>G	p.His82Arg	p.H82R	ENST00000405192	NM_001163147.1	82	cAt/cGt	6/12	0.195947547040089	3	FACETS	0.413	0.367	0.462	0.138	0.122	0.154	INDETERMINATE	1	TRUE	0	0.807560330678246	3		325	791	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90949294	90949294	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001446-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	89	307	0	ENST00000265433.3:c.2194C>A	p.Gln732Lys	p.Q732K	ENST00000265433	NM_002485.4	732	Caa/Aaa	15/16	0.432810275211997	3	FACETS	0.294	0.26	0.331	0.098	0.086	0.111	INDETERMINATE	1	TRUE	0	0.807560330678246	3		307	1051	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245961	46245961	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001446-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	177	319	0	ENST00000334344.6:c.4055A>G	p.Asp1352Gly	p.D1352G	ENST00000334344	NM_152641.2	1352	gAt/gGt	15/21	1	2	FACETS	0.539	0.497	0.583	0.539	0.497	0.583	SUBCLONAL	1	TRUE	1	0.807560330678246	2		319	813	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577035	7577035	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001446-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	242	336	0	ENST00000269305.4:c.903del	p.Ser303AlafsTer42	p.S303Afs*42	ENST00000269305	NM_001126112.2	301	ccA/cc	8/11	0.807560330678246	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.807560330678246	1		336	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs747342068	NA	P-0001450-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	228	158	0	ENST00000269305.4:c.394A>C	p.Lys132Gln	p.K132Q	ENST00000269305	NM_001126112.2	132	Aag/Cag	5/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.773531522624435	2		158	514	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0001450-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	331	366	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.773531522624435	2		366	776	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0001450-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	186	178	0	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.773531522624435	2		178	427	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849167	76849167	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001450-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	72	408	0	ENST00000373344.5:c.6109G>A	p.Val2037Ile	p.V2037I	ENST00000373344	NM_000489.3	2037	Gtc/Atc	26/35	0.453065332459662	1	FACETS	0.094	0.081	0.108	0.094	0.081	0.108	INDETERMINATE	1	TRUE	0	0.773531522624435	1		408	1216	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76812967	76812967	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001450-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	513	358	0	ENST00000373344.5:c.6654del	p.Asn2219IlefsTer31	p.N2219Ifs*31	ENST00000373344	NM_000489.3	2218	ccT/cc	30/35	0.453065332459662	1	FACETS	0.781	0.751	0.81	0.781	0.751	0.81	INDETERMINATE	1	TRUE	0	0.773531522624435	1		358	1042	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0001462-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	284	542	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.21595296050814	7	FACETS	1	0.979	1	1	0.995	1	CLONAL	7	FALSE	2	0.21595296050814	7		542	549	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657509	37657509	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001462-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	336	366	0	ENST00000447079.4:c.2426T>G	p.Phe809Cys	p.F809C	ENST00000447079	NM_015083.1	809	tTt/tGt	6/14	0.21595296050814	4	FACETS	0.948	0.912	0.983	1	0.997	1	CLONAL	8	FALSE	1	0.21595296050814	4		366	499	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657542	37657542	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001462-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	380	411	0	ENST00000447079.4:c.2459T>C	p.Leu820Ser	p.L820S	ENST00000447079	NM_015083.1	820	tTa/tCa	6/14	0.21595296050814	4	FACETS	1	0.985	1	1	0.997	1	CLONAL	7	FALSE	1	0.21595296050814	4		411	587	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0001468-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	184	221	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	0.995	1	CLONAL	4	TRUE	1	0.16	2		221	560	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001468-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	242	374	0	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	1	2	FACETS	1	0.981	1	1	0.996	1	CLONAL	3	TRUE	1	0.16	2		374	900	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937611	76937615	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTT	CTTTT	-	novel	NA	P-0001471-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	206	389	0	ENST00000373344.5:c.3133_3137del	p.Lys1045Ter	p.K1045*	ENST00000373344	NM_000489.3	1045	AAAAGt/t	9/35	0.562224040190285	1	FACETS	0.589	0.551	0.627	0.589	0.551	0.627	SUBCLONAL	1	TRUE	0	0.800607500064729	1		389	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0001471-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	294	166	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.800607500064729	2	FACETS	0.949	0.916	0.981	0.949	0.916	0.981	CLONAL	2	TRUE	0	0.800607500064729	2		166	387	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201822	66201822	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001471-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	156	184	0	ENST00000273854.3:c.2680G>C	p.Gly894Arg	p.G894R	ENST00000273854	NM_004439.5	894	Ggc/Cgc	16/18	1	2	FACETS	0.95	0.88	1	0.95	0.88	1	CLONAL	1	TRUE	1	0.800607500064729	2		184	410	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395737	45395737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001471-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	195	194	1	ENST00000262160.6:c.397C>T	p.Arg133Cys	p.R133C	ENST00000262160	NM_005901.5	133	Cgc/Tgc	4/11	0.800607500064729	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.800607500064729	1		195	279	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624242	89624243	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs121913290	NA	P-0001471-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	50	41	0	ENST00000371953.3:c.17_18del	p.Lys6ArgfsTer4	p.K6Rfs*4	ENST00000371953	NM_000314.4	6	AAa/a	1/9	0.800607500064729	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.800607500064729	1		41	72	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937001	48937005	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAA	CAGAA	-	rs1566192530	NA	P-0001471-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	155	181	0	ENST00000267163.4:c.772_776del	p.Asn258GlufsTer11	p.N258Efs*11	ENST00000267163	NM_000321.2	257	CAGAAc/c	8/27	0.800607500064729	1	FACETS	0.826	0.773	0.879	0.826	0.773	0.879	CLONAL	1	TRUE	0	0.800607500064729	1		181	281	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0001496-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	131	311	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.275831003588205	3	FACETS	1	0.986	1	0.729	0.667	0.792	INDETERMINATE	1	TRUE	1	0.538052367961772	3		311	424	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144146	11144146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001496-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	77	353	0	ENST00000358026.2:c.3727C>T	p.Arg1243Trp	p.R1243W	ENST00000358026	NM_001128849.1	1243	Cgg/Tgg	26/36	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.538052367961772	2		353	256	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575023	64575023	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs794728652	NA	P-0001509-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	237	215	1	ENST00000312049.6:c.783+1G>T		p.X261_splice	ENST00000312049	NM_130799.2	261			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		216	317	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0001514-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	62	201	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		201	829	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989481	85989481	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001515-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	238	402	1	ENST00000263360.6:c.1240C>T	p.Arg414Ter	p.R414*	ENST00000263360	NM_003797.3	414	Cga/Tga	12/12	0.823440145544865	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.823440145544865	1		403	312	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032764	30032765	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0001515-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	175	237	1	ENST00000338641.4:c.140_141del	p.Phe47Ter	p.F47*	ENST00000338641	NM_000268.3	47	TTt/t	2/16	0.823440145544865	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.823440145544865	1		238	247	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442440	49442440	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0001517-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	204	780	0	ENST00000301067.7:c.4131+2T>C		p.X1377_splice	ENST00000301067	NM_003482.3	1377			0.103407962943738	4	FACETS	1	0.948	1	1	0.948	1	INDETERMINATE	2	TRUE	2	0.705067266498449	4		780	487	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593613	+	missense_variant	Missense_Mutation	ONP	TTGT	TTGT	CTGA	novel	NA	P-0001517-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	131	694	2	ENST00000288135.5:c.1676_1679delinsCTGA	p.Val559_Val560delinsAlaAsp	p.V559_V560delinsAD	ENST00000288135	NM_000222.2	559	gTTGTt/gCTGAt	11/21	1	2	FACETS	0.918	0.841	0.997	0.918	0.841	0.997	CLONAL	1	TRUE	1	0.705067266498449	2		696	405	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0001518-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	33	330	2	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		332	1064	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230892	53230892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001518-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	22	260	0	ENST00000375401.3:c.1901G>A	p.Arg634His	p.R634H	ENST00000375401	NM_004187.3	634	cGc/cAc	14/26	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		260	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577595	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0001524-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	203	257	0	ENST00000269305.4:c.686_687del	p.Cys229TyrfsTer10	p.C229Yfs*10	ENST00000269305	NM_001126112.2	229	tGT/t	7/11	0.625296957141602	1	FACETS	0.761	0.712	0.811	0.761	0.712	0.811	SUBCLONAL	1	TRUE	0	0.677330267970383	1		257	521	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777665	9777665	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001524-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	286	344	1	ENST00000377346.4:c.1001A>G	p.Asn334Ser	p.N334S	ENST00000377346	NM_005026.3	334	aAc/aGc	8/24	0.518838809547607	1	FACETS	0.837	0.793	0.882	0.837	0.793	0.882	CLONAL	1	TRUE	0	0.677330267970383	1		345	667	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288645	33288645	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001524-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	259	222	0	ENST00000374542.5:c.907G>T	p.Gly303Cys	p.G303C	ENST00000374542	NM_001141970.1	303	Ggc/Tgc	3/8	0.276298568066934	3	FACETS	1	0.986	1	0.586	0.55	0.623	INDETERMINATE	1	TRUE	1	0.677330267970383	3		222	874	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376998	118376998	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001524-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	265	378	1	ENST00000534358.1:c.10391G>T	p.Ser3464Ile	p.S3464I	ENST00000534358	NM_005933.3	3464	aGc/aTc	27/36	0.677330267970383	1	FACETS	0.851	0.805	0.898	0.851	0.805	0.898	CLONAL	1	TRUE	0	0.677330267970383	1		379	608	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50490727	50490727	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001524-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	285	328	0	ENST00000394963.4:c.1364G>C	p.Trp455Ser	p.W455S	ENST00000394963	NM_003076.4	455	tGg/tCg	11/13	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.677330267970383	2		328	819	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416809	121416809	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs76845985	NA	P-0001524-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	230	396	0	ENST00000257555.6:c.238G>T	p.Asp80Tyr	p.D80Y	ENST00000257555		80	Gac/Tac	1/10	0.443307292616518	1	FACETS	0.608	0.569	0.648	0.608	0.569	0.648	SUBCLONAL	1	TRUE	0	0.677330267970383	1		396	739	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170552	11170552	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001524-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	112	187	0	ENST00000358026.2:c.4855G>T	p.Glu1619Ter	p.E1619*	ENST00000358026	NM_001128849.1	1619	Gaa/Taa	34/36	0.649268016419828	1	FACETS	0.741	0.677	0.808	0.741	0.677	0.808	SUBCLONAL	1	TRUE	0	0.677330267970383	1		187	295	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098819	+	inframe_deletion	In_Frame_Del	DEL	TTCACCTGTCTCTTCATCTAG	TTCACCTGTCTCTTCATCTAG	-	novel	NA	P-0001524-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	187	438	0	ENST00000397062.3:c.226_246del	p.Leu76_Glu82del	p.L76_E82del	ENST00000397062	NM_006164.4	76	CTAGATGAAGAGACAGGTGAA/-	2/5	1	2	FACETS	0.533	0.492	0.576	0.533	0.492	0.576	SUBCLONAL	1	TRUE	1	0.677330267970383	2		438	1036	SUCCESS
APC	324	MSKCC	GRCh37	5	112175891	112175891	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001524-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	242	302	0	ENST00000257430.4:c.4602del	p.Asn1535MetfsTer30	p.N1535Mfs*30	ENST00000257430	NM_000038.5	1534	Ggg/gg	16/16	0.625296957141602	1	FACETS	0.818	0.77	0.866	0.818	0.77	0.866	CLONAL	1	TRUE	0	0.677330267970383	1		302	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0001531-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	276	293	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.492232830184351	2	FACETS	0.962	0.912	1	0.962	0.912	1	CLONAL	2	TRUE	0	0.492232830184351	2		294	583	SUCCESS
APC	324	MSKCC	GRCh37	5	112175324	112175324	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1211642532	NA	P-0001531-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	231	256	0	ENST00000257430.4:c.4033G>T	p.Glu1345Ter	p.E1345*	ENST00000257430	NM_000038.5	1345	Gaa/Taa	16/16	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.492232830184351	2		256	876	SUCCESS
APC	324	MSKCC	GRCh37	5	112175328	112175328	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0001531-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	268	179	0	ENST00000257430.4:c.4037C>G	p.Ser1346Ter	p.S1346*	ENST00000257430	NM_000038.5	1346	tCa/tGa	16/16	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.492232830184351	2		179	886	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550460	29550460	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs763983337	NA	P-0001531-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	318	203	0	ENST00000356175.3:c.1722-2A>G		p.X574_splice	ENST00000356175	NM_000267.3	574			0.492232830184351	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.492232830184351	2		203	645	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0001543-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	159	294	1	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.505125383520331	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.505125383520331	1		295	444	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481898	56481898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001543-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1868	881	628	0	ENST00000267101.3:c.826C>T	p.Pro276Ser	p.P276S	ENST00000267101	NM_001982.3	276	Ccc/Tcc	7/28	0.505125383520331	8	FACETS	1	0.991	1			1	CLONAL	3	TRUE	NA	0.505125383520331	8		628	2749	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604796	48604798	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0001543-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	269	498	0	ENST00000342988.3:c.1619_1621del	p.Leu540del	p.L540del	ENST00000342988	NM_005359.5	540	CTT/-	12/12	0.505125383520331	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.505125383520331	1		498	722	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509447	106509447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001558-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	397	53	456	0	ENST00000359195.3:c.1441G>A	p.Val481Ile	p.V481I	ENST00000359195	NM_002649.2	481	Gtc/Atc	2/11	0.407455550731572	4	FACETS	0.789	0.674	0.915			1	CLONAL	1	TRUE	NA	0.425475856396594	4		456	450	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239082	98239082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781101191	NA	P-0001558-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	253	19	468	0	ENST00000331920.6:c.1561G>A	p.Ala521Thr	p.A521T	ENST00000331920	NM_000264.3	521	Gcc/Acc	11/24	NA	2	FACETS	0.328	0.249	0.421			1	INDETERMINATE	1	TRUE	NA	0.425475856396594	2		468	272	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0001559-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	58	62	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.63	0.543	0.725	0.63	0.543	0.725	SUBCLONAL	1	TRUE	1	0.435071603021334	2		62	423	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69229651	69229651	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001559-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	108	284	0	ENST00000462284.1:c.727G>C	p.Asp243His	p.D243H	ENST00000462284	NM_002392.5	243	Gat/Cat	9/11	0.228449501601635	4	FACETS	0.641	0.573	0.712			1	INDETERMINATE	1	TRUE	NA	0.435071603021334	4		284	1112	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0001561-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	149	412	0	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.176964288865701	3	FACETS	0.843	0.773	0.917	0.843	0.773	0.917	CLONAL	3	TRUE	0	0.198219368730833	3		412	653	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953909	17953909	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001561-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1282	106	332	0	ENST00000458235.1:c.493del	p.Leu165TrpfsTer21	p.L165Wfs*21	ENST00000458235	NM_000215.3	165	Ctg/tg	5/24	0.198219368730833	11	FACETS	1	0.98	1	0.162	0.144	0.181	CLONAL	1	TRUE	2	0.198219368730833	11		332	1388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0001577-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	148	293	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.432625012815749	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	TRUE	0	0.444428825441804	3		294	254	SUCCESS
APC	324	MSKCC	GRCh37	5	112163677	112163677	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0001577-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	272	658	0	ENST00000257430.4:c.1600A>T	p.Lys534Ter	p.K534*	ENST00000257430	NM_000038.5	534	Aaa/Taa	13/16	0.322390445192397	3	FACETS	1	0.987	1	0.761	0.72	0.804	CLONAL	2	TRUE	0	0.444428825441804	3		658	655	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545597	106545597	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001577-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	231	492	0	ENST00000359195.3:c.3074A>G	p.Asn1025Ser	p.N1025S	ENST00000359195	NM_002649.2	1025	aAc/aGc	11/11	0.444428825441804	3	FACETS	1	0.989	1	0.819	0.772	0.867	CLONAL	2	TRUE	0	0.444428825441804	3		492	517	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779482	3779482	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001608-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	211	478	0	ENST00000262367.5:c.5566C>T	p.Gln1856Ter	p.Q1856*	ENST00000262367	NM_004380.2	1856	Cag/Tag	31/31	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	FALSE	NA	0.448800014069927	2		478	660	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175462	108175462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1801516	NA	P-0001615-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	18	338	0	ENST00000278616.4:c.5557G>A	p.Asp1853Asn	p.D1853N	ENST00000278616	NM_000051.3	1853	Gat/Aat	37/63	1	2	FACETS	0.146	0.109	0.19	0.146	0.109	0.19	SUBCLONAL	1	TRUE	1	0.392677050805953	2		338	627	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539588	187539588	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs3733406	NA	P-0001615-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	70	334	1	ENST00000441802.2:c.8152A>G	p.Ile2718Val	p.I2718V	ENST00000441802	NM_005245.3	2718	Att/Gtt	10/27	1	2	FACETS	0.532	0.464	0.606	0.532	0.464	0.606	SUBCLONAL	1	TRUE	1	0.392677050805953	2		335	670	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0001630-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	19	505	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		505	566	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0001630-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	39	389	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		389	440	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604662	48604662	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001633-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	29	486	0	ENST00000342988.3:c.1484T>C	p.Leu495Pro	p.L495P	ENST00000342988	NM_005359.5	495	cTt/cCt	12/12	0.375145287111867	1	FACETS	0.247	0.197	0.303	0.247	0.197	0.303	SUBCLONAL	1	TRUE	0	0.375145287111867	1		486	509	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043597	6043604	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTTACTT	ACTTACTT	-	novel	NA	P-0001633-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	13	187	0	ENST00000265849.7:c.249_250+6del		p.X83_splice	ENST00000265849	NM_000535.5	83		3/15	1	2	FACETS	0.373	0.266	0.502	0.373	0.266	0.502	SUBCLONAL	1	TRUE	1	0.375145287111867	2		187	186	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220592	1220592	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001633-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	279	522	0	ENST00000326873.7:c.611del	p.Phe204SerfsTer83	p.F204Sfs*83	ENST00000326873	NM_000455.4	204	Ttc/tc	5/10	0.375145287111867	1	FACETS	0.842	0.795	0.889	1	0.995	1	CLONAL	2	TRUE	0	0.375145287111867	1		522	718	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457219	25457226	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGCAGT	CCAGCAGT	GTG	novel	NA	P-0001633-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	145	605	0	ENST00000264709.3:c.2661_2668delinsCAC	p.Arg887SerfsTer32	p.R887Sfs*32	ENST00000264709	NM_175629.2	887	agACTGCTGGgc/agCACgc	23/23	1	2	FACETS	0.826	0.753	0.902	0.826	0.753	0.902	CLONAL	1	TRUE	1	0.375145287111867	2		605	936	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0001642-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	74	448	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.181501493701799	2	FACETS	1	0.975	1	0.748	0.656	0.846	CLONAL	1	TRUE	0	0.189636295114532	2		448	522	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685300	89685300	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs878853936	NA	P-0001642-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	91	328	0	ENST00000371953.3:c.195C>A	p.Tyr65Ter	p.Y65*	ENST00000371953	NM_000314.4	65	taC/taA	3/9	0.189636295114532	3	FACETS	0.904	0.804	1			1	CLONAL	2	TRUE	NA	0.189636295114532	3		328	581	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422723	49422723	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001642-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	117	438	0	ENST00000301067.7:c.14270C>T	p.Pro4757Leu	p.P4757L	ENST00000301067	NM_003482.3	4757	cCt/cTt	45/54	0.189636295114532	4	FACETS	0.971	0.876	1	0.971	0.876	1	CLONAL	2	TRUE	2	0.189636295114532	4		438	756	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29105993	29105993	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs864622149	NA	P-0001642-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	104	406	0	ENST00000328354.6:c.846+1G>A		p.X282_splice	ENST00000328354	NM_007194.3	282			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.189636295114532	2		406	774	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660643	190660643	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001655-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	33	256	0	ENST00000441310.2:c.281G>T	p.Gly94Val	p.G94V	ENST00000441310	NM_000534.4	94	gGa/gTa	3/13	1	2	FACETS	0.441	0.358	0.536	0.441	0.358	0.536	SUBCLONAL	1	TRUE	1	0.232177898778912	2		256	644	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098787	47098787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001655-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	54	401	0	ENST00000409792.3:c.6487C>T	p.Pro2163Ser	p.P2163S	ENST00000409792	NM_014159.6	2163	Ccc/Tcc	15/21	1	2	FACETS	0.647	0.551	0.752	0.647	0.551	0.752	SUBCLONAL	1	TRUE	1	0.232177898778912	2		401	719	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098871	47098871	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001655-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	73	440	0	ENST00000409792.3:c.6403C>T	p.Gln2135Ter	p.Q2135*	ENST00000409792	NM_014159.6	2135	Cag/Tag	15/21	1	2	FACETS	0.748	0.653	0.851	0.748	0.653	0.851	SUBCLONAL	1	TRUE	1	0.232177898778912	2		440	841	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89874702	89874702	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001655-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	37	501	0	ENST00000389301.3:c.596G>A	p.Ser199Asn	p.S199N	ENST00000389301	NM_000135.2	199	aGc/aAc	6/43	0.1939587899758	1	FACETS	0.416	0.341	0.499	0.416	0.341	0.499	SUBCLONAL	1	TRUE	0	0.232177898778912	1		501	678	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108259	8108259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001655-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	42	440	0	ENST00000585124.1:c.965C>T	p.Ser322Leu	p.S322L	ENST00000585124	NM_004217.3	322	tCa/tTa	9/9	1	2	FACETS	0.459	0.382	0.545	0.459	0.382	0.545	SUBCLONAL	1	TRUE	1	0.232177898778912	2		440	788	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866376	42866376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777667088	NA	P-0001655-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	38	352	0	ENST00000398585.3:c.256G>A	p.Val86Met	p.V86M	ENST00000398585	NM_001135099.1	86	Gtg/Atg	3/14	1	2	FACETS	0.602	0.497	0.719	0.602	0.497	0.719	SUBCLONAL	1	TRUE	1	0.232177898778912	2		352	544	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41525908	41525912	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTC	TCTTC	-	novel	NA	P-0001655-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	36	430	0	ENST00000263253.7:c.1185_1189del	p.Ser396ThrfsTer13	p.S396Tfs*13	ENST00000263253	NM_001429.3	395	TCTTCt/t	5/31	0.204120501750549	1	FACETS	0.424	0.347	0.51	0.424	0.347	0.51	SUBCLONAL	1	TRUE	0	0.232177898778912	1		430	647	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0001658-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	304	330	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.131574168083953	4	FACETS	0.93	0.877	0.985			1	INDETERMINATE	2	TRUE	NA	0.399756459007508	4		332	1144	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0001658-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	173	618	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.160510396534083	3	FACETS	0.99	0.91	1	0.495	0.455	0.537	INDETERMINATE	1	TRUE	1	0.399756459007508	3		618	1049	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0001658-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	274	393	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.399756459007508	2		393	600	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001658-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	167	265	0	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	0.160510396534083	3	FACETS	0.803	0.741	0.867	0.803	0.741	0.867	INDETERMINATE	2	TRUE	1	0.399756459007508	3		265	624	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001658-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	283	570	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	0.399756459007508	3	FACETS	0.993	0.937	1	0.993	0.937	1	CLONAL	2	TRUE	1	0.399756459007508	3		570	855	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89869730	89869740	+	frameshift_variant	Frame_Shift_Del	DEL	AACAAACATTT	AACAAACATTT	-	novel	NA	P-0001658-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	134	724	0	ENST00000389301.3:c.719_729del	p.Gln240LeufsTer17	p.Q240Lfs*17	ENST00000389301	NM_000135.2	240	cAAATGTTTGTT/c	8/43	1	2	FACETS	0.696	0.632	0.764	0.696	0.632	0.764	SUBCLONAL	1	TRUE	1	0.399756459007508	2		724	963	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0001664-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	274	393	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.664566016811854	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.674638780270086	1		393	470	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663563	117663563	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001664-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	313	541	0	ENST00000368508.3:c.4669G>T	p.Val1557Leu	p.V1557L	ENST00000368508	NM_002944.2	1557	Gta/Tta	28/43	NA	2	FACETS	0.94	0.888	0.993			1	INDETERMINATE	1	TRUE	NA	0.674638780270086	2		541	987	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545734	106545734	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001664-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	348	458	1	ENST00000359195.3:c.3211C>A	p.Gln1071Lys	p.Q1071K	ENST00000359195	NM_002649.2	1071	Cag/Aag	11/11	0.674638780270086	3	FACETS	1	0.982	1	0.541	0.511	0.571	CLONAL	1	TRUE	1	0.674638780270086	3		459	1276	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752965	128752965	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001664-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	603	456	0	ENST00000377970.2:c.1126G>C	p.Val376Leu	p.V376L	ENST00000377970	NM_002467.4	376	Gtc/Ctc	3/3	0.674638780270086	3	FACETS	0.93	0.897	0.963	0.93	0.897	0.963	CLONAL	2	TRUE	1	0.674638780270086	3		456	1285	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514539	125514539	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0001664-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	183	304	0	ENST00000428830.2:c.1233+1G>A		p.X411_splice	ENST00000428830	NM_001114121.2	411			0.674638780270086	3	FACETS	0.824	0.761	0.89			1	CLONAL	1	TRUE	NA	0.674638780270086	3		304	880	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78933999	78933999	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001664-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	204	411	0	ENST00000306801.3:c.3599G>T	p.Ser1200Ile	p.S1200I	ENST00000306801	NM_020761.2	1200	aGc/aTc	30/34	1	2	FACETS	0.935	0.871	1	0.935	0.871	1	CLONAL	1	TRUE	1	0.674638780270086	2		411	647	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416752	121416752	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001664-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	249	497	0	ENST00000257555.6:c.183del	p.Asn62MetfsTer93	p.N62Mfs*93	ENST00000257555		61	Ccc/cc	1/10	1	2	FACETS	0.927	0.87	0.986	0.927	0.87	0.986	CLONAL	1	TRUE	1	0.674638780270086	2		497	796	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133598	55133598	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs751257703	NA	P-0001667-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	190	576	0	ENST00000257290.5:c.902A>T	p.Glu301Val	p.E301V	ENST00000257290	NM_006206.4	301	gAa/gTa	6/23	0.408609239352621	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.491087820089076	1		576	470	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907058	101907058	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001667-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	209	440	0	ENST00000374994.4:c.1019del	p.Leu340TrpfsTer2	p.L340Wfs*2	ENST00000374994	NM_004612.2	340	Ttg/tg	6/9	0.4100978409628	2	FACETS	0.774	0.724	0.824	0.774	0.724	0.824	SUBCLONAL	2	TRUE	0	0.491087820089076	2		440	550	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396835	139396835	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373841359	NA	P-0001684-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	17	339	0	ENST00000277541.6:c.5273G>A	p.Arg1758His	p.R1758H	ENST00000277541	NM_017617.3	1758	cGc/cAc	28/34	0.239224948967458	1	FACETS	0.899	0.677	1	0.899	0.677	1	CLONAL	1	TRUE	0	0.255706203850456	1		339	129	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0001690-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	159	402	1	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.158823131404031	2	FACETS	0.768	0.705	0.833	0.768	0.705	0.833	INDETERMINATE	2	TRUE	0	0.285700838545576	2		403	725	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0001690-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	126	405	2	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.285700838545576	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.285700838545576	1		407	747	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535373	66535373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747419095	NA	P-0001690-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	79	391	0	ENST00000273854.3:c.88G>A	p.Gly30Ser	p.G30S	ENST00000273854	NM_004439.5	30	Ggc/Agc	1/18	0.285700838545576	1	FACETS	0.99	0.873	1	0.99	0.873	1	CLONAL	1	TRUE	0	0.285700838545576	1		391	479	SUCCESS
APC	324	MSKCC	GRCh37	5	112175411	112175411	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001690-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	215	400	0	ENST00000257430.4:c.4120G>T	p.Glu1374Ter	p.E1374*	ENST00000257430	NM_000038.5	1374	Gaa/Taa	16/16	0.285700838545576	1	FACETS	1	0.959	1	1	0.994	1	CLONAL	2	TRUE	0	0.285700838545576	1		400	624	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460417	149460417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756076440	NA	P-0001690-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	106	507	0	ENST00000286301.3:c.220G>A	p.Ala74Thr	p.A74T	ENST00000286301	NM_005211.3	74	Gct/Act	3/22	0.285700838545576	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.285700838545576	1		507	602	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578188	7578188	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201592	NA	P-0001690-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	307	553	0	ENST00000269305.4:c.661G>T	p.Glu221Ter	p.E221*	ENST00000269305	NM_001126112.2	221	Gag/Tag	6/11	0.285700838545576	1	FACETS	1	0.958	1	1	0.997	1	CLONAL	3	TRUE	0	0.285700838545576	1		553	610	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241895	133241895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1483635586	NA	P-0001692-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	34	507	1	ENST00000320574.5:c.2461C>T	p.Arg821Cys	p.R821C	ENST00000320574	NM_006231.2	821	Cgc/Tgc	21/49	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.639012987166893	2		508	75	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152093	55152093	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121908585	NA	P-0001692-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	151	573	0	ENST00000257290.5:c.2525A>T	p.Asp842Val	p.D842V	ENST00000257290	NM_006206.4	842	gAc/gTc	18/23	0.639012987166893	6	FACETS	0.986	0.922	1			1	CLONAL	4	TRUE	NA	0.639012987166893	6		573	273	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436674	52436674	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001699-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	46	646	0	ENST00000460680.1:c.2000G>A	p.Arg667Lys	p.R667K	ENST00000460680	NM_004656.3	667	aGg/aAg	16/17	0.14688725157054	0	FACETS	1	0.872	1			1	CLONAL	4	TRUE	0	0.146980066646388	0		646	132	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873747	35873747	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001711-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	58	411	0	ENST00000303115.3:c.703T>A	p.Ser235Thr	p.S235T	ENST00000303115	NM_002185.3	235	Tca/Aca	5/8	0.284441470359747	4	FACETS	1	0.948	1	0.608	0.524	0.7	CLONAL	1	TRUE	2	0.289196955560087	4		411	425	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200677	128200677	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001720-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	110	223	1	ENST00000341105.2:c.1128C>A	p.Tyr376Ter	p.Y376*	ENST00000341105	NM_032638.4	376	taC/taA	5/6	0.455339912443794	1	FACETS	0.713	0.653	0.774	0.713	0.653	0.774	SUBCLONAL	1	TRUE	0	0.757485097654757	1		224	253	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0001723-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	281	405	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.374198885000602	3	FACETS	1	0.989	1	0.792	0.748	0.837	CLONAL	2	TRUE	0	0.374198885000602	3		405	750	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725054	89725054	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1554826026	NA	P-0001723-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	87	450	0	ENST00000371953.3:c.1037A>G	p.Tyr346Cys	p.Y346C	ENST00000371953	NM_000314.4	346	tAc/tGc	9/9	0.374198885000602	1	FACETS	0.977	0.871	1	0.977	0.871	1	CLONAL	1	TRUE	0	0.374198885000602	1		450	387	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0001729-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	210	330	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.597140656777525	4	FACETS	0.883	0.825	0.942	0.883	0.825	0.942	CLONAL	2	TRUE	2	0.637162025763976	4		332	611	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0001729-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	329	464	1	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.637162025763976	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.637162025763976	2		465	498	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680956	30680956	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001729-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	383	666	0	ENST00000376406.3:c.763G>T	p.Glu255Ter	p.E255*	ENST00000376406	NM_014641.2	255	Gaa/Taa	5/15	0.637162025763976	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.637162025763976	3		666	744	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610608	81610608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001736-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	65	554	0	ENST00000298171.2:c.2206G>A	p.Glu736Lys	p.E736K	ENST00000298171	NM_000369.2	736	Gaa/Aaa	10/10	1	2	FACETS	0.851	0.735	0.976	0.851	0.735	0.976	CLONAL	1	TRUE	1	0.15	2		554	1019	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0001736-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	29	471	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.3	2	FACETS	0.438	0.35	0.539			1	SUBCLONAL	1	TRUE	NA	0.15	2		471	883	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163293	32163293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001736-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	89	633	0	ENST00000375023.3:c.5933G>A	p.Arg1978Gln	p.R1978Q	ENST00000375023	NM_004557.3	1978	cGg/cAg	30/30	1	2	FACETS	0.99	0.875	1	0.99	0.875	1	CLONAL	1	TRUE	1	0.15	2		633	1199	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741731	145741731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001736-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	83	501	0	ENST00000428558.2:c.772G>A	p.Gly258Arg	p.G258R	ENST00000428558	NM_004260.3	258	Gga/Aga	5/22	0.218279894451679	3	FACETS	1	0.965	1	0.629	0.554	0.711	CLONAL	1	TRUE	1	0.15	3		501	945	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424400	49424400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001736-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	54	528	0	ENST00000301067.7:c.13823C>T	p.Ser4608Phe	p.S4608F	ENST00000301067	NM_003482.3	4608	tCc/tTc	41/54	1	2	FACETS	0.698	0.594	0.812	0.698	0.594	0.812	SUBCLONAL	1	TRUE	1	0.15	2		528	1032	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298107	15298107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210611177	NA	P-0001736-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	42	366	0	ENST00000263388.2:c.1649C>T	p.Ser550Phe	p.S550F	ENST00000263388	NM_000435.2	550	tCc/tTc	11/33	1	2	FACETS	0.807	0.672	0.957	0.807	0.672	0.957	CLONAL	1	TRUE	1	0.15	2		366	694	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556071	29556071	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001736-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	52	291	0	ENST00000356175.3:c.2439del	p.Lys814ArgfsTer7	p.K814Rfs*7	ENST00000356175	NM_000267.3	813	gTt/gt	21/57	1	2	FACETS	0.968	0.823	1	0.968	0.823	1	CLONAL	1	TRUE	1	0.15	2		291	716	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577540	7577541	+	missense_variant	Missense_Mutation	DNP	GT	GT	TA	novel	NA	P-0001736-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	35	401	0	ENST00000269305.4:c.740_741delinsTA	p.Asn247Ile	p.N247I	ENST00000269305	NM_001126112.2	247	aAC/aTA	7/11	0.3	2	FACETS	0.64	0.523	0.773			1	SUBCLONAL	1	TRUE	NA	0.15	2		401	729	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933010	39933010	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001738-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	390	255	0	ENST00000378444.4:c.1589A>T	p.Lys530Met	p.K530M	ENST00000378444	NM_001123385.1	530	aAg/aTg	4/15	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.764361307013456	1		255	535	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0001754-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	199	330	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.368553749369304	3	FACETS	0.93	0.873	0.988	1	0.991	1	CLONAL	3	TRUE	1	0.385735992951055	3		332	441	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0001754-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	38	62	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.385735992951055	2	FACETS	1	0.94	1	0.64	0.537	0.75	CLONAL	1	TRUE	0	0.385735992951055	2		62	154	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0001754-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	155	529	1	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.368553749369304	3	FACETS	0.837	0.77	0.906	0.837	0.77	0.906	CLONAL	2	TRUE	1	0.385735992951055	3		530	573	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858913	89858913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199967286	NA	P-0001754-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	105	294	0	ENST00000389301.3:c.1049G>A	p.Arg350Gln	p.R350Q	ENST00000389301	NM_000135.2	350	cGg/cAg	12/43	0.368553749369304	3	FACETS	0.945	0.848	1	0.473	0.424	0.525	CLONAL	1	TRUE	1	0.385735992951055	3		294	687	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257128	198257128	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001754-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	131	445	0	ENST00000335508.6:c.3814A>G	p.Ile1272Val	p.I1272V	ENST00000335508	NM_012433.2	1272	Atc/Gtc	25/25	0.215999548863028	5	FACETS	1	0.972	1	0.769	0.702	0.837	INDETERMINATE	2	TRUE	2	0.385735992951055	5		445	465	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052953	180052953	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs963089368	NA	P-0001754-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	93	424	0	ENST00000261937.6:c.1337C>T	p.Thr446Met	p.T446M	ENST00000261937	NM_182925.4	446	aCg/aTg	10/30	0.368553749369304	3	FACETS	0.851	0.757	0.951	0.425	0.378	0.476	CLONAL	1	TRUE	1	0.385735992951055	3		424	676	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28631496	28631496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001754-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	74	445	0	ENST00000241453.7:c.472G>A	p.Val158Met	p.V158M	ENST00000241453	NM_004119.2	158	Gtg/Atg	4/24	0.385735992951055	3	FACETS	0.793	0.695	0.899	0.397	0.347	0.45	SUBCLONAL	1	TRUE	1	0.385735992951055	3		445	577	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130367	2130367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397515225	NA	P-0001754-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	98	381	0	ENST00000219476.3:c.3599G>A	p.Arg1200Gln	p.R1200Q	ENST00000219476	NM_000548.3	1200	cGg/cAg	30/42	0.368553749369304	3	FACETS	0.82	0.732	0.914	0.41	0.366	0.457	CLONAL	1	TRUE	1	0.385735992951055	3		381	739	SUCCESS
APC	324	MSKCC	GRCh37	5	112173851	112173851	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001754-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	72	357	0	ENST00000257430.4:c.2560del	p.Arg854GlufsTer7	p.R854Efs*7	ENST00000257430	NM_000038.5	854	Aga/ga	16/16	0.368553749369304	3	FACETS	0.994	0.872	1	0.497	0.436	0.563	CLONAL	1	TRUE	1	0.385735992951055	3		357	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0001763-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	275	496	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.842916223224042	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.842916223224042	2		496	311	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0001763-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	405	699	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.742165437378963	3	FACETS	1	0.966	1			1	CLONAL	2	TRUE	NA	0.842916223224042	3		699	680	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984924	101984924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001763-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	138	396	0	ENST00000282441.5:c.371G>A	p.Arg124Gln	p.R124Q	ENST00000282441	NM_001130145.2	124	cGa/cAa	2/9	0.842916223224042	3	FACETS	1	0.952	1	0.527	0.483	0.571	CLONAL	1	TRUE	1	0.842916223224042	3		396	442	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432041	121432041	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057520504	NA	P-0001763-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	269	666	0	ENST00000257555.6:c.788G>A	p.Arg263His	p.R263H	ENST00000257555		263	cGt/cAt	4/10	0.842916223224042	3	FACETS	0.98	0.933	1	0.98	0.933	1	CLONAL	2	TRUE	1	0.842916223224042	3		666	463	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033898	49033898	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001763-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	159	649	0	ENST00000267163.4:c.2035A>T	p.Ile679Phe	p.I679F	ENST00000267163	NM_000321.2	679	Atc/Ttc	20/27	NA	2	FACETS	0.946	0.877	1			1	INDETERMINATE	1	TRUE	NA	0.842916223224042	2		649	399	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0001766-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	88	322	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.263682944520361	3	FACETS	0.951	0.848	1	0.951	0.848	1	CLONAL	2	TRUE	1	0.263682944520361	3		322	397	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0001771-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	12	286	0	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	NA	2	FACETS	0.952	0.682	1			1	INDETERMINATE	1	TRUE	NA	0.35	2		286	72	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0001771-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	44	378	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.225915265185882	2	FACETS	0.849	0.726	0.98	0.849	0.726	0.98	CLONAL	2	TRUE	0	0.35	2		378	148	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248385	59248385	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001771-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	35	185	0	ENST00000371222.2:c.358G>A	p.Glu120Lys	p.E120K	ENST00000371222	NM_002228.3	120	Gaa/Aaa	1/1	0.212062712316222	4	FACETS	1	0.888	1	0.553	0.456	0.661	CLONAL	1	TRUE	2	0.35	4		185	244	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237689	133237689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500820	NA	P-0001771-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	48	462	0	ENST00000320574.5:c.2926C>T	p.Arg976Cys	p.R976C	ENST00000320574	NM_006231.2	976	Cgc/Tgc	25/49	0.164756966477898	4	FACETS	0.842	0.719	0.973	0.842	0.719	0.973	INDETERMINATE	2	TRUE	2	0.35	4		462	220	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0001783-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	226	363	0	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	0.92830083969358	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.92830083969358	1		363	253	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244952	46244952	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001783-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	255	556	2	ENST00000334344.6:c.3046C>T	p.Gln1016Ter	p.Q1016*	ENST00000334344	NM_152641.2	1016	Caa/Taa	15/21	0.92830083969358	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.92830083969358	1		558	283	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343528	343528	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001783-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	241	512	0	ENST00000262320.3:c.2146G>T	p.Glu716Ter	p.E716*	ENST00000262320	NM_003502.3	716	Gag/Tag	8/11	0.927058852932187	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.92830083969358	1		512	269	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0001798-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	259	393	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.91014654335883	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.91014654335883	1		393	283	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337717	73337717	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001798-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	418	581	0	ENST00000377767.4:c.1999A>T	p.Met667Leu	p.M667L	ENST00000377767	NM_014953.3	667	Atg/Ttg	16/21	0.91014654335883	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.91014654335883	1		581	463	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0001801-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	161	571	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.794952928693681	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.806854242138449	2		571	197	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104712	193104712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	145	262	0	ENST00000367435.3:c.416G>A	p.Arg139Gln	p.R139Q	ENST00000367435	NM_024529.4	139	cGa/cAa	5/17	1	2	FACETS	0.976	0.889	1	0.976	0.889	1	CLONAL	1	TRUE	1	0.29	2		262	1025	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	191	467	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.217423926597132	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.29	1		467	928	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	155	315	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.892	0.815	0.973	0.892	0.815	0.973	CLONAL	1	TRUE	1	0.29	2		315	1198	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407979	139407979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200816814	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	79	242	0	ENST00000277541.6:c.2218G>A	p.Asp740Asn	p.D740N	ENST00000277541	NM_017617.3	740	Gac/Aac	14/34	1	2	FACETS	0.724	0.636	0.818	0.724	0.636	0.818	SUBCLONAL	1	TRUE	1	0.29	2		242	753	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226579931	226579931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765535441	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1332	131	419	0	ENST00000366794.5:c.371C>T	p.Thr124Met	p.T124M	ENST00000366794	NM_001618.3	124	aCg/aTg	3/23	1	2	FACETS	0.618	0.558	0.68	0.618	0.558	0.68	SUBCLONAL	1	TRUE	1	0.29	2		419	1463	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	294	232	1	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.3	2	FACETS	0.922	0.868	0.978			1	CLONAL	2	TRUE	NA	0.29	2		233	1099	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900288	101900288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111854391	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	144	251	0	ENST00000374994.4:c.722C>T	p.Ser241Leu	p.S241L	ENST00000374994	NM_004612.2	241	tCg/tTg	4/9	1	2	FACETS	0.9	0.819	0.984	0.9	0.819	0.984	CLONAL	1	TRUE	1	0.29	2		251	1104	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	147	297	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	0.3	2	FACETS	1	0.929	1			1	CLONAL	1	TRUE	NA	0.29	2		297	993	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572534	95572534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555370340	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	65	259	0	ENST00000393063.1:c.2831G>A	p.Arg944Gln	p.R944Q	ENST00000393063	NM_030621.3	944	cGa/cAa	19/28	1	2	FACETS	0.415	0.358	0.477	0.415	0.358	0.477	SUBCLONAL	1	TRUE	1	0.29	2		259	1081	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11193216	11193216	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	58	321	0	ENST00000361445.4:c.5285A>G	p.Gln1762Arg	p.Q1762R	ENST00000361445	NM_004958.3	1762	cAg/cGg	38/58	0.217423926597132	0	FACETS	0.324	0.277	0.375			1	SUBCLONAL	1	TRUE	0	0.29	0		321	876	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202864	16202864	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	107	319	0	ENST00000375759.3:c.572C>A	p.Pro191Gln	p.P191Q	ENST00000375759	NM_015001.2	191	cCa/cAa	3/15	0.160130682761253	1	FACETS	0.588	0.526	0.654	0.588	0.526	0.654	INDETERMINATE	1	TRUE	0	0.29	1		319	1073	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237633	16237633	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	86	300	0	ENST00000375759.3:c.1080G>T	p.Lys360Asn	p.K360N	ENST00000375759	NM_015001.2	360	aaG/aaT	5/15	0.160130682761253	1	FACETS	0.487	0.43	0.549	0.487	0.43	0.549	INDETERMINATE	1	TRUE	0	0.29	1		300	1041	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100172	27100172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775802127	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	78	242	0	ENST00000324856.7:c.3968G>A	p.Arg1323His	p.R1323H	ENST00000324856	NM_006015.4	1323	cGc/cAc	16/20	0.160130682761253	1	FACETS	0.534	0.468	0.605	0.534	0.468	0.605	INDETERMINATE	1	TRUE	0	0.29	1		242	861	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107078	27107078	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	82	216	0	ENST00000324856.7:c.6689T>C	p.Met2230Thr	p.M2230T	ENST00000324856	NM_006015.4	2230	aTg/aCg	20/20	0.160130682761253	1	FACETS	0.646	0.569	0.729	0.646	0.569	0.729	INDETERMINATE	1	TRUE	0	0.29	1		216	748	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803818	43803818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147938568	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	104	355	0	ENST00000372470.3:c.128G>A	p.Arg43Gln	p.R43Q	ENST00000372470	NM_005373.2	43	cGa/cAa	2/12	0.160130682761253	1	FACETS	0.63	0.563	0.701	0.63	0.563	0.701	INDETERMINATE	1	TRUE	0	0.29	1		355	974	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480621	120480621	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	91	262	0	ENST00000256646.2:c.3196C>A	p.Leu1066Ile	p.L1066I	ENST00000256646	NM_024408.3	1066	Ctc/Atc	20/34	1	2	FACETS	0.715	0.634	0.802	0.715	0.634	0.802	SUBCLONAL	1	TRUE	1	0.29	2		262	878	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845433	156845433	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	54	261	0	ENST00000524377.1:c.1476G>T	p.Glu492Asp	p.E492D	ENST00000524377	NM_002529.3	492	gaG/gaT	12/17	1	2	FACETS	0.444	0.378	0.517	0.444	0.378	0.517	SUBCLONAL	1	TRUE	1	0.29	2		261	838	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162722975	162722975	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	56	326	0	ENST00000367921.3:c.173C>A	p.Ala58Asp	p.A58D	ENST00000367921	NM_006182.2	58	gCc/gAc	4/18	1	2	FACETS	0.353	0.301	0.41	0.353	0.301	0.41	SUBCLONAL	1	TRUE	1	0.29	2		326	1094	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243778404	243778404	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	73	332	0	ENST00000263826.5:c.621T>G	p.Phe207Leu	p.F207L	ENST00000263826	NM_005465.4	207	ttT/ttG	6/13	1	2	FACETS	0.429	0.373	0.489	0.429	0.373	0.489	SUBCLONAL	1	TRUE	1	0.29	2		332	1174	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800978	243800978	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1383	203	449	0	ENST00000263826.5:c.496C>T	p.Arg166Ter	p.R166*	ENST00000263826	NM_005465.4	166	Cga/Tga	5/13	1	2	FACETS	0.883	0.816	0.953	0.883	0.816	0.953	CLONAL	1	TRUE	1	0.29	2		449	1586	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25498386	25498386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1274769751	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	80	345	0	ENST00000264709.3:c.475G>A	p.Glu159Lys	p.E159K	ENST00000264709	NM_175629.2	159	Gaa/Aaa	5/23	1	2	FACETS	0.509	0.447	0.577	0.509	0.447	0.577	SUBCLONAL	1	TRUE	1	0.29	2		345	1083	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965468	25965468	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1311	243	413	0	ENST00000435504.4:c.3738G>T	p.Glu1246Asp	p.E1246D	ENST00000435504		1246	gaG/gaT	13/13	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.29	2		413	1554	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606679	29606679	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs865931787	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	151	363	1	ENST00000389048.3:c.1201C>T	p.Arg401Ter	p.R401*	ENST00000389048	NM_004304.4	401	Cga/Tga	5/29	0.217423926597132	1	FACETS	0.874	0.798	0.953	0.874	0.798	0.953	CLONAL	1	TRUE	0	0.29	1		364	1019	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027541	48027541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587779923	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	96	235	0	ENST00000234420.5:c.2419G>A	p.Glu807Lys	p.E807K	ENST00000234420	NM_000179.2	807	Gaa/Aaa	4/10	1	2	FACETS	0.875	0.779	0.976	0.875	0.779	0.976	CLONAL	1	TRUE	1	0.29	2		235	757	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198262749	198262749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	99	337	0	ENST00000335508.6:c.3226G>A	p.Ala1076Thr	p.A1076T	ENST00000335508	NM_012433.2	1076	Gcc/Acc	22/25	1	2	FACETS	0.526	0.468	0.588	0.526	0.468	0.588	SUBCLONAL	1	TRUE	1	0.29	2		337	1298	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265468	198265468	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1185	207	378	0	ENST00000335508.6:c.2689C>A	p.Leu897Ile	p.L897I	ENST00000335508	NM_012433.2	897	Ctt/Att	18/25	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.29	2		378	1392	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248749	212248749	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	152	307	0	ENST00000342788.4:c.3518C>A	p.Ser1173Tyr	p.S1173Y	ENST00000342788	NM_005235.2	1173	tCt/tAt	28/28	1	2	FACETS	0.976	0.891	1	0.976	0.891	1	CLONAL	1	TRUE	1	0.29	2		307	1074	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645489	215645489	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881416	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1352	211	409	0	ENST00000260947.4:c.1109G>A	p.Arg370His	p.R370H	ENST00000260947	NM_000465.2	370	cGt/cAt	4/11	1	2	FACETS	0.931	0.862	1	0.931	0.862	1	CLONAL	1	TRUE	1	0.29	2		409	1563	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645633	215645633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774251286	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	153	345	0	ENST00000260947.4:c.965G>A	p.Arg322His	p.R322H	ENST00000260947	NM_000465.2	322	cGt/cAt	4/11	1	2	FACETS	0.899	0.821	0.981	0.899	0.821	0.981	CLONAL	1	TRUE	1	0.29	2		345	1174	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225365104	225365104	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1209	133	296	0	ENST00000264414.4:c.1586G>T	p.Arg529Ile	p.R529I	ENST00000264414	NM_003590.4	529	aGa/aTa	11/16	1	2	FACETS	0.683	0.619	0.752	0.683	0.619	0.752	SUBCLONAL	1	TRUE	1	0.29	2		296	1342	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662224	227662224	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	204	347	0	ENST00000305123.5:c.1231C>T	p.Arg411Ter	p.R411*	ENST00000305123	NM_005544.2	411	Cga/Tga	1/2	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.29	2		347	1298	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641904	12641904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752713997	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	138	210	0	ENST00000251849.4:c.845G>A	p.Arg282Gln	p.R282Q	ENST00000251849	NM_002880.3	282	cGa/cAa	8/17	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.29	2		210	913	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641905	12641905	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs755926381	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	68	210	0	ENST00000251849.4:c.844C>T	p.Arg282Ter	p.R282*	ENST00000251849	NM_002880.3	282	Cga/Tga	8/17	1	2	FACETS	0.52	0.452	0.595	0.52	0.452	0.595	SUBCLONAL	1	TRUE	1	0.29	2		210	901	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648462	30648462	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	69	230	0	ENST00000295754.5:c.87G>T	p.Gln29His	p.Q29H	ENST00000295754	NM_003242.5	29	caG/caT	1/7	1	2	FACETS	0.438	0.38	0.501	0.438	0.38	0.501	SUBCLONAL	1	TRUE	1	0.29	2		230	1087	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182748	38182748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765995806	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	92	298	0	ENST00000396334.3:c.901C>T	p.Arg301Cys	p.R301C	ENST00000396334	NM_002468.4	301	Cgc/Tgc	5/5	1	2	FACETS	0.525	0.465	0.59	0.525	0.465	0.59	SUBCLONAL	1	TRUE	1	0.29	2		298	1208	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275648	41275648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397514554	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	88	307	0	ENST00000349496.5:c.1543C>T	p.Arg515Ter	p.R515*	ENST00000349496	NM_001904.3	515	Cga/Tga	10/15	1	2	FACETS	0.502	0.443	0.565	0.502	0.443	0.565	SUBCLONAL	1	TRUE	1	0.29	2		307	1209	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147533	47147533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	165	328	0	ENST00000409792.3:c.4793G>A	p.Arg1598Gln	p.R1598Q	ENST00000409792	NM_014159.6	1598	cGa/cAa	6/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.29	2		328	1054	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164577	47164577	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	191	343	0	ENST00000409792.3:c.1549G>T	p.Glu517Ter	p.E517*	ENST00000409792	NM_014159.6	517	Gaa/Taa	3/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.29	2		343	1148	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165088	47165088	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	208	328	0	ENST00000409792.3:c.1038A>C	p.Glu346Asp	p.E346D	ENST00000409792	NM_014159.6	346	gaA/gaC	3/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.29	2		328	1198	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911429	134911429	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	148	236	0	ENST00000398015.3:c.1894G>T	p.Glu632Ter	p.E632*	ENST00000398015	NM_004441.4	632	Gaa/Taa	11/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.29	2		236	824	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413662	138413662	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1331108652	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	245	257	1	ENST00000289153.2:c.1858C>T	p.Arg620Ter	p.R620*	ENST00000289153	NM_006219.2	620	Cga/Tga	12/22	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.29	2		258	1141	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461582	138461582	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	154	337	0	ENST00000289153.2:c.439G>T	p.Glu147Ter	p.E147*	ENST00000289153	NM_006219.2	147	Gaa/Taa	3/22	1	2	FACETS	0.851	0.777	0.929	0.851	0.777	0.929	CLONAL	1	TRUE	1	0.29	2		337	1248	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231276	142231276	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756354361	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	283	325	0	ENST00000350721.4:c.4678G>A	p.Asp1560Asn	p.D1560N	ENST00000350721	NM_001184.3	1560	Gat/Aat	27/47	0.217423926597132	3	FACETS	0.785	0.736	0.835	0.785	0.736	0.835	SUBCLONAL	2	TRUE	1	0.29	3		325	1424	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281802	142281802	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1270	174	351	1	ENST00000350721.4:c.442G>T	p.Glu148Ter	p.E148*	ENST00000350721	NM_001184.3	148	Gaa/Taa	4/47	0.217423926597132	3	FACETS	0.952	0.873	1	0.476	0.436	0.517	CLONAL	1	TRUE	1	0.29	3		352	1444	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198200	185198200	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	291	293	0	ENST00000265026.3:c.2682G>T	p.Glu894Asp	p.E894D	ENST00000265026	NM_004721.4	894	gaG/gaT	13/14	0.217423926597132	3	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	1	0.29	3		293	1137	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446160	187446160	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1159893808	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	159	300	0	ENST00000232014.4:c.1528G>A	p.Asp510Asn	p.D510N	ENST00000232014	NM_001130845.1	510	Gat/Aat	6/10	0.217423926597132	3	FACETS	1	0.944	1	0.521	0.476	0.567	CLONAL	1	TRUE	1	0.29	3		300	1206	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455648	189455648	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	211	241	0	ENST00000264731.3:c.182T>G	p.Phe61Cys	p.F61C	ENST00000264731	NM_003722.4	61	tTt/tGt	2/14	0.217423926597132	3	FACETS	0.782	0.726	0.841	0.782	0.726	0.841	SUBCLONAL	2	TRUE	1	0.29	3		241	1065	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127309	55127309	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	77	316	0	ENST00000257290.5:c.97A>C	p.Asn33His	p.N33H	ENST00000257290	NM_006206.4	33	Aat/Cat	3/23	0.217423926597132	1	FACETS	0.467	0.408	0.53	0.467	0.408	0.53	SUBCLONAL	1	TRUE	0	0.29	1		316	973	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155215	55155215	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	77	293	0	ENST00000257290.5:c.2814G>T	p.Glu938Asp	p.E938D	ENST00000257290	NM_006206.4	938	gaG/gaT	21/23	0.217423926597132	1	FACETS	0.533	0.467	0.604	0.533	0.467	0.604	SUBCLONAL	1	TRUE	0	0.29	1		293	852	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561827	55561827	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	74	324	0	ENST00000288135.5:c.217G>T	p.Glu73Ter	p.E73*	ENST00000288135	NM_000222.2	73	Gaa/Taa	2/21	0.217423926597132	1	FACETS	0.416	0.363	0.474	0.416	0.363	0.474	SUBCLONAL	1	TRUE	0	0.29	1		324	1048	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383948	84383948	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	105	320	0	ENST00000321945.7:c.904A>C	p.Lys302Gln	p.K302Q	ENST00000321945	NM_139076.2	302	Aaa/Caa	9/9	1	2	FACETS	0.696	0.622	0.774	0.696	0.622	0.774	SUBCLONAL	1	TRUE	1	0.29	2		320	1041	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84393392	84393392	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	80	329	0	ENST00000321945.7:c.265T>G	p.Leu89Val	p.L89V	ENST00000321945	NM_139076.2	89	Tta/Gta	4/9	1	2	FACETS	0.497	0.436	0.564	0.497	0.436	0.564	SUBCLONAL	1	TRUE	1	0.29	2		329	1109	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541808	187541808	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	148	392	0	ENST00000441802.2:c.5932A>C	p.Lys1978Gln	p.K1978Q	ENST00000441802	NM_005245.3	1978	Aag/Cag	10/27	0.217423926597132	1	FACETS	0.7	0.638	0.766	0.7	0.638	0.766	SUBCLONAL	1	TRUE	0	0.29	1		392	1246	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542785	187542785	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	130	383	0	ENST00000441802.2:c.4955C>T	p.Ser1652Phe	p.S1652F	ENST00000441802	NM_005245.3	1652	tCt/tTt	10/27	0.217423926597132	1	FACETS	0.696	0.63	0.766	0.696	0.63	0.766	SUBCLONAL	1	TRUE	0	0.29	1		383	1101	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554966	187554966	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774134398	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	124	289	0	ENST00000441802.2:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000441802	NM_005245.3	1399	Gac/Aac	7/27	0.217423926597132	1	FACETS	0.728	0.658	0.803	0.728	0.658	0.803	SUBCLONAL	1	TRUE	0	0.29	1		289	1004	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629964	187629964	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	116	291	0	ENST00000441802.2:c.1018G>T	p.Asp340Tyr	p.D340Y	ENST00000441802	NM_005245.3	340	Gat/Tat	2/27	0.217423926597132	1	FACETS	0.769	0.692	0.85	0.769	0.692	0.85	SUBCLONAL	1	TRUE	0	0.29	1		291	890	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630723	187630723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	142	447	0	ENST00000441802.2:c.259G>A	p.Glu87Lys	p.E87K	ENST00000441802	NM_005245.3	87	Gag/Aag	2/27	0.217423926597132	1	FACETS	0.65	0.59	0.712	0.65	0.59	0.712	SUBCLONAL	1	TRUE	0	0.29	1		447	1289	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177065	56177065	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	136	259	0	ENST00000399503.3:c.2335A>G	p.Thr779Ala	p.T779A	ENST00000399503	NM_005921.1	779	Act/Gct	13/20	0.217423926597132	3	FACETS	1	0.972	1	0.587	0.533	0.643	CLONAL	1	TRUE	1	0.29	3		259	915	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177448	56177448	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1513	121	425	0	ENST00000399503.3:c.2421T>G	p.Asn807Lys	p.N807K	ENST00000399503	NM_005921.1	807	aaT/aaG	14/20	0.217423926597132	3	FACETS	0.585	0.526	0.647	0.292	0.263	0.324	SUBCLONAL	1	TRUE	1	0.29	3		425	1634	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591278	67591278	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	180	213	1	ENST00000274335.5:c.1776G>T	p.Lys592Asn	p.K592N	ENST00000274335		592	aaG/aaT	13/15	0.217423926597132	3	FACETS	1	0.987	1	0.679	0.625	0.735	CLONAL	1	TRUE	1	0.29	3		214	1047	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593380	67593380	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1264	83	326	0	ENST00000274335.5:c.2126C>A	p.Ser709Tyr	p.S709Y	ENST00000274335		709	tCc/tAc	15/15	0.217423926597132	3	FACETS	0.487	0.428	0.55	0.243	0.214	0.275	SUBCLONAL	1	TRUE	1	0.29	3		326	1347	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86681164	86681164	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	91	309	0	ENST00000274376.6:c.2805A>C	p.Lys935Asn	p.K935N	ENST00000274376	NM_002890.2	935	aaA/aaC	22/25	0.217423926597132	3	FACETS	0.589	0.521	0.661	0.294	0.26	0.331	SUBCLONAL	1	TRUE	1	0.29	3		309	1221	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86686647	86686647	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1304	191	350	0	ENST00000274376.6:c.3091G>T	p.Glu1031Ter	p.E1031*	ENST00000274376	NM_002890.2	1031	Gaa/Taa	25/25	0.217423926597132	3	FACETS	1	0.929	1	0.504	0.465	0.546	CLONAL	1	TRUE	1	0.29	3		350	1495	SUCCESS
APC	324	MSKCC	GRCh37	5	112164554	112164554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	29	147	0	ENST00000257430.4:c.1628T>C	p.Val543Ala	p.V543A	ENST00000257430	NM_000038.5	543	gTt/gCt	14/16	1	2	FACETS	0.357	0.286	0.439	0.357	0.286	0.439	SUBCLONAL	1	TRUE	1	0.29	2		147	560	SUCCESS
APC	324	MSKCC	GRCh37	5	112174956	112174956	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1114167614	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	134	262	0	ENST00000257430.4:c.3665C>A	p.Ser1222Ter	p.S1222*	ENST00000257430	NM_000038.5	1222	tCa/tAa	16/16	1	2	FACETS	0.961	0.872	1	0.961	0.872	1	CLONAL	1	TRUE	1	0.29	2		262	962	SUCCESS
APC	324	MSKCC	GRCh37	5	112175982	112175982	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	58	222	0	ENST00000257430.4:c.4691T>G	p.Leu1564Ter	p.L1564*	ENST00000257430	NM_000038.5	1564	tTa/tGa	16/16	1	2	FACETS	0.513	0.44	0.594	0.513	0.44	0.594	SUBCLONAL	1	TRUE	1	0.29	2		222	779	SUCCESS
APC	324	MSKCC	GRCh37	5	112179011	112179011	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876659753	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	70	271	0	ENST00000257430.4:c.7720C>A	p.Leu2574Ile	p.L2574I	ENST00000257430	NM_000038.5	2574	Ctt/Att	16/16	1	2	FACETS	0.486	0.422	0.555	0.486	0.422	0.555	SUBCLONAL	1	TRUE	1	0.29	2		271	994	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637645	176637645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	83	363	0	ENST00000439151.2:c.2245G>T	p.Asp749Tyr	p.D749Y	ENST00000439151	NM_022455.4	749	Gat/Tat	5/23	1	2	FACETS	0.533	0.469	0.603	0.533	0.469	0.603	SUBCLONAL	1	TRUE	1	0.29	2		363	1073	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401564	401564	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	62	344	0	ENST00000380956.4:c.886G>T	p.Glu296Ter	p.E296*	ENST00000380956	NM_001195286.1	296	Gag/Tag	7/9	1	2	FACETS	0.396	0.34	0.456	0.396	0.34	0.456	SUBCLONAL	1	TRUE	1	0.29	2		344	1081	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20483060	20483060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750169257	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	81	274	0	ENST00000346618.3:c.793G>A	p.Glu265Lys	p.E265K	ENST00000346618	NM_001949.4	265	Gag/Aag	4/7	1	2	FACETS	0.531	0.466	0.601	0.531	0.466	0.601	SUBCLONAL	1	TRUE	1	0.29	2		274	1052	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183070	32183070	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764454139	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	153	338	0	ENST00000375023.3:c.1954C>T	p.Pro652Ser	p.P652S	ENST00000375023	NM_004557.3	652	Cct/Tct	12/30	0.3	2	FACETS	1	0.964	1			1	CLONAL	1	TRUE	NA	0.29	2		338	960	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555057	106555057	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs940196192	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	85	208	0	ENST00000369096.4:c.2174G>A	p.Arg725Gln	p.R725Q	ENST00000369096	NM_001198.3	725	cGa/cAa	7/7	0.217423926597132	3	FACETS	0.75	0.662	0.845	0.375	0.331	0.423	SUBCLONAL	1	TRUE	1	0.29	3		208	895	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117629975	117629975	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	90	275	0	ENST00000368508.3:c.6551G>T	p.Arg2184Ile	p.R2184I	ENST00000368508	NM_002944.2	2184	aGa/aTa	41/43	1	2	FACETS	0.601	0.532	0.676	0.601	0.532	0.676	SUBCLONAL	1	TRUE	1	0.29	2		275	1032	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641051	117641051	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	201	414	0	ENST00000368508.3:c.5920G>T	p.Glu1974Ter	p.E1974*	ENST00000368508	NM_002944.2	1974	Gaa/Taa	36/43	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.29	2		414	1340	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683877	117683877	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1329	108	407	0	ENST00000368508.3:c.3270T>A	p.Asn1090Lys	p.N1090K	ENST00000368508	NM_002944.2	1090	aaT/aaA	21/43	1	2	FACETS	0.518	0.463	0.577	0.518	0.463	0.577	SUBCLONAL	1	TRUE	1	0.29	2		407	1437	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706936	117706936	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1315	112	340	0	ENST00000368508.3:c.2214G>T	p.Glu738Asp	p.E738D	ENST00000368508	NM_002944.2	738	gaG/gaT	15/43	1	2	FACETS	0.541	0.485	0.601	0.541	0.485	0.601	SUBCLONAL	1	TRUE	1	0.29	2		340	1427	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710586	117710586	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	96	281	0	ENST00000368508.3:c.1686G>T	p.Gln562His	p.Q562H	ENST00000368508	NM_002944.2	562	caG/caT	12/43	1	2	FACETS	0.644	0.572	0.721	0.644	0.572	0.721	SUBCLONAL	1	TRUE	1	0.29	2		281	1028	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714464	117714464	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	76	281	0	ENST00000368508.3:c.1185G>T	p.Glu395Asp	p.E395D	ENST00000368508	NM_002944.2	395	gaG/gaT	11/43	1	2	FACETS	0.527	0.461	0.599	0.527	0.461	0.599	SUBCLONAL	1	TRUE	1	0.29	2		281	994	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715380	117715380	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs957763915	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	87	371	0	ENST00000368508.3:c.1109C>A	p.Ser370Tyr	p.S370Y	ENST00000368508	NM_002944.2	370	tCt/tAt	10/43	1	2	FACETS	0.522	0.461	0.588	0.522	0.461	0.588	SUBCLONAL	1	TRUE	1	0.29	2		371	1149	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519777	137519777	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	60	167	0	ENST00000367739.4:c.862-1G>T		p.X288_splice	ENST00000367739	NM_000416.2	288			0.3	3	FACETS	0.628	0.54	0.725			1	SUBCLONAL	1	TRUE	NA	0.29	3		167	754	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137522105	137522105	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	77	246	0	ENST00000367739.4:c.774T>G	p.Phe258Leu	p.F258L	ENST00000367739	NM_000416.2	258	ttT/ttG	6/7	0.3	3	FACETS	0.523	0.457	0.594			1	SUBCLONAL	1	TRUE	NA	0.29	3		246	1163	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163749	152163749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1207112399	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	129	281	2	ENST00000206249.3:c.470G>A	p.Arg157Gln	p.R157Q	ENST00000206249	NM_000125.3	157	cGa/cAa	2/8	1	2	FACETS	0.867	0.785	0.954	0.867	0.785	0.954	CLONAL	1	TRUE	1	0.29	2		283	1026	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335667	81335667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1418	121	351	0	ENST00000222390.5:c.1693C>T	p.Leu565Phe	p.L565F	ENST00000222390	NM_000601.4	565	Ctc/Ttc	15/18	1	2	FACETS	0.542	0.488	0.6	0.542	0.488	0.6	SUBCLONAL	1	TRUE	1	0.29	2		351	1539	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92462625	92462625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576150359	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	130	136	0	ENST00000265734.4:c.13G>A	p.Gly5Ser	p.G5S	ENST00000265734	NM_001259.6	5	Ggc/Agc	2/8	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.29	2		136	640	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509723	106509723	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1228	105	326	0	ENST00000359195.3:c.1717G>T	p.Glu573Ter	p.E573*	ENST00000359195	NM_002649.2	573	Gaa/Taa	2/11	1	2	FACETS	0.543	0.485	0.606	0.543	0.485	0.606	SUBCLONAL	1	TRUE	1	0.29	2		326	1333	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524687	106524687	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	127	248	0	ENST00000359195.3:c.2848G>T	p.Asp950Tyr	p.D950Y	ENST00000359195	NM_002649.2	950	Gac/Tac	9/11	1	2	FACETS	0.885	0.8	0.974	0.885	0.8	0.974	CLONAL	1	TRUE	1	0.29	2		248	990	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845086	128845086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761395599	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	144	358	0	ENST00000249373.3:c.580G>A	p.Glu194Lys	p.E194K	ENST00000249373	NM_005631.4	194	Gaa/Aaa	3/12	0.3	1	FACETS	0.911	0.83	0.996	0.911	0.83	0.996	CLONAL	1	TRUE	0	0.29	1		358	932	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845580	151845580	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1287135873	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	77	253	0	ENST00000262189.6:c.13432C>T	p.Arg4478Ter	p.R4478*	ENST00000262189	NM_170606.2	4478	Cga/Tga	52/59	1	2	FACETS	0.525	0.46	0.596	0.525	0.46	0.596	SUBCLONAL	1	TRUE	1	0.29	2		253	1011	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945367	151945367	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	55	100	0	ENST00000262189.6:c.2152G>T	p.Glu718Ter	p.E718*	ENST00000262189	NM_170606.2	718	Gaa/Taa	14/59	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.29	2		100	370	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050770	5050770	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	180	320	0	ENST00000381652.3:c.553G>T	p.Asp185Tyr	p.D185Y	ENST00000381652	NM_004972.3	185	Gat/Tat	6/25	1	2	FACETS	0.949	0.873	1	0.949	0.873	1	CLONAL	1	TRUE	1	0.29	2		320	1308	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072546	5072546	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	80	274	0	ENST00000381652.3:c.1696G>T	p.Glu566Ter	p.E566*	ENST00000381652	NM_004972.3	566	Gaa/Taa	13/25	1	2	FACETS	0.522	0.458	0.591	0.522	0.458	0.591	SUBCLONAL	1	TRUE	1	0.29	2		274	1057	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126393	5126393	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	145	241	0	ENST00000381652.3:c.3238G>T	p.Glu1080Ter	p.E1080*	ENST00000381652	NM_004972.3	1080	Gaa/Taa	24/25	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.29	2		241	957	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528648	8528648	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1385	97	369	0	ENST00000356435.5:c.484G>T	p.Asp162Tyr	p.D162Y	ENST00000356435		162	Gat/Tat	4/35	1	2	FACETS	0.451	0.401	0.506	0.451	0.401	0.506	SUBCLONAL	1	TRUE	1	0.29	2		369	1482	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528710	8528710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768826930	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	191	300	0	ENST00000356435.5:c.422G>A	p.Arg141His	p.R141H	ENST00000356435		141	cGc/cAc	4/35	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.29	2		300	1264	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97897674	97897674	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	106	372	0	ENST00000289081.3:c.797G>T	p.Arg266Ile	p.R266I	ENST00000289081	NM_000136.2	266	aGa/aTa	8/15	1	2	FACETS	0.6	0.536	0.668	0.6	0.536	0.668	SUBCLONAL	1	TRUE	1	0.29	2		372	1218	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101909971	101909971	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	175	289	0	ENST00000374994.4:c.1291C>A	p.Leu431Ile	p.L431I	ENST00000374994	NM_004612.2	431	Ctt/Att	8/9	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.29	2		289	1162	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399507	139399507	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs933070856	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	64	231	0	ENST00000277541.6:c.4636G>A	p.Asp1546Asn	p.D1546N	ENST00000277541	NM_017617.3	1546	Gac/Aac	26/34	1	2	FACETS	0.559	0.483	0.641	0.559	0.483	0.641	SUBCLONAL	1	TRUE	1	0.29	2		231	790	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63661997	63661997	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1507	226	329	0	ENST00000279873.7:c.101G>T	p.Arg34Ile	p.R34I	ENST00000279873	NM_032199.2	34	aGa/aTa	2/10	0.3	3	FACETS	1	0.95	1			1	CLONAL	1	TRUE	NA	0.29	3		329	1733	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404720	70404720	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369109149	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	175	386	0	ENST00000373644.4:c.2234G>A	p.Arg745Gln	p.R745Q	ENST00000373644	NM_030625.2	745	cGa/cAa	4/12	0.3	1	FACETS	0.885	0.814	0.96	0.885	0.814	0.96	CLONAL	1	TRUE	0	0.29	1		386	1166	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405491	70405491	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	152	313	0	ENST00000373644.4:c.3005C>A	p.Ser1002Ter	p.S1002*	ENST00000373644	NM_030625.2	1002	tCa/tAa	4/12	0.3	1	FACETS	0.819	0.747	0.893	0.819	0.747	0.893	CLONAL	1	TRUE	0	0.29	1		313	1095	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683246	88683246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767763451	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	127	201	0	ENST00000372037.3:c.1456C>T	p.Arg486Trp	p.R486W	ENST00000372037	NM_004329.2	486	Cgg/Tgg	12/13	0.3	2	FACETS	1	0.941	1			1	CLONAL	1	TRUE	NA	0.29	2		201	833	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202491	67202491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375129435	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	104	345	0	ENST00000312629.5:c.1300C>T	p.Arg434Trp	p.R434W	ENST00000312629	NM_003952.2	434	Cgg/Tgg	15/15	0.3	3	FACETS	0.675	0.602	0.752			1	SUBCLONAL	1	TRUE	NA	0.29	3		345	1217	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124599	108124599	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	271	368	0	ENST00000278616.4:c.1957C>A	p.Leu653Ile	p.L653I	ENST00000278616	NM_000051.3	653	Ctt/Att	13/63	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.29	2		368	1292	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153473	108153473	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760928285	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1280	111	325	0	ENST00000278616.4:c.3613C>T	p.Arg1205Cys	p.R1205C	ENST00000278616	NM_000051.3	1205	Cgt/Tgt	25/63	1	2	FACETS	0.55	0.493	0.612	0.55	0.493	0.612	SUBCLONAL	1	TRUE	1	0.29	2		325	1391	SUCCESS
ATM	472	MSKCC	GRCh37	11	108168047	108168047	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	65	309	0	ENST00000278616.4:c.4943T>G	p.Val1648Gly	p.V1648G	ENST00000278616	NM_000051.3	1648	gTt/gGt	33/63	1	2	FACETS	0.377	0.326	0.434	0.377	0.326	0.434	SUBCLONAL	1	TRUE	1	0.29	2		309	1188	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216627	108216627	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	55	208	0	ENST00000278616.4:c.8576C>A	p.Ser2859Tyr	p.S2859Y	ENST00000278616	NM_000051.3	2859	tCt/tAt	58/63	1	2	FACETS	0.439	0.374	0.51	0.439	0.374	0.51	SUBCLONAL	1	TRUE	1	0.29	2		208	864	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373178	118373178	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200497972	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1294	114	423	0	ENST00000534358.1:c.6571C>T	p.Arg2191Ter	p.R2191*	ENST00000534358	NM_005933.3	2191	Cga/Tga	27/36	1	2	FACETS	0.558	0.501	0.62	0.558	0.501	0.62	SUBCLONAL	1	TRUE	1	0.29	2		423	1408	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374726	118374726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437799270	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	86	376	0	ENST00000534358.1:c.8119C>T	p.Arg2707Trp	p.R2707W	ENST00000534358	NM_005933.3	2707	Cgg/Tgg	27/36	1	2	FACETS	0.526	0.464	0.593	0.526	0.464	0.593	SUBCLONAL	1	TRUE	1	0.29	2		376	1127	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375181	118375181	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	178	354	0	ENST00000534358.1:c.8574G>T	p.Lys2858Asn	p.K2858N	ENST00000534358	NM_005933.3	2858	aaG/aaT	27/36	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.29	2		354	1031	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377107	118377107	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	187	354	0	ENST00000534358.1:c.10500G>T	p.Gln3500His	p.Q3500H	ENST00000534358	NM_005933.3	3500	caG/caT	27/36	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.29	2		354	1173	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416956	416956	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	211	389	0	ENST00000399788.2:c.3594A>C	p.Lys1198Asn	p.K1198N	ENST00000399788	NM_001042603.1	1198	aaA/aaC	23/28	0.3	2	FACETS	1	0.95	1			1	CLONAL	1	TRUE	NA	0.29	2		389	1410	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	441077	441077	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1275	230	353	0	ENST00000399788.2:c.1681G>A	p.Glu561Lys	p.E561K	ENST00000399788	NM_001042603.1	561	Gag/Aag	13/28	0.3	2	FACETS	1	0.963	1			1	CLONAL	1	TRUE	NA	0.29	2		353	1505	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023606	1023606	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	192	308	0	ENST00000358495.3:c.958G>T	p.Glu320Ter	p.E320*	ENST00000358495	NM_134424.2	320	Gaa/Taa	10/12	0.3	2	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.29	2		308	1158	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409117	4409117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776036883	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	148	301	0	ENST00000261254.3:c.812C>T	p.Ser271Leu	p.S271L	ENST00000261254	NM_001759.3	271	tCg/tTg	5/5	0.3	2	FACETS	0.92	0.839	1			1	CLONAL	1	TRUE	NA	0.29	2		301	1109	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435287	18435287	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1361	205	367	0	ENST00000266497.5:c.272C>A	p.Ser91Tyr	p.S91Y	ENST00000266497		91	tCt/tAt	1/31	1	2	FACETS	0.903	0.835	0.974	0.903	0.835	0.974	CLONAL	1	TRUE	1	0.29	2		367	1566	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446936	18446936	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs377755015	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	160	317	0	ENST00000266497.5:c.1021G>T	p.Glu341Ter	p.E341*	ENST00000266497		341	Gaa/Taa	4/31	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.29	2		317	1082	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573894	18573894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759658584	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	164	348	0	ENST00000266497.5:c.2212C>T	p.Arg738Cys	p.R738C	ENST00000266497		738	Cgt/Tgt	15/31	1	2	FACETS	0.95	0.871	1	0.95	0.871	1	CLONAL	1	TRUE	1	0.29	2		348	1190	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644423	18644423	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1258	187	368	0	ENST00000266497.5:c.2601C>A	p.Phe867Leu	p.F867L	ENST00000266497		867	ttC/ttA	18/31	1	2	FACETS	0.892	0.822	0.966	0.892	0.822	0.966	CLONAL	1	TRUE	1	0.29	2		368	1445	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378568	25378568	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	190	326	0	ENST00000311936.3:c.430A>C	p.Thr144Pro	p.T144P	ENST00000311936	NM_004985.3	144	Aca/Cca	4/5	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.29	2		326	1234	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125024	46125024	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	227	337	1	ENST00000334344.6:c.211G>T	p.Glu71Ter	p.E71*	ENST00000334344	NM_152641.2	71	Gaa/Taa	3/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.29	2		338	1423	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287322	46287322	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	168	238	0	ENST00000334344.6:c.5267T>G	p.Phe1756Cys	p.F1756C	ENST00000334344	NM_152641.2	1756	tTt/tGt	19/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.29	2		238	962	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425520	49425520	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1290	199	425	0	ENST00000301067.7:c.12968T>C	p.Leu4323Ser	p.L4323S	ENST00000301067	NM_003482.3	4323	tTa/tCa	39/54	1	2	FACETS	0.922	0.851	0.995	0.922	0.851	0.995	CLONAL	1	TRUE	1	0.29	2		425	1489	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58142372	58142372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1181	221	283	0	ENST00000257904.6:c.848G>A	p.Arg283Gln	p.R283Q	ENST00000257904	NM_000075.3	283	cGa/cAa	8/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.29	2		283	1402	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102874103	102874103	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1282	189	332	0	ENST00000307046.8:c.57C>A	p.Phe19Leu	p.F19L	ENST00000307046	NM_001111285.1	19	ttC/ttA	1/4	1	2	FACETS	0.886	0.816	0.959	0.886	0.816	0.959	CLONAL	1	TRUE	1	0.29	2		332	1471	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888257	112888257	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	177	346	0	ENST00000351677.2:c.273G>T	p.Lys91Asn	p.K91N	ENST00000351677	NM_002834.3	91	aaG/aaT	3/16	0.3	2	FACETS	1	0.974	1			1	CLONAL	1	TRUE	NA	0.29	2		346	1073	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626735	28626735	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	68	406	0	ENST00000241453.7:c.561G>T	p.Glu187Asp	p.E187D	ENST00000241453	NM_004119.2	187	gaG/gaT	5/24	0.217423926597132	0	FACETS	0.27	0.233	0.309			1	SUBCLONAL	1	TRUE	0	0.29	0		406	1235	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28644722	28644722	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	63	315	0	ENST00000241453.7:c.71C>A	p.Thr24Asn	p.T24N	ENST00000241453	NM_004119.2	24	aCt/aAt	2/24	0.217423926597132	0	FACETS	0.369	0.318	0.424			1	SUBCLONAL	1	TRUE	0	0.29	0		315	836	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004305	29004305	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	104	247	0	ENST00000282397.4:c.989-1G>T		p.X330_splice	ENST00000282397	NM_002019.4	330			1	2	FACETS	0.732	0.654	0.815	0.732	0.654	0.815	SUBCLONAL	1	TRUE	1	0.29	2		247	980	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914877	32914877	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs886040653	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	121	282	0	ENST00000380152.3:c.6385G>T	p.Glu2129Ter	p.E2129*	ENST00000380152		2129	Gaa/Taa	11/27	1	2	FACETS	0.783	0.706	0.865	0.783	0.706	0.865	SUBCLONAL	1	TRUE	1	0.29	2		282	1066	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937357	32937357	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	81	276	0	ENST00000380152.3:c.8018A>C	p.Lys2673Thr	p.K2673T	ENST00000380152		2673	aAa/aCa	18/27	1	2	FACETS	0.55	0.483	0.622	0.55	0.483	0.622	SUBCLONAL	1	TRUE	1	0.29	2		276	1016	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941657	48941657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1060503077	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	65	281	2	ENST00000267163.4:c.967G>T	p.Glu323Ter	p.E323*	ENST00000267163	NM_000321.2	323	Gaa/Taa	10/27	1	2	FACETS	0.382	0.33	0.44	0.382	0.33	0.44	SUBCLONAL	1	TRUE	1	0.29	2		283	1172	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337650	73337650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1319	111	357	0	ENST00000377767.4:c.2066G>A	p.Arg689Gln	p.R689Q	ENST00000377767	NM_014953.3	689	cGa/cAa	16/21	1	2	FACETS	0.535	0.479	0.595	0.535	0.479	0.595	SUBCLONAL	1	TRUE	1	0.29	2		357	1430	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95577791	95577791	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1555371642	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	121	246	0	ENST00000393063.1:c.2119G>A	p.Glu707Lys	p.E707K	ENST00000393063	NM_030621.3	707	Gaa/Aaa	15/28	1	2	FACETS	0.834	0.752	0.92	0.834	0.752	0.92	CLONAL	1	TRUE	1	0.29	2		246	1001	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95592991	95592991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1440	100	370	0	ENST00000393063.1:c.829G>A	p.Ala277Thr	p.A277T	ENST00000393063	NM_030621.3	277	Gca/Aca	8/28	1	2	FACETS	0.448	0.398	0.501	0.448	0.398	0.501	SUBCLONAL	1	TRUE	1	0.29	2		370	1540	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346819	91346819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140387675	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	166	387	0	ENST00000355112.3:c.3427G>A	p.Glu1143Lys	p.E1143K	ENST00000355112	NM_000057.2	1143	Gaa/Aaa	18/22	1	2	FACETS	0.927	0.85	1	0.927	0.85	1	CLONAL	1	TRUE	1	0.29	2		387	1235	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500588	99500588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150801101	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	113	244	0	ENST00000268035.6:c.4021G>A	p.Asp1341Asn	p.D1341N	ENST00000268035	NM_000875.3	1341	Gac/Aac	21/21	1	2	FACETS	0.957	0.861	1	0.957	0.861	1	CLONAL	1	TRUE	1	0.29	2		244	814	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777750	3777750	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	201	408	0	ENST00000262367.5:c.7298A>G	p.Asp2433Gly	p.D2433G	ENST00000262367	NM_004380.2	2433	gAc/gGc	31/31	0.3	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.29	1		408	1144	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663371	67663371	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139828150	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	65	278	0	ENST00000264010.4:c.1772C>T	p.Thr591Met	p.T591M	ENST00000264010	NM_006565.3	591	aCg/aTg	10/12	0.217423926597132	1	FACETS	0.392	0.339	0.45	0.392	0.339	0.45	SUBCLONAL	1	TRUE	0	0.29	1		278	978	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89871709	89871709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144560850	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	155	322	0	ENST00000389301.3:c.688G>A	p.Val230Ile	p.V230I	ENST00000389301	NM_000135.2	230	Gtc/Atc	7/43	0.217423926597132	1	FACETS	0.982	0.898	1	0.982	0.898	1	CLONAL	1	TRUE	0	0.29	1		322	931	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16047005	16047005	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	174	353	0	ENST00000268712.3:c.1088G>T	p.Gly363Val	p.G363V	ENST00000268712	NM_006311.3	363	gGg/gTg	11/46	0.217423926597132	1	FACETS	0.97	0.892	1	0.97	0.892	1	CLONAL	1	TRUE	0	0.29	1		353	1058	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684058	29684058	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	178	299	0	ENST00000356175.3:c.7756G>A	p.Glu2586Lys	p.E2586K	ENST00000356175	NM_000267.3	2586	Gaa/Aaa	52/57	0.3	3	FACETS	1	0.958	1			1	CLONAL	1	TRUE	NA	0.29	3		299	1321	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245988	41245988	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	175	402	0	ENST00000357654.3:c.1560A>C	p.Lys520Asn	p.K520N	ENST00000357654	NM_007294.3	520	aaA/aaC	10/23	1	2	FACETS	0.935	0.859	1	0.935	0.859	1	CLONAL	1	TRUE	1	0.29	2		402	1291	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216737	2216737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	47	213	0	ENST00000398665.3:c.2381G>A	p.Arg794Lys	p.R794K	ENST00000398665	NM_032482.2	794	aGg/aAg	20/28	0.3	1	FACETS	0.579	0.488	0.678	0.579	0.488	0.678	SUBCLONAL	1	TRUE	0	0.29	1		213	479	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222203	5222203	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	72	300	0	ENST00000357368.4:c.3132G>T	p.Met1044Ile	p.M1044I	ENST00000357368	NM_002850.3	1044	atG/atT	19/38	0.290742974369365	0	FACETS	0.432	0.377	0.492			1	SUBCLONAL	1	TRUE	0	0.29	0		300	816	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265097	5265097	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	64	404	0	ENST00000357368.4:c.490C>T	p.Pro164Ser	p.P164S	ENST00000357368	NM_002850.3	164	Cct/Tct	5/38	0.290742974369365	0	FACETS	0.389	0.336	0.447			1	SUBCLONAL	1	TRUE	0	0.29	0		404	806	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273593	5273593	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs146675930	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	66	258	0	ENST00000357368.4:c.239C>T	p.Thr80Met	p.T80M	ENST00000357368	NM_002850.3	80	aCg/aTg	4/38	0.290742974369365	0	FACETS	0.587	0.509	0.67			1	SUBCLONAL	1	TRUE	0	0.29	0		258	551	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262107	10262107	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	91	442	0	ENST00000340748.4:c.2184G>T	p.Lys728Asn	p.K728N	ENST00000340748		728	aaG/aaT	23/40	0.290742974369365	0	FACETS	0.411	0.364	0.462			1	SUBCLONAL	1	TRUE	0	0.29	0		442	1083	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355074	15355074	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	112	199	0	ENST00000263377.2:c.2549A>C	p.His850Pro	p.H850P	ENST00000263377	NM_058243.2	850	cAt/cCt	13/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.29	2		199	646	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308339	30308339	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1205	89	360	0	ENST00000262643.3:c.353A>C	p.Lys118Thr	p.K118T	ENST00000262643	NM_001238.2	118	aAa/aCa	6/12	1	2	FACETS	0.474	0.419	0.534	0.474	0.419	0.534	SUBCLONAL	1	TRUE	1	0.29	2		360	1294	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30311662	30311662	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1171	99	417	0	ENST00000262643.3:c.516C>A	p.Phe172Leu	p.F172L	ENST00000262643	NM_001238.2	172	ttC/ttA	7/12	1	2	FACETS	0.538	0.478	0.601	0.538	0.478	0.601	SUBCLONAL	1	TRUE	1	0.29	2		417	1270	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024619	31024619	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	100	344	0	ENST00000375687.4:c.4104G>T	p.Lys1368Asn	p.K1368N	ENST00000375687	NM_015338.5	1368	aaG/aaT	13/13	1	2	FACETS	0.555	0.494	0.62	0.555	0.494	0.62	SUBCLONAL	1	TRUE	1	0.29	2		344	1243	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375120	31375120	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs906767301	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	73	365	1	ENST00000328111.2:c.517G>A	p.Asp173Asn	p.D173N	ENST00000328111	NM_006892.3	173	Gac/Aac	6/23	1	2	FACETS	0.477	0.415	0.543	0.477	0.415	0.543	SUBCLONAL	1	TRUE	1	0.29	2		366	1056	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408920	41408920	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	75	331	0	ENST00000373198.4:c.506C>A	p.Ser169Ter	p.S169*	ENST00000373198	NM_133170.3	169	tCa/tAa	4/32	1	2	FACETS	0.477	0.416	0.542	0.477	0.416	0.542	SUBCLONAL	1	TRUE	1	0.29	2		331	1085	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931668	39931668	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	252	175	0	ENST00000378444.4:c.2931C>A	p.Phe977Leu	p.F977L	ENST00000378444	NM_001123385.1	977	ttC/ttA	4/15	0.3	2	FACETS	0.877	0.821	0.934	0.877	0.821	0.934	CLONAL	2	TRUE	0	0.29	2		175	991	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044502	47044502	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	85	184	0	ENST00000377604.3:c.1999G>T	p.Glu667Ter	p.E667*	ENST00000377604	NM_001204468.1	667	Gaa/Taa	18/24	0.3	2	FACETS	0.736	0.649	0.828	0.368	0.324	0.414	SUBCLONAL	1	TRUE	0	0.29	2		184	797	SUCCESS
AR	367	MSKCC	GRCh37	X	66942723	66942723	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057521122	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	80	248	0	ENST00000374690.3:c.2504A>G	p.Tyr835Cys	p.Y835C	ENST00000374690	NM_000044.3	835	tAc/tGc	7/8	0.3	2	FACETS	0.56	0.492	0.634	0.28	0.246	0.317	SUBCLONAL	1	TRUE	0	0.29	2		248	985	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972708	76972708	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	82	197	0	ENST00000373344.5:c.33G>T	p.Leu11Phe	p.L11F	ENST00000373344	NM_000489.3	11	ttG/ttT	2/35	0.3	2	FACETS	0.667	0.587	0.753	0.333	0.293	0.377	SUBCLONAL	1	TRUE	0	0.29	2		197	848	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034377	123034377	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	189	195	0	ENST00000355640.3:c.1134A>C	p.Glu378Asp	p.E378D	ENST00000355640		378	gaA/gaC	6/7	0.3	2	FACETS	0.866	0.802	0.931	0.866	0.802	0.931	CLONAL	2	TRUE	0	0.29	2		195	753	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210320	123210320	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	204	119	0	ENST00000218089.9:c.2672A>C	p.Lys891Thr	p.K891T	ENST00000218089	NM_001042749.1	891	aAg/aCg	26/35	0.3	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.29	2		119	692	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224793	123224793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	111	178	0	ENST00000218089.9:c.3557G>A	p.Arg1186Gln	p.R1186Q	ENST00000218089	NM_001042749.1	1186	cGa/cAa	32/35	0.3	2	FACETS	0.826	0.741	0.915	0.413	0.37	0.458	CLONAL	1	TRUE	0	0.29	2		178	927	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0001812-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	192	542	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.131973083811838	0	FACETS	0.585	0.541	0.63			1	INDETERMINATE	1	FALSE	0	0.423996018448975	0		542	892	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0001812-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	176	405	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.423996018448975	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	0	0.423996018448975	1		405	555	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0001812-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	282	591	2	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	1	0.423996018448975	2		593	1024	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716098	243716098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001812-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	148	421	1	ENST00000263826.5:c.1096C>T	p.Pro366Ser	p.P366S	ENST00000263826	NM_005465.4	366	Cct/Tct	10/13	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	FALSE	1	0.423996018448975	2		422	697	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0001820-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	13	519	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.3	1	FACETS	0.206	0.146	0.279	0.206	0.146	0.279	SUBCLONAL	1	TRUE	0	0.33	1		519	320	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121909229	NA	P-0001820-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	21	269	0	ENST00000371953.3:c.389G>C	p.Arg130Pro	p.R130P	ENST00000371953	NM_000314.4	130	cGa/cCa	5/9	0.226658037731954	4	FACETS	0.275	0.211	0.351	0.138	0.105	0.176	SUBCLONAL	1	TRUE	2	0.33	4		269	615	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0001828-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	277	520	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.252844515370234	2	FACETS	0.921	0.867	0.976	0.921	0.867	0.976	CLONAL	2	TRUE	0	0.345035367348652	2		520	872	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0001828-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	70	403	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	0.345035367348652	3	FACETS	0.856	0.754	0.963			1	CLONAL	2	TRUE	NA	0.345035367348652	3		403	278	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335021	65335021	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001828-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	136	568	0	ENST00000342505.4:c.620A>T	p.Gln207Leu	p.Q207L	ENST00000342505	NM_002227.2	207	cAg/cTg	6/25	0.226569572337791	4	FACETS	0.832	0.759	0.909	0.832	0.759	0.909	CLONAL	2	TRUE	2	0.345035367348652	4		568	637	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786479	135786479	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs781312535	NA	P-0001828-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	119	514	0	ENST00000298552.3:c.1051A>G	p.Met351Val	p.M351V	ENST00000298552	NM_001162426.1	351	Atg/Gtg	11/23	0.345035367348652	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.345035367348652	1		514	469	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679723	88679723	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001828-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	71	573	0	ENST00000360948.2:c.740G>C	p.Gly247Ala	p.G247A	ENST00000360948	NM_001012338.2	247	gGg/gCg	7/19	0.288644354006296	0	FACETS	0.89	0.784	1			1	CLONAL	1	TRUE	0	0.345035367348652	0		573	303	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578400	7578400	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs751477326	NA	P-0001828-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	45	397	0	ENST00000269305.4:c.530C>G	p.Pro177Arg	p.P177R	ENST00000269305	NM_001126112.2	177	cCc/cGc	5/11	0.345035367348652	3	FACETS	1	0.897	1			1	CLONAL	1	TRUE	NA	0.345035367348652	3		397	283	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226008	53226008	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001828-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	79	681	1	ENST00000375401.3:c.2841G>T	p.Leu947Phe	p.L947F	ENST00000375401	NM_004187.3	947	ttG/ttT	19/26	0.345035367348652	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.345035367348652	1		682	322	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185204	123185204	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001828-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	156	693	2	ENST00000218089.9:c.1156G>T	p.Val386Phe	p.V386F	ENST00000218089	NM_001042749.1	386	Gtt/Ttt	13/35	0.312872593471863	1	FACETS	0.827	0.757	0.9	0.827	0.757	0.9	CLONAL	1	TRUE	0	0.345035367348652	1		695	905	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519999	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	327	204	0	ENST00000269305.4:c.716A>G	p.Asn239Ser	p.N239S	ENST00000269305	NM_001126112.2	239	aAc/aGc	7/11	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.855921697212927	2		204	376	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955550	48955550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913304	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	452	309	0	ENST00000267163.4:c.1666C>T	p.Arg556Ter	p.R556*	ENST00000267163	NM_000321.2	556	Cga/Tga	17/27	0.814127590114334	2	FACETS	0.993	0.97	1	0.993	0.97	1	CLONAL	2	TRUE	0	0.855921697212927	2		309	532	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510572	38510572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786205678	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	430	270	0	ENST00000254066.5:c.826C>T	p.Arg276Trp	p.R276W	ENST00000254066	NM_000964.3	276	Cgg/Tgg	7/9	NA	2	FACETS	0.981	0.958	1			1	INDETERMINATE	2	TRUE	NA	0.855921697212927	2		270	512	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86667971	86667971	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770599456	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	208	337	0	ENST00000274376.6:c.1735C>T	p.Arg579Trp	p.R579W	ENST00000274376	NM_002890.2	579	Cgg/Tgg	13/25	0.855921697212927	4	FACETS	0.866	0.804	0.931	0.433	0.402	0.466	CLONAL	1	TRUE	2	0.855921697212927	4		337	1041	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259783	16259783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	668	325	0	ENST00000375759.3:c.7048G>A	p.Ala2350Thr	p.A2350T	ENST00000375759	NM_015001.2	2350	Gct/Act	11/15	0.822366354707178	3	FACETS	0.962	0.945	0.978	0.962	0.945	0.978	CLONAL	3	TRUE	0	0.855921697212927	3		325	772	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651115	206651115	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781821296	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	421	307	1	ENST00000367120.3:c.725C>T	p.Pro242Leu	p.P242L	ENST00000367120	NM_014002.3	242	cCg/cTg	8/22	0.82587829030691	2	FACETS	0.964	0.94	0.987	0.964	0.94	0.987	CLONAL	2	TRUE	0	0.855921697212927	2		308	510	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	205	319	0	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	0.816591043291353	2	FACETS	0.889	0.831	0.947	0.444	0.415	0.474	CLONAL	1	TRUE	0	0.855921697212927	2		319	539	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140715	55140715	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	425	352	0	ENST00000257290.5:c.1576A>T	p.Thr526Ser	p.T526S	ENST00000257290	NM_006206.4	526	Acg/Tcg	11/23	0.829925424429764	2	FACETS	0.89	0.864	0.915	0.89	0.864	0.915	CLONAL	2	TRUE	0	0.855921697212927	2		352	558	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602953	55602953	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776681643	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	355	292	1	ENST00000288135.5:c.2663G>A	p.Arg888Gln	p.R888Q	ENST00000288135	NM_000222.2	888	cGg/cAg	19/21	0.829925424429764	2	FACETS	0.953	0.927	0.979	0.953	0.927	0.979	CLONAL	2	TRUE	0	0.855921697212927	2		293	435	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293449	1293449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs551522837	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	357	295	1	ENST00000310581.5:c.1552G>A	p.Ala518Thr	p.A518T	ENST00000310581	NM_198253.2	518	Gct/Act	2/16	NA	2	FACETS	0.761	0.732	0.789			1	INDETERMINATE	2	TRUE	NA	0.855921697212927	2		296	548	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672299	30672299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374716229	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	430	274	0	ENST00000376406.3:c.4661G>A	p.Arg1554Gln	p.R1554Q	ENST00000376406	NM_014641.2	1554	cGg/cAg	10/15	0.855921697212927	4	FACETS	1	0.982	1			1	CLONAL	2	TRUE	NA	0.855921697212927	4		274	894	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196170	138196170	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs587778710	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	122	220	2	ENST00000237289.4:c.484C>T	p.Arg162Trp	p.R162W	ENST00000237289	NM_001270507.1	162	Cgg/Tgg	3/9	0.855921697212927	4	FACETS	0.693	0.627	0.763	0.347	0.313	0.382	SUBCLONAL	1	TRUE	2	0.855921697212927	4		222	763	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465558	8465558	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1400992051	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	464	421	0	ENST00000356435.5:c.3622G>A	p.Asp1208Asn	p.D1208N	ENST00000356435		1208	Gac/Aac	21/35	0.750825361863529	4	FACETS	0.975	0.935	1	0.975	0.935	1	CLONAL	2	TRUE	2	0.855921697212927	4		421	1032	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970927	21970927	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501274	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	422	247	2	ENST00000304494.5:c.431G>A	p.Arg144His	p.R144H	ENST00000304494	NM_000077.4	144	cGc/cAc	2/3	0.750825361863529	4	FACETS	0.945	0.904	0.987	0.945	0.904	0.987	CLONAL	2	TRUE	2	0.855921697212927	4		249	968	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404285	139404285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773902766	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	189	361	0	ENST00000277541.6:c.2869G>A	p.Gly957Arg	p.G957R	ENST00000277541	NM_017617.3	957	Ggg/Agg	18/34	0.750825361863529	4	FACETS	0.963	0.891	1	0.482	0.445	0.519	CLONAL	1	TRUE	2	0.855921697212927	4		361	851	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417596	139417596	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372660483	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	366	283	0	ENST00000277541.6:c.448G>A	p.Ala150Thr	p.A150T	ENST00000277541	NM_017617.3	150	Gcc/Acc	4/34	0.750825361863529	4	FACETS	0.922	0.878	0.965	0.922	0.878	0.965	CLONAL	2	TRUE	2	0.855921697212927	4		283	861	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123246935	123246935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113014479	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	432	325	0	ENST00000358487.5:c.1990C>T	p.Arg664Trp	p.R664W	ENST00000358487	NM_000141.4	664	Cgg/Tgg	15/18	0.750825361863529	4	FACETS	0.975	0.933	1	0.975	0.933	1	CLONAL	2	TRUE	2	0.855921697212927	4		325	961	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94211915	94211915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773766504	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	428	285	1	ENST00000323929.3:c.530C>T	p.Ala177Val	p.A177V	ENST00000323929	NM_005591.3	177	gCg/gTg	6/20	0.82587829030691	2	FACETS	0.952	0.928	0.976	0.952	0.928	0.976	CLONAL	2	TRUE	0	0.855921697212927	2		286	525	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118353197	118353197	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555039632	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	348	258	0	ENST00000534358.1:c.4073A>G	p.Lys1358Arg	p.K1358R	ENST00000534358	NM_005933.3	1358	aAa/aGa	8/36	0.82587829030691	2	FACETS	0.916	0.888	0.942	0.916	0.888	0.942	CLONAL	2	TRUE	0	0.855921697212927	2		258	444	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402115	402115	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	557	362	0	ENST00000399788.2:c.4676A>T	p.Glu1559Val	p.E1559V	ENST00000399788	NM_001042603.1	1559	gAa/gTa	27/28	NA	2	FACETS	0.968	0.947	0.988			1	INDETERMINATE	2	TRUE	NA	0.855921697212927	2		362	672	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245099	46245099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1251425183	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	350	314	0	ENST00000334344.6:c.3193C>T	p.Leu1065Phe	p.L1065F	ENST00000334344	NM_152641.2	1065	Ctt/Ttt	15/21	0.816591043291353	2	FACETS	0.909	0.881	0.935	0.909	0.881	0.935	CLONAL	2	TRUE	0	0.855921697212927	2		314	450	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438641	49438641	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759226682	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	424	278	1	ENST00000301067.7:c.4849C>T	p.Arg1617Trp	p.R1617W	ENST00000301067	NM_003482.3	1617	Cgg/Tgg	19/54	0.816591043291353	2	FACETS	0.956	0.932	0.979	0.956	0.932	0.979	CLONAL	2	TRUE	0	0.855921697212927	2		279	518	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549403	21549403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765566250	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	203	177	0	ENST00000382592.4:c.2873G>A	p.Arg958His	p.R958H	ENST00000382592	NM_014572.2	958	cGc/cAc	8/8	0.829925424429764	2	FACETS	0.937	0.901	0.971	0.937	0.901	0.971	CLONAL	2	TRUE	0	0.855921697212927	2		177	253	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354357	354357	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1456907312	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	350	335	0	ENST00000262320.3:c.1201C>T	p.Arg401Cys	p.R401C	ENST00000262320	NM_003502.3	401	Cgc/Tgc	5/11	0.573879119152046	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	2	0.855921697212927	4		335	757	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133801	2133801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397515209	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	236	178	2	ENST00000219476.3:c.3989C>T	p.Thr1330Met	p.T1330M	ENST00000219476	NM_000548.3	1330	aCg/aTg	33/42	0.573879119152046	4	FACETS	0.999	0.943	1	0.999	0.943	1	CLONAL	2	TRUE	2	0.855921697212927	4		180	512	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778741	3778741	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	132	236	0	ENST00000262367.5:c.6307C>T	p.Gln2103Ter	p.Q2103*	ENST00000262367	NM_004380.2	2103	Cag/Tag	31/31	0.573879119152046	4	FACETS	0.807	0.734	0.884	0.404	0.367	0.442	CLONAL	1	TRUE	2	0.855921697212927	4		236	709	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664600	29664600	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs876660207	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	316	231	2	ENST00000356175.3:c.6579G>C	p.Glu2193Asp	p.E2193D	ENST00000356175	NM_000267.3	2193	gaG/gaC	42/57	1	2	FACETS	0.881	0.851	0.91	1	0.997	1	CLONAL	2	TRUE	1	0.855921697212927	2		233	419	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223057	1223057	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	476	285	0	ENST00000326873.7:c.994T>A	p.Trp332Arg	p.W332R	ENST00000326873	NM_000455.4	332	Tgg/Agg	8/10	0.855921697212927	4	FACETS	1	0.968	1			1	CLONAL	2	TRUE	NA	0.855921697212927	4		285	1023	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213968	2213968	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376032475	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	245	160	0	ENST00000398665.3:c.1780G>A	p.Gly594Ser	p.G594S	ENST00000398665	NM_032482.2	594	Ggc/Agc	18/28	0.781490844393204	3	FACETS	0.822	0.778	0.867			1	CLONAL	2	TRUE	NA	0.855921697212927	3		160	497	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238995	5238995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	346	250	0	ENST00000357368.4:c.1784C>T	p.Ala595Val	p.A595V	ENST00000357368	NM_002850.3	595	gCg/gTg	13/38	0.573879119152046	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.855921697212927	4		250	716	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164757	36164757	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	45	266	0	ENST00000300305.3:c.1118C>T	p.Ser373Leu	p.S373L	ENST00000300305		373	tCg/tTg	8/8	0.824266391304689	2	FACETS	0.225	0.189	0.265	0.112	0.094	0.133	SUBCLONAL	1	TRUE	0	0.855921697212927	2		266	468	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1327780	1327780	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	199	310	0	ENST00000400841.2:c.101T>A	p.Ile34Asn	p.I34N	ENST00000400841		34	aTc/aAc	2/6	1	1	FACETS	0.911	0.867	0.954	0.911	0.867	0.954	CLONAL	1	TRUE	0	0.855921697212927	1		310	292	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923059	39923059	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	246	194	0	ENST00000378444.4:c.3649C>T	p.Arg1217Ter	p.R1217*	ENST00000378444	NM_001123385.1	1217	Cga/Tga	8/15	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.855921697212927	1		194	308	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652469	48652469	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	232	181	0	ENST00000376670.3:c.1140G>T	p.Met380Ile	p.M380I	ENST00000376670	NM_002049.3	380	atG/atT	6/6	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.855921697212927	1		181	275	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343006	70343006	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556334969	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	284	156	0	ENST00000374080.3:c.1547G>A	p.Arg516His	p.R516H	ENST00000374080		516	cGt/cAt	11/45	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.855921697212927	1		156	338	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531788	46531789	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	rs781568531	NA	P-0001851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	197	394	0	ENST00000262741.5:c.558_559del	p.Gln187ValfsTer6	p.Q187Vfs*6	ENST00000262741	NM_003629.3	186	tcTCag/tcag	5/10	0.855921697212927	3	FACETS	0.783	0.726	0.841	0.261	0.242	0.281	SUBCLONAL	1	TRUE	0	0.855921697212927	3		394	840	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891659	28891659	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001855-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	109	242	0	ENST00000282397.4:c.3362C>A	p.Ala1121Asp	p.A1121D	ENST00000282397	NM_002019.4	1121	gCt/gAt	25/30	0.192698705809964	3	FACETS	0.782	0.705	0.863	0.521	0.47	0.576	SUBCLONAL	2	TRUE	0	0.291988561543836	3		242	547	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212149	5212149	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1377011238	NA	P-0001855-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	57	222	0	ENST00000357368.4:c.4882C>T	p.Arg1628Cys	p.R1628C	ENST00000357368	NM_002850.3	1628	Cgc/Tgc	32/38	0.291988561543836	1	FACETS	0.786	0.676	0.906	0.786	0.676	0.906	CLONAL	1	TRUE	0	0.291988561543836	1		222	424	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045000	47045000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556782020	NA	P-0001855-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	46	110	0	ENST00000377604.3:c.2326C>T	p.Arg776Trp	p.R776W	ENST00000377604	NM_001204468.1	776	Cgg/Tgg	20/24	0.138891808069279	2	FACETS	1	0.955	1			1	INDETERMINATE	1	TRUE	NA	0.291988561543836	2		110	230	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577525	7577525	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001855-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	81	186	0	ENST00000269305.4:c.756del	p.Thr253ProfsTer92	p.T253Pfs*92	ENST00000269305	NM_001126112.2	252	ctC/ct	7/11	0.195561232257801	2	FACETS	0.826	0.734	0.923	0.826	0.734	0.923	CLONAL	2	TRUE	0	0.291988561543836	2		186	336	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0001860-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	478	591	2	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	0.291829173467582	4	FACETS	0.883	0.845	0.921	0.883	0.845	0.921	INDETERMINATE	2	TRUE	2	0.770515260102055	4		593	1244	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0001860-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	381	533	2	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.770515260102055	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.770515260102055	1		535	569	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175916344	175916344	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001860-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	440	509	0	ENST00000367669.3:c.2165A>C	p.Gln722Pro	p.Q722P	ENST00000367669	NM_022457.5	722	cAg/cCg	19/20	0.770515260102055	3	FACETS	1	0.988	1	0.553	0.527	0.58	CLONAL	1	TRUE	1	0.770515260102055	3		509	1430	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598190	52598190	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001860-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	497	612	0	ENST00000394830.3:c.3676G>C	p.Glu1226Gln	p.E1226Q	ENST00000394830	NM_018313.4	1226	Gaa/Caa	24/30	0.770515260102055	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.770515260102055	1		612	683	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2969662	2969662	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001860-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	198	474	0	ENST00000396946.4:c.1617C>A	p.Cys539Ter	p.C539*	ENST00000396946	NM_032415.4	539	tgC/tgA	12/25	0.770515260102055	2	FACETS	0.938	0.875	1	0.469	0.437	0.501	CLONAL	1	TRUE	0	0.770515260102055	2		474	548	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578192	7578192	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001860-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	368	521	0	ENST00000269305.4:c.657del	p.Tyr220MetfsTer27	p.Y220Mfs*27	ENST00000269305	NM_001126112.2	219	ccC/cc	6/11	0.770515260102055	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.770515260102055	1		521	545	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193121537	193121537	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001885-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	351	639	0	ENST00000367435.3:c.935T>C	p.Met312Thr	p.M312T	ENST00000367435	NM_024529.4	312	aTg/aCg	10/17	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.87	2		639	740	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686895	37686895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001885-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	170	671	1	ENST00000447079.4:c.3799C>T	p.Pro1267Ser	p.P1267S	ENST00000447079	NM_015083.1	1267	Cct/Tct	14/14	1	2	FACETS	0.9	0.837	0.965	0.9	0.837	0.965	CLONAL	1	TRUE	1	0.87	2		672	434	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0001895-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	22	411	1	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	1	2	FACETS	0.225	0.173	0.286	0.225	0.173	0.286	SUBCLONAL	1	FALSE	1	0.217052022923788	2		412	900	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0001895-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	63	389	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	0.707	0.61	0.813	0.707	0.61	0.813	SUBCLONAL	1	FALSE	1	0.217052022923788	2		389	821	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449800	29449800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs76742576	NA	P-0001895-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	92	297	0	ENST00000389048.3:c.3055G>A	p.Val1019Ile	p.V1019I	ENST00000389048	NM_004304.4	1019	Gtc/Atc	18/29	0.217052022923788	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	0	0.217052022923788	1		297	589	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226595556	226595558	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	novel	NA	P-0001895-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	92	302	0	ENST00000366794.5:c.73_75del	p.Ser25del	p.S25del	ENST00000366794	NM_001618.3	25	AGC/-	1/23	0.217052022923788	6	FACETS	1	0.971	1			1	CLONAL	1	FALSE	NA	0.217052022923788	6		302	938	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001897-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	31	303	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	0.237748989682261	5	FACETS	0.388	0.313	0.474	0.129	0.104	0.158	INDETERMINATE	1	TRUE	2	0.519661372086144	5		303	547	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203775	94203775	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001898-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	49	350	0	ENST00000323929.3:c.879G>T	p.Lys293Asn	p.K293N	ENST00000323929	NM_005591.3	293	aaG/aaT	9/20	0.267075560942529	3	FACETS	0.847	0.718	0.989	0.424	0.359	0.495	CLONAL	1	TRUE	1	0.267075560942529	3		350	491	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123499637	123499637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001898-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	98	498	0	ENST00000371139.4:c.164G>A	p.Arg55Gln	p.R55Q	ENST00000371139	NM_001114937.2	55	cGa/cAa	2/4	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.267075560942529	2		498	540	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349178	11349178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772494995	NA	P-0001907-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	89	32	82	0	ENST00000332029.2:c.158C>T	p.Thr53Met	p.T53M	ENST00000332029	NM_003745.1	53	aCg/aTg	2/2	0.323374961304262	5	FACETS	0.909	0.753	1	0.606	0.502	0.719	CLONAL	2	TRUE	2	0.515839325400558	5		82	121	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579361	7579361	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1064796722	NA	P-0001907-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	170	197	455	0	ENST00000269305.4:c.326T>G	p.Phe109Cys	p.F109C	ENST00000269305	NM_001126112.2	109	tTc/tGc	4/11	0.514619141831066	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.515839325400558	2		455	367	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334714	81334714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	470	546	0	ENST00000222390.5:c.2002C>T	p.Pro668Ser	p.P668S	ENST00000222390	NM_000601.4	668	Cca/Tca	17/18	1	2	FACETS	1	0.988	1	1	0.998	1	CLONAL	4	TRUE	1	0.224957482317692	2		546	974	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432883	432883	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	338	419	0	ENST00000399788.2:c.2033C>G	p.Ala678Gly	p.A678G	ENST00000399788	NM_001042603.1	678	gCa/gGa	15/28	0.224957482317692	1	FACETS	0.981	0.936	1	1	0.997	1	CLONAL	4	TRUE	0	0.224957482317692	1		419	680	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653796	89653798	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs1554893765	NA	P-0001932-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	164	455	1	ENST00000371953.3:c.97_99del	p.Ile33del	p.I33del	ENST00000371953	NM_000314.4	32	ATT/-	2/9	0.580599392086932	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.580599392086932	1		456	400	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942566	17942566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001932-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	53	164	0	ENST00000458235.1:c.2722G>A	p.Gly908Ser	p.G908S	ENST00000458235	NM_000215.3	908	Ggc/Agc	20/24	0.41525734848434	1	FACETS	0.508	0.437	0.584	0.508	0.437	0.584	SUBCLONAL	1	TRUE	0	0.580599392086932	1		164	255	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542372	187542372	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777812985	NA	P-0001936-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	84	252	0	ENST00000441802.2:c.5368G>A	p.Val1790Ile	p.V1790I	ENST00000441802	NM_005245.3	1790	Gtc/Atc	10/27	0.371047728861914	1	FACETS	0.477	0.425	0.532	0.477	0.425	0.532	INDETERMINATE	1	TRUE	0	0.696015589997426	1		252	330	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420460	49420460	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001936-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	71	229	0	ENST00000301067.7:c.15289C>T	p.Arg5097Ter	p.R5097*	ENST00000301067	NM_003482.3	5097	Cga/Tga	48/54	1	2	FACETS	0.487	0.427	0.551	0.487	0.427	0.551	SUBCLONAL	1	TRUE	1	0.696015589997426	2		229	419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0001941-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	41	415	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.500723267522983	3	FACETS	1	0.918	1	0.722	0.626	0.819	CLONAL	2	TRUE	0	0.564410609428635	3		415	86	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272166	15272206	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGCCCGGGCAGGCCAGCGTCAGCTTCTTGCCCCGCCCCC	GGGGCCCGGGCAGGCCAGCGTCAGCTTCTTGCCCCGCCCCC	-	novel	NA	P-0001941-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	22	62	0	ENST00000263388.2:c.6233_6273del	p.Arg2078ProfsTer3	p.R2078Pfs*3	ENST00000263388	NM_000435.2	2078	cGGGGGCGGGGCAAGAAGCTGACGCTGGCCTGCCCGGGCCCC/c	33/33	0.564410609428635	3	FACETS	0.952	0.802	1	1	0.945	1	CLONAL	3	TRUE	1	0.564410609428635	3		62	35	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913499	NA	P-0001975-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	188	362	1	ENST00000345146.2:c.394C>A	p.Arg132Ser	p.R132S	ENST00000345146	NM_005896.2	132	Cgt/Agt	4/10	1	2	FACETS	0.938	0.875	1	0.938	0.875	1	CLONAL	1	FALSE	1	0.794931506392884	2		363	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0001975-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	182	397	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.794931506392884	2		397	435	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937611	76937615	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTT	CTTTT	-	novel	NA	P-0001975-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	232	389	0	ENST00000373344.5:c.3133_3137del	p.Lys1045Ter	p.K1045*	ENST00000373344	NM_000489.3	1045	AAAAGt/t	9/35	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	0	0.794931506392884	1		389	324	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965595	25965595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001975-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	175	420	0	ENST00000435504.4:c.3611G>A	p.Ser1204Asn	p.S1204N	ENST00000435504		1204	aGt/aAt	13/13	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	FALSE	1	0.794931506392884	2		420	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577157	7577157	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0001975-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	163	378	0	ENST00000269305.4:c.783-2A>C		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.794931506392884	2		378	399	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891154	151891154	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001976-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	127	341	0	ENST00000262189.6:c.4600C>T	p.Gln1534Ter	p.Q1534*	ENST00000262189	NM_170606.2	1534	Cag/Tag	31/59	1	2	FACETS	0.985	0.897	1	0.985	0.897	1	CLONAL	1	TRUE	1	0.494114748157452	2		341	522	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654694	29654694	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001976-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	327	418	0	ENST00000356175.3:c.5383G>T	p.Glu1795Ter	p.E1795*	ENST00000356175	NM_000267.3	1795	Gag/Tag	37/57	0.483482569029054	3	FACETS	0.979	0.937	1	0.979	0.937	1	CLONAL	3	TRUE	0	0.494114748157452	3		418	562	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022388	31022388	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs868446207	NA	P-0001976-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	55	241	1	ENST00000375687.4:c.1873C>T	p.Arg625Ter	p.R625*	ENST00000375687	NM_015338.5	625	Cga/Tga	13/13	0.477140000358599	2	FACETS	0.931	0.806	1	0.466	0.403	0.533	CLONAL	1	TRUE	0	0.494114748157452	2		242	239	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589594	67589596	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	novel	NA	P-0001976-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	94	319	0	ENST00000274335.5:c.1358_1360del	p.Asn453del	p.N453del	ENST00000274335		453	AAC/-	10/15	0.494114748157452	3	FACETS	0.63	0.56	0.705	0.315	0.28	0.353	SUBCLONAL	1	TRUE	1	0.494114748157452	3		319	753	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653835	89653835	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001976-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	242	333	0	ENST00000371953.3:c.133del	p.Val45TyrfsTer9	p.V45Yfs*9	ENST00000371953	NM_000314.4	45	Gta/ta	2/9	0.477140000358599	2	FACETS	0.902	0.851	0.953	0.902	0.851	0.953	CLONAL	2	TRUE	0	0.494114748157452	2		333	543	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001979-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	86	227	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.353858333140989	2	FACETS	1	0.96	1	0.588	0.523	0.657	CLONAL	1	TRUE	0	0.353858333140989	2		227	413	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564590	55564590	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001983-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	110	346	0	ENST00000288135.5:c.478T>G	p.Leu160Val	p.L160V	ENST00000288135	NM_000222.2	160	Ttg/Gtg	3/21	0.369813003139733	1	FACETS	0.79	0.713	0.872	0.79	0.713	0.872	SUBCLONAL	1	FALSE	0	0.411757937035012	1		346	537	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138286	2138286	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137854219	NA	P-0001983-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	276	362	0	ENST00000219476.3:c.5219G>A	p.Trp1740Ter	p.W1740*	ENST00000219476	NM_000548.3	1740	tGg/tAg	41/42	0.380537642435137	3	FACETS	0.883	0.837	0.93	0.883	0.837	0.93	CLONAL	3	FALSE	0	0.411757937035012	3		362	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0001983-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	512	293	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.411757937035012	6	FACETS	0.933	0.903	0.963			1	CLONAL	6	FALSE	NA	0.411757937035012	6		293	810	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0001985-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	212	325	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.627920446223438	3	FACETS	0.938	0.911	0.962	1	0.995	1	CLONAL	4	TRUE	0	0.622716335420832	3		325	238	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55603410	55603410	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001985-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	27	374	0	ENST00000288135.5:c.2766G>T	p.Gln922His	p.Q922H	ENST00000288135	NM_000222.2	922	caG/caT	20/21	NA	2	FACETS	0.469	0.376	0.573			1	INDETERMINATE	1	TRUE	NA	0.622716335420832	2		374	185	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94170383	94170384	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0001985-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	110	378	0	ENST00000323929.3:c.1885_1886del	p.Gln629AlafsTer9	p.Q629Afs*9	ENST00000323929	NM_005591.3	629	CAg/g	17/20	0.627920446223438	5	FACETS	0.823	0.745	0.905	0.329	0.298	0.362	CLONAL	2	TRUE	0	0.622716335420832	5		378	415	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0001994-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	278	542	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.632948548024714	6	FACETS	0.943	0.903	0.982	1	0.992	1	CLONAL	5	TRUE	2	0.632948548024714	6		542	422	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272408	15272408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142007575	NA	P-0001994-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	20	374	0	ENST00000263388.2:c.6031G>A	p.Val2011Ile	p.V2011I	ENST00000263388	NM_000435.2	2011	Gta/Ata	33/33	NA	2	FACETS	0.506	0.391	0.636			1	INDETERMINATE	1	TRUE	NA	0.632948548024714	2		374	125	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0002013-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	76	311	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.998	0.889	1	1	0.984	1	CLONAL	2	FALSE	1	0.317224585926539	2		311	240	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0002013-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	230	505	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.317224585926539	10	FACETS	1	0.968	1			1	CLONAL	7	FALSE	NA	0.317224585926539	10		505	454	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255968	16255968	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0002016-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	30	415	0	ENST00000375759.3:c.3233C>G	p.Ser1078Ter	p.S1078*	ENST00000375759	NM_015001.2	1078	tCa/tGa	11/15	0.414813853244436	3	FACETS	0.62	0.501	0.754	0.207	0.167	0.252	SUBCLONAL	1	TRUE	0	0.444607297074537	3		415	266	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735510	204735510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759232662	NA	P-0002016-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	30	452	1	ENST00000302823.3:c.311C>T	p.Thr104Met	p.T104M	ENST00000302823	NM_005214.4	104	aCg/aTg	2/4	0.444607297074537	3	FACETS	0.465	0.375	0.567	0.232	0.187	0.284	SUBCLONAL	1	TRUE	1	0.444607297074537	3		453	355	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52692222	52692222	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002016-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	31	673	0	ENST00000394830.3:c.638C>G	p.Ser213Cys	p.S213C	ENST00000394830	NM_018313.4	213	tCt/tGt	6/30	0.13670411071547	1	FACETS	0.406	0.33	0.492	0.406	0.33	0.492	INDETERMINATE	1	TRUE	0	0.444607297074537	1		673	267	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266679	142266679	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002016-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	160	618	0	ENST00000350721.4:c.3245G>T	p.Arg1082Leu	p.R1082L	ENST00000350721	NM_001184.3	1082	cGt/cTt	16/47	0.444607297074537	5	FACETS	1	0.955	1	0.702	0.647	0.758	CLONAL	2	TRUE	2	0.444607297074537	5		618	570	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593648	55593648	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002016-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	83	576	2	ENST00000288135.5:c.1714G>T	p.Asp572Tyr	p.D572Y	ENST00000288135	NM_000222.2	572	Gac/Tac	11/21	0.317999618962099	3	FACETS	1	0.979	1	0.738	0.658	0.822	CLONAL	1	TRUE	1	0.444607297074537	3		578	309	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519130	187519130	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002016-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	33	508	0	ENST00000441802.2:c.12253C>G	p.Gln4085Glu	p.Q4085E	ENST00000441802	NM_005245.3	4085	Cag/Gag	23/27	0.444607297074537	1	FACETS	0.542	0.445	0.65	0.542	0.445	0.65	SUBCLONAL	1	TRUE	0	0.444607297074537	1		508	213	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542177	187542177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773207249	NA	P-0002016-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	50	673	0	ENST00000441802.2:c.5563C>T	p.Pro1855Ser	p.P1855S	ENST00000441802	NM_005245.3	1855	Cca/Tca	10/27	0.444607297074537	1	FACETS	0.764	0.655	0.881	0.764	0.655	0.881	SUBCLONAL	1	TRUE	0	0.444607297074537	1		673	229	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1255449	1255449	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1060503001	NA	P-0002016-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	28	449	0	ENST00000310581.5:c.3110C>G	p.Ser1037Cys	p.S1037C	ENST00000310581	NM_198253.2	1037	tCt/tGt	14/16	0.343605376236211	5	FACETS	0.714	0.572	0.875			1	SUBCLONAL	1	TRUE	NA	0.444607297074537	5		449	294	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679595	86679595	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0002016-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	54	607	0	ENST00000274376.6:c.2756C>G	p.Ser919Ter	p.S919*	ENST00000274376	NM_002890.2	919	tCa/tGa	21/25	0.444607297074537	3	FACETS	0.544	0.464	0.631	0.272	0.232	0.316	SUBCLONAL	1	TRUE	1	0.444607297074537	3		607	546	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030299	180030299	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002016-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	77	572	0	ENST00000261937.6:c.3985G>T	p.Gly1329Cys	p.G1329C	ENST00000261937	NM_182925.4	1329	Ggc/Tgc	30/30	0.444607297074537	3	FACETS	1	0.971	1	0.666	0.59	0.746	CLONAL	1	TRUE	1	0.444607297074537	3		572	318	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265628	152265628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002016-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	37	279	0	ENST00000206249.3:c.1081G>A	p.Ala361Thr	p.A361T	ENST00000206249	NM_000125.3	361	Gcg/Acg	4/8	0.319053959270341	2	FACETS	1	0.853	1	0.511	0.427	0.601	CLONAL	1	TRUE	0	0.444607297074537	2		279	163	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956934	2956934	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002016-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	24	390	0	ENST00000396946.4:c.2693A>G	p.Gln898Arg	p.Q898R	ENST00000396946	NM_032415.4	898	cAg/cGg	20/25	0.444607297074537	5	FACETS	0.598	0.469	0.746	0.199	0.156	0.249	SUBCLONAL	1	TRUE	2	0.444607297074537	5		390	301	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444333	50444333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775004468	NA	P-0002016-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	39	388	0	ENST00000331340.3:c.263C>T	p.Ser88Leu	p.S88L	ENST00000331340	NM_006060.4	88	tCg/tTg	4/8	0.444607297074537	5	FACETS	0.735	0.61	0.874	0.245	0.203	0.292	SUBCLONAL	1	TRUE	2	0.444607297074537	5		388	398	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399835	139399835	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002016-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	39	424	0	ENST00000277541.6:c.4513T>G	p.Cys1505Gly	p.C1505G	ENST00000277541	NM_017617.3	1505	Tgt/Ggt	25/34	0.444607297074537	3	FACETS	0.592	0.492	0.704	0.197	0.164	0.235	SUBCLONAL	1	TRUE	0	0.444607297074537	3		424	362	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239450	123239450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002016-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	50	469	0	ENST00000358487.5:c.2387C>T	p.Ser796Phe	p.S796F	ENST00000358487	NM_000141.4	796	tCt/tTt	18/18	0.444607297074537	5	FACETS	0.866	0.736	1	0.216	0.184	0.252	CLONAL	1	TRUE	1	0.444607297074537	5		469	433	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170479	108170479	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121434217	NA	P-0002016-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	48	570	0	ENST00000278616.4:c.5044G>C	p.Asp1682His	p.D1682H	ENST00000278616	NM_000051.3	1682	Gat/Cat	34/63	0.444607297074537	3	FACETS	0.614	0.52	0.717	0.205	0.173	0.239	SUBCLONAL	1	TRUE	0	0.444607297074537	3		570	430	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	464357	464357	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1445712907	NA	P-0002016-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	45	766	0	ENST00000399788.2:c.837G>C	p.Met279Ile	p.M279I	ENST00000399788	NM_001042603.1	279	atG/atC	7/28	NA	2	FACETS	0.564	0.475	0.661			1	INDETERMINATE	1	TRUE	NA	0.444607297074537	2		766	359	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893659	28893659	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002016-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	37	418	0	ENST00000282397.4:c.3187C>G	p.Leu1063Val	p.L1063V	ENST00000282397	NM_002019.4	1063	Ctg/Gtg	24/30	0.444607297074537	5	FACETS	0.793	0.655	0.946	0.159	0.131	0.19	CLONAL	1	TRUE	0	0.444607297074537	5		418	350	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144835	11144835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002016-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	82	389	0	ENST00000358026.2:c.3910C>T	p.Gln1304Ter	p.Q1304*	ENST00000358026	NM_001128849.1	1304	Cag/Tag	28/36	0.444607297074537	2	FACETS	0.862	0.775	0.951	0.862	0.775	0.951	CLONAL	2	TRUE	0	0.444607297074537	2		389	214	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716051	52716051	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002016-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	33	587	0	ENST00000322088.6:c.616A>G	p.Ile206Val	p.I206V	ENST00000322088	NM_014225.5	206	Atc/Gtc	5/15	0.444607297074537	5	FACETS	0.728	0.594	0.878	0.243	0.198	0.293	SUBCLONAL	1	TRUE	2	0.444607297074537	5		587	340	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345945	70345945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002016-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	42	336	0	ENST00000374080.3:c.2482G>C	p.Asp828His	p.D828H	ENST00000374080		828	Gat/Cat	18/45	0.189336291104374	2	FACETS	0.94	0.794	1			1	INDETERMINATE	1	TRUE	NA	0.444607297074537	2		336	201	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21968238	21968238	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002016-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	109	377	0	ENST00000304494.5:c.461del	p.Ile154ThrfsTer39	p.I154Tfs*39	ENST00000304494	NM_000077.4	154	aTc/ac	3/3	0.393676255540495	3	FACETS	1	0.97	1	0.76	0.694	0.826	CLONAL	2	TRUE	0	0.444607297074537	3		377	263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577576	7577578	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	novel	NA	P-0002016-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	63	427	0	ENST00000269305.4:c.703_705del	p.Asn235del	p.N235del	ENST00000269305	NM_001126112.2	235	AAC/-	7/11	0.298582698627384	2	FACETS	1	0.974	1	0.738	0.65	0.83	CLONAL	1	TRUE	0	0.444607297074537	2		427	192	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348131	348131	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002057-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	60	617	1	ENST00000262320.3:c.1375C>T	p.Leu459Phe	p.L459F	ENST00000262320	NM_003502.3	459	Ctc/Ttc	6/11	0.368246146640941	1	FACETS	0.39	0.336	0.45	0.39	0.336	0.45	SUBCLONAL	1	TRUE	0	0.382111168452444	1		618	651	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857404	68857429	+	frameshift_variant	Frame_Shift_Del	DEL	CCTTAGAGGTCAGCGTGTGTGACTGT	CCTTAGAGGTCAGCGTGTGTGACTGT	-	novel	NA	P-0002057-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	209	633	0	ENST00000261769.5:c.2039_2064del	p.Thr680ArgfsTer8	p.T680Rfs*8	ENST00000261769	NM_004360.3	680	aCCTTAGAGGTCAGCGTGTGTGACTGT/a	13/16	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.382111168452444	2		633	853	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0002072-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	164	593	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.329677699827774	3	FACETS	0.972	0.897	1	0.972	0.897	1	CLONAL	2	FALSE	1	0.329677699827774	3		593	596	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916781	178916781	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002077-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	53	625	0	ENST00000263967.3:c.168C>A	p.Tyr56Ter	p.Y56*	ENST00000263967	NM_006218.2	56	taC/taA	2/21	NA	2	FACETS	0.175	0.148	0.205			1	INDETERMINATE	1	TRUE	NA	0.58570911564368	2		625	1033	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608442	28608442	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002077-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	114	491	0	ENST00000241453.7:c.1700A>G	p.Lys567Arg	p.K567R	ENST00000241453	NM_004119.2	567	aAa/aGa	13/24	0.58570911564368	1	FACETS	0.526	0.476	0.579	0.526	0.476	0.579	SUBCLONAL	1	TRUE	0	0.58570911564368	1		491	523	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094876	143094876	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002103-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1442	133	488	0	ENST00000262992.4:c.1268T>G	p.Leu423Arg	p.L423R	ENST00000262992	NM_001101669.1	423	cTt/cGt	14/24	1	2	FACETS	0.732	0.662	0.806	0.732	0.662	0.806	SUBCLONAL	1	TRUE	1	0.230737822196674	2		488	1575	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171570	32171570	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002103-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	128	450	0	ENST00000375023.3:c.3208G>T	p.Gly1070Cys	p.G1070C	ENST00000375023	NM_004557.3	1070	Ggt/Tgt	20/30	1	2	FACETS	0.967	0.875	1	0.967	0.875	1	CLONAL	1	TRUE	1	0.230737822196674	2		450	1147	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781080	135781080	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0002103-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	150	620	0	ENST00000298552.3:c.1885A>T	p.Lys629Ter	p.K629*	ENST00000298552	NM_001162426.1	629	Aag/Tag	15/23	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.230737822196674	2		620	1261	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151868398	151868398	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002106-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	101	511	0	ENST00000262189.6:c.9404G>T	p.Gly3135Val	p.G3135V	ENST00000262189	NM_170606.2	3135	gGa/gTa	40/59	1	2	FACETS	0.356	0.317	0.397	0.356	0.317	0.397	SUBCLONAL	1	TRUE	1	0.574108500519969	2		511	988	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579366	7579369	+	frameshift_variant	Frame_Shift_Del	DEL	GTAG	GTAG	-	novel	NA	P-0002106-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	153	297	0	ENST00000269305.4:c.318_321del	p.Ser106ArgfsTer16	p.S106Rfs*16	ENST00000269305	NM_001126112.2	106	agCTAC/ag	4/11	0.574108500519969	1	FACETS	0.832	0.767	0.897	0.832	0.767	0.897	CLONAL	1	TRUE	0	0.574108500519969	1		297	457	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945549	151945553	+	protein_altering_variant	In_Frame_Del	DEL	GTAAC	GTAAC	TG	novel	NA	P-0002106-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	73	98	0	ENST00000262189.6:c.1966_1970delinsCA	p.Val656_Thr657delinsGln	p.V656_T657delinsQ	ENST00000262189	NM_170606.2	656	GTTACa/CAa	14/59	1	2	FACETS	0.99	0.876	1	0.99	0.876	1	CLONAL	1	TRUE	1	0.574108500519969	2		98	257	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002122-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	116	341	2	ENST00000269305.4:c.313G>T	p.Gly105Cys	p.G105C	ENST00000269305	NM_001126112.2	105	Ggc/Tgc	4/11	0.252334969881179	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.252334969881179	1		343	675	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319313	11319313	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002122-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	130	398	0	ENST00000361445.4:c.154C>T	p.Leu52Phe	p.L52F	ENST00000361445	NM_004958.3	52	Ctc/Ttc	2/58	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.252334969881179	2		398	923	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682398	52682398	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002122-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	197	495	0	ENST00000394830.3:c.775G>T	p.Ala259Ser	p.A259S	ENST00000394830	NM_018313.4	259	Gcc/Tcc	8/30	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.252334969881179	2		495	1089	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629648	187629648	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002122-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	129	536	0	ENST00000441802.2:c.1334C>G	p.Ala445Gly	p.A445G	ENST00000441802	NM_005245.3	445	gCg/gGg	2/27	0.252334969881179	1	FACETS	0.961	0.87	1	0.961	0.87	1	CLONAL	1	TRUE	0	0.252334969881179	1		536	930	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523145	176523145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746619070	NA	P-0002122-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	118	413	0	ENST00000292408.4:c.1909G>A	p.Val637Ile	p.V637I	ENST00000292408	NM_213647.1	637	Gtc/Atc	14/18	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.252334969881179	2		413	929	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549433	21549433	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002122-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	32	177	0	ENST00000382592.4:c.2843T>A	p.Ile948Asn	p.I948N	ENST00000382592	NM_014572.2	948	aTc/aAc	8/8	1	2	FACETS	0.667	0.542	0.809	0.667	0.542	0.809	SUBCLONAL	1	TRUE	1	0.252334969881179	2		177	380	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0002123-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	83	393	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.95	0.853	1	1	0.985	1	CLONAL	2	TRUE	1	0.381577998318681	2		393	229	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519226	187519226	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200611830	NA	P-0002147-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	202	383	0	ENST00000441802.2:c.12157G>A	p.Val4053Ile	p.V4053I	ENST00000441802	NM_005245.3	4053	Gtc/Atc	23/27	NA	2	FACETS	0.78	0.727	0.835			1	INDETERMINATE	1	TRUE	NA	0.807635967146502	2		383	641	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0002147-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	273	258	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.807635967146502	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.807635967146502	1		258	342	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685334	86685334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002147-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	243	164	0	ENST00000274376.6:c.3050G>T	p.Gly1017Val	p.G1017V	ENST00000274376	NM_002890.2	1017	gGt/gTt	24/25	0.5134856777768	4	FACETS	0.931	0.877	0.986	0.931	0.877	0.986	CLONAL	2	TRUE	2	0.807635967146502	4		164	584	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844245	68844245	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs878854697	NA	P-0002147-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	134	266	0	ENST00000261769.5:c.832+1G>A		p.X278_splice	ENST00000261769	NM_004360.3	278			0.807635967146502	1	FACETS	0.965	0.906	1	0.965	0.906	1	CLONAL	1	TRUE	0	0.807635967146502	1		266	205	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307212	65307212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150021823	NA	P-0002149-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	54	337	0	ENST00000342505.4:c.2476C>T	p.Arg826Cys	p.R826C	ENST00000342505	NM_002227.2	826	Cgc/Tgc	18/25	0.402036844468303	0	FACETS	0.263	0.224	0.304			1	SUBCLONAL	1	TRUE	0	0.478680571956889	0		337	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0002149-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	199	335	0	ENST00000269305.4:c.994-1G>T		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.475009015521216	1	FACETS	0.897	0.834	0.962	0.897	0.834	0.962	CLONAL	1	TRUE	0	0.478680571956889	1		335	705	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0002153-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	317	542	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.243067681039208	3	FACETS	1	0.994	1	0.727	0.686	0.77	CLONAL	1	TRUE	1	0.399756348059952	3		542	1308	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602290	10602290	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002153-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	335	487	0	ENST00000171111.5:c.1288G>T	p.Gly430Cys	p.G430C	ENST00000171111	NM_203500.1	430	Ggc/Tgc	3/6	0.266680530185499	3	FACETS	0.872	0.829	0.914	0.872	0.829	0.914	CLONAL	3	TRUE	0	0.399756348059952	3		487	769	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480327	89480327	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002153-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	124	702	0	ENST00000336596.2:c.2164C>A	p.Gln722Lys	p.Q722K	ENST00000336596	NM_005233.5	722	Cag/Aag	13/17	0.246229375841232	3	FACETS	0.658	0.594	0.726	0.329	0.297	0.363	SUBCLONAL	1	TRUE	1	0.399756348059952	3		702	1131	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230848	66230848	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760043343	NA	P-0002153-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	122	718	0	ENST00000273854.3:c.2123C>T	p.Thr708Ile	p.T708I	ENST00000273854	NM_004439.5	708	aCc/aTc	12/18	1	2	FACETS	0.483	0.435	0.534	0.483	0.435	0.534	SUBCLONAL	1	TRUE	1	0.399756348059952	2		718	1263	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439396	149439396	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002153-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	109	537	0	ENST00000286301.3:c.1999T>C	p.Cys667Arg	p.C667R	ENST00000286301	NM_005211.3	667	Tgc/Cgc	15/22	0.182368783391079	0	FACETS	0.415	0.373	0.461			1	INDETERMINATE	1	TRUE	0	0.399756348059952	0		537	788	SUCCESS
BLM	641	MSKCC	GRCh37	15	91328199	91328199	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002153-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	333	590	0	ENST00000355112.3:c.2711T>A	p.Met904Lys	p.M904K	ENST00000355112	NM_000057.2	904	aTg/aAg	14/22	0.243067681039208	3	FACETS	0.759	0.717	0.802	0.759	0.717	0.802	SUBCLONAL	2	TRUE	1	0.399756348059952	3		590	1317	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240279	5240279	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002153-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	333	590	0	ENST00000357368.4:c.1635G>T	p.Trp545Cys	p.W545C	ENST00000357368	NM_002850.3	545	tgG/tgT	12/38	0.266680530185499	3	FACETS	1	0.988	1	0.752	0.714	0.791	CLONAL	2	TRUE	0	0.399756348059952	3		590	886	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684105	29684106	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0002153-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	119	548	0	ENST00000356175.3:c.7804_7805del	p.Leu2602SerfsTer10	p.L2602Sfs*10	ENST00000356175	NM_000267.3	2601	gtTCta/gtta	52/57	0.246229375841232	3	FACETS	0.65	0.585	0.719	0.325	0.292	0.36	SUBCLONAL	1	TRUE	1	0.399756348059952	3		548	1099	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219350	1219363	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCATGCAGGAAA	TGGCATGCAGGAAA	-	novel	NA	P-0002153-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	293	508	0	ENST00000326873.7:c.404_417del	p.Gly135AlafsTer23	p.G135Afs*23	ENST00000326873	NM_000455.4	134	tgTGGCATGCAGGAAAtg/tgtg	3/10	0.266680530185499	3	FACETS	0.983	0.927	1	0.655	0.618	0.693	CLONAL	2	TRUE	0	0.399756348059952	3		508	895	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0002154-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	389	415	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.362484847860758	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.362484847860758	2		415	961	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002154-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	140	265	0	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.362484847860758	2		265	685	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55143638	55143638	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002154-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	97	299	0	ENST00000257290.5:c.1870G>T	p.Val624Phe	p.V624F	ENST00000257290	NM_006206.4	624	Gtt/Ttt	13/23	0.362484847860758	5	FACETS	0.811	0.721	0.907	0.27	0.24	0.303	CLONAL	1	TRUE	2	0.362484847860758	5		299	1019	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041214	29041214	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002154-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1339	620	401	1	ENST00000282397.4:c.214G>T	p.Glu72Ter	p.E72*	ENST00000282397	NM_002019.4	72	Gaa/Taa	3/30	0.362484847860758	6	FACETS	1	0.964	1	1	0.964	1	CLONAL	3	TRUE	3	0.362484847860758	6		402	1959	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937425	76937425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002154-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1279	189	419	0	ENST00000373344.5:c.3323C>T	p.Ser1108Leu	p.S1108L	ENST00000373344	NM_000489.3	1108	tCa/tTa	9/35	0.362484847860758	3	FACETS	0.839	0.773	0.908	0.42	0.386	0.454	CLONAL	1	TRUE	1	0.362484847860758	3		419	1468	SUCCESS
APC	324	MSKCC	GRCh37	5	112116525	112116526	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0002154-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	164	297	0	ENST00000257430.4:c.572_573del	p.Tyr191Ter	p.Y191*	ENST00000257430	NM_000038.5	190	gaATat/gaat	6/16	1	2	FACETS	0.949	0.871	1	0.949	0.871	1	CLONAL	1	TRUE	1	0.362484847860758	2		297	953	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048764	180048764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002161-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	34	545	0	ENST00000261937.6:c.1798G>A	p.Asp600Asn	p.D600N	ENST00000261937	NM_182925.4	600	Gat/Aat	13/30	0.331003367869795	1	FACETS	0.327	0.266	0.395	0.327	0.266	0.395	SUBCLONAL	1	FALSE	0	0.331003367869795	1		545	525	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0002161-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	107	415	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.331003367869795	3	FACETS	0.786	0.704	0.873	0.393	0.352	0.437	SUBCLONAL	1	FALSE	1	0.331003367869795	3		415	959	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0002161-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	286	405	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.331003367869795	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	FALSE	1	0.331003367869795	3		405	851	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920396	134920396	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002161-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	48	642	0	ENST00000398015.3:c.2211G>C	p.Glu737Asp	p.E737D	ENST00000398015	NM_004441.4	737	gaG/gaC	12/16	0.199555551235689	2	FACETS	0.523	0.441	0.612	0.261	0.22	0.306	SUBCLONAL	1	FALSE	0	0.331003367869795	2		642	555	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468063	50468063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002161-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	79	429	1	ENST00000331340.3:c.1298G>A	p.Arg433His	p.R433H	ENST00000331340	NM_006060.4	433	cGc/cAc	8/8	0.331003367869795	6	FACETS	1	0.963	1	0.25	0.22	0.283	CLONAL	1	FALSE	1	0.331003367869795	6		430	634	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541763	187541763	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1240672070	NA	P-0002191-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	242	422	1	ENST00000441802.2:c.5977A>G	p.Thr1993Ala	p.T1993A	ENST00000441802	NM_005245.3	1993	Acc/Gcc	10/27	1	2	FACETS	0.523	0.488	0.559	0.523	0.488	0.559	SUBCLONAL	1	TRUE	1	0.834712872221465	2		423	1109	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434994	56434994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002191-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	186	337	0	ENST00000407977.2:c.2143C>T	p.Pro715Ser	p.P715S	ENST00000407977		715	Cca/Tca	9/10	1	2	FACETS	0.514	0.475	0.555	0.514	0.475	0.555	SUBCLONAL	1	TRUE	1	0.834712872221465	2		337	867	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866393	37866393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002196-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	79	300	1	ENST00000269571.5:c.698C>T	p.Thr233Ile	p.T233I	ENST00000269571		233	aCt/aTt	6/27	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.17	2		301	812	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627361	37627361	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002196-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	103	422	3	ENST00000447079.4:c.1280del	p.Leu427CysfsTer9	p.L427Cfs*9	ENST00000447079	NM_015083.1	426	Ttt/tt	2/14	1	2	FACETS	0.979	0.873	1	0.979	0.873	1	CLONAL	1	TRUE	1	0.17	2		425	1238	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627744	37627744	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002196-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	100	465	0	ENST00000447079.4:c.1661del	p.Leu554CysfsTer56	p.L554Cfs*56	ENST00000447079	NM_015083.1	553	ccT/cc	2/14	1	2	FACETS	0.98	0.873	1	0.98	0.873	1	CLONAL	1	TRUE	1	0.17	2		465	1200	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120612013	120612014	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0002197-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	17	35	2	ENST00000256646.2:c.7_8delinsTT	p.Ala3Phe	p.A3F	ENST00000256646	NM_024408.3	3	GCc/TTc	1/34	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.895888875221782	NA		37	203	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143324171	143324171	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1161782093	NA	P-0002197-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	234	349	0	ENST00000262992.4:c.292T>G	p.Phe98Val	p.F98V	ENST00000262992	NM_001101669.1	98	Ttc/Gtc	5/24	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.895888875221782	2		349	517	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572033	64572033	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002197-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	1135	331	0	ENST00000312049.6:c.1606C>T	p.Gln536Ter	p.Q536*	ENST00000312049	NM_130799.2	536	Cag/Tag	10/10	0.895888875221782	2	FACETS	0.972	0.959	0.984	0.972	0.959	0.984	CLONAL	2	TRUE	0	0.895888875221782	2		331	1304	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604778	48604778	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767383	NA	P-0002197-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	250	382	0	ENST00000342988.3:c.1600C>T	p.Gln534Ter	p.Q534*	ENST00000342988	NM_005359.5	534	Cag/Tag	12/12	0.88363890746985	1	FACETS	0.963	0.928	0.996	0.963	0.928	0.996	CLONAL	1	TRUE	0	0.895888875221782	1		382	320	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0002203-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	112	542	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.125614119301862	6	FACETS	0.907	0.82	0.998	1	0.963	1	CLONAL	5	FALSE	2	0.125614119301862	6		542	492	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0002209-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	32	333	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		333	1004	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0002209-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	48	152	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		152	669	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0002213-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	167	330	2	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	0.251674087330552	2		332	934	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691039	NA	P-0002213-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	88	320	0	ENST00000269305.4:c.919+1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.251674087330552	1	FACETS	0.793	0.702	0.89	0.793	0.702	0.89	SUBCLONAL	1	TRUE	0	0.251674087330552	1		320	771	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0002218-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	434	322	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.454562361012569	4	FACETS	0.957	0.912	1			1	CLONAL	2	TRUE	NA	0.454562361012569	4		322	1451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121912651	NA	P-0002218-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	400	307	1	ENST00000269305.4:c.742C>G	p.Arg248Gly	p.R248G	ENST00000269305	NM_001126112.2	248	Cgg/Ggg	7/11	0.454562361012569	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.454562361012569	2		308	875	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941696	48941696	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002218-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	216	336	0	ENST00000267163.4:c.1010del	p.Leu337TrpfsTer12	p.L337Wfs*12	ENST00000267163	NM_000321.2	336	Ttt/tt	10/27	0.454562361012569	1	FACETS	0.918	0.856	0.982	0.918	0.856	0.982	CLONAL	1	TRUE	0	0.454562361012569	1		336	800	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577505	7577505	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs745425759	NA	P-0002227-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	313	209	0	ENST00000269305.4:c.776A>T	p.Asp259Val	p.D259V	ENST00000269305	NM_001126112.2	259	gAc/gTc	7/11	NA	2	FACETS	0.962	0.914	1			1	INDETERMINATE	2	TRUE	NA	0.45838512666526	2		209	710	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344641	70344641	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs752335726	NA	P-0002227-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	112	448	0	ENST00000374080.3:c.2002A>G	p.Ile668Val	p.I668V	ENST00000374080		668	Att/Gtt	14/45	0.158035771590928	4	FACETS	0.614	0.551	0.682	0.307	0.275	0.341	INDETERMINATE	1	TRUE	2	0.45838512666526	4		448	1160	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245456	153245457	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0002227-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	67	342	0	ENST00000281708.4:c.1734_1735del	p.Gly579AlafsTer25	p.G579Afs*25	ENST00000281708	NM_033632.3	578	acAGgg/acgg	11/12	1	2	FACETS	0.424	0.368	0.485	0.424	0.368	0.485	SUBCLONAL	1	TRUE	1	0.45838512666526	2		342	689	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183867	10183867	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002234-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	201	231	0	ENST00000256474.2:c.336C>A	p.Tyr112Ter	p.Y112*	ENST00000256474	NM_000551.3	112	taC/taA	1/3	0.653992659060997	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.653992659060997	1		231	386	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148529786	148529787	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0002234-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	85	483	0	ENST00000320356.2:c.302_303del	p.Leu101GlnfsTer24	p.L101Qfs*24	ENST00000320356	NM_004456.4	101	cTG/c	4/20	1	2	FACETS	0.89	0.796	0.988	0.89	0.796	0.988	CLONAL	1	TRUE	1	0.653992659060997	2		483	292	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0002237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	241	240	0	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	0.649909577027673	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.653320225912912	1		240	459	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099341	27099341	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	118	296	0	ENST00000324856.7:c.3578A>C	p.Asp1193Ala	p.D1193A	ENST00000324856	NM_006015.4	1193	gAt/gCt	14/20	0.469206623081208	1	FACETS	0.389	0.352	0.429	0.389	0.352	0.429	SUBCLONAL	1	TRUE	0	0.653320225912912	1		296	625	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416462	29416462	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	336	359	0	ENST00000389048.3:c.4491C>G	p.Asn1497Lys	p.N1497K	ENST00000389048	NM_004304.4	1497	aaC/aaG	29/29	0.340220316346655	1	FACETS	0.778	0.739	0.818	0.778	0.739	0.818	INDETERMINATE	1	TRUE	0	0.653320225912912	1		359	890	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456489	32456489	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	39	58	0	ENST00000332351.3:c.403C>G	p.Pro135Ala	p.P135A	ENST00000332351	NM_024426.4	135	Ccg/Gcg	1/10	0.653320225912912	1	FACETS	0.969	0.836	1	0.969	0.836	1	CLONAL	1	TRUE	0	0.653320225912912	1		58	83	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028754	47028754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	148	346	0	ENST00000377604.3:c.58G>A	p.Asp20Asn	p.D20N	ENST00000377604	NM_001204468.1	20	Gac/Aac	3/24	0.241235368936453	0	FACETS	0.213	0.195	0.233			1	INDETERMINATE	1	TRUE	0	0.653320225912912	0		346	736	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243882	41243894	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTTCATCCTCA	CTCTTCATCCTCA	-	novel	NA	P-0002237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	239	256	0	ENST00000357654.3:c.3654_3666del	p.Glu1219PhefsTer12	p.E1219Ffs*12	ENST00000357654	NM_007294.3	1218	agTGAGGATGAAGAG/ag	10/23	0.653320225912912	1	FACETS	0.972	0.918	1	0.972	0.918	1	CLONAL	1	TRUE	0	0.653320225912912	1		256	507	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041720	47041720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002247-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	52	274	0	ENST00000377604.3:c.1945C>T	p.Gln649Ter	p.Q649*	ENST00000377604	NM_001204468.1	649	Caa/Taa	17/24	0.168316576632964	1	FACETS	0.836	0.713	0.972	0.836	0.713	0.972	CLONAL	1	TRUE	0	0.22	1		274	503	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0002247-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	291	371	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.858	0.808	0.909	1	0.996	1	CLONAL	3	TRUE	1	0.22	2		371	1028	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78425878	78425878	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002247-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	33	185	0	ENST00000370768.2:c.1567C>A	p.Pro523Thr	p.P523T	ENST00000370768	NM_003902.3	523	Cct/Act	16/20	1	2	FACETS	0.624	0.507	0.755	0.624	0.507	0.755	SUBCLONAL	1	TRUE	1	0.22	2		185	481	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266831	198266831	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002247-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	66	321	0	ENST00000335508.6:c.2101G>T	p.Val701Phe	p.V701F	ENST00000335508	NM_012433.2	701	Gtt/Ttt	15/25	1	2	FACETS	0.881	0.764	1	0.881	0.764	1	CLONAL	1	TRUE	1	0.22	2		321	681	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267400	198267400	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002247-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	51	351	0	ENST00000335508.6:c.1957A>C	p.Lys653Gln	p.K653Q	ENST00000335508	NM_012433.2	653	Aaa/Caa	14/25	1	2	FACETS	0.675	0.573	0.788	0.675	0.573	0.788	SUBCLONAL	1	TRUE	1	0.22	2		351	687	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014114	70014114	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002247-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	53	376	0	ENST00000394351.3:c.975C>G	p.Ser325Arg	p.S325R	ENST00000394351	NM_000248.3	325	agC/agG	9/9	1	2	FACETS	0.608	0.517	0.708	0.608	0.517	0.708	SUBCLONAL	1	TRUE	1	0.22	2		376	793	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573368	55573368	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002247-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	80	354	0	ENST00000288135.5:c.1030G>C	p.Glu344Gln	p.E344Q	ENST00000288135	NM_000222.2	344	Gaa/Caa	6/21	1	2	FACETS	0.93	0.818	1	0.93	0.818	1	CLONAL	1	TRUE	1	0.22	2		354	782	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549752	187549752	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002247-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	44	395	0	ENST00000441802.2:c.4489A>G	p.Arg1497Gly	p.R1497G	ENST00000441802	NM_005245.3	1497	Aga/Gga	8/27	1	2	FACETS	0.552	0.462	0.653	0.552	0.462	0.653	SUBCLONAL	1	TRUE	1	0.22	2		395	724	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2952953	2952953	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002247-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	27	259	0	ENST00000396946.4:c.2987G>T	p.Gly996Val	p.G996V	ENST00000396946	NM_032415.4	996	gGa/gTa	22/25	NA	2	FACETS	0.535	0.425	0.661			1	INDETERMINATE	1	TRUE	NA	0.22	2		259	459	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484233	8484233	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002247-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	43	374	0	ENST00000356435.5:c.3299C>A	p.Thr1100Lys	p.T1100K	ENST00000356435		1100	aCg/aAg	19/35	1	2	FACETS	0.526	0.439	0.623	0.526	0.439	0.623	SUBCLONAL	1	TRUE	1	0.22	2		374	743	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625090	69625090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554980287	NA	P-0002247-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	31	177	0	ENST00000334134.2:c.703G>A	p.Glu235Lys	p.E235K	ENST00000334134	NM_005247.2	235	Gag/Aag	3/3	1	2	FACETS	0.744	0.602	0.904	0.744	0.602	0.904	CLONAL	1	TRUE	1	0.22	2		177	379	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435598	110435598	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002247-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	17	98	0	ENST00000375856.3:c.2803G>T	p.Ala935Ser	p.A935S	ENST00000375856	NM_003749.2	935	Gcg/Tcg	1/2	1	2	FACETS	0.809	0.606	1	0.809	0.606	1	CLONAL	1	TRUE	1	0.22	2		98	191	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831212	3831212	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002247-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	37	316	2	ENST00000262367.5:c.1669G>A	p.Ala557Thr	p.A557T	ENST00000262367	NM_004380.2	557	Gcc/Acc	7/31	1	2	FACETS	0.573	0.471	0.687	0.573	0.471	0.687	SUBCLONAL	1	TRUE	1	0.22	2		318	587	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778857	76778857	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002247-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	39	427	0	ENST00000373344.5:c.6722T>A	p.Leu2241His	p.L2241H	ENST00000373344	NM_000489.3	2241	cTt/cAt	31/35	0.168316576632964	1	FACETS	0.417	0.345	0.499	0.417	0.345	0.499	SUBCLONAL	1	TRUE	0	0.22	1		427	756	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613424	100613424	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002247-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	62	231	0	ENST00000308731.7:c.976G>T	p.Asp326Tyr	p.D326Y	ENST00000308731	NM_000061.2	326	Gac/Tac	12/19	0.168316576632964	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.22	1		231	462	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615625	100615625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147036606	NA	P-0002247-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	105	465	0	ENST00000308731.7:c.707G>A	p.Arg236Gln	p.R236Q	ENST00000308731	NM_000061.2	236	cGg/cAg	8/19	0.168316576632964	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.22	1		465	795	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123499637	123499637	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs111033630	NA	P-0002247-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	57	350	0	ENST00000371139.4:c.164G>T	p.Arg55Leu	p.R55L	ENST00000371139	NM_001114937.2	55	cGa/cTa	2/4	0.217165434383169	3	FACETS	0.667	0.571	0.773			1	SUBCLONAL	1	TRUE	NA	0.22	3		350	862	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057924	27057924	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002247-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	40	304	0	ENST00000324856.7:c.1636del	p.Gln546ArgfsTer73	p.Q546Rfs*73	ENST00000324856	NM_006015.4	544	caC/ca	3/20	1	2	FACETS	0.629	0.522	0.749	0.629	0.522	0.749	SUBCLONAL	1	TRUE	1	0.22	2		304	578	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546697	9546697	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002247-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	47	319	0	ENST00000353224.5:c.1325del	p.Pro442GlnfsTer36	p.P442Qfs*36	ENST00000353224	NM_177990.2	442	cCa/ca	5/10	1	2	FACETS	0.674	0.568	0.791	0.674	0.568	0.791	SUBCLONAL	1	TRUE	1	0.22	2		319	634	SUCCESS
APC	324	MSKCC	GRCh37	5	112175324	112175324	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1211642532	NA	P-0002251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	39	256	0	ENST00000257430.4:c.4033G>T	p.Glu1345Ter	p.E1345*	ENST00000257430	NM_000038.5	1345	Gaa/Taa	16/16	0.242951975633475	4	FACETS	0.862	0.718	1	0.431	0.359	0.51	INDETERMINATE	1	TRUE	2	0.460815722492806	4		256	287	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467635	66467635	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	46	439	0	ENST00000273854.3:c.634C>A	p.Leu212Ile	p.L212I	ENST00000273854	NM_004439.5	212	Ctt/Att	3/18	0.13751836075389	0	FACETS	0.422	0.358	0.492			1	INDETERMINATE	1	TRUE	0	0.460815722492806	0		439	255	SUCCESS
APC	324	MSKCC	GRCh37	5	112173803	112173803	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0002251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	124	401	0	ENST00000257430.4:c.2512A>T	p.Arg838Ter	p.R838*	ENST00000257430	NM_000038.5	838	Aga/Tga	16/16	0.242951975633475	4	FACETS	1	0.95	1	1	0.95	1	INDETERMINATE	2	TRUE	2	0.460815722492806	4		401	372	SUCCESS
APC	324	MSKCC	GRCh37	5	112175336	112175336	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	37	337	0	ENST00000257430.4:c.4045C>T	p.His1349Tyr	p.H1349Y	ENST00000257430	NM_000038.5	1349	Cac/Tac	16/16	0.242951975633475	4	FACETS	0.82	0.679	0.976	0.41	0.339	0.488	INDETERMINATE	1	TRUE	2	0.460815722492806	4		337	286	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973211	25973211	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1267191288	NA	P-0002277-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	241	294	0	ENST00000435504.4:c.1214del	p.Pro405GlnfsTer18	p.P405Qfs*18	ENST00000435504		405	cCa/ca	12/13	0.736830041435824	1	FACETS	0.965	0.916	1	0.965	0.916	1	CLONAL	1	TRUE	0	0.736830041435824	1		294	428	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0002278-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	129	452	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.239400937519598	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	1	0.239400937519598	4		452	385	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679161	88679161	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002278-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	21	502	0	ENST00000360948.2:c.876G>T	p.Met292Ile	p.M292I	ENST00000360948	NM_001012338.2	292	atG/atT	8/19	0.204732851745205	1	FACETS	0.757	0.586	0.955	0.757	0.586	0.955	CLONAL	1	TRUE	0	0.239400937519598	1		502	204	SUCCESS
AXL	558	MSKCC	GRCh37	19	41736922	41736922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002278-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	31	506	0	ENST00000301178.4:c.637G>A	p.Val213Ile	p.V213I	ENST00000301178	NM_021913.4	213	Gtc/Atc	5/20	1	2	FACETS	1	0.839	1	1	0.839	1	CLONAL	1	TRUE	1	0.239400937519598	2		506	250	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556676	41556676	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002278-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	37	343	0	ENST00000263253.7:c.3621G>C	p.Glu1207Asp	p.E1207D	ENST00000263253	NM_001429.3	1207	gaG/gaC	20/31	0.126611698267104	3	FACETS	1	0.937	1			1	INDETERMINATE	1	TRUE	NA	0.239400937519598	3		343	264	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569808	67569808	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002296-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	100	306	0	ENST00000274335.5:c.469A>C	p.Asn157His	p.N157H	ENST00000274335		157	Aac/Cac	3/15	1	2	FACETS	0.391	0.349	0.437	0.391	0.349	0.437	SUBCLONAL	1	TRUE	1	0.545631226060306	2		306	937	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468308	50468308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1270036178	NA	P-0002296-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	342	227	0	ENST00000331340.3:c.1543C>T	p.Arg515Cys	p.R515C	ENST00000331340	NM_006060.4	515	Cgc/Tgc	8/8	0.545631226060306	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.545631226060306	3		227	748	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242509	55242509	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002296-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	80	270	0	ENST00000275493.2:c.2279T>C	p.Leu760Pro	p.L760P	ENST00000275493	NM_005228.3	760	cTc/cCc	19/28	0.545631226060306	3	FACETS	0.407	0.357	0.461	0.204	0.178	0.231	SUBCLONAL	1	TRUE	1	0.545631226060306	3		270	917	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850907	128850907	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002296-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	226	395	1	ENST00000249373.3:c.1754A>C	p.Gln585Pro	p.Q585P	ENST00000249373	NM_005631.4	585	cAg/cCg	10/12	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.545631226060306	2		396	812	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275815	38275815	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002296-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	281	364	1	ENST00000425967.3:c.1454C>A	p.Thr485Asn	p.T485N	ENST00000425967	NM_001174067.1	485	aCt/aAt	11/19	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.545631226060306	2		365	916	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102094434	102094434	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002296-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	298	448	0	ENST00000282441.5:c.1114C>T	p.Gln372Ter	p.Q372*	ENST00000282441	NM_001130145.2	372	Cag/Tag	7/9	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.545631226060306	2		448	1068	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392119	118392129	+	frameshift_variant	Frame_Shift_Del	DEL	ATTACGACAGC	ATTACGACAGC	-	novel	NA	P-0002296-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	194	267	0	ENST00000534358.1:c.11631_11641del	p.Tyr3877Ter	p.Y3877*	ENST00000534358	NM_005933.3	3877	tATTACGACAGC/t	35/36	1	2	FACETS	0.788	0.73	0.849	0.788	0.73	0.849	SUBCLONAL	1	TRUE	1	0.545631226060306	2		267	902	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955475	48955541	+	frameshift_variant	Frame_Shift_Del	DEL	GTGATCGAAAGTTTTATCAAAGCAGAAGGCAACTTGACAAGAGAAATGATAAAACATTTAGAACGAT	GTGATCGAAAGTTTTATCAAAGCAGAAGGCAACTTGACAAGAGAAATGATAAAACATTTAGAACGAT	-	novel	NA	P-0002296-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	206	445	0	ENST00000267163.4:c.1595_1661del	p.Ile532AsnfsTer57	p.I532Nfs*57	ENST00000267163	NM_000321.2	531	GTGATCGAAAGTTTTATCAAAGCAGAAGGCAACTTGACAAGAGAAATGATAAAACATTTAGAACGATgt/gt	17/27	0.531969394001157	1	FACETS	0.754	0.702	0.808	0.754	0.702	0.808	SUBCLONAL	1	TRUE	0	0.545631226060306	1		445	728	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0002297-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	549	173	221	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.203753204810816	3	FACETS	0.76	0.701	0.82	0.76	0.701	0.82	INDETERMINATE	2	TRUE	1	0.374481066631909	3		221	722	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151921100	151921100	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002297-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	51	11	35	0	ENST00000262189.6:c.3323G>C	p.Arg1108Thr	p.R1108T	ENST00000262189	NM_170606.2	1108	aGa/aCa	20/59	1	2	FACETS	0.948	0.669	1	0.948	0.669	1	CLONAL	1	TRUE	1	0.374481066631909	2		35	62	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945689	151945690	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0002297-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	256	53	192	0	ENST00000262189.6:c.1829_1830del	p.Thr610SerfsTer4	p.T610Sfs*4	ENST00000262189	NM_170606.2	610	aCA/a	14/59	1	2	FACETS	0.916	0.786	1	0.916	0.786	1	CLONAL	1	TRUE	1	0.374481066631909	2		192	309	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0002308-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	195	505	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.25285602465623	3	FACETS	1	0.991	1	0.697	0.651	0.744	INDETERMINATE	1	TRUE	1	0.757532166045571	3		505	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0002308-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	125	366	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.25285602465623	3	FACETS	1	0.95	1	0.53	0.484	0.579	INDETERMINATE	1	TRUE	1	0.757532166045571	3		366	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0002318-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	1175	448	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	NA	2	FACETS	1	0.997	1			1	INDETERMINATE	2	TRUE	NA	0.758575008655874	2		448	1475	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962846	2962846	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002318-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	263	269	0	ENST00000396946.4:c.2062C>T	p.Arg688Ter	p.R688*	ENST00000396946	NM_032415.4	688	Cga/Tga	16/25	0.422227615945816	1	FACETS	0.425	0.398	0.452	0.425	0.398	0.452	INDETERMINATE	1	TRUE	0	0.758575008655874	1		269	1013	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376169	118376169	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002318-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1242	322	313	1	ENST00000534358.1:c.9562C>T	p.Leu3188Phe	p.L3188F	ENST00000534358	NM_005933.3	3188	Ctt/Ttt	27/36	0.287341676291493	1	FACETS	0.337	0.317	0.357	0.337	0.317	0.357	INDETERMINATE	1	TRUE	0	0.758575008655874	1		314	1564	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0002323-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	603	330	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.513160014013281	5	FACETS	1	0.982	1	1	0.982	1	CLONAL	4	TRUE	1	0.527140610776605	5		332	1005	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0002323-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	321	471	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.527140610776605	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.527140610776605	2		471	546	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790038	40790038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757402269	NA	P-0002323-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	600	382	0	ENST00000373198.4:c.2693C>T	p.Thr898Met	p.T898M	ENST00000373198	NM_133170.3	898	aCg/aTg	18/32	0.527140610776605	5	FACETS	1	0.985	1			1	CLONAL	4	TRUE	NA	0.527140610776605	5		382	993	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28931588	NA	P-0002323-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	488	435	0	ENST00000349496.5:c.94G>C	p.Asp32His	p.D32H	ENST00000349496	NM_001904.3	32	Gac/Cac	3/15	0.527140610776605	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.527140610776605	3		435	721	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266679	41266679	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002323-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	393	334	0	ENST00000349496.5:c.476T>C	p.Leu159Pro	p.L159P	ENST00000349496	NM_001904.3	159	cTg/cCg	4/15	0.527140610776605	3	FACETS	0.887	0.859	0.914	1	0.995	1	CLONAL	4	TRUE	0	0.527140610776605	3		334	531	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882084	36882084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002323-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	122	389	0	ENST00000358127.4:c.929C>T	p.Thr310Met	p.T310M	ENST00000358127	NM_001280556.1	310	aCg/aTg	8/10	0.377054375817966	3	FACETS	0.936	0.848	1	0.468	0.424	0.514	CLONAL	1	TRUE	1	0.527140610776605	3		389	625	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247830	59247831	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0002323-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	503	615	0	ENST00000371222.2:c.912_913del	p.Gln304HisfsTer5	p.Q304Hfs*5	ENST00000371222	NM_002228.3	304	caGGtg/catg	1/1	0.312631539663983	3	FACETS	0.881	0.85	0.913	0.881	0.85	0.913	INDETERMINATE	3	TRUE	0	0.527140610776605	3		615	912	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426625	49426625	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002328-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	85	284	0	ENST00000301067.7:c.11863C>G	p.Leu3955Val	p.L3955V	ENST00000301067	NM_003482.3	3955	Cta/Gta	39/54	0.23292496473642	3	FACETS	0.678	0.601	0.76	0.339	0.3	0.38	INDETERMINATE	1	TRUE	1	0.695205247685555	3		284	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0002343-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	350	467	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.446239019536597	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.543197050476643	1		467	713	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0002343-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	192	489	1	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.543197050476643	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.543197050476643	1		490	426	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32971177	32971191	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCTGGTAAGTTAAT	TTCTGGTAAGTTAAT	-	novel	NA	P-0002343-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	159	676	0	ENST00000380152.3:c.9644_9648+10del		p.X3215_splice	ENST00000380152		3215		26/27	0.528534466219633	3	FACETS	1	0.972	1	0.375	0.345	0.407	CLONAL	1	TRUE	0	0.543197050476643	3		676	661	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0002359-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	25	245	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.241	0.189	0.301	0.241	0.189	0.301	SUBCLONAL	1	TRUE	1	0.24	2		245	865	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176104201	176104201	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs766705212	NA	P-0002359-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	63	355	0	ENST00000367669.3:c.913C>A	p.Pro305Thr	p.P305T	ENST00000367669	NM_022457.5	305	Cct/Act	8/20	0.200864504042567	3	FACETS	0.687	0.593	0.79	0.343	0.296	0.395	SUBCLONAL	1	TRUE	1	0.24	3		355	856	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729875	30729875	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1553631693	NA	P-0002359-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	41	235	0	ENST00000295754.5:c.1397-1G>A		p.X466_splice	ENST00000295754	NM_003242.5	466			1	2	FACETS	0.842	0.702	0.996	0.842	0.702	0.996	CLONAL	1	TRUE	1	0.24	2		235	406	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356129	66356129	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002359-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	82	511	0	ENST00000273854.3:c.1368G>T	p.Gln456His	p.Q456H	ENST00000273854	NM_004439.5	456	caG/caT	5/18	1	2	FACETS	0.835	0.736	0.943	0.835	0.736	0.943	CLONAL	1	TRUE	1	0.24	2		511	818	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447041	49447041	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1033142865	NA	P-0002359-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	82	534	0	ENST00000301067.7:c.903C>G	p.Phe301Leu	p.F301L	ENST00000301067	NM_003482.3	301	ttC/ttG	7/54	0.108161888988865	3	FACETS	0.79	0.695	0.892	0.395	0.347	0.446	INDETERMINATE	1	TRUE	1	0.24	3		534	969	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218479	1218479	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0002359-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	68	444	0	ENST00000326873.7:c.354C>G	p.Tyr118Ter	p.Y118*	ENST00000326873	NM_000455.4	118	taC/taG	2/10	0.280847651117931	1	FACETS	0.86	0.748	0.98	0.86	0.748	0.98	CLONAL	1	TRUE	0	0.24	1		444	580	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610150	10610150	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002359-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	79	523	0	ENST00000171111.5:c.560T>A	p.Ile187Asn	p.I187N	ENST00000171111	NM_203500.1	187	aTc/aAc	2/6	0.280847651117931	1	FACETS	0.699	0.614	0.791	0.699	0.614	0.791	SUBCLONAL	1	TRUE	0	0.24	1		523	829	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169566	11169566	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0002359-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	52	368	0	ENST00000358026.2:c.4731+1G>C		p.X1577_splice	ENST00000358026	NM_001128849.1	1577			0.280847651117931	1	FACETS	0.899	0.767	1	0.899	0.767	1	CLONAL	1	TRUE	0	0.24	1		368	424	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224560	53224560	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002359-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	73	689	0	ENST00000375401.3:c.3153G>C	p.Leu1051Phe	p.L1051F	ENST00000375401	NM_004187.3	1051	ttG/ttC	21/26	0.3	1	FACETS	0.586	0.511	0.667	0.586	0.511	0.667	SUBCLONAL	1	TRUE	0	0.24	1		689	914	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0002366-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	255	221	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.932	0.875	0.991	0.932	0.875	0.991	CLONAL	1	TRUE	1	0.63821607253333	2		221	857	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002366-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	405	927	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.63821607253333	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.63821607253333	1		927	822	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292438	15292438	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs908559600	NA	P-0002366-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	88	627	1	ENST00000263388.2:c.2741C>T	p.Pro914Leu	p.P914L	ENST00000263388	NM_000435.2	914	cCa/cTa	17/33	1	2	FACETS	0.335	0.296	0.376	0.335	0.296	0.376	SUBCLONAL	1	TRUE	1	0.63821607253333	2		628	824	SUCCESS
APC	324	MSKCC	GRCh37	5	112178414	112178414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002366-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	97	635	0	ENST00000257430.4:c.7123C>T	p.Gln2375Ter	p.Q2375*	ENST00000257430	NM_000038.5	2375	Caa/Taa	16/16	1	2	FACETS	0.254	0.226	0.285	0.254	0.226	0.285	SUBCLONAL	1	TRUE	1	0.63821607253333	2		635	1196	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176618933	176618933	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002366-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1201	135	847	0	ENST00000439151.2:c.976C>G	p.Leu326Val	p.L326V	ENST00000439151	NM_022455.4	326	Ctc/Gtc	3/23	1	2	FACETS	0.317	0.287	0.348	0.317	0.287	0.348	SUBCLONAL	1	TRUE	1	0.63821607253333	2		847	1336	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056132	26056132	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002366-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	128	646	0	ENST00000343677.2:c.525G>C	p.Lys175Asn	p.K175N	ENST00000343677	NM_005319.3	175	aaG/aaC	1/1	1	2	FACETS	0.391	0.354	0.431	0.391	0.354	0.431	SUBCLONAL	1	TRUE	1	0.63821607253333	2		646	1025	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983974	2983974	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002366-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	89	1099	0	ENST00000396946.4:c.556G>C	p.Glu186Gln	p.E186Q	ENST00000396946	NM_032415.4	186	Gag/Cag	5/25	0.63821607253333	1	FACETS	0.211	0.187	0.238	0.211	0.187	0.238	SUBCLONAL	1	TRUE	0	0.63821607253333	1		1099	898	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115111972	115111972	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002366-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	141	246	0	ENST00000257566.3:c.1768C>T	p.Gln590Ter	p.Q590*	ENST00000257566	NM_016569.3	590	Cag/Tag	7/8	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.63821607253333	2		246	381	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250217	133250217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879254276	NA	P-0002366-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	161	753	1	ENST00000320574.5:c.1303G>A	p.Asp435Asn	p.D435N	ENST00000320574	NM_006231.2	435	Gat/Aat	13/49	0.123253193721006	0	FACETS	0.182	0.167	0.199			1	INDETERMINATE	1	TRUE	0	0.63821607253333	0		754	1001	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148708	20148708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002366-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	101	631	0	ENST00000379607.5:c.355G>A	p.Asp119Asn	p.D119N	ENST00000379607	NM_001412.3	119	Gat/Aat	6/7	0.123253193721006	0	FACETS	0.105	0.094	0.118			1	INDETERMINATE	1	TRUE	0	0.63821607253333	0		631	1086	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756662	756662	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002393-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	187	667	0	ENST00000314574.4:c.166A>G	p.Ser56Gly	p.S56G	ENST00000314574	NM_005433.3	56	Agt/Ggt	2/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.314163256262499	2		667	1021	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696721	176696721	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002393-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	176	465	0	ENST00000439151.2:c.5422del	p.His1808ThrfsTer13	p.H1808Tfs*13	ENST00000439151	NM_022455.4	1808	Cac/ac	16/23	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.314163256262499	2		465	913	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002394-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	197	520	1	ENST00000269305.4:c.880del	p.Glu294SerfsTer51	p.E294Sfs*51	ENST00000269305	NM_001126112.2	294	Gag/ag	8/11	0.29467148133375	1	FACETS	0.877	0.816	0.94	0.877	0.816	0.94	INDETERMINATE	1	TRUE	0	0.511238226175944	1		521	654	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022628	31022628	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002394-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	317	561	0	ENST00000375687.4:c.2113G>T	p.Glu705Ter	p.E705*	ENST00000375687	NM_015338.5	705	Gag/Tag	13/13	0.348882597846157	5	FACETS	0.793	0.747	0.84	0.528	0.498	0.56	SUBCLONAL	2	TRUE	2	0.511238226175944	5		561	1382	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106621	27106621	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002394-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	352	452	0	ENST00000324856.7:c.6232G>T	p.Glu2078Ter	p.E2078*	ENST00000324856	NM_006015.4	2078	Gag/Tag	20/20	0.443213843744589	2	FACETS	0.911	0.869	0.953	0.911	0.869	0.953	CLONAL	2	TRUE	0	0.511238226175944	2		452	756	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462305	89462305	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002394-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	201	418	0	ENST00000336596.2:c.1777C>A	p.Leu593Ile	p.L593I	ENST00000336596	NM_005233.5	593	Ctc/Atc	10/17	0.493923502374282	1	FACETS	0.816	0.759	0.875	0.816	0.759	0.875	CLONAL	1	TRUE	0	0.511238226175944	1		418	717	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494163	140494163	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1469574556	NA	P-0002394-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	194	312	0	ENST00000288602.6:c.1085G>T	p.Arg362Leu	p.R362L	ENST00000288602	NM_004333.4	362	cGa/cTa	8/18	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.511238226175944	2		312	635	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486245	8486245	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs146596907	NA	P-0002394-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	162	418	0	ENST00000356435.5:c.2572C>A	p.Leu858Ile	p.L858I	ENST00000356435		858	Cta/Ata	17/35	0.511238226175944	1	FACETS	0.938	0.867	1	0.938	0.867	1	CLONAL	1	TRUE	0	0.511238226175944	1		418	503	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974724	21974724	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002394-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	177	385	1	ENST00000304494.5:c.103G>T	p.Gly35Trp	p.G35W	ENST00000304494	NM_000077.4	35	Ggg/Tgg	1/3	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.511238226175944	NA		386	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574020	7574020	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002394-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	213	558	0	ENST00000269305.4:c.1007A>G	p.Glu336Gly	p.E336G	ENST00000269305	NM_001126112.2	336	gAg/gGg	10/11	0.29467148133375	1	FACETS	0.846	0.789	0.905	0.846	0.789	0.905	INDETERMINATE	1	TRUE	0	0.511238226175944	1		558	733	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022697	31022697	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002394-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	218	377	0	ENST00000375687.4:c.2182G>A	p.Glu728Lys	p.E728K	ENST00000375687	NM_015338.5	728	Gaa/Aaa	13/13	0.348882597846157	5	FACETS	0.759	0.706	0.814	0.506	0.47	0.543	SUBCLONAL	2	TRUE	2	0.511238226175944	5		377	993	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023105	31023105	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002394-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	296	500	0	ENST00000375687.4:c.2590G>A	p.Asp864Asn	p.D864N	ENST00000375687	NM_015338.5	864	Gac/Aac	13/13	0.348882597846157	5	FACETS	0.811	0.762	0.86	0.54	0.508	0.574	CLONAL	2	TRUE	2	0.511238226175944	5		500	1262	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023347	31023347	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002394-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	220	376	0	ENST00000375687.4:c.2832G>C	p.Leu944Phe	p.L944F	ENST00000375687	NM_015338.5	944	ttG/ttC	13/13	0.348882597846157	5	FACETS	0.767	0.714	0.822	0.511	0.476	0.548	SUBCLONAL	2	TRUE	2	0.511238226175944	5		376	991	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023684	31023684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002394-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	262	481	0	ENST00000375687.4:c.3169G>A	p.Asp1057Asn	p.D1057N	ENST00000375687	NM_015338.5	1057	Gat/Aat	13/13	0.348882597846157	5	FACETS	1	0.992	1	0.486	0.455	0.519	CLONAL	1	TRUE	2	0.511238226175944	5		481	1241	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023740	31023740	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002394-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	208	392	0	ENST00000375687.4:c.3225G>T	p.Lys1075Asn	p.K1075N	ENST00000375687	NM_015338.5	1075	aaG/aaT	13/13	0.348882597846157	5	FACETS	1	0.989	1	0.453	0.42	0.487	CLONAL	1	TRUE	2	0.511238226175944	5		392	1059	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023747	31023747	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002394-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	211	379	0	ENST00000375687.4:c.3232G>C	p.Asp1078His	p.D1078H	ENST00000375687	NM_015338.5	1078	Gat/Cat	13/13	0.348882597846157	5	FACETS	1	0.989	1	0.457	0.424	0.491	CLONAL	1	TRUE	2	0.511238226175944	5		379	1064	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023870	31023870	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002394-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	273	444	0	ENST00000375687.4:c.3355G>C	p.Glu1119Gln	p.E1119Q	ENST00000375687	NM_015338.5	1119	Gag/Cag	13/13	0.348882597846157	5	FACETS	0.778	0.73	0.829	0.519	0.486	0.553	SUBCLONAL	2	TRUE	2	0.511238226175944	5		444	1212	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024074	31024074	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002394-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	274	422	0	ENST00000375687.4:c.3559G>T	p.Gly1187Cys	p.G1187C	ENST00000375687	NM_015338.5	1187	Ggt/Tgt	13/13	0.348882597846157	5	FACETS	0.763	0.715	0.812	0.509	0.477	0.542	SUBCLONAL	2	TRUE	2	0.511238226175944	5		422	1241	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024146	31024146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002394-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	255	456	0	ENST00000375687.4:c.3631G>A	p.Asp1211Asn	p.D1211N	ENST00000375687	NM_015338.5	1211	Gac/Aac	13/13	0.348882597846157	5	FACETS	1	0.991	1	0.452	0.422	0.483	CLONAL	1	TRUE	2	0.511238226175944	5		456	1299	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024197	31024197	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002394-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	262	498	1	ENST00000375687.4:c.3682G>A	p.Glu1228Lys	p.E1228K	ENST00000375687	NM_015338.5	1228	Gaa/Aaa	13/13	0.348882597846157	5	FACETS	1	0.991	1	0.443	0.414	0.473	CLONAL	1	TRUE	2	0.511238226175944	5		499	1362	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024236	31024236	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372409311	NA	P-0002394-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	288	531	0	ENST00000375687.4:c.3721G>A	p.Glu1241Lys	p.E1241K	ENST00000375687	NM_015338.5	1241	Gaa/Aaa	13/13	0.348882597846157	5	FACETS	1	0.993	1	0.492	0.462	0.523	CLONAL	1	TRUE	2	0.511238226175944	5		531	1349	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31025054	31025054	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002394-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	232	350	0	ENST00000375687.4:c.4539G>T	p.Met1513Ile	p.M1513I	ENST00000375687	NM_015338.5	1513	atG/atT	13/13	0.348882597846157	5	FACETS	1	0.99	1	0.461	0.429	0.494	CLONAL	1	TRUE	2	0.511238226175944	5		350	1160	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579585	7579585	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002394-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	71	328	0	ENST00000269305.4:c.102del	p.Leu35CysfsTer9	p.L35Cfs*9	ENST00000269305	NM_001126112.2	34	ccC/cc	4/11	0.29467148133375	1	FACETS	0.41	0.359	0.466	0.41	0.359	0.466	INDETERMINATE	1	TRUE	0	0.511238226175944	1		328	504	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0002414-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	903	278	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.675828774909495	3	FACETS	0.885	0.865	0.906			1	CLONAL	3	TRUE	NA	0.675828774909495	3		278	1346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0002414-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	339	452	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.52438916853257	2	FACETS	1	0.995	1	0.731	0.697	0.765	CLONAL	1	TRUE	0	0.675828774909495	2		452	686	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0002414-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	205	312	1	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	0.399502190382754	3	FACETS	1	0.974	1	0.548	0.51	0.588	INDETERMINATE	1	TRUE	1	0.675828774909495	3		313	740	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562746	29562746	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs199474742	NA	P-0002414-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	211	540	1	ENST00000356175.3:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000356175	NM_000267.3	1276	Cga/Tga	28/57	0.5266475605203	3	FACETS	0.768	0.713	0.825	0.384	0.356	0.413	SUBCLONAL	1	TRUE	1	0.675828774909495	3		541	1088	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482847	67482847	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002414-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	479	366	0	ENST00000327367.4:c.1252del	p.Ser418AlafsTer58	p.S418Afs*58	ENST00000327367	NM_005902.3	417	ccA/cc	9/9	0.500076767855852	3	FACETS	1	0.996	1	0.832	0.804	0.859	CLONAL	2	TRUE	0	0.675828774909495	3		366	760	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954198	48954198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123331	NA	P-0002430-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	134	434	0	ENST00000267163.4:c.1399C>T	p.Arg467Ter	p.R467*	ENST00000267163	NM_000321.2	467	Cga/Tga	15/27	0.3	2	FACETS	1	0.912	1			1	CLONAL	1	TRUE	NA	0.25	2		434	1066	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814144	76814144	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002430-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	138	595	0	ENST00000373344.5:c.6500C>A	p.Ala2167Asp	p.A2167D	ENST00000373344	NM_000489.3	2167	gCt/gAt	29/35	0.105440855178993	0	FACETS	0.716	0.65	0.786			1	INDETERMINATE	1	TRUE	0	0.25	0		595	1156	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0002433-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	166	542	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.758	0.699	0.82	1	0.989	1	SUBCLONAL	2	TRUE	1	0.32285528891682	2		542	678	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0002433-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	195	378	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.312539548327447	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	0	0.32285528891682	2		378	601	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295773	212295773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1299031105	NA	P-0002433-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	154	386	1	ENST00000342788.4:c.2540G>A	p.Arg847His	p.R847H	ENST00000342788	NM_005235.2	847	cGt/cAt	21/28	0.32285528891682	6	FACETS	0.849	0.776	0.924			1	CLONAL	2	TRUE	NA	0.32285528891682	6		387	925	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057979	27057979	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002433-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	101	261	1	ENST00000324856.7:c.1687C>T	p.Gln563Ter	p.Q563*	ENST00000324856	NM_006015.4	563	Cag/Tag	3/20	1	2	FACETS	0.93	0.832	1	0.93	0.832	1	CLONAL	1	TRUE	1	0.32285528891682	2		262	673	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085668	16085668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002433-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	153	325	0	ENST00000281043.3:c.844G>A	p.Val282Met	p.V282M	ENST00000281043	NM_005378.4	282	Gtg/Atg	3/3	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.32285528891682	2		325	725	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047001	128047001	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002433-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	183	442	0	ENST00000285398.2:c.734C>T	p.Pro245Leu	p.P245L	ENST00000285398	NM_000122.1	245	cCc/cTc	6/15	0.32285528891682	4	FACETS	0.866	0.8	0.935			1	CLONAL	2	TRUE	NA	0.32285528891682	4		442	866	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894993	101894993	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0002433-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	185	424	0	ENST00000374994.4:c.546T>A	p.Tyr182Ter	p.Y182*	ENST00000374994	NM_004612.2	182	taT/taA	3/9	0.275383566359619	2	FACETS	0.904	0.838	0.971	0.904	0.838	0.971	CLONAL	2	TRUE	0	0.32285528891682	2		424	634	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424729	49424729	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002433-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	142	370	1	ENST00000301067.7:c.13618C>G	p.Arg4540Gly	p.R4540G	ENST00000301067	NM_003482.3	4540	Cgg/Ggg	40/54	0.32285528891682	3	FACETS	1	0.964	1	0.556	0.507	0.609	CLONAL	1	TRUE	1	0.32285528891682	3		371	918	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603039	48603039	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002433-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	222	268	0	ENST00000342988.3:c.1340T>A	p.Met447Lys	p.M447K	ENST00000342988	NM_005359.5	447	aTg/aAg	11/12	0.275383566359619	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.32285528891682	2		268	642	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853780	59853781	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0002433-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1237	83	469	0	ENST00000259008.2:c.2078_2079del	p.Cys693PhefsTer23	p.C693Ffs*23	ENST00000259008	NM_032043.2	693	tGT/t	14/20	0.32285528891682	9	FACETS	0.83	0.729	0.938			1	CLONAL	1	TRUE	NA	0.32285528891682	9		469	1320	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061191	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs879499034	NA	P-0002439-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	37	222	0	ENST00000250448.2:c.798C>A	p.Phe266Leu	p.F266L	ENST00000250448	NM_004496.3	266	ttC/ttA	2/2	1	2	FACETS	0.736	0.61	0.877	0.736	0.61	0.877	SUBCLONAL	1	TRUE	1	0.347686256090458	2		222	289	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42840410	42840411	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0002439-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	51	362	0	ENST00000398585.3:c.1337_1338del	p.Arg446MetfsTer8	p.R446Mfs*8	ENST00000398585	NM_001135099.1	446	aGA/a	12/14	1	2	FACETS	0.567	0.482	0.661	0.567	0.482	0.661	SUBCLONAL	1	TRUE	1	0.347686256090458	2		362	517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0002449-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	664	415	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.912824835032746	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.912824835032746	1		415	790	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843535	156843535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369367198	NA	P-0002449-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	149	309	0	ENST00000524377.1:c.961G>A	p.Val321Met	p.V321M	ENST00000524377	NM_002529.3	321	Gtg/Atg	8/17	0.912824835032746	1	FACETS	0.269	0.246	0.293	0.269	0.246	0.293	SUBCLONAL	1	TRUE	0	0.912824835032746	1		309	659	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514536	41514536	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002493-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	32	294	0	ENST00000373198.4:c.125G>T	p.Gly42Val	p.G42V	ENST00000373198	NM_133170.3	42	gGt/gTt	2/32	0.459173629599416	3	FACETS	0.363	0.295	0.441	0.182	0.147	0.221	SUBCLONAL	1	TRUE	1	0.552673968166904	3		294	407	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266073	41266108	+	inframe_deletion	In_Frame_Del	DEL	CACTGGCAGCAACAGTCTTACCTGGACTCTGGAATC	CACTGGCAGCAACAGTCTTACCTGGACTCTGGAATC	-	novel	NA	P-0002493-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	67	327	0	ENST00000349496.5:c.72_107del	p.Trp25_His36del	p.W25_H36del	ENST00000349496	NM_001904.3	24	CACTGGCAGCAACAGTCTTACCTGGACTCTGGAATC/-	3/15	1	2	FACETS	0.662	0.579	0.752	0.662	0.579	0.752	SUBCLONAL	1	TRUE	1	0.552673968166904	2		327	366	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0002506-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	40	62	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.169531684212035	3	FACETS	0.603	0.5	0.717	0.301	0.25	0.359	SUBCLONAL	1	TRUE	1	0.26	3		62	577	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0002506-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	219	525	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.270367144918342	4	FACETS	1	0.947	1	0.681	0.633	0.73	CLONAL	2	TRUE	1	0.26	4		525	1039	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0002506-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	59	232	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	1	2	FACETS	0.871	0.75	1	0.871	0.75	1	CLONAL	1	TRUE	1	0.26	2		232	521	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098328	47098328	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs771957568	NA	P-0002506-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	50	323	0	ENST00000409792.3:c.6946A>G	p.Thr2316Ala	p.T2316A	ENST00000409792	NM_014159.6	2316	Act/Gct	15/21	1	2	FACETS	0.527	0.446	0.616	0.527	0.446	0.616	SUBCLONAL	1	TRUE	1	0.26	2		323	730	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0002520-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	8	467	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.054	0.034	0.08	0.054	0.034	0.08	SUBCLONAL	1	TRUE	1	0.83	2		467	357	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0002530-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	579	934	282	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.455033140197378	11	FACETS	1	0.991	1			1	CLONAL	8	TRUE	NA	0.455033140197378	11		283	1513	SUCCESS
ALK	238	MSKCC	GRCh37	2	29541244	29541244	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002530-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	482	117	319	0	ENST00000389048.3:c.1573G>T	p.Asp525Tyr	p.D525Y	ENST00000389048	NM_004304.4	525	Gat/Tat	8/29	0.455033140197378	3	FACETS	1	0.94	1	0.527	0.476	0.58	CLONAL	1	TRUE	1	0.455033140197378	3		319	599	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772286	68772286	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002530-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	255	239	390	0	ENST00000261769.5:c.136del	p.Leu46TrpfsTer10	p.L46Wfs*10	ENST00000261769	NM_004360.3	45	caC/ca	2/16	0.448006784260591	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.455033140197378	2		390	494	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443609	52443620	+	inframe_deletion	In_Frame_Del	DEL	TGCACCCCCTTG	TGCACCCCCTTG	-	novel	NA	P-0002532-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	69	324	1	ENST00000460680.1:c.72_83del	p.Lys25_Gln28del	p.K25_Q28del	ENST00000460680	NM_004656.3	24	gtCAAGGGGGTGCAa/gta	3/17	0.321501246067627	3	FACETS	0.949	0.845	1	1	0.976	1	CLONAL	3	TRUE	1	0.321501246067627	3		325	175	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750271	133750271	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002555-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	106	345	0	ENST00000318560.5:c.1102A>G	p.Asn368Asp	p.N368D	ENST00000318560	NM_005157.4	368	Aac/Gac	7/11	1	2	FACETS	0.388	0.347	0.43	0.388	0.347	0.43	SUBCLONAL	1	TRUE	1	0.74	2		345	739	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0002565-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	111	542	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	0.919	0.831	1			1	INDETERMINATE	2	TRUE	NA	0.272739899102729	2		542	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0002565-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	249	415	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.247166856251876	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.272739899102729	2		415	863	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391214	89391214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs530556931	NA	P-0002565-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	48	243	0	ENST00000336596.2:c.1280C>T	p.Ala427Val	p.A427V	ENST00000336596	NM_005233.5	427	gCg/gTg	5/17	0.156953699487263	2	FACETS	1	0.941	1	0.613	0.522	0.713	INDETERMINATE	1	TRUE	0	0.272739899102729	2		243	287	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607555	43607555	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201553718	NA	P-0002565-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	102	326	0	ENST00000355710.3:c.1531G>A	p.Glu511Lys	p.E511K	ENST00000355710	NM_020975.4	511	Gag/Aag	8/20	0.272739899102729	5	FACETS	0.817	0.732	0.907	0.545	0.488	0.605	CLONAL	2	TRUE	2	0.272739899102729	5		326	645	SUCCESS
APC	324	MSKCC	GRCh37	5	112175651	112175651	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002565-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	95	478	0	ENST00000257430.4:c.4364del	p.Asn1455IlefsTer18	p.N1455Ifs*18	ENST00000257430	NM_000038.5	1454	Aaa/aa	16/16	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.272739899102729	2		478	478	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0002570-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	268	542	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.285809216627311	3	FACETS	0.861	0.813	0.911	0.861	0.813	0.911	INDETERMINATE	2	TRUE	1	0.575785558093219	3		542	696	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0002570-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	114	129	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.575785558093219	2	FACETS	1	0.983	1	0.664	0.607	0.723	CLONAL	1	TRUE	0	0.575785558093219	2		129	298	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0002571-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	286	408	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.571751861031035	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.571751861031035	1		408	669	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602581	10602581	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002571-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	247	433	0	ENST00000171111.5:c.997G>T	p.Gly333Cys	p.G333C	ENST00000171111	NM_203500.1	333	Ggc/Tgc	3/6	0.555671832241408	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.571751861031035	1		433	563	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465394	120465394	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002571-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	86	252	0	ENST00000256646.2:c.4867G>T	p.Val1623Phe	p.V1623F	ENST00000256646	NM_024408.3	1623	Gtc/Ttc	27/34	0.292249318096334	1	FACETS	0.505	0.449	0.565	0.505	0.449	0.565	INDETERMINATE	1	TRUE	0	0.571751861031035	1		252	425	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911589	134911589	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002571-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	228	456	0	ENST00000398015.3:c.2054G>T	p.Gly685Val	p.G685V	ENST00000398015	NM_004441.4	685	gGt/gTt	11/16	0.318671022021235	1	FACETS	0.785	0.734	0.836	0.785	0.734	0.836	INDETERMINATE	1	TRUE	0	0.571751861031035	1		456	726	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056022	26056022	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002571-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	209	402	0	ENST00000343677.2:c.635A>T	p.Lys212Met	p.K212M	ENST00000343677	NM_005319.3	212	aAg/aTg	1/1	0.571751861031035	3	FACETS	1	0.955	1	0.519	0.482	0.557	CLONAL	1	TRUE	1	0.571751861031035	3		402	906	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662368	117662368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002571-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	279	531	0	ENST00000368508.3:c.5009C>T	p.Thr1670Ile	p.T1670I	ENST00000368508	NM_002944.2	1670	aCt/aTt	30/43	0.571751861031035	1	FACETS	0.952	0.899	1	0.952	0.899	1	CLONAL	1	TRUE	0	0.571751861031035	1		531	732	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508721	106508721	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002571-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	223	453	0	ENST00000359195.3:c.715G>C	p.Asp239His	p.D239H	ENST00000359195	NM_002649.2	239	Gac/Cac	2/11	1	2	FACETS	0.914	0.853	0.978	0.914	0.853	0.978	CLONAL	1	TRUE	1	0.571751861031035	2		453	853	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220578	1220578	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1131690934	NA	P-0002571-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	156	386	0	ENST00000326873.7:c.598-2A>G		p.X200_splice	ENST00000326873	NM_000455.4	200			0.555671832241408	1	FACETS	0.939	0.869	1	0.939	0.869	1	CLONAL	1	TRUE	0	0.571751861031035	1		386	415	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29422343	29422343	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002571-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	147	348	0	ENST00000356175.3:c.17del	p.Pro6ArgfsTer18	p.P6Rfs*18	ENST00000356175	NM_000267.3	6	Ccg/cg	1/57	0.571751861031035	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.571751861031035	1		348	347	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115823	8115823	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002574-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	52	387	0	ENST00000346208.3:c.1169C>A	p.Ser390Ter	p.S390*	ENST00000346208		390	tCg/tAg	6/6	0.425020045707585	4	FACETS	0.455	0.387	0.529			1	INDETERMINATE	1	TRUE	NA	0.813468205010884	4		387	510	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433950	49433950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780306423	NA	P-0002574-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	99	212	0	ENST00000301067.7:c.7603C>T	p.Arg2535Cys	p.R2535C	ENST00000301067	NM_003482.3	2535	Cgt/Tgt	31/54	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.813468205010884	2		212	203	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493621	56493621	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs1343971705	NA	P-0002574-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	92	283	0	ENST00000267101.3:c.2938-1G>T		p.X980_splice	ENST00000267101	NM_001982.3	980			0.26131156686442	4	FACETS	0.862	0.779	0.946	0.862	0.779	0.946	INDETERMINATE	2	TRUE	2	0.813468205010884	4		283	238	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0002580-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	143	320	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.463183162328204	4	FACETS	0.909	0.827	0.994	0.454	0.413	0.497	CLONAL	1	TRUE	2	0.464164694955041	4		320	993	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0002580-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	222	525	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.463183162328204	4	FACETS	0.884	0.825	0.945	0.884	0.825	0.945	CLONAL	2	TRUE	2	0.464164694955041	4		525	792	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282211	38282211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793120	NA	P-0002590-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	273	240	0	ENST00000425967.3:c.845C>T	p.Ser282Phe	p.S282F	ENST00000425967	NM_001174067.1	282	tCc/tTc	8/19	0.456819553114031	6	FACETS	1	0.951	1	1	0.951	1	INDETERMINATE	3	TRUE	3	0.796380828368704	6		240	590	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550488	29550488	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs199474760	NA	P-0002590-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	131	393	0	ENST00000356175.3:c.1748A>G	p.Lys583Arg	p.K583R	ENST00000356175	NM_000267.3	583	aAg/aGg	16/57	0.796380828368704	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.796380828368704	1		393	179	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315338	30315338	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002590-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	124	308	0	ENST00000322652.5:c.1024-1G>A		p.X342_splice	ENST00000322652	NM_015355.2	342			0.796380828368704	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.796380828368704	1		308	176	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357153	70357153	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002590-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	224	274	0	ENST00000374080.3:c.5670del	p.Ser1891ProfsTer40	p.S1891Pfs*40	ENST00000374080		1890	Ccc/cc	39/45	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.796380828368704	1		274	267	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0002601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	36	100	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.413399120041414	3	FACETS	0.973	0.821	1	0.649	0.547	0.756	CLONAL	2	FALSE	0	0.413399120041414	3		100	108	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231764	66231764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	17	363	0	ENST00000273854.3:c.1936G>A	p.Gly646Arg	p.G646R	ENST00000273854	NM_004439.5	646	Gga/Aga	11/18	0.199759684350465	2	FACETS	0.409	0.306	0.531	0.205	0.153	0.266	INDETERMINATE	1	FALSE	0	0.413399120041414	2		363	201	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87367001	87367001	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0002601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	26	422	3	ENST00000277120.3:c.1396+1G>T		p.X466_splice	ENST00000277120		466			0.318163176512239	4	FACETS	0.859	0.684	1	0.429	0.342	0.528	CLONAL	1	FALSE	2	0.413399120041414	4		425	207	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578412	7578412	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519747	NA	P-0002601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	135	339	0	ENST00000269305.4:c.518T>C	p.Val173Ala	p.V173A	ENST00000269305	NM_001126112.2	173	gTg/gCg	5/11	0.404177363100113	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	3	FALSE	0	0.413399120041414	3		339	247	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432664	29432664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113994087	NA	P-0121427-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	280	236	0	ENST00000389048.3:c.3824G>A	p.Arg1275Gln	p.R1275Q	ENST00000389048	NM_004304.4	1275	cGa/cAa	25/29	0.594252019162626	3	FACETS	1	0.982	1	0.716	0.68	0.752	CLONAL	2	NA	0	0.594252019162626	3		236	569	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0002615-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	103	294	1	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.793514741871804	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.793514741871804	1		295	155	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018264	48018264	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0002615-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	118	239	0	ENST00000234420.5:c.457+2T>G		p.X153_splice	ENST00000234420	NM_000179.2	153			0.226666620045427	3	FACETS	0.753	0.691	0.815	0.753	0.691	0.815	INDETERMINATE	2	TRUE	1	0.793514741871804	3		239	276	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183776	10183777	+	missense_variant	Missense_Mutation	DNP	GC	GC	CT	novel	NA	P-0002615-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	102	314	1	ENST00000256474.2:c.245_246delinsCT	p.Arg82Pro	p.R82P	ENST00000256474	NM_000551.3	82	cGC/cCT	1/3	0.793514741871804	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.793514741871804	1		315	153	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508709	38508709	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002615-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	162	360	0	ENST00000254066.5:c.757A>G	p.Thr253Ala	p.T253A	ENST00000254066	NM_000964.3	253	Acc/Gcc	6/9	0.226666620045427	3	FACETS	0.779	0.725	0.834	0.779	0.725	0.834	INDETERMINATE	2	TRUE	1	0.793514741871804	3		360	366	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-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	118	311	0	ENST00000460680.1:c.1250_1250+13del		p.X417_splice	ENST00000460680	NM_004656.3	417		12/17	0.793514741871804	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.793514741871804	1		311	173	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235296	235296	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002615-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	89	252	0	ENST00000264932.6:c.1102C>G	p.Leu368Val	p.L368V	ENST00000264932	NM_004168.2	368	Ctg/Gtg	9/15	NA	2	FACETS	0.955	0.861	1			1	INDETERMINATE	1	TRUE	NA	0.793514741871804	2		252	235	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41905026	41905026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374294883	NA	P-0002615-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	185	347	1	ENST00000372991.4:c.521G>A	p.Arg174Gln	p.R174Q	ENST00000372991	NM_001760.3	174	cGa/cAa	3/5	0.760915787752456	3	FACETS	0.764	0.714	0.815	0.51	0.476	0.543	SUBCLONAL	2	TRUE	0	0.793514741871804	3		348	426	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874314	76874314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002619-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	90	411	0	ENST00000373344.5:c.5408G>A	p.Arg1803His	p.R1803H	ENST00000373344	NM_000489.3	1803	cGt/cAt	21/35	1	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.307427007194238	1		411	343	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772294	68772303	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGCCGCGT	GAGGCCGCGT	-	novel	NA	P-0002619-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	32	426	0	ENST00000261769.5:c.143_152del	p.Arg48ThrfsTer5	p.R48Tfs*5	ENST00000261769	NM_004360.3	48	aGAGGCCGCGTc/ac	2/16	0.307427007194238	1	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	0	0.307427007194238	1		426	154	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	463397	463397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002620-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	97	285	0	ENST00000399788.2:c.874G>A	p.Asp292Asn	p.D292N	ENST00000399788	NM_001042603.1	292	Gat/Aat	8/28	0.852297996552026	3	FACETS	0.253	0.224	0.284			1	SUBCLONAL	1	TRUE	NA	0.895105604697642	3		285	1240	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888199	112888199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918454	NA	P-0002620-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	148	310	0	ENST00000351677.2:c.215C>T	p.Ala72Val	p.A72V	ENST00000351677	NM_002834.3	72	gCc/gTc	3/16	1	2	FACETS	0.365	0.333	0.399	0.365	0.333	0.399	SUBCLONAL	1	TRUE	1	0.895105604697642	2		310	905	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888211	112888211	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121918465	NA	P-0002620-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	110	306	0	ENST00000351677.2:c.227A>G	p.Glu76Gly	p.E76G	ENST00000351677	NM_002834.3	76	gAg/gGg	3/16	1	2	FACETS	0.274	0.246	0.305	0.274	0.246	0.305	SUBCLONAL	1	TRUE	1	0.895105604697642	2		306	896	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045524	47045524	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002620-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	83	116	0	ENST00000377604.3:c.2491C>T	p.Pro831Ser	p.P831S	ENST00000377604	NM_001204468.1	831	Cca/Tca	22/24	1	1	FACETS	0.347	0.31	0.387	0.347	0.31	0.387	SUBCLONAL	1	TRUE	0	0.895105604697642	1		116	295	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164637	47164643	+	frameshift_variant	Frame_Shift_Del	DEL	TTTTACA	TTTTACA	-	novel	NA	P-0002620-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	366	272	0	ENST00000409792.3:c.1483_1489del	p.Cys495LeufsTer6	p.C495Lfs*6	ENST00000409792	NM_014159.6	495	TGTAAAAct/ct	3/21	1	2	FACETS	0.931	0.887	0.976	0.931	0.887	0.976	CLONAL	1	TRUE	1	0.895105604697642	2		272	878	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038884	12038884	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002620-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	118	309	0	ENST00000396373.4:c.1180del	p.Met394CysfsTer11	p.M394Cfs*11	ENST00000396373	NM_001987.4	393	Aaa/aa	7/8	0.865642145482771	3	FACETS	0.297	0.267	0.33	0.149	0.133	0.165	SUBCLONAL	1	TRUE	1	0.895105604697642	3		309	1283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0002629-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	21	230	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	1	2	FACETS	0.234	0.179	0.299	0.234	0.179	0.299	SUBCLONAL	1	TRUE	1	0.28	2		230	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934571	NA	P-0002629-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	21	228	0	ENST00000269305.4:c.747G>C	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agC	7/11	1	2	FACETS	0.236	0.181	0.301	0.236	0.181	0.301	SUBCLONAL	1	TRUE	1	0.28	2		228	636	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519896	NA	P-0002636-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	11	336	0	ENST00000281708.4:c.1514G>A	p.Arg505His	p.R505H	ENST00000281708	NM_033632.3	505	cGc/cAc	10/12	0.65729305398344	2	FACETS	0.063	0.043	0.088	0.031	0.021	0.044	SUBCLONAL	1	TRUE	0	0.718922923165539	2		336	487	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0002645-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	1002	520	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.34995231952872	6	FACETS	0.985	0.963	1			1	CLONAL	5	TRUE	NA	0.581477685720123	6		520	1513	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0002645-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	186	505	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.580781807238165	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.581477685720123	1		505	427	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015054	37015054	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374738065	NA	P-0002645-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	162	375	0	ENST00000358127.4:c.350G>A	p.Arg117Gln	p.R117Q	ENST00000358127	NM_001280556.1	117	cGg/cAg	3/10	0.580781807238165	1	FACETS	0.939	0.871	1	0.939	0.871	1	CLONAL	1	TRUE	0	0.581477685720123	1		375	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0002651-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	168	333	0	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	0.443162997707965	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.443162997707965	1		333	516	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540140	187540140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002651-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	183	410	2	ENST00000441802.2:c.7600G>A	p.Asp2534Asn	p.D2534N	ENST00000441802	NM_005245.3	2534	Gac/Aac	10/27	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.443162997707965	2		412	719	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549458	187549458	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002651-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	132	337	0	ENST00000441802.2:c.4660G>C	p.Asp1554His	p.D1554H	ENST00000441802	NM_005245.3	1554	Gac/Cac	9/27	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.443162997707965	2		337	580	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417398	139417398	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1317233337	NA	P-0002651-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	111	261	0	ENST00000277541.6:c.646G>C	p.Glu216Gln	p.E216Q	ENST00000277541	NM_017617.3	216	Gag/Cag	4/34	0.443162997707965	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	0	0.443162997707965	1		261	389	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342821	118342821	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002651-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	75	296	0	ENST00000534358.1:c.947C>G	p.Ser316Trp	p.S316W	ENST00000534358	NM_005933.3	316	tCg/tGg	3/36	0.208582419327447	1	FACETS	0.521	0.457	0.589	0.521	0.457	0.589	INDETERMINATE	1	TRUE	0	0.443162997707965	1		296	506	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243482	41243482	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002651-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	167	409	0	ENST00000357654.3:c.4066C>G	p.Gln1356Glu	p.Q1356E	ENST00000357654	NM_007294.3	1356	Caa/Gaa	10/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.443162997707965	2		409	673	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942065	17942065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1186986948	NA	P-0002651-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	59	329	0	ENST00000458235.1:c.2950C>T	p.Arg984Cys	p.R984C	ENST00000458235	NM_000215.3	984	Cgc/Tgc	21/24	1	2	FACETS	0.49	0.422	0.565	0.49	0.422	0.565	SUBCLONAL	1	TRUE	1	0.443162997707965	2		329	543	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217288	66217297	+	frameshift_variant	Frame_Shift_Del	DEL	TGAATCACAG	TGAATCACAG	-	novel	NA	P-0002651-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	70	204	0	ENST00000273854.3:c.2318_2327del	p.Thr773SerfsTer6	p.T773Sfs*6	ENST00000273854	NM_004439.5	773	aCTGTGATTCAg/ag	14/18	1	2	FACETS	0.708	0.62	0.804	0.708	0.62	0.804	SUBCLONAL	1	TRUE	1	0.443162997707965	2		204	446	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483145	29483145	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs886039548	NA	P-0002656-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	20	258	0	ENST00000356175.3:c.204+1G>A		p.X68_splice	ENST00000356175	NM_000267.3	68			0.248505223844254	2	FACETS	0.513	0.392	0.654	0.256	0.196	0.327	SUBCLONAL	1	TRUE	0	0.248505223844254	2		258	314	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939337	76939337	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002656-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	31	448	0	ENST00000373344.5:c.1411del	p.Ser471ValfsTer43	p.S471Vfs*43	ENST00000373344	NM_000489.3	471	Agt/gt	9/35	0.248505223844254	0	FACETS	0.411	0.332	0.501			1	SUBCLONAL	1	TRUE	0	0.248505223844254	0		448	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0002663-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	61	215	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.3	1	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	0	0.31	1		215	322	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0002663-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	153	320	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.278398907508113	2	FACETS	0.839	0.771	0.91	0.839	0.771	0.91	CLONAL	2	TRUE	0	0.31	2		320	588	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164268	47164268	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002663-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	76	309	0	ENST00000409792.3:c.1858C>T	p.Arg620Ter	p.R620*	ENST00000409792	NM_014159.6	620	Cga/Tga	3/21	1	2	FACETS	0.934	0.821	1	0.934	0.821	1	CLONAL	1	TRUE	1	0.31	2		309	525	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355867	73355867	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002663-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	59	228	0	ENST00000377767.4:c.104G>C	p.Gly35Ala	p.G35A	ENST00000377767	NM_014953.3	35	gGg/gCg	1/21	1	2	FACETS	0.803	0.692	0.923	0.803	0.692	0.923	CLONAL	1	TRUE	1	0.31	2		228	474	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677834	47677834	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002663-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	77	266	0	ENST00000347630.2:c.1031C>T	p.Ser344Leu	p.S344L	ENST00000347630	NM_001007230.1	344	tCa/tTa	11/11	0.29528357155821	3	FACETS	0.873	0.767	0.988	0.291	0.255	0.33	CLONAL	1	TRUE	0	0.31	3		266	657	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023553	27023557	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCC	GCGCC	-	novel	NA	P-0002663-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	92	225	0	ENST00000324856.7:c.659_663del	p.Ser220IlefsTer178	p.S220Ifs*178	ENST00000324856	NM_006015.4	220	aGCGCC/a	1/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.31	2		225	462	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183640	10183654	+	inframe_deletion	In_Frame_Del	DEL	GAGTCCGGCCCGGAA	GAGTCCGGCCCGGAA	-	rs863224839	NA	P-0002663-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	58	305	0	ENST00000256474.2:c.123_137del	p.Ser43_Glu47del	p.S43_E47del	ENST00000256474	NM_000551.3	37	GAGTCCGGCCCGGAA/-	1/3	1	2	FACETS	0.711	0.612	0.82	0.711	0.612	0.82	SUBCLONAL	1	TRUE	1	0.31	2		305	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0002664-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	289	428	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.620959695979376	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.662308130235364	1		428	581	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0002664-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	143	95	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.658271834699122	2	FACETS	0.986	0.927	1	0.986	0.927	1	CLONAL	2	TRUE	0	0.662308130235364	2		95	219	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928068	178928068	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002664-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	211	186	1	ENST00000263967.3:c.1346C>G	p.Pro449Arg	p.P449R	ENST00000263967	NM_006218.2	449	cCt/cGt	8/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.662308130235364	2		187	604	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135780967	135780967	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs118203610	NA	P-0002664-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	203	266	0	ENST00000298552.3:c.1997+1G>A		p.X666_splice	ENST00000298552	NM_001162426.1	666			1	2	FACETS	0.967	0.901	1	0.967	0.901	1	CLONAL	1	TRUE	1	0.662308130235364	2		266	634	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354330	354330	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002664-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	240	268	1	ENST00000262320.3:c.1228G>T	p.Glu410Ter	p.E410*	ENST00000262320	NM_003502.3	410	Gag/Tag	5/11	0.662308130235364	1	FACETS	0.983	0.929	1	0.983	0.929	1	CLONAL	1	TRUE	0	0.662308130235364	1		269	493	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	95	62	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.51	0.457	0.566	0.51	0.457	0.566	SUBCLONAL	1	TRUE	1	0.866389686193462	2		62	430	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	285	366	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	0.866389686193462	2		366	621	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685315	89685315	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1554897280	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	140	318	0	ENST00000371953.3:c.209+1G>A		p.X70_splice	ENST00000371953	NM_000314.4	70			NA	2	FACETS	0.439	0.4	0.48			1	INDETERMINATE	1	TRUE	NA	0.866389686193462	2		318	736	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39706221	39706221	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	145	460	0	ENST00000361337.2:c.280-1G>A		p.X94_splice	ENST00000361337	NM_003286.2	94			1	2	FACETS	0.431	0.394	0.471	0.431	0.394	0.471	SUBCLONAL	1	TRUE	1	0.866389686193462	2		460	776	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217302	11217302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	160	530	0	ENST00000361445.4:c.4376C>T	p.Ala1459Val	p.A1459V	ENST00000361445	NM_004958.3	1459	gCc/gTc	30/58	0.866389686193462	3	FACETS	0.514	0.471	0.56	0.257	0.235	0.28	SUBCLONAL	1	TRUE	1	0.866389686193462	3		530	1029	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256862	16256862	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772778845	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	153	477	0	ENST00000375759.3:c.4127G>A	p.Gly1376Asp	p.G1376D	ENST00000375759	NM_015001.2	1376	gGt/gAt	11/15	0.866389686193462	3	FACETS	0.529	0.484	0.577	0.265	0.242	0.289	SUBCLONAL	1	TRUE	1	0.866389686193462	3		477	956	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056167	27056167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1231021260	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	118	389	0	ENST00000324856.7:c.1163G>A	p.Gly388Asp	p.G388D	ENST00000324856	NM_006015.4	388	gGc/gAc	2/20	0.866389686193462	3	FACETS	0.506	0.457	0.559	0.253	0.228	0.28	SUBCLONAL	1	TRUE	1	0.866389686193462	3		389	771	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099846	27099846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	110	365	0	ENST00000324856.7:c.3725G>A	p.Ser1242Asn	p.S1242N	ENST00000324856	NM_006015.4	1242	aGt/aAt	15/20	0.866389686193462	3	FACETS	0.489	0.439	0.542	0.245	0.219	0.271	SUBCLONAL	1	TRUE	1	0.866389686193462	3		365	744	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471775	120471775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	159	562	0	ENST00000256646.2:c.3716G>A	p.Gly1239Asp	p.G1239D	ENST00000256646	NM_024408.3	1239	gGt/gAt	23/34	1	2	FACETS	0.517	0.475	0.561	0.517	0.475	0.561	SUBCLONAL	1	TRUE	1	0.866389686193462	2		562	710	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506301	120506301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	46	351	0	ENST00000256646.2:c.1811G>A	p.Cys604Tyr	p.C604Y	ENST00000256646	NM_024408.3	604	tGc/tAc	11/34	1	2	FACETS	0.174	0.146	0.205	0.174	0.146	0.205	SUBCLONAL	1	TRUE	1	0.866389686193462	2		351	609	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845950	156845950	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	34	458	0	ENST00000524377.1:c.1580C>T	p.Ala527Val	p.A527V	ENST00000524377	NM_002529.3	527	gCt/gTt	13/17	1	2	FACETS	0.135	0.11	0.164	0.135	0.11	0.164	SUBCLONAL	1	TRUE	1	0.866389686193462	2		458	581	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193181212	193181212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773264613	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	166	482	0	ENST00000367435.3:c.1048C>T	p.Pro350Ser	p.P350S	ENST00000367435	NM_024529.4	350	Ccc/Tcc	12/17	1	2	FACETS	0.422	0.387	0.458	0.422	0.387	0.458	SUBCLONAL	1	TRUE	1	0.866389686193462	2		482	908	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193205453	193205453	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1199579887	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	151	410	1	ENST00000367435.3:c.1384C>T	p.Pro462Ser	p.P462S	ENST00000367435	NM_024529.4	462	Cct/Tct	15/17	1	2	FACETS	0.477	0.437	0.52	0.477	0.437	0.52	SUBCLONAL	1	TRUE	1	0.866389686193462	2		411	730	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652330	206652330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	136	493	2	ENST00000367120.3:c.1037C>T	p.Ala346Val	p.A346V	ENST00000367120	NM_014002.3	346	gCc/gTc	10/22	1	2	FACETS	0.57	0.52	0.621	0.57	0.52	0.621	SUBCLONAL	1	TRUE	1	0.866389686193462	2		495	551	SUCCESS
FH	2271	MSKCC	GRCh37	1	241661270	241661270	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1131691250	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	144	345	0	ENST00000366560.3:c.1391G>A	p.Gly464Glu	p.G464E	ENST00000366560	NM_000143.3	464	gGg/gAg	10/10	1	2	FACETS	0.516	0.472	0.562	0.516	0.472	0.562	SUBCLONAL	1	TRUE	1	0.866389686193462	2		345	644	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243668585	243668585	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	157	443	0	ENST00000263826.5:c.1406C>T	p.Pro469Leu	p.P469L	ENST00000263826	NM_005465.4	469	cCt/cTt	13/13	1	2	FACETS	0.532	0.489	0.577	0.532	0.489	0.577	SUBCLONAL	1	TRUE	1	0.866389686193462	2		443	681	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551275	29551275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	134	490	0	ENST00000389048.3:c.1355G>A	p.Gly452Glu	p.G452E	ENST00000389048	NM_004304.4	452	gGg/gAg	6/29	1	2	FACETS	0.563	0.514	0.615	0.563	0.514	0.615	SUBCLONAL	1	TRUE	1	0.866389686193462	2		490	549	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641528	47641528	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63751454	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	138	364	0	ENST00000233146.2:c.913G>A	p.Ala305Thr	p.A305T	ENST00000233146	NM_000251.2	305	Gca/Aca	5/16	1	2	FACETS	0.542	0.495	0.591	0.542	0.495	0.591	SUBCLONAL	1	TRUE	1	0.866389686193462	2		364	588	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656880	47656880	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	129	343	0	ENST00000233146.2:c.1077-1G>A		p.X359_splice	ENST00000233146	NM_000251.2	359			1	2	FACETS	0.49	0.445	0.536	0.49	0.445	0.536	SUBCLONAL	1	TRUE	1	0.866389686193462	2		343	608	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707939	47707939	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1553370404	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	135	515	0	ENST00000233146.2:c.2563C>T	p.Gln855Ter	p.Q855*	ENST00000233146	NM_000251.2	855	Cag/Tag	15/16	1	2	FACETS	0.438	0.399	0.48	0.438	0.399	0.48	SUBCLONAL	1	TRUE	1	0.866389686193462	2		515	711	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027307	48027307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	171	453	0	ENST00000234420.5:c.2185G>A	p.Ala729Thr	p.A729T	ENST00000234420	NM_000179.2	729	Gcc/Acc	4/10	1	2	FACETS	0.503	0.463	0.544	0.503	0.463	0.544	SUBCLONAL	1	TRUE	1	0.866389686193462	2		453	785	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032053	48032053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	175	438	0	ENST00000234420.5:c.3443G>A	p.Gly1148Asp	p.G1148D	ENST00000234420	NM_000179.2	1148	gGc/gAc	6/10	1	2	FACETS	0.549	0.507	0.593	0.549	0.507	0.593	SUBCLONAL	1	TRUE	1	0.866389686193462	2		438	736	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032080	48032080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752212361	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	193	460	0	ENST00000234420.5:c.3470G>A	p.Gly1157Asp	p.G1157D	ENST00000234420	NM_000179.2	1157	gGt/gAt	6/10	1	2	FACETS	0.522	0.483	0.562	0.522	0.483	0.562	SUBCLONAL	1	TRUE	1	0.866389686193462	2		460	854	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033436	48033436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	222	551	0	ENST00000234420.5:c.3740C>T	p.Thr1247Ile	p.T1247I	ENST00000234420	NM_000179.2	1247	aCt/aTt	8/10	1	2	FACETS	0.541	0.504	0.58	0.541	0.504	0.58	SUBCLONAL	1	TRUE	1	0.866389686193462	2		551	947	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098752	178098752	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	164	549	0	ENST00000397062.3:c.293G>A	p.Gly98Glu	p.G98E	ENST00000397062	NM_006164.4	98	gGa/gAa	2/5	0.124002262712449	4	FACETS	0.946	0.87	1	0.473	0.435	0.513	INDETERMINATE	1	TRUE	2	0.866389686193462	4		549	747	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339006	225339006	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	186	611	0	ENST00000264414.4:c.2263G>A	p.Ala755Thr	p.A755T	ENST00000264414	NM_003590.4	755	Gca/Aca	16/16	1	2	FACETS	0.487	0.45	0.526	0.487	0.45	0.526	SUBCLONAL	1	TRUE	1	0.866389686193462	2		611	881	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662097	227662097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1014841546	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	103	417	1	ENST00000305123.5:c.1358C>T	p.Thr453Ile	p.T453I	ENST00000305123	NM_005544.2	453	aCc/aTc	1/2	1	2	FACETS	0.423	0.379	0.469	0.423	0.379	0.469	SUBCLONAL	1	TRUE	1	0.866389686193462	2		418	562	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627188	12627188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397516816	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	126	462	0	ENST00000251849.4:c.1528C>T	p.Leu510Phe	p.L510F	ENST00000251849	NM_002880.3	510	Ctc/Ttc	14/17	0.605641251260856	5	FACETS	0.527	0.475	0.581			1	SUBCLONAL	1	TRUE	NA	0.866389686193462	5		462	1270	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52677357	52677357	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	113	368	0	ENST00000394830.3:c.902C>T	p.Thr301Ile	p.T301I	ENST00000394830	NM_018313.4	301	aCt/aTt	10/30	0.866389686193462	3	FACETS	0.488	0.439	0.54	0.244	0.219	0.27	SUBCLONAL	1	TRUE	1	0.866389686193462	3		368	766	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665437	138665437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1053343902	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	61	284	0	ENST00000330315.3:c.128G>A	p.Gly43Glu	p.G43E	ENST00000330315	NM_023067.3	43	gGg/gAg	1/1	1	2	FACETS	0.508	0.442	0.579	0.508	0.442	0.579	SUBCLONAL	1	TRUE	1	0.866389686193462	2		284	277	SUCCESS
ATR	545	MSKCC	GRCh37	3	142254997	142254997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	180	418	0	ENST00000350721.4:c.3772C>T	p.His1258Tyr	p.H1258Y	ENST00000350721	NM_001184.3	1258	Cat/Tat	20/47	1	2	FACETS	0.516	0.476	0.557	0.516	0.476	0.557	SUBCLONAL	1	TRUE	1	0.866389686193462	2		418	806	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916959	178916959	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	114	311	0	ENST00000263967.3:c.346G>A	p.Glu116Lys	p.E116K	ENST00000263967	NM_006218.2	116	Gaa/Aaa	2/21	1	2	FACETS	0.486	0.439	0.536	0.486	0.439	0.536	SUBCLONAL	1	TRUE	1	0.866389686193462	2		311	541	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526151	189526151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	140	440	0	ENST00000264731.3:c.415G>A	p.Ala139Thr	p.A139T	ENST00000264731	NM_003722.4	139	Gcg/Acg	4/14	1	2	FACETS	0.57	0.521	0.621	0.57	0.521	0.621	SUBCLONAL	1	TRUE	1	0.866389686193462	2		440	567	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806206	1806206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	139	500	0	ENST00000260795.2:c.1225C>T	p.Pro409Ser	p.P409S	ENST00000260795		409	Ccc/Tcc	8/17	0.555943768723816	4	FACETS	0.578	0.525	0.633			1	SUBCLONAL	1	TRUE	NA	0.866389686193462	4		500	1037	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604623	55604623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2199	153	550	0	ENST00000288135.5:c.2831C>T	p.Pro944Leu	p.P944L	ENST00000288135	NM_000222.2	944	cCc/cTc	21/21	0.866389686193462	7	FACETS	0.475	0.432	0.521			1	SUBCLONAL	1	TRUE	NA	0.866389686193462	7		550	2352	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157804	106157804	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	132	395	0	ENST00000380013.4:c.2705G>A	p.Arg902Lys	p.R902K	ENST00000380013	NM_001127208.2	902	aGa/aAa	3/11	0.866389686193462	2	FACETS	0.565	0.516	0.617	0.283	0.258	0.309	SUBCLONAL	1	TRUE	0	0.866389686193462	2		395	539	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143235866	143235866	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	120	323	1	ENST00000262992.4:c.422G>A	p.Gly141Glu	p.G141E	ENST00000262992	NM_001101669.1	141	gGg/gAg	6/24	0.866389686193462	2	FACETS	0.616	0.56	0.674	0.308	0.28	0.337	SUBCLONAL	1	TRUE	0	0.866389686193462	2		324	450	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332940	153332940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	120	285	0	ENST00000281708.4:c.16C>T	p.Leu6Phe	p.L6F	ENST00000281708	NM_033632.3	6	Ctc/Ttc	2/12	0.866389686193462	2	FACETS	0.755	0.689	0.823	0.377	0.344	0.412	SUBCLONAL	1	TRUE	0	0.866389686193462	2		285	367	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264567	1264567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	79	475	0	ENST00000310581.5:c.2795G>A	p.Gly932Asp	p.G932D	ENST00000310581	NM_198253.2	932	gGc/gAc	11/16	0.106575605510535	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.866389686193462	0		475	447	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174859	56174859	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	152	527	0	ENST00000399503.3:c.2018G>A	p.Arg673Lys	p.R673K	ENST00000399503	NM_005921.1	673	aGa/aAa	11/20	1	2	FACETS	0.451	0.413	0.491	0.451	0.413	0.491	SUBCLONAL	1	TRUE	1	0.866389686193462	2		527	778	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183339	56183339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	108	334	0	ENST00000399503.3:c.4249G>A	p.Ala1417Thr	p.A1417T	ENST00000399503	NM_005921.1	1417	Gca/Aca	18/20	1	2	FACETS	0.458	0.413	0.506	0.458	0.413	0.506	SUBCLONAL	1	TRUE	1	0.866389686193462	2		334	544	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755674	57755674	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	31	431	0	ENST00000274289.3:c.113C>T	p.Pro38Leu	p.P38L	ENST00000274289	NM_006622.3	38	cCc/cTc	1/14	1	2	FACETS	0.165	0.133	0.201	0.165	0.133	0.201	SUBCLONAL	1	TRUE	1	0.866389686193462	2		431	435	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495361	149495361	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	75	407	0	ENST00000261799.4:c.3286G>A	p.Ala1096Thr	p.A1096T	ENST00000261799	NM_002609.3	1096	Gcg/Acg	23/23	0.106575605510535	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.866389686193462	0		407	362	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523122	176523122	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	103	475	1	ENST00000292408.4:c.1886C>T	p.Ala629Val	p.A629V	ENST00000292408	NM_213647.1	629	gCt/gTt	14/18	0.106575605510535	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.866389686193462	0		476	547	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700304	117700304	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780718091	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	151	468	0	ENST00000368508.3:c.2515G>A	p.Asp839Asn	p.D839N	ENST00000368508	NM_002944.2	839	Gac/Aac	17/43	1	2	FACETS	0.429	0.392	0.467	0.429	0.392	0.467	SUBCLONAL	1	TRUE	1	0.866389686193462	2		468	813	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715450	117715450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	179	448	0	ENST00000368508.3:c.1039G>A	p.Ala347Thr	p.A347T	ENST00000368508	NM_002944.2	347	Gcg/Acg	10/43	1	2	FACETS	0.581	0.537	0.627	0.581	0.537	0.627	SUBCLONAL	1	TRUE	1	0.866389686193462	2		448	711	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55270309	55270309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	152	636	0	ENST00000275493.2:c.3262C>T	p.Pro1088Ser	p.P1088S	ENST00000275493	NM_005228.3	1088	Cca/Tca	27/28	1	2	FACETS	0.514	0.471	0.558	0.514	0.471	0.558	SUBCLONAL	1	TRUE	1	0.866389686193462	2		636	683	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852158	128852158	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141955434	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	126	518	0	ENST00000249373.3:c.2230C>T	p.Pro744Ser	p.P744S	ENST00000249373	NM_005631.4	744	Cct/Tct	12/12	0.49362914235788	3	FACETS	0.577	0.523	0.634	0.289	0.261	0.317	INDETERMINATE	1	TRUE	1	0.866389686193462	3		518	722	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508812	148508812	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	129	368	0	ENST00000320356.2:c.1852C>T	p.His618Tyr	p.H618Y	ENST00000320356	NM_004456.4	618	Cat/Tat	16/20	0.49362914235788	3	FACETS	0.552	0.501	0.606	0.276	0.25	0.303	INDETERMINATE	1	TRUE	1	0.866389686193462	3		368	773	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271734	38271734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	99	509	0	ENST00000425967.3:c.2215G>A	p.Glu739Lys	p.E739K	ENST00000425967	NM_001174067.1	739	Gaa/Aaa	17/19	0.375487091672811	3	FACETS	0.475	0.424	0.529	0.238	0.212	0.265	INDETERMINATE	1	TRUE	1	0.866389686193462	3		509	689	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231053	98231053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	65	194	0	ENST00000331920.6:c.2230C>T	p.Leu744Phe	p.L744F	ENST00000331920	NM_000264.3	744	Ctc/Ttc	14/24	0.866389686193462	3	FACETS	0.46	0.399	0.525	0.153	0.133	0.175	SUBCLONAL	1	TRUE	0	0.866389686193462	3		194	468	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772626	135772626	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	257	737	0	ENST00000298552.3:c.2920C>T	p.Leu974Phe	p.L974F	ENST00000298552	NM_001162426.1	974	Ctc/Ttc	22/23	0.866389686193462	3	FACETS	0.746	0.698	0.795	0.249	0.232	0.265	SUBCLONAL	1	TRUE	0	0.866389686193462	3		737	1140	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607660	43607660	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	94	382	0	ENST00000355710.3:c.1636G>A	p.Gly546Arg	p.G546R	ENST00000355710	NM_020975.4	546	Gga/Aga	8/20	0.866389686193462	4	FACETS	0.506	0.45	0.566	0.169	0.15	0.189	SUBCLONAL	1	TRUE	1	0.866389686193462	4		382	800	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692911	89692911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909241	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	115	322	0	ENST00000371953.3:c.395G>A	p.Gly132Asp	p.G132D	ENST00000371953	NM_000314.4	132	gGt/gAt	5/9	NA	2	FACETS	0.432	0.39	0.477			1	INDETERMINATE	1	TRUE	NA	0.866389686193462	2		322	614	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352753	118352753	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	153	351	0	ENST00000534358.1:c.3958C>T	p.Pro1320Ser	p.P1320S	ENST00000534358	NM_005933.3	1320	Ccc/Tcc	7/36	1	2	FACETS	0.519	0.476	0.563	0.519	0.476	0.563	SUBCLONAL	1	TRUE	1	0.866389686193462	2		351	681	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038896	12038896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1654	310	527	0	ENST00000396373.4:c.1189G>A	p.Ala397Thr	p.A397T	ENST00000396373	NM_001987.4	397	Gcc/Acc	7/8	0.489173694624775	4	FACETS	0.68	0.639	0.723			1	INDETERMINATE	1	TRUE	NA	0.866389686193462	4		527	1964	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230523	46230523	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	174	362	0	ENST00000334344.6:c.773-1G>A		p.X258_splice	ENST00000334344	NM_152641.2	258			1	2	FACETS	0.552	0.509	0.596	0.552	0.509	0.596	SUBCLONAL	1	TRUE	1	0.866389686193462	2		362	728	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425416	49425416	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	134	534	0	ENST00000301067.7:c.13072G>A	p.Val4358Ile	p.V4358I	ENST00000301067	NM_003482.3	4358	Gtc/Atc	39/54	1	2	FACETS	0.528	0.481	0.576	0.528	0.481	0.576	SUBCLONAL	1	TRUE	1	0.866389686193462	2		534	586	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435143	49435143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	53	169	0	ENST00000301067.7:c.6410C>T	p.Thr2137Ile	p.T2137I	ENST00000301067	NM_003482.3	2137	aCc/aTc	31/54	1	2	FACETS	0.471	0.405	0.541	0.471	0.405	0.541	SUBCLONAL	1	TRUE	1	0.866389686193462	2		169	260	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436530	49436530	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	46	452	0	ENST00000301067.7:c.5776C>T	p.Leu1926Phe	p.L1926F	ENST00000301067	NM_003482.3	1926	Ctt/Ttt	26/54	1	2	FACETS	0.188	0.158	0.221	0.188	0.158	0.221	SUBCLONAL	1	TRUE	1	0.866389686193462	2		452	565	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438255	49438255	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	184	491	1	ENST00000301067.7:c.5014C>A	p.Pro1672Thr	p.P1672T	ENST00000301067	NM_003482.3	1672	Cct/Act	20/54	1	2	FACETS	0.591	0.547	0.636	0.591	0.547	0.636	SUBCLONAL	1	TRUE	1	0.866389686193462	2		492	719	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623547	28623547	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	154	400	0	ENST00000241453.7:c.1010G>A	p.Ser337Asn	p.S337N	ENST00000241453	NM_004119.2	337	aGt/aAt	8/24	NA	2	FACETS	0.57	0.523	0.618			1	INDETERMINATE	1	TRUE	NA	0.866389686193462	2		400	624	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335560	73335560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	226	566	0	ENST00000377767.4:c.2611G>A	p.Gly871Arg	p.G871R	ENST00000377767	NM_014953.3	871	Ggg/Agg	19/21	0.866389686193462	1	FACETS	0.605	0.57	0.64	0.605	0.57	0.64	SUBCLONAL	1	TRUE	0	0.866389686193462	1		566	489	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422070	81422070	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	40	387	0	ENST00000298171.2:c.46C>T	p.Pro16Ser	p.P16S	ENST00000298171	NM_000369.2	16	Ccc/Tcc	1/10	1	2	FACETS	0.198	0.164	0.236	0.198	0.164	0.236	SUBCLONAL	1	TRUE	1	0.866389686193462	2		387	466	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557687	95557687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	101	387	0	ENST00000393063.1:c.5380G>A	p.Glu1794Lys	p.E1794K	ENST00000393063	NM_030621.3	1794	Gag/Aag	26/28	1	2	FACETS	0.425	0.381	0.472	0.425	0.381	0.472	SUBCLONAL	1	TRUE	1	0.866389686193462	2		387	548	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774140	66774140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	118	564	0	ENST00000307102.5:c.616C>T	p.Leu206Phe	p.L206F	ENST00000307102	NM_002755.3	206	Ctc/Ttc	6/11	1	2	FACETS	0.417	0.376	0.459	0.417	0.376	0.459	SUBCLONAL	1	TRUE	1	0.866389686193462	2		564	654	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396238	396238	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	123	490	0	ENST00000262320.3:c.788C>T	p.Pro263Leu	p.P263L	ENST00000262320	NM_003502.3	263	cCc/cTc	2/11	1	2	FACETS	0.536	0.486	0.587	0.536	0.486	0.587	SUBCLONAL	1	TRUE	1	0.866389686193462	2		490	530	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892244	9892244	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	258	506	0	ENST00000330684.3:c.2246C>G	p.Thr749Ser	p.T749S	ENST00000330684	NM_001134407.1	749	aCc/aGc	11/13	NA	2	FACETS	1	0.963	1			1	INDETERMINATE	1	TRUE	NA	0.866389686193462	2		506	581	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619333	23619333	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	120	428	0	ENST00000261584.4:c.3202G>A	p.Gly1068Arg	p.G1068R	ENST00000261584	NM_024675.3	1068	Ggg/Agg	12/13	1	2	FACETS	0.415	0.375	0.457	0.415	0.375	0.457	SUBCLONAL	1	TRUE	1	0.866389686193462	2		428	668	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877381	89877381	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763338641	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	142	413	0	ENST00000389301.3:c.382C>T	p.Pro128Ser	p.P128S	ENST00000389301	NM_000135.2	128	Cca/Tca	4/43	1	2	FACETS	0.597	0.547	0.649	0.597	0.547	0.649	SUBCLONAL	1	TRUE	1	0.866389686193462	2		413	549	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663722	29663722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1026776734	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	201	567	0	ENST00000356175.3:c.6154C>T	p.Leu2052Phe	p.L2052F	ENST00000356175	NM_000267.3	2052	Ctt/Ttt	41/57	1	2	FACETS	0.46	0.426	0.495	0.46	0.426	0.495	SUBCLONAL	1	TRUE	1	0.866389686193462	2		567	1009	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246260	41246260	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	179	554	0	ENST00000357654.3:c.1288G>A	p.Asp430Asn	p.D430N	ENST00000357654	NM_007294.3	430	Gac/Aac	10/23	NA	2	FACETS	0.502	0.463	0.542			1	INDETERMINATE	1	TRUE	NA	0.866389686193462	2		554	823	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435399	56435399	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774676773	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	29	299	0	ENST00000407977.2:c.1738C>T	p.Pro580Ser	p.P580S	ENST00000407977		580	Cct/Tct	9/10	1	2	FACETS	0.176	0.141	0.216	0.176	0.141	0.216	SUBCLONAL	1	TRUE	1	0.866389686193462	2		299	381	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853791	59853791	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	201	584	1	ENST00000259008.2:c.2068G>A	p.Gly690Arg	p.G690R	ENST00000259008	NM_032043.2	690	Gga/Aga	14/20	1	2	FACETS	0.538	0.499	0.579	0.538	0.499	0.579	SUBCLONAL	1	TRUE	1	0.866389686193462	2		585	862	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533763	63533763	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777283610	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	77	359	0	ENST00000307078.5:c.1391C>T	p.Ser464Phe	p.S464F	ENST00000307078	NM_004655.3	464	tCc/tTc	6/11	1	2	FACETS	0.404	0.356	0.455	0.404	0.356	0.455	SUBCLONAL	1	TRUE	1	0.866389686193462	2		359	440	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78865601	78865601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	138	440	0	ENST00000306801.3:c.2065G>A	p.Glu689Lys	p.E689K	ENST00000306801	NM_020761.2	689	Gaa/Aaa	18/34	1	2	FACETS	0.539	0.492	0.588	0.539	0.492	0.588	SUBCLONAL	1	TRUE	1	0.866389686193462	2		440	591	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743308	743308	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1221	232	545	0	ENST00000314574.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000314574	NM_005433.3	278	Cga/Tga	7/12	0.40545499241296	4	FACETS	0.688	0.64	0.738			1	INDETERMINATE	1	TRUE	NA	0.866389686193462	4		545	1453	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39629551	39629551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	164	529	0	ENST00000262039.4:c.2245C>T	p.Leu749Phe	p.L749F	ENST00000262039	NM_002647.2	749	Ctt/Ttt	21/25	0.116649720716958	4	FACETS	0.706	0.647	0.767			1	INDETERMINATE	1	TRUE	NA	0.866389686193462	4		529	1001	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394694	45394694	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	111	386	0	ENST00000262160.6:c.655G>A	p.Glu219Lys	p.E219K	ENST00000262160	NM_005901.5	219	Gaa/Aaa	5/11	0.116649720716958	4	FACETS	0.645	0.58	0.714			1	INDETERMINATE	1	TRUE	NA	0.866389686193462	4		386	741	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5258066	5258066	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	136	431	0	ENST00000357368.4:c.668G>A	p.Gly223Asp	p.G223D	ENST00000357368	NM_002850.3	223	gGc/gAc	8/38	0.866389686193462	3	FACETS	0.578	0.526	0.633	0.289	0.263	0.317	SUBCLONAL	1	TRUE	1	0.866389686193462	3		431	778	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254548	10254548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	160	574	0	ENST00000340748.4:c.2962C>T	p.Pro988Ser	p.P988S	ENST00000340748		988	Cct/Tct	28/40	0.866389686193462	3	FACETS	0.586	0.537	0.637	0.293	0.268	0.319	SUBCLONAL	1	TRUE	1	0.866389686193462	3		574	903	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10257165	10257165	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	238	437	0	ENST00000340748.4:c.2708G>A	p.Arg903Lys	p.R903K	ENST00000340748		903	aGg/aAg	27/40	0.866389686193462	3	FACETS	0.967	0.906	1	0.484	0.453	0.516	CLONAL	1	TRUE	1	0.866389686193462	3		437	814	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272036	15272036	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	100	152	0	ENST00000263388.2:c.6403G>A	p.Val2135Met	p.V2135M	ENST00000263388	NM_000435.2	2135	Gtg/Atg	33/33	0.866389686193462	3	FACETS	0.927	0.836	1	0.463	0.418	0.511	CLONAL	1	TRUE	1	0.866389686193462	3		152	357	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15280973	15280973	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1477898406	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	79	483	0	ENST00000263388.2:c.5123C>T	p.Ala1708Val	p.A1708V	ENST00000263388	NM_000435.2	1708	gCc/gTc	28/33	0.866389686193462	3	FACETS	0.362	0.318	0.409	0.181	0.159	0.205	SUBCLONAL	1	TRUE	1	0.866389686193462	3		483	722	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951135	17951135	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	246	418	0	ENST00000458235.1:c.1158C>G	p.Ile386Met	p.I386M	ENST00000458235	NM_000215.3	386	atC/atG	9/24	0.866389686193462	3	FACETS	1	0.965	1	0.52	0.488	0.554	CLONAL	1	TRUE	1	0.866389686193462	3		418	782	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308074	30308074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	113	503	0	ENST00000262643.3:c.211C>T	p.Pro71Ser	p.P71S	ENST00000262643	NM_001238.2	71	Ccc/Tcc	5/12	0.866389686193462	3	FACETS	0.425	0.382	0.471	0.213	0.191	0.236	SUBCLONAL	1	TRUE	1	0.866389686193462	3		503	879	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655305	45655305	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769110368	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	152	473	2	ENST00000407780.3:c.547G>A	p.Ala183Thr	p.A183T	ENST00000407780	NM_001283052.1	183	Gct/Act	4/7	0.116649720716958	4	FACETS	0.926	0.849	1			1	INDETERMINATE	1	TRUE	NA	0.866389686193462	4		475	707	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573432	41573432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749435586	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	122	441	0	ENST00000263253.7:c.5717C>T	p.Thr1906Ile	p.T1906I	ENST00000263253	NM_001429.3	1906	aCc/aTc	31/31	NA	2	FACETS	0.551	0.5	0.604			1	INDETERMINATE	1	TRUE	NA	0.866389686193462	2		441	511	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855916	76855916	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	50	622	0	ENST00000373344.5:c.5684G>A	p.Ser1895Asn	p.S1895N	ENST00000373344	NM_000489.3	1895	aGc/aAc	23/35	0.427574386097149	1	FACETS	0.075	0.063	0.088	0.075	0.063	0.088	INDETERMINATE	1	TRUE	0	0.866389686193462	1		622	873	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937470	76937470	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1557137763	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	321	566	0	ENST00000373344.5:c.3278G>T	p.Arg1093Met	p.R1093M	ENST00000373344	NM_000489.3	1093	aGg/aTg	9/35	0.427574386097149	1	FACETS	0.562	0.534	0.591	0.562	0.534	0.591	INDETERMINATE	1	TRUE	0	0.866389686193462	1		566	747	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25368390	25368390	+	intron_variant	Intron	DEL	T	T	-	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2785	153	530	1	ENST00000311936.3:c.451-5545del		p.*151*	ENST00000311936	NM_004985.3	185/189			0.866389686193462	7	FACETS	0.381	0.346	0.417			1	SUBCLONAL	1	TRUE	NA	0.866389686193462	7		531	2938	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	907	561	0	ENST00000269305.4:c.641del	p.His214LeufsTer33	p.H214Lfs*33	ENST00000269305	NM_001126112.2	214	cAt/ct	6/11	0.866389686193462	3	FACETS	1	0.998	1	1	0.998	1	CLONAL	3	TRUE	0	0.866389686193462	3		561	934	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022297	31022297	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	65	560	1	ENST00000375687.4:c.1786del	p.Arg596GlyfsTer107	p.R596Gfs*107	ENST00000375687	NM_015338.5	594	tgC/tg	13/13	1	2	FACETS	0.197	0.17	0.226	0.197	0.17	0.226	SUBCLONAL	1	TRUE	1	0.866389686193462	2		561	763	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339981	70339981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002698-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	102	229	0	ENST00000374080.3:c.514G>A	p.Glu172Lys	p.E172K	ENST00000374080		172	Gag/Aag	4/45	0.44800279727086	2	FACETS	0.941	0.845	1			1	CLONAL	1	TRUE	NA	0.447157390395072	2		229	485	SUCCESS
CBL	867	MSKCC	GRCh37	11	119168158	119168158	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1565272311	NA	P-0002701-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	145	383	0	ENST00000264033.4:c.2218C>T	p.Gln740Ter	p.Q740*	ENST00000264033	NM_005188.3	740	Cag/Tag	14/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.670060551936499	2		383	383	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0002702-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	268	618	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.377518163402981	3	FACETS	1	0.994	1	0.737	0.697	0.777	INDETERMINATE	1	TRUE	1	0.865563638569313	3		618	602	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0002702-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	292	224	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	0.807219498779425	2	FACETS	0.883	0.852	0.912	0.883	0.852	0.912	CLONAL	2	TRUE	0	0.865563638569313	2		224	382	SUCCESS
APC	324	MSKCC	GRCh37	5	112175024	112175024	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0002702-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	140	380	0	ENST00000257430.4:c.3733A>T	p.Lys1245Ter	p.K1245*	ENST00000257430	NM_000038.5	1245	Aag/Tag	16/16	0.377518163402981	3	FACETS	1	0.946	1	0.52	0.477	0.564	INDETERMINATE	1	TRUE	1	0.865563638569313	3		380	446	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260238	19260238	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002702-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	129	363	0	ENST00000162023.5:c.55G>A	p.Val19Met	p.V19M	ENST00000162023		19	Gtg/Atg	7/13	0.865563638569313	3	FACETS	0.916	0.837	0.999	0.458	0.418	0.5	CLONAL	1	TRUE	1	0.865563638569313	3		363	466	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968808	15968808	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002702-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	352	343	0	ENST00000268712.3:c.4942del	p.Ala1648GlnfsTer8	p.A1648Qfs*8	ENST00000268712	NM_006311.3	1648	Gca/ca	33/46	0.807219498779425	2	FACETS	0.918	0.891	0.944	0.918	0.891	0.944	CLONAL	2	TRUE	0	0.865563638569313	2		343	443	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031895	26031895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1332600888	NA	P-0002707-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	62	157	1	ENST00000244661.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000244661	NM_003537.3	132	Cgc/Tgc	1/1	0.335135031538146	3	FACETS	1	0.944	1	0.584	0.507	0.667	CLONAL	1	FALSE	1	0.335135031538146	3		158	370	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638344	117638344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1484038087	NA	P-0002707-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	93	445	0	ENST00000368508.3:c.6097G>A	p.Asp2033Asn	p.D2033N	ENST00000368508	NM_002944.2	2033	Gac/Aac	38/43	0.335135031538146	3	FACETS	1	0.909	1	0.512	0.455	0.572	CLONAL	1	FALSE	1	0.335135031538146	3		445	633	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0002725-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	19	129	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.896	0.683	1	0.896	0.683	1	CLONAL	1	FALSE	1	0.222108936542952	2		129	191	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0002725-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	150	520	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.107506439639601	3	FACETS	0.86	0.789	0.932			1	INDETERMINATE	3	FALSE	NA	0.222108936542952	3		520	582	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794106	242794106	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs148456597	NA	P-0002725-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	55	562	0	ENST00000334409.5:c.622C>A	p.Pro208Thr	p.P208T	ENST00000334409	NM_005018.2	208	Ccc/Acc	4/5	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	FALSE	1	0.222108936542952	2		562	472	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129962	55129962	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002725-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	51	613	0	ENST00000257290.5:c.496G>T	p.Gly166Trp	p.G166W	ENST00000257290	NM_006206.4	166	Ggg/Tgg	4/23	0.222108936542952	1	FACETS	0.752	0.639	0.876	0.752	0.639	0.876	SUBCLONAL	1	FALSE	0	0.222108936542952	1		613	543	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525547	187525547	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002725-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	34	633	0	ENST00000441802.2:c.10532A>C	p.Tyr3511Ser	p.Y3511S	ENST00000441802	NM_005245.3	3511	tAc/tCc	18/27	1	2	FACETS	0.585	0.477	0.707	0.585	0.477	0.707	SUBCLONAL	1	FALSE	1	0.222108936542952	2		633	523	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499592	149499592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002725-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	58	528	0	ENST00000261799.4:c.2681G>T	p.Trp894Leu	p.W894L	ENST00000261799	NM_002609.3	894	tGg/tTg	19/23	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	FALSE	1	0.222108936542952	2		528	522	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504352	149504352	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002725-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	65	429	0	ENST00000261799.4:c.1850C>A	p.Ala617Asp	p.A617D	ENST00000261799	NM_002609.3	617	gCc/gAc	13/23	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	1	0.222108936542952	2		429	526	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878816	151878816	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002725-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	39	483	0	ENST00000262189.6:c.6129T>A	p.Phe2043Leu	p.F2043L	ENST00000262189	NM_170606.2	2043	ttT/ttA	36/59	1	2	FACETS	0.616	0.51	0.735	0.616	0.51	0.735	SUBCLONAL	1	FALSE	1	0.222108936542952	2		483	570	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194204	94194204	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0002725-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	38	571	0	ENST00000323929.3:c.1226-2A>G		p.X409_splice	ENST00000323929	NM_005591.3	409			1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	FALSE	1	0.222108936542952	2		571	302	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249302	133249302	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002725-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	109	559	0	ENST00000320574.5:c.1597G>T	p.Val533Leu	p.V533L	ENST00000320574	NM_006231.2	533	Gtg/Ttg	15/49	0.194475819804888	2	FACETS	0.964	0.87	1	0.964	0.87	1	CLONAL	2	FALSE	0	0.222108936542952	2		559	509	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472524	88472524	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002725-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	54	556	1	ENST00000360948.2:c.2031C>A	p.His677Gln	p.H677Q	ENST00000360948	NM_001012338.2	677	caC/caA	16/19	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	FALSE	1	0.222108936542952	2		557	480	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647209	23647209	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002725-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	55	688	0	ENST00000261584.4:c.658A>T	p.Ser220Cys	p.S220C	ENST00000261584	NM_024675.3	220	Agt/Tgt	4/13	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	FALSE	1	0.222108936542952	2		688	489	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385108	41385108	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002725-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	39	507	0	ENST00000373198.4:c.853G>T	p.Val285Leu	p.V285L	ENST00000373198	NM_133170.3	285	Gtg/Ttg	6/32	1	2	FACETS	0.777	0.644	0.925	0.777	0.644	0.925	CLONAL	1	FALSE	1	0.222108936542952	2		507	452	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76777741	76777741	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002725-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	54	666	0	ENST00000373344.5:c.6975G>T	p.Glu2325Asp	p.E2325D	ENST00000373344	NM_000489.3	2325	gaG/gaT	32/35	0.127475020994327	0	FACETS	0.778	0.665	0.902			1	INDETERMINATE	1	FALSE	0	0.222108936542952	0		666	486	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144113	11144113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002732-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	22	689	0	ENST00000358026.2:c.3694G>A	p.Gly1232Ser	p.G1232S	ENST00000358026	NM_001128849.1	1232	Ggc/Agc	26/36	1	2	FACETS	0.206	0.159	0.261	0.206	0.159	0.261	SUBCLONAL	1	TRUE	1	0.399722703985247	2		689	534	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0002744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	9	181	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.246	0.163	0.349	0.246	0.163	0.349	SUBCLONAL	1	TRUE	1	0.642339501964025	2		181	114	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727085	243727085	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	13	574	0	ENST00000263826.5:c.885A>T	p.Glu295Asp	p.E295D	ENST00000263826	NM_005465.4	295	gaA/gaT	9/13	NA	2	FACETS	0.205	0.146	0.277			1	INDETERMINATE	1	TRUE	NA	0.642339501964025	2		574	197	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202288	133202288	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	12	430	0	ENST00000320574.5:c.6600G>C	p.Glu2200Asp	p.E2200D	ENST00000320574	NM_006231.2	2200	gaG/gaC	47/49	NA	2	FACETS	0.374	0.265	0.504			1	INDETERMINATE	1	TRUE	NA	0.642339501964025	2		430	100	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039339	49039339	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0002744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	23	619	0	ENST00000267163.4:c.2326-2A>G		p.X776_splice	ENST00000267163	NM_000321.2	776			0.287117558696715	5	FACETS	0.633	0.496	0.791	0.211	0.165	0.264	INDETERMINATE	1	TRUE	2	0.642339501964025	5		619	222	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0002778-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	318	415	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.735709676622619	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.735709676622619	1		415	471	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0002778-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	406	398	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	0.735709676622619	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.735709676622619	2		398	536	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157792	106157792	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002778-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	99	388	1	ENST00000380013.4:c.2693G>A	p.Gly898Glu	p.G898E	ENST00000380013	NM_001127208.2	898	gGa/gAa	3/11	NA	2	FACETS	0.375	0.335	0.418			1	INDETERMINATE	1	TRUE	NA	0.735709676622619	2		389	717	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171760	36171760	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0002778-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	186	300	0	ENST00000300305.3:c.806-1G>C		p.X269_splice	ENST00000300305		269			0.277265940410187	1	FACETS	0.725	0.677	0.773	0.725	0.677	0.773	INDETERMINATE	1	TRUE	0	0.735709676622619	1		300	441	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0002779-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	133	533	2	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.206402095521464	2	FACETS	0.937	0.858	1	1	0.986	1	CLONAL	3	TRUE	0	0.212167649809308	2		535	446	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0002779-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	160	351	2	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.13860836243964	4	FACETS	0.986	0.908	1	1	0.989	1	CLONAL	3	TRUE	2	0.212167649809308	4		353	618	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675248	176675248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201483724	NA	P-0002779-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	97	416	0	ENST00000439151.2:c.4564G>A	p.Asp1522Asn	p.D1522N	ENST00000439151	NM_022455.4	1522	Gat/Aat	11/23	1	2	FACETS	0.839	0.75	0.933	1	0.984	1	CLONAL	2	TRUE	1	0.212167649809308	2		416	545	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086004	16086004	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1558536389	NA	P-0002779-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	46	299	0	ENST00000281043.3:c.1180C>T	p.Arg394Cys	p.R394C	ENST00000281043	NM_005378.4	394	Cgc/Tgc	3/3	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.212167649809308	2		299	342	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050355	128050355	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002779-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	55	374	0	ENST00000285398.2:c.302T>C	p.Val101Ala	p.V101A	ENST00000285398	NM_000122.1	101	gTg/gCg	3/15	0.204350982240838	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.212167649809308	1		374	401	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277967	41277967	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002779-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	63	339	0	ENST00000349496.5:c.1931T>C	p.Leu644Pro	p.L644P	ENST00000349496	NM_001904.3	644	cTt/cCt	12/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.212167649809308	2		339	472	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225543	133225543	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002779-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	67	370	0	ENST00000320574.5:c.4121A>C	p.Lys1374Thr	p.K1374T	ENST00000320574	NM_006231.2	1374	aAa/aCa	32/49	0.135411539795197	0	FACETS	0.699	0.611	0.793			1	SUBCLONAL	2	TRUE	0	0.212167649809308	0		370	356	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484597	57484597	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs137854533	NA	P-0002779-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	30	181	0	ENST00000371085.3:c.681G>C	p.Gln227His	p.Q227H	ENST00000371085	NM_000516.4	227	caG/caC	9/13	0.212167649809308	5	FACETS	1	0.925	1			1	CLONAL	1	TRUE	NA	0.212167649809308	5		181	281	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0002784-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	216	129	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.4433760924557	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	0	0.4433760924557	3		129	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0002784-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	222	415	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.4433760924557	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.4433760924557	1		415	673	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317012	11317012	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs151205593	NA	P-0002784-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	177	403	0	ENST00000361445.4:c.482A>G	p.Asn161Ser	p.N161S	ENST00000361445	NM_004958.3	161	aAt/aGt	4/58	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.4433760924557	2		403	737	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847351	68847351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs570930882	NA	P-0002784-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	180	417	0	ENST00000261769.5:c.1273G>A	p.Val425Ile	p.V425I	ENST00000261769	NM_004360.3	425	Gtc/Atc	9/16	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.4433760924557	2		417	781	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054241	30054241	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002786-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	181	424	0	ENST00000338641.4:c.663C>A	p.Tyr221Ter	p.Y221*	ENST00000338641	NM_000268.3	221	taC/taA	7/16	0.444807639082386	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.444807639082386	1		424	531	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0002789-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	30	62	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	0.180901685290273	2		62	254	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002789-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	95	520	1	ENST00000269305.4:c.880del	p.Glu294SerfsTer51	p.E294Sfs*51	ENST00000269305	NM_001126112.2	294	Gag/ag	8/11	1	2	FACETS	1	0.903	1	1	0.987	1	CLONAL	2	TRUE	1	0.180901685290273	2		521	519	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002795-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	242	349	0	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	0.177218079061721	2	FACETS	1	0.992	1	0.742	0.694	0.792	INDETERMINATE	1	TRUE	0	0.354374854734518	2		349	920	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277230	41277230	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002795-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	113	238	0	ENST00000349496.5:c.1699G>A	p.Glu567Lys	p.E567K	ENST00000349496	NM_001904.3	567	Gaa/Aaa	11/15	1	2	FACETS	0.969	0.874	1	0.969	0.874	1	CLONAL	1	TRUE	1	0.354374854734518	2		238	658	SUCCESS
APC	324	MSKCC	GRCh37	5	112175273	112175273	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123121	NA	P-0002795-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	76	226	0	ENST00000257430.4:c.3982C>T	p.Gln1328Ter	p.Q1328*	ENST00000257430	NM_000038.5	1328	Cag/Tag	16/16	1	2	FACETS	0.823	0.724	0.93	0.823	0.724	0.93	CLONAL	1	TRUE	1	0.354374854734518	2		226	521	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746086	162746086	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002806-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	768	147	474	0	ENST00000367921.3:c.2209A>T	p.Ser737Cys	p.S737C	ENST00000367921	NM_006182.2	737	Agt/Tgt	16/18	0.443585913864149	3	FACETS	0.885	0.808	0.966	0.443	0.404	0.483	CLONAL	1	TRUE	1	0.443585913864149	3		474	915	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123499643	123499645	+	missense_variant	Missense_Mutation	TNP	CCC	CCC	ACA	novel	NA	P-0002806-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	147	79	273	0	ENST00000371139.4:c.170_172delinsACA	p.Ser57_Gln58delinsTyrLys	p.S57_Q58delinsYK	ENST00000371139	NM_001114937.2	57	tCCCag/tACAag	2/4	1	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.443585913864149	1		273	226	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207102	1207102	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002806-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	606	126	394	0	ENST00000326873.7:c.191del	p.Lys64ArgfsTer32	p.K64Rfs*32	ENST00000326873	NM_000455.4	64	Aag/ag	1/10	0.367716954910211	1	FACETS	0.604	0.547	0.664	0.604	0.547	0.664	SUBCLONAL	1	TRUE	0	0.443585913864149	1		394	732	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380279	25380282	+	missense_variant	Missense_Mutation	ONP	CCTG	CCTG	ACTC	novel	NA	P-0002806-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	618	127	479	0	ENST00000311936.3:c.176_179delinsGAGT	p.Ala59_Gly60delinsGlyVal	p.A59_G60delinsGV	ENST00000311936	NM_004985.3	59	gCAGGt/gGAGTt	3/5	1	2	FACETS	0.769	0.697	0.844	0.769	0.697	0.844	SUBCLONAL	1	TRUE	1	0.443585913864149	2		479	745	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144865	11144865	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002816-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	163	345	0	ENST00000358026.2:c.3940G>T	p.Asp1314Tyr	p.D1314Y	ENST00000358026	NM_001128849.1	1314	Gat/Tat	28/36	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.710205582073444	2		345	456	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225556	2225556	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	38	482	0	ENST00000326181.6:c.1559A>G	p.Asn520Ser	p.N520S	ENST00000326181	NM_032271.2	520	aAc/aGc	17/21	0.276034866731699	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		482	149	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474064	29474064	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002826-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	294	466	0	ENST00000389048.3:c.2111C>A	p.Ala704Asp	p.A704D	ENST00000389048	NM_004304.4	704	gCc/gAc	12/29	0.406733100328321	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.406733100328321	4		466	962	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451442	187451442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002826-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	205	348	0	ENST00000232014.4:c.40C>T	p.His14Tyr	p.H14Y	ENST00000232014	NM_001130845.1	14	Cat/Tat	3/10	0.406733100328321		FACETS		0.927	1				CLONAL	2	TRUE	0	0.406733100328321	2		348	509	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521309	187521309	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002826-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	164	577	0	ENST00000441802.2:c.11846A>T	p.Tyr3949Phe	p.Y3949F	ENST00000441802	NM_005245.3	3949	tAt/tTt	22/27	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.406733100328321	2		577	796	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187525	32187525	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002826-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	80	280	0	ENST00000375023.3:c.1354T>A	p.Cys452Ser	p.C452S	ENST00000375023	NM_004557.3	452	Tgc/Agc	8/30	0.406733100328321	3	FACETS	0.919	0.811	1	0.46	0.405	0.518	CLONAL	1	TRUE	1	0.406733100328321	3		280	515	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374323	81374323	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002826-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	292	428	0	ENST00000222390.5:c.739C>G	p.Pro247Ala	p.P247A	ENST00000222390	NM_000601.4	247	Cct/Gct	6/18	0.406733100328321	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.406733100328321	3		428	788	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615036	43615036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1345166214	NA	P-0002826-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	108	489	0	ENST00000355710.3:c.2450G>A	p.Arg817His	p.R817H	ENST00000355710	NM_020975.4	817	cGc/cAc	14/20	0.406733100328321	3	FACETS	0.846	0.76	0.938	0.423	0.38	0.469	CLONAL	1	TRUE	1	0.406733100328321	3		489	755	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790512	3790512	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002826-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	116	400	0	ENST00000262367.5:c.4021C>T	p.Arg1341Ter	p.R1341*	ENST00000262367	NM_004380.2	1341	Cga/Tga	24/31	0.406733100328321	3	FACETS	0.883	0.796	0.975	0.442	0.398	0.488	CLONAL	1	TRUE	1	0.406733100328321	3		400	777	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858037	9858037	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002826-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	152	552	0	ENST00000330684.3:c.3364G>T	p.Gly1122Cys	p.G1122C	ENST00000330684	NM_001134407.1	1122	Ggt/Tgt	13/13	0.406733100328321	3	FACETS	0.903	0.825	0.985	0.452	0.412	0.493	CLONAL	1	TRUE	1	0.406733100328321	3		552	996	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641459	23641459	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002826-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	410	608	0	ENST00000261584.4:c.2016A>T	p.Glu672Asp	p.E672D	ENST00000261584	NM_024675.3	672	gaA/gaT	5/13	0.406733100328321	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.406733100328321	3		608	1090	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512269	38512269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002826-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	123	375	0	ENST00000254066.5:c.1180C>T	p.Arg394Trp	p.R394W	ENST00000254066	NM_000964.3	394	Cgg/Tgg	9/9	0.406733100328321	3	FACETS	1	0.907	1	0.501	0.454	0.551	CLONAL	1	TRUE	1	0.406733100328321	3		375	726	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218447	1218447	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0002826-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	647	471	0	ENST00000326873.7:c.322A>T	p.Lys108Ter	p.K108*	ENST00000326873	NM_000455.4	108	Aaa/Taa	2/10	0.400918495909688	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	4	TRUE	0	0.406733100328321	4		471	1058	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921643	39921643	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002826-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	38	400	0	ENST00000378444.4:c.4177A>T	p.Thr1393Ser	p.T1393S	ENST00000378444	NM_001123385.1	1393	Act/Tct	10/15	0.242152292706962	3	FACETS	0.35	0.288	0.419	0.117	0.096	0.14	INDETERMINATE	1	TRUE	0	0.406733100328321	3		400	643	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0002826-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	533	278	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.406733100328321	3	FACETS	0.949	0.914	0.984	1	0.997	1	CLONAL	3	TRUE	1	0.406733100328321	3		278	1108	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0002841-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	229	221	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.994	0.927	1	0.994	0.927	1	CLONAL	1	TRUE	1	0.501585272281144	2		221	919	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002841-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	246	315	0	ENST00000263967.3:c.333G>T	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaT	2/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.501585272281144	2		315	840	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458591	120458591	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002841-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	178	309	0	ENST00000256646.2:c.6754G>A	p.Asp2252Asn	p.D2252N	ENST00000256646	NM_024408.3	2252	Gat/Aat	34/34	0.491308949798205	3	FACETS	1	0.945	1	0.515	0.475	0.557	CLONAL	1	TRUE	1	0.501585272281144	3		309	862	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463227	25463227	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002841-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	181	433	0	ENST00000264709.3:c.2266G>C	p.Glu756Gln	p.E756Q	ENST00000264709	NM_175629.2	756	Gag/Cag	19/23	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.501585272281144	2		433	719	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88651921	88651921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002841-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	178	223	0	ENST00000372037.3:c.268G>A	p.Asp90Asn	p.D90N	ENST00000372037	NM_004329.2	90	Gac/Aac	5/13	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.501585272281144	2		223	696	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534316	534316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002841-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	105	265	1	ENST00000451590.1:c.7G>A	p.Glu3Lys	p.E3K	ENST00000451590	NM_001130442.1	3	Gaa/Aaa	2/5	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.501585272281144	2		266	407	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213538	2213538	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002841-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	130	339	0	ENST00000398665.3:c.1558G>A	p.Glu520Lys	p.E520K	ENST00000398665	NM_032482.2	520	Gag/Aag	17/28	1	2	FACETS	0.995	0.907	1	0.995	0.907	1	CLONAL	1	TRUE	1	0.501585272281144	2		339	521	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330581	65330581	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002841-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	299	510	2	ENST00000342505.4:c.1065del	p.Asn357ThrfsTer20	p.N357Tfs*20	ENST00000342505	NM_002227.2	355	gaG/ga	8/25	0.501585272281144	1	FACETS	0.826	0.778	0.874	0.826	0.778	0.874	CLONAL	1	TRUE	0	0.501585272281144	1		512	1082	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946319	55946334	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCACCATTCCACTGC	GGCACCATTCCACTGC	-	novel	NA	P-0002841-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	137	248	0	ENST00000263923.4:c.3849-4_3860del		p.X1283_splice	ENST00000263923	NM_002253.2	1283		30/30	0.267748782637269	3	FACETS	0.87	0.792	0.952	0.435	0.396	0.476	INDETERMINATE	1	TRUE	1	0.501585272281144	3		248	785	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578419	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587781845	NA	P-0002850-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	380	227	0	ENST00000269305.4:c.511G>T	p.Glu171Ter	p.E171*	ENST00000269305	NM_001126112.2	171	Gag/Tag	5/11	0.473536205288536	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	2	0.549112529664539	4		227	1029	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0002850-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	347	415	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.473536205288536	4	FACETS	0.863	0.818	0.91	0.863	0.818	0.91	CLONAL	2	TRUE	2	0.549112529664539	4		415	1134	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445028	49445028	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs75226229	NA	P-0002850-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	103	142	1	ENST00000301067.7:c.2438C>T	p.Pro813Leu	p.P813L	ENST00000301067	NM_003482.3	813	cCg/cTg	10/54	0.549112529664539	3	FACETS	0.84	0.754	0.931	0.42	0.377	0.466	CLONAL	1	TRUE	1	0.549112529664539	3		143	569	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257132	198257132	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002850-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	163	426	0	ENST00000335508.6:c.3810C>A	p.Asn1270Lys	p.N1270K	ENST00000335508	NM_012433.2	1270	aaC/aaA	25/25	1	2	FACETS	0.968	0.893	1	0.968	0.893	1	CLONAL	1	TRUE	1	0.549112529664539	2		426	613	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521706	89521706	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002850-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	282	350	0	ENST00000336596.2:c.2783G>C	p.Cys928Ser	p.C928S	ENST00000336596	NM_005233.5	928	tGc/tCc	16/17	0.549112529664539	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.549112529664539	2		350	510	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468194	50468194	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002850-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	351	323	2	ENST00000331340.3:c.1429T>A	p.Tyr477Asn	p.Y477N	ENST00000331340	NM_006060.4	477	Tac/Aac	8/8	0.473536205288536	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	2	0.549112529664539	4		325	976	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508683	106508683	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002850-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	262	360	0	ENST00000359195.3:c.677G>T	p.Arg226Leu	p.R226L	ENST00000359195	NM_002649.2	226	cGc/cTc	2/11	0.473536205288536	4	FACETS	1	0.992	1	0.718	0.673	0.765	CLONAL	1	TRUE	2	0.549112529664539	4		360	1029	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371963	55371963	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002850-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	107	150	0	ENST00000297316.4:c.653C>A	p.Pro218Gln	p.P218Q	ENST00000297316	NM_022454.3	218	cCg/cAg	2/2	0.549112529664539	4	FACETS	1	0.933	1			1	CLONAL	1	TRUE	NA	0.549112529664539	4		150	576	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94211901	94211901	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1446077946	NA	P-0002850-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	120	384	0	ENST00000323929.3:c.544G>A	p.Gly182Arg	p.G182R	ENST00000323929	NM_005591.3	182	Gga/Aga	6/20	0.549112529664539	3	FACETS	0.864	0.782	0.95	0.432	0.391	0.475	CLONAL	1	TRUE	1	0.549112529664539	3		384	645	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929185	32929185	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002850-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	277	469	0	ENST00000380152.3:c.7195A>T	p.Thr2399Ser	p.T2399S	ENST00000380152		2399	Aca/Tca	14/27	0.234745331024529	5	FACETS	0.96	0.903	1	0.64	0.602	0.679	INDETERMINATE	2	TRUE	2	0.549112529664539	5		469	958	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987078	36987078	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002850-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3599	287	269	0	ENST00000354822.5:c.611A>G	p.Tyr204Cys	p.Y204C	ENST00000354822	NM_001079668.2	204	tAc/tGc	3/3	0.549112529664539	19	FACETS	0.762	0.712	0.815			1	SUBCLONAL	2	TRUE	NA	0.549112529664539	19		269	3886	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2115571	2115571	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs149877669	NA	P-0002850-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	88	377	0	ENST00000219476.3:c.1651G>T	p.Ala551Ser	p.A551S	ENST00000219476	NM_000548.3	551	Gcc/Tcc	16/42	1	2	FACETS	0.34	0.3	0.382	0.34	0.3	0.382	SUBCLONAL	1	TRUE	1	0.549112529664539	2		377	944	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602760	10602760	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002850-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	462	368	0	ENST00000171111.5:c.818G>C	p.Cys273Ser	p.C273S	ENST00000171111	NM_203500.1	273	tGc/tCc	3/6	0.549112529664539	2	FACETS	0.989	0.951	1	0.989	0.951	1	CLONAL	2	TRUE	0	0.549112529664539	2		368	851	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735447	40735447	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs745862490	NA	P-0002850-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	452	378	0	ENST00000373198.4:c.3426G>T	p.Arg1142Ser	p.R1142S	ENST00000373198	NM_133170.3	1142	agG/agT	25/32	0.549112529664539	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.549112529664539	3		378	1015	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484596	57484596	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913494	NA	P-0002850-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	301	248	0	ENST00000371085.3:c.680A>T	p.Gln227Leu	p.Q227L	ENST00000371085	NM_000516.4	227	cAg/cTg	9/13	0.549112529664539	3	FACETS	0.969	0.919	1	0.969	0.919	1	CLONAL	2	TRUE	1	0.549112529664539	3		248	721	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817344	39817344	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002850-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	193	403	0	ENST00000288319.7:c.219C>A	p.Ser73Arg	p.S73R	ENST00000288319	NM_182918.3	73	agC/agA	2/10	0.549112529664539	4	FACETS	1	0.973	1	0.37	0.342	0.4	CLONAL	1	TRUE	1	0.549112529664539	4		403	980	SUCCESS
AR	367	MSKCC	GRCh37	X	66942725	66942725	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002850-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	163	235	0	ENST00000374690.3:c.2506A>G	p.Ile836Val	p.I836V	ENST00000374690	NM_000044.3	836	Atc/Gtc	7/8	0.366351886399226	0	FACETS	0.881	0.825	0.936			1	CLONAL	1	TRUE	NA	0.549112529664539	0		235	304	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859633	151859634	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0002850-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	253	357	0	ENST00000262189.6:c.11028_11029del	p.Cys3677TyrfsTer10	p.C3677Yfs*10	ENST00000262189	NM_170606.2	3676	ctATgt/ctgt	43/59	0.272402050206709	4	FACETS	0.803	0.753	0.854	0.803	0.753	0.854	INDETERMINATE	2	TRUE	2	0.549112529664539	4		357	889	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0002856-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	47	62	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.319076029039908	2	FACETS	1	0.964	1	0.748	0.64	0.863	CLONAL	1	TRUE	0	0.334412011826855	2		62	188	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0002856-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	142	420	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.329093273154409	3	FACETS	1	0.971	1	0.748	0.687	0.81	CLONAL	2	TRUE	0	0.334412011826855	3		420	442	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0002859-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	42	129	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.271660414623856	2		129	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0002859-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	101	323	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.271660414623856	1	FACETS	0.98	0.877	1	0.98	0.877	1	CLONAL	1	TRUE	0	0.271660414623856	1		323	656	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096252	178096252	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0002859-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	77	177	0	ENST00000397062.3:c.1079C>G	p.Ser360Ter	p.S360*	ENST00000397062	NM_006164.4	360	tCa/tGa	5/5	1	2	FACETS	0.887	0.779	1	0.887	0.779	1	CLONAL	1	TRUE	1	0.271660414623856	2		177	639	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293639	1293639	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002859-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	208	218	0	ENST00000310581.5:c.1362G>T	p.Gln454His	p.Q454H	ENST00000310581	NM_198253.2	454	caG/caT	2/16	0.271660414623856	5	FACETS	0.981	0.918	1	0.981	0.918	1	CLONAL	4	TRUE	1	0.271660414623856	5		218	549	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751386	57751386	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002859-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	110	234	0	ENST00000274289.3:c.1605G>A	p.Met535Ile	p.M535I	ENST00000274289	NM_006622.3	535	atG/atA	11/14	0.250785743809688	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.271660414623856	1		234	582	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433706	149433706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002859-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	99	273	0	ENST00000286301.3:c.2845G>A	p.Glu949Lys	p.E949K	ENST00000286301	NM_005211.3	949	Gag/Aag	22/22	0.271660414623856	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.271660414623856	1		273	601	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402803	20402803	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002859-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	12	42	0	ENST00000346618.3:c.340C>T	p.Gln114Ter	p.Q114*	ENST00000346618	NM_001949.4	114	Cag/Tag	1/7	1	2	FACETS	0.94	0.668	1	0.94	0.668	1	CLONAL	1	TRUE	1	0.271660414623856	2		42	94	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391284	139391284	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002859-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	72	300	0	ENST00000277541.6:c.6907A>T	p.Ser2303Cys	p.S2303C	ENST00000277541	NM_017617.3	2303	Agt/Tgt	34/34	0.271660414623856	1	FACETS	0.844	0.738	0.957	0.844	0.738	0.957	CLONAL	1	TRUE	0	0.271660414623856	1		300	543	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150330	108150330	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002859-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	23	212	0	ENST00000278616.4:c.3397G>C	p.Glu1133Gln	p.E1133Q	ENST00000278616	NM_000051.3	1133	Gaa/Caa	23/63	0.151071901732296	3	FACETS	0.427	0.332	0.538	0.142	0.11	0.18	INDETERMINATE	1	TRUE	0	0.271660414623856	3		212	450	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198472	108198472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881314	NA	P-0002859-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	56	197	0	ENST00000278616.4:c.7076C>T	p.Thr2359Ile	p.T2359I	ENST00000278616	NM_000051.3	2359	aCc/aTc	48/63	0.151071901732296	3	FACETS	0.803	0.688	0.929	0.268	0.229	0.31	INDETERMINATE	1	TRUE	0	0.271660414623856	3		197	583	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811633	102811633	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002859-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	137	425	0	ENST00000307046.8:c.551G>C	p.Ser184Thr	p.S184T	ENST00000307046	NM_001111285.1	184	aGt/aCt	4/4	1	2	FACETS	0.878	0.797	0.963	0.878	0.797	0.963	CLONAL	1	TRUE	1	0.271660414623856	2		425	1149	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727455	66727455	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs869025608	NA	P-0002859-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	71	235	0	ENST00000307102.5:c.171G>C	p.Lys57Asn	p.K57N	ENST00000307102	NM_002755.3	57	aaG/aaC	2/11	1	2	FACETS	0.843	0.736	0.959	0.843	0.736	0.959	CLONAL	1	TRUE	1	0.271660414623856	2		235	620	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922680	44922680	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002859-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	94	313	1	ENST00000377967.4:c.1541G>C	p.Gly514Ala	p.G514A	ENST00000377967	NM_021140.2	514	gGa/gCa	16/29	1	2	FACETS	0.934	0.831	1	0.934	0.831	1	CLONAL	1	TRUE	1	0.271660414623856	2		314	741	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243893	53243893	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002859-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	99	352	2	ENST00000375401.3:c.1100G>T	p.Arg367Leu	p.R367L	ENST00000375401	NM_004187.3	367	cGg/cTg	8/26	1	2	FACETS	0.892	0.796	0.995	0.892	0.796	0.995	CLONAL	1	TRUE	1	0.271660414623856	2		354	817	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339551	70339551	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002859-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	113	391	0	ENST00000374080.3:c.220A>T	p.Ser74Cys	p.S74C	ENST00000374080		74	Agc/Tgc	3/45	1	2	FACETS	0.922	0.829	1	0.922	0.829	1	CLONAL	1	TRUE	1	0.271660414623856	2		391	902	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937995	76937995	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002859-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	69	371	0	ENST00000373344.5:c.2753C>A	p.Thr918Asn	p.T918N	ENST00000373344	NM_000489.3	918	aCt/aAt	9/35	1	2	FACETS	0.617	0.536	0.705	0.617	0.536	0.705	SUBCLONAL	1	TRUE	1	0.271660414623856	2		371	823	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939693	76939693	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002859-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	106	393	0	ENST00000373344.5:c.1055T>G	p.Met352Arg	p.M352R	ENST00000373344	NM_000489.3	352	aTg/aGg	9/35	1	2	FACETS	0.814	0.728	0.905	0.814	0.728	0.905	CLONAL	1	TRUE	1	0.271660414623856	2		393	959	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123199756	123199756	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002859-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	77	333	0	ENST00000218089.9:c.2056C>G	p.Gln686Glu	p.Q686E	ENST00000218089	NM_001042749.1	686	Cag/Gag	21/35	1	2	FACETS	0.863	0.758	0.976	0.863	0.758	0.976	CLONAL	1	TRUE	1	0.271660414623856	2		333	657	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158700	26158700	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002859-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	20	61	0	ENST00000289316.2:c.303del	p.Leu102CysfsTer33	p.L102Cfs*33	ENST00000289316	NM_138720.2	101	ctG/ct	1/2	1	2	FACETS	0.969	0.747	1	0.969	0.747	1	CLONAL	1	TRUE	1	0.271660414623856	2		61	152	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513213	44513213	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	novel	NA	P-0002859-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	37	104	0	ENST00000291552.4:c.722G>C	p.Ter241SerextTer10	p.*241Sext*10	ENST00000291552	NM_006758.2	241	tGa/tCa	8/8	1	2	FACETS	0.973	0.806	1	0.973	0.806	1	CLONAL	1	TRUE	1	0.271660414623856	2		104	280	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939461	76939462	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0002859-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	59	380	0	ENST00000373344.5:c.1286_1287delinsAA	p.Thr429Lys	p.T429K	ENST00000373344	NM_000489.3	429	aCC/aAA	9/35	1	2	FACETS	0.548	0.471	0.633	0.548	0.471	0.633	SUBCLONAL	1	TRUE	1	0.271660414623856	2		380	792	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237595	16237595	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0002866-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	55	291	0	ENST00000375759.3:c.1043-1G>C		p.X348_splice	ENST00000375759	NM_015001.2	348			0.466162414670027	1	FACETS	0.411	0.352	0.475	0.411	0.352	0.475	SUBCLONAL	1	TRUE	0	0.466162414670027	1		291	440	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588144	69588144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002866-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	175	507	2	ENST00000168712.1:c.554G>A	p.Gly185Glu	p.G185E	ENST00000168712	NM_002007.2	185	gGg/gAg	3/3	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.466162414670027	2		509	750	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0002869-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	195	401	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.436907327972271	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.451011766152322	1		401	621	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244485	46244485	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs147193304	NA	P-0002869-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	44	336	0	ENST00000334344.6:c.2579A>G	p.Asn860Ser	p.N860S	ENST00000334344	NM_152641.2	860	aAt/aGt	15/21	0.451011766152322	1	FACETS	0.218	0.182	0.258	0.218	0.182	0.258	SUBCLONAL	1	TRUE	0	0.451011766152322	1		336	692	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101065	41101065	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002869-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	123	262	0	ENST00000373198.4:c.1291A>G	p.Asn431Asp	p.N431D	ENST00000373198	NM_133170.3	431	Aac/Gac	8/32	1	2	FACETS	0.8	0.724	0.879	0.8	0.724	0.879	SUBCLONAL	1	TRUE	1	0.451011766152322	2		262	682	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360591	70360591	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002869-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	124	124	0	ENST00000374080.3:c.6151C>T	p.Gln2051Ter	p.Q2051*	ENST00000374080		2051	Cag/Tag	42/45	0.248872040407469	0	FACETS	0.99	0.909	1			1	INDETERMINATE	1	TRUE	NA	0.451011766152322	0		124	305	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242481	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAA	AATTAAGAGAAGCAA	CACCAT	novel	NA	P-0002869-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	283	277	0	ENST00000275493.2:c.2237_2251delinsCACCAT	p.Glu746_Thr751delinsAlaProSer	p.E746_T751delinsAPS	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAAca/gCACCATca	19/28	0.341030674089342	4	FACETS	1	0.988	1	0.775	0.732	0.819	CLONAL	2	TRUE	1	0.451011766152322	4		277	783	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0002873-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	232	378	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.681445773933512	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.704742763472016	1		378	421	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246998	53246998	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002873-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	249	215	0	ENST00000375401.3:c.502C>T	p.Gln168Ter	p.Q168*	ENST00000375401	NM_004187.3	168	Cag/Tag	4/26	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.704742763472016	1		215	370	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889201	76889201	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0002885-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	368	504	2	ENST00000373344.5:c.4810-1G>A		p.X1604_splice	ENST00000373344	NM_000489.3	1604			0.817289031987045	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.831731083971105	2		506	442	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165638	118165652	+	inframe_deletion	In_Frame_Del	DEL	GACATCGTCCAGACC	GACATCGTCCAGACC	-	novel	NA	P-0002885-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	211	314	0	ENST00000369448.3:c.149_163del	p.Asp50_Thr54del	p.D50_T54del	ENST00000369448	NM_017709.3	50	GACATCGTCCAGACC/-	2/2	0.831731083971105	4	FACETS	0.924	0.858	0.992	0.462	0.429	0.496	CLONAL	1	TRUE	2	0.831731083971105	4		314	1006	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0002894-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	332	372	5	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.540802209118791	2	FACETS	0.965	0.923	1	0.965	0.923	1	CLONAL	2	TRUE	0	0.584313659596584	2		377	589	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180367	32180367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1382129029	NA	P-0002903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	63	439	0	ENST00000375023.3:c.2564G>A	p.Arg855His	p.R855H	ENST00000375023	NM_004557.3	855	cGc/cAc	17/30	0.487486726365659	2	FACETS	0.839	0.731	0.954	0.42	0.365	0.477	CLONAL	1	TRUE	0	0.487486726365659	2		439	308	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248854	133248854	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755090755	NA	P-0002903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	101	695	0	ENST00000320574.5:c.1741G>A	p.Ala581Thr	p.A581T	ENST00000320574	NM_006231.2	581	Gcc/Acc	16/49	0.487486726365659	2	FACETS	1	0.96	1	0.563	0.508	0.621	CLONAL	1	TRUE	0	0.487486726365659	2		695	368	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412913	49412913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	54	840	0	ENST00000418115.1:c.110C>T	p.Thr37Ile	p.T37I	ENST00000418115	NM_001664.2	37	aCa/aTa	2/5	0.487486726365659	2	FACETS	0.998	0.863	1	0.499	0.431	0.571	CLONAL	1	TRUE	0	0.487486726365659	2		840	222	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254906	16254906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	139	456	0	ENST00000375759.3:c.2171G>A	p.Arg724Gln	p.R724Q	ENST00000375759	NM_015001.2	724	cGa/cAa	11/15	0.487486726365659	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.487486726365659	2		456	265	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301854	65301854	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	50	424	0	ENST00000342505.4:c.3185C>T	p.Ser1062Phe	p.S1062F	ENST00000342505	NM_002227.2	1062	tCt/tTt	23/25	0.487486726365659	2	FACETS	1	0.911	1	0.54	0.465	0.62	CLONAL	1	TRUE	0	0.487486726365659	2		424	190	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306959	65306959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1358494508	NA	P-0002903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	15	642	0	ENST00000342505.4:c.2618G>A	p.Arg873His	p.R873H	ENST00000342505	NM_002227.2	873	cGc/cAc	19/25	0.487486726365659	2	FACETS	0.189	0.138	0.251	0.095	0.069	0.126	SUBCLONAL	1	TRUE	0	0.487486726365659	2		642	325	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335079	65335079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	43	661	0	ENST00000342505.4:c.562G>A	p.Glu188Lys	p.E188K	ENST00000342505	NM_002227.2	188	Gag/Aag	6/25	0.487486726365659	2	FACETS	0.754	0.636	0.882	0.377	0.318	0.441	SUBCLONAL	1	TRUE	0	0.487486726365659	2		661	234	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849887	156849887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759190964	NA	P-0002903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	20	602	0	ENST00000524377.1:c.2143G>A	p.Val715Met	p.V715M	ENST00000524377	NM_002529.3	715	Gtg/Atg	16/17	0.487486726365659	2	FACETS	0.21	0.16	0.269	0.105	0.08	0.135	SUBCLONAL	1	TRUE	0	0.487486726365659	2		602	390	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029144	26029144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	39	670	1	ENST00000435504.4:c.206G>A	p.Gly69Asp	p.G69D	ENST00000435504		69	gGc/gAc	4/13	0.487486726365659	2	FACETS	0.724	0.605	0.854	0.362	0.302	0.427	SUBCLONAL	1	TRUE	0	0.487486726365659	2		671	221	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193507	99193507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1471383993	NA	P-0002903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	182	524	2	ENST00000074304.5:c.2702G>A	p.Arg901His	p.R901H	ENST00000074304	NM_001134224.1	901	cGt/cAt	25/26	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	2	TRUE	NA	0.487486726365659	2		526	342	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103828	47103828	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs976581260	NA	P-0002903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	102	600	0	ENST00000409792.3:c.6118C>T	p.Arg2040Ter	p.R2040*	ENST00000409792	NM_014159.6	2040	Cga/Tga	14/21	0.487486726365659	2	FACETS	0.969	0.887	1	0.969	0.887	1	CLONAL	2	TRUE	0	0.487486726365659	2		600	216	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521114	187521114	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760053140	NA	P-0002903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	190	507	3	ENST00000441802.2:c.12041C>T	p.Thr4014Met	p.T4014M	ENST00000441802	NM_005245.3	4014	aCg/aTg	22/27	0.487486726365659	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.487486726365659	2		510	366	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629339	187629339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202126944	NA	P-0002903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	54	662	0	ENST00000441802.2:c.1643G>A	p.Arg548His	p.R548H	ENST00000441802	NM_005245.3	548	cGc/cAc	2/27	0.487486726365659	2	FACETS	0.669	0.575	0.772	0.335	0.287	0.386	SUBCLONAL	1	TRUE	0	0.487486726365659	2		662	331	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645172	86645172	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	43	435	0	ENST00000274376.6:c.1244A>T	p.Tyr415Phe	p.Y415F	ENST00000274376	NM_002890.2	415	tAt/tTt	8/25	0.200756113047407	6	FACETS	1	0.948	1	0.443	0.373	0.52	INDETERMINATE	1	TRUE	3	0.487486726365659	6		435	262	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721723	176721723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745704989	NA	P-0002903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	168	457	0	ENST00000439151.2:c.7354G>A	p.Ala2452Thr	p.A2452T	ENST00000439151	NM_022455.4	2452	Gct/Act	23/23	0.200756113047407	6	FACETS	1	0.952	1	1	0.952	1	INDETERMINATE	3	TRUE	3	0.487486726365659	6		457	440	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367275	50367275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778910457	NA	P-0002903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	68	454	1	ENST00000331340.3:c.82G>A	p.Asp28Asn	p.D28N	ENST00000331340	NM_006060.4	28	Gat/Aat	3/8	0.315026019828252	6	FACETS	1	0.924	1	0.362	0.315	0.413	CLONAL	1	TRUE	3	0.487486726365659	6		455	507	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623686	43623686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532862288	NA	P-0002903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	12	559	0	ENST00000355710.3:c.3314C>T	p.Ala1105Val	p.A1105V	ENST00000355710	NM_020975.4	1105	gCg/gTg	20/20	0.484241258665018	2	FACETS	0.239	0.168	0.327	0.119	0.084	0.164	SUBCLONAL	1	TRUE	0	0.487486726365659	2		559	206	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206633	108206633	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0002903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	111	687	0	ENST00000278616.4:c.8213T>A	p.Leu2738Ter	p.L2738*	ENST00000278616	NM_000051.3	2738	tTa/tAa	56/63	0.487486726365659	2	FACETS	0.889	0.815	0.965	0.889	0.815	0.965	CLONAL	2	TRUE	0	0.487486726365659	2		687	256	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245945	46245945	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1170525254	NA	P-0002903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	88	539	0	ENST00000334344.6:c.4039C>T	p.Gln1347Ter	p.Q1347*	ENST00000334344	NM_152641.2	1347	Caa/Taa	15/21	0.487486726365659	2	FACETS	0.96	0.872	1	0.96	0.872	1	CLONAL	2	TRUE	0	0.487486726365659	2		539	188	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50481162	50481162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	63	589	0	ENST00000394963.4:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000394963	NM_003076.4	183	cGa/cAa	5/13	0.487486726365659	2	FACETS	0.901	0.786	1	0.45	0.393	0.512	CLONAL	1	TRUE	0	0.487486726365659	2		589	287	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41001222	41001222	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	50	710	0	ENST00000267868.3:c.344-1G>A		p.X115_splice	ENST00000267868	NM_002875.4	115			0.487486726365659	2	FACETS	0.904	0.775	1	0.452	0.387	0.521	CLONAL	1	TRUE	0	0.487486726365659	2		710	227	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831226	3831226	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398406959	NA	P-0002903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	75	542	0	ENST00000262367.5:c.1655C>T	p.Pro552Leu	p.P552L	ENST00000262367	NM_004380.2	552	cCg/cTg	7/31	0.348318057627766	4	FACETS	0.848	0.752	0.948	0.848	0.752	0.948	CLONAL	2	TRUE	2	0.487486726365659	4		542	270	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805671	89805671	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201886956	NA	P-0002903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	149	568	0	ENST00000389301.3:c.4037C>T	p.Ala1346Val	p.A1346V	ENST00000389301	NM_000135.2	1346	gCg/gTg	41/43	0.348318057627766	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	2	0.487486726365659	4		568	420	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919545	78919545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776174012	NA	P-0002903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	131	533	0	ENST00000306801.3:c.3104C>T	p.Thr1035Met	p.T1035M	ENST00000306801	NM_020761.2	1035	aCg/aTg	26/34	0.487486726365659	2	FACETS	0.933	0.862	1	0.933	0.862	1	CLONAL	2	TRUE	0	0.487486726365659	2		533	288	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121109	3121109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773591539	NA	P-0002903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	25	589	0	ENST00000078429.4:c.1012C>T	p.Arg338Cys	p.R338C	ENST00000078429	NM_002067.2	338	Cgc/Tgc	7/7	0.487486726365659	3	FACETS	0.277	0.218	0.346	0.092	0.072	0.116	SUBCLONAL	1	TRUE	0	0.487486726365659	3		589	460	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937109	39937109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757971608	NA	P-0002903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	179	614	2	ENST00000378444.4:c.74C>T	p.Ala25Val	p.A25V	ENST00000378444	NM_001123385.1	25	gCg/gTg	2/15	0.487486726365659	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.487486726365659	1		616	371	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226022	53226022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	187	685	3	ENST00000375401.3:c.2827C>T	p.Arg943Ter	p.R943*	ENST00000375401	NM_004187.3	943	Cga/Tga	19/26	0.487486726365659	1	FACETS	0.831	0.782	0.88	1	0.993	1	CLONAL	2	TRUE	0	0.487486726365659	1		688	349	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026590	48026590	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	83	481	0	ENST00000234420.5:c.1468del	p.Glu490LysfsTer2	p.E490Kfs*2	ENST00000234420	NM_000179.2	490	Gaa/aa	4/10	0.487486726365659	2	FACETS	0.906	0.818	0.994	0.906	0.818	0.994	CLONAL	2	TRUE	0	0.487486726365659	2		481	188	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720856	89720875	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	ACTTTTCTCCAAATTTTAAG	ACTTTTCTCCAAATTTTAAG	-	novel	NA	P-0002903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	32	274	0	ENST00000371953.3:c.1007_1026del	p.Tyr336CysfsTer18	p.Y336Cfs*18	ENST00000371953	NM_000314.4	336	tACTTTTCTCCAAATTTTAAG/t	8/9	0.484241258665018	2	FACETS	0.772	0.648	0.902	0.772	0.648	0.902	CLONAL	2	TRUE	0	0.487486726365659	2		274	85	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0002922-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	216	221	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.378260975582222	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.40632172785321	3		221	622	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0002922-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	245	271	0	ENST00000269305.4:c.559+1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.254369995172211	3	FACETS	0.985	0.932	1			1	CLONAL	3	TRUE	NA	0.40632172785321	3		271	491	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs104886003	NA	P-0002922-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	44	178	0	ENST00000263967.3:c.1633G>C	p.Glu545Gln	p.E545Q	ENST00000263967	NM_006218.2	545	Gag/Cag	10/21	0.378260975582222	3	FACETS	0.663	0.557	0.78	0.332	0.278	0.39	SUBCLONAL	1	TRUE	1	0.40632172785321	3		178	393	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262489	16262489	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002922-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	25	159	0	ENST00000375759.3:c.9754G>T	p.Val3252Phe	p.V3252F	ENST00000375759	NM_015001.2	3252	Gtc/Ttc	11/15	0.254369995172211	3	FACETS	0.569	0.45	0.706			1	SUBCLONAL	1	TRUE	NA	0.40632172785321	3		159	260	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023609	27023609	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002922-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	51	263	0	ENST00000324856.7:c.715C>G	p.Pro239Ala	p.P239A	ENST00000324856	NM_006015.4	239	Ccg/Gcg	1/20	NA	2	FACETS	0.671	0.572	0.779			1	INDETERMINATE	1	TRUE	NA	0.40632172785321	2		263	374	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469128	25469128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002922-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	86	530	0	ENST00000264709.3:c.1330G>A	p.Glu444Lys	p.E444K	ENST00000264709	NM_175629.2	444	Gag/Aag	11/23	0.276061891897895	3	FACETS	0.509	0.449	0.573	0.254	0.224	0.287	SUBCLONAL	1	TRUE	1	0.40632172785321	3		530	1001	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537966	212537966	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002922-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	56	381	0	ENST00000342788.4:c.1639G>C	p.Glu547Gln	p.E547Q	ENST00000342788	NM_005235.2	547	Gag/Cag	14/28	0.256513667172976	3	FACETS	0.484	0.414	0.561	0.242	0.207	0.281	SUBCLONAL	1	TRUE	1	0.40632172785321	3		381	685	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043989	180043989	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1218205510	NA	P-0002922-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	52	385	0	ENST00000261937.6:c.3007G>A	p.Asp1003Asn	p.D1003N	ENST00000261937	NM_182925.4	1003	Gac/Aac	22/30	0.256513667172976	3	FACETS	0.473	0.402	0.551	0.237	0.201	0.276	SUBCLONAL	1	TRUE	1	0.40632172785321	3		385	651	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642495	117642495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs9489124	NA	P-0002922-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	52	487	1	ENST00000368508.3:c.5704G>A	p.Glu1902Lys	p.E1902K	ENST00000368508	NM_002944.2	1902	Gaa/Aaa	35/43	0.276061891897895	3	FACETS	0.327	0.277	0.382	0.163	0.138	0.191	SUBCLONAL	1	TRUE	1	0.40632172785321	3		488	942	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150373	157150373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762428637	NA	P-0002922-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	152	396	0	ENST00000346085.5:c.1555G>A	p.Asp519Asn	p.D519N	ENST00000346085	NM_020732.3	519	Gat/Aat	2/20	0.276061891897895	3	FACETS	1	0.977	1	0.596	0.546	0.649	CLONAL	1	TRUE	1	0.40632172785321	3		396	755	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741620	145741620	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002922-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1435	126	487	0	ENST00000428558.2:c.883G>C	p.Glu295Gln	p.E295Q	ENST00000428558	NM_004260.3	295	Gag/Cag	5/22	0.40632172785321	10	FACETS	1	0.933	1	0.13	0.117	0.144	CLONAL	1	TRUE	2	0.40632172785321	10		487	1561	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41021830	41021830	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1555429629	NA	P-0002922-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	44	392	0	ENST00000267868.3:c.772G>A	p.Glu258Lys	p.E258K	ENST00000267868	NM_002875.4	258	Gag/Aag	8/10	1	2	FACETS	0.291	0.243	0.344	0.291	0.243	0.344	SUBCLONAL	1	TRUE	1	0.40632172785321	2		392	745	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260605	10260605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002922-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	110	501	0	ENST00000340748.4:c.2257G>A	p.Asp753Asn	p.D753N	ENST00000340748		753	Gat/Aat	24/40	0.378260975582222	3	FACETS	0.552	0.494	0.613	0.276	0.247	0.307	SUBCLONAL	1	TRUE	1	0.40632172785321	3		501	1180	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790114	40790114	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002922-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	51	360	0	ENST00000373198.4:c.2617G>T	p.Asp873Tyr	p.D873Y	ENST00000373198	NM_133170.3	873	Gac/Tac	18/32	0.40632172785321	3	FACETS	0.449	0.381	0.525	0.15	0.127	0.175	SUBCLONAL	1	TRUE	0	0.40632172785321	3		360	672	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41521952	41521952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002922-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	55	485	0	ENST00000263253.7:c.814C>T	p.Leu272Phe	p.L272F	ENST00000263253	NM_001429.3	272	Ctc/Ttc	3/31	0.254369995172211	3	FACETS	0.348	0.297	0.405			1	SUBCLONAL	1	TRUE	NA	0.40632172785321	3		485	935	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0002937-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	168	311	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.253203068042004	3	FACETS	0.895	0.827	0.965			1	CLONAL	2	TRUE	NA	0.376070814028174	3		311	593	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678727	52678727	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002937-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	140	368	1	ENST00000394830.3:c.892C>T	p.Arg298Ter	p.R298*	ENST00000394830	NM_018313.4	298	Cga/Tga	9/30	0.326298151345871	3	FACETS	0.788	0.721	0.858			1	SUBCLONAL	2	TRUE	NA	0.376070814028174	3		369	561	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs878854073	NA	P-0002945-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	336	624	0	ENST00000269305.4:c.673-1G>A		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.278209021736382	3	FACETS	0.939	0.899	0.979	1	0.996	1	CLONAL	5	TRUE	0	0.278209021736382	3		624	586	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0002945-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	316	269	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.192648464805146	3	FACETS	0.86	0.813	0.908	1	0.992	1	CLONAL	3	TRUE	1	0.278209021736382	3		269	1003	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0002945-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	193	132	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.278209021736382	5	FACETS	0.986	0.925	1	1	0.988	1	CLONAL	5	TRUE	1	0.278209021736382	5		132	399	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0002945-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	565	751	1	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	0.278209021736382	5	FACETS	0.922	0.89	0.953	1	0.997	1	CLONAL	6	TRUE	1	0.278209021736382	5		752	1041	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178653	56178653	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002945-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	179	640	0	ENST00000399503.3:c.3626A>T	p.Gln1209Leu	p.Q1209L	ENST00000399503	NM_005921.1	1209	cAg/cTg	14/20	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.278209021736382	NA		640	796	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439695	140439695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776664982	NA	P-0002945-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	86	456	1	ENST00000288602.6:c.2044C>T	p.Arg682Trp	p.R682W	ENST00000288602	NM_004333.4	682	Cgg/Tgg	17/18	0.197925404041941	3	FACETS	0.917	0.817	1	0.917	0.817	1	CLONAL	2	TRUE	1	0.278209021736382	3		457	384	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948787	55948787	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs751902659	NA	P-0002946-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	97	514	1	ENST00000263923.4:c.3678C>A	p.Asn1226Lys	p.N1226K	ENST00000263923	NM_002253.2	1226	aaC/aaA	28/30	1	2	FACETS	0.93	0.838	1	0.93	0.838	1	CLONAL	1	TRUE	1	0.642094363025409	2		515	325	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518923	187518923	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002946-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	148	669	0	ENST00000441802.2:c.12281A>T	p.Lys4094Ile	p.K4094I	ENST00000441802	NM_005245.3	4094	aAa/aTa	24/27	1	2	FACETS	0.928	0.853	1	0.928	0.853	1	CLONAL	1	TRUE	1	0.642094363025409	2		669	497	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854962	76854962	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002946-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	142	979	0	ENST00000373344.5:c.5874G>A	p.Trp1958Ter	p.W1958*	ENST00000373344	NM_000489.3	1958	tgG/tgA	25/35	0.149498358828914	0	FACETS	0.339	0.311	0.368			1	INDETERMINATE	1	TRUE	0	0.642094363025409	0		979	467	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851754	134851754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56396912	NA	P-0002947-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	109	500	0	ENST00000398015.3:c.1160C>T	p.Thr387Met	p.T387M	ENST00000398015	NM_004441.4	387	aCg/aTg	5/16	0.12479949853322	5	FACETS	0.974	0.874	1	0.243	0.218	0.27	INDETERMINATE	1	TRUE	1	0.500746189034826	5		500	783	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923343	131923343	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002947-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	72	254	0	ENST00000265335.6:c.846G>A	p.Met282Ile	p.M282I	ENST00000265335		282	atG/atA	6/25	0.12479949853322	5	FACETS	0.995	0.871	1	0.249	0.217	0.282	INDETERMINATE	1	TRUE	1	0.500746189034826	5		254	506	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726685	88726685	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002957-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	219	475	0	ENST00000360948.2:c.359C>A	p.Pro120His	p.P120H	ENST00000360948	NM_001012338.2	120	cCc/cAc	4/19	0.497356833027631	3	FACETS	0.925	0.877	0.972	0.925	0.877	0.972	CLONAL	3	TRUE	0	0.543984100098444	3		475	369	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740138	162740138	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002957-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	478	542	0	ENST00000367921.3:c.1340T>A	p.Leu447Gln	p.L447Q	ENST00000367921	NM_006182.2	447	cTg/cAg	12/18	0.543984100098444	7	FACETS	0.959	0.928	0.989	1	0.995	1	CLONAL	6	TRUE	2	0.543984100098444	7		542	721	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281472	198281472	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002957-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	78	436	0	ENST00000335508.6:c.659A>G	p.Gln220Arg	p.Q220R	ENST00000335508	NM_012433.2	220	cAg/cGg	6/25	0.225824944174877	2	FACETS	1	0.978	1	0.699	0.627	0.774	INDETERMINATE	1	TRUE	0	0.543984100098444	2		436	205	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156936	89156936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002957-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	85	636	0	ENST00000336596.2:c.38G>A	p.Cys13Tyr	p.C13Y	ENST00000336596	NM_005233.5	13	tGc/tAc	1/17	0.147461615847888	1	FACETS	0.748	0.669	0.832	0.748	0.669	0.832	INDETERMINATE	1	TRUE	0	0.543984100098444	1		636	304	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521679	89521679	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs778067909	NA	P-0002957-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	74	483	0	ENST00000336596.2:c.2756G>T	p.Trp919Leu	p.W919L	ENST00000336596	NM_005233.5	919	tGg/tTg	16/17	0.147461615847888	1	FACETS	0.802	0.712	0.896	0.802	0.712	0.896	INDETERMINATE	1	TRUE	0	0.543984100098444	1		483	247	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188394	142188394	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs191588404	NA	P-0002957-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	155	319	0	ENST00000350721.4:c.6337G>C	p.Val2113Leu	p.V2113L	ENST00000350721	NM_001184.3	2113	Gta/Cta	38/47	0.514194728433281	4	FACETS	0.948	0.895	0.999	0.948	0.895	0.999	CLONAL	4	TRUE	0	0.543984100098444	4		319	232	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964325	55964325	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs145905001	NA	P-0002957-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	173	609	0	ENST00000263923.4:c.2488C>A	p.Pro830Thr	p.P830T	ENST00000263923	NM_002253.2	830	Ccc/Acc	17/30	0.543984100098444	8	FACETS	1	0.974	1	0.375	0.346	0.405	CLONAL	2	TRUE	2	0.543984100098444	8		609	744	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244249	153244249	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002957-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	83	420	0	ENST00000281708.4:c.1908T>A	p.Phe636Leu	p.F636L	ENST00000281708	NM_033632.3	636	ttT/ttA	12/12	0.435305930378464	3	FACETS	1	0.904	1			1	CLONAL	1	TRUE	NA	0.543984100098444	3		420	381	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630759	187630759	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002957-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	129	708	0	ENST00000441802.2:c.223G>T	p.Val75Phe	p.V75F	ENST00000441802	NM_005245.3	75	Gtt/Ttt	2/27	0.544714964603303	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.543984100098444	1		708	255	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665415	176665415	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002957-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	208	467	1	ENST00000439151.2:c.4099G>C	p.Glu1367Gln	p.E1367Q	ENST00000439151	NM_022455.4	1367	Gag/Cag	7/23	0.385338200202984	5	FACETS	0.947	0.888	1	0.947	0.888	1	CLONAL	3	TRUE	2	0.543984100098444	5		468	489	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394949	394949	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002957-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	115	329	0	ENST00000380956.4:c.345G>T	p.Gln115His	p.Q115H	ENST00000380956	NM_001195286.1	115	caG/caT	3/9	0.320027831555261	4	FACETS	1	0.943	1			1	INDETERMINATE	2	TRUE	NA	0.543984100098444	4		329	313	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469985	157469985	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554226099	NA	P-0002957-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	87	358	0	ENST00000346085.5:c.2779G>T	p.Gly927Ter	p.G927*	ENST00000346085	NM_020732.3	927	Gga/Tga	9/20	0.512719564627803	2	FACETS	0.833	0.755	0.912	0.833	0.755	0.912	CLONAL	2	TRUE	0	0.543984100098444	2		358	192	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560109	29560109	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002957-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	113	465	0	ENST00000356175.3:c.3586C>T	p.Leu1196Phe	p.L1196F	ENST00000356175	NM_000267.3	1196	Ctt/Ttt	27/57	0.414886273451249	4	FACETS	0.802	0.728	0.879	0.802	0.728	0.879	CLONAL	2	TRUE	2	0.543984100098444	4		465	400	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78820303	78820303	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763716081	NA	P-0002957-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	98	500	0	ENST00000306801.3:c.1243G>A	p.Ala415Thr	p.A415T	ENST00000306801	NM_020761.2	415	Gca/Aca	11/34	0.414886273451249	4	FACETS	1	0.974	1	0.637	0.571	0.705	CLONAL	1	TRUE	2	0.543984100098444	4		500	437	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60795890	60795890	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs750755544	NA	P-0002957-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	189	481	0	ENST00000333681.4:c.688A>G	p.Ile230Val	p.I230V	ENST00000333681		230	Atc/Gtc	3/3	0.40523690893355	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.543984100098444	3		481	413	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954635	17954635	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002957-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	160	456	0	ENST00000458235.1:c.259A>G	p.Ile87Val	p.I87V	ENST00000458235	NM_000215.3	87	Atc/Gtc	3/24	0.544714964603303	2	FACETS	0.987	0.924	1	0.987	0.924	1	CLONAL	2	TRUE	0	0.543984100098444	2		456	298	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380513	31380513	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002957-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	184	542	0	ENST00000328111.2:c.1003T>A	p.Trp335Arg	p.W335R	ENST00000328111	NM_006892.3	335	Tgg/Agg	9/23	0.544714964603303	4	FACETS	0.989	0.92	1	0.989	0.92	1	CLONAL	2	TRUE	2	0.543984100098444	4		542	528	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615113	100615113	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002957-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	128	664	0	ENST00000308731.7:c.802T>A	p.Tyr268Asn	p.Y268N	ENST00000308731	NM_000061.2	268	Tat/Aat	9/19	0.544714964603303	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.543984100098444	1		664	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002957-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	179	388	0	ENST00000269305.4:c.461del	p.Gly154AlafsTer16	p.G154Afs*16	ENST00000269305	NM_001126112.2	154	gGc/gc	5/11	0.521042626163124	3	FACETS	0.891	0.839	0.943	0.891	0.839	0.943	CLONAL	3	TRUE	0	0.543984100098444	3		388	313	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101030	41101030	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002957-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	191	458	0	ENST00000373198.4:c.1326del	p.Thr443ProfsTer14	p.T443Pfs*14	ENST00000373198	NM_133170.3	442	caG/ca	8/32	0.544714964603303	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	2	0.543984100098444	4		458	525	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0002963-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	282	366	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.557137486075573	2		366	843	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0002963-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	691	675	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	NA	2	FACETS	0.857	0.836	0.878			1	INDETERMINATE	3	TRUE	NA	0.557137486075573	2		676	965	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915063	131915063	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002963-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	222	462	2	ENST00000265335.6:c.420G>T	p.Met140Ile	p.M140I	ENST00000265335		140	atG/atT	4/25	0.190555062874437	4	FACETS	0.784	0.732	0.838	0.784	0.732	0.838	INDETERMINATE	2	TRUE	2	0.557137486075573	4		464	791	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0002972-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	471	448	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.699513180422766	2	FACETS	0.977	0.949	1	0.977	0.949	1	CLONAL	2	TRUE	0	0.753395774831437	2		448	640	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65312353	65312353	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375353661	NA	P-0002984-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	151	372	2	ENST00000342505.4:c.1966G>A	p.Val656Ile	p.V656I	ENST00000342505	NM_002227.2	656	Gtc/Atc	14/25	0.642016968390984	4	FACETS	0.922	0.845	1			1	CLONAL	1	FALSE	NA	0.815915516892758	4		374	729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0002984-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	470	401	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.815915516892758	3	FACETS	1	0.996	1	0.813	0.788	0.837	CLONAL	2	FALSE	0	0.815915516892758	3		401	665	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982371	25982371	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002984-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	221	287	0	ENST00000435504.4:c.919C>T	p.Leu307Phe	p.L307F	ENST00000435504		307	Ctc/Ttc	9/13	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	FALSE	NA	0.815915516892758	2		287	398	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451792	29451792	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002984-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	259	370	0	ENST00000389048.3:c.2773G>T	p.Gly925Ter	p.G925*	ENST00000389048	NM_004304.4	925	Gga/Tga	16/29	0.647198565699945	6	FACETS	0.983	0.923	1			1	CLONAL	2	FALSE	NA	0.815915516892758	6		370	850	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435363	110435363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002984-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	56	137	0	ENST00000375856.3:c.3038C>T	p.Pro1013Leu	p.P1013L	ENST00000375856	NM_003749.2	1013	cCg/cTg	1/2	0.619153197839915	1	FACETS	0.713	0.633	0.793	0.713	0.633	0.793	SUBCLONAL	1	FALSE	0	0.815915516892758	1		137	114	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0002990-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	201	527	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.986	0.916	1	0.986	0.916	1	CLONAL	1	TRUE	1	0.540882745123775	2		527	754	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421807	49421808	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0002990-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	235	652	0	ENST00000301067.7:c.14499_14500del	p.Glu4834SerfsTer2	p.E4834Sfs*2	ENST00000301067	NM_003482.3	4833	ggGGaa/ggaa	46/54	1	2	FACETS	0.997	0.932	1	0.997	0.932	1	CLONAL	1	TRUE	1	0.540882745123775	2		652	872	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257086	198257086	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0121465-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	121	588	0	ENST00000335508.6:c.3856A>G	p.Arg1286Gly	p.R1286G	ENST00000335508	NM_012433.2	1286	Aga/Gga	25/25	1	2	FACETS	0.872	0.79	0.959	0.872	0.79	0.959	CLONAL	1	NA	1	0.43818614183004	2		588	633	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393340	393340	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0121465-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	85	500	0	ENST00000380956.4:c.188A>G	p.Asn63Ser	p.N63S	ENST00000380956	NM_001195286.1	63	aAc/aGc	2/9	0.43818614183004	5	FACETS	0.548	0.482	0.618	0.183	0.16	0.206	SUBCLONAL	1	NA	2	0.43818614183004	5		500	1174	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49419966	49419966	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121465-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	96	492	0	ENST00000301067.7:c.15783G>T	p.Gln5261His	p.Q5261H	ENST00000301067	NM_003482.3	5261	caG/caT	48/54	0.43818614183004	3	FACETS	0.577	0.513	0.645	0.288	0.256	0.323	SUBCLONAL	1	NA	1	0.43818614183004	3		492	926	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445007	49445007	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0121465-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	53	161	0	ENST00000301067.7:c.2459A>T	p.Glu820Val	p.E820V	ENST00000301067	NM_003482.3	820	gAg/gTg	10/54	0.43818614183004	3	FACETS	0.804	0.688	0.929	0.402	0.344	0.465	CLONAL	1	NA	1	0.43818614183004	3		161	367	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790092	40790092	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121465-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	196	512	0	ENST00000373198.4:c.2639C>A	p.Pro880His	p.P880H	ENST00000373198	NM_133170.3	880	cCc/cAc	18/32	0.43818614183004	4	FACETS	1	0.969	1	0.545	0.503	0.588	CLONAL	1	NA	2	0.43818614183004	4		512	1181	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940500	76940500	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0121465-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	100	581	0	ENST00000373344.5:c.595-2A>T		p.X199_splice	ENST00000373344	NM_000489.3	199			1	2	FACETS	0.756	0.676	0.84	0.756	0.676	0.84	SUBCLONAL	1	NA	1	0.43818614183004	2		581	604	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970979	21970979	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs6413464	NA	P-0002997-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	78	508	0	ENST00000304494.5:c.379G>T	p.Ala127Ser	p.A127S	ENST00000304494	NM_000077.4	127	Gca/Tca	2/3	0.542402960000321	2	FACETS	1	0.979	1	0.715	0.643	0.788	CLONAL	1	TRUE	0	0.596367104109696	2		508	183	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0002997-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	103	524	0	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	0.289639186156666	2	FACETS	1	0.985	1	0.741	0.677	0.806	INDETERMINATE	1	TRUE	0	0.596367104109696	2		524	233	SUCCESS
FH	2271	MSKCC	GRCh37	1	241676926	241676926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776891545	NA	P-0002999-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	173	532	1	ENST00000366560.3:c.355G>A	p.Ala119Thr	p.A119T	ENST00000366560	NM_000143.3	119	Gca/Aca	3/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.587484513052757	2		533	557	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673736	176673736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002999-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	176	520	2	ENST00000439151.2:c.4436C>T	p.Ala1479Val	p.A1479V	ENST00000439151	NM_022455.4	1479	gCc/gTc	10/23	0.382938218101026	1	FACETS	0.862	0.801	0.924	0.862	0.801	0.924	CLONAL	1	TRUE	0	0.587484513052757	1		522	491	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221711	55221711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760101437	NA	P-0002999-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	14	435	0	ENST00000275493.2:c.755G>A	p.Arg252His	p.R252H	ENST00000275493	NM_005228.3	252	cGc/cAc	7/28	1	2	FACETS	0.077	0.055	0.105	0.077	0.055	0.105	SUBCLONAL	1	TRUE	1	0.587484513052757	2		435	615	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004241	29004241	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772440220	NA	P-0002999-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	126	606	0	ENST00000282397.4:c.1052G>A	p.Arg351Gln	p.R351Q	ENST00000282397	NM_002019.4	351	cGg/cAg	8/30	0.587484513052757	1	FACETS	0.544	0.494	0.596	0.544	0.494	0.596	SUBCLONAL	1	TRUE	0	0.587484513052757	1		606	557	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0003013-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	220	330	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.199155237521055	3	FACETS	0.961	0.898	1	0.641	0.598	0.684	INDETERMINATE	2	TRUE	0	0.384368496061606	3		332	710	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012347	176012347	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003013-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	101	368	0	ENST00000367669.3:c.1587G>T	p.Leu529Phe	p.L529F	ENST00000367669	NM_022457.5	529	ttG/ttT	14/20	1	2	FACETS	0.966	0.866	1	0.966	0.866	1	CLONAL	1	TRUE	1	0.384368496061606	2		368	544	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422066	81422066	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003013-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	82	230	0	ENST00000298171.2:c.42C>A	p.Asp14Glu	p.D14E	ENST00000298171	NM_000369.2	14	gaC/gaA	1/10	0.106006699121753	4	FACETS	1	0.966	1	0.626	0.554	0.702	INDETERMINATE	1	TRUE	2	0.384368496061606	4		230	472	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196093	138196093	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003028-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	65	456	0	ENST00000237289.4:c.407G>T	p.Arg136Leu	p.R136L	ENST00000237289	NM_001270507.1	136	cGc/cTc	3/9	0.206599492055532	3	FACETS	0.546	0.473	0.627	0.273	0.236	0.314	INDETERMINATE	1	TRUE	1	0.354595274516985	3		456	790	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061797	38061797	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003028-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	60	529	1	ENST00000250448.2:c.192C>A	p.Phe64Leu	p.F64L	ENST00000250448	NM_004496.3	64	ttC/ttA	2/2	1	2	FACETS	0.591	0.509	0.68	0.591	0.509	0.68	SUBCLONAL	1	TRUE	1	0.354595274516985	2		530	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0003038-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	229	255	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.664701623259475	1	FACETS	0.94	0.89	0.988	0.94	0.89	0.988	CLONAL	1	TRUE	0	0.745632321384348	1		255	410	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913355	NA	P-0003038-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	319	410	0	ENST00000288602.6:c.1406G>T	p.Gly469Val	p.G469V	ENST00000288602	NM_004333.4	469	gGa/gTa	11/18	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.745632321384348	2		410	807	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537921	212537921	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003038-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	287	362	0	ENST00000342788.4:c.1684A>G	p.Met562Val	p.M562V	ENST00000342788	NM_005235.2	562	Atg/Gtg	14/28	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.745632321384348	2		362	770	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249510	153249510	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1157879635	NA	P-0003038-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	159	275	0	ENST00000281708.4:c.1268G>T	p.Gly423Val	p.G423V	ENST00000281708	NM_033632.3	423	gGa/gTa	9/12	1	2	FACETS	0.9	0.832	0.97	0.9	0.832	0.97	CLONAL	1	TRUE	1	0.745632321384348	2		275	474	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021623	31021623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003038-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	339	227	0	ENST00000375687.4:c.1622G>A	p.Arg541Gln	p.R541Q	ENST00000375687	NM_015338.5	541	cGg/cAg	12/13	0.702706912579377	4	FACETS	0.971	0.924	1			1	CLONAL	2	TRUE	NA	0.745632321384348	4		227	817	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962593	100962606	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AGTAGTTGTGCTGC	AGTAGTTGTGCTGC	-	novel	NA	P-0003038-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	272	489	0	ENST00000325455.5:c.1791_1804del	p.Gln598MetfsTer6	p.Q598Mfs*6	ENST00000325455	NM_001202474.3	597	ggGCAGCACAACTACTta/ggta	3/8	1	2	FACETS	0.791	0.744	0.84	0.791	0.744	0.84	SUBCLONAL	1	TRUE	1	0.745632321384348	2		489	922	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947559	48947559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003043-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	348	285	0	ENST00000267163.4:c.1147del	p.Gln383AsnfsTer3	p.Q383Nfs*3	ENST00000267163	NM_000321.2	382	atC/at	12/27	0.730663210022843	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.911097917188082	1		285	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577042	7577042	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0003043-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	557	323	0	ENST00000269305.4:c.896del	p.Leu299ArgfsTer46	p.L299Rfs*46	ENST00000269305	NM_001126112.2	299	cTg/cg	8/11	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	2	TRUE	NA	0.911097917188082	2		323	594	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162474	47162474	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	95	379	0	ENST00000409792.3:c.3652C>T	p.Gln1218Ter	p.Q1218*	ENST00000409792	NM_014159.6	1218	Caa/Taa	3/21	0.335568884409967	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	2	TRUE	0	0.335568884409967	2		379	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578523	7578548	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCAAAACATCTTGTTGAGGGCAGG	TGGCAAAACATCTTGTTGAGGGCAGG	-	novel	NA	P-0003125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	44	211	0	ENST00000269305.4:c.382_407del	p.Pro128ThrfsTer12	p.P128Tfs*12	ENST00000269305	NM_001126112.2	128	CCTGCCCTCAACAAGATGTTTTGCCAa/a	5/11	0.335568884409967	2	FACETS	1	0.918	1	0.568	0.48	0.662	CLONAL	1	TRUE	0	0.335568884409967	2		211	231	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405643	139405650	+	frameshift_variant	Frame_Shift_Del	DEL	AGTCCTCG	AGTCCTCG	-	novel	NA	P-0003125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	26	228	0	ENST00000277541.6:c.2541_2548del	p.Glu848Ter	p.E848*	ENST00000277541	NM_017617.3	847	tcCGAGGACTat/tcat	16/34	1	2	FACETS	0.553	0.439	0.684	0.553	0.439	0.684	SUBCLONAL	1	TRUE	1	0.335568884409967	2		228	280	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578419	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587781845	NA	P-0003129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	185	227	0	ENST00000269305.4:c.511G>T	p.Glu171Ter	p.E171*	ENST00000269305	NM_001126112.2	171	Gag/Tag	5/11	0.559891675266659	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.559891675266659	2		227	308	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0003129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	338	542	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.48637102615321	3	FACETS	0.914	0.869	0.961			1	CLONAL	2	TRUE	NA	0.559891675266659	3		542	845	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270189	66270189	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	229	322	0	ENST00000273854.3:c.1693G>T	p.Ala565Ser	p.A565S	ENST00000273854	NM_004439.5	565	Gca/Tca	8/18	0.559891675266659	3	FACETS	0.901	0.846	0.956	0.901	0.846	0.956	CLONAL	2	TRUE	1	0.559891675266659	3		322	581	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446885	187446885	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	146	331	0	ENST00000232014.4:c.1308G>T	p.Glu436Asp	p.E436D	ENST00000232014	NM_001130845.1	436	gaG/gaT	5/10	0.524815484876643	3	FACETS	1	0.966	1	0.553	0.506	0.601	CLONAL	1	TRUE	1	0.559891675266659	3		331	604	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722039	176722039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	105	285	1	ENST00000439151.2:c.7670G>A	p.Gly2557Glu	p.G2557E	ENST00000439151	NM_022455.4	2557	gGa/gAa	23/23	0.559891675266659	2	FACETS	0.964	0.871	1	0.482	0.435	0.531	CLONAL	1	TRUE	0	0.559891675266659	2		286	389	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858446	27858446	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	134	507	0	ENST00000359303.2:c.125A>G	p.Tyr42Cys	p.Y42C	ENST00000359303	NM_003535.2	42	tAc/tGc	1/1	0.559891675266659	3	FACETS	0.826	0.751	0.904	0.413	0.375	0.452	CLONAL	1	TRUE	1	0.559891675266659	3		507	742	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343997	118343997	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	124	344	1	ENST00000534358.1:c.2123A>C	p.His708Pro	p.H708P	ENST00000534358	NM_005933.3	708	cAc/cCc	3/36	0.559891675266659	2	FACETS	0.9	0.819	0.985	0.45	0.409	0.493	CLONAL	1	TRUE	0	0.559891675266659	2		345	492	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120684	115120684	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	144	438	0	ENST00000257566.3:c.322G>T	p.Glu108Ter	p.E108*	ENST00000257566	NM_016569.3	108	Gag/Tag	1/8	0.524815484876643	3	FACETS	1	0.947	1	0.523	0.479	0.57	CLONAL	1	TRUE	1	0.559891675266659	3		438	629	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821290	72821290	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	157	511	0	ENST00000268489.5:c.10885C>G	p.Pro3629Ala	p.P3629A	ENST00000268489	NM_006885.3	3629	Ccc/Gcc	10/10	0.196473139688834	3	FACETS	1	0.93	1	0.338	0.31	0.367	INDETERMINATE	1	TRUE	0	0.559891675266659	3		511	708	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821409	72821409	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	111	490	0	ENST00000268489.5:c.10766C>G	p.Ser3589Cys	p.S3589C	ENST00000268489	NM_006885.3	3589	tCt/tGt	10/10	0.196473139688834	3	FACETS	0.842	0.758	0.929	0.281	0.252	0.31	INDETERMINATE	1	TRUE	0	0.559891675266659	3		490	603	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602340	10602340	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	239	345	0	ENST00000171111.5:c.1238G>T	p.Arg413Leu	p.R413L	ENST00000171111	NM_203500.1	413	cGt/cTt	3/6	0.559891675266659	2	FACETS	0.995	0.944	1	0.995	0.944	1	CLONAL	2	TRUE	0	0.559891675266659	2		345	429	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954190	17954190	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	301	377	0	ENST00000458235.1:c.419A>G	p.Gln140Arg	p.Q140R	ENST00000458235	NM_000215.3	140	cAg/cGg	4/24	0.559891675266659	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.559891675266659	2		377	480	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617565	100617565	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	156	414	0	ENST00000308731.7:c.504G>C	p.Leu168Phe	p.L168F	ENST00000308731	NM_000061.2	168	ttG/ttC	6/19	0.559891675266659	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.559891675266659	1		414	362	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271639	15271649	+	frameshift_variant	Frame_Shift_Del	DEL	GACCAGTCTGA	GACCAGTCTGA	-	novel	NA	P-0003129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	206	395	0	ENST00000263388.2:c.6790_6800del	p.Ser2264ArgfsTer5	p.S2264Rfs*5	ENST00000263388	NM_000435.2	2264	TCAGACTGGTCc/c	33/33	0.559891675266659	2	FACETS	0.971	0.916	1	0.971	0.916	1	CLONAL	2	TRUE	0	0.559891675266659	2		395	379	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355311	81355311	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	230	312	0	ENST00000222390.5:c.1063del	p.Arg355GlufsTer56	p.R355Efs*56	ENST00000222390	NM_000601.4	355	Cga/ga	9/18	0.486499223802521	5	FACETS	0.879	0.821	0.939	0.586	0.547	0.626	CLONAL	2	TRUE	2	0.559891675266659	5		312	860	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0003134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	273	221	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.983	0.925	1	1	0.995	1	CLONAL	2	TRUE	1	0.32	2		221	868	SUCCESS
FH	2271	MSKCC	GRCh37	1	241671916	241671916	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	149	324	1	ENST00000366560.3:c.725T>G	p.Leu242Arg	p.L242R	ENST00000366560	NM_000143.3	242	cTt/cGt	5/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.32	2		325	721	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252043	133252043	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	28	309	0	ENST00000320574.5:c.1167C>G	p.Phe389Leu	p.F389L	ENST00000320574	NM_006231.2	389	ttC/ttG	12/49	0.106009007849588	0	FACETS	0.221	0.176	0.273			1	INDETERMINATE	1	TRUE	0	0.32	0		309	538	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325762	30325762	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs771704089	NA	P-0003134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	54	215	0	ENST00000322652.5:c.1960C>T	p.Arg654Ter	p.R654*	ENST00000322652	NM_015355.2	654	Cga/Tga	16/16	0.256598184564535	3	FACETS	0.533	0.454	0.619			1	SUBCLONAL	1	TRUE	NA	0.32	3		215	735	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651409	52651409	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	313	444	0	ENST00000394830.3:c.1687T>G	p.Leu563Val	p.L563V	ENST00000394830	NM_018313.4	563	Ttg/Gtg	15/30	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.494154398847704	2		444	893	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589147	67589147	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	161	203	0	ENST00000274335.5:c.1135A>G	p.Lys379Glu	p.K379E	ENST00000274335		379	Aaa/Gaa	9/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.494154398847704	2		203	546	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112438	115112438	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1423724888	NA	P-0003150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	82	201	0	ENST00000257566.3:c.1302C>G	p.Asp434Glu	p.D434E	ENST00000257566	NM_016569.3	434	gaC/gaG	7/8	0.403243897222053	8	FACETS	0.981	0.88	1			1	CLONAL	4	TRUE	NA	0.403243897222053	8		201	229	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591153	67591153	+	splice_donor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0003150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	24	269	0	ENST00000274335.5:c.1745+1del		p.X582_splice	ENST00000274335		582			0.184581528195202	5	FACETS	0.692	0.544	0.863	0.231	0.181	0.288	INDETERMINATE	1	TRUE	2	0.403243897222053	5		269	276	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593604	55593604	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057520032	NA	P-0003153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	3413	490	2	ENST00000288135.5:c.1670G>C	p.Trp557Ser	p.W557S	ENST00000288135	NM_000222.2	557	tGg/tCg	11/21	0.582612426830187	27	FACETS	1	0.998	1			1	CLONAL	26	TRUE	NA	0.582612426830187	27		492	3700	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106701	2106701	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	123	457	0	ENST00000219476.3:c.705C>G	p.Ser235Arg	p.S235R	ENST00000219476	NM_000548.3	235	agC/agG	8/42	0.582612426830187	2	FACETS	0.977	0.891	1	0.489	0.445	0.534	CLONAL	1	TRUE	0	0.582612426830187	2		457	432	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732513	74732513	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	57	403	0	ENST00000359995.5:c.396T>A	p.Ser132Arg	p.S132R	ENST00000359995	NM_001195427.1	132	agT/agA	2/3	0.577093275485692	3	FACETS	0.459	0.393	0.53	0.229	0.196	0.265	SUBCLONAL	1	TRUE	1	0.582612426830187	3		403	551	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436010	49436013	+	missense_variant	Missense_Mutation	ONP	CCTC	CCTC	ACTG	novel	NA	P-0003153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	84	334	0	ENST00000301067.7:c.5968_5971delinsCAGT	p.Glu1990_Gly1991delinsGlnCys	p.E1990_G1991delinsQC	ENST00000301067	NM_003482.3	1990	GAGGgt/CAGTgt	28/54	0.582612426830187	3	FACETS	0.985	0.876	1	0.493	0.438	0.55	CLONAL	1	TRUE	1	0.582612426830187	3		334	378	SUCCESS
ALK	238	MSKCC	GRCh37	2	29436860	29436860	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs281864720	NA	P-0121588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	144	274	0	ENST00000389048.3:c.3733T>G	p.Phe1245Val	p.F1245V	ENST00000389048	NM_004304.4	1245	Ttc/Gtc	24/29	1	2	FACETS	0.909	0.83	0.992	0.909	0.83	0.992	CLONAL	1	NA	1	0.417319045445338	2		274	759	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159019	143159019	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0121588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	107	281	1	ENST00000262992.4:c.834C>G	p.Cys278Trp	p.C278W	ENST00000262992	NM_001101669.1	278	tgC/tgG	10/24	1	2	FACETS	0.824	0.741	0.913	0.824	0.741	0.913	CLONAL	1	NA	1	0.417319045445338	2		282	622	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0003160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	113	272	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	NA	2	FACETS	1	0.948	1			1	INDETERMINATE	1	TRUE	NA	0.337134785828945	2		272	621	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0003160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	66	418	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	0.337134785828945	1	FACETS	0.828	0.722	0.942	0.828	0.722	0.942	CLONAL	1	TRUE	0	0.337134785828945	1		418	393	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956511	93956511	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	128	479	0	ENST00000369303.4:c.2725A>T	p.Arg909Trp	p.R909W	ENST00000369303	NM_004440.3	909	Agg/Tgg	15/17	1	2	FACETS	0.804	0.727	0.884	0.804	0.727	0.884	CLONAL	1	TRUE	1	0.337134785828945	2		479	945	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953730	48953730	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs3092891	NA	P-0003160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	88	248	0	ENST00000267163.4:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000267163	NM_000321.2	445	Cga/Tga	14/27	1	2	FACETS	0.722	0.64	0.81	0.722	0.64	0.81	SUBCLONAL	1	TRUE	1	0.337134785828945	2		248	723	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207120	1207120	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	59	308	0	ENST00000326873.7:c.208G>T	p.Glu70Ter	p.E70*	ENST00000326873	NM_000455.4	70	Gag/Tag	1/10	0.300118685395649	0	FACETS	0.636	0.549	0.729			1	SUBCLONAL	1	TRUE	0	0.337134785828945	0		308	365	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42384946	42384946	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	131	424	0	ENST00000221972.3:c.580G>A	p.Asp194Asn	p.D194N	ENST00000221972	NM_021601.3	194	Gac/Aac	5/5	0.29277997721936	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.337134785828945	1		424	452	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306562	41306562	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	59	332	0	ENST00000373198.4:c.1097G>A	p.Gly366Asp	p.G366D	ENST00000373198	NM_133170.3	366	gGt/gAt	7/32	0.337134785828945	1	FACETS	0.685	0.591	0.786	0.685	0.591	0.786	SUBCLONAL	1	TRUE	0	0.337134785828945	1		332	425	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0003162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	545	388	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	0.899489734210895	2	FACETS	0.98	0.962	0.997	0.98	0.962	0.997	CLONAL	2	TRUE	0	0.899489734210895	2		388	618	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544703	65544703	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs387906650	NA	P-0003162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	303	345	0	ENST00000358664.4:c.223C>T	p.Arg75Ter	p.R75*	ENST00000358664	NM_002382.4	75	Cga/Tga	4/5	0.899489734210895	1	FACETS	0.965	0.934	0.995	0.965	0.934	0.995	CLONAL	1	TRUE	0	0.899489734210895	1		345	384	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166103	118166103	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	336	375	0	ENST00000369448.3:c.613C>T	p.His205Tyr	p.H205Y	ENST00000369448	NM_017709.3	205	Cac/Tac	2/2	0.899489734210895	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.899489734210895	1		375	389	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10244910	10244910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	561	380	1	ENST00000340748.4:c.4799C>T	p.Ala1600Val	p.A1600V	ENST00000340748		1600	gCc/gTc	39/40	0.883560004929751	3	FACETS	0.971	0.94	1	0.971	0.94	1	CLONAL	2	TRUE	1	0.899489734210895	3		381	931	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651496	52651496	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	120	630	1	ENST00000394830.3:c.1600C>T	p.Arg534Ter	p.R534*	ENST00000394830	NM_018313.4	534	Cga/Tga	15/30	0.279383285742657	1	FACETS	0.759	0.689	0.831	1	0.986	1	SUBCLONAL	2	TRUE	0	0.279383285742657	1		631	487	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555655	21555655	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0003177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	79	553	0	ENST00000382592.4:c.2615C>G	p.Ser872Ter	p.S872*	ENST00000382592	NM_014572.2	872	tCa/tGa	6/8	NA	2	FACETS	1	0.952	1			1	INDETERMINATE	1	TRUE	NA	0.279383285742657	2		553	490	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0003196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	95	542	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.247358484032319	1	FACETS	0.842	0.75	0.942	0.842	0.75	0.942	CLONAL	1	TRUE	0	0.247358484032319	1		542	799	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579529	7579529	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658483	NA	P-0003196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	68	221	0	ENST00000269305.4:c.158G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tGg/tAg	4/11	0.247358484032319	1	FACETS	0.891	0.776	1	0.891	0.776	1	CLONAL	1	TRUE	0	0.247358484032319	1		221	541	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050388	128050388	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1275332128	NA	P-0003196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	56	231	0	ENST00000285398.2:c.269C>G	p.Ser90Cys	p.S90C	ENST00000285398	NM_000122.1	90	tCt/tGt	3/15	1	2	FACETS	0.672	0.575	0.778	0.672	0.575	0.778	SUBCLONAL	1	TRUE	1	0.247358484032319	2		231	674	SUCCESS
ATR	545	MSKCC	GRCh37	3	142171969	142171969	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0003196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	56	309	0	ENST00000350721.4:c.7761+1G>T		p.X2587_splice	ENST00000350721	NM_001184.3	2587			1	2	FACETS	0.601	0.514	0.697	0.601	0.514	0.697	SUBCLONAL	1	TRUE	1	0.247358484032319	2		309	753	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129671	11129671	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	76	292	0	ENST00000358026.2:c.2481del	p.Ser828ProfsTer3	p.S828Pfs*3	ENST00000358026	NM_001128849.1	826	gCc/gc	17/36	0.247358484032319	1	FACETS	0.831	0.729	0.941	0.831	0.729	0.941	CLONAL	1	TRUE	0	0.247358484032319	1		292	648	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188210	10188210	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs5030830	NA	P-0003205-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	135	244	0	ENST00000256474.2:c.353T>C	p.Leu118Pro	p.L118P	ENST00000256474	NM_000551.3	118	cTc/cCc	2/3	0.309291094585602	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.309291094585602	1		244	712	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0003213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	169	201	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.481808952897455	5	FACETS	1	0.944	1	0.684	0.632	0.738	CLONAL	2	TRUE	2	0.481808952897455	5		201	589	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0003213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	88	320	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.481808952897455	5	FACETS	1	0.921	1	0.349	0.309	0.391	CLONAL	1	TRUE	2	0.481808952897455	5		320	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0003213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	66	216	0	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	0.481808952897455	2	FACETS	0.938	0.822	1	0.469	0.411	0.531	CLONAL	1	TRUE	0	0.481808952897455	2		216	292	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099030	27099030	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0003213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	101	287	0	ENST00000324856.7:c.3446C>G	p.Ser1149Ter	p.S1149*	ENST00000324856	NM_006015.4	1149	tCa/tGa	13/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.481808952897455	2		287	395	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803147	1803147	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	63	228	0	ENST00000260795.2:c.499C>G	p.Pro167Ala	p.P167A	ENST00000260795		167	Ccg/Gcg	4/17	0.143720961798855	5	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.481808952897455	5		228	320	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505550	157505550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	54	156	0	ENST00000346085.5:c.3531G>T	p.Lys1177Asn	p.K1177N	ENST00000346085	NM_020732.3	1177	aaG/aaT	13/20	1	2	FACETS	0.872	0.752	1	0.872	0.752	1	CLONAL	1	TRUE	1	0.481808952897455	2		156	257	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	135	419	0	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	0.481808952897455	4	FACETS	0.921	0.836	1			1	CLONAL	1	TRUE	NA	0.481808952897455	4		419	902	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227760	53227760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	98	429	0	ENST00000375401.3:c.2428G>A	p.Glu810Lys	p.E810K	ENST00000375401	NM_004187.3	810	Gag/Aag	17/26	0.274536389398774	5	FACETS	0.956	0.853	1			1	INDETERMINATE	1	TRUE	NA	0.481808952897455	5		429	733	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855903	76855903	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	105	339	0	ENST00000373344.5:c.5697G>C	p.Lys1899Asn	p.K1899N	ENST00000373344	NM_000489.3	1899	aaG/aaC	23/35	0.274536389398774	5	FACETS	0.955	0.856	1			1	INDETERMINATE	1	TRUE	NA	0.481808952897455	5		339	786	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028833	47028851	+	frameshift_variant	Frame_Shift_Del	DEL	GCGAGTATGGCAGCCAGGA	GCGAGTATGGCAGCCAGGA	-	novel	NA	P-0003213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	156	329	0	ENST00000377604.3:c.138_156del	p.Glu47AlafsTer81	p.E47Afs*81	ENST00000377604	NM_001204468.1	46	cGCGAGTATGGCAGCCAGGAg/cg	3/24	0.274536389398774	5	FACETS	1	0.924	1			1	INDETERMINATE	2	TRUE	NA	0.481808952897455	5		329	556	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779494	3779494	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	44	287	1	ENST00000262367.5:c.5554C>T	p.Gln1852Ter	p.Q1852*	ENST00000262367	NM_004380.2	1852	Cag/Tag	31/31	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.58083136144553	2		288	117	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926885	112926885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507544	NA	P-0003231-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	12	243	0	ENST00000351677.2:c.1505C>T	p.Ser502Leu	p.S502L	ENST00000351677	NM_002834.3	502	tCa/tTa	13/16	0.0892124314811108	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		243	468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0003234-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	426	505	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.536572692666502	2	FACETS	0.964	0.925	1	0.964	0.925	1	CLONAL	2	TRUE	0	0.536572692666502	2		505	824	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193181550	193181550	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003234-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	112	473	0	ENST00000367435.3:c.1097C>A	p.Ala366Glu	p.A366E	ENST00000367435	NM_024529.4	366	gCa/gAa	13/17	0.351878554472285	6	FACETS	0.963	0.865	1	0.241	0.216	0.267	CLONAL	1	TRUE	2	0.536572692666502	6		473	899	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162267	47162267	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003234-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	102	387	0	ENST00000409792.3:c.3859C>A	p.Gln1287Lys	p.Q1287K	ENST00000409792	NM_014159.6	1287	Cag/Aag	3/21	0.536572692666502	2	FACETS	0.98	0.883	1	0.49	0.441	0.54	CLONAL	1	TRUE	0	0.536572692666502	2		387	388	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196702	106196702	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003234-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	122	450	0	ENST00000380013.4:c.5035T>C	p.Tyr1679His	p.Y1679H	ENST00000380013	NM_001127208.2	1679	Tac/Cac	11/11	0.536572692666502	1	FACETS	0.909	0.831	0.99	0.909	0.831	0.99	CLONAL	1	TRUE	0	0.536572692666502	1		450	366	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508526	106508526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003234-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	226	124	0	ENST00000359195.3:c.520G>A	p.Glu174Lys	p.E174K	ENST00000359195	NM_002649.2	174	Gag/Aag	2/11	0.536572692666502	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	1	0.536572692666502	4		124	384	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213636	2213636	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003234-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	82	370	0	ENST00000398665.3:c.1656T>G	p.Asp552Glu	p.D552E	ENST00000398665	NM_032482.2	552	gaT/gaG	17/28	0.536572692666502	3	FACETS	0.448	0.394	0.506	0.224	0.197	0.253	SUBCLONAL	1	TRUE	1	0.536572692666502	3		370	865	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915996	127915997	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0003234-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	37	585	0	ENST00000373547.4:c.484_485del	p.Val162ProfsTer7	p.V162Pfs*7	ENST00000373547	NM_002721.4	162	GTc/c	6/7	1	2	FACETS	0.206	0.169	0.248	0.206	0.169	0.248	SUBCLONAL	1	TRUE	1	0.536572692666502	2		585	669	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0003239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	93	293	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.461042960030638	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	TRUE	0	0.461042960030638	3		294	149	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106861	27106861	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	68	312	0	ENST00000324856.7:c.6472C>T	p.Arg2158Ter	p.R2158*	ENST00000324856	NM_006015.4	2158	Cga/Tga	20/20	0.389720664519259	3	FACETS	0.912	0.808	1	0.912	0.808	1	CLONAL	2	TRUE	1	0.461042960030638	3		312	199	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011144	12011144	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	160	219	0	ENST00000353533.5:c.551C>G	p.Ser184Trp	p.S184W	ENST00000353533	NM_003010.3	184	tCg/tGg	5/11	0.461042960030638	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	3	TRUE	0	0.461042960030638	3		219	280	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610153	81610154	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0003239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	13	296	0	ENST00000298171.2:c.1754_1755del	p.Phe585CysfsTer72	p.F585Cfs*72	ENST00000298171	NM_000369.2	584	gTT/g	10/10	0.346927826244097	5	FACETS	0.536	0.383	0.721	0.179	0.127	0.241	SUBCLONAL	1	TRUE	2	0.461042960030638	5		296	178	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0003240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	216	520	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.378898287141826	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.38330773982109	1		520	852	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0003240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	80	289	2	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.38330773982109	1	FACETS	0.967	0.858	1	0.967	0.858	1	CLONAL	1	TRUE	0	0.38330773982109	1		291	349	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55960993	55960993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	158	313	0	ENST00000263923.4:c.2947C>T	p.Leu983Phe	p.L983F	ENST00000263923	NM_002253.2	983	Ctc/Ttc	21/30	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.38330773982109	2		313	689	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250242	110250242	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	81	260	0	ENST00000374672.4:c.433C>A	p.Pro145Thr	p.P145T	ENST00000374672	NM_004235.4	145	Ccc/Acc	3/5	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.38330773982109	2		260	375	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2194572	2194572	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	153	409	0	ENST00000398665.3:c.647A>G	p.Tyr216Cys	p.Y216C	ENST00000398665	NM_032482.2	216	tAc/tGc	7/28	0.38330773982109	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.38330773982109	1		409	473	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132442	11132442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	60	437	0	ENST00000358026.2:c.2658G>A	p.Met886Ile	p.M886I	ENST00000358026	NM_001128849.1	886	atG/atA	19/36	0.38330773982109	1	FACETS	0.432	0.372	0.497	0.432	0.372	0.497	SUBCLONAL	1	TRUE	0	0.38330773982109	1		437	586	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144442	11144442	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	38	294	0	ENST00000358026.2:c.3775-1G>A		p.X1259_splice	ENST00000358026	NM_001128849.1	1259			0.38330773982109	1	FACETS	0.371	0.307	0.443	0.371	0.307	0.443	SUBCLONAL	1	TRUE	0	0.38330773982109	1		294	432	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597401	10597402	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	A	novel	NA	P-0003240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	184	367	0	ENST00000171111.5:c.1801_1802delinsT	p.Arg601Ter	p.R601*	ENST00000171111	NM_203500.1	601	CGg/Tg	6/6	0.38330773982109	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.38330773982109	1		367	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0003243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	8	135	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	0.22670711632833	3	FACETS	1	0.749	1	0.592	0.389	0.84	CLONAL	1	TRUE	1	0.312629530982955	3		135	50	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0003243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	13	525	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.273005394363078	3	FACETS	0.981	0.724	1	0.981	0.724	1	CLONAL	2	TRUE	1	0.312629530982955	3		525	49	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0003243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	18	272	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.202299738430651	3	FACETS	0.888	0.698	1	0.888	0.698	1	CLONAL	3	TRUE	0	0.312629530982955	3		272	50	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231250	142231250	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	92	323	0	ENST00000350721.4:c.4704C>G	p.Asp1568Glu	p.D1568E	ENST00000350721	NM_001184.3	1568	gaC/gaG	27/47	0.58166523647196	3	FACETS	0.458	0.406	0.513	0.153	0.135	0.171	SUBCLONAL	1	TRUE	0	0.58166523647196	3		323	892	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557364	187557364	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757948428	NA	P-0003249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	333	253	0	ENST00000441802.2:c.3998C>T	p.Pro1333Leu	p.P1333L	ENST00000441802	NM_005245.3	1333	cCt/cTt	6/27	0.533968534122935	4	FACETS	0.869	0.828	0.91	0.869	0.828	0.91	CLONAL	3	TRUE	1	0.58166523647196	4		253	695	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500488	149500488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1060499540	NA	P-0003249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	87	288	0	ENST00000261799.4:c.2549A>T	p.Asp850Val	p.D850V	ENST00000261799	NM_002609.3	850	gAc/gTc	18/23	0.58166523647196	4	FACETS	0.529	0.467	0.595	0.264	0.233	0.298	SUBCLONAL	1	TRUE	2	0.58166523647196	4		288	895	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742995	145742995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1395545206	NA	P-0003249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	16	75	0	ENST00000428558.2:c.109G>A	p.Glu37Lys	p.E37K	ENST00000428558	NM_004260.3	37	Gag/Aag	2/22	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.58166523647196	NA		75	195	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242357	98242357	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	117	276	0	ENST00000331920.6:c.961C>A	p.Leu321Ile	p.L321I	ENST00000331920	NM_000264.3	321	Ctt/Att	7/24	0.330998547113247	6	FACETS	0.893	0.804	0.987	0.298	0.268	0.329	INDETERMINATE	1	TRUE	3	0.58166523647196	6		276	975	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652297	36652298	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0003249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	112	242	0	ENST00000244741.5:c.419_420del	p.Arg140GlnfsTer56	p.R140Qfs*56	ENST00000244741	NM_000389.4	140	cGA/c	2/3	0.58166523647196	4	FACETS	1	0.917	1	0.509	0.459	0.562	CLONAL	1	TRUE	2	0.58166523647196	4		242	598	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0003250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	235	201	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.356683655221658	3	FACETS	0.883	0.831	0.937	1	0.991	1	CLONAL	3	TRUE	1	0.356683655221658	3		201	586	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125222	47125222	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	45	231	0	ENST00000409792.3:c.6048G>T	p.Trp2016Cys	p.W2016C	ENST00000409792	NM_014159.6	2016	tgG/tgT	12/21	0.191489082907995	1	FACETS	0.438	0.368	0.516	0.438	0.368	0.516	INDETERMINATE	1	TRUE	0	0.356683655221658	1		231	473	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519646	176519646	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	20	144	0	ENST00000292408.4:c.919-1G>A		p.X307_splice	ENST00000292408	NM_213647.1	307			0.356683655221658	4	FACETS	0.385	0.294	0.493	0.193	0.147	0.247	SUBCLONAL	1	TRUE	2	0.356683655221658	4		144	395	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40447742	40447742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1366673239	NA	P-0003250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	58	559	0	ENST00000345506.4:c.481G>A	p.Glu161Lys	p.E161K	ENST00000345506	NM_003152.3	161	Gag/Aag	6/20	0.311585133930804	2	FACETS	0.392	0.336	0.453	0.196	0.168	0.227	SUBCLONAL	1	TRUE	0	0.356683655221658	2		559	830	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312413	91312413	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	198	436	1	ENST00000355112.3:c.2358G>T	p.Arg786Ser	p.R786S	ENST00000355112	NM_000057.2	786	agG/agT	11/22	1	2	FACETS	0.91	0.846	0.977	0.91	0.846	0.977	CLONAL	1	NA	1	0.608348908757625	2		437	715	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814153	76814153	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0121499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	217	260	0	ENST00000373344.5:c.6491G>C	p.Arg2164Thr	p.R2164T	ENST00000373344	NM_000489.3	2164	aGg/aCg	29/35	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	NA	0	0.608348908757625	1		260	366	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057976	27057976	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	47	416	0	ENST00000324856.7:c.1684C>T	p.Gln562Ter	p.Q562*	ENST00000324856	NM_006015.4	562	Cag/Tag	3/20	0.176927518132357	3	FACETS	0.903	0.773	1	0.903	0.773	1	INDETERMINATE	2	TRUE	1	0.311634179739294	3		416	193	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0003265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	642	221	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.871045258283562	3	FACETS	0.998	0.983	1	0.998	0.983	1	CLONAL	3	TRUE	0	0.871045258283562	3		221	707	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35860993	35860993	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0003265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	191	254	0	ENST00000303115.3:c.122C>G	p.Ser41Ter	p.S41*	ENST00000303115	NM_002185.3	41	tCa/tGa	2/8	0.871045258283562	5	FACETS	0.849	0.784	0.918	0.283	0.261	0.306	CLONAL	1	TRUE	2	0.871045258283562	5		254	1191	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519717	NA	P-0003265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	394	231	1	ENST00000206249.3:c.1607T>G	p.Leu536Arg	p.L536R	ENST00000206249	NM_000125.3	536	cTc/cGc	8/8	0.863088381980105	3	FACETS	0.988	0.951	1	0.659	0.634	0.684	CLONAL	2	TRUE	0	0.871045258283562	3		232	657	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302902	15302902	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	184	196	0	ENST00000263388.2:c.548G>C	p.Cys183Ser	p.C183S	ENST00000263388	NM_000435.2	183	tGc/tCc	4/33	0.871045258283562	3	FACETS	0.905	0.839	0.974	0.453	0.419	0.487	CLONAL	1	TRUE	1	0.871045258283562	3		196	670	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0003268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	32	366	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.272922086617644	1	FACETS	0.564	0.465	0.671	0.564	0.465	0.671	INDETERMINATE	1	TRUE	0	0.589036629524369	1		366	136	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203436	NA	P-0003268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	291	196	0	ENST00000269305.4:c.487T>C	p.Tyr163His	p.Y163H	ENST00000269305	NM_001126112.2	163	Tac/Cac	5/11	0.18014922250438	2	FACETS	1	0.992	1	1	0.992	1	INDETERMINATE	2	TRUE	0	0.589036629524369	2		196	433	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932089	39932089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	126	153	0	ENST00000378444.4:c.2510C>T	p.Pro837Leu	p.P837L	ENST00000378444	NM_001123385.1	837	cCc/cTc	4/15	0.26960260190538	0	FACETS	0.866	0.809	0.922			1	INDETERMINATE	1	TRUE	NA	0.589036629524369	0		153	203	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939761	76939761	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	44	253	0	ENST00000373344.5:c.987del	p.Lys330AsnfsTer2	p.K330Nfs*2	ENST00000373344	NM_000489.3	329	aaG/aa	9/35	0.26960260190538	0	FACETS	0.83	0.734	0.922			1	INDETERMINATE	1	TRUE	NA	0.589036629524369	0		253	74	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs587781433	NA	P-0003270-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	12	232	0	ENST00000269305.4:c.766A>C	p.Thr256Pro	p.T256P	ENST00000269305	NM_001126112.2	256	Aca/Cca	7/11	NA	2	FACETS	0.336	0.237	0.458			1	INDETERMINATE	1	TRUE	NA	0.405468895791416	2		232	176	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867709	45867709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200895828	NA	P-0003270-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	11	321	0	ENST00000391945.4:c.691G>A	p.Val231Met	p.V231M	ENST00000391945	NM_000400.3	231	Gtg/Atg	8/23	1	2	FACETS	0.31	0.214	0.429	0.31	0.214	0.429	SUBCLONAL	1	TRUE	1	0.405468895791416	2		321	175	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462571	29462571	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003270-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	20	338	0	ENST00000389048.3:c.2330A>G	p.Gln777Arg	p.Q777R	ENST00000389048	NM_004304.4	777	cAg/cGg	13/29	1	2	FACETS	0.346	0.265	0.441	0.346	0.265	0.441	SUBCLONAL	1	TRUE	1	0.405468895791416	2		338	285	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248726	212248726	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003270-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	38	276	0	ENST00000342788.4:c.3541C>T	p.Gln1181Ter	p.Q1181*	ENST00000342788	NM_005235.2	1181	Caa/Taa	28/28	0.214663811434351	4	FACETS	0.489	0.403	0.584	0.244	0.201	0.292	INDETERMINATE	1	TRUE	2	0.405468895791416	4		276	539	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627319	86627319	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0003270-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	66	201	0	ENST00000274376.6:c.692+2T>A		p.X231_splice	ENST00000274376	NM_002890.2	231			0.378431337859401	4	FACETS	0.77	0.669	0.88	0.385	0.334	0.44	SUBCLONAL	1	TRUE	2	0.405468895791416	4		201	594	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056402	26056402	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003270-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	68	234	0	ENST00000343677.2:c.255G>C	p.Lys85Asn	p.K85N	ENST00000343677	NM_005319.3	85	aaG/aaC	1/1	0.405468895791416	8	FACETS	1	0.923	1			1	CLONAL	1	TRUE	NA	0.405468895791416	8		234	683	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163826	152163826	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003270-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	45	344	1	ENST00000206249.3:c.547C>G	p.Arg183Gly	p.R183G	ENST00000206249	NM_000125.3	183	Cgc/Ggc	2/8	0.129847450496182	5	FACETS	0.689	0.579	0.811			1	INDETERMINATE	1	TRUE	NA	0.405468895791416	5		345	518	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271752	38271752	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003270-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	14	343	0	ENST00000425967.3:c.2197C>A	p.Pro733Thr	p.P733T	ENST00000425967	NM_001174067.1	733	Ccc/Acc	17/19	NA	2	FACETS	0.259	0.186	0.346			1	INDETERMINATE	1	TRUE	NA	0.405468895791416	2		343	267	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717778	89717778	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0003270-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	34	138	0	ENST00000371953.3:c.801+2T>G		p.X267_splice	ENST00000371953	NM_000314.4	267			NA	2	FACETS	0.526	0.431	0.632			1	INDETERMINATE	1	TRUE	NA	0.405468895791416	2		138	319	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654737	29654737	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs771529172	NA	P-0003270-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	36	272	0	ENST00000356175.3:c.5426G>T	p.Arg1809Leu	p.R1809L	ENST00000356175	NM_000267.3	1809	cGc/cTc	37/57	1	2	FACETS	0.352	0.288	0.423	0.352	0.288	0.423	SUBCLONAL	1	TRUE	1	0.405468895791416	2		272	505	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0003274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	237	320	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.148709554869801	10	FACETS	0.964	0.905	1	0.857	0.805	0.91	CLONAL	8	FALSE	1	0.148709554869801	10		320	659	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0003274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	240	525	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.148709554869801	10	FACETS	1	0.968	1	1	0.968	1	CLONAL	9	FALSE	1	0.148709554869801	10		525	550	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0003274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	129	505	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.148709554869801	2	FACETS	0.977	0.893	1	1	0.99	1	CLONAL	4	FALSE	0	0.148709554869801	2		505	444	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859870	151859870	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	168	187	0	ENST00000262189.6:c.10792C>A	p.Pro3598Thr	p.P3598T	ENST00000262189	NM_170606.2	3598	Cca/Aca	43/59	0.265661150614975	5	FACETS	1	0.982	1	0.808	0.745	0.872	CLONAL	2	TRUE	2	0.320341193614027	5		187	641	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715794	18715794	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs971525578	NA	P-0003293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	62	253	0	ENST00000266497.5:c.3625A>G	p.Thr1209Ala	p.T1209A	ENST00000266497		1209	Aca/Gca	25/31	0.320341193614027	4	FACETS	0.64	0.551	0.736	0.16	0.137	0.184	SUBCLONAL	1	TRUE	0	0.320341193614027	4		253	799	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207092	1207092	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs778376925	NA	P-0003293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	123	214	0	ENST00000326873.7:c.180C>G	p.Tyr60Ter	p.Y60*	ENST00000326873	NM_000455.4	60	taC/taG	1/10	NA	2	FACETS	0.774	0.704	0.847			1	INDETERMINATE	2	TRUE	NA	0.320341193614027	2		214	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579352	7579359	+	frameshift_variant	Frame_Shift_Del	DEL	CCCAGACG	CCCAGACG	ACCA	novel	NA	P-0003293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	96	180	0	ENST00000269305.4:c.328_335delinsTGGT	p.Arg110TrpfsTer12	p.R110Wfs*12	ENST00000269305	NM_001126112.2	110	CGTCTGGGc/TGGTc	4/11	0.240986808370228	2	FACETS	1	0.981	1	0.726	0.651	0.804	CLONAL	1	TRUE	0	0.320341193614027	2		180	413	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0003321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	132	393	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.453759855778544	2	FACETS	0.846	0.778	0.915	0.846	0.778	0.915	CLONAL	2	TRUE	0	0.453759855778544	2		393	344	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098806	178098806	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	89	501	1	ENST00000397062.3:c.239C>G	p.Thr80Arg	p.T80R	ENST00000397062	NM_006164.4	80	aCa/aGa	2/5	0.434154321739698	5	FACETS	0.776	0.691	0.864			1	SUBCLONAL	2	TRUE	NA	0.453759855778544	5		502	425	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155357	99155357	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	55	250	0	ENST00000074304.5:c.583G>T	p.Val195Phe	p.V195F	ENST00000074304	NM_001134224.1	195	Gtt/Ttt	9/26	0.150385493290345	4	FACETS	1	0.942	1	0.593	0.511	0.682	INDETERMINATE	1	TRUE	2	0.453759855778544	4		250	297	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430554	181430554	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	131	233	0	ENST00000325404.1:c.406G>C	p.Gly136Arg	p.G136R	ENST00000325404	NM_003106.3	136	Ggc/Cgc	1/1	0.453759855778544	5	FACETS	1	0.951	1	0.706	0.645	0.769	CLONAL	2	TRUE	2	0.453759855778544	5		233	458	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627953	187627953	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs762688063	NA	P-0003321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	109	550	0	ENST00000441802.2:c.3029T>C	p.Val1010Ala	p.V1010A	ENST00000441802	NM_005245.3	1010	gTt/gCt	2/27	0.453759855778544	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.453759855778544	1		550	302	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982095	93982095	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779416238	NA	P-0003321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	40	563	0	ENST00000369303.4:c.1370G>A	p.Arg457Gln	p.R457Q	ENST00000369303	NM_004440.3	457	cGg/cAg	6/17	0.162703586134693	1	FACETS	0.453	0.378	0.536	0.453	0.378	0.536	INDETERMINATE	1	TRUE	0	0.453759855778544	1		563	301	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117680998	117680998	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	36	349	0	ENST00000368508.3:c.3622C>A	p.His1208Asn	p.H1208N	ENST00000368508	NM_002944.2	1208	Cac/Aac	23/43	1	2	FACETS	0.632	0.523	0.753	0.632	0.523	0.753	SUBCLONAL	1	TRUE	1	0.453759855778544	2		349	251	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880135	151880135	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	77	414	1	ENST00000262189.6:c.5189G>T	p.Arg1730Leu	p.R1730L	ENST00000262189	NM_170606.2	1730	cGt/cTt	35/59	1	2	FACETS	0.888	0.785	0.999	0.888	0.785	0.999	CLONAL	1	TRUE	1	0.453759855778544	2		415	382	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371967	55371967	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	58	153	0	ENST00000297316.4:c.657G>T	p.Leu219Phe	p.L219F	ENST00000297316	NM_022454.3	219	ttG/ttT	2/2	0.203450056139549	4	FACETS	0.877	0.764	0.995	0.877	0.764	0.995	INDETERMINATE	2	TRUE	2	0.453759855778544	4		153	212	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786002	135786002	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	52	185	0	ENST00000298552.3:c.1219G>T	p.Val407Leu	p.V407L	ENST00000298552	NM_001162426.1	407	Gtg/Ttg	12/23	1	2	FACETS	0.81	0.695	0.934	0.81	0.695	0.934	CLONAL	1	TRUE	1	0.453759855778544	2		185	283	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414253	32414253	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	54	367	0	ENST00000332351.3:c.1298C>G	p.Ser433Cys	p.S433C	ENST00000332351	NM_024426.4	433	tCt/tGt	8/10	0.453759855778544	1	FACETS	0.876	0.759	1	0.876	0.759	1	CLONAL	1	TRUE	0	0.453759855778544	1		367	210	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121538	108121538	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1163918420	NA	P-0003321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	44	374	0	ENST00000278616.4:c.1346G>A	p.Gly449Glu	p.G449E	ENST00000278616	NM_000051.3	449	gGg/gAg	10/63	1	2	FACETS	0.69	0.582	0.808	0.69	0.582	0.808	SUBCLONAL	1	TRUE	1	0.453759855778544	2		374	281	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18762544	18762544	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	36	303	0	ENST00000266497.5:c.4040T>A	p.Val1347Glu	p.V1347E	ENST00000266497		1347	gTg/gAg	29/31	1	2	FACETS	0.721	0.598	0.857	0.721	0.598	0.857	SUBCLONAL	1	TRUE	1	0.453759855778544	2		303	220	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415908	49415908	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	33	325	0	ENST00000301067.7:c.16439A>G	p.Asn5480Ser	p.N5480S	ENST00000301067	NM_003482.3	5480	aAc/aGc	53/54	1	2	FACETS	0.493	0.403	0.594	0.493	0.403	0.594	SUBCLONAL	1	TRUE	1	0.453759855778544	2		325	295	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440545	49440545	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs794727143	NA	P-0003321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	100	383	0	ENST00000301067.7:c.4265G>A	p.Trp1422Ter	p.W1422*	ENST00000301067	NM_003482.3	1422	tGg/tAg	15/54	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.453759855778544	2		383	429	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444738	49444738	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	82	286	0	ENST00000301067.7:c.2728C>T	p.Pro910Ser	p.P910S	ENST00000301067	NM_003482.3	910	Cct/Tct	10/54	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.453759855778544	2		286	320	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347116	89347116	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	52	493	0	ENST00000301030.4:c.5834A>G	p.Glu1945Gly	p.E1945G	ENST00000301030	NM_001256183.1	1945	gAg/gGg	9/13	0.201375981941332	0	FACETS	0.359	0.306	0.415			1	INDETERMINATE	1	TRUE	0	0.453759855778544	0		493	349	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022877	31022877	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1402270258	NA	P-0003321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	41	309	1	ENST00000375687.4:c.2362G>T	p.Glu788Ter	p.E788*	ENST00000375687	NM_015338.5	788	Gaa/Taa	13/13	0.160558951900662	5	FACETS	0.721	0.601	0.854	0.24	0.2	0.285	INDETERMINATE	1	TRUE	2	0.453759855778544	5		310	421	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794409	42794410	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0003321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	87	527	0	ENST00000575354.2:c.1489_1490delinsAG	p.Pro497Ser	p.P497S	ENST00000575354	NM_015125.3	497	CCt/AGt	10/20	0.453759855778544	2	FACETS	0.799	0.71	0.893	0.399	0.355	0.447	SUBCLONAL	1	TRUE	0	0.453759855778544	2		527	480	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054194	30054194	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	80	395	0	ENST00000338641.4:c.616G>T	p.Glu206Ter	p.E206*	ENST00000338641	NM_000268.3	206	Gaa/Taa	7/16	0.753700250515458	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.794358258208741	1		395	114	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990351	81990351	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	27	407	0	ENST00000359376.3:c.3622G>A	p.Glu1208Lys	p.E1208K	ENST00000359376	NM_002661.3	1208	Gaa/Aaa	32/33	0.578778489585794	1	FACETS	0.163	0.129	0.202	0.163	0.129	0.202	SUBCLONAL	1	TRUE	0	0.578778489585794	1		407	406	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0003348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	38	378	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.219243185578657	2		378	277	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167577	NA	P-0003348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	21	272	0	ENST00000257430.4:c.4463del	p.Leu1488TyrfsTer19	p.L1488Yfs*19	ENST00000257430	NM_000038.5	1487	acT/ac	16/16	1	2	FACETS	1	0.8	1	1	0.8	1	CLONAL	1	TRUE	1	0.219243185578657	2		272	185	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106661	27106661	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	49	314	0	ENST00000324856.7:c.6272G>A	p.Trp2091Ter	p.W2091*	ENST00000324856	NM_006015.4	2091	tGg/tAg	20/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.219243185578657	2		314	333	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028106	48028106	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	26	317	0	ENST00000234420.5:c.2984A>C	p.Glu995Ala	p.E995A	ENST00000234420	NM_000179.2	995	gAg/gCg	4/10	1	2	FACETS	0.941	0.748	1	0.941	0.748	1	CLONAL	1	TRUE	1	0.219243185578657	2		317	252	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163764	32163764	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	68	225	0	ENST00000375023.3:c.5462G>T	p.Gly1821Val	p.G1821V	ENST00000375023	NM_004557.3	1821	gGg/gTg	30/30	0.219243185578657	3	FACETS	1	0.973	1	0.743	0.648	0.845	CLONAL	1	TRUE	1	0.219243185578657	3		225	463	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377160	118377160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	50	420	1	ENST00000534358.1:c.10553C>T	p.Ser3518Phe	p.S3518F	ENST00000534358	NM_005933.3	3518	tCt/tTt	27/36	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.219243185578657	2		421	377	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149219	119149219	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs587777540	NA	P-0003349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	107	383	0	ENST00000264033.4:c.1228-1G>A		p.X410_splice	ENST00000264033	NM_005188.3	410			0.446763347701558	3	FACETS	0.892	0.821	0.964	0.892	0.821	0.964	CLONAL	3	TRUE	0	0.470114240372807	3		383	210	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445685	49445685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs190079343	NA	P-0003349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	49	437	0	ENST00000301067.7:c.1781C>T	p.Pro594Leu	p.P594L	ENST00000301067	NM_003482.3	594	cCg/cTg	10/54	0.230951585890553	5	FACETS	1	0.932	1			1	INDETERMINATE	1	TRUE	NA	0.470114240372807	5		437	303	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480005	50480005	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	63	304	0	ENST00000394963.4:c.239G>A	p.Gly80Asp	p.G80D	ENST00000394963	NM_003076.4	80	gGc/gAc	2/13	0.230951585890553	5	FACETS	1	0.955	1			1	INDETERMINATE	1	TRUE	NA	0.470114240372807	5		304	370	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37680925	37680925	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0003349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	85	261	0	ENST00000447079.4:c.3096-2A>C		p.X1032_splice	ENST00000447079	NM_015083.1	1032			0.470114240372807	3	FACETS	0.767	0.686	0.852	0.767	0.686	0.852	SUBCLONAL	2	TRUE	1	0.470114240372807	3		261	291	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0003371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	55	330	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.312255263382964	3	FACETS	1	0.945	1	0.613	0.524	0.71	CLONAL	1	TRUE	1	0.17	3		332	573	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0003371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	80	329	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.312255263382964	3	FACETS	0.909	0.801	1			1	CLONAL	2	TRUE	NA	0.17	3		329	562	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992703	72992703	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1289295486	NA	P-0003383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1221	69	605	1	ENST00000268489.5:c.1342G>A	p.Asp448Asn	p.D448N	ENST00000268489	NM_006885.3	448	Gac/Aac	2/10	1	2	FACETS	0.517	0.449	0.592	0.517	0.449	0.592	SUBCLONAL	1	TRUE	1	0.206806090917793	2		606	1290	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	51	129	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.2187513136502	5	FACETS	0.856	0.735	0.987	0.571	0.49	0.658	INDETERMINATE	2	TRUE	2	0.390142624409924	5		129	242	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0003402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	45	261	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.390142624409924	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.390142624409924	1		261	156	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519754	29519754	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	21	283	0	ENST00000389048.3:c.1817G>A	p.Arg606Lys	p.R606K	ENST00000389048	NM_004304.4	606	aGg/aAg	9/29	0.390142624409924	1	FACETS	0.585	0.455	0.734	0.585	0.455	0.734	SUBCLONAL	1	TRUE	0	0.390142624409924	1		283	148	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027574	48027574	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786203612	NA	P-0003402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	30	216	0	ENST00000234420.5:c.2452C>G	p.Leu818Val	p.L818V	ENST00000234420	NM_000179.2	818	Ctt/Gtt	4/10	NA	2	FACETS	0.687	0.557	0.832			1	INDETERMINATE	1	TRUE	NA	0.390142624409924	2		216	224	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275259	41275259	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	80	332	0	ENST00000349496.5:c.1425C>G	p.His475Gln	p.H475Q	ENST00000349496	NM_001904.3	475	caC/caG	9/15	0.261830340279416	2	FACETS	0.795	0.709	0.884	0.795	0.709	0.884	SUBCLONAL	2	TRUE	0	0.390142624409924	2		332	258	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021828	71021828	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	84	286	0	ENST00000318789.4:c.1531-1G>A		p.X511_splice	ENST00000318789	NM_032682.5	511			NA	2	FACETS	0.763	0.683	0.848			1	INDETERMINATE	2	TRUE	NA	0.390142624409924	2		286	282	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199939	128199939	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	33	177	0	ENST00000341105.2:c.1366C>G	p.Pro456Ala	p.P456A	ENST00000341105	NM_032638.4	456	Ccg/Gcg	6/6	0.235727685479898	3	FACETS	0.802	0.666	0.949			1	CLONAL	2	TRUE	NA	0.390142624409924	3		177	126	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199945	128199945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	38	197	0	ENST00000341105.2:c.1360C>G	p.Pro454Ala	p.P454A	ENST00000341105	NM_032638.4	454	Ccc/Gcc	6/6	0.235727685479898	3	FACETS	0.837	0.705	0.979			1	CLONAL	2	TRUE	NA	0.390142624409924	3		197	139	SUCCESS
ATR	545	MSKCC	GRCh37	3	142285098	142285098	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	29	397	2	ENST00000350721.4:c.157G>T	p.Val53Leu	p.V53L	ENST00000350721	NM_001184.3	53	Gta/Tta	3/47	0.235727685479898	3	FACETS	0.5	0.402	0.612			1	SUBCLONAL	1	TRUE	NA	0.390142624409924	3		399	355	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805473	1805473	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188723332	NA	P-0003402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	30	481	0	ENST00000260795.2:c.985G>A	p.Val329Ile	p.V329I	ENST00000260795		329	Gtc/Atc	7/17	0.390142624409924	1	FACETS	0.699	0.569	0.844	0.699	0.569	0.844	SUBCLONAL	1	TRUE	0	0.390142624409924	1		481	177	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38955776	38955776	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	107	349	0	ENST00000357387.3:c.2530G>C	p.Glu844Gln	p.E844Q	ENST00000357387	NM_152756.3	844	Gag/Cag	26/38	0.2187513136502	5	FACETS	0.947	0.855	1	0.631	0.57	0.696	INDETERMINATE	2	TRUE	2	0.390142624409924	5		349	459	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622253	117622253	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	75	392	0	ENST00000368508.3:c.6617C>A	p.Pro2206His	p.P2206H	ENST00000368508	NM_002944.2	2206	cCt/cAt	42/43	0.169804863900079	0	FACETS	0.612	0.539	0.69			1	INDETERMINATE	1	TRUE	0	0.390142624409924	0		392	383	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975511	13975511	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	17	113	0	ENST00000405192.2:c.376C>T	p.Gln126Ter	p.Q126*	ENST00000405192	NM_001163147.1	126	Cag/Tag	7/12	0.390142624409924	3	FACETS	0.548	0.411	0.71	0.274	0.205	0.355	SUBCLONAL	1	TRUE	1	0.390142624409924	3		113	190	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151868351	151868351	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	92	298	0	ENST00000262189.6:c.9451C>T	p.Gln3151Ter	p.Q3151*	ENST00000262189	NM_170606.2	3151	Cag/Tag	40/59	0.390142624409924	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.390142624409924	1		298	286	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999276	100999276	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	92	660	0	ENST00000325455.5:c.526T>A	p.Ser176Thr	p.S176T	ENST00000325455	NM_001202474.3	176	Tcc/Acc	1/8	0.2187513136502	5	FACETS	1	0.968	1	0.799	0.718	0.883	INDETERMINATE	2	TRUE	2	0.390142624409924	5		660	312	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892236	9892236	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	23	434	0	ENST00000330684.3:c.2254A>G	p.Ser752Gly	p.S752G	ENST00000330684	NM_001134407.1	752	Agt/Ggt	11/13	0.372542178445993	1	FACETS	0.428	0.334	0.534	0.428	0.334	0.534	SUBCLONAL	1	TRUE	0	0.390142624409924	1		434	222	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350084	89350084	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	53	690	0	ENST00000301030.4:c.2866G>C	p.Glu956Gln	p.E956Q	ENST00000301030	NM_001256183.1	956	Gag/Cag	9/13	0.222643407763119	1	FACETS	0.746	0.641	0.86	0.746	0.641	0.86	INDETERMINATE	1	TRUE	0	0.390142624409924	1		690	293	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39607438	39607438	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1453724049	NA	P-0003402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	42	339	0	ENST00000262039.4:c.1516A>T	p.Thr506Ser	p.T506S	ENST00000262039	NM_002647.2	506	Act/Tct	14/25	0.324392546495259	3	FACETS	0.663	0.555	0.783	0.332	0.277	0.392	SUBCLONAL	1	TRUE	1	0.390142624409924	3		339	388	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4097279	4097279	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	55	316	1	ENST00000262948.5:c.982G>A	p.Glu328Lys	p.E328K	ENST00000262948	NM_030662.3	328	Gag/Aag	8/11	0.376340664666414	0	FACETS	0.864	0.75	0.984			1	CLONAL	1	TRUE	0	0.390142624409924	0		317	199	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143135	24143135	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	59	454	0	ENST00000263121.7:c.367C>T	p.Gln123Ter	p.Q123*	ENST00000263121	NM_003073.3	123	Cag/Tag	4/9	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.33	2		454	279	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143166	24143166	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	77	520	0	ENST00000263121.7:c.398C>T	p.Pro133Leu	p.P133L	ENST00000263121	NM_003073.3	133	cCc/cTc	4/9	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.33	2		520	336	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143204	24143204	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	78	530	0	ENST00000263121.7:c.436C>G	p.Pro146Ala	p.P146A	ENST00000263121	NM_003073.3	146	Cca/Gca	4/9	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.33	2		530	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0003439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	36	675	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.282850329792677	1	FACETS	0.776	0.645	0.919	0.776	0.645	0.919	CLONAL	1	TRUE	0	0.40274332066716	1		676	184	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257336	16257336	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0003439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	71	365	0	ENST00000375759.3:c.4601C>G	p.Ser1534Ter	p.S1534*	ENST00000375759	NM_015001.2	1534	tCa/tGa	11/15	0.282850329792677	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.40274332066716	1		365	251	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096027	178096027	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	57	289	0	ENST00000397062.3:c.1304G>T	p.Gly435Val	p.G435V	ENST00000397062	NM_006164.4	435	gGt/gTt	5/5	NA	2	FACETS	0.773	0.666	0.889			1	INDETERMINATE	1	TRUE	NA	0.40274332066716	2		289	366	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670550	134670550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	92	426	0	ENST00000398015.3:c.461G>T	p.Arg154Met	p.R154M	ENST00000398015	NM_004441.4	154	aGg/aTg	3/16	0.2909317534098	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.40274332066716	2		426	200	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0003439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	55	441	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	0.854	0.734	0.982	0.854	0.734	0.982	CLONAL	1	TRUE	1	0.40274332066716	2		441	320	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796754	135796754	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203434	NA	P-0003439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	56	397	0	ENST00000298552.3:c.733C>T	p.Arg245Ter	p.R245*	ENST00000298552	NM_001162426.1	245	Cga/Tga	8/23	0.396028997275771	1	FACETS	0.892	0.772	1	0.892	0.772	1	CLONAL	1	TRUE	0	0.40274332066716	1		397	249	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200479	67200479	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	30	332	4	ENST00000312629.5:c.673G>T	p.Val225Phe	p.V225F	ENST00000312629	NM_003952.2	225	Gtc/Ttc	8/15	1	2	FACETS	0.634	0.514	0.769	0.634	0.514	0.769	SUBCLONAL	1	TRUE	1	0.40274332066716	2		336	235	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971061	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGCACGTCCAGCCGCGCCCCGGCC	CGCGCACGTCCAGCCGCGCCCCGGCC	-	novel	NA	P-0003439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	49	175	0	ENST00000304494.5:c.297_322del	p.Ala100CysfsTer11	p.A100Cfs*11	ENST00000304494	NM_000077.4	99	cgGGCCGGGGCGCGGCTGGACGTGCGCGat/cgat	2/3	0.396028997275771	1	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	0	0.40274332066716	1		175	186	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927406	49927406	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	42	641	0	ENST00000296474.3:c.3898del	p.Leu1300TrpfsTer20	p.L1300Wfs*20	ENST00000296474	NM_002447.2	1300	Ctg/tg	19/20	0.282927595668412	0	FACETS	0.779	0.661	0.904			1	CLONAL	1	TRUE	0	0.40274332066716	0		641	160	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008053	29008054	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0003439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	33	394	0	ENST00000282397.4:c.715_716delinsAG	p.Pro239Arg	p.P239R	ENST00000282397	NM_002019.4	239	CCa/AGa	6/30	0.40274332066716	1	FACETS	0.654	0.538	0.783	0.654	0.538	0.783	SUBCLONAL	1	TRUE	0	0.40274332066716	1		394	200	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78426054	78426067	+	frameshift_variant	Frame_Shift_Del	DEL	GATTATAAGGTGCA	GATTATAAGGTGCA	-	novel	NA	P-0003446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	39	378	0	ENST00000370768.2:c.1458_1471del	p.Ala487TrpfsTer33	p.A487Wfs*33	ENST00000370768	NM_003902.3	486	ccTGCACCTTATAATCct/ccct	15/20	1	2	FACETS	0.395	0.327	0.472	0.395	0.327	0.472	SUBCLONAL	1	TRUE	1	0.32	2		378	617	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125848	47125848	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	44	407	0	ENST00000409792.3:c.5422C>T	p.Pro1808Ser	p.P1808S	ENST00000409792	NM_014159.6	1808	Ccc/Tcc	12/21	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.720853547845911	2		407	120	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041121	42041141	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCAGGTATAAAGTTCTTTTT	CCCAGGTATAAAGTTCTTTTT	-	novel	NA	P-0003460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	136	980	0	ENST00000219905.7:c.5499_5503+16del		p.X1833_splice	ENST00000219905	NM_001164273.1	1833		16/24	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.720853547845911	2		980	375	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0003465-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	47	375	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.218940323393585	3	FACETS	0.767	0.652	0.892	0.767	0.652	0.892	SUBCLONAL	2	TRUE	1	0.263696373239064	3		375	263	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2202720	2202720	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003465-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	24	404	0	ENST00000398665.3:c.729T>G	p.Phe243Leu	p.F243L	ENST00000398665	NM_032482.2	243	ttT/ttG	9/28	0.249863220331469	0	FACETS	0.888	0.703	1			1	CLONAL	1	TRUE	0	0.263696373239064	0		404	151	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412034	116412061	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTCCAGAAGGTATATTTCAGTTTATTG	TTTCCAGAAGGTATATTTCAGTTTATTG	-	novel	NA	P-0003480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	48	167	0	ENST00000397752.3:c.3021_3028+20del		p.X1007_splice	ENST00000397752	NM_000245.2	1007		14/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		167	307	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952138	178952138	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	40	320	2	ENST00000263967.3:c.3193C>T	p.His1065Tyr	p.H1065Y	ENST00000263967	NM_006218.2	1065	Cat/Tat	21/21	1	2	FACETS	0.606	0.504	0.719	0.606	0.504	0.719	SUBCLONAL	1	TRUE	1	0.317465922270108	2		322	416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578204	7578204	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	132	621	0	ENST00000269305.4:c.645T>A	p.Ser215Arg	p.S215R	ENST00000269305	NM_001126112.2	215	agT/agA	6/11	0.317465922270108	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.317465922270108	1		621	609	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012151	16012151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	79	625	0	ENST00000268712.3:c.2131G>A	p.Asp711Asn	p.D711N	ENST00000268712	NM_006311.3	711	Gat/Aat	19/46	0.317465922270108	1	FACETS	0.748	0.659	0.843	0.748	0.659	0.843	SUBCLONAL	1	TRUE	0	0.317465922270108	1		625	560	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242470	+	missense_variant	Missense_Mutation	DNP	TT	TT	CC	rs397517096	NA	P-0003495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	97	296	0	ENST00000275493.2:c.2239_2240delinsCC	p.Leu747Pro	p.L747P	ENST00000275493	NM_005228.3	747	TTa/CCa	19/28	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.317465922270108	2		296	534	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039147	49039147	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003496-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	98	168	0	ENST00000267163.4:c.2228del	p.Leu743Ter	p.L743*	ENST00000267163	NM_000321.2	742	gTt/gt	22/27	0.491716275439517	1	FACETS	0.958	0.888	1	0.958	0.888	1	CLONAL	1	TRUE	0	0.798290895520357	1		168	154	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023295	33023295	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003498-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	423	789	0	ENST00000300177.4:c.404A>G	p.Glu135Gly	p.E135G	ENST00000300177	NM_001191322.1	135	gAa/gGa	2/2	0.588869016046314	4	FACETS	0.914	0.871	0.957	0.914	0.871	0.957	CLONAL	2	TRUE	2	0.588869016046314	4		789	1249	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994869	73994869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003498-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	24	11	0	ENST00000318443.5:c.353G>A	p.Gly118Asp	p.G118D	ENST00000318443	NM_001024736.1	118	gGc/gAc	3/10	0.588869016046314	4	FACETS	1	0.879	1			1	CLONAL	3	TRUE	NA	0.588869016046314	4		11	41	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039204	49039241	+	frameshift_variant	Frame_Shift_Del	DEL	TGCAGAGACTGAAAACAAATATTTTGCAGTATGCTTCC	TGCAGAGACTGAAAACAAATATTTTGCAGTATGCTTCC	-	novel	NA	P-0003498-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	143	591	0	ENST00000267163.4:c.2282_2319del	p.Met761AsnfsTer21	p.M761Nfs*21	ENST00000267163	NM_000321.2	761	aTGCAGAGACTGAAAACAAATATTTTGCAGTATGCTTCC/a	22/27	0.411731516944943	1	FACETS	0.663	0.608	0.72	0.663	0.608	0.72	SUBCLONAL	1	TRUE	0	0.588869016046314	1		591	517	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872110	76872117	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTTGCA	AGCTTGCA	-	novel	NA	P-0003498-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	177	690	0	ENST00000373344.5:c.5530_5537del	p.Cys1844LeufsTer14	p.C1844Lfs*14	ENST00000373344	NM_000489.3	1844	TGCAAGCTc/c	22/35	0.588869016046314	1	FACETS	0.787	0.73	0.845	0.787	0.73	0.845	SUBCLONAL	1	TRUE	0	0.588869016046314	1		690	539	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872121	76872132	+	inframe_deletion	In_Frame_Del	DEL	AATAGAAGTCAT	AATAGAAGTCAT	-	novel	NA	P-0003498-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	178	726	0	ENST00000373344.5:c.5515_5526del	p.Met1839_Ile1842del	p.M1839_I1842del	ENST00000373344	NM_000489.3	1839	ATGACTTCTATT/-	22/35	0.588869016046314	1	FACETS	0.773	0.717	0.83	0.773	0.717	0.83	SUBCLONAL	1	TRUE	0	0.588869016046314	1		726	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0003501-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	203	415	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.487629779095064	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.487629779095064	1		415	618	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687566	29687566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144178015	NA	P-0003501-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	251	452	1	ENST00000356175.3:c.8159C>T	p.Thr2720Met	p.T2720M	ENST00000356175	NM_000267.3	2720	aCg/aTg	56/57	0.460391857877133	3	FACETS	1	0.986	1	0.598	0.56	0.638	CLONAL	1	TRUE	1	0.487629779095064	3		453	1070	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221995	1221995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201090	NA	P-0003503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	55	439	0	ENST00000326873.7:c.910C>T	p.Arg304Trp	p.R304W	ENST00000326873	NM_000455.4	304	Cgg/Tgg	7/10	0.726045772996419	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.726045772996419	1		439	80	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984987	101984987	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1288900479	NA	P-0003503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	18	220	0	ENST00000282441.5:c.434C>G	p.Thr145Ser	p.T145S	ENST00000282441	NM_001130145.2	145	aCt/aGt	2/9	0.420560317502184	1	FACETS	0.564	0.44	0.698	0.564	0.44	0.698	INDETERMINATE	1	TRUE	0	0.726045772996419	1		220	56	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061327	38061327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	54	560	0	ENST00000250448.2:c.662C>T	p.Ser221Leu	p.S221L	ENST00000250448	NM_004496.3	221	tCg/tTg	2/2	0.224869659959602	5	FACETS	1	0.95	1	0.779	0.684	0.877	INDETERMINATE	2	TRUE	2	0.726045772996419	5		560	133	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610507	10610507	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	58	454	0	ENST00000171111.5:c.203A>G	p.Asn68Ser	p.N68S	ENST00000171111	NM_203500.1	68	aAc/aGc	2/6	0.726045772996419	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.726045772996419	1		454	77	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916405	39916418	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GACCTGGTTCCATC	GACCTGGTTCCATC	-	novel	NA	P-0003503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	62	304	0	ENST00000378444.4:c.4585_4595+3del		p.X1529_splice	ENST00000378444	NM_001123385.1	1529		11/15	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.726045772996419	1		304	73	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782144	NA	P-0003511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	98	325	0	ENST00000269305.4:c.473G>C	p.Arg158Pro	p.R158P	ENST00000269305	NM_001126112.2	158	cGc/cCc	5/11	0.387684955376584	1	FACETS	0.987	0.89	1	0.987	0.89	1	CLONAL	1	TRUE	0	0.462639493440593	1		325	330	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164812	106164812	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	35	353	0	ENST00000380013.4:c.3680T>C	p.Val1227Ala	p.V1227A	ENST00000380013	NM_001127208.2	1227	gTg/gCg	6/11	0.310572513532495	1	FACETS	0.282	0.231	0.34	0.282	0.231	0.34	SUBCLONAL	1	TRUE	0	0.462639493440593	1		353	412	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923210	26923210	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0003511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	175	406	0	ENST00000381527.3:c.206T>G	p.Leu69Ter	p.L69*	ENST00000381527	NM_001260.1	69	tTa/tGa	3/13	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.462639493440593	2		406	705	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6414400	6414400	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	20	94	0	ENST00000356142.4:c.34G>A	p.Gly12Arg	p.G12R	ENST00000356142	NM_018890.3	12	Gga/Aga	1/7	0.3	3	FACETS	1	0.825	1	0.545	0.419	0.692	CLONAL	1	TRUE	1	0.21	3		94	193	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148928	119148928	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	111	288	0	ENST00000264033.4:c.1148T>G	p.Ile383Arg	p.I383R	ENST00000264033	NM_005188.3	383	aTa/aGa	8/16	1	2	FACETS	0.771	0.693	0.852	1	0.984	1	SUBCLONAL	2	TRUE	1	0.21	2		288	686	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244616	46244616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	56	330	0	ENST00000334344.6:c.2710C>T	p.Gln904Ter	p.Q904*	ENST00000334344	NM_152641.2	904	Cag/Tag	15/21	0.232702321863266	3	FACETS	0.666	0.569	0.773	0.333	0.284	0.387	SUBCLONAL	1	TRUE	1	0.21	3		330	885	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57569920	57569920	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	52	264	0	ENST00000316660.6:c.100G>T	p.Asp34Tyr	p.D34Y	ENST00000316660	NM_021127.2	34	Gac/Tac	2/2	1	2	FACETS	0.78	0.663	0.908	0.78	0.663	0.908	CLONAL	1	TRUE	1	0.21	2		264	635	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0003527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	450	330	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.475074172226123	3	FACETS	1	0.968	1	1	0.997	1	CLONAL	3	FALSE	1	0.475074172226123	3		332	777	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0003527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	109	245	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.475074172226123	3	FACETS	1	0.944	1	0.535	0.482	0.59	CLONAL	1	FALSE	1	0.475074172226123	3		245	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578520	7578520	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	145	253	0	ENST00000269305.4:c.410T>A	p.Leu137Gln	p.L137Q	ENST00000269305	NM_001126112.2	137	cTg/cAg	5/11	NA	2	FACETS	0.954	0.885	1			1	INDETERMINATE	2	FALSE	NA	0.475074172226123	2		253	320	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243668598	243668598	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776935	NA	P-0003527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	90	299	0	ENST00000263826.5:c.1393C>T	p.Arg465Trp	p.R465W	ENST00000263826	NM_005465.4	465	Cgg/Tgg	13/13	0.460258217466103	3	FACETS	1	0.893	1	0.501	0.446	0.559	CLONAL	1	FALSE	1	0.475074172226123	3		299	468	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159015	143159015	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0003527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	75	250	0	ENST00000262992.4:c.836+2T>C		p.X279_splice	ENST00000262992	NM_001101669.1	279			0.475074172226123	2	FACETS	1	0.928	1	0.533	0.472	0.598	CLONAL	1	FALSE	0	0.475074172226123	2		250	296	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112919929	112919929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1214510641	NA	P-0003527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	56	127	0	ENST00000351677.2:c.1144G>A	p.Val382Ile	p.V382I	ENST00000351677	NM_002834.3	382	Gtc/Atc	10/16	0.460258217466103	3	FACETS	1	0.956	1	0.634	0.55	0.724	CLONAL	1	FALSE	1	0.475074172226123	3		127	230	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087947	27087947	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003537-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	96	229	0	ENST00000324856.7:c.2234G>C	p.Ser745Thr	p.S745T	ENST00000324856	NM_006015.4	745	aGc/aCc	6/20	0.421018681998994	1	FACETS	0.42	0.375	0.468	0.42	0.375	0.468	SUBCLONAL	1	TRUE	0	0.596218034776977	1		229	538	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058537	72058537	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003537-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	155	407	0	ENST00000357731.5:c.903C>A	p.Asn301Lys	p.N301K	ENST00000357731	NM_173808.2	301	aaC/aaA	6/7	0.348854525468518	1	FACETS	0.439	0.402	0.478	0.439	0.402	0.478	INDETERMINATE	1	TRUE	0	0.596218034776977	1		407	831	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99163154	99163154	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003537-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	204	218	0	ENST00000074304.5:c.1160A>G	p.Lys387Arg	p.K387R	ENST00000074304	NM_001134224.1	387	aAa/aGa	13/26	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.596218034776977	2		218	568	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874551	35874551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003537-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	213	310	0	ENST00000303115.3:c.707G>T	p.Gly236Val	p.G236V	ENST00000303115	NM_002185.3	236	gGg/gTg	6/8	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.596218034776977	2		310	699	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569301	67569301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003537-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	190	226	0	ENST00000274335.5:c.418G>A	p.Glu140Lys	p.E140K	ENST00000274335		140	Gaa/Aaa	2/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.596218034776977	2		226	608	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218052	108218052	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1064794840	NA	P-0003537-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	314	234	0	ENST00000278616.4:c.8631G>C	p.Leu2877Phe	p.L2877F	ENST00000278616	NM_000051.3	2877	ttG/ttC	59/63	0.596218034776977	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.596218034776977	2		234	521	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434552	49434552	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003537-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	116	133	0	ENST00000301067.7:c.7001G>T	p.Arg2334Leu	p.R2334L	ENST00000301067	NM_003482.3	2334	cGg/cTg	31/54	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.596218034776977	2		133	360	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727490	88727490	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003537-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	127	227	0	ENST00000360948.2:c.289G>C	p.Val97Leu	p.V97L	ENST00000360948	NM_001012338.2	97	Gtg/Ctg	3/19	0.226414531190929	0	FACETS	0.418	0.381	0.455			1	INDETERMINATE	1	TRUE	0	0.596218034776977	0		227	412	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350927	89350927	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003537-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	288	434	0	ENST00000301030.4:c.2023G>C	p.Glu675Gln	p.E675Q	ENST00000301030	NM_001256183.1	675	Gag/Cag	9/13	0.267851165362621	0	FACETS	0.44	0.414	0.466			1	INDETERMINATE	1	TRUE	0	0.596218034776977	0		434	887	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207201	1207201	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0003537-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	139	136	0	ENST00000326873.7:c.289A>T	p.Lys97Ter	p.K97*	ENST00000326873	NM_000455.4	97	Aag/Tag	1/10	0.596218034776977	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.596218034776977	1		136	260	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602799	10602799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003537-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	219	245	0	ENST00000171111.5:c.779G>T	p.Arg260Leu	p.R260L	ENST00000171111	NM_203500.1	260	cGa/cTa	3/6	0.596218034776977	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.596218034776977	1		245	393	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790139	40790139	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003537-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	103	149	0	ENST00000373198.4:c.2592C>G	p.Ile864Met	p.I864M	ENST00000373198	NM_133170.3	864	atC/atG	18/32	0.412397095756782	1	FACETS	0.72	0.651	0.791	0.72	0.651	0.791	SUBCLONAL	1	TRUE	0	0.596218034776977	1		149	337	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508182	38508184	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs751811710	NA	P-0003537-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	86	266	1	ENST00000254066.5:c.499_501del	p.Lys167del	p.K167del	ENST00000254066	NM_000964.3	164	AAG/-	5/9	0.596218034776977	1	FACETS	0.487	0.433	0.544	0.487	0.433	0.544	SUBCLONAL	1	TRUE	0	0.596218034776977	1		267	416	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0003545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	48	132	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.356201582518039	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.356201582518039	1		132	198	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106652	27106652	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	73	416	1	ENST00000324856.7:c.6263T>C	p.Leu2088Pro	p.L2088P	ENST00000324856	NM_006015.4	2088	cTc/cCc	20/20	0.356201582518039	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.356201582518039	1		417	321	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0003551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	824	201	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.454843674108735	13	FACETS	1	0.994	1			1	CLONAL	11	TRUE	NA	0.454843674108735	13		201	1109	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0003551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	106	325	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.329543585119156	3	FACETS	1	0.91	1	0.667	0.607	0.728	CLONAL	2	TRUE	0	0.454843674108735	3		325	286	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254863	16254863	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	43	317	0	ENST00000375759.3:c.2128G>C	p.Glu710Gln	p.E710Q	ENST00000375759	NM_015001.2	710	Gag/Cag	11/15	0.275499139052903	4	FACETS	0.646	0.541	0.762	0.323	0.27	0.381	SUBCLONAL	1	TRUE	2	0.454843674108735	4		317	426	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858570	57858570	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	40	618	0	ENST00000228682.2:c.308C>G	p.Pro103Arg	p.P103R	ENST00000228682	NM_005269.2	103	cCc/cGc	4/12	0.368788221263043	1	FACETS	0.288	0.239	0.342	0.288	0.239	0.342	SUBCLONAL	1	TRUE	0	0.454843674108735	1		618	472	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56875697	56875697	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	229	505	0	ENST00000308159.5:c.2301T>G	p.Ser767Arg	p.S767R	ENST00000308159	NM_014669.4	767	agT/agG	21/22	0.454843674108735	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.454843674108735	1		505	523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578486	7578486	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	111	336	0	ENST00000269305.4:c.444T>A	p.Asp148Glu	p.D148E	ENST00000269305	NM_001126112.2	148	gaT/gaA	5/11	0.329543585119156	3	FACETS	1	0.935	1	0.686	0.626	0.748	CLONAL	2	TRUE	0	0.454843674108735	3		336	291	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0003552-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	94	192	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.238746066959965	3	FACETS	1	0.939	1	0.706	0.636	0.779	CLONAL	2	TRUE	0	0.348409080945499	3		192	299	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085690	16085690	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003552-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	114	379	0	ENST00000281043.3:c.866C>A	p.Ser289Tyr	p.S289Y	ENST00000281043	NM_005378.4	289	tCc/tAc	3/3	0.28597031124948	4	FACETS	0.752	0.679	0.828	0.752	0.679	0.828	SUBCLONAL	2	TRUE	2	0.348409080945499	4		379	587	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692812	89692820	+	inframe_deletion	In_Frame_Del	DEL	AACTTATCA	AACTTATCA	-	novel	NA	P-0003552-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	64	144	0	ENST00000371953.3:c.299_307del	p.Leu100_Lys102del	p.L100_K102del	ENST00000371953	NM_000314.4	99	gAACTTATCAaa/gaa	5/9	0.337033837639065	2	FACETS	1	0.971	1	0.718	0.628	0.812	CLONAL	1	TRUE	0	0.348409080945499	2		144	256	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	71	62	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.714188308843944	4	FACETS	1	0.925	1	0.534	0.47	0.601	CLONAL	1	TRUE	2	0.835890778355817	4		62	292	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0003570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	184	420	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.835540549829414	2	FACETS	0.987	0.949	1	0.987	0.949	1	CLONAL	2	TRUE	0	0.835890778355817	2		420	223	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461166	120461166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200693165	NA	P-0003570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	60	225	2	ENST00000256646.2:c.5792G>A	p.Arg1931His	p.R1931H	ENST00000256646	NM_024408.3	1931	cGc/cAc	32/34	0.714188308843944	4	FACETS	0.887	0.771	1	0.444	0.385	0.506	CLONAL	1	TRUE	2	0.835890778355817	4		227	297	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535450	66535450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	47	64	2	ENST00000273854.3:c.11C>T	p.Ser4Leu	p.S4L	ENST00000273854	NM_004439.5	4	tCg/tTg	1/18	0.544465965678893	4	FACETS	1	0.96	1	0.456	0.392	0.523	CLONAL	1	TRUE	1	0.835890778355817	4		66	151	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032045	26032045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	74	634	0	ENST00000244661.2:c.244G>A	p.Asp82Asn	p.D82N	ENST00000244661	NM_003537.3	82	Gat/Aat	1/1	0.544465965678893	4	FACETS	0.433	0.379	0.492	0.144	0.126	0.164	SUBCLONAL	1	TRUE	1	0.835890778355817	4		634	750	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22008910	22008910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	156	306	0	ENST00000276925.6:c.43G>A	p.Asp15Asn	p.D15N	ENST00000276925	NM_004936.3	15	Gat/Aat	1/2	0.444441913071028	5	FACETS	1	0.983	1	0.419	0.385	0.455	INDETERMINATE	1	TRUE	2	0.835890778355817	5		306	669	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230772	46230772	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	15	235	0	ENST00000334344.6:c.1021G>C	p.Glu341Gln	p.E341Q	ENST00000334344	NM_152641.2	341	Gag/Cag	8/21	0.65445174492445	3	FACETS	0.229	0.167	0.303	0.115	0.083	0.152	SUBCLONAL	1	TRUE	1	0.835890778355817	3		235	222	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913416	28913416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1423880278	NA	P-0003570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	34	324	1	ENST00000282397.4:c.2377G>A	p.Asp793Asn	p.D793N	ENST00000282397	NM_002019.4	793	Gac/Aac	17/30	0.255056882698791	3	FACETS	0.373	0.306	0.449	0.124	0.102	0.15	INDETERMINATE	1	TRUE	0	0.835890778355817	3		325	309	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923448	9923448	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	77	379	0	ENST00000330684.3:c.1839C>G	p.Phe613Leu	p.F613L	ENST00000330684	NM_001134407.1	613	ttC/ttG	9/13	0.555866129275107	4	FACETS	1	0.886	1	0.5	0.443	0.561	CLONAL	1	TRUE	2	0.835890778355817	4		379	338	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845758	68845758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373364873	NA	P-0003570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	51	269	0	ENST00000261769.5:c.1004G>A	p.Arg335Gln	p.R335Q	ENST00000261769	NM_004360.3	335	cGa/cAa	7/16	0.255056882698791	3	FACETS	0.706	0.606	0.814	0.235	0.202	0.272	INDETERMINATE	1	TRUE	0	0.835890778355817	3		269	245	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548880	29548880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	72	235	0	ENST00000356175.3:c.1654C>T	p.Leu552Phe	p.L552F	ENST00000356175	NM_000267.3	552	Ctt/Ttt	15/57	0.835890778355817	6	FACETS	0.784	0.686	0.89			1	SUBCLONAL	1	TRUE	NA	0.835890778355817	6		235	587	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627521	14627521	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	47	425	0	ENST00000254322.2:c.549G>T	p.Met183Ile	p.M183I	ENST00000254322	NM_006145.1	183	atG/atT	2/3	0.607101206798503	4	FACETS	0.332	0.279	0.39			1	SUBCLONAL	1	TRUE	NA	0.835890778355817	4		425	622	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0003579-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	208	311	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	0.995	1	CLONAL	3	TRUE	1	0.23	2		311	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0003579-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	656	593	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.3	4	FACETS	0.986	0.966	1			1	CLONAL	9	TRUE	NA	0.23	4		593	791	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854957	76854957	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0003579-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	391	252	0	ENST00000373344.5:c.5879C>G	p.Ser1960Ter	p.S1960*	ENST00000373344	NM_000489.3	1960	tCa/tGa	25/35	1	1	FACETS	0.97	0.94	0.998	1	0.998	1	CLONAL	6	TRUE	0	0.23	1		252	517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0003593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	158	455	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.290464281095307	1	FACETS	0.965	0.885	1	0.965	0.885	1	CLONAL	1	TRUE	0	0.336395775688025	1		455	810	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0003602-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	447	520	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.725330561224531	6	FACETS	0.975	0.933	1			1	CLONAL	3	TRUE	NA	0.725330561224531	6		520	1033	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0003602-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	346	505	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.725330561224531	2	FACETS	0.978	0.943	1	0.978	0.943	1	CLONAL	2	TRUE	0	0.725330561224531	2		505	488	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0003602-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	157	533	2	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.725330561224531	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.725330561224531	1		535	258	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934874	NA	P-0003619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	215	178	0	ENST00000269305.4:c.451C>G	p.Pro151Ala	p.P151A	ENST00000269305	NM_001126112.2	151	Ccc/Gcc	5/11	NA	2	FACETS	0.907	0.869	0.944			1	INDETERMINATE	2	TRUE	NA	0.820023621447458	2		178	289	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991736	25991736	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs530632623	NA	P-0003619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	96	190	0	ENST00000435504.4:c.506C>T	p.Ala169Val	p.A169V	ENST00000435504		169	gCg/gTg	7/13	0.820023621447458	3	FACETS	0.799	0.717	0.886	0.4	0.358	0.443	SUBCLONAL	1	TRUE	1	0.820023621447458	3		190	413	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0003623-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	8	496	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	1	2	FACETS	0.654	0.423	0.947	0.654	0.423	0.947	SUBCLONAL	1	TRUE	1	0.24	2		496	102	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412030	116412044	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TACTTTTCCAGAAGG	TACTTTTCCAGAAGG	-	novel	NA	P-0003623-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	39	198	0	ENST00000397752.3:c.3017_3028+3del		p.X1006_splice	ENST00000397752	NM_000245.2	1006		14/21	0.523403616198983	3	FACETS	1	0.922	1	0.599	0.498	0.71	CLONAL	1	TRUE	1	0.24	3		198	304	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244934	46244934	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0003623-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	10	410	0	ENST00000334344.6:c.3028A>T	p.Lys1010Ter	p.K1010*	ENST00000334344	NM_152641.2	1010	Aaa/Taa	15/21	0.218639855649223	3	FACETS	0.481	0.326	0.676	0.241	0.163	0.338	SUBCLONAL	1	TRUE	1	0.24	3		410	194	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0003632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	77	445	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	NA	2	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.201466019619378	2		446	593	SUCCESS
FH	2271	MSKCC	GRCh37	1	241661212	241661212	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	110	323	0	ENST00000366560.3:c.1449G>T	p.Lys483Asn	p.K483N	ENST00000366560	NM_000143.3	483	aaG/aaT	10/10	1	2	FACETS	0.772	0.694	0.855	1	0.984	1	SUBCLONAL	2	TRUE	1	0.201466019619378	2		323	707	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483979	212483979	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	80	357	0	ENST00000342788.4:c.2224G>C	p.Glu742Gln	p.E742Q	ENST00000342788	NM_005235.2	742	Gaa/Caa	19/28	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.201466019619378	2		357	667	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812191	212812191	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	99	319	0	ENST00000342788.4:c.385T>A	p.Phe129Ile	p.F129I	ENST00000342788	NM_005235.2	129	Ttt/Att	3/28	1	2	FACETS	0.834	0.746	0.927	1	0.984	1	CLONAL	2	TRUE	1	0.201466019619378	2		319	589	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670615	134670615	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	86	386	0	ENST00000398015.3:c.526G>T	p.Ala176Ser	p.A176S	ENST00000398015	NM_004441.4	176	Gct/Tct	3/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.201466019619378	2		386	678	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481637	20481637	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0003632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	54	275	0	ENST00000346618.3:c.706A>T	p.Lys236Ter	p.K236*	ENST00000346618	NM_001949.4	236	Aaa/Taa	3/7	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.201466019619378	2		275	483	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444360	50444360	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	47	212	1	ENST00000331340.3:c.290G>T	p.Arg97Met	p.R97M	ENST00000331340	NM_006060.4	97	aGg/aTg	4/8	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.201466019619378	2		213	438	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335719	81335720	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0003632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	52	250	1	ENST00000222390.5:c.1640_1641delinsTT	p.Trp547Phe	p.W547F	ENST00000222390	NM_000601.4	547	tGG/tTT	15/18	0.179359469313828	3	FACETS	0.958	0.815	1	0.479	0.407	0.558	CLONAL	1	TRUE	1	0.201466019619378	3		251	593	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971114	21971114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1060501269	NA	P-0003632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	27	177	0	ENST00000304494.5:c.244G>T	p.Val82Leu	p.V82L	ENST00000304494	NM_000077.4	82	Gtg/Ttg	2/3	0.201466019619378	1	FACETS	1	0.831	1	1	0.831	1	CLONAL	1	TRUE	0	0.201466019619378	1		177	231	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112479	115112479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs912240752	NA	P-0003632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	73	234	2	ENST00000257566.3:c.1261C>T	p.Arg421Trp	p.R421W	ENST00000257566	NM_016569.3	421	Cgg/Tgg	7/8	1	2	FACETS	0.956	0.841	1	1	0.982	1	CLONAL	2	TRUE	1	0.201466019619378	2		236	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578258	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0003632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	61	388	0	ENST00000269305.4:c.591_592delinsTT	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	197	gtGGaa/gtTTaa	6/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.201466019619378	2		388	456	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627316	37627316	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	74	280	0	ENST00000447079.4:c.1231G>T	p.Ala411Ser	p.A411S	ENST00000447079	NM_015083.1	411	Gct/Tct	2/14	1	2	FACETS	0.76	0.668	0.86	1	0.976	1	SUBCLONAL	2	TRUE	1	0.201466019619378	2		280	483	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092889	29092889	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	80	358	0	ENST00000328354.6:c.1095G>T	p.Lys365Asn	p.K365N	ENST00000328354	NM_007194.3	365	aaG/aaT	10/15	0.201466019619378	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.201466019619378	1		358	591	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931748	39931748	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	72	503	0	ENST00000378444.4:c.2851G>A	p.Asp951Asn	p.D951N	ENST00000378444	NM_001123385.1	951	Gat/Aat	4/15	0.201466019619378	1	FACETS	0.872	0.761	0.992	0.872	0.761	0.992	CLONAL	1	TRUE	0	0.201466019619378	1		503	737	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028850	47028850	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	59	367	0	ENST00000377604.3:c.154G>T	p.Glu52Ter	p.E52*	ENST00000377604	NM_001204468.1	52	Gag/Tag	3/24	0.201466019619378	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.201466019619378	1		367	480	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202644	108202647	+	frameshift_variant	Frame_Shift_Del	DEL	TTTG	TTTG	-	rs1555124506	NA	P-0003642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	39	323	0	ENST00000278616.4:c.7671_7674del	p.Phe2558LeufsTer5	p.F2558Lfs*5	ENST00000278616	NM_000051.3	2556	acTTTG/ac	52/63	0.3799435318589	2	FACETS	1	0.96	1	0.746	0.634	0.864	CLONAL	1	TRUE	0	0.44660410856181	2		323	117	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247863	59247864	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0003642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	91	650	0	ENST00000371222.2:c.879_880del	p.Glu293AspfsTer16	p.E293Dfs*16	ENST00000371222	NM_002228.3	293	gaGCtg/gatg	1/1	0.228293001949079	5	FACETS	1	0.956	1	0.746	0.67	0.825	INDETERMINATE	2	TRUE	2	0.44660410856181	5		650	304	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0003657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	36	349	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	0.427	0.35	0.513	0.427	0.35	0.513	SUBCLONAL	1	TRUE	1	0.29	2		349	582	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026752	48026752	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	25	266	0	ENST00000234420.5:c.1630G>T	p.Glu544Ter	p.E544*	ENST00000234420	NM_000179.2	544	Gaa/Taa	4/10	0.210758197751648	1	FACETS	0.337	0.265	0.421	0.337	0.265	0.421	SUBCLONAL	1	TRUE	0	0.29	1		266	437	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561808	55561808	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	31	357	0	ENST00000288135.5:c.198G>A	p.Trp66Ter	p.W66*	ENST00000288135	NM_000222.2	66	tgG/tgA	2/21	1	2	FACETS	0.347	0.279	0.423	0.347	0.279	0.423	SUBCLONAL	1	TRUE	1	0.29	2		357	617	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842408	68842408	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	159	474	0	ENST00000261769.5:c.469G>T	p.Val157Phe	p.V157F	ENST00000261769	NM_004360.3	157	Gtt/Ttt	4/16	0.3	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.29	1		474	723	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827886	40827886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201911869	NA	P-0003657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	96	312	0	ENST00000373198.4:c.2542G>A	p.Gly848Arg	p.G848R	ENST00000373198	NM_133170.3	848	Gga/Aga	17/32	0.193997993464436	1	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	0	0.29	1		312	561	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914756	39914756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	58	375	0	ENST00000378444.4:c.4606G>A	p.Asp1536Asn	p.D1536N	ENST00000378444	NM_001123385.1	1536	Gat/Aat	12/15	0.210758197751648	1	FACETS	0.623	0.535	0.718	0.623	0.535	0.718	SUBCLONAL	1	TRUE	0	0.29	1		375	549	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405133	70405133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1174505520	NA	P-0003660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	54	352	0	ENST00000373644.4:c.2647G>A	p.Asp883Asn	p.D883N	ENST00000373644	NM_030625.2	883	Gat/Aat	4/12	1	2	FACETS	0.422	0.36	0.491	0.422	0.36	0.491	SUBCLONAL	1	TRUE	1	0.355865449214034	2		352	719	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0003666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	105	159	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.29875766990229	2	FACETS	1	0.978	1	0.658	0.594	0.724	CLONAL	1	TRUE	0	0.406332039666878	2		159	393	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143341	30143341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	75	293	0	ENST00000389048.3:c.185C>T	p.Ser62Leu	p.S62L	ENST00000389048	NM_004304.4	62	tCg/tTg	1/29	0.295985996123484	3	FACETS	0.862	0.757	0.975	0.431	0.378	0.488	CLONAL	1	TRUE	1	0.406332039666878	3		293	515	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245033	46245033	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs139789595	NA	P-0003666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	501	397	0	ENST00000334344.6:c.3127C>T	p.Gln1043Ter	p.Q1043*	ENST00000334344	NM_152641.2	1043	Caa/Taa	15/21	0.406332039666878	3	FACETS	0.912	0.877	0.948	0.912	0.877	0.948	CLONAL	3	TRUE	0	0.406332039666878	3		397	1084	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589920	212589920	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0003666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	75	215	0	ENST00000342788.4:c.623-1G>T		p.X208_splice	ENST00000342788	NM_005235.2	208			0.295985996123484	3	FACETS	0.793	0.696	0.898	0.397	0.348	0.449	SUBCLONAL	1	TRUE	1	0.406332039666878	3		215	560	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896546	151896546	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0003666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	51	142	0	ENST00000262189.6:c.4093-2A>T		p.X1365_splice	ENST00000262189	NM_170606.2	1365			1	2	FACETS	0.585	0.498	0.68	0.585	0.498	0.68	SUBCLONAL	1	TRUE	1	0.406332039666878	2		142	429	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404834	70404834	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs765874881	NA	P-0003666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	203	278	0	ENST00000373644.4:c.2348G>T	p.Gly783Val	p.G783V	ENST00000373644	NM_030625.2	783	gGc/gTc	4/12	0.186550067038219	4	FACETS	0.787	0.73	0.845			1	INDETERMINATE	2	TRUE	NA	0.406332039666878	4		278	893	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593397	48593397	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	55	164	0	ENST00000342988.3:c.1148T>G	p.Ile383Arg	p.I383R	ENST00000342988	NM_005359.5	383	aTa/aGa	10/12	0.312785069544557	1	FACETS	0.556	0.477	0.642	0.556	0.477	0.642	SUBCLONAL	1	TRUE	0	0.406332039666878	1		164	388	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453200	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTGAGGT	TCTGAGGT	-	novel	NA	P-0003666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	68	160	0	ENST00000288602.6:c.1742-7_1742del		p.X581_splice	ENST00000288602	NM_004333.4	581		15/18	1	2	FACETS	0.714	0.622	0.812	0.714	0.622	0.812	SUBCLONAL	1	TRUE	1	0.406332039666878	2		160	469	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602614	10602617	+	missense_variant	Missense_Mutation	ONP	GCGC	GCGC	ACGG	novel	NA	P-0003666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	250	275	0	ENST00000171111.5:c.961_964delinsCCGT	p.Ala321_Pro322delinsProSer	p.A321_P322delinsPS	ENST00000171111	NM_203500.1	321	GCGCcc/CCGTcc	3/6	0.311655346091306	3	FACETS	0.863	0.814	0.912	0.863	0.814	0.912	CLONAL	3	TRUE	0	0.406332039666878	3		275	572	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654516	29654517	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0003666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	215	262	0	ENST00000356175.3:c.5206-1_5206delinsAA		p.X1736_splice	ENST00000356175	NM_000267.3	1736		37/57	0.29875766990229	2	FACETS	1	0.991	1	0.703	0.655	0.752	CLONAL	1	TRUE	0	0.406332039666878	2		262	753	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0003669-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	35	366	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		366	396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0003669-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	58	675	1	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		676	454	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909678	76909678	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003669-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	27	366	0	ENST00000373344.5:c.4227del	p.Ala1410GlnfsTer80	p.A1410Qfs*80	ENST00000373344	NM_000489.3	1409	aaA/aa	14/35	0.158991004850174	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		366	367	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849164	76849164	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0003703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	153	427	0	ENST00000373344.5:c.6110+2T>A		p.X2037_splice	ENST00000373344	NM_000489.3	2037			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		427	365	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0003704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	41	274	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	1	2	FACETS	0.977	0.818	1	0.977	0.818	1	CLONAL	1	TRUE	1	0.280595923209389	2		274	299	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0003704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	42	275	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	0.280528617383745	3	FACETS	1	0.955	1	0.714	0.601	0.837	CLONAL	1	TRUE	1	0.280595923209389	3		275	239	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277991	41277991	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	23	353	0	ENST00000349496.5:c.1954+1G>A		p.X652_splice	ENST00000349496	NM_001904.3	652			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		353	166	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127164	22127164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057519911	NA	P-0003711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	130	638	0	ENST00000215832.6:c.964G>A	p.Glu322Lys	p.E322K	ENST00000215832	NM_002745.4	322	Gag/Aag	7/9	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.369681641846566	2		638	620	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754908	29754908	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	65	259	0	ENST00000389048.3:c.1027G>C	p.Glu343Gln	p.E343Q	ENST00000389048	NM_004304.4	343	Gag/Cag	4/29	0.356771328597633	3	FACETS	0.92	0.8	1	0.46	0.4	0.525	CLONAL	1	TRUE	1	0.369681641846566	3		259	453	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663054	227663054	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	67	302	0	ENST00000305123.5:c.401G>T	p.Gly134Val	p.G134V	ENST00000305123	NM_005544.2	134	gGc/gTc	1/2	1	2	FACETS	0.811	0.707	0.923	0.811	0.707	0.923	CLONAL	1	TRUE	1	0.369681641846566	2		302	447	SUCCESS
ATR	545	MSKCC	GRCh37	3	142183938	142183938	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0003711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	91	450	0	ENST00000350721.4:c.7041+1G>T		p.X2347_splice	ENST00000350721	NM_001184.3	2347			1	2	FACETS	0.781	0.695	0.874	0.781	0.695	0.874	SUBCLONAL	1	TRUE	1	0.369681641846566	2		450	630	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242962	142242962	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	130	488	0	ENST00000350721.4:c.4025G>T	p.Gly1342Val	p.G1342V	ENST00000350721	NM_001184.3	1342	gGt/gTt	22/47	1	2	FACETS	0.898	0.815	0.986	0.898	0.815	0.986	CLONAL	1	TRUE	1	0.369681641846566	2		488	783	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123050	5123050	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	113	399	0	ENST00000381652.3:c.3106G>C	p.Asp1036His	p.D1036H	ENST00000381652	NM_004972.3	1036	Gat/Cat	23/25	0.369681641846566	1	FACETS	0.859	0.775	0.947	0.859	0.775	0.947	CLONAL	1	TRUE	0	0.369681641846566	1		399	580	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418361	49418361	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1555185217	NA	P-0003711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	87	246	0	ENST00000301067.7:c.16052G>A	p.Arg5351Gln	p.R5351Q	ENST00000301067	NM_003482.3	5351	cGg/cAg	50/54	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.369681641846566	2		246	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0003713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	84	366	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.264223772633378	3	FACETS	0.998	0.895	1	0.665	0.597	0.736	CLONAL	2	TRUE	0	0.410849620422371	3		366	247	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230813	66230813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748201189	NA	P-0003713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	27	442	0	ENST00000273854.3:c.2158G>A	p.Asp720Asn	p.D720N	ENST00000273854	NM_004439.5	720	Gat/Aat	12/18	0.41814824822665	1	FACETS	0.383	0.305	0.471	0.383	0.305	0.471	SUBCLONAL	1	TRUE	0	0.410849620422371	1		442	273	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566700	212566700	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	40	292	0	ENST00000342788.4:c.1481A>C	p.Glu494Ala	p.E494A	ENST00000342788	NM_005235.2	494	gAa/gCa	12/28	0.312833407410106	2	FACETS	0.62	0.517	0.734	0.31	0.258	0.367	SUBCLONAL	1	TRUE	0	0.410849620422371	2		292	314	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045890	143045890	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	27	286	0	ENST00000262992.4:c.1744C>T	p.Pro582Ser	p.P582S	ENST00000262992	NM_001101669.1	582	Ccc/Tcc	17/24	0.365690381384395	2	FACETS	0.667	0.535	0.816	0.334	0.267	0.408	SUBCLONAL	1	TRUE	0	0.410849620422371	2		286	197	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472483	88472483	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	36	370	0	ENST00000360948.2:c.2072T>C	p.Leu691Pro	p.L691P	ENST00000360948	NM_001012338.2	691	cTg/cCg	16/19	0.157215339136247	1	FACETS	0.534	0.441	0.636	0.534	0.441	0.636	INDETERMINATE	1	TRUE	0	0.410849620422371	1		370	261	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098473	11098473	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760562676	NA	P-0003713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	30	210	0	ENST00000358026.2:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000358026	NM_001128849.1	331	Cag/Tag	6/36	0.41814824822665	3	FACETS	1	0.9	1	0.583	0.476	0.701	CLONAL	1	TRUE	1	0.410849620422371	3		210	151	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054584	13054586	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs1398145751	NA	P-0003713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	82	628	0	ENST00000316448.5:c.1116_1118del	p.Glu372del	p.E372del	ENST00000316448	NM_004343.3	371	GAA/-	9/9	0.41814824822665	3	FACETS	0.953	0.843	1	0.476	0.421	0.535	CLONAL	1	TRUE	1	0.410849620422371	3		628	505	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0003716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	120	375	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.48514801583825	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.48514801583825	1		375	308	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142966	47142966	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1559720382	NA	P-0003716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	191	259	1	ENST00000409792.3:c.4997A>G	p.Tyr1666Cys	p.Y1666C	ENST00000409792	NM_014159.6	1666	tAt/tGt	8/21	NA	2	FACETS	0.843	0.788	0.899			1	INDETERMINATE	2	TRUE	NA	0.48514801583825	2		260	467	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913026	32913026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80358684	NA	P-0003716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	196	459	3	ENST00000380152.3:c.4534C>T	p.Arg1512Cys	p.R1512C	ENST00000380152		1512	Cgt/Tgt	11/27	0.423646006418336	0	FACETS	0.705	0.657	0.755			1	SUBCLONAL	1	TRUE	0	0.48514801583825	0		462	590	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991115	41991115	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	244	283	0	ENST00000219905.7:c.2068C>T	p.Gln690Ter	p.Q690*	ENST00000219905	NM_001164273.1	690	Cag/Tag	4/24	0.0701947676622967	3	FACETS	0.927	0.871	0.984			1	INDETERMINATE	2	TRUE	NA	0.48514801583825	3		283	674	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096901	11096901	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	100	270	1	ENST00000358026.2:c.392C>A	p.Ser131Tyr	p.S131Y	ENST00000358026	NM_001128849.1	131	tCt/tAt	4/36	0.481598545484153	1	FACETS	0.877	0.791	0.967	0.877	0.791	0.967	CLONAL	1	TRUE	0	0.48514801583825	1		271	356	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0003732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	138	298	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	0.110226678324775	4	FACETS	1	0.974	1			1	INDETERMINATE	2	TRUE	NA	0.290079759806547	4		298	527	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169377	11169377	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519916	NA	P-0003732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	169	577	0	ENST00000361445.4:c.7498A>T	p.Ile2500Phe	p.I2500F	ENST00000361445	NM_004958.3	2500	Att/Ttt	56/58	0.241617022332977	5	FACETS	0.897	0.825	0.973	0.598	0.55	0.649	CLONAL	2	TRUE	2	0.290079759806547	5		577	932	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086218	16086218	+	stop_lost	Nonstop_Mutation	SNP	A	A	T	novel	NA	P-0003732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	86	266	0	ENST00000281043.3:c.1394A>T	p.Ter465LeuextTer15	p.*465Lext*15	ENST00000281043	NM_005378.4	465	tAg/tTg	3/3	0.174677758385967	5	FACETS	0.933	0.829	1	0.622	0.553	0.696	CLONAL	2	TRUE	2	0.290079759806547	5		266	456	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44919400	44919400	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	75	161	0	ENST00000377967.4:c.1328A>G	p.Gln443Arg	p.Q443R	ENST00000377967	NM_021140.2	443	cAg/cGg	13/29	0.268679955719539	2	FACETS	0.976	0.866	1	0.976	0.866	1	CLONAL	2	TRUE	0	0.290079759806547	2		161	265	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038560	47038560	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0003732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	170	540	0	ENST00000377604.3:c.722C>G	p.Ser241Ter	p.S241*	ENST00000377604	NM_001204468.1	241	tCa/tGa	8/24	0.268679955719539	2	FACETS	0.98	0.906	1	0.98	0.906	1	CLONAL	2	TRUE	0	0.290079759806547	2		540	598	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80646057	80646057	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	16	77	0	ENST00000286548.4:c.95A>G	p.Asp32Gly	p.D32G	ENST00000286548	NM_002072.3	32	gAc/gGc	1/7	1	2	FACETS	0.453	0.336	0.592	0.453	0.336	0.592	SUBCLONAL	1	TRUE	1	0.403245956933119	2		77	175	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233062	69233062	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3479	440	184	0	ENST00000462284.1:c.927G>C	p.Trp309Cys	p.W309C	ENST00000462284	NM_002392.5	309	tgG/tgC	11/11	0.403245956933119	6	FACETS	1	0.953	1			1	CLONAL	1	TRUE	NA	0.403245956933119	6		184	3919	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378642	25378642	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	46	235	0	ENST00000311936.3:c.356A>G	p.Asp119Gly	p.D119G	ENST00000311936	NM_004985.3	119	gAt/gGt	4/5	0.315552998841859	3	FACETS	0.792	0.668	0.929	0.396	0.334	0.465	CLONAL	1	TRUE	1	0.315552998841859	3		235	426	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547026	9547026	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	13	33	0	ENST00000353224.5:c.996T>A	p.Asp332Glu	p.D332E	ENST00000353224	NM_177990.2	332	gaT/gaA	5/10	0.310369552835913	4	FACETS	1	0.8	1	0.38	0.274	0.506	CLONAL	1	TRUE	1	0.315552998841859	4		33	95	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023122	48023122	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	201	414	0	ENST00000234420.5:c.547T>A	p.Leu183Ile	p.L183I	ENST00000234420	NM_000179.2	183	Tta/Ata	3/10	0.48441115540252	4	FACETS	0.984	0.911	1	0.492	0.455	0.53	CLONAL	1	TRUE	2	0.576991362991974	4		414	1117	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805633	46805633	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	350	417	1	ENST00000290295.7:c.323C>A	p.Ala108Glu	p.A108E	ENST00000290295	NM_006361.5	108	gCg/gAg	1/2	0.47997490495399	4	FACETS	0.952	0.903	1			1	CLONAL	2	TRUE	NA	0.576991362991974	4		418	1005	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193554	99193554	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	181	216	0	ENST00000074304.5:c.2749del	p.Glu917SerfsTer27	p.E917Sfs*27	ENST00000074304	NM_001134224.1	917	Gag/ag	25/26	0.48441115540252	4	FACETS	0.904	0.84	0.97	0.904	0.84	0.97	CLONAL	2	TRUE	2	0.576991362991974	4		216	547	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608994	43609008	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGCCCTCAGGGGGC	CTGCCCTCAGGGGGC	-	novel	NA	P-0003750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	168	377	0	ENST00000355710.3:c.1760-10_1764del		p.X587_splice	ENST00000355710	NM_020975.4	587		10/20	0.525677581398127	3	FACETS	0.967	0.89	1	0.483	0.445	0.524	CLONAL	1	TRUE	1	0.576991362991974	3		377	776	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629033	14629035	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs764800868	NA	P-0003750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	103	348	0	ENST00000254322.2:c.127_129del	p.Glu43del	p.E43del	ENST00000254322	NM_006145.1	43	GAG/-	1/3	0.493549131106081	2	FACETS	0.753	0.677	0.833	0.377	0.338	0.417	SUBCLONAL	1	TRUE	0	0.576991362991974	2		348	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0003754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	108	181	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.766731001993219	3	FACETS	1	0.966	1	0.565	0.513	0.618	CLONAL	1	TRUE	1	0.870955579359171	3		181	315	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436170	51436170	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	133	89	0	ENST00000262662.1:c.129+1G>A		p.X43_splice	ENST00000262662		43			NA	2	FACETS	1	0.982	1			1	INDETERMINATE	2	TRUE	NA	0.870955579359171	2		89	148	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661972	29661972	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0003754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	116	220	0	ENST00000356175.3:c.5866A>T	p.Lys1956Ter	p.K1956*	ENST00000356175	NM_000267.3	1956	Aag/Tag	39/57	0.850793955992432	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.870955579359171	1		220	146	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577518	7577518	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519995	NA	P-0003763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	155	161	0	ENST00000269305.4:c.763A>T	p.Ile255Phe	p.I255F	ENST00000269305	NM_001126112.2	255	Atc/Ttc	7/11	0.22189190623996	5	FACETS	0.932	0.874	0.989			1	INDETERMINATE	5	TRUE	NA	0.405109385767688	5		161	264	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11292519	11292519	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	161	288	0	ENST00000361445.4:c.2488G>C	p.Asp830His	p.D830H	ENST00000361445	NM_004958.3	830	Gat/Cat	16/58	0.405109385767688	6	FACETS	0.804	0.737	0.873			1	CLONAL	2	TRUE	NA	0.405109385767688	6		288	895	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11308130	11308130	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758906272	NA	P-0003763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	94	193	0	ENST00000361445.4:c.862G>A	p.Glu288Lys	p.E288K	ENST00000361445	NM_004958.3	288	Gaa/Aaa	7/58	0.405109385767688	6	FACETS	1	0.974	1			1	CLONAL	1	TRUE	NA	0.405109385767688	6		193	635	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923816	39923816	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	98	343	0	ENST00000378444.4:c.3275T>C	p.Phe1092Ser	p.F1092S	ENST00000378444	NM_001123385.1	1092	tTt/tCt	7/15	0.410867468784549	3	FACETS	1	0.947	1	0.547	0.489	0.608	CLONAL	1	TRUE	1	0.405109385767688	3		343	532	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928807	49928861	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AACCCAGAGCCAGATGAACACTGACCCGCTGAGGTGAGCGGATGAACTGGAGCAG	AACCCAGAGCCAGATGAACACTGACCCGCTGAGGTGAGCGGATGAACTGGAGCAG	-	novel	NA	P-0003763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	69	337	0	ENST00000296474.3:c.3505_3534+25del		p.X1169_splice	ENST00000296474	NM_002447.2	1169		16/20	0.410867468784549	4	FACETS	0.985	0.86	1	0.328	0.286	0.373	CLONAL	1	TRUE	1	0.405109385767688	4		337	486	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955425	48955426	+	stop_gained	Nonsense_Mutation	DNP	TC	TC	AA	novel	NA	P-0003763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	24	200	0	ENST00000267163.4:c.1541_1542delinsAA	p.Phe514Ter	p.F514*	ENST00000267163	NM_000321.2	514	tTC/tAA	17/27	0.173951431876056	4	FACETS	0.435	0.34	0.544	0.217	0.17	0.272	INDETERMINATE	1	TRUE	2	0.405109385767688	4		200	383	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699544	117699544	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0003766-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	104	135	1	ENST00000369458.3:c.98-1G>T		p.X33_splice	ENST00000369458	NM_024626.3	33			1	2	FACETS	0.958	0.863	1	0.958	0.863	1	CLONAL	1	TRUE	1	0.481519902880737	2		136	451	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188196	10188196	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs869025637	NA	P-0003766-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	187	223	0	ENST00000256474.2:c.341-2A>G		p.X114_splice	ENST00000256474	NM_000551.3	114			0.476734754202457	1	FACETS	0.892	0.828	0.959	0.892	0.828	0.959	CLONAL	1	TRUE	0	0.481519902880737	1		223	661	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393233	393233	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003766-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	189	245	0	ENST00000380956.4:c.81G>A	p.Trp27Ter	p.W27*	ENST00000380956	NM_001195286.1	27	tgG/tgA	2/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.481519902880737	NA		245	833	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39704892	39704892	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs889429048	NA	P-0003766-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	115	198	0	ENST00000361337.2:c.237C>G	p.Asp79Glu	p.D79E	ENST00000361337	NM_003286.2	79	gaC/gaG	4/21	0.233007140425119	3	FACETS	1	0.945	1	0.533	0.482	0.587	INDETERMINATE	1	TRUE	1	0.481519902880737	3		198	556	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157749	106157749	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003766-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	164	198	0	ENST00000380013.4:c.2650del	p.Gln884LysfsTer37	p.Q884Kfs*37	ENST00000380013	NM_001127208.2	884	Caa/aa	3/11	0.476734754202457	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.481519902880737	1		198	499	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	45	129	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.605531527686538	2		129	145	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846177	151846177	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	109	308	0	ENST00000262189.6:c.12835C>T	p.Gln4279Ter	p.Q4279*	ENST00000262189	NM_170606.2	4279	Cag/Tag	52/59	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.605531527686538	2		308	348	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846233	151846233	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	77	220	0	ENST00000262189.6:c.12779C>G	p.Ser4260Cys	p.S4260C	ENST00000262189	NM_170606.2	4260	tCc/tGc	52/59	1	2	FACETS	0.949	0.844	1	0.949	0.844	1	CLONAL	1	TRUE	1	0.605531527686538	2		220	268	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100388	8100388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	197	515	0	ENST00000346208.3:c.362C>T	p.Ser121Phe	p.S121F	ENST00000346208		121	tCc/tTc	3/6	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.605531527686538	2		515	596	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115947	8115948	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0003772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	71	224	0	ENST00000346208.3:c.1293_1294del	p.Pro432ThrfsTer74	p.P432Tfs*74	ENST00000346208		431	ggACca/ggca	6/6	1	2	FACETS	0.754	0.664	0.85	0.754	0.664	0.85	SUBCLONAL	1	TRUE	1	0.605531527686538	2		224	311	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206661282	206661282	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	95	283	0	ENST00000367120.3:c.1648A>G	p.Met550Val	p.M550V	ENST00000367120	NM_014002.3	550	Atg/Gtg	16/22	0.274050140798304	3	FACETS	0.973	0.865	1	0.486	0.432	0.544	CLONAL	1	TRUE	1	0.25	3		283	879	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266059	41266307	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGT	AAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGT	-	novel	NA	P-0003775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	75	237	0	ENST00000349496.5:c.56_241+63del		p.X19_splice	ENST00000349496	NM_001904.3	19		3/15	1	2	FACETS	0.786	0.688	0.892	0.786	0.688	0.892	SUBCLONAL	1	TRUE	1	0.25	2		237	763	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0003789-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	213	520	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.406282795937891	4	FACETS	0.846	0.789	0.906	0.846	0.789	0.906	CLONAL	2	TRUE	2	0.496025638898129	4		520	759	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370841	55370841	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759612481	NA	P-0003789-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	103	196	0	ENST00000297316.4:c.143C>T	p.Ala48Val	p.A48V	ENST00000297316	NM_022454.3	48	gCg/gTg	1/2	0.406282795937891	4	FACETS	0.971	0.879	1	0.971	0.879	1	CLONAL	2	TRUE	2	0.496025638898129	4		196	320	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0003789-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	89	286	0	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	0.496025638898129	1	FACETS	0.967	0.869	1	0.967	0.869	1	CLONAL	1	TRUE	0	0.496025638898129	1		286	279	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952412	38952412	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003789-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	235	399	0	ENST00000357387.3:c.3013C>A	p.Pro1005Thr	p.P1005T	ENST00000357387	NM_152756.3	1005	Cca/Aca	30/38	0.496025638898129	3	FACETS	0.908	0.853	0.965	0.908	0.853	0.965	CLONAL	2	TRUE	1	0.496025638898129	3		399	651	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911483	114911483	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0003789-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	150	206	0	ENST00000543371.1:c.1002-1G>C		p.X334_splice	ENST00000543371	NM_001198531.1	334			0.413433597740849	3	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	1	0.496025638898129	3		206	377	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589527	69589527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003789-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	72	84	0	ENST00000168712.1:c.326C>T	p.Ala109Val	p.A109V	ENST00000168712	NM_002007.2	109	gCg/gTg	1/3	0.413433597740849	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.496025638898129	3		84	154	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578552	7578552	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003789-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	139	269	0	ENST00000269305.4:c.378C>A	p.Tyr126Ter	p.Y126*	ENST00000269305	NM_001126112.2	126	taC/taA	5/11	0.496025638898129	2	FACETS	0.944	0.875	1	0.944	0.875	1	CLONAL	2	TRUE	0	0.496025638898129	2		269	297	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0003791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	157	542	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.3	4	FACETS	0.758	0.694	0.825	0.758	0.694	0.825	SUBCLONAL	2	TRUE	2	0.29	4		542	921	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0003791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	215	267	1	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.3	3	FACETS	0.838	0.783	0.895	1	0.988	1	CLONAL	3	TRUE	1	0.29	3		268	675	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134885788	134885788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757743061	NA	P-0003791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	128	259	1	ENST00000398015.3:c.1699C>T	p.Arg567Trp	p.R567W	ENST00000398015	NM_004441.4	567	Cgg/Tgg	9/16	0.3	3	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.29	3		260	678	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215865	142215865	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	35	191	0	ENST00000350721.4:c.5728C>T	p.Leu1910Phe	p.L1910F	ENST00000350721	NM_001184.3	1910	Ctc/Ttc	33/47	0.3	4	FACETS	0.448	0.366	0.541	0.224	0.183	0.271	SUBCLONAL	1	TRUE	2	0.29	4		191	695	SUCCESS
APC	324	MSKCC	GRCh37	5	112174241	112174241	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1254176854	NA	P-0003791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	143	261	0	ENST00000257430.4:c.2950G>T	p.Glu984Ter	p.E984*	ENST00000257430	NM_000038.5	984	Gaa/Taa	16/16	0.3	3	FACETS	1	0.986	1	0.71	0.648	0.775	CLONAL	1	TRUE	1	0.29	3		261	795	SUCCESS
APC	324	MSKCC	GRCh37	5	112175282	112175282	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0003791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	71	264	0	ENST00000257430.4:c.3991A>T	p.Arg1331Ter	p.R1331*	ENST00000257430	NM_000038.5	1331	Aga/Tga	16/16	0.3	3	FACETS	0.842	0.734	0.958	0.421	0.367	0.479	CLONAL	1	TRUE	1	0.29	3		264	666	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796795	135796795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1322586198	NA	P-0003791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	75	292	0	ENST00000298552.3:c.692C>T	p.Pro231Leu	p.P231L	ENST00000298552	NM_001162426.1	231	cCg/cTg	8/23	0.280892387372047	3	FACETS	0.796	0.697	0.903	0.398	0.348	0.452	CLONAL	1	TRUE	1	0.29	3		292	744	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241024	133241024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	56	299	0	ENST00000320574.5:c.2493G>A	p.Met831Ile	p.M831I	ENST00000320574	NM_006231.2	831	atG/atA	22/49	0.180335716154647	2	FACETS	0.513	0.438	0.595	0.256	0.219	0.298	SUBCLONAL	1	TRUE	0	0.29	2		299	753	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794986	42794986	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	95	255	0	ENST00000575354.2:c.2066A>C	p.Lys689Thr	p.K689T	ENST00000575354	NM_015125.3	689	aAg/aCg	10/20	0.3	4	FACETS	1	0.929	1			1	CLONAL	1	TRUE	NA	0.29	4		255	799	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747062	40747062	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1195105599	NA	P-0003791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	63	270	0	ENST00000373198.4:c.3020A>G	p.Asn1007Ser	p.N1007S	ENST00000373198	NM_133170.3	1007	aAc/aGc	22/32	NA	2	FACETS	0.618	0.534	0.71			1	INDETERMINATE	1	TRUE	NA	0.29	2		270	703	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0003793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	113	187	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	0.671783230542704	1	FACETS	0.931	0.856	1	0.931	0.856	1	CLONAL	1	TRUE	0	0.671783230542704	1		187	240	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577586	7577586	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	370	304	0	ENST00000269305.4:c.695T>A	p.Ile232Asn	p.I232N	ENST00000269305	NM_001126112.2	232	aTc/aAc	7/11	0.654301273788412	2	FACETS	0.982	0.946	1	0.982	0.946	1	CLONAL	2	TRUE	0	0.671783230542704	2		304	561	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730859	40730859	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	959	245	0	ENST00000373198.4:c.3676C>T	p.Arg1226Ter	p.R1226*	ENST00000373198	NM_133170.3	1226	Cga/Tga	27/32	0.671783230542704	6	FACETS	0.947	0.926	0.968	0.947	0.926	0.968	CLONAL	5	TRUE	1	0.671783230542704	6		245	1413	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0003804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	219	396	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	1	2	FACETS	0.94	0.883	0.997	0.94	0.883	0.997	CLONAL	1	TRUE	1	0.917611771017109	2		396	508	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40500451	40500451	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	396	495	0	ENST00000264657.5:c.84G>C	p.Met28Ile	p.M28I	ENST00000264657	NM_139276.2	28	atG/atC	2/24	0.130517999001404	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.917611771017109	0		495	921	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828151	3828151	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	236	347	0	ENST00000262367.5:c.1974del	p.Tyr659ThrfsTer7	p.Y659Tfs*7	ENST00000262367	NM_004380.2	658	atC/at	10/31	1	2	FACETS	0.904	0.851	0.958	0.904	0.851	0.958	CLONAL	1	TRUE	1	0.917611771017109	2		347	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0003810-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	282	286	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.561868061706085	2	FACETS	0.976	0.931	1	0.976	0.931	1	CLONAL	2	TRUE	0	0.58111484857254	2		286	497	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56411684	56411684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1004957123	NA	P-0003810-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	82	538	0	ENST00000348428.3:c.1868C>T	p.Pro623Leu	p.P623L	ENST00000348428	NM_006785.3	623	cCg/cTg	15/17	0.561868061706085	2	FACETS	0.389	0.343	0.439	0.195	0.171	0.22	SUBCLONAL	1	TRUE	0	0.58111484857254	2		538	725	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0003813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	200	293	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	0.138832887318913	1	FACETS	1	0.984	1	1	0.984	1	INDETERMINATE	1	TRUE	0	0.483789085116794	1		293	534	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750720	128750720	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886556187	NA	P-0003813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	321	273	0	ENST00000377970.2:c.257C>T	p.Ser86Leu	p.S86L	ENST00000377970	NM_002467.4	86	tCg/tTg	2/3	0.237543395926257	6	FACETS	0.894	0.85	0.939			1	INDETERMINATE	4	TRUE	NA	0.483789085116794	6		273	730	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103487	77103487	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs996658283	NA	P-0003813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	62	297	1	ENST00000356341.3:c.79G>A	p.Gly27Ser	p.G27S	ENST00000356341	NM_002576.4	27	Ggc/Agc	2/15	1	2	FACETS	0.322	0.277	0.371	0.322	0.277	0.371	SUBCLONAL	1	TRUE	1	0.483789085116794	2		298	796	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244049	41244049	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	179	308	0	ENST00000357654.3:c.3499G>T	p.Glu1167Ter	p.E1167*	ENST00000357654	NM_007294.3	1167	Gaa/Taa	10/23	0.460571108527804	1	FACETS	0.817	0.755	0.88	0.817	0.755	0.88	CLONAL	1	TRUE	0	0.483789085116794	1		308	687	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544722	65544723	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0003828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	50	462	0	ENST00000358664.4:c.203_204del	p.Thr68ArgfsTer18	p.T68Rfs*18	ENST00000358664	NM_002382.4	68	aCA/a	4/5	0.283064421431484	5	FACETS	1	0.947	1	0.796	0.691	0.906	INDETERMINATE	2	FALSE	2	0.515461711646732	5		462	144	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521543	8521543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868728165	NA	P-0003831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	72	208	0	ENST00000356435.5:c.695G>A	p.Arg232His	p.R232H	ENST00000356435		232	cGc/cAc	9/35	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.538490678815817	NA		208	343	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352489	118352489	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	54	269	0	ENST00000534358.1:c.3694A>T	p.Ser1232Cys	p.S1232C	ENST00000534358	NM_005933.3	1232	Agt/Tgt	7/36	1	2	FACETS	0.396	0.339	0.46	0.396	0.339	0.46	SUBCLONAL	1	TRUE	1	0.538490678815817	2		269	506	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490328	29490328	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	115	308	0	ENST00000356175.3:c.413C>G	p.Ala138Gly	p.A138G	ENST00000356175	NM_000267.3	138	gCc/gGc	4/57	1	2	FACETS	0.761	0.688	0.838	0.761	0.688	0.838	SUBCLONAL	1	TRUE	1	0.538490678815817	2		308	561	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735446	40735446	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	63	388	0	ENST00000373198.4:c.3427G>T	p.Val1143Phe	p.V1143F	ENST00000373198	NM_133170.3	1143	Gtc/Ttc	25/32	1	2	FACETS	0.45	0.389	0.516	0.45	0.389	0.516	SUBCLONAL	1	TRUE	1	0.538490678815817	2		388	520	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0003846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	44	413	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	1	2	FACETS	0.595	0.498	0.703	0.595	0.498	0.703	SUBCLONAL	1	TRUE	1	0.24	2		413	616	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163696	32163696	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	26	253	1	ENST00000375023.3:c.5530C>G	p.Arg1844Gly	p.R1844G	ENST00000375023	NM_004557.3	1844	Cgg/Ggg	30/30	1	2	FACETS	0.72	0.571	0.89	0.72	0.571	0.89	SUBCLONAL	1	TRUE	1	0.24	2		254	301	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0003847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	37	221	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.667	0.553	0.794	0.667	0.553	0.794	SUBCLONAL	1	TRUE	1	0.413815564695485	2		221	268	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867274	68867274	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	83	296	0	ENST00000261769.5:c.2521del	p.Glu841LysfsTer5	p.E841Kfs*5	ENST00000261769	NM_004360.3	841	Gaa/aa	16/16	0.413815564695485	0	FACETS	0.746	0.665	0.832			1	SUBCLONAL	1	TRUE	0	0.413815564695485	0		296	315	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720849	89720849	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0003847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	118	161	0	ENST00000371953.3:c.1001del	p.Asn334ThrfsTer10	p.N334Tfs*10	ENST00000371953	NM_000314.4	334	Aac/ac	8/9	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	2	TRUE	NA	0.413815564695485	2		161	254	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984844	9984844	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	107	557	0	ENST00000330684.3:c.1121A>T	p.Lys374Met	p.K374M	ENST00000330684	NM_001134407.1	374	aAg/aTg	4/13	0.621427367687324	1	FACETS	0.746	0.681	0.812	0.746	0.681	0.812	SUBCLONAL	1	TRUE	0	0.712865363526576	1		557	259	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0003881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	206	274	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	1	2	FACETS	0.942	0.877	1	0.942	0.877	1	CLONAL	1	TRUE	1	0.603425259813229	2		274	725	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0003881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	122	275	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	0.86	0.783	0.941	0.86	0.783	0.941	CLONAL	1	TRUE	1	0.603425259813229	2		275	470	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610085	28610085	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	114	431	0	ENST00000241453.7:c.1405G>T	p.Asp469Tyr	p.D469Y	ENST00000241453	NM_004119.2	469	Gac/Tac	11/24	1	2	FACETS	0.445	0.4	0.492	0.445	0.4	0.492	SUBCLONAL	1	TRUE	1	0.603425259813229	2		431	850	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340254	116340256	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0003881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	263	330	0	ENST00000397752.3:c.1120_1122del	p.Phe374del	p.F374del	ENST00000397752	NM_000245.2	372	gaCTTc/gac	2/21	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.603425259813229	2		330	864	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41276089	41276094	+	inframe_deletion	In_Frame_Del	DEL	CAACGC	CAACGC	-	novel	NA	P-0003881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	100	402	0	ENST00000357654.3:c.20_25del	p.Arg7_Glu9delinsGln	p.R7_E9delinsQ	ENST00000357654	NM_007294.3	7	cGCGTTGaa/caa	2/23	0.198114849147663	0	FACETS	0.203	0.181	0.226			1	INDETERMINATE	1	TRUE	0	0.603425259813229	0		402	647	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777972	27777972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	53	583	0	ENST00000369163.2:c.121C>T	p.Arg41Cys	p.R41C	ENST00000369163	NM_003536.2	41	Cgc/Tgc	1/1	0.269174458985218	6	FACETS	0.84	0.715	0.978	0.28	0.238	0.326	CLONAL	1	TRUE	3	0.269174458985218	6		583	721	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0003882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	38	531	1	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.269174458985218	3	FACETS	0.508	0.419	0.609	0.169	0.139	0.203	SUBCLONAL	1	TRUE	0	0.269174458985218	3		532	630	SUCCESS
MET	4233	MSKCC	GRCh37	7	116409781	116409781	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	61	334	0	ENST00000397752.3:c.2666C>T	p.Ser889Phe	p.S889F	ENST00000397752	NM_000245.2	889	tCt/tTt	12/21	0.269174458985218	3	FACETS	1	0.883	1	0.512	0.442	0.588	CLONAL	1	TRUE	1	0.269174458985218	3		334	502	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372319	55372319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	33	227	0	ENST00000297316.4:c.1009C>T	p.Pro337Ser	p.P337S	ENST00000297316	NM_022454.3	337	Ccg/Tcg	2/2	0.269174458985218	3	FACETS	0.809	0.666	0.965	0.809	0.666	0.965	CLONAL	2	TRUE	1	0.269174458985218	3		227	172	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442528	49442528	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	27	337	0	ENST00000301067.7:c.4045A>C	p.Ser1349Arg	p.S1349R	ENST00000301067	NM_003482.3	1349	Agt/Cgt	13/54	0.269174458985218	6	FACETS	0.638	0.506	0.788	0.159	0.126	0.197	SUBCLONAL	1	TRUE	2	0.269174458985218	6		337	484	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061360	38061360	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	98	358	0	ENST00000250448.2:c.629A>G	p.Asn210Ser	p.N210S	ENST00000250448	NM_004496.3	210	aAc/aGc	2/2	0.269174458985218	6	FACETS	1	0.905	1	1	0.905	1	CLONAL	3	TRUE	3	0.269174458985218	6		358	371	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729083	66729083	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	90	397	0	ENST00000307102.5:c.292-1G>A		p.X98_splice	ENST00000307102	NM_002755.3	98			0.245697342158897	5	FACETS	1	0.961	1	0.778	0.695	0.866	CLONAL	2	TRUE	2	0.269174458985218	5		397	402	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584339	39584339	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	35	202	0	ENST00000262039.4:c.1004A>C	p.Lys335Thr	p.K335T	ENST00000262039	NM_002647.2	335	aAa/aCa	10/25	0.269174458985218	3	FACETS	0.883	0.726	1	0.442	0.363	0.53	CLONAL	1	TRUE	1	0.269174458985218	3		202	334	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741925	162741925	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	91	268	0	ENST00000367921.3:c.1616C>A	p.Ser539Ter	p.S539*	ENST00000367921	NM_006182.2	539	tCa/tAa	13/18	0.257196347196725	4	FACETS	1	0.922	1	1	0.922	1	CLONAL	2	TRUE	2	0.257196347196725	4		268	428	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439268	52439268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	41	147	0	ENST00000460680.1:c.974C>T	p.Ser325Phe	p.S325F	ENST00000460680	NM_004656.3	325	tCc/tTc	11/17	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.257196347196725	2		147	240	SUCCESS
APC	324	MSKCC	GRCh37	5	112175222	112175222	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	39	180	0	ENST00000257430.4:c.3931A>T	p.Ile1311Phe	p.I1311F	ENST00000257430	NM_000038.5	1311	Att/Ttt	16/16	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.257196347196725	2		180	215	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250016	110250016	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	37	148	0	ENST00000374672.4:c.659C>T	p.Pro220Leu	p.P220L	ENST00000374672	NM_004235.4	220	cCg/cTg	3/5	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.257196347196725	2		148	204	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719941	18719941	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	103	321	0	ENST00000266497.5:c.3838C>G	p.Leu1280Val	p.L1280V	ENST00000266497		1280	Cta/Gta	27/31	0.179822089384854	4	FACETS	1	0.969	1			1	CLONAL	2	TRUE	NA	0.257196347196725	4		321	423	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420885	49420885	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	76	201	0	ENST00000301067.7:c.14864C>A	p.Ser4955Tyr	p.S4955Y	ENST00000301067	NM_003482.3	4955	tCc/tAc	48/54	0.257196347196725	4	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	2	0.257196347196725	4		201	350	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778345	3778345	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	19	114	0	ENST00000262367.5:c.6703C>T	p.Gln2235Ter	p.Q2235*	ENST00000262367	NM_004380.2	2235	Caa/Taa	31/31	1	2	FACETS	0.947	0.724	1	0.947	0.724	1	CLONAL	1	TRUE	1	0.257196347196725	2		114	156	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207166	1207166	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0003937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	99	242	0	ENST00000326873.7:c.254T>A	p.Leu85Ter	p.L85*	ENST00000326873	NM_000455.4	85	tTg/tAg	1/10	0.257196347196725	2	FACETS	0.904	0.818	0.992	1	0.98	1	CLONAL	3	TRUE	0	0.257196347196725	2		242	284	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602496	10602496	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750532889	NA	P-0003937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	101	266	0	ENST00000171111.5:c.1082C>T	p.Pro361Leu	p.P361L	ENST00000171111	NM_203500.1	361	cCg/cTg	3/6	0.257196347196725	2	FACETS	0.867	0.785	0.951	1	0.978	1	CLONAL	3	TRUE	0	0.257196347196725	2		266	302	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138500	11138500	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	108	356	0	ENST00000358026.2:c.3256G>T	p.Asp1086Tyr	p.D1086Y	ENST00000358026	NM_001128849.1	1086	Gat/Tat	24/36	0.257196347196725	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	0	0.257196347196725	2		356	396	SUCCESS
AR	367	MSKCC	GRCh37	X	66766499	66766499	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1409800023	NA	P-0003937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	73	259	0	ENST00000374690.3:c.1511A>G	p.Tyr504Cys	p.Y504C	ENST00000374690	NM_000044.3	504	tAc/tGc	1/8	0.257196347196725	0	FACETS	0.921	0.818	1			1	CLONAL	2	TRUE	NA	0.257196347196725	0		259	229	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115739	108115774	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAACCCAAGAAAAAGGTATAAAGGAAATGTTTACTG	AAACCCAAGAAAAAGGTATAAAGGAAATGTTTACTG	-	novel	NA	P-0003937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	38	146	0	ENST00000278616.4:c.887_901+21del		p.X296_splice	ENST00000278616	NM_000051.3	296		7/63	0.257196347196725	2	FACETS	1	0.954	1	0.742	0.62	0.876	CLONAL	1	TRUE	0	0.257196347196725	2		146	199	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814954	139814954	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	76	566	0	ENST00000247668.2:c.949del	p.Leu317Ter	p.L317*	ENST00000247668	NM_021138.3	316	gCc/gc	8/11	0.217977766965583	4	FACETS	1	0.9	1	0.343	0.301	0.39	CLONAL	1	TRUE	1	0.257196347196725	4		566	721	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0004000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	108	192	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.482411945164077	2	FACETS	0.929	0.851	1	0.929	0.851	1	CLONAL	2	TRUE	0	0.482411945164077	2		192	241	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191552	10191552	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	103	180	0	ENST00000256474.2:c.545G>T	p.Arg182Met	p.R182M	ENST00000256474	NM_000551.3	182	aGg/aTg	3/3	0.466346811897679	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.482411945164077	1		180	293	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602664	55602664	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs1057519713	NA	P-0004014-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	33	172	0	ENST00000288135.5:c.2485G>C	p.Ala829Pro	p.A829P	ENST00000288135	NM_000222.2	829	Gct/Cct	18/21	0.418492108300404	1	FACETS	0.799	0.66	0.952	0.799	0.66	0.952	CLONAL	1	TRUE	0	0.418492108300404	1		172	156	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0004034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	78	210	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	0.407763847588439	2	FACETS	0.915	0.82	1	0.915	0.82	1	CLONAL	2	TRUE	0	0.407763847588439	2		210	209	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198848	67198848	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	92	263	0	ENST00000312629.5:c.319G>C	p.Val107Leu	p.V107L	ENST00000312629	NM_003952.2	107	Gtg/Ctg	5/15	0.407763847588439	4	FACETS	0.923	0.828	1			1	CLONAL	2	TRUE	NA	0.407763847588439	4		263	344	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040942	42040942	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1276129280	NA	P-0004034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	65	540	0	ENST00000219905.7:c.5320C>G	p.Leu1774Val	p.L1774V	ENST00000219905	NM_001164273.1	1774	Ctt/Gtt	16/24	0.222896265397464	1	FACETS	0.47	0.408	0.537	0.47	0.408	0.537	INDETERMINATE	1	TRUE	0	0.407763847588439	1		540	540	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222492	53222492	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	47	125	0	ENST00000375401.3:c.4340G>T	p.Gly1447Val	p.G1447V	ENST00000375401	NM_004187.3	1447	gGg/gTg	26/26	1	1	FACETS	0.778	0.675	0.883	1	0.97	1	SUBCLONAL	2	TRUE	0	0.407763847588439	1		125	118	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0004052-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	26	221	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.291452681818424	4	FACETS	1	0.908	1	1	0.908	1	INDETERMINATE	2	FALSE	2	0.654138558558084	4		221	57	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405174	139405174	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004052-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	11	379	0	ENST00000277541.6:c.2671T>C	p.Tyr891His	p.Y891H	ENST00000277541	NM_017617.3	891	Tac/Cac	17/34	1	2	FACETS	0.801	0.574	1	0.801	0.574	1	CLONAL	1	FALSE	1	0.654138558558084	2		379	42	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118355614	118355614	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004052-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	17	436	0	ENST00000534358.1:c.4256G>C	p.Gly1419Ala	p.G1419A	ENST00000534358	NM_005933.3	1419	gGc/gCc	10/36	0.279551107192344	5	FACETS	0.953	0.738	1	0.636	0.492	0.792	INDETERMINATE	2	FALSE	2	0.654138558558084	5		436	54	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521477	46521477	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	150	438	0	ENST00000262741.5:c.931C>G	p.Gln311Glu	p.Q311E	ENST00000262741	NM_003629.3	311	Caa/Gaa	7/10	0.520728540848162	2	FACETS	0.856	0.784	0.931	0.428	0.392	0.466	CLONAL	1	TRUE	0	0.520728540848162	2		438	673	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248055	59248055	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	111	171	0	ENST00000371222.2:c.688C>T	p.Gln230Ter	p.Q230*	ENST00000371222	NM_002228.3	230	Cag/Tag	1/1	0.520728540848162	2	FACETS	0.867	0.795	0.939	0.867	0.795	0.939	CLONAL	2	TRUE	0	0.520728540848162	2		171	246	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455225	29455225	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs61754865	NA	P-0004057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	98	313	0	ENST00000389048.3:c.2577G>C	p.Glu859Asp	p.E859D	ENST00000389048	NM_004304.4	859	gaG/gaC	15/29	0.520728540848162	3	FACETS	0.801	0.716	0.891	0.401	0.358	0.446	CLONAL	1	TRUE	1	0.520728540848162	3		313	592	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020875	26020875	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	447	624	0	ENST00000357647.3:c.158G>C	p.Arg53Pro	p.R53P	ENST00000357647	NM_003529.2	53	cGc/cCc	1/1	0.520728540848162	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.520728540848162	3		624	1044	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117861203	117861203	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1926	180	367	0	ENST00000297338.2:c.1686G>C	p.Gln562His	p.Q562H	ENST00000297338	NM_006265.2	562	caG/caC	13/14	0.520728540848162	9	FACETS	0.927	0.85	1	0.132	0.121	0.144	CLONAL	1	TRUE	2	0.520728540848162	9		367	2106	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292986	91292986	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	104	267	0	ENST00000355112.3:c.488C>A	p.Ser163Tyr	p.S163Y	ENST00000355112	NM_000057.2	163	tCt/tAt	3/22	0.520728540848162	3	FACETS	0.804	0.721	0.892	0.402	0.36	0.446	CLONAL	1	TRUE	1	0.520728540848162	3		267	626	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23640569	23640569	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555460219	NA	P-0004057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	161	338	0	ENST00000261584.4:c.2542G>C	p.Asp848His	p.D848H	ENST00000261584	NM_024675.3	848	Gat/Cat	6/13	0.465932083674192	4	FACETS	1	0.938	1			1	CLONAL	1	TRUE	NA	0.520728540848162	4		338	916	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519999	NA	P-0004057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	177	204	0	ENST00000269305.4:c.716A>G	p.Asn239Ser	p.N239S	ENST00000269305	NM_001126112.2	239	aAc/aGc	7/11	0.520728540848162	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.520728540848162	2		204	324	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297706	15297706	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	243	359	0	ENST00000263388.2:c.1934G>T	p.Cys645Phe	p.C645F	ENST00000263388	NM_000435.2	645	tGc/tTc	12/33	0.468345493826954	4	FACETS	0.931	0.873	0.99	0.931	0.873	0.99	CLONAL	2	TRUE	2	0.520728540848162	4		359	762	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164342	47164342	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0004069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	33	311	0	ENST00000409792.3:c.1784C>G	p.Ser595Ter	p.S595*	ENST00000409792	NM_014159.6	595	tCa/tGa	3/21	1	2	FACETS	0.458	0.372	0.556	0.458	0.372	0.556	SUBCLONAL	1	TRUE	1	0.244864376499618	2		311	588	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50358698	50358698	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0004069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	29	134	0	ENST00000331340.3:c.40+1G>T		p.X14_splice	ENST00000331340	NM_006060.4	14			1	2	FACETS	0.929	0.749	1	0.929	0.749	1	CLONAL	1	TRUE	1	0.244864376499618	2		134	255	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575420	64575420	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs150512958	NA	P-0004069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	79	316	0	ENST00000312049.6:c.597C>A	p.His199Gln	p.H199Q	ENST00000312049	NM_130799.2	199	caC/caA	3/10	0.244864376499618	1	FACETS	0.942	0.829	1	0.942	0.829	1	CLONAL	1	TRUE	0	0.244864376499618	1		316	601	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133308	30133308	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	73	427	1	ENST00000263025.4:c.190C>T	p.Arg64Cys	p.R64C	ENST00000263025	NM_002746.2	64	Cgc/Tgc	2/9	0.244864376499618	1	FACETS	0.718	0.627	0.816	0.718	0.627	0.816	SUBCLONAL	1	TRUE	0	0.244864376499618	1		428	729	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288690	33288690	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	36	209	0	ENST00000374542.5:c.862del	p.Asp288MetfsTer6	p.D288Mfs*6	ENST00000374542	NM_001141970.1	288	Gat/at	3/8	1	2	FACETS	0.833	0.686	0.997	0.833	0.686	0.997	CLONAL	1	TRUE	1	0.244864376499618	2		209	353	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754349	57754349	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	51	212	0	ENST00000274289.3:c.502del	p.Ala168LeufsTer4	p.A168Lfs*4	ENST00000274289	NM_006622.3	168	Gct/ct	4/14	0.141714301846794	3	FACETS	0.891	0.757	1	0.445	0.378	0.519	INDETERMINATE	1	TRUE	1	0.244864376499618	3		212	525	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0004070-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	379	181	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.696344510192127	3	FACETS	0.994	0.964	1			1	CLONAL	3	TRUE	NA	0.696344510192127	3		181	492	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199469669	NA	P-0004070-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	220	402	0	ENST00000374080.3:c.130G>T	p.Gly44Cys	p.G44C	ENST00000374080		44	Ggt/Tgt	2/45	0.486662480057849	1	FACETS	0.806	0.757	0.855	0.806	0.757	0.855	CLONAL	1	TRUE	0	0.696344510192127	1		402	511	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818332	170818332	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1288532134	NA	P-0004070-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	149	306	0	ENST00000296930.5:c.162G>C	p.Lys54Asn	p.K54N	ENST00000296930	NM_002520.6	54	aaG/aaC	3/11	0.633986767084583	4	FACETS	0.89	0.813	0.969	0.445	0.406	0.485	CLONAL	1	TRUE	2	0.696344510192127	4		306	816	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0004075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	98	415	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	0.14	2		415	1119	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0004075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	48	269	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.778	0.656	0.914	0.778	0.656	0.914	CLONAL	1	TRUE	1	0.14	2		269	881	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0004075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	15	112	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	1	2	FACETS	0.768	0.561	1	0.768	0.561	1	CLONAL	1	TRUE	1	0.14	2		112	279	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429797	78429797	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	139	273	0	ENST00000370768.2:c.991C>T	p.Arg331Ter	p.R331*	ENST00000370768	NM_003902.3	331	Cga/Tga	12/20	0.474982486872016	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.474982486872016	1		273	401	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144147	11144147	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	110	192	0	ENST00000358026.2:c.3728G>T	p.Arg1243Leu	p.R1243L	ENST00000358026	NM_001128849.1	1243	cGg/cTg	26/36	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.474982486872016	2		192	422	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133238255	133238275	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CATTGGTGAAGCCTTCCTGAG	CATTGGTGAAGCCTTCCTGAG	-	novel	NA	P-0004084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	33	196	0	ENST00000320574.5:c.2707-5_2722del		p.X903_splice	ENST00000320574	NM_006231.2	903		24/49	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		196	327	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570263	87570263	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	36	288	0	ENST00000277120.3:c.2003A>T	p.Gln668Leu	p.Q668L	ENST00000277120		668	cAg/cTg	17/19	0.244210316532983	3	FACETS	0.618	0.507	0.741	0.309	0.253	0.371	SUBCLONAL	1	TRUE	1	0.287387084162417	3		288	464	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645690	12645690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs869025501	NA	P-0004121-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	102	243	0	ENST00000251849.4:c.779C>T	p.Thr260Ile	p.T260I	ENST00000251849	NM_002880.3	260	aCa/aTa	7/17	0.244979628631873	3	FACETS	0.984	0.89	1	0.656	0.593	0.721	CLONAL	2	TRUE	0	0.37139827871861	3		243	331	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979498	55979498	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0004121-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	230	392	0	ENST00000263923.4:c.949A>T	p.Lys317Ter	p.K317*	ENST00000263923	NM_002253.2	317	Aag/Tag	7/30	0.3521726855988	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.37139827871861	2		392	578	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279443	1279443	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004121-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	92	357	0	ENST00000310581.5:c.2093G>A	p.Arg698Gln	p.R698Q	ENST00000310581	NM_198253.2	698	cGg/cAg	5/16	0.300734305322933	4	FACETS	0.944	0.846	1	0.944	0.846	1	CLONAL	2	TRUE	2	0.37139827871861	4		357	360	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047881	180047881	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004121-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	91	250	0	ENST00000261937.6:c.2294T>C	p.Val765Ala	p.V765A	ENST00000261937	NM_182925.4	765	gTg/gCg	15/30	0.309737024662419	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	2	TRUE	0	0.37139827871861	2		250	239	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041210	29041210	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004121-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	77	426	0	ENST00000282397.4:c.218G>A	p.Arg73Lys	p.R73K	ENST00000282397	NM_002019.4	73	aGg/aAg	3/30	0.244979628631873	3	FACETS	0.661	0.58	0.748	0.22	0.193	0.25	SUBCLONAL	1	TRUE	0	0.37139827871861	3		426	744	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647274	2647274	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004121-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	19	250	0	ENST00000342085.4:c.1552A>T	p.Thr518Ser	p.T518S	ENST00000342085	NM_002613.4	518	Acg/Tcg	13/14	0.3521726855988	2	FACETS	0.27	0.204	0.347	0.135	0.102	0.174	SUBCLONAL	1	TRUE	0	0.37139827871861	2		250	379	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778078	3778078	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004121-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	22	323	1	ENST00000262367.5:c.6970C>A	p.Gln2324Lys	p.Q2324K	ENST00000262367	NM_004380.2	2324	Cag/Aag	31/31	0.3521726855988	2	FACETS	0.305	0.235	0.385	0.152	0.117	0.193	SUBCLONAL	1	TRUE	0	0.37139827871861	2		324	389	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220694	1220694	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004121-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	192	399	0	ENST00000326873.7:c.712A>T	p.Ile238Phe	p.I238F	ENST00000326873	NM_000455.4	238	Atc/Ttc	5/10	0.37139827871861	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.37139827871861	2		399	437	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40742220	40742220	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004121-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	162	478	0	ENST00000392038.2:c.904A>T	p.Ser302Cys	p.S302C	ENST00000392038	NM_001626.4	302	Agt/Tgt	10/14	0.37139827871861	3	FACETS	0.804	0.741	0.87	0.804	0.741	0.87	CLONAL	2	TRUE	1	0.37139827871861	3		478	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579849	7579849	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004121-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	153	380	0	ENST00000269305.4:c.64del	p.Leu22TyrfsTer22	p.L22Yfs*22	ENST00000269305	NM_001126112.2	22	Cta/ta	2/11	0.37139827871861	2	FACETS	0.947	0.875	1	0.947	0.875	1	CLONAL	2	TRUE	0	0.37139827871861	2		380	435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0004122-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	105	224	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	0.336193833566605	1	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	0	0.336193833566605	1		224	512	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199897	128199897	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004122-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	65	152	0	ENST00000341105.2:c.1408C>A	p.Pro470Thr	p.P470T	ENST00000341105	NM_032638.4	470	Ccc/Acc	6/6	0.336193833566605	1	FACETS	0.76	0.662	0.867	0.76	0.662	0.867	SUBCLONAL	1	TRUE	0	0.336193833566605	1		152	423	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197903	123197903	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0004122-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	47	287	0	ENST00000218089.9:c.2025+2T>C		p.X675_splice	ENST00000218089	NM_001042749.1	675			1	2	FACETS	0.464	0.391	0.545	0.464	0.391	0.545	SUBCLONAL	1	TRUE	1	0.336193833566605	2		287	602	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343360	118343360	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs782591851	NA	P-0004138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	73	328	0	ENST00000534358.1:c.1486A>T	p.Ile496Phe	p.I496F	ENST00000534358	NM_005933.3	496	Att/Ttt	3/36	0.205513658783729	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	0	0.205513658783729	1		328	473	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969465	44969470	+	inframe_deletion	In_Frame_Del	DEL	CTGATG	CTGATG	-	novel	NA	P-0004138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	94	288	0	ENST00000377967.4:c.4148_4153del	p.Leu1383_Met1384del	p.L1383_M1384del	ENST00000377967	NM_021140.2	1383	CTGATG/-	28/29	0.13021660284922	0	FACETS	0.972	0.871	1			1	CLONAL	2	FALSE	NA	0.205513658783729	0		288	374	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0004140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	222	375	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.4653803171903	5	FACETS	0.942	0.88	1			1	CLONAL	2	TRUE	NA	0.597719646179663	5		375	748	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164966	47164966	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	230	343	0	ENST00000409792.3:c.1160C>G	p.Thr387Ser	p.T387S	ENST00000409792	NM_014159.6	387	aCt/aGt	3/21	0.56334787719144	2	FACETS	0.955	0.906	1	0.955	0.906	1	CLONAL	2	TRUE	0	0.597719646179663	2		343	403	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503718	186503718	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	158	662	0	ENST00000323963.5:c.395G>A	p.Cys132Tyr	p.C132Y	ENST00000323963		132	tGt/tAt	5/11	0.277898597585381	3	FACETS	0.822	0.754	0.894			1	INDETERMINATE	1	TRUE	NA	0.597719646179663	3		662	835	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535309	66535309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	87	356	1	ENST00000273854.3:c.152G>A	p.Arg51Gln	p.R51Q	ENST00000273854	NM_004439.5	51	cGg/cAg	1/18	0.550338699116801	3	FACETS	0.827	0.736	0.925	0.276	0.245	0.309	CLONAL	1	TRUE	0	0.597719646179663	3		357	457	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63829535	63829535	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	141	254	0	ENST00000279873.7:c.1178G>A	p.Cys393Tyr	p.C393Y	ENST00000279873	NM_032199.2	393	tGt/tAt	8/10	0.476584978705061	4	FACETS	0.872	0.802	0.945	0.872	0.802	0.945	CLONAL	2	TRUE	2	0.597719646179663	4		254	432	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915778	112915778	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs923052172	NA	P-0004140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	104	369	0	ENST00000351677.2:c.1051C>T	p.Arg351Ter	p.R351*	ENST00000351677	NM_002834.3	351	Cga/Tga	9/16	1	2	FACETS	0.817	0.736	0.901	0.817	0.736	0.901	CLONAL	1	TRUE	1	0.597719646179663	2		369	426	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128482	30128482	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	354	650	0	ENST00000263025.4:c.900C>G	p.Asp300Glu	p.D300E	ENST00000263025	NM_002746.2	300	gaC/gaG	6/9	0.263800339221617	5	FACETS	1	0.987	1	0.744	0.706	0.782	INDETERMINATE	2	TRUE	2	0.597719646179663	5		650	1007	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39644786	39644786	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	259	365	0	ENST00000262039.4:c.2515G>A	p.Val839Met	p.V839M	ENST00000262039	NM_002647.2	839	Gtg/Atg	23/25	0.562304832080764	3	FACETS	0.936	0.894	0.976	0.936	0.894	0.976	CLONAL	3	TRUE	0	0.597719646179663	3		365	401	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210408	2210408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	78	256	0	ENST00000398665.3:c.1015G>A	p.Glu339Lys	p.E339K	ENST00000398665	NM_032482.2	339	Gag/Aag	13/28	0.587129549008075	2	FACETS	0.985	0.877	1	0.492	0.438	0.549	CLONAL	1	TRUE	0	0.597719646179663	2		256	265	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560898	9560898	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767455314	NA	P-0004140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	263	408	1	ENST00000353224.5:c.884C>T	p.Pro295Leu	p.P295L	ENST00000353224	NM_177990.2	295	cCg/cTg	4/10	0.457213284519385	4	FACETS	0.856	0.805	0.909	0.856	0.805	0.909	CLONAL	2	TRUE	2	0.597719646179663	4		409	821	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573651	48573677	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GATGGGAGGCTTCAGGTTAGTCTTATA	GATGGGAGGCTTCAGGTTAGTCTTATA	T	novel	NA	P-0004140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	144	190	0	ENST00000342988.3:c.235_249+12delinsT		p.X79_splice	ENST00000342988	NM_005359.5	79		2/12	0.562304832080764	3	FACETS	0.884	0.829	0.938	0.884	0.829	0.938	CLONAL	3	TRUE	0	0.597719646179663	3		190	236	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108828	2108828	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs878854122	NA	P-0004147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	493	513	1	ENST00000219476.3:c.929A>G	p.Tyr310Cys	p.Y310C	ENST00000219476	NM_000548.3	310	tAt/tGt	10/42	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		514	970	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253911	NA	P-0004165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	27	151	0	ENST00000269305.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000269305	NM_001126112.2	180	Gag/Aag	5/11	0.210025822363192	1	FACETS	0.716	0.574	0.876	0.716	0.574	0.876	SUBCLONAL	1	FALSE	0	0.322751098007005	1		151	196	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0004165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	35	221	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.684	0.562	0.82	0.684	0.562	0.82	SUBCLONAL	1	FALSE	1	0.322751098007005	2		221	317	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120844	115120863	+	frameshift_variant	Frame_Shift_Del	DEL	GAGCGCCGCCGCGCCGTTGG	GAGCGCCGCCGCGCCGTTGG	-	novel	NA	P-0004165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	50	141	0	ENST00000257566.3:c.143_162del	p.Pro48LeufsTer56	p.P48Lfs*56	ENST00000257566	NM_016569.3	48	cCCAACGGCGCGGCGGCGCTC/c	1/8	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	FALSE	1	0.322751098007005	2		141	280	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578541	7578541	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	100	431	0	ENST00000269305.4:c.389T>G	p.Leu130Arg	p.L130R	ENST00000269305	NM_001126112.2	130	cTc/cGc	5/11	0.322861495685724	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.322861495685724	1		431	501	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197379	94197415	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTTCAAAACCTCCACTATAGTCCACCTGAAAACAC	AGGTTCAAAACCTCCACTATAGTCCACCTGAAAACAC	-	novel	NA	P-0004175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	96	579	0	ENST00000323929.3:c.1099-10_1125del		p.X367_splice	ENST00000323929	NM_005591.3	367		11/20	1	2	FACETS	0.723	0.644	0.808	0.723	0.644	0.808	SUBCLONAL	1	TRUE	1	0.322861495685724	2		579	822	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259161	36259161	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	351	399	0	ENST00000300305.3:c.330G>T	p.Lys110Asn	p.K110N	ENST00000300305		110	aaG/aaT	3/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.910860388129774	2		399	729	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859560	151859578	+	frameshift_variant	Frame_Shift_Del	DEL	TTTGCATACGTCTGTTGAT	TTTGCATACGTCTGTTGAT	-	novel	NA	P-0004181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	328	426	0	ENST00000262189.6:c.11084_11102del	p.Asn3695IlefsTer4	p.N3695Ifs*4	ENST00000262189	NM_170606.2	3695	aATCAACAGACGTATGCAAAt/at	43/59	0.904176625978977	1	FACETS	0.995	0.968	1	0.995	0.968	1	CLONAL	1	TRUE	0	0.910860388129774	1		426	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578521	7578531	+	frameshift_variant	Frame_Shift_Del	DEL	GTTGGCAAAAC	GTTGGCAAAAC	-	novel	NA	P-0004181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	269	318	0	ENST00000269305.4:c.399_409del	p.Met133IlefsTer12	p.M133Ifs*12	ENST00000269305	NM_001126112.2	133	atGTTTTGCCAACtg/attg	5/11	0.910860388129774	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.910860388129774	1		318	310	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845699	68845699	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	454	481	0	ENST00000261769.5:c.945del	p.Asn315LysfsTer41	p.N315Kfs*41	ENST00000261769	NM_004360.3	315	aaT/aa	7/16	0.846503403480729	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.910860388129774	1		481	521	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255106	16255107	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0004181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	813	352	0	ENST00000375759.3:c.2372_2373del	p.Thr791ArgfsTer2	p.T791Rfs*2	ENST00000375759	NM_015001.2	791	ACa/a	11/15	0.910860388129774	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.910860388129774	2		352	882	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248633	59248634	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0004181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	430	509	0	ENST00000371222.2:c.109_110del	p.Ser37HisfsTer69	p.S37Hfs*69	ENST00000371222	NM_002228.3	37	AGc/c	1/1	1	2	FACETS	0.998	0.956	1	0.998	0.956	1	CLONAL	1	TRUE	1	0.910860388129774	2		509	946	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288749	33288749	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	27	326	0	ENST00000374542.5:c.803A>G	p.Asn268Ser	p.N268S	ENST00000374542	NM_001141970.1	268	aAc/aGc	3/8	0.433760606805084	5	FACETS	0.592	0.471	0.73	0.197	0.157	0.244	SUBCLONAL	1	TRUE	2	0.433760606805084	5		326	347	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778800	76778800	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	57	503	0	ENST00000373344.5:c.6779A>G	p.His2260Arg	p.H2260R	ENST00000373344	NM_000489.3	2260	cAc/cGc	31/35	1	1	FACETS	0.944	0.821	1	0.944	0.821	1	CLONAL	1	TRUE	0	0.433760606805084	1		503	218	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573786	64573786	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1114167541	NA	P-0004185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	36	313	0	ENST00000312049.6:c.967del	p.Tyr323ThrfsTer45	p.Y323Tfs*45	ENST00000312049	NM_130799.2	323	Tac/ac	7/10	0.168440637005215	2	FACETS	0.629	0.52	0.75	0.314	0.26	0.375	INDETERMINATE	1	TRUE	0	0.433760606805084	2		313	264	SUCCESS
APC	324	MSKCC	GRCh37	5	112174025	112174025	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004205-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	37	242	0	ENST00000257430.4:c.2734T>G	p.Leu912Val	p.L912V	ENST00000257430	NM_000038.5	912	Tta/Gta	16/16	0.259678593551532	3	FACETS	0.958	0.801	1	0.958	0.801	1	CLONAL	2	TRUE	1	0.259678593551532	3		242	168	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439253	52439253	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004205-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	51	136	0	ENST00000460680.1:c.989del	p.Asn330ThrfsTer5	p.N330Tfs*5	ENST00000460680	NM_004656.3	330	aAc/ac	11/17	0.255532783331252	2	FACETS	0.909	0.782	1	0.909	0.782	1	CLONAL	2	TRUE	0	0.259678593551532	2		136	216	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0004219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	38	278	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.17754550125767	4	FACETS	0.955	0.787	1	0.477	0.393	0.572	CLONAL	1	TRUE	2	0.12	4		278	743	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0004219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	28	445	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.3	3	FACETS	0.874	0.697	1			1	CLONAL	1	TRUE	NA	0.12	3		446	566	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636160	28636160	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	153	549	0	ENST00000241453.7:c.212G>C	p.Ser71Thr	p.S71T	ENST00000241453	NM_004119.2	71	aGc/aCc	3/24	1	2	FACETS	0.913	0.838	0.992	1	0.994	1	CLONAL	4	TRUE	1	0.12	2		549	698	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604787	48604787	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519741	NA	P-0004219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	14	420	1	ENST00000342988.3:c.1609G>T	p.Asp537Tyr	p.D537Y	ENST00000342988	NM_005359.5	537	Gac/Tac	12/12	0.17754550125767	3	FACETS	0.516	0.371	0.693	0.258	0.185	0.347	SUBCLONAL	1	TRUE	1	0.12	3		421	479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0004221-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	154	505	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.462640863272394	1	FACETS	0.977	0.901	1	0.977	0.901	1	CLONAL	1	TRUE	0	0.490666159812328	1		505	485	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0004237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	28	402	1	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.531280896966797	2		403	95	SUCCESS
RET	5979	MSKCC	GRCh37	10	43598035	43598035	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	21	274	0	ENST00000355710.3:c.583T>C	p.Phe195Leu	p.F195L	ENST00000355710	NM_020975.4	195	Ttc/Ctc	3/20	0.162338614238979	1	FACETS	0.4	0.311	0.502	0.4	0.311	0.502	INDETERMINATE	1	TRUE	0	0.531280896966797	1		274	145	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881392	37881392	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	16	216	0	ENST00000269571.5:c.2584A>G	p.Thr862Ala	p.T862A	ENST00000269571		862	Aca/Gca	21/27	0.479545175934211	2	FACETS	0.386	0.287	0.503	0.193	0.143	0.252	SUBCLONAL	1	TRUE	0	0.531280896966797	2		216	156	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492824	56492824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	37	250	0	ENST00000407977.2:c.115G>A	p.Glu39Lys	p.E39K	ENST00000407977		39	Gaa/Aaa	2/10	0.531280896966797	5	FACETS	1	0.847	1			1	CLONAL	1	TRUE	NA	0.531280896966797	5		250	245	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715979	52715979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786205227	NA	P-0004237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	97	367	1	ENST00000322088.6:c.544C>T	p.Arg182Trp	p.R182W	ENST00000322088	NM_014225.5	182	Cgg/Tgg	5/15	0.227416418789356	6	FACETS	1	0.955	1	0.812	0.738	0.887	INDETERMINATE	3	TRUE	2	0.531280896966797	6		368	232	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004248-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	264	330	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.484995714517839	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.484995714517839	3		332	562	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023217	27023227	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCTAGGCCC	GCCCTAGGCCC	-	novel	NA	P-0004248-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	201	232	0	ENST00000324856.7:c.328_338del	p.Arg110GlufsTer3	p.R110Efs*3	ENST00000324856	NM_006015.4	108	gGCCCTAGGCCC/g	1/20	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.484995714517839	2		232	554	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458423	120458423	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004248-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	54	233	1	ENST00000256646.2:c.6922C>G	p.Gln2308Glu	p.Q2308E	ENST00000256646	NM_024408.3	2308	Cag/Gag	34/34	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.484995714517839	2		234	215	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266945	41266945	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004248-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	103	619	0	ENST00000349496.5:c.616A>T	p.Asn206Tyr	p.N206Y	ENST00000349496	NM_001904.3	206	Aat/Tat	5/15	1	2	FACETS	0.838	0.753	0.927	0.838	0.753	0.927	CLONAL	1	TRUE	1	0.484995714517839	2		619	507	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991455	72991455	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1316526787	NA	P-0004248-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	323	835	0	ENST00000268489.5:c.2590T>C	p.Tyr864His	p.Y864H	ENST00000268489	NM_006885.3	864	Tac/Cac	2/10	0.188479279362806	2	FACETS	0.88	0.836	0.924	0.88	0.836	0.924	INDETERMINATE	2	TRUE	0	0.484995714517839	2		835	757	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748476	40748476	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004248-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	305	595	0	ENST00000392038.2:c.406A>G	p.Met136Val	p.M136V	ENST00000392038	NM_001626.4	136	Atg/Gtg	5/14	1	2	FACETS	0.788	0.746	0.831	1	0.995	1	SUBCLONAL	2	TRUE	1	0.484995714517839	2		595	798	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101127	27101131	+	frameshift_variant	Frame_Shift_Del	DEL	CCAAT	CCAAT	-	novel	NA	P-0004248-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	161	631	1	ENST00000324856.7:c.4409_4413del	p.Thr1470SerfsTer19	p.T1470Sfs*19	ENST00000324856	NM_006015.4	1470	aCCAAT/a	18/20	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.484995714517839	2		632	662	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865199	57865199	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	100	515	0	ENST00000228682.2:c.2676G>T	p.Gln892His	p.Q892H	ENST00000228682	NM_005269.2	892	caG/caT	12/12	0.588860614200277	2	FACETS	0.864	0.778	0.954	0.432	0.389	0.477	CLONAL	1	TRUE	0	0.613915537210454	2		515	377	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979590	7979613	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTGTCATAGGTGAGCTCCGACA	GGCTGTCATAGGTGAGCTCCGACA	CG	novel	NA	P-0004261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	67	277	0	ENST00000319144.4:c.1412_1435delinsCG	p.Leu471ProfsTer36	p.L471Pfs*36	ENST00000319144	NM_001139.2	471	cTGTCGGAGCTCACCTATGACAGCCtc/cCGtc	11/15	0.209486325772814	4	FACETS	1	0.911	1			1	INDETERMINATE	1	TRUE	NA	0.613915537210454	4		277	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579312	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0004261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	91	146	0	ENST00000269305.4:c.375_375+1delinsTT		p.X125_splice	ENST00000269305	NM_001126112.2	125		4/11	0.209486325772814	4	FACETS	0.867	0.79	0.943			1	INDETERMINATE	3	TRUE	NA	0.613915537210454	4		146	184	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	222	330	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.259707268693586	4	FACETS	1	0.982	1			1	CLONAL	3	TRUE	NA	0.321558309106497	4		332	544	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998688	100998688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	56	1501	0	ENST00000325455.5:c.1114G>A	p.Asp372Asn	p.D372N	ENST00000325455	NM_001202474.3	372	Gac/Aac	1/8	1	2	FACETS	0.626	0.537	0.725	0.626	0.537	0.725	SUBCLONAL	1	TRUE	1	0.321558309106497	2		1501	556	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10267145	10267145	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	75	907	0	ENST00000340748.4:c.1273G>A	p.Gly425Ser	p.G425S	ENST00000340748		425	Ggc/Agc	17/40	1	2	FACETS	0.96	0.843	1	0.96	0.843	1	CLONAL	1	TRUE	1	0.321558309106497	2		907	486	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55154980	55154980	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	165	934	0	ENST00000257290.5:c.2689C>A	p.Pro897Thr	p.P897T	ENST00000257290	NM_006206.4	897	Ccc/Acc	20/23	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.46	2		934	699	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248033	98248033	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	141	952	0	ENST00000331920.6:c.518A>T	p.Glu173Val	p.E173V	ENST00000331920	NM_000264.3	173	gAa/gTa	3/24	1	2	FACETS	0.886	0.809	0.966	0.886	0.809	0.966	CLONAL	1	TRUE	1	0.46	2		952	692	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610306	10610306	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	33	888	0	ENST00000171111.5:c.404G>T	p.Arg135Leu	p.R135L	ENST00000171111	NM_203500.1	135	cGc/cTc	2/6	1	2	FACETS	0.231	0.187	0.28	0.231	0.187	0.28	SUBCLONAL	1	TRUE	1	0.46	2		888	622	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937135	76937135	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	131	611	0	ENST00000373344.5:c.3613T>G	p.Ser1205Ala	p.S1205A	ENST00000373344	NM_000489.3	1205	Tct/Gct	9/35	1	1	FACETS	0.815	0.755	0.876	1	0.99	1	CLONAL	2	TRUE	0	0.46	1		611	269	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610387	10610387	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	136	813	0	ENST00000171111.5:c.323del	p.Lys108ArgfsTer49	p.K108Rfs*49	ENST00000171111	NM_203500.1	108	aAg/ag	2/6	1	2	FACETS	0.984	0.898	1	0.984	0.898	1	CLONAL	1	TRUE	1	0.46	2		813	601	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913237	NA	P-0004302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	109	455	0	ENST00000369535.4:c.35G>T	p.Gly12Val	p.G12V	ENST00000369535	NM_002524.4	12	gGt/gTt	2/7	0.3	3	FACETS	1	0.909	1	1	0.909	1	CLONAL	2	FALSE	1	0.3	3		455	416	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148880	119148880	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs267606704	NA	P-0004302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	15	310	0	ENST00000264033.4:c.1100A>C	p.Gln367Pro	p.Q367P	ENST00000264033	NM_005188.3	367	cAa/cCa	8/16	0.1535959004327	3	FACETS	0.612	0.449	0.806	0.306	0.224	0.403	INDETERMINATE	1	FALSE	1	0.3	3		310	188	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593656	55593658	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0004302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	8	395	0	ENST00000288135.5:c.1724_1726del	p.Gln575del	p.Q575del	ENST00000288135	NM_000222.2	574	acACAa/aca	11/21	0.3	1	FACETS	0.229	0.147	0.335	0.229	0.147	0.335	SUBCLONAL	1	FALSE	0	0.3	1		395	198	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417944	32417944	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1172760612	NA	P-0004311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	199	301	2	ENST00000332351.3:c.1108C>T	p.Arg370Cys	p.R370C	ENST00000332351	NM_024426.4	370	Cgt/Tgt	7/10	1	2	FACETS	0.915	0.856	0.976	0.915	0.856	0.976	CLONAL	1	TRUE	1	0.864495094830579	2		303	503	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075154	16075154	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	120	317	0	ENST00000268712.3:c.398T>A	p.Leu133Gln	p.L133Q	ENST00000268712	NM_006311.3	133	cTg/cAg	4/46	1	2	FACETS	0.841	0.77	0.915	0.841	0.77	0.915	CLONAL	1	TRUE	1	0.864495094830579	2		317	330	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720843	89720843	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	33	193	0	ENST00000371953.3:c.996del	p.Ala333ProfsTer11	p.A333Pfs*11	ENST00000371953	NM_000314.4	332	Aaa/aa	8/9	1	2	FACETS	0.734	0.613	0.862	0.734	0.613	0.862	SUBCLONAL	1	TRUE	1	0.864495094830579	2		193	104	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711973	89711973	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	13	265	0	ENST00000371953.3:c.591del	p.Met198Ter	p.M198*	ENST00000371953	NM_000314.4	197	aaG/aa	6/9	1	2	FACETS	0.181	0.129	0.244	0.181	0.129	0.244	SUBCLONAL	1	TRUE	1	0.864495094830579	2		265	166	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552755	226552755	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	258	313	1	ENST00000366794.5:c.2606T>C	p.Phe869Ser	p.F869S	ENST00000366794	NM_001618.3	869	tTt/tCt	19/23	0.36870467395896	6	FACETS	0.892	0.847	0.937	1	0.99	1	INDETERMINATE	4	TRUE	3	0.734486677531269	6		314	486	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056184	26056184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201150687	NA	P-0004312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	95	318	0	ENST00000343677.2:c.473C>T	p.Ala158Val	p.A158V	ENST00000343677	NM_005319.3	158	gCg/gTg	1/1	0.734486677531269	3	FACETS	0.964	0.865	1			1	CLONAL	1	TRUE	NA	0.734486677531269	3		318	367	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200026	138200026	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780514490	NA	P-0004312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	14	152	0	ENST00000237289.4:c.1444G>A	p.Gly482Ser	p.G482S	ENST00000237289	NM_001270507.1	482	Ggc/Agc	7/9	0.637795760103246	4	FACETS	0.352	0.255	0.469	0.176	0.127	0.235	SUBCLONAL	1	TRUE	2	0.734486677531269	4		152	188	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578502	7578502	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555526241	NA	P-0004312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	177	236	1	ENST00000269305.4:c.428T>G	p.Val143Gly	p.V143G	ENST00000269305	NM_001126112.2	143	gTg/gGg	5/11	0.731043679197474	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.734486677531269	2		237	232	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075283	16075283	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	147	408	0	ENST00000268712.3:c.269A>G	p.Glu90Gly	p.E90G	ENST00000268712	NM_006311.3	90	gAa/gGa	4/46	0.731043679197474	2	FACETS	1	0.963	1	0.534	0.493	0.575	CLONAL	1	TRUE	0	0.734486677531269	2		408	375	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763458	41763458	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	111	399	0	ENST00000301178.4:c.2257G>C	p.Val753Leu	p.V753L	ENST00000301178	NM_021913.4	753	Gtg/Ctg	19/20	0.601307501221217	3	FACETS	1	0.975	1	0.604	0.549	0.661	CLONAL	1	TRUE	1	0.734486677531269	3		399	342	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359084	81359084	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747693036	NA	P-0004317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	30	272	0	ENST00000222390.5:c.877A>G	p.Met293Val	p.M293V	ENST00000222390	NM_000601.4	293	Atg/Gtg	8/18	0.166463707855487	0	FACETS	0.127	0.102	0.155			1	INDETERMINATE	1	TRUE	0	0.62243018845789	0		272	287	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114740	108114740	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0004317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	211	287	0	ENST00000278616.4:c.557T>A	p.Leu186Ter	p.L186*	ENST00000278616	NM_000051.3	186	tTa/tAa	6/63	0.627162768390476	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.62243018845789	1		287	392	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747850	41747850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	112	285	0	ENST00000226382.2:c.919G>A	p.Ala307Thr	p.A307T	ENST00000226382	NM_003924.3	307	Gcc/Acc	3/3	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.307251247625516	2		285	654	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528417	157528417	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1469600286	NA	P-0004326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	133	291	0	ENST00000346085.5:c.6142A>G	p.Ile2048Val	p.I2048V	ENST00000346085	NM_020732.3	2048	Att/Gtt	20/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.307251247625516	2		291	740	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487277	56487277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035001455	NA	P-0004326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	130	243	0	ENST00000267101.3:c.1423C>T	p.Arg475Trp	p.R475W	ENST00000267101	NM_001982.3	475	Cgg/Tgg	12/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.307251247625516	2		243	727	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842745	68842753	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ATACACTGT	ATACACTGT	-	novel	NA	P-0004326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	205	370	0	ENST00000261769.5:c.682_687+3del		p.X228_splice	ENST00000261769	NM_004360.3	228		5/16	0.299929800905583	2	FACETS	0.801	0.744	0.86	0.801	0.744	0.86	CLONAL	2	TRUE	0	0.307251247625516	2		370	833	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0004336-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	17	395	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.288	0.213	0.377	0.288	0.213	0.377	SUBCLONAL	1	TRUE	1	0.15	2		395	788	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432513	49432513	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004336-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	66	348	0	ENST00000301067.7:c.8626C>T	p.Gln2876Ter	p.Q2876*	ENST00000301067	NM_003482.3	2876	Cag/Tag	34/54	NA	2	FACETS	1	0.925	1			1	INDETERMINATE	1	TRUE	NA	0.15	2		348	799	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391076	89391076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764139832	NA	P-0004338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	162	463	0	ENST00000336596.2:c.1142G>A	p.Arg381His	p.R381H	ENST00000336596	NM_005233.5	381	cGc/cAc	5/17	1	2	FACETS	0.911	0.843	0.981	0.911	0.843	0.981	CLONAL	1	TRUE	1	0.734888526096554	2		463	484	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131111	55131111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5845	429	367	0	ENST00000257290.5:c.654G>A	p.Met218Ile	p.M218I	ENST00000257290	NM_006206.4	218	atG/atA	5/23	0.734888526096554	25	FACETS	0.879	0.831	0.929	0.073	0.069	0.078	CLONAL	2	TRUE	1	0.734888526096554	25		367	6274	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131142	55131142	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5810	644	394	0	ENST00000257290.5:c.685G>A	p.Glu229Lys	p.E229K	ENST00000257290	NM_006206.4	229	Gaa/Aaa	5/23	0.734888526096554	25	FACETS	0.856	0.818	0.894	0.107	0.102	0.112	CLONAL	3	TRUE	1	0.734888526096554	25		394	6454	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133814	55133814	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5933	642	466	1	ENST00000257290.5:c.1027C>T	p.Pro343Ser	p.P343S	ENST00000257290	NM_006206.4	343	Cca/Tca	7/23	0.734888526096554	25	FACETS	0.837	0.8	0.875	0.105	0.1	0.11	CLONAL	3	TRUE	1	0.734888526096554	25		467	6575	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651879	36651879	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0004338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	85	342	0	ENST00000244741.5:c.1A>G	p.Met1?	p.M1?	ENST00000244741	NM_000389.4	1	Atg/Gtg	2/3	0.127281703375578	3	FACETS	1	0.927	1	0.524	0.468	0.582	INDETERMINATE	1	TRUE	1	0.734888526096554	3		342	302	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658484	117658484	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	75	253	0	ENST00000368508.3:c.5099A>C	p.Tyr1700Ser	p.Y1700S	ENST00000368508	NM_002944.2	1700	tAc/tCc	31/43	NA	2	FACETS	0.804	0.714	0.898			1	INDETERMINATE	1	TRUE	NA	0.734888526096554	2		253	254	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690817	89690819	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs1554897864	NA	P-0004338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	40	129	0	ENST00000371953.3:c.226_228del	p.Tyr76del	p.Y76del	ENST00000371953	NM_000314.4	75	cATTat/cat	4/9	0.734888526096554	1	FACETS	0.725	0.623	0.829	0.725	0.623	0.829	SUBCLONAL	1	TRUE	0	0.734888526096554	1		129	95	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0004342-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	44	201	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.892	0.751	1	0.892	0.751	1	CLONAL	1	FALSE	1	0.3	2		201	329	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879092	151879092	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	59	251	0	ENST00000262189.6:c.5853T>G	p.Asp1951Glu	p.D1951E	ENST00000262189	NM_170606.2	1951	gaT/gaG	36/59	0.591902399270047	3	FACETS	0.827	0.717	0.944	0.413	0.358	0.472	CLONAL	1	TRUE	1	0.647058295428841	3		251	292	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115727	108115727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747727055	NA	P-0004355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	72	201	0	ENST00000278616.4:c.875C>T	p.Pro292Leu	p.P292L	ENST00000278616	NM_000051.3	292	cCg/cTg	7/63	0.614371378857733	1	FACETS	0.965	0.867	1	0.965	0.867	1	CLONAL	1	TRUE	0	0.647058295428841	1		201	156	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061204	38061229	+	protein_altering_variant	In_Frame_Del	DEL	CGGCGCAAGTAGCAGCCGTTCTCGAA	CGGCGCAAGTAGCAGCCGTTCTCGAA	TAGCGCTT	novel	NA	P-0004355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	87	193	0	ENST00000250448.2:c.760_785delinsAAGCGCTA	p.Phe254_Arg262delinsLysArgTyr	p.F254_R262delinsKRY	ENST00000250448	NM_004496.3	254	TTCGAGAACGGCTGCTACTTGCGCCGc/AAGCGCTAc	2/2	1	2	FACETS	0.764	0.695	0.833	1	0.984	1	SUBCLONAL	2	TRUE	1	0.647058295428841	2		193	176	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0004361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	69	520	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.994	0.864	1	0.994	0.864	1	CLONAL	1	TRUE	1	0.17	2		520	817	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0004361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	29	220	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	1	2	FACETS	0.571	0.457	0.702	0.571	0.457	0.702	SUBCLONAL	1	TRUE	1	0.17	2		220	597	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190670377	190670377	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0004361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	56	313	0	ENST00000441310.2:c.316-1G>T		p.X106_splice	ENST00000441310	NM_000534.4	106			1	2	FACETS	0.744	0.636	0.864	0.744	0.636	0.864	SUBCLONAL	1	TRUE	1	0.17	2		313	885	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003281	42003281	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0004361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1370	119	589	0	ENST00000219905.7:c.2818A>T	p.Lys940Ter	p.K940*	ENST00000219905	NM_001164273.1	940	Aag/Tag	8/24	0.291445960799263	1	FACETS	0.86	0.774	0.953	0.86	0.774	0.953	CLONAL	1	TRUE	0	0.17	1		589	1489	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679129	88679129	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0004361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	67	263	0	ENST00000360948.2:c.907+1G>T		p.X303_splice	ENST00000360948	NM_001012338.2	303			1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.17	2		263	670	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727529	88727529	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	47	145	0	ENST00000360948.2:c.250C>T	p.His84Tyr	p.H84Y	ENST00000360948	NM_001012338.2	84	Cac/Tac	3/19	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.17	2		145	537	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774132	56774132	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1188093917	NA	P-0004361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	49	282	0	ENST00000337432.4:c.483G>T	p.Glu161Asp	p.E161D	ENST00000337432	NM_058216.2	161	gaG/gaT	3/9	1	2	FACETS	0.61	0.515	0.716	0.61	0.515	0.716	SUBCLONAL	1	TRUE	1	0.17	2		282	945	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0004364-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	273	375	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.51355748941841	2	FACETS	0.968	0.919	1	0.968	0.919	1	CLONAL	2	TRUE	0	0.51355748941841	2		375	549	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105811	27105811	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0004364-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	159	593	0	ENST00000324856.7:c.5422A>T	p.Lys1808Ter	p.K1808*	ENST00000324856	NM_006015.4	1808	Aag/Tag	20/20	0.51355748941841	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.51355748941841	1		593	433	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276722	15276722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446718967	NA	P-0004364-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	148	666	0	ENST00000263388.2:c.5543G>A	p.Arg1848His	p.R1848H	ENST00000263388	NM_000435.2	1848	cGt/cAt	30/33	0.51355748941841	3	FACETS	1	0.929	1	0.509	0.465	0.554	CLONAL	1	TRUE	1	0.51355748941841	3		666	712	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462165	120462165	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	49	341	1	ENST00000256646.2:c.5551G>A	p.Ala1851Thr	p.A1851T	ENST00000256646	NM_024408.3	1851	Gca/Aca	31/34	1	2	FACETS	0.273	0.23	0.321	0.273	0.23	0.321	SUBCLONAL	1	TRUE	1	0.416215336642284	2		342	862	SUCCESS
ALK	238	MSKCC	GRCh37	2	29448375	29448375	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	235	563	0	ENST00000389048.3:c.3124T>G	p.Ser1042Ala	p.S1042A	ENST00000389048	NM_004304.4	1042	Tct/Gct	19/29	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.416215336642284	2		563	966	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294501	1294501	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	46	171	0	ENST00000310581.5:c.500C>A	p.Ala167Asp	p.A167D	ENST00000310581	NM_198253.2	167	gCc/gAc	2/16	0.260305799653706	2	FACETS	0.773	0.655	0.901	0.386	0.327	0.451	CLONAL	1	TRUE	0	0.416215336642284	2		171	286	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760663	133760663	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	184	443	0	ENST00000318560.5:c.2986C>T	p.Gln996Ter	p.Q996*	ENST00000318560	NM_005157.4	996	Cag/Tag	11/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.416215336642284	2		443	782	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117713	108117713	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	78	384	0	ENST00000278616.4:c.924G>A	p.Trp308Ter	p.W308*	ENST00000278616	NM_000051.3	308	tgG/tgA	8/63	1	2	FACETS	0.505	0.443	0.572	0.505	0.443	0.572	SUBCLONAL	1	TRUE	1	0.416215336642284	2		384	742	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173578	108173578	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0004385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	106	203	0	ENST00000278616.4:c.5320-2A>G		p.X1774_splice	ENST00000278616	NM_000051.3	1774			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.416215336642284	2		203	417	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322774	30322774	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	82	292	0	ENST00000322652.5:c.1787C>T	p.Thr596Ile	p.T596I	ENST00000322652	NM_015355.2	596	aCc/aTc	14/16	0.110647337104615	4	FACETS	0.726	0.639	0.819	0.363	0.319	0.41	INDETERMINATE	1	TRUE	2	0.416215336642284	4		292	769	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058361	42058362	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0004385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	121	690	0	ENST00000219905.7:c.8081_8082delinsTT	p.Ser2694Phe	p.S2694F	ENST00000219905	NM_001164273.1	2694	tCC/tTT	24/24	0.416215336642284	1	FACETS	0.532	0.48	0.586	0.532	0.48	0.586	SUBCLONAL	1	TRUE	0	0.416215336642284	1		690	866	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0004386-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	531	221	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.336378676698438	4	FACETS	1	0.988	1			1	CLONAL	4	TRUE	NA	0.516785417027806	4		221	756	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425853	49425853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772665565	NA	P-0004386-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	145	468	0	ENST00000301067.7:c.12635G>A	p.Arg4212Gln	p.R4212Q	ENST00000301067	NM_003482.3	4212	cGg/cAg	39/54	0.263595421123102	5	FACETS	1	0.985	1	0.462	0.422	0.504	INDETERMINATE	1	TRUE	2	0.516785417027806	5		468	719	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796466	42796466	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004386-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	217	413	1	ENST00000575354.2:c.3023A>G	p.Gln1008Arg	p.Q1008R	ENST00000575354	NM_015125.3	1008	cAg/cGg	13/20	0.52087763635246	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.516785417027806	2		414	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577533	7577547	+	inframe_deletion	In_Frame_Del	DEL	GCCTCCGGTTCATGC	GCCTCCGGTTCATGC	-	novel	NA	P-0004386-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	131	413	0	ENST00000269305.4:c.734_748del	p.Gly245_Pro250delinsAla	p.G245_P250delinsA	ENST00000269305	NM_001126112.2	245	gGCATGAACCGGAGGCcc/gcc	7/11	0.52087763635246	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.516785417027806	1		413	337	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256949	16256949	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004389-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	32	371	0	ENST00000375759.3:c.4214C>G	p.Ser1405Cys	p.S1405C	ENST00000375759	NM_015001.2	1405	tCt/tGt	11/15	1	2	FACETS	0.75	0.608	0.912	0.75	0.608	0.912	CLONAL	1	TRUE	1	0.16	2		371	533	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0004395-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	178	282	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.513992767772992	4	FACETS	0.949	0.885	1			1	CLONAL	2	TRUE	NA	0.790615862884643	4		283	425	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045025	47045025	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004395-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	264	367	1	ENST00000377604.3:c.2351A>T	p.His784Leu	p.H784L	ENST00000377604	NM_001204468.1	784	cAc/cTc	20/24	0.787122926672775	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.790615862884643	2		368	317	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12629089	12629089	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0004395-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	89	237	0	ENST00000251849.4:c.1417+1G>A		p.X473_splice	ENST00000251849	NM_002880.3	473			0.531557710915864	3	FACETS	0.875	0.782	0.972			1	CLONAL	1	TRUE	NA	0.790615862884643	3		237	359	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164973	47164973	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004395-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	89	278	0	ENST00000409792.3:c.1153A>G	p.Arg385Gly	p.R385G	ENST00000409792	NM_014159.6	385	Aga/Gga	3/21	0.790615862884643	3	FACETS	0.768	0.685	0.856	0.384	0.342	0.428	SUBCLONAL	1	TRUE	1	0.790615862884643	3		278	409	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739058	145739058	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004395-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	80	212	0	ENST00000428558.2:c.2097C>A	p.Asn699Lys	p.N699K	ENST00000428558	NM_004260.3	699	aaC/aaA	13/22	0.790615862884643	7	FACETS	1	0.894	1			1	CLONAL	1	TRUE	NA	0.790615862884643	7		212	593	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992693	72992693	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004395-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	165	619	0	ENST00000268489.5:c.1352G>T	p.Cys451Phe	p.C451F	ENST00000268489	NM_006885.3	451	tGc/tTc	2/10	0.483192239675829	3	FACETS	0.942	0.869	1			1	CLONAL	1	TRUE	NA	0.790615862884643	3		619	618	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221334	1221334	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004395-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	146	306	0	ENST00000326873.7:c.857T>G	p.Leu286Arg	p.L286R	ENST00000326873	NM_000455.4	286	cTg/cGg	6/10	0.790615862884643	2	FACETS	0.91	0.861	0.956	0.91	0.861	0.956	CLONAL	2	TRUE	0	0.790615862884643	2		306	203	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950111	44950111	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0004395-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	397	456	0	ENST00000377967.4:c.3878+2T>G		p.X1293_splice	ENST00000377967	NM_021140.2	1293			0.787122926672775	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.790615862884643	2		456	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0004396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	288	448	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.202736559008318	4	FACETS	1	0.983	1	1	0.996	1	CLONAL	7	FALSE	0	0.202736559008318	4		448	462	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0004396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	136	366	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.161255253461533	4	FACETS	1	0.961	1	1	0.989	1	CLONAL	3	FALSE	2	0.202736559008318	4		366	495	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912118	76912119	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0004396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	258	456	0	ENST00000373344.5:c.4145_4146del	p.Ser1382Ter	p.S1382*	ENST00000373344	NM_000489.3	1382	tCT/t	13/35	1	1	FACETS	1	0.986	1	1	0.996	1	CLONAL	4	FALSE	0	0.202736559008318	1		456	513	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0004408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	81	503	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.527862188627975	1	FACETS	0.682	0.606	0.762	0.682	0.606	0.762	SUBCLONAL	1	TRUE	0	0.527862188627975	1		503	331	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589581	67589583	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	novel	NA	P-0004408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	167	329	0	ENST00000274335.5:c.1345_1347del	p.Leu449del	p.L449del	ENST00000274335		448	aaATTa/aaa	10/15	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.527862188627975	2		329	568	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270180	66270180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763063348	NA	P-0004408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	106	400	0	ENST00000273854.3:c.1702G>A	p.Asp568Asn	p.D568N	ENST00000273854	NM_004439.5	568	Gat/Aat	8/18	0.525224238889987	1	FACETS	0.664	0.599	0.733	0.664	0.599	0.733	SUBCLONAL	1	TRUE	0	0.527862188627975	1		400	445	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949999	44949999	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0004408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	107	236	0	ENST00000377967.4:c.3768C>G	p.Tyr1256Ter	p.Y1256*	ENST00000377967	NM_021140.2	1256	taC/taG	26/29	0.191711396442292	0	FACETS	0.571	0.518	0.626			1	INDETERMINATE	1	TRUE	NA	0.527862188627975	0		236	335	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514605	103514605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773179441	NA	P-0004416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	244	267	1	ENST00000355739.4:c.1106C>T	p.Ala369Val	p.A369V	ENST00000355739	NM_000123.3	369	gCc/gTc	8/15	0.689400253761065	3	FACETS	0.936	0.897	0.973	0.936	0.897	0.973	CLONAL	3	TRUE	0	0.689400253761065	3		268	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577573	7577573	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0004416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	485	322	0	ENST00000269305.4:c.708C>G	p.Tyr236Ter	p.Y236*	ENST00000269305	NM_001126112.2	236	taC/taG	7/11	0.689400253761065	4	FACETS	0.937	0.912	0.962			1	CLONAL	4	TRUE	NA	0.689400253761065	4		322	634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0004423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	541	511	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.518226456733608	6	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	FALSE	3	0.699077417021655	6		512	1150	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288978	212288978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	182	312	0	ENST00000342788.4:c.2768G>A	p.Gly923Glu	p.G923E	ENST00000342788	NM_005235.2	923	gGa/gAa	23/28	0.566281284521662	4	FACETS	1	0.99	1	0.49	0.454	0.527	CLONAL	1	FALSE	1	0.699077417021655	4		312	602	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780711	9780711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs545136223	NA	P-0004423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	87	144	0	ENST00000377346.4:c.1513G>A	p.Glu505Lys	p.E505K	ENST00000377346	NM_005026.3	505	Gag/Aag	12/24	0.699077417021655	6	FACETS	1	0.96	1	0.295	0.262	0.33	CLONAL	1	FALSE	2	0.699077417021655	6		144	506	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202864	16202864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	643	282	0	ENST00000375759.3:c.572C>T	p.Pro191Leu	p.P191L	ENST00000375759	NM_015001.2	191	cCa/cTa	3/15	0.699077417021655	6	FACETS	0.938	0.908	0.968	0.938	0.908	0.968	CLONAL	4	FALSE	2	0.699077417021655	6		282	1176	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120467997	120467997	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	382	341	0	ENST00000256646.2:c.4442A>C	p.Asp1481Ala	p.D1481A	ENST00000256646	NM_024408.3	1481	gAt/gCt	25/34	0.565138523842643	6	FACETS	0.947	0.903	0.991	0.947	0.903	0.991	CLONAL	3	FALSE	3	0.699077417021655	6		341	923	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750398	41750398	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	108	197	0	ENST00000226382.2:c.230C>T	p.Pro77Leu	p.P77L	ENST00000226382	NM_003924.3	77	cCg/cTg	1/3	0.565138523842643	6	FACETS	1	0.977	1	0.433	0.389	0.478	CLONAL	1	FALSE	3	0.699077417021655	6		197	571	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554948	187554948	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1193354510	NA	P-0004423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	260	275	0	ENST00000441802.2:c.4213G>A	p.Asp1405Asn	p.D1405N	ENST00000441802	NM_005245.3	1405	Gac/Aac	7/27	0.699077417021655	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	FALSE	0	0.699077417021655	2		275	324	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434525	140434525	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	126	142	0	ENST00000288602.6:c.2173C>T	p.His725Tyr	p.H725Y	ENST00000288602	NM_004333.4	725	Cac/Tac	18/18	0.518226456733608	6	FACETS	0.879	0.8	0.96	0.586	0.533	0.64	CLONAL	2	FALSE	3	0.699077417021655	6		142	492	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878709	151878709	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1321521913	NA	P-0004423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	266	190	0	ENST00000262189.6:c.6236C>T	p.Pro2079Leu	p.P2079L	ENST00000262189	NM_170606.2	2079	cCa/cTa	36/59	0.518226456733608	6	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	FALSE	3	0.699077417021655	6		190	552	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741532	145741532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756986756	NA	P-0004423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	183	283	0	ENST00000428558.2:c.971C>T	p.Pro324Leu	p.P324L	ENST00000428558	NM_004260.3	324	cCc/cTc	5/22	0.566281284521662	4	FACETS	0.756	0.702	0.812	0.504	0.468	0.542	SUBCLONAL	2	FALSE	1	0.699077417021655	4		283	588	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974792	21974792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141798398	NA	P-0004423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	52	82	0	ENST00000304494.5:c.35C>T	p.Ser12Leu	p.S12L	ENST00000304494	NM_000077.4	12	tCg/tTg	1/3	0.566281284521662	4	FACETS	1	0.966	1	0.479	0.414	0.546	CLONAL	1	FALSE	1	0.699077417021655	4		82	176	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851230	63851230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1271514044	NA	P-0004423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	109	312	0	ENST00000279873.7:c.2008C>T	p.His670Tyr	p.H670Y	ENST00000279873	NM_032199.2	670	Cat/Tat	10/10	0.55535575541432	4	FACETS	0.889	0.8	0.982			1	CLONAL	1	FALSE	NA	0.699077417021655	4		312	596	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263912	104263912	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs1443773793	NA	P-0004423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	124	41	0	ENST00000369902.3:c.3G>A	p.Met1?	p.M1?	ENST00000369902	NM_016169.3	1	atG/atA	1/12	0.699077417021655	4	FACETS	0.841	0.778	0.903	1	0.984	1	CLONAL	3	FALSE	2	0.699077417021655	4		41	239	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205216	61205216	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	366	307	0	ENST00000301761.2:c.156G>T	p.Leu52Phe	p.L52F	ENST00000301761	NM_017841.2	52	ttG/ttT	2/4	0.699077417021655	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	FALSE	0	0.699077417021655	2		307	446	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549115	21549115	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776466850	NA	P-0004423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	180	287	0	ENST00000382592.4:c.3161G>A	p.Arg1054Gln	p.R1054Q	ENST00000382592	NM_014572.2	1054	cGa/cAa	8/8	0.699077417021655	6	FACETS	0.986	0.908	1			1	CLONAL	1	FALSE	NA	0.699077417021655	6		287	1252	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913021	32913021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	249	524	0	ENST00000380152.3:c.4529C>T	p.Pro1510Leu	p.P1510L	ENST00000380152		1510	cCc/cTc	11/27	0.699077417021655	5	FACETS	1	0.988	1	0.247	0.23	0.264	CLONAL	1	FALSE	0	0.699077417021655	5		524	1182	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954192	48954192	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	593	222	0	ENST00000267163.4:c.1393G>T	p.Glu465Ter	p.E465*	ENST00000267163	NM_000321.2	465	Gaa/Taa	15/27	0.699077417021655	5	FACETS	0.986	0.966	1	0.986	0.966	1	CLONAL	5	FALSE	0	0.699077417021655	5		222	705	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820669	3820669	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	110	156	0	ENST00000262367.5:c.2782C>T	p.Pro928Ser	p.P928S	ENST00000262367	NM_004380.2	928	Ccg/Tcg	14/31	0.699077417021655	6	FACETS	1	0.974	1	0.313	0.281	0.346	CLONAL	1	FALSE	2	0.699077417021655	6		156	603	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212139	5212139	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1235868511	NA	P-0004423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	182	329	0	ENST00000357368.4:c.4892T>C	p.Met1631Thr	p.M1631T	ENST00000357368	NM_002850.3	1631	aTg/aCg	32/38	0.699077417021655	4	FACETS	1	0.978	1	0.573	0.53	0.618	CLONAL	1	FALSE	2	0.699077417021655	4		329	772	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36022614	36022614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	400	282	0	ENST00000358208.4:c.487C>T	p.Arg163Trp	p.R163W	ENST00000358208		163	Cgg/Tgg	5/12	0.518226456733608	6	FACETS	0.945	0.902	0.988	0.945	0.902	0.988	CLONAL	3	FALSE	3	0.699077417021655	6		282	968	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866421	42866421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	163	287	0	ENST00000398585.3:c.211C>T	p.Pro71Ser	p.P71S	ENST00000398585	NM_001135099.1	71	Ccc/Tcc	3/14	0.699077417021655	4	FACETS	1	0.976	1	0.576	0.53	0.624	CLONAL	1	FALSE	2	0.699077417021655	4		287	688	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650040	206650041	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0004423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	105	141	2	ENST00000367120.3:c.560_561delinsAA	p.Arg187Gln	p.R187Q	ENST00000367120	NM_014002.3	187	cGG/cAA	7/22	0.565138523842643	6	FACETS	1	0.979	1	0.45	0.404	0.498	CLONAL	1	FALSE	3	0.699077417021655	6		143	534	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143129652	143129653	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0004423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	135	201	0	ENST00000262992.4:c.997_998delinsAA	p.Gly333Lys	p.G333K	ENST00000262992	NM_001101669.1	333	GGa/AAa	12/24	0.699077417021655	3	FACETS	1	0.988	1	0.499	0.46	0.54	CLONAL	1	FALSE	0	0.699077417021655	3		201	348	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451887	29451888	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0004423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	370	358	0	ENST00000389048.3:c.2677_2678delinsAA	p.Gly893Lys	p.G893K	ENST00000389048	NM_004304.4	893	GGa/AAa	16/29	0.566281284521662	4	FACETS	0.897	0.86	0.935	0.897	0.86	0.935	CLONAL	3	FALSE	1	0.699077417021655	4		358	668	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331686	8331688	+	missense_variant	Missense_Mutation	TNP	CTC	CTC	TTT	novel	NA	P-0004423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	190	332	0	ENST00000356435.5:c.5428_5430delinsAAA	p.Glu1810Lys	p.E1810K	ENST00000356435		1810	GAG/AAA	33/35	0.566281284521662	4	FACETS	1	0.989	1	0.459	0.426	0.493	CLONAL	1	FALSE	1	0.699077417021655	4		332	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578197	7578198	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0004423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	466	371	0	ENST00000269305.4:c.651_652delinsAA	p.Val218Met	p.V218M	ENST00000269305	NM_001126112.2	217	gtGGtg/gtAAtg	6/11	0.518226456733608	6	FACETS	0.938	0.899	0.978	0.938	0.899	0.978	CLONAL	3	FALSE	3	0.699077417021655	6		371	1136	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772451	56772452	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0004423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	348	316	0	ENST00000337432.4:c.305_306delinsTT	p.Thr102Ile	p.T102I	ENST00000337432	NM_058216.2	102	aCC/aTT	2/9	0.566281284521662	4	FACETS	0.951	0.912	0.99	0.951	0.912	0.99	CLONAL	3	FALSE	1	0.699077417021655	4		316	593	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376356	15376357	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0004423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	312	307	0	ENST00000263377.2:c.657_658delinsAA	p.Ala220Thr	p.A220T	ENST00000263377	NM_058243.2	219	caGGcc/caAAcc	5/20	0.699077417021655	4	FACETS	0.986	0.935	1	0.986	0.935	1	CLONAL	2	FALSE	2	0.699077417021655	4		307	769	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546606	9546607	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0004423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	199	284	0	ENST00000353224.5:c.1415_1416delinsAA	p.Gly472Glu	p.G472E	ENST00000353224	NM_177990.2	472	gGG/gAA	5/10	0.518226456733608	6	FACETS	1	0.99	1	0.491	0.455	0.528	CLONAL	1	FALSE	3	0.699077417021655	6		284	927	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546965	9546966	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0004423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	154	112	0	ENST00000353224.5:c.1056_1057delinsAA	p.Gly353Ser	p.G353S	ENST00000353224	NM_177990.2	352	agGGgc/agAAgc	5/10	0.518226456733608	6	FACETS	1	0.963	1	1	0.963	1	CLONAL	3	FALSE	3	0.699077417021655	6		112	334	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979281	40979282	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0004423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	251	183	0	ENST00000373198.4:c.1851_1852delinsAA	p.Gly618Arg	p.G618R	ENST00000373198	NM_133170.3	617	cgGGga/cgAAga	11/32	0.518226456733608	6	FACETS	0.985	0.929	1	0.985	0.929	1	CLONAL	3	FALSE	3	0.699077417021655	6		183	583	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0004431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	118	62	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.515851945573596	3	FACETS	0.858	0.784	0.933	0.858	0.784	0.933	CLONAL	2	TRUE	1	0.526777770799371	3		62	330	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0004431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	289	542	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.471200624258909	4	FACETS	0.971	0.916	1	0.971	0.916	1	CLONAL	2	TRUE	2	0.526777770799371	4		542	863	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0004431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	274	211	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	0.515851945573596	3	FACETS	0.997	0.943	1	0.997	0.943	1	CLONAL	2	TRUE	1	0.526777770799371	3		211	659	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212037	5212037	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	128	195	0	ENST00000357368.4:c.4994T>A	p.Ile1665Asn	p.I1665N	ENST00000357368	NM_002850.3	1665	aTc/aAc	32/38	0.515851945573596	3	FACETS	1	0.952	1	0.536	0.487	0.586	CLONAL	1	TRUE	1	0.526777770799371	3		195	573	SUCCESS
AR	367	MSKCC	GRCh37	X	66937442	66937442	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555996863	NA	P-0004431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	311	282	0	ENST00000374690.3:c.2296G>A	p.Ala766Thr	p.A766T	ENST00000374690	NM_000044.3	766	Gcc/Acc	5/8	0.485751187210117	3	FACETS	0.999	0.947	1	0.999	0.947	1	CLONAL	2	TRUE	1	0.526777770799371	3		282	747	SUCCESS
APC	324	MSKCC	GRCh37	5	112175243	112175243	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	88	136	0	ENST00000257430.4:c.3952del	p.Asp1318IlefsTer3	p.D1318Ifs*3	ENST00000257430	NM_000038.5	1318	Gat/at	16/16	0.515851945573596	3	FACETS	0.813	0.723	0.91	0.407	0.361	0.455	CLONAL	1	TRUE	1	0.526777770799371	3		136	519	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710540	114710540	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	171	295	0	ENST00000543371.1:c.28del	p.Asp10MetfsTer3	p.D10Mfs*3	ENST00000543371	NM_001198531.1	9	Ggg/gg	1/14	1	2	FACETS	0.848	0.781	0.917	0.848	0.781	0.917	CLONAL	1	TRUE	1	0.526777770799371	2		295	766	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0004432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	248	415	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.321000297201517	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.321000297201517	2		415	733	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686868	117686868	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	68	445	0	ENST00000368508.3:c.2849C>T	p.Ser950Phe	p.S950F	ENST00000368508	NM_002944.2	950	tCt/tTt	19/43	0.237400992126667	3	FACETS	0.878	0.765	1	0.439	0.382	0.5	CLONAL	1	TRUE	1	0.321000297201517	3		445	560	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061113	38061113	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	12	49	0	ENST00000250448.2:c.876G>C	p.Glu292Asp	p.E292D	ENST00000250448	NM_004496.3	292	gaG/gaC	2/2	0.321000297201517	5	FACETS	1	0.857	1	0.351	0.25	0.47	CLONAL	1	TRUE	1	0.321000297201517	5		49	79	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950340	17950340	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	73	450	2	ENST00000458235.1:c.1387C>A	p.His463Asn	p.H463N	ENST00000458235	NM_000215.3	463	Cac/Aac	10/24	0.321000297201517	3	FACETS	0.766	0.67	0.87	0.383	0.335	0.435	SUBCLONAL	1	TRUE	1	0.321000297201517	3		452	689	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0004432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	174	356	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	0.321000297201517	7	FACETS	0.948	0.876	1	0.711	0.657	0.767	CLONAL	3	TRUE	3	0.321000297201517	7		356	687	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828768	3828768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004436-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	336	373	0	ENST00000262367.5:c.1874G>A	p.Arg625His	p.R625H	ENST00000262367	NM_004380.2	625	cGc/cAc	9/31	0.134272354404247	1	FACETS	0.735	0.696	0.776	0.735	0.696	0.776	INDETERMINATE	1	TRUE	0	0.581013524529706	1		373	1116	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023327	27023327	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004436-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	83	99	0	ENST00000324856.7:c.437del	p.Pro146GlnfsTer86	p.P146Qfs*86	ENST00000324856	NM_006015.4	145	Ccc/cc	1/20	0.304435602756153	1	FACETS	0.711	0.635	0.791	0.711	0.635	0.791	INDETERMINATE	1	TRUE	0	0.581013524529706	1		99	285	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098804	178098804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553487942	NA	P-0004436-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	385	443	0	ENST00000397062.3:c.241G>A	p.Gly81Ser	p.G81S	ENST00000397062	NM_006164.4	81	Ggt/Agt	2/5	0.284782162611887	1	FACETS	0.84	0.799	0.881	0.84	0.799	0.881	INDETERMINATE	1	TRUE	0	0.581013524529706	1		443	1120	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206616	108206616	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1183442138	NA	P-0004436-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	305	316	0	ENST00000278616.4:c.8196C>G	p.Phe2732Leu	p.F2732L	ENST00000278616	NM_000051.3	2732	ttC/ttG	56/63	0.559480648381152	1	FACETS	0.95	0.9	1	0.95	0.9	1	CLONAL	1	TRUE	0	0.581013524529706	1		316	784	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120617	115120617	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004436-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	276	337	0	ENST00000257566.3:c.389G>A	p.Arg130Lys	p.R130K	ENST00000257566	NM_016569.3	130	aGg/aAg	1/8	NA	2	FACETS	0.976	0.918	1			1	INDETERMINATE	1	TRUE	NA	0.581013524529706	2		337	973	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221998	1221998	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690945	NA	P-0004436-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	204	335	3	ENST00000326873.7:c.913C>T	p.Gln305Ter	p.Q305*	ENST00000326873	NM_000455.4	305	Cag/Tag	7/10	0.581675725097255	1	FACETS	0.958	0.897	1	0.958	0.897	1	CLONAL	1	TRUE	0	0.581013524529706	1		338	520	SUCCESS
APC	324	MSKCC	GRCh37	5	112175171	112175171	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085373	NA	P-0004441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	100	393	0	ENST00000257430.4:c.3880C>T	p.Gln1294Ter	p.Q1294*	ENST00000257430	NM_000038.5	1294	Cag/Tag	16/16	1	2	FACETS	0.925	0.833	1	0.925	0.833	1	CLONAL	1	TRUE	1	0.545765546131404	2		393	396	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	123	464	0	ENST00000288602.6:c.1742A>T	p.Asn581Ile	p.N581I	ENST00000288602	NM_004333.4	581	aAt/aTt	15/18	1	2	FACETS	0.889	0.808	0.973	0.889	0.808	0.973	CLONAL	1	TRUE	1	0.545765546131404	2		464	507	SUCCESS
APC	324	MSKCC	GRCh37	5	112175136	112175136	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	104	447	0	ENST00000257430.4:c.3845C>A	p.Ser1282Ter	p.S1282*	ENST00000257430	NM_000038.5	1282	tCa/tAa	16/16	1	2	FACETS	0.905	0.816	0.998	0.905	0.816	0.998	CLONAL	1	TRUE	1	0.545765546131404	2		447	421	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441393	149441393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs573212436	NA	P-0004441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	33	663	1	ENST00000286301.3:c.1646G>A	p.Arg549His	p.R549H	ENST00000286301	NM_005211.3	549	cGc/cAc	12/22	1	2	FACETS	0.224	0.182	0.272	0.224	0.182	0.272	SUBCLONAL	1	TRUE	1	0.545765546131404	2		664	540	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524624	103524624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377353991	NA	P-0004441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1288	189	941	2	ENST00000355739.4:c.2755C>T	p.Arg919Trp	p.R919W	ENST00000355739	NM_000123.3	919	Cgg/Tgg	13/15	0.529265162868661	4	FACETS	0.725	0.668	0.785	0.362	0.334	0.393	SUBCLONAL	1	TRUE	2	0.545765546131404	4		943	1477	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578371	7578371	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	105	500	1	ENST00000269305.4:c.559G>C	p.Gly187Arg	p.G187R	ENST00000269305	NM_001126112.2	187	Ggt/Cgt	5/11	0.545765546131404	1	FACETS	0.942	0.856	1	0.942	0.856	1	CLONAL	1	TRUE	0	0.545765546131404	1		501	297	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214729	5214729	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	140	667	0	ENST00000357368.4:c.4337A>G	p.Tyr1446Cys	p.Y1446C	ENST00000357368	NM_002850.3	1446	tAc/tGc	29/38	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.545765546131404	2		667	503	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603039	48603066	+	frameshift_variant	Frame_Shift_Del	DEL	TGCAGCAGCAGGCGGCTACTGCACAAGC	TGCAGCAGCAGGCGGCTACTGCACAAGC	-	rs876660720	NA	P-0004441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	135	478	0	ENST00000342988.3:c.1349_1376del	p.Gln450LeufsTer17	p.Q450Lfs*17	ENST00000342988	NM_005359.5	447	aTGCAGCAGCAGGCGGCTACTGCACAAGCt/at	11/12	0.545765546131404	1	FACETS	0.89	0.817	0.965	0.89	0.817	0.965	CLONAL	1	TRUE	0	0.545765546131404	1		478	404	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0004476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	95	452	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.162748826869025	2	FACETS	0.859	0.774	0.948	0.43	0.387	0.474	INDETERMINATE	1	TRUE	0	0.697631504735206	2		452	317	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151216551	151216551	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	41	165	0	ENST00000262187.5:c.47C>T	p.Ser16Phe	p.S16F	ENST00000262187	NM_005614.3	16	tCt/tTt	1/8	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.697631504735206	2		165	103	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416586	29416586	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	120	317	0	ENST00000389048.3:c.4367C>A	p.Pro1456His	p.P1456H	ENST00000389048	NM_004304.4	1456	cCc/cAc	29/29	0.162748826869025	2	FACETS	1	0.978	1	0.599	0.55	0.649	INDETERMINATE	1	TRUE	0	0.697631504735206	2		317	287	SUCCESS
APC	324	MSKCC	GRCh37	5	112154981	112154981	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	109	376	0	ENST00000257430.4:c.1252G>T	p.Glu418Ter	p.E418*	ENST00000257430	NM_000038.5	418	Gaa/Taa	10/16	0.693949317885452	1	FACETS	0.942	0.867	1	0.942	0.867	1	CLONAL	1	TRUE	0	0.697631504735206	1		376	216	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751001	128751001	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1164555124	NA	P-0004476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	50	351	0	ENST00000377970.2:c.538G>T	p.Ala180Ser	p.A180S	ENST00000377970	NM_002467.4	180	Gcc/Tcc	2/3	0.593564141210191	4	FACETS	0.911	0.779	1	0.456	0.389	0.527	CLONAL	1	TRUE	2	0.697631504735206	4		351	267	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219229	94219229	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	56	308	0	ENST00000323929.3:c.175G>T	p.Gly59Cys	p.G59C	ENST00000323929	NM_005591.3	59	Ggt/Tgt	4/20	0.304382767028506	2	FACETS	0.836	0.728	0.95	0.418	0.364	0.475	INDETERMINATE	1	TRUE	0	0.697631504735206	2		308	192	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219241	94219241	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	48	297	0	ENST00000323929.3:c.163A>C	p.Ile55Leu	p.I55L	ENST00000323929	NM_005591.3	55	Att/Ctt	4/20	0.304382767028506	2	FACETS	0.824	0.709	0.946	0.412	0.354	0.473	INDETERMINATE	1	TRUE	0	0.697631504735206	2		297	167	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0004477-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	152	221	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.362181868228956	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.362181868228956	3		221	432	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776125	9776125	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004477-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	32	109	0	ENST00000377346.4:c.589G>C	p.Glu197Gln	p.E197Q	ENST00000377346	NM_005026.3	197	Gag/Cag	5/24	NA	2	FACETS	0.93	0.762	1			1	INDETERMINATE	1	TRUE	NA	0.362181868228956	2		109	190	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32899248	32899248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375125172	NA	P-0004477-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	92	266	0	ENST00000380152.3:c.352C>T	p.Arg118Cys	p.R118C	ENST00000380152		118	Cgc/Tgc	4/27	1	2	FACETS	0.966	0.861	1	0.966	0.861	1	CLONAL	1	TRUE	1	0.362181868228956	2		266	526	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0004492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	74	62	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.379327456163611	5	FACETS	0.948	0.83	1	0.316	0.276	0.359	CLONAL	1	TRUE	2	0.379327456163611	5		62	646	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127164	22127164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057519911	NA	P-0004492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	141	638	0	ENST00000215832.6:c.964G>A	p.Glu322Lys	p.E322K	ENST00000215832	NM_002745.4	322	Gag/Aag	7/9	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.379327456163611	2		638	668	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673753	37673753	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	130	694	0	ENST00000447079.4:c.2907del	p.Phe969LeufsTer4	p.F969Lfs*4	ENST00000447079	NM_015083.1	969	ttC/tt	10/14	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.379327456163611	2		694	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0004495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	77	604	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	0.886	0.775	1	0.886	0.775	1	CLONAL	1	TRUE	1	0.15	2		604	1159	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465997	69465997	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	70	460	0	ENST00000227507.2:c.835G>T	p.Glu279Ter	p.E279*	ENST00000227507	NM_053056.2	279	Gag/Tag	5/5	0.3	6	FACETS	0.988	0.858	1			1	CLONAL	1	TRUE	NA	0.15	6		460	1228	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022628	31022628	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	69	561	0	ENST00000375687.4:c.2113G>T	p.Glu705Ter	p.E705*	ENST00000375687	NM_015338.5	705	Gag/Tag	13/13	1	2	FACETS	0.862	0.749	0.986	0.862	0.749	0.986	CLONAL	1	TRUE	1	0.15	2		561	1067	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909336	41909336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1430025445	NA	P-0004495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	36	282	0	ENST00000372991.4:c.52G>A	p.Asp18Asn	p.D18N	ENST00000372991	NM_001760.3	18	Gac/Aac	1/5	1	2	FACETS	1	0.838	1	1	0.838	1	CLONAL	1	TRUE	1	0.15	2		282	470	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165759	108165759	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	59	532	0	ENST00000278616.4:c.4882A>T	p.Met1628Leu	p.M1628L	ENST00000278616	NM_000051.3	1628	Atg/Ttg	32/63	0.3	2	FACETS	0.679	0.582	0.785			1	SUBCLONAL	1	TRUE	NA	0.15	2		532	1159	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608224	28608224	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	70	740	0	ENST00000241453.7:c.1832A>T	p.Glu611Val	p.E611V	ENST00000241453	NM_004119.2	611	gAg/gTg	14/24	1	2	FACETS	0.743	0.645	0.85	0.743	0.645	0.85	SUBCLONAL	1	TRUE	1	0.15	2		740	1256	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936713	32936713	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	58	513	0	ENST00000380152.3:c.7859T>A	p.Val2620Asp	p.V2620D	ENST00000380152		2620	gTt/gAt	17/27	1	2	FACETS	0.795	0.681	0.92	0.795	0.681	0.92	CLONAL	1	TRUE	1	0.15	2		513	973	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530180	63530180	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	60	547	0	ENST00000307078.5:c.2255A>C	p.Lys752Thr	p.K752T	ENST00000307078	NM_004655.3	752	aAa/aCa	10/11	1	2	FACETS	0.878	0.754	1	0.878	0.754	1	CLONAL	1	TRUE	1	0.15	2		547	911	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868188	45868188	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758582720	NA	P-0004495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	58	489	0	ENST00000391945.4:c.502G>A	p.Val168Met	p.V168M	ENST00000391945	NM_000400.3	168	Gtg/Atg	7/23	1	2	FACETS	0.89	0.763	1	0.89	0.763	1	CLONAL	1	TRUE	1	0.15	2		489	869	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023604	27023604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	38	320	1	ENST00000324856.7:c.710G>A	p.Gly237Asp	p.G237D	ENST00000324856	NM_006015.4	237	gGc/gAc	1/20	0.143627259326026	4	FACETS	0.997	0.827	1	0.499	0.413	0.593	INDETERMINATE	1	TRUE	2	0.31	4		321	322	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225896	2225896	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	66	465	0	ENST00000326181.6:c.1688A>T	p.Tyr563Phe	p.Y563F	ENST00000326181	NM_032271.2	563	tAc/tTc	18/21	NA	2	FACETS	0.803	0.705	0.908			1	INDETERMINATE	2	TRUE	NA	0.31	2		465	265	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216520	2216520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	48	391	0	ENST00000398665.3:c.2164C>T	p.Leu722Phe	p.L722F	ENST00000398665	NM_032482.2	722	Ctc/Ttc	20/28	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.31	2		391	249	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169355	11169355	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	40	466	0	ENST00000361445.4:c.7520A>G	p.Lys2507Arg	p.K2507R	ENST00000361445	NM_004958.3	2507	aAg/aGg	56/58	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.37	2		466	212	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183748	10183748	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs869025619	NA	P-0004507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	85	318	0	ENST00000256474.2:c.217C>T	p.Gln73Ter	p.Q73*	ENST00000256474	NM_000551.3	73	Cag/Tag	1/3	0.3	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.37	1		318	321	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47079174	47079174	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0004507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	30	510	0	ENST00000409792.3:c.7332T>G	p.Tyr2444Ter	p.Y2444*	ENST00000409792	NM_014159.6	2444	taT/taG	18/21	0.3	1	FACETS	0.858	0.7	1	0.858	0.7	1	CLONAL	1	TRUE	0	0.37	1		510	154	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637669	52637669	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	55	449	0	ENST00000394830.3:c.2647G>T	p.Gly883Ter	p.G883*	ENST00000394830	NM_018313.4	883	Gga/Tga	18/30	0.3	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.37	1		449	206	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754956	29754956	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	124	295	0	ENST00000389048.3:c.979G>C	p.Ala327Pro	p.A327P	ENST00000389048	NM_004304.4	327	Gct/Cct	4/29	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.272583864526363	2		295	730	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0004508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	153	607	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.272583864526363	2		607	979	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278049	18278049	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs372272045	NA	P-0004508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	136	511	0	ENST00000222254.8:c.1669G>T	p.Asp557Tyr	p.D557Y	ENST00000222254	NM_005027.3	557	Gac/Tac	13/16	1	2	FACETS	0.986	0.895	1	0.986	0.895	1	CLONAL	1	TRUE	1	0.272583864526363	2		511	1012	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425080	49425086	+	frameshift_variant	Frame_Shift_Del	DEL	TTGCCCG	TTGCCCG	-	novel	NA	P-0004508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	175	621	0	ENST00000301067.7:c.13402_13408del	p.Ala4469MetfsTer48	p.A4469Mfs*48	ENST00000301067	NM_003482.3	4468	CGGGCAAag/ag	39/54	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.272583864526363	2		621	1131	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425091	49425103	+	protein_altering_variant	In_Frame_Del	DEL	AGCTTCTGCAAGA	AGCTTCTGCAAGA	T	novel	NA	P-0004508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	169	604	0	ENST00000301067.7:c.13385_13397delinsA	p.Leu4462_Leu4466delinsGln	p.L4462_L4466delinsQ	ENST00000301067	NM_003482.3	4462	cTCTTGCAGAAGCTa/cAa	39/54	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.272583864526363	2		604	1124	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	328	494	0	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	2	TRUE	NA	0.662712738122279	2		494	482	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43806100	43806100	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	385	508	0	ENST00000372470.3:c.896T>C	p.Val299Ala	p.V299A	ENST00000372470	NM_005373.2	299	gTt/gCt	6/12	0.647076499647144	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.662712738122279	4		508	911	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829714	76829714	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0004512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	317	502	1	ENST00000373344.5:c.6326+1G>A		p.X2109_splice	ENST00000373344	NM_000489.3	2109			0.364872507515527	5	FACETS	0.846	0.803	0.889	0.846	0.803	0.889	INDETERMINATE	3	TRUE	2	0.662712738122279	5		503	752	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055696	152055696	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	12	568	0	ENST00000262189.6:c.226G>A	p.Glu76Lys	p.E76K	ENST00000262189	NM_170606.2	76	Gaa/Aaa	2/59	0.315595369321451	5	FACETS	0.936	0.665	1	0.312	0.221	0.42	CLONAL	1	TRUE	2	0.461781050381439	5		568	94	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974926	15974926	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	10	472	0	ENST00000268712.3:c.3949C>A	p.Gln1317Lys	p.Q1317K	ENST00000268712	NM_006311.3	1317	Caa/Aaa	30/46	0.379635812727184	3	FACETS	0.711	0.488	0.981	0.355	0.244	0.491	CLONAL	1	TRUE	1	0.461781050381439	3		472	75	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195680	123195680	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	17	285	0	ENST00000218089.9:c.1594G>T	p.Ala532Ser	p.A532S	ENST00000218089	NM_001042749.1	532	Gcg/Tcg	17/35	0.371654734124702	2	FACETS	0.722	0.547	0.923			1	CLONAL	1	TRUE	NA	0.461781050381439	2		285	102	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061220	38061225	+	inframe_deletion	In_Frame_Del	DEL	CGTTCT	CGTTCT	-	novel	NA	P-0004522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	195	309	0	ENST00000250448.2:c.764_769del	p.Glu255_Asn256del	p.E255_N256del	ENST00000250448	NM_004496.3	255	gAGAACGgc/ggc	2/2	0.461781050381439	26	FACETS	1	0.942	1			1	CLONAL	11	TRUE	NA	0.461781050381439	26		309	498	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089737	27089737	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	22	243	0	ENST00000324856.7:c.2693del	p.Ala898ValfsTer21	p.A898Vfs*21	ENST00000324856	NM_006015.4	898	gCt/gt	8/20	0.37534185831535	5	FACETS	0.906	0.718	1			1	CLONAL	2	TRUE	NA	0.461781050381439	5		243	89	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0004547-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	123	311	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	NA	2	FACETS	0.648	0.587	0.714			1	INDETERMINATE	1	TRUE	NA	0.49981887649712	2		311	759	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105424	27105826	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGAAGACTTGGGGAGGTCTCTCAAGTCAATAATTCTGTTCTTAGGCCACTTTTCTCCCTTAATTTATTTCCTGTTCTTTCTCTTTTTAGCTCCCAGGGTTGCTAGAGCTCCTTGTAGAATATTTCCGACGATGCCTGATTGAGATCTTTGGCATTTTAAAGGAGTATGAGGTGGGTGACCCAGGACAGAGAACGCTACTGGATCCTGGGAGGTTCAGCAAGGTGTCTAGTCCAGCTCCCATGGAGGGTGGGGAAGAAGAAGAAGAACTTCTAGGTCCTAAACTAGAAGAGGAAGAAGAAGAGGAAGTAGTTGAAAATGATGAGGAGATAGCCTTTTCAGGCAAGGACAAGCCAGCTTCAGAGAATAGTGAGGAGAAGCTGATCAGTAAGTTTGACAAGCTTC	CAGAAGACTTGGGGAGGTCTCTCAAGTCAATAATTCTGTTCTTAGGCCACTTTTCTCCCTTAATTTATTTCCTGTTCTTTCTCTTTTTAGCTCCCAGGGTTGCTAGAGCTCCTTGTAGAATATTTCCGACGATGCCTGATTGAGATCTTTGGCATTTTAAAGGAGTATGAGGTGGGTGACCCAGGACAGAGAACGCTACTGGATCCTGGGAGGTTCAGCAAGGTGTCTAGTCCAGCTCCCATGGAGGGTGGGGAAGAAGAAGAAGAACTTCTAGGTCCTAAACTAGAAGAGGAAGAAGAAGAGGAAGTAGTTGAAAATGATGAGGAGATAGCCTTTTCAGGCAAGGACAAGCCAGCTTCAGAGAATAGTGAGGAGAAGCTGATCAGTAAGTTTGACAAGCTTC	-	novel	NA	P-0004547-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	49	106	0	ENST00000324856.7:c.5125-87_5440del		p.X1709_splice	ENST00000324856	NM_006015.4	1709		20/20	0.222198224478293	3	FACETS	1	0.967	1			1	INDETERMINATE	1	TRUE	NA	0.49981887649712	3		106	164	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0004548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	322	503	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.678866816863397	1	FACETS	0.984	0.938	1	0.984	0.938	1	CLONAL	1	TRUE	0	0.678866816863397	1		503	637	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844101	68844101	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	50	380	0	ENST00000261769.5:c.689T>C	p.Leu230Pro	p.L230P	ENST00000261769	NM_004360.3	230	cTc/cCc	6/16	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		380	401	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149596	202149596	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004573-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	47	444	0	ENST00000358485.4:c.1037G>A	p.Cys346Tyr	p.C346Y	ENST00000358485	NM_001080125.1	346	tGc/tAc	8/9	1	2	FACETS	0.846	0.712	0.995	0.846	0.712	0.995	CLONAL	1	TRUE	1	0.137002111532498	2		444	811	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149928	202149928	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004573-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	36	359	0	ENST00000358485.4:c.1369G>T	p.Asp457Tyr	p.D457Y	ENST00000358485	NM_001080125.1	457	Gac/Tac	8/9	1	2	FACETS	0.737	0.604	0.887	0.737	0.604	0.887	SUBCLONAL	1	TRUE	1	0.137002111532498	2		359	713	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592043	67592043	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004573-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	57	389	0	ENST00000274335.5:c.1859A>G	p.Asp620Gly	p.D620G	ENST00000274335		620	gAt/gGt	14/15	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.137002111532498	2		389	746	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710590	117710590	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199766618	NA	P-0004573-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	66	361	0	ENST00000368508.3:c.1682C>T	p.Pro561Leu	p.P561L	ENST00000368508	NM_002944.2	561	cCg/cTg	12/43	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.137002111532498	2		361	717	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874416	151874416	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004573-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	59	442	0	ENST00000262189.6:c.8122G>T	p.Glu2708Ter	p.E2708*	ENST00000262189	NM_170606.2	2708	Gaa/Taa	38/59	1	2	FACETS	0.985	0.846	1	0.985	0.846	1	CLONAL	1	TRUE	1	0.137002111532498	2		442	874	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138918	64138918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781635747	NA	P-0004573-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	29	220	0	ENST00000334205.4:c.2285C>T	p.Pro762Leu	p.P762L	ENST00000334205	NM_003942.2	762	cCc/cTc	17/17	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.137002111532498	2		220	369	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0004594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	12	411	1	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	0.170790260535022	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		412	275	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164419	47164419	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	12	337	0	ENST00000409792.3:c.1707del	p.Phe569LeufsTer10	p.F569Lfs*10	ENST00000409792	NM_014159.6	569	ttT/tt	3/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		337	233	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041557	42041565	+	frameshift_variant	Frame_Shift_Del	DEL	TCTGAAACC	TCTGAAACC	G	novel	NA	P-0004594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	14	637	0	ENST00000219905.7:c.5752_5760delinsG	p.Ser1918GlufsTer5	p.S1918Efs*5	ENST00000219905	NM_001164273.1	1918	TCTGAAACC/G	17/24	0.3	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		637	274	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553249	106553249	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1415765117	NA	P-0004613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	116	490	0	ENST00000369096.4:c.1214C>T	p.Ser405Leu	p.S405L	ENST00000369096	NM_001198.3	405	tCg/tTg	5/7	0.437114620495889	2	FACETS	0.705	0.637	0.777	0.353	0.318	0.389	SUBCLONAL	1	TRUE	0	0.549301703293808	2		490	599	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134691	2134691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	60	261	0	ENST00000219476.3:c.4468G>A	p.Glu1490Lys	p.E1490K	ENST00000219476	NM_000548.3	1490	Gag/Aag	34/42	0.338764385064773	4	FACETS	0.634	0.546	0.729	0.317	0.273	0.365	SUBCLONAL	1	TRUE	2	0.549301703293808	4		261	534	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578470	7578473	+	frameshift_variant	Frame_Shift_Del	DEL	CGGG	CGGG	-	novel	NA	P-0004613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	391	431	0	ENST00000269305.4:c.457_460del	p.Pro153AlafsTer16	p.P153Afs*16	ENST00000269305	NM_001126112.2	153	CCCGgc/gc	5/11	0.549301703293808	3	FACETS	0.891	0.856	0.926	0.891	0.856	0.926	CLONAL	3	TRUE	0	0.549301703293808	3		431	679	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242481	+	protein_altering_variant	In_Frame_Del	DEL	GGAATTAAGAGAAGCAA	GGAATTAAGAGAAGCAA	AATTC	rs727504332	NA	P-0004613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	554	384	1	ENST00000275493.2:c.2235_2251delinsAATTC	p.Glu746_Thr751delinsIlePro	p.E746_T751delinsIP	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCAAca/aaAATTCca	19/28	0.549301703293808	7	FACETS	0.98	0.947	1	0.817	0.789	0.844	CLONAL	5	TRUE	1	0.549301703293808	7		385	977	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437315	52437315	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0004636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	137	193	0	ENST00000460680.1:c.1730-1G>C		p.X577_splice	ENST00000460680	NM_004656.3	577			0.425249480357658	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.425249480357658	1		193	471	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142964	47142964	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	122	191	0	ENST00000409792.3:c.4999C>T	p.Gln1667Ter	p.Q1667*	ENST00000409792	NM_014159.6	1667	Cag/Tag	8/21	0.425249480357658	1	FACETS	0.811	0.736	0.89	0.811	0.736	0.89	CLONAL	1	TRUE	0	0.425249480357658	1		191	557	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634656	158634656	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	191	296	0	ENST00000263640.3:c.530A>C	p.Asp177Ala	p.D177A	ENST00000263640	NM_001105.4	177	gAc/gCc	5/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.425249480357658	2		296	844	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556678	41556678	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	104	115	0	ENST00000263253.7:c.3623T>A	p.Ile1208Asn	p.I1208N	ENST00000263253	NM_001429.3	1208	aTc/aAc	20/31	0.425249480357658	1	FACETS	0.935	0.843	1	0.935	0.843	1	CLONAL	1	TRUE	0	0.425249480357658	1		115	412	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593667	55593669	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	rs1060502543	NA	P-0004645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	201	395	0	ENST00000288135.5:c.1735_1737del	p.Asp579del	p.D579del	ENST00000288135	NM_000222.2	578	tATGat/tat	11/21	1	2	FACETS	0.749	0.697	0.803	0.749	0.697	0.803	SUBCLONAL	1	TRUE	1	0.781995101694589	2		395	686	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0004673-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	56	533	2	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.261048482717644	1	FACETS	0.684	0.586	0.791	0.684	0.586	0.791	SUBCLONAL	1	TRUE	0	0.261048482717644	1		535	545	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578294	212578294	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004673-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	55	676	0	ENST00000342788.4:c.963A>C	p.Lys321Asn	p.K321N	ENST00000342788	NM_005235.2	321	aaA/aaC	8/28	1	2	FACETS	0.592	0.505	0.687	0.592	0.505	0.687	SUBCLONAL	1	TRUE	1	0.261048482717644	2		676	712	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs377767347	NA	P-0004673-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	21	534	1	ENST00000342988.3:c.1082G>T	p.Arg361Leu	p.R361L	ENST00000342988	NM_005359.5	361	cGc/cTc	9/12	0.261048482717644	1	FACETS	0.257	0.197	0.327	0.257	0.197	0.327	SUBCLONAL	1	TRUE	0	0.261048482717644	1		535	545	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239862	105239862	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs751232562	NA	P-0000047-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	25	976	0	ENST00000349310.3:c.758A>G	p.Tyr253Cys	p.Y253C	ENST00000349310	NM_001014432.1	253	tAt/tGt	10/15	NA	2	FACETS	0.299	0.237	0.371			1	INDETERMINATE	1	TRUE	NA	0.68158263099611	2		976	245	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443574	52443592	+	frameshift_variant	Frame_Shift_Del	DEL	GACATTTGCTCTGAAGGTC	GACATTTGCTCTGAAGGTC	-	novel	NA	P-0000047-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	201	809	0	ENST00000460680.1:c.100_118del	p.Asp34ArgfsTer32	p.D34Rfs*32	ENST00000460680	NM_004656.3	34	GACCTTCAGAGCAAATGTCag/ag	3/17	0.562989740326345	3	FACETS	0.895	0.839	0.95	0.596	0.559	0.634	CLONAL	2	TRUE	0	0.68158263099611	3		809	442	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426031	138426031	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000064-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	549	131	328	0	ENST00000289153.2:c.1500A>C	p.Lys500Asn	p.K500N	ENST00000289153	NM_006219.2	500	aaA/aaC	9/22	NA	2	FACETS	0.815	0.741	0.892			1	INDETERMINATE	1	TRUE	NA	0.473021289229972	2		328	680	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043377	180043377	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771345898	NA	P-0000064-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	487	83	337	0	ENST00000261937.6:c.3209G>A	p.Arg1070His	p.R1070H	ENST00000261937	NM_182925.4	1070	cGc/cAc	23/30	NA	2	FACETS	0.616	0.544	0.692			1	INDETERMINATE	1	TRUE	NA	0.473021289229972	2		337	570	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481627	56481627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1429784531	NA	P-0000064-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	586	109	326	0	ENST00000267101.3:c.662C>T	p.Pro221Leu	p.P221L	ENST00000267101	NM_001982.3	221	cCc/cTc	6/28	0.397017902527397	4	FACETS	0.977	0.878	1	0.488	0.439	0.541	CLONAL	1	TRUE	2	0.473021289229972	4		326	695	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593558	48593558	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0000064-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	293	48	187	0	ENST00000342988.3:c.1308+1G>C		p.X436_splice	ENST00000342988	NM_005359.5	436			0.356970568031644	1	FACETS	0.454	0.385	0.53	0.454	0.385	0.53	SUBCLONAL	1	TRUE	0	0.473021289229972	1		187	341	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716212	52716212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555791268	NA	P-0000064-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	333	140	238	0	ENST00000322088.6:c.656C>T	p.Ser219Leu	p.S219L	ENST00000322088	NM_014225.5	219	tCg/tTg	6/15	0.393247825453955	4	FACETS	0.922	0.846	1			1	CLONAL	2	TRUE	NA	0.473021289229972	4		238	473	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165674	108165677	+	frameshift_variant	Frame_Shift_Del	DEL	AGTA	AGTA	-	rs1060501659	NA	P-0000064-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	378	222	342	0	ENST00000278616.4:c.4800_4803del	p.Ser1601PhefsTer7	p.S1601Ffs*7	ENST00000278616	NM_000051.3	1599	tcAGTA/tc	32/63	0.42776041262653	2	FACETS	0.782	0.733	0.832	0.782	0.733	0.832	SUBCLONAL	2	TRUE	0	0.473021289229972	2		342	600	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20483139	20483139	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000073-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	448	222	342	0	ENST00000346618.3:c.872C>A	p.Ser291Ter	p.S291*	ENST00000346618	NM_001949.4	291	tCa/tAa	4/7	1	2	FACETS	0.856	0.801	0.912	1	0.993	1	CLONAL	2	TRUE	1	0.387149345017862	2		342	670	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805077	89805077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374984587	NA	P-0000073-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	710	153	385	2	ENST00000389301.3:c.4300G>A	p.Ala1434Thr	p.A1434T	ENST00000389301	NM_000135.2	1434	Gcc/Acc	43/43	1	2	FACETS	0.916	0.838	0.997	0.916	0.838	0.997	CLONAL	1	TRUE	1	0.387149345017862	2		387	863	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094351	27094351	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000073-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	380	214	338	0	ENST00000324856.7:c.3060del	p.Lys1021ArgfsTer18	p.K1021Rfs*18	ENST00000324856	NM_006015.4	1020	aGg/ag	11/20	1	2	FACETS	0.931	0.871	0.992	1	0.994	1	CLONAL	2	TRUE	1	0.387149345017862	2		338	594	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007051	152007051	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000103-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	228	396	0	ENST00000262189.6:c.849A>T	p.Glu283Asp	p.E283D	ENST00000262189	NM_170606.2	283	gaA/gaT	6/59	0.500352026017007	4	FACETS	1	0.97	1			1	CLONAL	1	TRUE	NA	0.661956064125185	4		396	1067	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692953	89692953	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs786204933	NA	P-0000103-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	192	297	0	ENST00000371953.3:c.437T>G	p.Leu146Ter	p.L146*	ENST00000371953	NM_000314.4	146	tTa/tGa	5/9	0.490189697389438	1	FACETS	0.894	0.837	0.952	0.894	0.837	0.952	CLONAL	1	TRUE	0	0.661956064125185	1		297	434	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061655	38061655	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1343017631	NA	P-0000103-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	26	107	0	ENST00000250448.2:c.334G>C	p.Gly112Arg	p.G112R	ENST00000250448	NM_004496.3	112	Ggc/Cgc	2/2	0.658493728457369	4	FACETS	0.622	0.495	0.765	0.155	0.123	0.192	SUBCLONAL	1	TRUE	0	0.661956064125185	4		107	210	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579415	7579415	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000103-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	275	325	1	ENST00000269305.4:c.272G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tGg/tAg	4/11	0.633432445607864	2	FACETS	0.996	0.954	1	0.996	0.954	1	CLONAL	2	TRUE	0	0.661956064125185	2		326	417	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523329	9523329	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000103-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	202	474	0	ENST00000353224.5:c.1908G>C	p.Met636Ile	p.M636I	ENST00000353224	NM_177990.2	636	atG/atC	9/10	0.661956064125185	3	FACETS	0.727	0.673	0.783			1	SUBCLONAL	1	TRUE	NA	0.661956064125185	3		474	1117	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24135766	24135766	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000103-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	525	375	0	ENST00000263121.7:c.253G>T	p.Ala85Ser	p.A85S	ENST00000263121	NM_003073.3	85	Gcc/Tcc	3/9	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.661956064125185	2		375	747	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288735	11288735	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000110-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	162	411	3	ENST00000361445.4:c.3020C>A	p.Ala1007Asp	p.A1007D	ENST00000361445	NM_004958.3	1007	gCc/gAc	19/58	NA	2	FACETS	0.943	0.867	1			1	INDETERMINATE	1	TRUE	NA	0.488964519897046	2		414	703	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849080	156849080	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000110-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	228	484	1	ENST00000524377.1:c.1972G>T	p.Val658Leu	p.V658L	ENST00000524377	NM_002529.3	658	Gtg/Ttg	15/17	0.280845389639437	2	FACETS	1	0.977	1	0.551	0.514	0.589	INDETERMINATE	1	TRUE	0	0.488964519897046	2		485	846	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519777	29519777	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000110-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	46	383	0	ENST00000389048.3:c.1794G>T	p.Leu598Phe	p.L598F	ENST00000389048	NM_004304.4	598	ttG/ttT	9/29	0.293181292299445	3	FACETS	0.361	0.303	0.425	0.12	0.101	0.142	INDETERMINATE	1	TRUE	0	0.488964519897046	3		383	648	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176478	142176478	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000110-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	92	409	2	ENST00000350721.4:c.7623G>T	p.Arg2541Ser	p.R2541S	ENST00000350721	NM_001184.3	2541	agG/agT	45/47	0.419990724963442	3	FACETS	0.553	0.491	0.62	0.276	0.245	0.31	SUBCLONAL	1	TRUE	1	0.488964519897046	3		411	847	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430735	181430735	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000110-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	141	361	5	ENST00000325404.1:c.587C>A	p.Pro196His	p.P196H	ENST00000325404	NM_003106.3	196	cCc/cAc	1/1	0.419990724963442	3	FACETS	1	0.984	1	0.663	0.607	0.721	CLONAL	1	TRUE	1	0.488964519897046	3		366	541	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168698	32168698	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000110-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	136	457	0	ENST00000375023.3:c.4225C>A	p.Leu1409Ile	p.L1409I	ENST00000375023	NM_004557.3	1409	Ctc/Atc	23/30	0.488964519897046	3	FACETS	0.755	0.686	0.828	0.377	0.343	0.414	SUBCLONAL	1	TRUE	1	0.488964519897046	3		457	917	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404570	8404570	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000110-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	227	523	4	ENST00000356435.5:c.4177G>T	p.Asp1393Tyr	p.D1393Y	ENST00000356435		1393	Gat/Tat	25/35	0.230788417404394	4	FACETS	1	0.986	1	0.611	0.569	0.655	INDETERMINATE	1	TRUE	2	0.488964519897046	4		527	1131	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28882979	28882979	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1158779072	NA	P-0000110-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	215	494	2	ENST00000282397.4:c.3720+1G>A		p.X1240_splice	ENST00000282397	NM_002019.4	1240			0.321269101024997	3	FACETS	0.997	0.926	1	0.498	0.463	0.535	CLONAL	1	TRUE	1	0.488964519897046	3		496	1098	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061732	38061732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000110-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	48	223	0	ENST00000250448.2:c.257C>T	p.Pro86Leu	p.P86L	ENST00000250448	NM_004496.3	86	cCg/cTg	2/2	0.245282750268116	5	FACETS	0.772	0.653	0.902	0.257	0.217	0.301	INDETERMINATE	1	TRUE	2	0.488964519897046	5		223	441	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78831617	78831617	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000110-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	83	383	3	ENST00000306801.3:c.1426G>T	p.Val476Leu	p.V476L	ENST00000306801	NM_020761.2	476	Gtg/Ttg	13/34	0.321269101024997	3	FACETS	0.566	0.499	0.637	0.283	0.249	0.319	SUBCLONAL	1	TRUE	1	0.488964519897046	3		386	747	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291025	10291025	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0000110-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	71	319	3	ENST00000340748.4:c.445+1G>T		p.X149_splice	ENST00000340748		149			0.288779944538242	3	FACETS	0.579	0.505	0.659	0.29	0.252	0.33	INDETERMINATE	1	TRUE	1	0.488964519897046	3		322	624	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600344	10600344	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000110-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	125	466	3	ENST00000171111.5:c.1511A>G	p.Asn504Ser	p.N504S	ENST00000171111	NM_203500.1	504	aAc/aGc	4/6	0.288779944538242	3	FACETS	0.783	0.708	0.861	0.391	0.354	0.431	INDETERMINATE	1	TRUE	1	0.488964519897046	3		469	813	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953407	17953407	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000110-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	138	411	1	ENST00000458235.1:c.579C>A	p.Cys193Ter	p.C193*	ENST00000458235	NM_000215.3	193	tgC/tgA	6/24	0.419990724963442	3	FACETS	1	0.982	1	0.643	0.588	0.701	CLONAL	1	TRUE	1	0.488964519897046	3		412	546	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546850	9546850	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000110-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	60	378	1	ENST00000353224.5:c.1172G>T	p.Ser391Ile	p.S391I	ENST00000353224	NM_177990.2	391	aGt/aTt	5/10	0.273452997290532	3	FACETS	0.773	0.669	0.886	0.387	0.334	0.443	INDETERMINATE	1	TRUE	1	0.488964519897046	3		379	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000110-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	155	341	0	ENST00000269305.4:c.731del	p.Gly244AlafsTer3	p.G244Afs*3	ENST00000269305	NM_001126112.2	244	gGc/gc	7/11	0.280845389639437	2	FACETS	1	0.952	1	0.525	0.482	0.569	INDETERMINATE	1	TRUE	0	0.488964519897046	2		341	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0000127-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	95	153	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.360252959542125	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.360252959542125	1		153	392	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22143076	22143076	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000127-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	390	222	0	ENST00000215832.6:c.631A>G	p.Ile211Val	p.I211V	ENST00000215832	NM_002745.4	211	Att/Gtt	5/9	0.334919280605658	5	FACETS	1	0.988	1			1	CLONAL	3	TRUE	NA	0.360252959542125	5		222	1007	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720805	89720808	+	frameshift_variant	Frame_Shift_Del	DEL	CTTT	CTTT	-	rs398123330	NA	P-0000131-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	274	71	0	ENST00000371953.3:c.956_959del	p.Thr319LysfsTer24	p.T319Kfs*24	ENST00000371953	NM_000314.4	319	aCTTTa/aa	8/9	0.475841163716989	2	FACETS	0.765	0.723	0.808	0.765	0.723	0.808	SUBCLONAL	2	TRUE	0	0.528093399319423	2		71	678	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs786202525	NA	P-0000131-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	518	173	0	ENST00000269305.4:c.532del	p.His178ThrfsTer69	p.H178Tfs*69	ENST00000269305	NM_001126112.2	178	Cac/ac	5/11	0.528093399319423	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.528093399319423	1		173	1436	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0000145-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	71	347	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.875	0.765	0.994	0.875	0.765	0.994	CLONAL	1	TRUE	1	0.293446041229856	2		347	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577510	7577511	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0000145-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	48	292	0	ENST00000269305.4:c.770_771del	p.Leu257ArgfsTer6	p.L257Rfs*6	ENST00000269305	NM_001126112.2	257	cTG/c	7/11	0.269065975662446	1	FACETS	0.598	0.506	0.699	0.598	0.506	0.699	SUBCLONAL	1	TRUE	0	0.293446041229856	1		292	467	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0000148-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	1474	231	332	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.677	0.629	0.728	0.677	0.629	0.728	SUBCLONAL	1	TRUE	1	0.4	2		332	1705	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662307	67662307	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000148-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	944	74	378	0	ENST00000264010.4:c.1553C>G	p.Thr518Ser	p.T518S	ENST00000264010	NM_006565.3	518	aCc/aGc	9/12	1	2	FACETS	0.363	0.317	0.414	0.363	0.317	0.414	SUBCLONAL	1	TRUE	1	0.4	2		378	1018	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156731	20156731	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000148-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	1685	159	498	0	ENST00000379607.5:c.26G>T	p.Gly9Val	p.G9V	ENST00000379607	NM_001412.3	9	gGt/gTt	2/7	0.162892735113389	0	FACETS	0.259	0.236	0.283			1	INDETERMINATE	1	TRUE	0	0.4	0		498	1844	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849844	151849844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000175-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	152	418	0	ENST00000262189.6:c.12472G>A	p.Val4158Met	p.V4158M	ENST00000262189	NM_170606.2	4158	Gtg/Atg	49/59	0.170203317743698	4	FACETS	0.96	0.886	1	0.96	0.886	1	INDETERMINATE	2	TRUE	2	0.574750237577642	4		418	434	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000175-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	84	421	0	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	0.233672815507046	3	FACETS	1	0.974	1	0.656	0.586	0.728	INDETERMINATE	1	TRUE	1	0.574750237577642	3		421	287	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191385	185191385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000184-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1388	83	365	0	ENST00000265026.3:c.2266G>A	p.Asp756Asn	p.D756N	ENST00000265026	NM_004721.4	756	Gac/Aac	11/14	0.488976709580525	3	FACETS	0.287	0.252	0.325	0.144	0.126	0.163	SUBCLONAL	1	FALSE	1	0.488976709580525	3		365	1471	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151868347	151868347	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0000184-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	980	423	0	ENST00000262189.6:c.9453+2T>C		p.X3151_splice	ENST00000262189	NM_170606.2	3151			0.443562525429146	3	FACETS	0.936	0.912	0.96	0.936	0.912	0.96	CLONAL	3	FALSE	0	0.488976709580525	3		423	1777	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719930	18719930	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000184-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	72	488	1	ENST00000266497.5:c.3827G>T	p.Arg1276Ile	p.R1276I	ENST00000266497		1276	aGa/aTa	27/31	0.488976709580525	1	FACETS	0.224	0.195	0.256	0.224	0.195	0.256	SUBCLONAL	1	FALSE	0	0.488976709580525	1		489	992	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303439	91303439	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000184-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1442	122	479	0	ENST00000355112.3:c.1150G>T	p.Asp384Tyr	p.D384Y	ENST00000355112	NM_000057.2	384	Gat/Tat	6/22	0.249643269858807	3	FACETS	0.397	0.357	0.439	0.132	0.119	0.147	INDETERMINATE	1	FALSE	0	0.488976709580525	3		479	1564	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646903	23646903	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000184-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1283	152	481	0	ENST00000261584.4:c.964G>C	p.Glu322Gln	p.E322Q	ENST00000261584	NM_024675.3	322	Gag/Cag	4/13	1	2	FACETS	0.433	0.395	0.474	0.433	0.395	0.474	SUBCLONAL	1	FALSE	1	0.488976709580525	2		481	1435	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663398	67663398	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000184-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1241	126	438	0	ENST00000264010.4:c.1799G>C	p.Arg600Thr	p.R600T	ENST00000264010	NM_006565.3	600	aGa/aCa	10/12	1	2	FACETS	0.377	0.34	0.416	0.377	0.34	0.416	SUBCLONAL	1	FALSE	1	0.488976709580525	2		438	1367	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683503	29683503	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000184-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1399	96	376	0	ENST00000356175.3:c.7578G>C	p.Leu2526Phe	p.L2526F	ENST00000356175	NM_000267.3	2526	ttG/ttC	51/57	0.276849723722775	4	FACETS	0.391	0.347	0.439			1	INDETERMINATE	1	FALSE	NA	0.488976709580525	4		376	1495	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243698	41243698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000184-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1738	98	636	0	ENST00000357654.3:c.3850C>T	p.His1284Tyr	p.H1284Y	ENST00000357654	NM_007294.3	1284	Cac/Tac	10/23	0.144938445768128	2	FACETS	0.218	0.193	0.245	0.109	0.096	0.123	INDETERMINATE	1	FALSE	0	0.488976709580525	2		636	1836	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0000188-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	601	387	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.693062816154408	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.693062816154408	1		387	984	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685315	89685315	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1554897280	NA	P-0000188-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	224	419	0	ENST00000371953.3:c.209+1G>T		p.X70_splice	ENST00000371953	NM_000314.4	70			0.693062816154408	1	FACETS	0.994	0.94	1	0.994	0.94	1	CLONAL	1	TRUE	0	0.693062816154408	1		419	425	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0000188-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	407	446	0	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	0.672267335740276	2	FACETS	0.897	0.864	0.929	0.897	0.864	0.929	CLONAL	2	TRUE	0	0.693062816154408	2		446	655	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438565	52438565	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000188-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	461	381	0	ENST00000460680.1:c.1154del	p.Arg385GlnfsTer45	p.R385Qfs*45	ENST00000460680	NM_004656.3	385	cGa/ca	12/17	0.693062816154408	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.693062816154408	1		381	744	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192629	94192630	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs1245161888	NA	P-0000188-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	221	578	0	ENST00000323929.3:c.1444_1445del	p.Gln482AlafsTer4	p.Q482Afs*4	ENST00000323929	NM_005591.3	482	CAg/g	13/20	1	2	FACETS	0.545	0.506	0.585	0.545	0.506	0.585	SUBCLONAL	1	TRUE	1	0.693062816154408	2		578	1171	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0000189-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	293	473	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.144683645097098	3	FACETS	1	0.992	1	0.665	0.626	0.704	INDETERMINATE	1	FALSE	1	0.578207814629811	3		473	983	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374292	138374292	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000189-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	341	614	0	ENST00000289153.2:c.3152A>G	p.Glu1051Gly	p.E1051G	ENST00000289153	NM_006219.2	1051	gAa/gGa	22/22	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	FALSE	NA	0.578207814629811	2		614	1118	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434312	49434312	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000189-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	195	596	0	ENST00000301067.7:c.7241G>A	p.Ser2414Asn	p.S2414N	ENST00000301067	NM_003482.3	2414	aGt/aAt	31/54	0.144683645097098	3	FACETS	1	0.987	1	0.637	0.592	0.684	INDETERMINATE	1	FALSE	1	0.578207814629811	3		596	682	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151882675	151882675	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000197-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	74	341	1	ENST00000262189.6:c.5050A>C	p.Lys1684Gln	p.K1684Q	ENST00000262189	NM_170606.2	1684	Aaa/Caa	34/59	1	2	FACETS	0.835	0.728	0.95	0.835	0.728	0.95	CLONAL	1	FALSE	1	0.173861499512532	2		342	1020	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577587	7577587	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000197-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	51	318	0	ENST00000269305.4:c.694A>T	p.Ile232Phe	p.I232F	ENST00000269305	NM_001126112.2	232	Atc/Ttc	7/11	0.173861499512532	1	FACETS	0.861	0.731	1	0.861	0.731	1	CLONAL	1	FALSE	0	0.173861499512532	1		318	622	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756709	756709	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0000197-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1466	110	552	0	ENST00000314574.4:c.119C>G	p.Ser40Ter	p.S40*	ENST00000314574	NM_005433.3	40	tCa/tGa	2/12	1	2	FACETS	0.803	0.718	0.893	0.803	0.718	0.893	CLONAL	1	FALSE	1	0.173861499512532	2		552	1576	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777894	NA	P-0000208-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	192	575	0	ENST00000361445.4:c.6644C>T	p.Ser2215Phe	p.S2215F	ENST00000361445	NM_004958.3	2215	tCt/tTt	47/58	0.319986749731437	2	FACETS	0.906	0.836	0.979	0.453	0.418	0.49	CLONAL	1	TRUE	0	0.319986749731437	2		575	1325	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509386	46509386	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000208-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	204	472	0	ENST00000262741.5:c.1345G>A	p.Ala449Thr	p.A449T	ENST00000262741	NM_003629.3	449	Gcc/Acc	10/10	0.319986749731437	2	FACETS	1	0.961	1	0.53	0.49	0.571	CLONAL	1	TRUE	0	0.319986749731437	2		472	1204	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0000211-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	33	957	0	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	0.116417852962926	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		957	832	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0000212-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1502	136	450	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.977	0.885	1	0.977	0.885	1	CLONAL	1	TRUE	1	0.17	2		451	1638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0000212-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	116	542	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.3	2	FACETS	1	0.928	1			1	CLONAL	1	TRUE	NA	0.17	2		542	1312	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152244	99152245	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0000212-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1631	121	460	0	ENST00000074304.5:c.323_324del	p.Leu108HisfsTer13	p.L108Hfs*13	ENST00000074304	NM_001134224.1	108	cTT/c	6/26	1	2	FACETS	0.813	0.731	0.9	0.813	0.731	0.9	CLONAL	1	TRUE	1	0.17	2		460	1752	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713900	30713900	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000212-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	70	306	0	ENST00000295754.5:c.1225del	p.Ser409LeufsTer22	p.S409Lfs*22	ENST00000295754	NM_003242.5	409	Tct/ct	4/7	1	2	FACETS	0.709	0.616	0.81	0.709	0.616	0.81	SUBCLONAL	1	TRUE	1	0.17	2		306	1162	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0000216-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	84	140	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.398245944249352	3	FACETS	0.863	0.771	0.959	0.863	0.771	0.959	CLONAL	2	TRUE	1	0.398245944249352	3		142	293	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804950	43804950	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000216-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	157	272	0	ENST00000372470.3:c.400G>T	p.Ala134Ser	p.A134S	ENST00000372470	NM_005373.2	134	Gct/Tct	4/12	0.300203148855829	3	FACETS	1	0.988	1	0.483	0.443	0.523	CLONAL	1	TRUE	0	0.398245944249352	3		272	653	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527303	187527303	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774392890	NA	P-0000216-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	127	216	0	ENST00000441802.2:c.10271C>T	p.Thr3424Met	p.T3424M	ENST00000441802	NM_005245.3	3424	aCg/aTg	17/27	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.398245944249352	2		216	630	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751180	57751180	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000216-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	190	306	0	ENST00000274289.3:c.1687G>C	p.Glu563Gln	p.E563Q	ENST00000274289	NM_006622.3	563	Gag/Cag	12/14	0.398245944249352	5	FACETS	1	0.976	1			1	CLONAL	1	TRUE	NA	0.398245944249352	5		306	1337	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247514	123247514	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000216-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	192	449	0	ENST00000358487.5:c.1977G>C	p.Lys659Asn	p.K659N	ENST00000358487	NM_000141.4	659	aaG/aaC	14/18	0.398245944249352	2	FACETS	1	0.927	1	0.501	0.463	0.54	CLONAL	1	TRUE	0	0.398245944249352	2		449	962	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913476	NA	P-0000216-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	418	445	0	ENST00000358487.5:c.1647T>G	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaG	12/18	0.398245944249352	2	FACETS	0.983	0.938	1	0.983	0.938	1	CLONAL	2	TRUE	0	0.398245944249352	2		445	1068	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911530	32911530	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0000216-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	93	226	0	ENST00000380152.3:c.3038C>G	p.Ser1013Ter	p.S1013*	ENST00000380152		1013	tCa/tGa	11/27	0.213284263044604	4	FACETS	1	0.895	1	0.335	0.298	0.375	INDETERMINATE	1	TRUE	1	0.398245944249352	4		226	649	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591886	48591886	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000216-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	149	439	0	ENST00000342988.3:c.1049T>G	p.Val350Gly	p.V350G	ENST00000342988	NM_005359.5	350	gTt/gGt	9/12	NA	2	FACETS	1	0.945	1			1	INDETERMINATE	1	TRUE	NA	0.398245944249352	2		439	718	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59871055	59871055	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000216-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	57	460	0	ENST00000259008.2:c.1376G>C	p.Arg459Thr	p.R459T	ENST00000259008	NM_032043.2	459	aGa/aCa	10/20	NA	2	FACETS	0.326	0.279	0.378			1	INDETERMINATE	1	TRUE	NA	0.398245944249352	2		460	878	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87475990	87475990	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000218-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	80	518	0	ENST00000277120.3:c.1432A>G	p.Arg478Gly	p.R478G	ENST00000277120		478	Aga/Gga	13/19	1	2	FACETS	0.51	0.447	0.577	0.51	0.447	0.577	SUBCLONAL	1	TRUE	1	0.325269543899785	2		518	965	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891298	101891298	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000218-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	115	578	1	ENST00000374994.4:c.259G>A	p.Ala87Thr	p.A87T	ENST00000374994	NM_004612.2	87	Gca/Aca	2/9	1	2	FACETS	0.702	0.631	0.777	0.702	0.631	0.777	SUBCLONAL	1	TRUE	1	0.325269543899785	2		579	1007	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225145	53225145	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000218-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	170	817	0	ENST00000375401.3:c.3073G>A	p.Ala1025Thr	p.A1025T	ENST00000375401	NM_004187.3	1025	Gct/Act	20/26	0.325269543899785	1	FACETS	0.851	0.782	0.924	0.851	0.782	0.924	CLONAL	1	TRUE	0	0.325269543899785	1		817	1028	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0000221-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	369	276	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.245838883097442	3	FACETS	0.868	0.825	0.911	0.868	0.825	0.911	CLONAL	3	FALSE	0	0.310446388021726	3		276	1055	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0000231-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	46	289	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.0929354688307727	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		289	744	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0000234-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	54	169	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.254836639579576	4	FACETS	0.758	0.652	0.872	0.758	0.652	0.872	SUBCLONAL	2	TRUE	2	0.325435334327557	4		169	290	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0000234-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	148	259	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	0.254836639579576	4	FACETS	0.826	0.755	0.899	0.826	0.755	0.899	CLONAL	2	TRUE	2	0.325435334327557	4		259	730	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000234-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	58	207	0	ENST00000269305.4:c.715A>C	p.Asn239His	p.N239H	ENST00000269305	NM_001126112.2	239	Aac/Cac	7/11	0.246795418883961	2	FACETS	1	0.969	1	0.733	0.637	0.836	CLONAL	1	TRUE	0	0.325435334327557	2		207	243	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577550	+	frameshift_variant	Frame_Shift_Del	DEL	TGCCGC	TGCCGC	GGCGG	novel	NA	P-0000234-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	57	215	0	ENST00000269305.4:c.731_736delinsCCGCC	p.Gly244AlafsTer3	p.G244Afs*3	ENST00000269305	NM_001126112.2	244	gGCGGCAtg/gCCGCCtg	7/11	0.246795418883961	2	FACETS	1	0.97	1	0.742	0.644	0.846	CLONAL	1	TRUE	0	0.325435334327557	2		215	236	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0000269-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	77	495	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.345967231237703	4	FACETS	1	0.956	1	1	0.984	1	CLONAL	3	FALSE	2	0.512722762890303	4		496	139	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106829	27106829	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000269-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	191	187	0	ENST00000324856.7:c.6440T>C	p.Leu2147Ser	p.L2147S	ENST00000324856	NM_006015.4	2147	tTg/tCg	20/20	0.365386977314959	5	FACETS	1	0.987	1	1	0.995	1	CLONAL	5	FALSE	2	0.512722762890303	5		187	244	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0000269-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	90	405	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	0.414700152741316	5	FACETS	0.958	0.868	1			1	CLONAL	3	FALSE	NA	0.512722762890303	5		405	216	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106850	27106853	+	missense_variant	Missense_Mutation	ONP	TCCT	TCCT	CCCC	novel	NA	P-0000269-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	180	183	0	ENST00000324856.7:c.6461_6464delinsCCCC	p.Phe2154_Leu2155delinsSerPro	p.F2154_L2155delinsSP	ENST00000324856	NM_006015.4	2154	tTCCTc/tCCCCc	20/20	0.365386977314959	5	FACETS	1	0.982	1	1	0.994	1	CLONAL	5	FALSE	2	0.512722762890303	5		183	235	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52663002	52663002	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000275-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	141	576	0	ENST00000394830.3:c.1351G>C	p.Asp451His	p.D451H	ENST00000394830	NM_018313.4	451	Gat/Cat	13/30	0.590802756145326	1	FACETS	0.461	0.42	0.503	0.461	0.42	0.503	SUBCLONAL	1	TRUE	0	0.605363838296318	1		576	705	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118368760	118368760	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000275-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	138	358	0	ENST00000534358.1:c.5774A>G	p.His1925Arg	p.H1925R	ENST00000534358	NM_005933.3	1925	cAt/cGt	21/36	NA	2	FACETS	0.74	0.676	0.807			1	INDETERMINATE	1	TRUE	NA	0.605363838296318	2		358	616	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32971123	32971123	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000275-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	274	591	0	ENST00000380152.3:c.9590A>G	p.Asp3197Gly	p.D3197G	ENST00000380152		3197	gAc/gGc	26/27	NA	2	FACETS	0.915	0.86	0.972			1	INDETERMINATE	1	TRUE	NA	0.605363838296318	2		591	989	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0000275-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	284	474	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	1	2	FACETS	0.961	0.917	1	1	0.996	1	CLONAL	2	TRUE	1	0.605363838296318	2		474	488	SUCCESS
ATM	472	MSKCC	GRCh37	11	108127020	108127040	+	inframe_deletion	In_Frame_Del	DEL	ATAGCTGAAGAGGAAGCATAT	ATAGCTGAAGAGGAAGCATAT	-	novel	NA	P-0000275-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	58	601	0	ENST00000278616.4:c.2204_2224del	p.Ile735_Tyr741del	p.I735_Y741del	ENST00000278616	NM_000051.3	735	ATAGCTGAAGAGGAAGCATAT/-	14/63	1	2	FACETS	0.269	0.231	0.311	0.269	0.231	0.311	SUBCLONAL	1	TRUE	1	0.605363838296318	2		601	712	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000278-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	28	529	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	0.193	0.153	0.239	0.193	0.153	0.239	SUBCLONAL	1	TRUE	1	0.33	2		529	880	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437215	52437237	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCTGTCCGTGGCTTCCACGAC	CTGCTGTCCGTGGCTTCCACGAC	-	novel	NA	P-0000286-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	12	660	0	ENST00000460680.1:c.1807_1829del	p.Val603ArgfsTer32	p.V603Rfs*32	ENST00000460680	NM_004656.3	603	GTCGTGGAAGCCACGGACAGCAGa/a	14/17	1	2	FACETS	0.416	0.293	0.566	0.416	0.293	0.566	SUBCLONAL	1	TRUE	1	0.37	2		660	156	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005020	150005020	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000286-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	20	384	0	ENST00000253339.5:c.1205del	p.Asn402MetfsTer8	p.N402Mfs*8	ENST00000253339		402	aAt/at	3/7	1	2	FACETS	0.533	0.409	0.676	0.533	0.409	0.676	SUBCLONAL	1	TRUE	1	0.37	2		384	203	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0000295-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	34	495	1	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	0.17	2		496	359	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470953	25470953	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000295-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	33	376	0	ENST00000264709.3:c.808G>T	p.Gly270Trp	p.G270W	ENST00000264709	NM_175629.2	270	Ggg/Tgg	7/23	1	2	FACETS	0.799	0.65	0.967	0.799	0.65	0.967	CLONAL	1	TRUE	1	0.17	2		376	486	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736116	204736116	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000295-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	52	357	0	ENST00000302823.3:c.473C>G	p.Pro158Arg	p.P158R	ENST00000302823	NM_005214.4	158	cCa/cGa	3/4	1	2	FACETS	0.897	0.762	1	0.897	0.762	1	CLONAL	1	TRUE	1	0.17	2		357	682	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204914	128204914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750157738	NA	P-0000295-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	37	317	0	ENST00000341105.2:c.527C>T	p.Thr176Met	p.T176M	ENST00000341105	NM_032638.4	176	aCg/aTg	3/6	1	2	FACETS	0.963	0.794	1	0.963	0.794	1	CLONAL	1	TRUE	1	0.17	2		317	452	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053207	180053207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000295-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	29	271	0	ENST00000261937.6:c.1162G>A	p.Glu388Lys	p.E388K	ENST00000261937	NM_182925.4	388	Gag/Aag	9/30	1	2	FACETS	0.712	0.571	0.874	0.712	0.571	0.874	SUBCLONAL	1	TRUE	1	0.17	2		271	479	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056210	26056210	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000295-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	50	357	0	ENST00000343677.2:c.447G>T	p.Lys149Asn	p.K149N	ENST00000343677	NM_005319.3	149	aaG/aaT	1/1	1	2	FACETS	0.905	0.767	1	0.905	0.767	1	CLONAL	1	TRUE	1	0.17	2		357	650	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642534	117642534	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000295-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	40	539	0	ENST00000368508.3:c.5665C>G	p.Gln1889Glu	p.Q1889E	ENST00000368508	NM_002944.2	1889	Caa/Gaa	35/43	1	2	FACETS	0.631	0.523	0.752	0.631	0.523	0.752	SUBCLONAL	1	TRUE	1	0.17	2		539	746	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112553	115112553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000295-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	28	302	2	ENST00000257566.3:c.1187C>T	p.Ser396Phe	p.S396F	ENST00000257566	NM_016569.3	396	tCc/tTc	7/8	1	2	FACETS	0.711	0.568	0.876	0.711	0.568	0.876	SUBCLONAL	1	TRUE	1	0.17	2		304	463	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631693	90631693	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000295-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	29	315	0	ENST00000330062.3:c.576C>G	p.Phe192Leu	p.F192L	ENST00000330062	NM_002168.2	192	ttC/ttG	5/11	1	2	FACETS	0.698	0.559	0.856	0.698	0.559	0.856	SUBCLONAL	1	TRUE	1	0.17	2		315	489	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0000295-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	10	147	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	1	2	FACETS	0.514	0.347	0.723	0.514	0.347	0.723	SUBCLONAL	1	TRUE	1	0.17	2		147	229	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0000302-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	38	229	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	0.925	0.762	1	0.925	0.762	1	CLONAL	1	TRUE	1	0.1	2		229	822	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462563	29462563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1346365547	NA	P-0000307-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	115	268	0	ENST00000389048.3:c.2338G>A	p.Glu780Lys	p.E780K	ENST00000389048	NM_004304.4	780	Gag/Aag	13/29	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.314202673022527	2		268	534	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908839	101908839	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000307-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1301	73	451	0	ENST00000374994.4:c.1203C>G	p.Ile401Met	p.I401M	ENST00000374994	NM_004612.2	401	atC/atG	7/9	0.249996145873007	3	FACETS	0.391	0.341	0.447	0.13	0.113	0.149	SUBCLONAL	1	TRUE	0	0.314202673022527	3		451	1374	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438231	49438231	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000307-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	192	427	0	ENST00000301067.7:c.5038G>T	p.Glu1680Ter	p.E1680*	ENST00000301067	NM_003482.3	1680	Gag/Tag	20/54	0.254799090221874	4	FACETS	0.835	0.772	0.9			1	CLONAL	2	TRUE	NA	0.314202673022527	4		427	962	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443499	49443499	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369794887	NA	P-0000307-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	34	207	0	ENST00000301067.7:c.3872G>A	p.Arg1291Gln	p.R1291Q	ENST00000301067	NM_003482.3	1291	cGg/cAg	11/54	0.254799090221874	4	FACETS	0.562	0.459	0.679			1	SUBCLONAL	1	TRUE	NA	0.314202673022527	4		207	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000307-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	495	497	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.314202673022527	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.314202673022527	3		497	1086	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041563	47041563	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0000307-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	138	381	0	ENST00000377604.3:c.1788T>G	p.Tyr596Ter	p.Y596*	ENST00000377604	NM_001204468.1	596	taT/taG	17/24	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.314202673022527	NA		381	608	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303039	15303039	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000307-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	43	120	0	ENST00000263388.2:c.411del	p.Asp139MetfsTer97	p.D139Mfs*97	ENST00000263388	NM_000435.2	137	ggG/gg	4/33	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.314202673022527	2		120	213	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499342	89499342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000315-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	320	335	0	ENST00000336596.2:c.2512G>A	p.Asp838Asn	p.D838N	ENST00000336596	NM_005233.5	838	Gat/Aat	15/17	0.745407669914172	2	FACETS	0.958	0.923	0.992	0.958	0.923	0.992	CLONAL	2	TRUE	0	0.745407669914172	2		335	448	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968233	134968233	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000315-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	175	526	0	ENST00000398015.3:c.2746G>C	p.Val916Leu	p.V916L	ENST00000398015	NM_004441.4	916	Gtg/Ctg	15/16	0.713128252341116	5	FACETS	0.832	0.764	0.902			1	CLONAL	1	TRUE	NA	0.745407669914172	5		526	1196	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467863	66467863	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000315-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	425	477	0	ENST00000273854.3:c.406G>T	p.Asp136Tyr	p.D136Y	ENST00000273854	NM_004439.5	136	Gac/Tac	3/18	0.656396831721534	4	FACETS	0.974	0.931	1	0.974	0.931	1	CLONAL	2	TRUE	2	0.745407669914172	4		477	1022	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156669	106156669	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000315-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	364	340	0	ENST00000380013.4:c.1570G>T	p.Glu524Ter	p.E524*	ENST00000380013	NM_001127208.2	524	Gag/Tag	3/11	0.745407669914172	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.745407669914172	2		340	466	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630936	187630936	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000315-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	347	344	0	ENST00000441802.2:c.46C>T	p.Gln16Ter	p.Q16*	ENST00000441802	NM_005245.3	16	Caa/Taa	2/27	0.745407669914172	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.745407669914172	2		344	463	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294042	1294042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000315-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	303	532	0	ENST00000310581.5:c.959C>T	p.Pro320Leu	p.P320L	ENST00000310581	NM_198253.2	320	cCt/cTt	2/16	0.574906149055429	4	FACETS	0.952	0.903	1	0.952	0.903	1	CLONAL	2	TRUE	2	0.745407669914172	4		532	745	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004891	150004891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1392085429	NA	P-0000315-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	353	432	0	ENST00000253339.5:c.1334C>T	p.Pro445Leu	p.P445L	ENST00000253339		445	cCg/cTg	3/7	0.35233137604832	6	FACETS	0.951	0.905	0.997	0.951	0.905	0.997	INDETERMINATE	3	TRUE	3	0.745407669914172	6		432	827	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759418	133759418	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000315-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	927	708	0	ENST00000318560.5:c.1741G>C	p.Glu581Gln	p.E581Q	ENST00000318560	NM_005157.4	581	Gag/Cag	11/11	0.729613393333695	4	FACETS	0.974	0.958	0.99	0.974	0.958	0.99	CLONAL	4	TRUE	0	0.745407669914172	4		708	1114	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70432668	70432668	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000315-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	195	400	0	ENST00000373644.4:c.4690C>G	p.Gln1564Glu	p.Q1564E	ENST00000373644	NM_030625.2	1564	Caa/Gaa	8/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.745407669914172	2		400	470	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285670	46285670	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000315-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	225	447	0	ENST00000334344.6:c.5030G>T	p.Arg1677Leu	p.R1677L	ENST00000334344	NM_152641.2	1677	cGa/cTa	17/21	0.745407669914172	3	FACETS	0.937	0.874	1	0.469	0.437	0.501	CLONAL	1	TRUE	1	0.745407669914172	3		447	884	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435051	49435051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000315-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	75	173	0	ENST00000301067.7:c.6502C>T	p.Pro2168Ser	p.P2168S	ENST00000301067	NM_003482.3	2168	Ccc/Tcc	31/54	0.745407669914172	3	FACETS	1	0.902	1	0.51	0.452	0.57	CLONAL	1	TRUE	1	0.745407669914172	3		173	271	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923374	9923374	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000315-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	357	456	0	ENST00000330684.3:c.1913C>A	p.Ala638Asp	p.A638D	ENST00000330684	NM_001134407.1	638	gCt/gAt	9/13	0.608522912696991	4	FACETS	0.94	0.895	0.986			1	CLONAL	2	TRUE	NA	0.745407669914172	4		456	889	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579349	7579349	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1567555667	NA	P-0000315-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	241	374	0	ENST00000269305.4:c.338T>G	p.Phe113Cys	p.F113C	ENST00000269305	NM_001126112.2	113	tTc/tGc	4/11	NA	2	FACETS	0.983	0.943	1			1	INDETERMINATE	2	TRUE	NA	0.745407669914172	2		374	329	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216464	2216464	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs779346222	NA	P-0000315-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	243	344	0	ENST00000398665.3:c.2108A>T	p.His703Leu	p.H703L	ENST00000398665	NM_032482.2	703	cAc/cTc	20/28	0.323759986031644	5	FACETS	0.884	0.834	0.933	0.884	0.834	0.933	INDETERMINATE	3	TRUE	2	0.745407669914172	5		344	521	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39763596	39763596	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000315-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	351	390	0	ENST00000288319.7:c.856C>G	p.Gln286Glu	p.Q286E	ENST00000288319	NM_182918.3	286	Cag/Gag	8/10	0.745407669914172	3	FACETS	0.918	0.877	0.96	0.918	0.877	0.96	CLONAL	2	TRUE	1	0.745407669914172	3		390	704	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348205	70348205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000315-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	232	296	0	ENST00000374080.3:c.3269C>T	p.Ala1090Val	p.A1090V	ENST00000374080		1090	gCa/gTa	23/45	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.745407669914172	1		296	319	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953855	55953856	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0000315-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	168	416	0	ENST00000263923.4:c.3580_3581del	p.Leu1194AlafsTer15	p.L1194Afs*15	ENST00000263923	NM_002253.2	1194	CTg/g	27/30	0.656396831721534	4	FACETS	0.832	0.764	0.902	0.416	0.382	0.451	CLONAL	1	TRUE	2	0.745407669914172	4		416	946	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965470	90965470	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0000324-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	104	313	0	ENST00000265433.3:c.1845+2T>C		p.X615_splice	ENST00000265433	NM_002485.4	615			0.487558440569854	3	FACETS	0.968	0.87	1	0.484	0.435	0.536	CLONAL	1	TRUE	1	0.487558440569854	3		313	548	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726723	41726723	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000324-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	28	299	0	ENST00000301178.4:c.268G>A	p.Glu90Lys	p.E90K	ENST00000301178	NM_021913.4	90	Gag/Aag	2/20	1	2	FACETS	0.32	0.256	0.393	0.32	0.256	0.393	SUBCLONAL	1	TRUE	1	0.487558440569854	2		299	359	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552118	29552121	+	frameshift_variant	Frame_Shift_Del	DEL	AGAT	AGAT	-	novel	NA	P-0000324-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	54	282	0	ENST00000356175.3:c.1854_1857del	p.Asp618GlufsTer12	p.D618Efs*12	ENST00000356175	NM_000267.3	617	gcAGAT/gc	17/57	0.465386962834965	1	FACETS	0.566	0.487	0.651	0.566	0.487	0.651	SUBCLONAL	1	TRUE	0	0.487558440569854	1		282	296	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436624	52436624	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs387906848	NA	P-0000332-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	283	77	210	0	ENST00000460680.1:c.2050C>T	p.Gln684Ter	p.Q684*	ENST00000460680	NM_004656.3	684	Cag/Tag	16/17	0.185916258794013	6	FACETS	1	0.92	1	1	0.92	1	CLONAL	3	TRUE	3	0.185916258794013	6		210	360	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005717	150005717	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000332-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	112	33	109	0	ENST00000253339.5:c.508C>T	p.Gln170Ter	p.Q170*	ENST00000253339		170	Caa/Taa	3/7	0.185916258794013	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	2	TRUE	0	0.185916258794013	2		109	145	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579310	7579310	+	splice_donor_variant	Splice_Site	SNP	A	A	C	rs1555526469	NA	P-0000335-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	215	325	0	ENST00000269305.4:c.375+2T>G		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.660726581498721	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.660726581498721	1		325	419	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444452	50444452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000335-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	180	167	0	ENST00000331340.3:c.382G>A	p.Gly128Arg	p.G128R	ENST00000331340	NM_006060.4	128	Ggg/Agg	4/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.660726581498721	2		167	481	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656963	47656963	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs751249745	NA	P-0000355-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	181	348	0	ENST00000233146.2:c.1159C>G	p.Leu387Val	p.L387V	ENST00000233146	NM_000251.2	387	Ctt/Gtt	7/16	0.874082531736897	1	FACETS	0.449	0.417	0.482	0.449	0.417	0.482	SUBCLONAL	1	TRUE	0	0.874082531736897	1		348	519	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786037	3786037	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000355-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	333	445	0	ENST00000262367.5:c.4728G>T	p.Glu1576Asp	p.E1576D	ENST00000262367	NM_004380.2	1576	gaG/gaT	28/31	NA	2	FACETS	1	0.972	1			1	INDETERMINATE	1	TRUE	NA	0.874082531736897	2		445	740	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691025	NA	P-0000355-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	311	284	0	ENST00000269305.4:c.785G>T	p.Gly262Val	p.G262V	ENST00000269305	NM_001126112.2	262	gGt/gTt	8/11	0.874082531736897	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.874082531736897	1		284	376	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937744	76937745	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0000355-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	857	554	0	ENST00000373344.5:c.3003_3004del	p.Lys1001AsnfsTer3	p.K1001Nfs*3	ENST00000373344	NM_000489.3	1001	aaAGta/aata	9/35	0.252448911626932	1	FACETS	0.584	0.566	0.602	0.584	0.566	0.602	INDETERMINATE	1	TRUE	0	0.874082531736897	1		554	1891	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0000359-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	151	278	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	1	2	FACETS	0.597	0.547	0.65	0.597	0.547	0.65	SUBCLONAL	1	TRUE	1	0.69	2		278	733	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0000367-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	391	396	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	NA	2	FACETS	0.832	0.794	0.871			1	INDETERMINATE	2	TRUE	NA	0.487790964195185	2		396	963	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0000367-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	292	717	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.488076802458706	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.487790964195185	2		718	532	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696708	47696708	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000367-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	296	537	0	ENST00000347630.2:c.240C>G	p.Ser80Arg	p.S80R	ENST00000347630	NM_001007230.1	80	agC/agG	5/11	0.382299014352146	4	FACETS	0.823	0.775	0.872			1	CLONAL	2	TRUE	NA	0.487790964195185	4		537	1097	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157499	106157499	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000376-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	49	285	0	ENST00000380013.4:c.2400T>A	p.His800Gln	p.H800Q	ENST00000380013	NM_001127208.2	800	caT/caA	3/11	0.227592239040887	2	FACETS	0.683	0.58	0.796	0.341	0.29	0.398	SUBCLONAL	1	TRUE	0	0.364269248263579	2		285	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578287	7578287	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000376-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	78	394	0	ENST00000269305.4:c.562del	p.Leu188TrpfsTer59	p.L188Wfs*59	ENST00000269305	NM_001126112.2	188	Ctg/tg	6/11	0.308197851408404	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.364269248263579	1		394	313	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532897	187532897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774126688	NA	P-0000392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	52	247	0	ENST00000441802.2:c.9496G>A	p.Asp3166Asn	p.D3166N	ENST00000441802	NM_005245.3	3166	Gac/Aac	14/27	NA	2	FACETS	0.488	0.414	0.57			1	INDETERMINATE	1	FALSE	NA	0.237853938225444	2		247	896	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578532	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	19	163	0	ENST00000269305.4:c.398T>G	p.Met133Arg	p.M133R	ENST00000269305	NM_001126112.2	133	aTg/aGg	5/11	1	2	FACETS	0.401	0.304	0.517	0.401	0.304	0.517	SUBCLONAL	1	FALSE	1	0.237853938225444	2		163	398	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195125	123195125	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1275	81	327	0	ENST00000218089.9:c.1468G>T	p.Glu490Ter	p.E490*	ENST00000218089	NM_001042749.1	490	Gag/Tag	16/35	NA	2	FACETS	0.502	0.441	0.569			1	INDETERMINATE	1	FALSE	NA	0.237853938225444	2		327	1356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0000398-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	72	276	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.334594927521037	3	FACETS	1	0.967	1	0.658	0.578	0.743	CLONAL	1	FALSE	1	0.334594927521037	3		276	382	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198226	185198226	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770105218	NA	P-0000398-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	40	349	0	ENST00000265026.3:c.2708C>T	p.Ser903Leu	p.S903L	ENST00000265026	NM_004721.4	903	tCg/tTg	13/14	0.334594927521037	6	FACETS	0.726	0.602	0.863			1	SUBCLONAL	1	FALSE	NA	0.334594927521037	6		349	550	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0000404-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	189	396	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.342484083444178	3	FACETS	0.761	0.702	0.821	0.761	0.702	0.821	SUBCLONAL	2	TRUE	1	0.26	3		396	1080	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0000404-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	72	227	2	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	0.120060371577865	3	FACETS	0.808	0.705	0.919	0.404	0.352	0.46	INDETERMINATE	1	TRUE	1	0.26	3		229	775	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248357	212248357	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879163362	NA	P-0000404-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	114	273	0	ENST00000342788.4:c.3910C>T	p.Arg1304Trp	p.R1304W	ENST00000342788	NM_005235.2	1304	Cgg/Tgg	28/28	0.283622077349881	3	FACETS	1	0.976	1	0.642	0.578	0.709	CLONAL	1	TRUE	1	0.26	3		273	772	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928068	178928068	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000404-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	83	267	0	ENST00000263967.3:c.1346C>G	p.Pro449Arg	p.P449R	ENST00000263967	NM_006218.2	449	cCt/cGt	8/21	0.120060371577865	3	FACETS	0.88	0.775	0.992	0.44	0.387	0.496	INDETERMINATE	1	TRUE	1	0.26	3		267	820	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679733	30679733	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000404-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	68	416	0	ENST00000376406.3:c.1986G>C	p.Gln662His	p.Q662H	ENST00000376406	NM_014641.2	662	caG/caC	5/15	0.283622077349881	4	FACETS	0.73	0.633	0.835	0.365	0.316	0.418	SUBCLONAL	1	TRUE	2	0.26	4		416	903	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711885	89711885	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000404-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	88	274	0	ENST00000371953.3:c.504del	p.Ser170ValfsTer13	p.S170Vfs*13	ENST00000371953	NM_000314.4	168	aTt/at	6/9	0.3	4	FACETS	1	0.892	1			1	CLONAL	1	TRUE	NA	0.26	4		274	846	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023212	27023229	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGGGCCCTAGGCCCGC	CGCGGGCCCTAGGCCCGC	A	novel	NA	P-0000404-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	37	170	0	ENST00000324856.7:c.318_335delinsA	p.Asn106LysfsTer5	p.N106Kfs*5	ENST00000324856	NM_006015.4	106	aaCGCGGGCCCTAGGCCCGCc/aaAc	1/20	0.283622077349881	3	FACETS	1	0.905	1	0.572	0.474	0.681	CLONAL	1	TRUE	1	0.26	3		170	281	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303249	11303249	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000405-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	67	440	0	ENST00000361445.4:c.1334G>C	p.Arg445Thr	p.R445T	ENST00000361445	NM_004958.3	445	aGg/aCg	9/58	0.237534065173607	1	FACETS	0.614	0.532	0.702	0.614	0.532	0.702	SUBCLONAL	1	TRUE	0	0.237534065173607	1		440	810	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248471	212248471	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000405-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	89	567	0	ENST00000342788.4:c.3796T>C	p.Tyr1266His	p.Y1266H	ENST00000342788	NM_005235.2	1266	Tat/Cat	28/28	1	2	FACETS	0.617	0.545	0.695	0.617	0.545	0.695	SUBCLONAL	1	TRUE	1	0.237534065173607	2		567	1214	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356415	66356415	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000405-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	56	305	0	ENST00000273854.3:c.1082C>A	p.Pro361His	p.P361H	ENST00000273854	NM_004439.5	361	cCt/cAt	5/18	1	2	FACETS	0.676	0.578	0.783	0.676	0.578	0.783	SUBCLONAL	1	TRUE	1	0.237534065173607	2		305	698	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542810	187542810	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000405-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	67	533	0	ENST00000441802.2:c.4930A>G	p.Ser1644Gly	p.S1644G	ENST00000441802	NM_005245.3	1644	Agt/Ggt	10/27	NA	2	FACETS	0.465	0.403	0.534			1	INDETERMINATE	1	TRUE	NA	0.237534065173607	2		533	1212	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628452	187628452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000405-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	64	521	0	ENST00000441802.2:c.2530G>A	p.Val844Ile	p.V844I	ENST00000441802	NM_005245.3	844	Gtt/Att	2/27	NA	2	FACETS	0.619	0.534	0.711			1	INDETERMINATE	1	TRUE	NA	0.237534065173607	2		521	871	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331980	81331980	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000405-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	162	428	0	ENST00000222390.5:c.2104C>G	p.Arg702Gly	p.R702G	ENST00000222390	NM_000601.4	702	Cgt/Ggt	18/18	NA	2	FACETS	1	0.954	1			1	INDETERMINATE	1	TRUE	NA	0.237534065173607	2		428	1282	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737591	145737591	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs375297971	NA	P-0000405-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	90	435	0	ENST00000428558.2:c.3172C>G	p.Arg1058Gly	p.R1058G	ENST00000428558	NM_004260.3	1058	Cgt/Ggt	19/22	0.237534065173607	3	FACETS	1	0.977	1	0.703	0.625	0.786	CLONAL	1	TRUE	1	0.237534065173607	3		435	603	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517883	8517883	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000405-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1230	113	574	0	ENST00000356435.5:c.1508T>A	p.Leu503His	p.L503H	ENST00000356435		503	cTt/cAt	10/35	1	2	FACETS	0.708	0.635	0.786	0.708	0.635	0.786	SUBCLONAL	1	TRUE	1	0.237534065173607	2		574	1343	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434487	110434487	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000405-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	51	435	0	ENST00000375856.3:c.3914G>T	p.Gly1305Val	p.G1305V	ENST00000375856	NM_003749.2	1305	gGg/gTg	1/2	1	2	FACETS	0.668	0.567	0.779	0.668	0.567	0.779	SUBCLONAL	1	TRUE	1	0.237534065173607	2		435	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0000405-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	61	554	0	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.237534065173607	1	FACETS	0.651	0.561	0.75	0.651	0.561	0.75	SUBCLONAL	1	TRUE	0	0.237534065173607	1		554	695	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795484	42795484	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000405-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	45	416	0	ENST00000575354.2:c.2564G>T	p.Gly855Val	p.G855V	ENST00000575354	NM_015125.3	855	gGc/gTc	10/20	0.185792480154146	0	FACETS	0.645	0.542	0.758			1	SUBCLONAL	1	TRUE	0	0.237534065173607	0		416	448	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032866	30032866	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587776562	NA	P-0000405-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	41	306	0	ENST00000338641.4:c.240+1G>T		p.X80_splice	ENST00000338641	NM_000268.3	80			0.237534065173607	1	FACETS	0.546	0.454	0.649	0.546	0.454	0.649	SUBCLONAL	1	TRUE	0	0.237534065173607	1		306	557	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141498	11141498	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000405-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	51	603	0	ENST00000358026.2:c.3480del	p.Leu1161SerfsTer3	p.L1161Sfs*3	ENST00000358026	NM_001128849.1	1159	Ggg/gg	25/36	0.225449979304984	0	FACETS	0.486	0.413	0.568			1	SUBCLONAL	1	TRUE	0	0.237534065173607	0		603	673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0000413-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	18	351	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.286	0.214	0.37	0.286	0.214	0.37	SUBCLONAL	1	TRUE	1	0.33	2		351	382	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637999	176637999	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000417-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	60	238	0	ENST00000439151.2:c.2599C>T	p.Leu867Phe	p.L867F	ENST00000439151	NM_022455.4	867	Ctc/Ttc	5/23	0.178815635703865	3	FACETS	1	0.964	1	0.692	0.597	0.796	CLONAL	1	TRUE	1	0.178168127059226	3		238	530	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873789	151873789	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000417-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	50	258	0	ENST00000262189.6:c.8749G>T	p.Val2917Phe	p.V2917F	ENST00000262189	NM_170606.2	2917	Gtt/Ttt	38/59	0.178815635703865	3	FACETS	1	0.881	1	0.522	0.443	0.61	CLONAL	1	TRUE	1	0.178168127059226	3		258	585	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430840	47430840	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000417-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	53	511	0	ENST00000377045.4:c.1805C>A	p.Ala602Asp	p.A602D	ENST00000377045	NM_001654.4	602	gCc/gAc	16/16	0.178815635703865	1	FACETS	0.687	0.584	0.8	0.687	0.584	0.8	SUBCLONAL	1	TRUE	0	0.178168127059226	1		511	789	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511676	66511676	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000417-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	109	147	0	ENST00000358598.2:c.138del	p.Met47TrpfsTer82	p.M47Wfs*82	ENST00000358598	NM_212471.2	46	Ccc/cc	2/11	0.178815635703865	3	FACETS	0.983	0.888	1	1	0.983	1	CLONAL	3	TRUE	1	0.178168127059226	3		147	452	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809564	36809564	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	84	206	0	ENST00000373129.3:c.901G>A	p.Glu301Lys	p.E301K	ENST00000373129	NM_032017.1	301	Gag/Aag	10/12	0.132547391000648	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.216880671246854	3		206	362	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0000436-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	314	493	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.336228884127	NA		494	666	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632730	23632730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1220966608	NA	P-0000436-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	120	331	0	ENST00000261584.4:c.3066G>A	p.Met1022Ile	p.M1022I	ENST00000261584	NM_024675.3	1022	atG/atA	10/13	0.106018231552279	4	FACETS	0.795	0.72	0.874	0.795	0.72	0.874	INDETERMINATE	2	TRUE	2	0.336228884127	4		331	600	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584560	48584560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000436-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	183	275	0	ENST00000342988.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000342988	NM_005359.5	245	Cag/Tag	6/12	0.215464775285918	3	FACETS	0.943	0.874	1	0.629	0.582	0.677	CLONAL	2	TRUE	0	0.336228884127	3		275	674	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845391	76845391	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000436-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	64	457	0	ENST00000373344.5:c.6130C>T	p.Leu2044Phe	p.L2044F	ENST00000373344	NM_000489.3	2044	Ctc/Ttc	27/35	NA	2	FACETS	0.416	0.359	0.478			1	INDETERMINATE	1	TRUE	NA	0.336228884127	2		457	915	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0000445-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	161	229	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.896	0.824	0.972	0.896	0.824	0.972	CLONAL	1	FALSE	1	0.484271018022039	2		229	742	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739111	46739111	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs372225086	NA	P-0000445-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	251	608	0	ENST00000371975.4:c.1460C>G	p.Ser487Cys	p.S487C	ENST00000371975	NM_003579.3	487	tCt/tGt	13/18	1	2	FACETS	0.933	0.872	0.995	0.933	0.872	0.995	CLONAL	1	FALSE	1	0.484271018022039	2		608	1111	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0000446-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	269	449	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.3220583074586	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.38584494926581	1		449	836	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020768	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs926053251	NA	P-0000446-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	128	333	0	ENST00000358127.4:c.77T>G	p.Val26Gly	p.V26G	ENST00000358127	NM_001280556.1	26	gTt/gGt	2/10	1	2	FACETS	0.816	0.74	0.897	0.816	0.74	0.897	CLONAL	1	TRUE	1	0.38584494926581	2		333	813	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102199	27102199	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0000446-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	308	288	0	ENST00000324856.7:c.5124+1G>A		p.X1708_splice	ENST00000324856	NM_006015.4	1708			0.361205495254929	2	FACETS	0.975	0.923	1	0.975	0.923	1	CLONAL	2	TRUE	0	0.38584494926581	2		288	819	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508983	106508983	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000446-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	145	191	0	ENST00000359195.3:c.977T>C	p.Val326Ala	p.V326A	ENST00000359195	NM_002649.2	326	gTg/gCg	2/11	0.349389262741723	3	FACETS	1	0.985	1	0.676	0.618	0.736	CLONAL	1	TRUE	1	0.38584494926581	3		191	663	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215633997	215633999	+	missense_variant	Missense_Mutation	TNP	TTC	TTC	CTT	novel	NA	P-0000446-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	115	405	0	ENST00000260947.4:c.1352_1354delinsAAG	p.Gly451_Ser452delinsGluGly	p.G451_S452delinsEG	ENST00000260947	NM_000465.2	451	gGAAgt/gAAGgt	5/11	0.358664637633796	3	FACETS	0.643	0.578	0.712	0.214	0.192	0.238	SUBCLONAL	1	TRUE	0	0.38584494926581	3		405	1106	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0000455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	137	153	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.566734316681878	2	FACETS	0.853	0.794	0.911	0.853	0.794	0.911	CLONAL	2	TRUE	0	0.629999754334029	2		153	255	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176536	142176536	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	76	567	0	ENST00000350721.4:c.7565G>T	p.Gly2522Val	p.G2522V	ENST00000350721	NM_001184.3	2522	gGa/gTa	45/47	0.351215795998191	5	FACETS	0.884	0.777	0.999	0.295	0.259	0.333	INDETERMINATE	1	TRUE	2	0.629999754334029	5		567	531	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236696	236696	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143798161	NA	P-0000455-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	20	177	0	ENST00000264932.6:c.1414G>A	p.Glu472Lys	p.E472K	ENST00000264932	NM_004168.2	472	Gaa/Aaa	10/15	0.629999754334029	3	FACETS	0.663	0.513	0.833	0.331	0.256	0.417	SUBCLONAL	1	TRUE	1	0.629999754334029	3		177	126	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0000463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	481	493	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	2	TRUE	NA	0.674411910097263	2		494	633	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397745	49397745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	491	559	0	ENST00000418115.1:c.479C>T	p.Ser160Leu	p.S160L	ENST00000418115	NM_001664.2	160	tCa/tTa	5/5	NA	2	FACETS	0.941	0.91	0.971			1	INDETERMINATE	2	TRUE	NA	0.674411910097263	2		559	774	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977919	134977919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	442	440	0	ENST00000398015.3:c.2912C>T	p.Ser971Phe	p.S971F	ENST00000398015	NM_004441.4	971	tCt/tTt	16/16	0.674411910097263	6	FACETS	0.883	0.844	0.923	0.53	0.506	0.554	CLONAL	3	TRUE	1	0.674411910097263	6		440	1162	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594218	55594218	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1560418381	NA	P-0000463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	224	399	0	ENST00000288135.5:c.1921C>A	p.Leu641Ile	p.L641I	ENST00000288135	NM_000222.2	641	Ctc/Atc	13/21	0.366560178494051	3	FACETS	1	0.988	1	0.627	0.587	0.669	INDETERMINATE	1	TRUE	1	0.674411910097263	3		399	708	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163720	32163720	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253487294	NA	P-0000463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	129	304	0	ENST00000375023.3:c.5506G>A	p.Glu1836Lys	p.E1836K	ENST00000375023	NM_004557.3	1836	Gag/Aag	30/30	0.54999064848109	5	FACETS	1	0.935	1	0.682	0.625	0.741	CLONAL	2	TRUE	2	0.674411910097263	5		304	376	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790748	89790748	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	546	779	0	ENST00000336032.3:c.135C>G	p.Ile45Met	p.I45M	ENST00000336032	NM_006813.2	45	atC/atG	1/2	0.54999064848109	5	FACETS	0.945	0.91	0.98	0.945	0.91	0.98	CLONAL	3	TRUE	2	0.674411910097263	5		779	1149	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072624	5072624	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	306	209	0	ENST00000381652.3:c.1774G>A	p.Glu592Lys	p.E592K	ENST00000381652	NM_004972.3	592	Gag/Aag	13/25	0.646587843565398	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.674411910097263	2		209	439	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106035	8106035	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	215	261	0	ENST00000346208.3:c.855C>A	p.Asn285Lys	p.N285K	ENST00000346208		285	aaC/aaA	4/6	0.50253525850316	3	FACETS	1	0.959	1			1	CLONAL	2	TRUE	NA	0.674411910097263	3		261	418	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40367034	40367043	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCCGTGGA	GCGCCGTGGA	-	novel	NA	P-0000463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	190	655	0	ENST00000397332.2:c.154_163del	p.Ser52ProfsTer85	p.S52Pfs*85	ENST00000397332	NM_001033082.2	52	TCCACGGCGCcc/cc	2/3	0.362200774198171	4	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.674411910097263	4		655	680	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098969	178098970	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0000463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	716	385	0	ENST00000397062.3:c.75_76delinsAA	p.Gln26Lys	p.Q26K	ENST00000397062	NM_006164.4	25	agGCaa/agAAaa	2/5	0.66005560881937	5	FACETS	1	0.995	1			1	CLONAL	3	TRUE	NA	0.674411910097263	5		385	1261	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0000465-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	618	290	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.3	6	FACETS	0.969	0.938	1	1	0.997	1	CLONAL	8	TRUE	1	0.2	6		290	1116	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000465-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	254	200	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	1	2	FACETS	1	0.965	1	1	0.996	1	CLONAL	4	TRUE	1	0.2	2		200	616	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720670	89720670	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786204875	NA	P-0000473-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	22	83	0	ENST00000371953.3:c.821G>A	p.Trp274Ter	p.W274*	ENST00000371953	NM_000314.4	274	tGg/tAg	8/9	0.241646352145586	2	FACETS	1	0.923	1	0.74	0.582	0.919	CLONAL	1	TRUE	0	0.241646352145586	2		83	123	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578202	7578202	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057520004	NA	P-0000473-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	97	745	0	ENST00000269305.4:c.647T>A	p.Val216Glu	p.V216E	ENST00000269305	NM_001126112.2	216	gTg/gAg	6/11	0.233263575531148	2	FACETS	1	0.954	1	0.565	0.503	0.63	CLONAL	1	TRUE	0	0.241646352145586	2		745	711	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845405	42845405	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000473-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	178	373	0	ENST00000398585.3:c.857A>G	p.Asn286Ser	p.N286S	ENST00000398585	NM_001135099.1	286	aAc/aGc	9/14	0.241646352145586	5	FACETS	1	0.953	1	0.826	0.768	0.885	CLONAL	4	TRUE	0	0.241646352145586	5		373	486	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123156482	123156482	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000473-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1461	127	785	0	ENST00000218089.9:c.5T>A	p.Ile2Lys	p.I2K	ENST00000218089	NM_001042749.1	2	aTa/aAa	3/35	0.202525679390682	3	FACETS	0.742	0.669	0.819	0.371	0.334	0.41	SUBCLONAL	1	TRUE	1	0.241646352145586	3		785	1588	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978342	2978342	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000482-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	127	365	0	ENST00000396946.4:c.988G>T	p.Ala330Ser	p.A330S	ENST00000396946	NM_032415.4	330	Gcc/Tcc	7/25	0.330864525951222	1	FACETS	0.685	0.622	0.75	0.685	0.622	0.75	SUBCLONAL	1	TRUE	0	0.479496882125822	1		365	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577115	7577115	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519983	NA	P-0000482-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	210	533	0	ENST00000269305.4:c.823T>C	p.Cys275Arg	p.C275R	ENST00000269305	NM_001126112.2	275	Tgt/Cgt	8/11	0.471621138358321	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.479496882125822	1		533	602	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939062	76939065	+	frameshift_variant	Frame_Shift_Del	DEL	TTTT	TTTT	-	novel	NA	P-0000482-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	358	612	0	ENST00000373344.5:c.1683_1686del	p.Lys562Ter	p.K562*	ENST00000373344	NM_000489.3	561	gtAAAA/gt	9/35	0.246121160763383	1	FACETS	0.775	0.733	0.818	0.775	0.733	0.818	INDETERMINATE	1	TRUE	0	0.479496882125822	1		612	1465	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099799	157099799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375160616	NA	P-0000483-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	16	242	0	ENST00000346085.5:c.736G>A	p.Gly246Ser	p.G246S	ENST00000346085	NM_020732.3	246	Ggc/Agc	1/20	1	2	FACETS	0.33	0.243	0.433	0.33	0.243	0.433	SUBCLONAL	1	FALSE	1	0.331197347161262	2		242	293	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405998	70405998	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000483-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	72	471	0	ENST00000373644.4:c.3512A>T	p.Asn1171Ile	p.N1171I	ENST00000373644	NM_030625.2	1171	aAt/aTt	4/12	0.289853072156862	3	FACETS	0.63	0.55	0.718	0.315	0.275	0.359	SUBCLONAL	1	FALSE	1	0.331197347161262	3		471	804	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871790	12871799	+	frameshift_variant	Frame_Shift_Del	DEL	AACAGAAGAA	AACAGAAGAA	-	novel	NA	P-0000483-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	95	230	0	ENST00000228872.4:c.509_518del	p.Thr170MetfsTer52	p.T170Mfs*52	ENST00000228872	NM_004064.3	169	agAACAGAAGAA/ag	2/3	0.331197347161262	7	FACETS	0.758	0.675	0.846			1	SUBCLONAL	2	FALSE	NA	0.331197347161262	7		230	692	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0000489-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	17	140	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.757	0.584	0.947	0.757	0.584	0.947	CLONAL	1	TRUE	1	0.774445395495925	2		142	58	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000489-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	42	332	0	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	0.259348296144181	1	FACETS	0.511	0.437	0.59	0.511	0.437	0.59	INDETERMINATE	1	TRUE	0	0.774445395495925	1		332	130	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217302	11217302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000501-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	103	472	0	ENST00000361445.4:c.4376C>A	p.Ala1459Asp	p.A1459D	ENST00000361445	NM_004958.3	1459	gCc/gAc	30/58	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		472	1059	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17371320	17371320	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs74315370	NA	P-0000501-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	128	527	0	ENST00000375499.3:c.136C>T	p.Arg46Ter	p.R46*	ENST00000375499	NM_003000.2	46	Cga/Tga	2/8	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		527	1198	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0000502-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	121	717	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.326662709824975	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	0	0.326662709824975	1		718	583	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0000502-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	94	140	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.239952301528627	4	FACETS	0.896	0.802	0.995	0.896	0.802	0.995	CLONAL	2	FALSE	2	0.326662709824975	4		142	426	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0000502-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	32	251	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	FALSE	1	0.326662709824975	2		251	153	SUCCESS
ATM	472	MSKCC	GRCh37	11	108137949	108137949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879189597	NA	P-0000502-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	43	410	0	ENST00000278616.4:c.2518G>A	p.Asp840Asn	p.D840N	ENST00000278616	NM_000051.3	840	Gat/Aat	17/63	0.282924266428229	1	FACETS	0.336	0.281	0.398	0.336	0.281	0.398	SUBCLONAL	1	FALSE	0	0.326662709824975	1		410	655	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144080	11144080	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000502-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	82	430	0	ENST00000358026.2:c.3661A>G	p.Lys1221Glu	p.K1221E	ENST00000358026	NM_001128849.1	1221	Aag/Gag	26/36	0.122734612988954	0	FACETS	0.644	0.569	0.724			1	INDETERMINATE	1	FALSE	0	0.326662709824975	0		430	525	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039422	47039422	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000502-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	97	271	0	ENST00000377604.3:c.1045C>T	p.Gln349Ter	p.Q349*	ENST00000377604	NM_001204468.1	349	Cag/Tag	10/24	1	1	FACETS	0.789	0.711	0.869	1	0.984	1	SUBCLONAL	2	FALSE	0	0.326662709824975	1		271	315	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220444	1220444	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131690939	NA	P-0000502-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	80	608	0	ENST00000326873.7:c.540del	p.Asn181ThrfsTer106	p.N181Tfs*106	ENST00000326873	NM_000455.4	179	ccG/cc	4/10	0.321207261590253	0	FACETS	0.758	0.67	0.852			1	SUBCLONAL	1	FALSE	0	0.326662709824975	0		608	435	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918596	44918597	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0000502-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	191	371	0	ENST00000377967.4:c.1083_1084del	p.Tyr362Ter	p.Y362*	ENST00000377967	NM_021140.2	360	aCT/a	12/29	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	0	0.326662709824975	1		371	704	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402765	139402765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1386494518	NA	P-0000510-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	335	240	0	ENST00000277541.6:c.3244C>T	p.Arg1082Cys	p.R1082C	ENST00000277541	NM_017617.3	1082	Cgc/Tgc	20/34	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		240	709	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412646	139412646	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000510-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	237	265	0	ENST00000277541.6:c.1198T>G	p.Cys400Gly	p.C400G	ENST00000277541	NM_017617.3	400	Tgc/Ggc	7/34	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		265	629	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0000517-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	322	444	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	2	TRUE	NA	0.849835205495757	2		444	371	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105679	27105679	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000517-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	128	340	0	ENST00000324856.7:c.5290G>T	p.Glu1764Ter	p.E1764*	ENST00000324856	NM_006015.4	1764	Gaa/Taa	20/20	NA	2	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.849835205495757	2		340	284	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166241	118166241	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769480797	NA	P-0000517-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	56	334	0	ENST00000369448.3:c.751C>T	p.Leu251Phe	p.L251F	ENST00000369448	NM_017709.3	251	Ctt/Ttt	2/2	0.849835205495757	3	FACETS	0.508	0.436	0.584	0.254	0.218	0.292	SUBCLONAL	1	TRUE	1	0.849835205495757	3		334	370	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027086	48027086	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0000517-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	173	414	0	ENST00000234420.5:c.1964T>A	p.Leu655Ter	p.L655*	ENST00000234420	NM_000179.2	655	tTa/tAa	4/10	0.569438849109613	4	FACETS	1	0.983	1	0.404	0.374	0.436	CLONAL	1	TRUE	1	0.849835205495757	4		414	621	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504308	8504308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000517-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	192	417	0	ENST00000356435.5:c.1775G>A	p.Gly592Asp	p.G592D	ENST00000356435		592	gGc/gAc	12/35	0.643131471922079	5	FACETS	1	0.979	1	0.386	0.357	0.416	CLONAL	1	TRUE	2	0.849835205495757	5		417	888	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482611	56482611	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000517-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	159	473	0	ENST00000267101.3:c.1068G>T	p.Lys356Asn	p.K356N	ENST00000267101	NM_001982.3	356	aaG/aaT	9/28	0.569438849109613	4	FACETS	1	0.976	1	0.385	0.354	0.416	CLONAL	1	TRUE	1	0.849835205495757	4		473	600	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845625	68845625	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660645	NA	P-0000517-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	88	454	0	ENST00000261769.5:c.871G>T	p.Asp291Tyr	p.D291Y	ENST00000261769	NM_004360.3	291	Gat/Tat	7/16	NA	2	FACETS	0.62	0.554	0.689			1	INDETERMINATE	1	TRUE	NA	0.849835205495757	2		454	334	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78923303	78923303	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000517-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	125	459	0	ENST00000306801.3:c.3326T>A	p.Val1109Glu	p.V1109E	ENST00000306801	NM_020761.2	1109	gTg/gAg	28/34	0.833462771345059	3	FACETS	0.886	0.807	0.968	0.295	0.269	0.323	CLONAL	1	TRUE	0	0.849835205495757	3		459	473	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39713159	39713159	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000517-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	73	217	0	ENST00000361337.2:c.565G>A	p.Asp189Asn	p.D189N	ENST00000361337	NM_003286.2	189	Gat/Aat	8/21	0.704231652209223	5	FACETS	0.588	0.514	0.667			1	SUBCLONAL	1	TRUE	NA	0.849835205495757	5		217	665	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716210	52716215	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CTCGGT	CTCGGT	-	novel	NA	P-0000517-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	34	354	0	ENST00000322088.6:c.654_659del	p.Asp218_Val220delinsGlu	p.D218_V220delinsE	ENST00000322088	NM_014225.5	218	gaCTCGGTg/gag	6/15	0.849835205495757	3	FACETS	0.268	0.219	0.324			1	SUBCLONAL	1	TRUE	NA	0.849835205495757	3		354	425	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520239	176520240	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	C	novel	NA	P-0000517-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	96	326	0	ENST00000292408.4:c.1158_1159delinsC	p.Ala387ProfsTer64	p.A387Pfs*64	ENST00000292408	NM_213647.1	386	ctGGcc/ctCcc	9/18	0.837469874010861	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.849835205495757	1		326	125	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0000520-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	165	495	1	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	0.561124005879895	2		496	624	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972104	55972104	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1311687491	NA	P-0000520-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	174	441	0	ENST00000263923.4:c.1540G>A	p.Val514Ile	p.V514I	ENST00000263923	NM_002253.2	514	Gta/Ata	12/30	1	2	FACETS	0.853	0.787	0.921	0.853	0.787	0.921	CLONAL	1	TRUE	1	0.561124005879895	2		441	727	SUCCESS
APC	324	MSKCC	GRCh37	5	112174096	112174096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs137854575	NA	P-0000520-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	150	448	0	ENST00000257430.4:c.2805C>A	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	taC/taA	16/16	1	2	FACETS	0.936	0.86	1	0.936	0.86	1	CLONAL	1	TRUE	1	0.561124005879895	2		448	571	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120232	70120232	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000520-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	650	804	0	ENST00000245479.2:c.1234C>T	p.Gln412Ter	p.Q412*	ENST00000245479	NM_000346.3	412	Cag/Tag	3/3	0.561124005879895	2	FACETS	0.862	0.84	0.883	1	0.997	1	CLONAL	3	TRUE	0	0.561124005879895	2		804	896	SUCCESS
APC	324	MSKCC	GRCh37	5	112175248	112175249	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0000520-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	95	329	0	ENST00000257430.4:c.3959_3960del	p.Val1320GlufsTer11	p.V1320Efs*11	ENST00000257430	NM_000038.5	1319	ccTGtg/cctg	16/16	1	2	FACETS	0.763	0.683	0.847	0.763	0.683	0.847	SUBCLONAL	1	TRUE	1	0.561124005879895	2		329	444	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0000526-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	435	450	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.600533322524738	3	FACETS	0.996	0.955	1	0.996	0.955	1	CLONAL	2	TRUE	1	0.64632793189779	3		451	894	SUCCESS
APC	324	MSKCC	GRCh37	5	112163677	112163677	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0000526-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	355	477	0	ENST00000257430.4:c.1600A>T	p.Lys534Ter	p.K534*	ENST00000257430	NM_000038.5	534	Aaa/Taa	13/16	NA	2	FACETS	0.84	0.804	0.876			1	INDETERMINATE	2	TRUE	NA	0.64632793189779	2		477	654	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209721	98209721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749244396	NA	P-0000526-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	62	117	0	ENST00000331920.6:c.3817G>A	p.Glu1273Lys	p.E1273K	ENST00000331920	NM_000264.3	1273	Gaa/Aaa	23/24	0.600533322524738	3	FACETS	0.878	0.765	0.999	0.439	0.382	0.5	CLONAL	1	TRUE	1	0.64632793189779	3		117	289	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175528	108175528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs376603775	NA	P-0000526-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	327	282	0	ENST00000278616.4:c.5623C>T	p.Arg1875Ter	p.R1875*	ENST00000278616	NM_000051.3	1875	Cga/Tga	37/63	0.610242532289151	2	FACETS	0.942	0.903	0.981	0.942	0.903	0.981	CLONAL	2	TRUE	0	0.64632793189779	2		282	537	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434070	121434070	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766770471	NA	P-0000526-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	153	413	1	ENST00000257555.6:c.961C>T	p.Arg321Cys	p.R321C	ENST00000257555		321	Cgc/Tgc	5/10	NA	2	FACETS	0.612	0.561	0.666			1	INDETERMINATE	1	TRUE	NA	0.64632793189779	2		414	773	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793513	42793513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000526-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	133	288	0	ENST00000575354.2:c.1315G>A	p.Glu439Lys	p.E439K	ENST00000575354	NM_015125.3	439	Gag/Aag	8/20	0.180265977602734	3	FACETS	0.897	0.817	0.98	0.299	0.272	0.327	INDETERMINATE	1	TRUE	0	0.64632793189779	3		288	607	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186599	108186599	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876658415	NA	P-0000536-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	98	327	1	ENST00000278616.4:c.6056A>G	p.Tyr2019Cys	p.Y2019C	ENST00000278616	NM_000051.3	2019	tAt/tGt	41/63	0.272883085457419	1	FACETS	0.886	0.792	0.986	0.886	0.792	0.986	CLONAL	1	FALSE	0	0.30736418726873	1		328	609	SUCCESS
AXL	558	MSKCC	GRCh37	19	41759537	41759537	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000536-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	55	634	0	ENST00000301178.4:c.1960G>T	p.Ala654Ser	p.A654S	ENST00000301178	NM_021913.4	654	Gca/Tca	17/20	0.30736418726873	1	FACETS	0.359	0.306	0.418	0.359	0.306	0.418	SUBCLONAL	1	FALSE	0	0.30736418726873	1		634	843	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231055	53231055	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000536-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	123	275	0	ENST00000375401.3:c.1847A>T	p.Asn616Ile	p.N616I	ENST00000375401	NM_004187.3	616	aAc/aTc	13/26	0.30736418726873	0	FACETS	0.67	0.61	0.731			1	SUBCLONAL	2	FALSE	NA	0.30736418726873	0		275	414	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499382	89499382	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000546-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	136	286	0	ENST00000336596.2:c.2552C>G	p.Ala851Gly	p.A851G	ENST00000336596	NM_005233.5	851	gCt/gGt	15/17	0.217499625734627	4	FACETS	0.919	0.839	1	0.919	0.839	1	CLONAL	2	TRUE	2	0.348442989952778	4		286	573	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738975	145738975	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000546-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	44	182	0	ENST00000428558.2:c.2180C>G	p.Ala727Gly	p.A727G	ENST00000428558	NM_004260.3	727	gCc/gGc	13/22	0.320670878090645	4	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	2	0.348442989952778	4		182	147	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788617	3788617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519884	NA	P-0000546-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	46	445	0	ENST00000262367.5:c.4337G>A	p.Arg1446His	p.R1446H	ENST00000262367	NM_004380.2	1446	cGc/cAc	26/31	0.275303928198982	2	FACETS	0.559	0.471	0.657	0.28	0.235	0.329	SUBCLONAL	1	TRUE	0	0.348442989952778	2		445	472	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210451	2210451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138206172	NA	P-0000546-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	34	273	0	ENST00000398665.3:c.1058C>T	p.Ala353Val	p.A353V	ENST00000398665	NM_032482.2	353	gCg/gTg	13/28	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.348442989952778	2		273	144	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs17849781	NA	P-0000554-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	394	530	0	ENST00000269305.4:c.832C>A	p.Pro278Thr	p.P278T	ENST00000269305	NM_001126112.2	278	Cct/Act	8/11	0.373791694899407	2	FACETS	0.837	0.799	0.876	0.837	0.799	0.876	CLONAL	2	TRUE	0	0.486751967513352	2		530	967	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256499	16256499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000554-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	148	330	0	ENST00000375759.3:c.3764C>T	p.Ser1255Phe	p.S1255F	ENST00000375759	NM_015001.2	1255	tCt/tTt	11/15	0.347369475372085	3	FACETS	0.804	0.733	0.877			1	CLONAL	1	TRUE	NA	0.486751967513352	3		330	941	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259667	16259667	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000554-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	115	251	0	ENST00000375759.3:c.6932C>T	p.Ser2311Leu	p.S2311L	ENST00000375759	NM_015001.2	2311	tCa/tTa	11/15	0.347369475372085	3	FACETS	0.772	0.696	0.853			1	SUBCLONAL	1	TRUE	NA	0.486751967513352	3		251	761	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260717	16260717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000554-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	133	303	0	ENST00000375759.3:c.7982C>T	p.Ser2661Phe	p.S2661F	ENST00000375759	NM_015001.2	2661	tCc/tTc	11/15	0.347369475372085	3	FACETS	0.867	0.788	0.95			1	CLONAL	1	TRUE	NA	0.486751967513352	3		303	784	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661761	227661761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000554-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	114	265	0	ENST00000305123.5:c.1694G>A	p.Gly565Glu	p.G565E	ENST00000305123	NM_005544.2	565	gGa/gAa	1/2	0.346912884407105	3	FACETS	0.84	0.758	0.928	0.42	0.379	0.464	CLONAL	1	TRUE	1	0.486751967513352	3		265	693	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498465	89498465	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000554-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	139	200	0	ENST00000336596.2:c.2437G>T	p.Val813Phe	p.V813F	ENST00000336596	NM_005233.5	813	Gtt/Ttt	14/17	0.486751967513352	2	FACETS	1	0.982	1	0.628	0.576	0.681	CLONAL	1	TRUE	0	0.486751967513352	2		200	455	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136856	55136856	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000554-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1277	420	506	0	ENST00000257290.5:c.1178C>A	p.Thr393Asn	p.T393N	ENST00000257290	NM_006206.4	393	aCt/aAt	8/23	0.427496696470797	4	FACETS	0.756	0.718	0.795	0.756	0.718	0.795	SUBCLONAL	2	TRUE	2	0.486751967513352	4		506	1697	SUCCESS
APC	324	MSKCC	GRCh37	5	112179278	112179278	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000554-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	303	338	0	ENST00000257430.4:c.7987G>T	p.Asp2663Tyr	p.D2663Y	ENST00000257430	NM_000038.5	2663	Gac/Tac	16/16	0.375807940976785	2	FACETS	1	0.994	1	0.714	0.675	0.754	CLONAL	1	TRUE	0	0.486751967513352	2		338	872	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502144	157502144	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000554-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	123	262	0	ENST00000346085.5:c.3177G>T	p.Lys1059Asn	p.K1059N	ENST00000346085	NM_020732.3	1059	aaG/aaT	12/20	0.486751967513352	3	FACETS	0.826	0.747	0.909	0.413	0.373	0.455	CLONAL	1	TRUE	1	0.486751967513352	3		262	761	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985476	2985476	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000554-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1452	141	440	0	ENST00000396946.4:c.335C>T	p.Thr112Ile	p.T112I	ENST00000396946	NM_032415.4	112	aCt/aTt	4/25	0.486751967513352	4	FACETS	0.541	0.49	0.594	0.27	0.245	0.297	SUBCLONAL	1	TRUE	2	0.486751967513352	4		440	1593	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5081856	5081856	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000554-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	104	239	0	ENST00000381652.3:c.2566G>A	p.Gly856Ser	p.G856S	ENST00000381652	NM_004972.3	856	Ggc/Agc	19/25	0.366324832330875	3	FACETS	0.714	0.639	0.793	0.238	0.213	0.265	SUBCLONAL	1	TRUE	0	0.486751967513352	3		239	744	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180459	94180459	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000554-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1594	258	637	1	ENST00000323929.3:c.1709G>A	p.Arg570Lys	p.R570K	ENST00000323929	NM_005591.3	570	aGa/aAa	15/20	0.358758691577972	4	FACETS	0.851	0.794	0.91	0.426	0.397	0.455	CLONAL	1	TRUE	2	0.486751967513352	4		638	1852	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636134	28636134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200841206	NA	P-0000554-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	148	399	0	ENST00000241453.7:c.238G>A	p.Ala80Thr	p.A80T	ENST00000241453	NM_004119.2	80	Gct/Act	3/24	0.382720687437463	2	FACETS	0.851	0.778	0.926	0.425	0.389	0.463	CLONAL	1	TRUE	0	0.486751967513352	2		399	715	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339602	339602	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000554-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	141	472	0	ENST00000262320.3:c.2300G>C	p.Arg767Thr	p.R767T	ENST00000262320	NM_003502.3	767	aGa/aCa	10/11	0.358758691577972	4	FACETS	0.807	0.733	0.883	0.403	0.366	0.442	CLONAL	1	TRUE	2	0.486751967513352	4		472	1068	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857443	9857443	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000554-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	138	527	0	ENST00000330684.3:c.3958C>A	p.Leu1320Met	p.L1320M	ENST00000330684	NM_001134407.1	1320	Ctg/Atg	13/13	0.358758691577972	4	FACETS	0.662	0.6	0.727	0.331	0.3	0.364	SUBCLONAL	1	TRUE	2	0.486751967513352	4		527	1274	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7152894	7152894	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000554-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	136	349	0	ENST00000302850.5:c.2074G>A	p.Glu692Lys	p.E692K	ENST00000302850	NM_000208.2	692	Gaa/Aaa	10/22	0.373791694899407	2	FACETS	0.746	0.679	0.816	0.373	0.339	0.408	SUBCLONAL	1	TRUE	0	0.486751967513352	2		349	749	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426121	47426121	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000554-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1513	330	815	0	ENST00000377045.4:c.641C>A	p.Ser214Tyr	p.S214Y	ENST00000377045	NM_001654.4	214	tCc/tAc	7/16	0.346912884407105	3	FACETS	0.915	0.861	0.97	0.457	0.43	0.485	CLONAL	1	TRUE	1	0.486751967513352	3		815	1843	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650304	48650304	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000554-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1291	167	681	0	ENST00000376670.3:c.274C>A	p.Pro92Thr	p.P92T	ENST00000376670	NM_002049.3	92	Cca/Aca	3/6	0.346912884407105	3	FACETS	0.585	0.536	0.637	0.293	0.268	0.319	SUBCLONAL	1	TRUE	1	0.486751967513352	3		681	1458	SUCCESS
AR	367	MSKCC	GRCh37	X	66765730	66765730	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000554-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1632	480	898	0	ENST00000374690.3:c.742G>T	p.Gly248Cys	p.G248C	ENST00000374690	NM_000044.3	248	Ggc/Tgc	1/8	0.302554879084546	4	FACETS	1	0.995	1	0.694	0.661	0.728	CLONAL	1	TRUE	2	0.486751967513352	4		898	2112	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345955	70345955	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000554-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1812	201	688	0	ENST00000374080.3:c.2492C>T	p.Ala831Val	p.A831V	ENST00000374080		831	gCt/gTt	18/45	0.302554879084546	4	FACETS	0.61	0.563	0.66	0.305	0.281	0.33	SUBCLONAL	1	TRUE	2	0.486751967513352	4		688	2013	SUCCESS
APC	324	MSKCC	GRCh37	5	112155011	112155011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1302087242	NA	P-0000563-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	56	189	0	ENST00000257430.4:c.1282G>A	p.Glu428Lys	p.E428K	ENST00000257430	NM_000038.5	428	Gaa/Aaa	10/16	0.327618988770978	1	FACETS	0.979	0.845	1	0.979	0.845	1	CLONAL	1	TRUE	0	0.331523484343047	1		189	288	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0000563-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	25	367	0	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	0.331523484343047	1	FACETS	0.844	0.673	1	0.844	0.673	1	CLONAL	1	TRUE	0	0.331523484343047	1		367	149	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125470	7125470	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000563-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	18	425	0	ENST00000302850.5:c.3082G>A	p.Glu1028Lys	p.E1028K	ENST00000302850	NM_000208.2	1028	Gag/Aag	17/22	0.331523484343047	0	FACETS	0.321	0.242	0.414			1	SUBCLONAL	1	TRUE	0	0.331523484343047	0		425	226	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0000589-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	71	360	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.505215152212546	1	FACETS	0.68	0.598	0.766	0.68	0.598	0.766	SUBCLONAL	1	TRUE	0	0.505215152212546	1		360	309	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11273467	11273467	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs368318161	NA	P-0000609-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	84	350	0	ENST00000361445.4:c.3274G>T	p.Val1092Phe	p.V1092F	ENST00000361445	NM_004958.3	1092	Gtc/Ttc	21/58	0.250360533414033	1	FACETS	0.804	0.71	0.905	0.804	0.71	0.905	CLONAL	1	FALSE	0	0.250360533414033	1		350	730	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268071	55268071	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000609-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	162	500	0	ENST00000275493.2:c.2911A>G	p.Met971Val	p.M971V	ENST00000275493	NM_005228.3	971	Atg/Gtg	24/28	0.161374635134546	3	FACETS	1	0.971	1	0.569	0.52	0.62	CLONAL	1	FALSE	1	0.250360533414033	3		500	1280	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0000610-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	107	564	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.650028360432885	1	FACETS	0.903	0.826	0.982	0.903	0.826	0.982	CLONAL	1	TRUE	0	0.650028360432885	1		564	246	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979368	40979368	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000610-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	17	158	0	ENST00000373198.4:c.1765C>G	p.Pro589Ala	p.P589A	ENST00000373198	NM_133170.3	589	Cca/Gca	11/32	1	2	FACETS	0.317	0.238	0.41	0.317	0.238	0.41	SUBCLONAL	1	TRUE	1	0.650028360432885	2		158	165	SUCCESS
APC	324	MSKCC	GRCh37	5	112179354	112179354	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0000610-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	26	460	0	ENST00000257430.4:c.8066del	p.Lys2689ArgfsTer34	p.K2689Rfs*34	ENST00000257430	NM_000038.5	2688	gAa/ga	16/16	0.625866736038353	1	FACETS	0.261	0.208	0.321	0.261	0.208	0.321	SUBCLONAL	1	TRUE	0	0.650028360432885	1		460	207	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0000626-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	52	164	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.360110368991876	3	FACETS	1	0.939	1	0.592	0.507	0.683	CLONAL	1	FALSE	1	0.360110368991876	3		164	288	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0000626-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	21	409	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.344934405062531	4	FACETS	0.273	0.209	0.347	0.136	0.104	0.174	SUBCLONAL	1	FALSE	2	0.360110368991876	4		409	582	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645844	215645844	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758368819	NA	P-0000626-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	94	713	0	ENST00000260947.4:c.754C>T	p.Pro252Ser	p.P252S	ENST00000260947	NM_000465.2	252	Cct/Tct	4/11	0.291901428106333	4	FACETS	0.912	0.811	1	0.456	0.405	0.51	CLONAL	1	FALSE	2	0.360110368991876	4		713	779	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651496	52651496	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000626-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	66	588	0	ENST00000394830.3:c.1600C>T	p.Arg534Ter	p.R534*	ENST00000394830	NM_018313.4	534	Cga/Tga	15/30	NA	2	FACETS	0.545	0.473	0.624			1	INDETERMINATE	1	FALSE	NA	0.360110368991876	2		588	672	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119642274	119642274	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000626-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	30	349	0	ENST00000316626.5:c.423A>T	p.Arg141Ser	p.R141S	ENST00000316626		141	agA/agT	4/12	0.360110368991876	3	FACETS	0.331	0.266	0.405	0.166	0.133	0.203	SUBCLONAL	1	FALSE	1	0.360110368991876	3		349	594	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555293	106555293	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000626-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	28	217	0	ENST00000369096.4:c.2410C>A	p.Pro804Thr	p.P804T	ENST00000369096	NM_001198.3	804	Ccc/Acc	7/7	0.281458879860424	5	FACETS	0.785	0.629	0.963	0.262	0.209	0.321	CLONAL	1	FALSE	2	0.360110368991876	5		217	305	SUCCESS
APC	324	MSKCC	GRCh37	5	112175513	112175513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000635-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	257	274	0	ENST00000257430.4:c.4222G>T	p.Glu1408Ter	p.E1408*	ENST00000257430	NM_000038.5	1408	Gaa/Taa	16/16	0.220714635815545	2	FACETS	0.977	0.914	1	0.977	0.914	1	CLONAL	2	TRUE	0	0.230608417734699	2		274	1141	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004217	150004217	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1431439182	NA	P-0000635-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1408	186	388	1	ENST00000253339.5:c.2008C>T	p.Arg670Trp	p.R670W	ENST00000253339		670	Cgg/Tgg	3/7	0.230608417734699	1	FACETS	0.895	0.824	0.97	0.895	0.824	0.97	CLONAL	1	TRUE	0	0.230608417734699	1		389	1594	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421553	32421553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000635-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	68	142	0	ENST00000332351.3:c.1039C>T	p.Pro347Ser	p.P347S	ENST00000332351	NM_024426.4	347	Ccc/Tcc	6/10	1	2	FACETS	0.785	0.682	0.897	0.785	0.682	0.897	SUBCLONAL	1	TRUE	1	0.230608417734699	2		142	751	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0000635-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1250	171	315	2	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.230608417734699	2		317	1421	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987033	36987033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000635-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	78	205	0	ENST00000354822.5:c.656C>T	p.Pro219Leu	p.P219L	ENST00000354822	NM_001079668.2	219	cCg/cTg	3/3	1	2	FACETS	0.976	0.858	1	0.976	0.858	1	CLONAL	1	TRUE	1	0.230608417734699	2		205	693	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919673	96919673	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1231066976	NA	P-0000644-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	465	107	414	0	ENST00000258439.3:c.590G>A	p.Arg197His	p.R197H	ENST00000258439	NM_001193304.2	197	cGc/cAc	4/4	1	2	FACETS	0.732	0.658	0.809	0.732	0.658	0.809	SUBCLONAL	1	TRUE	1	0.511420665474434	2		414	572	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797206	42797206	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs750040712	NA	P-0000652-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	208	631	0	ENST00000575354.2:c.3568G>C	p.Gly1190Arg	p.G1190R	ENST00000575354	NM_015125.3	1190	Ggg/Cgg	15/20	1	2	FACETS	1	0.945	1	1	0.995	1	CLONAL	3	TRUE	1	0.219579738003962	2		631	623	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566507	41566507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000652-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	257	832	0	ENST00000263253.7:c.4384C>T	p.Arg1462Ter	p.R1462*	ENST00000263253	NM_001429.3	1462	Cga/Tga	27/31	1	2	FACETS	0.884	0.829	0.939	1	0.996	1	CLONAL	3	TRUE	1	0.219579738003962	2		832	883	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0000678-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	41	495	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.944	0.802	1	0.944	0.802	1	CLONAL	1	TRUE	1	0.607358524854383	2		496	143	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0000678-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	144	340	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.375595372457418	3	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	1	0.607358524854383	3		340	300	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245404	153245404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000678-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	79	201	0	ENST00000281708.4:c.1787C>T	p.Ser596Phe	p.S596F	ENST00000281708	NM_033632.3	596	tCt/tTt	11/12	0.187278924970114	4	FACETS	1	0.913	1	0.68	0.61	0.752	INDETERMINATE	2	TRUE	1	0.607358524854383	4		201	205	SUCCESS
APC	324	MSKCC	GRCh37	5	112154723	112154723	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775126020	NA	P-0000678-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	100	153	0	ENST00000257430.4:c.994C>T	p.Arg332Ter	p.R332*	ENST00000257430	NM_000038.5	332	Cga/Tga	10/16	0.5463530760369	5	FACETS	0.928	0.847	1	0.928	0.847	1	CLONAL	3	TRUE	2	0.607358524854383	5		153	226	SUCCESS
APC	324	MSKCC	GRCh37	5	112174152	112174152	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0000678-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	86	229	0	ENST00000257430.4:c.2861T>A	p.Leu954Ter	p.L954*	ENST00000257430	NM_000038.5	954	tTa/tAa	16/16	0.5463530760369	5	FACETS	0.999	0.895	1	0.666	0.597	0.737	CLONAL	2	TRUE	2	0.607358524854383	5		229	271	SUCCESS
APC	324	MSKCC	GRCh37	5	112175852	112175852	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000678-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	82	87	0	ENST00000257430.4:c.4561G>T	p.Glu1521Ter	p.E1521*	ENST00000257430	NM_000038.5	1521	Gaa/Taa	16/16	0.5463530760369	5	FACETS	0.977	0.885	1	0.977	0.885	1	CLONAL	3	TRUE	2	0.607358524854383	5		87	176	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14026284	14026284	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000678-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	108	164	0	ENST00000405192.2:c.160C>A	p.Gln54Lys	p.Q54K	ENST00000405192	NM_001163147.1	54	Cag/Aag	4/12	0.390744079032624	5	FACETS	1	0.97	1	0.771	0.702	0.841	CLONAL	2	TRUE	2	0.607358524854383	5		164	294	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396853	396853	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771405148	NA	P-0000678-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	102	322	0	ENST00000262320.3:c.173C>T	p.Thr58Met	p.T58M	ENST00000262320	NM_003502.3	58	aCg/aTg	2/11	0.415785564391461	4	FACETS	0.803	0.726	0.883	0.803	0.726	0.883	CLONAL	2	TRUE	2	0.607358524854383	4		322	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0000678-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	91	278	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	NA	2	FACETS	1	0.951	1			1	INDETERMINATE	2	TRUE	NA	0.607358524854383	2		278	144	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117648	70117648	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000678-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	105	334	0	ENST00000245479.2:c.116C>G	p.Ser39Cys	p.S39C	ENST00000245479	NM_000346.3	39	tCc/tGc	1/3	0.607358524854383	3	FACETS	0.959	0.877	1	0.959	0.877	1	CLONAL	2	TRUE	1	0.607358524854383	3		334	235	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602808	10602808	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000678-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	115	255	0	ENST00000171111.5:c.770G>A	p.Cys257Tyr	p.C257Y	ENST00000171111	NM_203500.1	257	tGc/tAc	3/6	0.375595372457418	3	FACETS	0.939	0.861	1	0.939	0.861	1	CLONAL	2	TRUE	1	0.607358524854383	3		255	263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0000688-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	152	493	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.340918687947179	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.340918687947179	1		494	537	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5462993	5462993	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000688-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	54	269	0	ENST00000381577.3:c.554A>T	p.Lys185Met	p.K185M	ENST00000381577	NM_014143.3	185	aAg/aTg	4/7	0.340918687947179	2	FACETS	0.425	0.362	0.494	0.212	0.181	0.247	SUBCLONAL	1	TRUE	0	0.340918687947179	2		269	746	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210894	133210894	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000688-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	49	374	0	ENST00000320574.5:c.5882G>T	p.Gly1961Val	p.G1961V	ENST00000320574	NM_006231.2	1961	gGg/gTg	43/49	0.340918687947179	1	FACETS	0.313	0.264	0.366	0.313	0.264	0.366	SUBCLONAL	1	TRUE	0	0.340918687947179	1		374	763	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342706	118342707	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0000688-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	49	222	0	ENST00000534358.1:c.837_838del	p.Pro280SerfsTer4	p.P280Sfs*4	ENST00000534358	NM_005933.3	278	CTc/c	3/36	0.233676308757234	1	FACETS	0.497	0.421	0.58	0.497	0.421	0.58	SUBCLONAL	1	TRUE	0	0.340918687947179	1		222	480	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435655	18435655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424459751	NA	P-0000691-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	16	167	0	ENST00000266497.5:c.640C>T	p.Pro214Ser	p.P214S	ENST00000266497		214	Ccc/Tcc	1/31	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.23	2		167	98	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0000695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	11	163	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.200740876081718	3	FACETS	1	0.788	1	0.587	0.41	0.801	CLONAL	1	FALSE	1	0.226837315118872	3		163	92	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0000695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	24	298	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	0.200740876081718	3	FACETS	0.899	0.715	1	0.899	0.715	1	CLONAL	2	FALSE	1	0.226837315118872	3		298	131	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs863224683	NA	P-0000695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	27	165	0	ENST00000269305.4:c.388C>G	p.Leu130Val	p.L130V	ENST00000269305	NM_001126112.2	130	Ctc/Gtc	5/11	0.226837315118872	1	FACETS	1	0.876	1	1	0.96	1	CLONAL	2	FALSE	0	0.226837315118872	1		165	96	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385221	41385221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375454640	NA	P-0000695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	109	282	0	ENST00000373198.4:c.740G>A	p.Arg247His	p.R247H	ENST00000373198	NM_133170.3	247	cGc/cAc	6/32	0.226837315118872	4	FACETS	1	0.94	1	1	0.989	1	CLONAL	5	FALSE	1	0.226837315118872	4		282	229	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357069	70357069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200279192	NA	P-0000695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	16	352	0	ENST00000374080.3:c.5584C>T	p.Arg1862Cys	p.R1862C	ENST00000374080		1862	Cgc/Tgc	39/45	0.226837315118872	0	FACETS	0.785	0.584	1			1	CLONAL	1	FALSE	NA	0.226837315118872	0		352	139	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0000706-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	103	290	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.21770709359854	5	FACETS	0.97	0.869	1	0.647	0.579	0.718	CLONAL	2	TRUE	2	0.21770709359854	5		290	647	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913315	NA	P-0000706-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	23	402	1	ENST00000326873.7:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000326873	NM_000455.4	194	Gac/Tac	4/10	0.152677763811509	3	FACETS	0.626	0.488	0.787			1	SUBCLONAL	1	TRUE	NA	0.21770709359854	3		403	374	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0000725-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	41	275	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	0.32	0.266	0.38	0.32	0.266	0.38	SUBCLONAL	1	TRUE	1	0.42314903780471	2		275	606	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939992	76939992	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000725-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	58	249	0	ENST00000373344.5:c.756G>T	p.Glu252Asp	p.E252D	ENST00000373344	NM_000489.3	252	gaG/gaT	9/35	1	1	FACETS	0.425	0.365	0.49	0.425	0.365	0.49	SUBCLONAL	1	TRUE	0	0.42314903780471	1		249	509	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061223	38061228	+	inframe_deletion	In_Frame_Del	DEL	TCTCGA	TCTCGA	-	novel	NA	P-0000725-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	306	304	0	ENST00000250448.2:c.761_766del	p.Phe254_Asn256delinsTyr	p.F254_N256delinsY	ENST00000250448	NM_004496.3	254	tTCGAGAac/tac	2/2	0.139110328890141	3	FACETS	0.935	0.883	0.988	0.935	0.883	0.988	INDETERMINATE	2	TRUE	1	0.42314903780471	3		304	937	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281291	142281291	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0000732-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	54	216	0	ENST00000350721.4:c.953T>G	p.Leu318Ter	p.L318*	ENST00000350721	NM_001184.3	318	tTa/tGa	4/47	NA	2	FACETS	0.468	0.4	0.542			1	INDETERMINATE	1	FALSE	NA	0.443957285642989	2		216	520	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281532	142281532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000732-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	45	291	0	ENST00000350721.4:c.712G>A	p.Glu238Lys	p.E238K	ENST00000350721	NM_001184.3	238	Gag/Aag	4/47	NA	2	FACETS	0.355	0.298	0.418			1	INDETERMINATE	1	FALSE	NA	0.443957285642989	2		291	571	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436632	52436633	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0000741-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	93	217	0	ENST00000460680.1:c.2041_2042del	p.Met681AlafsTer35	p.M681Afs*35	ENST00000460680	NM_004656.3	681	ATg/g	16/17	0.239953220007994	1	FACETS	0.968	0.897	1	1	0.991	1	CLONAL	5	TRUE	0	0.239953220007994	1		217	141	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0000744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	110	450	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.167095866498536	3	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.236675060002319	3		451	777	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0000744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	16	221	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.485	0.358	0.636	0.485	0.358	0.636	SUBCLONAL	1	TRUE	1	0.236675060002319	2		221	279	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0000744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	34	441	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.236675060002319	3	FACETS	0.663	0.541	0.8	0.331	0.27	0.4	SUBCLONAL	1	TRUE	1	0.236675060002319	3		441	485	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928425	69928425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781567478	NA	P-0000744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	13	198	0	ENST00000352241.4:c.245C>T	p.Ala82Val	p.A82V	ENST00000352241	NM_198159.2	82	gCg/gTg	2/10	0.128132862890867	5	FACETS	0.61	0.435	0.824			1	INDETERMINATE	1	TRUE	NA	0.236675060002319	5		198	244	SUCCESS
APC	324	MSKCC	GRCh37	5	112136980	112136980	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1554076133	NA	P-0000744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	31	246	0	ENST00000257430.4:c.734C>A	p.Ser245Ter	p.S245*	ENST00000257430	NM_000038.5	245	tCa/tAa	8/16	0.201705879322459	4	FACETS	0.864	0.699	1	0.432	0.349	0.525	CLONAL	1	TRUE	2	0.236675060002319	4		246	375	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8733795	8733795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138127948	NA	P-0000744-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	55	367	0	ENST00000356435.5:c.49C>T	p.Arg17Cys	p.R17C	ENST00000356435		17	Cgc/Tgc	1/35	0.226561434520164	3	FACETS	1	0.948	1	0.62	0.532	0.716	CLONAL	1	TRUE	1	0.236675060002319	3		367	419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780071	NA	P-0000769-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	176	446	0	ENST00000269305.4:c.580C>T	p.Leu194Phe	p.L194F	ENST00000269305	NM_001126112.2	194	Ctt/Ttt	6/11	0.361190899218332	2	FACETS	0.929	0.864	0.995	0.929	0.864	0.995	CLONAL	2	TRUE	0	0.414541157850607	2		446	457	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0000769-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	91	298	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	1	2	FACETS	0.989	0.883	1	0.989	0.883	1	CLONAL	1	TRUE	1	0.414541157850607	2		298	444	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248055	59248055	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000769-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	127	181	0	ENST00000371222.2:c.688C>T	p.Gln230Ter	p.Q230*	ENST00000371222	NM_002228.3	230	Cag/Tag	1/1	0.348491450491503	3	FACETS	1	0.962	1	0.723	0.663	0.784	CLONAL	2	TRUE	0	0.414541157850607	3		181	341	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046371	128046371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764717311	NA	P-0000769-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	29	297	0	ENST00000285398.2:c.892C>T	p.Arg298Trp	p.R298W	ENST00000285398	NM_000122.1	298	Cgg/Tgg	7/15	0.414541157850607	4	FACETS	0.348	0.279	0.428	0.116	0.093	0.143	SUBCLONAL	1	TRUE	1	0.414541157850607	4		297	568	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535384	66535384	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000769-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	78	266	0	ENST00000273854.3:c.77C>T	p.Ala26Val	p.A26V	ENST00000273854	NM_004439.5	26	gCg/gTg	1/18	0.274754085271388	4	FACETS	1	0.969	1	0.654	0.578	0.735	CLONAL	1	TRUE	2	0.414541157850607	4		266	407	SUCCESS
APC	324	MSKCC	GRCh37	5	112173656	112173656	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123117	NA	P-0000769-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	93	311	0	ENST00000257430.4:c.2365C>T	p.Gln789Ter	p.Q789*	ENST00000257430	NM_000038.5	789	Cag/Tag	16/16	1	2	FACETS	0.969	0.866	1	0.969	0.866	1	CLONAL	1	TRUE	1	0.414541157850607	2		311	463	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606319	93606319	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000769-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	106	396	0	ENST00000375746.1:c.139T>A	p.Tyr47Asn	p.Y47N	ENST00000375746	NM_001174167.1	47	Tac/Aac	2/14	0.405859258089917	3	FACETS	1	0.957	1	0.559	0.503	0.619	CLONAL	1	TRUE	1	0.414541157850607	3		396	552	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031268	36031268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367543247	NA	P-0000769-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	111	467	0	ENST00000358208.4:c.1387C>T	p.Arg463Trp	p.R463W	ENST00000358208		463	Cgg/Tgg	11/12	0.414541157850607	7	FACETS	1	0.936	1	0.212	0.189	0.235	CLONAL	1	TRUE	2	0.414541157850607	7		467	1031	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0000772-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	51	229	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.152274469935735	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	0	0.190699070725591	1		229	328	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84403395	84403395	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000772-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	46	312	0	ENST00000321945.7:c.90A>C	p.Glu30Asp	p.E30D	ENST00000321945	NM_139076.2	30	gaA/gaC	2/9	0.190699070725591	4	FACETS	0.795	0.667	0.935	0.265	0.222	0.312	CLONAL	1	FALSE	1	0.190699070725591	4		312	723	SUCCESS
APC	324	MSKCC	GRCh37	5	112175118	112175118	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1060503299	NA	P-0000772-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	44	185	0	ENST00000257430.4:c.3827C>A	p.Ser1276Ter	p.S1276*	ENST00000257430	NM_000038.5	1276	tCa/tAa	16/16	0.162039379402533	4	FACETS	1	0.879	1	0.529	0.444	0.624	CLONAL	1	FALSE	2	0.190699070725591	4		185	519	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553440	106553440	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000772-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	24	143	0	ENST00000369096.4:c.1405T>C	p.Ser469Pro	p.S469P	ENST00000369096	NM_001198.3	469	Tcg/Ccg	5/7	0.190699070725591	4	FACETS	1	0.805	1	0.513	0.403	0.64	CLONAL	1	FALSE	2	0.190699070725591	4		143	292	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273419	38273419	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000772-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	44	501	0	ENST00000425967.3:c.1916C>A	p.Ala639Asp	p.A639D	ENST00000425967	NM_001174067.1	639	gCc/gAc	14/19	1	2	FACETS	0.658	0.551	0.778	0.658	0.551	0.778	SUBCLONAL	1	FALSE	1	0.190699070725591	2		501	701	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720837	89720837	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1554825607	NA	P-0000772-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	75	196	0	ENST00000371953.3:c.988A>T	p.Lys330Ter	p.K330*	ENST00000371953	NM_000314.4	330	Aaa/Taa	8/9	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	1	FALSE	NA	0.190699070725591	2		196	533	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509612	29509612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000772-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	87	368	0	ENST00000356175.3:c.817C>T	p.Leu273Phe	p.L273F	ENST00000356175	NM_000267.3	273	Ctc/Ttc	8/57	0.162039379402533	4	FACETS	1	0.977	1	0.728	0.644	0.818	CLONAL	1	FALSE	2	0.190699070725591	4		368	746	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302827	15302827	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000772-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	23	231	0	ENST00000263388.2:c.623A>C	p.Asn208Thr	p.N208T	ENST00000263388	NM_000435.2	208	aAc/aCc	4/33	1	2	FACETS	0.939	0.734	1	0.939	0.734	1	CLONAL	1	FALSE	1	0.190699070725591	2		231	257	SUCCESS
APC	324	MSKCC	GRCh37	5	112175595	112175595	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000772-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	110	409	0	ENST00000257430.4:c.4304del	p.Arg1435LysfsTer38	p.R1435Kfs*38	ENST00000257430	NM_000038.5	1435	aGa/aa	16/16	0.162039379402533	4	FACETS	1	0.981	1	0.717	0.643	0.795	CLONAL	1	FALSE	2	0.190699070725591	4		409	958	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149251	119149251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267606708	NA	P-0000779-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1337	58	549	0	ENST00000264033.4:c.1259G>A	p.Arg420Gln	p.R420Q	ENST00000264033	NM_005188.3	420	cGa/cAa	9/16	1	2	FACETS	0.121	0.103	0.141	0.121	0.103	0.141	SUBCLONAL	1	TRUE	1	0.686894622865043	2		549	1395	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609383	39609383	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000779-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	445	339	0	ENST00000262039.4:c.1685A>C	p.Glu562Ala	p.E562A	ENST00000262039	NM_002647.2	562	gAa/gCa	15/25	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.686894622865043	2		339	1261	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0000791-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	22	378	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.481578394235626	4	FACETS	0.368	0.285	0.464	0.184	0.142	0.232	SUBCLONAL	1	TRUE	2	0.65531282356863	4		379	302	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0000791-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	8	435	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.65531282356863	2	FACETS	0.14	0.09	0.205	0.07	0.045	0.103	SUBCLONAL	1	TRUE	0	0.65531282356863	2		435	174	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132780	152132780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000791-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	32	465	0	ENST00000262189.6:c.92C>T	p.Ala31Val	p.A31V	ENST00000262189	NM_170606.2	31	gCc/gTc	1/59	0.65531282356863	2	FACETS	0.208	0.168	0.253	0.104	0.084	0.127	SUBCLONAL	1	TRUE	0	0.65531282356863	2		465	470	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233121	69233121	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000791-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	72	230	0	ENST00000462284.1:c.986G>C	p.Trp329Ser	p.W329S	ENST00000462284	NM_002392.5	329	tGg/tCg	11/11	0.481578394235626	4	FACETS	1	0.962	1	0.614	0.542	0.691	CLONAL	1	TRUE	2	0.65531282356863	4		230	296	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0000797-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	38	344	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		344	773	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099346	27099346	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000800-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	28	215	0	ENST00000324856.7:c.3583A>G	p.Ser1195Gly	p.S1195G	ENST00000324856	NM_006015.4	1195	Agt/Ggt	14/20	1	2	FACETS	0.228	0.182	0.282	0.228	0.182	0.282	SUBCLONAL	1	TRUE	1	0.457256872714132	2		215	536	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446330	29446330	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000800-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	49	196	0	ENST00000389048.3:c.3237G>T	p.Lys1079Asn	p.K1079N	ENST00000389048	NM_004304.4	1079	aaG/aaT	20/29	1	2	FACETS	0.493	0.418	0.575	0.493	0.418	0.575	SUBCLONAL	1	TRUE	1	0.457256872714132	2		196	435	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587144	189587144	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000800-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	277	217	0	ENST00000264731.3:c.1161G>C	p.Met387Ile	p.M387I	ENST00000264731	NM_003722.4	387	atG/atC	9/14	0.457256872714132	5	FACETS	1	0.945	1	0.671	0.63	0.712	CLONAL	2	TRUE	2	0.457256872714132	5		217	1015	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133553	55133553	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000800-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	154	227	0	ENST00000257290.5:c.857G>C	p.Gly286Ala	p.G286A	ENST00000257290	NM_006206.4	286	gGa/gCa	6/23	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.457256872714132	2		227	608	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158139	106158139	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000800-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	48	160	1	ENST00000380013.4:c.3040G>A	p.Ala1014Thr	p.A1014T	ENST00000380013	NM_001127208.2	1014	Gca/Aca	3/11	0.209937378064883	4	FACETS	0.559	0.472	0.655	0.28	0.236	0.328	INDETERMINATE	1	TRUE	2	0.457256872714132	4		161	547	SUCCESS
APC	324	MSKCC	GRCh37	5	112175876	112175876	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085992	NA	P-0000800-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	106	125	0	ENST00000257430.4:c.4585C>T	p.Gln1529Ter	p.Q1529*	ENST00000257430	NM_000038.5	1529	Cag/Tag	16/16	0.457256872714132	2	FACETS	0.865	0.788	0.943	0.865	0.788	0.943	CLONAL	2	TRUE	0	0.457256872714132	2		125	268	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672644	30672644	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000800-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	276	338	0	ENST00000376406.3:c.4316G>A	p.Arg1439Lys	p.R1439K	ENST00000376406	NM_014641.2	1439	aGg/aAg	10/15	0.403839414347244	4	FACETS	1	0.987	1			1	CLONAL	2	TRUE	NA	0.457256872714132	4		338	763	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157454327	157454327	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs766942261	NA	P-0000800-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	15	133	0	ENST00000346085.5:c.2537A>G	p.Gln846Arg	p.Q846R	ENST00000346085	NM_020732.3	846	cAg/cGg	8/20	1	2	FACETS	0.246	0.179	0.326	0.246	0.179	0.326	SUBCLONAL	1	TRUE	1	0.457256872714132	2		133	267	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410462	139410462	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000800-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	182	356	0	ENST00000277541.6:c.1640C>A	p.Pro547His	p.P547H	ENST00000277541	NM_017617.3	547	cCc/cAc	10/34	0.457256872714132	2	FACETS	0.943	0.881	1	0.943	0.881	1	CLONAL	2	TRUE	0	0.457256872714132	2		356	422	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291149	10291149	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000800-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	352	471	0	ENST00000340748.4:c.322G>C	p.Glu108Gln	p.E108Q	ENST00000340748		108	Gaa/Caa	4/40	0.457256872714132	1	FACETS	0.813	0.776	0.851	1	0.996	1	CLONAL	2	TRUE	0	0.457256872714132	1		471	730	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602619	10602619	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1239985410	NA	P-0000800-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	169	240	0	ENST00000171111.5:c.959G>T	p.Arg320Leu	p.R320L	ENST00000171111	NM_203500.1	320	cGg/cTg	3/6	0.457256872714132	1	FACETS	0.839	0.784	0.893	1	0.992	1	CLONAL	2	TRUE	0	0.457256872714132	1		240	340	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273219	18273219	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000800-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	218	357	0	ENST00000222254.8:c.1012G>T	p.Glu338Ter	p.E338*	ENST00000222254	NM_005027.3	338	Gag/Tag	9/16	0.340721030867917	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.457256872714132	1		357	541	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145609	24145609	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000800-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	54	159	0	ENST00000263121.7:c.628G>A	p.Glu210Lys	p.E210K	ENST00000263121	NM_003073.3	210	Gag/Aag	5/9	0.13938097561796	0	FACETS	0.548	0.473	0.628			1	INDETERMINATE	1	TRUE	0	0.457256872714132	0		159	234	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112422	115112422	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000800-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	137	256	0	ENST00000257566.3:c.1318del	p.Ala440ProfsTer192	p.A440Pfs*192	ENST00000257566	NM_016569.3	440	Gcc/cc	7/8	0.178176598724886	3	FACETS	0.84	0.771	0.912			1	INDETERMINATE	2	TRUE	NA	0.457256872714132	3		256	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576922	7576922	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000800-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	184	181	0	ENST00000269305.4:c.924del	p.Asn310ThrfsTer35	p.N310Tfs*35	ENST00000269305	NM_001126112.2	308	ctG/ct	9/11	0.457256872714132	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.457256872714132	2		181	367	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222960	5222962	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0000800-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	51	141	0	ENST00000357368.4:c.2841_2843del	p.Leu948del	p.L948del	ENST00000357368	NM_002850.3	947	ctTCTc/ctc	18/38	0.457256872714132	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.457256872714132	1		141	159	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143260	24143260	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000800-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	112	421	0	ENST00000263121.7:c.496del	p.Leu166PhefsTer10	p.L166Ffs*10	ENST00000263121	NM_003073.3	164	ttC/tt	4/9	0.13938097561796	0	FACETS	0.512	0.463	0.564			1	INDETERMINATE	1	TRUE	0	0.457256872714132	0		421	519	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431597	49431598	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0000800-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	123	245	0	ENST00000301067.7:c.9541_9542delinsTT	p.Glu3181Leu	p.E3181L	ENST00000301067	NM_003482.3	3181	GAg/TTg	34/54	0.222905845609992	5	FACETS	1	0.928	1	0.681	0.62	0.744	INDETERMINATE	2	TRUE	2	0.457256872714132	5		245	444	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692922	89692922	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201044	NA	P-0000805-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	465	165	279	0	ENST00000371953.3:c.406T>C	p.Cys136Arg	p.C136R	ENST00000371953	NM_000314.4	136	Tgt/Cgt	5/9	0.209208248270409	3	FACETS	1	0.982	1	0.818	0.754	0.884	CLONAL	2	TRUE	0	0.238982031476854	3		279	630	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932980	39932980	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238996683	NA	P-0000806-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	559	149	378	0	ENST00000378444.4:c.1619G>A	p.Arg540Gln	p.R540Q	ENST00000378444	NM_001123385.1	540	cGg/cAg	4/15	0.404027651148712	5	FACETS	0.837	0.766	0.91			1	CLONAL	2	TRUE	NA	0.404027651148712	5		378	708	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440855	52440855	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553645702	NA	P-0000806-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	293	77	239	0	ENST00000460680.1:c.649G>A	p.Ala217Thr	p.A217T	ENST00000460680	NM_004656.3	217	Gcc/Acc	8/17	0.404027651148712	3	FACETS	1	0.964	1	0.619	0.547	0.696	CLONAL	1	TRUE	1	0.404027651148712	3		239	370	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159041	24159041	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000806-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	350	62	164	0	ENST00000263121.7:c.713C>A	p.Ala238Asp	p.A238D	ENST00000263121	NM_003073.3	238	gCc/gAc	6/9	0.404027651148712	5	FACETS	1	0.948	1			1	CLONAL	1	TRUE	NA	0.404027651148712	5		164	412	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0000830-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	140	347	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.345387066116407	4	FACETS	1	0.988	1	0.741	0.679	0.804	INDETERMINATE	1	TRUE	2	0.665492766132702	4		347	473	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184960	32184960	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000853-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	44	335	0	ENST00000375023.3:c.1708C>T	p.Pro570Ser	p.P570S	ENST00000375023	NM_004557.3	570	Cct/Tct	10/30	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	FALSE	1	0.404299610135654	2		335	217	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401046	139401046	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000853-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	83	598	0	ENST00000277541.6:c.3947G>A	p.Cys1316Tyr	p.C1316Y	ENST00000277541	NM_017617.3	1316	tGc/tAc	24/34	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	FALSE	1	0.404299610135654	2		598	383	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81534603	81534603	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000853-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	66	387	0	ENST00000298171.2:c.248T>C	p.Val83Ala	p.V83A	ENST00000298171	NM_000369.2	83	gTa/gCa	3/10	0.173098957439052	0	FACETS	0.828	0.728	0.932			1	INDETERMINATE	1	FALSE	0	0.404299610135654	0		387	235	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226139	53226139	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000853-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	25	476	0	ENST00000375401.3:c.2710C>A	p.Leu904Met	p.L904M	ENST00000375401	NM_004187.3	904	Ctg/Atg	19/26	0.404299610135654	1	FACETS	0.305	0.24	0.379	0.305	0.24	0.379	SUBCLONAL	1	FALSE	0	0.404299610135654	1		476	324	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0000869-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	421	418	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.576332599606746	2	FACETS	0.954	0.918	0.989	0.954	0.918	0.989	CLONAL	2	TRUE	0	0.611450567376655	2		418	722	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295723	212295723	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000869-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	121	407	0	ENST00000342788.4:c.2590C>A	p.Leu864Ile	p.L864I	ENST00000342788	NM_005235.2	864	Cta/Ata	21/28	0.591657333316605	3	FACETS	0.902	0.818	0.99	0.451	0.409	0.495	CLONAL	1	TRUE	1	0.611450567376655	3		407	573	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987120	69987120	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000869-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	137	305	0	ENST00000394351.3:c.181G>T	p.Val61Phe	p.V61F	ENST00000394351	NM_000248.3	61	Gtc/Ttc	2/9	0.591657333316605	3	FACETS	0.808	0.736	0.884	0.404	0.368	0.442	CLONAL	1	TRUE	1	0.611450567376655	3		305	724	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205020	128205020	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000869-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	114	216	0	ENST00000341105.2:c.421T>C	p.Tyr141His	p.Y141H	ENST00000341105	NM_032638.4	141	Tac/Cac	3/6	0.591657333316605	3	FACETS	1	0.952	1	0.54	0.489	0.593	CLONAL	1	TRUE	1	0.611450567376655	3		216	451	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916860	178916862	+	missense_variant	Missense_Mutation	TNP	TTT	TTT	AAG	novel	NA	P-0000869-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	133	406	0	ENST00000263967.3:c.247_249delinsAAG	p.Phe83Lys	p.F83K	ENST00000263967	NM_006218.2	83	TTT/AAG	2/21	0.591657333316605	3	FACETS	0.991	0.904	1	0.496	0.452	0.541	CLONAL	1	TRUE	1	0.611450567376655	3		406	573	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172433	108172433	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	526	394	0	ENST00000278616.4:c.5236G>C	p.Gly1746Arg	p.G1746R	ENST00000278616	NM_000051.3	1746	Gga/Cga	35/63	0.465959387509079	4	FACETS	0.917	0.882	0.953	0.917	0.882	0.953	INDETERMINATE	2	TRUE	2	0.907644362893327	4		394	1205	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671746	67671746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	217	182	0	ENST00000264010.4:c.2155G>A	p.Glu719Lys	p.E719K	ENST00000264010	NM_006565.3	719	Gag/Aag	12/12	0.685360313385083	3	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.907644362893327	3		182	616	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764146326	NA	P-0000878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	812	313	0	ENST00000269305.4:c.841G>A	p.Asp281Asn	p.D281N	ENST00000269305	NM_001126112.2	281	Gac/Aac	8/11	0.907644362893327	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.907644362893327	2		313	848	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027248	49027248	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0000888-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	350	263	0	ENST00000267163.4:c.1814+1G>T		p.X605_splice	ENST00000267163	NM_000321.2	605			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		263	385	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0000890-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	168	278	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	1	2	FACETS	0.915	0.851	0.98	0.915	0.851	0.98	CLONAL	1	TRUE	1	0.893495606033366	2		278	411	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439712	51439712	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000890-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	82	220	0	ENST00000262662.1:c.277C>T	p.Gln93Ter	p.Q93*	ENST00000262662		93	Caa/Taa	4/4	0.893495606033366	1	FACETS	0.284	0.252	0.317	0.284	0.252	0.317	SUBCLONAL	1	TRUE	0	0.893495606033366	1		220	358	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148701	20148727	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AATGTATCAGTTTCATTGATTTTAGCT	AATGTATCAGTTTCATTGATTTTAGCT	-	novel	NA	P-0000890-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	44	141	0	ENST00000379607.5:c.338-2_362del		p.X113_splice	ENST00000379607	NM_001412.3	113		6/7	1	1	FACETS	0.505	0.436	0.575	0.505	0.436	0.575	SUBCLONAL	1	TRUE	0	0.893495606033366	1		141	108	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0000899-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	160	428	1	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	NA	2	FACETS	0.991	0.928	1			1	INDETERMINATE	2	TRUE	NA	0.548952393249107	2		429	294	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149204	61149204	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs763552533	NA	P-0000899-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	23	282	0	ENST00000295025.8:c.1394A>G	p.Asn465Ser	p.N465S	ENST00000295025	NM_002908.2	465	aAt/aGt	11/11	0.548952393249107	3	FACETS	0.324	0.252	0.406	0.162	0.126	0.203	SUBCLONAL	1	TRUE	1	0.548952393249107	3		282	330	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86669978	86669978	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0000899-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	124	212	0	ENST00000274376.6:c.1777-2A>T		p.X593_splice	ENST00000274376	NM_002890.2	593			0.534804959093606	2	FACETS	0.753	0.692	0.815	0.753	0.692	0.815	SUBCLONAL	2	TRUE	0	0.548952393249107	2		212	300	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526106	66526106	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000899-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	85	166	1	ENST00000358598.2:c.937G>T	p.Val313Phe	p.V313F	ENST00000358598	NM_212471.2	313	Gtt/Ttt	10/11	0.548952393249107	3	FACETS	0.956	0.85	1			1	CLONAL	1	TRUE	NA	0.548952393249107	3		167	413	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795741	42795762	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGGGTGGCTCAGCCCAGCTG	CCCGGGTGGCTCAGCCCAGCTG	-	novel	NA	P-0000899-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	34	444	0	ENST00000575354.2:c.2731_2752del	p.Pro911CysfsTer6	p.P911Cfs*6	ENST00000575354	NM_015125.3	910	ccCCCGGGTGGCTCAGCCCAGCTG/cc	11/20	0.432052024209516	5	FACETS	0.54	0.441	0.652	0.18	0.147	0.218	SUBCLONAL	1	TRUE	2	0.548952393249107	5		444	418	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0000903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	85	663	1	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.153804840256534	4	FACETS	0.603	0.531	0.68	0.301	0.265	0.34	INDETERMINATE	1	FALSE	2	0.326098157819376	4		664	1147	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	120	628	0	ENST00000397062.3:c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	NM_006164.4	34	Cga/Gga	2/5	0.326098157819376	4	FACETS	0.763	0.687	0.844	0.382	0.343	0.422	SUBCLONAL	1	FALSE	2	0.326098157819376	4		628	1279	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153596	55153596	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0000903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	65	528	0	ENST00000257290.5:c.2563-1G>C		p.X855_splice	ENST00000257290	NM_006206.4	855			NA	2	FACETS	0.575	0.498	0.659			1	INDETERMINATE	1	FALSE	NA	0.326098157819376	2		528	693	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484163	8484163	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	167	612	0	ENST00000356435.5:c.3369G>T	p.Met1123Ile	p.M1123I	ENST00000356435		1123	atG/atT	19/35	0.326098157819376	3	FACETS	1	0.978	1	0.59	0.541	0.64	CLONAL	1	FALSE	1	0.326098157819376	3		612	1010	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781032	135781032	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	101	798	0	ENST00000298552.3:c.1933C>T	p.Pro645Ser	p.P645S	ENST00000298552	NM_001162426.1	645	Cca/Tca	15/23	1	2	FACETS	0.706	0.63	0.787	0.706	0.63	0.787	SUBCLONAL	1	FALSE	1	0.326098157819376	2		798	877	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406651	70406651	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	95	793	1	ENST00000373644.4:c.4165G>C	p.Asp1389His	p.D1389H	ENST00000373644	NM_030625.2	1389	Gac/Cac	4/12	1	2	FACETS	0.599	0.532	0.67	0.599	0.532	0.67	SUBCLONAL	1	FALSE	1	0.326098157819376	2		794	973	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690619	88690619	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs965378877	NA	P-0000903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	76	341	0	ENST00000360948.2:c.411C>G	p.Asn137Lys	p.N137K	ENST00000360948	NM_001012338.2	137	aaC/aaG	5/19	0.216029225626467	3	FACETS	0.839	0.736	0.95	0.42	0.368	0.475	CLONAL	1	FALSE	1	0.326098157819376	3		341	646	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23635412	23635412	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	54	513	0	ENST00000261584.4:c.2752C>G	p.Pro918Ala	p.P918A	ENST00000261584	NM_024675.3	918	Cca/Gca	8/13	1	2	FACETS	0.535	0.456	0.621	0.535	0.456	0.621	SUBCLONAL	1	FALSE	1	0.326098157819376	2		513	619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577508	7577508	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	32	343	0	ENST00000269305.4:c.773A>T	p.Glu258Val	p.E258V	ENST00000269305	NM_001126112.2	258	gAa/gTa	7/11	NA	2	FACETS	0.764	0.623	0.921			1	INDETERMINATE	1	FALSE	NA	0.326098157819376	2		343	257	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101956	11101956	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000903-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	54	262	0	ENST00000358026.2:c.1376A>C	p.Gln459Pro	p.Q459P	ENST00000358026	NM_001128849.1	459	cAg/cCg	8/36	0.326098157819376	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	FALSE	0	0.326098157819376	1		262	253	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0000913-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	717	440	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.304272313062964	13	FACETS	0.987	0.953	1			1	CLONAL	7	TRUE	NA	0.304272313062964	13		440	1823	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0000913-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	360	315	0	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	0.254375823394975	2	FACETS	0.941	0.891	0.991	0.941	0.891	0.991	CLONAL	2	TRUE	0	0.304272313062964	2		315	1258	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944329	206944329	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000913-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1214	177	233	0	ENST00000423557.1:c.301C>T	p.Gln101Ter	p.Q101*	ENST00000423557	NM_000572.2	101	Caa/Taa	3/5	0.304272313062964	4	FACETS	1	0.965	1	0.545	0.501	0.592	CLONAL	1	TRUE	2	0.304272313062964	4		233	1391	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404581	8404581	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000913-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	149	275	0	ENST00000356435.5:c.4166T>G	p.Val1389Gly	p.V1389G	ENST00000356435		1389	gTa/gGa	25/35	0.304272313062964	1	FACETS	0.897	0.819	0.978	0.897	0.819	0.978	CLONAL	1	TRUE	0	0.304272313062964	1		275	926	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0000938-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	121	233	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.163046051598532	2	FACETS	1	0.981	1	0.66	0.6	0.723	INDETERMINATE	1	TRUE	0	0.384345751421522	2		233	477	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100081	27100081	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000938-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	146	418	0	ENST00000324856.7:c.3877G>T	p.Gly1293Ter	p.G1293*	ENST00000324856	NM_006015.4	1293	Gga/Tga	16/20	1	2	FACETS	0.74	0.675	0.809	0.74	0.675	0.809	SUBCLONAL	1	TRUE	1	0.384345751421522	2		418	1026	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639190	176639190	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000938-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	22	55	0	ENST00000439151.2:c.3790G>C	p.Glu1264Gln	p.E1264Q	ENST00000439151	NM_022455.4	1264	Gaa/Caa	5/23	0.213159719211733	3	FACETS	0.954	0.748	1	0.477	0.374	0.595	INDETERMINATE	1	TRUE	1	0.384345751421522	3		55	143	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0000946-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	88	140	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.450365362825678	2	FACETS	1	0.98	1	0.705	0.635	0.777	CLONAL	1	TRUE	0	0.519994549969828	2		142	240	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0000947-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	70	229	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.426559630639643	1	FACETS	0.716	0.629	0.808	0.716	0.629	0.808	SUBCLONAL	1	TRUE	0	0.454013234989556	1		229	333	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652129	36652129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34916193	NA	P-0000947-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	44	187	0	ENST00000244741.5:c.251G>A	p.Arg84Gln	p.R84Q	ENST00000244741	NM_000389.4	84	cGa/cAa	2/3	0.291107972439847	5	FACETS	0.512	0.429	0.605			1	SUBCLONAL	1	TRUE	NA	0.454013234989556	5		187	636	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38978753	38978753	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs760798451	NA	P-0000947-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	18	111	0	ENST00000357387.3:c.754-1G>A		p.X252_splice	ENST00000357387	NM_152756.3	252			0.286945760994961	4	FACETS	0.403	0.303	0.521	0.202	0.151	0.261	SUBCLONAL	1	TRUE	2	0.454013234989556	4		111	286	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100436	8100436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1220437638	NA	P-0000947-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	49	397	0	ENST00000346208.3:c.410C>T	p.Ser137Leu	p.S137L	ENST00000346208		137	tCg/tTg	3/6	0.13937094444317	5	FACETS	0.471	0.397	0.552	0.157	0.132	0.184	INDETERMINATE	1	TRUE	2	0.454013234989556	5		397	771	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692893	89692893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1114167656	NA	P-0000947-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	28	112	0	ENST00000371953.3:c.377C>T	p.Ala126Val	p.A126V	ENST00000371953	NM_000314.4	126	gCt/gTt	5/9	0.13937094444317	5	FACETS	0.964	0.776	1	0.321	0.258	0.393	INDETERMINATE	1	TRUE	2	0.454013234989556	5		112	215	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023681	1023681	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000947-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	33	133	0	ENST00000358495.3:c.883C>T	p.Pro295Ser	p.P295S	ENST00000358495	NM_134424.2	295	Cct/Tct	10/12	0.129934989236213	3	FACETS	0.498	0.406	0.602			1	INDETERMINATE	1	TRUE	NA	0.454013234989556	3		133	358	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779413	3779413	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000947-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	33	215	0	ENST00000262367.5:c.5635C>G	p.Gln1879Glu	p.Q1879E	ENST00000262367	NM_004380.2	1879	Cag/Gag	31/31	0.454013234989556	3	FACETS	0.297	0.241	0.36	0.148	0.12	0.18	SUBCLONAL	1	TRUE	1	0.454013234989556	3		215	601	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245724	41245724	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000947-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	27	274	0	ENST00000357654.3:c.1824G>C	p.Lys608Asn	p.K608N	ENST00000357654	NM_007294.3	608	aaG/aaC	10/23	1	2	FACETS	0.325	0.258	0.401	0.325	0.258	0.401	SUBCLONAL	1	TRUE	1	0.454013234989556	2		274	366	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927977	178927982	+	inframe_deletion	In_Frame_Del	DEL	CACTGT	CACTGT	-	novel	NA	P-0000947-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	45	88	0	ENST00000263967.3:c.1256_1261del	p.His419_Cys420del	p.H419_C420del	ENST00000263967	NM_006218.2	419	CACTGT/-	8/21	0.454013234989556	3	FACETS	1	0.952	1	0.657	0.56	0.762	CLONAL	1	TRUE	1	0.454013234989556	3		88	185	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0000950-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	207	290	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.269285727720924	4	FACETS	0.928	0.865	0.993	0.928	0.865	0.993	CLONAL	3	TRUE	1	0.269285727720924	4		290	701	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474079	29474079	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000950-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	34	343	1	ENST00000389048.3:c.2096C>A	p.Ala699Glu	p.A699E	ENST00000389048	NM_004304.4	699	gCa/gAa	12/29	0.269285727720924	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	0	0.269285727720924	1		344	189	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190742145	190742145	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000950-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	20	305	0	ENST00000441310.2:c.2782C>A	p.Leu928Ile	p.L928I	ENST00000441310	NM_000534.4	928	Ctt/Att	13/13	0.269285727720924	5	FACETS	0.529	0.404	0.677	0.176	0.134	0.226	SUBCLONAL	1	TRUE	2	0.269285727720924	5		305	394	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285196	198285196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000950-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	59	227	0	ENST00000335508.6:c.371G>A	p.Arg124Gln	p.R124Q	ENST00000335508	NM_012433.2	124	cGg/cAg	4/25	0.269285727720924	5	FACETS	0.767	0.662	0.88	0.511	0.441	0.587	SUBCLONAL	2	TRUE	2	0.269285727720924	5		227	401	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806215	1806215	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000950-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	14	362	0	ENST00000260795.2:c.1234C>A	p.His412Asn	p.H412N	ENST00000260795		412	Cac/Aac	8/17	0.269285727720924	0	FACETS	0.704	0.514	0.927			1	CLONAL	1	TRUE	0	0.269285727720924	0		362	108	SUCCESS
APC	324	MSKCC	GRCh37	5	112157607	112157607	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000950-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	188	225	0	ENST00000257430.4:c.1327G>T	p.Glu443Ter	p.E443*	ENST00000257430	NM_000038.5	443	Gaa/Taa	11/16	0.269285727720924	5	FACETS	0.911	0.848	0.975	1	0.985	1	CLONAL	4	TRUE	2	0.269285727720924	5		225	538	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175951	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1392778905	NA	P-0000950-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	43	125	0	ENST00000257430.4:c.4660G>T	p.Glu1554Ter	p.E1554*	ENST00000257430	NM_000038.5	1554	Gaa/Taa	16/16	0.269285727720924	5	FACETS	0.752	0.633	0.883	0.502	0.422	0.589	SUBCLONAL	2	TRUE	2	0.269285727720924	5		125	298	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845410	151845410	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000950-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	27	251	1	ENST00000262189.6:c.13602G>T	p.Gln4534His	p.Q4534H	ENST00000262189	NM_170606.2	4534	caG/caT	52/59	0.269285727720924	5	FACETS	0.687	0.546	0.848	0.229	0.182	0.283	SUBCLONAL	1	TRUE	2	0.269285727720924	5		252	410	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446201	70446201	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000950-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	24	376	0	ENST00000373644.4:c.5141C>A	p.Ser1714Ter	p.S1714*	ENST00000373644	NM_030625.2	1714	tCa/tAa	11/12	0.269285727720924	3	FACETS	0.502	0.393	0.628	0.251	0.196	0.314	SUBCLONAL	1	TRUE	1	0.269285727720924	3		376	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000950-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	38	152	0	ENST00000269305.4:c.380C>A	p.Ser127Tyr	p.S127Y	ENST00000269305	NM_001126112.2	127	tCc/tAc	5/11	0.269285727720924	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	2	TRUE	0	0.269285727720924	2		152	126	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15943773	15943773	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000950-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	147	377	0	ENST00000268712.3:c.6715C>A	p.Pro2239Thr	p.P2239T	ENST00000268712	NM_006311.3	2239	Cca/Aca	43/46	0.269285727720924	2	FACETS	0.892	0.823	0.962	1	0.986	1	CLONAL	3	TRUE	0	0.269285727720924	2		377	408	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684327	29684327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs560262404	NA	P-0000950-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	167	333	0	ENST00000356175.3:c.7847G>A	p.Arg2616Gln	p.R2616Q	ENST00000356175	NM_000267.3	2616	cGa/cAa	53/57	0.269285727720924	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.269285727720924	2		333	553	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047995	180047995	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762560832	NA	P-0000955-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	291	139	429	0	ENST00000261937.6:c.2180C>T	p.Ala727Val	p.A727V	ENST00000261937	NM_182925.4	727	gCg/gTg	15/30	0.168792589715424	2	FACETS	1	0.978	1	0.597	0.549	0.648	INDETERMINATE	1	TRUE	0	0.541094886935352	2		429	430	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0000955-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	171	319	358	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.535853652262959	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.541094886935352	2		358	490	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844246	68844246	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0000955-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	100	150	270	0	ENST00000261769.5:c.832+2T>C		p.X278_splice	ENST00000261769	NM_004360.3	278			NA	2	FACETS	1	0.98	1			1	INDETERMINATE	2	TRUE	NA	0.541094886935352	2		270	250	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950292	17950292	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000955-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	327	66	352	0	ENST00000458235.1:c.1435C>A	p.Pro479Thr	p.P479T	ENST00000458235	NM_000215.3	479	Ccc/Acc	10/24	1	2	FACETS	0.621	0.541	0.706	0.621	0.541	0.706	SUBCLONAL	1	TRUE	1	0.541094886935352	2		352	393	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52725470	52725470	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000955-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	407	71	424	0	ENST00000322088.6:c.1637A>T	p.Lys546Met	p.K546M	ENST00000322088	NM_014225.5	546	aAg/aTg	13/15	1	2	FACETS	0.549	0.48	0.623	0.549	0.48	0.623	SUBCLONAL	1	TRUE	1	0.541094886935352	2		424	478	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0000963-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	203	440	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.382019303244369	3	FACETS	1	0.989	1	0.671	0.625	0.719	CLONAL	1	TRUE	1	0.571877750424741	3		440	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579440	7579440	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs867725248	NA	P-0000963-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	74	215	0	ENST00000269305.4:c.247del	p.Ala83ArgfsTer40	p.A83Rfs*40	ENST00000269305	NM_001126112.2	83	Gcg/cg	4/11	0.571877750424741	1	FACETS	0.888	0.792	0.988	0.888	0.792	0.988	CLONAL	1	TRUE	0	0.571877750424741	1		215	208	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508291	38508291	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000963-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	174	433	0	ENST00000254066.5:c.599C>T	p.Pro200Leu	p.P200L	ENST00000254066	NM_000964.3	200	cCt/cTt	5/9	NA	2	FACETS	0.945	0.874	1			1	INDETERMINATE	1	TRUE	NA	0.571877750424741	2		433	644	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0000966-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	242	48	236	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.447	0.38	0.52	0.447	0.38	0.52	SUBCLONAL	1	TRUE	1	0.740167074489266	2		236	290	SUCCESS
AR	367	MSKCC	GRCh37	X	66943543	66943543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852581	NA	P-0000966-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	113	317	285	0	ENST00000374690.3:c.2623C>T	p.His875Tyr	p.H875Y	ENST00000374690	NM_000044.3	875	Cat/Tat	8/8	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.740167074489266	1		285	430	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864233	151864233	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000966-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	610	108	350	0	ENST00000262189.6:c.9748C>T	p.Gln3250Ter	p.Q3250*	ENST00000262189	NM_170606.2	3250	Cag/Tag	42/59	0.709370777903493	3	FACETS	0.557	0.5	0.617	0.278	0.25	0.309	SUBCLONAL	1	TRUE	1	0.740167074489266	3		350	718	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435675	56435675	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000966-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	193	39	161	0	ENST00000407977.2:c.1462C>T	p.Gln488Ter	p.Q488*	ENST00000407977		488	Cag/Tag	9/10	1	2	FACETS	0.454	0.379	0.536	0.454	0.379	0.536	SUBCLONAL	1	TRUE	1	0.740167074489266	2		161	232	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741807	40741807	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000966-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	386	31	339	0	ENST00000392038.2:c.1165C>T	p.Pro389Ser	p.P389S	ENST00000392038	NM_001626.4	389	Ccc/Tcc	11/14	1	2	FACETS	0.201	0.162	0.245	0.201	0.162	0.245	SUBCLONAL	1	TRUE	1	0.740167074489266	2		339	417	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485865	57485865	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750103665	NA	P-0000966-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	408	97	350	0	ENST00000371085.3:c.1166G>A	p.Arg389His	p.R389H	ENST00000371085	NM_000516.4	389	cGt/cAt	13/13	1	2	FACETS	0.519	0.464	0.577	0.519	0.464	0.577	SUBCLONAL	1	TRUE	1	0.740167074489266	2		350	505	SUCCESS
AR	367	MSKCC	GRCh37	X	66766151	66766151	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000966-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	58	173	184	0	ENST00000374690.3:c.1163A>G	p.Lys388Arg	p.K388R	ENST00000374690	NM_000044.3	388	aAg/aGg	1/8	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.740167074489266	1		184	231	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229240	123229240	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs867285087	NA	P-0000966-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	442	32	264	0	ENST00000218089.9:c.3724C>T	p.Arg1242Ter	p.R1242*	ENST00000218089	NM_001042749.1	1242	Cga/Tga	34/35	1	1	FACETS	0.115	0.093	0.14	0.115	0.093	0.14	SUBCLONAL	1	TRUE	0	0.740167074489266	1		264	474	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412882	49412886	+	frameshift_variant	Frame_Shift_Del	DEL	CTCGA	CTCGA	-	novel	NA	P-0000966-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	500	190	571	0	ENST00000418115.1:c.137_141del	p.Ile46SerfsTer20	p.I46Sfs*20	ENST00000418115	NM_001664.2	46	aTCGAG/a	2/5	0.123855345566764	3	FACETS	1	0.943	1	0.51	0.473	0.548	INDETERMINATE	1	TRUE	1	0.740167074489266	3		571	690	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022900	31022901	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0000966-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	296	171	364	0	ENST00000375687.4:c.2385_2386del	p.Trp796GlyfsTer3	p.W796Gfs*3	ENST00000375687	NM_015338.5	795	tcCTgg/tcgg	13/13	1	2	FACETS	0.989	0.919	1	0.989	0.919	1	CLONAL	1	TRUE	1	0.740167074489266	2		364	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0000977-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	115	153	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			NA	2	FACETS	0.858	0.782	0.935			1	INDETERMINATE	2	TRUE	NA	0.406254202450899	2		153	330	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257885	16257885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779004613	NA	P-0000977-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	32	191	2	ENST00000375759.3:c.5150C>T	p.Ala1717Val	p.A1717V	ENST00000375759	NM_015001.2	1717	gCg/gTg	11/15	1	2	FACETS	0.67	0.547	0.807	0.67	0.547	0.807	SUBCLONAL	1	TRUE	1	0.406254202450899	2		193	235	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372022	55372022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000977-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	26	205	0	ENST00000297316.4:c.712G>A	p.Ala238Thr	p.A238T	ENST00000297316	NM_022454.3	238	Gcc/Acc	2/2	0.319169426887601	2	FACETS	0.391	0.31	0.484	0.196	0.155	0.243	SUBCLONAL	1	TRUE	0	0.406254202450899	2		205	327	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974732	21974732	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs878853650	NA	P-0000977-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	189	579	0	ENST00000304494.5:c.95T>C	p.Leu32Pro	p.L32P	ENST00000304494	NM_000077.4	32	cTg/cCg	1/3	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.406254202450899	2		579	627	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117527	4117527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774875456	NA	P-0000977-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	44	197	0	ENST00000262948.5:c.193G>A	p.Gly65Ser	p.G65S	ENST00000262948	NM_030662.3	65	Ggc/Agc	2/11	0.335003104554857	1	FACETS	0.744	0.63	0.868	0.744	0.63	0.868	SUBCLONAL	1	TRUE	0	0.406254202450899	1		197	232	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644705	134644706	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0000977-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	40	372	0	ENST00000398015.3:c.106_107del	p.Ala36GlnfsTer14	p.A36Qfs*14	ENST00000398015	NM_004441.4	36	GCc/c	2/16	1	2	FACETS	0.425	0.353	0.506	0.425	0.353	0.506	SUBCLONAL	1	TRUE	1	0.406254202450899	2		372	463	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0000982-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	303	344	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.288906521580576	4	FACETS	0.939	0.889	0.99	0.939	0.889	0.99	CLONAL	3	FALSE	1	0.365912335216022	4		344	803	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0000982-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	72	175	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.288906521580576	4	FACETS	0.999	0.874	1	0.333	0.291	0.378	CLONAL	1	FALSE	1	0.365912335216022	4		175	538	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637453	47637453	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754478179	NA	P-0000982-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	192	419	0	ENST00000233146.2:c.587C>T	p.Pro196Leu	p.P196L	ENST00000233146	NM_000251.2	196	cCa/cTa	3/16	0.288906521580576	4	FACETS	0.844	0.786	0.904	0.844	0.786	0.904	CLONAL	3	FALSE	1	0.365912335216022	4		419	566	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0000982-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	334	384	1	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	0.365912335216022	5	FACETS	0.968	0.927	1	0.968	0.927	1	CLONAL	5	FALSE	0	0.365912335216022	5		385	584	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128848606	128848606	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000982-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	292	542	0	ENST00000249373.3:c.1271T>C	p.Met424Thr	p.M424T	ENST00000249373	NM_005631.4	424	aTg/aCg	7/12	0.365912335216022	4	FACETS	0.934	0.883	0.986	0.934	0.883	0.986	CLONAL	3	FALSE	1	0.365912335216022	4		542	778	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828861	26828861	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000982-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	476	460	1	ENST00000381527.3:c.83G>A	p.Gly28Asp	p.G28D	ENST00000381527	NM_001260.1	28	gGc/gAc	1/13	0.365912335216022	7	FACETS	1	0.983	1			1	CLONAL	5	FALSE	NA	0.365912335216022	7		461	957	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0000982-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	8757	387	11	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	0.365912335216022	45	FACETS	0.995	0.991	0.998			1	CLONAL	46	FALSE	NA	0.365912335216022	45		398	9276	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944260	206944260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746523858	NA	P-0000982-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	84	464	2	ENST00000423557.1:c.370C>T	p.Arg124Trp	p.R124W	ENST00000423557	NM_000572.2	124	Cgg/Tgg	3/5	0.359220006516729	4	FACETS	0.995	0.88	1	0.498	0.44	0.56	CLONAL	1	FALSE	2	0.365912335216022	4		466	630	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850765	63850765	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000982-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	145	553	0	ENST00000279873.7:c.1543G>C	p.Glu515Gln	p.E515Q	ENST00000279873	NM_032199.2	515	Gag/Cag	10/10	0.365912335216022	4	FACETS	1	0.973	1	0.291	0.265	0.318	CLONAL	1	FALSE	0	0.365912335216022	4		553	931	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58701067	58701067	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000982-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	100	1118	0	ENST00000305921.3:c.658G>C	p.Glu220Gln	p.E220Q	ENST00000305921	NM_003620.3	220	Gaa/Caa	2/6	0.365912335216022	5	FACETS	0.648	0.576	0.724	0.162	0.144	0.181	SUBCLONAL	1	FALSE	1	0.365912335216022	5		1118	1307	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0000997-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	334	409	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.620328467880593	3	FACETS	0.994	0.947	1	0.994	0.947	1	CLONAL	2	TRUE	1	0.620328467880593	3		409	710	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0000997-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	299	227	0	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	NA	2	FACETS	0.945	0.903	0.987			1	INDETERMINATE	2	TRUE	NA	0.620328467880593	2		227	510	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000997-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	325	227	0	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	NA	2	FACETS	0.916	0.876	0.956			1	INDETERMINATE	2	TRUE	NA	0.620328467880593	2		227	572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0000997-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	413	444	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.257802848859118	3	FACETS	1	0.972	1			1	INDETERMINATE	3	TRUE	NA	0.620328467880593	3		444	579	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094251	193094251	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000997-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	185	290	1	ENST00000367435.3:c.141G>T	p.Lys47Asn	p.K47N	ENST00000367435	NM_024529.4	47	aaG/aaT	2/17	0.566256199684716	4	FACETS	0.9	0.83	0.973	0.45	0.415	0.487	CLONAL	1	TRUE	2	0.620328467880593	4		291	1074	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570814	226570814	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000997-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	206	202	2	ENST00000366794.5:c.1082C>A	p.Thr361Asn	p.T361N	ENST00000366794	NM_001618.3	361	aCc/aAc	8/23	0.566256199684716	4	FACETS	1	0.987	1	0.638	0.592	0.684	CLONAL	1	TRUE	2	0.620328467880593	4		204	844	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736238	243736238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000997-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	104	137	0	ENST00000263826.5:c.809G>A	p.Arg270His	p.R270H	ENST00000263826	NM_005465.4	270	cGt/cAt	8/13	0.566256199684716	4	FACETS	0.801	0.718	0.889	0.401	0.359	0.445	CLONAL	1	TRUE	2	0.620328467880593	4		137	678	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497950	25497950	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000997-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	75	129	0	ENST00000264709.3:c.499C>T	p.Arg167Trp	p.R167W	ENST00000264709	NM_175629.2	167	Cgg/Tgg	6/23	NA	2	FACETS	0.677	0.597	0.762			1	INDETERMINATE	1	TRUE	NA	0.620328467880593	2		129	357	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958863	38958863	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000997-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	402	305	0	ENST00000357387.3:c.2249G>A	p.Trp750Ter	p.W750*	ENST00000357387	NM_152756.3	750	tGg/tAg	23/38	0.609240031700538	4	FACETS	0.934	0.89	0.979	0.467	0.445	0.49	CLONAL	2	TRUE	0	0.620328467880593	4		305	1124	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371005	55371005	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000997-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	70	136	0	ENST00000297316.4:c.307G>T	p.Gly103Cys	p.G103C	ENST00000297316	NM_022454.3	103	Ggc/Tgc	1/2	0.2037475379091	0	FACETS	0.332	0.293	0.373			1	INDETERMINATE	1	TRUE	0	0.620328467880593	0		136	258	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203549	108203549	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000997-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	134	132	0	ENST00000278616.4:c.7849G>A	p.Val2617Ile	p.V2617I	ENST00000278616	NM_000051.3	2617	Gtc/Atc	53/63	0.579320231226053	2	FACETS	0.991	0.908	1	0.495	0.454	0.539	CLONAL	1	TRUE	0	0.620328467880593	2		132	436	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610687	81610687	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767693393	NA	P-0000997-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	90	221	1	ENST00000298171.2:c.2285C>T	p.Thr762Met	p.T762M	ENST00000298171	NM_000369.2	762	aCg/aTg	10/10	0.186190175531169	1	FACETS	0.524	0.468	0.583	0.524	0.468	0.583	INDETERMINATE	1	TRUE	0	0.620328467880593	1		222	382	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853886	59853886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759142191	NA	P-0000997-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	136	302	0	ENST00000259008.2:c.1973G>A	p.Arg658Gln	p.R658Q	ENST00000259008	NM_032043.2	658	cGg/cAg	14/20	0.60616477336758	1	FACETS	0.595	0.544	0.648	0.595	0.544	0.648	SUBCLONAL	1	TRUE	0	0.620328467880593	1		302	508	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231335	5231335	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769069932	NA	P-0000997-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	45	211	0	ENST00000357368.4:c.2141G>A	p.Arg714His	p.R714H	ENST00000357368	NM_002850.3	714	cGc/cAc	14/38	0.234524742114509	1	FACETS	0.325	0.274	0.38	0.325	0.274	0.38	INDETERMINATE	1	TRUE	0	0.620328467880593	1		211	308	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17949084	17949084	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000997-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	169	259	2	ENST00000458235.1:c.1557C>G	p.Asp519Glu	p.D519E	ENST00000458235	NM_000215.3	519	gaC/gaG	11/24	0.294600025098447	4	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.620328467880593	4		261	697	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552732	226552739	+	frameshift_variant	Frame_Shift_Del	DEL	GACCCTGG	GACCCTGG	-	novel	NA	P-0000997-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	88	218	1	ENST00000366794.5:c.2622_2629del	p.Gln875SerfsTer6	p.Q875Sfs*6	ENST00000366794	NM_001618.3	874	tcCCAGGGTCtt/tctt	19/23	0.566256199684716	4	FACETS	0.557	0.492	0.625	0.278	0.246	0.313	SUBCLONAL	1	TRUE	2	0.620328467880593	4		219	826	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517201	NA	P-0001021-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	106	291	0	ENST00000263967.3:c.1637A>C	p.Gln546Pro	p.Q546P	ENST00000263967	NM_006218.2	546	cAg/cCg	10/21	0.708221182893352	3	FACETS	0.871	0.785	0.961	0.435	0.392	0.481	CLONAL	1	TRUE	1	0.7032726417938	3		291	468	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518099	8518099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764400127	NA	P-0001021-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1334	248	663	1	ENST00000356435.5:c.1292C>T	p.Ser431Leu	p.S431L	ENST00000356435		431	tCg/tTg	10/35	0.708221182893352	5	FACETS	0.916	0.854	0.981	0.305	0.284	0.327	CLONAL	1	TRUE	2	0.7032726417938	5		664	1582	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437616	110437616	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001021-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	228	436	0	ENST00000375856.3:c.785C>T	p.Ser262Leu	p.S262L	ENST00000375856	NM_003749.2	262	tCg/tTg	1/2	0.509536247018362	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.7032726417938	1		436	399	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061334	38061334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001021-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	391	872	0	ENST00000250448.2:c.655C>A	p.Arg219Ser	p.R219S	ENST00000250448	NM_004496.3	219	Cgc/Agc	2/2	0.708221182893352	3	FACETS	1	0.965	1	0.511	0.484	0.537	CLONAL	1	TRUE	1	0.7032726417938	3		872	1472	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647416	23647417	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	AA	novel	NA	P-0001021-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	225	827	0	ENST00000261584.4:c.450_451delinsTT	p.Gln150_Gln151delinsHisTer	p.Q150_Q151delinsH*	ENST00000261584	NM_024675.3	150	caGCag/caTTag	4/13	0.708221182893352	3	FACETS	0.674	0.626	0.723			1	SUBCLONAL	1	TRUE	NA	0.7032726417938	3		827	1284	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66781554	66781554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001027-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	27	427	0	ENST00000307102.5:c.962C>A	p.Pro321His	p.P321H	ENST00000307102	NM_002755.3	321	cCt/cAt	9/11	0.124655298014398	5	FACETS	1	0.808	1	0.675	0.539	0.829	CLONAL	2	FALSE	2	0.124655298014398	5		427	254	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263932	104263948	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCCCCCGGCCCCACC	GCGCCCCCGGCCCCACC	-	novel	NA	P-0001027-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	16	87	0	ENST00000369902.3:c.37_53del	p.Thr13TrpfsTer29	p.T13Wfs*29	ENST00000369902	NM_016169.3	8	gGCGCCCCCGGCCCCACC/g	1/12	1	2	FACETS	0.839	0.624	1	1	0.909	1	CLONAL	2	FALSE	1	0.124655298014398	2		87	153	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631839	90631839	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519906	NA	P-0001031-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	262	379	0	ENST00000330062.3:c.514A>T	p.Arg172Trp	p.R172W	ENST00000330062	NM_002168.2	172	Agg/Tgg	4/11	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.669642822053624	2		379	779	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217276	123217276	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001031-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	45	538	0	ENST00000218089.9:c.2930G>C	p.Gly977Ala	p.G977A	ENST00000218089	NM_001042749.1	977	gGc/gCc	29/35	0.642062936168039	1	FACETS	0.325	0.275	0.38	0.325	0.275	0.38	SUBCLONAL	1	TRUE	0	0.669642822053624	1		538	275	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300537	11300537	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001037-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	175	436	0	ENST00000361445.4:c.1609G>A	p.Asp537Asn	p.D537N	ENST00000361445	NM_004958.3	537	Gat/Aat	11/58	0.477687999409753	5	FACETS	0.992	0.912	1			1	CLONAL	1	TRUE	NA	0.553734894540409	5		436	1166	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213872	66213872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772452750	NA	P-0001037-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	215	514	0	ENST00000273854.3:c.2558G>A	p.Arg853Gln	p.R853Q	ENST00000273854	NM_004439.5	853	cGa/cAa	15/18	1	2	FACETS	0.956	0.891	1	0.956	0.891	1	CLONAL	1	TRUE	1	0.553734894540409	2		514	812	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294327	1294327	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001037-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	94	147	0	ENST00000310581.5:c.674G>A	p.Gly225Glu	p.G225E	ENST00000310581	NM_198253.2	225	gGg/gAg	2/16	0.553734894540409	11	FACETS	0.945	0.838	1			1	CLONAL	1	TRUE	NA	0.553734894540409	11		147	1255	SUCCESS
APC	324	MSKCC	GRCh37	5	112177049	112177049	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001037-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	57	374	0	ENST00000257430.4:c.5758C>T	p.Arg1920Ter	p.R1920*	ENST00000257430	NM_000038.5	1920	Cga/Tga	16/16	0.553734894540409	3	FACETS	0.277	0.237	0.322	0.139	0.118	0.161	SUBCLONAL	1	TRUE	1	0.553734894540409	3		374	948	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001037-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	2072	139	0	ENST00000397752.3:c.3028G>C	p.Asp1010His	p.D1010H	ENST00000397752	NM_000245.2	1010	Gat/Cat	14/21	0.553734894540409	18	FACETS	1	0.998	1			1	CLONAL	18	TRUE	NA	0.553734894540409	18		139	2209	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110251451	110251451	+	start_lost,splice_region_variant	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0001037-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	170	401	0	ENST00000374672.4:c.3G>A	p.Met1?	p.M1?	ENST00000374672	NM_004235.4	1	atG/atA	1/5	0.553734894540409	3	FACETS	1	0.927	1	0.335	0.309	0.363	CLONAL	1	TRUE	0	0.553734894540409	3		401	779	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118368773	118368773	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001037-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	88	159	0	ENST00000534358.1:c.5787C>G	p.Ile1929Met	p.I1929M	ENST00000534358	NM_005933.3	1929	atC/atG	21/36	0.553734894540409	3	FACETS	0.976	0.869	1	0.488	0.434	0.544	CLONAL	1	TRUE	1	0.553734894540409	3		159	416	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560263	95560263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001037-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	104	199	0	ENST00000393063.1:c.5326C>T	p.Gln1776Ter	p.Q1776*	ENST00000393063	NM_030621.3	1776	Cag/Tag	25/28	0.553734894540409	3	FACETS	0.895	0.804	0.99	0.447	0.402	0.495	CLONAL	1	TRUE	1	0.553734894540409	3		199	536	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030313	180030313	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs307821	NA	P-0001040-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	11	429	0	ENST00000261937.6:c.3971G>T	p.Arg1324Leu	p.R1324L	ENST00000261937	NM_182925.4	1324	cGg/cTg	30/30	0.186821295200089	0	FACETS	0.427	0.296	0.59			1	SUBCLONAL	1	TRUE	0	0.24	0		429	163	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578214	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs864309495	NA	P-0001040-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	20	453	0	ENST00000269305.4:c.635_636del	p.Phe212SerfsTer3	p.F212Sfs*3	ENST00000269305	NM_001126112.2	212	tTT/t	6/11	0.0886257456902134	0	FACETS	0.704	0.541	0.891			1	INDETERMINATE	1	TRUE	0	0.24	0		453	180	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143033	30143033	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001047-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	109	548	0	ENST00000389048.3:c.493C>A	p.Leu165Met	p.L165M	ENST00000389048	NM_004304.4	165	Ctg/Atg	1/29	0.228039714852121	0	FACETS	0.72	0.646	0.798			1	SUBCLONAL	1	TRUE	0	0.279156498080534	0		548	782	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030245	180030245	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001047-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	79	520	0	ENST00000261937.6:c.4039G>A	p.Asp1347Asn	p.D1347N	ENST00000261937	NM_182925.4	1347	Gac/Aac	30/30	0.228039714852121	0	FACETS	0.501	0.439	0.566			1	SUBCLONAL	1	TRUE	0	0.279156498080534	0		520	815	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873858	151873858	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001047-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	52	282	0	ENST00000262189.6:c.8680A>T	p.Ile2894Phe	p.I2894F	ENST00000262189	NM_170606.2	2894	Att/Ttt	38/59	0.165858743092982	1	FACETS	0.355	0.301	0.414	0.355	0.301	0.414	INDETERMINATE	1	TRUE	0	0.279156498080534	1		282	904	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917699	151917699	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001047-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	15	99	0	ENST00000262189.6:c.3621G>T	p.Lys1207Asn	p.K1207N	ENST00000262189	NM_170606.2	1207	aaG/aaT	23/59	0.165858743092982	1	FACETS	0.336	0.245	0.445	0.336	0.245	0.445	INDETERMINATE	1	TRUE	0	0.279156498080534	1		99	275	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570395	95570395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143841809	NA	P-0001047-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	31	106	0	ENST00000393063.1:c.3338C>T	p.Ser1113Phe	p.S1113F	ENST00000393063	NM_030621.3	1113	tCc/tTc	22/28	1	2	FACETS	0.49	0.396	0.597	0.49	0.396	0.597	SUBCLONAL	1	TRUE	1	0.279156498080534	2		106	453	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796921	78796921	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001047-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	68	271	0	ENST00000306801.3:c.1034G>C	p.Ser345Thr	p.S345T	ENST00000306801	NM_020761.2	345	aGt/aCt	9/34	0.165858743092982	1	FACETS	0.486	0.421	0.556	0.486	0.421	0.556	INDETERMINATE	1	TRUE	0	0.279156498080534	1		271	863	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0001054-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	190	450	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.236547724017184	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.236547724017184	3		451	775	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0001054-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	115	236	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.236547724017184	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.236547724017184	4		236	483	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606696	29606696	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769910087	NA	P-0001054-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	23	502	0	ENST00000389048.3:c.1184G>A	p.Arg395His	p.R395H	ENST00000389048	NM_004304.4	395	cGt/cAt	5/29	0.236547724017184	0	FACETS	0.45	0.351	0.565			1	SUBCLONAL	1	TRUE	0	0.236547724017184	0		502	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912655	NA	P-0001054-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	72	427	0	ENST00000269305.4:c.725G>C	p.Cys242Ser	p.C242S	ENST00000269305	NM_001126112.2	242	tGc/tCc	7/11	0.224584527167119	2	FACETS	0.86	0.762	0.962	1	0.969	1	CLONAL	3	TRUE	0	0.236547724017184	2		427	236	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591891	48591891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912581	NA	P-0001054-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	84	524	0	ENST00000342988.3:c.1054G>A	p.Gly352Arg	p.G352R	ENST00000342988	NM_005359.5	352	Gga/Aga	9/12	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.236547724017184	2		524	538	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260328	10260328	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148987580	NA	P-0001054-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	45	362	0	ENST00000340748.4:c.2339C>T	p.Thr780Met	p.T780M	ENST00000340748		780	aCg/aTg	25/40	0.236547724017184	1	FACETS	0.784	0.666	0.911	1	0.964	1	CLONAL	2	TRUE	0	0.236547724017184	1		362	214	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920227	76920227	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001054-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	37	591	0	ENST00000373344.5:c.3850C>A	p.Leu1284Ile	p.L1284I	ENST00000373344	NM_000489.3	1284	Ctt/Att	11/35	0.187459014204932	1	FACETS	0.474	0.39	0.568	0.474	0.39	0.568	SUBCLONAL	1	TRUE	0	0.236547724017184	1		591	582	SUCCESS
APC	324	MSKCC	GRCh37	5	112175765	112175774	+	frameshift_variant	Frame_Shift_Del	DEL	GCCACGGAAA	GCCACGGAAA	-	novel	NA	P-0001054-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	40	366	0	ENST00000257430.4:c.4475_4484del	p.Ala1492ValfsTer12	p.A1492Vfs*12	ENST00000257430	NM_000038.5	1492	GCCACGGAAAgt/gt	16/16	0.224584527167119	2	FACETS	0.917	0.763	1	0.458	0.381	0.543	CLONAL	1	TRUE	0	0.236547724017184	2		366	369	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146566	55146566	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001054-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	32	465	0	ENST00000257290.5:c.2240A>G	p.Glu747Gly	p.E747G	ENST00000257290	NM_006206.4	747	gAa/gGa	16/23	0.236547724017184	1	FACETS	0.523	0.424	0.635	0.523	0.424	0.635	SUBCLONAL	1	TRUE	0	0.236547724017184	1		465	456	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399521	139399521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001054-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	30	364	0	ENST00000277541.6:c.4622G>A	p.Ser1541Asn	p.S1541N	ENST00000277541	NM_017617.3	1541	aGc/aAc	26/34	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.236547724017184	2		364	192	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0001078-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	382	161	333	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.217928055518728	4	FACETS	0.921	0.85	0.994	0.921	0.85	0.994	INDETERMINATE	2	TRUE	2	0.474928819592791	4		333	543	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0001078-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	300	93	339	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	0.458416721219529	1	FACETS	0.76	0.68	0.843	0.76	0.68	0.843	SUBCLONAL	1	TRUE	0	0.474928819592791	1		339	393	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102098302	102098302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001078-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	474	168	452	0	ENST00000282441.5:c.1266G>T	p.Glu422Asp	p.E422D	ENST00000282441	NM_001130145.2	422	gaG/gaT	8/9	0.217928055518728	4	FACETS	0.813	0.75	0.878	0.813	0.75	0.878	INDETERMINATE	2	TRUE	2	0.474928819592791	4		452	642	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100658	67100658	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001078-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	487	192	551	0	ENST00000412916.2:c.356T>A	p.Leu119Gln	p.L119Q	ENST00000412916		119	cTg/cAg	4/6	0.474928819592791	1	FACETS	0.908	0.843	0.975	0.908	0.843	0.975	CLONAL	1	TRUE	0	0.474928819592791	1		551	679	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844181	68844184	+	missense_variant	Missense_Mutation	ONP	GACA	GACA	AATG	novel	NA	P-0001078-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	299	178	503	0	ENST00000261769.5:c.769_772delinsAATG	p.Asp257_Asn258delinsAsnAsp	p.D257_N258delinsND	ENST00000261769	NM_004360.3	257	GACAac/AATGac	6/16	0.474928819592791	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.474928819592791	1		503	477	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057519990	NA	P-0001084-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	125	407	0	ENST00000269305.4:c.796G>T	p.Gly266Ter	p.G266*	ENST00000269305	NM_001126112.2	266	Gga/Tga	8/11	0.345635877660327	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.345635877660327	1		407	470	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047527	49047527	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587778850	NA	P-0001084-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	92	308	0	ENST00000267163.4:c.2520+1G>A		p.X840_splice	ENST00000267163	NM_000321.2	840			0.275051342466407	2	FACETS	0.982	0.875	1	0.491	0.437	0.548	CLONAL	1	TRUE	0	0.345635877660327	2		308	542	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602493	10602493	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001084-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	140	347	0	ENST00000171111.5:c.1085G>C	p.Arg362Pro	p.R362P	ENST00000171111	NM_203500.1	362	cGg/cCg	3/6	0.345635877660327	1	FACETS	0.802	0.737	0.868	1	0.989	1	CLONAL	2	TRUE	0	0.345635877660327	1		347	418	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092724	27092724	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001084-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	124	286	0	ENST00000324856.7:c.2748del	p.Asn917IlefsTer2	p.N917Ifs*2	ENST00000324856	NM_006015.4	915	taC/ta	9/20	0.345635877660327	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.345635877660327	1		286	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0001086-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	143	289	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.206811360866362	3	FACETS	0.849	0.778	0.923	0.849	0.778	0.923	CLONAL	3	TRUE	0	0.22149626473109	3		289	563	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981462	55981462	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs545112274	NA	P-0001086-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	56	409	0	ENST00000263923.4:c.475G>A	p.Val159Met	p.V159M	ENST00000263923	NM_002253.2	159	Gtg/Atg	4/30	0.212476136350021	5	FACETS	0.66	0.563	0.766	0.22	0.187	0.256	SUBCLONAL	1	TRUE	2	0.22149626473109	5		409	1021	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	231001	231001	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143484394	NA	P-0001086-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	50	456	1	ENST00000264932.6:c.781C>T	p.Arg261Cys	p.R261C	ENST00000264932	NM_004168.2	261	Cgc/Tgc	7/15	0.22149626473109	5	FACETS	0.625	0.528	0.732			1	SUBCLONAL	1	TRUE	NA	0.22149626473109	5		457	963	SUCCESS
APC	324	MSKCC	GRCh37	5	112174798	112174798	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001086-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	38	315	0	ENST00000257430.4:c.3507G>C	p.Glu1169Asp	p.E1169D	ENST00000257430	NM_000038.5	1169	gaG/gaC	16/16	0.22149626473109	4	FACETS	0.602	0.496	0.721	0.201	0.165	0.241	SUBCLONAL	1	TRUE	1	0.22149626473109	4		315	696	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939009	131939009	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001086-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	27	193	0	ENST00000265335.6:c.2225T>C	p.Leu742Ser	p.L742S	ENST00000265335		742	tTg/tCg	14/25	0.212476136350021	5	FACETS	0.698	0.555	0.863	0.233	0.185	0.288	SUBCLONAL	1	TRUE	2	0.22149626473109	5		193	465	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980811	40980811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001086-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	31	439	0	ENST00000373198.4:c.1675G>A	p.Gly559Arg	p.G559R	ENST00000373198	NM_133170.3	559	Ggg/Agg	10/32	0.22149626473109	1	FACETS	0.408	0.329	0.498	0.408	0.329	0.498	SUBCLONAL	1	TRUE	0	0.22149626473109	1		439	610	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288894	33288894	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001095-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	151	225	0	ENST00000374542.5:c.658T>C	p.Ser220Pro	p.S220P	ENST00000374542	NM_001141970.1	220	Tcc/Ccc	3/8	0.723558218578814	1	FACETS	0.724	0.677	0.771	0.724	0.677	0.771	SUBCLONAL	1	TRUE	0	0.86434017006036	1		225	274	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90996784	90996784	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001095-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	850	618	0	ENST00000265433.3:c.6G>C	p.Trp2Cys	p.W2C	ENST00000265433	NM_002485.4	2	tgG/tgC	1/16	0.5160864282469	4	FACETS	0.835	0.812	0.857	0.835	0.812	0.857	INDETERMINATE	3	TRUE	1	0.86434017006036	4		618	1464	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0001108-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	183	493	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.3	1	FACETS	0.867	0.805	0.931	1	0.992	1	CLONAL	2	TRUE	0	0.3	1		494	598	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998995	11998995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001108-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	112	271	0	ENST00000353533.5:c.497G>A	p.Gly166Asp	p.G166D	ENST00000353533	NM_003010.3	166	gGt/gAt	4/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.3	2		271	709	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0001112-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	581	633	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.725100607725194	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.742940680506403	2		633	763	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136162	11136162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001112-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	188	513	0	ENST00000358026.2:c.3146C>T	p.Pro1049Leu	p.P1049L	ENST00000358026	NM_001128849.1	1049	cCc/cTc	22/36	0.742940680506403	1	FACETS	0.982	0.926	1	0.982	0.926	1	CLONAL	1	TRUE	0	0.742940680506403	1		513	324	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497672	120497672	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001112-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	143	287	0	ENST00000256646.2:c.2210G>T	p.Gly737Val	p.G737V	ENST00000256646	NM_024408.3	737	gGt/gTt	13/34	0.402760674926503	3	FACETS	1	0.985	1	0.65	0.599	0.703	INDETERMINATE	1	TRUE	1	0.742940680506403	3		287	406	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961074	55961074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001112-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	257	807	1	ENST00000263923.4:c.2866C>T	p.Pro956Ser	p.P956S	ENST00000263923	NM_002253.2	956	Cct/Tct	21/30	1	2	FACETS	0.924	0.869	0.98	0.924	0.869	0.98	CLONAL	1	TRUE	1	0.742940680506403	2		808	749	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700232	117700232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146533107	NA	P-0001112-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	292	526	0	ENST00000368508.3:c.2587C>T	p.Arg863Trp	p.R863W	ENST00000368508	NM_002944.2	863	Cgg/Tgg	17/43	1	2	FACETS	0.937	0.885	0.99	0.937	0.885	0.99	CLONAL	1	TRUE	1	0.742940680506403	2		526	839	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198233	138198233	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001112-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	204	342	0	ENST00000237289.4:c.826G>A	p.Val276Ile	p.V276I	ENST00000237289	NM_001270507.1	276	Gtt/Att	6/9	1	2	FACETS	0.838	0.781	0.897	0.838	0.781	0.897	CLONAL	1	TRUE	1	0.742940680506403	2		342	655	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524305	148524305	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001112-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	324	538	0	ENST00000320356.2:c.679A>G	p.Ile227Val	p.I227V	ENST00000320356	NM_004456.4	227	Att/Gtt	7/20	1	2	FACETS	0.939	0.889	0.989	0.939	0.889	0.989	CLONAL	1	TRUE	1	0.742940680506403	2		538	929	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945352	151945352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001112-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	53	98	0	ENST00000262189.6:c.2167G>A	p.Glu723Lys	p.E723K	ENST00000262189	NM_170606.2	723	Gaa/Aaa	14/59	1	2	FACETS	0.802	0.695	0.913	0.802	0.695	0.913	CLONAL	1	TRUE	1	0.742940680506403	2		98	178	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685313	89685313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs794727480	NA	P-0001112-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	271	506	0	ENST00000371953.3:c.208C>T	p.Leu70Phe	p.L70F	ENST00000371953	NM_000314.4	70	Ctt/Ttt	3/9	1	2	FACETS	0.814	0.766	0.864	0.814	0.766	0.864	CLONAL	1	TRUE	1	0.742940680506403	2		506	896	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428629	49428629	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001112-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	279	677	0	ENST00000301067.7:c.10321C>T	p.Gln3441Ter	p.Q3441*	ENST00000301067	NM_003482.3	3441	Cag/Tag	35/54	1	2	FACETS	0.952	0.898	1	0.952	0.898	1	CLONAL	1	TRUE	1	0.742940680506403	2		677	789	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001354	29001354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001112-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	237	407	0	ENST00000282397.4:c.1378C>T	p.Pro460Ser	p.P460S	ENST00000282397	NM_002019.4	460	Cct/Tct	10/30	0.673873141394437	1	FACETS	0.957	0.908	1	0.957	0.908	1	CLONAL	1	TRUE	0	0.742940680506403	1		407	419	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73343019	73343019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001112-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	565	472	0	ENST00000377767.4:c.1787G>A	p.Arg596Lys	p.R596K	ENST00000377767	NM_014953.3	596	aGa/aAa	14/21	0.7274347043344	2	FACETS	0.977	0.951	1	0.977	0.951	1	CLONAL	2	TRUE	0	0.742940680506403	2		472	778	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423632	88423632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1478926904	NA	P-0001112-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	150	411	0	ENST00000360948.2:c.2203C>T	p.Arg735Cys	p.R735C	ENST00000360948	NM_001012338.2	735	Cgc/Tgc	18/19	1	2	FACETS	0.845	0.778	0.913	0.845	0.778	0.913	CLONAL	1	TRUE	1	0.742940680506403	2		411	478	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288437	15288437	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001112-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	55	140	0	ENST00000263388.2:c.4302G>A	p.Trp1434Ter	p.W1434*	ENST00000263388	NM_000435.2	1434	tgG/tgA	24/33	NA	2	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.742940680506403	2		140	127	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930393	39930393	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001112-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	691	579	0	ENST00000378444.4:c.3071C>T	p.Ser1024Leu	p.S1024L	ENST00000378444	NM_001123385.1	1024	tCa/tTa	6/15	0.469256442984532	3	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.742940680506403	3		579	1057	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130435	29130436	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0001112-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	241	542	0	ENST00000328354.6:c.274_275delinsTT	p.Pro92Phe	p.P92F	ENST00000328354	NM_007194.3	92	CCc/TTc	2/15	1	2	FACETS	0.977	0.918	1	0.977	0.918	1	CLONAL	1	TRUE	1	0.742940680506403	2		542	664	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274248	10274249	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0001112-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	46	201	0	ENST00000330684.3:c.20_21delinsAA	p.Trp7Ter	p.W7*	ENST00000330684	NM_001134407.1	7	tGG/tAA	2/13	1	2	FACETS	0.789	0.677	0.907	0.789	0.677	0.907	CLONAL	1	TRUE	1	0.742940680506403	2		201	157	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0001125-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	112	186	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.17871389301225	5	FACETS	0.951	0.903	0.994	1	0.991	1	INDETERMINATE	5	TRUE	2	0.710166804350105	5		186	137	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0001128-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	33	333	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.756	0.616	0.913	0.756	0.616	0.913	CLONAL	1	TRUE	1	0.22	2		333	397	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0001128-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	9	328	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.231	0.152	0.333	0.231	0.152	0.333	SUBCLONAL	1	TRUE	1	0.22	2		328	354	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146520	55146520	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs749523527	NA	P-0001128-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	27	388	0	ENST00000257290.5:c.2194A>G	p.Met732Val	p.M732V	ENST00000257290	NM_006206.4	732	Atg/Gtg	16/23	0.201651782905258	0	FACETS	0.461	0.367	0.57			1	SUBCLONAL	1	TRUE	0	0.22	0		388	415	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911100	32911100	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001128-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	23	251	0	ENST00000380152.3:c.2608A>T	p.Ile870Phe	p.I870F	ENST00000380152		870	Att/Ttt	11/27	0.201651782905258	1	FACETS	0.521	0.406	0.655	0.521	0.406	0.655	SUBCLONAL	1	TRUE	0	0.22	1		251	357	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578206	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001128-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	11	625	0	ENST00000269305.4:c.643A>T	p.Ser215Cys	p.S215C	ENST00000269305	NM_001126112.2	215	Agt/Tgt	6/11	0.3	1	FACETS	0.263	0.181	0.366	0.263	0.181	0.366	SUBCLONAL	1	TRUE	0	0.22	1		625	338	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714574	52714574	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001128-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	21	578	0	ENST00000322088.6:c.332C>A	p.Ser111Tyr	p.S111Y	ENST00000322088	NM_014225.5	111	tCc/tAc	4/15	0.201651782905258	1	FACETS	0.438	0.336	0.556	0.438	0.336	0.556	SUBCLONAL	1	TRUE	0	0.22	1		578	388	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226576458	226576475	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TGAAGGAGACACAGGATA	TGAAGGAGACACAGGATA	-	novel	NA	P-0001128-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	36	566	0	ENST00000366794.5:c.618-19_618-2del		p.X206_splice	ENST00000366794	NM_001618.3	206			1	2	FACETS	0.726	0.596	0.871	0.726	0.596	0.871	SUBCLONAL	1	TRUE	1	0.22	2		566	451	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0001137-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	116	396	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.333911731757437	3	FACETS	1	0.951	1	0.361	0.326	0.399	CLONAL	1	TRUE	0	0.377955760917026	3		396	673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0001137-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	126	542	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.377955760917026	3	FACETS	0.942	0.86	1			1	CLONAL	2	TRUE	NA	0.377955760917026	3		542	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782329	NA	P-0001137-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	49	233	0	ENST00000269305.4:c.746G>C	p.Arg249Thr	p.R249T	ENST00000269305	NM_001126112.2	249	aGg/aCg	7/11	0.377955760917026	3	FACETS	0.803	0.682	0.935			1	CLONAL	1	TRUE	NA	0.377955760917026	3		233	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0001140-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	97	153	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.637878012975331	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.657127274581047	2		153	126	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650574	18650574	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001140-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	133	182	0	ENST00000266497.5:c.2785G>C	p.Asp929His	p.D929H	ENST00000266497		929	Gat/Cat	20/31	0.657127274581047	8	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.657127274581047	8		182	1004	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222757	5222757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779903263	NA	P-0001140-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	22	164	0	ENST00000357368.4:c.3046C>T	p.Arg1016Trp	p.R1016W	ENST00000357368	NM_002850.3	1016	Cgg/Tgg	18/38	0.657127274581047	1	FACETS	0.624	0.499	0.76	0.624	0.499	0.76	SUBCLONAL	1	TRUE	0	0.657127274581047	1		164	72	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204758	128204758	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001141-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	511	583	0	ENST00000341105.2:c.683C>A	p.Pro228His	p.P228H	ENST00000341105	NM_032638.4	228	cCc/cAc	3/6	0.4277099390218	5	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	2	0.4277099390218	5		583	1249	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927384	178927384	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001141-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	132	328	0	ENST00000263967.3:c.1147T>C	p.Trp383Arg	p.W383R	ENST00000263967	NM_006218.2	383	Tgg/Cgg	7/21	0.4277099390218	6	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.4277099390218	6		328	830	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953022	2953022	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141681466	NA	P-0001141-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	71	320	0	ENST00000396946.4:c.2918G>A	p.Arg973His	p.R973H	ENST00000396946	NM_032415.4	973	cGc/cAc	22/25	0.407593083576704	4	FACETS	0.686	0.598	0.781	0.343	0.299	0.391	SUBCLONAL	1	TRUE	2	0.4277099390218	4		320	691	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588891	52588891	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001164-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	48	190	0	ENST00000394830.3:c.4137G>C	p.Met1379Ile	p.M1379I	ENST00000394830	NM_018313.4	1379	atG/atC	27/30	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.75646649585317	NA		190	287	SUCCESS
AXL	558	MSKCC	GRCh37	19	41759538	41759538	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001174-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	37	404	0	ENST00000301178.4:c.1961C>A	p.Ala654Glu	p.A654E	ENST00000301178	NM_021913.4	654	gCa/gAa	17/20	1	2	FACETS	0.66	0.55	0.782	0.66	0.55	0.782	SUBCLONAL	1	TRUE	1	0.543945346091293	2		404	206	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577115	7577115	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519983	NA	P-0001183-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	247	533	0	ENST00000269305.4:c.823T>C	p.Cys275Arg	p.C275R	ENST00000269305	NM_001126112.2	275	Tgt/Cgt	8/11	0.743221403858782	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.743221403858782	1		533	324	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245429	153245429	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001183-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	95	475	0	ENST00000281708.4:c.1762G>T	p.Glu588Ter	p.E588*	ENST00000281708	NM_033632.3	588	Gaa/Taa	11/12	0.698995403686064	2	FACETS	0.595	0.532	0.66	0.297	0.266	0.33	SUBCLONAL	1	TRUE	0	0.743221403858782	2		475	430	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967279	38967279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746828213	NA	P-0001183-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	201	401	0	ENST00000357387.3:c.1202G>A	p.Arg401His	p.R401H	ENST00000357387	NM_152756.3	401	cGt/cAt	14/38	0.729594613311895	1	FACETS	0.974	0.92	1	0.974	0.92	1	CLONAL	1	TRUE	0	0.743221403858782	1		401	349	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59861749	59861749	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001183-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	60	523	0	ENST00000259008.2:c.1510A>T	p.Ile504Phe	p.I504F	ENST00000259008	NM_032043.2	504	Atc/Ttc	11/20	0.743221403858782	2	FACETS	0.334	0.288	0.384	0.167	0.144	0.192	SUBCLONAL	1	TRUE	0	0.743221403858782	2		523	483	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922166	39922166	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs981265184	NA	P-0001183-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	94	733	1	ENST00000378444.4:c.4006G>C	p.Asp1336His	p.D1336H	ENST00000378444	NM_001123385.1	1336	Gac/Cac	9/15	0.650878576838441	0	FACETS		NA	1			1	NA	1	TRUE	0	0.743221403858782	0		734	188	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928072	178928098	+	inframe_deletion	In_Frame_Del	DEL	TGGATTAGAAGATTTGCTGAACCCTAT	TGGATTAGAAGATTTGCTGAACCCTAT	-	novel	NA	P-0001183-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	27	380	0	ENST00000263967.3:c.1353_1379del	p.Leu452_Gly460del	p.L452_G460del	ENST00000263967	NM_006218.2	450	caTGGATTAGAAGATTTGCTGAACCCTATt/cat	8/21	1	2	FACETS	0.153	0.121	0.189	0.153	0.121	0.189	SUBCLONAL	1	TRUE	1	0.743221403858782	2		380	475	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571965	64571965	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001184-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	178	662	0	ENST00000312049.6:c.1674G>A	p.Met558Ile	p.M558I	ENST00000312049	NM_130799.2	558	atG/atA	10/10	0.491889615022738	1	FACETS	0.904	0.837	0.972	0.904	0.837	0.972	CLONAL	1	TRUE	0	0.491889615022738	1		662	604	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265876	16265886	+	frameshift_variant	Frame_Shift_Del	DEL	TCTCCAACATC	TCTCCAACATC	-	novel	NA	P-0001184-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	71	619	0	ENST00000375759.3:c.10954_10964del	p.Asn3652ProfsTer13	p.N3652Pfs*13	ENST00000375759	NM_015001.2	3650	aTCTCCAACATC/a	15/15	1	2	FACETS	0.363	0.316	0.413	0.363	0.316	0.413	SUBCLONAL	1	TRUE	1	0.491889615022738	2		619	796	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0001192-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	271	717	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.773970624336457	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	FALSE	0	0.773970624336457	2		718	307	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197766	66197766	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001192-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	135	955	0	ENST00000273854.3:c.2933A>C	p.Lys978Thr	p.K978T	ENST00000273854	NM_004439.5	978	aAg/aCg	17/18	0.773970624336457	2	FACETS	1	0.972	1	0.555	0.513	0.599	CLONAL	1	FALSE	0	0.773970624336457	2		955	314	SUCCESS
APC	324	MSKCC	GRCh37	5	112175000	112175000	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001192-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	150	371	0	ENST00000257430.4:c.3709C>T	p.Gln1237Ter	p.Q1237*	ENST00000257430	NM_000038.5	1237	Cag/Tag	16/16	0.773970624336457	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	FALSE	0	0.773970624336457	2		371	181	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170088	32170088	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775047010	NA	P-0001192-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	132	670	1	ENST00000375023.3:c.3520G>A	p.Gly1174Arg	p.G1174R	ENST00000375023	NM_004557.3	1174	Gga/Aga	21/30	0.588589424925131	6	FACETS	0.844	0.77	0.92	0.563	0.513	0.614	CLONAL	2	FALSE	3	0.773970624336457	6		671	515	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681101	117681101	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001192-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	147	1003	0	ENST00000368508.3:c.3519A>C	p.Gln1173His	p.Q1173H	ENST00000368508	NM_002944.2	1173	caA/caC	23/43	0.743126962150341	2	FACETS	1	0.967	1	0.54	0.499	0.58	CLONAL	1	FALSE	0	0.773970624336457	2		1003	352	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163751	152163751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751407371	NA	P-0001192-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	154	564	0	ENST00000206249.3:c.472C>T	p.Arg158Cys	p.R158C	ENST00000206249	NM_000125.3	158	Cgc/Tgc	2/8	0.371583786365031	6	FACETS	0.904	0.838	0.97	0.904	0.838	0.97	INDETERMINATE	3	FALSE	3	0.773970624336457	6		564	374	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8501027	8501027	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001192-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	110	583	0	ENST00000356435.5:c.1855A>T	p.Thr619Ser	p.T619S	ENST00000356435		619	Acc/Tcc	13/35	0.773970624336457	3	FACETS	1	0.966	1	0.566	0.514	0.62	CLONAL	1	FALSE	1	0.773970624336457	3		583	348	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908809	101908809	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001192-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	221	986	0	ENST00000374994.4:c.1173A>C	p.Lys391Asn	p.K391N	ENST00000374994	NM_004612.2	391	aaA/aaC	7/9	0.773970624336457	3	FACETS	0.957	0.904	1	0.957	0.904	1	CLONAL	2	FALSE	1	0.773970624336457	3		986	414	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125523678	125523678	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001192-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	22	877	0	ENST00000428830.2:c.1271T>C	p.Leu424Pro	p.L424P	ENST00000428830	NM_001114121.2	424	cTc/cCc	12/14	0.773970624336457	3	FACETS	0.302	0.234	0.38	0.151	0.117	0.19	SUBCLONAL	1	FALSE	1	0.773970624336457	3		877	261	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231140	46231140	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001192-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	64	791	0	ENST00000334344.6:c.1060C>A	p.Leu354Met	p.L354M	ENST00000334344	NM_152641.2	354	Ctg/Atg	9/21	0.319531752303021	5	FACETS	0.878	0.763	1	0.293	0.254	0.334	INDETERMINATE	1	FALSE	2	0.773970624336457	5		791	407	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727453	66727453	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397516790	NA	P-0001192-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	230	581	0	ENST00000307102.5:c.169A>G	p.Lys57Glu	p.K57E	ENST00000307102	NM_002755.3	57	Aag/Gag	2/11	0.773970624336457	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	FALSE	0	0.773970624336457	2		581	261	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627904	37627904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001192-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	103	888	0	ENST00000447079.4:c.1819G>A	p.Val607Ile	p.V607I	ENST00000447079	NM_015083.1	607	Gtt/Att	2/14	0.773970624336457	3	FACETS	0.744	0.669	0.824	0.372	0.334	0.412	SUBCLONAL	1	FALSE	1	0.773970624336457	3		888	496	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673794	37673794	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1308016883	NA	P-0001192-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	93	508	0	ENST00000447079.4:c.2948G>A	p.Arg983Gln	p.R983Q	ENST00000447079	NM_015083.1	983	cGa/cAa	10/14	0.773970624336457	3	FACETS	0.84	0.752	0.932	0.42	0.376	0.466	CLONAL	1	FALSE	1	0.773970624336457	3		508	397	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145660	11145660	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001192-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	59	536	0	ENST00000358026.2:c.4022A>G	p.Asp1341Gly	p.D1341G	ENST00000358026	NM_001128849.1	1341	gAc/gGc	29/36	0.773970624336457	2	FACETS	0.63	0.548	0.717	0.315	0.274	0.359	SUBCLONAL	1	FALSE	0	0.773970624336457	2		536	242	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0001202-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	178	426	0	ENST00000374080.3:c.3670C>T	p.Leu1224Phe	p.L1224F	ENST00000374080		1224	Ctc/Ttc	26/45	0.3	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		426	353	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525719	187525719	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001202-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	142	424	0	ENST00000441802.2:c.10360C>G	p.Pro3454Ala	p.P3454A	ENST00000441802	NM_005245.3	3454	Cca/Gca	18/27	0.118610872795145	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		424	487	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292632	91292632	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555418242	NA	P-0001202-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	188	433	0	ENST00000355112.3:c.134A>G	p.Asn45Ser	p.N45S	ENST00000355112	NM_000057.2	45	aAc/aGc	3/22	0.3	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		433	658	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891363	101891363	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001214-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	229	481	0	ENST00000374994.4:c.324A>C	p.Lys108Asn	p.K108N	ENST00000374994	NM_004612.2	108	aaA/aaC	2/9	1	2	FACETS	0.847	0.791	0.904	1	0.993	1	CLONAL	2	TRUE	1	0.329396731378983	2		481	821	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0001222-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	33	160	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.356792582812993	1	FACETS	0.975	0.806	1	0.975	0.806	1	CLONAL	1	TRUE	0	0.368293749235228	1		160	150	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156051	99156051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776096061	NA	P-0001222-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	50	427	0	ENST00000074304.5:c.731G>A	p.Arg244Gln	p.R244Q	ENST00000074304	NM_001134224.1	244	cGg/cAg	10/26	1	2	FACETS	0.418	0.354	0.489	0.418	0.354	0.489	SUBCLONAL	1	TRUE	1	0.368293749235228	2		427	649	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056020	26056020	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0001222-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	84	263	1	ENST00000343677.2:c.637A>T	p.Lys213Ter	p.K213*	ENST00000343677	NM_005319.3	213	Aaa/Taa	1/1	0.268965728413417	3	FACETS	0.984	0.871	1	0.492	0.435	0.552	CLONAL	1	TRUE	1	0.368293749235228	3		264	549	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779180	135779180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200827913	NA	P-0001222-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	88	289	0	ENST00000298552.3:c.2066G>A	p.Arg689His	p.R689H	ENST00000298552	NM_001162426.1	689	cGc/cAc	17/23	0.368293749235228	1	FACETS	0.835	0.743	0.932	0.835	0.743	0.932	CLONAL	1	TRUE	0	0.368293749235228	1		289	467	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805331	89805331	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001222-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	33	342	0	ENST00000389301.3:c.4219A>C	p.Ile1407Leu	p.I1407L	ENST00000389301	NM_000135.2	1407	Ata/Cta	42/43	0.143986179396429	0	FACETS	0.205	0.166	0.249			1	INDETERMINATE	1	TRUE	0	0.368293749235228	0		342	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0001222-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	74	260	0	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	0.317588734161086	1	FACETS	0.796	0.7	0.898	0.796	0.7	0.898	SUBCLONAL	1	TRUE	0	0.368293749235228	1		260	412	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976123	7976123	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001222-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	108	371	0	ENST00000319144.4:c.2072A>C	p.Asp691Ala	p.D691A	ENST00000319144	NM_001139.2	691	gAc/gCc	15/15	0.317588734161086	1	FACETS	0.967	0.872	1	0.967	0.872	1	CLONAL	1	TRUE	0	0.368293749235228	1		371	495	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141546	11141546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1298515852	NA	P-0001222-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	108	421	0	ENST00000358026.2:c.3523G>A	p.Asp1175Asn	p.D1175N	ENST00000358026	NM_001128849.1	1175	Gac/Aac	25/36	0.368293749235228	1	FACETS	0.891	0.803	0.984	0.891	0.803	0.984	CLONAL	1	TRUE	0	0.368293749235228	1		421	537	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724339	52724339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs969720045	NA	P-0001222-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	36	403	0	ENST00000322088.6:c.1471G>A	p.Gly491Arg	p.G491R	ENST00000322088	NM_014225.5	491	Gga/Aga	12/15	1	2	FACETS	0.285	0.233	0.343	0.285	0.233	0.343	SUBCLONAL	1	TRUE	1	0.368293749235228	2		403	686	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001242-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	83	241	0	ENST00000269305.4:c.736del	p.Met246Ter	p.M246*	ENST00000269305	NM_001126112.2	246	Atg/tg	7/11	0.144037237436831	3	FACETS	0.863	0.77	0.96			1	INDETERMINATE	3	FALSE	NA	0.243854584808035	3		241	295	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670327	134670327	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373140258	NA	P-0001242-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	29	405	0	ENST00000398015.3:c.238C>T	p.Arg80Trp	p.R80W	ENST00000398015	NM_004441.4	80	Cgg/Tgg	3/16	0.243854584808035	5	FACETS	0.871	0.699	1	0.29	0.233	0.356	CLONAL	1	FALSE	2	0.243854584808035	5		405	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0001257-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	128	289	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.15172537064672	3	FACETS	1	0.932	1			1	INDETERMINATE	2	TRUE	NA	0.468725069047604	3		289	332	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0001257-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	119	290	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.438471757673417	2	FACETS	0.976	0.899	1	0.976	0.899	1	CLONAL	2	TRUE	0	0.468725069047604	2		290	260	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515397	149515397	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17110944	NA	P-0001257-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	14	224	0	ENST00000261799.4:c.85A>T	p.Ile29Phe	p.I29F	ENST00000261799	NM_002609.3	29	Atc/Ttc	3/23	0.29483551080087	2	FACETS	0.231	0.166	0.309	0.115	0.083	0.155	SUBCLONAL	1	TRUE	0	0.468725069047604	2		224	259	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630597	187630597	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs41278611	NA	P-0001257-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	16	496	0	ENST00000441802.2:c.385G>C	p.Val129Leu	p.V129L	ENST00000441802	NM_005245.3	129	Gtg/Ctg	2/27	0.438471757673417	2	FACETS	0.227	0.167	0.298	0.113	0.083	0.149	SUBCLONAL	1	TRUE	0	0.468725069047604	2		496	301	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663795	241663795	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001257-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	39	141	0	ENST00000366560.3:c.1332G>T	p.Arg444Ser	p.R444S	ENST00000366560	NM_000143.3	444	agG/agT	9/10	0.293814449450015	6	FACETS	1	0.853	1	0.676	0.569	0.791	CLONAL	2	TRUE	3	0.468725069047604	6		141	159	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142931	30142931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001257-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	144	371	0	ENST00000389048.3:c.595G>A	p.Gly199Ser	p.G199S	ENST00000389048	NM_004304.4	199	Ggc/Agc	1/29	0.355349603078205	3	FACETS	0.837	0.77	0.906	0.837	0.77	0.906	CLONAL	2	TRUE	1	0.468725069047604	3		371	453	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025969	48025969	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001257-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	115	278	0	ENST00000234420.5:c.847G>T	p.Gly283Trp	p.G283W	ENST00000234420	NM_000179.2	283	Ggg/Tgg	4/10	0.355349603078205	3	FACETS	1	0.985	1	0.746	0.677	0.817	CLONAL	1	TRUE	1	0.468725069047604	3		278	406	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645471	215645471	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782333	NA	P-0001257-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	68	595	0	ENST00000260947.4:c.1127C>T	p.Ser376Leu	p.S376L	ENST00000260947	NM_000465.2	376	tCa/tTa	4/11	0.271897394930274	4	FACETS	1	0.942	1	0.568	0.497	0.645	INDETERMINATE	1	TRUE	2	0.468725069047604	4		595	375	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819735	170819735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001257-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	123	138	0	ENST00000296930.5:c.374C>T	p.Ser125Leu	p.S125L	ENST00000296930	NM_002520.6	125	tCa/tTa	5/11	0.447150187902828	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	0	0.468725069047604	3		138	191	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944985	31944985	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs3759295	NA	P-0001257-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	22	276	0	ENST00000340398.3:c.116A>C	p.His39Pro	p.H39P	ENST00000340398	NM_001013699.2	39	cAt/cCt	1/1	0.438471757673417	2	FACETS	0.248	0.191	0.313	0.124	0.095	0.157	SUBCLONAL	1	TRUE	0	0.468725069047604	2		276	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578548	7578548	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001257-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	114	192	0	ENST00000269305.4:c.382C>G	p.Pro128Ala	p.P128A	ENST00000269305	NM_001126112.2	128	Cct/Gct	5/11	0.15172537064672	3	FACETS	1	0.969	1			1	INDETERMINATE	2	TRUE	NA	0.468725069047604	3		192	268	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265205	5265205	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001257-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	119	235	0	ENST00000357368.4:c.382G>T	p.Asp128Tyr	p.D128Y	ENST00000357368	NM_002850.3	128	Gac/Tac	5/38	0.468725069047604	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.468725069047604	2		235	243	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420088	41420088	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001257-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	74	204	0	ENST00000373198.4:c.233A>G	p.Asn78Ser	p.N78S	ENST00000373198	NM_133170.3	78	aAc/aGc	3/32	0.330445664222375	4	FACETS	0.906	0.803	1	0.906	0.803	1	CLONAL	2	TRUE	2	0.468725069047604	4		204	256	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911382	39911382	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001257-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	88	488	0	ENST00000378444.4:c.5248G>T	p.Ala1750Ser	p.A1750S	ENST00000378444	NM_001123385.1	1750	Gcc/Tcc	15/15	0.173210296225224	1	FACETS	0.642	0.571	0.716	0.642	0.571	0.716	INDETERMINATE	1	TRUE	0	0.468725069047604	1		488	448	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608326	100608326	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001257-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	135	534	0	ENST00000308731.7:c.1764G>T	p.Trp588Cys	p.W588C	ENST00000308731	NM_000061.2	588	tgG/tgT	18/19	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.468725069047604	2		534	392	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196808	123196808	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001257-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	59	523	0	ENST00000218089.9:c.1695G>T	p.Glu565Asp	p.E565D	ENST00000218089	NM_001042749.1	565	gaG/gaT	18/35	NA	2	FACETS	0.871	0.756	0.995			1	INDETERMINATE	1	TRUE	NA	0.468725069047604	2		523	289	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955485	48955499	+	inframe_deletion	In_Frame_Del	DEL	GTTTTATCAAAGCAG	GTTTTATCAAAGCAG	-	novel	NA	P-0001257-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	48	355	0	ENST00000267163.4:c.1601_1615del	p.Ser534_Glu539delinsLys	p.S534_E539delinsK	ENST00000267163	NM_000321.2	534	aGTTTTATCAAAGCAGaa/aaa	17/27	0.15172537064672	3	FACETS	0.81	0.698	0.928			1	INDETERMINATE	2	TRUE	NA	0.468725069047604	3		355	156	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0001274-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	191	603	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.464738953415492	1	FACETS	0.869	0.806	0.934	0.869	0.806	0.934	CLONAL	1	TRUE	0	0.464738953415492	1		603	726	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152009027	152009027	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001274-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	116	273	0	ENST00000262189.6:c.595C>T	p.Arg199Ter	p.R199*	ENST00000262189	NM_170606.2	199	Cga/Tga	5/59	1	2	FACETS	0.987	0.894	1	0.987	0.894	1	CLONAL	1	TRUE	1	0.464738953415492	2		273	506	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523268	9523268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001274-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	210	617	0	ENST00000353224.5:c.1969del	p.Asp657ThrfsTer7	p.D657Tfs*7	ENST00000353224	NM_177990.2	657	Gac/ac	9/10	1	2	FACETS	0.915	0.849	0.982	0.915	0.849	0.982	CLONAL	1	TRUE	1	0.464738953415492	2		617	988	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0001289-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	167	495	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.394408622415427	1	FACETS	0.789	0.737	0.841	0.789	0.737	0.841	INDETERMINATE	1	TRUE	0	0.753729161083266	1		496	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0001289-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	180	351	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.47203905322697	1	FACETS	0.863	0.81	0.915	0.863	0.81	0.915	CLONAL	1	TRUE	0	0.753729161083266	1		351	345	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0001289-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	196	340	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.546818416349614	1	FACETS	0.748	0.702	0.796	0.748	0.702	0.796	SUBCLONAL	1	TRUE	0	0.753729161083266	1		340	433	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0001289-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	73	163	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.406702694448537	1	FACETS	0.493	0.437	0.551	0.493	0.437	0.551	INDETERMINATE	1	TRUE	0	0.753729161083266	1		163	245	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0001289-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	115	256	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	0.394408622415427	1	FACETS	0.723	0.663	0.783	0.723	0.663	0.783	INDETERMINATE	1	TRUE	0	0.753729161083266	1		256	263	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354435	354435	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001289-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	106	348	0	ENST00000262320.3:c.1123T>C	p.Tyr375His	p.Y375H	ENST00000262320	NM_003502.3	375	Tac/Cac	5/11	0.47203905322697	1	FACETS	0.375	0.337	0.414	0.375	0.337	0.414	SUBCLONAL	1	TRUE	0	0.753729161083266	1		348	468	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533093	63533093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750354919	NA	P-0001289-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	152	355	0	ENST00000307078.5:c.1801G>A	p.Gly601Ser	p.G601S	ENST00000307078	NM_004655.3	601	Ggc/Agc	7/11	0.149784892359852	3	FACETS	0.86	0.789	0.933			1	INDETERMINATE	1	TRUE	NA	0.753729161083266	3		355	646	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117870	70117870	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001289-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	131	193	0	ENST00000245479.2:c.338T>C	p.Met113Thr	p.M113T	ENST00000245479	NM_000346.3	113	aTg/aCg	1/3	0.149784892359852	3	FACETS	1	0.93	1			1	INDETERMINATE	1	TRUE	NA	0.753729161083266	3		193	469	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953977	131953977	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001290-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	99	113	0	ENST00000265335.6:c.3380C>G	p.Thr1127Ser	p.T1127S	ENST00000265335		1127	aCt/aGt	21/25	NA	2	FACETS	0.501	0.449	0.557			1	INDETERMINATE	1	TRUE	NA	0.741003113788105	2		113	533	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637841	176637841	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001290-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	243	175	0	ENST00000439151.2:c.2441G>T	p.Cys814Phe	p.C814F	ENST00000439151	NM_022455.4	814	tGc/tTc	5/23	1	2	FACETS	0.847	0.794	0.901	0.847	0.794	0.901	CLONAL	1	TRUE	1	0.741003113788105	2		175	774	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296192	15296192	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001290-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	107	158	0	ENST00000263388.2:c.2172G>C	p.Trp724Cys	p.W724C	ENST00000263388	NM_000435.2	724	tgG/tgC	14/33	0.741195064600189	1	FACETS	0.45	0.407	0.495	0.45	0.407	0.495	SUBCLONAL	1	TRUE	0	0.741003113788105	1		158	404	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84388632	84388659	+	frameshift_variant	Frame_Shift_Del	DEL	TACATTTCATTTATCTTATGTACCTCCT	TACATTTCATTTATCTTATGTACCTCCT	-	novel	NA	P-0001290-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1378	76	323	0	ENST00000321945.7:c.629_656del	p.Lys210MetfsTer8	p.K210Mfs*8	ENST00000321945	NM_139076.2	210	aAGGAGGTACATAAGATAAATGAAATGTAt/at	7/9	NA	2	FACETS	0.141	0.123	0.161			1	INDETERMINATE	1	TRUE	NA	0.741003113788105	2		323	1454	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604752	48604763	+	inframe_deletion	In_Frame_Del	DEL	TTGAAATTCACT	TTGAAATTCACT	-	novel	NA	P-0001310-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	156	351	0	ENST00000342988.3:c.1575_1586del	p.Glu526_Leu529del	p.E526_L529del	ENST00000342988	NM_005359.5	525	aTTGAAATTCACTta/ata	12/12	0.90834894588264	1	FACETS	0.499	0.462	0.535	0.499	0.462	0.535	SUBCLONAL	1	TRUE	0	0.90834894588264	1		351	376	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022561	31022580	+	frameshift_variant	Frame_Shift_Del	DEL	CACCCCTGGAAAGTGTACGT	CACCCCTGGAAAGTGTACGT	-	novel	NA	P-0001310-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	160	348	0	ENST00000375687.4:c.2048_2067del	p.Thr683ArgfsTer28	p.T683Rfs*28	ENST00000375687	NM_015338.5	682	agCACCCCTGGAAAGTGTACGTca/agca	13/13	1	2	FACETS	0.433	0.397	0.471	0.433	0.397	0.471	SUBCLONAL	1	TRUE	1	0.90834894588264	2		348	813	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69458752	69458754	+	missense_variant	Missense_Mutation	TNP	TGC	TGC	GCA	novel	NA	P-0001312-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	89	273	0	ENST00000227507.2:c.567_569inv	p.Cys189_Ala190delinsTrpHis	p.C189_A190delinsWH	ENST00000227507	NM_053056.2	189	tgTGCc/tgGCAc	3/5	0.287530835260094	4	FACETS	0.664	0.588	0.746	0.332	0.294	0.373	SUBCLONAL	1	TRUE	2	0.41281323832486	4		273	917	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	G	rs11575997	NA	P-0001312-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	453	318	0	ENST00000269305.4:c.993+1G>C		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.41281323832486	3	FACETS	0.888	0.851	0.925	0.888	0.851	0.925	CLONAL	3	TRUE	0	0.41281323832486	3		318	994	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0001320-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	191	235	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.964	1	1	0.995	1	CLONAL	3	TRUE	1	0.23115120295827	2		235	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0001320-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	422	344	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.23115120295827	2	FACETS	0.982	0.956	1	1	0.998	1	CLONAL	7	TRUE	0	0.23115120295827	2		344	531	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257801	133257801	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001320-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	63	402	0	ENST00000320574.5:c.127A>G	p.Lys43Glu	p.K43E	ENST00000320574	NM_006231.2	43	Aag/Gag	2/49	0.23115120295827	1	FACETS	0.917	0.794	1	0.917	0.794	1	CLONAL	1	TRUE	0	0.23115120295827	1		402	526	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101836	11101836	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001320-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	71	221	0	ENST00000358026.2:c.1256A>C	p.Glu419Ala	p.E419A	ENST00000358026	NM_001128849.1	419	gAg/gCg	8/36	0.23115120295827	1	FACETS	0.97	0.856	1	1	0.982	1	CLONAL	2	TRUE	0	0.23115120295827	1		221	280	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144146	11144146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001320-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	15	264	2	ENST00000358026.2:c.3727C>T	p.Arg1243Trp	p.R1243W	ENST00000358026	NM_001128849.1	1243	Cgg/Tgg	26/36	0.23115120295827	1	FACETS	0.39	0.285	0.517	0.39	0.285	0.517	SUBCLONAL	1	TRUE	0	0.23115120295827	1		266	294	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938279	76938280	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0001320-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	245	263	1	ENST00000373344.5:c.2468_2469del	p.Lys823ArgfsTer7	p.K823Rfs*7	ENST00000373344	NM_000489.3	823	aAA/a	9/35	0.208034278887758	0	FACETS	0.838	0.799	0.876			1	CLONAL	5	TRUE	NA	0.23115120295827	0		264	389	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0001335-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	301	347	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.407019268932245	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.407019268932245	3		347	526	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632305	215632305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1379944646	NA	P-0001335-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	77	544	0	ENST00000260947.4:c.1469C>T	p.Thr490Ile	p.T490I	ENST00000260947	NM_000465.2	490	aCc/aTc	6/11	0.407019268932245	3	FACETS	0.702	0.616	0.794	0.351	0.308	0.397	SUBCLONAL	1	TRUE	1	0.407019268932245	3		544	649	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115720	8115720	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001335-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	106	511	0	ENST00000346208.3:c.1066A>G	p.Met356Val	p.M356V	ENST00000346208		356	Atg/Gtg	6/6	0.288190764182289	5	FACETS	0.812	0.726	0.903	0.271	0.242	0.301	CLONAL	1	TRUE	2	0.407019268932245	5		511	1033	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127763	64127763	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001335-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	69	330	0	ENST00000334205.4:c.256C>T	p.Arg86Cys	p.R86C	ENST00000334205	NM_003942.2	86	Cgc/Tgc	3/17	0.407019268932245	5	FACETS	0.663	0.576	0.757			1	SUBCLONAL	1	TRUE	NA	0.407019268932245	5		330	824	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487301	56487301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001335-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	59	309	0	ENST00000267101.3:c.1447G>A	p.Asp483Asn	p.D483N	ENST00000267101	NM_001982.3	483	Gac/Aac	12/28	0.288190764182289	5	FACETS	0.66	0.567	0.762	0.22	0.189	0.254	SUBCLONAL	1	TRUE	2	0.407019268932245	5		309	707	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109667	115109691	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGTCCGGCTTGGCTTCCAAGCCG	CCTGTCCGGCTTGGCTTCCAAGCCG	-	novel	NA	P-0001335-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	157	586	0	ENST00000257566.3:c.2187_2211del	p.Gly730ProfsTer151	p.G730Pfs*151	ENST00000257566	NM_016569.3	729	agCGGCTTGGAAGCCAAGCCGGACAGG/ag	8/8	0.288190764182289	5	FACETS	1	0.981	1	0.414	0.379	0.451	CLONAL	1	TRUE	2	0.407019268932245	5		586	1000	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1567555907	NA	P-0001335-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	436	358	0	ENST00000269305.4:c.314del	p.Gly105AlafsTer18	p.G105Afs*18	ENST00000269305	NM_001126112.2	105	gGc/gc	4/11	0.407019268932245	3	FACETS	0.966	0.926	1	0.966	0.926	1	CLONAL	3	TRUE	0	0.407019268932245	3		358	890	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511513	38511518	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGACCG	AGACCG	-	novel	NA	P-0001335-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	93	277	0	ENST00000254066.5:c.1013-2_1016del		p.X338_splice	ENST00000254066	NM_000964.3	338		8/9	0.407019268932245	5	FACETS	0.966	0.859	1	0.241	0.214	0.27	CLONAL	1	TRUE	1	0.407019268932245	5		277	762	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691003	NA	P-0001373-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	185	182	0	ENST00000269305.4:c.96+1G>T		p.X32_splice	ENST00000269305	NM_001126112.2	32			0.685536243700265	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.685536243700265	1		182	348	SUCCESS
ATM	472	MSKCC	GRCh37	11	108168044	108168044	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001373-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	397	175	0	ENST00000278616.4:c.4940T>C	p.Leu1647Pro	p.L1647P	ENST00000278616	NM_000051.3	1647	cTa/cCa	33/63	0.685536243700265	2	FACETS	0.956	0.922	0.989	0.956	0.922	0.989	CLONAL	2	TRUE	0	0.685536243700265	2		175	606	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743505	46743507	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs768106067	NA	P-0001373-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	41	110	0	ENST00000371975.4:c.1889_1891del	p.Lys630del	p.K630del	ENST00000371975	NM_003579.3	629	gAGAag/gag	17/18	1	2	FACETS	0.267	0.222	0.317	0.267	0.222	0.317	SUBCLONAL	1	TRUE	1	0.685536243700265	2		110	448	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0001380-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	59	378	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.215794123944211	0	FACETS	0.881	0.759	1			1	CLONAL	1	FALSE	0	0.215794123944211	0		379	487	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591888	48591888	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001380-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	52	367	0	ENST00000342988.3:c.1051G>T	p.Asp351Tyr	p.D351Y	ENST00000342988	NM_005359.5	351	Gat/Tat	9/12	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	FALSE	1	0.215794123944211	2		367	453	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77048449	77048449	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001380-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	58	313	0	ENST00000356341.3:c.1136T>G	p.Phe379Cys	p.F379C	ENST00000356341	NM_002576.4	379	tTc/tGc	12/15	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	FALSE	1	0.215794123944211	2		313	476	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376690	31376690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001380-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	35	273	0	ENST00000328111.2:c.685G>A	p.Val229Met	p.V229M	ENST00000328111	NM_006892.3	229	Gtg/Atg	7/23	1	2	FACETS	0.965	0.793	1	0.965	0.793	1	CLONAL	1	FALSE	1	0.215794123944211	2		273	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577525	7577533	+	inframe_deletion	In_Frame_Del	DEL	GAGGATGGG	GAGGATGGG	-	novel	NA	P-0001380-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	34	221	0	ENST00000269305.4:c.748_756del	p.Pro250_Leu252del	p.P250_L252del	ENST00000269305	NM_001126112.2	250	CCCATCCTC/-	7/11	0.215794123944211	1	FACETS	0.937	0.768	1	0.937	0.768	1	CLONAL	1	FALSE	0	0.215794123944211	1		221	300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577560	7577560	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520002	NA	P-0001382-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	39	337	0	ENST00000269305.4:c.721T>C	p.Ser241Pro	p.S241P	ENST00000269305	NM_001126112.2	241	Tcc/Ccc	7/11	NA	2	FACETS	0.709	0.589	0.843			1	INDETERMINATE	1	TRUE	NA	0.292507443687485	2		337	376	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020768	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs926053251	NA	P-0001382-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	72	333	0	ENST00000358127.4:c.77T>G	p.Val26Gly	p.V26G	ENST00000358127	NM_001280556.1	26	gTt/gGt	2/10	0.220279145537095	1	FACETS	0.662	0.578	0.752	0.662	0.578	0.752	SUBCLONAL	1	TRUE	0	0.292507443687485	1		333	635	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100860	27100860	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001382-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	59	519	0	ENST00000324856.7:c.4142C>A	p.Ala1381Asp	p.A1381D	ENST00000324856	NM_006015.4	1381	gCc/gAc	18/20	1	2	FACETS	0.649	0.558	0.748	0.649	0.558	0.748	SUBCLONAL	1	TRUE	1	0.292507443687485	2		519	622	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0001389-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	31	160	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.219585172523493	2	FACETS	1	0.937	1	0.696	0.568	0.837	CLONAL	1	TRUE	0	0.239551561948618	2		160	186	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0001389-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	144	717	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.219585172523493	2	FACETS	0.907	0.829	0.987	0.907	0.829	0.987	CLONAL	2	TRUE	0	0.239551561948618	2		718	663	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0001389-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	182	440	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.239551561948618	7	FACETS	0.981	0.91	1			1	CLONAL	4	TRUE	NA	0.239551561948618	7		440	619	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438243	56438243	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001389-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	116	443	0	ENST00000407977.2:c.750del	p.Ser251AlafsTer168	p.S251Afs*168	ENST00000407977		250	gcC/gc	7/10	0.223771363820465	4	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	2	0.239551561948618	4		443	584	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560947	9560947	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001398-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	81	425	0	ENST00000353224.5:c.835C>A	p.Gln279Lys	p.Q279K	ENST00000353224	NM_177990.2	279	Cag/Aag	4/10	0.240938932920612	3	FACETS	1	0.971	1	0.662	0.585	0.744	CLONAL	1	TRUE	1	0.305284354101002	3		425	462	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657655	37657655	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001407-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	143	832	1	ENST00000447079.4:c.2572C>T	p.Arg858Trp	p.R858W	ENST00000447079	NM_015083.1	858	Cgg/Tgg	6/14	0.14944177443213	2	FACETS	1	0.971	1	1	0.992	1	CLONAL	4	TRUE	0	0.14944177443213	2		833	429	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673732	37673734	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0001407-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	106	837	0	ENST00000447079.4:c.2887_2889del	p.Val963del	p.V963del	ENST00000447079	NM_015083.1	962	gaTGTt/gat	10/14	0.14944177443213	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.14944177443213	2		837	628	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427687	49427687	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001410-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	239	380	0	ENST00000301067.7:c.10801C>T	p.Gln3601Ter	p.Q3601*	ENST00000301067	NM_003482.3	3601	Caa/Taa	39/54	0.660781772441777	3	FACETS	1	0.993	1			1	CLONAL	1	TRUE	NA	0.8278179047676	3		380	564	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593604	55593609	+	inframe_deletion	In_Frame_Del	DEL	GGAAGG	GGAAGG	-	novel	NA	P-0001410-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	1243	492	0	ENST00000288135.5:c.1670_1675del	p.Trp557_Val559delinsPhe	p.W557_V559delinsF	ENST00000288135	NM_000222.2	557	tGGAAGGtt/ttt	11/21	0.753194922184375	4	FACETS	0.946	0.933	0.958			1	CLONAL	4	TRUE	NA	0.8278179047676	4		492	1451	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787756	135787756	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001410-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	306	396	1	ENST00000298552.3:c.826del	p.Ser276LeufsTer42	p.S276Lfs*42	ENST00000298552	NM_001162426.1	276	Tct/ct	9/23	0.732177527867627	1	FACETS	0.874	0.836	0.91	0.874	0.836	0.91	CLONAL	1	TRUE	0	0.8278179047676	1		397	496	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0001419-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	433	229	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.409242786723055	3	FACETS	1	0.977	1	1	0.996	1	CLONAL	3	TRUE	1	0.409242786723055	3		229	830	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111554	8111554	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001419-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	469	428	0	ENST00000346208.3:c.1040T>G	p.Leu347Arg	p.L347R	ENST00000346208		347	cTt/cGt	5/6	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	3	TRUE	NA	0.409242786723055	2		428	720	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275757	41275757	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001426-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	183	301	0	ENST00000349496.5:c.1652C>A	p.Thr551Lys	p.T551K	ENST00000349496	NM_001904.3	551	aCg/aAg	10/15	0.614999977757324	4	FACETS	0.995	0.918	1	0.332	0.306	0.359	CLONAL	1	TRUE	1	0.614999977757324	4		301	966	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441448	52441448	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374928824	NA	P-0001426-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	270	417	0	ENST00000460680.1:c.404C>T	p.Pro135Leu	p.P135L	ENST00000460680	NM_004656.3	135	cCg/cTg	6/17	0.208924277307351	5	FACETS	0.846	0.794	0.899			1	INDETERMINATE	2	TRUE	NA	0.614999977757324	5		417	998	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938900	178938900	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001426-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	72	68	0	ENST00000263967.3:c.2142C>A	p.Asn714Lys	p.N714K	ENST00000263967	NM_006218.2	714	aaC/aaA	14/21	0.455688522365171	4	FACETS	0.879	0.781	0.981			1	CLONAL	2	TRUE	NA	0.614999977757324	4		68	215	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503838	149503838	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs864309711	NA	P-0001426-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	212	474	0	ENST00000261799.4:c.1998C>A	p.Asn666Lys	p.N666K	ENST00000261799	NM_002609.3	666	aaC/aaA	14/23	0.614999977757324	3	FACETS	1	0.973	1	0.545	0.507	0.584	CLONAL	1	TRUE	1	0.614999977757324	3		474	827	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508491	106508491	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001426-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	66	87	0	ENST00000359195.3:c.485T>C	p.Val162Ala	p.V162A	ENST00000359195	NM_002649.2	162	gTc/gCc	2/11	0.614999977757324	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	1	0.614999977757324	3		87	126	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370913	55370913	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001426-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	124	300	0	ENST00000297316.4:c.215T>A	p.Met72Lys	p.M72K	ENST00000297316	NM_022454.3	72	aTg/aAg	1/2	0.60160528791173	4	FACETS	0.877	0.794	0.964			1	CLONAL	1	TRUE	NA	0.614999977757324	4		300	743	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692911	89692911	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121909241	NA	P-0001426-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	173	266	0	ENST00000371953.3:c.395G>T	p.Gly132Val	p.G132V	ENST00000371953	NM_000314.4	132	gGt/gTt	5/9	0.614999977757324	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.614999977757324	1		266	307	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448143	49448143	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001426-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	346	355	0	ENST00000301067.7:c.457G>T	p.Glu153Ter	p.E153*	ENST00000301067	NM_003482.3	153	Gag/Tag	4/54	0.589127950238955	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.614999977757324	3		355	669	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857910	9857910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001426-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	370	368	0	ENST00000330684.3:c.3491C>T	p.Thr1164Met	p.T1164M	ENST00000330684	NM_001134407.1	1164	aCg/aTg	13/13	0.425906511373331	5	FACETS	0.834	0.794	0.874	0.834	0.794	0.874	CLONAL	3	TRUE	2	0.614999977757324	5		368	925	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0001426-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	437	441	0	ENST00000269305.4:c.96+1G>A		p.X32_splice	ENST00000269305	NM_001126112.2	32			0.614999977757324	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.614999977757324	2		441	623	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467911	66467922	+	inframe_deletion	In_Frame_Del	DEL	TGGAGATCCAAC	TGGAGATCCAAC	-	novel	NA	P-0001426-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	307	388	0	ENST00000273854.3:c.347_358del	p.Ser116_Ser119del	p.S116_S119del	ENST00000273854	NM_004439.5	116	aGTTGGATCTCCAat/aat	3/18	0.375739387982395	4	FACETS	0.85	0.803	0.897	0.85	0.803	0.897	CLONAL	2	TRUE	2	0.614999977757324	4		388	949	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061010	38061031	+	frameshift_variant	Frame_Shift_Del	DEL	CGGGGGCCGGCGCGCCCTCTAG	CGGGGGCCGGCGCGCCCTCTAG	-	novel	NA	P-0001426-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	85	219	0	ENST00000250448.2:c.958_979del	p.Leu320GlyfsTer23	p.L320Gfs*23	ENST00000250448	NM_004496.3	320	CTAGAGGGCGCGCCGGCCCCCGgg/gg	2/2	0.375739387982395	4	FACETS	0.803	0.719	0.89	0.803	0.719	0.89	CLONAL	2	TRUE	2	0.614999977757324	4		219	278	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0001427-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	32	450	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.179633931084348	1	FACETS	0.665	0.541	0.804	0.665	0.541	0.804	SUBCLONAL	1	TRUE	0	0.260105744831564	1		451	322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0001427-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	65	320	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			NA	2	FACETS	1	0.92	1			1	INDETERMINATE	2	TRUE	NA	0.260105744831564	2		320	235	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438209	49438209	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1183756465	NA	P-0001427-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	25	473	0	ENST00000301067.7:c.5060G>T	p.Arg1687Leu	p.R1687L	ENST00000301067	NM_003482.3	1687	cGc/cTc	20/54	0.156878427613731	2	FACETS	0.658	0.52	0.817	0.329	0.26	0.409	SUBCLONAL	1	TRUE	0	0.260105744831564	2		473	292	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492721	56492722	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0001427-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	60	394	0	ENST00000407977.2:c.217_218delinsTT	p.Ala73Phe	p.A73F	ENST00000407977		73	GCt/TTt	2/10	0.260105744831564	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.260105744831564	1		394	313	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913237	NA	P-0001444-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	179	207	454	0	ENST00000369535.4:c.35G>C	p.Gly12Ala	p.G12A	ENST00000369535	NM_002524.4	12	gGt/gCt	2/7	0.288818726246445	1	FACETS	0.798	0.753	0.843	1	0.994	1	INDETERMINATE	2	TRUE	0	0.502852844270587	1		454	386	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913399	NA	P-0001444-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	158	28	331	0	ENST00000349496.5:c.100G>C	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Cga	3/15	1	2	FACETS	0.599	0.482	0.729	0.599	0.482	0.729	SUBCLONAL	1	TRUE	1	0.502852844270587	2		331	186	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95556991	95556991	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001444-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	203	24	460	0	ENST00000393063.1:c.5613G>C	p.Glu1871Asp	p.E1871D	ENST00000393063	NM_030621.3	1871	gaG/gaC	28/28	0.181955379470695	1	FACETS	0.315	0.248	0.392	0.315	0.248	0.392	INDETERMINATE	1	TRUE	0	0.502852844270587	1		460	227	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0001452-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	332	495	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.388386023028727	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.47435867432205	3		496	795	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392871	118392871	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001452-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	171	265	0	ENST00000534358.1:c.11903G>T	p.Arg3968Leu	p.R3968L	ENST00000534358	NM_005933.3	3968	cGg/cTg	36/36	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.47435867432205	2		265	712	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916152	9916152	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001452-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	138	273	0	ENST00000330684.3:c.2137G>A	p.Val713Ile	p.V713I	ENST00000330684	NM_001134407.1	713	Gta/Ata	10/13	NA	2	FACETS	0.755	0.687	0.825			1	INDETERMINATE	1	TRUE	NA	0.47435867432205	2		273	771	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916166	9916166	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001452-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	133	268	0	ENST00000330684.3:c.2123T>A	p.Phe708Tyr	p.F708Y	ENST00000330684	NM_001134407.1	708	tTt/tAt	10/13	NA	2	FACETS	0.725	0.659	0.795			1	INDETERMINATE	1	TRUE	NA	0.47435867432205	2		268	773	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916194	9916194	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001452-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	131	268	0	ENST00000330684.3:c.2095C>A	p.Pro699Thr	p.P699T	ENST00000330684	NM_001134407.1	699	Ccc/Acc	10/13	NA	2	FACETS	0.749	0.681	0.822			1	INDETERMINATE	1	TRUE	NA	0.47435867432205	2		268	737	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266134	41266136	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs587776850	NA	P-0001452-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	48	200	0	ENST00000349496.5:c.133_135del	p.Ser45del	p.S45del	ENST00000349496	NM_001904.3	44	cCTTct/cct	3/15	1	2	FACETS	0.324	0.273	0.38	0.324	0.273	0.38	SUBCLONAL	1	TRUE	1	0.47435867432205	2		200	625	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0001454-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	78	308	1	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.245292832390845	3	FACETS	1	0.931	1	0.543	0.477	0.614	CLONAL	1	TRUE	1	0.245292832390845	3		309	657	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0001454-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	171	290	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.235028199294898	2	FACETS	0.946	0.872	1	0.946	0.872	1	CLONAL	2	TRUE	0	0.245292832390845	2		290	737	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0001454-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	24	288	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.344	0.269	0.431	0.344	0.269	0.431	SUBCLONAL	1	TRUE	1	0.245292832390845	2		288	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576919	7576919	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001454-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	38	318	0	ENST00000269305.4:c.927del	p.Asn310ThrfsTer35	p.N310Tfs*35	ENST00000269305	NM_001126112.2	309	ccC/cc	9/11	0.245292832390845	1	FACETS	0.764	0.633	0.909	0.764	0.633	0.909	CLONAL	1	TRUE	0	0.245292832390845	1		318	356	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029153	26029153	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001454-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	113	402	0	ENST00000435504.4:c.197G>T	p.Gly66Val	p.G66V	ENST00000435504		66	gGt/gTt	4/13	0.237790557572255	3	FACETS	1	0.983	1	0.729	0.657	0.806	CLONAL	1	TRUE	1	0.245292832390845	3		402	709	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750471	41750471	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001454-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	44	301	0	ENST00000226382.2:c.157G>T	p.Ala53Ser	p.A53S	ENST00000226382	NM_003924.3	53	Gcc/Tcc	1/3	0.217037146007209	3	FACETS	0.864	0.725	1	0.432	0.362	0.509	CLONAL	1	TRUE	1	0.245292832390845	3		301	466	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391508	84391508	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001454-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	17	156	0	ENST00000321945.7:c.324G>C	p.Gln108His	p.Q108H	ENST00000321945	NM_139076.2	108	caG/caC	5/9	0.217037146007209	3	FACETS	0.533	0.397	0.694	0.266	0.198	0.347	SUBCLONAL	1	TRUE	1	0.245292832390845	3		156	292	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637292	176637292	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001454-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	40	221	0	ENST00000439151.2:c.1892A>T	p.Lys631Met	p.K631M	ENST00000439151	NM_022455.4	631	aAg/aTg	5/23	0.217037146007209	3	FACETS	0.87	0.723	1	0.435	0.361	0.516	CLONAL	1	TRUE	1	0.245292832390845	3		221	421	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604539	43604539	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs142338976	NA	P-0001454-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	88	342	0	ENST00000355710.3:c.1124T>A	p.Leu375Gln	p.L375Q	ENST00000355710	NM_020975.4	375	cTg/cAg	6/20	0.245292832390845	3	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.245292832390845	3		342	606	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593602	55593613	+	inframe_deletion	In_Frame_Del	DEL	GTGGAAGGTTGT	GTGGAAGGTTGT	-	novel	NA	P-0001461-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	385	365	0	ENST00000288135.5:c.1668_1679del	p.Gln556_Val560delinsHis	p.Q556_V560delinsH	ENST00000288135	NM_000222.2	556	caGTGGAAGGTTGTt/cat	11/21	0.55969519088241	5	FACETS	0.934	0.888	0.98			1	CLONAL	2	TRUE	NA	0.771439058764071	5		365	1153	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0001464-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	138	153	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.858393926359908	1	FACETS	0.987	0.934	1	0.987	0.934	1	CLONAL	1	TRUE	0	0.858393926359908	1		153	186	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687052	176687052	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001464-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	40	334	0	ENST00000439151.2:c.5029G>T	p.Ala1677Ser	p.A1677S	ENST00000439151	NM_022455.4	1677	Gct/Tct	14/23	1	2	FACETS	0.117	0.096	0.14	0.117	0.096	0.14	SUBCLONAL	1	TRUE	1	0.858393926359908	2		334	798	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467955	50467955	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001464-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	157	141	0	ENST00000331340.3:c.1190C>T	p.Ser397Phe	p.S397F	ENST00000331340	NM_006060.4	397	tCc/tTc	8/8	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.858393926359908	2		141	354	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938099	76938100	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0001464-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	394	347	1	ENST00000373344.5:c.2648_2649del	p.Gln883ArgfsTer13	p.Q883Rfs*13	ENST00000373344	NM_000489.3	883	cAA/c	9/35	0.858393926359908	1	FACETS	0.991	0.96	1	0.991	0.96	1	CLONAL	1	TRUE	0	0.858393926359908	1		348	529	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0001469-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	234	225	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	NA	2	FACETS	0.981	0.918	1			1	INDETERMINATE	1	TRUE	NA	0.60063994850149	2		225	794	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0001469-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	152	169	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	0.865	0.795	0.938	0.865	0.795	0.938	CLONAL	1	TRUE	1	0.60063994850149	2		169	585	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467437	66467437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749830045	NA	P-0001469-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	165	146	0	ENST00000273854.3:c.832G>A	p.Ala278Thr	p.A278T	ENST00000273854	NM_004439.5	278	Gcc/Acc	3/18	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.60063994850149	2		146	541	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274210	10274210	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001469-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	102	110	0	ENST00000330684.3:c.59G>T	p.Gly20Val	p.G20V	ENST00000330684	NM_001134407.1	20	gGt/gTt	2/13	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.60063994850149	2		110	323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578393	7578393	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876660821	NA	P-0001469-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	217	131	1	ENST00000269305.4:c.537T>G	p.His179Gln	p.H179Q	ENST00000269305	NM_001126112.2	179	caT/caG	5/11	NA	2	FACETS	1	0.959	1			1	INDETERMINATE	2	TRUE	NA	0.60063994850149	2		132	357	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0001469-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	73	78	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.774	0.683	0.871	0.774	0.683	0.871	SUBCLONAL	1	TRUE	1	0.60063994850149	2		78	314	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0001473-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	74	140	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.402728915909657	3	FACETS	0.775	0.686	0.868	0.775	0.686	0.868	SUBCLONAL	2	TRUE	1	0.421880712574079	3		142	274	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183340	56183340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1358646708	NA	P-0001473-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	128	143	0	ENST00000399503.3:c.4250C>T	p.Ala1417Val	p.A1417V	ENST00000399503	NM_005921.1	1417	gCa/gTa	18/20	0.421880712574079	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.421880712574079	3		143	344	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770018	56770018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201523760	NA	P-0001473-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	29	292	0	ENST00000337432.4:c.14C>T	p.Thr5Met	p.T5M	ENST00000337432	NM_058216.2	5	aCg/aTg	1/9	1	2	FACETS	0.269	0.215	0.33	0.269	0.215	0.33	SUBCLONAL	1	TRUE	1	0.421880712574079	2		292	512	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098807	178098807	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001478-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	66	437	0	ENST00000397062.3:c.238A>G	p.Thr80Ala	p.T80A	ENST00000397062	NM_006164.4	80	Aca/Gca	2/5	1	2	FACETS	0.265	0.229	0.304	0.265	0.229	0.304	SUBCLONAL	1	TRUE	1	0.518738626542135	2		437	962	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659830	227659830	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001478-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	25	124	0	ENST00000305123.5:c.3625C>G	p.Gln1209Glu	p.Q1209E	ENST00000305123	NM_005544.2	1209	Caa/Gaa	1/2	1	2	FACETS	0.375	0.296	0.465	0.375	0.296	0.465	SUBCLONAL	1	TRUE	1	0.518738626542135	2		124	257	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679234	30679234	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001478-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	104	342	0	ENST00000376406.3:c.2176C>G	p.Pro726Ala	p.P726A	ENST00000376406	NM_014641.2	726	Cca/Gca	7/15	1	2	FACETS	0.467	0.418	0.52	0.467	0.418	0.52	SUBCLONAL	1	TRUE	1	0.518738626542135	2		342	858	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679794	30679794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001478-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	51	266	0	ENST00000376406.3:c.1925G>A	p.Arg642Lys	p.R642K	ENST00000376406	NM_014641.2	642	aGa/aAa	5/15	1	2	FACETS	0.261	0.221	0.305	0.261	0.221	0.305	SUBCLONAL	1	TRUE	1	0.518738626542135	2		266	753	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679855	30679855	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001478-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	37	247	0	ENST00000376406.3:c.1864G>A	p.Glu622Lys	p.E622K	ENST00000376406	NM_014641.2	622	Gag/Aag	5/15	1	2	FACETS	0.207	0.17	0.248	0.207	0.17	0.248	SUBCLONAL	1	TRUE	1	0.518738626542135	2		247	690	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679975	30679975	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001478-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	34	229	0	ENST00000376406.3:c.1744G>A	p.Glu582Lys	p.E582K	ENST00000376406	NM_014641.2	582	Gag/Aag	5/15	1	2	FACETS	0.199	0.162	0.241	0.199	0.162	0.241	SUBCLONAL	1	TRUE	1	0.518738626542135	2		229	659	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164129	32164129	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001478-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	77	234	0	ENST00000375023.3:c.5270G>C	p.Gly1757Ala	p.G1757A	ENST00000375023	NM_004557.3	1757	gGa/gCa	29/30	1	2	FACETS	0.457	0.401	0.518	0.457	0.401	0.518	SUBCLONAL	1	TRUE	1	0.518738626542135	2		234	649	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166482	32166482	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001478-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	91	327	0	ENST00000375023.3:c.4561G>C	p.Asp1521His	p.D1521H	ENST00000375023	NM_004557.3	1521	Gat/Cat	25/30	1	2	FACETS	0.408	0.361	0.458	0.408	0.361	0.458	SUBCLONAL	1	TRUE	1	0.518738626542135	2		327	860	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853293	151853293	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001478-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	66	185	0	ENST00000262189.6:c.11809G>T	p.Glu3937Ter	p.E3937*	ENST00000262189	NM_170606.2	3937	Gaa/Taa	45/59	0.518738626542135	1	FACETS	0.525	0.458	0.596	0.525	0.458	0.596	SUBCLONAL	1	TRUE	0	0.518738626542135	1		185	359	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442781	442781	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001478-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	82	214	0	ENST00000399788.2:c.1525C>G	p.His509Asp	p.H509D	ENST00000399788	NM_001042603.1	509	Cat/Gat	12/28	NA	2	FACETS	0.54	0.477	0.608			1	INDETERMINATE	1	TRUE	NA	0.518738626542135	2		214	585	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245928	46245928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001478-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	65	183	0	ENST00000334344.6:c.4022C>T	p.Ser1341Leu	p.S1341L	ENST00000334344	NM_152641.2	1341	tCa/tTa	15/21	1	2	FACETS	0.455	0.394	0.52	0.455	0.394	0.52	SUBCLONAL	1	TRUE	1	0.518738626542135	2		183	551	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246375	46246375	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001478-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	153	282	0	ENST00000334344.6:c.4469G>C	p.Gly1490Ala	p.G1490A	ENST00000334344	NM_152641.2	1490	gGa/gCa	15/21	1	2	FACETS	0.895	0.821	0.972	0.895	0.821	0.972	CLONAL	1	TRUE	1	0.518738626542135	2		282	659	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426688	49426688	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555188469	NA	P-0001478-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	64	118	0	ENST00000301067.7:c.11800C>T	p.Gln3934Ter	p.Q3934*	ENST00000301067	NM_003482.3	3934	Cag/Tag	39/54	1	2	FACETS	0.938	0.821	1	0.938	0.821	1	CLONAL	1	TRUE	1	0.518738626542135	2		118	263	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17117061	17117061	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001478-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	104	291	0	ENST00000285071.4:c.1648C>A	p.Leu550Met	p.L550M	ENST00000285071	NM_144997.5	550	Ctg/Atg	14/14	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.518738626542135	NA		291	496	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561018	9561018	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001478-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	140	228	0	ENST00000353224.5:c.764G>C	p.Ser255Thr	p.S255T	ENST00000353224	NM_177990.2	255	aGt/aCt	4/10	1	2	FACETS	0.871	0.795	0.949	0.871	0.795	0.949	CLONAL	1	TRUE	1	0.518738626542135	2		228	620	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609728	81609729	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0001478-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	86	312	0	ENST00000298171.2:c.1326_1327delinsAA	p.Ser442_His443delinsArgAsn	p.S442_H443delinsRN	ENST00000298171	NM_000369.2	442	agCCac/agAAac	10/10	1	2	FACETS	0.44	0.389	0.495	0.44	0.389	0.495	SUBCLONAL	1	TRUE	1	0.518738626542135	2		312	753	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508389	106508389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758375337	NA	P-0001479-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	65	40	0	ENST00000359195.3:c.383C>T	p.Thr128Met	p.T128M	ENST00000359195	NM_002649.2	128	aCg/aTg	2/11	0.290780031423541	6	FACETS	0.996	0.873	1			1	INDETERMINATE	2	TRUE	NA	0.489209959643621	6		40	264	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0001498-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	14	409	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		409	348	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793442	42793442	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748865223	NA	P-0001505-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	16	409	0	ENST00000575354.2:c.1244G>A	p.Arg415Gln	p.R415Q	ENST00000575354	NM_015125.3	415	cGg/cAg	8/20	0.179621741481199	1	FACETS	0.673	0.498	0.882	0.673	0.498	0.882	SUBCLONAL	1	TRUE	0	0.179621741481199	1		409	241	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0001510-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	125	229	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.256896278858433	1	FACETS	0.872	0.803	0.943	1	0.99	1	CLONAL	2	FALSE	0	0.388657001207758	1		229	297	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164711	47164711	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201984344	NA	P-0001510-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	236	413	0	ENST00000409792.3:c.1415G>A	p.Arg472His	p.R472H	ENST00000409792	NM_014159.6	472	cGt/cAt	3/21	0.247682773309077	3	FACETS	0.857	0.807	0.908	0.857	0.807	0.908	CLONAL	3	FALSE	0	0.388657001207758	3		413	564	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851937	128851937	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001510-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	70	432	0	ENST00000249373.3:c.2009G>A	p.Gly670Asp	p.G670D	ENST00000249373	NM_005631.4	670	gGc/gAc	12/12	0.256896278858433	1	FACETS	0.864	0.758	0.976	0.864	0.758	0.976	CLONAL	1	FALSE	0	0.388657001207758	1		432	336	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391377	139391377	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752505638	NA	P-0001510-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	137	406	0	ENST00000277541.6:c.6814C>T	p.Arg2272Cys	p.R2272C	ENST00000277541	NM_017617.3	2272	Cgt/Tgt	34/34	0.390605064939581	1	FACETS	0.95	0.879	1	1	0.991	1	CLONAL	2	FALSE	0	0.388657001207758	1		406	299	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141426	11141426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001510-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	174	497	0	ENST00000358026.2:c.3403C>T	p.Arg1135Trp	p.R1135W	ENST00000358026	NM_001128849.1	1135	Cgg/Tgg	25/36	0.390605064939581	1	FACETS	1	0.937	1	1	0.993	1	CLONAL	2	FALSE	0	0.388657001207758	1		497	360	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278106	41278106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001525-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	725	444	0	ENST00000349496.5:c.1982G>A	p.Arg661Gln	p.R661Q	ENST00000349496	NM_001904.3	661	cGa/cAa	13/15	0.559081905443507	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.560946717052028	2		444	1200	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0001525-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	386	343	0	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	0.559081905443507	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.560946717052028	2		343	684	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251982	8251982	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001525-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	223	487	0	ENST00000335790.3:c.95del	p.Lys32ArgfsTer6	p.K32Rfs*6	ENST00000335790	NM_002315.2	32	aAg/ag	2/4	1	2	FACETS	0.986	0.921	1	0.986	0.921	1	CLONAL	1	TRUE	1	0.560946717052028	2		487	806	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578467	7578467	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001528-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	214	286	0	ENST00000269305.4:c.463A>C	p.Thr155Pro	p.T155P	ENST00000269305	NM_001126112.2	155	Acc/Ccc	5/11	0.501129337592413	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.501129337592413	2		286	409	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056648	26056648	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs755438887	NA	P-0001528-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	72	89	0	ENST00000343677.2:c.9G>C	p.Glu3Asp	p.E3D	ENST00000343677	NM_005319.3	3	gaG/gaC	1/1	0.468223539879007	5	FACETS	1	0.943	1			1	CLONAL	2	TRUE	NA	0.501129337592413	5		89	228	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690802	89690802	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs1114167621	NA	P-0001528-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	202	273	0	ENST00000371953.3:c.210-1G>C		p.X70_splice	ENST00000371953	NM_000314.4	70			0.432295358684116	3	FACETS	0.864	0.814	0.914			1	CLONAL	3	TRUE	NA	0.501129337592413	3		273	389	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984924	101984924	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001533-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	232	168	0	ENST00000282441.5:c.371G>C	p.Arg124Pro	p.R124P	ENST00000282441	NM_001130145.2	124	cGa/cCa	2/9	0.88591751951629	3	FACETS	0.961	0.899	1	0.481	0.449	0.513	CLONAL	1	TRUE	1	0.90285627242838	3		168	776	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs17849781	NA	P-0001534-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	98	530	0	ENST00000269305.4:c.832C>A	p.Pro278Thr	p.P278T	ENST00000269305	NM_001126112.2	278	Cct/Act	8/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		530	1111	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913514	NA	P-0001542-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	158	426	0	ENST00000288135.5:c.2466T>A	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaA	17/21	0.453345174118771	5	FACETS	0.755	0.692	0.819	0.377	0.346	0.41	SUBCLONAL	2	TRUE	1	0.453345174118771	5		426	776	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0001550-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	300	290	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.334056887695628	4	FACETS	0.97	0.918	1	0.97	0.918	1	CLONAL	3	TRUE	1	0.334056887695628	4		290	823	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0001550-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	132	279	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.230861585539657	2	FACETS	0.761	0.695	0.83	0.761	0.695	0.83	SUBCLONAL	2	TRUE	0	0.334056887695628	2		279	519	SUCCESS
ALK	238	MSKCC	GRCh37	2	29497970	29497970	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001550-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	169	315	0	ENST00000389048.3:c.2036C>A	p.Pro679His	p.P679H	ENST00000389048	NM_004304.4	679	cCt/cAt	11/29	0.219175593513541	2	FACETS	0.775	0.715	0.837	0.775	0.715	0.837	SUBCLONAL	2	TRUE	0	0.334056887695628	2		315	653	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696189	52696189	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001550-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	119	434	0	ENST00000394830.3:c.488A>T	p.Asp163Val	p.D163V	ENST00000394830	NM_018313.4	163	gAt/gTt	5/30	0.25778940900585	3	FACETS	1	0.93	1	0.518	0.468	0.572	CLONAL	1	TRUE	1	0.334056887695628	3		434	802	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201693	66201693	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001550-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	74	383	0	ENST00000273854.3:c.2809C>A	p.Arg937Ser	p.R937S	ENST00000273854	NM_004439.5	937	Cgt/Agt	16/18	0.334056887695628	1	FACETS	0.799	0.702	0.903	0.799	0.702	0.903	CLONAL	1	TRUE	0	0.334056887695628	1		383	462	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944902	131944902	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0001550-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	48	264	0	ENST00000265335.6:c.2922+1G>A		p.X974_splice	ENST00000265335		974			0.14859017071478	3	FACETS	0.611	0.516	0.715	0.305	0.258	0.358	INDETERMINATE	1	TRUE	1	0.334056887695628	3		264	549	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386589	81386589	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001550-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	97	320	0	ENST00000222390.5:c.398G>T	p.Gly133Val	p.G133V	ENST00000222390	NM_000601.4	133	gGa/gTa	4/18	0.334056887695628	5	FACETS	1	0.964	1	0.398	0.355	0.444	CLONAL	1	TRUE	2	0.334056887695628	5		320	730	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517961	8517961	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001550-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	96	402	0	ENST00000356435.5:c.1430C>A	p.Thr477Asn	p.T477N	ENST00000356435		477	aCt/aAt	10/35	0.25778940900585	3	FACETS	0.918	0.818	1	0.459	0.409	0.512	CLONAL	1	TRUE	1	0.334056887695628	3		402	731	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114223	115114223	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001550-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	173	370	0	ENST00000257566.3:c.994G>C	p.Glu332Gln	p.E332Q	ENST00000257566	NM_016569.3	332	Gag/Cag	6/8	0.334056887695628	2	FACETS	0.781	0.722	0.843	0.781	0.722	0.843	SUBCLONAL	2	TRUE	0	0.334056887695628	2		370	663	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610637	10610637	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001550-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	33	261	0	ENST00000171111.5:c.73G>C	p.Glu25Gln	p.E25Q	ENST00000171111	NM_203500.1	25	Gag/Cag	2/6	0.334056887695628	3	FACETS	0.37	0.3	0.448	0.185	0.15	0.224	SUBCLONAL	1	TRUE	1	0.334056887695628	3		261	624	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39746924	39746924	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001550-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	89	208	0	ENST00000361337.2:c.1938C>G	p.Asn646Lys	p.N646K	ENST00000361337	NM_003286.2	646	aaC/aaG	18/21	0.305970160767161	4	FACETS	1	0.969	1			1	CLONAL	1	TRUE	NA	0.334056887695628	4		208	560	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778848	76778848	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001550-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	92	435	0	ENST00000373344.5:c.6731A>T	p.His2244Leu	p.H2244L	ENST00000373344	NM_000489.3	2244	cAt/cTt	31/35	1	2	FACETS	0.849	0.755	0.949	0.849	0.755	0.949	CLONAL	1	TRUE	1	0.334056887695628	2		435	649	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs104886003	NA	P-0001568-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	446	19	182	0	ENST00000263967.3:c.1633G>C	p.Glu545Gln	p.E545Q	ENST00000263967	NM_006218.2	545	Gag/Cag	10/21	0.238887399592422	3	FACETS	0.334	0.253	0.431	0.167	0.126	0.216	SUBCLONAL	1	TRUE	1	0.278674002703095	3		182	465	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113272	209113272	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001568-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	1078	84	403	0	ENST00000345146.2:c.235G>A	p.Asp79Asn	p.D79N	ENST00000345146	NM_005896.2	79	Gat/Aat	4/10	1	2	FACETS	0.519	0.457	0.586	0.519	0.457	0.586	SUBCLONAL	1	TRUE	1	0.278674002703095	2		403	1162	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057595	180057595	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001568-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	854	54	443	0	ENST00000261937.6:c.360C>G	p.Ile120Met	p.I120M	ENST00000261937	NM_182925.4	120	atC/atG	3/30	0.278674002703095	1	FACETS	0.367	0.313	0.428	0.367	0.313	0.428	SUBCLONAL	1	TRUE	0	0.278674002703095	1		443	908	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402737	20402737	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001568-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	703	38	246	0	ENST00000346618.3:c.274G>C	p.Glu92Gln	p.E92Q	ENST00000346618	NM_001949.4	92	Gag/Cag	1/7	0.15314764398523	4	FACETS	0.471	0.388	0.564	0.235	0.194	0.282	INDETERMINATE	1	TRUE	2	0.278674002703095	4		246	741	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519599	137519599	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001568-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	1133	85	410	0	ENST00000367739.4:c.1039G>C	p.Glu347Gln	p.E347Q	ENST00000367739	NM_000416.2	347	Gaa/Caa	7/7	NA	2	FACETS	0.501	0.441	0.565			1	INDETERMINATE	1	TRUE	NA	0.278674002703095	2		410	1218	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741836	145741836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001568-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	1469	84	416	0	ENST00000428558.2:c.667G>A	p.Gly223Ser	p.G223S	ENST00000428558	NM_004260.3	223	Ggt/Agt	5/22	0.278674002703095	4	FACETS	0.496	0.436	0.561	0.165	0.145	0.187	SUBCLONAL	1	TRUE	1	0.278674002703095	4		416	1553	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190766	108190766	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001568-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	732	46	295	0	ENST00000278616.4:c.6433G>T	p.Glu2145Ter	p.E2145*	ENST00000278616	NM_000051.3	2145	Gaa/Taa	44/63	0.278674002703095	2	FACETS	0.424	0.356	0.5	0.212	0.178	0.25	SUBCLONAL	1	TRUE	0	0.278674002703095	2		295	778	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26974662	26974662	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001568-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	725	117	384	0	ENST00000381527.3:c.1006T>G	p.Leu336Val	p.L336V	ENST00000381527	NM_001260.1	336	Tta/Gta	10/13	0.278674002703095	2	FACETS	0.997	0.899	1	0.499	0.449	0.551	CLONAL	1	TRUE	0	0.278674002703095	2		384	842	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436290	110436290	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001568-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	187	52	74	0	ENST00000375856.3:c.2111C>T	p.Ser704Phe	p.S704F	ENST00000375856	NM_003749.2	704	tCt/tTt	1/2	0.278674002703095	3	FACETS	0.89	0.765	1	0.89	0.765	1	CLONAL	2	TRUE	1	0.278674002703095	3		74	239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0001568-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	418	163	246	0	ENST00000269305.4:c.376-1G>T		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.278674002703095	1	FACETS	0.866	0.799	0.936	1	0.991	1	CLONAL	2	TRUE	0	0.278674002703095	1		246	581	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0001573-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	437	554	0	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.434579756021759	4	FACETS	0.99	0.957	1			1	CLONAL	4	TRUE	NA	0.518090459983599	4		554	647	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986893	36986893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1310962672	NA	P-0001573-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	77	242	0	ENST00000354822.5:c.796G>A	p.Gly266Ser	p.G266S	ENST00000354822	NM_001079668.2	266	Ggc/Agc	3/3	0.485098437173061	4	FACETS	0.994	0.887	1	0.994	0.887	1	CLONAL	2	TRUE	2	0.518090459983599	4		242	227	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759868	63759868	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766186442	NA	P-0001573-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	417	588	0	ENST00000279873.7:c.521C>T	p.Thr174Met	p.T174M	ENST00000279873	NM_032199.2	174	aCg/aTg	4/10	0.131689096528022	6	FACETS	1	0.985	1			1	INDETERMINATE	4	TRUE	NA	0.518090459983599	6		588	780	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937234	76937234	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001573-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	409	680	0	ENST00000373344.5:c.3514del	p.Thr1172LeufsTer18	p.T1172Lfs*18	ENST00000373344	NM_000489.3	1172	Act/ct	9/35	0.278092010426384	4	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.518090459983599	4		680	1083	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001581-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	129	230	0	ENST00000269305.4:c.853G>T	p.Glu285Ter	p.E285*	ENST00000269305	NM_001126112.2	285	Gag/Tag	8/11	0.3462476780543	1	FACETS	0.894	0.813	0.979	0.894	0.813	0.979	CLONAL	1	TRUE	0	0.371614221627992	1		230	632	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17355119	17355119	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001581-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	119	208	0	ENST00000375499.3:c.399G>A	p.Met133Ile	p.M133I	ENST00000375499	NM_003000.2	133	atG/atA	4/8	1	2	FACETS	0.888	0.803	0.979	0.888	0.803	0.979	CLONAL	1	TRUE	1	0.371614221627992	2		208	721	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40497584	40497584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774724351	NA	P-0001581-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	164	259	0	ENST00000264657.5:c.365C>T	p.Ala122Val	p.A122V	ENST00000264657	NM_139276.2	122	gCg/gTg	4/24	0.371614221627992	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.371614221627992	1		259	699	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0001597-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	249	378	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.218058272967818	1	FACETS	0.934	0.876	0.994	0.934	0.876	0.994	INDETERMINATE	1	TRUE	0	0.470656705179984	1		379	866	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180411	94180411	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753717905	NA	P-0001597-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	88	800	0	ENST00000323929.3:c.1757C>T	p.Ser586Leu	p.S586L	ENST00000323929	NM_005591.3	586	tCg/tTg	15/20	1	2	FACETS	0.356	0.315	0.401	0.356	0.315	0.401	SUBCLONAL	1	TRUE	1	0.470656705179984	2		800	1049	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130319	2130319	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1060500939	NA	P-0001597-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	87	568	0	ENST00000219476.3:c.3551C>A	p.Ala1184Glu	p.A1184E	ENST00000219476	NM_000548.3	1184	gCg/gAg	30/42	0.218058272967818	1	FACETS	0.378	0.334	0.425	0.378	0.334	0.425	INDETERMINATE	1	TRUE	0	0.470656705179984	1		568	748	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932914	39932914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147493277	NA	P-0001597-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	78	511	0	ENST00000378444.4:c.1685C>T	p.Ser562Leu	p.S562L	ENST00000378444	NM_001123385.1	562	tCg/tTg	4/15	0.361409977217308	1	FACETS	0.386	0.339	0.436	0.386	0.339	0.436	SUBCLONAL	1	TRUE	0	0.470656705179984	1		511	657	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0001616-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	792	542	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.305947243408285	5	FACETS	1	0.992	1			1	CLONAL	6	TRUE	NA	0.305947243408285	5		542	1210	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431011	181431011	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001616-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	221	356	0	ENST00000325404.1:c.863C>G	p.Ala288Gly	p.A288G	ENST00000325404	NM_003106.3	288	gCc/gGc	1/1	0.305947243408285	5	FACETS	0.958	0.891	1	0.639	0.594	0.685	CLONAL	2	TRUE	2	0.305947243408285	5		356	1100	SUCCESS
AXL	558	MSKCC	GRCh37	19	41725338	41725338	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001616-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	52	382	0	ENST00000301178.4:c.41C>G	p.Ala14Gly	p.A14G	ENST00000301178	NM_021913.4	14	gCc/gGc	1/20	0.152794435641114	4	FACETS	0.575	0.488	0.671	0.144	0.122	0.168	INDETERMINATE	1	TRUE	0	0.305947243408285	4		382	772	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0001623-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	138	495	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.38133976082617	2		496	600	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168793	56168793	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001623-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	157	357	0	ENST00000399503.3:c.1649del	p.Pro550LeufsTer7	p.P550Lfs*7	ENST00000399503	NM_005921.1	549	atC/at	9/20	0.241971940190926	4	FACETS	0.866	0.796	0.938	0.866	0.796	0.938	CLONAL	2	FALSE	2	0.38133976082617	4		357	657	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161230	56161230	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001623-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	154	415	0	ENST00000399503.3:c.1099C>T	p.Gln367Ter	p.Q367*	ENST00000399503	NM_005921.1	367	Caa/Taa	5/20	0.241971940190926	4	FACETS	0.79	0.725	0.858	0.79	0.725	0.858	SUBCLONAL	2	FALSE	2	0.38133976082617	4		415	706	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001635-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	187	468	0	ENST00000269305.4:c.403del	p.Cys135AlafsTer35	p.C135Afs*35	ENST00000269305	NM_001126112.2	135	Tgc/gc	5/11	0.439855264676942	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.439855264676942	1		468	485	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469967	157469967	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001635-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	213	485	0	ENST00000346085.5:c.2761C>A	p.Pro921Thr	p.P921T	ENST00000346085	NM_020732.3	921	Cct/Act	9/20	0.282931757588677	4	FACETS	0.865	0.806	0.926			1	CLONAL	2	TRUE	NA	0.439855264676942	4		485	806	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224772	123224772	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001635-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	229	769	1	ENST00000218089.9:c.3536C>A	p.Ala1179Glu	p.A1179E	ENST00000218089	NM_001042749.1	1179	gCa/gAa	32/35	1	2	FACETS	0.821	0.764	0.881	0.821	0.764	0.881	CLONAL	1	TRUE	1	0.439855264676942	2		770	1268	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0001640-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	127	164	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.400833269323594	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.400833269323594	2		164	292	SUCCESS
APC	324	MSKCC	GRCh37	5	112175240	112175240	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001640-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	82	1167	0	ENST00000257430.4:c.3949G>T	p.Glu1317Ter	p.E1317*	ENST00000257430	NM_000038.5	1317	Gaa/Taa	16/16	0.400833269323594	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	2	TRUE	0	0.400833269323594	2		1167	203	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29105993	29105993	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs864622149	NA	P-0001642-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	12	238	0	ENST00000328354.6:c.846+1G>A		p.X282_splice	ENST00000328354	NM_007194.3	282			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		238	138	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913255	NA	P-0001657-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	38	351	0	ENST00000369535.4:c.183A>T	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caT	3/7	1	2	FACETS	0.636	0.529	0.754	0.636	0.529	0.754	SUBCLONAL	1	TRUE	1	0.479774581611636	2		351	249	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0001669-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	118	461	3	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	1	2	FACETS	0.867	0.788	0.949	0.867	0.788	0.949	CLONAL	1	TRUE	1	0.642022802448413	2		464	424	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0001672-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	188	495	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.364110509266631	5	FACETS	1	0.984	1			1	INDETERMINATE	3	TRUE	NA	0.804070928663487	5		496	309	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001672-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	135	355	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.753570021834846	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.804070928663487	1		355	191	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200978	108200978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001672-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	79	291	0	ENST00000278616.4:c.7345G>A	p.Glu2449Lys	p.E2449K	ENST00000278616	NM_000051.3	2449	Gaa/Aaa	50/63	0.804070928663487	2	FACETS	1	0.937	1	0.528	0.475	0.582	CLONAL	1	TRUE	0	0.804070928663487	2		291	186	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517966	187517966	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0001672-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	205	335	2	ENST00000441802.2:c.12728C>G	p.Ser4243Ter	p.S4243*	ENST00000441802	NM_005245.3	4243	tCa/tGa	25/27	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.804070928663487	2		337	434	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541457	187541457	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001672-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	150	443	0	ENST00000441802.2:c.6283G>T	p.Glu2095Ter	p.E2095*	ENST00000441802	NM_005245.3	2095	Gag/Tag	10/27	1	2	FACETS	0.947	0.876	1	0.947	0.876	1	CLONAL	1	TRUE	1	0.804070928663487	2		443	394	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89791020	89791020	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001672-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	41	21	0	ENST00000336032.3:c.407G>A	p.Gly136Glu	p.G136E	ENST00000336032	NM_006813.2	136	gGa/gAa	1/2	0.381842263684475	5	FACETS	1	0.91	1	0.721	0.619	0.826	INDETERMINATE	2	TRUE	2	0.804070928663487	5		21	104	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657472	29657472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786203824	NA	P-0001672-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	78	330	0	ENST00000356175.3:c.5705C>T	p.Thr1902Met	p.T1902M	ENST00000356175	NM_000267.3	1902	aCg/aTg	38/57	0.753570021834846	1	FACETS	0.943	0.865	1	0.943	0.865	1	CLONAL	1	TRUE	0	0.804070928663487	1		330	123	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0001678-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	137	409	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.1660727148066	2	FACETS	1	0.959	1	0.547	0.498	0.599	INDETERMINATE	1	TRUE	0	0.31	2		409	808	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032866	30032866	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587776562	NA	P-0001678-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	362	306	0	ENST00000338641.4:c.240+1G>T		p.X80_splice	ENST00000338641	NM_000268.3	80			0.265549563688934	4	FACETS	1	0.987	1			1	CLONAL	3	TRUE	NA	0.31	4		306	929	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168731	32168731	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1245029988	NA	P-0001678-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	166	438	0	ENST00000375023.3:c.4192G>A	p.Ala1398Thr	p.A1398T	ENST00000375023	NM_004557.3	1398	Gca/Aca	23/30	1	2	FACETS	0.851	0.78	0.926	0.851	0.78	0.926	CLONAL	1	TRUE	1	0.31	2		438	1258	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573010	7573010	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0001678-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	112	203	0	ENST00000269305.4:c.1101-2A>T		p.X367_splice	ENST00000269305	NM_001126112.2	367			0.304997327168558	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.31	1		203	566	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162505	47162506	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0001678-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	168	482	0	ENST00000409792.3:c.3620_3621del	p.Ser1207Ter	p.S1207*	ENST00000409792	NM_014159.6	1207	tCT/t	3/21	0.304997327168558	1	FACETS	0.965	0.887	1	0.965	0.887	1	CLONAL	1	TRUE	0	0.31	1		482	949	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0001681-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	117	378	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.318714000246233	3	FACETS	0.901	0.839	0.961	1	0.989	1	CLONAL	5	TRUE	0	0.318714000246233	3		379	189	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056714	180056714	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001682-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	41	492	0	ENST00000261937.6:c.798G>T	p.Trp266Cys	p.W266C	ENST00000261937	NM_182925.4	266	tgG/tgT	6/30	0.485191027730446	3	FACETS	0.28	0.232	0.333	0.093	0.077	0.111	SUBCLONAL	1	TRUE	0	0.488431459137427	3		492	747	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469938	157469938	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001682-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	117	399	0	ENST00000346085.5:c.2732G>A	p.Gly911Glu	p.G911E	ENST00000346085	NM_020732.3	911	gGa/gAa	9/20	0.441970218023184	2	FACETS	0.895	0.811	0.984	0.448	0.405	0.492	CLONAL	1	TRUE	0	0.488431459137427	2		399	535	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0001700-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	375	333	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.674329677321285	3	FACETS	0.957	0.925	0.988	0.957	0.925	0.988	CLONAL	3	TRUE	0	0.674329677321285	3		333	518	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0001700-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	207	442	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	0.877	0.817	0.939	0.877	0.817	0.939	CLONAL	1	TRUE	1	0.674329677321285	2		442	700	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057781	27057781	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001700-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	275	638	0	ENST00000324856.7:c.1489C>T	p.Gln497Ter	p.Q497*	ENST00000324856	NM_006015.4	497	Caa/Taa	3/20	1	2	FACETS	0.992	0.935	1	0.992	0.935	1	CLONAL	1	TRUE	1	0.674329677321285	2		638	822	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372518	55372518	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001700-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	535	495	0	ENST00000297316.4:c.1208G>T	p.Ser403Ile	p.S403I	ENST00000297316	NM_022454.3	403	aGc/aTc	2/2	0.674329677321285	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.674329677321285	3		495	1004	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491290	2491290	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001704-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	386	312	0	ENST00000355716.4:c.333C>G	p.Cys111Trp	p.C111W	ENST00000355716	NM_003820.2	111	tgC/tgG	4/8	1	2	FACETS	0.863	0.833	0.892	1	0.997	1	CLONAL	2	TRUE	1	0.790568576120857	2		312	566	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775912	9775912	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001704-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	326	337	0	ENST00000377346.4:c.376C>G	p.His126Asp	p.H126D	ENST00000377346	NM_005026.3	126	Cac/Gac	5/24	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.790568576120857	2		337	809	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180840	106180840	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1297194836	NA	P-0001704-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	422	341	0	ENST00000380013.4:c.3868T>C	p.Ser1290Pro	p.S1290P	ENST00000380013	NM_001127208.2	1290	Tca/Cca	7/11	1	2	FACETS	0.955	0.911	0.999	0.955	0.911	0.999	CLONAL	1	TRUE	1	0.790568576120857	2		341	1118	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637076	93637076	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001704-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	494	325	1	ENST00000375746.1:c.1126G>T	p.Glu376Ter	p.E376*	ENST00000375746	NM_001174167.1	376	Gaa/Taa	9/14	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.790568576120857	2		326	1245	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249288	133249288	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001704-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	382	400	0	ENST00000320574.5:c.1611G>C	p.Glu537Asp	p.E537D	ENST00000320574	NM_006231.2	537	gaG/gaC	15/49	0.790568576120857	3	FACETS	0.957	0.908	1	0.478	0.454	0.504	CLONAL	1	TRUE	1	0.790568576120857	3		400	1409	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936995	48936995	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778842	NA	P-0001704-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	518	377	0	ENST00000267163.4:c.763C>T	p.Arg255Ter	p.R255*	ENST00000267163	NM_000321.2	255	Cga/Tga	8/27	0.790568576120857	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.790568576120857	1		377	783	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419938	152419938	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001715-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	55	449	0	ENST00000206249.3:c.1625A>G	p.Glu542Gly	p.E542G	ENST00000206249	NM_000125.3	542	gAg/gGg	8/8	0.491195771387148	4	FACETS	0.233	0.198	0.271	0.117	0.099	0.136	INDETERMINATE	1	TRUE	2	0.845638555518607	4		449	1030	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38966777	38966780	+	frameshift_variant	Frame_Shift_Del	DEL	CTAA	CTAA	-	novel	NA	P-0001715-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	259	454	0	ENST00000357387.3:c.1262_1265del	p.Val421GlufsTer6	p.V421Efs*6	ENST00000357387	NM_152756.3	421	gTTAGa/ga	15/38	0.845638555518607	4	FACETS	0.863	0.807	0.921	0.432	0.403	0.461	CLONAL	1	TRUE	2	0.845638555518607	4		454	1310	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416626	121416626	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001721-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	22	485	0	ENST00000257555.6:c.55T>C	p.Ser19Pro	p.S19P	ENST00000257555		19	Tca/Cca	1/10	0.78852924431391	1	FACETS	0.483	0.386	0.587	0.483	0.386	0.587	SUBCLONAL	1	TRUE	0	0.788450688881903	1		485	70	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577135	7577135	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001721-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	62	534	0	ENST00000269305.4:c.803A>T	p.Asn268Ile	p.N268I	ENST00000269305	NM_001126112.2	268	aAc/aTc	8/11	0.7751486572172	1	FACETS	0.787	0.705	0.87	0.787	0.705	0.87	SUBCLONAL	1	TRUE	0	0.788450688881903	1		534	121	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855934	68855934	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001721-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	45	531	0	ENST00000261769.5:c.1743del	p.Leu582CysfsTer2	p.L582Cfs*2	ENST00000261769	NM_004360.3	581	cTt/ct	12/16	0.78852924431391	1	FACETS	0.823	0.724	0.921	0.823	0.724	0.921	CLONAL	1	TRUE	0	0.788450688881903	1		531	84	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089730	27089730	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001735-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	25	158	0	ENST00000324856.7:c.2686G>T	p.Glu896Ter	p.E896*	ENST00000324856	NM_006015.4	896	Gaa/Taa	8/20	0.281387798266278	3	FACETS	0.571	0.453	0.706	0.286	0.226	0.353	INDETERMINATE	1	TRUE	1	0.52956934221689	3		158	209	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0001746-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	128	387	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	NA	2	FACETS	0.977	0.918	1			1	INDETERMINATE	2	TRUE	NA	0.689366706302882	2		387	190	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0001746-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	31	482	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.519761218697776	0	FACETS		NA	1			1	NA	1	TRUE	0	0.689366706302882	0		482	102	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277275	41277275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001746-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	67	701	0	ENST00000349496.5:c.1744C>T	p.Arg582Trp	p.R582W	ENST00000349496	NM_001904.3	582	Cgg/Tgg	11/15	1	2	FACETS	0.88	0.776	0.988	0.88	0.776	0.988	CLONAL	1	TRUE	1	0.689366706302882	2		701	221	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274722	142274722	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001746-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	33	517	1	ENST00000350721.4:c.2338C>A	p.Leu780Ile	p.L780I	ENST00000350721	NM_001184.3	780	Ctt/Att	10/47	1	2	FACETS	0.532	0.438	0.635	0.532	0.438	0.635	SUBCLONAL	1	TRUE	1	0.689366706302882	2		518	180	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874636	35874636	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001746-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	26	767	2	ENST00000303115.3:c.792G>T	p.Trp264Cys	p.W264C	ENST00000303115	NM_002185.3	264	tgG/tgT	6/8	1	2	FACETS	0.397	0.317	0.488	0.397	0.317	0.488	SUBCLONAL	1	TRUE	1	0.689366706302882	2		769	190	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692791	89692791	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1114167623	NA	P-0001746-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	47	421	0	ENST00000371953.3:c.275A>G	p.Asp92Gly	p.D92G	ENST00000371953	NM_000314.4	92	gAc/gGc	5/9	0.685075743690805	1	FACETS	0.921	0.808	1	0.921	0.808	1	CLONAL	1	TRUE	0	0.689366706302882	1		421	97	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0001746-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	63	340	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.343546938994221	1	FACETS	0.735	0.65	0.822	0.735	0.65	0.822	INDETERMINATE	1	TRUE	0	0.689366706302882	1		340	163	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0001747-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	179	542	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.632388327381081	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.632388327381081	1		542	332	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989475	85989475	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001747-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	37	520	2	ENST00000263360.6:c.1234G>A	p.Ala412Thr	p.A412T	ENST00000263360	NM_003797.3	412	Gct/Act	12/12	0.417451546404578	3	FACETS	0.667	0.554	0.791	0.333	0.277	0.396	SUBCLONAL	1	TRUE	1	0.632388327381081	3		522	231	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371676	55371683	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGCTGC	GCGGCTGC	-	novel	NA	P-0001747-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	72	351	0	ENST00000297316.4:c.369_376del	p.Leu124AlafsTer35	p.L124Afs*35	ENST00000297316	NM_022454.3	122	gaGCGGCTGCgc/gagc	2/2	0.632388327381081	6	FACETS	0.661	0.577	0.753			1	SUBCLONAL	1	TRUE	NA	0.632388327381081	6		351	780	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371727	55371729	+	inframe_deletion	In_Frame_Del	DEL	GCG	GCG	-	novel	NA	P-0001747-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	59	283	0	ENST00000297316.4:c.423_425del	p.Arg142del	p.R142del	ENST00000297316	NM_022454.3	139	ccGCGg/ccg	2/2	0.632388327381081	6	FACETS	0.681	0.585	0.785			1	SUBCLONAL	1	TRUE	NA	0.632388327381081	6		283	621	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371821	55371823	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	novel	NA	P-0001747-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	13	18	0	ENST00000297316.4:c.514_516del	p.Gly172del	p.G172del	ENST00000297316	NM_022454.3	171	GGC/-	2/2	0.632388327381081	6	FACETS	0.95	0.686	1			1	CLONAL	1	TRUE	NA	0.632388327381081	6		18	98	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0001762-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	141	495	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.364150360378111	4	FACETS	0.836	0.765	0.909	0.836	0.765	0.909	CLONAL	2	TRUE	2	0.441367620633522	4		496	551	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86658435	86658435	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001762-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	37	516	0	ENST00000274376.6:c.1400C>G	p.Thr467Arg	p.T467R	ENST00000274376	NM_002890.2	467	aCa/aGa	10/25	0.421164093122252	3	FACETS	0.343	0.282	0.411	0.171	0.141	0.206	SUBCLONAL	1	TRUE	1	0.441367620633522	3		516	597	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955108	17955108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56384680	NA	P-0001762-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	113	460	0	ENST00000458235.1:c.119G>A	p.Arg40His	p.R40H	ENST00000458235	NM_000215.3	40	cGc/cAc	2/24	0.218762369243171	5	FACETS	0.915	0.828	1	0.61	0.552	0.671	INDETERMINATE	2	TRUE	2	0.441367620633522	5		460	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576913	7576941	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTTGTTGGGCAGTGCTAGGAAAGAGGCAA	GTTGTTGGGCAGTGCTAGGAAAGAGGCAA	-	novel	NA	P-0001762-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	43	514	0	ENST00000269305.4:c.920-15_933del		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	0.316924040560509	2	FACETS	0.812	0.685	0.95	0.406	0.342	0.475	CLONAL	1	TRUE	0	0.441367620633522	2		514	240	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0001781-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	36	409	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.450472454325676	2	FACETS	0.913	0.769	1	0.457	0.384	0.533	CLONAL	1	TRUE	0	0.691602956681618	2		409	114	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935606	13935606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326846768	NA	P-0001781-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	155	575	0	ENST00000405192.2:c.1250G>A	p.Arg417His	p.R417H	ENST00000405192	NM_001163147.1	417	cGt/cAt	12/12	0.670449393879784	4	FACETS	0.872	0.815	0.928	1	0.988	1	CLONAL	3	TRUE	2	0.691602956681618	4		575	290	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80343503	80343503	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001781-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	17	574	0	ENST00000286548.4:c.816C>A	p.Phe272Leu	p.F272L	ENST00000286548	NM_002072.3	272	ttC/ttA	6/7	0.521328605139432	3	FACETS	0.264	0.197	0.343			1	SUBCLONAL	1	TRUE	NA	0.691602956681618	3		574	251	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021149	31021149	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1203866783	NA	P-0001781-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	126	624	0	ENST00000375687.4:c.1148A>G	p.Lys383Arg	p.K383R	ENST00000375687	NM_015338.5	383	aAa/aGa	12/13	0.691602956681618	7	FACETS	0.894	0.825	0.964			1	CLONAL	4	TRUE	NA	0.691602956681618	7		624	278	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199469669	NA	P-0001781-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	210	717	0	ENST00000374080.3:c.130G>T	p.Gly44Cys	p.G44C	ENST00000374080		44	Ggt/Tgt	2/45	0.444874192108317	3	FACETS	0.927	0.885	0.966			1	CLONAL	3	TRUE	NA	0.691602956681618	3		717	294	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938569	76938569	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001781-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	86	745	0	ENST00000373344.5:c.2179C>T	p.Gln727Ter	p.Q727*	ENST00000373344	NM_000489.3	727	Caa/Taa	9/35	NA	2	FACETS	0.864	0.793	0.933			1	INDETERMINATE	2	TRUE	NA	0.691602956681618	2		745	144	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0001799-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	293	351	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.680050253906716	3	FACETS	0.844	0.809	0.879	0.844	0.809	0.879	CLONAL	3	TRUE	0	0.680050253906716	3		351	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0001802-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	255	349	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.311220878619877	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	0	0.346976471766099	2		349	735	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719635	190719635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs531239757	NA	P-0001802-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	78	278	0	ENST00000441310.2:c.1637G>A	p.Cys546Tyr	p.C546Y	ENST00000441310	NM_000534.4	546	tGt/tAt	9/13	0.346976471766099	3	FACETS	0.85	0.747	0.96	0.425	0.373	0.48	CLONAL	1	TRUE	1	0.346976471766099	3		278	621	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209101832	209101832	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001802-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	161	549	0	ENST00000345146.2:c.1216A>G	p.Lys406Glu	p.K406E	ENST00000345146	NM_005896.2	406	Aag/Gag	10/10	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.346976471766099	2		549	893	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215987	142215987	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs759599412	NA	P-0001802-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	166	352	0	ENST00000350721.4:c.5606A>G	p.Gln1869Arg	p.Q1869R	ENST00000350721	NM_001184.3	1869	cAg/cGg	33/47	0.346976471766099	4	FACETS	0.798	0.733	0.864	0.798	0.733	0.864	SUBCLONAL	2	TRUE	2	0.346976471766099	4		352	808	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90634806	90634806	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001802-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	441	391	0	ENST00000330062.3:c.186C>G	p.Ile62Met	p.I62M	ENST00000330062	NM_002168.2	62	atC/atG	2/11	0.346976471766099	5	FACETS	0.972	0.927	1	0.972	0.927	1	CLONAL	3	TRUE	2	0.346976471766099	5		391	1326	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878160	48878161	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0001802-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	91	126	0	ENST00000267163.4:c.112_113delinsTT	p.Gly38Phe	p.G38F	ENST00000267163	NM_000321.2	38	GGc/TTc	1/27	NA	2	FACETS	0.979	0.882	1			1	INDETERMINATE	2	TRUE	NA	0.346976471766099	2		126	268	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0001824-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	13	378	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		379	609	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717630	89717630	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554825168	NA	P-0001844-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	59	151	0	ENST00000371953.3:c.655C>T	p.Gln219Ter	p.Q219*	ENST00000371953	NM_000314.4	219	Cag/Tag	7/9	0.355191911265156	4	FACETS	0.843	0.726	0.97			1	CLONAL	1	TRUE	NA	0.375404307963501	4		151	513	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0001844-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	13	149	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.183108324417404	4	FACETS	0.365	0.26	0.493	0.182	0.13	0.247	INDETERMINATE	1	TRUE	2	0.375404307963501	4		149	261	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448600	89448600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759973751	NA	P-0001844-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	33	218	0	ENST00000336596.2:c.1564C>T	p.Arg522Cys	p.R522C	ENST00000336596	NM_005233.5	522	Cgc/Tgc	7/17	0.183108324417404	4	FACETS	0.499	0.405	0.604	0.249	0.202	0.302	INDETERMINATE	1	TRUE	2	0.375404307963501	4		218	485	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119624681	119624681	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001844-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	137	175	0	ENST00000316626.5:c.734G>C	p.Cys245Ser	p.C245S	ENST00000316626		245	tGt/tCt	7/12	0.183108324417404	4	FACETS	0.868	0.793	0.947	0.868	0.793	0.947	INDETERMINATE	2	TRUE	2	0.375404307963501	4		175	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578490	7578490	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1453167097	NA	P-0001844-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	139	153	0	ENST00000269305.4:c.440T>G	p.Val147Gly	p.V147G	ENST00000269305	NM_001126112.2	147	gTt/gGt	5/11	0.183108324417404	4	FACETS	1	0.954	1	1	0.99	1	INDETERMINATE	3	TRUE	2	0.375404307963501	4		153	325	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961561	54961561	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779597046	NA	P-0001844-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	90	202	0	ENST00000312783.6:c.71G>A	p.Arg24His	p.R24H	ENST00000312783	NM_198436.1	24	cGt/cAt	4/10	0.360226045402636	4	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.375404307963501	4		202	457	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717612	89717612	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001844-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	139	130	0	ENST00000371953.3:c.638del	p.Pro213LeufsTer8	p.P213Lfs*8	ENST00000371953	NM_000314.4	213	Cct/ct	7/9	0.355191911265156	4	FACETS	1	0.975	1			1	CLONAL	2	TRUE	NA	0.375404307963501	4		130	439	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845894	151845894	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001845-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	104	274	0	ENST00000262189.6:c.13118C>A	p.Pro4373Gln	p.P4373Q	ENST00000262189	NM_170606.2	4373	cCa/cAa	52/59	1	2	FACETS	0.884	0.798	0.974	0.884	0.798	0.974	CLONAL	1	FALSE	1	0.586567776767224	2		274	401	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243048	105243048	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519804	NA	P-0001845-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	153	228	0	ENST00000349310.3:c.235C>A	p.Gln79Lys	p.Q79K	ENST00000349310	NM_001014432.1	79	Cag/Aag	5/15	1	2	FACETS	0.95	0.874	1	0.95	0.874	1	CLONAL	1	FALSE	1	0.586567776767224	2		228	549	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653152	29653152	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001845-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	86	178	0	ENST00000356175.3:c.5087A>G	p.Glu1696Gly	p.E1696G	ENST00000356175	NM_000267.3	1696	gAg/gGg	36/57	1	2	FACETS	0.965	0.863	1	0.965	0.863	1	CLONAL	1	FALSE	1	0.586567776767224	2		178	304	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105591	27105591	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0001849-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	70	337	0	ENST00000324856.7:c.5202T>G	p.Tyr1734Ter	p.Y1734*	ENST00000324856	NM_006015.4	1734	taT/taG	20/20	0.678762871167469	3	FACETS	0.845	0.742	0.954	0.422	0.371	0.477	CLONAL	1	TRUE	1	0.678762871167469	3		337	327	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540178	23540178	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001849-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	17	56	0	ENST00000380871.4:c.225G>C	p.Gln75His	p.Q75H	ENST00000380871	NM_006167.3	75	caG/caC	1/2	0.63627380521048	2	FACETS	0.737	0.565	0.928	0.368	0.282	0.464	CLONAL	1	TRUE	0	0.678762871167469	2		56	68	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451133	70451133	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001849-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	151	279	0	ENST00000373644.4:c.5973T>A	p.Asp1991Glu	p.D1991E	ENST00000373644	NM_030625.2	1991	gaT/gaA	12/12	0.56762803496091	5	FACETS	1	0.953	1	0.696	0.643	0.751	CLONAL	2	TRUE	2	0.678762871167469	5		279	430	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125523642	125523642	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001849-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	113	311	0	ENST00000428830.2:c.1235T>C	p.Val412Ala	p.V412A	ENST00000428830	NM_001114121.2	412	gTt/gCt	12/14	0.420827044568813	3	FACETS	0.794	0.726	0.863			1	SUBCLONAL	2	TRUE	NA	0.678762871167469	3		311	281	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305399	65305400	+	missense_variant	Missense_Mutation	DNP	AG	AG	GA	novel	NA	P-0001852-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	76	262	0	ENST00000342505.4:c.2728_2729delinsTC	p.Leu910Ser	p.L910S	ENST00000342505	NM_002227.2	910	CTg/TCg	20/25	1	2	FACETS	0.866	0.776	0.958	1	0.983	1	CLONAL	2	TRUE	1	0.464249765729935	2		262	189	SUCCESS
APC	324	MSKCC	GRCh37	5	112175180	112175199	+	frameshift_variant	Frame_Shift_Del	DEL	GATTCTGCTAATACCCTGCA	GATTCTGCTAATACCCTGCA	C	novel	NA	P-0001852-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	12	124	0	ENST00000257430.4:c.3889_3908delinsC	p.Asp1297GlnfsTer2	p.D1297Qfs*2	ENST00000257430	NM_000038.5	1297	GATTCTGCTAATACCCTGCAa/Ca	16/16	NA	2	FACETS	0.76	0.545	1			1	INDETERMINATE	1	TRUE	NA	0.464249765729935	2		124	68	SUCCESS
APC	324	MSKCC	GRCh37	5	112178276	112178276	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs146048493	NA	P-0001859-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	874	596	585	0	ENST00000257430.4:c.6985A>G	p.Ile2329Val	p.I2329V	ENST00000257430	NM_000038.5	2329	Att/Gtt	16/16	1	2	FACETS	0.892	0.858	0.925	1	0.997	1	CLONAL	2	FALSE	1	0.454720751924718	2		585	1470	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710536	117710536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001859-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	749	225	324	0	ENST00000368508.3:c.1736C>T	p.Pro579Leu	p.P579L	ENST00000368508	NM_002944.2	579	cCt/cTt	12/43	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	1	0.454720751924718	2		324	974	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946426	2946426	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471772603	NA	P-0001859-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	983	417	496	0	ENST00000396946.4:c.3311G>A	p.Arg1104Gln	p.R1104Q	ENST00000396946	NM_032415.4	1104	cGg/cAg	25/25	0.207095084630527	5	FACETS	1	0.987	1			1	INDETERMINATE	2	FALSE	NA	0.454720751924718	5		496	1400	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531782	46531782	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001859-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	940	655	682	0	ENST00000262741.5:c.565del	p.Gln189ArgfsTer23	p.Q189Rfs*23	ENST00000262741	NM_003629.3	189	Cag/ag	5/10	1	2	FACETS	0.903	0.871	0.936	1	0.998	1	CLONAL	2	FALSE	1	0.454720751924718	2		682	1595	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226562006	226562006	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001859-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	693	372	523	0	ENST00000366794.5:c.1991del	p.Lys664SerfsTer12	p.K664Sfs*12	ENST00000366794	NM_001618.3	664	aAg/ag	14/23	0.186633082131859	1	FACETS	1	0.991	1	1	0.991	1	INDETERMINATE	1	FALSE	0	0.454720751924718	1		523	1065	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880931	134880931	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001859-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	895	131	469	0	ENST00000398015.3:c.1494del	p.Gly499AlafsTer28	p.G499Afs*28	ENST00000398015	NM_004441.4	498	ccT/cc	7/16	0.372361918774893	1	FACETS	0.434	0.393	0.477	0.434	0.393	0.477	SUBCLONAL	1	FALSE	0	0.454720751924718	1		469	1026	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0001861-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	19	414	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	1	2	FACETS	0.444	0.337	0.57	0.444	0.337	0.57	SUBCLONAL	1	FALSE	1	0.3	2		414	285	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254684	16254684	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs777527531	NA	P-0001861-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	32	548	0	ENST00000375759.3:c.1949A>G	p.Tyr650Cys	p.Y650C	ENST00000375759	NM_015001.2	650	tAt/tGt	11/15	NA	2	FACETS	0.36	0.291	0.438			1	INDETERMINATE	1	FALSE	NA	0.3	2		548	593	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185221	123185221	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001861-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	37	271	0	ENST00000218089.9:c.1173A>G	p.Ile391Met	p.I391M	ENST00000218089	NM_001042749.1	391	atA/atG	13/35	0.282194821238213	2	FACETS	0.628	0.518	0.75			1	SUBCLONAL	1	FALSE	NA	0.3	2		271	393	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288357	33288357	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001886-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	283	399	0	ENST00000374542.5:c.1051G>C	p.Ala351Pro	p.A351P	ENST00000374542	NM_001141970.1	351	Gca/Cca	4/8	0.738598217156509	3	FACETS	0.853	0.819	0.886			1	CLONAL	3	TRUE	NA	0.738598217156509	3		399	410	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577445	64577445	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001886-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	274	561	0	ENST00000312049.6:c.137A>C	p.His46Pro	p.H46P	ENST00000312049	NM_130799.2	46	cAt/cCt	2/10	0.738598217156509	3	FACETS	0.92	0.886	0.953			1	CLONAL	3	TRUE	NA	0.738598217156509	3		561	368	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690819	89690820	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0001886-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	132	305	0	ENST00000371953.3:c.227_228del	p.Tyr76Ter	p.Y76*	ENST00000371953	NM_000314.4	76	TAt/t	4/9	0.722036366415083	2	FACETS	1	0.98	1	0.596	0.55	0.642	CLONAL	1	TRUE	0	0.738598217156509	2		305	300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555526268	NA	P-0001887-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	196	237	0	ENST00000269305.4:c.406C>G	p.Gln136Glu	p.Q136E	ENST00000269305	NM_001126112.2	136	Caa/Gaa	5/11	0.537153714469051	1	FACETS	0.856	0.799	0.915	0.856	0.799	0.915	CLONAL	1	TRUE	0	0.6	1		237	534	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0001909-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	174	549	1	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.681531780080033	2		550	489	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519818	29519818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772496459	NA	P-0001909-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	171	428	1	ENST00000389048.3:c.1753G>A	p.Ala585Thr	p.A585T	ENST00000389048	NM_004304.4	585	Gcc/Acc	9/29	0.603048444123644	3	FACETS	0.895	0.825	0.967	0.447	0.412	0.484	CLONAL	1	TRUE	1	0.681531780080033	3		429	752	SUCCESS
APC	324	MSKCC	GRCh37	5	112175419	112175419	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0001909-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	145	378	2	ENST00000257430.4:c.4128T>G	p.Tyr1376Ter	p.Y1376*	ENST00000257430	NM_000038.5	1376	taT/taG	16/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.681531780080033	2		380	388	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132875	64132875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746182941	NA	P-0001909-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	650	498	1	ENST00000334205.4:c.1009C>T	p.Arg337Trp	p.R337W	ENST00000334205	NM_003942.2	337	Cgg/Tgg	9/17	0.681531780080033	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.681531780080033	3		499	812	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577497	7577497	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0001909-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	167	295	0	ENST00000269305.4:c.782+2T>C		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.681531780080033	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.681531780080033	1		295	292	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593473	48593473	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001909-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	175	454	1	ENST00000342988.3:c.1224T>A	p.Phe408Leu	p.F408L	ENST00000342988	NM_005359.5	408	ttT/ttA	10/12	0.681531780080033	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.681531780080033	1		455	329	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441333	52441333	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0001917-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	72	452	0	ENST00000460680.1:c.438-1G>A		p.X146_splice	ENST00000460680	NM_004656.3	146			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		452	405	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0001924-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	33	378	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.197371982545484	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		379	379	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200786	128200786	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs745439347	NA	P-0001924-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	21	204	0	ENST00000341105.2:c.1019C>T	p.Ser340Leu	p.S340L	ENST00000341105	NM_032638.4	340	tCg/tTg	5/6	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		204	220	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964318	55964318	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001924-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	36	292	0	ENST00000263923.4:c.2495A>T	p.Asp832Val	p.D832V	ENST00000263923	NM_002253.2	832	gAc/gTc	17/30	0.197371982545484	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		292	304	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030479	49030479	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001924-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	33	282	1	ENST00000267163.4:c.1959del	p.Val654CysfsTer4	p.V654Cfs*4	ENST00000267163	NM_000321.2	652	Aaa/aa	19/27	0.3	4	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	4		283	329	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001924-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	18	193	0	ENST00000269305.4:c.383del	p.Pro128LeufsTer42	p.P128Lfs*42	ENST00000269305	NM_001126112.2	128	cCt/ct	5/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		193	204	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567670	226567670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001926-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	263	304	0	ENST00000366794.5:c.1496C>T	p.Ser499Leu	p.S499L	ENST00000366794	NM_001618.3	499	tCa/tTa	10/23	0.508984308541133	3	FACETS	1	0.976	1			1	CLONAL	2	TRUE	NA	0.695650075280557	3		304	488	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251745	212251745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001926-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	116	280	0	ENST00000342788.4:c.3314C>T	p.Ser1105Phe	p.S1105F	ENST00000342788	NM_005235.2	1105	tCc/tTc	27/28	0.695650075280557	3	FACETS	1	0.952	1	0.538	0.488	0.589	CLONAL	1	TRUE	1	0.695650075280557	3		280	418	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622060	43622060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001926-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	93	264	0	ENST00000355710.3:c.3077C>T	p.Ser1026Phe	p.S1026F	ENST00000355710	NM_020975.4	1026	tCc/tTc	19/20	0.402582954233285	1	FACETS	0.504	0.452	0.558	0.504	0.452	0.558	INDETERMINATE	1	TRUE	0	0.695650075280557	1		264	346	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972704	32972704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001926-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	249	289	0	ENST00000380152.3:c.10054C>T	p.Leu3352Phe	p.L3352F	ENST00000380152		3352	Ctt/Ttt	27/27	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.695650075280557	2		289	608	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941654	48941654	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs776534331	NA	P-0001926-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	165	277	0	ENST00000267163.4:c.964G>T	p.Glu322Ter	p.E322*	ENST00000267163	NM_000321.2	322	Gaa/Taa	10/27	0.608902198392078	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.695650075280557	1		277	304	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862796	9862796	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001926-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	83	215	0	ENST00000330684.3:c.2507T>G	p.Ile836Ser	p.I836S	ENST00000330684	NM_001134407.1	836	aTc/aGc	12/13	0.140955365947106	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.695650075280557	0		215	213	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578528	7578528	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001926-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	184	229	0	ENST00000269305.4:c.402T>A	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	ttT/ttA	5/11	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.695650075280557	2		229	437	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303019	15303019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568361985	NA	P-0001926-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	83	203	0	ENST00000263388.2:c.431G>A	p.Cys144Tyr	p.C144Y	ENST00000263388	NM_000435.2	144	tGc/tAc	4/33	0.402582954233285	1	FACETS	0.855	0.774	0.937	0.855	0.774	0.937	INDETERMINATE	1	TRUE	0	0.695650075280557	1		203	182	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929002	44929002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001926-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	385	181	0	ENST00000377967.4:c.2102C>T	p.Ser701Phe	p.S701F	ENST00000377967	NM_021140.2	701	tCt/tTt	17/29	0.695650075280557	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.695650075280557	2		181	458	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797783	42797784	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0001926-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	191	245	0	ENST00000575354.2:c.3835_3836delinsTT	p.Pro1279Phe	p.P1279F	ENST00000575354	NM_015125.3	1279	CCt/TTt	16/20	0.695650075280557	6	FACETS	0.873	0.809	0.939			1	CLONAL	2	TRUE	NA	0.695650075280557	6		245	752	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023831	27023832	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0001926-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	346	78	0	ENST00000324856.7:c.937_938delinsAA	p.Gly313Lys	p.G313K	ENST00000324856	NM_006015.4	313	GGg/AAg	1/20	0.695650075280557	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	1	0.695650075280557	4		78	501	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577142	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0001926-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	206	325	0	ENST00000269305.4:c.796_797delinsAA	p.Gly266Lys	p.G266K	ENST00000269305	NM_001126112.2	266	GGa/AAa	8/11	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.695650075280557	2		325	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0001941-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	123	717	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.331862952338962	2	FACETS	0.761	0.695	0.83	0.761	0.695	0.83	SUBCLONAL	2	TRUE	0	0.396917330066207	2		718	407	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272166	15272206	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGCCCGGGCAGGCCAGCGTCAGCTTCTTGCCCCGCCCCC	GGGGCCCGGGCAGGCCAGCGTCAGCTTCTTGCCCCGCCCCC	-	novel	NA	P-0001941-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	69	216	0	ENST00000263388.2:c.6233_6273del	p.Arg2078ProfsTer3	p.R2078Pfs*3	ENST00000263388	NM_000435.2	2078	cGGGGGCGGGGCAAGAAGCTGACGCTGGCCTGCCCGGGCCCC/c	33/33	0.258481540098335	3	FACETS	0.902	0.807	0.998	0.902	0.807	0.998	CLONAL	3	TRUE	0	0.396917330066207	3		216	154	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0001961-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	317	229	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.548208537029441	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.585670701471356	2		229	540	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0001961-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	164	140	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.585670701471356	3	FACETS	0.955	0.889	1	0.955	0.889	1	CLONAL	2	TRUE	1	0.585670701471356	3		142	379	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0001961-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	176	408	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.585670701471356	3	FACETS	0.926	0.854	1	0.463	0.427	0.501	CLONAL	1	TRUE	1	0.585670701471356	3		409	839	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604778	48604778	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767383	NA	P-0001961-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	353	469	0	ENST00000342988.3:c.1600C>T	p.Gln534Ter	p.Q534*	ENST00000342988	NM_005359.5	534	Cag/Tag	12/12	0.577955391078016	2	FACETS	0.94	0.9	0.98	0.94	0.9	0.98	CLONAL	2	TRUE	0	0.585670701471356	2		469	641	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181413	185181413	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001961-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	244	577	0	ENST00000265026.3:c.1354G>A	p.Glu452Lys	p.E452K	ENST00000265026	NM_004721.4	452	Gaa/Aaa	8/14	0.585670701471356	3	FACETS	0.979	0.915	1	0.49	0.457	0.523	CLONAL	1	TRUE	1	0.585670701471356	3		577	1100	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217180	66217180	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001961-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	45	535	0	ENST00000273854.3:c.2435T>C	p.Leu812Pro	p.L812P	ENST00000273854	NM_004439.5	812	cTt/cCt	14/18	1	2	FACETS	0.22	0.185	0.26	0.22	0.185	0.26	SUBCLONAL	1	TRUE	1	0.585670701471356	2		535	697	SUCCESS
APC	324	MSKCC	GRCh37	5	112175419	112175419	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0001961-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	260	368	0	ENST00000257430.4:c.4128T>A	p.Tyr1376Ter	p.Y1376*	ENST00000257430	NM_000038.5	1376	taT/taA	16/16	0.585670701471356	3	FACETS	0.908	0.857	0.96	0.908	0.857	0.96	CLONAL	2	TRUE	1	0.585670701471356	3		368	632	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004222	29004222	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001961-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	150	443	0	ENST00000282397.4:c.1071G>T	p.Met357Ile	p.M357I	ENST00000282397	NM_002019.4	357	atG/atT	8/30	0.582149487276626	4	FACETS	0.792	0.723	0.865	0.264	0.241	0.289	SUBCLONAL	1	TRUE	1	0.585670701471356	4		443	1025	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628326	90628326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147578332	NA	P-0001961-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	316	395	0	ENST00000330062.3:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000330062	NM_002168.2	362	cGg/cAg	9/11	0.571603613045322	3	FACETS	1	0.958	1	0.672	0.639	0.705	CLONAL	2	TRUE	0	0.585670701471356	3		395	692	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578419	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587781845	NA	P-0001968-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	60	356	0	ENST00000269305.4:c.511G>T	p.Glu171Ter	p.E171*	ENST00000269305	NM_001126112.2	171	Gag/Tag	5/11	0.175927209096793	1	FACETS	0.841	0.728	0.962	1	0.974	1	CLONAL	2	TRUE	0	0.175927209096793	1		356	370	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285246	212285246	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001968-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	73	442	0	ENST00000342788.4:c.3055G>C	p.Ala1019Pro	p.A1019P	ENST00000342788	NM_005235.2	1019	Gct/Cct	25/28	0.175927209096793	2	FACETS	0.868	0.761	0.982	0.868	0.761	0.982	CLONAL	2	TRUE	0	0.175927209096793	2		442	478	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587153	212587153	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001968-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	104	447	0	ENST00000342788.4:c.848A>G	p.Tyr283Cys	p.Y283C	ENST00000342788	NM_005235.2	283	tAc/tGc	7/28	0.175927209096793	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.175927209096793	2		447	508	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884860	134884860	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001968-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	48	417	0	ENST00000398015.3:c.1636G>T	p.Ala546Ser	p.A546S	ENST00000398015	NM_004441.4	546	Gca/Tca	8/16	NA	2	FACETS	1	0.95	1			1	INDETERMINATE	1	TRUE	NA	0.175927209096793	2		417	413	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532927	187532927	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001968-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	22	292	0	ENST00000441802.2:c.9466T>G	p.Leu3156Val	p.L3156V	ENST00000441802	NM_005245.3	3156	Tta/Gta	14/27	1	2	FACETS	0.646	0.5	0.816	0.646	0.5	0.816	SUBCLONAL	1	TRUE	1	0.175927209096793	2		292	387	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876976	151876976	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1358646492	NA	P-0001968-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	63	468	0	ENST00000262189.6:c.7385A>G	p.Gln2462Arg	p.Q2462R	ENST00000262189	NM_170606.2	2462	cAg/cGg	37/59	0.175927209096793	1	FACETS	0.758	0.657	0.866	1	0.971	1	SUBCLONAL	2	TRUE	0	0.175927209096793	1		468	431	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409769	139409769	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001968-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	70	261	0	ENST00000277541.6:c.1987G>T	p.Glu663Ter	p.E663*	ENST00000277541	NM_017617.3	663	Gag/Tag	12/34	0.175927209096793	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.175927209096793	2		261	342	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420490	49420490	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001968-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	45	369	0	ENST00000301067.7:c.15259G>A	p.Gly5087Arg	p.G5087R	ENST00000301067	NM_003482.3	5087	Gga/Aga	48/54	NA	2	FACETS	1	0.939	1			1	INDETERMINATE	1	TRUE	NA	0.175927209096793	2		369	408	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0001977-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	95	378	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.247191810576767	5	FACETS	0.976	0.882	1	1	0.987	1	CLONAL	4	TRUE	3	0.247191810576767	5		379	270	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0001977-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	32	278	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.247191810576767	5	FACETS	1	0.894	1	1	0.894	1	CLONAL	3	TRUE	2	0.247191810576767	5		278	107	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023735	27023735	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001977-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	24	105	0	ENST00000324856.7:c.841G>T	p.Ala281Ser	p.A281S	ENST00000324856	NM_006015.4	281	Gcg/Tcg	1/20	0.247191810576767	3	FACETS	1	0.889	1	1	0.889	1	CLONAL	2	TRUE	1	0.247191810576767	3		105	93	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798266	45798266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878854192	NA	P-0001977-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	14	304	0	ENST00000450313.1:c.670G>A	p.Ala224Thr	p.A224T	ENST00000450313	NM_012222.2	224	Gcc/Acc	8/16	0.247191810576767	3	FACETS	1	0.83	1	0.6	0.439	0.791	CLONAL	1	TRUE	1	0.247191810576767	3		304	106	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085647	16085647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1238492356	NA	P-0001977-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	14	303	0	ENST00000281043.3:c.823G>A	p.Glu275Lys	p.E275K	ENST00000281043	NM_005378.4	275	Gaa/Aaa	3/3	0.247191810576767	3	FACETS	1	0.774	1	0.535	0.39	0.707	CLONAL	1	TRUE	1	0.247191810576767	3		303	119	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55569972	55569972	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001977-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	32	435	0	ENST00000288135.5:c.839C>A	p.Ala280Glu	p.A280E	ENST00000288135	NM_000222.2	280	gCg/gAg	5/21	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.247191810576767	2		435	202	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867448	35867448	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001977-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	53	301	0	ENST00000303115.3:c.262C>A	p.Leu88Ile	p.L88I	ENST00000303115	NM_002185.3	88	Cta/Ata	3/8	0.247191810576767	6	FACETS	0.901	0.777	1	0.676	0.583	0.776	CLONAL	3	TRUE	2	0.247191810576767	6		301	237	SUCCESS
BLM	641	MSKCC	GRCh37	15	91328180	91328180	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001977-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	36	358	0	ENST00000355112.3:c.2692A>T	p.Arg898Trp	p.R898W	ENST00000355112	NM_000057.2	898	Agg/Tgg	14/22	0.247191810576767	3	FACETS	0.794	0.659	0.943	0.794	0.659	0.943	CLONAL	2	TRUE	1	0.247191810576767	3		358	206	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670713	67670713	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001977-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	15	361	0	ENST00000264010.4:c.1958G>T	p.Gly653Val	p.G653V	ENST00000264010	NM_006565.3	653	gGa/gTa	11/12	0.247191810576767	3	FACETS	1	0.755	1	0.513	0.378	0.672	CLONAL	1	TRUE	1	0.247191810576767	3		361	133	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220649	1220649	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001986-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	136	321	0	ENST00000326873.7:c.667G>T	p.Glu223Ter	p.E223*	ENST00000326873	NM_000455.4	223	Gag/Tag	5/10	NA	2	FACETS	1	0.978	1			1	INDETERMINATE	2	TRUE	NA	0.25766857580718	2		321	440	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705619	47705619	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001986-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	170	350	0	ENST00000233146.2:c.2419A>G	p.Thr807Ala	p.T807A	ENST00000233146	NM_000251.2	807	Act/Gct	14/16	0.25766857580718	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	1	0.25766857580718	4		350	484	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427271	427271	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0001986-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	65	250	0	ENST00000399788.2:c.2897+1G>T		p.X966_splice	ENST00000399788	NM_001042603.1	966			NA	2	FACETS	0.838	0.733	0.95			1	INDETERMINATE	2	TRUE	NA	0.25766857580718	2		250	301	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514410	103514410	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001986-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	93	285	0	ENST00000355739.4:c.911A>T	p.Asp304Val	p.D304V	ENST00000355739	NM_000123.3	304	gAt/gTt	8/15	0.229603376954245	4	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	2	0.25766857580718	4		285	422	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610073	10610073	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001986-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	145	378	0	ENST00000171111.5:c.637G>T	p.Glu213Ter	p.E213*	ENST00000171111	NM_203500.1	213	Gag/Tag	2/6	0.25766857580718	1	FACETS	0.862	0.796	0.93	1	0.993	1	CLONAL	3	TRUE	0	0.25766857580718	1		378	379	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20152120	20152120	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001986-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	104	422	0	ENST00000379607.5:c.210G>T	p.Trp70Cys	p.W70C	ENST00000379607	NM_001412.3	70	tgG/tgT	4/7	0.25766857580718	3	FACETS	0.866	0.778	0.959			1	CLONAL	2	TRUE	NA	0.25766857580718	3		422	526	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53241084	53241084	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001986-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	111	437	0	ENST00000375401.3:c.1127G>T	p.Cys376Phe	p.C376F	ENST00000375401	NM_004187.3	376	tGt/tTt	9/26	NA	2	FACETS	0.984	0.89	1			1	INDETERMINATE	2	TRUE	NA	0.25766857580718	2		437	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577585	7577590	+	inframe_deletion	In_Frame_Del	DEL	GATGGT	GATGGT	-	novel	NA	P-0001986-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	61	264	0	ENST00000269305.4:c.691_696del	p.Thr231_Ile232del	p.T231_I232del	ENST00000269305	NM_001126112.2	231	ACCATC/-	7/11	0.25766857580718	2	FACETS	0.789	0.686	0.899	0.789	0.686	0.899	SUBCLONAL	2	TRUE	0	0.25766857580718	2		264	300	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0001990-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	96	229	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.412700298178411	3	FACETS	1	0.92	1	0.518	0.462	0.576	CLONAL	1	TRUE	1	0.412700298178411	3		229	542	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0001990-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	192	267	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	0.412700298178411	3	FACETS	0.988	0.92	1	0.988	0.92	1	CLONAL	2	TRUE	1	0.412700298178411	3		267	568	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001990-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	205	276	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.412700298178411	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.412700298178411	2		276	433	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59793361	59793361	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001990-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	158	388	0	ENST00000259008.2:c.2443C>T	p.Gln815Ter	p.Q815*	ENST00000259008	NM_032043.2	815	Cag/Tag	17/20	0.412700298178411	3	FACETS	1	0.98	1	0.607	0.557	0.659	CLONAL	1	TRUE	1	0.412700298178411	3		388	761	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245058	53245058	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001990-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	283	390	0	ENST00000375401.3:c.882C>G	p.Ser294Arg	p.S294R	ENST00000375401	NM_004187.3	294	agC/agG	7/26	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	2	TRUE	NA	0.412700298178411	2		390	645	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0002008-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	30	289	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.507695576458431	1	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	0	0.536657763947739	1		289	79	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416704	29416704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002008-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	10	276	0	ENST00000389048.3:c.4249G>A	p.Asp1417Asn	p.D1417N	ENST00000389048	NM_004304.4	1417	Gac/Aac	29/29	0.415659596081298	0	FACETS	0.27	0.186	0.371			1	SUBCLONAL	1	TRUE	0	0.536657763947739	0		276	64	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163486	32163486	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002008-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	60	319	0	ENST00000375023.3:c.5740C>G	p.Arg1914Gly	p.R1914G	ENST00000375023	NM_004557.3	1914	Cgt/Ggt	30/30	0.536657763947739	5	FACETS	1	0.902	1	1	0.902	1	CLONAL	2	TRUE	3	0.536657763947739	5		319	195	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420003	152420003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774794965	NA	P-0002008-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	11	338	0	ENST00000206249.3:c.1690G>A	p.Asp564Asn	p.D564N	ENST00000206249	NM_000125.3	564	Gac/Aac	8/8	1	2	FACETS	0.586	0.412	0.793	0.586	0.412	0.793	SUBCLONAL	1	TRUE	1	0.536657763947739	2		338	70	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132914	64132914	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758970427	NA	P-0002008-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	37	395	0	ENST00000334205.4:c.1048C>T	p.Pro350Ser	p.P350S	ENST00000334205	NM_003942.2	350	Cct/Tct	9/17	0.287775158062482	4	FACETS	0.803	0.675	0.939			1	INDETERMINATE	2	TRUE	NA	0.536657763947739	4		395	132	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260954	16260954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465631567	NA	P-0002011-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	75	107	0	ENST00000375759.3:c.8219C>T	p.Thr2740Ile	p.T2740I	ENST00000375759	NM_015001.2	2740	aCc/aTc	11/15	1	2	FACETS	0.693	0.612	0.778	0.693	0.612	0.778	SUBCLONAL	1	TRUE	1	0.668304535677666	2		107	324	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101300	27101300	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002011-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	212	226	0	ENST00000324856.7:c.4582C>T	p.Arg1528Ter	p.R1528*	ENST00000324856	NM_006015.4	1528	Cga/Tga	18/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.668304535677666	2		226	523	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030479	49030479	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002050-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	938	282	1	ENST00000267163.4:c.1959del	p.Val654CysfsTer4	p.V654Cfs*4	ENST00000267163	NM_000321.2	652	Aaa/aa	19/27	0.947851321309242	4	FACETS	0.925	0.913	0.936	0.925	0.913	0.936	CLONAL	4	TRUE	0	0.947851321309242	4		283	1042	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187166	11187166	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002050-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	264	445	1	ENST00000361445.4:c.6252G>T	p.Trp2084Cys	p.W2084C	ENST00000361445	NM_004958.3	2084	tgG/tgT	45/58	NA	2	FACETS	0.829	0.782	0.877			1	INDETERMINATE	1	TRUE	NA	0.947851321309242	2		446	672	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43806111	43806111	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002050-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	257	414	0	ENST00000372470.3:c.907T>A	p.Trp303Arg	p.W303R	ENST00000372470	NM_005373.2	303	Tgg/Agg	6/12	0.297412657807192	2	FACETS	0.805	0.758	0.852	0.402	0.379	0.426	INDETERMINATE	1	TRUE	0	0.947851321309242	2		414	674	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950358	38950358	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs776195419	NA	P-0002050-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	509	479	0	ENST00000357387.3:c.3592A>G	p.Thr1198Ala	p.T1198A	ENST00000357387	NM_152756.3	1198	Aca/Gca	31/38	0.136668617265565	3	FACETS	0.763	0.734	0.792	0.763	0.734	0.792	INDETERMINATE	2	TRUE	1	0.947851321309242	3		479	1037	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180565	56180565	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002050-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	282	334	0	ENST00000399503.3:c.3894G>T	p.Met1298Ile	p.M1298I	ENST00000399503	NM_005921.1	1298	atG/atT	16/20	0.136668617265565	3	FACETS	1	0.994	1	0.741	0.703	0.779	INDETERMINATE	1	TRUE	1	0.947851321309242	3		334	592	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388090	81388090	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002050-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	353	487	0	ENST00000222390.5:c.285A>T	p.Gln95His	p.Q95H	ENST00000222390	NM_000601.4	95	caA/caT	3/18	0.947851321309242	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.947851321309242	1		487	372	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18747479	18747479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755020029	NA	P-0002050-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	436	394	0	ENST00000266497.5:c.3940G>A	p.Glu1314Lys	p.E1314K	ENST00000266497		1314	Gaa/Aaa	28/31	0.59171801950393	1	FACETS	0.717	0.692	0.741	0.717	0.692	0.741	SUBCLONAL	1	TRUE	0	0.947851321309242	1		394	675	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0002050-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	278	280	0	ENST00000269305.4:c.559+1G>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.917480443138091	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.947851321309242	1		280	291	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937312	76937312	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002050-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	342	248	0	ENST00000373344.5:c.3436A>G	p.Thr1146Ala	p.T1146A	ENST00000373344	NM_000489.3	1146	Act/Gct	9/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.947851321309242	1		248	357	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825335	134825358	+	inframe_deletion	In_Frame_Del	DEL	GCTCCCACTGCCCCTCCAACAGCC	GCTCCCACTGCCCCTCCAACAGCC	-	novel	NA	P-0002050-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	428	346	0	ENST00000398015.3:c.857_880del	p.His286_Ser293del	p.H286_S293del	ENST00000398015	NM_004441.4	284	tGCTCCCACTGCCCCTCCAACAGCCgc/tgc	4/16	0.947851321309242	2	FACETS	0.966	0.925	1	0.483	0.462	0.504	CLONAL	1	TRUE	0	0.947851321309242	2		346	935	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0002054-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	145	435	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.192916011384641	2	FACETS	0.842	0.777	0.909	0.842	0.777	0.909	INDETERMINATE	2	TRUE	0	0.441482845937924	2		435	390	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509127	66509127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145126637	NA	P-0002054-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	80	583	2	ENST00000273854.3:c.200G>A	p.Arg67His	p.R67H	ENST00000273854	NM_004439.5	67	cGc/cAc	2/18	0.441482845937924	3	FACETS	0.981	0.867	1	0.49	0.433	0.551	CLONAL	1	TRUE	1	0.441482845937924	3		585	451	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099478	27099478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002054-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	136	311	1	ENST00000324856.7:c.3715G>A	p.Ala1239Thr	p.A1239T	ENST00000324856	NM_006015.4	1239	Gct/Act	14/20	0.441482845937924	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.441482845937924	3		312	312	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156160	106156160	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0002054-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	90	441	0	ENST00000380013.4:c.1061C>G	p.Ser354Ter	p.S354*	ENST00000380013	NM_001127208.2	354	tCa/tGa	3/11	0.441482845937924	3	FACETS	1	0.934	1	0.534	0.476	0.596	CLONAL	1	TRUE	1	0.441482845937924	3		441	466	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129385	152129385	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002054-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	94	342	0	ENST00000206249.3:c.338C>T	p.Pro113Leu	p.P113L	ENST00000206249	NM_000125.3	113	cCg/cTg	1/8	0.160713762549724	3	FACETS	0.771	0.693	0.853	0.514	0.462	0.569	INDETERMINATE	2	TRUE	0	0.441482845937924	3		342	337	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402046	402046	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002054-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	86	619	0	ENST00000399788.2:c.4745A>C	p.Lys1582Thr	p.K1582T	ENST00000399788	NM_001042603.1	1582	aAg/aCg	27/28	NA	2	FACETS	0.787	0.699	0.881			1	INDETERMINATE	1	TRUE	NA	0.441482845937924	2		619	495	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913581	32913581	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002054-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	87	425	0	ENST00000380152.3:c.5089A>G	p.Ile1697Val	p.I1697V	ENST00000380152		1697	Ata/Gta	11/27	0.335611976696685	4	FACETS	1	0.947	1	0.557	0.494	0.623	CLONAL	1	TRUE	2	0.441482845937924	4		425	510	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816226	89816226	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002054-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	152	516	0	ENST00000389301.3:c.3151A>G	p.Ile1051Val	p.I1051V	ENST00000389301	NM_000135.2	1051	Att/Gtt	32/43	0.215689462493593	2	FACETS	1	0.944	1	1	0.944	1	INDETERMINATE	2	TRUE	0	0.441482845937924	2		516	338	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781371	NA	P-0002054-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	151	407	0	ENST00000269305.4:c.328C>T	p.Arg110Cys	p.R110C	ENST00000269305	NM_001126112.2	110	Cgt/Tgt	4/11	0.441482845937924	1	FACETS	1	0.941	1	1	0.993	1	CLONAL	2	TRUE	0	0.441482845937924	1		407	265	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143966	11143966	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002054-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	120	354	0	ENST00000358026.2:c.3547G>C	p.Asp1183His	p.D1183H	ENST00000358026	NM_001128849.1	1183	Gac/Cac	26/36	1	2	FACETS	0.783	0.716	0.853	1	0.987	1	SUBCLONAL	2	TRUE	1	0.441482845937924	2		354	347	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41525915	41525915	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002054-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	148	516	0	ENST00000263253.7:c.1190G>C	p.Arg397Pro	p.R397P	ENST00000263253	NM_001429.3	397	cGa/cCa	5/31	0.192916011384641	2	FACETS	1	0.987	1	0.698	0.643	0.756	INDETERMINATE	1	TRUE	0	0.441482845937924	2		516	480	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0002058-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	334	290	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	1	2	FACETS	0.966	0.918	1	1	0.996	1	CLONAL	2	TRUE	1	0.44	2		290	786	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441217	52441217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002064-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	251	332	0	ENST00000460680.1:c.553G>A	p.Gly185Arg	p.G185R	ENST00000460680	NM_004656.3	185	Ggg/Agg	7/17	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.356561204442831	2		332	577	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426000	138426000	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0002064-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	59	335	0	ENST00000289153.2:c.1530+1G>A		p.X510_splice	ENST00000289153	NM_006219.2	510			0.356561204442831	3	FACETS	0.615	0.529	0.709	0.308	0.264	0.355	SUBCLONAL	1	TRUE	1	0.356561204442831	3		335	634	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209308	133209308	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002064-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	226	415	0	ENST00000320574.5:c.6078G>T	p.Arg2026Ser	p.R2026S	ENST00000320574	NM_006231.2	2026	agG/agT	44/49	0.356561204442831	3	FACETS	1	0.988	1	0.819	0.768	0.871	CLONAL	2	TRUE	0	0.356561204442831	3		415	608	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934294	39934294	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587778099	NA	P-0002064-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	166	409	1	ENST00000378444.4:c.305G>C	p.Arg102Pro	p.R102P	ENST00000378444	NM_001123385.1	102	cGg/cCg	4/15	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.356561204442831	2		410	643	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0002075-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	93	188	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.345454478868096	4	FACETS	0.878	0.787	0.975	0.878	0.787	0.975	CLONAL	2	TRUE	2	0.367441343196497	4		188	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579580	7579580	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002075-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	185	372	0	ENST00000269305.4:c.107del	p.Pro36ArgfsTer8	p.P36Rfs*8	ENST00000269305	NM_001126112.2	36	cCg/cg	4/11	0.313768543966011	2	FACETS	0.888	0.825	0.952	0.888	0.825	0.952	CLONAL	2	TRUE	0	0.367441343196497	2		372	567	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209108272	209108272	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002075-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	231	528	0	ENST00000345146.2:c.577G>T	p.Ala193Ser	p.A193S	ENST00000345146	NM_005896.2	193	Gca/Tca	6/10	0.367441343196497	3	FACETS	1	0.99	1	0.688	0.641	0.736	CLONAL	1	TRUE	1	0.367441343196497	3		528	1082	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225360671	225360671	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002075-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	161	495	0	ENST00000264414.4:c.1720G>A	p.Glu574Lys	p.E574K	ENST00000264414	NM_003590.4	574	Gaa/Aaa	13/16	0.367441343196497	3	FACETS	1	0.966	1	0.549	0.504	0.597	CLONAL	1	TRUE	1	0.367441343196497	3		495	944	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445029	89445029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1201275406	NA	P-0002075-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	200	557	0	ENST00000336596.2:c.1349G>A	p.Arg450Lys	p.R450K	ENST00000336596	NM_005233.5	450	aGa/aAa	6/17	0.318202242497514	3	FACETS	1	0.985	1	0.417	0.386	0.449	CLONAL	1	TRUE	0	0.367441343196497	3		557	1031	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445035	89445035	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002075-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	204	549	0	ENST00000336596.2:c.1355G>T	p.Ser452Ile	p.S452I	ENST00000336596	NM_005233.5	452	aGc/aTc	6/17	0.318202242497514	3	FACETS	1	0.985	1	0.413	0.382	0.445	CLONAL	1	TRUE	0	0.367441343196497	3		549	1061	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963047	38963047	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002075-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	155	566	0	ENST00000357387.3:c.1497G>T	p.Gln499His	p.Q499H	ENST00000357387	NM_152756.3	499	caG/caT	17/38	0.367441343196497	3	FACETS	0.995	0.91	1	0.497	0.455	0.542	CLONAL	1	TRUE	1	0.367441343196497	3		566	1004	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751895	57751895	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs749968952	NA	P-0002075-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	204	616	0	ENST00000274289.3:c.1342A>G	p.Ile448Val	p.I448V	ENST00000274289	NM_006622.3	448	Ata/Gta	10/14	0.313768543966011	2	FACETS	1	0.991	1	0.729	0.677	0.781	CLONAL	1	TRUE	0	0.367441343196497	2		616	762	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721436	176721436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780750393	NA	P-0002075-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	202	439	1	ENST00000439151.2:c.7067C>T	p.Thr2356Met	p.T2356M	ENST00000439151	NM_022455.4	2356	aCg/aTg	23/23	0.313768543966011	2	FACETS	0.827	0.77	0.885	0.827	0.77	0.885	CLONAL	2	TRUE	0	0.367441343196497	2		440	665	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188419	32188419	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0002075-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	118	302	0	ENST00000375023.3:c.923-1G>T		p.X308_splice	ENST00000375023	NM_004557.3	308			0.181892966498382	5	FACETS	0.844	0.764	0.929	0.563	0.509	0.619	INDETERMINATE	2	TRUE	2	0.367441343196497	5		302	590	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370711	55370711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002075-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	63	186	0	ENST00000297316.4:c.13G>A	p.Asp5Asn	p.D5N	ENST00000297316	NM_022454.3	5	Gat/Aat	1/2	0.240080956118381	5	FACETS	1	0.9	1	0.349	0.302	0.4	CLONAL	1	TRUE	2	0.367441343196497	5		186	508	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333158	70333158	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002075-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	333	633	0	ENST00000373644.4:c.1063C>T	p.Gln355Ter	p.Q355*	ENST00000373644	NM_030625.2	355	Caa/Taa	2/12	0.316451614982475	3	FACETS	0.848	0.806	0.892	0.848	0.806	0.892	CLONAL	3	TRUE	0	0.367441343196497	3		633	843	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216494	108216494	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002075-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	121	547	0	ENST00000278616.4:c.8443G>C	p.Glu2815Gln	p.E2815Q	ENST00000278616	NM_000051.3	2815	Gag/Cag	58/63	0.181892966498382	5	FACETS	1	0.912	1	0.337	0.304	0.372	INDETERMINATE	1	TRUE	2	0.367441343196497	5		547	1010	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344997	118344997	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555036917	NA	P-0002075-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	105	377	0	ENST00000534358.1:c.3123G>C	p.Lys1041Asn	p.K1041N	ENST00000534358	NM_005933.3	1041	aaG/aaC	3/36	0.181892966498382	5	FACETS	0.947	0.847	1	0.316	0.282	0.351	INDETERMINATE	1	TRUE	2	0.367441343196497	5		377	936	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828827	26828827	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002075-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	132	350	0	ENST00000381527.3:c.49G>T	p.Glu17Ter	p.E17*	ENST00000381527	NM_001260.1	17	Gag/Tag	1/13	0.313768543966011	2	FACETS	1	0.963	1	0.556	0.506	0.609	CLONAL	1	TRUE	0	0.367441343196497	2		350	646	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26911769	26911769	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002075-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	90	391	0	ENST00000381527.3:c.194G>C	p.Arg65Thr	p.R65T	ENST00000381527	NM_001260.1	65	aGa/aCa	2/13	0.313768543966011	2	FACETS	0.811	0.721	0.907	0.406	0.36	0.454	CLONAL	1	TRUE	0	0.367441343196497	2		391	604	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81528560	81528560	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002075-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	97	485	0	ENST00000298171.2:c.239G>C	p.Arg80Thr	p.R80T	ENST00000298171	NM_000369.2	80	aGa/aCa	2/10	0.367441343196497	3	FACETS	0.954	0.852	1	0.477	0.426	0.532	CLONAL	1	TRUE	1	0.367441343196497	3		485	655	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779159	3779159	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002075-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	193	267	0	ENST00000262367.5:c.5889G>T	p.Glu1963Asp	p.E1963D	ENST00000262367	NM_004380.2	1963	gaG/gaT	31/31	0.338278863738823	2	FACETS	0.962	0.897	1	0.962	0.897	1	CLONAL	2	TRUE	0	0.367441343196497	2		267	546	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641458	23641458	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002075-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	174	680	0	ENST00000261584.4:c.2017G>C	p.Glu673Gln	p.E673Q	ENST00000261584	NM_024675.3	673	Gag/Cag	5/13	0.338278863738823	2	FACETS	0.98	0.902	1	0.49	0.451	0.531	CLONAL	1	TRUE	0	0.367441343196497	2		680	966	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116194	67116194	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002075-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	148	481	0	ENST00000412916.2:c.478C>G	p.His160Asp	p.H160D	ENST00000412916		160	Cat/Gat	5/6	0.338278863738823	2	FACETS	0.947	0.865	1	0.473	0.432	0.516	CLONAL	1	TRUE	0	0.367441343196497	2		481	851	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89869707	89869707	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0002075-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	217	627	0	ENST00000389301.3:c.752C>G	p.Ser251Ter	p.S251*	ENST00000389301	NM_000135.2	251	tCa/tGa	8/43	0.338278863738823	2	FACETS	1	0.973	1	0.548	0.509	0.588	CLONAL	1	TRUE	0	0.367441343196497	2		627	1078	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16001811	16001811	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0002075-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	140	358	0	ENST00000268712.3:c.2691-1G>A		p.X897_splice	ENST00000268712	NM_006311.3	897			0.313768543966011	2	FACETS	0.797	0.731	0.865	0.797	0.731	0.865	SUBCLONAL	2	TRUE	0	0.367441343196497	2		358	478	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682491	37682491	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002075-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	119	440	0	ENST00000447079.4:c.3682G>C	p.Glu1228Gln	p.E1228Q	ENST00000447079	NM_015083.1	1228	Gag/Cag	13/14	0.181892966498382	5	FACETS	1	0.957	1	0.37	0.334	0.409	INDETERMINATE	1	TRUE	2	0.367441343196497	5		440	904	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59770816	59770816	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002075-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	154	573	0	ENST00000259008.2:c.2550G>C	p.Arg850Ser	p.R850S	ENST00000259008	NM_032043.2	850	agG/agC	18/20	0.181892966498382	5	FACETS	1	0.979	1	0.408	0.372	0.445	INDETERMINATE	1	TRUE	2	0.367441343196497	5		573	1063	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78765248	78765248	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0002075-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	236	375	0	ENST00000306801.3:c.831-2A>T		p.X277_splice	ENST00000306801	NM_020761.2	277			0.181892966498382	5	FACETS	0.976	0.911	1	0.651	0.607	0.695	INDETERMINATE	2	TRUE	2	0.367441343196497	5		375	1021	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600381	10600381	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002075-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	230	526	0	ENST00000171111.5:c.1474C>T	p.Pro492Ser	p.P492S	ENST00000171111	NM_203500.1	492	Cca/Tca	4/6	0.313768543966011	2	FACETS	0.78	0.729	0.833	0.78	0.729	0.833	SUBCLONAL	2	TRUE	0	0.367441343196497	2		526	802	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297772	15297772	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002075-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	235	433	0	ENST00000263388.2:c.1868A>G	p.Asp623Gly	p.D623G	ENST00000263388	NM_000435.2	623	gAc/gGc	12/33	0.313768543966011	2	FACETS	0.828	0.776	0.883	0.828	0.776	0.883	CLONAL	2	TRUE	0	0.367441343196497	2		433	772	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742733	39742733	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002075-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	282	308	0	ENST00000361337.2:c.1576G>C	p.Glu526Gln	p.E526Q	ENST00000361337	NM_003286.2	526	Gag/Cag	15/21	0.354731645786947	4	FACETS	0.991	0.932	1	0.496	0.466	0.526	CLONAL	2	TRUE	0	0.367441343196497	4		308	1059	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564754	41564754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748959061	NA	P-0002075-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	170	592	0	ENST00000263253.7:c.4055C>T	p.Ser1352Phe	p.S1352F	ENST00000263253	NM_001429.3	1352	tCc/tTc	25/31	NA	2	FACETS	1	0.957	1			1	INDETERMINATE	1	TRUE	NA	0.367441343196497	2		592	872	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564818	41564818	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002075-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	150	517	0	ENST00000263253.7:c.4119C>G	p.Phe1373Leu	p.F1373L	ENST00000263253	NM_001429.3	1373	ttC/ttG	25/31	NA	2	FACETS	1	0.947	1			1	INDETERMINATE	1	TRUE	NA	0.367441343196497	2		517	779	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574245	41574245	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316927373	NA	P-0002075-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	153	454	0	ENST00000263253.7:c.6530C>T	p.Ser2177Leu	p.S2177L	ENST00000263253	NM_001429.3	2177	tCa/tTa	31/31	NA	2	FACETS	0.967	0.885	1			1	INDETERMINATE	1	TRUE	NA	0.367441343196497	2		454	861	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720640	89720665	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTTTTTTAGGACAAAATGTTTCAC	TTTTTTTTTAGGACAAAATGTTTCAC	-	novel	NA	P-0002075-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	95	139	0	ENST00000371953.3:c.802-7_820del		p.X268_splice	ENST00000371953	NM_000314.4	268		8/9	0.316451614982475	3	FACETS	1	0.968	1	0.782	0.707	0.858	CLONAL	2	TRUE	0	0.367441343196497	3		139	261	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472569	88472570	+	missense_variant	Missense_Mutation	DNP	CT	CT	AA	novel	NA	P-0002075-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	181	517	0	ENST00000360948.2:c.1985_1986delinsTT	p.Gln662Leu	p.Q662L	ENST00000360948	NM_001012338.2	662	cAG/cTT	16/19	0.313768543966011	2	FACETS	0.872	0.809	0.936	0.872	0.809	0.936	CLONAL	2	TRUE	0	0.367441343196497	2		517	565	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0002091-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	904	335	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.788944909681966	7	FACETS	0.938	0.919	0.957	0.938	0.919	0.957	CLONAL	6	TRUE	1	0.788944909681966	7		335	1210	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404534	70404534	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002091-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	607	508	0	ENST00000373644.4:c.2048A>C	p.Gln683Pro	p.Q683P	ENST00000373644	NM_030625.2	683	cAa/cCa	4/12	0.625376825920794	4	FACETS	1	0.967	1			1	CLONAL	2	TRUE	NA	0.788944909681966	4		508	1372	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941628	48941628	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0002091-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	999	305	0	ENST00000267163.4:c.940-2A>G		p.X314_splice	ENST00000267163	NM_000321.2	314			0.770041012641825	4	FACETS	0.971	0.956	0.984	0.971	0.956	0.984	CLONAL	4	TRUE	0	0.788944909681966	4		305	1167	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577113	7577113	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555525279	NA	P-0002091-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	927	440	0	ENST00000269305.4:c.825T>G	p.Cys275Trp	p.C275W	ENST00000269305	NM_001126112.2	275	tgT/tgG	8/11	0.75168482679249	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	4	TRUE	0	0.788944909681966	4		440	1044	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118945	3118945	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002091-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	151	346	0	ENST00000078429.4:c.629G>T	p.Arg210Leu	p.R210L	ENST00000078429	NM_002067.2	210	cGg/cTg	5/7	NA	2	FACETS	0.982	0.908	1			1	INDETERMINATE	1	TRUE	NA	0.788944909681966	2		346	390	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466856	57466856	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002091-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	124	271	0	ENST00000371085.3:c.75G>C	p.Lys25Asn	p.K25N	ENST00000371085	NM_000516.4	25	aaG/aaC	1/13	0.613863245376169	3	FACETS	0.927	0.844	1			1	CLONAL	1	TRUE	NA	0.788944909681966	3		271	473	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123159723	123159723	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002091-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1682	284	531	0	ENST00000218089.9:c.78T>A	p.Asp26Glu	p.D26E	ENST00000218089	NM_001042749.1	26	gaT/gaA	4/35	0.585379380260171	5	FACETS	0.8	0.748	0.853			1	SUBCLONAL	1	TRUE	NA	0.788944909681966	5		531	1966	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190708783	190708783	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002092-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	227	491	1	ENST00000441310.2:c.676C>T	p.Gln226Ter	p.Q226*	ENST00000441310	NM_000534.4	226	Cag/Tag	6/13	0.213733662617108	4	FACETS	0.817	0.762	0.873	0.817	0.762	0.873	INDETERMINATE	2	TRUE	2	0.458780560224177	4		492	884	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438566	52438566	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1553645164	NA	P-0002092-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	602	404	1	ENST00000460680.1:c.1153C>T	p.Arg385Ter	p.R385*	ENST00000460680	NM_004656.3	385	Cga/Tga	12/17	0.434049138889254	3	FACETS	0.976	0.944	1	0.976	0.944	1	CLONAL	3	TRUE	0	0.458780560224177	3		405	1102	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568668	41568668	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002092-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	99	247	0	ENST00000263253.7:c.4617+1G>A		p.X1539_splice	ENST00000263253	NM_001429.3	1539			1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.458780560224177	2		247	388	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0002108-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	400	410	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	0.636116658981041	3	FACETS	0.915	0.876	0.955	0.915	0.876	0.955	CLONAL	2	TRUE	1	0.704181300021932	3		410	839	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0002108-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	23	219	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.126	0.097	0.159	0.126	0.097	0.159	SUBCLONAL	1	TRUE	1	0.704181300021932	2		219	520	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197042	123197042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002108-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	239	586	0	ENST00000218089.9:c.1808G>A	p.Gly603Glu	p.G603E	ENST00000218089	NM_001042749.1	603	gGa/gAa	19/35	0.290299928603311	1	FACETS	0.437	0.408	0.467	0.437	0.408	0.467	INDETERMINATE	1	TRUE	0	0.704181300021932	1		586	1007	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518697	204518697	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002111-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	26	446	0	ENST00000367182.3:c.1360A>G	p.Thr454Ala	p.T454A	ENST00000367182	NM_001278516.1	454	Acg/Gcg	11/11	0.414745632326761	3	FACETS	0.935	0.751	1			1	CLONAL	1	FALSE	NA	0.539306207373805	3		446	131	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608322	28608322	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002111-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	22	510	0	ENST00000241453.7:c.1734G>T	p.Met578Ile	p.M578I	ENST00000241453	NM_004119.2	578	atG/atT	14/24	0.448219689200243	1	FACETS	0.448	0.351	0.557	0.448	0.351	0.557	SUBCLONAL	1	FALSE	0	0.539306207373805	1		510	133	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0002136-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	118	276	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.46374021209195	2	FACETS	0.967	0.891	1	0.967	0.891	1	CLONAL	2	TRUE	0	0.506597374824754	2		276	241	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248709	59248709	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002136-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	34	362	0	ENST00000371222.2:c.34G>C	p.Asp12His	p.D12H	ENST00000371222	NM_002228.3	12	Gat/Cat	1/1	0.417046088590738	4	FACETS	0.418	0.341	0.505	0.209	0.17	0.253	SUBCLONAL	1	TRUE	2	0.506597374824754	4		362	484	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294664	1294664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002136-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	25	68	0	ENST00000310581.5:c.337G>A	p.Glu113Lys	p.E113K	ENST00000310581	NM_198253.2	113	Gag/Aag	2/16	0.417046088590738	4	FACETS	1	0.935	1	0.743	0.599	0.902	CLONAL	1	TRUE	2	0.506597374824754	4		68	100	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005425	150005425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002136-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	149	381	0	ENST00000253339.5:c.800C>T	p.Ser267Leu	p.S267L	ENST00000253339		267	tCa/tTa	3/7	0.418566936721884	2	FACETS	0.87	0.807	0.934	0.87	0.807	0.934	CLONAL	2	TRUE	0	0.506597374824754	2		381	338	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231176	98231176	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002136-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	128	281	0	ENST00000331920.6:c.2107G>C	p.Glu703Gln	p.E703Q	ENST00000331920	NM_000264.3	703	Gag/Cag	14/24	0.375406376645773	5	FACETS	1	0.971	1	0.76	0.696	0.826	CLONAL	2	TRUE	2	0.506597374824754	5		281	390	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727458	66727458	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002136-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	49	361	2	ENST00000307102.5:c.174G>T	p.Gln58His	p.Q58H	ENST00000307102	NM_002755.3	58	caG/caT	2/11	0.506597374824754	5	FACETS	0.615	0.52	0.718	0.123	0.104	0.144	SUBCLONAL	1	TRUE	0	0.506597374824754	5		363	554	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60795877	60795877	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002136-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	51	364	0	ENST00000333681.4:c.701C>A	p.Ala234Asp	p.A234D	ENST00000333681		234	gCc/gAc	3/3	NA	2	FACETS	0.577	0.492	0.669			1	INDETERMINATE	1	TRUE	NA	0.506597374824754	2		364	349	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0002149-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	132	495	1	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	FALSE	1	0.327221238583793	2		496	741	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307212	65307212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150021823	NA	P-0002149-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	75	324	0	ENST00000342505.4:c.2476C>T	p.Arg826Cys	p.R826C	ENST00000342505	NM_002227.2	826	Cgc/Tgc	18/25	0.311703327217125	1	FACETS	0.747	0.656	0.845	0.747	0.656	0.845	SUBCLONAL	1	FALSE	0	0.327221238583793	1		324	513	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0002149-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	120	372	0	ENST00000269305.4:c.994-1G>T		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.269776151013424	0	FACETS	1	0.96	1			1	CLONAL	1	FALSE	0	0.327221238583793	0		372	448	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0002156-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	75	450	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.789	0.689	0.897	0.789	0.689	0.897	SUBCLONAL	1	TRUE	1	0.176394034946471	2		451	1078	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259610	89259610	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002156-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	69	261	0	ENST00000336596.2:c.754G>T	p.Val252Leu	p.V252L	ENST00000336596	NM_005233.5	252	Gta/Tta	3/17	0.176394034946471	2	FACETS	0.961	0.841	1	0.961	0.841	1	CLONAL	2	TRUE	0	0.176394034946471	2		261	407	SUCCESS
APC	324	MSKCC	GRCh37	5	112178759	112178759	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002156-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	73	574	0	ENST00000257430.4:c.7468G>C	p.Asp2490His	p.D2490H	ENST00000257430	NM_000038.5	2490	Gat/Cat	16/16	1	2	FACETS	0.877	0.765	0.998	0.877	0.765	0.998	CLONAL	1	TRUE	1	0.176394034946471	2		574	944	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163720	32163720	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002156-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	25	266	0	ENST00000375023.3:c.5506G>C	p.Glu1836Gln	p.E1836Q	ENST00000375023	NM_004557.3	1836	Gag/Cag	30/30	1	2	FACETS	0.768	0.605	0.956	0.768	0.605	0.956	CLONAL	1	TRUE	1	0.176394034946471	2		266	369	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383308	4383308	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002156-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	64	433	0	ENST00000261254.3:c.102G>T	p.Glu34Asp	p.E34D	ENST00000261254	NM_001759.3	34	gaG/gaT	1/5	NA	2	FACETS	1	0.894	1			1	INDETERMINATE	1	TRUE	NA	0.176394034946471	2		433	698	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435490	18435490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760928254	NA	P-0002156-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	70	466	0	ENST00000266497.5:c.475G>A	p.Glu159Lys	p.E159K	ENST00000266497		159	Gaa/Aaa	1/31	1	2	FACETS	0.946	0.823	1	0.946	0.823	1	CLONAL	1	TRUE	1	0.176394034946471	2		466	839	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248854	133248854	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755090755	NA	P-0002156-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	71	444	1	ENST00000320574.5:c.1741G>A	p.Ala581Thr	p.A581T	ENST00000320574	NM_006231.2	581	Gcc/Acc	16/49	1	2	FACETS	0.981	0.854	1	0.981	0.854	1	CLONAL	1	TRUE	1	0.176394034946471	2		445	821	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969442	44969442	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002156-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	95	362	0	ENST00000377967.4:c.4124T>C	p.Leu1375Pro	p.L1375P	ENST00000377967	NM_021140.2	1375	cTa/cCa	28/29	1	1	FACETS	0.824	0.735	0.918	1	0.983	1	CLONAL	2	TRUE	0	0.176394034946471	1		362	596	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092815	27092815	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002156-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	69	563	0	ENST00000324856.7:c.2840del	p.Pro947HisfsTer21	p.P947Hfs*21	ENST00000324856	NM_006015.4	946	Ccc/cc	9/20	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.176394034946471	2		563	766	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098806	178098806	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002172-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	27	345	0	ENST00000397062.3:c.239C>G	p.Thr80Arg	p.T80R	ENST00000397062	NM_006164.4	80	aCa/aGa	2/5	0.426099155453915	2	FACETS	0.111	0.087	0.138	0.056	0.043	0.069	SUBCLONAL	1	TRUE	0	0.426099155453915	2		345	1141	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498423	89498423	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1203973847	NA	P-0002172-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	163	270	0	ENST00000336596.2:c.2395C>T	p.Arg799Cys	p.R799C	ENST00000336596	NM_005233.5	799	Cgc/Tgc	14/17	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.426099155453915	2		270	721	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638918	176638918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770929380	NA	P-0002192-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	143	480	0	ENST00000439151.2:c.3518G>A	p.Arg1173His	p.R1173H	ENST00000439151	NM_022455.4	1173	cGc/cAc	5/23	0.362612917567702	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.362612917567702	1		480	613	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570087	212570087	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002192-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	55	511	0	ENST00000342788.4:c.1154A>G	p.Asp385Gly	p.D385G	ENST00000342788	NM_005235.2	385	gAc/gGc	10/28	0.362612917567702	3	FACETS	0.333	0.284	0.388	0.167	0.142	0.194	SUBCLONAL	1	TRUE	1	0.362612917567702	3		511	1075	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217259	66217259	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002192-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	42	349	0	ENST00000273854.3:c.2356G>A	p.Ala786Thr	p.A786T	ENST00000273854	NM_004439.5	786	Gca/Aca	14/18	0.204879272010386	3	FACETS	0.354	0.294	0.421	0.177	0.147	0.211	INDETERMINATE	1	TRUE	1	0.362612917567702	3		349	773	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673028	30673028	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002192-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	38	451	0	ENST00000376406.3:c.3932G>T	p.Arg1311Met	p.R1311M	ENST00000376406	NM_014641.2	1311	aGg/aTg	10/15	NA	2	FACETS	0.329	0.271	0.393			1	INDETERMINATE	1	TRUE	NA	0.362612917567702	2		451	638	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760723	133760723	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002192-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	93	449	0	ENST00000318560.5:c.3046C>A	p.Arg1016Ser	p.R1016S	ENST00000318560	NM_005157.4	1016	Cgc/Agc	11/11	1	2	FACETS	0.939	0.838	1	0.939	0.838	1	CLONAL	1	TRUE	1	0.362612917567702	2		449	546	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405621	139405621	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002192-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	27	343	0	ENST00000277541.6:c.2570G>A	p.Cys857Tyr	p.C857Y	ENST00000277541	NM_017617.3	857	tGc/tAc	16/34	1	2	FACETS	0.322	0.256	0.399	0.322	0.256	0.399	SUBCLONAL	1	TRUE	1	0.362612917567702	2		343	462	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996053	73996053	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465926642	NA	P-0002192-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	77	364	0	ENST00000318443.5:c.787G>A	p.Asp263Asn	p.D263N	ENST00000318443	NM_001024736.1	263	Gat/Aat	5/10	0.204879272010386	3	FACETS	1	0.881	1	0.501	0.44	0.565	INDETERMINATE	1	TRUE	1	0.362612917567702	3		364	501	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104405	2104405	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs878854107	NA	P-0002192-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	92	410	0	ENST00000219476.3:c.445A>G	p.Asn149Asp	p.N149D	ENST00000219476	NM_000548.3	149	Aat/Gat	5/42	1	2	FACETS	0.84	0.748	0.938	0.84	0.748	0.938	CLONAL	1	TRUE	1	0.362612917567702	2		410	604	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368217	31368217	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121908945	NA	P-0002192-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	93	320	0	ENST00000328111.2:c.88C>T	p.Gln30Ter	p.Q30*	ENST00000328111	NM_006892.3	30	Cag/Tag	2/23	0.340866163152496	3	FACETS	1	0.922	1	0.521	0.464	0.582	CLONAL	1	TRUE	1	0.362612917567702	3		320	581	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41558731	41558731	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002192-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	114	514	0	ENST00000263253.7:c.3676A>C	p.Ile1226Leu	p.I1226L	ENST00000263253	NM_001429.3	1226	Ata/Cta	21/31	1	2	FACETS	0.897	0.808	0.99	0.897	0.808	0.99	CLONAL	1	TRUE	1	0.362612917567702	2		514	701	SUCCESS
AR	367	MSKCC	GRCh37	X	66765124	66765124	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002192-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	114	341	0	ENST00000374690.3:c.136A>G	p.Ser46Gly	p.S46G	ENST00000374690	NM_000044.3	46	Agc/Ggc	1/8	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.362612917567702	2		341	612	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002202-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	624	408	1	ENST00000342988.3:c.1610A>T	p.Asp537Val	p.D537V	ENST00000342988	NM_005359.5	537	gAc/gTc	12/12	0.891726891409898	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.891726891409898	1		409	751	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287502	33287502	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0002202-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	614	367	0	ENST00000374542.5:c.1595T>A	p.Leu532Ter	p.L532*	ENST00000374542	NM_001141970.1	532	tTa/tAa	6/8	0.891726891409898	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.891726891409898	1		367	732	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575526	64575526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565648547	NA	P-0002202-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	609	367	0	ENST00000312049.6:c.491C>T	p.Ala164Val	p.A164V	ENST00000312049	NM_130799.2	164	gCc/gTc	3/10	0.891726891409898	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.891726891409898	1		367	732	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165074	47165074	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002228-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	138	397	0	ENST00000409792.3:c.1052T>A	p.Phe351Tyr	p.F351Y	ENST00000409792	NM_014159.6	351	tTt/tAt	3/21	0.412549535860508	3	FACETS	1	0.968	1	0.565	0.515	0.618	CLONAL	1	TRUE	1	0.412549535860508	3		397	714	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265578	152265578	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002228-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	24	189	0	ENST00000206249.3:c.1031G>A	p.Gly344Asp	p.G344D	ENST00000206249	NM_000125.3	344	gGc/gAc	4/8	0.309318096820594	3	FACETS	0.309	0.242	0.387	0.103	0.08	0.129	SUBCLONAL	1	TRUE	0	0.412549535860508	3		189	454	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563185	21563185	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002228-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	62	295	0	ENST00000382592.4:c.734A>G	p.His245Arg	p.H245R	ENST00000382592	NM_014572.2	245	cAc/cGc	4/8	0.3132139186006	4	FACETS	0.741	0.64	0.85			1	SUBCLONAL	1	TRUE	NA	0.412549535860508	4		295	573	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0002230-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	587	23	378	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		379	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764146326	NA	P-0002230-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	999	21	313	0	ENST00000269305.4:c.841G>A	p.Asp281Asn	p.D281N	ENST00000269305	NM_001126112.2	281	Gac/Aac	8/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		313	1020	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430590	181430590	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1386119066	NA	P-0121539-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	42	167	0	ENST00000325404.1:c.442G>A	p.Gly148Ser	p.G148S	ENST00000325404	NM_003106.3	148	Ggc/Agc	1/1	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	NA	1	0.222540087296286	2		167	287	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161856	47161856	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002253-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	72	1065	0	ENST00000409792.3:c.4270del	p.Arg1424GlufsTer8	p.R1424Efs*8	ENST00000409792	NM_014159.6	1424	Aga/ga	3/21	0.467965759805124	1	FACETS	0.665	0.587	0.745	0.665	0.587	0.745	SUBCLONAL	1	TRUE	0	0.585122050488808	1		1065	262	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289242	33289245	+	frameshift_variant	Frame_Shift_Del	DEL	CCGC	CCGC	-	novel	NA	P-0002253-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	202	514	0	ENST00000374542.5:c.307_310del	p.Ala103SerfsTer40	p.A103Sfs*40	ENST00000374542	NM_001141970.1	103	GCGGag/ag	3/8	0.303410658342595	5	FACETS	1	0.975	1	0.64	0.602	0.678	INDETERMINATE	3	TRUE	0	0.585122050488808	5		514	405	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575456	64575456	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002253-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	198	905	0	ENST00000312049.6:c.561del	p.Asn189MetfsTer35	p.N189Mfs*35	ENST00000312049	NM_130799.2	187	ggG/gg	3/10	0.540947529238738	2	FACETS	0.868	0.816	0.919	0.868	0.816	0.919	CLONAL	2	TRUE	0	0.585122050488808	2		905	390	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0002270-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	61	169	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.579035246794679	2	FACETS	0.827	0.721	0.939	0.413	0.36	0.47	CLONAL	1	TRUE	0	0.585724279731254	2		169	252	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807543	1807543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002270-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	142	443	0	ENST00000260795.2:c.1712G>A	p.Arg571Gln	p.R571Q	ENST00000260795		571	cGg/cAg	12/17	0.209286619020157	1	FACETS	0.781	0.718	0.846	0.781	0.718	0.846	INDETERMINATE	1	TRUE	0	0.585724279731254	1		443	439	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157293	106157293	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002270-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	153	554	0	ENST00000380013.4:c.2195del	p.Pro732HisfsTer19	p.P732Hfs*19	ENST00000380013	NM_001127208.2	732	Cca/ca	3/11	0.585724279731254	1	FACETS	0.901	0.833	0.97	0.901	0.833	0.97	CLONAL	1	TRUE	0	0.585724279731254	1		554	410	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231050	53231050	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002270-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	145	251	0	ENST00000375401.3:c.1852del	p.Cys618AlafsTer41	p.C618Afs*41	ENST00000375401	NM_004187.3	618	Tgc/gc	13/26	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.585724279731254	1		251	257	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782144	NA	P-0002279-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	112	261	0	ENST00000269305.4:c.473G>C	p.Arg158Pro	p.R158P	ENST00000269305	NM_001126112.2	158	cGc/cCc	5/11	0.318104921048244	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.318104921048244	1		261	514	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106687	27106687	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002279-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	136	534	0	ENST00000324856.7:c.6298C>T	p.Gln2100Ter	p.Q2100*	ENST00000324856	NM_006015.4	2100	Cag/Tag	20/20	0.318104921048244	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.318104921048244	1		534	677	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550867	150550867	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002279-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	178	460	0	ENST00000369026.2:c.789G>T	p.Arg263Ser	p.R263S	ENST00000369026	NM_021960.4	263	agG/agT	2/3	0.318104921048244	3	FACETS	0.77	0.711	0.832	0.77	0.711	0.832	SUBCLONAL	2	TRUE	1	0.318104921048244	3		460	842	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395006	139395006	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002279-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	77	258	0	ENST00000277541.6:c.5932C>T	p.Gln1978Ter	p.Q1978*	ENST00000277541	NM_017617.3	1978	Cag/Tag	31/34	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.318104921048244	2		258	409	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378667	25378667	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002279-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	175	599	0	ENST00000311936.3:c.331A>C	p.Met111Leu	p.M111L	ENST00000311936	NM_004985.3	111	Atg/Ctg	4/5	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.318104921048244	2		599	927	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974739	21974739	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002279-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	89	474	0	ENST00000304494.5:c.88del	p.Ala30ArgfsTer23	p.A30Rfs*23	ENST00000304494	NM_000077.4	30	Gcg/cg	1/3	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.318104921048244	2		474	478	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397792	116397792	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002289-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	114	815	1	ENST00000397752.3:c.2066A>T	p.His689Leu	p.H689L	ENST00000397752	NM_000245.2	689	cAc/cTc	8/21	1	2	FACETS	0.664	0.596	0.737	0.664	0.596	0.737	SUBCLONAL	1	FALSE	1	0.3	2		816	1144	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340407	8340407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201651279	NA	P-0002289-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	75	623	0	ENST00000356435.5:c.5189G>A	p.Arg1730Gln	p.R1730Q	ENST00000356435		1730	cGg/cAg	31/35	0.3	1	FACETS	0.604	0.529	0.685	0.604	0.529	0.685	SUBCLONAL	1	FALSE	0	0.3	1		623	704	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713386	40713386	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1462727415	NA	P-0002289-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	60	542	0	ENST00000373198.4:c.4129C>G	p.Arg1377Gly	p.R1377G	ENST00000373198	NM_133170.3	1377	Cga/Gga	30/32	0.3	0	FACETS	0.505	0.435	0.58			1	SUBCLONAL	1	FALSE	0	0.3	0		542	555	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225556	2225556	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002307-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	26	482	0	ENST00000326181.6:c.1559A>G	p.Asn520Ser	p.N520S	ENST00000326181	NM_032271.2	520	aAc/aGc	17/21	0.327968870832819	1	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	FALSE	0	0.327968870832819	1		482	114	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0002309-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	135	367	0	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.369974866543112	2		367	542	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0002309-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1192	360	379	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.369974866543112	8	FACETS	0.882	0.834	0.931			1	CLONAL	3	TRUE	NA	0.369974866543112	8		379	1552	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0002309-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	891	440	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.369974866543112	8	FACETS	1	0.982	1			1	CLONAL	7	TRUE	NA	0.369974866543112	8		440	1439	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0002309-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	135	259	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.269774473406114	2	FACETS	0.91	0.827	0.997	0.455	0.413	0.499	CLONAL	1	TRUE	0	0.369974866543112	2		259	802	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395904	395904	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002309-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	90	483	0	ENST00000380956.4:c.461T>C	p.Met154Thr	p.M154T	ENST00000380956	NM_001195286.1	154	aTg/aCg	4/9	0.294037908491572	3	FACETS	0.725	0.643	0.813	0.363	0.321	0.407	SUBCLONAL	1	TRUE	1	0.369974866543112	3		483	795	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148513825	148513825	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002309-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	78	446	0	ENST00000320356.2:c.1456C>T	p.Pro486Ser	p.P486S	ENST00000320356	NM_004456.4	486	Ccc/Tcc	12/20	0.243038368295727	3	FACETS	0.555	0.487	0.629	0.185	0.162	0.21	SUBCLONAL	1	TRUE	0	0.369974866543112	3		446	900	SUCCESS
EED	8726	MSKCC	GRCh37	11	85968616	85968618	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0002309-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	96	394	0	ENST00000263360.6:c.615_617del	p.Leu207del	p.L207del	ENST00000263360	NM_003797.3	204	aaTCTt/aat	6/12	0.243727648313777	4	FACETS	0.728	0.647	0.814	0.364	0.323	0.407	SUBCLONAL	1	TRUE	2	0.369974866543112	4		394	977	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0002336-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	582	347	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.768039053085538	6	FACETS	1	0.984	1	1	0.984	1	CLONAL	5	TRUE	1	0.753001505042443	6		347	765	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876659675	NA	P-0002336-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	248	332	2	ENST00000269305.4:c.764T>A	p.Ile255Asn	p.I255N	ENST00000269305	NM_001126112.2	255	aTc/aAc	7/11	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.753001505042443	2		334	295	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911617	131911617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002336-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	179	347	0	ENST00000265335.6:c.362C>T	p.Thr121Ile	p.T121I	ENST00000265335		121	aCa/aTa	3/25	0.704863034024009	5	FACETS	1	0.989	1			1	CLONAL	1	TRUE	NA	0.753001505042443	5		347	718	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371927	55371927	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002336-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	33	53	0	ENST00000297316.4:c.617G>T	p.Cys206Phe	p.C206F	ENST00000297316	NM_022454.3	206	tGc/tTc	2/2	0.552810778479125	4	FACETS	1	0.932	1	0.423	0.352	0.5	CLONAL	1	TRUE	1	0.753001505042443	4		53	121	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24135805	24135805	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002336-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	155	446	0	ENST00000263121.7:c.292G>C	p.Glu98Gln	p.E98Q	ENST00000263121	NM_003073.3	98	Gag/Cag	3/9	0.768039053085538	4	FACETS	0.941	0.863	1	0.314	0.287	0.341	CLONAL	1	TRUE	1	0.753001505042443	4		446	767	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100657	67100657	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002336-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	185	459	0	ENST00000412916.2:c.355del	p.Leu119TrpfsTer20	p.L119Wfs*20	ENST00000412916		119	Ctg/tg	4/6	0.768039053085538	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.753001505042443	1		459	264	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16052797	16052801	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAT	AAAAT	-	novel	NA	P-0002336-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	342	417	0	ENST00000268712.3:c.873_877del	p.Leu291PhefsTer2	p.L291Ffs*2	ENST00000268712	NM_006311.3	291	ttATTTTtt/tttt	9/46	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.753001505042443	2		417	433	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821883	59821884	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0002336-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	213	574	0	ENST00000259008.2:c.2166_2167del	p.Val723HisfsTer13	p.V723Hfs*13	ENST00000259008	NM_032043.2	722	acAGtc/actc	15/20	0.748566607005576	3	FACETS	1	0.955	1	0.516	0.48	0.552	CLONAL	1	TRUE	1	0.753001505042443	3		574	755	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0002363-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	28	275	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.167356192486981	2	FACETS	0.945	0.763	1	0.945	0.763	1	CLONAL	2	FALSE	0	0.167356192486981	2		275	177	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853050	151853050	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002363-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	57	230	0	ENST00000262189.6:c.11905del	p.Val3969LeufsTer18	p.V3969Lfs*18	ENST00000262189	NM_170606.2	3969	Gtt/tt	46/59	0.167356192486981	4	FACETS	1	0.931	1	0.755	0.651	0.868	CLONAL	2	FALSE	1	0.167356192486981	4		230	351	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0002369-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	31	405	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	1	2	FACETS	0.121	0.097	0.148	0.121	0.097	0.148	SUBCLONAL	1	TRUE	1	0.650167664093077	2		405	787	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577222	64577224	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs794728657	NA	P-0002369-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	264	633	0	ENST00000312049.6:c.358_360del	p.Lys120del	p.K120del	ENST00000312049	NM_130799.2	120	AAG/-	2/10	0.650167664093077	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.650167664093077	1		633	532	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717608	89717608	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1564566706	NA	P-0002369-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	31	427	0	ENST00000371953.3:c.635-2A>G		p.X212_splice	ENST00000371953	NM_000314.4	212			0.650167664093077	1	FACETS	0.193	0.156	0.235	0.193	0.156	0.235	SUBCLONAL	1	TRUE	0	0.650167664093077	1		427	333	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962849	2962849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs562372731	NA	P-0002369-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	149	621	0	ENST00000396946.4:c.2059G>A	p.Ala687Thr	p.A687T	ENST00000396946	NM_032415.4	687	Gcg/Acg	16/25	1	2	FACETS	0.783	0.719	0.85	0.783	0.719	0.85	SUBCLONAL	1	TRUE	1	0.650167664093077	2		621	585	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106863	27106867	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGA	AAAGA	-	novel	NA	P-0002369-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	104	448	0	ENST00000324856.7:c.6475_6479del	p.Lys2159ProfsTer64	p.K2159Pfs*64	ENST00000324856	NM_006015.4	2158	cgAAAGAac/cgac	20/20	0.650167664093077	1	FACETS	0.499	0.449	0.55	0.499	0.449	0.55	SUBCLONAL	1	TRUE	0	0.650167664093077	1		448	433	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778784	76778786	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0002369-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	57	1032	5	ENST00000373344.5:c.6793_6795del	p.Glu2265del	p.E2265del	ENST00000373344	NM_000489.3	2265	GAG/-	31/35	0.415067364598175	1	FACETS	0.171	0.146	0.198	0.171	0.146	0.198	SUBCLONAL	1	TRUE	0	0.650167664093077	1		1037	692	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198269892	198269892	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002377-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	77	356	0	ENST00000335508.6:c.1447G>T	p.Asp483Tyr	p.D483Y	ENST00000335508	NM_012433.2	483	Gat/Tat	11/25	0.400761484068362	3	FACETS	0.582	0.51	0.659	0.291	0.255	0.33	SUBCLONAL	1	TRUE	1	0.400761484068362	3		356	793	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335878	73335878	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002377-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	105	310	0	ENST00000377767.4:c.2417A>G	p.Asp806Gly	p.D806G	ENST00000377767	NM_014953.3	806	gAc/gGc	18/21	0.400761484068362	2	FACETS	1	0.92	1	0.513	0.461	0.567	CLONAL	1	TRUE	0	0.400761484068362	2		310	511	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0002379-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	18	636	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	NA	2	FACETS	0.139	0.104	0.181			1	INDETERMINATE	1	FALSE	NA	0.802181806932964	2		636	322	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572456	95572456	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002379-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	44	576	0	ENST00000393063.1:c.2909A>C	p.Glu970Ala	p.E970A	ENST00000393063	NM_030621.3	970	gAa/gCa	19/28	0.802181806932964	4	FACETS	0.232	0.194	0.275	0.116	0.097	0.138	SUBCLONAL	1	FALSE	2	0.802181806932964	4		576	851	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0002379-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	161	438	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	0.619942169768423	4	FACETS	1	0.98	1	0.598	0.551	0.647	CLONAL	1	FALSE	2	0.802181806932964	4		438	605	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389348	8389348	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002382-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	144	381	0	ENST00000356435.5:c.4270G>T	p.Ala1424Ser	p.A1424S	ENST00000356435		1424	Gcc/Tcc	26/35	0.236724199831495	3	FACETS	0.68	0.619	0.743	0.34	0.309	0.372	INDETERMINATE	1	TRUE	1	0.609673974390185	3		381	907	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844185	68844185	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002382-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	57	410	0	ENST00000261769.5:c.773A>G	p.Asn258Ser	p.N258S	ENST00000261769	NM_004360.3	258	aAc/aGc	6/16	0.236724199831495	3	FACETS	0.297	0.254	0.344	0.149	0.127	0.172	INDETERMINATE	1	TRUE	1	0.609673974390185	3		410	821	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487582	38487582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002382-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	345	400	0	ENST00000254066.5:c.112C>T	p.Pro38Ser	p.P38S	ENST00000254066	NM_000964.3	38	Cca/Tca	2/9	0.236724199831495	3	FACETS	0.807	0.766	0.848	0.807	0.766	0.848	INDETERMINATE	2	TRUE	1	0.609673974390185	3		400	915	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256974	41256974	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs80358146	NA	P-0002382-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	38	297	0	ENST00000357654.3:c.213-1G>A		p.X71_splice	ENST00000357654	NM_007294.3	71			0.236724199831495	3	FACETS	0.23	0.189	0.275	0.115	0.094	0.138	INDETERMINATE	1	TRUE	1	0.609673974390185	3		297	708	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850870	63850870	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002383-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	660	396	356	1	ENST00000279873.7:c.1648G>T	p.Glu550Ter	p.E550*	ENST00000279873	NM_032199.2	550	Gaa/Taa	10/10	1	2	FACETS	0.999	0.952	1	0.999	0.952	1	CLONAL	1	TRUE	1	0.751043929681774	2		357	1056	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577475	64577475	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002383-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	637	244	365	0	ENST00000312049.6:c.107T>A	p.Leu36His	p.L36H	ENST00000312049	NM_130799.2	36	cTc/cAc	2/10	1	2	FACETS	0.738	0.69	0.786	0.738	0.69	0.786	SUBCLONAL	1	TRUE	1	0.751043929681774	2		365	881	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544642	65544642	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002383-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	816	511	528	0	ENST00000358664.4:c.284T>A	p.Leu95Gln	p.L95Q	ENST00000358664	NM_002382.4	95	cTg/cAg	4/5	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.751043929681774	2		528	1327	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560493	65560493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002383-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	915	530	558	0	ENST00000358664.4:c.104G>A	p.Arg35His	p.R35H	ENST00000358664	NM_002382.4	35	cGt/cAt	3/5	1	2	FACETS	0.977	0.937	1	0.977	0.937	1	CLONAL	1	TRUE	1	0.751043929681774	2		558	1445	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956958	2956958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1347465052	NA	P-0002397-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	47	329	0	ENST00000396946.4:c.2669C>T	p.Ser890Leu	p.S890L	ENST00000396946	NM_032415.4	890	tCg/tTg	20/25	NA	2	FACETS	0.522	0.44	0.612			1	INDETERMINATE	1	FALSE	NA	0.340294147088718	2		329	529	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949089	151949089	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002397-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	149	458	0	ENST00000262189.6:c.1556A>G	p.His519Arg	p.H519R	ENST00000262189	NM_170606.2	519	cAc/cGc	11/59	0.294824080536267	4	FACETS	0.772	0.706	0.841	0.772	0.706	0.841	SUBCLONAL	2	FALSE	2	0.340294147088718	4		458	760	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288427	15288427	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002397-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	36	153	0	ENST00000263388.2:c.4312A>C	p.Asn1438His	p.N1438H	ENST00000263388	NM_000435.2	1438	Aac/Cac	24/33	0.152395016541166	4	FACETS	0.783	0.652	0.927	0.783	0.652	0.927	INDETERMINATE	2	FALSE	2	0.340294147088718	4		153	181	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279558	1279558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002415-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	69	380	0	ENST00000310581.5:c.1978G>A	p.Ala660Thr	p.A660T	ENST00000310581	NM_198253.2	660	Gca/Aca	5/16	0.216893816350673	0	FACETS	0.42	0.368	0.475			1	INDETERMINATE	1	TRUE	0	0.501416110654496	0		380	327	SUCCESS
APC	324	MSKCC	GRCh37	5	112176483	112176483	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002415-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	191	442	1	ENST00000257430.4:c.5192C>A	p.Ala1731Asp	p.A1731D	ENST00000257430	NM_000038.5	1731	gCt/gAt	16/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.501416110654496	2		443	741	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0002449-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	263	717	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		718	327	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944157	81944157	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761094228	NA	P-0002449-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	124	388	0	ENST00000359376.3:c.1766G>A	p.Arg589His	p.R589H	ENST00000359376	NM_002661.3	589	cGc/cAc	18/33	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		388	569	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0002458-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	89	450	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.836	0.742	0.936	1	0.987	1	CLONAL	3	TRUE	1	0.112848742160927	2		451	629	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0002458-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	49	259	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	0.971	0.828	1	1	0.979	1	CLONAL	3	TRUE	1	0.112848742160927	2		259	298	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032039	26032039	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002458-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	56	317	0	ENST00000244661.2:c.250C>A	p.Arg84Ser	p.R84S	ENST00000244661	NM_003537.3	84	Cgc/Agc	1/1	0.112848742160927	9	FACETS	0.93	0.798	1			1	CLONAL	3	TRUE	NA	0.112848742160927	9		317	496	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101707	27101712	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CATTGG	CATTGG	A	novel	NA	P-0002458-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	38	401	0	ENST00000324856.7:c.4989_4993+1delinsA		p.X1663_splice	ENST00000324856	NM_006015.4	1663		18/20	0.117696337349673	0	FACETS	0.776	0.642	0.925			1	CLONAL	2	TRUE	0	0.112848742160927	0		401	385	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604764	48604766	+	inframe_deletion	In_Frame_Del	DEL	TAC	TAC	-	novel	NA	P-0002458-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	67	537	0	ENST00000342988.3:c.1586_1588del	p.Leu529_His530delinsTyr	p.L529_H530delinsY	ENST00000342988	NM_005359.5	529	tTACac/tac	12/12	0.117696337349673	1	FACETS	1	0.896	1	1	0.981	1	CLONAL	2	TRUE	0	0.112848742160927	1		537	542	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0002491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	77	335	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.208607289489251	3	FACETS	1	0.969	1	0.665	0.584	0.752	CLONAL	1	TRUE	1	0.208607289489251	3		335	613	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0002491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	32	379	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.208607289489251	3	FACETS	0.552	0.447	0.671	0.276	0.223	0.336	SUBCLONAL	1	TRUE	1	0.208607289489251	3		379	614	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579716	7579716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1192416464	NA	P-0002491-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	74	272	0	ENST00000269305.4:c.80del	p.Pro27LeufsTer17	p.P27Lfs*17	ENST00000269305	NM_001126112.2	27	cCt/ct	3/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.208607289489251	2		272	498	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593602	55593616	+	protein_altering_variant	In_Frame_Del	DEL	GTGGAAGGTTGTTGA	GTGGAAGGTTGTTGA	ACCTTC	novel	NA	P-0002525-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	210	451	0	ENST00000288135.5:c.1668_1682delinsACCTTC	p.Trp557_Glu561delinsProSer	p.W557_E561delinsPS	ENST00000288135	NM_000222.2	556	caGTGGAAGGTTGTTGAg/caACCTTCg	11/21	NA	2	FACETS	0.963	0.902	1			1	INDETERMINATE	1	TRUE	NA	0.788580300637783	2		451	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0002544-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	12	418	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.126471813744215	0	FACETS	0.097	0.068	0.134			1	INDETERMINATE	1	TRUE	0	0.407164740474067	0		418	360	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0002544-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	50	290	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.643	0.547	0.748	0.643	0.547	0.748	SUBCLONAL	1	TRUE	1	0.407164740474067	2		290	382	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112269	115112270	+	missense_variant	Missense_Mutation	DNP	CG	CG	AA	novel	NA	P-0002544-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	17	63	0	ENST00000257566.3:c.1470_1471delinsTT	p.Ala491Ser	p.A491S	ENST00000257566	NM_016569.3	490	gcCGcg/gcTTcg	7/8	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.407164740474067	2		63	70	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9928013	9928013	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002544-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	69	380	0	ENST00000330684.3:c.1726T>A	p.Phe576Ile	p.F576I	ENST00000330684	NM_001134407.1	576	Ttt/Att	8/13	1	2	FACETS	0.892	0.781	1	0.892	0.781	1	CLONAL	1	TRUE	1	0.407164740474067	2		380	380	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577569	7577569	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519981	NA	P-0002564-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	132	264	0	ENST00000269305.4:c.712T>G	p.Cys238Gly	p.C238G	ENST00000269305	NM_001126112.2	238	Tgt/Ggt	7/11	NA	2	FACETS	1	0.962	1			1	INDETERMINATE	2	TRUE	NA	0.378455557095087	2		264	325	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0002573-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	664	295	1	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.481036213402919	4	FACETS	1	0.991	1	0.789	0.765	0.813	CLONAL	3	TRUE	0	0.593340483155952	4		296	1130	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0002573-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	1325	628	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.593340483155952	6	FACETS	1	0.997	1			1	CLONAL	5	TRUE	NA	0.593340483155952	6		628	1817	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218090	108218090	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002576-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	155	192	0	ENST00000278616.4:c.8669T>C	p.Leu2890Pro	p.L2890P	ENST00000278616	NM_000051.3	2890	cTa/cCa	59/63	0.454216406862968	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	3	TRUE	0	0.454216406862968	3		192	274	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420804	49420804	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002576-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	45	206	1	ENST00000301067.7:c.14945G>A	p.Trp4982Ter	p.W4982*	ENST00000301067	NM_003482.3	4982	tGg/tAg	48/54	0.454216406862968	3	FACETS	1	0.942	1	0.617	0.525	0.716	CLONAL	1	TRUE	1	0.454216406862968	3		207	197	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691808	30691820	+	frameshift_variant	Frame_Shift_Del	DEL	CCCAAGCTCCCCT	CCCAAGCTCCCCT	-	novel	NA	P-0002576-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	132	345	0	ENST00000295754.5:c.310_322del	p.Pro104ThrfsTer16	p.P104Tfs*16	ENST00000295754	NM_003242.5	104	CCCAAGCTCCCCTac/ac	3/7	0.414442043817266	4	FACETS	1	0.982	1	0.621	0.572	0.672	CLONAL	2	TRUE	0	0.454216406862968	4		345	340	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0002578-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	18	394	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.799667121671941	3	FACETS	0.076	0.056	0.099	0.038	0.028	0.05	SUBCLONAL	1	TRUE	1	0.872613505802647	3		394	784	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152092	55152093	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	rs121913264	NA	P-0002578-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	175	393	0	ENST00000257290.5:c.2524_2525delinsAT	p.Asp842Ile	p.D842I	ENST00000257290	NM_006206.4	842	GAc/ATc	18/23	1	2	FACETS	0.78	0.724	0.838	0.78	0.724	0.838	SUBCLONAL	1	TRUE	1	0.872613505802647	2		393	514	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106315	27106316	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0002578-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	190	378	0	ENST00000324856.7:c.5929_5930del	p.Leu1977CysfsTer21	p.L1977Cfs*21	ENST00000324856	NM_006015.4	1976	TCt/t	20/20	0.868115214188059	2	FACETS	0.949	0.887	1	0.474	0.443	0.506	CLONAL	1	TRUE	0	0.872613505802647	2		378	459	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828707	3828707	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002579-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	49	456	0	ENST00000262367.5:c.1935C>G	p.Asn645Lys	p.N645K	ENST00000262367	NM_004380.2	645	aaC/aaG	9/31	1	2	FACETS	0.795	0.672	0.932	0.795	0.672	0.932	CLONAL	1	FALSE	1	0.161678135042238	2		456	762	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0002591-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	469	296	495	1	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	0.69552505396487	2		496	765	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287415	38287415	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002591-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	475	357	231	0	ENST00000425967.3:c.242G>A	p.Gly81Asp	p.G81D	ENST00000425967	NM_001174067.1	81	gGt/gAt	4/19	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.69552505396487	2		231	832	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572986	7572986	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555524156	NA	P-0002591-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	163	101	245	0	ENST00000269305.4:c.1123C>T	p.Gln375Ter	p.Q375*	ENST00000269305	NM_001126112.2	375	Cag/Tag	11/11	0.480377190222363	0	FACETS		NA	1			1	NA	1	TRUE	0	0.69552505396487	0		245	264	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835627	68835627	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002591-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	240	405	342	0	ENST00000261769.5:c.220del	p.Arg74AspfsTer9	p.R74Dfs*9	ENST00000261769	NM_004360.3	73	aCc/ac	3/16	0.69552505396487	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.69552505396487	1		342	645	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577260	64577260	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs794728647	NA	P-0002621-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	71	504	0	ENST00000312049.6:c.322C>T	p.Arg108Ter	p.R108*	ENST00000312049	NM_130799.2	108	Cga/Tga	2/10	0.837652646615667	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.837652646615667	1		504	84	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991085	41991085	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002621-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	10	579	0	ENST00000219905.7:c.2038G>T	p.Asp680Tyr	p.D680Y	ENST00000219905	NM_001164273.1	680	Gat/Tat	4/24	0.837652646615667	1	FACETS	0.19	0.13	0.263	0.19	0.13	0.263	SUBCLONAL	1	TRUE	0	0.837652646615667	1		579	73	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991095	41991095	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002621-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	12	612	0	ENST00000219905.7:c.2048C>T	p.Thr683Ile	p.T683I	ENST00000219905	NM_001164273.1	683	aCa/aTa	4/24	0.837652646615667	1	FACETS	0.208	0.148	0.279	0.208	0.148	0.279	SUBCLONAL	1	TRUE	0	0.837652646615667	1		612	80	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0002625-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	177	91	169	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.62429841413052	2		169	268	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027813	152027813	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002625-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	349	160	260	0	ENST00000262189.6:c.262C>T	p.Gln88Ter	p.Q88*	ENST00000262189	NM_170606.2	88	Caa/Taa	3/59	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.62429841413052	2		260	509	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100462	102100462	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002625-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	353	335	269	0	ENST00000282441.5:c.1306T>A	p.Ser436Thr	p.S436T	ENST00000282441	NM_001130145.2	436	Tca/Aca	9/9	0.470491297227118	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.62429841413052	3		269	688	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061151	38061151	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002625-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	122	22	66	0	ENST00000250448.2:c.838A>G	p.Ser280Gly	p.S280G	ENST00000250448	NM_004496.3	280	Agc/Ggc	2/2	1	2	FACETS	0.489	0.383	0.61	0.489	0.383	0.61	SUBCLONAL	1	TRUE	1	0.62429841413052	2		66	144	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061099	38061108	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTCCTTGC	GGGTCCTTGC	-	novel	NA	P-0002625-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	98	20	66	0	ENST00000250448.2:c.881_890del	p.Arg294ProfsTer24	p.R294Pfs*24	ENST00000250448	NM_004496.3	294	cGCAAGGACCCc/cc	2/2	1	2	FACETS	0.543	0.421	0.682	0.543	0.421	0.682	SUBCLONAL	1	TRUE	1	0.62429841413052	2		66	118	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061120	38061140	+	inframe_deletion	In_Frame_Del	DEL	CCGCCCTTGGCGCCGCTGCCC	CCGCCCTTGGCGCCGCTGCCC	-	novel	NA	P-0002625-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	95	22	59	0	ENST00000250448.2:c.849_869del	p.Gly284_Gly290del	p.G284_G290del	ENST00000250448	NM_004496.3	283	ggGGGCAGCGGCGCCAAGGGCGGc/ggc	2/2	1	2	FACETS	0.602	0.474	0.747	0.602	0.474	0.747	SUBCLONAL	1	TRUE	1	0.62429841413052	2		59	117	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268033	55268033	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1368179445	NA	P-0002649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	24	284	2	ENST00000275493.2:c.2873G>A	p.Arg958His	p.R958H	ENST00000275493	NM_005228.3	958	cGc/cAc	24/28	1	2	FACETS	0.421	0.331	0.524	0.421	0.331	0.524	SUBCLONAL	1	TRUE	1	0.428779859046705	2		286	266	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923468	9923468	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	43	323	0	ENST00000330684.3:c.1819C>A	p.Leu607Ile	p.L607I	ENST00000330684	NM_001134407.1	607	Ctt/Att	9/13	0.19027531593519	4	FACETS	1	0.925	1	0.39	0.329	0.457	INDETERMINATE	1	TRUE	1	0.428779859046705	4		323	245	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867278	68867278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	68	267	1	ENST00000261769.5:c.2525C>T	p.Ala842Val	p.A842V	ENST00000261769	NM_004360.3	842	gCt/gTt	16/16	0.428779859046705	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.428779859046705	1		268	234	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250105	110250105	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	45	215	0	ENST00000374672.4:c.570del	p.Asn191ThrfsTer3	p.N191Tfs*3	ENST00000374672	NM_004235.4	190	atC/at	3/5	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.428779859046705	2		215	184	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478211	99478220	+	protein_altering_variant	In_Frame_Del	DEL	GCAAGCATGC	GCAAGCATGC	TGCTTTT	novel	NA	P-0002649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	46	198	0	ENST00000268035.6:c.3115_3124delinsTGCTTTT	p.Ala1039_Arg1042delinsCysPheCys	p.A1039_R1042delinsCFC	ENST00000268035	NM_000875.3	1039	GCAAGCATGCgt/TGCTTTTgt	16/21	1	2	FACETS	0.828	0.703	0.965	0.828	0.703	0.965	CLONAL	1	TRUE	1	0.428779859046705	2		198	259	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867272	68867272	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002649-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	65	255	0	ENST00000261769.5:c.2520del	p.Glu841LysfsTer5	p.E841Kfs*5	ENST00000261769	NM_004360.3	840	tCc/tc	16/16	0.428779859046705	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	0	0.428779859046705	1		255	230	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870952	12870952	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002652-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	181	336	0	ENST00000228872.4:c.179G>A	p.Trp60Ter	p.W60*	ENST00000228872	NM_004064.3	60	tGg/tAg	1/3	1	2	FACETS	0.931	0.865	0.999	0.931	0.865	0.999	CLONAL	1	TRUE	1	0.696731712416566	2		336	558	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916934	178916936	+	inframe_deletion	In_Frame_Del	DEL	CCG	CCG	-	rs1553820399	NA	P-0002652-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	227	275	0	ENST00000263967.3:c.321_323del	p.Arg108del	p.R108del	ENST00000263967	NM_006218.2	107	aaCCGt/aat	2/21	0.338790733115428	3	FACETS	0.761	0.715	0.809	0.761	0.715	0.809	INDETERMINATE	2	TRUE	1	0.696731712416566	3		275	577	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164595	36164597	+	inframe_deletion	In_Frame_Del	DEL	CGC	CGC	-	novel	NA	P-0002652-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	324	211	0	ENST00000300305.3:c.1278_1280del	p.Arg427del	p.R427del	ENST00000300305		426	ccGCGc/ccc	8/8	0.696731712416566	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.696731712416566	2		211	441	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164607	36164613	+	frameshift_variant	Frame_Shift_Del	DEL	CGCTCGC	CGCTCGC	-	novel	NA	P-0002652-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	336	220	0	ENST00000300305.3:c.1262_1268del	p.Gly421AlafsTer171	p.G421Afs*171	ENST00000300305		421	gGCGAGCGc/gc	8/8	0.696731712416566	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.696731712416566	2		220	455	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0002653-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	138	301	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.3	2		301	762	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289545	33289545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1436067809	NA	P-0002653-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	89	295	0	ENST00000374542.5:c.158C>T	p.Ser53Leu	p.S53L	ENST00000374542	NM_001141970.1	53	tCg/tTg	2/8	1	2	FACETS	0.83	0.736	0.93	0.83	0.736	0.93	CLONAL	1	FALSE	1	0.3	2		295	715	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191489	10191489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730882035	NA	P-0002654-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	75	291	1	ENST00000256474.2:c.482G>A	p.Arg161Gln	p.R161Q	ENST00000256474	NM_000551.3	161	cGa/cAa	3/3	0.269928224911838	1	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	0	0.291053299250827	1		292	435	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861064	35861064	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1442477462	NA	P-0002654-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	58	216	0	ENST00000303115.3:c.193A>C	p.Asn65His	p.N65H	ENST00000303115	NM_002185.3	65	Aac/Cac	2/8	0.291053299250827	3	FACETS	0.888	0.764	1	0.444	0.382	0.512	CLONAL	1	TRUE	1	0.291053299250827	3		216	514	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138567	37138567	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002654-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	31	279	0	ENST00000373509.5:c.101T>A	p.Leu34Gln	p.L34Q	ENST00000373509	NM_002648.3	34	cTg/cAg	2/6	1	2	FACETS	0.521	0.421	0.634	0.521	0.421	0.634	SUBCLONAL	1	TRUE	1	0.291053299250827	2		279	409	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239915	53239915	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002654-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	118	206	0	ENST00000375401.3:c.1526C>A	p.Ser509Ter	p.S509*	ENST00000375401	NM_004187.3	509	tCa/tAa	11/26	0.1559889041481	2	FACETS	1	0.972	1			1	INDETERMINATE	2	TRUE	NA	0.291053299250827	2		206	349	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553289	106553289	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0002662-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	275	258	0	ENST00000369096.4:c.1254C>G	p.Tyr418Ter	p.Y418*	ENST00000369096	NM_001198.3	418	taC/taG	5/7	1	2	FACETS	0.87	0.822	0.92	0.87	0.822	0.92	CLONAL	1	TRUE	1	0.869195419115632	2		258	727	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0002670-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	96	164	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.306214901413561	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	2	TRUE	0	0.331574131781723	2		164	285	SUCCESS
APC	324	MSKCC	GRCh37	5	112178805	112178805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147549623	NA	P-0002670-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	61	470	2	ENST00000257430.4:c.7514G>A	p.Arg2505Gln	p.R2505Q	ENST00000257430	NM_000038.5	2505	cGa/cAa	16/16	0.181038912394241	5	FACETS	0.986	0.851	1	0.329	0.283	0.378	INDETERMINATE	1	TRUE	2	0.331574131781723	5		472	559	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0002670-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	63	212	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	0.181038912394241	5	FACETS	0.918	0.8	1	0.612	0.533	0.696	INDETERMINATE	2	TRUE	2	0.331574131781723	5		212	310	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17371343	17371343	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143058777	NA	P-0002670-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	143	437	0	ENST00000375499.3:c.113G>A	p.Arg38His	p.R38H	ENST00000375499	NM_003000.2	38	cGt/cAt	2/8	0.328617615821654	2	FACETS	0.954	0.877	1	0.954	0.877	1	CLONAL	2	TRUE	0	0.331574131781723	2		437	452	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480320	56480320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002670-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	72	329	0	ENST00000267101.3:c.427C>A	p.Leu143Met	p.L143M	ENST00000267101	NM_001982.3	143	Ctg/Atg	4/28	0.331574131781723	3	FACETS	1	0.941	1	0.563	0.493	0.637	CLONAL	1	TRUE	1	0.331574131781723	3		329	450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577091	7577091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149633775	NA	P-0002670-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	184	449	0	ENST00000269305.4:c.847C>T	p.Arg283Cys	p.R283C	ENST00000269305	NM_001126112.2	283	Cgc/Tgc	8/11	0.306214901413561	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.331574131781723	2		449	495	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748596	40748596	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754546663	NA	P-0002670-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	43	351	0	ENST00000373198.4:c.2920C>T	p.Arg974Trp	p.R974W	ENST00000373198	NM_133170.3	974	Cgg/Tgg	21/32	0.331574131781723	6	FACETS	0.74	0.618	0.875	0.185	0.154	0.219	SUBCLONAL	1	TRUE	2	0.331574131781723	6		351	583	SUCCESS
APC	324	MSKCC	GRCh37	5	112174623	112174624	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	G	novel	NA	P-0002670-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	122	467	0	ENST00000257430.4:c.3332_3333delinsG	p.Glu1111GlyfsTer15	p.E1111Gfs*15	ENST00000257430	NM_000038.5	1111	gAA/gG	16/16	0.181038912394241	5	FACETS	1	0.936	1	0.693	0.629	0.76	INDETERMINATE	2	TRUE	2	0.331574131781723	5		467	530	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17350487	17350487	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002697-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	190	499	0	ENST00000375499.3:c.623G>T	p.Gly208Val	p.G208V	ENST00000375499	NM_003000.2	208	gGg/gTg	6/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.652447395928478	2		499	479	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266107	41266107	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002697-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	167	528	0	ENST00000349496.5:c.104T>G	p.Ile35Ser	p.I35S	ENST00000349496	NM_001904.3	35	aTc/aGc	3/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.652447395928478	2		528	437	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390382	118390382	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002697-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	141	582	0	ENST00000534358.1:c.11197del	p.Leu3733SerfsTer29	p.L3733Sfs*29	ENST00000534358	NM_005933.3	3732	ttC/tt	32/36	1	2	FACETS	0.936	0.859	1	0.936	0.859	1	CLONAL	1	TRUE	1	0.652447395928478	2		582	462	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0002709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	743	290	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.629333774267025	6	FACETS	1	0.995	1	0.88	0.856	0.904	CLONAL	4	TRUE	1	0.629333774267025	6		290	1212	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552200	29552200	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs146051850	NA	P-0002709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	334	617	0	ENST00000356175.3:c.1933A>G	p.Met645Val	p.M645V	ENST00000356175	NM_000267.3	645	Atg/Gtg	17/57	0.608980855187861	2	FACETS	0.92	0.881	0.959	0.92	0.881	0.959	CLONAL	2	TRUE	0	0.629333774267025	2		617	577	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11273560	11273560	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	106	400	0	ENST00000361445.4:c.3181G>T	p.Val1061Leu	p.V1061L	ENST00000361445	NM_004958.3	1061	Gta/Tta	21/58	1	2	FACETS	0.92	0.833	1	0.92	0.833	1	CLONAL	1	TRUE	1	0.629333774267025	2		400	366	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107156	27107156	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0002709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	99	312	1	ENST00000324856.7:c.6767C>G	p.Ser2256Ter	p.S2256*	ENST00000324856	NM_006015.4	2256	tCa/tGa	20/20	1	2	FACETS	0.939	0.847	1	0.939	0.847	1	CLONAL	1	TRUE	1	0.629333774267025	2		313	335	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521576	46521576	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	181	698	0	ENST00000262741.5:c.832G>T	p.Glu278Ter	p.E278*	ENST00000262741	NM_003629.3	278	Gag/Tag	7/10	0.629333774267025	3	FACETS	0.841	0.776	0.909	0.421	0.388	0.455	CLONAL	1	TRUE	1	0.629333774267025	3		698	899	SUCCESS
FH	2271	MSKCC	GRCh37	1	241671970	241671971	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0002709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	124	477	0	ENST00000366560.3:c.670_671delinsTT	p.Glu224Leu	p.E224L	ENST00000366560	NM_000143.3	224	GAg/TTg	5/10	0.629333774267025	3	FACETS	0.88	0.798	0.965	0.44	0.399	0.483	CLONAL	1	TRUE	1	0.629333774267025	3		477	589	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251865	212251865	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	150	305	0	ENST00000342788.4:c.3194T>A	p.Val1065Glu	p.V1065E	ENST00000342788	NM_005235.2	1065	gTa/gAa	27/28	0.612663949091142	2	FACETS	0.906	0.848	0.963	0.906	0.848	0.963	CLONAL	2	TRUE	0	0.629333774267025	2		305	263	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566735	212566735	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	265	543	0	ENST00000342788.4:c.1446C>A	p.Asn482Lys	p.N482K	ENST00000342788	NM_005235.2	482	aaC/aaA	12/28	0.612663949091142	2	FACETS	0.948	0.904	0.992	0.948	0.904	0.992	CLONAL	2	TRUE	0	0.629333774267025	2		543	444	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645738	215645738	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	288	544	0	ENST00000260947.4:c.860A>G	p.Glu287Gly	p.E287G	ENST00000260947	NM_000465.2	287	gAg/gGg	4/11	0.612663949091142	2	FACETS	0.957	0.915	0.999	0.957	0.915	0.999	CLONAL	2	TRUE	0	0.629333774267025	2		544	478	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668771	52668771	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0002709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	350	543	0	ENST00000394830.3:c.1148C>G	p.Ser383Ter	p.S383*	ENST00000394830	NM_018313.4	383	tCa/tGa	12/30	0.608980855187861	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.629333774267025	2		543	536	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259054	89259054	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1354537650	NA	P-0002709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	183	367	0	ENST00000336596.2:c.198G>T	p.Arg66Ser	p.R66S	ENST00000336596	NM_005233.5	66	agG/agT	3/17	0.608980855187861	2	FACETS	0.917	0.865	0.969	0.917	0.865	0.969	CLONAL	2	TRUE	0	0.629333774267025	2		367	317	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480469	89480469	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	196	480	0	ENST00000336596.2:c.2306G>T	p.Arg769Leu	p.R769L	ENST00000336596	NM_005233.5	769	cGt/cTt	13/17	0.608980855187861	2	FACETS	0.872	0.822	0.922	0.872	0.822	0.922	CLONAL	2	TRUE	0	0.629333774267025	2		480	357	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664814	138664814	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	35	46	0	ENST00000330315.3:c.751C>A	p.Pro251Thr	p.P251T	ENST00000330315	NM_023067.3	251	Ccg/Acg	1/1	0.485078098180223	4	FACETS	0.915	0.79	1			1	CLONAL	3	TRUE	NA	0.629333774267025	4		46	66	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747918	41747918	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	120	341	0	ENST00000226382.2:c.851C>T	p.Pro284Leu	p.P284L	ENST00000226382	NM_003924.3	284	cCg/cTg	3/3	0.621670135637277	2	FACETS	0.978	0.911	1	0.978	0.911	1	CLONAL	2	TRUE	0	0.629333774267025	2		341	195	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133573	55133573	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762106764	NA	P-0002709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	264	429	1	ENST00000257290.5:c.877C>T	p.Arg293Cys	p.R293C	ENST00000257290	NM_006206.4	293	Cgc/Tgc	6/23	0.621670135637277	2	FACETS	0.996	0.951	1	0.996	0.951	1	CLONAL	2	TRUE	0	0.629333774267025	2		430	421	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094963	143094963	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0002709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	107	407	1	ENST00000262992.4:c.1182-1G>T		p.X394_splice	ENST00000262992	NM_001101669.1	394			0.621670135637277	2	FACETS	0.897	0.812	0.986	0.449	0.406	0.493	CLONAL	1	TRUE	0	0.629333774267025	2		408	379	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001494	150001494	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs140832020	NA	P-0002709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	118	444	0	ENST00000253339.5:c.2110A>G	p.Met704Val	p.M704V	ENST00000253339		704	Atg/Gtg	4/7	0.612663949091142	2	FACETS	0.933	0.849	1	0.466	0.424	0.51	CLONAL	1	TRUE	0	0.629333774267025	2		444	402	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455150	50455150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	87	332	0	ENST00000331340.3:c.697C>T	p.Pro233Ser	p.P233S	ENST00000331340	NM_006060.4	233	Ccg/Tcg	6/8	0.623687513970121	3	FACETS	0.964	0.86	1	0.482	0.43	0.537	CLONAL	1	TRUE	1	0.629333774267025	3		332	377	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268962	55268962	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	311	530	0	ENST00000275493.2:c.3028G>T	p.Val1010Leu	p.V1010L	ENST00000275493	NM_005228.3	1010	Gtg/Ttg	25/28	0.623687513970121	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.629333774267025	3		530	616	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485963	8485963	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	487	574	0	ENST00000356435.5:c.2854A>T	p.Thr952Ser	p.T952S	ENST00000356435		952	Acc/Tcc	17/35	0.599346096726945	4	FACETS	0.94	0.912	0.966	0.94	0.912	0.966	CLONAL	4	TRUE	0	0.629333774267025	4		574	671	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097781	8097781	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	216	588	2	ENST00000346208.3:c.163G>T	p.Gly55Cys	p.G55C	ENST00000346208		55	Ggt/Tgt	2/6	0.629333774267025	2	FACETS	0.925	0.876	0.973	0.925	0.876	0.973	CLONAL	2	TRUE	0	0.629333774267025	2		590	371	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69456196	69456196	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	1163	522	0	ENST00000227507.2:c.115G>T	p.Ala39Ser	p.A39S	ENST00000227507	NM_053056.2	39	Gcg/Tcg	1/5	0.629333774267025	10	FACETS	1	0.991	1			1	CLONAL	8	TRUE	NA	0.629333774267025	10		522	1601	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416628	416628	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	138	521	0	ENST00000399788.2:c.3922G>C	p.Asp1308His	p.D1308H	ENST00000399788	NM_001042603.1	1308	Gac/Cac	23/28	0.629333774267025	7	FACETS	0.869	0.788	0.954			1	CLONAL	1	TRUE	NA	0.629333774267025	7		521	1299	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534801	18534801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759595930	NA	P-0002709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	129	444	0	ENST00000266497.5:c.1859C>T	p.Pro620Leu	p.P620L	ENST00000266497		620	cCg/cTg	12/31	0.629333774267025	6	FACETS	0.92	0.833	1	0.184	0.166	0.203	CLONAL	1	TRUE	1	0.629333774267025	6		444	1006	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488233	56488233	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	139	496	0	ENST00000267101.3:c.1752C>G	p.His584Gln	p.H584Q	ENST00000267101	NM_001982.3	584	caC/caG	15/28	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.629333774267025	2		496	422	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120839	115120839	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	93	394	0	ENST00000257566.3:c.167T>C	p.Leu56Pro	p.L56P	ENST00000257566	NM_016569.3	56	cTg/cCg	1/8	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.629333774267025	2		394	287	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912039	32912039	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1566228768	NA	P-0002709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	274	422	0	ENST00000380152.3:c.3547G>C	p.Glu1183Gln	p.E1183Q	ENST00000380152		1183	Gaa/Caa	11/27	0.621670135637277	2	FACETS	0.999	0.954	1	0.999	0.954	1	CLONAL	2	TRUE	0	0.629333774267025	2		422	436	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602625	10602625	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	251	525	0	ENST00000171111.5:c.953C>T	p.Pro318Leu	p.P318L	ENST00000171111	NM_203500.1	318	cCc/cTc	3/6	0.608980855187861	2	FACETS	0.978	0.932	1	0.978	0.932	1	CLONAL	2	TRUE	0	0.629333774267025	2		525	408	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521308	8521308	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	393	382	0	ENST00000356435.5:c.930del	p.Ile311LeufsTer4	p.I311Lfs*4	ENST00000356435		310	gtC/gt	9/35	0.599346096726945	4	FACETS	0.899	0.868	0.928	0.899	0.868	0.928	CLONAL	4	TRUE	0	0.629333774267025	4		382	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579463	7579463	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	213	380	0	ENST00000269305.4:c.224del	p.Pro75LeufsTer48	p.P75Lfs*48	ENST00000269305	NM_001126112.2	75	cCt/ct	4/11	0.612663949091142	2	FACETS	0.922	0.873	0.971	0.922	0.873	0.971	CLONAL	2	TRUE	0	0.629333774267025	2		380	367	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591888	48591888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519739	NA	P-0002733-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	126	640	0	ENST00000342988.3:c.1051G>A	p.Asp351Asn	p.D351N	ENST00000342988	NM_005359.5	351	Gat/Aat	9/12	0.215910764662985	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.215910764662985	1		640	910	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405971	49405971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002733-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	124	578	0	ENST00000418115.1:c.167C>T	p.Ala56Val	p.A56V	ENST00000418115	NM_001664.2	56	gCt/gTt	3/5	0.215910764662985	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.215910764662985	1		578	956	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0002737-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	9	169	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.362	0.24	0.518	0.362	0.24	0.518	SUBCLONAL	1	TRUE	1	0.28719734449058	2		169	173	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736329	243736329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002737-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	33	263	0	ENST00000263826.5:c.718G>A	p.Glu240Lys	p.E240K	ENST00000263826	NM_005465.4	240	Gag/Aag	8/13	1	2	FACETS	0.573	0.467	0.693	0.573	0.467	0.693	SUBCLONAL	1	TRUE	1	0.28719734449058	2		263	401	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025796	48025796	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1553412096	NA	P-0002737-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	34	272	0	ENST00000234420.5:c.674T>C	p.Ile225Thr	p.I225T	ENST00000234420	NM_000179.2	225	aTt/aCt	4/10	1	2	FACETS	0.752	0.616	0.903	0.752	0.616	0.903	CLONAL	1	TRUE	1	0.28719734449058	2		272	315	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688794	47688794	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1437667184	NA	P-0002737-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	175	271	0	ENST00000347630.2:c.506A>G	p.Asn169Ser	p.N169S	ENST00000347630	NM_001007230.1	169	aAc/aGc	7/11	0.185674408298644	3	FACETS	0.897	0.832	0.963	0.897	0.832	0.963	CLONAL	3	TRUE	0	0.28719734449058	3		271	518	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792700	33792700	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002737-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	24	45	0	ENST00000498907.2:c.621G>C	p.Gln207His	p.Q207H	ENST00000498907	NM_004364.3	207	caG/caC	1/1	0.253678016873144	1	FACETS	0.62	0.488	0.77	0.62	0.488	0.77	SUBCLONAL	1	TRUE	0	0.28719734449058	1		45	231	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577049	7577049	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002737-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	106	283	0	ENST00000269305.4:c.889del	p.His297ThrfsTer48	p.H297Tfs*48	ENST00000269305	NM_001126112.2	297	Cac/ac	8/11	0.172730267038418	0	FACETS	1	0.924	1			1	CLONAL	1	TRUE	0	0.28719734449058	0		283	510	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0002738-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	8	169	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.279970006535809	1	FACETS	0.497	0.323	0.716	0.497	0.323	0.716	SUBCLONAL	1	TRUE	0	0.342158579075175	1		169	78	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0002738-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	78	189	0	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	0.279970006535809	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.342158579075175	1		189	359	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717661	89717661	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0002738-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	19	145	0	ENST00000371953.3:c.686C>G	p.Ser229Ter	p.S229*	ENST00000371953	NM_000314.4	229	tCa/tGa	7/9	0.267374463850667	1	FACETS	0.731	0.561	0.925	0.731	0.561	0.925	CLONAL	1	TRUE	0	0.342158579075175	1		145	126	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154887	2154887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1212009594	NA	P-0002738-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	57	189	0	ENST00000434045.2:c.334G>A	p.Ala112Thr	p.A112T	ENST00000434045	NM_001127598.1	112	Gca/Aca	4/5	1	2	FACETS	0.756	0.65	0.87	0.756	0.65	0.87	SUBCLONAL	1	TRUE	1	0.342158579075175	2		189	441	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007061	152007061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002738-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	26	187	0	ENST00000262189.6:c.839G>A	p.Gly280Glu	p.G280E	ENST00000262189	NM_170606.2	280	gGg/gAg	6/59	0.154012221454555	2	FACETS	0.451	0.357	0.558	0.225	0.178	0.279	INDETERMINATE	1	TRUE	0	0.342158579075175	2		187	337	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0002743-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	115	140	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.287014415202332	3	FACETS	0.915	0.829	1	0.61	0.552	0.67	CLONAL	2	TRUE	0	0.294256897553142	3		142	490	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0002743-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	312	290	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.243838078093081	5	FACETS	0.93	0.878	0.984	0.93	0.878	0.984	CLONAL	3	TRUE	2	0.294256897553142	5		290	1095	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339518	116339518	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002743-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	100	517	0	ENST00000397752.3:c.380A>G	p.Asp127Gly	p.D127G	ENST00000397752	NM_000245.2	127	gAt/gGt	2/21	0.221272761593909	4	FACETS	1	0.903	1	0.506	0.451	0.564	CLONAL	1	TRUE	2	0.294256897553142	4		517	869	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420101	420101	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002743-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1253	122	709	0	ENST00000399788.2:c.3166C>T	p.Arg1056Trp	p.R1056W	ENST00000399788	NM_001042603.1	1056	Cgg/Tgg	21/28	0.155260809034598	5	FACETS	0.869	0.783	0.961			1	INDETERMINATE	1	TRUE	NA	0.294256897553142	5		709	1375	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117790	70117790	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002743-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	93	621	0	ENST00000245479.2:c.258G>A	p.Trp86Ter	p.W86*	ENST00000245479	NM_000346.3	86	tgG/tgA	1/3	1	2	FACETS	0.985	0.876	1	0.985	0.876	1	CLONAL	1	TRUE	1	0.294256897553142	2		621	642	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0002752-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	19	378	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.917	0.709	1	0.917	0.709	1	CLONAL	1	TRUE	1	0.445748057812182	2		379	93	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577560	7577560	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520002	NA	P-0002752-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	16	337	0	ENST00000269305.4:c.721T>C	p.Ser241Pro	p.S241P	ENST00000269305	NM_001126112.2	241	Tcc/Ccc	7/11	0.330936304616237	1	FACETS	0.672	0.506	0.862	0.672	0.506	0.862	SUBCLONAL	1	TRUE	0	0.445748057812182	1		337	83	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100829	27100829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002752-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	30	434	0	ENST00000324856.7:c.4111C>T	p.Arg1371Trp	p.R1371W	ENST00000324856	NM_006015.4	1371	Cgg/Tgg	18/20	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.445748057812182	2		434	113	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190656591	190656591	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002752-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	21	459	0	ENST00000441310.2:c.56C>T	p.Thr19Ile	p.T19I	ENST00000441310	NM_000534.4	19	aCt/aTt	2/13	1	2	FACETS	0.889	0.696	1	0.889	0.696	1	CLONAL	1	TRUE	1	0.445748057812182	2		459	106	SUCCESS
APC	324	MSKCC	GRCh37	5	112175288	112175288	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0002752-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	60	366	0	ENST00000257430.4:c.3997A>T	p.Lys1333Ter	p.K1333*	ENST00000257430	NM_000038.5	1333	Aaa/Taa	16/16	0.445748057812182	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.445748057812182	2		366	114	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0002780-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	31	379	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.195192519306971	4	FACETS	0.684	0.558	0.825	0.342	0.279	0.413	INDETERMINATE	1	TRUE	2	0.799414100576311	4		379	204	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0002780-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	81	440	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.195192519306971	4	FACETS	0.916	0.825	1	0.916	0.825	1	INDETERMINATE	2	TRUE	2	0.799414100576311	4		440	199	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543825	212543825	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002780-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	10	386	0	ENST00000342788.4:c.1574G>T	p.Arg525Leu	p.R525L	ENST00000342788	NM_005235.2	525	cGc/cTc	13/28	0.388088195602867	1	FACETS	0.083	0.056	0.118	0.083	0.056	0.118	INDETERMINATE	1	TRUE	0	0.799414100576311	1		386	180	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437813	52437813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002780-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	31	331	0	ENST00000460680.1:c.1348G>A	p.Glu450Lys	p.E450K	ENST00000460680	NM_004656.3	450	Gag/Aag	13/17	0.388088195602867	1	FACETS	0.419	0.347	0.498	0.419	0.347	0.498	INDETERMINATE	1	TRUE	0	0.799414100576311	1		331	111	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435665	18435665	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002780-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	34	211	0	ENST00000266497.5:c.650G>T	p.Trp217Leu	p.W217L	ENST00000266497		217	tGg/tTg	1/31	1	2	FACETS	0.512	0.424	0.609	0.512	0.424	0.609	SUBCLONAL	1	TRUE	1	0.799414100576311	2		211	166	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511499	38511541	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTTCTGCTTCCTCAGACCGCCAGGACCTGGAGCAGCCGGACC	GGTTCTGCTTCCTCAGACCGCCAGGACCTGGAGCAGCCGGACC	-	novel	NA	P-0002780-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	24	200	0	ENST00000254066.5:c.1013-14_1041del		p.X338_splice	ENST00000254066	NM_000964.3	338		8/9	1	2	FACETS	0.492	0.392	0.604	0.492	0.392	0.604	SUBCLONAL	1	TRUE	1	0.799414100576311	2		200	122	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0002814-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	105	276	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.284190256494181	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	2	TRUE	0	0.329831478476099	2		276	318	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113265	209113265	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002814-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	34	562	1	ENST00000345146.2:c.242A>G	p.Lys81Arg	p.K81R	ENST00000345146	NM_005896.2	81	aAg/aGg	4/10	0.294343981797084	3	FACETS	0.867	0.712	1	0.434	0.356	0.52	CLONAL	1	TRUE	1	0.329831478476099	3		563	277	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913527	NA	P-0002814-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	60	474	0	ENST00000311936.3:c.436G>C	p.Ala146Pro	p.A146P	ENST00000311936	NM_004985.3	146	Gca/Cca	4/5	0.314261761054932	3	FACETS	0.797	0.693	0.907	0.797	0.693	0.907	CLONAL	2	TRUE	1	0.329831478476099	3		474	266	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0002823-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	9	140	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.109	0.071	0.157	0.109	0.071	0.157	SUBCLONAL	1	TRUE	1	0.51	2		142	324	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0002823-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	29	626	0	ENST00000262160.6:c.1391C>G	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tGa	11/11	1	2	FACETS	0.256	0.205	0.314	0.256	0.205	0.314	SUBCLONAL	1	TRUE	1	0.51	2		626	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780071	NA	P-0002823-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	41	446	0	ENST00000269305.4:c.580C>T	p.Leu194Phe	p.L194F	ENST00000269305	NM_001126112.2	194	Ctt/Ttt	6/11	1	2	FACETS	0.276	0.229	0.328	0.276	0.229	0.328	SUBCLONAL	1	TRUE	1	0.51	2		446	582	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0002823-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	44	690	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	1	2	FACETS	0.225	0.188	0.267	0.225	0.188	0.267	SUBCLONAL	1	TRUE	1	0.51	2		690	766	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533676	63533676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367697282	NA	P-0002823-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	38	631	0	ENST00000307078.5:c.1478C>T	p.Ser493Leu	p.S493L	ENST00000307078	NM_004655.3	493	tCg/tTg	6/11	1	2	FACETS	0.319	0.263	0.381	0.319	0.263	0.381	SUBCLONAL	1	TRUE	1	0.51	2		631	467	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449565	149449565	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002823-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	39	734	0	ENST00000286301.3:c.1381G>C	p.Glu461Gln	p.E461Q	ENST00000286301	NM_005211.3	461	Gag/Cag	10/22	1	2	FACETS	0.252	0.208	0.302	0.252	0.208	0.302	SUBCLONAL	1	TRUE	1	0.51	2		734	606	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002823-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	43	386	0	ENST00000397752.3:c.3028G>A	p.Asp1010Asn	p.D1010N	ENST00000397752	NM_000245.2	1010	Gat/Aat	14/21	0.288684228301199	3	FACETS	0.551	0.462	0.649	0.276	0.231	0.325	INDETERMINATE	1	TRUE	1	0.51	3		386	384	SUCCESS
MET	4233	MSKCC	GRCh37	7	116414994	116414994	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002823-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	57	680	0	ENST00000397752.3:c.3088G>C	p.Asp1030His	p.D1030H	ENST00000397752	NM_000245.2	1030	Gac/Cac	15/21	0.288684228301199	3	FACETS	0.396	0.339	0.458	0.198	0.169	0.229	INDETERMINATE	1	TRUE	1	0.51	3		680	709	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742960	17742960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1241501765	NA	P-0002823-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	28	486	0	ENST00000250003.3:c.868G>A	p.Glu290Lys	p.E290K	ENST00000250003	NM_002478.4	290	Gag/Aag	3/3	1	2	FACETS	0.328	0.262	0.403	0.328	0.262	0.403	SUBCLONAL	1	TRUE	1	0.51	2		486	335	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456785	32456785	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773550149	NA	P-0002823-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	24	295	0	ENST00000332351.3:c.107C>T	p.Pro36Leu	p.P36L	ENST00000332351	NM_024426.4	36	cCg/cTg	1/10	1	2	FACETS	0.399	0.314	0.496	0.399	0.314	0.496	SUBCLONAL	1	TRUE	1	0.51	2		295	236	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033964	49033964	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002823-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	24	519	0	ENST00000267163.4:c.2101G>T	p.Asp701Tyr	p.D701Y	ENST00000267163	NM_000321.2	701	Gac/Tac	20/27	1	2	FACETS	0.199	0.155	0.249	0.199	0.155	0.249	SUBCLONAL	1	TRUE	1	0.51	2		519	474	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112562	2112562	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs45515894	NA	P-0002823-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	27	560	0	ENST00000219476.3:c.1322G>A	p.Trp441Ter	p.W441*	ENST00000219476	NM_000548.3	441	tGg/tAg	13/42	1	2	FACETS	0.224	0.177	0.277	0.224	0.177	0.277	SUBCLONAL	1	TRUE	1	0.51	2		560	473	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828148	3828148	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0002823-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	35	665	0	ENST00000262367.5:c.1977C>G	p.Tyr659Ter	p.Y659*	ENST00000262367	NM_004380.2	659	taC/taG	10/31	1	2	FACETS	0.196	0.16	0.237	0.196	0.16	0.237	SUBCLONAL	1	TRUE	1	0.51	2		665	700	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577543	7577543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1019340046	NA	P-0002823-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	29	519	0	ENST00000269305.4:c.738G>A	p.Met246Ile	p.M246I	ENST00000269305	NM_001126112.2	246	atG/atA	7/11	1	2	FACETS	0.208	0.166	0.255	0.208	0.166	0.255	SUBCLONAL	1	TRUE	1	0.51	2		519	548	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548347	41548347	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002823-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	29	548	0	ENST00000263253.7:c.3135G>T	p.Lys1045Asn	p.K1045N	ENST00000263253	NM_001429.3	1045	aaG/aaT	16/31	1	2	FACETS	0.219	0.175	0.269	0.219	0.175	0.269	SUBCLONAL	1	TRUE	1	0.51	2		548	519	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551118	41551118	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0002823-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	38	686	0	ENST00000263253.7:c.3261+1G>C		p.X1087_splice	ENST00000263253	NM_001429.3	1087			1	2	FACETS	0.225	0.185	0.269	0.225	0.185	0.269	SUBCLONAL	1	TRUE	1	0.51	2		686	663	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0002833-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	580	255	4	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.746116268648785	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.746116268648785	3		259	700	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813074	76813078	+	frameshift_variant	Frame_Shift_Del	DEL	GCTTA	GCTTA	-	novel	NA	P-0002833-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	147	238	0	ENST00000373344.5:c.6543_6547del	p.Lys2182ValfsTer8	p.K2182Vfs*8	ENST00000373344	NM_000489.3	2181	acTAAGCag/acag	30/35	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.746116268648785	1		238	210	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0002838-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	17	378	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.56	0.417	0.731	0.56	0.417	0.731	SUBCLONAL	1	TRUE	1	0.17	2		379	357	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0002838-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	43	409	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	TRUE	1	0.17	2		409	341	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443612	29443612	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1244270149	NA	P-0002838-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	38	280	0	ENST00000389048.3:c.3605G>A	p.Gly1202Glu	p.G1202E	ENST00000389048	NM_004304.4	1202	gGa/gAa	23/29	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.17	2		280	428	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578213	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs864309495	NA	P-0002840-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	305	668	0	ENST00000269305.4:c.636del	p.Arg213AspfsTer34	p.R213Dfs*34	ENST00000269305	NM_001126112.2	212	ttT/tt	6/11	0.219915802930071	0	FACETS	0.885	0.835	0.936			1	CLONAL	2	FALSE	0	0.246631753464079	0		668	1053	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440373	52440373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002840-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	59	391	0	ENST00000460680.1:c.679C>T	p.Arg227Cys	p.R227C	ENST00000460680	NM_004656.3	227	Cgc/Tgc	9/17	1	2	FACETS	0.593	0.509	0.685	0.593	0.509	0.685	SUBCLONAL	1	FALSE	1	0.246631753464079	2		391	807	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721879	176721879	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002840-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	129	451	0	ENST00000439151.2:c.7510G>C	p.Val2504Leu	p.V2504L	ENST00000439151	NM_022455.4	2504	Gtt/Ctt	23/23	0.201661353406754	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	FALSE	0	0.246631753464079	1		451	892	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441252	52441252	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002843-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	56	251	0	ENST00000460680.1:c.518A>G	p.Tyr173Cys	p.Y173C	ENST00000460680	NM_004656.3	173	tAt/tGt	7/17	1	2	FACETS	0.701	0.599	0.812	0.701	0.599	0.812	SUBCLONAL	1	TRUE	1	0.24	2		251	666	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183833	10183835	+	missense_variant	Missense_Mutation	TNP	TGC	TGC	CTA	novel	NA	P-0002843-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	53	148	0	ENST00000256474.2:c.302_304delinsCTA	p.Leu101_Pro102delinsProThr	p.L101_P102delinsPT	ENST00000256474	NM_000551.3	101	cTGCcg/cCTAcg	1/3	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.24	2		148	424	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029530	14029530	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002843-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	30	151	0	ENST00000311895.7:c.1741T>C	p.Tyr581His	p.Y581H	ENST00000311895	NM_005236.2	581	Tat/Cat	8/11	1	2	FACETS	0.564	0.454	0.69	0.564	0.454	0.69	SUBCLONAL	1	TRUE	1	0.24	2		151	443	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720958	119720958	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002848-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	510	133	591	0	ENST00000316626.5:c.217G>A	p.Ala73Thr	p.A73T	ENST00000316626		73	Gcc/Acc	2/12	0.423339767801317	0	FACETS	0.564	0.514	0.617			1	SUBCLONAL	1	TRUE	0	0.423064032314966	0		591	643	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405027	405027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568315642	NA	P-0002848-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	551	103	443	0	ENST00000380956.4:c.1109C>T	p.Ala370Val	p.A370V	ENST00000380956	NM_001195286.1	370	gCg/gTg	8/9	NA	2	FACETS	0.745	0.667	0.827			1	INDETERMINATE	1	TRUE	NA	0.423064032314966	2		443	654	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223241	2223241	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002848-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	636	60	507	0	ENST00000326181.6:c.853G>C	p.Glu285Gln	p.E285Q	ENST00000326181	NM_032271.2	285	Gag/Cag	10/21	0.40932290217924	3	FACETS	0.494	0.425	0.569	0.247	0.212	0.285	SUBCLONAL	1	TRUE	1	0.423064032314966	3		507	696	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684388	29684388	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0002848-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	364	404	524	0	ENST00000356175.3:c.7907+1G>T		p.X2636_splice	ENST00000356175	NM_000267.3	2636			NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.423064032314966	2		524	768	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510675	38510675	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002848-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	778	765	440	0	ENST00000254066.5:c.929T>C	p.Phe310Ser	p.F310S	ENST00000254066	NM_000964.3	310	tTt/tCt	7/9	0.423064032314966	11	FACETS	0.972	0.942	1			1	CLONAL	7	TRUE	NA	0.423064032314966	11		440	1543	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224550	123224550	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002848-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	726	97	604	1	ENST00000218089.9:c.3403G>A	p.Glu1135Lys	p.E1135K	ENST00000218089	NM_001042749.1	1135	Gag/Aag	31/35	0.293062190636293	2	FACETS	0.557	0.496	0.622	0.279	0.248	0.311	SUBCLONAL	1	TRUE	0	0.423064032314966	2		605	823	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577561	7577566	+	inframe_deletion	In_Frame_Del	DEL	ACTGTT	ACTGTT	-	novel	NA	P-0002848-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	245	251	400	0	ENST00000269305.4:c.715_720del	p.Asn239_Ser240del	p.N239_S240del	ENST00000269305	NM_001126112.2	239	AACAGT/-	7/11	0.424933353703353	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.423064032314966	2		400	496	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0002858-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	241	495	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.904193748926201	5	FACETS	0.993	0.974	1	0.993	0.974	1	CLONAL	5	TRUE	0	0.904193748926201	5		496	253	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453486	138453486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451809865	NA	P-0002858-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	53	241	0	ENST00000289153.2:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000289153	NM_006219.2	321	cGa/cAa	5/22	0.878822895844093	4	FACETS	0.9	0.775	1	0.225	0.193	0.259	CLONAL	1	TRUE	0	0.904193748926201	4		241	248	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743775	46743775	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002858-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	36	243	0	ENST00000371975.4:c.2065C>G	p.Gln689Glu	p.Q689E	ENST00000371975	NM_003579.3	689	Cag/Gag	18/18	0.407377462701611	3	FACETS	1	0.9	1	0.545	0.46	0.635	INDETERMINATE	1	TRUE	1	0.904193748926201	3		243	106	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458033	120458033	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002858-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	39	182	0	ENST00000256646.2:c.7312G>A	p.Asp2438Asn	p.D2438N	ENST00000256646	NM_024408.3	2438	Gat/Aat	34/34	0.407377462701611	3	FACETS	1	0.946	1	0.626	0.536	0.72	INDETERMINATE	1	TRUE	1	0.904193748926201	3		182	100	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458315	120458315	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002858-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	28	147	0	ENST00000256646.2:c.7030G>C	p.Glu2344Gln	p.E2344Q	ENST00000256646	NM_024408.3	2344	Gaa/Caa	34/34	0.407377462701611	3	FACETS	0.947	0.776	1	0.473	0.388	0.565	INDETERMINATE	1	TRUE	1	0.904193748926201	3		147	95	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458519	120458519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002858-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	31	180	0	ENST00000256646.2:c.6826G>A	p.Glu2276Lys	p.E2276K	ENST00000256646	NM_024408.3	2276	Gag/Aag	34/34	0.407377462701611	3	FACETS	1	0.945	1	0.673	0.566	0.783	INDETERMINATE	1	TRUE	1	0.904193748926201	3		180	74	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874261	155874261	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs483352822	NA	P-0002858-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	38	249	0	ENST00000368323.3:c.270G>C	p.Met90Ile	p.M90I	ENST00000368323	NM_006912.5	90	atG/atC	5/6	0.904193748926201	7	FACETS	1	0.914	1			1	CLONAL	1	TRUE	NA	0.904193748926201	7		249	236	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844182	156844182	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002858-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	32	233	0	ENST00000524377.1:c.1185C>G	p.Phe395Leu	p.F395L	ENST00000524377	NM_002529.3	395	ttC/ttG	9/17	0.826845950151772	5	FACETS	0.981	0.806	1	0.245	0.201	0.294	CLONAL	1	TRUE	1	0.904193748926201	5		233	170	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226549764	226549764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002858-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	35	190	0	ENST00000366794.5:c.2869G>A	p.Asp957Asn	p.D957N	ENST00000366794	NM_001618.3	957	Gat/Aat	22/23	0.826845950151772	5	FACETS	0.873	0.722	1	0.218	0.18	0.26	CLONAL	1	TRUE	1	0.904193748926201	5		190	209	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715667	30715667	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002858-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	39	187	0	ENST00000295754.5:c.1325T>A	p.Phe442Tyr	p.F442Y	ENST00000295754	NM_003242.5	442	tTc/tAc	5/7	0.815298340866959	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.904193748926201	1		187	47	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215931	142215931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002858-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	49	206	0	ENST00000350721.4:c.5662G>A	p.Glu1888Lys	p.E1888K	ENST00000350721	NM_001184.3	1888	Gaa/Aaa	33/47	0.878822895844093	4	FACETS	0.947	0.811	1	0.237	0.202	0.273	CLONAL	1	TRUE	0	0.904193748926201	4		206	218	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561872	55561872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002858-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	32	241	0	ENST00000288135.5:c.262G>A	p.Glu88Lys	p.E88K	ENST00000288135	NM_000222.2	88	Gaa/Aaa	2/21	NA	2	FACETS	0.863	0.726	1			1	INDETERMINATE	1	TRUE	NA	0.904193748926201	2		241	82	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193871	106193871	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002858-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	57	224	0	ENST00000380013.4:c.4333C>A	p.Gln1445Lys	p.Q1445K	ENST00000380013	NM_001127208.2	1445	Cag/Aag	10/11	0.407377462701611	3	FACETS	1	0.972	1	0.71	0.627	0.793	INDETERMINATE	1	TRUE	1	0.904193748926201	3		224	129	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404458	70404458	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002858-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	36	216	0	ENST00000373644.4:c.1972G>C	p.Asp658His	p.D658H	ENST00000373644	NM_030625.2	658	Gat/Cat	4/12	1	2	FACETS	0.773	0.654	0.899	0.773	0.654	0.899	SUBCLONAL	1	TRUE	1	0.904193748926201	2		216	103	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514089	69514089	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002858-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	37	227	0	ENST00000294312.3:c.592G>C	p.Asp198His	p.D198H	ENST00000294312	NM_005117.2	198	Gac/Cac	3/3	0.904193748926201	6	FACETS	0.881	0.73	1			1	CLONAL	1	TRUE	NA	0.904193748926201	6		227	261	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343271	118343271	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002858-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	13	233	0	ENST00000534358.1:c.1397C>G	p.Ser466Cys	p.S466C	ENST00000534358	NM_005933.3	466	tCt/tGt	3/36	0.847931650825225	1	FACETS	0.254	0.185	0.333	0.254	0.185	0.333	SUBCLONAL	1	TRUE	0	0.904193748926201	1		233	62	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420070	420070	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs191475834	NA	P-0002858-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	58	316	0	ENST00000399788.2:c.3197C>T	p.Ser1066Phe	p.S1066F	ENST00000399788	NM_001042603.1	1066	tCt/tTt	21/28	NA	2	FACETS	0.95	0.84	1			1	INDETERMINATE	1	TRUE	NA	0.904193748926201	2		316	135	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446951	18446951	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0002858-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	19	176	0	ENST00000266497.5:c.1034+2T>G		p.X345_splice	ENST00000266497		345			0.300841753392776	3	FACETS	0.504	0.387	0.638	0.252	0.193	0.319	INDETERMINATE	1	TRUE	1	0.904193748926201	3		176	121	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218205	69218205	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs759861388	NA	P-0002858-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	58	227	0	ENST00000462284.1:c.421C>G	p.Gln141Glu	p.Q141E	ENST00000462284	NM_002392.5	141	Caa/Gaa	6/11	0.36676038159133	4	FACETS	0.94	0.832	1	0.94	0.832	1	INDETERMINATE	2	TRUE	2	0.904193748926201	4		227	130	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226002	133226002	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002858-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	27	254	0	ENST00000320574.5:c.3895G>C	p.Glu1299Gln	p.E1299Q	ENST00000320574	NM_006231.2	1299	Gag/Cag	31/49	1	2	FACETS	0.671	0.549	0.802	0.671	0.549	0.802	SUBCLONAL	1	TRUE	1	0.904193748926201	2		254	89	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602354	28602354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1367367961	NA	P-0002858-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	30	291	0	ENST00000241453.7:c.2014G>A	p.Glu672Lys	p.E672K	ENST00000241453	NM_004119.2	672	Gag/Aag	16/24	NA	2	FACETS	0.799	0.666	0.94			1	INDETERMINATE	1	TRUE	NA	0.904193748926201	2		291	83	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608053	28608053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002858-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	31	313	0	ENST00000241453.7:c.1913C>T	p.Ser638Leu	p.S638L	ENST00000241453	NM_004119.2	638	tCa/tTa	15/24	NA	2	FACETS	0.879	0.738	1			1	INDETERMINATE	1	TRUE	NA	0.904193748926201	2		313	78	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438153	110438153	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1314168066	NA	P-0002858-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	16	98	0	ENST00000375856.3:c.248G>A	p.Arg83Gln	p.R83Q	ENST00000375856	NM_003749.2	83	cGg/cAg	1/2	0.265163123836228	4	FACETS	1	0.849	1	1	0.849	1	INDETERMINATE	2	TRUE	2	0.904193748926201	4		98	31	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239245	105239245	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002858-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	29	186	0	ENST00000349310.3:c.1142C>T	p.Ser381Leu	p.S381L	ENST00000349310	NM_001014432.1	381	tCa/tTa	12/15	NA	2	FACETS	0.957	0.802	1			1	INDETERMINATE	1	TRUE	NA	0.904193748926201	2		186	67	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396845	396845	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002858-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	19	253	0	ENST00000262320.3:c.181C>G	p.Pro61Ala	p.P61A	ENST00000262320	NM_003502.3	61	Ccg/Gcg	2/11	1	2	FACETS	0.824	0.653	1	0.824	0.653	1	CLONAL	1	TRUE	1	0.904193748926201	2		253	51	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916216	9916216	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002858-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	29	258	1	ENST00000330684.3:c.2073G>C	p.Glu691Asp	p.E691D	ENST00000330684	NM_001134407.1	691	gaG/gaC	10/13	1	2	FACETS	0.713	0.588	0.845	0.713	0.588	0.845	SUBCLONAL	1	TRUE	1	0.904193748926201	2		259	90	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618395	37618395	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002858-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	50	196	0	ENST00000447079.4:c.71C>A	p.Ser24Ter	p.S24*	ENST00000447079	NM_015083.1	24	tCa/tAa	1/14	0.78635874250506	6	FACETS	1	0.947	1			1	CLONAL	1	TRUE	NA	0.904193748926201	6		196	250	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41242963	41242963	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002858-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	28	214	0	ENST00000357654.3:c.4183C>G	p.Gln1395Glu	p.Q1395E	ENST00000357654	NM_007294.3	1395	Cag/Gag	11/23	0.254068901298937	4	FACETS	0.991	0.807	1			1	INDETERMINATE	1	TRUE	NA	0.904193748926201	4		214	119	SUCCESS
YES1	7525	MSKCC	GRCh37	18	742933	742933	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002858-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	51	280	0	ENST00000314574.4:c.1045G>A	p.Glu349Lys	p.E349K	ENST00000314574	NM_005433.3	349	Gaa/Aaa	8/12	0.623858141436767	1	FACETS	0.515	0.451	0.58	0.515	0.451	0.58	SUBCLONAL	1	TRUE	0	0.904193748926201	1		280	120	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106991	11106991	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002858-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	28	261	0	ENST00000358026.2:c.1696G>C	p.Glu566Gln	p.E566Q	ENST00000358026	NM_001128849.1	566	Gag/Cag	10/36	1	2	FACETS	0.815	0.674	0.962	0.815	0.674	0.962	CLONAL	1	TRUE	1	0.904193748926201	2		261	76	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921627	39921627	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002858-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	33	238	0	ENST00000378444.4:c.4193G>C	p.Arg1398Thr	p.R1398T	ENST00000378444	NM_001123385.1	1398	aGa/aCa	10/15	NA	2	FACETS	1	0.892	1			1	INDETERMINATE	1	TRUE	NA	0.904193748926201	2		238	69	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562849	176562849	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002858-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	81	237	0	ENST00000439151.2:c.745del	p.Glu249LysfsTer12	p.E249Kfs*12	ENST00000439151	NM_022455.4	249	Gaa/aa	2/23	0.407377462701611	3	FACETS	0.916	0.836	0.994	0.916	0.836	0.994	INDETERMINATE	2	TRUE	1	0.904193748926201	3		237	142	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0002861-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	1264	299	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.3	17	FACETS	1	0.99	1			1	CLONAL	13	TRUE	NA	0.31	17		299	2049	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0002861-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	62	289	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.3	3	FACETS	0.75	0.648	0.861	0.375	0.324	0.431	SUBCLONAL	1	TRUE	1	0.31	3		289	616	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462174	120462174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002861-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	37	296	0	ENST00000256646.2:c.5542G>A	p.Asp1848Asn	p.D1848N	ENST00000256646	NM_024408.3	1848	Gat/Aat	31/34	1	2	FACETS	0.35	0.287	0.42	0.35	0.287	0.42	SUBCLONAL	1	TRUE	1	0.31	2		296	682	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858231	9858231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002861-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	49	401	0	ENST00000330684.3:c.3170C>T	p.Ala1057Val	p.A1057V	ENST00000330684	NM_001134407.1	1057	gCc/gTc	13/13	1	2	FACETS	0.365	0.308	0.429	0.365	0.308	0.429	SUBCLONAL	1	TRUE	1	0.31	2		401	865	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858769	9858769	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002861-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	29	236	0	ENST00000330684.3:c.2632G>A	p.Glu878Lys	p.E878K	ENST00000330684	NM_001134407.1	878	Gaa/Aaa	13/13	1	2	FACETS	0.335	0.268	0.411	0.335	0.268	0.411	SUBCLONAL	1	TRUE	1	0.31	2		236	559	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0002871-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	14	169	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		169	339	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732963	30732963	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121918714	NA	P-0002871-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	32	269	0	ENST00000295754.5:c.1576G>C	p.Glu526Gln	p.E526Q	ENST00000295754	NM_003242.5	526	Gag/Cag	7/7	0.133753750570198	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		269	564	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860573	151860573	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002871-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	34	453	0	ENST00000262189.6:c.10089T>G	p.Cys3363Trp	p.C3363W	ENST00000262189	NM_170606.2	3363	tgT/tgG	43/59	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		453	676	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0002880-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	118	284	0	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	0.503590491513076	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	0	0.503590491513076	1		284	323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0002887-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	160	351	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.202174420337068	1	FACETS	0.936	0.86	1	1	0.991	1	CLONAL	2	TRUE	0	0.202174420337068	1		351	760	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426644	121426644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853243	NA	P-0002887-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	64	390	0	ENST00000257555.6:c.335C>T	p.Pro112Leu	p.P112L	ENST00000257555		112	cCg/cTg	2/10	0.202174420337068	3	FACETS	0.843	0.728	0.968	0.421	0.364	0.484	CLONAL	1	TRUE	1	0.202174420337068	3		390	827	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103513917	103513917	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1400865997	NA	P-0002887-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	63	433	0	ENST00000355739.4:c.733C>G	p.Gln245Glu	p.Q245E	ENST00000355739	NM_000123.3	245	Cag/Gag	7/15	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.202174420337068	2		433	617	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0002896-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	148	169	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.358128461788832	5	FACETS	0.939	0.865	1			1	CLONAL	3	TRUE	NA	0.358128461788832	5		169	451	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144624	55144624	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002896-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	162	398	0	ENST00000257290.5:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000257290	NM_006206.4	700	Aag/Gag	15/23	0.200210450468816	3	FACETS	0.771	0.709	0.835	0.514	0.473	0.557	INDETERMINATE	2	TRUE	0	0.358128461788832	3		398	692	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431629	6431629	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002896-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	48	191	0	ENST00000356142.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000356142	NM_018890.3	61	cAa/cGa	3/7	0.358128461788832	4	FACETS	0.778	0.658	0.91	0.389	0.329	0.455	CLONAL	1	TRUE	2	0.358128461788832	4		191	468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0002904-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	511	391	0	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	0.563654121568137	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.569306459417225	2		391	870	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023805	27023805	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002904-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	308	179	0	ENST00000324856.7:c.911C>A	p.Ser304Ter	p.S304*	ENST00000324856	NM_006015.4	304	tCg/tAg	1/20	0.563654121568137	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.569306459417225	2		179	480	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0002905-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	112	450	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.273154418989902	2		451	548	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794422	242794422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758959367	NA	P-0002905-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	85	420	1	ENST00000334409.5:c.520G>A	p.Val174Met	p.V174M	ENST00000334409	NM_005018.2	174	Gtg/Atg	3/5	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.273154418989902	2		421	424	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998901	11998901	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002905-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	187	386	1	ENST00000353533.5:c.403T>A	p.Ser135Thr	p.S135T	ENST00000353533	NM_003010.3	135	Tca/Aca	4/11	0.211100942776846	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	3	TRUE	0	0.273154418989902	3		387	508	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207204	1207204	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0002905-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	106	243	0	ENST00000326873.7:c.290+2T>A		p.X97_splice	ENST00000326873	NM_000455.4	97			0.273154418989902	1	FACETS	1	0.977	1	1	0.99	1	CLONAL	2	TRUE	0	0.273154418989902	1		243	273	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610423	10610423	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002905-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	186	410	0	ENST00000171111.5:c.287A>G	p.His96Arg	p.H96R	ENST00000171111	NM_203500.1	96	cAc/cGc	2/6	0.273154418989902	1	FACETS	1	0.954	1	1	0.995	1	CLONAL	3	TRUE	0	0.273154418989902	1		410	384	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573830	64573830	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1565644366	NA	P-0002913-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	283	219	0	ENST00000312049.6:c.923C>A	p.Ser308Ter	p.S308*	ENST00000312049	NM_130799.2	308	tCa/tAa	7/10	0.896936113835107	2	FACETS	0.992	0.967	1	0.992	0.967	1	CLONAL	2	TRUE	0	0.896936113835107	2		219	318	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0002921-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	154	396	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.33240694505535	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.33240694505535	2		396	434	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098953	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002921-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	83	571	0	ENST00000397062.3:c.92G>C	p.Gly31Ala	p.G31A	ENST00000397062	NM_006164.4	31	gGa/gCa	2/5	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.33240694505535	2		571	427	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437912	52437912	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0002921-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	47	246	0	ENST00000460680.1:c.1251-2A>T		p.X417_splice	ENST00000460680	NM_004656.3	417			0.33240694505535	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.33240694505535	1		246	179	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390149	89390149	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002921-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	66	572	0	ENST00000336596.2:c.898G>A	p.Gly300Ser	p.G300S	ENST00000336596	NM_005233.5	300	Ggt/Agt	4/17	0.33240694505535	1	FACETS	0.963	0.841	1	0.963	0.841	1	CLONAL	1	TRUE	0	0.33240694505535	1		572	344	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161408	185161408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002921-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	50	635	0	ENST00000265026.3:c.835G>A	p.Asp279Asn	p.D279N	ENST00000265026	NM_004721.4	279	Gat/Aat	4/14	0.33240694505535	1	FACETS	0.859	0.734	0.995	0.859	0.734	0.995	CLONAL	1	TRUE	0	0.33240694505535	1		635	292	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167813	56167813	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002921-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	37	543	2	ENST00000399503.3:c.1378G>T	p.Glu460Ter	p.E460*	ENST00000399503	NM_005921.1	460	Gaa/Taa	7/20	0.174651734063808	3	FACETS	0.568	0.468	0.68	0.284	0.234	0.34	INDETERMINATE	1	TRUE	1	0.33240694505535	3		545	457	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499688	8499688	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002921-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	125	675	1	ENST00000356435.5:c.2281G>T	p.Gly761Cys	p.G761C	ENST00000356435		761	Ggc/Tgc	14/35	0.286851631813171	2	FACETS	0.902	0.823	0.983	0.902	0.823	0.983	CLONAL	2	TRUE	0	0.33240694505535	2		676	417	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907047	101907047	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0002921-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	77	455	0	ENST00000374994.4:c.1007C>G	p.Ser336Ter	p.S336*	ENST00000374994	NM_004612.2	336	tCa/tGa	6/9	0.286851631813171	2	FACETS	1	0.977	1	0.742	0.658	0.832	CLONAL	1	TRUE	0	0.33240694505535	2		455	312	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346364	73346364	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002921-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	56	597	0	ENST00000377767.4:c.1436A>G	p.Asp479Gly	p.D479G	ENST00000377767	NM_014953.3	479	gAc/gGc	10/21	1	2	FACETS	0.896	0.771	1	0.896	0.771	1	CLONAL	1	TRUE	1	0.33240694505535	2		597	376	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384649	31384649	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002921-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	43	673	0	ENST00000328111.2:c.1351G>T	p.Glu451Ter	p.E451*	ENST00000328111	NM_006892.3	451	Gag/Tag	13/23	1	2	FACETS	0.602	0.504	0.71	0.602	0.504	0.71	SUBCLONAL	1	TRUE	1	0.33240694505535	2		673	430	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041606	47041606	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002921-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	83	741	0	ENST00000377604.3:c.1831G>T	p.Glu611Ter	p.E611*	ENST00000377604	NM_001204468.1	611	Gag/Tag	17/24	0.22284814671062	0	FACETS	0.591	0.522	0.664			1	SUBCLONAL	1	TRUE	0	0.33240694505535	0		741	564	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430395	47430395	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002921-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	105	747	0	ENST00000377045.4:c.1670G>T	p.Arg557Leu	p.R557L	ENST00000377045	NM_001654.4	557	cGg/cTg	15/16	0.22284814671062	0	FACETS	0.709	0.636	0.785			1	SUBCLONAL	1	TRUE	0	0.33240694505535	0		747	595	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938508	76938508	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002921-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	51	761	0	ENST00000373344.5:c.2240G>C	p.Ser747Thr	p.S747T	ENST00000373344	NM_000489.3	747	aGt/aCt	9/35	0.22284814671062	0	FACETS	0.56	0.477	0.649			1	SUBCLONAL	1	TRUE	0	0.33240694505535	0		761	366	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085972	16085972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs998174759	NA	P-0002939-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	153	519	1	ENST00000281043.3:c.1148G>A	p.Arg383His	p.R383H	ENST00000281043	NM_005378.4	383	cGc/cAc	3/3	1	2	FACETS	0.997	0.917	1	0.997	0.917	1	CLONAL	1	TRUE	1	0.539565533416542	2		520	569	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0002949-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	16	368	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		368	731	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028895	47028895	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002949-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	11	108	0	ENST00000377604.3:c.199G>T	p.Glu67Ter	p.E67*	ENST00000377604	NM_001204468.1	67	Gag/Tag	3/24	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		108	195	SUCCESS
AR	367	MSKCC	GRCh37	X	66941726	66941726	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002952-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	29	710	0	ENST00000374690.3:c.2370C>A	p.His790Gln	p.H790Q	ENST00000374690	NM_000044.3	790	caC/caA	6/8	0.240583905580255	0	FACETS	0.072	0.057	0.089			1	INDETERMINATE	1	TRUE	0	0.640462124195055	0		710	453	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0002959-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	71	298	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.79	0.689	0.899	0.79	0.689	0.899	SUBCLONAL	1	TRUE	1	0.267885121594324	2		298	671	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061249	38061249	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002959-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	89	359	0	ENST00000250448.2:c.740A>G	p.His247Arg	p.H247R	ENST00000250448	NM_004496.3	247	cAc/cGc	2/2	0.14373879475184	3	FACETS	1	0.95	1	0.563	0.499	0.631	INDETERMINATE	1	TRUE	1	0.267885121594324	3		359	669	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265680	10265680	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002959-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	33	419	0	ENST00000340748.4:c.1497del	p.Phe499LeufsTer3	p.F499Lfs*3	ENST00000340748		499	ttT/tt	19/40	0.198544840285482	1	FACETS	0.331	0.268	0.402	0.331	0.268	0.402	SUBCLONAL	1	TRUE	0	0.267885121594324	1		419	645	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0002968-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	46	368	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.188740141776728	3	FACETS	0.557	0.468	0.657	0.279	0.234	0.329	SUBCLONAL	1	TRUE	1	0.222744730579315	3		368	824	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164058	47164058	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0002977-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	47	354	0	ENST00000409792.3:c.2068A>T	p.Lys690Ter	p.K690*	ENST00000409792	NM_014159.6	690	Aaa/Taa	3/21	0.382275031807383	1	FACETS	0.865	0.737	1	0.865	0.737	1	CLONAL	1	TRUE	0	0.382275031807383	1		354	230	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390690	139390690	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002977-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	96	399	0	ENST00000277541.6:c.7501C>T	p.Gln2501Ter	p.Q2501*	ENST00000277541	NM_017617.3	2501	Cag/Tag	34/34	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.382275031807383	2		399	478	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857046	9857046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774039446	NA	P-0002977-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	165	433	0	ENST00000330684.3:c.4355G>A	p.Arg1452His	p.R1452H	ENST00000330684	NM_001134407.1	1452	cGc/cAc	13/13	0.238968611131753	3	FACETS	0.944	0.88	1	1	0.99	1	CLONAL	3	TRUE	1	0.382275031807383	3		433	363	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163333	47163333	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002977-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	87	461	0	ENST00000409792.3:c.2793del	p.Val932Ter	p.V932*	ENST00000409792	NM_014159.6	931	gaA/ga	3/21	0.382275031807383	1	FACETS	0.841	0.759	0.924	1	0.985	1	CLONAL	2	TRUE	0	0.382275031807383	1		461	219	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0002982-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	360	409	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.51926289517294	4	FACETS	0.852	0.816	0.887	0.852	0.816	0.887	CLONAL	3	TRUE	1	0.778095570251211	4		409	644	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557310	187557310	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002982-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	193	470	0	ENST00000441802.2:c.4052C>A	p.Pro1351Gln	p.P1351Q	ENST00000441802	NM_005245.3	1351	cCg/cAg	6/27	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.778095570251211	2		470	456	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370951	55370951	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002982-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	161	353	1	ENST00000297316.4:c.253C>G	p.Arg85Gly	p.R85G	ENST00000297316	NM_022454.3	85	Cgg/Ggg	1/2	0.224384883574224	4	FACETS	0.968	0.9	1	0.968	0.9	1	INDETERMINATE	2	TRUE	2	0.778095570251211	4		354	380	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0003011-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	41	311	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	0.3	3	FACETS	0.534	0.444	0.635	0.267	0.222	0.318	SUBCLONAL	1	TRUE	1	0.28	3		311	625	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293457	1293457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003011-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	115	371	0	ENST00000310581.5:c.1544G>A	p.Arg515Gln	p.R515Q	ENST00000310581	NM_198253.2	515	cGg/cAg	2/16	0.19781371430588	4	FACETS	0.797	0.719	0.879	0.797	0.719	0.879	SUBCLONAL	2	TRUE	2	0.28	4		371	660	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911539	39911539	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003011-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	250	299	0	ENST00000378444.4:c.5091T>A	p.Phe1697Leu	p.F1697L	ENST00000378444	NM_001123385.1	1697	ttT/ttA	15/15	0.3	2	FACETS	0.985	0.929	1			1	CLONAL	3	TRUE	NA	0.28	2		299	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578505	7578505	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003011-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	173	369	0	ENST00000269305.4:c.425del	p.Pro142LeufsTer28	p.P142Lfs*28	ENST00000269305	NM_001126112.2	142	cCt/ct	5/11	0.282162597165969	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	0	0.28	2		369	615	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0003036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	237	315	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	0.945	0.89	1	0.945	0.89	1	CLONAL	1	TRUE	1	0.925633701003421	2		315	542	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0003037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	28	290	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		290	553	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0003074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	96	340	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.197577920625504	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.197577920625504	3		340	461	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0003074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	54	342	0	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.197577920625504	2		342	478	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0003074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	127	334	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.197577920625504	3	FACETS	0.907	0.826	0.992	1	0.983	1	CLONAL	3	TRUE	1	0.197577920625504	3		334	519	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419986	41419986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372989163	NA	P-0003074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	51	388	1	ENST00000373198.4:c.335G>A	p.Arg112His	p.R112H	ENST00000373198	NM_133170.3	112	cGt/cAt	3/32	0.197577920625504	3	FACETS	0.995	0.846	1	0.498	0.423	0.58	CLONAL	1	TRUE	1	0.197577920625504	3		389	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0003074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	56	244	1	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	0.197577920625504	2	FACETS	0.926	0.799	1	0.926	0.799	1	CLONAL	2	TRUE	0	0.197577920625504	2		245	306	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954221	48954221	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs1131690886	NA	P-0003074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	82	374	0	ENST00000267163.4:c.1421+1G>C		p.X474_splice	ENST00000267163	NM_000321.2	474			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.197577920625504	2		374	579	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930888	39930888	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0003074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	65	514	0	ENST00000378444.4:c.3051+2T>C		p.X1017_splice	ENST00000378444	NM_001123385.1	1017			0.0960936391178231	1	FACETS	1	0.927	1	1	0.927	1	INDETERMINATE	1	TRUE	0	0.197577920625504	1		514	538	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394820	394820	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003100-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	182	267	0	ENST00000399788.2:c.4875G>A	p.Trp1625Ter	p.W1625*	ENST00000399788	NM_001042603.1	1625	tgG/tgA	28/28	0.630710974092966	6	FACETS	1	0.98	1	0.397	0.366	0.43	CLONAL	1	TRUE	3	0.630710974092966	6		267	1095	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578415	7578415	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003100-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	164	149	0	ENST00000269305.4:c.515T>A	p.Val172Asp	p.V172D	ENST00000269305	NM_001126112.2	172	gTt/gAt	5/11	0.597723773416112	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.630710974092966	1		149	321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0003110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	288	344	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.425422407797702	5	FACETS	1	0.981	1			1	CLONAL	2	TRUE	NA	0.617199450148716	5		344	826	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0003110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	207	224	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.425422407797702	5	FACETS	1	0.949	1			1	CLONAL	2	TRUE	NA	0.617199450148716	5		224	633	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033738	48033738	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	47	222	0	ENST00000234420.5:c.3949C>A	p.His1317Asn	p.H1317N	ENST00000234420	NM_000179.2	1317	Cat/Aat	9/10	0.250354700225546	5	FACETS	0.446	0.376	0.525	0.149	0.125	0.175	INDETERMINATE	1	TRUE	2	0.617199450148716	5		222	657	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586388	189586388	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	219	115	0	ENST00000264731.3:c.1012C>A	p.Arg338Ser	p.R338S	ENST00000264731	NM_003722.4	338	Cgc/Agc	8/14	0.617199450148716	4	FACETS	0.915	0.864	0.966	0.915	0.864	0.966	CLONAL	3	TRUE	1	0.617199450148716	4		115	418	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564527	55564527	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	91	244	0	ENST00000288135.5:c.415A>G	p.Thr139Ala	p.T139A	ENST00000288135	NM_000222.2	139	Aca/Gca	3/21	0.173395420679332	3	FACETS	0.682	0.607	0.762			1	INDETERMINATE	1	TRUE	NA	0.617199450148716	3		244	566	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180050970	180050970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	112	295	0	ENST00000261937.6:c.1513G>A	p.Asp505Asn	p.D505N	ENST00000261937	NM_182925.4	505	Gac/Aac	11/30	NA	2	FACETS	0.611	0.551	0.674			1	INDETERMINATE	1	TRUE	NA	0.617199450148716	2		295	594	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418336	139418336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768517628	NA	P-0003110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	117	230	0	ENST00000277541.6:c.236G>A	p.Arg79His	p.R79H	ENST00000277541	NM_017617.3	79	cGc/cAc	3/34	0.456419228300595	3	FACETS	0.996	0.903	1	0.498	0.451	0.547	CLONAL	1	TRUE	1	0.617199450148716	3		230	498	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130244	2130244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45473098	NA	P-0003110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	308	282	0	ENST00000219476.3:c.3476G>A	p.Arg1159Gln	p.R1159Q	ENST00000219476	NM_000548.3	1159	cGg/cAg	30/42	0.531893642382642	3	FACETS	0.981	0.932	1	0.654	0.621	0.686	CLONAL	2	TRUE	0	0.617199450148716	3		282	666	SUCCESS
APC	324	MSKCC	GRCh37	5	112154935	112154935	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	300	221	0	ENST00000257430.4:c.1206del	p.Glu403LysfsTer51	p.E403Kfs*51	ENST00000257430	NM_000038.5	402	cgT/cg	10/16	0.431583957239272	3	FACETS	1	0.987	1	0.732	0.697	0.767	CLONAL	2	TRUE	0	0.617199450148716	3		221	579	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780013	9780013	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	62	351	0	ENST00000377346.4:c.1277T>C	p.Phe426Ser	p.F426S	ENST00000377346	NM_005026.3	426	tTt/tCt	10/24	0.277767307037524	1	FACETS	0.255	0.22	0.294	0.255	0.22	0.294	INDETERMINATE	1	TRUE	0	0.519513154397414	1		351	692	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804956	43804956	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	152	332	0	ENST00000372470.3:c.406C>A	p.Pro136Thr	p.P136T	ENST00000372470	NM_005373.2	136	Ccc/Acc	4/12	0.277767307037524	1	FACETS	0.703	0.646	0.763	0.703	0.646	0.763	INDETERMINATE	1	TRUE	0	0.519513154397414	1		332	616	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613133	52613133	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	220	368	0	ENST00000394830.3:c.3395G>A	p.Trp1132Ter	p.W1132*	ENST00000394830	NM_018313.4	1132	tGg/tAg	22/30	0.519513154397414	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.519513154397414	1		368	581	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97897777	97897779	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs3831244	NA	P-0003117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	30	253	0	ENST00000289081.3:c.692_694del	p.Lys231del	p.K231del	ENST00000289081	NM_000136.2	231	aAGAtt/att	8/15	0.436786642333403	1	FACETS	0.227	0.182	0.277	0.227	0.182	0.277	SUBCLONAL	1	TRUE	0	0.519513154397414	1		253	377	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441471	52441471	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	225	350	0	ENST00000460680.1:c.381del	p.Gly128AspfsTer59	p.G128Dfs*59	ENST00000460680	NM_004656.3	127	aaA/aa	6/17	0.519513154397414	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.519513154397414	1		350	577	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0003136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	21	450	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.270583992568217	3	FACETS	0.868	0.689	1	1	0.908	1	CLONAL	3	TRUE	1	0.256126181975694	3		451	71	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	13	296	0	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	0.270583992568217	1	FACETS	1	0.833	1	1	0.924	1	CLONAL	2	TRUE	0	0.256126181975694	1		296	38	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0003136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	11	267	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	0.254933654680278	2	FACETS	1	0.779	1	1	0.779	1	CLONAL	2	TRUE	0	0.256126181975694	2		267	39	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252866	36252866	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs759068561	NA	P-0003136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	11	309	0	ENST00000300305.3:c.496C>T	p.Arg166Ter	p.R166*	ENST00000300305		166	Cga/Tga	4/8	0.270583992568217	4	FACETS	0.884	0.624	1	0.884	0.624	1	CLONAL	2	TRUE	2	0.256126181975694	4		309	61	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513732	41513732	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	18	297	0	ENST00000263253.7:c.636G>T	p.Met212Ile	p.M212I	ENST00000263253	NM_001429.3	212	atG/atT	2/31	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.256126181975694	2		297	112	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0003143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	61	290	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.176951536241659	5	FACETS	0.972	0.838	1	0.324	0.279	0.373	CLONAL	1	TRUE	2	0.25	5		290	690	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934874	NA	P-0003143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	53	225	0	ENST00000269305.4:c.451C>G	p.Pro151Ala	p.P151A	ENST00000269305	NM_001126112.2	151	Ccc/Gcc	5/11	0.176951536241659	3	FACETS	1	0.959	1	0.685	0.587	0.792	CLONAL	1	TRUE	1	0.25	3		225	348	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117730774	117730774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145609658	NA	P-0003152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	188	374	3	ENST00000368508.3:c.260C>T	p.Ala87Val	p.A87V	ENST00000368508	NM_002944.2	87	gCg/gTg	4/43	0.458886511724032	1	FACETS	0.586	0.545	0.629	0.586	0.545	0.629	SUBCLONAL	1	TRUE	0	0.704964661658418	1		377	589	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503795	186503795	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	331	483	0	ENST00000323963.5:c.472G>C	p.Gly158Arg	p.G158R	ENST00000323963		158	Ggt/Cgt	5/11	0.474167455949011	6	FACETS	1	0.994	1	0.365	0.344	0.386	CLONAL	1	TRUE	2	0.704964661658418	6		483	1551	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665670	86665670	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	277	227	0	ENST00000274376.6:c.1651G>T	p.Glu551Ter	p.E551*	ENST00000274376	NM_002890.2	551	Gaa/Taa	12/25	NA	2	FACETS	0.804	0.765	0.841			1	INDETERMINATE	2	TRUE	NA	0.704964661658418	2		227	489	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955128	93955128	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	177	451	0	ENST00000369303.4:c.2770A>G	p.Thr924Ala	p.T924A	ENST00000369303	NM_004440.3	924	Acc/Gcc	16/17	0.535751647769658	1	FACETS	0.496	0.458	0.534	0.496	0.458	0.534	SUBCLONAL	1	TRUE	0	0.704964661658418	1		451	656	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455114	50455114	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	103	224	0	ENST00000331340.3:c.661G>C	p.Glu221Gln	p.E221Q	ENST00000331340	NM_006060.4	221	Gag/Cag	6/8	1	2	FACETS	0.814	0.735	0.896	0.814	0.735	0.896	CLONAL	1	TRUE	1	0.704964661658418	2		224	359	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007900	45007900	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0003152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	33	119	0	ENST00000558401.1:c.346+1G>C		p.X116_splice	ENST00000558401	NM_004048.2	116			0.704964661658418	1	FACETS	0.257	0.21	0.309	0.257	0.21	0.309	SUBCLONAL	1	TRUE	0	0.704964661658418	1		119	236	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	314	174	0	ENST00000269305.4:c.542G>C	p.Arg181Pro	p.R181P	ENST00000269305	NM_001126112.2	181	cGc/cCc	5/11	0.547501268100788	4	FACETS	0.879	0.847	0.909	0.879	0.847	0.909	CLONAL	4	TRUE	0	0.704964661658418	4		174	432	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145676	11145676	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	25	226	0	ENST00000358026.2:c.4038G>T	p.Trp1346Cys	p.W1346C	ENST00000358026	NM_001128849.1	1346	tgG/tgT	29/36	0.704964661658418	2	FACETS	0.206	0.162	0.256	0.103	0.081	0.128	SUBCLONAL	1	TRUE	0	0.704964661658418	2		226	345	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741602	145741637	+	inframe_deletion	In_Frame_Del	DEL	CCCCTGGAGGGTCTTCCTCAACTGCTACAGCCCCAG	CCCCTGGAGGGTCTTCCTCAACTGCTACAGCCCCAG	-	novel	NA	P-0003152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	33	308	0	ENST00000428558.2:c.866_901del	p.Ala289_Gly300del	p.A289_G300del	ENST00000428558	NM_004260.3	289	gCTGGGGCTGTAGCAGTTGAGGAAGACCCTCCAGGGGaa/gaa	5/22	0.49782446522894	4	FACETS	0.271	0.22	0.329	0.136	0.11	0.165	SUBCLONAL	1	TRUE	2	0.704964661658418	4		308	589	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881489	48881490	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs587778862	NA	P-0003152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	290	252	0	ENST00000267163.4:c.219_220del	p.Arg73SerfsTer36	p.R73Sfs*36	ENST00000267163	NM_000321.2	71	AGa/a	2/27	0.66344414278266	2	FACETS	1	0.994	1	0.722	0.686	0.757	CLONAL	1	TRUE	0	0.704964661658418	2		252	570	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225603	2225603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	23	268	0	ENST00000326181.6:c.1606G>A	p.Gly536Ser	p.G536S	ENST00000326181	NM_032271.2	536	Ggc/Agc	17/21	1	2	FACETS	0.412	0.321	0.516	0.412	0.321	0.516	SUBCLONAL	1	TRUE	1	0.38	2		268	294	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226320	2226320	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	101	290	0	ENST00000326181.6:c.1933A>C	p.Ser645Arg	p.S645R	ENST00000326181	NM_032271.2	645	Agt/Cgt	20/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.38	2		290	409	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807877	3807877	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	102	290	0	ENST00000262367.5:c.3542T>G	p.Leu1181Arg	p.L1181R	ENST00000262367	NM_004380.2	1181	cTt/cGt	18/31	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.38	2		290	533	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28929495	NA	P-0003169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	102	352	0	ENST00000275493.2:c.2155G>A	p.Gly719Ser	p.G719S	ENST00000275493	NM_005228.3	719	Ggc/Agc	18/28	0.286624919341831	3	FACETS	1	0.982	1	0.745	0.668	0.825	CLONAL	1	FALSE	1	0.3	3		352	525	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0003169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	115	323	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.286624919341831	3	FACETS	1	0.984	1	0.745	0.673	0.82	CLONAL	1	FALSE	1	0.3	3		323	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573996	7573996	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	40	514	0	ENST00000269305.4:c.1031T>G	p.Leu344Arg	p.L344R	ENST00000269305	NM_001126112.2	344	cTg/cGg	10/11	0.3	1	FACETS	0.351	0.291	0.418	0.351	0.291	0.418	SUBCLONAL	1	FALSE	0	0.3	1		514	646	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	74	169	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.203914960565928	4	FACETS	1	0.919	1	1	0.919	1	INDETERMINATE	2	TRUE	2	0.358187800129601	4		169	268	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	201	281	1	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	0.358187800129601	5	FACETS	0.857	0.798	0.918	0.857	0.798	0.918	CLONAL	3	TRUE	2	0.358187800129601	5		282	671	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	135	334	0	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	0.300310664135872	4	FACETS	1	0.956	1			1	CLONAL	2	TRUE	NA	0.358187800129601	4		334	479	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158456	26158456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs62623440	NA	P-0003179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	252	310	0	ENST00000289316.2:c.59C>T	p.Thr20Ile	p.T20I	ENST00000289316	NM_138720.2	20	aCt/aTt	1/2	0.358187800129601	9	FACETS	1	0.975	1			1	CLONAL	3	TRUE	NA	0.358187800129601	9		310	979	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93640003	93640003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	45	291	0	ENST00000375746.1:c.1332G>A	p.Trp444Ter	p.W444*	ENST00000375746	NM_001174167.1	444	tgG/tgA	10/14	NA	2	FACETS	0.582	0.489	0.683			1	INDETERMINATE	1	TRUE	NA	0.358187800129601	2		291	432	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134043	41134043	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	118	613	0	ENST00000379561.5:c.1585C>T	p.Gln529Ter	p.Q529*	ENST00000379561	NM_002015.3	529	Cag/Tag	2/3	0.364087987119097	3	FACETS	1	0.947	1	0.537	0.485	0.592	CLONAL	1	TRUE	1	0.358187800129601	3		613	723	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129396	30129396	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	263	482	1	ENST00000263025.4:c.632G>C	p.Arg211Pro	p.R211P	ENST00000263025	NM_002746.2	211	cGg/cCg	4/9	NA	2	FACETS	0.925	0.87	0.981			1	INDETERMINATE	2	TRUE	NA	0.358187800129601	2		483	794	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576888	7576888	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0003179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	218	294	0	ENST00000269305.4:c.958A>T	p.Lys320Ter	p.K320*	ENST00000269305	NM_001126112.2	320	Aag/Tag	9/11	0.35873725192969	2	FACETS	0.854	0.804	0.905	1	0.99	1	CLONAL	3	TRUE	0	0.358187800129601	2		294	475	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0003186-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	69	229	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.200513146303733	5	FACETS	0.81	0.706	0.921	0.27	0.235	0.307	INDETERMINATE	1	FALSE	2	0.647373188178996	5		229	519	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0003186-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	190	378	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.409388185368538	4	FACETS	0.888	0.82	0.959			1	CLONAL	1	FALSE	NA	0.647373188178996	4		379	1089	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003186-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	78	323	0	ENST00000322088.6:c.767C>A	p.Ser256Tyr	p.S256Y	ENST00000322088	NM_014225.5	256	tCc/tAc	6/15	NA	2	FACETS	0.591	0.522	0.664			1	INDETERMINATE	1	FALSE	NA	0.647373188178996	2		323	408	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0003192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	295	449	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.159247897434418	3	FACETS	0.921	0.866	0.976			1	CLONAL	3	TRUE	NA	0.2051958247948	3		449	1148	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149590	61149590	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	36	353	0	ENST00000295025.8:c.1780G>T	p.Asp594Tyr	p.D594Y	ENST00000295025	NM_002908.2	594	Gat/Tat	11/11	0.2051958247948	6	FACETS	0.777	0.637	0.934	0.194	0.159	0.234	CLONAL	1	TRUE	2	0.2051958247948	6		353	637	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455299	29455299	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763771560	NA	P-0003201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	54	193	0	ENST00000389048.3:c.2503C>T	p.Pro835Ser	p.P835S	ENST00000389048	NM_004304.4	835	Ccg/Tcg	15/29	NA	2	FACETS	1	0.961	1			1	INDETERMINATE	1	TRUE	NA	0.289745280659068	2		193	272	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845620	128845620	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	46	193	0	ENST00000249373.3:c.917C>A	p.Pro306His	p.P306H	ENST00000249373	NM_005631.4	306	cCc/cAc	4/12	0.256765304580283	4	FACETS	0.809	0.687	0.942	0.809	0.687	0.942	CLONAL	2	TRUE	2	0.289745280659068	4		193	253	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971003	21971003	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	35	215	0	ENST00000304494.5:c.355G>T	p.Glu119Ter	p.E119*	ENST00000304494	NM_000077.4	119	Gag/Tag	2/3	0.289745280659068	2	FACETS	1	0.916	1	0.595	0.492	0.708	CLONAL	1	TRUE	0	0.289745280659068	2		215	203	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325644	87325644	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	88	305	0	ENST00000277120.3:c.521T>C	p.Leu174Ser	p.L174S	ENST00000277120		174	tTg/tCg	6/19	0.289745280659068	2	FACETS	0.832	0.743	0.926	0.832	0.743	0.926	CLONAL	2	TRUE	0	0.289745280659068	2		305	365	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104389868	104389868	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	84	310	0	ENST00000369902.3:c.1411G>T	p.Val471Phe	p.V471F	ENST00000369902	NM_016169.3	471	Gtc/Ttc	12/12	0.252368837602903	4	FACETS	0.815	0.722	0.912			1	CLONAL	2	TRUE	NA	0.289745280659068	4		310	459	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919323	48919323	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	56	172	0	ENST00000267163.4:c.488G>T	p.Ser163Ile	p.S163I	ENST00000267163	NM_000321.2	163	aGc/aTc	4/27	0.254980960034298	3	FACETS	1	0.959	1			1	CLONAL	1	TRUE	NA	0.289745280659068	3		172	332	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2111998	2111998	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs45517157	NA	P-0003201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	59	201	0	ENST00000219476.3:c.1246G>T	p.Asp416Tyr	p.D416Y	ENST00000219476	NM_000548.3	416	Gac/Tac	12/42	0.192373765128002	2	FACETS	0.808	0.703	0.92	0.808	0.703	0.92	CLONAL	2	TRUE	0	0.289745280659068	2		201	252	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578433	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555526101	NA	P-0003201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	71	176	0	ENST00000269305.4:c.497C>G	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	166	tCa/tGa	5/11	0.165811559795766	3	FACETS	1	0.914	1	0.695	0.614	0.781	INDETERMINATE	2	TRUE	0	0.289745280659068	3		176	269	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097084	11097084	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	122	335	0	ENST00000358026.2:c.579del	p.Gln194SerfsTer109	p.Q194Sfs*109	ENST00000358026	NM_001128849.1	192	aGg/ag	4/36	0.289745280659068	3	FACETS	0.94	0.86	1	0.94	0.86	1	CLONAL	3	TRUE	0	0.289745280659068	3		335	342	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0003207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	109	449	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.348954713007743	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.349710959841279	2		449	283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0003216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	460	339	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.79748692908721	2	FACETS	0.981	0.955	1	0.981	0.955	1	CLONAL	2	TRUE	0	0.808529951018079	2		339	580	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751983	57751983	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0003216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	239	206	0	ENST00000274289.3:c.1255-1G>T		p.X419_splice	ENST00000274289	NM_006622.3	419			0.808529951018079	2	FACETS	1	0.987	1	0.578	0.546	0.611	CLONAL	1	TRUE	0	0.808529951018079	2		206	511	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742733	39742733	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003217-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	162	308	0	ENST00000361337.2:c.1576G>C	p.Glu526Gln	p.E526Q	ENST00000361337	NM_003286.2	526	Gag/Cag	15/21	0.461075444289804	5	FACETS	0.99	0.907	1	0.33	0.302	0.359	CLONAL	1	TRUE	2	0.510544914079145	5		308	1132	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742856	145742856	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854641	NA	P-0003217-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	27	142	0	ENST00000428558.2:c.155C>T	p.Thr52Met	p.T52M	ENST00000428558	NM_004260.3	52	aCg/aTg	3/22	0.258738097077871	5	FACETS	0.584	0.465	0.719	0.195	0.155	0.24	INDETERMINATE	1	TRUE	2	0.510544914079145	5		142	320	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57862002	57862002	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003217-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	136	307	1	ENST00000228682.2:c.1303G>A	p.Ala435Thr	p.A435T	ENST00000228682	NM_005269.2	435	Gcc/Acc	10/12	0.381626170619939	3	FACETS	0.9	0.819	0.985	0.45	0.409	0.493	CLONAL	1	TRUE	1	0.510544914079145	3		308	743	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991104	41991104	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003217-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	103	306	0	ENST00000219905.7:c.2057C>A	p.Ser686Tyr	p.S686Y	ENST00000219905	NM_001164273.1	686	tCt/tAt	4/24	0.249158175424866	4	FACETS	0.942	0.844	1	0.471	0.422	0.523	INDETERMINATE	1	TRUE	2	0.510544914079145	4		306	647	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849629	68849629	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003217-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	79	309	0	ENST00000261769.5:c.1532A>T	p.Gln511Leu	p.Q511L	ENST00000261769	NM_004360.3	511	cAg/cTg	10/16	0.510544914079145	2	FACETS	0.449	0.395	0.508	0.225	0.197	0.254	SUBCLONAL	1	TRUE	0	0.510544914079145	2		309	689	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101155	41101155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1328848371	NA	P-0003217-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	77	155	0	ENST00000373198.4:c.1201C>T	p.Arg401Trp	p.R401W	ENST00000373198	NM_133170.3	401	Cgg/Tgg	8/32	0.461075444289804	5	FACETS	0.983	0.864	1	0.328	0.288	0.37	CLONAL	1	TRUE	2	0.510544914079145	5		155	542	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920474	50920474	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	83	235	0	ENST00000440232.2:c.3166A>G	p.Thr1056Ala	p.T1056A	ENST00000440232	NM_002691.3	1056	Acg/Gcg	26/27	0.226906484208191	1	FACETS	0.575	0.511	0.642	0.575	0.511	0.642	INDETERMINATE	1	TRUE	0	0.573540467755843	1		235	359	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171680	36171682	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs771972670	NA	P-0003226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	54	197	0	ENST00000300305.3:c.883_885del	p.Ser295del	p.S295del	ENST00000300305		295	TCT/-	7/8	0.573540467755843	1	FACETS	0.39	0.335	0.451	0.39	0.335	0.451	SUBCLONAL	1	TRUE	0	0.573540467755843	1		197	344	SUCCESS
APC	324	MSKCC	GRCh37	5	112175934	112175941	+	frameshift_variant	Frame_Shift_Del	DEL	ACCAAGAG	ACCAAGAG	-	novel	NA	P-0003226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	112	196	0	ENST00000257430.4:c.4644_4651del	p.Asn1548LysfsTer8	p.N1548Kfs*8	ENST00000257430	NM_000038.5	1548	aACCAAGAG/a	16/16	0.573540467755843	1	FACETS	0.824	0.75	0.901	0.824	0.75	0.901	CLONAL	1	TRUE	0	0.573540467755843	1		196	338	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	10	169	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.305399709394694	3	FACETS	0.759	0.52	1	0.379	0.26	0.526	CLONAL	1	TRUE	1	0.366918598419061	3		169	85	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047037	128047037	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	14	357	0	ENST00000285398.2:c.698C>A	p.Ser233Tyr	p.S233Y	ENST00000285398	NM_000122.1	233	tCc/tAc	6/15	1	2	FACETS	1	0.83	1	1	0.83	1	CLONAL	1	TRUE	1	0.366918598419061	2		357	65	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271460	26271460	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	35	554	0	ENST00000305910.3:c.153G>C	p.Glu51Asp	p.E51D	ENST00000305910	NM_003534.2	51	gaG/gaC	1/1	0.366918598419061	6	FACETS	1	0.9	1	0.745	0.62	0.88	CLONAL	2	TRUE	3	0.366918598419061	6		554	148	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874425	151874425	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	15	312	0	ENST00000262189.6:c.8113G>C	p.Glu2705Gln	p.E2705Q	ENST00000262189	NM_170606.2	2705	Gag/Cag	38/59	0.313357938415651	1	FACETS	0.71	0.527	0.923	0.71	0.527	0.923	CLONAL	1	TRUE	0	0.366918598419061	1		312	94	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955578	48955578	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0003233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	22	240	0	ENST00000267163.4:c.1694C>G	p.Ser565Ter	p.S565*	ENST00000267163	NM_000321.2	565	tCa/tGa	17/27	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.366918598419061	2		240	86	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103513946	103513946	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	11	279	0	ENST00000355739.4:c.762G>A	p.Met254Ile	p.M254I	ENST00000355739	NM_000123.3	254	atG/atA	7/15	1	2	FACETS	0.625	0.436	0.854	0.625	0.436	0.854	SUBCLONAL	1	TRUE	1	0.366918598419061	2		279	96	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647508	23647508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1251150895	NA	P-0003233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	14	295	0	ENST00000261584.4:c.359G>A	p.Arg120Lys	p.R120K	ENST00000261584	NM_024675.3	120	aGa/aAa	4/13	NA	2	FACETS	1	0.777	1			1	INDETERMINATE	1	TRUE	NA	0.366918598419061	2		295	72	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867343	68867343	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142927667	NA	P-0003233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	10	297	0	ENST00000261769.5:c.2590G>A	p.Glu864Lys	p.E864K	ENST00000261769	NM_004360.3	864	Gaa/Aaa	16/16	0.366918598419061	0	FACETS	0.704	0.49	0.957			1	CLONAL	1	TRUE	0	0.366918598419061	0		297	49	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41489079	41489079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373061594	NA	P-0003233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	29	231	0	ENST00000263253.7:c.71C>T	p.Ser24Leu	p.S24L	ENST00000263253	NM_001429.3	24	tCg/tTg	1/31	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.366918598419061	2		231	124	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849304	76849304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	21	426	0	ENST00000373344.5:c.5972C>T	p.Ser1991Phe	p.S1991F	ENST00000373344	NM_000489.3	1991	tCt/tTt	26/35	0.347838481397441	0	FACETS	0.594	0.475	0.721			1	SUBCLONAL	2	TRUE	0	0.366918598419061	0		426	61	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	12	140	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.461	0.323	0.631	0.461	0.323	0.631	SUBCLONAL	1	TRUE	1	0.19	2		142	274	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857508	68857508	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	55	195	0	ENST00000261769.5:c.2143G>T	p.Gly715Ter	p.G715*	ENST00000261769	NM_004360.3	715	Gga/Tga	13/16	1	2	FACETS	0.96	0.821	1	0.96	0.821	1	CLONAL	1	TRUE	1	0.19	2		195	603	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252888	36252896	+	inframe_deletion	In_Frame_Del	DEL	AAATCTTGC	AAATCTTGC	-	novel	NA	P-0003236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	84	266	0	ENST00000300305.3:c.466_474del	p.Ala156_Phe158del	p.A156_F158del	ENST00000300305		156	GCAAGATTT/-	4/8	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.19	2		266	816	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0003241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	48	160	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.145094828663327	3	FACETS	1	0.943	1	0.595	0.513	0.681	INDETERMINATE	1	TRUE	1	0.728616750890407	3		160	151	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712018	89712018	+	splice_donor_variant	Splice_Site	SNP	T	T	G	rs727504114	NA	P-0003241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	27	134	0	ENST00000371953.3:c.634+2T>G		p.X212_splice	ENST00000371953	NM_000314.4	212			0.145094828663327	3	FACETS	0.829	0.671	1	0.414	0.335	0.502	INDETERMINATE	1	TRUE	1	0.728616750890407	3		134	122	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842680	68842692	+	frameshift_variant	Frame_Shift_Del	DEL	ATTATTGAAAGAG	ATTATTGAAAGAG	GTT	novel	NA	P-0003241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	210	509	0	ENST00000261769.5:c.616_628delinsGTT	p.Ile206ValfsTer6	p.I206Vfs*6	ENST00000261769	NM_004360.3	206	ATTATTGAAAGAGaa/GTTaa	5/16	0.728616750890407	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.728616750890407	1		509	325	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691025	NA	P-0003244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	374	284	0	ENST00000269305.4:c.785G>T	p.Gly262Val	p.G262V	ENST00000269305	NM_001126112.2	262	gGt/gTt	8/11	0.448739003648777	2	FACETS	0.907	0.865	0.949	0.907	0.865	0.949	CLONAL	2	TRUE	0	0.479304169168844	2		284	860	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736316	243736316	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1487	156	340	0	ENST00000263826.5:c.731C>T	p.Ser244Phe	p.S244F	ENST00000263826	NM_005465.4	244	tCt/tTt	8/13	0.479304169168844	6	FACETS	0.776	0.708	0.848			1	SUBCLONAL	1	TRUE	NA	0.479304169168844	6		340	1643	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760404	133760404	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	97	227	0	ENST00000318560.5:c.2727G>T	p.Lys909Asn	p.K909N	ENST00000318560	NM_005157.4	909	aaG/aaT	11/11	0.479304169168844	5	FACETS	0.633	0.563	0.708			1	SUBCLONAL	1	TRUE	NA	0.479304169168844	5		227	1099	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760362	133760416	+	frameshift_variant	Frame_Shift_Del	DEL	CAAACCTGCCCCGCCGCCCCCACCAGCAGCCTCTGCAGGGAAGGCTGGAGGAAAG	CAAACCTGCCCCGCCGCCCCCACCAGCAGCCTCTGCAGGGAAGGCTGGAGGAAAG	-	novel	NA	P-0003244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	234	210	0	ENST00000318560.5:c.2686_2740del	p.Lys896ProfsTer28	p.K896Pfs*28	ENST00000318560	NM_005157.4	895	ctCAAACCTGCCCCGCCGCCCCCACCAGCAGCCTCTGCAGGGAAGGCTGGAGGAAAG/ct	11/11	0.479304169168844	5	FACETS	0.784	0.731	0.839			1	SUBCLONAL	2	TRUE	NA	0.479304169168844	5		210	1070	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271572	26271572	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	226	406	0	ENST00000305910.3:c.41del	p.Gly14AlafsTer23	p.G14Afs*23	ENST00000305910	NM_003534.2	14	gGc/gc	1/1	0.479304169168844	3	FACETS	0.867	0.806	0.931	0.434	0.403	0.466	CLONAL	1	TRUE	1	0.479304169168844	3		406	1348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0003258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	182	418	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.273591991760826	2	FACETS	0.967	0.895	1	0.967	0.895	1	CLONAL	2	TRUE	0	0.28398870552313	2		418	663	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137522064	137522064	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	52	258	0	ENST00000367739.4:c.815A>C	p.Lys272Thr	p.K272T	ENST00000367739	NM_000416.2	272	aAa/aCa	6/7	0.129765992456907	3	FACETS	1	0.91	1	0.364	0.311	0.422	INDETERMINATE	1	TRUE	0	0.28398870552313	3		258	383	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567686	226567686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1276677693	NA	P-0003258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	52	474	0	ENST00000366794.5:c.1480G>A	p.Ala494Thr	p.A494T	ENST00000366794	NM_001618.3	494	Gcc/Acc	10/23	0.28398870552313	3	FACETS	0.817	0.696	0.949	0.272	0.232	0.317	CLONAL	1	TRUE	0	0.28398870552313	3		474	512	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168613	32168613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	51	377	0	ENST00000375023.3:c.4310G>A	p.Gly1437Glu	p.G1437E	ENST00000375023	NM_004557.3	1437	gGg/gAg	23/30	0.254583177689086	3	FACETS	1	0.888	1	0.525	0.447	0.609	CLONAL	1	TRUE	1	0.28398870552313	3		377	391	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15365053	15365053	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	72	387	0	ENST00000263377.2:c.2068G>T	p.Ala690Ser	p.A690S	ENST00000263377	NM_058243.2	690	Gcc/Tcc	11/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.28398870552313	2		387	457	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410274	63410274	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	52	545	0	ENST00000330258.3:c.2893C>T	p.Pro965Ser	p.P965S	ENST00000330258	NM_152424.3	965	Cct/Tct	2/2	0.28398870552313	1	FACETS	0.656	0.559	0.762	0.656	0.559	0.762	SUBCLONAL	1	TRUE	0	0.28398870552313	1		545	479	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412400	63412400	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	75	739	0	ENST00000330258.3:c.767A>G	p.Lys256Arg	p.K256R	ENST00000330258	NM_152424.3	256	aAa/aGa	2/2	0.28398870552313	1	FACETS	0.675	0.592	0.766	0.675	0.592	0.766	SUBCLONAL	1	TRUE	0	0.28398870552313	1		739	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0003259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	98	351	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.25058762167187	2	FACETS	1	0.956	1	0.564	0.504	0.626	CLONAL	1	TRUE	0	0.33	2		351	527	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0003259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	140	225	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.25058762167187	2	FACETS	1	0.984	1	0.674	0.616	0.735	CLONAL	1	TRUE	0	0.33	2		225	629	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346550	81346550	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs148293411	NA	P-0003259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	110	386	0	ENST00000222390.5:c.1403G>A	p.Arg468His	p.R468H	ENST00000222390	NM_000601.4	468	cGt/cAt	11/18	0.261443990569154	3	FACETS	1	0.982	1	0.718	0.647	0.792	CLONAL	1	TRUE	1	0.33	3		386	541	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945961	17945961	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	161	585	0	ENST00000458235.1:c.1978G>C	p.Ala660Pro	p.A660P	ENST00000458235	NM_000215.3	660	Gct/Cct	15/24	0.261443990569154	3	FACETS	0.86	0.791	0.931	0.86	0.791	0.931	CLONAL	2	TRUE	1	0.33	3		585	661	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28631580	28631580	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	233	215	0	ENST00000241453.7:c.388A>T	p.Ile130Phe	p.I130F	ENST00000241453	NM_004119.2	130	Att/Ttt	4/24	0.928073041415253	2	FACETS	0.916	0.863	0.97			1	CLONAL	1	TRUE	NA	0.94	2		215	541	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0003275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	96	290	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA	2	FACETS	1	0.943	1			1	INDETERMINATE	1	TRUE	NA	0.2	2		290	878	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246548	41246548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	67	424	0	ENST00000357654.3:c.1000C>T	p.Pro334Ser	p.P334S	ENST00000357654	NM_007294.3	334	Ccc/Tcc	10/23	0.3	1	FACETS	0.792	0.688	0.906	0.792	0.688	0.906	CLONAL	1	TRUE	0	0.2	1		424	761	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176338	24176338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	64	321	1	ENST00000263121.7:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000263121	NM_003073.3	377	Cgt/Tgt	9/9	1	2	FACETS	0.808	0.698	0.927	0.808	0.698	0.927	CLONAL	1	TRUE	1	0.2	2		322	792	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003284-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	8	140	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.321	0.206	0.471	0.321	0.206	0.471	SUBCLONAL	1	TRUE	1	0.2	2		142	249	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374944	45374944	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003284-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	47	306	0	ENST00000262160.6:c.899A>G	p.Asp300Gly	p.D300G	ENST00000262160	NM_005901.5	300	gAt/gGt	8/11	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.2	2		306	439	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121913370	NA	P-0003284-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	28	188	0	ENST00000288602.6:c.1742A>G	p.Asn581Ser	p.N581S	ENST00000288602	NM_004333.4	581	aAt/aGt	15/18	1	2	FACETS	0.946	0.758	1	0.946	0.758	1	CLONAL	1	TRUE	1	0.2	2		188	296	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106861	27106861	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003284-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	71	232	1	ENST00000324856.7:c.6472C>T	p.Arg2158Ter	p.R2158*	ENST00000324856	NM_006015.4	2158	Cga/Tga	20/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.2	2		233	546	SUCCESS
APC	324	MSKCC	GRCh37	5	112170647	112170647	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003284-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	28	250	0	ENST00000257430.4:c.1744-1G>A		p.X582_splice	ENST00000257430	NM_000038.5	582			1	2	FACETS	0.753	0.602	0.925	0.753	0.602	0.925	CLONAL	1	TRUE	1	0.2	2		250	372	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905466	11905466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144209028	NA	P-0003284-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	34	192	0	ENST00000396373.4:c.116G>A	p.Arg39Gln	p.R39Q	ENST00000396373	NM_001987.4	39	cGa/cAa	2/8	0.127546060967048	0	FACETS	0.485	0.395	0.586			1	SUBCLONAL	1	TRUE	0	0.2	0		192	561	SUCCESS
APC	324	MSKCC	GRCh37	5	112176029	112176029	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0003284-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	26	245	0	ENST00000257430.4:c.4738del	p.Ile1580PhefsTer70	p.I1580Ffs*70	ENST00000257430	NM_000038.5	1580	Att/tt	16/16	1	2	FACETS	0.657	0.52	0.814	0.657	0.52	0.814	SUBCLONAL	1	TRUE	1	0.2	2		245	396	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482760	67482761	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0003284-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	95	397	0	ENST00000327367.4:c.1166_1167del	p.Val389AspfsTer8	p.V389Dfs*8	ENST00000327367	NM_005902.3	388	acTGtg/actg	9/9	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.2	2		397	679	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0003301-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	69	340	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.17	2		340	658	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0003301-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	38	165	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	1	2	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	TRUE	1	0.17	2		165	439	SUCCESS
APC	324	MSKCC	GRCh37	5	112175360	112175360	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003301-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	28	257	0	ENST00000257430.4:c.4069G>T	p.Gly1357Ter	p.G1357*	ENST00000257430	NM_000038.5	1357	Gga/Tga	16/16	1	2	FACETS	0.734	0.586	0.903	0.734	0.586	0.903	CLONAL	1	TRUE	1	0.17	2		257	449	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014355	70014355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752915964	NA	P-0003301-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1249	67	650	0	ENST00000394351.3:c.1216C>T	p.Arg406Trp	p.R406W	ENST00000394351	NM_000248.3	406	Cgg/Tgg	9/9	1	2	FACETS	0.599	0.518	0.687	0.599	0.518	0.687	SUBCLONAL	1	TRUE	1	0.17	2		650	1316	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0003314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	73	450	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.803	0.703	0.91	0.803	0.703	0.91	CLONAL	1	TRUE	1	0.341781993964027	2		451	532	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0003314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	13	181	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	1	2	FACETS	0.181	0.128	0.246	0.181	0.128	0.246	SUBCLONAL	1	TRUE	1	0.341781993964027	2		181	420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057519990	NA	P-0003314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	120	407	0	ENST00000269305.4:c.796G>T	p.Gly266Ter	p.G266*	ENST00000269305	NM_001126112.2	266	Gga/Tga	8/11	0.304355890264046	1	FACETS	0.951	0.861	1	0.951	0.861	1	CLONAL	1	TRUE	0	0.341781993964027	1		407	612	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363178	40363178	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	123	239	0	ENST00000397332.2:c.1051G>C	p.Val351Leu	p.V351L	ENST00000397332	NM_001033082.2	351	Gtg/Ctg	3/3	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.341781993964027	2		239	645	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666423	206666423	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	207	202	0	ENST00000367120.3:c.1903G>T	p.Ala635Ser	p.A635S	ENST00000367120	NM_014002.3	635	Gcc/Tcc	19/22	0.242353628785428	4	FACETS	1	0.987	1	0.832	0.776	0.89	CLONAL	2	TRUE	1	0.341781993964027	4		202	651	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361159	66361159	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	83	202	0	ENST00000273854.3:c.1013G>T	p.Cys338Phe	p.C338F	ENST00000273854	NM_004439.5	338	tGt/tTt	4/18	1	2	FACETS	0.89	0.787	0.999	0.89	0.787	0.999	CLONAL	1	TRUE	1	0.341781993964027	2		202	546	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943451	17943451	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	117	242	0	ENST00000458235.1:c.2557G>T	p.Ala853Ser	p.A853S	ENST00000458235	NM_000215.3	853	Gcc/Tcc	19/24	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.341781993964027	2		242	656	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966724	44966724	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	96	280	0	ENST00000377967.4:c.3948G>T	p.Glu1316Asp	p.E1316D	ENST00000377967	NM_021140.2	1316	gaG/gaT	27/29	1	2	FACETS	0.913	0.815	1	0.913	0.815	1	CLONAL	1	TRUE	1	0.341781993964027	2		280	615	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941669	48941670	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0003314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	75	154	0	ENST00000267163.4:c.982_983del	p.Asn328Ter	p.N328*	ENST00000267163	NM_000321.2	327	AAa/a	10/27	0.304355890264046	1	FACETS	0.848	0.746	0.957	0.848	0.746	0.957	CLONAL	1	TRUE	0	0.341781993964027	1		154	429	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0003322-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	17	288	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.189	0.14	0.248	0.189	0.14	0.248	SUBCLONAL	1	TRUE	1	0.230903549527761	2		288	778	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0003322-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	70	329	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	1	2	FACETS	0.849	0.74	0.968	0.849	0.74	0.968	CLONAL	1	TRUE	1	0.230903549527761	2		329	714	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242483	55242506	+	inframe_deletion	In_Frame_Del	DEL	ATCTCCGAAAGCCAACAAGGAAAT	ATCTCCGAAAGCCAACAAGGAAAT	-	rs727504232	NA	P-0003322-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	75	262	0	ENST00000275493.2:c.2253_2276del	p.Ser752_Ile759del	p.S752_I759del	ENST00000275493	NM_005228.3	751	acATCTCCGAAAGCCAACAAGGAAATc/acc	19/28	0.230903549527761	7	FACETS	1	0.966	1			1	CLONAL	1	TRUE	NA	0.230903549527761	7		262	777	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0003324-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	44	308	1	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.674	0.564	0.796	0.674	0.564	0.796	SUBCLONAL	1	TRUE	1	0.21	2		309	622	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0003324-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	57	290	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.808	0.692	0.934	0.808	0.692	0.934	CLONAL	1	TRUE	1	0.21	2		290	672	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966967	25966967	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003324-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	27	343	0	ENST00000435504.4:c.2239G>T	p.Gly747Cys	p.G747C	ENST00000435504		747	Ggt/Tgt	13/13	1	2	FACETS	0.494	0.392	0.611	0.494	0.392	0.611	SUBCLONAL	1	TRUE	1	0.21	2		343	521	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959010	2959010	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003324-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	22	245	0	ENST00000396946.4:c.2506A>T	p.Ser836Cys	p.S836C	ENST00000396946	NM_032415.4	836	Agc/Tgc	18/25	0.0869114041161068	3	FACETS	0.555	0.429	0.702	0.278	0.214	0.351	INDETERMINATE	1	TRUE	1	0.21	3		245	417	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140508735	140508735	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003324-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	65	341	0	ENST00000288602.6:c.565G>T	p.Gly189Cys	p.G189C	ENST00000288602	NM_004333.4	189	Ggt/Tgt	4/18	0.183984806926598	3	FACETS	1	0.949	1	0.399	0.346	0.456	CLONAL	1	TRUE	0	0.21	3		341	572	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0003330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	129	409	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.983	0.898	1	0.983	0.898	1	CLONAL	1	TRUE	1	0.565536292815224	2		409	464	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0003334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	135	450	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.33387729914445	1	FACETS	1	0.985	1	1	0.985	1	INDETERMINATE	1	TRUE	0	0.608718979745846	1		451	248	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0003334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	317	164	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	2	TRUE	NA	0.608718979745846	2		164	506	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443345	187443345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	181	260	1	ENST00000232014.4:c.1781G>A	p.Arg594Gln	p.R594Q	ENST00000232014	NM_001130845.1	594	cGa/cAa	8/10	0.290664620208057	4	FACETS	0.797	0.739	0.857			1	INDETERMINATE	2	TRUE	NA	0.608718979745846	4		261	600	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650073	206650073	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	187	268	0	ENST00000367120.3:c.593T>A	p.Phe198Tyr	p.F198Y	ENST00000367120	NM_014002.3	198	tTc/tAc	7/22	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.608718979745846	2		268	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0003344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	473	717	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.721057405857648	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.721057405857648	2		718	618	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343153	118343153	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142138730	NA	P-0003344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	150	339	0	ENST00000534358.1:c.1279C>T	p.Arg427Trp	p.R427W	ENST00000534358	NM_005933.3	427	Cgg/Tgg	3/36	0.721057405857648	3	FACETS	1	0.95	1	0.523	0.481	0.567	CLONAL	1	TRUE	1	0.721057405857648	3		339	541	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244082	153244082	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	200	371	0	ENST00000281708.4:c.2075C>G	p.Thr692Ser	p.T692S	ENST00000281708	NM_033632.3	692	aCt/aGt	12/12	0.721057405857648	3	FACETS	1	0.983	1	0.391	0.364	0.418	CLONAL	1	TRUE	0	0.721057405857648	3		371	644	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271237	1271237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757820442	NA	P-0003344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	78	284	0	ENST00000310581.5:c.2465G>A	p.Gly822Asp	p.G822D	ENST00000310581	NM_198253.2	822	gGc/gAc	8/16	NA	2	FACETS	0.792	0.705	0.884			1	INDETERMINATE	1	TRUE	NA	0.721057405857648	2		284	273	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630233	100630233	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	233	242	1	ENST00000308731.7:c.40T>C	p.Ser14Pro	p.S14P	ENST00000308731	NM_000061.2	14	Tcc/Ccc	2/19	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.721057405857648	1		243	317	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102080268	102080269	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0003344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	216	405	0	ENST00000282441.5:c.1005_1006del	p.Ser336HisfsTer14	p.S336Hfs*14	ENST00000282441	NM_001130145.2	335	ccCAgc/ccgc	6/9	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.721057405857648	2		405	551	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469484	25469499	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTACCTTCTGGTGGC	TTTACCTTCTGGTGGC	-	novel	NA	P-0003344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	222	301	0	ENST00000264709.3:c.1269_1279+5del		p.X423_splice	ENST00000264709	NM_175629.2	423		10/23	0.686246803576066	4	FACETS	0.901	0.845	0.958	0.901	0.845	0.958	CLONAL	2	TRUE	2	0.721057405857648	4		301	588	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781340	135781340	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	208	607	0	ENST00000298552.3:c.1625A>C	p.Lys542Thr	p.K542T	ENST00000298552	NM_001162426.1	542	aAg/aCg	15/23	1	2	FACETS	0.967	0.897	1	0.967	0.897	1	CLONAL	1	TRUE	1	0.387748405247424	2		607	1109	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101387	27101394	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTCTGC	CCCTCTGC	-	novel	NA	P-0003345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	103	300	0	ENST00000324856.7:c.4673_4680del	p.Ser1558CysfsTer11	p.S1558Cfs*11	ENST00000324856	NM_006015.4	1557	CCCTCTGCc/c	18/20	1	2	FACETS	0.729	0.652	0.81	0.729	0.652	0.81	SUBCLONAL	1	TRUE	1	0.387748405247424	2		300	729	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063328	67063345	+	inframe_deletion	In_Frame_Del	DEL	CGACCAGAGAAGCAAGTT	CGACCAGAGAAGCAAGTT	-	novel	NA	P-0003345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	56	214	0	ENST00000412916.2:c.21_38del	p.Asp7_Phe12del	p.D7_F12del	ENST00000412916		6	ccCGACCAGAGAAGCAAGTTc/ccc	1/6	0.387748405247424	1	FACETS	0.693	0.597	0.797	0.693	0.597	0.797	SUBCLONAL	1	TRUE	0	0.387748405247424	1		214	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0003364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	127	211	0	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	0.273361307890479	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	2	TRUE	0	0.330678547218715	2		211	382	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741812	145741812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1001434106	NA	P-0003364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	387	430	0	ENST00000428558.2:c.691G>A	p.Gly231Ser	p.G231S	ENST00000428558	NM_004260.3	231	Ggt/Agt	5/22	0.270814095010339	4	FACETS	1	0.989	1			1	CLONAL	3	TRUE	NA	0.330678547218715	4		430	937	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873679	35873679	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	108	488	0	ENST00000216797.5:c.172G>C	p.Glu58Gln	p.E58Q	ENST00000216797	NM_020529.2	58	Gag/Cag	1/6	1	2	FACETS	0.787	0.706	0.873	0.787	0.706	0.873	SUBCLONAL	1	TRUE	1	0.330678547218715	2		488	830	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442757	99442757	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	111	338	0	ENST00000268035.6:c.1154C>G	p.Thr385Arg	p.T385R	ENST00000268035	NM_000875.3	385	aCg/aGg	5/21	0.165349968991269	3	FACETS	1	0.912	1			1	INDETERMINATE	1	TRUE	NA	0.330678547218715	3		338	770	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76764029	76764029	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	53	494	0	ENST00000373344.5:c.7279A>G	p.Thr2427Ala	p.T2427A	ENST00000373344	NM_000489.3	2427	Act/Gct	35/35	0.234582156722847	1	FACETS	0.346	0.294	0.403	0.346	0.294	0.403	SUBCLONAL	1	TRUE	0	0.330678547218715	1		494	774	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418718	49418741	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GATTCCACACGGCTAAGAAGCAGG	GATTCCACACGGCTAAGAAGCAGG	-	novel	NA	P-0003364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	60	201	0	ENST00000301067.7:c.15785-12_15796del		p.X5262_splice	ENST00000301067	NM_003482.3	5262		49/54	1	2	FACETS	0.856	0.74	0.982	0.856	0.74	0.982	CLONAL	1	TRUE	1	0.330678547218715	2		201	424	SUCCESS
ATR	545	MSKCC	GRCh37	3	142218520	142218523	+	frameshift_variant	Frame_Shift_Del	DEL	CTTC	CTTC	-	novel	NA	P-0003364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	67	390	0	ENST00000350721.4:c.5326_5329del	p.Glu1776GlnfsTer47	p.E1776Qfs*47	ENST00000350721	NM_001184.3	1776	GAAGca/ca	31/47	NA	2	FACETS	0.475	0.412	0.544			1	INDETERMINATE	1	TRUE	NA	0.330678547218715	2		390	853	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143994	11143994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003381-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	107	299	1	ENST00000358026.2:c.3575G>A	p.Arg1192His	p.R1192H	ENST00000358026	NM_001128849.1	1192	cGc/cAc	26/36	1	2	FACETS	0.924	0.836	1	0.924	0.836	1	CLONAL	1	TRUE	1	0.598527465847958	2		300	387	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941715	48941716	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0003381-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	101	269	0	ENST00000267163.4:c.1027_1028del	p.Leu343SerfsTer3	p.L343Sfs*3	ENST00000267163	NM_000321.2	342	aCT/a	10/27	0.598527465847958	1	FACETS	0.957	0.872	1	0.957	0.872	1	CLONAL	1	TRUE	0	0.598527465847958	1		269	247	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578245	7578245	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780072	NA	P-0003390-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	8	519	0	ENST00000269305.4:c.604C>T	p.Arg202Cys	p.R202C	ENST00000269305	NM_001126112.2	202	Cgt/Tgt	6/11	NA	2	FACETS	0.386	0.248	0.566			1	INDETERMINATE	1	TRUE	NA	0.177157077879151	2		519	234	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433068	49433074	+	frameshift_variant	Frame_Shift_Del	DEL	CTAGGGA	CTAGGGA	-	novel	NA	P-0003390-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	63	474	0	ENST00000301067.7:c.8297_8303del	p.Phe2766SerfsTer19	p.F2766Sfs*19	ENST00000301067	NM_003482.3	2766	tTCCCTAGc/tc	33/54	1				0.736	0.958				CLONAL	3	TRUE	1	0.177157077879151	2		474	281	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618887	37618887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747496820	NA	P-0003398-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	110	290	0	ENST00000447079.4:c.563G>A	p.Arg188Gln	p.R188Q	ENST00000447079	NM_015083.1	188	cGg/cAg	1/14	1	2	FACETS	0.915	0.836	0.996	0.915	0.836	0.996	CLONAL	1	TRUE	1	0.877099595249008	2		290	274	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0003401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	209	332	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.139734430012153	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.2	3		332	968	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191492	10191492	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397516444	NA	P-0003406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	96	334	0	ENST00000256474.2:c.485G>A	p.Cys162Tyr	p.C162Y	ENST00000256474	NM_000551.3	162	tGc/tAc	3/3	0.535598645452059	1	FACETS	0.833	0.752	0.917	0.833	0.752	0.917	CLONAL	1	TRUE	0	0.563330711883046	1		334	294	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239927	53239927	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782012138	NA	P-0003406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	142	309	0	ENST00000375401.3:c.1514G>A	p.Gly505Asp	p.G505D	ENST00000375401	NM_004187.3	505	gGc/gAc	11/26	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.563330711883046	1		309	278	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199835	108199835	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	122	298	0	ENST00000278616.4:c.7180del	p.Ser2394GlnfsTer12	p.S2394Qfs*12	ENST00000278616	NM_000051.3	2393	Ttt/tt	49/63	1	2	FACETS	0.942	0.857	1	0.942	0.857	1	CLONAL	1	TRUE	1	0.563330711883046	2		298	460	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0003437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	115	340	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.99	0.891	1	0.99	0.891	1	CLONAL	1	TRUE	1	0.279626642197895	2		340	831	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0003437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	242	493	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.236316085966998	2	FACETS	0.776	0.725	0.829	0.776	0.725	0.829	SUBCLONAL	2	TRUE	0	0.279626642197895	2		494	1115	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0003437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	89	373	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	0.747	0.661	0.839	0.747	0.661	0.839	SUBCLONAL	1	TRUE	1	0.279626642197895	2		373	852	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0003437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	77	163	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	0.279626642197895	2		163	523	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048131	180048131	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	52	413	0	ENST00000261937.6:c.2142C>A	p.Asp714Glu	p.D714E	ENST00000261937	NM_182925.4	714	gaC/gaA	14/30	1	2	FACETS	0.392	0.332	0.458	0.392	0.332	0.458	SUBCLONAL	1	TRUE	1	0.279626642197895	2		413	949	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895656	28895656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	137	408	0	ENST00000282397.4:c.3118G>A	p.Asp1040Asn	p.D1040N	ENST00000282397	NM_002019.4	1040	Gat/Aat	23/30	0.279626642197895	4	FACETS	0.924	0.838	1	0.308	0.279	0.339	CLONAL	1	TRUE	1	0.279626642197895	4		408	1357	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0003444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	1356	290	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.515118994342165	6	FACETS	0.985	0.965	1			1	CLONAL	5	TRUE	NA	0.515118994342165	6		290	2170	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0003444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	278	466	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.487884126835956	1	FACETS	0.967	0.911	1	0.967	0.911	1	CLONAL	1	TRUE	0	0.515118994342165	1		466	829	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750437	41750437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	181	314	0	ENST00000226382.2:c.191C>T	p.Ser64Phe	p.S64F	ENST00000226382	NM_003924.3	64	tCc/tTc	1/3	1	2	FACETS	0.994	0.92	1	0.994	0.92	1	CLONAL	1	TRUE	1	0.515118994342165	2		314	707	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845320	156845320	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	158	545	0	ENST00000524377.1:c.1363G>C	p.Val455Leu	p.V455L	ENST00000524377	NM_002529.3	455	Gtg/Ctg	12/17	1	2	FACETS	0.573	0.524	0.624	0.573	0.524	0.624	SUBCLONAL	1	TRUE	1	0.515118994342165	2		545	1071	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097307	178097307	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	128	227	0	ENST00000397062.3:c.407C>G	p.Ser136Cys	p.S136C	ENST00000397062	NM_006164.4	136	tCt/tGt	4/5	1	2	FACETS	0.852	0.775	0.933	0.852	0.775	0.933	CLONAL	1	TRUE	1	0.515118994342165	2		227	583	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199889	108199889	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	82	292	0	ENST00000278616.4:c.7231G>A	p.Glu2411Lys	p.E2411K	ENST00000278616	NM_000051.3	2411	Gaa/Aaa	49/63	NA	2	FACETS	0.428	0.377	0.483			1	INDETERMINATE	1	TRUE	NA	0.515118994342165	2		292	743	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199922	108199922	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	69	261	0	ENST00000278616.4:c.7264G>C	p.Glu2422Gln	p.E2422Q	ENST00000278616	NM_000051.3	2422	Gag/Cag	49/63	NA	2	FACETS	0.426	0.371	0.486			1	INDETERMINATE	1	TRUE	NA	0.515118994342165	2		261	629	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040911	47040911	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs782684857	NA	P-0003444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	182	200	0	ENST00000377604.3:c.1441G>T	p.Glu481Ter	p.E481*	ENST00000377604	NM_001204468.1	481	Gag/Tag	14/24	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.515118994342165	1		200	419	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781057	135781058	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs118203599	NA	P-0003444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	303	640	0	ENST00000298552.3:c.1907_1908del	p.Glu636GlyfsTer51	p.E636Gfs*51	ENST00000298552	NM_001162426.1	636	gAG/g	15/23	0.515118994342165	1	FACETS	0.889	0.839	0.94	0.889	0.839	0.94	CLONAL	1	TRUE	0	0.515118994342165	1		640	982	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517963	187517963	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	97	301	0	ENST00000441802.2:c.12731A>C	p.Asp4244Ala	p.D4244A	ENST00000441802	NM_005245.3	4244	gAc/gCc	25/27	0.736957414303842	2	FACETS	0.453	0.405	0.504	0.227	0.202	0.252	SUBCLONAL	1	TRUE	0	0.736957414303842	2		301	581	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334837	81334838	+	missense_variant	Missense_Mutation	DNP	CA	CA	AT	novel	NA	P-0003462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	184	305	1	ENST00000222390.5:c.1878_1879delinsAT	p.Asp626_Gly627delinsGluCys	p.D626_G627delinsEC	ENST00000222390	NM_000601.4	626	gaTGgc/gaATgc	17/18	1	2	FACETS	0.881	0.818	0.945	0.881	0.818	0.945	CLONAL	1	TRUE	1	0.736957414303842	2		306	567	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92354983	92354983	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	165	297	0	ENST00000265734.4:c.494G>T	p.Gly165Val	p.G165V	ENST00000265734	NM_001259.6	165	gGc/gTc	4/8	1	2	FACETS	0.905	0.837	0.974	0.905	0.837	0.974	CLONAL	1	TRUE	1	0.736957414303842	2		297	495	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207675	102207675	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	382	500	0	ENST00000263464.3:c.1657G>T	p.Glu553Ter	p.E553*	ENST00000263464	NM_001165.4	553	Gaa/Taa	9/9	0.389935130373629	1	FACETS	0.826	0.789	0.862	0.826	0.789	0.862	INDETERMINATE	1	TRUE	0	0.736957414303842	1		500	793	SUCCESS
ATM	472	MSKCC	GRCh37	11	108154953	108154953	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0003462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	103	142	0	ENST00000278616.4:c.3747-1G>T		p.X1249_splice	ENST00000278616	NM_000051.3	1249			0.389935130373629	1	FACETS	0.671	0.611	0.733	0.671	0.611	0.733	INDETERMINATE	1	TRUE	0	0.736957414303842	1		142	263	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109870	115109871	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0003462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	75	107	0	ENST00000257566.3:c.2007_2008delinsAA	p.Leu670Met	p.L670M	ENST00000257566	NM_016569.3	669	ccCCtg/ccAAtg	8/8	0.389935130373629	1	FACETS	1	0.955	1	1	0.955	1	INDETERMINATE	1	TRUE	0	0.736957414303842	1		107	120	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112187	115112187	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	121	258	0	ENST00000257566.3:c.1553T>G	p.Leu518Arg	p.L518R	ENST00000257566	NM_016569.3	518	cTc/cGc	7/8	0.389935130373629	1	FACETS	0.816	0.753	0.88	0.816	0.753	0.88	INDETERMINATE	1	TRUE	0	0.736957414303842	1		258	254	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225535	133225535	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	99	285	0	ENST00000320574.5:c.4129G>T	p.Glu1377Ter	p.E1377*	ENST00000320574	NM_006231.2	1377	Gag/Tag	32/49	0.389935130373629	1	FACETS	0.396	0.356	0.439	0.396	0.356	0.439	INDETERMINATE	1	TRUE	0	0.736957414303842	1		285	428	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782177	NA	P-0003462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	363	436	0	ENST00000269305.4:c.644G>T	p.Ser215Ile	p.S215I	ENST00000269305	NM_001126112.2	215	aGt/aTt	6/11	NA	2	FACETS	0.926	0.893	0.958			1	INDETERMINATE	2	TRUE	NA	0.736957414303842	2		436	532	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63545761	63545761	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	161	315	2	ENST00000307078.5:c.833A>T	p.Asp278Val	p.D278V	ENST00000307078	NM_004655.3	278	gAt/gTt	3/11	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.736957414303842	2		317	427	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145486	24145486	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	160	289	0	ENST00000263121.7:c.505G>C	p.Asp169His	p.D169H	ENST00000263121	NM_003073.3	169	Gat/Cat	5/9	0.736957414303842	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.736957414303842	1		289	270	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720726	89720726	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	44	41	0	ENST00000371953.3:c.878del	p.Gly293GlufsTer14	p.G293Efs*14	ENST00000371953	NM_000314.4	293	Gga/ga	8/9	0.736957414303842	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.736957414303842	1		41	69	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663692	117663692	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	25	241	0	ENST00000368508.3:c.4540A>G	p.Ile1514Val	p.I1514V	ENST00000368508	NM_002944.2	1514	Ata/Gta	28/43	1	2	FACETS	0.137	0.107	0.171	0.137	0.107	0.171	SUBCLONAL	1	TRUE	1	0.8	2		241	456	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190503	32190503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003472-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	119	323	0	ENST00000375023.3:c.236G>A	p.Ser79Asn	p.S79N	ENST00000375023	NM_004557.3	79	aGc/aAc	3/30	0.33502581932243	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.33502581932243	1		323	429	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0003479-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	324	440	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.375158707239372	9	FACETS	1	0.972	1	0.693	0.656	0.731	CLONAL	4	FALSE	3	0.375158707239372	9		440	961	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719175	61719175	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003479-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	52	471	0	ENST00000401558.2:c.1882C>T	p.Gln628Ter	p.Q628*	ENST00000401558	NM_003400.3	628	Caa/Taa	16/25	0.37602780171587	4	FACETS	0.451	0.383	0.527			1	SUBCLONAL	1	FALSE	NA	0.375158707239372	4		471	845	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012596	36012596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003479-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	31	258	0	ENST00000358208.4:c.40C>T	p.Arg14Trp	p.R14W	ENST00000358208		14	Cgg/Tgg	2/12	0.375158707239372	5	FACETS	0.561	0.453	0.684			1	SUBCLONAL	1	FALSE	NA	0.375158707239372	5		258	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577572	7577572	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003479-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	114	381	0	ENST00000269305.4:c.709del	p.Met237CysfsTer10	p.M237Cfs*10	ENST00000269305	NM_001126112.2	237	Atg/tg	7/11	0.37602780171587	3	FACETS	0.986	0.897	1			1	CLONAL	2	FALSE	NA	0.375158707239372	3		381	366	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712568	52712593	+	frameshift_variant	Frame_Shift_Del	DEL	CCTTATAGTCTCGGATGGTATTATAG	CCTTATAGTCTCGGATGGTATTATAG	-	novel	NA	P-0003488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	115	313	0	ENST00000394830.3:c.159_184del	p.Tyr54Ter	p.Y54*	ENST00000394830	NM_018313.4	53	ctCTATAATACCATCCGAGACTATAAGGat/ctat	3/30	0.564099045829886	2	FACETS	1	0.981	1	0.629	0.577	0.682	CLONAL	1	TRUE	0	0.68227803391341	2		313	268	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153438	108153438	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	45	244	0	ENST00000278616.4:c.3581del	p.Leu1194Ter	p.L1194*	ENST00000278616	NM_000051.3	1193	gTt/gt	25/63	NA	2	FACETS	0.505	0.428	0.59			1	INDETERMINATE	1	TRUE	NA	0.68227803391341	2		244	261	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832590	72832591	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0003488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	47	330	2	ENST00000268489.5:c.3990_3991delinsTT	p.Lys1330_Asn1331delinsAsnTyr	p.K1330_N1331delinsNY	ENST00000268489	NM_006885.3	1330	aaGAac/aaTTac	9/10	0.297274221790787	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.68227803391341	0		332	156	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0003489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	26	259	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.322	0.254	0.401	0.322	0.254	0.401	SUBCLONAL	1	TRUE	1	0.20174056751671	2		259	800	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0003489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	174	315	2	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	1	0.947	1	1	0.993	1	CLONAL	2	TRUE	1	0.20174056751671	2		317	833	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0003489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	57	407	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.20174056751671	1	FACETS	0.656	0.561	0.759	0.656	0.561	0.759	SUBCLONAL	1	TRUE	0	0.20174056751671	1		407	775	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748072	72748072	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	49	534	0	ENST00000357731.5:c.106C>T	p.Gln36Ter	p.Q36*	ENST00000357731	NM_173808.2	36	Cag/Tag	1/7	1	2	FACETS	0.533	0.45	0.625	0.533	0.45	0.625	SUBCLONAL	1	TRUE	1	0.20174056751671	2		534	911	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142949	47142949	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	82	271	1	ENST00000409792.3:c.5014G>T	p.Gly1672Ter	p.G1672*	ENST00000409792	NM_014159.6	1672	Gga/Tga	8/21	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.20174056751671	2		272	720	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052606	42052606	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	85	474	0	ENST00000219905.7:c.7277G>T	p.Arg2426Leu	p.R2426L	ENST00000219905	NM_001164273.1	2426	cGg/cTg	20/24	0.20174056751671	1	FACETS	0.658	0.58	0.743	0.658	0.58	0.743	SUBCLONAL	1	TRUE	0	0.20174056751671	1		474	1151	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23652447	23652447	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs750720488	NA	P-0003489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	36	350	0	ENST00000261584.4:c.32G>T	p.Cys11Phe	p.C11F	ENST00000261584	NM_024675.3	11	tGt/tTt	1/13	1	2	FACETS	0.564	0.462	0.678	0.564	0.462	0.678	SUBCLONAL	1	TRUE	1	0.20174056751671	2		350	633	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864483	56864483	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	151	478	0	ENST00000308159.5:c.971A>G	p.Tyr324Cys	p.Y324C	ENST00000308159	NM_014669.4	324	tAc/tGc	10/22	0.20174056751671	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.20174056751671	1		478	1185	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929255	44929255	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	69	246	0	ENST00000377967.4:c.2355G>T	p.Met785Ile	p.M785I	ENST00000377967	NM_021140.2	785	atG/atT	17/29	0.168813373384338	2	FACETS	0.996	0.867	1			1	CLONAL	1	TRUE	NA	0.20174056751671	2		246	687	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0003500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	328	495	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.935	0.884	0.987	0.935	0.884	0.987	CLONAL	1	TRUE	1	0.613229432952929	2		496	1144	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894228	NA	P-0003500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	462	378	0	ENST00000451590.1:c.37G>C	p.Gly13Arg	p.G13R	ENST00000451590	NM_001130442.1	13	Ggt/Cgt	2/5	0.381102063238134	1	FACETS	0.992	0.951	1	0.992	0.951	1	CLONAL	1	TRUE	0	0.613229432952929	1		378	1053	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549644	187549644	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	176	289	0	ENST00000441802.2:c.4597A>G	p.Met1533Val	p.M1533V	ENST00000441802	NM_005245.3	1533	Atg/Gtg	8/27	NA	2	FACETS	0.983	0.911	1			1	INDETERMINATE	1	TRUE	NA	0.613229432952929	2		289	584	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276900	123276900	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	230	488	0	ENST00000358487.5:c.1017A>C	p.Glu339Asp	p.E339D	ENST00000358487	NM_000141.4	339	gaA/gaC	8/18	0.613229432952929	1	FACETS	0.586	0.547	0.627	0.586	0.547	0.627	SUBCLONAL	1	TRUE	0	0.613229432952929	1		488	887	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019738	123019738	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	358	239	0	ENST00000355640.3:c.227del	p.Gly76GlufsTer54	p.G76Efs*54	ENST00000355640		76	Gga/ga	2/7	1	1	FACETS	0.85	0.808	0.893	0.85	0.808	0.893	CLONAL	1	TRUE	0	0.613229432952929	1		239	952	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821509	72821510	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0003500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	305	536	0	ENST00000268489.5:c.10665_10666del	p.His3555GlnfsTer15	p.H3555Qfs*15	ENST00000268489	NM_006885.3	3555	caCAga/caga	10/10	1	2	FACETS	0.89	0.839	0.942	0.89	0.839	0.942	CLONAL	1	TRUE	1	0.613229432952929	2		536	1118	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437206	52437206	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35448940	NA	P-0003504-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	127	445	0	ENST00000460680.1:c.1838C>T	p.Thr613Met	p.T613M	ENST00000460680	NM_004656.3	613	aCg/aTg	14/17	0.474810059691157	3	FACETS	0.942	0.854	1	0.471	0.427	0.517	CLONAL	1	TRUE	1	0.474810059691157	3		445	703	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061208	38061208	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003504-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	57	188	0	ENST00000250448.2:c.781C>A	p.Arg261Ser	p.R261S	ENST00000250448	NM_004496.3	261	Cgc/Agc	2/2	1	2	FACETS	0.854	0.739	0.978	0.854	0.739	0.978	CLONAL	1	TRUE	1	0.474810059691157	2		188	281	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731631	47731631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003504-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	32	61	0	ENST00000449228.1:c.161G>A	p.Arg54Gln	p.R54Q	ENST00000449228	NM_001127240.2	54	cGa/cAa	2/4	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.474810059691157	2		61	101	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0003510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	124	450	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.261876185937215	4	FACETS	1	0.973	1	0.591	0.537	0.647	INDETERMINATE	1	FALSE	2	0.670471698415353	4		451	523	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0003510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	54	482	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.327	0.28	0.38	0.327	0.28	0.38	SUBCLONAL	1	FALSE	1	0.670471698415353	2		482	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578496	7578496	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	78	326	0	ENST00000269305.4:c.434T>G	p.Leu145Arg	p.L145R	ENST00000269305	NM_001126112.2	145	cTg/cGg	5/11	0.16956229036539	2	FACETS	0.705	0.625	0.79	0.353	0.312	0.395	INDETERMINATE	1	FALSE	0	0.670471698415353	2		326	330	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874812	151874812	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	83	322	0	ENST00000262189.6:c.7726del	p.Ala2576LeufsTer7	p.A2576Lfs*7	ENST00000262189	NM_170606.2	2576	Gct/ct	38/59	0.208538273738707	3	FACETS	0.719	0.637	0.806	0.359	0.318	0.403	INDETERMINATE	1	FALSE	1	0.670471698415353	3		322	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782144	NA	P-0003511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	64	261	0	ENST00000269305.4:c.473G>C	p.Arg158Pro	p.R158P	ENST00000269305	NM_001126112.2	158	cGc/cCc	5/11	1	2	FACETS	0.792	0.69	0.901	1	0.974	1	CLONAL	2	TRUE	1	0.236879076617561	2		261	341	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164812	106164812	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	21	270	0	ENST00000380013.4:c.3680T>C	p.Val1227Ala	p.V1227A	ENST00000380013	NM_001127208.2	1227	gTg/gCg	6/11	0.236879076617561	1	FACETS	0.418	0.321	0.531	0.418	0.321	0.531	SUBCLONAL	1	TRUE	0	0.236879076617561	1		270	374	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923210	26923210	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0003511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	152	395	0	ENST00000381527.3:c.206T>G	p.Leu69Ter	p.L69*	ENST00000381527	NM_001260.1	69	tTa/tGa	3/13	1	2	FACETS	1	0.972	1	1	0.992	1	CLONAL	2	TRUE	1	0.236879076617561	2		395	569	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923033	44923033	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	31	271	0	ENST00000377967.4:c.1894T>A	p.Trp632Arg	p.W632R	ENST00000377967	NM_021140.2	632	Tgg/Agg	16/29	1	1	FACETS	0.669	0.542	0.812	0.669	0.542	0.812	SUBCLONAL	1	TRUE	0	0.236879076617561	1		271	345	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115927	8115928	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0003511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	30	291	0	ENST00000346208.3:c.1273_1274delinsAT	p.Pro425Ile	p.P425I	ENST00000346208		425	CCa/ATa	6/6	0.236879076617561	3	FACETS	0.657	0.529	0.803	0.329	0.264	0.402	SUBCLONAL	1	TRUE	1	0.236879076617561	3		291	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0003518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	135	229	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.509802766763389	1	FACETS	0.812	0.756	0.867	1	0.991	1	CLONAL	2	TRUE	0	0.509802766763389	1		229	243	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0003518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	119	355	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.509802766763389	2		355	448	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16062133	16062133	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	101	486	0	ENST00000268712.3:c.673C>A	p.Pro225Thr	p.P225T	ENST00000268712	NM_006311.3	225	Cct/Act	6/46	0.509802766763389	1	FACETS	0.677	0.609	0.749	0.677	0.609	0.749	SUBCLONAL	1	TRUE	0	0.509802766763389	1		486	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576875	7576875	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	264	265	0	ENST00000269305.4:c.971A>C	p.Asp324Ala	p.D324A	ENST00000269305	NM_001126112.2	324	gAt/gCt	9/11	0.843323570032185	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.843101040958796	1		265	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576869	7576870	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0003535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	257	260	0	ENST00000269305.4:c.976_977del	p.Glu326IlefsTer10	p.E326Ifs*10	ENST00000269305	NM_001126112.2	326	GAa/a	9/11	0.843323570032185	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.843101040958796	1		260	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520006	NA	P-0003538-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	92	474	0	ENST00000269305.4:c.821T>C	p.Val274Ala	p.V274A	ENST00000269305	NM_001126112.2	274	gTt/gCt	8/11	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.28800225479881	2		474	627	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932083	36932083	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003538-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	90	436	0	ENST00000361632.4:c.2386C>T	p.Pro796Ser	p.P796S	ENST00000361632		796	Ccc/Tcc	16/16	0.28800225479881	3	FACETS	1	0.908	1	0.513	0.455	0.575	CLONAL	1	TRUE	1	0.28800225479881	3		436	697	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024488	16024488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568152376	NA	P-0003538-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	85	359	0	ENST00000268712.3:c.1730G>A	p.Ser577Asn	p.S577N	ENST00000268712	NM_006311.3	577	aGt/aAt	16/46	1	2	FACETS	0.938	0.83	1	0.938	0.83	1	CLONAL	1	TRUE	1	0.28800225479881	2		359	629	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0003544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	289	378	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	0.922	0.888	0.955			1	INDETERMINATE	2	TRUE	NA	0.787394556581172	2		379	398	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191513	10191513	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1131690962	NA	P-0003546-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	130	294	0	ENST00000256474.2:c.506T>C	p.Leu169Pro	p.L169P	ENST00000256474	NM_000551.3	169	cTa/cCa	3/3	0.556039831220205	1	FACETS	0.947	0.87	1	0.947	0.87	1	CLONAL	1	TRUE	0	0.565816333932012	1		294	348	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164757	47164757	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003546-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	117	215	0	ENST00000409792.3:c.1369G>T	p.Glu457Ter	p.E457*	ENST00000409792	NM_014159.6	457	Gag/Tag	3/21	0.556039831220205	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.565816333932012	1		215	280	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609061	43609061	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003546-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	271	635	0	ENST00000355710.3:c.1817A>T	p.Tyr606Phe	p.Y606F	ENST00000355710	NM_020975.4	606	tAt/tTt	10/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.565816333932012	2		635	797	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406490	70406490	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003546-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	160	302	0	ENST00000373644.4:c.4004C>T	p.Pro1335Leu	p.P1335L	ENST00000373644	NM_030625.2	1335	cCa/cTa	4/12	1	2	FACETS	0.992	0.915	1	0.992	0.915	1	CLONAL	1	TRUE	1	0.565816333932012	2		302	570	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915518	112915518	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003546-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	222	418	0	ENST00000351677.2:c.917A>G	p.Asn306Ser	p.N306S	ENST00000351677	NM_002834.3	306	aAt/aGt	8/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.565816333932012	2		418	739	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624937	9624937	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003546-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	182	343	0	ENST00000353224.5:c.40C>G	p.Pro14Ala	p.P14A	ENST00000353224	NM_177990.2	14	Ccg/Gcg	3/10	1	2	FACETS	0.922	0.853	0.992	0.922	0.853	0.992	CLONAL	1	TRUE	1	0.565816333932012	2		343	698	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598129	52598139	+	frameshift_variant	Frame_Shift_Del	DEL	AATTTCTTCAT	AATTTCTTCAT	-	novel	NA	P-0003546-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	199	436	0	ENST00000394830.3:c.3727_3737del	p.Met1243GlnfsTer11	p.M1243Qfs*11	ENST00000394830	NM_018313.4	1243	ATGAAGAAATTc/c	24/30	0.556039831220205	1	FACETS	0.968	0.905	1	0.968	0.905	1	CLONAL	1	TRUE	0	0.565816333932012	1		436	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	411	401	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.838453540204121	2		401	475	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	339	239	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	0.838453540204121	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.838453540204121	3		239	528	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066446	94066446	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	596	403	0	ENST00000369303.4:c.1313C>A	p.Thr438Asn	p.T438N	ENST00000369303	NM_004440.3	438	aCt/aAt	5/17	0.838453540204121	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.838453540204121	2		403	707	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166597	118166597	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	137	137	0	ENST00000369448.3:c.1107C>A	p.Ser369Arg	p.S369R	ENST00000369448	NM_017709.3	369	agC/agA	2/2	0.432892107572702	3	FACETS	1	0.987	1	0.688	0.635	0.742	INDETERMINATE	1	TRUE	1	0.838453540204121	3		137	337	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226576371	226576371	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	240	397	1	ENST00000366794.5:c.703G>T	p.Glu235Ter	p.E235*	ENST00000366794	NM_001618.3	235	Gaa/Taa	5/23	0.838453540204121	4	FACETS	0.952	0.888	1	0.317	0.296	0.339	CLONAL	1	TRUE	1	0.838453540204121	4		398	1106	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727024	243727024	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	258	206	0	ENST00000263826.5:c.946G>T	p.Glu316Ter	p.E316*	ENST00000263826	NM_005465.4	316	Gag/Tag	9/13	0.838453540204121	4	FACETS	1	0.987	1	0.4	0.374	0.425	CLONAL	1	TRUE	1	0.838453540204121	4		206	944	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449859	29449859	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1376365612	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	407	383	0	ENST00000389048.3:c.2996C>A	p.Pro999His	p.P999H	ENST00000389048	NM_004304.4	999	cCt/cAt	18/29	0.838453540204121	3	FACETS	0.941	0.904	0.978	0.941	0.904	0.978	CLONAL	2	TRUE	1	0.838453540204121	3		383	732	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519758	29519758	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	261	256	0	ENST00000389048.3:c.1813G>C	p.Asp605His	p.D605H	ENST00000389048	NM_004304.4	605	Gac/Cac	9/29	0.838453540204121	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.838453540204121	3		256	428	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281560	198281560	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	209	272	1	ENST00000335508.6:c.571C>T	p.Gln191Ter	p.Q191*	ENST00000335508	NM_012433.2	191	Cag/Tag	6/25	0.838453540204121	3	FACETS	0.92	0.857	0.985	0.46	0.428	0.493	CLONAL	1	TRUE	1	0.838453540204121	3		273	769	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578260	212578260	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs768893584	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	530	334	0	ENST00000342788.4:c.997G>T	p.Ala333Ser	p.A333S	ENST00000342788	NM_005235.2	333	Gct/Tct	8/28	0.838453540204121	3	FACETS	0.958	0.926	0.991	0.958	0.926	0.991	CLONAL	2	TRUE	1	0.838453540204121	3		334	936	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795126	242795126	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	125	140	0	ENST00000334409.5:c.83C>A	p.Pro28Gln	p.P28Q	ENST00000334409	NM_005018.2	28	cCa/cAa	2/5	0.570277297159883	3	FACETS	1	0.946	1			1	CLONAL	2	TRUE	NA	0.838453540204121	3		140	208	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231276	142231276	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	413	311	0	ENST00000350721.4:c.4678G>T	p.Asp1560Tyr	p.D1560Y	ENST00000350721	NM_001184.3	1560	Gat/Tat	27/47	0.814232460140683	3	FACETS	0.93	0.893	0.966	0.93	0.893	0.966	CLONAL	2	TRUE	1	0.838453540204121	3		311	752	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447214	187447214	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1016920638	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	130	191	0	ENST00000232014.4:c.979G>T	p.Gly327Cys	p.G327C	ENST00000232014	NM_001130845.1	327	Ggt/Tgt	5/10	0.838453540204121	3	FACETS	0.887	0.81	0.968	0.444	0.405	0.484	CLONAL	1	TRUE	1	0.838453540204121	3		191	496	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604182	189604182	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	234	270	0	ENST00000264731.3:c.1350-1G>A		p.X450_splice	ENST00000264731	NM_003722.4	450			0.838453540204121	3	FACETS	0.979	0.916	1	0.49	0.458	0.522	CLONAL	1	TRUE	1	0.838453540204121	3		270	809	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467476	66467476	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	363	269	0	ENST00000273854.3:c.793C>G	p.His265Asp	p.H265D	ENST00000273854	NM_004439.5	265	Cat/Gat	3/18	0.828746063569121	2	FACETS	0.982	0.955	1	0.982	0.955	1	CLONAL	2	TRUE	0	0.838453540204121	2		269	441	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510091	187510091	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	353	245	0	ENST00000441802.2:c.13422G>T	p.Leu4474Phe	p.L4474F	ENST00000441802	NM_005245.3	4474	ttG/ttT	27/27	0.828746063569121	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.838453540204121	2		245	407	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047936	180047936	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs774978737	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	197	257	0	ENST00000261937.6:c.2239C>A	p.Leu747Met	p.L747M	ENST00000261937	NM_182925.4	747	Ctg/Atg	15/30	0.814232460140683	3	FACETS	0.921	0.868	0.974	0.921	0.868	0.974	CLONAL	2	TRUE	1	0.838453540204121	3		257	362	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271309	26271309	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	677	786	0	ENST00000305910.3:c.304G>T	p.Val102Leu	p.V102L	ENST00000305910	NM_003534.2	102	Gtg/Ttg	1/1	0.513898920567021	6	FACETS	0.971	0.938	1	0.971	0.938	1	CLONAL	3	TRUE	3	0.838453540204121	6		786	1484	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778179	27778179	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	760	825	3	ENST00000369163.2:c.328C>G	p.Leu110Val	p.L110V	ENST00000369163	NM_003536.2	110	Ctg/Gtg	1/1	0.513898920567021	6	FACETS	0.952	0.921	0.983	0.952	0.921	0.983	CLONAL	3	TRUE	3	0.838453540204121	6		828	1699	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956509	93956509	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	535	403	2	ENST00000369303.4:c.2726+1G>T		p.X909_splice	ENST00000369303	NM_004440.3	909			0.838453540204121	2	FACETS	0.991	0.969	1	0.991	0.969	1	CLONAL	2	TRUE	0	0.838453540204121	2		405	644	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004745	150004745	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1342174778	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	347	233	2	ENST00000253339.5:c.1480A>G	p.Ile494Val	p.I494V	ENST00000253339		494	Att/Gtt	3/7	0.838453540204121	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.838453540204121	2		235	400	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860435	151860435	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	526	307	0	ENST00000262189.6:c.10227G>C	p.Glu3409Asp	p.E3409D	ENST00000262189	NM_170606.2	3409	gaG/gaC	43/59	0.802669533404959	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	2	0.838453540204121	4		307	1077	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759848	133759848	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	219	253	0	ENST00000318560.5:c.2171A>G	p.His724Arg	p.H724R	ENST00000318560	NM_005157.4	724	cAt/cGt	11/11	0.828746063569121	2	FACETS	1	0.983	1	0.558	0.525	0.591	CLONAL	1	TRUE	0	0.838453540204121	2		253	468	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998680	100998680	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	714	521	2	ENST00000325455.5:c.1122C>A	p.Tyr374Ter	p.Y374*	ENST00000325455	NM_001202474.3	374	taC/taA	1/8	0.810194603457829	5	FACETS	0.981	0.952	1	0.981	0.952	1	CLONAL	3	TRUE	2	0.838453540204121	5		523	1306	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150312	108150312	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	310	213	0	ENST00000278616.4:c.3379G>T	p.Ala1127Ser	p.A1127S	ENST00000278616	NM_000051.3	1127	Gct/Tct	23/63	0.810194603457829	5	FACETS	0.879	0.83	0.928	0.586	0.553	0.619	CLONAL	2	TRUE	2	0.838453540204121	5		213	950	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534713	18534713	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	322	204	2	ENST00000266497.5:c.1771G>T	p.Gly591Trp	p.G591W	ENST00000266497		591	Ggg/Tgg	12/31	0.802669533404959	4	FACETS	0.959	0.912	1	0.959	0.912	1	CLONAL	2	TRUE	2	0.838453540204121	4		206	736	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246315	46246315	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	430	263	0	ENST00000334344.6:c.4409C>A	p.Ser1470Ter	p.S1470*	ENST00000334344	NM_152641.2	1470	tCa/tAa	15/21	0.812672599119608	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.838453540204121	2		263	504	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415848	49415848	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	342	292	0	ENST00000301067.7:c.16499G>T	p.Arg5500Leu	p.R5500L	ENST00000301067	NM_003482.3	5500	cGg/cTg	53/54	0.812672599119608	2	FACETS	0.96	0.931	0.986	0.96	0.931	0.986	CLONAL	2	TRUE	0	0.838453540204121	2		292	425	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861998	57861998	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	387	420	0	ENST00000228682.2:c.1299G>T	p.Glu433Asp	p.E433D	ENST00000228682	NM_005269.2	433	gaG/gaT	10/12	0.812672599119608	2	FACETS	0.999	0.974	1	0.999	0.974	1	CLONAL	2	TRUE	0	0.838453540204121	2		420	462	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858348	9858348	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	187	200	0	ENST00000330684.3:c.3053T>A	p.Val1018Glu	p.V1018E	ENST00000330684	NM_001134407.1	1018	gTg/gAg	13/13	0.838453540204121	2	FACETS	0.996	0.959	1	0.996	0.959	1	CLONAL	2	TRUE	0	0.838453540204121	2		200	224	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556073	29556073	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	348	187	0	ENST00000356175.3:c.2440A>T	p.Lys814Ter	p.K814*	ENST00000356175	NM_000267.3	814	Aag/Tag	21/57	0.838453540204121	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.838453540204121	2		187	412	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39570424	39570424	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	338	168	0	ENST00000262039.4:c.620G>T	p.Ser207Ile	p.S207I	ENST00000262039	NM_002647.2	207	aGt/aTt	6/25	0.828746063569121	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.838453540204121	2		168	389	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191227	2191227	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	215	258	0	ENST00000398665.3:c.481G>T	p.Asp161Tyr	p.D161Y	ENST00000398665	NM_032482.2	161	Gac/Tac	5/28	0.828203635197136	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.838453540204121	2		258	255	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026137	36026137	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	125	345	1	ENST00000358208.4:c.739G>T	p.Val247Leu	p.V247L	ENST00000358208		247	Gtg/Ttg	7/12	0.838453540204121	3	FACETS	0.815	0.742	0.892	0.408	0.371	0.446	CLONAL	1	TRUE	1	0.838453540204121	3		346	519	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40864893	40864893	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	406	273	0	ENST00000373198.4:c.2375A>T	p.Asn792Ile	p.N792I	ENST00000373198	NM_133170.3	792	aAt/aTt	16/32	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	1	TRUE	NA	0.838453540204121	2		273	697	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306757	41306757	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	220	180	0	ENST00000373198.4:c.902G>C	p.Gly301Ala	p.G301A	ENST00000373198	NM_133170.3	301	gGg/gCg	7/32	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.838453540204121	2		180	354	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242903	142242904	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0003562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	419	359	0	ENST00000350721.4:c.4083_4084delinsTT	p.Leu1361_Gly1362delinsPheTrp	p.L1361_G1362delinsFW	ENST00000350721	NM_001184.3	1361	ttGGgg/ttTTgg	22/47	0.814232460140683	3	FACETS	0.813	0.779	0.848	0.813	0.779	0.848	CLONAL	2	TRUE	1	0.838453540204121	3		359	872	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0003563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	205	378	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.962	0.898	1	0.962	0.898	1	CLONAL	1	TRUE	1	0.734934365015877	2		379	580	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0003572-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	192	323	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.467875813001868	6	FACETS	1	0.964	1	0.532	0.493	0.572	CLONAL	2	TRUE	2	0.467875813001868	6		323	747	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28929495	NA	P-0003572-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	233	321	0	ENST00000275493.2:c.2155G>T	p.Gly719Cys	p.G719C	ENST00000275493	NM_005228.3	719	Ggc/Tgc	18/28	0.467875813001868	6	FACETS	1	0.979	1	0.557	0.52	0.594	CLONAL	2	TRUE	2	0.467875813001868	6		321	866	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0003572-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	218	328	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.187635883961175	3	FACETS	1	0.968	1	0.699	0.656	0.743	INDETERMINATE	2	TRUE	0	0.467875813001868	3		328	548	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577541	7577541	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201762	NA	P-0003572-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	322	229	1	ENST00000269305.4:c.740A>T	p.Asn247Ile	p.N247I	ENST00000269305	NM_001126112.2	247	aAc/aTc	7/11	0.466847139249719	4	FACETS	0.941	0.901	0.98	0.941	0.901	0.98	CLONAL	4	TRUE	0	0.467875813001868	4		230	537	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974687	21974687	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003572-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	92	332	0	ENST00000304494.5:c.140G>T	p.Arg47Met	p.R47M	ENST00000304494	NM_000077.4	47	aGg/aTg	1/3	0.467875813001868	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.467875813001868	1		332	273	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020673	37020673	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003589-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	154	310	1	ENST00000358127.4:c.172C>G	p.Leu58Val	p.L58V	ENST00000358127	NM_001280556.1	58	Ctt/Gtt	2/10	0.720749727735259	3	FACETS	1	0.988	1	0.465	0.431	0.5	CLONAL	1	TRUE	0	0.778196289006815	3		311	394	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223917	53223917	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782205045	NA	P-0003589-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	139	165	0	ENST00000375401.3:c.3442G>A	p.Val1148Met	p.V1148M	ENST00000375401	NM_004187.3	1148	Gtg/Atg	23/26	0.778196289006815	2	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.778196289006815	2		165	298	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354698	70354698	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003589-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	123	201	0	ENST00000374080.3:c.4863G>T	p.Gln1621His	p.Q1621H	ENST00000374080		1621	caG/caT	35/45	0.778196289006815	2	FACETS	1	0.942	1			1	CLONAL	1	TRUE	NA	0.778196289006815	2		201	306	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0003595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	153	409	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	1	TRUE	NA	0.584097770138614	2		409	428	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0003595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	202	462	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	0.57200723902206	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.584097770138614	1		462	377	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517959	187517959	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	114	374	0	ENST00000441802.2:c.12735A>G	p.Ile4245Met	p.I4245M	ENST00000441802	NM_005245.3	4245	atA/atG	25/27	NA	2	FACETS	0.929	0.843	1			1	INDETERMINATE	1	TRUE	NA	0.584097770138614	2		374	420	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508689	106508689	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	98	336	0	ENST00000359195.3:c.683C>A	p.Thr228Asn	p.T228N	ENST00000359195	NM_002649.2	228	aCc/aAc	2/11	0.241783678276259	2	FACETS	0.854	0.767	0.944	0.427	0.383	0.472	INDETERMINATE	1	TRUE	0	0.584097770138614	2		336	393	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450747	70450747	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	139	374	0	ENST00000373644.4:c.5587A>C	p.Lys1863Gln	p.K1863Q	ENST00000373644	NM_030625.2	1863	Aag/Cag	12/12	NA	2	FACETS	0.907	0.83	0.986			1	INDETERMINATE	1	TRUE	NA	0.584097770138614	2		374	525	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114799860	114799860	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	115	609	0	ENST00000543371.1:c.527G>T	p.Arg176Leu	p.R176L	ENST00000543371	NM_001198531.1	176	cGg/cTg	5/14	0.585486835223206	4	FACETS	0.763	0.687	0.843	0.254	0.229	0.281	SUBCLONAL	1	TRUE	1	0.584097770138614	4		609	818	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169100	119169100	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	47	322	0	ENST00000264033.4:c.2284A>T	p.Thr762Ser	p.T762S	ENST00000264033	NM_005188.3	762	Act/Tct	15/16	0.576065737918454	2	FACETS	0.371	0.313	0.434	0.185	0.156	0.217	SUBCLONAL	1	TRUE	0	0.584097770138614	2		322	434	SUCCESS
AR	367	MSKCC	GRCh37	X	66937401	66937401	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	217	570	0	ENST00000374690.3:c.2255G>A	p.Trp752Ter	p.W752*	ENST00000374690	NM_000044.3	752	tGg/tAg	5/8	0.515584999168723	1	FACETS	0.941	0.882	1	0.941	0.882	1	CLONAL	1	TRUE	0	0.584097770138614	1		570	559	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971037	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0003595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	103	159	1	ENST00000304494.5:c.321_322del	p.Asp108CysfsTer11	p.D108Cfs*11	ENST00000304494	NM_000077.4	107	cgCGat/cgat	2/3	0.585486835223206	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.584097770138614	1		160	219	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0003597-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	171	229	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.373099947054319	3	FACETS	1	0.984	1	0.767	0.719	0.814	CLONAL	2	TRUE	0	0.617849758076153	3		229	315	SUCCESS
AR	367	MSKCC	GRCh37	X	66943552	66943552	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137852578	NA	P-0003597-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	196	269	0	ENST00000374690.3:c.2632A>G	p.Thr878Ala	p.T878A	ENST00000374690	NM_000044.3	878	Act/Gct	8/8	0.617849758076153	4	FACETS	1	0.989	1			1	CLONAL	1	TRUE	NA	0.617849758076153	4		269	756	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442530	52442530	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003597-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	153	347	0	ENST00000460680.1:c.215T>C	p.Ile72Thr	p.I72T	ENST00000460680	NM_004656.3	72	aTt/aCt	4/17	0.349065218279662	6	FACETS	1	0.977	1	0.771	0.71	0.832	INDETERMINATE	2	TRUE	3	0.617849758076153	6		347	479	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857679	9857679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886042648	NA	P-0003597-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	262	341	0	ENST00000330684.3:c.3722G>A	p.Arg1241Gln	p.R1241Q	ENST00000330684	NM_001134407.1	1241	cGg/cAg	13/13	0.617849758076153	5	FACETS	0.941	0.89	0.992	0.941	0.89	0.992	CLONAL	3	TRUE	2	0.617849758076153	5		341	579	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540230	23540235	+	inframe_deletion	In_Frame_Del	DEL	GGCTCC	GGCTCC	-	rs753037741	NA	P-0003597-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	34	138	0	ENST00000380871.4:c.168_173del	p.Pro62_Glu63del	p.P62_E63del	ENST00000380871	NM_006167.3	56	ccGGAGCCa/cca	1/2	0.290349993465379	2	FACETS	1	0.919	1	0.579	0.488	0.675	INDETERMINATE	1	TRUE	0	0.617849758076153	2		138	95	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	164	304	0	ENST00000269305.4:c.472C>G	p.Arg158Gly	p.R158G	ENST00000269305	NM_001126112.2	158	Cgc/Ggc	5/11	0.3	3	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.77	3		304	400	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589586	67589591	+	inframe_deletion	In_Frame_Del	DEL	ATGAAT	ATGAAT	-	novel	NA	P-0003600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	200	322	0	ENST00000274335.5:c.1351_1356del	p.Glu451_Tyr452del	p.E451_Y452del	ENST00000274335		450	cATGAATat/cat	10/15	0.127349265852525	3	FACETS	1	0.984	1	0.593	0.552	0.634	INDETERMINATE	1	TRUE	1	0.77	3		322	607	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472471	88472471	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs779320655	NA	P-0003600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	231	502	1	ENST00000360948.2:c.2084T>C	p.Ile695Thr	p.I695T	ENST00000360948	NM_001012338.2	695	aTt/aCt	16/19	1	2	FACETS	0.985	0.925	1	0.985	0.925	1	CLONAL	1	TRUE	1	0.77	2		503	609	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0003616-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	43	426	0	ENST00000374080.3:c.3670C>T	p.Leu1224Phe	p.L1224F	ENST00000374080		1224	Ctc/Ttc	26/45	0.24917238774003	0	FACETS	0.807	0.722	0.885			1	CLONAL	3	FALSE	NA	0.360671901298039	0		426	63	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430562	80430562	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003616-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	28	167	0	ENST00000286548.4:c.446G>A	p.Arg149Gln	p.R149Q	ENST00000286548	NM_002072.3	149	cGa/cAa	3/7	1	2	FACETS	1	0.887	1	1	0.963	1	CLONAL	2	FALSE	1	0.360671901298039	2		167	71	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759985	63759985	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003616-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	79	266	0	ENST00000279873.7:c.638T>C	p.Ile213Thr	p.I213T	ENST00000279873	NM_032199.2	213	aTt/aCt	4/10	0.281048581121455	3	FACETS	1	0.91	1	1	0.982	1	CLONAL	3	FALSE	1	0.360671901298039	3		266	171	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181276	123181278	+	inframe_deletion	In_Frame_Del	DEL	AAT	AAT	-	novel	NA	P-0003616-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	36	218	0	ENST00000218089.9:c.741_743del	p.Gln247_Tyr248delinsHis	p.Q247_Y248delinsH	ENST00000218089	NM_001042749.1	247	cAATat/cat	9/35	0.24917238774003	0	FACETS	0.626	0.529	0.727			1	SUBCLONAL	2	FALSE	NA	0.360671901298039	0		218	102	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0003617-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	16	298	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		298	363	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023156	31023156	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003617-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	24	255	0	ENST00000375687.4:c.2641A>G	p.Arg881Gly	p.R881G	ENST00000375687	NM_015338.5	881	Aga/Gga	13/13	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		255	463	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0003624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	39	495	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.12	2		496	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0003624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	29	216	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			1	2	FACETS	0.888	0.712	1	0.888	0.712	1	CLONAL	1	TRUE	1	0.12	2		216	544	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	144	201	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.474208225989502	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.474208225989502	1		201	351	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026102	71026127	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGCGTTGCGTCGGAAGTAAGCAAA	GCCGCGTTGCGTCGGAAGTAAGCAAA	-	novel	NA	P-0003634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	165	247	0	ENST00000318789.4:c.1495_1520del	p.Phe499HisfsTer9	p.F499Hfs*9	ENST00000318789	NM_032682.5	499	TTTGCTTACTTCCGACGCAACGCGGCc/c	17/21	0.474208225989502	1	FACETS	0.886	0.818	0.957	0.886	0.818	0.957	CLONAL	1	TRUE	0	0.474208225989502	1		247	599	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266756	18266756	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003639-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	37	274	0	ENST00000222254.8:c.67C>A	p.Leu23Met	p.L23M	ENST00000222254	NM_005027.3	23	Ctg/Atg	2/16	0.851751641082964	3	FACETS	0.303	0.25	0.362	0.151	0.125	0.181	SUBCLONAL	1	TRUE	1	0.851751641082964	3		274	409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0003643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	354	229	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.501535318120235	3	FACETS	0.954	0.924	0.982	1	0.997	1	CLONAL	7	TRUE	0	0.26	3		229	461	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0003643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	171	235	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.153444436976865	4	FACETS	1	0.978	1	1	0.992	1	INDETERMINATE	3	TRUE	2	0.26	4		235	486	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931992	39931992	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0003643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	118	269	0	ENST00000378444.4:c.2607T>G	p.Tyr869Ter	p.Y869*	ENST00000378444	NM_001123385.1	869	taT/taG	4/15	0.3	2	FACETS	0.934	0.854	1	1	0.985	1	CLONAL	3	TRUE	0	0.26	2		269	324	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937320	76937320	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	114	186	0	ENST00000373344.5:c.3428del	p.Lys1143ArgfsTer47	p.K1143Rfs*47	ENST00000373344	NM_000489.3	1143	aAg/ag	9/35	1	1	FACETS	1	0.978	1	1	0.993	1	CLONAL	5	TRUE	0	0.26	1		186	143	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814927	139814927	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003659-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	60	497	0	ENST00000247668.2:c.920A>T	p.His307Leu	p.H307L	ENST00000247668	NM_021138.3	307	cAc/cTc	8/11	0.3	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		497	295	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0003662-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	31	340	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.595	0.479	0.726	0.595	0.479	0.726	SUBCLONAL	1	TRUE	1	0.15	2		340	695	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0003662-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	17	276	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.405	0.301	0.531	0.405	0.301	0.531	SUBCLONAL	1	TRUE	1	0.15	2		276	559	SUCCESS
APC	324	MSKCC	GRCh37	5	112175417	112175418	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	rs1554085533	NA	P-0003662-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	46	317	0	ENST00000257430.4:c.4127_4128del	p.Tyr1376CysfsTer9	p.Y1376Cfs*9	ENST00000257430	NM_000038.5	1376	TAt/t	16/16	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.15	2		317	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0003676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	151	624	0	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	0.722095671256908	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.733265536117546	2		624	205	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169278	32169278	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0003676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	47	339	0	ENST00000375023.3:c.3756-1G>C		p.X1252_splice	ENST00000375023	NM_004557.3	1252			0.716621851042321	3	FACETS	1	0.961	1	0.453	0.392	0.516	CLONAL	1	TRUE	0	0.733265536117546	3		339	129	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934575	NA	P-0003686-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	105	229	0	ENST00000269305.4:c.733G>C	p.Gly245Arg	p.G245R	ENST00000269305	NM_001126112.2	245	Ggc/Cgc	7/11	0.218870948324091	2	FACETS	0.862	0.778	0.949	0.862	0.778	0.949	CLONAL	2	TRUE	0	0.297895428408114	2		229	409	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249438	110249438	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003686-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	124	442	0	ENST00000374672.4:c.1135C>G	p.Pro379Ala	p.P379A	ENST00000374672	NM_004235.4	379	Ccc/Gcc	4/5	0.297895428408114	3	FACETS	1	0.95	1	0.539	0.487	0.594	CLONAL	1	TRUE	1	0.297895428408114	3		442	887	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110768	2110768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003686-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	169	408	0	ENST00000219476.3:c.1073G>A	p.Trp358Ter	p.W358*	ENST00000219476	NM_000548.3	358	tGg/tAg	11/42	0.292579879030724	2	FACETS	0.982	0.907	1	0.982	0.907	1	CLONAL	2	TRUE	0	0.297895428408114	2		408	578	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0003692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	182	450	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	0.973	0.905	1			1	INDETERMINATE	1	FALSE	NA	0.721905786309421	2		451	518	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0003692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	161	313	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	0.987	0.914	1	0.987	0.914	1	CLONAL	1	FALSE	1	0.721905786309421	2		313	452	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267489	198267489	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1039242157	NA	P-0003696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	120	319	0	ENST00000335508.6:c.1868A>G	p.Tyr623Cys	p.Y623C	ENST00000335508	NM_012433.2	623	tAt/tGt	14/25	1	2	FACETS	0.879	0.805	0.954	1	0.992	1	CLONAL	3	TRUE	1	0.29	2		319	314	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237793	16237793	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	43	232	0	ENST00000375759.3:c.1241del	p.Pro414GlnfsTer16	p.P414Qfs*16	ENST00000375759	NM_015001.2	414	Cca/ca	5/15	1	2	FACETS	0.918	0.771	1	0.918	0.771	1	CLONAL	1	TRUE	1	0.29	2		232	323	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437302	52437302	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	191	399	0	ENST00000460680.1:c.1742del	p.Gly581ValfsTer36	p.G581Vfs*36	ENST00000460680	NM_004656.3	581	gGt/gt	14/17	1	2	FACETS	0.931	0.884	0.976	1	0.996	1	CLONAL	5	TRUE	1	0.29	2		399	283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0003705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	179	229	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.289585286678647	3	FACETS	0.953	0.886	1	0.953	0.886	1	CLONAL	3	TRUE	0	0.289585286678647	3		229	495	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0003705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	211	334	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.289585286678647	8	FACETS	1	0.978	1			1	CLONAL	3	TRUE	NA	0.289585286678647	8		334	812	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233039	55233039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	84	493	0	ENST00000275493.2:c.1789G>A	p.Ala597Thr	p.A597T	ENST00000275493	NM_005228.3	597	Gca/Aca	15/28	0.285280123035483	5	FACETS	1	0.954	1	0.388	0.343	0.437	CLONAL	1	TRUE	2	0.289585286678647	5		493	714	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0003706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	56	408	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	0.405328618633925	5	FACETS	1	0.934	1	0.379	0.328	0.435	INDETERMINATE	1	FALSE	2	0.85986519846954	5		408	262	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325792	65325792	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	66	225	0	ENST00000342505.4:c.1330A>G	p.Ile444Val	p.I444V	ENST00000342505	NM_002227.2	444	Atc/Gtc	9/25	0.85986519846954	4	FACETS	1	0.972	1	0.696	0.615	0.782	CLONAL	1	FALSE	2	0.85986519846954	4		225	205	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532626	187532626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	42	469	0	ENST00000441802.2:c.9767G>A	p.Ser3256Asn	p.S3256N	ENST00000441802	NM_005245.3	3256	aGt/aAt	14/27	1	2	FACETS	0.543	0.459	0.633	0.543	0.459	0.633	SUBCLONAL	1	FALSE	1	0.85986519846954	2		469	180	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0003714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	229	322	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.628289936873784	5	FACETS	1	0.988	1	0.811	0.762	0.861	CLONAL	2	TRUE	2	0.628289936873784	5		322	582	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042766	42042766	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	148	631	1	ENST00000219905.7:c.6961G>T	p.Asp2321Tyr	p.D2321Y	ENST00000219905	NM_001164273.1	2321	Gat/Tat	17/24	0.534380635885917	0	FACETS	0.572	0.532	0.613			1	SUBCLONAL	1	TRUE	0	0.628289936873784	0		632	306	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77054904	77054906	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	novel	NA	P-0003714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	129	531	0	ENST00000356341.3:c.956_958del	p.Met319del	p.M319del	ENST00000356341	NM_002576.4	319	aTGAgg/agg	10/15	1	2	FACETS	0.982	0.899	1	0.982	0.899	1	CLONAL	1	TRUE	1	0.628289936873784	2		531	418	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0003715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	27	290	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.211022385781083	3	FACETS	0.894	0.709	1	0.447	0.354	0.554	CLONAL	1	TRUE	1	0.1	3		290	634	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437220	220437220	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	29	511	2	ENST00000243786.2:c.124G>T	p.Gly42Trp	p.G42W	ENST00000243786	NM_002191.3	42	Ggg/Tgg	1/2	0.188951349274141	3	FACETS	1	0.888	1	0.584	0.468	0.717	CLONAL	1	TRUE	1	0.1	3		513	521	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213771	66213771	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0003715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	42	254	0	ENST00000273854.3:c.2658+1G>T		p.X886_splice	ENST00000273854	NM_004439.5	886			1	2	FACETS	0.921	0.769	1	1	0.966	1	CLONAL	2	TRUE	1	0.1	2		254	456	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143066999	143066999	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	72	319	0	ENST00000262992.4:c.1714C>G	p.Pro572Ala	p.P572A	ENST00000262992	NM_001101669.1	572	Cca/Gca	16/24	0.211022385781083	3	FACETS	0.96	0.84	1	0.96	0.84	1	CLONAL	3	TRUE	0	0.1	3		319	525	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93953201	93953201	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	34	484	0	ENST00000369303.4:c.2940C>A	p.Ser980Arg	p.S980R	ENST00000369303	NM_004440.3	980	agC/agA	17/17	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.1	NA		484	598	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968283	2968283	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	33	314	0	ENST00000396946.4:c.1703C>A	p.Pro568Gln	p.P568Q	ENST00000396946	NM_032415.4	568	cCg/cAg	13/25	0.211022385781083	3	FACETS	0.833	0.678	1	0.833	0.678	1	CLONAL	2	TRUE	1	0.1	3		314	416	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528735	8528735	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	23	258	0	ENST00000356435.5:c.397C>A	p.Gln133Lys	p.Q133K	ENST00000356435		133	Cag/Aag	4/35	0.188951349274141	3	FACETS	1	0.822	1	0.533	0.415	0.671	CLONAL	1	TRUE	1	0.1	3		258	453	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243484	46243484	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	48	302	0	ENST00000334344.6:c.1837C>T	p.Gln613Ter	p.Q613*	ENST00000334344	NM_152641.2	613	Cag/Tag	14/21	0.211022385781083	3	FACETS	1	0.923	1	1	0.923	1	CLONAL	2	TRUE	1	0.1	3		302	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0003715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	27	176	1	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	NA	2	FACETS	1	0.928	1			1	INDETERMINATE	1	TRUE	NA	0.1	2		177	377	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16040679	16040679	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	41	369	0	ENST00000268712.3:c.1455G>C	p.Glu485Asp	p.E485D	ENST00000268712	NM_006311.3	485	gaG/gaC	14/46	NA	2	FACETS	1	0.95	1			1	INDETERMINATE	1	TRUE	NA	0.1	2		369	575	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16040727	16040727	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0003715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	26	254	0	ENST00000268712.3:c.1408-1G>C		p.X470_splice	ENST00000268712	NM_006311.3	470			NA	2	FACETS	1	0.871	1			1	INDETERMINATE	1	TRUE	NA	0.1	2		254	454	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486028	29486028	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	21	184	0	ENST00000356175.3:c.205A>G	p.Arg69Gly	p.R69G	ENST00000356175	NM_000267.3	69	Aga/Gga	3/57	0.188951349274141	3	FACETS	1	0.879	1	0.621	0.478	0.789	CLONAL	1	TRUE	1	0.1	3		184	355	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022668	31022668	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	28	298	0	ENST00000375687.4:c.2153G>T	p.Arg718Ile	p.R718I	ENST00000375687	NM_015338.5	718	aGa/aTa	13/13	0.188951349274141	3	FACETS	1	0.933	1	0.733	0.586	0.901	CLONAL	1	TRUE	1	0.1	3		298	401	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0003722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	180	442	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	0.33507945430245	2	FACETS	1	0.99	1	0.743	0.689	0.799	CLONAL	1	TRUE	0	0.412646835283903	2		442	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057520005	NA	P-0003722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	268	575	1	ENST00000269305.4:c.820G>T	p.Val274Phe	p.V274F	ENST00000269305	NM_001126112.2	274	Gtt/Ttt	8/11	0.33507945430245	2	FACETS	0.864	0.814	0.914	0.864	0.814	0.914	CLONAL	2	TRUE	0	0.412646835283903	2		576	752	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400777	72400777	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	130	543	1	ENST00000357731.5:c.394C>A	p.His132Asn	p.H132N	ENST00000357731	NM_173808.2	132	Cat/Aat	2/7	0.347527186521846	3	FACETS	0.856	0.776	0.94	0.428	0.388	0.47	CLONAL	1	TRUE	1	0.412646835283903	3		544	888	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569259	67569259	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	60	254	0	ENST00000274335.5:c.376G>T	p.Asp126Tyr	p.D126Y	ENST00000274335		126	Gac/Tac	2/15	0.33507945430245	2	FACETS	0.697	0.603	0.8	0.349	0.301	0.4	SUBCLONAL	1	TRUE	0	0.412646835283903	2		254	417	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77043873	77043873	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	161	570	0	ENST00000356341.3:c.1453C>T	p.Gln485Ter	p.Q485*	ENST00000356341	NM_002576.4	485	Cag/Tag	14/15	0.324191987956464	5	FACETS	1	0.96	1	0.361	0.33	0.393	CLONAL	1	TRUE	2	0.412646835283903	5		570	1167	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444978	49444978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1286510393	NA	P-0003722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	19	81	0	ENST00000301067.7:c.2488G>A	p.Glu830Lys	p.E830K	ENST00000301067	NM_003482.3	830	Gaa/Aaa	10/54	0.412646835283903	3	FACETS	0.756	0.579	0.96			1	CLONAL	1	TRUE	NA	0.412646835283903	3		81	147	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649396	23649396	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	99	400	0	ENST00000261584.4:c.103C>T	p.Leu35Phe	p.L35F	ENST00000261584	NM_024675.3	35	Ctt/Ttt	2/13	1	2	FACETS	0.751	0.671	0.835	0.751	0.671	0.835	SUBCLONAL	1	TRUE	1	0.412646835283903	2		400	639	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664598	29664598	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	215	243	0	ENST00000356175.3:c.6577G>T	p.Glu2193Ter	p.E2193*	ENST00000356175	NM_000267.3	2193	Gag/Tag	42/57	0.412646835283903	3	FACETS	1	0.986	1			1	CLONAL	2	TRUE	NA	0.412646835283903	3		243	530	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40371810	40371810	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	181	321	0	ENST00000293328.3:c.601G>T	p.Glu201Ter	p.E201*	ENST00000293328	NM_012448.3	201	Gag/Tag	6/19	0.200010044214566	3	FACETS	1	0.985	1			1	INDETERMINATE	2	TRUE	NA	0.412646835283903	3		321	439	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610123	10610123	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	240	471	0	ENST00000171111.5:c.587G>T	p.Cys196Phe	p.C196F	ENST00000171111	NM_203500.1	196	tGt/tTt	2/6	0.33507945430245	2	FACETS	0.838	0.787	0.891	0.838	0.787	0.891	CLONAL	2	TRUE	0	0.412646835283903	2		471	694	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76812936	76812936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	92	375	0	ENST00000373344.5:c.6685C>T	p.Pro2229Ser	p.P2229S	ENST00000373344	NM_000489.3	2229	Ccc/Tcc	30/35	1	2	FACETS	0.663	0.589	0.741	0.663	0.589	0.741	SUBCLONAL	1	TRUE	1	0.412646835283903	2		375	673	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907627	76907627	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	120	530	0	ENST00000373344.5:c.4534C>A	p.Arg1512Ser	p.R1512S	ENST00000373344	NM_000489.3	1512	Cgt/Agt	15/35	1	2	FACETS	0.638	0.576	0.705	0.638	0.576	0.705	SUBCLONAL	1	TRUE	1	0.412646835283903	2		530	911	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007156	62007156	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	13	389	0	ENST00000392795.3:c.526G>T	p.Val176Leu	p.V176L	ENST00000392795	NM_001039933.1	176	Gtg/Ttg	4/6	0.253889233524921	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		389	128	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0003731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	304	387	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.689879377251195	1	FACETS	0.814	0.773	0.854	0.814	0.773	0.854	CLONAL	1	TRUE	0	0.730645390763988	1		387	649	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0003731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	400	368	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.221938926401723	3	FACETS	0.792	0.756	0.828	0.792	0.756	0.828	INDETERMINATE	2	TRUE	1	0.730645390763988	3		368	944	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446175	49446175	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	136	185	0	ENST00000301067.7:c.1291G>T	p.Glu431Ter	p.E431*	ENST00000301067	NM_003482.3	431	Gag/Tag	10/54	0.730645390763988	2	FACETS	1	0.98	1	0.593	0.548	0.639	CLONAL	1	TRUE	0	0.730645390763988	2		185	314	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871698	35871698	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	299	552	1	ENST00000216797.5:c.808G>C	p.Gly270Arg	p.G270R	ENST00000216797	NM_020529.2	270	Ggc/Cgc	5/6	0.2304577743317	1	FACETS	0.497	0.468	0.526	0.497	0.468	0.526	INDETERMINATE	1	TRUE	0	0.730645390763988	1		553	1046	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576885	7576885	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0003731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	31	306	0	ENST00000269305.4:c.961A>T	p.Lys321Ter	p.K321*	ENST00000269305	NM_001126112.2	321	Aaa/Taa	9/11	0.689879377251195	1	FACETS	0.108	0.087	0.132	0.108	0.087	0.132	SUBCLONAL	1	TRUE	0	0.730645390763988	1		306	498	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424970	49424970	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783691	NA	P-0003731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	211	265	0	ENST00000301067.7:c.13518del	p.Ser4507AlafsTer12	p.S4507Afs*12	ENST00000301067	NM_003482.3	4506	ccC/cc	39/54	0.730645390763988	2	FACETS	1	0.976	1	0.542	0.507	0.577	CLONAL	1	TRUE	0	0.730645390763988	2		265	533	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0003748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	80	495	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.307442958507601	3	FACETS	0.756	0.671	0.845	0.756	0.671	0.845	SUBCLONAL	2	TRUE	1	0.380675189680934	3		496	331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578430	7578431	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0003748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	24	201	0	ENST00000269305.4:c.499_500del	p.Gln167AlafsTer13	p.Q167Afs*13	ENST00000269305	NM_001126112.2	167	CAg/g	5/11	1	2	FACETS	0.657	0.518	0.814	0.657	0.518	0.814	SUBCLONAL	1	TRUE	1	0.380675189680934	2		201	192	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027998	48027998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757653982	NA	P-0003749-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	87	171	0	ENST00000234420.5:c.2876G>A	p.Arg959His	p.R959H	ENST00000234420	NM_000179.2	959	cGc/cAc	4/10	0.211432929720401	5	FACETS	0.876	0.78	0.978	0.584	0.52	0.652	INDETERMINATE	2	TRUE	2	0.368897165456237	5		171	418	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460348	149460348	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003749-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	32	137	0	ENST00000286301.3:c.289A>C	p.Ile97Leu	p.I97L	ENST00000286301	NM_005211.3	97	Atc/Ctc	3/22	0.169077941663298	4	FACETS	1	0.922	1	0.628	0.515	0.754	INDETERMINATE	1	TRUE	2	0.368897165456237	4		137	189	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006042	22006042	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746854404	NA	P-0003749-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	93	156	0	ENST00000276925.6:c.361G>A	p.Glu121Lys	p.E121K	ENST00000276925	NM_004936.3	121	Gag/Aag	2/2	0.368897165456237	5	FACETS	1	0.921	1			1	CLONAL	2	TRUE	NA	0.368897165456237	5		156	379	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900680	3900680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003749-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	43	123	0	ENST00000262367.5:c.416G>A	p.Ser139Asn	p.S139N	ENST00000262367	NM_004380.2	139	aGc/aAc	2/31	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.368897165456237	2		123	196	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667364	241667367	+	frameshift_variant	Frame_Shift_Del	DEL	TTCA	TTCA	-	rs756469140	NA	P-0003749-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	279	387	2	ENST00000366560.3:c.1083_1086del	p.Glu362GlnfsTer10	p.E362Qfs*10	ENST00000366560	NM_000143.3	361	aaTGAA/aa	7/10	0.368897165456237	5	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	2	0.368897165456237	5		389	736	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201776	66201776	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	212	249	0	ENST00000273854.3:c.2726A>T	p.Gln909Leu	p.Q909L	ENST00000273854	NM_004439.5	909	cAg/cTg	16/18	1	2	FACETS	1	0.981	1	1	0.995	1	CLONAL	3	FALSE	1	0.285413415561154	2		249	450	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865281	57865281	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368469814	NA	P-0003758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	243	369	0	ENST00000228682.2:c.2758G>A	p.Ala920Thr	p.A920T	ENST00000228682	NM_005269.2	920	Gcc/Acc	12/12	0.285413415561154	4	FACETS	1	0.989	1	0.831	0.778	0.886	CLONAL	2	FALSE	1	0.285413415561154	4		369	878	SUCCESS
APC	324	MSKCC	GRCh37	5	112103004	112103252	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCTATGGGTTCATTTCCAAGAAGAGGGTTTGTAAATGGAAGCAGAGAAAGTACTGGATATTTAGAAGAACTTGAGAAAGAGAGGTAACTTTTCTTCATATAGTAAACATTGCCTTGTGTACTCCAGTTTATTGTTATTTTGTAATATAATATTTAAATTGTGAATTTATAGTAGGTGATAGCTAACACTTAGAGCATTTTGCATTTTTAAACTCAAAGATAGCATGTTATTGATTGCACTTACATTAA	TCCTATGGGTTCATTTCCAAGAAGAGGGTTTGTAAATGGAAGCAGAGAAAGTACTGGATATTTAGAAGAACTTGAGAAAGAGAGGTAACTTTTCTTCATATAGTAAACATTGCCTTGTGTACTCCAGTTTATTGTTATTTTGTAATATAATATTTAAATTGTGAATTTATAGTAGGTGATAGCTAACACTTAGAGCATTTTGCATTTTTAAACTCAAAGATAGCATGTTATTGATTGCACTTACATTAA	-	novel	NA	P-0003758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	105	233	0	ENST00000257430.4:c.339_422+165del		p.X113_splice	ENST00000257430	NM_000038.5	113		4/16	0.285413415561154	0	FACETS	0.903	0.832	0.974			1	CLONAL	3	FALSE	0	0.285413415561154	0		233	194	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954366	48954366	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	277	165	0	ENST00000267163.4:c.1488del	p.Thr497HisfsTer22	p.T497Hfs*22	ENST00000267163	NM_000321.2	496	gCc/gc	16/27	0.184093288125385	1	FACETS	1	0.992	1	1	0.997	1	CLONAL	5	FALSE	0	0.285413415561154	1		165	314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0003765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	26	493	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.091	0.071	0.114	0.091	0.071	0.114	SUBCLONAL	1	TRUE	1	0.740889296973414	2		494	770	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692892	89692892	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554898129	NA	P-0003765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	66	183	0	ENST00000371953.3:c.376G>T	p.Ala126Ser	p.A126S	ENST00000371953	NM_000314.4	126	Gct/Tct	5/9	0.190829800369455	2	FACETS	0.806	0.71	0.907	0.403	0.355	0.454	INDETERMINATE	1	TRUE	0	0.740889296973414	2		183	221	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921737	111921737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1170116948	NA	P-0003765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	360	263	0	ENST00000393256.3:c.526G>A	p.Glu176Lys	p.E176K	ENST00000393256	NM_006538.4	176	Gaa/Aaa	4/4	0.469391911969203	2	FACETS	0.76	0.729	0.792	0.76	0.729	0.792	SUBCLONAL	2	TRUE	0	0.740889296973414	2		263	639	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586502	189586502	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757536818	NA	P-0003765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	120	151	1	ENST00000264731.3:c.1126C>T	p.Arg376Cys	p.R376C	ENST00000264731	NM_003722.4	376	Cgc/Tgc	8/14	1	2	FACETS	0.973	0.89	1	0.973	0.89	1	CLONAL	1	TRUE	1	0.740889296973414	2		152	333	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86668008	86668008	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	46	260	0	ENST00000274376.6:c.1772G>A	p.Arg591His	p.R591H	ENST00000274376	NM_002890.2	591	cGt/cAt	13/25	1	2	FACETS	0.235	0.197	0.276	0.235	0.197	0.276	SUBCLONAL	1	TRUE	1	0.740889296973414	2		260	529	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465952	69465952	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	202	312	0	ENST00000227507.2:c.790C>T	p.Gln264Ter	p.Q264*	ENST00000227507	NM_053056.2	264	Cag/Tag	5/5	1	2	FACETS	0.897	0.836	0.959	0.897	0.836	0.959	CLONAL	1	TRUE	1	0.740889296973414	2		312	608	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290890	15290890	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	241	399	1	ENST00000263388.2:c.3320T>C	p.Met1107Thr	p.M1107T	ENST00000263388	NM_000435.2	1107	aTg/aCg	20/33	1	2	FACETS	0.937	0.88	0.996	0.937	0.88	0.996	CLONAL	1	TRUE	1	0.740889296973414	2		400	694	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954587	17954587	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs761583890	NA	P-0003765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	115	179	0	ENST00000458235.1:c.307C>T	p.Arg103Cys	p.R103C	ENST00000458235	NM_000215.3	103	Cgc/Tgc	3/24	1	2	FACETS	0.844	0.768	0.922	0.844	0.768	0.922	CLONAL	1	TRUE	1	0.740889296973414	2		179	368	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265540	198265540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003773-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	175	345	0	ENST00000335508.6:c.2617G>A	p.Glu873Lys	p.E873K	ENST00000335508	NM_012433.2	873	Gag/Aag	18/25	1	2	FACETS	0.88	0.81	0.951	0.88	0.81	0.951	CLONAL	1	TRUE	1	0.451702149850815	2		345	881	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349348	73349348	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0003773-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	165	269	1	ENST00000377767.4:c.987+1G>T		p.X329_splice	ENST00000377767	NM_014953.3	329			0.451702149850815	1	FACETS	0.949	0.876	1	0.949	0.876	1	CLONAL	1	TRUE	0	0.451702149850815	1		270	596	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779565	3779565	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003773-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	38	363	0	ENST00000262367.5:c.5483A>G	p.Tyr1828Cys	p.Y1828C	ENST00000262367	NM_004380.2	1828	tAc/tGc	31/31	1	2	FACETS	0.234	0.193	0.281	0.234	0.193	0.281	SUBCLONAL	1	TRUE	1	0.451702149850815	2		363	719	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627283	86627283	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003773-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	46	293	0	ENST00000274376.6:c.660del	p.Ser222AlafsTer3	p.S222Afs*3	ENST00000274376	NM_002890.2	220	Ttt/tt	2/25	0.180451698084622	3	FACETS	0.369	0.31	0.434	0.184	0.155	0.217	INDETERMINATE	1	TRUE	1	0.451702149850815	3		293	677	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266105	41266119	+	protein_altering_variant	In_Frame_Del	DEL	AATCCATTCTGGTGC	AATCCATTCTGGTGC	TGT	novel	NA	P-0003773-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	102	307	0	ENST00000349496.5:c.102_116delinsTGT	p.Ile35_Ala39delinsVal	p.I35_A39delinsV	ENST00000349496	NM_001904.3	34	ggAATCCATTCTGGTGCc/ggTGTc	3/15	0.418578363541128	2	FACETS	0.619	0.553	0.688	0.309	0.276	0.344	SUBCLONAL	1	TRUE	0	0.451702149850815	2		307	730	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0003773-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	112	278	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	1	2	FACETS	0.824	0.743	0.909	0.824	0.743	0.909	CLONAL	1	TRUE	1	0.451702149850815	2		278	602	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0003780-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	410	450	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.241699619736697	4	FACETS	0.977	0.935	1			1	CLONAL	4	TRUE	NA	0.31	4		451	887	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0003780-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	168	308	1	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.290766665640182	4	FACETS	0.844	0.776	0.915	0.844	0.776	0.915	CLONAL	2	TRUE	2	0.31	4		309	841	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0003780-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	273	542	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.263378821153603	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.31	2		542	842	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649679	48649679	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150572851	NA	P-0003780-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	246	581	1	ENST00000376670.3:c.163G>A	p.Ala55Thr	p.A55T	ENST00000376670	NM_002049.3	55	Gct/Act	2/6	0.296617511028918	3	FACETS	0.881	0.824	0.94			1	CLONAL	2	TRUE	NA	0.31	3		582	1040	SUCCESS
APC	324	MSKCC	GRCh37	5	112175630	112175630	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003780-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	146	551	0	ENST00000257430.4:c.4339C>T	p.Gln1447Ter	p.Q1447*	ENST00000257430	NM_000038.5	1447	Caa/Taa	16/16	0.295300281338062	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.31	1		551	740	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655380	67655380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003780-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	123	462	1	ENST00000264010.4:c.1243C>T	p.Arg415Trp	p.R415W	ENST00000264010	NM_006565.3	415	Cgg/Tgg	7/12	0.288792468047363	3	FACETS	1	0.913	1	0.505	0.456	0.557	CLONAL	1	TRUE	1	0.31	3		463	907	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775532	39775532	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003780-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	182	347	0	ENST00000288319.7:c.488T>C	p.Ile163Thr	p.I163T	ENST00000288319	NM_182918.3	163	aTc/aCc	4/10	0.290766665640182	4	FACETS	0.975	0.901	1	0.975	0.901	1	CLONAL	2	TRUE	2	0.31	4		347	789	SUCCESS
ATM	472	MSKCC	GRCh37	11	108225582	108225583	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs786203030	NA	P-0003786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	42	160	0	ENST00000278616.4:c.8833_8834del	p.Leu2945ValfsTer10	p.L2945Vfs*10	ENST00000278616	NM_000051.3	2944	aCT/a	61/63	0.771917602840587	1	FACETS	0.891	0.782	0.997	0.891	0.782	0.997	CLONAL	1	TRUE	0	0.771917602840587	1		160	75	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0003803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	360	717	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.763780748470929	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.763780748470929	1		718	466	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0003803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	286	324	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.763780748470929	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.763780748470929	1		324	377	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261542	142261542	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	139	434	0	ENST00000350721.4:c.3415C>G	p.Leu1139Val	p.L1139V	ENST00000350721	NM_001184.3	1139	Ctg/Gtg	17/47	1	2	FACETS	0.352	0.32	0.386	0.352	0.32	0.386	SUBCLONAL	1	TRUE	1	0.763780748470929	2		434	1033	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171632	32171632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61729679	NA	P-0003803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	264	296	0	ENST00000375023.3:c.3146C>T	p.Pro1049Leu	p.P1049L	ENST00000375023	NM_004557.3	1049	cCc/cTc	20/30	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.763780748470929	2		296	622	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495328	56495328	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138861245	NA	P-0003803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	346	413	0	ENST00000267101.3:c.3518G>A	p.Arg1173Gln	p.R1173Q	ENST00000267101	NM_001982.3	1173	cGg/cAg	28/28	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.763780748470929	2		413	819	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118885	70118885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	269	306	0	ENST00000245479.2:c.457C>T	p.Pro153Ser	p.P153S	ENST00000245479	NM_000346.3	153	Ccc/Tcc	2/3	1	2	FACETS	0.969	0.914	1	0.969	0.914	1	CLONAL	1	TRUE	1	0.763780748470929	2		306	727	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0003814-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	61	378	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.211789244989787	3	FACETS	0.755	0.65	0.87	0.377	0.325	0.435	SUBCLONAL	1	TRUE	1	0.211789244989787	3		379	844	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045875	26045875	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003814-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	61	465	0	ENST00000540144.1:c.237C>G	p.Phe79Leu	p.F79L	ENST00000540144	NM_003531.2	79	ttC/ttG	1/1	0.211789244989787	5	FACETS	0.731	0.628	0.843	0.244	0.209	0.281	SUBCLONAL	1	TRUE	2	0.211789244989787	5		465	1039	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101091	27101095	+	frameshift_variant	Frame_Shift_Del	DEL	AGTTT	AGTTT	-	novel	NA	P-0003814-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	50	274	0	ENST00000324856.7:c.4373_4377del	p.Gln1458ArgfsTer31	p.Q1458Rfs*31	ENST00000324856	NM_006015.4	1458	cAGTTT/c	18/20	1	2	FACETS	0.851	0.722	0.993	0.851	0.722	0.993	CLONAL	1	TRUE	1	0.211789244989787	2		274	555	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0003820-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	288	235	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.993	0.94	1	0.993	0.94	1	CLONAL	1	TRUE	1	0.87	2		235	667	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106194030	106194030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1298652864	NA	P-0003820-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	118	239	0	ENST00000380013.4:c.4492C>T	p.Arg1498Cys	p.R1498C	ENST00000380013	NM_001127208.2	1498	Cgt/Tgt	10/11	1	2	FACETS	0.327	0.294	0.361	0.327	0.294	0.361	SUBCLONAL	1	TRUE	1	0.87	2		239	830	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99440009	99440009	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003820-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	147	206	2	ENST00000268035.6:c.977G>T	p.Gly326Val	p.G326V	ENST00000268035	NM_000875.3	326	gGt/gTt	4/21	1	2	FACETS	0.469	0.428	0.511	0.469	0.428	0.511	SUBCLONAL	1	TRUE	1	0.87	2		208	721	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578397	7578397	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1555526004	NA	P-0003820-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	326	131	0	ENST00000269305.4:c.533A>C	p.His178Pro	p.H178P	ENST00000269305	NM_001126112.2	178	cAc/cCc	5/11	0.877203232703016	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.87	2		131	359	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829815	76829815	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0003820-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	257	165	0	ENST00000373344.5:c.6226A>T	p.Lys2076Ter	p.K2076*	ENST00000373344	NM_000489.3	2076	Aag/Tag	28/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.87	1		165	295	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578419	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587781845	NA	P-0003829-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	166	356	0	ENST00000269305.4:c.511G>T	p.Glu171Ter	p.E171*	ENST00000269305	NM_001126112.2	171	Gag/Tag	5/11	0.657188869926217	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.657188869926217	1		356	279	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29105993	29105993	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs864622149	NA	P-0003829-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	173	238	0	ENST00000328354.6:c.846+1G>A		p.X282_splice	ENST00000328354	NM_007194.3	282			0.657188869926217	1	FACETS	0.948	0.885	1	0.948	0.885	1	CLONAL	1	TRUE	0	0.657188869926217	1		238	373	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389329	8389329	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866195026	NA	P-0003829-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	129	705	0	ENST00000356435.5:c.4289G>A	p.Gly1430Glu	p.G1430E	ENST00000356435		1430	gGa/gAa	26/35	1	2	FACETS	0.557	0.505	0.611	0.557	0.505	0.611	SUBCLONAL	1	TRUE	1	0.657188869926217	2		705	705	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804252	43804252	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003829-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	142	610	0	ENST00000372470.3:c.252G>C	p.Met84Ile	p.M84I	ENST00000372470	NM_005373.2	84	atG/atC	3/12	0.173648823078538	6	FACETS	0.996	0.907	1			1	INDETERMINATE	1	TRUE	NA	0.657188869926217	6		610	1004	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942559	17942559	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003829-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	72	356	0	ENST00000458235.1:c.2729T>C	p.Leu910Ser	p.L910S	ENST00000458235	NM_000215.3	910	tTg/tCg	20/24	0.34878043368884	3	FACETS	0.603	0.528	0.683	0.301	0.264	0.342	INDETERMINATE	1	TRUE	1	0.657188869926217	3		356	483	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183724	10183724	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs869025616	NA	P-0003838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	84	291	0	ENST00000256474.2:c.193T>C	p.Ser65Pro	p.S65P	ENST00000256474	NM_000551.3	65	Tcg/Ccg	1/3	0.437932261309576	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.437932261309576	1		291	253	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162813	47162813	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0003838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	74	255	0	ENST00000409792.3:c.3313A>T	p.Arg1105Ter	p.R1105*	ENST00000409792	NM_014159.6	1105	Aga/Tga	3/21	0.330072181095295	0	FACETS	0.745	0.661	0.833			1	SUBCLONAL	1	TRUE	0	0.437932261309576	0		255	255	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702555	52702555	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	82	418	1	ENST00000394830.3:c.343G>T	p.Asp115Tyr	p.D115Y	ENST00000394830	NM_018313.4	115	Gac/Tac	4/30	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.437932261309576	NA		419	383	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374245	138374245	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	38	490	0	ENST00000289153.2:c.3199G>T	p.Asp1067Tyr	p.D1067Y	ENST00000289153	NM_006219.2	1067	Gac/Tac	22/22	1	2	FACETS	0.342	0.282	0.409	0.342	0.282	0.409	SUBCLONAL	1	TRUE	1	0.437932261309576	2		490	507	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201119	108201119	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	46	176	4	ENST00000278616.4:c.7486G>T	p.Gly2496Ter	p.G2496*	ENST00000278616	NM_000051.3	2496	Gga/Tga	50/63	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.437932261309576	2		180	205	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748545	40748545	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	106	427	0	ENST00000392038.2:c.337C>G	p.Arg113Gly	p.R113G	ENST00000392038	NM_001626.4	113	Cgg/Ggg	5/14	0.149902814166411	0	FACETS	0.62	0.559	0.683			1	INDETERMINATE	1	TRUE	0	0.437932261309576	0		427	439	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031679	36031679	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1405253806	NA	P-0003838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	31	443	1	ENST00000358208.4:c.1508G>A	p.Arg503Gln	p.R503Q	ENST00000358208		503	cGg/cAg	12/12	1	2	FACETS	0.295	0.238	0.36	0.295	0.238	0.36	SUBCLONAL	1	TRUE	1	0.437932261309576	2		444	480	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725463	117725463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	107	452	0	ENST00000368508.3:c.418G>A	p.Gly140Arg	p.G140R	ENST00000368508	NM_002944.2	140	Gga/Aga	5/43	0.3	2	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.28	2		452	601	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26911760	26911760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	146	445	1	ENST00000381527.3:c.185C>T	p.Ser62Leu	p.S62L	ENST00000381527	NM_001260.1	62	tCg/tTg	2/13	1	2	FACETS	0.974	0.89	1	0.974	0.89	1	CLONAL	1	FALSE	1	0.384905314070886	2		446	779	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368476	225368476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	50	478	0	ENST00000264414.4:c.1270G>A	p.Glu424Lys	p.E424K	ENST00000264414	NM_003590.4	424	Gaa/Aaa	9/16	0.387547316632521	3	FACETS	0.31	0.262	0.364			1	SUBCLONAL	1	FALSE	NA	0.384905314070886	3		478	999	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401414	139401414	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	14	132	0	ENST00000277541.6:c.3655G>T	p.Glu1219Ter	p.E1219*	ENST00000277541	NM_017617.3	1219	Gag/Tag	23/34	NA	2	FACETS	0.573	0.417	0.758			1	INDETERMINATE	1	FALSE	NA	0.384905314070886	2		132	127	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114724324	114724324	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	97	800	0	ENST00000543371.1:c.391C>T	p.Gln131Ter	p.Q131*	ENST00000543371	NM_001198531.1	131	Cag/Tag	4/14	NA	2	FACETS	0.52	0.462	0.581			1	INDETERMINATE	1	FALSE	NA	0.384905314070886	2		800	970	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220464	133220464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	65	384	0	ENST00000320574.5:c.4249G>A	p.Glu1417Lys	p.E1417K	ENST00000320574	NM_006231.2	1417	Gag/Aag	33/49	1	2	FACETS	0.705	0.613	0.805	0.705	0.613	0.805	SUBCLONAL	1	FALSE	1	0.384905314070886	2		384	479	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78923339	78923339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1441841406	NA	P-0003848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	18	300	0	ENST00000306801.3:c.3362C>T	p.Thr1121Met	p.T1121M	ENST00000306801	NM_020761.2	1121	aCg/aTg	28/34	0.164072521929548	4	FACETS	0.458	0.344	0.591	0.229	0.172	0.296	INDETERMINATE	1	FALSE	2	0.384905314070886	4		300	283	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426683	47426683	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	43	574	0	ENST00000377045.4:c.928G>T	p.Val310Leu	p.V310L	ENST00000377045	NM_001654.4	310	Gtg/Ttg	10/16	0.208568038223845	3	FACETS	0.343	0.286	0.407	0.172	0.143	0.204	INDETERMINATE	1	FALSE	1	0.384905314070886	3		574	776	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253409	226253411	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0003848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	19	114	0	ENST00000366813.1:c.183_185del	p.Leu62del	p.L62del	ENST00000366813		61	CTT/-	2/3	0.384905314070886	5	FACETS	0.475	0.36	0.61	0.158	0.12	0.204	SUBCLONAL	1	FALSE	2	0.384905314070886	5		114	328	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162496	47162496	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	123	512	0	ENST00000409792.3:c.3630del	p.Asp1211MetfsTer25	p.D1211Mfs*25	ENST00000409792	NM_014159.6	1210	gaA/ga	3/21	0.387547316632521	4	FACETS	0.944	0.852	1			1	CLONAL	1	FALSE	NA	0.384905314070886	4		512	938	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579508	7579508	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	49	339	0	ENST00000269305.4:c.179del	p.Pro60GlnfsTer63	p.P60Qfs*63	ENST00000269305	NM_001126112.2	60	cCa/ca	4/11	0.387547316632521	3	FACETS	0.816	0.693	0.95	0.408	0.346	0.475	CLONAL	1	FALSE	1	0.384905314070886	3		339	372	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0003851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	742	387	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.681013471281915	3	FACETS	0.98	0.957	1	0.98	0.957	1	CLONAL	3	TRUE	0	0.681013471281915	3		387	994	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532693	187532693	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	224	362	0	ENST00000441802.2:c.9700G>A	p.Glu3234Lys	p.E3234K	ENST00000441802	NM_005245.3	3234	Gaa/Aaa	14/27	NA	2	FACETS	0.992	0.929	1			1	INDETERMINATE	1	TRUE	NA	0.681013471281915	2		362	663	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655381	67655381	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	204	358	1	ENST00000264010.4:c.1244G>A	p.Arg415Gln	p.R415Q	ENST00000264010	NM_006565.3	415	cGg/cAg	7/12	0.653108313561943	3	FACETS	0.866	0.804	0.931	0.433	0.402	0.466	CLONAL	1	TRUE	1	0.681013471281915	3		359	927	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735458	40735458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1243407933	NA	P-0003851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	166	317	0	ENST00000373198.4:c.3415C>T	p.Arg1139Trp	p.R1139W	ENST00000373198	NM_133170.3	1139	Cgg/Tgg	25/32	0.569957112230448	3	FACETS	0.911	0.839	0.986			1	CLONAL	1	TRUE	NA	0.681013471281915	3		317	717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0003854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	49	351	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.942	0.805	1	1	0.973	1	CLONAL	2	TRUE	1	0.2	2		351	260	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220649	1220649	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	62	321	0	ENST00000326873.7:c.667G>T	p.Glu223Ter	p.E223*	ENST00000326873	NM_000455.4	223	Gag/Tag	5/10	0.208235384038736	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	2	TRUE	0	0.2	2		321	298	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587162	212587162	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	124	404	0	ENST00000342788.4:c.839A>G	p.Asn280Ser	p.N280S	ENST00000342788	NM_005235.2	280	aAt/aGt	7/28	0.191434879492306	2	FACETS	0.91	0.825	1	0.91	0.825	1	CLONAL	2	TRUE	0	0.2	2		404	681	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938938	178938938	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	18	133	0	ENST00000263967.3:c.2180C>T	p.Thr727Ile	p.T727I	ENST00000263967	NM_006218.2	727	aCa/aTa	14/21	0.301414380746316	3	FACETS	0.93	0.702	1			1	CLONAL	1	TRUE	NA	0.2	3		133	213	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146743	185146743	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	67	304	0	ENST00000265026.3:c.374G>T	p.Ser125Ile	p.S125I	ENST00000265026	NM_004721.4	125	aGt/aTt	2/14	0.191434879492306	2	FACETS	0.957	0.837	1	0.957	0.837	1	CLONAL	2	TRUE	0	0.2	2		304	350	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532615	187532615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	28	394	0	ENST00000441802.2:c.9778G>A	p.Glu3260Lys	p.E3260K	ENST00000441802	NM_005245.3	3260	Gaa/Aaa	14/27	1	2	FACETS	0.66	0.527	0.812	0.66	0.527	0.812	SUBCLONAL	1	TRUE	1	0.2	2		394	424	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619982	21619982	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	42	462	1	ENST00000382592.4:c.184C>A	p.Gln62Lys	p.Q62K	ENST00000382592	NM_014572.2	62	Cag/Aag	2/8	0.223615804527329	1	FACETS	0.913	0.763	1	0.913	0.763	1	CLONAL	1	TRUE	0	0.2	1		463	414	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66679750	66679750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	59	433	1	ENST00000307102.5:c.65G>T	p.Gly22Val	p.G22V	ENST00000307102	NM_002755.3	22	gGg/gTg	1/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.2	2		434	397	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911128	40911128	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0003854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	165	561	0	ENST00000373198.4:c.2176+1G>T		p.X726_splice	ENST00000373198	NM_133170.3	726			0.230005839227552	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.2	3		561	820	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913381	NA	P-0003858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	34	192	0	ENST00000304494.5:c.322G>A	p.Asp108Asn	p.D108N	ENST00000304494	NM_000077.4	108	Gat/Aat	2/3	1	2	FACETS	0.901	0.738	1	0.901	0.738	1	CLONAL	1	TRUE	1	0.22	2		192	343	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6048638	6048638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	38	234	0	ENST00000265849.7:c.13G>A	p.Glu5Lys	p.E5K	ENST00000265849	NM_000535.5	5	Gag/Aag	1/15	1	2	FACETS	0.768	0.635	0.916	0.768	0.635	0.916	CLONAL	1	TRUE	1	0.22	2		234	450	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218052	108218052	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1064794840	NA	P-0003858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	40	245	0	ENST00000278616.4:c.8631G>C	p.Leu2877Phe	p.L2877F	ENST00000278616	NM_000051.3	2877	ttG/ttC	59/63	0.297936362981803	3	FACETS	0.719	0.597	0.856	0.36	0.298	0.428	SUBCLONAL	1	TRUE	1	0.22	3		245	561	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649694	206649694	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	44	141	0	ENST00000367120.3:c.529G>A	p.Glu177Lys	p.E177K	ENST00000367120	NM_014002.3	177	Gag/Aag	6/22	1	2	FACETS	0.885	0.749	1	1	0.968	1	CLONAL	2	TRUE	1	0.22	2		141	226	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978935	25978935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	77	339	0	ENST00000435504.4:c.988G>A	p.Glu330Lys	p.E330K	ENST00000435504		330	Gaa/Aaa	10/13	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.22	2		339	688	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512506	149512506	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0003858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	12	141	0	ENST00000261799.4:c.935-1G>C		p.X312_splice	ENST00000261799	NM_002609.3	312			1	2	FACETS	0.491	0.345	0.671	0.491	0.345	0.671	SUBCLONAL	1	TRUE	1	0.22	2		141	222	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224498	108224498	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	76	257	0	ENST00000278616.4:c.8677G>C	p.Ala2893Pro	p.A2893P	ENST00000278616	NM_000051.3	2893	Gct/Cct	60/63	0.297936362981803	3	FACETS	1	0.973	1	0.711	0.625	0.804	CLONAL	1	TRUE	1	0.22	3		257	539	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224504	108224504	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	79	258	1	ENST00000278616.4:c.8683G>A	p.Glu2895Lys	p.E2895K	ENST00000278616	NM_000051.3	2895	Gaa/Aaa	60/63	0.297936362981803	3	FACETS	1	0.974	1	0.708	0.624	0.798	CLONAL	1	TRUE	1	0.22	3		259	563	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649235	23649235	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	43	381	0	ENST00000261584.4:c.147G>T	p.Lys49Asn	p.K49N	ENST00000261584	NM_024675.3	49	aaG/aaT	3/13	1	2	FACETS	0.566	0.472	0.67	0.566	0.472	0.67	SUBCLONAL	1	TRUE	1	0.22	2		381	691	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928869	44928869	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	60	212	0	ENST00000377967.4:c.1969G>T	p.Glu657Ter	p.E657*	ENST00000377967	NM_021140.2	657	Gaa/Taa	17/29	1	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.22	1		212	391	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617217	100617217	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	85	198	0	ENST00000308731.7:c.532G>T	p.Gly178Trp	p.G178W	ENST00000308731	NM_000061.2	178	Ggg/Tgg	7/19	1	1	FACETS	0.919	0.819	1	1	0.984	1	CLONAL	2	TRUE	0	0.22	1		198	374	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057329	180057329	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs758916231	NA	P-0003861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	16	272	0	ENST00000261937.6:c.409C>G	p.Gln137Glu	p.Q137E	ENST00000261937	NM_182925.4	137	Cag/Gag	4/30	1	2	FACETS	0.491	0.363	0.645	0.491	0.363	0.645	SUBCLONAL	1	TRUE	1	0.22	2		272	296	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148981	119148981	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	58	357	0	ENST00000264033.4:c.1201T>A	p.Cys401Ser	p.C401S	ENST00000264033	NM_005188.3	401	Tgc/Agc	8/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.22	2		357	393	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836428	89836428	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759117757	NA	P-0003861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	31	212	0	ENST00000389301.3:c.2321C>T	p.Pro774Leu	p.P774L	ENST00000389301	NM_000135.2	774	cCg/cTg	26/43	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.22	2		212	251	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578480	7578495	+	frameshift_variant	Frame_Shift_Del	DEL	TGTGGAATCAACCCAC	TGTGGAATCAACCCAC	-	novel	NA	P-0003861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	41	260	0	ENST00000269305.4:c.435_450del	p.Trp146ProfsTer19	p.W146Pfs*19	ENST00000269305	NM_001126112.2	145	ctGTGGGTTGATTCCACA/ct	5/11	0.3	2	FACETS	1	0.926	1			1	CLONAL	1	TRUE	NA	0.22	2		260	311	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942685	48942685	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913301	NA	P-0003867-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	399	466	0	ENST00000267163.4:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000267163	NM_000321.2	358	Cga/Tga	11/27	0.771418991996423	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.771418991996423	1		466	585	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0003880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	264	405	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	0.188898901887212	1	FACETS	1	0.992	1	1	0.992	1	INDETERMINATE	1	TRUE	0	0.37137735139492	1		405	829	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087360	27087360	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0003880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	32	315	0	ENST00000324856.7:c.1934C>G	p.Ser645Ter	p.S645*	ENST00000324856	NM_006015.4	645	tCa/tGa	5/20	0.332961341177537	1	FACETS	0.237	0.192	0.289	0.237	0.192	0.289	SUBCLONAL	1	TRUE	0	0.37137735139492	1		315	591	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78923342	78923342	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749994413	NA	P-0003880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	62	215	0	ENST00000306801.3:c.3365C>T	p.Thr1122Met	p.T1122M	ENST00000306801	NM_020761.2	1122	aCg/aTg	28/34	0.357132233267181	2	FACETS	0.681	0.59	0.781	0.341	0.295	0.391	SUBCLONAL	1	TRUE	0	0.37137735139492	2		215	490	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023576	27023604	+	frameshift_variant	Frame_Shift_Del	DEL	GCCTACGCGCTGAGCTCCCCGAGAGGTGG	GCCTACGCGCTGAGCTCCCCGAGAGGTGG	A	novel	NA	P-0003880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	130	303	0	ENST00000324856.7:c.682_710delinsA	p.Ala228ThrfsTer126	p.A228Tfs*126	ENST00000324856	NM_006015.4	228	GCCTACGCGCTGAGCTCCCCGAGAGGTGGc/Ac	1/20	0.332961341177537	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.37137735139492	1		303	399	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0003890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	415	344	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.739132996269536	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	0	0.739132996269536	1		344	641	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0003890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	160	339	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	1	2	FACETS	0.947	0.877	1	0.947	0.877	1	CLONAL	1	FALSE	1	0.739132996269536	2		339	457	SUCCESS
APC	324	MSKCC	GRCh37	5	112175561	112175561	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	268	356	0	ENST00000257430.4:c.4271del	p.Pro1424GlnfsTer49	p.P1424Qfs*49	ENST00000257430	NM_000038.5	1424	Cca/ca	16/16	0.739132996269536	1	FACETS	0.941	0.895	0.986	0.941	0.895	0.986	CLONAL	1	FALSE	0	0.739132996269536	1		356	486	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969932	81969932	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024473204	NA	P-0003890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	497	543	0	ENST00000359376.3:c.3001C>T	p.Arg1001Cys	p.R1001C	ENST00000359376	NM_002661.3	1001	Cgc/Tgc	27/33	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.739132996269536	2		543	1329	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953858	17953869	+	inframe_deletion	In_Frame_Del	DEL	CCGGCCGCTGGG	CCGGCCGCTGGG	-	novel	NA	P-0003890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	311	269	0	ENST00000458235.1:c.533_544del	p.Ala178_Pro181del	p.A178_P181del	ENST00000458235	NM_000215.3	178	gCCCAGCGGCCGGga/gga	5/24	1	2	FACETS	0.939	0.888	0.991	0.939	0.888	0.991	CLONAL	1	FALSE	1	0.739132996269536	2		269	896	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0003923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	120	323	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.414446050100682	2		323	516	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	72	140	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.414446050100682	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.414446050100682	1		142	248	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0003923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	158	379	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.414446050100682	2		379	656	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0003923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	142	259	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.414446050100682	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.414446050100682	1		259	490	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28929495	NA	P-0003923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	103	321	0	ENST00000275493.2:c.2155G>T	p.Gly719Cys	p.G719C	ENST00000275493	NM_005228.3	719	Ggc/Tgc	18/28	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.414446050100682	2		321	490	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814578	43814578	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs898662151	NA	P-0003923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	179	396	3	ENST00000372470.3:c.1373G>T	p.Arg458Leu	p.R458L	ENST00000372470	NM_005373.2	458	cGt/cTt	9/12	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.414446050100682	2		399	800	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249026	55249026	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	104	276	2	ENST00000275493.2:c.2324G>A	p.Cys775Tyr	p.C775Y	ENST00000275493	NM_005228.3	775	tGc/tAc	20/28	1	2	FACETS	0.895	0.803	0.991	0.895	0.803	0.991	CLONAL	1	TRUE	1	0.414446050100682	2		278	561	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047294	77047294	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	152	317	0	ENST00000356341.3:c.1250A>T	p.Glu417Val	p.E417V	ENST00000356341	NM_002576.4	417	gAg/gTg	13/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.414446050100682	2		317	640	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610490	81610490	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	169	328	0	ENST00000298171.2:c.2088T>A	p.Phe696Leu	p.F696L	ENST00000298171	NM_000369.2	696	ttT/ttA	10/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.414446050100682	2		328	733	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584749	48584752	+	frameshift_variant	Frame_Shift_Del	DEL	ACAC	ACAC	-	novel	NA	P-0003923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	159	287	0	ENST00000342988.3:c.829_832del	p.Thr277LeufsTer58	p.T277Lfs*58	ENST00000342988	NM_005359.5	276	tACACa/ta	7/12	0.414446050100682	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.414446050100682	1		287	536	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906409	50906418	+	frameshift_variant	Frame_Shift_Del	DEL	TGCGGCCCTG	TGCGGCCCTG	GGGGGCCTT	novel	NA	P-0003923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	187	510	0	ENST00000440232.2:c.1070_1079delinsGGGGGCCTT	p.Leu357ArgfsTer36	p.L357Rfs*36	ENST00000440232	NM_002691.3	357	cTGCGGCCCTGt/cGGGGGCCTTt	9/27	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.414446050100682	2		510	862	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741925	162741925	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003937-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	134	268	0	ENST00000367921.3:c.1616C>A	p.Ser539Ter	p.S539*	ENST00000367921	NM_006182.2	539	tCa/tAa	13/18	0.283570589087317	4	FACETS	0.885	0.809	0.964	0.885	0.809	0.964	CLONAL	2	TRUE	2	0.437906497795659	4		268	497	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439268	52439268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003937-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	66	147	0	ENST00000460680.1:c.974C>T	p.Ser325Phe	p.S325F	ENST00000460680	NM_004656.3	325	tCc/tTc	11/17	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.437906497795659	2		147	261	SUCCESS
APC	324	MSKCC	GRCh37	5	112175222	112175222	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003937-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	45	180	0	ENST00000257430.4:c.3931A>T	p.Ile1311Phe	p.I1311F	ENST00000257430	NM_000038.5	1311	Att/Ttt	16/16	1	2	FACETS	0.875	0.742	1	0.875	0.742	1	CLONAL	1	TRUE	1	0.437906497795659	2		180	235	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719941	18719941	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003937-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	106	321	0	ENST00000266497.5:c.3838C>G	p.Leu1280Val	p.L1280V	ENST00000266497		1280	Cta/Gta	27/31	NA	2	FACETS	1	0.952	1			1	INDETERMINATE	1	TRUE	NA	0.437906497795659	2		321	444	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420885	49420885	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003937-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	128	201	0	ENST00000301067.7:c.14864C>A	p.Ser4955Tyr	p.S4955Y	ENST00000301067	NM_003482.3	4955	tCc/tAc	48/54	0.437906497795659	4	FACETS	0.916	0.836	0.999	0.916	0.836	0.999	CLONAL	2	TRUE	2	0.437906497795659	4		201	459	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778345	3778345	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003937-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	35	114	0	ENST00000262367.5:c.6703C>T	p.Gln2235Ter	p.Q2235*	ENST00000262367	NM_004380.2	2235	Caa/Taa	31/31	1	2	FACETS	1	0.836	1	1	0.836	1	CLONAL	1	TRUE	1	0.437906497795659	2		114	159	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207166	1207166	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0003937-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	126	242	0	ENST00000326873.7:c.254T>A	p.Leu85Ter	p.L85*	ENST00000326873	NM_000455.4	85	tTg/tAg	1/10	0.437906497795659	2	FACETS	0.875	0.803	0.948	0.875	0.803	0.948	CLONAL	2	TRUE	0	0.437906497795659	2		242	329	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602496	10602496	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750532889	NA	P-0003937-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	198	266	0	ENST00000171111.5:c.1082C>T	p.Pro361Leu	p.P361L	ENST00000171111	NM_203500.1	361	cCg/cTg	3/6	0.437906497795659	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.437906497795659	2		266	380	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138500	11138500	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003937-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	211	356	0	ENST00000358026.2:c.3256G>T	p.Asp1086Tyr	p.D1086Y	ENST00000358026	NM_001128849.1	1086	Gat/Tat	24/36	0.437906497795659	2	FACETS	0.985	0.925	1	0.985	0.925	1	CLONAL	2	TRUE	0	0.437906497795659	2		356	489	SUCCESS
AR	367	MSKCC	GRCh37	X	66766499	66766499	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1409800023	NA	P-0003937-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	86	259	0	ENST00000374690.3:c.1511A>G	p.Tyr504Cys	p.Y504C	ENST00000374690	NM_000044.3	504	tAc/tGc	1/8	0.437906497795659	2	FACETS	1	0.94	1			1	CLONAL	1	TRUE	NA	0.437906497795659	2		259	363	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115739	108115774	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAACCCAAGAAAAAGGTATAAAGGAAATGTTTACTG	AAACCCAAGAAAAAGGTATAAAGGAAATGTTTACTG	-	novel	NA	P-0003937-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	107	146	0	ENST00000278616.4:c.887_901+21del		p.X296_splice	ENST00000278616	NM_000051.3	296		7/63	0.437906497795659	3	FACETS	0.852	0.781	0.924	0.852	0.781	0.924	CLONAL	3	TRUE	0	0.437906497795659	3		146	233	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814954	139814954	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003937-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	185	566	0	ENST00000247668.2:c.949del	p.Leu317Ter	p.L317*	ENST00000247668	NM_021138.3	316	gCc/gc	8/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.437906497795659	2		566	736	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980313	7980313	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003971-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	68	11	131	0	ENST00000319144.4:c.1270T>C	p.Tyr424His	p.Y424H	ENST00000319144	NM_001139.2	424	Tac/Cac	9/15	0.208767675598873	7	FACETS	1	0.711	1	0.406	0.284	0.552	CLONAL	2	TRUE	2	0.208767675598873	7		131	79	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593284	67593299	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGCTATGGCTTTGC	CTGGCTATGGCTTTGC	-	novel	NA	P-0003971-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	127	20	367	0	ENST00000274335.5:c.2031_2046del	p.Gly678SerfsTer9	p.G678Sfs*9	ENST00000274335		677	aCTGGCTATGGCTTTGCc/ac	15/15	0.208767675598873	9	FACETS	1	0.845	1			1	CLONAL	2	TRUE	NA	0.208767675598873	9		367	147	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856060	151856060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751794784	NA	P-0003986-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	83	388	0	ENST00000262189.6:c.11558G>A	p.Arg3853Gln	p.R3853Q	ENST00000262189	NM_170606.2	3853	cGg/cAg	44/59	0.705384407908113	3	FACETS	0.679	0.601	0.761			1	SUBCLONAL	1	TRUE	NA	0.705384407908113	3		388	469	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492966	8492966	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003986-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	12	156	0	ENST00000356435.5:c.2363C>T	p.Ser788Phe	p.S788F	ENST00000356435		788	tCt/tTt	16/35	0.14308316479356	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.705384407908113	0		156	140	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261434	16261434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	21	200	0	ENST00000375759.3:c.8699C>T	p.Ser2900Leu	p.S2900L	ENST00000375759	NM_015001.2	2900	tCg/tTg	11/15	1	2	FACETS	0.727	0.561	0.921	0.727	0.561	0.921	CLONAL	1	FALSE	1	0.216313864480818	2		200	267	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0003996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	57	603	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.216313864480818	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	0	0.216313864480818	1		603	371	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610033	43610033	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	34	524	0	ENST00000355710.3:c.1985A>C	p.Lys662Thr	p.K662T	ENST00000355710	NM_020975.4	662	aAg/aCg	11/20	1	2	FACETS	0.788	0.644	0.949	0.788	0.644	0.949	CLONAL	1	FALSE	1	0.216313864480818	2		524	399	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604688	48604688	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	30	259	0	ENST00000342988.3:c.1510A>C	p.Ser504Arg	p.S504R	ENST00000342988	NM_005359.5	504	Agt/Cgt	12/12	0.216313864480818	1	FACETS	1	0.83	1	1	0.83	1	CLONAL	1	FALSE	0	0.216313864480818	1		259	241	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909491	50909491	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139557851	NA	P-0003996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	41	607	0	ENST00000440232.2:c.1295G>A	p.Arg432Gln	p.R432Q	ENST00000440232	NM_002691.3	432	cGg/cAg	11/27	0.216313864480818	0	FACETS	0.764	0.637	0.904			1	CLONAL	1	FALSE	0	0.216313864480818	0		607	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0004025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	94	344	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.25	2		344	622	SUCCESS
APC	324	MSKCC	GRCh37	5	112164557	112164557	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs144056494	NA	P-0004025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	35	84	0	ENST00000257430.4:c.1631T>C	p.Ile544Thr	p.I544T	ENST00000257430	NM_000038.5	544	aTt/aCt	14/16	1	2	FACETS	1	0.823	1	1	0.823	1	CLONAL	1	TRUE	1	0.25	2		84	280	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922294	100922294	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1315135533	NA	P-0004025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	59	253	0	ENST00000325455.5:c.2218C>T	p.Arg740Ter	p.R740*	ENST00000325455	NM_001202474.3	740	Cga/Tga	5/8	1	2	FACETS	0.837	0.72	0.964	0.837	0.72	0.964	CLONAL	1	TRUE	1	0.25	2		253	564	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226294	2226294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	53	182	0	ENST00000326181.6:c.1907C>T	p.Thr636Met	p.T636M	ENST00000326181	NM_032271.2	636	aCg/aTg	20/21	0.297436986477322	1	FACETS	0.753	0.642	0.873	0.753	0.642	0.873	SUBCLONAL	1	TRUE	0	0.25	1		182	493	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790027	40790027	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	53	135	0	ENST00000373198.4:c.2704A>G	p.Arg902Gly	p.R902G	ENST00000373198	NM_133170.3	902	Aga/Gga	18/32	0.16697287769214	2	FACETS	0.857	0.731	0.994	0.428	0.365	0.497	CLONAL	1	TRUE	0	0.25	2		135	495	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0004041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	126	298	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.921	0.84	1	0.921	0.84	1	CLONAL	1	TRUE	1	0.621937111964392	2		298	440	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763098116	NA	P-0004041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	228	443	0	ENST00000269305.4:c.830G>A	p.Cys277Tyr	p.C277Y	ENST00000269305	NM_001126112.2	277	tGt/tAt	8/11	0.521424951616791	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.621937111964392	1		443	459	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257894	198257894	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	163	383	0	ENST00000335508.6:c.3558G>T	p.Gln1186His	p.Q1186H	ENST00000335508	NM_012433.2	1186	caG/caT	24/25	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.621937111964392	2		383	501	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89880930	89880930	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004061-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	421	484	0	ENST00000389301.3:c.281T>C	p.Ile94Thr	p.I94T	ENST00000389301	NM_000135.2	94	aTa/aCa	3/43	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.804838064025708	2		484	1005	SUCCESS
APC	324	MSKCC	GRCh37	5	112176740	112176743	+	frameshift_variant	Frame_Shift_Del	DEL	AAAA	AAAA	-	novel	NA	P-0004061-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	278	465	0	ENST00000257430.4:c.5450_5453del	p.Lys1817IlefsTer45	p.K1817Ifs*45	ENST00000257430	NM_000038.5	1817	AAAAat/at	16/16	0.764080956998662	1	FACETS	0.978	0.937	1	0.978	0.937	1	CLONAL	1	TRUE	0	0.804838064025708	1		465	422	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593604	55593604	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057520032	NA	P-0004068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	187	291	0	ENST00000288135.5:c.1670G>C	p.Trp557Ser	p.W557S	ENST00000288135	NM_000222.2	557	tGg/tCg	11/21	0.183153686967796	3	FACETS	0.941	0.871	1	1	0.989	1	CLONAL	3	TRUE	1	0.183153686967796	3		291	790	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394896	394896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	127	171	0	ENST00000380956.4:c.292C>T	p.Arg98Trp	p.R98W	ENST00000380956	NM_001195286.1	98	Cgg/Tgg	3/9	1	2	FACETS	1	0.962	1	1	0.992	1	CLONAL	3	TRUE	1	0.183153686967796	2		171	422	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399409	139399411	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	rs761020817	NA	P-0004068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	138	197	3	ENST00000277541.6:c.4732_4734del	p.Val1578del	p.V1578del	ENST00000277541	NM_017617.3	1578	GTG/-	26/34	1	2	FACETS	1	0.955	1	1	0.993	1	CLONAL	3	TRUE	1	0.183153686967796	2		200	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0004073-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	362	717	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.983	0.934	1	1	0.996	1	CLONAL	2	TRUE	1	0.361300417275069	2		718	1019	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0004073-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	151	235	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.986	0.91	1	1	0.992	1	CLONAL	2	TRUE	1	0.361300417275069	2		235	424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0004073-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	273	175	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	0.996	1	CLONAL	2	TRUE	1	0.361300417275069	2		175	708	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285648	46285648	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004073-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	60	263	0	ENST00000334344.6:c.5008G>T	p.Glu1670Ter	p.E1670*	ENST00000334344	NM_152641.2	1670	Gaa/Taa	17/21	0.245969753350589	1	FACETS	0.754	0.653	0.863	0.754	0.653	0.863	SUBCLONAL	1	TRUE	0	0.361300417275069	1		263	361	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16055282	16055282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004073-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	183	272	0	ENST00000268712.3:c.820G>A	p.Val274Met	p.V274M	ENST00000268712	NM_006311.3	274	Gtg/Atg	8/46	1	2	FACETS	0.914	0.849	0.981	1	0.993	1	CLONAL	2	TRUE	1	0.361300417275069	2		272	554	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939548	76939549	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	C	novel	NA	P-0004073-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	132	193	0	ENST00000373344.5:c.1199_1200delinsG	p.Ala400GlyfsTer14	p.A400Gfs*14	ENST00000373344	NM_000489.3	400	gCT/gG	9/35	0.282544680330716	0	FACETS	0.778	0.73	0.824			1	SUBCLONAL	3	TRUE	NA	0.361300417275069	0		193	200	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913381	NA	P-0004085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	129	192	0	ENST00000304494.5:c.322G>A	p.Asp108Asn	p.D108N	ENST00000304494	NM_000077.4	108	Gat/Aat	2/3	0.254199533117458	1	FACETS	0.834	0.766	0.904	1	0.992	1	CLONAL	3	TRUE	0	0.254199533117458	1		192	354	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429779	78429779	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	126	257	0	ENST00000370768.2:c.1009G>A	p.Glu337Lys	p.E337K	ENST00000370768	NM_003902.3	337	Gaa/Aaa	12/20	0.237634038563512	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	0	0.254199533117458	2		257	468	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658609	206658609	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	142	216	0	ENST00000367120.3:c.1582G>A	p.Val528Met	p.V528M	ENST00000367120	NM_014002.3	528	Gtg/Atg	15/22	0.254199533117458	2	FACETS	0.96	0.885	1	1	0.988	1	CLONAL	3	TRUE	0	0.254199533117458	2		216	388	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800946	243800946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	45	381	0	ENST00000263826.5:c.528G>A	p.Met176Ile	p.M176I	ENST00000263826	NM_005465.4	176	atG/atA	5/13	0.254199533117458	2	FACETS	0.484	0.406	0.572	0.242	0.203	0.286	SUBCLONAL	1	TRUE	0	0.254199533117458	2		381	731	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911585	134911585	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	60	202	0	ENST00000398015.3:c.2050G>C	p.Glu684Gln	p.E684Q	ENST00000398015	NM_004441.4	684	Gag/Cag	11/16	0.208349346647719	3	FACETS	1	0.954	1	0.627	0.542	0.72	CLONAL	1	TRUE	1	0.254199533117458	3		202	424	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281863	142281863	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	78	215	0	ENST00000350721.4:c.381C>G	p.Ile127Met	p.I127M	ENST00000350721	NM_001184.3	127	atC/atG	4/47	0.208349346647719	3	FACETS	0.791	0.698	0.89	0.791	0.698	0.89	SUBCLONAL	2	TRUE	1	0.254199533117458	3		215	437	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456477	189456477	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	36	253	0	ENST00000264731.3:c.238C>A	p.Pro80Thr	p.P80T	ENST00000264731	NM_003722.4	80	Cca/Aca	3/14	0.208349346647719	3	FACETS	0.469	0.385	0.565	0.235	0.192	0.283	SUBCLONAL	1	TRUE	1	0.254199533117458	3		253	680	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176684141	176684141	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	84	279	0	ENST00000439151.2:c.4955C>T	p.Ser1652Phe	p.S1652F	ENST00000439151	NM_022455.4	1652	tCt/tTt	13/23	0.254199533117458	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.254199533117458	1		279	397	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673161	30673161	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	168	250	0	ENST00000376406.3:c.3799C>T	p.Gln1267Ter	p.Q1267*	ENST00000376406	NM_014641.2	1267	Cag/Tag	10/15	0.224689457550863	4	FACETS	0.903	0.838	0.969			1	CLONAL	4	TRUE	NA	0.254199533117458	4		250	459	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138642	37138642	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs936800231	NA	P-0004085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	30	178	0	ENST00000373509.5:c.176C>G	p.Ser59Cys	p.S59C	ENST00000373509	NM_002648.3	59	tCc/tGc	2/6	0.254199533117458	5	FACETS	0.729	0.587	0.891	0.243	0.195	0.297	SUBCLONAL	1	TRUE	2	0.254199533117458	5		178	447	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199839	108199839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779861	NA	P-0004085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	175	251	0	ENST00000278616.4:c.7181C>T	p.Ser2394Leu	p.S2394L	ENST00000278616	NM_000051.3	2394	tCa/tTa	49/63	0.208349346647719	3	FACETS	0.969	0.898	1	1	0.99	1	CLONAL	3	TRUE	1	0.254199533117458	3		251	534	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28908251	28908251	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	84	325	0	ENST00000282397.4:c.2504G>C	p.Arg835Thr	p.R835T	ENST00000282397	NM_002019.4	835	aGa/aCa	18/30	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.254199533117458	2		325	545	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993420	72993420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1382582139	NA	P-0004085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	116	474	1	ENST00000268489.5:c.625G>A	p.Glu209Lys	p.E209K	ENST00000268489	NM_006885.3	209	Gag/Aag	2/10	0.254199533117458	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.254199533117458	1		475	630	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216755	7216755	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	41	366	0	ENST00000380728.2:c.668C>G	p.Ser223Cys	p.S223C	ENST00000380728		223	tCt/tGt	8/11	0.254199533117458	1	FACETS	0.488	0.406	0.58	0.488	0.406	0.58	SUBCLONAL	1	TRUE	0	0.254199533117458	1		366	577	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243589	41243589	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	25	391	0	ENST00000357654.3:c.3959C>G	p.Ser1320Cys	p.S1320C	ENST00000357654	NM_007294.3	1320	tCt/tGt	10/23	0.254199533117458	1	FACETS	0.355	0.279	0.443	0.355	0.279	0.443	SUBCLONAL	1	TRUE	0	0.254199533117458	1		391	483	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543605	9543605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1159424856	NA	P-0004085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	218	356	0	ENST00000353224.5:c.1549G>A	p.Asp517Asn	p.D517N	ENST00000353224	NM_177990.2	517	Gat/Aat	6/10	1	2	FACETS	1	0.937	1	1	0.994	1	CLONAL	2	TRUE	1	0.254199533117458	2		356	853	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229229	123229229	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0004085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	174	170	0	ENST00000218089.9:c.3713C>G	p.Ser1238Ter	p.S1238*	ENST00000218089	NM_001042749.1	1238	tCa/tGa	34/35	1	1	FACETS	0.96	0.895	1	1	0.994	1	CLONAL	3	TRUE	0	0.254199533117458	1		170	415	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433971	49434101	+	frameshift_variant	Frame_Shift_Del	DEL	CAAATGCACCCGTCCCAGGGGACCGGACAAAATTGGGGGGCTGCCCACTTGGGACCTTGGCATGGAGCTCACCTGCTGGCCCCGCGGGCAGGGCTGCTGGGAACCCCCCAGCCCCCAGCGAAGTGTGGGCT	CAAATGCACCCGTCCCAGGGGACCGGACAAAATTGGGGGGCTGCCCACTTGGGACCTTGGCATGGAGCTCACCTGCTGGCCCCGCGGGCAGGGCTGCTGGGAACCCCCCAGCCCCCAGCGAAGTGTGGGCT	-	novel	NA	P-0004085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	38	166	0	ENST00000301067.7:c.7452_7582del	p.Ala2485GlyfsTer126	p.A2485Gfs*126	ENST00000301067	NM_003482.3	2484	ctAGCCCACACTTCGCTGGGGGCTGGGGGGTTCCCAGCAGCCCTGCCCGCGGGGCCAGCAGGTGAGCTCCATGCCAAGGTCCCAAGTGGGCAGCCCCCCAATTTTGTCCGGTCCCCTGGGACGGGTGCATTTGtg/cttg	31/54	0.254199533117458	3	FACETS	1	0.948	1	0.705	0.587	0.835	CLONAL	1	TRUE	1	0.254199533117458	3		166	239	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224531	108224546	+	frameshift_variant	Frame_Shift_Del	DEL	GAGACAGTTCCTTTTA	GAGACAGTTCCTTTTA	-	novel	NA	P-0004085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	37	245	0	ENST00000278616.4:c.8712_8727del	p.Glu2904AspfsTer29	p.E2904Dfs*29	ENST00000278616	NM_000051.3	2904	GAGACAGTTCCTTTTAga/ga	60/63	0.208349346647719	3	FACETS	0.689	0.568	0.825	0.345	0.284	0.413	SUBCLONAL	1	TRUE	1	0.254199533117458	3		245	476	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042326	42042326	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	85	637	0	ENST00000219905.7:c.6522del	p.Trp2174Ter	p.W2174*	ENST00000219905	NM_001164273.1	2174	tGg/tg	17/24	0.254199533117458	0	FACETS	0.959	0.85	1			1	CLONAL	1	TRUE	0	0.254199533117458	0		637	520	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440519	49440520	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CA	CA	-	novel	NA	P-0004085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	123	254	0	ENST00000301067.7:c.4290_4291del	p.Cys1430Ter	p.C1430*	ENST00000301067	NM_003482.3	1430	tgTGag/tgag	15/54	0.254199533117458	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.254199533117458	3		254	492	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0004088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	42	280	0	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	0.3	2	FACETS	0.529	0.44	0.629			1	SUBCLONAL	1	TRUE	NA	0.14	2		280	1134	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398831	398831	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs538810711	NA	P-0004088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1253	80	342	3	ENST00000380956.4:c.641G>T	p.Cys214Phe	p.C214F	ENST00000380956	NM_001195286.1	214	tGc/tTc	6/9	1	2	FACETS	0.857	0.752	0.972	0.857	0.752	0.972	CLONAL	1	TRUE	1	0.14	2		345	1333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0004105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	135	418	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.424628441777165	1	FACETS	0.762	0.695	0.833	0.762	0.695	0.833	SUBCLONAL	1	TRUE	0	0.424628441777165	1		418	657	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947383	38947383	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	87	297	0	ENST00000357387.3:c.4297A>G	p.Ile1433Val	p.I1433V	ENST00000357387	NM_152756.3	1433	Ata/Gta	32/38	1	2	FACETS	0.773	0.686	0.866	0.773	0.686	0.866	SUBCLONAL	1	TRUE	1	0.424628441777165	2		297	530	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405292	70405292	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1330901615	NA	P-0004105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	64	336	0	ENST00000373644.4:c.2806A>G	p.Thr936Ala	p.T936A	ENST00000373644	NM_030625.2	936	Act/Gct	4/12	0.29515648545968	1	FACETS	0.383	0.331	0.439	0.383	0.331	0.439	SUBCLONAL	1	TRUE	0	0.424628441777165	1		336	620	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348228	70348228	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	146	417	1	ENST00000374080.3:c.3292G>C	p.Ala1098Pro	p.A1098P	ENST00000374080		1098	Gcc/Ccc	23/45	0.372328718925855	1	FACETS	0.723	0.661	0.788	0.723	0.661	0.788	SUBCLONAL	1	TRUE	0	0.424628441777165	1		418	749	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242493	+	protein_altering_variant	In_Frame_Del	DEL	TAAGAGAAGCAACATCTCCGAAAG	TAAGAGAAGCAACATCTCCGAAAG	CGATGT	novel	NA	P-0004105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	66	282	0	ENST00000275493.2:c.2240_2263delinsCGATGT	p.Leu747_Ala755delinsSerMetSer	p.L747_A755delinsSMS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCCGAAAGcc/tCGATGTcc	19/28	1	2	FACETS	0.505	0.438	0.577	0.505	0.438	0.577	SUBCLONAL	1	TRUE	1	0.424628441777165	2		282	616	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982031	93982031	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	46	454	0	ENST00000369303.4:c.1434C>G	p.Ile478Met	p.I478M	ENST00000369303	NM_004440.3	478	atC/atG	6/17	0.181187971647421	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.775921744718984	0		454	624	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015109	37015109	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	205	426	0	ENST00000358127.4:c.295A>T	p.Ile99Phe	p.I99F	ENST00000358127	NM_001280556.1	99	Atc/Ttc	3/10	0.782933805292654	3	FACETS	0.981	0.913	1	0.49	0.456	0.526	CLONAL	1	TRUE	1	0.782933805292654	3		426	743	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782620	NA	P-0004107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	354	240	1	ENST00000269305.4:c.427G>A	p.Val143Met	p.V143M	ENST00000269305	NM_001126112.2	143	Gtg/Atg	5/11	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.782933805292654	2		241	415	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657562	37657562	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	762	376	0	ENST00000447079.4:c.2479G>T	p.Gly827Cys	p.G827C	ENST00000447079	NM_015083.1	827	Ggt/Tgt	6/14	0.773659650600745	5	FACETS	0.881	0.858	0.904			1	CLONAL	4	TRUE	NA	0.782933805292654	5		376	1201	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158549	26158554	+	inframe_deletion	In_Frame_Del	DEL	CCGACA	CCGACA	-	novel	NA	P-0004107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	173	211	0	ENST00000289316.2:c.155_160del	p.Asp52_Thr53del	p.D52_T53del	ENST00000289316	NM_138720.2	51	cCCGACAcc/ccc	1/2	0.324109321501286	6	FACETS	0.792	0.731	0.855	0.528	0.487	0.57	INDETERMINATE	2	TRUE	3	0.782933805292654	6		211	716	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0004110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	199	290	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.31	2		290	912	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2972201	2972201	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	90	227	0	ENST00000396946.4:c.1538C>T	p.Pro513Leu	p.P513L	ENST00000396946	NM_032415.4	513	cCc/cTc	11/25	0.168974260922456	1	FACETS	1	0.895	1	1	0.895	1	INDETERMINATE	1	TRUE	0	0.31	1		227	488	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514940	103514940	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1008091379	NA	P-0004110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	96	199	0	ENST00000355739.4:c.1441G>T	p.Val481Leu	p.V481L	ENST00000355739	NM_000123.3	481	Gtg/Ttg	8/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.31	2		199	518	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610227	10610227	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	214	615	0	ENST00000171111.5:c.483G>T	p.Met161Ile	p.M161I	ENST00000171111	NM_203500.1	161	atG/atT	2/6	0.295728048523137	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.31	1		615	805	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221321	1221322	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0004110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	156	356	0	ENST00000326873.7:c.848_849del	p.Ser283Ter	p.S283*	ENST00000326873	NM_000455.4	282	CTc/c	6/10	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.31	2		356	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0004130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	228	473	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.287937174160008	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.287937174160008	1		473	1104	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199967	128199967	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	86	238	0	ENST00000341105.2:c.1338C>G	p.Phe446Leu	p.F446L	ENST00000341105	NM_032638.4	446	ttC/ttG	6/6	1	2	FACETS	0.685	0.605	0.771	0.685	0.605	0.771	SUBCLONAL	1	TRUE	1	0.287937174160008	2		238	872	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549308	187549308	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	114	307	0	ENST00000441802.2:c.4810G>A	p.Gly1604Arg	p.G1604R	ENST00000441802	NM_005245.3	1604	Gga/Aga	9/27	0.287937174160008	1	FACETS	0.858	0.772	0.949	0.858	0.772	0.949	CLONAL	1	TRUE	0	0.287937174160008	1		307	790	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78519437	78519437	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	46	197	0	ENST00000306801.3:c.8C>A	p.Ser3Tyr	p.S3Y	ENST00000306801	NM_020761.2	3	tCc/tAc	1/34	1	2	FACETS	0.643	0.541	0.755	0.643	0.541	0.755	SUBCLONAL	1	TRUE	1	0.287937174160008	2		197	497	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208290	5208290	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	238	489	0	ENST00000357368.4:c.5600A>C	p.Lys1867Thr	p.K1867T	ENST00000357368	NM_002850.3	1867	aAg/aCg	36/38	0.287937174160008	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.287937174160008	1		489	1042	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997826	149997826	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	148	309	1	ENST00000253339.5:c.2641del	p.Asp881IlefsTer11	p.D881Ifs*11	ENST00000253339		881	Gat/at	5/7	0.287937174160008	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.287937174160008	1		310	747	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176085759	176085759	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0004130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	145	343	0	ENST00000367669.3:c.1026+1del		p.X342_splice	ENST00000367669	NM_022457.5	342			0.196637660935907	1	FACETS	0.908	0.828	0.993	0.908	0.828	0.993	CLONAL	1	TRUE	0	0.287937174160008	1		343	949	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120526	94120536	+	frameshift_variant	Frame_Shift_Del	DEL	TCCAATCTCTC	TCCAATCTCTC	-	novel	NA	P-0004130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1710	317	612	0	ENST00000369303.4:c.515_525del	p.Arg172ThrfsTer35	p.R172Tfs*35	ENST00000369303	NM_004440.3	172	aGAGAGATTGGA/a	3/17	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.287937174160008	2		612	2027	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359053	81359053	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	33	454	0	ENST00000222390.5:c.908C>G	p.Thr303Ser	p.T303S	ENST00000222390	NM_000601.4	303	aCt/aGt	8/18	1	2	FACETS	0.94	0.764	1	0.94	0.764	1	CLONAL	1	TRUE	1	0.12	2		454	585	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508349	106508349	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	16	107	0	ENST00000359195.3:c.343G>T	p.Val115Leu	p.V115L	ENST00000359195	NM_002649.2	115	Gtg/Ttg	2/11	1	2	FACETS	0.844	0.623	1	0.844	0.623	1	CLONAL	1	TRUE	1	0.12	2		107	316	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161390	2161390	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	55	448	0	ENST00000434045.2:c.137G>T	p.Arg46Leu	p.R46L	ENST00000434045	NM_001127598.1	46	cGc/cTc	2/5	1	2	FACETS	0.887	0.756	1	0.887	0.756	1	CLONAL	1	TRUE	1	0.12	2		448	1033	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220703	1220703	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	41	347	0	ENST00000326873.7:c.721G>C	p.Ala241Pro	p.A241P	ENST00000326873	NM_000455.4	241	Gct/Cct	5/10	1	2	FACETS	0.943	0.783	1	0.943	0.783	1	CLONAL	1	TRUE	1	0.12	2		347	725	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602764	10602764	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	44	358	2	ENST00000171111.5:c.814C>T	p.Arg272Cys	p.R272C	ENST00000171111	NM_203500.1	272	Cgc/Tgc	3/6	1	2	FACETS	0.872	0.729	1	0.872	0.729	1	CLONAL	1	TRUE	1	0.12	2		360	841	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577137	7577138	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0004131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	40	431	0	ENST00000269305.4:c.800_801delinsTT	p.Arg267Leu	p.R267L	ENST00000269305	NM_001126112.2	267	cGG/cTT	8/11	1	2	FACETS	0.645	0.533	0.77	0.645	0.533	0.77	SUBCLONAL	1	TRUE	1	0.12	2		431	1034	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0004158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	149	275	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.231693831396999	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	FALSE	0	0.231693831396999	3		275	418	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152641	99152641	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	36	382	0	ENST00000074304.5:c.437A>G	p.Asp146Gly	p.D146G	ENST00000074304	NM_001134224.1	146	gAc/gGc	7/26	0.231693831396999	6	FACETS	0.783	0.642	0.941	0.196	0.16	0.236	CLONAL	1	FALSE	2	0.231693831396999	6		382	581	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430771	47430771	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764281834	NA	P-0004158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	99	369	1	ENST00000377045.4:c.1736G>A	p.Arg579Gln	p.R579Q	ENST00000377045	NM_001654.4	579	cGg/cAg	16/16	NA	2	FACETS	0.828	0.742	0.919			1	INDETERMINATE	2	FALSE	NA	0.231693831396999	2		370	516	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577382	64577382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757766498	NA	P-0004164-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	208	402	0	ENST00000312049.6:c.200C>T	p.Pro67Leu	p.P67L	ENST00000312049	NM_130799.2	67	cCc/cTc	2/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.476405551444287	2		402	816	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0004166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	47	334	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.16856499521673	5	FACETS	0.706	0.597	0.825			1	INDETERMINATE	1	TRUE	NA	0.708078305718579	5		334	388	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894230	NA	P-0004166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	33	132	0	ENST00000451590.1:c.35G>T	p.Gly12Val	p.G12V	ENST00000451590	NM_001130442.1	12	gGc/gTc	2/5	0.201247504933501	4	FACETS	0.49	0.4	0.591	0.245	0.2	0.296	INDETERMINATE	1	TRUE	2	0.708078305718579	4		132	325	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974695	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691187	NA	P-0004166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	94	159	0	ENST00000304494.5:c.132del	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	taC/ta	1/3	0.708078305718579	1	FACETS	0.991	0.909	1	0.991	0.909	1	CLONAL	1	TRUE	0	0.708078305718579	1		159	173	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054006	42054006	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	76	287	0	ENST00000219905.7:c.7468C>T	p.Arg2490Ter	p.R2490*	ENST00000219905	NM_001164273.1	2490	Cga/Tga	21/24	NA	2	FACETS	1	0.904	1			1	INDETERMINATE	1	TRUE	NA	0.708078305718579	2		287	212	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578238	7578255	+	inframe_deletion	In_Frame_Del	DEL	TCCACACGCAAATTTCCT	TCCACACGCAAATTTCCT	-	rs1567551704	NA	P-0004166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	247	202	0	ENST00000269305.4:c.594_611del	p.Gly199_Glu204del	p.G199_E204del	ENST00000269305	NM_001126112.2	198	gaAGGAAATTTGCGTGTGGAg/gag	6/11	0.706802505032957	3	FACETS	0.882	0.844	0.919	0.882	0.844	0.919	CLONAL	3	TRUE	0	0.708078305718579	3		202	357	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	438	139	0	ENST00000397752.3:c.3028G>C	p.Asp1010His	p.D1010H	ENST00000397752	NM_000245.2	1010	Gat/Cat	14/21	0.378515315027425	6	FACETS	0.927	0.893	0.96			1	CLONAL	6	TRUE	NA	0.378515315027425	6		139	731	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575432	67575432	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1261761196	NA	P-0004169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	73	155	0	ENST00000274335.5:c.505A>G	p.Thr169Ala	p.T169A	ENST00000274335		169	Aca/Gca	4/15	0.312471461994498	4	FACETS	0.869	0.76	0.986			1	CLONAL	1	TRUE	NA	0.378515315027425	4		155	612	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134571	41134571	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs760394095	NA	P-0004169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	116	353	1	ENST00000379561.5:c.1057G>T	p.Ala353Ser	p.A353S	ENST00000379561	NM_002015.3	353	Gca/Tca	2/3	1	2	FACETS	0.574	0.516	0.636	0.574	0.516	0.636	SUBCLONAL	1	TRUE	1	0.378515315027425	2		354	1067	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354416	40354416	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	140	443	0	ENST00000293328.3:c.2179G>T	p.Asp727Tyr	p.D727Y	ENST00000293328	NM_012448.3	727	Gac/Tac	18/19	NA	2	FACETS	0.76	0.692	0.833			1	INDETERMINATE	1	TRUE	NA	0.378515315027425	2		443	973	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792782	33792782	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	17	58	0	ENST00000498907.2:c.539C>G	p.Pro180Arg	p.P180R	ENST00000498907	NM_004364.3	180	cCt/cGt	1/1	1	2	FACETS	0.713	0.537	0.917	0.713	0.537	0.917	CLONAL	1	TRUE	1	0.378515315027425	2		58	126	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710608	40710608	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	58	131	0	ENST00000373198.4:c.4243G>A	p.Glu1415Lys	p.E1415K	ENST00000373198	NM_133170.3	1415	Gag/Aag	31/32	0.253667819370514	3	FACETS	0.738	0.635	0.85	0.369	0.317	0.425	SUBCLONAL	1	TRUE	1	0.378515315027425	3		131	494	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044886	47044889	+	frameshift_variant	Frame_Shift_Del	DEL	AGTG	AGTG	-	rs1131691421	NA	P-0004169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	68	163	1	ENST00000377604.3:c.2214_2217del	p.Ser738ArgfsTer63	p.S738Rfs*63	ENST00000377604	NM_001204468.1	738	AGTGag/ag	20/24	0.378515315027425	1	FACETS	0.702	0.613	0.797	0.702	0.613	0.797	SUBCLONAL	1	TRUE	0	0.378515315027425	1		164	415	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0004173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	57	307	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.238320823641651	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	0	0.236951103426529	1		307	284	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692961	89692961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060500122	NA	P-0004173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	55	191	0	ENST00000371953.3:c.445C>T	p.Gln149Ter	p.Q149*	ENST00000371953	NM_000314.4	149	Caa/Taa	5/9	1	2	FACETS	0.784	0.676	0.901	1	0.97	1	CLONAL	2	FALSE	1	0.236951103426529	2		191	296	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931589	NA	P-0004173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	42	260	0	ENST00000349496.5:c.101G>A	p.Gly34Glu	p.G34E	ENST00000349496	NM_001904.3	34	gGa/gAa	3/15	1	2	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	FALSE	1	0.236951103426529	2		260	353	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155653	56155653	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	43	196	0	ENST00000399503.3:c.745C>G	p.Arg249Gly	p.R249G	ENST00000399503	NM_005921.1	249	Cgc/Ggc	3/20	0.148022389965407	4	FACETS	1	0.936	1	0.624	0.523	0.734	CLONAL	1	FALSE	2	0.236951103426529	4		196	360	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846086	68846086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876661091	NA	P-0004173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	35	340	0	ENST00000261769.5:c.1057G>A	p.Glu353Lys	p.E353K	ENST00000261769	NM_004360.3	353	Gag/Aag	8/16	0.236951103426529	1	FACETS	1	0.835	1	1	0.835	1	CLONAL	1	FALSE	0	0.236951103426529	1		340	257	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591145	67591154	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TACTTGATGT	TACTTGATGT	-	novel	NA	P-0004173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	42	204	0	ENST00000274335.5:c.1738_1745+2del		p.X580_splice	ENST00000274335		580		12/15	0.236951103426529	9	FACETS	1	0.956	1			1	CLONAL	1	FALSE	NA	0.236951103426529	9		204	435	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692951	89692953	+	frameshift_variant	Frame_Shift_Del	DEL	TTT	TTT	A	novel	NA	P-0004173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	42	204	0	ENST00000371953.3:c.435_437delinsA	p.Phe145LeufsTer34	p.F145Lfs*34	ENST00000371953	NM_000314.4	145	ttTTTa/ttAa	5/9	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	FALSE	1	0.236951103426529	2		204	308	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0004182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	160	387	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.440259111454207	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.440259111454207	1		387	380	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0004182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	81	140	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.291997892977566	4	FACETS	0.801	0.711	0.894	0.801	0.711	0.894	CLONAL	2	TRUE	2	0.440259111454207	4		142	331	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17371294	17371294	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	41	461	0	ENST00000375499.3:c.162C>A	p.Asp54Glu	p.D54E	ENST00000375499	NM_003000.2	54	gaC/gaA	2/8	NA	2	FACETS	0.478	0.398	0.565			1	INDETERMINATE	1	TRUE	NA	0.440259111454207	2		461	390	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638571	176638571	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	140	436	0	ENST00000439151.2:c.3171del	p.Gln1058SerfsTer5	p.Q1058Sfs*5	ENST00000439151	NM_022455.4	1057	aaT/aa	5/23	0.440259111454207	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.440259111454207	1		436	407	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0004191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	67	347	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.731	0.637	0.832	0.731	0.637	0.832	SUBCLONAL	1	TRUE	1	0.402761987601638	2		347	455	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521120	187521120	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752997628	NA	P-0004191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	53	225	1	ENST00000441802.2:c.12035C>T	p.Thr4012Met	p.T4012M	ENST00000441802	NM_005245.3	4012	aCg/aTg	22/27	NA	2	FACETS	0.522	0.445	0.606			1	INDETERMINATE	1	TRUE	NA	0.402761987601638	2		226	504	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950417	38950417	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1384531742	NA	P-0004191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	48	344	0	ENST00000357387.3:c.3533T>C	p.Ile1178Thr	p.I1178T	ENST00000357387	NM_152756.3	1178	aTt/aCt	31/38	0.179509768182989	4	FACETS	0.666	0.563	0.779	0.333	0.281	0.39	INDETERMINATE	1	TRUE	2	0.402761987601638	4		344	502	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8497267	8497267	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs747543296	NA	P-0004191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	36	212	0	ENST00000356435.5:c.2324G>A	p.Trp775Ter	p.W775*	ENST00000356435		775	tGg/tAg	15/35	0.112042126615861	4	FACETS	0.645	0.53	0.772	0.322	0.265	0.386	INDETERMINATE	1	TRUE	2	0.402761987601638	4		212	389	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23635345	23635345	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	80	339	0	ENST00000261584.4:c.2819A>G	p.Glu940Gly	p.E940G	ENST00000261584	NM_024675.3	940	gAa/gGa	8/13	1	2	FACETS	0.728	0.642	0.819	0.728	0.642	0.819	SUBCLONAL	1	TRUE	1	0.402761987601638	2		339	546	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862208	68862208	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0004191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	32	152	0	ENST00000261769.5:c.2295+1G>A		p.X765_splice	ENST00000261769	NM_004360.3	765			0.214212251116967	0	FACETS	0.358	0.292	0.432			1	INDETERMINATE	1	TRUE	0	0.402761987601638	0		152	265	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42384773	42384773	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782714583	NA	P-0004192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	61	467	0	ENST00000221972.3:c.535G>A	p.Gly179Arg	p.G179R	ENST00000221972	NM_021601.3	179	Ggg/Agg	4/5	1	2	FACETS	0.996	0.857	1	0.996	0.857	1	CLONAL	1	TRUE	1	0.15	2		467	817	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631837	90631837	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004200-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	80	186	1	ENST00000330062.3:c.516G>T	p.Arg172Ser	p.R172S	ENST00000330062	NM_002168.2	172	agG/agT	4/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.3	2		187	459	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	65	450	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.252713010331898	1	FACETS	0.379	0.328	0.433	0.379	0.328	0.433	INDETERMINATE	1	TRUE	0	0.434862345460578	1		451	618	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546404	46546404	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	96	326	0	ENST00000262741.5:c.125C>G	p.Pro42Arg	p.P42R	ENST00000262741	NM_003629.3	42	cCt/cGt	2/10	1	2	FACETS	0.44	0.391	0.492	0.44	0.391	0.492	SUBCLONAL	1	TRUE	1	0.434862345460578	2		326	1004	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66737006	66737006	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	89	275	0	ENST00000307102.5:c.529C>G	p.Leu177Val	p.L177V	ENST00000307102	NM_002755.3	177	Ctg/Gtg	5/11	0.42202942038434	3	FACETS	0.437	0.386	0.491	0.218	0.193	0.246	SUBCLONAL	1	TRUE	1	0.434862345460578	3		275	1141	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795414	42795438	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCCCCAGCAGCTTCAGGTGGCAC	CTGCCCCAGCAGCTTCAGGTGGCAC	-	novel	NA	P-0004207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	53	147	0	ENST00000575354.2:c.2505_2529del	p.Gln835HisfsTer81	p.Q835Hfs*81	ENST00000575354	NM_015125.3	832	CTGCCCCAGCAGCTTCAGGTGGCACct/ct	10/20	1	2	FACETS	0.502	0.428	0.582	0.502	0.428	0.582	SUBCLONAL	1	TRUE	1	0.434862345460578	2		147	486	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986870	36986886	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGGTGCCCCCGCCGC	CCCGGTGCCCCCGCCGC	-	novel	NA	P-0004207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	47	106	0	ENST00000354822.5:c.803_819del	p.Gly268ValfsTer165	p.G268Vfs*165	ENST00000354822	NM_001079668.2	268	gGCGGCGGGGGCACCGGG/g	3/3	1	2	FACETS	0.865	0.736	1	0.865	0.736	1	CLONAL	1	TRUE	1	0.434862345460578	2		106	250	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691039	NA	P-0004210-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	161	313	1	ENST00000269305.4:c.919+1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		314	352	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0004211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	146	290	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.911	0.834	0.991	0.911	0.834	0.991	CLONAL	1	TRUE	1	0.497976049717822	2		290	644	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0004211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	26	342	0	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	1	2	FACETS	0.122	0.096	0.153	0.122	0.096	0.153	SUBCLONAL	1	TRUE	1	0.497976049717822	2		342	854	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560460	65560460	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	40	405	0	ENST00000358664.4:c.137T>G	p.Leu46Trp	p.L46W	ENST00000358664	NM_002382.4	46	tTg/tGg	3/5	0.497976049717822	1	FACETS	0.191	0.158	0.228	0.191	0.158	0.228	SUBCLONAL	1	TRUE	0	0.497976049717822	1		405	632	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543360	65543386	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCGCCTTCTCCAGTGCACGGACTAAA	CTCGCCTTCTCCAGTGCACGGACTAAA	-	novel	NA	P-0004211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	155	550	0	ENST00000358664.4:c.296-5_317del		p.X99_splice	ENST00000358664	NM_002382.4	99		5/5	0.497976049717822	1	FACETS	0.806	0.741	0.873	0.806	0.741	0.873	CLONAL	1	TRUE	0	0.497976049717822	1		550	580	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	251	450	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.526157641451322	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.526157641451322	2		451	458	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0004220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	63	333	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.2012582600111	2	FACETS	0.837	0.745	0.931	0.837	0.745	0.931	INDETERMINATE	2	TRUE	0	0.526157641451322	2		333	143	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0004220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	77	370	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.941	0.834	1	0.941	0.834	1	CLONAL	1	TRUE	1	0.526157641451322	2		370	311	SUCCESS
APC	324	MSKCC	GRCh37	5	112175621	112175621	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	144	692	0	ENST00000257430.4:c.4330C>T	p.Gln1444Ter	p.Q1444*	ENST00000257430	NM_000038.5	1444	Caa/Taa	16/16	1	2	FACETS	0.764	0.707	0.823	1	0.989	1	SUBCLONAL	2	TRUE	1	0.526157641451322	2		692	358	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169361	11169361	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519777	NA	P-0004220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	76	699	0	ENST00000361445.4:c.7514G>C	p.Arg2505Pro	p.R2505P	ENST00000361445	NM_004958.3	2505	cGa/cCa	56/58	NA	2	FACETS	0.917	0.812	1			1	INDETERMINATE	1	TRUE	NA	0.526157641451322	2		699	315	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438703	49438703	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	175	438	0	ENST00000301067.7:c.4787G>T	p.Gly1596Val	p.G1596V	ENST00000301067	NM_003482.3	1596	gGc/gTc	19/54	0.51488171774105	3	FACETS	0.943	0.888	0.997	0.943	0.888	0.997	CLONAL	3	TRUE	0	0.526157641451322	3		438	297	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144446	58144446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140644696	NA	P-0004220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	228	352	0	ENST00000257904.6:c.625C>T	p.Arg209Cys	p.R209C	ENST00000257904	NM_000075.3	209	Cgt/Tgt	5/8	0.297007329384626	5	FACETS	1	0.986	1			1	INDETERMINATE	3	TRUE	NA	0.526157641451322	5		352	457	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374881	45374881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	265	511	0	ENST00000262160.6:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000262160	NM_005901.5	321	cGa/cAa	8/11	0.526157641451322	3	FACETS	0.979	0.934	1	0.979	0.934	1	CLONAL	3	TRUE	0	0.526157641451322	3		511	433	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604750	48604750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	304	496	0	ENST00000342988.3:c.1572G>T	p.Trp524Cys	p.W524C	ENST00000342988	NM_005359.5	524	tgG/tgT	12/12	0.526157641451322	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.526157641451322	3		496	436	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160230	22160230	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	110	440	0	ENST00000215832.6:c.401T>C	p.Leu134Pro	p.L134P	ENST00000215832	NM_002745.4	134	cTc/cCc	3/9	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.526157641451322	2		440	343	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358533	67358599	+	frameshift_variant	Frame_Shift_Del	DEL	GCCTGCTGGGCTGGAAGAAGGGCGAGCAGAACGGGCAGGAGGAGAAATGGTGCGAGAAGGCGGTCAA	GCCTGCTGGGCTGGAAGAAGGGCGAGCAGAACGGGCAGGAGGAGAAATGGTGCGAGAAGGCGGTCAA	-	novel	NA	P-0004220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	53	376	0	ENST00000327367.4:c.42_108del	p.Leu15AlafsTer79	p.L15Afs*79	ENST00000327367	NM_005902.3	14	cGCCTGCTGGGCTGGAAGAAGGGCGAGCAGAACGGGCAGGAGGAGAAATGGTGCGAGAAGGCGGTCAAg/cg	1/9	0.219751909237305	4	FACETS	1	0.965	1	0.715	0.617	0.819	INDETERMINATE	1	TRUE	2	0.526157641451322	4		376	215	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120205	70120226	+	frameshift_variant	Frame_Shift_Del	DEL	AGCCCCAGCCACTACAGCGAGC	AGCCCCAGCCACTACAGCGAGC	-	novel	NA	P-0004220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	114	379	0	ENST00000245479.2:c.1210_1231del	p.Pro404SerfsTer59	p.P404Sfs*59	ENST00000245479	NM_000346.3	403	AGCCCCAGCCACTACAGCGAGCag/ag	3/3	0.447834717133376	3	FACETS	1	0.97	1			1	CLONAL	2	TRUE	NA	0.526157641451322	3		379	244	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593586	55593591	+	inframe_deletion	In_Frame_Del	DEL	CCATGT	CCATGT	-	novel	NA	P-0004235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	253	297	0	ENST00000288135.5:c.1652_1657del	p.Pro551_Tyr553delinsHis	p.P551_Y553delinsH	ENST00000288135	NM_000222.2	551	cCCATGTat/cat	11/21	0.863960069368346	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.863960069368346	2		297	291	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0004238-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	45	440	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.167272094442209	5	FACETS		NA	1			1	NA	NA	FALSE	2	NA	5		440	399	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575705	55575708	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTA	AGTA	-	novel	NA	P-0004238-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	43	258	0	ENST00000288135.5:c.1231+5_1231+8del		p.X411_splice	ENST00000288135	NM_000222.2	411		7/21	0.167272094442209	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		258	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0004264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	30	229	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.568	0.457	0.695	0.568	0.457	0.695	SUBCLONAL	1	TRUE	1	0.203834371746281	2		229	518	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0004264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	179	495	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.203834371746281	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.203834371746281	3		496	804	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0004264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	166	358	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.134378407554803	5	FACETS	0.942	0.864	1	0.471	0.432	0.512	CLONAL	2	TRUE	1	0.203834371746281	5		358	1129	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11292540	11292540	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	40	359	0	ENST00000361445.4:c.2467A>T	p.Ile823Phe	p.I823F	ENST00000361445	NM_004958.3	823	Atc/Ttc	16/58	1	2	FACETS	0.51	0.422	0.608	0.51	0.422	0.608	SUBCLONAL	1	TRUE	1	0.203834371746281	2		359	770	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023303	27023303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	15	84	0	ENST00000324856.7:c.409C>T	p.His137Tyr	p.H137Y	ENST00000324856	NM_006015.4	137	Cac/Tac	1/20	1	2	FACETS	0.759	0.556	1	0.759	0.556	1	CLONAL	1	TRUE	1	0.203834371746281	2		84	194	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940133	49940133	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	57	577	0	ENST00000296474.3:c.910C>A	p.Pro304Thr	p.P304T	ENST00000296474	NM_002447.2	304	Cca/Aca	1/20	0.169868702752308	0	FACETS	0.532	0.455	0.616			1	SUBCLONAL	1	TRUE	0	0.203834371746281	0		577	837	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0004264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	19	188	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.203834371746281	3	FACETS	0.696	0.529	0.894	0.348	0.264	0.447	SUBCLONAL	1	TRUE	1	0.203834371746281	3		188	295	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099283	157099283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	42	157	0	ENST00000346085.5:c.220G>A	p.Glu74Lys	p.E74K	ENST00000346085	NM_020732.3	74	Gaa/Aaa	1/20	0.134378407554803	5	FACETS	1	0.955	1	0.368	0.307	0.434	CLONAL	1	TRUE	1	0.203834371746281	5		157	366	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752738	128752738	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	50	252	0	ENST00000377970.2:c.899G>A	p.Gly300Glu	p.G300E	ENST00000377970	NM_002467.4	300	gGa/gAa	3/3	0.159384176874516	3	FACETS	0.749	0.634	0.875	0.374	0.317	0.438	SUBCLONAL	1	TRUE	1	0.203834371746281	3		252	722	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090778	5090778	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	48	321	0	ENST00000381652.3:c.2926G>A	p.Asp976Asn	p.D976N	ENST00000381652	NM_004972.3	976	Gat/Aat	22/25	NA	2	FACETS	0.63	0.531	0.739			1	INDETERMINATE	1	TRUE	NA	0.203834371746281	2		321	748	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103515	77103515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	34	340	0	ENST00000356341.3:c.51G>A	p.Met17Ile	p.M17I	ENST00000356341	NM_002576.4	17	atG/atA	2/15	NA	2	FACETS	0.521	0.425	0.631			1	INDETERMINATE	1	TRUE	NA	0.203834371746281	2		340	640	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590677	95590677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1327	76	557	1	ENST00000393063.1:c.1232C>T	p.Ser411Leu	p.S411L	ENST00000393063	NM_030621.3	411	tCa/tTa	9/28	0.159384176874516	3	FACETS	0.586	0.511	0.666	0.293	0.255	0.333	SUBCLONAL	1	TRUE	1	0.203834371746281	3		558	1403	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821625	72821625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201772357	NA	P-0004264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	11	53	0	ENST00000268489.5:c.10550G>A	p.Gly3517Asp	p.G3517D	ENST00000268489	NM_006885.3	3517	gGc/gAc	10/10	0.157137699149064	0	FACETS	0.699	0.486	0.96			1	SUBCLONAL	1	TRUE	0	0.203834371746281	0		53	123	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357577	89357577	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	39	529	0	ENST00000301030.4:c.241G>A	p.Glu81Lys	p.E81K	ENST00000301030	NM_001256183.1	81	Gag/Aag	5/13	0.157137699149064	0	FACETS	0.397	0.328	0.474			1	SUBCLONAL	1	TRUE	0	0.203834371746281	0		529	768	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677936	58677936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1367540274	NA	P-0004264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	41	277	0	ENST00000305921.3:c.161C>T	p.Ser54Leu	p.S54L	ENST00000305921	NM_003620.3	54	tCg/tTg	1/6	1	2	FACETS	0.705	0.586	0.837	0.705	0.586	0.837	SUBCLONAL	1	TRUE	1	0.203834371746281	2		277	571	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376413	15376413	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs374747220	NA	P-0004264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	66	602	0	ENST00000263377.2:c.601C>G	p.Gln201Glu	p.Q201E	ENST00000263377	NM_058243.2	201	Caa/Gaa	5/20	1	2	FACETS	0.674	0.583	0.773	0.674	0.583	0.773	SUBCLONAL	1	TRUE	1	0.203834371746281	2		602	961	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420076	41420076	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	26	232	0	ENST00000373198.4:c.245G>C	p.Arg82Thr	p.R82T	ENST00000373198	NM_133170.3	82	aGa/aCa	3/32	0.203834371746281	1	FACETS	0.579	0.458	0.717	0.579	0.458	0.717	SUBCLONAL	1	TRUE	0	0.203834371746281	1		232	396	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6414401	6414401	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	25	117	0	ENST00000356142.4:c.35G>T	p.Gly12Val	p.G12V	ENST00000356142	NM_018890.3	12	gGa/gTa	1/7	0.335473716024773	7	FACETS	0.939	0.741	1	0.235	0.185	0.292	CLONAL	1	TRUE	3	0.335473716024773	7		117	292	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417912	138417912	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	73	485	0	ENST00000289153.2:c.1607C>T	p.Pro536Leu	p.P536L	ENST00000289153	NM_006219.2	536	cCt/cTt	11/22	0.623041922770117	4	FACETS	1	0.906	1	0.344	0.303	0.388	CLONAL	1	TRUE	1	0.69468591800214	4		485	345	SUCCESS
APC	324	MSKCC	GRCh37	5	112164642	112164642	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	79	347	0	ENST00000257430.4:c.1716G>C	p.Leu572Phe	p.L572F	ENST00000257430	NM_000038.5	572	ttG/ttC	14/16	NA	2	FACETS	1	0.931	1			1	INDETERMINATE	1	TRUE	NA	0.69468591800214	2		347	216	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374438	81374438	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0004280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	54	447	1	ENST00000222390.5:c.626-2A>T		p.X209_splice	ENST00000222390	NM_000601.4	209			1	2	FACETS	0.925	0.806	1	0.925	0.806	1	CLONAL	1	TRUE	1	0.69468591800214	2		448	168	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829283	72829283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773115759	NA	P-0004280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	274	705	2	ENST00000268489.5:c.7298C>T	p.Ala2433Val	p.A2433V	ENST00000268489	NM_006885.3	2433	gCg/gTg	9/10	0.25478521439143	2	FACETS	0.812	0.773	0.85	0.812	0.773	0.85	INDETERMINATE	2	TRUE	0	0.69468591800214	2		707	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0004287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	239	411	0	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	0.498164438612428	2	FACETS	0.956	0.903	1	0.956	0.903	1	CLONAL	2	TRUE	0	0.498164438612428	2		411	502	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144882	47144882	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	128	533	0	ENST00000409792.3:c.4871C>G	p.Ser1624Cys	p.S1624C	ENST00000409792	NM_014159.6	1624	tCt/tGt	7/21	0.498164438612428	2	FACETS	0.886	0.817	0.956	0.886	0.817	0.956	CLONAL	2	TRUE	0	0.498164438612428	2		533	290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0004288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	305	516	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	0.169314065105769	3	FACETS	0.971	0.938	1			1	CLONAL	10	FALSE	NA	0.17131819705158	3		516	398	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913499	NA	P-0004288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	145	659	0	ENST00000345146.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000345146	NM_005896.2	132	Cgt/Ggt	4/10	1	2	FACETS	1	0.969	1	1	0.994	1	CLONAL	4	FALSE	1	0.17131819705158	2		659	386	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0004301-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	85	140	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.905	0.808	1	0.905	0.808	1	CLONAL	1	TRUE	1	0.579757511147556	2		142	324	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696652	47696652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004301-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	207	474	0	ENST00000347630.2:c.296G>A	p.Arg99Gln	p.R99Q	ENST00000347630	NM_001007230.1	99	cGg/cAg	5/11	1	2	FACETS	0.961	0.895	1	0.961	0.895	1	CLONAL	1	TRUE	1	0.579757511147556	2		474	743	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0004310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	62	351	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	NA	2	FACETS	1	0.96	1			1	INDETERMINATE	1	TRUE	NA	0.508733971575238	2		351	197	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0004310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	34	140	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.868	0.72	1	0.868	0.72	1	CLONAL	1	TRUE	1	0.508733971575238	2		142	154	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0004335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	29	378	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		379	691	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0004335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	20	308	1	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.0800417837312223	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		309	483	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597401	10597401	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	38	540	0	ENST00000171111.5:c.1802G>T	p.Arg601Leu	p.R601L	ENST00000171111	NM_203500.1	601	cGg/cTg	6/6	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		540	638	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158153	47158153	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	99	493	0	ENST00000409792.3:c.4546T>C	p.Cys1516Arg	p.C1516R	ENST00000409792	NM_014159.6	1516	Tgt/Cgt	4/21	0.160188664259503	2	FACETS	0.808	0.721	0.9	0.404	0.36	0.45	INDETERMINATE	1	TRUE	0	0.319138719048543	2		493	768	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577084	+	frameshift_variant	Frame_Shift_Del	DEL	TCCT	TCCT	CC	novel	NA	P-0004354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	448	467	1	ENST00000269305.4:c.854_857delinsGG	p.Glu285GlyfsTer20	p.E285Gfs*20	ENST00000269305	NM_001126112.2	285	gAGGAa/gGGa	8/11	0.949929228984096	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.949929228984096	1		468	469	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412884	49412884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	204	642	0	ENST00000418115.1:c.139G>A	p.Glu47Lys	p.E47K	ENST00000418115	NM_001664.2	47	Gag/Aag	2/5	1	2	FACETS	0.965	0.898	1	0.965	0.898	1	CLONAL	1	TRUE	1	0.56	2		642	755	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526176	189526176	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	187	485	0	ENST00000264731.3:c.440C>G	p.Ser147Trp	p.S147W	ENST00000264731	NM_003722.4	147	tCg/tGg	4/14	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.56	2		485	573	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938403	44938403	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	169	293	0	ENST00000377967.4:c.2951T>C	p.Phe984Ser	p.F984S	ENST00000377967	NM_021140.2	984	tTc/tCc	20/29	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.56	1		293	325	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874320	76874320	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	22	391	0	ENST00000373344.5:c.5402A>G	p.Lys1801Arg	p.K1801R	ENST00000373344	NM_000489.3	1801	aAa/aGa	21/35	1	1	FACETS	0.193	0.149	0.244	0.193	0.149	0.244	SUBCLONAL	1	TRUE	0	0.56	1		391	293	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004369-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	143	450	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.250881701737379	1	FACETS	0.718	0.659	0.778	0.718	0.659	0.778	INDETERMINATE	1	TRUE	0	0.584884070465114	1		451	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0004369-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	221	164	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.584884070465114	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.584884070465114	2		164	365	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845224	128845224	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376509030	NA	P-0004369-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	188	212	1	ENST00000249373.3:c.718G>A	p.Val240Ile	p.V240I	ENST00000249373	NM_005631.4	240	Gtc/Atc	3/12	0.584884070465114	3	FACETS	0.982	0.919	1	0.982	0.919	1	CLONAL	2	TRUE	1	0.584884070465114	3		213	423	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244311	5244311	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004369-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	193	455	0	ENST00000357368.4:c.1171G>A	p.Gly391Ser	p.G391S	ENST00000357368	NM_002850.3	391	Ggc/Agc	11/38	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.584884070465114	2		455	659	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531821	46531821	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	86	564	1	ENST00000262741.5:c.526G>C	p.Ala176Pro	p.A176P	ENST00000262741	NM_003629.3	176	Gca/Cca	5/10	1	2	FACETS	0.601	0.531	0.676	0.601	0.531	0.676	SUBCLONAL	1	TRUE	1	0.371212459971069	2		565	771	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870999	12870999	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	54	370	0	ENST00000228872.4:c.226T>G	p.Trp76Gly	p.W76G	ENST00000228872	NM_004064.3	76	Tgg/Ggg	1/3	0.258580574532578	3	FACETS	0.614	0.524	0.712	0.307	0.262	0.356	SUBCLONAL	1	TRUE	1	0.371212459971069	3		370	562	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056100	26056100	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1235205455	NA	P-0004381-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	32	292	0	ENST00000343677.2:c.557C>T	p.Ala186Val	p.A186V	ENST00000343677	NM_005319.3	186	gCc/gTc	1/1	0.210714980646548	6	FACETS	0.734	0.595	0.893	0.245	0.198	0.298	SUBCLONAL	1	FALSE	3	0.210714980646548	6		292	588	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23625374	23625374	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760373091	NA	P-0004381-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	67	519	0	ENST00000261584.4:c.3152T>C	p.Ile1051Thr	p.I1051T	ENST00000261584	NM_024675.3	1051	aTt/aCt	11/13	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.210714980646548	2		519	451	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231375	5231375	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs757257991	NA	P-0004381-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	20	396	0	ENST00000357368.4:c.2101G>C	p.Glu701Gln	p.E701Q	ENST00000357368	NM_002850.3	701	Gag/Cag	14/38	1	2	FACETS	0.517	0.395	0.661	0.517	0.395	0.661	SUBCLONAL	1	FALSE	1	0.210714980646548	2		396	367	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0004388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	397	358	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.405614362196809	3	FACETS	0.949	0.905	0.994	0.949	0.905	0.994	CLONAL	2	TRUE	1	0.498667176681094	3		358	1048	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031973	26031973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	380	1342	0	ENST00000244661.2:c.316G>C	p.Glu106Gln	p.E106Q	ENST00000244661	NM_003537.3	106	Gag/Cag	1/1	0.405614362196809	3	FACETS	0.821	0.78	0.862	0.821	0.78	0.862	CLONAL	2	TRUE	1	0.498667176681094	3		1342	1160	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	253	1357	0	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	0.104516386650639	0	FACETS	0.502	0.469	0.535			1	INDETERMINATE	1	TRUE	0	0.498667176681094	0		1357	1014	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781634	9781634	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	133	751	0	ENST00000377346.4:c.1944C>G	p.Phe648Leu	p.F648L	ENST00000377346	NM_005026.3	648	ttC/ttG	15/24	1	2	FACETS	0.859	0.782	0.939	0.859	0.782	0.939	CLONAL	1	TRUE	1	0.498667176681094	2		751	621	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932338	36932338	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	240	1637	0	ENST00000361632.4:c.2131T>C	p.Ser711Pro	p.S711P	ENST00000361632		711	Tcc/Ccc	16/16	1	2	FACETS	0.927	0.866	0.991	0.927	0.866	0.991	CLONAL	1	TRUE	1	0.498667176681094	2		1637	1038	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682991	241682991	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1226883651	NA	P-0004388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	138	546	0	ENST00000366560.3:c.32C>G	p.Ser11Trp	p.S11W	ENST00000366560	NM_000143.3	11	tCg/tGg	1/10	0.197704604395618	5	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.498667176681094	5		546	651	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226907	142226907	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	132	779	0	ENST00000350721.4:c.4897C>G	p.Leu1633Val	p.L1633V	ENST00000350721	NM_001184.3	1633	Cta/Gta	28/47	1	2	FACETS	0.807	0.734	0.883	0.807	0.734	0.883	CLONAL	1	TRUE	1	0.498667176681094	2		779	656	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549689	187549689	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	147	666	0	ENST00000441802.2:c.4552G>T	p.Glu1518Ter	p.E1518*	ENST00000441802	NM_005245.3	1518	Gag/Tag	8/27	1	2	FACETS	0.931	0.853	1	0.931	0.853	1	CLONAL	1	TRUE	1	0.498667176681094	2		666	633	SUCCESS
APC	324	MSKCC	GRCh37	5	112176446	112176446	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	124	605	0	ENST00000257430.4:c.5155G>C	p.Glu1719Gln	p.E1719Q	ENST00000257430	NM_000038.5	1719	Gag/Cag	16/16	0.498667176681094	3	FACETS	0.864	0.783	0.95	0.432	0.391	0.475	CLONAL	1	TRUE	1	0.498667176681094	3		605	719	SUCCESS
APC	324	MSKCC	GRCh37	5	112177184	112177184	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	114	698	0	ENST00000257430.4:c.5893C>G	p.His1965Asp	p.H1965D	ENST00000257430	NM_000038.5	1965	Cat/Gat	16/16	0.498667176681094	3	FACETS	0.815	0.734	0.9	0.407	0.367	0.45	CLONAL	1	TRUE	1	0.498667176681094	3		698	701	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528335	157528335	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	167	998	0	ENST00000346085.5:c.6060G>C	p.Leu2020Phe	p.L2020F	ENST00000346085	NM_020732.3	2020	ttG/ttC	20/20	0.405614362196809	3	FACETS	0.988	0.908	1	0.494	0.454	0.536	CLONAL	1	TRUE	1	0.498667176681094	3		998	847	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381439	81381439	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	167	846	0	ENST00000222390.5:c.622G>C	p.Glu208Gln	p.E208Q	ENST00000222390	NM_000601.4	208	Gaa/Caa	5/18	1	2	FACETS	0.971	0.895	1	0.971	0.895	1	CLONAL	1	TRUE	1	0.498667176681094	2		846	690	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874386	151874386	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	162	819	0	ENST00000262189.6:c.8152G>C	p.Glu2718Gln	p.E2718Q	ENST00000262189	NM_170606.2	2718	Gaa/Caa	38/59	1	2	FACETS	0.954	0.878	1	0.954	0.878	1	CLONAL	1	TRUE	1	0.498667176681094	2		819	681	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403413	139403413	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	182	1034	0	ENST00000277541.6:c.3080C>T	p.Ser1027Leu	p.S1027L	ENST00000277541	NM_017617.3	1027	tCa/tTa	19/34	1	2	FACETS	0.911	0.842	0.983	0.911	0.842	0.983	CLONAL	1	TRUE	1	0.498667176681094	2		1034	801	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692794	89692794	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121909238	NA	P-0004388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	68	550	1	ENST00000371953.3:c.278A>G	p.His93Arg	p.H93R	ENST00000371953	NM_000314.4	93	cAt/cGt	5/9	0.498667176681094	1	FACETS	0.846	0.746	0.951	0.846	0.746	0.951	CLONAL	1	TRUE	0	0.498667176681094	1		551	242	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417852	32417852	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1218	67	799	0	ENST00000332351.3:c.1200G>C	p.Lys400Asn	p.K400N	ENST00000332351	NM_024426.4	400	aaG/aaC	7/10	0.474455001400836	5	FACETS	0.366	0.316	0.419			1	SUBCLONAL	1	TRUE	NA	0.498667176681094	5		799	1285	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588863	69588863	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747806374	NA	P-0004388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2037	186	983	0	ENST00000168712.1:c.373G>A	p.Val125Met	p.V125M	ENST00000168712	NM_002007.2	125	Gtg/Atg	2/3	0.498667176681094	8	FACETS	0.838	0.77	0.909			1	CLONAL	1	TRUE	NA	0.498667176681094	8		983	2223	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433246	49433246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs974587965	NA	P-0004388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	182	976	0	ENST00000301067.7:c.8201G>A	p.Arg2734Gln	p.R2734Q	ENST00000301067	NM_003482.3	2734	cGa/cAa	32/54	1	2	FACETS	0.999	0.924	1	0.999	0.924	1	CLONAL	1	TRUE	1	0.498667176681094	2		976	731	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811655	102811655	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	229	1556	0	ENST00000307046.8:c.529G>C	p.Glu177Gln	p.E177Q	ENST00000307046	NM_001111285.1	177	Gag/Cag	4/4	1	2	FACETS	0.948	0.884	1	0.948	0.884	1	CLONAL	1	TRUE	1	0.498667176681094	2		1556	969	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873811	35873811	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	127	698	0	ENST00000216797.5:c.40G>C	p.Glu14Gln	p.E14Q	ENST00000216797	NM_020529.2	14	Gag/Cag	1/6	0.498667176681094	3	FACETS	0.973	0.883	1	0.487	0.441	0.534	CLONAL	1	TRUE	1	0.498667176681094	3		698	654	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99460028	99460028	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1427403890	NA	P-0004388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	175	778	0	ENST00000268035.6:c.2124G>C	p.Glu708Asp	p.E708D	ENST00000268035	NM_000875.3	708	gaG/gaC	10/21	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.498667176681094	2		778	665	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56792541	56792541	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	256	1305	0	ENST00000308159.5:c.271G>C	p.Glu91Gln	p.E91Q	ENST00000308159	NM_014669.4	91	Gag/Cag	3/22	0.104516386650639	0	FACETS	0.509	0.477	0.542			1	INDETERMINATE	1	TRUE	0	0.498667176681094	0		1305	1011	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276185	15276185	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	183	890	0	ENST00000263388.2:c.5809G>C	p.Glu1937Gln	p.E1937Q	ENST00000263388	NM_000435.2	1937	Gag/Cag	31/33	1	2	FACETS	0.967	0.894	1	0.967	0.894	1	CLONAL	1	TRUE	1	0.498667176681094	2		890	759	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651603	48651603	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	207	1472	1	ENST00000376670.3:c.769C>T	p.Gln257Ter	p.Q257*	ENST00000376670	NM_002049.3	257	Cag/Tag	5/6	0.120817156779721	0	FACETS	0.439	0.407	0.472			1	INDETERMINATE	1	TRUE	0	0.498667176681094	0		1473	948	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061192	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0004388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	204	461	0	ENST00000250448.2:c.797_798del	p.Phe266Ter	p.F266*	ENST00000250448	NM_004496.3	266	tTC/t	2/2	0.498667176681094	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.498667176681094	3		461	489	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188240	10188240	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	42	829	0	ENST00000256474.2:c.383T>C	p.Leu128Pro	p.L128P	ENST00000256474	NM_000551.3	128	cTt/cCt	2/3	0.306166243756763	1	FACETS	0.96	0.808	1	0.96	0.808	1	CLONAL	1	FALSE	0	0.306166243756763	1		829	242	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047193	77047193	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1473604815	NA	P-0004397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	33	965	0	ENST00000356341.3:c.1351G>A	p.Gly451Ser	p.G451S	ENST00000356341	NM_002576.4	451	Ggc/Agc	13/15	1	2	FACETS	0.707	0.577	0.852	0.707	0.577	0.852	SUBCLONAL	1	FALSE	1	0.306166243756763	2		965	305	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984927	101984927	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	39	491	0	ENST00000282441.5:c.374C>G	p.Ala125Gly	p.A125G	ENST00000282441	NM_001130145.2	125	gCt/gGt	2/9	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	1	0.306166243756763	2		491	197	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163371	47163371	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	35	790	0	ENST00000409792.3:c.2755del	p.Glu919SerfsTer3	p.E919Sfs*3	ENST00000409792	NM_014159.6	919	Gag/ag	3/21	0.306166243756763	1	FACETS	0.983	0.814	1	0.983	0.814	1	CLONAL	1	FALSE	0	0.306166243756763	1		790	197	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272518	11272518	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	22	210	0	ENST00000361445.4:c.3412A>T	p.Thr1138Ser	p.T1138S	ENST00000361445	NM_004958.3	1138	Act/Tct	23/58	0.420010502061167	3	FACETS	0.72	0.562	0.901	0.36	0.281	0.451	CLONAL	1	TRUE	1	0.420010502061167	3		210	176	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437227	220437227	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1342413931	NA	P-0004417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	24	482	1	ENST00000243786.2:c.131C>T	p.Pro44Leu	p.P44L	ENST00000243786	NM_002191.3	44	cCc/cTc	1/2	0.420010502061167	3	FACETS	0.324	0.253	0.406	0.162	0.126	0.203	SUBCLONAL	1	TRUE	1	0.420010502061167	3		483	427	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665421	176665421	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	50	303	0	ENST00000439151.2:c.4105C>G	p.Pro1369Ala	p.P1369A	ENST00000439151	NM_022455.4	1369	Ccg/Gcg	7/23	1	2	FACETS	0.872	0.746	1	0.872	0.746	1	CLONAL	1	TRUE	1	0.420010502061167	2		303	273	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434609	49434609	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	16	214	0	ENST00000301067.7:c.6944A>C	p.His2315Pro	p.H2315P	ENST00000301067	NM_003482.3	2315	cAc/cCc	31/54	0.420010502061167	3	FACETS	0.421	0.311	0.551	0.21	0.155	0.276	SUBCLONAL	1	TRUE	1	0.420010502061167	3		214	219	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933761	39933761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763713717	NA	P-0004417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	78	158	1	ENST00000378444.4:c.838G>A	p.Val280Ile	p.V280I	ENST00000378444	NM_001123385.1	280	Gtc/Atc	4/15	0.420010502061167	2	FACETS	0.829	0.741	0.92			1	CLONAL	2	TRUE	NA	0.420010502061167	2		159	224	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984933	101984933	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004425-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	74	226	0	ENST00000282441.5:c.380C>T	p.Ser127Phe	p.S127F	ENST00000282441	NM_001130145.2	127	tCc/tTc	2/9	NA	2	FACETS	1	0.952	1			1	INDETERMINATE	1	TRUE	NA	0.858530453739428	2		226	157	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0004433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	23	140	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.5	0.39	0.628	0.5	0.39	0.628	SUBCLONAL	1	TRUE	1	0.271180807369585	2		142	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578213	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs864309495	NA	P-0004433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	105	668	0	ENST00000269305.4:c.636del	p.Arg213AspfsTer34	p.R213Dfs*34	ENST00000269305	NM_001126112.2	212	ttT/tt	6/11	0.271180807369585	1	FACETS	0.53	0.473	0.59	0.53	0.473	0.59	SUBCLONAL	1	TRUE	0	0.271180807369585	1		668	1264	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11270891	11270891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	42	820	0	ENST00000361445.4:c.3634C>A	p.Leu1212Ile	p.L1212I	ENST00000361445	NM_004958.3	1212	Ctc/Atc	24/58	1	2	FACETS	0.424	0.353	0.504	0.424	0.353	0.504	SUBCLONAL	1	TRUE	1	0.271180807369585	2		820	730	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281475	142281475	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	71	933	0	ENST00000350721.4:c.769C>G	p.Gln257Glu	p.Q257E	ENST00000350721	NM_001184.3	257	Cag/Gag	4/47	1	2	FACETS	0.652	0.568	0.743	0.652	0.568	0.743	SUBCLONAL	1	TRUE	1	0.271180807369585	2		933	803	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919271	178919271	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	83	680	1	ENST00000263967.3:c.756A>T	p.Leu252Phe	p.L252F	ENST00000263967	NM_006218.2	252	ttA/ttT	4/21	1	2	FACETS	0.679	0.598	0.766	0.679	0.598	0.766	SUBCLONAL	1	TRUE	1	0.271180807369585	2		681	902	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741784	145741784	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	124	913	1	ENST00000428558.2:c.719C>T	p.Ser240Leu	p.S240L	ENST00000428558	NM_004260.3	240	tCa/tTa	5/22	NA	2	FACETS	0.93	0.84	1			1	INDETERMINATE	1	TRUE	NA	0.271180807369585	2		914	983	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760320	133760321	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0004433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	152	775	0	ENST00000318560.5:c.2645_2646del	p.Ser882Ter	p.S882*	ENST00000318560	NM_005157.4	881	tcCTct/tcct	11/11	0.23479145901134	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.271180807369585	1		775	935	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105628	11105630	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0004433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	81	696	0	ENST00000358026.2:c.1548_1550del	p.Lys517del	p.K517del	ENST00000358026	NM_001128849.1	515	cAGAag/cag	9/36	1	2	FACETS	0.73	0.642	0.825	0.73	0.642	0.825	SUBCLONAL	1	TRUE	1	0.271180807369585	2		696	818	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660348	227660350	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0004433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	35	396	0	ENST00000305123.5:c.3105_3107del	p.Ser1038del	p.S1038del	ENST00000305123	NM_005544.2	1035	tcCTCa/tca	1/2	1	2	FACETS	0.513	0.42	0.618	0.513	0.42	0.618	SUBCLONAL	1	TRUE	1	0.271180807369585	2		396	503	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0004450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	240	358	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.727365753786451	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.727365753786451	1		358	383	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0004450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	103	140	2	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.911	0.825	0.999	0.911	0.825	0.999	CLONAL	1	TRUE	1	0.727365753786451	2		142	311	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149562	202149562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	209	280	0	ENST00000358485.4:c.1003G>A	p.Glu335Lys	p.E335K	ENST00000358485	NM_001080125.1	335	Gag/Aag	8/9	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.727365753786451	2		280	534	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149574	202149574	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	210	284	0	ENST00000358485.4:c.1015G>C	p.Glu339Gln	p.E339Q	ENST00000358485	NM_001080125.1	339	Gag/Cag	8/9	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.727365753786451	2		284	535	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439878	220439878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148455844	NA	P-0004450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	188	376	0	ENST00000243786.2:c.731C>T	p.Ser244Phe	p.S244F	ENST00000243786	NM_002191.3	244	tCt/tTt	2/2	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.727365753786451	2		376	485	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059211	47059211	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	250	212	0	ENST00000409792.3:c.7450C>T	p.Gln2484Ter	p.Q2484*	ENST00000409792	NM_014159.6	2484	Cag/Tag	20/21	0.721799195698477	2	FACETS	0.982	0.942	1	0.982	0.942	1	CLONAL	2	TRUE	0	0.727365753786451	2		212	350	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542342	187542342	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	124	188	0	ENST00000441802.2:c.5398G>C	p.Asp1800His	p.D1800H	ENST00000441802	NM_005245.3	1800	Gat/Cat	10/27	1	2	FACETS	0.927	0.847	1	0.927	0.847	1	CLONAL	1	TRUE	1	0.727365753786451	2		188	368	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950024	38950024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	130	224	0	ENST00000357387.3:c.3926C>T	p.Ala1309Val	p.A1309V	ENST00000357387	NM_152756.3	1309	gCt/gTt	31/38	1	2	FACETS	0.826	0.755	0.898	0.826	0.755	0.898	CLONAL	1	TRUE	1	0.727365753786451	2		224	433	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984157	2984157	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	63	117	0	ENST00000396946.4:c.373G>C	p.Glu125Gln	p.E125Q	ENST00000396946	NM_032415.4	125	Gag/Cag	5/25	1	2	FACETS	0.821	0.721	0.926	0.821	0.721	0.926	CLONAL	1	TRUE	1	0.727365753786451	2		117	211	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417337	139417337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs537766290	NA	P-0004450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	89	161	0	ENST00000277541.6:c.707C>T	p.Thr236Met	p.T236M	ENST00000277541	NM_017617.3	236	aCg/aTg	4/34	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.727365753786451	2		161	235	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446328	70446328	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	266	367	0	ENST00000373644.4:c.5268G>C	p.Lys1756Asn	p.K1756N	ENST00000373644	NM_030625.2	1756	aaG/aaC	11/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.727365753786451	2		367	703	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246017	46246017	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	234	290	0	ENST00000334344.6:c.4111C>G	p.His1371Asp	p.H1371D	ENST00000334344	NM_152641.2	1371	Cat/Gat	15/21	1	2	FACETS	0.96	0.901	1	0.96	0.901	1	CLONAL	1	TRUE	1	0.727365753786451	2		290	670	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557738	21557738	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	200	323	0	ENST00000382592.4:c.2107G>A	p.Asp703Asn	p.D703N	ENST00000382592	NM_014572.2	703	Gat/Aat	5/8	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.727365753786451	2		323	532	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250978	99250978	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	138	320	0	ENST00000268035.6:c.282G>C	p.Glu94Asp	p.E94D	ENST00000268035	NM_000875.3	94	gaG/gaC	2/21	1	2	FACETS	0.713	0.652	0.776	0.713	0.652	0.776	SUBCLONAL	1	TRUE	1	0.727365753786451	2		320	532	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770065	56770065	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs752608224	NA	P-0004450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	132	253	0	ENST00000337432.4:c.61C>G	p.Pro21Ala	p.P21A	ENST00000337432	NM_058216.2	21	Cca/Gca	1/9	1	2	FACETS	0.699	0.638	0.763	0.699	0.638	0.763	SUBCLONAL	1	TRUE	1	0.727365753786451	2		253	519	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303646	30303646	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771972554	NA	P-0004450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	131	268	0	ENST00000262643.3:c.74C>T	p.Ser25Leu	p.S25L	ENST00000262643	NM_001238.2	25	tCg/tTg	3/12	1	2	FACETS	0.84	0.768	0.913	0.84	0.768	0.913	CLONAL	1	TRUE	1	0.727365753786451	2		268	429	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385038	31385038	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	133	233	0	ENST00000328111.2:c.1423C>T	p.Gln475Ter	p.Q475*	ENST00000328111	NM_006892.3	475	Cag/Tag	14/23	1	2	FACETS	0.912	0.836	0.99	0.912	0.836	0.99	CLONAL	1	TRUE	1	0.727365753786451	2		233	401	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412392	63412392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	238	402	1	ENST00000330258.3:c.775G>A	p.Glu259Lys	p.E259K	ENST00000330258	NM_152424.3	259	Gaa/Aaa	2/2	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.727365753786451	2		403	614	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938094	76938094	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	134	337	0	ENST00000373344.5:c.2654G>C	p.Arg885Thr	p.R885T	ENST00000373344	NM_000489.3	885	aGa/aCa	9/35	1	2	FACETS	0.576	0.524	0.629	0.576	0.524	0.629	SUBCLONAL	1	TRUE	1	0.727365753786451	2		337	640	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102081	27102091	+	frameshift_variant	Frame_Shift_Del	DEL	ATGGCGGGTAA	ATGGCGGGTAA	G	novel	NA	P-0004450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	184	329	0	ENST00000324856.7:c.5007_5017delinsG	p.Trp1670Ter	p.W1670*	ENST00000324856	NM_006015.4	1669	gcATGGCGGGTAAtg/gcGtg	19/20	1	2	FACETS	0.96	0.893	1	0.96	0.893	1	CLONAL	1	TRUE	1	0.727365753786451	2		329	527	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578467	7578467	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	216	286	0	ENST00000269305.4:c.463A>C	p.Thr155Pro	p.T155P	ENST00000269305	NM_001126112.2	155	Acc/Ccc	5/11	0.591669850800301	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.591669850800301	2		286	365	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659245	86659245	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554048066	NA	P-0004453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	209	373	0	ENST00000274376.6:c.1534C>T	p.Arg512Ter	p.R512*	ENST00000274376	NM_002890.2	512	Cga/Tga	11/25	0.591669850800301	2	FACETS	0.92	0.869	0.971	0.92	0.869	0.971	CLONAL	2	TRUE	0	0.591669850800301	2		373	384	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959434	26959434	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	155	454	0	ENST00000381527.3:c.601G>T	p.Ala201Ser	p.A201S	ENST00000381527	NM_001260.1	201	Gcc/Tcc	6/13	0.244009005352006	5	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.591669850800301	5		454	778	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830703	72830703	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	221	656	1	ENST00000268489.5:c.5878T>A	p.Tyr1960Asn	p.Y1960N	ENST00000268489	NM_006885.3	1960	Tat/Aat	9/10	0.591669850800301	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.591669850800301	1		657	506	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247935	10247935	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	88	161	0	ENST00000340748.4:c.4267G>T	p.Ala1423Ser	p.A1423S	ENST00000340748		1423	Gcc/Tcc	36/40	0.493523268842386	4	FACETS	1	0.937	1	0.538	0.479	0.601	CLONAL	1	TRUE	2	0.591669850800301	4		161	440	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098405	11098405	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770322996	NA	P-0004453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	181	256	0	ENST00000358026.2:c.923C>T	p.Thr308Met	p.T308M	ENST00000358026	NM_001128849.1	308	aCg/aTg	6/36	0.591669850800301	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	0	0.591669850800301	2		256	304	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258625	19258625	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	286	347	0	ENST00000162023.5:c.275G>T	p.Gly92Val	p.G92V	ENST00000162023		92	gGc/gTc	8/13	0.591669850800301	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.591669850800301	2		347	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519980	NA	P-0004459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	40	181	1	ENST00000269305.4:c.528C>G	p.Cys176Trp	p.C176W	ENST00000269305	NM_001126112.2	176	tgC/tgG	5/11	0.351269664489489	1	FACETS	0.84	0.707	0.984	0.84	0.707	0.984	CLONAL	1	TRUE	0	0.420222372565087	1		182	179	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56363666	56363666	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763701192	NA	P-0004459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	33	340	2	ENST00000348428.3:c.445C>T	p.Arg149Trp	p.R149W	ENST00000348428	NM_006785.3	149	Cgg/Tgg	3/17	0.420222372565087	1	FACETS	0.379	0.309	0.458	0.379	0.309	0.458	SUBCLONAL	1	TRUE	0	0.420222372565087	1		342	327	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108780	2108780	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	28	295	1	ENST00000219476.3:c.881G>T	p.Gly294Val	p.G294V	ENST00000219476	NM_000548.3	294	gGa/gTa	10/42	1	2	FACETS	0.418	0.334	0.513	0.418	0.334	0.513	SUBCLONAL	1	TRUE	1	0.420222372565087	2		296	319	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2111969	2111969	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	16	210	0	ENST00000219476.3:c.1217G>C	p.Arg406Thr	p.R406T	ENST00000219476	NM_000548.3	406	aGa/aCa	12/42	1	2	FACETS	0.333	0.246	0.436	0.333	0.246	0.436	SUBCLONAL	1	TRUE	1	0.420222372565087	2		210	229	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845646	151845646	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0004468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	214	196	0	ENST00000262189.6:c.13366A>T	p.Arg4456Ter	p.R4456*	ENST00000262189	NM_170606.2	4456	Aga/Tga	52/59	0.233775176466953	5	FACETS	0.844	0.787	0.903			1	INDETERMINATE	2	FALSE	NA	0.667153586890707	5		196	760	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571952	64571952	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs794728632	NA	P-0004468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	712	435	0	ENST00000312049.6:c.1687G>T	p.Glu563Ter	p.E563*	ENST00000312049	NM_130799.2	563	Gag/Tag	10/10	NA	2	FACETS	0.902	0.876	0.928			1	INDETERMINATE	2	FALSE	NA	0.667153586890707	2		435	1183	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236216	108236216	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	134	221	0	ENST00000278616.4:c.9152G>T	p.Gly3051Val	p.G3051V	ENST00000278616	NM_000051.3	3051	gGa/gTa	63/63	0.667153586890707	1	FACETS	0.904	0.836	0.973	0.904	0.836	0.973	CLONAL	1	FALSE	0	0.667153586890707	1		221	296	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762464	41762464	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	149	182	0	ENST00000301178.4:c.2144G>A	p.Trp715Ter	p.W715*	ENST00000301178	NM_021913.4	715	tGg/tAg	18/20	0.442035247187987	1	FACETS	0.597	0.549	0.646	0.597	0.549	0.646	SUBCLONAL	1	FALSE	0	0.667153586890707	1		182	499	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162451	47162451	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121572-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	213	185	0	ENST00000409792.3:c.3675G>T	p.Arg1225Ser	p.R1225S	ENST00000409792	NM_014159.6	1225	agG/agT	3/21	1	2	FACETS	0.859	0.799	0.922	0.859	0.799	0.922	CLONAL	1	NA	1	0.54236484149116	2		185	914	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39573291	39573291	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0121572-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1398	217	200	0	ENST00000262039.4:c.772C>T	p.Pro258Ser	p.P258S	ENST00000262039	NM_002647.2	258	Ccc/Tcc	7/25	0.305869997415337	6	FACETS	1	0.951	1	0.344	0.319	0.371	INDETERMINATE	1	NA	3	0.54236484149116	6		200	1615	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0004500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	619	495	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.3	2	FACETS	1	0.997	1	1	0.998	1	INDETERMINATE	3	TRUE	0	0.54	2		496	702	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	159	441	0	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS	0.763	0.708	0.818	1	0.99	1	SUBCLONAL	2	TRUE	1	0.54	2		441	386	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0004500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	301	517	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	0.791	0.75	0.832	1	0.995	1	SUBCLONAL	2	TRUE	1	0.54	2		517	705	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521708	89521708	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	279	489	0	ENST00000336596.2:c.2785A>C	p.Lys929Gln	p.K929Q	ENST00000336596	NM_005233.5	929	Aag/Cag	16/17	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.54	2		489	699	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106674	27106674	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	190	497	0	ENST00000324856.7:c.6286del	p.Ser2096GlnfsTer39	p.S2096Qfs*39	ENST00000324856	NM_006015.4	2095	ccT/cc	20/20	1	2	FACETS	0.85	0.796	0.904	1	0.993	1	CLONAL	2	TRUE	1	0.54	2		497	414	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70005651	70005651	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	32	243	0	ENST00000394351.3:c.680T>C	p.Leu227Pro	p.L227P	ENST00000394351	NM_000248.3	227	cTa/cCa	7/9	0.640561674974951	2	FACETS	0.233	0.189	0.283	0.116	0.094	0.142	SUBCLONAL	1	TRUE	0	0.640561674974951	2		243	429	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091774	29091774	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587780170	NA	P-0004506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	16	156	0	ENST00000328354.6:c.1183G>C	p.Val395Leu	p.V395L	ENST00000328354	NM_007194.3	395	Gtt/Ctt	11/15	1	2	FACETS	0.171	0.126	0.225	0.171	0.126	0.225	SUBCLONAL	1	TRUE	1	0.640561674974951	2		156	292	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922051	39922051	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	67	202	0	ENST00000378444.4:c.4121G>T	p.Arg1374Met	p.R1374M	ENST00000378444	NM_001123385.1	1374	aGg/aTg	9/15	0.559343566424014	2	FACETS	0.344	0.299	0.393			1	SUBCLONAL	1	TRUE	NA	0.640561674974951	2		202	608	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870953	12870953	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004543-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	53	284	0	ENST00000228872.4:c.180G>C	p.Trp60Cys	p.W60C	ENST00000228872	NM_004064.3	60	tgG/tgC	1/3	1	2	FACETS	0.694	0.595	0.801	0.694	0.595	0.801	SUBCLONAL	1	TRUE	1	0.48032876772008	2		284	318	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0004549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	259	378	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.34272653604993	5	FACETS	1	0.987	1	0.779	0.732	0.826	CLONAL	2	TRUE	2	0.503171146524619	5		379	773	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729636	41729636	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	281	520	0	ENST00000242208.4:c.893G>A	p.Arg298Gln	p.R298Q	ENST00000242208	NM_002192.2	298	cGg/cAg	3/3	0.444180945942783	3	FACETS	0.886	0.836	0.937			1	CLONAL	2	TRUE	NA	0.503171146524619	3		520	789	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577062	7577062	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	272	428	0	ENST00000269305.4:c.876del	p.Glu294SerfsTer51	p.E294Sfs*51	ENST00000269305	NM_001126112.2	292	aaA/aa	8/11	0.514914111296899	4	FACETS	1	0.984	1			1	CLONAL	2	TRUE	NA	0.503171146524619	4		428	729	SUCCESS
APC	324	MSKCC	GRCh37	5	112175770	112175773	+	frameshift_variant	Frame_Shift_Del	DEL	GGAA	GGAA	-	novel	NA	P-0004549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	151	293	0	ENST00000257430.4:c.4479_4482del	p.Glu1494ValfsTer12	p.E1494Vfs*12	ENST00000257430	NM_000038.5	1493	acGGAA/ac	16/16	0.459707449151033	3	FACETS	0.884	0.816	0.953	0.589	0.544	0.635	CLONAL	2	TRUE	0	0.503171146524619	3		293	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004552-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	270	336	0	ENST00000269305.4:c.166G>T	p.Glu56Ter	p.E56*	ENST00000269305	NM_001126112.2	56	Gaa/Taa	4/11	0.597811359723957	2	FACETS	0.859	0.819	0.899	0.859	0.819	0.899	CLONAL	2	TRUE	0	0.686274238854901	2		336	458	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543740	29543740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004552-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	50	290	0	ENST00000389048.3:c.1423C>T	p.Pro475Ser	p.P475S	ENST00000389048	NM_004304.4	475	Cct/Tct	7/29	0.356589015651169	5	FACETS	0.411	0.347	0.48	0.137	0.115	0.16	INDETERMINATE	1	TRUE	2	0.686274238854901	5		290	720	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610154	10610154	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	448	504	0	ENST00000171111.5:c.556G>T	p.Gly186Cys	p.G186C	ENST00000171111	NM_203500.1	186	Ggc/Tgc	2/6	0.80939428016468	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.80939428016468	2		504	546	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0004591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	487	345	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.80939428016468	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.80939428016468	2		345	597	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555950	226555950	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	265	288	0	ENST00000366794.5:c.2227G>T	p.Asp743Tyr	p.D743Y	ENST00000366794	NM_001618.3	743	Gac/Tac	16/23	0.80939428016468	5	FACETS	1	0.944	1	0.501	0.472	0.53	CLONAL	2	TRUE	1	0.80939428016468	5		288	724	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221279	1221309	+	frameshift_variant	Frame_Shift_Del	DEL	GGGAAGGGGAGCTACGCCATCCCGGGCGACT	GGGAAGGGGAGCTACGCCATCCCGGGCGACT	-	novel	NA	P-0004591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	317	408	1	ENST00000326873.7:c.803_833del	p.Gly268ValfsTer9	p.G268Vfs*9	ENST00000326873	NM_000455.4	268	GGGAAGGGGAGCTACGCCATCCCGGGCGACTgt/gt	6/10	NA	2	FACETS	0.928	0.896	0.958			1	INDETERMINATE	2	TRUE	NA	0.80939428016468	2		409	422	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	115	551	0	ENST00000267163.4:c.958del	p.Arg320AspfsTer12	p.R320Dfs*12	ENST00000267163	NM_000321.2	320	Cga/ga	10/27	0.46537229622539	1	FACETS	0.823	0.746	0.903	0.823	0.746	0.903	CLONAL	1	TRUE	0	0.46537229622539	1		551	461	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041610	47041610	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004603-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	336	1775	0	ENST00000377604.3:c.1835G>T	p.Arg612Met	p.R612M	ENST00000377604	NM_001204468.1	612	aGg/aTg	17/24	0.649795704093824	3	FACETS	1	0.994	1	0.684	0.65	0.718	CLONAL	1	TRUE	1	0.912320801054856	3		1775	784	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412878	63412878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1350779419	NA	P-0004603-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	255	1805	2	ENST00000330258.3:c.289G>A	p.Asp97Asn	p.D97N	ENST00000330258	NM_152424.3	97	Gat/Aat	2/2	0.649795704093824	3	FACETS	1	0.989	1	0.607	0.572	0.643	CLONAL	1	TRUE	1	0.912320801054856	3		1807	670	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937798	76937798	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004603-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	130	2023	2	ENST00000373344.5:c.2950C>T	p.Gln984Ter	p.Q984*	ENST00000373344	NM_000489.3	984	Cag/Tag	9/35	0.649795704093824	3	FACETS	1	0.928	1	0.507	0.464	0.552	CLONAL	1	TRUE	1	0.912320801054856	3		2025	409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578414	7578414	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004605-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	203	307	0	ENST00000269305.4:c.516del	p.Val173Ter	p.V173*	ENST00000269305	NM_001126112.2	172	gtT/gt	5/11	0.472644344141928	2	FACETS	1	0.992	1	0.716	0.672	0.761	CLONAL	1	TRUE	0	0.623047325456678	2		307	455	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998975	100998975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004605-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	170	615	0	ENST00000325455.5:c.827C>T	p.Ser276Leu	p.S276L	ENST00000325455	NM_001202474.3	276	tCa/tTa	1/8	0.623047325456678	3	FACETS	0.959	0.884	1	0.48	0.442	0.519	CLONAL	1	TRUE	1	0.623047325456678	3		615	746	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416773	121416773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779442858	NA	P-0004605-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	173	413	0	ENST00000257555.6:c.202C>T	p.Arg68Trp	p.R68W	ENST00000257555		68	Cgg/Tgg	1/10	1	2	FACETS	0.707	0.651	0.764	0.707	0.651	0.764	SUBCLONAL	1	TRUE	1	0.623047325456678	2		413	786	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557921	29557921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004605-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	104	143	0	ENST00000356175.3:c.3175G>A	p.Asp1059Asn	p.D1059N	ENST00000356175	NM_000267.3	1059	Gat/Aat	24/57	0.472644344141928	2	FACETS	0.773	0.708	0.838	0.773	0.708	0.838	SUBCLONAL	2	TRUE	0	0.623047325456678	2		143	216	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211130	2211130	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004605-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	344	596	0	ENST00000398665.3:c.1384C>T	p.Gln462Ter	p.Q462*	ENST00000398665	NM_032482.2	462	Cag/Tag	15/28	0.336345146097245	1	FACETS	0.977	0.931	1	0.977	0.931	1	INDETERMINATE	1	TRUE	0	0.623047325456678	1		596	778	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554294	29554312	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGCAGGAAACACTGAGGTA	TGCAGGAAACACTGAGGTA	-	novel	NA	P-0004605-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	152	391	0	ENST00000356175.3:c.2313_2325+6del		p.X771_splice	ENST00000356175	NM_000267.3	771		19/57	0.472644344141928	2	FACETS	1	0.984	1	0.626	0.579	0.673	CLONAL	1	TRUE	0	0.623047325456678	2		391	390	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0004607-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	1950	299	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.487755044778617	18	FACETS	0.989	0.978	1			1	CLONAL	17	TRUE	NA	0.487755044778617	18		299	2331	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400822	72400822	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004607-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	134	619	0	ENST00000357731.5:c.349A>G	p.Thr117Ala	p.T117A	ENST00000357731	NM_173808.2	117	Acg/Gcg	2/7	0.487755044778617	3	FACETS	0.768	0.697	0.842	0.384	0.348	0.421	SUBCLONAL	1	TRUE	1	0.487755044778617	3		619	890	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715721	30715721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893816	NA	P-0004607-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	153	270	1	ENST00000295754.5:c.1379G>A	p.Arg460His	p.R460H	ENST00000295754	NM_003242.5	460	cGc/cAc	5/7	0.451562835423784	2	FACETS	0.815	0.755	0.876	0.815	0.755	0.876	CLONAL	2	TRUE	0	0.487755044778617	2		271	385	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20486939	20486939	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004607-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	88	395	0	ENST00000346618.3:c.904C>G	p.Gln302Glu	p.Q302E	ENST00000346618	NM_001949.4	302	Caa/Gaa	5/7	0.166017152105042	4	FACETS	0.94	0.835	1	0.47	0.417	0.527	INDETERMINATE	1	TRUE	2	0.487755044778617	4		395	571	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99486178	99486178	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004607-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	46	306	0	ENST00000268035.6:c.3484G>C	p.Glu1162Gln	p.E1162Q	ENST00000268035	NM_000875.3	1162	Gag/Cag	19/21	1	2	FACETS	0.518	0.438	0.607	0.518	0.438	0.607	SUBCLONAL	1	TRUE	1	0.487755044778617	2		306	364	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577569	7577569	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519981	NA	P-0004607-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	112	292	0	ENST00000269305.4:c.712T>C	p.Cys238Arg	p.C238R	ENST00000269305	NM_001126112.2	238	Tgt/Cgt	7/11	0.487755044778617	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.487755044778617	1		292	297	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207118	1207118	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004607-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	116	362	0	ENST00000326873.7:c.206C>A	p.Ser69Ter	p.S69*	ENST00000326873	NM_000455.4	69	tCg/tAg	1/10	0.487755044778617	1	FACETS	0.838	0.761	0.919	0.838	0.761	0.919	CLONAL	1	TRUE	0	0.487755044778617	1		362	429	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218423	1218423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004607-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	48	348	0	ENST00000326873.7:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000326873	NM_000455.4	100	Caa/Taa	2/10	0.487755044778617	1	FACETS	0.336	0.284	0.393	0.336	0.284	0.393	SUBCLONAL	1	TRUE	0	0.487755044778617	1		348	443	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319453	11319453	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	115	499	0	ENST00000361445.4:c.14G>C	p.Gly5Ala	p.G5A	ENST00000361445	NM_004958.3	5	gGa/gCa	2/58	0.600092518113623	2	FACETS	1	0.916	1	0.503	0.458	0.549	CLONAL	1	TRUE	0	0.665190761948529	2		499	344	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675877	30675877	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	184	973	0	ENST00000376406.3:c.2479G>A	p.Glu827Lys	p.E827K	ENST00000376406	NM_014641.2	827	Gag/Aag	8/15	0.563454521252951	3	FACETS	1	0.981	1	0.391	0.362	0.42	CLONAL	1	TRUE	0	0.665190761948529	3		973	629	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441912	40441912	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	724	1190	0	ENST00000345506.4:c.157G>A	p.Asp53Asn	p.D53N	ENST00000345506	NM_003152.3	53	Gac/Aac	4/20	0.644049529580213	4	FACETS	0.928	0.906	0.948	0.928	0.906	0.948	CLONAL	4	TRUE	0	0.665190761948529	4		1190	977	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577512	7577513	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0004612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	172	466	0	ENST00000269305.4:c.768_769del	p.Leu257GlyfsTer6	p.L257Gfs*6	ENST00000269305	NM_001126112.2	256	acACtg/actg	7/11	0.594766442778013	2	FACETS	0.826	0.776	0.876	0.826	0.776	0.876	CLONAL	2	TRUE	0	0.665190761948529	2		466	313	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439278	52439278	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	70	139	0	ENST00000460680.1:c.964C>T	p.Gln322Ter	p.Q322*	ENST00000460680	NM_004656.3	322	Caa/Taa	11/17	1	2	FACETS	0.829	0.723	0.943	1	0.977	1	CLONAL	2	TRUE	1	0.15	2		139	563	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964134	28964134	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	37	270	0	ENST00000282397.4:c.1768A>C	p.Ile590Leu	p.I590L	ENST00000282397	NM_002019.4	590	Att/Ctt	13/30	0.129111554560168	1	FACETS	0.79	0.65	0.946	0.79	0.65	0.946	CLONAL	1	TRUE	0	0.15	1		270	578	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564825	41564825	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004657-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	83	493	0	ENST00000263253.7:c.4126A>G	p.Met1376Val	p.M1376V	ENST00000263253	NM_001429.3	1376	Atg/Gtg	25/31	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		493	599	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207102	1207102	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0004658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	58	380	0	ENST00000326873.7:c.190A>T	p.Lys64Ter	p.K64*	ENST00000326873	NM_000455.4	64	Aag/Tag	1/10	0.268852406072359	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.268852406072359	1		380	314	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480549	120480549	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	73	433	0	ENST00000256646.2:c.3268C>T	p.Pro1090Ser	p.P1090S	ENST00000256646	NM_024408.3	1090	Cca/Tca	20/34	0.181510048687772	3	FACETS	1	0.946	1	0.574	0.502	0.65	CLONAL	1	TRUE	1	0.268852406072359	3		433	537	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215617190	215617190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	80	311	0	ENST00000260947.4:c.1658C>T	p.Ser553Leu	p.S553L	ENST00000260947	NM_000465.2	553	tCa/tTa	7/11	0.217684665298434	4	FACETS	1	0.956	1	0.592	0.521	0.668	CLONAL	1	TRUE	2	0.268852406072359	4		311	638	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561686	55561686	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs759129060	NA	P-0004658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	36	192	0	ENST00000288135.5:c.76C>T	p.Gln26Ter	p.Q26*	ENST00000288135	NM_000222.2	26	Caa/Taa	2/21	0.181510048687772	3	FACETS	0.983	0.811	1	0.492	0.405	0.588	CLONAL	1	TRUE	1	0.268852406072359	3		192	309	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102098222	102098222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	40	293	0	ENST00000282441.5:c.1186G>A	p.Glu396Lys	p.E396K	ENST00000282441	NM_001130145.2	396	Gag/Aag	8/9	1	2	FACETS	0.629	0.523	0.748	0.629	0.523	0.748	SUBCLONAL	1	TRUE	1	0.268852406072359	2		293	473	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828812	72828812	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	121	694	0	ENST00000268489.5:c.7769C>G	p.Ser2590Cys	p.S2590C	ENST00000268489	NM_006885.3	2590	tCt/tGt	9/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.268852406072359	2		694	760	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30302714	30302714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	20	147	0	ENST00000322652.5:c.805G>A	p.Glu269Lys	p.E269K	ENST00000322652	NM_015355.2	269	Gaa/Aaa	7/16	1	2	FACETS	0.641	0.492	0.815	0.641	0.492	0.815	SUBCLONAL	1	TRUE	1	0.268852406072359	2		147	232	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2202733	2202733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	60	528	0	ENST00000398665.3:c.742G>A	p.Glu248Lys	p.E248K	ENST00000398665	NM_032482.2	248	Gag/Aag	9/28	0.268852406072359	1	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	0	0.268852406072359	1		528	377	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600420	10600420	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	52	488	0	ENST00000171111.5:c.1435G>T	p.Asp479Tyr	p.D479Y	ENST00000171111	NM_203500.1	479	Gac/Tac	4/6	0.268852406072359	1	FACETS	0.861	0.735	0.998	0.861	0.735	0.998	CLONAL	1	TRUE	0	0.268852406072359	1		488	389	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105605	11105605	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0004658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	44	344	0	ENST00000358026.2:c.1521C>G	p.Tyr507Ter	p.Y507*	ENST00000358026	NM_001128849.1	507	taC/taG	9/36	0.268852406072359	1	FACETS	0.816	0.687	0.959	0.816	0.687	0.959	CLONAL	1	TRUE	0	0.268852406072359	1		344	347	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791735	42791735	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	51	401	0	ENST00000575354.2:c.621C>A	p.Phe207Leu	p.F207L	ENST00000575354	NM_015125.3	207	ttC/ttA	5/20	0.268852406072359	1	FACETS	0.977	0.835	1	0.977	0.835	1	CLONAL	1	TRUE	0	0.268852406072359	1		401	336	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039420	47039422	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0004658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	45	261	0	ENST00000377604.3:c.1043_1045del	p.Ile348_Gln349delinsLys	p.I348_Q349delinsK	ENST00000377604	NM_001204468.1	348	aTCCag/aag	10/24	1	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.268852406072359	1		261	220	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904958	101904981	+	inframe_deletion	In_Frame_Del	DEL	CTTCACATGGAGATTGTTGGTACC	CTTCACATGGAGATTGTTGGTACC	-	novel	NA	P-0004658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	59	306	0	ENST00000374994.4:c.947_970del	p.Leu316_Thr323del	p.L316_T323del	ENST00000374994	NM_004612.2	316	CTTCACATGGAGATTGTTGGTACC/-	5/9	0.160421446736955	2	FACETS	0.948	0.817	1	0.474	0.408	0.545	INDETERMINATE	1	TRUE	0	0.268852406072359	2		306	463	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0004670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	11	435	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	1	2	FACETS	0.111	0.076	0.155	0.111	0.076	0.155	SUBCLONAL	1	TRUE	1	0.382203232756517	2		435	518	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873672	35873672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	76	424	0	ENST00000303115.3:c.628G>A	p.Asp210Asn	p.D210N	ENST00000303115	NM_002185.3	210	Gat/Aat	5/8	1	2	FACETS	0.65	0.57	0.735	0.65	0.57	0.735	SUBCLONAL	1	TRUE	1	0.382203232756517	2		424	612	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150022917	150022917	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	28	341	0	ENST00000253339.5:c.346G>C	p.Glu116Gln	p.E116Q	ENST00000253339		116	Gag/Cag	1/7	1	2	FACETS	0.268	0.213	0.33	0.268	0.213	0.33	SUBCLONAL	1	TRUE	1	0.382203232756517	2		341	547	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835794	68835794	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	97	370	0	ENST00000261769.5:c.385C>T	p.Gln129Ter	p.Q129*	ENST00000261769	NM_004360.3	129	Cag/Tag	3/16	0.382203232756517	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.382203232756517	1		370	398	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351514	89351514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754010341	NA	P-0004670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	52	861	1	ENST00000301030.4:c.1436C>T	p.Ser479Leu	p.S479L	ENST00000301030	NM_001256183.1	479	tCg/tTg	9/13	0.382203232756517	1	FACETS	0.332	0.282	0.387	0.332	0.282	0.387	SUBCLONAL	1	TRUE	0	0.382203232756517	1		862	663	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119203	3119203	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0004670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	79	497	0	ENST00000078429.4:c.736-1G>A		p.X246_splice	ENST00000078429	NM_002067.2	246			0.382203232756517	1	FACETS	0.816	0.721	0.916	0.816	0.721	0.916	CLONAL	1	TRUE	0	0.382203232756517	1		497	410	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119354	3119354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1208131352	NA	P-0004670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	70	393	0	ENST00000078429.4:c.886G>A	p.Asp296Asn	p.D296N	ENST00000078429	NM_002067.2	296	Gat/Aat	6/7	0.382203232756517	1	FACETS	0.854	0.749	0.965	0.854	0.749	0.965	CLONAL	1	TRUE	0	0.382203232756517	1		393	347	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121176	3121176	+	stop_lost	Nonstop_Mutation	SNP	G	G	T	novel	NA	P-0004670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	59	338	0	ENST00000078429.4:c.1079G>T	p.Ter360LeuextTer48	p.*360Lext*48	ENST00000078429	NM_002067.2	360	tGa/tTa	7/7	0.382203232756517	1	FACETS	0.78	0.676	0.893	0.78	0.676	0.893	SUBCLONAL	1	TRUE	0	0.382203232756517	1		338	320	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005346	29005346	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	56	673	0	ENST00000282397.4:c.915C>A	p.Asp305Glu	p.D305E	ENST00000282397	NM_002019.4	305	gaC/gaA	7/30	1	2	FACETS	0.42	0.36	0.487	0.42	0.36	0.487	SUBCLONAL	1	TRUE	1	0.45	2		673	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0004681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	200	311	0	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.757476423238902	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.757476423238902	2		311	240	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0004681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	68	672	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	NA	2	FACETS	0.514	0.45	0.583			1	INDETERMINATE	1	TRUE	NA	0.757476423238902	2		672	349	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442854	187442854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867576130	NA	P-0004681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	8	263	0	ENST00000232014.4:c.1852C>T	p.Arg618Cys	p.R618C	ENST00000232014	NM_001130845.1	618	Cgt/Tgt	9/10	0.165927898873679	4	FACETS	0.136	0.087	0.2	0.068	0.043	0.1	INDETERMINATE	1	TRUE	2	0.757476423238902	4		263	273	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157834	106157834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs4145756	NA	P-0004681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	243	455	2	ENST00000380013.4:c.2735C>T	p.Ala912Val	p.A912V	ENST00000380013	NM_001127208.2	912	gCg/gTg	3/11	0.371808248500987	4	FACETS	1	0.949	1	1	0.949	1	INDETERMINATE	2	TRUE	2	0.757476423238902	4		457	560	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180040082	180040082	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	29	539	0	ENST00000261937.6:c.3360C>G	p.Ile1120Met	p.I1120M	ENST00000261937	NM_182925.4	1120	atC/atG	25/30	NA	2	FACETS	0.314	0.253	0.382			1	INDETERMINATE	1	TRUE	NA	0.757476423238902	2		539	244	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777876	27777876	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	62	787	0	ENST00000369163.2:c.25C>G	p.Arg9Gly	p.R9G	ENST00000369163	NM_003536.2	9	Cgc/Ggc	1/1	0.607225601887201	3	FACETS	0.423	0.365	0.485	0.141	0.121	0.162	SUBCLONAL	1	TRUE	0	0.757476423238902	3		787	534	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951817	2951817	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	140	513	0	ENST00000396946.4:c.3133G>T	p.Val1045Leu	p.V1045L	ENST00000396946	NM_032415.4	1045	Gtg/Ttg	23/25	0.733182791235985	3	FACETS	1	0.981	1	0.611	0.562	0.662	CLONAL	1	TRUE	1	0.757476423238902	3		513	417	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104352399	104352399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	48	582	0	ENST00000369902.3:c.515C>T	p.Ser172Leu	p.S172L	ENST00000369902	NM_016169.3	172	tCa/tTa	4/12	0.757476423238902	1	FACETS	0.368	0.314	0.425	0.368	0.314	0.425	SUBCLONAL	1	TRUE	0	0.757476423238902	1		582	214	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437730	110437730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1209394395	NA	P-0004681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	279	411	0	ENST00000375856.3:c.671G>A	p.Arg224His	p.R224H	ENST00000375856	NM_003749.2	224	cGc/cAc	1/2	0.757476423238902	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.757476423238902	2		411	337	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841322	15841322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	33	560	2	ENST00000307771.7:c.1406C>T	p.Ser469Leu	p.S469L	ENST00000307771	NM_005089.3	469	tCg/tTg	11/11	0.510190931350164	1	FACETS	0.113	0.092	0.137	0.113	0.092	0.137	SUBCLONAL	1	TRUE	0	0.757476423238902	1		562	479	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447588	187447588	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	69	317	0	ENST00000232014.4:c.605del	p.Pro202LeufsTer122	p.P202Lfs*122	ENST00000232014	NM_001130845.1	202	cCt/ct	5/10	0.165927898873679	4	FACETS	0.982	0.862	1	0.491	0.431	0.555	INDETERMINATE	1	TRUE	2	0.757476423238902	4		317	326	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643798	52643808	+	frameshift_variant	Frame_Shift_Del	DEL	TAGTCAGATAG	TAGTCAGATAG	-	novel	NA	P-0004681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	51	462	0	ENST00000394830.3:c.2088_2098del	p.Tyr697Ter	p.Y697*	ENST00000394830	NM_018313.4	696	taCTATCTGACTAtt/tatt	17/30	NA	2	FACETS	0.393	0.335	0.455			1	INDETERMINATE	1	TRUE	NA	0.757476423238902	2		462	343	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0004686-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	482	628	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.606082573716582	2	FACETS	0.889	0.857	0.921	0.889	0.857	0.921	CLONAL	2	TRUE	0	0.636353716230953	2		628	852	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455123	50455123	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004686-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	246	458	0	ENST00000331340.3:c.670C>T	p.His224Tyr	p.H224Y	ENST00000331340	NM_006060.4	224	Cac/Tac	6/8	0.616591523050257	3	FACETS	0.982	0.918	1	0.491	0.459	0.524	CLONAL	1	TRUE	1	0.636353716230953	3		458	1038	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156728	20156728	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004686-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	413	792	0	ENST00000379607.5:c.29A>C	p.Lys10Thr	p.K10T	ENST00000379607	NM_001412.3	10	aAa/aCa	2/7	0.626936492492529	1	FACETS	0.969	0.927	1	0.969	0.927	1	CLONAL	1	TRUE	0	0.636353716230953	1		792	913	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363378	40363378	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000037-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	629	124	497	0	ENST00000397332.2:c.851T>G	p.Ile284Ser	p.I284S	ENST00000397332	NM_001033082.2	284	aTt/aGt	3/3	0.395905920731061	1	FACETS	0.654	0.592	0.719	0.654	0.592	0.719	SUBCLONAL	1	TRUE	0	0.402368712540842	1		497	753	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202730	133202730	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000037-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	650	145	532	0	ENST00000320574.5:c.6504C>G	p.Asp2168Glu	p.D2168E	ENST00000320574	NM_006231.2	2168	gaC/gaG	46/49	0.392907634856383	1	FACETS	0.724	0.661	0.79	0.724	0.661	0.79	SUBCLONAL	1	TRUE	0	0.402368712540842	1		532	795	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0000037-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	293	230	388	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.402368712540842	1	FACETS	0.873	0.822	0.924	1	0.994	1	CLONAL	2	TRUE	0	0.402368712540842	1		388	523	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15960850	15960850	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000037-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	307	118	408	1	ENST00000268712.3:c.6370C>A	p.Leu2124Ile	p.L2124I	ENST00000268712	NM_006311.3	2124	Ctt/Att	40/46	0.402368712540842	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.402368712540842	1		409	425	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090639	71090639	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000042-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	232	610	0	ENST00000318789.4:c.709A>G	p.Ser237Gly	p.S237G	ENST00000318789	NM_032682.5	237	Agt/Ggt	11/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.644720550302239	2		610	691	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0000060-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	217	314	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.548787492484951	1	FACETS	0.757	0.717	0.797	1	0.994	1	SUBCLONAL	2	TRUE	0	0.548787492484951	1		314	379	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0000060-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	359	470	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.525125971254054	4	FACETS	0.89	0.844	0.937	0.89	0.844	0.937	CLONAL	2	TRUE	2	0.548787492484951	4		470	1138	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717618	89717618	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000060-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	106	204	0	ENST00000371953.3:c.643T>C	p.Phe215Leu	p.F215L	ENST00000371953	NM_000314.4	215	Ttt/Ctt	7/9	0.165945140258729	2	FACETS	0.522	0.468	0.579	0.261	0.234	0.29	INDETERMINATE	1	TRUE	0	0.548787492484951	2		204	740	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945237	32945237	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs398122710	NA	P-0000060-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	148	181	0	ENST00000380152.3:c.8632G>A	p.Glu2878Lys	p.E2878K	ENST00000380152		2878	Gaa/Aaa	20/27	0.501754792954645	1	FACETS	0.887	0.818	0.959	0.887	0.818	0.959	CLONAL	1	TRUE	0	0.548787492484951	1		181	441	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851867	128851867	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000060-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	137	309	0	ENST00000249373.3:c.1943del	p.Pro648GlnfsTer128	p.P648Qfs*128	ENST00000249373	NM_005631.4	647	Ccc/cc	12/12	0.548787492484951	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.548787492484951	1		309	337	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551364	150551381	+	frameshift_variant	Frame_Shift_Del	DEL	GTCGTAAGGTCTCCAGCG	GTCGTAAGGTCTCCAGCG	ATCC	novel	NA	P-0000060-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1561	122	514	0	ENST00000369026.2:c.626_643delinsGGAT	p.Ala209GlyfsTer63	p.A209Gfs*63	ENST00000369026	NM_021960.4	209	gCGCTGGAGACCTTACGACgg/gGGATgg	1/3	0.548787492484951	5	FACETS	0.482	0.433	0.533			1	SUBCLONAL	1	TRUE	NA	0.548787492484951	5		514	1683	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204864	NA	P-0000102-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	37	327	0	ENST00000371953.3:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000371953	NM_000314.4	171	Cag/Tag	6/9	0.288227940115063	1	FACETS	0.321	0.263	0.385	0.321	0.263	0.385	SUBCLONAL	1	TRUE	0	0.288227940115063	1		327	685	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628788	187628788	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000102-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	61	402	0	ENST00000441802.2:c.2194G>C	p.Val732Leu	p.V732L	ENST00000441802	NM_005245.3	732	Gtg/Ctg	2/27	1	2	FACETS	0.559	0.481	0.644	0.559	0.481	0.644	SUBCLONAL	1	TRUE	1	0.288227940115063	2		402	757	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0000102-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	124	278	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	0.262711045867602	2	FACETS	0.893	0.812	0.976	0.893	0.812	0.976	CLONAL	2	TRUE	0	0.288227940115063	2		278	482	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162045	22162060	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCAGGGTTCTCTGG	CCTCAGGGTTCTCTGG	-	novel	NA	P-0000102-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	35	388	0	ENST00000215832.6:c.195_210del	p.Cys65TrpfsTer3	p.C65Wfs*3	ENST00000215832	NM_002745.4	65	tgCCAGAGAACCCTGAGG/tg	2/9	0.288227940115063	1	FACETS	0.304	0.248	0.367	0.304	0.248	0.367	SUBCLONAL	1	TRUE	0	0.288227940115063	1		388	684	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0000108-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1311	119	412	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.628082686618573	6	FACETS	0.598	0.538	0.662			1	SUBCLONAL	1	TRUE	NA	0.628082686618573	6		413	1430	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0000108-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	397	358	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	0.545681204811507	3	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.628082686618573	3		358	673	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574829	41574829	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs768061933	NA	P-0000108-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	196	345	0	ENST00000263253.7:c.7114A>G	p.Met2372Val	p.M2372V	ENST00000263253	NM_001429.3	2372	Atg/Gtg	31/31	0.292698331743967	5	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.628082686618573	5		345	922	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0000113-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	41	206	228	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.856169086920237	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.856169086920237	1		228	247	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748512	162748512	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000113-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	240	146	135	0	ENST00000367921.3:c.2426G>A	p.Gly809Glu	p.G809E	ENST00000367921	NM_006182.2	809	gGg/gAg	17/18	1	2	FACETS	0.884	0.816	0.953	0.884	0.816	0.953	CLONAL	1	TRUE	1	0.856169086920237	2		135	386	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113220	209113220	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000113-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	936	335	406	2	ENST00000345146.2:c.287A>T	p.Asn96Ile	p.N96I	ENST00000345146	NM_005896.2	96	aAt/aTt	4/10	0.856169086920237	3	FACETS	0.879	0.831	0.929	0.44	0.415	0.465	CLONAL	1	TRUE	1	0.856169086920237	3		408	1271	SUCCESS
FIP1L1	81608	MSKCC	GRCh37	4	54292094	54292094	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000113-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	513	114	222	0	ENST00000358575.5:c.934G>T	p.Glu312Ter	p.E312*	ENST00000358575	NM_001134937.1	312	Gaa/Taa	11/18	1	2	FACETS	0.425	0.383	0.469	0.425	0.383	0.469	SUBCLONAL	1	TRUE	1	0.856169086920237	2		222	627	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280008	66280008	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000113-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	357	269	258	0	ENST00000273854.3:c.1681C>A	p.Pro561Thr	p.P561T	ENST00000273854	NM_004439.5	561	Cca/Aca	7/18	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.856169086920237	2		258	626	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672323	86672323	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554049422	NA	P-0000113-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	114	257	315	0	ENST00000274376.6:c.2125C>T	p.Arg709Ter	p.R709*	ENST00000274376	NM_002890.2	709	Cga/Tga	16/25	0.856169086920237	1	FACETS	0.925	0.887	0.963	0.925	0.887	0.963	CLONAL	1	TRUE	0	0.856169086920237	1		315	371	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953975	131953975	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000113-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	34	151	192	0	ENST00000265335.6:c.3378G>T	p.Lys1126Asn	p.K1126N	ENST00000265335		1126	aaG/aaT	21/25	0.856169086920237	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.856169086920237	1		192	185	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129397	152129397	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000113-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	459	193	179	0	ENST00000206249.3:c.350T>A	p.Leu117Gln	p.L117Q	ENST00000206249	NM_000125.3	117	cTg/cAg	1/8	0.856169086920237	3	FACETS	0.987	0.918	1	0.494	0.459	0.53	CLONAL	1	TRUE	1	0.856169086920237	3		179	652	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334790	81334790	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000113-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	429	274	367	0	ENST00000222390.5:c.1926C>A	p.Cys642Ter	p.C642*	ENST00000222390	NM_000601.4	642	tgC/tgA	17/18	NA	2	FACETS	0.91	0.86	0.962			1	INDETERMINATE	1	TRUE	NA	0.856169086920237	2		367	703	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878604	151878604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000113-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	506	188	174	0	ENST00000262189.6:c.6341G>A	p.Arg2114Lys	p.R2114K	ENST00000262189	NM_170606.2	2114	aGg/aAg	36/59	0.856169086920237	3	FACETS	0.904	0.838	0.971			1	CLONAL	1	TRUE	NA	0.856169086920237	3		174	694	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600430	43600430	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000113-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	288	200	152	1	ENST00000355710.3:c.656A>T	p.Asp219Val	p.D219V	ENST00000355710	NM_020975.4	219	gAc/gTc	4/20	0.174193388740997	3	FACETS	1	0.991	1	0.684	0.64	0.728	INDETERMINATE	1	TRUE	1	0.856169086920237	3		153	488	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001399	29001399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000113-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	85	234	217	0	ENST00000282397.4:c.1333C>T	p.Pro445Ser	p.P445S	ENST00000282397	NM_002019.4	445	Cca/Tca	10/30	0.856169086920237	1	FACETS	0.98	0.94	1	0.98	0.94	1	CLONAL	1	TRUE	0	0.856169086920237	1		217	319	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32931929	32931929	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000113-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	119	349	384	0	ENST00000380152.3:c.7668T>A	p.Asn2556Lys	p.N2556K	ENST00000380152		2556	aaT/aaA	16/27	0.856169086920237	1	FACETS	0.996	0.963	1	0.996	0.963	1	CLONAL	1	TRUE	0	0.856169086920237	1		384	468	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954300	48954300	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1461382798	NA	P-0000113-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	80	252	330	0	ENST00000267163.4:c.1422-1G>A		p.X474_splice	ENST00000267163	NM_000321.2	474			0.856169086920237	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.856169086920237	1		330	332	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514480	41514480	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000113-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	372	278	212	0	ENST00000373198.4:c.181G>T	p.Glu61Ter	p.E61*	ENST00000373198	NM_133170.3	61	Gag/Tag	2/32	0.546568806954619	3	FACETS	1	0.994	1			1	CLONAL	1	TRUE	NA	0.856169086920237	3		212	650	SUCCESS
AR	367	MSKCC	GRCh37	X	66766247	66766247	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000113-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	270	176	151	0	ENST00000374690.3:c.1259C>A	p.Ala420Glu	p.A420E	ENST00000374690	NM_000044.3	420	gCg/gAg	1/8	NA	2	FACETS	0.922	0.858	0.986			1	INDETERMINATE	1	TRUE	NA	0.856169086920237	2		151	446	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419930	41419930	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000113-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	507	378	248	0	ENST00000373198.4:c.391del	p.Gln131LysfsTer17	p.Q131Kfs*17	ENST00000373198	NM_133170.3	131	Caa/aa	3/32	0.546568806954619	3	FACETS	1	0.995	1			1	CLONAL	1	TRUE	NA	0.856169086920237	3		248	885	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665213	138665218	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGCG	CGCGCG	T	novel	NA	P-0000113-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	680	293	282	0	ENST00000330315.3:c.347_352delinsA	p.Pro116GlnfsTer121	p.P116Qfs*121	ENST00000330315	NM_023067.3	116	cCGCGCGag/cAag	1/1	0.856169086920237	3	FACETS	1	0.947	1	0.502	0.473	0.532	CLONAL	1	TRUE	1	0.856169086920237	3		282	973	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0000114-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	409	262	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.439697731182784	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.439697731182784	3		262	1086	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0000114-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	183	357	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.773	0.712	0.836	0.773	0.712	0.836	SUBCLONAL	1	TRUE	1	0.439697731182784	2		357	1077	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36022615	36022615	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000114-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	76	398	0	ENST00000358208.4:c.488G>A	p.Arg163Gln	p.R163Q	ENST00000358208		163	cGg/cAg	5/12	0.189034753036397	3	FACETS	0.517	0.452	0.586	0.258	0.226	0.293	INDETERMINATE	1	TRUE	1	0.439697731182784	3		398	816	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344107	70344107	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000114-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1443	121	537	0	ENST00000374080.3:c.1843A>T	p.Thr615Ser	p.T615S	ENST00000374080		615	Act/Tct	13/45	0.439697731182784	3	FACETS	0.429	0.386	0.475	0.215	0.193	0.238	SUBCLONAL	1	TRUE	1	0.439697731182784	3		537	1564	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175462	108175462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1801516	NA	P-0000133-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	687	17	290	0	ENST00000278616.4:c.5557G>A	p.Asp1853Asn	p.D1853N	ENST00000278616	NM_000051.3	1853	Gat/Aat	37/63	1	2	FACETS	0.372	0.276	0.487	0.372	0.276	0.487	SUBCLONAL	1	TRUE	1	0.13	2		290	704	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0000133-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	233	20	78	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.13	2		78	253	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6045627	6045627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs10254120	NA	P-0000133-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	206	13	86	0	ENST00000265849.7:c.59G>A	p.Arg20Gln	p.R20Q	ENST00000265849	NM_000535.5	20	cGg/cAg	2/15	1	2	FACETS	0.913	0.652	1	0.913	0.652	1	CLONAL	1	TRUE	1	0.13	2		86	219	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578513	7578513	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000133-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	374	23	242	0	ENST00000269305.4:c.417G>C	p.Lys139Asn	p.K139N	ENST00000269305	NM_001126112.2	139	aaG/aaC	5/11	0.184403461504337	1	FACETS	0.833	0.649	1	0.833	0.649	1	CLONAL	1	TRUE	0	0.13	1		242	397	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058756	180058756	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000140-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	28	324	0	ENST00000261937.6:c.81G>T	p.Met27Ile	p.M27I	ENST00000261937	NM_182925.4	27	atG/atT	2/30	NA	2	FACETS	0.365	0.292	0.447			1	INDETERMINATE	1	TRUE	NA	0.52596479729734	2		324	292	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0000148-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	311	350	359	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.67772011047622	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	FALSE	1	0.711373482165002	3		359	661	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465943	69465943	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000148-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	510	29	285	0	ENST00000227507.2:c.781C>T	p.Gln261Ter	p.Q261*	ENST00000227507	NM_053056.2	261	Cag/Tag	5/5	1	2	FACETS	0.151	0.121	0.186	0.151	0.121	0.186	SUBCLONAL	1	FALSE	1	0.711373482165002	2		285	539	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662307	67662307	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000148-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	295	116	235	1	ENST00000264010.4:c.1553C>G	p.Thr518Ser	p.T518S	ENST00000264010	NM_006565.3	518	aCc/aGc	9/12	1	2	FACETS	0.794	0.721	0.869	0.794	0.721	0.869	SUBCLONAL	1	FALSE	1	0.711373482165002	2		236	411	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156731	20156731	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000148-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	321	215	397	0	ENST00000379607.5:c.26G>T	p.Gly9Val	p.G9V	ENST00000379607	NM_001412.3	9	gGt/gTt	2/7	0.229969034268759	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.711373482165002	0		397	536	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663406	227663406	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000151-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	19	128	0	ENST00000305123.5:c.49G>T	p.Gly17Cys	p.G17C	ENST00000305123	NM_005544.2	17	Ggc/Tgc	1/2	0.806883813142656	3	FACETS	0.348	0.265	0.444	0.116	0.088	0.148	SUBCLONAL	1	TRUE	0	0.806883813142656	3		128	190	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352766	70352766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866231134	NA	P-0000153-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	68	793	1	ENST00000374080.3:c.4487G>A	p.Arg1496His	p.R1496H	ENST00000374080		1496	cGc/cAc	32/45	0.25369454966572	0	FACETS	0.377	0.327	0.432			1	SUBCLONAL	1	TRUE	0	0.283520237761165	0		794	911	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0000156-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	101	261	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.31314604032644	1	FACETS	0.691	0.628	0.755	0.691	0.628	0.755	INDETERMINATE	1	TRUE	0	0.719785449039881	1		261	260	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427057	49427057	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000156-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	235	324	0	ENST00000301067.7:c.11431C>T	p.Gln3811Ter	p.Q3811*	ENST00000301067	NM_003482.3	3811	Cag/Tag	39/54	0.242599769179559	1	FACETS	0.808	0.762	0.855	0.808	0.762	0.855	INDETERMINATE	1	TRUE	0	0.719785449039881	1		324	517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587781525	NA	P-0000156-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	402	447	0	ENST00000269305.4:c.842A>G	p.Asp281Gly	p.D281G	ENST00000269305	NM_001126112.2	281	gAc/gGc	8/11	0.719785449039881	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.719785449039881	1		447	696	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0000157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1389	126	454	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		454	1515	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0000157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	75	264	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.91	0.795	1	0.91	0.795	1	CLONAL	1	TRUE	1	0.16	2		265	1030	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0000157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	121	332	2	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.16	NA		334	1277	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805008	43805008	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	129	432	0	ENST00000372470.3:c.458G>A	p.Ser153Asn	p.S153N	ENST00000372470	NM_005373.2	153	aGc/aAc	4/12	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.16	2		432	1264	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43817946	43817946	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1768	123	562	0	ENST00000372470.3:c.1625A>G	p.Tyr542Cys	p.Y542C	ENST00000372470	NM_005373.2	542	tAc/tGc	11/12	1	2	FACETS	0.813	0.732	0.9	0.813	0.732	0.9	CLONAL	1	TRUE	1	0.16	2		562	1891	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874530	155874530	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs869025191	NA	P-0000157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1267	111	423	1	ENST00000368323.3:c.229G>A	p.Ala77Thr	p.A77T	ENST00000368323	NM_006912.5	77	Gct/Act	4/6	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.16	2		424	1378	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844187	156844187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752761451	NA	P-0000157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	103	419	0	ENST00000524377.1:c.1190C>T	p.Pro397Leu	p.P397L	ENST00000524377	NM_002529.3	397	cCg/cTg	9/17	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.16	2		419	1216	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	45	201	0	ENST00000263967.3:c.333G>T	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaT	2/21	1	2	FACETS	0.771	0.646	0.909	0.771	0.646	0.909	CLONAL	1	TRUE	1	0.16	2		201	730	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549742	187549742	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	65	341	0	ENST00000441802.2:c.4499T>A	p.Leu1500Gln	p.L1500Q	ENST00000441802	NM_005245.3	1500	cTg/cAg	8/27	1	2	FACETS	0.683	0.59	0.785	0.683	0.59	0.785	SUBCLONAL	1	TRUE	1	0.16	2		341	1189	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38991078	38991078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	39	201	0	ENST00000357387.3:c.556G>A	p.Ala186Thr	p.A186T	ENST00000357387	NM_152756.3	186	Gca/Aca	7/38	1	2	FACETS	0.676	0.559	0.808	0.676	0.559	0.808	SUBCLONAL	1	TRUE	1	0.16	2		201	721	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199963	138199963	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	45	164	0	ENST00000237289.4:c.1381C>A	p.Pro461Thr	p.P461T	ENST00000237289	NM_001270507.1	461	Cca/Aca	7/9	1	2	FACETS	0.848	0.712	1	0.848	0.712	1	CLONAL	1	TRUE	1	0.16	2		164	663	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522348	157522348	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	93	296	1	ENST00000346085.5:c.4620C>A	p.Tyr1540Ter	p.Y1540*	ENST00000346085	NM_020732.3	1540	taC/taA	18/20	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.16	2		297	1050	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336414	80336414	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	41	133	0	ENST00000286548.4:c.905C>T	p.Ala302Val	p.A302V	ENST00000286548	NM_002072.3	302	gCc/gTc	7/7	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.16	NA		133	482	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650109	93650109	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1210	98	353	0	ENST00000375746.1:c.1660G>A	p.Asp554Asn	p.D554N	ENST00000375746	NM_001174167.1	554	Gat/Aat	12/14	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.16	NA		353	1308	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797298	135797298	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	71	238	0	ENST00000298552.3:c.571C>A	p.Leu191Ile	p.L191I	ENST00000298552	NM_001162426.1	191	Ctt/Att	7/23	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.16	NA		238	917	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399386	139399386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201360886	NA	P-0000157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	91	341	0	ENST00000277541.6:c.4757G>A	p.Arg1586His	p.R1586H	ENST00000277541	NM_017617.3	1586	cGc/cAc	26/34	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.16	NA		341	975	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596039	43596039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	77	312	0	ENST00000355710.3:c.206G>A	p.Gly69Asp	p.G69D	ENST00000355710	NM_020975.4	69	gGc/gAc	2/20	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.16	NA		312	876	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090976	77090976	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1655	100	498	0	ENST00000356341.3:c.254T>A	p.Ile85Asn	p.I85N	ENST00000356341	NM_002576.4	85	aTt/aAt	3/15	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.16	NA		498	1755	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427537	49427537	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	102	302	0	ENST00000301067.7:c.10951C>T	p.Gln3651Ter	p.Q3651*	ENST00000301067	NM_003482.3	3651	Caa/Taa	39/54	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.16	NA		302	1034	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444495	49444495	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1223112534	NA	P-0000157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	61	181	0	ENST00000301067.7:c.2876A>G	p.Tyr959Cys	p.Y959C	ENST00000301067	NM_003482.3	959	tAc/tGc	11/54	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.16	NA		181	762	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257828	133257828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771051323	NA	P-0000157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	102	394	0	ENST00000320574.5:c.100C>T	p.Arg34Cys	p.R34C	ENST00000320574	NM_006231.2	34	Cgc/Tgc	2/49	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.16	NA		394	1139	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226309	2226309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	110	346	0	ENST00000326181.6:c.1922G>A	p.Arg641His	p.R641H	ENST00000326181	NM_032271.2	641	cGt/cAt	20/21	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.16	NA		346	1038	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968867	15968867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772605440	NA	P-0000157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	79	262	0	ENST00000268712.3:c.4883G>A	p.Arg1628His	p.R1628H	ENST00000268712	NM_006311.3	1628	cGt/cAt	33/46	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.16	NA		262	1026	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653158	29653158	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	70	213	0	ENST00000356175.3:c.5093T>C	p.Ile1698Thr	p.I1698T	ENST00000356175	NM_000267.3	1698	aTa/aCa	36/57	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.16	NA		213	824	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119348	3119348	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745554999	NA	P-0000157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	116	430	2	ENST00000078429.4:c.880G>A	p.Glu294Lys	p.E294K	ENST00000078429	NM_002067.2	294	Gag/Aag	6/7	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.16	NA		432	1229	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117120	7117120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1365	127	525	1	ENST00000302850.5:c.4096G>A	p.Gly1366Arg	p.G1366R	ENST00000302850	NM_000208.2	1366	Gga/Aga	22/22	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.16	NA		526	1492	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743993	41743993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1356	147	546	0	ENST00000301178.4:c.928G>A	p.Ala310Thr	p.A310T	ENST00000301178	NM_021913.4	310	Gca/Aca	7/20	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.16	NA		546	1503	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817481	39817481	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	81	329	0	ENST00000288319.7:c.82C>A	p.Leu28Met	p.L28M	ENST00000288319	NM_182918.3	28	Ctg/Atg	2/10	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.16	NA		329	1097	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240701	53240701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1179564010	NA	P-0000157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2205	212	826	1	ENST00000375401.3:c.1379G>A	p.Arg460Gln	p.R460Q	ENST00000375401	NM_004187.3	460	cGg/cAg	10/26	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.16	NA		827	2417	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	68	216	2	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.16	2		218	683	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106078	27106078	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	61	166	0	ENST00000324856.7:c.5693del	p.Pro1898HisfsTer25	p.P1898Hfs*25	ENST00000324856	NM_006015.4	1897	Ccc/cc	20/20	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.16	2		166	675	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090086	37090086	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	87	344	0	ENST00000231790.2:c.1975del	p.Arg659AspfsTer2	p.R659Dfs*2	ENST00000231790	NM_000249.3	659	Cga/ga	17/19	1	2	FACETS	0.86	0.759	0.97	0.86	0.759	0.97	CLONAL	1	TRUE	1	0.16	2		344	1264	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240742	55240742	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	75	369	0	ENST00000275493.2:c.1989del	p.Ile664SerfsTer41	p.I664Sfs*41	ENST00000275493	NM_005228.3	662	ctG/ct	17/28	1	2	FACETS	0.889	0.776	1	0.889	0.776	1	CLONAL	1	TRUE	1	0.16	2		369	1055	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112154	115112154	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	114	415	0	ENST00000257566.3:c.1586del	p.Gly529AlafsTer103	p.G529Afs*103	ENST00000257566	NM_016569.3	529	gGc/gc	7/8	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.16	NA		415	1187	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024505	16024505	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000157-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1615	154	504	1	ENST00000268712.3:c.1713del	p.Arg572GlufsTer18	p.R572Efs*18	ENST00000268712	NM_006311.3	571	ggG/gg	16/46	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.16	NA		505	1769	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0000167-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	80	190	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	0.962	0.85	1	0.962	0.85	1	CLONAL	1	TRUE	1	0.370603992645261	2		190	449	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0000167-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	13	131	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	1	2	FACETS	0.216	0.153	0.293	0.216	0.153	0.293	SUBCLONAL	1	TRUE	1	0.370603992645261	2		131	325	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553702	29553702	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000167-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	57	113	0	ENST00000356175.3:c.2251G>A	p.Gly751Arg	p.G751R	ENST00000356175	NM_000267.3	751	Gga/Aga	18/57	0.370603992645261	1	FACETS	0.905	0.783	1	0.905	0.783	1	CLONAL	1	TRUE	0	0.370603992645261	1		113	277	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849521	68849521	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000167-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	178	456	0	ENST00000261769.5:c.1424del	p.Val475GlyfsTer6	p.V475Gfs*6	ENST00000261769	NM_004360.3	475	gTg/gg	10/16	0.370603992645261	1	FACETS	0.979	0.904	1	0.979	0.904	1	CLONAL	1	TRUE	0	0.370603992645261	1		456	799	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63816914	63816914	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000182-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	813	200	349	0	ENST00000279873.7:c.885G>T	p.Lys295Asn	p.K295N	ENST00000279873	NM_032199.2	295	aaG/aaT	6/10	1	2	FACETS	0.63	0.583	0.678	0.63	0.583	0.678	SUBCLONAL	1	TRUE	1	0.626973687896658	2		349	1013	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417829	32417829	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0000182-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	792	319	460	0	ENST00000332351.3:c.1223T>G	p.Leu408Ter	p.L408*	ENST00000332351	NM_024426.4	408	tTa/tGa	7/10	1	2	FACETS	0.916	0.865	0.968	0.916	0.865	0.968	CLONAL	1	TRUE	1	0.626973687896658	2		460	1111	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0000183-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	391	470	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.388236612726557	3	FACETS	0.94	0.893	0.987	0.94	0.893	0.987	CLONAL	2	TRUE	1	0.4	3		470	1248	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0000183-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	227	553	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.99	0.921	1	0.99	0.921	1	CLONAL	1	TRUE	1	0.4	2		553	1147	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168491	56168492	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0000183-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	237	445	0	ENST00000399503.3:c.1450_1451del	p.Glu484ThrfsTer8	p.E484Tfs*8	ENST00000399503	NM_005921.1	483	AGa/a	8/20	0.118980914323349	3	FACETS	1	0.972	1	0.542	0.504	0.58	INDETERMINATE	1	TRUE	1	0.4	3		445	1313	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720837	89720837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0000183-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	47	224	0	ENST00000371953.3:c.990del	p.Asp331ThrfsTer13	p.D331Tfs*13	ENST00000371953	NM_000314.4	330	Aaa/aa	8/9	0.388236612726557	1	FACETS	0.359	0.303	0.422	0.359	0.303	0.422	SUBCLONAL	1	TRUE	0	0.4	1		224	523	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556301	29556308	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGTCAG	CCTGTCAG	-	novel	NA	P-0000199-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	106	145	500	0	ENST00000356175.3:c.2669_2676del	p.Pro890GlnfsTer13	p.P890Qfs*13	ENST00000356175	NM_000267.3	890	CCTGTCAGc/c	21/57	0.783828958298007	1	FACETS	0.896	0.839	0.953	0.896	0.839	0.953	CLONAL	1	FALSE	0	0.783828958298007	1		500	251	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0000204-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	2161	470	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.531596542420709	8	FACETS	1	0.993	1			1	CLONAL	7	TRUE	NA	0.531596542420709	8		470	2984	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303726	65303726	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000204-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1290	410	489	0	ENST00000342505.4:c.3029T>G	p.Leu1010Arg	p.L1010R	ENST00000342505	NM_002227.2	1010	cTt/cGt	22/25	1	2	FACETS	0.907	0.861	0.954	0.907	0.861	0.954	CLONAL	1	TRUE	1	0.531596542420709	2		489	1700	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971163	21971163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs780893836	NA	P-0000204-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	35	107	0	ENST00000579755.1:c.238C>G	p.Pro80Ala	p.P80A	ENST00000579755		80	Cca/Gca	2/3	0.511813729091954	1	FACETS	0.441	0.364	0.526	0.441	0.364	0.526	SUBCLONAL	1	TRUE	0	0.531596542420709	1		107	219	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424092	49424092	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs748791941	NA	P-0000204-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1226	426	486	0	ENST00000301067.7:c.13970C>G	p.Ser4657Cys	p.S4657C	ENST00000301067	NM_003482.3	4657	tCt/tGt	42/54	1	2	FACETS	0.97	0.923	1	0.97	0.923	1	CLONAL	1	TRUE	1	0.531596542420709	2		486	1652	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562249	95562249	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000204-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1292	392	548	0	ENST00000393063.1:c.5008G>C	p.Glu1670Gln	p.E1670Q	ENST00000393063	NM_030621.3	1670	Gaa/Caa	24/28	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.531596542420709	NA		548	1684	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562693	95562693	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000204-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	332	395	0	ENST00000393063.1:c.4564G>C	p.Asp1522His	p.D1522H	ENST00000393063	NM_030621.3	1522	Gac/Cac	24/28	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.531596542420709	NA		395	1353	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560815	9560815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388617807	NA	P-0000204-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	285	406	1	ENST00000353224.5:c.967G>A	p.Glu323Lys	p.E323K	ENST00000353224	NM_177990.2	323	Gag/Aag	4/10	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.531596542420709	NA		407	1202	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0000207-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	123	190	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.388540349144615	2		190	515	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0000207-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	102	429	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.388540349144615	2		429	501	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862205	68862205	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs876658575	NA	P-0000207-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	160	311	0	ENST00000261769.5:c.2293C>T	p.Gln765Ter	p.Q765*	ENST00000261769	NM_004360.3	765	Cag/Tag	14/16	0.388540349144615	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.388540349144615	1		311	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0000214-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	458	398	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.4267795948908	2	FACETS	0.916	0.877	0.956	0.916	0.877	0.956	CLONAL	2	FALSE	0	0.437891248436312	2		398	1142	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954198	48954198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123331	NA	P-0000214-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	384	422	1	ENST00000267163.4:c.1399C>T	p.Arg467Ter	p.R467*	ENST00000267163	NM_000321.2	467	Cga/Tga	15/27	0.4267795948908	2	FACETS	0.949	0.905	0.993	0.949	0.905	0.993	CLONAL	2	FALSE	0	0.437891248436312	2		423	924	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0000220-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	836	581	470	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.997	0.959	1	0.997	0.959	1	CLONAL	1	TRUE	1	0.822885794262353	2		470	1417	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670234	134670234	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000220-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	1003	577	446	1	ENST00000398015.3:c.145G>T	p.Asp49Tyr	p.D49Y	ENST00000398015	NM_004441.4	49	Gat/Tat	3/16	NA	2	FACETS	0.888	0.853	0.923			1	INDETERMINATE	1	TRUE	NA	0.822885794262353	2		447	1580	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2115535	2115535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000220-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	3291	861	741	0	ENST00000219476.3:c.1615C>T	p.Leu539Phe	p.L539F	ENST00000219476	NM_000548.3	539	Ctc/Ttc	16/42	0.660297506410537	4	FACETS	0.919	0.886	0.952	0.459	0.443	0.476	CLONAL	1	TRUE	2	0.822885794262353	4		741	4152	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39613847	39613847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000220-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	1210	501	591	0	ENST00000262039.4:c.1765G>A	p.Glu589Lys	p.E589K	ENST00000262039	NM_002647.2	589	Gaa/Aaa	16/25	1	2	FACETS	0.712	0.68	0.744	0.712	0.68	0.744	SUBCLONAL	1	TRUE	1	0.822885794262353	2		591	1711	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24133963	24133963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000220-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	374	368	346	0	ENST00000263121.7:c.114G>A	p.Met38Ile	p.M38I	ENST00000263121	NM_003073.3	38	atG/atA	2/9	0.791541229473315	1	FACETS	0.709	0.678	0.741	0.709	0.678	0.741	SUBCLONAL	1	TRUE	0	0.822885794262353	1		346	742	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178518	56178518	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0000220-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	791	508	450	0	ENST00000399503.3:c.3491del	p.Asp1164ValfsTer8	p.D1164Vfs*8	ENST00000399503	NM_005921.1	1164	gAt/gt	14/20	1	2	FACETS	0.95	0.911	0.99	0.95	0.911	0.99	CLONAL	1	TRUE	1	0.822885794262353	2		450	1299	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849572	68849572	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000220-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	452	1657	694	0	ENST00000261769.5:c.1475del	p.Arg492LysfsTer30	p.R492Kfs*30	ENST00000261769	NM_004360.3	492	aGa/aa	10/16	NA	2	FACETS	0.955	0.941	0.968			1	INDETERMINATE	2	TRUE	NA	0.822885794262353	2		694	2109	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0000230-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	197	607	2	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.270217393169155	2		609	1110	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0000230-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	124	628	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.270217393169155	1	FACETS	0.827	0.747	0.911	0.827	0.747	0.911	CLONAL	1	TRUE	0	0.270217393169155	1		628	960	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793663	NA	P-0000230-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1495	163	509	0	ENST00000263967.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000263967	NM_006218.2	93	cGg/cAg	2/21	1	2	FACETS	0.728	0.665	0.794	0.728	0.665	0.794	SUBCLONAL	1	TRUE	1	0.270217393169155	2		509	1658	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69456152	69456152	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000230-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1337	243	668	0	ENST00000227507.2:c.71A>G	p.Asn24Ser	p.N24S	ENST00000227507	NM_053056.2	24	aAc/aGc	1/5	0.24708468566276	4	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.270217393169155	4		668	1580	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0000238-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	226	262	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.184482673291274	3	FACETS	0.95	0.891	1	1	0.99	1	CLONAL	4	TRUE	0	0.224237518988738	3		262	590	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439855	52439855	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000238-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	167	391	0	ENST00000460680.1:c.857del	p.Lys286SerfsTer49	p.K286Sfs*49	ENST00000460680	NM_004656.3	286	aAg/ag	10/17	0.224237518988738	1	FACETS	1	0.928	1	1	0.994	1	CLONAL	3	TRUE	0	0.224237518988738	1		391	441	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565852	55565852	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000239-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	65	279	0	ENST00000288135.5:c.676G>T	p.Gly226Trp	p.G226W	ENST00000288135	NM_000222.2	226	Ggg/Tgg	4/21	1	2	FACETS	0.748	0.647	0.859	0.748	0.647	0.859	SUBCLONAL	1	TRUE	1	0.175656245158239	2		279	989	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910914	32910914	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000239-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	33	164	0	ENST00000380152.3:c.2422G>T	p.Glu808Ter	p.E808*	ENST00000380152		808	Gaa/Taa	11/27	NA	2	FACETS	0.642	0.522	0.779			1	INDETERMINATE	1	TRUE	NA	0.175656245158239	2		164	585	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039816	47039816	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0000239-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	77	245	0	ENST00000377604.3:c.1161-2A>T		p.X387_splice	ENST00000377604	NM_001204468.1	387			1	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.175656245158239	1		245	648	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245033	53245033	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1556851514	NA	P-0000239-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	56	387	0	ENST00000375401.3:c.907G>C	p.Glu303Gln	p.E303Q	ENST00000375401	NM_004187.3	303	Gaa/Caa	7/26	1	1	FACETS	0.529	0.451	0.615	0.529	0.451	0.615	SUBCLONAL	1	TRUE	0	0.175656245158239	1		387	1099	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0000241-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	253	358	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.317066459437019	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.317066459437019	1		358	898	SUCCESS
APC	324	MSKCC	GRCh37	5	112178879	112178879	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881265	NA	P-0000241-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	79	319	0	ENST00000257430.4:c.7588C>T	p.Arg2530Trp	p.R2530W	ENST00000257430	NM_000038.5	2530	Cgg/Tgg	16/16	0.317066459437019	3	FACETS	0.81	0.712	0.915	0.405	0.356	0.458	CLONAL	1	TRUE	1	0.317066459437019	3		319	713	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209286	98209286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369882883	NA	P-0000241-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1378	187	662	0	ENST00000331920.6:c.4252G>A	p.Val1418Ile	p.V1418I	ENST00000331920	NM_000264.3	1418	Gtc/Atc	23/24	0.317066459437019	4	FACETS	0.993	0.914	1	0.331	0.304	0.359	CLONAL	1	TRUE	1	0.317066459437019	4		662	1565	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047135	77047135	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000241-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	133	436	0	ENST00000356341.3:c.1409T>A	p.Leu470Gln	p.L470Q	ENST00000356341	NM_002576.4	470	cTg/cAg	13/15	0.280853862062682	3	FACETS	0.92	0.834	1	0.46	0.417	0.506	CLONAL	1	TRUE	1	0.317066459437019	3		436	1056	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000241-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	260	402	1	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	0.285923525793045	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.317066459437019	2		403	770	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0000241-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	195	120	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.315037249222674	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.317066459437019	2		120	577	SUCCESS
APC	324	MSKCC	GRCh37	5	112174693	112174697	+	frameshift_variant	Frame_Shift_Del	DEL	CTATG	CTATG	-	novel	NA	P-0000241-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	189	274	0	ENST00000257430.4:c.3402_3406del	p.Asp1134GlufsTer3	p.D1134Efs*3	ENST00000257430	NM_000038.5	1134	gaCTATGaa/gaaa	16/16	0.317066459437019	3	FACETS	0.869	0.804	0.935	0.869	0.804	0.935	CLONAL	2	TRUE	1	0.317066459437019	3		274	795	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0000241-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	101	419	1	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.317066459437019	3	FACETS	0.855	0.764	0.953	0.428	0.382	0.477	CLONAL	1	TRUE	1	0.317066459437019	3		420	863	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0000263-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	94	703	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.938	0.838	1	0.938	0.838	1	CLONAL	1	TRUE	1	0.4	2		704	501	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460516	149460516	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000263-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	46	245	0	ENST00000286301.3:c.121C>T	p.Arg41Ter	p.R41*	ENST00000286301	NM_005211.3	41	Cga/Tga	3/22	0.172014428343698	3	FACETS	0.687	0.579	0.805	0.343	0.289	0.403	INDETERMINATE	1	TRUE	1	0.4	3		245	402	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871864	12871864	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000263-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	10	72	0	ENST00000228872.4:c.581G>A	p.Arg194Lys	p.R194K	ENST00000228872	NM_004064.3	194	aGa/aAa	2/3	0.175545470637492	3	FACETS	0.37	0.251	0.52			1	INDETERMINATE	1	TRUE	NA	0.4	3		72	162	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823843	3823843	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000263-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	51	246	0	ENST00000262367.5:c.2372G>C	p.Ser791Thr	p.S791T	ENST00000262367	NM_004380.2	791	aGc/aCc	13/31	1	2	FACETS	0.59	0.502	0.686	0.59	0.502	0.686	SUBCLONAL	1	TRUE	1	0.4	2		246	432	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851789	134851789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000273-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	699	298	884	3	ENST00000398015.3:c.1195C>T	p.His399Tyr	p.H399Y	ENST00000398015	NM_004441.4	399	Cac/Tac	5/16	0.409608995379435	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.409608995379435	1		887	997	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518651	103518651	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000273-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	630	165	558	2	ENST00000355739.4:c.2239C>A	p.Gln747Lys	p.Q747K	ENST00000355739	NM_000123.3	747	Cag/Aag	10/15	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.409608995379435	NA		560	795	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038275	30038275	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0000273-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	931	325	1091	2	ENST00000338641.4:c.447+1G>A		p.X149_splice	ENST00000338641	NM_000268.3	149			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.409608995379435	NA		1093	1256	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100308	27100308	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000298-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	51	489	0	ENST00000324856.7:c.4020del	p.Asn1341IlefsTer140	p.N1341Ifs*140	ENST00000324856	NM_006015.4	1340	ggC/gg	17/20	0.379797799322714	1	FACETS	0.713	0.61	0.825	0.713	0.61	0.825	SUBCLONAL	1	FALSE	0	0.379797799322714	1		489	305	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0000301-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	40	304	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.244597009804019	6	FACETS	0.575	0.476	0.686			1	SUBCLONAL	1	TRUE	NA	0.244597009804019	6		304	847	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000301-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	91	402	0	ENST00000269305.4:c.859G>T	p.Glu287Ter	p.E287*	ENST00000269305	NM_001126112.2	287	Gag/Tag	8/11	0.228030770501044	1	FACETS	0.93	0.826	1	0.93	0.826	1	CLONAL	1	TRUE	0	0.244597009804019	1		402	702	SUCCESS
ALK	238	MSKCC	GRCh37	2	29420441	29420441	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000318-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	236	674	0	ENST00000389048.3:c.4040G>T	p.Arg1347Leu	p.R1347L	ENST00000389048	NM_004304.4	1347	cGg/cTg	27/29	0.634944859129554	4	FACETS	0.883	0.823	0.946			1	CLONAL	1	TRUE	NA	0.718820816924616	4		674	1278	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231724	66231724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000318-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1209	76	668	0	ENST00000273854.3:c.1976C>T	p.Pro659Leu	p.P659L	ENST00000273854	NM_004439.5	659	cCc/cTc	11/18	0.634944859129554	4	FACETS	0.283	0.247	0.322			1	SUBCLONAL	1	TRUE	NA	0.718820816924616	4		668	1285	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015039	37015039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs185643174	NA	P-0000318-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	191	517	0	ENST00000358127.4:c.365G>A	p.Arg122Gln	p.R122Q	ENST00000358127	NM_001280556.1	122	cGg/cAg	3/10	0.717704547859784	4	FACETS	1	0.943	1			1	CLONAL	1	TRUE	NA	0.718820816924616	4		517	893	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140500237	140500237	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000329-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	250	316	0	ENST00000288602.6:c.905A>G	p.Gln302Arg	p.Q302R	ENST00000288602	NM_004333.4	302	cAg/cGg	7/18	0.758279419554077	3	FACETS	1	0.978	1	0.364	0.341	0.387	CLONAL	1	TRUE	0	0.768428075036938	3		316	825	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160489	108160489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749770110	NA	P-0000329-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	600	614	0	ENST00000278616.4:c.4397G>A	p.Arg1466Gln	p.R1466Q	ENST00000278616	NM_000051.3	1466	cGa/cAa	29/63	0.764178464118351	2	FACETS	0.95	0.925	0.974	0.95	0.925	0.974	CLONAL	2	TRUE	0	0.768428075036938	2		614	822	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0000329-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	977	659	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	0.748506543228607	2	FACETS	0.99	0.971	1	0.99	0.971	1	CLONAL	2	TRUE	0	0.768428075036938	2		659	1284	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713427	40713427	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000329-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	532	403	0	ENST00000373198.4:c.4088G>T	p.Arg1363Leu	p.R1363L	ENST00000373198	NM_133170.3	1363	cGg/cTg	30/32	0.733074874517621	3	FACETS	0.994	0.96	1	0.994	0.96	1	CLONAL	2	TRUE	1	0.768428075036938	3		403	964	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579310	7579310	+	splice_donor_variant	Splice_Site	SNP	A	A	C	rs1555526469	NA	P-0000335-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	36	316	0	ENST00000269305.4:c.375+2T>G		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.377570129899091	2	FACETS	0.538	0.443	0.643	0.269	0.221	0.322	SUBCLONAL	1	TRUE	0	0.419814919028453	2		316	319	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444452	50444452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000335-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	80	168	0	ENST00000331340.3:c.382G>A	p.Gly128Arg	p.G128R	ENST00000331340	NM_006060.4	128	Ggg/Agg	4/8	0.269444458333711	4	FACETS	1	0.906	1	1	0.906	1	CLONAL	2	TRUE	2	0.419814919028453	4		168	266	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0000344-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	161	358	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.188684153531155	5	FACETS	1	0.964	1	0.724	0.665	0.786	CLONAL	2	TRUE	2	0.274595732860649	5		358	762	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921379	178921379	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000344-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	40	547	0	ENST00000263967.3:c.861G>C	p.Leu287Phe	p.L287F	ENST00000263967	NM_006218.2	287	ttG/ttC	5/21	0.274595732860649	5	FACETS	0.519	0.429	0.619	0.13	0.107	0.155	SUBCLONAL	1	TRUE	1	0.274595732860649	5		547	793	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88428948	88428948	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000344-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	84	736	0	ENST00000360948.2:c.2152A>T	p.Asn718Tyr	p.N718Y	ENST00000360948	NM_001012338.2	718	Aat/Tat	17/19	0.274050502190941	2	FACETS	0.9	0.802	1	0.9	0.802	1	CLONAL	2	TRUE	0	0.274595732860649	2		736	340	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597402	10597402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770453522	NA	P-0000344-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	167	575	0	ENST00000171111.5:c.1801C>T	p.Arg601Trp	p.R601W	ENST00000171111	NM_203500.1	601	Cgg/Tgg	6/6	0.274595732860649	1	FACETS	1	0.938	1	1	0.993	1	CLONAL	2	TRUE	0	0.274595732860649	1		575	517	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221312	1221312	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000344-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	120	527	0	ENST00000326873.7:c.836del	p.Gly279AlafsTer8	p.G279Afs*8	ENST00000326873	NM_000455.4	279	Ggc/gc	6/10	0.274595732860649	1	FACETS	0.82	0.745	0.897	1	0.987	1	CLONAL	2	TRUE	0	0.274595732860649	1		527	460	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620446	52620446	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000362-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	140	367	0	ENST00000394830.3:c.3307G>T	p.Glu1103Ter	p.E1103*	ENST00000394830	NM_018313.4	1103	Gaa/Taa	21/30	0.247282372955022	0	FACETS	0.744	0.68	0.81			1	SUBCLONAL	2	TRUE	0	0.247282372955022	0		367	573	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0000388-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	92	556	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.327501374332214	2		556	532	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332758	65332758	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs746120026	NA	P-0000388-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	195	472	0	ENST00000342505.4:c.781G>T	p.Val261Leu	p.V261L	ENST00000342505	NM_002227.2	261	Gtg/Ttg	7/25	0.17879763314756	2	FACETS	1	0.949	1	1	0.949	1	INDETERMINATE	2	TRUE	0	0.327501374332214	2		472	582	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521724	89521724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000388-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	124	353	0	ENST00000336596.2:c.2801G>A	p.Gly934Asp	p.G934D	ENST00000336596	NM_005233.5	934	gGt/gAt	16/17	0.327501374332214	3	FACETS	0.992	0.905	1	0.992	0.905	1	CLONAL	2	TRUE	1	0.327501374332214	3		353	444	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14026280	14026280	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000388-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	204	417	0	ENST00000405192.2:c.164A>T	p.Glu55Val	p.E55V	ENST00000405192	NM_001163147.1	55	gAa/gTa	4/12	0.313238520702755	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.327501374332214	4		417	673	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524968	8524968	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000388-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	87	445	0	ENST00000356435.5:c.636C>A	p.Ser212Arg	p.S212R	ENST00000356435		212	agC/agA	7/35	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.327501374332214	2		445	433	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438665	49438665	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000388-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	92	393	0	ENST00000301067.7:c.4825C>T	p.His1609Tyr	p.H1609Y	ENST00000301067	NM_003482.3	1609	Cac/Tac	19/54	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.327501374332214	2		393	391	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117427	115117427	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000388-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	66	348	0	ENST00000257566.3:c.747G>T	p.Gln249His	p.Q249H	ENST00000257566	NM_016569.3	249	caG/caT	4/8	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.327501374332214	2		348	382	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014071	14014071	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs368281878	NA	P-0000388-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	34	509	0	ENST00000311895.7:c.49G>T	p.Glu17Ter	p.E17*	ENST00000311895	NM_005236.2	17	Gag/Tag	1/11	0.251222188435782	2	FACETS	0.473	0.386	0.571	0.236	0.193	0.286	SUBCLONAL	1	TRUE	0	0.327501374332214	2		509	439	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926532	59926532	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000388-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	372	695	0	ENST00000259008.2:c.465A>T	p.Gln155His	p.Q155H	ENST00000259008	NM_032043.2	155	caA/caT	5/20	NA	2	FACETS	0.971	0.928	1			1	INDETERMINATE	3	TRUE	NA	0.327501374332214	2		695	780	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133860	55133860	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0000388-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	89	443	0	ENST00000257290.5:c.1076del	p.Asn359IlefsTer15	p.N359Ifs*15	ENST00000257290	NM_006206.4	358	gAa/ga	7/23	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.327501374332214	2		443	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579456	7579456	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000388-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	147	303	0	ENST00000269305.4:c.231del	p.Ala78GlnfsTer45	p.A78Qfs*45	ENST00000269305	NM_001126112.2	77	ccA/cc	4/11	0.327501374332214	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.327501374332214	2		303	362	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677320	29677320	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000388-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	184	481	0	ENST00000356175.3:c.7379del	p.Gly2460ValfsTer8	p.G2460Vfs*8	ENST00000356175	NM_000267.3	2460	Ggt/gt	49/57	0.327501374332214	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.327501374332214	2		481	498	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584514	48584514	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000388-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	154	290	1	ENST00000342988.3:c.692del	p.Gly231AlafsTer10	p.G231Afs*10	ENST00000342988	NM_005359.5	229	ctG/ct	6/12	0.327501374332214	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.327501374332214	2		291	382	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637865	176637865	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs377684553	NA	P-0000409-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	168	319	0	ENST00000439151.2:c.2465C>G	p.Ser822Cys	p.S822C	ENST00000439151	NM_022455.4	822	tCt/tGt	5/23	0.220470165938177	1	FACETS	0.863	0.799	0.929	0.863	0.799	0.929	INDETERMINATE	1	FALSE	0	0.550126501791691	1		319	513	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407454	407454	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0000409-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	180	286	0	ENST00000380956.4:c.1213-1G>T		p.X405_splice	ENST00000380956	NM_001195286.1	405			0.562970886271853	4	FACETS	1	0.981	1			1	CLONAL	1	FALSE	NA	0.550126501791691	4		286	850	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572054	64572054	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000409-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	209	238	0	ENST00000312049.6:c.1585C>G	p.Pro529Ala	p.P529A	ENST00000312049	NM_130799.2	529	Cct/Gct	10/10	0.562970886271853	4	FACETS	1	0.985	1			1	CLONAL	1	FALSE	NA	0.550126501791691	4		238	966	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987093	36987093	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000409-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	471	221	0	ENST00000354822.5:c.596C>T	p.Ser199Leu	p.S199L	ENST00000354822	NM_001079668.2	199	tCg/tTg	3/3	0.562970886271853	3	FACETS	1	0.995	1			1	CLONAL	3	FALSE	NA	0.550126501791691	3		221	635	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs17849781	NA	P-0000409-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	511	451	0	ENST00000269305.4:c.832C>A	p.Pro278Thr	p.P278T	ENST00000269305	NM_001126112.2	278	Cct/Act	8/11	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	2	FALSE	NA	0.550126501791691	2		451	766	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41197814	41197814	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000409-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	288	263	0	ENST00000357654.3:c.5473G>C	p.Gly1825Arg	p.G1825R	ENST00000357654	NM_007294.3	1825	Ggg/Cgg	23/23	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	2	FALSE	NA	0.550126501791691	2		263	470	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0000426-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	159	412	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.206439586166365	5	FACETS	1	0.939	1			1	CLONAL	4	FALSE	NA	0.206439586166365	5		413	495	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199974	128199974	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs781161922	NA	P-0000426-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	56	299	0	ENST00000341105.2:c.1331C>A	p.Pro444Gln	p.P444Q	ENST00000341105	NM_032638.4	444	cCg/cAg	6/6	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.206439586166365	NA		299	321	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220476	1220476	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000426-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	219	472	0	ENST00000326873.7:c.569T>G	p.Leu190Arg	p.L190R	ENST00000326873	NM_000455.4	190	cTc/cGc	4/10	0.206439586166365	5	FACETS	0.885	0.825	0.946	0.885	0.825	0.946	CLONAL	4	FALSE	1	0.206439586166365	5		472	785	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600369	10600369	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000426-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	223	557	1	ENST00000171111.5:c.1486G>T	p.Glu496Ter	p.E496*	ENST00000171111	NM_203500.1	496	Gag/Tag	4/6	0.206439586166365	5	FACETS	1	0.968	1	0.798	0.744	0.854	CLONAL	3	FALSE	1	0.206439586166365	5		558	886	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144090	11144090	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000426-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	78	435	0	ENST00000358026.2:c.3671T>C	p.Val1224Ala	p.V1224A	ENST00000358026	NM_001128849.1	1224	gTg/gCg	26/36	0.206439586166365	5	FACETS	0.829	0.729	0.936	0.414	0.364	0.468	CLONAL	2	FALSE	1	0.206439586166365	5		435	597	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420191	88420191	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000426-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	52	434	0	ENST00000360948.2:c.2495del	p.Pro832GlnfsTer15	p.P832Qfs*15	ENST00000360948	NM_001012338.2	832	cCa/ca	19/19	0.184002267910243	0	FACETS	1	0.955	1			1	CLONAL	1	FALSE	0	0.206439586166365	0		434	305	SUCCESS
AR	367	MSKCC	GRCh37	X	66937397	66937398	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0000426-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	36	740	0	ENST00000374690.3:c.2251_2252delinsTT	p.Gly751Phe	p.G751F	ENST00000374690	NM_000044.3	751	GGc/TTc	5/8	0.206439586166365	0	FACETS	0.632	0.519	0.758			1	SUBCLONAL	1	FALSE	0	0.206439586166365	0		740	438	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0000427-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	368	73	240	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	1	2	FACETS	0.853	0.748	0.964	0.853	0.748	0.964	CLONAL	1	TRUE	1	0.388295959005393	2		240	441	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280095	66280095	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1206356192	NA	P-0000427-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	509	119	276	0	ENST00000273854.3:c.1594C>T	p.Pro532Ser	p.P532S	ENST00000273854	NM_004439.5	532	Cca/Tca	7/18	0.199696970516578	1	FACETS	0.787	0.712	0.865	0.787	0.712	0.865	INDETERMINATE	1	TRUE	0	0.388295959005393	1		276	628	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540465	187540465	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000427-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	334	68	169	0	ENST00000441802.2:c.7275G>T	p.Leu2425Phe	p.L2425F	ENST00000441802	NM_005245.3	2425	ttG/ttT	10/27	0.388295959005393	1	FACETS	0.702	0.613	0.797	0.702	0.613	0.797	SUBCLONAL	1	TRUE	0	0.388295959005393	1		169	402	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047286	180047286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000427-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	758	215	363	0	ENST00000261937.6:c.2429C>T	p.Thr810Met	p.T810M	ENST00000261937	NM_182925.4	810	aCg/aTg	17/30	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.388295959005393	2		363	973	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491483	18491483	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0000427-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	302	70	156	0	ENST00000266497.5:c.1395+1G>C		p.X465_splice	ENST00000266497		465			1	2	FACETS	0.969	0.85	1	0.969	0.85	1	CLONAL	1	TRUE	1	0.388295959005393	2		156	372	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207078	1207078	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000427-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	397	196	263	0	ENST00000326873.7:c.166G>T	p.Gly56Trp	p.G56W	ENST00000326873	NM_000455.4	56	Ggg/Tgg	1/10	0.388295959005393	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.388295959005393	1		263	593	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2193751	2193751	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000427-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	446	159	312	0	ENST00000398665.3:c.557A>C	p.Glu186Ala	p.E186A	ENST00000398665	NM_032482.2	186	gAg/gCg	6/28	0.388295959005393	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.388295959005393	1		312	605	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141508	11141508	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000427-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	416	216	276	0	ENST00000358026.2:c.3485G>T	p.Gly1162Val	p.G1162V	ENST00000358026	NM_001128849.1	1162	gGc/gTc	25/36	0.388295959005393	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.388295959005393	1		276	632	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710553	40710553	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000427-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	399	97	142	0	ENST00000373198.4:c.4298G>C	p.Arg1433Pro	p.R1433P	ENST00000373198	NM_133170.3	1433	cGt/cCt	31/32	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.388295959005393	2		142	496	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599949	10599950	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0000427-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	554	247	403	0	ENST00000171111.5:c.1626_1627del	p.Glu542AspfsTer31	p.E542Dfs*31	ENST00000171111	NM_203500.1	542	gaGAcg/gacg	5/6	0.388295959005393	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.388295959005393	1		403	801	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306733	41306734	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0000427-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	399	86	205	0	ENST00000373198.4:c.925_926delinsAA	p.Pro309Lys	p.P309K	ENST00000373198	NM_133170.3	309	CCa/AAa	7/32	1	2	FACETS	0.913	0.811	1	0.913	0.811	1	CLONAL	1	TRUE	1	0.388295959005393	2		205	485	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026440	48026440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000453-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	112	481	0	ENST00000234420.5:c.1318G>A	p.Ala440Thr	p.A440T	ENST00000234420	NM_000179.2	440	Gct/Act	4/10	1	2	FACETS	0.752	0.677	0.83	0.752	0.677	0.83	SUBCLONAL	1	TRUE	1	0.459231938897178	2		481	649	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433718	49433718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372935294	NA	P-0000453-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	193	438	0	ENST00000301067.7:c.7835C>T	p.Pro2612Leu	p.P2612L	ENST00000301067	NM_003482.3	2612	cCt/cTt	31/54	0.418263557306346	3	FACETS	0.923	0.86	0.987	0.923	0.86	0.987	CLONAL	2	TRUE	1	0.459231938897178	3		438	560	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109924	115109924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754142951	NA	P-0000453-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	77	196	0	ENST00000257566.3:c.1954G>A	p.Gly652Ser	p.G652S	ENST00000257566	NM_016569.3	652	Ggc/Agc	8/8	0.451054054415338	2	FACETS	1	0.935	1	0.541	0.479	0.606	CLONAL	1	TRUE	0	0.459231938897178	2		196	310	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0000453-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	275	325	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.369000406354387	5	FACETS	1	0.971	1			1	CLONAL	3	TRUE	NA	0.459231938897178	5		325	648	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581229	48581229	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs377767331	NA	P-0000453-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	277	390	0	ENST00000342988.3:c.533C>G	p.Ser178Ter	p.S178*	ENST00000342988	NM_005359.5	178	tCa/tGa	5/12	0.459231938897178	2	FACETS	0.931	0.881	0.981	0.931	0.881	0.981	CLONAL	2	TRUE	0	0.459231938897178	2		390	648	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761014	59761017	+	frameshift_variant	Frame_Shift_Del	DEL	ATAG	ATAG	-	rs778664039	NA	P-0000453-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	240	593	0	ENST00000259008.2:c.3390_3393del	p.Tyr1131LeufsTer18	p.Y1131Lfs*18	ENST00000259008	NM_032043.2	1130	atCTAT/at	20/20	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.459231938897178	2		593	839	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183532	10183532	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1060503557	NA	P-0000459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	50	513	0	ENST00000256474.2:c.1A>G	p.Met1?	p.M1?	ENST00000256474	NM_000551.3	1	Atg/Gtg	1/3	0.170829110085404	4	FACETS	0.846	0.735	0.96	0.846	0.735	0.96	INDETERMINATE	2	TRUE	2	0.74976601574824	4		513	138	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971000	21971000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	10	347	0	ENST00000304494.5:c.358G>T	p.Glu120Ter	p.E120*	ENST00000304494	NM_000077.4	120	Gag/Tag	2/3	0.74976601574824	1	FACETS	0.333	0.232	0.454	0.333	0.232	0.454	SUBCLONAL	1	TRUE	0	0.74976601574824	1		347	50	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243881	46243881	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs993030810	NA	P-0000459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	78	528	0	ENST00000334344.6:c.1975T>C	p.Ser659Pro	p.S659P	ENST00000334344	NM_152641.2	659	Tct/Cct	15/21	0.251021155336679	3	FACETS	0.782	0.703	0.862	0.782	0.703	0.862	INDETERMINATE	2	TRUE	1	0.74976601574824	3		528	183	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831438	89831438	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs762804216	NA	P-0000459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	86	521	0	ENST00000389301.3:c.2638C>T	p.Arg880Ter	p.R880*	ENST00000389301	NM_000135.2	880	Cga/Tga	28/43	0.110205355882133	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.74976601574824	0		521	217	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599973	10599973	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	12	685	0	ENST00000171111.5:c.1603G>T	p.Glu535Ter	p.E535*	ENST00000171111	NM_203500.1	535	Gag/Tag	5/6	0.74976601574824	1	FACETS	0.135	0.095	0.184	0.135	0.095	0.184	SUBCLONAL	1	TRUE	0	0.74976601574824	1		685	148	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602646	10602646	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	39	500	1	ENST00000171111.5:c.932A>G	p.His311Arg	p.H311R	ENST00000171111	NM_203500.1	311	cAc/cGc	3/6	0.74976601574824	1	FACETS	0.707	0.607	0.809	0.707	0.607	0.809	SUBCLONAL	1	TRUE	0	0.74976601574824	1		501	92	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0000459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	53	655	1	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.630515257374014	1	FACETS	0.982	0.879	1	0.982	0.879	1	CLONAL	1	TRUE	0	0.74976601574824	1		656	90	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550459	29550460	+	splice_acceptor_variant,intron_variant	Splice_Site	DNP	CA	CA	GC	novel	NA	P-0000459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	38	311	0	ENST00000356175.3:c.1722-3_1722-2delinsGC		p.X574_splice	ENST00000356175	NM_000267.3	574			1	2	FACETS	0.786	0.663	0.916	0.786	0.663	0.916	CLONAL	1	TRUE	1	0.74976601574824	2		311	129	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000468-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	234	63	273	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.414173490811571	2	FACETS	0.899	0.784	1	0.45	0.392	0.511	CLONAL	1	TRUE	0	0.471725153770915	2		273	297	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056146	27056146	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1557591022	NA	P-0000468-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	267	73	269	0	ENST00000324856.7:c.1142C>G	p.Ser381Cys	p.S381C	ENST00000324856	NM_006015.4	381	tCc/tGc	2/20	0.108319665339208	3	FACETS	1	0.944	1			1	INDETERMINATE	1	TRUE	NA	0.471725153770915	3		269	340	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170240	32170240	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000468-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	261	64	261	0	ENST00000375023.3:c.3368C>A	p.Pro1123His	p.P1123H	ENST00000375023	NM_004557.3	1123	cCt/cAt	21/30	1	2	FACETS	0.835	0.728	0.949	0.835	0.728	0.949	CLONAL	1	TRUE	1	0.471725153770915	2		261	325	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404899	70404899	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000468-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	302	92	435	0	ENST00000373644.4:c.2413A>T	p.Ser805Cys	p.S805C	ENST00000373644	NM_030625.2	805	Agc/Tgc	4/12	1	2	FACETS	0.99	0.886	1	0.99	0.886	1	CLONAL	1	TRUE	1	0.471725153770915	2		435	394	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385034	31385034	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000468-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	244	68	307	0	ENST00000328111.2:c.1419del	p.Tyr474IlefsTer116	p.Y474Ifs*116	ENST00000328111	NM_006892.3	473	ggC/gg	14/23	1	2	FACETS	0.924	0.811	1	0.924	0.811	1	CLONAL	1	TRUE	1	0.471725153770915	2		307	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0000469-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	105	294	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	2	FALSE	NA	0.759301747603988	2		294	134	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0000469-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	216	261	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.661959393421302	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	FALSE	2	0.759301747603988	4		261	474	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178253	56178253	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000469-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	198	401	1	ENST00000399503.3:c.3226C>G	p.Pro1076Ala	p.P1076A	ENST00000399503	NM_005921.1	1076	Ccc/Gcc	14/20	0.759301747603988	4	FACETS	0.934	0.865	1	0.467	0.432	0.503	CLONAL	1	FALSE	2	0.759301747603988	4		402	982	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631302	117631302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138376257	NA	P-0000469-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	219	608	0	ENST00000368508.3:c.6376C>T	p.Arg2126Trp	p.R2126W	ENST00000368508	NM_002944.2	2126	Cgg/Tgg	40/43	0.752930050067675	3	FACETS	1	0.955	1	0.515	0.481	0.551	CLONAL	1	FALSE	1	0.759301747603988	3		608	772	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206911	162206911	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000469-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	38	260	0	ENST00000366898.1:c.764C>T	p.Ser255Phe	p.S255F	ENST00000366898	NM_004562.2	255	tCc/tTc	7/12	0.752930050067675	3	FACETS	0.351	0.291	0.419	0.176	0.145	0.21	SUBCLONAL	1	FALSE	1	0.759301747603988	3		260	393	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54948558	54948558	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000469-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	428	509	0	ENST00000312783.6:c.760C>T	p.His254Tyr	p.H254Y	ENST00000312783	NM_198436.1	254	Cat/Tat	8/10	0.515046814757747	5	FACETS	1	0.99	1			1	CLONAL	2	FALSE	NA	0.759301747603988	5		509	1076	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632691	23632691	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0000469-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	219	371	0	ENST00000261584.4:c.3105del	p.Ile1035MetfsTer6	p.I1035Mfs*6	ENST00000261584	NM_024675.3	1035	atT/at	10/13	0.2919157775725	4	FACETS	0.921	0.864	0.979	0.614	0.576	0.653	INDETERMINATE	2	FALSE	1	0.759301747603988	4		371	551	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099872	157099873	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0000469-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	276	320	0	ENST00000346085.5:c.809_810delinsTA	p.Ser270Leu	p.S270L	ENST00000346085	NM_020732.3	270	tCC/tTA	1/20	0.752930050067675	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	FALSE	1	0.759301747603988	3		320	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0000470-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	182	228	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	1	0.961	1			1	INDETERMINATE	2	TRUE	NA	0.586895486805221	2		228	303	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0000470-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	234	470	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.578326025817037	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.586895486805221	2		470	366	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451308	70451308	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000470-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	40	464	0	ENST00000373644.4:c.6148C>A	p.Gln2050Lys	p.Q2050K	ENST00000373644	NM_030625.2	2050	Cag/Aag	12/12	0.531754247306922	2	FACETS	0.226	0.187	0.27	0.113	0.093	0.135	SUBCLONAL	1	TRUE	0	0.586895486805221	2		464	602	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033947	49033947	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000470-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	208	323	0	ENST00000267163.4:c.2084T>A	p.Met695Lys	p.M695K	ENST00000267163	NM_000321.2	695	aTg/aAg	20/27	0.578326025817037	2	FACETS	0.923	0.871	0.974	0.923	0.871	0.974	CLONAL	2	TRUE	0	0.586895486805221	2		323	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0000488-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	25	228	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		228	353	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217302	11217302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000501-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	112	567	2	ENST00000361445.4:c.4376C>A	p.Ala1459Asp	p.A1459D	ENST00000361445	NM_004958.3	1459	gCc/gAc	30/58	1	2	FACETS	0.346	0.31	0.384	0.346	0.31	0.384	SUBCLONAL	1	TRUE	1	0.6	2		569	1079	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17371320	17371320	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs74315370	NA	P-0000501-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	216	555	0	ENST00000375499.3:c.136C>T	p.Arg46Ter	p.R46*	ENST00000375499	NM_003000.2	46	Cga/Tga	2/8	1	2	FACETS	0.718	0.667	0.77	0.718	0.667	0.77	SUBCLONAL	1	TRUE	1	0.6	2		555	1003	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098944	178098944	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000527-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	288	519	0	ENST00000397062.3:c.101G>T	p.Arg34Leu	p.R34L	ENST00000397062	NM_006164.4	34	cGa/cTa	2/5	0.302662466778135	3	FACETS	0.821	0.772	0.872	0.821	0.772	0.872	CLONAL	2	TRUE	1	0.347162190659251	3		519	1186	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245523	153245523	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000527-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	125	322	0	ENST00000281708.4:c.1668T>G	p.Ser556Arg	p.S556R	ENST00000281708	NM_033632.3	556	agT/agG	11/12	0.27110889020271	2	FACETS	1	0.974	1	0.599	0.544	0.657	CLONAL	1	TRUE	0	0.347162190659251	2		322	601	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754849	57754849	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000527-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	96	507	0	ENST00000274289.3:c.341C>T	p.Pro114Leu	p.P114L	ENST00000274289	NM_006622.3	114	cCt/cTt	2/14	0.302662466778135	3	FACETS	0.684	0.608	0.765	0.342	0.304	0.383	SUBCLONAL	1	TRUE	1	0.347162190659251	3		507	949	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115639	108115639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876659531	NA	P-0000527-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	207	435	0	ENST00000278616.4:c.787C>T	p.Leu263Phe	p.L263F	ENST00000278616	NM_000051.3	263	Ctt/Ttt	7/63	0.302662466778135	3	FACETS	1	0.991	1	0.73	0.678	0.785	CLONAL	1	TRUE	1	0.347162190659251	3		435	958	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442898	49442898	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000527-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	54	320	0	ENST00000301067.7:c.4010A>G	p.Glu1337Gly	p.E1337G	ENST00000301067	NM_003482.3	1337	gAg/gGg	12/54	0.317773262275535	5	FACETS	0.824	0.704	0.956	0.275	0.234	0.319	CLONAL	1	TRUE	2	0.347162190659251	5		320	574	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832709	3832709	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000527-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	55	349	0	ENST00000262367.5:c.1549C>T	p.Gln517Ter	p.Q517*	ENST00000262367	NM_004380.2	517	Cag/Tag	6/31	0.299054730296564	3	FACETS	0.508	0.434	0.59			1	SUBCLONAL	1	TRUE	NA	0.347162190659251	3		349	732	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835612	68835612	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1284989530	NA	P-0000527-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	116	519	0	ENST00000261769.5:c.203A>G	p.Tyr68Cys	p.Y68C	ENST00000261769	NM_004360.3	68	tAt/tGt	3/16	0.27110889020271	2	FACETS	0.776	0.699	0.858	0.388	0.349	0.429	SUBCLONAL	1	TRUE	0	0.347162190659251	2		519	861	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657056	45657056	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000527-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	90	365	0	ENST00000407780.3:c.100G>T	p.Glu34Ter	p.E34*	ENST00000407780	NM_001283052.1	34	Gag/Tag	3/7	0.317773262275535	5	FACETS	0.785	0.699	0.877	0.524	0.466	0.585	SUBCLONAL	2	TRUE	2	0.347162190659251	5		365	502	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951087	48951088	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs1131690889	NA	P-0000527-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	105	241	0	ENST00000267163.4:c.1251_1252del	p.Arg418SerfsTer9	p.R418Sfs*9	ENST00000267163	NM_000321.2	417	AAa/a	13/27	0.233307767615913	2	FACETS	1	0.966	1	0.584	0.525	0.646	CLONAL	1	TRUE	0	0.347162190659251	2		241	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579330	7579330	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000527-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	63	300	0	ENST00000269305.4:c.357del	p.Lys120SerfsTer3	p.K120Sfs*3	ENST00000269305	NM_001126112.2	119	gcC/gc	4/11	0.347162190659251	1	FACETS	0.898	0.782	1	0.898	0.782	1	CLONAL	1	TRUE	0	0.347162190659251	1		300	334	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0000530-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	39	322	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	0.185168018510085	1	FACETS	0.848	0.712	0.995	0.848	0.712	0.995	INDETERMINATE	1	TRUE	0	0.412490418081376	1		322	177	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0000531-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	19	358	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.100376879834172	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		358	695	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037408	12037408	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000569-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	111	298	0	ENST00000396373.4:c.1039C>T	p.Gln347Ter	p.Q347*	ENST00000396373	NM_001987.4	347	Cag/Tag	6/8	0.198392838885576	2	FACETS	1	0.982	1	0.715	0.646	0.788	CLONAL	1	FALSE	0	0.316723248618997	2		298	490	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0000583-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	810	406	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.299497100671409	8	FACETS	0.998	0.967	1	0.998	0.967	1	CLONAL	6	TRUE	2	0.28	8		406	1778	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031973	26031973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000583-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	78	224	0	ENST00000244661.2:c.316G>C	p.Glu106Gln	p.E106Q	ENST00000244661	NM_003537.3	106	Gag/Cag	1/1	0.282802779859433	3	FACETS	0.955	0.839	1	0.478	0.419	0.54	CLONAL	1	TRUE	1	0.28	3		224	665	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0000583-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	765	309	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.299497100671409	8	FACETS	1	0.991	1	1	0.991	1	CLONAL	6	TRUE	2	0.28	8		309	1589	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000583-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	62	316	0	ENST00000269305.4:c.517G>C	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ctg	5/11	1	2	FACETS	0.654	0.564	0.752	0.654	0.564	0.752	SUBCLONAL	1	TRUE	1	0.28	2		316	677	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099329	193099329	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000583-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	199	354	0	ENST00000367435.3:c.263G>C	p.Arg88Thr	p.R88T	ENST00000367435	NM_024529.4	88	aGa/aCa	3/17	0.282802779859433	3	FACETS	1	0.987	1	0.651	0.602	0.703	CLONAL	1	TRUE	1	0.28	3		354	1244	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97888824	97888824	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000583-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1188	125	511	0	ENST00000289081.3:c.883G>T	p.Asp295Tyr	p.D295Y	ENST00000289081	NM_000136.2	295	Gat/Tat	9/15	1	2	FACETS	0.68	0.613	0.751	0.68	0.613	0.751	SUBCLONAL	1	TRUE	1	0.28	2		511	1313	SUCCESS
ATM	472	MSKCC	GRCh37	11	108099990	108099990	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000583-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	36	160	0	ENST00000278616.4:c.271C>T	p.Gln91Ter	p.Q91*	ENST00000278616	NM_000051.3	91	Cag/Tag	4/63	0.169086041732842	2	FACETS	0.501	0.411	0.602	0.251	0.205	0.301	SUBCLONAL	1	TRUE	0	0.28	2		160	513	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190715	108190715	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000583-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	51	363	0	ENST00000278616.4:c.6382T>G	p.Leu2128Val	p.L2128V	ENST00000278616	NM_000051.3	2128	Ttg/Gtg	44/63	0.169086041732842	2	FACETS	0.376	0.318	0.439	0.188	0.159	0.22	SUBCLONAL	1	TRUE	0	0.28	2		363	970	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347782	347782	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000583-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1428	103	622	0	ENST00000262320.3:c.1724C>A	p.Ser575Tyr	p.S575Y	ENST00000262320	NM_003502.3	575	tCc/tAc	6/11	0.195984294822879	5	FACETS	0.682	0.608	0.762	0.227	0.202	0.254	SUBCLONAL	1	TRUE	2	0.28	5		622	1531	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789649	3789649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000583-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2002	139	566	0	ENST00000262367.5:c.4210G>A	p.Gly1404Ser	p.G1404S	ENST00000262367	NM_004380.2	1404	Ggc/Agc	25/31	0.195984294822879	5	FACETS	0.659	0.596	0.725	0.22	0.198	0.242	SUBCLONAL	1	TRUE	2	0.28	5		566	2141	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0000611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	318	377	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.68193817228224	4	FACETS	1	0.992	1	0.435	0.411	0.46	CLONAL	1	TRUE	1	0.847288342596823	4		378	1062	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0000611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	559	245	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.44777163110314	5	FACETS	1	0.994	1			1	INDETERMINATE	5	TRUE	NA	0.847288342596823	5		245	591	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0000611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	944	308	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.722581752810449	5	FACETS	0.977	0.951	1	0.977	0.951	1	CLONAL	3	TRUE	2	0.847288342596823	5		308	1727	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144148	55144148	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519700	NA	P-0000611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2994	467	287	0	ENST00000257290.5:c.1977C>G	p.Asn659Lys	p.N659K	ENST00000257290	NM_006206.4	659	aaC/aaG	14/23	0.847288342596823	13	FACETS	0.901	0.856	0.948			1	CLONAL	2	TRUE	NA	0.847288342596823	13		287	3461	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685313	89685313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	80	271	0	ENST00000371953.3:c.208C>A	p.Leu70Ile	p.L70I	ENST00000371953	NM_000314.4	70	Ctt/Att	3/9	0.847288342596823	3	FACETS	0.234	0.205	0.265			1	SUBCLONAL	1	TRUE	NA	0.847288342596823	3		271	1149	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937446	76937446	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	914	233	0	ENST00000373344.5:c.3302C>A	p.Ser1101Ter	p.S1101*	ENST00000373344	NM_000489.3	1101	tCa/tAa	9/35	0.70135800397326	2	FACETS	1	0.998	1			1	CLONAL	2	TRUE	NA	0.847288342596823	2		233	958	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413171	139413172	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0000611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	613	362	0	ENST00000277541.6:c.970_971del	p.Val324GlnfsTer6	p.V324Qfs*6	ENST00000277541	NM_017617.3	324	GTc/c	6/34	0.847288342596823	3	FACETS	0.893	0.873	0.912	0.893	0.873	0.912	CLONAL	3	TRUE	0	0.847288342596823	3		362	769	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399273	139399273	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000620-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	27	346	0	ENST00000277541.6:c.4870G>C	p.Glu1624Gln	p.E1624Q	ENST00000277541	NM_017617.3	1624	Gag/Cag	26/34	1	2	FACETS	0.333	0.266	0.41	0.333	0.266	0.41	SUBCLONAL	1	TRUE	1	0.61637010593138	2		346	263	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292988	91292988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000620-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	38	455	0	ENST00000355112.3:c.490G>A	p.Glu164Lys	p.E164K	ENST00000355112	NM_000057.2	164	Gag/Aag	3/22	0.166593450958334	4	FACETS	0.492	0.407	0.587	0.246	0.203	0.294	INDETERMINATE	1	TRUE	2	0.61637010593138	4		455	405	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0000620-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	8	264	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.071	0.045	0.105	0.071	0.045	0.105	SUBCLONAL	1	TRUE	1	0.61637010593138	2		264	364	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913514	NA	P-0000654-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	3294	435	0	ENST00000288135.5:c.2466T>G	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaG	17/21	0.717173417901932	12	FACETS	1	0.998	1			1	CLONAL	12	TRUE	NA	0.717173417901932	12		435	3487	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155045	108155045	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000654-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	129	644	0	ENST00000278616.4:c.3838A>C	p.Lys1280Gln	p.K1280Q	ENST00000278616	NM_000051.3	1280	Aaa/Caa	26/63	0.124373663521175	6	FACETS	0.801	0.725	0.882			1	INDETERMINATE	1	TRUE	NA	0.717173417901932	6		644	1093	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37628012	37628030	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GATAGGTAAGTCCTATAGT	GATAGGTAAGTCCTATAGT	-	novel	NA	P-0000654-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	129	642	0	ENST00000447079.4:c.1929_1931+16del		p.X643_splice	ENST00000447079	NM_015083.1	643		2/14	0.717173417901932	3	FACETS	0.53	0.479	0.582	0.265	0.239	0.291	SUBCLONAL	1	TRUE	1	0.717173417901932	3		642	923	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0000655-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	81	413	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.483	0.425	0.545	0.483	0.425	0.545	SUBCLONAL	1	TRUE	1	0.48282184222481	2		413	695	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427658	72427658	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000655-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	161	370	0	ENST00000477973.2:c.832T>G	p.Ser278Ala	p.S278A	ENST00000477973	NM_012234.5	278	Tcc/Gcc	4/4	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.48282184222481	2		370	612	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370903	55370903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000655-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	52	328	0	ENST00000297316.4:c.205C>T	p.Arg69Trp	p.R69W	ENST00000297316	NM_022454.3	69	Cgg/Tgg	1/2	0.176640771429255	4	FACETS	0.699	0.596	0.812	0.349	0.298	0.406	INDETERMINATE	1	TRUE	2	0.48282184222481	4		328	457	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380277	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913238	NA	P-0000655-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	193	484	0	ENST00000311936.3:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	61	Caa/Aaa	3/5	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.48282184222481	2		484	750	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061469	38061469	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000655-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	109	292	0	ENST00000250448.2:c.520T>A	p.Ser174Thr	p.S174T	ENST00000250448	NM_004496.3	174	Tcg/Acg	2/2	0.484173083592581	3	FACETS	1	0.966	1	0.579	0.522	0.638	CLONAL	1	TRUE	1	0.48282184222481	3		292	484	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178656	32178656	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000673-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	149	205	0	ENST00000375023.3:c.2738C>G	p.Ser913Cys	p.S913C	ENST00000375023	NM_004557.3	913	tCc/tGc	18/30	0.683506548114781	3	FACETS	0.896	0.821	0.974	0.448	0.41	0.487	CLONAL	1	TRUE	1	0.683506548114781	3		205	653	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32191686	32191686	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000673-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	225	421	0	ENST00000375023.3:c.20T>A	p.Leu7Gln	p.L7Q	ENST00000375023	NM_004557.3	7	cTg/cAg	1/30	0.683506548114781	3	FACETS	0.952	0.887	1	0.476	0.443	0.509	CLONAL	1	TRUE	1	0.683506548114781	3		421	928	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104356920	104356920	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000673-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	152	208	0	ENST00000369902.3:c.780G>T	p.Glu260Asp	p.E260D	ENST00000369902	NM_016169.3	260	gaG/gaT	7/12	0.683506548114781	2	FACETS	0.799	0.734	0.865	0.399	0.367	0.433	SUBCLONAL	1	TRUE	0	0.683506548114781	2		208	557	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912279	32912279	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000673-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	224	198	0	ENST00000380152.3:c.3787A>C	p.Ser1263Arg	p.S1263R	ENST00000380152		1263	Agt/Cgt	11/27	NA	2	FACETS	0.87	0.813	0.929			1	INDETERMINATE	1	TRUE	NA	0.683506548114781	2		198	753	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0000674-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	301	412	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	0.966	0.911	1			1	INDETERMINATE	1	FALSE	NA	0.637436533438054	2		413	978	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0000674-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	113	76	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.637436533438054	2		76	329	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000674-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	172	389	0	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.637436533438054	2		389	488	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683892	117683892	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000674-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	302	339	0	ENST00000368508.3:c.3255C>G	p.Phe1085Leu	p.F1085L	ENST00000368508	NM_002944.2	1085	ttC/ttG	21/43	NA	2	FACETS	0.916	0.864	0.97			1	INDETERMINATE	1	FALSE	NA	0.637436533438054	2		339	1034	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555526097	NA	P-0000674-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	142	170	0	ENST00000269305.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000269305	NM_001126112.2	167	Cag/Tag	5/11	0.610845578062867	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	0	0.637436533438054	1		170	287	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355259	15355259	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000674-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	13	42	0	ENST00000263377.2:c.2364G>C	p.Gln788His	p.Q788H	ENST00000263377	NM_058243.2	788	caG/caC	13/20	1	2	FACETS	0.392	0.282	0.523	0.392	0.282	0.523	SUBCLONAL	1	FALSE	1	0.637436533438054	2		42	104	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782177	NA	P-0000681-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	162	175	0	ENST00000269305.4:c.644G>T	p.Ser215Ile	p.S215I	ENST00000269305	NM_001126112.2	215	aGt/aTt	6/11	0.216462471903038	0	FACETS	0.828	0.759	0.9			1	CLONAL	1	TRUE	0	0.282127238590256	0		175	996	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797759	45797759	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0000681-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	75	149	0	ENST00000450313.1:c.934-1G>T		p.X312_splice	ENST00000450313	NM_012222.2	312			1	2	FACETS	0.55	0.48	0.625	0.55	0.48	0.625	SUBCLONAL	1	TRUE	1	0.282127238590256	2		149	967	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635608	47635608	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1330621664	NA	P-0000681-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	93	113	0	ENST00000233146.2:c.280C>G	p.Leu94Val	p.L94V	ENST00000233146	NM_000251.2	94	Ctg/Gtg	2/16	1	2	FACETS	0.856	0.761	0.958	0.856	0.761	0.958	CLONAL	1	TRUE	1	0.282127238590256	2		113	770	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732725	204732725	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000681-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	121	119	0	ENST00000302823.3:c.60G>T	p.Trp20Cys	p.W20C	ENST00000302823	NM_005214.4	20	tgG/tgT	1/4	1	2	FACETS	0.81	0.73	0.894	0.81	0.73	0.894	CLONAL	1	TRUE	1	0.282127238590256	2		119	1059	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468414	89468414	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000681-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	173	87	0	ENST00000336596.2:c.1948G>T	p.Val650Leu	p.V650L	ENST00000336596	NM_005233.5	650	Gtg/Ttg	11/17	0.241860545148629	2	FACETS	0.796	0.734	0.861	0.796	0.734	0.861	SUBCLONAL	2	TRUE	0	0.282127238590256	2		87	770	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679595	86679595	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000681-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	308	101	0	ENST00000274376.6:c.2756C>T	p.Ser919Leu	p.S919L	ENST00000274376	NM_002890.2	919	tCa/tTa	21/25	0.115294772803753	3	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.282127238590256	3		101	1021	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150533	157150533	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000681-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	60	53	0	ENST00000346085.5:c.1715G>C	p.Gly572Ala	p.G572A	ENST00000346085	NM_020732.3	572	gGa/gCa	2/20	0.282127238590256	1	FACETS	0.805	0.695	0.924	0.805	0.695	0.924	CLONAL	1	TRUE	0	0.282127238590256	1		53	454	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0000681-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	74	109	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	1	2	FACETS	0.641	0.56	0.729	0.641	0.56	0.729	SUBCLONAL	1	TRUE	1	0.282127238590256	2		109	818	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398067	4398067	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000681-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	104	132	0	ENST00000261254.3:c.631A>T	p.Ile211Phe	p.I211F	ENST00000261254	NM_001759.3	211	Atc/Ttc	4/5	0.172058909876923	1	FACETS	0.844	0.756	0.938	0.844	0.756	0.938	CLONAL	1	TRUE	0	0.282127238590256	1		132	750	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440412	49440412	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000681-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	86	93	0	ENST00000301067.7:c.4398G>T	p.Lys1466Asn	p.K1466N	ENST00000301067	NM_003482.3	1466	aaG/aaT	15/54	0.282127238590256	3	FACETS	1	0.936	1	0.543	0.48	0.609	CLONAL	1	TRUE	1	0.282127238590256	3		93	641	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222326	2222326	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000681-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	65	162	0	ENST00000326181.6:c.610G>A	p.Glu204Lys	p.E204K	ENST00000326181	NM_032271.2	204	Gag/Aag	8/21	0.173890023395587	1	FACETS	0.461	0.398	0.529	0.461	0.398	0.529	SUBCLONAL	1	TRUE	0	0.282127238590256	1		162	859	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7168073	7168073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754537233	NA	P-0000681-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	55	126	0	ENST00000302850.5:c.1516C>T	p.Arg506Trp	p.R506W	ENST00000302850	NM_000208.2	506	Cgg/Tgg	7/22	0.173890023395587	1	FACETS	0.412	0.352	0.479	0.412	0.352	0.479	SUBCLONAL	1	TRUE	0	0.282127238590256	1		126	812	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164775	36164775	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867474432	NA	P-0000681-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	123	142	0	ENST00000300305.3:c.1100G>A	p.Gly367Asp	p.G367D	ENST00000300305		367	gGc/gAc	8/8	1	2	FACETS	0.968	0.874	1	0.968	0.874	1	CLONAL	1	TRUE	1	0.282127238590256	2		142	901	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039611	47039611	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000681-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	108	115	0	ENST00000377604.3:c.1063G>T	p.Glu355Ter	p.E355*	ENST00000377604	NM_001204468.1	355	Gag/Tag	11/24	0.143768099797064	3	FACETS	1	0.964	1	0.582	0.522	0.645	INDETERMINATE	1	TRUE	1	0.282127238590256	3		115	751	SUCCESS
AR	367	MSKCC	GRCh37	X	66765309	66765309	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0000681-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	167	186	0	ENST00000374690.3:c.321C>G	p.Tyr107Ter	p.Y107*	ENST00000374690	NM_000044.3	107	taC/taG	1/8	0.143768099797064	3	FACETS	1	0.944	1	0.519	0.476	0.565	INDETERMINATE	1	TRUE	1	0.282127238590256	3		186	1301	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341596	70341596	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs773615925	NA	P-0000681-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1228	148	169	1	ENST00000374080.3:c.1031C>A	p.Thr344Asn	p.T344N	ENST00000374080		344	aCt/aAt	7/45	0.143768099797064	3	FACETS	0.87	0.792	0.952	0.435	0.396	0.476	INDETERMINATE	1	TRUE	1	0.282127238590256	3		170	1376	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857648	59857649	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0000681-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	87	106	0	ENST00000259008.2:c.1908_1909delinsCT	p.Glu636_Ala637delinsAspSer	p.E636_A637delinsDS	ENST00000259008	NM_032043.2	636	gaGGct/gaCTct	13/20	1	2	FACETS	0.943	0.835	1	0.943	0.835	1	CLONAL	1	TRUE	1	0.282127238590256	2		106	654	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212289026	212289026	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs905615345	NA	P-0000683-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	52	258	0	ENST00000342788.4:c.2720G>C	p.Gly907Ala	p.G907A	ENST00000342788	NM_005235.2	907	gGa/gCa	23/28	0.317006885888683	1	FACETS	0.607	0.529	0.688	0.607	0.529	0.688	INDETERMINATE	1	TRUE	0	0.745920145700907	1		258	144	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259452	89259452	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000683-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	34	344	0	ENST00000336596.2:c.596T>A	p.Phe199Tyr	p.F199Y	ENST00000336596	NM_005233.5	199	tTc/tAc	3/17	0.35831201123223	1	FACETS	0.379	0.314	0.449	0.379	0.314	0.449	INDETERMINATE	1	TRUE	0	0.745920145700907	1		344	151	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959898	38959898	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1378200700	NA	P-0000683-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	12	242	0	ENST00000357387.3:c.2034A>C	p.Lys678Asn	p.K678N	ENST00000357387	NM_152756.3	678	aaA/aaC	21/38	0.317006885888683	1	FACETS	0.114	0.08	0.156	0.114	0.08	0.156	INDETERMINATE	1	TRUE	0	0.745920145700907	1		242	177	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099315	4099315	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000683-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	101	397	0	ENST00000262948.5:c.803C>G	p.Pro268Arg	p.P268R	ENST00000262948	NM_030662.3	268	cCc/cGc	7/11	0.358503827582311	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.745920145700907	0		397	330	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244383	5244383	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000683-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	30	362	0	ENST00000357368.4:c.1099T>A	p.Tyr367Asn	p.Y367N	ENST00000357368	NM_002850.3	367	Tat/Aat	11/38	0.358503827582311	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.745920145700907	0		362	148	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578230	7578230	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000683-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	162	429	0	ENST00000269305.4:c.619del	p.Asp207MetfsTer40	p.D207Mfs*40	ENST00000269305	NM_001126112.2	207	Gat/at	6/11	0.634011489404271	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.745920145700907	1		429	245	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0000698-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	56	314	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.821	0.708	0.943	1	0.972	1	CLONAL	2	TRUE	1	0.22	2		314	310	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106793	27106793	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000698-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	71	385	0	ENST00000324856.7:c.6404T>A	p.Ile2135Asn	p.I2135N	ENST00000324856	NM_006015.4	2135	aTt/aAt	20/20	1	2	FACETS	0.765	0.67	0.866	1	0.975	1	SUBCLONAL	2	TRUE	1	0.22	2		385	422	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913283	NA	P-0000698-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	50	350	2	ENST00000263967.3:c.3129G>T	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atT	21/21	1	2	FACETS	0.789	0.674	0.914	1	0.967	1	CLONAL	2	TRUE	1	0.22	2		352	288	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589578	67589585	+	frameshift_variant	Frame_Shift_Del	DEL	AAAATTAC	AAAATTAC	T	novel	NA	P-0000698-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	31	228	0	ENST00000274335.5:c.1341_1348delinsT	p.Lys447AsnfsTer31	p.K447Nfs*31	ENST00000274335		447	aaAAAATTACat/aaTat	10/15	0.3	7	FACETS	0.881	0.716	1			1	CLONAL	2	TRUE	NA	0.22	7		228	248	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0000702-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	156	190	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	0.978	0.899	1	0.978	0.899	1	CLONAL	1	TRUE	1	0.493877802170525	2		190	646	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031973	26031973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000702-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	55	224	0	ENST00000244661.2:c.316G>C	p.Glu106Gln	p.E106Q	ENST00000244661	NM_003537.3	106	Gag/Cag	1/1	1	2	FACETS	0.752	0.648	0.865	0.752	0.648	0.865	SUBCLONAL	1	TRUE	1	0.493877802170525	2		224	296	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567824	226567824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000702-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	149	170	0	ENST00000366794.5:c.1342G>A	p.Glu448Lys	p.E448K	ENST00000366794	NM_001618.3	448	Gaa/Aaa	10/23	0.469284160953749	5	FACETS	0.97	0.885	1	0.242	0.221	0.265	CLONAL	1	TRUE	1	0.493877802170525	5		170	1083	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266494	198266494	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs756424171	NA	P-0000702-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	122	157	0	ENST00000335508.6:c.2342A>G	p.Asp781Gly	p.D781G	ENST00000335508	NM_012433.2	781	gAt/gGt	16/25	1	2	FACETS	0.823	0.746	0.904	0.823	0.746	0.904	CLONAL	1	TRUE	1	0.493877802170525	2		157	600	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851900	128851900	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000702-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	102	177	0	ENST00000249373.3:c.1972G>C	p.Glu658Gln	p.E658Q	ENST00000249373	NM_005631.4	658	Gag/Cag	12/12	1	2	FACETS	0.782	0.702	0.867	0.782	0.702	0.867	SUBCLONAL	1	TRUE	1	0.493877802170525	2		177	528	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725076	47725076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs571014601	NA	P-0000702-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	145	236	0	ENST00000449228.1:c.668G>A	p.Arg223Gln	p.R223Q	ENST00000449228	NM_001127240.2	223	cGa/cAa	4/4	1	2	FACETS	0.919	0.841	1	0.919	0.841	1	CLONAL	1	TRUE	1	0.493877802170525	2		236	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0000736-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	199	607	2	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.799474185950553	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.799474185950553	1		609	294	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000736-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	127	391	0	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	0.399711894266647	1	FACETS	0.392	0.357	0.429	0.392	0.357	0.429	INDETERMINATE	1	TRUE	0	0.799474185950553	1		391	486	SUCCESS
APC	324	MSKCC	GRCh37	5	112170691	112170691	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000736-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	138	304	1	ENST00000257430.4:c.1787C>A	p.Ser596Ter	p.S596*	ENST00000257430	NM_000038.5	596	tCa/tAa	15/16	0.277308001529754	1	FACETS	0.691	0.64	0.742	0.691	0.64	0.742	INDETERMINATE	1	TRUE	0	0.799474185950553	1		305	300	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310820	123310820	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747502397	NA	P-0000736-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	58	464	0	ENST00000358487.5:c.608G>A	p.Arg203His	p.R203H	ENST00000358487	NM_000141.4	203	cGc/cAc	5/18	0.569066658596879	1	FACETS	0.209	0.18	0.241	0.209	0.18	0.241	SUBCLONAL	1	TRUE	0	0.799474185950553	1		464	417	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730802	40730802	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747513450	NA	P-0000736-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	126	175	0	ENST00000373198.4:c.3733G>A	p.Gly1245Arg	p.G1245R	ENST00000373198	NM_133170.3	1245	Gga/Aga	27/32	0.392799317302316	5	FACETS	1	0.986	1	0.496	0.452	0.542	INDETERMINATE	1	TRUE	2	0.799474185950553	5		175	466	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739064	40739064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780908301	NA	P-0000736-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	184	255	0	ENST00000373198.4:c.3220G>A	p.Val1074Ile	p.V1074I	ENST00000373198	NM_133170.3	1074	Gtt/Att	24/32	0.392799317302316	5	FACETS	1	0.957	1	0.691	0.644	0.74	INDETERMINATE	2	TRUE	2	0.799474185950553	5		255	488	SUCCESS
APC	324	MSKCC	GRCh37	5	112175417	112175418	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	rs1554085533	NA	P-0000736-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	60	206	0	ENST00000257430.4:c.4127_4128del	p.Tyr1376CysfsTer9	p.Y1376Cfs*9	ENST00000257430	NM_000038.5	1376	TAt/t	16/16	0.277308001529754	1	FACETS	0.356	0.31	0.405	0.356	0.31	0.405	INDETERMINATE	1	TRUE	0	0.799474185950553	1		206	253	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119866	70119866	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000736-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	327	343	0	ENST00000245479.2:c.868del	p.Asp290MetfsTer93	p.D290Mfs*93	ENST00000245479	NM_000346.3	290	Gat/at	3/3	0.379055271077002	4	FACETS	0.992	0.943	1			1	INDETERMINATE	2	TRUE	NA	0.799474185950553	4		343	742	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645396	215645396	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000738-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	46	425	0	ENST00000260947.4:c.1202G>A	p.Ser401Asn	p.S401N	ENST00000260947	NM_000465.2	401	aGt/aAt	4/11	1	2	FACETS	0.651	0.548	0.764	0.651	0.548	0.764	SUBCLONAL	1	TRUE	1	0.284374699023894	2		425	497	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12647767	12647767	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000738-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	56	358	0	ENST00000251849.4:c.613G>C	p.Gly205Arg	p.G205R	ENST00000251849	NM_002880.3	205	Gga/Cga	6/17	1	2	FACETS	0.92	0.79	1	0.92	0.79	1	CLONAL	1	TRUE	1	0.284374699023894	2		358	428	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702621	52702621	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000738-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	41	353	0	ENST00000394830.3:c.277G>A	p.Asp93Asn	p.D93N	ENST00000394830	NM_018313.4	93	Gac/Aac	4/30	1	2	FACETS	0.697	0.581	0.825	0.697	0.581	0.825	SUBCLONAL	1	TRUE	1	0.284374699023894	2		353	414	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516926	187516926	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000738-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	71	316	0	ENST00000441802.2:c.13055C>G	p.Pro4352Arg	p.P4352R	ENST00000441802	NM_005245.3	4352	cCt/cGt	26/27	0.284374699023894	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.284374699023894	1		316	372	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818313	170818313	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000738-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	56	687	0	ENST00000296930.5:c.143G>C	p.Ser48Thr	p.S48T	ENST00000296930	NM_002520.6	48	aGt/aCt	3/11	0.284374699023894	2	FACETS	0.545	0.466	0.631	0.272	0.233	0.316	SUBCLONAL	1	TRUE	0	0.284374699023894	2		687	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578199	7578199	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0000738-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	75	489	0	ENST00000269305.4:c.650del	p.Val217GlyfsTer30	p.V217Gfs*30	ENST00000269305	NM_001126112.2	217	gTg/gg	6/11	0.284374699023894	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.284374699023894	1		489	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0000745-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	27	228	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.157349384451379	2	FACETS	0.895	0.727	1	0.895	0.727	1	INDETERMINATE	2	TRUE	0	0.276705222293227	2		228	109	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0000745-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	72	454	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.772	0.674	0.878	0.772	0.674	0.878	SUBCLONAL	1	TRUE	1	0.276705222293227	2		454	674	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0000745-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	51	252	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.933	0.795	1	0.933	0.795	1	CLONAL	1	TRUE	1	0.276705222293227	2		252	395	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015293	128015293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770995913	NA	P-0000745-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	78	174	0	ENST00000285398.2:c.2228G>A	p.Arg743His	p.R743H	ENST00000285398	NM_000122.1	743	cGc/cAc	15/15	0.276705222293227	4	FACETS	0.93	0.828	1	0.93	0.828	1	CLONAL	3	TRUE	1	0.276705222293227	4		174	258	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0000745-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	81	287	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.204178635372434	3	FACETS	1	0.923	1	0.699	0.621	0.78	CLONAL	2	TRUE	0	0.276705222293227	3		287	318	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39613803	39613803	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000745-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	22	248	0	ENST00000262039.4:c.1721A>T	p.Gln574Leu	p.Q574L	ENST00000262039	NM_002647.2	574	cAg/cTg	16/25	1	2	FACETS	0.396	0.306	0.5	0.396	0.306	0.5	SUBCLONAL	1	TRUE	1	0.276705222293227	2		248	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0000749-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	190	371	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.0833963064421189	0	FACETS	0.712	0.668	0.756			1	INDETERMINATE	2	TRUE	0	0.41	0		371	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0000749-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	51	294	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.0833963064421189	0	FACETS	1	0.921	1			1	INDETERMINATE	1	TRUE	0	0.41	0		294	136	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0000749-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	129	377	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.3	3	FACETS	1	0.948	1			1	CLONAL	2	TRUE	NA	0.41	3		378	363	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0000749-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	13	197	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	0.3	4	FACETS	0.295	0.21	0.4			1	SUBCLONAL	1	TRUE	NA	0.41	4		197	303	SUCCESS
APC	324	MSKCC	GRCh37	5	112154694	112154694	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000749-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	103	223	0	ENST00000257430.4:c.965T>G	p.Leu322Arg	p.L322R	ENST00000257430	NM_000038.5	322	cTt/cGt	10/16	0.0833963064421189	0	FACETS	0.941	0.853	1			1	INDETERMINATE	1	TRUE	0	0.41	0		223	315	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271725	38271725	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000749-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	22	393	0	ENST00000425967.3:c.2224A>G	p.Lys742Glu	p.K742E	ENST00000425967	NM_001174067.1	742	Aag/Gag	17/19	1	2	FACETS	0.436	0.339	0.549	0.436	0.339	0.549	SUBCLONAL	1	TRUE	1	0.41	2		393	246	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862116	68862116	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782464	NA	P-0000749-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	20	397	0	ENST00000261769.5:c.2204C>T	p.Ala735Val	p.A735V	ENST00000261769	NM_004360.3	735	gCg/gTg	14/16	0.230670357318409	1	FACETS	0.243	0.186	0.311	0.243	0.186	0.311	INDETERMINATE	1	TRUE	0	0.41	1		397	319	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888758	76888758	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000749-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	265	296	0	ENST00000373344.5:c.5071C>T	p.Gln1691Ter	p.Q1691*	ENST00000373344	NM_000489.3	1691	Caa/Taa	19/35	0.3	0	FACETS		NA	1			1	NA	3	TRUE	0	0.41	0		296	325	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0000754-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	309	454	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.609740783554812	2		454	902	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0000754-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	264	521	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.498184589466746	1	FACETS	0.624	0.585	0.663	0.624	0.585	0.663	SUBCLONAL	1	TRUE	0	0.609740783554812	1		521	965	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160745	56160745	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000754-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	190	424	0	ENST00000399503.3:c.1019T>G	p.Val340Gly	p.V340G	ENST00000399503	NM_005921.1	340	gTg/gGg	4/20	1	2	FACETS	0.806	0.747	0.868	0.806	0.747	0.868	CLONAL	1	TRUE	1	0.609740783554812	2		424	773	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111957672	111957672	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000754-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	259	436	0	ENST00000375549.3:c.41T>G	p.Leu14Arg	p.L14R	ENST00000375549	NM_003002.3	14	cTa/cGa	1/4	1	2	FACETS	0.807	0.756	0.859	0.807	0.756	0.859	CLONAL	1	TRUE	1	0.609740783554812	2		436	1053	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880257	37880257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000754-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	362	493	0	ENST00000269571.5:c.2301C>G	p.Ile767Met	p.I767M	ENST00000269571		767	atC/atG	19/27	1	2	FACETS	0.911	0.863	0.96	0.911	0.863	0.96	CLONAL	1	TRUE	1	0.609740783554812	2		493	1303	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5207956	5207956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1290109580	NA	P-0000754-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	292	539	1	ENST00000357368.4:c.5755C>T	p.Arg1919Trp	p.R1919W	ENST00000357368	NM_002850.3	1919	Cgg/Tgg	37/38	0.288108776937756	1	FACETS	0.641	0.604	0.68	0.641	0.604	0.68	INDETERMINATE	1	TRUE	0	0.609740783554812	1		540	1038	SUCCESS
APC	324	MSKCC	GRCh37	5	112175569	112175587	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTGGACAAACCATGCCA	CCCTGGACAAACCATGCCA	-	novel	NA	P-0000754-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	320	461	0	ENST00000257430.4:c.4280_4298del	p.Pro1427GlnfsTer40	p.P1427Qfs*40	ENST00000257430	NM_000038.5	1426	agCCCTGGACAAACCATGCCA/ag	16/16	0.609740783554812	2	FACETS	1	0.993	1	0.663	0.629	0.697	CLONAL	1	TRUE	0	0.609740783554812	2		461	792	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0000761-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	70	377	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.978	0.874	1	1	0.984	1	CLONAL	2	TRUE	1	0.425839510776901	2		378	168	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0000761-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	69	256	0	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	0.425839510776901	1	FACETS	1	0.968	1	1	0.989	1	CLONAL	3	TRUE	0	0.425839510776901	1		256	81	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0000762-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	108	454	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.6911424128043	3	FACETS	0.815	0.735	0.898			1	CLONAL	1	TRUE	NA	0.783019413669573	3		454	471	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0000762-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	162	472	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.537907777633188	4	FACETS	0.811	0.751	0.872	0.811	0.751	0.872	CLONAL	2	TRUE	2	0.783019413669573	4		472	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0000762-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	185	543	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.269494574382123	3	FACETS	0.768	0.718	0.819	0.512	0.478	0.546	INDETERMINATE	2	TRUE	0	0.783019413669573	3		543	428	SUCCESS
APC	324	MSKCC	GRCh37	5	112173510	112173510	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000762-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	116	311	0	ENST00000257430.4:c.2220del	p.Asn741IlefsTer20	p.N741Ifs*20	ENST00000257430	NM_000038.5	740	gCc/gc	16/16	0.537907777633188	4	FACETS	1	0.981	1	0.667	0.606	0.73	CLONAL	1	TRUE	2	0.783019413669573	4		311	396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0000770-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	73	314	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	NA	2	FACETS	0.962	0.86	1			1	INDETERMINATE	2	TRUE	NA	0.421658282357617	2		314	180	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519411	137519411	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000770-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	25	178	0	ENST00000367739.4:c.1227A>C	p.Arg409Ser	p.R409S	ENST00000367739	NM_000416.2	409	agA/agC	7/7	0.330188734926885	5	FACETS	0.547	0.431	0.68			1	SUBCLONAL	1	TRUE	NA	0.421658282357617	5		178	354	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0000771-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	29	859	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	0.335348313151349	3	FACETS	0.671	0.54	0.819	0.335	0.27	0.41	SUBCLONAL	1	TRUE	1	0.335348313151349	3		859	301	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs11554290	NA	P-0000771-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	34	1231	0	ENST00000369535.4:c.182A>C	p.Gln61Pro	p.Q61P	ENST00000369535	NM_002524.4	61	cAa/cCa	3/7	1	2	FACETS	0.395	0.322	0.478	0.395	0.322	0.478	SUBCLONAL	1	TRUE	1	0.335348313151349	2		1231	513	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347916	70347916	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000771-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	85	759	0	ENST00000374080.3:c.3155G>T	p.Ser1052Ile	p.S1052I	ENST00000374080		1052	aGc/aTc	22/45	1	1	FACETS	0.913	0.811	1	0.913	0.811	1	CLONAL	1	TRUE	0	0.335348313151349	1		759	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0000780-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	212	248	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.697511300315379	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.697511300315379	2		248	304	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562864	21562864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1211577619	NA	P-0000780-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	88	187	0	ENST00000382592.4:c.1055G>A	p.Arg352Gln	p.R352Q	ENST00000382592	NM_014572.2	352	cGg/cAg	4/8	NA	2	FACETS	0.723	0.646	0.804			1	INDETERMINATE	1	TRUE	NA	0.697511300315379	2		187	349	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0000787-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	323	300	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.74	2		300	798	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0000798-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	157	358	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	0.610936552478997	2		358	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0000798-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	314	255	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.576058458165413	2	FACETS	0.961	0.919	1	0.961	0.919	1	CLONAL	2	TRUE	0	0.610936552478997	2		255	535	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0000798-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	243	287	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.576058458165413	2	FACETS	0.916	0.87	0.963	0.916	0.87	0.963	CLONAL	2	TRUE	0	0.610936552478997	2		287	434	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951925	2951925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147381531	NA	P-0000798-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	135	242	0	ENST00000396946.4:c.3025G>A	p.Val1009Ile	p.V1009I	ENST00000396946	NM_032415.4	1009	Gtc/Atc	23/25	0.599007700447057	4	FACETS	0.957	0.871	1	0.319	0.29	0.349	CLONAL	1	TRUE	1	0.610936552478997	4		242	744	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022346	31022346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372418554	NA	P-0000798-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1249	70	447	0	ENST00000375687.4:c.1831G>A	p.Ala611Thr	p.A611T	ENST00000375687	NM_015338.5	611	Gcc/Acc	13/13	0.536044907097891	4	FACETS	0.28	0.243	0.32	0.093	0.081	0.107	SUBCLONAL	1	TRUE	1	0.610936552478997	4		447	1319	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342648	70342648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000798-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1302	489	734	0	ENST00000374080.3:c.1409G>A	p.Arg470His	p.R470H	ENST00000374080		470	cGc/cAc	10/45	0.514402725656566	3	FACETS	1	0.992	1	0.583	0.557	0.611	CLONAL	1	TRUE	1	0.610936552478997	3		734	1791	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357138	70357138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762659794	NA	P-0000798-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1682	725	1064	0	ENST00000374080.3:c.5653G>A	p.Val1885Ile	p.V1885I	ENST00000374080		1885	Gtc/Atc	39/45	0.514402725656566	3	FACETS	1	0.996	1	0.644	0.62	0.668	CLONAL	1	TRUE	1	0.610936552478997	3		1064	2407	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128018857	128018857	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000799-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	197	537	0	ENST00000285398.2:c.2011G>T	p.Ala671Ser	p.A671S	ENST00000285398	NM_000122.1	671	Gct/Tct	13/15	0.382164635666301	3	FACETS	0.939	0.867	1	0.469	0.433	0.507	CLONAL	1	TRUE	1	0.382164635666301	3		537	1308	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6414400	6414400	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000799-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	74	122	0	ENST00000356142.4:c.34G>A	p.Gly12Arg	p.G12R	ENST00000356142	NM_018890.3	12	Gga/Aga	1/7	0.382164635666301	6	FACETS	1	0.947	1	0.288	0.252	0.327	CLONAL	1	TRUE	2	0.382164635666301	6		122	593	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560514	65560514	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000799-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	150	296	0	ENST00000358664.4:c.83A>G	p.His28Arg	p.H28R	ENST00000358664	NM_002382.4	28	cAt/cGt	3/5	0.242485141849514	5	FACETS	1	0.976	1	0.399	0.363	0.435	CLONAL	1	TRUE	2	0.382164635666301	5		296	1033	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0000807-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	135	556	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.197010420805622	3	FACETS	1	0.964	1	1	0.989	1	CLONAL	3	TRUE	1	0.17	3		556	520	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602581	10602581	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000807-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	26	325	0	ENST00000171111.5:c.997G>T	p.Gly333Cys	p.G333C	ENST00000171111	NM_203500.1	333	Ggc/Tgc	3/6	0.206418889100162	1	FACETS	0.804	0.637	0.996	0.804	0.637	0.996	CLONAL	1	TRUE	0	0.17	1		325	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0000807-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	52	437	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.17	2		437	554	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0000807-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	16	172	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	1	2	FACETS	0.788	0.583	1	0.788	0.583	1	CLONAL	1	TRUE	1	0.17	2		172	239	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582180	189582180	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000807-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	23	245	0	ENST00000264731.3:c.739C>A	p.His247Asn	p.H247N	ENST00000264731	NM_003722.4	247	Cat/Aat	5/14	1	2	FACETS	0.767	0.597	0.962	0.767	0.597	0.962	CLONAL	1	TRUE	1	0.17	2		245	353	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472559	88472559	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000807-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	26	396	0	ENST00000360948.2:c.1996G>T	p.Gly666Cys	p.G666C	ENST00000360948	NM_001012338.2	666	Ggt/Tgt	16/19	1	2	FACETS	0.672	0.532	0.834	0.672	0.532	0.834	SUBCLONAL	1	TRUE	1	0.17	2		396	455	SUCCESS
APC	324	MSKCC	GRCh37	5	112178700	112178700	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000816-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	324	479	0	ENST00000257430.4:c.7409G>C	p.Arg2470Thr	p.R2470T	ENST00000257430	NM_000038.5	2470	aGa/aCa	16/16	0.633081354182474	4	FACETS	0.951	0.901	1			1	CLONAL	2	TRUE	NA	0.633081354182474	4		479	879	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534294	534294	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000816-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	90	410	0	ENST00000451590.1:c.29G>C	p.Gly10Ala	p.G10A	ENST00000451590	NM_001130442.1	10	gGc/gCc	2/5	0.597402208405008	3	FACETS	1	0.933	1	0.352	0.315	0.392	CLONAL	1	TRUE	0	0.633081354182474	3		410	354	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678490	88678490	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1199513223	NA	P-0000816-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	92	507	0	ENST00000360948.2:c.1046A>G	p.His349Arg	p.H349R	ENST00000360948	NM_001012338.2	349	cAt/cGt	9/19	0.343936337659712	5	FACETS	1	0.948	1	0.369	0.329	0.412	INDETERMINATE	1	TRUE	2	0.633081354182474	5		507	512	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028659	12028659	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000816-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	298	409	0	ENST00000353533.5:c.862T>C	p.Ser288Pro	p.S288P	ENST00000353533	NM_003010.3	288	Tct/Cct	8/11	0.600735841610345	2	FACETS	0.928	0.887	0.969	0.928	0.887	0.969	CLONAL	2	TRUE	0	0.633081354182474	2		409	507	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490340	29490340	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0000816-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	349	434	0	ENST00000356175.3:c.425T>A	p.Leu142Ter	p.L142*	ENST00000356175	NM_000267.3	142	tTa/tAa	4/57	0.600735841610345	2	FACETS	0.974	0.935	1	0.974	0.935	1	CLONAL	2	TRUE	0	0.633081354182474	2		434	566	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482619	56482619	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000817-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	34	303	0	ENST00000267101.3:c.1076G>A	p.Gly359Asp	p.G359D	ENST00000267101	NM_001982.3	359	gGc/gAc	9/28	1	2	FACETS	0.586	0.479	0.706	0.586	0.479	0.706	SUBCLONAL	1	TRUE	1	0.3	2		303	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519975	NA	P-0000817-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	37	220	0	ENST00000269305.4:c.403T>C	p.Cys135Arg	p.C135R	ENST00000269305	NM_001126112.2	135	Tgc/Cgc	5/11	1	2	FACETS	0.999	0.829	1	0.999	0.829	1	CLONAL	1	TRUE	1	0.3	2		220	247	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691025	NA	P-0000826-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	89	356	0	ENST00000269305.4:c.785G>T	p.Gly262Val	p.G262V	ENST00000269305	NM_001126112.2	262	gGt/gTt	8/11	0.198600376684463	4	FACETS	1	0.956	1	0.764	0.68	0.851	CLONAL	2	TRUE	1	0.214495341372564	4		356	440	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0000826-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	110	194	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.214495341372564	3	FACETS	0.887	0.802	0.975	0.887	0.802	0.975	CLONAL	3	TRUE	0	0.214495341372564	3		194	427	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047211	180047211	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000826-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	16	483	0	ENST00000261937.6:c.2504C>T	p.Ala835Val	p.A835V	ENST00000261937	NM_182925.4	835	gCc/gTc	17/30	1	2	FACETS	0.502	0.371	0.66	0.502	0.371	0.66	SUBCLONAL	1	TRUE	1	0.214495341372564	2		483	297	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117639364	117639364	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1383276210	NA	P-0000826-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	57	388	0	ENST00000368508.3:c.5992G>A	p.Ala1998Thr	p.A1998T	ENST00000368508	NM_002944.2	1998	Gca/Aca	37/43	0.168334988708843	4	FACETS	1	0.934	1	0.578	0.496	0.668	CLONAL	1	TRUE	2	0.214495341372564	4		388	558	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164211	47164211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761234986	NA	P-0000827-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	22	290	1	ENST00000409792.3:c.1915G>A	p.Glu639Lys	p.E639K	ENST00000409792	NM_014159.6	639	Gaa/Aaa	3/21	1	2	FACETS	0.316	0.244	0.399	0.316	0.244	0.399	SUBCLONAL	1	TRUE	1	0.363931295076947	2		291	383	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577064	7577064	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0000827-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	27	371	0	ENST00000269305.4:c.874A>T	p.Lys292Ter	p.K292*	ENST00000269305	NM_001126112.2	292	Aaa/Taa	8/11	1	2	FACETS	0.217	0.171	0.269	0.217	0.171	0.269	SUBCLONAL	1	TRUE	1	0.363931295076947	2		371	685	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0000827-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	22	459	0	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	1	2	FACETS	0.242	0.187	0.307	0.242	0.187	0.307	SUBCLONAL	1	TRUE	1	0.363931295076947	2		459	499	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374956	45374956	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000827-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	25	355	0	ENST00000262160.6:c.887C>A	p.Ser296Ter	p.S296*	ENST00000262160	NM_005901.5	296	tCa/tAa	8/11	1	2	FACETS	0.32	0.252	0.399	0.32	0.252	0.399	SUBCLONAL	1	TRUE	1	0.363931295076947	2		355	429	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618601	37618601	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000842-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	106	195	0	ENST00000447079.4:c.277C>T	p.Arg93Ter	p.R93*	ENST00000447079	NM_015083.1	93	Cga/Tga	1/14	0.296461514600333	2	FACETS	0.846	0.77	0.924	1	0.979	1	CLONAL	3	TRUE	0	0.29	2		195	288	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0000843-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	151	163	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	0.497174054437753	3	FACETS	1	0.986	1	0.812	0.76	0.864	CLONAL	2	TRUE	0	0.592965621450926	3		163	271	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0000843-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	380	383	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.592965621450926	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.592965621450926	2		385	585	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955165	17955165	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752820429	NA	P-0000843-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	380	173	0	ENST00000458235.1:c.62C>T	p.Thr21Met	p.T21M	ENST00000458235	NM_000215.3	21	aCg/aTg	2/24	0.580194295684493	5	FACETS	0.931	0.894	0.968			1	CLONAL	4	TRUE	NA	0.592965621450926	5		173	650	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000861-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	12	273	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.281179633375214	1	FACETS	0.31	0.217	0.423	0.31	0.217	0.423	SUBCLONAL	1	TRUE	0	0.281179633375214	1		273	237	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857688	78857688	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000861-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	48	275	0	ENST00000306801.3:c.1758G>C	p.Gln586His	p.Q586H	ENST00000306801	NM_020761.2	586	caG/caC	16/34	0.281179633375214	3	FACETS	0.774	0.655	0.906	0.387	0.327	0.453	CLONAL	1	TRUE	1	0.281179633375214	3		275	503	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417921	138417921	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs866345647	NA	P-0000861-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	48	162	0	ENST00000289153.2:c.1598del	p.Lys533SerfsTer6	p.K533Sfs*6	ENST00000289153	NM_006219.2	533	aAg/ag	11/22	1	2	FACETS	0.858	0.727	1	0.858	0.727	1	CLONAL	1	TRUE	1	0.281179633375214	2		162	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0000868-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	284	189	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.378366299989428	2	FACETS	0.971	0.919	1	0.971	0.919	1	CLONAL	2	TRUE	0	0.43805591751938	2		189	668	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288967	212288967	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs537458255	NA	P-0000868-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	52	197	0	ENST00000342788.4:c.2779C>T	p.Arg927Ter	p.R927*	ENST00000342788	NM_005235.2	927	Cga/Tga	23/28	0.254482905892638	4	FACETS	1	0.896	1	0.529	0.452	0.611	INDETERMINATE	1	TRUE	2	0.43805591751938	4		197	323	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55569944	55569944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000868-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	69	124	0	ENST00000288135.5:c.811C>T	p.Arg271Cys	p.R271C	ENST00000288135	NM_000222.2	271	Cgt/Tgt	5/21	0.43805591751938	3	FACETS	0.838	0.741	0.94	0.838	0.741	0.94	CLONAL	2	TRUE	1	0.43805591751938	3		124	229	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0000868-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	145	561	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.43805591751938	3	FACETS	0.993	0.926	1	0.993	0.926	1	CLONAL	3	TRUE	0	0.43805591751938	3		561	271	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748580	40748580	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000868-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	84	96	0	ENST00000373198.4:c.2936C>G	p.Thr979Ser	p.T979S	ENST00000373198	NM_133170.3	979	aCt/aGt	21/32	0.43805591751938	9	FACETS	1	0.914	1	0.149	0.131	0.169	CLONAL	1	TRUE	2	0.43805591751938	9		96	929	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099065	157099065	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0000871-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	37	41	0	ENST00000346085.5:c.2T>C	p.Met1?	p.M1?	ENST00000346085	NM_020732.3	1	aTg/aCg	1/20	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.733804081803576	2		41	87	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257817	16257817	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000871-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	102	108	0	ENST00000375759.3:c.5083del	p.Glu1695AsnfsTer6	p.E1695Nfs*6	ENST00000375759	NM_015001.2	1694	gtG/gt	11/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.733804081803576	2		108	228	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0000900-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	4979	335	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.573454938827307	33	FACETS	0.988	0.983	0.992			1	CLONAL	33	TRUE	NA	0.573454938827307	33		335	5269	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648456	30648456	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000900-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	194	328	0	ENST00000295754.5:c.81C>G	p.His27Gln	p.H27Q	ENST00000295754	NM_003242.5	27	caC/caG	1/7	0.573454938827307	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.573454938827307	1		328	414	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0000903-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1280	240	253	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.716	0.667	0.768	0.716	0.667	0.768	SUBCLONAL	1	TRUE	1	0.440829228364209	2		253	1520	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000903-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1336	303	599	0	ENST00000397062.3:c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	NM_006164.4	34	Cga/Gga	2/5	1	2	FACETS	0.839	0.788	0.891	0.839	0.788	0.891	CLONAL	1	TRUE	1	0.440829228364209	2		599	1639	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153596	55153596	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0000903-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	179	524	0	ENST00000257290.5:c.2563-1G>C		p.X855_splice	ENST00000257290	NM_006206.4	855			0.210900648022605	0	FACETS	0.447	0.412	0.484			1	INDETERMINATE	1	TRUE	0	0.440829228364209	0		524	1015	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484163	8484163	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000903-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	405	524	0	ENST00000356435.5:c.3369G>T	p.Met1123Ile	p.M1123I	ENST00000356435		1123	atG/atT	19/35	0.440829228364209	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.440829228364209	1		524	1108	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781032	135781032	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000903-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1300	316	741	1	ENST00000298552.3:c.1933C>T	p.Pro645Ser	p.P645S	ENST00000298552	NM_001162426.1	645	Cca/Tca	15/23	1	2	FACETS	0.887	0.835	0.941	0.887	0.835	0.941	CLONAL	1	TRUE	1	0.440829228364209	2		742	1616	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406651	70406651	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000903-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1265	303	700	0	ENST00000373644.4:c.4165G>C	p.Asp1389His	p.D1389H	ENST00000373644	NM_030625.2	1389	Gac/Cac	4/12	1	2	FACETS	0.877	0.824	0.931	0.877	0.824	0.931	CLONAL	1	TRUE	1	0.440829228364209	2		700	1568	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690619	88690619	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs965378877	NA	P-0000903-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	85	378	0	ENST00000360948.2:c.411C>G	p.Asn137Lys	p.N137K	ENST00000360948	NM_001012338.2	137	aaC/aaG	5/19	1	2	FACETS	0.493	0.435	0.554	0.493	0.435	0.554	SUBCLONAL	1	TRUE	1	0.440829228364209	2		378	783	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23635412	23635412	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000903-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	202	475	0	ENST00000261584.4:c.2752C>G	p.Pro918Ala	p.P918A	ENST00000261584	NM_024675.3	918	Cca/Gca	8/13	0.250117068980284	1	FACETS	0.616	0.57	0.664	0.616	0.57	0.664	INDETERMINATE	1	TRUE	0	0.440829228364209	1		475	1159	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577508	7577508	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000903-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	184	279	0	ENST00000269305.4:c.773A>T	p.Glu258Val	p.E258V	ENST00000269305	NM_001126112.2	258	gAa/gTa	7/11	0.440829228364209	1	FACETS	0.915	0.848	0.985	0.915	0.848	0.985	CLONAL	1	TRUE	0	0.440829228364209	1		279	711	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101956	11101956	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000903-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	128	288	0	ENST00000358026.2:c.1376A>C	p.Gln459Pro	p.Q459P	ENST00000358026	NM_001128849.1	459	cAg/cCg	8/36	0.440829228364209	1	FACETS	0.808	0.736	0.884	0.808	0.736	0.884	CLONAL	1	TRUE	0	0.440829228364209	1		288	560	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474110	29474110	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000903-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	48	417	0	ENST00000389048.3:c.2065G>T	p.Gly689Trp	p.G689W	ENST00000389048	NM_004304.4	689	Ggg/Tgg	12/29	1	2	FACETS	0.25	0.21	0.294	0.25	0.21	0.294	SUBCLONAL	1	TRUE	1	0.440829228364209	2		417	872	SUCCESS
FH	2271	MSKCC	GRCh37	1	241661270	241661270	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691250	NA	P-0000907-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	206	314	0	ENST00000366560.3:c.1391G>T	p.Gly464Val	p.G464V	ENST00000366560	NM_000143.3	464	gGg/gTg	10/10	1	2	FACETS	0.842	0.782	0.904	0.842	0.782	0.904	CLONAL	1	TRUE	1	0.539999285499964	2		314	906	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871286	35871286	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000907-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	61	343	0	ENST00000303115.3:c.508C>G	p.Arg170Gly	p.R170G	ENST00000303115	NM_002185.3	170	Cgc/Ggc	4/8	0.446175907077362	3	FACETS	0.279	0.239	0.322	0.093	0.079	0.108	SUBCLONAL	1	TRUE	0	0.539999285499964	3		343	1029	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499685	8499685	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000907-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	236	315	0	ENST00000356435.5:c.2284C>A	p.Gln762Lys	p.Q762K	ENST00000356435		762	Cag/Aag	14/35	0.483177152126793	1	FACETS	0.797	0.745	0.849	0.797	0.745	0.849	SUBCLONAL	1	TRUE	0	0.539999285499964	1		315	801	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123623	108123623	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000907-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	83	357	0	ENST00000278616.4:c.1882C>T	p.Gln628Ter	p.Q628*	ENST00000278616	NM_000051.3	628	Caa/Taa	12/63	0.276995523491703	2	FACETS	0.279	0.245	0.315	0.139	0.122	0.158	INDETERMINATE	1	TRUE	0	0.539999285499964	2		357	1103	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913343	NA	P-0000907-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	371	466	0	ENST00000269305.4:c.817C>A	p.Arg273Ser	p.R273S	ENST00000269305	NM_001126112.2	273	Cgt/Agt	8/11	0.501117716315328	1	FACETS	0.985	0.937	1	0.985	0.937	1	CLONAL	1	TRUE	0	0.539999285499964	1		466	1018	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220649	1220649	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000907-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	175	381	0	ENST00000326873.7:c.667G>T	p.Glu223Ter	p.E223*	ENST00000326873	NM_000455.4	223	Gag/Tag	5/10	0.539999285499964	1	FACETS	0.886	0.822	0.952	0.886	0.822	0.952	CLONAL	1	TRUE	0	0.539999285499964	1		381	534	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290037	15290037	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000907-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	566	423	0	ENST00000263388.2:c.3517G>T	p.Gly1173Trp	p.G1173W	ENST00000263388	NM_000435.2	1173	Ggg/Tgg	22/33	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.539999285499964	2		423	977	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850973	63850973	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000917-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	67	316	0	ENST00000279873.7:c.1751A>G	p.Glu584Gly	p.E584G	ENST00000279873	NM_032199.2	584	gAg/gGg	10/10	1	2	FACETS	0.895	0.776	1	0.895	0.776	1	CLONAL	1	TRUE	1	0.15	2		316	998	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657443	29657443	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000917-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	96	462	0	ENST00000356175.3:c.5676G>C	p.Lys1892Asn	p.K1892N	ENST00000356175	NM_000267.3	1892	aaG/aaC	38/57	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.15	2		462	1137	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591931	48591931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000917-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	51	327	0	ENST00000342988.3:c.1094G>A	p.Gly365Asp	p.G365D	ENST00000342988	NM_005359.5	365	gGt/gAt	9/12	1	2	FACETS	0.737	0.624	0.861	0.737	0.624	0.861	SUBCLONAL	1	TRUE	1	0.15	2		327	923	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190665	11190665	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000923-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	196	276	0	ENST00000361445.4:c.5534A>T	p.Glu1845Val	p.E1845V	ENST00000361445	NM_004958.3	1845	gAg/gTg	39/58	0.287806622598429	4	FACETS	0.863	0.804	0.923			1	CLONAL	3	TRUE	NA	0.35	4		276	584	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163691	47163691	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs537620848	NA	P-0000923-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	175	282	0	ENST00000409792.3:c.2435T>C	p.Ile812Thr	p.I812T	ENST00000409792	NM_014159.6	812	aTt/aCt	3/21	0.303249791073653	1	FACETS	0.95	0.885	1	1	0.993	1	CLONAL	2	TRUE	0	0.35	1		282	434	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0000924-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	1355	358	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.433445228410136	4	FACETS	0.937	0.92	0.954			1	CLONAL	5	TRUE	NA	0.433445228410136	4		358	1913	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597395	10597395	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000924-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	274	334	0	ENST00000171111.5:c.1808G>T	p.Gly603Val	p.G603V	ENST00000171111	NM_203500.1	603	gGg/gTg	6/6	0.433445228410136	1	FACETS	0.777	0.735	0.82	1	0.994	1	SUBCLONAL	2	TRUE	0	0.433445228410136	1		334	637	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743560	46743560	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1221995564	NA	P-0000924-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	107	246	0	ENST00000371975.4:c.1941T>A	p.Asp647Glu	p.D647E	ENST00000371975	NM_003579.3	647	gaT/gaA	17/18	1	2	FACETS	0.984	0.886	1	0.984	0.886	1	CLONAL	1	TRUE	1	0.433445228410136	2		246	502	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983863	2983863	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000924-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	179	377	0	ENST00000396946.4:c.667C>T	p.Arg223Ter	p.R223*	ENST00000396946	NM_032415.4	223	Cga/Tga	5/25	0.33405030832174	5	FACETS	0.776	0.716	0.839	0.517	0.477	0.559	SUBCLONAL	2	TRUE	2	0.433445228410136	5		377	878	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484300	8484300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000924-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	275	368	0	ENST00000356435.5:c.3232G>A	p.Glu1078Lys	p.E1078K	ENST00000356435		1078	Gag/Aag	19/35	0.322545884314325	2	FACETS	1	0.994	1	0.746	0.702	0.79	CLONAL	1	TRUE	0	0.433445228410136	2		368	851	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971155	21971155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000924-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	57	69	0	ENST00000304494.5:c.203C>A	p.Ala68Glu	p.A68E	ENST00000304494	NM_000077.4	68	gCg/gAg	2/3	0.322545884314325	2	FACETS	0.974	0.86	1	0.974	0.86	1	CLONAL	2	TRUE	0	0.433445228410136	2		69	135	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061046	38061046	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs537882736	NA	P-0000924-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	40	124	0	ENST00000250448.2:c.943G>T	p.Gly315Trp	p.G315W	ENST00000250448	NM_004496.3	315	Ggg/Tgg	2/2	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.433445228410136	2		124	181	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577126	7577126	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000924-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	249	378	0	ENST00000269305.4:c.812A>T	p.Glu271Val	p.E271V	ENST00000269305	NM_001126112.2	271	gAg/gTg	8/11	0.344484462009374	2	FACETS	0.83	0.781	0.881	0.83	0.781	0.881	CLONAL	2	TRUE	0	0.433445228410136	2		378	692	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0000942-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	34	235	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	1	2	FACETS	0.87	0.71	1	0.87	0.71	1	CLONAL	1	TRUE	1	0.17	2		235	460	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261533	16261533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000942-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	32	208	0	ENST00000375759.3:c.8798C>T	p.Thr2933Ile	p.T2933I	ENST00000375759	NM_015001.2	2933	aCc/aTc	11/15	0.201286347101575	3	FACETS	0.888	0.72	1	0.444	0.36	0.539	CLONAL	1	TRUE	1	0.17	3		208	460	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164820	47164820	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000942-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	18	247	0	ENST00000409792.3:c.1306A>T	p.Arg436Trp	p.R436W	ENST00000409792	NM_014159.6	436	Agg/Tgg	3/21	1	2	FACETS	0.711	0.535	0.918	0.711	0.535	0.918	CLONAL	1	TRUE	1	0.17	2		247	298	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685301	89685301	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000942-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	47	233	0	ENST00000371953.3:c.196A>G	p.Lys66Glu	p.K66E	ENST00000371953	NM_000314.4	66	Aag/Gag	3/9	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.17	2		233	496	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919308	48919308	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0000942-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	25	236	0	ENST00000267163.4:c.473T>A	p.Leu158Ter	p.L158*	ENST00000267163	NM_000321.2	158	tTg/tAg	4/27	0.201286347101575	3	FACETS	0.725	0.571	0.904	0.363	0.285	0.452	CLONAL	1	TRUE	1	0.17	3		236	440	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130180	2130180	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45451497	NA	P-0000942-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	45	323	0	ENST00000219476.3:c.3412C>T	p.Arg1138Ter	p.R1138*	ENST00000219476	NM_000548.3	1138	Cga/Tga	30/42	0.3	0	FACETS	0.927	0.779	1			1	CLONAL	1	TRUE	0	0.17	0		323	474	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651917	36651932	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCAGCAAGGCCTGC	CGGCAGCAAGGCCTGC	-	novel	NA	P-0000942-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	78	156	0	ENST00000244741.5:c.41_56del	p.Gly14AlafsTer12	p.G14Afs*12	ENST00000244741	NM_000389.4	13	tgCGGCAGCAAGGCCTGC/tg	2/3	0.539114213101135	4	FACETS	0.806	0.708	0.911	0.806	0.708	0.911	CLONAL	2	TRUE	2	0.17	4		156	666	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0000950-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	627	358	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.682510628942842	5	FACETS	0.944	0.917	0.971	0.944	0.917	0.971	CLONAL	4	TRUE	1	0.705236631201602	5		358	969	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285196	198285196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000950-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	320	227	0	ENST00000335508.6:c.371G>A	p.Arg124Gln	p.R124Q	ENST00000335508	NM_012433.2	124	cGg/cAg	4/25	0.705236631201602	4	FACETS	1	0.993	1	0.821	0.783	0.86	CLONAL	2	TRUE	1	0.705236631201602	4		227	628	SUCCESS
APC	324	MSKCC	GRCh37	5	112157607	112157607	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000950-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	667	225	0	ENST00000257430.4:c.1327G>T	p.Glu443Ter	p.E443*	ENST00000257430	NM_000038.5	443	Gaa/Taa	11/16	0.705236631201602	6	FACETS	1	0.98	1			1	CLONAL	4	TRUE	NA	0.705236631201602	6		225	1126	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175951	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1392778905	NA	P-0000950-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	145	125	0	ENST00000257430.4:c.4660G>T	p.Glu1554Ter	p.E1554*	ENST00000257430	NM_000038.5	1554	Gaa/Taa	16/16	0.705236631201602	6	FACETS	0.85	0.779	0.924			1	CLONAL	2	TRUE	NA	0.705236631201602	6		125	583	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000950-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	192	152	0	ENST00000269305.4:c.380C>A	p.Ser127Tyr	p.S127Y	ENST00000269305	NM_001126112.2	127	tCc/tAc	5/11	0.488145759859492	3	FACETS	0.874	0.831	0.915			1	CLONAL	3	TRUE	NA	0.705236631201602	3		152	281	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684327	29684327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs560262404	NA	P-0000950-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	578	333	0	ENST00000356175.3:c.7847G>A	p.Arg2616Gln	p.R2616Q	ENST00000356175	NM_000267.3	2616	cGa/cAa	53/57	0.406859874500739	4	FACETS	0.916	0.893	0.938	1	0.998	1	INDETERMINATE	4	TRUE	2	0.705236631201602	4		333	763	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706977	117706977	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764959275	NA	P-0000950-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	311	331	0	ENST00000368508.3:c.2173G>A	p.Asp725Asn	p.D725N	ENST00000368508	NM_002944.2	725	Gac/Aac	15/43	0.412092202369362	6	FACETS	0.875	0.829	0.922	0.875	0.829	0.922	INDETERMINATE	3	TRUE	3	0.705236631201602	6		331	810	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521502	8521502	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000950-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	241	226	0	ENST00000356435.5:c.736G>T	p.Glu246Ter	p.E246*	ENST00000356435		246	Gaa/Taa	9/35	0.316867277682932	6	FACETS	1	0.987	1	0.79	0.742	0.84	INDETERMINATE	2	TRUE	3	0.705236631201602	6		226	695	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450070	32450070	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000950-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	66	236	0	ENST00000332351.3:c.742G>T	p.Asp248Tyr	p.D248Y	ENST00000332351	NM_024426.4	248	Gat/Tat	2/10	0.666756284734673	4	FACETS	0.961	0.84	1	0.32	0.28	0.364	CLONAL	1	TRUE	1	0.705236631201602	4		236	332	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380223	25380223	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000950-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	140	296	0	ENST00000311936.3:c.235C>A	p.Leu79Ile	p.L79I	ENST00000311936	NM_004985.3	79	Ctt/Att	3/5	0.682510628942842	5	FACETS	1	0.912	1	0.25	0.228	0.274	CLONAL	1	TRUE	1	0.705236631201602	5		296	816	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929232	44929232	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000950-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	146	238	0	ENST00000377967.4:c.2332C>A	p.Pro778Thr	p.P778T	ENST00000377967	NM_021140.2	778	Cct/Act	17/29	0.547185679745156	2	FACETS	0.605	0.554	0.659			1	SUBCLONAL	1	TRUE	NA	0.705236631201602	2		238	684	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027109	49027141	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTCATCATGTTTCATATAGGATTCACCTTTAT	TTTCATCATGTTTCATATAGGATTCACCTTTAT	A	novel	NA	P-0000950-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	102	292	0	ENST00000267163.4:c.1696-20_1708delinsA		p.X566_splice	ENST00000267163	NM_000321.2	566		18/27	0.705236631201602	5	FACETS	0.881	0.796	0.968	0.352	0.318	0.388	CLONAL	2	TRUE	0	0.705236631201602	5		292	338	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0000982-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	95	120	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.373610086196922	3	FACETS	1	0.955	1	0.566	0.505	0.63	CLONAL	1	TRUE	1	0.373745460721255	3		120	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0000982-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	305	511	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.373610086196922	3	FACETS	0.984	0.929	1	0.984	0.929	1	CLONAL	2	TRUE	1	0.373745460721255	3		511	984	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637453	47637453	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754478179	NA	P-0000982-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	81	112	1	ENST00000233146.2:c.587C>T	p.Pro196Leu	p.P196L	ENST00000233146	NM_000251.2	196	cCa/cTa	3/16	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.373745460721255	2		113	394	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0000982-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	127	81	0	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	0.373745460721255	3	FACETS	0.93	0.858	1	0.93	0.858	1	CLONAL	3	TRUE	0	0.373745460721255	3		81	289	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940662	131940662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000982-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	24	148	0	ENST00000265335.6:c.2689G>A	p.Glu897Lys	p.E897K	ENST00000265335		897	Gaa/Aaa	16/25	0.373745460721255	3	FACETS	0.404	0.317	0.506	0.135	0.105	0.169	SUBCLONAL	1	TRUE	0	0.373745460721255	3		148	377	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128848606	128848606	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000982-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	99	179	0	ENST00000249373.3:c.1271T>C	p.Met424Thr	p.M424T	ENST00000249373	NM_005631.4	424	aTg/aCg	7/12	0.196728914597257	3	FACETS	1	0.957	1	0.378	0.338	0.42	INDETERMINATE	1	TRUE	0	0.373745460721255	3		179	555	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372337	55372337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1281266243	NA	P-0000982-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	52	120	1	ENST00000297316.4:c.1027C>T	p.Arg343Trp	p.R343W	ENST00000297316	NM_022454.3	343	Cgg/Tgg	2/2	0.291497340875405	4	FACETS	0.812	0.692	0.943	0.406	0.346	0.472	CLONAL	1	TRUE	2	0.373745460721255	4		121	471	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828861	26828861	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000982-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	377	135	0	ENST00000381527.3:c.83G>A	p.Gly28Asp	p.G28D	ENST00000381527	NM_001260.1	28	gGc/gAc	1/13	0.368096761324072	5	FACETS	0.892	0.851	0.934	0.892	0.851	0.934	CLONAL	4	TRUE	1	0.373745460721255	5		135	882	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0000982-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	3946	114	3	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	0.373745460721255	39	FACETS	1	0.996	1			1	CLONAL	38	TRUE	NA	0.373745460721255	39		117	4386	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0000987-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	2276	335	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.319322013870205	55	FACETS	1	0.993	1			1	CLONAL	47	TRUE	NA	0.319322013870205	55		335	2851	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150552000	150552000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000987-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	152	586	0	ENST00000369026.2:c.7G>A	p.Gly3Ser	p.G3S	ENST00000369026	NM_021960.4	3	Ggc/Agc	1/3	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.319322013870205	2		586	909	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504377	8504377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000987-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	40	322	0	ENST00000356435.5:c.1706C>T	p.Ser569Leu	p.S569L	ENST00000356435		569	tCa/tTa	12/35	0.291545302633217	2	FACETS	0.591	0.491	0.702	0.295	0.245	0.351	SUBCLONAL	1	TRUE	0	0.319322013870205	2		322	424	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28886185	28886185	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000987-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	39	539	0	ENST00000282397.4:c.3437G>C	p.Arg1146Thr	p.R1146T	ENST00000282397	NM_002019.4	1146	aGa/aCa	26/30	0.31387552079046	1	FACETS	0.383	0.317	0.457	0.383	0.317	0.457	SUBCLONAL	1	TRUE	0	0.319322013870205	1		539	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0000987-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	118	305	0	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	0.291545302633217	2	FACETS	1	0.984	1	0.736	0.667	0.808	CLONAL	1	TRUE	0	0.319322013870205	2		305	502	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015055	37015055	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1414110836	NA	P-0000995-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	165	366	0	ENST00000358127.4:c.349C>T	p.Arg117Trp	p.R117W	ENST00000358127	NM_001280556.1	117	Cgg/Tgg	3/10	1	2	FACETS	0.838	0.77	0.909	0.838	0.77	0.909	CLONAL	1	TRUE	1	0.457836613520942	2		366	860	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44919324	44919324	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000995-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	51	144	0	ENST00000377967.4:c.1252A>G	p.Ser418Gly	p.S418G	ENST00000377967	NM_021140.2	418	Agt/Ggt	13/29	0.372319877775237	2	FACETS	0.743	0.635	0.859			1	SUBCLONAL	1	TRUE	NA	0.457836613520942	2		144	300	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434593	110434595	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	novel	NA	P-0000995-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	32	163	2	ENST00000375856.3:c.3806_3808del	p.Gln1269del	p.Q1269del	ENST00000375856	NM_003749.2	1269	cAGCcg/ccg	1/2	0.457836613520942	5	FACETS	0.473	0.383	0.574	0.095	0.076	0.115	SUBCLONAL	1	TRUE	0	0.457836613520942	5		165	499	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346750	91346750	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0001003-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	115	293	0	ENST00000355112.3:c.3359-1G>T		p.X1120_splice	ENST00000355112	NM_000057.2	1120			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		293	246	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0001005-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	81	218	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	0.202269577700679	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	0	0.264748122924869	1		218	494	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916947	178916947	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001005-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	128	243	0	ENST00000263967.3:c.334A>T	p.Ile112Phe	p.I112F	ENST00000263967	NM_006218.2	112	Atc/Ttc	2/21	1	2	FACETS	0.854	0.772	0.941	0.854	0.772	0.941	CLONAL	1	FALSE	1	0.264748122924869	2		243	1132	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178681	108178681	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001005-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	40	169	0	ENST00000278616.4:c.5732C>T	p.Ala1911Val	p.A1911V	ENST00000278616	NM_000051.3	1911	gCt/gTt	38/63	1	2	FACETS	0.509	0.422	0.606	0.509	0.422	0.606	SUBCLONAL	1	FALSE	1	0.264748122924869	2		169	594	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001005-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	118	363	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.264748122924869	1	FACETS	0.818	0.737	0.904	0.818	0.737	0.904	CLONAL	1	FALSE	0	0.264748122924869	1		363	945	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354234	70354234	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001005-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1642	93	535	0	ENST00000374080.3:c.4645C>T	p.Arg1549Cys	p.R1549C	ENST00000374080		1549	Cgc/Tgc	34/45	1	2	FACETS	0.405	0.358	0.455	0.405	0.358	0.455	SUBCLONAL	1	FALSE	1	0.264748122924869	2		535	1735	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398280	25398281	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0001005-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2007	148	491	0	ENST00000311936.3:c.38_39delinsAA	p.Gly13Glu	p.G13E	ENST00000311936	NM_004985.3	13	gGC/gAA	2/5	0.247297792783999	3	FACETS	0.587	0.534	0.644	0.294	0.267	0.322	SUBCLONAL	1	FALSE	1	0.264748122924869	3		491	2155	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057520000	NA	P-0001007-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	544	401	0	ENST00000269305.4:c.452C>A	p.Pro151His	p.P151H	ENST00000269305	NM_001126112.2	151	cCc/cAc	5/11	0.914451584640269	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	FALSE	0	0.92681571329789	2		401	570	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661537	227661537	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777987963	NA	P-0001007-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	135	518	1	ENST00000305123.5:c.1918G>A	p.Val640Ile	p.V640I	ENST00000305123	NM_005544.2	640	Gta/Ata	1/2	1	2	FACETS	0.346	0.314	0.379	0.346	0.314	0.379	SUBCLONAL	1	FALSE	1	0.92681571329789	2		519	842	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692887	89692887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660535	NA	P-0001007-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	80	194	0	ENST00000371953.3:c.371G>A	p.Cys124Tyr	p.C124Y	ENST00000371953	NM_000314.4	124	tGt/tAt	5/9	0.481583807245625	1	FACETS	0.298	0.264	0.333	0.298	0.264	0.333	INDETERMINATE	1	FALSE	0	0.92681571329789	1		194	311	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557630	95557630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001007-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	383	589	0	ENST00000393063.1:c.5437G>A	p.Glu1813Lys	p.E1813K	ENST00000393063	NM_030621.3	1813	Gag/Aag	26/28	0.884737677226548	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	0	0.92681571329789	1		589	443	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720857	89720857	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs786201816	NA	P-0001011-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	47	109	1	ENST00000371953.3:c.1008C>G	p.Tyr336Ter	p.Y336*	ENST00000371953	NM_000314.4	336	taC/taG	8/9	0.262592453688554	3	FACETS	0.782	0.668	0.904	0.782	0.668	0.904	CLONAL	2	FALSE	1	0.345535808077622	3		110	204	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578532	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001011-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	67	203	0	ENST00000269305.4:c.398T>A	p.Met133Lys	p.M133K	ENST00000269305	NM_001126112.2	133	aTg/aAg	5/11	0.242031527136396	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	0	0.345535808077622	1		203	246	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0001013-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	94	454	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.308285493510846	3	FACETS	0.402	0.357	0.451	0.201	0.178	0.226	INDETERMINATE	1	TRUE	1	0.557508896470952	3		454	1072	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103411	77103411	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001013-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	50	749	0	ENST00000356341.3:c.155A>T	p.Asp52Val	p.D52V	ENST00000356341	NM_002576.4	52	gAc/gTc	2/15	0.176489461460022	5	FACETS	0.48	0.406	0.561	0.16	0.135	0.187	INDETERMINATE	1	TRUE	2	0.557508896470952	5		749	686	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636744	2636744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370494924	NA	P-0001013-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	17	519	0	ENST00000342085.4:c.1193C>T	p.Ser398Leu	p.S398L	ENST00000342085	NM_002613.4	398	tCa/tTa	11/14	0.319556839235504	1	FACETS	0.141	0.105	0.185	0.141	0.105	0.185	INDETERMINATE	1	TRUE	0	0.557508896470952	1		519	311	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182575	99182575	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1231375445	NA	P-0001023-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	20	349	0	ENST00000074304.5:c.2378G>A	p.Arg793Gln	p.R793Q	ENST00000074304	NM_001134224.1	793	cGa/cAa	22/26	0.260367632475779	3	FACETS	0.623	0.477	0.794	0.312	0.238	0.397	SUBCLONAL	1	TRUE	1	0.26	3		349	279	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649968	88649968	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001023-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	32	424	0	ENST00000372037.3:c.217A>G	p.Asn73Asp	p.N73D	ENST00000372037	NM_004329.2	73	Aat/Gat	4/13	1	2	FACETS	0.606	0.492	0.735	0.606	0.492	0.735	SUBCLONAL	1	TRUE	1	0.26	2		424	406	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0001023-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	94	513	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.260367632475779	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.26	3		513	330	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004804	16004804	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001023-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	30	521	0	ENST00000268712.3:c.2450C>T	p.Thr817Ile	p.T817I	ENST00000268712	NM_006311.3	817	aCc/aTc	20/46	0.260367632475779	3	FACETS	0.495	0.398	0.605	0.247	0.199	0.303	SUBCLONAL	1	TRUE	1	0.26	3		521	527	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312638	30312638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001023-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	187	449	0	ENST00000262643.3:c.619C>T	p.Pro207Ser	p.P207S	ENST00000262643	NM_001238.2	207	Cct/Tct	8/12	0.299053702890106	6	FACETS	0.856	0.792	0.923			1	CLONAL	3	TRUE	NA	0.26	6		449	851	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313019	30313019	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001023-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	73	474	0	ENST00000262643.3:c.822C>G	p.Ile274Met	p.I274M	ENST00000262643	NM_001238.2	274	atC/atG	9/12	0.299053702890106	6	FACETS	1	0.954	1			1	CLONAL	1	TRUE	NA	0.26	6		474	711	SUCCESS
ATM	472	MSKCC	GRCh37	11	108225544	108225544	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001038-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	411	370	0	ENST00000278616.4:c.8793T>G	p.Cys2931Trp	p.C2931W	ENST00000278616	NM_000051.3	2931	tgT/tgG	61/63	0.888058612556992	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.889429688154216	1		370	510	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574006	7574011	+	inframe_deletion	In_Frame_Del	DEL	ACATCT	ACATCT	-	novel	NA	P-0001038-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	349	507	0	ENST00000269305.4:c.1016_1021del	p.Glu339_Phe341delinsVal	p.E339_F341delinsV	ENST00000269305	NM_001126112.2	339	gAGATGTtc/gtc	10/11	0.889429688154216	1	FACETS	0.923	0.892	0.953	0.923	0.892	0.953	CLONAL	1	TRUE	0	0.889429688154216	1		507	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587782272	NA	P-0001046-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	351	417	0	ENST00000269305.4:c.994-1G>C		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.38988085967126	3	FACETS	0.919	0.877	0.961	0.919	0.877	0.961	CLONAL	3	TRUE	0	0.421818300402302	3		417	731	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938529	76938536	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTTGAG	TCTTTGAG	-	novel	NA	P-0001046-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	313	535	0	ENST00000373344.5:c.2212_2219del	p.Leu738GlyfsTer13	p.L738Gfs*13	ENST00000373344	NM_000489.3	738	CTCAAAGAg/g	9/35	0.421818300402302	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.421818300402302	1		535	1028	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0001050-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	148	298	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.264452715378913	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	0	0.264452715378913	3		298	365	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439780	52439780	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0001050-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	143	619	0	ENST00000460680.1:c.931+1G>A		p.X311_splice	ENST00000460680	NM_004656.3	311			1	2	FACETS	0.759	0.694	0.828	1	0.987	1	SUBCLONAL	2	TRUE	1	0.264452715378913	2		619	712	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438305	56438305	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001050-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	23	266	0	ENST00000407977.2:c.688G>T	p.Asp230Tyr	p.D230Y	ENST00000407977		230	Gat/Tat	7/10	0.180593517021733	3	FACETS	0.646	0.504	0.81	0.323	0.252	0.405	SUBCLONAL	1	TRUE	1	0.264452715378913	3		266	305	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0001076-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	244	377	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.144799516644715	4	FACETS	1	0.978	1	1	0.978	1	INDETERMINATE	2	FALSE	2	0.665262844725778	4		378	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0001076-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	560	459	0	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	NA	2	FACETS	0.895	0.879	0.91			1	INDETERMINATE	3	FALSE	NA	0.665262844725778	2		459	627	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175534	108175534	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001076-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	142	472	0	ENST00000278616.4:c.5629T>C	p.Phe1877Leu	p.F1877L	ENST00000278616	NM_000051.3	1877	Ttc/Ctc	37/63	0.144799516644715	4	FACETS	1	0.957	1	0.539	0.492	0.587	INDETERMINATE	1	FALSE	2	0.665262844725778	4		472	660	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909629	76909629	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs919106518	NA	P-0001076-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	266	632	1	ENST00000373344.5:c.4276C>T	p.Arg1426Ter	p.R1426*	ENST00000373344	NM_000489.3	1426	Cga/Tga	14/35	0.665262844725778	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	0	0.665262844725778	1		633	440	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149511596	149511596	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377445092	NA	P-0001089-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	39	367	0	ENST00000261799.4:c.1189C>T	p.Arg397Trp	p.R397W	ENST00000261799	NM_002609.3	397	Cgg/Tgg	8/23	0.186984136453777	3	FACETS	0.317	0.262	0.379	0.158	0.131	0.19	INDETERMINATE	1	TRUE	1	0.4699202446932	3		367	647	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707647	176707647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001089-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	56	298	0	ENST00000439151.2:c.5704G>A	p.Glu1902Lys	p.E1902K	ENST00000439151	NM_022455.4	1902	Gag/Aag	18/23	0.145304725560515	1	FACETS	0.304	0.26	0.352	0.304	0.26	0.352	INDETERMINATE	1	TRUE	0	0.4699202446932	1		298	600	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750874	128750874	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001089-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	1696	571	0	ENST00000377970.2:c.411G>T	p.Glu137Asp	p.E137D	ENST00000377970	NM_002467.4	137	gaG/gaT	2/3	0.4699202446932	11	FACETS	0.959	0.944	0.974			1	CLONAL	10	TRUE	NA	0.4699202446932	11		571	2344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540652	NA	P-0001089-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	123	257	0	ENST00000269305.4:c.743G>C	p.Arg248Pro	p.R248P	ENST00000269305	NM_001126112.2	248	cGg/cCg	7/11	0.351041598992877	2	FACETS	1	0.983	1	0.675	0.616	0.735	CLONAL	1	TRUE	0	0.4699202446932	2		257	388	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685986	29685986	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0001089-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	277	475	0	ENST00000356175.3:c.8051-1G>T		p.X2684_splice	ENST00000356175	NM_000267.3	2684			0.123977007510642	1	FACETS	1	0.968	1	1	0.968	1	INDETERMINATE	1	TRUE	0	0.4699202446932	1		475	866	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245606	41245606	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001089-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	80	451	0	ENST00000357654.3:c.1942G>C	p.Glu648Gln	p.E648Q	ENST00000357654	NM_007294.3	648	Gaa/Caa	10/23	0.464315519000759	1	FACETS	0.341	0.3	0.386	0.341	0.3	0.386	SUBCLONAL	1	TRUE	0	0.4699202446932	1		451	763	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412015	116412035	+	inframe_deletion	In_Frame_Del	DEL	TGTAGACTACCGAGCTACTTT	TGTAGACTACCGAGCTACTTT	-	novel	NA	P-0001089-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	652	260	0	ENST00000397752.3:c.3001_3021del	p.Val1001_Phe1007del	p.V1001_F1007del	ENST00000397752	NM_000245.2	1000	tcTGTAGACTACCGAGCTACTTTt/tct	14/21	0.4699202446932	12	FACETS	1	0.986	1			1	CLONAL	6	TRUE	NA	0.4699202446932	12		260	1491	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441252	52441252	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001093-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	64	267	0	ENST00000460680.1:c.518A>G	p.Tyr173Cys	p.Y173C	ENST00000460680	NM_004656.3	173	tAt/tGt	7/17	0.216233925742028	1	FACETS	0.921	0.799	1	0.921	0.799	1	CLONAL	1	TRUE	0	0.251109408072179	1		267	484	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468079	120468079	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001093-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	26	240	0	ENST00000256646.2:c.4360G>T	p.Asp1454Tyr	p.D1454Y	ENST00000256646	NM_024408.3	1454	Gac/Tac	25/34	1	2	FACETS	0.462	0.365	0.574	0.462	0.365	0.574	SUBCLONAL	1	TRUE	1	0.251109408072179	2		240	448	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165204	47165204	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0001093-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	36	295	0	ENST00000409792.3:c.922A>T	p.Lys308Ter	p.K308*	ENST00000409792	NM_014159.6	308	Aag/Tag	3/21	0.216233925742028	1	FACETS	0.381	0.312	0.459	0.381	0.312	0.459	SUBCLONAL	1	TRUE	0	0.251109408072179	1		295	658	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201843	66201843	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001093-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	33	210	0	ENST00000273854.3:c.2659G>T	p.Val887Leu	p.V887L	ENST00000273854	NM_004439.5	887	Gtg/Ttg	16/18	1	2	FACETS	0.533	0.434	0.646	0.533	0.434	0.646	SUBCLONAL	1	TRUE	1	0.251109408072179	2		210	493	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176618953	176618953	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001093-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	42	352	0	ENST00000439151.2:c.996G>T	p.Lys332Asn	p.K332N	ENST00000439151	NM_022455.4	332	aaG/aaT	3/23	0.245800605662303	1	FACETS	0.476	0.396	0.564	0.476	0.396	0.564	SUBCLONAL	1	TRUE	0	0.251109408072179	1		352	615	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859522	151859522	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001093-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	86	314	0	ENST00000262189.6:c.11140A>G	p.Lys3714Glu	p.K3714E	ENST00000262189	NM_170606.2	3714	Aaa/Gaa	43/59	0.169296376134282	3	FACETS	1	0.945	1	0.557	0.493	0.626	CLONAL	1	TRUE	1	0.251109408072179	3		314	692	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741707	145741707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543009701	NA	P-0001093-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	36	255	0	ENST00000428558.2:c.796G>A	p.Glu266Lys	p.E266K	ENST00000428558	NM_004260.3	266	Gag/Aag	5/22	0.219276285912474	4	FACETS	0.787	0.647	0.944	0.393	0.323	0.472	CLONAL	1	TRUE	2	0.251109408072179	4		255	456	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77051801	77051801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs534472752	NA	P-0001093-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	52	292	0	ENST00000356341.3:c.1006G>A	p.Val336Met	p.V336M	ENST00000356341	NM_002576.4	336	Gtg/Atg	11/15	1	2	FACETS	0.687	0.584	0.8	0.687	0.584	0.8	SUBCLONAL	1	TRUE	1	0.251109408072179	2		292	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0001093-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	19	170	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	1	2	FACETS	0.449	0.34	0.577	0.449	0.34	0.577	SUBCLONAL	1	TRUE	1	0.251109408072179	2		170	337	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019426	31019426	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001093-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	51	328	0	ENST00000375687.4:c.923T>C	p.Leu308Pro	p.L308P	ENST00000375687	NM_015338.5	308	cTa/cCa	10/13	1	2	FACETS	0.639	0.542	0.745	0.639	0.542	0.745	SUBCLONAL	1	TRUE	1	0.251109408072179	2		328	636	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405828	157405828	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001093-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	26	211	0	ENST00000346085.5:c.2072del	p.Gly691GlufsTer6	p.G691Efs*6	ENST00000346085	NM_020732.3	690	acG/ac	6/20	0.216233925742028	1	FACETS	0.371	0.293	0.461	0.371	0.293	0.461	SUBCLONAL	1	TRUE	0	0.251109408072179	1		211	488	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074295	30074296	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0001110-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	94	272	0	ENST00000338641.4:c.1557_1558delinsTT	p.Met519_Glu520delinsIleTer	p.M519_E520delinsI*	ENST00000338641	NM_000268.3	519	atGGag/atTTag	14/16	0.463158671734767	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.460490077168955	1		272	293	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433655	49433655	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001129-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	129	284	0	ENST00000301067.7:c.7898C>A	p.Ser2633Ter	p.S2633*	ENST00000301067	NM_003482.3	2633	tCa/tAa	31/54	1	2	FACETS	0.967	0.89	1	1	0.993	1	CLONAL	5	TRUE	1	0.17	2		284	314	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0001131-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	815	335	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.447748474944235	6	FACETS	1	0.995	1			1	CLONAL	4	TRUE	NA	0.447748474944235	6		335	1573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0001131-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	137	485	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			1	2	FACETS	0.67	0.609	0.734	0.67	0.609	0.734	SUBCLONAL	1	TRUE	1	0.447748474944235	2		485	914	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306996	65306996	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs375979659	NA	P-0001131-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	69	448	2	ENST00000342505.4:c.2581C>A	p.Pro861Thr	p.P861T	ENST00000342505	NM_002227.2	861	Cca/Aca	19/25	0.405187301359214	1	FACETS	0.243	0.211	0.279	0.243	0.211	0.279	SUBCLONAL	1	TRUE	0	0.447748474944235	1		450	983	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950211	38950211	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001131-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	86	283	0	ENST00000357387.3:c.3739A>C	p.Thr1247Pro	p.T1247P	ENST00000357387	NM_152756.3	1247	Act/Cct	31/38	0.172089994289756	4	FACETS	0.511	0.451	0.576	0.256	0.225	0.288	INDETERMINATE	1	TRUE	2	0.447748474944235	4		283	1088	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5065038	5065038	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001131-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	334	430	0	ENST00000381652.3:c.1212T>G	p.Ile404Met	p.I404M	ENST00000381652	NM_004972.3	404	atT/atG	9/25	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.447748474944235	2		430	1137	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497635	125497635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767992502	NA	P-0001131-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	122	310	0	ENST00000428830.2:c.199G>A	p.Val67Ile	p.V67I	ENST00000428830	NM_001114121.2	67	Gta/Ata	3/14	1	2	FACETS	0.477	0.43	0.527	0.477	0.43	0.527	SUBCLONAL	1	TRUE	1	0.447748474944235	2		310	1142	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724250	52724250	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001131-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	82	388	0	ENST00000322088.6:c.1382C>T	p.Ala461Val	p.A461V	ENST00000322088	NM_014225.5	461	gCa/gTa	12/15	NA	2	FACETS	0.454	0.4	0.513			1	INDETERMINATE	1	TRUE	NA	0.447748474944235	2		388	806	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579556	7579560	+	frameshift_variant	Frame_Shift_Del	DEL	ATCAA	ATCAA	-	novel	NA	P-0001131-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	37	296	0	ENST00000269305.4:c.127_131del	p.Leu43AlafsTer7	p.L43Afs*7	ENST00000269305	NM_001126112.2	43	TTGATg/g	4/11	1	2	FACETS	0.281	0.231	0.337	0.281	0.231	0.337	SUBCLONAL	1	TRUE	1	0.447748474944235	2		296	589	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0001154-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	196	351	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.384648263920123	4	FACETS	0.923	0.857	0.992			1	CLONAL	2	TRUE	NA	0.391822975236801	4		351	754	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163512	47163512	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001155-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	111	279	0	ENST00000409792.3:c.2614C>T	p.Gln872Ter	p.Q872*	ENST00000409792	NM_014159.6	872	Caa/Taa	3/21	NA	2	FACETS	0.884	0.796	0.977			1	INDETERMINATE	1	TRUE	NA	0.386421512980273	2		279	650	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204864	NA	P-0001165-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	543	327	0	ENST00000371953.3:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000371953	NM_000314.4	171	Cag/Tag	6/9	0.669640019114129	3	FACETS	0.839	0.815	0.861	0.839	0.815	0.861	CLONAL	3	TRUE	0	0.798912608346761	3		327	756	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578538	7578538	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1131691037	NA	P-0001165-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	297	279	0	ENST00000269305.4:c.392A>T	p.Asn131Ile	p.N131I	ENST00000269305	NM_001126112.2	131	aAc/aTc	5/11	0.716095854148945	2	FACETS	0.9	0.866	0.933	0.9	0.866	0.933	CLONAL	2	TRUE	0	0.798912608346761	2		279	413	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845384	76845384	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001165-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	628	630	0	ENST00000373344.5:c.6137C>A	p.Ser2046Tyr	p.S2046Y	ENST00000373344	NM_000489.3	2046	tCt/tAt	27/35	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	1	TRUE	NA	0.798912608346761	2		630	1315	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0001170-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	254	338	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.449926503911604	3	FACETS	0.967	0.917	1	0.967	0.917	1	CLONAL	3	TRUE	0	0.449926503911604	3		338	477	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0001170-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	112	354	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.449926503911604	1	FACETS	0.76	0.696	0.824	1	0.987	1	SUBCLONAL	2	TRUE	0	0.449926503911604	1		354	254	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589848	212589848	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001170-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	121	268	0	ENST00000342788.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000342788	NM_005235.2	232	Cga/Tga	6/28	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.449926503911604	2		268	515	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900288	101900288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111854391	NA	P-0001170-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	42	377	0	ENST00000374994.4:c.722C>T	p.Ser241Leu	p.S241L	ENST00000374994	NM_004612.2	241	tCg/tTg	4/9	1	2	FACETS	0.348	0.29	0.413	0.348	0.29	0.413	SUBCLONAL	1	TRUE	1	0.449926503911604	2		377	536	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442974	49442974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768072508	NA	P-0001170-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	45	328	0	ENST00000301067.7:c.3934C>T	p.Arg1312Cys	p.R1312C	ENST00000301067	NM_003482.3	1312	Cgc/Tgc	12/54	1	2	FACETS	0.59	0.498	0.691	0.59	0.498	0.691	SUBCLONAL	1	TRUE	1	0.449926503911604	2		328	339	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016603	12016603	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001170-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	183	404	0	ENST00000353533.5:c.739G>T	p.Asp247Tyr	p.D247Y	ENST00000353533	NM_003010.3	247	Gac/Tac	7/11	0.449926503911604	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.449926503911604	1		404	447	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040639	47040639	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001170-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	197	236	0	ENST00000377604.3:c.1274G>A	p.Trp425Ter	p.W425*	ENST00000377604	NM_001204468.1	425	tGg/tAg	13/24	1	1	FACETS	1	0.979	1	1	0.995	1	CLONAL	2	TRUE	0	0.449926503911604	1		236	318	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105621	27105621	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001170-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	109	447	0	ENST00000324856.7:c.5232del	p.Leu1745TrpfsTer25	p.L1745Wfs*25	ENST00000324856	NM_006015.4	1744	ctA/ct	20/20	0.325266166313334	1	FACETS	0.786	0.709	0.866	0.786	0.709	0.866	SUBCLONAL	1	TRUE	0	0.449926503911604	1		447	478	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0001172-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	35	401	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	0.783	0.641	0.943	0.783	0.641	0.943	CLONAL	1	TRUE	1	0.17	2		402	526	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844174	68844174	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001172-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	57	617	0	ENST00000261769.5:c.762T>A	p.Asp254Glu	p.D254E	ENST00000261769	NM_004360.3	254	gaT/gaA	6/16	1	2	FACETS	0.996	0.854	1	0.996	0.854	1	CLONAL	1	TRUE	1	0.17	2		617	673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0001180-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	55	228	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.316942085733665	2		228	340	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417096	417096	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001180-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	30	292	0	ENST00000399788.2:c.3454A>T	p.Met1152Leu	p.M1152L	ENST00000399788	NM_001042603.1	1152	Atg/Ttg	23/28	NA	2	FACETS	0.373	0.3	0.457			1	INDETERMINATE	1	TRUE	NA	0.316942085733665	2		292	507	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844174	68844174	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001197-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	24	617	0	ENST00000261769.5:c.762T>A	p.Asp254Glu	p.D254E	ENST00000261769	NM_004360.3	254	gaT/gaA	6/16	0.221285637257315	3	FACETS	1	0.912	1	0.672	0.53	0.833	CLONAL	1	TRUE	1	0.21	3		617	188	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180232	38180232	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001197-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	22	637	0	ENST00000396334.3:c.80T>C	p.Val27Ala	p.V27A	ENST00000396334	NM_002468.4	27	gTc/gCc	1/5	0.291725956076583	3	FACETS	1	0.836	1	0.546	0.425	0.685	CLONAL	1	TRUE	1	0.21	3		637	212	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577075	7577075	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001197-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	18	645	0	ENST00000269305.4:c.863del	p.Asn288IlefsTer57	p.N288Ifs*57	ENST00000269305	NM_001126112.2	288	aAt/at	8/11	1	2	FACETS	0.912	0.69	1	0.912	0.69	1	CLONAL	1	TRUE	1	0.21	2		645	188	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119776	70119776	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001203-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	95	768	2	ENST00000245479.2:c.778C>T	p.Pro260Ser	p.P260S	ENST00000245479	NM_000346.3	260	Cca/Tca	3/3	0.451504818244521	2	FACETS	1	0.97	1	1	0.989	1	CLONAL	3	TRUE	0	0.451504818244521	2		770	131	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579317	7579324	+	frameshift_variant	Frame_Shift_Del	DEL	AAGTCACA	AAGTCACA	-	novel	NA	P-0001203-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	23	279	0	ENST00000269305.4:c.363_370del	p.Val122HisfsTer24	p.V122Hfs*24	ENST00000269305	NM_001126112.2	121	tcTGTGACTTgc/tcgc	4/11	0.451504818244521	2	FACETS	0.943	0.771	1	0.943	0.771	1	CLONAL	2	TRUE	0	0.451504818244521	2		279	54	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0001209-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	52	859	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	1	2	FACETS	0.685	0.585	0.795	0.685	0.585	0.795	SUBCLONAL	1	TRUE	1	0.373748800648585	2		859	406	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480078	120480078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001209-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	80	214	0	ENST00000256646.2:c.3349G>A	p.Glu1117Lys	p.E1117K	ENST00000256646	NM_024408.3	1117	Gaa/Aaa	21/34	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.373748800648585	2		214	304	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483351	120483351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001209-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	67	200	0	ENST00000256646.2:c.3010G>A	p.Asp1004Asn	p.D1004N	ENST00000256646	NM_024408.3	1004	Gat/Aat	19/34	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.373748800648585	2		200	262	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845946	156845946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001209-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	213	513	0	ENST00000524377.1:c.1576C>T	p.Leu526Phe	p.L526F	ENST00000524377	NM_002529.3	526	Ctt/Ttt	13/17	0.261733906235604	4	FACETS	1	0.986	1	0.807	0.754	0.861	CLONAL	2	TRUE	1	0.373748800648585	4		513	647	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443579	29443579	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001209-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	81	293	0	ENST00000389048.3:c.3638C>A	p.Pro1213His	p.P1213H	ENST00000389048	NM_004304.4	1213	cCt/cAt	23/29	0.202432818954238	0	FACETS	0.732	0.649	0.819			1	INDETERMINATE	1	TRUE	0	0.373748800648585	0		293	371	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186878	142186878	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001209-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	44	418	0	ENST00000350721.4:c.6585G>T	p.Lys2195Asn	p.K2195N	ENST00000350721	NM_001184.3	2195	aaG/aaT	39/47	1	2	FACETS	0.806	0.68	0.945	0.806	0.68	0.945	CLONAL	1	TRUE	1	0.373748800648585	2		418	292	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39074231	39074231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs980024517	NA	P-0001209-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	52	425	0	ENST00000357387.3:c.79C>T	p.Pro27Ser	p.P27S	ENST00000357387	NM_152756.3	27	Ccg/Tcg	2/38	1	2	FACETS	0.75	0.641	0.869	0.75	0.641	0.869	SUBCLONAL	1	TRUE	1	0.373748800648585	2		425	371	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090449	5090449	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001209-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	76	490	0	ENST00000381652.3:c.2765G>C	p.Arg922Pro	p.R922P	ENST00000381652	NM_004972.3	922	cGg/cCg	21/25	NA	2	FACETS	1	0.889	1			1	INDETERMINATE	1	TRUE	NA	0.373748800648585	2		490	403	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521411	8521411	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001209-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	70	489	0	ENST00000356435.5:c.827T>C	p.Leu276Pro	p.L276P	ENST00000356435		276	cTg/cCg	9/35	0.373748800648585	1	FACETS	0.804	0.704	0.91	0.804	0.704	0.91	CLONAL	1	TRUE	0	0.373748800648585	1		489	379	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1040397	1040397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35008685	NA	P-0001209-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	100	597	0	ENST00000358495.3:c.175G>A	p.Gly59Arg	p.G59R	ENST00000358495	NM_134424.2	59	Gga/Aga	3/12	NA	2	FACETS	0.984	0.881	1			1	INDETERMINATE	1	TRUE	NA	0.373748800648585	2		597	544	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118788	115118788	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001209-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	93	472	0	ENST00000257566.3:c.553T>G	p.Tyr185Asp	p.Y185D	ENST00000257566	NM_016569.3	185	Tac/Gac	2/8	1	2	FACETS	0.935	0.834	1	0.935	0.834	1	CLONAL	1	TRUE	1	0.373748800648585	2		472	532	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910761	32910761	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs886040419	NA	P-0001209-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	81	416	0	ENST00000380152.3:c.2269A>G	p.Lys757Glu	p.K757E	ENST00000380152		757	Aaa/Gaa	11/27	0.371611382021863	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.373748800648585	1		416	339	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033886	49033886	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs137853295	NA	P-0001209-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	88	565	0	ENST00000267163.4:c.2023G>T	p.Glu675Ter	p.E675*	ENST00000267163	NM_000321.2	675	Gaa/Taa	20/27	0.371611382021863	1	FACETS	0.884	0.788	0.987	0.884	0.788	0.987	CLONAL	1	TRUE	0	0.373748800648585	1		565	433	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678560	88678560	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001209-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	47	267	0	ENST00000360948.2:c.976C>A	p.Arg326Ser	p.R326S	ENST00000360948	NM_001012338.2	326	Cgt/Agt	9/19	1	2	FACETS	0.833	0.707	0.97	0.833	0.707	0.97	CLONAL	1	TRUE	1	0.373748800648585	2		267	302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579346	7579346	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs781724995	NA	P-0001209-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	107	373	0	ENST00000269305.4:c.341T>A	p.Leu114Ter	p.L114*	ENST00000269305	NM_001126112.2	114	tTg/tAg	4/11	0.373748800648585	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.373748800648585	1		373	420	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610417	10610417	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001209-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	127	460	0	ENST00000171111.5:c.293T>G	p.Val98Gly	p.V98G	ENST00000171111	NM_203500.1	98	gTg/gGg	2/6	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.373748800648585	2		460	670	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347819	70347819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001209-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	146	385	0	ENST00000374080.3:c.3058G>A	p.Glu1020Lys	p.E1020K	ENST00000374080		1020	Gag/Aag	22/45	0.304175624253875	0	FACETS	0.585	0.539	0.632			1	SUBCLONAL	2	TRUE	NA	0.373748800648585	0		385	418	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0001218-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	35	470	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		470	704	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0001226-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	109	409	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.200298517703677	1	FACETS	0.931	0.839	1	1	0.987	1	CLONAL	2	TRUE	0	0.200298517703677	1		409	526	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0001226-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	42	261	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.200298517703677	3	FACETS	1	0.921	1	0.588	0.492	0.695	CLONAL	1	TRUE	1	0.200298517703677	3		261	392	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636086	28636086	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001226-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	35	477	0	ENST00000241453.7:c.286G>T	p.Asp96Tyr	p.D96Y	ENST00000241453	NM_004119.2	96	Gac/Tac	3/24	0.200298517703677	0	FACETS	0.458	0.374	0.553			1	SUBCLONAL	1	TRUE	0	0.200298517703677	0		477	610	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586109	29586109	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001226-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	288	343	0	ENST00000356175.3:c.4329C>G	p.Phe1443Leu	p.F1443L	ENST00000356175	NM_000267.3	1443	ttC/ttG	32/57	0.200298517703677	8	FACETS	0.885	0.831	0.941			1	CLONAL	4	TRUE	NA	0.200298517703677	8		343	1300	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170774	11170774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568565786	NA	P-0001226-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	39	376	0	ENST00000358026.2:c.4918C>T	p.Arg1640Trp	p.R1640W	ENST00000358026	NM_001128849.1	1640	Cgg/Tgg	35/36	0.200298517703677	0	FACETS	0.654	0.542	0.779			1	SUBCLONAL	1	TRUE	0	0.200298517703677	0		376	476	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609942	43609947	+	inframe_deletion	In_Frame_Del	DEL	GAGCTG	GAGCTG	-	rs121913312	NA	P-0001234-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	100	558	0	ENST00000355710.3:c.1894_1899del	p.Glu632_Leu633del	p.E632_L633del	ENST00000355710	NM_020975.4	632	GAGCTG/-	11/20	0.233401771995412	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		558	577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0001235-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	110	314	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.342495366349024	2		314	557	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0001235-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	44	556	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.326186456849082	2	FACETS	0.491	0.412	0.58	0.246	0.206	0.29	SUBCLONAL	1	TRUE	0	0.342495366349024	2		556	523	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047071	128047071	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1558962721	NA	P-0001235-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	93	422	0	ENST00000285398.2:c.664A>C	p.Lys222Gln	p.K222Q	ENST00000285398	NM_000122.1	222	Aag/Cag	6/15	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.342495366349024	2		422	514	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715619	30715619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730880224	NA	P-0001235-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	61	273	0	ENST00000295754.5:c.1277C>T	p.Ala426Val	p.A426V	ENST00000295754	NM_003242.5	426	gCt/gTt	5/7	0.342495366349024	1	FACETS	0.663	0.574	0.76	0.663	0.574	0.76	SUBCLONAL	1	TRUE	0	0.342495366349024	1		273	445	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0001279-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	203	377	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.948	0.883	1	1	0.995	1	CLONAL	5	TRUE	1	0.13	2		378	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0001279-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	246	693	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.365616933123537	3	FACETS	0.925	0.869	0.983			1	CLONAL	6	TRUE	NA	0.13	3		693	726	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114322	143114322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001279-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	75	228	0	ENST00000262992.4:c.1099G>A	p.Gly367Arg	p.G367R	ENST00000262992	NM_001101669.1	367	Gga/Aga	13/24	0.148133334338665	3	FACETS	0.898	0.787	1	0.898	0.787	1	CLONAL	2	TRUE	1	0.13	3		228	684	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332868	152332868	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745723014	NA	P-0001279-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	184	220	0	ENST00000206249.3:c.1174G>A	p.Val392Ile	p.V392I	ENST00000206249	NM_000125.3	392	Gtc/Atc	5/8	1	2	FACETS	0.918	0.851	0.986	1	0.995	1	CLONAL	5	TRUE	1	0.13	2		220	617	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944566	32944566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41293517	NA	P-0001279-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	70	377	0	ENST00000380152.3:c.8359C>T	p.Arg2787Cys	p.R2787C	ENST00000380152		2787	Cgc/Tgc	19/27	0.148133334338665	0	FACETS	1	0.962	1			1	CLONAL	1	TRUE	0	0.13	0		377	725	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203436	NA	P-0001279-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	129	164	0	ENST00000269305.4:c.487T>C	p.Tyr163His	p.Y163H	ENST00000269305	NM_001126112.2	163	Tac/Cac	5/11	0.365616933123537	3	FACETS	1	0.938	1			1	CLONAL	5	TRUE	NA	0.13	3		164	410	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907808	76907812	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTT	CTCTT	-	novel	NA	P-0001279-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	209	334	0	ENST00000373344.5:c.4349_4353del	p.Glu1450GlyfsTer15	p.E1450Gfs*15	ENST00000373344	NM_000489.3	1450	gAAGAG/g	15/35	0.365616933123537	0	FACETS	1	0.946	1			1	CLONAL	5	TRUE	0	0.13	0		334	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0001284-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	125	398	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.368223701146935	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.368223701146935	1		398	419	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672854	86672854	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001284-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	102	186	0	ENST00000274376.6:c.2341G>T	p.Glu781Ter	p.E781*	ENST00000274376	NM_002890.2	781	Gaa/Taa	17/25	0.301567827558719	3	FACETS	1	0.937	1	0.696	0.63	0.765	CLONAL	2	TRUE	0	0.368223701146935	3		186	314	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718143	117718143	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001284-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	88	447	0	ENST00000368508.3:c.714del	p.Lys238AsnfsTer2	p.K238Nfs*2	ENST00000368508	NM_002944.2	238	aaA/aa	7/43	0.368223701146935	1	FACETS	0.867	0.771	0.967	0.867	0.771	0.967	CLONAL	1	TRUE	0	0.368223701146935	1		447	450	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906599	32906599	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001284-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	114	444	0	ENST00000380152.3:c.984del	p.Arg329GlyfsTer20	p.R329Gfs*20	ENST00000380152		328	acT/ac	10/27	0.295882850452425	2	FACETS	1	0.975	1	0.617	0.558	0.678	CLONAL	1	TRUE	0	0.368223701146935	2		444	502	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0001294-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	296	530	0	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		530	1263	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862740	9862740	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs796052564	NA	P-0001297-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	74	233	0	ENST00000330684.3:c.2563G>A	p.Asp855Asn	p.D855N	ENST00000330684	NM_001134407.1	855	Gac/Aac	12/13	0.295082347504147	1	FACETS	0.805	0.71	0.906	1	0.979	1	CLONAL	2	TRUE	0	0.24	1		233	337	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929196	44929196	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001297-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	179	268	0	ENST00000377967.4:c.2296G>T	p.Asp766Tyr	p.D766Y	ENST00000377967	NM_021140.2	766	Gat/Tat	17/29	0.3	3	FACETS	1	0.982	1	0.8	0.74	0.862	CLONAL	2	TRUE	0	0.24	3		268	696	SUCCESS
AR	367	MSKCC	GRCh37	X	66931257	66931257	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001297-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	116	323	0	ENST00000374690.3:c.1899G>T	p.Lys633Asn	p.K633N	ENST00000374690	NM_000044.3	633	aaG/aaT	4/8	0.3	3	FACETS	1	0.983	1	0.485	0.437	0.536	CLONAL	1	TRUE	0	0.24	3		323	744	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404185	139404186	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0001297-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	27	200	0	ENST00000277541.6:c.2968_2969del	p.Ser990LeufsTer34	p.S990Lfs*34	ENST00000277541	NM_017617.3	990	AGc/c	18/34	0.3	0	FACETS	1	0.903	1			1	CLONAL	1	TRUE	0	0.24	0		200	141	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0001300-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	98	335	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.659	0.588	0.734	0.659	0.588	0.734	SUBCLONAL	1	TRUE	1	0.43109344850279	2		335	690	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045004	47045004	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001300-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	190	392	0	ENST00000377604.3:c.2330A>G	p.His777Arg	p.H777R	ENST00000377604	NM_001204468.1	777	cAc/cGc	20/24	0.43109344850279	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.43109344850279	1		392	634	SUCCESS
APC	324	MSKCC	GRCh37	5	112164664	112164665	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0001300-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	93	160	0	ENST00000257430.4:c.1741_1742del	p.Lys581GlyfsTer20	p.K581Gfs*20	ENST00000257430	NM_000038.5	580	AAa/a	14/16	0.428139497258995	1	FACETS	0.853	0.763	0.946	0.853	0.763	0.946	CLONAL	1	TRUE	0	0.43109344850279	1		160	397	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0001306-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	78	261	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.897	0.794	1	0.897	0.794	1	CLONAL	1	FALSE	1	0.483017349292965	2		261	360	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846093	68846093	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0001306-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	190	499	0	ENST00000261769.5:c.1064T>G	p.Leu355Ter	p.L355*	ENST00000261769	NM_004360.3	355	tTa/tGa	8/16	0.302381292151119	0	FACETS	0.589	0.547	0.633			1	SUBCLONAL	1	FALSE	0	0.483017349292965	0		499	690	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0001315-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1202	537	456	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.91424827661451	3	FACETS	0.97	0.929	1	0.485	0.464	0.506	CLONAL	1	TRUE	1	0.934521954401916	3		456	1739	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513547	41513547	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs780440242	NA	P-0001315-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	325	354	0	ENST00000263253.7:c.451A>G	p.Thr151Ala	p.T151A	ENST00000263253	NM_001429.3	151	Aca/Gca	2/31	0.934521954401916	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.934521954401916	1		354	360	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039132	49039133	+	splice_acceptor_variant	Splice_Site	DEL	AG	AG	-	novel	NA	P-0001315-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	269	306	0	ENST00000267163.4:c.2212-1_2212del		p.X738_splice	ENST00000267163	NM_000321.2	738			0.934521954401916	1	FACETS	0.95	0.92	0.977	0.95	0.92	0.977	CLONAL	1	TRUE	0	0.934521954401916	1		306	323	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121805	2121807	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs137854104	NA	P-0001315-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	297	432	0	ENST00000219476.3:c.1973_1975del	p.Lys658del	p.K658del	ENST00000219476	NM_000548.3	656	gAGAag/gag	19/42	1	2	FACETS	0.837	0.793	0.883	0.837	0.793	0.883	CLONAL	1	TRUE	1	0.934521954401916	2		432	759	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486063	29486064	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs771115661	NA	P-0001315-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	443	498	0	ENST00000356175.3:c.246_247del	p.Gln83ValfsTer23	p.Q83Vfs*23	ENST00000356175	NM_000267.3	80	taTCtc/tatc	3/57	1	2	FACETS	0.829	0.793	0.866	0.829	0.793	0.866	CLONAL	1	TRUE	1	0.934521954401916	2		498	1143	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562738	29562739	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555615472	NA	P-0001315-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	511	630	0	ENST00000356175.3:c.3822_3823del	p.Phe1275ProfsTer8	p.F1275Pfs*8	ENST00000356175	NM_000267.3	1273	aCT/a	28/57	1	2	FACETS	0.872	0.837	0.908	0.872	0.837	0.908	CLONAL	1	TRUE	1	0.934521954401916	2		630	1254	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0001316-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	76	228	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.417072921627266	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	0	0.417072921627266	1		228	220	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0001316-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	202	412	1	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	FALSE	1	0.417072921627266	2		413	743	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190938	185190938	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001316-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	177	655	0	ENST00000265026.3:c.1819A>C	p.Lys607Gln	p.K607Q	ENST00000265026	NM_004721.4	607	Aaa/Caa	11/14	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.417072921627266	2		655	735	SUCCESS
APC	324	MSKCC	GRCh37	5	112170647	112170647	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0001316-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	111	323	0	ENST00000257430.4:c.1744-1G>A		p.X582_splice	ENST00000257430	NM_000038.5	582			1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	1	0.417072921627266	2		323	499	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114174	115114174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001316-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	159	485	0	ENST00000257566.3:c.1043G>A	p.Cys348Tyr	p.C348Y	ENST00000257566	NM_016569.3	348	tGc/tAc	6/8	0.353353998274342	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	FALSE	0	0.417072921627266	1		485	591	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217299	11217310	+	inframe_deletion	In_Frame_Del	DEL	AGGGCATCCTCC	AGGGCATCCTCC	-	novel	NA	P-0001316-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	81	450	0	ENST00000361445.4:c.4368_4379del	p.Trp1456_Leu1460delinsCys	p.W1456_L1460delinsC	ENST00000361445	NM_004958.3	1456	tgGGAGGATGCCCTt/tgt	30/58	0.143817534536414	0	FACETS	0.497	0.439	0.558			1	INDETERMINATE	1	FALSE	0	0.417072921627266	0		450	456	SUCCESS
APC	324	MSKCC	GRCh37	5	112176027	112176027	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001316-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	92	245	0	ENST00000257430.4:c.4737del	p.Ile1580PhefsTer70	p.I1580Ffs*70	ENST00000257430	NM_000038.5	1579	aTt/at	16/16	1	2	FACETS	0.902	0.805	1	0.902	0.805	1	CLONAL	1	FALSE	1	0.417072921627266	2		245	489	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138068	2138077	+	frameshift_variant	Frame_Shift_Del	DEL	CACCAGCGTG	CACCAGCGTG	-	novel	NA	P-0001342-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	367	458	0	ENST00000219476.3:c.5088_5097del	p.Asp1696GlufsTer127	p.D1696Efs*127	ENST00000219476	NM_000548.3	1696	gaCACCAGCGTG/ga	40/42	0.160885263107461	5	FACETS	0.989	0.947	1			1	INDETERMINATE	4	TRUE	NA	0.453097840291968	5		458	688	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0001350-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	308	470	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	0.663349649624196	2		470	896	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193459	99193459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1330981099	NA	P-0001350-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	297	356	0	ENST00000074304.5:c.2654G>A	p.Arg885His	p.R885H	ENST00000074304	NM_001134224.1	885	cGc/cAc	25/26	1	2	FACETS	0.897	0.846	0.95	0.897	0.846	0.95	CLONAL	1	TRUE	1	0.663349649624196	2		356	998	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846168	68846168	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0001350-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	261	276	0	ENST00000261769.5:c.1137+2T>G		p.X379_splice	ENST00000261769	NM_004360.3	379			0.663349649624196	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.663349649624196	1		276	515	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0001359-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	691	125	359	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.225012569056482	4	FACETS	1	0.983	1	0.716	0.648	0.788	CLONAL	1	FALSE	2	0.272268066292981	4		359	816	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682800	190682800	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs765594171	NA	P-0001359-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	506	139	212	0	ENST00000441310.2:c.476A>T	p.Tyr159Phe	p.Y159F	ENST00000441310	NM_000534.4	159	tAc/tTc	5/13	0.272268066292981	4	FACETS	1	0.919	1	1	0.919	1	CLONAL	2	FALSE	2	0.272268066292981	4		212	645	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139179	108139179	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs113482790	NA	P-0001359-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	489	109	282	0	ENST00000278616.4:c.2681A>G	p.Asp894Gly	p.D894G	ENST00000278616	NM_000051.3	894	gAt/gGt	18/63	0.272268066292981	3	FACETS	0.761	0.685	0.841	0.761	0.685	0.841	SUBCLONAL	2	FALSE	1	0.272268066292981	3		282	598	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0001411-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1361	169	412	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.3	1	FACETS	0.942	0.863	1	0.942	0.863	1	CLONAL	1	TRUE	0	0.21	1		413	1530	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0001411-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	127	395	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.21	2		395	1137	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371639	55371639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1270815957	NA	P-0001411-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	58	396	0	ENST00000297316.4:c.329C>T	p.Thr110Met	p.T110M	ENST00000297316	NM_022454.3	110	aCg/aTg	2/2	1	2	FACETS	0.826	0.709	0.954	0.826	0.709	0.954	CLONAL	1	TRUE	1	0.21	2		396	669	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32905069	32905069	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs372188754	NA	P-0001411-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	96	242	0	ENST00000380152.3:c.695A>G	p.Tyr232Cys	p.Y232C	ENST00000380152		232	tAt/tGt	9/27	1	2	FACETS	0.953	0.848	1	0.953	0.848	1	CLONAL	1	TRUE	1	0.21	2		242	959	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0001416-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	70	255	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.164492260124113	6	FACETS	0.955	0.844	1	0.795	0.703	0.892	CLONAL	5	TRUE	0	0.164492260124113	6		255	237	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367797	15367797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1195390127	NA	P-0001416-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	23	195	0	ENST00000263377.2:c.1529G>A	p.Arg510Gln	p.R510Q	ENST00000263377	NM_058243.2	510	cGg/cAg	8/20	0.0442635830897207	4	FACETS	1	0.8	1	1	0.8	1	INDETERMINATE	2	TRUE	2	0.164492260124113	4		195	160	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437159	52437162	+	frameshift_variant	Frame_Shift_Del	DEL	GTGA	GTGA	-	rs1559585778	NA	P-0001416-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	41	299	0	ENST00000460680.1:c.1882_1885del	p.Ser628ProfsTer8	p.S628Pfs*8	ENST00000460680	NM_004656.3	628	TCACcc/cc	14/17	0.0640324952640299	3	FACETS	0.89	0.75	1			1	INDETERMINATE	3	TRUE	NA	0.164492260124113	3		299	202	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638017	176638017	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001417-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	147	415	0	ENST00000439151.2:c.2617G>C	p.Gly873Arg	p.G873R	ENST00000439151	NM_022455.4	873	Ggt/Cgt	5/23	1	2	FACETS	0.934	0.858	1	0.934	0.858	1	CLONAL	1	TRUE	1	0.596989973890818	2		415	527	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665392	176665392	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001417-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	191	405	0	ENST00000439151.2:c.4076C>A	p.Ser1359Ter	p.S1359*	ENST00000439151	NM_022455.4	1359	tCa/tAa	7/23	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.596989973890818	2		405	627	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638017	176638017	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001417-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	59	415	0	ENST00000439151.2:c.2617G>C	p.Gly873Arg	p.G873R	ENST00000439151	NM_022455.4	873	Ggt/Cgt	5/23	1	2	FACETS	0.897	0.786	1	0.897	0.786	1	CLONAL	1	TRUE	1	0.730946825347781	2		415	180	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665392	176665392	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001417-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	113	405	0	ENST00000439151.2:c.4076C>A	p.Ser1359Ter	p.S1359*	ENST00000439151	NM_022455.4	1359	tCa/tAa	7/23	1	2	FACETS	0.928	0.846	1	0.928	0.846	1	CLONAL	1	TRUE	1	0.730946825347781	2		405	333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0001421-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	228	314	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.616733386804818	3	FACETS	0.989	0.955	1			1	CLONAL	3	TRUE	NA	0.76771645005638	3		314	277	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019198	31019198	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767144159	NA	P-0001421-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	241	540	0	ENST00000375687.4:c.793C>T	p.Arg265Cys	p.R265C	ENST00000375687	NM_015338.5	265	Cgt/Tgt	9/13	0.589973526328288	6	FACETS	0.854	0.799	0.911	0.569	0.532	0.608	CLONAL	2	TRUE	3	0.76771645005638	6		540	932	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0001440-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	182	276	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.353306000053194	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	0	0.373001070855489	3		276	349	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335065	65335065	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001440-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	104	300	0	ENST00000342505.4:c.576G>T	p.Met192Ile	p.M192I	ENST00000342505	NM_002227.2	192	atG/atT	6/25	0.373001070855489	4	FACETS	1	0.93	1	0.35	0.313	0.389	CLONAL	1	TRUE	1	0.373001070855489	4		300	730	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702662	52702662	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0001440-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	175	303	0	ENST00000394830.3:c.237-1G>C		p.X79_splice	ENST00000394830	NM_018313.4	79			0.373001070855489	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.373001070855489	2		303	440	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433934	149433934	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001440-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	99	370	0	ENST00000286301.3:c.2714A>T	p.Gln905Leu	p.Q905L	ENST00000286301	NM_005211.3	905	cAg/cTg	21/22	0.373001070855489	3	FACETS	1	0.933	1	0.353	0.315	0.393	CLONAL	1	TRUE	0	0.373001070855489	3		370	595	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967566	26967566	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs369889152	NA	P-0001440-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	233	438	0	ENST00000381527.3:c.709C>T	p.Arg237Ter	p.R237*	ENST00000381527	NM_001260.1	237	Cga/Tga	7/13	1	2	FACETS	0.869	0.814	0.925	1	0.994	1	CLONAL	2	TRUE	1	0.373001070855489	2		438	719	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440912	52440912	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1205668341	NA	P-0001440-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	85	293	1	ENST00000460680.1:c.592del	p.Glu198ArgfsTer33	p.E198Rfs*33	ENST00000460680	NM_004656.3	198	Gag/ag	8/17	0.373001070855489	2	FACETS	0.863	0.765	0.968	0.432	0.382	0.484	CLONAL	1	TRUE	0	0.373001070855489	2		294	528	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0001456-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	31	302	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	NA	2	FACETS	0.476	0.386	0.577			1	INDETERMINATE	1	FALSE	NA	0.466622423576597	2		302	279	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478851	56478851	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001456-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	73	384	0	ENST00000267101.3:c.307C>G	p.Arg103Gly	p.R103G	ENST00000267101	NM_001982.3	103	Cgc/Ggc	3/28	0.178606547034998	4	FACETS	1	0.941	1	0.56	0.492	0.632	INDETERMINATE	1	FALSE	2	0.466622423576597	4		384	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782177	NA	P-0001456-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	21	362	0	ENST00000269305.4:c.644G>C	p.Ser215Thr	p.S215T	ENST00000269305	NM_001126112.2	215	aGt/aCt	6/11	1	2	FACETS	0.333	0.257	0.422	0.333	0.257	0.422	SUBCLONAL	1	FALSE	1	0.466622423576597	2		362	270	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164703	36164703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001456-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	48	262	0	ENST00000300305.3:c.1172C>T	p.Ala391Val	p.A391V	ENST00000300305		391	gCg/gTg	8/8	0.162212823844104	3	FACETS	1	0.89	1	0.526	0.449	0.61	INDETERMINATE	1	FALSE	1	0.466622423576597	3		262	241	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0001459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	21	261	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.389686401287222	2		261	97	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691025	NA	P-0001459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	226	356	0	ENST00000269305.4:c.785G>T	p.Gly262Val	p.G262V	ENST00000269305	NM_001126112.2	262	gGt/gTt	8/11	0.345394667942295	3	FACETS	0.87	0.818	0.922	0.87	0.818	0.922	CLONAL	3	TRUE	0	0.389686401287222	3		356	531	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371734	55371734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	34	129	0	ENST00000297316.4:c.424C>T	p.Arg142Cys	p.R142C	ENST00000297316	NM_022454.3	142	Cgc/Tgc	2/2	0.389686401287222	4	FACETS	0.811	0.665	0.974	0.406	0.332	0.487	CLONAL	1	TRUE	2	0.389686401287222	4		129	299	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858913	89858913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199967286	NA	P-0001459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	29	152	0	ENST00000389301.3:c.1049G>A	p.Arg350Gln	p.R350Q	ENST00000389301	NM_000135.2	350	cGg/cAg	12/43	0.117709210670446	4	FACETS	0.455	0.364	0.558	0.227	0.182	0.279	INDETERMINATE	1	TRUE	2	0.389686401287222	4		152	455	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735470	40735470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761910971	NA	P-0001459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	139	312	0	ENST00000373198.4:c.3403G>A	p.Val1135Met	p.V1135M	ENST00000373198	NM_133170.3	1135	Gtg/Atg	25/32	0.385647611105128	4	FACETS	0.847	0.774	0.923	0.847	0.774	0.923	CLONAL	2	TRUE	2	0.389686401287222	4		312	585	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001459-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	55	280	0	ENST00000257430.4:c.3340del	p.Arg1114GlufsTer12	p.R1114Efs*12	ENST00000257430	NM_000038.5	1114	Cga/ga	16/16	0.233024803317507	1	FACETS	0.848	0.732	0.973	0.848	0.732	0.973	INDETERMINATE	1	TRUE	0	0.389686401287222	1		280	268	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0001463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	93	261	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.273263518433234	4	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	2	0.273263518433234	4		261	411	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652129	36652129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34916193	NA	P-0001463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	108	217	0	ENST00000244741.5:c.251G>A	p.Arg84Gln	p.R84Q	ENST00000244741	NM_000389.4	84	cGa/cAa	2/3	0.273263518433234	3	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.273263518433234	3		217	638	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087917	27087917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142353005	NA	P-0001463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	40	211	0	ENST00000324856.7:c.2204G>A	p.Ser735Asn	p.S735N	ENST00000324856	NM_006015.4	735	aGc/aAc	6/20	0.273263518433234	3	FACETS	0.511	0.424	0.609	0.256	0.212	0.305	SUBCLONAL	1	TRUE	1	0.273263518433234	3		211	651	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441310	52441310	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	268	311	0	ENST00000460680.1:c.460G>T	p.Glu154Ter	p.E154*	ENST00000460680	NM_004656.3	154	Gag/Tag	7/17	0.273263518433234	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.273263518433234	2		311	858	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970899	55970899	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	127	347	0	ENST00000263923.4:c.1898C>A	p.Ser633Tyr	p.S633Y	ENST00000263923	NM_002253.2	633	tCc/tAc	13/30	0.273263518433234	3	FACETS	1	0.917	1	0.507	0.459	0.559	CLONAL	1	TRUE	1	0.273263518433234	3		347	1041	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891615	151891615	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	90	191	0	ENST00000262189.6:c.4417C>T	p.Gln1473Ter	p.Q1473*	ENST00000262189	NM_170606.2	1473	Cag/Tag	29/59	NA	2	FACETS	1	0.947	1			1	INDETERMINATE	1	TRUE	NA	0.273263518433234	2		191	592	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504390	8504390	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	81	222	0	ENST00000356435.5:c.1693G>A	p.Glu565Lys	p.E565K	ENST00000356435		565	Gag/Aag	12/35	NA	2	FACETS	1	0.92	1			1	INDETERMINATE	1	TRUE	NA	0.273263518433234	2		222	562	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125523707	125523707	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	113	314	0	ENST00000428830.2:c.1300G>C	p.Asp434His	p.D434H	ENST00000428830	NM_001114121.2	434	Gat/Cat	12/14	1	2	FACETS	0.998	0.897	1	0.998	0.897	1	CLONAL	1	TRUE	1	0.273263518433234	2		314	829	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243484	46243484	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	94	296	0	ENST00000334344.6:c.1837C>G	p.Gln613Glu	p.Q613E	ENST00000334344	NM_152641.2	613	Cag/Gag	14/21	1	2	FACETS	0.849	0.755	0.95	0.849	0.755	0.95	CLONAL	1	TRUE	1	0.273263518433234	2		296	810	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253176	133253176	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	107	299	0	ENST00000320574.5:c.865G>A	p.Glu289Lys	p.E289K	ENST00000320574	NM_006231.2	289	Gag/Aag	9/49	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.273263518433234	2		299	668	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136858	2136858	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	89	226	0	ENST00000219476.3:c.4975C>G	p.Leu1659Val	p.L1659V	ENST00000219476	NM_000548.3	1659	Ctt/Gtt	38/42	0.218243725326406	4	FACETS	1	0.928	1	0.532	0.471	0.597	CLONAL	1	TRUE	2	0.273263518433234	4		226	779	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166342	7166342	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	52	345	0	ENST00000302850.5:c.1684G>C	p.Asp562His	p.D562H	ENST00000302850	NM_000208.2	562	Gac/Cac	8/22	1	2	FACETS	0.482	0.409	0.563	0.482	0.409	0.563	SUBCLONAL	1	TRUE	1	0.273263518433234	2		345	789	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39746883	39746883	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	55	126	0	ENST00000361337.2:c.1897C>T	p.Gln633Ter	p.Q633*	ENST00000361337	NM_003286.2	633	Cag/Tag	18/21	0.273263518433234	5	FACETS	1	0.875	1	0.341	0.292	0.396	CLONAL	1	TRUE	2	0.273263518433234	5		126	554	SUCCESS
AR	367	MSKCC	GRCh37	X	66863117	66863117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	166	535	0	ENST00000374690.3:c.1636C>T	p.His546Tyr	p.H546Y	ENST00000374690	NM_000044.3	546	Cat/Tat	2/8	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.273263518433234	2		535	1122	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613331	100613331	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	91	369	0	ENST00000308731.7:c.1069G>C	p.Glu357Gln	p.E357Q	ENST00000308731	NM_000061.2	357	Gag/Cag	12/19	1	2	FACETS	0.766	0.68	0.859	0.766	0.68	0.859	SUBCLONAL	1	TRUE	1	0.273263518433234	2		369	869	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147720	61147721	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0001463-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	94	245	0	ENST00000295025.8:c.1030_1031delinsAT	p.Glu344Met	p.E344M	ENST00000295025	NM_002908.2	344	GAg/ATg	10/11	0.273263518433234	3	FACETS	0.914	0.812	1	0.457	0.406	0.511	CLONAL	1	TRUE	1	0.273263518433234	3		245	856	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0001472-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	162	338	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.407503614644137	3	FACETS	1	0.965	1			1	CLONAL	3	FALSE	NA	0.438842132064946	3		338	288	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876181	35876181	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001472-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	22	268	0	ENST00000303115.3:c.973C>T	p.Gln325Ter	p.Q325*	ENST00000303115	NM_002185.3	325	Caa/Taa	8/8	0.386908078222418	4	FACETS	0.443	0.343	0.558	0.221	0.171	0.279	SUBCLONAL	1	FALSE	2	0.438842132064946	4		268	326	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625435	69625435	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376445217	NA	P-0001472-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	155	292	0	ENST00000334134.2:c.358C>T	p.Arg120Trp	p.R120W	ENST00000334134	NM_005247.2	120	Cgg/Tgg	3/3	0.386908078222418	4	FACETS	0.934	0.86	1	0.934	0.86	1	CLONAL	2	FALSE	2	0.438842132064946	4		292	544	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124561	108124563	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs876659575	NA	P-0001472-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	90	240	0	ENST00000278616.4:c.1924_1926del	p.Glu642del	p.E642del	ENST00000278616	NM_000051.3	640	aAAGaa/aaa	13/63	0.386908078222418	4	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	FALSE	2	0.438842132064946	4		240	255	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576904	7576904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001472-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	370	255	0	ENST00000269305.4:c.942del	p.Ser315LeufsTer30	p.S315Lfs*30	ENST00000269305	NM_001126112.2	314	tcC/tc	9/11	0.438842132064946	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	4	FALSE	0	0.438842132064946	4		255	546	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382185	152382185	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001483-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	69	217	0	ENST00000206249.3:c.1295C>T	p.Ser432Leu	p.S432L	ENST00000206249	NM_000125.3	432	tCa/tTa	6/8	0.314715119167013	3	FACETS	1	0.967	1			1	CLONAL	1	TRUE	NA	0.395559165029446	3		217	317	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55130030	55130030	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001483-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	41	412	0	ENST00000257290.5:c.564C>G	p.Ile188Met	p.I188M	ENST00000257290	NM_006206.4	188	atC/atG	4/23	0.248563056557488	1	FACETS	0.554	0.464	0.654	0.554	0.464	0.654	SUBCLONAL	1	TRUE	0	0.395559165029446	1		412	300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0001489-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	91	367	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	0.748995642445412	1	FACETS	0.993	0.914	1	0.993	0.914	1	CLONAL	1	TRUE	0	0.748995642445412	1		367	153	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231357	5231357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001489-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	93	657	0	ENST00000357368.4:c.2119G>A	p.Glu707Lys	p.E707K	ENST00000357368	NM_002850.3	707	Gag/Aag	14/38	NA	2	FACETS	0.556	0.496	0.618			1	INDETERMINATE	1	TRUE	NA	0.748995642445412	2		657	447	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115875	8115879	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCT	GCCCT	-	novel	NA	P-0001489-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	96	676	0	ENST00000346208.3:c.1221_1225del	p.Pro408GlnfsTer97	p.P408Qfs*97	ENST00000346208		407	tcGCCCTtc/tctc	6/6	0.257725455581422	3	FACETS	0.684	0.612	0.761	0.228	0.204	0.254	INDETERMINATE	1	TRUE	0	0.748995642445412	3		676	515	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421897	49421897	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001493-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	166	493	0	ENST00000301067.7:c.14410G>C	p.Ala4804Pro	p.A4804P	ENST00000301067	NM_003482.3	4804	Gcg/Ccg	46/54	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.265549258646093	2		493	912	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911181	32911181	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs979372317	NA	P-0001493-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	89	488	0	ENST00000380152.3:c.2689G>T	p.Glu897Ter	p.E897*	ENST00000380152		897	Gaa/Taa	11/27	0.265549258646093	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.265549258646093	1		488	510	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061215	38061235	+	inframe_deletion	In_Frame_Del	DEL	GCAGCCGTTCTCGAACATGTT	GCAGCCGTTCTCGAACATGTT	-	novel	NA	P-0001493-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	127	481	0	ENST00000250448.2:c.754_774del	p.Asn252_Cys258del	p.N252_C258del	ENST00000250448	NM_004496.3	252	AACATGTTCGAGAACGGCTGC/-	2/2	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.265549258646093	2		481	831	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0001499-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	120	228	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.250714628601002	4	FACETS	1	0.948	1	0.539	0.486	0.595	CLONAL	1	FALSE	2	0.290142898896359	4		228	990	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001499-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	81	389	0	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	0.178773858884867	2	FACETS	1	0.963	1	0.611	0.54	0.686	CLONAL	1	FALSE	0	0.290142898896359	2		389	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576881	7576881	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001499-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	109	432	0	ENST00000269305.4:c.965del	p.Pro322HisfsTer23	p.P322Hfs*23	ENST00000269305	NM_001126112.2	322	cCa/ca	9/11	0.250714628601002	4	FACETS	0.846	0.762	0.934	0.846	0.762	0.934	CLONAL	2	FALSE	2	0.290142898896359	4		432	573	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115722	8115722	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001505-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	134	437	0	ENST00000346208.3:c.1068G>A	p.Met356Ile	p.M356I	ENST00000346208		356	atG/atA	6/6	1	2	FACETS	0.778	0.71	0.849	1	0.987	1	SUBCLONAL	2	TRUE	1	0.312610314909647	2		437	551	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793442	42793442	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748865223	NA	P-0001505-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	46	259	0	ENST00000575354.2:c.1244G>A	p.Arg415Gln	p.R415Q	ENST00000575354	NM_015125.3	415	cGg/cAg	8/20	NA	2	FACETS	0.892	0.754	1			1	INDETERMINATE	1	TRUE	NA	0.312610314909647	2		259	330	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788617	3788617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519884	NA	P-0001511-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	61	826	0	ENST00000262367.5:c.4337G>A	p.Arg1446His	p.R1446H	ENST00000262367	NM_004380.2	1446	cGc/cAc	26/31	1	2	FACETS	0.563	0.483	0.649	0.563	0.483	0.649	SUBCLONAL	1	TRUE	1	0.197491166797791	2		826	1098	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989553	212989553	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs756650586	NA	P-0001511-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	115	611	0	ENST00000342788.4:c.158A>G	p.Tyr53Cys	p.Y53C	ENST00000342788	NM_005235.2	53	tAt/tGt	2/28	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.197491166797791	2		611	910	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59934523	59934523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001511-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	150	756	0	ENST00000259008.2:c.275C>T	p.Ser92Leu	p.S92L	ENST00000259008	NM_032043.2	92	tCa/tTa	4/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.197491166797791	2		756	1288	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374293	138374293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001521-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	291	618	0	ENST00000289153.2:c.3151G>A	p.Glu1051Lys	p.E1051K	ENST00000289153	NM_006219.2	1051	Gaa/Aaa	22/22	1	2	FACETS	0.98	0.924	1	0.98	0.924	1	CLONAL	1	TRUE	1	0.640213653130523	2		618	928	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286214	66286214	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001521-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	255	586	0	ENST00000273854.3:c.1472A>T	p.Glu491Val	p.E491V	ENST00000273854	NM_004439.5	491	gAa/gTa	6/18	1	2	FACETS	0.96	0.901	1	0.96	0.901	1	CLONAL	1	TRUE	1	0.640213653130523	2		586	830	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628482	187628482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001521-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	224	566	0	ENST00000441802.2:c.2500G>A	p.Asp834Asn	p.D834N	ENST00000441802	NM_005245.3	834	Gac/Aac	2/27	1	2	FACETS	0.835	0.779	0.893	0.835	0.779	0.893	CLONAL	1	TRUE	1	0.640213653130523	2		566	838	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392161	81392161	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001521-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	686	460	0	ENST00000222390.5:c.116T>G	p.Ile39Ser	p.I39S	ENST00000222390	NM_000601.4	39	aTt/aGt	2/18	0.640213653130523	4	FACETS	0.959	0.93	0.988	0.959	0.93	0.988	CLONAL	3	TRUE	1	0.640213653130523	4		460	1222	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772907	135772907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203732	NA	P-0001521-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	331	651	0	ENST00000298552.3:c.2716C>T	p.Gln906Ter	p.Q906*	ENST00000298552	NM_001162426.1	906	Caa/Taa	21/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.640213653130523	2		651	1000	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781467	135781467	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203537	NA	P-0001521-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	176	333	0	ENST00000298552.3:c.1498C>T	p.Arg500Ter	p.R500*	ENST00000298552	NM_001162426.1	500	Cga/Tga	15/23	1	2	FACETS	0.958	0.888	1	0.958	0.888	1	CLONAL	1	TRUE	1	0.640213653130523	2		333	574	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623896	28623896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001521-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	135	343	0	ENST00000241453.7:c.758C>T	p.Pro253Leu	p.P253L	ENST00000241453	NM_004119.2	253	cCt/cTt	7/24	1	2	FACETS	0.921	0.843	1	0.921	0.843	1	CLONAL	1	TRUE	1	0.640213653130523	2		343	458	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0001547-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	669	470	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.239802021228567	6	FACETS	1	0.991	1	1	0.991	1	CLONAL	5	TRUE	1	0.239802021228567	6		470	1545	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27093058	27093058	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0001547-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	319	294	0	ENST00000324856.7:c.2988+1G>T		p.X996_splice	ENST00000324856	NM_006015.4	996			1	2	FACETS	0.838	0.792	0.885	1	0.996	1	CLONAL	3	TRUE	1	0.239802021228567	2		294	1058	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252086	133252086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778572159	NA	P-0001547-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	79	332	0	ENST00000320574.5:c.1124G>A	p.Arg375Gln	p.R375Q	ENST00000320574	NM_006231.2	375	cGg/cAg	12/49	1	2	FACETS	0.775	0.681	0.877	0.775	0.681	0.877	SUBCLONAL	1	TRUE	1	0.239802021228567	2		332	850	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435798	110435798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1240854451	NA	P-0001547-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	16	41	0	ENST00000375856.3:c.2603C>T	p.Ser868Leu	p.S868L	ENST00000375856	NM_003749.2	868	tCg/tTg	1/2	0.239802021228567	5	FACETS	1	0.889	1	0.357	0.266	0.464	CLONAL	1	TRUE	1	0.239802021228567	5		41	127	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438291	56438291	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001547-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	150	276	0	ENST00000407977.2:c.702G>C	p.Gln234His	p.Q234H	ENST00000407977		234	caG/caC	7/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.239802021228567	2		276	846	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106210	27106210	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001547-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	93	282	0	ENST00000324856.7:c.5823del	p.Phe1941LeufsTer15	p.F1941Lfs*15	ENST00000324856	NM_006015.4	1941	Ttt/tt	20/20	1	2	FACETS	0.773	0.685	0.866	0.773	0.685	0.866	SUBCLONAL	1	TRUE	1	0.239802021228567	2		282	1004	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782144	NA	P-0001564-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	82	418	0	ENST00000269305.4:c.473G>C	p.Arg158Pro	p.R158P	ENST00000269305	NM_001126112.2	158	cGc/cCc	5/11	0.339644068690779	1	FACETS	0.878	0.782	0.978	0.878	0.782	0.978	CLONAL	1	TRUE	0	0.473640696987914	1		418	301	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890142	76890145	+	frameshift_variant	Frame_Shift_Del	DEL	TTTC	TTTC	-	novel	NA	P-0001564-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	170	786	0	ENST00000373344.5:c.4749_4752del	p.Lys1583AsnfsTer22	p.K1583Nfs*22	ENST00000373344	NM_000489.3	1583	aaGAAA/aa	17/35	0.328611239208329	1	FACETS	0.813	0.75	0.878	0.813	0.75	0.878	CLONAL	1	TRUE	0	0.473640696987914	1		786	674	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711939	89711940	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0001564-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	90	460	0	ENST00000371953.3:c.557_558del	p.Leu186ArgfsTer3	p.L186Rfs*3	ENST00000371953	NM_000314.4	186	cTG/c	6/9	0.473640696987914	1	FACETS	0.861	0.771	0.955	0.861	0.771	0.955	CLONAL	1	TRUE	0	0.473640696987914	1		460	337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0001565-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	337	280	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.776278271771414	1	FACETS	0.971	0.932	1	0.971	0.932	1	CLONAL	1	TRUE	0	0.776278271771414	1		280	547	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0001565-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	412	252	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.776278271771414	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	1	0.776278271771414	4		252	609	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244905	46244905	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001565-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	447	455	0	ENST00000334344.6:c.2999C>A	p.Pro1000His	p.P1000H	ENST00000334344	NM_152641.2	1000	cCt/cAt	15/21	1	2	FACETS	0.866	0.826	0.906	0.866	0.826	0.906	CLONAL	1	TRUE	1	0.776278271771414	2		455	1330	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426550	49426550	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001565-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	597	431	0	ENST00000301067.7:c.11938C>T	p.Gln3980Ter	p.Q3980*	ENST00000301067	NM_003482.3	3980	Cag/Tag	39/54	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.776278271771414	2		431	1486	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716327	52716327	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001565-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	369	305	0	ENST00000322088.6:c.771G>C	p.Trp257Cys	p.W257C	ENST00000322088	NM_014225.5	257	tgG/tgC	6/15	NA	2	FACETS	0.988	0.94	1			1	INDETERMINATE	1	TRUE	NA	0.776278271771414	2		305	962	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961338	54961338	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs369728775	NA	P-0001565-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	329	338	0	ENST00000312783.6:c.294C>G	p.Ser98Arg	p.S98R	ENST00000312783	NM_198436.1	98	agC/agG	4/10	NA	2	FACETS	0.899	0.852	0.947			1	INDETERMINATE	1	TRUE	NA	0.776278271771414	2		338	943	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0001571-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	293	693	308	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.303758220364817	3	FACETS	0.947	0.923	0.97	0.947	0.923	0.97	INDETERMINATE	3	TRUE	0	0.657651264822962	3		308	986	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0001571-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	226	462	418	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.61830016906142	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.657651264822962	2		418	688	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551535	150551535	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs773866164	NA	P-0001571-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	1824	427	608	0	ENST00000369026.2:c.472G>C	p.Gly158Arg	p.G158R	ENST00000369026	NM_021960.4	158	Ggg/Cgg	1/3	0.382650749587513	6	FACETS	1	0.994	1	0.445	0.422	0.469	INDETERMINATE	1	TRUE	3	0.657651264822962	6		608	2251	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275760	41275760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001571-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	500	359	525	2	ENST00000349496.5:c.1655C>T	p.Ser552Phe	p.S552F	ENST00000349496	NM_001904.3	552	tCc/tTc	10/15	0.310783375236137	1	FACETS	0.853	0.812	0.894	0.853	0.812	0.894	INDETERMINATE	1	TRUE	0	0.657651264822962	1		527	859	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391146	89391146	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001571-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	534	93	425	0	ENST00000336596.2:c.1212C>A	p.Asn404Lys	p.N404K	ENST00000336596	NM_005233.5	404	aaC/aaA	5/17	0.647046967488595	1	FACETS	0.303	0.269	0.338	0.303	0.269	0.338	SUBCLONAL	1	TRUE	0	0.657651264822962	1		425	627	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205872	128205872	+	start_lost	Translation_Start_Site	SNP	C	C	A	novel	NA	P-0001571-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	314	58	180	0	ENST00000341105.2:c.3G>T	p.Met1?	p.M1?	ENST00000341105	NM_032638.4	1	atG/atT	2/6	0.332574079187564	2	FACETS	0.474	0.409	0.545	0.237	0.204	0.273	INDETERMINATE	1	TRUE	0	0.657651264822962	2		180	372	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55963864	55963864	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001571-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	800	758	608	1	ENST00000263923.4:c.2579C>A	p.Ala860Glu	p.A860E	ENST00000263923	NM_002253.2	860	gCa/gAa	18/30	0.657651264822962	3	FACETS	0.983	0.952	1	0.983	0.952	1	CLONAL	2	TRUE	1	0.657651264822962	3		609	1558	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539963	187539963	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001571-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	353	651	463	0	ENST00000441802.2:c.7777G>C	p.Ala2593Pro	p.A2593P	ENST00000441802	NM_005245.3	2593	Gca/Cca	10/27	0.657651264822962	2	FACETS	0.986	0.958	1	0.986	0.958	1	CLONAL	2	TRUE	0	0.657651264822962	2		463	1004	SUCCESS
APC	324	MSKCC	GRCh37	5	112177701	112177701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554087411	NA	P-0001571-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	670	138	375	0	ENST00000257430.4:c.6410C>T	p.Ser2137Phe	p.S2137F	ENST00000257430	NM_000038.5	2137	tCc/tTc	16/16	0.61830016906142	2	FACETS	0.519	0.473	0.568	0.26	0.236	0.284	SUBCLONAL	1	TRUE	0	0.657651264822962	2		375	808	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048868	180048868	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001571-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	1124	119	446	0	ENST00000261937.6:c.1694C>G	p.Ser565Cys	p.S565C	ENST00000261937	NM_182925.4	565	tCc/tGc	13/30	0.548725281377151	3	FACETS	0.387	0.348	0.428			1	SUBCLONAL	1	TRUE	NA	0.657651264822962	3		446	1243	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056966	180056966	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001571-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	1323	143	645	0	ENST00000261937.6:c.653A>G	p.Asn218Ser	p.N218S	ENST00000261937	NM_182925.4	218	aAc/aGc	5/30	0.548725281377151	3	FACETS	0.394	0.358	0.433			1	SUBCLONAL	1	TRUE	NA	0.657651264822962	3		645	1466	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413103	139413103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746187371	NA	P-0001571-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	1102	229	498	0	ENST00000277541.6:c.1039G>A	p.Gly347Ser	p.G347S	ENST00000277541	NM_017617.3	347	Ggc/Agc	6/34	0.630584652056024	3	FACETS	0.695	0.646	0.746	0.232	0.215	0.249	SUBCLONAL	1	TRUE	0	0.657651264822962	3		498	1331	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432139	121432139	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001571-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	812	155	565	0	ENST00000257555.6:c.886G>T	p.Gly296Ter	p.G296*	ENST00000257555		296	Gga/Tga	4/10	0.332574079187564	2	FACETS	0.487	0.446	0.531	0.244	0.223	0.266	INDETERMINATE	1	TRUE	0	0.657651264822962	2		565	967	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202265	133202265	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001571-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	505	596	481	0	ENST00000320574.5:c.6623A>G	p.Gln2208Arg	p.Q2208R	ENST00000320574	NM_006231.2	2208	cAg/cGg	47/49	0.332574079187564	2	FACETS	0.823	0.796	0.85	0.823	0.796	0.85	INDETERMINATE	2	TRUE	0	0.657651264822962	2		481	1101	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823824	3823824	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001571-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	795	101	466	0	ENST00000262367.5:c.2391C>G	p.Asn797Lys	p.N797K	ENST00000262367	NM_004380.2	797	aaC/aaG	13/31	NA	2	FACETS	0.343	0.306	0.382			1	INDETERMINATE	1	TRUE	NA	0.657651264822962	2		466	896	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974774	21974774	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001571-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	198	254	299	0	ENST00000304494.5:c.53del	p.Thr18ArgfsTer8	p.T18Rfs*8	ENST00000304494	NM_000077.4	18	aCg/ag	1/3	0.641417618661003	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.657651264822962	1		299	452	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712007	89712008	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0001571-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	282	135	167	0	ENST00000371953.3:c.625_626delinsTT	p.Gly209Leu	p.G209L	ENST00000371953	NM_000314.4	209	GGa/TTa	6/9	1	2	FACETS	0.985	0.903	1	0.985	0.903	1	CLONAL	1	TRUE	1	0.657651264822962	2		167	417	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0001574-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	364	358	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA	2	FACETS	0.838	0.794	0.884			1	INDETERMINATE	1	TRUE	NA	0.613901543407557	2		358	1415	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099008	27099008	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001574-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	435	411	0	ENST00000324856.7:c.3424C>T	p.Gln1142Ter	p.Q1142*	ENST00000324856	NM_006015.4	1142	Cag/Tag	13/20	0.535626339760909	2	FACETS	0.843	0.809	0.876	0.843	0.809	0.876	CLONAL	2	TRUE	0	0.613901543407557	2		411	841	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138201360	138201360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001574-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	270	293	1	ENST00000237289.4:c.2059C>T	p.His687Tyr	p.H687Y	ENST00000237289	NM_001270507.1	687	Cat/Tat	8/9	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.613901543407557	2		294	634	SUCCESS
MET	4233	MSKCC	GRCh37	7	116409781	116409781	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001574-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	418	461	3	ENST00000397752.3:c.2666C>G	p.Ser889Cys	p.S889C	ENST00000397752	NM_000245.2	889	tCt/tGt	12/21	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.613901543407557	2		464	1136	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218500	1218500	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1131690951	NA	P-0001574-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	308	325	5	ENST00000326873.7:c.374+1A>G		p.X125_splice	ENST00000326873	NM_000455.4	125			0.472450233448522	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.613901543407557	1		330	695	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126772	5126772	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001574-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	251	433	0	ENST00000381652.3:c.3382del	p.Asp1128IlefsTer39	p.D1128Ifs*39	ENST00000381652	NM_004972.3	1127	aGg/ag	25/25	NA	2	FACETS	0.912	0.854	0.97			1	INDETERMINATE	1	TRUE	NA	0.613901543407557	2		433	897	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610211	10610211	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001574-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	434	489	1	ENST00000171111.5:c.499del	p.Val167LeufsTer63	p.V167Lfs*63	ENST00000171111	NM_203500.1	167	Gtt/tt	2/6	0.613901543407557	1	FACETS	0.971	0.929	1	0.971	0.929	1	CLONAL	1	TRUE	0	0.613901543407557	1		490	1009	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265331	16265331	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001580-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	277	330	0	ENST00000375759.3:c.10823C>A	p.Ala3608Glu	p.A3608E	ENST00000375759	NM_015001.2	3608	gCg/gAg	14/15	0.471061547577697	3	FACETS	0.888	0.838	0.939	0.888	0.838	0.939	CLONAL	2	FALSE	1	0.521531625714674	3		330	754	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564083	139564083	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs574267042	NA	P-0001580-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	136	304	0	ENST00000308874.7:c.223C>T	p.Arg75Cys	p.R75C	ENST00000308874		75	Cgc/Tgc	5/10	0.521531625714674	3	FACETS	1	0.919	1	0.504	0.459	0.551	CLONAL	1	FALSE	1	0.521531625714674	3		304	652	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0001583-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	189	258	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	NA	2	FACETS	0.985	0.912	1			1	INDETERMINATE	1	TRUE	NA	0.491465150293247	2		258	781	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0001583-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	207	409	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.965	0.897	1	0.965	0.897	1	CLONAL	1	TRUE	1	0.491465150293247	2		409	873	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0001583-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	229	472	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.491465150293247	1	FACETS	0.857	0.801	0.915	0.857	0.801	0.915	CLONAL	1	TRUE	0	0.491465150293247	1		472	820	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254644	16254644	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001583-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	387	325	0	ENST00000375759.3:c.1909C>T	p.Arg637Ter	p.R637*	ENST00000375759	NM_015001.2	637	Cga/Tga	11/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.491465150293247	2		325	1430	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057642	27057642	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0001583-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	311	327	0	ENST00000324856.7:c.1351-1G>C		p.X451_splice	ENST00000324856	NM_006015.4	451			1	2	FACETS	0.971	0.914	1	0.971	0.914	1	CLONAL	1	TRUE	1	0.491465150293247	2		327	1304	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0001583-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	212	253	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.491465150293247	2		253	733	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702600	52702600	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0001583-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	289	293	0	ENST00000394830.3:c.298A>T	p.Lys100Ter	p.K100*	ENST00000394830	NM_018313.4	100	Aaa/Taa	4/30	0.491465150293247	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.491465150293247	1		293	763	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938835	178938835	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500029	NA	P-0001583-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	44	12	0	ENST00000263967.3:c.2077C>T	p.Arg693Cys	p.R693C	ENST00000263967	NM_006218.2	693	Cgt/Tgt	14/21	1	2	FACETS	1	0.913	1	1	0.977	1	CLONAL	2	TRUE	1	0.491465150293247	2		12	85	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280022	66280022	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001583-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	245	282	0	ENST00000273854.3:c.1667A>C	p.Glu556Ala	p.E556A	ENST00000273854	NM_004439.5	556	gAg/gCg	7/18	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.491465150293247	2		282	984	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4387986	4387986	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001583-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	347	281	0	ENST00000261254.3:c.472G>A	p.Asp158Asn	p.D158N	ENST00000261254	NM_001759.3	158	Gac/Aac	3/5	0.302830876903128	3	FACETS	1	0.994	1	0.691	0.654	0.73	CLONAL	1	TRUE	1	0.491465150293247	3		281	1272	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125251	47125260	+	frameshift_variant	Frame_Shift_Del	DEL	CACTTATATC	CACTTATATC	-	novel	NA	P-0001583-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	215	352	0	ENST00000409792.3:c.6010_6019del	p.Asp2004IlefsTer13	p.D2004Ifs*13	ENST00000409792	NM_014159.6	2004	GATATAAGTGat/at	12/21	0.491465150293247	1	FACETS	0.775	0.721	0.83	0.775	0.721	0.83	SUBCLONAL	1	TRUE	0	0.491465150293247	1		352	852	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133724	55133724	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001591-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1292	323	709	0	ENST00000257290.5:c.937G>C	p.Gly313Arg	p.G313R	ENST00000257290	NM_006206.4	313	Ggt/Cgt	7/23	1	2	FACETS	0.929	0.875	0.985	0.929	0.875	0.985	CLONAL	1	TRUE	1	0.430525223444692	2		709	1615	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141018	55141018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121908589	NA	P-0001591-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	329	575	0	ENST00000257290.5:c.1664A>G	p.Tyr555Cys	p.Y555C	ENST00000257290	NM_006206.4	555	tAt/tGt	12/23	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.430525223444692	2		575	1156	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027020	71027020	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	88	369	1	ENST00000318789.4:c.1307G>A	p.Arg436His	p.R436H	ENST00000318789	NM_032682.5	436	cGc/cAc	15/21	0.638628224797047	4	FACETS	0.881	0.783	0.984			1	CLONAL	1	TRUE	NA	0.705587770843902	4		370	483	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434856	99434856	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201956526	NA	P-0001596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1306	329	262	0	ENST00000268035.6:c.943G>A	p.Gly315Ser	p.G315S	ENST00000268035	NM_000875.3	315	Ggc/Agc	3/21	0.705587770843902	21	FACETS	1	0.982	1			1	CLONAL	4	TRUE	NA	0.705587770843902	21		262	1635	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573090	41573090	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	53	524	0	ENST00000263253.7:c.5375A>G	p.His1792Arg	p.H1792R	ENST00000263253	NM_001429.3	1792	cAt/cGt	31/31	NA	2	FACETS	0.766	0.663	0.876			1	INDETERMINATE	1	TRUE	NA	0.705587770843902	2		524	196	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577537	7577538	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	684	413	2	ENST00000269305.4:c.743_744delinsAA	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGG/cAA	7/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.925172120479527	2		415	1401	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498004	29498004	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1208550472	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	1017	646	0	ENST00000389048.3:c.2002G>A	p.Glu668Lys	p.E668K	ENST00000389048	NM_004304.4	668	Gaa/Aaa	11/29	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.925172120479527	2		646	2098	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416417	49416417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565753611	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	999	488	1	ENST00000301067.7:c.16294C>T	p.Arg5432Trp	p.R5432W	ENST00000301067	NM_003482.3	5432	Cgg/Tgg	51/54	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.925172120479527	2		489	2127	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101270	27101270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	705	477	1	ENST00000324856.7:c.4552C>T	p.Pro1518Ser	p.P1518S	ENST00000324856	NM_006015.4	1518	Ccc/Tcc	18/20	1	2	FACETS	0.92	0.888	0.951	0.92	0.888	0.951	CLONAL	1	TRUE	1	0.925172120479527	2		478	1657	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807544	36807544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775585540	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	671	473	1	ENST00000373129.3:c.1120G>A	p.Glu374Lys	p.E374K	ENST00000373129	NM_032017.1	374	Gag/Aag	12/12	1	2	FACETS	0.981	0.947	1	0.981	0.947	1	CLONAL	1	TRUE	1	0.925172120479527	2		474	1479	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36824421	36824421	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	816	488	0	ENST00000373129.3:c.115C>T	p.Pro39Ser	p.P39S	ENST00000373129	NM_032017.1	39	Ccc/Tcc	4/12	1	2	FACETS	0.982	0.951	1	0.982	0.951	1	CLONAL	1	TRUE	1	0.925172120479527	2		488	1797	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335121	65335121	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	744	455	1	ENST00000342505.4:c.520C>T	p.Arg174Ter	p.R174*	ENST00000342505	NM_002227.2	174	Cga/Tga	6/25	1	2	FACETS	0.973	0.941	1	0.973	0.941	1	CLONAL	1	TRUE	1	0.925172120479527	2		456	1653	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555956	226555956	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	739	433	0	ENST00000366794.5:c.2221C>T	p.Pro741Ser	p.P741S	ENST00000366794	NM_001618.3	741	Ccc/Tcc	16/23	1	2	FACETS	0.986	0.954	1	0.986	0.954	1	CLONAL	1	TRUE	1	0.925172120479527	2		433	1620	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965914	25965914	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1432015161	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	906	543	0	ENST00000435504.4:c.3292G>A	p.Glu1098Lys	p.E1098K	ENST00000435504		1098	Gaa/Aaa	13/13	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.925172120479527	2		543	1885	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027143	48027143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	677	593	0	ENST00000234420.5:c.2021G>A	p.Gly674Glu	p.G674E	ENST00000234420	NM_000179.2	674	gGa/gAa	4/10	1	2	FACETS	0.942	0.909	0.974	0.942	0.909	0.974	CLONAL	1	TRUE	1	0.925172120479527	2		593	1554	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151181	202151181	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	498	382	0	ENST00000358485.4:c.1482-1G>A		p.X494_splice	ENST00000358485	NM_001080125.1	494			1	2	FACETS	0.995	0.956	1	0.995	0.956	1	CLONAL	1	TRUE	1	0.925172120479527	2		382	1082	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417901	138417901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1373	484	520	0	ENST00000289153.2:c.1618G>A	p.Glu540Lys	p.E540K	ENST00000289153	NM_006219.2	540	Gaa/Aaa	11/22	0.925172120479527	3	FACETS	0.824	0.786	0.863	0.275	0.262	0.288	CLONAL	1	TRUE	0	0.925172120479527	3		520	1857	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928082	178928082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	511	505	0	ENST00000263967.3:c.1360G>A	p.Asp454Asn	p.D454N	ENST00000263967	NM_006218.2	454	Gat/Aat	8/21	0.925172120479527	3	FACETS	0.966	0.924	1	0.322	0.308	0.337	CLONAL	1	TRUE	0	0.925172120479527	3		505	1672	SUCCESS
APC	324	MSKCC	GRCh37	5	112179098	112179098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	657	426	1	ENST00000257430.4:c.7807G>A	p.Glu2603Lys	p.E2603K	ENST00000257430	NM_000038.5	2603	Gaa/Aaa	16/16	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.925172120479527	2		427	1366	SUCCESS
APC	324	MSKCC	GRCh37	5	112179224	112179224	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	731	516	0	ENST00000257430.4:c.7933T>C	p.Tyr2645His	p.Y2645H	ENST00000257430	NM_000038.5	2645	Tat/Cat	16/16	1	2	FACETS	0.967	0.935	0.998	0.967	0.935	0.998	CLONAL	1	TRUE	1	0.925172120479527	2		516	1635	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435604	149435604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	661	425	0	ENST00000286301.3:c.2539G>A	p.Glu847Lys	p.E847K	ENST00000286301	NM_005211.3	847	Gag/Aag	19/22	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.925172120479527	2		425	1419	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401694	401694	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	736	450	0	ENST00000380956.4:c.1016C>T	p.Pro339Leu	p.P339L	ENST00000380956	NM_001195286.1	339	cCc/cTc	7/9	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.925172120479527	2		450	1531	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117717422	117717422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	699	525	0	ENST00000368508.3:c.785C>T	p.Ser262Phe	p.S262F	ENST00000368508	NM_002944.2	262	tCt/tTt	8/43	1	2	FACETS	0.99	0.957	1	0.99	0.957	1	CLONAL	1	TRUE	1	0.925172120479527	2		525	1527	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376091	8376091	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	490	329	0	ENST00000356435.5:c.4507-1G>A		p.X1503_splice	ENST00000356435		1503			0.925172120479527	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.925172120479527	1		329	536	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333350	70333350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	788	594	0	ENST00000373644.4:c.1255C>T	p.Leu419Phe	p.L419F	ENST00000373644	NM_030625.2	419	Ctt/Ttt	2/12	1	2	FACETS	0.999	0.967	1	0.999	0.967	1	CLONAL	1	TRUE	1	0.925172120479527	2		594	1706	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419117	419117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1443684874	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	886	604	1	ENST00000399788.2:c.3230G>A	p.Arg1077Gln	p.R1077Q	ENST00000399788	NM_001042603.1	1077	cGg/cAg	22/28	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.925172120479527	2		605	1911	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495085	56495085	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	943	478	2	ENST00000267101.3:c.3442C>A	p.Pro1148Thr	p.P1148T	ENST00000267101	NM_001982.3	1148	Cca/Aca	27/28	1	2	FACETS	0.999	0.97	1	0.999	0.97	1	CLONAL	1	TRUE	1	0.925172120479527	2		480	2041	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609361	81609361	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772172530	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	882	595	0	ENST00000298171.2:c.959G>A	p.Ser320Asn	p.S320N	ENST00000298171	NM_000369.2	320	aGc/aAc	10/10	1	2	FACETS	0.973	0.944	1	0.973	0.944	1	CLONAL	1	TRUE	1	0.925172120479527	2		595	1959	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609507	81609507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	869	544	0	ENST00000298171.2:c.1105G>A	p.Glu369Lys	p.E369K	ENST00000298171	NM_000369.2	369	Gag/Aag	10/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.925172120479527	2		544	1878	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	338196	338196	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	999	611	1	ENST00000262320.3:c.2515G>T	p.Glu839Ter	p.E839*	ENST00000262320	NM_003502.3	839	Gag/Tag	11/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.925172120479527	2		612	2149	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124364	2124364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	776	462	0	ENST00000219476.3:c.2519C>T	p.Ala840Val	p.A840V	ENST00000219476	NM_000548.3	840	gCc/gTc	22/42	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.925172120479527	2		462	1592	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226174	2226174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	751	448	0	ENST00000326181.6:c.1871C>T	p.Ser624Phe	p.S624F	ENST00000326181	NM_032271.2	624	tCc/tTc	19/21	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.925172120479527	2		448	1552	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041722	14041722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	884	517	0	ENST00000311895.7:c.2269C>T	p.Leu757Phe	p.L757F	ENST00000311895	NM_005236.2	757	Ctt/Ttt	11/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.925172120479527	2		517	1907	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226527	41226527	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1286565832	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	552	449	0	ENST00000357654.3:c.4496C>T	p.Ser1499Phe	p.S1499F	ENST00000357654	NM_007294.3	1499	tCt/tTt	14/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.925172120479527	2		449	1181	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63537656	63537656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201387209	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	818	555	0	ENST00000307078.5:c.976C>T	p.Arg326Cys	p.R326C	ENST00000307078	NM_004655.3	326	Cgt/Tgt	4/11	1	2	FACETS	0.973	0.943	1	0.973	0.943	1	CLONAL	1	TRUE	1	0.925172120479527	2		555	1817	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244384	5244384	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	648	415	0	ENST00000357368.4:c.1098A>T	p.Glu366Asp	p.E366D	ENST00000357368	NM_002850.3	366	gaA/gaT	11/38	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.925172120479527	2		415	1317	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860782	45860782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	644	469	0	ENST00000391945.4:c.1327G>A	p.Ala443Thr	p.A443T	ENST00000391945	NM_000400.3	443	Gcc/Acc	14/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.925172120479527	2		469	1361	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485400	57485400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	734	406	1	ENST00000371085.3:c.982C>T	p.Pro328Ser	p.P328S	ENST00000371085	NM_000516.4	328	Ccc/Tcc	12/13	1	2	FACETS	0.926	0.895	0.957	0.926	0.895	0.957	CLONAL	1	TRUE	1	0.925172120479527	2		407	1714	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36265239	36265239	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	586	457	0	ENST00000300305.3:c.80C>T	p.Pro27Leu	p.P27L	ENST00000300305		27	cCt/cTt	2/8	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.925172120479527	2		457	1246	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295824	212295825	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	552	464	0	ENST00000342788.4:c.2488_2489delinsAA	p.Gly830Lys	p.G830K	ENST00000342788	NM_005235.2	830	GGa/AAa	21/28	1	2	FACETS	0.977	0.941	1	0.977	0.941	1	CLONAL	1	TRUE	1	0.925172120479527	2		464	1221	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138430	37138431	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	600	203	0	ENST00000373509.5:c.79_80delinsTT	p.Pro27Phe	p.P27F	ENST00000373509	NM_002648.3	27	CCc/TTc	1/6	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.925172120479527	2		203	1092	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413899	139413900	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	618	450	0	ENST00000277541.6:c.860_861delinsAA	p.Trp287Ter	p.W287*	ENST00000277541	NM_017617.3	287	tGG/tAA	5/34	1	2	FACETS	0.932	0.899	0.966	0.932	0.899	0.966	CLONAL	1	TRUE	1	0.925172120479527	2		450	1433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577531	7577532	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	616	414	0	ENST00000269305.4:c.749_750delinsTT	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCC/cTT	7/11	1	2	FACETS	0.948	0.914	0.983	0.948	0.914	0.983	CLONAL	1	TRUE	1	0.925172120479527	2		414	1404	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059191	47059192	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	658	474	0	ENST00000409792.3:c.7469_7470delinsAA	p.Arg2490Gln	p.R2490Q	ENST00000409792	NM_014159.6	2490	cGG/cAA	20/21	0.925172120479527	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.925172120479527	1		474	748	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49430996	49430997	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	659	488	0	ENST00000301067.7:c.10142_10143delinsTT	p.Pro3381Leu	p.P3381L	ENST00000301067	NM_003482.3	3381	cCC/cTT	34/54	1	2	FACETS	0.933	0.9	0.966	0.933	0.9	0.966	CLONAL	1	TRUE	1	0.925172120479527	2		488	1527	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219121	133219122	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	731	535	0	ENST00000320574.5:c.4922_4923delinsTT	p.Thr1641Ile	p.T1641I	ENST00000320574	NM_006231.2	1641	aCC/aTT	37/49	1	2	FACETS	0.906	0.875	0.936	0.906	0.875	0.936	CLONAL	1	TRUE	1	0.925172120479527	2		535	1745	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56171018	56171019	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	588	314	0	ENST00000399503.3:c.1846_1847delinsAA	p.Gly616Lys	p.G616K	ENST00000399503	NM_005921.1	616	GGg/AAg	10/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.925172120479527	2		314	1222	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534289	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	660	448	0	ENST00000451590.1:c.34_35delinsAA	p.Gly12Asn	p.G12N	ENST00000451590	NM_001130442.1	12	GGc/AAc	2/5	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.925172120479527	2		448	1355	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118355646	118355647	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0001601-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	611	498	1	ENST00000534358.1:c.4288_4289delinsTT	p.Pro1430Phe	p.P1430F	ENST00000534358	NM_005933.3	1430	CCc/TTc	10/36	1	2	FACETS	0.954	0.919	0.988	0.954	0.919	0.988	CLONAL	1	TRUE	1	0.925172120479527	2		499	1385	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209465	98209465	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001602-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	555	428	0	ENST00000331920.6:c.4073G>T	p.Gly1358Val	p.G1358V	ENST00000331920	NM_000264.3	1358	gGc/gTc	23/24	1	2	FACETS	0.89	0.855	0.927	0.89	0.855	0.927	CLONAL	1	TRUE	1	0.815263693307491	2		428	1529	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977587	2977587	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	210	584	0	ENST00000396946.4:c.1097A>T	p.Asn366Ile	p.N366I	ENST00000396946	NM_032415.4	366	aAc/aTc	8/25	0.584671020509115	5	FACETS	1	0.979	1	0.285	0.264	0.306	CLONAL	1	TRUE	1	0.739965711352078	5		584	1051	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	401998	401998	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3157	435	668	1	ENST00000399788.2:c.4793C>T	p.Ser1598Leu	p.S1598L	ENST00000399788	NM_001042603.1	1598	tCa/tTa	27/28	0.739965711352078	8	FACETS	1	0.977	1	0.263	0.249	0.278	CLONAL	1	TRUE	4	0.739965711352078	8		669	3592	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402181	402181	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3909	507	746	0	ENST00000399788.2:c.4610A>C	p.Lys1537Thr	p.K1537T	ENST00000399788	NM_001042603.1	1537	aAa/aCa	27/28	0.739965711352078	8	FACETS	0.999	0.95	1	0.25	0.237	0.263	CLONAL	1	TRUE	4	0.739965711352078	8		746	4416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587780070	NA	P-0001611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	387	376	0	ENST00000269305.4:c.535C>G	p.His179Asp	p.H179D	ENST00000269305	NM_001126112.2	179	Cat/Gat	5/11	0.729294736720686	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.739965711352078	2		376	506	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40739841	40739841	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001611-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2519	138	347	0	ENST00000392038.2:c.1384C>G	p.Leu462Val	p.L462V	ENST00000392038	NM_001626.4	462	Ctg/Gtg	14/14	0.739965711352078	15	FACETS	0.816	0.738	0.898			1	CLONAL	1	TRUE	NA	0.739965711352078	15		347	2657	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0001613-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	1173	335	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.506699443791709	11	FACETS	0.98	0.962	0.997			1	CLONAL	10	TRUE	NA	0.506699443791709	11		335	1550	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782664	NA	P-0001613-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	194	299	0	ENST00000269305.4:c.711G>C	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atC	7/11	0.467746560186368	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	0	0.506699443791709	2		299	382	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2949706	2949706	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001613-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	60	482	0	ENST00000396946.4:c.3238G>C	p.Glu1080Gln	p.E1080Q	ENST00000396946	NM_032415.4	1080	Gag/Cag	24/25	0.506699443791709	3	FACETS	0.321	0.275	0.371	0.16	0.137	0.186	SUBCLONAL	1	TRUE	1	0.506699443791709	3		482	925	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510781	120510781	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001613-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	191	452	0	ENST00000256646.2:c.1183C>G	p.Leu395Val	p.L395V	ENST00000256646	NM_024408.3	395	Cta/Gta	7/34	0.273326220024038	5	FACETS	1	0.989	1	0.467	0.431	0.503	INDETERMINATE	1	TRUE	2	0.506699443791709	5		452	948	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933533	49933533	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001613-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	239	724	1	ENST00000296474.3:c.2657G>T	p.Gly886Val	p.G886V	ENST00000296474	NM_002447.2	886	gGg/gTg	11/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.506699443791709	2		725	878	SUCCESS
ATR	545	MSKCC	GRCh37	3	142212096	142212096	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001613-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	96	495	0	ENST00000350721.4:c.5956G>A	p.Glu1986Lys	p.E1986K	ENST00000350721	NM_001184.3	1986	Gaa/Aaa	35/47	0.262958408012936	4	FACETS	0.698	0.621	0.78			1	INDETERMINATE	1	TRUE	NA	0.506699443791709	4		495	818	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131930625	131930625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1273705472	NA	P-0001613-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	50	347	0	ENST00000265335.6:c.1858G>A	p.Glu620Lys	p.E620K	ENST00000265335		620	Gag/Aag	12/25	0.506699443791709	3	FACETS	0.424	0.359	0.495	0.212	0.179	0.248	SUBCLONAL	1	TRUE	1	0.506699443791709	3		347	584	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149188	61149188	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001618-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	100	448	0	ENST00000295025.8:c.1378G>A	p.Ala460Thr	p.A460T	ENST00000295025	NM_002908.2	460	Gct/Act	11/11	1	2	FACETS	0.662	0.594	0.734	0.662	0.594	0.734	SUBCLONAL	1	TRUE	1	0.622697004432042	2		448	485	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044348	128044348	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913047	NA	P-0001618-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	62	500	1	ENST00000285398.2:c.1273C>T	p.Arg425Ter	p.R425*	ENST00000285398	NM_000122.1	425	Cga/Tga	8/15	1	2	FACETS	0.582	0.506	0.664	0.582	0.506	0.664	SUBCLONAL	1	TRUE	1	0.622697004432042	2		501	342	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434563	99434563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs950258270	NA	P-0001618-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	97	293	0	ENST00000268035.6:c.650G>A	p.Ser217Asn	p.S217N	ENST00000268035	NM_000875.3	217	aGc/aAc	3/21	0.26662415769817	0	FACETS	0.297	0.266	0.329			1	INDETERMINATE	1	TRUE	0	0.622697004432042	0		293	396	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223958	2223958	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001618-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	36	564	0	ENST00000326181.6:c.1172C>G	p.Thr391Ser	p.T391S	ENST00000326181	NM_032271.2	391	aCc/aGc	13/21	0.410561285344725	1	FACETS	0.208	0.171	0.25	0.208	0.171	0.25	SUBCLONAL	1	TRUE	0	0.622697004432042	1		564	382	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814282	76814282	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001618-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	68	573	0	ENST00000373344.5:c.6362C>A	p.Ser2121Tyr	p.S2121Y	ENST00000373344	NM_000489.3	2121	tCt/tAt	29/35	0.622697004432042	1	FACETS	0.283	0.246	0.323	0.283	0.246	0.323	SUBCLONAL	1	TRUE	0	0.622697004432042	1		573	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577596	7577596	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001618-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	153	353	0	ENST00000269305.4:c.685del	p.Cys229ValfsTer18	p.C229Vfs*18	ENST00000269305	NM_001126112.2	229	Tgt/gt	7/11	NA	2	FACETS	0.89	0.833	0.947			1	INDETERMINATE	2	TRUE	NA	0.622697004432042	2		353	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578266	7578266	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs942158624	NA	P-0001634-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	106	635	0	ENST00000269305.4:c.583A>T	p.Ile195Phe	p.I195F	ENST00000269305	NM_001126112.2	195	Atc/Ttc	6/11	0.447615606314765	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.453631468379548	1		635	349	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29105993	29105993	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs864622149	NA	P-0001642-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	18	295	0	ENST00000328354.6:c.846+1G>A		p.X282_splice	ENST00000328354	NM_007194.3	282			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		295	128	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0001662-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	17	276	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.148685709785336	1	FACETS	0.378	0.281	0.493	0.378	0.281	0.493	SUBCLONAL	1	TRUE	0	0.2	1		276	405	SUCCESS
AR	367	MSKCC	GRCh37	X	66931247	66931247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868669253	NA	P-0001662-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	40	314	0	ENST00000374690.3:c.1889G>A	p.Arg630Gln	p.R630Q	ENST00000374690	NM_000044.3	630	cGg/cAg	4/8	1	1	FACETS	0.807	0.671	0.959	0.807	0.671	0.959	CLONAL	1	TRUE	0	0.2	1		314	446	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0001670-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	181	472	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.874	0.806	0.945	0.874	0.806	0.945	CLONAL	1	TRUE	1	0.42219369894083	2		472	981	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0001670-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	232	368	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	0.252009065145933	3	FACETS	0.868	0.812	0.925	0.578	0.541	0.617	INDETERMINATE	2	TRUE	0	0.42219369894083	3		368	767	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0001670-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	223	703	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.422874519470061	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.42219369894083	1		704	589	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0001670-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	88	339	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.671	0.595	0.752	0.671	0.595	0.752	SUBCLONAL	1	TRUE	1	0.42219369894083	2		339	621	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0001677-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	169	314	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.977	0.901	1	1	0.992	1	CLONAL	2	TRUE	1	0.25	2		314	692	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0001677-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	80	264	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.742	0.652	0.839	0.742	0.652	0.839	SUBCLONAL	1	TRUE	1	0.25	2		265	863	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0001681-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	71	412	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		413	1041	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0001688-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	325	259	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.599755228806998	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.599755228806998	2		260	507	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0001688-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	17	217	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	NA	2	FACETS	0.142	0.106	0.186			1	INDETERMINATE	1	TRUE	NA	0.599755228806998	2		217	398	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160227	22160227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001688-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	249	321	0	ENST00000215832.6:c.404G>A	p.Arg135Lys	p.R135K	ENST00000215832	NM_002745.4	135	aGa/aAa	3/9	0.599755228806998	2	FACETS	0.969	0.908	1	0.484	0.454	0.516	CLONAL	1	TRUE	0	0.599755228806998	2		321	857	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150031	202150031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167464002	NA	P-0001688-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	243	235	0	ENST00000358485.4:c.1472G>A	p.Arg491Gln	p.R491Q	ENST00000358485	NM_001080125.1	491	cGa/cAa	8/9	0.282726593227784	2	FACETS	0.855	0.809	0.9	0.855	0.809	0.9	INDETERMINATE	2	TRUE	0	0.599755228806998	2		235	474	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157758	106157758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001688-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	174	335	0	ENST00000380013.4:c.2659G>A	p.Glu887Lys	p.E887K	ENST00000380013	NM_001127208.2	887	Gag/Aag	3/11	0.244996392036068	3	FACETS	0.89	0.821	0.963	0.445	0.41	0.482	INDETERMINATE	1	TRUE	1	0.599755228806998	3		335	847	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038431	180038431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001688-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	47	345	0	ENST00000261937.6:c.3586G>A	p.Glu1196Lys	p.E1196K	ENST00000261937	NM_182925.4	1196	Gag/Aag	27/30	0.47877227415227	1	FACETS	0.196	0.165	0.231	0.196	0.165	0.231	SUBCLONAL	1	TRUE	0	0.599755228806998	1		345	559	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428445	49428445	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001688-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	66	348	0	ENST00000301067.7:c.10360C>T	p.Gln3454Ter	p.Q3454*	ENST00000301067	NM_003482.3	3454	Caa/Taa	36/54	1	2	FACETS	0.312	0.27	0.357	0.312	0.27	0.357	SUBCLONAL	1	TRUE	1	0.599755228806998	2		348	706	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548886	29548886	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs953440640	NA	P-0001688-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	138	269	0	ENST00000356175.3:c.1660C>T	p.Gln554Ter	p.Q554*	ENST00000356175	NM_000267.3	554	Cag/Tag	15/57	1	2	FACETS	0.732	0.668	0.798	0.732	0.668	0.798	SUBCLONAL	1	TRUE	1	0.599755228806998	2		269	629	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110623	4110623	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201129499	NA	P-0001688-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	175	298	1	ENST00000262948.5:c.334C>T	p.Arg112Trp	p.R112W	ENST00000262948	NM_030662.3	112	Cgg/Tgg	3/11	0.451927156474442	3	FACETS	1	0.931	1			1	CLONAL	1	TRUE	NA	0.599755228806998	3		299	752	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0001695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	336	307	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.323270773277292	5	FACETS	1	0.991	1	0.793	0.754	0.832	INDETERMINATE	2	TRUE	2	0.802097265023665	5		307	776	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450066	32450066	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	217	271	0	ENST00000332351.3:c.746C>A	p.Pro249His	p.P249H	ENST00000332351	NM_024426.4	249	cCc/cAc	2/10	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.802097265023665	2		271	429	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560434	65560434	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	452	288	0	ENST00000358664.4:c.163G>T	p.Gly55Ter	p.G55*	ENST00000358664	NM_002382.4	55	Gga/Tga	3/5	0.765669395971274	2	FACETS	0.927	0.9	0.953	0.927	0.9	0.953	CLONAL	2	TRUE	0	0.802097265023665	2		288	608	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912664	NA	P-0001695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	385	360	0	ENST00000269305.4:c.1010G>C	p.Arg337Pro	p.R337P	ENST00000269305	NM_001126112.2	337	cGc/cCc	10/11	0.323270773277292	5	FACETS	1	0.986	1	0.723	0.689	0.757	INDETERMINATE	2	TRUE	2	0.802097265023665	5		360	975	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017781	31017781	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	343	307	1	ENST00000375687.4:c.643G>T	p.Ala215Ser	p.A215S	ENST00000375687	NM_015338.5	215	Gct/Tct	8/13	0.257457629196572	5	FACETS	0.866	0.826	0.907	0.866	0.826	0.907	INDETERMINATE	3	TRUE	2	0.802097265023665	5		308	725	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038536	47038536	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	404	382	0	ENST00000377604.3:c.698G>T	p.Cys233Phe	p.C233F	ENST00000377604	NM_001204468.1	233	tGc/tTc	8/24	0.323270773277292	5	FACETS	0.837	0.8	0.874	0.837	0.8	0.874	INDETERMINATE	3	TRUE	2	0.802097265023665	5		382	884	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179117	123179117	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001695-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	495	314	0	ENST00000218089.9:c.566G>T	p.Ser189Ile	p.S189I	ENST00000218089	NM_001042749.1	189	aGt/aTt	8/35	0.323270773277292	5	FACETS	1	0.994	1	0.804	0.772	0.837	INDETERMINATE	2	TRUE	2	0.802097265023665	5		314	1127	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0001698-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	359	470	1	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.827384730365931	2	FACETS	0.971	0.944	0.997	0.971	0.944	0.997	CLONAL	2	TRUE	0	0.839971550564423	2		471	440	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256462	16256462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001698-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	204	473	0	ENST00000375759.3:c.3727C>T	p.Arg1243Trp	p.R1243W	ENST00000375759	NM_015001.2	1243	Cgg/Tgg	11/15	NA	2	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.839971550564423	2		473	478	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61706070	61706070	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1314305335	NA	P-0001698-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	44	629	0	ENST00000401558.2:c.3101T>G	p.Phe1034Cys	p.F1034C	ENST00000401558	NM_003400.3	1034	tTt/tGt	25/25	0.614873336041654	4	FACETS	0.223	0.186	0.264	0.074	0.062	0.088	SUBCLONAL	1	TRUE	1	0.839971550564423	4		629	864	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622575	28622575	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001698-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	134	347	0	ENST00000241453.7:c.1042G>T	p.Gly348Ter	p.G348*	ENST00000241453	NM_004119.2	348	Gga/Tga	9/24	1	2	FACETS	0.95	0.875	1	0.95	0.875	1	CLONAL	1	TRUE	1	0.839971550564423	2		347	336	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	360063	360063	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001698-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	172	583	0	ENST00000262320.3:c.1026del	p.Ile343SerfsTer71	p.I343Sfs*71	ENST00000262320	NM_003502.3	342	ggG/gg	4/11	0.813356520089705	3	FACETS	0.956	0.884	1	0.478	0.442	0.516	CLONAL	1	TRUE	1	0.839971550564423	3		583	608	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335684	81335684	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001699-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	41	488	0	ENST00000222390.5:c.1676A>G	p.Glu559Gly	p.E559G	ENST00000222390	NM_000601.4	559	gAg/gGg	15/18	NA	2	FACETS	0.257	0.213	0.306			1	INDETERMINATE	1	TRUE	NA	0.444681377306262	2		488	718	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524194	18524194	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs758959571	NA	P-0001699-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	157	550	0	ENST00000266497.5:c.1706C>A	p.Thr569Asn	p.T569N	ENST00000266497		569	aCc/aAc	11/31	0.444681377306262	1	FACETS	0.879	0.808	0.952	0.879	0.808	0.952	CLONAL	1	TRUE	0	0.444681377306262	1		550	625	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857815	57857815	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001699-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	280	613	0	ENST00000228682.2:c.134A>T	p.Asn45Ile	p.N45I	ENST00000228682	NM_005269.2	45	aAc/aTc	3/12	1	2	FACETS	0.878	0.823	0.934	0.878	0.823	0.934	CLONAL	1	TRUE	1	0.444681377306262	2		613	1435	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0001706-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	132	359	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.134719228609487	3	FACETS	0.919	0.844	0.997	1	0.986	1	INDETERMINATE	3	TRUE	1	0.29	3		359	378	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809730	36809730	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001706-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	81	362	0	ENST00000373129.3:c.875C>T	p.Thr292Ile	p.T292I	ENST00000373129	NM_032017.1	292	aCc/aTc	9/12	0.134719228609487	3	FACETS	1	0.953	1	1	0.953	1	INDETERMINATE	2	TRUE	1	0.29	3		362	283	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844362	156844362	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs764171953	NA	P-0001706-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	100	551	0	ENST00000524377.1:c.1196-1G>A		p.X399_splice	ENST00000524377	NM_002529.3	399			0.519172869934945	3	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	1	0.29	3		551	373	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206943235	206943235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760677075	NA	P-0001706-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	114	421	0	ENST00000423557.1:c.383G>A	p.Arg128Gln	p.R128Q	ENST00000423557	NM_000572.2	128	cGa/cAa	4/5	0.519172869934945	3	FACETS	1	0.91	1	1	0.91	1	CLONAL	2	TRUE	1	0.29	3		421	448	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170944	99170944	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001706-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	67	393	0	ENST00000074304.5:c.1573G>A	p.Glu525Lys	p.E525K	ENST00000074304	NM_001134224.1	525	Gag/Aag	16/26	1	2	FACETS	0.939	0.827	1	1	0.981	1	CLONAL	2	TRUE	1	0.29	2		393	246	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911579	134911579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs959853730	NA	P-0001706-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	57	431	0	ENST00000398015.3:c.2044C>T	p.Arg682Cys	p.R682C	ENST00000398015	NM_004441.4	682	Cgc/Tgc	11/16	0.3	0	FACETS	1	0.939	1			1	CLONAL	1	TRUE	0	0.29	0		431	243	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607173	189607173	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001706-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	77	506	0	ENST00000264731.3:c.1552G>A	p.Gly518Arg	p.G518R	ENST00000264731	NM_003722.4	518	Gga/Aga	12/14	1	2	FACETS	0.928	0.824	1	1	0.983	1	CLONAL	2	TRUE	1	0.29	2		506	286	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801140	1801140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001706-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	73	459	0	ENST00000260795.2:c.269G>A	p.Gly90Glu	p.G90E	ENST00000260795		90	gGg/gAg	2/17	0.212514426617915	0	FACETS	0.987	0.883	1			1	CLONAL	2	TRUE	0	0.29	0		459	181	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536173	106536173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001706-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	100	348	0	ENST00000369096.4:c.140C>T	p.Thr47Ile	p.T47I	ENST00000369096	NM_001198.3	47	aCt/aTt	2/7	0.3	4	FACETS	1	0.92	1			1	CLONAL	2	TRUE	NA	0.29	4		348	433	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683659	162683659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769099303	NA	P-0001706-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	78	465	0	ENST00000366898.1:c.310C>T	p.Arg104Trp	p.R104W	ENST00000366898	NM_004562.2	104	Cgg/Tgg	3/12	0.3	0	FACETS	0.71	0.632	0.792			1	SUBCLONAL	2	TRUE	0	0.29	0		465	269	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341890	8341890	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001706-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	56	599	1	ENST00000356435.5:c.4750C>T	p.His1584Tyr	p.H1584Y	ENST00000356435		1584	Cat/Tat	29/35	0.3	0	FACETS	0.626	0.543	0.714			1	SUBCLONAL	2	TRUE	0	0.29	0		600	219	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245858	46245858	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001706-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	107	435	0	ENST00000334344.6:c.3952C>T	p.Gln1318Ter	p.Q1318*	ENST00000334344	NM_152641.2	1318	Cag/Tag	15/21	0.134719228609487	5	FACETS	1	0.962	1	1	0.962	1	INDETERMINATE	3	TRUE	2	0.29	5		435	317	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636143	28636143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371663652	NA	P-0001706-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	53	463	0	ENST00000241453.7:c.229G>A	p.Glu77Lys	p.E77K	ENST00000241453	NM_004119.2	77	Gaa/Aaa	3/24	0.3	0	FACETS	0.998	0.859	1			1	CLONAL	1	TRUE	0	0.29	0		463	260	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008336	29008336	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001706-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	70	456	0	ENST00000282397.4:c.535C>T	p.Pro179Ser	p.P179S	ENST00000282397	NM_002019.4	179	Cct/Tct	5/30	0.3	0	FACETS	0.68	0.6	0.764			1	SUBCLONAL	2	TRUE	0	0.29	0		456	252	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609522	81609522	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001706-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	95	527	0	ENST00000298171.2:c.1120C>T	p.Gln374Ter	p.Q374*	ENST00000298171	NM_000369.2	374	Cag/Tag	10/10	0.3	1	FACETS	0.878	0.79	0.969	1	0.986	1	CLONAL	2	TRUE	0	0.29	1		527	319	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645118	67645118	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001706-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	109	535	0	ENST00000264010.4:c.383C>T	p.Thr128Ile	p.T128I	ENST00000264010	NM_006565.3	128	aCc/aTc	3/12	1	2	FACETS	0.949	0.859	1	1	0.988	1	CLONAL	2	TRUE	1	0.29	2		535	396	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685571	29685571	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001706-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	122	444	0	ENST00000356175.3:c.7981C>T	p.His2661Tyr	p.H2661Y	ENST00000356175	NM_000267.3	2661	Cat/Tat	54/57	0.260590265516495	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.29	3		444	406	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745208	41745208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878962530	NA	P-0001706-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	67	464	0	ENST00000301178.4:c.1274C>T	p.Ala425Val	p.A425V	ENST00000301178	NM_021913.4	425	gCc/gTc	9/20	0.3	0	FACETS	0.675	0.594	0.76			1	SUBCLONAL	2	TRUE	0	0.29	0		464	243	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944629	40944629	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001706-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	45	225	0	ENST00000373198.4:c.1873C>T	p.Gln625Ter	p.Q625*	ENST00000373198	NM_133170.3	625	Cag/Tag	12/32	0.3	0	FACETS	0.77	0.661	0.886			1	SUBCLONAL	2	TRUE	0	0.29	0		225	143	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246680	46246681	+	splice_donor_variant	Splice_Site	DNP	GT	GT	AA	novel	NA	P-0001706-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	41	175	0	ENST00000334344.6:c.4773+1_4773+2delinsAA		p.X1591_splice	ENST00000334344	NM_152641.2	1591			0.134719228609487	5	FACETS	1	0.926	1	0.782	0.661	0.912	INDETERMINATE	2	TRUE	2	0.29	5		175	173	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0001707-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	817	253	335	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.3	1	FACETS	0.791	0.74	0.844	1	0.993	1	SUBCLONAL	2	TRUE	0	0.26	1		335	1070	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913338	NA	P-0001707-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	867	90	367	0	ENST00000288602.6:c.1781A>T	p.Asp594Val	p.D594V	ENST00000288602	NM_004333.4	594	gAt/gTt	15/18	NA	2	FACETS	0.723	0.64	0.812			1	INDETERMINATE	1	TRUE	NA	0.26	2		367	957	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0001707-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	786	141	325	0	ENST00000269305.4:c.920-2A>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.3	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.26	1		325	927	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0001733-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	297	570	3	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.491847498062456	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.521431971623248	1		573	836	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875627	35875627	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369971728	NA	P-0001733-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1179	173	507	0	ENST00000303115.3:c.814G>A	p.Val272Ile	p.V272I	ENST00000303115	NM_002185.3	272	Gta/Ata	7/8	0.521431971623248	4	FACETS	0.747	0.685	0.811	0.249	0.228	0.271	SUBCLONAL	1	TRUE	1	0.521431971623248	4		507	1352	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509006	106509006	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201525740	NA	P-0001733-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	159	358	1	ENST00000359195.3:c.1000G>A	p.Gly334Ser	p.G334S	ENST00000359195	NM_002649.2	334	Ggc/Agc	2/11	0.439164962142075	2	FACETS	0.785	0.72	0.852	0.392	0.36	0.426	SUBCLONAL	1	TRUE	0	0.521431971623248	2		359	777	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31369176	31369176	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760640013	NA	P-0001733-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	312	531	1	ENST00000328111.2:c.160C>T	p.Arg54Ter	p.R54*	ENST00000328111	NM_006892.3	54	Cga/Tga	3/23	0.334434869882632	3	FACETS	1	0.987	1	0.576	0.542	0.61	CLONAL	1	TRUE	1	0.521431971623248	3		532	1310	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805610	89805610	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001749-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	70	312	0	ENST00000389301.3:c.4098G>T	p.Gln1366His	p.Q1366H	ENST00000389301	NM_000135.2	1366	caG/caT	41/43	0.26991339163795	1	FACETS	0.465	0.404	0.531	0.465	0.404	0.531	SUBCLONAL	1	TRUE	0	0.26991339163795	1		312	965	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523637	41523637	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001749-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	102	367	0	ENST00000263253.7:c.1053C>A	p.Cys351Ter	p.C351*	ENST00000263253	NM_001429.3	351	tgC/tgA	4/31	NA	2	FACETS	0.633	0.564	0.706			1	INDETERMINATE	1	TRUE	NA	0.26991339163795	2		367	1194	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001751-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	246	336	0	ENST00000206249.3:c.1609T>G	p.Tyr537Asp	p.Y537D	ENST00000206249	NM_000125.3	537	Tat/Gat	8/8	NA	2	FACETS	0.877	0.825	0.929			1	INDETERMINATE	2	FALSE	NA	0.441098557697897	2		336	636	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778564	3778564	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001751-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	133	482	0	ENST00000262367.5:c.6484G>A	p.Gly2162Arg	p.G2162R	ENST00000262367	NM_004380.2	2162	Gga/Aga	31/31	0.357660336288438	1	FACETS	0.756	0.688	0.826	0.756	0.688	0.826	SUBCLONAL	1	FALSE	0	0.441098557697897	1		482	622	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0001752-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	49	394	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.138024814054439	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.138024814054439	1		394	559	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788651	3788651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001752-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	83	483	0	ENST00000262367.5:c.4303G>A	p.Asp1435Asn	p.D1435N	ENST00000262367	NM_004380.2	1435	Gat/Aat	26/31	0.138024814054439	0	FACETS	0.701	0.619	0.79			1	SUBCLONAL	2	TRUE	0	0.138024814054439	0		483	739	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432664	29432664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113994087	NA	P-0001768-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	109	534	0	ENST00000389048.3:c.3824G>A	p.Arg1275Gln	p.R1275Q	ENST00000389048	NM_004304.4	1275	cGa/cAa	25/29	0.247540644818278	3	FACETS	1	0.983	1	0.724	0.654	0.799	CLONAL	1	TRUE	1	0.36012386643378	3		534	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579341	7579345	+	frameshift_variant	Frame_Shift_Del	DEL	AATGC	AATGC	-	novel	NA	P-0001768-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	155	454	0	ENST00000269305.4:c.342_346del	p.Leu114PhefsTer33	p.L114Ffs*33	ENST00000269305	NM_001126112.2	114	ttGCATTct/ttct	4/11	NA	2	FACETS	1	0.941	1			1	INDETERMINATE	2	TRUE	NA	0.36012386643378	2		454	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0001785-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	407	622	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.470946928636507	3	FACETS	0.924	0.89	0.959	0.924	0.89	0.959	CLONAL	3	TRUE	0	0.549397469614328	3		622	681	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022517	31022517	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001785-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	227	360	0	ENST00000375687.4:c.2002G>T	p.Gly668Cys	p.G668C	ENST00000375687	NM_015338.5	668	Ggt/Tgt	13/13	0.262957775158705	6	FACETS	0.992	0.931	1	0.744	0.698	0.79	INDETERMINATE	3	TRUE	2	0.549397469614328	6		360	583	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0001788-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	491	382	2	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.833389766606389	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.836183821939973	1		384	651	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0001788-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	561	414	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	0.385835600251422	1	FACETS	0.737	0.712	0.763	0.737	0.712	0.763	INDETERMINATE	1	TRUE	0	0.836183821939973	1		414	1059	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439250	52439275	+	frameshift_variant	Frame_Shift_Del	DEL	TTGTTGGGAGGGCTGTGGGATGGGGC	TTGTTGGGAGGGCTGTGGGATGGGGC	-	novel	NA	P-0001788-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	228	394	0	ENST00000460680.1:c.967_992del	p.Ala323ThrfsTer66	p.A323Tfs*66	ENST00000460680	NM_004656.3	323	GCCCCATCCCACAGCCCTCCCAACAAa/a	11/17	0.836183821939973	1	FACETS	0.483	0.452	0.514	0.483	0.452	0.514	SUBCLONAL	1	TRUE	0	0.836183821939973	1		394	657	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0001793-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	38	259	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.203781415537335	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.226433239472623	1		260	218	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0001793-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	12	553	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.938	0.665	1	0.938	0.665	1	CLONAL	1	TRUE	1	0.226433239472623	2		553	113	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578340	212578340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1448870993	NA	P-0001793-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	19	524	0	ENST00000342788.4:c.917G>A	p.Arg306His	p.R306H	ENST00000342788	NM_005235.2	306	cGt/cAt	8/28	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.226433239472623	2		524	114	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131893092	131893092	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001793-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	18	582	1	ENST00000265335.6:c.76A>T	p.Thr26Ser	p.T26S	ENST00000265335		26	Act/Tct	1/25	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.226433239472623	2		583	121	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098944	178098944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001794-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	187	734	0	ENST00000397062.3:c.101G>A	p.Arg34Gln	p.R34Q	ENST00000397062	NM_006164.4	34	cGa/cAa	2/5	0.489610660971783	3	FACETS	0.928	0.865	0.993	0.928	0.865	0.993	CLONAL	2	TRUE	1	0.503162336107299	3		734	501	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553761	106553761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001794-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	76	671	0	ENST00000369096.4:c.1726G>A	p.Glu576Lys	p.E576K	ENST00000369096	NM_001198.3	576	Gaa/Aaa	5/7	0.203192679746709	6	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.503162336107299	6		671	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578282	7578306	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCCAGACCTAAGAGCAATCAGTGA	GGCCAGACCTAAGAGCAATCAGTGA	-	novel	NA	P-0001794-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	31	610	0	ENST00000269305.4:c.560-17_567del		p.X187_splice	ENST00000269305	NM_001126112.2	187		6/11	NA	2	FACETS	0.57	0.464	0.689			1	INDETERMINATE	1	TRUE	NA	0.503162336107299	2		610	216	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0001795-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	477	646	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.433094541990149	2	FACETS	1	0.992	1	0.558	0.536	0.58	INDETERMINATE	1	FALSE	0	0.878853119250811	2		646	973	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371708	225371708	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001795-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1252	350	613	0	ENST00000264414.4:c.896T>G	p.Met299Arg	p.M299R	ENST00000264414	NM_003590.4	299	aTg/aGg	7/16	0.450171228811687	5	FACETS	1	0.988	1	0.384	0.363	0.406	INDETERMINATE	1	FALSE	2	0.878853119250811	5		613	1602	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143326463	143326463	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001796-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	228	454	0	ENST00000262992.4:c.151G>T	p.Val51Leu	p.V51L	ENST00000262992	NM_001101669.1	51	Gtg/Ttg	4/24	0.56618559967544	3	FACETS	1	0.992	1	0.465	0.435	0.495	CLONAL	1	TRUE	0	0.663153980421128	3		454	657	SUCCESS
APC	324	MSKCC	GRCh37	5	112154849	112154849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs947634162	NA	P-0001796-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	161	660	2	ENST00000257430.4:c.1120C>T	p.Arg374Trp	p.R374W	ENST00000257430	NM_000038.5	374	Cgg/Tgg	10/16	0.611989123915883	4	FACETS	0.86	0.789	0.935	0.287	0.263	0.312	CLONAL	1	TRUE	1	0.663153980421128	4		662	939	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100357	8100357	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200765508	NA	P-0001796-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	151	727	0	ENST00000346208.3:c.331C>T	p.Pro111Ser	p.P111S	ENST00000346208		111	Ccc/Tcc	3/6	0.20832150595489	4	FACETS	0.807	0.737	0.88	0.403	0.368	0.44	INDETERMINATE	1	TRUE	2	0.663153980421128	4		727	939	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552600	18552600	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001796-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	157	681	0	ENST00000266497.5:c.2011G>C	p.Glu671Gln	p.E671Q	ENST00000266497		671	Gaa/Caa	14/31	0.365951397801711	1	FACETS	0.52	0.478	0.563	0.52	0.478	0.563	INDETERMINATE	1	TRUE	0	0.663153980421128	1		681	609	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476370	88476370	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001796-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	98	566	0	ENST00000360948.2:c.1762G>A	p.Glu588Lys	p.E588K	ENST00000360948	NM_001012338.2	588	Gag/Aag	15/19	0.594043699743092	2	FACETS	0.519	0.464	0.578	0.26	0.232	0.289	SUBCLONAL	1	TRUE	0	0.663153980421128	2		566	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579415	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	G	novel	NA	P-0001796-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	488	563	0	ENST00000269305.4:c.272_273delinsC	p.Trp91SerfsTer32	p.W91Sfs*32	ENST00000269305	NM_001126112.2	91	tGG/tC	4/11	0.377697125299888	4	FACETS	1	0.995	1			1	INDETERMINATE	3	TRUE	NA	0.663153980421128	4		563	720	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0001807-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	287	359	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.652352485478179	5	FACETS	1	0.965	1	1	0.965	1	CLONAL	3	FALSE	2	0.722215686370179	5		359	543	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0001807-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	101	514	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.722215686370179	3	FACETS	1	0.924	1	0.514	0.464	0.567	CLONAL	1	FALSE	1	0.722215686370179	3		514	370	SUCCESS
APC	324	MSKCC	GRCh37	5	112176212	112176212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755126540	NA	P-0001807-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	116	471	0	ENST00000257430.4:c.4921G>A	p.Val1641Met	p.V1641M	ENST00000257430	NM_000038.5	1641	Gtg/Atg	16/16	0.722215686370179	3	FACETS	1	0.952	1	0.537	0.488	0.588	CLONAL	1	FALSE	1	0.722215686370179	3		471	407	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0001807-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	199	235	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	0.722215686370179	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	FALSE	0	0.722215686370179	2		235	267	SUCCESS
APC	324	MSKCC	GRCh37	5	112175182	112175182	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001807-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	140	239	0	ENST00000257430.4:c.3892del	p.Ser1298LeufsTer7	p.S1298Lfs*7	ENST00000257430	NM_000038.5	1297	gaT/ga	16/16	0.722215686370179	3	FACETS	0.999	0.931	1	0.999	0.931	1	CLONAL	2	FALSE	1	0.722215686370179	3		239	264	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0001814-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	430	459	1	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	0.199999144843653	4	FACETS	0.985	0.944	1	0.985	0.944	1	INDETERMINATE	2	TRUE	2	0.920630312707565	4		460	911	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434943	56434943	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775335997	NA	P-0001814-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	601	550	0	ENST00000407977.2:c.2194C>T	p.Arg732Cys	p.R732C	ENST00000407977		732	Cgc/Tgc	9/10	0.558728030980458	4	FACETS	0.959	0.924	0.993			1	CLONAL	2	TRUE	NA	0.920630312707565	4		550	1308	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199350	16199350	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001833-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	53	605	1	ENST00000375759.3:c.123G>T	p.Arg41Ser	p.R41S	ENST00000375759	NM_015001.2	41	agG/agT	2/15	0.3	1	FACETS	0.488	0.415	0.569	0.488	0.415	0.569	SUBCLONAL	1	TRUE	0	0.21	1		606	925	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965734	25965734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001833-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	56	644	0	ENST00000435504.4:c.3472G>A	p.Ala1158Thr	p.A1158T	ENST00000435504		1158	Gcc/Acc	13/13	1	2	FACETS	0.637	0.544	0.739	0.637	0.544	0.739	SUBCLONAL	1	TRUE	1	0.21	2		644	837	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793392	242793392	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001833-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	37	516	0	ENST00000334409.5:c.685C>T	p.Gln229Ter	p.Q229*	ENST00000334409	NM_005018.2	229	Cag/Tag	5/5	1	2	FACETS	0.605	0.498	0.726	0.605	0.498	0.726	SUBCLONAL	1	TRUE	1	0.21	2		516	582	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294373	1294373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001833-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	25	309	0	ENST00000310581.5:c.628G>A	p.Ala210Thr	p.A210T	ENST00000310581	NM_198253.2	210	Gcc/Acc	2/16	1	2	FACETS	0.572	0.45	0.713	0.572	0.45	0.713	SUBCLONAL	1	TRUE	1	0.21	2		309	416	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513316	149513316	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001833-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	26	405	0	ENST00000261799.4:c.767G>T	p.Arg256Leu	p.R256L	ENST00000261799	NM_002609.3	256	cGg/cTg	6/23	0.147623016669992	1	FACETS	0.497	0.393	0.617	0.497	0.393	0.617	SUBCLONAL	1	TRUE	0	0.21	1		405	446	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386589	81386589	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001833-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	50	503	0	ENST00000222390.5:c.398G>A	p.Gly133Glu	p.G133E	ENST00000222390	NM_000601.4	133	gGa/gAa	4/18	1	2	FACETS	0.572	0.484	0.67	0.572	0.484	0.67	SUBCLONAL	1	TRUE	1	0.21	2		503	832	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771774	135771774	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001833-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	46	720	0	ENST00000298552.3:c.3343G>A	p.Glu1115Lys	p.E1115K	ENST00000298552	NM_001162426.1	1115	Gag/Aag	23/23	1	2	FACETS	0.486	0.408	0.573	0.486	0.408	0.573	SUBCLONAL	1	TRUE	1	0.21	2		720	901	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620417	43620417	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001833-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	33	343	0	ENST00000355710.3:c.3026T>A	p.Met1009Lys	p.M1009K	ENST00000355710	NM_020975.4	1009	aTg/aAg	18/20	1	2	FACETS	0.595	0.484	0.721	0.595	0.484	0.721	SUBCLONAL	1	TRUE	1	0.21	2		343	528	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78765301	78765301	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001833-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	58	509	0	ENST00000306801.3:c.882G>C	p.Leu294Phe	p.L294F	ENST00000306801	NM_020761.2	294	ttG/ttC	7/34	1	2	FACETS	0.679	0.582	0.786	0.679	0.582	0.786	SUBCLONAL	1	TRUE	1	0.21	2		509	813	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138459	11138459	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs1568498107	NA	P-0001833-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	33	390	0	ENST00000358026.2:c.3216-1G>T		p.X1072_splice	ENST00000358026	NM_001128849.1	1072			0.228806116185588	1	FACETS	0.538	0.437	0.652	0.538	0.437	0.652	SUBCLONAL	1	TRUE	0	0.21	1		390	523	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523697	176523697	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001833-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	34	626	0	ENST00000292408.4:c.2110del	p.Glu704ArgfsTer18	p.E704Rfs*18	ENST00000292408	NM_213647.1	703	cGg/cg	16/18	0.147623016669992	1	FACETS	0.52	0.424	0.629	0.52	0.424	0.629	SUBCLONAL	1	TRUE	0	0.21	1		626	557	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393428	139393429	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0001833-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	76	470	0	ENST00000277541.6:c.6102_6103delinsTT	p.Trp2034_Ala2035delinsCysSer	p.W2034_A2035delinsCS	ENST00000277541	NM_017617.3	2034	tgGGcc/tgTTcc	33/34	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.21	2		470	555	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044978	47044978	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001840-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	150	333	0	ENST00000377604.3:c.2307del	p.Ser770AlafsTer32	p.S770Afs*32	ENST00000377604	NM_001204468.1	768	ttC/tt	20/24	0.331981683913686	4	FACETS	0.86	0.793	0.93			1	CLONAL	3	TRUE	NA	0.340041195624544	4		333	458	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061754	38061754	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001840-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	66	271	0	ENST00000250448.2:c.235C>A	p.Pro79Thr	p.P79T	ENST00000250448	NM_004496.3	79	Ccc/Acc	2/2	0.340041195624544	3	FACETS	1	0.963	1	0.434	0.379	0.493	CLONAL	1	TRUE	0	0.340041195624544	3		271	349	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0001842-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	17	553	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.305468876603286	5	FACETS	0.286	0.212	0.374	0.071	0.053	0.094	SUBCLONAL	1	TRUE	1	0.305468876603286	5		553	568	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599321	55599321	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913507	NA	P-0001842-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	17	511	0	ENST00000288135.5:c.2447A>T	p.Asp816Val	p.D816V	ENST00000288135	NM_000222.2	816	gAc/gTc	17/21	0.305468876603286	5	FACETS	0.34	0.252	0.444			1	SUBCLONAL	1	TRUE	NA	0.305468876603286	5		511	478	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94201059	94201059	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	rs374389299	NA	P-0001842-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	49	491	0	ENST00000323929.3:c.1018A>T	p.Ile340Phe	p.I340F	ENST00000323929	NM_005591.3	340	Att/Ttt	10/20	0.305468876603286	2	FACETS	1	0.854	1	0.501	0.427	0.583	CLONAL	1	TRUE	0	0.305468876603286	2		491	320	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0001857-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	25	264	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	0.126734027249751	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		264	475	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117737	70117737	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001857-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	50	322	0	ENST00000245479.2:c.206del	p.Phe69SerfsTer41	p.F69Sfs*41	ENST00000245479	NM_000346.3	69	Ttc/tc	1/3	0.3	3	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	3		322	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0001867-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	230	347	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.507572148559416	2	FACETS	0.834	0.787	0.882	0.834	0.787	0.882	CLONAL	2	TRUE	0	0.570905675100965	2		347	483	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521611	46521611	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001867-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	156	422	0	ENST00000262741.5:c.797G>T	p.Arg266Leu	p.R266L	ENST00000262741	NM_003629.3	266	cGt/cTt	7/10	1	2	FACETS	0.926	0.852	1	0.926	0.852	1	CLONAL	1	TRUE	1	0.570905675100965	2		422	590	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582133	52582133	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001867-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	170	319	0	ENST00000394830.3:c.4695G>C	p.Leu1565Phe	p.L1565F	ENST00000394830	NM_018313.4	1565	ttG/ttC	30/30	0.525035594431666	1	FACETS	0.961	0.893	1	0.961	0.893	1	CLONAL	1	TRUE	0	0.570905675100965	1		319	443	SUCCESS
APC	324	MSKCC	GRCh37	5	112173371	112173371	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001867-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	249	363	0	ENST00000257430.4:c.2080G>A	p.Asp694Asn	p.D694N	ENST00000257430	NM_000038.5	694	Gac/Aac	16/16	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.570905675100965	NA		363	530	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244073	46244073	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs746167865	NA	P-0001867-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	138	377	0	ENST00000334344.6:c.2167A>G	p.Ile723Val	p.I723V	ENST00000334344	NM_152641.2	723	Ata/Gta	15/21	1	2	FACETS	0.826	0.755	0.901	0.826	0.755	0.901	CLONAL	1	TRUE	1	0.570905675100965	2		377	585	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436964	49436964	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001867-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	112	359	0	ENST00000301067.7:c.5539G>C	p.Glu1847Gln	p.E1847Q	ENST00000301067	NM_003482.3	1847	Gag/Cag	25/54	1	2	FACETS	0.904	0.819	0.993	0.904	0.819	0.993	CLONAL	1	TRUE	1	0.570905675100965	2		359	434	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448190	49448190	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001867-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	95	381	0	ENST00000301067.7:c.410G>T	p.Trp137Leu	p.W137L	ENST00000301067	NM_003482.3	137	tGg/tTg	4/54	1	2	FACETS	0.725	0.649	0.806	0.725	0.649	0.806	SUBCLONAL	1	TRUE	1	0.570905675100965	2		381	459	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114144	115114144	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001867-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	143	367	0	ENST00000257566.3:c.1073C>A	p.Ser358Tyr	p.S358Y	ENST00000257566	NM_016569.3	358	tCc/tAc	6/8	1	2	FACETS	0.984	0.903	1	0.984	0.903	1	CLONAL	1	TRUE	1	0.570905675100965	2		367	509	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646591	23646591	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001867-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	124	315	0	ENST00000261584.4:c.1276G>A	p.Glu426Lys	p.E426K	ENST00000261584	NM_024675.3	426	Gag/Aag	4/13	0.296031375648935	1	FACETS	0.678	0.617	0.741	0.678	0.617	0.741	INDETERMINATE	1	TRUE	0	0.570905675100965	1		315	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577138	7577138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780075	NA	P-0001867-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	122	343	0	ENST00000269305.4:c.800G>A	p.Arg267Gln	p.R267Q	ENST00000269305	NM_001126112.2	267	cGg/cAg	8/11	0.507572148559416	2	FACETS	0.915	0.833	1	0.458	0.416	0.501	CLONAL	1	TRUE	0	0.570905675100965	2		343	467	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075152	16075152	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001867-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	144	283	0	ENST00000268712.3:c.400C>G	p.Pro134Ala	p.P134A	ENST00000268712	NM_006311.3	134	Cca/Gca	4/46	1	2	FACETS	0.868	0.795	0.944	0.868	0.795	0.944	CLONAL	1	TRUE	1	0.570905675100965	2		283	581	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591888	48591888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519739	NA	P-0001867-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	154	452	0	ENST00000342988.3:c.1051G>A	p.Asp351Asn	p.D351N	ENST00000342988	NM_005359.5	351	Gat/Aat	9/12	0.517426680022988	1	FACETS	0.862	0.797	0.93	0.862	0.797	0.93	CLONAL	1	TRUE	0	0.570905675100965	1		452	447	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610465	10610465	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001867-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	128	367	0	ENST00000171111.5:c.245A>C	p.Gln82Pro	p.Q82P	ENST00000171111	NM_203500.1	82	cAg/cCg	2/6	0.570905675100965	1	FACETS	0.9	0.826	0.976	0.9	0.826	0.976	CLONAL	1	TRUE	0	0.570905675100965	1		367	356	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344320	118344320	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781874908	NA	P-0001877-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	52	612	0	ENST00000534358.1:c.2446C>T	p.Pro816Ser	p.P816S	ENST00000534358	NM_005933.3	816	Cca/Tca	3/36	0.447313429926732	2	FACETS	0.688	0.588	0.796	0.344	0.294	0.398	SUBCLONAL	1	TRUE	0	0.447313429926732	2		612	338	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519998	NA	P-0001877-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	133	879	0	ENST00000269305.4:c.581T>C	p.Leu194Pro	p.L194P	ENST00000269305	NM_001126112.2	194	cTt/cCt	6/11	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	2	TRUE	NA	0.447313429926732	2		879	268	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676263	29676263	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001877-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	179	624	0	ENST00000356175.3:c.7253del	p.Leu2418Ter	p.L2418*	ENST00000356175	NM_000267.3	2418	Tta/ta	48/57	0.447313429926732	2	FACETS	0.964	0.9	1	0.964	0.9	1	CLONAL	2	TRUE	0	0.447313429926732	2		624	415	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0001883-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	177	470	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.436168117415544	3	FACETS	0.842	0.78	0.906	0.842	0.78	0.906	CLONAL	2	TRUE	1	0.436168117415544	3		470	587	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242715	66242715	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0001883-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	59	418	0	ENST00000273854.3:c.1856+1G>C		p.X619_splice	ENST00000273854	NM_004439.5	619			0.374883787722691	2	FACETS	0.529	0.456	0.609	0.265	0.228	0.305	SUBCLONAL	1	TRUE	0	0.436168117415544	2		418	511	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741178	145741178	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs558779399	NA	P-0001883-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	48	495	0	ENST00000428558.2:c.1228G>C	p.Asp410His	p.D410H	ENST00000428558	NM_004260.3	410	Gat/Cat	6/22	0.305922295519445	5	FACETS	0.919	0.779	1	0.306	0.259	0.358	CLONAL	1	TRUE	2	0.436168117415544	5		495	396	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407524	139407524	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001883-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	36	409	0	ENST00000277541.6:c.2416T>C	p.Cys806Arg	p.C806R	ENST00000277541	NM_017617.3	806	Tgt/Cgt	15/34	0.436168117415544	1	FACETS	0.466	0.385	0.556	0.466	0.385	0.556	SUBCLONAL	1	TRUE	0	0.436168117415544	1		409	277	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577027	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	GTGCTCCCTG	GTGCTCCCTG	-	novel	NA	P-0001883-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	127	500	1	ENST00000269305.4:c.902_911del	p.Pro301LeufsTer41	p.P301Lfs*41	ENST00000269305	NM_001126112.2	301	cCAGGGAGCACt/ct	8/11	0.377865690774427	2	FACETS	0.844	0.774	0.915	0.844	0.774	0.915	CLONAL	2	TRUE	0	0.436168117415544	2		501	345	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0001892-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	209	391	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	1	2	FACETS	1	0.964	1	1	0.994	1	CLONAL	2	FALSE	1	0.332283072082708	2		391	601	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0001892-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	42	459	1	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	1	2	FACETS	0.297	0.247	0.353	0.297	0.247	0.353	SUBCLONAL	1	FALSE	1	0.332283072082708	2		460	852	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6439807	6439807	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001892-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	523	481	0	ENST00000356142.4:c.333T>A	p.Asn111Lys	p.N111K	ENST00000356142	NM_018890.3	111	aaT/aaA	5/7	0.332283072082708	6	FACETS	0.893	0.856	0.931	0.714	0.685	0.745	CLONAL	4	FALSE	1	0.332283072082708	6		481	1467	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593609	55593611	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	rs121913685	NA	P-0001892-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	4262	497	0	ENST00000288135.5:c.1679_1681del	p.Val560del	p.V560del	ENST00000288135	NM_000222.2	559	GTT/-	11/21	0.332283072082708	34	FACETS	0.995	0.987	1			1	CLONAL	30	FALSE	NA	0.332283072082708	34		497	5426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578530	7578530	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001915-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	394	422	0	ENST00000269305.4:c.400T>G	p.Phe134Val	p.F134V	ENST00000269305	NM_001126112.2	134	Ttt/Gtt	5/11	0.415464616302074	2	FACETS	0.997	0.952	1	0.997	0.952	1	CLONAL	2	TRUE	0	0.414534360617121	2		422	953	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430522	181430522	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001915-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1344	147	388	0	ENST00000325404.1:c.374A>G	p.Tyr125Cys	p.Y125C	ENST00000325404	NM_003106.3	125	tAc/tGc	1/1	0.414534360617121	6	FACETS	0.87	0.792	0.953			1	CLONAL	1	TRUE	NA	0.414534360617121	6		388	1491	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681045	117681045	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1440151759	NA	P-0001915-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1218	247	580	0	ENST00000368508.3:c.3575A>G	p.Asp1192Gly	p.D1192G	ENST00000368508	NM_002944.2	1192	gAt/gGt	23/43	0.415464616302074	3	FACETS	0.982	0.916	1	0.491	0.458	0.526	CLONAL	1	TRUE	1	0.414534360617121	3		580	1465	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005276	150005276	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001915-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	486	558	0	ENST00000253339.5:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000253339		317	Cag/Tag	3/7	0.415464616302074	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.414534360617121	3		558	1339	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129360	2129360	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001915-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1277	171	524	1	ENST00000219476.3:c.3215G>T	p.Ser1072Ile	p.S1072I	ENST00000219476	NM_000548.3	1072	aGc/aTc	28/42	0.415464616302074	4	FACETS	0.806	0.739	0.876	0.269	0.246	0.292	CLONAL	1	TRUE	1	0.414534360617121	4		525	1448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0001923-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	179	693	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.371073818712579	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.371073818712579	2		693	462	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695864	117695864	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001923-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	112	278	0	ENST00000369458.3:c.573C>A	p.Phe191Leu	p.F191L	ENST00000369458	NM_024626.3	191	ttC/ttA	4/6	0.371073818712579	2	FACETS	0.888	0.808	0.97	0.888	0.808	0.97	CLONAL	2	TRUE	0	0.371073818712579	2		278	340	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663872	29663872	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001923-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	116	347	0	ENST00000356175.3:c.6304C>G	p.His2102Asp	p.H2102D	ENST00000356175	NM_000267.3	2102	Cat/Gat	41/57	0.282578438577922	3	FACETS	1	0.974	1			1	CLONAL	1	TRUE	NA	0.371073818712579	3		347	603	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218470	1218471	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0001954-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	25	536	0	ENST00000326873.7:c.348_349del	p.Leu117IlefsTer45	p.L117Ifs*45	ENST00000326873	NM_000455.4	115	gaTGtg/gatg	2/10	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		536	367	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156271	106156271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777619320	NA	P-0001957-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	66	300	0	ENST00000380013.4:c.1172C>T	p.Ser391Phe	p.S391F	ENST00000380013	NM_001127208.2	391	tCc/tTc	3/11	0.333084818318997	5	FACETS	1	0.965	1	0.819	0.728	0.912	INDETERMINATE	2	TRUE	2	0.66	5		300	162	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112248	115112248	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001957-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	28	52	0	ENST00000257566.3:c.1492C>A	p.Leu498Met	p.L498M	ENST00000257566	NM_016569.3	498	Ctg/Atg	7/8	0.429643305380902	4	FACETS	1	0.869	1			1	CLONAL	2	TRUE	NA	0.66	4		52	67	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990733	7990733	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001957-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	43	250	0	ENST00000319144.4:c.28A>G	p.Thr10Ala	p.T10A	ENST00000319144	NM_001139.2	10	Aca/Gca	1/15	0.333084818318997	5	FACETS	0.87	0.742	1	0.58	0.495	0.671	INDETERMINATE	2	TRUE	2	0.66	5		250	149	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856058	68856058	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001957-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	57	410	1	ENST00000261769.5:c.1866del	p.Asn622LysfsTer9	p.N622Kfs*9	ENST00000261769	NM_004360.3	622	aaT/aa	12/16	0.377006297209126	2	FACETS	0.8	0.713	0.885	0.8	0.713	0.885	INDETERMINATE	2	TRUE	0	0.66	2		411	108	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0001964-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	40	387	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.385278405862372	1	FACETS	0.901	0.798	0.998	1	0.979	1	CLONAL	3	FALSE	0	0.385278405862372	1		387	62	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0001964-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	77	454	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.227832261000147	3	FACETS	1	0.94	1	1	0.94	1	INDETERMINATE	3	FALSE	0	0.385278405862372	3		454	151	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0001964-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	47	336	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	NA	2	FACETS	0.847	0.743	0.951			1	INDETERMINATE	3	FALSE	NA	0.385278405862372	2		336	96	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0001980-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	88	314	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.384413970532506	2		314	376	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024480	16024480	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1432273966	NA	P-0001980-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	45	405	0	ENST00000268712.3:c.1738C>T	p.Arg580Cys	p.R580C	ENST00000268712	NM_006311.3	580	Cgc/Tgc	16/46	1	2	FACETS	0.431	0.362	0.508	0.431	0.362	0.508	SUBCLONAL	1	FALSE	1	0.384413970532506	2		405	543	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727455	66727455	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs869025608	NA	P-0001987-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	146	411	0	ENST00000307102.5:c.171G>T	p.Lys57Asn	p.K57N	ENST00000307102	NM_002755.3	57	aaG/aaT	2/11	0.341366725790938	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.341366725790938	2		411	395	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098944	178098944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001987-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	101	734	0	ENST00000397062.3:c.101G>A	p.Arg34Gln	p.R34Q	ENST00000397062	NM_006164.4	34	cGa/cAa	2/5	0.341366725790938	4	FACETS	1	0.919	1	0.345	0.308	0.384	CLONAL	1	TRUE	1	0.341366725790938	4		734	768	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782664	NA	P-0001987-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	106	299	0	ENST00000269305.4:c.711G>C	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atC	7/11	0.294615172046138	2	FACETS	0.989	0.898	1	0.989	0.898	1	CLONAL	2	TRUE	0	0.341366725790938	2		299	314	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202920	16202920	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001987-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	64	409	0	ENST00000375759.3:c.628A>T	p.Thr210Ser	p.T210S	ENST00000375759	NM_015001.2	210	Aca/Tca	3/15	0.25448530282234	1	FACETS	0.81	0.704	0.923	0.81	0.704	0.923	CLONAL	1	TRUE	0	0.341366725790938	1		409	384	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911519	134911519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752762812	NA	P-0001987-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	64	384	0	ENST00000398015.3:c.1984C>T	p.Arg662Cys	p.R662C	ENST00000398015	NM_004441.4	662	Cgt/Tgt	11/16	0.341366725790938	2	FACETS	0.91	0.791	1	0.455	0.395	0.519	CLONAL	1	TRUE	0	0.341366725790938	2		384	412	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456447	189456447	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001987-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	78	465	0	ENST00000264731.3:c.208C>T	p.Gln70Ter	p.Q70*	ENST00000264731	NM_003722.4	70	Cag/Tag	3/14	1	2	FACETS	0.901	0.794	1	0.901	0.794	1	CLONAL	1	TRUE	1	0.341366725790938	2		465	507	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361157	66361157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001987-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	74	458	0	ENST00000273854.3:c.1015G>A	p.Glu339Lys	p.E339K	ENST00000273854	NM_004439.5	339	Gaa/Aaa	4/18	0.341366725790938	4	FACETS	0.882	0.772	1	0.441	0.386	0.501	CLONAL	1	TRUE	2	0.341366725790938	4		458	659	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106162495	106162495	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0001987-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	116	336	0	ENST00000380013.4:c.3410-1G>C		p.X1137_splice	ENST00000380013	NM_001127208.2	1137			0.341366725790938	4	FACETS	0.882	0.798	0.969	0.882	0.798	0.969	CLONAL	2	TRUE	2	0.341366725790938	4		336	517	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067089	143067089	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001987-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	168	594	0	ENST00000262992.4:c.1624C>A	p.Leu542Met	p.L542M	ENST00000262992	NM_001101669.1	542	Ctg/Atg	16/24	0.341366725790938	4	FACETS	0.921	0.848	0.996	0.921	0.848	0.996	CLONAL	2	TRUE	2	0.341366725790938	4		594	717	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143235912	143235912	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001987-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	53	342	0	ENST00000262992.4:c.376C>T	p.Arg126Ter	p.R126*	ENST00000262992	NM_001101669.1	126	Cga/Tga	6/24	0.341366725790938	4	FACETS	0.745	0.635	0.866	0.373	0.317	0.433	SUBCLONAL	1	TRUE	2	0.341366725790938	4		342	559	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38942426	38942426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001987-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	90	414	0	ENST00000357387.3:c.5107G>A	p.Asp1703Asn	p.D1703N	ENST00000357387	NM_152756.3	1703	Gat/Aat	38/38	0.341366725790938	7	FACETS	1	0.942	1	0.22	0.195	0.248	CLONAL	1	TRUE	2	0.341366725790938	7		414	887	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174918	56174918	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001987-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	67	324	0	ENST00000399503.3:c.2077G>C	p.Asp693His	p.D693H	ENST00000399503	NM_005921.1	693	Gat/Cat	11/20	0.326576108141053	2	FACETS	1	0.904	1	0.521	0.455	0.591	CLONAL	1	TRUE	0	0.341366725790938	2		324	377	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589219	67589219	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001987-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	86	478	0	ENST00000274335.5:c.1207G>A	p.Glu403Lys	p.E403K	ENST00000274335		403	Gaa/Aaa	9/15	0.326576108141053	2	FACETS	0.952	0.845	1	0.476	0.422	0.534	CLONAL	1	TRUE	0	0.341366725790938	2		478	529	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031891	26031891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001987-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	59	187	0	ENST00000244661.2:c.398G>A	p.Gly133Glu	p.G133E	ENST00000244661	NM_003537.3	133	gGa/gAa	1/1	0.341366725790938	4	FACETS	1	0.96	1			1	CLONAL	1	TRUE	NA	0.341366725790938	4		187	353	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983881	2983881	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs767395417	NA	P-0001987-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	117	500	0	ENST00000396946.4:c.649A>T	p.Met217Leu	p.M217L	ENST00000396946	NM_032415.4	217	Atg/Ttg	5/25	0.341366725790938	3	FACETS	0.773	0.7	0.849			1	SUBCLONAL	2	TRUE	NA	0.341366725790938	3		500	519	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334708	81334708	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001987-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	79	553	0	ENST00000222390.5:c.2008G>A	p.Glu670Lys	p.E670K	ENST00000222390	NM_000601.4	670	Gag/Aag	17/18	0.341366725790938	4	FACETS	0.789	0.693	0.892	0.394	0.346	0.446	SUBCLONAL	1	TRUE	2	0.341366725790938	4		553	787	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737311	145737311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779826649	NA	P-0001987-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	81	418	0	ENST00000428558.2:c.3376G>A	p.Glu1126Lys	p.E1126K	ENST00000428558	NM_004260.3	1126	Gag/Aag	20/22	0.341366725790938	6	FACETS	1	0.923	1	0.213	0.187	0.241	CLONAL	1	TRUE	1	0.341366725790938	6		418	750	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741427	17741427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001987-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	55	390	0	ENST00000250003.3:c.98C>T	p.Pro33Leu	p.P33L	ENST00000250003	NM_002478.4	33	cCg/cTg	1/3	0.288251873943739	3	FACETS	0.846	0.725	0.977	0.423	0.362	0.489	CLONAL	1	TRUE	1	0.341366725790938	3		390	446	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145430	58145430	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894340	NA	P-0001987-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	74	378	0	ENST00000257904.6:c.71G>T	p.Arg24Leu	p.R24L	ENST00000257904	NM_000075.3	24	cGt/cTt	2/8	0.326576108141053	2	FACETS	0.859	0.753	0.971	0.429	0.376	0.486	CLONAL	1	TRUE	0	0.341366725790938	2		378	505	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264509	30264509	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001987-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	26	146	0	ENST00000322652.5:c.244G>A	p.Asp82Asn	p.D82N	ENST00000322652	NM_015355.2	82	Gac/Aac	1/16	0.337325885309699	4	FACETS	0.933	0.743	1	0.233	0.185	0.287	CLONAL	1	TRUE	0	0.341366725790938	4		146	219	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7119503	7119503	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001987-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	77	566	0	ENST00000302850.5:c.3751G>C	p.Asp1251His	p.D1251H	ENST00000302850	NM_000208.2	1251	Gat/Cat	21/22	0.341366725790938	2	FACETS	0.897	0.789	1	0.448	0.394	0.506	CLONAL	1	TRUE	0	0.341366725790938	2		566	503	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951100	17951100	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001987-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	70	369	0	ENST00000458235.1:c.1193C>G	p.Ser398Cys	p.S398C	ENST00000458235	NM_000215.3	398	tCc/tGc	9/24	0.321782357254109	3	FACETS	1	0.908	1	0.349	0.305	0.396	CLONAL	1	TRUE	0	0.341366725790938	3		369	459	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713427	40713427	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752787425	NA	P-0001987-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	63	352	0	ENST00000373198.4:c.4088G>A	p.Arg1363Gln	p.R1363Q	ENST00000373198	NM_133170.3	1363	cGg/cAg	30/32	0.288251873943739	3	FACETS	1	0.953	1	0.61	0.531	0.696	CLONAL	1	TRUE	1	0.341366725790938	3		352	354	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735506	40735506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001987-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	51	412	0	ENST00000373198.4:c.3367G>A	p.Ala1123Thr	p.A1123T	ENST00000373198	NM_133170.3	1123	Gcc/Acc	25/32	0.288251873943739	3	FACETS	0.813	0.693	0.945	0.407	0.346	0.473	CLONAL	1	TRUE	1	0.341366725790938	3		412	430	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051602	30051639	+	frameshift_variant	Frame_Shift_Del	DEL	TGACTCCGGAAATGTGGGAGGAGAGAATTACTGCTTGG	TGACTCCGGAAATGTGGGAGGAGAGAATTACTGCTTGG	-	novel	NA	P-0001997-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	177	886	0	ENST00000338641.4:c.537_574del	p.Met179IlefsTer11	p.M179Ifs*11	ENST00000338641	NM_000268.3	179	aTGACTCCGGAAATGTGGGAGGAGAGAATTACTGCTTGG/a	6/16	0.3	2	FACETS	0.957	0.905	1	1	0.995	1	CLONAL	7	TRUE	0	0.19	2		886	278	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0002010-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	154	470	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	NA	2	FACETS	0.966	0.886	1			1	INDETERMINATE	1	TRUE	NA	0.46	2		470	693	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404791	70404791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002010-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	536	339	0	ENST00000373644.4:c.2305G>A	p.Glu769Lys	p.E769K	ENST00000373644	NM_030625.2	769	Gaa/Aaa	4/12	0.3	5	FACETS	0.91	0.877	0.943	0.91	0.877	0.943	CLONAL	4	TRUE	1	0.46	5		339	1082	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223541	53223541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002010-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	54	192	0	ENST00000375401.3:c.3818C>T	p.Pro1273Leu	p.P1273L	ENST00000375401	NM_004187.3	1273	cCc/cTc	23/26	0.143081741139576	0	FACETS	0.54	0.466	0.618			1	INDETERMINATE	1	TRUE	0	0.46	0		192	235	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088788	27088788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002010-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	249	305	0	ENST00000324856.7:c.2402del	p.Gly801ValfsTer32	p.G801Vfs*32	ENST00000324856	NM_006015.4	799	caG/ca	7/20	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	2	TRUE	NA	0.46	2		305	512	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436624	52436624	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs387906848	NA	P-0002019-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	135	370	0	ENST00000460680.1:c.2050C>T	p.Gln684Ter	p.Q684*	ENST00000460680	NM_004656.3	684	Cag/Tag	16/17	0.581438919257692	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.581438919257692	1		370	320	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272308	38272308	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs869320694	NA	P-0002020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	205	478	0	ENST00000425967.3:c.2059A>G	p.Lys687Glu	p.K687E	ENST00000425967	NM_001174067.1	687	Aag/Gag	15/19	0.856911447762836	1	FACETS	0.991	0.95	1	0.991	0.95	1	CLONAL	1	TRUE	0	0.871308349199601	1		478	268	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224505	108224505	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	207	483	0	ENST00000278616.4:c.8684A>C	p.Glu2895Ala	p.E2895A	ENST00000278616	NM_000051.3	2895	gAa/gCa	60/63	0.871308349199601	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.871308349199601	1		483	259	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971393	15971393	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002047-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	60	441	0	ENST00000268712.3:c.4556del	p.Ser1519Ter	p.S1519*	ENST00000268712	NM_006311.3	1519	tCg/tg	32/46	0.282270125470262	5	FACETS	1	0.908	1	0.354	0.306	0.406	INDETERMINATE	1	FALSE	2	0.518381404201124	5		441	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0002053-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	145	401	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.284448945532852	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	0	0.288282823280304	2		402	484	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851510	128851510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002053-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	112	504	0	ENST00000249373.3:c.1835C>T	p.Ala612Val	p.A612V	ENST00000249373	NM_005631.4	612	gCt/gTt	11/12	0.288282823280304	5	FACETS	1	0.951	1	0.366	0.328	0.406	CLONAL	1	TRUE	2	0.288282823280304	5		504	1014	SUCCESS
BLM	641	MSKCC	GRCh37	15	91352420	91352420	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002053-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	115	412	0	ENST00000355112.3:c.3805G>A	p.Asp1269Asn	p.D1269N	ENST00000355112	NM_000057.2	1269	Gac/Aac	20/22	0.288282823280304	4	FACETS	1	0.946	1	0.36	0.323	0.398	CLONAL	1	TRUE	1	0.288282823280304	4		412	953	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139563042	139563063	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTGTCTCCGAGTCGTTCGTG	CCCTGTCTCCGAGTCGTTCGTG	-	novel	NA	P-0002053-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	86	395	0	ENST00000308874.7:c.115_136del	p.Pro39SerfsTer151	p.P39Sfs*151	ENST00000308874		38	gaCCCTGTCTCCGAGTCGTTCGTG/ga	4/10	0.288282823280304	6	FACETS	1	0.936	1	0.363	0.32	0.409	CLONAL	1	TRUE	3	0.288282823280304	6		395	864	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0002060-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	133	299	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.182409550642717	3	FACETS	0.93	0.848	1	0.93	0.848	1	CLONAL	3	TRUE	0	0.184014686696596	3		299	566	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486334	8486334	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536936783	NA	P-0002060-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	20	134	0	ENST00000356435.5:c.2483G>A	p.Arg828Gln	p.R828Q	ENST00000356435		828	cGg/cAg	17/35	0.180734364565987	2	FACETS	0.91	0.697	1	0.455	0.348	0.579	CLONAL	1	TRUE	0	0.184014686696596	2		134	239	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219336	1219336	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002060-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	120	336	0	ENST00000326873.7:c.388G>T	p.Glu130Ter	p.E130*	ENST00000326873	NM_000455.4	130	Gag/Tag	3/10	0.182612456062918	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	2	TRUE	0	0.184014686696596	2		336	648	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602404	10602404	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002060-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	102	384	0	ENST00000171111.5:c.1174G>C	p.Ala392Pro	p.A392P	ENST00000171111	NM_203500.1	392	Gcc/Ccc	3/6	0.182612456062918	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	2	TRUE	0	0.184014686696596	2		384	554	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0002070-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	319	556	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.450703323277361	2		556	1306	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0002070-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	348	336	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.231523906044418	3	FACETS	0.829	0.786	0.874	0.829	0.786	0.874	INDETERMINATE	2	TRUE	1	0.450703323277361	3		336	1141	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405951	49405951	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002070-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	141	358	0	ENST00000418115.1:c.187C>A	p.Gln63Lys	p.Q63K	ENST00000418115	NM_001664.2	63	Cag/Aag	3/5	1	2	FACETS	0.644	0.586	0.705	0.644	0.586	0.705	SUBCLONAL	1	TRUE	1	0.450703323277361	2		358	971	SUCCESS
ATM	472	MSKCC	GRCh37	11	108225543	108225543	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501563	NA	P-0002070-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	100	339	1	ENST00000278616.4:c.8792G>A	p.Cys2931Tyr	p.C2931Y	ENST00000278616	NM_000051.3	2931	tGt/tAt	61/63	0.339399411674591	0	FACETS	0.381	0.34	0.424			1	SUBCLONAL	1	TRUE	0	0.450703323277361	0		340	640	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457342	67457342	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs138550573	NA	P-0002070-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	179	345	2	ENST00000327367.4:c.316A>G	p.Met106Val	p.M106V	ENST00000327367	NM_005902.3	106	Atg/Gtg	2/9	0.238609082315826	1	FACETS	0.892	0.825	0.961	0.892	0.825	0.961	INDETERMINATE	1	TRUE	0	0.450703323277361	1		347	690	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041653	14041653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753924297	NA	P-0002070-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	126	390	0	ENST00000311895.7:c.2200G>A	p.Gly734Ser	p.G734S	ENST00000311895	NM_005236.2	734	Ggc/Agc	11/11	0.411477196105591	1	FACETS	0.496	0.448	0.545	0.496	0.448	0.545	SUBCLONAL	1	TRUE	0	0.450703323277361	1		390	874	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645415	67645415	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002070-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	184	272	0	ENST00000264010.4:c.680A>G	p.Asp227Gly	p.D227G	ENST00000264010	NM_006565.3	227	gAt/gGt	3/12	0.411477196105591	1	FACETS	0.898	0.832	0.967	0.898	0.832	0.967	CLONAL	1	TRUE	0	0.450703323277361	1		272	704	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645504	67645504	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002070-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	108	156	0	ENST00000264010.4:c.769A>G	p.Ile257Val	p.I257V	ENST00000264010	NM_006565.3	257	Att/Gtt	3/12	0.411477196105591	1	FACETS	0.949	0.859	1	0.949	0.859	1	CLONAL	1	TRUE	0	0.450703323277361	1		156	391	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306741	41306741	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002070-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	73	286	0	ENST00000373198.4:c.918G>T	p.Trp306Cys	p.W306C	ENST00000373198	NM_133170.3	306	tgG/tgT	7/32	0.231523906044418	3	FACETS	0.588	0.514	0.668	0.294	0.257	0.334	INDETERMINATE	1	TRUE	1	0.450703323277361	3		286	675	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966591	25966591	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0002087-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	62	355	0	ENST00000435504.4:c.2615C>G	p.Ser872Ter	p.S872*	ENST00000435504		872	tCa/tGa	13/13	1	2	FACETS	0.616	0.531	0.709	0.616	0.531	0.709	SUBCLONAL	1	FALSE	1	0.266200432369712	2		355	756	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456425	89456425	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002087-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	76	467	0	ENST00000336596.2:c.1601C>A	p.Ser534Tyr	p.S534Y	ENST00000336596	NM_005233.5	534	tCc/tAc	8/17	0.144167077917212	3	FACETS	0.575	0.503	0.654	0.288	0.251	0.327	INDETERMINATE	1	FALSE	1	0.266200432369712	3		467	1125	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979551	55979551	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002087-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1185	71	514	0	ENST00000263923.4:c.896G>T	p.Arg299Leu	p.R299L	ENST00000263923	NM_002253.2	299	cGg/cTg	7/30	1	2	FACETS	0.425	0.369	0.485	0.425	0.369	0.485	SUBCLONAL	1	FALSE	1	0.266200432369712	2		514	1256	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439341	149439341	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002087-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	90	473	0	ENST00000286301.3:c.2054C>A	p.Pro685His	p.P685H	ENST00000286301	NM_005211.3	685	cCc/cAc	15/22	0.181270537032683	1	FACETS	0.66	0.585	0.741	0.66	0.585	0.741	SUBCLONAL	1	FALSE	0	0.266200432369712	1		473	888	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681737	30681737	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002087-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	58	460	0	ENST00000376406.3:c.360G>C	p.Leu120Phe	p.L120F	ENST00000376406	NM_014641.2	120	ttG/ttC	3/15	1	2	FACETS	0.452	0.387	0.523	0.452	0.387	0.523	SUBCLONAL	1	FALSE	1	0.266200432369712	2		460	965	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739026	145739026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002087-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	195	307	0	ENST00000428558.2:c.2129G>T	p.Arg710Leu	p.R710L	ENST00000428558	NM_004260.3	710	cGc/cTc	13/22	0.133910872728142	5	FACETS	1	0.982	1	0.59	0.546	0.635	INDETERMINATE	2	FALSE	1	0.266200432369712	5		307	869	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390588	139390588	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002087-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	47	529	0	ENST00000277541.6:c.7603G>T	p.Gly2535Cys	p.G2535C	ENST00000277541	NM_017617.3	2535	Ggc/Tgc	34/34	1	2	FACETS	0.417	0.351	0.491	0.417	0.351	0.491	SUBCLONAL	1	FALSE	1	0.266200432369712	2		529	846	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606847	43606847	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002087-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	66	299	0	ENST00000355710.3:c.1456G>T	p.Val486Leu	p.V486L	ENST00000355710	NM_020975.4	486	Gtg/Ttg	7/20	1	2	FACETS	0.806	0.7	0.922	0.806	0.7	0.922	CLONAL	1	FALSE	1	0.266200432369712	2		299	615	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256135	123256135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141929882	NA	P-0002087-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	93	531	0	ENST00000358487.5:c.1774C>T	p.Arg592Cys	p.R592C	ENST00000358487	NM_000141.4	592	Cgt/Tgt	13/18	1	2	FACETS	0.646	0.573	0.725	0.646	0.573	0.725	SUBCLONAL	1	FALSE	1	0.266200432369712	2		531	1081	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498245	498245	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002087-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	25	182	0	ENST00000399788.2:c.13G>T	p.Gly5Trp	p.G5W	ENST00000399788	NM_001042603.1	5	Ggg/Tgg	1/28	0.257537223988656	1	FACETS	0.416	0.328	0.519	0.416	0.328	0.519	SUBCLONAL	1	FALSE	0	0.266200432369712	1		182	391	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891063	112891063	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002087-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	62	394	0	ENST00000351677.2:c.397G>T	p.Gly133Cys	p.G133C	ENST00000351677	NM_002834.3	133	Ggt/Tgt	4/16	NA	2	FACETS	0.553	0.476	0.636			1	INDETERMINATE	1	FALSE	NA	0.266200432369712	2		394	843	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562091	21562091	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002087-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1185	65	674	0	ENST00000382592.4:c.1828G>T	p.Val610Leu	p.V610L	ENST00000382592	NM_014572.2	610	Gtg/Ttg	4/8	NA	2	FACETS	0.391	0.337	0.449			1	INDETERMINATE	1	FALSE	NA	0.266200432369712	2		674	1250	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919313	48919313	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002087-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	78	318	0	ENST00000267163.4:c.478G>T	p.Ala160Ser	p.A160S	ENST00000267163	NM_000321.2	160	Gca/Tca	4/27	1	2	FACETS	0.735	0.645	0.832	0.735	0.645	0.832	SUBCLONAL	1	FALSE	1	0.266200432369712	2		318	797	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312379	91312379	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002087-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	56	431	0	ENST00000355112.3:c.2324G>C	p.Arg775Thr	p.R775T	ENST00000355112	NM_000057.2	775	aGa/aCa	11/22	1	2	FACETS	0.381	0.325	0.443	0.381	0.325	0.443	SUBCLONAL	1	FALSE	1	0.266200432369712	2		431	1104	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0002087-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	58	495	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.181270537032683	1	FACETS	0.431	0.369	0.499	0.431	0.369	0.499	SUBCLONAL	1	FALSE	0	0.266200432369712	1		495	877	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216458	2216458	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002087-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	37	372	0	ENST00000398665.3:c.2102T>A	p.Leu701Gln	p.L701Q	ENST00000398665	NM_032482.2	701	cTg/cAg	20/28	0.266200432369712	1	FACETS	0.344	0.283	0.413	0.344	0.283	0.413	SUBCLONAL	1	FALSE	0	0.266200432369712	1		372	700	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602772	10602772	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002087-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	39	429	0	ENST00000171111.5:c.806G>T	p.Arg269Leu	p.R269L	ENST00000171111	NM_203500.1	269	cGg/cTg	3/6	0.266200432369712	1	FACETS	0.37	0.305	0.442	0.37	0.305	0.442	SUBCLONAL	1	FALSE	0	0.266200432369712	1		429	687	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107191	11107191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002087-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	69	394	0	ENST00000358026.2:c.1783C>T	p.Gln595Ter	p.Q595*	ENST00000358026	NM_001128849.1	595	Cag/Tag	11/36	0.266200432369712	1	FACETS	0.648	0.564	0.74	0.648	0.564	0.74	SUBCLONAL	1	FALSE	0	0.266200432369712	1		394	693	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313222	30313222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002087-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	78	559	0	ENST00000262643.3:c.916C>T	p.His306Tyr	p.H306Y	ENST00000262643	NM_001238.2	306	Cat/Tat	10/12	0.266200432369712	1	FACETS	0.53	0.465	0.601	0.53	0.465	0.601	SUBCLONAL	1	FALSE	0	0.266200432369712	1		559	958	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794086	42794086	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002087-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	33	211	0	ENST00000575354.2:c.1447G>A	p.Asp483Asn	p.D483N	ENST00000575354	NM_015125.3	483	Gac/Aac	9/20	0.266200432369712	1	FACETS	0.386	0.313	0.468	0.386	0.313	0.468	SUBCLONAL	1	FALSE	0	0.266200432369712	1		211	557	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599338	55599338	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002094-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	124	343	0	ENST00000288135.5:c.2464A>T	p.Asn822Tyr	p.N822Y	ENST00000288135	NM_000222.2	822	Aat/Tat	17/21	0.250933174453305	1	FACETS	0.773	0.702	0.847	1	0.986	1	SUBCLONAL	2	FALSE	0	0.250933174453305	1		343	559	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0002095-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	32	412	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.111218396916848	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		413	788	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501195	NA	P-0002125-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	48	300	0	ENST00000269305.4:c.313G>A	p.Gly105Ser	p.G105S	ENST00000269305	NM_001126112.2	105	Ggc/Agc	4/11	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.13	2		300	626	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120508094	120508094	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1475043862	NA	P-0002125-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	59	273	0	ENST00000256646.2:c.1663G>A	p.Glu555Lys	p.E555K	ENST00000256646	NM_024408.3	555	Gaa/Aaa	10/34	1	2	FACETS	0.989	0.848	1	0.989	0.848	1	CLONAL	1	TRUE	1	0.13	2		273	918	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666420	206666420	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002125-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	86	292	0	ENST00000367120.3:c.1900G>A	p.Glu634Lys	p.E634K	ENST00000367120	NM_014002.3	634	Gaa/Aaa	19/22	1	2	FACETS	0.895	0.792	1	1	0.983	1	CLONAL	2	TRUE	1	0.13	2		292	739	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527338	157527338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002125-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	50	291	0	ENST00000346085.5:c.5063G>A	p.Arg1688Lys	p.R1688K	ENST00000346085	NM_020732.3	1688	aGa/aAa	20/20	1	2	FACETS	0.821	0.694	0.961	0.821	0.694	0.961	CLONAL	1	TRUE	1	0.13	2		291	937	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399504	139399504	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002125-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	62	264	0	ENST00000277541.6:c.4639C>T	p.Gln1547Ter	p.Q1547*	ENST00000277541	NM_017617.3	1547	Cag/Tag	26/34	1	2	FACETS	0.786	0.679	0.902	1	0.972	1	CLONAL	2	TRUE	1	0.13	2		264	607	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432459	49432459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002125-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	46	311	0	ENST00000301067.7:c.8680C>T	p.Pro2894Ser	p.P2894S	ENST00000301067	NM_003482.3	2894	Ccg/Tcg	34/54	1	2	FACETS	0.95	0.798	1	0.95	0.798	1	CLONAL	1	TRUE	1	0.13	2		311	745	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292874	91292874	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778106	NA	P-0002125-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	53	338	0	ENST00000355112.3:c.376C>T	p.Pro126Ser	p.P126S	ENST00000355112	NM_000057.2	126	Cca/Tca	3/22	1	2	FACETS	0.807	0.685	0.94	0.807	0.685	0.94	CLONAL	1	TRUE	1	0.13	2		338	1011	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134559	2134559	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002125-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	37	322	0	ENST00000219476.3:c.4336C>T	p.Pro1446Ser	p.P1446S	ENST00000219476	NM_000548.3	1446	Cct/Tct	34/42	1	2	FACETS	0.949	0.781	1	0.949	0.781	1	CLONAL	1	TRUE	1	0.13	2		322	600	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577514	7577514	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002125-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	35	268	0	ENST00000269305.4:c.767C>G	p.Thr256Arg	p.T256R	ENST00000269305	NM_001126112.2	256	aCa/aGa	7/11	1	2	FACETS	1	0.837	1	1	0.837	1	CLONAL	1	TRUE	1	0.13	2		268	526	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980318	7980318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774333332	NA	P-0002125-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	31	176	0	ENST00000319144.4:c.1265C>T	p.Pro422Leu	p.P422L	ENST00000319144	NM_001139.2	422	cCc/cTc	9/15	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.13	2		176	351	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47684611	47684611	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0002125-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	59	293	0	ENST00000347630.2:c.837+1G>T		p.X279_splice	ENST00000347630	NM_001007230.1	279			1	2	FACETS	0.927	0.795	1	0.927	0.795	1	CLONAL	1	TRUE	1	0.13	2		293	979	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138500	11138500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002125-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	57	366	0	ENST00000358026.2:c.3256G>A	p.Asp1086Asn	p.D1086N	ENST00000358026	NM_001128849.1	1086	Gat/Aat	24/36	1	2	FACETS	0.999	0.855	1	0.999	0.855	1	CLONAL	1	TRUE	1	0.13	2		366	878	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179029	123179029	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002125-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	44	198	0	ENST00000218089.9:c.478C>T	p.Pro160Ser	p.P160S	ENST00000218089	NM_001042749.1	160	Cca/Tca	8/35	1	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.13	1		198	541	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941638	48941642	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTT	TCTTT	-	novel	NA	P-0002125-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	58	336	0	ENST00000267163.4:c.948_952del	p.Leu317Ter	p.L317*	ENST00000267163	NM_000321.2	316	aaTCTTTct/aact	10/27	1	2	FACETS	0.833	0.713	0.965	0.833	0.713	0.965	CLONAL	1	TRUE	1	0.13	2		336	1071	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0002126-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	226	398	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.239425877505838	2	FACETS	0.946	0.885	1	0.946	0.885	1	CLONAL	2	FALSE	0	0.315424264890298	2		398	757	SUCCESS
ATR	545	MSKCC	GRCh37	3	142257388	142257388	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002126-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	227	349	0	ENST00000350721.4:c.3661C>A	p.Pro1221Thr	p.P1221T	ENST00000350721	NM_001184.3	1221	Cct/Act	19/47	0.296091227073544	2	FACETS	0.883	0.825	0.943	0.883	0.825	0.943	CLONAL	2	FALSE	0	0.315424264890298	2		349	815	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136984	64136984	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1157020356	NA	P-0002126-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	53	252	0	ENST00000334205.4:c.1495C>T	p.Arg499Trp	p.R499W	ENST00000334205	NM_003942.2	499	Cgg/Tgg	13/17	0.263486492322009	3	FACETS	0.648	0.552	0.754	0.324	0.276	0.377	SUBCLONAL	1	FALSE	1	0.315424264890298	3		252	600	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0002128-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	157	314	0	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	0.98	1	CLONAL	1	TRUE	1	0.596568100963287	2		314	446	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0002128-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	150	377	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.998	0.918	1	0.998	0.918	1	CLONAL	1	TRUE	1	0.596568100963287	2		378	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0002128-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	173	511	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	0.596568100963287	2		511	491	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940431	76940431	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002128-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	164	572	0	ENST00000373344.5:c.662G>A	p.Arg221Lys	p.R221K	ENST00000373344	NM_000489.3	221	aGg/aAg	8/35	0.407592275553973	1	FACETS	0.738	0.682	0.795	0.738	0.682	0.795	SUBCLONAL	1	TRUE	0	0.596568100963287	1		572	523	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589526	67589600	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AATCTTTCTAGGATCAAGTTGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACACTC	AATCTTTCTAGGATCAAGTTGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACACTC	-	novel	NA	P-0002128-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	74	311	0	ENST00000274335.5:c.1300-10_1364del		p.X434_splice	ENST00000274335		434		10/15	0.186506898236016	3	FACETS	0.834	0.735	0.941	0.417	0.367	0.471	INDETERMINATE	1	TRUE	1	0.596568100963287	3		311	386	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439286	52439286	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002135-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	183	239	0	ENST00000460680.1:c.956C>A	p.Ser319Ter	p.S319*	ENST00000460680	NM_004656.3	319	tCa/tAa	11/17	0.781881046113234	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.788228463113189	1		239	271	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106492	108106492	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587781688	NA	P-0002135-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	492	229	0	ENST00000278616.4:c.427A>G	p.Asn143Asp	p.N143D	ENST00000278616	NM_000051.3	143	Aac/Gac	5/63	0.771880531700054	2	FACETS	0.991	0.965	1	0.991	0.965	1	CLONAL	2	TRUE	0	0.788228463113189	2		229	630	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0002142-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	138	470	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	0.27	2		470	796	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0002142-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	84	591	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.193325987957762	1	FACETS	0.828	0.732	0.931	0.828	0.732	0.931	CLONAL	1	TRUE	0	0.27	1		591	650	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391168	89391168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772463834	NA	P-0002142-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	74	452	0	ENST00000336596.2:c.1234G>A	p.Val412Ile	p.V412I	ENST00000336596	NM_005233.5	412	Gtt/Att	5/17	1	2	FACETS	0.921	0.807	1	0.921	0.807	1	CLONAL	1	TRUE	1	0.27	2		452	595	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279534	1279534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1368095577	NA	P-0002142-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	30	543	1	ENST00000310581.5:c.2002G>A	p.Glu668Lys	p.E668K	ENST00000310581	NM_198253.2	668	Gag/Aag	5/16	0.3	1	FACETS	0.514	0.414	0.627	0.514	0.414	0.627	SUBCLONAL	1	TRUE	0	0.27	1		544	374	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930634	32930634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56070345	NA	P-0002142-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	53	512	1	ENST00000380152.3:c.7505G>A	p.Arg2502His	p.R2502H	ENST00000380152		2502	cGc/cAc	15/27	0.193325987957762	1	FACETS	0.465	0.395	0.541	0.465	0.395	0.541	SUBCLONAL	1	TRUE	0	0.27	1		513	731	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561423	9561423	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201131316	NA	P-0002142-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	43	592	0	ENST00000353224.5:c.359C>T	p.Ala120Val	p.A120V	ENST00000353224	NM_177990.2	120	gCg/gTg	4/10	1	2	FACETS	0.54	0.451	0.639	0.54	0.451	0.639	SUBCLONAL	1	TRUE	1	0.27	2		592	590	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0002151-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1282	128	412	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.192790232855031	5	FACETS	1	0.973	1	0.405	0.365	0.447	CLONAL	1	TRUE	2	0.192790232855031	5		413	1410	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355283	81355283	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002151-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	197	516	0	ENST00000222390.5:c.1091G>T	p.Trp364Leu	p.W364L	ENST00000222390	NM_000601.4	364	tGg/tTg	9/18	0.188171529876607	4	FACETS	0.908	0.839	0.981	0.908	0.839	0.981	CLONAL	2	TRUE	2	0.192790232855031	4		516	1342	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508872	106508872	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002151-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	89	379	0	ENST00000359195.3:c.866A>G	p.Asn289Ser	p.N289S	ENST00000359195	NM_002649.2	289	aAc/aGc	2/11	0.188171529876607	4	FACETS	1	0.972	1	0.667	0.591	0.749	CLONAL	1	TRUE	2	0.192790232855031	4		379	825	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319910	8319910	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002151-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	183	604	0	ENST00000356435.5:c.5591T>A	p.Met1864Lys	p.M1864K	ENST00000356435		1864	aTg/aAg	34/35	0.192790232855031	3	FACETS	0.848	0.781	0.918	0.848	0.781	0.918	CLONAL	2	TRUE	1	0.192790232855031	3		604	1227	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100285	8100285	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002151-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	68	414	0	ENST00000346208.3:c.259C>A	p.Pro87Thr	p.P87T	ENST00000346208		87	Ccg/Acg	3/6	0.0793350480053707	4	FACETS	1	0.969	1	0.711	0.618	0.81	INDETERMINATE	1	TRUE	2	0.192790232855031	4		414	592	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186830	108186830	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002151-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	112	455	1	ENST00000278616.4:c.6188G>T	p.Gly2063Val	p.G2063V	ENST00000278616	NM_000051.3	2063	gGa/gTa	42/63	0.192790232855031	3	FACETS	1	0.976	1	0.649	0.582	0.719	CLONAL	1	TRUE	1	0.192790232855031	3		456	982	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786802	3786802	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002151-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	50	430	0	ENST00000262367.5:c.4409A>T	p.His1470Leu	p.H1470L	ENST00000262367	NM_004380.2	1470	cAc/cTc	27/31	0.192790232855031	1	FACETS	0.83	0.703	0.968	0.83	0.703	0.968	CLONAL	1	TRUE	0	0.192790232855031	1		430	565	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016651	12016651	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002151-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	91	410	0	ENST00000353533.5:c.787G>T	p.Asp263Tyr	p.D263Y	ENST00000353533	NM_003010.3	263	Gat/Tat	7/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.192790232855031	2		410	829	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291941	15291941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002151-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	21	304	0	ENST00000263388.2:c.2825del	p.Gly942AlafsTer2	p.G942Afs*2	ENST00000263388	NM_000435.2	942	gGc/gc	18/33	0.150709159477538	0	FACETS	0.6	0.462	0.761			1	SUBCLONAL	1	TRUE	0	0.192790232855031	0		304	293	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0002176-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	155	553	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.237252111882341	4	FACETS	1	0.965	1	0.55	0.504	0.599	INDETERMINATE	1	TRUE	2	0.472452179532524	4		553	878	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1268741	1268741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060503009	NA	P-0002176-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	90	261	0	ENST00000310581.5:c.2476G>A	p.Val826Ile	p.V826I	ENST00000310581	NM_198253.2	826	Gtc/Atc	9/16	0.472452179532524	1	FACETS	0.786	0.703	0.874	0.786	0.703	0.874	SUBCLONAL	1	TRUE	0	0.472452179532524	1		261	370	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061310	38061310	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs745876197	NA	P-0002176-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	287	318	0	ENST00000250448.2:c.679T>C	p.Cys227Arg	p.C227R	ENST00000250448	NM_004496.3	227	Tgc/Cgc	2/2	0.237252111882341	4	FACETS	0.784	0.737	0.832	0.784	0.737	0.832	INDETERMINATE	2	TRUE	2	0.472452179532524	4		318	1141	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0002178-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	71	235	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	NA	2	FACETS	1	0.967	1			1	INDETERMINATE	1	TRUE	NA	0.26	2		235	410	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220400	1220400	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002178-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	66	388	0	ENST00000326873.7:c.493G>C	p.Glu165Gln	p.E165Q	ENST00000326873	NM_000455.4	165	Gag/Cag	4/10	NA	2	FACETS	1	0.957	1			1	INDETERMINATE	1	TRUE	NA	0.26	2		388	408	SUCCESS
REL	5966	MSKCC	GRCh37	2	61144017	61144017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1317515438	NA	P-0002178-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	133	307	0	ENST00000295025.8:c.400G>A	p.Glu134Lys	p.E134K	ENST00000295025	NM_002908.2	134	Gaa/Aaa	5/11	0.278803375979347	4	FACETS	0.929	0.845	1			1	CLONAL	2	TRUE	NA	0.26	4		307	694	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274974	142274974	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002178-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	121	250	0	ENST00000350721.4:c.2086G>T	p.Val696Phe	p.V696F	ENST00000350721	NM_001184.3	696	Gtc/Ttc	10/47	0.188248468160337	5	FACETS	1	0.952	1	0.72	0.652	0.791	CLONAL	2	TRUE	2	0.26	5		250	599	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197704	66197704	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002178-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	56	308	0	ENST00000273854.3:c.2995C>T	p.Gln999Ter	p.Q999*	ENST00000273854	NM_004439.5	999	Cag/Tag	17/18	0.202427559711344	3	FACETS	0.741	0.634	0.858	0.37	0.317	0.429	SUBCLONAL	1	TRUE	1	0.26	3		308	657	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158626	26158626	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002178-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	27	109	0	ENST00000289316.2:c.229G>C	p.Glu77Gln	p.E77Q	ENST00000289316	NM_138720.2	77	Gag/Cag	1/2	0.3	13	FACETS	1	0.922	1			1	CLONAL	1	TRUE	NA	0.26	13		109	366	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782136	135782136	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002178-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	52	460	0	ENST00000298552.3:c.1420G>T	p.Glu474Ter	p.E474*	ENST00000298552	NM_001162426.1	474	Gaa/Taa	14/23	1	2	FACETS	0.62	0.527	0.722	0.62	0.527	0.722	SUBCLONAL	1	TRUE	1	0.26	2		460	645	SUCCESS
RET	5979	MSKCC	GRCh37	10	43613863	43613863	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002178-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	33	284	0	ENST00000355710.3:c.2327T>C	p.Phe776Ser	p.F776S	ENST00000355710	NM_020975.4	776	tTc/tCc	13/20	1	2	FACETS	0.586	0.477	0.709	0.586	0.477	0.709	SUBCLONAL	1	TRUE	1	0.26	2		284	433	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70432777	70432777	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002178-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	42	447	0	ENST00000373644.4:c.4799G>C	p.Arg1600Thr	p.R1600T	ENST00000373644	NM_030625.2	1600	aGa/aCa	8/12	0.227663536751119	1	FACETS	0.448	0.373	0.531	0.448	0.373	0.531	SUBCLONAL	1	TRUE	0	0.26	1		447	628	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050906	49050906	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002178-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	121	306	1	ENST00000267163.4:c.2590G>T	p.Glu864Ter	p.E864*	ENST00000267163	NM_000321.2	864	Gaa/Taa	25/27	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.26	2		307	671	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1206925	1206925	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002178-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	59	145	0	ENST00000326873.7:c.13G>C	p.Asp5His	p.D5H	ENST00000326873	NM_000455.4	5	Gac/Cac	1/10	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.26	NA		145	320	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1206952	1206952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002178-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	70	182	0	ENST00000326873.7:c.40G>A	p.Glu14Lys	p.E14K	ENST00000326873	NM_000455.4	14	Gag/Aag	1/10	NA	2	FACETS	0.754	0.662	0.853			1	INDETERMINATE	2	TRUE	NA	0.26	2		182	357	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207114	1207114	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002178-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	87	338	0	ENST00000326873.7:c.202G>C	p.Asp68His	p.D68H	ENST00000326873	NM_000455.4	68	Gac/Cac	1/10	NA	2	FACETS	1	0.96	1			1	INDETERMINATE	1	TRUE	NA	0.26	2		338	565	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0002184-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1309	460	456	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.761041128118987	3	FACETS	0.943	0.899	0.989	0.472	0.449	0.495	CLONAL	1	TRUE	1	0.761041128118987	3		456	1769	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0002184-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	734	591	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	NA	2	FACETS	0.962	0.939	0.983			1	INDETERMINATE	2	TRUE	NA	0.761041128118987	2		591	1003	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741915	17741915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002184-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	48	48	0	ENST00000250003.3:c.586G>A	p.Asp196Asn	p.D196N	ENST00000250003	NM_002478.4	196	Gac/Aac	1/3	0.248822968994455	1	FACETS	0.588	0.509	0.669	0.588	0.509	0.669	INDETERMINATE	1	TRUE	0	0.761041128118987	1		48	133	SUCCESS
ATR	545	MSKCC	GRCh37	3	142232374	142232374	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0002188-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	216	359	0	ENST00000350721.4:c.4610T>A	p.Leu1537Ter	p.L1537*	ENST00000350721	NM_001184.3	1537	tTa/tAa	26/47	0.447354606867932	5	FACETS	1	0.991	1	0.733	0.681	0.787	CLONAL	1	FALSE	3	0.447354606867932	5		359	1101	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625080	69625080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782166974	NA	P-0002188-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	51	196	0	ENST00000334134.2:c.713C>T	p.Ala238Val	p.A238V	ENST00000334134	NM_005247.2	238	gCg/gTg	3/3	0.447354606867932	17	FACETS	1	0.954	1			1	CLONAL	1	FALSE	NA	0.447354606867932	17		196	734	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374366	31374366	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757657111	NA	P-0002188-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	163	388	0	ENST00000328111.2:c.365G>A	p.Arg122His	p.R122H	ENST00000328111	NM_006892.3	122	cGt/cAt	5/23	0.447876167723022	3	FACETS	1	0.986	1			1	CLONAL	1	FALSE	NA	0.447354606867932	3		388	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579345	7579364	+	frameshift_variant	Frame_Shift_Del	DEL	CAAGAAGCCCAGACGGAAAC	CAAGAAGCCCAGACGGAAAC	-	novel	NA	P-0002188-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	344	318	0	ENST00000269305.4:c.323_342del	p.Gly108AlafsTer34	p.G108Afs*34	ENST00000269305	NM_001126112.2	108	gGTTTCCGTCTGGGCTTCTTG/g	4/11	0.447876167723022	6	FACETS	1	0.986	1	1	0.986	1	CLONAL	6	FALSE	0	0.447354606867932	6		318	468	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0002206-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	32	261	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.281	0.227	0.342	0.281	0.227	0.342	SUBCLONAL	1	TRUE	1	0.377767928270765	2		261	603	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721176	61721176	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002206-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	75	401	1	ENST00000401558.2:c.1098T>A	p.Phe366Leu	p.F366L	ENST00000401558	NM_003400.3	366	ttT/ttA	12/25	1	2	FACETS	0.379	0.331	0.431	0.379	0.331	0.431	SUBCLONAL	1	TRUE	1	0.377767928270765	2		402	1048	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0002207-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	404	335	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.453954089033813	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.483470142181604	2		335	751	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995188	15995188	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002207-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	93	636	0	ENST00000268712.3:c.3005G>C	p.Arg1002Thr	p.R1002T	ENST00000268712	NM_006311.3	1002	aGa/aCa	22/46	0.483470142181604	1	FACETS	0.365	0.324	0.408	0.365	0.324	0.408	SUBCLONAL	1	TRUE	0	0.483470142181604	1		636	800	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024029	27024029	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002207-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	13	45	0	ENST00000324856.7:c.1135C>G	p.Gln379Glu	p.Q379E	ENST00000324856	NM_006015.4	379	Cag/Gag	1/20	1	2	FACETS	0.464	0.333	0.619	0.464	0.333	0.619	SUBCLONAL	1	TRUE	1	0.483470142181604	2		45	116	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710794	117710794	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002207-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	166	539	0	ENST00000368508.3:c.1478G>T	p.Arg493Leu	p.R493L	ENST00000368508	NM_002944.2	493	cGc/cTc	12/43	0.426199893062023	2	FACETS	0.789	0.725	0.856	0.395	0.362	0.428	SUBCLONAL	1	TRUE	0	0.483470142181604	2		539	870	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347415	91347415	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002207-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	45	389	2	ENST00000355112.3:c.3577G>C	p.Glu1193Gln	p.E1193Q	ENST00000355112	NM_000057.2	1193	Gaa/Caa	19/22	0.432208750453906	2	FACETS	0.342	0.287	0.403	0.171	0.143	0.202	SUBCLONAL	1	TRUE	0	0.483470142181604	2		391	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578446	7578446	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002207-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	164	368	0	ENST00000269305.4:c.484A>T	p.Ile162Phe	p.I162F	ENST00000269305	NM_001126112.2	162	Atc/Ttc	5/11	0.483470142181604	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.483470142181604	1		368	439	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799254	42799254	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002207-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	32	195	0	ENST00000575354.2:c.4738G>C	p.Glu1580Gln	p.E1580Q	ENST00000575354	NM_015125.3	1580	Gag/Cag	20/20	0.483470142181604	1	FACETS	0.256	0.208	0.311	0.256	0.208	0.311	SUBCLONAL	1	TRUE	0	0.483470142181604	1		195	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0002215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	76	371	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.16	2		371	761	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0002215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	50	287	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	1	2	FACETS	0.862	0.73	1	0.862	0.73	1	CLONAL	1	TRUE	1	0.16	2		287	725	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845144	128845144	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002215-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	71	359	1	ENST00000249373.3:c.638G>T	p.Cys213Phe	p.C213F	ENST00000249373	NM_005631.4	213	tGc/tTc	3/12	1	2	FACETS	0.998	0.869	1	0.998	0.869	1	CLONAL	1	TRUE	1	0.16	2		360	889	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349127	11349127	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002225-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	98	133	0	ENST00000332029.2:c.209C>T	p.Ala70Val	p.A70V	ENST00000332029	NM_003745.1	70	gCc/gTc	2/2	0.121014488144176	4	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.470077089625526	4		133	481	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091333	193091333	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs28942098	NA	P-0002226-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	751	237	0	ENST00000367435.3:c.3G>A	p.Met1?	p.M1?	ENST00000367435	NM_024529.4	1	atG/atA	1/17	0.731885871821767	3	FACETS	0.992	0.973	1	0.992	0.973	1	CLONAL	3	TRUE	0	0.754726903089502	3		237	921	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970864	55970864	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs774211387	NA	P-0002226-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	453	587	0	ENST00000263923.4:c.1933C>G	p.Gln645Glu	p.Q645E	ENST00000263923	NM_002253.2	645	Caa/Gaa	13/30	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.754726903089502	2		587	1162	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609812	117609812	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002226-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	567	609	0	ENST00000368508.3:c.6887A>G	p.Glu2296Gly	p.E2296G	ENST00000368508	NM_002944.2	2296	gAa/gGa	43/43	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.754726903089502	2		609	1372	SUCCESS
MET	4233	MSKCC	GRCh37	7	116409781	116409781	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002226-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	102	416	0	ENST00000397752.3:c.2666C>T	p.Ser889Phe	p.S889F	ENST00000397752	NM_000245.2	889	tCt/tTt	12/21	1	2	FACETS	0.255	0.227	0.284	0.255	0.227	0.284	SUBCLONAL	1	TRUE	1	0.754726903089502	2		416	1061	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285666	46285666	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002226-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1597	91	513	0	ENST00000334344.6:c.5026C>G	p.Gln1676Glu	p.Q1676E	ENST00000334344	NM_152641.2	1676	Cag/Gag	17/21	0.754726903089502	3	FACETS	0.197	0.174	0.222	0.098	0.087	0.111	SUBCLONAL	1	TRUE	1	0.754726903089502	3		513	1688	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911322	32911322	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs80358533	NA	P-0002226-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	369	377	0	ENST00000380152.3:c.2830A>T	p.Lys944Ter	p.K944*	ENST00000380152		944	Aaa/Taa	11/27	1	2	FACETS	0.993	0.944	1	0.993	0.944	1	CLONAL	1	TRUE	1	0.754726903089502	2		377	985	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577526	7577526	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121912653	NA	P-0002242-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	611	380	0	ENST00000269305.4:c.755T>C	p.Leu252Pro	p.L252P	ENST00000269305	NM_001126112.2	252	cTc/cCc	7/11	0.914376855628532	3	FACETS	0.995	0.982	1	0.995	0.982	1	CLONAL	3	TRUE	0	0.919861569217099	3		380	650	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161856	47161856	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002253-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	102	459	0	ENST00000409792.3:c.4270del	p.Arg1424GlufsTer8	p.R1424Efs*8	ENST00000409792	NM_014159.6	1424	Aga/ga	3/21	0.372308805805632	3	FACETS	0.846	0.757	0.941	0.282	0.252	0.314	CLONAL	1	TRUE	0	0.372308805805632	3		459	768	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289242	33289245	+	frameshift_variant	Frame_Shift_Del	DEL	CCGC	CCGC	-	novel	NA	P-0002253-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	128	266	0	ENST00000374542.5:c.307_310del	p.Ala103SerfsTer40	p.A103Sfs*40	ENST00000374542	NM_001141970.1	103	GCGGag/ag	3/8	0.261853348376895	3	FACETS	1	0.953	1	0.706	0.647	0.767	CLONAL	2	TRUE	0	0.372308805805632	3		266	385	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575456	64575456	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002253-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	177	404	0	ENST00000312049.6:c.561del	p.Asn189MetfsTer35	p.N189Mfs*35	ENST00000312049	NM_130799.2	187	ggG/gg	3/10	0.364160371855511	2	FACETS	0.863	0.8	0.927	0.863	0.8	0.927	CLONAL	2	TRUE	0	0.372308805805632	2		404	551	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188049	151188049	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002253-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	129	589	0	ENST00000262187.5:c.104A>C	p.Tyr35Ser	p.Y35S	ENST00000262187	NM_005614.3	35	tAc/tCc	2/8	0.372308805805632	3	FACETS	0.881	0.798	0.969	0.441	0.399	0.485	CLONAL	1	TRUE	1	0.372308805805632	3		589	933	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584762	52584762	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0002255-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	102	694	0	ENST00000394830.3:c.4359+1G>A		p.X1453_splice	ENST00000394830	NM_018313.4	1453			0.483428940811094	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.483428940811094	1		694	287	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779166	135779166	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397514789	NA	P-0002255-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	83	549	0	ENST00000298552.3:c.2080C>T	p.Gln694Ter	p.Q694*	ENST00000298552	NM_001162426.1	694	Cag/Tag	17/23	0.410375244861871	0	FACETS	0.662	0.592	0.735			1	SUBCLONAL	1	TRUE	0	0.483428940811094	0		549	268	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100415	8100415	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002255-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	78	752	0	ENST00000346208.3:c.389T>A	p.Leu130His	p.L130H	ENST00000346208		130	cTc/cAc	3/6	0.106894865259987	4	FACETS	1	0.97	1	0.654	0.578	0.734	INDETERMINATE	1	TRUE	2	0.483428940811094	4		752	366	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682777	190682777	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002259-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	134	407	0	ENST00000441310.2:c.453T>A	p.Asn151Lys	p.N151K	ENST00000441310	NM_000534.4	151	aaT/aaA	5/13	0.299791080658833	4	FACETS	1	0.985	1	0.722	0.657	0.789	CLONAL	1	TRUE	2	0.418017615743061	4		407	630	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0002275-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	79	456	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		456	902	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094339	193094339	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002275-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	45	363	0	ENST00000367435.3:c.229C>T	p.Arg77Cys	p.R77C	ENST00000367435	NM_024529.4	77	Cgt/Tgt	2/17	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		363	820	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599332	55599332	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519710	NA	P-0002293-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	579	486	0	ENST00000288135.5:c.2458G>T	p.Asp820Tyr	p.D820Y	ENST00000288135	NM_000222.2	820	Gat/Tat	17/21	NA	2	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.813055936392132	2		486	1402	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593608	55593613	+	inframe_deletion	In_Frame_Del	DEL	GGTTGT	GGTTGT	-	novel	NA	P-0002293-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	718	547	0	ENST00000288135.5:c.1674_1679del	p.Lys558_Val560delinsAsn	p.K558_V560delinsN	ENST00000288135	NM_000222.2	558	aaGGTTGTt/aat	11/21	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.813055936392132	2		547	1759	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135804251	135804251	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002293-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	47	376	0	ENST00000298552.3:c.9del	p.Gln3HisfsTer23	p.Q3Hfs*23	ENST00000298552	NM_001162426.1	3	caA/ca	3/23	0.813055936392132	1	FACETS	0.117	0.098	0.138	0.117	0.098	0.138	SUBCLONAL	1	TRUE	0	0.813055936392132	1		376	586	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696425	47696425	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519967	NA	P-0002306-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	60	521	0	ENST00000347630.2:c.398T>C	p.Phe133Ser	p.F133S	ENST00000347630	NM_001007230.1	133	tTc/tCc	6/11	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.15	2		521	703	SUCCESS
ATM	472	MSKCC	GRCh37	11	108159726	108159726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002306-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	46	573	0	ENST00000278616.4:c.4132C>T	p.Pro1378Ser	p.P1378S	ENST00000278616	NM_000051.3	1378	Cca/Tca	28/63	1	2	FACETS	0.806	0.677	0.949	0.806	0.677	0.949	CLONAL	1	TRUE	1	0.15	2		573	761	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577525	7577527	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0002306-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	45	368	0	ENST00000269305.4:c.754_756del	p.Leu252del	p.L252del	ENST00000269305	NM_001126112.2	252	CTC/-	7/11	1	2	FACETS	0.705	0.591	0.832	0.705	0.591	0.832	SUBCLONAL	1	TRUE	1	0.15	2		368	851	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002310-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	486	210	1	ENST00000269305.4:c.383del	p.Pro128LeufsTer42	p.P128Lfs*42	ENST00000269305	NM_001126112.2	128	cCt/ct	5/11	0.690528406873484	4	FACETS	0.946	0.921	0.97			1	CLONAL	4	TRUE	NA	0.690528406873484	4		211	629	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0002313-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	143	377	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.821	0.755	0.889	0.821	0.755	0.889	CLONAL	1	TRUE	1	0.770578387975159	2		378	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0002313-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	379	409	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	0.770578387975159	2		409	965	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0002313-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	484	591	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.770578387975159	2		591	1224	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332818	65332818	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002313-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	64	438	0	ENST00000342505.4:c.721A>T	p.Asn241Tyr	p.N241Y	ENST00000342505	NM_002227.2	241	Aat/Tat	7/25	1	2	FACETS	0.491	0.428	0.559	0.491	0.428	0.559	SUBCLONAL	1	TRUE	1	0.770578387975159	2		438	338	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699237	117699237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002313-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	97	509	0	ENST00000369458.3:c.404C>T	p.Ser135Phe	p.S135F	ENST00000369458	NM_024626.3	135	tCt/tTt	3/6	1	2	FACETS	0.476	0.425	0.529	0.476	0.425	0.529	SUBCLONAL	1	TRUE	1	0.770578387975159	2		509	529	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685502	29685502	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002313-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	16	336	0	ENST00000356175.3:c.7912A>G	p.Asn2638Asp	p.N2638D	ENST00000356175	NM_000267.3	2638	Aat/Gat	54/57	1	2	FACETS	0.169	0.125	0.223	0.169	0.125	0.223	SUBCLONAL	1	TRUE	1	0.770578387975159	2		336	245	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748841	41748841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002313-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	207	563	0	ENST00000301178.4:c.1366G>A	p.Gly456Arg	p.G456R	ENST00000301178	NM_021913.4	456	Gga/Aga	11/20	1	2	FACETS	0.428	0.397	0.462	0.428	0.397	0.462	SUBCLONAL	1	TRUE	1	0.770578387975159	2		563	1254	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938248	76938248	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002313-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	125	588	0	ENST00000373344.5:c.2500del	p.Ala834ProfsTer35	p.A834Pfs*35	ENST00000373344	NM_000489.3	834	Gcc/cc	9/35	0.644388940158877	1	FACETS	0.795	0.735	0.854	0.795	0.735	0.854	SUBCLONAL	1	TRUE	0	0.770578387975159	1		588	251	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851558	134851558	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs770155473	NA	P-0002337-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	221	461	0	ENST00000398015.3:c.964G>A	p.Val322Ile	p.V322I	ENST00000398015	NM_004441.4	322	Gtc/Atc	5/16	1	2	FACETS	0.946	0.886	1	0.946	0.886	1	CLONAL	1	TRUE	1	0.75718124217407	2		461	617	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629232	187629232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182393996	NA	P-0002337-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	152	681	0	ENST00000441802.2:c.1750G>A	p.Val584Met	p.V584M	ENST00000441802	NM_005245.3	584	Gtg/Atg	2/27	1	2	FACETS	0.477	0.437	0.52	0.477	0.437	0.52	SUBCLONAL	1	TRUE	1	0.75718124217407	2		681	841	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578551	7578551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002337-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	393	230	1	ENST00000269305.4:c.379T>C	p.Ser127Pro	p.S127P	ENST00000269305	NM_001126112.2	127	Tcc/Ccc	5/11	0.75718124217407	2	FACETS	0.932	0.901	0.962	0.932	0.901	0.962	CLONAL	2	TRUE	0	0.75718124217407	2		231	557	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347881	70347907	+	inframe_deletion	In_Frame_Del	DEL	CAAGAGTCTTAGTGAGAACCCTGCTAA	CAAGAGTCTTAGTGAGAACCCTGCTAA	-	novel	NA	P-0002337-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	438	790	0	ENST00000374080.3:c.3121_3147del	p.Lys1041_Asn1049del	p.K1041_N1049del	ENST00000374080		1040	ggCAAGAGTCTTAGTGAGAACCCTGCTAAc/ggc	22/45	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.75718124217407	2		790	1132	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0002356-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	1150	693	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.432567308448387	6	FACETS	0.997	0.972	1	0.997	0.972	1	INDETERMINATE	3	TRUE	3	0.947035347128004	6		693	2350	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469669	NA	P-0002356-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	630	756	0	ENST00000374080.3:c.130G>A	p.Gly44Ser	p.G44S	ENST00000374080		44	Ggt/Agt	2/45	0.349363843387455	1	FACETS	0.556	0.537	0.575	0.556	0.537	0.575	INDETERMINATE	1	TRUE	0	0.947035347128004	1		756	1259	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170354	119170354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507498	NA	P-0002356-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	523	520	0	ENST00000264033.4:c.2584G>A	p.Glu862Lys	p.E862K	ENST00000264033	NM_005188.3	862	Gag/Aag	16/16	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.947035347128004	2		520	1014	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579336	7579351	+	frameshift_variant	Frame_Shift_Del	DEL	CCCAGAATGCAAGAAG	CCCAGAATGCAAGAAG	-	novel	NA	P-0002356-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	532	481	0	ENST00000269305.4:c.336_351del	p.Phe113GlnfsTer5	p.F113Qfs*5	ENST00000269305	NM_001126112.2	112	ggCTTCTTGCATTCTGGG/gg	4/11	0.432567308448387	6	FACETS	1	0.991	1	0.74	0.709	0.771	INDETERMINATE	2	TRUE	3	0.947035347128004	6		481	1465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0002362-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	27	591	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.661	0.528	0.81	0.661	0.528	0.81	SUBCLONAL	1	FALSE	1	0.363307966565364	2		591	225	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0002374-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	171	511	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.447441197003215	1	FACETS	0.937	0.866	1	0.937	0.866	1	CLONAL	1	TRUE	0	0.462263492538469	1		511	607	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446237	29446237	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs140606509	NA	P-0002374-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	142	486	0	ENST00000389048.3:c.3330G>C	p.Glu1110Asp	p.E1110D	ENST00000389048	NM_004304.4	1110	gaG/gaC	20/29	1	2	FACETS	0.838	0.765	0.915	0.838	0.765	0.915	CLONAL	1	TRUE	1	0.462263492538469	2		486	733	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160670	56160670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002374-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	148	400	0	ENST00000399503.3:c.944G>A	p.Arg315Lys	p.R315K	ENST00000399503	NM_005921.1	315	aGa/aAa	4/20	1	2	FACETS	0.799	0.731	0.871	0.799	0.731	0.871	SUBCLONAL	1	TRUE	1	0.462263492538469	2		400	801	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103513930	103513930	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002374-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	47	456	0	ENST00000355739.4:c.746A>T	p.His249Leu	p.H249L	ENST00000355739	NM_000123.3	249	cAt/cTt	7/15	1	2	FACETS	0.217	0.182	0.256	0.217	0.182	0.256	SUBCLONAL	1	TRUE	1	0.462263492538469	2		456	938	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007731	62007731	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1443194987	NA	P-0002374-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	45	230	0	ENST00000392795.3:c.136C>T	p.Arg46Trp	p.R46W	ENST00000392795	NM_001039933.1	46	Cgg/Tgg	3/6	0.396440910677489	3	FACETS	0.542	0.456	0.637	0.271	0.228	0.319	SUBCLONAL	1	TRUE	1	0.462263492538469	3		230	442	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374161	118374161	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002374-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	147	452	0	ENST00000534358.1:c.7554del	p.Arg2519GlyfsTer7	p.R2519Gfs*7	ENST00000534358	NM_005933.3	2518	ccA/cc	27/36	0.39751360383703	1	FACETS	0.787	0.721	0.856	0.787	0.721	0.856	SUBCLONAL	1	TRUE	0	0.462263492538469	1		452	621	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0002417-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	312	259	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	NA	2	FACETS	0.966	0.924	1			1	INDETERMINATE	2	TRUE	NA	0.613093570040094	2		260	527	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184750	185184750	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs752255390	NA	P-0002417-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	252	323	0	ENST00000265026.3:c.1642C>T	p.Arg548Trp	p.R548W	ENST00000265026	NM_004721.4	548	Cgg/Tgg	10/14	1	2	FACETS	0.976	0.916	1	0.976	0.916	1	CLONAL	1	TRUE	1	0.613093570040094	2		323	842	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115750	8115750	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs104894164	NA	P-0002417-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	342	482	0	ENST00000346208.3:c.1096C>T	p.Arg366Ter	p.R366*	ENST00000346208		366	Cga/Tga	6/6	0.613093570040094	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.613093570040094	1		482	748	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552598	18552598	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002417-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	102	380	0	ENST00000266497.5:c.2009C>G	p.Ser670Cys	p.S670C	ENST00000266497		670	tCt/tGt	14/31	NA	2	FACETS	0.441	0.394	0.49			1	INDETERMINATE	1	TRUE	NA	0.613093570040094	2		380	755	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0002425-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	136	512	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	1	2	FACETS	0.803	0.73	0.879	0.803	0.73	0.879	CLONAL	1	TRUE	1	0.401914477246625	2		512	843	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948129	55948129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002425-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	230	362	0	ENST00000263923.4:c.3842C>T	p.Ser1281Phe	p.S1281F	ENST00000263923	NM_002253.2	1281	tCt/tTt	29/30	1	2	FACETS	0.994	0.926	1	0.994	0.926	1	CLONAL	1	TRUE	1	0.401914477246625	2		362	1151	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031919	26031919	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1270004025	NA	P-0002425-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	145	204	0	ENST00000244661.2:c.370G>C	p.Asp124His	p.D124H	ENST00000244661	NM_003537.3	124	Gac/Cac	1/1	0.146029196164723	3	FACETS	1	0.973	1	0.582	0.531	0.634	INDETERMINATE	1	TRUE	1	0.401914477246625	3		204	745	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37141754	37141754	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002425-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	218	358	0	ENST00000373509.5:c.829G>C	p.Asp277His	p.D277H	ENST00000373509	NM_002648.3	277	Gat/Cat	6/6	0.146029196164723	3	FACETS	1	0.985	1	0.605	0.562	0.649	INDETERMINATE	1	TRUE	1	0.401914477246625	3		358	1077	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370798	55370798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1406469266	NA	P-0002425-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	119	201	0	ENST00000297316.4:c.100G>A	p.Glu34Lys	p.E34K	ENST00000297316	NM_022454.3	34	Gag/Aag	1/2	0.146029196164723	3	FACETS	1	0.985	1	0.742	0.674	0.814	INDETERMINATE	1	TRUE	1	0.401914477246625	3		201	479	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937009	48937009	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002425-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	269	377	0	ENST00000267163.4:c.777G>T	p.Arg259Ser	p.R259S	ENST00000267163	NM_000321.2	259	agG/agT	8/27	0.401914477246625	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.401914477246625	1		377	1010	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587781525	NA	P-0002425-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	211	391	0	ENST00000269305.4:c.842A>T	p.Asp281Val	p.D281V	ENST00000269305	NM_001126112.2	281	gAc/gTc	8/11	0.401914477246625	1	FACETS	0.97	0.902	1	0.97	0.902	1	CLONAL	1	TRUE	0	0.401914477246625	1		391	865	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119789	70119789	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002425-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	202	335	0	ENST00000245479.2:c.791G>C	p.Arg264Thr	p.R264T	ENST00000245479	NM_000346.3	264	aGa/aCa	3/3	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.401914477246625	2		335	855	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206827	36206827	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002425-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	105	230	0	ENST00000300305.3:c.685G>C	p.Glu229Gln	p.E229Q	ENST00000300305		229	Gag/Cag	6/8	1	2	FACETS	0.904	0.812	1	0.904	0.812	1	CLONAL	1	TRUE	1	0.401914477246625	2		230	578	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206873	36206873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002425-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	118	216	0	ENST00000300305.3:c.639G>T	p.Gln213His	p.Q213H	ENST00000300305		213	caG/caT	6/8	1	2	FACETS	0.964	0.872	1	0.964	0.872	1	CLONAL	1	TRUE	1	0.401914477246625	2		216	609	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0002434-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	347	454	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.662951894137352	2		454	954	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979610	7979610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781269323	NA	P-0002434-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	183	298	0	ENST00000319144.4:c.1415C>T	p.Ser472Leu	p.S472L	ENST00000319144	NM_001139.2	472	tCg/tTg	11/15	0.662951894137352	1	FACETS	0.902	0.844	0.961	0.902	0.844	0.961	CLONAL	1	TRUE	0	0.662951894137352	1		298	409	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39570492	39570492	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002434-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	245	329	0	ENST00000262039.4:c.688G>T	p.Glu230Ter	p.E230*	ENST00000262039	NM_002647.2	230	Gaa/Taa	6/25	1	2	FACETS	0.878	0.822	0.935	0.878	0.822	0.935	CLONAL	1	TRUE	1	0.662951894137352	2		329	842	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164856	47164856	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1278528667	NA	P-0002445-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	73	284	0	ENST00000409792.3:c.1270C>T	p.Arg424Ter	p.R424*	ENST00000409792	NM_014159.6	424	Cga/Tga	3/21	1	2	FACETS	0.92	0.809	1	0.92	0.809	1	CLONAL	1	TRUE	1	0.398539812467274	2		284	398	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711904	89711904	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs786201867	NA	P-0002445-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	160	346	0	ENST00000371953.3:c.522T>A	p.Tyr174Ter	p.Y174*	ENST00000371953	NM_000314.4	174	taT/taA	6/9	0.398539812467274	2	FACETS	0.938	0.869	1	0.938	0.869	1	CLONAL	2	TRUE	0	0.398539812467274	2		346	428	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844241	68844241	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002445-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	80	275	0	ENST00000261769.5:c.830del	p.Pro277GlnfsTer5	p.P277Qfs*5	ENST00000261769	NM_004360.3	277	Cca/ca	6/16	0.398539812467274	1	FACETS	0.906	0.803	1	0.906	0.803	1	CLONAL	1	TRUE	0	0.398539812467274	1		275	355	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309725	104309725	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0002448-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	21	557	0	ENST00000369902.3:c.318-2A>G		p.X106_splice	ENST00000369902	NM_016169.3	106			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		557	303	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2493219	2493219	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002480-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	42	355	0	ENST00000355716.4:c.659G>C	p.Gly220Ala	p.G220A	ENST00000355716	NM_003820.2	220	gGc/gCc	6/8	1	2	FACETS	0.73	0.612	0.861	0.73	0.612	0.861	SUBCLONAL	1	TRUE	1	0.342390900952109	2		355	336	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37048532	37048532	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002480-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	68	314	0	ENST00000231790.2:c.431G>A	p.Gly144Asp	p.G144D	ENST00000231790	NM_000249.3	144	gGc/gAc	5/19	0.261184668499538	3	FACETS	0.849	0.739	0.967	0.424	0.369	0.484	CLONAL	1	TRUE	1	0.342390900952109	3		314	548	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385309	4385309	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002480-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	125	362	0	ENST00000261254.3:c.334C>G	p.Leu112Val	p.L112V	ENST00000261254	NM_001759.3	112	Ctc/Gtc	2/5	0.342390900952109	8	FACETS	0.94	0.851	1	0.47	0.425	0.517	CLONAL	2	TRUE	4	0.342390900952109	8		362	787	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479178	50479178	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002480-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	29	181	0	ENST00000394963.4:c.26C>A	p.Ser9Tyr	p.S9Y	ENST00000394963	NM_003076.4	9	tCt/tAt	1/13	0.342390900952109	3	FACETS	0.684	0.55	0.835	0.342	0.275	0.418	SUBCLONAL	1	TRUE	1	0.342390900952109	3		181	290	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0002496-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	28	530	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.605483937805525	3	FACETS	0.106	0.084	0.131	0.053	0.042	0.066	SUBCLONAL	1	TRUE	1	0.605483937805525	3		530	1141	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568561	41568561	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002496-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	537	281	0	ENST00000263253.7:c.4511T>C	p.Phe1504Ser	p.F1504S	ENST00000263253	NM_001429.3	1504	tTc/tCc	28/31	0.605483937805525	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.605483937805525	2		281	738	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591126	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAGAAAGAC	GAGAAAGAC	-	novel	NA	P-0002496-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	222	200	0	ENST00000274335.5:c.1723_1731del	p.Lys575_Arg577del	p.K575_R577del	ENST00000274335		573	ctGAGAAAGACg/ctg	12/15	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.605483937805525	2		200	638	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097819	27097819	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0002508-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	32	304	0	ENST00000324856.7:c.3406+2T>A		p.X1136_splice	ENST00000324856	NM_006015.4	1136			0.723091718750146	1	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	0	0.723091718750146	1		304	55	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220443	1220443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202466	NA	P-0002508-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	37	477	0	ENST00000326873.7:c.536C>T	p.Pro179Leu	p.P179L	ENST00000326873	NM_000455.4	179	cCg/cTg	4/10	0.723091718750146	1	FACETS	0.86	0.741	0.979	0.86	0.741	0.979	CLONAL	1	TRUE	0	0.723091718750146	1		477	76	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0002524-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	273	395	335	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.317938475271678	13	FACETS	1	0.977	1			1	CLONAL	10	TRUE	NA	0.317938475271678	13		335	668	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0002524-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	190	62	280	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.281147163177231	3	FACETS	0.897	0.783	1	0.598	0.522	0.678	CLONAL	2	TRUE	0	0.317938475271678	3		280	252	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0002524-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	313	14	351	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.242183288185753	2	FACETS	0.269	0.194	0.361	0.135	0.097	0.181	SUBCLONAL	1	TRUE	0	0.317938475271678	2		351	327	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398255	25398255	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913236	NA	P-0002524-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	334	10	449	0	ENST00000311936.3:c.64C>A	p.Gln22Lys	p.Q22K	ENST00000311936	NM_004985.3	22	Cag/Aag	2/5	0.242183288185753	2	FACETS	0.183	0.123	0.259	0.091	0.061	0.13	SUBCLONAL	1	TRUE	0	0.317938475271678	2		449	344	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400182	41400182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002524-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	253	34	352	0	ENST00000373198.4:c.577C>T	p.Pro193Ser	p.P193S	ENST00000373198	NM_133170.3	193	Cct/Tct	5/32	0.316043385178093	4	FACETS	0.982	0.806	1	0.491	0.403	0.59	CLONAL	1	TRUE	2	0.317938475271678	4		352	287	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0002534-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	782	335	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.248894836168001	18	FACETS	0.975	0.951	0.998			1	CLONAL	17	TRUE	NA	0.248894836168001	18		335	1134	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577495	7577512	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGACCTGGAGTCTTCCAG	TGACCTGGAGTCTTCCAG	-	novel	NA	P-0002534-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	52	234	0	ENST00000269305.4:c.769_782+4del		p.X257_splice	ENST00000269305	NM_001126112.2	257		7/11	0.209624684835371	2	FACETS	0.945	0.814	1	0.945	0.814	1	CLONAL	2	TRUE	0	0.248894836168001	2		234	221	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0002536-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	367	591	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.791282410317499	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.791282410317499	1		591	543	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024854	31024854	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002536-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	307	492	0	ENST00000375687.4:c.4339C>T	p.Leu1447Phe	p.L1447F	ENST00000375687	NM_015338.5	1447	Ctc/Ttc	13/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.791282410317499	2		492	758	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0002549-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	30	363	1	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.858	0.692	1	0.858	0.692	1	CLONAL	1	TRUE	1	0.22	2		364	318	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727455	66727455	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs869025608	NA	P-0002549-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	76	411	0	ENST00000307102.5:c.171G>T	p.Lys57Asn	p.K57N	ENST00000307102	NM_002755.3	57	aaG/aaT	2/11	0.185829477622946	2	FACETS	0.789	0.695	0.889	0.789	0.695	0.889	SUBCLONAL	2	TRUE	0	0.22	2		411	438	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445094	89445094	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002549-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	37	499	0	ENST00000336596.2:c.1414G>C	p.Val472Leu	p.V472L	ENST00000336596	NM_005233.5	472	Gtc/Ctc	6/17	1	2	FACETS	0.678	0.559	0.812	0.678	0.559	0.812	SUBCLONAL	1	TRUE	1	0.22	2		499	496	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619249	43619249	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758800351	NA	P-0002549-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	17	339	0	ENST00000355710.3:c.2932G>A	p.Glu978Lys	p.E978K	ENST00000355710	NM_020975.4	978	Gag/Aag	17/20	0.3	2	FACETS	0.461	0.344	0.602			1	SUBCLONAL	1	TRUE	NA	0.22	2		339	335	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473698	67473698	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002549-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	57	463	0	ENST00000327367.4:c.778T>G	p.Phe260Val	p.F260V	ENST00000327367	NM_005902.3	260	Ttc/Gtc	6/9	0.185829477622946	2	FACETS	1	0.96	1	0.673	0.579	0.774	CLONAL	1	TRUE	0	0.22	2		463	385	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368283	45368283	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002549-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	84	504	0	ENST00000262160.6:c.1319T>G	p.Leu440Arg	p.L440R	ENST00000262160	NM_005901.5	440	cTt/cGt	11/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.22	2		504	634	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944512	40944512	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002549-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	53	525	0	ENST00000373198.4:c.1990T>C	p.Phe664Leu	p.F664L	ENST00000373198	NM_133170.3	664	Ttt/Ctt	12/32	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.22	2		525	473	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347197	70347197	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002549-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	56	571	0	ENST00000374080.3:c.2861T>G	p.Val954Gly	p.V954G	ENST00000374080		954	gTc/gGc	21/45	0.0915477665914305	0	FACETS	0.683	0.585	0.791			1	INDETERMINATE	1	TRUE	0	0.22	0		571	581	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650735	12650735	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs775525868	NA	P-0002552-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	446	274	0	ENST00000251849.4:c.420C>G	p.Asn140Lys	p.N140K	ENST00000251849	NM_002880.3	140	aaC/aaG	4/17	1	2	FACETS	0.923	0.883	0.963	0.923	0.883	0.963	CLONAL	1	TRUE	1	0.912838738411585	2		274	1059	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665348	117665348	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0002552-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	122	287	0	ENST00000368508.3:c.4399A>T	p.Arg1467Ter	p.R1467*	ENST00000368508	NM_002944.2	1467	Aga/Tga	27/43	NA	2	FACETS	0.227	0.204	0.251			1	INDETERMINATE	1	TRUE	NA	0.912838738411585	2		287	1179	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544649	65544654	+	frameshift_variant	Frame_Shift_Del	DEL	CATTCT	CATTCT	G	novel	NA	P-0002552-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	454	313	0	ENST00000358664.4:c.272_277delinsC	p.Gln91ProfsTer53	p.Q91Pfs*53	ENST00000358664	NM_002382.4	91	cAGAATGct/cCct	4/5	0.905148172107373	1	FACETS	0.996	0.972	1	0.996	0.972	1	CLONAL	1	TRUE	0	0.912838738411585	1		313	543	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562642	29562642	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002552-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	630	385	0	ENST00000356175.3:c.3722del	p.Arg1241GlnfsTer25	p.R1241Qfs*25	ENST00000356175	NM_000267.3	1241	cGa/ca	28/57	1	2	FACETS	0.983	0.948	1	0.983	0.948	1	CLONAL	1	TRUE	1	0.912838738411585	2		385	1404	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106655	27106655	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002558-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	73	360	0	ENST00000324856.7:c.6266T>C	p.Leu2089Pro	p.L2089P	ENST00000324856	NM_006015.4	2089	cTa/cCa	20/20	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.312996832616427	2		360	447	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849143	156849143	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs775191394	NA	P-0002558-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	71	356	0	ENST00000524377.1:c.2035G>T	p.Asp679Tyr	p.D679Y	ENST00000524377	NM_002529.3	679	Gac/Tac	15/17	0.187012736496016	3	FACETS	0.79	0.695	0.891	0.79	0.695	0.891	INDETERMINATE	2	TRUE	1	0.312996832616427	3		356	332	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278077	41278077	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0002558-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	50	454	0	ENST00000349496.5:c.1955-2A>G		p.X652_splice	ENST00000349496	NM_001904.3	652			0.312996832616427	1	FACETS	0.456	0.386	0.533	0.456	0.386	0.533	SUBCLONAL	1	TRUE	0	0.312996832616427	1		454	591	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531004	187531004	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002558-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	70	378	0	ENST00000441802.2:c.10019A>G	p.Tyr3340Cys	p.Y3340C	ENST00000441802	NM_005245.3	3340	tAc/tGc	15/27	1	2	FACETS	0.678	0.591	0.772	0.678	0.591	0.772	SUBCLONAL	1	TRUE	1	0.312996832616427	2		378	660	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207061	1207067	+	frameshift_variant	Frame_Shift_Del	DEL	TGATGGG	TGATGGG	-	novel	NA	P-0002558-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	65	317	0	ENST00000326873.7:c.149_155del	p.Leu50ArgfsTer12	p.L50Rfs*12	ENST00000326873	NM_000455.4	50	cTGATGGGg/cg	1/10	0.272024484896812	0	FACETS	0.873	0.762	0.991			1	CLONAL	1	TRUE	0	0.312996832616427	0		317	327	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033972	48033972	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002567-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	163	438	0	ENST00000234420.5:c.4056A>T	p.Lys1352Asn	p.K1352N	ENST00000234420	NM_000179.2	1352	aaA/aaT	10/10	0.482859647656586	3	FACETS	0.931	0.855	1	0.466	0.427	0.506	CLONAL	1	TRUE	1	0.482859647656586	3		438	900	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692790	89692790	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554898067	NA	P-0002567-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	238	296	0	ENST00000371953.3:c.274G>T	p.Asp92Tyr	p.D92Y	ENST00000371953	NM_000314.4	92	Gac/Tac	5/9	0.482859647656586	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.482859647656586	2		296	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578259	7578259	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1567551903	NA	P-0002567-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	322	704	0	ENST00000269305.4:c.590T>A	p.Val197Glu	p.V197E	ENST00000269305	NM_001126112.2	197	gTg/gAg	6/11	0.482859647656586	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.482859647656586	2		704	634	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220579	123220579	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002567-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	458	560	0	ENST00000218089.9:c.3236C>G	p.Thr1079Arg	p.T1079R	ENST00000218089	NM_001042749.1	1079	aCa/aGa	30/35	0.452546774036707	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.482859647656586	3		560	754	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0002568-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	42	298	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		298	541	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0002568-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	39	530	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.24956465592505	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		530	884	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0002577-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	443	454	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.335711869799446	6	FACETS	0.985	0.945	1			1	CLONAL	5	TRUE	NA	0.335711869799446	6		454	896	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0002577-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	41	429	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.183428419645364	3	FACETS	0.551	0.458	0.654	0.184	0.152	0.218	INDETERMINATE	1	TRUE	0	0.335711869799446	3		429	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0002577-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	236	497	0	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	0.335711869799446	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.335711869799446	2		497	668	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692993	89692993	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519724	NA	P-0002577-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	79	332	0	ENST00000371953.3:c.477G>T	p.Arg159Ser	p.R159S	ENST00000371953	NM_000314.4	159	agG/agT	5/9	0.329489380638922	3	FACETS	0.823	0.73	0.921	0.823	0.73	0.921	CLONAL	2	TRUE	1	0.335711869799446	3		332	334	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs121913292	NA	P-0002577-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	99	361	0	ENST00000371953.3:c.389del	p.Arg130GlnfsTer4	p.R130Qfs*4	ENST00000371953	NM_000314.4	130	cGa/ca	5/9	0.329489380638922	3	FACETS	0.895	0.805	0.988	0.895	0.805	0.988	CLONAL	2	TRUE	1	0.335711869799446	3		361	385	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945137	44945137	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0002581-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	15	213	0	ENST00000377967.4:c.3461C>G	p.Ser1154Ter	p.S1154*	ENST00000377967	NM_021140.2	1154	tCa/tGa	24/29	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		213	284	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588785	29588789	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTG	ACCTG	-	novel	NA	P-0002588-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	65	333	0	ENST00000356175.3:c.4571_4575del	p.Tyr1524TrpfsTer17	p.Y1524Wfs*17	ENST00000356175	NM_000267.3	1524	tACCTG/t	34/57	0.458338918359896	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.538883769169853	1		333	162	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876659675	NA	P-0002592-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	506	381	0	ENST00000269305.4:c.764T>A	p.Ile255Asn	p.I255N	ENST00000269305	NM_001126112.2	255	aTc/aAc	7/11	0.469242017412217	4	FACETS	1	0.975	1			1	CLONAL	4	TRUE	NA	0.469242017412217	4		381	786	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693929	47693929	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002592-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	350	516	0	ENST00000233146.2:c.1643G>T	p.Gly548Val	p.G548V	ENST00000233146	NM_000251.2	548	gGt/gTt	10/16	0.350571797654776	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	2	0.469242017412217	4		516	1064	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447793	49447793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002592-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	248	297	0	ENST00000301067.7:c.641G>A	p.Cys214Tyr	p.C214Y	ENST00000301067	NM_003482.3	214	tGc/tAc	5/54	0.469242017412217	4	FACETS	0.944	0.885	1	0.944	0.885	1	CLONAL	2	TRUE	2	0.469242017412217	4		297	823	SUCCESS
BLM	641	MSKCC	GRCh37	15	91334069	91334069	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs772671554	NA	P-0002592-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	147	354	1	ENST00000355112.3:c.3014T>C	p.Ile1005Thr	p.I1005T	ENST00000355112	NM_000057.2	1005	aTa/aCa	15/22	0.318487087537407	5	FACETS	0.769	0.704	0.837	0.513	0.469	0.558	SUBCLONAL	2	TRUE	2	0.469242017412217	5		355	694	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018264	48018264	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0002615-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	94	206	0	ENST00000234420.5:c.457+2T>G		p.X153_splice	ENST00000234420	NM_000179.2	153			1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.53395341254903	2		206	310	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183776	10183777	+	missense_variant	Missense_Mutation	DNP	GC	GC	CT	novel	NA	P-0002615-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	40	256	1	ENST00000256474.2:c.245_246delinsCT	p.Arg82Pro	p.R82P	ENST00000256474	NM_000551.3	82	cGC/cCT	1/3	0.53395341254903	1	FACETS	0.525	0.441	0.618	0.525	0.441	0.618	SUBCLONAL	1	TRUE	0	0.53395341254903	1		257	209	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508709	38508709	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002615-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	115	250	0	ENST00000254066.5:c.757A>G	p.Thr253Ala	p.T253A	ENST00000254066	NM_000964.3	253	Acc/Gcc	6/9	0.381269190565387	1	FACETS	0.96	0.875	1	0.96	0.875	1	CLONAL	1	TRUE	0	0.53395341254903	1		250	329	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-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	73	197	0	ENST00000460680.1:c.1250_1250+13del		p.X417_splice	ENST00000460680	NM_004656.3	417		12/17	0.53395341254903	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.53395341254903	1		197	187	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0002616-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	504	358	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.341671153996806	5	FACETS	0.952	0.914	0.99			1	CLONAL	4	TRUE	NA	0.341671153996806	5		358	1172	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576042	29576042	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002632-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	71	463	1	ENST00000356175.3:c.4015C>T	p.Leu1339Phe	p.L1339F	ENST00000356175	NM_000267.3	1339	Ctc/Ttc	30/57	1	2	FACETS	0.52	0.454	0.591	0.52	0.454	0.591	SUBCLONAL	1	TRUE	1	0.472245609778918	2		464	578	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722019	176722020	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0002632-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	65	302	0	ENST00000439151.2:c.7650_7651del	p.Glu2550AspfsTer14	p.E2550Dfs*14	ENST00000439151	NM_022455.4	2550	gaGCca/gaca	23/23	1	2	FACETS	0.803	0.7	0.912	0.803	0.7	0.912	CLONAL	1	TRUE	1	0.472245609778918	2		302	343	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0002633-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	103	591	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.591886935515392	2	FACETS	1	0.976	1	0.617	0.56	0.675	CLONAL	1	TRUE	0	0.591886935515392	2		591	282	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0002633-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	67	251	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	0.591886935515392	2	FACETS	1	0.951	1	0.572	0.506	0.64	CLONAL	1	TRUE	0	0.591886935515392	2		251	198	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002633-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	17	322	2	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	0.591886935515392	2	FACETS	0.676	0.514	0.859	0.338	0.257	0.43	SUBCLONAL	1	TRUE	0	0.591886935515392	2		324	85	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0002633-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	254	476	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.591886935515392	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.591886935515392	2		476	406	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330619	65330619	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763659890	NA	P-0002633-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	58	495	0	ENST00000342505.4:c.1027C>T	p.Arg343Trp	p.R343W	ENST00000342505	NM_002227.2	343	Cgg/Tgg	8/25	NA	2	FACETS	0.573	0.495	0.657			1	INDETERMINATE	1	TRUE	NA	0.591886935515392	2		495	342	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846363	156846363	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs763758904	NA	P-0002633-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	47	407	2	ENST00000524377.1:c.1804C>T	p.Arg602Ter	p.R602*	ENST00000524377	NM_002529.3	602	Cga/Tga	14/17	0.591886935515392	2	FACETS	1	0.949	1	0.611	0.528	0.697	CLONAL	1	TRUE	0	0.591886935515392	2		409	130	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746017	162746017	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002633-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	90	460	0	ENST00000367921.3:c.2140C>T	p.Arg714Ter	p.R714*	ENST00000367921	NM_006182.2	714	Cga/Tga	16/18	0.591886935515392	2	FACETS	1	0.951	1	0.549	0.494	0.606	CLONAL	1	TRUE	0	0.591886935515392	2		460	277	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47643433	47643433	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs587779198	NA	P-0002633-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	105	342	0	ENST00000233146.2:c.943-2A>G		p.X315_splice	ENST00000233146	NM_000251.2	315			0.591886935515392	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.591886935515392	2		342	158	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005398	150005398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775507536	NA	P-0002633-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	78	438	0	ENST00000253339.5:c.827G>A	p.Arg276His	p.R276H	ENST00000253339		276	cGc/cAc	3/7	0.545231242320255	2	FACETS	1	0.902	1	0.507	0.451	0.565	CLONAL	1	TRUE	0	0.591886935515392	2		438	260	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974121	2974121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760308478	NA	P-0002633-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	36	351	2	ENST00000396946.4:c.1484C>T	p.Pro495Leu	p.P495L	ENST00000396946	NM_032415.4	495	cCg/cTg	10/25	0.370438064573599	4	FACETS	0.817	0.676	0.972	0.409	0.338	0.486	CLONAL	1	TRUE	2	0.591886935515392	4		353	237	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371633	55371633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs931390946	NA	P-0002633-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	17	315	0	ENST00000297316.4:c.323C>T	p.Ala108Val	p.A108V	ENST00000297316	NM_022454.3	108	gCg/gTg	2/2	0.519381826361453	3	FACETS	0.653	0.493	0.838	0.218	0.164	0.28	SUBCLONAL	1	TRUE	0	0.591886935515392	3		315	114	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646396	23646396	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs577969558	NA	P-0002633-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	90	496	1	ENST00000261584.4:c.1471G>A	p.Ala491Thr	p.A491T	ENST00000261584	NM_024675.3	491	Gct/Act	4/13	0.591886935515392	2	FACETS	1	0.949	1	0.545	0.49	0.602	CLONAL	1	TRUE	0	0.591886935515392	2		497	279	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814313	76814313	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002633-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	87	197	0	ENST00000373344.5:c.6331C>T	p.Arg2111Ter	p.R2111*	ENST00000373344	NM_000489.3	2111	Cga/Tga	29/35	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.591886935515392	1		197	142	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220588	123220588	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002633-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	112	231	0	ENST00000218089.9:c.3245G>A	p.Arg1082Gln	p.R1082Q	ENST00000218089	NM_001042749.1	1082	cGg/cAg	30/35	1	1	FACETS	0.775	0.722	0.825	1	0.989	1	SUBCLONAL	2	TRUE	0	0.591886935515392	1		231	172	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967049	25967052	+	frameshift_variant	Frame_Shift_Del	DEL	TCTG	TCTG	-	novel	NA	P-0002633-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	34	389	0	ENST00000435504.4:c.2154_2157del	p.Asp718GlufsTer80	p.D718Efs*80	ENST00000435504		718	gaCAGA/ga	13/13	0.591886935515392	2	FACETS	0.586	0.483	0.699	0.293	0.241	0.35	SUBCLONAL	1	TRUE	0	0.591886935515392	2		389	196	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139564	47139566	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0002633-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	129	388	0	ENST00000409792.3:c.5021_5023del	p.Glu1674del	p.E1674del	ENST00000409792	NM_014159.6	1674	gAAGcc/gcc	9/21	0.591886935515392	2	FACETS	0.875	0.812	0.939	0.875	0.812	0.939	CLONAL	2	TRUE	0	0.591886935515392	2		388	249	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98244305	98244306	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	A	novel	NA	P-0002633-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	182	494	1	ENST00000331920.6:c.671_672delinsT	p.Tyr224PhefsTer4	p.Y224Ffs*4	ENST00000331920	NM_000264.3	224	tAC/tT	5/24	0.591886935515392	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.591886935515392	2		495	295	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030465	49030466	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0002633-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	103	360	0	ENST00000267163.4:c.1941_1942del	p.Ser648ThrfsTer4	p.S648Tfs*4	ENST00000267163	NM_000321.2	647	cTT/c	19/27	0.519381826361453	3	FACETS	1	0.935	1	0.683	0.625	0.742	CLONAL	2	TRUE	0	0.591886935515392	3		360	220	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553478	29553478	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781807	NA	P-0002633-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	135	345	1	ENST00000356175.3:c.2033del	p.Pro678ArgfsTer10	p.P678Rfs*10	ENST00000356175	NM_000267.3	676	aCc/ac	18/57	NA	2	FACETS	0.867	0.805	0.929			1	INDETERMINATE	2	TRUE	NA	0.591886935515392	2		346	263	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41558737	41558740	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	rs1555910482	NA	P-0002633-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	65	487	0	ENST00000263253.7:c.3684_3687del	p.Lys1228AsnfsTer48	p.K1228Nfs*48	ENST00000263253	NM_001429.3	1228	AAAGaa/aa	21/31	0.406030986968376	1	FACETS	0.609	0.534	0.688	0.609	0.534	0.688	SUBCLONAL	1	TRUE	0	0.591886935515392	1		487	254	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0002635-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	253	289	0	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	0.376340685598227	2	FACETS	0.956	0.899	1	0.956	0.899	1	CLONAL	2	FALSE	0	0.380291226083753	2		289	696	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602341	10602341	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002635-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	240	282	0	ENST00000171111.5:c.1237del	p.Arg413ValfsTer45	p.R413Vfs*45	ENST00000171111	NM_203500.1	413	Cgt/gt	3/6	0.376340685598227	2	FACETS	0.995	0.936	1	0.995	0.936	1	CLONAL	2	FALSE	0	0.380291226083753	2		282	634	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969951	161969951	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002635-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	241	253	0	ENST00000366898.1:c.1018G>T	p.Gly340Trp	p.G340W	ENST00000366898	NM_004562.2	340	Ggg/Tgg	9/12	0.351967626355189	3	FACETS	0.857	0.807	0.907	0.857	0.807	0.907	CLONAL	3	FALSE	0	0.380291226083753	3		253	587	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0002635-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	189	318	0	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	0.376340685598227	2	FACETS	0.817	0.76	0.877	0.817	0.76	0.877	CLONAL	2	FALSE	0	0.380291226083753	2		318	608	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341727	8341727	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs369304072	NA	P-0002635-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	226	399	0	ENST00000356435.5:c.4913G>T	p.Gly1638Val	p.G1638V	ENST00000356435		1638	gGa/gTa	29/35	0.376340685598227	2	FACETS	0.825	0.772	0.88	0.825	0.772	0.88	CLONAL	2	FALSE	0	0.380291226083753	2		399	720	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333771	70333771	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002635-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	253	310	0	ENST00000373644.4:c.1676C>A	p.Thr559Asn	p.T559N	ENST00000373644	NM_030625.2	559	aCc/aAc	2/12	0.238415483730818	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	FALSE	2	0.380291226083753	4		310	847	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222006	1222006	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0002635-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	203	205	1	ENST00000326873.7:c.920+1G>T		p.X307_splice	ENST00000326873	NM_000455.4	307			0.376340685598227	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	FALSE	0	0.380291226083753	2		206	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578517	7578517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750600586	NA	P-0002639-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	107	169	0	ENST00000269305.4:c.413C>T	p.Ala138Val	p.A138V	ENST00000269305	NM_001126112.2	138	gCc/gTc	5/11	0.262459018010937	1	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	0	0.262459018010937	1		169	704	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101660	27101661	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0002639-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	43	203	0	ENST00000324856.7:c.4942_4943delinsAA	p.Ala1648Asn	p.A1648N	ENST00000324856	NM_006015.4	1648	GCc/AAc	18/20	1	2	FACETS	0.412	0.344	0.489	0.412	0.344	0.489	SUBCLONAL	1	TRUE	1	0.262459018010937	2		203	795	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665131	138665131	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002639-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	47	149	0	ENST00000330315.3:c.434G>T	p.Arg145Leu	p.R145L	ENST00000330315	NM_023067.3	145	cGc/cTc	1/1	0.240052296176838	3	FACETS	0.869	0.734	1	0.435	0.367	0.509	CLONAL	1	TRUE	1	0.262459018010937	3		149	466	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612091	189612091	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002639-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	128	245	0	ENST00000264731.3:c.1843C>G	p.His615Asp	p.H615D	ENST00000264731	NM_003722.4	615	Cat/Gat	14/14	0.240052296176838	3	FACETS	1	0.947	1	0.535	0.483	0.589	CLONAL	1	TRUE	1	0.262459018010937	3		245	1032	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535351	66535351	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs963468479	NA	P-0002639-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	93	166	0	ENST00000273854.3:c.110G>T	p.Arg37Leu	p.R37L	ENST00000273854	NM_004439.5	37	cGg/cTg	1/18	0.262459018010937	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.262459018010937	1		166	573	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473762	67473762	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002639-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	98	225	0	ENST00000327367.4:c.842C>A	p.Ala281Glu	p.A281E	ENST00000327367	NM_005902.3	281	gCa/gAa	6/9	0.262459018010937	1	FACETS	0.982	0.877	1	0.982	0.877	1	CLONAL	1	TRUE	0	0.262459018010937	1		225	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578528	7578528	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002639-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	91	168	0	ENST00000269305.4:c.402T>G	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	ttT/ttG	5/11	0.262459018010937	1	FACETS	0.917	0.815	1	0.917	0.815	1	CLONAL	1	TRUE	0	0.262459018010937	1		168	657	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610127	10610127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002639-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	121	247	0	ENST00000171111.5:c.583G>C	p.Gly195Arg	p.G195R	ENST00000171111	NM_203500.1	195	Ggc/Cgc	2/6	0.262459018010937	1	FACETS	0.979	0.885	1	0.979	0.885	1	CLONAL	1	TRUE	0	0.262459018010937	1		247	818	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913566	39913566	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002639-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	68	275	0	ENST00000378444.4:c.4762G>T	p.Gly1588Cys	p.G1588C	ENST00000378444	NM_001123385.1	1588	Ggt/Tgt	13/15	0.177038620869193	1	FACETS	0.441	0.383	0.505	0.441	0.383	0.505	SUBCLONAL	1	TRUE	0	0.262459018010937	1		275	1020	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937114	76937114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002639-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	240	269	0	ENST00000373344.5:c.3634G>A	p.Asp1212Asn	p.D1212N	ENST00000373344	NM_000489.3	1212	Gat/Aat	9/35	0.262459018010937	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.262459018010937	3		269	939	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152095	11152095	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002639-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	94	219	1	ENST00000358026.2:c.4381del	p.Arg1461AlafsTer34	p.R1461Afs*34	ENST00000358026	NM_001128849.1	1460	aCc/ac	31/36	0.262459018010937	1	FACETS	0.863	0.768	0.964	0.863	0.768	0.964	CLONAL	1	TRUE	0	0.262459018010937	1		220	721	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917796	29917796	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002640-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	66	249	0	ENST00000389048.3:c.872G>C	p.Arg291Pro	p.R291P	ENST00000389048	NM_004304.4	291	cGc/cCc	3/29	1	2	FACETS	0.861	0.76	0.965	0.861	0.76	0.965	CLONAL	1	TRUE	1	0.766724809715163	2		249	200	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845941	151845941	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002658-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	291	316	0	ENST00000262189.6:c.13071G>A	p.Trp4357Ter	p.W4357*	ENST00000262189	NM_170606.2	4357	tgG/tgA	52/59	0.648707158956192	3	FACETS	1	0.985	1			1	CLONAL	3	TRUE	NA	0.838734382029991	3		316	324	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033916	49033916	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs878853949	NA	P-0002658-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	450	270	0	ENST00000267163.4:c.2053C>T	p.Gln685Ter	p.Q685*	ENST00000267163	NM_000321.2	685	Cag/Tag	20/27	0.838734382029991	4	FACETS	1	0.996	1	1	0.996	1	CLONAL	4	TRUE	0	0.838734382029991	4		270	476	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43806103	43806103	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002658-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	118	276	0	ENST00000372470.3:c.899C>A	p.Thr300Asn	p.T300N	ENST00000372470	NM_005373.2	300	aCc/aAc	6/12	0.743619482531069	3	FACETS	1	0.971	1			1	CLONAL	1	TRUE	NA	0.838734382029991	3		276	347	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468382	89468382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs570346631	NA	P-0002658-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	195	185	0	ENST00000336596.2:c.1916G>A	p.Arg639His	p.R639H	ENST00000336596	NM_005233.5	639	cGc/cAc	11/17	0.838734382029991	4	FACETS	0.99	0.928	1			1	CLONAL	2	TRUE	NA	0.838734382029991	4		185	432	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38968044	38968044	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs748169007	NA	P-0002658-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	138	219	0	ENST00000357387.3:c.1060+1G>A		p.X354_splice	ENST00000357387	NM_152756.3	354			0.736600530787301	4	FACETS	0.945	0.874	1			1	CLONAL	2	TRUE	NA	0.838734382029991	4		219	320	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056203	26056203	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0002658-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	189	345	0	ENST00000343677.2:c.454A>T	p.Lys152Ter	p.K152*	ENST00000343677	NM_005319.3	152	Aag/Tag	1/1	0.458302628197691	4	FACETS	0.9	0.851	0.947	1	0.992	1	INDETERMINATE	3	TRUE	2	0.838734382029991	4		345	307	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163642	32163642	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs775494392	NA	P-0002658-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	47	179	0	ENST00000375023.3:c.5584C>G	p.Arg1862Gly	p.R1862G	ENST00000375023	NM_004557.3	1862	Cgg/Ggg	30/30	0.806175850930628	3	FACETS	0.816	0.698	0.942	0.408	0.349	0.471	CLONAL	1	TRUE	1	0.838734382029991	3		179	195	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32189009	32189009	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002658-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	171	267	1	ENST00000375023.3:c.545G>C	p.Cys182Ser	p.C182S	ENST00000375023	NM_004557.3	182	tGc/tCc	4/30	0.806175850930628	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.838734382029991	3		268	274	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409852	139409852	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1485274124	NA	P-0002658-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	302	247	1	ENST00000277541.6:c.1904G>A	p.Gly635Glu	p.G635E	ENST00000277541	NM_017617.3	635	gGa/gAa	12/34	0.838734382029991	4	FACETS	1	0.995	1	1	0.995	1	CLONAL	4	TRUE	0	0.838734382029991	4		248	316	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518488	69518488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002658-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	88	123	0	ENST00000294312.3:c.157C>T	p.His53Tyr	p.H53Y	ENST00000294312	NM_005117.2	53	Cac/Tac	1/3	0.838734382029991	3	FACETS	0.986	0.905	1	0.986	0.905	1	CLONAL	2	TRUE	1	0.838734382029991	3		123	151	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203596	108203596	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002658-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	69	169	0	ENST00000278616.4:c.7896C>G	p.Asn2632Lys	p.N2632K	ENST00000278616	NM_000051.3	2632	aaC/aaG	53/63	0.838734382029991	3	FACETS	1	0.9	1	0.51	0.45	0.572	CLONAL	1	TRUE	1	0.838734382029991	3		169	229	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425357	49425357	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1327126544	NA	P-0002658-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	44	319	0	ENST00000301067.7:c.13131G>A	p.Trp4377Ter	p.W4377*	ENST00000301067	NM_003482.3	4377	tgG/tgA	39/54	0.589881578311226	2	FACETS	0.35	0.295	0.41	0.175	0.147	0.205	SUBCLONAL	1	TRUE	0	0.838734382029991	2		319	300	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012455	29012455	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002658-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	373	258	2	ENST00000282397.4:c.416A>G	p.Tyr139Cys	p.Y139C	ENST00000282397	NM_002019.4	139	tAc/tGc	4/30	0.838734382029991	4	FACETS	1	0.995	1	1	0.995	1	CLONAL	4	TRUE	0	0.838734382029991	4		260	393	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433285	49433285	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002658-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	134	245	0	ENST00000301067.7:c.8162del	p.Gly2721ValfsTer12	p.G2721Vfs*12	ENST00000301067	NM_003482.3	2721	gGt/gt	32/54	0.589881578311226	2	FACETS	0.94	0.894	0.982	0.94	0.894	0.982	CLONAL	2	TRUE	0	0.838734382029991	2		245	170	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578245	7578277	+	inframe_deletion	In_Frame_Del	DEL	GCAAATTTCCTTCCACTCGGATAAGATGCTGAG	GCAAATTTCCTTCCACTCGGATAAGATGCTGAG	-	novel	NA	P-0002658-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	200	319	1	ENST00000269305.4:c.572_604del	p.Pro191_Leu201del	p.P191_L201del	ENST00000269305	NM_001126112.2	191	cCTCAGCATCTTATCCGAGTGGAAGGAAATTTGCgt/cgt	6/11	0.838734382029991	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.838734382029991	2		320	224	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226573297	226573297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377195931	NA	P-0002669-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	119	278	0	ENST00000366794.5:c.919G>A	p.Asp307Asn	p.D307N	ENST00000366794	NM_001618.3	307	Gat/Aat	7/23	0.536398528198346	3	FACETS	0.927	0.849	1	0.927	0.849	1	CLONAL	2	TRUE	1	0.535425047753311	3		278	304	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17350571	17350571	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786201161	NA	P-0002669-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	117	171	0	ENST00000375499.3:c.541-2A>G		p.X181_splice	ENST00000375499	NM_003000.2	181			0.536398528198346	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	2	0.535425047753311	4		171	281	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057727	27057727	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002669-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	165	343	0	ENST00000324856.7:c.1435C>T	p.Gln479Ter	p.Q479*	ENST00000324856	NM_006015.4	479	Cag/Tag	3/20	0.536398528198346	4	FACETS	0.98	0.907	1	0.98	0.907	1	CLONAL	2	TRUE	2	0.535425047753311	4		343	483	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117024	193117024	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002669-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	124	367	0	ENST00000367435.3:c.757C>A	p.Leu253Ile	p.L253I	ENST00000367435	NM_024529.4	253	Ctt/Att	8/17	0.536398528198346	3	FACETS	1	0.983	1	0.68	0.62	0.742	CLONAL	1	TRUE	1	0.535425047753311	3		367	432	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635624	47635624	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002669-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	102	300	0	ENST00000233146.2:c.296G>T	p.Arg99Ile	p.R99I	ENST00000233146	NM_000251.2	99	aGa/aTa	2/16	0.536398528198346	3	FACETS	1	0.96	1	0.567	0.51	0.626	CLONAL	1	TRUE	1	0.535425047753311	3		300	426	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058737	47058737	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002669-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	141	219	0	ENST00000409792.3:c.7541A>T	p.His2514Leu	p.H2514L	ENST00000409792	NM_014159.6	2514	cAc/cTc	21/21	0.536398528198346	3	FACETS	0.905	0.845	0.963	0.905	0.845	0.963	CLONAL	3	TRUE	0	0.535425047753311	3		219	246	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169201	32169201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1342965791	NA	P-0002669-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	110	200	0	ENST00000375023.3:c.3832G>A	p.Gly1278Ser	p.G1278S	ENST00000375023	NM_004557.3	1278	Ggc/Agc	22/30	0.486753293844138	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.535425047753311	1		200	202	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501301	140501301	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002669-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	98	233	0	ENST00000288602.6:c.771G>T	p.Gln257His	p.Q257H	ENST00000288602	NM_004333.4	257	caG/caT	6/18	0.536398528198346	3	FACETS	1	0.979	1	0.68	0.613	0.751	CLONAL	1	TRUE	1	0.535425047753311	3		233	341	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552600	18552600	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002669-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	135	335	0	ENST00000266497.5:c.2011G>T	p.Glu671Ter	p.E671*	ENST00000266497		671	Gaa/Taa	14/31	0.342717545912989	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.535425047753311	1		335	256	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431843	49431843	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs778257510	NA	P-0002669-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	107	176	0	ENST00000301067.7:c.9296G>T	p.Arg3099Leu	p.R3099L	ENST00000301067	NM_003482.3	3099	cGc/cTc	34/54	0.536398528198346	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.535425047753311	3		176	237	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563018	21563018	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002669-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	38	296	0	ENST00000382592.4:c.901G>T	p.Gly301Cys	p.G301C	ENST00000382592	NM_014572.2	301	Ggc/Tgc	4/8	NA	2	FACETS	0.639	0.533	0.756			1	INDETERMINATE	1	TRUE	NA	0.535425047753311	2		296	222	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610141	28610141	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002669-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	79	317	2	ENST00000241453.7:c.1349C>A	p.Ala450Glu	p.A450E	ENST00000241453	NM_004119.2	450	gCg/gAg	11/24	NA	2	FACETS	0.86	0.763	0.963			1	INDETERMINATE	1	TRUE	NA	0.535425047753311	2		319	343	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28624268	28624268	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002669-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	172	385	0	ENST00000241453.7:c.706G>T	p.Glu236Ter	p.E236*	ENST00000241453	NM_004119.2	236	Gaa/Taa	6/24	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.535425047753311	2		385	435	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027174	49027174	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002669-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	271	361	0	ENST00000267163.4:c.1741G>T	p.Gly581Ter	p.G581*	ENST00000267163	NM_000321.2	581	Gga/Tga	18/27	0.536398528198346	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.535425047753311	3		361	405	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799136	88799136	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0002669-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	64	212	0	ENST00000360948.2:c.248+1G>A		p.X83_splice	ENST00000360948	NM_001012338.2	83			0.444968202992732	0	FACETS		NA	1			1	NA	2	TRUE	0	0.535425047753311	0		212	92	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577102	7577103	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TA	novel	NA	P-0002669-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	205	298	0	ENST00000269305.4:c.835_836delinsTA	p.Gly279Ter	p.G279*	ENST00000269305	NM_001126112.2	279	GGg/TAg	8/11	0.536398528198346	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	TRUE	0	0.535425047753311	3		298	311	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964832	15964832	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002669-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	181	361	0	ENST00000268712.3:c.5764A>G	p.Arg1922Gly	p.R1922G	ENST00000268712	NM_006311.3	1922	Aga/Gga	37/46	0.536398528198346	3	FACETS	0.858	0.807	0.909	0.858	0.807	0.909	CLONAL	3	TRUE	0	0.535425047753311	3		361	333	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435153	56435155	+	stop_gained	Nonsense_Mutation	TNP	CGG	CGG	AGA	novel	NA	P-0002669-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	46	137	0	ENST00000407977.2:c.1982_1984delinsTCT	p.Ser661_Glu662delinsPheTer	p.S661_E662delinsF*	ENST00000407977		661	tCCGag/tTCTag	9/10	0.536398528198346	3	FACETS	0.951	0.809	1	0.476	0.404	0.553	CLONAL	1	TRUE	1	0.535425047753311	3		137	229	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597431	10597431	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002669-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	256	196	1	ENST00000171111.5:c.1772G>T	p.Trp591Leu	p.W591L	ENST00000171111	NM_203500.1	591	tGg/tTg	6/6	0.536398528198346	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	4	TRUE	0	0.535425047753311	4		197	340	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839815	42839815	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0002669-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	83	219	0	ENST00000398585.3:c.1426-2A>T		p.X476_splice	ENST00000398585	NM_001135099.1	476			NA	2	FACETS	0.866	0.784	0.949			1	INDETERMINATE	2	TRUE	NA	0.535425047753311	2		219	179	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484193	8484193	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002669-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	149	333	0	ENST00000356435.5:c.3339del	p.Phe1114SerfsTer10	p.F1114Sfs*10	ENST00000356435		1113	gcC/gc	19/35	0.35425969647732	3	FACETS	1	0.939	1			1	CLONAL	2	TRUE	NA	0.535425047753311	3		333	348	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0002673-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	276	412	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.32313787648528	5	FACETS	1	0.968	1	0.779	0.734	0.825	CLONAL	3	TRUE	1	0.32313787648528	5		413	814	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626377	12626377	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002673-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	178	400	0	ENST00000251849.4:c.1772A>C	p.Lys591Thr	p.K591T	ENST00000251849	NM_002880.3	591	aAa/aCa	16/17	0.32313787648528	3	FACETS	0.997	0.923	1	0.997	0.923	1	CLONAL	2	TRUE	1	0.32313787648528	3		400	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579346	7579346	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002673-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	116	256	0	ENST00000269305.4:c.341del	p.Leu114CysfsTer9	p.L114Cfs*9	ENST00000269305	NM_001126112.2	114	tTg/tg	4/11	0.32313787648528	2	FACETS	0.907	0.824	0.992	0.907	0.824	0.992	CLONAL	2	TRUE	0	0.32313787648528	2		256	396	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0002682-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	72	259	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.737984257895053	2		260	185	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0002682-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	81	205	0	ENST00000262160.6:c.1391C>G	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tGa	11/11	0.737984257895053	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.737984257895053	1		205	131	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855984	68855984	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121964877	NA	P-0002682-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	109	289	0	ENST00000261769.5:c.1792C>T	p.Arg598Ter	p.R598*	ENST00000261769	NM_004360.3	598	Cga/Tga	12/16	0.737984257895053	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.737984257895053	1		289	180	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572986	7572986	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555524156	NA	P-0002682-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	78	161	0	ENST00000269305.4:c.1123C>T	p.Gln375Ter	p.Q375*	ENST00000269305	NM_001126112.2	375	Cag/Tag	11/11	0.737984257895053	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.737984257895053	1		161	108	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11293486	11293486	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002682-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	120	314	0	ENST00000361445.4:c.2390A>T	p.Asn797Ile	p.N797I	ENST00000361445	NM_004958.3	797	aAt/aTt	15/58	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.737984257895053	2		314	307	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176104168	176104168	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002682-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	36	194	0	ENST00000367669.3:c.946G>A	p.Glu316Lys	p.E316K	ENST00000367669	NM_022457.5	316	Gaa/Aaa	8/20	0.737984257895053	4	FACETS	0.606	0.5	0.723	0.202	0.166	0.241	SUBCLONAL	1	TRUE	1	0.737984257895053	4		194	280	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715353	61715353	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002682-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	60	269	0	ENST00000401558.2:c.2260G>T	p.Glu754Ter	p.E754*	ENST00000401558	NM_003400.3	754	Gaa/Taa	19/25	1	2	FACETS	0.704	0.614	0.799	0.704	0.614	0.799	SUBCLONAL	1	TRUE	1	0.737984257895053	2		269	231	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215617239	215617239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002682-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	98	284	0	ENST00000260947.4:c.1609G>A	p.Glu537Lys	p.E537K	ENST00000260947	NM_000465.2	537	Gaa/Aaa	7/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.737984257895053	2		284	246	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125785	47125785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002682-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	94	156	0	ENST00000409792.3:c.5485C>T	p.Gln1829Ter	p.Q1829*	ENST00000409792	NM_014159.6	1829	Cag/Tag	12/21	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.737984257895053	2		156	253	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155622	106155622	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343154406	NA	P-0002682-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	113	175	0	ENST00000380013.4:c.523G>A	p.Glu175Lys	p.E175K	ENST00000380013	NM_001127208.2	175	Gaa/Aaa	3/11	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.737984257895053	2		175	301	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155988	106155988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749991352	NA	P-0002682-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	100	220	0	ENST00000380013.4:c.889G>A	p.Asp297Asn	p.D297N	ENST00000380013	NM_001127208.2	297	Gat/Aat	3/11	1	2	FACETS	0.916	0.829	1	0.916	0.829	1	CLONAL	1	TRUE	1	0.737984257895053	2		220	296	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293718	1293718	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002682-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	94	131	0	ENST00000310581.5:c.1283G>A	p.Arg428Gln	p.R428Q	ENST00000310581	NM_198253.2	428	cGg/cAg	2/16	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.737984257895053	2		131	247	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939060	131939060	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002682-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	50	221	0	ENST00000265335.6:c.2276G>T	p.Arg759Ile	p.R759I	ENST00000265335		759	aGa/aTa	14/25	1	2	FACETS	0.766	0.66	0.877	0.766	0.66	0.877	SUBCLONAL	1	TRUE	1	0.737984257895053	2		221	177	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405086	405086	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002682-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	110	258	0	ENST00000380956.4:c.1168G>C	p.Glu390Gln	p.E390Q	ENST00000380956	NM_001195286.1	390	Gag/Cag	8/9	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.737984257895053	2		258	275	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538863	23538863	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002682-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	118	229	0	ENST00000380871.4:c.576G>C	p.Glu192Asp	p.E192D	ENST00000380871	NM_006167.3	192	gaG/gaC	2/2	0.737984257895053	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.737984257895053	1		229	175	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913233	32913233	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002682-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	113	188	0	ENST00000380152.3:c.4741G>T	p.Glu1581Ter	p.E1581*	ENST00000380152		1581	Gag/Tag	11/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.737984257895053	2		188	247	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984698	11984698	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002682-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	48	69	0	ENST00000353533.5:c.244G>T	p.Glu82Ter	p.E82*	ENST00000353533	NM_003010.3	82	Gag/Tag	3/11	0.737984257895053	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.737984257895053	1		69	77	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245866	41245866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002682-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	105	288	0	ENST00000357654.3:c.1682C>T	p.Ser561Phe	p.S561F	ENST00000357654	NM_007294.3	561	tCt/tTt	10/23	0.737984257895053	1	FACETS	0.911	0.839	0.983	0.911	0.839	0.983	CLONAL	1	TRUE	0	0.737984257895053	1		288	197	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533676	63533676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367697282	NA	P-0002682-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	92	239	0	ENST00000307078.5:c.1478C>T	p.Ser493Leu	p.S493L	ENST00000307078	NM_004655.3	493	tCg/tTg	6/11	0.737984257895053	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.737984257895053	1		239	155	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265400	10265400	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002682-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	99	208	0	ENST00000340748.4:c.1646C>G	p.Ser549Cys	p.S549C	ENST00000340748		549	tCc/tGc	20/40	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.737984257895053	2		208	257	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207153	1207155	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs587782056	NA	P-0002682-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	91	245	0	ENST00000326873.7:c.250_252del	p.Lys84del	p.K84del	ENST00000326873	NM_000455.4	81	AAG/-	1/10	1	2	FACETS	0.894	0.804	0.986	0.894	0.804	0.986	CLONAL	1	TRUE	1	0.737984257895053	2		245	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0002683-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	220	98	255	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.479816387105469	1	FACETS	0.976	0.881	1	0.976	0.881	1	CLONAL	1	TRUE	0	0.479816387105469	1		255	318	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0002683-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	388	360	454	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.275763350181139	5	FACETS	1	0.991	1			1	INDETERMINATE	3	TRUE	NA	0.479816387105469	5		454	748	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437766	52437766	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002683-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	411	98	260	0	ENST00000460680.1:c.1395C>G	p.Ile465Met	p.I465M	ENST00000460680	NM_004656.3	465	atC/atG	13/17	0.479816387105469	3	FACETS	0.995	0.891	1			1	CLONAL	1	TRUE	NA	0.479816387105469	3		260	509	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427784	72427784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1438865674	NA	P-0002683-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	216	20	110	1	ENST00000477973.2:c.706C>T	p.Arg236Trp	p.R236W	ENST00000477973	NM_012234.5	236	Cgg/Tgg	4/4	1	2	FACETS	0.353	0.271	0.449	0.353	0.271	0.449	SUBCLONAL	1	TRUE	1	0.479816387105469	2		111	236	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541163	187541163	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002683-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	351	88	214	0	ENST00000441802.2:c.6577G>C	p.Glu2193Gln	p.E2193Q	ENST00000441802	NM_005245.3	2193	Gag/Cag	10/27	1	2	FACETS	0.836	0.744	0.932	0.836	0.744	0.932	CLONAL	1	TRUE	1	0.479816387105469	2		214	439	SUCCESS
ATM	472	MSKCC	GRCh37	11	108138070	108138070	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0002683-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	181	110	211	0	ENST00000278616.4:c.2638+1G>T		p.X880_splice	ENST00000278616	NM_000051.3	880			0.479816387105469	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.479816387105469	1		211	291	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602329	28602329	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002683-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	299	78	303	0	ENST00000241453.7:c.2039C>A	p.Ala680Glu	p.A680E	ENST00000241453	NM_004119.2	680	gCg/gAg	16/24	0.404568426562179	1	FACETS	0.656	0.58	0.736	0.656	0.58	0.736	SUBCLONAL	1	TRUE	0	0.479816387105469	1		303	377	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602417	28602417	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002683-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	289	36	248	0	ENST00000241453.7:c.1951G>C	p.Asp651His	p.D651H	ENST00000241453	NM_004119.2	651	Gac/Cac	16/24	0.404568426562179	1	FACETS	0.351	0.289	0.42	0.351	0.289	0.42	SUBCLONAL	1	TRUE	0	0.479816387105469	1		248	325	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245624	41245624	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs80357344	NA	P-0002683-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	400	138	257	0	ENST00000357654.3:c.1924G>C	p.Asp642His	p.D642H	ENST00000357654	NM_007294.3	642	Gat/Cat	10/23	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.479816387105469	2		257	538	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044742	47044745	+	frameshift_variant	Frame_Shift_Del	DEL	GAAA	GAAA	CG	novel	NA	P-0002683-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	234	53	288	0	ENST00000377604.3:c.2142_2145delinsCG	p.Lys715ValfsTer4	p.K715Vfs*4	ENST00000377604	NM_001204468.1	714	ccGAAA/ccCG	19/24	0.36923367566965	0	FACETS	0.4	0.344	0.462			1	SUBCLONAL	1	TRUE	0	0.479816387105469	0		288	287	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0002691-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	169	377	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.885	0.826	0.943	1	0.994	1	CLONAL	3	TRUE	1	0.358702916992058	2		378	355	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937611	76937615	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTT	CTTTT	-	novel	NA	P-0002691-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	141	312	0	ENST00000373344.5:c.3133_3137del	p.Lys1045Ter	p.K1045*	ENST00000373344	NM_000489.3	1045	AAAAGt/t	9/35	0.358702916992058	1	FACETS	1	0.97	1	1	0.992	1	CLONAL	2	TRUE	0	0.358702916992058	1		312	297	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125034	46125035	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0002691-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	25	214	0	ENST00000334344.6:c.221_222del	p.Glu74GlyfsTer10	p.E74Gfs*10	ENST00000334344	NM_152641.2	74	gAA/g	3/21	1	2	FACETS	0.297	0.233	0.37	0.297	0.233	0.37	SUBCLONAL	1	TRUE	1	0.358702916992058	2		214	470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578396	+	inframe_deletion	In_Frame_Del	DEL	TGG	TGG	-	novel	NA	P-0002691-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	216	181	0	ENST00000269305.4:c.534_536del	p.His179del	p.H179del	ENST00000269305	NM_001126112.2	178	caCCAt/cat	5/11	0.358702916992058	2	FACETS	0.979	0.95	1	1	0.996	1	CLONAL	5	TRUE	0	0.358702916992058	2		181	246	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	164	261	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.35088486442723	3	FACETS	0.822	0.758	0.888	0.822	0.758	0.888	CLONAL	2	TRUE	1	0.390968729794264	3		261	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	81	440	0	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	0.390968729794264	1	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	0	0.390968729794264	1		440	332	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141586	202141586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760898260	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	145	531	0	ENST00000358485.4:c.874C>T	p.Arg292Trp	p.R292W	ENST00000358485	NM_001080125.1	292	Cgg/Tgg	7/9	1	2	FACETS	0.858	0.782	0.936	0.858	0.782	0.936	CLONAL	1	TRUE	1	0.390968729794264	2		531	865	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263850	133263850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	36	212	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	0.390968729794264	NA		212	188	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307502	118307502	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782112520	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	73	478	0	ENST00000534358.1:c.275C>T	p.Ser92Leu	p.S92L	ENST00000534358	NM_005933.3	92	tCg/tTg	1/36	NA	2	FACETS	0.879	0.772	0.993			1	INDETERMINATE	1	TRUE	NA	0.390968729794264	2		478	425	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011144	12011144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	138	519	0	ENST00000353533.5:c.551C>T	p.Ser184Leu	p.S184L	ENST00000353533	NM_003010.3	184	tCg/tTg	5/11	0.390968729794264	1	FACETS	0.853	0.778	0.931	0.853	0.778	0.931	CLONAL	1	TRUE	0	0.390968729794264	1		519	666	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306987	65306987	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	140	524	0	ENST00000342505.4:c.2590G>T	p.Glu864Ter	p.E864*	ENST00000342505	NM_002227.2	864	Gaa/Taa	19/25	0.344864290690485	2	FACETS	0.912	0.831	0.997	0.456	0.415	0.499	CLONAL	1	TRUE	0	0.390968729794264	2		524	785	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309819	65309819	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	110	551	0	ENST00000342505.4:c.2331G>C	p.Trp777Cys	p.W777C	ENST00000342505	NM_002227.2	777	tgG/tgC	17/25	0.344864290690485	2	FACETS	0.844	0.759	0.933	0.422	0.379	0.467	CLONAL	1	TRUE	0	0.390968729794264	2		551	667	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111000	193111000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	85	377	0	ENST00000367435.3:c.533C>T	p.Ser178Leu	p.S178L	ENST00000367435	NM_024529.4	178	tCa/tTa	7/17	0.344864290690485	2	FACETS	0.697	0.616	0.783	0.348	0.308	0.392	SUBCLONAL	1	TRUE	0	0.390968729794264	2		377	624	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111022	193111022	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	99	406	0	ENST00000367435.3:c.555C>G	p.Ile185Met	p.I185M	ENST00000367435	NM_024529.4	185	atC/atG	7/17	0.344864290690485	2	FACETS	0.699	0.624	0.779	0.35	0.312	0.39	SUBCLONAL	1	TRUE	0	0.390968729794264	2		406	724	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266893	41266893	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	156	563	0	ENST00000349496.5:c.564C>G	p.Ile188Met	p.I188M	ENST00000349496	NM_001904.3	188	atC/atG	5/15	1	2	FACETS	0.976	0.894	1	0.976	0.894	1	CLONAL	1	TRUE	1	0.390968729794264	2		563	818	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405870	49405870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	116	676	0	ENST00000418115.1:c.268G>A	p.Asp90Asn	p.D90N	ENST00000418115	NM_001664.2	90	Gat/Aat	3/5	0.371754687125999	1	FACETS	0.692	0.624	0.763	0.692	0.624	0.763	SUBCLONAL	1	TRUE	0	0.390968729794264	1		676	690	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390170	89390170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148593404	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	154	587	0	ENST00000336596.2:c.919G>A	p.Glu307Lys	p.E307K	ENST00000336596	NM_005233.5	307	Gag/Aag	4/17	0.371754687125999	1	FACETS	0.947	0.87	1	0.947	0.87	1	CLONAL	1	TRUE	0	0.390968729794264	1		587	669	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204891	128204891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	105	559	0	ENST00000341105.2:c.550G>A	p.Asp184Asn	p.D184N	ENST00000341105	NM_032638.4	184	Gac/Aac	3/6	0.385084277845394	3	FACETS	1	0.935	1	0.528	0.474	0.585	CLONAL	1	TRUE	1	0.390968729794264	3		559	608	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	231100	231100	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1560992565	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	68	300	0	ENST00000264932.6:c.880C>G	p.Gln294Glu	p.Q294E	ENST00000264932	NM_004168.2	294	Cag/Gag	7/15	1	2	FACETS	0.824	0.72	0.936	0.824	0.72	0.936	CLONAL	1	TRUE	1	0.390968729794264	2		300	422	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953918	131953918	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	127	363	0	ENST00000265335.6:c.3321G>A	p.Met1107Ile	p.M1107I	ENST00000265335		1107	atG/atA	21/25	0.0778675923143435	3	FACETS	0.958	0.868	1	0.479	0.434	0.526	INDETERMINATE	1	TRUE	1	0.390968729794264	3		363	811	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953955	131953955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	98	322	0	ENST00000265335.6:c.3358G>A	p.Asp1120Asn	p.D1120N	ENST00000265335		1120	Gat/Aat	21/25	0.0778675923143435	3	FACETS	0.865	0.772	0.964	0.432	0.386	0.482	INDETERMINATE	1	TRUE	1	0.390968729794264	3		322	693	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953963	131953963	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	84	307	0	ENST00000265335.6:c.3366T>A	p.Asp1122Glu	p.D1122E	ENST00000265335		1122	gaT/gaA	21/25	0.0778675923143435	3	FACETS	0.799	0.706	0.898	0.399	0.353	0.449	INDETERMINATE	1	TRUE	1	0.390968729794264	3		307	643	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523718	176523718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140492176	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	59	519	0	ENST00000292408.4:c.2129G>A	p.Arg710Gln	p.R710Q	ENST00000292408	NM_213647.1	710	cGa/cAa	16/18	1	2	FACETS	0.87	0.752	0.996	0.87	0.752	0.996	CLONAL	1	TRUE	1	0.390968729794264	2		519	347	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176715836	176715836	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	176	611	0	ENST00000439151.2:c.6168C>G	p.Phe2056Leu	p.F2056L	ENST00000439151	NM_022455.4	2056	ttC/ttG	21/23	1	2	FACETS	0.928	0.855	1	0.928	0.855	1	CLONAL	1	TRUE	1	0.390968729794264	2		611	970	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481439	20481439	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	102	395	0	ENST00000346618.3:c.508C>A	p.Pro170Thr	p.P170T	ENST00000346618	NM_001949.4	170	Cca/Aca	3/7	NA	2	FACETS	0.875	0.785	0.971			1	INDETERMINATE	1	TRUE	NA	0.390968729794264	2		395	596	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652203	36652203	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	80	412	0	ENST00000244741.5:c.325G>C	p.Asp109His	p.D109H	ENST00000244741	NM_000389.4	109	Gac/Cac	2/3	1	2	FACETS	0.869	0.768	0.977	0.869	0.768	0.977	CLONAL	1	TRUE	1	0.390968729794264	2		412	471	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525098	157525098	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	161	500	1	ENST00000346085.5:c.4993G>T	p.Asp1665Tyr	p.D1665Y	ENST00000346085	NM_020732.3	1665	Gac/Tac	19/20	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.390968729794264	2		501	812	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846012	151846012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398375188	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	99	487	0	ENST00000262189.6:c.13000C>T	p.Arg4334Trp	p.R4334W	ENST00000262189	NM_170606.2	4334	Cgg/Tgg	52/59	1	2	FACETS	0.776	0.693	0.863	0.776	0.693	0.863	SUBCLONAL	1	TRUE	1	0.390968729794264	2		487	653	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450084	32450084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	82	508	0	ENST00000332351.3:c.728C>T	p.Ser243Leu	p.S243L	ENST00000332351	NM_024426.4	243	tCa/tTa	2/10	1	2	FACETS	0.918	0.813	1	0.918	0.813	1	CLONAL	1	TRUE	1	0.390968729794264	2		508	457	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482351	56482351	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	158	602	0	ENST00000267101.3:c.899C>G	p.Ser300Cys	p.S300C	ENST00000267101	NM_001982.3	300	tCc/tGc	8/28	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.390968729794264	2		602	749	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495375	56495375	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	123	591	0	ENST00000267101.3:c.3565G>A	p.Glu1189Lys	p.E1189K	ENST00000267101	NM_001982.3	1189	Gaa/Aaa	28/28	1	2	FACETS	0.777	0.702	0.855	0.777	0.702	0.855	SUBCLONAL	1	TRUE	1	0.390968729794264	2		591	810	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919675	28919675	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	129	509	0	ENST00000282397.4:c.2262G>C	p.Lys754Asn	p.K754N	ENST00000282397	NM_002019.4	754	aaG/aaC	16/30	1	2	FACETS	0.927	0.842	1	0.927	0.842	1	CLONAL	1	TRUE	1	0.390968729794264	2		509	712	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929131	32929131	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777305503	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	166	590	0	ENST00000380152.3:c.7141C>T	p.Pro2381Ser	p.P2381S	ENST00000380152		2381	Cca/Tca	14/27	0.331752097070116	3	FACETS	0.91	0.834	0.989			1	CLONAL	1	TRUE	NA	0.390968729794264	3		590	1116	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972596	32972596	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	124	459	0	ENST00000380152.3:c.9946G>C	p.Glu3316Gln	p.E3316Q	ENST00000380152		3316	Gaa/Caa	27/27	0.331752097070116	3	FACETS	0.951	0.861	1			1	CLONAL	1	TRUE	NA	0.390968729794264	3		459	797	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105240300	105240300	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs971568277	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	61	455	0	ENST00000349310.3:c.651C>G	p.Phe217Leu	p.F217L	ENST00000349310	NM_001014432.1	217	ttC/ttG	9/15	0.390968729794264	1	FACETS	0.719	0.624	0.822	0.719	0.624	0.822	SUBCLONAL	1	TRUE	0	0.390968729794264	1		455	349	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242021	105242021	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	205	601	0	ENST00000349310.3:c.403G>C	p.Glu135Gln	p.E135Q	ENST00000349310	NM_001014432.1	135	Gag/Cag	6/15	0.390968729794264	1	FACETS	0.963	0.905	1	1	0.994	1	CLONAL	2	TRUE	0	0.390968729794264	1		601	438	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127688	2127688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779832805	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	88	564	1	ENST00000219476.3:c.2927G>A	p.Arg976Gln	p.R976Q	ENST00000219476	NM_000548.3	976	cGg/cAg	26/42	0.100775634710781	3	FACETS	0.947	0.841	1	0.316	0.28	0.354	INDETERMINATE	1	TRUE	0	0.390968729794264	3		565	568	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857082	9857082	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs752489703	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	105	543	0	ENST00000330684.3:c.4319C>G	p.Ser1440Cys	p.S1440C	ENST00000330684	NM_001134407.1	1440	tCt/tGt	13/13	0.100775634710781	3	FACETS	0.831	0.744	0.923	0.277	0.248	0.308	INDETERMINATE	1	TRUE	0	0.390968729794264	3		543	773	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9928088	9928088	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	119	377	0	ENST00000330684.3:c.1652-1G>A		p.X551_splice	ENST00000330684	NM_001134407.1	551			0.100775634710781	3	FACETS	1	0.952	1	0.362	0.327	0.399	INDETERMINATE	1	TRUE	0	0.390968729794264	3		377	670	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664405	29664405	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	131	498	0	ENST00000356175.3:c.6384G>C	p.Leu2128Phe	p.L2128F	ENST00000356175	NM_000267.3	2128	ttG/ttC	42/57	0.344864290690485	2	FACETS	0.775	0.703	0.851	0.387	0.351	0.426	SUBCLONAL	1	TRUE	0	0.390968729794264	2		498	865	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533788	63533788	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	61	433	0	ENST00000307078.5:c.1366G>A	p.Gly456Ser	p.G456S	ENST00000307078	NM_004655.3	456	Ggc/Agc	6/11	0.390968729794264	1	FACETS	0.812	0.706	0.926	0.812	0.706	0.926	CLONAL	1	TRUE	0	0.390968729794264	1		433	309	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117707	70117707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367592961	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	128	710	0	ENST00000245479.2:c.175G>A	p.Asp59Asn	p.D59N	ENST00000245479	NM_000346.3	59	Gat/Aat	1/3	0.390968729794264	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.390968729794264	1		710	429	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223448	2223448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	50	412	0	ENST00000398665.3:c.3559G>A	p.Glu1187Lys	p.E1187K	ENST00000398665	NM_032482.2	1187	Gag/Aag	25/28	0.341945099075666	0	FACETS	0.608	0.521	0.703			1	SUBCLONAL	1	TRUE	0	0.390968729794264	0		412	256	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796942	42796942	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs774372702	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	71	514	0	ENST00000575354.2:c.3400C>G	p.Leu1134Val	p.L1134V	ENST00000575354	NM_015125.3	1134	Ctg/Gtg	14/20	1	2	FACETS	0.863	0.756	0.977	0.863	0.756	0.977	CLONAL	1	TRUE	1	0.390968729794264	2		514	421	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182858	123182858	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	152	549	0	ENST00000218089.9:c.823C>T	p.Gln275Ter	p.Q275*	ENST00000218089	NM_001042749.1	275	Cag/Tag	10/35	0.322705256468645	1	FACETS	0.717	0.655	0.781	0.717	0.655	0.781	SUBCLONAL	1	TRUE	0	0.390968729794264	1		549	873	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	338123	338123	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	novel	NA	P-0002713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	79	592	0	ENST00000262320.3:c.2588G>C	p.Ter863SerextTer1	p.*863Sext*1	ENST00000262320	NM_003502.3	863	tGa/tCa	11/11	0.100775634710781	3	FACETS	0.817	0.72	0.922	0.272	0.24	0.308	INDETERMINATE	1	TRUE	0	0.390968729794264	3		592	591	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880923	134880924	+	missense_variant	Missense_Mutation	DNP	CT	CT	AG	novel	NA	P-0002720-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	83	479	0	ENST00000398015.3:c.1486_1487inv	p.Leu496Arg	p.L496R	ENST00000398015	NM_004441.4	496	CTg/AGg	7/16	0.456976107436788	2	FACETS	1	0.948	1	0.555	0.494	0.619	CLONAL	1	TRUE	0	0.467292216767136	2		479	320	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039340	49039340	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0002720-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	253	602	0	ENST00000267163.4:c.2326-1del		p.X776_splice	ENST00000267163	NM_000321.2	776			0.463219588117482	2	FACETS	0.864	0.814	0.914	0.864	0.814	0.914	CLONAL	2	TRUE	0	0.467292216767136	2		602	627	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427754	72427754	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002723-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	30	366	0	ENST00000477973.2:c.736C>T	p.Gln246Ter	p.Q246*	ENST00000477973	NM_012234.5	246	Cag/Tag	4/4	0.765831635088966	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.765831635088966	1		366	37	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871126	12871126	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0002723-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	25	315	0	ENST00000228872.4:c.353T>A	p.Leu118Ter	p.L118*	ENST00000228872	NM_004064.3	118	tTa/tAa	1/3	0.680120490354486	3	FACETS	1	0.863	1	1	0.863	1	CLONAL	2	TRUE	1	0.765831635088966	3		315	44	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0002724-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	323	228	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.599012220718289	2	FACETS	0.973	0.931	1	0.973	0.931	1	CLONAL	2	TRUE	0	0.599012220718289	2		228	554	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0002724-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	210	561	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.465156210253037	3	FACETS	1	0.959	1	0.522	0.485	0.56	CLONAL	1	TRUE	1	0.599012220718289	3		561	873	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212464	5212464	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002724-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	284	484	0	ENST00000357368.4:c.4653G>T	p.Gln1551His	p.Q1551H	ENST00000357368	NM_002850.3	1551	caG/caT	31/38	0.599012220718289	3	FACETS	1	0.986	1	0.579	0.544	0.615	CLONAL	1	TRUE	1	0.599012220718289	3		484	1064	SUCCESS
APC	324	MSKCC	GRCh37	5	112175561	112175561	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002724-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	378	473	0	ENST00000257430.4:c.4271del	p.Pro1424GlnfsTer49	p.P1424Qfs*49	ENST00000257430	NM_000038.5	1424	Cca/ca	16/16	0.465156210253037	3	FACETS	0.935	0.892	0.978	0.935	0.892	0.978	CLONAL	2	TRUE	1	0.599012220718289	3		473	877	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0002729-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	62	228	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.0769794824236965	2	FACETS	0.989	0.858	1	1	0.979	1	CLONAL	4	FALSE	0	0.0769794824236965	2		228	407	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0002729-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	144	377	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	0.994	1	CLONAL	6	FALSE	1	0.0769794824236965	2		378	599	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0002729-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	215	383	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.0769794824236965	2	FACETS	0.975	0.913	1	1	0.996	1	CLONAL	10	FALSE	0	0.0769794824236965	2		385	573	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0002730-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	252	358	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	0.469468432855744	2		358	959	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0002730-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	193	491	0	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	0.469468432855744	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.469468432855744	1		491	565	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100720	8100720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002730-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	142	599	0	ENST00000346208.3:c.694G>A	p.Gly232Arg	p.G232R	ENST00000346208		232	Gga/Aga	3/6	1	2	FACETS	0.837	0.764	0.913	0.837	0.764	0.913	CLONAL	1	TRUE	1	0.469468432855744	2		599	723	SUCCESS
APC	324	MSKCC	GRCh37	5	112164582	112164582	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167594	NA	P-0002730-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	260	355	0	ENST00000257430.4:c.1657del	p.Trp553GlyfsTer5	p.W553Gfs*5	ENST00000257430	NM_000038.5	552	tcT/tc	14/16	0.469468432855744	2	FACETS	0.928	0.877	0.979	0.928	0.877	0.979	CLONAL	2	TRUE	0	0.469468432855744	2		355	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912657	NA	P-0002731-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	888	392	0	ENST00000269305.4:c.814G>C	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ctg	8/11	0.677732935883852	3	FACETS	0.935	0.914	0.955	0.935	0.914	0.955	CLONAL	3	TRUE	0	0.677732935883852	3		392	1251	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653080	29653080	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002731-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	485	273	0	ENST00000356175.3:c.5015A>G	p.His1672Arg	p.H1672R	ENST00000356175	NM_000267.3	1672	cAt/cGt	36/57	0.677732935883852	3	FACETS	0.949	0.921	0.976	0.949	0.921	0.976	CLONAL	3	TRUE	0	0.677732935883852	3		273	673	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600417	10600417	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002731-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	663	366	0	ENST00000171111.5:c.1438G>T	p.Gly480Trp	p.G480W	ENST00000171111	NM_203500.1	480	Ggg/Tgg	4/6	0.448159573659907	3	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.677732935883852	3		366	1066	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219412	1219422	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTGCGTGCGC	GGTGCGTGCGC	-	novel	NA	P-0002731-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	299	202	0	ENST00000326873.7:c.464+2_464+12del		p.X155_splice	ENST00000326873	NM_000455.4	155		3/10	NA	2	FACETS	0.886	0.847	0.924			1	INDETERMINATE	2	TRUE	NA	0.677732935883852	2		202	498	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023208	27023208	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002731-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	73	124	0	ENST00000324856.7:c.314G>T	p.Gly105Val	p.G105V	ENST00000324856	NM_006015.4	105	gGg/gTg	1/20	0.595078160238385	2	FACETS	0.816	0.722	0.914	0.408	0.361	0.457	CLONAL	1	TRUE	0	0.677732935883852	2		124	264	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720987	119720987	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002731-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	209	396	0	ENST00000316626.5:c.188G>C	p.Gly63Ala	p.G63A	ENST00000316626		63	gGa/gCa	2/12	0.595078160238385	2	FACETS	0.818	0.762	0.876	0.409	0.381	0.438	CLONAL	1	TRUE	0	0.677732935883852	2		396	754	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016322	150016322	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002731-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	155	304	0	ENST00000253339.5:c.384C>A	p.Asn128Lys	p.N128K	ENST00000253339		128	aaC/aaA	2/7	NA	2	FACETS	0.765	0.703	0.829			1	INDETERMINATE	1	TRUE	NA	0.677732935883852	2		304	598	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738648	145738648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767102398	NA	P-0002731-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	255	142	0	ENST00000428558.2:c.2416G>A	p.Gly806Arg	p.G806R	ENST00000428558	NM_004260.3	806	Ggg/Agg	15/22	0.677732935883852	6	FACETS	0.914	0.856	0.973	0.457	0.428	0.487	CLONAL	2	TRUE	2	0.677732935883852	6		142	970	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563201	21563201	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002731-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	188	296	0	ENST00000382592.4:c.718G>C	p.Glu240Gln	p.E240Q	ENST00000382592	NM_014572.2	240	Gag/Cag	4/8	1	2	FACETS	0.852	0.791	0.915	0.852	0.791	0.915	CLONAL	1	TRUE	1	0.677732935883852	2		296	651	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058472	42058472	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002731-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	638	565	0	ENST00000219905.7:c.8193del	p.Asp2732ThrfsTer20	p.D2732Tfs*20	ENST00000219905	NM_001164273.1	2731	gTt/gt	24/24	0.595078160238385	2	FACETS	0.857	0.83	0.883	0.857	0.83	0.883	CLONAL	2	TRUE	0	0.677732935883852	2		565	1099	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434745	49434745	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777903880	NA	P-0002753-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	214	239	0	ENST00000301067.7:c.6808G>A	p.Glu2270Lys	p.E2270K	ENST00000301067	NM_003482.3	2270	Gag/Aag	31/54	0.53783501236625	4	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	2	0.53783501236625	4		239	607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578175	7578175	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0002753-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	220	261	0	ENST00000269305.4:c.672+2T>C		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.513629161182767	2	FACETS	0.891	0.84	0.943	0.891	0.84	0.943	CLONAL	2	TRUE	0	0.53783501236625	2		261	459	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591832	48591832	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002753-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	218	282	0	ENST00000342988.3:c.995A>T	p.Asp332Val	p.D332V	ENST00000342988	NM_005359.5	332	gAt/gTt	9/12	0.53783501236625	4	FACETS	0.921	0.86	0.982	0.921	0.86	0.982	CLONAL	2	TRUE	2	0.53783501236625	4		282	677	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5246017	5246017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002753-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	170	181	1	ENST00000357368.4:c.758G>A	p.Ser253Asn	p.S253N	ENST00000357368	NM_002850.3	253	aGc/aAc	10/38	0.513629161182767	2	FACETS	0.914	0.854	0.973	0.914	0.854	0.973	CLONAL	2	TRUE	0	0.53783501236625	2		182	346	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874417	76874419	+	missense_variant	Missense_Mutation	TNP	AAT	AAT	CAG	novel	NA	P-0002753-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	210	151	0	ENST00000373344.5:c.5303_5305delinsCTG	p.Asn1768_Leu1769delinsThrVal	p.N1768_L1769delinsTV	ENST00000373344	NM_000489.3	1768	aATTta/aCTGta	21/35	0.416782263224452	2	FACETS	1	0.99	1			1	CLONAL	2	TRUE	NA	0.53783501236625	2		151	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0002759-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	136	545	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.254007609038655	2	FACETS	0.782	0.716	0.85	0.782	0.716	0.85	SUBCLONAL	2	TRUE	0	0.367786529703143	2		545	473	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741751	145741751	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002759-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	58	511	0	ENST00000428558.2:c.752G>T	p.Ser251Ile	p.S251I	ENST00000428558	NM_004260.3	251	aGc/aTc	5/22	1	2	FACETS	0.649	0.558	0.748	0.649	0.558	0.748	SUBCLONAL	1	TRUE	1	0.367786529703143	2		511	486	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426955	70426955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002759-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	44	471	0	ENST00000373644.4:c.4615G>A	p.Glu1539Lys	p.E1539K	ENST00000373644	NM_030625.2	1539	Gag/Aag	7/12	0.174872519380529	1	FACETS	0.534	0.448	0.627	0.534	0.448	0.627	INDETERMINATE	1	TRUE	0	0.367786529703143	1		471	366	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141526	11141526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002759-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	89	559	0	ENST00000358026.2:c.3503C>T	p.Ala1168Val	p.A1168V	ENST00000358026	NM_001128849.1	1168	gCa/gTa	25/36	0.367786529703143	1	FACETS	0.956	0.853	1	0.956	0.853	1	CLONAL	1	TRUE	0	0.367786529703143	1		559	413	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871948	45871948	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002759-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	92	586	0	ENST00000391945.4:c.300G>C	p.Glu100Asp	p.E100D	ENST00000391945	NM_000400.3	100	gaG/gaC	5/23	0.367786529703143	1	FACETS	0.865	0.772	0.963	0.865	0.772	0.963	CLONAL	1	TRUE	0	0.367786529703143	1		586	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578466	7578466	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786202752	NA	P-0002767-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	316	345	0	ENST00000269305.4:c.464C>A	p.Thr155Asn	p.T155N	ENST00000269305	NM_001126112.2	155	aCc/aAc	5/11	0.4824302290579	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.4824302290579	2		345	648	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0002782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	220	454	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.941	0.877	1	0.941	0.877	1	CLONAL	1	TRUE	1	0.525992642033449	2		454	889	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0002782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	123	336	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	NA	2	FACETS	0.546	0.494	0.602			1	INDETERMINATE	1	TRUE	NA	0.525992642033449	2		336	856	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258409	16258409	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	33	437	0	ENST00000375759.3:c.5674C>T	p.Pro1892Ser	p.P1892S	ENST00000375759	NM_015001.2	1892	Cca/Tca	11/15	1	2	FACETS	0.195	0.158	0.237	0.195	0.158	0.237	SUBCLONAL	1	TRUE	1	0.525992642033449	2		437	644	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446362	29446362	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	90	388	0	ENST00000389048.3:c.3205A>C	p.Met1069Leu	p.M1069L	ENST00000389048	NM_004304.4	1069	Atg/Ctg	20/29	NA	2	FACETS	0.609	0.541	0.681			1	INDETERMINATE	1	TRUE	NA	0.525992642033449	2		388	562	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098801	178098801	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	141	465	0	ENST00000397062.3:c.244G>C	p.Glu82Gln	p.E82Q	ENST00000397062	NM_006164.4	82	Gaa/Caa	2/5	1	2	FACETS	0.565	0.514	0.618	0.565	0.514	0.618	SUBCLONAL	1	TRUE	1	0.525992642033449	2		465	949	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418394	49418394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1565756106	NA	P-0002782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	97	272	0	ENST00000301067.7:c.16019G>A	p.Arg5340Gln	p.R5340Q	ENST00000301067	NM_003482.3	5340	cGa/cAa	50/54	1	2	FACETS	0.606	0.541	0.674	0.606	0.541	0.674	SUBCLONAL	1	TRUE	1	0.525992642033449	2		272	609	SUCCESS
APC	324	MSKCC	GRCh37	5	112128161	112128161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002782-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	167	407	0	ENST00000257430.4:c.664del	p.Gln222SerfsTer71	p.Q222Sfs*71	ENST00000257430	NM_000038.5	222	Cag/ag	7/16	1	2	FACETS	0.754	0.693	0.817	0.754	0.693	0.817	SUBCLONAL	1	TRUE	1	0.525992642033449	2		407	842	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726624	41726624	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002800-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	86	228	0	ENST00000301178.4:c.169C>T	p.Gln57Ter	p.Q57*	ENST00000301178	NM_021913.4	57	Cag/Tag	2/20	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.276846408377619	2		228	602	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458146	120458146	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002800-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	84	215	0	ENST00000256646.2:c.7199del	p.Arg2400GlnfsTer16	p.R2400Qfs*16	ENST00000256646	NM_024408.3	2400	cGa/ca	34/34	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.276846408377619	2		215	581	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023653	1023676	+	inframe_deletion	In_Frame_Del	DEL	ACAGTTACAGGAGTGCTGTGCGTC	ACAGTTACAGGAGTGCTGTGCGTC	-	novel	NA	P-0002800-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	115	225	0	ENST00000358495.3:c.888_911del	p.Thr297_Val304del	p.T297_V304del	ENST00000358495	NM_134424.2	296	gtGACGCACAGCACTCCTGTAACTGTc/gtc	10/12	0.267483905579403	3	FACETS	1	0.982	1	0.705	0.636	0.778	CLONAL	1	TRUE	1	0.276846408377619	3		225	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002800-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	76	161	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.276846408377619	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.276846408377619	1		161	449	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210246	123210261	+	protein_altering_variant	In_Frame_Del	DEL	AGCATTTTGTAAGCTA	AGCATTTTGTAAGCTA	C	novel	NA	P-0002800-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	113	267	0	ENST00000218089.9:c.2598_2613delinsC	p.Ala867_Leu871del	p.A867_L871del	ENST00000218089	NM_001042749.1	866	gcAGCATTTTGTAAGCTA/gcC	26/35	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.276846408377619	2		267	780	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490660	20490660	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0002800-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	63	152	0	ENST00000346618.3:c.1397G>C	p.Ter466SerextTer5	p.*466Sext*5	ENST00000346618	NM_001949.4	466	tGa/tCa	7/7	1	2	FACETS	0.956	0.829	1	0.956	0.829	1	CLONAL	1	TRUE	1	0.276846408377619	2		152	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579867	7579867	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002803-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	60	238	0	ENST00000269305.4:c.46del	p.Gln16ArgfsTer28	p.Q16Rfs*28	ENST00000269305	NM_001126112.2	16	Cag/ag	2/11	1	2	FACETS	0.746	0.643	0.858	0.746	0.643	0.858	SUBCLONAL	1	FALSE	1	0.3	2		238	536	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348236	70348236	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002810-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	77	579	1	ENST00000374080.3:c.3300C>A	p.Cys1100Ter	p.C1100*	ENST00000374080		1100	tgC/tgA	23/45	NA	2	FACETS	0.396	0.347	0.449			1	INDETERMINATE	1	TRUE	NA	0.470299183152643	2		580	827	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181792	56181792	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002813-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	49	347	0	ENST00000399503.3:c.4016G>A	p.Gly1339Glu	p.G1339E	ENST00000399503	NM_005921.1	1339	gGa/gAa	17/20	0.159029092135276	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	2	TRUE	0	0.159029092135276	2		347	275	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577077	7577077	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs748891343	NA	P-0002813-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	38	422	0	ENST00000269305.4:c.861G>C	p.Glu287Asp	p.E287D	ENST00000269305	NM_001126112.2	287	gaG/gaC	8/11	0.12382270556358	1	FACETS	0.772	0.641	0.916	1	0.955	1	CLONAL	2	TRUE	0	0.159029092135276	1		422	285	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188261	10188261	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0002820-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	78	565	0	ENST00000256474.2:c.404T>G	p.Leu135Ter	p.L135*	ENST00000256474	NM_000551.3	135	tTa/tGa	2/3	0.177872796878326	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.23	1		565	489	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143130	24143130	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0002820-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	44	430	0	ENST00000263121.7:c.363-1G>T		p.X121_splice	ENST00000263121	NM_003073.3	121			0.247907937555575	1	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	0	0.23	1		430	330	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982762	90982769	+	frameshift_variant	Frame_Shift_Del	DEL	AACTGCGG	AACTGCGG	-	novel	NA	P-0002820-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	96	487	0	ENST00000265433.3:c.719_726del	p.Ser240CysfsTer8	p.S240Cfs*8	ENST00000265433	NM_002485.4	240	tCCGCAGTT/t	7/16	0.177872796878326	4	FACETS	0.754	0.672	0.841	0.754	0.672	0.841	SUBCLONAL	2	TRUE	2	0.23	4		487	681	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069467	30069468	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0002820-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	27	237	0	ENST00000338641.4:c.1336_1337del	p.Arg446GlufsTer48	p.R446Efs*48	ENST00000338641	NM_000268.3	444	tcAGag/tcag	12/16	0.247907937555575	1	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	0	0.23	1		237	167	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420258	88420258	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002828-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	58	556	0	ENST00000360948.2:c.2428G>C	p.Glu810Gln	p.E810Q	ENST00000360948	NM_001012338.2	810	Gaa/Caa	19/19	1	2	FACETS	0.593	0.51	0.684	0.593	0.51	0.684	SUBCLONAL	1	TRUE	1	0.361391275754354	2		556	541	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440373	52440373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002840-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	23	360	0	ENST00000460680.1:c.679C>T	p.Arg227Cys	p.R227C	ENST00000460680	NM_004656.3	227	Cgc/Tgc	9/17	1	2	FACETS	0.516	0.4	0.65	0.516	0.4	0.65	SUBCLONAL	1	TRUE	1	0.14	2		360	637	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721879	176721879	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002840-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	44	420	0	ENST00000439151.2:c.7510G>C	p.Val2504Leu	p.V2504L	ENST00000439151	NM_022455.4	2504	Gtt/Ctt	23/23	1	2	FACETS	0.892	0.746	1	0.892	0.746	1	CLONAL	1	TRUE	1	0.14	2		420	705	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578213	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs864309495	NA	P-0002840-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	95	698	0	ENST00000269305.4:c.636del	p.Arg213AspfsTer34	p.R213Dfs*34	ENST00000269305	NM_001126112.2	212	ttT/tt	6/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.14	2		698	1036	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441252	52441252	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002843-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	74	267	0	ENST00000460680.1:c.518A>G	p.Tyr173Cys	p.Y173C	ENST00000460680	NM_004656.3	173	tAt/tGt	7/17	0.200425544588583	1	FACETS	0.741	0.648	0.842	0.741	0.648	0.842	SUBCLONAL	1	TRUE	0	0.242633609466978	1		267	723	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183833	10183835	+	missense_variant	Missense_Mutation	TNP	TGC	TGC	CTA	novel	NA	P-0002843-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	88	296	0	ENST00000256474.2:c.302_304delinsCTA	p.Leu101_Pro102delinsProThr	p.L101_P102delinsPT	ENST00000256474	NM_000551.3	101	cTGCcg/cCTAcg	1/3	0.166200966962431	2	FACETS	1	0.976	1	0.696	0.618	0.779	CLONAL	1	TRUE	0	0.242633609466978	2		296	521	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86686656	86686656	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002843-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	78	466	0	ENST00000274376.6:c.3100C>G	p.Gln1034Glu	p.Q1034E	ENST00000274376	NM_002890.2	1034	Caa/Gaa	25/25	1	2	FACETS	0.918	0.807	1	0.918	0.807	1	CLONAL	1	TRUE	1	0.242633609466978	2		466	700	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029530	14029530	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002843-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	83	290	0	ENST00000311895.7:c.1741T>C	p.Tyr581His	p.Y581H	ENST00000311895	NM_005236.2	581	Tat/Cat	8/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.242633609466978	2		290	562	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0002844-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	309	456	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.558063475991695	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.558063475991695	3		456	639	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974730	21974730	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002844-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	128	343	0	ENST00000304494.5:c.97G>T	p.Glu33Ter	p.E33*	ENST00000304494	NM_000077.4	33	Gag/Tag	1/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.558063475991695	2		343	398	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0002847-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	121	470	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.19709020564757	2	FACETS	1	0.981	1	0.629	0.575	0.683	INDETERMINATE	1	TRUE	0	0.585058562681797	2		470	329	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0002847-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	167	255	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.592975314303704	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.585058562681797	2		255	268	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300105	15300105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002847-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	130	492	0	ENST00000263388.2:c.1171G>A	p.Asp391Asn	p.D391N	ENST00000263388	NM_000435.2	391	Gat/Aat	7/33	0.592975314303704	1	FACETS	0.756	0.707	0.803	1	0.99	1	SUBCLONAL	2	TRUE	0	0.585058562681797	1		492	208	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527252	187527252	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002847-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	53	412	0	ENST00000441802.2:c.10322C>G	p.Ser3441Cys	p.S3441C	ENST00000441802	NM_005245.3	3441	tCc/tGc	17/27	0.47894457115472	0	FACETS	0.411	0.356	0.469			1	SUBCLONAL	1	TRUE	0	0.585058562681797	0		412	183	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16055293	16055293	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0002847-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	133	460	0	ENST00000268712.3:c.809C>G	p.Ser270Ter	p.S270*	ENST00000268712	NM_006311.3	270	tCa/tGa	8/46	0.592975314303704	4	FACETS	1	0.93	1			1	CLONAL	1	TRUE	NA	0.585058562681797	4		460	702	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223377	2223377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002847-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	133	470	0	ENST00000398665.3:c.3488C>T	p.Pro1163Leu	p.P1163L	ENST00000398665	NM_032482.2	1163	cCc/cTc	25/28	0.592975314303704	1	FACETS	0.759	0.71	0.806	1	0.991	1	SUBCLONAL	2	TRUE	0	0.585058562681797	1		470	212	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0002851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	154	262	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.947	0.869	1	0.947	0.869	1	CLONAL	1	TRUE	1	0.48119538686987	2		262	676	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128030530	128030530	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	38	333	0	ENST00000285398.2:c.1738A>G	p.Ile580Val	p.I580V	ENST00000285398	NM_000122.1	580	Atc/Gtc	11/15	1	2	FACETS	0.226	0.186	0.271	0.226	0.186	0.271	SUBCLONAL	1	TRUE	1	0.48119538686987	2		333	698	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609902	117609902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781588795	NA	P-0002851-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	148	469	1	ENST00000368508.3:c.6797C>T	p.Thr2266Met	p.T2266M	ENST00000368508	NM_002944.2	2266	aCg/aTg	43/43	0.406559164789635	1	FACETS	0.62	0.567	0.676	0.62	0.567	0.676	SUBCLONAL	1	TRUE	0	0.48119538686987	1		470	753	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360578	118360578	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002863-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1414	197	566	0	ENST00000534358.1:c.4551A>C	p.Lys1517Asn	p.K1517N	ENST00000534358	NM_005933.3	1517	aaA/aaC	12/36	0.454740787015202	1	FACETS	0.397	0.366	0.43	0.397	0.366	0.43	SUBCLONAL	1	TRUE	0	0.470773135473565	1		566	1611	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360595	118360595	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002863-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1455	127	513	0	ENST00000534358.1:c.4568A>C	p.Lys1523Thr	p.K1523T	ENST00000534358	NM_005933.3	1523	aAa/aCa	12/36	0.454740787015202	1	FACETS	0.261	0.235	0.288	0.261	0.235	0.288	SUBCLONAL	1	TRUE	0	0.470773135473565	1		513	1582	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0002878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	56	322	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.229150133853223	2		322	372	SUCCESS
APC	324	MSKCC	GRCh37	5	112175513	112175513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	78	258	0	ENST00000257430.4:c.4222G>T	p.Glu1408Ter	p.E1408*	ENST00000257430	NM_000038.5	1408	Gaa/Taa	16/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.229150133853223	2		258	476	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387092	31387092	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764722946	NA	P-0002878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	253	364	2	ENST00000328111.2:c.1717C>T	p.Arg573Trp	p.R573W	ENST00000328111	NM_006892.3	573	Cgg/Tgg	16/23	0.206804090149869	4	FACETS	0.952	0.892	1	0.952	0.892	1	CLONAL	3	TRUE	1	0.229150133853223	4		366	950	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0002878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	130	354	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.201302054600207	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.229150133853223	1		354	685	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247312	153247312	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	80	312	0	ENST00000281708.4:c.1490T>C	p.Leu497Ser	p.L497S	ENST00000281708	NM_033632.3	497	tTg/tCg	10/12	0.201302054600207	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.229150133853223	1		312	418	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971195	13971195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777866452	NA	P-0002878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	126	278	0	ENST00000405192.2:c.734C>T	p.Ala245Val	p.A245V	ENST00000405192	NM_001163147.1	245	gCg/gTg	8/12	0.229150133853223	3	FACETS	0.915	0.83	1	0.915	0.83	1	CLONAL	2	TRUE	1	0.229150133853223	3		278	670	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873347	151873347	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	59	332	0	ENST00000262189.6:c.9191A>G	p.Gln3064Arg	p.Q3064R	ENST00000262189	NM_170606.2	3064	cAa/cGa	38/59	0.229150133853223	3	FACETS	0.92	0.791	1	0.46	0.395	0.53	CLONAL	1	TRUE	1	0.229150133853223	3		332	624	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141493	11141493	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	60	355	0	ENST00000358026.2:c.3470G>A	p.Arg1157Gln	p.R1157Q	ENST00000358026	NM_001128849.1	1157	cGg/cAg	25/36	1	2	FACETS	0.694	0.596	0.8	0.694	0.596	0.8	SUBCLONAL	1	TRUE	1	0.229150133853223	2		355	755	SUCCESS
APC	324	MSKCC	GRCh37	5	112174458	112174458	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002878-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	19	284	0	ENST00000257430.4:c.3167del	p.Ile1056LysfsTer5	p.I1056Kfs*5	ENST00000257430	NM_000038.5	1056	aTa/aa	16/16	1	2	FACETS	0.452	0.342	0.581	0.452	0.342	0.581	SUBCLONAL	1	TRUE	1	0.229150133853223	2		284	367	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0002890-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	139	406	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.286201308927823	7	FACETS	1	0.984	1	0.233	0.211	0.256	CLONAL	1	TRUE	1	0.286201308927823	7		406	1191	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0002890-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	507	335	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.286201308927823	7	FACETS	0.973	0.936	1	0.973	0.936	1	CLONAL	6	TRUE	1	0.286201308927823	7		335	1041	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502650	149502650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368867827	NA	P-0002890-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	47	188	0	ENST00000261799.4:c.2138C>T	p.Ala713Val	p.A713V	ENST00000261799	NM_002609.3	713	gCg/gTg	15/23	0.286201308927823	3	FACETS	0.642	0.541	0.753	0.321	0.27	0.377	SUBCLONAL	1	TRUE	1	0.286201308927823	3		188	585	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575671	48575671	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002890-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	116	275	0	ENST00000342988.3:c.431C>A	p.Ser144Ter	p.S144*	ENST00000342988	NM_005359.5	144	tCa/tAa	4/12	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.286201308927823	2		275	729	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279325	18279325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002890-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	135	198	0	ENST00000222254.8:c.1777G>A	p.Glu593Lys	p.E593K	ENST00000222254	NM_005027.3	593	Gag/Aag	14/16	0.249910402468036	4	FACETS	0.945	0.861	1			1	CLONAL	2	TRUE	NA	0.286201308927823	4		198	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577089	7577090	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0002890-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	143	366	1	ENST00000269305.4:c.848_849del	p.Arg283HisfsTer22	p.R283Hfs*22	ENST00000269305	NM_001126112.2	283	cGC/c	8/11	NA	2	FACETS	0.823	0.753	0.896			1	INDETERMINATE	2	TRUE	NA	0.286201308927823	2		367	607	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591857	48591857	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002898-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	41	545	0	ENST00000342988.3:c.1020G>C	p.Lys340Asn	p.K340N	ENST00000342988	NM_005359.5	340	aaG/aaC	9/12	1	2	FACETS	0.701	0.585	0.829	0.701	0.585	0.829	SUBCLONAL	1	FALSE	1	0.321475963559253	2		545	364	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0002898-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	66	488	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	0.0996015699972819	4	FACETS	1	0.939	1	0.569	0.495	0.649	INDETERMINATE	1	FALSE	2	0.321475963559253	4		488	477	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969468	44969471	+	frameshift_variant	Frame_Shift_Del	DEL	ATGC	ATGC	-	novel	NA	P-0002898-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	52	279	0	ENST00000377967.4:c.4151_4154del	p.Met1384LysfsTer8	p.M1384Kfs*8	ENST00000377967	NM_021140.2	1384	ATGCaa/aa	28/29	1	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	FALSE	0	0.321475963559253	1		279	235	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0002909-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	10	512	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.13804354514015	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		512	401	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0002909-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	15	409	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		409	325	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188198	10188198	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002941-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	81	644	0	ENST00000256474.2:c.341G>C	p.Gly114Ala	p.G114A	ENST00000256474	NM_000551.3	114	gGt/gCt	2/3	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.24	2		644	637	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436619	52436619	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002941-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	61	655	0	ENST00000460680.1:c.2055del	p.Gly686AlafsTer6	p.G686Afs*6	ENST00000460680	NM_004656.3	685	gaA/ga	16/17	1	2	FACETS	0.909	0.785	1	0.909	0.785	1	CLONAL	1	TRUE	1	0.24	2		655	559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0002944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	101	371	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.391021893134089	1	FACETS	0.964	0.867	1	0.964	0.867	1	CLONAL	1	TRUE	0	0.410405188407222	1		371	406	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115045	3115045	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	26	504	0	ENST00000078429.4:c.580T>C	p.Phe194Leu	p.F194L	ENST00000078429	NM_002067.2	194	Ttc/Ctc	4/7	0.410405188407222	1	FACETS	0.414	0.329	0.511	0.414	0.329	0.511	SUBCLONAL	1	TRUE	0	0.410405188407222	1		504	243	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0002948-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	14	228	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.256	0.184	0.344	0.256	0.184	0.344	SUBCLONAL	1	FALSE	1	0.3	2		228	364	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803526	43803526	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002948-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	42	440	0	ENST00000372470.3:c.7T>C	p.Ser3Pro	p.S3P	ENST00000372470	NM_005373.2	3	Tcc/Ccc	1/12	1	2	FACETS	0.511	0.426	0.605	0.511	0.426	0.605	SUBCLONAL	1	FALSE	1	0.3	2		440	548	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0002951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	272	693	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.378926752897044	2	FACETS	0.881	0.832	0.931	0.881	0.832	0.931	CLONAL	2	TRUE	0	0.441598798438426	2		693	699	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0002951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	116	326	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	0.367585798384595	3	FACETS	1	0.985	1	0.749	0.68	0.821	CLONAL	1	TRUE	1	0.441598798438426	3		326	428	SUCCESS
APC	324	MSKCC	GRCh37	5	112175235	112175235	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	59	401	0	ENST00000257430.4:c.3944C>A	p.Ser1315Ter	p.S1315*	ENST00000257430	NM_000038.5	1315	tCa/tAa	16/16	0.367585798384595	3	FACETS	0.643	0.554	0.74	0.322	0.277	0.37	SUBCLONAL	1	TRUE	1	0.441598798438426	3		401	507	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78426167	78426167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	57	288	0	ENST00000370768.2:c.1358C>T	p.Pro453Leu	p.P453L	ENST00000370768	NM_003902.3	453	cCt/cTt	15/20	1	2	FACETS	0.644	0.554	0.741	0.644	0.554	0.741	SUBCLONAL	1	TRUE	1	0.441598798438426	2		288	401	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175996783	175996783	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs766620891	NA	P-0002951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	130	605	0	ENST00000367669.3:c.1654A>G	p.Ile552Val	p.I552V	ENST00000367669	NM_022457.5	552	Att/Gtt	15/20	0.364769251719054	3	FACETS	0.882	0.8	0.968	0.441	0.4	0.484	CLONAL	1	TRUE	1	0.441598798438426	3		605	815	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332070	81332070	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	26	422	0	ENST00000222390.5:c.2014G>A	p.Asp672Asn	p.D672N	ENST00000222390	NM_000601.4	672	Gat/Aat	18/18	0.367585798384595	3	FACETS	0.332	0.262	0.412	0.166	0.131	0.206	SUBCLONAL	1	TRUE	1	0.441598798438426	3		422	433	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0002959-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	33	262	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.772	0.632	0.929	0.772	0.632	0.929	CLONAL	1	TRUE	1	0.326097231398672	2		262	262	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061249	38061249	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002959-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	37	698	0	ENST00000250448.2:c.740A>G	p.His247Arg	p.H247R	ENST00000250448	NM_004496.3	247	cAc/cGc	2/2	0.315259362644896	3	FACETS	1	0.88	1	0.539	0.447	0.64	CLONAL	1	TRUE	1	0.326097231398672	3		698	245	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265680	10265680	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002959-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	17	768	0	ENST00000340748.4:c.1497del	p.Phe499LeufsTer3	p.F499Lfs*3	ENST00000340748		499	ttT/tt	19/40	1	2	FACETS	0.385	0.287	0.501	0.385	0.287	0.501	SUBCLONAL	1	TRUE	1	0.326097231398672	2		768	271	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335035	81335035	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002962-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	148	349	0	ENST00000222390.5:c.1792G>C	p.Asp598His	p.D598H	ENST00000222390	NM_000601.4	598	Gat/Cat	16/18	0.281008434639395	3	FACETS	1	0.982	1	0.642	0.586	0.7	CLONAL	1	TRUE	1	0.305993889902755	3		349	869	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601230	28601230	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002962-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	144	393	0	ENST00000241453.7:c.2202T>A	p.Asn734Lys	p.N734K	ENST00000241453	NM_004119.2	734	aaT/aaA	17/24	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.305993889902755	2		393	904	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519966	NA	P-0002962-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	208	459	1	ENST00000347630.2:c.397T>A	p.Phe133Ile	p.F133I	ENST00000347630	NM_001007230.1	133	Ttc/Atc	6/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.305993889902755	2		460	996	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519912	NA	P-0002962-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	262	288	0	ENST00000374080.3:c.3670C>G	p.Leu1224Val	p.L1224V	ENST00000374080		1224	Ctc/Gtc	26/45	1	1	FACETS	1	0.991	1	1	0.996	1	CLONAL	2	TRUE	0	0.305993889902755	1		288	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0002969-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	160	255	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.407847429336763	2	FACETS	0.995	0.924	1	0.995	0.924	1	CLONAL	2	TRUE	0	0.409139158265925	2		255	393	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155653	56155653	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200234617	NA	P-0002969-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	44	207	0	ENST00000399503.3:c.745C>T	p.Arg249Cys	p.R249C	ENST00000399503	NM_005921.1	249	Cgc/Tgc	3/20	0.407847429336763	2	FACETS	0.494	0.415	0.582	0.247	0.207	0.291	SUBCLONAL	1	TRUE	0	0.409139158265925	2		207	435	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255917	16255917	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002969-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	30	185	0	ENST00000375759.3:c.3182C>G	p.Ala1061Gly	p.A1061G	ENST00000375759	NM_015001.2	1061	gCc/gGc	11/15	0.198591883165564	1	FACETS	0.309	0.248	0.377	0.309	0.248	0.377	INDETERMINATE	1	TRUE	0	0.409139158265925	1		185	378	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812197	43812197	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002969-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	72	391	0	ENST00000372470.3:c.1062C>G	p.Phe354Leu	p.F354L	ENST00000372470	NM_005373.2	354	ttC/ttG	7/12	0.198591883165564	1	FACETS	0.583	0.511	0.661	0.583	0.511	0.661	INDETERMINATE	1	TRUE	0	0.409139158265925	1		391	480	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176118155	176118155	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002969-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	27	314	0	ENST00000367669.3:c.818G>T	p.Arg273Ile	p.R273I	ENST00000367669	NM_022457.5	273	aGa/aTa	6/20	1	2	FACETS	0.312	0.248	0.386	0.312	0.248	0.386	SUBCLONAL	1	TRUE	1	0.409139158265925	2		314	423	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667414	241667414	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002969-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	54	334	0	ENST00000366560.3:c.1036G>T	p.Gly346Cys	p.G346C	ENST00000366560	NM_000143.3	346	Ggt/Tgt	7/10	0.409139158265925	3	FACETS	0.46	0.392	0.535			1	SUBCLONAL	1	TRUE	NA	0.409139158265925	3		334	691	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662185	227662185	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs768932529	NA	P-0002969-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	201	307	0	ENST00000305123.5:c.1270G>T	p.Gly424Cys	p.G424C	ENST00000305123	NM_005544.2	424	Ggt/Tgt	1/2	0.355299172181363	3	FACETS	0.99	0.923	1	0.99	0.923	1	CLONAL	2	TRUE	1	0.409139158265925	3		307	598	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794882	242794882	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002969-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	91	306	0	ENST00000334409.5:c.327C>A	p.Ser109Arg	p.S109R	ENST00000334409	NM_005018.2	109	agC/agA	2/5	0.355299172181363	3	FACETS	1	0.936	1	0.536	0.477	0.598	CLONAL	1	TRUE	1	0.409139158265925	3		306	500	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231213	142231213	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002969-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	111	333	0	ENST00000350721.4:c.4741G>T	p.Val1581Leu	p.V1581L	ENST00000350721	NM_001184.3	1581	Gtg/Ttg	27/47	0.198591883165564	1	FACETS	0.867	0.783	0.955	0.867	0.783	0.955	INDETERMINATE	1	TRUE	0	0.409139158265925	1		333	498	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531001	187531001	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002969-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	111	292	0	ENST00000441802.2:c.10022C>A	p.Thr3341Lys	p.T3341K	ENST00000441802	NM_005245.3	3341	aCg/aAg	15/27	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.409139158265925	2		292	527	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056641	26056641	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774100132	NA	P-0002969-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	61	71	0	ENST00000343677.2:c.16C>T	p.Pro6Ser	p.P6S	ENST00000343677	NM_005319.3	6	Cct/Tct	1/1	0.407847429336763	2	FACETS	0.887	0.782	0.996	0.887	0.782	0.996	CLONAL	2	TRUE	0	0.409139158265925	2		71	168	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671021	30671021	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002969-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	86	275	0	ENST00000376406.3:c.5725G>C	p.Val1909Leu	p.V1909L	ENST00000376406	NM_014641.2	1909	Gtg/Ctg	12/15	0.407847429336763	2	FACETS	0.789	0.699	0.884	0.394	0.349	0.442	SUBCLONAL	1	TRUE	0	0.409139158265925	2		275	533	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170323	32170323	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002969-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	130	186	0	ENST00000375023.3:c.3285C>G	p.His1095Gln	p.H1095Q	ENST00000375023	NM_004557.3	1095	caC/caG	21/30	0.407847429336763	2	FACETS	0.948	0.872	1	0.948	0.872	1	CLONAL	2	TRUE	0	0.409139158265925	2		186	335	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467844	50467844	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs896917396	NA	P-0002969-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	136	205	0	ENST00000331340.3:c.1079G>T	p.Arg360Leu	p.R360L	ENST00000331340	NM_006060.4	360	cGc/cTc	8/8	0.238631897348438	2	FACETS	0.894	0.822	0.967	0.894	0.822	0.967	INDETERMINATE	2	TRUE	0	0.409139158265925	2		205	372	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006645	62006645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002969-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	161	336	0	ENST00000392795.3:c.634G>A	p.Val212Met	p.V212M	ENST00000392795	NM_001039933.1	212	Gtg/Atg	6/6	0.409139158265925	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.409139158265925	1		336	447	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221947	1221947	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0002969-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	142	307	0	ENST00000326873.7:c.863-1G>T		p.X288_splice	ENST00000326873	NM_000455.4	288			0.409139158265925	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.409139158265925	1		307	398	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600447	10600447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002969-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	170	357	0	ENST00000171111.5:c.1408C>T	p.Arg470Cys	p.R470C	ENST00000171111	NM_203500.1	470	Cgt/Tgt	4/6	0.409139158265925	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.409139158265925	1		357	494	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141519	11141519	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002969-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	171	305	1	ENST00000358026.2:c.3496C>T	p.Gln1166Ter	p.Q1166*	ENST00000358026	NM_001128849.1	1166	Cag/Tag	25/36	0.409139158265925	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.409139158265925	1		306	479	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938646	76938646	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs797044563	NA	P-0002969-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	109	214	1	ENST00000373344.5:c.2102G>T	p.Arg701Leu	p.R701L	ENST00000373344	NM_000489.3	701	cGt/cTt	9/35	0.15768320874966	0	FACETS	1	0.923	1			1	INDETERMINATE	1	TRUE	NA	0.409139158265925	0		215	310	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617162	100617162	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002969-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	158	210	0	ENST00000308731.7:c.587A>T	p.Gln196Leu	p.Q196L	ENST00000308731	NM_000061.2	196	cAg/cTg	7/19	0.15768320874966	0	FACETS	0.658	0.612	0.704			1	INDETERMINATE	2	TRUE	NA	0.409139158265925	0		210	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0002970-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	168	298	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.201650518530013	2	FACETS	1	0.988	1	0.727	0.669	0.788	CLONAL	1	TRUE	0	0.283464689813667	2		298	815	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0002970-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	133	262	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.254810773221232	3	FACETS	0.843	0.763	0.927	0.421	0.381	0.464	CLONAL	1	TRUE	1	0.283464689813667	3		262	1271	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713559	30713559	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0002970-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	200	315	0	ENST00000295754.5:c.884C>G	p.Ser295Ter	p.S295*	ENST00000295754	NM_003242.5	295	tCa/tGa	4/7	0.208015789666732	2	FACETS	0.935	0.868	1	0.935	0.868	1	CLONAL	2	TRUE	0	0.283464689813667	2		315	755	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719737	61719737	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002970-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1239	311	634	0	ENST00000401558.2:c.1531G>A	p.Glu511Lys	p.E511K	ENST00000401558	NM_003400.3	511	Gag/Aag	14/25	0.283464689813667	3	FACETS	0.808	0.76	0.858	0.808	0.76	0.858	CLONAL	2	TRUE	1	0.283464689813667	3		634	1550	SUCCESS
FIP1L1	81608	MSKCC	GRCh37	4	54280808	54280808	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002970-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	92	455	0	ENST00000358575.5:c.797C>G	p.Thr266Arg	p.T266R	ENST00000358575	NM_001134937.1	266	aCa/aGa	10/18	0.283464689813667	2	FACETS	0.557	0.493	0.625	0.278	0.246	0.313	SUBCLONAL	1	TRUE	0	0.283464689813667	2		455	1166	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540343	187540343	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0002970-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	326	398	0	ENST00000441802.2:c.7397C>G	p.Ser2466Ter	p.S2466*	ENST00000441802	NM_005245.3	2466	tCa/tGa	10/27	0.283464689813667	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.283464689813667	2		398	1095	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176671232	176671232	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002970-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	327	538	0	ENST00000439151.2:c.4339G>T	p.Glu1447Ter	p.E1447*	ENST00000439151	NM_022455.4	1447	Gaa/Taa	9/23	0.283464689813667	2	FACETS	0.882	0.832	0.933	0.882	0.832	0.933	CLONAL	2	TRUE	0	0.283464689813667	2		538	1308	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38064170	38064170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1406059545	NA	P-0002970-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	152	458	0	ENST00000250448.2:c.8G>A	p.Gly3Glu	p.G3E	ENST00000250448	NM_004496.3	3	gGa/gAa	1/2	0.283464689813667	3	FACETS	0.992	0.905	1	0.496	0.452	0.542	CLONAL	1	TRUE	1	0.283464689813667	3		458	1234	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820792	3820792	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002970-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	91	422	0	ENST00000262367.5:c.2659C>G	p.Gln887Glu	p.Q887E	ENST00000262367	NM_004380.2	887	Cag/Gag	14/31	0.283464689813667	3	FACETS	0.69	0.611	0.774	0.345	0.305	0.387	SUBCLONAL	1	TRUE	1	0.283464689813667	3		422	1063	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820954	3820954	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002970-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	56	207	0	ENST00000262367.5:c.2497C>G	p.Leu833Val	p.L833V	ENST00000262367	NM_004380.2	833	Ctc/Gtc	14/31	0.283464689813667	3	FACETS	0.787	0.674	0.911	0.394	0.337	0.456	CLONAL	1	TRUE	1	0.283464689813667	3		207	573	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888799	76888799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002970-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	331	350	2	ENST00000373344.5:c.5030G>A	p.Gly1677Asp	p.G1677D	ENST00000373344	NM_000489.3	1677	gGt/gAt	19/35	0.283464689813667	2	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.283464689813667	2		352	969	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257536	16257536	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1285412482	NA	P-0002971-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	39	405	0	ENST00000375759.3:c.4801G>A	p.Asp1601Asn	p.D1601N	ENST00000375759	NM_015001.2	1601	Gac/Aac	11/15	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		405	704	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257536	16257536	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1285412482	NA	P-0002971-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	112	405	0	ENST00000375759.3:c.4801G>A	p.Asp1601Asn	p.D1601N	ENST00000375759	NM_015001.2	1601	Gac/Aac	11/15	1	2	FACETS	0.99	0.896	1	0.99	0.896	1	CLONAL	1	TRUE	1	0.470216808894073	2		405	481	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255375	16255375	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002971-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	161	471	0	ENST00000375759.3:c.2640G>C	p.Leu880Phe	p.L880F	ENST00000375759	NM_015001.2	880	ttG/ttC	11/15	1	2	FACETS	0.861	0.791	0.935	0.861	0.791	0.935	CLONAL	1	TRUE	1	0.470216808894073	2		471	795	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0002994-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	408	383	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.547750203632909	2	FACETS	0.882	0.854	0.909	1	0.996	1	CLONAL	3	FALSE	0	0.547750203632909	2		385	563	SUCCESS
APC	324	MSKCC	GRCh37	5	112175175	112175175	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002994-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	40	237	0	ENST00000257430.4:c.3885del	p.Ala1296GlnfsTer9	p.A1296Qfs*9	ENST00000257430	NM_000038.5	1295	gAa/ga	16/16	0.33891543564085	2	FACETS	0.596	0.499	0.703	0.298	0.249	0.352	SUBCLONAL	1	FALSE	0	0.547750203632909	2		237	245	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397532	116397532	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs773826297	NA	P-0002994-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	275	564	1	ENST00000397752.3:c.1904A>G	p.Asn635Ser	p.N635S	ENST00000397752	NM_000245.2	635	aAt/aGt	7/21	0.547750203632909	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	FALSE	1	0.547750203632909	4		565	503	SUCCESS
APC	324	MSKCC	GRCh37	5	112174091	112174094	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1131691143	NA	P-0002994-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	143	435	4	ENST00000257430.4:c.2802_2805del	p.Tyr935IlefsTer19	p.Y935Ifs*19	ENST00000257430	NM_000038.5	934	ACTTac/ac	16/16	0.33891543564085	2	FACETS	0.853	0.792	0.915	0.853	0.792	0.915	CLONAL	2	FALSE	0	0.547750203632909	2		439	306	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0002995-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	656	703	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.63270189999759	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.627745027657704	3		704	810	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117311	115117311	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002995-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	389	491	0	ENST00000257566.3:c.863del	p.Lys288ArgfsTer2	p.K288Rfs*2	ENST00000257566	NM_016569.3	288	aAg/ag	4/8	0.63270189999759	4	FACETS	1	0.987	1			1	CLONAL	2	TRUE	NA	0.627745027657704	4		491	929	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855965	68856011	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCCCCATACCAGAACCTCGAACTATATTCTTCTGTGAGAGGAATC	CGCCCCCATACCAGAACCTCGAACTATATTCTTCTGTGAGAGGAATC	-	novel	NA	P-0002995-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	506	677	0	ENST00000261769.5:c.1774_1820del	p.Ala592LysfsTer9	p.A592Kfs*9	ENST00000261769	NM_004360.3	591	aaCGCCCCCATACCAGAACCTCGAACTATATTCTTCTGTGAGAGGAATCca/aaca	12/16	0.338688056031861	3	FACETS	1	0.995	1			1	INDETERMINATE	3	TRUE	NA	0.627745027657704	3		677	651	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0002996-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	53	358	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.12	2		358	813	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199935	128199935	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002996-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	24	368	2	ENST00000341105.2:c.1370C>A	p.Thr457Lys	p.T457K	ENST00000341105	NM_032638.4	457	aCg/aAg	6/6	1	2	FACETS	0.907	0.71	1	0.907	0.71	1	CLONAL	1	TRUE	1	0.12	2		370	441	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432074	121432074	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002996-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	35	525	1	ENST00000257555.6:c.821A>T	p.Glu274Val	p.E274V	ENST00000257555		274	gAa/gTa	4/10	1	2	FACETS	0.906	0.741	1	0.906	0.741	1	CLONAL	1	TRUE	1	0.12	2		526	644	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546688	9546688	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002996-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	37	493	0	ENST00000353224.5:c.1334C>A	p.Pro445His	p.P445H	ENST00000353224	NM_177990.2	445	cCc/cAc	5/10	1	2	FACETS	0.937	0.771	1	0.937	0.771	1	CLONAL	1	TRUE	1	0.12	2		493	658	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0003016-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	33	213	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	1	2	FACETS	0.803	0.653	0.974	0.803	0.653	0.974	CLONAL	1	TRUE	1	0.14	2		213	587	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211146	55211146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003016-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	39	396	0	ENST00000275493.2:c.389C>T	p.Thr130Ile	p.T130I	ENST00000275493	NM_005228.3	130	aCc/aTc	3/28	1	2	FACETS	0.981	0.812	1	0.981	0.812	1	CLONAL	1	TRUE	1	0.14	2		396	568	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444884	49444884	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123739	NA	P-0003016-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	22	236	0	ENST00000301067.7:c.2582C>T	p.Ser861Phe	p.S861F	ENST00000301067	NM_003482.3	861	tCc/tTc	10/54	1	2	FACETS	0.852	0.66	1	0.852	0.66	1	CLONAL	1	TRUE	1	0.14	2		236	369	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918582	44918582	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003016-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	40	318	0	ENST00000377967.4:c.1065G>A	p.Trp355Ter	p.W355*	ENST00000377967	NM_021140.2	355	tgG/tgA	12/29	1	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.14	1		318	407	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968197	134968197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780597750	NA	P-0003021-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	30	603	0	ENST00000398015.3:c.2710G>A	p.Asp904Asn	p.D904N	ENST00000398015	NM_004441.4	904	Gac/Aac	15/16	0.309805736433715	4	FACETS	1	0.847	1	0.526	0.426	0.639	CLONAL	1	TRUE	2	0.309805736433715	4		603	241	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246445	105246445	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003021-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	33	569	0	ENST00000349310.3:c.155T>A	p.Leu52His	p.L52H	ENST00000349310	NM_001014432.1	52	cTc/cAc	4/15	0.309805736433715	3	FACETS	1	0.894	1	0.567	0.465	0.68	CLONAL	1	TRUE	1	0.309805736433715	3		569	217	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100196	27100196	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0003021-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	62	343	0	ENST00000324856.7:c.3992del	p.Gln1331ArgfsTer150	p.Q1331Rfs*150	ENST00000324856	NM_006015.4	1331	cAg/cg	16/20	0.309805736433715	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.309805736433715	3		343	192	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599333	55599333	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913682	NA	P-0003022-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	60	283	0	ENST00000288135.5:c.2459A>G	p.Asp820Gly	p.D820G	ENST00000288135	NM_000222.2	820	gAt/gGt	17/21	0.281773601767414	3	FACETS	0.996	0.868	1	0.996	0.868	1	CLONAL	2	FALSE	1	0.281773601767414	3		283	244	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499120	149499120	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003025-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	125	368	0	ENST00000261799.4:c.2708del	p.Pro903LeufsTer7	p.P903Lfs*7	ENST00000261799	NM_002609.3	903	cCt/ct	20/23	0.272138771875184	4	FACETS	0.87	0.793	0.949	0.87	0.793	0.949	INDETERMINATE	2	FALSE	2	0.469341321829328	4		368	450	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518506	204518506	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1393081884	NA	P-0003033-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	490	269	0	ENST00000367182.3:c.1169A>G	p.Asn390Ser	p.N390S	ENST00000367182	NM_001278516.1	390	aAc/aGc	11/11	0.784301024096685	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.784301024096685	3		269	857	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402475	139402475	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003033-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	233	295	0	ENST00000277541.6:c.3442G>T	p.Glu1148Ter	p.E1148*	ENST00000277541	NM_017617.3	1148	Gag/Tag	21/34	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.784301024096685	2		295	562	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579381	7579381	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003033-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	179	208	0	ENST00000269305.4:c.306del	p.Tyr103ThrfsTer20	p.Y103Tfs*20	ENST00000269305	NM_001126112.2	102	acC/ac	4/11	0.724487816400704	1	FACETS	0.907	0.854	0.958	0.907	0.854	0.958	CLONAL	1	TRUE	0	0.784301024096685	1		208	306	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570341	95570341	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	203	223	0	ENST00000393063.1:c.3392A>T	p.Asn1131Ile	p.N1131I	ENST00000393063	NM_030621.3	1131	aAt/aTt	22/28	NA	2	FACETS	0.99	0.925	1			1	INDETERMINATE	1	TRUE	NA	0.745479029973011	2		223	550	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922880	44922884	+	frameshift_variant	Frame_Shift_Del	DEL	ACATC	ACATC	T	novel	NA	P-0003099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	39	287	0	ENST00000377967.4:c.1741_1745delinsT	p.Thr581Ter	p.T581*	ENST00000377967	NM_021140.2	581	ACATCa/Ta	16/29	1	1	FACETS	0.122	0.101	0.146	0.122	0.101	0.146	SUBCLONAL	1	TRUE	0	0.745479029973011	1		287	538	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627753	187627757	+	frameshift_variant	Frame_Shift_Del	DEL	AGCCA	AGCCA	-	novel	NA	P-0003099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	362	502	0	ENST00000441802.2:c.3225_3229del	p.Gly1076TrpfsTer9	p.G1076Wfs*9	ENST00000441802	NM_005245.3	1075	gaTGGCTct/gact	2/27	NA	2	FACETS	0.99	0.941	1			1	INDETERMINATE	1	TRUE	NA	0.745479029973011	2		502	981	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952147	178952147	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	70	188	0	ENST00000263967.3:c.3202A>T	p.Asn1068Tyr	p.N1068Y	ENST00000263967	NM_006218.2	1068	Aac/Tac	21/21	0.555875992124481	4	FACETS	0.63	0.549	0.717	0.21	0.183	0.239	SUBCLONAL	1	TRUE	1	0.555875992124481	4		188	622	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741760	145741760	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759352592	NA	P-0003103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	106	254	0	ENST00000428558.2:c.743G>A	p.Arg248His	p.R248H	ENST00000428558	NM_004260.3	248	cGt/cAt	5/22	0.555875992124481	3	FACETS	1	0.961	1	0.565	0.51	0.623	CLONAL	1	TRUE	1	0.555875992124481	3		254	431	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41554467	41554467	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1489896703	NA	P-0003103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	123	320	0	ENST00000263253.7:c.3553A>G	p.Ile1185Val	p.I1185V	ENST00000263253	NM_001429.3	1185	Ata/Gta	19/31	1	2	FACETS	0.814	0.739	0.892	0.814	0.739	0.892	CLONAL	1	TRUE	1	0.555875992124481	2		320	544	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0003116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	193	335	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.228020356117903	3	FACETS	1	0.989	1	0.689	0.638	0.742	CLONAL	1	TRUE	1	0.366567822589401	3		335	904	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912660	NA	P-0003116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	207	297	0	ENST00000269305.4:c.839G>T	p.Arg280Ile	p.R280I	ENST00000269305	NM_001126112.2	280	aGa/aTa	8/11	0.297702101506482	2	FACETS	0.804	0.749	0.861	0.804	0.749	0.861	CLONAL	2	TRUE	0	0.366567822589401	2		297	702	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123048	5123048	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	190	246	0	ENST00000381652.3:c.3104C>T	p.Ser1035Leu	p.S1035L	ENST00000381652	NM_004972.3	1035	tCa/tTa	23/25	0.366567822589401	1	FACETS	0.989	0.915	1	0.989	0.915	1	CLONAL	1	TRUE	0	0.366567822589401	1		246	856	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213918	66213918	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	125	304	0	ENST00000273854.3:c.2512G>A	p.Gly838Arg	p.G838R	ENST00000273854	NM_004439.5	838	Gga/Aga	15/18	1	2	FACETS	0.888	0.804	0.976	0.888	0.804	0.976	CLONAL	1	TRUE	1	0.366567822589401	2		304	768	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268975	55268975	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	150	243	0	ENST00000275493.2:c.3041A>T	p.Asp1014Val	p.D1014V	ENST00000275493	NM_005228.3	1014	gAc/gTc	25/28	0.228020356117903	3	FACETS	1	0.984	1	0.655	0.6	0.713	CLONAL	1	TRUE	1	0.366567822589401	3		243	739	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878947	117878947	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	183	457	0	ENST00000297338.2:c.22C>G	p.Leu8Val	p.L8V	ENST00000297338	NM_006265.2	8	Ctc/Gtc	2/14	1	2	FACETS	0.751	0.691	0.813	0.751	0.691	0.813	SUBCLONAL	1	TRUE	1	0.366567822589401	2		457	1330	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003746	45003746	+	start_lost	Translation_Start_Site	SNP	T	T	C	rs1057519879	NA	P-0003116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	94	253	0	ENST00000558401.1:c.2T>C	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	aTg/aCg	1/4	0.366567822589401	1	FACETS	0.709	0.632	0.791	0.709	0.632	0.791	SUBCLONAL	1	TRUE	0	0.366567822589401	1		253	591	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129662	2129662	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1163066622	NA	P-0003116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	67	236	0	ENST00000219476.3:c.3389C>G	p.Ser1130Cys	p.S1130C	ENST00000219476	NM_000548.3	1130	tCc/tGc	29/42	0.267517885020573	3	FACETS	0.865	0.753	0.986	0.433	0.376	0.493	CLONAL	1	TRUE	1	0.366567822589401	3		236	500	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646794	23646794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	163	370	0	ENST00000261584.4:c.1073C>T	p.Pro358Leu	p.P358L	ENST00000261584	NM_024675.3	358	cCc/cTc	4/13	0.267517885020573	3	FACETS	0.88	0.806	0.958	0.44	0.403	0.479	CLONAL	1	TRUE	1	0.366567822589401	3		370	1196	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325416	1325416	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	84	298	0	ENST00000400841.2:c.259G>A	p.Asp87Asn	p.D87N	ENST00000400841		87	Gac/Aac	3/6	NA	2	FACETS	0.588	0.519	0.663			1	INDETERMINATE	1	TRUE	NA	0.366567822589401	2		298	779	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424260	47424260	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	35	353	1	ENST00000377045.4:c.265G>T	p.Glu89Ter	p.E89*	ENST00000377045	NM_001654.4	89	Gag/Tag	4/16	0.366567822589401	1	FACETS	0.228	0.186	0.276	0.228	0.186	0.276	SUBCLONAL	1	TRUE	0	0.366567822589401	1		354	683	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920216	76920216	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	138	517	0	ENST00000373344.5:c.3861T>A	p.Asp1287Glu	p.D1287E	ENST00000373344	NM_000489.3	1287	gaT/gaA	11/35	1	2	FACETS	0.616	0.559	0.676	0.616	0.559	0.676	SUBCLONAL	1	TRUE	1	0.366567822589401	2		517	1223	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0003116-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	73	335	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.18	2		335	778	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912660	NA	P-0003116-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	101	297	0	ENST00000269305.4:c.839G>T	p.Arg280Ile	p.R280I	ENST00000269305	NM_001126112.2	280	aGa/aTa	8/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.18	2		297	993	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123048	5123048	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003116-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	57	246	0	ENST00000381652.3:c.3104C>T	p.Ser1035Leu	p.S1035L	ENST00000381652	NM_004972.3	1035	tCa/tTa	23/25	1	2	FACETS	0.803	0.687	0.929	0.803	0.687	0.929	CLONAL	1	TRUE	1	0.18	2		246	789	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268975	55268975	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003116-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	53	243	0	ENST00000275493.2:c.3041A>T	p.Asp1014Val	p.D1014V	ENST00000275493	NM_005228.3	1014	gAc/gTc	25/28	1	2	FACETS	0.721	0.613	0.84	0.721	0.613	0.84	SUBCLONAL	1	TRUE	1	0.18	2		243	817	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920216	76920216	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003116-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1173	112	517	0	ENST00000373344.5:c.3861T>A	p.Asp1287Glu	p.D1287E	ENST00000373344	NM_000489.3	1287	gaT/gaA	11/35	1	2	FACETS	0.968	0.868	1	0.968	0.868	1	CLONAL	1	TRUE	1	0.18	2		517	1285	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	169	306	1	ENST00000397062.3:c.92G>A	p.Gly31Glu	p.G31E	ENST00000397062	NM_006164.4	31	gGa/gAa	2/5	1	2	FACETS	0.9	0.831	0.972	0.9	0.831	0.972	CLONAL	1	TRUE	1	0.58585527790493	2		307	641	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727453	66727453	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397516790	NA	P-0003147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	356	331	0	ENST00000307102.5:c.169A>G	p.Lys57Glu	p.K57E	ENST00000307102	NM_002755.3	57	Aag/Gag	2/11	0.227096909100423	4	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.58585527790493	4		331	787	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382143	152382143	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	169	290	0	ENST00000206249.3:c.1253T>A	p.Val418Glu	p.V418E	ENST00000206249	NM_000125.3	418	gTa/gAa	6/8	0.560032565921818	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.58585527790493	1		290	395	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170432	119170432	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	196	353	3	ENST00000264033.4:c.2662G>A	p.Ala888Thr	p.A888T	ENST00000264033	NM_005188.3	888	Gcc/Acc	16/16	1	2	FACETS	0.912	0.846	0.979	0.912	0.846	0.979	CLONAL	1	TRUE	1	0.58585527790493	2		356	734	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131215	55131215	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	rs1214333123	NA	P-0121460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	322	245	0	ENST00000257290.5:c.758T>A	p.Val253Glu	p.V253E	ENST00000257290	NM_006206.4	253	gTg/gAg	5/23	1	2	FACETS	0.884	0.84	0.929	0.884	0.84	0.929	CLONAL	1	NA	1	0.973636079220386	2		245	748	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982070	93982070	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0121460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	660	475	0	ENST00000369303.4:c.1395A>T	p.Glu465Asp	p.E465D	ENST00000369303	NM_004440.3	465	gaA/gaT	6/17	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	NA	NA	0.973636079220386	2		475	1313	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817912	3817912	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0121460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	67	244	0	ENST00000262367.5:c.3061-2A>G		p.X1021_splice	ENST00000262367	NM_004380.2	1021			1	2	FACETS	0.203	0.176	0.233	0.203	0.176	0.233	SUBCLONAL	1	NA	1	0.973636079220386	2		244	677	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843611	3843611	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0121460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	119	197	0	ENST00000262367.5:c.992C>A	p.Ser331Ter	p.S331*	ENST00000262367	NM_004380.2	331	tCa/tAa	4/31	1	2	FACETS	0.392	0.354	0.431	0.392	0.354	0.431	SUBCLONAL	1	NA	1	0.973636079220386	2		197	624	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937684	76937684	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0121460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	574	212	0	ENST00000373344.5:c.3064C>T	p.Arg1022Ter	p.R1022*	ENST00000373344	NM_000489.3	1022	Cga/Tga	9/35	1	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	NA	0	0.973636079220386	1		212	583	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0003156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	740	304	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.275696439268155	20	FACETS	0.98	0.954	1			1	CLONAL	17	TRUE	NA	0.275696439268155	20		304	1122	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186599	108186599	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876658415	NA	P-0003156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	88	322	0	ENST00000278616.4:c.6056A>G	p.Tyr2019Cys	p.Y2019C	ENST00000278616	NM_000051.3	2019	tAt/tGt	41/63	0.275696439268155	2	FACETS	0.942	0.842	1	0.942	0.842	1	CLONAL	2	TRUE	0	0.275696439268155	2		322	339	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630465	187630465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1439256953	NA	P-0003156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	335	468	0	ENST00000441802.2:c.517G>A	p.Ala173Thr	p.A173T	ENST00000441802	NM_005245.3	173	Gcc/Acc	2/27	0.275696439268155	4	FACETS	0.878	0.833	0.923	1	0.99	1	CLONAL	4	TRUE	1	0.275696439268155	4		468	883	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206912	102206912	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	91	524	0	ENST00000263464.3:c.1540C>G	p.Leu514Val	p.L514V	ENST00000263464	NM_001165.4	514	Ctg/Gtg	7/9	0.275696439268155	2	FACETS	0.947	0.841	1	0.474	0.42	0.53	CLONAL	1	TRUE	0	0.275696439268155	2		524	697	SUCCESS
ATM	472	MSKCC	GRCh37	11	108168100	108168100	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	51	345	0	ENST00000278616.4:c.4996G>C	p.Glu1666Gln	p.E1666Q	ENST00000278616	NM_000051.3	1666	Gaa/Caa	33/63	0.275696439268155	2	FACETS	1	0.873	1	0.512	0.437	0.595	CLONAL	1	TRUE	0	0.275696439268155	2		345	361	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15838440	15838440	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0003156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	72	256	0	ENST00000307771.7:c.937+1G>T		p.X313_splice	ENST00000307771	NM_005089.3	313			0.245314221888593	2	FACETS	1	0.971	1			1	CLONAL	1	TRUE	NA	0.275696439268155	2		256	377	SUCCESS
AR	367	MSKCC	GRCh37	X	66931318	66931318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200737258	NA	P-0003156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	114	288	0	ENST00000374690.3:c.1960G>A	p.Glu654Lys	p.E654K	ENST00000374690	NM_000044.3	654	Gag/Aag	4/8	0.245314221888593	2	FACETS	0.911	0.825	1			1	CLONAL	2	TRUE	NA	0.275696439268155	2		288	454	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044718	47044719	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0003156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	120	193	0	ENST00000377604.3:c.2119_2120del	p.Gln707AlafsTer12	p.Q707Afs*12	ENST00000377604	NM_001204468.1	706	agACag/agag	19/24	0.245314221888593	2	FACETS	0.939	0.861	1			1	CLONAL	3	TRUE	NA	0.275696439268155	2		193	309	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0003157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	57	235	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	1	2	FACETS	0.512	0.438	0.594	0.512	0.438	0.594	SUBCLONAL	1	TRUE	1	0.25	2		235	890	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	73	167	0	ENST00000397752.3:c.3028G>A	p.Asp1010Asn	p.D1010N	ENST00000397752	NM_000245.2	1010	Gat/Aat	14/21	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.25	2		167	552	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058708	47058708	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	48	247	0	ENST00000409792.3:c.7570T>C	p.Cys2524Arg	p.C2524R	ENST00000409792	NM_014159.6	2524	Tgt/Cgt	21/21	1	2	FACETS	0.441	0.371	0.518	0.441	0.371	0.518	SUBCLONAL	1	TRUE	1	0.25	2		247	871	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058716	47058716	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	45	225	0	ENST00000409792.3:c.7562T>C	p.Leu2521Pro	p.L2521P	ENST00000409792	NM_014159.6	2521	cTg/cCg	21/21	1	2	FACETS	0.438	0.367	0.517	0.438	0.367	0.517	SUBCLONAL	1	TRUE	1	0.25	2		225	822	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142966	47142966	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1559720382	NA	P-0003157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	57	332	0	ENST00000409792.3:c.4997A>G	p.Tyr1666Cys	p.Y1666C	ENST00000409792	NM_014159.6	1666	tAt/tGt	8/21	1	2	FACETS	0.545	0.467	0.632	0.545	0.467	0.632	SUBCLONAL	1	TRUE	1	0.25	2		332	836	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042305	42042306	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0003157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	116	517	0	ENST00000219905.7:c.6500_6501del	p.Leu2167ArgfsTer27	p.L2167Rfs*27	ENST00000219905	NM_001164273.1	2167	cTG/c	17/24	0.3	1	FACETS	0.688	0.618	0.762	0.688	0.618	0.762	SUBCLONAL	1	TRUE	0	0.25	1		517	1181	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610136	10610136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	262	417	0	ENST00000171111.5:c.574G>A	p.Glu192Lys	p.E192K	ENST00000171111	NM_203500.1	192	Gag/Aag	2/6	0.215833391342433	3	FACETS	1	0.989	1	0.608	0.571	0.645	INDETERMINATE	1	TRUE	1	0.746469209281691	3		417	793	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101385	27101385	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	204	330	0	ENST00000324856.7:c.4667G>T	p.Gly1556Val	p.G1556V	ENST00000324856	NM_006015.4	1556	gGt/gTt	18/20	0.52352648493786	3	FACETS	0.96	0.892	1			1	CLONAL	1	TRUE	NA	0.746469209281691	3		330	782	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468463	89468463	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	245	353	0	ENST00000336596.2:c.1997A>G	p.Asp666Gly	p.D666G	ENST00000336596	NM_005233.5	666	gAc/gGc	11/17	0.746469209281691	6	FACETS	0.824	0.77	0.879			1	CLONAL	2	TRUE	NA	0.746469209281691	6		353	993	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55130071	55130071	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	373	360	0	ENST00000257290.5:c.605C>A	p.Pro202Gln	p.P202Q	ENST00000257290	NM_006206.4	202	cCa/cAa	4/23	0.746469209281691	3	FACETS	0.948	0.907	0.988	0.948	0.907	0.988	CLONAL	2	TRUE	1	0.746469209281691	3		360	724	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511337	157511337	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	89	156	0	ENST00000346085.5:c.3855G>A	p.Met1285Ile	p.M1285I	ENST00000346085	NM_020732.3	1285	atG/atA	15/20	0.670646066657281	2	FACETS	1	0.911	1	0.505	0.456	0.556	CLONAL	1	TRUE	0	0.746469209281691	2		156	236	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843246	128843246	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	167	354	0	ENST00000249373.3:c.353G>T	p.Cys118Phe	p.C118F	ENST00000249373	NM_005631.4	118	tGc/tTc	2/12	0.637032571903246	3	FACETS	0.855	0.787	0.925	0.285	0.262	0.309	CLONAL	1	TRUE	0	0.746469209281691	3		354	719	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430648	80430648	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	103	178	0	ENST00000286548.4:c.360G>C	p.Lys120Asn	p.K120N	ENST00000286548	NM_002072.3	120	aaG/aaC	3/7	0.637032571903246	3	FACETS	0.806	0.736	0.877	0.538	0.491	0.585	CLONAL	2	TRUE	0	0.746469209281691	3		178	235	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405200	70405200	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0003165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	86	256	0	ENST00000373644.4:c.2714C>G	p.Ser905Ter	p.S905*	ENST00000373644	NM_030625.2	905	tCa/tGa	4/12	0.300990376162022	3	FACETS	0.867	0.773	0.966	0.289	0.257	0.322	INDETERMINATE	1	TRUE	0	0.746469209281691	3		256	365	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741696	17741696	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	176	297	0	ENST00000250003.3:c.367A>T	p.Ser123Cys	p.S123C	ENST00000250003	NM_002478.4	123	Agc/Tgc	1/3	0.65611809308958	2	FACETS	0.916	0.85	0.983	0.458	0.425	0.492	CLONAL	1	TRUE	0	0.746469209281691	2		297	515	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865296	57865296	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	975	584	1	ENST00000228682.2:c.2773T>A	p.Tyr925Asn	p.Y925N	ENST00000228682	NM_005269.2	925	Tac/Aac	12/12	0.746469209281691	4	FACETS	0.971	0.948	0.994	0.971	0.948	0.994	CLONAL	3	TRUE	1	0.746469209281691	4		585	1566	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237751	133237751	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0003165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	140	293	0	ENST00000320574.5:c.2865-1G>T		p.X955_splice	ENST00000320574	NM_006231.2	955			1	2	FACETS	0.734	0.672	0.798	0.734	0.672	0.798	SUBCLONAL	1	TRUE	1	0.746469209281691	2		293	511	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434700	110434700	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	153	268	0	ENST00000375856.3:c.3701G>T	p.Ser1234Ile	p.S1234I	ENST00000375856	NM_003749.2	1234	aGc/aTc	1/2	1	2	FACETS	0.755	0.695	0.817	0.755	0.695	0.817	SUBCLONAL	1	TRUE	1	0.746469209281691	2		268	543	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808885	3808885	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	335	299	0	ENST00000262367.5:c.3339G>T	p.Gln1113His	p.Q1113H	ENST00000262367	NM_004380.2	1113	caG/caT	17/31	0.746469209281691	3	FACETS	0.862	0.821	0.903	0.862	0.821	0.903	CLONAL	2	TRUE	1	0.746469209281691	3		299	715	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057520006	NA	P-0003165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	552	446	0	ENST00000269305.4:c.821T>A	p.Val274Asp	p.V274D	ENST00000269305	NM_001126112.2	274	gTt/gAt	8/11	0.65611809308958	2	FACETS	0.863	0.836	0.889	0.863	0.836	0.889	CLONAL	2	TRUE	0	0.746469209281691	2		446	857	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995182	15995182	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	219	418	0	ENST00000268712.3:c.3011G>T	p.Trp1004Leu	p.W1004L	ENST00000268712	NM_006311.3	1004	tGg/tTg	22/46	0.65611809308958	2	FACETS	0.889	0.831	0.948	0.445	0.415	0.474	CLONAL	1	TRUE	0	0.746469209281691	2		418	660	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627955	37627955	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	233	404	0	ENST00000447079.4:c.1870A>T	p.Thr624Ser	p.T624S	ENST00000447079	NM_015083.1	624	Act/Tct	2/14	0.628473871645718	3	FACETS	1	0.961	1	0.519	0.485	0.554	CLONAL	1	TRUE	1	0.746469209281691	3		404	826	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39647380	39647380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1306170227	NA	P-0003165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	336	357	0	ENST00000262039.4:c.2552C>T	p.Ser851Leu	p.S851L	ENST00000262039	NM_002647.2	851	tCg/tTg	24/25	0.512499274072948	3	FACETS	0.916	0.874	0.958	0.916	0.874	0.958	CLONAL	2	TRUE	1	0.746469209281691	3		357	675	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716006	52716006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	162	447	0	ENST00000322088.6:c.571G>A	p.Glu191Lys	p.E191K	ENST00000322088	NM_014225.5	191	Gag/Aag	5/15	NA	2	FACETS	0.64	0.589	0.693			1	INDETERMINATE	1	TRUE	NA	0.746469209281691	2		447	678	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420070	41420070	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	89	261	0	ENST00000373198.4:c.251C>A	p.Ser84Tyr	p.S84Y	ENST00000373198	NM_133170.3	84	tCt/tAt	3/32	0.293731390847489	5	FACETS	0.813	0.721	0.91	0.163	0.144	0.182	INDETERMINATE	1	TRUE	0	0.746469209281691	5		261	622	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514606	44514606	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	115	230	0	ENST00000291552.4:c.550G>C	p.Glu184Gln	p.E184Q	ENST00000291552	NM_006758.2	184	Gag/Cag	7/8	0.628473871645718	3	FACETS	0.774	0.699	0.851	0.387	0.349	0.426	SUBCLONAL	1	TRUE	1	0.746469209281691	3		230	547	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341534	70341534	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	672	514	0	ENST00000374080.3:c.969G>C	p.Gln323His	p.Q323H	ENST00000374080		323	caG/caC	7/45	0.746469209281691	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.746469209281691	3		514	1220	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939457	76939457	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	137	489	0	ENST00000373344.5:c.1291G>T	p.Glu431Ter	p.E431*	ENST00000373344	NM_000489.3	431	Gag/Tag	9/35	0.746469209281691	3	FACETS	0.765	0.697	0.835	0.382	0.348	0.418	SUBCLONAL	1	TRUE	1	0.746469209281691	3		489	659	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532758	46532758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	100	262	0	ENST00000262741.5:c.320del	p.Gly107GlufsTer6	p.G107Efs*6	ENST00000262741	NM_003629.3	107	gGa/ga	4/10	0.593450092009809	4	FACETS	0.705	0.63	0.784	0.352	0.315	0.392	SUBCLONAL	1	TRUE	2	0.746469209281691	4		262	664	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203726	94203727	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0003165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	143	301	0	ENST00000323929.3:c.927_928delinsTT	p.Met309_Glu310delinsIleTer	p.M309_E310delinsI*	ENST00000323929	NM_005591.3	309	atGGag/atTTag	9/20	0.434227261167629	5	FACETS	1	0.939	1	0.345	0.315	0.377	INDETERMINATE	1	TRUE	2	0.746469209281691	5		301	784	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941633	48941633	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	197	348	0	ENST00000267163.4:c.943G>T	p.Glu315Ter	p.E315*	ENST00000267163	NM_000321.2	315	Gaa/Taa	10/27	0.489204958419758	1	FACETS	0.838	0.783	0.895	0.838	0.783	0.895	CLONAL	1	TRUE	0	0.617594948789672	1		348	526	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42057138	42057138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780211238	NA	P-0003172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	436	698	0	ENST00000219905.7:c.7799C>T	p.Pro2600Leu	p.P2600L	ENST00000219905	NM_001164273.1	2600	cCg/cTg	23/24	0.594020240288315	1	FACETS	0.933	0.893	0.974	0.933	0.893	0.974	CLONAL	1	TRUE	0	0.617594948789672	1		698	1046	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618616	37618616	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	445	409	0	ENST00000447079.4:c.292G>T	p.Glu98Ter	p.E98*	ENST00000447079	NM_015083.1	98	Gaa/Taa	1/14	NA	2	FACETS	0.982	0.947	1			1	INDETERMINATE	2	TRUE	NA	0.617594948789672	2		409	734	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576827	7576857	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGATAAGAGGTCCCAAGACTTAGTACCTGAA	TGATAAGAGGTCCCAAGACTTAGTACCTGAA	-	novel	NA	P-0003172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	116	291	0	ENST00000269305.4:c.989_993+26del		p.X330_splice	ENST00000269305	NM_001126112.2	330		9/11	0.440155713537881	1	FACETS	0.766	0.699	0.835	0.766	0.699	0.835	SUBCLONAL	1	TRUE	0	0.617594948789672	1		291	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0003175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	27	401	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.120583461419232	2		402	340	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412905	49412905	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519951	NA	P-0003175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	55	522	0	ENST00000418115.1:c.118G>C	p.Glu40Gln	p.E40Q	ENST00000418115	NM_001664.2	40	Gag/Cag	2/5	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.120583461419232	2		522	659	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200219	123200219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	40	364	2	ENST00000218089.9:c.2198C>T	p.Ala733Val	p.A733V	ENST00000218089	NM_001042749.1	733	gCa/gTa	23/35	NA	2	FACETS	0.929	0.77	1			1	INDETERMINATE	1	TRUE	NA	0.120583461419232	2		366	714	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095593	178095593	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	61	473	0	ENST00000397062.3:c.1738G>A	p.Glu580Lys	p.E580K	ENST00000397062	NM_006164.4	580	Gaa/Aaa	5/5	0.120583461419232	3	FACETS	0.798	0.688	0.918	0.798	0.688	0.918	CLONAL	2	TRUE	1	0.120583461419232	3		473	672	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096493	178096493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	39	297	0	ENST00000397062.3:c.838G>A	p.Asp280Asn	p.D280N	ENST00000397062	NM_006164.4	280	Gat/Aat	5/5	0.120583461419232	3	FACETS	1	0.941	1	0.675	0.559	0.805	CLONAL	1	TRUE	1	0.120583461419232	3		297	508	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955567	55955567	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	47	485	0	ENST00000263923.4:c.3378G>T	p.Arg1126Ser	p.R1126S	ENST00000263923	NM_002253.2	1126	agG/agT	25/30	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.120583461419232	2		485	646	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197346	26197346	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	30	544	0	ENST00000356476.2:c.133G>T	p.Gly45Cys	p.G45C	ENST00000356476		45	Ggc/Tgc	1/1	0.120583461419232	3	FACETS	1	0.83	1	0.517	0.416	0.633	CLONAL	1	TRUE	1	0.120583461419232	3		544	510	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729514	41729514	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs775755149	NA	P-0003175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	37	509	0	ENST00000242208.4:c.1015A>G	p.Ile339Val	p.I339V	ENST00000242208	NM_002192.2	339	Atc/Gtc	3/3	0.120583461419232	5	FACETS	1	0.933	1	0.434	0.357	0.52	CLONAL	1	TRUE	2	0.120583461419232	5		509	557	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240814	55240814	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	16	173	0	ENST00000275493.2:c.2058G>C	p.Arg686Ser	p.R686S	ENST00000275493	NM_005228.3	686	agG/agC	17/28	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.120583461419232	2		173	189	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390602	139390602	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	22	422	0	ENST00000277541.6:c.7589C>G	p.Ser2530Cys	p.S2530C	ENST00000277541	NM_017617.3	2530	tCc/tGc	34/34	1	2	FACETS	0.96	0.743	1	0.96	0.743	1	CLONAL	1	TRUE	1	0.120583461419232	2		422	380	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111498	8111498	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	28	330	2	ENST00000346208.3:c.984G>T	p.Trp328Cys	p.W328C	ENST00000346208		328	tgG/tgT	5/6	NA	2	FACETS	1	0.84	1			1	INDETERMINATE	1	TRUE	NA	0.120583461419232	2		332	438	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925682	114925682	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	42	627	0	ENST00000543371.1:c.1760C>A	p.Ala587Asp	p.A587D	ENST00000543371	NM_001198531.1	587	gCc/gAc	14/14	0.120583461419232	1	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	0	0.120583461419232	1		627	586	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623581	28623581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757718855	NA	P-0003175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	49	305	0	ENST00000241453.7:c.976G>A	p.Gly326Arg	p.G326R	ENST00000241453	NM_004119.2	326	Gga/Aga	8/24	NA	2	FACETS	1	0.957	1			1	INDETERMINATE	1	TRUE	NA	0.120583461419232	2		305	577	SUCCESS
BLM	641	MSKCC	GRCh37	15	91337453	91337453	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	68	307	2	ENST00000355112.3:c.3076A>C	p.Met1026Leu	p.M1026L	ENST00000355112	NM_000057.2	1026	Atg/Ctg	16/22	0.120583461419232	3	FACETS	0.906	0.788	1	0.604	0.525	0.689	CLONAL	2	TRUE	0	0.120583461419232	3		309	660	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916121	9916121	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	19	296	0	ENST00000330684.3:c.2168G>T	p.Gly723Val	p.G723V	ENST00000330684	NM_001134407.1	723	gGg/gTg	10/13	NA	2	FACETS	0.976	0.74	1			1	INDETERMINATE	1	TRUE	NA	0.120583461419232	2		296	323	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952316	17952316	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	24	273	0	ENST00000458235.1:c.1024G>T	p.Val342Leu	p.V342L	ENST00000458235	NM_000215.3	342	Gtg/Ttg	8/24	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.120583461419232	2		273	301	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651311	45651311	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	39	428	0	ENST00000407780.3:c.714G>C	p.Glu238Asp	p.E238D	ENST00000407780	NM_001283052.1	238	gaG/gaC	5/7	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.120583461419232	2		428	534	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148698	20148698	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	40	362	0	ENST00000379607.5:c.365G>T	p.Gly122Val	p.G122V	ENST00000379607	NM_001412.3	122	gGt/gTt	6/7	0.120583461419232	1	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	0	0.120583461419232	1		362	597	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939820	76939820	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	59	563	0	ENST00000373344.5:c.928G>C	p.Glu310Gln	p.E310Q	ENST00000373344	NM_000489.3	310	Gaa/Caa	9/35	0.120583461419232	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.120583461419232	1		563	746	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542634	187542634	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	45	396	0	ENST00000441802.2:c.5106del	p.Asp1703MetfsTer33	p.D1703Mfs*33	ENST00000441802	NM_005245.3	1702	aaA/aa	10/27	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.120583461419232	2		396	544	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445244	49445244	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	12	192	0	ENST00000301067.7:c.2222del	p.Pro741ArgfsTer189	p.P741Rfs*189	ENST00000301067	NM_003482.3	741	cCg/cg	10/54	1	2	FACETS	0.897	0.63	1	0.897	0.63	1	CLONAL	1	TRUE	1	0.120583461419232	2		192	222	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729769	162729770	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	TT	novel	NA	P-0003175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	25	224	0	ENST00000367921.3:c.855_855+1delinsTT		p.X285_splice	ENST00000367921	NM_006182.2	285		8/18	0.120583461419232	3	FACETS	1	0.863	1	0.567	0.446	0.705	CLONAL	1	TRUE	1	0.120583461419232	3		224	388	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784040	9784040	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	198	406	0	ENST00000377346.4:c.2608C>T	p.Arg870Ter	p.R870*	ENST00000377346	NM_005026.3	870	Cga/Tga	21/24	0.47372753230751	1	FACETS	0.331	0.307	0.355	0.331	0.307	0.355	INDETERMINATE	1	TRUE	0	0.909532210225566	1		406	717	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332459	70332459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751344073	NA	P-0003181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	196	478	0	ENST00000373644.4:c.364G>A	p.Val122Ile	p.V122I	ENST00000373644	NM_030625.2	122	Gta/Ata	2/12	0.47372753230751	1	FACETS	0.304	0.282	0.327	0.304	0.282	0.327	INDETERMINATE	1	TRUE	0	0.909532210225566	1		478	773	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057874	27057874	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003193-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	131	392	0	ENST00000324856.7:c.1582C>T	p.Gln528Ter	p.Q528*	ENST00000324856	NM_006015.4	528	Cag/Tag	3/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.398702898954102	2		392	490	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156731	20156731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003193-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	194	338	0	ENST00000379607.5:c.26G>A	p.Gly9Asp	p.G9D	ENST00000379607	NM_001412.3	9	gGt/gAt	2/7	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	1	0.398702898954102	2		338	663	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089664	27089665	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0003193-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	128	323	0	ENST00000324856.7:c.2620_2621del	p.Asn874TyrfsTer61	p.N874Yfs*61	ENST00000324856	NM_006015.4	874	AAt/t	8/20	1	2	FACETS	0.799	0.731	0.869	1	0.988	1	SUBCLONAL	2	FALSE	1	0.398702898954102	2		323	402	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913492	NA	P-0003199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	108	241	0	ENST00000286548.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000286548	NM_002072.3	209	cAa/cTa	5/7	1	2	FACETS	0.86	0.78	0.942	0.86	0.78	0.942	CLONAL	1	TRUE	1	0.738818731857271	2		241	340	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443599	52443601	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0003199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	204	300	0	ENST00000460680.1:c.91_93del	p.Glu31del	p.E31del	ENST00000460680	NM_004656.3	31	GAG/-	3/17	0.738818731857271	1	FACETS	0.967	0.914	1	0.967	0.914	1	CLONAL	1	TRUE	0	0.738818731857271	1		300	360	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845368	156845368	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003200-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	36	392	1	ENST00000524377.1:c.1411T>A	p.Leu471Met	p.L471M	ENST00000524377	NM_002529.3	471	Ttg/Atg	12/17	1	2	FACETS	0.562	0.46	0.676	0.562	0.46	0.676	SUBCLONAL	1	TRUE	1	0.2	2		393	641	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670844	134670844	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003200-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	25	130	0	ENST00000398015.3:c.755G>C	p.Arg252Pro	p.R252P	ENST00000398015	NM_004441.4	252	cGa/cCa	3/16	1	2	FACETS	0.969	0.766	1	0.969	0.766	1	CLONAL	1	TRUE	1	0.2	2		130	258	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286913	33286913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003200-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	29	240	0	ENST00000374542.5:c.2024C>T	p.Ser675Phe	p.S675F	ENST00000374542	NM_001141970.1	675	tCc/tTc	7/8	0.288622815193725	3	FACETS	0.639	0.512	0.784	0.32	0.256	0.392	SUBCLONAL	1	TRUE	1	0.2	3		240	499	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3929852	3929852	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003200-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	125	363	0	ENST00000262367.5:c.66C>G	p.Phe22Leu	p.F22L	ENST00000262367	NM_004380.2	22	ttC/ttG	1/31	1	2	FACETS	0.814	0.737	0.895	1	0.987	1	CLONAL	2	TRUE	1	0.2	2		363	768	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448598	89448613	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGCAAGTTTGAGTT	GCCGCAAGTTTGAGTT	-	novel	NA	P-0003200-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	76	305	0	ENST00000336596.2:c.1562_1577del	p.Ser521MetfsTer19	p.S521Mfs*19	ENST00000336596	NM_005233.5	521	aGCCGCAAGTTTGAGTTt/at	7/17	0.297955323257758	1	FACETS	0.954	0.836	1	0.954	0.836	1	CLONAL	1	TRUE	0	0.2	1		305	717	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0003211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	230	308	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.991	0.929	1	0.991	0.929	1	CLONAL	1	TRUE	1	0.713942533420612	2		308	650	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	98	261	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	0.713942533420612	2		261	258	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0003211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	256	332	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	0.965	0.908	1	0.965	0.908	1	CLONAL	1	TRUE	1	0.713942533420612	2		332	743	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0003211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	194	275	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.976	0.909	1	0.976	0.909	1	CLONAL	1	TRUE	1	0.713942533420612	2		275	557	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131926976	131926976	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs193921012	NA	P-0003211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	178	338	0	ENST00000265335.6:c.1513A>G	p.Ile505Val	p.I505V	ENST00000265335		505	Ata/Gta	10/25	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.713942533420612	2		338	483	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831068	72831068	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	361	403	1	ENST00000268489.5:c.5513A>C	p.Gln1838Pro	p.Q1838P	ENST00000268489	NM_006885.3	1838	cAg/cCg	9/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.713942533420612	2		404	988	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022592	31022592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs373221034	NA	P-0003211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	343	288	0	ENST00000375687.4:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000375687	NM_015338.5	693	Cga/Tga	13/13	0.713942533420612	3	FACETS	1	0.982	1	0.543	0.513	0.573	CLONAL	1	TRUE	1	0.713942533420612	3		288	1201	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579841	7579841	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	381	342	0	ENST00000269305.4:c.72del	p.Lys24AsnfsTer20	p.K24Nfs*20	ENST00000269305	NM_001126112.2	24	aaA/aa	2/11	0.713942533420612	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.713942533420612	1		342	661	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372518	55372518	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003221-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	128	202	0	ENST00000297316.4:c.1208G>T	p.Ser403Ile	p.S403I	ENST00000297316	NM_022454.3	403	aGc/aTc	2/2	1	2	FACETS	0.997	0.908	1	0.997	0.908	1	CLONAL	1	TRUE	1	0.451059556346212	2		202	569	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624274	89624274	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs587782187	NA	P-0003221-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	83	110	0	ENST00000371953.3:c.48T>A	p.Tyr16Ter	p.Y16*	ENST00000371953	NM_000314.4	16	taT/taA	1/9	0.447634267172118	3	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	1	0.451059556346212	3		110	216	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685300	89685300	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs878853936	NA	P-0003221-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	45	177	0	ENST00000371953.3:c.195C>G	p.Tyr65Ter	p.Y65*	ENST00000371953	NM_000314.4	65	taC/taG	3/9	0.447634267172118	3	FACETS	0.835	0.705	0.976	0.417	0.352	0.488	CLONAL	1	TRUE	1	0.451059556346212	3		177	293	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003223-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	51	252	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.506734407213817	2		252	198	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912359	97912359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554302947	NA	P-0003223-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	99	271	0	ENST00000289081.3:c.532G>A	p.Glu178Lys	p.E178K	ENST00000289081	NM_000136.2	178	Gag/Aag	7/15	1	2	FACETS	0.907	0.814	1	0.907	0.814	1	CLONAL	1	TRUE	1	0.506734407213817	2		271	431	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857481	68857481	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003223-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	128	336	0	ENST00000261769.5:c.2116C>T	p.Gln706Ter	p.Q706*	ENST00000261769	NM_004360.3	706	Caa/Taa	13/16	0.506734407213817	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.506734407213817	1		336	375	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554906	187554906	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	146	486	0	ENST00000441802.2:c.4255G>T	p.Ala1419Ser	p.A1419S	ENST00000441802	NM_005245.3	1419	Gca/Tca	7/27	1	2	FACETS	0.894	0.82	0.971	0.894	0.82	0.971	CLONAL	1	TRUE	1	0.5699454381828	2		486	573	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692835	89692835	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs57374291	NA	P-0003262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	43	123	0	ENST00000371953.3:c.319G>T	p.Asp107Tyr	p.D107Y	ENST00000371953	NM_000314.4	107	Gat/Tat	5/9	0.5699454381828	1	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	0	0.5699454381828	1		123	102	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538949	187538949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1251415716	NA	P-0121481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	249	376	0	ENST00000441802.2:c.8791G>A	p.Asp2931Asn	p.D2931N	ENST00000441802	NM_005245.3	2931	Gac/Aac	10/27	0.570522000443448	2	FACETS	1	0.97	1	0.528	0.495	0.562	CLONAL	1	NA	0	0.570522000443448	2		376	826	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434515	110434515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0121481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	109	165	0	ENST00000375856.3:c.3886G>A	p.Ala1296Thr	p.A1296T	ENST00000375856	NM_003749.2	1296	Gct/Act	1/2	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	NA	1	0.570522000443448	2		165	322	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42840389	42840389	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0121481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	203	327	0	ENST00000398585.3:c.1359T>A	p.Tyr453Ter	p.Y453*	ENST00000398585	NM_001135099.1	453	taT/taA	12/14	0.367703345772864	2	FACETS	1	0.973	1	0.543	0.506	0.581	CLONAL	1	NA	0	0.570522000443448	2		327	655	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888760	76888760	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	227	416	0	ENST00000373344.5:c.5069C>A	p.Ala1690Asp	p.A1690D	ENST00000373344	NM_000489.3	1690	gCt/gAt	19/35	0.570522000443448	1	FACETS	0.961	0.902	1	0.961	0.902	1	CLONAL	1	NA	0	0.570522000443448	1		416	592	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144118	11144129	+	inframe_deletion	In_Frame_Del	DEL	GTTCGACCAGAA	GTTCGACCAGAA	-	novel	NA	P-0121481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	163	286	0	ENST00000358026.2:c.3701_3712del	p.Phe1234_Lys1237del	p.F1234_K1237del	ENST00000358026	NM_001128849.1	1233	atGTTCGACCAGAAg/atg	26/36	0.570522000443448	2	FACETS	0.906	0.834	0.979	0.453	0.417	0.49	CLONAL	1	NA	0	0.570522000443448	2		286	631	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0003269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	158	377	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.237377126351315	3	FACETS	0.853	0.785	0.923	1	0.984	1	CLONAL	3	TRUE	1	0.237377126351315	3		378	582	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0003269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	125	470	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.232670967106141	4	FACETS	0.992	0.9	1	0.992	0.9	1	CLONAL	2	TRUE	2	0.237377126351315	4		470	657	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261454	16261454	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	40	246	0	ENST00000375759.3:c.8719C>A	p.Pro2907Thr	p.P2907T	ENST00000375759	NM_015001.2	2907	Cca/Aca	11/15	NA	2	FACETS	0.994	0.829	1			1	INDETERMINATE	1	TRUE	NA	0.237377126351315	2		246	339	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590466	67590466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	139	285	0	ENST00000274335.5:c.1528G>A	p.Glu510Lys	p.E510K	ENST00000274335		510	Gaa/Aaa	11/15	0.237377126351315	3	FACETS	1	0.921	1	1	0.921	1	CLONAL	2	TRUE	1	0.237377126351315	3		285	649	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211593	98211593	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	31	224	0	ENST00000331920.6:c.3562A>T	p.Asn1188Tyr	p.N1188Y	ENST00000331920	NM_000264.3	1188	Aac/Tac	22/24	0.162197578066985	4	FACETS	1	0.833	1	0.515	0.417	0.625	CLONAL	1	TRUE	2	0.237377126351315	4		224	314	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527568	29527569	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555610903	NA	P-0003269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	55	352	0	ENST00000356175.3:c.1019_1020del	p.Ser340CysfsTer12	p.S340Cfs*12	ENST00000356175	NM_000267.3	339	aaCTct/aact	9/57	0.237377126351315	3	FACETS	0.777	0.664	0.901	0.389	0.332	0.451	CLONAL	1	TRUE	1	0.237377126351315	3		352	667	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657341	29657345	+	frameshift_variant	Frame_Shift_Del	DEL	CTTAA	CTTAA	-	novel	NA	P-0003269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	89	371	0	ENST00000356175.3:c.5577_5581del	p.Thr1860TyrfsTer3	p.T1860Yfs*3	ENST00000356175	NM_000267.3	1858	gcCTTAAct/gcct	38/57	0.237377126351315	3	FACETS	1	0.962	1	0.601	0.533	0.674	CLONAL	1	TRUE	1	0.237377126351315	3		371	698	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89811386	89811388	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs1380850249	NA	P-0003269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	112	448	0	ENST00000389301.3:c.3605_3607del	p.Glu1202del	p.E1202del	ENST00000389301	NM_000135.2	1202	gAAGgc/ggc	36/43	0.171803747868982	3	FACETS	0.898	0.81	0.99	0.898	0.81	0.99	CLONAL	2	TRUE	1	0.237377126351315	3		448	588	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0003273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	523	363	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.253848331612154	17	FACETS	1	0.976	1			1	CLONAL	16	TRUE	NA	0.253848331612154	17		363	744	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0003280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	544	321	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.521428776758395	3	FACETS	0.919	0.888	0.95	1	0.997	1	CLONAL	3	TRUE	1	0.521428776758395	3		321	954	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451507	70451507	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs757251233	NA	P-0003280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	80	441	0	ENST00000373644.4:c.6347A>G	p.Asn2116Ser	p.N2116S	ENST00000373644	NM_030625.2	2116	aAt/aGt	12/12	0.190217911785667	2	FACETS	0.563	0.496	0.634	0.282	0.248	0.317	INDETERMINATE	1	TRUE	0	0.521428776758395	2		441	545	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699331	18699331	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003297-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	82	278	0	ENST00000266497.5:c.3432A>T	p.Gln1144His	p.Q1144H	ENST00000266497		1144	caA/caT	24/31	1	2	FACETS	0.241	0.212	0.272	0.241	0.212	0.272	SUBCLONAL	1	TRUE	1	0.99	2		278	688	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs760043106	NA	P-0003299-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	330	252	0	ENST00000269305.4:c.584T>A	p.Ile195Asn	p.I195N	ENST00000269305	NM_001126112.2	195	aTc/aAc	6/11	0.422759273623748	3	FACETS	0.886	0.847	0.925	0.886	0.847	0.925	CLONAL	3	TRUE	0	0.529573780809708	3		252	593	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437782	52437782	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0003299-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	314	407	0	ENST00000460680.1:c.1379C>G	p.Ser460Ter	p.S460*	ENST00000460680	NM_004656.3	460	tCa/tGa	13/17	0.441930883192987	2	FACETS	0.897	0.853	0.941	0.897	0.853	0.941	CLONAL	2	TRUE	0	0.529573780809708	2		407	661	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332613	153332613	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003299-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	129	264	0	ENST00000281708.4:c.343G>T	p.Glu115Ter	p.E115*	ENST00000281708	NM_033632.3	115	Gag/Tag	2/12	0.26941248621593	3	FACETS	1	0.96	1	0.547	0.498	0.599	INDETERMINATE	1	TRUE	1	0.529573780809708	3		264	563	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619118	43619118	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0003299-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	89	186	0	ENST00000355710.3:c.2802-1G>T		p.X934_splice	ENST00000355710	NM_020975.4	934			0.167001273127388	4	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.529573780809708	4		186	361	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266771	198266771	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	31	241	0	ENST00000335508.6:c.2161A>T	p.Ile721Phe	p.I721F	ENST00000335508	NM_012433.2	721	Atc/Ttc	15/25	0.164188005187065	3	FACETS	0.798	0.648	0.966	0.798	0.648	0.966	CLONAL	2	TRUE	1	0.164188005187065	3		241	256	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86642492	86642492	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	11	171	0	ENST00000274376.6:c.1053G>A	p.Trp351Ter	p.W351*	ENST00000274376	NM_002890.2	351	tgG/tgA	7/25	1	2	FACETS	0.684	0.472	0.946	0.684	0.472	0.946	SUBCLONAL	1	TRUE	1	0.164188005187065	2		171	196	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729648	41729648	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	20	360	0	ENST00000242208.4:c.881T>G	p.Met294Arg	p.M294R	ENST00000242208	NM_002192.2	294	aTg/aGg	3/3	1	2	FACETS	1	0.827	1	1	0.827	1	CLONAL	1	TRUE	1	0.164188005187065	2		360	222	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345882	152345882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	21	350	0	ENST00000359321.1:c.688G>A	p.Ala230Thr	p.A230T	ENST00000359321	NM_005431.1	230	Gca/Aca	3/3	1	2	FACETS	0.695	0.535	0.883	0.695	0.535	0.883	SUBCLONAL	1	TRUE	1	0.164188005187065	2		350	368	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738149	145738149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371890521	NA	P-0003302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	12	269	0	ENST00000428558.2:c.2761G>A	p.Glu921Lys	p.E921K	ENST00000428558	NM_004260.3	921	Gag/Aag	17/22	0.135479874810387	3	FACETS	0.815	0.574	1	0.408	0.287	0.556	CLONAL	1	TRUE	1	0.164188005187065	3		269	194	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683977	29683977	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0003302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	17	259	0	ENST00000356175.3:c.7676-1G>C		p.X2559_splice	ENST00000356175	NM_000267.3	2559			0.164188005187065	3	FACETS	1	0.748	1	0.5	0.374	0.65	CLONAL	1	TRUE	1	0.164188005187065	3		259	224	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164935	123164935	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	15	284	0	ENST00000218089.9:c.248T>A	p.Met83Lys	p.M83K	ENST00000218089	NM_001042749.1	83	aTg/aAg	5/35	0.164188005187065	1	FACETS	0.626	0.457	0.828	0.626	0.457	0.828	SUBCLONAL	1	TRUE	0	0.164188005187065	1		284	268	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098959	178098982	+	inframe_deletion	In_Frame_Del	DEL	TCTATATCTTGCCTCCAAAGTATG	TCTATATCTTGCCTCCAAAGTATG	-	novel	NA	P-0003302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	31	212	0	ENST00000397062.3:c.63_86del	p.Ile22_Asp29del	p.I22_D29del	ENST00000397062	NM_006164.4	21	gaCATACTTTGGAGGCAAGATATAGAt/gat	2/5	0.164188005187065	3	FACETS	0.76	0.617	0.92	0.76	0.617	0.92	CLONAL	2	TRUE	1	0.164188005187065	3		212	269	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0003307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	204	300	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	0.982	0.917	1	0.982	0.917	1	CLONAL	1	TRUE	1	0.712933886308249	2		300	583	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0003307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	626	388	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	0.700367377011993	3	FACETS	0.967	0.944	0.989	0.967	0.944	0.989	CLONAL	3	TRUE	0	0.712933886308249	3		388	821	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0003308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	237	228	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.619059069144915	3	FACETS	0.939	0.896	0.98			1	CLONAL	3	TRUE	NA	0.619059069144915	3		228	356	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	62	252	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.521825667534047	5	FACETS	0.847	0.742	0.958	0.565	0.494	0.639	CLONAL	2	TRUE	2	0.619059069144915	5		252	228	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0003308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	222	323	1	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.619059069144915	4	FACETS	0.933	0.882	0.983	0.933	0.882	0.983	CLONAL	3	TRUE	1	0.619059069144915	4		324	415	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680546	241680546	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1472397242	NA	P-0003308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	86	438	0	ENST00000366560.3:c.203A>G	p.Tyr68Cys	p.Y68C	ENST00000366560	NM_000143.3	68	tAt/tGt	2/10	0.579077749493907	3	FACETS	0.803	0.714	0.898	0.402	0.357	0.449	CLONAL	1	TRUE	1	0.619059069144915	3		438	453	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610715	52610715	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0003308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	77	288	0	ENST00000394830.3:c.3459-1G>T		p.X1153_splice	ENST00000394830	NM_018313.4	1153			0.356089743653026	5	FACETS	1	0.961	1	0.405	0.357	0.456	INDETERMINATE	1	TRUE	2	0.619059069144915	5		288	395	SUCCESS
APC	324	MSKCC	GRCh37	5	112175322	112175322	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1114167578	NA	P-0003308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	50	265	0	ENST00000257430.4:c.4031C>G	p.Ser1344Ter	p.S1344*	ENST00000257430	NM_000038.5	1344	tCa/tGa	16/16	0.619059069144915	4	FACETS	0.713	0.607	0.828	0.238	0.202	0.276	SUBCLONAL	1	TRUE	1	0.619059069144915	4		265	367	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649545	48649545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782258887	NA	P-0003308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	85	552	0	ENST00000376670.3:c.29G>A	p.Gly10Glu	p.G10E	ENST00000376670	NM_002049.3	10	gGg/gAg	2/6	0.602022745394756	4	FACETS	0.756	0.669	0.849			1	SUBCLONAL	1	TRUE	NA	0.619059069144915	4		552	588	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361078	70361107	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGCAGCAGCAGCAACAGCAACAGCAGCAGC	AGCAGCAGCAGCAACAGCAACAGCAGCAGC	-	rs773480549	NA	P-0003308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	84	146	0	ENST00000374080.3:c.6300_6329del		p.X2100_splice	ENST00000374080		2100		43/45	0.248420938139934	5	FACETS	0.952	0.851	1			1	INDETERMINATE	2	TRUE	NA	0.619059069144915	5		146	275	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891349	101891349	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	63	214	0	ENST00000374994.4:c.310G>T	p.Asp104Tyr	p.D104Y	ENST00000374994	NM_004612.2	104	Gac/Tac	2/9	0.313112930822055	1	FACETS	0.954	0.83	1	0.954	0.83	1	CLONAL	1	TRUE	0	0.332692564307308	1		214	331	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0003324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	64	454	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.936	0.811	1	0.936	0.811	1	CLONAL	1	TRUE	1	0.25	2		454	547	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0003324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	105	262	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.302139349908509	3	FACETS	0.923	0.83	1	0.923	0.83	1	CLONAL	2	TRUE	1	0.25	3		262	512	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508547	106508547	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	42	141	0	ENST00000359195.3:c.541G>T	p.Val181Leu	p.V181L	ENST00000359195	NM_002649.2	181	Gtg/Ttg	2/11	1	2	FACETS	0.957	0.802	1	0.957	0.802	1	CLONAL	1	TRUE	1	0.25	2		141	351	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5064985	5064985	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	66	389	1	ENST00000381652.3:c.1159G>T	p.Val387Leu	p.V387L	ENST00000381652	NM_004972.3	387	Gta/Tta	9/25	1	2	FACETS	0.98	0.851	1	0.98	0.851	1	CLONAL	1	TRUE	1	0.25	2		390	539	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426779	47426779	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	91	298	0	ENST00000377045.4:c.1024C>A	p.Gln342Lys	p.Q342K	ENST00000377045	NM_001654.4	342	Cag/Aag	10/16	0.302139349908509	1	FACETS	0.874	0.776	0.979	0.874	0.776	0.979	CLONAL	1	TRUE	0	0.25	1		298	729	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937179	76937179	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	156	572	0	ENST00000373344.5:c.3569G>T	p.Arg1190Ile	p.R1190I	ENST00000373344	NM_000489.3	1190	aGa/aTa	9/35	1	2	FACETS	0.8	0.733	0.869	1	0.989	1	SUBCLONAL	2	TRUE	1	0.25	2		572	780	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0003333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	126	377	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.244515484468373	4	FACETS	1	0.958	1	1	0.958	1	INDETERMINATE	2	TRUE	2	0.497370946059145	4		378	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0003333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	275	591	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.380798702507199	5	FACETS	1	0.987	1			1	CLONAL	5	TRUE	NA	0.497370946059145	5		591	365	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630021	187630021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374843828	NA	P-0003333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	68	195	0	ENST00000441802.2:c.961G>A	p.Gly321Ser	p.G321S	ENST00000441802	NM_005245.3	321	Ggt/Agt	2/27	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.497370946059145	2		195	214	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937664	76937697	+	frameshift_variant	Frame_Shift_Del	DEL	AAAATGACAAATTTCTTCTCGCTCAGGTAACTTT	AAAATGACAAATTTCTTCTCGCTCAGGTAACTTT	-	novel	NA	P-0003333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	146	183	0	ENST00000373344.5:c.3051_3084del	p.Glu1017AspfsTer5	p.E1017Dfs*5	ENST00000373344	NM_000489.3	1017	gaAAAGTTACCTGAGCGAGAAGAAATTTGTCATTTT/ga	9/35	1	1	FACETS	1	0.985	1	1	0.994	1	CLONAL	2	TRUE	0	0.497370946059145	1		183	197	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879250	151879250	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	11	328	0	ENST00000262189.6:c.5695G>T	p.Ala1899Ser	p.A1899S	ENST00000262189	NM_170606.2	1899	Gca/Tca	36/59	0.433840659995815	3	FACETS	0.785	0.551	1			1	CLONAL	1	TRUE	NA	0.444910443940686	3		328	77	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2208947	2208947	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	21	452	0	ENST00000398665.3:c.977T>A	p.Phe326Tyr	p.F326Y	ENST00000398665	NM_032482.2	326	tTt/tAt	12/28	NA	2	FACETS	1	0.859	1			1	INDETERMINATE	1	TRUE	NA	0.444910443940686	2		452	84	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0003351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1185	166	476	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.771	0.706	0.839	0.771	0.706	0.839	SUBCLONAL	1	TRUE	1	0.318817348491919	2		476	1351	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772227	68772227	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs786201058	NA	P-0003351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	106	407	0	ENST00000261769.5:c.76G>T	p.Glu26Ter	p.E26*	ENST00000261769	NM_004360.3	26	Gag/Tag	2/16	0.318817348491919	1	FACETS	0.733	0.657	0.813	0.733	0.657	0.813	SUBCLONAL	1	TRUE	0	0.318817348491919	1		407	763	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16021276	16021276	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	109	262	0	ENST00000268712.3:c.1981C>T	p.Gln661Ter	p.Q661*	ENST00000268712	NM_006311.3	661	Caa/Taa	18/46	0.261018324874637	1	FACETS	0.669	0.6	0.742	0.669	0.6	0.742	SUBCLONAL	1	TRUE	0	0.318817348491919	1		262	859	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0003368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	169	412	1	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	0.959	1	0.991	1	CLONAL	2	TRUE	1	0.202268791448987	2		413	945	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0003368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	59	240	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.199703386375294	1	FACETS	0.993	0.855	1	0.993	0.855	1	CLONAL	1	TRUE	0	0.202268791448987	1		240	528	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120529700	120529700	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	49	250	0	ENST00000256646.2:c.757G>T	p.Glu253Ter	p.E253*	ENST00000256646	NM_024408.3	253	Gaa/Taa	5/34	1	2	FACETS	0.7	0.592	0.82	0.7	0.592	0.82	SUBCLONAL	1	TRUE	1	0.202268791448987	2		250	692	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163630	32163630	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	50	211	0	ENST00000375023.3:c.5596G>C	p.Ala1866Pro	p.A1866P	ENST00000375023	NM_004557.3	1866	Gcc/Ccc	30/30	0.164407074833022	3	FACETS	1	0.955	1	0.677	0.576	0.788	CLONAL	1	TRUE	1	0.202268791448987	3		211	402	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545635	106545635	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	68	314	0	ENST00000359195.3:c.3112G>T	p.Gly1038Ter	p.G1038*	ENST00000359195	NM_002649.2	1038	Gga/Tga	11/11	0.164407074833022	3	FACETS	0.808	0.701	0.924	0.404	0.35	0.462	CLONAL	1	TRUE	1	0.202268791448987	3		314	916	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233976	133233976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775271152	NA	P-0003368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	56	262	0	ENST00000320574.5:c.3418G>A	p.Ala1140Thr	p.A1140T	ENST00000320574	NM_006231.2	1140	Gcc/Acc	28/49	0.146469427800923	1	FACETS	0.929	0.796	1	0.929	0.796	1	CLONAL	1	TRUE	0	0.202268791448987	1		262	536	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133234477	133234477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376921543	NA	P-0003368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	67	278	0	ENST00000320574.5:c.3355C>T	p.Leu1119Phe	p.L1119F	ENST00000320574	NM_006231.2	1119	Ctt/Ttt	27/49	0.146469427800923	1	FACETS	0.933	0.811	1	0.933	0.811	1	CLONAL	1	TRUE	0	0.202268791448987	1		278	638	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032315	42032315	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	104	629	0	ENST00000219905.7:c.4499A>T	p.Asn1500Ile	p.N1500I	ENST00000219905	NM_001164273.1	1500	aAt/aTt	14/24	0.151704400131536	1	FACETS	0.796	0.711	0.887	0.796	0.711	0.887	SUBCLONAL	1	TRUE	0	0.202268791448987	1		629	1161	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39745000	39745000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	57	313	0	ENST00000361337.2:c.1790C>T	p.Thr597Met	p.T597M	ENST00000361337	NM_003286.2	597	aCg/aTg	17/21	0.164407074833022	3	FACETS	0.694	0.594	0.804	0.347	0.297	0.402	SUBCLONAL	1	TRUE	1	0.202268791448987	3		313	894	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	62	208	0	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.249301641203217	2		208	447	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55087020	55087020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180577495	NA	P-0003393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	12	141	0	ENST00000275493.2:c.50C>T	p.Ala17Val	p.A17V	ENST00000275493	NM_005228.3	17	gCg/gTg	1/28	1	2	FACETS	0.465	0.327	0.635	0.465	0.327	0.635	SUBCLONAL	1	TRUE	1	0.249301641203217	2		141	207	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111524	8111524	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	59	227	0	ENST00000346208.3:c.1010T>A	p.Val337Asp	p.V337D	ENST00000346208		337	gTc/gAc	5/6	1	2	FACETS	0.857	0.738	0.987	0.857	0.738	0.987	CLONAL	1	TRUE	1	0.249301641203217	2		227	552	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884997	111884997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	71	384	0	ENST00000341259.2:c.995G>A	p.Arg332Lys	p.R332K	ENST00000341259	NM_005475.2	332	aGg/aAg	5/8	1	2	FACETS	0.805	0.702	0.916	0.805	0.702	0.916	CLONAL	1	TRUE	1	0.249301641203217	2		384	708	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063679	67063679	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	31	166	0	ENST00000412916.2:c.128G>C	p.Arg43Pro	p.R43P	ENST00000412916		43	cGc/cCc	2/6	0.249301641203217	1	FACETS	0.844	0.686	1	0.844	0.686	1	CLONAL	1	TRUE	0	0.249301641203217	1		166	258	SUCCESS
APC	324	MSKCC	GRCh37	5	112175118	112175118	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1060503299	NA	P-0003397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	19	173	0	ENST00000257430.4:c.3827C>A	p.Ser1276Ter	p.S1276*	ENST00000257430	NM_000038.5	1276	tCa/tAa	16/16	1	2	FACETS	0.874	0.663	1	0.874	0.663	1	CLONAL	1	TRUE	1	0.15	2		173	290	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157519961	157519961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554234953	NA	P-0003397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	55	347	0	ENST00000346085.5:c.4030C>T	p.Gln1344Ter	p.Q1344*	ENST00000346085	NM_020732.3	1344	Cag/Tag	17/20	0.103055645948947	3	FACETS	1	0.951	1	0.641	0.548	0.743	CLONAL	1	TRUE	1	0.15	3		347	615	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920449	114920449	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	47	477	0	ENST00000543371.1:c.1390A>G	p.Arg464Gly	p.R464G	ENST00000543371	NM_001198531.1	464	Agg/Ggg	13/14	1	2	FACETS	0.716	0.602	0.843	0.716	0.602	0.843	SUBCLONAL	1	TRUE	1	0.15	2		477	875	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5081862	5081862	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	111	195	0	ENST00000381652.3:c.2571+1G>A		p.X857_splice	ENST00000381652	NM_004972.3	857			1	2	FACETS	0.955	0.873	1	0.955	0.873	1	CLONAL	1	TRUE	1	0.867669334269415	2		195	268	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563482	87563482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194954580	NA	P-0003405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	139	297	0	ENST00000277120.3:c.1870G>A	p.Val624Met	p.V624M	ENST00000277120		624	Gtg/Atg	16/19	1	2	FACETS	0.959	0.886	1	0.959	0.886	1	CLONAL	1	TRUE	1	0.867669334269415	2		297	334	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514891	44514891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1392951313	NA	P-0003405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	168	295	0	ENST00000291552.4:c.356G>A	p.Arg119His	p.R119H	ENST00000291552	NM_006758.2	119	cGt/cAt	6/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.867669334269415	2		295	372	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63810726	63810743	+	inframe_deletion	In_Frame_Del	DEL	CAACAACAATTCCGATGG	CAACAACAATTCCGATGG	-	novel	NA	P-0003414-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	52	475	0	ENST00000279873.7:c.816_833del	p.Asn272_Gly277del	p.N272_G277del	ENST00000279873	NM_032199.2	271	tcCAACAACAATTCCGATGGc/tcc	5/10	0.338338959617109	4	FACETS	0.735	0.626	0.855			1	SUBCLONAL	1	TRUE	NA	0.348967151589082	4		475	547	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416575	29416575	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	35	307	0	ENST00000389048.3:c.4378G>C	p.Glu1460Gln	p.E1460Q	ENST00000389048	NM_004304.4	1460	Gag/Cag	29/29	0.267437987524371	2	FACETS	0.563	0.465	0.673	0.282	0.232	0.337	INDETERMINATE	1	TRUE	0	0.519881658738531	2		307	239	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182514	99182514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	10	332	0	ENST00000074304.5:c.2317C>T	p.Pro773Ser	p.P773S	ENST00000074304	NM_001134224.1	773	Cct/Tct	22/26	0.519881658738531	3	FACETS	0.255	0.173	0.359	0.128	0.086	0.18	SUBCLONAL	1	TRUE	1	0.519881658738531	3		332	190	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168608	32168608	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs184540431	NA	P-0003415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	20	237	1	ENST00000375023.3:c.4315G>A	p.Ala1439Thr	p.A1439T	ENST00000375023	NM_004557.3	1439	Gca/Aca	23/30	0.483105954181491	4	FACETS	0.692	0.533	0.876	0.346	0.266	0.438	SUBCLONAL	1	TRUE	2	0.519881658738531	4		238	169	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857475	9857475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	65	296	0	ENST00000330684.3:c.3926G>A	p.Arg1309Gln	p.R1309Q	ENST00000330684	NM_001134407.1	1309	cGg/cAg	13/13	0.342842554186118	4	FACETS	0.83	0.729	0.935	0.83	0.729	0.935	CLONAL	2	TRUE	2	0.519881658738531	4		296	229	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945714	17945714	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	16	366	0	ENST00000458235.1:c.2146T>C	p.Trp716Arg	p.W716R	ENST00000458235	NM_000215.3	716	Tgg/Cgg	16/24	0.257417659347229	3	FACETS	0.354	0.262	0.464			1	INDETERMINATE	1	TRUE	NA	0.519881658738531	3		366	219	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650523	48650523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	67	525	0	ENST00000376670.3:c.493G>A	p.Gly165Ser	p.G165S	ENST00000376670	NM_002049.3	165	Ggc/Agc	3/6	0.442612984048221	1	FACETS	0.963	0.852	1	0.963	0.852	1	CLONAL	1	TRUE	0	0.519881658738531	1		525	198	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525050	9525050	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	72	397	0	ENST00000353224.5:c.1835del	p.Pro612LeufsTer3	p.P612Lfs*3	ENST00000353224	NM_177990.2	612	cCt/ct	8/10	0.41836919558738	4	FACETS	1	0.95	1	0.578	0.508	0.653	CLONAL	1	TRUE	2	0.519881658738531	4		397	364	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0003424-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	300	339	0	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	0.476111836977432	2	FACETS	0.988	0.951	1	1	0.996	1	CLONAL	3	TRUE	0	0.476111836977432	2		339	425	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814303	76814306	+	frameshift_variant	Frame_Shift_Del	DEL	ATAA	ATAA	-	novel	NA	P-0003424-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	187	461	0	ENST00000373344.5:c.6338_6341del	p.Phe2113SerfsTer9	p.F2113Sfs*9	ENST00000373344	NM_000489.3	2113	tTTATc/tc	29/35	0.476111836977432	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.476111836977432	1		461	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0003432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	59	371	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.486898764183138	2	FACETS	0.813	0.719	0.908	0.813	0.719	0.908	CLONAL	2	TRUE	0	0.526187136833815	2		371	138	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272482	142272482	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	70	521	0	ENST00000350721.4:c.2633G>A	p.Arg878Lys	p.R878K	ENST00000350721	NM_001184.3	878	aGg/aAg	12/47	0.356150465902369	5	FACETS	1	0.917	1	0.696	0.616	0.78	CLONAL	2	TRUE	2	0.526187136833815	5		521	228	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0003432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	33	109	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.511806151926665	3	FACETS	0.9	0.758	1	0.9	0.758	1	CLONAL	2	TRUE	1	0.526187136833815	3		109	88	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572593	64572593	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	65	397	2	ENST00000312049.6:c.1263C>A	p.Cys421Ter	p.C421*	ENST00000312049	NM_130799.2	421	tgC/tgA	9/10	0.432935397715081	2	FACETS	0.98	0.88	1	0.98	0.88	1	CLONAL	2	TRUE	0	0.526187136833815	2		399	126	SUCCESS
AR	367	MSKCC	GRCh37	X	66765779	66765779	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	23	302	0	ENST00000374690.3:c.791G>A	p.Arg264Gln	p.R264Q	ENST00000374690	NM_000044.3	264	cGg/cAg	1/8	0.368397165902	2	FACETS	1	0.865	1			1	CLONAL	1	TRUE	NA	0.526187136833815	2		302	79	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579716	7579716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1192416464	NA	P-0003468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	351	349	0	ENST00000269305.4:c.80del	p.Pro27LeufsTer17	p.P27Lfs*17	ENST00000269305	NM_001126112.2	27	cCt/ct	3/11	0.94799220896102	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.967334706117891	1		349	360	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508038	106508038	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1273593548	NA	P-0003468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	87	143	0	ENST00000359195.3:c.32T>G	p.Val11Gly	p.V11G	ENST00000359195	NM_002649.2	11	gTg/gGg	2/11	1	2	FACETS	0.504	0.449	0.561	0.504	0.449	0.561	SUBCLONAL	1	TRUE	1	0.967334706117891	2		143	357	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914070	32914070	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs431825332	NA	P-0003468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	266	555	4	ENST00000380152.3:c.5578A>T	p.Lys1860Ter	p.K1860*	ENST00000380152		1860	Aaa/Taa	11/27	0.720464155642869	0	FACETS		NA	1			1	NA	1	TRUE	0	0.967334706117891	0		559	290	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420308	88420308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367985043	NA	P-0003468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	258	255	0	ENST00000360948.2:c.2378G>A	p.Arg793Gln	p.R793Q	ENST00000360948	NM_001012338.2	793	cGa/cAa	19/19	0.967334706117891	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.967334706117891	1		255	265	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265017	46265019	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0003468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	236	491	0	ENST00000371998.3:c.1890_1892del	p.Asp631del	p.D631del	ENST00000371998		629	tcTGAt/tct	12/23	1	2	FACETS	0.492	0.459	0.526	0.492	0.459	0.526	SUBCLONAL	1	TRUE	1	0.967334706117891	2		491	992	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579716	7579716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1192416464	NA	P-0003468-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	218	349	0	ENST00000269305.4:c.80del	p.Pro27LeufsTer17	p.P27Lfs*17	ENST00000269305	NM_001126112.2	27	cCt/ct	3/11	0.816973726978343	1	FACETS	0.998	0.953	1	0.998	0.953	1	CLONAL	1	TRUE	0	0.82530552964366	1		349	311	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508038	106508038	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1273593548	NA	P-0003468-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	78	143	0	ENST00000359195.3:c.32T>G	p.Val11Gly	p.V11G	ENST00000359195	NM_002649.2	11	gTg/gGg	2/11	1	2	FACETS	0.463	0.409	0.521	0.463	0.409	0.521	SUBCLONAL	1	TRUE	1	0.82530552964366	2		143	408	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914070	32914070	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs431825332	NA	P-0003468-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	105	555	4	ENST00000380152.3:c.5578A>T	p.Lys1860Ter	p.K1860*	ENST00000380152		1860	Aaa/Taa	11/27	0.677537112409824	0	FACETS		NA	1			1	NA	1	TRUE	0	0.82530552964366	0		559	191	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420308	88420308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367985043	NA	P-0003468-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	185	255	0	ENST00000360948.2:c.2378G>A	p.Arg793Gln	p.R793Q	ENST00000360948	NM_001012338.2	793	cGa/cAa	19/19	0.82530552964366	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.82530552964366	1		255	235	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265017	46265019	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0003468-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	82	491	0	ENST00000371998.3:c.1890_1892del	p.Asp631del	p.D631del	ENST00000371998		629	tcTGAt/tct	12/23	NA	2	FACETS	0.445	0.393	0.499			1	INDETERMINATE	1	TRUE	NA	0.82530552964366	2		491	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0003477-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	150	203	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.624232699309016	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.658412201728859	1		203	300	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268338	142268338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003477-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	91	208	0	ENST00000350721.4:c.3154G>A	p.Ala1052Thr	p.A1052T	ENST00000350721	NM_001184.3	1052	Gcc/Acc	15/47	1	2	FACETS	0.464	0.412	0.519	0.464	0.412	0.519	SUBCLONAL	1	TRUE	1	0.658412201728859	2		208	596	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762412	41762412	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003477-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	34	417	0	ENST00000301178.4:c.2092T>C	p.Tyr698His	p.Y698H	ENST00000301178	NM_021913.4	698	Tac/Cac	18/20	1	2	FACETS	0.152	0.123	0.184	0.152	0.123	0.184	SUBCLONAL	1	TRUE	1	0.658412201728859	2		417	680	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524489	44524489	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003477-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	226	214	0	ENST00000291552.4:c.68A>G	p.Lys23Arg	p.K23R	ENST00000291552	NM_006758.2	23	aAa/aGa	2/8	0.300774580379494	3	FACETS	1	0.981	1	0.566	0.528	0.605	INDETERMINATE	1	TRUE	1	0.658412201728859	3		214	806	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627302	86627302	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003478-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	44	178	0	ENST00000274376.6:c.677T>C	p.Val226Ala	p.V226A	ENST00000274376	NM_002890.2	226	gTt/gCt	2/25	1	2	FACETS	0.285	0.239	0.336	0.285	0.239	0.336	SUBCLONAL	1	TRUE	1	0.605399799225121	2		178	510	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046029	180046029	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003478-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	43	96	0	ENST00000261937.6:c.2842C>T	p.Pro948Ser	p.P948S	ENST00000261937	NM_182925.4	948	Ccc/Tcc	20/30	1	2	FACETS	0.899	0.766	1	0.899	0.766	1	CLONAL	1	TRUE	1	0.605399799225121	2		96	158	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069315	30069315	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	191	315	0	ENST00000338641.4:c.1180G>T	p.Glu394Ter	p.E394*	ENST00000338641	NM_000268.3	394	Gag/Tag	12/16	0.287439453616822	1	FACETS	0.983	0.911	1	0.983	0.911	1	CLONAL	1	TRUE	0	0.402104685006977	1		315	772	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444926	49444926	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	46	83	0	ENST00000301067.7:c.2540A>C	p.Glu847Ala	p.E847A	ENST00000301067	NM_003482.3	847	gAg/gCg	10/54	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.402104685006977	2		83	227	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003213	42003213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1209	317	628	0	ENST00000219905.7:c.2750C>T	p.Ser917Phe	p.S917F	ENST00000219905	NM_001164273.1	917	tCc/tTc	8/24	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.402104685006977	2		628	1526	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439722	49439722	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	193	401	0	ENST00000301067.7:c.4722del	p.Met1575Ter	p.M1575*	ENST00000301067	NM_003482.3	1574	ccC/cc	18/54	0.347722793907708	1	FACETS	0.74	0.684	0.798	0.74	0.684	0.798	SUBCLONAL	1	TRUE	0	0.402104685006977	1		401	1037	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577507	+	missense_variant	Missense_Mutation	DNP	CT	CT	GA	novel	NA	P-0003487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	149	221	0	ENST00000269305.4:c.774_775delinsTC	p.Glu258_Asp259delinsAspHis	p.E258_D259delinsDH	ENST00000269305	NM_001126112.2	258	gaAGac/gaTCac	7/11	0.343262059388745	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.402104685006977	1		221	521	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496970	29496970	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs753529924	NA	P-0003490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	167	260	0	ENST00000356175.3:c.541C>T	p.Gln181Ter	p.Q181*	ENST00000356175	NM_000267.3	181	Cag/Tag	5/57	0.569541717144026	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.569541717144026	1		260	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782144	NA	P-0003511-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	158	418	0	ENST00000269305.4:c.473G>C	p.Arg158Pro	p.R158P	ENST00000269305	NM_001126112.2	158	cGc/cCc	5/11	NA	2	FACETS	1	0.937	1			1	INDETERMINATE	2	FALSE	NA	0.317962932059238	2		418	489	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923210	26923210	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0003511-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	81	395	0	ENST00000381527.3:c.206T>G	p.Leu69Ter	p.L69*	ENST00000381527	NM_001260.1	69	tTa/tGa	3/13	0.317962932059238	3	FACETS	0.978	0.87	1	0.978	0.87	1	CLONAL	2	FALSE	1	0.317962932059238	3		395	302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs587781433	NA	P-0003539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	147	297	0	ENST00000269305.4:c.766A>C	p.Thr256Pro	p.T256P	ENST00000269305	NM_001126112.2	256	Aca/Cca	7/11	0.453405113390654	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.453405113390654	2		297	317	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721622	49721622	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs200268600	NA	P-0003539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	10	25	0	ENST00000449682.2:c.2017G>A	p.Gly673Ser	p.G673S	ENST00000449682	NM_020998.3	673	Ggt/Agt	18/18	1	2	FACETS	1	0.83	1	1	0.83	1	CLONAL	1	TRUE	1	0.453405113390654	2		25	34	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1040474	1040474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	79	387	0	ENST00000358495.3:c.98C>T	p.Ala33Val	p.A33V	ENST00000358495	NM_134424.2	33	gCa/gTa	3/12	0.453405113390654	7	FACETS	0.663	0.581	0.752	0.111	0.096	0.126	SUBCLONAL	1	TRUE	1	0.453405113390654	7		387	1121	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441768	49441827	+	frameshift_variant	Frame_Shift_Del	DEL	GGTGATAGCACTGAGAGCACTGCGAACAGGCAAGGAGGTGGCCCTCTGCCCCCCGGCCAA	GGTGATAGCACTGAGAGCACTGCGAACAGGCAAGGAGGTGGCCCTCTGCCCCCCGGCCAA	TG	novel	NA	P-0003539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	97	488	1	ENST00000301067.7:c.4157_4216delinsCA	p.Phe1386SerfsTer12	p.F1386Sfs*12	ENST00000301067	NM_003482.3	1386	tTTGGCCGGGGGGCAGAGGGCCACCTCCTTGCCTGTTCGCAGTGCTCTCAGTGCTATCACCct/tCAct	14/54	0.454095577727501	3	FACETS	0.782	0.698	0.872	0.391	0.349	0.436	SUBCLONAL	1	TRUE	1	0.453405113390654	3		489	671	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0003558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	165	454	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	0.993	1	CLONAL	2	TRUE	1	0.306997966822639	2		454	471	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604790	48604790	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1568211615	NA	P-0003558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	80	398	0	ENST00000342988.3:c.1612G>T	p.Glu538Ter	p.E538*	ENST00000342988	NM_005359.5	538	Gaa/Taa	12/12	0.306997966822639	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.306997966822639	1		398	303	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106763	27106763	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	64	375	0	ENST00000324856.7:c.6374T>G	p.Leu2125Arg	p.L2125R	ENST00000324856	NM_006015.4	2125	cTc/cGc	20/20	1	2	FACETS	0.906	0.796	1	1	0.979	1	CLONAL	2	TRUE	1	0.306997966822639	2		375	230	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964083	28964083	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	79	472	0	ENST00000282397.4:c.1819C>A	p.Gln607Lys	p.Q607K	ENST00000282397	NM_002019.4	607	Caa/Aaa	13/30	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.306997966822639	2		472	366	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434958	49434958	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs398123753	NA	P-0003558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	20	179	0	ENST00000301067.7:c.6595del	p.Tyr2199IlefsTer65	p.Y2199Ifs*65	ENST00000301067	NM_003482.3	2199	Tat/at	31/54	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.306997966822639	2		179	100	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888189	112888189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507511	NA	P-0121515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	63	445	0	ENST00000351677.2:c.205G>A	p.Glu69Lys	p.E69K	ENST00000351677	NM_002834.3	69	Gag/Aag	3/16	1	2	FACETS	1	0.92	1	1	0.985	1	CLONAL	3	NA	1	0.186313813750166	2		445	212	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0003573-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	203	335	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.381312663060603	4	FACETS	0.983	0.914	1	0.983	0.914	1	CLONAL	2	TRUE	2	0.392341610393251	4		335	733	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201856	152201856	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003573-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	104	374	0	ENST00000206249.3:c.710G>A	p.Cys237Tyr	p.C237Y	ENST00000206249	NM_000125.3	237	tGc/tAc	3/8	1	2	FACETS	0.998	0.897	1	0.998	0.897	1	CLONAL	1	TRUE	1	0.392341610393251	2		374	531	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030398	49030398	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003573-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	125	322	1	ENST00000267163.4:c.1873A>G	p.Thr625Ala	p.T625A	ENST00000267163	NM_000321.2	625	Act/Gct	19/27	0.267693788205632	3	FACETS	1	0.936	1	0.521	0.471	0.572	CLONAL	1	TRUE	1	0.392341610393251	3		323	732	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3113463	3113463	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003573-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	79	375	0	ENST00000078429.4:c.457C>G	p.Leu153Val	p.L153V	ENST00000078429	NM_002067.2	153	Ctc/Gtc	3/7	0.230014562915404	1	FACETS	0.556	0.49	0.628	0.556	0.49	0.628	INDETERMINATE	1	TRUE	0	0.392341610393251	1		375	582	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0003591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	33	382	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.110025724504325	1	FACETS	0.487	0.399	0.585	0.487	0.399	0.585	INDETERMINATE	1	TRUE	0	0.440408999215633	1		382	240	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480304	89480304	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1368854829	NA	P-0003591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	39	369	0	ENST00000336596.2:c.2141A>G	p.His714Arg	p.H714R	ENST00000336596	NM_005233.5	714	cAc/cGc	13/17	0.345520187347357	4	FACETS	0.955	0.797	1			1	CLONAL	1	TRUE	NA	0.440408999215633	4		369	267	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350407	89350407	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	46	902	0	ENST00000301030.4:c.2543C>T	p.Ser848Leu	p.S848L	ENST00000301030	NM_001256183.1	848	tCa/tTa	9/13	0.430767700749529	0	FACETS	0.46	0.39	0.536			1	SUBCLONAL	1	TRUE	0	0.440408999215633	0		902	254	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351394	89351394	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	60	737	0	ENST00000301030.4:c.1556C>G	p.Ser519Cys	p.S519C	ENST00000301030	NM_001256183.1	519	tCt/tGt	9/13	0.430767700749529	0	FACETS	0.709	0.62	0.803			1	SUBCLONAL	1	TRUE	0	0.440408999215633	0		737	215	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003592-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	112	536	1	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	0.411129925121017	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.411129925121017	1		537	392	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470497	25470497	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs758881009	NA	P-0003592-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	50	480	0	ENST00000264709.3:c.977G>T	p.Arg326Leu	p.R326L	ENST00000264709	NM_175629.2	326	cGc/cTc	8/23	0.374592453974239	3	FACETS	0.516	0.438	0.603	0.258	0.219	0.302	SUBCLONAL	1	TRUE	1	0.411129925121017	3		480	568	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349988	70349988	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003592-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	278	277	0	ENST00000374080.3:c.3971T>A	p.Ile1324Asn	p.I1324N	ENST00000374080		1324	aTt/aAt	28/45	0.371031397611215	2	FACETS	1	0.961	1			1	CLONAL	3	TRUE	NA	0.411129925121017	2		277	448	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	164	228	1	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	0.93	0.86	1	0.93	0.86	1	CLONAL	1	TRUE	1	0.712784833808939	2		229	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0003599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	356	303	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.712784833808939	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	0	0.712784833808939	3		304	448	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0003599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	309	246	1	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	0.712784833808939	3	FACETS	0.993	0.947	1	0.993	0.947	1	CLONAL	2	TRUE	1	0.712784833808939	3		247	592	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589584	67589613	+	inframe_deletion	In_Frame_Del	DEL	ACATGAATATAACACTCAGTTTCAAGAAAA	ACATGAATATAACACTCAGTTTCAAGAAAA	-	novel	NA	P-0003599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	147	280	0	ENST00000274335.5:c.1348_1377del	p.His450_Lys459del	p.H450_K459del	ENST00000274335		449	ttACATGAATATAACACTCAGTTTCAAGAAAAa/tta	10/15	1	2	FACETS	0.778	0.715	0.844	0.778	0.715	0.844	SUBCLONAL	1	TRUE	1	0.712784833808939	2		280	530	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949720	151949720	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	84	480	2	ENST00000262189.6:c.1380C>A	p.Tyr460Ter	p.Y460*	ENST00000262189	NM_170606.2	460	taC/taA	10/59	0.212549913766679	5	FACETS	1	0.894	1	0.668	0.596	0.743	INDETERMINATE	2	TRUE	2	0.473101519516356	5		482	303	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118831	115118831	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	34	413	0	ENST00000257566.3:c.510G>T	p.Trp170Cys	p.W170C	ENST00000257566	NM_016569.3	170	tgG/tgT	2/8	NA	2	FACETS	0.423	0.346	0.509			1	INDETERMINATE	1	TRUE	NA	0.473101519516356	2		413	340	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564567	41564568	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0003601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	57	428	0	ENST00000263253.7:c.3990_3991del	p.Asp1330GlufsTer34	p.D1330Efs*34	ENST00000263253	NM_001429.3	1330	gAC/g	24/31	0.430007797201638	1	FACETS	0.708	0.613	0.809	0.708	0.613	0.809	SUBCLONAL	1	TRUE	0	0.473101519516356	1		428	260	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564459	41564469	+	frameshift_variant	Frame_Shift_Del	DEL	CATCTACCAGA	CATCTACCAGA	-	novel	NA	P-0003601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	34	337	0	ENST00000263253.7:c.3882_3892del	p.Ser1295TrpfsTer10	p.S1295Wfs*10	ENST00000263253	NM_001429.3	1294	cCATCTACCAGA/c	24/31	0.430007797201638	1	FACETS	0.427	0.35	0.512	0.427	0.35	0.512	SUBCLONAL	1	TRUE	0	0.473101519516356	1		337	257	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86686617	86686617	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	123	261	0	ENST00000274376.6:c.3061C>T	p.His1021Tyr	p.H1021Y	ENST00000274376	NM_002890.2	1021	Cac/Tac	25/25	1	2	FACETS	0.908	0.822	0.999	0.908	0.822	0.999	CLONAL	1	TRUE	1	0.349051577207948	2		261	776	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741936	17741936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	11	44	0	ENST00000250003.3:c.607C>T	p.Arg203Cys	p.R203C	ENST00000250003	NM_002478.4	203	Cgc/Tgc	1/3	0.349051577207948	1	FACETS	0.46	0.32	0.632	0.46	0.32	0.632	SUBCLONAL	1	TRUE	0	0.349051577207948	1		44	113	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0003611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	92	409	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.392596248488935	1	FACETS	0.86	0.768	0.957	0.86	0.768	0.957	CLONAL	1	TRUE	0	0.392596248488935	1		409	438	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430533	181430533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1366316849	NA	P-0003611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	85	260	0	ENST00000325404.1:c.385G>A	p.Gly129Ser	p.G129S	ENST00000325404	NM_003106.3	129	Ggc/Agc	1/1	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.392596248488935	2		260	433	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671830	30671830	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	81	341	0	ENST00000376406.3:c.5130T>G	p.Ile1710Met	p.I1710M	ENST00000376406	NM_014641.2	1710	atT/atG	10/15	0.222094924786686	4	FACETS	0.762	0.671	0.86	0.381	0.335	0.43	INDETERMINATE	1	TRUE	2	0.392596248488935	4		341	754	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741459	17741459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866461266	NA	P-0003611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	107	368	0	ENST00000250003.3:c.130G>A	p.Glu44Lys	p.E44K	ENST00000250003	NM_002478.4	44	Gaa/Aaa	1/3	1	2	FACETS	0.883	0.794	0.978	0.883	0.794	0.978	CLONAL	1	TRUE	1	0.392596248488935	2		368	617	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098419	108098419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587779858	NA	P-0003611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	80	199	0	ENST00000278616.4:c.68G>A	p.Arg23Gln	p.R23Q	ENST00000278616	NM_000051.3	23	cGa/cAa	2/63	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.392596248488935	2		199	340	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56798140	56798140	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	98	405	0	ENST00000337432.4:c.871G>T	p.Asp291Tyr	p.D291Y	ENST00000337432	NM_058216.2	291	Gat/Tat	6/9	0.392596248488935	1	FACETS	0.708	0.633	0.787	0.708	0.633	0.787	SUBCLONAL	1	TRUE	0	0.392596248488935	1		405	567	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523285	9523285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767541766	NA	P-0003611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	105	394	0	ENST00000353224.5:c.1952C>T	p.Ala651Val	p.A651V	ENST00000353224	NM_177990.2	651	gCg/gTg	9/10	1	2	FACETS	0.75	0.672	0.833	0.75	0.672	0.833	SUBCLONAL	1	TRUE	1	0.392596248488935	2		394	713	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852482	42852482	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	124	361	0	ENST00000398585.3:c.604A>T	p.Arg202Trp	p.R202W	ENST00000398585	NM_001135099.1	202	Agg/Tgg	6/14	1	2	FACETS	0.87	0.788	0.956	0.87	0.788	0.956	CLONAL	1	TRUE	1	0.392596248488935	2		361	726	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974769	21974772	+	frameshift_variant	Frame_Shift_Del	DEL	CGGC	CGGC	-	novel	NA	P-0003611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	55	170	0	ENST00000304494.5:c.55_58del	p.Ala19ArgfsTer6	p.A19Rfs*6	ENST00000304494	NM_000077.4	19	GCCGcg/cg	1/3	0.392596248488935	1	FACETS	0.894	0.772	1	0.894	0.772	1	CLONAL	1	TRUE	0	0.392596248488935	1		170	252	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380276	+	missense_variant	Missense_Mutation	DNP	TT	TT	GC	novel	NA	P-0003611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	104	323	0	ENST00000311936.3:c.182_183delinsGC	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAA/cGC	3/5	1	2	FACETS	0.79	0.708	0.876	0.79	0.708	0.876	SUBCLONAL	1	TRUE	1	0.392596248488935	2		323	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0003630-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	60	298	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.838	0.724	0.96	1	0.974	1	CLONAL	2	TRUE	1	0.18	2		298	398	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438139	110438139	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003630-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	21	137	0	ENST00000375856.3:c.262G>A	p.Ala88Thr	p.A88T	ENST00000375856	NM_003749.2	88	Gcg/Acg	1/2	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.18	2		137	187	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286558	33286558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003644-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	38	224	0	ENST00000374542.5:c.2185G>A	p.Asp729Asn	p.D729N	ENST00000374542	NM_001141970.1	729	Gat/Aat	8/8	1	2	FACETS	0.632	0.522	0.755	0.632	0.522	0.755	SUBCLONAL	1	TRUE	1	0.254627004193137	2		224	472	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151216551	151216551	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003644-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	32	228	0	ENST00000262187.5:c.47C>T	p.Ser16Phe	p.S16F	ENST00000262187	NM_005614.3	16	tCt/tTt	1/8	0.254627004193137	3	FACETS	0.723	0.587	0.876	0.361	0.293	0.438	SUBCLONAL	1	TRUE	1	0.254627004193137	3		228	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577115	7577115	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519983	NA	P-0003647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	412	408	0	ENST00000269305.4:c.823T>C	p.Cys275Arg	p.C275R	ENST00000269305	NM_001126112.2	275	Tgt/Cgt	8/11	NA	2	FACETS	0.95	0.916	0.984			1	INDETERMINATE	2	TRUE	NA	0.657840875397925	2		408	659	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520000	106520000	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs759433704	NA	P-0003647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	160	316	0	ENST00000359195.3:c.2428C>A	p.Pro810Thr	p.P810T	ENST00000359195	NM_002649.2	810	Cca/Aca	6/11	0.657840875397925	3	FACETS	0.658	0.602	0.715	0.329	0.301	0.358	SUBCLONAL	1	TRUE	1	0.657840875397925	3		316	983	SUCCESS
ATR	545	MSKCC	GRCh37	3	142297540	142297540	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	157	294	0	ENST00000350721.4:c.7G>C	p.Glu3Gln	p.E3Q	ENST00000350721	NM_001184.3	3	Gaa/Caa	1/47	0.471085579636882	3	FACETS	1	0.982	1	0.611	0.563	0.66	CLONAL	1	TRUE	1	0.657840875397925	3		294	519	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968266	2968266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773909937	NA	P-0003647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	145	324	1	ENST00000396946.4:c.1720G>A	p.Val574Ile	p.V574I	ENST00000396946	NM_032415.4	574	Gtc/Atc	13/25	0.415219727626141	4	FACETS	0.903	0.825	0.986			1	CLONAL	1	TRUE	NA	0.657840875397925	4		325	809	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868976	117868976	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1579	185	398	0	ENST00000297338.2:c.723C>G	p.Ile241Met	p.I241M	ENST00000297338	NM_006265.2	241	atC/atG	7/14	0.657840875397925	8	FACETS	0.948	0.872	1			1	CLONAL	1	TRUE	NA	0.657840875397925	8		398	1764	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955156	17955156	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	271	226	0	ENST00000458235.1:c.71G>C	p.Gly24Ala	p.G24A	ENST00000458235	NM_000215.3	24	gGt/gCt	2/24	0.556301969577636	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	2	0.657840875397925	4		226	659	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795338	39795338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	258	282	0	ENST00000288319.7:c.382C>T	p.Pro128Ser	p.P128S	ENST00000288319	NM_182918.3	128	Cca/Tca	3/10	0.657840875397925	5	FACETS	1	0.99	1	0.812	0.765	0.858	CLONAL	2	TRUE	2	0.657840875397925	5		282	640	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548249	41548249	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	158	244	0	ENST00000263253.7:c.3037G>C	p.Glu1013Gln	p.E1013Q	ENST00000263253	NM_001429.3	1013	Gaa/Caa	16/31	0.459437759106507	5	FACETS	1	0.972	1			1	CLONAL	1	TRUE	NA	0.657840875397925	5		244	838	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239597	53239597	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	117	306	0	ENST00000375401.3:c.1745C>T	p.Pro582Leu	p.P582L	ENST00000375401	NM_004187.3	582	cCa/cTa	12/26	0.467460085105669	4	FACETS	0.683	0.616	0.755			1	SUBCLONAL	1	TRUE	NA	0.657840875397925	4		306	863	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944769	31944812	+	frameshift_variant	Frame_Shift_Del	DEL	GCACACAGGTTAGTATCTTCCAACAGACCCACCAGGTACGCTTC	GCACACAGGTTAGTATCTTCCAACAGACCCACCAGGTACGCTTC	-	novel	NA	P-0003647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	138	190	0	ENST00000340398.3:c.289_332del	p.Glu97HisfsTer4	p.E97Hfs*4	ENST00000340398	NM_001013699.2	97	GAAGCGTACCTGGTGGGTCTGTTGGAAGATACTAACCTGTGTGCc/c	1/1	0.657840875397925	3	FACETS	1	0.985	1	0.447	0.41	0.484	CLONAL	1	TRUE	0	0.657840875397925	3		190	416	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944819	31944820	+	missense_variant	Missense_Mutation	DNP	CT	CT	TA	novel	NA	P-0003647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	146	443	0	ENST00000340398.3:c.281_282delinsTA	p.Glu94Val	p.E94V	ENST00000340398	NM_001013699.2	94	gAG/gTA	1/1	0.657840875397925	3	FACETS	0.736	0.673	0.803	0.245	0.224	0.268	SUBCLONAL	1	TRUE	0	0.657840875397925	3		443	801	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074231	8074231	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	92	479	0	ENST00000377482.5:c.428C>A	p.Ala143Asp	p.A143D	ENST00000377482	NM_018948.3	143	gCc/gAc	4/4	NA	2	FACETS	1	0.945	1			1	INDETERMINATE	1	TRUE	NA	0.190716939361959	2		479	870	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085678	16085678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747134309	NA	P-0003672-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	116	362	0	ENST00000281043.3:c.854G>A	p.Arg285Gln	p.R285Q	ENST00000281043	NM_005378.4	285	cGg/cAg	3/3	NA	2	FACETS	0.818	0.742	0.898			1	INDETERMINATE	1	TRUE	NA	0.604519763742021	2		362	469	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922340	178922340	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003672-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	131	353	0	ENST00000263967.3:c.1109A>G	p.Asn370Ser	p.N370S	ENST00000263967	NM_006218.2	370	aAt/aGt	6/21	1	2	FACETS	0.719	0.654	0.786	0.719	0.654	0.786	SUBCLONAL	1	TRUE	1	0.604519763742021	2		353	603	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438526	49438526	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003672-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	112	331	0	ENST00000301067.7:c.4963+1G>A		p.X1655_splice	ENST00000301067	NM_003482.3	1655			1	2	FACETS	0.94	0.853	1	0.94	0.853	1	CLONAL	1	TRUE	1	0.604519763742021	2		331	394	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060694	38060694	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003672-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	162	467	1	ENST00000250448.2:c.1295C>T	p.Thr432Met	p.T432M	ENST00000250448	NM_004496.3	432	aCg/aTg	2/2	0.604519763742021	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.604519763742021	1		468	368	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052726	42052726	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003672-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	161	388	0	ENST00000219905.7:c.7397G>C	p.Arg2466Pro	p.R2466P	ENST00000219905	NM_001164273.1	2466	cGa/cCa	20/24	NA	2	FACETS	0.992	0.916	1			1	INDETERMINATE	1	TRUE	NA	0.604519763742021	2		388	537	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050644	30050644	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0003672-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	101	310	0	ENST00000338641.4:c.448-2A>G		p.X150_splice	ENST00000338641	NM_000268.3	150			0.604519763742021	1	FACETS	0.788	0.713	0.864	0.788	0.713	0.864	SUBCLONAL	1	TRUE	0	0.604519763742021	1		310	296	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125250	47125278	+	frameshift_variant	Frame_Shift_Del	DEL	TCACTTATATCCACTGTTTTATCTGGCTG	TCACTTATATCCACTGTTTTATCTGGCTG	-	novel	NA	P-0003672-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	187	328	0	ENST00000409792.3:c.5992_6020del	p.Gln1998PhefsTer25	p.Q1998Ffs*25	ENST00000409792	NM_014159.6	1998	CAGCCAGATAAAACAGTGGATATAAGTGAt/t	12/21	1	2	FACETS	0.985	0.915	1	0.985	0.915	1	CLONAL	1	TRUE	1	0.604519763742021	2		328	628	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163800	47163803	+	frameshift_variant	Frame_Shift_Del	DEL	TAAC	TAAC	-	novel	NA	P-0003672-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	177	334	0	ENST00000409792.3:c.2323_2326del	p.Val775LysfsTer22	p.V775Kfs*22	ENST00000409792	NM_014159.6	775	GTTAaa/aa	3/21	1	2	FACETS	0.941	0.872	1	0.941	0.872	1	CLONAL	1	TRUE	1	0.604519763742021	2		334	622	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0003679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	44	329	0	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.32704905746659	4	FACETS	0.419	0.35	0.496			1	SUBCLONAL	1	TRUE	NA	0.338283263769281	4		329	830	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874639	35874639	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	45	280	0	ENST00000303115.3:c.795A>T	p.Lys265Asn	p.K265N	ENST00000303115	NM_002185.3	265	aaA/aaT	6/8	0.288567126943297	3	FACETS	0.513	0.431	0.605	0.257	0.215	0.303	SUBCLONAL	1	TRUE	1	0.338283263769281	3		280	606	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729972	41729972	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	79	465	0	ENST00000242208.4:c.557T>C	p.Leu186Ser	p.L186S	ENST00000242208	NM_002192.2	186	tTg/tCg	3/3	0.338283263769281	5	FACETS	0.667	0.585	0.756			1	SUBCLONAL	1	TRUE	NA	0.338283263769281	5		465	1055	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370827	55370827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	36	141	0	ENST00000297316.4:c.129G>T	p.Lys43Asn	p.K43N	ENST00000297316	NM_022454.3	43	aaG/aaT	1/2	0.338283263769281	4	FACETS	0.819	0.674	0.979	0.409	0.337	0.49	CLONAL	1	TRUE	2	0.338283263769281	4		141	348	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687597	29687597	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	78	308	0	ENST00000356175.3:c.8190T>G	p.Ser2730Arg	p.S2730R	ENST00000356175	NM_000267.3	2730	agT/agG	56/57	0.338283263769281	3	FACETS	0.756	0.664	0.855	0.378	0.332	0.428	SUBCLONAL	1	TRUE	1	0.338283263769281	3		308	713	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860421	42860421	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	67	285	0	ENST00000398585.3:c.456C>A	p.Asn152Lys	p.N152K	ENST00000398585	NM_001135099.1	152	aaC/aaA	5/14	0.338283263769281	3	FACETS	0.772	0.671	0.881	0.386	0.335	0.441	SUBCLONAL	1	TRUE	1	0.338283263769281	3		285	600	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340974	70340974	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	85	152	0	ENST00000374080.3:c.708del	p.Glu237ArgfsTer19	p.E237Rfs*19	ENST00000374080		236	aCc/ac	5/45	0.338283263769281	2	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.338283263769281	2		152	349	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134441	30134441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003695-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	17	477	0	ENST00000263025.4:c.90G>A	p.Met30Ile	p.M30I	ENST00000263025	NM_002746.2	30	atG/atA	1/9	1	2	FACETS	0.462	0.345	0.6	0.462	0.345	0.6	SUBCLONAL	1	TRUE	1	0.33	2		477	223	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831467	72831467	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0003695-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	32	610	0	ENST00000268489.5:c.5114C>G	p.Ser1705Ter	p.S1705*	ENST00000268489	NM_006885.3	1705	tCa/tGa	9/10	0.183392953281942	1	FACETS	0.42	0.34	0.509	0.42	0.34	0.509	INDETERMINATE	1	TRUE	0	0.33	1		610	386	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696431	47696431	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519969	NA	P-0003695-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	41	359	0	ENST00000347630.2:c.392G>C	p.Trp131Ser	p.W131S	ENST00000347630	NM_001007230.1	131	tGg/tCg	6/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.33	NA		359	337	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918713	44918713	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0003695-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	24	160	0	ENST00000377967.4:c.1194+2T>C		p.X398_splice	ENST00000377967	NM_021140.2	398			0.200916645346257	0	FACETS	0.672	0.533	0.829			1	SUBCLONAL	1	TRUE	NA	0.33	0		160	145	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873236	71873236	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	129	635	0	ENST00000357731.5:c.958T>G	p.Tyr320Asp	p.Y320D	ENST00000357731	NM_173808.2	320	Tat/Gat	7/7	1	2	FACETS	0.859	0.779	0.942	0.859	0.779	0.942	CLONAL	1	TRUE	1	0.396291162269502	2		635	758	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592280	29592300	+	inframe_deletion	In_Frame_Del	DEL	TTTGAAAACGTTAAGTATTTT	TTTGAAAACGTTAAGTATTTT	-	novel	NA	P-0003701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	84	440	0	ENST00000356175.3:c.4695_4715del	p.Leu1566_Phe1572del	p.L1566_F1572del	ENST00000356175	NM_000267.3	1565	gcTTTGAAAACGTTAAGTATTTTc/gcc	35/57	0.396291162269502	1	FACETS	0.85	0.755	0.95	0.85	0.755	0.95	CLONAL	1	TRUE	0	0.396291162269502	1		440	400	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0003733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	11	217	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		217	318	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0003733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	18	215	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		215	380	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058420	42058421	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0003733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	71	493	1	ENST00000219905.7:c.8140_8141delinsTT	p.Gly2714Phe	p.G2714F	ENST00000219905	NM_001164273.1	2714	GGt/TTt	24/24	0.3	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		494	907	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500868	149500868	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1320275282	NA	P-0003751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	198	216	1	ENST00000261799.4:c.2362C>T	p.Arg788Ter	p.R788*	ENST00000261799	NM_002609.3	788	Cga/Tga	17/23	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.740057563136679	2		217	514	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061450	38061450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	174	201	0	ENST00000250448.2:c.539C>T	p.Thr180Ile	p.T180I	ENST00000250448	NM_004496.3	180	aCc/aTc	2/2	1	2	FACETS	0.968	0.899	1	0.968	0.899	1	CLONAL	1	TRUE	1	0.740057563136679	2		201	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0003753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	53	400	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	1	2	FACETS	0.913	0.777	1	0.913	0.777	1	CLONAL	1	TRUE	1	0.15179713239111	2		400	765	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0003753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	13	348	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.15179713239111	1	FACETS	0.258	0.183	0.351	0.258	0.183	0.351	SUBCLONAL	1	TRUE	0	0.15179713239111	1		348	614	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0003753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	43	293	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	0.816	0.682	0.967	0.816	0.682	0.967	CLONAL	1	TRUE	1	0.15179713239111	2		293	694	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0003753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	21	165	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	1	2	FACETS	0.709	0.545	0.901	0.709	0.545	0.901	CLONAL	1	TRUE	1	0.15179713239111	2		165	390	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0003753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	27	326	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	1	2	FACETS	1	0.804	1	1	0.804	1	CLONAL	1	TRUE	1	0.15179713239111	2		326	352	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554630	63554630	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555583747	NA	P-0003753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	39	170	0	ENST00000307078.5:c.109C>T	p.Gln37Ter	p.Q37*	ENST00000307078	NM_004655.3	37	Cag/Tag	2/11	0.15179713239111	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.15179713239111	1		170	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578226	7578226	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1464727668	NA	P-0003761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	117	335	0	ENST00000269305.4:c.623A>T	p.Asp208Val	p.D208V	ENST00000269305	NM_001126112.2	208	gAc/gTc	6/11	0.225135297093479	2	FACETS	1	0.982	1	0.675	0.613	0.74	INDETERMINATE	1	TRUE	0	0.392997886231088	2		335	441	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0003778-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	171	470	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.626666226411432	3	FACETS	0.908	0.837	0.983	0.454	0.418	0.492	CLONAL	1	TRUE	1	0.626666226411432	3		470	789	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949126	151949126	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003778-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	204	347	0	ENST00000262189.6:c.1519C>T	p.Gln507Ter	p.Q507*	ENST00000262189	NM_170606.2	507	Cag/Tag	11/59	1	2	FACETS	0.991	0.924	1	0.991	0.924	1	CLONAL	1	TRUE	1	0.626666226411432	2		347	657	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653800	89653800	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003778-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	159	264	0	ENST00000371953.3:c.98T>G	p.Ile33Ser	p.I33S	ENST00000371953	NM_000314.4	33	aTt/aGt	2/9	0.522114102841747	1	FACETS	0.949	0.883	1	0.949	0.883	1	CLONAL	1	TRUE	0	0.626666226411432	1		264	367	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578480	7578488	+	inframe_deletion	In_Frame_Del	DEL	TGTGGAATC	TGTGGAATC	-	novel	NA	P-0003778-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	439	233	0	ENST00000269305.4:c.442_450del	p.Asp148_Thr150del	p.D148_T150del	ENST00000269305	NM_001126112.2	148	GATTCCACA/-	5/11	0.362469795378869	4	FACETS	0.967	0.939	0.995			1	INDETERMINATE	4	TRUE	NA	0.626666226411432	4		233	589	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0003787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	25	113	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.989	0.78	1	0.989	0.78	1	CLONAL	1	TRUE	1	0.16	2		113	316	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	31	168	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	0.784	0.633	0.956	0.784	0.633	0.956	CLONAL	1	TRUE	1	0.16	2		168	494	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155369	99155369	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs954252241	NA	P-0003787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	41	225	0	ENST00000074304.5:c.595G>A	p.Asp199Asn	p.D199N	ENST00000074304	NM_001134224.1	199	Gat/Aat	9/26	1	2	FACETS	0.972	0.809	1	0.972	0.809	1	CLONAL	1	TRUE	1	0.16	2		225	527	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982743	7982743	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764382022	NA	P-0003787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	33	208	0	ENST00000319144.4:c.1042G>C	p.Glu348Gln	p.E348Q	ENST00000319144	NM_001139.2	348	Gag/Cag	8/15	1	2	FACETS	0.783	0.636	0.948	0.783	0.636	0.948	CLONAL	1	TRUE	1	0.16	2		208	527	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266702	18266702	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	27	129	0	ENST00000222254.8:c.13G>A	p.Glu5Lys	p.E5K	ENST00000222254	NM_005027.3	5	Gag/Aag	2/16	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.16	2		129	277	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179197	123179197	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003794-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	62	401	0	ENST00000218089.9:c.646C>T	p.Arg216Ter	p.R216*	ENST00000218089	NM_001042749.1	216	Cga/Tga	8/35	0.500589057969068	2	FACETS	0.455	0.393	0.522	0.227	0.196	0.261	SUBCLONAL	1	TRUE	0	0.500589057969068	2		401	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0003794-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	483	348	0	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	0.502271739375328	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.500589057969068	3		348	767	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003794-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	219	228	1	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	0.502271739375328	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.500589057969068	2		229	394	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220130	133220130	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754518522	NA	P-0003794-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	27	301	0	ENST00000320574.5:c.4307G>A	p.Arg1436Gln	p.R1436Q	ENST00000320574	NM_006231.2	1436	cGg/cAg	34/49	0.502271739375328	1	FACETS	0.23	0.183	0.284	0.23	0.183	0.284	SUBCLONAL	1	TRUE	0	0.500589057969068	1		301	351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0003819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	304	161	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	0.545623279223133	3	FACETS	0.908	0.868	0.948	0.908	0.868	0.948	CLONAL	3	TRUE	0	0.557217979071806	3		161	512	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289234	33289234	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	80	210	0	ENST00000374542.5:c.318C>A	p.Cys106Ter	p.C106*	ENST00000374542	NM_001141970.1	106	tgC/tgA	3/8	0.250104988097375	5	FACETS	0.723	0.636	0.817	0.241	0.212	0.273	INDETERMINATE	1	TRUE	2	0.557217979071806	5		210	729	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549075	87549075	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0003819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	71	244	0	ENST00000277120.3:c.1634-2A>T		p.X545_splice	ENST00000277120		545			NA	2	FACETS	0.348	0.303	0.396			1	INDETERMINATE	1	TRUE	NA	0.557217979071806	2		244	733	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972848	32972848	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	41	255	0	ENST00000380152.3:c.10198A>T	p.Ser3400Cys	p.S3400C	ENST00000380152		3400	Agt/Tgt	27/27	0.530135154733642	2	FACETS	0.186	0.154	0.222	0.093	0.077	0.111	SUBCLONAL	1	TRUE	0	0.557217979071806	2		255	790	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0003824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	31	549	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.749	0.605	0.912	0.749	0.605	0.912	CLONAL	1	FALSE	1	0.173521604279857	2		549	477	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0003824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	131	240	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	1	2	FACETS	0.927	0.85	1	1	0.993	1	CLONAL	4	FALSE	1	0.173521604279857	2		240	407	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206943213	206943213	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1252096113	NA	P-0003824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	27	527	0	ENST00000423557.1:c.405G>C	p.Lys135Asn	p.K135N	ENST00000423557	NM_000572.2	135	aaG/aaC	4/5	0.17196359285393	3	FACETS	1	0.915	1	0.655	0.523	0.805	CLONAL	1	FALSE	1	0.173521604279857	3		527	258	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398218	25398218	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs104894366	NA	P-0003824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	165	604	0	ENST00000311936.3:c.101C>G	p.Pro34Arg	p.P34R	ENST00000311936	NM_004985.3	34	cCa/cGa	2/5	NA	2	FACETS	1	0.952	1			1	INDETERMINATE	4	FALSE	NA	0.173521604279857	2		604	459	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443509	49443509	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0003824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	117	502	0	ENST00000301067.7:c.3862A>T	p.Lys1288Ter	p.K1288*	ENST00000301067	NM_003482.3	1288	Aag/Tag	11/54	NA	2	FACETS	1	0.963	1			1	INDETERMINATE	4	FALSE	NA	0.173521604279857	2		502	307	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577177	64577183	+	frameshift_variant	Frame_Shift_Del	DEL	CTTGAAG	CTTGAAG	-	novel	NA	P-0003824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	139	645	1	ENST00000312049.6:c.399_405del	p.Tyr133Ter	p.Y133*	ENST00000312049	NM_130799.2	133	taCTTCAAG/ta	2/10	1	2	FACETS	0.88	0.808	0.955	1	0.993	1	CLONAL	4	FALSE	1	0.173521604279857	2		646	455	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649896	88649903	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTTAGC	ACCTTAGC	-	novel	NA	P-0003824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	28	362	0	ENST00000372037.3:c.148_155del	p.Leu50ArgfsTer18	p.L50Rfs*18	ENST00000372037	NM_004329.2	49	ACCTTAGCa/a	4/13	0.173521604279857	1	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	FALSE	0	0.173521604279857	1		362	279	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0003825-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	351	388	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	1	0.972	1	1	0.997	1	CLONAL	3	FALSE	1	0.3	2		388	760	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778017	27778017	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003825-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	750	801	0	ENST00000369163.2:c.166C>T	p.Gln56Ter	p.Q56*	ENST00000369163	NM_003536.2	56	Cag/Tag	1/1	0.111479032537817	4	FACETS	0.953	0.922	0.984	1	0.998	1	INDETERMINATE	4	FALSE	2	0.3	4		801	1705	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380280	25380280	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894359	NA	P-0003834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	126	497	0	ENST00000311936.3:c.178G>A	p.Gly60Ser	p.G60S	ENST00000311936	NM_004985.3	60	Ggt/Agt	3/5	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.48	2		497	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578199	7578199	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	95	730	0	ENST00000269305.4:c.650T>G	p.Val217Gly	p.V217G	ENST00000269305	NM_001126112.2	217	gTg/gGg	6/11	1	2	FACETS	0.652	0.581	0.727	0.652	0.581	0.727	SUBCLONAL	1	TRUE	1	0.48	2		730	607	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003838-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	56	252	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.836	0.724	0.955	0.836	0.724	0.955	CLONAL	1	TRUE	1	0.562778177528031	2		252	238	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183724	10183724	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs869025616	NA	P-0003838-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	61	291	0	ENST00000256474.2:c.193T>C	p.Ser65Pro	p.S65P	ENST00000256474	NM_000551.3	65	Tcg/Ccg	1/3	0.530546032424587	1	FACETS	0.775	0.679	0.875	0.775	0.679	0.875	SUBCLONAL	1	TRUE	0	0.562778177528031	1		291	201	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162813	47162813	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0003838-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	84	255	0	ENST00000409792.3:c.3313A>T	p.Arg1105Ter	p.R1105*	ENST00000409792	NM_014159.6	1105	Aga/Tga	3/21	0.562778177528031	1	FACETS	0.89	0.799	0.984	0.89	0.799	0.984	CLONAL	1	TRUE	0	0.562778177528031	1		255	241	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702555	52702555	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003838-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	147	418	1	ENST00000394830.3:c.343G>T	p.Asp115Tyr	p.D115Y	ENST00000394830	NM_018313.4	115	Gac/Tac	4/30	0.562778177528031	1	FACETS	0.836	0.77	0.904	0.836	0.77	0.904	CLONAL	1	TRUE	0	0.562778177528031	1		419	449	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201119	108201119	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003838-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	82	176	4	ENST00000278616.4:c.7486G>T	p.Gly2496Ter	p.G2496*	ENST00000278616	NM_000051.3	2496	Gga/Tga	50/63	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.562778177528031	2		180	280	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748545	40748545	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003838-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	114	427	0	ENST00000392038.2:c.337C>G	p.Arg113Gly	p.R113G	ENST00000392038	NM_001626.4	113	Cgg/Ggg	5/14	0.151778776842976	0	FACETS	0.433	0.393	0.475			1	INDETERMINATE	1	TRUE	0	0.562778177528031	0		427	409	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610077	10610077	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003838-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	103	414	0	ENST00000171111.5:c.633T>G	p.Phe211Leu	p.F211L	ENST00000171111	NM_203500.1	211	ttT/ttG	2/6	1	2	FACETS	0.817	0.735	0.903	0.817	0.735	0.903	CLONAL	1	TRUE	1	0.562778177528031	2		414	448	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411883	116411920	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCTTTCTCTCTGTTTTAAGATCTGGGCAGTGAATTAG	TTCTTTCTCTCTGTTTTAAGATCTGGGCAGTGAATTAG	-	novel	NA	P-0003840-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	400	189	0	ENST00000397752.3:c.2888-17_2908del		p.X963_splice	ENST00000397752	NM_000245.2	963		14/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		189	559	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680854	30680854	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003852-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	237	490	0	ENST00000376406.3:c.865C>G	p.Leu289Val	p.L289V	ENST00000376406	NM_014641.2	289	Ctg/Gtg	5/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.57672593066324	2		490	786	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360844	118360844	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003852-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	34	161	0	ENST00000534358.1:c.4576A>T	p.Ile1526Phe	p.I1526F	ENST00000534358	NM_005933.3	1526	Atc/Ttc	13/36	1	2	FACETS	0.329	0.269	0.397	0.329	0.269	0.397	SUBCLONAL	1	TRUE	1	0.57672593066324	2		161	358	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0003852-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	173	334	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	0.897	0.828	0.968	0.897	0.828	0.968	CLONAL	1	TRUE	1	0.57672593066324	2		334	669	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217276	11217276	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	121	382	0	ENST00000361445.4:c.4402G>T	p.Asp1468Tyr	p.D1468Y	ENST00000361445	NM_004958.3	1468	Gac/Tac	30/58	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.476844919260526	2		382	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0003860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	83	213	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.473948523240196	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.476844919260526	1		213	254	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0003860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	122	556	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.473948523240196	1	FACETS	0.908	0.828	0.992	0.908	0.828	0.992	CLONAL	1	TRUE	0	0.476844919260526	1		556	429	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510561	38510561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1457382271	NA	P-0003860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	95	266	0	ENST00000254066.5:c.815G>A	p.Arg272Gln	p.R272Q	ENST00000254066	NM_000964.3	272	cGg/cAg	7/9	0.47621097535792	3	FACETS	0.945	0.844	1			1	CLONAL	1	TRUE	NA	0.476844919260526	3		266	522	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375492	40375492	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	153	700	1	ENST00000293328.3:c.458T>G	p.Leu153Arg	p.L153R	ENST00000293328	NM_012448.3	153	cTg/cGg	5/19	0.429524529661325	0	FACETS	0.575	0.528	0.623			1	SUBCLONAL	1	TRUE	0	0.476844919260526	0		701	584	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437558	56437558	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	67	335	0	ENST00000407977.2:c.904T>A	p.Trp302Arg	p.W302R	ENST00000407977		302	Tgg/Agg	8/10	0.476844919260526	1	FACETS	0.591	0.517	0.671	0.591	0.517	0.671	SUBCLONAL	1	TRUE	0	0.476844919260526	1		335	362	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526486	66526486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772571340	NA	P-0003860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	120	246	0	ENST00000358598.2:c.1042G>A	p.Val348Ile	p.V348I	ENST00000358598	NM_212471.2	348	Gtt/Att	11/11	0.473948523240196	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.476844919260526	1		246	340	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420022	41420022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	73	348	0	ENST00000373198.4:c.299C>T	p.Thr100Ile	p.T100I	ENST00000373198	NM_133170.3	100	aCc/aTc	3/32	1	2	FACETS	0.843	0.742	0.951	0.843	0.742	0.951	CLONAL	1	TRUE	1	0.476844919260526	2		348	363	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	554	556	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.406122016711771	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	4	TRUE	0	0.417569081109576	4		556	894	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419837	41419837	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs267605939	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	70	259	0	ENST00000373198.4:c.484C>T	p.Gln162Ter	p.Q162*	ENST00000373198	NM_133170.3	162	Cag/Tag	3/32	0.417569081109576	6	FACETS	0.859	0.749	0.979	0.286	0.249	0.327	CLONAL	1	TRUE	3	0.417569081109576	6		259	716	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	143	240	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.417569081109576	2	FACETS	0.967	0.894	1	0.967	0.894	1	CLONAL	2	TRUE	0	0.417569081109576	2		240	354	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520017	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	164	285	0	ENST00000326873.7:c.647C>T	p.Ser216Phe	p.S216F	ENST00000326873	NM_000455.4	216	tCc/tTc	5/10	0.417569081109576	2	FACETS	0.987	0.917	1	0.987	0.917	1	CLONAL	2	TRUE	0	0.417569081109576	2		285	398	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845941	151845941	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	250	316	0	ENST00000262189.6:c.13071G>A	p.Trp4357Ter	p.W4357*	ENST00000262189	NM_170606.2	4357	tgG/tgA	52/59	0.417569081109576	5	FACETS	0.989	0.925	1	0.659	0.617	0.702	CLONAL	2	TRUE	2	0.417569081109576	5		316	985	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188582	11188582	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	201	322	0	ENST00000361445.4:c.5839G>C	p.Asp1947His	p.D1947H	ENST00000361445	NM_004958.3	1947	Gat/Cat	42/58	0.417569081109576	3	FACETS	0.978	0.912	1	0.978	0.912	1	CLONAL	2	TRUE	1	0.417569081109576	3		322	595	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366887	40366887	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	89	295	0	ENST00000397332.2:c.310G>A	p.Glu104Lys	p.E104K	ENST00000397332	NM_001033082.2	104	Gaa/Aaa	2/3	0.417569081109576	3	FACETS	1	0.962	1	0.591	0.526	0.659	CLONAL	1	TRUE	1	0.417569081109576	3		295	436	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818313	43818313	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	113	302	0	ENST00000372470.3:c.1778G>C	p.Arg593Thr	p.R593T	ENST00000372470	NM_005373.2	593	aGa/aCa	12/12	0.417569081109576	3	FACETS	1	0.938	1	0.527	0.475	0.581	CLONAL	1	TRUE	1	0.417569081109576	3		302	621	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749994	162749994	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	88	307	0	ENST00000367921.3:c.2526C>G	p.Phe842Leu	p.F842L	ENST00000367921	NM_006182.2	842	ttC/ttG	18/18	0.417569081109576	5	FACETS	0.85	0.753	0.955	0.213	0.188	0.239	CLONAL	1	TRUE	1	0.417569081109576	5		307	806	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518519	204518519	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	96	279	0	ENST00000367182.3:c.1182C>G	p.Phe394Leu	p.F394L	ENST00000367182	NM_001278516.1	394	ttC/ttG	11/11	0.417569081109576	5	FACETS	1	0.901	1	0.253	0.225	0.283	CLONAL	1	TRUE	1	0.417569081109576	5		279	739	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967092	25967092	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	60	262	0	ENST00000435504.4:c.2114G>C	p.Gly705Ala	p.G705A	ENST00000435504		705	gGt/gCt	13/13	0.417569081109576	3	FACETS	0.825	0.713	0.946	0.413	0.356	0.473	CLONAL	1	TRUE	1	0.417569081109576	3		262	421	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698126	47698126	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1114167816	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	132	342	0	ENST00000233146.2:c.1684G>C	p.Glu562Gln	p.E562Q	ENST00000233146	NM_000251.2	562	Gag/Cag	11/16	0.417569081109576	3	FACETS	1	0.957	1	0.544	0.494	0.595	CLONAL	1	TRUE	1	0.417569081109576	3		342	703	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935493	49935493	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	132	471	0	ENST00000296474.3:c.1871C>G	p.Ser624Ter	p.S624*	ENST00000296474	NM_002447.2	624	tCa/tGa	5/20	0.417569081109576	2	FACETS	1	0.916	1	0.503	0.458	0.551	CLONAL	1	TRUE	0	0.417569081109576	2		471	628	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390953	89390953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	218	338	0	ENST00000336596.2:c.1019C>T	p.Ser340Leu	p.S340L	ENST00000336596	NM_005233.5	340	tCa/tTa	5/17	0.417569081109576	3	FACETS	0.932	0.871	0.995	0.932	0.871	0.995	CLONAL	2	TRUE	1	0.417569081109576	3		338	677	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178942495	178942495	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	102	244	0	ENST00000263967.3:c.2302G>C	p.Glu768Gln	p.E768Q	ENST00000263967	NM_006218.2	768	Gag/Cag	16/21	0.417569081109576	3	FACETS	0.96	0.86	1	0.48	0.43	0.533	CLONAL	1	TRUE	1	0.417569081109576	3		244	615	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747882	41747882	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	81	234	0	ENST00000226382.2:c.887C>G	p.Ser296Cys	p.S296C	ENST00000226382	NM_003924.3	296	tCt/tGt	3/3	0.299668797460161	3	FACETS	1	0.9	1	0.51	0.451	0.573	CLONAL	1	TRUE	1	0.417569081109576	3		234	460	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535283	66535283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs547670481	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	105	237	0	ENST00000273854.3:c.178G>A	p.Glu60Lys	p.E60K	ENST00000273854	NM_004439.5	60	Gaa/Aaa	1/18	0.299668797460161	3	FACETS	0.781	0.706	0.86	0.781	0.706	0.86	SUBCLONAL	2	TRUE	1	0.417569081109576	3		237	389	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157521	106157521	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	112	336	0	ENST00000380013.4:c.2422G>T	p.Glu808Ter	p.E808*	ENST00000380013	NM_001127208.2	808	Gaa/Taa	3/11	0.299668797460161	3	FACETS	1	0.935	1	0.525	0.473	0.579	CLONAL	1	TRUE	1	0.417569081109576	3		336	618	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541019	187541019	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	75	231	0	ENST00000441802.2:c.6721C>G	p.Pro2241Ala	p.P2241A	ENST00000441802	NM_005245.3	2241	Cct/Gct	10/27	0.299668797460161	3	FACETS	1	0.956	1	0.59	0.52	0.664	CLONAL	1	TRUE	1	0.417569081109576	3		231	368	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950054	38950054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	107	291	0	ENST00000357387.3:c.3896G>A	p.Arg1299Lys	p.R1299K	ENST00000357387	NM_152756.3	1299	aGa/aAa	31/38	0.291672741266609	5	FACETS	1	0.971	1	0.408	0.366	0.452	CLONAL	1	TRUE	2	0.417569081109576	5		291	681	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161970011	161970011	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	139	360	0	ENST00000366898.1:c.958G>T	p.Ala320Ser	p.A320S	ENST00000366898	NM_004562.2	320	Gca/Tca	9/12	0.414267596897123	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.417569081109576	1		360	461	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444362	50444362	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	148	201	0	ENST00000331340.3:c.292G>T	p.Asp98Tyr	p.D98Y	ENST00000331340	NM_006060.4	98	Gac/Tac	4/8	0.291672741266609	5	FACETS	1	0.973	1	0.756	0.695	0.82	CLONAL	2	TRUE	2	0.417569081109576	5		201	508	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386565	81386565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868138405	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	211	335	0	ENST00000222390.5:c.422C>T	p.Ser141Phe	p.S141F	ENST00000222390	NM_000601.4	141	tCt/tTt	4/18	0.291672741266609	5	FACETS	0.987	0.918	1	0.658	0.612	0.705	CLONAL	2	TRUE	2	0.417569081109576	5		335	833	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412037	116412037	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	74	233	0	ENST00000397752.3:c.3022C>G	p.Pro1008Ala	p.P1008A	ENST00000397752	NM_000245.2	1008	Cca/Gca	14/21	0.291672741266609	5	FACETS	0.921	0.806	1	0.307	0.268	0.348	CLONAL	1	TRUE	2	0.417569081109576	5		233	626	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851993	128851993	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1200280970	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	143	270	0	ENST00000249373.3:c.2065C>A	p.Pro689Thr	p.P689T	ENST00000249373	NM_005631.4	689	Cct/Act	12/12	0.291672741266609	5	FACETS	1	0.968	1	0.74	0.679	0.803	CLONAL	2	TRUE	2	0.417569081109576	5		270	502	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90949279	90949279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	86	301	0	ENST00000265433.3:c.2209G>A	p.Glu737Lys	p.E737K	ENST00000265433	NM_002485.4	737	Gag/Aag	15/16	0.239288705085836	5	FACETS	0.896	0.792	1	0.299	0.264	0.336	INDETERMINATE	1	TRUE	2	0.417569081109576	5		301	748	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389380	8389380	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	229	288	0	ENST00000356435.5:c.4238C>A	p.Ala1413Asp	p.A1413D	ENST00000356435		1413	gCc/gAc	26/35	0.417569081109576	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.417569081109576	3		288	576	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549090	87549090	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	111	345	0	ENST00000277120.3:c.1647C>G	p.Ile549Met	p.I549M	ENST00000277120		549	atC/atG	15/19	0.262984430828278	3	FACETS	0.981	0.883	1	0.327	0.294	0.362	CLONAL	1	TRUE	0	0.417569081109576	3		345	655	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814713	139814713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753016580	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	97	368	0	ENST00000247668.2:c.706G>A	p.Glu236Lys	p.E236K	ENST00000247668	NM_021138.3	236	Gag/Aag	8/11	0.417569081109576	3	FACETS	0.921	0.822	1	0.46	0.411	0.513	CLONAL	1	TRUE	1	0.417569081109576	3		368	610	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600525	43600525	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	73	332	0	ENST00000355710.3:c.751G>C	p.Glu251Gln	p.E251Q	ENST00000355710	NM_020975.4	251	Gag/Cag	4/20	0.417569081109576	3	FACETS	0.895	0.785	1	0.448	0.392	0.507	CLONAL	1	TRUE	1	0.417569081109576	3		332	472	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999795	100999795	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	155	407	0	ENST00000325455.5:c.7G>A	p.Glu3Lys	p.E3K	ENST00000325455	NM_001202474.3	3	Gag/Aag	1/8	0.239288705085836	5	FACETS	0.986	0.907	1	0.658	0.604	0.713	INDETERMINATE	2	TRUE	2	0.417569081109576	5		407	612	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503138	125503138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	117	376	0	ENST00000428830.2:c.505G>A	p.Gly169Ser	p.G169S	ENST00000428830	NM_001114121.2	169	Ggt/Agt	6/14	0.239288705085836	5	FACETS	0.96	0.865	1	0.32	0.288	0.354	INDETERMINATE	1	TRUE	2	0.417569081109576	5		376	949	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427491	427491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774366438	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	130	390	0	ENST00000399788.2:c.2678G>A	p.Arg893Gln	p.R893Q	ENST00000399788	NM_001042603.1	893	cGa/cAa	19/28	0.406122016711771	4	FACETS	1	0.928	1	0.257	0.233	0.282	CLONAL	1	TRUE	0	0.417569081109576	4		390	859	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915689	112915689	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	226	309	0	ENST00000351677.2:c.962C>G	p.Ser321Ter	p.S321*	ENST00000351677	NM_002834.3	321	tCa/tGa	9/16	NA	2	FACETS	1	0.942	1			1	INDETERMINATE	2	TRUE	NA	0.417569081109576	2		309	540	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133236053	133236053	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	85	248	0	ENST00000320574.5:c.3103G>A	p.Glu1035Lys	p.E1035K	ENST00000320574	NM_006231.2	1035	Gag/Aag	26/49	0.417569081109576	2	FACETS	0.923	0.82	1	0.462	0.41	0.517	CLONAL	1	TRUE	0	0.417569081109576	2		248	441	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911595	32911595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	168	556	0	ENST00000380152.3:c.3103G>A	p.Glu1035Lys	p.E1035K	ENST00000380152		1035	Gaa/Aaa	11/27	1	2	FACETS	0.904	0.831	0.98	0.904	0.831	0.98	CLONAL	1	TRUE	1	0.417569081109576	2		556	890	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527685	103527685	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	102	316	0	ENST00000355739.4:c.2993G>C	p.Arg998Thr	p.R998T	ENST00000355739	NM_000123.3	998	aGa/aCa	15/15	0.417569081109576	4	FACETS	0.873	0.781	0.972	0.291	0.26	0.324	CLONAL	1	TRUE	1	0.417569081109576	4		316	793	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420166	88420166	+	stop_lost	Nonstop_Mutation	SNP	C	C	A	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	142	276	0	ENST00000360948.2:c.2520G>T	p.Ter840TyrextTer38	p.*840Yext*38	ENST00000360948	NM_001012338.2	840	taG/taT	19/19	0.239288705085836	5	FACETS	0.933	0.853	1	0.622	0.569	0.677	INDETERMINATE	2	TRUE	2	0.417569081109576	5		276	593	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472652	88472652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	34	197	0	ENST00000360948.2:c.1903G>A	p.Asp635Asn	p.D635N	ENST00000360948	NM_001012338.2	635	Gat/Aat	16/19	0.239288705085836	5	FACETS	0.681	0.557	0.82	0.227	0.185	0.274	INDETERMINATE	1	TRUE	2	0.417569081109576	5		197	389	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99451967	99451967	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs745748508	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	95	325	0	ENST00000268035.6:c.1301G>C	p.Trp434Ser	p.W434S	ENST00000268035	NM_000875.3	434	tGg/tCg	6/21	0.417569081109576	5	FACETS	0.794	0.706	0.888			1	SUBCLONAL	1	TRUE	NA	0.417569081109576	5		325	932	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992515	72992515	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	291	464	0	ENST00000268489.5:c.1530G>T	p.Glu510Asp	p.E510D	ENST00000268489	NM_006885.3	510	gaG/gaT	2/10	0.417569081109576	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.417569081109576	2		464	656	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685633	29685633	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	104	323	0	ENST00000356175.3:c.8043C>A	p.Tyr2681Ter	p.Y2681*	ENST00000356175	NM_000267.3	2681	taC/taA	54/57	0.291672741266609	5	FACETS	1	0.954	1	0.372	0.333	0.413	CLONAL	1	TRUE	2	0.417569081109576	5		323	726	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56432330	56432330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771349279	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	89	252	0	ENST00000407977.2:c.2326G>A	p.Glu776Lys	p.E776K	ENST00000407977		776	Gag/Aag	10/10	0.263001940663727	4	FACETS	1	0.901	1	0.508	0.451	0.569	CLONAL	1	TRUE	2	0.417569081109576	4		252	595	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677881	58677881	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	194	344	0	ENST00000305921.3:c.106G>T	p.Glu36Ter	p.E36*	ENST00000305921	NM_003620.3	36	Gaa/Taa	1/6	0.263001940663727	4	FACETS	0.986	0.916	1	0.986	0.916	1	CLONAL	2	TRUE	2	0.417569081109576	4		344	668	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761478	59761478	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs864622628	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	205	291	0	ENST00000259008.2:c.2929G>T	p.Ala977Ser	p.A977S	ENST00000259008	NM_032043.2	977	Gca/Tca	20/20	0.263001940663727	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	2	0.417569081109576	4		291	673	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534386	63534386	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	79	247	0	ENST00000307078.5:c.1135G>C	p.Glu379Gln	p.E379Q	ENST00000307078	NM_004655.3	379	Gaa/Caa	5/11	0.239288705085836	5	FACETS	1	0.953	1	0.388	0.341	0.437	INDETERMINATE	1	TRUE	2	0.417569081109576	5		247	529	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60795989	60795989	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1344438049	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	60	247	0	ENST00000333681.4:c.589G>A	p.Ala197Thr	p.A197T	ENST00000333681		197	Gcc/Acc	3/3	1	2	FACETS	0.948	0.823	1	0.948	0.823	1	CLONAL	1	TRUE	1	0.417569081109576	2		247	303	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276653	15276653	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	93	285	0	ENST00000263388.2:c.5612C>G	p.Ser1871Ter	p.S1871*	ENST00000263388	NM_000435.2	1871	tCa/tGa	30/33	0.239288705085836	5	FACETS	1	0.956	1	0.382	0.34	0.427	INDETERMINATE	1	TRUE	2	0.417569081109576	5		285	632	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942524	17942524	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	42	217	0	ENST00000458235.1:c.2764G>C	p.Asp922His	p.D922H	ENST00000458235	NM_000215.3	922	Gat/Cat	20/24	0.239288705085836	5	FACETS	0.852	0.713	1	0.284	0.237	0.336	INDETERMINATE	1	TRUE	2	0.417569081109576	5		217	384	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525055	9525055	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	336	371	0	ENST00000353224.5:c.1830G>T	p.Met610Ile	p.M610I	ENST00000353224	NM_177990.2	610	atG/atT	8/10	0.252430138995507	3	FACETS	1	0.975	1			1	CLONAL	3	TRUE	NA	0.417569081109576	3		371	630	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023626	31023626	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	80	355	0	ENST00000375687.4:c.3111G>T	p.Trp1037Cys	p.W1037C	ENST00000375687	NM_015338.5	1037	tgG/tgT	13/13	0.417569081109576	6	FACETS	0.743	0.652	0.84	0.248	0.217	0.28	SUBCLONAL	1	TRUE	3	0.417569081109576	6		355	947	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860356	42860356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	158	369	0	ENST00000398585.3:c.521C>T	p.Ser174Leu	p.S174L	ENST00000398585	NM_001135099.1	174	tCa/tTa	5/14	0.417569081109576	2	FACETS	0.85	0.787	0.915	0.85	0.787	0.915	CLONAL	2	TRUE	0	0.417569081109576	2		369	445	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547924	41547924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367954257	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	118	335	0	ENST00000263253.7:c.2905G>A	p.Glu969Lys	p.E969K	ENST00000263253	NM_001429.3	969	Gag/Aag	15/31	0.252430138995507	3	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.417569081109576	3		335	569	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566552	41566552	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	196	312	0	ENST00000263253.7:c.4429G>C	p.Glu1477Gln	p.E1477Q	ENST00000263253	NM_001429.3	1477	Gag/Cag	27/31	0.252430138995507	3	FACETS	0.878	0.817	0.941			1	CLONAL	2	TRUE	NA	0.417569081109576	3		312	646	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412673	63412673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	221	401	0	ENST00000330258.3:c.494C>T	p.Pro165Leu	p.P165L	ENST00000330258	NM_152424.3	165	cCa/cTa	2/2	0.417569081109576	2	FACETS	0.982	0.922	1	0.982	0.922	1	CLONAL	2	TRUE	0	0.417569081109576	2		401	539	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045829	26045830	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0003869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	113	654	0	ENST00000540144.1:c.191_192delinsAA	p.Arg64Gln	p.R64Q	ENST00000540144	NM_003531.2	64	cGG/cAA	1/1	0.417569081109576	3	FACETS	0.696	0.625	0.771	0.348	0.312	0.386	SUBCLONAL	1	TRUE	1	0.417569081109576	3		654	940	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944812	31944812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866971809	NA	P-0003875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	175	422	0	ENST00000340398.3:c.289G>A	p.Glu97Lys	p.E97K	ENST00000340398	NM_001013699.2	97	Gaa/Aaa	1/1	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.511943934132505	2		422	560	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165785	118165785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1302106502	NA	P-0003875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	82	237	0	ENST00000369448.3:c.295C>T	p.Leu99Phe	p.L99F	ENST00000369448	NM_017709.3	99	Ctt/Ttt	2/2	0.511943934132505	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.511943934132505	1		237	223	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900262	101900262	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	92	315	1	ENST00000374994.4:c.696G>T	p.Lys232Asn	p.K232N	ENST00000374994	NM_004612.2	232	aaG/aaT	4/9	0.511943934132505	1	FACETS	0.938	0.845	1	0.938	0.845	1	CLONAL	1	TRUE	0	0.511943934132505	1		316	285	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835629	68835629	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658932	NA	P-0003875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	175	427	0	ENST00000261769.5:c.220C>T	p.Arg74Ter	p.R74*	ENST00000261769	NM_004360.3	74	Cga/Tga	3/16	0.511943934132505	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.511943934132505	1		427	505	SUCCESS
AR	367	MSKCC	GRCh37	X	66941720	66941720	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	149	543	0	ENST00000374690.3:c.2364G>C	p.Met788Ile	p.M788I	ENST00000374690	NM_000044.3	788	atG/atC	6/8	0.27468760386967	1	FACETS	0.636	0.582	0.692	0.636	0.582	0.692	INDETERMINATE	1	TRUE	0	0.511943934132505	1		543	681	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106434	27106434	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	104	291	0	ENST00000324856.7:c.6046del	p.Leu2016CysfsTer14	p.L2016Cfs*14	ENST00000324856	NM_006015.4	2015	atC/at	20/20	0.511943934132505	1	FACETS	0.991	0.899	1	0.991	0.899	1	CLONAL	1	TRUE	0	0.511943934132505	1		291	305	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0003884-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	395	591	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.59736755504566	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.59736755504566	1		591	905	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144880	47144880	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003884-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	522	448	0	ENST00000409792.3:c.4873C>T	p.Arg1625Cys	p.R1625C	ENST00000409792	NM_014159.6	1625	Cgt/Tgt	7/21	0.560218954584806	2	FACETS	0.896	0.864	0.928	0.896	0.864	0.928	CLONAL	2	TRUE	0	0.59736755504566	2		448	975	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624296	89624296	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs786201995	NA	P-0003884-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	162	273	0	ENST00000371953.3:c.70G>C	p.Asp24His	p.D24H	ENST00000371953	NM_000314.4	24	Gac/Cac	1/9	0.59736755504566	1	FACETS	0.818	0.757	0.88	0.818	0.757	0.88	CLONAL	1	TRUE	0	0.59736755504566	1		273	465	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710670	114710670	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0003884-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	458	831	0	ENST00000543371.1:c.155C>G	p.Ser52Ter	p.S52*	ENST00000543371	NM_001198531.1	52	tCa/tGa	1/14	0.59736755504566	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.59736755504566	1		831	996	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984782	11984782	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1164096095	NA	P-0003884-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	84	284	0	ENST00000353533.5:c.328C>T	p.Arg110Ter	p.R110*	ENST00000353533	NM_003010.3	110	Cga/Tga	3/11	0.59736755504566	1	FACETS	0.48	0.426	0.537	0.48	0.426	0.537	SUBCLONAL	1	TRUE	0	0.59736755504566	1		284	411	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	9	261	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.239	0.158	0.344	0.239	0.158	0.344	SUBCLONAL	1	TRUE	1	0.271611313656718	2		261	277	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279674	123279674	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs77543610	NA	P-0003885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	14	88	0	ENST00000358487.5:c.758C>G	p.Pro253Arg	p.P253R	ENST00000358487	NM_000141.4	253	cCt/cGt	7/18	0.271611313656718	1	FACETS	0.331	0.239	0.443	0.331	0.239	0.443	SUBCLONAL	1	TRUE	0	0.271611313656718	1		88	269	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649669	206649669	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	27	120	0	ENST00000367120.3:c.504G>C	p.Glu168Asp	p.E168D	ENST00000367120	NM_014002.3	168	gaG/gaC	6/22	0.207552107156227	3	FACETS	0.471	0.374	0.583	0.236	0.187	0.292	SUBCLONAL	1	TRUE	1	0.271611313656718	3		120	479	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612711	228612711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	66	582	0	ENST00000366696.1:c.316G>A	p.Glu106Lys	p.E106K	ENST00000366696	NM_003493.2	106	Gag/Aag	1/1	0.207552107156227	3	FACETS	0.468	0.405	0.538	0.234	0.202	0.269	SUBCLONAL	1	TRUE	1	0.271611313656718	3		582	1179	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437173	220437173	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746580263	NA	P-0003885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	80	496	1	ENST00000243786.2:c.77G>A	p.Arg26Gln	p.R26Q	ENST00000243786	NM_002191.3	26	cGg/cAg	1/2	1	2	FACETS	0.624	0.548	0.706	0.624	0.548	0.706	SUBCLONAL	1	TRUE	1	0.271611313656718	2		497	944	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793342	242793342	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	50	249	0	ENST00000334409.5:c.735G>C	p.Gln245His	p.Q245H	ENST00000334409	NM_005018.2	245	caG/caC	5/5	1	2	FACETS	0.604	0.511	0.705	0.604	0.511	0.705	SUBCLONAL	1	TRUE	1	0.271611313656718	2		249	610	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71064794	71064794	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	48	232	0	ENST00000318789.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000318789	NM_032682.5	294	Gag/Tag	12/21	1	2	FACETS	0.59	0.498	0.692	0.59	0.498	0.692	SUBCLONAL	1	TRUE	1	0.271611313656718	2		232	599	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204726	128204726	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	54	362	0	ENST00000341105.2:c.715C>T	p.Gln239Ter	p.Q239*	ENST00000341105	NM_032638.4	239	Cag/Tag	3/6	1	2	FACETS	0.516	0.439	0.6	0.516	0.439	0.6	SUBCLONAL	1	TRUE	1	0.271611313656718	2		362	771	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204866	128204866	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773786765	NA	P-0003885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	43	312	0	ENST00000341105.2:c.575C>T	p.Ser192Phe	p.S192F	ENST00000341105	NM_032638.4	192	tCt/tTt	3/6	1	2	FACETS	0.442	0.369	0.524	0.442	0.369	0.524	SUBCLONAL	1	TRUE	1	0.271611313656718	2		312	716	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845954	151845954	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	51	313	0	ENST00000262189.6:c.13058G>C	p.Arg4353Thr	p.R4353T	ENST00000262189	NM_170606.2	4353	aGa/aCa	52/59	0.207552107156227	3	FACETS	0.543	0.46	0.634	0.271	0.23	0.317	SUBCLONAL	1	TRUE	1	0.271611313656718	3		313	786	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325550	87325550	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0003885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	92	264	0	ENST00000277120.3:c.429-2A>G		p.X143_splice	ENST00000277120		143			1	2	FACETS	0.971	0.863	1	0.971	0.863	1	CLONAL	1	TRUE	1	0.271611313656718	2		264	698	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443917	18443917	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	50	249	0	ENST00000266497.5:c.890C>A	p.Ser297Ter	p.S297*	ENST00000266497		297	tCa/tAa	3/31	1	2	FACETS	0.811	0.689	0.945	0.811	0.689	0.945	CLONAL	1	TRUE	1	0.271611313656718	2		249	454	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434666	49434666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	30	227	0	ENST00000301067.7:c.6887C>T	p.Ser2296Phe	p.S2296F	ENST00000301067	NM_003482.3	2296	tCt/tTt	31/54	1	2	FACETS	0.41	0.329	0.502	0.41	0.329	0.502	SUBCLONAL	1	TRUE	1	0.271611313656718	2		227	539	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40993322	40993322	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	69	253	0	ENST00000267868.3:c.148G>C	p.Glu50Gln	p.E50Q	ENST00000267868	NM_002875.4	50	Gag/Cag	3/10	1	2	FACETS	0.723	0.629	0.824	0.723	0.629	0.824	SUBCLONAL	1	TRUE	1	0.271611313656718	2		253	703	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786710	3786710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	71	443	0	ENST00000262367.5:c.4501G>A	p.Glu1501Lys	p.E1501K	ENST00000262367	NM_004380.2	1501	Gag/Aag	27/31	1	2	FACETS	0.531	0.462	0.606	0.531	0.462	0.606	SUBCLONAL	1	TRUE	1	0.271611313656718	2		443	985	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790482	3790482	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	48	310	0	ENST00000262367.5:c.4051C>G	p.His1351Asp	p.H1351D	ENST00000262367	NM_004380.2	1351	Cac/Gac	24/31	1	2	FACETS	0.435	0.366	0.511	0.435	0.366	0.511	SUBCLONAL	1	TRUE	1	0.271611313656718	2		310	813	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038623	14038623	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	48	219	0	ENST00000311895.7:c.1948G>C	p.Asp650His	p.D650H	ENST00000311895	NM_005236.2	650	Gat/Cat	10/11	1	2	FACETS	0.544	0.459	0.638	0.544	0.459	0.638	SUBCLONAL	1	TRUE	1	0.271611313656718	2		219	650	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844229	68844229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	38	256	0	ENST00000261769.5:c.817G>A	p.Glu273Lys	p.E273K	ENST00000261769	NM_004360.3	273	Gaa/Aaa	6/16	0.271611313656718	1	FACETS	0.432	0.356	0.516	0.432	0.356	0.516	SUBCLONAL	1	TRUE	0	0.271611313656718	1		256	560	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15975531	15975531	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	29	292	0	ENST00000268712.3:c.3823C>T	p.Arg1275Ter	p.R1275*	ENST00000268712	NM_006311.3	1275	Cga/Tga	29/46	1	2	FACETS	0.388	0.311	0.477	0.388	0.311	0.477	SUBCLONAL	1	TRUE	1	0.271611313656718	2		292	550	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131361	17131361	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	65	364	0	ENST00000285071.4:c.91C>G	p.Gln31Glu	p.Q31E	ENST00000285071	NM_144997.5	31	Caa/Gaa	4/14	1	2	FACETS	0.614	0.531	0.704	0.614	0.531	0.704	SUBCLONAL	1	TRUE	1	0.271611313656718	2		364	780	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245606	41245606	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs886039984	NA	P-0003885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	59	289	0	ENST00000357654.3:c.1942G>T	p.Glu648Ter	p.E648*	ENST00000357654	NM_007294.3	648	Gaa/Taa	10/23	0.192017331990081	1	FACETS	0.578	0.496	0.666	0.578	0.496	0.666	SUBCLONAL	1	TRUE	0	0.271611313656718	1		289	650	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395632	45395632	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	42	260	0	ENST00000262160.6:c.502C>T	p.Gln168Ter	p.Q168*	ENST00000262160	NM_005901.5	168	Cag/Tag	4/11	1	2	FACETS	0.474	0.395	0.563	0.474	0.395	0.563	SUBCLONAL	1	TRUE	1	0.271611313656718	2		260	652	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561441	9561441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	35	194	0	ENST00000353224.5:c.341G>A	p.Ser114Asn	p.S114N	ENST00000353224	NM_177990.2	114	aGc/aAc	4/10	1	2	FACETS	0.499	0.409	0.602	0.499	0.409	0.602	SUBCLONAL	1	TRUE	1	0.271611313656718	2		194	516	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101007	41101007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375946335	NA	P-0003885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	40	228	0	ENST00000373198.4:c.1349G>A	p.Arg450Gln	p.R450Q	ENST00000373198	NM_133170.3	450	cGa/cAa	8/32	1	2	FACETS	0.504	0.418	0.601	0.504	0.418	0.601	SUBCLONAL	1	TRUE	1	0.271611313656718	2		228	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579838	7579844	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CAGTTTC	CAGTTTC	-	novel	NA	P-0003885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	81	286	0	ENST00000269305.4:c.69_74+1del		p.X23_splice	ENST00000269305	NM_001126112.2	23		2/11	1	2	FACETS	0.827	0.728	0.933	0.827	0.728	0.933	CLONAL	1	TRUE	1	0.271611313656718	2		286	721	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14031702	14031702	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	41	220	0	ENST00000311895.7:c.1891del	p.Glu631LysfsTer4	p.E631Kfs*4	ENST00000311895	NM_005236.2	631	Gaa/aa	9/11	1	2	FACETS	0.539	0.448	0.64	0.539	0.448	0.64	SUBCLONAL	1	TRUE	1	0.271611313656718	2		220	560	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168687	56168687	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003893-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	147	236	0	ENST00000399503.3:c.1543del	p.Leu515SerfsTer42	p.L515Sfs*42	ENST00000399503	NM_005921.1	514	tCc/tc	9/20	0.157436702141091	7	FACETS	1	0.945	1	0.883	0.814	0.954	CLONAL	6	FALSE	0	0.157436702141091	7		236	421	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0003903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	220	470	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.661544066697451	4	FACETS	0.949	0.89	1	0.949	0.89	1	CLONAL	2	TRUE	2	0.661544066697451	4		470	582	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	312	245	0	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.658678443947073	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.661544066697451	2		245	435	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641212	93641212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200320837	NA	P-0003903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	337	246	0	ENST00000375746.1:c.1558C>T	p.Arg520Cys	p.R520C	ENST00000375746	NM_001174167.1	520	Cgt/Tgt	11/14	0.661544066697451	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.661544066697451	3		246	640	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0003938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	44	262	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.22	2		262	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578520	7578520	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	58	181	0	ENST00000269305.4:c.410T>A	p.Leu137Gln	p.L137Q	ENST00000269305	NM_001126112.2	137	cTg/cAg	5/11	1	2	FACETS	0.845	0.737	0.959	1	0.982	1	CLONAL	3	TRUE	1	0.22	2		181	208	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015052	27015052	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs776697460	NA	P-0003938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	37	343	0	ENST00000335756.4:c.154C>T	p.Arg52Ter	p.R52*	ENST00000335756	NM_001809.3	52	Cga/Tga	2/5	1	2	FACETS	0.689	0.568	0.825	0.689	0.568	0.825	SUBCLONAL	1	TRUE	1	0.22	2		343	488	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528612	89528612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	35	189	0	ENST00000336596.2:c.2912C>T	p.Ala971Val	p.A971V	ENST00000336596	NM_005233.5	971	gCt/gTt	17/17	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.22	2		189	292	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127960	64127960	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	70	242	3	ENST00000334205.4:c.358G>A	p.Gly120Ser	p.G120S	ENST00000334205	NM_003942.2	120	Ggc/Agc	4/17	1	2	FACETS	0.86	0.754	0.973	1	0.979	1	CLONAL	2	TRUE	1	0.22	2		245	370	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012709	36012729	+	inframe_deletion	In_Frame_Del	DEL	CGCGGCCTTCGCCCCCGCGGC	CGCGGCCTTCGCCCCCGCGGC	-	novel	NA	P-0003938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	33	74	0	ENST00000358208.4:c.156_176del	p.Ala53_Ala59del	p.A53_A59del	ENST00000358208		51	agCGCGGCCTTCGCCCCCGCGGCc/agc	2/12	1	2	FACETS	1	0.838	1	1	0.964	1	CLONAL	2	TRUE	1	0.22	2		74	148	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094373	27094374	+	stop_gained	Nonsense_Mutation	DNP	TC	TC	AA	novel	NA	P-0003938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	28	128	1	ENST00000324856.7:c.3081_3082delinsAA	p.Tyr1027_Leu1028delinsTer	p.Y1027_L1028delins*	ENST00000324856	NM_006015.4	1027	taTCtg/taAAtg	11/20	0.15463087589996	1	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	TRUE	0	0.22	1		129	211	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436076	49436076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003949-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	41	85	0	ENST00000301067.7:c.5905C>T	p.Pro1969Ser	p.P1969S	ENST00000301067	NM_003482.3	1969	Ccc/Tcc	28/54	0.56415681431103	4	FACETS	1	0.926	1			1	CLONAL	1	TRUE	NA	0.56415681431103	4		85	193	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134885819	134885819	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1410311147	NA	P-0003984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	20	191	0	ENST00000398015.3:c.1730A>G	p.Asp577Gly	p.D577G	ENST00000398015	NM_004441.4	577	gAt/gGt	9/16	1	2	FACETS	0.427	0.326	0.544	0.427	0.326	0.544	SUBCLONAL	1	TRUE	1	0.32	2		191	293	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333346	70333346	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	13	334	0	ENST00000373644.4:c.1251A>T	p.Glu417Asp	p.E417D	ENST00000373644	NM_030625.2	417	gaA/gaT	2/12	1	2	FACETS	0.353	0.252	0.477	0.353	0.252	0.477	SUBCLONAL	1	TRUE	1	0.32	2		334	230	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579473	7579480	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGAGCA	GGGGAGCA	-	novel	NA	P-0003984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	28	182	0	ENST00000269305.4:c.207_214del	p.Ala70ArgfsTer76	p.A70Rfs*76	ENST00000269305	NM_001126112.2	69	gcTGCTCCCCcc/gccc	4/11	1	2	FACETS	0.535	0.428	0.657	0.535	0.428	0.657	SUBCLONAL	1	TRUE	1	0.32	2		182	327	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0003999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	57	368	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	0.342546620382078	3	FACETS	0.942	0.81	1	0.314	0.27	0.362	CLONAL	1	TRUE	0	0.342546620382078	3		368	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	178	278	0	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	0.284016951729523	2	FACETS	0.923	0.856	0.992	0.923	0.856	0.992	CLONAL	2	TRUE	0	0.342546620382078	2		278	563	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593301	67593301	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	58	243	0	ENST00000274335.5:c.2047G>T	p.Glu683Ter	p.E683*	ENST00000274335		683	Gag/Tag	15/15	0.283004213111695	2	FACETS	0.54	0.464	0.624	0.27	0.232	0.312	SUBCLONAL	1	TRUE	0	0.342546620382078	2		243	627	SUCCESS
APC	324	MSKCC	GRCh37	5	112175358	112175358	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1554085480	NA	P-0003999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	94	138	0	ENST00000257430.4:c.4067C>G	p.Ser1356Ter	p.S1356*	ENST00000257430	NM_000038.5	1356	tCa/tGa	16/16	0.283004213111695	2	FACETS	0.93	0.838	1	0.93	0.838	1	CLONAL	2	TRUE	0	0.342546620382078	2		138	295	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967988	93967988	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	118	378	0	ENST00000369303.4:c.1939G>A	p.Val647Ile	p.V647I	ENST00000369303	NM_004440.3	647	Gtc/Atc	11/17	0.283004213111695	2	FACETS	0.772	0.695	0.852	0.386	0.347	0.426	SUBCLONAL	1	TRUE	0	0.342546620382078	2		378	893	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041668	42041668	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs755505535	NA	P-0003999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	193	432	1	ENST00000219905.7:c.5863G>T	p.Val1955Phe	p.V1955F	ENST00000219905	NM_001164273.1	1955	Gtt/Ttt	17/24	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.342546620382078	2		433	1020	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900910	114901013	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGACGGTGTCTTTCTCTGTTCTCCTCCCCACAGTCTAACAAAGTGCCAGTGGTGCAGCACCCTCACCATGTCCACCCCCTCACGCCTCTTATCACGTACAGCAA	TGACGGTGTCTTTCTCTGTTCTCCTCCCCACAGTCTAACAAAGTGCCAGTGGTGCAGCACCCTCACCATGTCCACCCCCTCACGCCTCTTATCACGTACAGCAA	-	novel	NA	P-0003999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	95	256	0	ENST00000543371.1:c.553-30_626del		p.X185_splice	ENST00000543371	NM_001198531.1	185		6/14	1	2	FACETS	0.965	0.861	1	0.965	0.861	1	CLONAL	1	TRUE	1	0.342546620382078	2		256	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578493	7578493	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1206165503	NA	P-0004035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	198	151	0	ENST00000269305.4:c.437G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tGg/tAg	5/11	0.70332027487932	1	FACETS	0.943	0.888	0.999	0.943	0.888	0.999	CLONAL	1	TRUE	0	0.70332027487932	1		151	387	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916924	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	513	419	0	ENST00000263967.3:c.311C>G	p.Pro104Arg	p.P104R	ENST00000263967	NM_006218.2	104	cCa/cGa	2/21	0.691005255113156	2	FACETS	0.973	0.931	1	0.486	0.465	0.507	CLONAL	1	TRUE	0	0.70332027487932	2		419	1500	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720699	89720699	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs786202840	NA	P-0004035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	43	13	0	ENST00000371953.3:c.850G>T	p.Glu284Ter	p.E284*	ENST00000371953	NM_000314.4	284	Gag/Tag	8/9	0.70332027487932	1	FACETS	0.979	0.858	1	0.979	0.858	1	CLONAL	1	TRUE	0	0.70332027487932	1		13	81	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953735	48953735	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0004035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	232	171	0	ENST00000267163.4:c.1338C>G	p.Tyr446Ter	p.Y446*	ENST00000267163	NM_000321.2	446	taC/taG	14/27	0.70332027487932	1	FACETS	0.936	0.885	0.987	0.936	0.885	0.987	CLONAL	1	TRUE	0	0.70332027487932	1		171	457	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188396	142188396	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs535888898	NA	P-0004055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	47	178	0	ENST00000350721.4:c.6335G>A	p.Arg2112His	p.R2112H	ENST00000350721	NM_001184.3	2112	cGt/cAt	38/47	0.184204749369244	3	FACETS	0.869	0.74	1	0.435	0.37	0.504	INDETERMINATE	1	TRUE	1	0.591217421407087	3		178	237	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534304	187534304	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1298661702	NA	P-0004055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	148	271	0	ENST00000441802.2:c.9422G>A	p.Gly3141Glu	p.G3141E	ENST00000441802	NM_005245.3	3141	gGa/gAa	13/27	0.352489073103888	6	FACETS	1	0.983	1	0.33	0.301	0.36	INDETERMINATE	1	TRUE	2	0.591217421407087	6		271	828	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495422	149495422	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1002145058	NA	P-0004055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	176	383	0	ENST00000261799.4:c.3225G>C	p.Gln1075His	p.Q1075H	ENST00000261799	NM_002609.3	1075	caG/caC	23/23	0.434278271252597	2	FACETS	0.883	0.817	0.952	0.442	0.408	0.476	CLONAL	1	TRUE	0	0.591217421407087	2		383	674	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959004	2959004	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0004055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	94	208	0	ENST00000396946.4:c.2510+2T>A		p.X837_splice	ENST00000396946	NM_032415.4	837			0.390089377803023	3	FACETS	1	0.927	1	0.348	0.311	0.386	CLONAL	1	TRUE	0	0.591217421407087	3		208	395	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432765	49432765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1272325227	NA	P-0004055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	26	102	0	ENST00000301067.7:c.8374G>A	p.Val2792Ile	p.V2792I	ENST00000301067	NM_003482.3	2792	Gta/Ata	34/54	0.325917625220453	3	FACETS	0.717	0.574	0.877	0.239	0.191	0.293	INDETERMINATE	1	TRUE	0	0.591217421407087	3		102	159	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994769	73994769	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1182	83	328	0	ENST00000318443.5:c.253C>A	p.Gln85Lys	p.Q85K	ENST00000318443	NM_001024736.1	85	Cag/Aag	3/10	0.591217421407087	6	FACETS	0.484	0.426	0.548			1	SUBCLONAL	1	TRUE	NA	0.591217421407087	6		328	1265	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755478	39755478	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	102	184	0	ENST00000288319.7:c.1287C>A	p.Asn429Lys	p.N429K	ENST00000288319	NM_182918.3	429	aaC/aaA	10/10	0.591217421407087	3	FACETS	0.741	0.664	0.823	0.371	0.332	0.412	SUBCLONAL	1	TRUE	1	0.591217421407087	3		184	603	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341199	70341199	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	291	194	0	ENST00000374080.3:c.758A>T	p.Glu253Val	p.E253V	ENST00000374080		253	gAg/gTg	6/45	0.591217421407087	2	FACETS	0.984	0.94	1			1	CLONAL	2	TRUE	NA	0.591217421407087	2		194	500	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012227	152012275	+	frameshift_variant	Frame_Shift_Del	DEL	TCTGTCCTCTTTGTTTTCGTGGTGCTGAGTTTTGCATTTTCTCATAGGT	TCTGTCCTCTTTGTTTTCGTGGTGCTGAGTTTTGCATTTTCTCATAGGT	-	novel	NA	P-0004055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	54	320	0	ENST00000262189.6:c.538_586del	p.Thr180GlufsTer10	p.T180Efs*10	ENST00000262189	NM_170606.2	180	ACCTATGAGAAAATGCAAAACTCAGCACCACGAAAACAAAGAGGACAGAga/ga	4/59	0.434278271252597	2	FACETS	0.597	0.513	0.688	0.298	0.256	0.344	SUBCLONAL	1	TRUE	0	0.591217421407087	2		320	306	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573989	7573997	+	inframe_deletion	In_Frame_Del	DEL	CTCATTCAG	CTCATTCAG	-	novel	NA	P-0004055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	317	434	0	ENST00000269305.4:c.1030_1038del	p.Leu344_Glu346del	p.L344_E346del	ENST00000269305	NM_001126112.2	344	CTGAATGAG/-	10/11	0.325917625220453	3	FACETS	0.864	0.819	0.909	0.576	0.546	0.606	INDETERMINATE	2	TRUE	0	0.591217421407087	3		434	804	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543888	212543897	+	frameshift_variant	Frame_Shift_Del	DEL	TTGCACACCA	TTGCACACCA	-	novel	NA	P-0004055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	104	310	0	ENST00000342788.4:c.1502_1511del	p.Met501ThrfsTer30	p.M501Tfs*30	ENST00000342788	NM_005235.2	501	aTGGTGTGCAAc/ac	13/28	0.591217421407087	3	FACETS	0.658	0.589	0.73	0.329	0.294	0.365	SUBCLONAL	1	TRUE	1	0.591217421407087	3		310	693	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660371	227660371	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	40	126	0	ENST00000305123.5:c.3084G>T	p.Arg1028Ser	p.R1028S	ENST00000305123	NM_005544.2	1028	agG/agT	1/2	0.329103962571678	3	FACETS	0.913	0.762	1	0.457	0.381	0.54	CLONAL	1	TRUE	1	0.329103962571678	3		126	310	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462338	89462338	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	75	298	0	ENST00000336596.2:c.1810G>T	p.Asp604Tyr	p.D604Y	ENST00000336596	NM_005233.5	604	Gac/Tac	10/17	0.30069407205593	3	FACETS	0.808	0.708	0.916	0.269	0.236	0.306	CLONAL	1	TRUE	0	0.329103962571678	3		298	657	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670265	134670265	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	141	260	0	ENST00000398015.3:c.176A>T	p.Gln59Leu	p.Q59L	ENST00000398015	NM_004441.4	59	cAg/cTg	3/16	0.30069407205593	3	FACETS	0.976	0.895	1	0.651	0.596	0.707	CLONAL	2	TRUE	0	0.329103962571678	3		260	511	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467970	66467970	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	74	317	0	ENST00000273854.3:c.299A>T	p.Gln100Leu	p.Q100L	ENST00000273854	NM_004439.5	100	cAa/cTa	3/18	0.329103962571678	3	FACETS	0.761	0.666	0.864	0.381	0.333	0.432	SUBCLONAL	1	TRUE	1	0.329103962571678	3		317	688	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636850	176636850	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	111	291	0	ENST00000439151.2:c.1450G>T	p.Glu484Ter	p.E484*	ENST00000439151	NM_022455.4	484	Gaa/Taa	5/23	0.231564636090432	3	FACETS	1	0.982	1	0.472	0.425	0.521	CLONAL	1	TRUE	0	0.329103962571678	3		291	555	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778080	27778080	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1512	199	664	0	ENST00000369163.2:c.229C>A	p.Gln77Lys	p.Q77K	ENST00000369163	NM_003536.2	77	Cag/Aag	1/1	0.329103962571678	5	FACETS	1	0.958	1	0.352	0.324	0.381	CLONAL	1	TRUE	2	0.329103962571678	5		664	1711	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2972169	2972169	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	38	210	0	ENST00000396946.4:c.1570G>T	p.Ala524Ser	p.A524S	ENST00000396946	NM_032415.4	524	Gcc/Tcc	11/25	0.329103962571678	4	FACETS	0.458	0.378	0.549	0.153	0.126	0.183	SUBCLONAL	1	TRUE	1	0.329103962571678	4		210	670	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509630	106509630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	139	323	0	ENST00000359195.3:c.1624C>T	p.Arg542Trp	p.R542W	ENST00000359195	NM_002649.2	542	Cgg/Tgg	2/11	0.329103962571678	10	FACETS	0.794	0.721	0.871			1	SUBCLONAL	2	TRUE	NA	0.329103962571678	10		323	1232	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151181876	151181876	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1571	155	452	1	ENST00000262187.5:c.139A>G	p.Ile47Val	p.I47V	ENST00000262187	NM_005614.3	47	Atc/Gtc	3/8	0.329103962571678	8	FACETS	1	0.958	1			1	CLONAL	1	TRUE	NA	0.329103962571678	8		453	1726	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878887	151878887	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	56	234	0	ENST00000262189.6:c.6058C>A	p.Gln2020Lys	p.Q2020K	ENST00000262189	NM_170606.2	2020	Caa/Aaa	36/59	0.329103962571678	8	FACETS	0.858	0.734	0.995			1	CLONAL	1	TRUE	NA	0.329103962571678	8		234	788	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044413	5044413	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	104	382	0	ENST00000381652.3:c.361C>G	p.Pro121Ala	p.P121A	ENST00000381652	NM_004972.3	121	Cct/Gct	5/25	0.329103962571678	6	FACETS	1	0.903	1	0.337	0.301	0.376	CLONAL	1	TRUE	3	0.329103962571678	6		382	1036	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484335	8484335	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	80	301	0	ENST00000356435.5:c.3197G>T	p.Arg1066Leu	p.R1066L	ENST00000356435		1066	cGa/cTa	19/35	0.329103962571678	6	FACETS	0.981	0.862	1	0.327	0.287	0.37	CLONAL	1	TRUE	3	0.329103962571678	6		301	822	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485807	8485807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	71	263	0	ENST00000356435.5:c.3010C>A	p.Pro1004Thr	p.P1004T	ENST00000356435		1004	Cca/Aca	17/35	0.329103962571678	6	FACETS	0.962	0.838	1	0.321	0.279	0.365	CLONAL	1	TRUE	3	0.329103962571678	6		263	744	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486143	8486143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370631792	NA	P-0004065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	81	348	0	ENST00000356435.5:c.2674G>A	p.Val892Ile	p.V892I	ENST00000356435		892	Gtc/Atc	17/35	0.329103962571678	6	FACETS	0.966	0.85	1	0.322	0.283	0.364	CLONAL	1	TRUE	3	0.329103962571678	6		348	845	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760961	133760961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1003322722	NA	P-0004065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	101	400	1	ENST00000318560.5:c.3284G>A	p.Arg1095Gln	p.R1095Q	ENST00000318560	NM_005157.4	1095	cGg/cAg	11/11	0.329103962571678	3	FACETS	0.926	0.827	1	0.463	0.413	0.516	CLONAL	1	TRUE	1	0.329103962571678	3		401	772	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115937	8115937	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	145	186	0	ENST00000346208.3:c.1283T>A	p.Leu428Gln	p.L428Q	ENST00000346208		428	cTg/cAg	6/6	0.329103962571678	6	FACETS	0.844	0.774	0.917	0.844	0.774	0.917	CLONAL	3	TRUE	3	0.329103962571678	6		186	577	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69458635	69458635	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	84	274	0	ENST00000227507.2:c.450G>T	p.Trp150Cys	p.W150C	ENST00000227507	NM_053056.2	150	tgG/tgT	3/5	0.329103962571678	5	FACETS	0.888	0.783	1	0.296	0.261	0.334	CLONAL	1	TRUE	2	0.329103962571678	5		274	859	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69458654	69458654	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	98	305	0	ENST00000227507.2:c.469C>T	p.Pro157Ser	p.P157S	ENST00000227507	NM_053056.2	157	Ccg/Tcg	3/5	0.329103962571678	5	FACETS	0.94	0.837	1	0.313	0.279	0.35	CLONAL	1	TRUE	2	0.329103962571678	5		305	946	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644460	18644460	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs558526586	NA	P-0004065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	91	330	0	ENST00000266497.5:c.2638C>A	p.Pro880Thr	p.P880T	ENST00000266497		880	Cct/Act	18/31	NA	2	FACETS	0.879	0.782	0.983			1	INDETERMINATE	1	TRUE	NA	0.329103962571678	2		330	629	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549216	21549216	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	133	497	0	ENST00000382592.4:c.3060G>T	p.Lys1020Asn	p.K1020N	ENST00000382592	NM_014572.2	1020	aaG/aaT	8/8	NA	2	FACETS	1	0.945	1			1	INDETERMINATE	1	TRUE	NA	0.329103962571678	2		497	766	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28886210	28886210	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	70	291	0	ENST00000282397.4:c.3412C>A	p.His1138Asn	p.H1138N	ENST00000282397	NM_002019.4	1138	Cac/Aac	26/30	NA	2	FACETS	0.921	0.805	1			1	INDETERMINATE	1	TRUE	NA	0.329103962571678	2		291	462	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610593	81610593	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs756463066	NA	P-0004065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	94	347	0	ENST00000298171.2:c.2191G>T	p.Gly731Cys	p.G731C	ENST00000298171	NM_000369.2	731	Ggt/Tgt	10/10	0.267809693282107	4	FACETS	1	0.951	1	0.561	0.499	0.626	CLONAL	1	TRUE	2	0.329103962571678	4		347	677	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95579541	95579541	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	56	170	0	ENST00000393063.1:c.1928G>T	p.Ser643Ile	p.S643I	ENST00000393063	NM_030621.3	643	aGt/aTt	13/28	0.267809693282107	4	FACETS	0.822	0.705	0.951	0.411	0.352	0.476	CLONAL	1	TRUE	2	0.329103962571678	4		170	550	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0004065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	98	232	1	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	0.292286190713366	2	FACETS	1	0.982	1	0.743	0.667	0.822	CLONAL	1	TRUE	0	0.329103962571678	2		233	401	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400681	56400681	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	146	541	0	ENST00000348428.3:c.1275G>T	p.Met425Ile	p.M425I	ENST00000348428	NM_006785.3	425	atG/atT	11/17	0.301768967651678	1	FACETS	0.855	0.78	0.933	0.855	0.78	0.933	CLONAL	1	TRUE	0	0.329103962571678	1		541	867	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543632	9543632	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	70	351	0	ENST00000353224.5:c.1522G>T	p.Asp508Tyr	p.D508Y	ENST00000353224	NM_177990.2	508	Gac/Tac	6/10	0.329103962571678	3	FACETS	0.811	0.707	0.923	0.405	0.353	0.462	CLONAL	1	TRUE	1	0.329103962571678	3		351	611	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546958	9546958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771448843	NA	P-0004065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	31	123	0	ENST00000353224.5:c.1064C>T	p.Ala355Val	p.A355V	ENST00000353224	NM_177990.2	355	gCc/gTc	5/10	0.329103962571678	3	FACETS	0.781	0.634	0.946	0.39	0.317	0.473	CLONAL	1	TRUE	1	0.329103962571678	3		123	281	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730802	40730802	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	49	224	0	ENST00000373198.4:c.3733G>T	p.Gly1245Ter	p.G1245*	ENST00000373198	NM_133170.3	1245	Gga/Tga	27/32	NA	2	FACETS	0.765	0.65	0.892			1	INDETERMINATE	1	TRUE	NA	0.329103962571678	2		224	389	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652279	48652279	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	135	497	0	ENST00000376670.3:c.950G>T	p.Arg317Leu	p.R317L	ENST00000376670	NM_002049.3	317	cGg/cTg	6/6	0.294370198495711	2	FACETS	1	0.953	1	0.538	0.489	0.589	CLONAL	1	TRUE	0	0.329103962571678	2		497	763	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412682	63412682	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	87	316	0	ENST00000330258.3:c.485T>A	p.Met162Lys	p.M162K	ENST00000330258	NM_152424.3	162	aTg/aAg	2/2	0.294370198495711	2	FACETS	0.834	0.739	0.935	0.417	0.369	0.468	CLONAL	1	TRUE	0	0.329103962571678	2		316	634	SUCCESS
AR	367	MSKCC	GRCh37	X	66765470	66765470	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	74	330	0	ENST00000374690.3:c.482C>A	p.Pro161Gln	p.P161Q	ENST00000374690	NM_000044.3	161	cCa/cAa	1/8	0.294370198495711	2	FACETS	0.85	0.746	0.962	0.425	0.373	0.481	CLONAL	1	TRUE	0	0.329103962571678	2		330	529	SUCCESS
AR	367	MSKCC	GRCh37	X	66765898	66765898	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	64	372	0	ENST00000374690.3:c.910G>T	p.Glu304Ter	p.E304*	ENST00000374690	NM_000044.3	304	Gaa/Taa	1/8	0.294370198495711	2	FACETS	0.648	0.561	0.743	0.324	0.28	0.372	SUBCLONAL	1	TRUE	0	0.329103962571678	2		372	600	SUCCESS
AR	367	MSKCC	GRCh37	X	66766187	66766187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	56	141	0	ENST00000374690.3:c.1199C>T	p.Ala400Val	p.A400V	ENST00000374690	NM_000044.3	400	gCg/gTg	1/8	0.294370198495711	2	FACETS	1	0.874	1	0.508	0.437	0.584	CLONAL	1	TRUE	0	0.329103962571678	2		141	335	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345955	70345955	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	95	468	0	ENST00000374080.3:c.2492C>T	p.Ala831Val	p.A831V	ENST00000374080		831	gCt/gTt	18/45	1	2	FACETS	0.715	0.636	0.799	0.715	0.636	0.799	SUBCLONAL	1	TRUE	1	0.329103962571678	2		468	808	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190896	106190896	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	146	170	0	ENST00000380013.4:c.4174A>C	p.Ser1392Arg	p.S1392R	ENST00000380013	NM_001127208.2	1392	Agc/Cgc	9/11	1	2	FACETS	0.848	0.781	0.918	0.848	0.781	0.918	CLONAL	1	TRUE	1	0.775149436353721	2		170	444	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933406	100933406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150584881	NA	P-0004079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	271	424	0	ENST00000325455.5:c.1984G>A	p.Val662Ile	p.V662I	ENST00000325455	NM_001202474.3	662	Gtt/Att	4/8	1	2	FACETS	0.93	0.877	0.984	0.93	0.877	0.984	CLONAL	1	TRUE	1	0.775149436353721	2		424	752	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152009026	152009026	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	16	186	0	ENST00000262189.6:c.596del	p.Arg199HisfsTer7	p.R199Hfs*7	ENST00000262189	NM_170606.2	199	cGa/ca	5/59	0.766434531865656	1	FACETS	0.111	0.082	0.146	0.111	0.082	0.146	SUBCLONAL	1	TRUE	0	0.775149436353721	1		186	227	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0004081-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	108	213	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.162131379741272	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.222384491774546	2		213	443	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0004081-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	110	253	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.162131379741272	2	FACETS	0.793	0.714	0.876	0.793	0.714	0.876	SUBCLONAL	2	TRUE	0	0.222384491774546	2		253	624	SUCCESS
APC	324	MSKCC	GRCh37	5	112175246	112175246	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1057517558	NA	P-0004081-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	122	176	0	ENST00000257430.4:c.3956del	p.Pro1319LeufsTer2	p.P1319Lfs*2	ENST00000257430	NM_000038.5	1319	Cct/ct	16/16	0.200169804808017	3	FACETS	1	0.975	1	0.806	0.733	0.883	CLONAL	2	TRUE	0	0.222384491774546	3		176	504	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710972	114710976	+	frameshift_variant	Frame_Shift_Del	DEL	AGACG	AGACG	-	novel	NA	P-0004081-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	106	336	0	ENST00000543371.1:c.196_200del	p.Arg66AlafsTer29	p.R66Afs*29	ENST00000543371	NM_001198531.1	66	AGACGg/g	2/14	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.222384491774546	2		336	778	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684287	29684287	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	153	368	0	ENST00000356175.3:c.7807G>C	p.Ala2603Pro	p.A2603P	ENST00000356175	NM_000267.3	2603	Gct/Cct	53/57	0.623024257665634	3	FACETS	1	0.945	1	0.519	0.476	0.563	CLONAL	1	TRUE	1	0.623024257665634	3		368	621	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933958	39933958	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0004082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	239	291	0	ENST00000378444.4:c.641C>G	p.Ser214Ter	p.S214*	ENST00000378444	NM_001123385.1	214	tCa/tGa	4/15	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.623024257665634	1		291	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578551	7578551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	198	230	1	ENST00000269305.4:c.379T>C	p.Ser127Pro	p.S127P	ENST00000269305	NM_001126112.2	127	Tcc/Ccc	5/11	0.690377371420543	2	FACETS	0.97	0.923	1	0.97	0.923	1	CLONAL	2	TRUE	0	0.706339873580207	2		231	289	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105764	27105764	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	34	323	0	ENST00000324856.7:c.5375G>T	p.Gly1792Val	p.G1792V	ENST00000324856	NM_006015.4	1792	gGc/gTc	20/20	NA	2	FACETS	0.145	0.117	0.175			1	INDETERMINATE	1	TRUE	NA	0.706339873580207	2		323	666	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141632	202141632	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	396	394	0	ENST00000358485.4:c.920G>T	p.Arg307Leu	p.R307L	ENST00000358485	NM_001080125.1	307	cGg/cTg	7/9	0.627482487719837	2	FACETS	0.963	0.93	0.996	0.963	0.93	0.996	CLONAL	2	TRUE	0	0.706339873580207	2		394	582	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86642511	86642511	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	217	236	0	ENST00000274376.6:c.1072A>G	p.Lys358Glu	p.K358E	ENST00000274376	NM_002890.2	358	Aaa/Gaa	7/25	0.627482487719837	2	FACETS	0.766	0.724	0.808	0.766	0.724	0.808	SUBCLONAL	2	TRUE	0	0.706339873580207	2		236	401	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2969699	2969699	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	46	338	0	ENST00000396946.4:c.1580A>G	p.His527Arg	p.H527R	ENST00000396946	NM_032415.4	527	cAc/cGc	12/25	0.203537256135384	2	FACETS	0.235	0.197	0.277	0.118	0.098	0.139	INDETERMINATE	1	TRUE	0	0.706339873580207	2		338	554	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223522	55223522	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0004099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	278	593	0	ENST00000275493.2:c.890-1G>T		p.X297_splice	ENST00000275493	NM_005228.3	297			0.203537256135384	2	FACETS	0.859	0.809	0.911	0.43	0.404	0.456	INDETERMINATE	1	TRUE	0	0.706339873580207	2		593	916	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625094	69625094	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	55	221	0	ENST00000334134.2:c.699G>T	p.Gln233His	p.Q233H	ENST00000334134	NM_005247.2	233	caG/caT	3/3	0.203537256135384	2	FACETS	0.533	0.459	0.613	0.267	0.229	0.307	INDETERMINATE	1	TRUE	0	0.706339873580207	2		221	292	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944915	31944915	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs995848674	NA	P-0004099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	126	302	0	ENST00000340398.3:c.186C>G	p.Ile62Met	p.I62M	ENST00000340398	NM_001013699.2	62	atC/atG	1/1	0.178703694131158	3	FACETS	0.916	0.834	1	0.305	0.278	0.334	INDETERMINATE	1	TRUE	0	0.706339873580207	3		302	527	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123836	46123836	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	65	262	1	ENST00000334344.6:c.102T>A	p.Phe34Leu	p.F34L	ENST00000334344	NM_152641.2	34	ttT/ttA	2/21	0.178703694131158	3	FACETS	0.421	0.365	0.481	0.14	0.121	0.161	INDETERMINATE	1	TRUE	0	0.706339873580207	3		263	592	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222176	2222176	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	294	411	0	ENST00000398665.3:c.3008C>G	p.Ala1003Gly	p.A1003G	ENST00000398665	NM_032482.2	1003	gCc/gGc	24/28	0.706339873580207	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.706339873580207	1		411	407	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955199	17955199	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	139	303	0	ENST00000458235.1:c.28C>A	p.Leu10Met	p.L10M	ENST00000458235	NM_000215.3	10	Ctg/Atg	2/24	0.458386450040687	1	FACETS	0.723	0.667	0.78	0.723	0.667	0.78	SUBCLONAL	1	TRUE	0	0.706339873580207	1		303	352	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624771	9624771	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0004099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	40	191	0	ENST00000353224.5:c.204+2T>C		p.X68_splice	ENST00000353224	NM_177990.2	68			0.686084638670192	3	FACETS	0.447	0.372	0.529	0.149	0.124	0.177	SUBCLONAL	1	TRUE	0	0.706339873580207	3		191	343	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593477	215593478	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0004099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	334	315	0	ENST00000260947.4:c.2256_2257delinsTT	p.Gln752_Gly753delinsHisCys	p.Q752_G753delinsHC	ENST00000260947	NM_000465.2	752	caGGgc/caTTgc	11/11	0.627482487719837	2	FACETS	0.835	0.8	0.87	0.835	0.8	0.87	CLONAL	2	TRUE	0	0.706339873580207	2		315	566	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30323815	30323815	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0004100-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	70	329	0	ENST00000322652.5:c.1795-2A>G		p.X599_splice	ENST00000322652	NM_015355.2	599			0.861119177592192	1	FACETS	0.355	0.313	0.399	0.355	0.313	0.399	SUBCLONAL	1	TRUE	0	0.861119177592192	1		329	261	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325757	30325758	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0004100-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	41	287	0	ENST00000322652.5:c.1956_1957del	p.Cys653SerfsTer12	p.C653Sfs*12	ENST00000322652	NM_015355.2	652	tTA/t	16/16	0.861119177592192	1	FACETS	0.303	0.255	0.354	0.303	0.255	0.354	SUBCLONAL	1	TRUE	0	0.861119177592192	1		287	179	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0004108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	55	456	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.269607425254393	3	FACETS	0.765	0.655	0.886	0.765	0.655	0.886	SUBCLONAL	2	TRUE	1	0.15	3		456	515	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717624	89717624	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	93	233	0	ENST00000371953.3:c.649G>T	p.Val217Phe	p.V217F	ENST00000371953	NM_000314.4	217	Gtc/Ttc	7/9	0.590080104382984	1	FACETS	0.922	0.834	1	0.922	0.834	1	CLONAL	1	TRUE	0	0.590080104382984	1		233	241	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918796	50918796	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748904485	NA	P-0004111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	281	705	0	ENST00000440232.2:c.2666G>A	p.Arg889His	p.R889H	ENST00000440232	NM_002691.3	889	cGc/cAc	21/27	1	2	FACETS	0.987	0.929	1	0.987	0.929	1	CLONAL	1	TRUE	1	0.590080104382984	2		705	965	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566521	41566521	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	215	423	0	ENST00000263253.7:c.4398G>C	p.Trp1466Cys	p.W1466C	ENST00000263253	NM_001429.3	1466	tgG/tgC	27/31	1	2	FACETS	0.966	0.901	1	0.966	0.901	1	CLONAL	1	TRUE	1	0.590080104382984	2		423	754	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0004116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	116	147	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.322363751529724	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.324480391908743	2		147	322	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412375	139412375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1341448592	NA	P-0004116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	29	164	0	ENST00000277541.6:c.1270G>A	p.Glu424Lys	p.E424K	ENST00000277541	NM_017617.3	424	Gag/Aag	8/34	0.324480391908743	3	FACETS	0.527	0.423	0.646	0.264	0.211	0.323	SUBCLONAL	1	TRUE	1	0.324480391908743	3		164	394	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459530	50459530	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	39	203	0	ENST00000331340.3:c.819A>C	p.Lys273Asn	p.K273N	ENST00000331340	NM_006060.4	273	aaA/aaC	7/8	0.288446474578447	5	FACETS	0.637	0.527	0.76	0.212	0.175	0.254	SUBCLONAL	1	TRUE	2	0.324480391908743	5		203	561	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552756	226552756	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	92	378	0	ENST00000366794.5:c.2605T>G	p.Phe869Val	p.F869V	ENST00000366794	NM_001618.3	869	Ttt/Gtt	19/23	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.324480391908743	2		378	543	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727146	243727146	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	46	249	0	ENST00000263826.5:c.824A>T	p.Glu275Val	p.E275V	ENST00000263826	NM_005465.4	275	gAg/gTg	9/13	1	2	FACETS	0.727	0.614	0.852	0.727	0.614	0.852	SUBCLONAL	1	TRUE	1	0.324480391908743	2		249	390	SUCCESS
ALK	238	MSKCC	GRCh37	2	29450509	29450509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774004991	NA	P-0004116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	99	430	0	ENST00000389048.3:c.2845G>A	p.Glu949Lys	p.E949K	ENST00000389048	NM_004304.4	949	Gaa/Aaa	17/29	0.324480391908743	3	FACETS	0.877	0.782	0.977	0.438	0.391	0.489	CLONAL	1	TRUE	1	0.324480391908743	3		430	809	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637653	52637653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	100	372	0	ENST00000394830.3:c.2663C>T	p.Ser888Leu	p.S888L	ENST00000394830	NM_018313.4	888	tCa/tTa	18/30	1	2	FACETS	0.896	0.801	0.997	0.896	0.801	0.997	CLONAL	1	TRUE	1	0.324480391908743	2		372	688	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468391	89468391	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	90	259	0	ENST00000336596.2:c.1925T>G	p.Leu642Arg	p.L642R	ENST00000336596	NM_005233.5	642	cTt/cGt	11/17	1	2	FACETS	0.799	0.715	0.887	1	0.983	1	SUBCLONAL	2	TRUE	1	0.324480391908743	2		259	347	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670223	134670223	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	146	241	0	ENST00000398015.3:c.134T>G	p.Val45Gly	p.V45G	ENST00000398015	NM_004441.4	45	gTc/gGc	3/16	0.324480391908743	3	FACETS	0.909	0.834	0.988			1	CLONAL	2	TRUE	NA	0.324480391908743	3		241	575	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467712	66467712	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs757810079	NA	P-0004116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	105	347	0	ENST00000273854.3:c.557T>G	p.Leu186Arg	p.L186R	ENST00000273854	NM_004439.5	186	cTt/cGt	3/18	0.210302958301648	2	FACETS	1	0.966	1	0.588	0.529	0.651	CLONAL	1	TRUE	0	0.324480391908743	2		347	550	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673157	30673157	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1309983671	NA	P-0004116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	62	253	0	ENST00000376406.3:c.3803C>T	p.Ala1268Val	p.A1268V	ENST00000376406	NM_014641.2	1268	gCt/gTt	10/15	0.261190062584752	4	FACETS	1	0.95	1	0.605	0.525	0.693	CLONAL	1	TRUE	2	0.324480391908743	4		253	418	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442946	49442946	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	52	283	0	ENST00000301067.7:c.3962G>C	p.Gly1321Ala	p.G1321A	ENST00000301067	NM_003482.3	1321	gGa/gCa	12/54	0.324480391908743	2	FACETS	0.661	0.563	0.768	0.33	0.281	0.384	SUBCLONAL	1	TRUE	0	0.324480391908743	2		283	485	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348473	56348473	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	112	815	0	ENST00000348428.3:c.281A>C	p.Lys94Thr	p.K94T	ENST00000348428	NM_006785.3	94	aAg/aCg	2/17	1	2	FACETS	0.597	0.535	0.662	0.597	0.535	0.662	SUBCLONAL	1	TRUE	1	0.324480391908743	2		815	1157	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650817	48650818	+	missense_variant	Missense_Mutation	DNP	GC	GC	TG	novel	NA	P-0004116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	202	397	0	ENST00000376670.3:c.686_687delinsTG	p.Gly229Val	p.G229V	ENST00000376670	NM_002049.3	229	gGC/gTG	4/6	1	1	FACETS	0.959	0.896	1	1	0.994	1	CLONAL	2	TRUE	0	0.324480391908743	1		397	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs786203436	NA	P-0004117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	157	193	0	ENST00000269305.4:c.487T>A	p.Tyr163Asn	p.Y163N	ENST00000269305	NM_001126112.2	163	Tac/Aac	5/11	0.289966173095493	2	FACETS	0.987	0.918	1	0.987	0.918	1	CLONAL	2	TRUE	0	0.446684755219227	2		193	356	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242470	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs397517097	NA	P-0004117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	122	270	0	ENST00000275493.2:c.2240T>C	p.Leu747Ser	p.L747S	ENST00000275493	NM_005228.3	747	tTa/tCa	19/28	0.309089359659581	5	FACETS	0.754	0.683	0.828	0.503	0.455	0.552	SUBCLONAL	2	TRUE	2	0.446684755219227	5		270	605	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720661	89720661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs142420551	NA	P-0004117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	45	78	0	ENST00000371953.3:c.812T>C	p.Phe271Ser	p.F271S	ENST00000371953	NM_000314.4	271	tTt/tCt	8/9	0.297784016110253	3	FACETS	0.785	0.672	0.905	0.523	0.448	0.604	CLONAL	2	TRUE	0	0.446684755219227	3		78	157	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242476	55242490	+	inframe_deletion	In_Frame_Del	DEL	AAGCAACATCTCCGA	AAGCAACATCTCCGA	-	novel	NA	P-0004117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	110	265	0	ENST00000275493.2:c.2250_2264del	p.Thr751_Ala755del	p.T751_A755del	ENST00000275493	NM_005228.3	749	gAAGCAACATCTCCGAaa/gaa	19/28	0.309089359659581	5	FACETS	1	0.981	1	0.466	0.42	0.515	CLONAL	1	TRUE	2	0.446684755219227	5		265	588	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0004127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	42	252	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.598016865670624	2		252	125	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776057	9776057	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148638384	NA	P-0004127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	177	536	0	ENST00000377346.4:c.521C>T	p.Ser174Leu	p.S174L	ENST00000377346	NM_005026.3	174	tCg/tTg	5/24	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.598016865670624	2		536	529	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0004127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	80	146	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.598016865670624	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.598016865670624	2		146	124	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520181	176520181	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520036	NA	P-0004127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	52	489	0	ENST00000292408.4:c.1100A>G	p.Tyr367Cys	p.Y367C	ENST00000292408	NM_213647.1	367	tAt/tGt	9/18	0.592707174347527	2	FACETS	0.289	0.246	0.337	0.145	0.123	0.169	SUBCLONAL	1	TRUE	0	0.598016865670624	2		489	601	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880451	155880451	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	197	507	0	ENST00000368323.3:c.102G>C	p.Lys34Asn	p.K34N	ENST00000368323	NM_006912.5	34	aaG/aaC	2/6	0.598016865670624	3	FACETS	1	0.951	1	0.516	0.479	0.555	CLONAL	1	TRUE	1	0.598016865670624	3		507	829	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713606	30713606	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	46	352	0	ENST00000295754.5:c.931G>T	p.Glu311Ter	p.E311*	ENST00000295754	NM_003242.5	311	Gag/Tag	4/7	1	2	FACETS	0.321	0.27	0.377	0.321	0.27	0.377	SUBCLONAL	1	TRUE	1	0.598016865670624	2		352	480	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165831	47165831	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	107	751	0	ENST00000409792.3:c.295G>A	p.Asp99Asn	p.D99N	ENST00000409792	NM_014159.6	99	Gat/Aat	3/21	1	2	FACETS	0.684	0.616	0.756	0.684	0.616	0.756	SUBCLONAL	1	TRUE	1	0.598016865670624	2		751	523	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751180	57751180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	149	557	1	ENST00000274289.3:c.1687G>A	p.Glu563Lys	p.E563K	ENST00000274289	NM_006622.3	563	Gag/Aag	12/14	0.592707174347527	2	FACETS	0.985	0.906	1	0.492	0.453	0.533	CLONAL	1	TRUE	0	0.598016865670624	2		558	506	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017519	112017519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	227	814	1	ENST00000368678.4:c.994G>A	p.Glu332Lys	p.E332K	ENST00000368678		332	Gag/Aag	9/13	NA	2	FACETS	1	0.954	1			1	INDETERMINATE	1	TRUE	NA	0.598016865670624	2		815	741	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508793	106508793	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370152741	NA	P-0004127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	175	566	0	ENST00000359195.3:c.787G>A	p.Glu263Lys	p.E263K	ENST00000359195	NM_002649.2	263	Gaa/Aaa	2/11	1	2	FACETS	0.994	0.92	1	0.994	0.92	1	CLONAL	1	TRUE	1	0.598016865670624	2		566	589	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859835	151859835	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	136	402	0	ENST00000262189.6:c.10827G>T	p.Lys3609Asn	p.K3609N	ENST00000262189	NM_170606.2	3609	aaG/aaT	43/59	1	2	FACETS	0.964	0.882	1	0.964	0.882	1	CLONAL	1	TRUE	1	0.598016865670624	2		402	472	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965561	90965561	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	111	723	0	ENST00000265433.3:c.1756G>T	p.Asp586Tyr	p.D586Y	ENST00000265433	NM_002485.4	586	Gat/Tat	11/16	0.598016865670624	3	FACETS	1	0.931	1	0.519	0.469	0.571	CLONAL	1	TRUE	1	0.598016865670624	3		723	465	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215779	98215779	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	167	523	0	ENST00000331920.6:c.3430G>C	p.Glu1144Gln	p.E1144Q	ENST00000331920	NM_000264.3	1144	Gag/Cag	20/24	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.598016865670624	2		523	547	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173675	108173675	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	69	473	0	ENST00000278616.4:c.5415G>A	p.Trp1805Ter	p.W1805*	ENST00000278616	NM_000051.3	1805	tgG/tgA	36/63	1	2	FACETS	0.99	0.875	1	0.99	0.875	1	CLONAL	1	TRUE	1	0.598016865670624	2		473	233	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347622	118347622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	194	671	0	ENST00000534358.1:c.3259C>T	p.Pro1087Ser	p.P1087S	ENST00000534358	NM_005933.3	1087	Cct/Tct	4/36	1	2	FACETS	0.942	0.875	1	0.942	0.875	1	CLONAL	1	TRUE	1	0.598016865670624	2		671	689	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871245	12871245	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	37	79	1	ENST00000228872.4:c.472G>T	p.Asp158Tyr	p.D158Y	ENST00000228872	NM_004064.3	158	Gac/Tac	1/3	0.13384622754963	4	FACETS	0.755	0.635	0.883	0.755	0.635	0.883	INDETERMINATE	2	TRUE	2	0.598016865670624	4		80	131	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121438985	121438985	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	195	730	0	ENST00000257555.6:c.1886C>T	p.Ser629Phe	p.S629F	ENST00000257555		629	tCc/tTc	10/10	0.592707174347527	2	FACETS	0.991	0.922	1	0.496	0.461	0.532	CLONAL	1	TRUE	0	0.598016865670624	2		730	658	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061191	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	129	355	0	ENST00000250448.2:c.798C>G	p.Phe266Leu	p.F266L	ENST00000250448	NM_004496.3	266	ttC/ttG	2/2	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.598016865670624	2		355	411	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95595891	95595891	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	116	654	0	ENST00000393063.1:c.652G>C	p.Glu218Gln	p.E218Q	ENST00000393063	NM_030621.3	218	Gaa/Caa	7/28	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.598016865670624	2		654	336	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041753	42041753	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0004127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	202	1062	0	ENST00000219905.7:c.5948C>G	p.Ser1983Ter	p.S1983*	ENST00000219905	NM_001164273.1	1983	tCa/tGa	17/24	0.291027800811935	1	FACETS	0.78	0.728	0.834	0.78	0.728	0.834	INDETERMINATE	1	TRUE	0	0.598016865670624	1		1062	607	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041948	42041948	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	152	945	0	ENST00000219905.7:c.6143C>G	p.Ser2048Cys	p.S2048C	ENST00000219905	NM_001164273.1	2048	tCt/tGt	17/24	0.291027800811935	1	FACETS	0.704	0.648	0.762	0.704	0.648	0.762	INDETERMINATE	1	TRUE	0	0.598016865670624	1		945	506	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627854	37627854	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	161	700	0	ENST00000447079.4:c.1769C>T	p.Ser590Leu	p.S590L	ENST00000447079	NM_015083.1	590	tCa/tTa	2/14	1	2	FACETS	0.871	0.802	0.942	0.871	0.802	0.942	CLONAL	1	TRUE	1	0.598016865670624	2		700	618	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612221	1612221	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	167	568	0	ENST00000344749.5:c.1798G>T	p.Glu600Ter	p.E600*	ENST00000344749	NM_001136139.2	600	Gag/Tag	18/19	1	2	FACETS	0.96	0.886	1	0.96	0.886	1	CLONAL	1	TRUE	1	0.598016865670624	2		568	582	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10286275	10286275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	195	707	0	ENST00000340748.4:c.541C>T	p.Gln181Ter	p.Q181*	ENST00000340748		181	Cag/Tag	6/40	1	2	FACETS	0.984	0.914	1	0.984	0.914	1	CLONAL	1	TRUE	1	0.598016865670624	2		707	663	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354038	15354038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201742792	NA	P-0004127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	13	109	0	ENST00000263377.2:c.2842G>A	p.Val948Met	p.V948M	ENST00000263377	NM_058243.2	948	Gtg/Atg	14/20	1	2	FACETS	0.41	0.295	0.547	0.41	0.295	0.547	SUBCLONAL	1	TRUE	1	0.598016865670624	2		109	106	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17941394	17941394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	94	373	0	ENST00000458235.1:c.3014C>T	p.Ser1005Phe	p.S1005F	ENST00000458235	NM_000215.3	1005	tCt/tTt	22/24	1	2	FACETS	0.806	0.722	0.894	0.806	0.722	0.894	CLONAL	1	TRUE	1	0.598016865670624	2		373	390	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341198	70341198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	165	718	0	ENST00000374080.3:c.757G>A	p.Glu253Lys	p.E253K	ENST00000374080		253	Gag/Aag	6/45	1	2	FACETS	0.776	0.714	0.84	0.776	0.714	0.84	SUBCLONAL	1	TRUE	1	0.598016865670624	2		718	711	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178382	56178382	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	319	555	0	ENST00000399503.3:c.3357del	p.Lys1119AsnfsTer4	p.K1119Nfs*4	ENST00000399503	NM_005921.1	1119	Aaa/aa	14/20	0.592707174347527	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.598016865670624	2		555	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0004152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	162	202	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.643013307559584	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	0	0.643013307559584	1		202	314	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309900	65309900	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0004152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	178	213	0	ENST00000342505.4:c.2252-2A>G		p.X751_splice	ENST00000342505	NM_002227.2	751			0.643013307559584	1	FACETS	0.882	0.822	0.942	0.882	0.822	0.942	CLONAL	1	FALSE	0	0.643013307559584	1		213	426	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005131	150005131	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	223	285	0	ENST00000253339.5:c.1094C>A	p.Ala365Asp	p.A365D	ENST00000253339		365	gCt/gAt	3/7	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.643013307559584	2		285	603	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129191	152129191	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs760465612	NA	P-0004152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	317	366	0	ENST00000206249.3:c.144G>T	p.Lys48Asn	p.K48N	ENST00000206249	NM_000125.3	48	aaG/aaT	1/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.643013307559584	2		366	934	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265517	152265517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	191	209	0	ENST00000206249.3:c.970C>T	p.Pro324Ser	p.P324S	ENST00000206249	NM_000125.3	324	Ccc/Tcc	4/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.643013307559584	2		209	561	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856030	151856030	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	352	407	0	ENST00000262189.6:c.11588C>T	p.Pro3863Leu	p.P3863L	ENST00000262189	NM_170606.2	3863	cCt/cTt	44/59	0.643013307559584	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	0	0.643013307559584	1		407	721	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742111	145742111	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	116	106	0	ENST00000428558.2:c.392G>T	p.Gly131Val	p.G131V	ENST00000428558	NM_004260.3	131	gGa/gTa	5/22	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	1	0.643013307559584	2		106	329	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635167	87635167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	230	242	0	ENST00000277120.3:c.2219G>A	p.Ser740Asn	p.S740N	ENST00000277120		740	aGc/aAc	18/19	0.643013307559584	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	0	0.643013307559584	1		242	440	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741928	17741928	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	39	28	0	ENST00000250003.3:c.599C>A	p.Ser200Tyr	p.S200Y	ENST00000250003	NM_002478.4	200	tCc/tAc	1/3	1	2	FACETS	0.842	0.711	0.983	0.842	0.711	0.983	CLONAL	1	FALSE	1	0.643013307559584	2		28	144	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573153	64573153	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	216	274	1	ENST00000312049.6:c.1139C>A	p.Ala380Asp	p.A380D	ENST00000312049	NM_130799.2	380	gCc/gAc	8/10	1	2	FACETS	0.971	0.907	1	0.971	0.907	1	CLONAL	1	FALSE	1	0.643013307559584	2		275	692	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564823	41564823	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	247	286	0	ENST00000263253.7:c.4124G>T	p.Gly1375Val	p.G1375V	ENST00000263253	NM_001429.3	1375	gGc/gTc	25/31	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	FALSE	NA	0.643013307559584	2		286	713	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099479	27099479	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0004153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	161	213	0	ENST00000324856.7:c.3715+1G>A		p.X1239_splice	ENST00000324856	NM_006015.4	1239			0.2171397983647	2	FACETS	0.923	0.853	0.996	0.462	0.426	0.498	INDETERMINATE	1	TRUE	0	0.679705753246439	2		213	513	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636823	8636823	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	239	260	0	ENST00000356435.5:c.86C>A	p.Thr29Lys	p.T29K	ENST00000356435		29	aCa/aAa	2/35	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.679705753246439	2		260	682	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579364	+	frameshift_variant	Frame_Shift_Del	DEL	CGGAAAC	CGGAAAC	-	novel	NA	P-0004153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	171	238	0	ENST00000269305.4:c.323_329del	p.Gly108ValfsTer13	p.G108Vfs*13	ENST00000269305	NM_001126112.2	108	gGTTTCCGt/gt	4/11	0.679705753246439	1	FACETS	0.992	0.929	1	0.992	0.929	1	CLONAL	1	TRUE	0	0.679705753246439	1		238	335	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591077	67591077	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	216	212	0	ENST00000274335.5:c.1670del	p.Arg557GlnfsTer7	p.R557Qfs*7	ENST00000274335		557	cGa/ca	12/15	0.679705753246439	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.679705753246439	1		212	371	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44935948	44935955	+	frameshift_variant	Frame_Shift_Del	DEL	AGGTAAAA	AGGTAAAA	-	novel	NA	P-0004153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	274	461	0	ENST00000377967.4:c.2710_2717del	p.Gly904TrpfsTer4	p.G904Wfs*4	ENST00000377967	NM_021140.2	903	ctAGGTAAAAat/ctat	18/29	0.679705753246439	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.679705753246439	1		461	483	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0004159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	117	338	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.95	0.858	1	0.95	0.858	1	CLONAL	1	FALSE	1	0.367270958167948	2		338	671	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	213	454	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.219881502487555	2	FACETS	1	0.987	1	0.637	0.592	0.683	INDETERMINATE	1	FALSE	0	0.367270958167948	2		454	911	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200631	67200631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763667411	NA	P-0004159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	100	224	0	ENST00000312629.5:c.742C>T	p.Arg248Trp	p.R248W	ENST00000312629	NM_003952.2	248	Cgg/Tgg	9/15	1	2	FACETS	0.972	0.871	1	0.972	0.871	1	CLONAL	1	FALSE	1	0.367270958167948	2		224	560	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106228	27106228	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	75	191	0	ENST00000324856.7:c.5839C>T	p.Gln1947Ter	p.Q1947*	ENST00000324856	NM_006015.4	1947	Cag/Tag	20/20	0.167160788996404	0	FACETS	0.518	0.455	0.585			1	INDETERMINATE	1	FALSE	0	0.367270958167948	0		191	499	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225698	26225698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1171	186	750	1	ENST00000360408.1:c.316G>A	p.Glu106Lys	p.E106K	ENST00000360408	NM_003532.2	106	Gag/Aag	1/1	1	2	FACETS	0.746	0.687	0.808	0.746	0.687	0.808	SUBCLONAL	1	FALSE	1	0.367270958167948	2		751	1357	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625158	69625158	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377265856	NA	P-0004159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	138	276	0	ENST00000334134.2:c.635G>A	p.Arg212Gln	p.R212Q	ENST00000334134	NM_005247.2	212	cGg/cAg	3/3	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.367270958167948	2		276	607	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929213	32929213	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1339	168	515	0	ENST00000380152.3:c.7223C>A	p.Pro2408Gln	p.P2408Q	ENST00000380152		2408	cCa/cAa	14/27	0.361536541816461	3	FACETS	0.719	0.658	0.782	0.24	0.219	0.261	SUBCLONAL	1	FALSE	0	0.367270958167948	3		515	1507	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350635	89350635	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765315608	NA	P-0004159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1297	174	745	0	ENST00000301030.4:c.2315G>A	p.Arg772Gln	p.R772Q	ENST00000301030	NM_001256183.1	772	cGg/cAg	9/13	0.167160788996404	0	FACETS	0.408	0.374	0.443			1	INDETERMINATE	1	FALSE	0	0.367270958167948	0		745	1471	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976483	7976483	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	69	210	0	ENST00000319144.4:c.1909C>T	p.Arg637Ter	p.R637*	ENST00000319144	NM_001139.2	637	Cga/Tga	14/15	1	2	FACETS	0.706	0.616	0.804	0.706	0.616	0.804	SUBCLONAL	1	FALSE	1	0.367270958167948	2		210	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0004172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	144	228	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.318559981356338	2	FACETS	0.928	0.853	1	0.928	0.853	1	CLONAL	2	FALSE	0	0.329470548583309	2		228	471	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0004172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	99	412	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.211885323600754	5	FACETS	0.841	0.753	0.934	0.561	0.502	0.623	CLONAL	2	FALSE	2	0.329470548583309	5		413	534	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0004172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	97	185	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.329470548583309	3	FACETS	0.862	0.774	0.954	0.862	0.774	0.954	CLONAL	2	FALSE	1	0.329470548583309	3		185	398	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120495	70120505	+	frameshift_variant	Frame_Shift_Del	DEL	ACAACCCGTCT	ACAACCCGTCT	-	novel	NA	P-0004172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	255	215	0	ENST00000245479.2:c.1500_1510del	p.Gln500HisfsTer74	p.Q500Hfs*74	ENST00000245479	NM_000346.3	499	gaACAACCCGTCTac/gaac	3/3	0.318559981356338	2	FACETS	0.98	0.92	1	0.98	0.92	1	CLONAL	2	FALSE	0	0.329470548583309	2		215	790	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061414	38061414	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs926601303	NA	P-0004172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	153	146	0	ENST00000250448.2:c.575C>T	p.Thr192Met	p.T192M	ENST00000250448	NM_004496.3	192	aCg/aTg	2/2	0.329470548583309	3	FACETS	0.921	0.847	0.999	0.921	0.847	0.999	CLONAL	2	FALSE	1	0.329470548583309	3		146	587	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412941	63412941	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	337	289	0	ENST00000330258.3:c.226G>T	p.Gly76Ter	p.G76*	ENST00000330258	NM_152424.3	76	Gga/Tga	2/2	0.171982760664699	2	FACETS	0.936	0.886	0.987	0.936	0.886	0.987	INDETERMINATE	2	FALSE	0	0.329470548583309	2		289	1093	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352972	70352972	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0004172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	122	233	1	ENST00000374080.3:c.4528-1G>C		p.X1510_splice	ENST00000374080		1510			0.171982760664699	2	FACETS	0.812	0.733	0.895	0.406	0.366	0.448	INDETERMINATE	1	FALSE	0	0.329470548583309	2		234	912	SUCCESS
APC	324	MSKCC	GRCh37	5	112175786	112175786	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	60	123	0	ENST00000257430.4:c.4496del	p.Gly1499AspfsTer8	p.G1499Dfs*8	ENST00000257430	NM_000038.5	1499	Gga/ga	16/16	0.329470548583309	3	FACETS	0.871	0.752	1	0.436	0.376	0.501	CLONAL	1	FALSE	1	0.329470548583309	3		123	487	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832113	72832113	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004193-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	77	919	0	ENST00000268489.5:c.4468G>A	p.Glu1490Lys	p.E1490K	ENST00000268489	NM_006885.3	1490	Gag/Aag	9/10	0.628117197851111	1	FACETS	0.289	0.254	0.327	0.289	0.254	0.327	SUBCLONAL	1	TRUE	0	0.628117197851111	1		919	581	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0004201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	157	190	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.499484787330579	3	FACETS	1	0.969	1	0.555	0.51	0.603	CLONAL	1	TRUE	1	0.499170163453794	3		190	708	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764146326	NA	P-0004201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	273	473	0	ENST00000269305.4:c.841G>T	p.Asp281Tyr	p.D281Y	ENST00000269305	NM_001126112.2	281	Gac/Tac	8/11	0.487065147388463	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.499170163453794	2		473	533	SUCCESS
ATR	545	MSKCC	GRCh37	3	142254009	142254009	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	187	272	0	ENST00000350721.4:c.3858G>T	p.Gln1286His	p.Q1286H	ENST00000350721	NM_001184.3	1286	caG/caT	21/47	0.499170163453794	9	FACETS	0.808	0.744	0.874			1	CLONAL	2	TRUE	NA	0.499170163453794	9		272	1274	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520456	176520456	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	282	405	1	ENST00000292408.4:c.1301G>T	p.Arg434Leu	p.R434L	ENST00000292408	NM_213647.1	434	cGa/cTa	10/18	0.491275938365323	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.499170163453794	4		406	766	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511318	157511318	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	66	221	0	ENST00000346085.5:c.3836A>G	p.Lys1279Arg	p.K1279R	ENST00000346085	NM_020732.3	1279	aAg/aGg	15/20	0.499484787330579	3	FACETS	0.884	0.771	1	0.442	0.385	0.502	CLONAL	1	TRUE	1	0.499170163453794	3		221	374	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	464404	464404	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	256	400	0	ENST00000399788.2:c.790C>G	p.Arg264Gly	p.R264G	ENST00000399788	NM_001042603.1	264	Cga/Gga	7/28	0.459994206821264	4	FACETS	0.984	0.925	1			1	CLONAL	2	TRUE	NA	0.499170163453794	4		400	781	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528192	103528192	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	59	143	0	ENST00000355739.4:c.3500C>A	p.Ser1167Tyr	p.S1167Y	ENST00000355739	NM_000123.3	1167	tCt/tAt	15/15	0.48707983475958	2	FACETS	1	0.946	1	0.579	0.506	0.657	CLONAL	1	TRUE	0	0.499170163453794	2		143	204	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902651	50902651	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1270501754	NA	P-0004201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	314	587	0	ENST00000440232.2:c.226G>C	p.Asp76His	p.D76H	ENST00000440232	NM_002691.3	76	Gat/Cat	3/27	0.49421553849522	5	FACETS	0.981	0.926	1	0.393	0.37	0.415	CLONAL	2	TRUE	0	0.499170163453794	5		587	1121	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593262	67593263	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0004201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	331	465	0	ENST00000274335.5:c.2011_2012del	p.Val671HisfsTer15	p.V671Hfs*15	ENST00000274335		670	TGt/t	15/15	NA	2	FACETS	0.965	0.92	1			1	INDETERMINATE	2	TRUE	NA	0.499170163453794	2		465	687	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098806	178098806	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	175	397	0	ENST00000397062.3:c.239C>G	p.Thr80Arg	p.T80R	ENST00000397062	NM_006164.4	80	aCa/aGa	2/5	0.25724059903854	5	FACETS	0.888	0.82	0.958			1	CLONAL	3	FALSE	NA	0.25724059903854	5		397	708	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578207	7578215	+	inframe_deletion	In_Frame_Del	DEL	ATGTCGAAA	ATGTCGAAA	-	novel	NA	P-0004215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	112	379	0	ENST00000269305.4:c.634_642del	p.Phe212_His214del	p.F212_H214del	ENST00000269305	NM_001126112.2	212	TTTCGACAT/-	6/11	0.123372478232888	3	FACETS	1	0.969	1			1	INDETERMINATE	2	FALSE	NA	0.25724059903854	3		379	423	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227832	55227832	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	rs1171743336	NA	P-0004225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	48	414	0	ENST00000275493.2:c.1299T>A	p.His433Gln	p.H433Q	ENST00000275493	NM_005228.3	433	caT/caA	12/28	1	2	FACETS	0.25	0.211	0.293	0.25	0.211	0.293	SUBCLONAL	1	TRUE	1	0.729859532561861	2		414	526	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944246	81944246	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763166039	NA	P-0004225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	434	870	3	ENST00000359376.3:c.1855G>A	p.Glu619Lys	p.E619K	ENST00000359376	NM_002661.3	619	Gag/Aag	18/33	1	2	FACETS	0.937	0.894	0.981	0.937	0.894	0.981	CLONAL	1	TRUE	1	0.729859532561861	2		873	1269	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983152	149983152	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	80	476	1	ENST00000253339.5:c.3106A>G	p.Thr1036Ala	p.T1036A	ENST00000253339		1036	Aca/Gca	7/7	0.395466933971492	2	FACETS	1	0.899	1	0.508	0.45	0.57	CLONAL	1	TRUE	0	0.395466933971492	2		477	398	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273218	55273218	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	285	613	0	ENST00000275493.2:c.3541G>C	p.Ala1181Pro	p.A1181P	ENST00000275493	NM_005228.3	1181	Gcc/Ccc	28/28	0.395466933971492	5	FACETS	1	0.967	1	1	0.967	1	CLONAL	3	TRUE	2	0.395466933971492	5		613	742	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850921	63850921	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	60	391	0	ENST00000279873.7:c.1699C>A	p.Pro567Thr	p.P567T	ENST00000279873	NM_032199.2	567	Cct/Act	10/10	0.3951115900344	3	FACETS	0.83	0.717	0.952	0.415	0.358	0.476	CLONAL	1	TRUE	1	0.395466933971492	3		391	438	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032296	10032296	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	94	295	0	ENST00000330684.3:c.527T>A	p.Ile176Asn	p.I176N	ENST00000330684	NM_001134407.1	176	aTc/aAc	3/13	0.36053763502597	2	FACETS	0.947	0.857	1	0.947	0.857	1	CLONAL	2	TRUE	0	0.395466933971492	2		295	251	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510741	38510741	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	36	232	0	ENST00000254066.5:c.995T>A	p.Ile332Asn	p.I332N	ENST00000254066	NM_000964.3	332	aTc/aAc	7/9	0.3951115900344	3	FACETS	0.89	0.736	1	0.445	0.368	0.53	CLONAL	1	TRUE	1	0.395466933971492	3		232	245	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692858	89692875	+	inframe_deletion	In_Frame_Del	DEL	AGATGACAATCATGTTGC	AGATGACAATCATGTTGC	-	novel	NA	P-0004227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	41	108	0	ENST00000371953.3:c.344_361del	p.Asp115_Ala120del	p.D115_A120del	ENST00000371953	NM_000314.4	114	gaAGATGACAATCATGTTGCa/gaa	5/9	0.395466933971492	1	FACETS	0.808	0.694	0.925	1	0.967	1	CLONAL	2	TRUE	0	0.395466933971492	1		108	103	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099349	27099368	+	frameshift_variant	Frame_Shift_Del	DEL	GACTCCACATTCCAGAAGCG	GACTCCACATTCCAGAAGCG	-	novel	NA	P-0004227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	82	459	0	ENST00000324856.7:c.3588_3607del	p.Asp1196GlufsTer17	p.D1196Efs*17	ENST00000324856	NM_006015.4	1196	GACTCCACATTCCAGAAGCGg/g	14/20	0.395466933971492	2	FACETS	0.945	0.837	1	0.472	0.418	0.53	CLONAL	1	TRUE	0	0.395466933971492	2		459	439	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0004240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	9	261	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.267	0.176	0.383	0.267	0.176	0.383	SUBCLONAL	1	TRUE	1	0.286722329875806	2		261	235	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534539	140534539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	47	188	0	ENST00000288602.6:c.374C>T	p.Ser125Phe	p.S125F	ENST00000288602	NM_004333.4	125	tCt/tTt	3/18	1	2	FACETS	0.884	0.748	1	0.884	0.748	1	CLONAL	1	TRUE	1	0.286722329875806	2		188	371	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891274	101891274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	99	299	0	ENST00000374994.4:c.235C>T	p.Pro79Ser	p.P79S	ENST00000374994	NM_004612.2	79	Cct/Tct	2/9	0.193092244342456	2	FACETS	1	0.969	1	0.613	0.549	0.682	CLONAL	1	TRUE	0	0.286722329875806	2		299	563	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054468	42054468	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	116	377	0	ENST00000219905.7:c.7652C>G	p.Ser2551Cys	p.S2551C	ENST00000219905	NM_001164273.1	2551	tCt/tGt	22/24	1	2	FACETS	0.865	0.779	0.957	0.865	0.779	0.957	CLONAL	1	TRUE	1	0.286722329875806	2		377	935	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054533	42054533	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs759572856	NA	P-0004240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	98	301	0	ENST00000219905.7:c.7717C>G	p.Leu2573Val	p.L2573V	ENST00000219905	NM_001164273.1	2573	Ctt/Gtt	22/24	1	2	FACETS	0.721	0.642	0.805	0.721	0.642	0.805	SUBCLONAL	1	TRUE	1	0.286722329875806	2		301	948	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942024	44942024	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	91	240	0	ENST00000377967.4:c.3274del	p.Asp1092MetfsTer12	p.D1092Mfs*12	ENST00000377967	NM_021140.2	1092	Gat/at	22/29	1	2	FACETS	0.986	0.876	1	0.986	0.876	1	CLONAL	1	TRUE	1	0.286722329875806	2		240	644	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008548	70008548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771113831	NA	P-0004243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	97	238	0	ENST00000394351.3:c.835C>T	p.Arg279Trp	p.R279W	ENST00000394351	NM_000248.3	279	Cgg/Tgg	8/9	NA	2	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.701000360221369	2		238	250	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415668	152415668	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	90	226	0	ENST00000206249.3:c.1518G>C	p.Gln506His	p.Q506H	ENST00000206249	NM_000125.3	506	caG/caC	7/8	0.500644109716713	4	FACETS	1	0.971	1			1	CLONAL	1	TRUE	NA	0.701000360221369	4		226	349	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627919	37627919	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	449	346	0	ENST00000447079.4:c.1834C>T	p.Gln612Ter	p.Q612*	ENST00000447079	NM_015083.1	612	Caa/Taa	2/14	0.701000360221369	3	FACETS	1	0.994	1			1	CLONAL	3	TRUE	NA	0.701000360221369	3		346	541	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400734	56400734	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	405	525	0	ENST00000348428.3:c.1328A>C	p.Gln443Pro	p.Q443P	ENST00000348428	NM_006785.3	443	cAa/cCa	11/17	0.500644109716713	4	FACETS	1	0.969	1			1	CLONAL	2	TRUE	NA	0.701000360221369	4		525	965	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061209	38061209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	557	146	0	ENST00000250448.2:c.780del	p.Leu260PhefsTer61	p.L260Ffs*61	ENST00000250448	NM_004496.3	260	ttG/tt	2/2	0.701000360221369	10	FACETS	1	0.99	1			1	CLONAL	8	TRUE	NA	0.701000360221369	10		146	734	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0004244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	34	521	2	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			1	2	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	TRUE	1	0.22	2		523	298	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412910	49412910	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	44	1262	0	ENST00000418115.1:c.113T>G	p.Val38Gly	p.V38G	ENST00000418115	NM_001664.2	38	gTg/gGg	2/5	1	2	FACETS	0.553	0.463	0.654	0.553	0.463	0.654	SUBCLONAL	1	TRUE	1	0.22	2		1262	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0004276-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	181	123	0	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.340201813104403	3	FACETS	0.955	0.896	1	0.955	0.896	1	CLONAL	3	TRUE	0	0.434514574230269	3		123	354	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190708756	190708756	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004276-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	296	303	0	ENST00000441310.2:c.649G>T	p.Ala217Ser	p.A217S	ENST00000441310	NM_000534.4	217	Gct/Tct	6/13	0.388288685586693	4	FACETS	0.876	0.829	0.923	1	0.993	1	CLONAL	3	TRUE	2	0.434514574230269	4		303	744	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723762	49723762	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004276-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	65	60	0	ENST00000449682.2:c.1000G>C	p.Glu334Gln	p.E334Q	ENST00000449682	NM_020998.3	334	Gaa/Caa	8/18	0.434514574230269	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.434514574230269	1		60	180	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154825	2154825	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004276-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	92	338	0	ENST00000434045.2:c.396C>A	p.Asp132Glu	p.D132E	ENST00000434045	NM_001127598.1	132	gaC/gaA	4/5	1	2	FACETS	0.556	0.493	0.622	0.556	0.493	0.622	SUBCLONAL	1	TRUE	1	0.434514574230269	2		338	762	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878062	48878062	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004276-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	87	142	2	ENST00000267163.4:c.19del	p.Arg7GlufsTer58	p.R7Efs*58	ENST00000267163	NM_000321.2	5	aCc/ac	1/27	0.434514574230269	2	FACETS	0.758	0.681	0.839	0.758	0.681	0.839	SUBCLONAL	2	TRUE	0	0.434514574230269	2		144	264	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747906	41747906	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	17	325	0	ENST00000226382.2:c.863G>C	p.Gly288Ala	p.G288A	ENST00000226382	NM_003924.3	288	gGg/gCg	3/3	1	2	FACETS	0.693	0.517	0.901	0.693	0.517	0.901	SUBCLONAL	1	FALSE	1	0.188719125321548	2		325	260	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977546	2977546	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	46	300	0	ENST00000396946.4:c.1138G>T	p.Asp380Tyr	p.D380Y	ENST00000396946	NM_032415.4	380	Gac/Tac	8/25	0.188719125321548	5	FACETS	0.883	0.747	1			1	CLONAL	2	FALSE	NA	0.188719125321548	5		300	354	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346947	73346947	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	18	339	2	ENST00000377767.4:c.1270G>T	p.Gly424Ter	p.G424*	ENST00000377767	NM_014953.3	424	Gga/Tga	9/21	0.188719125321548	6	FACETS	1	0.781	1			1	CLONAL	1	FALSE	NA	0.188719125321548	6		341	253	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15975458	15975458	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0004277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	29	393	0	ENST00000268712.3:c.3895+1G>T		p.X1299_splice	ENST00000268712	NM_006311.3	1299			0.188719125321548	3	FACETS	1	0.822	1	1	0.822	1	CLONAL	2	FALSE	1	0.188719125321548	3		393	166	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579552	7579552	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	28	236	0	ENST00000269305.4:c.135del	p.Ser46ProfsTer77	p.S46Pfs*77	ENST00000269305	NM_001126112.2	45	ctG/ct	4/11	0.112714695433033	5	FACETS	1	0.934	1	0.368	0.295	0.45	INDETERMINATE	1	FALSE	1	0.188719125321548	5		236	259	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161697	56161704	+	frameshift_variant	Frame_Shift_Del	DEL	AAGGATCA	AAGGATCA	-	novel	NA	P-0004277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	44	324	0	ENST00000399503.3:c.1197_1204del	p.Arg399SerfsTer5	p.R399Sfs*5	ENST00000399503	NM_005921.1	398	tcAAGGATCAaa/tcaa	6/20	0.188719125321548	3	FACETS	1	0.862	1	1	0.862	1	CLONAL	2	FALSE	1	0.188719125321548	3		324	250	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0004284-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	35	291	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.182628930358703	1	FACETS	0.322	0.264	0.387	0.322	0.264	0.387	INDETERMINATE	1	FALSE	0	0.408797829087794	1		291	423	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951964	178951964	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004284-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	36	424	0	ENST00000263967.3:c.3019G>C	p.Gly1007Arg	p.G1007R	ENST00000263967	NM_006218.2	1007	Ggc/Cgc	21/21	1	2	FACETS	0.267	0.219	0.322	0.267	0.219	0.322	SUBCLONAL	1	FALSE	1	0.408797829087794	2		424	659	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183797	10183797	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs5030807	NA	P-0004284-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	78	307	0	ENST00000256474.2:c.266T>C	p.Leu89Pro	p.L89P	ENST00000256474	NM_000551.3	89	cTc/cCc	1/3	0.373148878287592	1	FACETS	0.88	0.779	0.986	0.88	0.779	0.986	CLONAL	1	FALSE	0	0.408797829087794	1		307	345	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508193	106508193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373644334	NA	P-0004284-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	30	173	0	ENST00000359195.3:c.187G>A	p.Gly63Ser	p.G63S	ENST00000359195	NM_002649.2	63	Ggc/Agc	2/11	0.189390588000674	3	FACETS	0.532	0.429	0.649	0.266	0.214	0.325	INDETERMINATE	1	FALSE	1	0.408797829087794	3		173	332	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28971155	28971155	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004284-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	38	421	0	ENST00000282397.4:c.1602T>G	p.Ile534Met	p.I534M	ENST00000282397	NM_002019.4	534	atT/atG	12/30	0.139008325349833	0	FACETS	0.185	0.153	0.222			1	INDETERMINATE	1	FALSE	0	0.408797829087794	0		421	593	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593605	55593608	+	protein_altering_variant	In_Frame_Del	DEL	GAAG	GAAG	C	novel	NA	P-0004305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	360	642	0	ENST00000288135.5:c.1671_1674delinsC	p.Trp557_Lys558delinsCys	p.W557_K558delinsC	ENST00000288135	NM_000222.2	557	tgGAAG/tgC	11/21	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.458994993061946	2		642	1513	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0004315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	179	412	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.332321459392778	3	FACETS	0.841	0.777	0.907	0.841	0.777	0.907	CLONAL	2	TRUE	1	0.332321459392778	3		413	747	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602369	10602369	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	214	499	0	ENST00000171111.5:c.1209G>T	p.Trp403Cys	p.W403C	ENST00000171111	NM_203500.1	403	tgG/tgT	3/6	0.312037353378726	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.332321459392778	2		499	601	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257876	16257876	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	86	229	0	ENST00000375759.3:c.5141T>C	p.Met1714Thr	p.M1714T	ENST00000375759	NM_015001.2	1714	aTg/aCg	11/15	0.312037353378726	2	FACETS	0.999	0.897	1	0.999	0.897	1	CLONAL	2	TRUE	0	0.332321459392778	2		229	259	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981064	55981064	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs576918743	NA	P-0004315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	95	413	0	ENST00000263923.4:c.635T>C	p.Ile212Thr	p.I212T	ENST00000263923	NM_002253.2	212	aTt/aCt	5/30	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.332321459392778	2		413	566	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398312	25398312	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	96	382	0	ENST00000311936.3:c.7G>T	p.Glu3Ter	p.E3*	ENST00000311936	NM_004985.3	3	Gaa/Taa	2/5	0.332321459392778	3	FACETS	1	0.948	1	0.552	0.493	0.615	CLONAL	1	TRUE	1	0.332321459392778	3		382	610	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432450	49432450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	96	496	0	ENST00000301067.7:c.8689G>A	p.Gly2897Ser	p.G2897S	ENST00000301067	NM_003482.3	2897	Ggt/Agt	34/54	0.332321459392778	3	FACETS	1	0.914	1	0.514	0.458	0.574	CLONAL	1	TRUE	1	0.332321459392778	3		496	655	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869558	102869558	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	93	202	0	ENST00000307046.8:c.83C>T	p.Ser28Phe	p.S28F	ENST00000307046	NM_001111285.1	28	tCc/tTc	2/4	0.332321459392778	3	FACETS	0.894	0.802	0.991	0.894	0.802	0.991	CLONAL	2	TRUE	1	0.332321459392778	3		202	365	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220443	1220443	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	206	522	0	ENST00000326873.7:c.536C>G	p.Pro179Arg	p.P179R	ENST00000326873	NM_000455.4	179	cCg/cGg	4/10	0.312037353378726	2	FACETS	0.997	0.93	1	0.997	0.93	1	CLONAL	2	TRUE	0	0.332321459392778	2		522	622	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0004315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	196	473	0	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	0.312037353378726	2	FACETS	0.953	0.887	1	0.953	0.887	1	CLONAL	2	TRUE	0	0.332321459392778	2		473	619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0004324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	78	325	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.509040370364499	1	FACETS	0.964	0.86	1	0.964	0.86	1	CLONAL	1	TRUE	0	0.509040370364499	1		325	237	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222986	1222986	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs864622488	NA	P-0004324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	222	233	0	ENST00000326873.7:c.923G>T	p.Trp308Leu	p.W308L	ENST00000326873	NM_000455.4	308	tGg/tTg	8/10	0.509040370364499	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.509040370364499	2		233	357	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179197	123179197	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	79	401	0	ENST00000218089.9:c.646C>T	p.Arg216Ter	p.R216*	ENST00000218089	NM_001042749.1	216	Cga/Tga	8/35	0.424095878263629	0	FACETS	0.69	0.617	0.764			1	SUBCLONAL	1	TRUE	0	0.509040370364499	0		401	221	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285243	212285243	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1332523099	NA	P-0004324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	55	476	0	ENST00000342788.4:c.3058G>A	p.Glu1020Lys	p.E1020K	ENST00000342788	NM_005235.2	1020	Gag/Aag	25/28	0.28189549221641	1	FACETS	0.703	0.609	0.804	0.703	0.609	0.804	INDETERMINATE	1	TRUE	0	0.509040370364499	1		476	229	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502264	186502264	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	65	699	0	ENST00000323963.5:c.73G>C	p.Glu25Gln	p.E25Q	ENST00000323963		25	Gag/Cag	2/11	1	2	FACETS	0.504	0.437	0.576	0.504	0.437	0.576	SUBCLONAL	1	TRUE	1	0.509040370364499	2		699	507	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244204	153244204	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	54	545	0	ENST00000281708.4:c.1953G>C	p.Leu651Phe	p.L651F	ENST00000281708	NM_033632.3	651	ttG/ttC	12/12	1	2	FACETS	0.456	0.39	0.528	0.456	0.39	0.528	SUBCLONAL	1	TRUE	1	0.509040370364499	2		545	465	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528895	157528895	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs763772159	NA	P-0004324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	94	351	0	ENST00000346085.5:c.6620G>C	p.Arg2207Thr	p.R2207T	ENST00000346085	NM_020732.3	2207	aGa/aCa	20/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.509040370364499	2		351	346	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965668	90965668	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	37	607	0	ENST00000265433.3:c.1649A>T	p.Lys550Ile	p.K550I	ENST00000265433	NM_002485.4	550	aAa/aTa	11/16	1	2	FACETS	0.348	0.287	0.416	0.348	0.287	0.416	SUBCLONAL	1	TRUE	1	0.509040370364499	2		607	418	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753194	128753194	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	90	305	0	ENST00000377970.2:c.1355C>T	p.Ser452Phe	p.S452F	ENST00000377970	NM_002467.4	452	tCt/tTt	3/3	1	2	FACETS	0.948	0.848	1	0.948	0.848	1	CLONAL	1	TRUE	1	0.509040370364499	2		305	373	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737401	145737401	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	66	271	0	ENST00000428558.2:c.3286C>A	p.Arg1096Ser	p.R1096S	ENST00000428558	NM_004260.3	1096	Cgc/Agc	20/22	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.509040370364499	2		271	258	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426771	121426771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	101	458	1	ENST00000257555.6:c.462G>A	p.Met154Ile	p.M154I	ENST00000257555		154	atG/atA	2/10	1	2	FACETS	0.882	0.793	0.975	0.882	0.793	0.975	CLONAL	1	TRUE	1	0.509040370364499	2		459	450	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030485	49030485	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	71	291	0	ENST00000267163.4:c.1960G>T	p.Val654Leu	p.V654L	ENST00000267163	NM_000321.2	654	Gtg/Ttg	19/27	0.509040370364499	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.509040370364499	1		291	191	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670025	29670025	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0004324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	159	405	1	ENST00000356175.3:c.7000-2A>G		p.X2334_splice	ENST00000356175	NM_000267.3	2334			0.509040370364499	2	FACETS	0.903	0.841	0.965	0.903	0.841	0.965	CLONAL	2	TRUE	0	0.509040370364499	2		406	346	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673797	30673797	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004325-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	30	278	0	ENST00000376406.3:c.3163T>G	p.Ser1055Ala	p.S1055A	ENST00000376406	NM_014641.2	1055	Tct/Gct	10/15	1	2	FACETS	0.47	0.378	0.575	0.47	0.378	0.575	SUBCLONAL	1	TRUE	1	0.264338545552067	2		278	483	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165695	118165695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745917069	NA	P-0004339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	100	453	0	ENST00000369448.3:c.205G>A	p.Val69Ile	p.V69I	ENST00000369448	NM_017709.3	69	Gtc/Atc	2/2	1	2	FACETS	0.819	0.732	0.91	0.819	0.732	0.91	CLONAL	1	TRUE	1	0.381670370414207	2		453	640	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149808	202149808	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	35	390	0	ENST00000358485.4:c.1249C>T	p.Gln417Ter	p.Q417*	ENST00000358485	NM_001080125.1	417	Cag/Tag	8/9	1	2	FACETS	0.307	0.251	0.37	0.307	0.251	0.37	SUBCLONAL	1	TRUE	1	0.381670370414207	2		390	598	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164591	47164591	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0004339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	55	285	0	ENST00000409792.3:c.1535C>G	p.Ser512Ter	p.S512*	ENST00000409792	NM_014159.6	512	tCa/tGa	3/21	0.335166716389329	1	FACETS	0.698	0.6	0.804	0.698	0.6	0.804	SUBCLONAL	1	TRUE	0	0.381670370414207	1		285	334	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165153	47165153	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	100	317	0	ENST00000409792.3:c.973G>T	p.Glu325Ter	p.E325*	ENST00000409792	NM_014159.6	325	Gaa/Taa	3/21	0.335166716389329	1	FACETS	0.902	0.81	0.999	0.902	0.81	0.999	CLONAL	1	TRUE	0	0.381670370414207	1		317	470	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165678	47165678	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	106	483	0	ENST00000409792.3:c.448C>T	p.His150Tyr	p.H150Y	ENST00000409792	NM_014159.6	150	Cat/Tat	3/21	0.335166716389329	1	FACETS	0.843	0.759	0.932	0.843	0.759	0.932	CLONAL	1	TRUE	0	0.381670370414207	1		483	533	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160642	56160642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749900834	NA	P-0004339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	108	448	0	ENST00000399503.3:c.916C>T	p.Arg306Cys	p.R306C	ENST00000399503	NM_005921.1	306	Cgc/Tgc	4/20	1	2	FACETS	0.943	0.849	1	0.943	0.849	1	CLONAL	1	TRUE	1	0.381670370414207	2		448	600	SUCCESS
APC	324	MSKCC	GRCh37	5	112176386	112176386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	71	265	0	ENST00000257430.4:c.5095G>A	p.Glu1699Lys	p.E1699K	ENST00000257430	NM_000038.5	1699	Gag/Aag	16/16	1	2	FACETS	0.825	0.722	0.935	0.825	0.722	0.935	CLONAL	1	TRUE	1	0.381670370414207	2		265	451	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778004	27778004	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	240	1168	0	ENST00000369163.2:c.153G>C	p.Glu51Asp	p.E51D	ENST00000369163	NM_003536.2	51	gaG/gaC	1/1	1	2	FACETS	0.91	0.848	0.975	0.91	0.848	0.975	CLONAL	1	TRUE	1	0.381670370414207	2		1168	1382	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117778	108117778	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	53	273	0	ENST00000278616.4:c.989G>T	p.Gly330Val	p.G330V	ENST00000278616	NM_000051.3	330	gGa/gTa	8/63	1	2	FACETS	0.608	0.519	0.705	0.608	0.519	0.705	SUBCLONAL	1	TRUE	1	0.381670370414207	2		273	457	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437836	110437836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	52	244	0	ENST00000375856.3:c.565C>T	p.Pro189Ser	p.P189S	ENST00000375856	NM_003749.2	189	Ccc/Tcc	1/2	1	2	FACETS	0.873	0.748	1	0.873	0.748	1	CLONAL	1	TRUE	1	0.381670370414207	2		244	312	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68934917	68934917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	90	411	0	ENST00000487270.1:c.986C>T	p.Pro329Leu	p.P329L	ENST00000487270	NM_133509.3	329	cCc/cTc	10/11	1	2	FACETS	0.686	0.609	0.769	0.686	0.609	0.769	SUBCLONAL	1	TRUE	1	0.381670370414207	2		411	687	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591895	48591895	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs377767346	NA	P-0004339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	82	440	0	ENST00000342988.3:c.1058A>G	p.Tyr353Cys	p.Y353C	ENST00000342988	NM_005359.5	353	tAc/tGc	9/12	0.335166716389329	1	FACETS	0.641	0.567	0.721	0.641	0.567	0.721	SUBCLONAL	1	TRUE	0	0.381670370414207	1		440	542	SUCCESS
AXL	558	MSKCC	GRCh37	19	41749520	41749520	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0004339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	136	561	0	ENST00000301178.4:c.1446-1G>C		p.X482_splice	ENST00000301178	NM_021913.4	482			1	2	FACETS	0.909	0.827	0.995	0.909	0.827	0.995	CLONAL	1	TRUE	1	0.381670370414207	2		561	784	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0004357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	268	248	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.843401776324016	1	FACETS	0.93	0.891	0.968	0.93	0.891	0.968	CLONAL	1	TRUE	0	0.843401776324016	1		248	395	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967143	25967143	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	212	235	0	ENST00000435504.4:c.2063G>A	p.Gly688Glu	p.G688E	ENST00000435504		688	gGg/gAg	13/13	NA	2	FACETS	0.707	0.659	0.756			1	INDETERMINATE	1	TRUE	NA	0.843401776324016	2		235	711	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654625	29654649	+	frameshift_variant	Frame_Shift_Del	DEL	CTAGTAGATGAGAACCAGTTCACCT	CTAGTAGATGAGAACCAGTTCACCT	-	novel	NA	P-0004357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	530	391	0	ENST00000356175.3:c.5314_5338del	p.Leu1772Ter	p.L1772*	ENST00000356175	NM_000267.3	1772	CTAGTAGATGAGAACCAGTTCACCTta/ta	37/57	1	2	FACETS	0.931	0.908	0.953	1	0.998	1	CLONAL	2	TRUE	1	0.843401776324016	2		391	675	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0004358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	594	703	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.409197099911057	4	FACETS	0.93	0.899	0.961	0.93	0.899	0.961	CLONAL	4	TRUE	0	0.409197099911057	4		704	1100	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242662	16242662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	124	369	0	ENST00000375759.3:c.1283G>T	p.Arg428Met	p.R428M	ENST00000375759	NM_015001.2	428	aGg/aTg	6/15	0.301791356727527	3	FACETS	0.805	0.728	0.887	0.402	0.364	0.444	CLONAL	1	TRUE	1	0.409197099911057	3		369	907	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428228	49428228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757247893	NA	P-0004358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	45	314	0	ENST00000301067.7:c.10472G>A	p.Arg3491His	p.R3491H	ENST00000301067	NM_003482.3	3491	cGt/cAt	37/54	0.264751364486655	3	FACETS	0.47	0.394	0.553	0.235	0.197	0.277	SUBCLONAL	1	TRUE	1	0.409197099911057	3		314	564	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15978986	15978986	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	49	297	0	ENST00000268712.3:c.3532C>A	p.Pro1178Thr	p.P1178T	ENST00000268712	NM_006311.3	1178	Cca/Aca	27/46	0.409197099911057	4	FACETS	0.366	0.308	0.429	0.091	0.077	0.108	SUBCLONAL	1	TRUE	0	0.409197099911057	4		297	923	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351431	70351431	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	129	399	0	ENST00000374080.3:c.4079C>G	p.Ser1360Cys	p.S1360C	ENST00000374080		1360	tCc/tGc	29/45	0.220176737808562	1	FACETS	0.65	0.59	0.714	0.65	0.59	0.714	INDETERMINATE	1	TRUE	0	0.409197099911057	1		399	771	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352348	70352348	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	93	443	0	ENST00000374080.3:c.4375T>A	p.Ser1459Thr	p.S1459T	ENST00000374080		1459	Tcc/Acc	31/45	0.220176737808562	1	FACETS	0.46	0.409	0.515	0.46	0.409	0.515	INDETERMINATE	1	TRUE	0	0.409197099911057	1		443	786	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917740	151917755	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTAACTGTGAGGCT	CTGTAACTGTGAGGCT	-	novel	NA	P-0004358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	51	41	0	ENST00000262189.6:c.3565_3580del	p.Ser1189PhefsTer11	p.S1189Ffs*11	ENST00000262189	NM_170606.2	1189	AGCCTCACAGTTACAGtt/tt	23/59	1	2	FACETS	1	0.956	1	1	0.981	1	CLONAL	2	TRUE	1	0.409197099911057	2		41	104	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0004364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	385	456	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.680870145882469	2	FACETS	0.996	0.961	1	0.996	0.961	1	CLONAL	2	TRUE	0	0.680870145882469	2		456	568	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105811	27105811	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0004364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	220	593	0	ENST00000324856.7:c.5422A>T	p.Lys1808Ter	p.K1808*	ENST00000324856	NM_006015.4	1808	Aag/Tag	20/20	0.680870145882469	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.680870145882469	1		593	369	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276722	15276722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446718967	NA	P-0004364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	221	666	0	ENST00000263388.2:c.5543G>A	p.Arg1848His	p.R1848H	ENST00000263388	NM_000435.2	1848	cGt/cAt	30/33	0.680870145882469	3	FACETS	1	0.979	1	0.559	0.522	0.598	CLONAL	1	TRUE	1	0.680870145882469	3		666	778	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0004390-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	48	358	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.149753620080555	3	FACETS	1	0.952	1	0.673	0.57	0.786	CLONAL	1	TRUE	1	0.18	3		358	432	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0004390-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	22	336	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.3	3	FACETS	0.688	0.533	0.87			1	SUBCLONAL	1	TRUE	NA	0.18	3		336	387	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222934	5222934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768350891	NA	P-0004390-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	15	182	0	ENST00000357368.4:c.2869G>A	p.Glu957Lys	p.E957K	ENST00000357368	NM_002850.3	957	Gag/Aag	18/38	1	2	FACETS	0.992	0.729	1	0.992	0.729	1	CLONAL	1	TRUE	1	0.18	2		182	168	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0004390-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	15	251	0	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	1	2	FACETS	0.581	0.424	0.769	0.581	0.424	0.769	SUBCLONAL	1	TRUE	1	0.18	2		251	287	SUCCESS
ATM	472	MSKCC	GRCh37	11	108137925	108137925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2229022	NA	P-0004390-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	38	326	0	ENST00000278616.4:c.2494C>T	p.Arg832Cys	p.R832C	ENST00000278616	NM_000051.3	832	Cgt/Tgt	17/63	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.18	2		326	389	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592355	29592366	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGGTAAGAAAT	GAGGTAAGAAAT	-	novel	NA	P-0004390-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	23	315	0	ENST00000356175.3:c.4770_4772+9del		p.X1590_splice	ENST00000356175	NM_000267.3	1590		35/57	1	2	FACETS	0.704	0.548	0.884	0.704	0.548	0.884	SUBCLONAL	1	TRUE	1	0.18	2		315	363	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0004392-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	156	259	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.262974430930259	2	FACETS	0.98	0.909	1	1	0.99	1	CLONAL	3	TRUE	0	0.272064989311284	2		260	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574035	7574035	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs867389695	NA	P-0004392-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	121	650	0	ENST00000269305.4:c.994-2A>G		p.X332_splice	ENST00000269305	NM_001126112.2	332			NA	2	FACETS	0.898	0.816	0.984			1	INDETERMINATE	2	TRUE	NA	0.272064989311284	2		650	495	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878464	151878464	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004392-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	73	334	0	ENST00000262189.6:c.6481C>T	p.Gln2161Ter	p.Q2161*	ENST00000262189	NM_170606.2	2161	Caa/Taa	36/59	0.272064989311284	4	FACETS	0.91	0.801	1	0.91	0.801	1	CLONAL	2	TRUE	2	0.272064989311284	4		334	375	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353717	15353717	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004398-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	94	415	0	ENST00000263377.2:c.3163T>C	p.Ser1055Pro	p.S1055P	ENST00000263377	NM_058243.2	1055	Tca/Cca	14/20	0.354222072887092	3	FACETS	0.878	0.782	0.981	0.439	0.391	0.491	CLONAL	1	TRUE	1	0.361049585630376	3		415	700	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0004410-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	200	245	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.873568027427842	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.873568027427842	1		245	242	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412905	49412905	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519951	NA	P-0004410-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	166	522	0	ENST00000418115.1:c.118G>C	p.Glu40Gln	p.E40Q	ENST00000418115	NM_001664.2	40	Gag/Cag	2/5	0.873568027427842	1	FACETS	0.956	0.909	0.999	0.956	0.909	0.999	CLONAL	1	TRUE	0	0.873568027427842	1		522	224	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793365	242793365	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004410-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	261	261	0	ENST00000334409.5:c.712C>A	p.Pro238Thr	p.P238T	ENST00000334409	NM_005018.2	238	Ccc/Acc	5/5	0.826534768307685	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.873568027427842	1		261	324	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111663	56111663	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004410-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	143	153	0	ENST00000399503.3:c.263C>G	p.Ser88Trp	p.S88W	ENST00000399503	NM_005921.1	88	tCg/tGg	1/20	0.873568027427842	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.873568027427842	1		153	182	SUCCESS
APC	324	MSKCC	GRCh37	5	112111363	112111363	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004410-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	103	308	0	ENST00000257430.4:c.460G>C	p.Glu154Gln	p.E154Q	ENST00000257430	NM_000038.5	154	Gaa/Caa	5/16	0.873568027427842	1	FACETS	0.991	0.933	1	0.991	0.933	1	CLONAL	1	TRUE	0	0.873568027427842	1		308	134	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	401928	401928	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004410-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	124	383	0	ENST00000399788.2:c.4863C>A	p.Asp1621Glu	p.D1621E	ENST00000399788	NM_001042603.1	1621	gaC/gaA	27/28	0.333008783865075	5	FACETS	1	0.975	1			1	INDETERMINATE	1	TRUE	NA	0.873568027427842	5		383	544	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727843	78727843	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004410-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	245	355	0	ENST00000306801.3:c.688C>G	p.Gln230Glu	p.Q230E	ENST00000306801	NM_020761.2	230	Cag/Gag	6/34	0.873568027427842	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.873568027427842	1		355	305	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266723	18266723	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1308748759	NA	P-0004410-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	184	173	0	ENST00000222254.8:c.34C>G	p.Leu12Val	p.L12V	ENST00000222254	NM_005027.3	12	Ctg/Gtg	2/16	1	2	FACETS	0.977	0.913	1	0.977	0.913	1	CLONAL	1	TRUE	1	0.873568027427842	2		173	431	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912463	50912463	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004410-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	252	390	0	ENST00000440232.2:c.1977C>G	p.Ile659Met	p.I659M	ENST00000440232	NM_002691.3	659	atC/atG	16/27	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.873568027427842	2		390	564	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057303	30057303	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1450914413	NA	P-0004410-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	99	257	0	ENST00000338641.4:c.785G>A	p.Arg262Gln	p.R262Q	ENST00000338641	NM_000268.3	262	cGa/cAa	8/16	1	2	FACETS	0.96	0.874	1	0.96	0.874	1	CLONAL	1	TRUE	1	0.873568027427842	2		257	236	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565509	41565509	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004410-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	103	326	0	ENST00000263253.7:c.4175G>A	p.Arg1392Lys	p.R1392K	ENST00000263253	NM_001429.3	1392	aGa/aAa	26/31	1	2	FACETS	0.947	0.863	1	0.947	0.863	1	CLONAL	1	TRUE	1	0.873568027427842	2		326	249	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007805	45007810	+	inframe_deletion	In_Frame_Del	DEL	CTTGTA	CTTGTA	-	novel	NA	P-0004410-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	92	235	0	ENST00000558401.1:c.254_259del	p.Leu85_Tyr86del	p.L85_Y86del	ENST00000558401	NM_004048.2	84	ctCTTGTAc/ctc	2/4	0.816965710270014	1	FACETS	0.906	0.843	0.965	0.906	0.843	0.965	CLONAL	1	TRUE	0	0.873568027427842	1		235	131	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280012	66280012	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004410-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	119	299	0	ENST00000273854.3:c.1677del	p.Thr560ProfsTer15	p.T560Pfs*15	ENST00000273854	NM_004439.5	559	acC/ac	7/18	NA	2	FACETS	0.998	0.917	1			1	INDETERMINATE	1	TRUE	NA	0.873568027427842	2		299	273	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197751	123197759	+	inframe_deletion	In_Frame_Del	DEL	TACAGATGT	TACAGATGT	-	novel	NA	P-0004410-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	166	249	0	ENST00000218089.9:c.1876_1884del	p.Thr626_Val628del	p.T626_V628del	ENST00000218089	NM_001042749.1	625	gaTACAGATGTt/gat	20/35	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.873568027427842	1		249	191	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268223	153268224	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	AC	AC	CA	novel	NA	P-0004410-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	108	144	0	ENST00000281708.4:c.585-1_585delinsTG		p.X195_splice	ENST00000281708	NM_033632.3	195		4/12	0.873568027427842	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.873568027427842	1		144	139	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183696	10183696	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	129	227	0	ENST00000256474.2:c.166del	p.Ala56ProfsTer11	p.A56Pfs*11	ENST00000256474	NM_000551.3	55	gaG/ga	1/3	0.567742900972959	1	FACETS	0.998	0.918	1	0.998	0.918	1	CLONAL	1	FALSE	0	0.567742900972959	1		227	326	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776215	135776218	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs118203707	NA	P-0004413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	164	371	0	ENST00000298552.3:c.2509_2512del	p.Asn837ValfsTer11	p.N837Vfs*11	ENST00000298552	NM_001162426.1	837	AACAgt/gt	20/23	0.567742900972959	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	0	0.567742900972959	1		371	400	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276864	15276864	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004429-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	55	346	0	ENST00000263388.2:c.5401G>C	p.Gly1801Arg	p.G1801R	ENST00000263388	NM_000435.2	1801	Ggg/Cgg	30/33	0.26235583725155	3	FACETS	1	0.943	1	0.591	0.51	0.677	INDETERMINATE	1	TRUE	1	0.450861041009089	3		346	253	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0004430-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	77	456	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		456	241	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0004439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	325	228	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.397356531102987	3	FACETS	0.862	0.825	0.9	0.862	0.825	0.9	CLONAL	3	TRUE	0	0.561587743724519	3		228	573	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0004439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	622	315	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.561594413637209	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	2	0.561587743724519	4		315	1598	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955146	93955146	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	507	517	1	ENST00000369303.4:c.2752A>G	p.Asn918Asp	p.N918D	ENST00000369303	NM_004440.3	918	Aac/Gac	16/17	0.561594413637209	3	FACETS	0.874	0.838	0.911	0.874	0.838	0.911	CLONAL	2	TRUE	1	0.561587743724519	3		518	1323	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420607	49420607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123724	NA	P-0004439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	245	287	1	ENST00000301067.7:c.15142C>T	p.Arg5048Cys	p.R5048C	ENST00000301067	NM_003482.3	5048	Cgt/Tgt	48/54	0.557093147826472	3	FACETS	1	0.981	1	0.561	0.524	0.599	CLONAL	1	TRUE	1	0.561587743724519	3		288	996	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427267	49427267	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	302	223	0	ENST00000301067.7:c.11221C>T	p.Gln3741Ter	p.Q3741*	ENST00000301067	NM_003482.3	3741	Caa/Taa	39/54	0.557093147826472	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	1	0.561587743724519	3		223	686	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347729	347729	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	737	283	0	ENST00000262320.3:c.1777del	p.Ala593ProfsTer112	p.A593Pfs*112	ENST00000262320	NM_003502.3	593	Gcc/cc	6/11	0.525922028767476	4	FACETS	0.997	0.973	1	1	0.998	1	CLONAL	4	TRUE	2	0.561587743724519	4		283	1028	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0004446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	17	456	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.494	0.367	0.647	0.494	0.367	0.647	SUBCLONAL	1	TRUE	1	0.13	2		456	529	SUCCESS
AR	367	MSKCC	GRCh37	X	66943543	66943543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852581	NA	P-0004448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	54	269	0	ENST00000374690.3:c.2623C>T	p.His875Tyr	p.H875Y	ENST00000374690	NM_000044.3	875	Cat/Tat	8/8	1	1	FACETS	0.342	0.293	0.396	0.342	0.293	0.396	SUBCLONAL	1	TRUE	0	0.572798048379046	1		269	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0004449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	83	314	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.574746035581362	2		314	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0004449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	86	228	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	0.574746035581362	2		228	220	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0004449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	645	412	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.494738604418949	5	FACETS	1	0.995	1			1	CLONAL	4	TRUE	NA	0.574746035581362	5		413	957	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041067	180041067	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0004449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	64	345	0	ENST00000261937.6:c.3331+1G>T		p.X1111_splice	ENST00000261937	NM_182925.4	1111			1	2	FACETS	0.985	0.865	1	0.985	0.865	1	CLONAL	1	TRUE	1	0.574746035581362	2		345	226	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828005	72828005	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373169458	NA	P-0004449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	163	732	0	ENST00000268489.5:c.8576C>T	p.Thr2859Met	p.T2859M	ENST00000268489	NM_006885.3	2859	aCg/aTg	9/10	0.454493618039731	1	FACETS	0.923	0.856	0.991	0.923	0.856	0.991	CLONAL	1	TRUE	0	0.574746035581362	1		732	438	SUCCESS
AR	367	MSKCC	GRCh37	X	66765803	66765803	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	57	528	0	ENST00000374690.3:c.815T>C	p.Leu272Pro	p.L272P	ENST00000374690	NM_000044.3	272	cTt/cCt	1/8	0.271964676173915	1	FACETS	0.411	0.354	0.472	0.411	0.354	0.472	INDETERMINATE	1	TRUE	0	0.574746035581362	1		528	344	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748169	72748169	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004463-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	68	216	0	ENST00000357731.5:c.9G>C	p.Met3Ile	p.M3I	ENST00000357731	NM_173808.2	3	atG/atC	1/7	1	2	FACETS	0.528	0.459	0.602	0.528	0.459	0.602	SUBCLONAL	1	TRUE	1	0.432915863392777	2		216	595	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750722	128750722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004463-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	43	213	0	ENST00000377970.2:c.259C>T	p.Pro87Ser	p.P87S	ENST00000377970	NM_002467.4	87	Ccc/Tcc	2/3	0.432915863392777	1	FACETS	0.337	0.282	0.398	0.337	0.282	0.398	SUBCLONAL	1	TRUE	0	0.432915863392777	1		213	462	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112412	115112412	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004463-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	29	108	0	ENST00000257566.3:c.1328C>T	p.Ser443Leu	p.S443L	ENST00000257566	NM_016569.3	443	tCg/tTg	7/8	0.432915863392777	1	FACETS	0.372	0.299	0.455	0.372	0.299	0.455	SUBCLONAL	1	TRUE	0	0.432915863392777	1		108	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577571	7577571	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs765848205	NA	P-0004463-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	75	114	0	ENST00000269305.4:c.710T>A	p.Met237Lys	p.M237K	ENST00000269305	NM_001126112.2	237	aTg/aAg	7/11	0.432915863392777	1	FACETS	0.956	0.847	1	0.956	0.847	1	CLONAL	1	TRUE	0	0.432915863392777	1		114	284	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244882	41244882	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004463-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	54	187	0	ENST00000357654.3:c.2666C>G	p.Ser889Cys	p.S889C	ENST00000357654	NM_007294.3	889	tCt/tGt	10/23	0.430319750547895	2	FACETS	0.35	0.298	0.407	0.175	0.149	0.204	SUBCLONAL	1	TRUE	0	0.432915863392777	2		187	713	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210418	2210418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760131961	NA	P-0004463-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	19	110	0	ENST00000398665.3:c.1025G>A	p.Arg342Gln	p.R342Q	ENST00000398665	NM_032482.2	342	cGg/cAg	13/28	0.322072822986577	1	FACETS	0.283	0.215	0.363	0.283	0.215	0.363	SUBCLONAL	1	TRUE	0	0.432915863392777	1		110	243	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798191	42798191	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004463-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	28	157	0	ENST00000575354.2:c.4145C>T	p.Ser1382Leu	p.S1382L	ENST00000575354	NM_015125.3	1382	tCa/tTa	17/20	0.189092614962567	3	FACETS	0.286	0.228	0.353	0.143	0.114	0.177	INDETERMINATE	1	TRUE	1	0.432915863392777	3		157	550	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797786	42797786	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004473-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	748	192	0	ENST00000575354.2:c.3838G>A	p.Gly1280Arg	p.G1280R	ENST00000575354	NM_015125.3	1280	Ggg/Agg	16/20	0.471611801962506	5	FACETS	1	0.995	1			1	CLONAL	4	TRUE	NA	0.569863237120349	5		192	1122	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007475	62007475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1389559363	NA	P-0004482-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	362	376	0	ENST00000392795.3:c.392C>T	p.Ser131Leu	p.S131L	ENST00000392795	NM_001039933.1	131	tCg/tTg	3/6	1	2	FACETS	0.923	0.88	0.967	0.923	0.88	0.967	CLONAL	1	TRUE	1	0.936137984641597	2		376	838	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0004499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	121	545	1	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.534964039490284	2		546	345	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233730	233730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1483236652	NA	P-0004499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	37	183	0	ENST00000264932.6:c.1034G>A	p.Arg345Gln	p.R345Q	ENST00000264932	NM_004168.2	345	cGg/cAg	8/15	0.534964039490284	4	FACETS	0.786	0.652	0.935	0.393	0.326	0.468	CLONAL	1	TRUE	2	0.534964039490284	4		183	270	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0004526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	23	497	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	0.361	0.28	0.456	0.361	0.28	0.456	SUBCLONAL	1	TRUE	1	0.19	2		497	670	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061123	38061171	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCC	CCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCC	-	novel	NA	P-0004526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	18	87	0	ENST00000250448.2:c.818_866del	p.Gly273AlafsTer32	p.G273Afs*32	ENST00000250448	NM_004496.3	273	gGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGCGGCGCCAAGGGc/gc	2/2	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.19	2		87	146	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743895	41743895	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	152	516	1	ENST00000301178.4:c.830A>G	p.Asp277Gly	p.D277G	ENST00000301178	NM_021913.4	277	gAc/gGc	7/20	0.137219161102947	0	FACETS	0.619	0.569	0.67			1	INDETERMINATE	1	TRUE	0	0.470056524891617	0		517	554	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692812	89692812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	155	226	0	ENST00000371953.3:c.297del	p.Glu99AspfsTer14	p.E99Dfs*14	ENST00000371953	NM_000314.4	99	gAa/ga	5/9	0.137219161102947	0	FACETS	0.963	0.894	1			1	INDETERMINATE	1	TRUE	0	0.470056524891617	0		226	363	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913400	NA	P-0004533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	13	532	0	ENST00000349496.5:c.98C>A	p.Ser33Tyr	p.S33Y	ENST00000349496	NM_001904.3	33	tCt/tAt	3/15	NA	2	FACETS	0.195	0.138	0.265			1	INDETERMINATE	1	TRUE	NA	0.263863540196957	2		532	505	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857531	68857531	+	splice_donor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0004533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	45	270	0	ENST00000261769.5:c.2164+2del		p.X722_splice	ENST00000261769	NM_004360.3	722			NA	2	FACETS	1	0.9	1			1	INDETERMINATE	1	TRUE	NA	0.263863540196957	2		270	313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578484	7578502	+	frameshift_variant	Frame_Shift_Del	DEL	GAATCAACCCACAGCTGCA	GAATCAACCCACAGCTGCA	-	novel	NA	P-0004533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	66	371	0	ENST00000269305.4:c.428_446del	p.Val143AlafsTer21	p.V143Afs*21	ENST00000269305	NM_001126112.2	143	gTGCAGCTGTGGGTTGATTCc/gc	5/11	0.263863540196957	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.263863540196957	1		371	401	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846036	68846037	+	splice_acceptor_variant	Splice_Site	DEL	AG	AG	-	rs786201045	NA	P-0004533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	71	522	0	ENST00000261769.5:c.1009_1010del		p.X337_splice	ENST00000261769	NM_004360.3	337			NA	2	FACETS	0.968	0.846	1			1	INDETERMINATE	1	TRUE	NA	0.263863540196957	2		522	556	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579398	7579398	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	117	337	0	ENST00000269305.4:c.289del	p.Val97SerfsTer26	p.V97Sfs*26	ENST00000269305	NM_001126112.2	97	Gtc/tc	4/11	0.189292365955295	3	FACETS	0.948	0.855	1	0.948	0.855	1	CLONAL	2	TRUE	1	0.189292365955295	3		337	714	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0004553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	22	412	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		413	720	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0004553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	20	336	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		336	888	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562842	21562843	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0004563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	23	298	0	ENST00000382592.4:c.1076_1077delinsCT	p.Leu359Pro	p.L359P	ENST00000382592	NM_014572.2	359	cTG/cCT	4/8	1	2	FACETS	0.384	0.299	0.483	0.384	0.299	0.483	SUBCLONAL	1	TRUE	1	0.29	2		298	413	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852118	63852118	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0121433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	127	355	0	ENST00000279873.7:c.2901del	p.Lys967AsnfsTer15	p.K967Nfs*15	ENST00000279873	NM_032199.2	966	Aaa/aa	10/10	1	2	FACETS	0.697	0.636	0.76	0.697	0.636	0.76	SUBCLONAL	1	NA	1	0.815370444665848	2		355	447	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955059	17955059	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0121433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	199	483	2	ENST00000458235.1:c.168G>C	p.Gln56His	p.Q56H	ENST00000458235	NM_000215.3	56	caG/caC	2/24	0.815370444665848	2	FACETS	1	0.968	1	0.527	0.494	0.561	CLONAL	1	NA	0	0.815370444665848	2		485	463	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932085	39932085	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0121433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	225	546	0	ENST00000378444.4:c.2514del	p.Lys839SerfsTer17	p.K839Sfs*17	ENST00000378444	NM_001123385.1	838	ccC/cc	4/15	1	2	FACETS	0.835	0.782	0.889	0.835	0.782	0.889	CLONAL	1	NA	1	0.815370444665848	2		546	661	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845361	156845361	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	137	536	1	ENST00000524377.1:c.1404C>A	p.Phe468Leu	p.F468L	ENST00000524377	NM_002529.3	468	ttC/ttA	12/17	1	2	FACETS	0.451	0.411	0.494	0.451	0.411	0.494	SUBCLONAL	1	TRUE	1	0.818368103957627	2		537	742	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789685	3789685	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	138	514	0	ENST00000262367.5:c.4174C>T	p.Arg1392Ter	p.R1392*	ENST00000262367	NM_004380.2	1392	Cga/Tga	25/31	1	2	FACETS	0.455	0.414	0.498	0.455	0.414	0.498	SUBCLONAL	1	TRUE	1	0.818368103957627	2		514	741	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955966	55955966	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757722266	NA	P-0004600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	517	231	0	ENST00000263923.4:c.3196C>T	p.Arg1066Cys	p.R1066C	ENST00000263923	NM_002253.2	1066	Cgc/Tgc	24/30	0.316676837590378	6	FACETS	0.958	0.921	0.996	0.958	0.921	0.996	INDETERMINATE	3	TRUE	3	0.814867189734006	6		231	1161	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081519	143081519	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	851	216	0	ENST00000262992.4:c.1555G>T	p.Glu519Ter	p.E519*	ENST00000262992	NM_001101669.1	519	Gaa/Taa	15/24	0.7304851736158	5	FACETS	0.909	0.888	0.931	0.728	0.71	0.745	CLONAL	4	TRUE	0	0.814867189734006	5		216	1276	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151868429	151868429	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0004600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	222	214	0	ENST00000262189.6:c.9375-2A>C		p.X3125_splice	ENST00000262189	NM_170606.2	3125			NA	2	FACETS	0.865	0.81	0.921			1	INDETERMINATE	1	TRUE	NA	0.814867189734006	2		214	630	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345855	152345855	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	392	356	0	ENST00000359321.1:c.715A>T	p.Met239Leu	p.M239L	ENST00000359321	NM_005431.1	239	Atg/Ttg	3/3	NA	2	FACETS	0.923	0.88	0.967			1	INDETERMINATE	1	TRUE	NA	0.814867189734006	2		356	1042	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492311	56492311	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	314	270	0	ENST00000267101.3:c.2644A>T	p.Ser882Cys	p.S882C	ENST00000267101	NM_001982.3	882	Agt/Tgt	22/28	0.798169233543107	3	FACETS	0.927	0.875	0.981	0.464	0.437	0.491	CLONAL	1	TRUE	1	0.814867189734006	3		270	1170	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	183	298	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.678626218401356	1	FACETS	0.938	0.879	0.997	0.938	0.879	0.997	CLONAL	1	TRUE	0	0.678626218401356	1		298	380	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65349005	65349005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	122	440	1	ENST00000342505.4:c.160G>A	p.Glu54Lys	p.E54K	ENST00000342505	NM_002227.2	54	Gag/Aag	3/25	0.333916787995671	1	FACETS	0.403	0.365	0.443	0.403	0.365	0.443	INDETERMINATE	1	TRUE	0	0.678626218401356	1		441	589	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076784	72076784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	95	677	0	ENST00000357731.5:c.713G>A	p.Gly238Glu	p.G238E	ENST00000357731	NM_173808.2	238	gGa/gAa	5/7	0.333916787995671	1	FACETS	0.348	0.31	0.387	0.348	0.31	0.387	INDETERMINATE	1	TRUE	0	0.678626218401356	1		677	532	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166491	118166491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	106	467	0	ENST00000369448.3:c.1001C>T	p.Ser334Phe	p.S334F	ENST00000369448	NM_017709.3	334	tCc/tTc	2/2	0.333916787995671	1	FACETS	0.321	0.288	0.356	0.321	0.288	0.356	INDETERMINATE	1	TRUE	0	0.678626218401356	1		467	643	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226589969	226589969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770918209	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	238	528	0	ENST00000366794.5:c.232C>T	p.Arg78Trp	p.R78W	ENST00000366794	NM_001618.3	78	Cgg/Tgg	2/23	1	2	FACETS	0.963	0.903	1	0.963	0.903	1	CLONAL	1	TRUE	1	0.678626218401356	2		528	728	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793373	242793373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	278	488	1	ENST00000334409.5:c.704C>T	p.Pro235Leu	p.P235L	ENST00000334409	NM_005018.2	235	cCg/cTg	5/5	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.678626218401356	2		489	730	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440915	52440916	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	260	469	0	ENST00000460680.1:c.588_589delinsAA	p.Trp196_Gly197delinsTer	p.W196_G197delins*	ENST00000460680	NM_004656.3	196	tgGGgg/tgAAgg	8/17	0.678626218401356	1	FACETS	0.987	0.936	1	0.987	0.936	1	CLONAL	1	TRUE	0	0.678626218401356	1		469	513	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026095	71026095	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	88	451	1	ENST00000318789.4:c.1527G>A	p.Trp509Ter	p.W509*	ENST00000318789	NM_032682.5	509	tgG/tgA	17/21	0.678626218401356	1	FACETS	0.916	0.833	1	0.916	0.833	1	CLONAL	1	TRUE	0	0.678626218401356	1		452	187	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356179	66356179	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	113	480	0	ENST00000273854.3:c.1318G>A	p.Glu440Lys	p.E440K	ENST00000273854	NM_004439.5	440	Gag/Aag	5/18	1	2	FACETS	0.863	0.783	0.945	0.863	0.783	0.945	CLONAL	1	TRUE	1	0.678626218401356	2		480	386	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361151	66361151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	79	604	0	ENST00000273854.3:c.1021G>A	p.Asp341Asn	p.D341N	ENST00000273854	NM_004439.5	341	Gat/Aat	4/18	1	2	FACETS	0.995	0.889	1	0.995	0.889	1	CLONAL	1	TRUE	1	0.678626218401356	2		604	234	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630936	187630936	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	119	525	0	ENST00000441802.2:c.46C>T	p.Gln16Ter	p.Q16*	ENST00000441802	NM_005245.3	16	Caa/Taa	2/27	0.463051229575638	3	FACETS	0.932	0.846	1	0.466	0.423	0.511	CLONAL	1	TRUE	1	0.678626218401356	3		525	504	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502728	149502729	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	237	421	0	ENST00000261799.4:c.2059_2060delinsAA	p.Gly687Lys	p.G687K	ENST00000261799	NM_002609.3	687	GGa/AAa	15/23	0.333916787995671	1	FACETS	0.848	0.799	0.898	0.848	0.799	0.898	INDETERMINATE	1	TRUE	0	0.678626218401356	1		421	544	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045945	26045946	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	414	1002	0	ENST00000540144.1:c.307_308delinsAA	p.Gly103Lys	p.G103K	ENST00000540144	NM_003531.2	103	GGa/AAa	1/1	0.148373707722403	4	FACETS	0.776	0.738	0.814	0.776	0.738	0.814	INDETERMINATE	2	TRUE	2	0.678626218401356	4		1002	1320	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967868	93967868	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	111	1031	0	ENST00000369303.4:c.2059G>A	p.Gly687Arg	p.G687R	ENST00000369303	NM_004440.3	687	Ggg/Agg	11/17	0.296432654427445	1	FACETS	0.686	0.625	0.749	0.686	0.625	0.749	INDETERMINATE	1	TRUE	0	0.678626218401356	1		1031	315	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982072	93982072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1334631229	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	137	740	0	ENST00000369303.4:c.1393G>A	p.Glu465Lys	p.E465K	ENST00000369303	NM_004440.3	465	Gaa/Aaa	6/17	0.296432654427445	1	FACETS	0.662	0.608	0.717	0.662	0.608	0.717	INDETERMINATE	1	TRUE	0	0.678626218401356	1		740	403	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94129037	94129038	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	157	781	0	ENST00000369303.4:c.22_23delinsTT	p.Pro8Phe	p.P8F	ENST00000369303	NM_004440.3	8	CCt/TTt	1/17	0.296432654427445	1	FACETS	0.585	0.539	0.632	0.585	0.539	0.632	INDETERMINATE	1	TRUE	0	0.678626218401356	1		781	523	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647465	117647465	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs867760368	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	122	814	0	ENST00000368508.3:c.5479C>T	p.Gln1827Ter	p.Q1827*	ENST00000368508	NM_002944.2	1827	Cag/Tag	33/43	0.296432654427445	1	FACETS	0.769	0.705	0.834	0.769	0.705	0.834	INDETERMINATE	1	TRUE	0	0.678626218401356	1		814	309	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709028	117709028	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	132	700	0	ENST00000368508.3:c.1929G>A	p.Met643Ile	p.M643I	ENST00000368508	NM_002944.2	643	atG/atA	13/43	0.296432654427445	1	FACETS	0.657	0.603	0.713	0.657	0.603	0.713	INDETERMINATE	1	TRUE	0	0.678626218401356	1		700	391	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714387	117714387	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs778189552	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	87	446	0	ENST00000368508.3:c.1262G>A	p.Gly421Glu	p.G421E	ENST00000368508	NM_002944.2	421	gGg/gAg	11/43	0.296432654427445	1	FACETS	0.856	0.775	0.937	0.856	0.775	0.937	INDETERMINATE	1	TRUE	0	0.678626218401356	1		446	198	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455147	50455147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	109	305	0	ENST00000331340.3:c.694C>T	p.Leu232Phe	p.L232F	ENST00000331340	NM_006060.4	232	Ctt/Ttt	6/8	1	2	FACETS	0.979	0.89	1	0.979	0.89	1	CLONAL	1	TRUE	1	0.678626218401356	2		305	328	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	169	227	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.678626218401356	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.678626218401356	1		227	267	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427141	49427141	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs752477959	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	245	634	0	ENST00000301067.7:c.11347C>T	p.Gln3783Ter	p.Q3783*	ENST00000301067	NM_003482.3	3783	Caa/Taa	39/54	1	2	FACETS	0.905	0.848	0.963	0.905	0.848	0.963	CLONAL	1	TRUE	1	0.678626218401356	2		634	798	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592714	28592714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	91	445	0	ENST00000241453.7:c.2431G>A	p.Asp811Asn	p.D811N	ENST00000241453	NM_004119.2	811	Gac/Aac	20/24	1	2	FACETS	0.906	0.814	1	0.906	0.814	1	CLONAL	1	TRUE	1	0.678626218401356	2		445	296	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022913	33022913	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1435968313	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	316	930	0	ENST00000300177.4:c.22G>A	p.Val8Met	p.V8M	ENST00000300177	NM_001191322.1	8	Gtg/Atg	2/2	NA	2	FACETS	0.907	0.857	0.958			1	INDETERMINATE	1	TRUE	NA	0.678626218401356	2		930	1027	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121898	2121898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	256	423	0	ENST00000219476.3:c.2060C>T	p.Ser687Phe	p.S687F	ENST00000219476	NM_000548.3	687	tCc/tTc	19/42	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.678626218401356	2		423	700	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821328	72821328	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567505030	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	299	562	0	ENST00000268489.5:c.10847C>T	p.Ser3616Phe	p.S3616F	ENST00000268489	NM_006885.3	3616	tCt/tTt	10/10	1	2	FACETS	0.958	0.904	1	0.958	0.904	1	CLONAL	1	TRUE	1	0.678626218401356	2		562	920	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618388	37618388	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	226	410	2	ENST00000447079.4:c.64C>T	p.Gln22Ter	p.Q22*	ENST00000447079	NM_015083.1	22	Cag/Tag	1/14	NA	2	FACETS	0.957	0.896	1			1	INDETERMINATE	1	TRUE	NA	0.678626218401356	2		412	696	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40443989	40443989	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	310	697	0	ENST00000345506.4:c.286-1G>A		p.X96_splice	ENST00000345506	NM_003152.3	96			1	2	FACETS	0.928	0.877	0.981	0.928	0.877	0.981	CLONAL	1	TRUE	1	0.678626218401356	2		697	984	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40478213	40478213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	284	652	0	ENST00000264657.5:c.1286C>T	p.Ser429Phe	p.S429F	ENST00000264657	NM_139276.2	429	tCc/tTc	15/24	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.678626218401356	2		652	797	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117204	7117204	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	263	643	0	ENST00000302850.5:c.4012G>T	p.Glu1338Ter	p.E1338*	ENST00000302850	NM_000208.2	1338	Gag/Tag	22/22	0.678626218401356	1	FACETS	0.43	0.402	0.458	0.43	0.402	0.458	SUBCLONAL	1	TRUE	0	0.678626218401356	1		643	1191	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272243	15272243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs541777668	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	365	246	0	ENST00000263388.2:c.6196C>T	p.Pro2066Ser	p.P2066S	ENST00000263388	NM_000435.2	2066	Ccc/Tcc	33/33	0.678626218401356	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.678626218401356	3		246	641	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955168	17955168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	240	415	0	ENST00000458235.1:c.59C>T	p.Ser20Phe	p.S20F	ENST00000458235	NM_000215.3	20	tCc/tTc	2/24	1	2	FACETS	0.998	0.936	1	0.998	0.936	1	CLONAL	1	TRUE	1	0.678626218401356	2		415	709	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918997	50918997	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568638506	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	357	589	0	ENST00000440232.2:c.2734C>T	p.Pro912Ser	p.P912S	ENST00000440232	NM_002691.3	912	Ccc/Tcc	22/27	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.678626218401356	2		589	1042	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735458	40735458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1243407933	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	480	603	2	ENST00000373198.4:c.3415C>T	p.Arg1139Trp	p.R1139W	ENST00000373198	NM_133170.3	1139	Cgg/Tgg	25/32	0.632717909690301	3	FACETS	0.966	0.928	1	0.966	0.928	1	CLONAL	2	TRUE	1	0.678626218401356	3		605	981	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032794	30032794	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121434259	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	164	511	0	ENST00000338641.4:c.169C>T	p.Arg57Ter	p.R57*	ENST00000338641	NM_000268.3	57	Cga/Tga	2/16	1	2	FACETS	0.928	0.858	1	0.928	0.858	1	CLONAL	1	TRUE	1	0.678626218401356	2		511	521	SUCCESS
AR	367	MSKCC	GRCh37	X	66765700	66765700	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	214	763	0	ENST00000374690.3:c.712G>A	p.Glu238Lys	p.E238K	ENST00000374690	NM_000044.3	238	Gag/Aag	1/8	0.46392878484553	1	FACETS	0.54	0.503	0.578	0.54	0.503	0.578	SUBCLONAL	1	TRUE	0	0.678626218401356	1		763	772	SUCCESS
AR	367	MSKCC	GRCh37	X	66766105	66766105	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	171	379	0	ENST00000374690.3:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000374690	NM_000044.3	373	Gga/Aga	1/8	0.46392878484553	1	FACETS	0.626	0.58	0.673	0.626	0.58	0.673	SUBCLONAL	1	TRUE	0	0.678626218401356	1		379	532	SUCCESS
AR	367	MSKCC	GRCh37	X	66766387	66766387	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1346818973	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	24	69	0	ENST00000374690.3:c.1399G>A	p.Gly467Ser	p.G467S	ENST00000374690	NM_000044.3	467	Ggc/Agc	1/8	0.46392878484553	1	FACETS	0.497	0.399	0.605	0.497	0.399	0.605	SUBCLONAL	1	TRUE	0	0.678626218401356	1		69	94	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034426	123034426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	226	525	0	ENST00000355640.3:c.1183G>A	p.Glu395Lys	p.E395K	ENST00000355640		395	Gaa/Aaa	6/7	0.463051229575638	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.678626218401356	3		525	358	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266133	+	inframe_deletion	In_Frame_Del	DEL	CTGGTGCCACTACCACAGCTC	CTGGTGCCACTACCACAGCTC	-	novel	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	102	503	0	ENST00000349496.5:c.112_132del	p.Gly38_Pro44del	p.G38_P44del	ENST00000349496	NM_001904.3	37	tCTGGTGCCACTACCACAGCTCct/tct	3/15	0.678626218401356	1	FACETS	0.856	0.781	0.932	0.856	0.781	0.932	CLONAL	1	TRUE	0	0.678626218401356	1		503	232	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412196	139412207	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGACGCACCGGG	CGACGCACCGGG	-	novel	NA	P-0004614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	258	436	0	ENST00000277541.6:c.1438_1441+8del		p.X480_splice	ENST00000277541	NM_017617.3	480		8/34	0.678626218401356	1	FACETS	0.977	0.926	1	0.977	0.926	1	CLONAL	1	TRUE	0	0.678626218401356	1		436	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0004615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	167	387	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.374625567046904	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.402045766567699	2		387	407	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391978	139391978	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	188	419	1	ENST00000277541.6:c.6213G>T	p.Glu2071Asp	p.E2071D	ENST00000277541	NM_017617.3	2071	gaG/gaT	34/34	0.374625567046904	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.402045766567699	2		420	431	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568828	212568828	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0004615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	56	416	0	ENST00000342788.4:c.1289+1G>T		p.X430_splice	ENST00000342788	NM_005235.2	430			0.402045766567699	3	FACETS	0.742	0.637	0.856	0.371	0.318	0.428	SUBCLONAL	1	TRUE	1	0.402045766567699	3		416	451	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162987	47162987	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	186	449	0	ENST00000409792.3:c.3139G>A	p.Asp1047Asn	p.D1047N	ENST00000409792	NM_014159.6	1047	Gat/Aat	3/21	0.374625567046904	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.402045766567699	2		449	457	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247432	71247432	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	158	389	0	ENST00000318789.4:c.101A>T	p.Glu34Val	p.E34V	ENST00000318789	NM_032682.5	34	gAg/gTg	6/21	0.374625567046904	2	FACETS	0.949	0.88	1	0.949	0.88	1	CLONAL	2	TRUE	0	0.402045766567699	2		389	414	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956604	93956604	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	92	783	1	ENST00000369303.4:c.2632G>T	p.Ala878Ser	p.A878S	ENST00000369303	NM_004440.3	878	Gct/Tct	15/17	0.133846956337158	3	FACETS	0.776	0.69	0.869			1	INDETERMINATE	1	TRUE	NA	0.402045766567699	3		784	708	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120438	94120438	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	227	796	0	ENST00000369303.4:c.613T>A	p.Cys205Ser	p.C205S	ENST00000369303	NM_004440.3	205	Tgc/Agc	3/17	0.133846956337158	3	FACETS	0.913	0.853	0.973			1	INDETERMINATE	2	TRUE	NA	0.402045766567699	3		796	743	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459521	50459521	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	124	355	0	ENST00000331340.3:c.810C>A	p.Asn270Lys	p.N270K	ENST00000331340	NM_006060.4	270	aaC/aaA	7/8	0.400191366418441	4	FACETS	0.765	0.695	0.839	0.765	0.695	0.839	SUBCLONAL	2	TRUE	2	0.402045766567699	4		355	565	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453149	140453149	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913361	NA	P-0004615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	74	405	0	ENST00000288602.6:c.1786G>T	p.Gly596Cys	p.G596C	ENST00000288602	NM_004333.4	596	Ggt/Tgt	15/18	0.20247636570074	4	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.402045766567699	4		405	407	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95598873	95598873	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	134	449	0	ENST00000393063.1:c.286A>C	p.Thr96Pro	p.T96P	ENST00000393063	NM_030621.3	96	Acg/Ccg	4/28	0.402045766567699	3	FACETS	0.933	0.855	1	0.933	0.855	1	CLONAL	2	TRUE	1	0.402045766567699	3		449	429	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476326	88476326	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	58	412	0	ENST00000360948.2:c.1806G>T	p.Lys602Asn	p.K602N	ENST00000360948	NM_001012338.2	602	aaG/aaT	15/19	1	2	FACETS	0.702	0.605	0.807	0.702	0.605	0.807	SUBCLONAL	1	TRUE	1	0.402045766567699	2		412	411	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223317	2223317	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	164	358	1	ENST00000326181.6:c.929A>T	p.Gln310Leu	p.Q310L	ENST00000326181	NM_032271.2	310	cAg/cTg	10/21	0.402045766567699	3	FACETS	0.97	0.897	1	0.97	0.897	1	CLONAL	2	TRUE	1	0.402045766567699	3		359	505	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624852	9624852	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	84	491	0	ENST00000353224.5:c.125T>A	p.Leu42Gln	p.L42Q	ENST00000353224	NM_177990.2	42	cTg/cAg	3/10	0.395417413016053	3	FACETS	1	0.908	1	0.514	0.455	0.577	CLONAL	1	TRUE	1	0.402045766567699	3		491	488	SUCCESS
AR	367	MSKCC	GRCh37	X	66942828	66942828	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0004615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	155	505	0	ENST00000374690.3:c.2607+2T>C		p.X869_splice	ENST00000374690	NM_000044.3	869			1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.402045766567699	2		505	521	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610255	10610256	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0004615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	185	542	0	ENST00000171111.5:c.454_455del	p.Val152ProfsTer21	p.V152Pfs*21	ENST00000171111	NM_203500.1	152	GTc/c	2/6	0.392096633730561	2	FACETS	0.906	0.843	0.969	0.906	0.843	0.969	CLONAL	2	TRUE	0	0.402045766567699	2		542	508	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	133	252	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.261992329955644	3	FACETS	0.799	0.729	0.871			1	SUBCLONAL	2	TRUE	NA	0.38478982348045	3		252	516	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537184	41537184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	111	558	1	ENST00000263253.7:c.2011C>T	p.Pro671Ser	p.P671S	ENST00000263253	NM_001429.3	671	Cca/Tca	10/31	0.311831335075268	2	FACETS	0.674	0.605	0.747	0.337	0.302	0.374	SUBCLONAL	1	TRUE	0	0.38478982348045	2		559	856	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354044	15354044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	45	101	0	ENST00000263377.2:c.2836C>T	p.Pro946Ser	p.P946S	ENST00000263377	NM_058243.2	946	Cct/Tct	14/20	0.322678390518446	3	FACETS	1	0.846	1	0.5	0.423	0.584	CLONAL	1	TRUE	1	0.38478982348045	3		101	279	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203756	94203756	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	87	450	0	ENST00000323929.3:c.898C>T	p.Pro300Ser	p.P300S	ENST00000323929	NM_005591.3	300	Cct/Tct	9/20	0.322678390518446	3	FACETS	0.599	0.529	0.674	0.3	0.264	0.337	SUBCLONAL	1	TRUE	1	0.38478982348045	3		450	900	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419837	41419837	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs267605939	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	115	259	0	ENST00000373198.4:c.484C>T	p.Gln162Ter	p.Q162*	ENST00000373198	NM_133170.3	162	Cag/Tag	3/32	0.26749047557633	3	FACETS	0.734	0.66	0.812	0.245	0.22	0.271	SUBCLONAL	1	TRUE	0	0.38478982348045	3		259	971	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969912	161969912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1460011098	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	119	465	0	ENST00000366898.1:c.1057G>A	p.Glu353Lys	p.E353K	ENST00000366898	NM_004562.2	353	Gaa/Aaa	9/12	0.311831335075268	2	FACETS	0.774	0.699	0.854	0.387	0.349	0.427	SUBCLONAL	1	TRUE	0	0.38478982348045	2		465	799	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300429	11300429	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	86	321	0	ENST00000361445.4:c.1717C>G	p.Leu573Val	p.L573V	ENST00000361445	NM_004958.3	573	Ctc/Gtc	11/58	0.330990342480398	3	FACETS	0.72	0.637	0.81	0.36	0.318	0.405	SUBCLONAL	1	TRUE	1	0.38478982348045	3		321	740	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101280	27101280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	139	529	0	ENST00000324856.7:c.4562C>T	p.Pro1521Leu	p.P1521L	ENST00000324856	NM_006015.4	1521	cCc/cTc	18/20	0.330990342480398	3	FACETS	0.813	0.739	0.891	0.406	0.369	0.446	CLONAL	1	TRUE	1	0.38478982348045	3		529	1060	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166571	118166571	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	103	360	0	ENST00000369448.3:c.1081C>T	p.Pro361Ser	p.P361S	ENST00000369448	NM_017709.3	361	Cct/Tct	2/2	0.271365771580807	4	FACETS	0.756	0.675	0.842	0.378	0.337	0.421	SUBCLONAL	1	TRUE	2	0.38478982348045	4		360	981	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458438	120458438	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	148	261	0	ENST00000256646.2:c.6907C>T	p.Pro2303Ser	p.P2303S	ENST00000256646	NM_024408.3	2303	Ccc/Tcc	34/34	0.271365771580807	4	FACETS	0.894	0.82	0.971	0.894	0.82	0.971	CLONAL	2	TRUE	2	0.38478982348045	4		261	596	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462203	120462203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1416097171	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	194	361	0	ENST00000256646.2:c.5513G>A	p.Arg1838Gln	p.R1838Q	ENST00000256646	NM_024408.3	1838	cGa/cAa	31/34	0.271365771580807	4	FACETS	0.914	0.848	0.982	0.914	0.848	0.982	CLONAL	2	TRUE	2	0.38478982348045	4		361	764	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849798	156849798	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	116	408	0	ENST00000524377.1:c.2054G>A	p.Gly685Asp	p.G685D	ENST00000524377	NM_002529.3	685	gGc/gAc	16/17	0.330990342480398	3	FACETS	0.826	0.744	0.913	0.413	0.372	0.457	CLONAL	1	TRUE	1	0.38478982348045	3		408	870	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746018	162746018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	118	563	1	ENST00000367921.3:c.2141G>A	p.Arg714Gln	p.R714Q	ENST00000367921	NM_006182.2	714	cGa/cAa	16/18	0.330990342480398	3	FACETS	0.782	0.705	0.864	0.391	0.352	0.432	SUBCLONAL	1	TRUE	1	0.38478982348045	3		564	935	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226580017	226580017	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	71	342	0	ENST00000366794.5:c.287-2A>C		p.X96_splice	ENST00000366794	NM_001618.3	96			0.330990342480398	3	FACETS	0.649	0.566	0.739	0.325	0.283	0.37	SUBCLONAL	1	TRUE	1	0.38478982348045	3		342	678	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265579	198265579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	310	664	0	ENST00000335508.6:c.2578G>A	p.Glu860Lys	p.E860K	ENST00000335508	NM_012433.2	860	Gaa/Aaa	18/25	0.311831335075268	2	FACETS	0.816	0.771	0.862	0.816	0.771	0.862	CLONAL	2	TRUE	0	0.38478982348045	2		664	987	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137620	202137620	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	160	654	0	ENST00000358485.4:c.728-1G>C		p.X243_splice	ENST00000358485	NM_001080125.1	243			0.311831335075268	2	FACETS	0.797	0.729	0.867	0.398	0.364	0.434	SUBCLONAL	1	TRUE	0	0.38478982348045	2		654	1044	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259496	89259496	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	80	537	1	ENST00000336596.2:c.640G>A	p.Asp214Asn	p.D214N	ENST00000336596	NM_005233.5	214	Gac/Aac	3/17	0.38478982348045	1	FACETS	0.583	0.514	0.657	0.583	0.514	0.657	SUBCLONAL	1	TRUE	0	0.38478982348045	1		538	576	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143352343	143352343	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	112	519	0	ENST00000262992.4:c.70C>T	p.Pro24Ser	p.P24S	ENST00000262992	NM_001101669.1	24	Ccc/Tcc	2/24	1	2	FACETS	0.735	0.661	0.813	0.735	0.661	0.813	SUBCLONAL	1	TRUE	1	0.38478982348045	2		519	792	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43745248	43745248	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	365	715	1	ENST00000523873.1:c.161C>T	p.Pro54Leu	p.P54L	ENST00000523873		54	cCa/cTa	3/8	0.38478982348045	3	FACETS	0.875	0.83	0.922	0.875	0.83	0.922	CLONAL	2	TRUE	1	0.38478982348045	3		716	1292	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555135	106555135	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	114	357	0	ENST00000369096.4:c.2252T>G	p.Val751Gly	p.V751G	ENST00000369096	NM_001198.3	751	gTg/gGg	7/7	NA	2	FACETS	0.793	0.714	0.876			1	INDETERMINATE	1	TRUE	NA	0.38478982348045	2		357	747	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647414	117647414	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	121	669	2	ENST00000368508.3:c.5530A>T	p.Ile1844Phe	p.I1844F	ENST00000368508	NM_002944.2	1844	Atc/Ttc	33/43	0.38478982348045	1	FACETS	0.609	0.55	0.671	0.609	0.55	0.671	SUBCLONAL	1	TRUE	0	0.38478982348045	1		671	834	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935595	13935595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776609162	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	67	381	0	ENST00000405192.2:c.1261G>A	p.Glu421Lys	p.E421K	ENST00000405192	NM_001163147.1	421	Gag/Aag	12/12	0.271365771580807	4	FACETS	0.576	0.499	0.659	0.288	0.249	0.33	SUBCLONAL	1	TRUE	2	0.38478982348045	4		381	837	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860308	151860308	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	426	561	0	ENST00000262189.6:c.10354C>T	p.Pro3452Ser	p.P3452S	ENST00000262189	NM_170606.2	3452	Ccc/Tcc	43/59	0.38478982348045	3	FACETS	0.892	0.853	0.931	0.892	0.853	0.931	CLONAL	3	TRUE	0	0.38478982348045	3		561	987	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874334	151874334	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	493	471	0	ENST00000262189.6:c.8204T>A	p.Leu2735Ter	p.L2735*	ENST00000262189	NM_170606.2	2735	tTa/tAa	38/59	0.38478982348045	3	FACETS	0.972	0.934	1	0.972	0.934	1	CLONAL	3	TRUE	0	0.38478982348045	3		471	1048	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272377	38272377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	160	590	0	ENST00000425967.3:c.1990G>A	p.Glu664Lys	p.E664K	ENST00000425967	NM_001174067.1	664	Gag/Aag	15/19	0.336916615591126	4	FACETS	0.885	0.809	0.965	0.443	0.404	0.483	CLONAL	1	TRUE	2	0.38478982348045	4		590	1301	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371815	55371815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	18	64	0	ENST00000297316.4:c.505C>T	p.Pro169Ser	p.P169S	ENST00000297316	NM_022454.3	169	Ccc/Tcc	2/2	0.336916615591126	4	FACETS	1	0.858	1	0.594	0.454	0.755	CLONAL	1	TRUE	2	0.38478982348045	4		64	109	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518111	8518111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	231	422	1	ENST00000356435.5:c.1280G>A	p.Arg427Gln	p.R427Q	ENST00000356435		427	cGa/cAa	10/35	0.322678390518446	3	FACETS	0.771	0.719	0.824	0.771	0.719	0.824	SUBCLONAL	2	TRUE	1	0.38478982348045	3		423	929	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908786	101908786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	137	600	0	ENST00000374994.4:c.1150C>T	p.Leu384Phe	p.L384F	ENST00000374994	NM_004612.2	384	Ctc/Ttc	7/9	0.322678390518446	3	FACETS	0.837	0.76	0.917	0.418	0.38	0.459	CLONAL	1	TRUE	1	0.38478982348045	3		600	1015	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609039	43609039	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	169	610	2	ENST00000355710.3:c.1795C>T	p.Pro599Ser	p.P599S	ENST00000355710	NM_020975.4	599	Ccc/Tcc	10/20	NA	2	FACETS	0.768	0.705	0.834			1	INDETERMINATE	1	TRUE	NA	0.38478982348045	2		612	1144	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343391	118343391	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs936693402	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	129	463	0	ENST00000534358.1:c.1517C>T	p.Thr506Ile	p.T506I	ENST00000534358	NM_005933.3	506	aCc/aTc	3/36	0.322678390518446	3	FACETS	1	0.909	1	0.501	0.454	0.55	CLONAL	1	TRUE	1	0.38478982348045	3		463	798	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416732	121416732	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1338145634	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	142	507	2	ENST00000257555.6:c.161G>A	p.Arg54Gln	p.R54Q	ENST00000257555		54	cGa/cAa	1/10	0.322678390518446	3	FACETS	0.949	0.865	1	0.475	0.432	0.519	CLONAL	1	TRUE	1	0.38478982348045	3		509	927	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895689	28895689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	131	610	0	ENST00000282397.4:c.3085C>T	p.Leu1029Phe	p.L1029F	ENST00000282397	NM_002019.4	1029	Ctt/Ttt	23/30	0.311831335075268	2	FACETS	0.746	0.676	0.819	0.373	0.338	0.41	SUBCLONAL	1	TRUE	0	0.38478982348045	2		610	913	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435438	110435438	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	124	224	0	ENST00000375856.3:c.2963C>T	p.Ser988Phe	p.S988F	ENST00000375856	NM_003749.2	988	tCt/tTt	1/2	0.311831335075268	2	FACETS	0.769	0.702	0.839	0.769	0.702	0.839	SUBCLONAL	2	TRUE	0	0.38478982348045	2		224	419	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423566	88423566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1361200565	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	335	576	1	ENST00000360948.2:c.2269G>A	p.Gly757Arg	p.G757R	ENST00000360948	NM_001012338.2	757	Ggg/Agg	18/19	0.328425301792876	5	FACETS	0.879	0.832	0.926	0.659	0.624	0.695	CLONAL	3	TRUE	1	0.38478982348045	5		577	1042	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679753	88679753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	131	520	0	ENST00000360948.2:c.710C>T	p.Pro237Leu	p.P237L	ENST00000360948	NM_001012338.2	237	cCc/cTc	7/19	0.328425301792876	5	FACETS	0.854	0.773	0.94	0.214	0.193	0.235	CLONAL	1	TRUE	1	0.38478982348045	5		520	1257	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823918	3823918	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	135	412	0	ENST00000262367.5:c.2297C>T	p.Pro766Leu	p.P766L	ENST00000262367	NM_004380.2	766	cCt/cTt	13/31	0.335205032186009	2	FACETS	0.909	0.827	0.995	0.454	0.413	0.498	CLONAL	1	TRUE	0	0.38478982348045	2		412	772	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923318	9923318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867335598	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	106	541	0	ENST00000330684.3:c.1969G>A	p.Glu657Lys	p.E657K	ENST00000330684	NM_001134407.1	657	Gaa/Aaa	9/13	0.335205032186009	2	FACETS	0.721	0.646	0.8	0.361	0.323	0.4	SUBCLONAL	1	TRUE	0	0.38478982348045	2		541	764	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2225445	2225445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	408	619	1	ENST00000398665.3:c.3655G>A	p.Glu1219Lys	p.E1219K	ENST00000398665	NM_032482.2	1219	Gaa/Aaa	26/28	0.354339432829503	2	FACETS	0.944	0.9	0.989	0.944	0.9	0.989	CLONAL	2	TRUE	0	0.38478982348045	2		620	1123	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7132234	7132234	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	170	478	0	ENST00000302850.5:c.2777G>A	p.Arg926Gln	p.R926Q	ENST00000302850	NM_000208.2	926	cGg/cAg	14/22	0.322678390518446	3	FACETS	1	0.922	1	0.502	0.461	0.545	CLONAL	1	TRUE	1	0.38478982348045	3		478	1050	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909505	50909505	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1265	202	779	0	ENST00000440232.2:c.1309C>T	p.Gln437Ter	p.Q437*	ENST00000440232	NM_002691.3	437	Cag/Tag	11/27	0.271365771580807	4	FACETS	0.991	0.916	1	0.496	0.458	0.535	CLONAL	1	TRUE	2	0.38478982348045	4		779	1467	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022862	31022862	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	118	488	0	ENST00000375687.4:c.2347C>T	p.Pro783Ser	p.P783S	ENST00000375687	NM_015338.5	783	Ccg/Tcg	13/13	0.334862945760659	4	FACETS	0.788	0.709	0.871	0.263	0.236	0.291	SUBCLONAL	1	TRUE	1	0.38478982348045	4		488	1078	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36421162	36421162	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750755857	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	108	389	0	ENST00000300305.3:c.35C>T	p.Ser12Leu	p.S12L	ENST00000300305		12	tCg/tTg	1/8	0.330990342480398	3	FACETS	0.771	0.691	0.856	0.386	0.345	0.428	SUBCLONAL	1	TRUE	1	0.38478982348045	3		389	868	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526061	189526062	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	254	436	0	ENST00000264731.3:c.325_326delinsTT	p.Pro109Leu	p.P109L	ENST00000264731	NM_003722.4	109	CCa/TTa	4/14	0.38478982348045	3	FACETS	0.88	0.826	0.937	0.88	0.826	0.937	CLONAL	2	TRUE	1	0.38478982348045	3		436	894	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753997	57753998	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	82	361	0	ENST00000274289.3:c.626_627delinsAA	p.Gly209Glu	p.G209E	ENST00000274289	NM_006622.3	209	gGG/gAA	5/14	0.330990342480398	3	FACETS	0.695	0.613	0.784	0.348	0.306	0.392	SUBCLONAL	1	TRUE	1	0.38478982348045	3		361	731	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577537	7577538	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0004641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	281	413	2	ENST00000269305.4:c.743_744delinsAA	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGG/cAA	7/11	0.311831335075268	2	FACETS	0.975	0.921	1	0.975	0.921	1	CLONAL	2	TRUE	0	0.38478982348045	2		415	749	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152093	55152093	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121908585	NA	P-0004651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	268	262	0	ENST00000257290.5:c.2525A>T	p.Asp842Val	p.D842V	ENST00000257290	NM_006206.4	842	gAc/gTc	18/23	NA	2	FACETS	0.862	0.813	0.91			1	INDETERMINATE	2	TRUE	NA	0.462158089413753	2		262	673	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562638	29562641	+	frameshift_variant	Frame_Shift_Del	DEL	GCTC	GCTC	-	novel	NA	P-0004657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	34	605	0	ENST00000356175.3:c.3719_3722del	p.Ala1240GlufsTer25	p.A1240Efs*25	ENST00000356175	NM_000267.3	1240	GCTCga/ga	28/57	1	2	FACETS	0.484	0.399	0.576	0.484	0.399	0.576	SUBCLONAL	1	FALSE	1	0.760133632829946	2		605	185	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0004666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	169	288	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.514047567991114	3	FACETS	1	0.947	1	0.519	0.477	0.562	CLONAL	1	TRUE	1	0.514047567991114	3		288	797	SUCCESS
APC	324	MSKCC	GRCh37	5	112116601	112116601	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs863225370	NA	P-0004666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	237	253	0	ENST00000257430.4:c.645+1G>A		p.X215_splice	ENST00000257430	NM_000038.5	215			0.514047567991114	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	3	TRUE	0	0.514047567991114	3		253	381	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55228007	55228007	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	252	396	0	ENST00000275493.2:c.1474A>C	p.Ser492Arg	p.S492R	ENST00000275493	NM_005228.3	492	Agc/Cgc	12/28	0.511858257176924	5	FACETS	0.776	0.726	0.828	0.388	0.363	0.414	SUBCLONAL	2	TRUE	1	0.514047567991114	5		396	1119	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057520000	NA	P-0004666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	269	300	0	ENST00000269305.4:c.452C>G	p.Pro151Arg	p.P151R	ENST00000269305	NM_001126112.2	151	cCc/cGc	5/11	0.514047567991114	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.514047567991114	2		300	456	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796465	42796465	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	294	393	1	ENST00000575354.2:c.3022C>T	p.Gln1008Ter	p.Q1008*	ENST00000575354	NM_015125.3	1008	Cag/Tag	13/20	0.514047567991114	3	FACETS	1	0.986	1			1	CLONAL	2	TRUE	NA	0.514047567991114	3		394	647	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747137	40747137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752831315	NA	P-0004666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	102	355	0	ENST00000373198.4:c.2945C>T	p.Pro982Leu	p.P982L	ENST00000373198	NM_133170.3	982	cCg/cTg	22/32	0.301522246059268	6	FACETS	0.78	0.696	0.87			1	INDETERMINATE	1	TRUE	NA	0.514047567991114	6		355	1032	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818397	43818397	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004668-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	80	399	0	ENST00000372470.3:c.1862T>C	p.Ile621Thr	p.I621T	ENST00000372470	NM_005373.2	621	aTt/aCt	12/12	1	2	FACETS	0.806	0.713	0.905	0.806	0.713	0.905	CLONAL	1	TRUE	1	0.480537847774275	2		399	413	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460381	149460381	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004668-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	42	377	1	ENST00000286301.3:c.256G>A	p.Glu86Lys	p.E86K	ENST00000286301	NM_005211.3	86	Gag/Aag	3/22	1	2	FACETS	0.433	0.362	0.511	0.433	0.362	0.511	SUBCLONAL	1	TRUE	1	0.480537847774275	2		378	404	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842326	68842326	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0004668-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	77	436	0	ENST00000261769.5:c.388-1G>A		p.X130_splice	ENST00000261769	NM_004360.3	130			0.480537847774275	1	FACETS	0.674	0.596	0.757	0.674	0.596	0.757	SUBCLONAL	1	TRUE	0	0.480537847774275	1		436	361	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0004678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	193	335	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.219518607245264	3	FACETS	0.886	0.822	0.952	0.886	0.822	0.952	CLONAL	2	TRUE	1	0.348119389094418	3		335	735	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20488447	20488447	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	54	743	0	ENST00000346618.3:c.1103A>G	p.His368Arg	p.H368R	ENST00000346618	NM_001949.4	368	cAc/cGc	6/7	0.30118051017166	3	FACETS	0.366	0.311	0.426	0.183	0.155	0.213	SUBCLONAL	1	TRUE	1	0.348119389094418	3		743	995	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578259	7578259	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1567551903	NA	P-0004684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	89	704	0	ENST00000269305.4:c.590T>A	p.Val197Glu	p.V197E	ENST00000269305	NM_001126112.2	197	gTg/gAg	6/11	0.209285256565438	1	FACETS	0.766	0.678	0.861	0.766	0.678	0.861	SUBCLONAL	1	FALSE	0	0.209285256565438	1		704	994	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690393	117690419	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGATCTCCGATTCTGTGAAGTGAGAGA	TGATCTCCGATTCTGTGAAGTGAGAGA	-	novel	NA	P-0004684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	81	483	0	ENST00000369458.3:c.725-15_736del		p.X242_splice	ENST00000369458	NM_024626.3	242		5/6	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.209285256565438	2		483	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578227	7578227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	68	608	1	ENST00000269305.4:c.622G>A	p.Asp208Asn	p.D208N	ENST00000269305	NM_001126112.2	208	Gac/Aac	6/11	0.3	1	FACETS	0.621	0.539	0.71	0.621	0.539	0.71	SUBCLONAL	1	TRUE	0	0.23	1		609	843	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917490	178917490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	62	349	0	ENST00000263967.3:c.365G>A	p.Gly122Asp	p.G122D	ENST00000263967	NM_006218.2	122	gGc/gAc	3/21	1	2	FACETS	0.982	0.849	1	0.982	0.849	1	CLONAL	1	TRUE	1	0.23	2		349	549	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877402	89877402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780035612	NA	P-0004696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	94	474	1	ENST00000389301.3:c.361G>A	p.Val121Met	p.V121M	ENST00000389301	NM_000135.2	121	Gtg/Atg	4/43	1	2	FACETS	0.975	0.867	1	0.975	0.867	1	CLONAL	1	TRUE	1	0.23	2		475	838	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	45	542	0	ENST00000269305.4:c.859G>C	p.Glu287Gln	p.E287Q	ENST00000269305	NM_001126112.2	287	Gag/Cag	8/11	0.3	1	FACETS	0.464	0.388	0.547	0.464	0.388	0.547	SUBCLONAL	1	TRUE	0	0.23	1		542	747	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020146	123020146	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	133	629	0	ENST00000355640.3:c.635del	p.Pro212LeufsTer33	p.P212Lfs*33	ENST00000355640		212	Cct/ct	2/7	0.3	3	FACETS	1	0.967	1			1	CLONAL	1	TRUE	NA	0.23	3		629	1125	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439198	52439198	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	67	388	0	ENST00000460680.1:c.1044del	p.Asn349ThrfsTer13	p.N349Tfs*13	ENST00000460680	NM_004656.3	348	ccC/cc	11/17	0.3	1	FACETS	0.962	0.837	1	0.962	0.837	1	CLONAL	1	TRUE	0	0.23	1		388	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0000026-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	261	370	506	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.545731890261	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.545731890261	2		507	631	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0000026-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	325	468	213	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.545731890261	5	FACETS	0.983	0.948	1			1	CLONAL	4	TRUE	NA	0.545731890261	5		213	793	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004871	150004871	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000026-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	716	109	450	0	ENST00000253339.5:c.1354C>G	p.Pro452Ala	p.P452A	ENST00000253339		452	Cct/Gct	3/7	0.527041660926406	3	FACETS	0.616	0.553	0.683	0.308	0.276	0.342	SUBCLONAL	1	TRUE	1	0.545731890261	3		450	825	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467844	50467844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000026-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	469	135	323	0	ENST00000331340.3:c.1079G>A	p.Arg360His	p.R360H	ENST00000331340	NM_006060.4	360	cGc/cAc	8/8	0.527041660926406	3	FACETS	1	0.942	1	0.521	0.475	0.569	CLONAL	1	TRUE	1	0.545731890261	3		323	604	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246437	46246437	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000037-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	102	76	366	0	ENST00000334344.6:c.4531G>T	p.Glu1511Ter	p.E1511*	ENST00000334344	NM_152641.2	1511	Gaa/Taa	15/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.74313801889422	2		366	178	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396733	396733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000037-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	58	105	349	2	ENST00000262320.3:c.293G>A	p.Gly98Glu	p.G98E	ENST00000262320	NM_003502.3	98	gGg/gAg	2/11	0.73416063415706	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.74313801889422	1		351	163	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041504	14041504	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000037-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	25	68	202	0	ENST00000311895.7:c.2051T>C	p.Ile684Thr	p.I684T	ENST00000311895	NM_005236.2	684	aTa/aCa	11/11	0.73416063415706	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.74313801889422	1		202	93	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198280	138198283	+	frameshift_variant	Frame_Shift_Del	DEL	GACA	GACA	-	novel	NA	P-0000098-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	111	302	0	ENST00000237289.4:c.875_878del	p.Thr292IlefsTer6	p.T292Ifs*6	ENST00000237289	NM_001270507.1	291	ttGACA/tt	6/9	1	2	FACETS	0.787	0.714	0.863	0.787	0.714	0.863	SUBCLONAL	1	TRUE	1	0.73429843538019	2		302	384	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467698	66467698	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753230187	NA	P-0000115-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	124	285	0	ENST00000273854.3:c.571C>T	p.Arg191Cys	p.R191C	ENST00000273854	NM_004439.5	191	Cgt/Tgt	3/18	0.161449170580763	2	FACETS	0.996	0.902	1	0.996	0.902	1	CLONAL	2	TRUE	0	0.161449170580763	2		285	771	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636817	8636817	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000115-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	63	247	0	ENST00000356435.5:c.92T>A	p.Val31Asp	p.V31D	ENST00000356435		31	gTt/gAt	2/35	1	2	FACETS	0.831	0.717	0.956	0.831	0.717	0.956	CLONAL	1	TRUE	1	0.161449170580763	2		247	939	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421038	49421038	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000115-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	53	135	0	ENST00000301067.7:c.14711G>T	p.Arg4904Leu	p.R4904L	ENST00000301067	NM_003482.3	4904	cGa/cTa	48/54	0.161449170580763	3	FACETS	1	0.881	1	0.52	0.443	0.605	CLONAL	1	TRUE	1	0.161449170580763	3		135	682	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781504	NA	P-0000115-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	81	216	0	ENST00000269305.4:c.314G>A	p.Gly105Asp	p.G105D	ENST00000269305	NM_001126112.2	105	gGc/gAc	4/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.161449170580763	2		216	740	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528155	29528155	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000115-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	50	337	0	ENST00000356175.3:c.1163C>G	p.Pro388Arg	p.P388R	ENST00000356175	NM_000267.3	388	cCt/cGt	10/57	1	2	FACETS	0.635	0.536	0.743	0.635	0.536	0.743	SUBCLONAL	1	TRUE	1	0.161449170580763	2		337	976	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123505203	123505203	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000115-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	113	267	0	ENST00000371139.4:c.349A>G	p.Ile117Val	p.I117V	ENST00000371139	NM_001114937.2	117	Ata/Gta	4/4	0.161449170580763	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	0	0.161449170580763	2		267	678	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0000138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	241	124	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.500266368018607	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.500266368018607	3		124	549	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0000138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	562	358	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.500266368018607	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.500266368018607	3		358	1357	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609894	117609894	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs202153378	NA	P-0000138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	321	617	0	ENST00000368508.3:c.6805C>T	p.Arg2269Ter	p.R2269*	ENST00000368508	NM_002944.2	2269	Cga/Tga	43/43	0.500266368018607	2	FACETS	0.936	0.882	0.991	0.468	0.441	0.496	CLONAL	1	TRUE	0	0.500266368018607	2		617	1371	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266845	18266845	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	167	243	0	ENST00000222254.8:c.156G>C	p.Gln52His	p.Q52H	ENST00000222254	NM_005027.3	52	caG/caC	2/16	0.500266368018607	3	FACETS	1	0.957	1	0.53	0.488	0.574	CLONAL	1	TRUE	1	0.500266368018607	3		243	787	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352234	70352234	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1514	334	515	0	ENST00000374080.3:c.4261G>C	p.Glu1421Gln	p.E1421Q	ENST00000374080		1421	Gag/Cag	31/45	0.49546557716636	4	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.500266368018607	4		515	1848	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115745	8115745	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1369	444	625	1	ENST00000346208.3:c.1091G>C	p.Arg364Thr	p.R364T	ENST00000346208		364	aGa/aCa	6/6	0.500266368018607	3	FACETS	1	0.993	1	0.612	0.582	0.643	CLONAL	1	TRUE	1	0.500266368018607	3		626	1813	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188064	11188064	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	181	256	0	ENST00000361445.4:c.6030G>T	p.Met2010Ile	p.M2010I	ENST00000361445	NM_004958.3	2010	atG/atT	43/58	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.500266368018607	2		256	671	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303670	65303670	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1772	303	564	0	ENST00000342505.4:c.3085G>A	p.Glu1029Lys	p.E1029K	ENST00000342505	NM_002227.2	1029	Gaa/Aaa	22/25	0.500266368018607	4	FACETS	0.876	0.822	0.932	0.292	0.274	0.311	CLONAL	1	TRUE	1	0.500266368018607	4		564	2075	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466499	120466499	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1712	389	535	2	ENST00000256646.2:c.4620G>C	p.Glu1540Asp	p.E1540D	ENST00000256646	NM_024408.3	1540	gaG/gaC	26/34	0.500266368018607	4	FACETS	1	0.986	1	0.37	0.35	0.391	CLONAL	1	TRUE	1	0.500266368018607	4		537	2101	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707933	47707933	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1553370397	NA	P-0000138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	262	337	0	ENST00000233146.2:c.2557G>T	p.Glu853Ter	p.E853*	ENST00000233146	NM_000251.2	853	Gag/Tag	15/16	0.500266368018607	3	FACETS	1	0.983	1	0.569	0.533	0.607	CLONAL	1	TRUE	1	0.500266368018607	3		337	1150	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145528	61145528	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0000138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1289	73	310	0	ENST00000295025.8:c.641-1G>C		p.X214_splice	ENST00000295025	NM_002908.2	214			0.500266368018607	3	FACETS	0.268	0.233	0.306	0.134	0.116	0.153	SUBCLONAL	1	TRUE	1	0.500266368018607	3		310	1362	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281160	142281160	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1347	403	490	0	ENST00000350721.4:c.1084G>C	p.Glu362Gln	p.E362Q	ENST00000350721	NM_001184.3	362	Gaa/Caa	4/47	0.500266368018607	3	FACETS	1	0.989	1	0.575	0.546	0.606	CLONAL	1	TRUE	1	0.500266368018607	3		490	1750	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534464	187534464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	226	383	0	ENST00000441802.2:c.9262G>A	p.Glu3088Lys	p.E3088K	ENST00000441802	NM_005245.3	3088	Gag/Aag	13/27	0.500266368018607	2	FACETS	1	0.96	1	0.52	0.485	0.556	CLONAL	1	TRUE	0	0.500266368018607	2		383	869	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876293	35876293	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	249	352	0	ENST00000303115.3:c.1085G>T	p.Gly362Val	p.G362V	ENST00000303115	NM_002185.3	362	gGa/gTa	8/8	0.500266368018607	4	FACETS	1	0.96	1	0.52	0.485	0.557	CLONAL	1	TRUE	2	0.500266368018607	4		352	1435	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522551	176522551	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774571806	NA	P-0000138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	257	454	0	ENST00000292408.4:c.1648G>A	p.Val550Met	p.V550M	ENST00000292408	NM_213647.1	550	Gtg/Atg	13/18	0.500266368018607	4	FACETS	1	0.971	1	0.534	0.499	0.571	CLONAL	1	TRUE	2	0.500266368018607	4		454	1443	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508765	148508765	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs751723382	NA	P-0000138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	277	415	0	ENST00000320356.2:c.1899C>G	p.Ile633Met	p.I633M	ENST00000320356	NM_004456.4	633	atC/atG	16/20	0.500266368018607	3	FACETS	0.967	0.906	1	0.483	0.453	0.515	CLONAL	1	TRUE	1	0.500266368018607	3		415	1432	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517851	8517851	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1620	347	557	0	ENST00000356435.5:c.1540G>C	p.Gly514Arg	p.G514R	ENST00000356435		514	Gga/Cga	10/35	0.500266368018607	4	FACETS	1	0.975	1	0.529	0.499	0.56	CLONAL	1	TRUE	2	0.500266368018607	4		557	1967	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98009746	98009746	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1471	319	557	1	ENST00000289081.3:c.218A>G	p.Lys73Arg	p.K73R	ENST00000289081	NM_000136.2	73	aAa/aGa	3/15	0.500266368018607	3	FACETS	0.891	0.838	0.945	0.445	0.419	0.473	CLONAL	1	TRUE	1	0.500266368018607	3		558	1790	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98009780	98009780	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1215	262	470	0	ENST00000289081.3:c.184G>C	p.Glu62Gln	p.E62Q	ENST00000289081	NM_000136.2	62	Gaa/Caa	3/15	0.500266368018607	3	FACETS	0.887	0.829	0.947	0.443	0.414	0.474	CLONAL	1	TRUE	1	0.500266368018607	3		470	1477	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446212	70446212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	310	470	0	ENST00000373644.4:c.5152G>A	p.Glu1718Lys	p.E1718K	ENST00000373644	NM_030625.2	1718	Gag/Aag	11/12	0.500266368018607	2	FACETS	1	0.968	1	0.52	0.49	0.551	CLONAL	1	TRUE	0	0.500266368018607	2		470	1192	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486595	56486595	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	310	405	0	ENST00000267101.3:c.1174G>T	p.Glu392Ter	p.E392*	ENST00000267101	NM_001982.3	392	Gag/Tag	10/28	0.331402897184089	5	FACETS	0.784	0.738	0.831	0.522	0.492	0.554	SUBCLONAL	2	TRUE	2	0.500266368018607	5		405	1384	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248872	133248872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	265	411	0	ENST00000320574.5:c.1723G>A	p.Glu575Lys	p.E575K	ENST00000320574	NM_006231.2	575	Gag/Aag	16/49	0.500266368018607	3	FACETS	1	0.968	1			1	CLONAL	1	TRUE	NA	0.500266368018607	3		411	1259	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578246	28578246	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	338	519	0	ENST00000241453.7:c.2925C>A	p.Phe975Leu	p.F975L	ENST00000241453	NM_004119.2	975	ttC/ttA	24/24	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.500266368018607	2		519	1162	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346932	73346932	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	350	445	1	ENST00000377767.4:c.1285G>T	p.Glu429Ter	p.E429*	ENST00000377767	NM_014953.3	429	Gaa/Taa	9/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.500266368018607	2		446	1312	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029088	14029088	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	231	262	0	ENST00000311895.7:c.1299G>T	p.Leu433Phe	p.L433F	ENST00000311895	NM_005236.2	433	ttG/ttT	8/11	0.500266368018607	4	FACETS	1	0.963	1	0.526	0.49	0.565	CLONAL	1	TRUE	2	0.500266368018607	4		262	1316	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552209	29552209	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	325	439	0	ENST00000356175.3:c.1942G>T	p.Glu648Ter	p.E648*	ENST00000356175	NM_000267.3	648	Gaa/Taa	17/57	0.500266368018607	2	FACETS	1	0.973	1	0.525	0.495	0.555	CLONAL	1	TRUE	0	0.500266368018607	2		439	1238	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685536	29685536	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1131691074	NA	P-0000138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	295	407	0	ENST00000356175.3:c.7946C>A	p.Ser2649Ter	p.S2649*	ENST00000356175	NM_000267.3	2649	tCa/tAa	54/57	0.500266368018607	2	FACETS	1	0.97	1	0.524	0.493	0.555	CLONAL	1	TRUE	0	0.500266368018607	2		407	1126	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244352	41244352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1768	102	611	0	ENST00000357654.3:c.3196G>A	p.Glu1066Lys	p.E1066K	ENST00000357654	NM_007294.3	1066	Gaa/Aaa	10/23	0.500266368018607	4	FACETS	0.327	0.291	0.366	0.082	0.072	0.092	SUBCLONAL	1	TRUE	0	0.500266368018607	4		611	1870	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216292	2216292	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	207	293	0	ENST00000398665.3:c.1936G>A	p.Glu646Lys	p.E646K	ENST00000398665	NM_032482.2	646	Gag/Aag	20/28	0.500266368018607	2	FACETS	1	0.979	1	0.562	0.523	0.602	CLONAL	1	TRUE	0	0.500266368018607	2		293	736	SUCCESS
AXL	558	MSKCC	GRCh37	19	41759575	41759575	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1210	345	538	1	ENST00000301178.4:c.1998G>C	p.Lys666Asn	p.K666N	ENST00000301178	NM_021913.4	666	aaG/aaC	17/20	0.500266368018607	3	FACETS	1	0.984	1	0.554	0.523	0.586	CLONAL	1	TRUE	1	0.500266368018607	3		539	1555	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929487	44929487	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1469	422	627	0	ENST00000377967.4:c.2587C>G	p.Gln863Glu	p.Q863E	ENST00000377967	NM_021140.2	863	Cag/Gag	17/29	0.500266368018607	3	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.500266368018607	3		627	1891	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873674	151873674	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	234	309	0	ENST00000262189.6:c.8864del	p.Pro2955LeufsTer4	p.P2955Lfs*4	ENST00000262189	NM_170606.2	2955	cCt/ct	38/59	0.500266368018607	3	FACETS	1	0.952	1	0.513	0.478	0.549	CLONAL	1	TRUE	1	0.500266368018607	3		309	1140	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120666	115120667	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CC	CC	-	novel	NA	P-0000138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1395	382	583	0	ENST00000257566.3:c.339_340del	p.Trp113Ter	p.W113*	ENST00000257566	NM_016569.3	113	tgGGat/tgat	1/8	0.500266368018607	3	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.500266368018607	3		583	1777	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0000138-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	101	124	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.275205403390055	3	FACETS	0.847	0.76	0.938	0.847	0.76	0.938	CLONAL	2	TRUE	1	0.275205403390055	3		124	493	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0000138-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	239	358	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.275205403390055	3	FACETS	0.82	0.764	0.877	0.82	0.764	0.877	CLONAL	2	TRUE	1	0.275205403390055	3		358	1205	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193772	106193772	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000138-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	44	276	0	ENST00000380013.4:c.4234G>C	p.Asp1412His	p.D1412H	ENST00000380013	NM_001127208.2	1412	Gat/Cat	10/11	0.217476794048209	3	FACETS	0.454	0.379	0.537	0.151	0.126	0.179	SUBCLONAL	1	TRUE	0	0.275205403390055	3		276	801	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522551	176522551	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000138-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	35	411	0	ENST00000292408.4:c.1648G>C	p.Val550Leu	p.V550L	ENST00000292408	NM_213647.1	550	Gtg/Ctg	13/18	0.27041595213629	4	FACETS	0.34	0.277	0.411	0.17	0.138	0.206	SUBCLONAL	1	TRUE	2	0.275205403390055	4		411	954	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609894	117609894	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs202153378	NA	P-0000138-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1542	100	617	0	ENST00000368508.3:c.6805C>T	p.Arg2269Ter	p.R2269*	ENST00000368508	NM_002944.2	2269	Cga/Tga	43/43	0.262281275024826	2	FACETS	0.443	0.393	0.495	0.221	0.196	0.248	SUBCLONAL	1	TRUE	0	0.275205403390055	2		617	1642	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864343	151864343	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000138-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1367	95	507	0	ENST00000262189.6:c.9638C>T	p.Ser3213Leu	p.S3213L	ENST00000262189	NM_170606.2	3213	tCa/tTa	42/59	0.275205403390055	3	FACETS	0.537	0.476	0.603	0.269	0.238	0.302	SUBCLONAL	1	TRUE	1	0.275205403390055	3		507	1462	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372190	55372190	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000138-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	41	131	0	ENST00000297316.4:c.880C>A	p.His294Asn	p.H294N	ENST00000297316	NM_022454.3	294	Cac/Aac	2/2	0.240553480377276	4	FACETS	1	0.911	1	0.571	0.477	0.674	CLONAL	1	TRUE	2	0.275205403390055	4		131	333	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106094	8106094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000138-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	40	233	0	ENST00000346208.3:c.914G>A	p.Arg305Gln	p.R305Q	ENST00000346208		305	cGa/cAa	4/6	0.245385369559569	3	FACETS	0.507	0.42	0.604	0.254	0.21	0.302	SUBCLONAL	1	TRUE	1	0.275205403390055	3		233	652	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480435	50480435	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000138-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	55	314	0	ENST00000394963.4:c.397C>G	p.Leu133Val	p.L133V	ENST00000394963	NM_003076.4	133	Cta/Gta	3/13	0.224730379607861	4	FACETS	0.519	0.442	0.603			1	SUBCLONAL	1	TRUE	NA	0.275205403390055	4		314	983	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888189	112888189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507511	NA	P-0000138-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1229	29	446	0	ENST00000351677.2:c.205G>A	p.Glu69Lys	p.E69K	ENST00000351677	NM_002834.3	69	Gag/Aag	3/16	0.275205403390055	3	FACETS	0.191	0.152	0.235			1	SUBCLONAL	1	TRUE	NA	0.275205403390055	3		446	1258	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574698	95574698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000138-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1301	82	389	0	ENST00000393063.1:c.2399G>A	p.Arg800Lys	p.R800K	ENST00000393063	NM_030621.3	800	aGa/aAa	16/28	0.275205403390055	3	FACETS	0.49	0.43	0.555	0.245	0.215	0.278	SUBCLONAL	1	TRUE	1	0.275205403390055	3		389	1383	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679703	88679703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000138-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	70	348	0	ENST00000360948.2:c.760C>T	p.His254Tyr	p.H254Y	ENST00000360948	NM_001012338.2	254	Cac/Tac	7/19	1	2	FACETS	0.739	0.644	0.842	0.739	0.644	0.842	SUBCLONAL	1	TRUE	1	0.275205403390055	2		348	688	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266845	18266845	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000138-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	69	243	0	ENST00000222254.8:c.156G>C	p.Gln52His	p.Q52H	ENST00000222254	NM_005027.3	52	caG/caC	2/16	1	2	FACETS	0.739	0.643	0.842	0.739	0.643	0.842	SUBCLONAL	1	TRUE	1	0.275205403390055	2		243	679	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352234	70352234	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000138-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	81	515	0	ENST00000374080.3:c.4261G>C	p.Glu1421Gln	p.E1421Q	ENST00000374080		1421	Gag/Cag	31/45	0.275205403390055	3	FACETS	0.565	0.496	0.64	0.283	0.248	0.32	SUBCLONAL	1	TRUE	1	0.275205403390055	3		515	1185	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468399	120468399	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000187-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	50	212	0	ENST00000256646.2:c.4040G>C	p.Gly1347Ala	p.G1347A	ENST00000256646	NM_024408.3	1347	gGa/gCa	25/34	0.422109243896188	3	FACETS	0.34	0.287	0.398			1	SUBCLONAL	1	TRUE	NA	0.422109243896188	3		212	844	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718755	190718755	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000187-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	229	392	0	ENST00000441310.2:c.913G>C	p.Asp305His	p.D305H	ENST00000441310	NM_000534.4	305	Gat/Cat	8/13	NA	2	FACETS	0.886	0.824	0.949			1	INDETERMINATE	1	TRUE	NA	0.422109243896188	2		392	1225	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917490	178917490	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000187-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	240	278	0	ENST00000263967.3:c.365G>C	p.Gly122Ala	p.G122A	ENST00000263967	NM_006218.2	122	gGc/gCc	3/21	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.422109243896188	NA		278	1185	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66735669	66735669	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000187-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	342	364	0	ENST00000307102.5:c.490C>G	p.Gln164Glu	p.Q164E	ENST00000307102	NM_002755.3	164	Caa/Gaa	4/11	0.384370654600424	3	FACETS	0.842	0.797	0.888	0.561	0.531	0.592	CLONAL	2	TRUE	0	0.422109243896188	3		364	1165	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23625382	23625382	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000187-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	237	395	0	ENST00000261584.4:c.3144G>C	p.Lys1048Asn	p.K1048N	ENST00000261584	NM_024675.3	1048	aaG/aaC	11/13	0.422109243896188	2	FACETS	0.981	0.915	1	0.49	0.457	0.525	CLONAL	1	TRUE	0	0.422109243896188	2		395	1145	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577560	7577560	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0000187-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	292	280	1	ENST00000269305.4:c.721del	p.Ser241ProfsTer6	p.S241Pfs*6	ENST00000269305	NM_001126112.2	241	Tcc/cc	7/11	0.390091301437562	2	FACETS	0.973	0.921	1	0.973	0.921	1	CLONAL	2	TRUE	0	0.422109243896188	2		281	711	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0000204-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	834	294	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.291345486903408	10	FACETS	0.993	0.965	1			1	CLONAL	8	TRUE	NA	0.291345486903408	10		294	1560	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303726	65303726	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000204-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	148	596	0	ENST00000342505.4:c.3029T>G	p.Leu1010Arg	p.L1010R	ENST00000342505	NM_002227.2	1010	cTt/cGt	22/25	0.290462609576153	3	FACETS	1	0.917	1	0.503	0.458	0.55	CLONAL	1	TRUE	1	0.291345486903408	3		596	1157	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424092	49424092	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs748791941	NA	P-0000204-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	129	534	0	ENST00000301067.7:c.13970C>G	p.Ser4657Cys	p.S4657C	ENST00000301067	NM_003482.3	4657	tCt/tGt	42/54	0.290462609576153	3	FACETS	1	0.928	1	0.514	0.466	0.566	CLONAL	1	TRUE	1	0.291345486903408	3		534	986	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562249	95562249	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000204-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	149	645	0	ENST00000393063.1:c.5008G>C	p.Glu1670Gln	p.E1670Q	ENST00000393063	NM_030621.3	1670	Gaa/Caa	24/28	0.291345486903408	3	FACETS	1	0.918	1	0.504	0.459	0.551	CLONAL	1	TRUE	1	0.291345486903408	3		645	1163	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562693	95562693	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000204-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	149	583	0	ENST00000393063.1:c.4564G>C	p.Asp1522His	p.D1522H	ENST00000393063	NM_030621.3	1522	Gac/Cac	24/28	0.291345486903408	3	FACETS	1	0.935	1	0.515	0.47	0.563	CLONAL	1	TRUE	1	0.291345486903408	3		583	1137	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880257	37880257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000204-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	99	476	0	ENST00000269571.5:c.2301C>G	p.Ile767Met	p.I767M	ENST00000269571		767	atC/atG	19/27	0.177941305269784	3	FACETS	0.857	0.764	0.957			1	CLONAL	1	TRUE	NA	0.291345486903408	3		476	908	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000224-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	205	344	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	0.792	0.736	0.85	0.792	0.736	0.85	SUBCLONAL	1	TRUE	1	0.6226143595589	2		344	831	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950061	38950061	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000224-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	410	400	0	ENST00000357387.3:c.3889C>T	p.Pro1297Ser	p.P1297S	ENST00000357387	NM_152756.3	1297	Cct/Tct	31/38	1	2	FACETS	0.942	0.896	0.989	0.942	0.896	0.989	CLONAL	1	TRUE	1	0.6226143595589	2		400	1398	SUCCESS
ATM	472	MSKCC	GRCh37	11	108099967	108099967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000224-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	189	191	0	ENST00000278616.4:c.248C>T	p.Ser83Leu	p.S83L	ENST00000278616	NM_000051.3	83	tCa/tTa	4/63	0.6226143595589	1	FACETS	0.848	0.791	0.906	0.848	0.791	0.906	CLONAL	1	TRUE	0	0.6226143595589	1		191	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0000296-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	22	323	0	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.406819289818188	1	FACETS	0.681	0.535	0.844	0.681	0.535	0.844	SUBCLONAL	1	TRUE	0	0.427199957959217	1		323	119	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911514	131911514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143802516	NA	P-0000296-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	101	217	0	ENST00000265335.6:c.259C>T	p.Arg87Cys	p.R87C	ENST00000265335		87	Cgt/Tgt	3/25	0.348163652264926	1	FACETS	0.837	0.753	0.926	0.837	0.753	0.926	CLONAL	1	TRUE	0	0.427199957959217	1		217	444	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630768	90630768	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs749395621	NA	P-0000296-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	30	206	0	ENST00000330062.3:c.718A>G	p.Ile240Val	p.I240V	ENST00000330062	NM_002168.2	240	Atc/Gtc	6/11	1	2	FACETS	0.462	0.373	0.562	0.462	0.373	0.562	SUBCLONAL	1	TRUE	1	0.427199957959217	2		206	304	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0000339-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	523	454	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.86841346852487	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.86841346852487	1		454	634	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196463	106196463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000339-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	578	564	1	ENST00000380013.4:c.4796C>T	p.Ser1599Phe	p.S1599F	ENST00000380013	NM_001127208.2	1599	tCc/tTc	11/11	0.236549996079779	3	FACETS	1	0.996	1	0.675	0.649	0.701	INDETERMINATE	1	TRUE	1	0.86841346852487	3		565	1415	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372110	55372110	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000339-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	122	116	0	ENST00000297316.4:c.800C>A	p.Ala267Asp	p.A267D	ENST00000297316	NM_022454.3	267	gCc/gAc	2/2	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.86841346852487	2		116	268	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037952	49037952	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000339-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	331	359	0	ENST00000267163.4:c.2193del	p.Pro732LeufsTer12	p.P732Lfs*12	ENST00000267163	NM_000321.2	731	cTt/ct	21/27	0.86841346852487	1	FACETS	0.938	0.904	0.97	0.938	0.904	0.97	CLONAL	1	TRUE	0	0.86841346852487	1		359	460	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0000349-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	196	427	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.252887010660636	3	FACETS	1	0.95	1	1	0.95	1	CLONAL	3	TRUE	0	0.252887010660636	3		427	569	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724593	162724593	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000349-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	92	528	0	ENST00000367921.3:c.365A>G	p.Tyr122Cys	p.Y122C	ENST00000367921	NM_006182.2	122	tAc/tGc	5/18	0.252887010660636	5	FACETS	0.912	0.813	1	0.608	0.542	0.679	CLONAL	2	TRUE	2	0.252887010660636	5		528	550	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955632	55955632	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000349-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	77	831	0	ENST00000263923.4:c.3313C>A	p.Pro1105Thr	p.P1105T	ENST00000263923	NM_002253.2	1105	Cca/Aca	25/30	0.252616130721335	1	FACETS	0.778	0.688	0.873	1	0.979	1	SUBCLONAL	2	TRUE	0	0.252887010660636	1		831	342	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185820	32185820	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201418371	NA	P-0000349-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	36	531	0	ENST00000375023.3:c.1576G>A	p.Ala526Thr	p.A526T	ENST00000375023	NM_004557.3	526	Gcg/Acg	9/30	0.143230849240989	1	FACETS	0.61	0.501	0.731	0.61	0.501	0.731	INDETERMINATE	1	TRUE	0	0.252887010660636	1		531	408	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504401	8504401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757922864	NA	P-0000349-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	23	420	0	ENST00000356435.5:c.1682G>A	p.Arg561Gln	p.R561Q	ENST00000356435		561	cGa/cAa	12/35	1	2	FACETS	0.579	0.452	0.727	0.579	0.452	0.727	SUBCLONAL	1	TRUE	1	0.252887010660636	2		420	314	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625330	69625330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143483033	NA	P-0000349-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	159	844	0	ENST00000334134.2:c.463G>A	p.Val155Met	p.V155M	ENST00000334134	NM_005247.2	155	Gtg/Atg	3/3	1	2	FACETS	0.964	0.892	1	1	0.994	1	CLONAL	3	TRUE	1	0.252887010660636	2		844	435	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794023	42794023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000349-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	58	620	0	ENST00000575354.2:c.1384G>A	p.Asp462Asn	p.D462N	ENST00000575354	NM_015125.3	462	Gac/Aac	9/20	1	2	FACETS	0.846	0.727	0.976	0.846	0.727	0.976	CLONAL	1	TRUE	1	0.252887010660636	2		620	542	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0000352-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	199	538	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.331232952499138	3	FACETS	0.94	0.873	1	0.94	0.873	1	CLONAL	2	TRUE	1	0.331232952499138	3		538	745	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0000352-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	91	527	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.105697873596729	4	FACETS	0.999	0.887	1	0.5	0.443	0.56	INDETERMINATE	1	TRUE	2	0.331232952499138	4		527	732	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259439	55259439	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs397517126	NA	P-0000352-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	170	453	0	ENST00000275493.2:c.2497T>G	p.Leu833Val	p.L833V	ENST00000275493	NM_005228.3	833	Ttg/Gtg	21/28	0.331232952499138	3	FACETS	0.849	0.783	0.917	0.849	0.783	0.917	CLONAL	2	TRUE	1	0.331232952499138	3		453	705	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970971	21970971	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000352-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	105	649	1	ENST00000304494.5:c.387C>A	p.Tyr129Ter	p.Y129*	ENST00000304494	NM_000077.4	129	taC/taA	2/3	0.177321164103894	1	FACETS	0.969	0.871	1	0.969	0.871	1	INDETERMINATE	1	TRUE	0	0.331232952499138	1		650	546	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0000354-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	37	258	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.248328207027454	4	FACETS	0.669	0.552	0.8	0.334	0.276	0.4	SUBCLONAL	1	TRUE	2	0.369583339251741	4		258	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs786202525	NA	P-0000396-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	166	284	0	ENST00000269305.4:c.532del	p.His178ThrfsTer69	p.H178Tfs*69	ENST00000269305	NM_001126112.2	178	Cac/ac	5/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	NA	NA		284	285	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775676	9775676	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000396-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	234	365	0	ENST00000377346.4:c.219C>G	p.Ile73Met	p.I73M	ENST00000377346	NM_005026.3	73	atC/atG	4/24	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	NA	NA		365	267	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274901	142274901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369939610	NA	P-0000396-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	350	398	0	ENST00000350721.4:c.2159G>A	p.Gly720Asp	p.G720D	ENST00000350721	NM_001184.3	720	gGc/gAc	10/47	0.3	3	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	3		398	976	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191274	185191274	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000396-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	68	220	0	ENST00000265026.3:c.2155G>T	p.Gly719Cys	p.G719C	ENST00000265026	NM_004721.4	719	Ggt/Tgt	11/14	0.3	3	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	3		220	888	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129157	152129157	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000396-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	247	749	0	ENST00000206249.3:c.110G>T	p.Arg37Leu	p.R37L	ENST00000206249	NM_000125.3	37	cGg/cTg	1/8	0.3	3	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	3		749	1058	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466022	69466022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000396-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	197	274	0	ENST00000227507.2:c.860C>T	p.Pro287Leu	p.P287L	ENST00000227507	NM_053056.2	287	cCc/cTc	5/5	0.3	3	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	3		274	321	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423612	88423612	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000396-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	118	382	0	ENST00000360948.2:c.2223C>A	p.Ser741Arg	p.S741R	ENST00000360948	NM_001012338.2	741	agC/agA	18/19	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	NA	NA		382	908	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781351	3781351	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1555471874	NA	P-0000396-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	312	290	0	ENST00000262367.5:c.5014A>T	p.Arg1672Ter	p.R1672*	ENST00000262367	NM_004380.2	1672	Aga/Tga	30/31	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		290	540	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15978914	15978914	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000396-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	390	518	0	ENST00000268712.3:c.3604G>C	p.Glu1202Gln	p.E1202Q	ENST00000268712	NM_006311.3	1202	Gag/Cag	27/46	0.3	3	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	3		518	672	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0000433-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	84	124	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.524188006401311	8	FACETS	1	0.957	1	0.384	0.341	0.429	CLONAL	2	FALSE	2	0.524188006401311	8		124	358	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915621	131915621	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000433-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	93	143	0	ENST00000265335.6:c.619C>G	p.Gln207Glu	p.Q207E	ENST00000265335		207	Caa/Gaa	5/25	0.214125372630775	3	FACETS	1	0.974	1	0.642	0.576	0.711	INDETERMINATE	1	FALSE	1	0.524188006401311	3		143	349	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203489	108203489	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000433-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	55	94	0	ENST00000278616.4:c.7789G>C	p.Asp2597His	p.D2597H	ENST00000278616	NM_000051.3	2597	Gat/Cat	53/63	0.509975722117501	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	FALSE	0	0.524188006401311	1		94	146	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030426	49030426	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0000433-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	160	218	0	ENST00000267163.4:c.1901C>G	p.Ser634Ter	p.S634*	ENST00000267163	NM_000321.2	634	tCa/tGa	19/27	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	FALSE	NA	0.524188006401311	2		218	455	SUCCESS
AR	367	MSKCC	GRCh37	X	66766450	66766450	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000433-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	44	121	0	ENST00000374690.3:c.1462C>T	p.Gln488Ter	p.Q488*	ENST00000374690	NM_000044.3	488	Cag/Tag	1/8	0.524188006401311	0	FACETS		NA	1			1	NA	2	FALSE	NA	0.524188006401311	0		121	79	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53241030	53241031	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0000458-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	45	335	2	ENST00000375401.3:c.1180_1181del	p.Leu394AlafsTer11	p.L394Afs*11	ENST00000375401	NM_004187.3	394	CTg/g	9/26	1	1	FACETS	0.886	0.742	1	0.886	0.742	1	CLONAL	1	TRUE	0	0.12	1		337	796	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578529	7578529	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs780442292	NA	P-0000478-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	283	15	273	0	ENST00000269305.4:c.401T>G	p.Phe134Cys	p.F134C	ENST00000269305	NM_001126112.2	134	tTt/tGt	5/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		273	298	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0000495-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	347	294	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.257035831175692	5	FACETS	0.92	0.876	0.963			1	CLONAL	4	TRUE	NA	0.382707999554608	5		294	776	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665107	138665107	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000495-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	16	223	0	ENST00000330315.3:c.458T>C	p.Phe153Ser	p.F153S	ENST00000330315	NM_023067.3	153	tTc/tCc	1/1	NA	2	FACETS	0.478	0.355	0.624			1	INDETERMINATE	1	TRUE	NA	0.382707999554608	2		223	175	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963103	38963103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757132584	NA	P-0000495-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	96	485	0	ENST00000357387.3:c.1441G>A	p.Glu481Lys	p.E481K	ENST00000357387	NM_152756.3	481	Gaa/Aaa	17/38	0.328609888915353	3	FACETS	0.687	0.611	0.768	0.343	0.305	0.384	SUBCLONAL	1	TRUE	1	0.382707999554608	3		485	870	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444347	50444347	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000495-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	38	224	0	ENST00000331340.3:c.277A>C	p.Asn93His	p.N93H	ENST00000331340	NM_006060.4	93	Aat/Cat	4/8	0.269631578641088	4	FACETS	0.536	0.443	0.641	0.268	0.221	0.321	SUBCLONAL	1	TRUE	2	0.382707999554608	4		224	512	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395204	139395204	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375978224	NA	P-0000495-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	39	414	0	ENST00000277541.6:c.5734G>A	p.Asp1912Asn	p.D1912N	ENST00000277541	NM_017617.3	1912	Gac/Aac	31/34	0.328609888915353	3	FACETS	0.361	0.298	0.431	0.18	0.149	0.216	SUBCLONAL	1	TRUE	1	0.382707999554608	3		414	673	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223226	41223226	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000495-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	40	300	0	ENST00000357654.3:c.4705A>G	p.Ser1569Gly	p.S1569G	ENST00000357654	NM_007294.3	1569	Agc/Ggc	15/23	0.145741233955336	5	FACETS	0.699	0.58	0.83	0.175	0.145	0.208	INDETERMINATE	1	TRUE	1	0.382707999554608	5		300	471	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214685	5214685	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000495-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	87	501	0	ENST00000357368.4:c.4381T>A	p.Tyr1461Asn	p.Y1461N	ENST00000357368	NM_002850.3	1461	Tac/Aac	29/38	NA	2	FACETS	0.897	0.796	1			1	INDETERMINATE	1	TRUE	NA	0.382707999554608	2		501	507	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765681	41765681	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000495-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	56	552	0	ENST00000301178.4:c.2557A>T	p.Ser853Cys	p.S853C	ENST00000301178	NM_021913.4	853	Agc/Tgc	20/20	0.236635066178039	2	FACETS	0.462	0.396	0.535	0.231	0.198	0.268	SUBCLONAL	1	TRUE	0	0.382707999554608	2		552	633	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514648	44514648	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000495-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	67	307	0	ENST00000291552.4:c.508A>T	p.Asn170Tyr	p.N170Y	ENST00000291552	NM_006758.2	170	Aac/Tac	7/8	0.382707999554608	5	FACETS	0.991	0.862	1			1	CLONAL	1	TRUE	NA	0.382707999554608	5		307	556	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567546196	NA	P-0000495-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	122	382	0	ENST00000269305.4:c.949del	p.Gln317SerfsTer28	p.Q317Sfs*28	ENST00000269305	NM_001126112.2	317	Cag/ag	9/11	0.382707999554608	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.382707999554608	1		382	421	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0000525-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	554	364	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.398615957562911	3	FACETS	1	0.992	1	1	0.997	1	CLONAL	3	TRUE	1	0.398615957562911	3		364	1017	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0000525-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	332	573	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.398615957562911	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.398615957562911	1		573	1162	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259206	36259206	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000525-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	200	431	0	ENST00000300305.3:c.285del	p.Asn96ThrfsTer26	p.N96Tfs*26	ENST00000300305		95	ccC/cc	3/8	0.274137030200146	3	FACETS	0.904	0.835	0.975	0.452	0.417	0.488	CLONAL	1	TRUE	1	0.398615957562911	3		431	1332	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263850	133263850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000525-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	112	159	0	ENST00000320574.5:c.52G>A	p.Glu18Lys	p.E18K	ENST00000320574	NM_006231.2	18	Gag/Aag	1/49	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.398615957562911	2		159	388	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015042	71015042	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs772816590	NA	P-0000525-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	237	347	1	ENST00000318789.4:c.1888G>A	p.Val630Met	p.V630M	ENST00000318789	NM_032682.5	630	Gtg/Atg	20/21	0.274137030200146	3	FACETS	1	0.986	1	0.61	0.569	0.653	CLONAL	1	TRUE	1	0.398615957562911	3		348	1169	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72861848	72861848	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000525-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	252	370	0	ENST00000325599.8:c.1034G>A	p.Arg345Lys	p.R345K	ENST00000325599	NM_018130.2	345	aGg/aAg	9/11	0.274137030200146	3	FACETS	0.849	0.796	0.904	0.849	0.796	0.904	CLONAL	2	TRUE	1	0.398615957562911	3		370	893	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953785	48953785	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0000525-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	138	302	0	ENST00000267163.4:c.1388C>G	p.Ser463Ter	p.S463*	ENST00000267163	NM_000321.2	463	tCa/tGa	14/27	0.398615957562911	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.398615957562911	1		302	529	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0000538-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	90	448	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.503821784936112	2	FACETS	0.925	0.841	1	0.925	0.841	1	CLONAL	2	TRUE	0	0.506853776768881	2		448	192	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846071	68846071	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000538-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	67	461	0	ENST00000261769.5:c.1042G>A	p.Ala348Thr	p.A348T	ENST00000261769	NM_004360.3	348	Gct/Act	8/16	0.253378300176176	3	FACETS	1	0.964	1	0.64	0.562	0.721	INDETERMINATE	1	TRUE	1	0.506853776768881	3		461	259	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578410	7578410	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000538-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	43	249	0	ENST00000269305.4:c.520A>T	p.Arg174Trp	p.R174W	ENST00000269305	NM_001126112.2	174	Agg/Tgg	5/11	0.506853776768881	1	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	0	0.506853776768881	1		249	116	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577557	7577557	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519982	NA	P-0000557-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	25	223	0	ENST00000269305.4:c.724T>G	p.Cys242Gly	p.C242G	ENST00000269305	NM_001126112.2	242	Tgc/Ggc	7/11	0.268231724912787	1	FACETS	0.815	0.647	1	0.815	0.647	1	CLONAL	1	TRUE	0	0.268231724912787	1		223	198	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916929	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519931	NA	P-0000576-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	372	352	0	ENST00000263967.3:c.316G>C	p.Gly106Arg	p.G106R	ENST00000263967	NM_006218.2	106	Ggc/Cgc	2/21	1	2	FACETS	0.886	0.844	0.928	0.886	0.844	0.928	CLONAL	1	TRUE	1	0.93431767361743	2		352	899	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260593	1260593	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0000576-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1393	112	461	0	ENST00000310581.5:c.2966T>A	p.Leu989Ter	p.L989*	ENST00000310581	NM_198253.2	989	tTg/tAg	12/16	1	2	FACETS	0.159	0.142	0.177	0.159	0.142	0.177	SUBCLONAL	1	TRUE	1	0.93431767361743	2		461	1505	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538834	23538834	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000576-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	478	375	0	ENST00000380871.4:c.605A>G	p.Glu202Gly	p.E202G	ENST00000380871	NM_006167.3	202	gAg/gGg	2/2	1	2	FACETS	0.975	0.936	1	0.975	0.936	1	CLONAL	1	TRUE	1	0.93431767361743	2		375	1049	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0000592-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	47	228	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.396	0.334	0.463	0.396	0.334	0.463	SUBCLONAL	1	FALSE	1	0.546034343498117	2		228	435	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206647678	206647678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000592-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	21	245	0	ENST00000367120.3:c.92C>T	p.Ser31Phe	p.S31F	ENST00000367120	NM_014002.3	31	tCc/tTc	4/22	0.546034343498117	3	FACETS	0.304	0.234	0.386	0.152	0.117	0.193	SUBCLONAL	1	FALSE	1	0.546034343498117	3		245	322	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000592-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	248	421	0	ENST00000263967.3:c.3129G>C	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atC	21/21	1	2	FACETS	0.963	0.902	1	0.963	0.902	1	CLONAL	1	FALSE	1	0.546034343498117	2		421	943	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028618	12028618	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000592-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	179	363	0	ENST00000353533.5:c.821G>C	p.Arg274Thr	p.R274T	ENST00000353533	NM_003010.3	274	aGa/aCa	8/11	0.332189943133995	0	FACETS	0.511	0.473	0.549			1	SUBCLONAL	1	FALSE	0	0.546034343498117	0		363	583	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842605	68842605	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0000592-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	133	377	0	ENST00000261769.5:c.542del	p.Asn181ThrfsTer34	p.N181Tfs*34	ENST00000261769	NM_004360.3	181	Aac/ac	5/16	0.42463629445305	0	FACETS	0.577	0.53	0.626			1	SUBCLONAL	1	FALSE	0	0.546034343498117	0		377	383	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462123	120462123	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000619-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	205	381	0	ENST00000256646.2:c.5593C>T	p.Gln1865Ter	p.Q1865*	ENST00000256646	NM_024408.3	1865	Cag/Tag	31/34	1	2	FACETS	0.957	0.896	1	0.957	0.896	1	CLONAL	1	TRUE	1	0.849931668698144	2		381	504	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748458	162748458	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1433624804	NA	P-0000619-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	225	422	0	ENST00000367921.3:c.2372A>G	p.Gln791Arg	p.Q791R	ENST00000367921	NM_006182.2	791	cAg/cGg	17/18	0.849931668698144	4	FACETS	0.921	0.858	0.987	0.307	0.286	0.329	CLONAL	1	TRUE	1	0.849931668698144	4		422	1063	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0000622-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	496	301	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.279123543647107	3	FACETS	1	0.994	1	0.796	0.762	0.83	CLONAL	2	TRUE	0	0.361387116246564	3		301	1358	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519775	29519775	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000622-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	63	348	0	ENST00000389048.3:c.1796C>A	p.Pro599His	p.P599H	ENST00000389048	NM_004304.4	599	cCt/cAt	9/29	1	2	FACETS	0.474	0.409	0.545	0.474	0.409	0.545	SUBCLONAL	1	TRUE	1	0.361387116246564	2		348	735	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191005	185191005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000622-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1523	143	923	0	ENST00000265026.3:c.1886C>T	p.Pro629Leu	p.P629L	ENST00000265026	NM_004721.4	629	cCt/cTt	11/14	0.262254983600708	2	FACETS	0.475	0.431	0.522	0.238	0.215	0.261	SUBCLONAL	1	TRUE	0	0.361387116246564	2		923	1666	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455653	189455653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000622-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	117	316	0	ENST00000264731.3:c.187G>A	p.Glu63Lys	p.E63K	ENST00000264731	NM_003722.4	63	Gaa/Aaa	2/14	0.262254983600708	2	FACETS	0.959	0.866	1	0.48	0.433	0.529	CLONAL	1	TRUE	0	0.361387116246564	2		316	675	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130067	143130067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000622-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	79	492	0	ENST00000262992.4:c.949G>A	p.Glu317Lys	p.E317K	ENST00000262992	NM_001101669.1	317	Gaa/Aaa	11/24	1	2	FACETS	0.454	0.398	0.514	0.454	0.398	0.514	SUBCLONAL	1	TRUE	1	0.361387116246564	2		492	963	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680755	30680755	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000622-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	96	648	0	ENST00000376406.3:c.964C>T	p.Gln322Ter	p.Q322*	ENST00000376406	NM_014641.2	322	Cag/Tag	5/15	1	2	FACETS	0.443	0.393	0.496	0.443	0.393	0.496	SUBCLONAL	1	TRUE	1	0.361387116246564	2		648	1199	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518153	8518153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000622-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	70	427	0	ENST00000356435.5:c.1238C>T	p.Ser413Leu	p.S413L	ENST00000356435		413	tCa/tTa	10/35	0.322359096786704	2	FACETS	0.417	0.362	0.476	0.209	0.181	0.238	SUBCLONAL	1	TRUE	0	0.361387116246564	2		427	929	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038912	12038912	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000622-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	535	511	0	ENST00000396373.4:c.1205A>G	p.Tyr402Cys	p.Y402C	ENST00000396373	NM_001987.4	402	tAc/tGc	7/8	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.361387116246564	NA		511	1339	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426639	49426662	+	inframe_deletion	In_Frame_Del	DEL	TGTTGAAGCTGTTGCTGCTGCTGT	TGTTGAAGCTGTTGCTGCTGCTGT	-	rs771018434	NA	P-0000622-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	52	381	0	ENST00000301067.7:c.11826_11849del	p.Gln3947_Gln3954del	p.Q3947_Q3954del	ENST00000301067	NM_003482.3	3942	caACAGCAGCAGCAACAGCTTCAACAg/cag	39/54	0.279123543647107	3	FACETS	0.429	0.364	0.501	0.143	0.121	0.167	SUBCLONAL	1	TRUE	0	0.361387116246564	3		381	792	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784026	9784026	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0000640-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	134	351	0	ENST00000377346.4:c.2595-1G>A		p.X865_splice	ENST00000377346	NM_005026.3	865			0.111508271386128	1	FACETS	0.97	0.887	1	1	0.993	1	CLONAL	5	FALSE	0	0.111508271386128	1		351	468	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662421	67662421	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000640-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	164	518	1	ENST00000264010.4:c.1667T>C	p.Val556Ala	p.V556A	ENST00000264010	NM_006565.3	556	gTc/gCc	9/12	0.111508271386128	1	FACETS	1	0.961	1	1	0.995	1	CLONAL	5	FALSE	0	0.111508271386128	1		519	523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882025	NA	P-0000647-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	161	890	0	ENST00000269305.4:c.646G>C	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ctg	6/11	0.304343719134637	0	FACETS	0.765	0.702	0.831			1	SUBCLONAL	1	FALSE	0	0.323782049174313	0		890	879	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0000651-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	403	375	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.659186125554539	1	FACETS	0.83	0.802	0.859	0.83	0.802	0.859	CLONAL	1	TRUE	0	0.892670752939573	1		376	602	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0000651-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	426	506	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.892670752939573	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.892670752939573	2		507	444	SUCCESS
AR	367	MSKCC	GRCh37	X	66942741	66942741	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs9332969	NA	P-0000651-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1655	213	824	0	ENST00000374690.3:c.2522G>A	p.Arg841His	p.R841H	ENST00000374690	NM_000044.3	841	cGt/cAt	7/8	0.137943754662017	3	FACETS	0.369	0.342	0.399	0.185	0.171	0.2	INDETERMINATE	1	TRUE	1	0.892670752939573	3		824	1868	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119485	193119485	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000651-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1181	131	402	0	ENST00000367435.3:c.880G>A	p.Asp294Asn	p.D294N	ENST00000367435	NM_024529.4	294	Gat/Aat	9/17	0.5050405520151	4	FACETS	0.423	0.383	0.466	0.212	0.191	0.233	INDETERMINATE	1	TRUE	2	0.892670752939573	4		402	1312	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243469	41243469	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000651-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	289	797	0	ENST00000357654.3:c.4079G>A	p.Ser1360Asn	p.S1360N	ENST00000357654	NM_007294.3	1360	aGc/aAc	10/23	1	2	FACETS	0.479	0.449	0.509	0.479	0.449	0.509	SUBCLONAL	1	TRUE	1	0.892670752939573	2		797	1353	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549698	187549699	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0000651-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	111	285	0	ENST00000441802.2:c.4542_4543del	p.Thr1516PhefsTer2	p.T1516Ffs*2	ENST00000441802	NM_005245.3	1514	ctCTat/ctat	8/27	0.892670752939573	2	FACETS	0.565	0.511	0.621	0.283	0.255	0.311	SUBCLONAL	1	TRUE	0	0.892670752939573	2		285	440	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890142	76890145	+	frameshift_variant	Frame_Shift_Del	DEL	TTTC	TTTC	-	novel	NA	P-0000651-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	599	710	0	ENST00000373344.5:c.4749_4752del	p.Lys1583AsnfsTer22	p.K1583Nfs*22	ENST00000373344	NM_000489.3	1583	aaGAAA/aa	17/35	NA	2	FACETS	0.877	0.843	0.91			1	INDETERMINATE	1	TRUE	NA	0.892670752939573	2		710	1531	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427658	72427658	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000655-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	67	388	0	ENST00000477973.2:c.832T>G	p.Ser278Ala	p.S278A	ENST00000477973	NM_012234.5	278	Tcc/Gcc	4/4	0.127339651016884	5	FACETS	0.849	0.747	0.958			1	INDETERMINATE	2	TRUE	NA	0.564755438121427	5		388	258	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380277	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913238	NA	P-0000655-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	77	366	1	ENST00000311936.3:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	61	Caa/Aaa	3/5	NA	2	FACETS	0.931	0.826	1			1	INDETERMINATE	1	TRUE	NA	0.564755438121427	2		367	293	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061469	38061469	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000655-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	227	363	0	ENST00000250448.2:c.520T>A	p.Ser174Thr	p.S174T	ENST00000250448	NM_004496.3	174	Tcg/Acg	2/2	0.34376058491339	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.564755438121427	4		363	592	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380277	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913238	NA	P-0000655-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	59	366	1	ENST00000311936.3:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	61	Caa/Aaa	3/5	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.15	2		367	787	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0000690-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	178	124	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.409601164210763	5	FACETS	0.928	0.862	0.995	0.928	0.862	0.995	CLONAL	3	TRUE	2	0.409601164210763	5		124	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0000690-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	145	185	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.409601164210763	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.409601164210763	1		185	406	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448571	89448571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000690-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	262	267	0	ENST00000336596.2:c.1535G>A	p.Arg512Gln	p.R512Q	ENST00000336596	NM_005233.5	512	cGa/cAa	7/17	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.409601164210763	2		267	913	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0000694-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	71	294	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.30611945225756	4	FACETS	1	0.939	1			1	CLONAL	2	TRUE	NA	0.18	4		294	416	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610503	215610503	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000694-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	30	369	1	ENST00000260947.4:c.1753C>A	p.Leu585Ile	p.L585I	ENST00000260947	NM_000465.2	585	Ctc/Atc	8/11	1	2	FACETS	0.958	0.773	1	0.958	0.773	1	CLONAL	1	TRUE	1	0.18	2		370	348	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206579	108206579	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs745901025	NA	P-0000694-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	26	199	0	ENST00000278616.4:c.8159A>G	p.Asp2720Gly	p.D2720G	ENST00000278616	NM_000051.3	2720	gAt/gGt	56/63	1	2	FACETS	1	0.804	1	1	0.804	1	CLONAL	1	TRUE	1	0.18	2		199	285	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908766	101908766	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0000709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	627	532	0	ENST00000374994.4:c.1131-1G>A		p.X377_splice	ENST00000374994	NM_004612.2	377			0.590249098734569	1	FACETS	0.944	0.909	0.979	0.944	0.909	0.979	CLONAL	1	FALSE	0	0.590249098734569	1		532	1587	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435720	110435720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	56	72	0	ENST00000375856.3:c.2681C>T	p.Ser894Phe	p.S894F	ENST00000375856	NM_003749.2	894	tCc/tTc	1/2	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	FALSE	1	0.590249098734569	2		72	173	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101650	27101651	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0000709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	231	358	0	ENST00000324856.7:c.4934_4935del	p.Ser1645CysfsTer2	p.S1645Cfs*2	ENST00000324856	NM_006015.4	1644	ggCTct/ggct	18/20	0.590249098734569	1	FACETS	0.865	0.811	0.919	0.865	0.811	0.919	CLONAL	1	FALSE	0	0.590249098734569	1		358	638	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691783	30691783	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000711-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	244	408	0	ENST00000295754.5:c.285A>G	p.Ile95Met	p.I95M	ENST00000295754	NM_003242.5	95	atA/atG	3/7	0.507851100712607	7	FACETS	1	0.982	1			1	CLONAL	3	TRUE	NA	0.507851100712607	7		408	656	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955570	48955575	+	frameshift_variant	Frame_Shift_Del	DEL	ATGGCT	ATGGCT	G	novel	NA	P-0000711-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	100	309	0	ENST00000267163.4:c.1686_1691delinsG	p.Trp563LeufsTer7	p.W563Lfs*7	ENST00000267163	NM_000321.2	562	gcATGGCTc/gcGc	17/27	0.451013680661558	3	FACETS	0.914	0.83	1			1	CLONAL	2	TRUE	NA	0.507851100712607	3		309	270	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0000713-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	13	394	1	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.742	1	1	0.742	1	CLONAL	1	FALSE	1	0.174210300904303	2		395	144	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050694	30050694	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000750-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	21	369	0	ENST00000338641.4:c.496G>T	p.Glu166Ter	p.E166*	ENST00000338641	NM_000268.3	166	Gag/Tag	5/16	0.488310858821283	1	FACETS	0.209	0.161	0.265	0.209	0.161	0.265	SUBCLONAL	1	TRUE	0	0.488310858821283	1		369	311	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057326	30057326	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000750-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	32	248	0	ENST00000338641.4:c.808G>T	p.Glu270Ter	p.E270*	ENST00000338641	NM_000268.3	270	Gag/Tag	8/16	0.488310858821283	1	FACETS	0.505	0.414	0.607	0.505	0.414	0.607	SUBCLONAL	1	TRUE	0	0.488310858821283	1		248	196	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437431	52437431	+	splice_donor_variant	Splice_Site	DEL	C	C	-	rs1559586374	NA	P-0000750-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	30	148	0	ENST00000460680.1:c.1729+1del		p.X577_splice	ENST00000460680	NM_004656.3	577			0.28717938812121	0	FACETS	0.642	0.53	0.76			1	INDETERMINATE	1	TRUE	0	0.488310858821283	0		148	98	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893355	32893355	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000809-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	145	280	0	ENST00000380152.3:c.209C>G	p.Ser70Cys	p.S70C	ENST00000380152		70	tCt/tGt	3/27	0.694591786548899	1	FACETS	0.482	0.443	0.524	0.482	0.443	0.524	SUBCLONAL	1	TRUE	0	0.739778300243498	1		280	512	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665752	29665755	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1555535032	NA	P-0000809-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	163	282	0	ENST00000356175.3:c.6789_6792del	p.Tyr2264ThrfsTer5	p.Y2264Tfs*5	ENST00000356175	NM_000267.3	2263	ACTTac/ac	45/57	NA	2	FACETS	0.862	0.797	0.929			1	INDETERMINATE	1	TRUE	NA	0.739778300243498	2		282	511	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061208	38061208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000847-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	144	325	1	ENST00000250448.2:c.781C>T	p.Arg261Cys	p.R261C	ENST00000250448	NM_004496.3	261	Cgc/Tgc	2/2	1	2	FACETS	0.82	0.749	0.895	1	0.989	1	CLONAL	2	FALSE	1	0.224164465446511	2		326	783	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904938	101904938	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200518416	NA	P-0000852-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	155	109	0	ENST00000374994.4:c.926C>T	p.Thr309Met	p.T309M	ENST00000374994	NM_004612.2	309	aCg/aTg	5/9	0.184371366018314	6	FACETS	0.864	0.801	0.929			1	INDETERMINATE	3	FALSE	NA	0.808280265544157	6		109	387	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0000852-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	74	685	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	0.180687835906933	1	FACETS	0.583	0.522	0.647	0.583	0.522	0.647	INDETERMINATE	1	FALSE	0	0.808280265544157	1		685	187	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156720	20156720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000852-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	348	94	0	ENST00000379607.5:c.37C>T	p.Arg13Cys	p.R13C	ENST00000379607	NM_001412.3	13	Cgc/Tgc	2/7	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	FALSE	0	0.808280265544157	1		94	420	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462768	69462768	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000912-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	107	701	2	ENST00000227507.2:c.581A>G	p.Lys194Arg	p.K194R	ENST00000227507	NM_053056.2	194	aAg/aGg	4/5	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.378403238460016	2		703	394	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696425	47696425	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519967	NA	P-0000912-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	151	921	0	ENST00000347630.2:c.398T>C	p.Phe133Ser	p.F133S	ENST00000347630	NM_001007230.1	133	tTc/tCc	6/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.378403238460016	2		921	601	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0000931-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	113	414	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.221029048762343	2		414	940	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000965-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	385	344	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.751187713230634	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.760283084035488	1		344	625	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098969	178098969	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000965-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	471	547	1	ENST00000397062.3:c.76C>A	p.Gln26Lys	p.Q26K	ENST00000397062	NM_006164.4	26	Caa/Aaa	2/5	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.760283084035488	2		548	1213	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650676	18650676	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000965-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	195	249	0	ENST00000266497.5:c.2887G>C	p.Asp963His	p.D963H	ENST00000266497		963	Gac/Cac	20/31	NA	2	FACETS	0.913	0.851	0.976			1	INDETERMINATE	1	TRUE	NA	0.760283084035488	2		249	562	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434618	49434618	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0000993-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	260	312	0	ENST00000301067.7:c.6935C>G	p.Ser2312Ter	p.S2312*	ENST00000301067	NM_003482.3	2312	tCa/tGa	31/54	1	2	FACETS	0.984	0.927	1	0.984	0.927	1	CLONAL	1	TRUE	1	0.74955588850217	2		312	705	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206647673	206647673	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0000993-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	441	172	0	ENST00000367120.3:c.88-1G>A		p.X30_splice	ENST00000367120	NM_014002.3	30			0.439908431182769	3	FACETS	1	0.994	1	0.765	0.738	0.791	INDETERMINATE	2	TRUE	0	0.74955588850217	3		172	705	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084189	47084189	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000993-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	184	202	0	ENST00000409792.3:c.7100C>T	p.Ser2367Phe	p.S2367F	ENST00000409792	NM_014159.6	2367	tCt/tTt	17/21	0.74955588850217	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.74955588850217	1		202	303	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147551	47147551	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000993-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	273	297	0	ENST00000409792.3:c.4775G>T	p.Arg1592Leu	p.R1592L	ENST00000409792	NM_014159.6	1592	cGa/cTa	6/21	0.74955588850217	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.74955588850217	1		297	436	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519141	187519141	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0000993-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	278	302	0	ENST00000441802.2:c.12242T>A	p.Leu4081Ter	p.L4081*	ENST00000441802	NM_005245.3	4081	tTa/tAa	23/27	0.74955588850217	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.74955588850217	1		302	438	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947395	38947395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000993-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	113	322	0	ENST00000357387.3:c.4285C>T	p.Leu1429Phe	p.L1429F	ENST00000357387	NM_152756.3	1429	Ctc/Ttc	32/38	0.74955588850217	4	FACETS	0.453	0.406	0.502	0.151	0.135	0.168	SUBCLONAL	1	TRUE	1	0.74955588850217	4		322	1165	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0000993-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	215	338	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	0.74955588850217	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.74955588850217	1		338	347	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672030	30672030	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000993-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	225	552	0	ENST00000376406.3:c.4930A>G	p.Arg1644Gly	p.R1644G	ENST00000376406	NM_014641.2	1644	Agg/Ggg	10/15	0.388551106068417	1	FACETS	0.41	0.382	0.439	0.41	0.382	0.439	INDETERMINATE	1	TRUE	0	0.74955588850217	1		552	916	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2972213	2972213	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000993-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	444	251	0	ENST00000396946.4:c.1526G>T	p.Arg509Ile	p.R509I	ENST00000396946	NM_032415.4	509	aGa/aTa	11/25	0.324938142653104	3	FACETS	1	0.995	1	0.787	0.76	0.813	INDETERMINATE	2	TRUE	0	0.74955588850217	3		251	690	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860254	151860254	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000993-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	415	469	0	ENST00000262189.6:c.10408C>T	p.Gln3470Ter	p.Q3470*	ENST00000262189	NM_170606.2	3470	Cag/Tag	43/59	0.74955588850217	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.74955588850217	1		469	633	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420213	49420213	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000993-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	329	317	0	ENST00000301067.7:c.15536G>T	p.Arg5179Leu	p.R5179L	ENST00000301067	NM_003482.3	5179	cGt/cTt	48/54	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.74955588850217	2		317	856	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448398	49448398	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000993-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	422	470	0	ENST00000301067.7:c.313C>T	p.Pro105Ser	p.P105S	ENST00000301067	NM_003482.3	105	Ccc/Tcc	3/54	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.74955588850217	2		470	1119	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347933	347933	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000993-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	261	992	0	ENST00000262320.3:c.1573G>C	p.Asp525His	p.D525H	ENST00000262320	NM_003502.3	525	Gac/Cac	6/11	0.449523415992216	1	FACETS	0.362	0.338	0.386	0.362	0.338	0.386	INDETERMINATE	1	TRUE	0	0.74955588850217	1		992	1204	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0000993-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	260	175	0	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.738448632308944	2	FACETS	0.943	0.904	0.98	0.943	0.904	0.98	CLONAL	2	TRUE	0	0.74955588850217	2		175	368	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448335	56448335	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000993-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	274	238	0	ENST00000407977.2:c.312C>G	p.Ile104Met	p.I104M	ENST00000407977		104	atC/atG	3/10	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.74955588850217	2		238	721	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7152939	7152939	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0000993-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	179	228	0	ENST00000302850.5:c.2030-1G>T		p.X677_splice	ENST00000302850	NM_000208.2	677			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.74955588850217	2		228	462	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302839	15302839	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000993-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	183	222	0	ENST00000263388.2:c.611C>T	p.Ser204Leu	p.S204L	ENST00000263388	NM_000435.2	204	tCa/tTa	4/33	1	2	FACETS	0.913	0.849	0.978	0.913	0.849	0.978	CLONAL	1	TRUE	1	0.74955588850217	2		222	535	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0001014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	15	251	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	0.455710876066505	2	FACETS	1	0.858	1	0.61	0.461	0.775	CLONAL	1	TRUE	0	0.455710876066505	2		251	54	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440548	49440548	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001014-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	32	316	0	ENST00000301067.7:c.4262G>T	p.Gly1421Val	p.G1421V	ENST00000301067	NM_003482.3	1421	gGc/gTc	15/54	0.448793146084637	5	FACETS	1	0.899	1	0.384	0.314	0.462	CLONAL	1	TRUE	2	0.455710876066505	5		316	205	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0001043-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	94	294	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.231036605011344	4	FACETS	1	0.968	1	1	0.986	1	CLONAL	3	TRUE	2	0.30586198411469	4		294	231	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001043-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	9	486	1	ENST00000263967.3:c.278G>T	p.Arg93Leu	p.R93L	ENST00000263967	NM_006218.2	93	cGg/cTg	2/21	0.231036605011344	4	FACETS	0.198	0.13	0.285	0.099	0.065	0.143	SUBCLONAL	1	TRUE	2	0.30586198411469	4		487	388	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638392	176638392	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001043-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	98	463	0	ENST00000439151.2:c.2992T>G	p.Leu998Val	p.L998V	ENST00000439151	NM_022455.4	998	Tta/Gta	5/23	0.228381621096628	3	FACETS	0.889	0.805	0.976	1	0.979	1	CLONAL	3	TRUE	1	0.30586198411469	3		463	277	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106022	8106022	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001043-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	288	302	3	ENST00000346208.3:c.842A>G	p.His281Arg	p.H281R	ENST00000346208		281	cAc/cGc	4/6	0.30586198411469	5	FACETS	1	0.973	1	1	0.995	1	CLONAL	6	TRUE	1	0.30586198411469	5		305	448	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168793	56168793	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001043-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	179	426	0	ENST00000399503.3:c.1649del	p.Pro550LeufsTer7	p.P550Lfs*7	ENST00000399503	NM_005921.1	549	atC/at	9/20	0.30586198411469	7	FACETS	1	0.952	1	1	0.952	1	CLONAL	4	TRUE	3	0.30586198411469	7		426	501	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170991	56170991	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001043-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	113	190	0	ENST00000399503.3:c.1823del	p.Gly608AlafsTer48	p.G608Afs*48	ENST00000399503	NM_005921.1	607	Ggg/gg	10/20	0.30586198411469	7	FACETS	1	0.924	1	1	0.924	1	CLONAL	4	TRUE	3	0.30586198411469	7		190	321	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143033	30143033	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001047-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	609	548	1	ENST00000389048.3:c.493C>A	p.Leu165Met	p.L165M	ENST00000389048	NM_004304.4	165	Ctg/Atg	1/29	0.594578330705151	3	FACETS	0.992	0.964	1	0.992	0.964	1	CLONAL	3	TRUE	0	0.591966279080514	3		549	896	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030245	180030245	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001047-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	358	529	0	ENST00000261937.6:c.4039G>A	p.Asp1347Asn	p.D1347N	ENST00000261937	NM_182925.4	1347	Gac/Aac	30/30	0.591966279080514	6	FACETS	0.893	0.845	0.942	0.595	0.563	0.628	CLONAL	2	TRUE	3	0.591966279080514	6		529	1479	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873858	151873858	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001047-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	179	400	0	ENST00000262189.6:c.8680A>T	p.Ile2894Phe	p.I2894F	ENST00000262189	NM_170606.2	2894	Att/Ttt	38/59	1	2	FACETS	0.846	0.782	0.912	0.846	0.782	0.912	CLONAL	1	TRUE	1	0.591966279080514	2		400	715	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917699	151917699	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001047-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	30	79	0	ENST00000262189.6:c.3621G>T	p.Lys1207Asn	p.K1207N	ENST00000262189	NM_170606.2	1207	aaG/aaT	23/59	1	2	FACETS	0.699	0.571	0.839	0.699	0.571	0.839	SUBCLONAL	1	TRUE	1	0.591966279080514	2		79	145	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570395	95570395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143841809	NA	P-0001047-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	130	189	0	ENST00000393063.1:c.3338C>T	p.Ser1113Phe	p.S1113F	ENST00000393063	NM_030621.3	1113	tCc/tTc	22/28	0.528096572737482	4	FACETS	0.892	0.817	0.969	0.892	0.817	0.969	CLONAL	2	TRUE	2	0.591966279080514	4		189	392	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796921	78796921	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001047-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	422	313	1	ENST00000306801.3:c.1034G>C	p.Ser345Thr	p.S345T	ENST00000306801	NM_020761.2	345	aGt/aCt	9/34	0.591966279080514	6	FACETS	0.933	0.89	0.975	0.699	0.668	0.732	CLONAL	3	TRUE	2	0.591966279080514	6		314	1113	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188175	11188175	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001047-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	122	257	0	ENST00000361445.4:c.5919C>G	p.Ile1973Met	p.I1973M	ENST00000361445	NM_004958.3	1973	atC/atG	43/58	0.528096572737482	4	FACETS	0.878	0.795	0.967	0.439	0.397	0.484	CLONAL	1	TRUE	2	0.591966279080514	4		257	747	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145334	61145334	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001047-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	107	196	0	ENST00000295025.8:c.544A>C	p.Asn182His	p.N182H	ENST00000295025	NM_002908.2	182	Aat/Cat	6/11	0.591966279080514	7	FACETS	1	0.965	1			1	CLONAL	1	TRUE	NA	0.591966279080514	7		196	765	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542108	187542108	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001047-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	111	217	0	ENST00000441802.2:c.5632G>A	p.Val1878Met	p.V1878M	ENST00000441802	NM_005245.3	1878	Gtg/Atg	10/27	0.594578330705151	2	FACETS	1	0.933	1	0.517	0.469	0.566	CLONAL	1	TRUE	0	0.591966279080514	2		217	363	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917610	151917610	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001047-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	44	159	0	ENST00000262189.6:c.3710G>A	p.Arg1237Gln	p.R1237Q	ENST00000262189	NM_170606.2	1237	cGa/cAa	23/59	1	2	FACETS	0.804	0.683	0.933	0.804	0.683	0.933	CLONAL	1	TRUE	1	0.591966279080514	2		159	185	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917730	151917730	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001047-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	18	53	0	ENST00000262189.6:c.3590G>C	p.Arg1197Thr	p.R1197T	ENST00000262189	NM_170606.2	1197	aGa/aCa	23/59	1	2	FACETS	0.563	0.43	0.716	0.563	0.43	0.716	SUBCLONAL	1	TRUE	1	0.591966279080514	2		53	108	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346430	152346430	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780126	NA	P-0001047-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	222	404	0	ENST00000359321.1:c.140A>G	p.His47Arg	p.H47R	ENST00000359321	NM_005431.1	47	cAt/cGt	3/3	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.591966279080514	2		404	742	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401198	139401198	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001047-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	182	401	0	ENST00000277541.6:c.3871T>G	p.Phe1291Val	p.F1291V	ENST00000277541	NM_017617.3	1291	Ttc/Gtc	23/34	0.471257608738012	4	FACETS	1	0.986	1	0.641	0.592	0.691	CLONAL	1	TRUE	2	0.591966279080514	4		401	764	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831272	3831272	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001047-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	127	274	0	ENST00000262367.5:c.1609A>C	p.Thr537Pro	p.T537P	ENST00000262367	NM_004380.2	537	Aca/Cca	7/31	0.594578330705151	5	FACETS	0.918	0.832	1	0.306	0.277	0.337	CLONAL	1	TRUE	2	0.591966279080514	5		274	882	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249707	110249709	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	rs1202210342	NA	P-0001047-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	42	333	0	ENST00000374672.4:c.966_968del	p.Glu323del	p.E323del	ENST00000374672	NM_004235.4	322	gaGGAa/gaa	3/5	0.471257608738012	4	FACETS	0.316	0.263	0.376	0.158	0.131	0.188	SUBCLONAL	1	TRUE	2	0.591966279080514	4		333	714	SUCCESS
AR	367	MSKCC	GRCh37	X	66765057	66765057	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001087-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	148	698	0	ENST00000374690.3:c.69C>A	p.Phe23Leu	p.F23L	ENST00000374690	NM_000044.3	23	ttC/ttA	1/8	0.627224651267239	1	FACETS	0.315	0.288	0.343	0.315	0.288	0.343	SUBCLONAL	1	TRUE	0	0.840743671935497	1		698	648	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855032	76855060	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCCCTTTTTTCTTCTTTCTAAAAACAAA	TTCCCTTTTTTCTTCTTTCTAAAAACAAA	GTTTT	novel	NA	P-0001087-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	311	574	0	ENST00000373344.5:c.5787-11_5804delinsAAAAC		p.X1929_splice	ENST00000373344	NM_000489.3	1929		25/35	0.627224651267239	1	FACETS	0.468	0.442	0.494	0.468	0.442	0.494	SUBCLONAL	1	TRUE	0	0.840743671935497	1		574	916	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0001114-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	113	228	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.143898856572227	4	FACETS	1	0.978	1	1	0.978	1	INDETERMINATE	2	TRUE	2	0.64612272115244	4		228	241	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519925	NA	P-0001114-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	160	384	0	ENST00000263967.3:c.1357G>C	p.Glu453Gln	p.E453Q	ENST00000263967	NM_006218.2	453	Gaa/Caa	8/21	0.143898856572227	4	FACETS	0.768	0.708	0.829	0.768	0.708	0.829	INDETERMINATE	2	TRUE	2	0.64612272115244	4		384	531	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891615	151891615	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001114-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	182	340	0	ENST00000262189.6:c.4417C>T	p.Gln1473Ter	p.Q1473*	ENST00000262189	NM_170606.2	1473	Cag/Tag	29/59	0.120144066013315	4	FACETS	0.893	0.831	0.957	0.893	0.831	0.957	INDETERMINATE	2	TRUE	2	0.64612272115244	4		340	519	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65304159	65304159	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001114-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	146	732	0	ENST00000342505.4:c.2956C>T	p.Gln986Ter	p.Q986*	ENST00000342505	NM_002227.2	986	Cag/Tag	21/25	0.64612272115244	1	FACETS	0.72	0.663	0.778	0.72	0.663	0.778	SUBCLONAL	1	TRUE	0	0.64612272115244	1		732	425	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948160	178948160	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001114-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	118	207	0	ENST00000263967.3:c.2932G>C	p.Glu978Gln	p.E978Q	ENST00000263967	NM_006218.2	978	Gag/Cag	20/21	0.143898856572227	4	FACETS	1	0.983	1	0.701	0.637	0.767	INDETERMINATE	1	TRUE	2	0.64612272115244	4		207	429	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177399	56177399	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001114-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	157	302	0	ENST00000399503.3:c.2372A>G	p.Tyr791Cys	p.Y791C	ENST00000399503	NM_005921.1	791	tAt/tGt	14/20	0.222203304463644	4	FACETS	0.769	0.709	0.831	0.769	0.709	0.831	INDETERMINATE	2	TRUE	2	0.64612272115244	4		302	520	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187983	32187983	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001114-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	115	441	0	ENST00000375023.3:c.1238C>A	p.Thr413Lys	p.T413K	ENST00000375023	NM_004557.3	413	aCa/aAa	7/30	1	2	FACETS	0.944	0.859	1	0.944	0.859	1	CLONAL	1	TRUE	1	0.64612272115244	2		441	377	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211469	98211469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781080456	NA	P-0001114-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	168	430	0	ENST00000331920.6:c.3686C>T	p.Thr1229Met	p.T1229M	ENST00000331920	NM_000264.3	1229	aCg/aTg	22/24	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.64612272115244	2		430	418	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396271	139396271	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001114-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	106	455	0	ENST00000277541.6:c.5567C>G	p.Ser1856Cys	p.S1856C	ENST00000277541	NM_017617.3	1856	tCt/tGt	30/34	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.64612272115244	2		455	318	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399191	139399191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1243453790	NA	P-0001114-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	77	383	0	ENST00000277541.6:c.4952C>T	p.Ser1651Leu	p.S1651L	ENST00000277541	NM_017617.3	1651	tCg/tTg	26/34	1	2	FACETS	0.989	0.881	1	0.989	0.881	1	CLONAL	1	TRUE	1	0.64612272115244	2		383	241	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442781	442781	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001114-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	233	402	0	ENST00000399788.2:c.1525C>A	p.His509Asn	p.H509N	ENST00000399788	NM_001042603.1	509	Cat/Aat	12/28	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.64612272115244	2		402	625	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239673	105239673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001114-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	204	659	1	ENST00000349310.3:c.872C>T	p.Thr291Ile	p.T291I	ENST00000349310	NM_001014432.1	291	aCa/aTa	11/15	0.143898856572227	4	FACETS	1	0.959	1	1	0.959	1	INDETERMINATE	2	TRUE	2	0.64612272115244	4		660	504	SUCCESS
BLM	641	MSKCC	GRCh37	15	91326061	91326061	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001114-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	172	420	0	ENST00000355112.3:c.2565G>A	p.Met855Ile	p.M855I	ENST00000355112	NM_000057.2	855	atG/atA	13/22	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.64612272115244	2		420	531	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562694	29562694	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001114-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	236	638	0	ENST00000356175.3:c.3774G>A	p.Trp1258Ter	p.W1258*	ENST00000356175	NM_000267.3	1258	tgG/tgA	28/57	0.64612272115244	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.64612272115244	1		638	449	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525048	9525048	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001114-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	309	570	0	ENST00000353224.5:c.1837G>A	p.Glu613Lys	p.E613K	ENST00000353224	NM_177990.2	613	Gag/Aag	8/10	0.64612272115244	3	FACETS	0.966	0.919	1	0.966	0.919	1	CLONAL	2	TRUE	1	0.64612272115244	3		570	655	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611065	100611065	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001114-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	126	677	0	ENST00000308731.7:c.1541C>T	p.Ser514Leu	p.S514L	ENST00000308731	NM_000061.2	514	tCa/tTa	15/19	0.28823377974203	0	FACETS	0.303	0.276	0.331			1	INDETERMINATE	1	TRUE	0	0.64612272115244	0		677	456	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007346	143007346	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	69	108	510	1	ENST00000262992.4:c.2438T>A	p.Ile813Asn	p.I813N	ENST00000262992	NM_001101669.1	813	aTc/aAc	22/24	0.810153234688705	1	FACETS	0.896	0.832	0.959	0.896	0.832	0.959	CLONAL	1	TRUE	0	0.810153234688705	1		511	177	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220260	55220260	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	140	99	658	0	ENST00000275493.2:c.650A>T	p.Gln217Leu	p.Q217L	ENST00000275493	NM_005228.3	217	cAg/cTg	6/28	0.222636085730387	1	FACETS	0.608	0.553	0.664	0.608	0.553	0.664	INDETERMINATE	1	TRUE	0	0.810153234688705	1		658	239	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484363	8484363	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	150	122	493	0	ENST00000356435.5:c.3169G>C	p.Gly1057Arg	p.G1057R	ENST00000356435		1057	Ggg/Cgg	19/35	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.810153234688705	2		493	272	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881462	48881462	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	39	203	328	0	ENST00000267163.4:c.184C>T	p.Gln62Ter	p.Q62*	ENST00000267163	NM_000321.2	62	Cag/Tag	2/27	0.723651064271768	3	FACETS	0.97	0.936	1	0.97	0.936	1	CLONAL	3	TRUE	0	0.810153234688705	3		328	242	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0001124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	42	88	568	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.810153234688705	1	FACETS	0.994	0.921	1	0.994	0.921	1	CLONAL	1	TRUE	0	0.810153234688705	1		568	130	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937694	76937694	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1184990999	NA	P-0001149-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	208	700	0	ENST00000373344.5:c.3054G>T	p.Lys1018Asn	p.K1018N	ENST00000373344	NM_000489.3	1018	aaG/aaT	9/35	0.267580658228977	0	FACETS	0.859	0.797	0.924			1	CLONAL	3	TRUE	0	0.13	0		700	1080	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189396	56189396	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001149-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	110	411	0	ENST00000399503.3:c.4430del	p.Leu1477CysfsTer13	p.L1477Cfs*13	ENST00000399503	NM_005921.1	1476	caT/ca	20/20	0.3	4	FACETS	1	0.97	1			1	CLONAL	2	TRUE	NA	0.13	4		411	788	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115839	8115843	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCT	CCTCT	-	novel	NA	P-0001149-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	138	491	0	ENST00000346208.3:c.1187_1191del	p.Leu396GlnfsTer109	p.L396Qfs*109	ENST00000346208		395	gcCCTCTcc/gccc	6/6	1	2	FACETS	0.919	0.837	1	1	0.992	1	CLONAL	3	TRUE	1	0.13	2		491	770	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178163	56178169	+	stop_gained,protein_altering_variant	Nonsense_Mutation	DEL	TTTACTC	TTTACTC	GAGT	novel	NA	P-0001149-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	75	349	0	ENST00000399503.3:c.3136_3142delinsGAGT	p.Phe1046_Gln1048delinsGluTer	p.F1046_Q1048delinsE*	ENST00000399503	NM_005921.1	1046	TTTACTCag/GAGTag	14/20	0.3	4	FACETS	0.922	0.808	1			1	CLONAL	2	TRUE	NA	0.13	4		349	707	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0001158-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	15	506	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.292642650895069	1	FACETS	0.556	0.407	0.735	0.556	0.407	0.735	SUBCLONAL	1	TRUE	0	0.21	1		507	230	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518267	8518267	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001158-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	15	315	0	ENST00000356435.5:c.1124C>A	p.Thr375Asn	p.T375N	ENST00000356435		375	aCc/aAc	10/35	1	2	FACETS	0.501	0.366	0.664	0.501	0.366	0.664	SUBCLONAL	1	TRUE	1	0.21	2		315	285	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781059	135781059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001158-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	20	504	0	ENST00000298552.3:c.1906G>A	p.Glu636Lys	p.E636K	ENST00000298552	NM_001162426.1	636	Gag/Aag	15/23	1	2	FACETS	0.569	0.434	0.726	0.569	0.434	0.726	SUBCLONAL	1	TRUE	1	0.21	2		504	335	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478786	56478786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324972550	NA	P-0001158-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	42	314	0	ENST00000267101.3:c.242G>A	p.Arg81Gln	p.R81Q	ENST00000267101	NM_001982.3	81	cGa/cAa	3/28	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.21	2		314	313	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604697	48604697	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001158-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	17	268	0	ENST00000342988.3:c.1519A>G	p.Lys507Glu	p.K507E	ENST00000342988	NM_005359.5	507	Aaa/Gaa	12/12	1	2	FACETS	0.618	0.461	0.804	0.618	0.461	0.804	SUBCLONAL	1	TRUE	1	0.21	2		268	262	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220649	1220649	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001163-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	122	513	0	ENST00000326873.7:c.667G>T	p.Glu223Ter	p.E223*	ENST00000326873	NM_000455.4	223	Gag/Tag	5/10	0.259244138954509	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.259244138954509	1		513	676	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913351	NA	P-0001163-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	132	436	0	ENST00000288602.6:c.1397G>C	p.Gly466Ala	p.G466A	ENST00000288602	NM_004333.4	466	gGa/gCa	11/18	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.259244138954509	2		436	741	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920482	134920482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001163-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	119	578	0	ENST00000398015.3:c.2297C>T	p.Ser766Phe	p.S766F	ENST00000398015	NM_004441.4	766	tCc/tTc	12/16	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.259244138954509	2		578	805	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036946	180036946	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001163-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	117	735	0	ENST00000261937.6:c.3766G>C	p.Glu1256Gln	p.E1256Q	ENST00000261937	NM_182925.4	1256	Gag/Cag	28/30	0.192777936417063	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	0	0.259244138954509	1		735	782	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602806	10602806	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001163-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	100	430	0	ENST00000171111.5:c.772G>T	p.Glu258Ter	p.E258*	ENST00000171111	NM_203500.1	258	Gaa/Taa	3/6	0.259244138954509	0	FACETS	1	0.963	1			1	CLONAL	1	TRUE	0	0.259244138954509	0		430	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579400	7579400	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001163-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	54	342	0	ENST00000269305.4:c.287del	p.Ser96LeufsTer27	p.S96Lfs*27	ENST00000269305	NM_001126112.2	96	tCt/tt	4/11	0.259244138954509	1	FACETS	0.947	0.812	1	0.947	0.812	1	CLONAL	1	TRUE	0	0.259244138954509	1		342	383	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	162	228	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.799455275259785	3	FACETS	0.792	0.729	0.858			1	SUBCLONAL	1	TRUE	NA	0.799455275259785	3		228	716	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	1032	583	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.799455275259785	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.799455275259785	2		583	1243	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11181344	11181344	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	418	408	0	ENST00000361445.4:c.6892G>C	p.Asp2298His	p.D2298H	ENST00000361445	NM_004958.3	2298	Gac/Cac	49/58	0.47001313838544	3	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.799455275259785	3		408	1188	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248163	59248163	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	29	23	0	ENST00000371222.2:c.580G>T	p.Gly194Cys	p.G194C	ENST00000371222	NM_002228.3	194	Ggc/Tgc	1/1	0.799455275259785	2	FACETS	1	0.841	1	0.504	0.42	0.591	CLONAL	1	TRUE	0	0.799455275259785	2		23	72	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958588	175958588	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	436	385	0	ENST00000367669.3:c.1757G>C	p.Arg586Pro	p.R586P	ENST00000367669	NM_022457.5	586	cGt/cCt	16/20	0.799455275259785	3	FACETS	1	0.976	1	0.346	0.329	0.363	CLONAL	1	TRUE	0	0.799455275259785	3		385	1471	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456439	29456439	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	336	756	0	ENST00000389048.3:c.2479G>T	p.Val827Leu	p.V827L	ENST00000389048	NM_004304.4	827	Gta/Tta	14/29	0.777356845950957	2	FACETS	0.614	0.579	0.649	0.307	0.289	0.325	SUBCLONAL	1	TRUE	0	0.799455275259785	2		756	1370	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635588	47635588	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587781447	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	447	400	0	ENST00000233146.2:c.260C>G	p.Ser87Cys	p.S87C	ENST00000233146	NM_000251.2	87	tCt/tGt	2/16	0.777356845950957	2	FACETS	1	0.996	1	0.662	0.636	0.687	CLONAL	1	TRUE	0	0.799455275259785	2		400	845	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637440	47637440	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs768006988	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	473	388	0	ENST00000233146.2:c.574A>T	p.Ile192Phe	p.I192F	ENST00000233146	NM_000251.2	192	Atc/Ttc	3/16	0.777356845950957	2	FACETS	1	0.996	1	0.684	0.659	0.709	CLONAL	1	TRUE	0	0.799455275259785	2		388	865	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026875	48026875	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1558662820	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	257	593	0	ENST00000234420.5:c.1753C>G	p.Leu585Val	p.L585V	ENST00000234420	NM_000179.2	585	Cta/Gta	4/10	0.777356845950957	2	FACETS	0.593	0.555	0.632	0.297	0.277	0.316	SUBCLONAL	1	TRUE	0	0.799455275259785	2		593	1084	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193486	99193486	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	832	548	0	ENST00000074304.5:c.2681G>T	p.Ser894Ile	p.S894I	ENST00000074304	NM_001134224.1	894	aGc/aTc	25/26	0.348696147693735	3	FACETS	1	0.99	1	0.689	0.67	0.707	INDETERMINATE	2	TRUE	0	0.799455275259785	3		548	1410	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728705	190728705	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	631	334	0	ENST00000441310.2:c.2093A>T	p.Gln698Leu	p.Q698L	ENST00000441310	NM_000534.4	698	cAg/cTg	10/13	0.799455275259785	3	FACETS	0.777	0.75	0.805			1	SUBCLONAL	2	TRUE	NA	0.799455275259785	3		334	1421	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212615412	212615412	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	189	411	0	ENST00000342788.4:c.574T>A	p.Ser192Thr	p.S192T	ENST00000342788	NM_005235.2	192	Tcc/Acc	5/28	0.363632353051919	2	FACETS	0.437	0.404	0.473	0.219	0.202	0.237	INDETERMINATE	1	TRUE	0	0.799455275259785	2		411	1081	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593707	215593707	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	118	237	0	ENST00000260947.4:c.2027A>T	p.Tyr676Phe	p.Y676F	ENST00000260947	NM_000465.2	676	tAc/tTc	11/11	0.363632353051919	2	FACETS	0.443	0.4	0.488	0.221	0.2	0.244	INDETERMINATE	1	TRUE	0	0.799455275259785	2		237	667	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162197	47162197	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	293	366	0	ENST00000409792.3:c.3929C>G	p.Ser1310Ter	p.S1310*	ENST00000409792	NM_014159.6	1310	tCa/tGa	3/21	0.303243281487062	3	FACETS	0.875	0.823	0.929	0.438	0.411	0.465	INDETERMINATE	1	TRUE	1	0.799455275259785	3		366	1172	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428190	72428190	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	423	370	0	ENST00000477973.2:c.699+1G>T		p.X233_splice	ENST00000477973	NM_012234.5	233			0.303243281487062	3	FACETS	1	0.994	1	0.624	0.595	0.653	INDETERMINATE	1	TRUE	1	0.799455275259785	3		370	1187	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664847	138664847	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767088367	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	45	22	0	ENST00000330315.3:c.718G>A	p.Gly240Ser	p.G240S	ENST00000330315	NM_023067.3	240	Ggc/Agc	1/1	0.303243281487062	3	FACETS	1	0.921	1	1	0.921	1	INDETERMINATE	2	TRUE	1	0.799455275259785	3		22	75	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167804	185167804	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1440	557	476	0	ENST00000265026.3:c.1127C>G	p.Ser376Cys	p.S376C	ENST00000265026	NM_004721.4	376	tCc/tGc	6/14	0.799455275259785	3	FACETS	0.977	0.935	1			1	CLONAL	1	TRUE	NA	0.799455275259785	3		476	1997	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201810	66201810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	222	375	0	ENST00000273854.3:c.2692C>T	p.Pro898Ser	p.P898S	ENST00000273854	NM_004439.5	898	Cca/Tca	16/18	0.398601790454206	1	FACETS	0.412	0.384	0.44	0.412	0.384	0.44	INDETERMINATE	1	TRUE	0	0.799455275259785	1		375	810	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201827	66201827	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	328	338	0	ENST00000273854.3:c.2675A>T	p.Glu892Val	p.E892V	ENST00000273854	NM_004439.5	892	gAg/gTg	16/18	0.398601790454206	1	FACETS	0.683	0.65	0.717	0.683	0.65	0.717	INDETERMINATE	1	TRUE	0	0.799455275259785	1		338	721	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467953	66467953	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	227	408	0	ENST00000273854.3:c.316G>T	p.Glu106Ter	p.E106*	ENST00000273854	NM_004439.5	106	Gaa/Taa	3/18	0.398601790454206	1	FACETS	0.395	0.368	0.422	0.395	0.368	0.422	INDETERMINATE	1	TRUE	0	0.799455275259785	1		408	864	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143352410	143352410	+	start_lost	Translation_Start_Site	SNP	C	C	A	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	536	453	0	ENST00000262992.4:c.3G>T	p.Met1?	p.M1?	ENST00000262992	NM_001101669.1	1	atG/atT	2/24	0.398601790454206	1	FACETS	0.787	0.759	0.815	0.787	0.759	0.815	INDETERMINATE	1	TRUE	0	0.799455275259785	1		453	1023	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876524	35876524	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1449	379	268	0	ENST00000303115.3:c.1316C>A	p.Thr439Asn	p.T439N	ENST00000303115	NM_002185.3	439	aCt/aAt	8/8	0.738457337755927	5	FACETS	1	0.988	1	0.285	0.27	0.301	CLONAL	1	TRUE	1	0.799455275259785	5		268	1828	SUCCESS
APC	324	MSKCC	GRCh37	5	112177106	112177106	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	800	458	0	ENST00000257430.4:c.5815G>C	p.Asp1939His	p.D1939H	ENST00000257430	NM_000038.5	1939	Gac/Cac	16/16	0.762506121992231	2	FACETS	0.949	0.928	0.968	0.949	0.928	0.968	CLONAL	2	TRUE	0	0.799455275259785	2		458	1055	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512446	149512446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1291265658	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	571	367	0	ENST00000261799.4:c.994C>T	p.Arg332Trp	p.R332W	ENST00000261799	NM_002609.3	332	Cgg/Tgg	7/23	0.762506121992231	2	FACETS	0.885	0.861	0.909	0.885	0.861	0.909	CLONAL	2	TRUE	0	0.799455275259785	2		367	807	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523702	176523702	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	747	595	0	ENST00000292408.4:c.2113G>T	p.Gly705Ter	p.G705*	ENST00000292408	NM_213647.1	705	Gga/Tga	16/18	0.762506121992231	2	FACETS	0.959	0.939	0.979	0.959	0.939	0.979	CLONAL	2	TRUE	0	0.799455275259785	2		595	974	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671949	30671949	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	559	521	1	ENST00000376406.3:c.5011A>C	p.Thr1671Pro	p.T1671P	ENST00000376406	NM_014641.2	1671	Acc/Ccc	10/15	0.189009069740781	3	FACETS	1	0.997	1	0.715	0.688	0.743	INDETERMINATE	1	TRUE	1	0.799455275259785	3		522	1368	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170060	32170060	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	540	532	0	ENST00000375023.3:c.3548G>T	p.Gly1183Val	p.G1183V	ENST00000375023	NM_004557.3	1183	gGa/gTa	21/30	0.189009069740781	3	FACETS	1	0.996	1	0.718	0.69	0.746	INDETERMINATE	1	TRUE	1	0.799455275259785	3		532	1317	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704623	117704623	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	574	424	1	ENST00000368508.3:c.2353G>T	p.Val785Leu	p.V785L	ENST00000368508	NM_002944.2	785	Gtg/Ttg	16/43	0.189009069740781	3	FACETS	1	0.997	1	0.721	0.693	0.749	INDETERMINATE	1	TRUE	1	0.799455275259785	3		425	1394	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137522064	137522064	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	214	268	0	ENST00000367739.4:c.815A>C	p.Lys272Thr	p.K272T	ENST00000367739	NM_000416.2	272	aAa/aCa	6/7	0.189009069740781	3	FACETS	0.695	0.645	0.747	0.348	0.322	0.374	INDETERMINATE	1	TRUE	1	0.799455275259785	3		268	1078	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983870	2983870	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	509	601	0	ENST00000396946.4:c.660G>C	p.Met220Ile	p.M220I	ENST00000396946	NM_032415.4	220	atG/atC	5/25	0.436125572543069	3	FACETS	1	0.99	1	0.553	0.529	0.578	INDETERMINATE	1	TRUE	1	0.799455275259785	3		601	1611	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971366	13971366	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	118	223	0	ENST00000405192.2:c.563G>C	p.Arg188Pro	p.R188P	ENST00000405192	NM_001163147.1	188	cGc/cCc	8/12	0.436125572543069	3	FACETS	0.575	0.519	0.635	0.288	0.259	0.318	INDETERMINATE	1	TRUE	1	0.799455275259785	3		223	718	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233096	55233096	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	302	247	0	ENST00000275493.2:c.1846G>T	p.Val616Leu	p.V616L	ENST00000275493	NM_005228.3	616	Gtg/Ttg	15/28	0.436125572543069	3	FACETS	1	0.99	1	0.597	0.564	0.631	INDETERMINATE	1	TRUE	1	0.799455275259785	3		247	885	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534411	140534411	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	1116	320	1	ENST00000288602.6:c.502G>T	p.Val168Leu	p.V168L	ENST00000288602	NM_004333.4	168	Gtg/Ttg	3/18	0.799455275259785	4	FACETS	0.953	0.932	0.974	0.953	0.932	0.974	CLONAL	3	TRUE	1	0.799455275259785	4		321	1757	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148507438	148507438	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1912	228	415	0	ENST00000320356.2:c.2016C>G	p.Phe672Leu	p.F672L	ENST00000320356	NM_004456.4	672	ttC/ttG	17/20	0.799455275259785	4	FACETS	0.48	0.445	0.516	0.16	0.148	0.172	SUBCLONAL	1	TRUE	1	0.799455275259785	4		415	2140	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860506	151860506	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1959	511	477	0	ENST00000262189.6:c.10156G>C	p.Asp3386His	p.D3386H	ENST00000262189	NM_170606.2	3386	Gat/Cat	43/59	0.799455275259785	4	FACETS	0.931	0.888	0.976	0.31	0.296	0.326	CLONAL	1	TRUE	1	0.799455275259785	4		477	2470	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151871215	151871215	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	790	355	0	ENST00000262189.6:c.9374+1G>C		p.X3125_splice	ENST00000262189	NM_170606.2	3125			0.799455275259785	4	FACETS	0.916	0.886	0.946	0.611	0.591	0.631	CLONAL	2	TRUE	1	0.799455275259785	4		355	1941	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151932996	151932996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372408170	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	46	74	0	ENST00000262189.6:c.2675G>A	p.Gly892Glu	p.G892E	ENST00000262189	NM_170606.2	892	gGa/gAa	16/59	0.799455275259785	4	FACETS	0.386	0.324	0.453	0.129	0.108	0.151	SUBCLONAL	1	TRUE	1	0.799455275259785	4		74	537	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054592	5054592	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	506	218	0	ENST00000381652.3:c.644G>T	p.Arg215Leu	p.R215L	ENST00000381652	NM_004972.3	215	cGa/cTa	7/25	NA	2	FACETS	0.998	0.974	1			1	INDETERMINATE	2	TRUE	NA	0.799455275259785	2		218	634	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5463097	5463097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763507364	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	527	202	0	ENST00000381577.3:c.658C>T	p.His220Tyr	p.H220Y	ENST00000381577	NM_014143.3	220	Cat/Tat	4/7	NA	2	FACETS	0.982	0.958	1			1	INDETERMINATE	2	TRUE	NA	0.799455275259785	2		202	671	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341725	8341725	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	945	571	1	ENST00000356435.5:c.4915G>T	p.Glu1639Ter	p.E1639*	ENST00000356435		1639	Gag/Tag	29/35	NA	2	FACETS	0.965	0.947	0.983			1	INDETERMINATE	2	TRUE	NA	0.799455275259785	2		572	1225	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88635778	88635778	+	start_lost	Translation_Start_Site	SNP	G	G	T	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	95	207	0	ENST00000372037.3:c.3G>T	p.Met1?	p.M1?	ENST00000372037	NM_004329.2	1	atG/atT	3/13	NA	2	FACETS	0.468	0.418	0.521			1	INDETERMINATE	1	TRUE	NA	0.799455275259785	2		207	508	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61197647	61197647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1356	296	650	1	ENST00000301761.2:c.29C>T	p.Ser10Leu	p.S10L	ENST00000301761	NM_017841.2	10	tCg/tTg	1/4	NA	2	FACETS	0.448	0.42	0.477			1	INDETERMINATE	1	TRUE	NA	0.799455275259785	2		651	1652	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136949	64136949	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	187	162	0	ENST00000334205.4:c.1460G>T	p.Arg487Leu	p.R487L	ENST00000334205	NM_003942.2	487	cGg/cTg	13/17	0.747163254612043	3	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.799455275259785	3		162	458	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137699	64137699	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	511	612	0	ENST00000334205.4:c.1800C>A	p.Tyr600Ter	p.Y600*	ENST00000334205	NM_003942.2	600	taC/taA	15/17	0.747163254612043	3	FACETS	1	0.994	1			1	CLONAL	1	TRUE	NA	0.799455275259785	3		612	1496	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198974	67198974	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs936208933	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	178	317	0	ENST00000312629.5:c.445G>C	p.Glu149Gln	p.E149Q	ENST00000312629	NM_003952.2	149	Gag/Cag	5/15	0.747163254612043	3	FACETS	0.567	0.521	0.614			1	SUBCLONAL	1	TRUE	NA	0.799455275259785	3		317	1100	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77054940	77054940	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	561	617	0	ENST00000356341.3:c.922A>G	p.Lys308Glu	p.K308E	ENST00000356341	NM_002576.4	308	Aag/Gag	10/15	0.52909711274224	3	FACETS	1	0.992	1	0.569	0.546	0.593	CLONAL	1	TRUE	1	0.799455275259785	3		617	1725	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165748	108165748	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1214	251	401	0	ENST00000278616.4:c.4871A>T	p.His1624Leu	p.H1624L	ENST00000278616	NM_000051.3	1624	cAt/cTt	32/63	0.52909711274224	3	FACETS	0.6	0.56	0.642	0.3	0.28	0.321	SUBCLONAL	1	TRUE	1	0.799455275259785	3		401	1465	SUCCESS
CBL	867	MSKCC	GRCh37	11	119146835	119146835	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	428	420	0	ENST00000264033.4:c.998G>T	p.Arg333Met	p.R333M	ENST00000264033	NM_005188.3	333	aGg/aTg	6/16	0.52909711274224	3	FACETS	1	0.991	1	0.574	0.547	0.601	CLONAL	1	TRUE	1	0.799455275259785	3		420	1306	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443917	18443917	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1305	242	476	0	ENST00000266497.5:c.890C>G	p.Ser297Ter	p.S297*	ENST00000266497		297	tCa/tGa	3/31	0.404261151161362	3	FACETS	0.548	0.51	0.587	0.183	0.17	0.196	INDETERMINATE	1	TRUE	0	0.799455275259785	3		476	1547	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205332	46205332	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	323	342	0	ENST00000334344.6:c.416C>T	p.Ser139Leu	p.S139L	ENST00000334344	NM_152641.2	139	tCg/tTg	4/21	0.404261151161362	3	FACETS	1	0.987	1	0.378	0.357	0.399	INDETERMINATE	1	TRUE	0	0.799455275259785	3		342	998	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432551	49432551	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	873	429	0	ENST00000301067.7:c.8588G>T	p.Gly2863Val	p.G2863V	ENST00000301067	NM_003482.3	2863	gGc/gTc	34/54	0.799455275259785	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	1	0.799455275259785	3		429	1313	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144442	58144442	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs373619077	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	273	217	0	ENST00000257904.6:c.629G>C	p.Arg210Pro	p.R210P	ENST00000257904	NM_000075.3	210	cGa/cCa	5/8	0.799455275259785	3	FACETS	0.989	0.929	1	0.494	0.464	0.525	CLONAL	1	TRUE	1	0.799455275259785	3		217	967	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249764	133249764	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1164814923	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	193	343	2	ENST00000320574.5:c.1459A>G	p.Met487Val	p.M487V	ENST00000320574	NM_006231.2	487	Atg/Gtg	14/49	NA	2	FACETS	0.653	0.606	0.702			1	INDETERMINATE	1	TRUE	NA	0.799455275259785	2		345	739	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562717	21562717	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	109	62	0	ENST00000382592.4:c.1202C>A	p.Pro401Gln	p.P401Q	ENST00000382592	NM_014572.2	401	cCa/cAa	4/8	0.348696147693735	3	FACETS	1	0.929	1	0.67	0.619	0.719	INDETERMINATE	2	TRUE	0	0.799455275259785	3		62	190	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955473	48955473	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1173	240	417	2	ENST00000267163.4:c.1589A>T	p.Lys530Ile	p.K530I	ENST00000267163	NM_000321.2	530	aAa/aTa	17/27	0.486679810591517	3	FACETS	0.595	0.554	0.637	0.198	0.184	0.213	SUBCLONAL	1	TRUE	0	0.799455275259785	3		419	1413	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033875	49033875	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1206	468	487	0	ENST00000267163.4:c.2012C>T	p.Ser671Phe	p.S671F	ENST00000267163	NM_000321.2	671	tCt/tTt	20/27	0.486679810591517	3	FACETS	0.979	0.934	1	0.326	0.311	0.342	CLONAL	1	TRUE	0	0.799455275259785	3		487	1674	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68301819	68301819	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	452	471	0	ENST00000487270.1:c.221G>T	p.Arg74Met	p.R74M	ENST00000487270	NM_133509.3	74	aGg/aTg	4/11	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.799455275259785	2		471	1060	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483985	88483985	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	199	326	1	ENST00000360948.2:c.1586-1G>C		p.X529_splice	ENST00000360948	NM_001012338.2	529			0.308892229089078	1	FACETS	0.452	0.42	0.485	0.452	0.42	0.485	INDETERMINATE	1	TRUE	0	0.799455275259785	1		327	661	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292656	91292656	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	426	323	0	ENST00000355112.3:c.158C>G	p.Ser53Ter	p.S53*	ENST00000355112	NM_000057.2	53	tCa/tGa	3/22	0.308892229089078	1	FACETS	0.676	0.647	0.705	0.676	0.647	0.705	INDETERMINATE	1	TRUE	0	0.799455275259785	1		323	946	SUCCESS
BLM	641	MSKCC	GRCh37	15	91328153	91328153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	238	355	0	ENST00000355112.3:c.2665G>T	p.Asp889Tyr	p.D889Y	ENST00000355112	NM_000057.2	889	Gat/Tat	14/22	0.308892229089078	1	FACETS	0.411	0.384	0.438	0.411	0.384	0.438	INDETERMINATE	1	TRUE	0	0.799455275259785	1		355	870	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478253	99478253	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	120	153	0	ENST00000268035.6:c.3157G>T	p.Val1053Leu	p.V1053L	ENST00000268035	NM_000875.3	1053	Gtg/Ttg	16/21	0.308892229089078	1	FACETS	0.434	0.395	0.475	0.434	0.395	0.475	INDETERMINATE	1	TRUE	0	0.799455275259785	1		153	415	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341293	341293	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	459	533	0	ENST00000262320.3:c.2191G>T	p.Val731Leu	p.V731L	ENST00000262320	NM_003502.3	731	Gtg/Ttg	9/11	NA	2	FACETS	0.959	0.918	1			1	INDETERMINATE	1	TRUE	NA	0.799455275259785	2		533	1197	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849470	89849470	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs778045457	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	472	567	0	ENST00000389301.3:c.1511G>T	p.Arg504Leu	p.R504L	ENST00000389301	NM_000135.2	504	cGc/cTc	16/43	NA	2	FACETS	0.964	0.923	1			1	INDETERMINATE	1	TRUE	NA	0.799455275259785	2		567	1225	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866091	37866091	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	479	423	0	ENST00000269571.5:c.600G>T	p.Lys200Asn	p.K200N	ENST00000269571		200	aaG/aaT	5/27	0.47001313838544	3	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.799455275259785	3		423	1380	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41203127	41203127	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs398122694	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	307	234	0	ENST00000357654.3:c.5285G>T	p.Arg1762Met	p.R1762M	ENST00000357654	NM_007294.3	1762	aGg/aTg	20/23	0.404261151161362	3	FACETS	1	0.992	1	0.429	0.406	0.453	INDETERMINATE	1	TRUE	0	0.799455275259785	3		234	835	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772460	56772460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1342	253	453	0	ENST00000337432.4:c.314C>T	p.Ser105Leu	p.S105L	ENST00000337432	NM_058216.2	105	tCa/tTa	2/9	0.404261151161362	3	FACETS	0.555	0.518	0.594	0.185	0.172	0.198	INDETERMINATE	1	TRUE	0	0.799455275259785	3		453	1595	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117632	70117632	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	566	543	0	ENST00000245479.2:c.100C>A	p.Pro34Thr	p.P34T	ENST00000245479	NM_000346.3	34	Ccc/Acc	1/3	0.799455275259785	3	FACETS	1	0.995	1	0.618	0.593	0.643	CLONAL	1	TRUE	1	0.799455275259785	3		543	1604	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117797	70117797	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	529	570	0	ENST00000245479.2:c.265G>T	p.Val89Leu	p.V89L	ENST00000245479	NM_000346.3	89	Gtg/Ttg	1/3	0.799455275259785	3	FACETS	1	0.994	1	0.607	0.582	0.633	CLONAL	1	TRUE	1	0.799455275259785	3		570	1525	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724581	724581	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs750831029	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	130	267	0	ENST00000314574.4:c.1475C>A	p.Pro492Gln	p.P492Q	ENST00000314574	NM_005433.3	492	cCg/cAg	12/12	NA	2	FACETS	0.397	0.36	0.436			1	INDETERMINATE	1	TRUE	NA	0.799455275259785	2		267	819	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349876	15349876	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	261	179	0	ENST00000263377.2:c.3776G>C	p.Arg1259Pro	p.R1259P	ENST00000263377	NM_058243.2	1259	cGc/cCc	18/20	0.429660146888207	1	FACETS	0.83	0.789	0.871	0.83	0.789	0.871	INDETERMINATE	1	TRUE	0	0.799455275259785	1		179	472	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266954	18266954	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	37	55	0	ENST00000222254.8:c.265C>A	p.Arg89Ser	p.R89S	ENST00000222254	NM_005027.3	89	Cgc/Agc	2/16	0.429660146888207	1	FACETS	0.459	0.387	0.536	0.459	0.387	0.536	INDETERMINATE	1	TRUE	0	0.799455275259785	1		55	121	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279639	18279639	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	199	345	0	ENST00000222254.8:c.1912G>T	p.Gly638Cys	p.G638C	ENST00000222254	NM_005027.3	638	Ggc/Tgc	15/16	0.429660146888207	1	FACETS	0.374	0.347	0.402	0.374	0.347	0.402	INDETERMINATE	1	TRUE	0	0.799455275259785	1		345	798	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314572	30314572	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	453	583	3	ENST00000262643.3:c.1121G>T	p.Arg374Leu	p.R374L	ENST00000262643	NM_001238.2	374	cGa/cTa	12/12	0.486679810591517	3	FACETS	1	0.974	1	0.344	0.328	0.361	CLONAL	1	TRUE	0	0.799455275259785	3		586	1537	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791519	42791519	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368616680	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1716	260	658	0	ENST00000575354.2:c.500G>A	p.Gly167Glu	p.G167E	ENST00000575354	NM_015125.3	167	gGa/gAa	4/20	0.486679810591517	3	FACETS	0.461	0.43	0.493	0.154	0.143	0.165	SUBCLONAL	1	TRUE	0	0.799455275259785	3		658	1976	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793127	42793127	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1351	265	465	0	ENST00000575354.2:c.1019G>T	p.Arg340Leu	p.R340L	ENST00000575354	NM_015125.3	340	cGg/cTg	7/20	0.486679810591517	3	FACETS	0.574	0.536	0.613	0.191	0.178	0.205	SUBCLONAL	1	TRUE	0	0.799455275259785	3		465	1616	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793543	42793543	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	344	317	0	ENST00000575354.2:c.1345G>C	p.Asp449His	p.D449H	ENST00000575354	NM_015125.3	449	Gat/Cat	8/20	0.486679810591517	3	FACETS	1	0.988	1	0.377	0.357	0.397	CLONAL	1	TRUE	0	0.799455275259785	3		317	1066	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715961	52715961	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	395	502	0	ENST00000322088.6:c.526G>C	p.Asp176His	p.D176H	ENST00000322088	NM_014225.5	176	Gat/Cat	5/15	0.486679810591517	3	FACETS	1	0.968	1	0.342	0.324	0.359	CLONAL	1	TRUE	0	0.799455275259785	3		502	1350	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023121	31023121	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1434	198	399	0	ENST00000375687.4:c.2606G>T	p.Gly869Val	p.G869V	ENST00000375687	NM_015338.5	869	gGt/gTt	13/13	0.432760956680173	4	FACETS	0.546	0.504	0.59	0.137	0.126	0.148	INDETERMINATE	1	TRUE	0	0.799455275259785	4		399	1632	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376681	31376681	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	366	402	0	ENST00000328111.2:c.676G>T	p.Gly226Trp	p.G226W	ENST00000328111	NM_006892.3	226	Ggg/Tgg	7/23	0.432760956680173	4	FACETS	1	0.993	1	0.324	0.307	0.342	INDETERMINATE	1	TRUE	0	0.799455275259785	4		402	1270	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39744994	39744994	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1493	188	482	0	ENST00000361337.2:c.1784C>A	p.Ser595Tyr	p.S595Y	ENST00000361337	NM_003286.2	595	tCc/tAc	17/21	0.432760956680173	4	FACETS	0.503	0.463	0.546	0.126	0.115	0.137	INDETERMINATE	1	TRUE	0	0.799455275259785	4		482	1681	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714438	40714438	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	144	340	0	ENST00000373198.4:c.3959T>A	p.Val1320Glu	p.V1320E	ENST00000373198	NM_133170.3	1320	gTg/gAg	29/32	0.585795938261469	3	FACETS	0.465	0.423	0.509	0.155	0.141	0.17	SUBCLONAL	1	TRUE	0	0.799455275259785	3		340	1085	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748580	40748580	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	168	331	0	ENST00000373198.4:c.2936C>A	p.Thr979Asn	p.T979N	ENST00000373198	NM_133170.3	979	aCt/aAt	21/32	0.585795938261469	3	FACETS	0.463	0.424	0.504	0.154	0.141	0.168	SUBCLONAL	1	TRUE	0	0.799455275259785	3		331	1270	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961363	54961363	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	105	186	0	ENST00000312783.6:c.269G>T	p.Arg90Met	p.R90M	ENST00000312783	NM_198436.1	90	aGg/aTg	4/10	0.585795938261469	3	FACETS	0.46	0.412	0.511	0.153	0.137	0.171	SUBCLONAL	1	TRUE	0	0.799455275259785	3		186	799	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095918	29095918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587783051	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	239	560	0	ENST00000328354.6:c.916G>A	p.Gly306Arg	p.G306R	ENST00000328354	NM_007194.3	306	Ggg/Agg	9/15	NA	2	FACETS	0.543	0.507	0.581			1	INDETERMINATE	1	TRUE	NA	0.799455275259785	2		560	1101	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225199	53225199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781854324	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	569	404	0	ENST00000375401.3:c.3019C>T	p.Arg1007Cys	p.R1007C	ENST00000375401	NM_004187.3	1007	Cgt/Tgt	20/26	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.799455275259785	1		404	734	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335655	81335655	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	565	449	0	ENST00000222390.5:c.1705del	p.Gln569SerfsTer13	p.Q569Sfs*13	ENST00000222390	NM_000601.4	569	Cag/ag	15/18	0.436125572543069	3	FACETS	1	0.994	1	0.59	0.566	0.614	INDETERMINATE	1	TRUE	1	0.799455275259785	3		449	1677	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858680	9858681	+	missense_variant	Missense_Mutation	DNP	CA	CA	AT	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	881	531	0	ENST00000330684.3:c.2720_2721delinsAT	p.Met907Asn	p.M907N	ENST00000330684	NM_001134407.1	907	aTG/aAT	13/13	NA	2	FACETS	0.978	0.959	0.996			1	INDETERMINATE	2	TRUE	NA	0.799455275259785	2		531	1127	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161482	2161483	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	291	691	0	ENST00000434045.2:c.44_45delinsAG	p.Thr15Lys	p.T15K	ENST00000434045	NM_001127598.1	15	aCC/aAG	2/5	NA	2	FACETS	0.64	0.602	0.679			1	INDETERMINATE	1	TRUE	NA	0.799455275259785	2		691	1137	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942724	44942726	+	missense_variant	Missense_Mutation	TNP	GAG	GAG	AAT	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	483	225	0	ENST00000377967.4:c.3304_3306delinsAAT	p.Glu1102Asn	p.E1102N	ENST00000377967	NM_021140.2	1102	GAG/AAT	23/29	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.799455275259785	1		225	624	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391977	139391978	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0001171-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	504	643	0	ENST00000277541.6:c.6213_6214delinsTT	p.Glu2071_Gly2072delinsAspCys	p.E2071_G2072delinsDC	ENST00000277541	NM_017617.3	2071	gaGGgc/gaTTgc	34/34	0.400670391049824	1	FACETS	0.726	0.698	0.754	0.726	0.698	0.754	INDETERMINATE	1	TRUE	0	0.799455275259785	1		643	1043	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484191	120484191	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001177-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	74	530	0	ENST00000256646.2:c.2939A>G	p.Asp980Gly	p.D980G	ENST00000256646	NM_024408.3	980	gAt/gGt	18/34	0.133063411650532	4	FACETS	1	0.969	1	0.677	0.594	0.766	INDETERMINATE	1	TRUE	2	0.283448799984244	4		530	495	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125455	47125455	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001177-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	48	840	0	ENST00000409792.3:c.5815del	p.Asp1939IlefsTer6	p.D1939Ifs*6	ENST00000409792	NM_014159.6	1939	Gat/at	12/21	NA	2	FACETS	0.571	0.482	0.669			1	INDETERMINATE	1	TRUE	NA	0.283448799984244	2		840	593	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0001190-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	245	269	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.310615718301007	2	FACETS	0.919	0.876	0.962	0.919	0.876	0.962	INDETERMINATE	2	TRUE	0	0.678105593492915	2		269	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0001190-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	207	646	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.654027534521883	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.678105593492915	1		647	349	SUCCESS
APC	324	MSKCC	GRCh37	5	112175758	112175758	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001190-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	115	439	0	ENST00000257430.4:c.4467del	p.Leu1489PhefsTer18	p.L1489Ffs*18	ENST00000257430	NM_000038.5	1489	ttA/tt	16/16	0.678105593492915	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.678105593492915	1		439	173	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001241-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	27	300	0	ENST00000397752.3:c.3028G>T	p.Asp1010Tyr	p.D1010Y	ENST00000397752	NM_000245.2	1010	Gat/Tat	14/21	0.314358346516251	2	FACETS	0.937	0.766	1	0.937	0.766	1	CLONAL	2	TRUE	0	0.323914262953736	2		300	89	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916531	39916531	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001241-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	13	689	0	ENST00000378444.4:c.4472A>G	p.Asn1491Ser	p.N1491S	ENST00000378444	NM_001123385.1	1491	aAt/aGt	11/15	0.323914262953736	0	FACETS	0.262	0.187	0.354			1	SUBCLONAL	1	TRUE	0	0.323914262953736	0		689	207	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0001287-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	61	203	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	NA	2	FACETS	0.492	0.425	0.566			1	INDETERMINATE	1	TRUE	NA	0.458898205387885	2		203	540	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105955	27105955	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001287-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	93	162	1	ENST00000324856.7:c.5566C>T	p.Gln1856Ter	p.Q1856*	ENST00000324856	NM_006015.4	1856	Cag/Tag	20/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.458898205387885	2		163	281	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0001287-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	113	157	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.458898205387885	2		157	355	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206599	108206599	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001287-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	199	240	0	ENST00000278616.4:c.8179G>T	p.Val2727Phe	p.V2727F	ENST00000278616	NM_000051.3	2727	Gtc/Ttc	56/63	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.458898205387885	2		240	819	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604789	48604789	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001287-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	201	318	0	ENST00000342988.3:c.1611C>G	p.Asp537Glu	p.D537E	ENST00000342988	NM_005359.5	537	gaC/gaG	12/12	0.339108311066606	2	FACETS	1	0.988	1	0.654	0.608	0.7	CLONAL	1	TRUE	0	0.458898205387885	2		318	670	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226697	2226697	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194208604	NA	P-0001287-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	35	269	0	ENST00000398665.3:c.4177G>A	p.Gly1393Ser	p.G1393S	ENST00000398665	NM_032482.2	1393	Ggc/Agc	27/28	1	2	FACETS	0.551	0.453	0.659	0.551	0.453	0.659	SUBCLONAL	1	TRUE	1	0.458898205387885	2		269	277	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431098	181431098	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001287-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	53	146	0	ENST00000325404.1:c.950del	p.Met317SerfsTer54	p.M317Sfs*54	ENST00000325404	NM_003106.3	317	aTg/ag	1/1	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.458898205387885	2		146	195	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973068	25973068	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001323-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	333	715	0	ENST00000435504.4:c.1357G>A	p.Val453Met	p.V453M	ENST00000435504		453	Gtg/Atg	12/13	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.583147864610585	2		715	1101	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453475	138453475	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0001323-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1345	264	769	0	ENST00000289153.2:c.972+1G>T		p.X324_splice	ENST00000289153	NM_006219.2	324			NA	2	FACETS	0.563	0.526	0.601			1	INDETERMINATE	1	TRUE	NA	0.583147864610585	2		769	1609	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191200	185191200	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001323-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	263	369	1	ENST00000265026.3:c.2081C>G	p.Ser694Trp	p.S694W	ENST00000265026	NM_004721.4	694	tCg/tGg	11/14	0.205453343970154	3	FACETS	1	0.969	1	1	0.969	1	INDETERMINATE	2	TRUE	1	0.583147864610585	3		370	564	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518517	69518517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001323-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	118	412	0	ENST00000294312.3:c.128G>A	p.Arg43His	p.R43H	ENST00000294312	NM_005117.2	43	cGc/cAc	1/3	1	2	FACETS	0.671	0.607	0.738	0.671	0.607	0.738	SUBCLONAL	1	TRUE	1	0.583147864610585	2		412	603	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913837	32913837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359507	NA	P-0001325-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	195	337	0	ENST00000380152.3:c.5351del	p.Asn1784ThrfsTer7	p.N1784Tfs*7	ENST00000380152		1782	cAa/ca	11/27	1	2	FACETS	0.813	0.762	0.865	1	0.993	1	CLONAL	2	TRUE	1	0.547645068393133	2		337	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0001325-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	286	506	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.228725382966387	3	FACETS	1	0.991	1	1	0.991	1	INDETERMINATE	2	TRUE	1	0.547645068393133	3		507	553	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0001325-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	238	392	2	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	NA	2	FACETS	0.752	0.708	0.797			1	INDETERMINATE	2	TRUE	NA	0.547645068393133	2		394	578	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0001325-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	227	335	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.228725382966387	3	FACETS	1	0.969	1	1	0.969	1	INDETERMINATE	2	TRUE	1	0.547645068393133	3		335	506	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9770626	9770626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761349863	NA	P-0001325-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	718	506	0	ENST00000377346.4:c.113G>A	p.Arg38His	p.R38H	ENST00000377346	NM_005026.3	38	cGc/cAc	3/24	0.456912916720375	4	FACETS	0.885	0.86	0.909	1	0.997	1	CLONAL	4	TRUE	1	0.547645068393133	4		506	1147	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784113	9784113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771951762	NA	P-0001325-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	449	279	0	ENST00000377346.4:c.2681G>A	p.Arg894Gln	p.R894Q	ENST00000377346	NM_005026.3	894	cGg/cAg	21/24	0.456912916720375	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	1	0.547645068393133	4		279	732	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17349180	17349180	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138996609	NA	P-0001325-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	200	293	0	ENST00000375499.3:c.688C>T	p.Arg230Cys	p.R230C	ENST00000375499	NM_003000.2	230	Cgc/Tgc	7/8	0.456912916720375	4	FACETS	0.814	0.758	0.873	0.543	0.505	0.582	CLONAL	2	TRUE	1	0.547645068393133	4		293	694	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125722	47125722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376063996	NA	P-0001325-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	288	387	0	ENST00000409792.3:c.5548C>T	p.Arg1850Cys	p.R1850C	ENST00000409792	NM_014159.6	1850	Cgt/Tgt	12/21	1	2	FACETS	0.769	0.728	0.81	1	0.995	1	SUBCLONAL	2	TRUE	1	0.547645068393133	2		387	684	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525017	187525017	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001325-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	245	262	0	ENST00000441802.2:c.10663T>C	p.Ser3555Pro	p.S3555P	ENST00000441802	NM_005245.3	3555	Tct/Cct	19/27	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.547645068393133	NA		262	451	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517609	176517609	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs755455944	NA	P-0001325-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	305	513	0	ENST00000292408.4:c.310C>T	p.Arg104Ter	p.R104*	ENST00000292408	NM_213647.1	104	Cga/Tga	3/18	0.154826577888671	0	FACETS	0.737	0.699	0.774			1	INDETERMINATE	1	TRUE	0	0.547645068393133	0		513	684	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469811	157469811	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145635490	NA	P-0001325-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	396	450	0	ENST00000346085.5:c.2605G>A	p.Gly869Ser	p.G869S	ENST00000346085	NM_020732.3	869	Ggc/Agc	9/20	1	2	FACETS	0.938	0.899	0.977	1	0.997	1	CLONAL	2	TRUE	1	0.547645068393133	2		450	771	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738383	145738383	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369250614	NA	P-0001325-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	167	439	1	ENST00000428558.2:c.2602G>A	p.Val868Met	p.V868M	ENST00000428558	NM_004260.3	868	Gtg/Atg	16/22	0.532220951488863	4	FACETS	0.753	0.69	0.819	0.251	0.23	0.273	SUBCLONAL	1	TRUE	1	0.547645068393133	4		440	1254	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104268939	104268939	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001325-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	493	534	0	ENST00000369902.3:c.196G>T	p.Asp66Tyr	p.D66Y	ENST00000369902	NM_016169.3	66	Gac/Tac	2/12	0.273662792652437	3	FACETS	1	0.995	1	1	0.995	1	INDETERMINATE	2	TRUE	1	0.547645068393133	3		534	946	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129428	64129428	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61736650	NA	P-0001325-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	338	434	0	ENST00000334205.4:c.860C>T	p.Ala287Val	p.A287V	ENST00000334205	NM_003942.2	287	gCg/gTg	8/17	1	2	FACETS	0.872	0.831	0.913	1	0.996	1	CLONAL	2	TRUE	1	0.547645068393133	2		434	708	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390716	118390716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555052977	NA	P-0001325-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	298	367	1	ENST00000534358.1:c.11366G>A	p.Arg3789His	p.R3789H	ENST00000534358	NM_005933.3	3789	cGt/cAt	33/36	1	2	FACETS	0.896	0.852	0.941	1	0.996	1	CLONAL	2	TRUE	1	0.547645068393133	2		368	607	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944812	31944812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866971809	NA	P-0001325-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	229	284	0	ENST00000340398.3:c.289G>A	p.Glu97Lys	p.E97K	ENST00000340398	NM_001013699.2	97	Gaa/Aaa	1/1	1	2	FACETS	0.838	0.79	0.887	1	0.994	1	CLONAL	2	TRUE	1	0.547645068393133	2		284	499	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900776	3900776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766844540	NA	P-0001325-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	122	199	0	ENST00000262367.5:c.320C>T	p.Pro107Leu	p.P107L	ENST00000262367	NM_004380.2	107	cCg/cTg	2/31	1	2	FACETS	0.771	0.708	0.834	1	0.988	1	SUBCLONAL	2	TRUE	1	0.547645068393133	2		199	289	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857895	9857895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761399460	NA	P-0001325-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	258	462	0	ENST00000330684.3:c.3506G>A	p.Arg1169Gln	p.R1169Q	ENST00000330684	NM_001134407.1	1169	cGg/cAg	13/13	1	2	FACETS	0.863	0.817	0.909	1	0.995	1	CLONAL	2	TRUE	1	0.547645068393133	2		462	546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0001325-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	156	210	0	ENST00000269305.4:c.673-2A>C		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.228725382966387	3	FACETS	1	0.962	1	1	0.962	1	INDETERMINATE	2	TRUE	1	0.547645068393133	3		210	345	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37871997	37871997	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756345214	NA	P-0001325-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	325	475	1	ENST00000269571.5:c.1318G>A	p.Ala440Thr	p.A440T	ENST00000269571		440	Gcc/Acc	12/27	0.228725382966387	3	FACETS	0.995	0.945	1	0.995	0.945	1	INDETERMINATE	2	TRUE	1	0.547645068393133	3		476	760	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226443	2226443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773019943	NA	P-0001325-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	301	421	0	ENST00000398665.3:c.3923C>T	p.Pro1308Leu	p.P1308L	ENST00000398665	NM_032482.2	1308	cCg/cTg	27/28	0.494278068436379	4	FACETS	0.83	0.783	0.878	0.553	0.522	0.586	CLONAL	2	TRUE	1	0.547645068393133	4		421	1025	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389135	31389135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1165118132	NA	P-0001325-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	350	463	0	ENST00000328111.2:c.2048G>A	p.Arg683His	p.R683H	ENST00000328111	NM_006892.3	683	cGc/cAc	19/23	0.228725382966387	3	FACETS	1	0.986	1	1	0.986	1	INDETERMINATE	2	TRUE	1	0.547645068393133	3		463	751	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263661	16263663	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-	rs768147844	NA	P-0001325-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	310	201	0	ENST00000375759.3:c.10036_10038del	p.Pro3346del	p.P3346del	ENST00000375759	NM_015001.2	3344	CCT/-	12/15	0.456912916720375	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	1	0.547645068393133	4		201	548	SUCCESS
APC	324	MSKCC	GRCh37	5	112173831	112173831	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001325-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	218	282	0	ENST00000257430.4:c.2544del	p.Asp849IlefsTer12	p.D849Ifs*12	ENST00000257430	NM_000038.5	847	gAa/ga	16/16	NA	2	FACETS	0.885	0.834	0.936			1	INDETERMINATE	2	TRUE	NA	0.547645068393133	2		282	450	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916766	48916766	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001325-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	227	303	0	ENST00000267163.4:c.299del	p.Gly100GlufsTer11	p.G100Efs*11	ENST00000267163	NM_000321.2	99	tGg/tg	3/27	0.445985833706188	0	FACETS		NA	1			1	NA	2	TRUE	0	0.547645068393133	0		303	250	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061169	38061169	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1489466891	NA	P-0001325-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	154	185	1	ENST00000250448.2:c.820del	p.Ala274ProfsTer47	p.A274Pfs*47	ENST00000250448	NM_004496.3	274	Gcc/cc	2/2	1	2	FACETS	0.907	0.846	0.969	1	0.992	1	CLONAL	2	TRUE	1	0.547645068393133	2		186	310	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021194	31021194	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781178976	NA	P-0001329-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	198	17	220	0	ENST00000375687.4:c.1193G>A	p.Gly398Asp	p.G398D	ENST00000375687	NM_015338.5	398	gGt/gAt	12/13	1	2	FACETS	0.616	0.46	0.799	0.616	0.46	0.799	SUBCLONAL	1	FALSE	1	0.256864091909116	2		220	215	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195686	123195686	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001329-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	89	16	332	0	ENST00000218089.9:c.1600G>A	p.Glu534Lys	p.E534K	ENST00000218089	NM_001042749.1	534	Gaa/Aaa	17/35	0.211210282289288	0	FACETS	0.882	0.66	1			1	CLONAL	1	FALSE	NA	0.256864091909116	0		332	105	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138068	2138077	+	frameshift_variant	Frame_Shift_Del	DEL	CACCAGCGTG	CACCAGCGTG	-	novel	NA	P-0001342-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	28	532	0	ENST00000219476.3:c.5088_5097del	p.Asp1696GlufsTer127	p.D1696Efs*127	ENST00000219476	NM_000548.3	1696	gaCACCAGCGTG/ga	40/42	0.282396824723857	1	FACETS	0.946	0.777	1	1	0.957	1	CLONAL	2	TRUE	0	0.282396824723857	1		532	90	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0001367-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	58	221	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.236898698388692	0	FACETS	0.865	0.763	0.97			1	CLONAL	3	FALSE	0	0.236898698388692	0		221	144	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0001367-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	74	357	4	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	0.158606494014063	0	FACETS	0.854	0.756	0.958			1	CLONAL	2	FALSE	0	0.236898698388692	0		361	279	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842698	68842698	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001367-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	176	459	0	ENST00000261769.5:c.635del	p.Gly212AspfsTer3	p.G212Dfs*3	ENST00000261769	NM_004360.3	212	Gga/ga	5/16	0.236898698388692	0	FACETS	0.851	0.793	0.911			1	CLONAL	3	FALSE	0	0.236898698388692	0		459	444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0001376-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	63	152	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	0.637968400362387	1	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	0	0.637968400362387	1		152	134	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606967	47606967	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001376-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	143	286	0	ENST00000263735.4:c.717A>T	p.Gln239His	p.Q239H	ENST00000263735	NM_002354.2	239	caA/caT	7/9	0.103683076344722	5	FACETS	1	0.971	1	0.555	0.512	0.6	INDETERMINATE	2	TRUE	1	0.637968400362387	5		286	395	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161243	56161243	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0001376-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	151	245	1	ENST00000399503.3:c.1112C>G	p.Ser371Ter	p.S371*	ENST00000399503	NM_005921.1	371	tCa/tGa	5/20	0.637968400362387	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.637968400362387	1		246	321	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717678	89717678	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554825200	NA	P-0001376-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	377	222	0	ENST00000371953.3:c.703G>T	p.Glu235Ter	p.E235*	ENST00000371953	NM_000314.4	235	Gaa/Taa	7/9	0.637968400362387	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.637968400362387	3		222	488	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242635	46242635	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001376-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	110	196	0	ENST00000334344.6:c.1597G>T	p.Glu533Ter	p.E533*	ENST00000334344	NM_152641.2	533	Gaa/Taa	13/21	NA	2	FACETS	1	0.927	1			1	INDETERMINATE	1	TRUE	NA	0.637968400362387	2		196	337	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023095	33023095	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001376-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	36	155	0	ENST00000300177.4:c.204G>C	p.Met68Ile	p.M68I	ENST00000300177	NM_001191322.1	68	atG/atC	2/2	0.637968400362387	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.637968400362387	1		155	68	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0001395-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	176	58	124	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.318431505796814	3	FACETS	0.9	0.782	1	0.9	0.782	1	CLONAL	2	TRUE	1	0.319517983306641	3		124	234	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161270	56161270	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001395-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	499	90	415	0	ENST00000399503.3:c.1139T>C	p.Leu380Ser	p.L380S	ENST00000399503	NM_005921.1	380	tTa/tCa	5/20	0.288399731028089	5	FACETS	1	0.977	1	0.472	0.419	0.528	CLONAL	1	TRUE	2	0.319517983306641	5		415	589	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484345	8484347	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs1282828198	NA	P-0001395-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	723	92	524	0	ENST00000356435.5:c.3185_3187del	p.Glu1062del	p.E1062del	ENST00000356435		1062	gAAGtg/gtg	19/35	0.224094154601307	5	FACETS	1	0.92	1	0.348	0.309	0.391	CLONAL	1	TRUE	2	0.319517983306641	5		524	815	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244091	46244091	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs199620718	NA	P-0001423-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	211	386	0	ENST00000334344.6:c.2185C>G	p.Pro729Ala	p.P729A	ENST00000334344	NM_152641.2	729	Cct/Gct	15/21	0.784916780298717	3	FACETS	1	0.965	1	0.527	0.491	0.564	CLONAL	1	TRUE	1	0.784916780298717	3		386	710	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651682	206651682	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001457-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	136	201	0	ENST00000367120.3:c.992C>G	p.Thr331Arg	p.T331R	ENST00000367120	NM_014002.3	331	aCg/aGg	9/22	0.703811609888643	4	FACETS	1	0.958	1			1	CLONAL	1	TRUE	NA	0.78808789718727	4		201	570	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917777	29917777	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001457-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	162	307	1	ENST00000389048.3:c.891G>C	p.Glu297Asp	p.E297D	ENST00000389048	NM_004304.4	297	gaG/gaC	3/29	0.553589364257576	6	FACETS	1	0.985	1	0.437	0.402	0.475	CLONAL	1	TRUE	3	0.78808789718727	6		308	807	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170837530	170837530	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs776815873	NA	P-0001457-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	224	204	0	ENST00000296930.5:c.847-1G>T		p.X283_splice	ENST00000296930	NM_002520.6	283			0.78808789718727	3	FACETS	1	0.97	1			1	CLONAL	1	TRUE	NA	0.78808789718727	3		204	744	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578522	7578522	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001457-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	322	164	0	ENST00000269305.4:c.408del	p.Gln136HisfsTer34	p.Q136Hfs*34	ENST00000269305	NM_001126112.2	136	caA/ca	5/11	0.78808789718727	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.78808789718727	2		164	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0001470-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	54	454	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.20374072236499	3	FACETS	0.866	0.756	0.981	0.866	0.756	0.981	CLONAL	3	FALSE	0	0.311965885748182	3		454	154	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0001470-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	39	321	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.311965885748182	3	FACETS	1	0.911	1	1	0.967	1	CLONAL	3	FALSE	1	0.311965885748182	3		321	89	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001470-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	12	161	0	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	0.267202919951667	4	FACETS	1	0.858	1	0.701	0.501	0.936	CLONAL	1	FALSE	2	0.311965885748182	4		161	72	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919643	96919643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751044006	NA	P-0001470-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	40	331	0	ENST00000258439.3:c.620C>T	p.Ala207Val	p.A207V	ENST00000258439	NM_001193304.2	207	gCg/gTg	4/4	0.192324657371687	4	FACETS	0.924	0.778	1	0.924	0.778	1	CLONAL	2	FALSE	2	0.311965885748182	4		331	182	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796955	42796955	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149948572	NA	P-0001470-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	44	381	0	ENST00000575354.2:c.3413C>T	p.Pro1138Leu	p.P1138L	ENST00000575354	NM_015125.3	1138	cCg/cTg	14/20	0.311965885748182	4	FACETS	0.777	0.658	0.908	0.389	0.329	0.454	CLONAL	2	FALSE	0	0.311965885748182	4		381	238	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100304	8100304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001474-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	329	596	0	ENST00000346208.3:c.278C>T	p.Ser93Phe	p.S93F	ENST00000346208		93	tCc/tTc	3/6	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.765427054762629	2		596	769	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204684	108204684	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs34099398	NA	P-0001474-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	79	292	0	ENST00000278616.4:c.7999A>T	p.Met2667Leu	p.M2667L	ENST00000278616	NM_000051.3	2667	Atg/Ttg	54/63	0.765427054762629	1	FACETS	0.995	0.912	1	0.995	0.912	1	CLONAL	1	FALSE	0	0.765427054762629	1		292	128	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112505	115112524	+	frameshift_variant	Frame_Shift_Del	DEL	ACCGCGGGGCTGCCCTTGTC	ACCGCGGGGCTGCCCTTGTC	-	novel	NA	P-0001474-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	139	480	0	ENST00000257566.3:c.1216_1235del	p.Asp406GlnfsTer8	p.D406Qfs*8	ENST00000257566	NM_016569.3	406	GACAAGGGCAGCCCCGCGGTc/c	7/8	1	2	FACETS	0.596	0.545	0.65	0.596	0.545	0.65	SUBCLONAL	1	FALSE	1	0.765427054762629	2		480	609	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584444	39584444	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001482-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	211	329	0	ENST00000262039.4:c.1109A>T	p.His370Leu	p.H370L	ENST00000262039	NM_002647.2	370	cAt/cTt	10/25	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.722129478683356	2		329	537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0001495-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	196	282	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.299231747634081	6	FACETS	0.974	0.934	1	1	0.995	1	CLONAL	8	TRUE	2	0.33	6		282	253	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268156	153268156	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001495-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	256	587	0	ENST00000281708.4:c.652C>T	p.Gln218Ter	p.Q218*	ENST00000281708	NM_033632.3	218	Caa/Taa	4/12	0.299231747634081	4	FACETS	0.907	0.862	0.951	1	0.995	1	CLONAL	5	TRUE	1	0.33	4		587	455	SUCCESS
APC	324	MSKCC	GRCh37	5	112175430	112175430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660713	NA	P-0001495-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	70	375	0	ENST00000257430.4:c.4139C>T	p.Thr1380Ile	p.T1380I	ENST00000257430	NM_000038.5	1380	aCc/aTc	16/16	0.299231747634081	4	FACETS	1	0.933	1	0.723	0.638	0.813	CLONAL	2	TRUE	1	0.33	4		375	260	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373919	118373919	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001495-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	103	520	0	ENST00000534358.1:c.7312G>A	p.Glu2438Lys	p.E2438K	ENST00000534358	NM_005933.3	2438	Gaa/Aaa	27/36	0.299231747634081	5	FACETS	1	0.962	1	1	0.962	1	CLONAL	3	TRUE	2	0.33	5		520	279	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9787087	9787087	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001495-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	66	385	0	ENST00000377346.4:c.3120del	p.Asp1041ThrfsTer28	p.D1041Tfs*28	ENST00000377346	NM_005026.3	1040	Aaa/aa	24/24	0.242502969488303	3	FACETS	0.801	0.701	0.906			1	CLONAL	2	TRUE	NA	0.33	3		385	291	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373928	118373928	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001495-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	109	538	0	ENST00000534358.1:c.7323del	p.Glu2442LysfsTer14	p.E2442Kfs*14	ENST00000534358	NM_005933.3	2441	Aaa/aa	27/36	0.299231747634081	5	FACETS	1	0.963	1	1	0.963	1	CLONAL	3	TRUE	2	0.33	5		538	297	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026090	71026090	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0001512-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	292	220	1	ENST00000318789.4:c.1530+2T>G		p.X510_splice	ENST00000318789	NM_032682.5	510			1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.841833461961785	2		221	608	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152093	55152093	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121908585	NA	P-0001512-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	345	317	0	ENST00000257290.5:c.2525A>T	p.Asp842Val	p.D842V	ENST00000257290	NM_006206.4	842	gAc/gTc	18/23	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.841833461961785	2		317	769	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192104	108192104	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs766706861	NA	P-0001541-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	22	35	539	0	ENST00000278616.4:c.6529C>T	p.Gln2177Ter	p.Q2177*	ENST00000278616	NM_000051.3	2177	Cag/Tag	45/63	0.83568416849777	1	FACETS	0.855	0.747	0.958	0.855	0.747	0.958	CLONAL	1	TRUE	0	0.836136441570921	1		539	57	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256238	133256238	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0001541-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	51	15	480	0	ENST00000320574.5:c.424-1G>T		p.X142_splice	ENST00000320574	NM_006231.2	142			0.69587181177422	1	FACETS	0.316	0.237	0.406	0.316	0.237	0.406	SUBCLONAL	1	TRUE	0	0.836136441570921	1		480	66	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743942	41743942	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001541-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	138	33	635	0	ENST00000301178.4:c.877C>A	p.Gln293Lys	p.Q293K	ENST00000301178	NM_021913.4	293	Cag/Aag	7/20	1	2	FACETS	0.462	0.38	0.551	0.462	0.38	0.551	SUBCLONAL	1	TRUE	1	0.836136441570921	2		635	171	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0001551-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1722	335	582	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	1	2	FACETS	0.752	0.708	0.797	1	0.994	1	SUBCLONAL	2	TRUE	1	0.216647890100521	2		582	2057	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0001555-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	931	558	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.711566751510474	3	FACETS		NA	1			1	NA	4	TRUE	NA	0.705339900136453	3		558	1006	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190770	106190770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001555-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	931	551	0	ENST00000380013.4:c.4048G>A	p.Glu1350Lys	p.E1350K	ENST00000380013	NM_001127208.2	1350	Gaa/Aaa	9/11	0.711566751510474	3	FACETS	1	0.998	1	1	0.998	1	CLONAL	3	TRUE	0	0.705339900136453	3		551	1032	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030460	49030461	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0001555-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2264	1357	592	0	ENST00000267163.4:c.1939_1940del	p.Leu647PhefsTer5	p.L647Ffs*5	ENST00000267163	NM_000321.2	645	acCTct/acct	19/27	0.705339900136453	11	FACETS	1	0.996	1	0.739	0.72	0.758	CLONAL	4	TRUE	5	0.705339900136453	11		592	3621	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421039	49421039	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398123721	NA	P-0001598-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	133	355	0	ENST00000301067.7:c.14710C>T	p.Arg4904Ter	p.R4904*	ENST00000301067	NM_003482.3	4904	Cga/Tga	48/54	1	2	FACETS	0.352	0.319	0.387	0.352	0.319	0.387	SUBCLONAL	1	TRUE	1	0.769937537959993	2		355	981	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0001598-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	24	171	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.769937537959993	1	FACETS	0.095	0.074	0.119	0.095	0.074	0.119	SUBCLONAL	1	TRUE	0	0.769937537959993	1		172	404	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806119	1806119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931614	NA	P-0001598-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	709	712	2	ENST00000260795.2:c.1138G>A	p.Gly380Arg	p.G380R	ENST00000260795		380	Ggg/Agg	8/17	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.769937537959993	2		714	1717	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717615	89717615	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909227	NA	P-0001598-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	158	186	0	ENST00000371953.3:c.640C>T	p.Gln214Ter	p.Q214*	ENST00000371953	NM_000314.4	214	Cag/Tag	7/9	0.769937537959993	1	FACETS	0.46	0.424	0.497	0.46	0.424	0.497	SUBCLONAL	1	TRUE	0	0.769937537959993	1		186	549	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807335	1807335	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001598-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	538	319	0	ENST00000260795.2:c.1584G>C	p.Met528Ile	p.M528I	ENST00000260795		528	atG/atC	11/17	1	2	FACETS	0.96	0.922	1	0.96	0.922	1	CLONAL	1	TRUE	1	0.769937537959993	2		319	1455	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022015	5022015	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001598-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	1045	266	0	ENST00000381652.3:c.28G>C	p.Glu10Gln	p.E10Q	ENST00000381652	NM_004972.3	10	Gaa/Caa	3/25	0.700799874419282	3	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.769937537959993	3		266	1816	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0001598-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	174	219	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.769937537959993	1	FACETS	0.491	0.455	0.529	0.491	0.455	0.529	SUBCLONAL	1	TRUE	0	0.769937537959993	1		219	566	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263310	123263310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001598-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	484	241	0	ENST00000358487.5:c.1433G>A	p.Arg478Lys	p.R478K	ENST00000358487	NM_000141.4	478	aGa/aAa	10/18	0.769937537959993	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.769937537959993	1		241	714	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41020973	41020973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001598-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1256	270	309	0	ENST00000267868.3:c.595C>T	p.His199Tyr	p.H199Y	ENST00000267868	NM_002875.4	199	Cac/Tac	7/10	1	2	FACETS	0.46	0.43	0.49	0.46	0.43	0.49	SUBCLONAL	1	TRUE	1	0.769937537959993	2		309	1526	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669542	88669542	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001598-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	245	291	0	ENST00000360948.2:c.1356G>C	p.Met452Ile	p.M452I	ENST00000360948	NM_001012338.2	452	atG/atC	12/19	1	2	FACETS	0.47	0.438	0.503	0.47	0.438	0.503	SUBCLONAL	1	TRUE	1	0.769937537959993	2		291	1354	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0001609-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	124	427	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.130492505519478	4	FACETS	0.973	0.879	1	0.973	0.879	1	CLONAL	2	TRUE	2	0.15538936039299	4		427	948	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0001609-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	129	528	1	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.15538936039299	4	FACETS	1	0.922	1	1	0.922	1	CLONAL	2	TRUE	2	0.15538936039299	4		529	940	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0001609-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	52	128	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.15538936039299	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	0	0.15538936039299	2		128	292	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860403	151860403	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1177151751	NA	P-0001609-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	115	447	0	ENST00000262189.6:c.10259A>G	p.Asp3420Gly	p.D3420G	ENST00000262189	NM_170606.2	3420	gAt/gGt	43/59	0.130492505519478	4	FACETS	0.76	0.683	0.842	0.76	0.683	0.842	SUBCLONAL	2	TRUE	2	0.15538936039299	4		447	1125	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137522036	137522040	+	frameshift_variant	Frame_Shift_Del	DEL	TATGC	TATGC	-	novel	NA	P-0001609-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	249	301	0	ENST00000367739.4:c.839_843del	p.Ser280AsnfsTer20	p.S280Nfs*20	ENST00000367739	NM_000416.2	280	aGCATA/a	6/7	0.15538936039299	11	FACETS	0.955	0.895	1	0.637	0.596	0.679	CLONAL	6	TRUE	2	0.15538936039299	11		301	950	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0001619-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	12	228	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		228	583	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0001628-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	123	586	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.250834142730339	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.31	1		586	513	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263770	16263770	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001628-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	115	506	0	ENST00000375759.3:c.10139C>T	p.Pro3380Leu	p.P3380L	ENST00000375759	NM_015001.2	3380	cCa/cTa	12/15	1	2	FACETS	0.756	0.684	0.83	1	0.985	1	SUBCLONAL	2	TRUE	1	0.31	2		506	491	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740248	162740248	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001628-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	152	586	1	ENST00000367921.3:c.1450C>T	p.Pro484Ser	p.P484S	ENST00000367921	NM_006182.2	484	Cca/Tca	12/18	0.215636502459885	3	FACETS	1	0.986	1	0.708	0.648	0.771	CLONAL	1	TRUE	1	0.31	3		587	800	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104538	193104538	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001628-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	133	532	0	ENST00000367435.3:c.325G>T	p.Asp109Tyr	p.D109Y	ENST00000367435	NM_024529.4	109	Gac/Tac	4/17	0.255870670542245	4	FACETS	0.914	0.833	0.999	0.914	0.833	0.999	CLONAL	2	TRUE	2	0.31	4		532	615	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206667251	206667251	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0001628-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	108	359	0	ENST00000367120.3:c.2046-2A>T		p.X682_splice	ENST00000367120	NM_014002.3	682			0.255870670542245	4	FACETS	0.911	0.821	1	0.911	0.821	1	CLONAL	2	TRUE	2	0.31	4		359	501	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967180	25967180	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001628-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	67	451	0	ENST00000435504.4:c.2026G>T	p.Ala676Ser	p.A676S	ENST00000435504		676	Gct/Tct	13/13	1	2	FACETS	0.866	0.754	0.987	0.866	0.754	0.987	CLONAL	1	TRUE	1	0.31	2		451	499	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705514	47705514	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001628-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	115	654	0	ENST00000233146.2:c.2314A>T	p.Thr772Ser	p.T772S	ENST00000233146	NM_000251.2	772	Aca/Tca	14/16	0.250834142730339	1	FACETS	0.981	0.886	1	0.981	0.886	1	CLONAL	1	TRUE	0	0.31	1		654	639	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971034	55971034	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1258995310	NA	P-0001628-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	197	586	0	ENST00000263923.4:c.1763C>T	p.Pro588Leu	p.P588L	ENST00000263923	NM_002253.2	588	cCa/cTa	13/30	0.270331617259971	2	FACETS	0.94	0.874	1	0.94	0.874	1	CLONAL	2	TRUE	0	0.31	2		586	676	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231721	66231721	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs200980371	NA	P-0001628-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	162	580	1	ENST00000273854.3:c.1979A>G	p.Asn660Ser	p.N660S	ENST00000273854	NM_004439.5	660	aAt/aGt	11/18	0.270331617259971	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.31	2		581	490	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971232	13971232	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001628-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	153	610	0	ENST00000405192.2:c.697G>T	p.Asp233Tyr	p.D233Y	ENST00000405192	NM_001163147.1	233	Gac/Tac	8/12	0.292251194026693	3	FACETS	0.859	0.788	0.932	0.859	0.788	0.932	CLONAL	2	TRUE	1	0.31	3		610	664	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508186	106508186	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001628-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	45	256	0	ENST00000359195.3:c.180C>A	p.His60Gln	p.H60Q	ENST00000359195	NM_002649.2	60	caC/caA	2/11	0.292251194026693	3	FACETS	0.838	0.706	0.984	0.419	0.353	0.492	CLONAL	1	TRUE	1	0.31	3		256	400	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90990460	90990460	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876661071	NA	P-0001628-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	116	516	0	ENST00000265433.3:c.572C>T	p.Pro191Leu	p.P191L	ENST00000265433	NM_002485.4	191	cCa/cTa	5/16	0.238797918628833	4	FACETS	0.772	0.697	0.851	0.772	0.697	0.851	SUBCLONAL	2	TRUE	2	0.31	4		516	635	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533791	533791	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001628-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	61	550	0	ENST00000451590.1:c.265T>A	p.Ser89Thr	p.S89T	ENST00000451590	NM_001130442.1	89	Tct/Act	3/5	1	2	FACETS	0.782	0.676	0.898	0.782	0.676	0.898	SUBCLONAL	1	TRUE	1	0.31	2		550	503	SUCCESS
ATM	472	MSKCC	GRCh37	11	108137926	108137926	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199875915	NA	P-0001628-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	79	567	0	ENST00000278616.4:c.2495G>T	p.Arg832Leu	p.R832L	ENST00000278616	NM_000051.3	832	cGt/cTt	17/63	1	2	FACETS	0.999	0.881	1	0.999	0.881	1	CLONAL	1	TRUE	1	0.31	2		567	510	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435175	18435175	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1410295044	NA	P-0001628-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	212	659	0	ENST00000266497.5:c.160T>A	p.Tyr54Asn	p.Y54N	ENST00000266497		54	Tac/Aac	1/31	0.297316040366511	2	FACETS	0.894	0.833	0.957	0.894	0.833	0.957	CLONAL	2	TRUE	0	0.31	2		659	765	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975470	26975470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1185691679	NA	P-0001628-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	88	476	0	ENST00000381527.3:c.1096G>A	p.Asp366Asn	p.D366N	ENST00000381527	NM_001260.1	366	Gac/Aac	11/13	0.121136627849668	0	FACETS	0.73	0.648	0.816			1	INDETERMINATE	1	TRUE	0	0.31	0		476	537	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786131	3786131	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001628-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	123	690	0	ENST00000262367.5:c.4634G>T	p.Trp1545Leu	p.W1545L	ENST00000262367	NM_004380.2	1545	tGg/tTg	28/31	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.31	2		690	560	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59770806	59770806	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001628-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	114	580	0	ENST00000259008.2:c.2560A>T	p.Ser854Cys	p.S854C	ENST00000259008	NM_032043.2	854	Agt/Tgt	18/20	1	2	FACETS	0.832	0.754	0.913	1	0.987	1	CLONAL	2	TRUE	1	0.31	2		580	442	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78858901	78858901	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001628-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	184	509	0	ENST00000306801.3:c.1936A>T	p.Met646Leu	p.M646L	ENST00000306801	NM_020761.2	646	Atg/Ttg	17/34	NA	2	FACETS	1	0.932	1			1	INDETERMINATE	2	TRUE	NA	0.31	2		509	591	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2208944	2208944	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001628-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	131	570	0	ENST00000398665.3:c.974A>G	p.Tyr325Cys	p.Y325C	ENST00000398665	NM_032482.2	325	tAt/tGt	12/28	0.297316040366511	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.31	1		570	521	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795222	42795222	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1449714309	NA	P-0001628-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	141	541	0	ENST00000575354.2:c.2302C>G	p.Pro768Ala	p.P768A	ENST00000575354	NM_015125.3	768	Ccg/Gcg	10/20	0.297316040366511	3	FACETS	0.861	0.787	0.938			1	CLONAL	2	TRUE	NA	0.31	3		541	610	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057263	30057263	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0001628-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	175	527	0	ENST00000338641.4:c.745A>T	p.Arg249Ter	p.R249*	ENST00000338641	NM_000268.3	249	Aga/Tga	8/16	0.250141046489182	3	FACETS	1	0.98	1	0.772	0.715	0.83	CLONAL	2	TRUE	0	0.31	3		527	563	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923703	39923703	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001628-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	115	675	0	ENST00000378444.4:c.3388C>A	p.Leu1130Ile	p.L1130I	ENST00000378444	NM_001123385.1	1130	Ctc/Atc	7/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.31	2		675	624	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345273	70345273	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001628-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	98	517	0	ENST00000374080.3:c.2299G>C	p.Ala767Pro	p.A767P	ENST00000374080		767	Gcc/Ccc	16/45	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.31	2		517	499	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918936	76918936	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001628-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	118	913	2	ENST00000373344.5:c.4055C>A	p.Ser1352Tyr	p.S1352Y	ENST00000373344	NM_000489.3	1352	tCt/tAt	12/35	0.207989689355636	0	FACETS	0.718	0.648	0.791			1	SUBCLONAL	1	TRUE	0	0.31	0		915	732	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478649	99478651	+	inframe_deletion	In_Frame_Del	DEL	AAT	AAT	-	novel	NA	P-0001628-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	83	452	0	ENST00000268035.6:c.3291_3293del	p.Met1098del	p.M1098del	ENST00000268035	NM_000875.3	1097	gaAATg/gag	17/21	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.31	2		452	481	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602408	10602408	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001628-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	124	551	0	ENST00000171111.5:c.1170del	p.Ser391AlafsTer9	p.S391Afs*9	ENST00000171111	NM_203500.1	390	tcC/tc	3/6	0.297316040366511	1	FACETS	0.813	0.741	0.886	1	0.988	1	CLONAL	2	TRUE	0	0.31	1		551	416	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141524	11141524	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001628-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	124	514	0	ENST00000358026.2:c.3502del	p.Ala1168GlnfsTer4	p.A1168Qfs*4	ENST00000358026	NM_001128849.1	1167	tcG/tc	25/36	0.297316040366511	1	FACETS	0.793	0.724	0.866	1	0.987	1	SUBCLONAL	2	TRUE	0	0.31	1		514	426	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0001661-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	104	364	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.966	0.874	1	0.966	0.874	1	CLONAL	1	FALSE	1	0.631730707141684	2		364	341	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493665	56493665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1195904336	NA	P-0001675-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	39	528	0	ENST00000267101.3:c.2981G>A	p.Gly994Asp	p.G994D	ENST00000267101	NM_001982.3	994	gGt/gAt	25/28	0.3	7	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	7		528	737	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122502	17122502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001675-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	24	650	0	ENST00000285071.4:c.893G>A	p.Ser298Asn	p.S298N	ENST00000285071	NM_144997.5	298	aGc/aAc	9/14	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		650	391	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575089	48575089	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001675-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	25	519	1	ENST00000342988.3:c.283T>C	p.Tyr95His	p.Y95H	ENST00000342988	NM_005359.5	95	Tat/Cat	3/12	0.161461686018387	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		520	411	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938029	76938029	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001717-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	210	358	0	ENST00000373344.5:c.2719C>T	p.Arg907Ter	p.R907*	ENST00000373344	NM_000489.3	907	Cga/Tga	9/35	0.582085409539733	2	FACETS	0.807	0.76	0.854			1	CLONAL	2	FALSE	NA	0.606701270237414	2		358	429	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0001722-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	143	337	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	1	FACETS	1	0.98	1	1	0.994	1	CLONAL	3	TRUE	0	0.3	1		337	241	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0001722-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	193	606	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	0.194302860392473	3	FACETS	1	0.981	1			1	CLONAL	2	TRUE	NA	0.3	3		606	640	SUCCESS
APC	324	MSKCC	GRCh37	5	112154943	112154943	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001722-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	202	608	0	ENST00000257430.4:c.1214G>T	p.Arg405Leu	p.R405L	ENST00000257430	NM_000038.5	405	cGa/cTa	10/16	1	2	FACETS	0.986	0.918	1	1	0.994	1	CLONAL	2	TRUE	1	0.3	2		608	683	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188866	32188866	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001722-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	117	525	0	ENST00000375023.3:c.688C>A	p.Arg230Ser	p.R230S	ENST00000375023	NM_004557.3	230	Cgt/Agt	4/30	0.149356591746684	4	FACETS	0.894	0.814	0.977	1	0.982	1	INDETERMINATE	3	TRUE	2	0.3	4		525	378	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750529	128750529	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001722-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	197	665	0	ENST00000377970.2:c.66C>A	p.Phe22Leu	p.F22L	ENST00000377970	NM_002467.4	22	ttC/ttA	2/3	0.229885402795788	3	FACETS	0.999	0.927	1	0.999	0.927	1	CLONAL	2	TRUE	1	0.3	3		665	756	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486070	29486070	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs746824139	NA	P-0001722-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	154	546	0	ENST00000356175.3:c.247C>T	p.Gln83Ter	p.Q83*	ENST00000356175	NM_000267.3	83	Cag/Tag	3/57	1	2	FACETS	0.85	0.781	0.921	1	0.99	1	CLONAL	2	TRUE	1	0.3	2		546	604	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466537	120466538	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0001722-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	185	635	0	ENST00000256646.2:c.4581_4582del	p.Cys1527TrpfsTer10	p.C1527Wfs*10	ENST00000256646	NM_024408.3	1527	tgTGgt/tggt	26/34	0.229885402795788	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.3	3		635	680	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445397	29445397	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001775-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	64	535	0	ENST00000389048.3:c.3436C>A	p.Gln1146Lys	p.Q1146K	ENST00000389048	NM_004304.4	1146	Caa/Aaa	21/29	0.134635715698928	3	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.294828599019654	3		535	372	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921559	39921559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746716983	NA	P-0001775-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	85	584	0	ENST00000378444.4:c.4261C>T	p.Arg1421Cys	p.R1421C	ENST00000378444	NM_001123385.1	1421	Cgc/Tgc	10/15	0.134635715698928	3	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.294828599019654	3		584	450	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602952	55602952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1237984655	NA	P-0001806-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	88	246	0	ENST00000288135.5:c.2662C>T	p.Arg888Trp	p.R888W	ENST00000288135	NM_000222.2	888	Cgg/Tgg	19/21	NA	2	FACETS	0.8	0.719	0.884			1	INDETERMINATE	1	TRUE	NA	0.817869668627245	2		246	269	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981142	55981142	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001806-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	87	381	0	ENST00000263923.4:c.557C>A	p.Thr186Asn	p.T186N	ENST00000263923	NM_002253.2	186	aCt/aAt	5/30	NA	2	FACETS	0.698	0.624	0.774			1	INDETERMINATE	1	TRUE	NA	0.817869668627245	2		381	305	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs786203436	NA	P-0001806-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	130	268	0	ENST00000269305.4:c.487T>A	p.Tyr163Asn	p.Y163N	ENST00000269305	NM_001126112.2	163	Tac/Aac	5/11	0.755014088448648	1	FACETS	0.843	0.785	0.899	0.843	0.785	0.899	CLONAL	1	TRUE	0	0.817869668627245	1		268	223	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778503	3778505	+	frameshift_variant	Frame_Shift_Del	DEL	ATG	ATG	TT	novel	NA	P-0001806-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	108	462	0	ENST00000262367.5:c.6543_6545delinsAA	p.Asn2181LysfsTer5	p.N2181Kfs*5	ENST00000262367	NM_004380.2	2181	aaCATg/aaAAg	31/31	0.817869668627245	1	FACETS	0.667	0.611	0.723	0.667	0.611	0.723	SUBCLONAL	1	TRUE	0	0.817869668627245	1		462	234	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573196	64573196	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001827-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	236	570	0	ENST00000312049.6:c.1096del	p.Glu366LysfsTer2	p.E366Kfs*2	ENST00000312049	NM_130799.2	366	Gaa/aa	8/10	0.603071538375452	1	FACETS	0.846	0.797	0.897	0.846	0.797	0.897	CLONAL	1	TRUE	0	0.65693573506712	1		570	570	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044978	47044978	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001840-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	357	367	0	ENST00000377604.3:c.2307del	p.Ser770AlafsTer32	p.S770Afs*32	ENST00000377604	NM_001204468.1	768	ttC/tt	20/24	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	1	TRUE	NA	0.433622611799499	2		367	1098	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0001874-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	352	294	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	0.594392454657828	2		294	1164	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106058	8106058	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001874-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	219	435	0	ENST00000346208.3:c.878T>A	p.Met293Lys	p.M293K	ENST00000346208		293	aTg/aAg	4/6	1	2	FACETS	0.869	0.81	0.93	0.869	0.81	0.93	CLONAL	1	TRUE	1	0.594392454657828	2		435	848	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38064108	38064108	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001874-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	364	406	0	ENST00000250448.2:c.70G>A	p.Glu24Lys	p.E24K	ENST00000250448	NM_004496.3	24	Gag/Aag	1/2	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.594392454657828	2		406	1129	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063346	67063346	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001874-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	251	380	0	ENST00000412916.2:c.36C>G	p.Phe12Leu	p.F12L	ENST00000412916		12	ttC/ttG	1/6	0.594392454657828	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.594392454657828	1		380	571	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0001874-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	478	604	2	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.594392454657828	2		606	1376	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170966	56170966	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001874-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	287	440	0	ENST00000399503.3:c.1796del	p.Asn599MetfsTer57	p.N599Mfs*57	ENST00000399503	NM_005921.1	598	gcA/gc	10/20	0.277914264658908	3	FACETS	1	0.991	1	0.633	0.596	0.671	INDETERMINATE	1	TRUE	1	0.594392454657828	3		440	989	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177781	56177781	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001874-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	330	454	0	ENST00000399503.3:c.2757del	p.Lys919AsnfsTer2	p.K919Nfs*2	ENST00000399503	NM_005921.1	918	acA/ac	14/20	0.277914264658908	3	FACETS	1	0.992	1	0.631	0.596	0.666	INDETERMINATE	1	TRUE	1	0.594392454657828	3		454	1142	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156713	20156713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001893-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	143	437	0	ENST00000379607.5:c.44G>A	p.Gly15Asp	p.G15D	ENST00000379607	NM_001412.3	15	gGt/gAt	2/7	0.169342196816816	0	FACETS	0.981	0.912	1			1	CLONAL	5	FALSE	0	0.169342196816816	0		437	286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0001899-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	837	433	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.295525614466682	1	FACETS	0.696	0.677	0.716	0.696	0.677	0.716	INDETERMINATE	1	TRUE	0	0.883300197646804	1		434	1520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577564	7577564	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057522275	NA	P-0001899-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	348	258	0	ENST00000269305.4:c.717C>G	p.Asn239Lys	p.N239K	ENST00000269305	NM_001126112.2	239	aaC/aaG	7/11	0.295525614466682	1	FACETS	0.404	0.382	0.425	0.404	0.382	0.425	INDETERMINATE	1	TRUE	0	0.883300197646804	1		258	1090	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0001902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	272	65	124	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.16692314154222	2	FACETS	1	0.877	1	0.502	0.438	0.571	INDETERMINATE	1	TRUE	0	0.383962797344219	2		124	337	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0001902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	593	51	329	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.413	0.35	0.481	0.413	0.35	0.481	SUBCLONAL	1	TRUE	1	0.383962797344219	2		329	644	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923215	26923215	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs769996123	NA	P-0001902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	596	53	479	0	ENST00000381527.3:c.211C>T	p.Arg71Ter	p.R71*	ENST00000381527	NM_001260.1	71	Cga/Tga	3/13	NA	2	FACETS	0.425	0.362	0.495			1	INDETERMINATE	1	TRUE	NA	0.383962797344219	2		479	649	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16247461	16247461	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763959899	NA	P-0001902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	541	52	507	0	ENST00000375759.3:c.1732G>A	p.Gly578Ser	p.G578S	ENST00000375759	NM_015001.2	578	Ggt/Agt	9/15	1	2	FACETS	0.457	0.388	0.532	0.457	0.388	0.532	SUBCLONAL	1	TRUE	1	0.383962797344219	2		507	593	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105592	27105592	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	475	100	580	0	ENST00000324856.7:c.5203G>T	p.Glu1735Ter	p.E1735*	ENST00000324856	NM_006015.4	1735	Gag/Tag	20/20	1	2	FACETS	0.906	0.811	1	0.906	0.811	1	CLONAL	1	TRUE	1	0.383962797344219	2		580	575	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726580	46726580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	485	48	511	0	ENST00000371975.4:c.659C>T	p.Ser220Phe	p.S220F	ENST00000371975	NM_003579.3	220	tCc/tTc	7/18	1	2	FACETS	0.469	0.396	0.549	0.469	0.396	0.549	SUBCLONAL	1	TRUE	1	0.383962797344219	2		511	533	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445265	29445265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1005846150	NA	P-0001902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	420	26	378	1	ENST00000389048.3:c.3460G>A	p.Glu1154Lys	p.E1154K	ENST00000389048	NM_004304.4	1154	Gaa/Aaa	22/29	1	2	FACETS	0.304	0.24	0.377	0.304	0.24	0.377	SUBCLONAL	1	TRUE	1	0.383962797344219	2		379	446	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936093	178936093	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913275	NA	P-0001902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	315	72	255	0	ENST00000263967.3:c.1635G>T	p.Glu545Asp	p.E545D	ENST00000263967	NM_006218.2	545	gaG/gaT	10/21	0.16692314154222	2	FACETS	0.969	0.851	1	0.485	0.425	0.548	INDETERMINATE	1	TRUE	0	0.383962797344219	2		255	387	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430422	181430422	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	470	34	515	0	ENST00000325404.1:c.274G>T	p.Asp92Tyr	p.D92Y	ENST00000325404	NM_003106.3	92	Gac/Tac	1/1	0.16692314154222	2	FACETS	0.351	0.286	0.425	0.176	0.143	0.213	INDETERMINATE	1	TRUE	0	0.383962797344219	2		515	504	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1795709	1795709	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	149	13	135	0	ENST00000260795.2:c.48C>G	p.Ile16Met	p.I16M	ENST00000260795		16	atC/atG	1/17	NA	2	FACETS	0.418	0.299	0.562			1	INDETERMINATE	1	TRUE	NA	0.383962797344219	2		135	162	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750466	57750466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	506	80	536	0	ENST00000274289.3:c.2002G>A	p.Glu668Lys	p.E668K	ENST00000274289	NM_006622.3	668	Gaa/Aaa	14/14	1	2	FACETS	0.711	0.627	0.802	0.711	0.627	0.802	SUBCLONAL	1	TRUE	1	0.383962797344219	2		536	586	SUCCESS
APC	324	MSKCC	GRCh37	5	112175677	112175677	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	489	45	419	0	ENST00000257430.4:c.4386G>C	p.Lys1462Asn	p.K1462N	ENST00000257430	NM_000038.5	1462	aaG/aaC	16/16	1	2	FACETS	0.439	0.368	0.517	0.439	0.368	0.517	SUBCLONAL	1	TRUE	1	0.383962797344219	2		419	534	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675372	30675372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	447	45	463	0	ENST00000376406.3:c.2984C>T	p.Ser995Phe	p.S995F	ENST00000376406	NM_014641.2	995	tCc/tTc	8/15	1	2	FACETS	0.476	0.4	0.561	0.476	0.4	0.561	SUBCLONAL	1	TRUE	1	0.383962797344219	2		463	492	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169159	32169159	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	377	74	431	0	ENST00000375023.3:c.3874G>C	p.Glu1292Gln	p.E1292Q	ENST00000375023	NM_004557.3	1292	Gag/Cag	22/30	1	2	FACETS	0.855	0.751	0.966	0.855	0.751	0.966	CLONAL	1	TRUE	1	0.383962797344219	2		431	451	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190561	32190561	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	338	39	305	0	ENST00000375023.3:c.178G>C	p.Glu60Gln	p.E60Q	ENST00000375023	NM_004557.3	60	Gag/Cag	3/30	1	2	FACETS	0.539	0.447	0.641	0.539	0.447	0.641	SUBCLONAL	1	TRUE	1	0.383962797344219	2		305	377	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151833948	151833948	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	506	47	418	0	ENST00000262189.6:c.14705G>C	p.Gly4902Ala	p.G4902A	ENST00000262189	NM_170606.2	4902	gGa/gCa	59/59	1	2	FACETS	0.443	0.373	0.52	0.443	0.373	0.52	SUBCLONAL	1	TRUE	1	0.383962797344219	2		418	553	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852416	63852416	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749976442	NA	P-0001902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	446	41	442	0	ENST00000279873.7:c.3194G>A	p.Gly1065Glu	p.G1065E	ENST00000279873	NM_032199.2	1065	gGa/gAa	10/10	1	2	FACETS	0.439	0.365	0.52	0.439	0.365	0.52	SUBCLONAL	1	TRUE	1	0.383962797344219	2		442	487	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571969	64571969	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	438	103	579	0	ENST00000312049.6:c.1670A>T	p.Lys557Met	p.K557M	ENST00000312049	NM_130799.2	557	aAg/aTg	10/10	0.16692314154222	2	FACETS	0.992	0.89	1	0.496	0.445	0.549	INDETERMINATE	1	TRUE	0	0.383962797344219	2		579	541	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061240	38061240	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	350	96	447	1	ENST00000250448.2:c.749C>A	p.Ser250Tyr	p.S250Y	ENST00000250448	NM_004496.3	250	tCc/tAc	2/2	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.383962797344219	2		448	446	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817908	3817908	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	463	58	498	0	ENST00000262367.5:c.3063G>A	p.Met1021Ile	p.M1021I	ENST00000262367	NM_004380.2	1021	atG/atA	16/31	1	2	FACETS	0.58	0.498	0.668	0.58	0.498	0.668	SUBCLONAL	1	TRUE	1	0.383962797344219	2		498	521	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935794	15935794	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0001902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	418	33	337	0	ENST00000268712.3:c.7139C>G	p.Ser2380Ter	p.S2380*	ENST00000268712	NM_006311.3	2380	tCa/tGa	46/46	1	2	FACETS	0.381	0.31	0.461	0.381	0.31	0.461	SUBCLONAL	1	TRUE	1	0.383962797344219	2		337	451	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004826	16004826	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	570	50	528	0	ENST00000268712.3:c.2428G>C	p.Val810Leu	p.V810L	ENST00000268712	NM_006311.3	810	Gtt/Ctt	20/46	1	2	FACETS	0.42	0.356	0.491	0.42	0.356	0.491	SUBCLONAL	1	TRUE	1	0.383962797344219	2		528	620	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117491	4117491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	215	24	256	0	ENST00000262948.5:c.229G>A	p.Glu77Lys	p.E77K	ENST00000262948	NM_030662.3	77	Gag/Aag	2/11	1	2	FACETS	0.523	0.411	0.651	0.523	0.411	0.651	SUBCLONAL	1	TRUE	1	0.383962797344219	2		256	239	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291496	15291496	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs774701967	NA	P-0001902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	404	27	346	0	ENST00000263388.2:c.3138G>T	p.Gln1046His	p.Q1046H	ENST00000263388	NM_000435.2	1046	caG/caT	19/33	1	2	FACETS	0.326	0.259	0.403	0.326	0.259	0.403	SUBCLONAL	1	TRUE	1	0.383962797344219	2		346	431	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31369162	31369162	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1437320413	NA	P-0001902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	532	43	505	0	ENST00000328111.2:c.146G>A	p.Arg49Gln	p.R49Q	ENST00000328111	NM_006892.3	49	cGa/cAa	3/23	1	2	FACETS	0.39	0.325	0.461	0.39	0.325	0.461	SUBCLONAL	1	TRUE	1	0.383962797344219	2		505	575	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849497	68849497	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	393	121	537	0	ENST00000261769.5:c.1401del	p.Thr468ProfsTer13	p.T468Pfs*13	ENST00000261769	NM_004360.3	467	aCc/ac	10/16	0.383962797344219	1	FACETS	0.991	0.9	1	0.991	0.9	1	CLONAL	1	TRUE	0	0.383962797344219	1		537	514	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61713073	61713075	+	frameshift_variant	Frame_Shift_Del	DEL	GAG	GAG	AA	novel	NA	P-0001902-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	488	30	452	0	ENST00000401558.2:c.2336_2338delinsTT	p.Pro779LeufsTer28	p.P779Lfs*28	ENST00000401558	NM_003400.3	779	cCTCtg/cTTtg	20/25	1	2	FACETS	0.302	0.242	0.369	0.302	0.242	0.369	SUBCLONAL	1	TRUE	1	0.383962797344219	2		452	518	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512309	38512309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	281	124	336	0	ENST00000254066.5:c.1220C>T	p.Pro407Leu	p.P407L	ENST00000254066	NM_000964.3	407	cCg/cTg	9/9	0.335393498787884	6	FACETS	1	0.927	1			1	CLONAL	3	TRUE	NA	0.335393498787884	6		336	405	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296093	15296093	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	207	70	448	0	ENST00000263388.2:c.2271C>G	p.His757Gln	p.H757Q	ENST00000263388	NM_000435.2	757	caC/caG	14/33	1	2	FACETS	0.753	0.664	0.848	1	0.976	1	SUBCLONAL	2	TRUE	1	0.335393498787884	2		448	277	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0001921-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	114	375	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.155244063889762	1	FACETS	0.883	0.797	0.972	1	0.987	1	CLONAL	2	TRUE	0	0.208139830524968	1		376	556	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0001921-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	279	497	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.208139830524968	7	FACETS	0.914	0.861	0.968	0.914	0.861	0.968	CLONAL	5	TRUE	2	0.208139830524968	7		497	892	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0001921-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	363	506	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.208139830524968	7	FACETS	0.986	0.945	1	1	0.996	1	CLONAL	8	TRUE	2	0.208139830524968	7		507	672	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361135	66361135	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001921-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	153	521	0	ENST00000273854.3:c.1037A>G	p.Glu346Gly	p.E346G	ENST00000273854	NM_004439.5	346	gAg/gGg	4/18	0.176049373515145	5	FACETS	1	0.947	1	0.699	0.639	0.762	CLONAL	2	TRUE	2	0.208139830524968	5		521	920	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814319	76814319	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0001921-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	185	190	0	ENST00000373344.5:c.6327-2A>G		p.X2109_splice	ENST00000373344	NM_000489.3	2109			1	1	FACETS	1	0.978	1	1	0.995	1	CLONAL	5	TRUE	0	0.208139830524968	1		190	298	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001927-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	52	500	0	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.15	2		500	582	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439694	51439694	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001927-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	50	177	0	ENST00000262662.1:c.259C>T	p.Gln87Ter	p.Q87*	ENST00000262662		87	Cag/Tag	4/4	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.15	2		177	485	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699325	117699325	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001927-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	35	215	0	ENST00000369458.3:c.316G>T	p.Asp106Tyr	p.D106Y	ENST00000369458	NM_024626.3	106	Gat/Tat	3/6	1	2	FACETS	0.701	0.573	0.845	0.701	0.573	0.845	SUBCLONAL	1	TRUE	1	0.15	2		215	666	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607552	43607552	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001927-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	16	108	0	ENST00000355710.3:c.1528G>T	p.Ala510Ser	p.A510S	ENST00000355710	NM_020975.4	510	Gcc/Tcc	8/20	1	2	FACETS	0.702	0.518	0.922	0.702	0.518	0.922	CLONAL	1	TRUE	1	0.15	2		108	304	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203753	94203753	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863225441	NA	P-0001927-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	27	209	0	ENST00000323929.3:c.901C>T	p.Leu301Phe	p.L301F	ENST00000323929	NM_005591.3	301	Ctt/Ttt	9/20	1	2	FACETS	0.69	0.547	0.853	0.69	0.547	0.853	SUBCLONAL	1	TRUE	1	0.15	2		209	522	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602290	10602290	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001927-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	21	166	0	ENST00000171111.5:c.1288G>T	p.Gly430Cys	p.G430C	ENST00000171111	NM_203500.1	430	Ggc/Tgc	3/6	1	2	FACETS	0.678	0.521	0.862	0.678	0.521	0.862	SUBCLONAL	1	TRUE	1	0.15	2		166	413	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923724	39923724	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001927-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	33	91	0	ENST00000378444.4:c.3367G>T	p.Asp1123Tyr	p.D1123Y	ENST00000378444	NM_001123385.1	1123	Gac/Tac	7/15	1	1	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	0	0.15	1		91	337	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040650	47040650	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001927-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	31	86	0	ENST00000377604.3:c.1285G>T	p.Glu429Ter	p.E429*	ENST00000377604	NM_001204468.1	429	Gag/Tag	13/24	1	1	FACETS	0.842	0.685	1	1	0.952	1	CLONAL	2	TRUE	0	0.15	1		86	227	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099124	27099124	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0001943-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	29	398	0	ENST00000324856.7:c.3539+1G>T		p.X1180_splice	ENST00000324856	NM_006015.4	1180			0.192331878443653	4	FACETS	0.848	0.683	1	0.424	0.341	0.517	INDETERMINATE	1	TRUE	2	0.348079914300137	4		398	265	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47108569	47108569	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001943-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	46	305	0	ENST00000409792.3:c.6100G>T	p.Glu2034Ter	p.E2034*	ENST00000409792	NM_014159.6	2034	Gaa/Taa	13/21	NA	2	FACETS	0.934	0.792	1			1	INDETERMINATE	1	TRUE	NA	0.348079914300137	2		305	283	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542782	187542782	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001943-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	42	456	0	ENST00000441802.2:c.4958T>G	p.Val1653Gly	p.V1653G	ENST00000441802	NM_005245.3	1653	gTg/gGg	10/27	0.197643053176205	3	FACETS	1	0.887	1	0.535	0.449	0.628	INDETERMINATE	1	TRUE	1	0.348079914300137	3		456	265	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693009	89693009	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0001955-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	99	184	0	ENST00000371953.3:c.492+1G>C		p.X164_splice	ENST00000371953	NM_000314.4	164			0.610770767994224	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.610770767994224	2		184	152	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729180	66729180	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs397516793	NA	P-0001955-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	137	424	0	ENST00000307102.5:c.388T>C	p.Tyr130His	p.Y130H	ENST00000307102	NM_002755.3	130	Tat/Cat	3/11	0.610770767994224	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.610770767994224	3		424	280	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416963	416963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001974-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	264	425	0	ENST00000399788.2:c.3587C>T	p.Ser1196Phe	p.S1196F	ENST00000399788	NM_001042603.1	1196	tCc/tTc	23/28	0.808989924582088	1	FACETS	0.996	0.956	1	0.996	0.956	1	CLONAL	1	TRUE	0	0.834905722538925	1		425	370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0001989-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	610	341	0	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.756367470761317	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.756367470761317	3		341	689	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566825	212566825	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001989-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	129	316	0	ENST00000342788.4:c.1356A>C	p.Glu452Asp	p.E452D	ENST00000342788	NM_005235.2	452	gaA/gaC	12/28	0.744402116590831	3	FACETS	0.94	0.857	1	0.313	0.285	0.342	CLONAL	1	TRUE	0	0.756367470761317	3		316	500	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383765	15383765	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001989-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1201	326	348	0	ENST00000263377.2:c.146A>G	p.Glu49Gly	p.E49G	ENST00000263377	NM_058243.2	49	gAg/gGg	2/20	0.756367470761317	8	FACETS	0.923	0.87	0.977			1	CLONAL	2	TRUE	NA	0.756367470761317	8		348	1527	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524799	187524802	+	frameshift_variant	Frame_Shift_Del	DEL	GATG	GATG	-	novel	NA	P-0001989-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	286	318	0	ENST00000441802.2:c.10878_10881del	p.Asp3626GlufsTer13	p.D3626Efs*13	ENST00000441802	NM_005245.3	3626	gaCATC/ga	19/27	0.756367470761317	5	FACETS	1	0.964	1	0.685	0.646	0.723	CLONAL	2	TRUE	2	0.756367470761317	5		318	786	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577392	64577392	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001993-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	188	545	1	ENST00000312049.6:c.190C>T	p.Gln64Ter	p.Q64*	ENST00000312049	NM_130799.2	64	Cag/Tag	2/10	0.619389056371567	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.619389056371567	1		546	413	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2105402	2105402	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs137854306	NA	P-0001993-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	66	354	0	ENST00000219476.3:c.482-1G>A		p.X161_splice	ENST00000219476	NM_000548.3	161			0.619389056371567	1	FACETS	0.581	0.511	0.656	0.581	0.511	0.656	SUBCLONAL	1	TRUE	0	0.619389056371567	1		354	253	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288980	33288980	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001993-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	230	313	0	ENST00000374542.5:c.572del	p.Leu191TrpfsTer38	p.L191Wfs*38	ENST00000374542	NM_001141970.1	191	tTg/tg	3/8	0.619389056371567	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.619389056371567	1		313	438	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0002001-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	102	301	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.586602460959119	3	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	1	0.586602460959119	3		301	218	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0002001-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	23	188	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.575823657018641	5	FACETS	1	0.889	1	0.302	0.239	0.373	CLONAL	1	TRUE	1	0.586602460959119	5		188	122	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058678	47058678	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002001-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	91	567	0	ENST00000409792.3:c.7600G>C	p.Glu2534Gln	p.E2534Q	ENST00000409792	NM_014159.6	2534	Gag/Cag	21/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.586602460959119	2		567	242	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519446	137519446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002001-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	45	355	0	ENST00000367739.4:c.1192C>T	p.His398Tyr	p.H398Y	ENST00000367739	NM_000416.2	398	Cac/Tac	7/7	0.544507438822709	3	FACETS	0.898	0.762	1	0.299	0.254	0.348	CLONAL	1	TRUE	0	0.586602460959119	3		355	221	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426875	70426875	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002001-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	39	417	0	ENST00000373644.4:c.4535C>G	p.Thr1512Ser	p.T1512S	ENST00000373644	NM_030625.2	1512	aCt/aGt	7/12	0.538503104272509	1	FACETS	0.407	0.34	0.48	0.407	0.34	0.48	SUBCLONAL	1	TRUE	0	0.586602460959119	1		417	231	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257249	133257249	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500889	NA	P-0002001-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	81	554	0	ENST00000320574.5:c.229C>T	p.Arg77Cys	p.R77C	ENST00000320574	NM_006231.2	77	Cgc/Tgc	3/49	0.586602460959119	3	FACETS	1	0.916	1	0.519	0.461	0.581	CLONAL	1	TRUE	1	0.586602460959119	3		554	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519988	NA	P-0002001-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	218	504	0	ENST00000269305.4:c.808T>G	p.Phe270Val	p.F270V	ENST00000269305	NM_001126112.2	270	Ttt/Gtt	8/11	0.586602460959119	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.586602460959119	2		504	337	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40743877	40743877	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002001-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	53	398	1	ENST00000392038.2:c.830A>G	p.Lys277Arg	p.K277R	ENST00000392038	NM_001626.4	277	aAg/aGg	9/14	0.503899351794374	4	FACETS	0.542	0.462	0.629	0.181	0.154	0.21	SUBCLONAL	1	TRUE	1	0.586602460959119	4		399	529	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544654	65544654	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002001-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	200	527	0	ENST00000358664.4:c.272del	p.Gln91ArgfsTer79	p.Q91Rfs*79	ENST00000358664	NM_002382.4	91	cAg/cg	4/5	0.586602460959119	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.586602460959119	2		527	311	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223973	2223973	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	179	522	0	ENST00000326181.6:c.1187A>G	p.Gln396Arg	p.Q396R	ENST00000326181	NM_032271.2	396	cAg/cGg	13/21	0.105093694791867	5	FACETS	1	0.983	1	0.817	0.754	0.883	INDETERMINATE	2	TRUE	2	0.224272116042243	5		522	870	SUCCESS
AR	367	MSKCC	GRCh37	X	66942785	66942785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886041132	NA	P-0002096-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	130	756	0	ENST00000374690.3:c.2566C>T	p.Arg856Cys	p.R856C	ENST00000374690	NM_000044.3	856	Cgc/Tgc	7/8	0.544964733776886	1	FACETS	0.482	0.44	0.524	0.482	0.44	0.524	SUBCLONAL	1	TRUE	0	0.776767155194084	1		756	425	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0002119-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	22	260	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.363426776313127	2	FACETS	0.92	0.741	1	0.92	0.741	1	CLONAL	2	TRUE	0	0.385703138966635	2		260	62	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520006	NA	P-0002119-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	85	421	1	ENST00000269305.4:c.821T>C	p.Val274Ala	p.V274A	ENST00000269305	NM_001126112.2	274	gTt/gCt	8/11	0.363426776313127	2	FACETS	0.938	0.843	1	0.938	0.843	1	CLONAL	2	TRUE	0	0.385703138966635	2		422	235	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685316	89685316	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs878853937	NA	P-0002119-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	48	213	0	ENST00000371953.3:c.209+2T>C		p.X70_splice	ENST00000371953	NM_000314.4	70			0.166715757679302	5	FACETS	0.834	0.719	0.956	0.834	0.719	0.956	INDETERMINATE	3	TRUE	2	0.385703138966635	5		213	157	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	398	294	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.116329264248517	4	FACETS	0.869	0.829	0.91	0.869	0.829	0.91	INDETERMINATE	2	TRUE	2	0.861939199528427	4		294	989	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	580	372	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.861939199528427	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.861939199528427	1		372	698	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	412	316	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	1	2	FACETS	0.966	0.923	1	0.966	0.923	1	CLONAL	1	TRUE	1	0.861939199528427	2		316	990	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023692	27023692	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	340	173	0	ENST00000324856.7:c.798C>A	p.Phe266Leu	p.F266L	ENST00000324856	NM_006015.4	266	ttC/ttA	1/20	0.860771067138674	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.861939199528427	1		173	424	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546348	46546348	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1415075907	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	665	411	0	ENST00000262741.5:c.181C>T	p.Gln61Ter	p.Q61*	ENST00000262741	NM_003629.3	61	Cag/Tag	2/10	0.860771067138674	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.861939199528427	1		411	845	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301842	65301842	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	413	257	0	ENST00000342505.4:c.3197C>G	p.Ser1066Cys	p.S1066C	ENST00000342505	NM_002227.2	1066	tCt/tGt	23/25	0.860771067138674	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.861939199528427	1		257	544	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301898	65301898	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	269	168	0	ENST00000342505.4:c.3141G>A	p.Trp1047Ter	p.W1047*	ENST00000342505	NM_002227.2	1047	tgG/tgA	23/25	0.860771067138674	1	FACETS	0.981	0.944	1	0.981	0.944	1	CLONAL	1	TRUE	0	0.861939199528427	1		168	362	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303735	65303735	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	462	321	0	ENST00000342505.4:c.3020G>C	p.Arg1007Thr	p.R1007T	ENST00000342505	NM_002227.2	1007	aGa/aCa	22/25	0.860771067138674	1	FACETS	0.947	0.919	0.975	0.947	0.919	0.975	CLONAL	1	TRUE	0	0.861939199528427	1		321	644	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880514	155880514	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1607	501	347	0	ENST00000368323.3:c.39C>G	p.Ser13Arg	p.S13R	ENST00000368323	NM_006912.5	13	agC/agG	2/6	0.762917974115222	5	FACETS	1	0.994	1			1	CLONAL	1	TRUE	NA	0.861939199528427	5		347	2108	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161326547	161326547	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	88	64	0	ENST00000367975.2:c.322C>G	p.Leu108Val	p.L108V	ENST00000367975	NM_003001.3	108	Ctg/Gtg	5/6	0.861939199528427	3	FACETS	0.849	0.759	0.944			1	CLONAL	1	TRUE	NA	0.861939199528427	3		64	344	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015190	128015190	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	377	367	0	ENST00000285398.2:c.2331C>G	p.Phe777Leu	p.F777L	ENST00000285398	NM_000122.1	777	ttC/ttG	15/15	1	2	FACETS	0.915	0.872	0.959	0.915	0.872	0.959	CLONAL	1	TRUE	1	0.861939199528427	2		367	956	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015230	128015230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs189511674	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	400	365	0	ENST00000285398.2:c.2291C>T	p.Ser764Leu	p.S764L	ENST00000285398	NM_000122.1	764	tCg/tTg	15/15	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.861939199528427	2		365	925	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371665	225371665	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1171731002	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	629	397	0	ENST00000264414.4:c.939G>A	p.Met313Ile	p.M313I	ENST00000264414	NM_003590.4	313	atG/atA	7/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.861939199528427	2		397	1452	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142964	47142964	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	469	363	0	ENST00000409792.3:c.4999C>T	p.Gln1667Ter	p.Q1667*	ENST00000409792	NM_014159.6	1667	Cag/Tag	8/21	1	2	FACETS	0.928	0.888	0.967	0.928	0.888	0.967	CLONAL	1	TRUE	1	0.861939199528427	2		363	1173	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183575	185183575	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs185398541	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	379	337	0	ENST00000265026.3:c.1429G>C	p.Glu477Gln	p.E477Q	ENST00000265026	NM_004721.4	477	Gag/Cag	9/14	0.116329264248517	4	FACETS	0.895	0.853	0.937	0.895	0.853	0.937	INDETERMINATE	2	TRUE	2	0.861939199528427	4		337	915	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599284	55599284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145602440	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	487	275	0	ENST00000288135.5:c.2410C>T	p.Arg804Trp	p.R804W	ENST00000288135	NM_000222.2	804	Cgg/Tgg	17/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.861939199528427	2		275	1116	SUCCESS
APC	324	MSKCC	GRCh37	5	112174068	112174068	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	446	283	0	ENST00000257430.4:c.2777C>G	p.Ser926Cys	p.S926C	ENST00000257430	NM_000038.5	926	tCt/tGt	16/16	1	2	FACETS	0.997	0.955	1	0.997	0.955	1	CLONAL	1	TRUE	1	0.861939199528427	2		283	1038	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925464	131925464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	382	241	0	ENST00000265335.6:c.1387G>A	p.Glu463Lys	p.E463K	ENST00000265335		463	Gaa/Aaa	9/25	1	2	FACETS	0.967	0.922	1	0.967	0.922	1	CLONAL	1	TRUE	1	0.861939199528427	2		241	917	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652251	36652251	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	376	277	0	ENST00000244741.5:c.373G>C	p.Glu125Gln	p.E125Q	ENST00000244741	NM_000389.4	125	Gag/Cag	2/3	1	2	FACETS	0.998	0.952	1	0.998	0.952	1	CLONAL	1	TRUE	1	0.861939199528427	2		277	874	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450326	50450326	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	360	332	0	ENST00000331340.3:c.510G>C	p.Glu170Asp	p.E170D	ENST00000331340	NM_006060.4	170	gaG/gaC	5/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.861939199528427	2		332	822	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240762	55240762	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768336804	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	252	315	0	ENST00000275493.2:c.2006G>A	p.Arg669Gln	p.R669Q	ENST00000275493	NM_005228.3	669	cGa/cAa	17/28	0.151003009665005	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.861939199528427	0		315	669	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089863	5089863	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	344	267	0	ENST00000381652.3:c.2761G>A	p.Gly921Ser	p.G921S	ENST00000381652	NM_004972.3	921	Ggt/Agt	20/25	1	2	FACETS	0.968	0.92	1	0.968	0.92	1	CLONAL	1	TRUE	1	0.861939199528427	2		267	825	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5462911	5462911	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	434	338	0	ENST00000381577.3:c.472G>A	p.Glu158Lys	p.E158K	ENST00000381577	NM_014143.3	158	Gag/Aag	4/7	1	2	FACETS	0.963	0.921	1	0.963	0.921	1	CLONAL	1	TRUE	1	0.861939199528427	2		338	1046	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755898	133755898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	303	287	0	ENST00000318560.5:c.1525G>A	p.Glu509Lys	p.E509K	ENST00000318560	NM_005157.4	509	Gag/Aag	10/11	1	2	FACETS	0.937	0.888	0.987	0.937	0.888	0.987	CLONAL	1	TRUE	1	0.861939199528427	2		287	750	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047169	77047169	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6231	422	322	0	ENST00000356341.3:c.1375G>A	p.Glu459Lys	p.E459K	ENST00000356341	NM_002576.4	459	Gaa/Aaa	13/15	0.861939199528427	10	FACETS	0.655	0.618	0.692			1	SUBCLONAL	1	TRUE	NA	0.861939199528427	10		322	6653	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691194	18691194	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	443	321	0	ENST00000266497.5:c.3305C>G	p.Ala1102Gly	p.A1102G	ENST00000266497		1102	gCt/gGt	23/31	NA	2	FACETS	0.954	0.912	0.995			1	INDETERMINATE	1	TRUE	NA	0.861939199528427	2		321	1078	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246664	46246664	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	226	126	0	ENST00000334344.6:c.4758G>T	p.Gln1586His	p.Q1586H	ENST00000334344	NM_152641.2	1586	caG/caT	15/21	0.116329264248517	4	FACETS	1	0.974	1	1	0.974	1	INDETERMINATE	2	TRUE	2	0.861939199528427	4		126	462	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549383	21549383	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749117314	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	230	221	0	ENST00000382592.4:c.2893G>A	p.Asp965Asn	p.D965N	ENST00000382592	NM_014572.2	965	Gat/Aat	8/8	NA	2	FACETS	1	0.962	1			1	INDETERMINATE	1	TRUE	NA	0.861939199528427	2		221	519	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588626	28588626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs548609046	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	460	391	0	ENST00000241453.7:c.2822C>T	p.Ser941Leu	p.S941L	ENST00000241453	NM_004119.2	941	tCg/tTg	23/24	NA	2	FACETS	0.999	0.958	1			1	INDETERMINATE	1	TRUE	NA	0.861939199528427	2		391	1068	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304464	91304464	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	370	249	0	ENST00000355112.3:c.1861G>C	p.Glu621Gln	p.E621Q	ENST00000355112	NM_000057.2	621	Gag/Cag	7/22	1	2	FACETS	0.924	0.88	0.969	0.924	0.88	0.969	CLONAL	1	TRUE	1	0.861939199528427	2		249	929	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789661	3789661	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	474	410	0	ENST00000262367.5:c.4198G>C	p.Glu1400Gln	p.E1400Q	ENST00000262367	NM_004380.2	1400	Gag/Cag	25/31	0.861939199528427	3	FACETS	0.997	0.952	1	0.498	0.476	0.522	CLONAL	1	TRUE	1	0.861939199528427	3		410	1579	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014026	14014026	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373789508	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	406	286	0	ENST00000311895.7:c.4G>A	p.Glu2Lys	p.E2K	ENST00000311895	NM_005236.2	2	Gag/Aag	1/11	0.861939199528427	3	FACETS	0.971	0.923	1	0.486	0.461	0.51	CLONAL	1	TRUE	1	0.861939199528427	3		286	1388	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321730	30321730	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	330	304	0	ENST00000322652.5:c.1585C>G	p.Leu529Val	p.L529V	ENST00000322652	NM_015355.2	529	Ctt/Gtt	13/16	1	2	FACETS	0.89	0.845	0.936	0.89	0.845	0.936	CLONAL	1	TRUE	1	0.861939199528427	2		304	860	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223126	1223126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769403473	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	360	347	0	ENST00000326873.7:c.1063G>A	p.Asp355Asn	p.D355N	ENST00000326873	NM_000455.4	355	Gac/Aac	8/10	0.201272014527982	1	FACETS	0.505	0.48	0.53	0.505	0.48	0.53	INDETERMINATE	1	TRUE	0	0.861939199528427	1		347	942	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955183	17955183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1457535594	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	266	259	0	ENST00000458235.1:c.44C>T	p.Ser15Leu	p.S15L	ENST00000458235	NM_000215.3	15	tCa/tTa	2/24	0.201272014527982	1	FACETS	0.508	0.479	0.538	0.508	0.479	0.538	INDETERMINATE	1	TRUE	0	0.861939199528427	1		259	691	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022877	31022877	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	432	285	0	ENST00000375687.4:c.2362G>A	p.Glu788Lys	p.E788K	ENST00000375687	NM_015338.5	788	Gaa/Aaa	13/13	1	2	FACETS	0.997	0.954	1	0.997	0.954	1	CLONAL	1	TRUE	1	0.861939199528427	2		285	1005	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39726959	39726959	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	335	237	0	ENST00000361337.2:c.957G>C	p.Met319Ile	p.M319I	ENST00000361337	NM_003286.2	319	atG/atC	11/21	1	2	FACETS	0.963	0.916	1	0.963	0.916	1	CLONAL	1	TRUE	1	0.861939199528427	2		237	807	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145531	24145531	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776374083	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	419	341	0	ENST00000263121.7:c.550G>A	p.Glu184Lys	p.E184K	ENST00000263121	NM_003073.3	184	Gag/Aag	5/9	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.861939199528427	2		341	899	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357219	70357219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002124-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	368	261	2	ENST00000374080.3:c.5734C>T	p.Arg1912Cys	p.R1912C	ENST00000374080		1912	Cgc/Tgc	39/45	0.201272014527982	1	FACETS	0.693	0.663	0.723	0.693	0.663	0.723	INDETERMINATE	1	TRUE	0	0.861939199528427	1		263	701	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727126	243727126	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002139-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	110	381	0	ENST00000263826.5:c.844G>A	p.Asp282Asn	p.D282N	ENST00000263826	NM_005465.4	282	Gat/Aat	9/13	0.636758474434016	3	FACETS	0.408	0.366	0.454	0.204	0.183	0.227	SUBCLONAL	1	TRUE	1	0.636758474434016	3		381	1116	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170975	56170975	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002139-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	198	279	0	ENST00000399503.3:c.1803G>C	p.Glu601Asp	p.E601D	ENST00000399503	NM_005921.1	601	gaG/gaC	10/20	0.351640541100614	1	FACETS	0.764	0.713	0.816	0.764	0.713	0.816	INDETERMINATE	1	TRUE	0	0.636758474434016	1		279	555	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631163	176631163	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002139-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	394	428	0	ENST00000439151.2:c.1106T>C	p.Phe369Ser	p.F369S	ENST00000439151	NM_022455.4	369	tTt/tCt	4/23	0.601954255989952	2	FACETS	0.864	0.829	0.899	0.864	0.829	0.899	CLONAL	2	TRUE	0	0.636758474434016	2		428	716	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631174	176631174	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002139-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	404	431	0	ENST00000439151.2:c.1117T>C	p.Ser373Pro	p.S373P	ENST00000439151	NM_022455.4	373	Tct/Cct	4/23	0.601954255989952	2	FACETS	0.86	0.825	0.894	0.86	0.825	0.894	CLONAL	2	TRUE	0	0.636758474434016	2		431	738	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851505	151851505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002139-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	115	286	0	ENST00000262189.6:c.11986G>A	p.Asp3996Asn	p.D3996N	ENST00000262189	NM_170606.2	3996	Gat/Aat	47/59	0.320580428119785	1	FACETS	0.393	0.354	0.433	0.393	0.354	0.433	INDETERMINATE	1	TRUE	0	0.636758474434016	1		286	627	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233081	69233081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002139-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	134	341	0	ENST00000462284.1:c.946G>A	p.Glu316Lys	p.E316K	ENST00000462284	NM_002392.5	316	Gaa/Aaa	11/11	1	2	FACETS	0.563	0.512	0.617	0.563	0.512	0.617	SUBCLONAL	1	TRUE	1	0.636758474434016	2		341	747	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593533	48593533	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002139-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	175	301	0	ENST00000342988.3:c.1284G>C	p.Lys428Asn	p.K428N	ENST00000342988	NM_005359.5	428	aaG/aaC	10/12	0.636758474434016	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.636758474434016	1		301	369	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0002152-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	329	269	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.155143826182154	3	FACETS	0.836	0.79	0.882	0.557	0.527	0.588	INDETERMINATE	2	TRUE	0	0.440227201184763	3		269	1091	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608399	43608399	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002152-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	198	372	0	ENST00000355710.3:c.1747C>T	p.Gln583Ter	p.Q583*	ENST00000355710	NM_020975.4	583	Cag/Tag	9/20	0.343130881973399	3	FACETS	0.862	0.797	0.93	0.431	0.398	0.465	CLONAL	1	TRUE	1	0.440227201184763	3		372	1273	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095590	178095590	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002177-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1368	226	474	0	ENST00000397062.3:c.1741T>A	p.Tyr581Asn	p.Y581N	ENST00000397062	NM_006164.4	581	Tac/Aac	5/5	0.339836552156039	3	FACETS	0.976	0.906	1	0.488	0.453	0.525	CLONAL	1	TRUE	1	0.339836552156039	3		474	1594	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431439	49431439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002177-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	195	421	0	ENST00000301067.7:c.9700G>A	p.Asp3234Asn	p.D3234N	ENST00000301067	NM_003482.3	3234	Gac/Aac	34/54	0.339836552156039	3	FACETS	1	0.973	1	0.555	0.513	0.6	CLONAL	1	TRUE	1	0.339836552156039	3		421	1209	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41011079	41011079	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002177-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	318	438	0	ENST00000267868.3:c.512T>C	p.Leu171Pro	p.L171P	ENST00000267868	NM_002875.4	171	cTg/cCg	6/10	0.339836552156039	3	FACETS	0.971	0.916	1	0.971	0.916	1	CLONAL	2	TRUE	1	0.339836552156039	3		438	1128	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519068	66519068	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0002177-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1212	107	304	0	ENST00000358598.2:c.348+1G>T		p.X116_splice	ENST00000358598	NM_212471.2	116			0.339836552156039	5	FACETS	0.721	0.644	0.803	0.24	0.214	0.268	SUBCLONAL	1	TRUE	2	0.339836552156039	5		304	1319	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631246	117631250	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TACAT	TACAT	-	novel	NA	P-0002177-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	202	452	0	ENST00000368508.3:c.6428_6432del	p.Asp2143ValfsTer25	p.D2143Vfs*25	ENST00000368508	NM_002944.2	2143	gATGTA/g	40/43	0.339836552156039	2	FACETS	1	0.945	1	0.513	0.475	0.553	CLONAL	1	TRUE	0	0.339836552156039	2		452	1159	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117717359	117717359	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002190-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	234	324	0	ENST00000368508.3:c.848C>G	p.Ser283Cys	p.S283C	ENST00000368508	NM_002944.2	283	tCt/tGt	8/43	0.359703099011017	1	FACETS	0.79	0.741	0.841	0.79	0.741	0.841	SUBCLONAL	1	TRUE	0	0.593850229800108	1		324	701	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0002229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	140	124	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.362555451903034	5	FACETS	1	0.94	1			1	CLONAL	3	TRUE	NA	0.362555451903034	5		124	388	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120876	115120877	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0002229-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	205	290	0	ENST00000257566.3:c.129_130del	p.Leu44AspfsTer66	p.L44Dfs*66	ENST00000257566	NM_016569.3	43	gcGCtg/gctg	1/8	0.263651433398663	4	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	2	0.362555451903034	4		290	763	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0002234-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	248	294	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.342660449223613	5	FACETS	1	0.965	1	1	0.965	1	CLONAL	4	TRUE	1	0.342660449223613	5		294	533	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163431	47163431	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0002234-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	178	638	0	ENST00000409792.3:c.2695A>T	p.Lys899Ter	p.K899*	ENST00000409792	NM_014159.6	899	Aaa/Taa	3/21	0.342660449223613	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.342660449223613	2		638	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579366	7579366	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0002234-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	284	459	0	ENST00000269305.4:c.321C>G	p.Tyr107Ter	p.Y107*	ENST00000269305	NM_001126112.2	107	taC/taG	4/11	0.342660449223613	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.342660449223613	2		459	827	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577526	7577526	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121912653	NA	P-0002242-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	180	380	0	ENST00000269305.4:c.755T>C	p.Leu252Pro	p.L252P	ENST00000269305	NM_001126112.2	252	cTc/cCc	7/11	0.231705293139969	2	FACETS	0.984	0.915	1	0.984	0.915	1	CLONAL	2	TRUE	0	0.348970189382659	2		380	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0002256-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	930	553	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.557623470024143	4	FACETS	0.938	0.917	0.959			1	CLONAL	4	TRUE	NA	0.56341472263629	4		553	1375	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262372	16262372	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760187317	NA	P-0002256-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	200	117	0	ENST00000375759.3:c.9637G>A	p.Ala3213Thr	p.A3213T	ENST00000375759	NM_015001.2	3213	Gcg/Acg	11/15	0.308130728531091	4	FACETS	1	0.982	1			1	INDETERMINATE	3	TRUE	NA	0.56341472263629	4		117	340	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549655	187549655	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002256-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	160	177	0	ENST00000441802.2:c.4586C>A	p.Thr1529Asn	p.T1529N	ENST00000441802	NM_005245.3	1529	aCc/aAc	8/27	0.56341472263629	3	FACETS	1	0.968	1	0.367	0.337	0.397	CLONAL	1	TRUE	0	0.56341472263629	3		177	662	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912353	32912353	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002256-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	201	507	0	ENST00000380152.3:c.3861T>A	p.Asn1287Lys	p.N1287K	ENST00000380152		1287	aaT/aaA	11/27	NA	2	FACETS	0.785	0.728	0.844			1	INDETERMINATE	1	TRUE	NA	0.56341472263629	2		507	909	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0002291-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	45	497	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.879	0.736	1	0.879	0.736	1	CLONAL	1	TRUE	1	0.13	2		497	788	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0002291-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	26	124	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.827	1	1	0.827	1	CLONAL	1	TRUE	1	0.13	2		124	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0002291-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	63	433	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.977	0.843	1	0.977	0.843	1	CLONAL	1	TRUE	1	0.13	2		434	992	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851477	128851477	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1216671158	NA	P-0002291-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	36	444	1	ENST00000249373.3:c.1802C>T	p.Ala601Val	p.A601V	ENST00000249373	NM_005631.4	601	gCg/gTg	11/12	1	2	FACETS	0.804	0.659	0.967	0.804	0.659	0.967	CLONAL	1	TRUE	1	0.13	2		445	689	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090489	71090496	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGAGTG	TGGGAGTG	-	novel	NA	P-0002291-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	46	469	0	ENST00000318789.4:c.852_859del	p.His284GlnfsTer8	p.H284Qfs*8	ENST00000318789	NM_032682.5	284	caCACTCCCAaa/caaa	11/21	1	2	FACETS	0.865	0.726	1	0.865	0.726	1	CLONAL	1	TRUE	1	0.13	2		469	818	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061334	38061334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002304-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	1076	435	494	0	ENST00000250448.2:c.655C>A	p.Arg219Ser	p.R219S	ENST00000250448	NM_004496.3	219	Cgc/Agc	2/2	1	2	FACETS	0.983	0.936	1	0.983	0.936	1	CLONAL	1	TRUE	1	0.585660219025389	2		494	1511	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721946	176721946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002304-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	592	304	411	0	ENST00000439151.2:c.7577C>T	p.Pro2526Leu	p.P2526L	ENST00000439151	NM_022455.4	2526	cCc/cTc	23/23	0.241499750322563	1	FACETS	0.819	0.774	0.865	0.819	0.774	0.865	INDETERMINATE	1	TRUE	0	0.585660219025389	1		411	896	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151927376	151927376	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002304-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	91	48	53	0	ENST00000262189.6:c.2800G>T	p.Asp934Tyr	p.D934Y	ENST00000262189	NM_170606.2	934	Gat/Tat	17/59	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.585660219025389	2		53	139	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500912	8500912	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002304-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	951	73	484	0	ENST00000356435.5:c.1970A>T	p.Asp657Val	p.D657V	ENST00000356435		657	gAc/gTc	13/35	1	2	FACETS	0.243	0.212	0.278	0.243	0.212	0.278	SUBCLONAL	1	TRUE	1	0.585660219025389	2		484	1024	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061104	38061134	+	frameshift_variant	Frame_Shift_Del	DEL	CTTGCGGCTCTCAGGGCCGCCCTTGGCGCCG	CTTGCGGCTCTCAGGGCCGCCCTTGGCGCCG	-	novel	NA	P-0002304-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	126	51	45	0	ENST00000250448.2:c.855_885del	p.Ser285ArgfsTer26	p.S285Rfs*26	ENST00000250448	NM_004496.3	285	agCGGCGCCAAGGGCGGCCCTGAGAGCCGCAAG/ag	2/2	1	2	FACETS	0.984	0.851	1	0.984	0.851	1	CLONAL	1	TRUE	1	0.585660219025389	2		45	177	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0002351-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	75	412	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.220979275357088	1	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	0	0.234884971884682	1		412	545	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498290	29498290	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002351-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	83	458	0	ENST00000389048.3:c.1890C>G	p.Ile630Met	p.I630M	ENST00000389048	NM_004304.4	630	atC/atG	10/29	0.220979275357088	1	FACETS	0.787	0.693	0.887	0.787	0.693	0.887	SUBCLONAL	1	TRUE	0	0.234884971884682	1		458	793	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225365113	225365113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002351-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	105	416	0	ENST00000264414.4:c.1577C>T	p.Pro526Leu	p.P526L	ENST00000264414	NM_003590.4	526	cCa/cTa	11/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.234884971884682	2		416	791	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265544	152265544	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002351-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	73	330	0	ENST00000206249.3:c.997C>A	p.Pro333Thr	p.P333T	ENST00000206249	NM_000125.3	333	Cct/Act	4/8	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.234884971884682	2		330	601	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508556	106508556	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002351-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	129	211	0	ENST00000359195.3:c.550C>A	p.Arg184Ser	p.R184S	ENST00000359195	NM_002649.2	184	Cgc/Agc	2/11	0.196747724624439	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.234884971884682	3		211	552	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480514	123480514	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002351-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	81	426	0	ENST00000371139.4:c.22C>G	p.His8Asp	p.H8D	ENST00000371139	NM_001114937.2	8	Cat/Gat	1/4	1	2	FACETS	0.853	0.75	0.963	0.853	0.75	0.963	CLONAL	1	TRUE	1	0.234884971884682	2		426	809	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206664151	206664151	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0002351-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	76	374	0	ENST00000367120.3:c.1695del		p.X565_splice	ENST00000367120	NM_014002.3	565			1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.234884971884682	2		374	647	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873888	151873888	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002364-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	225	109	402	0	ENST00000262189.6:c.8650C>T	p.Arg2884Ter	p.R2884*	ENST00000262189	NM_170606.2	2884	Cga/Tga	38/59	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.584709737277696	2		402	334	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160188	22160188	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749425404	NA	P-0002364-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	267	112	369	0	ENST00000215832.6:c.443G>A	p.Arg148His	p.R148H	ENST00000215832	NM_002745.4	148	cGt/cAt	3/9	NA	2	FACETS	1	0.917	1			1	INDETERMINATE	1	TRUE	NA	0.584709737277696	2		369	379	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879491	151879491	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002364-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	257	105	382	0	ENST00000262189.6:c.5454del	p.Asn1818LysfsTer31	p.N1818Kfs*31	ENST00000262189	NM_170606.2	1818	aaT/aa	36/59	1	2	FACETS	0.992	0.897	1	0.992	0.897	1	CLONAL	1	TRUE	1	0.584709737277696	2		382	362	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0002419-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	188	427	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	0.845	0.782	0.911			1	INDETERMINATE	1	TRUE	NA	0.521517262413503	2		427	853	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0002419-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	171	597	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.447313286679665	1	FACETS	0.885	0.819	0.952	0.885	0.819	0.952	CLONAL	1	TRUE	0	0.521517262413503	1		597	548	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593554	48593554	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002419-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	114	271	1	ENST00000342988.3:c.1307del	p.Lys436ArgfsTer40	p.K436Rfs*40	ENST00000342988	NM_005359.5	435	atA/at	10/12	0.447313286679665	1	FACETS	0.738	0.669	0.81	0.738	0.669	0.81	SUBCLONAL	1	TRUE	0	0.521517262413503	1		272	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0002428-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	43	558	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.285125575937467	1	FACETS	0.813	0.683	0.956	0.813	0.683	0.956	CLONAL	1	TRUE	0	0.285125575937467	1		558	318	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630335	47630335	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002428-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	35	303	0	ENST00000233146.2:c.5C>G	p.Ala2Gly	p.A2G	ENST00000233146	NM_000251.2	2	gCg/gGg	1/16	1	2	FACETS	0.575	0.471	0.691	0.575	0.471	0.691	SUBCLONAL	1	TRUE	1	0.285125575937467	2		303	427	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286761	212286761	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002428-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	99	370	0	ENST00000342788.4:c.2935C>T	p.Arg979Ter	p.R979*	ENST00000342788	NM_005235.2	979	Cga/Tga	24/28	0.285125575937467	4	FACETS	0.932	0.835	1	0.932	0.835	1	CLONAL	2	TRUE	2	0.285125575937467	4		370	479	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355257	81355257	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002428-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	81	401	0	ENST00000222390.5:c.1117C>T	p.Arg373Ter	p.R373*	ENST00000222390	NM_000601.4	373	Cga/Tga	9/18	0.285125575937467	5	FACETS	1	0.975	1	0.481	0.424	0.542	CLONAL	1	TRUE	2	0.285125575937467	5		401	562	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508533	106508533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773456619	NA	P-0002428-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	31	150	2	ENST00000359195.3:c.527C>T	p.Thr176Met	p.T176M	ENST00000359195	NM_002649.2	176	aCg/aTg	2/11	0.285125575937467	5	FACETS	0.839	0.679	1	0.28	0.226	0.34	CLONAL	1	TRUE	2	0.285125575937467	5		152	370	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842633	68842633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002428-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	150	368	0	ENST00000261769.5:c.569A>G	p.Tyr190Cys	p.Y190C	ENST00000261769	NM_004360.3	190	tAc/tGc	5/16	NA	2	FACETS	0.953	0.883	1			1	INDETERMINATE	3	TRUE	NA	0.285125575937467	2		368	368	SUCCESS
APC	324	MSKCC	GRCh37	5	112170822	112170822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1114167575	NA	P-0002438-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	306	509	0	ENST00000257430.4:c.1918C>T	p.Arg640Trp	p.R640W	ENST00000257430	NM_000038.5	640	Cgg/Tgg	15/16	0.233595926026995	5	FACETS	1	0.989	1	0.785	0.743	0.829	INDETERMINATE	2	TRUE	2	0.540643776028545	5		509	870	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149447875	149447875	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs546270503	NA	P-0002438-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	143	385	1	ENST00000286301.3:c.1529C>T	p.Pro510Leu	p.P510L	ENST00000286301	NM_005211.3	510	cCg/cTg	11/22	0.233595926026995	5	FACETS	1	0.956	1	0.36	0.328	0.394	INDETERMINATE	1	TRUE	2	0.540643776028545	5		386	887	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983044	149983044	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002438-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	168	597	1	ENST00000253339.5:c.3214G>T	p.Glu1072Ter	p.E1072*	ENST00000253339		1072	Gaa/Taa	7/7	0.471677056408948	4	FACETS	0.957	0.879	1	0.478	0.439	0.519	CLONAL	1	TRUE	2	0.540643776028545	4		598	1001	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348715	118348715	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002438-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	155	410	0	ENST00000534358.1:c.3368A>T	p.Glu1123Val	p.E1123V	ENST00000534358	NM_005933.3	1123	gAa/gTa	5/36	1	2	FACETS	0.769	0.705	0.835	0.769	0.705	0.835	SUBCLONAL	1	TRUE	1	0.540643776028545	2		410	746	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435350	110435350	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002438-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	207	141	0	ENST00000375856.3:c.3051G>T	p.Leu1017Phe	p.L1017F	ENST00000375856	NM_003749.2	1017	ttG/ttT	1/2	0.540643776028545	4	FACETS	1	0.984	1			1	CLONAL	2	TRUE	NA	0.540643776028545	4		141	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0002438-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	246	328	2	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.540643776028545	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.540643776028545	2		330	433	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267491	198267491	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs763149798	NA	P-0002466-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	125	346	0	ENST00000335508.6:c.1866G>C	p.Glu622Asp	p.E622D	ENST00000335508	NM_012433.2	622	gaG/gaC	14/25	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.504859196284831	2		346	427	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176503	142176503	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002466-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	105	615	0	ENST00000350721.4:c.7598G>C	p.Arg2533Pro	p.R2533P	ENST00000350721	NM_001184.3	2533	cGa/cCa	45/47	NA	2	FACETS	0.902	0.813	0.996			1	INDETERMINATE	1	TRUE	NA	0.504859196284831	2		615	461	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231221	98231221	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554695039	NA	P-0002466-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	96	287	0	ENST00000331920.6:c.2062C>T	p.Gln688Ter	p.Q688*	ENST00000331920	NM_000264.3	688	Cag/Tag	14/24	0.504859196284831	1	FACETS	0.974	0.879	1	0.974	0.879	1	CLONAL	1	TRUE	0	0.504859196284831	1		287	292	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231404	5231404	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002522-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	15	312	0	ENST00000357368.4:c.2072A>T	p.Gln691Leu	p.Q691L	ENST00000357368	NM_002850.3	691	cAg/cTg	14/38	0.227156990884017	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		312	145	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0002528-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	405	50	258	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		258	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0002547-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	293	342	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.376885813752908	3	FACETS	1	0.99	1	0.79	0.748	0.832	CLONAL	2	TRUE	0	0.432240966164118	3		343	696	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0002547-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	307	514	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.255440663946337	2	FACETS	0.787	0.743	0.83	0.787	0.743	0.83	INDETERMINATE	2	TRUE	0	0.432240966164118	2		514	903	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0002547-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	141	305	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.432240966164118	2		305	608	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180207	38180207	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1300885784	NA	P-0002547-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	138	431	0	ENST00000396334.3:c.55C>T	p.Pro19Ser	p.P19S	ENST00000396334	NM_002468.4	19	Ccc/Tcc	1/5	1	2	FACETS	0.855	0.779	0.934	0.855	0.779	0.934	CLONAL	1	TRUE	1	0.432240966164118	2		431	747	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519988	NA	P-0002547-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	84	527	1	ENST00000269305.4:c.808T>C	p.Phe270Leu	p.F270L	ENST00000269305	NM_001126112.2	270	Ttt/Ctt	8/11	0.376885813752908	3	FACETS	0.437	0.384	0.493	0.146	0.128	0.165	SUBCLONAL	1	TRUE	0	0.432240966164118	3		528	1082	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747079	40747079	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002547-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1535	144	459	0	ENST00000373198.4:c.3003C>G	p.Ser1001Arg	p.S1001R	ENST00000373198	NM_133170.3	1001	agC/agG	22/32	0.432240966164118	6	FACETS	0.74	0.672	0.812	0.247	0.224	0.271	SUBCLONAL	1	TRUE	3	0.432240966164118	6		459	1679	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0002566-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	177	364	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.380121280858602	5	FACETS	1	0.98	1	1	0.992	1	CLONAL	5	TRUE	1	0.380121280858602	5		364	272	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0002566-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	39	312	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.289516683990258	3	FACETS	1	0.941	1			1	CLONAL	1	TRUE	NA	0.380121280858602	3		312	189	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6029533	6029533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002566-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	46	520	0	ENST00000265849.7:c.1042G>A	p.Glu348Lys	p.E348K	ENST00000265849	NM_000535.5	348	Gaa/Aaa	10/15	0.380121280858602	5	FACETS	0.943	0.796	1	0.314	0.265	0.369	CLONAL	1	TRUE	2	0.380121280858602	5		520	403	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188164	11188164	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587777893	NA	P-0002569-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	238	184	0	ENST00000361445.4:c.5930C>A	p.Thr1977Lys	p.T1977K	ENST00000361445	NM_004958.3	1977	aCa/aAa	43/58	0.683671182083989	3	FACETS	0.99	0.936	1	0.99	0.936	1	CLONAL	2	TRUE	1	0.683671182083989	3		184	472	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551591	150551591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002569-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	174	186	0	ENST00000369026.2:c.416C>T	p.Ala139Val	p.A139V	ENST00000369026	NM_021960.4	139	gCt/gTt	1/3	0.683671182083989	4	FACETS	0.938	0.863	1	0.469	0.431	0.508	CLONAL	1	TRUE	2	0.683671182083989	4		186	914	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347510	91347510	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002569-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	115	248	0	ENST00000355112.3:c.3672A>C	p.Glu1224Asp	p.E1224D	ENST00000355112	NM_000057.2	1224	gaA/gaC	19/22	0.683671182083989	3	FACETS	1	0.965	1	0.563	0.511	0.616	CLONAL	1	TRUE	1	0.683671182083989	3		248	401	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313481	30313481	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002569-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	143	269	0	ENST00000262643.3:c.1081C>G	p.Gln361Glu	p.Q361E	ENST00000262643	NM_001238.2	361	Cag/Gag	11/12	0.683671182083989	4	FACETS	1	0.949	1	0.526	0.481	0.574	CLONAL	1	TRUE	2	0.683671182083989	4		269	669	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53241043	53241043	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002569-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	135	161	0	ENST00000375401.3:c.1168C>T	p.Arg390Trp	p.R390W	ENST00000375401	NM_004187.3	390	Cgg/Tgg	9/26	0.683671182083989	2	FACETS	0.859	0.786	0.933			1	CLONAL	1	TRUE	NA	0.683671182083989	2		161	460	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0002631-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	70	427	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.282092997961134	1	FACETS	0.67	0.585	0.761	0.67	0.585	0.761	SUBCLONAL	1	TRUE	0	0.34	1		427	510	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652869	212652869	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002631-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	49	540	0	ENST00000342788.4:c.437G>T	p.Gly146Val	p.G146V	ENST00000342788	NM_005235.2	146	gGa/gTa	4/28	1	2	FACETS	0.753	0.639	0.877	0.753	0.639	0.877	SUBCLONAL	1	TRUE	1	0.34	2		540	383	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867443	35867443	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1020619032	NA	P-0002631-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	83	540	0	ENST00000303115.3:c.257G>A	p.Arg86Lys	p.R86K	ENST00000303115	NM_002185.3	86	aGg/aAg	3/8	1	2	FACETS	0.998	0.884	1	0.998	0.884	1	CLONAL	1	TRUE	1	0.34	2		540	489	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399488	139399488	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002631-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	71	459	0	ENST00000277541.6:c.4655C>A	p.Ala1552Glu	p.A1552E	ENST00000277541	NM_017617.3	1552	gCg/gAg	26/34	1	2	FACETS	0.723	0.631	0.821	0.723	0.631	0.821	SUBCLONAL	1	TRUE	1	0.34	2		459	578	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591924	48591924	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs377767348	NA	P-0002631-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	89	664	0	ENST00000342988.3:c.1087T>C	p.Cys363Arg	p.C363R	ENST00000342988	NM_005359.5	363	Tgt/Cgt	9/12	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.34	2		664	504	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600530	10600530	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1568397317	NA	P-0002631-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	82	492	0	ENST00000171111.5:c.1326-1G>A		p.X442_splice	ENST00000171111	NM_203500.1	442			0.282092997961134	1	FACETS	0.755	0.668	0.849	0.755	0.668	0.849	SUBCLONAL	1	TRUE	0	0.34	1		492	530	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0002665-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	26	203	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	NA	2	FACETS	0.637	0.513	0.774			1	INDETERMINATE	1	TRUE	NA	0.680514666095502	2		203	120	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0002665-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	62	269	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.366454334326742	1	FACETS	0.771	0.682	0.862	0.771	0.682	0.862	INDETERMINATE	1	TRUE	0	0.680514666095502	1		269	156	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394805	45394805	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002665-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	66	265	0	ENST00000262160.6:c.544C>T	p.Arg182Ter	p.R182*	ENST00000262160	NM_005901.5	182	Cga/Tga	5/11	0.680514666095502	1	FACETS	0.826	0.736	0.917	0.826	0.736	0.917	CLONAL	1	TRUE	0	0.680514666095502	1		265	155	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473722	67473722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs794727798	NA	P-0002665-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	129	290	1	ENST00000327367.4:c.802C>T	p.Arg268Cys	p.R268C	ENST00000327367	NM_005902.3	268	Cgc/Tgc	6/9	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.680514666095502	2		291	368	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473779	67473779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906850	NA	P-0002665-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	87	205	0	ENST00000327367.4:c.859C>T	p.Arg287Trp	p.R287W	ENST00000327367	NM_005902.3	287	Cgg/Tgg	6/9	1	2	FACETS	0.958	0.86	1	0.958	0.86	1	CLONAL	1	TRUE	1	0.680514666095502	2		205	267	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99482445	99482445	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002665-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	89	213	1	ENST00000268035.6:c.3313G>T	p.Ala1105Ser	p.A1105S	ENST00000268035	NM_000875.3	1105	Gca/Tca	18/21	1	2	FACETS	0.98	0.881	1	0.98	0.881	1	CLONAL	1	TRUE	1	0.680514666095502	2		214	267	SUCCESS
APC	324	MSKCC	GRCh37	5	112175772	112175772	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002665-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	67	208	1	ENST00000257430.4:c.4483del	p.Ser1495ValfsTer12	p.S1495Vfs*12	ENST00000257430	NM_000038.5	1494	gAa/ga	16/16	NA	2	FACETS	0.817	0.719	0.92			1	INDETERMINATE	1	TRUE	NA	0.680514666095502	2		209	241	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0002712-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	20	746	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	1	2	FACETS	0.1	0.075	0.128	0.1	0.075	0.128	SUBCLONAL	1	TRUE	1	0.42	2		746	956	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371708	225371708	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002712-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	79	711	0	ENST00000264414.4:c.896T>G	p.Met299Arg	p.M299R	ENST00000264414	NM_003590.4	299	aTg/aGg	7/16	1	2	FACETS	0.358	0.314	0.406	0.358	0.314	0.406	SUBCLONAL	1	TRUE	1	0.42	2		711	1051	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095828	29095828	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002712-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	69	790	0	ENST00000328354.6:c.1006C>T	p.Gln336Ter	p.Q336*	ENST00000328354	NM_007194.3	336	Cag/Tag	9/15	0.3	3	FACETS	0.403	0.35	0.461	0.202	0.175	0.231	SUBCLONAL	1	TRUE	1	0.42	3		790	986	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0002721-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	89	342	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.31749170345173	3	FACETS	1	0.916	1	1	0.916	1	CLONAL	3	TRUE	0	0.403128199188214	3		343	176	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0002721-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	67	418	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	1	TRUE	NA	0.403128199188214	2		418	223	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845391	151845391	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002721-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	105	408	0	ENST00000262189.6:c.13621C>T	p.Arg4541Ter	p.R4541*	ENST00000262189	NM_170606.2	4541	Cga/Tga	52/59	0.403128199188214	5	FACETS	0.917	0.832	1	0.917	0.832	1	CLONAL	3	TRUE	2	0.403128199188214	5		408	304	SUCCESS
APC	324	MSKCC	GRCh37	5	112175233	112175248	+	frameshift_variant	Frame_Shift_Del	DEL	GTCAGCTGAAGATCCT	GTCAGCTGAAGATCCT	-	novel	NA	P-0002721-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	24	321	0	ENST00000257430.4:c.3944_3959del	p.Ser1315Ter	p.S1315*	ENST00000257430	NM_000038.5	1314	agGTCAGCTGAAGATCCT/ag	16/16	NA	2	FACETS	0.601	0.474	0.746			1	INDETERMINATE	1	TRUE	NA	0.403128199188214	2		321	198	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046342	180046342	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768185411	NA	P-0002746-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	37	381	0	ENST00000261937.6:c.2672G>A	p.Arg891His	p.R891H	ENST00000261937	NM_182925.4	891	cGc/cAc	19/30	0.238193305769946	1	FACETS	0.767	0.64	0.904	0.767	0.64	0.904	INDETERMINATE	1	TRUE	0	0.428507557624067	1		381	177	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104377046	104377046	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002746-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	57	491	0	ENST00000369902.3:c.1158-1G>A		p.X386_splice	ENST00000369902	NM_016169.3	386			0.428507557624067	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.428507557624067	1		491	174	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117453	115117453	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs751111385	NA	P-0002746-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	31	386	0	ENST00000257566.3:c.721A>G	p.Ile241Val	p.I241V	ENST00000257566	NM_016569.3	241	Ata/Gta	4/8	0.206087988419174	1	FACETS	0.689	0.564	0.827	0.689	0.564	0.827	INDETERMINATE	1	TRUE	0	0.428507557624067	1		386	165	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420315	88420315	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773244598	NA	P-0002746-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	12	484	0	ENST00000360948.2:c.2371C>T	p.Arg791Trp	p.R791W	ENST00000360948	NM_001012338.2	791	Cgg/Tgg	19/19	0.230200260583726	2	FACETS	0.255	0.179	0.348	0.127	0.089	0.174	INDETERMINATE	1	TRUE	0	0.428507557624067	2		484	220	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531024	187531025	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0002746-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	86	669	0	ENST00000441802.2:c.9998_9999del	p.Pro3333ArgfsTer13	p.P3333Rfs*13	ENST00000441802	NM_005245.3	3333	cCT/c	15/27	0.428507557624067	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.428507557624067	1		669	304	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578365	7578383	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTCACCATCGCTATCTGA	GCTCACCATCGCTATCTGA	-	novel	NA	P-0002746-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	63	423	0	ENST00000269305.4:c.547_559+6del		p.X183_splice	ENST00000269305	NM_001126112.2	183		5/11	0.206087988419174	1	FACETS	0.996	0.873	1	0.996	0.873	1	INDETERMINATE	1	TRUE	0	0.428507557624067	1		423	232	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0002756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	54	228	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	0.723382846852057	2		228	112	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114276	115114276	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0002756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	123	281	0	ENST00000257566.3:c.942-1G>C		p.X314_splice	ENST00000257566	NM_016569.3	314			0.258126744564817	3	FACETS	0.754	0.692	0.817	0.754	0.692	0.817	INDETERMINATE	2	TRUE	1	0.723382846852057	3		281	307	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0002799-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	335	395	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.758826907758406	4	FACETS	0.951	0.928	0.973	0.951	0.928	0.973	CLONAL	4	TRUE	0	0.834451973855658	4		396	387	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948202	55948202	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002799-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	42	333	0	ENST00000263923.4:c.3769C>A	p.Gln1257Lys	p.Q1257K	ENST00000263923	NM_002253.2	1257	Cag/Aag	29/30	0.672474978006345	3	FACETS	0.401	0.335	0.473	0.2	0.167	0.237	SUBCLONAL	1	TRUE	1	0.834451973855658	3		333	356	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	401996	401996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002799-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	73	451	0	ENST00000399788.2:c.4795G>A	p.Gly1599Arg	p.G1599R	ENST00000399788	NM_001042603.1	1599	Gga/Aga	27/28	0.742772739619086	4	FACETS	0.484	0.423	0.55			1	SUBCLONAL	1	TRUE	NA	0.834451973855658	4		451	663	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339311	70339311	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002799-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	52	358	0	ENST00000374080.3:c.188G>T	p.Ser63Ile	p.S63I	ENST00000374080		63	aGc/aTc	2/45	0.422490191095546	4	FACETS	0.446	0.379	0.518	0.223	0.189	0.259	INDETERMINATE	1	TRUE	2	0.834451973855658	4		358	513	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	464400	464400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	616	51	595	0	ENST00000399788.2:c.794G>A	p.Arg265Lys	p.R265K	ENST00000399788	NM_001042603.1	265	aGa/aAa	7/28	0.264945975253061	2	FACETS	0.397	0.336	0.463	0.198	0.168	0.232	SUBCLONAL	1	TRUE	0	0.385625255108776	2		595	667	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435648	110435648	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002808-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	210	46	172	0	ENST00000375856.3:c.2753A>C	p.Glu918Ala	p.E918A	ENST00000375856	NM_003749.2	918	gAg/gCg	1/2	0.193596813437019	1	FACETS	0.752	0.638	0.876	0.752	0.638	0.876	INDETERMINATE	1	TRUE	0	0.385625255108776	1		172	256	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0002827-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	157	260	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.293377971304377	5	FACETS	1	0.931	1			1	CLONAL	4	TRUE	NA	0.293377971304377	5		260	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0002827-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	72	221	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.269067270127964	2	FACETS	0.959	0.848	1	0.959	0.848	1	CLONAL	2	TRUE	0	0.293377971304377	2		221	256	SUCCESS
AR	367	MSKCC	GRCh37	X	66766276	66766276	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755088348	NA	P-0002827-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	43	264	1	ENST00000374690.3:c.1288G>A	p.Ala430Thr	p.A430T	ENST00000374690	NM_000044.3	430	Gcc/Acc	1/8	0.110426083562247	5	FACETS	1	0.913	1	0.284	0.238	0.335	INDETERMINATE	1	TRUE	1	0.293377971304377	5		265	371	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681655	30681655	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002827-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	83	467	0	ENST00000376406.3:c.442G>A	p.Glu148Lys	p.E148K	ENST00000376406	NM_014641.2	148	Gaa/Aaa	3/15	0.293377971304377	3	FACETS	1	0.948	1	0.566	0.5	0.637	CLONAL	1	TRUE	1	0.293377971304377	3		467	573	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441588	6441588	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764451724	NA	P-0002827-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	17	57	0	ENST00000356142.4:c.435C>G	p.Ile145Met	p.I145M	ENST00000356142	NM_018890.3	145	atC/atG	6/7	0.275992700947681	4	FACETS	0.781	0.592	0.997			1	CLONAL	2	TRUE	NA	0.293377971304377	4		57	96	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0002837-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	168	558	1	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.239917436395639	2	FACETS	0.915	0.843	0.989	0.915	0.843	0.989	CLONAL	2	TRUE	0	0.263053435754031	2		559	698	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837925	156837925	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002837-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	194	411	2	ENST00000524377.1:c.458C>A	p.Ser153Tyr	p.S153Y	ENST00000524377	NM_002529.3	153	tCt/tAt	5/17	0.21688895114458	4	FACETS	0.855	0.794	0.919			1	CLONAL	3	TRUE	NA	0.263053435754031	4		413	726	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55124948	55124948	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002837-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	197	532	0	ENST00000257290.5:c.13C>T	p.His5Tyr	p.H5Y	ENST00000257290	NM_006206.4	5	Cat/Tat	2/23	0.263053435754031	3	FACETS	0.956	0.886	1			1	CLONAL	2	TRUE	NA	0.263053435754031	3		532	886	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455153	50455154	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0002837-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	96	238	0	ENST00000331340.3:c.700_701delinsTT	p.Gly234Phe	p.G234F	ENST00000331340	NM_006060.4	234	GGc/TTc	6/8	0.236621801233361	4	FACETS	0.97	0.869	1	0.97	0.869	1	CLONAL	2	TRUE	2	0.263053435754031	4		238	475	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346571	81346571	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002837-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	184	473	0	ENST00000222390.5:c.1382G>T	p.Trp461Leu	p.W461L	ENST00000222390	NM_000601.4	461	tGg/tTg	11/18	0.236621801233361	4	FACETS	0.982	0.907	1	0.982	0.907	1	CLONAL	2	TRUE	2	0.263053435754031	4		473	900	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524287	148524287	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002837-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	143	431	0	ENST00000320356.2:c.697G>T	p.Asp233Tyr	p.D233Y	ENST00000320356	NM_004456.4	233	Gat/Tat	7/20	0.236621801233361	4	FACETS	0.855	0.78	0.934	0.855	0.78	0.934	CLONAL	2	TRUE	2	0.263053435754031	4		431	803	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857758	9857758	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002837-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	167	506	0	ENST00000330684.3:c.3643A>G	p.Arg1215Gly	p.R1215G	ENST00000330684	NM_001134407.1	1215	Aga/Gga	13/13	0.247531597305329	3	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	1	0.263053435754031	3		506	702	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220391	1220395	+	missense_variant	Missense_Mutation	ONP	GACGG	GACGG	TACTT	novel	NA	P-0002837-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	123	402	2	ENST00000326873.7:c.484_488delinsTACTT	p.Asp162_Gly163delinsTyrPhe	p.D162_G163delinsYF	ENST00000326873	NM_000455.4	162	GACGGc/TACTTc	4/10	0.239917436395639	2	FACETS	0.956	0.87	1	0.956	0.87	1	CLONAL	2	TRUE	0	0.263053435754031	2		404	489	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398280	25398281	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0002837-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	172	362	2	ENST00000311936.3:c.38_39delinsAA	p.Gly13Glu	p.G13E	ENST00000311936	NM_004985.3	13	gGC/gAA	2/5	0.236621801233361	4	FACETS	0.904	0.832	0.979	0.904	0.832	0.979	CLONAL	2	TRUE	2	0.263053435754031	4		364	914	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138376579	138376580	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0002854-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	945	112	436	0	ENST00000289153.2:c.2894_2895delinsAA	p.Ile965Lys	p.I965K	ENST00000289153	NM_006219.2	965	aTC/aAA	20/22	0.25979278486406	3	FACETS	0.768	0.689	0.852	0.384	0.344	0.426	SUBCLONAL	1	TRUE	1	0.320191016222788	3		436	1057	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0002893-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	43	269	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.684	0.572	0.809	0.684	0.572	0.809	SUBCLONAL	1	FALSE	1	0.208813818228935	2		269	602	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0002893-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	26	433	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.209868554711543	1	FACETS	0.437	0.345	0.543	0.437	0.345	0.543	SUBCLONAL	1	FALSE	0	0.208813818228935	1		433	510	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097786	27097786	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002893-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	28	368	0	ENST00000324856.7:c.3375G>T	p.Lys1125Asn	p.K1125N	ENST00000324856	NM_006015.4	1125	aaG/aaT	12/20	1	2	FACETS	0.686	0.548	0.843	0.686	0.548	0.843	SUBCLONAL	1	FALSE	1	0.208813818228935	2		368	391	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599344	55599344	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002893-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	29	384	0	ENST00000288135.5:c.2470G>T	p.Val824Leu	p.V824L	ENST00000288135	NM_000222.2	824	Gtg/Ttg	17/21	1	2	FACETS	0.627	0.503	0.769	0.627	0.503	0.769	SUBCLONAL	1	FALSE	1	0.208813818228935	2		384	443	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032255	10032255	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs886051634	NA	P-0002893-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	21	320	0	ENST00000330684.3:c.568A>G	p.Thr190Ala	p.T190A	ENST00000330684	NM_001134407.1	190	Aca/Gca	3/13	0.208813818228935	1	FACETS	0.637	0.491	0.806	0.637	0.491	0.806	SUBCLONAL	1	FALSE	0	0.208813818228935	1		320	283	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044453	47044453	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0002893-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	21	271	0	ENST00000377604.3:c.1951-1G>C		p.X651_splice	ENST00000377604	NM_001204468.1	651			1	1	FACETS	0.933	0.723	1	0.933	0.723	1	CLONAL	1	FALSE	0	0.208813818228935	1		271	193	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0002920-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	382	484	0	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	0.299794486495969	3	FACETS	0.857	0.823	0.892			1	INDETERMINATE	3	TRUE	NA	0.552529052765504	3		484	686	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007733	62007733	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002920-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	121	357	0	ENST00000392795.3:c.134C>A	p.Ser45Ter	p.S45*	ENST00000392795	NM_001039933.1	45	tCg/tAg	3/6	0.477265071512719	3	FACETS	1	0.985	1	0.715	0.652	0.78	CLONAL	1	TRUE	1	0.552529052765504	3		357	391	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0002989-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	29	427	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.225	0.179	0.277	0.225	0.179	0.277	SUBCLONAL	1	TRUE	1	0.24	2		427	1074	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0002989-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	47	390	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	1	2	FACETS	0.474	0.399	0.558	0.474	0.399	0.558	SUBCLONAL	1	TRUE	1	0.24	2		390	826	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544755	65544755	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0002989-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	59	315	0	ENST00000358664.4:c.172-1G>T		p.X58_splice	ENST00000358664	NM_002382.4	58			1	2	FACETS	0.676	0.581	0.781	0.676	0.581	0.781	SUBCLONAL	1	TRUE	1	0.24	2		315	727	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591135	67591137	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0002989-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	290	348	0	ENST00000274335.5:c.1728_1730del	p.Arg577del	p.R577del	ENST00000274335		576	acGAGa/aca	12/15	0.3	5	FACETS	1	0.983	1			1	CLONAL	3	TRUE	NA	0.24	5		348	985	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0003005-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	62	294	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		294	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003005-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	66	281	2	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		283	544	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0003005-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	37	868	0	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		868	981	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955574	48955574	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	26	416	0	ENST00000267163.4:c.1690del	p.Leu564SerfsTer47	p.L564Sfs*47	ENST00000267163	NM_000321.2	564	Ctc/tc	17/27	0.151142199547359	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		416	468	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085942	16085942	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	155	257	0	ENST00000281043.3:c.1118G>T	p.Arg373Leu	p.R373L	ENST00000281043	NM_005378.4	373	cGa/cTa	3/3	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.407038533131127	2		257	709	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183787	10183787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123481	NA	P-0003039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	106	209	0	ENST00000256474.2:c.256C>T	p.Pro86Ser	p.P86S	ENST00000256474	NM_000551.3	86	Ccc/Tcc	1/3	0.407038533131127	1	FACETS	0.838	0.755	0.926	0.838	0.755	0.926	CLONAL	1	FALSE	0	0.407038533131127	1		209	495	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442068	52442068	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1553645950	NA	P-0003039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	119	266	0	ENST00000460680.1:c.281A>G	p.His94Arg	p.H94R	ENST00000460680	NM_004656.3	94	cAt/cGt	5/17	0.407038533131127	1	FACETS	0.995	0.904	1	0.995	0.904	1	CLONAL	1	FALSE	0	0.407038533131127	1		266	468	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431661	431661	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	119	431	0	ENST00000399788.2:c.2348A>G	p.Lys783Arg	p.K783R	ENST00000399788	NM_001042603.1	783	aAa/aGa	17/28	1	2	FACETS	0.925	0.837	1	0.925	0.837	1	CLONAL	1	FALSE	1	0.407038533131127	2		431	632	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145035	58145035	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0003039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	105	299	0	ENST00000257904.6:c.309T>A	p.Tyr103Ter	p.Y103*	ENST00000257904	NM_000075.3	103	taT/taA	3/8	1	2	FACETS	0.938	0.843	1	0.938	0.843	1	CLONAL	1	FALSE	1	0.407038533131127	2		299	550	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290180	15290180	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371437217	NA	P-0003039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	102	292	0	ENST00000263388.2:c.3455C>T	p.Thr1152Met	p.T1152M	ENST00000263388	NM_000435.2	1152	aCg/aTg	21/33	1	2	FACETS	0.61	0.545	0.68	0.61	0.545	0.68	SUBCLONAL	1	FALSE	1	0.407038533131127	2		292	821	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0003077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	592	427	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.524629491312067	2	FACETS	0.858	0.832	0.884	0.858	0.832	0.884	CLONAL	2	TRUE	0	0.732213339301255	2		427	942	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	G	rs11575997	NA	P-0003077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	527	395	0	ENST00000269305.4:c.993+1G>C		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.732213339301255	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.732213339301255	2		395	651	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459157	120459157	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	229	375	0	ENST00000256646.2:c.6188A>G	p.Asp2063Gly	p.D2063G	ENST00000256646	NM_024408.3	2063	gAt/gGt	34/34	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.732213339301255	2		375	593	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488661	212488661	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	110	554	0	ENST00000342788.4:c.2188G>T	p.Gly730Ter	p.G730*	ENST00000342788	NM_005235.2	730	Gga/Tga	18/28	0.179540816056975	2	FACETS	0.353	0.317	0.392	0.177	0.158	0.196	INDETERMINATE	1	TRUE	0	0.732213339301255	2		554	851	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250870	153250870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	583	654	0	ENST00000281708.4:c.1190G>A	p.Gly397Asp	p.G397D	ENST00000281708	NM_033632.3	397	gGt/gAt	8/12	0.45957134535028	2	FACETS	0.845	0.819	0.871	0.845	0.819	0.871	CLONAL	2	TRUE	0	0.732213339301255	2		654	942	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039609	180039609	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs954889734	NA	P-0003077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	79	512	1	ENST00000261937.6:c.3434G>A	p.Arg1145His	p.R1145H	ENST00000261937	NM_182925.4	1145	cGc/cAc	26/30	NA	2	FACETS	0.388	0.342	0.438			1	INDETERMINATE	1	TRUE	NA	0.732213339301255	2		513	556	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354300	70354300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs962560401	NA	P-0003077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	673	355	0	ENST00000374080.3:c.4711G>A	p.Asp1571Asn	p.D1571N	ENST00000374080		1571	Gac/Aac	34/45	0.564611328881068	2	FACETS	1	0.998	1			1	CLONAL	2	TRUE	NA	0.732213339301255	2		355	777	SUCCESS
APC	324	MSKCC	GRCh37	5	112174099	112174099	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	375	522	0	ENST00000257430.4:c.2810del	p.Phe937SerfsTer18	p.F937Sfs*18	ENST00000257430	NM_000038.5	936	aaT/aa	16/16	0.548429763066951	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.732213339301255	1		522	526	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564815	41564817	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0003077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	282	534	0	ENST00000263253.7:c.4119_4121del	p.Phe1374del	p.F1374del	ENST00000263253	NM_001429.3	1372	tgCTTc/tgc	25/31	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.732213339301255	2		534	685	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0003080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	518	370	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.732290898961809	2	FACETS	0.968	0.942	0.994	0.968	0.942	0.994	CLONAL	2	TRUE	0	0.769836721668821	2		370	695	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716154	243716154	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	518	402	1	ENST00000263826.5:c.1040A>G	p.Tyr347Cys	p.Y347C	ENST00000263826	NM_005465.4	347	tAc/tGc	10/13	0.76629154730767	2	FACETS	0.949	0.923	0.975	0.949	0.923	0.975	CLONAL	2	TRUE	0	0.769836721668821	2		403	709	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275399	142275399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202162034	NA	P-0003080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	59	188	0	ENST00000350721.4:c.1904G>A	p.Arg635Gln	p.R635Q	ENST00000350721	NM_001184.3	635	cGa/cAa	9/47	0.769836721668821	5	FACETS	0.479	0.411	0.552	0.12	0.102	0.138	SUBCLONAL	1	TRUE	1	0.769836721668821	5		188	690	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280209	142280209	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs777982083	NA	P-0003080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	942	353	1	ENST00000350721.4:c.1225G>T	p.Glu409Ter	p.E409*	ENST00000350721	NM_001184.3	409	Gag/Tag	5/47	0.769836721668821	5	FACETS	0.982	0.961	1	0.982	0.961	1	CLONAL	4	TRUE	1	0.769836721668821	5		354	1342	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582020	189582020	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	689	283	0	ENST00000264731.3:c.580-1G>A		p.X194_splice	ENST00000264731	NM_003722.4	194			0.769836721668821	3	FACETS	0.859	0.838	0.88			1	CLONAL	3	TRUE	NA	0.769836721668821	3		283	962	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412729	139412729	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	210	224	0	ENST00000277541.6:c.1115T>G	p.Leu372Arg	p.L372R	ENST00000277541	NM_017617.3	372	cTc/cGc	7/34	0.769836721668821	1	FACETS	0.948	0.898	0.997	0.948	0.898	0.997	CLONAL	1	TRUE	0	0.769836721668821	1		224	354	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404855	70404855	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	94	341	0	ENST00000373644.4:c.2369C>T	p.Ser790Phe	p.S790F	ENST00000373644	NM_030625.2	790	tCt/tTt	4/12	0.360297427437639	1	FACETS	0.275	0.245	0.306	0.275	0.245	0.306	INDETERMINATE	1	TRUE	0	0.769836721668821	1		341	547	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047132	77047132	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	134	392	0	ENST00000356341.3:c.1412G>A	p.Arg471Lys	p.R471K	ENST00000356341	NM_002576.4	471	aGa/aAa	13/15	NA	2	FACETS	0.468	0.425	0.513			1	INDETERMINATE	1	TRUE	NA	0.769836721668821	2		392	744	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245532	46245532	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	97	228	0	ENST00000334344.6:c.3626G>C	p.Gly1209Ala	p.G1209A	ENST00000334344	NM_152641.2	1209	gGa/gCa	15/21	1	2	FACETS	0.487	0.436	0.542	0.487	0.436	0.542	SUBCLONAL	1	TRUE	1	0.769836721668821	2		228	517	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0003101-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	76	308	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.707581302510086	2	FACETS	0.985	0.91	1	0.985	0.91	1	CLONAL	2	TRUE	0	0.707581302510086	2		308	109	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857047	9857047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568622613	NA	P-0003101-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	76	577	2	ENST00000330684.3:c.4354C>T	p.Arg1452Cys	p.R1452C	ENST00000330684	NM_001134407.1	1452	Cgc/Tgc	13/13	0.231516722938833	1	FACETS	0.793	0.713	0.875	0.793	0.713	0.875	INDETERMINATE	1	TRUE	0	0.707581302510086	1		579	175	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417868	138417868	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003101-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	59	380	0	ENST00000289153.2:c.1651T>C	p.Cys551Arg	p.C551R	ENST00000289153	NM_006219.2	551	Tgt/Cgt	11/22	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.707581302510086	2		380	134	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881505	48881505	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0003101-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	53	422	0	ENST00000267163.4:c.227T>G	p.Leu76Ter	p.L76*	ENST00000267163	NM_000321.2	76	tTa/tGa	2/27	0.576974030989908	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.707581302510086	1		422	88	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577043	7577046	+	frameshift_variant	Frame_Shift_Del	DEL	GCTC	GCTC	-	novel	NA	P-0003101-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	72	532	0	ENST00000269305.4:c.892_895del	p.Glu298CysfsTer46	p.E298Cfs*46	ENST00000269305	NM_001126112.2	298	GAGCtg/tg	8/11	0.707581302510086	1	FACETS	0.889	0.8	0.977	0.889	0.8	0.977	CLONAL	1	TRUE	0	0.707581302510086	1		532	148	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599333	55599333	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913682	NA	P-0003105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	332	243	0	ENST00000288135.5:c.2459A>T	p.Asp820Val	p.D820V	ENST00000288135	NM_000222.2	820	gAt/gTt	17/21	0.39191327985675	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.39191327985675	2		243	734	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398220	25398220	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	183	300	0	ENST00000311936.3:c.99T>A	p.Asp33Glu	p.D33E	ENST00000311936	NM_004985.3	33	gaT/gaA	2/5	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.39191327985675	2		300	879	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858648	9858648	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003139-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1169	341	611	0	ENST00000330684.3:c.2753C>A	p.Pro918His	p.P918H	ENST00000330684	NM_001134407.1	918	cCc/cAc	13/13	0.279700003190087	5	FACETS	1	0.987	1	0.573	0.541	0.606	CLONAL	2	FALSE	1	0.279700003190087	5		611	1510	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	80	124	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.281050194364721	3	FACETS	0.981	0.871	1	0.981	0.871	1	CLONAL	2	TRUE	1	0.281050194364721	3		124	331	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	90	344	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.20938518043034	3	FACETS	1	0.931	1	0.356	0.316	0.399	CLONAL	1	TRUE	0	0.281050194364721	3		344	684	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158304	106158304	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	49	391	0	ENST00000380013.4:c.3205A>C	p.Thr1069Pro	p.T1069P	ENST00000380013	NM_001127208.2	1069	Acc/Ccc	3/11	1	2	FACETS	0.445	0.375	0.521	0.445	0.375	0.521	SUBCLONAL	1	TRUE	1	0.281050194364721	2		391	784	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391373	139391373	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	28	276	0	ENST00000277541.6:c.6818T>C	p.Leu2273Pro	p.L2273P	ENST00000277541	NM_017617.3	2273	cTc/cCc	34/34	1	2	FACETS	0.369	0.294	0.455	0.369	0.294	0.455	SUBCLONAL	1	TRUE	1	0.281050194364721	2		276	540	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003179-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	83	124	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.267120504263989	5	FACETS	1	0.968	1	0.812	0.728	0.899	INDETERMINATE	2	FALSE	2	0.480835799587546	5		124	244	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003179-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	215	397	0	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	0.480835799587546	4	FACETS	0.78	0.726	0.835	0.78	0.726	0.835	SUBCLONAL	2	FALSE	2	0.480835799587546	4		397	849	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003179-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	216	354	0	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	0.297961923582976	5	FACETS	0.893	0.831	0.956	0.595	0.554	0.638	CLONAL	2	FALSE	2	0.480835799587546	5		354	866	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158456	26158456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs62623440	NA	P-0003179-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	279	337	0	ENST00000289316.2:c.59C>T	p.Thr20Ile	p.T20I	ENST00000289316	NM_138720.2	20	aCt/aTt	1/2	0.480835799587546	4	FACETS	0.904	0.85	0.958	0.904	0.85	0.958	CLONAL	2	FALSE	2	0.480835799587546	4		337	951	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93640003	93640003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003179-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	93	286	0	ENST00000375746.1:c.1332G>A	p.Trp444Ter	p.W444*	ENST00000375746	NM_001174167.1	444	tgG/tgA	10/14	0.288848229555507	4	FACETS	0.81	0.721	0.906	0.405	0.36	0.453	CLONAL	1	FALSE	2	0.480835799587546	4		286	707	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134043	41134043	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003179-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	195	696	0	ENST00000379561.5:c.1585C>T	p.Gln529Ter	p.Q529*	ENST00000379561	NM_002015.3	529	Cag/Tag	2/3	0.274216581230114	3	FACETS	0.788	0.728	0.851	0.394	0.364	0.426	INDETERMINATE	1	FALSE	1	0.480835799587546	3		696	1277	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129396	30129396	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003179-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	409	465	0	ENST00000263025.4:c.632G>C	p.Arg211Pro	p.R211P	ENST00000263025	NM_002746.2	211	cGg/cCg	4/9	0.297961923582976	5	FACETS	1	0.992	1	0.803	0.765	0.842	CLONAL	2	FALSE	2	0.480835799587546	5		465	1215	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576888	7576888	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0003179-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	549	355	0	ENST00000269305.4:c.958A>T	p.Lys320Ter	p.K320*	ENST00000269305	NM_001126112.2	320	Aag/Tag	9/11	0.474012034468842	4	FACETS	0.917	0.887	0.947			1	CLONAL	4	FALSE	NA	0.480835799587546	4		355	922	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937410	178937410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	92	70	0	ENST00000263967.3:c.1798G>A	p.Glu600Lys	p.E600K	ENST00000263967	NM_006218.2	600	Gaa/Aaa	12/21	0.334039013491408	6	FACETS	1	0.971	1	1	0.971	1	INDETERMINATE	3	TRUE	3	0.87594650023504	6		70	169	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467986	66467986	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	188	403	0	ENST00000273854.3:c.283C>T	p.Pro95Ser	p.P95S	ENST00000273854	NM_004439.5	95	Cct/Tct	3/18	0.87594650023504	3	FACETS	1	0.961	1	0.525	0.488	0.563	CLONAL	1	TRUE	1	0.87594650023504	3		403	588	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652025	36652025	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	374	410	0	ENST00000244741.5:c.147G>A	p.Trp49Ter	p.W49*	ENST00000244741	NM_000389.4	49	tgG/tgA	2/3	0.875265155192956	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.87594650023504	2		410	424	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735470	40735470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761910971	NA	P-0003195-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	57	362	1	ENST00000373198.4:c.3403G>A	p.Val1135Met	p.V1135M	ENST00000373198	NM_133170.3	1135	Gtg/Atg	25/32	0.199828589965787	3	FACETS	0.785	0.675	0.904	0.392	0.337	0.452	INDETERMINATE	1	TRUE	1	0.396467283350609	3		363	439	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410051	139410051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61755997	NA	P-0003195-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	48	310	2	ENST00000277541.6:c.1787C>T	p.Thr596Met	p.T596M	ENST00000277541	NM_017617.3	596	aCg/aTg	11/34	1	2	FACETS	0.585	0.495	0.683	0.585	0.495	0.683	SUBCLONAL	1	TRUE	1	0.396467283350609	2		312	414	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625269	69625269	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003195-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	30	360	0	ENST00000334134.2:c.524C>A	p.Ser175Tyr	p.S175Y	ENST00000334134	NM_005247.2	175	tCc/tAc	3/3	1	2	FACETS	0.361	0.291	0.441	0.361	0.291	0.441	SUBCLONAL	1	TRUE	1	0.396467283350609	2		360	419	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106910	11106910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003195-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	33	280	0	ENST00000358026.2:c.1615C>T	p.Arg539Cys	p.R539C	ENST00000358026	NM_001128849.1	539	Cgc/Tgc	10/36	0.274186286849196	1	FACETS	0.375	0.306	0.453	0.375	0.306	0.453	SUBCLONAL	1	TRUE	0	0.396467283350609	1		280	356	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343453	70343453	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003195-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	30	361	0	ENST00000374080.3:c.1627G>A	p.Glu543Lys	p.E543K	ENST00000374080		543	Gaa/Aaa	12/45	0.274186286849196	1	FACETS	0.253	0.203	0.309	0.253	0.203	0.309	SUBCLONAL	1	TRUE	0	0.396467283350609	1		361	480	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911686	32911686	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs397507657	NA	P-0003195-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	115	463	0	ENST00000380152.3:c.3195del	p.Asn1066IlefsTer11	p.N1066Ifs*11	ENST00000380152		1065	aTt/at	11/27	0.396467283350609	0	FACETS	0.703	0.636	0.773			1	SUBCLONAL	1	TRUE	0	0.396467283350609	0		463	498	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16097831	16097837	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTGTT	CTTTGTT	-	novel	NA	P-0003195-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	64	223	0	ENST00000268712.3:c.47_53del	p.Glu16ValfsTer33	p.E16Vfs*33	ENST00000268712	NM_006311.3	16	gAACAAAGt/gt	2/46	0.396467283350609	1	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	0	0.396467283350609	1		223	248	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0003204-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	326	562	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.237767266329415	9	FACETS	1	0.99	1	1	0.997	1	CLONAL	13	TRUE	0	0.237767266329415	9		564	375	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003204-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	95	283	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.237767266329415	1	FACETS	1	0.965	1	1	0.991	1	CLONAL	3	TRUE	0	0.237767266329415	1		283	209	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61197625	61197625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149277592	NA	P-0003204-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	98	333	0	ENST00000301761.2:c.7G>A	p.Val3Met	p.V3M	ENST00000301761	NM_017841.2	3	Gtg/Atg	1/4	0.237767266329415	5	FACETS	0.928	0.843	1			1	CLONAL	5	TRUE	NA	0.237767266329415	5		333	241	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188210	10188210	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs5030830	NA	P-0003205-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	121	346	0	ENST00000256474.2:c.353T>C	p.Leu118Pro	p.L118P	ENST00000256474	NM_000551.3	118	cTc/cCc	2/3	0.423936462287806	1	FACETS	0.941	0.855	1	0.941	0.855	1	CLONAL	1	TRUE	0	0.423936462287806	1		346	478	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003254-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	55	228	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.527877721021239	3	FACETS	1	0.958	1	0.64	0.555	0.729	CLONAL	1	TRUE	1	0.53075082201228	3		228	205	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0003254-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	291	269	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.405886742722473	5	FACETS	0.929	0.879	0.979			1	CLONAL	3	TRUE	NA	0.53075082201228	5		269	707	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174416	11174416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003254-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	118	410	2	ENST00000361445.4:c.7259C>T	p.Ala2420Val	p.A2420V	ENST00000361445	NM_004958.3	2420	gCc/gTc	53/58	1	2	FACETS	0.921	0.835	1	0.921	0.835	1	CLONAL	1	TRUE	1	0.53075082201228	2		412	483	SUCCESS
APC	324	MSKCC	GRCh37	5	112173995	112173995	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003254-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	199	310	0	ENST00000257430.4:c.2704G>T	p.Glu902Ter	p.E902*	ENST00000257430	NM_000038.5	902	Gaa/Taa	16/16	0.53075082201228	4	FACETS	0.983	0.916	1	0.983	0.916	1	CLONAL	2	TRUE	2	0.53075082201228	4		310	584	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851976	128851976	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003254-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	90	298	0	ENST00000249373.3:c.2048G>T	p.Cys683Phe	p.C683F	ENST00000249373	NM_005631.4	683	tGc/tTc	12/12	0.491117753171852	5	FACETS	0.832	0.738	0.933	0.277	0.246	0.311	CLONAL	1	TRUE	2	0.53075082201228	5		298	732	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751263	128751263	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003254-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	125	132	0	ENST00000377970.2:c.800C>A	p.Ser267Tyr	p.S267Y	ENST00000377970	NM_002467.4	267	tCt/tAt	2/3	0.53075082201228	4	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	2	0.53075082201228	4		132	344	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759979	133759979	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003254-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	236	409	0	ENST00000318560.5:c.2302G>C	p.Gly768Arg	p.G768R	ENST00000318560	NM_005157.4	768	Ggg/Cgg	11/11	0.53075082201228	4	FACETS	0.94	0.881	1	0.94	0.881	1	CLONAL	2	TRUE	2	0.53075082201228	4		409	724	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711350	114711350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243981730	NA	P-0003254-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	69	230	0	ENST00000543371.1:c.365C>T	p.Ser122Leu	p.S122L	ENST00000543371	NM_001198531.1	122	tCg/tTg	3/14	0.503621103833078	3	FACETS	1	0.914	1	0.526	0.461	0.594	CLONAL	1	TRUE	1	0.53075082201228	3		230	313	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5225773	5225773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1012604149	NA	P-0003254-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	122	317	0	ENST00000357368.4:c.2459G>A	p.Arg820His	p.R820H	ENST00000357368	NM_002850.3	820	cGc/cAc	17/38	0.503621103833078	3	FACETS	1	0.925	1	0.511	0.464	0.561	CLONAL	1	TRUE	1	0.53075082201228	3		317	569	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954290	17954290	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003254-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	237	347	0	ENST00000458235.1:c.319C>A	p.Pro107Thr	p.P107T	ENST00000458235	NM_000215.3	107	Ccc/Acc	4/24	0.503621103833078	3	FACETS	0.923	0.868	0.979	0.923	0.868	0.979	CLONAL	2	TRUE	1	0.53075082201228	3		347	612	SUCCESS
APC	324	MSKCC	GRCh37	5	112174909	112174909	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003254-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	193	392	0	ENST00000257430.4:c.3618del	p.Ser1206ArgfsTer59	p.S1206Rfs*59	ENST00000257430	NM_000038.5	1206	agT/ag	16/16	0.53075082201228	4	FACETS	0.893	0.831	0.958	0.893	0.831	0.958	CLONAL	2	TRUE	2	0.53075082201228	4		392	623	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0003276-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	524	373	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.558251330054672	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.558251330054672	2		373	936	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579369	7579369	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555526581	NA	P-0003276-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	146	196	0	ENST00000269305.4:c.318C>G	p.Ser106Arg	p.S106R	ENST00000269305	NM_001126112.2	106	agC/agG	4/11	0.558251330054672	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.558251330054672	1		196	364	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245033	46245033	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs139789595	NA	P-0003276-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	525	375	0	ENST00000334344.6:c.3127C>T	p.Gln1043Ter	p.Q1043*	ENST00000334344	NM_152641.2	1043	Caa/Taa	15/21	0.558251330054672	2	FACETS	0.988	0.953	1	0.988	0.953	1	CLONAL	2	TRUE	0	0.558251330054672	2		375	952	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207019	1207054	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	ACCAGCCGCGCCGCAAGCGGGCCAAGCTCATCGGCA	ACCAGCCGCGCCGCAAGCGGGCCAAGCTCATCGGCA	-	novel	NA	P-0003276-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	245	171	0	ENST00000326873.7:c.108_143del	p.Tyr36_Lys48delinsTer	p.Y36_K48delins*	ENST00000326873	NM_000455.4	36	tACCAGCCGCGCCGCAAGCGGGCCAAGCTCATCGGCAag/tag	1/10	0.282645814555722	1	FACETS	1	0.994	1	1	0.994	1	INDETERMINATE	1	TRUE	0	0.558251330054672	1		171	447	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925652	114925654	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0003276-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	301	542	2	ENST00000543371.1:c.1734_1736del	p.Ser579del	p.S579del	ENST00000543371	NM_001198531.1	577	aCTTct/act	14/14	0.363937342073716	1	FACETS	0.758	0.715	0.803	0.758	0.715	0.803	SUBCLONAL	1	TRUE	0	0.558251330054672	1		544	1025	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599867	10599868	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0003276-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	325	386	0	ENST00000171111.5:c.1708_1708+1delinsTT		p.X570_splice	ENST00000171111	NM_203500.1	570		5/6	0.558251330054672	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.558251330054672	1		386	731	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937102	76937102	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs782062542	NA	P-0003335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	81	844	0	ENST00000373344.5:c.3646A>G	p.Ile1216Val	p.I1216V	ENST00000373344	NM_000489.3	1216	Ata/Gta	9/35	1	2	FACETS	0.928	0.83	1	0.928	0.83	1	CLONAL	1	TRUE	1	0.704177034497947	2		844	248	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367257	50367257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1245618829	NA	P-0003338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	31	297	0	ENST00000331340.3:c.64G>A	p.Asp22Asn	p.D22N	ENST00000331340	NM_006060.4	22	Gat/Aat	3/8	0.665980858439008	5	FACETS	0.399	0.322	0.487	0.133	0.107	0.163	SUBCLONAL	1	FALSE	2	0.705292156077138	5		297	453	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322774	30322774	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	14	245	0	ENST00000322652.5:c.1787C>A	p.Thr596Asn	p.T596N	ENST00000322652	NM_015355.2	596	aCc/aAc	14/16	0.484806848992689	3	FACETS	0.233	0.168	0.312	0.117	0.084	0.156	SUBCLONAL	1	FALSE	1	0.705292156077138	3		245	230	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0003357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	39	380	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.481782386862217	5	FACETS	0.926	0.785	1			1	CLONAL	2	FALSE	NA	0.704534269043681	5		380	123	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371785	55371785	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	18	50	1	ENST00000297316.4:c.475C>A	p.Leu159Met	p.L159M	ENST00000297316	NM_022454.3	159	Ctg/Atg	2/2	0.704534269043681	5	FACETS	0.762	0.589	0.952	0.508	0.393	0.635	CLONAL	2	FALSE	2	0.704534269043681	5		51	69	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607646	43607646	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	21	201	0	ENST00000355710.3:c.1622G>T	p.Cys541Phe	p.C541F	ENST00000355710	NM_020975.4	541	tGt/tTt	8/20	0.41594167846674	3	FACETS	0.74	0.579	0.92			1	INDETERMINATE	1	FALSE	NA	0.704534269043681	3		201	109	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1036375	1036375	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	26	396	0	ENST00000358495.3:c.403A>G	p.Lys135Glu	p.K135E	ENST00000358495	NM_134424.2	135	Aag/Gag	6/12	0.364063227619556	5	FACETS	1	0.874	1	0.375	0.301	0.457	INDETERMINATE	1	FALSE	2	0.704534269043681	5		396	135	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990661	7990661	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	29	352	0	ENST00000319144.4:c.100C>A	p.His34Asn	p.H34N	ENST00000319144	NM_001139.2	34	Cat/Aat	1/15	0.481782386862217	5	FACETS	1	0.905	1			1	CLONAL	1	FALSE	NA	0.704534269043681	5		352	142	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552158	29552158	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	17	264	0	ENST00000356175.3:c.1891G>T	p.Gly631Ter	p.G631*	ENST00000356175	NM_000267.3	631	Gga/Tga	17/57	0.704534269043681	4	FACETS	1	0.837	1	0.563	0.431	0.712	CLONAL	1	FALSE	2	0.704534269043681	4		264	73	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43745370	43745370	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003422-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	58	757	0	ENST00000523873.1:c.283G>T	p.Val95Leu	p.V95L	ENST00000523873		95	Gtg/Ttg	3/8	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.23	2		757	499	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962929	2962929	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003422-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	36	484	0	ENST00000396946.4:c.1979G>T	p.Arg660Leu	p.R660L	ENST00000396946	NM_032415.4	660	cGg/cTg	16/25	0.112188822285461	4	FACETS	1	0.908	1	0.583	0.481	0.698	INDETERMINATE	1	TRUE	2	0.23	4		484	330	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0003422-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	45	280	0	ENST00000397752.3:c.3028+1G>C		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.171636468548076	3	FACETS	1	0.906	1	0.727	0.619	0.844	CLONAL	2	TRUE	0	0.23	3		280	200	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8525035	8525035	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	92	341	1	ENST00000356435.5:c.569G>A	p.Gly190Glu	p.G190E	ENST00000356435		190	gGa/gAa	7/35	0.302880287074631	1	FACETS	0.432	0.385	0.483	0.432	0.385	0.483	INDETERMINATE	1	TRUE	0	0.53	1		342	590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs879253911	NA	P-0003450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	184	211	0	ENST00000269305.4:c.538G>T	p.Glu180Ter	p.E180*	ENST00000269305	NM_001126112.2	180	Gag/Tag	5/11	NA	2	FACETS	0.972	0.917	1			1	INDETERMINATE	2	TRUE	NA	0.600780302625361	2		211	315	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217781	2217781	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1468620969	NA	P-0003450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	219	364	0	ENST00000398665.3:c.2555A>C	p.Glu852Ala	p.E852A	ENST00000398665	NM_032482.2	852	gAg/gCg	22/28	0.364136520576205	5	FACETS	1	0.983	1	0.757	0.709	0.807	CLONAL	2	TRUE	2	0.600780302625361	5		364	610	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931464	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0003450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	14169	210	3	ENST00000374690.3:c.2105_2106delinsAT	p.Leu702His	p.L702H	ENST00000374690	NM_000044.3	702	cTC/cAT	4/8	0.600780302625361	28	FACETS	1	0.999	1			1	CLONAL	27	TRUE	NA	0.600780302625361	28		213	15335	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	9	228	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		228	220	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514067	69514067	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	34	363	0	ENST00000294312.3:c.614G>C	p.Gly205Ala	p.G205A	ENST00000294312	NM_005117.2	205	gGa/gCa	3/3	0.3	3	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	3		363	668	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514211	69514211	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	38	420	0	ENST00000294312.3:c.470G>C	p.Arg157Thr	p.R157T	ENST00000294312	NM_005117.2	157	aGa/aCa	3/3	0.3	3	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	3		420	747	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514332	69514332	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	31	301	0	ENST00000294312.3:c.349G>T	p.Glu117Ter	p.E117*	ENST00000294312	NM_005117.2	117	Gag/Tag	3/3	0.3	3	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	3		301	565	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0003475-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	197	301	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.672544650000747	4	FACETS	1	0.991	1	0.724	0.674	0.775	CLONAL	1	FALSE	2	0.810644759137572	4		301	608	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691039	NA	P-0003475-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	159	313	0	ENST00000269305.4:c.919+1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.368953845539532	3	FACETS	0.964	0.903	1	0.643	0.602	0.683	INDETERMINATE	2	FALSE	0	0.810644759137572	3		313	286	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0003475-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	116	378	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	0.810644759137572	3	FACETS	0.689	0.622	0.758	0.344	0.311	0.379	SUBCLONAL	1	FALSE	1	0.810644759137572	3		378	584	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790494	3790494	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867855180	NA	P-0003475-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	64	370	2	ENST00000262367.5:c.4039C>T	p.Arg1347Trp	p.R1347W	ENST00000262367	NM_004380.2	1347	Cgg/Tgg	24/31	NA	2	FACETS	0.371	0.322	0.423			1	INDETERMINATE	1	FALSE	NA	0.810644759137572	2		372	426	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56871638	56871638	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs199837299	NA	P-0003475-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	99	298	0	ENST00000308159.5:c.2018G>A	p.Arg673Gln	p.R673Q	ENST00000308159	NM_014669.4	673	cGg/cAg	18/22	0.596731239665881	3	FACETS	0.698	0.625	0.774	0.349	0.312	0.387	SUBCLONAL	1	FALSE	1	0.810644759137572	3		298	492	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119774	70119774	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0003475-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	248	372	0	ENST00000245479.2:c.776T>A	p.Leu259Ter	p.L259*	ENST00000245479	NM_000346.3	259	tTg/tAg	3/3	0.810644759137572	3	FACETS	1	0.982	1			1	CLONAL	2	FALSE	NA	0.810644759137572	3		372	405	SUCCESS
APC	324	MSKCC	GRCh37	5	112175761	112175761	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003475-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	146	386	0	ENST00000257430.4:c.4473del	p.Phe1491LeufsTer16	p.F1491Lfs*16	ENST00000257430	NM_000038.5	1490	caT/ca	16/16	0.810644759137572	3	FACETS	1	0.989	1	0.721	0.667	0.776	CLONAL	1	FALSE	1	0.810644759137572	3		386	351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578201	7578202	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0003484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	417	412	0	ENST00000269305.4:c.647_648del	p.Val216GlyfsTer5	p.V216Gfs*5	ENST00000269305	NM_001126112.2	216	gTG/g	6/11	0.840439371246666	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.840439371246666	1		412	548	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156729	20156729	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs757280897	NA	P-0003491-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	377	385	0	ENST00000379607.5:c.28A>G	p.Lys10Glu	p.K10E	ENST00000379607	NM_001412.3	10	Aaa/Gaa	2/7	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.602951695410839	2		385	1251	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224250	98224250	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003494-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	118	498	0	ENST00000331920.6:c.2591A>G	p.Glu864Gly	p.E864G	ENST00000331920	NM_000264.3	864	gAa/gGa	16/24	0.325227938167861	3	FACETS	0.484	0.435	0.535	0.242	0.217	0.268	INDETERMINATE	1	TRUE	1	0.643114532767269	3		498	1003	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0003531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	778	427	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.593456809325348	7	FACETS	0.908	0.881	0.934			1	CLONAL	5	TRUE	NA	0.593456809325348	7		427	1435	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032210	26032210	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	286	274	0	ENST00000244661.2:c.79C>T	p.Arg27Cys	p.R27C	ENST00000244661	NM_003537.3	27	Cgc/Tgc	1/1	0.593456809325348	4	FACETS	0.982	0.927	1	0.982	0.927	1	CLONAL	2	TRUE	2	0.593456809325348	4		274	782	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044488	5044488	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	313	396	0	ENST00000381652.3:c.436G>C	p.Asp146His	p.D146H	ENST00000381652	NM_004972.3	146	Gat/Cat	5/25	0.593456809325348	4	FACETS	0.896	0.847	0.946	0.896	0.847	0.946	CLONAL	2	TRUE	2	0.593456809325348	4		396	938	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0003531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	185	260	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	2	TRUE	NA	0.593456809325348	2		260	300	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677993	58677993	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761219249	NA	P-0003531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	205	155	0	ENST00000305921.3:c.218G>A	p.Arg73Gln	p.R73Q	ENST00000305921	NM_003620.3	73	cGa/cAa	1/6	0.593456809325348	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.593456809325348	4		155	457	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162552	47162552	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	212	227	0	ENST00000409792.3:c.3574del	p.Ala1192ProfsTer44	p.A1192Pfs*44	ENST00000409792	NM_014159.6	1192	Gcc/cc	3/21	0.593456809325348	2	FACETS	0.96	0.909	1	0.96	0.909	1	CLONAL	2	TRUE	0	0.593456809325348	2		227	372	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0003556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	75	345	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	0.799	0.704	0.899	0.799	0.704	0.899	SUBCLONAL	1	TRUE	1	0.490455025038049	2		345	383	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128748869	128748869	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	217	548	0	ENST00000377970.2:c.30G>C	p.Gln10His	p.Q10H	ENST00000377970	NM_002467.4	10	caG/caC	1/3	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.490455025038049	2		548	623	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499826	8499826	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	96	334	0	ENST00000356435.5:c.2143C>A	p.Pro715Thr	p.P715T	ENST00000356435		715	Cct/Act	14/35	0.173373681540532	5	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.490455025038049	5		334	521	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0003573-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	71	538	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.315069318455934	2		538	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577520	7577520	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1330865474	NA	P-0003573-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	60	338	0	ENST00000269305.4:c.761T>G	p.Ile254Ser	p.I254S	ENST00000269305	NM_001126112.2	254	aTc/aGc	7/11	0.315069318455934	1	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	0	0.315069318455934	1		338	302	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984963	55984963	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003575-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	69	364	0	ENST00000263923.4:c.166C>T	p.Gln56Ter	p.Q56*	ENST00000263923	NM_002253.2	56	Cag/Tag	3/30	0.509087359817886	1	FACETS	0.394	0.345	0.447	0.394	0.345	0.447	SUBCLONAL	1	TRUE	0	0.640169649935285	1		364	372	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222593	69222593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194693256	NA	P-0003575-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	65	337	0	ENST00000462284.1:c.566G>A	p.Arg189His	p.R189H	ENST00000462284	NM_002392.5	189	cGc/cAc	8/11	1	2	FACETS	0.389	0.337	0.445	0.389	0.337	0.445	SUBCLONAL	1	TRUE	1	0.640169649935285	2		337	522	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578532	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28934873	NA	P-0003575-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	271	187	0	ENST00000269305.4:c.398T>C	p.Met133Thr	p.M133T	ENST00000269305	NM_001126112.2	133	aTg/aCg	5/11	0.368779830987218	3	FACETS	0.983	0.944	1	1	0.995	1	INDETERMINATE	3	TRUE	1	0.640169649935285	3		187	379	SUCCESS
APC	324	MSKCC	GRCh37	5	112173730	112173730	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003575-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	227	301	0	ENST00000257430.4:c.2442del	p.Phe814LeufsTer6	p.F814Lfs*6	ENST00000257430	NM_000038.5	813	aaT/aa	16/16	0.602268429892444	3	FACETS	0.931	0.876	0.985	0.931	0.876	0.985	CLONAL	2	TRUE	1	0.640169649935285	3		301	503	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0003584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	179	269	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.272578004590067	3	FACETS	1	0.979	1			1	CLONAL	2	TRUE	NA	0.272578004590067	3		269	644	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440384	52440384	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	29	216	0	ENST00000460680.1:c.668A>T	p.Tyr223Phe	p.Y223F	ENST00000460680	NM_004656.3	223	tAc/tTc	9/17	1	2	FACETS	0.647	0.52	0.791	0.647	0.52	0.791	SUBCLONAL	1	TRUE	1	0.272578004590067	2		216	329	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391162	89391162	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	62	368	0	ENST00000336596.2:c.1228G>T	p.Asp410Tyr	p.D410Y	ENST00000336596	NM_005233.5	410	Gat/Tat	5/17	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.272578004590067	2		368	418	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538936	187538936	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	67	535	0	ENST00000441802.2:c.8804G>C	p.Gly2935Ala	p.G2935A	ENST00000441802	NM_005245.3	2935	gGg/gCg	10/27	1	2	FACETS	0.795	0.691	0.908	0.795	0.691	0.908	CLONAL	1	TRUE	1	0.272578004590067	2		535	618	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729881	41729881	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	86	719	0	ENST00000242208.4:c.648C>A	p.Ser216Arg	p.S216R	ENST00000242208	NM_002192.2	216	agC/agA	3/3	1	2	FACETS	0.909	0.804	1	0.909	0.804	1	CLONAL	1	TRUE	1	0.272578004590067	2		719	694	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230734	46230734	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	29	461	0	ENST00000334344.6:c.983G>T	p.Arg328Met	p.R328M	ENST00000334344	NM_152641.2	328	aGg/aTg	8/21	NA	2	FACETS	0.421	0.337	0.516			1	INDETERMINATE	1	TRUE	NA	0.272578004590067	2		461	506	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934087	39934087	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	25	503	0	ENST00000378444.4:c.512C>A	p.Pro171His	p.P171H	ENST00000378444	NM_001123385.1	171	cCt/cAt	4/15	0.272578004590067	1	FACETS	0.347	0.272	0.432	0.347	0.272	0.432	SUBCLONAL	1	TRUE	0	0.272578004590067	1		503	457	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038563	47038563	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0003584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	68	509	0	ENST00000377604.3:c.724+1G>T		p.X242_splice	ENST00000377604	NM_001204468.1	242			0.272578004590067	1	FACETS	0.83	0.724	0.945	0.83	0.724	0.945	CLONAL	1	TRUE	0	0.272578004590067	1		509	519	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410226	63410226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	32	435	0	ENST00000330258.3:c.2941G>A	p.Asp981Asn	p.D981N	ENST00000330258	NM_152424.3	981	Gac/Aac	2/2	0.241521974587967	1	FACETS	0.377	0.305	0.458	0.377	0.305	0.458	SUBCLONAL	1	TRUE	0	0.272578004590067	1		435	538	SUCCESS
AR	367	MSKCC	GRCh37	X	66766532	66766532	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	79	626	0	ENST00000374690.3:c.1544C>A	p.Pro515His	p.P515H	ENST00000374690	NM_000044.3	515	cCc/cAc	1/8	0.241521974587967	1	FACETS	0.764	0.672	0.863	0.764	0.672	0.863	SUBCLONAL	1	TRUE	0	0.272578004590067	1		626	655	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588875	29588876	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	TT	novel	NA	P-0003584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	60	412	0	ENST00000356175.3:c.4661_4661+1delinsTT		p.X1554_splice	ENST00000356175	NM_000267.3	1554		34/57	0.241521974587967	1	FACETS	0.809	0.698	0.929	0.809	0.698	0.929	CLONAL	1	TRUE	0	0.272578004590067	1		412	470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003592-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	175	500	0	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	0.372537630691515	1	FACETS	0.839	0.774	0.906	0.839	0.774	0.906	CLONAL	1	TRUE	0	0.44259969951315	1		500	734	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470497	25470497	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs758881009	NA	P-0003592-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	58	413	0	ENST00000264709.3:c.977G>T	p.Arg326Leu	p.R326L	ENST00000264709	NM_175629.2	326	cGc/cTc	8/23	0.368540386739832	3	FACETS	0.388	0.332	0.449	0.194	0.166	0.225	SUBCLONAL	1	TRUE	1	0.44259969951315	3		413	825	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349988	70349988	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003592-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	454	254	0	ENST00000374080.3:c.3971T>A	p.Ile1324Asn	p.I1324N	ENST00000374080		1324	aTt/aAt	28/45	0.428488285072682	2	FACETS	0.924	0.892	0.956			1	CLONAL	3	TRUE	NA	0.44259969951315	2		254	740	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0003602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	87	562	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.385307557333266	1	FACETS	0.962	0.858	1	0.962	0.858	1	CLONAL	1	TRUE	0	0.385307557333266	1		564	379	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30733024	30733024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	85	279	0	ENST00000295754.5:c.1637G>A	p.Arg546Lys	p.R546K	ENST00000295754	NM_003242.5	546	aGg/aAg	7/7	0.190464126298564	3	FACETS	1	0.976	1	0.692	0.616	0.773	INDETERMINATE	1	TRUE	1	0.385307557333266	3		279	380	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720808	89720808	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs1114167667	NA	P-0003602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	39	117	0	ENST00000371953.3:c.959T>G	p.Leu320Ter	p.L320*	ENST00000371953	NM_000314.4	320	tTa/tGa	8/9	0.385307557333266	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.385307557333266	1		117	120	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0003603-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	46	123	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.40447319118102	2		123	167	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99162464	99162464	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003603-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	30	256	0	ENST00000074304.5:c.982G>C	p.Asp328His	p.D328H	ENST00000074304	NM_001134224.1	328	Gat/Cat	12/26	0.26173431896188	3	FACETS	0.303	0.243	0.371	0.101	0.081	0.124	SUBCLONAL	1	TRUE	0	0.40447319118102	3		256	589	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527224	187527224	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003603-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	63	240	0	ENST00000441802.2:c.10350G>T	p.Gln3450His	p.Q3450H	ENST00000441802	NM_005245.3	3450	caG/caT	17/27	0.275027005801362	2	FACETS	0.735	0.637	0.84	0.367	0.318	0.42	SUBCLONAL	1	TRUE	0	0.40447319118102	2		240	424	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005006	150005006	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003603-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	76	265	0	ENST00000253339.5:c.1219C>T	p.Gln407Ter	p.Q407*	ENST00000253339		407	Cag/Tag	3/7	0.31848431131788	2	FACETS	0.75	0.659	0.847	0.375	0.329	0.424	SUBCLONAL	1	TRUE	0	0.40447319118102	2		265	501	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891642	28891642	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003603-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	39	373	2	ENST00000282397.4:c.3379C>A	p.Pro1127Thr	p.P1127T	ENST00000282397	NM_002019.4	1127	Cct/Act	25/30	0.372913023461752	1	FACETS	0.321	0.266	0.383	0.321	0.266	0.383	SUBCLONAL	1	TRUE	0	0.40447319118102	1		375	479	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944600	32944600	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs276174906	NA	P-0003603-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	143	491	1	ENST00000380152.3:c.8393C>G	p.Pro2798Arg	p.P2798R	ENST00000380152		2798	cCt/cGt	19/27	0.372913023461752	1	FACETS	0.755	0.689	0.824	0.755	0.689	0.824	SUBCLONAL	1	TRUE	0	0.40447319118102	1		492	747	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129108	2129108	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003603-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	66	329	0	ENST00000219476.3:c.3042C>G	p.Ser1014Arg	p.S1014R	ENST00000219476	NM_000548.3	1014	agC/agG	27/42	0.359549496597844	3	FACETS	0.633	0.549	0.723	0.316	0.274	0.362	SUBCLONAL	1	TRUE	1	0.40447319118102	3		329	620	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943751	9943751	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003603-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	25	226	0	ENST00000330684.3:c.1190C>A	p.Ser397Tyr	p.S397Y	ENST00000330684	NM_001134407.1	397	tCc/tAc	5/13	0.359549496597844	3	FACETS	0.306	0.241	0.382	0.153	0.12	0.191	SUBCLONAL	1	TRUE	1	0.40447319118102	3		226	485	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912103	50912103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237089094	NA	P-0003603-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	116	635	0	ENST00000440232.2:c.1837G>A	p.Ala613Thr	p.A613T	ENST00000440232	NM_002691.3	613	Gcc/Acc	15/27	1	2	FACETS	0.746	0.672	0.824	0.746	0.672	0.824	SUBCLONAL	1	TRUE	1	0.40447319118102	2		635	769	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058094	27058098	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTA	AGGTA	-	novel	NA	P-0003603-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	13	87	0	ENST00000324856.7:c.1803+1_1803+5del		p.X601_splice	ENST00000324856	NM_006015.4	601		3/20	0.283377307684083	1	FACETS	0.331	0.237	0.445	0.331	0.237	0.445	SUBCLONAL	1	TRUE	0	0.40447319118102	1		87	155	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879062	151879100	+	inframe_deletion	In_Frame_Del	DEL	GTCATTATTTGTCGTGGAAGAAGAACATAAATCTCTGAC	GTCATTATTTGTCGTGGAAGAAGAACATAAATCTCTGAC	-	novel	NA	P-0003603-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	71	241	0	ENST00000262189.6:c.5845_5883del	p.Val1949_Asp1961del	p.V1949_D1961del	ENST00000262189	NM_170606.2	1949	GTCAGAGATTTATGTTCTTCTTCCACGACAAATAATGAC/-	36/59	1	2	FACETS	0.82	0.719	0.929	0.82	0.719	0.929	CLONAL	1	TRUE	1	0.40447319118102	2		241	428	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910937	32910937	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80359330	NA	P-0003603-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	129	588	0	ENST00000380152.3:c.2446del	p.Glu816LysfsTer9	p.E816Kfs*9	ENST00000380152		815	atG/at	11/27	0.372913023461752	1	FACETS	0.618	0.56	0.678	0.618	0.56	0.678	SUBCLONAL	1	TRUE	0	0.40447319118102	1		588	824	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579406	7579406	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	72	240	0	ENST00000269305.4:c.281C>A	p.Ser94Ter	p.S94*	ENST00000269305	NM_001126112.2	94	tCa/tAa	4/11	0.393462405782488	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.393462405782488	1		240	247	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302857	15302857	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	94	308	0	ENST00000263388.2:c.593C>G	p.Ala198Gly	p.A198G	ENST00000263388	NM_000435.2	198	gCg/gGg	4/33	0.393462405782488	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.393462405782488	1		308	308	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117639399	117639399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003631-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	47	531	1	ENST00000368508.3:c.5957C>T	p.Ser1986Phe	p.S1986F	ENST00000368508	NM_002944.2	1986	tCc/tTc	37/43	0.3	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		532	463	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096192	71096192	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	78	356	0	ENST00000318789.4:c.565C>T	p.Gln189Ter	p.Q189*	ENST00000318789	NM_032682.5	189	Cag/Tag	10/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		356	565	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045804	26045804	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1415819059	NA	P-0003637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	95	1014	0	ENST00000540144.1:c.166C>T	p.Gln56Ter	p.Q56*	ENST00000540144	NM_003531.2	56	Cag/Tag	1/1	0.227519326074845	4	FACETS		NA	1			1	NA	NA	FALSE	2	NA	4		1014	735	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696431	47696431	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	26	549	0	ENST00000347630.2:c.392G>T	p.Trp131Leu	p.W131L	ENST00000347630	NM_001007230.1	131	tGg/tTg	6/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		549	515	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	91	210	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.332404996128376	1	FACETS	0.888	0.793	0.989	0.888	0.793	0.989	CLONAL	1	TRUE	0	0.376346010963123	1		210	442	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940405	49940405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	111	499	0	ENST00000296474.3:c.638C>T	p.Pro213Leu	p.P213L	ENST00000296474	NM_002447.2	213	cCa/cTa	1/20	1	2	FACETS	0.48	0.43	0.533	0.48	0.43	0.533	SUBCLONAL	1	TRUE	1	0.376346010963123	2		499	1229	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32920982	32920982	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	42	222	0	ENST00000380152.3:c.6956G>T	p.Arg2319Ile	p.R2319I	ENST00000380152		2319	aGa/aTa	13/27	1	2	FACETS	0.752	0.63	0.884	0.752	0.63	0.884	SUBCLONAL	1	TRUE	1	0.376346010963123	2		222	297	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961360	54961360	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	294	188	2	ENST00000312783.6:c.272C>A	p.Pro91Gln	p.P91Q	ENST00000312783	NM_198436.1	91	cCa/cAa	4/10	0.376346010963123	7	FACETS	1	0.984	1			1	CLONAL	3	TRUE	NA	0.376346010963123	7		190	909	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961430	54961430	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	112	88	0	ENST00000312783.6:c.202C>G	p.His68Asp	p.H68D	ENST00000312783	NM_198436.1	68	Cac/Gac	4/10	0.376346010963123	7	FACETS	0.965	0.875	1			1	CLONAL	3	TRUE	NA	0.376346010963123	7		88	399	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961474	54961474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	203	177	0	ENST00000312783.6:c.158C>T	p.Ser53Phe	p.S53F	ENST00000312783	NM_198436.1	53	tCt/tTt	4/10	0.376346010963123	7	FACETS	0.894	0.831	0.959			1	CLONAL	3	TRUE	NA	0.376346010963123	7		177	781	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961480	54961480	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	217	197	0	ENST00000312783.6:c.152C>T	p.Ser51Leu	p.S51L	ENST00000312783	NM_198436.1	51	tCa/tTa	4/10	0.376346010963123	7	FACETS	0.892	0.831	0.955			1	CLONAL	3	TRUE	NA	0.376346010963123	7		197	836	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0003708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	566	427	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.649358958661365	5	FACETS	1	0.974	1	1	0.974	1	CLONAL	4	TRUE	1	0.649358958661365	5		427	857	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704583	117704583	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	137	524	0	ENST00000368508.3:c.2393G>T	p.Gly798Val	p.G798V	ENST00000368508	NM_002944.2	798	gGt/gTt	16/43	0.61476661159126	3	FACETS	0.962	0.879	1	0.481	0.439	0.525	CLONAL	1	TRUE	1	0.649358958661365	3		524	581	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0003727-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	270	395	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.751099344709891	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.76992980044808	3		396	308	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411884	116411903	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTTTCTCTCTGTTTTAAGA	TCTTTCTCTCTGTTTTAAGA	-	novel	NA	P-0003735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	48	266	0	ENST00000397752.3:c.2888-16_2891del		p.X963_splice	ENST00000397752	NM_000245.2	963		14/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		266	320	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0003774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	362	373	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.507963918880905	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.507963918880905	2		373	706	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0003774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	237	319	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.507963918880905	1	FACETS	0.979	0.918	1	0.979	0.918	1	CLONAL	1	TRUE	0	0.507963918880905	1		319	711	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165602	118165602	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs921184290	NA	P-0003774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	138	226	0	ENST00000369448.3:c.112C>T	p.Arg38Ter	p.R38*	ENST00000369448	NM_017709.3	38	Cga/Tga	2/2	1	2	FACETS	0.958	0.876	1	0.958	0.876	1	CLONAL	1	TRUE	1	0.507963918880905	2		226	567	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713506	30713506	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	101	170	0	ENST00000295754.5:c.831G>C	p.Lys277Asn	p.K277N	ENST00000295754	NM_003242.5	277	aaG/aaC	4/7	0.507963918880905	1	FACETS	0.942	0.852	1	0.942	0.852	1	CLONAL	1	TRUE	0	0.507963918880905	1		170	315	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59770823	59770823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374334794	NA	P-0003774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	163	330	1	ENST00000259008.2:c.2543G>A	p.Arg848His	p.R848H	ENST00000259008	NM_032043.2	848	cGc/cAc	18/20	1	2	FACETS	0.949	0.874	1	0.949	0.874	1	CLONAL	1	TRUE	1	0.507963918880905	2		331	676	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0003802-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	119	171	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.255183218447574	2	FACETS	0.965	0.876	1	0.965	0.876	1	CLONAL	2	TRUE	0	0.264703780761991	2		172	466	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0003802-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	92	299	1	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.264703780761991	2		300	596	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088729	27088729	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003802-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	72	291	0	ENST00000324856.7:c.2338C>T	p.Gln780Ter	p.Q780*	ENST00000324856	NM_006015.4	780	Cag/Tag	7/20	1	2	FACETS	0.928	0.812	1	0.928	0.812	1	CLONAL	1	TRUE	1	0.264703780761991	2		291	586	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412967	49412967	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003802-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	119	426	0	ENST00000418115.1:c.56C>G	p.Thr19Arg	p.T19R	ENST00000418115	NM_001664.2	19	aCa/aGa	2/5	1	2	FACETS	0.941	0.849	1	0.941	0.849	1	CLONAL	1	TRUE	1	0.264703780761991	2		426	955	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279674	123279674	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs77543610	NA	P-0003802-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	57	112	1	ENST00000358487.5:c.758C>G	p.Pro253Arg	p.P253R	ENST00000358487	NM_000141.4	253	cCt/cGt	7/18	0.255183218447574	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	2	TRUE	0	0.264703780761991	2		113	209	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654643	67654643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs968244943	NA	P-0003802-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	133	345	0	ENST00000264010.4:c.1130G>A	p.Arg377His	p.R377H	ENST00000264010	NM_006565.3	377	cGt/cAt	6/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.264703780761991	2		345	766	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591108	67591125	+	inframe_deletion	In_Frame_Del	DEL	ACCAGACCTTATCCAGCT	ACCAGACCTTATCCAGCT	-	novel	NA	P-0003802-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	45	216	0	ENST00000274335.5:c.1701_1718del	p.Pro568_Leu573del	p.P568_L573del	ENST00000274335		567	aaACCAGACCTTATCCAGCTg/aag	12/15	1	2	FACETS	0.659	0.554	0.775	0.659	0.554	0.775	SUBCLONAL	1	TRUE	1	0.264703780761991	2		216	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0003816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	377	370	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.48448623648403	3	FACETS	0.995	0.955	1	0.995	0.955	1	CLONAL	3	FALSE	0	0.482373354362334	3		370	650	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458562	120458562	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	42	284	0	ENST00000256646.2:c.6783G>C	p.Glu2261Asp	p.E2261D	ENST00000256646	NM_024408.3	2261	gaG/gaC	34/34	0.342498706588639	6	FACETS	0.483	0.402	0.574	0.121	0.1	0.144	SUBCLONAL	1	FALSE	2	0.482373354362334	6		284	708	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77060289	77060289	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	182	279	0	ENST00000356341.3:c.880C>G	p.Gln294Glu	p.Q294E	ENST00000356341	NM_002576.4	294	Cag/Gag	9/15	0.358198610170871	4	FACETS	0.784	0.726	0.845	0.784	0.726	0.845	SUBCLONAL	2	FALSE	2	0.482373354362334	4		279	713	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129683	30129683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	78	513	0	ENST00000263025.4:c.530C>T	p.Thr177Ile	p.T177I	ENST00000263025	NM_002746.2	177	aCc/aTc	3/9	0.45741043822141	5	FACETS	0.59	0.517	0.669	0.118	0.103	0.134	SUBCLONAL	1	FALSE	0	0.482373354362334	5		513	944	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533761	63533764	+	frameshift_variant	Frame_Shift_Del	DEL	GGGA	GGGA	-	novel	NA	P-0003816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	65	239	0	ENST00000307078.5:c.1390_1393del	p.Ser464AlafsTer42	p.S464Afs*42	ENST00000307078	NM_004655.3	464	TCCCgc/gc	6/11	0.215355899393808	4	FACETS	0.977	0.85	1			1	INDETERMINATE	1	FALSE	NA	0.482373354362334	4		239	409	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164066	108164078	+	frameshift_variant	Frame_Shift_Del	DEL	GATAGATAACAAG	GATAGATAACAAG	-	novel	NA	P-0003816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	35	256	0	ENST00000278616.4:c.4642_4654del	p.Asp1548MetfsTer11	p.D1548Mfs*11	ENST00000278616	NM_000051.3	1546	gtGATAGATAACAAG/gt	31/63	0.474238507103946	2	FACETS	0.377	0.309	0.453	0.188	0.154	0.227	SUBCLONAL	1	FALSE	0	0.482373354362334	2		256	385	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448564	89448564	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1184230536	NA	P-0003830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	28	273	0	ENST00000336596.2:c.1528C>T	p.Arg510Ter	p.R510*	ENST00000336596	NM_005233.5	510	Cga/Tga	7/17	0.548839428026461	3	FACETS	0.36	0.288	0.442	0.18	0.144	0.221	SUBCLONAL	1	TRUE	1	0.637397643478628	3		273	322	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993681	72993681	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1169166147	NA	P-0003830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	71	352	0	ENST00000268489.5:c.364G>A	p.Glu122Lys	p.E122K	ENST00000268489	NM_006885.3	122	Gag/Aag	2/10	0.637397643478628	1	FACETS	0.453	0.398	0.511	0.453	0.398	0.511	SUBCLONAL	1	TRUE	0	0.637397643478628	1		352	335	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523525	41523525	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	87	233	1	ENST00000263253.7:c.941G>T	p.Gly314Val	p.G314V	ENST00000263253	NM_001429.3	314	gGc/gTc	4/31	1	2	FACETS	0.978	0.878	1	0.978	0.878	1	CLONAL	1	TRUE	1	0.637397643478628	2		234	279	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535442	66535442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	209	86	0	ENST00000273854.3:c.19C>T	p.Arg7Trp	p.R7W	ENST00000273854	NM_004439.5	7	Cgg/Tgg	1/18	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.798694088168813	2		86	434	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509978	106509978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764518673	NA	P-0003864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	216	286	0	ENST00000359195.3:c.1972C>T	p.His658Tyr	p.H658Y	ENST00000359195	NM_002649.2	658	Cat/Tat	2/11	1	2	FACETS	0.891	0.834	0.949	0.891	0.834	0.949	CLONAL	1	TRUE	1	0.798694088168813	2		286	607	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835937	151835937	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	341	394	0	ENST00000262189.6:c.14587G>A	p.Glu4863Lys	p.E4863K	ENST00000262189	NM_170606.2	4863	Gag/Aag	58/59	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.798694088168813	2		394	835	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244298	46244298	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	257	326	0	ENST00000334344.6:c.2392C>T	p.Gln798Ter	p.Q798*	ENST00000334344	NM_152641.2	798	Cag/Tag	15/21	1	2	FACETS	0.87	0.818	0.922	0.87	0.818	0.922	CLONAL	1	TRUE	1	0.798694088168813	2		326	740	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856445	111856445	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	323	140	0	ENST00000341259.2:c.496C>T	p.Pro166Ser	p.P166S	ENST00000341259	NM_005475.2	166	Ccc/Tcc	2/8	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.798694088168813	2		140	707	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856464	111856464	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763418967	NA	P-0003864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	345	151	0	ENST00000341259.2:c.515C>A	p.Thr172Asn	p.T172N	ENST00000341259	NM_005475.2	172	aCc/aAc	2/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.798694088168813	2		151	794	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62009584	62009584	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	417	297	0	ENST00000392795.3:c.38G>A	p.Trp13Ter	p.W13*	ENST00000392795	NM_001039933.1	13	tGg/tAg	1/6	0.211618735641075	3	FACETS	1	0.995	1	0.663	0.633	0.694	INDETERMINATE	1	TRUE	1	0.798694088168813	3		297	1102	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0003998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	219	344	0	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	0.577242117714276	2	FACETS	0.845	0.796	0.894	0.845	0.796	0.894	CLONAL	2	TRUE	0	0.577242117714276	2		344	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578412	7578412	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519747	NA	P-0003998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	225	169	0	ENST00000269305.4:c.518T>C	p.Val173Ala	p.V173A	ENST00000269305	NM_001126112.2	173	gTg/gCg	5/11	0.514243595017508	4	FACETS	1	0.988	1	0.844	0.803	0.886	CLONAL	3	TRUE	0	0.577242117714276	4		169	364	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061227	38061227	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	396	243	0	ENST00000250448.2:c.762C>G	p.Phe254Leu	p.F254L	ENST00000250448	NM_004496.3	254	ttC/ttG	2/2	0.577242117714276	6	FACETS	0.931	0.891	0.97	0.931	0.891	0.97	CLONAL	4	TRUE	2	0.577242117714276	6		243	794	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0004020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	152	724	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.212263955276611	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.212263955276611	2		724	654	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798590	45798590	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	53	189	0	ENST00000450313.1:c.504G>T	p.Glu168Asp	p.E168D	ENST00000450313	NM_012222.2	168	gaG/gaT	6/16	1	2	FACETS	0.972	0.829	1	0.972	0.829	1	CLONAL	1	TRUE	1	0.212263955276611	2		189	514	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922322	178922322	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	47	179	0	ENST00000263967.3:c.1091G>C	p.Gly364Ala	p.G364A	ENST00000263967	NM_006218.2	364	gGa/gCa	6/21	1	2	FACETS	0.798	0.673	0.936	0.798	0.673	0.936	CLONAL	1	TRUE	1	0.212263955276611	2		179	555	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7126618	7126618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	75	156	0	ENST00000302850.5:c.2990C>T	p.Pro997Leu	p.P997L	ENST00000302850	NM_000208.2	997	cCt/cTt	16/22	0.212263955276611	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.212263955276611	1		156	444	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045872	47045872	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0004020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	151	218	0	ENST00000377604.3:c.2668-1G>T		p.X890_splice	ENST00000377604	NM_001204468.1	890			0.210103518389306	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.212263955276611	2		218	666	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36814382	36814382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	10	412	0	ENST00000373129.3:c.658G>A	p.Gly220Arg	p.G220R	ENST00000373129	NM_032017.1	220	Ggg/Agg	8/12	0.15559404246529	3	FACETS	0.447	0.303	0.626	0.223	0.151	0.313	INDETERMINATE	1	TRUE	1	0.345331531374611	3		412	152	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233086	66233087	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	A	novel	NA	P-0004039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	10	242	0	ENST00000273854.3:c.1912_1913delinsT	p.His638LeufsTer10	p.H638Lfs*10	ENST00000273854	NM_004439.5	638	CAt/Tt	10/18	0.15559404246529	3	FACETS	0.672	0.459	0.935	0.336	0.229	0.468	INDETERMINATE	1	TRUE	1	0.345331531374611	3		242	101	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0004067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	951	724	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.572313666327281	7	FACETS	0.947	0.926	0.969	0.947	0.926	0.969	CLONAL	6	TRUE	1	0.572313666327281	7		724	1421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0004067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	189	466	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.572313666327281	3	FACETS	0.972	0.909	1	0.972	0.909	1	CLONAL	2	TRUE	1	0.572313666327281	3		466	437	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798461	45798461	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779997419	NA	P-0004067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	548	357	0	ENST00000450313.1:c.550C>T	p.Arg184Trp	p.R184W	ENST00000450313	NM_012222.2	184	Cgg/Tgg	7/16	0.381050167208897	3	FACETS	1	0.981	1			1	CLONAL	3	TRUE	NA	0.572313666327281	3		357	810	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465650	8465650	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763141884	NA	P-0004067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	205	276	0	ENST00000356435.5:c.3530G>T	p.Arg1177Leu	p.R1177L	ENST00000356435		1177	cGc/cTc	21/35	0.572313666327281	4	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.572313666327281	4		276	907	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486222	8486222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	367	226	0	ENST00000356435.5:c.2595G>A	p.Met865Ile	p.M865I	ENST00000356435		865	atG/atA	17/35	0.572313666327281	4	FACETS	0.89	0.851	0.93			1	CLONAL	3	TRUE	NA	0.572313666327281	4		226	755	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18576880	18576880	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1257	174	297	0	ENST00000266497.5:c.2288C>T	p.Ala763Val	p.A763V	ENST00000266497		763	gCt/gTt	16/31	0.572313666327281	7	FACETS	1	0.942	1	0.172	0.158	0.187	CLONAL	1	TRUE	1	0.572313666327281	7		297	1431	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993789	72993789	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	155	286	0	ENST00000268489.5:c.256G>T	p.Ala86Ser	p.A86S	ENST00000268489	NM_006885.3	86	Gcc/Tcc	2/10	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.572313666327281	2		286	531	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321324	1321324	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	183	210	0	ENST00000400841.2:c.431G>C	p.Gly144Ala	p.G144A	ENST00000400841		144	gGg/gCg	4/6	0.572313666327281	2	FACETS	0.795	0.744	0.847	0.795	0.744	0.847	SUBCLONAL	2	TRUE	0	0.572313666327281	2		210	402	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045025	47045025	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	266	294	0	ENST00000377604.3:c.2351A>T	p.His784Leu	p.H784L	ENST00000377604	NM_001204468.1	784	cAc/cTc	20/24	0.572313666327281	2	FACETS	0.962	0.915	1	0.962	0.915	1	CLONAL	2	TRUE	0	0.572313666327281	2		294	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0004067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	84	156	0	ENST00000269305.4:c.375+1del		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.572313666327281	3	FACETS	1	0.937	1	0.538	0.479	0.6	CLONAL	1	TRUE	1	0.572313666327281	3		156	351	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491645	56491645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004086-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	100	283	0	ENST00000267101.3:c.2537G>T	p.Ser846Ile	p.S846I	ENST00000267101	NM_001982.3	846	aGt/aTt	21/28	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.325565646295965	2		283	562	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004086-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	51	181	0	ENST00000269305.4:c.383del	p.Pro128LeufsTer42	p.P128Lfs*42	ENST00000269305	NM_001126112.2	128	cCt/ct	5/11	0.26512302959652	1	FACETS	0.944	0.808	1	0.944	0.808	1	CLONAL	1	TRUE	0	0.325565646295965	1		181	278	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231286	98231286	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752043221	NA	P-0004086-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	55	179	0	ENST00000331920.6:c.1997C>T	p.Thr666Met	p.T666M	ENST00000331920	NM_000264.3	666	aCg/aTg	14/24	1	2	FACETS	0.918	0.789	1	0.918	0.789	1	CLONAL	1	TRUE	1	0.325565646295965	2		179	368	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440879	52440882	+	frameshift_variant	Frame_Shift_Del	DEL	CCCG	CCCG	-	novel	NA	P-0004086-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	128	289	0	ENST00000460680.1:c.622_625del	p.Arg208SerfsTer22	p.R208Sfs*22	ENST00000460680	NM_004656.3	208	CGGGtc/tc	8/17	0.281978909678744	2	FACETS	0.806	0.735	0.88	0.806	0.735	0.88	CLONAL	2	TRUE	0	0.325565646295965	2		289	488	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056425	26056427	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	rs774779034	NA	P-0004086-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	46	170	0	ENST00000343677.2:c.230_232del	p.Asn77del	p.N77del	ENST00000343677	NM_005319.3	77	aACAgc/agc	1/1	1	2	FACETS	0.719	0.607	0.842	0.719	0.607	0.842	SUBCLONAL	1	TRUE	1	0.325565646295965	2		170	393	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202963	16202963	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs764161970	NA	P-0004095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	34	158	0	ENST00000375759.3:c.671T>C	p.Ile224Thr	p.I224T	ENST00000375759	NM_015001.2	224	aTt/aCt	3/15	1	2	FACETS	0.388	0.316	0.469	0.388	0.316	0.469	SUBCLONAL	1	TRUE	1	0.317427306123596	2		158	552	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025868	48025868	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs752135996	NA	P-0004095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	67	216	0	ENST00000234420.5:c.746G>C	p.Arg249Thr	p.R249T	ENST00000234420	NM_000179.2	249	aGg/aCg	4/10	0.317427306123596	3	FACETS	0.608	0.527	0.695	0.304	0.263	0.348	SUBCLONAL	1	TRUE	1	0.317427306123596	3		216	805	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249909	110249959	+	inframe_deletion	In_Frame_Del	DEL	CAGGGCTGCCTTTGCTGACGCTGATGACCGACGGGCTGCCGTACTCGCTGC	CAGGGCTGCCTTTGCTGACGCTGATGACCGACGGGCTGCCGTACTCGCTGC	-	rs869299423	NA	P-0004095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	43	78	0	ENST00000374672.4:c.716_766del	p.Gly239_Pro255del	p.G239_P255del	ENST00000374672	NM_004235.4	239	gGCAGCGAGTACGGCAGCCCGTCGGTCATCAGCGTCAGCAAAGGCAGCCCTGac/gac	3/5	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.317427306123596	2		78	253	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176973	56176973	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0004121-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	167	348	0	ENST00000399503.3:c.2243C>G	p.Ser748Ter	p.S748*	ENST00000399503	NM_005921.1	748	tCa/tGa	13/20	1	2	FACETS	0.576	0.529	0.624	0.576	0.529	0.624	SUBCLONAL	1	TRUE	1	0.698827916259883	2		348	830	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183345	56183345	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004121-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	68	221	0	ENST00000399503.3:c.4255G>A	p.Glu1419Lys	p.E1419K	ENST00000399503	NM_005921.1	1419	Gag/Aag	18/20	1	2	FACETS	0.419	0.366	0.477	0.419	0.366	0.477	SUBCLONAL	1	TRUE	1	0.698827916259883	2		221	464	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163686	32163686	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004121-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	49	200	0	ENST00000375023.3:c.5540C>T	p.Ser1847Leu	p.S1847L	ENST00000375023	NM_004557.3	1847	tCa/tTa	30/30	1	2	FACETS	0.49	0.418	0.569	0.49	0.418	0.569	SUBCLONAL	1	TRUE	1	0.698827916259883	2		200	286	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0004123-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	241	355	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.425528228298727	5	FACETS	0.979	0.915	1	0.653	0.61	0.696	CLONAL	2	TRUE	2	0.425528228298727	5		355	948	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0004123-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	221	481	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	NA	2	FACETS	0.8	0.749	0.853			1	INDETERMINATE	2	TRUE	NA	0.425528228298727	2		481	649	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921555	178921555	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004123-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	63	231	0	ENST00000263967.3:c.1037T>A	p.Val346Glu	p.V346E	ENST00000263967	NM_006218.2	346	gTa/gAa	5/21	0.287831622336021	2	FACETS	0.526	0.455	0.603	0.263	0.227	0.302	SUBCLONAL	1	TRUE	0	0.425528228298727	2		231	563	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43749764	43749764	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004123-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	73	526	0	ENST00000523873.1:c.617G>C	p.Cys206Ser	p.C206S	ENST00000523873		206	tGc/tCc	7/8	0.414402596172007	3	FACETS	0.343	0.299	0.391	0.172	0.149	0.196	SUBCLONAL	1	TRUE	1	0.425528228298727	3		526	1213	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266099	41266119	+	inframe_deletion	In_Frame_Del	DEL	CTCTGGAATCCATTCTGGTGC	CTCTGGAATCCATTCTGGTGC	-	novel	NA	P-0004123-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	82	332	0	ENST00000349496.5:c.97_117del	p.Ser33_Ala39del	p.S33_A39del	ENST00000349496	NM_001904.3	32	gaCTCTGGAATCCATTCTGGTGCc/gac	3/15	0.352522396690364	2	FACETS	0.596	0.525	0.671	0.298	0.262	0.336	SUBCLONAL	1	TRUE	0	0.425528228298727	2		332	647	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0004129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	101	228	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	0.663732347125459	2		228	285	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241679	55241681	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	rs397517086	NA	P-0004129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	1087	471	1	ENST00000275493.2:c.2127_2129del	p.Glu709_Thr710delinsAsp	p.E709_T710delinsD	ENST00000275493	NM_005228.3	709	gaAACt/gat	18/28	0.663732347125459	9	FACETS	1	0.986	1			1	CLONAL	7	TRUE	NA	0.663732347125459	9		472	1544	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149436878	149436878	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	105	381	0	ENST00000286301.3:c.2291A>C	p.Gln764Pro	p.Q764P	ENST00000286301	NM_005211.3	764	cAg/cCg	17/22	1	2	FACETS	0.914	0.828	1	0.914	0.828	1	CLONAL	1	TRUE	1	0.663732347125459	2		381	346	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945036	151945036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771250133	NA	P-0004129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	98	215	0	ENST00000262189.6:c.2483C>T	p.Pro828Leu	p.P828L	ENST00000262189	NM_170606.2	828	cCa/cTa	14/59	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.663732347125459	2		215	261	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46124999	46124999	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0004129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	121	326	0	ENST00000334344.6:c.187-1G>T		p.X63_splice	ENST00000334344	NM_152641.2	63			1	2	FACETS	0.581	0.526	0.638	0.581	0.526	0.638	SUBCLONAL	1	TRUE	1	0.663732347125459	2		326	628	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035965	47035965	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	155	277	0	ENST00000377604.3:c.643G>T	p.Glu215Ter	p.E215*	ENST00000377604	NM_001204468.1	215	Gag/Tag	7/24	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.663732347125459	1		277	242	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412320	63412320	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	166	350	0	ENST00000330258.3:c.847G>T	p.Glu283Ter	p.E283*	ENST00000330258	NM_152424.3	283	Gag/Tag	2/2	0.326712631604379	0	FACETS	0.704	0.667	0.739			1	INDETERMINATE	1	TRUE	NA	0.663732347125459	0		350	239	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356506	70356506	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0004129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	116	194	0	ENST00000374080.3:c.5400+1G>T		p.X1800_splice	ENST00000374080		1800			0.326712631604379	0	FACETS	0.676	0.632	0.718			1	INDETERMINATE	1	TRUE	NA	0.663732347125459	0		194	174	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0004140-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	52	258	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.382888237700476	3	FACETS	0.369	0.313	0.43	0.184	0.156	0.215	SUBCLONAL	1	TRUE	1	0.419864849750872	3		258	813	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63829535	63829535	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004140-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	42	205	0	ENST00000279873.7:c.1178G>A	p.Cys393Tyr	p.C393Y	ENST00000279873	NM_032199.2	393	tGt/tAt	8/10	0.419864849750872	6	FACETS	0.564	0.469	0.669			1	SUBCLONAL	1	TRUE	NA	0.419864849750872	6		205	653	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128482	30128482	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004140-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	48	285	0	ENST00000263025.4:c.900C>G	p.Asp300Glu	p.D300E	ENST00000263025	NM_002746.2	300	gaC/gaG	6/9	0.249180431582238	4	FACETS	0.519	0.438	0.609	0.26	0.219	0.305	INDETERMINATE	1	TRUE	2	0.419864849750872	4		285	625	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39644786	39644786	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004140-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	43	208	0	ENST00000262039.4:c.2515G>A	p.Val839Met	p.V839M	ENST00000262039	NM_002647.2	839	Gtg/Atg	23/25	0.287239069521749	5	FACETS	0.47	0.392	0.556			1	SUBCLONAL	1	TRUE	NA	0.419864849750872	5		208	711	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560898	9560898	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767455314	NA	P-0004140-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	34	265	0	ENST00000353224.5:c.884C>T	p.Pro295Leu	p.P295L	ENST00000353224	NM_177990.2	295	cCg/cTg	4/10	0.305153447978255	5	FACETS	0.434	0.354	0.525	0.145	0.118	0.175	SUBCLONAL	1	TRUE	2	0.419864849750872	5		265	608	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573651	48573677	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GATGGGAGGCTTCAGGTTAGTCTTATA	GATGGGAGGCTTCAGGTTAGTCTTATA	T	novel	NA	P-0004140-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	22	123	0	ENST00000342988.3:c.235_249+12delinsT		p.X79_splice	ENST00000342988	NM_005359.5	79		2/12	0.287239069521749	5	FACETS	0.402	0.311	0.508			1	SUBCLONAL	1	TRUE	NA	0.419864849750872	5		123	425	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828957	72828957	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	141	590	0	ENST00000268489.5:c.7624T>C	p.Phe2542Leu	p.F2542L	ENST00000268489	NM_006885.3	2542	Ttt/Ctt	9/10	0.174184071807009	0	FACETS	0.468	0.427	0.51			1	INDETERMINATE	1	TRUE	0	0.492703098022916	0		590	621	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541542	29541542	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137854557	NA	P-0004157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	17	330	0	ENST00000356175.3:c.1466A>G	p.Tyr489Cys	p.Y489C	ENST00000356175	NM_000267.3	489	tAt/tGt	13/57	NA	2	FACETS	0.285	0.212	0.37			1	INDETERMINATE	1	TRUE	NA	0.543152747078052	2		330	220	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0004187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	186	294	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.44767338274521	3	FACETS	0.841	0.782	0.901	0.841	0.782	0.901	CLONAL	2	TRUE	1	0.500066945851848	3		294	553	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948136	178948136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	219	309	0	ENST00000263967.3:c.2908G>A	p.Glu970Lys	p.E970K	ENST00000263967	NM_006218.2	970	Gaa/Aaa	20/21	0.44767338274521	3	FACETS	0.851	0.796	0.907	0.851	0.796	0.907	CLONAL	2	TRUE	1	0.500066945851848	3		309	643	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259610	16259610	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	148	384	0	ENST00000375759.3:c.6875C>A	p.Ser2292Ter	p.S2292*	ENST00000375759	NM_015001.2	2292	tCa/tAa	11/15	1	2	FACETS	0.848	0.776	0.923	0.848	0.776	0.923	CLONAL	1	TRUE	1	0.500066945851848	2		384	698	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842339	68842339	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	164	525	2	ENST00000261769.5:c.400G>T	p.Gly134Ter	p.G134*	ENST00000261769	NM_004360.3	134	Gga/Tga	4/16	0.500066945851848	1	FACETS	0.845	0.78	0.913	0.845	0.78	0.913	CLONAL	1	TRUE	0	0.500066945851848	1		527	582	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092811	27092811	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	167	453	0	ENST00000324856.7:c.2834del	p.Gly945AspfsTer23	p.G945Dfs*23	ENST00000324856	NM_006015.4	944	caG/ca	9/20	1	2	FACETS	0.976	0.9	1	0.976	0.9	1	CLONAL	1	TRUE	1	0.500066945851848	2		453	684	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0004204-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	282	646	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.850077498148838	2		647	643	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0004204-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	120	182	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.843	0.771	0.917	0.843	0.771	0.917	CLONAL	1	TRUE	1	0.850077498148838	2		182	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577555	7577555	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs375874539	NA	P-0004204-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	155	231	0	ENST00000269305.4:c.726C>G	p.Cys242Trp	p.C242W	ENST00000269305	NM_001126112.2	242	tgC/tgG	7/11	1	2	FACETS	0.942	0.873	1	0.942	0.873	1	CLONAL	1	TRUE	1	0.850077498148838	2		231	387	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350098	81350098	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004204-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	289	362	0	ENST00000222390.5:c.1234T>C	p.Cys412Arg	p.C412R	ENST00000222390	NM_000601.4	412	Tgt/Cgt	10/18	1	2	FACETS	0.984	0.932	1	0.984	0.932	1	CLONAL	1	TRUE	1	0.850077498148838	2		362	691	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134900	41134900	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004204-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	325	501	0	ENST00000379561.5:c.728G>T	p.Gly243Val	p.G243V	ENST00000379561	NM_002015.3	243	gGt/gTt	2/3	1	2	FACETS	0.918	0.871	0.966	0.918	0.871	0.966	CLONAL	1	TRUE	1	0.850077498148838	2		501	833	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557638	95557638	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004204-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	227	346	0	ENST00000393063.1:c.5429A>T	p.Asp1810Val	p.D1810V	ENST00000393063	NM_030621.3	1810	gAt/gTt	26/28	1	2	FACETS	0.863	0.809	0.917	0.863	0.809	0.917	CLONAL	1	TRUE	1	0.850077498148838	2		346	619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520006	NA	P-0004213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	390	316	0	ENST00000269305.4:c.821T>G	p.Val274Gly	p.V274G	ENST00000269305	NM_001126112.2	274	gTt/gGt	8/11	0.606860053034617	2	FACETS	0.968	0.932	1	0.968	0.932	1	CLONAL	2	TRUE	0	0.644751330529565	2		316	625	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239454	123239454	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024846807	NA	P-0004213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	179	330	0	ENST00000358487.5:c.2383G>A	p.Asp795Asn	p.D795N	ENST00000358487	NM_000141.4	795	Gat/Aat	18/18	0.617058786317164	2	FACETS	0.883	0.818	0.95	0.441	0.409	0.475	CLONAL	1	TRUE	0	0.644751330529565	2		330	629	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796006	78796006	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	161	226	0	ENST00000306801.3:c.896C>G	p.Pro299Arg	p.P299R	ENST00000306801	NM_020761.2	299	cCt/cGt	8/34	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.644751330529565	2		226	492	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342756	87342756	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	246	147	0	ENST00000277120.3:c.1041G>C	p.Gln347His	p.Q347H	ENST00000277120		347	caG/caC	9/19	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.832976124551535	2		147	549	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073710	8073710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143947835	NA	P-0004250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1475	509	571	0	ENST00000377482.5:c.949C>T	p.Pro317Ser	p.P317S	ENST00000377482	NM_018948.3	317	Ccc/Tcc	4/4	0.302451221327188	4	FACETS	1	0.995	1			1	INDETERMINATE	1	TRUE	NA	0.6436568502891	4		571	1984	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140760	55140760	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1327	86	351	0	ENST00000257290.5:c.1621T>A	p.Ser541Thr	p.S541T	ENST00000257290	NM_006206.4	541	Tca/Aca	11/23	NA	2	FACETS	0.189	0.166	0.214			1	INDETERMINATE	1	TRUE	NA	0.6436568502891	2		351	1413	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525729	187525729	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0004250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	80	222	0	ENST00000441802.2:c.10351-1G>T		p.X3451_splice	ENST00000441802	NM_005245.3	3451			0.213048834881009	1	FACETS	0.272	0.24	0.307	0.272	0.24	0.307	INDETERMINATE	1	TRUE	0	0.6436568502891	1		222	619	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492862	8492862	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	173	275	0	ENST00000356435.5:c.2467G>T	p.Val823Phe	p.V823F	ENST00000356435		823	Gtt/Ttt	16/35	0.228732496035119	3	FACETS	0.649	0.596	0.704	0.216	0.198	0.235	INDETERMINATE	1	TRUE	0	0.6436568502891	3		275	1095	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528638	8528638	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	211	364	0	ENST00000356435.5:c.494C>G	p.Pro165Arg	p.P165R	ENST00000356435		165	cCt/cGt	4/35	0.228732496035119	3	FACETS	0.624	0.578	0.672	0.208	0.192	0.224	INDETERMINATE	1	TRUE	0	0.6436568502891	3		364	1388	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959044	28959044	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	155	393	0	ENST00000282397.4:c.2094C>A	p.Asn698Lys	p.N698K	ENST00000282397	NM_002019.4	698	aaC/aaA	14/30	NA	2	FACETS	0.442	0.404	0.482			1	INDETERMINATE	1	TRUE	NA	0.6436568502891	2		393	1090	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315339	30315339	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	148	258	0	ENST00000322652.5:c.1024A>T	p.Arg342Trp	p.R342W	ENST00000322652	NM_015355.2	342	Agg/Tgg	10/16	0.203132071751484	5	FACETS	1	0.922	1	0.337	0.307	0.368	INDETERMINATE	1	TRUE	2	0.6436568502891	5		258	895	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207088	1207099	+	inframe_deletion	In_Frame_Del	DEL	CTTACGGCAAGG	CTTACGGCAAGG	-	novel	NA	P-0004250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	221	332	0	ENST00000326873.7:c.176_187del	p.Ser59_Val63delinsLeu	p.S59_V63delinsL	ENST00000326873	NM_000455.4	59	tCTTACGGCAAGGtg/ttg	1/10	NA	2	FACETS	0.606	0.563	0.65			1	INDETERMINATE	1	TRUE	NA	0.6436568502891	2		332	1133	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222176	2222176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	133	343	0	ENST00000398665.3:c.3010del	p.His1004ThrfsTer64	p.H1004Tfs*64	ENST00000398665	NM_032482.2	1003	gCc/gc	24/28	0.333923454850314	1	FACETS	0.37	0.336	0.405	0.37	0.336	0.405	INDETERMINATE	1	TRUE	0	0.6436568502891	1		343	758	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579472	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	A	novel	NA	P-0004250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	131	249	0	ENST00000269305.4:c.215_216delinsT	p.Pro72LeufsTer51	p.P72Lfs*51	ENST00000269305	NM_001126112.2	72	cCC/cT	4/11	1	2	FACETS	0.691	0.629	0.756	0.691	0.629	0.756	SUBCLONAL	1	TRUE	1	0.6436568502891	2		249	589	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759651	133759651	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	122	296	1	ENST00000318560.5:c.1974G>T	p.Lys658Asn	p.K658N	ENST00000318560	NM_005157.4	658	aaG/aaT	11/11	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.477405531150241	2		297	500	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256179	123256179	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	159	329	0	ENST00000358487.5:c.1730G>A	p.Arg577Gln	p.R577Q	ENST00000358487	NM_000141.4	577	cGa/cAa	13/18	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.477405531150241	2		329	660	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303467	30303467	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	25	34	0	ENST00000262643.3:c.5C>T	p.Pro2Leu	p.P2L	ENST00000262643	NM_001238.2	2	cCg/cTg	2/12	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.477405531150241	2		34	82	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000103	30000103	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0004266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	186	366	0	ENST00000338641.4:c.114+2T>A		p.X38_splice	ENST00000338641	NM_000268.3	38			0.477405531150241	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.477405531150241	1		366	521	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713832	30713832	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	21	136	0	ENST00000295754.5:c.1157T>C	p.Leu386Pro	p.L386P	ENST00000295754	NM_003242.5	386	cTc/cCc	4/7	0.316304716570368	4	FACETS	0.631	0.488	0.796	0.315	0.244	0.398	SUBCLONAL	1	TRUE	2	0.474035865126143	4		136	207	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527570	29527570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	44	267	0	ENST00000356175.3:c.1019C>T	p.Ser340Phe	p.S340F	ENST00000356175	NM_000267.3	340	tCt/tTt	9/57	0.459328918470578	3	FACETS	0.581	0.488	0.684	0.291	0.244	0.342	SUBCLONAL	1	TRUE	1	0.474035865126143	3		267	395	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711965	89711965	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786204901	NA	P-0004347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	151	161	0	ENST00000371953.3:c.585del	p.His196ThrfsTer3	p.H196Tfs*3	ENST00000371953	NM_000314.4	195	Ttt/tt	6/9	0.474035865126143	3	FACETS	0.948	0.886	1	0.948	0.886	1	CLONAL	3	TRUE	0	0.474035865126143	3		161	277	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577543	7577543	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	117	177	0	ENST00000269305.4:c.738del	p.Met246IlefsTer99	p.M246Ifs*99	ENST00000269305	NM_001126112.2	246	atG/at	7/11	0.439879603681085	3	FACETS	0.974	0.903	1	0.974	0.903	1	CLONAL	3	TRUE	0	0.474035865126143	3		177	209	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0004374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	56	124	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.250636213702566	4	FACETS	0.759	0.654	0.872	0.759	0.654	0.872	SUBCLONAL	2	FALSE	2	0.290372955107183	4		124	328	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845391	151845391	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	39	408	0	ENST00000262189.6:c.13621C>T	p.Arg4541Ter	p.R4541*	ENST00000262189	NM_170606.2	4541	Cga/Tga	52/59	1	2	FACETS	0.608	0.504	0.724	0.608	0.504	0.724	SUBCLONAL	1	FALSE	1	0.290372955107183	2		408	442	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610647	52610647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	37	508	0	ENST00000394830.3:c.3526G>A	p.Glu1176Lys	p.E1176K	ENST00000394830	NM_018313.4	1176	Gaa/Aaa	23/30	0.208386289707637	3	FACETS	0.579	0.477	0.694	0.29	0.238	0.347	SUBCLONAL	1	FALSE	1	0.290372955107183	3		508	504	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71008442	71008442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	34	597	0	ENST00000318789.4:c.1990G>A	p.Asp664Asn	p.D664N	ENST00000318789	NM_032682.5	664	Gac/Aac	21/21	0.225274397468769	4	FACETS	0.477	0.388	0.577			1	SUBCLONAL	1	FALSE	NA	0.290372955107183	4		597	634	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665197	138665197	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	70	492	2	ENST00000330315.3:c.368G>A	p.Arg123His	p.R123H	ENST00000330315	NM_023067.3	123	cGc/cAc	1/1	0.250636213702566	4	FACETS	0.751	0.658	0.851	0.751	0.658	0.851	SUBCLONAL	2	FALSE	2	0.290372955107183	4		494	414	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928083	178928083	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	92	384	0	ENST00000263967.3:c.1361A>G	p.Asp454Gly	p.D454G	ENST00000263967	NM_006218.2	454	gAt/gGt	8/21	0.250636213702566	4	FACETS	1	0.977	1	0.696	0.62	0.778	CLONAL	1	FALSE	2	0.290372955107183	4		384	587	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181765	56181765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1287268127	NA	P-0004374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	102	323	1	ENST00000399503.3:c.3989C>T	p.Ser1330Leu	p.S1330L	ENST00000399503	NM_005921.1	1330	tCg/tTg	17/20	0.243320118688264	4	FACETS	0.899	0.808	0.996	0.6	0.538	0.664	CLONAL	2	FALSE	1	0.290372955107183	4		324	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578362	7578385	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTGCTCACCATCGCTATCTGAGC	GCTGCTCACCATCGCTATCTGAGC	-	novel	NA	P-0004374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	44	290	0	ENST00000269305.4:c.545_559+9del		p.X182_splice	ENST00000269305	NM_001126112.2	182		5/11	0.179036184386305	2	FACETS	1	0.95	1	0.665	0.563	0.775	CLONAL	1	FALSE	0	0.290372955107183	2		290	228	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0004375-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	35	228	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.721	0.594	0.863	0.721	0.594	0.863	SUBCLONAL	1	TRUE	1	0.359487765554165	2		228	270	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419957	41419957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369230837	NA	P-0004375-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	64	473	0	ENST00000373198.4:c.364G>A	p.Val122Ile	p.V122I	ENST00000373198	NM_133170.3	122	Gtc/Atc	3/32	0.359487765554165	3	FACETS	0.431	0.372	0.495			1	SUBCLONAL	1	TRUE	NA	0.359487765554165	3		473	975	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593448	215593449	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0004375-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	130	420	0	ENST00000260947.4:c.2285_2286delinsTT	p.Trp762Phe	p.W762F	ENST00000260947	NM_000465.2	762	tGG/tTT	11/11	0.351621366353134	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.359487765554165	1		420	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747342068	NA	P-0004391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	27	462	0	ENST00000269305.4:c.394A>G	p.Lys132Glu	p.K132E	ENST00000269305	NM_001126112.2	132	Aag/Gag	5/11	1	2	FACETS	0.281	0.223	0.347	0.281	0.223	0.347	SUBCLONAL	1	TRUE	1	0.37	2		462	520	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122673	108122680	+	frameshift_variant	Frame_Shift_Del	DEL	AAGGAATC	AAGGAATC	-	novel	NA	P-0004394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	162	176	0	ENST00000278616.4:c.1719_1726del	p.Lys573AsnfsTer13	p.K573Nfs*13	ENST00000278616	NM_000051.3	573	AAGGAATCa/a	11/63	0.715134823899035	2	FACETS	0.878	0.827	0.927	0.878	0.827	0.927	CLONAL	2	TRUE	0	0.715134823899035	2		176	258	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0004403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	55	223	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.93	0.798	1	0.93	0.798	1	CLONAL	1	TRUE	1	0.282266508706794	2		223	419	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0004403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	65	448	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.282266508706794	1	FACETS	0.953	0.83	1	0.953	0.83	1	CLONAL	1	TRUE	0	0.282266508706794	1		448	415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0004403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	54	250	0	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	0.222662255691602	2	FACETS	0.843	0.728	0.965	0.843	0.728	0.965	CLONAL	2	TRUE	0	0.282266508706794	2		250	227	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685309	89685309	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs773176120	NA	P-0004403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	41	395	1	ENST00000371953.3:c.204C>G	p.Tyr68Ter	p.Y68*	ENST00000371953	NM_000314.4	68	taC/taG	3/9	0.282266508706794	1	FACETS	0.807	0.675	0.953	0.807	0.675	0.953	CLONAL	1	TRUE	0	0.282266508706794	1		396	309	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575096	48575096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555685159	NA	P-0004403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	58	513	1	ENST00000342988.3:c.290G>A	p.Arg97His	p.R97H	ENST00000342988	NM_005359.5	97	cGt/cAt	3/12	0.275461614902177	1	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	0	0.282266508706794	1		514	335	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411164	63411164	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	55	578	0	ENST00000330258.3:c.2003del	p.Ala668GlufsTer51	p.A668Efs*51	ENST00000330258	NM_152424.3	668	gCa/ga	2/2	0.1540714865024	0	FACETS	0.768	0.66	0.886			1	INDETERMINATE	1	TRUE	0	0.282266508706794	0		578	364	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0004409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	68	527	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.203543516527466	2		527	617	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188261	10188261	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0004412-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	76	427	0	ENST00000256474.2:c.404T>A	p.Leu135Ter	p.L135*	ENST00000256474	NM_000551.3	135	tTa/tAa	2/3	0.386270537108875	1	FACETS	0.882	0.783	0.985	0.882	0.783	0.985	CLONAL	1	TRUE	0	0.495004356802943	1		427	262	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725457	117725457	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004412-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	17	478	0	ENST00000368508.3:c.424T>A	p.Trp142Arg	p.W142R	ENST00000368508	NM_002944.2	142	Tgg/Agg	5/43	1	2	FACETS	0.206	0.153	0.269	0.206	0.153	0.269	SUBCLONAL	1	TRUE	1	0.495004356802943	2		478	333	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588853	52588853	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004412-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	61	304	0	ENST00000394830.3:c.4175del	p.Gly1392AlafsTer40	p.G1392Afs*40	ENST00000394830	NM_018313.4	1392	gGc/gc	27/30	0.330550051490613	1	FACETS	0.887	0.777	1	0.887	0.777	1	CLONAL	1	TRUE	0	0.495004356802943	1		304	209	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820613	44820614	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0004412-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	85	253	0	ENST00000377967.4:c.312_313del	p.Leu105IlefsTer20	p.L105Ifs*20	ENST00000377967	NM_021140.2	104	CTc/c	3/29	0.394085383609255	2	FACETS	1	0.932	1			1	CLONAL	2	TRUE	NA	0.495004356802943	2		253	167	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0004455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	83	885	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.314078352536925	1	FACETS	0.539	0.476	0.606	0.539	0.476	0.606	SUBCLONAL	1	TRUE	0	0.428433055107564	1		885	565	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027249	49027249	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0004455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	113	292	0	ENST00000267163.4:c.1814+2T>C		p.X605_splice	ENST00000267163	NM_000321.2	605			0.244385669158012	1	FACETS	0.748	0.676	0.824	0.748	0.676	0.824	INDETERMINATE	1	TRUE	0	0.428433055107564	1		292	554	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551984	150551984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1445925900	NA	P-0004455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	91	387	0	ENST00000369026.2:c.23C>T	p.Ala8Val	p.A8V	ENST00000369026	NM_021960.4	8	gCg/gTg	1/3	0.223797051952127	3	FACETS	0.735	0.652	0.823	0.367	0.326	0.412	INDETERMINATE	1	TRUE	1	0.428433055107564	3		387	702	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652074	36652074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	74	408	0	ENST00000244741.5:c.196G>A	p.Glu66Lys	p.E66K	ENST00000244741	NM_000389.4	66	Gag/Aag	2/3	0.318605918410473	1	FACETS	0.575	0.505	0.65	0.575	0.505	0.65	SUBCLONAL	1	TRUE	0	0.428433055107564	1		408	472	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553290	106553290	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	87	359	0	ENST00000369096.4:c.1255G>A	p.Gly419Ser	p.G419S	ENST00000369096	NM_001198.3	419	Ggc/Agc	5/7	1	2	FACETS	0.574	0.508	0.644	0.574	0.508	0.644	SUBCLONAL	1	TRUE	1	0.428433055107564	2		359	708	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404908	70404908	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	105	391	1	ENST00000373644.4:c.2422G>T	p.Ala808Ser	p.A808S	ENST00000373644	NM_030625.2	808	Gct/Tct	4/12	0.314078352536925	1	FACETS	0.635	0.57	0.703	0.635	0.57	0.703	SUBCLONAL	1	TRUE	0	0.428433055107564	1		392	607	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530126	212530126	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	97	439	0	ENST00000342788.4:c.1793del	p.Gln598ArgfsTer55	p.Q598Rfs*55	ENST00000342788	NM_005235.2	598	cAg/cg	15/28	1	2	FACETS	0.572	0.51	0.639	0.572	0.51	0.639	SUBCLONAL	1	TRUE	1	0.428433055107564	2		439	791	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265528	152265533	+	inframe_deletion	In_Frame_Del	DEL	CTATTC	CTATTC	-	novel	NA	P-0004455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	78	296	0	ENST00000206249.3:c.982_987del	p.Tyr328_Ser329del	p.Y328_S329del	ENST00000206249	NM_000125.3	327	ctCTATTCc/ctc	4/8	0.428433055107564	3	FACETS	0.608	0.534	0.688	0.304	0.267	0.344	SUBCLONAL	1	TRUE	1	0.428433055107564	3		296	727	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004501-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	173	465	0	ENST00000335508.6:c.1874G>T	p.Arg625Leu	p.R625L	ENST00000335508	NM_012433.2	625	cGt/cTt	14/25	1	2	FACETS	0.99	0.915	1	0.99	0.915	1	CLONAL	1	TRUE	1	0.53258207148425	2		465	656	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411087	63411087	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004501-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	166	648	0	ENST00000330258.3:c.2080G>C	p.Asp694His	p.D694H	ENST00000330258	NM_152424.3	694	Gac/Cac	2/2	1	2	FACETS	0.93	0.858	1	0.93	0.858	1	CLONAL	1	TRUE	1	0.53258207148425	2		648	670	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0004502-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	69	506	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.344905746177581	1	FACETS	0.983	0.862	1	0.983	0.862	1	CLONAL	1	FALSE	0	0.344905746177581	1		507	337	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0004502-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	63	373	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.267494768230693	1	FACETS	0.679	0.589	0.777	0.679	0.589	0.777	SUBCLONAL	1	FALSE	0	0.344905746177581	1		373	445	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920437	114920437	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004502-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	148	678	0	ENST00000543371.1:c.1378T>C	p.Cys460Arg	p.C460R	ENST00000543371	NM_001198531.1	460	Tgc/Cgc	13/14	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.344905746177581	2		678	611	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211650	5211650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004502-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	97	429	0	ENST00000357368.4:c.5185G>A	p.Gly1729Ser	p.G1729S	ENST00000357368	NM_002850.3	1729	Ggt/Agt	33/38	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.344905746177581	2		429	482	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41558757	41558757	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1340775159	NA	P-0004502-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	111	580	0	ENST00000263253.7:c.3702A>T	p.Arg1234Ser	p.R1234S	ENST00000263253	NM_001429.3	1234	agA/agT	21/31	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.344905746177581	2		580	498	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248632	59248632	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004502-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	108	472	0	ENST00000371222.2:c.111del	p.Ser37ArgfsTer2	p.S37Rfs*2	ENST00000371222	NM_002228.3	37	agC/ag	1/1	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.344905746177581	2		472	557	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0004521-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	273	228	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.489802799002496	2	FACETS	0.994	0.942	1	0.994	0.942	1	CLONAL	2	TRUE	0	0.489802799002496	2		228	561	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0004521-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	456	404	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.488671658633573	2	FACETS	0.915	0.877	0.953	0.915	0.877	0.953	CLONAL	2	TRUE	0	0.489802799002496	2		404	1018	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258254	16258254	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004521-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	197	427	0	ENST00000375759.3:c.5519T>C	p.Val1840Ala	p.V1840A	ENST00000375759	NM_015001.2	1840	gTc/gCc	11/15	1	2	FACETS	0.892	0.826	0.96	0.892	0.826	0.96	CLONAL	1	TRUE	1	0.489802799002496	2		427	902	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023905	27023905	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004521-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	47	62	0	ENST00000324856.7:c.1011G>A	p.Trp337Ter	p.W337*	ENST00000324856	NM_006015.4	337	tgG/tgA	1/20	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.489802799002496	2		62	154	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023169	27023212	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGGCCCGGCGCGGAGCCGGACCTGAAGAACTCGAACGGGAAC	GCGGGCCCGGCGCGGAGCCGGACCTGAAGAACTCGAACGGGAAC	-	novel	NA	P-0004521-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	32	60	0	ENST00000324856.7:c.283_326del	p.Gly95Ter	p.G95*	ENST00000324856	NM_006015.4	92	gGCGGGCCCGGCGCGGAGCCGGACCTGAAGAACTCGAACGGGAAC/g	1/20	1	2	FACETS	0.871	0.717	1	0.871	0.717	1	CLONAL	1	TRUE	1	0.489802799002496	2		60	150	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0004527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	233	258	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.527970079559869	4	FACETS	0.969	0.919	1	0.969	0.919	1	CLONAL	3	TRUE	1	0.647559024675904	4		258	408	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699316	117699316	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	43	410	0	ENST00000369458.3:c.325A>G	p.Ile109Val	p.I109V	ENST00000369458	NM_024626.3	109	Ata/Gta	3/6	NA	2	FACETS	0.46	0.386	0.54			1	INDETERMINATE	1	TRUE	NA	0.647559024675904	2		410	289	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12647754	12647754	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1329039538	NA	P-0004527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	62	464	0	ENST00000251849.4:c.626T>C	p.Leu209Pro	p.L209P	ENST00000251849	NM_002880.3	209	cTa/cCa	6/17	NA	2	FACETS	0.622	0.541	0.708			1	INDETERMINATE	1	TRUE	NA	0.647559024675904	2		464	308	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440382	187440382	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	45	194	0	ENST00000232014.4:c.1985A>G	p.Lys662Arg	p.K662R	ENST00000232014	NM_001130845.1	662	aAg/aGg	10/10	1	2	FACETS	0.635	0.539	0.738	0.635	0.539	0.738	SUBCLONAL	1	TRUE	1	0.647559024675904	2		194	219	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84403366	84403366	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	30	437	0	ENST00000321945.7:c.119A>G	p.Glu40Gly	p.E40G	ENST00000321945	NM_139076.2	40	gAa/gGa	2/9	1	2	FACETS	0.512	0.416	0.618	0.512	0.416	0.618	SUBCLONAL	1	TRUE	1	0.647559024675904	2		437	181	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220008	5220008	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	68	228	0	ENST00000357368.4:c.3707T>C	p.Leu1236Pro	p.L1236P	ENST00000357368	NM_002850.3	1236	cTg/cCg	22/38	1	2	FACETS	0.745	0.654	0.84	0.745	0.654	0.84	SUBCLONAL	1	TRUE	1	0.647559024675904	2		228	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0004536-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	149	395	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.297127560055977	5	FACETS	1	0.975	1	0.775	0.71	0.842	CLONAL	2	TRUE	2	0.28	5		396	650	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272804	142272804	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	140	442	0	ENST00000350721.4:c.2395G>A	p.Glu799Lys	p.E799K	ENST00000350721	NM_001184.3	799	Gaa/Aaa	11/47	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.497603232568354	2		442	560	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612154	189612154	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	77	401	0	ENST00000264731.3:c.1906G>T	p.Glu636Ter	p.E636*	ENST00000264731	NM_003722.4	636	Gag/Tag	14/14	1	2	FACETS	0.554	0.487	0.626	0.554	0.487	0.626	SUBCLONAL	1	TRUE	1	0.497603232568354	2		401	559	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177754	56177754	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	73	398	0	ENST00000399503.3:c.2727G>C	p.Glu909Asp	p.E909D	ENST00000399503	NM_005921.1	909	gaG/gaC	14/20	0.125128251704559	4	FACETS	0.782	0.685	0.886	0.391	0.342	0.443	INDETERMINATE	1	TRUE	2	0.497603232568354	4		398	562	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520447	176520447	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	57	437	0	ENST00000292408.4:c.1292C>A	p.Ser431Tyr	p.S431Y	ENST00000292408	NM_213647.1	431	tCc/tAc	10/18	1	2	FACETS	0.498	0.428	0.574	0.498	0.428	0.574	SUBCLONAL	1	TRUE	1	0.497603232568354	2		437	460	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722206	176722207	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0004537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	42	481	0	ENST00000439151.2:c.7837_7838delinsAT	p.Glu2613Ile	p.E2613I	ENST00000439151	NM_022455.4	2613	GAa/ATa	23/23	1	2	FACETS	0.304	0.253	0.36	0.304	0.253	0.36	SUBCLONAL	1	TRUE	1	0.497603232568354	2		481	556	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553166	106553166	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	47	350	0	ENST00000369096.4:c.1131G>C	p.Leu377Phe	p.L377F	ENST00000369096	NM_001198.3	377	ttG/ttC	5/7	1	2	FACETS	0.452	0.382	0.529	0.452	0.382	0.529	SUBCLONAL	1	TRUE	1	0.497603232568354	2		350	418	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137524774	137524774	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	139	407	0	ENST00000367739.4:c.595C>A	p.Gln199Lys	p.Q199K	ENST00000367739	NM_000416.2	199	Cag/Aag	5/7	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.497603232568354	2		407	545	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92404075	92404075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1178575524	NA	P-0004537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	77	458	1	ENST00000265734.4:c.304G>A	p.Asp102Asn	p.D102N	ENST00000265734	NM_001259.6	102	Gat/Aat	3/8	0.178875979672377	3	FACETS	0.633	0.556	0.715	0.316	0.278	0.358	INDETERMINATE	1	TRUE	1	0.497603232568354	3		459	611	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712017	89712017	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0004537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	53	147	0	ENST00000371953.3:c.634+1G>A		p.X212_splice	ENST00000371953	NM_000314.4	212			0.360355351396783	1	FACETS	0.904	0.785	1	0.904	0.785	1	CLONAL	1	TRUE	0	0.497603232568354	1		147	177	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515177	103515177	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	58	398	0	ENST00000355739.4:c.1678C>G	p.Leu560Val	p.L560V	ENST00000355739	NM_000123.3	560	Ctt/Gtt	8/15	0.497603232568354	1	FACETS	0.497	0.429	0.571	0.497	0.429	0.571	SUBCLONAL	1	TRUE	0	0.497603232568354	1		398	352	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0004537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	111	422	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.497603232568354	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.497603232568354	1		422	296	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968268	15968268	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	31	539	0	ENST00000268712.3:c.5017C>A	p.Pro1673Thr	p.P1673T	ENST00000268712	NM_006311.3	1673	Cct/Act	34/46	0.497603232568354	1	FACETS	0.197	0.159	0.241	0.197	0.159	0.241	SUBCLONAL	1	TRUE	0	0.497603232568354	1		539	474	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16001793	16001793	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0004537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	84	467	0	ENST00000268712.3:c.2708C>G	p.Ser903Ter	p.S903*	ENST00000268712	NM_006311.3	903	tCa/tGa	21/46	0.497603232568354	1	FACETS	0.576	0.511	0.645	0.576	0.511	0.645	SUBCLONAL	1	TRUE	0	0.497603232568354	1		467	440	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509567	29509567	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	97	429	0	ENST00000356175.3:c.772G>T	p.Glu258Ter	p.E258*	ENST00000356175	NM_000267.3	258	Gaa/Taa	8/57	0.497603232568354	1	FACETS	0.683	0.612	0.757	0.683	0.612	0.757	SUBCLONAL	1	TRUE	0	0.497603232568354	1		429	429	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47685245	47685245	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	141	499	0	ENST00000347630.2:c.705G>C	p.Glu235Asp	p.E235D	ENST00000347630	NM_001007230.1	235	gaG/gaC	8/11	0.497603232568354	1	FACETS	0.963	0.885	1	0.963	0.885	1	CLONAL	1	TRUE	0	0.497603232568354	1		499	442	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342170	70342170	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	73	539	0	ENST00000374080.3:c.1222G>C	p.Glu408Gln	p.E408Q	ENST00000374080		408	Gag/Cag	8/45	0.191436172189761	1	FACETS	0.392	0.343	0.445	0.392	0.343	0.445	INDETERMINATE	1	TRUE	0	0.497603232568354	1		539	562	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	20	86	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	1	0.819	1	1	0.819	1	CLONAL	1	TRUE	1	0.16	2		86	231	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007620	45007620	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs111947448	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	34	144	0	ENST00000558401.1:c.68-1G>T		p.X23_splice	ENST00000558401	NM_004048.2	23			1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.16	2		144	387	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965666	90965666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	50	373	1	ENST00000265433.3:c.1651del	p.Arg551GlyfsTer8	p.R551Gfs*8	ENST00000265433	NM_002485.4	551	Agg/gg	11/16	1	2	FACETS	0.915	0.775	1	0.915	0.775	1	CLONAL	1	TRUE	1	0.16	2		374	683	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	50	276	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.673	0.569	0.788	0.673	0.569	0.788	SUBCLONAL	1	TRUE	1	0.16	2		276	929	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	22	159	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.737	0.571	0.931	0.737	0.571	0.931	CLONAL	1	TRUE	1	0.16	2		159	373	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343697	118343697	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	45	242	0	ENST00000534358.1:c.1823G>A	p.Arg608Gln	p.R608Q	ENST00000534358	NM_005933.3	608	cGa/cAa	3/36	1	2	FACETS	0.982	0.824	1	0.982	0.824	1	CLONAL	1	TRUE	1	0.16	2		242	573	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99454555	99454555	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61740877	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	45	223	0	ENST00000268035.6:c.1474G>A	p.Val492Ile	p.V492I	ENST00000268035	NM_000875.3	492	Gtc/Atc	7/21	1	2	FACETS	0.787	0.66	0.928	0.787	0.66	0.928	CLONAL	1	TRUE	1	0.16	2		223	715	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183540	185183540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	35	243	0	ENST00000265026.3:c.1394C>T	p.Ala465Val	p.A465V	ENST00000265026	NM_004721.4	465	gCg/gTg	9/14	1	2	FACETS	0.846	0.693	1	0.846	0.693	1	CLONAL	1	TRUE	1	0.16	2		243	517	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539018	187539018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374444088	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	41	430	0	ENST00000441802.2:c.8722G>A	p.Val2908Ile	p.V2908I	ENST00000441802	NM_005245.3	2908	Gtc/Atc	10/27	1	2	FACETS	0.81	0.673	0.962	0.81	0.673	0.962	CLONAL	1	TRUE	1	0.16	2		430	633	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	30	294	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	0.672	0.54	0.822	0.672	0.54	0.822	SUBCLONAL	1	TRUE	1	0.16	2		294	558	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115252317	115252317	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	37	357	0	ENST00000369535.4:c.323A>G	p.Asp108Gly	p.D108G	ENST00000369535	NM_002524.4	108	gAt/gGt	4/7	1	2	FACETS	0.69	0.568	0.828	0.69	0.568	0.828	SUBCLONAL	1	TRUE	1	0.16	2		357	670	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277254	41277254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs797044875	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	48	262	0	ENST00000349496.5:c.1723G>A	p.Gly575Arg	p.G575R	ENST00000349496	NM_001904.3	575	Gga/Aga	11/15	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.16	2		262	535	SUCCESS
ATR	545	MSKCC	GRCh37	3	142177928	142177928	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762621866	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	38	233	0	ENST00000350721.4:c.7375C>T	p.Arg2459Cys	p.R2459C	ENST00000350721	NM_001184.3	2459	Cgt/Tgt	44/47	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.16	2		233	436	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293833	1293833	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	53	267	0	ENST00000310581.5:c.1168C>T	p.Arg390Trp	p.R390W	ENST00000310581	NM_198253.2	390	Cgg/Tgg	2/16	1	2	FACETS	0.817	0.695	0.951	0.817	0.695	0.951	CLONAL	1	TRUE	1	0.16	2		267	811	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562403	176562403	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	30	249	0	ENST00000439151.2:c.299C>A	p.Pro100His	p.P100H	ENST00000439151	NM_022455.4	100	cCt/cAt	2/23	1	2	FACETS	0.775	0.623	0.947	0.775	0.623	0.947	CLONAL	1	TRUE	1	0.16	2		249	484	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287346	33287346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371054058	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	44	325	0	ENST00000374542.5:c.1751C>T	p.Thr584Met	p.T584M	ENST00000374542	NM_001141970.1	584	aCg/aTg	6/8	1	2	FACETS	0.799	0.669	0.945	0.799	0.669	0.945	CLONAL	1	TRUE	1	0.16	2		325	688	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157488293	157488293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750810656	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	34	148	0	ENST00000346085.5:c.2999C>T	p.Ala1000Val	p.A1000V	ENST00000346085	NM_020732.3	1000	gCg/gTg	10/20	1	2	FACETS	0.71	0.578	0.858	0.71	0.578	0.858	SUBCLONAL	1	TRUE	1	0.16	2		148	599	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729727	41729727	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	64	434	0	ENST00000242208.4:c.802G>A	p.Glu268Lys	p.E268K	ENST00000242208	NM_002192.2	268	Gaa/Aaa	3/3	1	2	FACETS	0.82	0.708	0.942	0.82	0.708	0.942	CLONAL	1	TRUE	1	0.16	2		434	976	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468032	50468032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757907717	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	59	257	0	ENST00000331340.3:c.1267C>T	p.Arg423Cys	p.R423C	ENST00000331340	NM_006060.4	423	Cgc/Tgc	8/8	1	2	FACETS	0.905	0.777	1	0.905	0.777	1	CLONAL	1	TRUE	1	0.16	2		257	815	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856027	151856027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774117324	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	45	389	0	ENST00000262189.6:c.11591G>A	p.Arg3864His	p.R3864H	ENST00000262189	NM_170606.2	3864	cGc/cAc	44/59	1	2	FACETS	0.916	0.769	1	0.916	0.769	1	CLONAL	1	TRUE	1	0.16	2		389	614	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346031	152346031	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	53	461	0	ENST00000359321.1:c.539T>C	p.Leu180Ser	p.L180S	ENST00000359321	NM_005431.1	180	tTa/tCa	3/3	1	2	FACETS	0.923	0.785	1	0.923	0.785	1	CLONAL	1	TRUE	1	0.16	2		461	718	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563405	87563405	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147652140	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	48	226	0	ENST00000277120.3:c.1793G>A	p.Arg598His	p.R598H	ENST00000277120		598	cGc/cAc	16/19	1	2	FACETS	0.89	0.751	1	0.89	0.751	1	CLONAL	1	TRUE	1	0.16	2		226	674	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606304	93606304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	62	277	0	ENST00000375746.1:c.124C>T	p.Arg42Cys	p.R42C	ENST00000375746	NM_001174167.1	42	Cgc/Tgc	2/14	1	2	FACETS	0.84	0.723	0.967	0.84	0.723	0.967	CLONAL	1	TRUE	1	0.16	2		277	923	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787731	135787731	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151309813	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	38	323	2	ENST00000298552.3:c.851G>A	p.Arg284His	p.R284H	ENST00000298552	NM_001162426.1	284	cGc/cAc	9/23	1	2	FACETS	0.783	0.646	0.936	0.783	0.646	0.936	CLONAL	1	TRUE	1	0.16	2		325	607	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115907	8115907	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769298101	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	55	198	0	ENST00000346208.3:c.1253C>T	p.Thr418Met	p.T418M	ENST00000346208		418	aCg/aTg	6/6	1	2	FACETS	0.817	0.697	0.948	0.817	0.697	0.948	CLONAL	1	TRUE	1	0.16	2		198	842	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369241	118369241	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs781805661	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	40	176	0	ENST00000534358.1:c.5959G>A	p.Glu1987Lys	p.E1987K	ENST00000534358	NM_005933.3	1987	Gaa/Aaa	22/36	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.16	2		176	402	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905391	11905391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781494988	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	51	224	1	ENST00000396373.4:c.41G>A	p.Arg14Gln	p.R14Q	ENST00000396373	NM_001987.4	14	cGa/cAa	2/8	0.3	2	FACETS	0.828	0.702	0.967			1	CLONAL	1	TRUE	NA	0.16	2		225	770	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489582	56489582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56387488	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	26	189	0	ENST00000267101.3:c.2047C>T	p.Arg683Trp	p.R683W	ENST00000267101	NM_001982.3	683	Cgg/Tgg	17/28	1	2	FACETS	0.689	0.544	0.855	0.689	0.544	0.855	SUBCLONAL	1	TRUE	1	0.16	2		189	472	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813307	102813307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764732420	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	48	242	0	ENST00000307046.8:c.382G>A	p.Asp128Asn	p.D128N	ENST00000307046	NM_001111285.1	128	Gac/Aac	3/4	1	2	FACETS	0.66	0.556	0.775	0.66	0.556	0.775	SUBCLONAL	1	TRUE	1	0.16	2		242	909	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426776	121426776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150513055	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	79	366	1	ENST00000257555.6:c.467C>T	p.Thr156Met	p.T156M	ENST00000257555		156	aCg/aTg	2/10	1	2	FACETS	0.921	0.808	1	0.921	0.808	1	CLONAL	1	TRUE	1	0.16	2		367	1072	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337731	73337731	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	36	292	0	ENST00000377767.4:c.1985T>C	p.Met662Thr	p.M662T	ENST00000377767	NM_014953.3	662	aTg/aCg	16/21	1	2	FACETS	0.832	0.683	0.999	0.832	0.683	0.999	CLONAL	1	TRUE	1	0.16	2		292	541	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434592	110434592	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	46	171	2	ENST00000375856.3:c.3809C>A	p.Pro1270Gln	p.P1270Q	ENST00000375856	NM_003749.2	1270	cCg/cAg	1/2	1	2	FACETS	0.917	0.771	1	0.917	0.771	1	CLONAL	1	TRUE	1	0.16	2		173	627	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434745	110434745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	41	264	0	ENST00000375856.3:c.3656C>T	p.Pro1219Leu	p.P1219L	ENST00000375856	NM_003749.2	1219	cCg/cTg	1/2	1	2	FACETS	0.679	0.564	0.808	0.679	0.564	0.808	SUBCLONAL	1	TRUE	1	0.16	2		264	755	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872045	35872045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	66	402	0	ENST00000216797.5:c.568G>A	p.Ala190Thr	p.A190T	ENST00000216797	NM_020529.2	190	Gcc/Acc	4/6	1	2	FACETS	0.857	0.742	0.982	0.857	0.742	0.982	CLONAL	1	TRUE	1	0.16	2		402	963	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634318	23634318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	47	385	0	ENST00000261584.4:c.2968G>A	p.Glu990Lys	p.E990K	ENST00000261584	NM_024675.3	990	Gaa/Aaa	9/13	1	2	FACETS	0.813	0.684	0.955	0.813	0.684	0.955	CLONAL	1	TRUE	1	0.16	2		385	723	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662394	67662394	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	60	326	0	ENST00000264010.4:c.1640A>G	p.Asp547Gly	p.D547G	ENST00000264010	NM_006565.3	547	gAc/gGc	9/12	1	2	FACETS	0.757	0.65	0.874	0.757	0.65	0.874	SUBCLONAL	1	TRUE	1	0.16	2		326	991	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40376843	40376843	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769688321	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	65	538	0	ENST00000293328.3:c.329G>A	p.Arg110His	p.R110H	ENST00000293328	NM_012448.3	110	cGc/cAc	4/19	0.3	1	FACETS	0.731	0.632	0.84	0.731	0.632	0.84	SUBCLONAL	1	TRUE	0	0.16	1		538	1022	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436149	56436149	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	60	317	0	ENST00000407977.2:c.988C>T	p.Arg330Ter	p.R330*	ENST00000407977		330	Cga/Tga	9/10	1	2	FACETS	0.975	0.839	1	0.975	0.839	1	CLONAL	1	TRUE	1	0.16	2		317	769	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530162	63530162	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777885192	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	61	341	2	ENST00000307078.5:c.2273C>T	p.Ala758Val	p.A758V	ENST00000307078	NM_004655.3	758	gCg/gTg	10/11	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.16	2		343	743	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611735	1611735	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375296938	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	67	366	1	ENST00000344749.5:c.1927G>A	p.Glu643Lys	p.E643K	ENST00000344749	NM_001136139.2	643	Gaa/Aaa	19/19	1	2	FACETS	0.751	0.65	0.861	0.751	0.65	0.861	SUBCLONAL	1	TRUE	1	0.16	2		367	1115	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141492	11141492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	69	311	1	ENST00000358026.2:c.3469C>T	p.Arg1157Trp	p.R1157W	ENST00000358026	NM_001128849.1	1157	Cgg/Tgg	25/36	1	2	FACETS	0.884	0.768	1	0.884	0.768	1	CLONAL	1	TRUE	1	0.16	2		312	976	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905495	50905495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774030917	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	59	360	1	ENST00000440232.2:c.623C>T	p.Pro208Leu	p.P208L	ENST00000440232	NM_002691.3	208	cCg/cTg	6/27	1	2	FACETS	0.674	0.577	0.779	0.674	0.577	0.779	SUBCLONAL	1	TRUE	1	0.16	2		361	1095	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716039	52716039	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	57	326	0	ENST00000322088.6:c.604A>G	p.Lys202Glu	p.K202E	ENST00000322088	NM_014225.5	202	Aag/Gag	5/15	1	2	FACETS	0.738	0.631	0.856	0.738	0.631	0.856	SUBCLONAL	1	TRUE	1	0.16	2		326	965	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164469	36164469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	35	101	0	ENST00000300305.3:c.1406C>T	p.Ser469Phe	p.S469F	ENST00000300305		469	tCc/tTc	8/8	1	2	FACETS	0.879	0.719	1	0.879	0.719	1	CLONAL	1	TRUE	1	0.16	2		101	498	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225926	53225926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	59	334	0	ENST00000375401.3:c.2923G>A	p.Glu975Lys	p.E975K	ENST00000375401	NM_004187.3	975	Gaa/Aaa	19/26	0.3	1	FACETS	0.648	0.556	0.75	0.648	0.556	0.75	SUBCLONAL	1	TRUE	0	0.16	1		334	1047	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0004608-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	125	724	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.26	2		724	818	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0004608-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	89	488	1	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.26	2		489	641	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622630	158622630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004608-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	135	1020	2	ENST00000263640.3:c.869C>T	p.Ser290Leu	p.S290L	ENST00000263640	NM_001105.4	290	tCg/tTg	8/11	1	2	FACETS	0.937	0.85	1	0.937	0.85	1	CLONAL	1	TRUE	1	0.26	2		1022	1108	SUCCESS
APC	324	MSKCC	GRCh37	5	112173531	112173531	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004608-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	109	539	0	ENST00000257430.4:c.2240C>A	p.Ser747Ter	p.S747*	ENST00000257430	NM_000038.5	747	tCa/tAa	16/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.26	2		539	658	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374389	31374389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371009965	NA	P-0004608-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	158	633	0	ENST00000328111.2:c.388C>T	p.Arg130Cys	p.R130C	ENST00000328111	NM_006892.3	130	Cgc/Tgc	5/23	1	2	FACETS	0.938	0.857	1	0.938	0.857	1	CLONAL	1	TRUE	1	0.26	2		633	1296	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770587	40770587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776338672	NA	P-0004608-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	54	567	0	ENST00000373198.4:c.2795G>A	p.Arg932His	p.R932H	ENST00000373198	NM_133170.3	932	cGc/cAc	19/32	1	2	FACETS	0.472	0.402	0.549	0.472	0.402	0.549	SUBCLONAL	1	TRUE	1	0.26	2		567	880	SUCCESS
AR	367	MSKCC	GRCh37	X	66766199	66766199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035114992	NA	P-0004608-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	65	339	0	ENST00000374690.3:c.1211C>T	p.Ala404Val	p.A404V	ENST00000374690	NM_000044.3	404	gCg/gTg	1/8	0.231708902181357	1	FACETS	0.619	0.536	0.709	0.619	0.536	0.709	SUBCLONAL	1	TRUE	0	0.26	1		339	703	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734156	58734156	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs747947002	NA	P-0004608-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1515	179	967	0	ENST00000305921.3:c.1216del	p.Thr406ProfsTer3	p.T406Pfs*3	ENST00000305921	NM_003620.3	405	gAa/ga	5/6	1	2	FACETS	0.813	0.746	0.883	0.813	0.746	0.883	CLONAL	1	TRUE	1	0.26	2		967	1694	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022643	31022643	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs772303842	NA	P-0004608-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1250	201	650	0	ENST00000375687.4:c.2129del	p.Gly710GlufsTer15	p.G710Efs*15	ENST00000375687	NM_015338.5	710	Gga/ga	13/13	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.26	2		650	1451	SUCCESS
APC	324	MSKCC	GRCh37	5	112175903	112175903	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004608-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	98	453	0	ENST00000257430.4:c.4612del	p.Glu1538AsnfsTer27	p.E1538Nfs*27	ENST00000257430	NM_000038.5	1538	Gaa/aa	16/16	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.26	2		453	733	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958519	90958519	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs748073091	NA	P-0004621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	49	352	0	ENST00000265433.3:c.1919A>G	p.Asn640Ser	p.N640S	ENST00000265433	NM_002485.4	640	aAt/aGt	13/16	0.452435559026233	7	FACETS	1	0.948	1	0.321	0.272	0.373	CLONAL	1	FALSE	3	0.452435559026233	7		352	360	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0004625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	773	282	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.220107852610734	3	FACETS	1	0.995	1	1	0.998	1	CLONAL	7	TRUE	0	0.220107852610734	3		282	1040	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0004625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	103	375	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.991	0.905	1	1	0.992	1	CLONAL	4	TRUE	1	0.220107852610734	2		376	236	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740518	58740518	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	67	687	0	ENST00000305921.3:c.1423G>T	p.Glu475Ter	p.E475*	ENST00000305921	NM_003620.3	475	Gaa/Taa	6/6	0.255327626523171	3	FACETS	1	0.932	1	0.557	0.484	0.636	CLONAL	1	TRUE	1	0.23	3		687	583	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344023	70344023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	41	342	0	ENST00000374080.3:c.1759G>A	p.Glu587Lys	p.E587K	ENST00000374080		587	Gag/Aag	13/45	1	1	FACETS	0.968	0.809	1	0.968	0.809	1	CLONAL	1	TRUE	0	0.23	1		342	326	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412033	116412050	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTCCAGAAGGTATATT	TTTTCCAGAAGGTATATT	-	novel	NA	P-0004655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	23	316	0	ENST00000397752.3:c.3019_3028+8del		p.X1007_splice	ENST00000397752	NM_000245.2	1007		14/21	0.3	1	FACETS	0.898	0.705	1	0.898	0.705	1	CLONAL	1	TRUE	0	0.23	1		316	197	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0004677-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	277	447	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	1	2	FACETS	0.995	0.937	1	0.995	0.937	1	CLONAL	1	TRUE	1	0.641317879486863	2		447	868	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127319	17127319	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774358971	NA	P-0004737-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	183	484	0	ENST00000285071.4:c.535C>T	p.Arg179Trp	p.R179W	ENST00000285071	NM_144997.5	179	Cgg/Tgg	6/14	1	2	FACETS	0.965	0.89	1	0.965	0.89	1	CLONAL	1	TRUE	1	0.36009571807948	2		484	1053	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440661	56440661	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004737-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	195	565	2	ENST00000407977.2:c.557T>C	p.Ile186Thr	p.I186T	ENST00000407977		186	aTt/aCt	5/10	1	2	FACETS	0.948	0.877	1	0.948	0.877	1	CLONAL	1	TRUE	1	0.36009571807948	2		567	1142	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220370	1220371	+	splice_acceptor_variant	Splice_Site	DEL	AG	AG	-	novel	NA	P-0004737-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	213	480	0	ENST00000326873.7:c.465-2_465-1del		p.X155_splice	ENST00000326873	NM_000455.4	155			0.36009571807948	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.36009571807948	1		480	938	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599341	55599341	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519761	NA	P-0004760-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	53	295	0	ENST00000288135.5:c.2467T>G	p.Tyr823Asp	p.Y823D	ENST00000288135	NM_000222.2	823	Tat/Gat	17/21	0.385013640184594	6	FACETS	1	0.965	1			1	CLONAL	1	TRUE	NA	0.4	6		295	322	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593615	+	inframe_deletion	In_Frame_Del	DEL	AGTGGAAGGTTGTTG	AGTGGAAGGTTGTTG	-	novel	NA	P-0004760-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	124	445	0	ENST00000288135.5:c.1669_1683del	p.Trp557_Glu561del	p.W557_E561del	ENST00000288135	NM_000222.2	556	cAGTGGAAGGTTGTTGag/cag	11/21	0.385013640184594	6	FACETS	1	0.917	1			1	CLONAL	3	TRUE	NA	0.4	6		445	371	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	189	427	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.350585955609965	3	FACETS	0.925	0.858	0.994	0.925	0.858	0.994	CLONAL	2	TRUE	1	0.350585955609965	3		427	685	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46733241	46733241	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	139	268	0	ENST00000371975.4:c.1002G>C	p.Glu334Asp	p.E334D	ENST00000371975	NM_003579.3	334	gaG/gaC	9/18	1	2	FACETS	0.968	0.882	1	0.968	0.882	1	CLONAL	1	TRUE	1	0.350585955609965	2		268	819	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	121	427	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	0.328348300587657	2		427	602	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912580	NA	P-0004796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	106	355	0	ENST00000342988.3:c.1157G>A	p.Gly386Asp	p.G386D	ENST00000342988	NM_005359.5	386	gGt/gAt	10/12	0.328348300587657	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.328348300587657	1		355	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577575	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587782289	NA	P-0004796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	107	447	0	ENST00000269305.4:c.706T>G	p.Tyr236Asp	p.Y236D	ENST00000269305	NM_001126112.2	236	Tac/Gac	7/11	0.328348300587657	1	FACETS	0.867	0.779	0.96	0.867	0.779	0.96	CLONAL	1	TRUE	0	0.328348300587657	1		447	628	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0004808-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	129	228	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.525535782333209	4	FACETS	0.935	0.865	1	0.935	0.865	1	CLONAL	3	TRUE	1	0.525535782333209	4		228	267	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102199	27102199	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0004843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	197	438	0	ENST00000324856.7:c.5124+1G>C		p.X1708_splice	ENST00000324856	NM_006015.4	1708			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		438	979	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0004850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	366	433	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.542972707974534	1	FACETS	0.997	0.95	1	0.997	0.95	1	CLONAL	1	TRUE	0	0.580636178794551	1		434	897	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792755	33792757	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs746430067	NA	P-0004850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	18	60	0	ENST00000498907.2:c.564_566del	p.Pro189del	p.P189del	ENST00000498907	NM_004364.3	188	ccGCCc/ccc	1/1	1	2	FACETS	0.504	0.384	0.643	0.504	0.384	0.643	SUBCLONAL	1	TRUE	1	0.580636178794551	2		60	123	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162050	47162050	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	297	402	0	ENST00000409792.3:c.4076C>T	p.Ser1359Phe	p.S1359F	ENST00000409792	NM_014159.6	1359	tCc/tTc	3/21	1	2	FACETS	0.829	0.78	0.88	0.829	0.78	0.88	CLONAL	1	TRUE	1	0.580636178794551	2		402	1234	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163124	47163124	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs200816574	NA	P-0004850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	306	407	0	ENST00000409792.3:c.3002C>G	p.Ser1001Cys	p.S1001C	ENST00000409792	NM_014159.6	1001	tCt/tGt	3/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.580636178794551	2		407	1046	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403476	138403476	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	360	431	0	ENST00000289153.2:c.2306C>T	p.Ser769Leu	p.S769L	ENST00000289153	NM_006219.2	769	tCa/tTa	15/22	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.580636178794551	2		431	1158	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176521	142176521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	405	465	0	ENST00000350721.4:c.7580G>A	p.Gly2527Glu	p.G2527E	ENST00000350721	NM_001184.3	2527	gGa/gAa	45/47	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.580636178794551	2		465	1347	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77085411	77085411	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0004850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3044	300	460	0	ENST00000356341.3:c.440-1G>A		p.X147_splice	ENST00000356341	NM_002576.4	147			0.580636178794551	9	FACETS	0.937	0.877	0.999			1	CLONAL	1	TRUE	NA	0.580636178794551	9		460	3344	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0004859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	116	294	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.285021100120101	3	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	1	0.349188427494379	3		294	382	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578530	7578530	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	19	342	0	ENST00000269305.4:c.400T>G	p.Phe134Val	p.F134V	ENST00000269305	NM_001126112.2	134	Ttt/Gtt	5/11	0.349188427494379	3	FACETS	0.316	0.239	0.407	0.158	0.119	0.204	SUBCLONAL	1	TRUE	1	0.349188427494379	3		342	404	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178622	56178622	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	160	325	0	ENST00000399503.3:c.3595C>T	p.Gln1199Ter	p.Q1199*	ENST00000399503	NM_005921.1	1199	Cag/Tag	14/20	0.349188427494379	3	FACETS	0.949	0.882	1	1	0.989	1	CLONAL	3	TRUE	1	0.349188427494379	3		325	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0004869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	812	927	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.921528116163147	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.921528116163147	2		927	873	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307962	11307962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	55	847	0	ENST00000361445.4:c.1030G>A	p.Gly344Arg	p.G344R	ENST00000361445	NM_004958.3	344	Gga/Aga	7/58	0.916394406295626	2	FACETS	0.157	0.134	0.183	0.079	0.067	0.092	SUBCLONAL	1	TRUE	0	0.921528116163147	2		847	760	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695885	117695885	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	267	693	0	ENST00000369458.3:c.552A>C	p.Gln184His	p.Q184H	ENST00000369458	NM_024626.3	184	caA/caC	4/6	0.921528116163147	3	FACETS	1	0.956	1	0.509	0.479	0.54	CLONAL	1	TRUE	1	0.921528116163147	3		693	831	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198283294	198283294	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	284	767	0	ENST00000335508.6:c.434C>G	p.Pro145Arg	p.P145R	ENST00000335508	NM_012433.2	145	cCt/cGt	5/25	0.81451957746764	3	FACETS	1	0.994	1	0.72	0.683	0.758	CLONAL	1	TRUE	1	0.921528116163147	3		767	625	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72861838	72861838	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs142487191	NA	P-0004869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	201	657	0	ENST00000325599.8:c.1044A>G	p.Ile348Met	p.I348M	ENST00000325599	NM_018130.2	348	atA/atG	9/11	NA	2	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.921528116163147	2		657	417	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670540	134670540	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	230	873	1	ENST00000398015.3:c.451T>C	p.Phe151Leu	p.F151L	ENST00000398015	NM_004441.4	151	Ttt/Ctt	3/16	NA	2	FACETS	0.954	0.899	1			1	INDETERMINATE	1	TRUE	NA	0.921528116163147	2		874	523	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129057	152129057	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	56	875	0	ENST00000206249.3:c.10A>G	p.Thr4Ala	p.T4A	ENST00000206249	NM_000125.3	4	Acc/Gcc	1/8	0.329743433124324	1	FACETS	0.111	0.095	0.129	0.111	0.095	0.129	INDETERMINATE	1	TRUE	0	0.921528116163147	1		875	590	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508727	106508727	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	466	665	1	ENST00000359195.3:c.721C>A	p.Pro241Thr	p.P241T	ENST00000359195	NM_002649.2	241	Ccc/Acc	2/11	0.835365307119262	3	FACETS	0.964	0.931	0.998	0.964	0.931	0.998	CLONAL	2	TRUE	1	0.921528116163147	3		666	766	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659550	88659550	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0004869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	41	486	0	ENST00000372037.3:c.334-1G>A		p.X112_splice	ENST00000372037	NM_004329.2	112			0.319787640537131	5	FACETS	0.344	0.285	0.408			1	INDETERMINATE	1	TRUE	NA	0.921528116163147	5		486	617	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106666	2106666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772558666	NA	P-0004869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	427	875	0	ENST00000219476.3:c.670G>A	p.Ala224Thr	p.A224T	ENST00000219476	NM_000548.3	224	Gcc/Acc	8/42	0.555239287564306	3	FACETS	0.873	0.839	0.907	0.873	0.839	0.907	CLONAL	2	TRUE	1	0.921528116163147	3		875	775	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101973	11101973	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	629	763	1	ENST00000358026.2:c.1393G>T	p.Glu465Ter	p.E465*	ENST00000358026	NM_001128849.1	465	Gag/Tag	8/36	0.921528116163147	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.921528116163147	2		764	678	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553615	29553616	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TA	novel	NA	P-0004869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	29	569	0	ENST00000356175.3:c.2164_2165delinsTA	p.Gly722Ter	p.G722*	ENST00000356175	NM_000267.3	722	GGg/TAg	18/57	0.921528116163147	2	FACETS	0.142	0.114	0.175	0.071	0.057	0.088	SUBCLONAL	1	TRUE	0	0.921528116163147	2		569	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0004893-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	247	497	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	NA	2	FACETS	0.881	0.824	0.94			1	INDETERMINATE	2	TRUE	NA	0.26171662513776	2		497	1071	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620093	21620093	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004893-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	60	362	0	ENST00000382592.4:c.73G>T	p.Gly25Trp	p.G25W	ENST00000382592	NM_014572.2	25	Ggg/Tgg	2/8	0.241209733340258	1	FACETS	0.381	0.327	0.441	0.381	0.327	0.441	SUBCLONAL	1	TRUE	0	0.26171662513776	1		362	1045	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659675	NA	P-0004894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	105	182	0	ENST00000269305.4:c.764T>C	p.Ile255Thr	p.I255T	ENST00000269305	NM_001126112.2	255	aTc/aCc	7/11	0.314178765696947	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.314178765696947	2		182	283	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591892	48591892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767345	NA	P-0004894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	38	310	0	ENST00000342988.3:c.1055G>A	p.Gly352Glu	p.G352E	ENST00000342988	NM_005359.5	352	gGa/gAa	9/12	0.271884222620279	2	FACETS	0.65	0.538	0.775	0.325	0.269	0.388	SUBCLONAL	1	TRUE	0	0.314178765696947	2		310	372	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004905-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	164	427	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.163811000574686	4	FACETS	1	0.98	1			1	CLONAL	2	TRUE	NA	0.234389653438864	4		427	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0004905-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	53	369	0	ENST00000269305.4:c.97-1G>A		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.234389653438864	1	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	0	0.234389653438864	1		369	386	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440741	56440741	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004905-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	34	470	0	ENST00000407977.2:c.477G>A	p.Trp159Ter	p.W159*	ENST00000407977		159	tgG/tgA	5/10	0.234389653438864	1	FACETS	0.529	0.432	0.639	0.529	0.432	0.639	SUBCLONAL	1	TRUE	0	0.234389653438864	1		470	484	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0004906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	31	269	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.792	0.639	0.967	0.792	0.639	0.967	CLONAL	1	TRUE	1	0.13	2		269	602	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0004906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	74	344	0	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	0.23445542640308	3	FACETS	0.814	0.712	0.924	0.814	0.712	0.924	CLONAL	2	TRUE	1	0.13	3		344	745	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0004906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	23	572	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.0985679813663427	0	FACETS	0.597	0.464	0.751			1	SUBCLONAL	1	TRUE	0	0.13	0		572	516	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732918	30732918	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060501984	NA	P-0004906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	34	389	0	ENST00000295754.5:c.1531C>T	p.Gln511Ter	p.Q511*	ENST00000295754	NM_003242.5	511	Cag/Tag	7/7	1	2	FACETS	1	0.838	1	1	0.838	1	CLONAL	1	TRUE	1	0.13	2		389	508	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974714	21974714	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	20	261	0	ENST00000304494.5:c.113C>A	p.Pro38His	p.P38H	ENST00000304494	NM_000077.4	38	cCc/cAc	1/3	1	2	FACETS	0.908	0.694	1	0.908	0.694	1	CLONAL	1	TRUE	1	0.13	2		261	339	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0004909-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	204	294	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	2	TRUE	NA	0.557459949150195	2		294	342	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879885	37879885	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004909-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	136	513	0	ENST00000269571.5:c.2180G>C	p.Gly727Ala	p.G727A	ENST00000269571		727	gGa/gCa	18/27	0.493325912577216	1	FACETS	0.978	0.9	1	0.978	0.9	1	CLONAL	1	TRUE	0	0.557459949150195	1		513	360	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057520005	NA	P-0004909-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	166	566	0	ENST00000269305.4:c.820G>C	p.Val274Leu	p.V274L	ENST00000269305	NM_001126112.2	274	Gtt/Ctt	8/11	0.504717149629331	1	FACETS	0.922	0.854	0.991	0.922	0.854	0.991	CLONAL	1	TRUE	0	0.557459949150195	1		566	466	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911628	32911628	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004909-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	117	576	0	ENST00000380152.3:c.3136G>C	p.Glu1046Gln	p.E1046Q	ENST00000380152		1046	Gaa/Caa	11/27	0.45737047710356	0	FACETS	0.409	0.371	0.449			1	SUBCLONAL	1	TRUE	0	0.557459949150195	0		576	454	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023676	27023676	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs867647567	NA	P-0004909-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	120	385	0	ENST00000324856.7:c.782C>A	p.Ser261Ter	p.S261*	ENST00000324856	NM_006015.4	261	tCg/tAg	1/20	1	2	FACETS	0.978	0.89	1	0.978	0.89	1	CLONAL	1	TRUE	1	0.557459949150195	2		385	440	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089768	27089768	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004909-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	62	136	0	ENST00000324856.7:c.2724C>G	p.Ile908Met	p.I908M	ENST00000324856	NM_006015.4	908	atC/atG	8/20	1	2	FACETS	0.959	0.839	1	0.959	0.839	1	CLONAL	1	TRUE	1	0.557459949150195	2		136	232	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612091	189612091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004909-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	70	397	0	ENST00000264731.3:c.1843C>T	p.His615Tyr	p.H615Y	ENST00000264731	NM_003722.4	615	Cat/Tat	14/14	0.557459949150195	3	FACETS	0.497	0.433	0.566	0.249	0.216	0.283	SUBCLONAL	1	TRUE	1	0.557459949150195	3		397	646	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39074439	39074439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1298143494	NA	P-0004909-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	106	271	0	ENST00000357387.3:c.41G>A	p.Arg14Gln	p.R14Q	ENST00000357387	NM_152756.3	14	cGa/cAa	1/38	0.557459949150195	3	FACETS	1	0.955	1	0.551	0.497	0.608	CLONAL	1	TRUE	1	0.557459949150195	3		271	441	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522671	176522671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004909-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	156	510	1	ENST00000292408.4:c.1768G>T	p.Val590Phe	p.V590F	ENST00000292408	NM_213647.1	590	Gtc/Ttc	13/18	0.557459949150195	4	FACETS	0.821	0.751	0.894			1	CLONAL	1	TRUE	NA	0.557459949150195	4		511	1062	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178623	32178623	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004909-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	139	446	0	ENST00000375023.3:c.2771G>T	p.Gly924Val	p.G924V	ENST00000375023	NM_004557.3	924	gGc/gTc	18/30	1	2	FACETS	0.974	0.892	1	0.974	0.892	1	CLONAL	1	TRUE	1	0.557459949150195	2		446	512	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276944	123276944	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868243618	NA	P-0004909-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	108	357	0	ENST00000358487.5:c.973G>A	p.Glu325Lys	p.E325K	ENST00000358487	NM_000141.4	325	Gag/Aag	8/18	1	2	FACETS	0.814	0.734	0.897	0.814	0.734	0.897	CLONAL	1	TRUE	1	0.557459949150195	2		357	476	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007725	45007725	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004909-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	60	456	0	ENST00000558401.1:c.172G>C	p.Asp58His	p.D58H	ENST00000558401	NM_004048.2	58	Gac/Cac	2/4	1	2	FACETS	0.464	0.4	0.533	0.464	0.4	0.533	SUBCLONAL	1	TRUE	1	0.557459949150195	2		456	464	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007752	45007752	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004909-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	69	461	0	ENST00000558401.1:c.199G>C	p.Glu67Gln	p.E67Q	ENST00000558401	NM_004048.2	67	Gaa/Caa	2/4	1	2	FACETS	0.517	0.451	0.588	0.517	0.451	0.588	SUBCLONAL	1	TRUE	1	0.557459949150195	2		461	479	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763201	59763201	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004909-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	51	403	0	ENST00000259008.2:c.2901G>C	p.Glu967Asp	p.E967D	ENST00000259008	NM_032043.2	967	gaG/gaC	19/20	1	2	FACETS	0.451	0.384	0.524	0.451	0.384	0.524	SUBCLONAL	1	TRUE	1	0.557459949150195	2		403	406	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875940	76875940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004909-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	124	553	0	ENST00000373344.5:c.5195C>T	p.Ser1732Phe	p.S1732F	ENST00000373344	NM_000489.3	1732	tCt/tTt	20/35	0.493325912577216	1	FACETS	0.689	0.627	0.753	0.689	0.627	0.753	SUBCLONAL	1	TRUE	0	0.557459949150195	1		553	466	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0004914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	283	75	0				ENST00000310581	NM_198253.2	-/1132			0.429659276294109	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	2	0.628390782676896	4		75	634	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0004914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	314	361	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.429659276294109	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	2	0.628390782676896	4		362	682	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0004914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	603	480	1	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.186214096622987	3	FACETS	0.954	0.928	0.98			1	INDETERMINATE	3	TRUE	NA	0.628390782676896	3		481	881	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	448	415	0	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	0.429659276294109	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	2	0.628390782676896	4		415	999	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11269484	11269484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	271	396	0	ENST00000361445.4:c.3686C>T	p.Pro1229Leu	p.P1229L	ENST00000361445	NM_004958.3	1229	cCt/cTt	25/58	0.429659276294109	4	FACETS	0.75	0.705	0.797	0.75	0.705	0.797	SUBCLONAL	2	TRUE	2	0.628390782676896	4		396	936	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872710	136872710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	363	612	0	ENST00000241393.3:c.788C>T	p.Ser263Phe	p.S263F	ENST00000241393	NM_003467.2	263	tCc/tTc	2/2	0.202527214072686	2	FACETS	1	0.993	1	0.617	0.586	0.647	INDETERMINATE	1	TRUE	0	0.628390782676896	2		612	937	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285320	212285320	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	169	306	0	ENST00000342788.4:c.2981A>G	p.Lys994Arg	p.K994R	ENST00000342788	NM_005235.2	994	aAg/aGg	25/28	0.202527214072686	2	FACETS	1	0.989	1	0.671	0.624	0.718	INDETERMINATE	1	TRUE	0	0.628390782676896	2		306	401	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204933	128204933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	526	545	1	ENST00000341105.2:c.508C>T	p.Leu170Phe	p.L170F	ENST00000341105	NM_032638.4	170	Ctt/Ttt	3/6	0.628390782676896	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	1	0.628390782676896	3		546	895	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515296	149515296	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	251	413	0	ENST00000261799.4:c.186G>A	p.Trp62Ter	p.W62*	ENST00000261799	NM_002609.3	62	tgG/tgA	3/23	0.281767838309788	5	FACETS	0.888	0.832	0.945			1	INDETERMINATE	2	TRUE	NA	0.628390782676896	5		413	874	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965562	93965562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	319	538	0	ENST00000369303.4:c.2366C>T	p.Ala789Val	p.A789V	ENST00000369303	NM_004440.3	789	gCt/gTt	13/17	0.587557343282968	2	FACETS	0.847	0.809	0.886	0.847	0.809	0.886	CLONAL	2	TRUE	0	0.628390782676896	2		538	599	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686321	117686321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	225	301	0	ENST00000368508.3:c.3020G>A	p.Gly1007Glu	p.G1007E	ENST00000368508	NM_002944.2	1007	gGa/gAa	20/43	0.587557343282968	2	FACETS	0.916	0.868	0.963	0.916	0.868	0.963	CLONAL	2	TRUE	0	0.628390782676896	2		301	391	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860679	151860679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	435	466	0	ENST00000262189.6:c.9983G>A	p.Arg3328Lys	p.R3328K	ENST00000262189	NM_170606.2	3328	aGa/aAa	43/59	0.585002800253715	5	FACETS	1	0.985	1	0.713	0.68	0.746	CLONAL	2	TRUE	2	0.628390782676896	5		466	1257	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202099	67202099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237305807	NA	P-0004914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	445	445	0	ENST00000312629.5:c.1202G>A	p.Gly401Asp	p.G401D	ENST00000312629	NM_003952.2	401	gGc/gAc	14/15	0.602458369047746	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.628390782676896	4		445	1113	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202896	133202896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	194	280	0	ENST00000320574.5:c.6338C>T	p.Ser2113Phe	p.S2113F	ENST00000320574	NM_006231.2	2113	tCc/tTc	46/49	0.205710003300442	2	FACETS	1	0.989	1	0.646	0.604	0.689	INDETERMINATE	1	TRUE	0	0.628390782676896	2		280	478	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986535	36986535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301600327	NA	P-0004914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	560	373	3	ENST00000354822.5:c.1154C>T	p.Ser385Leu	p.S385L	ENST00000354822	NM_001079668.2	385	tCg/tTg	3/3	0.483604787771273	3	FACETS	1	0.985	1			1	CLONAL	3	TRUE	NA	0.628390782676896	3		376	768	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035146	42035146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	461	554	0	ENST00000219905.7:c.4988C>T	p.Thr1663Ile	p.T1663I	ENST00000219905	NM_001164273.1	1663	aCc/aTc	15/24	0.523845435027333	4	FACETS	0.941	0.9	0.983	0.941	0.9	0.983	CLONAL	2	TRUE	2	0.628390782676896	4		554	1269	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916226	9916226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	220	397	0	ENST00000330684.3:c.2063G>A	p.Gly688Glu	p.G688E	ENST00000330684	NM_001134407.1	688	gGa/gAa	10/13	0.628390782676896	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.628390782676896	1		397	454	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435377	56435377	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571903323	NA	P-0004914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	413	339	0	ENST00000407977.2:c.1760C>T	p.Pro587Leu	p.P587L	ENST00000407977		587	cCc/cTc	9/10	0.552575512801805	3	FACETS	0.944	0.912	0.975	0.944	0.912	0.975	CLONAL	3	TRUE	0	0.628390782676896	3		339	610	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040645	47040645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556779001	NA	P-0004914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	378	450	0	ENST00000377604.3:c.1280C>T	p.Thr427Ile	p.T427I	ENST00000377604	NM_001204468.1	427	aCc/aTc	13/24	0.523845435027333	4	FACETS	0.953	0.907	1	0.953	0.907	1	CLONAL	2	TRUE	2	0.628390782676896	4		450	1028	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413117	63413117	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	472	450	1	ENST00000330258.3:c.50C>T	p.Ser17Phe	p.S17F	ENST00000330258	NM_152424.3	17	tCt/tTt	2/2	0.523845435027333	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.628390782676896	4		451	1137	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019807	123019807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1174668840	NA	P-0004914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	240	369	0	ENST00000355640.3:c.295G>A	p.Glu99Lys	p.E99K	ENST00000355640		99	Gaa/Aaa	2/7	0.523845435027333	4	FACETS	0.927	0.87	0.984	0.927	0.87	0.984	CLONAL	2	TRUE	2	0.628390782676896	4		369	671	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974715	21974732	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCCCCCGCCTCCA	GCAGCGCCCCCGCCTCCA	-	novel	NA	P-0004914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	181	206	0	ENST00000304494.5:c.95_112del	p.Leu32_Leu37del	p.L32_L37del	ENST00000304494	NM_000077.4	32	cTGGAGGCGGGGGCGCTGCcc/ccc	1/3	0.628390782676896	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.628390782676896	1		206	339	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073288	8073289	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0004914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	479	551	0	ENST00000377482.5:c.1370_1371delinsTT	p.Ser457Phe	p.S457F	ENST00000377482	NM_018948.3	457	tCC/tTT	4/4	0.429659276294109	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	2	0.628390782676896	4		551	1133	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118353210	118353211	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0004914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	308	262	0	ENST00000534358.1:c.4086_4086+1delinsAA		p.X1362_splice	ENST00000534358	NM_005933.3	1362		8/36	0.602458369047746	4	FACETS	0.926	0.876	0.977	0.926	0.876	0.977	CLONAL	2	TRUE	2	0.628390782676896	4		262	862	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004944-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	394	427	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.749353547564791	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.760895270392041	2		427	502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0004944-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	638	383	2	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.723431046149555	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.760895270392041	3		385	753	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604764	48604766	+	inframe_deletion	In_Frame_Del	DEL	TAC	TAC	-	novel	NA	P-0004944-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	192	465	1	ENST00000342988.3:c.1586_1588del	p.Leu529_His530delinsTyr	p.L529_H530delinsY	ENST00000342988	NM_005359.5	529	tTACac/tac	12/12	0.758711331601454	1	FACETS	0.942	0.889	0.994	0.942	0.889	0.994	CLONAL	1	TRUE	0	0.760895270392041	1		466	332	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447384	187447384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780987785	NA	P-0004944-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	54	383	0	ENST00000232014.4:c.809G>A	p.Arg270Gln	p.R270Q	ENST00000232014	NM_001130845.1	270	cGa/cAa	5/10	0.760895270392041	4	FACETS	0.239	0.203	0.279	0.08	0.067	0.093	SUBCLONAL	1	TRUE	1	0.760895270392041	4		383	1045	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223570	55223570	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004944-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	238	569	0	ENST00000275493.2:c.937G>T	p.Ala313Ser	p.A313S	ENST00000275493	NM_005228.3	313	Gcc/Tcc	8/28	0.315948855845632	5	FACETS	1	0.977	1	0.368	0.343	0.394	INDETERMINATE	1	TRUE	2	0.760895270392041	5		569	1214	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109744	115109744	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004944-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	317	530	0	ENST00000257566.3:c.2134G>A	p.Ala712Thr	p.A712T	ENST00000257566	NM_016569.3	712	Gcg/Acg	8/8	0.485396263457449	5	FACETS	1	0.994	1	0.491	0.463	0.52	CLONAL	1	TRUE	2	0.760895270392041	5		530	1211	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424214	49424214	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004944-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	152	201	0	ENST00000301067.7:c.13848del	p.Ser4617ValfsTer23	p.S4617Vfs*23	ENST00000301067	NM_003482.3	4616	ctG/ct	42/54	0.53240828003892	4	FACETS	1	0.94	1			1	CLONAL	2	TRUE	NA	0.760895270392041	4		201	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004965-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	119	466	0	ENST00000269305.4:c.380C>A	p.Ser127Tyr	p.S127Y	ENST00000269305	NM_001126112.2	127	tCc/tAc	5/11	0.515783146344165	1	FACETS	0.946	0.863	1	0.946	0.863	1	CLONAL	1	TRUE	0	0.515783146344165	1		466	362	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138375075	138375075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1405576100	NA	P-0004965-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	124	598	1	ENST00000289153.2:c.2984G>A	p.Arg995Gln	p.R995Q	ENST00000289153	NM_006219.2	995	cGg/cAg	21/22	0.50093529534167	1	FACETS	0.776	0.706	0.848	0.776	0.706	0.848	SUBCLONAL	1	TRUE	0	0.515783146344165	1		599	460	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0004990-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	69	373	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.928	0.813	1	1	0.98	1	CLONAL	2	TRUE	1	0.21	2		373	354	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843448	156843448	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004990-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	33	188	0	ENST00000524377.1:c.874A>T	p.Thr292Ser	p.T292S	ENST00000524377	NM_002529.3	292	Acg/Tcg	8/17	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.21	2		188	298	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048661	180048661	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004990-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	18	247	0	ENST00000261937.6:c.1901C>A	p.Ala634Asp	p.A634D	ENST00000261937	NM_182925.4	634	gCc/gAc	13/30	1	2	FACETS	0.56	0.421	0.724	0.56	0.421	0.724	SUBCLONAL	1	TRUE	1	0.21	2		247	306	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513255	106513255	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004990-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	40	266	0	ENST00000359195.3:c.2159A>C	p.Tyr720Ser	p.Y720S	ENST00000359195	NM_002649.2	720	tAt/tCt	4/11	1	2	FACETS	0.89	0.74	1	0.89	0.74	1	CLONAL	1	TRUE	1	0.21	2		266	428	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922217	100922217	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004990-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	20	448	0	ENST00000325455.5:c.2295G>C	p.Trp765Cys	p.W765C	ENST00000325455	NM_001202474.3	765	tgG/tgC	5/8	1	2	FACETS	0.515	0.393	0.658	0.515	0.393	0.658	SUBCLONAL	1	TRUE	1	0.21	2		448	370	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645288	67645288	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004990-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	28	304	0	ENST00000264010.4:c.553C>T	p.Pro185Ser	p.P185S	ENST00000264010	NM_006565.3	185	Ccc/Tcc	3/12	1	2	FACETS	0.719	0.575	0.883	0.719	0.575	0.883	SUBCLONAL	1	TRUE	1	0.21	2		304	371	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412370	63412370	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004990-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	28	424	1	ENST00000330258.3:c.797C>A	p.Ala266Asp	p.A266D	ENST00000330258	NM_152424.3	266	gCc/gAc	2/2	0.3	1	FACETS	0.607	0.485	0.747	0.607	0.485	0.747	SUBCLONAL	1	TRUE	0	0.21	1		425	393	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074123	8074235	+	frameshift_variant	Frame_Shift_Del	DEL	GTATCTGAGCTAGTTAGGAATTCCACCTCACAGTCTGTGTCATCCAGAGAGAGGGCTTCAGAGATTGGCAACGGTGGAAGAGGCCTAGAACCCCGTTCACAAAGAGGGGCACA	GTATCTGAGCTAGTTAGGAATTCCACCTCACAGTCTGTGTCATCCAGAGAGAGGGCTTCAGAGATTGGCAACGGTGGAAGAGGCCTAGAACCCCGTTCACAAAGAGGGGCACA	-	novel	NA	P-0004990-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	48	495	0	ENST00000377482.5:c.424_536del	p.Cys142ArgfsTer11	p.C142Rfs*11	ENST00000377482	NM_018948.3	142	TGTGCCCCTCTTTGTGAACGGGGTTCTAGGCCTCTTCCACCGTTGCCAATCTCTGAAGCCCTCTCTCTGGATGACACAGACTGTGAGGTGGAATTCCTAACTAGCTCAGATACa/a	4/4	1	2	FACETS	0.971	0.821	1	0.971	0.821	1	CLONAL	1	TRUE	1	0.21	2		495	471	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0005005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	64	294	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	0.233763369516457	2		294	424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576885	7576903	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTCTTTGGCTGGGGAGA	TCTTCTTTGGCTGGGGAGA	-	novel	NA	P-0005005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	72	431	0	ENST00000269305.4:c.943_961del	p.Ser315AsnfsTer24	p.S315Nfs*24	ENST00000269305	NM_001126112.2	315	TCTCCCCAGCCAAAGAAGAaa/aa	9/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.233763369516457	2		431	437	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112058	115112058	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	139	541	0	ENST00000257566.3:c.1682T>C	p.Met561Thr	p.M561T	ENST00000257566	NM_016569.3	561	aTg/aCg	7/8	0.640214796223643	1	FACETS	0.966	0.894	1	0.966	0.894	1	CLONAL	1	TRUE	0	0.629788707483616	1		541	313	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134255	2134255	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	145	568	0	ENST00000219476.3:c.4032G>C	p.Glu1344Asp	p.E1344D	ENST00000219476	NM_000548.3	1344	gaG/gaC	34/42	NA	2	FACETS	0.891	0.818	0.966			1	INDETERMINATE	1	TRUE	NA	0.629788707483616	2		568	517	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546829	9546829	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	180	573	1	ENST00000353224.5:c.1193C>A	p.Ala398Asp	p.A398D	ENST00000353224	NM_177990.2	398	gCt/gAt	5/10	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.629788707483616	2		574	474	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152063	11152082	+	frameshift_variant	Frame_Shift_Del	DEL	CGACGCCGGCTCCTCCACCC	CGACGCCGGCTCCTCCACCC	-	novel	NA	P-0005046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	418	553	0	ENST00000358026.2:c.4351_4370del	p.Ala1451HisfsTer29	p.A1451Hfs*29	ENST00000358026	NM_001128849.1	1449	agCGACGCCGGCTCCTCCACCCcg/agcg	31/36	0.640214796223643	1	FACETS	0.794	0.769	0.817	1	0.997	1	SUBCLONAL	2	TRUE	0	0.629788707483616	1		553	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578266	7578266	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	389	626	0	ENST00000269305.4:c.583del	p.Ile195SerfsTer52	p.I195Sfs*52	ENST00000269305	NM_001126112.2	195	Atc/tc	6/11	0.640214796223643	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.629788707483616	1		626	579	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149983	202150006	+	inframe_deletion	In_Frame_Del	DEL	CAGAGGGAACCTGGTACATCCAGT	CAGAGGGAACCTGGTACATCCAGT	-	novel	NA	P-0005046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	191	601	0	ENST00000358485.4:c.1426_1449del	p.Glu476_Ser483del	p.E476_S483del	ENST00000358485	NM_001080125.1	475	gCAGAGGGAACCTGGTACATCCAGTca/gca	8/9	0.338200981897938	3	FACETS	1	0.987	1	0.636	0.591	0.682	INDETERMINATE	1	TRUE	1	0.629788707483616	3		601	627	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641298	23641298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555460461	NA	P-0005049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	76	570	0	ENST00000261584.4:c.2177C>T	p.Pro726Leu	p.P726L	ENST00000261584	NM_024675.3	726	cCt/cTt	5/13	1	2	FACETS	0.169	0.147	0.192	0.169	0.147	0.192	SUBCLONAL	1	TRUE	1	0.8	2		570	1127	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0005062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	314	258	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.835999668307866	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.838560339026668	2		258	360	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0005129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	275	223	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.486853970007785	3	FACETS	0.966	0.912	1	0.966	0.912	1	CLONAL	2	TRUE	1	0.526790716773543	3		223	683	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0005129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	67	75	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.526790716773543	2		75	252	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416704	29416704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	160	139	0	ENST00000389048.3:c.4249G>A	p.Asp1417Asn	p.D1417N	ENST00000389048	NM_004304.4	1417	Gac/Aac	29/29	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.526790716773543	2		139	550	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965504	25965504	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	191	327	0	ENST00000435504.4:c.3702G>T	p.Glu1234Asp	p.E1234D	ENST00000435504		1234	gaG/gaT	13/13	1	2	FACETS	0.844	0.781	0.909	0.844	0.781	0.909	CLONAL	1	TRUE	1	0.526790716773543	2		327	859	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988507	36988507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	173	189	0	ENST00000354822.5:c.146C>T	p.Pro49Leu	p.P49L	ENST00000354822	NM_001079668.2	49	cCc/cTc	2/3	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.526790716773543	2		189	653	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557639	95557639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775912475	NA	P-0005129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	107	323	0	ENST00000393063.1:c.5428G>A	p.Asp1810Asn	p.D1810N	ENST00000393063	NM_030621.3	1810	Gat/Aat	26/28	1	2	FACETS	0.891	0.804	0.982	0.891	0.804	0.982	CLONAL	1	TRUE	1	0.526790716773543	2		323	456	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472646	88472646	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs759908835	NA	P-0005129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	122	182	0	ENST00000360948.2:c.1909A>G	p.Met637Val	p.M637V	ENST00000360948	NM_001012338.2	637	Atg/Gtg	16/19	1	2	FACETS	0.919	0.835	1	0.919	0.835	1	CLONAL	1	TRUE	1	0.526790716773543	2		182	504	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678572	88678572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1161765368	NA	P-0005129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	112	162	0	ENST00000360948.2:c.964G>A	p.Glu322Lys	p.E322K	ENST00000360948	NM_001012338.2	322	Gag/Aag	9/19	1	2	FACETS	0.847	0.765	0.932	0.847	0.765	0.932	CLONAL	1	TRUE	1	0.526790716773543	2		162	502	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778617	3778617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1254533716	NA	P-0005129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	160	157	0	ENST00000262367.5:c.6431C>T	p.Ala2144Val	p.A2144V	ENST00000262367	NM_004380.2	2144	gCc/gTc	31/31	1	2	FACETS	0.96	0.883	1	0.96	0.883	1	CLONAL	1	TRUE	1	0.526790716773543	2		157	633	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637607	52637611	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCA	CTCCA	-	novel	NA	P-0005129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	128	281	0	ENST00000394830.3:c.2705_2709del	p.Val902GlufsTer15	p.V902Efs*15	ENST00000394830	NM_018313.4	902	gTGGAG/g	18/30	0.214936194408769	1	FACETS	0.96	0.879	1	0.96	0.879	1	INDETERMINATE	1	TRUE	0	0.526790716773543	1		281	373	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508728	148508728	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs267601395	NA	P-0005146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	601	515	0	ENST00000320356.2:c.1936T>C	p.Tyr646His	p.Y646H	ENST00000320356	NM_004456.4	646	Tac/Cac	16/20	0.617525953156679	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.616561915644166	3		515	1197	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593667	55593669	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	rs1060502543	NA	P-0005146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	481	420	0	ENST00000288135.5:c.1735_1737del	p.Asp579del	p.D579del	ENST00000288135	NM_000222.2	578	tATGat/tat	11/21	0.398170720932517	5	FACETS	1	0.992	1			1	CLONAL	3	TRUE	NA	0.616561915644166	5		420	899	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045780	26045780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1295	116	1084	0	ENST00000540144.1:c.142G>A	p.Ala48Thr	p.A48T	ENST00000540144	NM_003531.2	48	Gcc/Acc	1/1	1	2	FACETS	0.267	0.239	0.296	0.267	0.239	0.296	SUBCLONAL	1	TRUE	1	0.616561915644166	2		1084	1411	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622089	43622089	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	28	357	0	ENST00000355710.3:c.3106G>C	p.Glu1036Gln	p.E1036Q	ENST00000355710	NM_020975.4	1036	Gag/Cag	19/20	1	2	FACETS	0.174	0.138	0.214	0.174	0.138	0.214	SUBCLONAL	1	TRUE	1	0.616561915644166	2		357	523	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114917823	114917823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	349	698	0	ENST00000543371.1:c.1313C>T	p.Thr438Ile	p.T438I	ENST00000543371	NM_001198531.1	438	aCc/aTc	12/14	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.616561915644166	2		698	1104	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148958	119148958	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	163	447	0	ENST00000264033.4:c.1178T>G	p.Ile393Ser	p.I393S	ENST00000264033	NM_005188.3	393	aTt/aGt	8/16	1	2	FACETS	0.811	0.747	0.877	0.811	0.747	0.877	CLONAL	1	TRUE	1	0.616561915644166	2		447	652	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527891	103527891	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	57	430	0	ENST00000355739.4:c.3199T>G	p.Ser1067Ala	p.S1067A	ENST00000355739	NM_000123.3	1067	Tca/Gca	15/15	1	2	FACETS	0.273	0.234	0.316	0.273	0.234	0.316	SUBCLONAL	1	TRUE	1	0.616561915644166	2		430	677	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348280	89348280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371945379	NA	P-0005146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	324	983	0	ENST00000301030.4:c.4670C>T	p.Pro1557Leu	p.P1557L	ENST00000301030	NM_001256183.1	1557	cCa/cTa	9/13	0.151034224650068	0	FACETS	0.374	0.353	0.395			1	INDETERMINATE	1	TRUE	0	0.616561915644166	0		983	1077	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576857	7576857	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	205	407	0	ENST00000269305.4:c.989T>A	p.Leu330His	p.L330H	ENST00000269305	NM_001126112.2	330	cTt/cAt	9/11	0.616561915644166	1	FACETS	0.998	0.936	1	0.998	0.936	1	CLONAL	1	TRUE	0	0.616561915644166	1		407	461	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562365	95562365	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	12	498	0	ENST00000393063.1:c.4892C>T	p.Ser1631Phe	p.S1631F	ENST00000393063	NM_030621.3	1631	tCt/tTt	24/28	0.275106625642878	3	FACETS	0.919	0.661	1			1	INDETERMINATE	1	TRUE	NA	0.522614634013746	3		498	63	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979549	2979551	+	inframe_deletion	In_Frame_Del	DEL	TTT	TTT	-	novel	NA	P-0005171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	28	381	1	ENST00000396946.4:c.696_698del	p.Lys233del	p.K233del	ENST00000396946	NM_032415.4	232	ctAAAg/ctg	6/25	1	2	FACETS	0.809	0.647	0.992	0.809	0.647	0.992	CLONAL	1	FALSE	1	0.212450414169315	2		382	326	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0005189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	107	724	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.209586887690744	2	FACETS	0.767	0.691	0.848	0.767	0.691	0.848	SUBCLONAL	2	TRUE	0	0.262641725282495	2		724	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0005189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	92	498	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.262641725282495	2		498	612	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821421	72821421	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	63	606	0	ENST00000268489.5:c.10754C>G	p.Ser3585Cys	p.S3585C	ENST00000268489	NM_006885.3	3585	tCt/tGt	10/10	1	2	FACETS	0.656	0.567	0.754	0.656	0.567	0.754	SUBCLONAL	1	TRUE	1	0.262641725282495	2		606	731	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222730	5222730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374875451	NA	P-0005189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	51	157	0	ENST00000357368.4:c.3073G>A	p.Val1025Ile	p.V1025I	ENST00000357368	NM_002850.3	1025	Gtc/Atc	18/38	0.1722262262906	2	FACETS	1	0.961	1	0.706	0.605	0.816	CLONAL	1	TRUE	0	0.262641725282495	2		157	275	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273219	18273219	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	131	514	0	ENST00000222254.8:c.1012G>A	p.Glu338Lys	p.E338K	ENST00000222254	NM_005027.3	338	Gag/Aag	9/16	0.1722262262906	2	FACETS	0.806	0.733	0.881	0.806	0.733	0.881	CLONAL	2	TRUE	0	0.262641725282495	2		514	619	SUCCESS
APC	324	MSKCC	GRCh37	5	112173762	112173765	+	frameshift_variant	Frame_Shift_Del	DEL	CATA	CATA	ATT	novel	NA	P-0005189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	44	441	0	ENST00000257430.4:c.2471_2474delinsATT	p.Pro824HisfsTer3	p.P824Hfs*3	ENST00000257430	NM_000038.5	824	cCATAt/cATTt	16/16	1	2	FACETS	0.627	0.526	0.74	0.627	0.526	0.74	SUBCLONAL	1	TRUE	1	0.262641725282495	2		441	534	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0005208-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	49	580	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.3	3	FACETS	0.804	0.681	0.939			1	CLONAL	1	TRUE	NA	0.26	3		580	530	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680532	241680532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201878591	NA	P-0005235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	173	389	1	ENST00000366560.3:c.217G>A	p.Val73Met	p.V73M	ENST00000366560	NM_000143.3	73	Gtg/Atg	2/10	0.398356162009443	1	FACETS	0.381	0.351	0.412	0.381	0.351	0.412	INDETERMINATE	1	TRUE	0	0.758967599907871	1		390	742	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0005243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	105	375	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.903	0.818	0.99	1	0.991	1	CLONAL	4	TRUE	1	0.177811281818802	2		376	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0005243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	188	342	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.180124081703839	2	FACETS	1	0.963	1	1	0.995	1	CLONAL	8	TRUE	0	0.177811281818802	2		343	261	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938029	76938029	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	115	358	0	ENST00000373344.5:c.2719C>T	p.Arg907Ter	p.R907*	ENST00000373344	NM_000489.3	907	Cga/Tga	9/35	1	1	FACETS	1	0.966	1	1	0.993	1	CLONAL	6	TRUE	0	0.177811281818802	1		358	185	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938041	76938042	+	missense_variant	Missense_Mutation	DNP	CC	CC	GA	novel	NA	P-0005243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	101	363	0	ENST00000373344.5:c.2706_2707delinsTC	p.Met902_Glu903delinsIleGln	p.M902_E903delinsIQ	ENST00000373344	NM_000489.3	902	atGGaa/atTCaa	9/35	1	1	FACETS	0.964	0.888	1	1	0.992	1	CLONAL	6	TRUE	0	0.177811281818802	1		363	179	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0005252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	8	301	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.746	1	1	0.746	1	CLONAL	1	TRUE	1	0.364183822100075	2		301	38	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0005252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	15	433	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.268976044110053	3	FACETS	1	0.771	1	1	0.771	1	CLONAL	2	TRUE	1	0.364183822100075	3		433	48	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602488	10602488	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1397945617	NA	P-0005252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	43	405	0	ENST00000171111.5:c.1090G>T	p.Gly364Cys	p.G364C	ENST00000171111	NM_203500.1	364	Ggc/Tgc	3/6	0.271070556718077	0	FACETS	0.725	0.643	0.803			1	SUBCLONAL	3	TRUE	0	0.364183822100075	0		405	69	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699385	117699385	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	17	529	0	ENST00000369458.3:c.256G>T	p.Gly86Cys	p.G86C	ENST00000369458	NM_024626.3	86	Ggc/Tgc	3/6	0.364183822100075	3	FACETS	0.849	0.652	1	0.849	0.652	1	CLONAL	2	TRUE	1	0.364183822100075	3		529	65	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471018	25471018	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	26	504	0	ENST00000264709.3:c.743A>G	p.Gln248Arg	p.Q248R	ENST00000264709	NM_175629.2	248	cAg/cGg	7/23	0.348028681121788	4	FACETS	0.994	0.805	1			1	CLONAL	2	TRUE	NA	0.364183822100075	4		504	98	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629366	187629366	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	16	574	0	ENST00000441802.2:c.1616G>C	p.Arg539Pro	p.R539P	ENST00000441802	NM_005245.3	539	cGt/cCt	2/27	0.364183822100075	1	FACETS	0.971	0.761	1	1	0.934	1	CLONAL	2	TRUE	0	0.364183822100075	1		574	37	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168967	32168967	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	13	402	0	ENST00000375023.3:c.4066G>C	p.Asp1356His	p.D1356H	ENST00000375023	NM_004557.3	1356	Gac/Cac	22/30	NA	2	FACETS	0.785	0.567	1			1	INDETERMINATE	1	TRUE	NA	0.364183822100075	2		402	91	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427527	427527	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	22	536	0	ENST00000399788.2:c.2642G>T	p.Gly881Val	p.G881V	ENST00000399788	NM_001042603.1	881	gGc/gTc	19/28	NA	2	FACETS	0.875	0.718	1			1	INDETERMINATE	3	TRUE	NA	0.364183822100075	2		536	46	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443468	49443468	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	13	273	0	ENST00000301067.7:c.3903A>T	p.Lys1301Asn	p.K1301N	ENST00000301067	NM_003482.3	1301	aaA/aaT	11/54	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.364183822100075	2		273	48	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435372	121435372	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201811844	NA	P-0005252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	11	447	0	ENST00000257555.6:c.1405C>T	p.His469Tyr	p.H469Y	ENST00000257555		469	Cac/Tac	7/10	1	2	FACETS	0.805	0.565	1	0.805	0.565	1	CLONAL	1	TRUE	1	0.364183822100075	2		447	75	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561202	9561202	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0005252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	11	485	0	ENST00000353224.5:c.580A>T	p.Arg194Ter	p.R194*	ENST00000353224	NM_177990.2	194	Aga/Tga	4/10	1	2	FACETS	0.755	0.542	0.996	1	0.871	1	CLONAL	2	TRUE	1	0.364183822100075	2		485	40	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31379461	31379461	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	10	533	0	ENST00000328111.2:c.868G>T	p.Ala290Ser	p.A290S	ENST00000328111	NM_006892.3	290	Gcc/Tcc	8/23	1	2	FACETS	1	0.774	1	1	0.774	1	CLONAL	1	TRUE	1	0.364183822100075	2		533	48	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939705	76939705	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	33	646	0	ENST00000373344.5:c.1043T>A	p.Val348Glu	p.V348E	ENST00000373344	NM_000489.3	348	gTg/gAg	9/35	0.258382338161033	1	FACETS	1	0.945	1	1	0.973	1	CLONAL	2	TRUE	0	0.364183822100075	1		646	60	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	126	560	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.189897309391239	1	FACETS	0.947	0.86	1	1	0.989	1	CLONAL	2	TRUE	0	0.189897309391239	1		560	634	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182123	99182123	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	103	489	0	ENST00000074304.5:c.2188G>T	p.Glu730Ter	p.E730*	ENST00000074304	NM_001134224.1	730	Gag/Tag	21/26	1	2	FACETS	0.824	0.739	0.915	1	0.984	1	CLONAL	2	TRUE	1	0.189897309391239	2		489	658	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49399949	49399949	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	101	527	0	ENST00000418115.1:c.388G>T	p.Glu130Ter	p.E130*	ENST00000418115	NM_001664.2	130	Gag/Tag	4/5	1	2	FACETS	0.812	0.727	0.903	1	0.984	1	CLONAL	2	TRUE	1	0.189897309391239	2		527	655	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131094	55131094	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	100	483	0	ENST00000257290.5:c.637G>C	p.Glu213Gln	p.E213Q	ENST00000257290	NM_006206.4	213	Gag/Cag	5/23	0.175357024246844	2	FACETS	0.896	0.802	0.995	0.896	0.802	0.995	CLONAL	2	TRUE	0	0.189897309391239	2		483	588	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157256612	157256612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	68	442	0	ENST00000346085.5:c.1939G>A	p.Glu647Lys	p.E647K	ENST00000346085	NM_020732.3	647	Gaa/Aaa	5/20	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.189897309391239	2		442	641	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114124	115114124	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	42	509	0	ENST00000257566.3:c.1093C>A	p.Leu365Ile	p.L365I	ENST00000257566	NM_016569.3	365	Ctc/Atc	6/8	NA	2	FACETS	0.65	0.541	0.771			1	INDETERMINATE	1	TRUE	NA	0.189897309391239	2		509	681	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89809336	89809336	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	76	318	0	ENST00000389301.3:c.3637C>A	p.Pro1213Thr	p.P1213T	ENST00000389301	NM_000135.2	1213	Cct/Act	37/43	1	2	FACETS	0.933	0.822	1	1	0.982	1	CLONAL	2	TRUE	1	0.189897309391239	2		318	429	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249037	55249038	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0005261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	136	432	0	ENST00000275493.2:c.2335_2336delinsTT	p.Gly779Phe	p.G779F	ENST00000275493	NM_005228.3	779	GGc/TTc	20/28	0.189850193088724	4	FACETS	0.849	0.774	0.928	1	0.98	1	CLONAL	3	TRUE	2	0.189897309391239	4		432	669	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041640	47041642	+	stop_gained	Nonsense_Mutation	TNP	CGG	CGG	AGT	novel	NA	P-0005261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	70	591	1	ENST00000377604.3:c.1865_1867delinsAGT	p.Ser622_Ala623delinsTer	p.S622_A623delins*	ENST00000377604	NM_001204468.1	622	tCGGcc/tAGTcc	17/24	0.189897309391239	0	FACETS	1	0.908	1			1	CLONAL	1	TRUE	0	0.189897309391239	0		592	569	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0005268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	275	294	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.262920869869047	6	FACETS	1	0.965	1			1	CLONAL	3	TRUE	NA	0.428429902008402	6		294	771	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874292	151874292	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0005268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	98	406	0	ENST00000262189.6:c.8246T>G	p.Leu2749Ter	p.L2749*	ENST00000262189	NM_170606.2	2749	tTa/tGa	38/59	NA	2	FACETS	0.888	0.795	0.986			1	INDETERMINATE	1	TRUE	NA	0.428429902008402	2		406	515	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59878705	59878705	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005276-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	218	550	0	ENST00000259008.2:c.1049G>T	p.Cys350Phe	p.C350F	ENST00000259008	NM_032043.2	350	tGt/tTt	8/20	0.864514868654306	3	FACETS	0.807	0.751	0.864	0.404	0.375	0.432	CLONAL	1	TRUE	1	0.864514868654306	3		550	895	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047706	180047706	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005295-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	77	574	0	ENST00000261937.6:c.2309A>C	p.Asp770Ala	p.D770A	ENST00000261937	NM_182925.4	770	gAt/gCt	16/30	1	2	FACETS	0.986	0.864	1	0.986	0.864	1	CLONAL	1	TRUE	1	0.18	2		574	868	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252864	10252864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005295-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	46	463	0	ENST00000340748.4:c.3101G>A	p.Ser1034Asn	p.S1034N	ENST00000340748		1034	aGc/aAc	29/40	1	2	FACETS	0.668	0.561	0.787	0.668	0.561	0.787	SUBCLONAL	1	TRUE	1	0.18	2		463	765	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600507	10600507	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005295-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	43	441	0	ENST00000171111.5:c.1348T>C	p.Trp450Arg	p.W450R	ENST00000171111	NM_203500.1	450	Tgg/Cgg	4/6	1	2	FACETS	0.648	0.541	0.768	0.648	0.541	0.768	SUBCLONAL	1	TRUE	1	0.18	2		441	737	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038259	30038259	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1060503667	NA	P-0005295-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	131	561	0	ENST00000338641.4:c.432C>G	p.Tyr144Ter	p.Y144*	ENST00000338641	NM_000268.3	144	taC/taG	4/16	1	2	FACETS	0.846	0.768	0.929	1	0.988	1	CLONAL	2	TRUE	1	0.18	2		561	860	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0005314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	43	124	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.992	0.843	1	0.992	0.843	1	CLONAL	1	TRUE	1	0.507090741130264	2		124	171	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0005314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	67	188	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.782	0.695	0.871	1	0.979	1	SUBCLONAL	2	TRUE	1	0.507090741130264	2		188	169	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0005314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	117	346	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.507090741130264	1	FACETS	0.764	0.693	0.837	0.764	0.693	0.837	SUBCLONAL	1	TRUE	0	0.507090741130264	1		346	451	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258959	16258959	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0005314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	357	455	0	ENST00000375759.3:c.6224C>G	p.Ser2075Ter	p.S2075*	ENST00000375759	NM_015001.2	2075	tCa/tGa	11/15	0.327045106500249	3	FACETS	0.919	0.881	0.958	1	0.995	1	CLONAL	3	TRUE	1	0.507090741130264	3		455	640	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46725710	46725710	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	100	337	0	ENST00000371975.4:c.346G>C	p.Asp116His	p.D116H	ENST00000371975	NM_003579.3	116	Gat/Cat	5/18	0.327045106500249	3	FACETS	1	0.939	1	0.533	0.478	0.59	CLONAL	1	TRUE	1	0.507090741130264	3		337	464	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466818	25466818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	138	360	0	ENST00000264709.3:c.1885G>A	p.Glu629Lys	p.E629K	ENST00000264709	NM_175629.2	629	Gag/Aag	16/23	1	2	FACETS	0.919	0.84	1	0.919	0.84	1	CLONAL	1	TRUE	1	0.507090741130264	2		360	592	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799653	72799653	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	146	330	0	ENST00000325599.8:c.1516G>C	p.Asp506His	p.D506H	ENST00000325599	NM_018130.2	506	Gat/Cat	11/11	1	2	FACETS	0.942	0.863	1	0.942	0.863	1	CLONAL	1	TRUE	1	0.507090741130264	2		330	611	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138376646	138376646	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	50	214	0	ENST00000289153.2:c.2828G>T	p.Gly943Val	p.G943V	ENST00000289153	NM_006219.2	943	gGa/gTa	20/22	1	2	FACETS	0.996	0.857	1	0.996	0.857	1	CLONAL	1	TRUE	1	0.507090741130264	2		214	198	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521373	187521373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1414670349	NA	P-0005314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	44	287	0	ENST00000441802.2:c.11782G>A	p.Asp3928Asn	p.D3928N	ENST00000441802	NM_005245.3	3928	Gac/Aac	22/27	0.268658868154564	1	FACETS	0.578	0.49	0.674	0.578	0.49	0.674	INDETERMINATE	1	TRUE	0	0.507090741130264	1		287	224	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562864	176562864	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	144	309	0	ENST00000439151.2:c.760C>A	p.Leu254Ile	p.L254I	ENST00000439151	NM_022455.4	254	Ctc/Atc	2/23	0.208571787380557	5	FACETS	1	0.958	1			1	INDETERMINATE	1	TRUE	NA	0.507090741130264	5		309	921	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675606	30675606	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	168	423	0	ENST00000376406.3:c.2750G>C	p.Arg917Thr	p.R917T	ENST00000376406	NM_014641.2	917	aGa/aCa	8/15	0.327045106500249	3	FACETS	1	0.986	1	0.652	0.602	0.704	CLONAL	1	TRUE	1	0.507090741130264	3		423	637	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468182	50468182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	49	268	0	ENST00000331340.3:c.1417G>A	p.Asp473Asn	p.D473N	ENST00000331340	NM_006060.4	473	Gat/Aat	8/8	1	2	FACETS	0.567	0.482	0.659	0.567	0.482	0.659	SUBCLONAL	1	TRUE	1	0.507090741130264	2		268	341	SUCCESS
ATM	472	MSKCC	GRCh37	11	108225599	108225599	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	57	263	0	ENST00000278616.4:c.8848G>C	p.Glu2950Gln	p.E2950Q	ENST00000278616	NM_000051.3	2950	Gag/Cag	61/63	1	2	FACETS	0.842	0.729	0.963	0.842	0.729	0.963	CLONAL	1	TRUE	1	0.507090741130264	2		263	267	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022675	12022675	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	78	189	0	ENST00000396373.4:c.781G>A	p.Glu261Lys	p.E261K	ENST00000396373	NM_001987.4	261	Gag/Aag	5/8	0.403461869715739	4	FACETS	1	0.964	1	0.62	0.548	0.696	CLONAL	1	TRUE	2	0.507090741130264	4		189	374	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829710	72829710	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	118	534	0	ENST00000268489.5:c.6871C>T	p.Gln2291Ter	p.Q2291*	ENST00000268489	NM_006885.3	2291	Cag/Tag	9/10	0.507090741130264	1	FACETS	0.968	0.883	1	0.968	0.883	1	CLONAL	1	TRUE	0	0.507090741130264	1		534	359	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119314	3119314	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	117	355	0	ENST00000078429.4:c.846G>C	p.Lys282Asn	p.K282N	ENST00000078429	NM_002067.2	282	aaG/aaC	6/7	1	2	FACETS	0.886	0.802	0.973	0.886	0.802	0.973	CLONAL	1	TRUE	1	0.507090741130264	2		355	521	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924382	131924382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757836195	NA	P-0005316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	83	165	0	ENST00000265335.6:c.1055G>A	p.Arg352His	p.R352H	ENST00000265335		352	cGt/cAt	8/25	0.582273597132236	3	FACETS	1	0.909	1	0.512	0.455	0.572	CLONAL	1	TRUE	1	0.584664124524654	3		165	358	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939093	36939093	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	387	547	0	ENST00000361632.4:c.616G>C	p.Glu206Gln	p.E206Q	ENST00000361632		206	Gag/Cag	5/16	0.55594215752905	2	FACETS	0.892	0.855	0.929	0.892	0.855	0.929	CLONAL	2	TRUE	0	0.584664124524654	2		547	742	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156204	106156204	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150072691	NA	P-0005316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	216	186	2	ENST00000380013.4:c.1105C>T	p.Arg369Trp	p.R369W	ENST00000380013	NM_001127208.2	369	Cgg/Tgg	3/11	0.571467278406278	2	FACETS	0.955	0.903	1	0.955	0.903	1	CLONAL	2	TRUE	0	0.584664124524654	2		188	387	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072550	5072550	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587778408	NA	P-0005316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	222	253	0	ENST00000381652.3:c.1700T>A	p.Val567Glu	p.V567E	ENST00000381652	NM_004972.3	567	gTa/gAa	13/25	0.273704560464406	1	FACETS	1	0.992	1	1	0.992	1	INDETERMINATE	1	TRUE	0	0.584664124524654	1		253	400	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195886	102195886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	516	609	0	ENST00000263464.3:c.646G>A	p.Glu216Lys	p.E216K	ENST00000263464	NM_001165.4	216	Gaa/Aaa	2/9	0.560846625675644	3	FACETS	0.962	0.925	1	0.962	0.925	1	CLONAL	2	TRUE	1	0.584664124524654	3		609	1185	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28599058	28599058	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	224	197	0	ENST00000241453.7:c.2230C>T	p.Gln744Ter	p.Q744*	ENST00000241453	NM_004119.2	744	Cag/Tag	18/24	0.584664124524654	2	FACETS	0.906	0.856	0.955	0.906	0.856	0.955	CLONAL	2	TRUE	0	0.584664124524654	2		197	423	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437500	110437500	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1431016182	NA	P-0005316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	241	313	0	ENST00000375856.3:c.901C>T	p.Arg301Trp	p.R301W	ENST00000375856	NM_003749.2	301	Cgg/Tgg	1/2	0.55594215752905	2	FACETS	0.963	0.914	1	0.963	0.914	1	CLONAL	2	TRUE	0	0.584664124524654	2		313	428	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220578	1220578	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0005316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	144	281	0	ENST00000326873.7:c.598-2A>T		p.X200_splice	ENST00000326873	NM_000455.4	200			0.584664124524654	2	FACETS	0.864	0.804	0.924	0.864	0.804	0.924	CLONAL	2	TRUE	0	0.584664124524654	2		281	285	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610153	10610153	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	373	448	1	ENST00000171111.5:c.557G>T	p.Gly186Val	p.G186V	ENST00000171111	NM_203500.1	186	gGc/gTc	2/6	NA	2	FACETS	1	0.963	1			1	INDETERMINATE	2	TRUE	NA	0.584664124524654	2		449	636	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442077	52442077	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	119	280	0	ENST00000460680.1:c.272G>T	p.Cys91Phe	p.C91F	ENST00000460680	NM_004656.3	91	tGt/tTt	5/17	0.39208743345565	1	FACETS	0.519	0.472	0.566	0.519	0.472	0.566	INDETERMINATE	1	FALSE	0	0.748093862951738	1		280	384	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183788	10183788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882034	NA	P-0005317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	73	296	0	ENST00000256474.2:c.257C>T	p.Pro86Leu	p.P86L	ENST00000256474	NM_000551.3	86	cCc/cTc	1/3	NA	2	FACETS	0.72	0.637	0.807			1	INDETERMINATE	1	FALSE	NA	0.748093862951738	2		296	271	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099791	157099804	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCCGGCGGCCGC	GCCCCGGCGGCCGC	-	novel	NA	P-0005317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	197	278	0	ENST00000346085.5:c.730_743del	p.Pro244TrpfsTer5	p.P244Wfs*5	ENST00000346085	NM_020732.3	243	gGCCCCGGCGGCCGC/g	1/20	NA	2	FACETS	0.74	0.687	0.794			1	INDETERMINATE	1	FALSE	NA	0.748093862951738	2		278	712	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110669	2110669	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0005325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	259	315	0	ENST00000219476.3:c.976-2A>G		p.X326_splice	ENST00000219476	NM_000548.3	326			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		315	643	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519920	NA	P-0005333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	32	235	0	ENST00000397062.3:c.85G>C	p.Asp29His	p.D29H	ENST00000397062	NM_006164.4	29	Gat/Cat	2/5	1	2	FACETS	0.258	0.209	0.314	0.258	0.209	0.314	SUBCLONAL	1	TRUE	1	0.46529878121555	2		235	533	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891141	151891141	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	173	415	0	ENST00000262189.6:c.4613T>C	p.Leu1538Ser	p.L1538S	ENST00000262189	NM_170606.2	1538	tTg/tCg	31/59	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.46529878121555	2		415	634	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191529	10191546	+	inframe_deletion	In_Frame_Del	DEL	TTACAGGAGACTGGACAT	TTACAGGAGACTGGACAT	-	novel	NA	P-0005333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	162	435	0	ENST00000256474.2:c.522_539del	p.Tyr175_Ile180del	p.Y175_I180del	ENST00000256474	NM_000551.3	174	aaTTACAGGAGACTGGACATc/aac	3/3	0.46529878121555	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.46529878121555	1		435	426	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713685	52713691	+	frameshift_variant	Frame_Shift_Del	DEL	CACTGCT	CACTGCT	-	novel	NA	P-0005333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	197	420	0	ENST00000394830.3:c.37_43del	p.Ser14AlafsTer29	p.S14Afs*29	ENST00000394830	NM_018313.4	13	AGCAGTGtc/tc	2/30	0.46529878121555	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.46529878121555	1		420	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0005420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	923	433	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.63920744115466	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.63920744115466	3		434	1172	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0005420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	495	527	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.63920744115466	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.63920744115466	2		527	696	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023821	27023821	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005422-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	54	326	0	ENST00000324856.7:c.927G>C	p.Gln309His	p.Q309H	ENST00000324856	NM_006015.4	309	caG/caC	1/20	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.18	2		326	463	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572006	64572006	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005422-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	65	659	1	ENST00000312049.6:c.1633C>A	p.Pro545Thr	p.P545T	ENST00000312049	NM_130799.2	545	Ccg/Acg	10/10	1	2	FACETS	0.716	0.619	0.823	0.716	0.619	0.823	SUBCLONAL	1	TRUE	1	0.18	2		660	1008	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438146	56438146	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005422-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	65	532	0	ENST00000407977.2:c.847C>T	p.Gln283Ter	p.Q283*	ENST00000407977		283	Cag/Tag	7/10	1	2	FACETS	0.979	0.847	1	0.979	0.847	1	CLONAL	1	TRUE	1	0.18	2		532	738	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349198	70349198	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005422-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	81	335	1	ENST00000374080.3:c.3610G>T	p.Asp1204Tyr	p.D1204Y	ENST00000374080		1204	Gac/Tac	26/45	1	1	FACETS	0.806	0.712	0.906	1	0.98	1	CLONAL	2	TRUE	0	0.18	1		336	508	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78420955	78420955	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005422-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	46	442	0	ENST00000370768.2:c.1765del	p.Tyr589ThrfsTer76	p.Y589Tfs*76	ENST00000370768	NM_003902.3	589	Tac/ac	18/20	1	2	FACETS	0.685	0.575	0.807	0.685	0.575	0.807	SUBCLONAL	1	TRUE	1	0.18	2		442	746	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0005439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	335	558	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.44875664869133	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.458717822682291	2		558	631	SUCCESS
APC	324	MSKCC	GRCh37	5	112175761	112175761	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	95	386	0	ENST00000257430.4:c.4473del	p.Phe1491LeufsTer16	p.F1491Lfs*16	ENST00000257430	NM_000038.5	1490	caT/ca	16/16	0.217382627694274	3	FACETS	1	0.964	1	0.589	0.528	0.654	INDETERMINATE	1	TRUE	1	0.458717822682291	3		386	432	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0005439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	181	479	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.458717822682291	5	FACETS	1	0.961	1	0.705	0.653	0.758	CLONAL	2	TRUE	2	0.458717822682291	5		479	630	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0005439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	107	457	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.217382627694274	3	FACETS	1	0.967	1	0.586	0.528	0.647	INDETERMINATE	1	TRUE	1	0.458717822682291	3		457	489	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959241	2959241	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369433934	NA	P-0005439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	159	391	1	ENST00000396946.4:c.2275C>T	p.Arg759Trp	p.R759W	ENST00000396946	NM_032415.4	759	Cgg/Tgg	18/25	0.458717822682291	5	FACETS	0.98	0.903	1	0.653	0.602	0.707	CLONAL	2	TRUE	2	0.458717822682291	5		392	597	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274192	10274192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765986049	NA	P-0005439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	44	314	0	ENST00000330684.3:c.77C>T	p.Ala26Val	p.A26V	ENST00000330684	NM_001134407.1	26	gCg/gTg	2/13	0.418214184058444	3	FACETS	1	0.951	1	0.659	0.56	0.764	CLONAL	1	TRUE	1	0.458717822682291	3		314	179	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117702	70117711	+	frameshift_variant	Frame_Shift_Del	DEL	AGCCCGATCT	AGCCCGATCT	-	novel	NA	P-0005439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	480	724	0	ENST00000245479.2:c.170_179del	p.Glu57GlyfsTer50	p.E57Gfs*50	ENST00000245479	NM_000346.3	57	gAGCCCGATCTg/gg	1/3	0.458717822682291	5	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	2	0.458717822682291	5		724	1085	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120893	115120893	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005463-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	37	447	0	ENST00000257566.3:c.113del	p.Pro38ArgfsTer7	p.P38Rfs*7	ENST00000257566	NM_016569.3	38	cCg/cg	1/8	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		447	562	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14021892	14021892	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005501-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	62	444	1	ENST00000311895.7:c.592G>T	p.Val198Leu	p.V198L	ENST00000311895	NM_005236.2	198	Gta/Tta	4/11	1	2	FACETS	0.863	0.746	0.991	0.863	0.746	0.991	CLONAL	1	TRUE	1	0.245614873287019	2		445	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579315	7579315	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1555526478	NA	P-0005501-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	224	574	3	ENST00000269305.4:c.372C>A	p.Cys124Ter	p.C124*	ENST00000269305	NM_001126112.2	124	tgC/tgA	4/11	NA	2	FACETS	0.999	0.931	1			1	INDETERMINATE	2	TRUE	NA	0.245614873287019	2		577	913	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618805	37618806	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0005501-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	139	863	0	ENST00000447079.4:c.482_483del	p.Tyr161TrpfsTer38	p.Y161Wfs*38	ENST00000447079	NM_015083.1	161	TAt/t	1/14	0.245614873287019	1	FACETS	0.784	0.712	0.861	0.784	0.712	0.861	SUBCLONAL	1	TRUE	0	0.245614873287019	1		863	1266	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061223	38061228	+	inframe_deletion	In_Frame_Del	DEL	TCTCGA	TCTCGA	-	novel	NA	P-0005535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	665	409	1	ENST00000250448.2:c.761_766del	p.Phe254_Asn256delinsTyr	p.F254_N256delinsY	ENST00000250448	NM_004496.3	254	tTCGAGAac/tac	2/2	0.456743594957098	10	FACETS	1	0.988	1			1	CLONAL	5	TRUE	NA	0.456743594957098	10		410	1563	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031973	26031973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2609	734	977	3	ENST00000244661.2:c.316G>A	p.Glu106Lys	p.E106K	ENST00000244661	NM_003537.3	106	Gag/Aag	1/1	0.456743594957098	10	FACETS	0.906	0.871	0.942			1	CLONAL	3	TRUE	NA	0.456743594957098	10		980	3343	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131951789	131951789	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	64	551	0	ENST00000265335.6:c.3131A>C	p.Glu1044Ala	p.E1044A	ENST00000265335		1044	gAa/gCa	20/25	1	2	FACETS	0.326	0.281	0.375	0.326	0.281	0.375	SUBCLONAL	1	TRUE	1	0.456743594957098	2		551	860	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871066	12871066	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	470	342	0	ENST00000228872.4:c.293C>T	p.Ala98Val	p.A98V	ENST00000228872	NM_004064.3	98	gCc/gTc	1/3	0.456743594957098	10	FACETS	1	0.987	1			1	CLONAL	5	TRUE	NA	0.456743594957098	10		342	1090	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579448	7579464	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGCTGCTGGTGCAGG	GGAGCTGCTGGTGCAGG	-	novel	NA	P-0005535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	256	543	0	ENST00000269305.4:c.223_239del	p.Pro75TyrfsTer68	p.P75Yfs*68	ENST00000269305	NM_001126112.2	75	CCTGCACCAGCAGCTCCt/t	4/11	NA	2	FACETS	1	0.961	1			1	INDETERMINATE	2	TRUE	NA	0.456743594957098	2		543	550	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871053	12871053	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	466	356	0	ENST00000228872.4:c.285del	p.Gly97ValfsTer22	p.G97Vfs*22	ENST00000228872	NM_004064.3	94	Ccc/cc	1/3	0.456743594957098	10	FACETS	1	0.983	1			1	CLONAL	5	TRUE	NA	0.456743594957098	10		356	1101	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579875	7579875	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	412	554	0	ENST00000269305.4:c.38del	p.Pro13LeufsTer2	p.P13Lfs*2	ENST00000269305	NM_001126112.2	13	cCt/ct	2/11	0.511980940381572	2	FACETS	0.967	0.927	1	0.967	0.927	1	CLONAL	2	TRUE	0	0.511980940381572	2		554	832	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0005544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	111	373	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	0.19	2		373	1078	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777874	3777874	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	64	744	1	ENST00000262367.5:c.7174G>A	p.Ala2392Thr	p.A2392T	ENST00000262367	NM_004380.2	2392	Gcc/Acc	31/31	0.140642282553185	0	FACETS	0.595	0.514	0.684			1	SUBCLONAL	1	TRUE	0	0.19	0		745	917	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956172	55956172	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	70	493	1	ENST00000263923.4:c.3143G>T	p.Gly1048Val	p.G1048V	ENST00000263923	NM_002253.2	1048	gGc/gTc	23/30	1	2	FACETS	0.677	0.588	0.773	0.677	0.588	0.773	SUBCLONAL	1	TRUE	1	0.19	2		494	1089	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397818	116397819	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	novel	NA	P-0005544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1297	69	501	0	ENST00000397752.3:c.2092_2093delinsTT	p.Thr698Phe	p.T698F	ENST00000397752	NM_000245.2	698	ACt/TTt	8/21	0.140642282553185	3	FACETS	0.582	0.505	0.667	0.291	0.252	0.334	SUBCLONAL	1	TRUE	1	0.19	3		501	1366	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243048	105243048	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519804	NA	P-0005570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	603	438	1	ENST00000349310.3:c.235C>A	p.Gln79Lys	p.Q79K	ENST00000349310	NM_001014432.1	79	Cag/Aag	5/15	0.3	3	FACETS	1	0.996	1			1	INDETERMINATE	1	TRUE	NA	0.73	3		439	1725	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752800	128752800	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	77	230	0	ENST00000377970.2:c.961C>G	p.Gln321Glu	p.Q321E	ENST00000377970	NM_002467.4	321	Cag/Gag	3/3	0.3	4	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.73	4		230	254	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860539	151860541	+	frameshift_variant	Frame_Shift_Del	DEL	GAT	GAT	AA	novel	NA	P-0005570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	218	358	0	ENST00000262189.6:c.10121_10123delinsTT	p.Asn3374IlefsTer10	p.N3374Ifs*10	ENST00000262189	NM_170606.2	3374	aATCca/aTTca	43/59	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.73	2		358	580	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0005579-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	74	301	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.190265386886927	3	FACETS	0.977	0.854	1	0.977	0.854	1	CLONAL	2	TRUE	1	0.1	3		301	795	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0005579-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	66	558	1	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.1	2		559	1051	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720650	89720650	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1257124719	NA	P-0005602-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	40	95	0	ENST00000371953.3:c.802-1G>A		p.X268_splice	ENST00000371953	NM_000314.4	268			0.541603160720861	1	FACETS	0.798	0.677	0.926	0.798	0.677	0.926	CLONAL	1	TRUE	0	0.541603160720861	1		95	135	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115712	8115875	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAGAACAGCTCGTTTAACCCGGCCGCCCTCTCCAGACACATGTCCTCCCTGAGCCACATCTCG	CCCTGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAGAACAGCTCGTTTAACCCGGCCGCCCTCTCCAGACACATGTCCTCCCTGAGCCACATCTCG	-	novel	NA	P-0005602-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	129	541	0	ENST00000346208.3:c.1062_1225del	p.Thr355GlnfsTer97	p.T355Qfs*97	ENST00000346208		353	cCCCTGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAGAACAGCTCGTTTAACCCGGCCGCCCTCTCCAGACACATGTCCTCCCTGAGCCACATCTCG/c	6/6	NA	2	FACETS	0.479	0.433	0.527			1	INDETERMINATE	1	TRUE	NA	0.541603160720861	2		541	995	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133470	55133470	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005602-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	86	422	1	ENST00000257290.5:c.774C>G	p.Ile258Met	p.I258M	ENST00000257290	NM_006206.4	258	atC/atG	6/23	0.297473636021466	1	FACETS	0.223	0.196	0.252	0.223	0.196	0.252	INDETERMINATE	1	TRUE	0	0.541603160720861	1		423	1038	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133488	55133488	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005602-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	92	487	0	ENST00000257290.5:c.792C>G	p.Ile264Met	p.I264M	ENST00000257290	NM_006206.4	264	atC/atG	6/23	0.297473636021466	1	FACETS	0.219	0.194	0.246	0.219	0.194	0.246	INDETERMINATE	1	TRUE	0	0.541603160720861	1		487	1132	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133890	55133890	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1060501521	NA	P-0005602-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	98	427	0	ENST00000257290.5:c.1103A>G	p.Glu368Gly	p.E368G	ENST00000257290	NM_006206.4	368	gAa/gGa	7/23	0.297473636021466	1	FACETS	0.275	0.244	0.307	0.275	0.244	0.307	INDETERMINATE	1	TRUE	0	0.541603160720861	1		427	960	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573115	64573115	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1060499984	NA	P-0005602-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	173	185	0	ENST00000312049.6:c.1177C>G	p.Gln393Glu	p.Q393E	ENST00000312049	NM_130799.2	393	Caa/Gaa	8/10	0.526197512206452	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.541603160720861	1		185	432	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233372	69233372	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs780673045	NA	P-0005602-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8167	584	381	0	ENST00000462284.1:c.1237A>G	p.Ser413Gly	p.S413G	ENST00000462284	NM_002392.5	413	Agc/Ggc	11/11	0.541603160720861	20	FACETS	1	0.996	1			1	CLONAL	1	TRUE	NA	0.541603160720861	20		381	8751	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233391	69233391	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs200828111	NA	P-0005602-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8951	647	440	0	ENST00000462284.1:c.1256A>G	p.Glu419Gly	p.E419G	ENST00000462284	NM_002392.5	419	gAg/gGg	11/11	0.541603160720861	20	FACETS	1	0.996	1			1	CLONAL	1	TRUE	NA	0.541603160720861	20		440	9598	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0005620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	116	124	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	FALSE	1	0.627994318946316	2		124	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0005620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	186	528	1	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.627994318946316	1	FACETS	0.924	0.863	0.985	0.924	0.863	0.985	CLONAL	1	FALSE	0	0.627994318946316	1		529	440	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619057	37619057	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2114	946	447	0	ENST00000447079.4:c.733G>A	p.Asp245Asn	p.D245N	ENST00000447079	NM_015083.1	245	Gat/Aat	1/14	0.627994318946316	14	FACETS	0.939	0.909	0.969			1	CLONAL	5	FALSE	NA	0.627994318946316	14		447	3060	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618964	37618964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1905	921	350	0	ENST00000447079.4:c.640G>A	p.Asp214Asn	p.D214N	ENST00000447079	NM_015083.1	214	Gac/Aac	1/14	0.627994318946316	14	FACETS	0.99	0.958	1			1	CLONAL	5	FALSE	NA	0.627994318946316	14		350	2826	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618980	37618980	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1721	756	320	0	ENST00000447079.4:c.656G>A	p.Arg219Lys	p.R219K	ENST00000447079	NM_015083.1	219	aGa/aAa	1/14	0.627994318946316	14	FACETS	0.927	0.894	0.961			1	CLONAL	5	FALSE	NA	0.627994318946316	14		320	2477	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619027	37619027	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1787	793	351	0	ENST00000447079.4:c.703G>T	p.Asp235Tyr	p.D235Y	ENST00000447079	NM_015083.1	235	Gat/Tat	1/14	0.627994318946316	14	FACETS	0.933	0.901	0.967			1	CLONAL	5	FALSE	NA	0.627994318946316	14		351	2580	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619223	37619223	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1504	880	325	0	ENST00000447079.4:c.899G>C	p.Arg300Thr	p.R300T	ENST00000447079	NM_015083.1	300	aGa/aCa	1/14	0.627994318946316	14	FACETS	0.934	0.904	0.964			1	CLONAL	6	FALSE	NA	0.627994318946316	14		325	2384	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619264	37619264	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1205	637	269	0	ENST00000447079.4:c.940G>C	p.Glu314Gln	p.E314Q	ENST00000447079	NM_015083.1	314	Gaa/Caa	1/14	0.627994318946316	14	FACETS	1	0.986	1			1	CLONAL	5	FALSE	NA	0.627994318946316	14		269	1842	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619310	37619310	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	528	214	0	ENST00000447079.4:c.986G>T	p.Arg329Leu	p.R329L	ENST00000447079	NM_015083.1	329	cGa/cTa	1/14	0.627994318946316	14	FACETS	0.995	0.953	1			1	CLONAL	5	FALSE	NA	0.627994318946316	14		214	1612	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005644-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	29	601	0	ENST00000269305.4:c.853G>T	p.Glu285Ter	p.E285*	ENST00000269305	NM_001126112.2	285	Gag/Tag	8/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		601	979	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005677-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	103	145	0				ENST00000310581	NM_198253.2	-/1132			0.3	4	FACETS	0.939	0.85	1	0.939	0.85	1	CLONAL	3	FALSE	1	0.3	4		145	317	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041720	47041720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005677-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	188	321	0	ENST00000377604.3:c.1945C>T	p.Gln649Ter	p.Q649*	ENST00000377604	NM_001204468.1	649	Caa/Taa	17/24	0.3	2	FACETS	1	0.983	1			1	CLONAL	2	FALSE	NA	0.3	2		321	531	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057193	30057193	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0005677-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	121	373	0	ENST00000338641.4:c.676-1G>A		p.X226_splice	ENST00000338641	NM_000268.3	226			0.216191384334452	2	FACETS	1	0.983	1	0.7	0.635	0.769	CLONAL	1	FALSE	0	0.3	2		373	576	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350783	89350783	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005677-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	122	1075	0	ENST00000301030.4:c.2167G>C	p.Asp723His	p.D723H	ENST00000301030	NM_001256183.1	723	Gac/Cac	9/13	0.3	1	FACETS	0.602	0.543	0.665	0.602	0.543	0.665	SUBCLONAL	1	FALSE	0	0.3	1		1075	1148	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021538	31021538	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs763708711	NA	P-0005677-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	59	326	0	ENST00000375687.4:c.1537G>T	p.Glu513Ter	p.E513*	ENST00000375687	NM_015338.5	513	Gaa/Taa	12/13	1	2	FACETS	0.722	0.621	0.831	0.722	0.621	0.831	SUBCLONAL	1	FALSE	1	0.3	2		326	545	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937175	39937175	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005677-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	159	259	1	ENST00000378444.4:c.8C>T	p.Ser3Leu	p.S3L	ENST00000378444	NM_001123385.1	3	tCa/tTa	2/15	0.3	2	FACETS	1	0.98	1			1	CLONAL	2	FALSE	NA	0.3	2		260	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0005708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	103	885	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.30692339596138	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	0	0.30692339596138	1		885	395	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	172	427	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.891	0.823	0.961	1	0.992	1	CLONAL	2	FALSE	1	0.30692339596138	2		427	629	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270192	198270192	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	67	576	0	ENST00000335508.6:c.1244T>C	p.Leu415Pro	p.L415P	ENST00000335508	NM_012433.2	415	cTt/cCt	10/25	1	2	FACETS	0.854	0.744	0.974	0.854	0.744	0.974	CLONAL	1	FALSE	1	0.30692339596138	2		576	511	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106904	27106904	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	35	735	1	ENST00000324856.7:c.6516del	p.Asn2173ThrfsTer27	p.N2173Tfs*27	ENST00000324856	NM_006015.4	2172	gCc/gc	20/20	1	2	FACETS	0.675	0.554	0.809	0.675	0.554	0.809	SUBCLONAL	1	FALSE	1	0.30692339596138	2		736	338	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0005709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	78	606	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.3	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.2	1		606	666	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546847	9546847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	108	370	0	ENST00000353224.5:c.1175C>T	p.Ser392Leu	p.S392L	ENST00000353224	NM_177990.2	392	tCg/tTg	5/10	0.758499225817003	1	FACETS	0.677	0.619	0.737	0.677	0.619	0.737	SUBCLONAL	1	TRUE	0	0.758499225817003	1		370	261	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0005733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	420	306	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.705570861084797	3	FACETS	0.924	0.897	0.95	0.924	0.897	0.95	CLONAL	3	TRUE	0	0.758499225817003	3		306	551	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254623	16254623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749814808	NA	P-0005733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	355	600	0	ENST00000375759.3:c.1888C>T	p.Arg630Cys	p.R630C	ENST00000375759	NM_015001.2	630	Cgt/Tgt	11/15	0.159076464082686	3	FACETS	1	0.995	1	0.708	0.673	0.743	INDETERMINATE	1	TRUE	1	0.758499225817003	3		600	912	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159128	143159128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	271	339	0	ENST00000262992.4:c.725C>T	p.Pro242Leu	p.P242L	ENST00000262992	NM_001101669.1	242	cCc/cTc	10/24	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.758499225817003	2		339	709	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500561	149500561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	121	364	0	ENST00000261799.4:c.2476G>A	p.Asp826Asn	p.D826N	ENST00000261799	NM_002609.3	826	Gac/Aac	18/23	0.296680960857222	1	FACETS	0.5	0.456	0.546	0.5	0.456	0.546	INDETERMINATE	1	TRUE	0	0.758499225817003	1		364	396	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781200	135781200	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1299279813	NA	P-0005733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	407	952	0	ENST00000298552.3:c.1765C>T	p.Pro589Ser	p.P589S	ENST00000298552	NM_001162426.1	589	Cca/Tca	15/23	0.758499225817003	1	FACETS	0.918	0.881	0.953	0.918	0.881	0.953	CLONAL	1	TRUE	0	0.758499225817003	1		952	726	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274723	123274723	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1441011501	NA	P-0005733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	122	445	0	ENST00000358487.5:c.1195C>T	p.Arg399Ter	p.R399*	ENST00000358487	NM_000141.4	399	Cga/Tga	9/18	0.323232989466898	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.758499225817003	0		445	352	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135623	64135623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	315	565	1	ENST00000334205.4:c.1091C>T	p.Pro364Leu	p.P364L	ENST00000334205	NM_003942.2	364	cCc/cTc	10/17	0.200501089884339	1	FACETS	0.58	0.549	0.612	0.58	0.549	0.612	INDETERMINATE	1	TRUE	0	0.758499225817003	1		566	889	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577469	64577469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs794728616	NA	P-0005733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	315	516	1	ENST00000312049.6:c.113C>T	p.Ser38Phe	p.S38F	ENST00000312049	NM_130799.2	38	tCc/tTc	2/10	0.200501089884339	1	FACETS	0.649	0.616	0.683	0.649	0.616	0.683	INDETERMINATE	1	TRUE	0	0.758499225817003	1		517	794	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989562	85989562	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs767548896	NA	P-0005733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	228	334	0	ENST00000263360.6:c.1321C>T	p.Arg441Ter	p.R441*	ENST00000263360	NM_003797.3	441	Cga/Tga	12/12	0.200501089884339	1	FACETS	0.612	0.574	0.65	0.612	0.574	0.65	INDETERMINATE	1	TRUE	0	0.758499225817003	1		334	610	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118782	115118782	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	93	402	0	ENST00000257566.3:c.559C>T	p.His187Tyr	p.H187Y	ENST00000257566	NM_016569.3	187	Cac/Tac	2/8	0.200501089884339	1	FACETS	0.429	0.384	0.475	0.429	0.384	0.475	INDETERMINATE	1	TRUE	0	0.758499225817003	1		402	355	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219905	133219905	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	250	515	0	ENST00000320574.5:c.4456C>T	p.His1486Tyr	p.H1486Y	ENST00000320574	NM_006231.2	1486	Cat/Tat	35/49	0.200501089884339	1	FACETS	0.643	0.606	0.681	0.643	0.606	0.681	INDETERMINATE	1	TRUE	0	0.758499225817003	1		515	636	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914811	32914811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	410	871	0	ENST00000380152.3:c.6319C>T	p.Pro2107Ser	p.P2107S	ENST00000380152		2107	Cct/Tct	11/27	1	2	FACETS	0.911	0.868	0.954	0.911	0.868	0.954	CLONAL	1	TRUE	1	0.758499225817003	2		871	1187	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042616	42042616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	566	851	1	ENST00000219905.7:c.6811C>T	p.Gln2271Ter	p.Q2271*	ENST00000219905	NM_001164273.1	2271	Cag/Tag	17/24	0.22514064085229	3	FACETS	0.781	0.751	0.811	0.781	0.751	0.811	INDETERMINATE	2	TRUE	1	0.758499225817003	3		852	1318	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892232	9892232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	131	470	0	ENST00000330684.3:c.2258G>A	p.Gly753Glu	p.G753E	ENST00000330684	NM_001134407.1	753	gGg/gAg	11/13	0.758499225817003	1	FACETS	0.544	0.499	0.591	0.544	0.499	0.591	SUBCLONAL	1	TRUE	0	0.758499225817003	1		470	394	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419965	41419965	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	175	498	0	ENST00000373198.4:c.356C>T	p.Ala119Val	p.A119V	ENST00000373198	NM_133170.3	119	gCc/gTc	3/32	NA	2	FACETS	0.727	0.672	0.783			1	INDETERMINATE	1	TRUE	NA	0.758499225817003	2		498	635	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354585	70354585	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	139	527	0	ENST00000374080.3:c.4750G>A	p.Asp1584Asn	p.D1584N	ENST00000374080		1584	Gac/Aac	35/45	0.515974155285493	1	FACETS	0.343	0.312	0.374	0.343	0.312	0.374	SUBCLONAL	1	TRUE	0	0.758499225817003	1		527	664	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888754	76888754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	159	506	0	ENST00000373344.5:c.5075G>A	p.Gly1692Glu	p.G1692E	ENST00000373344	NM_000489.3	1692	gGa/gAa	19/35	0.515974155285493	1	FACETS	0.404	0.371	0.438	0.404	0.371	0.438	SUBCLONAL	1	TRUE	0	0.758499225817003	1		506	644	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0005749-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	243	592	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	0.194877993389183	4	FACETS	0.962	0.908	1	0.962	0.908	1	INDETERMINATE	2	TRUE	2	0.854985987328826	4		592	548	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913492	NA	P-0005749-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	163	364	0	ENST00000286548.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000286548	NM_002072.3	209	cAa/cTa	5/7	0.235699329611547	4	FACETS	0.926	0.861	0.991	0.926	0.861	0.991	INDETERMINATE	2	TRUE	2	0.854985987328826	4		364	382	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0005758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	49	342	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.803	0.678	0.942	0.803	0.678	0.942	CLONAL	1	TRUE	1	0.13	2		343	939	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0005758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	33	329	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.666	0.541	0.809	0.666	0.541	0.809	SUBCLONAL	1	TRUE	1	0.13	2		329	762	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724427	117724427	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs549177200	NA	P-0005758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	32	483	1	ENST00000368508.3:c.452C>T	p.Pro151Leu	p.P151L	ENST00000368508	NM_002944.2	151	cCg/cTg	6/43	0.222613282352083	0	FACETS	0.72	0.583	0.875			1	SUBCLONAL	1	TRUE	0	0.13	0		484	595	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573586	48573586	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	48	469	0	ENST00000342988.3:c.170T>C	p.Leu57Ser	p.L57S	ENST00000342988	NM_005359.5	57	tTa/tCa	2/12	1	2	FACETS	0.864	0.728	1	0.864	0.728	1	CLONAL	1	TRUE	1	0.13	2		469	855	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939069	76939069	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	42	516	0	ENST00000373344.5:c.1679C>T	p.Ser560Phe	p.S560F	ENST00000373344	NM_000489.3	560	tCt/tTt	9/35	0.163492061241759	1	FACETS	0.771	0.641	0.915	0.771	0.641	0.915	CLONAL	1	TRUE	0	0.13	1		516	784	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100126	27100126	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1158725246	NA	P-0005791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	259	546	0	ENST00000324856.7:c.3922A>C	p.Asn1308His	p.N1308H	ENST00000324856	NM_006015.4	1308	Aat/Cat	16/20	1	2	FACETS	0.985	0.925	1	0.985	0.925	1	CLONAL	1	TRUE	1	0.627648093020406	2		546	838	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750513	57750513	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	236	528	0	ENST00000274289.3:c.1955C>G	p.Ser652Cys	p.S652C	ENST00000274289	NM_006622.3	652	tCt/tGt	14/14	0.627648093020406	3	FACETS	0.744	0.693	0.797	0.372	0.346	0.399	SUBCLONAL	1	TRUE	1	0.627648093020406	3		528	1328	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6038873	6038873	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	255	469	1	ENST00000265849.7:c.571T>C	p.Tyr191His	p.Y191H	ENST00000265849	NM_000535.5	191	Tac/Cac	6/15	1	2	FACETS	0.974	0.915	1	0.974	0.915	1	CLONAL	1	TRUE	1	0.627648093020406	2		470	834	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139440194	139440194	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	196	146	0	ENST00000277541.6:c.45del	p.Ala16ArgfsTer17	p.A16Rfs*17	ENST00000277541	NM_017617.3	15	ccC/cc	1/34	0.627648093020406	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.627648093020406	2		146	303	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0005793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	16	342	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.26	2		343	88	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	11	427	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.268960802482141	3	FACETS	1	0.725	1	1	0.725	1	CLONAL	2	TRUE	1	0.26	3		427	47	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005815-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	278	427	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.662687133769408	3	FACETS	0.923	0.875	0.972	0.923	0.875	0.972	CLONAL	2	TRUE	1	0.662687133769408	3		427	605	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111886006	111886006	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005815-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	280	710	0	ENST00000341259.2:c.1628A>C	p.Glu543Ala	p.E543A	ENST00000341259	NM_005475.2	543	gAg/gCg	8/8	0.653865668840796	3	FACETS	0.967	0.908	1	0.483	0.454	0.514	CLONAL	1	TRUE	1	0.662687133769408	3		710	1164	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348955	89348955	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005815-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	266	715	0	ENST00000301030.4:c.3995A>G	p.Asp1332Gly	p.D1332G	ENST00000301030	NM_001256183.1	1332	gAc/gGc	9/13	0.653865668840796	3	FACETS	0.919	0.861	0.979	0.459	0.43	0.49	CLONAL	1	TRUE	1	0.662687133769408	3		715	1163	SUCCESS
AR	367	MSKCC	GRCh37	X	66766067	66766067	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005815-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	190	448	0	ENST00000374690.3:c.1079A>T	p.Gln360Leu	p.Q360L	ENST00000374690	NM_000044.3	360	cAg/cTg	1/8	0.590740537921584	4	FACETS	1	0.987	1	0.431	0.399	0.463	CLONAL	1	TRUE	1	0.662687133769408	4		448	738	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578485	7578485	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1064793929	NA	P-0005815-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	662	446	0	ENST00000269305.4:c.445del	p.Ser149ProfsTer21	p.S149Pfs*21	ENST00000269305	NM_001126112.2	149	Tcc/cc	5/11	0.662687133769408	3	FACETS	0.981	0.957	1	0.981	0.957	1	CLONAL	3	TRUE	0	0.662687133769408	3		446	904	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0005831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	37	258	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.444	0.364	0.534	0.444	0.364	0.534	SUBCLONAL	1	TRUE	1	0.17	2		258	981	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124339	2124339	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	101	903	0	ENST00000219476.3:c.2494C>G	p.His832Asp	p.H832D	ENST00000219476	NM_000548.3	832	Cac/Gac	22/42	0.564692384681287	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.564692384681287	2		903	167	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0005856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	90	682	0	ENST00000269305.4:c.560-2A>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.545832145155273	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	0	0.564692384681287	2		682	155	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0005858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	1044	433	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.665438549891057	3	FACETS	0.987	0.961	1	0.987	0.961	1	CLONAL	2	TRUE	1	0.677736221533878	3		434	2089	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0005858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1490	551	395	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.665438549891057	3	FACETS	1	0.986	1	0.533	0.51	0.557	CLONAL	1	TRUE	1	0.677736221533878	3		396	2041	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0005858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1218	543	460	1	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	0.465539876263459	6	FACETS	1	0.987	1	0.536	0.513	0.559	CLONAL	2	TRUE	2	0.677736221533878	6		461	1761	SUCCESS
APC	324	MSKCC	GRCh37	5	112163677	112163677	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0005858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1528	477	646	0	ENST00000257430.4:c.1600A>T	p.Lys534Ter	p.K534*	ENST00000257430	NM_000038.5	534	Aaa/Taa	13/16	0.665438549891057	3	FACETS	0.94	0.896	0.985	0.47	0.448	0.493	CLONAL	1	TRUE	1	0.677736221533878	3		646	2005	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857925	9857925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs534440095	NA	P-0005858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1595	397	507	0	ENST00000330684.3:c.3476G>A	p.Arg1159His	p.R1159H	ENST00000330684	NM_001134407.1	1159	cGc/cAc	13/13	0.677736221533878	3	FACETS	0.787	0.746	0.83			1	SUBCLONAL	1	TRUE	NA	0.677736221533878	3		507	1992	SUCCESS
APC	324	MSKCC	GRCh37	5	112173378	112173378	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1621	500	709	0	ENST00000257430.4:c.2087A>T	p.Glu696Val	p.E696V	ENST00000257430	NM_000038.5	696	gAa/gTa	16/16	0.665438549891057	3	FACETS	0.931	0.888	0.975	0.466	0.444	0.488	CLONAL	1	TRUE	1	0.677736221533878	3		709	2121	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	703	559	2	ENST00000257430.4:c.4199del	p.Ser1400Ter	p.S1400*	ENST00000257430	NM_000038.5	1400	tCg/tg	16/16	0.665438549891057	3	FACETS	0.922	0.892	0.953	0.922	0.892	0.953	CLONAL	2	TRUE	1	0.677736221533878	3		561	1506	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0005961-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	59	258	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.764	0.656	0.882	0.764	0.656	0.882	SUBCLONAL	1	TRUE	1	0.19	2		258	813	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241873	72241873	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1252345844	NA	P-0005961-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1275	72	785	2	ENST00000357731.5:c.517C>T	p.Arg173Ter	p.R173*	ENST00000357731	NM_173808.2	173	Cga/Tga	3/7	1	2	FACETS	0.563	0.489	0.642	0.563	0.489	0.642	SUBCLONAL	1	TRUE	1	0.19	2		787	1347	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692790	89692790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005961-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	35	294	0	ENST00000371953.3:c.274G>A	p.Asp92Asn	p.D92N	ENST00000371953	NM_000314.4	92	Gac/Aac	5/9	1	2	FACETS	0.789	0.646	0.949	0.789	0.646	0.949	CLONAL	1	TRUE	1	0.19	2		294	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578537	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs879254214	NA	P-0005961-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	103	456	1	ENST00000269305.4:c.393_395del	p.Asn131del	p.N131del	ENST00000269305	NM_001126112.2	131	aaCAAg/aag	5/11	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.19	2		457	992	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0005962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	19	422	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	1	2	FACETS	0.721	0.546	0.929	0.721	0.546	0.929	CLONAL	1	TRUE	1	0.11	2		422	479	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0005962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	20	312	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	1	2	FACETS	0.419	0.318	0.538	0.419	0.318	0.538	SUBCLONAL	1	TRUE	1	0.11	2		312	868	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0005998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	104	395	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.818	0.732	0.91	1	0.984	1	CLONAL	2	FALSE	1	0.147256873782501	2		396	863	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0005998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	71	269	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.147256873782501	2		269	780	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855262	76855262	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	54	222	0	ENST00000373344.5:c.5725G>A	p.Glu1909Lys	p.E1909K	ENST00000373344	NM_000489.3	1909	Gaa/Aaa	24/35	0.143634197352276	2	FACETS	1	0.93	1			1	CLONAL	1	FALSE	NA	0.147256873782501	2		222	634	SUCCESS
APC	324	MSKCC	GRCh37	5	112174516	112174520	+	frameshift_variant	Frame_Shift_Del	DEL	TCCTG	TCCTG	-	novel	NA	P-0005998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	71	293	0	ENST00000257430.4:c.3226_3230del	p.Pro1076LeufsTer3	p.P1076Lfs*3	ENST00000257430	NM_000038.5	1075	taTCCTGtt/tatt	16/16	0.147256873782501	3	FACETS	1	0.96	1	0.631	0.55	0.719	CLONAL	1	FALSE	1	0.147256873782501	3		293	820	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599341	55599341	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519761	NA	P-0006017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	137	295	0	ENST00000288135.5:c.2467T>G	p.Tyr823Asp	p.Y823D	ENST00000288135	NM_000222.2	823	Tat/Gat	17/21	0.436854120505241	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.436854120505241	2		295	264	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741694	17741694	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	740	407	0	ENST00000250003.3:c.365T>G	p.Leu122Arg	p.L122R	ENST00000250003	NM_002478.4	122	cTg/cGg	1/3	0.852800246603357	3	FACETS	0.988	0.978	0.998	0.988	0.978	0.998	CLONAL	3	TRUE	0	0.942924968313263	3		407	779	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0006033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	222	412	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	0.932924486049393	2	FACETS	1	0.955	1	0.507	0.478	0.537	CLONAL	1	TRUE	0	0.942924968313263	2		412	464	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876084	35876084	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0006033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	172	368	0	ENST00000303115.3:c.877-1G>C		p.X293_splice	ENST00000303115	NM_002185.3	293			0.942924968313263	5	FACETS	0.936	0.861	1	0.312	0.287	0.338	CLONAL	1	TRUE	2	0.942924968313263	5		368	941	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522551	176522551	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	2373	384	0	ENST00000292408.4:c.1648G>T	p.Val550Leu	p.V550L	ENST00000292408	NM_213647.1	550	Gtg/Ttg	13/18	0.942924968313263	15	FACETS	0.97	0.958	0.982			1	CLONAL	12	TRUE	NA	0.942924968313263	15		384	3083	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034920	42034920	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs368677841	NA	P-0006042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	382	525	1	ENST00000219905.7:c.4762C>T	p.Gln1588Ter	p.Q1588*	ENST00000219905	NM_001164273.1	1588	Cag/Tag	15/24	0.67606225502402	4	FACETS	0.849	0.808	0.891	0.849	0.808	0.891	CLONAL	2	TRUE	2	0.732981304350091	4		526	1064	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576870	7576870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	385	402	0	ENST00000269305.4:c.976G>A	p.Glu326Lys	p.E326K	ENST00000269305	NM_001126112.2	326	Gaa/Aaa	9/11	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	2	TRUE	NA	0.732981304350091	2		402	472	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199469672	NA	P-0006042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	509	553	0	ENST00000374080.3:c.131G>T	p.Gly44Val	p.G44V	ENST00000374080		44	gGt/gTt	2/45	0.413571852825015	5	FACETS	0.971	0.935	1	0.971	0.935	1	INDETERMINATE	3	TRUE	2	0.732981304350091	5		553	1001	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578466	7578466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006047-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	119	433	0	ENST00000269305.4:c.464C>T	p.Thr155Ile	p.T155I	ENST00000269305	NM_001126112.2	155	aCc/aTc	5/11	0.221019985384052	1	FACETS	0.934	0.842	1	0.934	0.842	1	CLONAL	1	TRUE	0	0.231746366193781	1		433	972	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39607452	39607452	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006047-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	124	538	1	ENST00000262039.4:c.1530T>A	p.Asp510Glu	p.D510E	ENST00000262039	NM_002647.2	510	gaT/gaA	14/25	0.221019985384052	1	FACETS	0.926	0.836	1	0.926	0.836	1	CLONAL	1	TRUE	0	0.231746366193781	1		539	1022	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0006061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	57	551	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.847	0.727	0.979	0.847	0.727	0.979	CLONAL	1	TRUE	1	0.228107089788087	2		551	590	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597813	43597813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770548816	NA	P-0006061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	98	660	1	ENST00000355710.3:c.361G>A	p.Val121Ile	p.V121I	ENST00000355710	NM_020975.4	121	Gtc/Atc	3/20	1	2	FACETS	0.733	0.651	0.819	0.733	0.651	0.819	SUBCLONAL	1	TRUE	1	0.228107089788087	2		661	1173	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222987	1222987	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	99	328	0	ENST00000326873.7:c.924G>A	p.Trp308Ter	p.W308*	ENST00000326873	NM_000455.4	308	tgG/tgA	8/10	0.177702625495753	2	FACETS	1	0.981	1	0.736	0.658	0.818	CLONAL	1	TRUE	0	0.228107089788087	2		328	590	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0006096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	10	724	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.487	0.331	0.683	0.487	0.331	0.683	SUBCLONAL	1	TRUE	1	0.27	2		724	152	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0006096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	11	342	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.566	0.392	0.78	0.566	0.392	0.78	SUBCLONAL	1	TRUE	1	0.27	2		343	144	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339175	65339175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180823763	NA	P-0006108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	187	374	0	ENST00000342505.4:c.361G>A	p.Asp121Asn	p.D121N	ENST00000342505	NM_002227.2	121	Gac/Aac	5/25	1	2	FACETS	0.896	0.829	0.966	0.896	0.829	0.966	CLONAL	1	TRUE	1	0.492282998037675	2		374	848	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495537	56495537	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	235	444	0	ENST00000267101.3:c.3727C>G	p.Leu1243Val	p.L1243V	ENST00000267101	NM_001982.3	1243	Ctc/Gtc	28/28	1	2	FACETS	0.911	0.85	0.974	0.911	0.85	0.974	CLONAL	1	TRUE	1	0.492282998037675	2		444	1048	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530188	63530188	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	51	495	0	ENST00000307078.5:c.2247G>C	p.Glu749Asp	p.E749D	ENST00000307078	NM_004655.3	749	gaG/gaC	10/11	1	2	FACETS	0.217	0.184	0.254	0.217	0.184	0.254	SUBCLONAL	1	TRUE	1	0.492282998037675	2		495	954	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0006123-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	159	301	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.202163471480625	4	FACETS	0.766	0.701	0.833	0.766	0.701	0.833	SUBCLONAL	2	TRUE	2	0.28088152587692	4		301	947	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867546	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGC	GGCGGCGGC	-	rs11466445	NA	P-0006123-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	10	23	0	ENST00000374994.4:c.70_78del	p.Ala24_Ala26del	p.A24_A26del	ENST00000374994	NM_004612.2	17	ctGGCGGCGGCg/ctg	1/9	0.204357014013538	3	FACETS	0.923	0.645	1	0.923	0.645	1	CLONAL	2	TRUE	1	0.28088152587692	3		23	44	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875096	151875096	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0006123-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	29	136	0	ENST00000262189.6:c.7443-1G>C		p.X2481_splice	ENST00000262189	NM_170606.2	2481			0.167214000356268	4	FACETS	1	0.828	1	0.515	0.414	0.627	INDETERMINATE	1	TRUE	2	0.28088152587692	4		136	257	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216552	108216553	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0006123-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	155	628	0	ENST00000278616.4:c.8502_8503del	p.Phe2834LeufsTer13	p.F2834Lfs*13	ENST00000278616	NM_000051.3	2834	tTC/t	58/63	0.170446523802574	2	FACETS	1	0.959	1	0.541	0.495	0.59	CLONAL	1	TRUE	0	0.28088152587692	2		628	1020	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481586	56481587	+	missense_variant	Missense_Mutation	DNP	GA	GA	CC	novel	NA	P-0006132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	63	388	0	ENST00000267101.3:c.621_622delinsCC	p.Lys207_Thr208delinsAsnPro	p.K207_T208delinsNP	ENST00000267101	NM_001982.3	207	aaGAcc/aaCCcc	6/28	0.167744441247525	4	FACETS	0.997	0.861	1	0.499	0.43	0.573	CLONAL	1	TRUE	2	0.204872360756789	4		388	743	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0006140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	56	373	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.781	0.668	0.904	0.781	0.668	0.904	CLONAL	1	TRUE	1	0.22	2		373	652	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984019	2984019	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	116	498	0	ENST00000396946.4:c.511G>T	p.Val171Leu	p.V171L	ENST00000396946	NM_032415.4	171	Gtg/Ttg	5/25	1	2	FACETS	0.979	0.881	1	0.979	0.881	1	CLONAL	1	TRUE	1	0.22	2		498	1077	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248598	59248598	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	110	514	0	ENST00000371222.2:c.145C>A	p.Leu49Met	p.L49M	ENST00000371222	NM_002228.3	49	Ctg/Atg	1/1	1	2	FACETS	0.867	0.776	0.963	0.867	0.776	0.963	CLONAL	1	TRUE	1	0.22	2		514	1154	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567767	226567767	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	159	518	0	ENST00000366794.5:c.1399A>C	p.Lys467Gln	p.K467Q	ENST00000366794	NM_001618.3	467	Aag/Cag	10/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.22	2		518	1207	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143226639	143226639	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0006140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	64	394	1	ENST00000262992.4:c.475A>T	p.Lys159Ter	p.K159*	ENST00000262992	NM_001101669.1	159	Aag/Tag	7/24	1	2	FACETS	0.759	0.656	0.871	0.759	0.656	0.871	SUBCLONAL	1	TRUE	1	0.22	2		395	767	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544661	65544661	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0006140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	115	513	0	ENST00000358664.4:c.265A>T	p.Lys89Ter	p.K89*	ENST00000358664	NM_002382.4	89	Aag/Tag	4/5	1	2	FACETS	0.965	0.868	1	0.965	0.868	1	CLONAL	1	TRUE	1	0.22	2		513	1083	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989709	15989709	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	94	405	0	ENST00000268712.3:c.3064G>T	p.Val1022Phe	p.V1022F	ENST00000268712	NM_006311.3	1022	Gtt/Ttt	23/46	1	2	FACETS	0.842	0.747	0.943	0.842	0.747	0.943	CLONAL	1	TRUE	1	0.22	2		405	1015	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342661	70342661	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	71	593	0	ENST00000374080.3:c.1422C>A	p.Ser474Arg	p.S474R	ENST00000374080		474	agC/agA	10/45	1	2	FACETS	0.544	0.473	0.621	0.544	0.473	0.621	SUBCLONAL	1	TRUE	1	0.22	2		593	1187	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183771	10183771	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	79	294	1	ENST00000256474.2:c.240T>A	p.Ser80Arg	p.S80R	ENST00000256474	NM_000551.3	80	agT/agA	1/3	0.164492784525875	2	FACETS	0.724	0.638	0.816	0.362	0.319	0.408	INDETERMINATE	1	TRUE	0	0.409483079356802	2		295	533	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157495253	157495253	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0006158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	96	316	0	ENST00000346085.5:c.3135+2T>C		p.X1045_splice	ENST00000346085	NM_020732.3	1045			0.124014252258137	3	FACETS	1	0.971	1	0.622	0.557	0.691	INDETERMINATE	1	TRUE	1	0.409483079356802	3		316	454	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729724	41729724	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	111	493	0	ENST00000242208.4:c.805G>C	p.Gly269Arg	p.G269R	ENST00000242208	NM_002192.2	269	Ggg/Cgg	3/3	0.332109355185299	3	FACETS	0.776	0.697	0.859	0.388	0.348	0.43	SUBCLONAL	1	TRUE	1	0.409483079356802	3		493	842	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435502	18435502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	22	330	0	ENST00000266497.5:c.487G>A	p.Glu163Lys	p.E163K	ENST00000266497		163	Gaa/Aaa	1/31	NA	2	FACETS	0.45	0.349	0.565			1	INDETERMINATE	1	TRUE	NA	0.409483079356802	2		330	239	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042233	42042233	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	97	622	0	ENST00000219905.7:c.6428C>A	p.Ser2143Ter	p.S2143*	ENST00000219905	NM_001164273.1	2143	tCa/tAa	17/24	1	2	FACETS	0.802	0.716	0.892	0.802	0.716	0.892	CLONAL	1	TRUE	1	0.409483079356802	2		622	591	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643630	52643630	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	50	281	0	ENST00000394830.3:c.2266del	p.Leu756CysfsTer19	p.L756Cfs*19	ENST00000394830	NM_018313.4	756	Ctg/tg	17/30	0.164492784525875	2	FACETS	0.836	0.714	0.969	0.418	0.357	0.485	INDETERMINATE	1	TRUE	0	0.409483079356802	2		281	292	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006205-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	206	427	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.270550632177811	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.271046864706958	3		427	830	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89815102	89815102	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006205-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	120	588	0	ENST00000389301.3:c.3313T>A	p.Cys1105Ser	p.C1105S	ENST00000389301	NM_000135.2	1105	Tgc/Agc	33/43	0.150474053832615	1	FACETS	0.883	0.797	0.974	0.883	0.797	0.974	INDETERMINATE	1	TRUE	0	0.271046864706958	1		588	867	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006205-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	203	399	0	ENST00000269305.4:c.377A>C	p.Tyr126Ser	p.Y126S	ENST00000269305	NM_001126112.2	126	tAc/tCc	5/11	0.243066654700411	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.271046864706958	2		399	669	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248528	59248528	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	366	587	0	ENST00000371222.2:c.215C>A	p.Ala72Glu	p.A72E	ENST00000371222	NM_002228.3	72	gCg/gAg	1/1	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.578180097042801	2		587	1169	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562037	21562037	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	281	843	0	ENST00000382592.4:c.1882G>A	p.Glu628Lys	p.E628K	ENST00000382592	NM_014572.2	628	Gag/Aag	4/8	0.578180097042801	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.578180097042801	1		843	676	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0006264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	436	364	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.507537308711969	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.507537308711969	3		364	1066	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421039	49421039	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398123721	NA	P-0006264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	270	355	0	ENST00000301067.7:c.14710C>T	p.Arg4904Ter	p.R4904*	ENST00000301067	NM_003482.3	4904	Cga/Tga	48/54	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.507537308711969	2		355	1045	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0006264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	311	454	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.44732157371655	1	FACETS	0.996	0.942	1	0.996	0.942	1	CLONAL	1	TRUE	0	0.507537308711969	1		454	918	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059260	27059260	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	402	434	2	ENST00000324856.7:c.1897C>T	p.Gln633Ter	p.Q633*	ENST00000324856	NM_006015.4	633	Cag/Tag	4/20	0.471395676537937	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.507537308711969	3		436	906	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001155	150001155	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	232	519	2	ENST00000253339.5:c.2449G>A	p.Glu817Lys	p.E817K	ENST00000253339		817	Gaa/Aaa	4/7	1	2	FACETS	0.888	0.828	0.95	0.888	0.828	0.95	CLONAL	1	TRUE	1	0.507537308711969	2		521	1029	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258790	16258790	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	614	482	1	ENST00000375759.3:c.6055C>T	p.Pro2019Ser	p.P2019S	ENST00000375759	NM_015001.2	2019	Ccc/Tcc	11/15	0.507537308711969	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.507537308711969	2		483	1114	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023220	27023220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1167372383	NA	P-0006264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	306	240	0	ENST00000324856.7:c.326C>T	p.Pro109Leu	p.P109L	ENST00000324856	NM_006015.4	109	cCt/cTt	1/20	0.471395676537937	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.507537308711969	3		240	683	SUCCESS
APC	324	MSKCC	GRCh37	5	112178036	112178036	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	126	452	0	ENST00000257430.4:c.6745A>C	p.Lys2249Gln	p.K2249Q	ENST00000257430	NM_000038.5	2249	Aaa/Caa	16/16	1	2	FACETS	0.669	0.606	0.735	0.669	0.606	0.735	SUBCLONAL	1	TRUE	1	0.507537308711969	2		452	742	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515340	149515340	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1323411468	NA	P-0006264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	278	388	0	ENST00000261799.4:c.142A>G	p.Ser48Gly	p.S48G	ENST00000261799	NM_002609.3	48	Agc/Ggc	3/23	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.507537308711969	2		388	1081	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32182001	32182001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	356	566	2	ENST00000375023.3:c.2053G>A	p.Gly685Arg	p.G685R	ENST00000375023	NM_004557.3	685	Ggg/Agg	13/30	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.507537308711969	2		568	1329	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538822	23538822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	208	360	0	ENST00000380871.4:c.617C>T	p.Ser206Phe	p.S206F	ENST00000380871	NM_006167.3	206	tCc/tTc	2/2	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.507537308711969	2		360	781	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750696	128750696	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	295	418	0	ENST00000377970.2:c.233C>T	p.Pro78Leu	p.P78L	ENST00000377970	NM_002467.4	78	cCt/cTt	2/3	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.507537308711969	2		418	1073	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373515	118373515	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	171	359	0	ENST00000534358.1:c.6908G>A	p.Ser2303Asn	p.S2303N	ENST00000534358	NM_005933.3	2303	aGc/aAc	27/36	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.507537308711969	2		359	649	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856413	111856413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531156627	NA	P-0006264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	195	226	0	ENST00000341259.2:c.464C>T	p.Pro155Leu	p.P155L	ENST00000341259	NM_005475.2	155	cCa/cTa	2/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.507537308711969	2		226	599	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590801	95590801	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	402	384	0	ENST00000393063.1:c.1108C>G	p.Leu370Val	p.L370V	ENST00000393063	NM_030621.3	370	Ctg/Gtg	9/28	0.507537308711969	3	FACETS	0.974	0.929	1	0.974	0.929	1	CLONAL	2	TRUE	1	0.507537308711969	3		384	1020	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030883	36030883	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	292	367	0	ENST00000358208.4:c.1162C>G	p.Arg388Gly	p.R388G	ENST00000358208		388	Cgg/Ggg	10/12	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.507537308711969	2		367	956	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942029	44942029	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	205	383	1	ENST00000377967.4:c.3279C>A	p.Asp1093Glu	p.D1093E	ENST00000377967	NM_021140.2	1093	gaC/gaA	22/29	0.26968353244661	1	FACETS	0.848	0.789	0.908	0.848	0.789	0.908	INDETERMINATE	1	TRUE	0	0.507537308711969	1		384	711	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546693	9546693	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	233	364	0	ENST00000353224.5:c.1329del	p.Asp444ThrfsTer34	p.D444Tfs*34	ENST00000353224	NM_177990.2	443	ggA/gg	5/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.507537308711969	2		364	868	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11168339	11168340	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0006264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	355	352	0	ENST00000361445.4:c.7532_7533delinsAA	p.Arg2511Gln	p.R2511Q	ENST00000361445	NM_004958.3	2511	cGG/cAA	57/58	0.507537308711969	2	FACETS	0.94	0.897	0.983	0.94	0.897	0.983	CLONAL	2	TRUE	0	0.507537308711969	2		352	744	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562950	21562951	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0006264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	295	371	0	ENST00000382592.4:c.968_969delinsTT	p.Pro323Leu	p.P323L	ENST00000382592	NM_014572.2	323	cCC/cTT	4/8	0.507537308711969	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.507537308711969	1		371	718	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	496	269	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.342960452950122	8	FACETS	1	0.99	1			1	CLONAL	5	TRUE	NA	0.342960452950122	8		269	1082	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735470	40735470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761910971	NA	P-0006266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	141	362	1	ENST00000373198.4:c.3403G>A	p.Val1135Met	p.V1135M	ENST00000373198	NM_133170.3	1135	Gtg/Atg	25/32	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.342960452950122	2		363	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519996	NA	P-0006266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	192	347	0	ENST00000269305.4:c.395A>T	p.Lys132Met	p.K132M	ENST00000269305	NM_001126112.2	132	aAg/aTg	5/11	0.200261716188198	3	FACETS	1	0.981	1	0.764	0.712	0.818	INDETERMINATE	2	TRUE	0	0.342960452950122	3		347	572	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974658	21974895	+	splice_donor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	CTGCAGACCCTCTACCCACCTGGATCGGCCTCCGACCGTAACTATTCGGTGCGTTGGGCAGCGCCCCCGCCTCCAGCAGCGCCCGCACCTCCTCTACCCGACCCCGGGCCGCGGCCGTGGCCAGCCAGTCAGCCGAAGGCTCCATGCTGCTCCCCGCCGCCGGCTCCATGCTGCTCCCCGCCGCCCGCTGCCTGCTCTCCCCCTCTCCGCAGCCGCCGAGCGCACGCGGTCCGCCCCA	CTGCAGACCCTCTACCCACCTGGATCGGCCTCCGACCGTAACTATTCGGTGCGTTGGGCAGCGCCCCCGCCTCCAGCAGCGCCCGCACCTCCTCTACCCGACCCCGGGCCGCGGCCGTGGCCAGCCAGTCAGCCGAAGGCTCCATGCTGCTCCCCGCCGCCGGCTCCATGCTGCTCCCCGCCGCCCGCTGCCTGCTCTCCCCCTCTCCGCAGCCGCCGAGCGCACGCGGTCCGCCCCA	-	novel	NA	P-0006266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	110	427	0	ENST00000304494.5:c.-69_150+19del		p.X23_splice	ENST00000304494	NM_000077.4	23		1/3	0.322842206788897	2	FACETS	1	0.97	1	0.598	0.54	0.66	CLONAL	1	TRUE	0	0.342960452950122	2		427	536	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99160428	99160428	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006283-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	59	361	0	ENST00000074304.5:c.907C>G	p.Leu303Val	p.L303V	ENST00000074304	NM_001134224.1	303	Ctc/Gtc	11/26	0.302259010105864	5	FACETS	0.924	0.796	1	0.308	0.265	0.355	CLONAL	1	TRUE	2	0.420796100665574	5		361	495	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024477	16024477	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1183742719	NA	P-0006283-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	88	310	2	ENST00000268712.3:c.1741C>A	p.Arg581Ser	p.R581S	ENST00000268712	NM_006311.3	581	Cgt/Agt	16/46	0.367651986639659	2	FACETS	0.907	0.807	1	0.454	0.403	0.507	CLONAL	1	TRUE	0	0.420796100665574	2		312	461	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845341	42845341	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006283-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	48	314	1	ENST00000398585.3:c.921G>T	p.Gln307His	p.Q307H	ENST00000398585	NM_001135099.1	307	caG/caT	9/14	0.367651986639659	2	FACETS	0.75	0.638	0.873	0.375	0.319	0.437	SUBCLONAL	1	TRUE	0	0.420796100665574	2		315	304	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029315	16029421	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGTACTCCCTATATCTACAAAAATAAAAATAAAATAAAAATAAACATTTAACTTATTATATAACTAATTATTTAACTCACTTGGAGTCTTCTTTTTCATCTTTTTC	CTGTACTCCCTATATCTACAAAAATAAAAATAAAATAAAAATAAACATTTAACTTATTATATAACTAATTATTTAACTCACTTGGAGTCTTCTTTTTCATCTTTTTC	-	novel	NA	P-0006283-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	20	77	0	ENST00000268712.3:c.1609_1634+81del		p.X537_splice	ENST00000268712	NM_006311.3	537		15/46	0.367651986639659	2	FACETS	1	0.796	1	0.511	0.398	0.637	CLONAL	1	TRUE	0	0.420796100665574	2		77	93	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0006310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	281	228	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.283476799844792	8	FACETS	0.952	0.902	1	1	0.988	1	CLONAL	6	TRUE	3	0.283476799844792	8		228	642	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220644	1220644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1167609100	NA	P-0006310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	110	578	1	ENST00000326873.7:c.662C>T	p.Pro221Leu	p.P221L	ENST00000326873	NM_000455.4	221	cCg/cTg	5/10	1	2	FACETS	0.937	0.842	1	0.937	0.842	1	CLONAL	1	TRUE	1	0.283476799844792	2		579	828	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438542	52438542	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	231	427	1	ENST00000460680.1:c.1177C>T	p.Gln393Ter	p.Q393*	ENST00000460680	NM_004656.3	393	Cag/Tag	12/17	0.360415998157748	2	FACETS	0.87	0.815	0.926	0.87	0.815	0.926	CLONAL	2	TRUE	0	0.38477141521971	2		428	690	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528621	89528621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780470195	NA	P-0006370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	277	327	2	ENST00000336596.2:c.2921C>T	p.Thr974Met	p.T974M	ENST00000336596	NM_005233.5	974	aCg/aTg	17/17	0.336392729997923	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.339024346025416	3		329	902	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779662	3779662	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	39	322	1	ENST00000262367.5:c.5386C>T	p.Gln1796Ter	p.Q1796*	ENST00000262367	NM_004380.2	1796	Cag/Tag	31/31	1	2	FACETS	0.327	0.27	0.391	0.327	0.27	0.391	SUBCLONAL	1	TRUE	1	0.339024346025416	2		323	703	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0006372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	18	499	1	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	1	2	FACETS	0.617	0.463	0.801	0.617	0.463	0.801	SUBCLONAL	1	TRUE	1	0.11	2		500	530	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398286	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0006372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	40	397	0	ENST00000311936.3:c.33_34delinsCT	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	11	gcTGgt/gcCTgt	2/5	1	2	FACETS	0.946	0.784	1	0.946	0.784	1	CLONAL	1	TRUE	1	0.11	2		397	769	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262483	16262483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369155141	NA	P-0006379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	23	165	0	ENST00000375759.3:c.9748G>A	p.Val3250Ile	p.V3250I	ENST00000375759	NM_015001.2	3250	Gtc/Atc	11/15	1	2	FACETS	0.46	0.359	0.576	0.46	0.359	0.576	SUBCLONAL	1	TRUE	1	0.363809922723765	2		165	275	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372289	55372289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs748072355	NA	P-0006379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	26	270	0	ENST00000297316.4:c.979C>A	p.Pro327Thr	p.P327T	ENST00000297316	NM_022454.3	327	Ccc/Acc	2/2	1	2	FACETS	0.275	0.217	0.342	0.275	0.217	0.342	SUBCLONAL	1	TRUE	1	0.363809922723765	2		270	520	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717609	89717609	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs876661024	NA	P-0006379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	29	221	0	ENST00000371953.3:c.635-1G>A		p.X212_splice	ENST00000371953	NM_000314.4	212			1	2	FACETS	0.498	0.4	0.609	0.498	0.4	0.609	SUBCLONAL	1	TRUE	1	0.363809922723765	2		221	320	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442443	49442443	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	109	483	0	ENST00000301067.7:c.4130A>T	p.Gln1377Leu	p.Q1377L	ENST00000301067	NM_003482.3	1377	cAg/cTg	13/54	1	2	FACETS	0.771	0.692	0.855	0.771	0.692	0.855	SUBCLONAL	1	TRUE	1	0.363809922723765	2		483	777	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188321	10188321	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs869025657	NA	P-0006381-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	113	391	1	ENST00000256474.2:c.463+1G>A		p.X155_splice	ENST00000256474	NM_000551.3	155			0.486264343439576	1	FACETS	0.918	0.834	1	0.918	0.834	1	CLONAL	1	TRUE	0	0.486264343439576	1		392	383	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562336	21562336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765917652	NA	P-0006381-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	130	282	0	ENST00000382592.4:c.1583C>T	p.Ser528Leu	p.S528L	ENST00000382592	NM_014572.2	528	tCg/tTg	4/8	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.486264343439576	2		282	485	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440866	52440866	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1220529268	NA	P-0006409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	93	963	1	ENST00000460680.1:c.638G>A	p.Arg213His	p.R213H	ENST00000460680	NM_004656.3	213	cGt/cAt	8/17	0.499577468957126	1	FACETS	0.287	0.254	0.322	0.287	0.254	0.322	SUBCLONAL	1	TRUE	0	0.518906613944542	1		964	925	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620685	52620685	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	93	417	0	ENST00000394830.3:c.3068C>G	p.Pro1023Arg	p.P1023R	ENST00000394830	NM_018313.4	1023	cCa/cGa	21/30	0.499577468957126	1	FACETS	0.84	0.755	0.928	0.84	0.755	0.928	CLONAL	1	TRUE	0	0.518906613944542	1		417	316	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396443	396443	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	232	1092	0	ENST00000262320.3:c.583G>T	p.Glu195Ter	p.E195*	ENST00000262320	NM_003502.3	195	Gaa/Taa	2/11	0.518906613944542	1	FACETS	0.857	0.801	0.913	0.857	0.801	0.913	CLONAL	1	TRUE	0	0.518906613944542	1		1092	773	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051038	180051066	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTCTTGCTGCTGCCGCCGCCGGCTGCC	AGGTCTTGCTGCTGCCGCCGCCGGCTGCC	-	novel	NA	P-0006409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	160	855	0	ENST00000261937.6:c.1422-5_1445del		p.X474_splice	ENST00000261937	NM_182925.4	474		11/30	0.27551893819288	0	FACETS	0.396	0.364	0.43			1	INDETERMINATE	1	TRUE	0	0.518906613944542	0		855	749	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0006410-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	1049	454	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.907802924255196	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.907802924255196	2		454	1097	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814303	76814306	+	frameshift_variant	Frame_Shift_Del	DEL	ATAA	ATAA	-	novel	NA	P-0006410-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	258	378	0	ENST00000373344.5:c.6338_6341del	p.Phe2113SerfsTer9	p.F2113Sfs*9	ENST00000373344	NM_000489.3	2113	tTTATc/tc	29/35	1	1	FACETS	0.985	0.953	1	0.985	0.953	1	CLONAL	1	TRUE	0	0.907802924255196	1		378	315	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777134	9777134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1445282622	NA	P-0006410-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	350	755	1	ENST00000377346.4:c.898C>T	p.Arg300Cys	p.R300C	ENST00000377346	NM_005026.3	300	Cgt/Tgt	7/24	0.106117703647406	5	FACETS	0.981	0.932	1	0.491	0.466	0.516	INDETERMINATE	2	TRUE	1	0.907802924255196	5		756	928	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935411	36935411	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006410-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	595	1003	0	ENST00000361632.4:c.1316C>T	p.Ala439Val	p.A439V	ENST00000361632		439	gCc/gTc	10/16	0.106117703647406	5	FACETS	0.899	0.868	0.929	0.674	0.651	0.697	INDETERMINATE	3	TRUE	1	0.907802924255196	5		1003	1148	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252156	226252156	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006410-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	34	91	0	ENST00000366813.1:c.104G>T	p.Gly35Val	p.G35V	ENST00000366813		35	gGg/gTg	1/3	0.106117703647406	5	FACETS	0.921	0.776	1	0.461	0.388	0.538	INDETERMINATE	2	TRUE	1	0.907802924255196	5		91	96	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133558	55133560	+	inframe_deletion	In_Frame_Del	DEL	TAC	TAC	-	novel	NA	P-0006410-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	444	551	0	ENST00000257290.5:c.862_864del	p.Tyr288del	p.Y288del	ENST00000257290	NM_006206.4	288	TAC/-	6/23	0.847818903574766	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.907802924255196	3		551	703	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0006426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	481	685	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	0.491099676891322	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.491099676891322	3		685	1191	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993182	72993182	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	362	1049	0	ENST00000268489.5:c.863A>C	p.Lys288Thr	p.K288T	ENST00000268489	NM_006885.3	288	aAa/aCa	2/10	0.491099676891322	1	FACETS	0.936	0.888	0.985	0.936	0.888	0.985	CLONAL	1	TRUE	0	0.491099676891322	1		1049	1188	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159751	20159751	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	247	461	4	ENST00000379607.5:c.8A>T	p.Lys3Met	p.K3M	ENST00000379607	NM_001412.3	3	aAg/aTg	1/7	0.491099676891322	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.491099676891322	1		465	710	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747342068	NA	P-0006434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	173	462	0	ENST00000269305.4:c.394A>G	p.Lys132Glu	p.K132E	ENST00000269305	NM_001126112.2	132	Aag/Gag	5/11	0.68656748310288	1	FACETS	0.935	0.875	0.995	0.935	0.875	0.995	CLONAL	1	TRUE	0	0.68656748310288	1		462	354	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	161	397	0	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	1	2	FACETS	0.965	0.892	1	0.965	0.892	1	CLONAL	1	TRUE	1	0.68656748310288	2		397	486	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828162	243828162	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1399248274	NA	P-0006434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	46	384	1	ENST00000263826.5:c.196C>T	p.Arg66Ter	p.R66*	ENST00000263826	NM_005465.4	66	Cga/Tga	3/13	NA	2	FACETS	0.307	0.259	0.361			1	INDETERMINATE	1	TRUE	NA	0.68656748310288	2		385	436	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258970	153258970	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	156	398	0	ENST00000281708.4:c.845C>A	p.Ser282Ter	p.S282*	ENST00000281708	NM_033632.3	282	tCa/tAa	5/12	0.49477354217538	1	FACETS	0.775	0.719	0.832	0.775	0.719	0.832	SUBCLONAL	1	TRUE	0	0.68656748310288	1		398	385	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183252	56183252	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	77	429	0	ENST00000399503.3:c.4162G>C	p.Asp1388His	p.D1388H	ENST00000399503	NM_005921.1	1388	Gat/Cat	18/20	0.533668501326203	1	FACETS	0.39	0.344	0.438	0.39	0.344	0.438	SUBCLONAL	1	TRUE	0	0.68656748310288	1		429	378	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045765	26045765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1319062216	NA	P-0006434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	150	841	1	ENST00000540144.1:c.127C>T	p.Arg43Cys	p.R43C	ENST00000540144	NM_003531.2	43	Cgc/Tgc	1/1	0.421258185901386	2	FACETS	0.493	0.45	0.538	0.247	0.225	0.269	SUBCLONAL	1	TRUE	0	0.68656748310288	2		842	886	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711344	114711344	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	113	257	0	ENST00000543371.1:c.359C>T	p.Ser120Leu	p.S120L	ENST00000543371	NM_001198531.1	120	tCg/tTg	3/14	0.533668501326203	1	FACETS	0.472	0.427	0.519	0.472	0.427	0.519	SUBCLONAL	1	TRUE	0	0.68656748310288	1		257	458	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223313	2223313	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	73	499	0	ENST00000326181.6:c.925G>A	p.Asp309Asn	p.D309N	ENST00000326181	NM_032271.2	309	Gac/Aac	10/21	0.304516189260437	2	FACETS	0.516	0.453	0.583	0.258	0.226	0.292	INDETERMINATE	1	TRUE	0	0.68656748310288	2		499	412	SUCCESS
AR	367	MSKCC	GRCh37	X	66942821	66942821	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	182	529	0	ENST00000374690.3:c.2602C>A	p.Gln868Lys	p.Q868K	ENST00000374690	NM_000044.3	868	Cag/Aag	7/8	0.68656748310288	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.68656748310288	1		529	337	SUCCESS
APC	324	MSKCC	GRCh37	5	112175433	112175434	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0006434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	158	329	0	ENST00000257430.4:c.4143_4144del	p.Leu1382HisfsTer3	p.L1382Hfs*3	ENST00000257430	NM_000038.5	1381	cCA/c	16/16	0.68656748310288	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.68656748310288	1		329	281	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932646	39932646	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006451-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	393	715	0	ENST00000378444.4:c.1953del	p.Tyr653ThrfsTer16	p.Y653Tfs*16	ENST00000378444	NM_001123385.1	651	atT/at	4/15	1	2	FACETS	0.962	0.913	1	0.962	0.913	1	CLONAL	1	TRUE	1	0.525955756972079	2		715	1553	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057905	27057905	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	302	511	0	ENST00000324856.7:c.1613del	p.Gln538ArgfsTer81	p.Q538Rfs*81	ENST00000324856	NM_006015.4	538	cAg/cg	3/20	0.778563586478437	1	FACETS	0.777	0.739	0.815	0.777	0.739	0.815	SUBCLONAL	1	TRUE	0	0.778563586478437	1		511	610	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0006485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	135	301	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.431611729768586	1	FACETS	0.806	0.735	0.88	0.806	0.735	0.88	CLONAL	1	TRUE	0	0.431611729768586	1		301	609	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0006485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	26	228	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.185	0.146	0.23	0.185	0.146	0.23	SUBCLONAL	1	TRUE	1	0.431611729768586	2		228	651	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057874	27057874	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	263	934	0	ENST00000324856.7:c.1582C>T	p.Gln528Ter	p.Q528*	ENST00000324856	NM_006015.4	528	Cag/Tag	3/20	1	2	FACETS	0.962	0.9	1	0.962	0.9	1	CLONAL	1	TRUE	1	0.431611729768586	2		934	1267	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617518	158617518	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs984482376	NA	P-0006485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	305	1118	5	ENST00000263640.3:c.1138C>T	p.Arg380Cys	p.R380C	ENST00000263640	NM_001105.4	380	Cgc/Tgc	9/11	1	2	FACETS	0.961	0.904	1	0.961	0.904	1	CLONAL	1	TRUE	1	0.431611729768586	2		1123	1470	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967266	134967266	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	223	788	0	ENST00000398015.3:c.2605C>A	p.Pro869Thr	p.P869T	ENST00000398015	NM_004441.4	869	Ccc/Acc	14/16	1	2	FACETS	0.979	0.912	1	0.979	0.912	1	CLONAL	1	TRUE	1	0.431611729768586	2		788	1055	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190903	185190903	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1222	262	1133	3	ENST00000265026.3:c.1784G>A	p.Ser595Asn	p.S595N	ENST00000265026	NM_004721.4	595	aGc/aAc	11/14	1	2	FACETS	0.818	0.765	0.874	0.818	0.765	0.874	CLONAL	1	TRUE	1	0.431611729768586	2		1136	1484	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187558011	187558011	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0006485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	115	478	1	ENST00000441802.2:c.3700A>T	p.Lys1234Ter	p.K1234*	ENST00000441802	NM_005245.3	1234	Aaa/Taa	5/27	1	2	FACETS	0.786	0.709	0.867	0.786	0.709	0.867	SUBCLONAL	1	TRUE	1	0.431611729768586	2		479	678	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398881	398881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	184	742	0	ENST00000380956.4:c.691C>T	p.Pro231Ser	p.P231S	ENST00000380956	NM_001195286.1	231	Ccc/Tcc	6/9	1	2	FACETS	0.927	0.856	1	0.927	0.856	1	CLONAL	1	TRUE	1	0.431611729768586	2		742	920	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271224	26271224	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1502	318	1574	0	ENST00000305910.3:c.389G>T	p.Arg130Leu	p.R130L	ENST00000305910	NM_003534.2	130	cGc/cTc	1/1	1	2	FACETS	0.81	0.761	0.859	0.81	0.761	0.859	CLONAL	1	TRUE	1	0.431611729768586	2		1574	1820	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007101	152007101	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1270	196	742	0	ENST00000262189.6:c.799G>A	p.Glu267Lys	p.E267K	ENST00000262189	NM_170606.2	267	Gaa/Aaa	6/59	0.370883486798828	3	FACETS	0.753	0.695	0.814	0.377	0.347	0.407	SUBCLONAL	1	TRUE	1	0.431611729768586	3		742	1466	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813092	76813092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	227	937	0	ENST00000373344.5:c.6529G>A	p.Asp2177Asn	p.D2177N	ENST00000373344	NM_000489.3	2177	Gat/Aat	30/35	1	2	FACETS	0.822	0.765	0.882	0.822	0.765	0.882	CLONAL	1	TRUE	1	0.431611729768586	2		937	1279	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781284	3781290	+	frameshift_variant	Frame_Shift_Del	DEL	TCCACCA	TCCACCA	-	novel	NA	P-0006485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	425	981	0	ENST00000262367.5:c.5075_5081del	p.Leu1692ArgfsTer50	p.L1692Rfs*50	ENST00000262367	NM_004380.2	1692	cTGGTGGAg/cg	30/31	0.370883486798828	3	FACETS	0.895	0.853	0.939	0.895	0.853	0.939	CLONAL	2	TRUE	1	0.431611729768586	3		981	1337	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0006488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	262	258	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.351555782578434	5	FACETS	0.909	0.854	0.965	0.909	0.854	0.965	CLONAL	3	TRUE	2	0.351555782578434	5		258	835	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0006488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	69	223	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.318997997575001	3	FACETS	0.774	0.675	0.882	0.387	0.337	0.441	SUBCLONAL	1	TRUE	1	0.351555782578434	3		223	596	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467675	50467675	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759124417	NA	P-0006488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	135	545	0	ENST00000331340.3:c.910G>A	p.Glu304Lys	p.E304K	ENST00000331340	NM_006060.4	304	Gaa/Aaa	8/8	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.351555782578434	2		545	686	SUCCESS
APC	324	MSKCC	GRCh37	5	112178162	112178162	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561610839	NA	P-0006488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	68	448	0	ENST00000257430.4:c.6871C>T	p.Gln2291Ter	p.Q2291*	ENST00000257430	NM_000038.5	2291	Caa/Taa	16/16	1	2	FACETS	0.783	0.683	0.891	0.783	0.683	0.891	SUBCLONAL	1	TRUE	1	0.351555782578434	2		448	494	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971027	21971028	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0006488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	170	348	0	ENST00000304494.5:c.330_331delinsAA	p.Trp110_Gly111delinsTer	p.W110_G111delins*	ENST00000304494	NM_000077.4	110	tgGGgc/tgAAgc	2/3	0.307023599730427	3	FACETS	1	0.978	1	0.763	0.707	0.82	CLONAL	2	TRUE	0	0.351555782578434	3		348	497	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600428	10600429	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0006488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1456	148	719	0	ENST00000171111.5:c.1426_1427delinsAA	p.Gly476Lys	p.G476K	ENST00000171111	NM_203500.1	476	GGg/AAg	4/6	0.351555782578434	3	FACETS	0.617	0.561	0.676	0.309	0.28	0.338	SUBCLONAL	1	TRUE	1	0.351555782578434	3		719	1604	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0006569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	41	355	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	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.14	2		355	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0006569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	23	493	1	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	1	2	FACETS	0.538	0.418	0.678	0.538	0.418	0.678	SUBCLONAL	1	TRUE	1	0.14	2		494	611	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0006569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	29	306	1	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	0.946	0.759	1	0.946	0.759	1	CLONAL	1	TRUE	1	0.14	2		307	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0006575-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	516	454	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.511757438621828	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.511757438621828	2		454	955	SUCCESS
APC	324	MSKCC	GRCh37	5	112175411	112175411	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006575-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	78	242	0	ENST00000257430.4:c.4120G>T	p.Glu1374Ter	p.E1374*	ENST00000257430	NM_000038.5	1374	Gaa/Taa	16/16	0.511757438621828	3	FACETS	0.772	0.68	0.87	0.386	0.34	0.435	SUBCLONAL	1	TRUE	1	0.511757438621828	3		242	496	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947199	178947199	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006575-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	110	332	0	ENST00000263967.3:c.2635C>T	p.Gln879Ter	p.Q879*	ENST00000263967	NM_006218.2	879	Cag/Tag	18/21	0.472799038317748	3	FACETS	0.918	0.827	1	0.459	0.413	0.507	CLONAL	1	TRUE	1	0.511757438621828	3		332	588	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521499	187521499	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006575-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	76	202	0	ENST00000441802.2:c.11656C>A	p.Leu3886Met	p.L3886M	ENST00000441802	NM_005245.3	3886	Ctg/Atg	22/27	0.511757438621828	2	FACETS	0.911	0.806	1	0.456	0.403	0.511	CLONAL	1	TRUE	0	0.511757438621828	2		202	326	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391610	139391610	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006575-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	160	346	0	ENST00000277541.6:c.6581C>G	p.Ser2194Cys	p.S2194C	ENST00000277541	NM_017617.3	2194	tCc/tGc	34/34	0.472799038317748	3	FACETS	1	0.974	1	0.569	0.523	0.617	CLONAL	1	TRUE	1	0.511757438621828	3		346	690	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298120	15298120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376606994	NA	P-0006575-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	398	448	0	ENST00000263388.2:c.1636G>A	p.Val546Met	p.V546M	ENST00000263388	NM_000435.2	546	Gtg/Atg	11/33	0.412918415844235	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	2	0.511757438621828	4		448	1135	SUCCESS
APC	324	MSKCC	GRCh37	5	112175412	112175412	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006575-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	222	243	0	ENST00000257430.4:c.4122del	p.Glu1374AspfsTer41	p.E1374Dfs*41	ENST00000257430	NM_000038.5	1374	gAa/ga	16/16	0.511757438621828	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.511757438621828	3		243	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0006577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	32	562	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.061	0.049	0.075	0.061	0.049	0.075	SUBCLONAL	1	TRUE	1	0.939584703286886	2		564	1119	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540172	187540172	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	241	543	1	ENST00000441802.2:c.7568T>G	p.Ile2523Ser	p.I2523S	ENST00000441802	NM_005245.3	2523	aTt/aGt	10/27	1	2	FACETS	0.474	0.442	0.507	0.474	0.442	0.507	SUBCLONAL	1	TRUE	1	0.939584703286886	2		544	1082	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123353298	123353298	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143978938	NA	P-0006577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	282	533	4	ENST00000358487.5:c.34G>A	p.Val12Met	p.V12M	ENST00000358487	NM_000141.4	12	Gtg/Atg	2/18	1	2	FACETS	0.513	0.482	0.546	0.513	0.482	0.546	SUBCLONAL	1	TRUE	1	0.939584703286886	2		537	1169	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0006593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	75	433	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.3	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.14	1		434	942	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	40	269	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.992	0.823	1	0.992	0.823	1	CLONAL	1	TRUE	1	0.14	2		269	576	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820925	3820925	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	42	268	0	ENST00000262367.5:c.2526G>T	p.Gln842His	p.Q842H	ENST00000262367	NM_004380.2	842	caG/caT	14/31	1	2	FACETS	0.912	0.76	1	0.912	0.76	1	CLONAL	1	TRUE	1	0.14	2		268	658	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624298	89624298	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1320222638	NA	P-0006594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	185	148	0	ENST00000371953.3:c.72C>G	p.Asp24Glu	p.D24E	ENST00000371953	NM_000314.4	24	gaC/gaG	1/9	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.68	2		148	477	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425016	49425016	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1298743172	NA	P-0006594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	312	351	0	ENST00000301067.7:c.13472T>C	p.Ile4491Thr	p.I4491T	ENST00000301067	NM_003482.3	4491	aTt/aCt	39/54	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.68	2		351	814	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863427	57863427	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2309	289	471	1	ENST00000228682.2:c.1522C>T	p.Gln508Ter	p.Q508*	ENST00000228682	NM_005269.2	508	Caa/Taa	11/12	0.684982819894621	5	FACETS	0.661	0.618	0.705			1	SUBCLONAL	1	TRUE	NA	0.68	5		472	2598	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0006622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	86	228	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.946	0.838	1	0.946	0.838	1	CLONAL	1	TRUE	1	0.29	2		228	627	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55231427	55231427	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs778985185	NA	P-0006622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	52	457	0	ENST00000275493.2:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000275493	NM_005228.3	545	Gag/Aag	14/28	1	2	FACETS	0.36	0.305	0.421	0.36	0.305	0.421	SUBCLONAL	1	TRUE	1	0.29	2		457	995	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115900	8115922	+	frameshift_variant	Frame_Shift_Del	DEL	CTGACCACGCCCACGCCGATGCA	CTGACCACGCCCACGCCGATGCA	-	novel	NA	P-0006622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	124	383	0	ENST00000346208.3:c.1247_1269del	p.Leu416ProfsTer83	p.L416Pfs*83	ENST00000346208		416	CTGACCACGCCCACGCCGATGCAc/c	6/6	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.29	2		383	802	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082466	16082466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006630-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	125	320	0	ENST00000281043.3:c.280G>A	p.Glu94Lys	p.E94K	ENST00000281043	NM_005378.4	94	Gag/Aag	2/3	0.460665246646592	2	FACETS	0.28	0.253	0.309	0.14	0.126	0.155	INDETERMINATE	1	TRUE	0	0.907987733164877	2		320	983	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99185084	99185084	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006630-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	906	482	0	ENST00000074304.5:c.2486G>T	p.Arg829Leu	p.R829L	ENST00000074304	NM_001134224.1	829	cGg/cTg	23/26	0.460665246646592	2	FACETS	1	0.998	1	0.749	0.732	0.766	INDETERMINATE	1	TRUE	0	0.907987733164877	2		482	1332	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970852	55970852	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006630-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	306	516	0	ENST00000263923.4:c.1945A>T	p.Thr649Ser	p.T649S	ENST00000263923	NM_002253.2	649	Acc/Tcc	13/30	0.493243564459807	1	FACETS	0.372	0.351	0.394	0.372	0.351	0.394	INDETERMINATE	1	TRUE	0	0.907987733164877	1		516	988	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129090	152129090	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006630-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	326	419	0	ENST00000206249.3:c.43C>G	p.Leu15Val	p.L15V	ENST00000206249	NM_000125.3	15	Ctg/Gtg	1/8	1	2	FACETS	0.559	0.528	0.592	0.559	0.528	0.592	SUBCLONAL	1	TRUE	1	0.907987733164877	2		419	1284	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861978	57861978	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006630-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	1179	569	0	ENST00000228682.2:c.1279A>T	p.Ser427Cys	p.S427C	ENST00000228682	NM_005269.2	427	Agc/Tgc	10/12	0.454420602641564	2	FACETS	0.764	0.749	0.779	0.764	0.749	0.779	INDETERMINATE	2	TRUE	0	0.907987733164877	2		569	1700	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951110	48951110	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006630-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	718	438	0	ENST00000267163.4:c.1272C>A	p.Tyr424Ter	p.Y424*	ENST00000267163	NM_000321.2	424	taC/taA	13/27	0.900868965614209	2	FACETS	0.995	0.98	1	0.995	0.98	1	CLONAL	2	TRUE	0	0.907987733164877	2		438	795	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678351	88678351	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006630-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	313	454	1	ENST00000360948.2:c.1185C>A	p.Phe395Leu	p.F395L	ENST00000360948	NM_001012338.2	395	ttC/ttA	9/19	0.493243564459807	1	FACETS	0.366	0.345	0.387	0.366	0.345	0.387	INDETERMINATE	1	TRUE	0	0.907987733164877	1		455	1029	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943790	9943790	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006630-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	165	231	0	ENST00000330684.3:c.1151G>A	p.Ser384Asn	p.S384N	ENST00000330684	NM_001134407.1	384	aGc/aAc	5/13	0.468372426420317	3	FACETS	0.521	0.477	0.566	0.174	0.159	0.189	INDETERMINATE	1	TRUE	0	0.907987733164877	3		231	1015	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579329	7579329	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs121912658	NA	P-0006630-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	775	421	0	ENST00000269305.4:c.358A>T	p.Lys120Ter	p.K120*	ENST00000269305	NM_001126112.2	120	Aag/Tag	4/11	0.907987733164877	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.907987733164877	1		421	859	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936781	78936782	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0006630-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	582	414	3	ENST00000306801.3:c.3864_3865del	p.Asn1288LysfsTer51	p.N1288Kfs*51	ENST00000306801	NM_020761.2	1288	aAC/a	33/34	0.425664149711653	3	FACETS	1	0.994	1	0.589	0.566	0.613	INDETERMINATE	1	TRUE	1	0.907987733164877	3		417	1581	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0006640-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	244	355	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.295803793446511	4	FACETS	0.888	0.83	0.949	0.888	0.83	0.949	CLONAL	2	TRUE	2	0.334140944687378	4		355	1097	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225400277	225400277	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs755957972	NA	P-0006640-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	130	356	0	ENST00000264414.4:c.346A>G	p.Met116Val	p.M116V	ENST00000264414	NM_003590.4	116	Atg/Gtg	3/16	1	2	FACETS	0.912	0.827	1	0.912	0.827	1	CLONAL	1	TRUE	1	0.334140944687378	2		356	853	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493802	56493802	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200017094	NA	P-0006640-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	104	313	0	ENST00000267101.3:c.3118C>T	p.Arg1040Trp	p.R1040W	ENST00000267101	NM_001982.3	1040	Cgg/Tgg	25/28	NA	2	FACETS	0.647	0.578	0.72			1	INDETERMINATE	1	TRUE	NA	0.334140944687378	2		313	962	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494012	56494012	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006640-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	163	324	0	ENST00000267101.3:c.3184C>G	p.Leu1062Val	p.L1062V	ENST00000267101	NM_001982.3	1062	Ctt/Gtt	26/28	NA	2	FACETS	0.851	0.78	0.926			1	INDETERMINATE	1	TRUE	NA	0.334140944687378	2		324	1146	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095905	178095905	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	187	395	0	ENST00000397062.3:c.1426C>G	p.Leu476Val	p.L476V	ENST00000397062	NM_006164.4	476	Ctc/Gtc	5/5	0.686832565945341	6	FACETS	0.949	0.874	1	0.158	0.145	0.172	CLONAL	1	TRUE	0	0.686832565945341	6		395	1362	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260663	1260663	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	811	454	9	ENST00000310581.5:c.2896G>C	p.Ala966Pro	p.A966P	ENST00000310581	NM_198253.2	966	Gct/Cct	12/16	0.686832565945341	6	FACETS	0.971	0.94	1			1	CLONAL	3	TRUE	NA	0.686832565945341	6		463	1925	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372430	55372430	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1526	263	451	0	ENST00000297316.4:c.1120G>T	p.Glu374Ter	p.E374*	ENST00000297316	NM_022454.3	374	Gag/Tag	2/2	0.686832565945341	7	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.686832565945341	7		451	1789	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914812	32914812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	269	564	1	ENST00000380152.3:c.6320C>T	p.Pro2107Leu	p.P2107L	ENST00000380152		2107	cCt/cTt	11/27	0.690055120583747	2	FACETS	1	0.988	1	0.586	0.553	0.62	CLONAL	1	TRUE	0	0.686832565945341	2		565	668	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934536	9934536	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1412	285	521	0	ENST00000330684.3:c.1619G>A	p.Ser540Asn	p.S540N	ENST00000330684	NM_001134407.1	540	aGt/aAt	7/13	0.623028675781974	5	FACETS	0.993	0.93	1			1	CLONAL	1	TRUE	NA	0.686832565945341	5		521	1697	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589526	69589558	+	inframe_deletion	In_Frame_Del	DEL	CGCGTGCGCGCCGCCGATGCGGCCGTCGGGGAG	CGCGTGCGCGCCGCCGATGCGGCCGTCGGGGAG	-	novel	NA	P-0006656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	52	140	0	ENST00000168712.1:c.295_327del	p.Leu99_Ala109del	p.L99_A109del	ENST00000168712	NM_002007.2	99	CTCCCCGACGGCCGCATCGGCGGCGCGCACGCG/-	1/3	0.690055120583747	3	FACETS	0.685	0.587	0.791	0.342	0.293	0.396	SUBCLONAL	1	TRUE	1	0.686832565945341	3		140	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579321	7579322	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs587780067	NA	P-0006656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	988	391	3	ENST00000269305.4:c.365_366del	p.Val122AspfsTer26	p.V122Dfs*26	ENST00000269305	NM_001126112.2	122	gTG/g	4/11	0.600262159031607	4	FACETS	1	0.997	1			1	CLONAL	4	TRUE	NA	0.686832565945341	4		394	1162	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578191	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs530941076	NA	P-0006675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	420	389	0	ENST00000269305.4:c.658T>C	p.Tyr220His	p.Y220H	ENST00000269305	NM_001126112.2	220	Tat/Cat	6/11	0.446488211976059	1	FACETS	0.889	0.846	0.932	0.889	0.846	0.932	CLONAL	1	TRUE	0	0.514694057478277	1		389	1364	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521670	89521670	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	260	414	0	ENST00000336596.2:c.2747C>G	p.Thr916Arg	p.T916R	ENST00000336596	NM_005233.5	916	aCa/aGa	16/17	0.483029437801458	1	FACETS	0.901	0.846	0.956	0.901	0.846	0.956	CLONAL	1	TRUE	0	0.514694057478277	1		414	833	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467446	66467446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773861301	NA	P-0006675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	310	346	0	ENST00000273854.3:c.823C>T	p.His275Tyr	p.H275Y	ENST00000273854	NM_004439.5	275	Cac/Tac	3/18	0.508662256833416	1	FACETS	0.936	0.884	0.988	0.936	0.884	0.988	CLONAL	1	TRUE	0	0.514694057478277	1		346	956	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778153	3778153	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	317	350	0	ENST00000262367.5:c.6895C>A	p.Gln2299Lys	p.Q2299K	ENST00000262367	NM_004380.2	2299	Cag/Aag	31/31	1	2	FACETS	0.951	0.897	1	0.951	0.897	1	CLONAL	1	TRUE	1	0.514694057478277	2		350	1295	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	40	269	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.845	1	1	0.845	1	CLONAL	1	TRUE	1	0.14	2		269	561	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0006699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	150	342	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.952	1	1	0.992	1	CLONAL	2	TRUE	1	0.21	2		343	676	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286820	212286820	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1337583184	NA	P-0006699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	97	323	0	ENST00000342788.4:c.2876T>C	p.Ile959Thr	p.I959T	ENST00000342788	NM_005235.2	959	aTt/aCt	24/28	0.3	3	FACETS	0.978	0.875	1	0.978	0.875	1	CLONAL	2	TRUE	1	0.21	3		323	522	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450397	50450397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	73	303	0	ENST00000331340.3:c.581C>T	p.Thr194Met	p.T194M	ENST00000331340	NM_006060.4	194	aCg/aTg	5/8	0.172379721872921	4	FACETS	1	0.967	1	0.671	0.587	0.761	CLONAL	1	TRUE	2	0.21	4		303	627	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517857	8517857	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs746567652	NA	P-0006699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	160	447	0	ENST00000356435.5:c.1534C>G	p.Gln512Glu	p.Q512E	ENST00000356435		512	Cag/Gag	10/35	0.177333506232844	2	FACETS	0.861	0.789	0.936	0.861	0.789	0.936	CLONAL	2	TRUE	0	0.21	2		447	885	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241459	105241459	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1200003171	NA	P-0006699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	82	480	1	ENST00000349310.3:c.521G>A	p.Arg174His	p.R174H	ENST00000349310	NM_001014432.1	174	cGc/cAc	7/15	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.21	2		481	737	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281344	15281344	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	42	362	0	ENST00000263388.2:c.4912G>T	p.Glu1638Ter	p.E1638*	ENST00000263388	NM_000435.2	1638	Gaa/Taa	27/33	1	2	FACETS	0.758	0.632	0.897	0.758	0.632	0.897	SUBCLONAL	1	TRUE	1	0.21	2		362	528	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750689	39750689	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	75	204	0	ENST00000361337.2:c.2089C>T	p.Gln697Ter	p.Q697*	ENST00000361337	NM_003286.2	697	Cag/Tag	20/21	0.232570081461953	4	FACETS	0.895	0.786	1	0.895	0.786	1	CLONAL	2	TRUE	2	0.21	4		204	483	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006702-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	374	269	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.238204729662624	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	1	0.238204729662624	4		269	1126	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593417	48593417	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006702-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	102	366	0	ENST00000342988.3:c.1168G>T	p.Glu390Ter	p.E390*	ENST00000342988	NM_005359.5	390	Gaa/Taa	10/12	0.238204729662624	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.238204729662624	1		366	720	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853209	68853209	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006702-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	129	520	0	ENST00000261769.5:c.1592A>G	p.Asn531Ser	p.N531S	ENST00000261769	NM_004360.3	531	aAc/aGc	11/16	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.238204729662624	2		520	1077	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578191	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs530941076	NA	P-0006702-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	140	477	0	ENST00000269305.4:c.658T>A	p.Tyr220Asn	p.Y220N	ENST00000269305	NM_001126112.2	220	Tat/Aat	6/11	0.238204729662624	1	FACETS	0.936	0.851	1	0.936	0.851	1	CLONAL	1	TRUE	0	0.238204729662624	1		477	1106	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691025	NA	P-0006703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	438	523	0	ENST00000269305.4:c.785G>T	p.Gly262Val	p.G262V	ENST00000269305	NM_001126112.2	262	gGt/gTt	8/11	0.429238850974615	2	FACETS	0.824	0.788	0.861	0.824	0.788	0.861	CLONAL	2	TRUE	0	0.486221798118629	2		523	1093	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17120481	17120481	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	379	451	0	ENST00000285071.4:c.1078T>A	p.Ser360Thr	p.S360T	ENST00000285071	NM_144997.5	360	Tct/Act	10/14	0.429238850974615	2	FACETS	0.837	0.798	0.877	0.837	0.798	0.877	CLONAL	2	TRUE	0	0.486221798118629	2		451	931	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176085809	176085827	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATAATACTACTGCAAAATG	ATAATACTACTGCAAAATG	-	novel	NA	P-0006703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	530	558	0	ENST00000367669.3:c.969-10_977del		p.X323_splice	ENST00000367669	NM_022457.5	323		9/20	0.486221798118629	3	FACETS	0.848	0.812	0.884	0.848	0.812	0.884	CLONAL	2	TRUE	1	0.486221798118629	3		558	1598	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0006730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	119	258	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.422914043095959	2		258	533	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0006730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	56	219	0	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	0.422914043095959	1	FACETS	0.637	0.548	0.732	0.637	0.548	0.732	SUBCLONAL	1	TRUE	0	0.422914043095959	1		219	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578433	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555526101	NA	P-0006730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	219	410	0	ENST00000269305.4:c.497C>G	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	166	tCa/tGa	5/11	0.422914043095959	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.422914043095959	1		410	765	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271192	153271192	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0006730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	93	333	0	ENST00000281708.4:c.584+2T>G		p.X195_splice	ENST00000281708	NM_033632.3	195			1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.422914043095959	2		333	406	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738696	145738696	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762402665	NA	P-0006730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1537	129	309	2	ENST00000428558.2:c.2368G>A	p.Gly790Arg	p.G790R	ENST00000428558	NM_004260.3	790	Ggg/Agg	15/22	0.422914043095959	9	FACETS	0.908	0.82	1			1	CLONAL	1	TRUE	NA	0.422914043095959	9		311	1666	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836985	89836985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs539161141	NA	P-0006730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	179	415	0	ENST00000389301.3:c.2209G>A	p.Ala737Thr	p.A737T	ENST00000389301	NM_000135.2	737	Gct/Act	24/43	1	2	FACETS	0.836	0.77	0.904	0.836	0.77	0.904	CLONAL	1	TRUE	1	0.422914043095959	2		415	1013	SUCCESS
APC	324	MSKCC	GRCh37	5	112175746	112175746	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006737-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	27	453	0	ENST00000257430.4:c.4455del	p.Asp1486IlefsTer21	p.D1486Ifs*21	ENST00000257430	NM_000038.5	1485	gcT/gc	16/16	1	2	FACETS	0.69	0.547	0.853	0.69	0.547	0.853	SUBCLONAL	1	TRUE	1	0.15	2		453	522	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579344	7579345	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0006737-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	108	604	3	ENST00000269305.4:c.342_343del	p.His115PhefsTer33	p.H115Ffs*33	ENST00000269305	NM_001126112.2	114	ttGCat/ttat	4/11	0.151152856393374	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	2	TRUE	0	0.15	2		607	707	SUCCESS
APC	324	MSKCC	GRCh37	5	112174842	112174842	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006737-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	122	451	0	ENST00000257430.4:c.3552del	p.Thr1185GlnfsTer80	p.T1185Qfs*80	ENST00000257430	NM_000038.5	1184	gCc/gc	16/16	1	2	FACETS	1	0.952	1	1	0.99	1	CLONAL	2	TRUE	1	0.15	2		451	750	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0006781-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	622	329	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.386931840611182	3	FACETS	0.906	0.878	0.933			1	CLONAL	4	TRUE	NA	0.395895381130563	3		329	1039	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572348	41572348	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006781-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	218	315	0	ENST00000263253.7:c.4877G>T	p.Gly1626Val	p.G1626V	ENST00000263253	NM_001429.3	1626	gGt/gTt	30/31	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.395895381130563	2		315	757	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872115	76872116	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	TT	novel	NA	P-0006781-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	141	228	0	ENST00000373344.5:c.5531_5532delinsAA	p.Cys1844Ter	p.C1844*	ENST00000373344	NM_000489.3	1844	tGC/tAA	22/35	0.395895381130563	0	FACETS	0.925	0.85	1			1	CLONAL	1	TRUE	NA	0.395895381130563	0		228	465	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56871580	56871580	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006801-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1317	84	1188	2	ENST00000308159.5:c.1960A>G	p.Ser654Gly	p.S654G	ENST00000308159	NM_014669.4	654	Agt/Ggt	18/22	NA	2	FACETS	0.17	0.15	0.193			1	INDETERMINATE	1	TRUE	NA	0.703333170580488	2		1190	1401	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0006802-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	489	466	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	1	2	FACETS	0.924	0.885	0.964	0.924	0.885	0.964	CLONAL	1	TRUE	1	0.78972838651222	2		466	1340	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431961	49431962	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0006802-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	360	331	0	ENST00000301067.7:c.9177_9178del	p.Asp3061GlnfsTer7	p.D3061Qfs*7	ENST00000301067	NM_003482.3	3059	acTGgg/acgg	34/54	0.757205036903698	1	FACETS	0.97	0.932	1	0.97	0.932	1	CLONAL	1	TRUE	0	0.78972838651222	1		331	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578488	7578488	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006818-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	395	478	0	ENST00000269305.4:c.442del	p.Asp148IlefsTer22	p.D148Ifs*22	ENST00000269305	NM_001126112.2	148	Gat/at	5/11	0.329093176318696	1	FACETS	0.821	0.78	0.861	1	0.996	1	CLONAL	2	FALSE	0	0.329093176318696	1		478	1222	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0006826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	55	124	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.526494552841515	5	FACETS	0.757	0.648	0.876	0.189	0.162	0.219	SUBCLONAL	1	TRUE	1	0.526494552841515	5		124	494	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449827	8449827	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	140	298	1	ENST00000356435.5:c.3886G>C	p.Glu1296Gln	p.E1296Q	ENST00000356435		1296	Gag/Cag	23/35	1	2	FACETS	0.888	0.812	0.967	0.888	0.812	0.967	CLONAL	1	TRUE	1	0.526494552841515	2		299	599	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256141	133256141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1250780418	NA	P-0006826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	241	461	2	ENST00000320574.5:c.520G>A	p.Val174Met	p.V174M	ENST00000320574	NM_006231.2	174	Gtg/Atg	6/49	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.526494552841515	2		463	842	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003545	42003545	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs765013304	NA	P-0006826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	309	580	0	ENST00000219905.7:c.3082C>G	p.Gln1028Glu	p.Q1028E	ENST00000219905	NM_001164273.1	1028	Caa/Gaa	8/24	1	2	FACETS	0.915	0.862	0.969	0.915	0.862	0.969	CLONAL	1	TRUE	1	0.526494552841515	2		580	1283	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343537	343537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745327595	NA	P-0006826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	266	569	0	ENST00000262320.3:c.2137C>T	p.Arg713Cys	p.R713C	ENST00000262320	NM_003502.3	713	Cgt/Tgt	8/11	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.526494552841515	2		569	1006	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578206	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs886039484	NA	P-0006837-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	385	545	0	ENST00000269305.4:c.643A>C	p.Ser215Arg	p.S215R	ENST00000269305	NM_001126112.2	215	Agt/Cgt	6/11	0.547481980097824	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.547481980097824	1		545	994	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138376590	138376590	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006837-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	389	506	1	ENST00000289153.2:c.2884T>A	p.Tyr962Asn	p.Y962N	ENST00000289153	NM_006219.2	962	Tat/Aat	20/22	0.284398326070869	1	FACETS	0.887	0.843	0.931	0.887	0.843	0.931	INDETERMINATE	1	TRUE	0	0.547481980097824	1		507	1164	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653859	89653860	+	stop_gained	Nonsense_Mutation	DNP	GT	GT	TG	novel	NA	P-0006837-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	197	328	0	ENST00000371953.3:c.157_158delinsTG	p.Val53Ter	p.V53*	ENST00000371953	NM_000314.4	53	GTa/TGa	2/9	0.547481980097824	1	FACETS	0.912	0.85	0.975	0.912	0.85	0.975	CLONAL	1	TRUE	0	0.547481980097824	1		328	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0006845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	20	497	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.473	0.36	0.606	0.473	0.36	0.606	SUBCLONAL	1	TRUE	1	0.15	2		497	564	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0006845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	38	381	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.15	2		381	456	SUCCESS
APC	324	MSKCC	GRCh37	5	112174814	112174814	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085081	NA	P-0006845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	46	397	1	ENST00000257430.4:c.3523C>T	p.Gln1175Ter	p.Q1175*	ENST00000257430	NM_000038.5	1175	Cag/Tag	16/16	1	2	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	TRUE	1	0.15	2		398	610	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845128	128845128	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878919378	NA	P-0006845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	35	395	3	ENST00000249373.3:c.622G>A	p.Glu208Lys	p.E208K	ENST00000249373	NM_005631.4	208	Gag/Aag	3/12	1	2	FACETS	0.74	0.605	0.892	0.74	0.605	0.892	SUBCLONAL	1	TRUE	1	0.15	2		398	631	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974679	21974679	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs864622636	NA	P-0006845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	27	361	1	ENST00000304494.5:c.148C>T	p.Gln50Ter	p.Q50*	ENST00000304494	NM_000077.4	50	Cag/Tag	1/3	1	2	FACETS	0.826	0.656	1	0.826	0.656	1	CLONAL	1	TRUE	1	0.15	2		362	436	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393199	393199	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006877-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	99	420	0	ENST00000380956.4:c.47C>T	p.Ala16Val	p.A16V	ENST00000380956	NM_001195286.1	16	gCg/gTg	2/9	0.160672291254619	5	FACETS	0.883	0.788	0.984			1	INDETERMINATE	1	TRUE	NA	0.565277099110021	5		420	733	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288851	33288851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs913125455	NA	P-0006877-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	151	208	1	ENST00000374542.5:c.701G>A	p.Arg234His	p.R234H	ENST00000374542	NM_001141970.1	234	cGc/cAc	3/8	0.449041554865197	4	FACETS	1	0.983	1	0.428	0.392	0.465	CLONAL	1	TRUE	1	0.565277099110021	4		209	651	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129130	152129130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006877-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	70	546	3	ENST00000206249.3:c.83G>A	p.Arg28His	p.R28H	ENST00000206249	NM_000125.3	28	cGt/cAt	1/8	0.449041554865197	4	FACETS	0.493	0.429	0.562	0.164	0.143	0.188	SUBCLONAL	1	TRUE	1	0.565277099110021	4		549	787	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622179	162622179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781608005	NA	P-0006877-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	115	322	0	ENST00000366898.1:c.518C>T	p.Thr173Met	p.T173M	ENST00000366898	NM_004562.2	173	aCg/aTg	4/12	0.449041554865197	4	FACETS	1	0.939	1	0.351	0.317	0.387	CLONAL	1	TRUE	1	0.565277099110021	4		322	605	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636739	8636739	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006877-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	65	186	1	ENST00000356435.5:c.170G>A	p.Trp57Ter	p.W57*	ENST00000356435		57	tGg/tAg	2/35	0.548428378471793	2	FACETS	0.489	0.425	0.559	0.245	0.212	0.28	SUBCLONAL	1	TRUE	0	0.565277099110021	2		187	470	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400024	139400024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006877-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	92	366	0	ENST00000277541.6:c.4324C>T	p.Pro1442Ser	p.P1442S	ENST00000277541	NM_017617.3	1442	Ccg/Tcg	25/34	0.258080044425398	5	FACETS	0.826	0.734	0.925	0.165	0.146	0.185	INDETERMINATE	1	TRUE	0	0.565277099110021	5		366	728	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405072	70405072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs555162188	NA	P-0006877-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	83	484	0	ENST00000373644.4:c.2586A>G	p.Ile862Met	p.I862M	ENST00000373644	NM_030625.2	862	atA/atG	4/12	0.565277099110021	3	FACETS	0.429	0.378	0.485	0.215	0.189	0.243	SUBCLONAL	1	TRUE	1	0.565277099110021	3		484	877	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405530	70405530	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1282487969	NA	P-0006877-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	67	298	0	ENST00000373644.4:c.3044T>C	p.Ile1015Thr	p.I1015T	ENST00000373644	NM_030625.2	1015	aTt/aCt	4/12	0.565277099110021	3	FACETS	0.514	0.447	0.587	0.257	0.223	0.294	SUBCLONAL	1	TRUE	1	0.565277099110021	3		298	591	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434090	49434090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779629382	NA	P-0006877-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	113	242	1	ENST00000301067.7:c.7463C>T	p.Ser2488Leu	p.S2488L	ENST00000301067	NM_003482.3	2488	tCg/tTg	31/54	0.565277099110021	3	FACETS	1	0.969	1	0.583	0.528	0.64	CLONAL	1	TRUE	1	0.565277099110021	3		243	440	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591888	48591888	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519739	NA	P-0006877-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	32	472	0	ENST00000342988.3:c.1051G>C	p.Asp351His	p.D351H	ENST00000342988	NM_005359.5	351	Gat/Cat	9/12	1	2	FACETS	0.146	0.117	0.178	0.146	0.117	0.178	SUBCLONAL	1	TRUE	1	0.565277099110021	2		472	777	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577567	7577567	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1555525537	NA	P-0006877-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	501	448	0	ENST00000269305.4:c.714del	p.Cys238Ter	p.C238*	ENST00000269305	NM_001126112.2	238	tgT/tg	7/11	0.258080044425398	5	FACETS	1	0.991	1	0.854	0.827	0.881	INDETERMINATE	4	TRUE	0	0.565277099110021	5		448	767	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0006886-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	846	538	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.859645758966479	3	FACETS	1	0.997	1			1	CLONAL	2	FALSE	NA	0.859645758966479	3		538	1237	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259442	55259442	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397517127	NA	P-0006886-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	768	393	0	ENST00000275493.2:c.2500G>T	p.Val834Leu	p.V834L	ENST00000275493	NM_005228.3	834	Gtg/Ttg	21/28	0.859645758966479	3	FACETS	1	0.997	1			1	CLONAL	2	FALSE	NA	0.859645758966479	3		393	1095	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349224	11349224	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006886-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	44	57	0	ENST00000332029.2:c.112C>T	p.Arg38Cys	p.R38C	ENST00000332029	NM_003745.1	38	Cgc/Tgc	2/2	0.859645758966479	3	FACETS	0.989	0.846	1	0.494	0.423	0.571	CLONAL	1	FALSE	1	0.859645758966479	3		57	148	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348510	56348510	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006886-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	459	670	2	ENST00000348428.3:c.318G>C	p.Leu106Phe	p.L106F	ENST00000348428	NM_006785.3	106	ttG/ttC	2/17	0.858944845765054	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	0	0.859645758966479	1		672	605	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162125	47162125	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006886-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	332	294	0	ENST00000409792.3:c.4001del	p.Asp1334ValfsTer39	p.D1334Vfs*39	ENST00000409792	NM_014159.6	1334	gAt/gt	3/21	NA	2	FACETS	0.931	0.902	0.957			1	INDETERMINATE	2	FALSE	NA	0.859645758966479	2		294	415	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057948	27057957	+	frameshift_variant	Frame_Shift_Del	DEL	ACAGCCACAG	ACAGCCACAG	-	novel	NA	P-0006886-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	217	429	0	ENST00000324856.7:c.1656_1665del	p.Gln553LeufsTer63	p.Q553Lfs*63	ENST00000324856	NM_006015.4	552	tcACAGCCACAG/tc	3/20	0.683220095479439	3	FACETS	0.934	0.871	0.998	0.467	0.435	0.499	CLONAL	1	FALSE	1	0.859645758966479	3		429	773	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0006889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	446	433	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.636228094116362	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.636228094116362	1		434	879	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0006889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	220	223	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.963	0.9	1	0.963	0.9	1	CLONAL	1	TRUE	1	0.636228094116362	2		223	718	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0006889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	185	304	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.636228094116362	2		304	549	SUCCESS
APC	324	MSKCC	GRCh37	5	112175182	112175182	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	124	240	0	ENST00000257430.4:c.3892del	p.Ser1298LeufsTer7	p.S1298Lfs*7	ENST00000257430	NM_000038.5	1297	gaT/ga	16/16	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.636228094116362	2		240	389	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933539	36933539	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148104401	NA	P-0006889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	356	577	1	ENST00000361632.4:c.1748G>A	p.Arg583His	p.R583H	ENST00000361632		583	cGt/cAt	13/16	1	2	FACETS	0.977	0.926	1	0.977	0.926	1	CLONAL	1	TRUE	1	0.636228094116362	2		578	1146	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798118	45798118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200495564	NA	P-0006889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	203	287	0	ENST00000450313.1:c.733C>T	p.Arg245Cys	p.R245C	ENST00000450313	NM_012222.2	245	Cgt/Tgt	9/16	1	2	FACETS	0.983	0.916	1	0.983	0.916	1	CLONAL	1	TRUE	1	0.636228094116362	2		287	649	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724421	117724421	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs752552490	NA	P-0006889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	450	508	0	ENST00000368508.3:c.458A>G	p.Tyr153Cys	p.Y153C	ENST00000368508	NM_002944.2	153	tAt/tGt	6/43	0.376071460316414	3	FACETS	0.957	0.918	0.997	0.957	0.918	0.997	INDETERMINATE	2	TRUE	1	0.636228094116362	3		508	974	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445424	29445424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762571775	NA	P-0006932-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	407	484	0	ENST00000389048.3:c.3409G>A	p.Gly1137Arg	p.G1137R	ENST00000389048	NM_004304.4	1137	Gga/Aga	21/29	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.950788919171052	2		484	829	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652961	29652968	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTAAAA	CTTTAAAA	-	novel	NA	P-0006932-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	408	473	0	ENST00000356175.3:c.4897_4904del	p.Phe1633ArgfsTer5	p.F1633Rfs*5	ENST00000356175	NM_000267.3	1632	cgCTTTAAAAca/cgca	36/57	1	2	FACETS	0.878	0.838	0.917	0.878	0.838	0.917	CLONAL	1	TRUE	1	0.950788919171052	2		473	978	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593602	55593617	+	protein_altering_variant	In_Frame_Del	DEL	GTGGAAGGTTGTTGAG	GTGGAAGGTTGTTGAG	ACAA	novel	NA	P-0006932-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	720	492	0	ENST00000288135.5:c.1668_1683delinsACAA	p.Trp557_Glu561delinsGln	p.W557_E561delinsQ	ENST00000288135	NM_000222.2	556	caGTGGAAGGTTGTTGAG/caACAA	11/21	0.950788919171052	3	FACETS	0.877	0.851	0.903	0.877	0.851	0.903	CLONAL	2	TRUE	1	0.950788919171052	3		492	1274	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595517	55595519	+	missense_variant	Missense_Mutation	TNP	TAC	TAC	GAT	novel	NA	P-0006932-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	379	418	0	ENST00000288135.5:c.2007_2009delinsGAT	p.Ile669_Thr670delinsMetIle	p.I669_T670delinsMI	ENST00000288135	NM_000222.2	669	atTACa/atGATa	14/21	0.950788919171052	3	FACETS	0.915	0.869	0.963	0.458	0.434	0.482	CLONAL	1	TRUE	1	0.950788919171052	3		418	1285	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0006967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	740	558	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.714752972602465	2	FACETS	0.996	0.972	1	0.996	0.972	1	CLONAL	2	FALSE	0	0.714752972602465	2		558	1040	SUCCESS
APC	324	MSKCC	GRCh37	5	112175225	112175225	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	534	360	0	ENST00000257430.4:c.3934G>T	p.Gly1312Ter	p.G1312*	ENST00000257430	NM_000038.5	1312	Gga/Tga	16/16	0.691239934687665	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	FALSE	0	0.714752972602465	3		360	669	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0007007-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	127	388	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	0.217499747395392	1	FACETS	0.997	0.902	1	0.997	0.902	1	CLONAL	1	TRUE	0	0.217499747395392	1		388	1044	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681010	117681010	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007007-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	85	316	0	ENST00000368508.3:c.3610C>G	p.Leu1204Val	p.L1204V	ENST00000368508	NM_002944.2	1204	Ctc/Gtc	23/43	1	2	FACETS	0.851	0.751	0.959	0.851	0.751	0.959	CLONAL	1	TRUE	1	0.217499747395392	2		316	918	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014094	70014094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764672619	NA	P-0007007-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1445	188	682	2	ENST00000394351.3:c.955C>A	p.Pro319Thr	p.P319T	ENST00000394351	NM_000248.3	319	Ccc/Acc	9/9	0.217499747395392	1	FACETS	0.944	0.869	1	0.944	0.869	1	CLONAL	1	TRUE	0	0.217499747395392	1		684	1633	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190831	106190831	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007007-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	113	398	1	ENST00000380013.4:c.4109G>T	p.Gly1370Val	p.G1370V	ENST00000380013	NM_001127208.2	1370	gGg/gTg	9/11	1	2	FACETS	0.886	0.795	0.983	0.886	0.795	0.983	CLONAL	1	TRUE	1	0.217499747395392	2		399	1173	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439873	52439873	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007007-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	109	337	0	ENST00000460680.1:c.839del	p.Gln280ArgfsTer55	p.Q280Rfs*55	ENST00000460680	NM_004656.3	280	cAg/cg	10/17	0.217499747395392	1	FACETS	0.919	0.824	1	0.919	0.824	1	CLONAL	1	TRUE	0	0.217499747395392	1		337	972	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	49	269	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.864	0.73	1	0.864	0.73	1	CLONAL	1	TRUE	1	0.14	2		269	810	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0007030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	75	548	0	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.14	2		548	1003	SUCCESS
APC	324	MSKCC	GRCh37	5	112175556	112175556	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs368327191	NA	P-0007030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	52	421	0	ENST00000257430.4:c.4265A>G	p.Asp1422Gly	p.D1422G	ENST00000257430	NM_000038.5	1422	gAt/gGt	16/16	1	2	FACETS	0.831	0.705	0.97	0.831	0.705	0.97	CLONAL	1	TRUE	1	0.14	2		421	894	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0007032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	48	228	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.999	0.845	1	0.999	0.845	1	CLONAL	1	FALSE	1	0.209427432601535	2		228	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	126	474	1	ENST00000269305.4:c.880del	p.Glu294SerfsTer51	p.E294Sfs*51	ENST00000269305	NM_001126112.2	294	Gag/ag	8/11	0.135959969582004	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	FALSE	0	0.209427432601535	1		475	1003	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692886	89692886	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	42	232	0	ENST00000371953.3:c.370T>A	p.Cys124Ser	p.C124S	ENST00000371953	NM_000314.4	124	Tgt/Agt	5/9	1	2	FACETS	0.83	0.693	0.983	0.83	0.693	0.983	CLONAL	1	FALSE	1	0.209427432601535	2		232	483	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191489	10191489	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	100	418	2	ENST00000256474.2:c.482G>T	p.Arg161Leu	p.R161L	ENST00000256474	NM_000551.3	161	cGa/cTa	3/3	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.209427432601535	2		420	830	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063320	67063320	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	76	240	1	ENST00000412916.2:c.10G>T	p.Val4Phe	p.V4F	ENST00000412916		4	Gtc/Ttc	1/6	0.208643076141053	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	0	0.209427432601535	1		241	512	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209714	98209714	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007040-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	259	439	0	ENST00000331920.6:c.3824G>C	p.Arg1275Thr	p.R1275T	ENST00000331920	NM_000264.3	1275	aGg/aCg	23/24	0.275858085354226	2	FACETS	0.976	0.917	1	0.976	0.917	1	CLONAL	2	TRUE	0	0.33862346583203	2		439	784	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396401	396401	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007040-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	78	569	0	ENST00000262320.3:c.625G>C	p.Glu209Gln	p.E209Q	ENST00000262320	NM_003502.3	209	Gaa/Caa	2/11	0.275858085354226	2	FACETS	0.473	0.415	0.537	0.237	0.207	0.269	SUBCLONAL	1	TRUE	0	0.33862346583203	2		569	973	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375538	40375538	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1035414287	NA	P-0007040-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1482	219	979	0	ENST00000293328.3:c.412T>C	p.Ser138Pro	p.S138P	ENST00000293328	NM_012448.3	138	Tcc/Ccc	5/19	0.275858085354226	2	FACETS	0.76	0.705	0.819	0.38	0.352	0.41	SUBCLONAL	1	TRUE	0	0.33862346583203	2		979	1701	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151855575	151856039	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTCGTGTCCTTGAATTGTTTGTTTTTTTTTTGTTTTTTTTTTTGAGACACAGTCTCATTCTGTCACCCAGGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAACCTCTGCCATCCAGGCTCAAGCAATTCTCGTGCCTCAGCCTCCCAAGTAGCTGGAATTACAGGCGTGTACCACCACGCCCAGTAAATGTTTGTATTTTTCGTAGAGATGAGGTTTTGCCATGTTGGCTAAGCTCATCTAGAACTCATGCCTCAAGTGATCCACCTGCCTCAGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACTGCCCCCAGCCTATATCCTTGACTTTTAAAAGAGGCTGCTCTAAATGACTCACCCTCACCTGTTTCAAGTGGGTAAACGTGTCAGTGCTAGAGTACATAGCTTGTTTCTCCTCTTCGTCCTTTTTCCTTTTCTTTGAGCGAGGTGCTGCTT	TCTCGTGTCCTTGAATTGTTTGTTTTTTTTTTGTTTTTTTTTTTGAGACACAGTCTCATTCTGTCACCCAGGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAACCTCTGCCATCCAGGCTCAAGCAATTCTCGTGCCTCAGCCTCCCAAGTAGCTGGAATTACAGGCGTGTACCACCACGCCCAGTAAATGTTTGTATTTTTCGTAGAGATGAGGTTTTGCCATGTTGGCTAAGCTCATCTAGAACTCATGCCTCAAGTGATCCACCTGCCTCAGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACTGCCCCCAGCCTATATCCTTGACTTTTAAAAGAGGCTGCTCTAAATGACTCACCCTCACCTGTTTCAAGTGGGTAAACGTGTCAGTGCTAGAGTACATAGCTTGTTTCTCCTCTTCGTCCTTTTTCCTTTTCTTTGAGCGAGGTGCTGCTT	-	novel	NA	P-0007040-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	0	61	0	0	ENST00000262189.6:c.11579_11670+373del		p.X3860_splice	ENST00000262189	NM_170606.2	3860		44/59	0.33862346583203	3	FACETS		NA	1	1	0.988	1	NA	7	TRUE	1	0.33862346583203	3		0	61	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579371	7579390	+	frameshift_variant	Frame_Shift_Del	DEL	TGCCCTGGTAGGTTTTCTGG	TGCCCTGGTAGGTTTTCTGG	-	novel	NA	P-0007040-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	198	575	0	ENST00000269305.4:c.297_316del	p.Gln100LeufsTer42	p.Q100Lfs*42	ENST00000269305	NM_001126112.2	99	tcCCAGAAAACCTACCAGGGCAgc/tcgc	4/11	0.275858085354226	2	FACETS	1	0.984	1	0.607	0.562	0.654	CLONAL	1	TRUE	0	0.33862346583203	2		575	963	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907159	32907159	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007040-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	160	513	0	ENST00000380152.3:c.1544del	p.Thr515IlefsTer10	p.T515Ifs*10	ENST00000380152		515	aCt/at	10/27	0.33862346583203	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.33862346583203	1		513	654	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0007082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	177	410	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.332168948702908	4	FACETS	1	0.942	1	0.76	0.707	0.814	CLONAL	3	TRUE	0	0.332168948702908	4		410	467	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0007082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	52	479	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.659	0.562	0.766	0.659	0.562	0.766	SUBCLONAL	1	TRUE	1	0.332168948702908	2		479	475	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051582	30051583	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	TT	novel	NA	P-0007111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	133	497	2	ENST00000338641.4:c.517-1_517delinsTT		p.X173_splice	ENST00000338641	NM_000268.3	173		6/16	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		499	613	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832299	72832299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	127	918	4	ENST00000268489.5:c.4282G>A	p.Ala1428Thr	p.A1428T	ENST00000268489	NM_006885.3	1428	Gcc/Acc	9/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.157729288091635	2		922	1093	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0007148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	108	610	2	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	NA	2	FACETS	0.907	0.814	1			1	INDETERMINATE	2	TRUE	NA	0.157729288091635	2		612	755	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0007163-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	13	228	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.144883658868097	3	FACETS	0.567	0.403	0.768	0.284	0.201	0.384	SUBCLONAL	1	TRUE	1	0.144544358571771	3		228	340	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100198	27100198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007163-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	86	255	1	ENST00000324856.7:c.3994C>T	p.Gln1332Ter	p.Q1332*	ENST00000324856	NM_006015.4	1332	Cag/Tag	16/20	0.144883658868097	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.144544358571771	3		256	524	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81968097	81968097	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007163-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	52	668	0	ENST00000359376.3:c.2803G>T	p.Val935Phe	p.V935F	ENST00000359376	NM_002661.3	935	Gtc/Ttc	26/33	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.144544358571771	2		668	669	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344236	70344236	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007163-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	32	69	0	ENST00000374080.3:c.1972G>C	p.Glu658Gln	p.E658Q	ENST00000374080		658	Gaa/Caa	13/45	0.144544358571771	3	FACETS	0.95	0.786	1			1	CLONAL	4	TRUE	NA	0.144544358571771	3		69	125	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0007226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	464	342	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.845420281432801	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.845420281432801	2		343	536	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0007226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	1959	551	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.845420281432801	6	FACETS	1	0.998	1	0.883	0.87	0.897	CLONAL	4	TRUE	1	0.845420281432801	6		551	2824	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482843	67482843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	837	358	0	ENST00000327367.4:c.1247C>T	p.Ser416Phe	p.S416F	ENST00000327367	NM_005902.3	416	tCc/tTc	9/9	0.844677151585052	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.845420281432801	3		358	930	SUCCESS
APC	324	MSKCC	GRCh37	5	112173582	112173582	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0007226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	304	394	0	ENST00000257430.4:c.2291T>A	p.Leu764Ter	p.L764*	ENST00000257430	NM_000038.5	764	tTa/tAa	16/16	1	2	FACETS	0.971	0.92	1	0.971	0.92	1	CLONAL	1	TRUE	1	0.845420281432801	2		394	741	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888168	81888168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754914807	NA	P-0007226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	727	546	2	ENST00000359376.3:c.313G>A	p.Val105Ile	p.V105I	ENST00000359376	NM_002661.3	105	Gtc/Atc	3/33	0.845420281432801	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.845420281432801	2		548	847	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044962	47044962	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	34	245	0	ENST00000377604.3:c.2288T>G	p.Leu763Arg	p.L763R	ENST00000377604	NM_001204468.1	763	cTc/cGc	20/24	1	1	FACETS	0.136	0.111	0.164	0.136	0.111	0.164	SUBCLONAL	1	TRUE	0	0.845420281432801	1		245	341	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513662	41513669	+	frameshift_variant	Frame_Shift_Del	DEL	ATCAAGTC	ATCAAGTC	-	novel	NA	P-0007226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	352	559	0	ENST00000263253.7:c.568_575del	p.Gln190GlufsTer29	p.Q190Efs*29	ENST00000263253	NM_001429.3	189	aATCAAGTC/a	2/31	0.838487568968622	3	FACETS	1	0.964	1	0.511	0.484	0.538	CLONAL	1	TRUE	1	0.845420281432801	3		559	1160	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340407	8340407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201651279	NA	P-0007228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	125	504	2	ENST00000356435.5:c.5189G>A	p.Arg1730Gln	p.R1730Q	ENST00000356435		1730	cGg/cAg	31/35	0.242107756172088	4	FACETS	0.882	0.8	0.969	0.882	0.8	0.969	CLONAL	2	TRUE	2	0.259788506967917	4		506	687	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577122	7577123	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0007228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	153	556	0	ENST00000269305.4:c.815_816del	p.Val272AlafsTer33	p.V272Afs*33	ENST00000269305	NM_001126112.2	272	gTG/g	8/11	0.259788506967917	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.259788506967917	2		556	557	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502855	186502855	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	621	582	1	ENST00000323963.5:c.313C>A	p.Leu105Ile	p.L105I	ENST00000323963		105	Cta/Ata	4/11	0.676393242165917	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.733706590349694	4		583	1419	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270110	66270110	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	297	412	0	ENST00000273854.3:c.1772G>A	p.Gly591Asp	p.G591D	ENST00000273854	NM_004439.5	591	gGc/gAc	8/18	0.733706590349694	2	FACETS	0.916	0.879	0.952	0.916	0.879	0.952	CLONAL	2	TRUE	0	0.733706590349694	2		412	442	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93627354	93627354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	396	407	0	ENST00000375746.1:c.821C>T	p.Pro274Leu	p.P274L	ENST00000375746	NM_001174167.1	274	cCa/cTa	6/14	0.712818647675451	4	FACETS	0.93	0.887	0.974	0.93	0.887	0.974	CLONAL	2	TRUE	2	0.733706590349694	4		407	1006	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139392010	139392010	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	354	252	0	ENST00000277541.6:c.6181G>T	p.Glu2061Ter	p.E2061*	ENST00000277541	NM_017617.3	2061	Gag/Tag	34/34	0.733706590349694	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.733706590349694	2		252	447	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398053	4398053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	793	419	0	ENST00000261254.3:c.617G>A	p.Ser206Asn	p.S206N	ENST00000261254	NM_001759.3	206	aGt/aAt	4/5	0.427206791068949	4	FACETS	0.938	0.919	0.956			1	INDETERMINATE	4	TRUE	NA	0.733706590349694	4		419	999	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409154	4409154	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	714	385	1	ENST00000261254.3:c.849C>A	p.Asp283Glu	p.D283E	ENST00000261254	NM_001759.3	283	gaC/gaA	5/5	0.427206791068949	4	FACETS	0.958	0.938	0.976			1	INDETERMINATE	4	TRUE	NA	0.733706590349694	4		386	881	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811603	102811603	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	429	383	0	ENST00000307046.8:c.581G>T	p.Gly194Val	p.G194V	ENST00000307046	NM_001111285.1	194	gGa/gTa	4/4	0.733706590349694	4	FACETS	0.923	0.882	0.965	0.923	0.882	0.965	CLONAL	2	TRUE	2	0.733706590349694	4		383	1098	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813444	102813444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752694732	NA	P-0007229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	338	289	1	ENST00000307046.8:c.245G>A	p.Ser82Asn	p.S82N	ENST00000307046	NM_001111285.1	82	aGc/aAc	3/4	0.733706590349694	4	FACETS	0.988	0.94	1	0.988	0.94	1	CLONAL	2	TRUE	2	0.733706590349694	4		290	808	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001398	29001398	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	330	308	0	ENST00000282397.4:c.1334C>G	p.Pro445Arg	p.P445R	ENST00000282397	NM_002019.4	445	cCa/cGa	10/30	0.733706590349694	2	FACETS	0.999	0.965	1	0.999	0.965	1	CLONAL	2	TRUE	0	0.733706590349694	2		308	450	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916851	48916851	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0007229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	174	200	0	ENST00000267163.4:c.380+1G>T		p.X127_splice	ENST00000267163	NM_000321.2	127			0.733706590349694	2	FACETS	0.96	0.912	1	0.96	0.912	1	CLONAL	2	TRUE	0	0.733706590349694	2		200	247	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934576	NA	P-0007229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	676	488	1	ENST00000269305.4:c.818G>C	p.Arg273Pro	p.R273P	ENST00000269305	NM_001126112.2	273	cGt/cCt	8/11	0.733706590349694	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.733706590349694	2		489	890	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244444	41244444	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	380	299	0	ENST00000357654.3:c.3104T>A	p.Val1035Asp	p.V1035D	ENST00000357654	NM_007294.3	1035	gTt/gAt	10/23	0.417628573722178	6	FACETS	0.989	0.944	1	0.989	0.944	1	INDETERMINATE	3	TRUE	3	0.733706590349694	6		299	861	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805949	46805949	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs546307661	NA	P-0007229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	349	334	0	ENST00000290295.7:c.7C>A	p.Pro3Thr	p.P3T	ENST00000290295	NM_006361.5	3	Ccc/Acc	1/2	0.417628573722178	6	FACETS	0.847	0.804	0.89	0.847	0.804	0.89	INDETERMINATE	3	TRUE	3	0.733706590349694	6		334	924	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145764	11145764	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	670	445	0	ENST00000358026.2:c.4126G>T	p.Glu1376Ter	p.E1376*	ENST00000358026	NM_001128849.1	1376	Gag/Tag	29/36	0.733706590349694	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.733706590349694	2		445	870	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380506	31380506	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	585	440	0	ENST00000328111.2:c.996G>A	p.Met332Ile	p.M332I	ENST00000328111	NM_006892.3	332	atG/atA	9/23	0.733706590349694	4	FACETS	1	0.984	1			1	CLONAL	2	TRUE	NA	0.733706590349694	4		440	1332	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36028594	36028594	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	1159	430	1	ENST00000358208.4:c.936G>C	p.Gln312His	p.Q312H	ENST00000358208		312	caG/caC	8/12	0.733706590349694	4	FACETS	0.953	0.932	0.974			1	CLONAL	3	TRUE	NA	0.733706590349694	4		431	1916	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21272326	21272326	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	235	416	0	ENST00000354336.3:c.104T>C	p.Met35Thr	p.M35T	ENST00000354336	NM_005207.3	35	aTg/aCg	1/3	0.733706590349694	3	FACETS	0.984	0.919	1	0.492	0.459	0.525	CLONAL	1	TRUE	1	0.733706590349694	3		416	890	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29085135	29085135	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	24	12	0	ENST00000328354.6:c.1530G>T	p.Gln510His	p.Q510H	ENST00000328354	NM_007194.3	510	caG/caT	14/15	0.733706590349694	3	FACETS	0.828	0.682	0.978	0.828	0.682	0.978	CLONAL	2	TRUE	1	0.733706590349694	3		12	54	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143044462	143044463	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0007229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	340	362	0	ENST00000262992.4:c.1999_2000delinsAT	p.Gly667Ile	p.G667I	ENST00000262992	NM_001101669.1	667	GGa/ATa	18/24	0.733706590349694	2	FACETS	0.936	0.902	0.97	0.936	0.902	0.97	CLONAL	2	TRUE	0	0.733706590349694	2		362	495	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859516	151859516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	190	530	0	ENST00000262189.6:c.11146G>A	p.Glu3716Lys	p.E3716K	ENST00000262189	NM_170606.2	3716	Gaa/Aaa	43/59	0.511854440076387	6	FACETS	1	0.981	1	0.582	0.541	0.625	CLONAL	2	TRUE	2	0.511854440076387	6		530	645	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549865	187549865	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs750386635	NA	P-0007269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	219	468	0	ENST00000441802.2:c.4376C>G	p.Ser1459Ter	p.S1459*	ENST00000441802	NM_005245.3	1459	tCa/tGa	8/27	0.515301638308254	2	FACETS	0.844	0.803	0.884	1	0.992	1	CLONAL	3	TRUE	0	0.511854440076387	2		468	338	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371795	55371795	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779291044	NA	P-0007269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	10	79	0	ENST00000297316.4:c.485C>T	p.Pro162Leu	p.P162L	ENST00000297316	NM_022454.3	162	cCg/cTg	2/2	0.307279949094292	6	FACETS	0.824	0.574	1	0.549	0.382	0.745	CLONAL	2	TRUE	3	0.511854440076387	6		79	48	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820582	3820582	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	118	277	0	ENST00000262367.5:c.2869C>G	p.Pro957Ala	p.P957A	ENST00000262367	NM_004380.2	957	Cct/Gct	14/31	0.307279949094292	6	FACETS	0.978	0.895	1	0.978	0.895	1	CLONAL	3	TRUE	3	0.511854440076387	6		277	318	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820765	3820765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	218	610	3	ENST00000262367.5:c.2686G>A	p.Gly896Arg	p.G896R	ENST00000262367	NM_004380.2	896	Ggg/Agg	14/31	0.307279949094292	6	FACETS	0.88	0.823	0.938	0.88	0.823	0.938	CLONAL	3	TRUE	3	0.511854440076387	6		613	653	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220416	1220760	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGGCATTGTGCACAAGGACATCAAGCCGGGGAACCTGCTGCTCACCACCGGTGGCACCCTCAAAATCTCCGACCTGGGCGTGGCCGAGGTAGGCACGTGCTAGGGGGGGCCCTGGGGCGCCCCCTCCCGGGCACTCCCTGAGGGCTGCACGGCACCGCCACAGGCACTGCACCCGTTCGCGGCGGACGACACCTGCCGGACCAGCCAGGGCTCCCCGGCTTTCCAGCCGCCCGAGATTGCCAACGGCCTGGACACCTTCTCCGGCTTCAAGGTGGACATCTGGTCGGCTGGGGTCACCCTGTAAGTGCCCCGCCCCCCCGGGCACTCACCACACGCACACTCCG	AGGGCATTGTGCACAAGGACATCAAGCCGGGGAACCTGCTGCTCACCACCGGTGGCACCCTCAAAATCTCCGACCTGGGCGTGGCCGAGGTAGGCACGTGCTAGGGGGGGCCCTGGGGCGCCCCCTCCCGGGCACTCCCTGAGGGCTGCACGGCACCGCCACAGGCACTGCACCCGTTCGCGGCGGACGACACCTGCCGGACCAGCCAGGGCTCCCCGGCTTTCCAGCCGCCCGAGATTGCCAACGGCCTGGACACCTTCTCCGGCTTCAAGGTGGACATCTGGTCGGCTGGGGTCACCCTGTAAGTGCCCCGCCCCCCCGGGCACTCACCACACGCACACTCCG	-	novel	NA	P-0007269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	139	553	0	ENST00000326873.7:c.513_734+48del		p.X171_splice	ENST00000326873	NM_000455.4	171		4-5/10	0.515301638308254	4	FACETS	0.897	0.831	0.964	0.673	0.623	0.723	CLONAL	3	TRUE	0	0.511854440076387	4		553	305	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0007288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	32	228	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.753	0.616	0.904	0.753	0.616	0.904	CLONAL	1	TRUE	1	0.431721090880403	2		228	197	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0007288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	88	364	0	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	0.431721090880403	2		364	395	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645412	67645412	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	109	491	0	ENST00000264010.4:c.677A>G	p.Tyr226Cys	p.Y226C	ENST00000264010	NM_006565.3	226	tAc/tGc	3/12	0.431721090880403	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.431721090880403	1		491	287	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654639	67654639	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	33	542	0	ENST00000264010.4:c.1126G>A	p.Glu376Lys	p.E376K	ENST00000264010	NM_006565.3	376	Gag/Aag	6/12	0.431721090880403	1	FACETS	0.362	0.295	0.437	0.362	0.295	0.437	SUBCLONAL	1	TRUE	0	0.431721090880403	1		542	331	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160626	56160700	+	inframe_deletion	In_Frame_Del	DEL	CCCTGAGGAAACAAACCGCCGTGTTAACAAAGTGATGCGGGCCAGACTGTACTTACTGCAGCAGATAGGGCCTAA	CCCTGAGGAAACAAACCGCCGTGTTAACAAAGTGATGCGGGCCAGACTGTACTTACTGCAGCAGATAGGGCCTAA	-	novel	NA	P-0007288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	71	431	0	ENST00000399503.3:c.901_975del	p.Pro301_Asn325del	p.P301_N325del	ENST00000399503	NM_005921.1	300	agCCCTGAGGAAACAAACCGCCGTGTTAACAAAGTGATGCGGGCCAGACTGTACTTACTGCAGCAGATAGGGCCTAAc/agc	4/20	1	2	FACETS	0.942	0.828	1	0.942	0.828	1	CLONAL	1	TRUE	1	0.431721090880403	2		431	349	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217872	7217875	+	frameshift_variant	Frame_Shift_Del	DEL	CTTC	CTTC	-	novel	NA	P-0007288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	37	604	0	ENST00000380728.2:c.136_139del	p.Glu46AsnfsTer16	p.E46Nfs*16	ENST00000380728		46	GAAGaa/aa	3/11	1	2	FACETS	0.317	0.261	0.381	0.317	0.261	0.381	SUBCLONAL	1	TRUE	1	0.431721090880403	2		604	540	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180581	56180584	+	frameshift_variant	Frame_Shift_Del	DEL	CCAA	CCAA	-	novel	NA	P-0007288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	71	527	0	ENST00000399503.3:c.3910_3913del	p.Pro1304ThrfsTer31	p.P1304Tfs*31	ENST00000399503	NM_005921.1	1304	CCAAac/ac	16/20	1	2	FACETS	0.959	0.843	1	0.959	0.843	1	CLONAL	1	TRUE	1	0.431721090880403	2		527	343	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413139	63413139	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1373608390	NA	P-0007295-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	206	136	0	ENST00000330258.3:c.28C>T	p.Gln10Ter	p.Q10*	ENST00000330258	NM_152424.3	10	Cag/Tag	2/2	1	1	FACETS	0.821	0.784	0.856	1	0.995	1	CLONAL	2	TRUE	0	0.608463316797953	1		136	287	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974979	15974979	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007295-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	368	205	0	ENST00000268712.3:c.3896G>T	p.Gly1299Val	p.G1299V	ENST00000268712	NM_006311.3	1299	gGg/gTg	30/46	0.608463316797953	3	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.608463316797953	3		205	698	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191488	10191488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs5030818	NA	P-0007299-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	89	360	0	ENST00000256474.2:c.481C>T	p.Arg161Ter	p.R161*	ENST00000256474	NM_000551.3	161	Cga/Tga	3/3	NA	2	FACETS	0.983	0.881	1			1	INDETERMINATE	2	TRUE	NA	0.282883522207119	2		360	320	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564327	86564327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007299-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	77	356	0	ENST00000274376.6:c.59G>A	p.Gly20Glu	p.G20E	ENST00000274376	NM_002890.2	20	gGa/gAa	1/25	0.174590334622165	5	FACETS	1	0.939	1	0.732	0.647	0.822	CLONAL	2	TRUE	2	0.282883522207119	5		356	353	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969143	93969143	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007299-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	39	669	0	ENST00000369303.4:c.1853A>G	p.Asn618Ser	p.N618S	ENST00000369303	NM_004440.3	618	aAt/aGt	10/17	0.282883522207119	1	FACETS	0.781	0.65	0.926	0.781	0.65	0.926	CLONAL	1	TRUE	0	0.282883522207119	1		669	303	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781382	135781382	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007299-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	162	694	0	ENST00000298552.3:c.1583del	p.Gly528AlafsTer4	p.G528Afs*4	ENST00000298552	NM_001162426.1	528	gGc/gc	15/23	0.282883522207119	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.282883522207119	2		694	532	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248131	59248131	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007299-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	20	54	0	ENST00000371222.2:c.612G>C	p.Gln204His	p.Q204H	ENST00000371222	NM_002228.3	204	caG/caC	1/1	0.222468939588957	3	FACETS	1	0.8	1	1	0.8	1	CLONAL	2	TRUE	1	0.282883522207119	3		54	79	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88672102	88672102	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007299-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	25	265	0	ENST00000372037.3:c.636G>T	p.Gln212His	p.Q212H	ENST00000372037	NM_004329.2	212	caG/caT	8/13	0.222468939588957	3	FACETS	1	0.929	1	0.726	0.579	0.889	CLONAL	1	TRUE	1	0.282883522207119	3		265	139	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0007359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	19	448	2	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		450	720	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0007369-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	201	364	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.965	0.901	1	0.965	0.901	1	CLONAL	1	TRUE	1	0.74	2		364	563	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630147	187630147	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007369-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	207	387	0	ENST00000441802.2:c.835del	p.Asp279MetfsTer11	p.D279Mfs*11	ENST00000441802	NM_005245.3	279	Gat/at	2/27	1	2	FACETS	0.99	0.926	1	0.99	0.926	1	CLONAL	1	TRUE	1	0.74	2		387	565	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437210	220437210	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	205	764	0	ENST00000243786.2:c.114G>C	p.Leu38Phe	p.L38F	ENST00000243786	NM_002191.3	38	ttG/ttC	1/2	0.394184281646218	4	FACETS	1	0.975	1	0.558	0.517	0.601	CLONAL	1	TRUE	2	0.521141492707865	4		764	1072	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158551	26158551	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776173606	NA	P-0007376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	68	257	0	ENST00000289316.2:c.154G>A	p.Asp52Asn	p.D52N	ENST00000289316	NM_138720.2	52	Gac/Aac	1/2	0.521141492707865	3	FACETS	0.818	0.715	0.929	0.409	0.357	0.465	CLONAL	1	TRUE	1	0.521141492707865	3		257	402	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979366	93979366	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139833485	NA	P-0007376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	188	677	2	ENST00000369303.4:c.1462C>T	p.Arg488Trp	p.R488W	ENST00000369303	NM_004440.3	488	Cgg/Tgg	7/17	1	2	FACETS	0.929	0.86	1	0.929	0.86	1	CLONAL	1	TRUE	1	0.521141492707865	2		679	777	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682317	37682317	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	131	541	1	ENST00000447079.4:c.3508T>A	p.Ser1170Thr	p.S1170T	ENST00000447079	NM_015083.1	1170	Tca/Aca	13/14	0.521141492707865	2	FACETS	0.815	0.742	0.891	0.407	0.371	0.446	CLONAL	1	TRUE	0	0.521141492707865	2		542	617	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623879	28623879	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	98	436	0	ENST00000241453.7:c.775del	p.Gln259AsnfsTer6	p.Q259Nfs*6	ENST00000241453	NM_004119.2	259	Caa/aa	7/24	0.521141492707865	4	FACETS	0.902	0.806	1	0.301	0.268	0.335	CLONAL	1	TRUE	1	0.521141492707865	4		436	634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0007416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	132	342	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.810833582196475	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.810833582196475	2		343	158	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735602	204735602	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	64	178	0	ENST00000302823.3:c.403T>A	p.Tyr135Asn	p.Y135N	ENST00000302823	NM_005214.4	135	Tac/Aac	2/4	0.810833582196475	3	FACETS	1	0.928	1	0.539	0.474	0.606	CLONAL	1	TRUE	1	0.810833582196475	3		178	206	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007422-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	119	427	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.158120732020609	5	FACETS	1	0.983	1	0.485	0.437	0.536	CLONAL	1	FALSE	2	0.249892593445143	5		427	900	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926873	112926873	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397507542	NA	P-0007422-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	82	408	0	ENST00000351677.2:c.1493G>T	p.Arg498Leu	p.R498L	ENST00000351677	NM_002834.3	498	cGg/cTg	13/16	NA	2	FACETS	0.879	0.774	0.991			1	INDETERMINATE	1	FALSE	NA	0.249892593445143	2		408	747	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986560	36986615	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTGGATACCTGGCCCTGCAGCGCCGCGGGGCTGGCGGCGTGGTGCGCCAGGTCC	GGCTGGATACCTGGCCCTGCAGCGCCGCGGGGCTGGCGGCGTGGTGCGCCAGGTCC	-	novel	NA	P-0007422-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	26	309	0	ENST00000354822.5:c.1074_1129del	p.Asp359ValfsTer61	p.D359Vfs*61	ENST00000354822	NM_001079668.2	358	ccGGACCTGGCGCACCACGCCGCCAGCCCCGCGGCGCTGCAGGGCCAGGTATCCAGCCtg/cctg	3/3	0.249892593445143	1	FACETS	0.514	0.407	0.637	0.514	0.407	0.637	SUBCLONAL	1	FALSE	0	0.249892593445143	1		309	354	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987082	36987082	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007422-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	44	226	0	ENST00000354822.5:c.607del	p.Val203CysfsTer25	p.V203Cfs*25	ENST00000354822	NM_001079668.2	203	Gtg/tg	3/3	0.249892593445143	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	0	0.249892593445143	1		226	246	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0007484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	705	454	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.775650822031188	3	FACETS	0.989	0.972	1	0.989	0.972	1	CLONAL	3	TRUE	0	0.804524702537999	3		454	828	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955053	55955053	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs747565731	NA	P-0007484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	214	945	0	ENST00000263923.4:c.3492G>T	p.Leu1164Phe	p.L1164F	ENST00000263923	NM_002253.2	1164	ttG/ttT	26/30	0.271157990056499	5	FACETS	1	0.981	1	0.743	0.696	0.789	INDETERMINATE	2	TRUE	2	0.804524702537999	5		945	527	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845501	63845501	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	67	784	1	ENST00000279873.7:c.1240G>T	p.Asp414Tyr	p.D414Y	ENST00000279873	NM_032199.2	414	Gat/Tat	9/10	0.242613883310879	2	FACETS	0.511	0.447	0.579	0.255	0.223	0.29	INDETERMINATE	1	TRUE	0	0.804524702537999	2		785	326	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56477640	56477640	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	39	1085	0	ENST00000267101.3:c.188T>C	p.Leu63Pro	p.L63P	ENST00000267101	NM_001982.3	63	cTt/cCt	2/28	0.804524702537999	3	FACETS	0.185	0.153	0.222	0.062	0.051	0.074	SUBCLONAL	1	TRUE	0	0.804524702537999	3		1085	733	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827932	72827932	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	266	1521	1	ENST00000268489.5:c.8649G>T	p.Met2883Ile	p.M2883I	ENST00000268489	NM_006885.3	2883	atG/atT	9/10	0.802500007459936	2	FACETS	0.773	0.727	0.821	0.387	0.363	0.411	SUBCLONAL	1	TRUE	0	0.804524702537999	2		1522	855	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24134033	24134033	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	44	1140	0	ENST00000263121.7:c.184A>C	p.Lys62Gln	p.K62Q	ENST00000263121	NM_003073.3	62	Aaa/Caa	2/9	0.775650822031188	3	FACETS	0.209	0.174	0.247	0.07	0.058	0.083	SUBCLONAL	1	TRUE	0	0.804524702537999	3		1140	734	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227948	53227948	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007547-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	455	367	2	ENST00000375401.3:c.2366G>A	p.Arg789His	p.R789H	ENST00000375401	NM_004187.3	789	cGc/cAc	16/26	0.469471649049951	3	FACETS	1	0.994	1			1	CLONAL	2	FALSE	NA	0.469471649049951	3		369	974	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653782	89653782	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs886041877	NA	P-0007571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	276	290	0	ENST00000371953.3:c.80A>G	p.Tyr27Cys	p.Y27C	ENST00000371953	NM_000314.4	27	tAt/tGt	2/9	1	2	FACETS	0.944	0.891	0.998	1	0.996	1	CLONAL	4	TRUE	1	0.2	2		290	731	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs121913468	NA	P-0007571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	427	397	0	ENST00000269571.5:c.2305G>C	p.Asp769His	p.D769H	ENST00000269571		769	Gac/Cac	19/27	0.3	3	FACETS	1	0.99	1			1	CLONAL	4	TRUE	NA	0.2	3		397	1046	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0007571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	314	270	0	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	1	0.985	1	1	0.997	1	CLONAL	3	TRUE	1	0.2	2		270	945	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711891	89711891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	292	256	1	ENST00000371953.3:c.509G>A	p.Ser170Asn	p.S170N	ENST00000371953	NM_000314.4	170	aGt/aAt	6/9	1	2	FACETS	0.906	0.856	0.956	1	0.997	1	CLONAL	4	TRUE	1	0.2	2		257	806	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136300	202136319	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTTGCAAGAGGAAATCTC	CTTTTGCAAGAGGAAATCTC	-	novel	NA	P-0007571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	246	384	0	ENST00000358485.4:c.545_564del	p.Leu182GlnfsTer6	p.L182Qfs*6	ENST00000358485	NM_001080125.1	182	CTTTTGCAAGAGGAAATCTCc/c	3/9	1	2	FACETS	1	0.937	1	1	0.996	1	CLONAL	3	TRUE	1	0.2	2		384	820	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589592	67589594	+	inframe_deletion	In_Frame_Del	DEL	ATA	ATA	-	novel	NA	P-0007571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	366	266	0	ENST00000274335.5:c.1356_1358del	p.Asn453del	p.N453del	ENST00000274335		452	tATAac/tac	10/15	1	2	FACETS	0.897	0.853	0.942	1	0.997	1	CLONAL	4	TRUE	1	0.2	2		266	1020	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0007580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	121	442	1	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.379246807027646	5	FACETS	1	0.967	1	1	0.967	1	CLONAL	4	TRUE	1	0.379246807027646	5		443	231	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241711	55241711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	109	394	0	ENST00000275493.2:c.2159C>T	p.Ser720Phe	p.S720F	ENST00000275493	NM_005228.3	720	tCc/tTc	18/28	0.379246807027646	5	FACETS	0.909	0.832	0.987	0.909	0.832	0.987	CLONAL	4	TRUE	1	0.379246807027646	5		394	248	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs786201838	NA	P-0007580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	88	464	0	ENST00000269305.4:c.578A>C	p.His193Pro	p.H193P	ENST00000269305	NM_001126112.2	193	cAt/cCt	6/11	0.379246807027646	3	FACETS	0.92	0.834	1			1	CLONAL	3	TRUE	NA	0.379246807027646	3		464	200	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579410	7579410	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567556123	NA	P-0007581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	68	402	0	ENST00000269305.4:c.277del	p.Leu93CysfsTer30	p.L93Cfs*30	ENST00000269305	NM_001126112.2	93	Ctg/tg	4/11	0.258272346224946	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.258272346224946	1		402	393	SUCCESS
APC	324	MSKCC	GRCh37	5	112175358	112175358	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1554085480	NA	P-0007581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	44	248	0	ENST00000257430.4:c.4067C>G	p.Ser1356Ter	p.S1356*	ENST00000257430	NM_000038.5	1356	tCa/tGa	16/16	1	2	FACETS	0.933	0.785	1	0.933	0.785	1	CLONAL	1	TRUE	1	0.258272346224946	2		248	365	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99179990	99179990	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	46	477	0	ENST00000074304.5:c.1933A>T	p.Ser645Cys	p.S645C	ENST00000074304	NM_001134224.1	645	Agt/Tgt	19/26	1	2	FACETS	0.652	0.549	0.767	0.652	0.549	0.767	SUBCLONAL	1	TRUE	1	0.258272346224946	2		477	546	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006093	22006093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1419378636	NA	P-0007581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	35	316	0	ENST00000276925.6:c.310G>A	p.Ala104Thr	p.A104T	ENST00000276925	NM_004936.3	104	Gcg/Acg	2/2	1	2	FACETS	0.633	0.519	0.762	0.633	0.519	0.762	SUBCLONAL	1	TRUE	1	0.258272346224946	2		316	428	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346856	73346856	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	41	405	0	ENST00000377767.4:c.1361A>C	p.Lys454Thr	p.K454T	ENST00000377767	NM_014953.3	454	aAg/aCg	9/21	0.258272346224946	5	FACETS	0.552	0.458	0.657	0.11	0.091	0.132	SUBCLONAL	1	TRUE	0	0.258272346224946	5		405	798	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041098	42041098	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	82	859	1	ENST00000219905.7:c.5476T>G	p.Leu1826Val	p.L1826V	ENST00000219905	NM_001164273.1	1826	Tta/Gta	16/24	0.258272346224946	1	FACETS	0.563	0.495	0.636	0.563	0.495	0.636	SUBCLONAL	1	TRUE	0	0.258272346224946	1		860	982	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40491357	40491357	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	42	609	0	ENST00000264657.5:c.443T>G	p.Leu148Arg	p.L148R	ENST00000264657	NM_139276.2	148	cTt/cGt	5/24	1	2	FACETS	0.42	0.35	0.499	0.42	0.35	0.499	SUBCLONAL	1	TRUE	1	0.258272346224946	2		609	774	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435014	56435014	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	29	389	0	ENST00000407977.2:c.2123A>G	p.Lys708Arg	p.K708R	ENST00000407977		708	aAg/aGg	9/10	1	2	FACETS	0.436	0.349	0.535	0.436	0.349	0.535	SUBCLONAL	1	TRUE	1	0.258272346224946	2		389	515	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281283	15281283	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	15	240	0	ENST00000263388.2:c.4973T>C	p.Leu1658Pro	p.L1658P	ENST00000263388	NM_000435.2	1658	cTc/cCc	27/33	0.258272346224946	1	FACETS	0.452	0.33	0.597	0.452	0.33	0.597	SUBCLONAL	1	TRUE	0	0.258272346224946	1		240	224	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538372	9538372	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	49	320	0	ENST00000353224.5:c.1626A>C	p.Glu542Asp	p.E542D	ENST00000353224	NM_177990.2	542	gaA/gaC	7/10	0.258272346224946	3	FACETS	0.762	0.645	0.891	0.381	0.322	0.446	SUBCLONAL	1	TRUE	1	0.258272346224946	3		320	562	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929269	44929269	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	68	328	0	ENST00000377967.4:c.2369A>C	p.Asn790Thr	p.N790T	ENST00000377967	NM_021140.2	790	aAc/aCc	17/29	1	1	FACETS	0.822	0.716	0.936	0.822	0.716	0.936	CLONAL	1	TRUE	0	0.258272346224946	1		328	558	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240764	53240764	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	52	409	0	ENST00000375401.3:c.1316A>C	p.Glu439Ala	p.E439A	ENST00000375401	NM_004187.3	439	gAg/gCg	10/26	1	1	FACETS	0.757	0.646	0.88	0.757	0.646	0.88	SUBCLONAL	1	TRUE	0	0.258272346224946	1		409	463	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	124	269	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.586327793316602	3	FACETS	0.787	0.725	0.848	0.787	0.725	0.848	SUBCLONAL	2	TRUE	1	0.828665197862777	3		269	269	SUCCESS
APC	324	MSKCC	GRCh37	5	112175198	112175198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	118	210	0	ENST00000257430.4:c.3907C>T	p.Gln1303Ter	p.Q1303*	ENST00000257430	NM_000038.5	1303	Caa/Taa	16/16	0.828665197862777	2	FACETS	0.969	0.919	1	0.969	0.919	1	CLONAL	2	TRUE	0	0.828665197862777	2		210	147	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661411	227661411	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	104	271	0	ENST00000305123.5:c.2044A>T	p.Ser682Cys	p.S682C	ENST00000305123	NM_005544.2	682	Agc/Tgc	1/2	1	2	FACETS	0.789	0.715	0.866	0.789	0.715	0.866	SUBCLONAL	1	TRUE	1	0.828665197862777	2		271	318	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910587	29910587	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	33	140	0	ENST00000376809.5:c.127G>T	p.Glu43Ter	p.E43*	ENST00000376809	NM_002116.7	43	Gag/Tag	2/8	1	2	FACETS	0.357	0.293	0.429	0.357	0.293	0.429	SUBCLONAL	1	TRUE	1	0.828665197862777	2		140	223	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798773	42798773	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269420975	NA	P-0007645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	90	250	0	ENST00000575354.2:c.4345G>A	p.Val1449Met	p.V1449M	ENST00000575354	NM_015125.3	1449	Gtg/Atg	19/20	0.407660050998732	1	FACETS	0.36	0.322	0.4	0.36	0.322	0.4	INDETERMINATE	1	TRUE	0	0.828665197862777	1		250	353	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936096	+	missense_variant	Missense_Mutation	DNP	AG	AG	CC	novel	NA	P-0007645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	105	244	0	ENST00000263967.3:c.1637_1638delinsCC	p.Gln546Pro	p.Q546P	ENST00000263967	NM_006218.2	546	cAG/cCC	10/21	0.437889558914739	1	FACETS	0.773	0.713	0.833	0.773	0.713	0.833	INDETERMINATE	1	TRUE	0	0.828665197862777	1		244	192	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782177	NA	P-0007661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	317	531	0	ENST00000269305.4:c.644G>A	p.Ser215Asn	p.S215N	ENST00000269305	NM_001126112.2	215	aGt/aAt	6/11	0.3	2	FACETS	0.935	0.882	0.991			1	CLONAL	3	TRUE	NA	0.17	2		531	1329	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427012	49427012	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	255	304	0	ENST00000301067.7:c.11476C>T	p.Gln3826Ter	p.Q3826*	ENST00000301067	NM_003482.3	3826	Cag/Tag	39/54	0.490657282802725	3	FACETS	1	0.981	1	1	0.994	1	CLONAL	3	TRUE	1	0.17	3		304	972	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293471	1293471	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	76	373	0	ENST00000310581.5:c.1530G>A	p.Trp510Ter	p.W510*	ENST00000310581	NM_198253.2	510	tgG/tgA	2/16	0.16868392831725	3	FACETS	1	0.879	1	0.502	0.439	0.57	CLONAL	1	TRUE	1	0.17	3		373	966	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777978	27777978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1639	407	986	1	ENST00000369163.2:c.127C>T	p.Arg43Trp	p.R43W	ENST00000369163	NM_003536.2	43	Cgg/Tgg	1/1	0.202189117819804	5	FACETS	0.979	0.928	1	0.979	0.928	1	CLONAL	3	TRUE	2	0.17	5		987	2046	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374436	118374440	+	frameshift_variant	Frame_Shift_Del	DEL	AGGAG	AGGAG	-	novel	NA	P-0007661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	159	378	0	ENST00000534358.1:c.7829_7833del	p.Gln2610ArgfsTer5	p.Q2610Rfs*5	ENST00000534358	NM_005933.3	2610	cAGGAG/c	27/36	0.202189117819804	4	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	2	0.17	4		378	1039	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0007671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	184	868	0	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	0.405255039715547	4	FACETS	1	0.965	1	0.542	0.499	0.586	CLONAL	1	TRUE	2	0.405255039715547	4		868	1178	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0007671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	299	348	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.405255039715547	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.405255039715547	4		348	999	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	115	406	0	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	0.405255039715547	3	FACETS	0.967	0.872	1	0.483	0.436	0.534	CLONAL	1	TRUE	1	0.405255039715547	3		406	706	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754325	57754325	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1197	70	552	1	ENST00000274289.3:c.526G>T	p.Val176Leu	p.V176L	ENST00000274289	NM_006622.3	176	Gtg/Ttg	4/14	0.405255039715547	6	FACETS	0.494	0.429	0.565	0.123	0.107	0.142	SUBCLONAL	1	TRUE	2	0.405255039715547	6		553	1267	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217306	7217306	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	388	673	0	ENST00000380728.2:c.399del	p.Ser134AlafsTer211	p.S134Afs*211	ENST00000380728		133	ggG/gg	6/11	0.361985815817979	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.405255039715547	2		673	884	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028668	12028668	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	312	641	0	ENST00000353533.5:c.871del	p.Trp291GlyfsTer27	p.W291Gfs*27	ENST00000353533	NM_003010.3	291	Tgg/gg	8/11	0.361985815817979	2	FACETS	0.907	0.859	0.956	0.907	0.859	0.956	CLONAL	2	TRUE	0	0.405255039715547	2		641	849	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0007776-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1174	99	301	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.741	0.659	0.828	0.741	0.659	0.828	SUBCLONAL	1	TRUE	1	0.21	2		301	1273	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111110	193111110	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007776-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1287	153	366	0	ENST00000367435.3:c.643G>T	p.Asp215Tyr	p.D215Y	ENST00000367435	NM_024529.4	215	Gat/Tat	7/17	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.21	2		366	1440	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193121549	193121549	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007776-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1275	143	479	0	ENST00000367435.3:c.947A>G	p.His316Arg	p.H316R	ENST00000367435	NM_024529.4	316	cAt/cGt	10/17	1	2	FACETS	0.96	0.873	1	0.96	0.873	1	CLONAL	1	TRUE	1	0.21	2		479	1418	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858549	27858549	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007776-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1329	108	650	0	ENST00000359303.2:c.22G>A	p.Ala8Thr	p.A8T	ENST00000359303	NM_003535.2	8	Gct/Act	1/1	1	2	FACETS	0.716	0.64	0.797	0.716	0.64	0.797	SUBCLONAL	1	TRUE	1	0.21	2		650	1437	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610096	10610096	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007776-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	62	423	0	ENST00000171111.5:c.614A>T	p.Glu205Val	p.E205V	ENST00000171111	NM_203500.1	205	gAg/gTg	2/6	0.133045372550116	1	FACETS	0.525	0.452	0.605	0.525	0.452	0.605	SUBCLONAL	1	TRUE	0	0.21	1		423	1006	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948788	17948788	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007776-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	70	555	0	ENST00000458235.1:c.1654G>T	p.Glu552Ter	p.E552*	ENST00000458235	NM_000215.3	552	Gag/Tag	12/24	0.133045372550116	1	FACETS	0.501	0.435	0.573	0.501	0.435	0.573	SUBCLONAL	1	TRUE	0	0.21	1		555	1190	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0007793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	139	294	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	0.375631750335242	2		294	694	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0007793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	264	392	2	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.375631750335242	3	FACETS	0.815	0.765	0.867	0.815	0.765	0.867	CLONAL	2	TRUE	1	0.375631750335242	3		394	1024	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	286	269	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.375631750335242	2	FACETS	0.977	0.923	1	0.977	0.923	1	CLONAL	2	TRUE	0	0.375631750335242	2		269	779	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796982	45796982	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	165	318	0	ENST00000450313.1:c.1348A>G	p.Lys450Glu	p.K450E	ENST00000450313	NM_012222.2	450	Aag/Gag	14/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.375631750335242	2		318	742	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683229	88683229	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs535109719	NA	P-0007793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	90	203	0	ENST00000372037.3:c.1439G>A	p.Arg480Gln	p.R480Q	ENST00000372037	NM_004329.2	480	cGg/cAg	12/13	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.375631750335242	2		203	460	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473601	67473601	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	134	317	0	ENST00000327367.4:c.681C>A	p.Cys227Ter	p.C227*	ENST00000327367	NM_005902.3	227	tgC/tgA	6/9	1	2	FACETS	0.988	0.899	1	0.988	0.899	1	CLONAL	1	TRUE	1	0.375631750335242	2		317	722	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029237	14029237	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	170	470	0	ENST00000311895.7:c.1448G>T	p.Arg483Ile	p.R483I	ENST00000311895	NM_005236.2	483	aGa/aTa	8/11	1	2	FACETS	0.981	0.902	1	0.981	0.902	1	CLONAL	1	TRUE	1	0.375631750335242	2		470	923	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374914	45374914	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	279	380	0	ENST00000262160.6:c.929G>C	p.Arg310Thr	p.R310T	ENST00000262160	NM_005901.5	310	aGg/aCg	8/11	0.375631750335242	2	FACETS	0.99	0.935	1	0.99	0.935	1	CLONAL	2	TRUE	0	0.375631750335242	2		380	750	SUCCESS
APC	324	MSKCC	GRCh37	5	112170766	112170766	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1064795792	NA	P-0007793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	150	443	0	ENST00000257430.4:c.1862del	p.Thr621IlefsTer9	p.T621Ifs*9	ENST00000257430	NM_000038.5	621	aCt/at	15/16	0.375631750335242	3	FACETS	0.974	0.889	1	0.487	0.444	0.532	CLONAL	1	TRUE	1	0.375631750335242	3		443	974	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0007808-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	247	124	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.657434531202697	4	FACETS	0.895	0.85	0.941	0.895	0.85	0.941	CLONAL	3	TRUE	1	0.690999669486084	4		124	450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0007808-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	559	582	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.68706652939373	2	FACETS	0.941	0.912	0.969	0.941	0.912	0.969	CLONAL	2	TRUE	0	0.690999669486084	2		582	860	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500413	99500413	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007808-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	259	563	0	ENST00000268035.6:c.3846C>G	p.Ser1282Arg	p.S1282R	ENST00000268035	NM_000875.3	1282	agC/agG	21/21	0.358433988252165	1	FACETS	0.757	0.714	0.801	0.757	0.714	0.801	INDETERMINATE	1	TRUE	0	0.690999669486084	1		563	648	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548908	29548908	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007808-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	175	349	0	ENST00000356175.3:c.1682G>A	p.Trp561Ter	p.W561*	ENST00000356175	NM_000267.3	561	tGg/tAg	15/57	0.68706652939373	2	FACETS	0.864	0.815	0.913	0.864	0.815	0.913	CLONAL	2	TRUE	0	0.690999669486084	2		349	293	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060953	38060968	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCCCCTGTCGCCGT	CGCCCCCTGTCGCCGT	-	novel	NA	P-0007808-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	129	226	1	ENST00000250448.2:c.1021_1036del	p.Thr341ProfsTer4	p.T341Pfs*4	ENST00000250448	NM_004496.3	341	ACGGCGACAGGGGGCGcc/cc	2/2	1	2	FACETS	0.904	0.827	0.983	0.904	0.827	0.983	CLONAL	1	TRUE	1	0.690999669486084	2		227	413	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0007816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	112	301	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.234113105231151	2		301	876	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755527	57755527	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	64	121	0	ENST00000274289.3:c.260T>A	p.Val87Glu	p.V87E	ENST00000274289	NM_006622.3	87	gTg/gAg	1/14	1	2	FACETS	0.818	0.713	0.931	1	0.976	1	CLONAL	2	TRUE	1	0.234113105231151	2		121	334	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198852	67198852	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	75	192	0	ENST00000312629.5:c.323G>C	p.Arg108Pro	p.R108P	ENST00000312629	NM_003952.2	108	cGc/cCc	5/15	1	2	FACETS	0.971	0.851	1	0.971	0.851	1	CLONAL	1	TRUE	1	0.234113105231151	2		192	660	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590599	95590599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	59	317	0	ENST00000393063.1:c.1310C>T	p.Pro437Leu	p.P437L	ENST00000393063	NM_030621.3	437	cCt/cTt	9/28	1	2	FACETS	0.44	0.377	0.51	0.44	0.377	0.51	SUBCLONAL	1	TRUE	1	0.234113105231151	2		317	1145	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226618	1226618	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs730881992	NA	P-0007816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	46	154	0	ENST00000326873.7:c.1274G>C	p.Arg425Pro	p.R425P	ENST00000326873	NM_000455.4	425	cGc/cCc	9/10	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.234113105231151	2		154	328	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028898	47028898	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0007816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	71	139	0	ENST00000377604.3:c.201+1G>T		p.X67_splice	ENST00000377604	NM_001204468.1	67			1	2	FACETS	0.8	0.702	0.905	1	0.977	1	CLONAL	2	TRUE	1	0.234113105231151	2		139	379	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0007848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	66	423	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	0.926	0.802	1	0.926	0.802	1	CLONAL	1	TRUE	1	0.18	2		423	792	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0007874-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	20	188	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.172372339004341	4	FACETS	0.453	0.345	0.578	0.226	0.172	0.289	INDETERMINATE	1	FALSE	2	0.3	4		188	383	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0007874-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	83	403	0	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	1	2	FACETS	0.949	0.839	1	0.949	0.839	1	CLONAL	1	FALSE	1	0.3	2		403	583	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061213	38061213	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007874-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	70	303	0	ENST00000250448.2:c.776A>C	p.Tyr259Ser	p.Y259S	ENST00000250448	NM_004496.3	259	tAc/tCc	2/2	0.172372339004341	4	FACETS	0.782	0.685	0.885	0.782	0.685	0.885	INDETERMINATE	2	FALSE	2	0.3	4		303	388	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007922-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	221	813	2	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	0.751847693598246	5	FACETS	0.896	0.832	0.963	0.299	0.277	0.321	CLONAL	1	TRUE	2	0.768621283071647	5		815	1381	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274737	123274737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs971411400	NA	P-0007922-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	19027	515	7	ENST00000358487.5:c.1181C>T	p.Thr394Ile	p.T394I	ENST00000358487	NM_000141.4	394	aCa/aTa	9/18	0.768621283071647	95	FACETS	0.998	0.996	1			1	CLONAL	94	TRUE	NA	0.768621283071647	95		522	19390	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274768	123274768	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554927408	NA	P-0007922-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	18405	477	5	ENST00000358487.5:c.1150G>A	p.Gly384Arg	p.G384R	ENST00000358487	NM_000141.4	384	Ggg/Agg	9/18	0.768621283071647	95	FACETS	0.997	0.996	0.999			1	CLONAL	94	TRUE	NA	0.768621283071647	95		482	18770	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817493	39817493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755303168	NA	P-0007922-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	183	449	1	ENST00000288319.7:c.70G>A	p.Gly24Arg	p.G24R	ENST00000288319	NM_182918.3	24	Gga/Aga	2/10	0.768621283071647	6	FACETS	0.937	0.862	1	0.234	0.215	0.254	CLONAL	1	TRUE	2	0.768621283071647	6		450	1290	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007972-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	99	269	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.934	0.833	1	0.934	0.833	1	CLONAL	1	TRUE	1	0.252693361086986	2		269	839	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755362	39755362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007972-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	94	528	0	ENST00000288319.7:c.1403C>T	p.Thr468Ile	p.T468I	ENST00000288319	NM_182918.3	468	aCc/aTc	10/10	1	2	FACETS	0.791	0.703	0.886	0.791	0.703	0.886	SUBCLONAL	1	TRUE	1	0.252693361086986	2		528	940	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	35	421	0	ENST00000263967.3:c.3129G>C	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atC	21/21	1	2	FACETS	0.477	0.39	0.574	0.477	0.39	0.574	SUBCLONAL	1	TRUE	1	0.26	2		421	565	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0008011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	29	269	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.155694614142288	3	FACETS	0.358	0.286	0.44	0.179	0.143	0.22	INDETERMINATE	1	TRUE	1	0.26	3		269	705	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0008011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	38	597	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	1	2	FACETS	0.308	0.254	0.37	0.308	0.254	0.37	SUBCLONAL	1	TRUE	1	0.26	2		597	948	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0008011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	23	464	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.3	1	FACETS	0.259	0.201	0.326	0.259	0.201	0.326	SUBCLONAL	1	TRUE	0	0.26	1		464	595	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90990535	90990535	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	83	315	0	ENST00000265433.3:c.497T>C	p.Ile166Thr	p.I166T	ENST00000265433	NM_002485.4	166	aTt/aCt	5/16	0.189924792084697	4	FACETS	1	0.953	1	0.387	0.341	0.436	CLONAL	1	TRUE	1	0.26	4		315	693	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0008035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	26	375	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.834	0.682	0.994	1	0.962	1	CLONAL	3	FALSE	1	0.273541265599788	2		376	76	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0008035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	54	446	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	0.0999390833145095	3	FACETS	0.951	0.899	0.989			1	INDETERMINATE	8	FALSE	NA	0.273541265599788	3		446	59	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868655	37868657	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0008035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	13	387	0	ENST00000269571.5:c.1106_1108del	p.Lys369del	p.K369del	ENST00000269571		368	AAG/-	9/27	1	2	FACETS	1	0.848	1	1	0.926	1	CLONAL	2	FALSE	1	0.273541265599788	2		387	39	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385192	4385194	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0008035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	25	348	0	ENST00000261254.3:c.222_224del	p.Glu75del	p.E75del	ENST00000261254	NM_001759.3	73	GAA/-	2/5	NA	2	FACETS	1	0.872	1			1	INDETERMINATE	3	FALSE	NA	0.273541265599788	2		348	57	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938696	76938697	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0008035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	35	240	0	ENST00000373344.5:c.2051_2052del	p.Thr684SerfsTer2	p.T684Sfs*2	ENST00000373344	NM_000489.3	684	aCA/a	9/35	0.273541265599788	0	FACETS	0.808	0.724	0.881			1	CLONAL	5	FALSE	NA	0.273541265599788	0		240	46	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0008038-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	86	427	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.813	0.718	0.915	0.813	0.718	0.915	CLONAL	1	TRUE	1	0.256713791666346	2		427	824	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729394	41729394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008038-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1486	158	813	1	ENST00000242208.4:c.1135C>T	p.Arg379Trp	p.R379W	ENST00000242208	NM_002192.2	379	Cgg/Tgg	3/3	0.256713791666346	3	FACETS	0.845	0.771	0.923	0.422	0.385	0.462	CLONAL	1	TRUE	1	0.256713791666346	3		814	1644	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222727	5222727	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746980740	NA	P-0008038-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	38	184	0	ENST00000357368.4:c.3076C>T	p.Arg1026Cys	p.R1026C	ENST00000357368	NM_002850.3	1026	Cgc/Tgc	18/38	0.20802837258992	3	FACETS	0.952	0.789	1	0.476	0.394	0.567	CLONAL	1	TRUE	1	0.256713791666346	3		184	351	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0008095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	42	269	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.218199503473567	1	FACETS	0.354	0.298	0.415	0.354	0.298	0.415	INDETERMINATE	1	TRUE	0	0.682949090495753	1		269	229	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188865	32188865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138205668	NA	P-0008095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	81	490	1	ENST00000375023.3:c.689G>A	p.Arg230His	p.R230H	ENST00000375023	NM_004557.3	230	cGt/cAt	4/30	0.682949090495753	3	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	1	0.682949090495753	3		491	152	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0008095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	177	646	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.681734502254228	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.682949090495753	2		647	248	SUCCESS
APC	324	MSKCC	GRCh37	5	112175198	112175198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	24	210	0	ENST00000257430.4:c.3907C>T	p.Gln1303Ter	p.Q1303*	ENST00000257430	NM_000038.5	1303	Caa/Taa	16/16	0.33472611311817	1	FACETS	0.593	0.479	0.716	0.593	0.479	0.716	INDETERMINATE	1	TRUE	0	0.682949090495753	1		210	78	SUCCESS
APC	324	MSKCC	GRCh37	5	112164658	112164658	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	40	351	0	ENST00000257430.4:c.1732G>T	p.Glu578Ter	p.E578*	ENST00000257430	NM_000038.5	578	Gaa/Taa	14/16	0.33472611311817	1	FACETS	0.857	0.739	0.977	0.857	0.739	0.977	INDETERMINATE	1	TRUE	0	0.682949090495753	1		351	90	SUCCESS
APC	324	MSKCC	GRCh37	5	112176206	112176206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	33	599	1	ENST00000257430.4:c.4915C>T	p.Pro1639Ser	p.P1639S	ENST00000257430	NM_000038.5	1639	Cca/Tca	16/16	0.33472611311817	1	FACETS	0.366	0.301	0.437	0.366	0.301	0.437	INDETERMINATE	1	TRUE	0	0.682949090495753	1		600	174	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203436	NA	P-0008101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	209	453	0	ENST00000269305.4:c.487T>C	p.Tyr163His	p.Y163H	ENST00000269305	NM_001126112.2	163	Tac/Cac	5/11	0.388954969061521	2	FACETS	0.939	0.88	0.999	0.939	0.88	0.999	CLONAL	2	TRUE	0	0.431425784772439	2		453	516	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217290	11217290	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	147	592	1	ENST00000361445.4:c.4388A>T	p.Tyr1463Phe	p.Y1463F	ENST00000361445	NM_004958.3	1463	tAt/tTt	30/58	0.431138824819443	3	FACETS	1	0.967	1	0.372	0.34	0.406	CLONAL	1	TRUE	0	0.431425784772439	3		593	742	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625390	69625390	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs574433541	NA	P-0008101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	62	495	0	ENST00000334134.2:c.403C>G	p.Arg135Gly	p.R135G	ENST00000334134	NM_005247.2	135	Cgg/Ggg	3/3	0.431425784772439	4	FACETS	0.521	0.449	0.6	0.13	0.112	0.15	SUBCLONAL	1	TRUE	0	0.431425784772439	4		495	789	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100936	41100936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757806313	NA	P-0008101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	61	390	1	ENST00000373198.4:c.1420G>A	p.Glu474Lys	p.E474K	ENST00000373198	NM_133170.3	474	Gag/Aag	8/32	0.431425784772439	3	FACETS	0.617	0.533	0.709	0.309	0.266	0.355	SUBCLONAL	1	TRUE	1	0.431425784772439	3		391	557	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430566	80430566	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	131	273	0	ENST00000286548.4:c.442C>T	p.Arg148Ter	p.R148*	ENST00000286548	NM_002072.3	148	Cga/Tga	3/7	0.569393046691827	5	FACETS	0.834	0.761	0.91	0.556	0.507	0.607	CLONAL	2	TRUE	2	0.605392980710013	5		273	495	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271350	26271365	+	frameshift_variant	Frame_Shift_Del	DEL	GAACTCTGAAAGCGCA	GAACTCTGAAAGCGCA	-	novel	NA	P-0008125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1467	315	1063	0	ENST00000305910.3:c.248_263del	p.Leu83ProfsTer3	p.L83Pfs*3	ENST00000305910	NM_003534.2	83	cTGCGCTTTCAGAGTTCc/cc	1/1	0.551395002372345	3	FACETS	0.761	0.715	0.808	0.254	0.238	0.27	SUBCLONAL	1	TRUE	0	0.605392980710013	3		1063	1782	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0008141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	261	223	0	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	0.433289545086558	3	FACETS	0.932	0.884	0.981	0.932	0.884	0.981	CLONAL	3	TRUE	0	0.433289545086558	3		223	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579366	7579366	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs770776262	NA	P-0008141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	292	364	0	ENST00000269305.4:c.321C>A	p.Tyr107Ter	p.Y107*	ENST00000269305	NM_001126112.2	107	taC/taA	4/11	0.433289545086558	2	FACETS	0.982	0.931	1	0.982	0.931	1	CLONAL	2	TRUE	0	0.433289545086558	2		364	686	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550952	150550952	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	62	118	0	ENST00000369026.2:c.704T>A	p.Leu235Gln	p.L235Q	ENST00000369026	NM_021960.4	235	cTg/cAg	2/3	0.433289545086558	3	FACETS	1	0.916	1	0.536	0.466	0.611	CLONAL	1	TRUE	1	0.433289545086558	3		118	325	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212252690	212252690	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	191	367	0	ENST00000342788.4:c.3163G>T	p.Ala1055Ser	p.A1055S	ENST00000342788	NM_005235.2	1055	Gcc/Tcc	26/28	0.433289545086558	3	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	1	0.433289545086558	3		367	531	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945649	38945649	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	119	445	0	ENST00000357387.3:c.4577T>C	p.Ile1526Thr	p.I1526T	ENST00000357387	NM_152756.3	1526	aTt/aCt	34/38	0.47524434503061	3	FACETS	0.533	0.479	0.589	0.266	0.239	0.295	SUBCLONAL	1	TRUE	1	0.505202748955583	3		445	1108	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572060	64572060	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs104894261	NA	P-0008150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	668	620	0	ENST00000312049.6:c.1579C>T	p.Arg527Ter	p.R527*	ENST00000312049	NM_130799.2	527	Cga/Tga	10/10	0.505202748955583	2	FACETS	0.94	0.909	0.972	0.94	0.909	0.972	CLONAL	2	TRUE	0	0.505202748955583	2		620	1406	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650813	37650813	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1226401359	NA	P-0008150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	320	587	0	ENST00000447079.4:c.2285A>G	p.Asn762Ser	p.N762S	ENST00000447079	NM_015083.1	762	aAt/aGt	5/14	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.505202748955583	2		587	1248	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165759	108165759	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008161-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	209	489	0	ENST00000278616.4:c.4882A>G	p.Met1628Val	p.M1628V	ENST00000278616	NM_000051.3	1628	Atg/Gtg	32/63	0.466622739853309	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.466622739853309	1		489	637	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220478	1220478	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0008161-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	189	478	0	ENST00000326873.7:c.571A>T	p.Lys191Ter	p.K191*	ENST00000326873	NM_000455.4	191	Aaa/Taa	4/10	0.466622739853309	1	FACETS	0.951	0.883	1	0.951	0.883	1	CLONAL	1	TRUE	0	0.466622739853309	1		478	653	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599929	10599929	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008161-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	524	608	0	ENST00000171111.5:c.1647del	p.Met550Ter	p.M550*	ENST00000171111	NM_203500.1	549	ccC/cc	5/6	0.390256635877395	3	FACETS	0.86	0.828	0.892			1	CLONAL	3	TRUE	NA	0.466622739853309	3		608	1074	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233024	55233024	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144943614	NA	P-0008179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	444	467	1	ENST00000275493.2:c.1774G>A	p.Val592Ile	p.V592I	ENST00000275493	NM_005228.3	592	Gtc/Atc	15/28	0.498046216298644	4	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	2	0.529644024821329	4		468	1277	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	463304	463304	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	445	647	0	ENST00000399788.2:c.967C>G	p.Leu323Val	p.L323V	ENST00000399788	NM_001042603.1	323	Cta/Gta	8/28	0.522587899445996	4	FACETS	0.961	0.917	1	0.961	0.917	1	CLONAL	2	TRUE	2	0.529644024821329	4		647	1337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934575	NA	P-0008206-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	527	399	0	ENST00000269305.4:c.733G>C	p.Gly245Arg	p.G245R	ENST00000269305	NM_001126112.2	245	Ggc/Cgc	7/11	0.867204740868913	1	FACETS	0.997	0.972	1	0.997	0.972	1	CLONAL	1	TRUE	0	0.876044856638042	1		399	678	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0008215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	310	506	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.557761791520397	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.547724499602854	2		507	486	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906916	32906919	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	rs80359277	NA	P-0008215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	57	213	0	ENST00000380152.3:c.1310_1313del	p.Lys437IlefsTer22	p.K437Ifs*22	ENST00000380152		434	aAAAGa/aa	10/27	0.389227518612434	4	FACETS	0.688	0.591	0.794			1	SUBCLONAL	1	TRUE	NA	0.547724499602854	4		213	468	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20483132	20483132	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1691	131	359	1	ENST00000346618.3:c.865G>A	p.Glu289Lys	p.E289K	ENST00000346618	NM_001949.4	289	Gag/Aag	4/7	0.547724499602854	9	FACETS	0.766	0.692	0.845			1	SUBCLONAL	1	TRUE	NA	0.547724499602854	9		360	1822	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206921	162206921	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	70	228	0	ENST00000366898.1:c.754C>T	p.Gln252Ter	p.Q252*	ENST00000366898	NM_004562.2	252	Cag/Tag	7/12	0.492112793487354	1	FACETS	0.663	0.584	0.746	0.663	0.584	0.746	SUBCLONAL	1	TRUE	0	0.547724499602854	1		228	280	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223597	55223597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776791214	NA	P-0008215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	32	284	1	ENST00000275493.2:c.964G>A	p.Gly322Ser	p.G322S	ENST00000275493	NM_005228.3	322	Ggc/Agc	8/28	0.557761791520397	1	FACETS	0.256	0.208	0.311	0.256	0.208	0.311	SUBCLONAL	1	TRUE	0	0.547724499602854	1		285	331	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151882690	151882690	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	60	159	0	ENST00000262189.6:c.5035G>T	p.Ala1679Ser	p.A1679S	ENST00000262189	NM_170606.2	1679	Gcc/Tcc	34/59	0.308339682422657	5	FACETS	1	0.915	1			1	INDETERMINATE	1	TRUE	NA	0.547724499602854	5		159	370	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0008225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	135	375	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.964	1	1	0.991	1	CLONAL	2	FALSE	1	0.201781050936227	2		376	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912660	NA	P-0008225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	432	532	2	ENST00000269305.4:c.839G>T	p.Arg280Ile	p.R280I	ENST00000269305	NM_001126112.2	280	aGa/aTa	8/11	0.201781050936227	2	FACETS	1	0.983	1	1	0.997	1	CLONAL	5	FALSE	0	0.201781050936227	2		534	821	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907844	76907844	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0008225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	95	127	0	ENST00000373344.5:c.4318-1G>C		p.X1440_splice	ENST00000373344	NM_000489.3	1440			1	1	FACETS	1	0.958	1	1	0.991	1	CLONAL	4	FALSE	0	0.201781050936227	1		127	195	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0008285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	22	294	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.233	0.18	0.296	0.233	0.18	0.296	SUBCLONAL	1	TRUE	1	0.23	2		294	820	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0008285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	171	538	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.278269505814686	3	FACETS	0.9	0.828	0.975	0.9	0.828	0.975	CLONAL	2	TRUE	1	0.23	3		538	921	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441422	52441422	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	118	470	0	ENST00000460680.1:c.430C>G	p.His144Asp	p.H144D	ENST00000460680	NM_004656.3	144	Cat/Gat	6/17	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.23	2		470	972	SUCCESS
APC	324	MSKCC	GRCh37	5	112179392	112179392	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1270065034	NA	P-0008285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	107	529	0	ENST00000257430.4:c.8101C>G	p.Gln2701Glu	p.Q2701E	ENST00000257430	NM_000038.5	2701	Cag/Gag	16/16	0.278269505814686	3	FACETS	0.849	0.759	0.945	0.424	0.379	0.473	CLONAL	1	TRUE	1	0.23	3		529	1222	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0008305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	234	558	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.433854581187215	1	FACETS	0.843	0.787	0.901	0.843	0.787	0.901	CLONAL	1	TRUE	0	0.433854581187215	1		558	1002	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383072	42383072	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	192	491	0	ENST00000221972.3:c.92A>G	p.Gln31Arg	p.Q31R	ENST00000221972	NM_021601.3	31	cAg/cGg	2/5	1	2	FACETS	0.809	0.747	0.873	0.809	0.747	0.873	CLONAL	1	TRUE	1	0.433854581187215	2		491	1094	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791337	42791337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769885524	NA	P-0008305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	69	348	2	ENST00000575354.2:c.397G>A	p.Gly133Ser	p.G133S	ENST00000575354	NM_015125.3	133	Ggc/Agc	3/20	1	2	FACETS	0.361	0.313	0.412	0.361	0.313	0.412	SUBCLONAL	1	TRUE	1	0.433854581187215	2		350	882	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491164	120491164	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	348	371	0	ENST00000256646.2:c.2625C>G	p.Asp875Glu	p.D875E	ENST00000256646	NM_024408.3	875	gaC/gaG	17/34	0.606580114130835	4	FACETS	0.971	0.922	1	0.971	0.922	1	CLONAL	2	TRUE	2	0.606580114130835	4		371	949	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937405	76937428	+	frameshift_variant	Frame_Shift_Del	DEL	ATTTCTCAGTATCAGATGATGAAC	ATTTCTCAGTATCAGATGATGAAC	GAAAT	novel	NA	P-0008312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	110	523	0	ENST00000373344.5:c.3320_3343delinsATTTC	p.Cys1107TyrfsTer5	p.C1107Yfs*5	ENST00000373344	NM_000489.3	1107	tGTTCATCATCTGATACTGAGAAATat/tATTTCat	9/35	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.606580114130835	2		523	267	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0008321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	271	604	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.293315631587359	3	FACETS	0.898	0.848	0.949	0.898	0.848	0.949	CLONAL	3	TRUE	0	0.33778902174262	3		604	696	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100948	41100948	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	195	379	0	ENST00000373198.4:c.1408C>T	p.Arg470Ter	p.R470*	ENST00000373198	NM_133170.3	470	Cga/Tga	8/32	0.311569671243013	4	FACETS	0.953	0.884	1			1	CLONAL	2	TRUE	NA	0.33778902174262	4		379	810	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0008321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	244	429	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.305900012384434	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.33778902174262	2		429	681	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056292	180056292	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	367	608	0	ENST00000261937.6:c.952C>T	p.Arg318Ter	p.R318*	ENST00000261937	NM_182925.4	318	Cga/Tga	7/30	0.293315631587359	3	FACETS	1	0.993	1	0.831	0.79	0.872	CLONAL	2	TRUE	0	0.33778902174262	3		608	1019	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357165	89357165	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1360155126	NA	P-0008321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	204	532	0	ENST00000301030.4:c.469A>G	p.Thr157Ala	p.T157A	ENST00000301030	NM_001256183.1	157	Acc/Gcc	6/13	0.33778902174262	3	FACETS	1	0.981	1	0.589	0.545	0.635	CLONAL	1	TRUE	1	0.33778902174262	3		532	1198	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383707	42383707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782414774	NA	P-0008321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	478	567	0	ENST00000221972.3:c.482C>T	p.Thr161Met	p.T161M	ENST00000221972	NM_021601.3	161	aCg/aTg	3/5	0.193007321948421	5	FACETS	0.877	0.84	0.915	1	0.993	1	INDETERMINATE	4	TRUE	2	0.33778902174262	5		567	1215	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983883	2983885	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	rs1033891819	NA	P-0008321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1202	138	641	0	ENST00000396946.4:c.645_647del	p.Lys215del	p.K215del	ENST00000396946	NM_032415.4	215	aaGAAc/aac	5/25	0.193007321948421	5	FACETS	0.919	0.833	1	0.306	0.277	0.337	INDETERMINATE	1	TRUE	2	0.33778902174262	5		641	1340	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420190	49420190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775954885	NA	P-0008331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	80	448	1	ENST00000301067.7:c.15559G>A	p.Ala5187Thr	p.A5187T	ENST00000301067	NM_003482.3	5187	Gcc/Acc	48/54	1	2	FACETS	0.959	0.844	1	0.959	0.844	1	CLONAL	1	TRUE	1	0.240451295942519	2		449	694	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423587	88423587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1366437707	NA	P-0008331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	52	546	1	ENST00000360948.2:c.2248G>A	p.Glu750Lys	p.E750K	ENST00000360948	NM_001012338.2	750	Gag/Aag	18/19	1	2	FACETS	0.855	0.728	0.993	0.855	0.728	0.993	CLONAL	1	TRUE	1	0.240451295942519	2		547	506	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339062	225339062	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	39	635	0	ENST00000264414.4:c.2207C>G	p.Pro736Arg	p.P736R	ENST00000264414	NM_003590.4	736	cCa/cGa	16/16	1	2	FACETS	0.904	0.751	1	0.904	0.751	1	CLONAL	1	TRUE	1	0.240451295942519	2		635	359	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183806	10183806	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	37	318	0	ENST00000256474.2:c.275A>G	p.Asp92Gly	p.D92G	ENST00000256474	NM_000551.3	92	gAc/gGc	1/3	0.240451295942519	1	FACETS	0.95	0.787	1	0.95	0.787	1	CLONAL	1	TRUE	0	0.240451295942519	1		318	285	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643328	52643328	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0008331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	55	447	0	ENST00000394830.3:c.2567+1G>T		p.X856_splice	ENST00000394830	NM_018313.4	856			0.240451295942519	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.240451295942519	1		447	271	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376168	225376198	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTACAATTGGTTCTTCCGTTGATTTGTCA	CTTTACAATTGGTTCTTCCGTTGATTTGTCA	-	novel	NA	P-0008331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	35	768	0	ENST00000264414.4:c.756_786del	p.Asp253TrpfsTer11	p.D253Wfs*11	ENST00000264414	NM_003590.4	252	ctTGACAAATCAACGGAAGAACCAATTGTAAAG/ct	6/16	1	2	FACETS	0.687	0.563	0.826	0.687	0.563	0.826	SUBCLONAL	1	TRUE	1	0.240451295942519	2		768	424	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162414	47162414	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	61	479	0	ENST00000409792.3:c.3712del	p.Ser1238LeufsTer21	p.S1238Lfs*21	ENST00000409792	NM_014159.6	1238	Tct/ct	3/21	0.240451295942519	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.240451295942519	1		479	316	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183811	10183818	+	protein_altering_variant	In_Frame_Del	DEL	GAGCCGCA	GAGCCGCA	TC	novel	NA	P-0008331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	36	304	0	ENST00000256474.2:c.280_287delinsTC	p.Glu94_Gln96delinsSer	p.E94_Q96delinsS	ENST00000256474	NM_000551.3	94	GAGCCGCAg/TCg	1/3	0.240451295942519	1	FACETS	0.918	0.758	1	0.918	0.758	1	CLONAL	1	TRUE	0	0.240451295942519	1		304	287	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0008382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	385	375	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.949	0.906	0.994	0.949	0.906	0.994	CLONAL	1	TRUE	1	0.873007613971146	2		376	929	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0008382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	1080	562	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	2	TRUE	NA	0.873007613971146	2		564	1208	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056021	26056021	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs987043105	NA	P-0008382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	198	244	0	ENST00000343677.2:c.636G>C	p.Lys212Asn	p.K212N	ENST00000343677	NM_005319.3	212	aaG/aaC	1/1	1	2	FACETS	0.864	0.807	0.922	0.864	0.807	0.922	CLONAL	1	TRUE	1	0.873007613971146	2		244	525	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163318	32163318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs969543760	NA	P-0008382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	622	607	0	ENST00000375023.3:c.5908C>T	p.Pro1970Ser	p.P1970S	ENST00000375023	NM_004557.3	1970	Cct/Tct	30/30	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.873007613971146	2		607	1406	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101150	27101150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	472	483	0	ENST00000324856.7:c.4432C>T	p.Pro1478Ser	p.P1478S	ENST00000324856	NM_006015.4	1478	Cca/Tca	18/20	1	2	FACETS	0.949	0.909	0.989	0.949	0.909	0.989	CLONAL	1	TRUE	1	0.873007613971146	2		483	1140	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28886234	28886234	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	221	352	0	ENST00000282397.4:c.3388T>A	p.Tyr1130Asn	p.Y1130N	ENST00000282397	NM_002019.4	1130	Tat/Aat	26/30	0.3841477755077	1	FACETS	0.395	0.368	0.421	0.395	0.368	0.421	INDETERMINATE	1	TRUE	0	0.873007613971146	1		352	723	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187560904	187560905	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0008382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	478	512	0	ENST00000441802.2:c.3613_3614del	p.Glu1206ThrfsTer4	p.E1206Tfs*4	ENST00000441802	NM_005245.3	1205	CGa/a	4/27	0.873007613971146	1	FACETS	0.979	0.953	1	0.979	0.953	1	CLONAL	1	TRUE	0	0.873007613971146	1		512	630	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875981	76875984	+	frameshift_variant	Frame_Shift_Del	DEL	ACAA	ACAA	-	novel	NA	P-0008382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	474	294	0	ENST00000373344.5:c.5151_5154del	p.Cys1718MetfsTer6	p.C1718Mfs*6	ENST00000373344	NM_000489.3	1717	gtTTGT/gt	20/35	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.873007613971146	1		294	589	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685282	89685282	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1114167671	NA	P-0008382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	20	243	0	ENST00000371953.3:c.179del	p.Lys60SerfsTer39	p.K60Sfs*39	ENST00000371953	NM_000314.4	59	tcA/tc	3/9	0.873007613971146	1	FACETS	0.082	0.063	0.106	0.082	0.063	0.106	SUBCLONAL	1	TRUE	0	0.873007613971146	1		243	313	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913517	NA	P-0008391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	330	433	0	ENST00000288135.5:c.1676T>C	p.Val559Ala	p.V559A	ENST00000288135	NM_000222.2	559	gTt/gCt	11/21	1	2	FACETS	0.988	0.933	1	0.988	0.933	1	CLONAL	1	TRUE	1	0.51467863315565	2		433	1298	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0008427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	3659	355	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.611986311173523	14	FACETS	0.981	0.972	0.991			1	CLONAL	12	TRUE	NA	0.611986311173523	14		355	4744	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs17849781	NA	P-0008427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	839	500	0	ENST00000269305.4:c.832C>G	p.Pro278Ala	p.P278A	ENST00000269305	NM_001126112.2	278	Cct/Gct	8/11	0.611986311173523	2	FACETS	0.99	0.964	1	0.99	0.964	1	CLONAL	2	TRUE	0	0.611986311173523	2		500	1385	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916765	48916781	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGGAATCTGTATCTT	TGGGGAATCTGTATCTT	-	novel	NA	P-0008427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	472	338	0	ENST00000267163.4:c.296_312del	p.Trp99TyrfsTer5	p.W99Yfs*5	ENST00000267163	NM_000321.2	99	TGGGGAATCTGTATCTTt/t	3/27	0.566813586317447	3	FACETS	1	0.994	1	0.775	0.747	0.804	CLONAL	2	TRUE	0	0.611986311173523	3		338	866	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0008436-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	87	269	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	0.876	0.775	0.985			1	INDETERMINATE	1	TRUE	NA	0.231741989714785	2		269	857	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0008446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	9	185	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	1	2	FACETS	0.517	0.341	0.743	0.517	0.341	0.743	SUBCLONAL	1	TRUE	1	0.12	2		185	290	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0008446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	17	427	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.49	0.364	0.641	0.49	0.364	0.641	SUBCLONAL	1	TRUE	1	0.12	2		427	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0008455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	208	228	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.877636097232087	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.877636097232087	1		228	261	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087566	27087566	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	110	237	0	ENST00000324856.7:c.2140C>A	p.Leu714Ile	p.L714I	ENST00000324856	NM_006015.4	714	Ctc/Atc	5/20	0.314146414447692	1	FACETS	0.342	0.31	0.376	0.342	0.31	0.376	INDETERMINATE	1	TRUE	0	0.877636097232087	1		237	411	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132774	152132774	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	64	197	0	ENST00000262189.6:c.98A>G	p.Asp33Gly	p.D33G	ENST00000262189	NM_170606.2	33	gAc/gGc	1/59	0.314146414447692	1	FACETS	0.258	0.225	0.294	0.258	0.225	0.294	INDETERMINATE	1	TRUE	0	0.877636097232087	1		197	317	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863656	68863656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	47	393	0	ENST00000261769.5:c.2395C>T	p.Pro799Ser	p.P799S	ENST00000261769	NM_004360.3	799	Ccc/Tcc	15/16	1	2	FACETS	0.399	0.336	0.468	0.399	0.336	0.468	SUBCLONAL	1	TRUE	1	0.46	2		393	512	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217630	7217630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	80	663	0	ENST00000380728.2:c.297del	p.Lys99AsnfsTer10	p.K99Nfs*10	ENST00000380728		99	aaA/aa	4/11	1	2	FACETS	0.376	0.33	0.425	0.376	0.33	0.425	SUBCLONAL	1	TRUE	1	0.46	2		663	926	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0008489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	155	454	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.187224234906448	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.187224234906448	2		454	784	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464875	120464875	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	217	157	0	ENST00000256646.2:c.5197G>T	p.Asp1733Tyr	p.D1733Y	ENST00000256646	NM_024408.3	1733	Gat/Tat	28/34	0.187224234906448	13	FACETS	0.961	0.896	1			1	CLONAL	6	TRUE	NA	0.187224234906448	13		157	816	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641217	23641217	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	47	263	0	ENST00000261584.4:c.2258G>T	p.Arg753Leu	p.R753L	ENST00000261584	NM_024675.3	753	cGa/cTa	5/13	1	2	FACETS	0.812	0.685	0.954	0.812	0.685	0.954	CLONAL	1	TRUE	1	0.187224234906448	2		263	618	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593678	215593678	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	41	242	0	ENST00000260947.4:c.2056del	p.His686IlefsTer28	p.H686Ifs*28	ENST00000260947	NM_000465.2	686	Cat/at	11/11	1	2	FACETS	0.837	0.697	0.994	0.837	0.697	0.994	CLONAL	1	TRUE	1	0.187224234906448	2		242	523	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76919024	76919024	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	483	328	1	ENST00000373344.5:c.3967G>T	p.Glu1323Ter	p.E1323*	ENST00000373344	NM_000489.3	1323	Gaa/Taa	12/35	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.83780539822876	1		329	578	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794431	242794431	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747408754	NA	P-0008533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	454	569	0	ENST00000334409.5:c.511G>A	p.Val171Ile	p.V171I	ENST00000334409	NM_005018.2	171	Gtt/Att	3/5	1	2	FACETS	1	0.954	1	1	0.997	1	CLONAL	2	TRUE	1	0.312585209882466	2		569	1452	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405044	405044	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	159	484	0	ENST00000380956.4:c.1126C>G	p.Arg376Gly	p.R376G	ENST00000380956	NM_001195286.1	376	Cgc/Ggc	8/9	1	2	FACETS	0.76	0.699	0.824	1	0.989	1	SUBCLONAL	2	TRUE	1	0.312585209882466	2		484	669	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549398	21549398	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	136	234	0	ENST00000382592.4:c.2878G>A	p.Gly960Arg	p.G960R	ENST00000382592	NM_014572.2	960	Ggg/Agg	8/8	1	2	FACETS	0.928	0.85	1	1	0.99	1	CLONAL	2	TRUE	1	0.312585209882466	2		234	469	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528225	103528225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188710607	NA	P-0008533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	26	74	0	ENST00000355739.4:c.3533G>A	p.Arg1178His	p.R1178H	ENST00000355739	NM_000123.3	1178	cGt/cAt	15/15	1	2	FACETS	0.84	0.681	1	1	0.947	1	CLONAL	2	TRUE	1	0.312585209882466	2		74	99	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804346	46804346	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	386	674	0	ENST00000290295.7:c.661A>T	p.Ile221Phe	p.I221F	ENST00000290295	NM_006361.5	221	Att/Ttt	2/2	0.312585209882466	3	FACETS	0.899	0.852	0.946	0.899	0.852	0.946	CLONAL	2	TRUE	1	0.312585209882466	3		674	1589	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038227	30038227	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	256	711	0	ENST00000338641.4:c.400C>G	p.Pro134Ala	p.P134A	ENST00000338641	NM_000268.3	134	Cct/Gct	4/16	0.30087804705974	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.312585209882466	1		711	927	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0008563-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	255	489	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.19800391407916	2	FACETS	1	0.99	1	0.66	0.616	0.705	CLONAL	1	TRUE	0	0.28	2		490	1380	SUCCESS
APC	324	MSKCC	GRCh37	5	112170779	112170779	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008563-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	69	748	2	ENST00000257430.4:c.1875G>T	p.Gln625His	p.Q625H	ENST00000257430	NM_000038.5	625	caG/caT	15/16	0.219779490942274	3	FACETS	0.535	0.464	0.611	0.267	0.232	0.306	SUBCLONAL	1	TRUE	1	0.28	3		750	1051	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122365	2122365	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs137854361	NA	P-0008563-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	84	348	2	ENST00000219476.3:c.2220+1G>A		p.X740_splice	ENST00000219476	NM_000548.3	740			0.212752999148811	4	FACETS	0.789	0.695	0.889	0.263	0.231	0.297	SUBCLONAL	1	TRUE	1	0.28	4		350	974	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937996	76938021	+	frameshift_variant	Frame_Shift_Del	DEL	TGGAAGCACTTGCTTGCTGCTTCTTA	TGGAAGCACTTGCTTGCTGCTTCTTA	-	novel	NA	P-0008563-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	66	341	0	ENST00000373344.5:c.2727_2752del	p.Lys910Ter	p.K910*	ENST00000373344	NM_000489.3	909	ccTAAGAAGCAGCAAGCAAGTGCTTCCAct/ccct	9/35	0.300955419371794	0	FACETS	0.716	0.623	0.816			1	SUBCLONAL	1	TRUE	NA	0.28	0		341	474	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138294	2138311	+	inframe_deletion	In_Frame_Del	DEL	CGGCTCCGCCACATCAAG	CGGCTCCGCCACATCAAG	-	rs137854218	NA	P-0008563-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	70	438	0	ENST00000219476.3:c.5238_5255del	p.His1746_Arg1751del	p.H1746_R1751del	ENST00000219476	NM_000548.3	1743	CGGCTCCGCCACATCAAG/-	41/42	0.212752999148811	4	FACETS	0.556	0.483	0.636	0.185	0.161	0.212	SUBCLONAL	1	TRUE	1	0.28	4		438	1151	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0008668-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	220	355	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.3	5	FACETS	0.93	0.865	0.996			1	CLONAL	3	TRUE	NA	0.21	5		355	988	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0008668-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	135	286	0	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	0.18013403783901	2	FACETS	0.881	0.801	0.964	0.881	0.801	0.964	CLONAL	2	TRUE	0	0.21	2		286	730	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574277	95574277	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008668-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	71	402	0	ENST00000393063.1:c.2590G>T	p.Ala864Ser	p.A864S	ENST00000393063	NM_030621.3	864	Gca/Tca	17/28	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.21	2		402	614	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0008674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	180	580	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.264146781881421	3	FACETS	0.955	0.883	1	0.955	0.883	1	CLONAL	2	TRUE	1	0.291790168528194	3		580	740	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0008674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	88	684	1	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.285935086897064	1	FACETS	0.853	0.757	0.956	0.853	0.757	0.956	CLONAL	1	TRUE	0	0.291790168528194	1		685	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0008674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	257	485	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	0.257063194634549	3	FACETS	0.917	0.862	0.972	0.917	0.862	0.972	CLONAL	3	TRUE	0	0.291790168528194	3		485	734	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0008674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	315	485	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.291790168528194	4	FACETS	0.956	0.904	1	0.956	0.904	1	CLONAL	3	TRUE	1	0.291790168528194	4		485	972	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056145	27056145	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	83	382	0	ENST00000324856.7:c.1141T>C	p.Ser381Pro	p.S381P	ENST00000324856	NM_006015.4	381	Tcc/Ccc	2/20	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.291790168528194	2		382	555	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26970478	26970478	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	192	633	0	ENST00000381527.3:c.847T>A	p.Phe283Ile	p.F283I	ENST00000381527	NM_001260.1	283	Ttc/Atc	8/13	0.280070426770442	2	FACETS	0.978	0.908	1	0.978	0.908	1	CLONAL	2	TRUE	0	0.291790168528194	2		633	673	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577392	64577392	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	403	545	1	ENST00000312049.6:c.190C>T	p.Gln64Ter	p.Q64*	ENST00000312049	NM_130799.2	64	Cag/Tag	2/10	0.737638750003663	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.813588969294848	1		546	537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0008714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	105	553	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.284438911484465	3	FACETS	1	0.98	1	0.701	0.631	0.775	CLONAL	1	FALSE	1	0.341813727707598	3		553	513	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748403	162748403	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	156	442	0	ENST00000367921.3:c.2317T>C	p.Phe773Leu	p.F773L	ENST00000367921	NM_006182.2	773	Ttt/Ctt	17/18	0.341813727707598	5	FACETS	0.878	0.81	0.949	0.878	0.81	0.949	CLONAL	3	FALSE	2	0.341813727707598	5		442	524	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480182	20480182	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	16	351	0	ENST00000346618.3:c.499C>G	p.Pro167Ala	p.P167A	ENST00000346618	NM_001949.4	167	Cca/Gca	2/7	0.127413876791483	6	FACETS	0.609	0.45	0.798	0.203	0.15	0.266	INDETERMINATE	1	FALSE	3	0.341813727707598	6		351	259	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0008723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	30	301	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.505	0.404	0.619	0.505	0.404	0.619	SUBCLONAL	1	TRUE	1	0.12	2		301	991	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610136	10610136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	61	417	0	ENST00000171111.5:c.574G>A	p.Glu192Lys	p.E192K	ENST00000171111	NM_203500.1	192	Gag/Aag	2/6	1	2	FACETS	0.964	0.829	1	0.964	0.829	1	CLONAL	1	TRUE	1	0.12	2		417	1055	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182641	38182641	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs387907272	NA	P-0008723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	34	372	0	ENST00000396334.3:c.794T>C	p.Leu265Pro	p.L265P	ENST00000396334	NM_002468.4	265	cTg/cCg	5/5	1	2	FACETS	0.604	0.491	0.732	0.604	0.491	0.732	SUBCLONAL	1	TRUE	1	0.12	2		372	938	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577404	64577404	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1454	148	574	1	ENST00000312049.6:c.178G>T	p.Glu60Ter	p.E60*	ENST00000312049	NM_130799.2	60	Gag/Tag	2/10	0.092855378201937	3	FACETS	0.816	0.742	0.894	0.816	0.742	0.894	CLONAL	2	TRUE	1	0.12	3		575	1602	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73352346	73352346	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1492	83	638	0	ENST00000377767.4:c.559G>C	p.Glu187Gln	p.E187Q	ENST00000377767	NM_014953.3	187	Gaa/Caa	3/21	1	2	FACETS	0.878	0.772	0.994	0.878	0.772	0.994	CLONAL	1	TRUE	1	0.12	2		638	1575	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168944	11168944	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	47	359	0	ENST00000358026.2:c.4534C>T	p.Gln1512Ter	p.Q1512*	ENST00000358026	NM_001128849.1	1512	Cag/Tag	32/36	1	2	FACETS	0.949	0.799	1	0.949	0.799	1	CLONAL	1	TRUE	1	0.12	2		359	825	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106951	27106951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008764-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	130	291	1	ENST00000324856.7:c.6562C>T	p.Gln2188Ter	p.Q2188*	ENST00000324856	NM_006015.4	2188	Cag/Tag	20/20	0.627096635683755	3	FACETS	0.952	0.867	1	0.476	0.433	0.521	CLONAL	1	TRUE	1	0.627096635683755	3		292	572	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865143	57865143	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008764-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5207	428	1024	3	ENST00000228682.2:c.2620C>A	p.Pro874Thr	p.P874T	ENST00000228682	NM_005269.2	874	Cct/Act	12/12	0.627096635683755	11	FACETS	0.926	0.876	0.978			1	CLONAL	1	TRUE	NA	0.627096635683755	11		1027	5635	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865294	57865294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008764-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4538	307	863	0	ENST00000228682.2:c.2771C>T	p.Ser924Phe	p.S924F	ENST00000228682	NM_005269.2	924	tCc/tTc	12/12	0.627096635683755	11	FACETS	0.772	0.723	0.824			1	SUBCLONAL	1	TRUE	NA	0.627096635683755	11		863	4845	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865652	57865652	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008764-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4906	339	1021	0	ENST00000228682.2:c.3129C>G	p.Asp1043Glu	p.D1043E	ENST00000228682	NM_005269.2	1043	gaC/gaG	12/12	0.627096635683755	11	FACETS	0.788	0.74	0.838			1	SUBCLONAL	1	TRUE	NA	0.627096635683755	11		1021	5245	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865707	57865707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748413929	NA	P-0008764-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4573	320	1007	0	ENST00000228682.2:c.3184C>T	p.Pro1062Ser	p.P1062S	ENST00000228682	NM_005269.2	1062	Cct/Tct	12/12	0.627096635683755	11	FACETS	0.797	0.747	0.849			1	SUBCLONAL	1	TRUE	NA	0.627096635683755	11		1007	4893	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685497	29685497	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0008764-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	128	266	0	ENST00000356175.3:c.7908-1G>A		p.X2636_splice	ENST00000356175	NM_000267.3	2636			0.627096635683755	3	FACETS	1	0.924	1	0.508	0.462	0.555	CLONAL	1	TRUE	1	0.627096635683755	3		266	528	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937687	76937687	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008764-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	307	355	0	ENST00000373344.5:c.3061G>T	p.Glu1021Ter	p.E1021*	ENST00000373344	NM_000489.3	1021	Gag/Tag	9/35	0.587452666904394	2	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.627096635683755	2		355	899	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0008766-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	412	427	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.326580406662107	2	FACETS	0.779	0.745	0.813	0.779	0.745	0.813	INDETERMINATE	2	TRUE	0	0.594243209484599	2		427	890	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0008766-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	422	573	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.594243209484599	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.594243209484599	1		573	914	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436026	56436026	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771831816	NA	P-0008766-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	153	302	0	ENST00000407977.2:c.1111C>T	p.Arg371Ter	p.R371*	ENST00000407977		371	Cga/Tga	9/10	0.210873505119846	3	FACETS	1	0.988	1	0.709	0.654	0.766	INDETERMINATE	1	TRUE	1	0.594243209484599	3		302	471	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266825	198266825	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs760147216	NA	P-0008766-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	316	463	0	ENST00000335508.6:c.2107A>C	p.Thr703Pro	p.T703P	ENST00000335508	NM_012433.2	703	Acc/Ccc	15/25	0.289872733632826	1	FACETS	0.787	0.744	0.83	0.787	0.744	0.83	INDETERMINATE	1	TRUE	0	0.594243209484599	1		463	950	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929202	44929202	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0008766-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	564	680	0	ENST00000377967.4:c.2302A>T	p.Lys768Ter	p.K768*	ENST00000377967	NM_021140.2	768	Aag/Tag	17/29	0.594243209484599	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.594243209484599	1		680	1235	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099837	27099837	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008766-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	226	367	0	ENST00000324856.7:c.3716del	p.Ala1239ValfsTer30	p.A1239Vfs*30	ENST00000324856	NM_006015.4	1239	gCt/gt	15/20	0.299965734275022	1	FACETS	0.875	0.821	0.93	0.875	0.821	0.93	INDETERMINATE	1	TRUE	0	0.594243209484599	1		367	611	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522482	187522482	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs79448797	NA	P-0008810-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	200	626	0	ENST00000441802.2:c.11581A>G	p.Thr3861Ala	p.T3861A	ENST00000441802	NM_005245.3	3861	Aca/Gca	21/27	0.420125733958525	1	FACETS	0.368	0.34	0.397	0.368	0.34	0.397	SUBCLONAL	1	TRUE	0	0.633016670930423	1		626	1174	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828221	72828222	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0008810-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1218	309	836	0	ENST00000268489.5:c.8359_8360del	p.Pro2787CysfsTer3	p.P2787Cfs*3	ENST00000268489	NM_006885.3	2787	CCt/t	9/10	0.351649148483268	1	FACETS	0.437	0.411	0.464	0.437	0.411	0.464	INDETERMINATE	1	TRUE	0	0.633016670930423	1		836	1527	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984744	72984744	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008810-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	456	738	0	ENST00000268489.5:c.2840del	p.Cys947SerfsTer19	p.C947Sfs*19	ENST00000268489	NM_006885.3	947	tGc/tc	3/10	0.351649148483268	1	FACETS	0.853	0.816	0.891	0.853	0.816	0.891	INDETERMINATE	1	TRUE	0	0.633016670930423	1		738	1154	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0008870-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	342	685	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.810479370979827	2		685	820	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578528	7578528	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	226	342	0	ENST00000269305.4:c.402T>G	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	ttT/ttG	5/11	0.489687887347635	1	FACETS	0.996	0.932	1	0.996	0.932	1	CLONAL	1	TRUE	0	0.489687887347635	1		342	700	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0008934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	438	261	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	0.471133958097644	4	FACETS	1	0.991	1	0.764	0.73	0.799	CLONAL	2	TRUE	1	0.489687887347635	4		261	1162	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294088	1294088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	245	380	0	ENST00000310581.5:c.913G>A	p.Ala305Thr	p.A305T	ENST00000310581	NM_198253.2	305	Gcg/Acg	2/16	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.489687887347635	2		380	858	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0008953-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	901	269	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.3	7	FACETS	0.989	0.962	1			1	CLONAL	6	FALSE	NA	0.3	7		269	1771	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800977	243800977	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008953-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	131	476	0	ENST00000263826.5:c.497G>A	p.Arg166Gln	p.R166Q	ENST00000263826	NM_005465.4	166	cGa/cAa	5/13	0.230579182218033	3	FACETS	0.73	0.66	0.804	0.365	0.33	0.402	SUBCLONAL	1	FALSE	1	0.3	3		476	1376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs967461896	NA	P-0008953-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	200	218	0	ENST00000269305.4:c.526T>G	p.Cys176Gly	p.C176G	ENST00000269305	NM_001126112.2	176	Tgc/Ggc	5/11	0.3	4	FACETS	0.904	0.842	0.968	0.904	0.842	0.968	CLONAL	3	FALSE	1	0.3	4		218	639	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512402	38512402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008953-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	119	239	5	ENST00000254066.5:c.1319del	p.Pro440ArgfsTer203	p.P440Rfs*203	ENST00000254066	NM_000964.3	438	gCc/gc	9/9	0.188086937828707	4	FACETS	1	0.979	1	0.66	0.596	0.728	CLONAL	1	FALSE	2	0.3	4		244	781	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575055	48575056	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	CA	novel	NA	P-0008953-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	141	355	0	ENST00000342988.3:c.250-1_250delinsCA		p.X84_splice	ENST00000342988	NM_005359.5	84		3/12	NA	2	FACETS	1	0.968	1			1	INDETERMINATE	1	FALSE	NA	0.3	2		355	828	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790412	3790412	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009007-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	46	317	2	ENST00000262367.5:c.4121G>A	p.Gly1374Glu	p.G1374E	ENST00000262367	NM_004380.2	1374	gGg/gAg	24/31	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		319	756	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	210	427	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.871	0.807	0.938	0.871	0.807	0.938	CLONAL	1	TRUE	1	0.360502107748541	2		427	1337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579508	7579508	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	143	518	0	ENST00000269305.4:c.179del	p.Pro60GlnfsTer63	p.P60Qfs*63	ENST00000269305	NM_001126112.2	60	cCa/ca	4/11	0.360502107748541	1	FACETS	0.945	0.864	1	0.945	0.864	1	CLONAL	1	TRUE	0	0.360502107748541	1		518	688	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259099	89259099	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	196	449	2	ENST00000336596.2:c.243G>T	p.Trp81Cys	p.W81C	ENST00000336596	NM_005233.5	81	tgG/tgT	3/17	0.360502107748541	1	FACETS	0.946	0.876	1	0.946	0.876	1	CLONAL	1	TRUE	0	0.360502107748541	1		451	942	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271736	18271736	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	141	434	0	ENST00000222254.8:c.423C>A	p.Asp141Glu	p.D141E	ENST00000222254	NM_005027.3	141	gaC/gaA	4/16	1	2	FACETS	0.913	0.832	0.998	0.913	0.832	0.998	CLONAL	1	TRUE	1	0.360502107748541	2		434	857	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190321	32190321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1033015617	NA	P-0009042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	21	233	0	ENST00000375023.3:c.418C>T	p.Arg140Cys	p.R140C	ENST00000375023	NM_004557.3	140	Cgc/Tgc	3/30	0.191275459500782	3	FACETS	0.498	0.384	0.632	0.249	0.192	0.316	SUBCLONAL	1	FALSE	1	0.3	3		233	323	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242478	55242478	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913229	NA	P-0009042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	94	338	0	ENST00000275493.2:c.2248G>C	p.Ala750Pro	p.A750P	ENST00000275493	NM_005228.3	750	Gca/Cca	19/28	0.191275459500782	3	FACETS	0.962	0.856	1	0.481	0.428	0.538	CLONAL	1	FALSE	1	0.3	3		338	749	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729508	41729508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	173	732	2	ENST00000242208.4:c.1021G>A	p.Ala341Thr	p.A341T	ENST00000242208	NM_002192.2	341	Gct/Act	3/3	0.191275459500782	3	FACETS	1	0.943	1	0.517	0.475	0.562	CLONAL	1	FALSE	1	0.3	3		734	1282	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739837	145739837	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	45	459	0	ENST00000428558.2:c.1693G>C	p.Val565Leu	p.V565L	ENST00000428558	NM_004260.3	565	Gtc/Ctc	10/22	1	2	FACETS	0.504	0.423	0.594	0.504	0.423	0.594	SUBCLONAL	1	FALSE	1	0.3	2		459	595	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830793	72830793	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	103	726	0	ENST00000268489.5:c.5788T>C	p.Ser1930Pro	p.S1930P	ENST00000268489	NM_006885.3	1930	Tcc/Ccc	9/10	0.3	1	FACETS	0.555	0.495	0.618	0.555	0.495	0.618	SUBCLONAL	1	FALSE	0	0.3	1		726	1052	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953916	17953916	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0009042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	47	375	0	ENST00000458235.1:c.486T>A	p.Cys162Ter	p.C162*	ENST00000458235	NM_000215.3	162	tgT/tgA	5/24	1	2	FACETS	0.587	0.495	0.688	0.587	0.495	0.688	SUBCLONAL	1	FALSE	1	0.3	2		375	534	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242478	+	protein_altering_variant	In_Frame_Del	DEL	GAATTAAGAGAAG	GAATTAAGAGAAG	ATTC	novel	NA	P-0009042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	92	350	0	ENST00000275493.2:c.2236_2248delinsATTC	p.Glu746_Ala750delinsIlePro	p.E746_A750delinsIP	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGca/ATTCca	19/28	0.191275459500782	3	FACETS	0.957	0.85	1	0.479	0.425	0.536	CLONAL	1	FALSE	1	0.3	3		350	737	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0009051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	183	646	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.462263932144795	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.462263932144795	2		647	354	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979572	55979572	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	84	479	0	ENST00000263923.4:c.875T>C	p.Leu292Ser	p.L292S	ENST00000263923	NM_002253.2	292	tTa/tCa	7/30	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.462263932144795	2		479	285	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0009066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	319	282	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.18423622157337	3	FACETS	1	0.987	1			1	CLONAL	3	TRUE	NA	0.251491577009263	3		282	846	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0009066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	72	269	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	0.992	0.868	1			1	INDETERMINATE	1	TRUE	NA	0.251491577009263	2		269	577	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794714	42794714	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	56	304	0	ENST00000575354.2:c.1795del	p.Arg599GlyfsTer129	p.R599Gfs*129	ENST00000575354	NM_015125.3	598	ttC/tt	10/20	1	2	FACETS	0.649	0.555	0.752	0.649	0.555	0.752	SUBCLONAL	1	TRUE	1	0.251491577009263	2		304	686	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626698	12626698	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	48	348	0	ENST00000251849.4:c.1591G>T	p.Val531Phe	p.V531F	ENST00000251849	NM_002880.3	531	Gtc/Ttc	15/17	0.251491577009263	1	FACETS	0.431	0.363	0.506	0.431	0.363	0.506	SUBCLONAL	1	TRUE	0	0.251491577009263	1		348	775	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279547	1279547	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	90	318	0	ENST00000310581.5:c.1989C>G	p.Ser663Arg	p.S663R	ENST00000310581	NM_198253.2	663	agC/agG	5/16	0.170928810946444	3	FACETS	1	0.955	1	0.576	0.511	0.646	CLONAL	1	TRUE	1	0.251491577009263	3		318	699	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412344	139412344	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	43	232	2	ENST00000277541.6:c.1301G>A	p.Gly434Asp	p.G434D	ENST00000277541	NM_017617.3	434	gGc/gAc	8/34	1	2	FACETS	0.612	0.511	0.723	0.612	0.511	0.723	SUBCLONAL	1	TRUE	1	0.251491577009263	2		234	559	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413099	139413099	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	49	407	0	ENST00000277541.6:c.1043C>A	p.Ala348Asp	p.A348D	ENST00000277541	NM_017617.3	348	gCc/gAc	6/34	1	2	FACETS	0.468	0.395	0.549	0.468	0.395	0.549	SUBCLONAL	1	TRUE	1	0.251491577009263	2		407	832	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235885	133235885	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	69	189	0	ENST00000320574.5:c.3271G>T	p.Glu1091Ter	p.E1091*	ENST00000320574	NM_006231.2	1091	Gag/Tag	26/49	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.251491577009263	2		189	443	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40460265	40460265	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	205	609	0	ENST00000345506.4:c.1976G>T	p.Arg659Leu	p.R659L	ENST00000345506	NM_003152.3	659	cGg/cTg	17/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.251491577009263	2		609	1342	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76812962	76812962	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1557059602	NA	P-0009066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	111	243	0	ENST00000373344.5:c.6659C>T	p.Ser2220Leu	p.S2220L	ENST00000373344	NM_000489.3	2220	tCa/tTa	30/35	1	1	FACETS	1	0.933	1	1	0.989	1	CLONAL	2	TRUE	0	0.251491577009263	1		243	373	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259178	36259178	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	447	475	0	ENST00000300305.3:c.313C>T	p.His105Tyr	p.H105Y	ENST00000300305		105	Cac/Tac	3/8	0.466633020183186	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.467674497567269	2		475	899	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990456	69990456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs869025259	NA	P-0009067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	63	462	0	ENST00000394351.3:c.415G>A	p.Asp139Asn	p.D139N	ENST00000394351	NM_000248.3	139	Gat/Aat	4/9	NA	2	FACETS	0.337	0.291	0.388			1	INDETERMINATE	1	TRUE	NA	0.467674497567269	2		462	799	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277552	142277552	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	71	423	0	ENST00000350721.4:c.1799A>G	p.Tyr600Cys	p.Y600C	ENST00000350721	NM_001184.3	600	tAt/tGt	8/47	0.428777012717773	3	FACETS	0.453	0.394	0.516	0.226	0.197	0.258	SUBCLONAL	1	TRUE	1	0.467674497567269	3		423	827	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398827	398827	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0009067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	88	519	0	ENST00000380956.4:c.638-1G>T		p.X213_splice	ENST00000380956	NM_001195286.1	213			0.253308999493148	4	FACETS	0.503	0.444	0.566	0.252	0.222	0.283	INDETERMINATE	1	TRUE	2	0.467674497567269	4		519	1098	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045182	47045182	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	83	256	0	ENST00000377604.3:c.2423A>T	p.Asp808Val	p.D808V	ENST00000377604	NM_001204468.1	808	gAc/gTc	21/24	0.389605579457986	2	FACETS	0.578	0.51	0.65			1	SUBCLONAL	1	TRUE	NA	0.467674497567269	2		256	614	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs587781702	NA	P-0009069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	67	333	0	ENST00000269305.4:c.920-1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		333	753	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0009075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	65	348	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.96	0.845	1	1	0.986	1	CLONAL	4	TRUE	1	0.157511618672115	2		348	215	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0009075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	115	410	1	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	1	0.965	1	1	0.992	1	CLONAL	3	TRUE	1	0.157511618672115	2		411	430	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725043	89725043	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1057517809	NA	P-0009075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	126	392	0	ENST00000371953.3:c.1027-1G>A		p.X343_splice	ENST00000371953	NM_000314.4	343			0.157511618672115	5	FACETS	1	0.943	1	1	0.99	1	CLONAL	7	TRUE	1	0.157511618672115	5		392	275	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690817	89690819	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs1554897864	NA	P-0009075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	62	220	0	ENST00000371953.3:c.226_228del	p.Tyr76del	p.Y76del	ENST00000371953	NM_000314.4	75	cATTat/cat	4/9	0.157511618672115	5	FACETS	0.936	0.821	1	1	0.95	1	CLONAL	5	TRUE	1	0.157511618672115	5		220	208	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656262	18656262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774333984	NA	P-0009075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	87	364	0	ENST00000266497.5:c.2941C>T	p.Arg981Cys	p.R981C	ENST00000266497		981	Cgc/Tgc	21/31	0.157511618672115	6	FACETS	1	0.94	1	1	0.94	1	CLONAL	4	TRUE	2	0.157511618672115	6		364	337	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461609	138461609	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs373262346	NA	P-0009075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	63	268	0	ENST00000289153.2:c.412G>C	p.Asp138His	p.D138H	ENST00000289153	NM_006219.2	138	Gat/Cat	3/22	1	2	FACETS	0.952	0.837	1	1	0.986	1	CLONAL	4	TRUE	1	0.157511618672115	2		268	210	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057964	27057964	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	326	223	0	ENST00000324856.7:c.1672del	p.Ser558LeufsTer61	p.S558Lfs*61	ENST00000324856	NM_006015.4	558	Tct/ct	3/20	0.157511618672115	3	FACETS	0.973	0.938	1	1	0.997	1	CLONAL	10	TRUE	0	0.157511618672115	3		223	459	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	63	427	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	0.228545334275322	2		427	428	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845366	151845366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	59	282	1	ENST00000262189.6:c.13646G>A	p.Arg4549His	p.R4549H	ENST00000262189	NM_170606.2	4549	cGc/cAc	52/59	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.228545334275322	2		283	370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578293	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGGAGGGGCCAGACCTAA	GAGGAGGGGCCAGACCTAA	-	novel	NA	P-0009091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	57	366	0	ENST00000269305.4:c.560-4_574del		p.X187_splice	ENST00000269305	NM_001126112.2	187		6/11	0.228693669970542	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.228545334275322	1		366	298	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068433	26068433	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0009132-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	180	290	2	ENST00000435504.4:c.58-1G>T		p.X20_splice	ENST00000435504		20			1	2	FACETS	0.976	0.903	1	0.976	0.903	1	CLONAL	1	TRUE	1	0.540109518419822	2		292	683	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478132	99478132	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009132-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	511	469	0	ENST00000268035.6:c.3036G>T	p.Met1012Ile	p.M1012I	ENST00000268035	NM_000875.3	1012	atG/atT	16/21	0.540109518419822	2	FACETS	0.928	0.893	0.962	0.928	0.893	0.962	CLONAL	2	TRUE	0	0.540109518419822	2		469	1020	SUCCESS
YES1	7525	MSKCC	GRCh37	18	742920	742920	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009132-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	203	428	0	ENST00000314574.4:c.1058A>T	p.Lys353Ile	p.K353I	ENST00000314574	NM_005433.3	353	aAa/aTa	8/12	1	2	FACETS	0.839	0.779	0.901	0.839	0.779	0.901	CLONAL	1	TRUE	1	0.540109518419822	2		428	896	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913517	NA	P-0009156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	289	619	0	ENST00000288135.5:c.1676T>A	p.Val559Asp	p.V559D	ENST00000288135	NM_000222.2	559	gTt/gAt	11/21	1	2	FACETS	0.919	0.863	0.977	0.919	0.863	0.977	CLONAL	1	TRUE	1	0.458649192928127	2		619	1371	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	98	294	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.75	0.673	0.831	0.75	0.673	0.831	SUBCLONAL	1	TRUE	1	0.59	2		294	443	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	51	335	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.66	0.565	0.762	0.66	0.565	0.762	SUBCLONAL	1	TRUE	1	0.59	2		335	262	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	111	258	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.836	0.756	0.919	0.836	0.756	0.919	CLONAL	1	TRUE	1	0.59	2		258	450	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	86	604	0	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.972	0.869	1	0.972	0.869	1	CLONAL	1	TRUE	1	0.59	2		604	300	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	75	480	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.775	0.685	0.871	0.775	0.685	0.871	SUBCLONAL	1	TRUE	1	0.59	2		480	328	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	145	484	5	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	1	2	FACETS	0.953	0.874	1	0.953	0.874	1	CLONAL	1	TRUE	1	0.59	2		489	516	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509085	66509085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	97	519	2	ENST00000273854.3:c.242del	p.Asn81MetfsTer24	p.N81Mfs*24	ENST00000273854	NM_004439.5	81	aAt/at	2/18	1	2	FACETS	0.707	0.633	0.785	0.707	0.633	0.785	SUBCLONAL	1	TRUE	1	0.59	2		521	465	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610083	81610083	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	30	513	0	ENST00000298171.2:c.1681A>C	p.Ser561Arg	p.S561R	ENST00000298171	NM_000369.2	561	Agt/Cgt	10/10	1	2	FACETS	0.328	0.265	0.4	0.328	0.265	0.4	SUBCLONAL	1	TRUE	1	0.59	2		513	310	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604775	48604775	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	116	517	0	ENST00000342988.3:c.1597C>A	p.Leu533Ile	p.L533I	ENST00000342988	NM_005359.5	533	Ctc/Atc	12/12	1	2	FACETS	0.998	0.908	1	0.998	0.908	1	CLONAL	1	TRUE	1	0.59	2		517	394	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	122	789	6	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	1	2	FACETS	0.887	0.807	0.971	0.887	0.807	0.971	CLONAL	1	TRUE	1	0.59	2		795	466	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522454	157522454	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	106	509	0	ENST00000346085.5:c.4726C>T	p.Pro1576Ser	p.P1576S	ENST00000346085	NM_020732.3	1576	Ccg/Tcg	18/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.59	2		509	324	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101655	27101655	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	75	520	0	ENST00000324856.7:c.4937T>G	p.Val1646Gly	p.V1646G	ENST00000324856	NM_006015.4	1646	gTt/gGt	18/20	1	2	FACETS	0.752	0.664	0.845	0.752	0.664	0.845	SUBCLONAL	1	TRUE	1	0.59	2		520	338	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732969	30732969	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	113	395	0	ENST00000295754.5:c.1582C>A	p.Arg528Ser	p.R528S	ENST00000295754	NM_003242.5	528	Cgt/Agt	7/7	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.59	2		395	353	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165917	47165917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	158	704	0	ENST00000409792.3:c.209G>A	p.Arg70Gln	p.R70Q	ENST00000409792	NM_014159.6	70	cGa/cAa	3/21	1	2	FACETS	0.93	0.856	1	0.93	0.856	1	CLONAL	1	TRUE	1	0.59	2		704	576	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939821	49939821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	211	816	1	ENST00000296474.3:c.1222C>T	p.Pro408Ser	p.P408S	ENST00000296474	NM_002447.2	408	Ccc/Tcc	1/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.59	2		817	668	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664795	138664795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113777439	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	35	110	0	ENST00000330315.3:c.770C>T	p.Pro257Leu	p.P257L	ENST00000330315	NM_023067.3	257	cCg/cTg	1/1	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.59	2		110	87	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747937	41747937	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138545772	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	71	373	0	ENST00000226382.2:c.832G>A	p.Gly278Ser	p.G278S	ENST00000226382	NM_003924.3	278	Ggc/Agc	3/3	1	2	FACETS	0.963	0.851	1	0.963	0.851	1	CLONAL	1	TRUE	1	0.59	2		373	250	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534340	187534340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1208705070	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	147	557	0	ENST00000441802.2:c.9386C>T	p.Pro3129Leu	p.P3129L	ENST00000441802	NM_005245.3	3129	cCt/cTt	13/27	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.59	2		557	467	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39074216	39074216	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	77	340	0	ENST00000357387.3:c.94C>T	p.Arg32Ter	p.R32*	ENST00000357387	NM_152756.3	32	Cga/Tga	2/38	1	2	FACETS	0.929	0.825	1	0.929	0.825	1	CLONAL	1	TRUE	1	0.59	2		340	281	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402690	20402690	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	98	436	0	ENST00000346618.3:c.227G>T	p.Ser76Ile	p.S76I	ENST00000346618	NM_001949.4	76	aGc/aTc	1/7	1	2	FACETS	0.837	0.752	0.926	0.837	0.752	0.926	CLONAL	1	TRUE	1	0.59	2		436	397	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168928	32168928	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs930453331	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	126	744	0	ENST00000375023.3:c.4105C>T	p.Pro1369Ser	p.P1369S	ENST00000375023	NM_004557.3	1369	Ccc/Tcc	22/30	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.59	2		744	424	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759406	133759406	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1371645607	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	196	883	3	ENST00000318560.5:c.1729C>T	p.Arg577Ter	p.R577*	ENST00000318560	NM_005157.4	577	Cga/Tga	11/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.59	2		886	604	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434595	110434595	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs555841746	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	73	357	0	ENST00000375856.3:c.3806A>C	p.Gln1269Pro	p.Q1269P	ENST00000375856	NM_003749.2	1269	cAg/cCg	1/2	1	2	FACETS	0.99	0.877	1	0.99	0.877	1	CLONAL	1	TRUE	1	0.59	2		357	250	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647720	2647720	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	135	683	2	ENST00000342085.4:c.1623G>T	p.Glu541Asp	p.E541D	ENST00000342085	NM_002613.4	541	gaG/gaT	14/14	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.59	2		685	395	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884277	37884277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	88	462	0	ENST00000269571.5:c.3748G>A	p.Gly1250Ser	p.G1250S	ENST00000269571		1250	Ggt/Agt	27/27	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.59	2		462	295	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438279	56438279	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1224543746	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	83	457	0	ENST00000407977.2:c.714G>A	p.Trp238Ter	p.W238*	ENST00000407977		238	tgG/tgA	7/10	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.59	2		457	276	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554617	63554617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751061508	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	66	375	2	ENST00000307078.5:c.122G>A	p.Gly41Asp	p.G41D	ENST00000307078	NM_004655.3	41	gGc/gAc	2/11	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.59	2		377	210	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117726	70117726	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	123	787	0	ENST00000245479.2:c.194A>C	p.Glu65Ala	p.E65A	ENST00000245479	NM_000346.3	65	gAg/gCg	1/3	1	2	FACETS	0.766	0.696	0.84	0.766	0.696	0.84	SUBCLONAL	1	TRUE	1	0.59	2		787	544	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265302	10265302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	86	486	2	ENST00000340748.4:c.1744C>T	p.Arg582Trp	p.R582W	ENST00000340748		582	Cgg/Tgg	20/40	1	2	FACETS	0.908	0.811	1	0.908	0.811	1	CLONAL	1	TRUE	1	0.59	2		488	321	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953390	17953390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs545218078	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	70	447	0	ENST00000458235.1:c.596G>A	p.Arg199His	p.R199H	ENST00000458235	NM_000215.3	199	cGc/cAc	6/24	1	2	FACETS	0.993	0.878	1	0.993	0.878	1	CLONAL	1	TRUE	1	0.59	2		447	239	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798822	42798822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	109	585	4	ENST00000575354.2:c.4394G>A	p.Arg1465His	p.R1465H	ENST00000575354	NM_015125.3	1465	cGc/cAc	19/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.59	2		589	309	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309542	30309542	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	159	707	0	ENST00000307677.4:c.480G>T	p.Gln160His	p.Q160H	ENST00000307677	NM_138578.1	160	caG/caT	2/3	0.108006775023598	0	FACETS	0.394	0.363	0.426			1	INDETERMINATE	1	TRUE	0	0.59	0		707	561	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222717	53222717	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	90	321	0	ENST00000375401.3:c.4219del	p.Asp1407ThrfsTer5	p.D1407Tfs*5	ENST00000375401	NM_004187.3	1407	Gac/ac	25/26	1	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.59	1		321	194	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969885	161969885	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	52	434	0	ENST00000366898.1:c.1083+1del		p.X361_splice	ENST00000366898	NM_004562.2	361			1	2	FACETS	0.805	0.694	0.924	0.805	0.694	0.924	CLONAL	1	TRUE	1	0.59	2		434	219	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575133	48575133	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	163	643	1	ENST00000342988.3:c.330del	p.Lys110AsnfsTer12	p.K110Nfs*12	ENST00000342988	NM_005359.5	109	ctA/ct	3/12	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.59	2		644	534	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480133	20480133	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	124	664	0	ENST00000346618.3:c.454del	p.Thr152ProfsTer43	p.T152Pfs*43	ENST00000346618	NM_001949.4	150	ttA/tt	2/7	1	2	FACETS	0.823	0.748	0.9	0.823	0.748	0.9	CLONAL	1	TRUE	1	0.59	2		664	511	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265049	46265049	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	81	1066	0	ENST00000371998.3:c.1924del	p.Leu642Ter	p.L642*	ENST00000371998		640	tCc/tc	12/23	0.108006775023598	0	FACETS	0.159	0.14	0.18			1	INDETERMINATE	1	TRUE	0	0.59	0		1066	707	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0009228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	313	329	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.325540905256629	4	FACETS	0.916	0.867	0.967	0.916	0.867	0.967	INDETERMINATE	2	TRUE	2	0.588703250807094	4		329	922	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028285	48028285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587779254	NA	P-0009228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	107	308	0	ENST00000234420.5:c.3163G>A	p.Ala1055Thr	p.A1055T	ENST00000234420	NM_000179.2	1055	Gca/Aca	4/10	0.290867229443584	2	FACETS	0.481	0.431	0.534	0.24	0.215	0.267	INDETERMINATE	1	TRUE	0	0.588703250807094	2		308	756	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579573	7579573	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	326	270	0	ENST00000269305.4:c.114del	p.Ala39GlnfsTer5	p.A39Qfs*5	ENST00000269305	NM_001126112.2	38	caA/ca	4/11	0.588703250807094	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.588703250807094	1		270	686	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369393	40369393	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0009228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	466	768	0	ENST00000293328.3:c.1257+2T>C		p.X419_splice	ENST00000293328	NM_012448.3	419			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.588703250807094	2		768	1552	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098949	47098949	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	28	411	0	ENST00000409792.3:c.6325C>T	p.Arg2109Ter	p.R2109*	ENST00000409792	NM_014159.6	2109	Cga/Tga	15/21	1	2	FACETS	0.218	0.174	0.269	0.218	0.174	0.269	SUBCLONAL	1	TRUE	1	0.543236347654528	2		411	472	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391716	139391716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371742334	NA	P-0009255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	115	434	0	ENST00000277541.6:c.6475C>T	p.Arg2159Cys	p.R2159C	ENST00000277541	NM_017617.3	2159	Cgc/Tgc	34/34	1	2	FACETS	0.511	0.46	0.565	0.511	0.46	0.565	SUBCLONAL	1	TRUE	1	0.543236347654528	2		434	828	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0009262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	216	573	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.179241238344596	2	FACETS	1	0.988	1	0.657	0.609	0.706	CLONAL	1	TRUE	0	0.246705175783048	2		573	1333	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012465	29012465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373801409	NA	P-0009262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	57	286	0	ENST00000282397.4:c.406G>A	p.Val136Ile	p.V136I	ENST00000282397	NM_002019.4	136	Gta/Ata	4/30	0.179241238344596	2	FACETS	0.684	0.586	0.791	0.342	0.293	0.396	SUBCLONAL	1	TRUE	0	0.246705175783048	2		286	676	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136143	11136143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770014321	NA	P-0009262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	125	301	0	ENST00000358026.2:c.3127C>T	p.Arg1043Trp	p.R1043W	ENST00000358026	NM_001128849.1	1043	Cgg/Tgg	22/36	1	2	FACETS	0.799	0.721	0.881	0.799	0.721	0.881	SUBCLONAL	1	TRUE	1	0.246705175783048	2		301	1269	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604792	48604815	+	inframe_deletion	In_Frame_Del	DEL	AGTACTTCATACCATGCCGATTGC	AGTACTTCATACCATGCCGATTGC	-	novel	NA	P-0009262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	80	337	0	ENST00000342988.3:c.1616_1639del	p.Val539_Ala546del	p.V539_A546del	ENST00000342988	NM_005359.5	538	gaAGTACTTCATACCATGCCGATTGCa/gaa	12/12	0.246705175783048	1	FACETS	0.607	0.533	0.687	0.607	0.533	0.687	SUBCLONAL	1	TRUE	0	0.246705175783048	1		337	936	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380277	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913238	NA	P-0009271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	731	366	1	ENST00000311936.3:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	61	Caa/Aaa	3/5	0.757462438853175	3	FACETS	0.978	0.949	1	0.978	0.949	1	CLONAL	2	TRUE	1	0.757462438853175	3		367	1360	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100998	27100998	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	336	372	0	ENST00000324856.7:c.4280del	p.Val1427AspfsTer54	p.V1427Dfs*54	ENST00000324856	NM_006015.4	1427	gTa/ga	18/20	0.742172357595449	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.757462438853175	1		372	537	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913351	NA	P-0009272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	167	436	0	ENST00000288602.6:c.1397G>C	p.Gly466Ala	p.G466A	ENST00000288602	NM_004333.4	466	gGa/gCa	11/18	0.321429037777466	5	FACETS	1	0.938	1	0.681	0.627	0.737	CLONAL	2	TRUE	2	0.321429037777466	5		436	754	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0009272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	204	466	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.321429037777466	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.321429037777466	2		466	599	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155255	185155255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	143	377	1	ENST00000265026.3:c.496G>T	p.Glu166Ter	p.E166*	ENST00000265026	NM_004721.4	166	Gag/Tag	3/14	0.117444314912065	4	FACETS	0.803	0.733	0.876	0.803	0.733	0.876	INDETERMINATE	2	TRUE	2	0.321429037777466	4		378	732	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542665	187542665	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs750325428	NA	P-0009272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	168	591	0	ENST00000441802.2:c.5075A>G	p.His1692Arg	p.H1692R	ENST00000441802	NM_005245.3	1692	cAt/cGt	10/27	0.117444314912065	4	FACETS	0.751	0.69	0.814	0.751	0.69	0.814	INDETERMINATE	2	TRUE	2	0.321429037777466	4		591	920	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55272957	55272957	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	134	388	1	ENST00000275493.2:c.3280A>T	p.Asn1094Tyr	p.N1094Y	ENST00000275493	NM_005228.3	1094	Aac/Tac	28/28	0.321429037777466	5	FACETS	0.829	0.754	0.908	0.553	0.503	0.606	CLONAL	2	TRUE	2	0.321429037777466	5		389	745	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633488	69633488	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	112	325	0	ENST00000334134.2:c.214G>C	p.Ala72Pro	p.A72P	ENST00000334134	NM_005247.2	72	Gcc/Ccc	1/3	0.215081527424956	4	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	2	0.321429037777466	4		325	448	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849596	68849596	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	242	561	0	ENST00000261769.5:c.1499G>C	p.Gly500Ala	p.G500A	ENST00000261769	NM_004360.3	500	gGc/gCc	10/16	0.117444314912065	4	FACETS	1	0.969	1	1	0.969	1	INDETERMINATE	2	TRUE	2	0.321429037777466	4		561	938	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877420	89877420	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	223	498	0	ENST00000389301.3:c.343G>T	p.Gly115Trp	p.G115W	ENST00000389301	NM_000135.2	115	Ggg/Tgg	4/43	0.117444314912065	4	FACETS	0.963	0.897	1	0.963	0.897	1	INDETERMINATE	2	TRUE	2	0.321429037777466	4		498	952	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557286	29557286	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	168	549	0	ENST00000356175.3:c.2999G>C	p.Arg1000Pro	p.R1000P	ENST00000356175	NM_000267.3	1000	cGt/cCt	23/57	0.321429037777466	2	FACETS	0.786	0.725	0.849	0.786	0.725	0.849	SUBCLONAL	2	TRUE	0	0.321429037777466	2		549	665	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874439	76874439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	198	261	0	ENST00000373344.5:c.5283G>A	p.Met1761Ile	p.M1761I	ENST00000373344	NM_000489.3	1761	atG/atA	21/35	0.279196867499304	2	FACETS	0.883	0.827	0.94			1	CLONAL	3	TRUE	NA	0.321429037777466	2		261	465	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611089	100611089	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	179	343	0	ENST00000308731.7:c.1517G>T	p.Cys506Phe	p.C506F	ENST00000308731	NM_000061.2	506	tGt/tTt	15/19	0.279196867499304	2	FACETS	1	0.986	1			1	CLONAL	2	TRUE	NA	0.321429037777466	2		343	448	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098370	11098370	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	203	605	2	ENST00000358026.2:c.888del	p.Ser297AlafsTer6	p.S297Afs*6	ENST00000358026	NM_001128849.1	296	acG/ac	6/36	0.316066318421577	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.321429037777466	2		607	616	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009299-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	104	427	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	0.973	0.869	1			1	INDETERMINATE	1	FALSE	NA	0.184555293608843	2		427	1158	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685287	89685287	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs398123316	NA	P-0009299-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	35	72	0	ENST00000371953.3:c.182A>G	p.His61Arg	p.H61R	ENST00000371953	NM_000314.4	61	cAt/cGt	3/9	0.184555293608843	3	FACETS	0.549	0.449	0.663	0.275	0.224	0.332	SUBCLONAL	1	FALSE	1	0.184555293608843	3		72	754	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057627	180057627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756234174	NA	P-0009299-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	130	844	0	ENST00000261937.6:c.328G>A	p.Val110Ile	p.V110I	ENST00000261937	NM_182925.4	110	Gtc/Atc	3/30	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.184555293608843	2		844	1289	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438208	56438208	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0009299-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	53	539	0	ENST00000407977.2:c.785C>G	p.Ser262Ter	p.S262*	ENST00000407977		262	tCa/tGa	7/10	1	2	FACETS	0.601	0.511	0.701	0.601	0.511	0.701	SUBCLONAL	1	FALSE	1	0.184555293608843	2		539	955	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573657	48573657	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009299-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	51	50	0	ENST00000342988.3:c.241A>G	p.Arg81Gly	p.R81G	ENST00000342988	NM_005359.5	81	Agg/Ggg	2/12	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	FALSE	1	0.184555293608843	2		50	478	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578473	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGGGTGCCGGG	CGCGGGTGCCGGG	-	novel	NA	P-0009299-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	60	498	0	ENST00000269305.4:c.457_469del	p.Pro153SerfsTer13	p.P153Sfs*13	ENST00000269305	NM_001126112.2	153	CCCGGCACCCGCGtc/tc	5/11	1	2	FACETS	0.69	0.592	0.796	0.69	0.592	0.796	SUBCLONAL	1	FALSE	1	0.184555293608843	2		498	943	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0009302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	37	200	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	NA	2	FACETS	0.846	0.705	1			1	INDETERMINATE	1	TRUE	NA	0.455441332334801	2		200	192	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0009302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	124	662	7	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.455441332334801	2		669	421	SUCCESS
APC	324	MSKCC	GRCh37	5	112175366	112175366	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs863225352	NA	P-0009302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	36	236	0	ENST00000257430.4:c.4075A>T	p.Lys1359Ter	p.K1359*	ENST00000257430	NM_000038.5	1359	Aaa/Taa	16/16	NA	2	FACETS	0.729	0.604	0.866			1	INDETERMINATE	1	TRUE	NA	0.455441332334801	2		236	217	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0009309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	305	375	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.544264365283914	2		376	874	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0009309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	577	395	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.721200512168247	2	FACETS	0.9	0.877	0.923	1	0.997	1	CLONAL	3	TRUE	0	0.544264365283914	2		396	785	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0009309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	22	168	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	1	2	FACETS	0.236	0.182	0.298	0.236	0.182	0.298	SUBCLONAL	1	TRUE	1	0.544264365283914	2		168	343	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891409	76891411	+	inframe_deletion	In_Frame_Del	DEL	CTA	CTA	-	novel	NA	P-0009309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	423	488	0	ENST00000373344.5:c.4694_4696del	p.Val1565del	p.V1565del	ENST00000373344	NM_000489.3	1565	gTAGat/gat	16/35	0.721200512168247	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.544264365283914	1		488	770	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715678	30715678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039551	NA	P-0009334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	235	394	3	ENST00000295754.5:c.1336G>A	p.Asp446Asn	p.D446N	ENST00000295754	NM_003242.5	446	Gat/Aat	5/7	0.457040575762501	2	FACETS	0.763	0.716	0.811	0.763	0.716	0.811	SUBCLONAL	2	TRUE	0	0.457040575762501	2		397	674	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674234	86674234	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	183	326	1	ENST00000274376.6:c.2366G>A	p.Arg789Gln	p.R789Q	ENST00000274376	NM_002890.2	789	cGa/cAa	18/25	0.457040575762501	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.457040575762501	2		327	389	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958367	90958367	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0009334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	190	415	0	ENST00000265433.3:c.2070+1G>T		p.X690_splice	ENST00000265433	NM_002485.4	690			0.457531433641245	4	FACETS	0.84	0.779	0.903	0.84	0.779	0.903	CLONAL	2	TRUE	2	0.457040575762501	4		415	721	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405192	139405192	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	379	514	0	ENST00000277541.6:c.2653C>T	p.Gln885Ter	p.Q885*	ENST00000277541	NM_017617.3	885	Cag/Tag	17/34	0.416797289709604	3	FACETS	0.864	0.826	0.902	0.864	0.826	0.902	CLONAL	3	TRUE	0	0.457040575762501	3		514	786	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273901	10273901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	281	551	3	ENST00000330684.3:c.368C>T	p.Pro123Leu	p.P123L	ENST00000330684	NM_001134407.1	123	cCc/cTc	2/13	0.286078935104226	4	FACETS	0.89	0.838	0.945	0.89	0.838	0.945	CLONAL	2	TRUE	2	0.457040575762501	4		554	1006	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654550	29654550	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	477	497	1	ENST00000356175.3:c.5239G>T	p.Glu1747Ter	p.E1747*	ENST00000356175	NM_000267.3	1747	Gag/Tag	37/57	0.450031502479869	3	FACETS	0.917	0.882	0.952	0.917	0.882	0.952	CLONAL	3	TRUE	0	0.457040575762501	3		498	932	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579489	+	frameshift_variant	Frame_Shift_Del	DEL	CGGGGGGAGCAGCCTCTGGC	CGGGGGGAGCAGCCTCTGGC	-	novel	NA	P-0009334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	302	336	0	ENST00000269305.4:c.198_217del	p.Met66IlefsTer76	p.M66Ifs*76	ENST00000269305	NM_001126112.2	66	atGCCAGAGGCTGCTCCCCCCGtg/attg	4/11	0.450031502479869	3	FACETS	0.914	0.87	0.958	0.914	0.87	0.958	CLONAL	3	TRUE	0	0.457040575762501	3		336	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs878854073	NA	P-0009337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	75	195	0	ENST00000269305.4:c.673-1G>A		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.189195680780989	2	FACETS	1	0.956	1	0.593	0.523	0.667	INDETERMINATE	1	TRUE	0	0.343825033865274	2		195	368	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423601	88423601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	85	387	1	ENST00000360948.2:c.2234G>A	p.Arg745Gln	p.R745Q	ENST00000360948	NM_001012338.2	745	cGg/cAg	18/19	0.343825033865274	0	FACETS	0.762	0.677	0.852			1	SUBCLONAL	1	TRUE	0	0.343825033865274	0		388	426	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423598	88423598	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	47	402	0	ENST00000360948.2:c.2237A>C	p.Lys746Thr	p.K746T	ENST00000360948	NM_001012338.2	746	aAg/aCg	18/19	0.343825033865274	0	FACETS	0.408	0.344	0.478			1	SUBCLONAL	1	TRUE	0	0.343825033865274	0		402	440	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65300248	65300271	+	frameshift_variant	Frame_Shift_Del	DEL	TTTTAAAAGTGCTTCAAATCCTTC	TTTTAAAAGTGCTTCAAATCCTTC	AA	novel	NA	P-0009337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	27	240	0	ENST00000342505.4:c.3439_3462delinsTT	p.Glu1147PhefsTer6	p.E1147Ffs*6	ENST00000342505	NM_002227.2	1147	GAAGGATTTGAAGCACTTTTAAAA/TT	25/25	0.168602787485161	3	FACETS	0.38	0.302	0.47	0.19	0.151	0.235	INDETERMINATE	1	TRUE	1	0.343825033865274	3		240	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0009339-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	533	395	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.475287527856321	3	FACETS	0.985	0.952	1	0.985	0.952	1	CLONAL	3	TRUE	0	0.475287527856321	3		396	939	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508514	106508514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1406220505	NA	P-0009339-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	52	150	0	ENST00000359195.3:c.508G>A	p.Asp170Asn	p.D170N	ENST00000359195	NM_002649.2	170	Gac/Aac	2/11	0.475287527856321	3	FACETS	1	0.954	1	0.636	0.548	0.729	CLONAL	1	TRUE	1	0.475287527856321	3		150	213	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0009344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	2729	294	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.406382302090858	16	FACETS	1	0.992	1			1	CLONAL	16	TRUE	NA	0.406382302090858	16		294	3222	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0009344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	283	568	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.21455113742342	2	FACETS	0.763	0.718	0.808	0.763	0.718	0.808	INDETERMINATE	2	TRUE	0	0.406382302090858	2		568	913	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437376	110437376	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs776945626	NA	P-0009344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	43	42	0	ENST00000375856.3:c.1025C>G	p.Ser342Trp	p.S342W	ENST00000375856	NM_003749.2	342	tCg/tGg	1/2	0.400985135258805	2	FACETS	0.767	0.655	0.884	0.767	0.655	0.884	SUBCLONAL	2	TRUE	0	0.406382302090858	2		42	138	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143261	30143261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1468357046	NA	P-0009344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	79	269	1	ENST00000389048.3:c.265G>A	p.Gly89Ser	p.G89S	ENST00000389048	NM_004304.4	89	Ggc/Agc	1/29	0.293167303549082	3	FACETS	0.761	0.669	0.858	0.38	0.334	0.429	SUBCLONAL	1	TRUE	1	0.406382302090858	3		270	615	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281088	142281088	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	119	601	0	ENST00000350721.4:c.1156G>T	p.Glu386Ter	p.E386*	ENST00000350721	NM_001184.3	386	Gag/Tag	4/47	0.307663902009066	2	FACETS	0.759	0.685	0.836	0.379	0.342	0.418	SUBCLONAL	1	TRUE	0	0.406382302090858	2		601	772	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962845	2962845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764342695	NA	P-0009344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	188	453	1	ENST00000396946.4:c.2063G>A	p.Arg688Gln	p.R688Q	ENST00000396946	NM_032415.4	688	cGa/cAa	16/25	0.406382302090858	3	FACETS	1	0.987	1	0.65	0.601	0.701	CLONAL	1	TRUE	1	0.406382302090858	3		454	856	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983923	15983923	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0009344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	127	471	0	ENST00000268712.3:c.3296C>G	p.Ser1099Ter	p.S1099*	ENST00000268712	NM_006311.3	1099	tCa/tGa	24/46	0.21455113742342	2	FACETS	0.736	0.667	0.809	0.368	0.333	0.405	INDETERMINATE	1	TRUE	0	0.406382302090858	2		471	849	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900171	101900171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564161322	NA	P-0009353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	43	153	0	ENST00000374994.4:c.605C>T	p.Ala202Val	p.A202V	ENST00000374994	NM_004612.2	202	gCg/gTg	4/9	0.288237240364353	2	FACETS	1	0.939	1	0.615	0.522	0.716	CLONAL	1	TRUE	0	0.384036717744106	2		153	182	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445238	29445238	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	45	124	0	ENST00000389048.3:c.3487G>C	p.Asp1163His	p.D1163H	ENST00000389048	NM_004304.4	1163	Gat/Cat	22/29	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.384036717744106	NA		124	145	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677844	47677844	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	59	162	0	ENST00000347630.2:c.1021A>G	p.Met341Val	p.M341V	ENST00000347630	NM_001007230.1	341	Atg/Gtg	11/11	0.384036717744106	4	FACETS	1	0.887	1	1	0.887	1	CLONAL	2	TRUE	2	0.384036717744106	4		162	209	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526126	63526126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854728	NA	P-0009353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	26	166	0	ENST00000307078.5:c.2500C>T	p.Arg834Trp	p.R834W	ENST00000307078	NM_004655.3	834	Cgg/Tgg	11/11	0.384036717744106	4	FACETS	0.811	0.646	0.999	0.406	0.323	0.5	CLONAL	1	TRUE	2	0.384036717744106	4		166	231	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188217	32188217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	27	313	0	ENST00000375023.3:c.1124G>A	p.Gly375Asp	p.G375D	ENST00000375023	NM_004557.3	375	gGc/gAc	6/30	0.204763622485775	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		313	522	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0009417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	247	258	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.396526415890178	6	FACETS	0.899	0.847	0.952	0.899	0.847	0.952	CLONAL	4	TRUE	2	0.396526415890178	6		258	621	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	97	145	0				ENST00000310581	NM_198253.2	-/1132			0.396526415890178	5	FACETS	0.876	0.791	0.963	0.876	0.791	0.963	CLONAL	3	TRUE	2	0.396526415890178	5		145	297	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908122	41908122	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	115	244	0	ENST00000372991.4:c.400C>G	p.Pro134Ala	p.P134A	ENST00000372991	NM_001760.3	134	Ccc/Gcc	2/5	0.396526415890178	6	FACETS	0.884	0.799	0.974			1	CLONAL	2	TRUE	NA	0.396526415890178	6		244	588	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433865	49433865	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	137	285	0	ENST00000301067.7:c.7688A>G	p.Asn2563Ser	p.N2563S	ENST00000301067	NM_003482.3	2563	aAc/aGc	31/54	0.396526415890178	4	FACETS	0.835	0.762	0.91	0.835	0.762	0.91	CLONAL	2	TRUE	2	0.396526415890178	4		285	578	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0009434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	349	301	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.145586809971618	2	FACETS	1	0.992	1	1	0.992	1	INDETERMINATE	2	TRUE	0	0.312997550195038	2		301	906	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827599	72827599	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	56	576	0	ENST00000268489.5:c.8982C>G	p.Phe2994Leu	p.F2994L	ENST00000268489	NM_006885.3	2994	ttC/ttG	9/10	1	2	FACETS	0.432	0.369	0.501	0.432	0.369	0.501	SUBCLONAL	1	TRUE	1	0.312997550195038	2		576	829	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577111	7577111	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs786202082	NA	P-0009434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	149	452	0	ENST00000269305.4:c.827C>G	p.Ala276Gly	p.A276G	ENST00000269305	NM_001126112.2	276	gCc/gGc	8/11	0.312997550195038	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.312997550195038	1		452	600	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5256125	5256125	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	35	333	0	ENST00000357368.4:c.712C>T	p.Arg238Ter	p.R238*	ENST00000357368	NM_002850.3	238	Cga/Tga	9/38	0.234848731860929	0	FACETS	0.43	0.353	0.517			1	SUBCLONAL	1	TRUE	0	0.312997550195038	0		333	357	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986560	36986585	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTGGATACCTGGCCCTGCAGCGCC	GGCTGGATACCTGGCCCTGCAGCGCC	-	novel	NA	P-0009434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	18	303	0	ENST00000354822.5:c.1104_1129del	p.Ala369ValfsTer61	p.A369Vfs*61	ENST00000354822	NM_001079668.2	368	gcGGCGCTGCAGGGCCAGGTATCCAGCCtg/gctg	3/3	1	2	FACETS	0.386	0.29	0.499	0.386	0.29	0.499	SUBCLONAL	1	TRUE	1	0.312997550195038	2		303	298	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0009443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	16	364	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.147991049230605	4	FACETS	0.298	0.219	0.393	0.149	0.109	0.197	SUBCLONAL	1	TRUE	2	0.235474843202073	4		364	563	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0009443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	160	580	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.215956501372632	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.235474843202073	2		580	569	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713757	30713757	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	183	155	0	ENST00000295754.5:c.1082T>G	p.Leu361Arg	p.L361R	ENST00000295754	NM_003242.5	361	cTc/cGc	4/7	0.235474843202073	3	FACETS	0.922	0.859	0.986	1	0.986	1	CLONAL	4	TRUE	0	0.235474843202073	3		155	471	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348230	348230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748733363	NA	P-0009443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	89	141	0	ENST00000262320.3:c.1276G>A	p.Asp426Asn	p.D426N	ENST00000262320	NM_003502.3	426	Gat/Aat	6/11	0.207982832775693	3	FACETS	0.88	0.783	0.983	0.88	0.783	0.983	CLONAL	2	TRUE	1	0.235474843202073	3		141	480	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974699	21974699	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	103	289	0	ENST00000304494.5:c.128del	p.Ser43IlefsTer10	p.S43Ifs*10	ENST00000304494	NM_000077.4	43	aGt/at	1/3	0.207982832775693	3	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	1	0.235474843202073	3		289	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577147	7577149	+	frameshift_variant	Frame_Shift_Del	DEL	AGA	AGA	T	novel	NA	P-0009443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	158	299	0	ENST00000269305.4:c.789_791delinsA	p.Asn263LysfsTer8	p.N263Kfs*8	ENST00000269305	NM_001126112.2	263	aaTCTa/aaAa	8/11	NA	2	FACETS	1	0.928	1			1	INDETERMINATE	2	TRUE	NA	0.235474843202073	2		299	664	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0009483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	33	269	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.782	0.635	0.949	0.782	0.635	0.949	CLONAL	1	TRUE	1	0.12	2		269	703	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0009483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	36	394	1	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.867	0.711	1	0.867	0.711	1	CLONAL	1	TRUE	1	0.12	2		395	692	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46715720	46715720	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	62	675	0	ENST00000371975.4:c.139T>A	p.Phe47Ile	p.F47I	ENST00000371975	NM_003579.3	47	Ttc/Atc	3/18	1	2	FACETS	0.91	0.784	1	0.91	0.784	1	CLONAL	1	TRUE	1	0.12	2		675	1135	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523157	176523157	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	46	457	1	ENST00000292408.4:c.1921G>A	p.Asp641Asn	p.D641N	ENST00000292408	NM_213647.1	641	Gac/Aac	14/18	1	2	FACETS	0.945	0.794	1	0.945	0.794	1	CLONAL	1	TRUE	1	0.12	2		458	811	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481418	140481418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913349	NA	P-0009483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	35	556	1	ENST00000288602.6:c.1390G>A	p.Gly464Arg	p.G464R	ENST00000288602	NM_004333.4	464	Gga/Aga	11/18	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.12	NA		557	807	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988428	41988428	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1230	68	843	3	ENST00000219905.7:c.1220C>T	p.Thr407Ile	p.T407I	ENST00000219905	NM_001164273.1	407	aCa/aTa	3/24	0.3	1	FACETS	0.821	0.711	0.94	0.821	0.711	0.94	CLONAL	1	TRUE	0	0.12	1		846	1298	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602763	10602763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774469695	NA	P-0009483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	43	456	2	ENST00000171111.5:c.815G>A	p.Arg272His	p.R272H	ENST00000171111	NM_203500.1	272	cGc/cAc	3/6	1	2	FACETS	0.956	0.798	1	0.956	0.798	1	CLONAL	1	TRUE	1	0.12	2		458	750	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845319	76845319	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	62	735	0	ENST00000373344.5:c.6202C>A	p.Pro2068Thr	p.P2068T	ENST00000373344	NM_000489.3	2068	Ccc/Acc	27/35	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.12	2		735	932	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176433	123176433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	86	615	0	ENST00000218089.9:c.400G>A	p.Glu134Lys	p.E134K	ENST00000218089	NM_001042749.1	134	Gaa/Aaa	7/35	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.12	2		615	1046	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587467	29587470	+	frameshift_variant	Frame_Shift_Del	DEL	TGCT	TGCT	-	novel	NA	P-0009483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	61	442	0	ENST00000356175.3:c.4453_4456del	p.Ala1485TyrfsTer67	p.A1485Yfs*67	ENST00000356175	NM_000267.3	1483	gTGCTt/gt	33/57	0.3	3	FACETS	1	0.965	1			1	CLONAL	1	TRUE	NA	0.12	3		442	759	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0009515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	298	395	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.655037177869663	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.655037177869663	1		396	586	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0009515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	331	329	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.353356493536227	1	FACETS	0.737	0.699	0.776	0.737	0.699	0.776	INDETERMINATE	1	TRUE	0	0.655037177869663	1		329	922	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955550	48955550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913304	NA	P-0009515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	376	327	1	ENST00000267163.4:c.1666C>T	p.Arg556Ter	p.R556*	ENST00000267163	NM_000321.2	556	Cga/Tga	17/27	0.226693165669065	2	FACETS	1	0.996	1	0.728	0.696	0.761	INDETERMINATE	1	TRUE	0	0.655037177869663	2		328	788	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341212	70341212	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	326	512	0	ENST00000374080.3:c.771G>T	p.Trp257Cys	p.W257C	ENST00000374080		257	tgG/tgT	6/45	0.262191947394738	1	FACETS	0.54	0.51	0.571	0.54	0.51	0.571	INDETERMINATE	1	TRUE	0	0.655037177869663	1		512	1239	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117538	4117538	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009521-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	51	155	0	ENST00000262948.5:c.182A>C	p.Lys61Thr	p.K61T	ENST00000262948	NM_030662.3	61	aAa/aCa	2/11	0.55	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.551138027080006	1		155	126	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032804	30032804	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009521-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	153	385	0	ENST00000338641.4:c.179G>A	p.Trp60Ter	p.W60*	ENST00000338641	NM_000268.3	60	tGg/tAg	2/16	0.55	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.551138027080006	1		385	333	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0009557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	37	123	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.867294697546295	2		123	63	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0009557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	132	363	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.816963237999108	2	FACETS	0.982	0.94	1	0.982	0.94	1	CLONAL	2	TRUE	0	0.867294697546295	2		363	155	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649694	206649694	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	128	351	0	ENST00000367120.3:c.529G>C	p.Glu177Gln	p.E177Q	ENST00000367120	NM_014002.3	177	Gag/Cag	6/22	0.763775608720262	6	FACETS	1	0.97	1	0.749	0.687	0.813	CLONAL	2	TRUE	3	0.867294697546295	6		351	359	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225611	26225611	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	121	1491	0	ENST00000360408.1:c.229C>G	p.Gln77Glu	p.Q77E	ENST00000360408	NM_003532.2	77	Cag/Gag	1/1	0.733071487933332	4	FACETS	0.919	0.833	1	0.459	0.416	0.505	CLONAL	1	TRUE	2	0.867294697546295	4		1491	567	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211833	123211833	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	93	922	0	ENST00000218089.9:c.2700C>G	p.Ile900Met	p.I900M	ENST00000218089	NM_001042749.1	900	atC/atG	27/35	0.764177458644865	2	FACETS	0.851	0.769	0.935	0.426	0.384	0.468	CLONAL	1	TRUE	0	0.867294697546295	2		922	252	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0009604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	63	301	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.14	2		301	859	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371604	225371604	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	52	408	0	ENST00000264414.4:c.1000G>T	p.Glu334Ter	p.E334*	ENST00000264414	NM_003590.4	334	Gaa/Taa	7/16	1	2	FACETS	0.948	0.805	1	0.948	0.805	1	CLONAL	1	TRUE	1	0.14	2		408	784	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158626973	158626973	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1302	83	890	0	ENST00000263640.3:c.697G>T	p.Ala233Ser	p.A233S	ENST00000263640	NM_001105.4	233	Gcc/Tcc	7/11	1	2	FACETS	0.377	0.331	0.427	0.377	0.331	0.427	SUBCLONAL	1	TRUE	1	0.317900408736006	2		890	1385	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696241	52696241	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	170	681	1	ENST00000394830.3:c.436C>T	p.Arg146Ter	p.R146*	ENST00000394830	NM_018313.4	146	Cga/Tga	5/30	0.311037138955063	1	FACETS	0.904	0.831	0.98	0.904	0.831	0.98	CLONAL	1	TRUE	0	0.317900408736006	1		682	995	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78829265	78829265	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	130	477	0	ENST00000306801.3:c.1316T>C	p.Val439Ala	p.V439A	ENST00000306801	NM_020761.2	439	gTg/gCg	12/34	1	2	FACETS	0.917	0.831	1	0.917	0.831	1	CLONAL	1	TRUE	1	0.317900408736006	2		477	892	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155757	106155757	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009639-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	144	363	0	ENST00000380013.4:c.658C>A	p.His220Asn	p.H220N	ENST00000380013	NM_001127208.2	220	Cac/Aac	3/11	0.394762750747573	1	FACETS	0.861	0.787	0.938	0.861	0.787	0.938	CLONAL	1	TRUE	0	0.394762750747573	1		363	680	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0009655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2040	77	701	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.3	12	FACETS	0.566	0.494	0.644	0.051	0.044	0.059	SUBCLONAL	1	TRUE	1	0.36	12		702	2117	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0009655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	1136	410	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.3	12	FACETS	1	0.994	1	0.77	0.751	0.788	CLONAL	8	TRUE	1	0.36	12		410	2087	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs786201057	NA	P-0009655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	55	520	1	ENST00000269305.4:c.374C>A	p.Thr125Lys	p.T125K	ENST00000269305	NM_001126112.2	125	aCg/aAg	4/11	1	2	FACETS	0.505	0.432	0.585	0.505	0.432	0.585	SUBCLONAL	1	TRUE	1	0.36	2		521	605	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0009663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	37	364	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.206286311818162	2		364	261	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023544	31023544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs116112525	NA	P-0009663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	48	399	1	ENST00000375687.4:c.3029C>T	p.Thr1010Met	p.T1010M	ENST00000375687	NM_015338.5	1010	aCg/aTg	13/13	1	2	FACETS	0.902	0.769	1	1	0.971	1	CLONAL	2	TRUE	1	0.206286311818162	2		400	258	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962846	2962846	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	64	441	2	ENST00000396946.4:c.2062C>T	p.Arg688Ter	p.R688*	ENST00000396946	NM_032415.4	688	Cga/Tga	16/25	1	2	FACETS	0.884	0.77	1	1	0.978	1	CLONAL	2	TRUE	1	0.206286311818162	2		443	351	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340450	8340450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200354236	NA	P-0009663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	34	491	0	ENST00000356435.5:c.5146G>A	p.Ala1716Thr	p.A1716T	ENST00000356435		1716	Gct/Act	31/35	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.206286311818162	2		491	230	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0009700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	394	294	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.373453806733767	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.373453806733767	3		294	1225	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0009700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	220	506	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.300678424424395	2	FACETS	1	0.992	1	0.747	0.697	0.798	CLONAL	1	TRUE	0	0.373453806733767	2		507	789	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042434	16042434	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1568277803	NA	P-0009700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	187	565	0	ENST00000268712.3:c.1240C>T	p.Arg414Ter	p.R414*	ENST00000268712	NM_006311.3	414	Cga/Tga	12/46	0.300678424424395	2	FACETS	0.897	0.827	0.969	0.448	0.413	0.485	CLONAL	1	TRUE	0	0.373453806733767	2		565	1117	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949065	151949065	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0009700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	170	512	0	ENST00000262189.6:c.1580T>G	p.Leu527Ter	p.L527*	ENST00000262189	NM_170606.2	527	tTa/tGa	11/59	0.271675352627297	3	FACETS	0.923	0.848	1	0.462	0.424	0.502	CLONAL	1	TRUE	1	0.373453806733767	3		512	1170	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960134	151960134	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1251	154	612	0	ENST00000262189.6:c.1266G>A	p.Met422Ile	p.M422I	ENST00000262189	NM_170606.2	422	atG/atA	9/59	0.271675352627297	3	FACETS	0.697	0.635	0.761	0.348	0.317	0.381	SUBCLONAL	1	TRUE	1	0.373453806733767	3		612	1405	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851653	63851653	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	108	445	0	ENST00000279873.7:c.2431G>C	p.Asp811His	p.D811H	ENST00000279873	NM_032199.2	811	Gat/Cat	10/10	0.300678424424395	2	FACETS	0.751	0.674	0.833	0.376	0.337	0.417	SUBCLONAL	1	TRUE	0	0.373453806733767	2		445	770	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782901	66782901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371140798	NA	P-0009700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	74	413	0	ENST00000307102.5:c.1130C>T	p.Ser377Phe	p.S377F	ENST00000307102	NM_002755.3	377	tCc/tTc	11/11	0.245127515414468	3	FACETS	0.643	0.563	0.731	0.322	0.281	0.366	SUBCLONAL	1	TRUE	1	0.373453806733767	3		413	731	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641767	23641767	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786203747	NA	P-0009700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	102	482	0	ENST00000261584.4:c.1708G>C	p.Glu570Gln	p.E570Q	ENST00000261584	NM_024675.3	570	Gag/Cag	5/13	0.220608486248896	4	FACETS	0.602	0.536	0.672	0.301	0.268	0.336	INDETERMINATE	1	TRUE	2	0.373453806733767	4		482	1247	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346798	89346798	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0009700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	85	620	0	ENST00000301030.4:c.6152C>G	p.Ser2051Ter	p.S2051*	ENST00000301030	NM_001256183.1	2051	tCa/tGa	9/13	0.321487919711356	3	FACETS	0.617	0.544	0.695	0.308	0.272	0.348	SUBCLONAL	1	TRUE	1	0.373453806733767	3		620	876	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0009710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	52	269	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.15227406092366	3	FACETS	1	0.951	1	0.645	0.55	0.747	CLONAL	1	TRUE	1	0.23	3		269	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0009710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1289	276	431	0	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	0.3	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.23	1		431	1565	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964310	55964310	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	33	504	0	ENST00000263923.4:c.2503A>G	p.Lys835Glu	p.K835E	ENST00000263923	NM_002253.2	835	Aag/Gag	17/30	0.3	0	FACETS	0.815	0.667	0.981			1	CLONAL	1	TRUE	0	0.23	0		504	271	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557327	187557327	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	53	524	1	ENST00000441802.2:c.4035G>T	p.Trp1345Cys	p.W1345C	ENST00000441802	NM_005245.3	1345	tgG/tgT	6/27	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.23	2		525	434	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047993	180047993	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3129	470	426	0	ENST00000261937.6:c.2182G>C	p.Asp728His	p.D728H	ENST00000261937	NM_182925.4	728	Gac/Cac	15/30	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.23	2		426	3599	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910377	29910377	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2844	227	438	0	ENST00000376809.5:c.47C>A	p.Ala16Asp	p.A16D	ENST00000376809	NM_002116.7	16	gCc/gAc	1/8	1	2	FACETS	0.643	0.595	0.693	0.643	0.595	0.693	SUBCLONAL	1	TRUE	1	0.23	2		438	3071	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560499	65560499	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	41	535	1	ENST00000358664.4:c.98G>T	p.Arg33Leu	p.R33L	ENST00000358664	NM_002382.4	33	cGa/cTa	3/5	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.23	2		536	316	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41022099	41022099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	112	555	0	ENST00000267868.3:c.823G>A	p.Gly275Arg	p.G275R	ENST00000267868	NM_002875.4	275	Gga/Aga	9/10	0.15227406092366	3	FACETS	1	0.98	1	0.689	0.62	0.763	CLONAL	1	TRUE	1	0.23	3		555	788	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041750	14041750	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	75	440	0	ENST00000311895.7:c.2297C>A	p.Pro766His	p.P766H	ENST00000311895	NM_005236.2	766	cCt/cAt	11/11	1	2	FACETS	0.94	0.823	1	0.94	0.823	1	CLONAL	1	TRUE	1	0.23	2		440	694	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523334	9523334	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	78	593	3	ENST00000353224.5:c.1903G>A	p.Glu635Lys	p.E635K	ENST00000353224	NM_177990.2	635	Gaa/Aaa	9/10	1	2	FACETS	0.98	0.861	1	0.98	0.861	1	CLONAL	1	TRUE	1	0.23	2		596	692	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041266	47041266	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0009710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1335	178	625	0	ENST00000377604.3:c.1693+1G>A		p.X565_splice	ENST00000377604	NM_001204468.1	565			1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.23	2		625	1513	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626635	100626635	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	131	676	1	ENST00000308731.7:c.295C>A	p.Pro99Thr	p.P99T	ENST00000308731	NM_000061.2	99	Cct/Act	4/19	0.3	2	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.23	2		677	855	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123022568	123022568	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	52	489	1	ENST00000355640.3:c.977G>T	p.Gly326Val	p.G326V	ENST00000355640		326	gGg/gTg	3/7	0.3	5	FACETS	0.989	0.841	1			1	CLONAL	1	TRUE	NA	0.23	5		490	615	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372693	81372694	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0009710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	69	511	0	ENST00000222390.5:c.840_841delinsTT	p.Trp280_Glu281delinsCysTer	p.W280_E281delinsC*	ENST00000222390	NM_000601.4	280	tgGGag/tgTTag	7/18	0.15227406092366	0	FACETS	0.779	0.679	0.887			1	SUBCLONAL	1	TRUE	0	0.23	0		511	593	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945049	31945050	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0009710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3298	374	640	3	ENST00000340398.3:c.51_52delinsAA	p.Arg18Ser	p.R18S	ENST00000340398	NM_001013699.2	17	ccCCgc/ccAAgc	1/1	0.15227406092366	3	FACETS	0.988	0.931	1	0.494	0.465	0.523	CLONAL	1	TRUE	1	0.23	3		643	3672	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115923	8115923	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	193	269	0	ENST00000346208.3:c.1271del	p.Pro424ArgfsTer51	p.P424Rfs*51	ENST00000346208		423	caC/ca	6/6	1	2	FACETS	0.845	0.783	0.908	0.845	0.783	0.908	CLONAL	1	TRUE	1	0.607711492113045	2		269	752	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653250	29653250	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	57	227	0	ENST00000356175.3:c.5185G>A	p.Asp1729Asn	p.D1729N	ENST00000356175	NM_000267.3	1729	Gac/Aac	36/57	NA	2	FACETS	0.349	0.3	0.404			1	INDETERMINATE	1	TRUE	NA	0.607711492113045	2		227	537	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30946609	30946609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	229	320	2	ENST00000375687.4:c.31C>T	p.Arg11Cys	p.R11C	ENST00000375687	NM_015338.5	11	Cgc/Tgc	1/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.607711492113045	2		322	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578277	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs1555525902	NA	P-0009729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	243	520	0	ENST00000269305.4:c.572_574del	p.Pro191del	p.P191del	ENST00000269305	NM_001126112.2	191	cCTCag/cag	6/11	0.316139689926169	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.444866132898705	1		520	755	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940431	13940431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	91	418	0	ENST00000405192.2:c.1075C>T	p.Pro359Ser	p.P359S	ENST00000405192	NM_001163147.1	359	Cca/Tca	11/12	1	2	FACETS	0.478	0.424	0.536	0.478	0.424	0.536	SUBCLONAL	1	TRUE	1	0.444866132898705	2		418	856	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0009736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	682	258	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.781769849370272	6	FACETS	0.995	0.966	1			1	CLONAL	4	TRUE	NA	0.781769849370272	6		258	1124	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636739	8636739	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	294	186	1	ENST00000356435.5:c.170G>A	p.Trp57Ter	p.W57*	ENST00000356435		57	tGg/tAg	2/35	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.781769849370272	2		187	359	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518715	176518715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	115	180	1	ENST00000292408.4:c.633G>A	p.Met211Ile	p.M211I	ENST00000292408	NM_213647.1	211	atG/atA	6/18	0.773481999338968	3	FACETS	0.945	0.857	1	0.473	0.428	0.518	CLONAL	1	TRUE	1	0.781769849370272	3		181	433	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421528	32421528	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	144	192	0	ENST00000332351.3:c.1064G>A	p.Arg355Lys	p.R355K	ENST00000332351	NM_024426.4	355	aGa/aAa	6/10	0.593882692975654	4	FACETS	1	0.974	1	0.385	0.352	0.418	CLONAL	1	TRUE	1	0.781769849370272	4		192	569	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940000	76940000	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1311466929	NA	P-0009736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	543	213	0	ENST00000373344.5:c.748C>T	p.Arg250Ter	p.R250*	ENST00000373344	NM_000489.3	250	Cga/Tga	9/35	0.673233040766936	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.781769849370272	2		213	611	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268985	142268985	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs911751877	NA	P-0009736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	363	330	0	ENST00000350721.4:c.2965C>T	p.Arg989Cys	p.R989C	ENST00000350721	NM_001184.3	989	Cgt/Tgt	14/47	0.385976478562675	5	FACETS	1	0.991	1	0.771	0.735	0.808	INDETERMINATE	2	TRUE	2	0.781769849370272	5		330	872	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217469	142217469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	298	299	0	ENST00000350721.4:c.5528C>T	p.Ser1843Phe	p.S1843F	ENST00000350721	NM_001184.3	1843	tCc/tTc	32/47	0.385976478562675	5	FACETS	1	0.972	1	0.695	0.658	0.734	INDETERMINATE	2	TRUE	2	0.781769849370272	5		299	794	SUCCESS
APC	324	MSKCC	GRCh37	5	112177763	112177763	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	348	210	0	ENST00000257430.4:c.6472C>T	p.Pro2158Ser	p.P2158S	ENST00000257430	NM_000038.5	2158	Ccc/Tcc	16/16	0.773481999338968	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.781769849370272	3		210	546	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553525	106553525	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1443004497	NA	P-0009736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	74	126	0	ENST00000369096.4:c.1490C>T	p.Ser497Phe	p.S497F	ENST00000369096	NM_001198.3	497	tCc/tTc	5/7	1	2	FACETS	0.915	0.816	1	0.915	0.816	1	CLONAL	1	TRUE	1	0.781769849370272	2		126	207	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945123	151945123	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs762303674	NA	P-0009736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	33	133	0	ENST00000262189.6:c.2396A>T	p.Asn799Ile	p.N799I	ENST00000262189	NM_170606.2	799	aAt/aTt	14/59	0.781769849370272	7	FACETS	0.662	0.539	0.799			1	SUBCLONAL	1	TRUE	NA	0.781769849370272	7		133	377	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434955	49434955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	150	113	0	ENST00000301067.7:c.6598C>T	p.Pro2200Ser	p.P2200S	ENST00000301067	NM_003482.3	2200	Cct/Tct	31/54	0.781769849370272	4	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	2	0.781769849370272	4		113	338	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624831	9624831	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	166	248	0	ENST00000353224.5:c.146G>A	p.Arg49Lys	p.R49K	ENST00000353224	NM_177990.2	49	aGg/aAg	3/10	0.753982332833824	3	FACETS	1	0.952	1			1	CLONAL	1	TRUE	NA	0.781769849370272	3		248	567	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440271	187440272	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	149	157	0	ENST00000232014.4:c.2095_2096delinsTT	p.Pro699Phe	p.P699F	ENST00000232014	NM_001130845.1	699	CCt/TTt	10/10	0.385976478562675	5	FACETS	0.856	0.787	0.926	0.57	0.525	0.617	INDETERMINATE	2	TRUE	2	0.781769849370272	5		157	484	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349368	89349369	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0009736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	414	701	1	ENST00000301030.4:c.3581_3582delinsAA	p.Gly1194Glu	p.G1194E	ENST00000301030	NM_001256183.1	1194	gGG/gAA	9/13	0.773481999338968	3	FACETS	0.948	0.901	0.996	0.474	0.45	0.498	CLONAL	1	TRUE	1	0.781769849370272	3		702	1554	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806119	1806119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931614	NA	P-0009745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1415	314	712	2	ENST00000260795.2:c.1138G>A	p.Gly380Arg	p.G380R	ENST00000260795		380	Ggg/Agg	8/17	1	2	FACETS	0.788	0.741	0.837	0.788	0.741	0.837	SUBCLONAL	1	TRUE	1	0.460775853544747	2		714	1729	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0009745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	172	260	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	0.460775853544747	2		260	679	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0009761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	143	228	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.58471206943613	3	FACETS	0.959	0.877	1	0.48	0.438	0.523	CLONAL	1	TRUE	1	0.58471206943613	3		228	659	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148507497	148507497	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	173	339	0	ENST00000320356.2:c.1957C>G	p.Gln653Glu	p.Q653E	ENST00000320356	NM_004456.4	653	Caa/Gaa	17/20	1	2	FACETS	0.822	0.758	0.888	0.822	0.758	0.888	CLONAL	1	TRUE	1	0.58471206943613	2		339	720	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913136	44913136	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	452	424	0	ENST00000377967.4:c.811C>T	p.Gln271Ter	p.Q271*	ENST00000377967	NM_021140.2	271	Cag/Tag	10/29	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.58471206943613	1		424	801	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069931	5069931	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0009761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	331	285	0	ENST00000381652.3:c.1520C>G	p.Ser507Ter	p.S507*	ENST00000381652	NM_004972.3	507	tCa/tGa	12/25	0.58471206943613	2	FACETS	0.904	0.864	0.945	0.904	0.864	0.945	CLONAL	2	TRUE	0	0.58471206943613	2		285	626	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89825063	89825063	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779162871	NA	P-0009761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	318	520	0	ENST00000389301.3:c.2903C>T	p.Ser968Leu	p.S968L	ENST00000389301	NM_000135.2	968	tCg/tTg	30/43	1	2	FACETS	0.954	0.901	1	0.954	0.901	1	CLONAL	1	TRUE	1	0.58471206943613	2		520	1140	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737036	162737036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	318	484	0	ENST00000367921.3:c.1180G>A	p.Asp394Asn	p.D394N	ENST00000367921	NM_006182.2	394	Gat/Aat	11/18	0.58471206943613	3	FACETS	1	0.98	1	0.543	0.512	0.575	CLONAL	1	TRUE	1	0.58471206943613	3		484	1295	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745985	162745985	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	259	493	0	ENST00000367921.3:c.2108C>G	p.Ser703Cys	p.S703C	ENST00000367921	NM_006182.2	703	tCt/tGt	16/18	0.58471206943613	3	FACETS	0.936	0.876	0.998	0.468	0.438	0.499	CLONAL	1	TRUE	1	0.58471206943613	3		493	1223	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937054	178937054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	125	243	0	ENST00000263967.3:c.1735G>A	p.Glu579Lys	p.E579K	ENST00000263967	NM_006218.2	579	Gaa/Aaa	11/21	0.58471206943613	3	FACETS	0.98	0.89	1	0.49	0.445	0.537	CLONAL	1	TRUE	1	0.58471206943613	3		243	564	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193871	106193871	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	267	481	1	ENST00000380013.4:c.4333C>T	p.Gln1445Ter	p.Q1445*	ENST00000380013	NM_001127208.2	1445	Cag/Tag	10/11	1	2	FACETS	0.903	0.848	0.96	0.903	0.848	0.96	CLONAL	1	TRUE	1	0.58471206943613	2		482	1011	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509379	149509379	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145823245	NA	P-0009761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	265	423	1	ENST00000261799.4:c.1520G>A	p.Arg507His	p.R507H	ENST00000261799	NM_002609.3	507	cGc/cAc	10/23	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.58471206943613	2		424	871	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641162	117641162	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	469	796	0	ENST00000368508.3:c.5809C>G	p.Leu1937Val	p.L1937V	ENST00000368508	NM_002944.2	1937	Ctt/Gtt	36/43	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.58471206943613	2		796	1591	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522271	157522271	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	260	445	0	ENST00000346085.5:c.4543C>G	p.His1515Asp	p.H1515D	ENST00000346085	NM_020732.3	1515	Cac/Gac	18/20	1	2	FACETS	0.973	0.913	1	0.973	0.913	1	CLONAL	1	TRUE	1	0.58471206943613	2		445	914	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441961	6441961	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	203	386	0	ENST00000356142.4:c.520C>G	p.Leu174Val	p.L174V	ENST00000356142	NM_018890.3	174	Ctg/Gtg	7/7	1	2	FACETS	0.928	0.863	0.995	0.928	0.863	0.995	CLONAL	1	TRUE	1	0.58471206943613	2		386	748	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413123	139413123	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	470	603	1	ENST00000277541.6:c.1019C>A	p.Ala340Asp	p.A340D	ENST00000277541	NM_017617.3	340	gCc/gAc	6/34	0.229284615204243	5	FACETS	0.946	0.903	0.99	0.631	0.602	0.66	INDETERMINATE	2	TRUE	2	0.58471206943613	5		604	1595	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417620	139417620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	357	463	0	ENST00000277541.6:c.424G>A	p.Asp142Asn	p.D142N	ENST00000277541	NM_017617.3	142	Gac/Aac	4/34	0.229284615204243	5	FACETS	0.89	0.843	0.939	0.594	0.562	0.626	INDETERMINATE	2	TRUE	2	0.58471206943613	5		463	1287	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256216	123256216	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	245	426	0	ENST00000358487.5:c.1693G>C	p.Glu565Gln	p.E565Q	ENST00000358487	NM_000141.4	565	Gag/Cag	13/18	1	2	FACETS	0.952	0.892	1	0.952	0.892	1	CLONAL	1	TRUE	1	0.58471206943613	2		426	880	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49423006	49423006	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	251	399	0	ENST00000301067.7:c.14089G>A	p.Glu4697Lys	p.E4697K	ENST00000301067	NM_003482.3	4697	Gag/Aag	44/54	1	2	FACETS	0.918	0.86	0.978	0.918	0.86	0.978	CLONAL	1	TRUE	1	0.58471206943613	2		399	935	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622508	28622508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	313	476	1	ENST00000241453.7:c.1109C>T	p.Ser370Phe	p.S370F	ENST00000241453	NM_004119.2	370	tCt/tTt	9/24	NA	2	FACETS	0.992	0.937	1			1	INDETERMINATE	1	TRUE	NA	0.58471206943613	2		477	1079	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845664	72845664	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	404	668	1	ENST00000268489.5:c.3676C>T	p.Pro1226Ser	p.P1226S	ENST00000268489	NM_006885.3	1226	Ccc/Tcc	7/10	1	2	FACETS	0.968	0.92	1	0.968	0.92	1	CLONAL	1	TRUE	1	0.58471206943613	2		669	1428	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618676	37618676	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1021200845	NA	P-0009761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	250	526	1	ENST00000447079.4:c.352C>T	p.Arg118Cys	p.R118C	ENST00000447079	NM_015083.1	118	Cgt/Tgt	1/14	1	2	FACETS	0.736	0.688	0.786	0.736	0.688	0.786	SUBCLONAL	1	TRUE	1	0.58471206943613	2		527	1162	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030079	36030079	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	253	424	0	ENST00000358208.4:c.1114C>G	p.Gln372Glu	p.Q372E	ENST00000358208		372	Cag/Gag	9/12	1	2	FACETS	0.978	0.917	1	0.978	0.917	1	CLONAL	1	TRUE	1	0.58471206943613	2		424	885	SUCCESS
AR	367	MSKCC	GRCh37	X	66905924	66905924	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	379	321	0	ENST00000374690.3:c.1841C>G	p.Ser614Cys	p.S614C	ENST00000374690	NM_000044.3	614	tCt/tGt	3/8	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.58471206943613	1		321	670	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732271	74732272	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1205	488	790	1	ENST00000359995.5:c.637_638delinsTT	p.Pro213Phe	p.P213F	ENST00000359995	NM_001195427.1	213	CCt/TTt	2/3	1		FACETS		0.942	1				CLONAL	1	TRUE	1	0.58471206943613	2		791	1693	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0009826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	49	497	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.749	0.632	0.878	0.749	0.632	0.878	SUBCLONAL	1	TRUE	1	0.14	2		497	935	SUCCESS
APC	324	MSKCC	GRCh37	5	112175223	112175223	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	41	247	0	ENST00000257430.4:c.3933del	p.Ile1311MetfsTer10	p.I1311Mfs*10	ENST00000257430	NM_000038.5	1311	aTt/at	16/16	1	2	FACETS	0.889	0.739	1	0.889	0.739	1	CLONAL	1	TRUE	1	0.14	2		247	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0009835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	246	327	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.50252526889843	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.50252526889843	1		327	719	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136318	202136318	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	190	346	0	ENST00000358485.4:c.562T>G	p.Ser188Ala	p.S188A	ENST00000358485	NM_001080125.1	188	Tcc/Gcc	3/9	1	2	FACETS	0.895	0.828	0.964	0.895	0.828	0.964	CLONAL	1	TRUE	1	0.50252526889843	2		346	845	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699337	47699337	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	256	512	0	ENST00000347630.2:c.171T>G	p.Phe57Leu	p.F57L	ENST00000347630	NM_001007230.1	57	ttT/ttG	4/11	0.50252526889843	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.50252526889843	1		512	735	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912660	NA	P-0009894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	213	532	2	ENST00000269305.4:c.839G>T	p.Arg280Ile	p.R280I	ENST00000269305	NM_001126112.2	280	aGa/aTa	8/11	0.24430935221427	1	FACETS	0.752	0.698	0.807	1	0.991	1	SUBCLONAL	2	TRUE	0	0.24430935221427	1		534	1018	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259581	89259581	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	82	354	0	ENST00000336596.2:c.725T>A	p.Met242Lys	p.M242K	ENST00000336596	NM_005233.5	242	aTg/aAg	3/17	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.24430935221427	2		354	509	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149447854	149447854	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	132	596	0	ENST00000286301.3:c.1550C>A	p.Pro517Gln	p.P517Q	ENST00000286301	NM_005211.3	517	cCa/cAa	11/22	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.24430935221427	2		596	910	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066586	94066586	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	169	857	0	ENST00000369303.4:c.1173G>T	p.Gln391His	p.Q391H	ENST00000369303	NM_004440.3	391	caG/caT	5/17	0.24430935221427	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.24430935221427	1		857	1190	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730061	41730061	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1197	241	963	0	ENST00000242208.4:c.468G>A	p.Trp156Ter	p.W156*	ENST00000242208	NM_002192.2	156	tgG/tgA	3/3	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.24430935221427	2		963	1438	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434442	121434442	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	129	642	0	ENST00000257555.6:c.1206C>A	p.Asn402Lys	p.N402K	ENST00000257555		402	aaC/aaA	6/10	0.186831353318942	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.24430935221427	1		642	845	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216382	2216382	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0009894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	125	462	0	ENST00000398665.3:c.2026A>T	p.Lys676Ter	p.K676*	ENST00000398665	NM_032482.2	676	Aag/Tag	20/28	0.24430935221427	1	FACETS	0.772	0.701	0.846	1	0.986	1	SUBCLONAL	2	TRUE	0	0.24430935221427	1		462	582	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602697	10602697	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	164	510	1	ENST00000171111.5:c.881A>T	p.Asp294Val	p.D294V	ENST00000171111	NM_203500.1	294	gAc/gTc	3/6	0.24430935221427	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.24430935221427	1		511	867	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041649	47041649	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	198	308	0	ENST00000377604.3:c.1874G>T	p.Gly625Val	p.G625V	ENST00000377604	NM_001204468.1	625	gGa/gTa	17/24	1	1	FACETS	0.845	0.789	0.903	1	0.995	1	CLONAL	3	TRUE	0	0.24430935221427	1		308	561	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221311	1221317	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCCCC	TGGCCCC	-	novel	NA	P-0009894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	159	618	0	ENST00000326873.7:c.834_840del	p.Gly279ArgfsTer6	p.G279Rfs*6	ENST00000326873	NM_000455.4	278	tgTGGCCCC/tg	6/10	0.24430935221427	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.24430935221427	1		618	845	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0009916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	137	394	1	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.654694191218642	2		395	398	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105639	27105639	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	121	359	0	ENST00000324856.7:c.5250del	p.Phe1750LeufsTer20	p.F1750Lfs*20	ENST00000324856	NM_006015.4	1750	ttC/tt	20/20	0.447971273334628	1	FACETS	0.772	0.707	0.839	0.772	0.707	0.839	SUBCLONAL	1	TRUE	0	0.654694191218642	1		359	322	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41201170	41201171	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0009916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	81	390	0	ENST00000357654.3:c.5373_5374delinsAT	p.Val1792Leu	p.V1792L	ENST00000357654	NM_007294.3	1791	gtGGtg/gtATtg	21/23	0.607775597163643	3	FACETS	0.491	0.432	0.554	0.245	0.216	0.277	SUBCLONAL	1	TRUE	1	0.654694191218642	3		390	669	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1620984	1620984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772853413	NA	P-0009932-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	428	538	2	ENST00000344749.5:c.1076C>T	p.Ser359Phe	p.S359F	ENST00000344749	NM_001136139.2	359	tCc/tTc	13/19	1	2	FACETS	0.928	0.887	0.97	0.928	0.887	0.97	CLONAL	1	TRUE	1	0.869837095500655	2		540	1060	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528764	8528764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009932-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	214	296	0	ENST00000356435.5:c.368G>A	p.Arg123Lys	p.R123K	ENST00000356435		123	aGg/aAg	4/35	1	2	FACETS	0.859	0.804	0.914	0.859	0.804	0.914	CLONAL	1	TRUE	1	0.869837095500655	2		296	573	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0009949-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	17	405	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	0.837	0.632	1	0.837	0.632	1	CLONAL	1	FALSE	1	0.324776750411541	2		405	125	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0009949-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	124	392	1	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	0.324776750411541	5	FACETS	1	0.938	1	1	0.938	1	CLONAL	4	FALSE	1	0.324776750411541	5		393	278	SUCCESS
APC	324	MSKCC	GRCh37	5	112175271	112175271	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009949-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	19	226	0	ENST00000257430.4:c.3980C>A	p.Ser1327Ter	p.S1327*	ENST00000257430	NM_000038.5	1327	tCa/tAa	16/16	1	2	FACETS	1	0.833	1	1	0.833	1	CLONAL	1	FALSE	1	0.324776750411541	2		226	106	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711367	114711367	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0009949-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	94	182	0	ENST00000543371.1:c.381+1G>A		p.X127_splice	ENST00000543371	NM_001198531.1	127			0.324776750411541	1	FACETS	1	0.957	1	1	0.991	1	CLONAL	3	FALSE	0	0.324776750411541	1		182	153	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572556	64572556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767854775	NA	P-0009949-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	85	247	0	ENST00000312049.6:c.1300G>A	p.Val434Met	p.V434M	ENST00000312049	NM_130799.2	434	Gtg/Atg	9/10	0.324776750411541	9	FACETS	0.995	0.891	1			1	CLONAL	4	FALSE	NA	0.324776750411541	9		247	281	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244166	5244166	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009949-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	22	352	0	ENST00000357368.4:c.1316G>A	p.Ser439Asn	p.S439N	ENST00000357368	NM_002850.3	439	aGc/aAc	11/38	0.26461801282791	0	FACETS	0.795	0.626	0.985			1	CLONAL	1	FALSE	0	0.324776750411541	0		352	115	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945509	17945509	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210023814	NA	P-0009949-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	35	272	1	ENST00000458235.1:c.2221C>T	p.Arg741Trp	p.R741W	ENST00000458235	NM_000215.3	741	Cgg/Tgg	17/24	0.315327418944153	4	FACETS	1	0.942	1	0.458	0.378	0.545	CLONAL	1	FALSE	1	0.324776750411541	4		273	208	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0009959-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	298	301	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.397014797917663	2		301	1390	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220717	1220717	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0009959-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	209	419	0	ENST00000326873.7:c.734+1G>A		p.X245_splice	ENST00000326873	NM_000455.4	245			0.397014797917663	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.397014797917663	1		419	781	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493634	56493634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009959-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	269	524	1	ENST00000267101.3:c.2950C>T	p.Pro984Ser	p.P984S	ENST00000267101	NM_001982.3	984	Cct/Tct	25/28	1	2	FACETS	0.96	0.898	1	0.96	0.898	1	CLONAL	1	TRUE	1	0.397014797917663	2		525	1412	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	54	427	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.678	0.577	0.788	0.678	0.577	0.788	SUBCLONAL	1	TRUE	1	0.216864893995747	2		427	735	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440715	56440715	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs368233607	NA	P-0009974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	81	426	0	ENST00000407977.2:c.503A>G	p.Asp168Gly	p.D168G	ENST00000407977		168	gAc/gGc	5/10	1	2	FACETS	0.903	0.795	1	0.903	0.795	1	CLONAL	1	TRUE	1	0.216864893995747	2		426	827	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617161	100617161	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	35	300	0	ENST00000308731.7:c.588G>C	p.Gln196His	p.Q196H	ENST00000308731	NM_000061.2	196	caG/caC	7/19	1	1	FACETS	0.515	0.421	0.62	0.515	0.421	0.62	SUBCLONAL	1	TRUE	0	0.216864893995747	1		300	559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577043	7577062	+	frameshift_variant	Frame_Shift_Del	DEL	GCTCGTGGTGAGGCTCCCCT	GCTCGTGGTGAGGCTCCCCT	-	novel	NA	P-0009974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	68	404	0	ENST00000269305.4:c.876_895del	p.Lys292AsnfsTer7	p.K292Nfs*7	ENST00000269305	NM_001126112.2	292	aaAGGGGAGCCTCACCACGAGCtg/aatg	8/11	1	2	FACETS	0.918	0.798	1	0.918	0.798	1	CLONAL	1	TRUE	1	0.216864893995747	2		404	683	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0009981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	514	329	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.360945576850017	5	FACETS	1	0.991	1	0.838	0.804	0.872	CLONAL	3	TRUE	1	0.360945576850017	5		329	1310	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251604	212251604	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	90	400	0	ENST00000342788.4:c.3455C>A	p.Thr1152Asn	p.T1152N	ENST00000342788	NM_005235.2	1152	aCt/aAt	27/28	0.360945576850017	5	FACETS	0.682	0.603	0.767	0.227	0.201	0.256	SUBCLONAL	1	TRUE	2	0.360945576850017	5		400	1127	SUCCESS
ATM	472	MSKCC	GRCh37	11	108168053	108168053	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs55870064	NA	P-0009981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	230	531	0	ENST00000278616.4:c.4949A>G	p.Asn1650Ser	p.N1650S	ENST00000278616	NM_000051.3	1650	aAt/aGt	33/63	0.293488381878905	4	FACETS	0.773	0.72	0.828	0.773	0.72	0.828	SUBCLONAL	2	TRUE	2	0.360945576850017	4		531	1122	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	398	506	0	ENST00000269305.4:c.455C>G	p.Pro152Arg	p.P152R	ENST00000269305	NM_001126112.2	152	cCg/cGg	5/11	0.321514637903476	3	FACETS	0.858	0.819	0.898	0.858	0.819	0.898	CLONAL	3	TRUE	0	0.360945576850017	3		506	1011	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0009984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1290	145	582	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.15	2		582	1435	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468488	89468488	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	58	392	0	ENST00000336596.2:c.2022G>T	p.Met674Ile	p.M674I	ENST00000336596	NM_005233.5	674	atG/atT	11/17	1	2	FACETS	0.779	0.667	0.902	0.779	0.667	0.902	CLONAL	1	TRUE	1	0.15	2		392	993	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799220	45799220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	95	321	0	ENST00000450313.1:c.213G>T	p.Gln71His	p.Q71H	ENST00000450313	NM_012222.2	71	caG/caT	3/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.15	2		321	988	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729662	162729662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	82	381	0	ENST00000367921.3:c.748G>T	p.Val250Leu	p.V250L	ENST00000367921	NM_006182.2	250	Gtg/Ttg	8/18	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.15	2		381	1027	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922372	178922372	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	125	362	0	ENST00000263967.3:c.1141C>G	p.Pro381Ala	p.P381A	ENST00000263967	NM_006218.2	381	Ccc/Gcc	6/21	1	2	FACETS	0.752	0.679	0.829	1	0.985	1	SUBCLONAL	2	TRUE	1	0.15	2		362	1108	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532590	187532590	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0009984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	72	385	0	ENST00000441802.2:c.9803C>G	p.Ser3268Ter	p.S3268*	ENST00000441802	NM_005245.3	3268	tCa/tGa	14/27	0.152288802059521	1	FACETS	0.873	0.761	0.995	0.873	0.761	0.995	CLONAL	1	TRUE	0	0.15	1		385	1017	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020778	112020778	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1700	201	621	0	ENST00000368678.4:c.793C>A	p.Arg265Ser	p.R265S	ENST00000368678		265	Cgt/Agt	8/13	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.15	2		621	1901	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729901	41729901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1630	96	632	1	ENST00000242208.4:c.628G>A	p.Val210Ile	p.V210I	ENST00000242208	NM_002192.2	210	Gta/Ata	3/3	1	2	FACETS	0.742	0.658	0.832	0.742	0.658	0.832	SUBCLONAL	1	TRUE	1	0.15	2		633	1726	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729975	41729975	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1737	94	602	1	ENST00000242208.4:c.554G>T	p.Ser185Ile	p.S185I	ENST00000242208	NM_002192.2	185	aGc/aTc	3/3	1	2	FACETS	0.685	0.606	0.769	0.685	0.606	0.769	SUBCLONAL	1	TRUE	1	0.15	2		603	1831	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363928	118363928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1228	78	389	0	ENST00000534358.1:c.5161G>A	p.Gly1721Arg	p.G1721R	ENST00000534358	NM_005933.3	1721	Ggg/Agg	16/36	0.133067477887449	3	FACETS	0.856	0.749	0.972	0.428	0.374	0.486	CLONAL	1	TRUE	1	0.15	3		389	1306	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28644750	28644750	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0009984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	45	319	1	ENST00000241453.7:c.44-1G>C		p.X15_splice	ENST00000241453	NM_004119.2	15			1	2	FACETS	0.732	0.613	0.864	0.732	0.613	0.864	SUBCLONAL	1	TRUE	1	0.15	2		320	820	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220488	1220488	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	95	346	0	ENST00000326873.7:c.581A>G	p.Asp194Gly	p.D194G	ENST00000326873	NM_000455.4	194	gAc/gGc	4/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.15	2		346	857	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11114057	11114057	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	156	504	0	ENST00000358026.2:c.1985C>A	p.Ser662Ter	p.S662*	ENST00000358026	NM_001128849.1	662	tCa/tAa	13/36	1	2	FACETS	0.806	0.736	0.879	1	0.989	1	CLONAL	2	TRUE	1	0.15	2		504	1291	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39746878	39746878	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	59	205	0	ENST00000361337.2:c.1892A>G	p.Asn631Ser	p.N631S	ENST00000361337	NM_003286.2	631	aAc/aGc	18/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.15	2		205	558	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396287	139396293	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCATC	CGGCATC	-	novel	NA	P-0009984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	119	432	0	ENST00000277541.6:c.5545_5551del	p.Asp1849LeufsTer36	p.D1849Lfs*36	ENST00000277541	NM_017617.3	1849	GATGCCGct/ct	30/34	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.15	2		432	1145	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434179	49434179	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000067-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	315	678	0	ENST00000301067.7:c.7374G>T	p.Gln2458His	p.Q2458H	ENST00000301067	NM_003482.3	2458	caG/caT	31/54	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.844689550536377	2		678	715	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947579	48947579	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs587778845	NA	P-0000067-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	795	546	1	ENST00000267163.4:c.1166T>A	p.Leu389Ter	p.L389*	ENST00000267163	NM_000321.2	389	tTa/tAa	12/27	0.844689550536377	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.844689550536377	3		547	854	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2111969	2111969	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000067-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	549	590	1	ENST00000219476.3:c.1217G>A	p.Arg406Lys	p.R406K	ENST00000219476	NM_000548.3	406	aGa/aAa	12/42	0.844689550536377	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.844689550536377	2		591	600	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0000067-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	410	327	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	2	TRUE	NA	0.844689550536377	2		327	452	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448582	89448582	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000689-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	138	464	0	ENST00000336596.2:c.1546G>C	p.Gly516Arg	p.G516R	ENST00000336596	NM_005233.5	516	Gga/Cga	7/17	1	2	FACETS	0.714	0.648	0.784	0.714	0.648	0.784	SUBCLONAL	1	TRUE	1	0.31272410344536	2		464	1236	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220718	1220718	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0000689-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	169	328	0	ENST00000326873.7:c.734+2T>G		p.X245_splice	ENST00000326873	NM_000455.4	245			NA	2	FACETS	0.89	0.822	0.96			1	INDETERMINATE	2	TRUE	NA	0.31272410344536	2		328	607	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143190	24143190	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000689-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	123	415	0	ENST00000263121.7:c.422A>T	p.His141Leu	p.H141L	ENST00000263121	NM_003073.3	141	cAc/cTc	4/9	0.145051667885159	1	FACETS	0.667	0.602	0.736	0.667	0.602	0.736	INDETERMINATE	1	TRUE	0	0.31272410344536	1		415	995	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0000690-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	113	229	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.380567635906716	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.380567635906716	3		229	303	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0000690-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	103	268	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.35482542946549	1	FACETS	0.774	0.695	0.858	0.774	0.695	0.858	SUBCLONAL	1	TRUE	0	0.380567635906716	1		268	566	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448571	89448571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000690-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	123	404	0	ENST00000336596.2:c.1535G>A	p.Arg512Gln	p.R512Q	ENST00000336596	NM_005233.5	512	cGa/cAa	7/17	0.35482542946549	1	FACETS	0.726	0.657	0.798	0.726	0.657	0.798	SUBCLONAL	1	TRUE	0	0.380567635906716	1		404	721	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188207	10188207	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001232-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	226	309	0	ENST00000256474.2:c.350G>T	p.Trp117Leu	p.W117L	ENST00000256474	NM_000551.3	117	tGg/tTg	2/3	0.274863214404795	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	0	0.279546352629167	2		309	794	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741998	40741998	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs374756725	NA	P-0001232-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	223	340	0	ENST00000392038.2:c.974A>G	p.Asn325Ser	p.N325S	ENST00000392038	NM_001626.4	325	aAt/aGt	11/14	0.103454037086952	5	FACETS	0.891	0.831	0.953	0.668	0.623	0.715	INDETERMINATE	3	TRUE	1	0.279546352629167	5		340	847	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52663010	52663013	+	frameshift_variant	Frame_Shift_Del	DEL	AAAT	AAAT	-	novel	NA	P-0001232-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	191	255	1	ENST00000394830.3:c.1340_1343del	p.His447ArgfsTer5	p.H447Rfs*5	ENST00000394830	NM_018313.4	447	cATTTg/cg	13/30	0.274863214404795	2	FACETS	0.936	0.868	1	0.936	0.868	1	CLONAL	2	TRUE	0	0.279546352629167	2		256	730	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056329	26056329	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001232-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	78	235	0	ENST00000343677.2:c.328A>G	p.Lys110Glu	p.K110E	ENST00000343677	NM_005319.3	110	Aag/Gag	1/1	0.274863214404795	2	FACETS	0.886	0.779	1	0.443	0.389	0.501	CLONAL	1	TRUE	0	0.279546352629167	2		235	630	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0001357-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	2372	411	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.349313629232269	23	FACETS	1	0.994	1			1	CLONAL	21	TRUE	NA	0.349313629232269	23		411	2990	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577098	7577098	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001357-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	115	529	0	ENST00000269305.4:c.840A>T	p.Arg280Ser	p.R280S	ENST00000269305	NM_001126112.2	280	agA/agT	8/11	0.349313629232269	3	FACETS	0.811	0.729	0.897	0.405	0.364	0.449	CLONAL	1	TRUE	1	0.349313629232269	3		529	954	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946306	2946306	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs573740263	NA	P-0001357-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	196	372	0	ENST00000396946.4:c.3431G>T	p.Arg1144Leu	p.R1144L	ENST00000396946	NM_032415.4	1144	cGc/cTc	25/25	0.26230935290796	5	FACETS	1	0.956	1	0.694	0.644	0.747	CLONAL	2	TRUE	2	0.349313629232269	5		372	821	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1555525367	NA	P-0001357-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	229	362	0	ENST00000269305.4:c.783-1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.349313629232269	3	FACETS	0.899	0.839	0.96	0.899	0.839	0.96	CLONAL	2	TRUE	1	0.349313629232269	3		362	857	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117570	70117570	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001357-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	45	352	0	ENST00000245479.2:c.38A>C	p.Glu13Ala	p.E13A	ENST00000245479	NM_000346.3	13	gAg/gCg	1/3	0.349313629232269	3	FACETS	0.416	0.348	0.491	0.208	0.174	0.246	SUBCLONAL	1	TRUE	1	0.349313629232269	3		352	728	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152044	11152044	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001357-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	164	264	0	ENST00000358026.2:c.4328G>T	p.Arg1443Leu	p.R1443L	ENST00000358026	NM_001128849.1	1443	cGg/cTg	31/36	0.322790890720942	2	FACETS	0.894	0.827	0.964	0.894	0.827	0.964	CLONAL	2	TRUE	0	0.349313629232269	2		264	525	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0001785-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	416	739	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.490604685419342	2	FACETS	0.963	0.922	1	0.963	0.922	1	CLONAL	2	TRUE	0	0.489988683174561	2		739	882	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022517	31022517	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001785-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	122	408	0	ENST00000375687.4:c.2002G>T	p.Gly668Cys	p.G668C	ENST00000375687	NM_015338.5	668	Ggt/Tgt	13/13	0.395054412960706	3	FACETS	0.979	0.887	1	0.49	0.443	0.538	CLONAL	1	TRUE	1	0.489988683174561	3		408	633	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175781	24175781	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001785-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	113	767	0	ENST00000263121.7:c.1009G>C	p.Glu337Gln	p.E337Q	ENST00000263121	NM_003073.3	337	Gag/Cag	8/9	0.490604685419342	2	FACETS	0.529	0.475	0.586	0.264	0.237	0.293	SUBCLONAL	1	TRUE	0	0.489988683174561	2		767	872	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0001961-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	219	353	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.498031411097968	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.498031411097968	2		353	415	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0001961-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	101	219	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.498031411097968	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.498031411097968	3		219	229	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0001961-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	54	360	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.498031411097968	3	FACETS	0.833	0.716	0.961	0.417	0.358	0.481	CLONAL	1	TRUE	1	0.498031411097968	3		361	325	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604778	48604778	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767383	NA	P-0001961-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	133	312	0	ENST00000342988.3:c.1600C>T	p.Gln534Ter	p.Q534*	ENST00000342988	NM_005359.5	534	Cag/Tag	12/12	0.463015817151888	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	0	0.498031411097968	2		312	265	SUCCESS
APC	324	MSKCC	GRCh37	5	112175419	112175419	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0001961-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	89	250	0	ENST00000257430.4:c.4128T>A	p.Tyr1376Ter	p.Y1376*	ENST00000257430	NM_000038.5	1376	taT/taA	16/16	0.498031411097968	3	FACETS	0.954	0.861	1	0.954	0.861	1	CLONAL	2	TRUE	1	0.498031411097968	3		250	234	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628326	90628326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147578332	NA	P-0001961-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	107	401	0	ENST00000330062.3:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000330062	NM_002168.2	362	cGg/cAg	9/11	0.473014521515079	3	FACETS	1	0.924	1	0.343	0.309	0.38	CLONAL	1	TRUE	0	0.498031411097968	3		401	521	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78831665	78831665	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001961-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	30	363	1	ENST00000306801.3:c.1474G>T	p.Val492Phe	p.V492F	ENST00000306801	NM_020761.2	492	Gtt/Ttt	13/34	0.498031411097968	3	FACETS	0.329	0.264	0.402	0.164	0.132	0.201	SUBCLONAL	1	TRUE	1	0.498031411097968	3		364	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0002123-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	247	273	2	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.485891723196971	1	FACETS	0.842	0.789	0.895	0.842	0.789	0.895	CLONAL	1	TRUE	0	0.528140212821388	1		275	818	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041698	29041698	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002123-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	188	538	0	ENST00000282397.4:c.121C>A	p.His41Asn	p.H41N	ENST00000282397	NM_002019.4	41	Cac/Aac	2/30	1	2	FACETS	0.812	0.751	0.875	0.812	0.751	0.875	CLONAL	1	TRUE	1	0.528140212821388	2		538	877	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89833611	89833611	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002123-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	119	624	0	ENST00000389301.3:c.2539A>C	p.Lys847Gln	p.K847Q	ENST00000389301	NM_000135.2	847	Aag/Cag	27/43	0.528140212821388	1	FACETS	0.325	0.293	0.36	0.325	0.293	0.36	SUBCLONAL	1	TRUE	0	0.528140212821388	1		624	1020	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174807	56174807	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002131-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	101	330	0	ENST00000399503.3:c.1969del	p.Thr657HisfsTer2	p.T657Hfs*2	ENST00000399503	NM_005921.1	656	Aaa/aa	11/20	0.413134152549335	9	FACETS	1	0.962	1	0.924	0.85	0.996	CLONAL	6	FALSE	2	0.413134152549335	9		330	185	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002221-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	164	145	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.956	0.887	1			1	INDETERMINATE	1	TRUE	NA	0.805571552155871	2		145	426	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0002221-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	351	316	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.927	0.881	0.974	0.927	0.881	0.974	CLONAL	1	TRUE	1	0.805571552155871	2		316	940	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720839	176720839	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002221-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	388	492	0	ENST00000439151.2:c.6470G>A	p.Trp2157Ter	p.W2157*	ENST00000439151	NM_022455.4	2157	tGg/tAg	23/23	1	2	FACETS	0.915	0.871	0.959	0.915	0.871	0.959	CLONAL	1	TRUE	1	0.805571552155871	2		492	1053	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574572	64574572	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0002221-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	450	543	1	ENST00000312049.6:c.825-2A>T		p.X275_splice	ENST00000312049	NM_130799.2	275			0.805571552155871	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.805571552155871	1		544	656	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673161	30673161	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002221-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	431	612	0	ENST00000376406.3:c.3799C>T	p.Gln1267Ter	p.Q1267*	ENST00000376406	NM_014641.2	1267	Cag/Tag	10/15	1	2	FACETS	0.86	0.821	0.9	0.86	0.821	0.9	CLONAL	1	TRUE	1	0.805571552155871	2		612	1244	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056237	26056245	+	inframe_deletion	In_Frame_Del	DEL	CTTCTTGGG	CTTCTTGGG	-	rs749190253	NA	P-0002221-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	138	415	0	ENST00000343677.2:c.412_420del	p.Pro138_Lys140del	p.P138_K140del	ENST00000343677	NM_005319.3	138	CCCAAGAAG/-	1/1	1	2	FACETS	0.306	0.277	0.336	0.306	0.277	0.336	SUBCLONAL	1	TRUE	1	0.805571552155871	2		415	1120	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002647-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	217	145	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.851239713920442	2		145	465	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584663	187584663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002647-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	522	443	0	ENST00000441802.2:c.3370G>A	p.Glu1124Lys	p.E1124K	ENST00000441802	NM_005245.3	1124	Gag/Aag	3/27	0.851239713920442	1	FACETS	0.602	0.578	0.625	0.602	0.578	0.625	SUBCLONAL	1	TRUE	0	0.851239713920442	1		443	1171	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720802	89720802	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002647-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	77	86	0	ENST00000371953.3:c.953T>C	p.Leu318Pro	p.L318P	ENST00000371953	NM_000314.4	318	cTt/cCt	8/9	0.851239713920442	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.851239713920442	1		86	103	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003314	143003314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1451831325	NA	P-0002647-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	256	210	1	ENST00000262992.4:c.2512C>T	p.Arg838Cys	p.R838C	ENST00000262992	NM_001101669.1	838	Cgt/Tgt	23/24	1	2	FACETS	0.798	0.75	0.846	0.798	0.75	0.846	SUBCLONAL	1	TRUE	1	0.851239713920442	2		211	754	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742094	145742094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002647-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	143	150	0	ENST00000428558.2:c.409G>A	p.Ala137Thr	p.A137T	ENST00000428558	NM_004260.3	137	Gca/Aca	5/22	1	2	FACETS	0.923	0.852	0.995	0.923	0.852	0.995	CLONAL	1	TRUE	1	0.851239713920442	2		150	364	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061110	38061110	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002647-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	50	84	0	ENST00000250448.2:c.879C>G	p.Ser293Arg	p.S293R	ENST00000250448	NM_004496.3	293	agC/agG	2/2	1	2	FACETS	0.783	0.679	0.892	0.783	0.679	0.892	SUBCLONAL	1	TRUE	1	0.851239713920442	2		84	150	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0002916-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	48	229	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.335869745374599	2	FACETS	0.842	0.716	0.979	0.421	0.358	0.49	CLONAL	1	TRUE	0	0.380264093829082	2		229	300	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241679	55241681	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	rs397517086	NA	P-0002916-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	264	541	0	ENST00000275493.2:c.2127_2129del	p.Glu709_Thr710delinsAsp	p.E709_T710delinsD	ENST00000275493	NM_005228.3	709	gaAACt/gat	18/28	0.380264093829082	9	FACETS	1	0.987	1			1	CLONAL	2	TRUE	NA	0.380264093829082	9		541	1345	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678409	88678409	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002916-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	51	850	0	ENST00000360948.2:c.1127A>G	p.Tyr376Cys	p.Y376C	ENST00000360948	NM_001012338.2	376	tAt/tGt	9/19	0.335869745374599	2	FACETS	0.428	0.364	0.5	0.214	0.182	0.25	SUBCLONAL	1	TRUE	0	0.380264093829082	2		850	626	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151855982	151855982	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747193976	NA	P-0002916-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	43	641	0	ENST00000262189.6:c.11636A>G	p.Tyr3879Cys	p.Y3879C	ENST00000262189	NM_170606.2	3879	tAc/tGc	44/59	0.308692581121325	5	FACETS	0.442	0.368	0.524	0.147	0.122	0.175	SUBCLONAL	1	TRUE	2	0.380264093829082	5		641	804	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938859	76938859	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002916-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	45	796	0	ENST00000373344.5:c.1889G>T	p.Gly630Val	p.G630V	ENST00000373344	NM_000489.3	630	gGa/gTa	9/35	0.363180122753032	2	FACETS	0.36	0.301	0.424	0.18	0.15	0.212	SUBCLONAL	1	TRUE	0	0.380264093829082	2		796	658	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573999	7573999	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003289-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	646	455	0	ENST00000269305.4:c.1028del	p.Glu343GlyfsTer2	p.E343Gfs*2	ENST00000269305	NM_001126112.2	343	gAg/gg	10/11	0.79313696378177	2	FACETS	0.958	0.936	0.98	0.958	0.936	0.98	CLONAL	2	TRUE	0	0.802382542180154	2		455	840	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937937	36937937	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003289-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	99	473	2	ENST00000361632.4:c.899C>T	p.Ala300Val	p.A300V	ENST00000361632		300	gCc/gTc	7/16	1	2	FACETS	0.26	0.232	0.291	0.26	0.232	0.291	SUBCLONAL	1	TRUE	1	0.802382542180154	2		475	948	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935584	49935584	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003289-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	447	472	0	ENST00000296474.3:c.1780T>A	p.Phe594Ile	p.F594I	ENST00000296474	NM_002447.2	594	Ttc/Atc	5/20	NA	2	FACETS	0.951	0.909	0.993			1	INDETERMINATE	1	TRUE	NA	0.802382542180154	2		472	1172	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443896	49443896	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs763628601	NA	P-0003289-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	247	332	0	ENST00000301067.7:c.3475G>C	p.Glu1159Gln	p.E1159Q	ENST00000301067	NM_003482.3	1159	Gag/Cag	11/54	0.751927283551396	4	FACETS	1	0.977	1	0.274	0.256	0.292	CLONAL	1	TRUE	0	0.802382542180154	4		332	1013	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930687	32930687	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs80358981	NA	P-0003289-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	508	316	0	ENST00000380152.3:c.7558C>T	p.Arg2520Ter	p.R2520*	ENST00000380152		2520	Cga/Tga	15/27	0.79313696378177	2	FACETS	0.98	0.955	1	0.98	0.955	1	CLONAL	2	TRUE	0	0.802382542180154	2		316	646	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130561	29130561	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003289-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1173	314	399	0	ENST00000328354.6:c.149G>C	p.Ser50Thr	p.S50T	ENST00000328354	NM_007194.3	50	aGc/aCc	2/15	0.802382542180154	4	FACETS	0.949	0.893	1	0.316	0.297	0.336	CLONAL	1	TRUE	1	0.802382542180154	4		399	1487	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045186	47045186	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556782204	NA	P-0003289-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	249	356	0	ENST00000377604.3:c.2427G>A	p.Met809Ile	p.M809I	ENST00000377604	NM_001204468.1	809	atG/atA	21/24	NA	2	FACETS	0.816	0.766	0.866			1	INDETERMINATE	1	TRUE	NA	0.802382542180154	2		356	761	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0003752-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	130	375	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.272918589595585	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	0	0.328827394615846	2		377	387	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0003752-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	70	433	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.328827394615846	6	FACETS	0.827	0.72	0.944	0.207	0.18	0.236	CLONAL	1	TRUE	2	0.328827394615846	6		433	853	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0003752-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	366	411	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.328827394615846	6	FACETS	1	0.982	1	1	0.982	1	CLONAL	4	TRUE	2	0.328827394615846	6		411	869	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881462	48881462	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003752-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	115	416	1	ENST00000267163.4:c.184C>T	p.Gln62Ter	p.Q62*	ENST00000267163	NM_000321.2	62	Cag/Tag	2/27	0.328827394615846	4	FACETS	1	0.933	1	0.69	0.626	0.757	CLONAL	2	TRUE	1	0.328827394615846	4		417	449	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475063	40475063	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003752-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	250	635	0	ENST00000264657.5:c.1847A>G	p.Glu616Gly	p.E616G	ENST00000264657	NM_139276.2	616	gAa/gGa	20/24	NA	2	FACETS	0.991	0.931	1			1	INDETERMINATE	2	TRUE	NA	0.328827394615846	2		635	767	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794603	42794603	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003752-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	236	390	0	ENST00000575354.2:c.1683G>C	p.Glu561Asp	p.E561D	ENST00000575354	NM_015125.3	561	gaG/gaC	10/20	0.328827394615846	3	FACETS	0.896	0.842	0.951	1	0.991	1	CLONAL	3	TRUE	1	0.328827394615846	3		390	622	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799185	88799185	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003752-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	59	521	0	ENST00000360948.2:c.200G>T	p.Gly67Val	p.G67V	ENST00000360948	NM_001012338.2	67	gGg/gTg	2/19	0.233441238933174	2	FACETS	0.735	0.634	0.846	0.368	0.317	0.423	SUBCLONAL	1	TRUE	0	0.328827394615846	2		521	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0003822-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	871	641	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.770168603701614	2		642	1100	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0003822-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	155	411	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.39689200735739	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.770168603701614	0		411	533	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937611	76937615	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTT	CTTTT	-	novel	NA	P-0003822-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	410	588	0	ENST00000373344.5:c.3133_3137del	p.Lys1045Ter	p.K1045*	ENST00000373344	NM_000489.3	1045	AAAAGt/t	9/35	0.156775130415478	1	FACETS	0.547	0.521	0.573	0.547	0.521	0.573	INDETERMINATE	1	TRUE	0	0.770168603701614	1		588	1197	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778083	3778083	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003822-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	348	568	0	ENST00000262367.5:c.6965C>T	p.Ser2322Leu	p.S2322L	ENST00000262367	NM_004380.2	2322	tCa/tTa	31/31	0.179940448091082	1	FACETS	0.613	0.582	0.644	0.613	0.582	0.644	INDETERMINATE	1	TRUE	0	0.770168603701614	1		568	907	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367347	50367347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003822-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	122	182	0	ENST00000331340.3:c.154G>A	p.Val52Ile	p.V52I	ENST00000331340	NM_006060.4	52	Gtc/Atc	3/8	1	2	FACETS	0.834	0.761	0.909	0.834	0.761	0.909	CLONAL	1	TRUE	1	0.770168603701614	2		182	380	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913517	NA	P-0003927-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	422	351	0	ENST00000288135.5:c.1676T>G	p.Val559Gly	p.V559G	ENST00000288135	NM_000222.2	559	gTt/gGt	11/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.729053190276756	2		351	1090	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003935-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	47	229	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.76626113632176	4	FACETS	0.568	0.481	0.664	0.284	0.24	0.332	SUBCLONAL	1	TRUE	2	0.841548856206427	4		229	362	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781504	NA	P-0003935-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	458	298	2	ENST00000269305.4:c.314G>T	p.Gly105Val	p.G105V	ENST00000269305	NM_001126112.2	105	gGc/gTc	4/11	0.787628718684494	3	FACETS	0.929	0.906	0.95	0.929	0.906	0.95	CLONAL	3	TRUE	0	0.841548856206427	3		300	555	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263850	133263850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003935-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	116	147	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	0.841548856206427	NA		147	363	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38946624	38946624	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003935-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	770	182	0	ENST00000357387.3:c.4345A>T	p.Asn1449Tyr	p.N1449Y	ENST00000357387	NM_152756.3	1449	Aac/Tac	33/38	0.841548856206427	6	FACETS	0.919	0.898	0.94	0.919	0.898	0.94	CLONAL	5	TRUE	1	0.841548856206427	6		182	1068	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178687	108178687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003935-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	76	77	0	ENST00000278616.4:c.5738T>C	p.Val1913Ala	p.V1913A	ENST00000278616	NM_000051.3	1913	gTg/gCg	38/63	0.841548856206427	3	FACETS	0.705	0.622	0.793	0.352	0.311	0.397	SUBCLONAL	1	TRUE	1	0.841548856206427	3		77	364	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	430210	430210	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003935-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	848	302	0	ENST00000399788.2:c.2492A>T	p.Gln831Leu	p.Q831L	ENST00000399788	NM_001042603.1	831	cAa/cTa	18/28	0.841548856206427	3	FACETS	0.971	0.956	0.986			1	CLONAL	3	TRUE	NA	0.841548856206427	3		302	983	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030378	49030378	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs267603840	NA	P-0003935-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	542	210	0	ENST00000267163.4:c.1853C>A	p.Ser618Ter	p.S618*	ENST00000267163	NM_000321.2	618	tCa/tAa	19/27	0.841548856206427	3	FACETS	0.981	0.962	0.998	0.981	0.962	0.998	CLONAL	3	TRUE	0	0.841548856206427	3		210	622	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755443	39755443	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003935-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	199	307	0	ENST00000288319.7:c.1322C>T	p.Thr441Ile	p.T441I	ENST00000288319	NM_182918.3	441	aCa/aTa	10/10	0.72719018436753	3	FACETS	1	0.962	1	0.525	0.489	0.562	CLONAL	1	TRUE	1	0.841548856206427	3		307	640	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572318	41572318	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003935-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	285	322	0	ENST00000263253.7:c.4847A>T	p.Asp1616Val	p.D1616V	ENST00000263253	NM_001429.3	1616	gAt/gTt	30/31	0.522116158669256	3	FACETS	0.876	0.834	0.919	0.876	0.834	0.919	CLONAL	2	TRUE	1	0.841548856206427	3		322	549	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117799	108117799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202160435	NA	P-0003936-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	51	209	1	ENST00000278616.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000278616	NM_000051.3	337	cGt/cAt	8/63	0.318478980087155	1	FACETS	0.273	0.232	0.32	0.273	0.232	0.32	SUBCLONAL	1	TRUE	0	0.394529125415075	1		210	759	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs760043106	NA	P-0003936-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	266	318	0	ENST00000269305.4:c.584T>A	p.Ile195Asn	p.I195N	ENST00000269305	NM_001126112.2	195	aTc/aAc	6/11	0.369204077775157	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.394529125415075	1		318	886	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843724	156843724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003936-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	135	402	0	ENST00000524377.1:c.1150G>A	p.Glu384Lys	p.E384K	ENST00000524377	NM_002529.3	384	Gag/Aag	8/17	0.319179541062154	2	FACETS	0.598	0.542	0.657	0.299	0.271	0.329	SUBCLONAL	1	TRUE	0	0.394529125415075	2		402	1144	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557388	187557388	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003936-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	60	220	0	ENST00000441802.2:c.3974T>G	p.Ile1325Ser	p.I1325S	ENST00000441802	NM_005245.3	1325	aTt/aGt	6/27	0.394529125415075	1	FACETS	0.564	0.487	0.647	0.564	0.487	0.647	SUBCLONAL	1	TRUE	0	0.394529125415075	1		220	433	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189484	56189484	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003936-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	67	222	0	ENST00000399503.3:c.4516C>T	p.Pro1506Ser	p.P1506S	ENST00000399503	NM_005921.1	1506	Cca/Tca	20/20	0.369204077775157	1	FACETS	0.483	0.419	0.551	0.483	0.419	0.551	SUBCLONAL	1	TRUE	0	0.394529125415075	1		222	565	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112292	115112292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1282046318	NA	P-0003936-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	13	64	0	ENST00000257566.3:c.1448C>T	p.Thr483Met	p.T483M	ENST00000257566	NM_016569.3	483	aCg/aTg	7/8	0.394529125415075	1	FACETS	0.365	0.261	0.49	0.365	0.261	0.49	SUBCLONAL	1	TRUE	0	0.394529125415075	1		64	145	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931463	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622007	NA	P-0003945-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	55	441	326	0	ENST00000374690.3:c.2105T>A	p.Leu702His	p.L702H	ENST00000374690	NM_000044.3	702	cTc/cAc	4/8	1	1	FACETS	0.925	0.906	0.942	1	0.998	1	CLONAL	3	FALSE	0	0.485365197387073	1		326	496	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711879	89711879	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003945-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	76	103	378	0	ENST00000371953.3:c.497T>G	p.Val166Gly	p.V166G	ENST00000371953	NM_000314.4	166	gTa/gGa	6/9	0.464506559080852	0	FACETS	0.61	0.563	0.656			1	SUBCLONAL	2	FALSE	0	0.485365197387073	0		378	179	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0003964-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	321	409	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.347263411164877	5	FACETS	0.891	0.842	0.941	0.891	0.842	0.941	CLONAL	3	TRUE	2	0.347263411164877	5		409	1052	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738230	145738230	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs186739072	NA	P-0003964-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	152	329	0	ENST00000428558.2:c.2755G>A	p.Ala919Thr	p.A919T	ENST00000428558	NM_004260.3	919	Gcc/Acc	16/22	0.347263411164877	5	FACETS	1	0.962	1	0.72	0.661	0.782	CLONAL	2	TRUE	2	0.347263411164877	5		329	616	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022020	5022020	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003964-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	75	489	0	ENST00000381652.3:c.33G>T	p.Met11Ile	p.M11I	ENST00000381652	NM_004972.3	11	atG/atT	3/25	0.312374605257972	3	FACETS	0.697	0.61	0.791	0.349	0.305	0.396	SUBCLONAL	1	TRUE	1	0.347263411164877	3		489	727	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633317	8633317	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003964-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	127	614	0	ENST00000356435.5:c.352G>A	p.Glu118Lys	p.E118K	ENST00000356435		118	Gaa/Aaa	3/35	0.312374605257972	3	FACETS	0.888	0.803	0.977	0.444	0.401	0.489	CLONAL	1	TRUE	1	0.347263411164877	3		614	967	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635188	87635188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003964-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	63	335	0	ENST00000277120.3:c.2240C>T	p.Thr747Met	p.T747M	ENST00000277120		747	aCg/aTg	18/19	0.312374605257972	3	FACETS	0.86	0.745	0.985	0.43	0.372	0.493	CLONAL	1	TRUE	1	0.347263411164877	3		335	495	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210798	133210798	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003964-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	103	616	0	ENST00000320574.5:c.5978A>T	p.Gln1993Leu	p.Q1993L	ENST00000320574	NM_006231.2	1993	cAg/cTg	43/49	0.286282969160086	3	FACETS	0.834	0.746	0.928	0.417	0.373	0.464	CLONAL	1	TRUE	1	0.347263411164877	3		616	835	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602584	10602584	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1208201314	NA	P-0003964-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	127	398	0	ENST00000171111.5:c.994G>T	p.Gly332Cys	p.G332C	ENST00000171111	NM_203500.1	332	Ggc/Tgc	3/6	0.347263411164877	1	FACETS	0.752	0.687	0.818	1	0.987	1	SUBCLONAL	2	TRUE	0	0.347263411164877	1		398	402	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610694	10610694	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003964-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	55	150	0	ENST00000171111.5:c.16A>T	p.Arg6Trp	p.R6W	ENST00000171111	NM_203500.1	6	Agg/Tgg	2/6	0.347263411164877	1	FACETS	0.855	0.748	0.966	1	0.976	1	CLONAL	2	TRUE	0	0.347263411164877	1		150	153	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582044	189582057	+	frameshift_variant	Frame_Shift_Del	DEL	CTACTGCCAAATTG	CTACTGCCAAATTG	-	novel	NA	P-0003964-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	45	386	0	ENST00000264731.3:c.604_617del	p.Tyr202LysfsTer29	p.Y202Kfs*29	ENST00000264731	NM_003722.4	201	ctCTACTGCCAAATTGca/ctca	5/14	0.312374605257972	3	FACETS	0.481	0.403	0.567	0.24	0.201	0.284	SUBCLONAL	1	TRUE	1	0.347263411164877	3		386	633	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577530	7577530	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004023-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	23	318	0	ENST00000269305.4:c.751A>T	p.Ile251Phe	p.I251F	ENST00000269305	NM_001126112.2	251	Atc/Ttc	7/11	0.608544826437173	2	FACETS	0.111	0.086	0.141	0.056	0.043	0.071	SUBCLONAL	1	TRUE	0	0.651828299056036	2		318	633	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0004430-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	523	622	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.631410670900836	4	FACETS	0.856	0.826	0.886	1	0.996	1	CLONAL	3	FALSE	2	0.752833223995377	4		624	948	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0004430-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	286	411	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.263830377989263	5	FACETS	1	0.985	1	0.745	0.704	0.786	INDETERMINATE	2	FALSE	2	0.752833223995377	5		411	724	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132617	11132617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1445478818	NA	P-0004430-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	23	477	0	ENST00000358026.2:c.2833G>A	p.Ala945Thr	p.A945T	ENST00000358026	NM_001128849.1	945	Gca/Aca	19/36	0.178438439114942	3	FACETS	0.227	0.177	0.286	0.114	0.088	0.143	INDETERMINATE	1	FALSE	1	0.752833223995377	3		477	370	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918976	76918977	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0004430-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	185	350	0	ENST00000373344.5:c.4014_4015del	p.His1338GlnfsTer11	p.H1338Qfs*11	ENST00000373344	NM_000489.3	1338	caTAgg/cagg	12/35	0.381789559243507	2	FACETS	1	0.953	1			1	INDETERMINATE	1	FALSE	NA	0.752833223995377	2		350	478	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435603	110435603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004516-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	43	70	0	ENST00000375856.3:c.2798C>T	p.Pro933Leu	p.P933L	ENST00000375856	NM_003749.2	933	cCg/cTg	1/2	0.301852666028924	3	FACETS	0.77	0.653	0.897	0.77	0.653	0.897	SUBCLONAL	2	TRUE	1	0.346572438754512	3		70	189	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0004701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	182	578	0	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	0.361506296072347	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.361506296072347	2		578	477	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260309	16260309	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	62	271	0	ENST00000375759.3:c.7574C>G	p.Ser2525Cys	p.S2525C	ENST00000375759	NM_015001.2	2525	tCt/tGt	11/15	1	2	FACETS	0.896	0.777	1	0.896	0.777	1	CLONAL	1	TRUE	1	0.361506296072347	2		271	383	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105565	27105565	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	98	472	0	ENST00000324856.7:c.5176G>T	p.Glu1726Ter	p.E1726*	ENST00000324856	NM_006015.4	1726	Gag/Tag	20/20	1	2	FACETS	0.927	0.829	1	0.927	0.829	1	CLONAL	1	TRUE	1	0.361506296072347	2		472	585	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551876	150551876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs919674275	NA	P-0004701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	54	244	0	ENST00000369026.2:c.131C>T	p.Ala44Val	p.A44V	ENST00000369026	NM_021960.4	44	gCc/gTc	1/3	0.349006612420595	4	FACETS	0.529	0.451	0.615	0.264	0.225	0.308	SUBCLONAL	1	TRUE	2	0.361506296072347	4		244	769	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524307	176524307	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	198	435	1	ENST00000292408.4:c.2168G>T	p.Arg723Leu	p.R723L	ENST00000292408	NM_213647.1	723	cGt/cTt	17/18	0.361506296072347	3	FACETS	0.891	0.828	0.956	0.891	0.828	0.956	CLONAL	2	TRUE	1	0.361506296072347	3		436	726	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056964	180056964	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	75	452	0	ENST00000261937.6:c.655C>A	p.Pro219Thr	p.P219T	ENST00000261937	NM_182925.4	219	Ccc/Acc	5/30	0.361506296072347	3	FACETS	0.631	0.552	0.716	0.315	0.276	0.358	SUBCLONAL	1	TRUE	1	0.361506296072347	3		452	777	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112035646	112035646	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	130	494	0	ENST00000368678.4:c.248G>T	p.Gly83Val	p.G83V	ENST00000368678		83	gGa/gTa	4/13	0.146106980467665	3	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.361506296072347	3		494	655	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739747	145739747	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0004701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	65	389	0	ENST00000428558.2:c.1705-1G>T		p.X569_splice	ENST00000428558	NM_004260.3	569			0.223811209668556	3	FACETS	0.741	0.643	0.847	0.247	0.214	0.283	SUBCLONAL	1	TRUE	0	0.361506296072347	3		389	573	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156609	2156609	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs868067982	NA	P-0004701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	108	464	0	ENST00000434045.2:c.313G>T	p.Gly105Cys	p.G105C	ENST00000434045	NM_001127598.1	105	Ggc/Tgc	3/5	0.361506296072347	2	FACETS	1	0.944	1	0.535	0.482	0.592	CLONAL	1	TRUE	0	0.361506296072347	2		464	558	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975663	26975663	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	29	482	0	ENST00000381527.3:c.1171C>T	p.Gln391Ter	p.Q391*	ENST00000381527	NM_001260.1	391	Caa/Taa	12/13	0.361506296072347	2	FACETS	0.312	0.249	0.383	0.156	0.124	0.192	SUBCLONAL	1	TRUE	0	0.361506296072347	2		482	515	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954183	32954183	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	42	478	0	ENST00000380152.3:c.9157G>C	p.Glu3053Gln	p.E3053Q	ENST00000380152		3053	Gag/Cag	24/27	0.361506296072347	2	FACETS	0.428	0.357	0.507	0.214	0.178	0.254	SUBCLONAL	1	TRUE	0	0.361506296072347	2		478	543	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457642	67457642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	232	494	0	ENST00000327367.4:c.452C>T	p.Pro151Leu	p.P151L	ENST00000327367	NM_005902.3	151	cCc/cTc	3/9	0.216341629283564	4	FACETS	1	0.985	1			1	INDETERMINATE	2	TRUE	NA	0.361506296072347	4		494	745	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39567846	39567846	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	42	251	0	ENST00000262039.4:c.602T>C	p.Ile201Thr	p.I201T	ENST00000262039	NM_002647.2	201	aTa/aCa	5/25	1	2	FACETS	0.638	0.534	0.753	0.638	0.534	0.753	SUBCLONAL	1	TRUE	1	0.361506296072347	2		251	364	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262096	10262096	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	130	554	0	ENST00000340748.4:c.2195C>G	p.Ser732Cys	p.S732C	ENST00000340748		732	tCt/tGt	23/40	0.361506296072347	2	FACETS	1	0.95	1	0.534	0.485	0.585	CLONAL	1	TRUE	0	0.361506296072347	2		554	674	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938380	76938380	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	158	527	0	ENST00000373344.5:c.2368T>G	p.Phe790Val	p.F790V	ENST00000373344	NM_000489.3	790	Ttt/Gtt	9/35	0.361506296072347	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.361506296072347	1		527	563	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs397518442	NA	P-0004701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	266	437	0	ENST00000326873.7:c.650del	p.Pro217ArgfsTer70	p.P217Rfs*70	ENST00000326873	NM_000455.4	216	tCc/tc	5/10	0.361506296072347	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.361506296072347	2		437	630	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955873	55955873	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	108	462	0	ENST00000263923.4:c.3289del	p.Glu1097LysfsTer5	p.E1097Kfs*5	ENST00000263923	NM_002253.2	1097	Gaa/aa	24/30	0.361506296072347	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.361506296072347	1		462	418	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846094	151846094	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	93	306	0	ENST00000262189.6:c.12918del	p.Ile4307SerfsTer19	p.I4307Sfs*19	ENST00000262189	NM_170606.2	4306	ccC/cc	52/59	0.326528675680871	3	FACETS	1	0.933	1	0.532	0.474	0.594	CLONAL	1	TRUE	1	0.361506296072347	3		306	571	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793598	89793606	+	inframe_deletion	In_Frame_Del	DEL	ACCAAGATC	ACCAAGATC	-	novel	NA	P-0004701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	95	408	0	ENST00000336032.3:c.670_678del	p.Lys224_Thr226del	p.K224_T226del	ENST00000336032	NM_006813.2	223	ACCAAGATC/-	2/2	0.308364387675823	3	FACETS	0.985	0.878	1			1	CLONAL	1	TRUE	NA	0.361506296072347	3		408	630	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332075	81332075	+	splice_acceptor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0004701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	73	295	0	ENST00000222390.5:c.2011-2del		p.X671_splice	ENST00000222390	NM_000601.4	671			0.361506296072347	3	FACETS	1	0.929	1	0.542	0.476	0.613	CLONAL	1	TRUE	1	0.361506296072347	3		295	440	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0004710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	282	409	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.3	3	FACETS	0.872	0.82	0.926	1	0.991	1	CLONAL	3	TRUE	1	0.23	3		409	1045	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0004710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	93	381	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	1	2	FACETS	0.807	0.716	0.905	0.807	0.716	0.905	CLONAL	1	TRUE	1	0.23	2		381	1002	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508268	106508268	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs147631551	NA	P-0004710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	32	188	0	ENST00000359195.3:c.262T>A	p.Tyr88Asn	p.Y88N	ENST00000359195	NM_002649.2	88	Tac/Aac	2/11	1	2	FACETS	0.447	0.361	0.544	0.447	0.361	0.544	SUBCLONAL	1	TRUE	1	0.23	2		188	623	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748074	72748074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	102	535	0	ENST00000357731.5:c.104G>A	p.Gly35Glu	p.G35E	ENST00000357731	NM_173808.2	35	gGa/gAa	1/7	1	2	FACETS	0.692	0.617	0.772	0.692	0.617	0.772	SUBCLONAL	1	TRUE	1	0.23	2		535	1282	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838360	156838360	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	61	449	0	ENST00000524377.1:c.638T>A	p.Leu213Gln	p.L213Q	ENST00000524377	NM_002529.3	213	cTg/cAg	6/17	1	2	FACETS	0.481	0.414	0.556	0.481	0.414	0.556	SUBCLONAL	1	TRUE	1	0.23	2		449	1102	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451770	29451770	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs755261455	NA	P-0004710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	113	427	0	ENST00000389048.3:c.2795G>C	p.Gly932Ala	p.G932A	ENST00000389048	NM_004304.4	932	gGa/gCa	16/29	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.23	2		427	924	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52675969	52675969	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0004710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	108	457	0	ENST00000394830.3:c.1087+1G>T		p.X363_splice	ENST00000394830	NM_018313.4	363			1	2	FACETS	0.787	0.704	0.875	0.787	0.704	0.875	SUBCLONAL	1	TRUE	1	0.23	2		457	1194	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181767	56181767	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	54	224	0	ENST00000399503.3:c.3991G>T	p.Val1331Leu	p.V1331L	ENST00000399503	NM_005921.1	1331	Gtg/Ttg	17/20	1	2	FACETS	0.65	0.554	0.756	0.65	0.554	0.756	SUBCLONAL	1	TRUE	1	0.23	2		224	722	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635133	87635133	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	57	291	0	ENST00000277120.3:c.2185A>T	p.Thr729Ser	p.T729S	ENST00000277120		729	Aca/Tca	18/19	1	2	FACETS	0.771	0.661	0.891	0.771	0.661	0.891	SUBCLONAL	1	TRUE	1	0.23	2		291	643	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413590	32413590	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0004710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	62	259	0	ENST00000332351.3:c.1360A>T	p.Lys454Ter	p.K454*	ENST00000332351	NM_024426.4	454	Aaa/Taa	9/10	1	2	FACETS	0.77	0.664	0.885	0.77	0.664	0.885	SUBCLONAL	1	TRUE	1	0.23	2		259	700	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998393	100998393	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	19	105	0	ENST00000325455.5:c.1409C>A	p.Pro470His	p.P470H	ENST00000325455	NM_001202474.3	470	cCc/cAc	1/8	1	2	FACETS	0.498	0.377	0.639	0.498	0.377	0.639	SUBCLONAL	1	TRUE	1	0.23	2		105	332	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	459905	459905	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	174	479	0	ENST00000399788.2:c.1190T>A	p.Leu397Gln	p.L397Q	ENST00000399788	NM_001042603.1	397	cTg/cAg	10/28	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.23	2		479	1296	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425064	49425064	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1246024040	NA	P-0004710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1209	113	505	1	ENST00000301067.7:c.13424G>T	p.Ser4475Ile	p.S4475I	ENST00000301067	NM_003482.3	4475	aGc/aTc	39/54	1	2	FACETS	0.743	0.667	0.825	0.743	0.667	0.825	SUBCLONAL	1	TRUE	1	0.23	2		506	1322	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597518	28597518	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	134	418	0	ENST00000241453.7:c.2387C>A	p.Ala796Asp	p.A796D	ENST00000241453	NM_004119.2	796	gCc/gAc	19/24	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.23	2		418	1155	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622559	28622559	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs769899577	NA	P-0004710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	65	249	0	ENST00000241453.7:c.1058C>A	p.Thr353Asn	p.T353N	ENST00000241453	NM_004119.2	353	aCc/aAc	9/24	1	2	FACETS	0.931	0.807	1	0.931	0.807	1	CLONAL	1	TRUE	1	0.23	2		249	607	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060796	38060796	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1230	130	594	0	ENST00000250448.2:c.1193A>T	p.His398Leu	p.H398L	ENST00000250448	NM_004496.3	398	cAc/cTc	2/2	1	2	FACETS	0.831	0.751	0.916	0.831	0.751	0.916	CLONAL	1	TRUE	1	0.23	2		594	1360	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420351	88420351	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	25	156	0	ENST00000360948.2:c.2335G>T	p.Val779Phe	p.V779F	ENST00000360948	NM_001012338.2	779	Gtc/Ttc	19/19	1	2	FACETS	0.491	0.386	0.612	0.491	0.386	0.612	SUBCLONAL	1	TRUE	1	0.23	2		156	443	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45873464	45873464	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs748033766	NA	P-0004710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	76	367	0	ENST00000391945.4:c.32A>G	p.Tyr11Cys	p.Y11C	ENST00000391945	NM_000400.3	11	tAc/tGc	2/23	1	2	FACETS	0.676	0.591	0.767	0.676	0.591	0.767	SUBCLONAL	1	TRUE	1	0.23	2		367	978	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36024605	36024605	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	55	445	0	ENST00000358208.4:c.594G>T	p.Lys198Asn	p.K198N	ENST00000358208		198	aaG/aaT	6/12	1	2	FACETS	0.44	0.374	0.511	0.44	0.374	0.511	SUBCLONAL	1	TRUE	1	0.23	2		445	1088	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944436	40944436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	118	486	0	ENST00000373198.4:c.2066G>A	p.Gly689Asp	p.G689D	ENST00000373198	NM_133170.3	689	gGc/gAc	12/32	1	2	FACETS	0.816	0.734	0.903	0.816	0.734	0.903	CLONAL	1	TRUE	1	0.23	2		486	1258	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41525923	41525923	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	112	348	0	ENST00000263253.7:c.1198A>T	p.Ile400Phe	p.I400F	ENST00000263253	NM_001429.3	400	Att/Ttt	5/31	1	2	FACETS	0.873	0.783	0.968	0.873	0.783	0.968	CLONAL	1	TRUE	1	0.23	2		348	1116	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228252	53228252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1191	77	540	0	ENST00000375401.3:c.2150C>T	p.Ser717Leu	p.S717L	ENST00000375401	NM_004187.3	717	tCa/tTa	15/26	0.288841050657185	1	FACETS	0.467	0.409	0.531	0.467	0.409	0.531	SUBCLONAL	1	TRUE	0	0.23	1		540	1268	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0004727-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	39	412	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		412	864	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004762-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	20	407	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.221	0.169	0.282	0.221	0.169	0.282	SUBCLONAL	1	TRUE	1	0.69	2		407	262	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0004762-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	100	219	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.69	2		219	211	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0004762-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	110	233	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.993	0.904	1	0.993	0.904	1	CLONAL	1	TRUE	1	0.69	2		233	321	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0004762-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	117	166	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.829	0.754	0.907	0.829	0.754	0.907	CLONAL	1	TRUE	1	0.69	2		166	409	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182709	38182709	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370623345	NA	P-0004762-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	87	511	0	ENST00000396334.3:c.862G>A	p.Asp288Asn	p.D288N	ENST00000396334	NM_002468.4	288	Gac/Aac	5/5	1	2	FACETS	0.894	0.802	0.99	0.894	0.802	0.99	CLONAL	1	TRUE	1	0.69	2		511	282	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732894	44732894	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004762-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	199	228	0	ENST00000377967.4:c.97G>T	p.Glu33Ter	p.E33*	ENST00000377967	NM_021140.2	33	Gag/Tag	1/29	1	1	FACETS		NA	1	1	0.995	1	NA	2	TRUE	0	0.69	1		228	238	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741972	162741972	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	895	428	1	ENST00000367921.3:c.1663G>T	p.Val555Leu	p.V555L	ENST00000367921	NM_006182.2	555	Gtg/Ttg	13/18	0.738723038608722	3	FACETS	0.925	0.899	0.952	0.925	0.899	0.952	CLONAL	2	NA	1	0.738723038608722	3		429	1793	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200425	138200425	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0121432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	279	264	0	ENST00000237289.4:c.1843T>G	p.Phe615Val	p.F615V	ENST00000237289	NM_001270507.1	615	Ttt/Gtt	7/9	0.727589548251337	1	FACETS	0.876	0.832	0.919	0.876	0.832	0.919	CLONAL	1	NA	0	0.738723038608722	1		264	544	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042006	14042006	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	332	364	0	ENST00000311895.7:c.2553C>A	p.Phe851Leu	p.F851L	ENST00000311895	NM_005236.2	851	ttC/ttA	11/11	0.18086396302401	4	FACETS	0.802	0.76	0.845	0.401	0.38	0.423	INDETERMINATE	2	NA	0	0.738723038608722	4		364	974	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775765	9775765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004779-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	53	378	0	ENST00000377346.4:c.308C>T	p.Ala103Val	p.A103V	ENST00000377346	NM_005026.3	103	gCc/gTc	4/24	NA	2	FACETS	0.663	0.564	0.772			1	INDETERMINATE	1	TRUE	NA	0.195878915718409	2		378	816	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024187	112024187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004779-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	59	566	0	ENST00000368678.4:c.598G>A	p.Val200Ile	p.V200I	ENST00000368678		200	Gtc/Atc	7/13	1	2	FACETS	0.675	0.579	0.78	0.675	0.579	0.78	SUBCLONAL	1	TRUE	1	0.195878915718409	2		566	893	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870787	12870787	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004779-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	35	153	0	ENST00000228872.4:c.14G>T	p.Arg5Leu	p.R5L	ENST00000228872	NM_004064.3	5	cGa/cTa	1/3	0.195878915718409	8	FACETS	1	0.908	1			1	CLONAL	1	TRUE	NA	0.195878915718409	8		153	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1131691023	NA	P-0004779-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	116	447	2	ENST00000269305.4:c.470T>C	p.Val157Ala	p.V157A	ENST00000269305	NM_001126112.2	157	gTc/gCc	5/11	1	2	FACETS	0.785	0.708	0.867	1	0.985	1	SUBCLONAL	2	TRUE	1	0.195878915718409	2		449	754	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0004789-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	118	412	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	0.85	0.768	0.936			1	INDETERMINATE	1	TRUE	NA	0.420689366474275	2		412	660	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0004789-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	127	375	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.420689366474275	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.420689366474275	1		377	463	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0004789-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	128	284	1	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	0.420689366474275	1	FACETS	0.905	0.824	0.989	0.905	0.824	0.989	CLONAL	1	TRUE	0	0.420689366474275	1		285	531	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951101	48951171	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TATAGGATACATCTTTAAAGAGAAATTTGCTAAAGCTGTGGGACAGGGTTGTGTCGAAATTGGATCACAGG	TATAGGATACATCTTTAAAGAGAAATTTGCTAAAGCTGTGGGACAGGGTTGTGTCGAAATTGGATCACAGG	-	novel	NA	P-0004789-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	174	368	0	ENST00000267163.4:c.1265_1332+3del		p.X422_splice	ENST00000267163	NM_000321.2	422		13/27	0.420689366474275	3	FACETS	0.81	0.749	0.873	0.54	0.499	0.582	CLONAL	2	TRUE	0	0.420689366474275	3		368	618	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106253	27106271	+	frameshift_variant	Frame_Shift_Del	DEL	TAGAGGACGAACCCCACAG	TAGAGGACGAACCCCACAG	-	novel	NA	P-0004789-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	130	398	1	ENST00000324856.7:c.5866_5884del	p.Glu1956ArgfsTer53	p.E1956Rfs*53	ENST00000324856	NM_006015.4	1955	cTAGAGGACGAACCCCACAGt/ct	20/20	1	2	FACETS	0.908	0.825	0.994	0.908	0.825	0.994	CLONAL	1	TRUE	1	0.420689366474275	2		399	681	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0004798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	180	316	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.252770590214012	3	FACETS	0.958	0.89	1	0.958	0.89	1	CLONAL	3	TRUE	0	0.26797831278952	3		316	530	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0004798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	105	476	2	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.26797831278952	2	FACETS	0.755	0.679	0.835	0.755	0.679	0.835	SUBCLONAL	2	TRUE	0	0.26797831278952	2		478	519	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0004798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	129	400	0	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	0.926	0.844	1	1	0.989	1	CLONAL	2	TRUE	1	0.26797831278952	2		400	520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0004798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	159	502	1	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.26797831278952	2		503	888	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174416	11174416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	125	603	0	ENST00000361445.4:c.7259C>T	p.Ala2420Val	p.A2420V	ENST00000361445	NM_004958.3	2420	gCc/gTc	53/58	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.26797831278952	2		603	911	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736188	204736188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	36	494	0	ENST00000302823.3:c.545C>T	p.Thr182Ile	p.T182I	ENST00000302823	NM_005214.4	182	aCa/aTa	3/4	0.261293117770975	3	FACETS	0.44	0.361	0.53	0.147	0.12	0.177	SUBCLONAL	1	TRUE	0	0.26797831278952	3		494	692	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535435	66535435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	39	129	1	ENST00000273854.3:c.26C>T	p.Ala9Val	p.A9V	ENST00000273854	NM_004439.5	9	gCg/gTg	1/18	1	2	FACETS	0.832	0.699	0.976	1	0.963	1	CLONAL	2	TRUE	1	0.26797831278952	2		130	175	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528897	157528897	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	82	447	0	ENST00000346085.5:c.6622G>A	p.Val2208Met	p.V2208M	ENST00000346085	NM_020732.3	2208	Gtg/Atg	20/20	0.145712770392731	3	FACETS	0.934	0.823	1	0.467	0.411	0.527	INDETERMINATE	1	TRUE	1	0.26797831278952	3		447	743	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196798	108196798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	26	365	0	ENST00000278616.4:c.6821C>T	p.Ala2274Val	p.A2274V	ENST00000278616	NM_000051.3	2274	gCa/gTa	47/63	1	2	FACETS	0.545	0.432	0.675	0.545	0.432	0.675	SUBCLONAL	1	TRUE	1	0.26797831278952	2		365	356	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211778	5211778	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs370553812	NA	P-0004798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	89	467	0	ENST00000357368.4:c.5057G>A	p.Arg1686Gln	p.R1686Q	ENST00000357368	NM_002850.3	1686	cGg/cAg	33/38	1	2	FACETS	0.958	0.85	1	0.958	0.85	1	CLONAL	1	TRUE	1	0.26797831278952	2		467	693	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933299	39933309	+	frameshift_variant	Frame_Shift_Del	DEL	TGGTAACGGTC	TGGTAACGGTC	-	novel	NA	P-0004798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	207	364	0	ENST00000378444.4:c.1290_1300del	p.Thr431ArgfsTer5	p.T431Rfs*5	ENST00000378444	NM_001123385.1	430	caGACCGTTACCAaa/caaa	4/15	0.160479272372506	2	FACETS	0.853	0.796	0.91			1	INDETERMINATE	3	TRUE	NA	0.26797831278952	2		364	604	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0004801-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	69	412	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.178310771578681	2	FACETS	1	0.887	1	0.511	0.444	0.583	CLONAL	1	TRUE	0	0.18796713326362	2		412	719	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0004801-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	193	455	0	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	0.178310771578681	2	FACETS	0.869	0.802	0.938	0.869	0.802	0.938	CLONAL	2	TRUE	0	0.18796713326362	2		455	1182	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403185	213403185	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004801-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	44	287	0	ENST00000342788.4:c.70G>A	p.Asp24Asn	p.D24N	ENST00000342788	NM_005235.2	24	Gat/Aat	1/28	0.18796713326362	3	FACETS	0.786	0.657	0.928	0.393	0.328	0.464	CLONAL	1	TRUE	1	0.18796713326362	3		287	652	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856015	45856015	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144511865	NA	P-0004801-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	123	337	0	ENST00000391945.4:c.1891C>T	p.Arg631Cys	p.R631C	ENST00000391945	NM_000400.3	631	Cgc/Tgc	20/23	0.18796713326362	3	FACETS	0.807	0.729	0.889	0.807	0.729	0.889	CLONAL	2	TRUE	1	0.18796713326362	3		337	887	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795407	39795407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371043321	NA	P-0004801-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	86	417	1	ENST00000288319.7:c.313G>A	p.Gly105Ser	p.G105S	ENST00000288319	NM_182918.3	105	Ggc/Agc	3/10	0.18796713326362	3	FACETS	0.928	0.818	1	0.309	0.272	0.349	CLONAL	1	TRUE	0	0.18796713326362	3		418	1079	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363770	118363775	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGGCTG	AGGCTG	-	novel	NA	P-0004801-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	56	247	0	ENST00000534358.1:c.5005-2_5008del		p.X1669_splice	ENST00000534358	NM_005933.3	1669		16/36	0.18796713326362	3	FACETS	0.894	0.765	1	0.447	0.382	0.518	CLONAL	1	TRUE	1	0.18796713326362	3		247	729	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912329	29912345	+	frameshift_variant	Frame_Shift_Del	DEL	TCTCCTTGGAGCTGTGA	TCTCCTTGGAGCTGTGA	-	novel	NA	P-0004801-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	113	393	0	ENST00000376809.5:c.950_966del	p.Leu317HisfsTer17	p.L317Hfs*17	ENST00000376809	NM_002116.7	316	gtTCTCCTTGGAGCTGTGAtc/gttc	5/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.18796713326362	2		393	869	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0004809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	60	538	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.717	0.616	0.826	0.717	0.616	0.826	SUBCLONAL	1	TRUE	1	0.22	2		538	761	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0004809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	64	303	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.3	2	FACETS	1	0.961	1			1	CLONAL	1	TRUE	NA	0.22	2		303	449	SUCCESS
APC	324	MSKCC	GRCh37	5	112175621	112175621	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	93	338	0	ENST00000257430.4:c.4330C>T	p.Gln1444Ter	p.Q1444*	ENST00000257430	NM_000038.5	1444	Caa/Taa	16/16	0.166253659242165	3	FACETS	1	0.972	1	0.652	0.579	0.729	CLONAL	1	TRUE	1	0.22	3		338	720	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0004809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	54	179	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	0.166253659242165	3	FACETS	0.734	0.626	0.854	0.367	0.313	0.427	SUBCLONAL	1	TRUE	1	0.22	3		179	742	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416139	29416139	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	36	281	0	ENST00000389048.3:c.4814A>T	p.Glu1605Val	p.E1605V	ENST00000389048	NM_004304.4	1605	gAg/gTg	29/29	1	2	FACETS	0.647	0.531	0.777	0.647	0.531	0.777	SUBCLONAL	1	TRUE	1	0.22	2		281	506	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488760	212488760	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	42	237	0	ENST00000342788.4:c.2089C>A	p.Pro697Thr	p.P697T	ENST00000342788	NM_005235.2	697	Cca/Aca	18/28	1	2	FACETS	0.794	0.663	0.939	0.794	0.663	0.939	CLONAL	1	TRUE	1	0.22	2		237	481	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713744	30713744	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs104893814	NA	P-0004809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	109	212	0	ENST00000295754.5:c.1069G>T	p.Gly357Trp	p.G357W	ENST00000295754	NM_003242.5	357	Ggg/Tgg	4/7	1	2	FACETS	0.865	0.779	0.955	1	0.986	1	CLONAL	2	TRUE	1	0.22	2		212	573	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136031	64136031	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	38	207	0	ENST00000334205.4:c.1292G>C	p.Arg431Pro	p.R431P	ENST00000334205	NM_003942.2	431	cGc/cCc	11/17	1	2	FACETS	0.909	0.753	1	0.909	0.753	1	CLONAL	1	TRUE	1	0.22	2		207	380	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562219	21562219	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	42	324	0	ENST00000382592.4:c.1700G>T	p.Gly567Val	p.G567V	ENST00000382592	NM_014572.2	567	gGa/gTa	4/8	0.3	2	FACETS	0.495	0.412	0.587			1	SUBCLONAL	1	TRUE	NA	0.22	2		324	772	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029218	14029218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41557814	NA	P-0004809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	65	316	0	ENST00000311895.7:c.1429C>T	p.Arg477Trp	p.R477W	ENST00000311895	NM_005236.2	477	Cgg/Tgg	8/11	1	2	FACETS	0.703	0.608	0.806	0.703	0.608	0.806	SUBCLONAL	1	TRUE	1	0.22	2		316	841	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696410	47696410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	59	309	0	ENST00000347630.2:c.413G>A	p.Arg138His	p.R138H	ENST00000347630	NM_001007230.1	138	cGt/cAt	6/11	1	2	FACETS	0.854	0.734	0.985	0.854	0.734	0.985	CLONAL	1	TRUE	1	0.22	2		309	628	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091862	29091862	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1060502716	NA	P-0004809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	11	46	0	ENST00000328354.6:c.1096-1G>T		p.X366_splice	ENST00000328354	NM_007194.3	366			0.0810983429577531	0	FACETS	0.857	0.599	1			1	INDETERMINATE	1	TRUE	0	0.22	0		46	91	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410021	63410021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1258291174	NA	P-0004809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	42	206	1	ENST00000330258.3:c.3146G>A	p.Arg1049Gln	p.R1049Q	ENST00000330258	NM_152424.3	1049	cGa/cAa	2/2	1	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.22	1		207	294	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411828	63411837	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGATAAGA	CAGGATAAGA	-	novel	NA	P-0004809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	56	196	0	ENST00000330258.3:c.1330_1339del	p.Ser444AlafsTer2	p.S444Afs*2	ENST00000330258	NM_152424.3	444	TCTTATCCTGgc/gc	2/2	1	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.22	1		196	324	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427819	72428218	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTAAGTAAGTTATGGATCAAAAACAGCTTCTGGCAGAATATCATCAATACGCACAAGACTTCATGACACTGTGGCAATGAATCCGAACTGCCTACCACACATGCCAAAGCCGACTACAGAGTGTGCTACTCAGTTTTAGCAATAATCCAACAAGCACGGATAGCAAAGCTTGGGACCAATGTAAAATTACTATTATCTGTTTCCTGTTCTGGCCACAGTATTTAAAAAAGAGAAAAAGTCACCAGCCCCACCCATACTTAGCTCTTCACCTTCTTAGCCTACAAACCCAAGGCACAAAACCACCCTGGATTCATGATTACGATTAAGTAAATCAGAGCAGTGATTTAGTATGTCATTCTAGTTTCCAAGTACCTTGAGGTGTGATTTGTTTCGCTGGTCT	TTAAGTAAGTTATGGATCAAAAACAGCTTCTGGCAGAATATCATCAATACGCACAAGACTTCATGACACTGTGGCAATGAATCCGAACTGCCTACCACACATGCCAAAGCCGACTACAGAGTGTGCTACTCAGTTTTAGCAATAATCCAACAAGCACGGATAGCAAAGCTTGGGACCAATGTAAAATTACTATTATCTGTTTCCTGTTCTGGCCACAGTATTTAAAAAAGAGAAAAAGTCACCAGCCCCACCCATACTTAGCTCTTCACCTTCTTAGCCTACAAACCCAAGGCACAAAACCACCCTGGATTCATGATTACGATTAAGTAAATCAGAGCAGTGATTTAGTATGTCATTCTAGTTTCCAAGTACCTTGAGGTGTGATTTGTTTCGCTGGTCT	-	novel	NA	P-0004826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	50	115	0	ENST00000477973.2:c.672_700-31del		p.X224_splice	ENST00000477973	NM_012234.5	224		3/4	1	2	FACETS	0.908	0.781	1	0.908	0.781	1	CLONAL	1	TRUE	1	0.553322177675002	2		115	199	SUCCESS
APC	324	MSKCC	GRCh37	5	112175847	112175848	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0004826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	134	335	0	ENST00000257430.4:c.4556_4557del	p.Asp1519GlyfsTer13	p.D1519Gfs*13	ENST00000257430	NM_000038.5	1519	gAT/g	16/16	0.553322177675002	1	FACETS	0.855	0.784	0.927	0.855	0.784	0.927	CLONAL	1	TRUE	0	0.553322177675002	1		335	410	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835956	151835963	+	protein_altering_variant	In_Frame_Del	DEL	CACACAAT	CACACAAT	AC	novel	NA	P-0004826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	39	433	0	ENST00000262189.6:c.14561_14568delinsGT	p.Asn4854_Val4856delinsSer	p.N4854_V4856delinsS	ENST00000262189	NM_170606.2	4854	aATTGTGTG/aGT	58/59	1	2	FACETS	0.187	0.154	0.224	0.187	0.154	0.224	SUBCLONAL	1	TRUE	1	0.553322177675002	2		433	753	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0004845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	249	375	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.378906718873054	2	FACETS	0.979	0.928	1	0.979	0.928	1	CLONAL	2	FALSE	0	0.527480212993961	2		377	482	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0004845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	259	396	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	0.472698222123036	4	FACETS	0.912	0.857	0.969	0.912	0.857	0.969	CLONAL	2	FALSE	2	0.527480212993961	4		396	822	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0004845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	142	437	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.527480212993961	4	FACETS	1	0.958	1	0.542	0.494	0.592	CLONAL	1	FALSE	2	0.527480212993961	4		437	759	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0004845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	322	596	1	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.472698222123036	4	FACETS	0.959	0.908	1	0.959	0.908	1	CLONAL	2	FALSE	2	0.527480212993961	4		597	972	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480376	89480376	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	132	421	0	ENST00000336596.2:c.2213C>A	p.Ser738Ter	p.S738*	ENST00000336596	NM_005233.5	738	tCa/tAa	13/17	0.514668984148883	3	FACETS	0.895	0.813	0.98	0.447	0.406	0.49	CLONAL	1	FALSE	1	0.527480212993961	3		421	707	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589596	67589617	+	protein_altering_variant	In_Frame_Del	DEL	CACTCAGTTTCAAGAAAAAAGT	CACTCAGTTTCAAGAAAAAAGT	A	novel	NA	P-0004845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	217	374	0	ENST00000274335.5:c.1359_1380delinsA	p.Asn453_Ser460delinsLys	p.N453_S460delinsK	ENST00000274335		453	aaCACTCAGTTTCAAGAAAAAAGT/aaA	10/15	0.472698222123036	4	FACETS	1	0.991	1	0.739	0.689	0.792	CLONAL	1	FALSE	2	0.527480212993961	4		374	850	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166356	7166356	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762498057	NA	P-0004854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	348	399	0	ENST00000302850.5:c.1670C>T	p.Thr557Met	p.T557M	ENST00000302850	NM_000208.2	557	aCg/aTg	8/22	0.377334699414742	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.427409359688842	3		399	945	SUCCESS
AR	367	MSKCC	GRCh37	X	66941796	66941796	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	114	518	0	ENST00000374690.3:c.2440T>G	p.Phe814Val	p.F814V	ENST00000374690	NM_000044.3	814	Ttc/Gtc	6/8	0.427409359688842	1	FACETS	0.592	0.533	0.653	0.592	0.533	0.653	SUBCLONAL	1	TRUE	0	0.427409359688842	1		518	709	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044500	12044500	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367662793	NA	P-0121477-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	217	413	0	ENST00000353533.5:c.1123G>A	p.Val375Ile	p.V375I	ENST00000353533	NM_003010.3	375	Gtt/Att	11/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	NA	1	0.623414670874465	2		413	574	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817803	3817803	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0121477-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	292	534	0	ENST00000262367.5:c.3168del	p.Val1057Ter	p.V1057*	ENST00000262367	NM_004380.2	1056	aaA/aa	16/31	1	2	FACETS	0.968	0.912	1	0.968	0.912	1	CLONAL	1	NA	1	0.623414670874465	2		534	968	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903731	41903731	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	256	311	0	ENST00000372991.4:c.826C>T	p.Gln276Ter	p.Q276*	ENST00000372991	NM_001760.3	276	Caa/Taa	5/5	0.810137194315165	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.810137194315165	1		311	334	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575035	64575035	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886039416	NA	P-0004885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	182	234	0	ENST00000312049.6:c.772C>T	p.Gln258Ter	p.Q258*	ENST00000312049	NM_130799.2	258	Cag/Tag	4/10	0.810137194315165	1	FACETS	0.994	0.943	1	0.994	0.943	1	CLONAL	1	TRUE	0	0.810137194315165	1		234	269	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120523	2120523	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45517199	NA	P-0004885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	478	370	0	ENST00000219476.3:c.1783C>T	p.Gln595Ter	p.Q595*	ENST00000219476	NM_000548.3	595	Cag/Tag	17/42	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.810137194315165	2		370	570	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786748	3786748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	504	327	0	ENST00000262367.5:c.4463C>T	p.Pro1488Leu	p.P1488L	ENST00000262367	NM_004380.2	1488	cCa/cTa	27/31	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.810137194315165	2		327	596	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944333	76944336	+	frameshift_variant	Frame_Shift_Del	DEL	GAAG	GAAG	-	novel	NA	P-0004885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	222	150	0	ENST00000373344.5:c.569_572del	p.Pro190HisfsTer15	p.P190Hfs*15	ENST00000373344	NM_000489.3	190	cCTTCa/ca	7/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.810137194315165	1		150	264	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0004889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	429	739	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.470151189323126	3	FACETS	0.891	0.855	0.927			1	CLONAL	3	TRUE	NA	0.470151189323126	3		739	843	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483305	120483305	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	60	689	0	ENST00000256646.2:c.3056G>C	p.Gly1019Ala	p.G1019A	ENST00000256646	NM_024408.3	1019	gGa/gCa	19/34	0.470151189323126	5	FACETS	0.459	0.394	0.53	0.153	0.131	0.177	SUBCLONAL	1	TRUE	2	0.470151189323126	5		689	949	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166770	32166770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs947409717	NA	P-0004889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	44	704	0	ENST00000375023.3:c.4468C>T	p.Arg1490Trp	p.R1490W	ENST00000375023	NM_004557.3	1490	Cgg/Tgg	24/30	0.261206126241561	5	FACETS	0.405	0.338	0.479	0.135	0.112	0.16	INDETERMINATE	1	TRUE	2	0.470151189323126	5		704	789	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500582	99500582	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	151	567	0	ENST00000268035.6:c.4015A>T	p.Ser1339Cys	p.S1339C	ENST00000268035	NM_000875.3	1339	Agc/Tgc	21/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.470151189323126	2		567	609	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277247	41277253	+	frameshift_variant	Frame_Shift_Del	DEL	TTGTACC	TTGTACC	-	novel	NA	P-0004889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	104	529	0	ENST00000349496.5:c.1716_1722del	p.Cys573GlufsTer6	p.C573Efs*6	ENST00000349496	NM_001904.3	572	ggTTGTACC/gg	11/15	0.416004485860864	3	FACETS	0.897	0.805	0.995	0.449	0.402	0.498	CLONAL	1	TRUE	1	0.470151189323126	3		529	609	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023151	27023179	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	-	novel	NA	P-0004898-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	88	72	0	ENST00000324856.7:c.267_295del	p.Ser90ProfsTer11	p.S90Pfs*11	ENST00000324856	NM_006015.4	86	gGCGGAGCCGGCAGCGGCGGCGGGCCCGGC/g	1/20	1	2	FACETS	0.911	0.828	0.994	1	0.989	1	CLONAL	3	TRUE	1	0.35	2		72	184	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405954	49405954	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004898-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	380	710	1	ENST00000418115.1:c.184G>A	p.Gly62Arg	p.G62R	ENST00000418115	NM_001664.2	62	Ggg/Agg	3/5	0.294632940569669	2	FACETS	0.885	0.84	0.93	0.885	0.84	0.93	CLONAL	2	TRUE	0	0.35	2		711	1227	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173733	108173733	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004898-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	91	428	0	ENST00000278616.4:c.5473C>T	p.Gln1825Ter	p.Q1825*	ENST00000278616	NM_000051.3	1825	Caa/Taa	36/63	1	2	FACETS	0.821	0.73	0.919	0.821	0.73	0.919	CLONAL	1	TRUE	1	0.35	2		428	633	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061412	38061412	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1310740071	NA	P-0004898-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	140	478	0	ENST00000250448.2:c.577C>G	p.Leu193Val	p.L193V	ENST00000250448	NM_004496.3	193	Ctg/Gtg	2/2	0.297907550715249	1	FACETS	0.99	0.903	1	0.99	0.903	1	CLONAL	1	TRUE	0	0.35	1		478	667	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849541	68849541	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004898-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	174	742	1	ENST00000261769.5:c.1444G>T	p.Glu482Ter	p.E482*	ENST00000261769	NM_004360.3	482	Gaa/Taa	10/16	0.297917190682572	1	FACETS	0.863	0.795	0.935	0.863	0.795	0.935	CLONAL	1	TRUE	0	0.35	1		743	950	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2208950	2208950	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1243763226	NA	P-0004898-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	378	662	0	ENST00000398665.3:c.980C>G	p.Ser327Cys	p.S327C	ENST00000398665	NM_032482.2	327	tCt/tGt	12/28	0.297917190682572	3	FACETS	0.998	0.948	1	0.998	0.948	1	CLONAL	2	TRUE	1	0.35	3		662	1271	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39763587	39763587	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004898-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	130	533	0	ENST00000288319.7:c.865C>T	p.Gln289Ter	p.Q289*	ENST00000288319	NM_182918.3	289	Cag/Tag	8/10	1	2	FACETS	0.906	0.822	0.994	0.906	0.822	0.994	CLONAL	1	TRUE	1	0.35	2		533	820	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0004907-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	85	595	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.909	0.802	1	0.909	0.802	1	CLONAL	1	FALSE	1	0.228930623621304	2		595	817	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0004907-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	63	166	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.864	0.747	0.991	0.864	0.747	0.991	CLONAL	1	FALSE	1	0.228930623621304	2		166	637	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41525969	41525969	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004907-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	50	229	1	ENST00000263253.7:c.1244T>C	p.Leu415Pro	p.L415P	ENST00000263253	NM_001429.3	415	cTc/cCc	5/31	0.172883478626833	3	FACETS	0.947	0.804	1	0.474	0.402	0.552	CLONAL	1	FALSE	1	0.228930623621304	3		230	514	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213863	66213863	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004907-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	28	292	0	ENST00000273854.3:c.2567C>T	p.Thr856Ile	p.T856I	ENST00000273854	NM_004439.5	856	aCt/aTt	15/18	0.228930623621304	0	FACETS	0.783	0.628	0.957			1	CLONAL	1	FALSE	0	0.228930623621304	0		292	241	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969323	44969323	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0004907-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	40	260	0	ENST00000377967.4:c.4006-1G>A		p.X1336_splice	ENST00000377967	NM_021140.2	1336			0.19672272756928	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	FALSE	0	0.228930623621304	1		260	263	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039436	47039436	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004907-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	79	252	0	ENST00000377604.3:c.1059C>G	p.Ile353Met	p.I353M	ENST00000377604	NM_001204468.1	353	atC/atG	10/24	0.19672272756928	1	FACETS	0.609	0.534	0.69	0.609	0.534	0.69	SUBCLONAL	1	FALSE	0	0.228930623621304	1		252	1004	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	135	145	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		145	201	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	169	145	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		145	432	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0004940-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	149	401	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.502852550656905	2	FACETS	1	0.987	1	0.676	0.625	0.727	CLONAL	1	TRUE	0	0.602580218250503	2		401	366	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0004940-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	113	455	0	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	0.602580218250503	1	FACETS	0.695	0.631	0.761	0.695	0.631	0.761	SUBCLONAL	1	TRUE	0	0.602580218250503	1		455	377	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436320	52436327	+	frameshift_variant	Frame_Shift_Del	DEL	TTGTAGGG	TTGTAGGG	-	novel	NA	P-0004940-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	199	560	0	ENST00000460680.1:c.2167_2174del	p.Pro723GlyfsTer38	p.P723Gfs*38	ENST00000460680	NM_004656.3	723	CCCTACAAg/g	17/17	0.187217988428348	2	FACETS	0.746	0.692	0.803	0.373	0.346	0.402	INDETERMINATE	1	TRUE	0	0.602580218250503	2		560	885	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0004958-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	400	551	1	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.36470168659818	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.36470168659818	2		552	1079	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188854	32188854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1183058401	NA	P-0004958-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	339	573	1	ENST00000375023.3:c.700C>T	p.Arg234Trp	p.R234W	ENST00000375023	NM_004557.3	234	Cgg/Tgg	4/30	0.342384732733094	3	FACETS	0.982	0.93	1	0.982	0.93	1	CLONAL	2	TRUE	1	0.36470168659818	3		574	1119	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444125	49444130	+	inframe_deletion	In_Frame_Del	DEL	TTCAGG	TTCAGG	-	novel	NA	P-0004958-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	140	659	0	ENST00000301067.7:c.3241_3246del	p.Pro1081_Glu1082del	p.P1081_E1082del	ENST00000301067	NM_003482.3	1081	CCTGAA/-	11/54	0.362532107106579	3	FACETS	0.76	0.69	0.833	0.38	0.345	0.417	SUBCLONAL	1	TRUE	1	0.36470168659818	3		659	1195	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346485	89346485	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004958-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	90	894	0	ENST00000301030.4:c.6465del	p.Val2156TrpfsTer19	p.V2156Wfs*19	ENST00000301030	NM_001256183.1	2155	ccC/cc	9/13	0.217373797608096	2	FACETS	0.399	0.353	0.449	0.2	0.176	0.225	INDETERMINATE	1	TRUE	0	0.36470168659818	2		894	1236	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544714	65544714	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004963-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	324	620	0	ENST00000358664.4:c.212T>G	p.Ile71Ser	p.I71S	ENST00000358664	NM_002382.4	71	aTc/aGc	4/5	0.625719405156503	1	FACETS	0.882	0.837	0.927	0.882	0.837	0.927	CLONAL	1	TRUE	0	0.625719405156503	1		620	807	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438548	49438548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779260688	NA	P-0004973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	174	439	0	ENST00000301067.7:c.4942G>A	p.Asp1648Asn	p.D1648N	ENST00000301067	NM_003482.3	1648	Gat/Aat	19/54	0.547430204294629	3	FACETS	1	0.986	1	0.645	0.596	0.695	CLONAL	1	TRUE	1	0.544893486905411	3		439	630	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0004983-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	24	299	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		299	464	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894230	NA	P-0004983-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	28	326	0	ENST00000451590.1:c.35G>A	p.Gly12Asp	p.G12D	ENST00000451590	NM_001130442.1	12	gGc/gAc	2/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		326	479	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953808	55953808	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004996-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1182	148	639	5	ENST00000263923.4:c.3628C>A	p.Pro1210Thr	p.P1210T	ENST00000263923	NM_002253.2	1210	Ccc/Acc	27/30	1	2	FACETS	0.322	0.293	0.353	0.322	0.293	0.353	SUBCLONAL	1	TRUE	1	0.690116832882142	2		644	1330	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985747	60985749	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0004996-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	77	229	0	ENST00000333681.4:c.151_153del	p.Ser51del	p.S51del	ENST00000333681		51	TCC/-	2/3	1	2	FACETS	0.392	0.344	0.443	0.392	0.344	0.443	SUBCLONAL	1	TRUE	1	0.690116832882142	2		229	569	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487577	38487577	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004996-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2012	126	633	0	ENST00000254066.5:c.110del	p.Pro37ArgfsTer5	p.P37Rfs*5	ENST00000254066	NM_000964.3	36	tCc/tc	2/9	0.690116832882142	3	FACETS	0.23	0.207	0.254	0.115	0.103	0.127	SUBCLONAL	1	TRUE	1	0.690116832882142	3		633	2138	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494334	2494334	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005038-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	25	412	0	ENST00000355716.4:c.725A>G	p.Gln242Arg	p.Q242R	ENST00000355716	NM_003820.2	242	cAg/cGg	7/8	1	2	FACETS	0.97	0.769	1	0.97	0.769	1	CLONAL	1	TRUE	1	0.23	2		412	224	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310503	65310503	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005038-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	43	593	0	ENST00000342505.4:c.2185A>T	p.Ser729Cys	p.S729C	ENST00000342505	NM_002227.2	729	Agt/Tgt	16/25	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.23	2		593	312	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873495	151873495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005038-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	21	579	2	ENST00000262189.6:c.9043C>T	p.Pro3015Ser	p.P3015S	ENST00000262189	NM_170606.2	3015	Cct/Tct	38/59	1	2	FACETS	0.652	0.503	0.826	0.652	0.503	0.826	SUBCLONAL	1	TRUE	1	0.23	2		581	280	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575153	64575153	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0005038-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	15	329	0	ENST00000312049.6:c.655-1G>A		p.X219_splice	ENST00000312049	NM_130799.2	219			1	2	FACETS	0.988	0.729	1	0.988	0.729	1	CLONAL	1	TRUE	1	0.23	2		329	132	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26971328	26971328	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005038-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	26	499	0	ENST00000381527.3:c.899A>G	p.His300Arg	p.H300R	ENST00000381527	NM_001260.1	300	cAt/cGt	9/13	1	2	FACETS	1	0.803	1	1	0.803	1	CLONAL	1	TRUE	1	0.23	2		499	224	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481576	40481576	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005038-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	30	698	0	ENST00000264657.5:c.1229A>G	p.His410Arg	p.H410R	ENST00000264657	NM_139276.2	410	cAc/cGc	13/24	1	2	FACETS	0.69	0.556	0.842	0.69	0.556	0.842	SUBCLONAL	1	TRUE	1	0.23	2		698	378	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0005041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	20	369	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.576	0.439	0.737	0.576	0.439	0.737	SUBCLONAL	1	TRUE	1	0.14	2		369	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782177	NA	P-0005041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	31	662	1	ENST00000269305.4:c.644G>T	p.Ser215Ile	p.S215I	ENST00000269305	NM_001126112.2	215	aGt/aTt	6/11	1	2	FACETS	0.797	0.643	0.971	0.797	0.643	0.971	CLONAL	1	TRUE	1	0.14	2		663	556	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943709	9943709	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	142	554	1	ENST00000330684.3:c.1232T>C	p.Leu411Pro	p.L411P	ENST00000330684	NM_001134407.1	411	cTg/cCg	5/13	0.309037372388807	3	FACETS	1	0.975	1	0.592	0.54	0.647	CLONAL	1	TRUE	1	0.339022134465383	3		555	827	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990337	81990337	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	140	861	0	ENST00000359376.3:c.3608T>C	p.Leu1203Pro	p.L1203P	ENST00000359376	NM_002661.3	1203	cTg/cCg	32/33	0.156935555336084	2	FACETS	0.825	0.75	0.904	0.413	0.375	0.452	INDETERMINATE	1	TRUE	0	0.339022134465383	2		861	1001	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45873792	45873792	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0005047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	233	458	1	ENST00000391945.4:c.5+2T>A		p.X2_splice	ENST00000391945	NM_000400.3	2			0.339022134465383	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.339022134465383	3		459	708	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578507	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGG	CAGGG	-	novel	NA	P-0005047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	282	796	0	ENST00000269305.4:c.423_427del	p.Pro142AlafsTer5	p.P142Afs*5	ENST00000269305	NM_001126112.2	141	tgCCCTGtg/tgtg	5/11	0.339022134465383	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.339022134465383	2		796	741	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520006	NA	P-0005060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	436	645	0	ENST00000269305.4:c.821T>G	p.Val274Gly	p.V274G	ENST00000269305	NM_001126112.2	274	gTt/gGt	8/11	NA	2	FACETS	0.85	0.812	0.887			1	INDETERMINATE	2	TRUE	NA	0.480029157894308	2		645	1069	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652836	212652836	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	178	674	0	ENST00000342788.4:c.470A>G	p.Tyr157Cys	p.Y157C	ENST00000342788	NM_005235.2	157	tAt/tGt	4/28	1	2	FACETS	0.978	0.904	1	0.978	0.904	1	CLONAL	1	TRUE	1	0.480029157894308	2		674	758	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169946	32169946	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	450	675	2	ENST00000375023.3:c.3662G>A	p.Trp1221Ter	p.W1221*	ENST00000375023	NM_004557.3	1221	tGg/tAg	21/30	0.237676349073991	2	FACETS	1	0.996	1	0.719	0.686	0.752	INDETERMINATE	1	TRUE	0	0.480029157894308	2		677	1304	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0005065-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	299	556	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.641149247356579	2		556	392	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518464	204518464	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777416962	NA	P-0005065-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	34	429	0	ENST00000367182.3:c.1127C>T	p.Ala376Val	p.A376V	ENST00000367182	NM_001278516.1	376	gCg/gTg	11/11	0.543153501484933	3	FACETS	0.233	0.19	0.282	0.117	0.095	0.141	SUBCLONAL	1	TRUE	1	0.641149247356579	3		429	601	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405948	49405948	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005065-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	83	526	0	ENST00000418115.1:c.190G>A	p.Glu64Lys	p.E64K	ENST00000418115	NM_001664.2	64	Gaa/Aaa	3/5	0.444002403401943	3	FACETS	0.698	0.618	0.783	0.349	0.309	0.392	SUBCLONAL	1	TRUE	1	0.641149247356579	3		526	490	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244137	153244137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140856583	NA	P-0005065-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	15	448	0	ENST00000281708.4:c.2020C>T	p.Arg674Trp	p.R674W	ENST00000281708	NM_033632.3	674	Cgg/Tgg	12/12	0.336671903862299	1	FACETS	0.147	0.107	0.194	0.147	0.107	0.194	INDETERMINATE	1	TRUE	0	0.641149247356579	1		448	217	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589001	67589001	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005065-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	13	326	0	ENST00000274335.5:c.1092G>A	p.Met364Ile	p.M364I	ENST00000274335		364	atG/atA	8/15	0.335009976536678	0	FACETS	0.073	0.052	0.099			1	INDETERMINATE	1	TRUE	0	0.641149247356579	0		326	198	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907116	101907116	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005065-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	30	464	0	ENST00000374994.4:c.1076A>G	p.Asp359Gly	p.D359G	ENST00000374994	NM_004612.2	359	gAt/gGt	6/9	0.23338077826528	2	FACETS	0.23	0.185	0.281	0.115	0.092	0.141	INDETERMINATE	1	TRUE	0	0.641149247356579	2		464	407	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0005103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	432	538	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.562513617704253	6	FACETS	1	0.991	1	1	0.991	1	CLONAL	4	TRUE	2	0.562513617704253	6		538	747	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0005103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	337	755	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.549439290534176	2	FACETS	0.971	0.928	1	0.971	0.928	1	CLONAL	2	TRUE	0	0.562513617704253	2		755	617	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0005103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	89	598	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.560113924155391	3	FACETS	1	0.9	1	0.504	0.45	0.562	CLONAL	1	TRUE	1	0.562513617704253	3		598	402	SUCCESS
APC	324	MSKCC	GRCh37	5	112173656	112173656	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123117	NA	P-0005103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	132	540	0	ENST00000257430.4:c.2365C>T	p.Gln789Ter	p.Q789*	ENST00000257430	NM_000038.5	789	Cag/Tag	16/16	0.560113924155391	3	FACETS	0.859	0.79	0.93	0.859	0.79	0.93	CLONAL	2	TRUE	1	0.562513617704253	3		540	350	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927985	49927985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035118897	NA	P-0005103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	368	939	2	ENST00000296474.3:c.3743G>A	p.Arg1248His	p.R1248H	ENST00000296474	NM_002447.2	1248	cGc/cAc	18/20	0.557224513634149	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.562513617704253	3		941	768	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675555	30675555	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	368	870	0	ENST00000376406.3:c.2801A>G	p.Glu934Gly	p.E934G	ENST00000376406	NM_014641.2	934	gAa/gGa	8/15	0.562608626719296	3	FACETS	0.99	0.944	1	0.99	0.944	1	CLONAL	2	TRUE	1	0.562513617704253	3		870	847	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579592	7579592	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0005110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	41	210	0	ENST00000269305.4:c.97-2A>T		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.843412546275167	1	FACETS	0.198	0.165	0.234	0.198	0.165	0.234	SUBCLONAL	1	TRUE	0	0.843412546275167	1		210	284	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974763	15974763	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	42	340	0	ENST00000268712.3:c.4112T>C	p.Val1371Ala	p.V1371A	ENST00000268712	NM_006311.3	1371	gTc/gCc	30/46	0.843412546275167	1	FACETS	0.135	0.113	0.16	0.135	0.113	0.16	SUBCLONAL	1	TRUE	0	0.843412546275167	1		340	426	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306569	41306569	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	46	296	0	ENST00000373198.4:c.1090C>T	p.Arg364Ter	p.R364*	ENST00000373198	NM_133170.3	364	Cga/Tga	7/32	1	2	FACETS	0.134	0.112	0.158	0.134	0.112	0.158	SUBCLONAL	1	TRUE	1	0.843412546275167	2		296	815	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073804	8073804	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1557463619	NA	P-0005110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	353	420	0	ENST00000377482.5:c.855del	p.Arg286GlufsTer9	p.R286Efs*9	ENST00000377482	NM_018948.3	285	ccC/cc	4/4	0.843412546275167	1	FACETS	0.978	0.944	1	0.978	0.944	1	CLONAL	1	TRUE	0	0.843412546275167	1		420	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0005122-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	547	556	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	NA	2	FACETS	0.872	0.848	0.895			1	INDETERMINATE	2	TRUE	NA	0.821131645355844	2		556	764	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170814991	170814991	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005122-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	111	242	0	ENST00000296930.5:c.39G>T	p.Arg13Ser	p.R13S	ENST00000296930	NM_002520.6	13	agG/agT	1/11	0.727741006394309	2	FACETS	0.861	0.784	0.94	0.431	0.392	0.47	CLONAL	1	TRUE	0	0.821131645355844	2		242	314	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788618	3788618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398124146	NA	P-0005122-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	221	556	0	ENST00000262367.5:c.4336C>T	p.Arg1446Cys	p.R1446C	ENST00000262367	NM_004380.2	1446	Cgc/Tgc	26/31	0.75831754378013	4	FACETS	0.817	0.759	0.877	0.272	0.253	0.293	CLONAL	1	TRUE	1	0.821131645355844	4		556	1200	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14021961	14021961	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005122-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	685	487	0	ENST00000311895.7:c.661A>G	p.Thr221Ala	p.T221A	ENST00000311895	NM_005236.2	221	Acc/Gcc	4/11	0.75831754378013	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	1	0.821131645355844	4		487	1013	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004877	16004877	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005122-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	226	465	0	ENST00000268712.3:c.2377G>C	p.Ala793Pro	p.A793P	ENST00000268712	NM_006311.3	793	Gca/Cca	20/46	0.698251568075932	1	FACETS	0.832	0.789	0.874	0.832	0.789	0.874	CLONAL	1	TRUE	0	0.821131645355844	1		465	390	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2199923	2199923	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1397211295	NA	P-0005122-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	432	462	0	ENST00000398665.3:c.692G>A	p.Arg231Gln	p.R231Q	ENST00000398665	NM_032482.2	231	cGa/cAa	8/28	0.734277381420019	2	FACETS	0.892	0.865	0.918	0.892	0.865	0.918	CLONAL	2	TRUE	0	0.821131645355844	2		462	590	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411199	63411199	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005122-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	281	267	0	ENST00000330258.3:c.1968G>A	p.Met656Ile	p.M656I	ENST00000330258	NM_152424.3	656	atG/atA	2/2	0.781571872551235	2	FACETS	0.749	0.705	0.794			1	SUBCLONAL	1	TRUE	NA	0.821131645355844	2		267	914	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411625	63411625	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005122-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	859	409	0	ENST00000330258.3:c.1542C>A	p.Ser514Arg	p.S514R	ENST00000330258	NM_152424.3	514	agC/agA	2/2	0.781571872551235	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.821131645355844	2		409	985	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0005138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	332	353	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.337749277893055	2	FACETS	1	0.994	1	0.676	0.642	0.71	INDETERMINATE	1	TRUE	0	0.615333426990639	2		353	798	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0005138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	141	411	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.653	0.596	0.712	0.653	0.596	0.712	SUBCLONAL	1	TRUE	1	0.615333426990639	2		411	702	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939354	76939354	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	184	580	0	ENST00000373344.5:c.1394C>A	p.Ser465Ter	p.S465*	ENST00000373344	NM_000489.3	465	tCa/tAa	9/35	1	2	FACETS	0.614	0.566	0.663	0.614	0.566	0.663	SUBCLONAL	1	TRUE	1	0.615333426990639	2		580	974	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0005157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	328	758	1	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.794691041714734	NA		759	828	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441972	52441972	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0005157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	317	545	0	ENST00000460680.1:c.375+2T>C		p.X125_splice	ENST00000460680	NM_004656.3	125			0.794691041714734	1	FACETS	0.997	0.958	1	0.997	0.958	1	CLONAL	1	TRUE	0	0.794691041714734	1		545	482	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245449	153245449	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	259	439	0	ENST00000281708.4:c.1742A>C	p.Gln581Pro	p.Q581P	ENST00000281708	NM_033632.3	581	cAg/cCg	11/12	1	2	FACETS	0.949	0.894	1	0.949	0.894	1	CLONAL	1	TRUE	1	0.794691041714734	2		439	687	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26970452	26970452	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	346	456	0	ENST00000381527.3:c.821C>G	p.Pro274Arg	p.P274R	ENST00000381527	NM_001260.1	274	cCt/cGt	8/13	NA	2	FACETS	0.921	0.875	0.969			1	INDETERMINATE	1	TRUE	NA	0.794691041714734	2		456	945	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056342	27056343	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0005161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	305	253	0	ENST00000324856.7:c.1338_1339del	p.Gln449AlafsTer173	p.Q449Afs*173	ENST00000324856	NM_006015.4	446	tcTTat/tcat	2/20	0.815205720328041	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.815205720328041	1		253	405	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710889	117710889	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	70	401	0	ENST00000368508.3:c.1383G>T	p.Lys461Asn	p.K461N	ENST00000368508	NM_002944.2	461	aaG/aaT	12/43	0.18713105902456	7	FACETS	1	0.956	1	0.31	0.269	0.354	CLONAL	1	NA	3	0.18713105902456	7		401	886	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138195990	138195990	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0121457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	59	220	0	ENST00000237289.4:c.304A>C	p.Asn102His	p.N102H	ENST00000237289	NM_001270507.1	102	Aat/Cat	3/9	0.18713105902456	7	FACETS	1	0.867	1	0.503	0.433	0.578	CLONAL	2	NA	3	0.18713105902456	7		220	460	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778738	76778738	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0121457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	133	467	0	ENST00000373344.5:c.6841G>A	p.Glu2281Lys	p.E2281K	ENST00000373344	NM_000489.3	2281	Gag/Aag	31/35	0.152794886885538	1	FACETS	0.975	0.887	1	1	0.99	1	CLONAL	2	NA	0	0.18713105902456	1		467	661	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952141	178952141	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	90	285	0	ENST00000263967.3:c.3196G>A	p.Ala1066Thr	p.A1066T	ENST00000263967	NM_006218.2	1066	Gca/Aca	21/21	1	2	FACETS	0.841	0.749	0.939	0.841	0.749	0.939	CLONAL	1	TRUE	1	0.418055294894483	2		285	512	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170827901	170827901	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0005170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	152	396	0	ENST00000296930.5:c.641C>G	p.Ser214Ter	p.S214*	ENST00000296930	NM_002520.6	214	tCa/tGa	8/11	0.418055294894483	1	FACETS	0.625	0.571	0.681	0.625	0.571	0.681	SUBCLONAL	1	TRUE	0	0.418055294894483	1		396	921	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207203	1207203	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1131690950	NA	P-0005170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	150	201	0	ENST00000326873.7:c.290+1G>A		p.X97_splice	ENST00000326873	NM_000455.4	97			0.412371218187422	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.418055294894483	1		201	472	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600474	10600474	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	185	329	0	ENST00000171111.5:c.1381A>T	p.Ile461Phe	p.I461F	ENST00000171111	NM_203500.1	461	Atc/Ttc	4/6	0.418055294894483	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.418055294894483	1		329	666	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0005179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	121	412	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	0.366066006816132	2		412	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0005179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	48	275	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.366066006816132	1	FACETS	0.657	0.558	0.765	0.657	0.558	0.765	SUBCLONAL	1	TRUE	0	0.366066006816132	1		275	326	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0005179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	74	397	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.366066006816132	1	FACETS	0.703	0.617	0.795	0.703	0.617	0.795	SUBCLONAL	1	TRUE	0	0.366066006816132	1		397	470	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736387	85736387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs187744101	NA	P-0005179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	86	865	0	ENST00000370580.1:c.260G>A	p.Arg87Gln	p.R87Q	ENST00000370580	NM_003921.4	87	cGg/cAg	2/3	1	2	FACETS	0.456	0.402	0.514	0.456	0.402	0.514	SUBCLONAL	1	TRUE	1	0.366066006816132	2		865	1031	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267359	198267359	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs377023736	NA	P-0005179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	91	554	0	ENST00000335508.6:c.1998G>C	p.Lys666Asn	p.K666N	ENST00000335508	NM_012433.2	666	aaG/aaC	14/25	0.267148890631355	3	FACETS	0.937	0.833	1	0.312	0.277	0.349	CLONAL	1	TRUE	0	0.366066006816132	3		554	628	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341842	8341842	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	29	639	0	ENST00000356435.5:c.4798G>T	p.Asp1600Tyr	p.D1600Y	ENST00000356435		1600	Gac/Tac	29/35	1	2	FACETS	0.274	0.219	0.337	0.274	0.219	0.337	SUBCLONAL	1	TRUE	1	0.366066006816132	2		639	578	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970982	21970982	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	69	513	0	ENST00000304494.5:c.376G>T	p.Val126Phe	p.V126F	ENST00000304494	NM_000077.4	126	Gtc/Ttc	2/3	1	2	FACETS	0.672	0.586	0.765	0.672	0.586	0.765	SUBCLONAL	1	TRUE	1	0.366066006816132	2		513	561	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974748	21974748	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1554656411	NA	P-0005179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	40	264	0	ENST00000304494.5:c.79G>T	p.Glu27Ter	p.E27*	ENST00000304494	NM_000077.4	27	Gag/Tag	1/3	1				0.52	0.74				SUBCLONAL	1	TRUE	1	0.366066006816132	2		264	350	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820792	3820792	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	79	424	0	ENST00000262367.5:c.2659C>A	p.Gln887Lys	p.Q887K	ENST00000262367	NM_004380.2	887	Cag/Aag	14/31	1	2	FACETS	0.765	0.674	0.863	0.765	0.674	0.863	SUBCLONAL	1	TRUE	1	0.366066006816132	2		424	564	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131262	17131262	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	94	553	0	ENST00000285071.4:c.190G>T	p.Ala64Ser	p.A64S	ENST00000285071	NM_144997.5	64	Gca/Tca	4/14	0.366066006816132	1	FACETS	0.759	0.677	0.846	0.759	0.677	0.846	SUBCLONAL	1	TRUE	0	0.366066006816132	1		553	553	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222868	5222868	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1028304582	NA	P-0005179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	95	259	0	ENST00000357368.4:c.2935C>T	p.Arg979Ter	p.R979*	ENST00000357368	NM_002850.3	979	Cga/Tga	18/38	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.366066006816132	2		259	372	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006898	47006898	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1556762493	NA	P-0005179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	120	512	2	ENST00000377604.3:c.17+1G>T		p.X6_splice	ENST00000377604	NM_001204468.1	6			0.234993631836495	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.366066006816132	1		514	520	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007841	45007841	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	37	364	0	ENST00000558401.1:c.288del	p.Asp96GlufsTer7	p.D96Efs*7	ENST00000558401	NM_004048.2	96	gaT/ga	2/4	0.366066006816132	1	FACETS	0.406	0.335	0.485	0.406	0.335	0.485	SUBCLONAL	1	TRUE	0	0.366066006816132	1		364	407	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797481	45797485	+	frameshift_variant	Frame_Shift_Del	DEL	CGAGG	CGAGG	T	novel	NA	P-0005179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	76	464	0	ENST00000450313.1:c.1034_1038delinsA	p.Pro345GlnfsTer62	p.P345Qfs*62	ENST00000450313	NM_012222.2	345	cCCTCG/cA	12/16	1	2	FACETS	0.701	0.616	0.793	0.701	0.616	0.793	SUBCLONAL	1	TRUE	1	0.366066006816132	2		464	592	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	13	407	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.603	0.434	0.806	0.603	0.434	0.806	SUBCLONAL	1	TRUE	1	0.368345135358198	2		407	117	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0005185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	27	269	0	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.368345135358198	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.368345135358198	1		269	96	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974721	21974721	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	42	291	3	ENST00000304494.5:c.106del	p.Ala36ArgfsTer17	p.A36Rfs*17	ENST00000304494	NM_000077.4	36	Gcg/cg	1/3	1	2	FACETS	0.864	0.737	0.997	1	0.969	1	CLONAL	2	TRUE	1	0.368345135358198	2		294	132	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964926	15964984	+	frameshift_variant	Frame_Shift_Del	DEL	GCCACTTGGAAAGGCTGAAGAAGTGTATAAACACTGAACAGATCTCTTCTCCACCTCCA	GCCACTTGGAAAGGCTGAAGAAGTGTATAAACACTGAACAGATCTCTTCTCCACCTCCA	-	novel	NA	P-0005185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	20	572	0	ENST00000268712.3:c.5612_5670del	p.Leu1871GlnfsTer12	p.L1871Qfs*12	ENST00000268712	NM_006311.3	1871	cTGGAGGTGGAGAAGAGATCTGTTCAGTGTTTATACACTTCTTCAGCCTTTCCAAGTGGC/c	37/46	0.368345135358198	1	FACETS	0.942	0.735	1	0.942	0.735	1	CLONAL	1	TRUE	0	0.368345135358198	1		572	94	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984697	11984718	+	frameshift_variant	Frame_Shift_Del	DEL	TGAGTCATCAGGAAAACTGAAG	TGAGTCATCAGGAAAACTGAAG	-	novel	NA	P-0005185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	10	224	0	ENST00000353533.5:c.243_264del	p.Glu82SerfsTer14	p.E82Sfs*14	ENST00000353533	NM_003010.3	81	atTGAGTCATCAGGAAAACTGAAG/at	3/11	0.368345135358198	1	FACETS	0.984	0.688	1	0.984	0.688	1	CLONAL	1	TRUE	0	0.368345135358198	1		224	45	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691022	NA	P-0005196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	293	419	0	ENST00000269305.4:c.1024del	p.Arg342GlufsTer3	p.R342Efs*3	ENST00000269305	NM_001126112.2	342	Cga/ga	10/11	0.467909826792149	2	FACETS	0.944	0.896	0.994	0.944	0.896	0.994	CLONAL	2	TRUE	0	0.467909826792149	2		419	663	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503671	186503671	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0005196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	568	331	0	ENST00000323963.5:c.349-1G>T		p.X117_splice	ENST00000323963		117			0.467909826792149	6	FACETS	0.949	0.914	0.984	0.949	0.914	0.984	CLONAL	4	TRUE	2	0.467909826792149	6		331	1238	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972008	55972008	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	244	230	0	ENST00000263923.4:c.1636C>T	p.His546Tyr	p.H546Y	ENST00000263923	NM_002253.2	546	Cac/Tac	12/30	0.411654276382207	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.467909826792149	4		230	695	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525471	137525471	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	391	230	0	ENST00000367739.4:c.544G>T	p.Glu182Ter	p.E182*	ENST00000367739	NM_000416.2	182	Gag/Tag	4/7	0.467909826792149	4	FACETS	0.932	0.896	0.968	0.932	0.896	0.968	CLONAL	4	TRUE	0	0.467909826792149	4		230	658	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264392	30264392	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	134	109	0	ENST00000322652.5:c.127G>T	p.Gly43Cys	p.G43C	ENST00000322652	NM_015355.2	43	Ggc/Tgc	1/16	0.467909826792149	2	FACETS	0.868	0.812	0.923	1	0.988	1	CLONAL	3	TRUE	0	0.467909826792149	2		109	220	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788617	3788617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519884	NA	P-0005203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	228	452	0	ENST00000262367.5:c.4337G>A	p.Arg1446His	p.R1446H	ENST00000262367	NM_004380.2	1446	cGc/cAc	26/31	0.727195684675246	3	FACETS	0.999	0.933	1	0.5	0.466	0.534	CLONAL	1	TRUE	1	0.729064875123279	3		452	854	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890192	76890192	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	193	514	0	ENST00000373344.5:c.4702G>T	p.Val1568Phe	p.V1568F	ENST00000373344	NM_000489.3	1568	Gtt/Ttt	17/35	1	2	FACETS	0.897	0.835	0.961	0.897	0.835	0.961	CLONAL	1	TRUE	1	0.729064875123279	2		514	590	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195683	123195683	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	107	487	0	ENST00000218089.9:c.1597G>T	p.Ala533Ser	p.A533S	ENST00000218089	NM_001042749.1	533	Gct/Tct	17/35	1	2	FACETS	0.392	0.352	0.435	0.392	0.352	0.435	SUBCLONAL	1	TRUE	1	0.729064875123279	2		487	748	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266512	198266512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	180	348	0	ENST00000335508.6:c.2324G>A	p.Arg775Gln	p.R775Q	ENST00000335508	NM_012433.2	775	cGa/cAa	16/25	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.84	2		348	402	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097668	11097668	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	255	408	0	ENST00000358026.2:c.848C>G	p.Pro283Arg	p.P283R	ENST00000358026	NM_001128849.1	283	cCc/cGc	5/36	1	2	FACETS	0.975	0.919	1	0.975	0.919	1	CLONAL	1	TRUE	1	0.84	2		408	623	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035011	42035011	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	356	736	0	ENST00000219905.7:c.4855del	p.Ser1619LeufsTer31	p.S1619Lfs*31	ENST00000219905	NM_001164273.1	1618	aTt/at	15/24	1	2	FACETS	0.817	0.776	0.86	0.817	0.776	0.86	CLONAL	1	TRUE	1	0.84	2		736	1037	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	66	415	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.262548826113419	4	FACETS	0.952	0.847	1	0.952	0.847	1	INDETERMINATE	2	TRUE	2	0.764847320015669	4		415	160	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267490	198267490	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	19	380	0	ENST00000335508.6:c.1867T>C	p.Tyr623His	p.Y623H	ENST00000335508	NM_012433.2	623	Tat/Cat	14/25	0.270252074291669	2	FACETS	0.502	0.387	0.631	0.251	0.193	0.316	INDETERMINATE	1	TRUE	0	0.764847320015669	2		380	99	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592123	67592123	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	43	473	0	ENST00000274335.5:c.1939C>G	p.Leu647Val	p.L647V	ENST00000274335		647	Ctt/Gtt	14/15	0.498857089118158	4	FACETS	0.757	0.649	0.872			1	SUBCLONAL	2	TRUE	NA	0.764847320015669	4		473	131	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905504	50905504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373192520	NA	P-0005219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	44	626	0	ENST00000440232.2:c.632G>A	p.Arg211His	p.R211H	ENST00000440232	NM_002691.3	211	cGc/cAc	6/27	0.764847320015669	1	FACETS	0.597	0.514	0.683	0.597	0.514	0.683	SUBCLONAL	1	TRUE	0	0.764847320015669	1		626	119	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608879	100608879	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0005219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	28	645	0	ENST00000308731.7:c.1729A>T	p.Lys577Ter	p.K577*	ENST00000308731	NM_000061.2	577	Aaa/Taa	17/19	NA	2	FACETS	0.6	0.488	0.723			1	INDETERMINATE	1	TRUE	NA	0.764847320015669	2		645	122	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0005222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	149	316	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.140351825261508	3	FACETS	1	0.987	1	0.72	0.659	0.783	INDETERMINATE	1	TRUE	1	0.356112782894119	3		316	685	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0005222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	38	233	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.827	0.688	0.981	0.827	0.688	0.981	CLONAL	1	TRUE	1	0.356112782894119	2		233	258	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0005222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	93	526	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.140351825261508	3	FACETS	0.792	0.704	0.886	0.396	0.352	0.443	INDETERMINATE	1	TRUE	1	0.356112782894119	3		526	777	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032069	10032069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868215122	NA	P-0005222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	114	673	0	ENST00000330684.3:c.754G>A	p.Asp252Asn	p.D252N	ENST00000330684	NM_001134407.1	252	Gat/Aat	3/13	1	2	FACETS	0.788	0.71	0.872	0.788	0.71	0.872	SUBCLONAL	1	TRUE	1	0.356112782894119	2		673	812	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164268	47164268	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	71	437	0	ENST00000409792.3:c.1858C>T	p.Arg620Ter	p.R620*	ENST00000409792	NM_014159.6	620	Cga/Tga	3/21	1	2	FACETS	0.809	0.708	0.918	0.809	0.708	0.918	CLONAL	1	TRUE	1	0.356112782894119	2		437	493	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252865	36252865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060499616	NA	P-0005222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	85	387	0	ENST00000300305.3:c.497G>A	p.Arg166Gln	p.R166Q	ENST00000300305		166	cGa/cAa	4/8	1	2	FACETS	0.741	0.656	0.833	0.741	0.656	0.833	SUBCLONAL	1	TRUE	1	0.356112782894119	2		387	644	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156675	55156675	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553906671	NA	P-0005222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	57	419	0	ENST00000257290.5:c.3076G>A	p.Asp1026Asn	p.D1026N	ENST00000257290	NM_006206.4	1026	Gac/Aac	22/23	0.302802480298491	1	FACETS	0.441	0.378	0.51	0.441	0.378	0.51	SUBCLONAL	1	TRUE	0	0.356112782894119	1		419	596	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961116	55961116	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	51	476	0	ENST00000263923.4:c.2824G>C	p.Gly942Arg	p.G942R	ENST00000263923	NM_002253.2	942	Ggg/Cgg	21/30	0.302802480298491	1	FACETS	0.37	0.314	0.432	0.37	0.314	0.432	SUBCLONAL	1	TRUE	0	0.356112782894119	1		476	636	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945638	38945638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	109	432	0	ENST00000357387.3:c.4588G>A	p.Gly1530Ser	p.G1530S	ENST00000357387	NM_152756.3	1530	Ggt/Agt	34/38	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.356112782894119	2		432	598	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665397	176665397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	133	507	1	ENST00000439151.2:c.4081C>T	p.Leu1361Phe	p.L1361F	ENST00000439151	NM_022455.4	1361	Ctt/Ttt	7/23	1	2	FACETS	0.926	0.841	1	0.926	0.841	1	CLONAL	1	TRUE	1	0.356112782894119	2		508	807	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486113	8486113	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	90	504	0	ENST00000356435.5:c.2704G>A	p.Gly902Ser	p.G902S	ENST00000356435		902	Ggc/Agc	17/35	0.356112782894119	1	FACETS	0.804	0.715	0.897	0.804	0.715	0.897	CLONAL	1	TRUE	0	0.356112782894119	1		504	517	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98247986	98247986	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	135	422	0	ENST00000331920.6:c.565C>T	p.His189Tyr	p.H189Y	ENST00000331920	NM_000264.3	189	Cat/Tat	3/24	0.356112782894119	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.356112782894119	1		422	617	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434610	99434610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1307066736	NA	P-0005222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	170	437	0	ENST00000268035.6:c.697C>T	p.Pro233Ser	p.P233S	ENST00000268035	NM_000875.3	233	Ccc/Tcc	3/21	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.356112782894119	2		437	910	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216536	7216536	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	169	721	0	ENST00000380728.2:c.799G>A	p.Asp267Asn	p.D267N	ENST00000380728		267	Gac/Aac	9/11	0.302802480298491	1	FACETS	0.81	0.744	0.879	0.81	0.744	0.879	CLONAL	1	TRUE	0	0.356112782894119	1		721	963	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741023	40741023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	86	534	0	ENST00000392038.2:c.1295C>T	p.Ser432Phe	p.S432F	ENST00000392038	NM_001626.4	432	tCc/tTc	13/14	0.302802480298491	1	FACETS	0.543	0.48	0.611	0.543	0.48	0.611	SUBCLONAL	1	TRUE	0	0.356112782894119	1		534	731	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791557	42791557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	148	523	0	ENST00000575354.2:c.538G>A	p.Glu180Lys	p.E180K	ENST00000575354	NM_015125.3	180	Gaa/Aaa	4/20	0.302802480298491	1	FACETS	0.865	0.791	0.942	0.865	0.791	0.942	CLONAL	1	TRUE	0	0.356112782894119	1		523	790	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118817	61118817	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0005231-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	28	498	0	ENST00000295025.8:c.11-1G>C		p.X4_splice	ENST00000295025	NM_002908.2	4			0.185614356280868	3	FACETS	0.816	0.652	1	0.408	0.326	0.502	CLONAL	1	TRUE	1	0.185614356280868	3		498	404	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711874	89711874	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs786204862	NA	P-0005231-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	67	420	0	ENST00000371953.3:c.493-1G>A		p.X165_splice	ENST00000371953	NM_000314.4	165			0.185614356280868	3	FACETS	1	0.925	1	1	0.925	1	CLONAL	2	TRUE	1	0.185614356280868	3		420	364	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883638	37883638	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200796676	NA	P-0005231-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	43	434	1	ENST00000269571.5:c.3250G>T	p.Asp1084Tyr	p.D1084Y	ENST00000269571		1084	Gat/Tat	26/27	0.185614356280868	3	FACETS	1	0.942	1	0.646	0.541	0.761	CLONAL	1	TRUE	1	0.185614356280868	3		435	392	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183753	10183761	+	inframe_deletion	In_Frame_Del	DEL	CATCTTCTG	CATCTTCTG	-	novel	NA	P-0005231-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	82	377	0	ENST00000256474.2:c.224_232del	p.Ile75_Cys77del	p.I75_C77del	ENST00000256474	NM_000551.3	74	gtCATCTTCTGc/gtc	1/3	0.185614356280868	3	FACETS	0.836	0.742	0.936	1	0.967	1	CLONAL	3	TRUE	1	0.185614356280868	3		377	385	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058665	47058679	+	inframe_deletion	In_Frame_Del	DEL	TGTTTCACATTCTCA	TGTTTCACATTCTCA	-	novel	NA	P-0005231-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	67	531	0	ENST00000409792.3:c.7599_7613del	p.Glu2534_His2538del	p.E2534_H2538del	ENST00000409792	NM_014159.6	2533	aaTGAGAATGTGAAACAc/aac	21/21	0.185614356280868	3	FACETS	0.82	0.714	0.934	0.82	0.714	0.934	CLONAL	2	TRUE	1	0.185614356280868	3		531	481	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626767	28626767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	105	813	0	ENST00000241453.7:c.529G>A	p.Glu177Lys	p.E177K	ENST00000241453	NM_004119.2	177	Gaa/Aaa	5/24	1	2	FACETS	0.737	0.659	0.819	0.737	0.659	0.819	SUBCLONAL	1	TRUE	1	0.334553260239212	2		813	852	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747042	40747042	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0005241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	29	574	1	ENST00000373198.4:c.3039+1G>A		p.X1013_splice	ENST00000373198	NM_133170.3	1013			1	2	FACETS	0.304	0.243	0.374	0.304	0.243	0.374	SUBCLONAL	1	TRUE	1	0.334553260239212	2		575	570	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	109	407	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		407	961	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0005250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	106	622	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.167929661079023	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		624	952	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954211	48954242	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAAATTTTAGGTAAATTTTTTACTTTTAGTAA	AAAATTTTAGGTAAATTTTTTACTTTTAGTAA	-	novel	NA	P-0005250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	79	656	0	ENST00000267163.4:c.1420_1421+30del		p.X474_splice	ENST00000267163	NM_000321.2	474		15/27	0.167929661079023	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		656	1167	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575192	48575192	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	108	599	0	ENST00000342988.3:c.386A>G	p.Asn129Ser	p.N129S	ENST00000342988	NM_005359.5	129	aAt/aGt	3/12	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		599	992	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005251-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	111	145	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.85	2		145	238	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0005251-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	145	166	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.855	0.789	0.923	0.855	0.789	0.923	CLONAL	1	TRUE	1	0.85	2		166	399	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285253	212285253	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005251-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	163	719	0	ENST00000342788.4:c.3048G>C	p.Met1016Ile	p.M1016I	ENST00000342788	NM_005235.2	1016	atG/atC	25/28	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.85	2		719	382	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379354	225379354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005251-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	35	609	0	ENST00000264414.4:c.514G>A	p.Glu172Lys	p.E172K	ENST00000264414	NM_003590.4	172	Gag/Aag	4/16	1	2	FACETS	0.198	0.162	0.239	0.198	0.162	0.239	SUBCLONAL	1	TRUE	1	0.85	2		609	415	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803147	1803147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005251-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	199	738	2	ENST00000260795.2:c.499C>T	p.Pro167Ser	p.P167S	ENST00000260795		167	Ccg/Tcg	4/17	1	2	FACETS	0.792	0.739	0.847	0.792	0.739	0.847	SUBCLONAL	1	TRUE	1	0.85	2		740	591	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955118	93955118	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005251-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	280	976	0	ENST00000369303.4:c.2780C>T	p.Ser927Leu	p.S927L	ENST00000369303	NM_004440.3	927	tCa/tTa	16/17	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.85	2		976	615	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151882717	151882717	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0005251-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	40	212	0	ENST00000262189.6:c.5009-1G>C		p.X1670_splice	ENST00000262189	NM_170606.2	1670			1	2	FACETS	0.951	0.816	1	0.951	0.816	1	CLONAL	1	TRUE	1	0.85	2		212	99	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151919124	151919124	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0005251-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	37	530	0	ENST00000262189.6:c.3461C>G	p.Ser1154Ter	p.S1154*	ENST00000262189	NM_170606.2	1154	tCa/tGa	22/59	1	2	FACETS	0.203	0.167	0.244	0.203	0.167	0.244	SUBCLONAL	1	TRUE	1	0.85	2		530	428	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425806	49425806	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005251-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	196	482	0	ENST00000301067.7:c.12682C>T	p.Gln4228Ter	p.Q4228*	ENST00000301067	NM_003482.3	4228	Cag/Tag	39/54	1	2	FACETS	0.93	0.869	0.992	0.93	0.869	0.992	CLONAL	1	TRUE	1	0.85	2		482	496	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438728	49438728	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1290729871	NA	P-0005251-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	263	682	0	ENST00000301067.7:c.4762G>T	p.Glu1588Ter	p.E1588*	ENST00000301067	NM_003482.3	1588	Gaa/Taa	19/54	1	2	FACETS	0.88	0.83	0.932	0.88	0.83	0.932	CLONAL	1	TRUE	1	0.85	2		682	703	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99192881	99192881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1013771934	NA	P-0005251-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	250	700	0	ENST00000268035.6:c.71C>T	p.Ser24Leu	p.S24L	ENST00000268035	NM_000875.3	24	tCg/tTg	1/21	1	2	FACETS	0.856	0.805	0.908	0.856	0.805	0.908	CLONAL	1	TRUE	1	0.85	2		700	687	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092917	29092917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908703	NA	P-0005251-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	158	774	0	ENST00000328354.6:c.1067C>T	p.Ser356Leu	p.S356L	ENST00000328354	NM_007194.3	356	tCa/tTa	10/15	1	2	FACETS	0.989	0.918	1	0.989	0.918	1	CLONAL	1	TRUE	1	0.85	2		774	376	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	69	407	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.156549799828669	5	FACETS	0.667	0.58	0.762	0.222	0.193	0.254	INDETERMINATE	1	TRUE	2	0.43	5		407	791	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0005275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	54	493	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.156549799828669	3	FACETS	0.549	0.469	0.637	0.274	0.234	0.319	INDETERMINATE	1	TRUE	1	0.43	3		495	556	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974770	21974775	+	inframe_deletion	In_Frame_Del	DEL	GGCCGT	GGCCGT	-	novel	NA	P-0005275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	23	290	0	ENST00000304494.5:c.52_57del	p.Thr18_Ala19del	p.T18_A19del	ENST00000304494	NM_000077.4	18	ACGGCC/-	1/3	1	2	FACETS	0.53	0.415	0.661	0.53	0.415	0.661	SUBCLONAL	1	TRUE	1	0.43	2		290	202	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0005277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	152	303	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		303	675	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641706	12641706	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	168	521	0	ENST00000251849.4:c.935T>A	p.Val312Glu	p.V312E	ENST00000251849	NM_002880.3	312	gTg/gAg	9/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		521	949	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144879	47144879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	430	569	0	ENST00000409792.3:c.4874G>A	p.Arg1625His	p.R1625H	ENST00000409792	NM_014159.6	1625	cGt/cAt	7/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		569	863	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909634	76909634	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	245	700	0	ENST00000373344.5:c.4271A>G	p.Lys1424Arg	p.K1424R	ENST00000373344	NM_000489.3	1424	aAa/aGa	14/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		700	931	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0005294-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	104	370	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	0.488979681921989	2		370	406	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276328	15276328	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0005294-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	125	411	0	ENST00000263388.2:c.5668-2A>C		p.X1890_splice	ENST00000263388	NM_000435.2	1890			0.229650631539721	5	FACETS	1	0.979	1	0.428	0.388	0.47	INDETERMINATE	1	TRUE	2	0.488979681921989	5		411	690	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443695	29443695	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs863225281	NA	P-0121533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	15	244	0	ENST00000389048.3:c.3522C>A	p.Phe1174Leu	p.F1174L	ENST00000389048	NM_004304.4	1174	ttC/ttA	23/29	1	2	FACETS		NA	1			1	NA	NA	NA	1	NA	2		244	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934574	NA	P-0005331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	579	539	1	ENST00000269305.4:c.844C>G	p.Arg282Gly	p.R282G	ENST00000269305	NM_001126112.2	282	Cgg/Ggg	8/11	0.580567731283786	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.580567731283786	3		540	819	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	11	145	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.45	0.312	0.621	0.45	0.312	0.621	SUBCLONAL	1	TRUE	1	0.307208795307042	2		145	159	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309857	65309857	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	44	474	0	ENST00000342505.4:c.2293G>C	p.Glu765Gln	p.E765Q	ENST00000342505	NM_002227.2	765	Gag/Cag	17/25	1	2	FACETS	0.772	0.649	0.907	0.772	0.649	0.907	CLONAL	1	TRUE	1	0.307208795307042	2		474	371	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183763	10183763	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs869025621	NA	P-0005332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	77	339	0	ENST00000256474.2:c.232A>T	p.Asn78Tyr	p.N78Y	ENST00000256474	NM_000551.3	78	Aat/Tat	1/3	0.20665137821023	2	FACETS	1	0.953	1	0.582	0.513	0.655	CLONAL	1	TRUE	0	0.307208795307042	2		339	431	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781440	135781440	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203542	NA	P-0005332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	93	650	1	ENST00000298552.3:c.1525C>T	p.Arg509Ter	p.R509*	ENST00000298552	NM_001162426.1	509	Cga/Tga	15/23	0.307208795307042	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.307208795307042	1		651	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0005340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	12	556	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		556	520	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0005421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	60	233	0				ENST00000310581	NM_198253.2	-/1132			0.273357563001567	1	FACETS	0.962	0.832	1	0.962	0.832	1	CLONAL	1	TRUE	0	0.273357563001567	1		233	394	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622672	158622672	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1260691632	NA	P-0005421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2121	137	785	5	ENST00000263640.3:c.827G>A	p.Ser276Asn	p.S276N	ENST00000263640	NM_001105.4	276	aGt/aAt	8/11	1	2	FACETS	0.444	0.401	0.489	0.444	0.401	0.489	SUBCLONAL	1	TRUE	1	0.273357563001567	2		790	2258	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510167	187510167	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	76	381	0	ENST00000441802.2:c.13346C>A	p.Pro4449Gln	p.P4449Q	ENST00000441802	NM_005245.3	4449	cCa/cAa	27/27	1	2	FACETS	0.518	0.453	0.589	0.518	0.453	0.589	SUBCLONAL	1	TRUE	1	0.273357563001567	2		381	1073	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539951	187539951	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs777631605	NA	P-0005421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	126	411	0	ENST00000441802.2:c.7789C>T	p.Arg2597Ter	p.R2597*	ENST00000441802	NM_005245.3	2597	Cga/Tga	10/27	1	2	FACETS	0.861	0.778	0.948	0.861	0.778	0.948	CLONAL	1	TRUE	1	0.273357563001567	2		411	1071	SUCCESS
APC	324	MSKCC	GRCh37	5	112177901	112177901	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs752654519	NA	P-0005421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	70	462	0	ENST00000257430.4:c.6610C>T	p.Arg2204Ter	p.R2204*	ENST00000257430	NM_000038.5	2204	Cga/Tga	16/16	1	2	FACETS	0.393	0.341	0.45	0.393	0.341	0.45	SUBCLONAL	1	TRUE	1	0.273357563001567	2		462	1302	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	CT	rs121913227	NA	P-0005421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	212	455	0	ENST00000288602.6:c.1798_1799delinsAG	p.Val600Arg	p.V600R	ENST00000288602	NM_004333.4	600	GTg/AGg	15/18	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.273357563001567	2		455	1254	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524945	8524945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1304	92	529	1	ENST00000356435.5:c.659C>T	p.Pro220Leu	p.P220L	ENST00000356435		220	cCt/cTt	7/35	1	2	FACETS	0.482	0.427	0.542	0.482	0.427	0.542	SUBCLONAL	1	TRUE	1	0.273357563001567	2		530	1396	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845516	63845516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1985	124	490	0	ENST00000279873.7:c.1255C>T	p.Pro419Ser	p.P419S	ENST00000279873	NM_032199.2	419	Cca/Tca	9/10	0.273357563001567	6	FACETS	0.665	0.599	0.736			1	SUBCLONAL	1	TRUE	NA	0.273357563001567	6		490	2109	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165783	108165783	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060501627	NA	P-0005421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1270	191	479	1	ENST00000278616.4:c.4906C>T	p.Gln1636Ter	p.Q1636*	ENST00000278616	NM_000051.3	1636	Cag/Tag	32/63	1	2	FACETS	0.956	0.882	1	0.956	0.882	1	CLONAL	1	TRUE	1	0.273357563001567	2		480	1461	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204627	108204627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	47	287	0	ENST00000278616.4:c.7942C>T	p.Pro2648Ser	p.P2648S	ENST00000278616	NM_000051.3	2648	Cca/Tca	54/63	1	2	FACETS	0.369	0.31	0.435	0.369	0.31	0.435	SUBCLONAL	1	TRUE	1	0.273357563001567	2		287	931	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423503	88423503	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	174	542	1	ENST00000360948.2:c.2332G>A	p.Glu778Lys	p.E778K	ENST00000360948	NM_001012338.2	778	Gag/Aag	18/19	1	2	FACETS	0.998	0.916	1	0.998	0.916	1	CLONAL	1	TRUE	1	0.273357563001567	2		543	1276	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476406	88476406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1395756451	NA	P-0005421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	68	245	0	ENST00000360948.2:c.1726G>A	p.Asp576Asn	p.D576N	ENST00000360948	NM_001012338.2	576	Gat/Aat	15/19	1	2	FACETS	0.946	0.824	1	0.946	0.824	1	CLONAL	1	TRUE	1	0.273357563001567	2		245	526	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830078	72830078	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1641	252	774	0	ENST00000268489.5:c.6503A>G	p.Asn2168Ser	p.N2168S	ENST00000268489	NM_006885.3	2168	aAc/aGc	9/10	1	2	FACETS	0.974	0.908	1	0.974	0.908	1	CLONAL	1	TRUE	1	0.273357563001567	2		774	1893	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39542596	39542596	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs138532795	NA	P-0005421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1416	206	450	0	ENST00000262039.4:c.400G>A	p.Gly134Ser	p.G134S	ENST00000262039	NM_002647.2	134	Ggc/Agc	3/25	1	2	FACETS	0.929	0.859	1	0.929	0.859	1	CLONAL	1	TRUE	1	0.273357563001567	2		450	1622	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385246	41385246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	151	531	1	ENST00000373198.4:c.715G>A	p.Val239Ile	p.V239I	ENST00000373198	NM_133170.3	239	Gtc/Atc	6/32	0.273357563001567	0	FACETS	0.622	0.567	0.68			1	SUBCLONAL	1	TRUE	0	0.273357563001567	0		532	1290	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256361	46256361	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2767	307	818	0	ENST00000371998.3:c.589T>C	p.Cys197Arg	p.C197R	ENST00000371998		197	Tgc/Cgc	7/23	0.163974969175458	4	FACETS	0.93	0.872	0.991			1	INDETERMINATE	1	TRUE	NA	0.273357563001567	4		818	3074	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0005430-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	273	578	0	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	0.405096291760862	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	0	0.404966596132923	3		578	502	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005430-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	188	315	0	ENST00000257430.4:c.4199C>A	p.Ser1400Ter	p.S1400*	ENST00000257430	NM_000038.5	1400	tCg/tAg	16/16	0.404966596132923	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.404966596132923	2		315	452	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944829	31944829	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005430-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	793	885	0	ENST00000340398.3:c.272C>T	p.Ala91Val	p.A91V	ENST00000340398	NM_001013699.2	91	gCg/gTg	1/1	0.405096291760862	3	FACETS	0.927	0.898	0.956	1	0.997	1	CLONAL	3	TRUE	1	0.404966596132923	3		885	1693	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467650	66467650	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0005430-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	79	454	0	ENST00000273854.3:c.619A>T	p.Lys207Ter	p.K207*	ENST00000273854	NM_004439.5	207	Aaa/Taa	3/18	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.404966596132923	2		454	373	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503225	125503225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005430-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	79	447	0	ENST00000428830.2:c.592C>T	p.Leu198Phe	p.L198F	ENST00000428830	NM_001114121.2	198	Ctt/Ttt	6/14	0.404966596132923	2	FACETS	0.956	0.846	1	0.478	0.423	0.537	CLONAL	1	TRUE	0	0.404966596132923	2		447	408	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937434	32937434	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005430-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	104	612	1	ENST00000380152.3:c.8095A>G	p.Asn2699Asp	p.N2699D	ENST00000380152		2699	Aat/Gat	18/27	0.404966596132923	6	FACETS	1	0.962	1	0.232	0.207	0.258	CLONAL	1	TRUE	1	0.404966596132923	6		613	802	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727490	88727490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1222179640	NA	P-0005430-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	164	603	2	ENST00000360948.2:c.289G>A	p.Val97Met	p.V97M	ENST00000360948	NM_001012338.2	97	Gtg/Atg	3/19	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.404966596132923	2		605	675	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223055	1223055	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371264852	NA	P-0005430-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	135	741	2	ENST00000326873.7:c.992G>A	p.Arg331Gln	p.R331Q	ENST00000326873	NM_000455.4	331	cGg/cAg	8/10	0.405096291760862	3	FACETS	1	0.926	1	0.51	0.464	0.559	CLONAL	1	TRUE	1	0.404966596132923	3		743	786	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086193	16086195	+	missense_variant	Missense_Mutation	TNP	AAA	AAA	TAT	novel	NA	P-0005430-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	64	456	0	ENST00000281043.3:c.1369_1371delinsTAT	p.Lys457Tyr	p.K457Y	ENST00000281043	NM_005378.4	457	AAA/TAT	3/3	0.367232618108893	3	FACETS	0.605	0.524	0.694	0.303	0.262	0.347	SUBCLONAL	1	TRUE	1	0.404966596132923	3		456	628	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637555	176637556	+	missense_variant	Missense_Mutation	DNP	GC	GC	CT	novel	NA	P-0005430-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	173	492	0	ENST00000439151.2:c.2155_2156delinsCT	p.Ala719Leu	p.A719L	ENST00000439151	NM_022455.4	719	GCa/CTa	5/23	0.405096291760862	3	FACETS	0.941	0.88	1	0.941	0.88	1	CLONAL	3	TRUE	0	0.404966596132923	3		492	364	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0005440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	727	537	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.899614824876981	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.899614824876981	2		537	776	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111698	56111698	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	209	271	0	ENST00000399503.3:c.298G>T	p.Gly100Trp	p.G100W	ENST00000399503	NM_005921.1	100	Ggg/Tgg	1/20	0.899614824876981	2	FACETS	1	0.955	1	0.509	0.479	0.541	CLONAL	1	TRUE	0	0.899614824876981	2		271	456	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169952	32169952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151325272	NA	P-0005440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1344	394	690	0	ENST00000375023.3:c.3656G>A	p.Arg1219Gln	p.R1219Q	ENST00000375023	NM_004557.3	1219	cGg/cAg	21/30	0.703497054718937	4	FACETS	0.957	0.908	1			1	CLONAL	1	TRUE	NA	0.899614824876981	4		690	1738	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0005446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	592	755	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.755316462714419	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.811560734544892	1		755	817	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319373	11319373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1446194159	NA	P-0005446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	200	556	0	ENST00000361445.4:c.94C>T	p.Arg32Trp	p.R32W	ENST00000361445	NM_004958.3	32	Cgg/Tgg	2/58	0.407116285246236	1	FACETS	0.378	0.351	0.406	0.378	0.351	0.406	INDETERMINATE	1	TRUE	0	0.811560734544892	1		556	775	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025849	48025849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377216828	NA	P-0005446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	279	785	0	ENST00000234420.5:c.727C>T	p.Arg243Cys	p.R243C	ENST00000234420	NM_000179.2	243	Cgc/Tgc	4/10	0.399582519370897	1	FACETS	0.373	0.35	0.397	0.373	0.35	0.397	INDETERMINATE	1	TRUE	0	0.811560734544892	1		785	1095	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749491	41749491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	135	450	0	ENST00000226382.2:c.304C>T	p.Arg102Cys	p.R102C	ENST00000226382	NM_003924.3	102	Cgc/Tgc	2/3	0.399582519370897	1	FACETS	0.304	0.276	0.332	0.304	0.276	0.332	INDETERMINATE	1	TRUE	0	0.811560734544892	1		450	651	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143236	58143236	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0005446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	394	482	0	ENST00000257904.6:c.683+1G>C		p.X228_splice	ENST00000257904	NM_000075.3	228			0.407116285246236	1	FACETS	0.757	0.725	0.789	0.757	0.725	0.789	INDETERMINATE	1	TRUE	0	0.811560734544892	1		482	762	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108875	2108875	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs137854200	NA	P-0005446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	204	514	0	ENST00000219476.3:c.975+1G>T		p.X325_splice	ENST00000219476	NM_000548.3	325			1	2	FACETS	0.486	0.45	0.523	0.486	0.45	0.523	SUBCLONAL	1	TRUE	1	0.811560734544892	2		514	1034	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	139	407	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.164949590693736	2	FACETS	0.824	0.751	0.9	0.824	0.751	0.9	CLONAL	2	TRUE	0	0.227987376807315	2		407	740	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176132973	176132973	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	94	414	0	ENST00000367669.3:c.620T>G	p.Leu207Trp	p.L207W	ENST00000367669	NM_022457.5	207	tTg/tGg	4/20	1	2	FACETS	0.899	0.799	1	0.899	0.799	1	CLONAL	1	TRUE	1	0.227987376807315	2		414	917	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204864	NA	P-0005456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	82	325	0	ENST00000371953.3:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000371953	NM_000314.4	171	Cag/Tag	6/9	0.33671903097307	1	FACETS	0.818	0.724	0.919	0.818	0.724	0.919	CLONAL	1	TRUE	0	0.33671903097307	1		325	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	101	300	0	ENST00000269305.4:c.542G>C	p.Arg181Pro	p.R181P	ENST00000269305	NM_001126112.2	181	cGc/cCc	5/11	0.33671903097307	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.33671903097307	1		300	464	SUCCESS
ATR	545	MSKCC	GRCh37	3	142184042	142184042	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	107	323	0	ENST00000350721.4:c.6938C>G	p.Ser2313Cys	p.S2313C	ENST00000350721	NM_001184.3	2313	tCt/tGt	41/47	0.284042699506445	3	FACETS	1	0.934	1	0.527	0.473	0.584	CLONAL	1	TRUE	1	0.33671903097307	3		323	705	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129934	55129934	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	126	509	0	ENST00000257290.5:c.468G>C	p.Glu156Asp	p.E156D	ENST00000257290	NM_006206.4	156	gaG/gaC	4/23	0.33671903097307	1	FACETS	0.88	0.798	0.967	0.88	0.798	0.967	CLONAL	1	TRUE	0	0.33671903097307	1		509	707	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911155	29911155	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs45482492	NA	P-0005456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	75	229	0	ENST00000376809.5:c.454G>T	p.Glu152Ter	p.E152*	ENST00000376809	NM_002116.7	152	Gag/Tag	3/8	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.33671903097307	2		229	395	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864461	162864461	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs146288080	NA	P-0005456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	61	463	0	ENST00000366898.1:c.52G>C	p.Asp18His	p.D18H	ENST00000366898	NM_004562.2	18	Gat/Cat	2/12	1	2	FACETS	0.477	0.411	0.55	0.477	0.411	0.55	SUBCLONAL	1	TRUE	1	0.33671903097307	2		463	759	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579310	7579310	+	splice_donor_variant	Splice_Site	SNP	A	A	T	rs1555526469	NA	P-0005465-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	166	397	0	ENST00000269305.4:c.375+2T>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		397	537	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005472-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	70	145	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.507456557533481	2		145	265	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455076	50455076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1184423158	NA	P-0005472-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	62	383	2	ENST00000331340.3:c.623G>A	p.Arg208Gln	p.R208Q	ENST00000331340	NM_006060.4	208	cGa/cAa	6/8	0.507456557533481	3	FACETS	0.979	0.852	1	0.489	0.426	0.558	CLONAL	1	TRUE	1	0.507456557533481	3		385	313	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450136	32450136	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766425764	NA	P-0005472-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	146	413	0	ENST00000332351.3:c.676C>T	p.Pro226Ser	p.P226S	ENST00000332351	NM_024426.4	226	Ccc/Tcc	2/10	0.330499554905323	1	FACETS	0.944	0.869	1	0.944	0.869	1	CLONAL	1	TRUE	0	0.507456557533481	1		413	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579854	7579858	+	frameshift_variant	Frame_Shift_Del	DEL	GAAAA	GAAAA	T	novel	NA	P-0005472-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	132	462	0	ENST00000269305.4:c.55_59delinsA	p.Phe19LysfsTer24	p.F19Kfs*24	ENST00000269305	NM_001126112.2	19	TTTTCa/Aa	2/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.507456557533481	2		462	432	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152093	55152093	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121908585	NA	P-0005481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	227	446	0	ENST00000257290.5:c.2525A>T	p.Asp842Val	p.D842V	ENST00000257290	NM_006206.4	842	gAc/gTc	18/23	1	2	FACETS	0.969	0.904	1	0.969	0.904	1	CLONAL	1	TRUE	1	0.539879469494141	2		446	868	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637431	47637431	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs63750821	NA	P-0005499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	373	569	0	ENST00000233146.2:c.565G>T	p.Ala189Ser	p.A189S	ENST00000233146	NM_000251.2	189	Gct/Tct	3/16	1	2	FACETS	0.935	0.892	0.979	0.935	0.892	0.979	CLONAL	1	TRUE	1	0.917719339211747	2		569	869	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449795	8449795	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs144935952	NA	P-0005499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	339	436	2	ENST00000356435.5:c.3918C>A	p.Asn1306Lys	p.N1306K	ENST00000356435		1306	aaC/aaA	23/35	NA	2	FACETS	0.866	0.823	0.91			1	INDETERMINATE	1	TRUE	NA	0.917719339211747	2		438	853	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435417	56435417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112997544	NA	P-0005499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	309	407	0	ENST00000407977.2:c.1720G>A	p.Gly574Arg	p.G574R	ENST00000407977		574	Gga/Aga	9/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.917719339211747	2		407	581	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713383	40713383	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs773803715	NA	P-0005499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	426	494	0	ENST00000373198.4:c.4132C>T	p.Arg1378Ter	p.R1378*	ENST00000373198	NM_133170.3	1378	Cga/Tga	30/32	1	2	FACETS	0.96	0.919	1	0.96	0.919	1	CLONAL	1	TRUE	1	0.917719339211747	2		494	967	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652252	48652252	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	667	931	0	ENST00000376670.3:c.923A>G	p.Lys308Arg	p.K308R	ENST00000376670	NM_002049.3	308	aAg/aGg	6/6	1	2	FACETS	0.961	0.928	0.995	0.961	0.928	0.995	CLONAL	1	TRUE	1	0.917719339211747	2		931	1512	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411132	63411132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41307359	NA	P-0005499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	510	753	1	ENST00000330258.3:c.2035C>T	p.Arg679Trp	p.R679W	ENST00000330258	NM_152424.3	679	Cgg/Tgg	2/2	1	2	FACETS	0.954	0.916	0.992	0.954	0.916	0.992	CLONAL	1	TRUE	1	0.917719339211747	2		754	1165	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271931	18271976	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGGCACTGCCCGCGCCGCTCGTGACCCCCGAGGCCTCGGCCGAG	GCTGGCACTGCCCGCGCCGCTCGTGACCCCCGAGGCCTCGGCCGAG	-	novel	NA	P-0005499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	53	332	0	ENST00000222254.8:c.536_581del	p.Leu179ArgfsTer147	p.L179Rfs*147	ENST00000222254	NM_005027.3	178	ctGCTGGCACTGCCCGCGCCGCTCGTGACCCCCGAGGCCTCGGCCGAG/ct	5/16	0.390292751426551	3	FACETS	0.284	0.242	0.331	0.142	0.121	0.166	INDETERMINATE	1	TRUE	1	0.917719339211747	3		332	593	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339185	70339260	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAAGGAAAAAACAACTAAACGCCGCTTTCCTGCCTCAGGATGAACTGACGGCCTTGAATGTAAAACAAGGTTTCAA	TAAGGAAAAAACAACTAAACGCCGCTTTCCTGCCTCAGGATGAACTGACGGCCTTGAATGTAAAACAAGGTTTCAA	-	novel	NA	P-0005499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	271	494	0	ENST00000374080.3:c.100-35_140del		p.X34_splice	ENST00000374080		34		2/45	1	2	FACETS	0.789	0.743	0.834	0.789	0.743	0.834	SUBCLONAL	1	TRUE	1	0.917719339211747	2		494	749	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256531	+	missense_variant	Missense_Mutation	DNP	GT	GT	TG	novel	NA	P-0005499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	310	489	1	ENST00000369535.4:c.180_181delinsCA	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	60	ggACaa/ggCAaa	3/7	0.917719339211747	1	FACETS	0.999	0.971	1	0.999	0.971	1	CLONAL	1	TRUE	0	0.917719339211747	1		490	366	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0005502-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	804	755	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	2	TRUE	NA	0.422159257343348	2		755	1648	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939103	36939103	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005502-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1562	566	1047	1	ENST00000361632.4:c.606G>A	p.Trp202Ter	p.W202*	ENST00000361632		202	tgG/tgA	5/16	0.422159257343348	2	FACETS	1	0.995	1	0.63	0.603	0.657	CLONAL	1	TRUE	0	0.422159257343348	2		1048	2128	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718114	117718114	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs759261834	NA	P-0005502-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	296	522	0	ENST00000368508.3:c.743T>A	p.Phe248Tyr	p.F248Y	ENST00000368508	NM_002944.2	248	tTc/tAc	7/43	0.352763927851502	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	2	0.422159257343348	4		522	982	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024570	14024570	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005502-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	150	354	0	ENST00000311895.7:c.796A>G	p.Ile266Val	p.I266V	ENST00000311895	NM_005236.2	266	Atc/Gtc	5/11	0.422159257343348	3	FACETS	0.79	0.726	0.856	0.79	0.726	0.856	SUBCLONAL	2	TRUE	1	0.422159257343348	3		354	545	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044474	12044474	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005502-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	350	398	0	ENST00000353533.5:c.1097T>C	p.Phe366Ser	p.F366S	ENST00000353533	NM_003010.3	366	tTt/tCt	11/11	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.422159257343348	2		398	687	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	98	502	0	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	0.484767049014131	2	FACETS	1	0.943	1	0.536	0.481	0.592	CLONAL	1	TRUE	0	0.476490455512393	2		502	384	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134829	41134829	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	177	1050	1	ENST00000379561.5:c.799C>T	p.Arg267Ter	p.R267*	ENST00000379561	NM_002015.3	267	Cga/Tga	2/3	0.484767049014131	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.476490455512393	1		1051	553	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246062	41246062	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28897676	NA	P-0005508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	91	397	0	ENST00000357654.3:c.1486C>T	p.Arg496Cys	p.R496C	ENST00000357654	NM_007294.3	496	Cgt/Tgt	10/23	0.484767049014131	3	FACETS	0.843	0.75	0.942	0.422	0.375	0.471	CLONAL	1	TRUE	1	0.476490455512393	3		397	561	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246457	41246457	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	107	594	0	ENST00000357654.3:c.1091C>G	p.Pro364Arg	p.P364R	ENST00000357654	NM_007294.3	364	cCt/cGt	10/23	0.484767049014131	3	FACETS	0.858	0.771	0.95	0.429	0.385	0.475	CLONAL	1	TRUE	1	0.476490455512393	3		594	648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578509	7578509	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519978	NA	P-0005524-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	267	482	0	ENST00000269305.4:c.421T>G	p.Cys141Gly	p.C141G	ENST00000269305	NM_001126112.2	141	Tgc/Ggc	5/11	0.694205921685478	1	FACETS	0.939	0.89	0.987	0.939	0.89	0.987	CLONAL	1	TRUE	0	0.694205921685478	1		482	535	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050948	49050948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005524-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	156	337	0	ENST00000267163.4:c.2632G>A	p.Asp878Asn	p.D878N	ENST00000267163	NM_000321.2	878	Gat/Aat	25/27	0.694205921685478	1	FACETS	0.858	0.798	0.918	0.858	0.798	0.918	CLONAL	1	TRUE	0	0.694205921685478	1		337	342	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576033	29576033	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005524-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	280	518	0	ENST00000356175.3:c.4006C>T	p.Gln1336Ter	p.Q1336*	ENST00000356175	NM_000267.3	1336	Cag/Tag	30/57	0.694205921685478	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.694205921685478	1		518	505	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267899	7267899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748177213	NA	P-0005524-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	66	213	1	ENST00000302850.5:c.109G>A	p.Gly37Ser	p.G37S	ENST00000302850	NM_000208.2	37	Ggc/Agc	2/22	0.694205921685478	6	FACETS	0.47	0.406	0.539			1	SUBCLONAL	1	TRUE	NA	0.694205921685478	6		214	967	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866493	42866493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005524-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	279	677	0	ENST00000398585.3:c.139G>A	p.Ala47Thr	p.A47T	ENST00000398585	NM_001135099.1	47	Gct/Act	3/14	1	2	FACETS	0.85	0.799	0.901	0.85	0.799	0.901	CLONAL	1	TRUE	1	0.694205921685478	2		677	946	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	141	407	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	0.257999619950802	2		407	738	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955949	55955949	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	40	453	0	ENST00000263923.4:c.3213G>A	p.Trp1071Ter	p.W1071*	ENST00000263923	NM_002253.2	1071	tgG/tgA	24/30	0.209702197387379	1	FACETS	0.46	0.381	0.548	0.46	0.381	0.548	SUBCLONAL	1	TRUE	0	0.257999619950802	1		453	587	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89478254	89478254	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0005527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	25	358	0	ENST00000336596.2:c.2075-2A>G		p.X692_splice	ENST00000336596	NM_005233.5	692			0.128086112950909	0	FACETS	0.335	0.264	0.418			1	INDETERMINATE	1	TRUE	0	0.257999619950802	0		358	429	SUCCESS
ATM	472	MSKCC	GRCh37	11	108214100	108214100	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1060501713	NA	P-0005527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	132	285	0	ENST00000278616.4:c.8418+2T>C		p.X2806_splice	ENST00000278616	NM_000051.3	2806			0.257999619950802	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.257999619950802	2		285	482	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112884138	112884138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	38	330	0	ENST00000351677.2:c.73G>A	p.Val25Ile	p.V25I	ENST00000351677	NM_002834.3	25	Gtt/Att	2/16	1	2	FACETS	0.498	0.411	0.596	0.498	0.411	0.596	SUBCLONAL	1	TRUE	1	0.257999619950802	2		330	591	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041382	47041382	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	81	592	2	ENST00000377604.3:c.1726G>T	p.Glu576Ter	p.E576*	ENST00000377604	NM_001204468.1	576	Gag/Tag	16/24	0.189535997745326	0	FACETS	0.596	0.524	0.673			1	SUBCLONAL	1	TRUE	0	0.257999619950802	0		594	782	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0005544-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	93	412	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	0.19	2		412	767	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0005544-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	61	549	1	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	0.576	0.495	0.665	0.576	0.495	0.665	SUBCLONAL	1	TRUE	1	0.19	2		550	1115	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178210	142178210	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005544-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	42	292	0	ENST00000350721.4:c.7208G>T	p.Gly2403Val	p.G2403V	ENST00000350721	NM_001184.3	2403	gGa/gTa	43/47	1	2	FACETS	0.879	0.734	1	0.879	0.734	1	CLONAL	1	TRUE	1	0.19	2		292	503	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057799	180057799	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs747701670	NA	P-0005544-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	31	233	0	ENST00000261937.6:c.156G>C	p.Arg52Ser	p.R52S	ENST00000261937	NM_182925.4	52	agG/agC	3/30	1	2	FACETS	0.752	0.608	0.915	0.752	0.608	0.915	CLONAL	1	TRUE	1	0.19	2		233	434	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186601	108186601	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005544-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	48	353	0	ENST00000278616.4:c.6058G>T	p.Gly2020Cys	p.G2020C	ENST00000278616	NM_000051.3	2020	Ggc/Tgc	41/63	1	2	FACETS	0.729	0.615	0.855	0.729	0.615	0.855	SUBCLONAL	1	TRUE	1	0.19	2		353	693	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038831	47038831	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005544-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	32	287	0	ENST00000377604.3:c.838G>T	p.Gly280Ter	p.G280*	ENST00000377604	NM_001204468.1	280	Gga/Tga	9/24	1	2	FACETS	0.671	0.544	0.815	0.671	0.544	0.815	SUBCLONAL	1	TRUE	1	0.19	2		287	502	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504998	186504998	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	468	650	0	ENST00000323963.5:c.854A>G	p.Lys285Arg	p.K285R	ENST00000323963		285	aAg/aGg	8/11	1	2	FACETS	0.965	0.923	1	0.965	0.923	1	CLONAL	1	TRUE	1	0.742921476820463	2		650	1305	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862830	9862830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	112	382	1	ENST00000330684.3:c.2473G>A	p.Ala825Thr	p.A825T	ENST00000330684	NM_001134407.1	825	Gct/Act	12/13	0.198058316242334	1	FACETS	0.702	0.631	0.777	0.702	0.631	0.777	SUBCLONAL	1	TRUE	0	0.32	1		383	838	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577593	7577594	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0005546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	111	275	0	ENST00000269305.4:c.687_688del	p.Thr230HisfsTer9	p.T230Hfs*9	ENST00000269305	NM_001126112.2	229	tgTAcc/tgcc	7/11	0.304077304459979	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.32	1		275	548	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0005553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1633	534	433	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.573680901279277	6	FACETS	0.922	0.882	0.964			1	CLONAL	2	TRUE	NA	0.573680901279277	6		433	2167	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0005553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	1009	383	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.573680901279277	6	FACETS	0.994	0.968	1			1	CLONAL	4	TRUE	NA	0.573680901279277	6		383	1900	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075166	16075166	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	474	449	0	ENST00000268712.3:c.386T>C	p.Leu129Ser	p.L129S	ENST00000268712	NM_006311.3	129	tTa/tCa	4/46	0.567184745286085	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.573680901279277	2		449	794	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839668	42839668	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	83	615	1	ENST00000398585.3:c.1571A>T	p.Gln524Leu	p.Q524L	ENST00000398585	NM_001135099.1	524	cAa/cTa	13/14	0.38817004961363	3	FACETS	0.307	0.27	0.348	0.102	0.09	0.116	SUBCLONAL	1	TRUE	0	0.573680901279277	3		616	1212	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579531	7579531	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	496	583	0	ENST00000269305.4:c.156del	p.Gln52HisfsTer71	p.Q52Hfs*71	ENST00000269305	NM_001126112.2	52	caA/ca	4/11	0.567184745286085	2	FACETS	0.986	0.951	1	0.986	0.951	1	CLONAL	2	TRUE	0	0.573680901279277	2		583	877	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216624	108216626	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs786203976	NA	P-0005554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	275	287	0	ENST00000278616.4:c.8578_8580del	p.Ser2860del	p.S2860del	ENST00000278616	NM_000051.3	2858	aCTTct/act	58/63	0.535578924933042	5	FACETS	1	0.979	1	0.724	0.681	0.767	CLONAL	2	TRUE	2	0.535578924933042	5		287	853	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430864	181430864	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	784	527	0	ENST00000325404.1:c.716C>A	p.Ser239Tyr	p.S239Y	ENST00000325404	NM_003106.3	239	tCc/tAc	1/1	0.541663088151675	3	FACETS	0.885	0.865	0.904	1	0.997	1	CLONAL	4	TRUE	0	0.535578924933042	3		527	1049	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729706	41729706	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	203	640	0	ENST00000242208.4:c.823G>T	p.Gly275Cys	p.G275C	ENST00000242208	NM_002192.2	275	Ggt/Tgt	3/3	0.186907058475512	3	FACETS	1	0.955	1	0.347	0.321	0.373	INDETERMINATE	1	TRUE	0	0.535578924933042	3		640	924	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8338983	8338983	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	212	493	0	ENST00000356435.5:c.5318C>A	p.Pro1773His	p.P1773H	ENST00000356435		1773	cCc/cAc	32/35	0.541663088151675	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.535578924933042	1		493	494	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514736	103514736	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	182	394	0	ENST00000355739.4:c.1237G>A	p.Gly413Arg	p.G413R	ENST00000355739	NM_000123.3	413	Ggg/Agg	8/15	NA	2	FACETS	1	0.932	1			1	INDETERMINATE	1	TRUE	NA	0.535578924933042	2		394	675	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16062108	16062108	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	520	486	0	ENST00000268712.3:c.698G>T	p.Arg233Leu	p.R233L	ENST00000268712	NM_006311.3	233	cGc/cTc	6/46	0.541663088151675	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.535578924933042	2		486	802	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39576601	39576601	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0005554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	297	330	0	ENST00000262039.4:c.892-1G>A		p.X298_splice	ENST00000262039	NM_002647.2	298			0.541663088151675	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.535578924933042	3		330	610	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220706	1220706	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878853992	NA	P-0005554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	528	338	0	ENST00000326873.7:c.724G>A	p.Gly242Arg	p.G242R	ENST00000326873	NM_000455.4	242	Ggg/Agg	5/10	0.541663088151675	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.535578924933042	3		338	747	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600008	10600008	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	553	423	0	ENST00000171111.5:c.1568G>T	p.Gly523Val	p.G523V	ENST00000171111	NM_203500.1	523	gGg/gTg	5/6	0.541663088151675	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.535578924933042	3		423	821	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26970431	26970431	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	366	481	1	ENST00000381527.3:c.802del	p.Glu268LysfsTer3	p.E268Kfs*3	ENST00000381527	NM_001260.1	267	tGg/tg	8/13	0.428937327810881	4	FACETS	0.997	0.947	1			1	CLONAL	2	TRUE	NA	0.535578924933042	4		482	1053	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	16	495	0	ENST00000263967.3:c.3129G>C	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atC	21/21	0.219248144147668	5	FACETS	0.268	0.197	0.354	0.067	0.049	0.089	SUBCLONAL	1	FALSE	1	0.219248144147668	5		495	723	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612911	228612911	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1587	112	935	0	ENST00000366696.1:c.116C>T	p.Pro39Leu	p.P39L	ENST00000366696	NM_003493.2	39	cCg/cTg	1/1	0.219248144147668	5	FACETS	0.799	0.716	0.888	0.266	0.238	0.296	SUBCLONAL	1	FALSE	2	0.219248144147668	5		935	1699	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916728	178916728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1497	35	1108	0	ENST00000263967.3:c.115G>A	p.Glu39Lys	p.E39K	ENST00000263967	NM_006218.2	39	Gag/Aag	2/21	0.219248144147668	5	FACETS	0.277	0.225	0.335	0.069	0.056	0.084	SUBCLONAL	1	FALSE	1	0.219248144147668	5		1108	1532	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553135	106553135	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	63	356	1	ENST00000369096.4:c.1100C>A	p.Ser367Tyr	p.S367Y	ENST00000369096	NM_001198.3	367	tCt/tAt	5/7	0.219248144147668	1	FACETS	0.796	0.688	0.913	0.796	0.688	0.913	CLONAL	1	FALSE	0	0.219248144147668	1		357	643	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151167722	151167722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	28	363	0	ENST00000262187.5:c.397G>A	p.Glu133Lys	p.E133K	ENST00000262187	NM_005614.3	133	Gaa/Aaa	7/8	0.104795183740051	5	FACETS	0.727	0.58	0.895	0.242	0.193	0.299	INDETERMINATE	1	FALSE	2	0.219248144147668	5		363	467	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372025	55372025	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	52	244	0	ENST00000297316.4:c.715G>A	p.Ala239Thr	p.A239T	ENST00000297316	NM_022454.3	239	Gcc/Acc	2/2	0.104795183740051	5	FACETS	1	0.945	1	0.416	0.354	0.484	INDETERMINATE	1	FALSE	2	0.219248144147668	5		244	505	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061549	38061549	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	28	259	0	ENST00000250448.2:c.440A>C	p.Asn147Thr	p.N147T	ENST00000250448	NM_004496.3	147	aAc/aCc	2/2	0.198219878254767	3	FACETS	0.6	0.479	0.739	0.3	0.239	0.37	SUBCLONAL	1	FALSE	1	0.219248144147668	3		259	472	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732322	74732322	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1349459208	NA	P-0005611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4167	509	1170	0	ENST00000359995.5:c.587C>T	p.Ser196Phe	p.S196F	ENST00000359995	NM_001195427.1	196	tCc/tTc	2/3	0.219248144147668	5	FACETS	1	0.994	1	0.44	0.418	0.462	CLONAL	1	FALSE	2	0.219248144147668	5		1170	4676	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732373	74732373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4339	422	1198	2	ENST00000359995.5:c.536C>T	p.Ser179Phe	p.S179F	ENST00000359995	NM_001195427.1	179	tCt/tTt	2/3	0.219248144147668	5	FACETS	1	0.98	1	0.358	0.338	0.379	CLONAL	1	FALSE	2	0.219248144147668	5		1200	4761	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732484	74732484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755334722	NA	P-0005611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3317	399	888	0	ENST00000359995.5:c.425C>T	p.Ser142Phe	p.S142F	ENST00000359995	NM_001195427.1	142	tCt/tTt	2/3	0.219248144147668	5	FACETS	1	0.993	1	0.434	0.41	0.459	CLONAL	1	FALSE	2	0.219248144147668	5		888	3716	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0005625-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	312	316	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.673730337741821	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.673730337741821	3		316	600	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0005625-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	361	353	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.673730337741821	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.673730337741821	2		353	523	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467663	50467663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005625-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	318	475	0	ENST00000331340.3:c.898G>A	p.Glu300Lys	p.E300K	ENST00000331340	NM_006060.4	300	Gag/Aag	8/8	0.664162453292946	4	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	2	0.673730337741821	4		475	790	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776099	9776099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748146002	NA	P-0005625-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	112	283	0	ENST00000377346.4:c.563G>A	p.Arg188Gln	p.R188Q	ENST00000377346	NM_005026.3	188	cGg/cAg	5/24	NA	2	FACETS	0.891	0.809	0.976			1	INDETERMINATE	1	TRUE	NA	0.673730337741821	2		283	373	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089745	27089745	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005625-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	94	269	0	ENST00000324856.7:c.2701A>G	p.Met901Val	p.M901V	ENST00000324856	NM_006015.4	901	Atg/Gtg	8/20	0.100337181271526	4	FACETS	0.902	0.815	0.991	0.902	0.815	0.991	INDETERMINATE	2	TRUE	2	0.673730337741821	4		269	259	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843736	156843736	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1008878777	NA	P-0005625-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	232	652	0	ENST00000524377.1:c.1162G>A	p.Glu388Lys	p.E388K	ENST00000524377	NM_002529.3	388	Gag/Aag	8/17	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.673730337741821	2		652	607	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730910	40730910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370873414	NA	P-0005625-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	173	303	4	ENST00000373198.4:c.3625C>T	p.Arg1209Trp	p.R1209W	ENST00000373198	NM_133170.3	1209	Cgg/Tgg	27/32	0.211750000918913	5	FACETS	1	0.984	1			1	INDETERMINATE	2	TRUE	NA	0.673730337741821	5		307	429	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790065	40790065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780417311	NA	P-0005625-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	200	386	1	ENST00000373198.4:c.2666G>A	p.Arg889Gln	p.R889Q	ENST00000373198	NM_133170.3	889	cGg/cAg	18/32	0.211750000918913	5	FACETS	1	0.934	1			1	INDETERMINATE	2	TRUE	NA	0.673730337741821	5		387	596	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100962	41100962	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005625-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	218	469	0	ENST00000373198.4:c.1394C>T	p.Ser465Phe	p.S465F	ENST00000373198	NM_133170.3	465	tCt/tTt	8/32	0.211750000918913	5	FACETS	1	0.97	1			1	INDETERMINATE	2	TRUE	NA	0.673730337741821	5		469	614	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005629-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	105	407	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.44	2		407	477	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287478	33287478	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005629-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	22	323	0	ENST00000374542.5:c.1619C>T	p.Pro540Leu	p.P540L	ENST00000374542	NM_001141970.1	540	cCc/cTc	6/8	0.3	4	FACETS	0.33	0.255	0.418			1	SUBCLONAL	1	TRUE	NA	0.44	4		323	436	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044971	47044971	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005629-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	63	506	0	ENST00000377604.3:c.2297G>C	p.Arg766Pro	p.R766P	ENST00000377604	NM_001204468.1	766	cGc/cCc	20/24	0.281105046446631	1	FACETS	0.466	0.404	0.534	0.466	0.404	0.534	SUBCLONAL	1	TRUE	0	0.44	1		506	479	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136172	11136172	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005629-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	40	437	1	ENST00000358026.2:c.3157del	p.Gln1053SerfsTer53	p.Q1053Sfs*53	ENST00000358026	NM_001128849.1	1052	ttC/tt	22/36	0.195009945452399	2	FACETS	0.423	0.351	0.502	0.211	0.175	0.251	INDETERMINATE	1	TRUE	0	0.44	2		438	430	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207037	1207037	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005629-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	123	400	0	ENST00000326873.7:c.127del	p.Ala43ProfsTer8	p.A43Pfs*8	ENST00000326873	NM_000455.4	42	cGg/cg	1/10	0.195009945452399	2	FACETS	1	0.926	1	0.511	0.464	0.56	INDETERMINATE	1	TRUE	0	0.44	2		400	547	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188188	108188194	+	frameshift_variant	Frame_Shift_Del	DEL	AAGAACT	AAGAACT	TC	novel	NA	P-0005629-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	62	440	0	ENST00000278616.4:c.6287_6293delinsTC	p.Glu2096ValfsTer29	p.E2096Vfs*29	ENST00000278616	NM_000051.3	2096	gAAGAACTt/gTCt	43/63	0.195009945452399	2	FACETS	0.752	0.652	0.858	0.376	0.326	0.429	INDETERMINATE	1	TRUE	0	0.44	2		440	375	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	61	145	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.562	0.485	0.647	0.562	0.485	0.647	SUBCLONAL	1	TRUE	1	0.342238110317594	2		145	634	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0005643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	116	316	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.185937611563232	3	FACETS	1	0.979	1	0.662	0.598	0.729	INDETERMINATE	1	TRUE	1	0.342238110317594	3		316	600	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0005643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	60	401	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.612	0.527	0.704	0.612	0.527	0.704	SUBCLONAL	1	TRUE	1	0.342238110317594	2		401	573	SUCCESS
APC	324	MSKCC	GRCh37	5	112174388	112174388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	37	248	1	ENST00000257430.4:c.3097G>A	p.Asp1033Asn	p.D1033N	ENST00000257430	NM_000038.5	1033	Gat/Aat	16/16	0.0974951386961058	4	FACETS	0.711	0.587	0.85	0.356	0.293	0.425	INDETERMINATE	1	TRUE	2	0.342238110317594	4		249	408	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624270	89624270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123324	NA	P-0005643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	45	152	0	ENST00000371953.3:c.44G>A	p.Arg15Lys	p.R15K	ENST00000371953	NM_000314.4	15	aGa/aAa	1/9	0.342238110317594	1	FACETS	0.529	0.445	0.621	0.529	0.445	0.621	SUBCLONAL	1	TRUE	0	0.342238110317594	1		152	412	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350115	81350115	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	27	901	0	ENST00000222390.5:c.1217C>G	p.Thr406Arg	p.T406R	ENST00000222390	NM_000601.4	406	aCa/aGa	10/18	1	2	FACETS	0.15	0.119	0.185	0.15	0.119	0.185	SUBCLONAL	1	TRUE	1	0.889186301159223	2		901	406	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436080	116436080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752669237	NA	P-0005651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	24	911	1	ENST00000397752.3:c.4075G>A	p.Val1359Ile	p.V1359I	ENST00000397752	NM_000245.2	1359	Gta/Ata	21/21	1	2	FACETS	0.183	0.143	0.229	0.183	0.143	0.229	SUBCLONAL	1	TRUE	1	0.889186301159223	2		912	295	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874196	151874196	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	131	724	0	ENST00000262189.6:c.8342T>C	p.Ile2781Thr	p.I2781T	ENST00000262189	NM_170606.2	2781	aTt/aCt	38/59	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.889186301159223	2		724	289	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200951	108200951	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1565529306	NA	P-0005651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	102	645	0	ENST00000278616.4:c.7318A>G	p.Lys2440Glu	p.K2440E	ENST00000278616	NM_000051.3	2440	Aag/Gag	50/63	0.884142424784421	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.889186301159223	1		645	118	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347665	118347665	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	166	917	0	ENST00000534358.1:c.3302G>A	p.Arg1101Gln	p.R1101Q	ENST00000534358	NM_005933.3	1101	cGa/cAa	4/36	0.884142424784421	1	FACETS	0.988	0.944	1	0.988	0.944	1	CLONAL	1	TRUE	0	0.889186301159223	1		917	210	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478860	56478860	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs757425458	NA	P-0005651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	56	1196	1	ENST00000267101.3:c.316C>T	p.Arg106Ter	p.R106*	ENST00000267101	NM_001982.3	106	Cga/Tga	3/28	1	2	FACETS	0.277	0.237	0.32	0.277	0.237	0.32	SUBCLONAL	1	TRUE	1	0.889186301159223	2		1197	455	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	510	407	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.547518877654116	3	FACETS	0.924	0.887	0.962	0.924	0.887	0.962	CLONAL	2	FALSE	1	0.556720403042399	3		407	1267	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921566	178921566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793349	NA	P-0005652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	181	295	0	ENST00000263967.3:c.1048G>A	p.Asp350Asn	p.D350N	ENST00000263967	NM_006218.2	350	Gac/Aac	5/21	1	2	FACETS	0.944	0.873	1	0.944	0.873	1	CLONAL	1	FALSE	1	0.556720403042399	2		295	689	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0005652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	378	630	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	NA	2	FACETS	0.929	0.889	0.968			1	INDETERMINATE	2	FALSE	NA	0.556720403042399	2		630	731	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604741	48604749	+	inframe_deletion	In_Frame_Del	DEL	ACCTTGCTG	ACCTTGCTG	-	novel	NA	P-0005652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	243	532	0	ENST00000342988.3:c.1563_1571del	p.Pro522_Trp524del	p.P522_W524del	ENST00000342988	NM_005359.5	521	acACCTTGCTGg/acg	12/12	0.556720403042399	1	FACETS	0.84	0.788	0.893	0.84	0.788	0.893	CLONAL	1	FALSE	0	0.556720403042399	1		532	750	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574030	7574030	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	29	474	0	ENST00000269305.4:c.997del	p.Arg333ValfsTer12	p.R333Vfs*12	ENST00000269305	NM_001126112.2	333	Cgt/gt	10/11	0.247338994599391	4	FACETS	0.44	0.353	0.539	0.22	0.176	0.27	INDETERMINATE	1	FALSE	2	0.557705202786129	4		474	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934578	NA	P-0005655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	56	305	0	ENST00000269305.4:c.524G>T	p.Arg175Leu	p.R175L	ENST00000269305	NM_001126112.2	175	cGc/cTc	5/11	0.247338994599391	4	FACETS	1	0.963	1	0.674	0.584	0.77	INDETERMINATE	1	FALSE	2	0.557705202786129	4		305	232	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300570	11300570	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764486955	NA	P-0005655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	102	450	0	ENST00000361445.4:c.1576C>T	p.Arg526Cys	p.R526C	ENST00000361445	NM_004958.3	526	Cgt/Tgt	11/58	0.278582844260797	4	FACETS	1	0.927	1			1	INDETERMINATE	1	FALSE	NA	0.557705202786129	4		450	547	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937383	76937383	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	62	365	0	ENST00000373344.5:c.3365del	p.Cys1122LeufsTer8	p.C1122Lfs*8	ENST00000373344	NM_000489.3	1122	tGt/tt	9/35	0.179848890220198	2	FACETS	0.444	0.384	0.509	0.222	0.192	0.255	INDETERMINATE	1	FALSE	0	0.557705202786129	2		365	501	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513488	149513488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465364786	NA	P-0005679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	96	236	0	ENST00000261799.4:c.715G>A	p.Gly239Arg	p.G239R	ENST00000261799	NM_002609.3	239	Ggg/Agg	5/23	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.265837122648894	2		236	700	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11313987	11313987	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005694-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	183	724	0	ENST00000361445.4:c.749C>G	p.Ala250Gly	p.A250G	ENST00000361445	NM_004958.3	250	gCc/gGc	6/58	0.269331234752763	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.274712274819528	1		724	1044	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131895027	131895027	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005694-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	83	389	0	ENST00000265335.6:c.181A>C	p.Thr61Pro	p.T61P	ENST00000265335		61	Acc/Ccc	2/25	0.145678809592545	4	FACETS	0.949	0.836	1	0.474	0.418	0.535	INDETERMINATE	1	TRUE	2	0.274712274819528	4		389	812	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115796	8115796	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005694-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1284	245	833	3	ENST00000346208.3:c.1142C>A	p.Ser381Ter	p.S381*	ENST00000346208		381	tCa/tAa	6/6	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.274712274819528	2		836	1529	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483910	88483910	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1170771297	NA	P-0005694-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	144	669	4	ENST00000360948.2:c.1660C>A	p.Leu554Met	p.L554M	ENST00000360948	NM_001012338.2	554	Ctg/Atg	14/19	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.274712274819528	2		673	795	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576106	88576106	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005694-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	170	703	1	ENST00000360948.2:c.1567T>A	p.Cys523Ser	p.C523S	ENST00000360948	NM_001012338.2	523	Tgc/Agc	13/19	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.274712274819528	2		704	928	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553474	29553474	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs779546178	NA	P-0005694-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	245	608	3	ENST00000356175.3:c.2023G>T	p.Gly675Ter	p.G675*	ENST00000356175	NM_000267.3	675	Gga/Tga	18/57	0.105236580570397	3	FACETS	0.835	0.779	0.892	0.835	0.779	0.892	INDETERMINATE	2	TRUE	1	0.274712274819528	3		611	1215	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556193	29556193	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555614261	NA	P-0005694-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	72	265	2	ENST00000356175.3:c.2560C>T	p.Gln854Ter	p.Q854*	ENST00000356175	NM_000267.3	854	Cag/Tag	21/57	0.105236580570397	3	FACETS	1	0.972	1	0.708	0.621	0.801	INDETERMINATE	1	TRUE	1	0.274712274819528	3		267	421	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061118	38061121	+	frameshift_variant	Frame_Shift_Del	DEL	GGCC	GGCC	-	novel	NA	P-0005698-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	153	159	0	ENST00000250448.2:c.868_871del	p.Gly290LeufsTer30	p.G290Lfs*30	ENST00000250448	NM_004496.3	290	GGCCct/ct	2/2	0.322329498819064	3	FACETS	0.881	0.82	0.943	1	0.988	1	CLONAL	3	TRUE	1	0.434829480934168	3		159	324	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0005707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	152	546	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.237947436845283	3	FACETS	1	0.962	1	0.713	0.658	0.77	CLONAL	2	TRUE	0	0.370923609556266	3		546	454	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445035	89445035	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	107	702	0	ENST00000336596.2:c.1355G>T	p.Ser452Ile	p.S452I	ENST00000336596	NM_005233.5	452	aGc/aTc	6/17	1	2	FACETS	0.92	0.827	1	0.92	0.827	1	CLONAL	1	TRUE	1	0.370923609556266	2		702	627	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038792	47038792	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1556777844	NA	P-0005707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	132	581	0	ENST00000377604.3:c.799C>T	p.Gln267Ter	p.Q267*	ENST00000377604	NM_001204468.1	267	Cag/Tag	9/24	0.30790266662471	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.370923609556266	3		581	368	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727107	243727107	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	146	593	0	ENST00000263826.5:c.863C>G	p.Thr288Arg	p.T288R	ENST00000263826	NM_005465.4	288	aCa/aGa	9/13	0.255947442285764	4	FACETS	1	0.985	1	0.687	0.627	0.749	CLONAL	1	TRUE	2	0.370923609556266	4		593	786	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47168137	47168137	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0005707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	80	632	1	ENST00000409792.3:c.87+1G>T		p.X29_splice	ENST00000409792	NM_014159.6	29			1	2	FACETS	0.875	0.772	0.984	0.875	0.772	0.984	CLONAL	1	TRUE	1	0.370923609556266	2		633	493	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801519	1801519	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	143	715	0	ENST00000260795.2:c.425A>T	p.Glu142Val	p.E142V	ENST00000260795		142	gAg/gTg	3/17	0.307107351371806	3	FACETS	0.762	0.697	0.829	0.762	0.697	0.829	SUBCLONAL	2	TRUE	1	0.370923609556266	3		715	600	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923688	131923688	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	247	671	0	ENST00000265335.6:c.958A>T	p.Arg320Trp	p.R320W	ENST00000265335		320	Agg/Tgg	7/25	0.307107351371806	3	FACETS	0.892	0.836	0.95	0.892	0.836	0.95	CLONAL	2	TRUE	1	0.370923609556266	3		671	885	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514478	149514478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1399184006	NA	P-0005707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	86	722	0	ENST00000261799.4:c.466C>A	p.Leu156Met	p.L156M	ENST00000261799	NM_002609.3	156	Ctg/Atg	4/23	1	2	FACETS	0.818	0.725	0.917	0.818	0.725	0.917	CLONAL	1	TRUE	1	0.370923609556266	2		722	567	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401528	401528	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs767774669	NA	P-0005707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	156	635	1	ENST00000380956.4:c.850G>T	p.Ala284Ser	p.A284S	ENST00000380956	NM_001195286.1	284	Gcc/Tcc	7/9	0.307107351371806	3	FACETS	0.852	0.784	0.923	0.852	0.784	0.923	CLONAL	2	TRUE	1	0.370923609556266	3		636	585	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729954	41729954	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	201	1008	2	ENST00000242208.4:c.575C>A	p.Ala192Asp	p.A192D	ENST00000242208	NM_002192.2	192	gCc/gAc	3/3	0.30790266662471	3	FACETS	1	0.985	1	0.622	0.576	0.67	CLONAL	1	TRUE	1	0.370923609556266	3		1010	1032	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751019	128751019	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1347	71	448	0	ENST00000377970.2:c.556T>A	p.Cys186Ser	p.C186S	ENST00000377970	NM_002467.4	186	Tgc/Agc	2/3	0.370923609556266	13	FACETS	0.821	0.713	0.938			1	CLONAL	1	TRUE	NA	0.370923609556266	13		448	1418	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425124	49425124	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	89	759	1	ENST00000301067.7:c.13364G>C	p.Arg4455Pro	p.R4455P	ENST00000301067	NM_003482.3	4455	cGc/cCc	39/54	0.30790266662471	3	FACETS	0.948	0.842	1	0.474	0.421	0.531	CLONAL	1	TRUE	1	0.370923609556266	3		760	600	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432038	49432038	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	209	821	0	ENST00000301067.7:c.9101A>T	p.Asn3034Ile	p.N3034I	ENST00000301067	NM_003482.3	3034	aAt/aTt	34/54	0.30790266662471	3	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	1	0.370923609556266	3		821	664	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922007	39922007	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	83	777	0	ENST00000378444.4:c.4165G>T	p.Asp1389Tyr	p.D1389Y	ENST00000378444	NM_001123385.1	1389	Gat/Tat	9/15	0.30790266662471	3	FACETS	0.904	0.799	1	0.452	0.399	0.508	CLONAL	1	TRUE	1	0.370923609556266	3		777	587	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247099	53247099	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	124	987	0	ENST00000375401.3:c.401G>T	p.Trp134Leu	p.W134L	ENST00000375401	NM_004187.3	134	tGg/tTg	4/26	0.30790266662471	3	FACETS	0.97	0.878	1	0.485	0.439	0.534	CLONAL	1	TRUE	1	0.370923609556266	3		987	817	SUCCESS
AR	367	MSKCC	GRCh37	X	66931523	66931523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769862197	NA	P-0005707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	88	649	0	ENST00000374690.3:c.2165C>T	p.Ala722Val	p.A722V	ENST00000374690	NM_000044.3	722	gCc/gTc	4/8	0.30790266662471	3	FACETS	0.922	0.818	1	0.461	0.409	0.517	CLONAL	1	TRUE	1	0.370923609556266	3		649	610	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877415	40877415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	164	611	2	ENST00000373198.4:c.2281del	p.Asp761ThrfsTer4	p.D761Tfs*4	ENST00000373198	NM_133170.3	761	Gac/ac	15/32	0.365656374544561	2	FACETS	0.837	0.774	0.903	0.837	0.774	0.903	CLONAL	2	TRUE	0	0.370923609556266	2		613	528	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223099	1223109	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGCGGACGA	GGCGCGGACGA	-	novel	NA	P-0005707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	162	769	0	ENST00000326873.7:c.1038_1048del	p.Ala347ArgfsTer9	p.A347Rfs*9	ENST00000326873	NM_000455.4	346	GGCGCGGACGAg/g	8/10	0.365656374544561	2	FACETS	0.981	0.909	1	0.981	0.909	1	CLONAL	2	TRUE	0	0.370923609556266	2		769	445	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223078	1223092	+	inframe_deletion	In_Frame_Del	DEL	CCGTACTTGGAGGAC	CCGTACTTGGAGGAC	-	novel	NA	P-0005707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	164	757	0	ENST00000326873.7:c.1016_1030del	p.Pro339_Asp343del	p.P339_D343del	ENST00000326873	NM_000455.4	339	CCGTACTTGGAGGAC/-	8/10	0.365656374544561	2	FACETS	0.955	0.885	1	0.955	0.885	1	CLONAL	2	TRUE	0	0.370923609556266	2		757	463	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0005732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	427	549	1	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.90511234059591	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.90511234059591	1		550	451	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845344	156845344	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	238	900	0	ENST00000524377.1:c.1387G>T	p.Ala463Ser	p.A463S	ENST00000524377	NM_002529.3	463	Gcc/Tcc	12/17	0.473857980512682	3	FACETS	0.63	0.587	0.674	0.315	0.293	0.337	INDETERMINATE	1	TRUE	1	0.90511234059591	3		900	1213	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466816	25466816	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	330	636	0	ENST00000264709.3:c.1887G>T	p.Glu629Asp	p.E629D	ENST00000264709	NM_175629.2	629	gaG/gaT	16/23	1	2	FACETS	0.981	0.934	1	0.981	0.934	1	CLONAL	1	TRUE	1	0.90511234059591	2		636	743	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738275	190738275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	141	247	0	ENST00000441310.2:c.2527C>T	p.Pro843Ser	p.P843S	ENST00000441310	NM_000534.4	843	Cca/Tca	12/13	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.90511234059591	2		247	296	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55603391	55603391	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	138	677	0	ENST00000288135.5:c.2747C>A	p.Thr916Lys	p.T916K	ENST00000288135	NM_000222.2	916	aCa/aAa	20/21	0.55852642944844	1	FACETS	0.312	0.285	0.34	0.312	0.285	0.34	SUBCLONAL	1	TRUE	0	0.90511234059591	1		677	535	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748573	43748573	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	587	966	1	ENST00000523873.1:c.527G>A	p.Trp176Ter	p.W176*	ENST00000523873		176	tGg/tAg	6/8	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.90511234059591	2		967	1208	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940369	13940369	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	158	287	0	ENST00000405192.2:c.1137G>C	p.Met379Ile	p.M379I	ENST00000405192	NM_001163147.1	379	atG/atC	11/12	1	2	FACETS	0.995	0.925	1	0.995	0.925	1	CLONAL	1	TRUE	1	0.90511234059591	2		287	351	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386620	81386620	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0005732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	123	252	0	ENST00000222390.5:c.368-1G>T		p.X123_splice	ENST00000222390	NM_000601.4	123			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.90511234059591	2		252	240	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520000	106520000	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	246	521	0	ENST00000359195.3:c.2428C>G	p.Pro810Ala	p.P810A	ENST00000359195	NM_002649.2	810	Cca/Gca	6/11	0.169664222337012	3	FACETS	1	0.992	1	0.688	0.648	0.727	INDETERMINATE	1	TRUE	1	0.90511234059591	3		521	574	SUCCESS
ATM	472	MSKCC	GRCh37	11	108137989	108137989	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555082235	NA	P-0005732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	240	719	1	ENST00000278616.4:c.2558C>T	p.Ser853Leu	p.S853L	ENST00000278616	NM_000051.3	853	tCa/tTa	17/63	1	2	FACETS	0.587	0.549	0.627	0.587	0.549	0.627	SUBCLONAL	1	TRUE	1	0.90511234059591	2		720	903	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304138	91304138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567041193	NA	P-0005732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	287	559	2	ENST00000355112.3:c.1535G>A	p.Gly512Glu	p.G512E	ENST00000355112	NM_000057.2	512	gGa/gAa	7/22	0.535773298154542	1	FACETS	0.74	0.707	0.773	0.74	0.707	0.773	INDETERMINATE	1	TRUE	0	0.90511234059591	1		561	469	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740365	58740365	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs780886952	NA	P-0005732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	467	848	0	ENST00000305921.3:c.1270G>T	p.Glu424Ter	p.E424*	ENST00000305921	NM_003620.3	424	Gag/Tag	6/6	0.169664222337012	3	FACETS	0.753	0.723	0.784	0.753	0.723	0.784	INDETERMINATE	2	TRUE	1	0.90511234059591	3		848	995	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095922	29095922	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	133	450	0	ENST00000328354.6:c.912G>T	p.Met304Ile	p.M304I	ENST00000328354	NM_007194.3	304	atG/atT	9/15	0.442403158893151	1	FACETS	0.339	0.31	0.37	0.339	0.31	0.37	INDETERMINATE	1	TRUE	0	0.90511234059591	1		450	474	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921460	39921460	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs967564648	NA	P-0005732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	356	764	0	ENST00000378444.4:c.4360C>T	p.Arg1454Trp	p.R1454W	ENST00000378444	NM_001123385.1	1454	Cgg/Tgg	10/15	NA	2	FACETS	0.897	0.854	0.941			1	INDETERMINATE	1	TRUE	NA	0.90511234059591	2		764	877	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422458	47422458	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	459	1035	0	ENST00000377045.4:c.92C>A	p.Thr31Lys	p.T31K	ENST00000377045	NM_001654.4	31	aCg/aAg	2/16	NA	2	FACETS	0.957	0.917	0.997			1	INDETERMINATE	1	TRUE	NA	0.90511234059591	2		1035	1060	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553520	29553520	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060500364	NA	P-0005732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	309	587	1	ENST00000356175.3:c.2071del	p.Leu691CysfsTer57	p.L691Cfs*57	ENST00000356175	NM_000267.3	690	gCc/gc	18/57	NA	2	FACETS	1	0.958	1			1	INDETERMINATE	1	TRUE	NA	0.90511234059591	2		588	677	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788615	3788617	+	missense_variant	Missense_Mutation	TNP	TGC	TGC	AGA	novel	NA	P-0005732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	330	575	0	ENST00000262367.5:c.4337_4339delinsTCT	p.Arg1446_Thr1447delinsLeuSer	p.R1446_T1447delinsLS	ENST00000262367	NM_004380.2	1446	cGCAca/cTCTca	26/31	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.90511234059591	2		575	700	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0005736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	30	561	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.220001741859248	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.220001741859248	1		561	170	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955538	48955538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913303	NA	P-0005736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	35	362	0	ENST00000267163.4:c.1654C>T	p.Arg552Ter	p.R552*	ENST00000267163	NM_000321.2	552	Cga/Tga	17/27	1	2	FACETS	0.799	0.662	0.951	1	0.955	1	CLONAL	2	TRUE	1	0.220001741859248	2		362	199	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965150	25965150	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	29	438	0	ENST00000435504.4:c.4056C>G	p.Ser1352Arg	p.S1352R	ENST00000435504		1352	agC/agG	13/13	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.220001741859248	2		438	196	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788602	3788602	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	32	454	0	ENST00000262367.5:c.4352A>G	p.His1451Arg	p.H1451R	ENST00000262367	NM_004380.2	1451	cAt/cGt	26/31	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.220001741859248	2		454	215	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846124	68846129	+	inframe_deletion	In_Frame_Del	DEL	CACTGA	CACTGA	-	novel	NA	P-0005736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	29	403	0	ENST00000261769.5:c.1098_1103del	p.Asp367_Thr368del	p.D367_T368del	ENST00000261769	NM_004360.3	365	gtCACTGAc/gtc	8/16	0.220001741859248	0	FACETS	1	0.871	1			1	CLONAL	1	TRUE	0	0.220001741859248	0		403	187	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188207	10188207	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005753-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	105	309	0	ENST00000256474.2:c.350G>T	p.Trp117Leu	p.W117L	ENST00000256474	NM_000551.3	117	tGg/tTg	2/3	0.416469070446134	2	FACETS	0.857	0.781	0.934	0.857	0.781	0.934	CLONAL	2	TRUE	0	0.471162955461079	2		309	260	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260696	16260696	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005753-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	44	216	0	ENST00000375759.3:c.7961T>C	p.Leu2654Pro	p.L2654P	ENST00000375759	NM_015001.2	2654	cTc/cCc	11/15	0.390004349696824	3	FACETS	0.782	0.66	0.917	0.391	0.33	0.459	CLONAL	1	TRUE	1	0.471162955461079	3		216	295	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087880	27087880	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005753-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	57	222	0	ENST00000324856.7:c.2167C>T	p.Gln723Ter	p.Q723*	ENST00000324856	NM_006015.4	723	Cag/Tag	6/20	0.390004349696824	3	FACETS	0.817	0.704	0.939	0.408	0.352	0.47	CLONAL	1	TRUE	1	0.471162955461079	3		222	366	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265477	198265477	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005753-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	30	199	0	ENST00000335508.6:c.2680G>T	p.Asp894Tyr	p.D894Y	ENST00000335508	NM_012433.2	894	Gat/Tat	18/25	0.18754273479128	6	FACETS	0.658	0.53	0.802	0.219	0.176	0.268	INDETERMINATE	1	TRUE	3	0.471162955461079	6		199	376	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125356	47125356	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005753-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	149	282	0	ENST00000409792.3:c.5914G>T	p.Glu1972Ter	p.E1972*	ENST00000409792	NM_014159.6	1972	Gaa/Taa	12/21	0.416469070446134	2	FACETS	0.789	0.729	0.85	0.789	0.729	0.85	SUBCLONAL	2	TRUE	0	0.471162955461079	2		282	401	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959168	28959168	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005753-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	31	204	0	ENST00000282397.4:c.1970A>C	p.Asp657Ala	p.D657A	ENST00000282397	NM_002019.4	657	gAt/gCt	14/30	0.471162955461079	5	FACETS	0.507	0.41	0.617	0.169	0.136	0.206	SUBCLONAL	1	TRUE	2	0.471162955461079	5		204	443	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90633839	90633839	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005753-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	72	261	0	ENST00000330062.3:c.245T>G	p.Phe82Cys	p.F82C	ENST00000330062	NM_002168.2	82	tTt/tGt	3/11	0.390004349696824	3	FACETS	0.935	0.821	1	0.467	0.41	0.529	CLONAL	1	TRUE	1	0.471162955461079	3		261	404	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643430	52643430	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005753-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	99	298	0	ENST00000394830.3:c.2466del	p.Phe822LeufsTer3	p.F822Lfs*3	ENST00000394830	NM_018313.4	822	ttT/tt	17/30	0.416469070446134	2	FACETS	1	0.969	1	0.597	0.538	0.658	CLONAL	1	TRUE	0	0.471162955461079	2		298	352	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230361	46230371	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TATCATTACAG	TATCATTACAG	-	novel	NA	P-0005753-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	65	175	0	ENST00000334344.6:c.706-10_706del		p.X236_splice	ENST00000334344	NM_152641.2	236			0.320634291691382	4	FACETS	1	0.966	1	0.67	0.585	0.76	CLONAL	1	TRUE	2	0.471162955461079	4		175	303	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005779-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	171	145	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.801798280207665	2		145	381	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801782	3801782	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005779-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	206	381	1	ENST00000262367.5:c.3724A>T	p.Thr1242Ser	p.T1242S	ENST00000262367	NM_004380.2	1242	Aca/Tca	20/31	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.801798280207665	2		382	439	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132434	11132434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005779-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	316	579	1	ENST00000358026.2:c.2650C>T	p.His884Tyr	p.H884Y	ENST00000358026	NM_001128849.1	884	Cac/Tac	19/36	0.801798280207665	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.801798280207665	1		580	429	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39726885	39726885	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005779-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	174	400	1	ENST00000361337.2:c.883A>T	p.Thr295Ser	p.T295S	ENST00000361337	NM_003286.2	295	Acc/Tcc	11/21	0.648472913303471	3	FACETS	1	0.975	1	0.557	0.516	0.599	CLONAL	1	TRUE	1	0.801798280207665	3		401	546	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573129	41573129	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005779-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	470	386	0	ENST00000263253.7:c.5414T>C	p.Phe1805Ser	p.F1805S	ENST00000263253	NM_001429.3	1805	tTc/tCc	31/31	0.583253859029552	3	FACETS	1	0.973	1			1	CLONAL	2	TRUE	NA	0.801798280207665	3		386	812	SUCCESS
APC	324	MSKCC	GRCh37	5	112174758	112174761	+	frameshift_variant	Frame_Shift_Del	DEL	AAGA	AAGA	-	rs1554085029	NA	P-0005782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	22	464	0	ENST00000257430.4:c.3467_3470del	p.Glu1156GlyfsTer8	p.E1156Gfs*8	ENST00000257430	NM_000038.5	1156	gAAGAg/gg	16/16	0.810103084455976	1	FACETS	0.176	0.137	0.22	0.176	0.137	0.22	SUBCLONAL	1	TRUE	0	0.810103084455976	1		464	184	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436086	51436086	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	16	269	0	ENST00000262662.1:c.46G>A	p.Gly16Arg	p.G16R	ENST00000262662		16	Ggg/Agg	3/4	1	2	FACETS	0.167	0.123	0.22	0.167	0.123	0.22	SUBCLONAL	1	TRUE	1	0.810103084455976	2		269	236	SUCCESS
APC	324	MSKCC	GRCh37	5	112163701	112163701	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	53	619	0	ENST00000257430.4:c.1624C>T	p.Gln542Ter	p.Q542*	ENST00000257430	NM_000038.5	542	Cag/Tag	13/16	0.810103084455976	1	FACETS	0.297	0.255	0.342	0.297	0.255	0.342	SUBCLONAL	1	TRUE	0	0.810103084455976	1		619	262	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249717	110249717	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	282	535	0	ENST00000374672.4:c.958G>C	p.Gly320Arg	p.G320R	ENST00000374672	NM_004235.4	320	Ggt/Cgt	3/5	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.810103084455976	2		535	691	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514875	103514875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1344944718	NA	P-0005782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	111	452	0	ENST00000355739.4:c.1376C>T	p.Ala459Val	p.A459V	ENST00000355739	NM_000123.3	459	gCc/gTc	8/15	0.501266650358052	3	FACETS	1	0.949	1	0.533	0.484	0.584	CLONAL	1	TRUE	1	0.810103084455976	3		452	361	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938568	44938568	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	16	309	0	ENST00000377967.4:c.3116A>T	p.Gln1039Leu	p.Q1039L	ENST00000377967	NM_021140.2	1039	cAg/cTg	20/29	1	1	FACETS	0.117	0.086	0.153	0.117	0.086	0.153	SUBCLONAL	1	TRUE	0	0.810103084455976	1		309	201	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579410	7579410	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567556123	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	764	638	0	ENST00000269305.4:c.277del	p.Leu93CysfsTer30	p.L93Cfs*30	ENST00000269305	NM_001126112.2	93	Ctg/tg	4/11	0.528021026195537	3	FACETS	0.933	0.907	0.958	0.933	0.907	0.958	CLONAL	3	TRUE	0	0.546768307536946	3		638	1272	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286731	212286731	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	102	400	0	ENST00000342788.4:c.2964+1G>T		p.X988_splice	ENST00000342788	NM_005235.2	988			0.155538251723547	4	FACETS	1	0.98	1	0.695	0.626	0.768	INDETERMINATE	1	TRUE	2	0.546768307536946	4		400	415	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044901	47044901	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	362	843	0	ENST00000377604.3:c.2227G>T	p.Glu743Ter	p.E743*	ENST00000377604	NM_001204468.1	743	Gag/Tag	20/24	NA	2	FACETS	0.901	0.853	0.951			1	INDETERMINATE	1	TRUE	NA	0.546768307536946	2		843	1469	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196627	106196627	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	105	556	0	ENST00000380013.4:c.4960C>G	p.Gln1654Glu	p.Q1654E	ENST00000380013	NM_001127208.2	1654	Cag/Gag	11/11	0.546768307536946	3	FACETS	0.618	0.554	0.687	0.309	0.277	0.344	SUBCLONAL	1	TRUE	1	0.546768307536946	3		556	791	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101374	27101374	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	180	591	0	ENST00000324856.7:c.4656G>T	p.Gln1552His	p.Q1552H	ENST00000324856	NM_006015.4	1552	caG/caT	18/20	0.166369981976982	2	FACETS	0.654	0.603	0.708	0.327	0.301	0.354	INDETERMINATE	1	TRUE	0	0.546768307536946	2		591	1006	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933165	36933165	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	521	943	0	ENST00000361632.4:c.1952G>T	p.Ser651Ile	p.S651I	ENST00000361632		651	aGc/aTc	14/16	0.166369981976982	2	FACETS	1	0.996	1	0.679	0.651	0.708	INDETERMINATE	1	TRUE	0	0.546768307536946	2		943	1403	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797106	45797106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778540	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	459	703	2	ENST00000450313.1:c.1309C>T	p.Arg437Trp	p.R437W	ENST00000450313	NM_012222.2	437	Cgg/Tgg	13/16	0.425441741185921	3	FACETS	1	0.996	1			1	CLONAL	1	TRUE	NA	0.546768307536946	3		705	1478	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509362	46509362	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	111	697	2	ENST00000262741.5:c.1369C>A	p.Pro457Thr	p.P457T	ENST00000262741	NM_003629.3	457	Ccc/Acc	10/10	0.425441741185921	3	FACETS	0.647	0.581	0.717			1	SUBCLONAL	1	TRUE	NA	0.546768307536946	3		699	799	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551699	150551699	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	99	251	2	ENST00000369026.2:c.308G>T	p.Arg103Leu	p.R103L	ENST00000369026	NM_021960.4	103	cGc/cTc	1/3	0.546768307536946	4	FACETS	0.849	0.758	0.945	0.424	0.379	0.473	CLONAL	1	TRUE	2	0.546768307536946	4		253	660	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745476	162745476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471671366	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	358	637	0	ENST00000367921.3:c.1891C>T	p.Arg631Trp	p.R631W	ENST00000367921	NM_006182.2	631	Cgg/Tgg	15/18	0.546768307536946	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.546768307536946	4		637	994	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226595555	226595555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1262	407	675	0	ENST00000366794.5:c.76G>A	p.Glu26Lys	p.E26K	ENST00000366794	NM_001618.3	26	Gag/Aag	1/23	0.546768307536946	4	FACETS	1	0.994	1	0.69	0.655	0.726	CLONAL	1	TRUE	2	0.546768307536946	4		675	1669	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143339	30143339	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	361	619	0	ENST00000389048.3:c.187C>A	p.Leu63Ile	p.L63I	ENST00000389048	NM_004304.4	63	Ctc/Atc	1/29	0.546768307536946	3	FACETS	1	0.992	1	0.632	0.598	0.666	CLONAL	1	TRUE	1	0.546768307536946	3		619	1331	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285248	212285248	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	160	633	1	ENST00000342788.4:c.3053A>T	p.Asp1018Val	p.D1018V	ENST00000342788	NM_005235.2	1018	gAt/gTt	25/28	0.155538251723547	4	FACETS	1	0.988	1	0.731	0.673	0.791	INDETERMINATE	1	TRUE	2	0.546768307536946	4		634	619	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588853	52588853	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	168	543	0	ENST00000394830.3:c.4175G>T	p.Gly1392Val	p.G1392V	ENST00000394830	NM_018313.4	1392	gGc/gTc	27/30	0.166369981976982	2	FACETS	0.648	0.595	0.703	0.324	0.297	0.352	INDETERMINATE	1	TRUE	0	0.546768307536946	2		543	949	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259406	89259406	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	142	934	0	ENST00000336596.2:c.550C>G	p.Gln184Glu	p.Q184E	ENST00000336596	NM_005233.5	184	Caa/Gaa	3/17	0.406954005647377	4	FACETS	0.623	0.566	0.683	0.311	0.283	0.342	SUBCLONAL	1	TRUE	2	0.546768307536946	4		934	1290	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138409981	138409981	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	127	406	1	ENST00000289153.2:c.1897G>T	p.Glu633Ter	p.E633*	ENST00000289153	NM_006219.2	633	Gaa/Taa	13/22	0.406954005647377	4	FACETS	1	0.985	1	0.723	0.659	0.79	CLONAL	1	TRUE	2	0.546768307536946	4		407	497	SUCCESS
ATR	545	MSKCC	GRCh37	3	142211975	142211975	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	122	387	0	ENST00000350721.4:c.6077A>T	p.Lys2026Met	p.K2026M	ENST00000350721	NM_001184.3	2026	aAg/aTg	35/47	0.406954005647377	4	FACETS	0.799	0.728	0.873	0.799	0.728	0.873	SUBCLONAL	2	TRUE	2	0.546768307536946	4		387	432	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447532	187447532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1433	151	509	2	ENST00000232014.4:c.661G>A	p.Ala221Thr	p.A221T	ENST00000232014	NM_001130845.1	221	Gcc/Acc	5/10	0.546768307536946	6	FACETS	0.73	0.665	0.799			1	SUBCLONAL	1	TRUE	NA	0.546768307536946	6		511	1584	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586462	189586462	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	282	568	0	ENST00000264731.3:c.1086G>T	p.Gln362His	p.Q362H	ENST00000264731	NM_003722.4	362	caG/caT	8/14	0.546768307536946	6	FACETS	1	0.948	1			1	CLONAL	2	TRUE	NA	0.546768307536946	6		568	1070	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155232	106155232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	133	674	1	ENST00000380013.4:c.133C>T	p.His45Tyr	p.H45Y	ENST00000380013	NM_001127208.2	45	Cat/Tat	3/11	0.546768307536946	3	FACETS	0.771	0.7	0.845	0.385	0.35	0.423	SUBCLONAL	1	TRUE	1	0.546768307536946	3		675	804	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871286	35871286	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	141	419	0	ENST00000303115.3:c.508C>A	p.Arg170Ser	p.R170S	ENST00000303115	NM_002185.3	170	Cgc/Agc	4/8	0.155538251723547	4	FACETS	0.892	0.82	0.967	0.892	0.82	0.967	INDETERMINATE	2	TRUE	2	0.546768307536946	4		419	447	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38964932	38964932	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	181	623	1	ENST00000357387.3:c.1362T>A	p.Asn454Lys	p.N454K	ENST00000357387	NM_152756.3	454	aaT/aaA	16/38	0.155538251723547	4	FACETS	0.808	0.748	0.869	0.808	0.748	0.869	INDETERMINATE	2	TRUE	2	0.546768307536946	4		624	634	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111822	56111822	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	32	15	0	ENST00000399503.3:c.422C>T	p.Ala141Val	p.A141V	ENST00000399503	NM_005921.1	141	gCc/gTc	1/20	0.546768307536946	6	FACETS	1	0.874	1			1	CLONAL	5	TRUE	NA	0.546768307536946	6		15	49	SUCCESS
APC	324	MSKCC	GRCh37	5	112175932	112175932	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	261	531	0	ENST00000257430.4:c.4641A>T	p.Glu1547Asp	p.E1547D	ENST00000257430	NM_000038.5	1547	gaA/gaT	16/16	0.546768307536946	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.546768307536946	2		531	469	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131976481	131976481	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	297	614	0	ENST00000265335.6:c.3736G>T	p.Ala1246Ser	p.A1246S	ENST00000265335		1246	Gca/Tca	24/25	0.546768307536946	2	FACETS	0.929	0.884	0.973	0.929	0.884	0.973	CLONAL	2	TRUE	0	0.546768307536946	2		614	585	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180037013	180037013	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	561	718	0	ENST00000261937.6:c.3699G>T	p.Trp1233Cys	p.W1233C	ENST00000261937	NM_182925.4	1233	tgG/tgT	28/30	0.546768307536946	2	FACETS	0.971	0.937	1	0.971	0.937	1	CLONAL	2	TRUE	0	0.546768307536946	2		718	1057	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536247	106536247	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	438	608	0	ENST00000369096.4:c.214G>T	p.Asp72Tyr	p.D72Y	ENST00000369096	NM_001198.3	72	Gat/Tat	2/7	0.257167311710949	5	FACETS	1	0.975	1	0.811	0.782	0.84	INDETERMINATE	4	TRUE	0	0.546768307536946	5		608	719	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335634	81335634	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	187	597	0	ENST00000222390.5:c.1726G>C	p.Gly576Arg	p.G576R	ENST00000222390	NM_000601.4	576	Gga/Cga	15/18	0.406954005647377	4	FACETS	1	0.989	1	0.713	0.66	0.767	CLONAL	1	TRUE	2	0.546768307536946	4		597	742	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386511	81386511	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	168	548	1	ENST00000222390.5:c.476A>T	p.Glu159Val	p.E159V	ENST00000222390	NM_000601.4	159	gAa/gTa	4/18	0.406954005647377	4	FACETS	1	0.982	1	0.61	0.561	0.661	CLONAL	1	TRUE	2	0.546768307536946	4		549	779	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151947021	151947021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	233	539	1	ENST00000262189.6:c.1753G>T	p.Glu585Ter	p.E585*	ENST00000262189	NM_170606.2	585	Gaa/Taa	13/59	0.546768307536946	5	FACETS	0.931	0.871	0.993	0.621	0.58	0.662	CLONAL	2	TRUE	2	0.546768307536946	5		540	833	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457183	5457183	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs768536942	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	24	573	0	ENST00000381577.3:c.157C>G	p.Leu53Val	p.L53V	ENST00000381577	NM_014143.3	53	Cta/Gta	3/7	0.546768307536946	1	FACETS	0.148	0.115	0.185	0.148	0.115	0.185	SUBCLONAL	1	TRUE	0	0.546768307536946	1		573	432	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650109	93650109	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs765007451	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	301	791	0	ENST00000375746.1:c.1660G>T	p.Asp554Tyr	p.D554Y	ENST00000375746	NM_001174167.1	554	Gat/Tat	12/14	0.386877277114952	4	FACETS	0.799	0.753	0.846			1	SUBCLONAL	2	TRUE	NA	0.546768307536946	4		791	1066	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609123	43609123	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2294	285	1082	1	ENST00000355710.3:c.1879G>T	p.Asp627Tyr	p.D627Y	ENST00000355710	NM_020975.4	627	Gat/Tat	10/20	0.546768307536946	4	FACETS	0.625	0.584	0.668	0.313	0.292	0.334	SUBCLONAL	1	TRUE	2	0.546768307536946	4		1083	2579	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615072	43615072	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1592	211	741	0	ENST00000355710.3:c.2486G>T	p.Ser829Ile	p.S829I	ENST00000355710	NM_020975.4	829	aGt/aTt	14/20	0.546768307536946	4	FACETS	0.662	0.612	0.714	0.331	0.306	0.357	SUBCLONAL	1	TRUE	2	0.546768307536946	4		741	1803	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205796	108205796	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	188	543	0	ENST00000278616.4:c.8111G>T	p.Cys2704Phe	p.C2704F	ENST00000278616	NM_000051.3	2704	tGt/tTt	55/63	0.546768307536946	2	FACETS	0.929	0.873	0.986	0.929	0.873	0.986	CLONAL	2	TRUE	0	0.546768307536946	2		543	370	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023614	1023614	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	107	628	0	ENST00000358495.3:c.950T>A	p.Val317Glu	p.V317E	ENST00000358495	NM_134424.2	317	gTg/gAg	10/12	0.546768307536946	3	FACETS	0.53	0.474	0.589	0.265	0.237	0.295	SUBCLONAL	1	TRUE	1	0.546768307536946	3		628	941	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398244	25398244	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	144	539	0	ENST00000311936.3:c.75G>C	p.Gln25His	p.Q25H	ENST00000311936	NM_004985.3	25	caG/caC	2/5	0.546768307536946	3	FACETS	1	0.951	1	0.528	0.483	0.575	CLONAL	1	TRUE	1	0.546768307536946	3		539	635	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869579	102869579	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	225	412	0	ENST00000307046.8:c.64-2A>T		p.X22_splice	ENST00000307046	NM_001111285.1	22			0.425441741185921	3	FACETS	0.87	0.816	0.925			1	CLONAL	2	TRUE	NA	0.546768307536946	3		412	602	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134698	41134698	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	963	1045	1	ENST00000379561.5:c.930G>T	p.Trp310Cys	p.W310C	ENST00000379561	NM_002015.3	310	tgG/tgT	2/3	0.534841500174444	3	FACETS	0.944	0.921	0.967	0.944	0.921	0.967	CLONAL	3	TRUE	0	0.546768307536946	3		1046	1584	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050869	49050869	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1346717703	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	84	405	0	ENST00000267163.4:c.2553G>T	p.Met851Ile	p.M851I	ENST00000267163	NM_000321.2	851	atG/atT	25/27	0.534841500174444	3	FACETS	1	0.955	1	0.38	0.338	0.424	CLONAL	1	TRUE	0	0.546768307536946	3		405	343	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060780	38060780	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2781	332	1174	2	ENST00000250448.2:c.1209C>A	p.Asn403Lys	p.N403K	ENST00000250448	NM_004496.3	403	aaC/aaA	2/2	0.546768307536946	5	FACETS	0.71	0.667	0.755	0.178	0.166	0.189	SUBCLONAL	1	TRUE	1	0.546768307536946	5		1176	3113	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560440	65560440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	651	584	0	ENST00000358664.4:c.157C>T	p.Leu53Phe	p.L53F	ENST00000358664	NM_002382.4	53	Ctc/Ttc	3/5	0.546768307536946	5	FACETS	1	0.987	1	1	0.987	1	CLONAL	4	TRUE	1	0.546768307536946	5		584	1052	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058501	42058501	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	409	1318	1	ENST00000219905.7:c.8221G>T	p.Glu2741Ter	p.E2741*	ENST00000219905	NM_001164273.1	2741	Gag/Tag	24/24	0.546768307536946	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.546768307536946	1		1319	880	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007787	45007787	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	227	573	0	ENST00000558401.1:c.234G>T	p.Lys78Asn	p.K78N	ENST00000558401	NM_004048.2	78	aaG/aaT	2/4	0.546768307536946	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.546768307536946	1		573	440	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250908	99250908	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	353	552	0	ENST00000268035.6:c.212G>T	p.Arg71Leu	p.R71L	ENST00000268035	NM_000875.3	71	cGc/cTc	2/21	0.207408437770186	4	FACETS	0.873	0.827	0.919	0.873	0.827	0.919	INDETERMINATE	2	TRUE	2	0.546768307536946	4		552	1144	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024717	14024717	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs762885572	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	167	518	1	ENST00000311895.7:c.943G>T	p.Ala315Ser	p.A315S	ENST00000311895	NM_005236.2	315	Gca/Tca	5/11	0.201432996144932	2	FACETS	1	0.977	1	0.57	0.527	0.614	INDETERMINATE	1	TRUE	0	0.546768307536946	2		519	536	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782331	56782331	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1290	181	856	0	ENST00000308159.5:c.172G>T	p.Val58Phe	p.V58F	ENST00000308159	NM_014669.4	58	Gtc/Ttc	2/22	0.257167311710949	5	FACETS	0.819	0.753	0.888	0.164	0.15	0.178	INDETERMINATE	1	TRUE	0	0.546768307536946	5		856	1471	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56870529	56870529	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	437	927	0	ENST00000308159.5:c.1799A>T	p.Lys600Met	p.K600M	ENST00000308159	NM_014669.4	600	aAg/aTg	17/22	0.257167311710949	5	FACETS	0.955	0.909	1	0.382	0.363	0.401	INDETERMINATE	2	TRUE	0	0.546768307536946	5		927	1524	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346769	89346769	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1526	215	813	1	ENST00000301030.4:c.6181G>T	p.Gly2061Trp	p.G2061W	ENST00000301030	NM_001256183.1	2061	Ggg/Tgg	9/13	0.257167311710949	5	FACETS	0.822	0.761	0.886	0.164	0.152	0.178	INDETERMINATE	1	TRUE	0	0.546768307536946	5		814	1741	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688753	47688753	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	239	550	2	ENST00000347630.2:c.547G>T	p.Glu183Ter	p.E183*	ENST00000347630	NM_001007230.1	183	Gag/Tag	7/11	0.479383488827554	3	FACETS	1	0.992	1	0.481	0.451	0.513	CLONAL	1	TRUE	0	0.546768307536946	3		552	771	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533925	63533925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555578117	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	220	369	0	ENST00000307078.5:c.1229C>T	p.Thr410Ile	p.T410I	ENST00000307078	NM_004655.3	410	aCa/aTa	6/11	0.546768307536946	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.546768307536946	1		369	504	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610427	10610427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	935	441	0	ENST00000171111.5:c.283G>A	p.Ala95Thr	p.A95T	ENST00000171111	NM_203500.1	95	Gcc/Acc	2/6	0.534841500174444	3	FACETS	0.984	0.961	1	0.984	0.961	1	CLONAL	3	TRUE	0	0.546768307536946	3		441	1475	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610439	10610439	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs202181679	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	957	657	0	ENST00000171111.5:c.271G>T	p.Ala91Ser	p.A91S	ENST00000171111	NM_203500.1	91	Gcc/Tcc	2/6	0.534841500174444	3	FACETS	0.998	0.975	1	0.998	0.975	1	CLONAL	3	TRUE	0	0.546768307536946	3		657	1489	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098340	11098340	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	1087	640	0	ENST00000358026.2:c.860-2A>G		p.X287_splice	ENST00000358026	NM_001128849.1	287			0.546768307536946	4	FACETS	1	0.986	1			1	CLONAL	4	TRUE	NA	0.546768307536946	4		640	1526	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375462	15375462	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1463	444	740	0	ENST00000263377.2:c.965G>C	p.Arg322Pro	p.R322P	ENST00000263377	NM_058243.2	322	cGg/cCg	6/20	0.546768307536946	4	FACETS	1	0.994	1	0.329	0.313	0.346	CLONAL	1	TRUE	0	0.546768307536946	4		740	1907	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523261	9523261	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	135	749	1	ENST00000353224.5:c.1976T>A	p.Leu659Ter	p.L659*	ENST00000353224	NM_177990.2	659	tTa/tAa	9/10	NA	2	FACETS	0.703	0.64	0.769			1	INDETERMINATE	1	TRUE	NA	0.546768307536946	2		750	702	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525116	9525116	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	105	629	0	ENST00000353224.5:c.1769G>T	p.Cys590Phe	p.C590F	ENST00000353224	NM_177990.2	590	tGt/tTt	8/10	NA	2	FACETS	0.621	0.558	0.689			1	INDETERMINATE	1	TRUE	NA	0.546768307536946	2		629	618	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546560	9546560	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	103	460	0	ENST00000353224.5:c.1462C>G	p.Arg488Gly	p.R488G	ENST00000353224	NM_177990.2	488	Cga/Gga	5/10	NA	2	FACETS	0.584	0.523	0.649			1	INDETERMINATE	1	TRUE	NA	0.546768307536946	2		460	645	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419893	41419893	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	324	634	2	ENST00000373198.4:c.428C>A	p.Thr143Asn	p.T143N	ENST00000373198	NM_133170.3	143	aCt/aAt	3/32	0.546768307536946	3	FACETS	1	0.992	1	0.645	0.61	0.682	CLONAL	1	TRUE	1	0.546768307536946	3		636	1169	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656921	45656921	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	477	863	0	ENST00000407780.3:c.235C>A	p.Arg79Ser	p.R79S	ENST00000407780	NM_001283052.1	79	Cgc/Agc	3/7	0.528021026195537	3	FACETS	1	0.996	1	0.486	0.464	0.508	CLONAL	1	TRUE	0	0.546768307536946	3		863	1525	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556692	41556692	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	169	368	0	ENST00000263253.7:c.3637G>T	p.Val1213Phe	p.V1213F	ENST00000263253	NM_001429.3	1213	Gtt/Ttt	20/31	0.466458570864874	2	FACETS	0.873	0.816	0.931	0.873	0.816	0.931	CLONAL	2	TRUE	0	0.546768307536946	2		368	354	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317514	1317514	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1261	532	938	1	ENST00000400841.2:c.551G>T	p.Trp184Leu	p.W184L	ENST00000400841		184	tGg/tTg	5/6	0.293181997392707	4	FACETS	0.839	0.803	0.876			1	INDETERMINATE	2	TRUE	NA	0.546768307536946	4		939	1793	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937761	76937761	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	142	730	0	ENST00000373344.5:c.2987C>A	p.Ser996Ter	p.S996*	ENST00000373344	NM_000489.3	996	tCa/tAa	9/35	0.386877277114952	4	FACETS	1	0.955	1			1	CLONAL	1	TRUE	NA	0.546768307536946	4		730	749	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611069	100611069	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs781869026	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	268	904	0	ENST00000308731.7:c.1537G>C	p.Glu513Gln	p.E513Q	ENST00000308731	NM_000061.2	513	Gag/Cag	15/19	0.386877277114952	4	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.546768307536946	4		904	1242	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630140	100630140	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	225	793	0	ENST00000308731.7:c.133G>T	p.Glu45Ter	p.E45*	ENST00000308731	NM_000061.2	45	Gaa/Taa	2/19	0.386877277114952	4	FACETS	0.983	0.914	1			1	CLONAL	1	TRUE	NA	0.546768307536946	4		793	1295	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100431	157100488	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCGGCGGCGGGGGCGGCGGCGGGCGGCCAGCAGGCGGCCGCGGGCATGGGCTTG	GGCGGCGGCGGCGGGGGCGGCGGCGGGCGGCCAGCAGGCGGCCGCGGGCATGGGCTTG	-	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	19	27	0	ENST00000346085.5:c.1371_1428del	p.Ala458ArgfsTer25	p.A458Rfs*25	ENST00000346085	NM_020732.3	456	caGGCGGCGGCGGCGGGGGCGGCGGCGGGCGGCCAGCAGGCGGCCGCGGGCATGGGCTTG/ca	1/20	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.546768307536946	NA		27	66	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106229	2106257	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTCTGTGGACATAGAGGTCAGTGCCTCC	CCTCTGTGGACATAGAGGTCAGTGCCTCC	-	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	288	738	0	ENST00000219476.3:c.636_648+16del		p.X212_splice	ENST00000219476	NM_000548.3	212		7/42	NA	2	FACETS	0.951	0.894	1			1	INDETERMINATE	1	TRUE	NA	0.546768307536946	2		738	1108	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631596	119631596	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	347	691	2	ENST00000316626.5:c.670del	p.Ala224HisfsTer4	p.A224Hfs*4	ENST00000316626		224	Gca/ca	6/12	0.406954005647377	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	2	0.546768307536946	4		693	828	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0005792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	911	436	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.900471208620821	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.900471208620821	1		436	1055	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537911	212537911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755861643	NA	P-0005792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	517	568	2	ENST00000342788.4:c.1694G>A	p.Gly565Asp	p.G565D	ENST00000342788	NM_005235.2	565	gGc/gAc	14/28	1	2	FACETS	0.985	0.946	1	0.985	0.946	1	CLONAL	1	TRUE	1	0.900471208620821	2		570	1166	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247472	71247472	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	1180	624	0	ENST00000318789.4:c.61G>T	p.Gly21Cys	p.G21C	ENST00000318789	NM_032682.5	21	Ggc/Tgc	6/21	0.752312369345582	3	FACETS	1	0.987	1			1	CLONAL	2	TRUE	NA	0.900471208620821	3		624	1879	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247367	153247367	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747241612	NA	P-0005792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	387	354	0	ENST00000281708.4:c.1435C>G	p.Arg479Gly	p.R479G	ENST00000281708	NM_033632.3	479	Cga/Gga	10/12	0.900471208620821	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.900471208620821	1		354	457	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202269	138202269	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	613	558	0	ENST00000237289.4:c.2186G>A	p.Ser729Asn	p.S729N	ENST00000237289	NM_001270507.1	729	aGc/aAc	9/9	1	2	FACETS	0.989	0.954	1	0.989	0.954	1	CLONAL	1	TRUE	1	0.900471208620821	2		558	1376	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508990	106508990	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	488	481	0	ENST00000359195.3:c.984C>A	p.Asp328Glu	p.D328E	ENST00000359195	NM_002649.2	328	gaC/gaA	2/11	1	2	FACETS	0.984	0.944	1	0.984	0.944	1	CLONAL	1	TRUE	1	0.900471208620821	2		481	1102	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864853	57864853	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1392	1033	1089	2	ENST00000228682.2:c.2330A>T	p.Gln777Leu	p.Q777L	ENST00000228682	NM_005269.2	777	cAa/cTa	12/12	1	2	FACETS	0.946	0.919	0.973	0.946	0.919	0.973	CLONAL	1	TRUE	1	0.900471208620821	2		1091	2425	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617654	39617654	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0005792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	3298	461	0	ENST00000262039.4:c.1840-2A>T		p.X614_splice	ENST00000262039	NM_002647.2	614			0.900471208620821	8	FACETS	1	0.995	1			1	CLONAL	7	TRUE	NA	0.900471208620821	8		461	3852	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229527	5229527	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	437	177	0	ENST00000357368.4:c.2324A>G	p.Lys775Arg	p.K775R	ENST00000357368	NM_002850.3	775	aAg/aGg	15/38	0.900471208620821	3	FACETS	0.951	0.916	0.986	0.951	0.916	0.986	CLONAL	2	TRUE	1	0.900471208620821	3		177	740	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099134	157099135	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0005792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	212	205	0	ENST00000346085.5:c.74_75del	p.Leu25GlnfsTer206	p.L25Qfs*206	ENST00000346085	NM_020732.3	24	gCT/g	1/20	1	2	FACETS	0.815	0.762	0.868	0.815	0.762	0.868	CLONAL	1	TRUE	1	0.900471208620821	2		205	578	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576098	29576098	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1135402852	NA	P-0005792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	624	797	0	ENST00000356175.3:c.4076del	p.Pro1359LeufsTer26	p.P1359Lfs*26	ENST00000356175	NM_000267.3	1357	ttC/tt	30/57	1	2	FACETS	0.865	0.833	0.898	0.865	0.833	0.898	CLONAL	1	TRUE	1	0.900471208620821	2		797	1602	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0005805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	131	383	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.611399289342151	6	FACETS	0.932	0.85	1	0.466	0.425	0.509	CLONAL	2	TRUE	2	0.611399289342151	6		383	511	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955432	48955432	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	157	378	0	ENST00000267163.4:c.1548G>A	p.Trp516Ter	p.W516*	ENST00000267163	NM_000321.2	516	tgG/tgA	17/27	0.611399289342151	2	FACETS	0.984	0.952	1	1	0.994	1	CLONAL	3	TRUE	0	0.611399289342151	2		378	174	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252950	36252950	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	90	475	0	ENST00000300305.3:c.412G>A	p.Glu138Lys	p.E138K	ENST00000300305		138	Gaa/Aaa	4/8	0.611399289342151	7	FACETS	0.797	0.71	0.889	0.399	0.355	0.445	SUBCLONAL	2	TRUE	3	0.611399289342151	7		475	467	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41999981	42000035	+	frameshift_variant	Frame_Shift_Del	DEL	GGGAGTACAGTTACCTTTGGCTCCAGCTACTAGCTTTCCTTTTTGGAACCTTACA	GGGAGTACAGTTACCTTTGGCTCCAGCTACTAGCTTTCCTTTTTGGAACCTTACA	-	novel	NA	P-0005805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	264	1087	2	ENST00000219905.7:c.2246_2300del	p.Gly749GlufsTer50	p.G749Efs*50	ENST00000219905	NM_001164273.1	748	ttGGGAGTACAGTTACCTTTGGCTCCAGCTACTAGCTTTCCTTTTTGGAACCTTACA/tt	6/24	0.488995862879002	4	FACETS	0.904	0.858	0.95	0.904	0.858	0.95	CLONAL	3	TRUE	1	0.611399289342151	4		1089	513	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0005810-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	139	585	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	0.883	0.803	0.967	0.883	0.803	0.967	CLONAL	1	TRUE	1	0.329643899862872	2		585	955	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97887405	97887405	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1160107777	NA	P-0005810-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	145	660	0	ENST00000289081.3:c.959A>G	p.Gln320Arg	p.Q320R	ENST00000289081	NM_000136.2	320	cAg/cGg	10/15	1	2	FACETS	0.779	0.709	0.852	0.779	0.709	0.852	SUBCLONAL	1	TRUE	1	0.329643899862872	2		660	1130	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0005816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	90	384	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.729	0.65	0.812	0.729	0.65	0.812	SUBCLONAL	1	FALSE	1	0.571615560313195	2		384	432	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028689	12028689	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1323703671	NA	P-0005816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	52	654	0	ENST00000353533.5:c.891+1G>T		p.X297_splice	ENST00000353533	NM_003010.3	297			0.571615560313195	1	FACETS	0.252	0.214	0.293	0.252	0.214	0.293	SUBCLONAL	1	FALSE	0	0.571615560313195	1		654	516	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912191	114912191	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005820-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	483	863	1	ENST00000543371.1:c.1261G>A	p.Asp421Asn	p.D421N	ENST00000543371	NM_001198531.1	421	Gat/Aat	11/14	0.620772038115807	1	FACETS	0.972	0.933	1	0.972	0.933	1	CLONAL	1	TRUE	0	0.620772038115807	1		864	1104	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577604	7577604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005820-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	237	382	0	ENST00000269305.4:c.677G>A	p.Gly226Asp	p.G226D	ENST00000269305	NM_001126112.2	226	gGc/gAc	7/11	0.606439360557636	0	FACETS	0.585	0.552	0.618			1	SUBCLONAL	1	TRUE	0	0.620772038115807	0		382	495	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162807	47162807	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005822-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	95	403	0	ENST00000409792.3:c.3319G>T	p.Glu1107Ter	p.E1107*	ENST00000409792	NM_014159.6	1107	Gag/Tag	3/21	0.539860367642681	1	FACETS	0.908	0.82	0.999	0.908	0.82	0.999	CLONAL	1	TRUE	0	0.539860367642681	1		403	283	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598097	52598097	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0005822-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	143	577	0	ENST00000394830.3:c.3769A>T	p.Lys1257Ter	p.K1257*	ENST00000394830	NM_018313.4	1257	Aaa/Taa	24/30	0.539860367642681	1	FACETS	0.881	0.81	0.954	0.881	0.81	0.954	CLONAL	1	TRUE	0	0.539860367642681	1		577	439	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007901	45007901	+	splice_donor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0005822-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	88	279	0	ENST00000558401.1:c.346+2del		p.X116_splice	ENST00000558401	NM_004048.2	116			0.539860367642681	1	FACETS	0.832	0.747	0.921	0.832	0.747	0.921	CLONAL	1	TRUE	0	0.539860367642681	1		279	286	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005825-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	249	401	0	ENST00000397062.3:c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	NM_006164.4	34	Cga/Gga	2/5	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.829566195439979	2		401	584	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041178	47041178	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005825-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	543	742	0	ENST00000377604.3:c.1608del	p.Lys536AsnfsTer168	p.K536Nfs*168	ENST00000377604	NM_001204468.1	536	Aaa/aa	15/24	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.829566195439979	2		742	1269	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099988	27099989	+	splice_donor_variant	Splice_Site	DNP	GT	GT	TA	novel	NA	P-0005825-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	346	647	0	ENST00000324856.7:c.3866+1_3866+2delinsTA		p.X1289_splice	ENST00000324856	NM_006015.4	1289			1	2	FACETS	0.888	0.844	0.934	0.888	0.844	0.934	CLONAL	1	TRUE	1	0.829566195439979	2		647	939	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575154	64575154	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0005830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	645	329	0	ENST00000312049.6:c.655-2A>C		p.X219_splice	ENST00000312049	NM_130799.2	219			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		329	754	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778200	27778200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1885	411	1177	1	ENST00000369163.2:c.349C>T	p.Arg117Trp	p.R117W	ENST00000369163	NM_003536.2	117	Cgg/Tgg	1/1	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.315586959335485	2		1178	2296	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867274	68867274	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	136	404	0	ENST00000261769.5:c.2521G>T	p.Glu841Ter	p.E841*	ENST00000261769	NM_004360.3	841	Gaa/Taa	16/16	1	2	FACETS	0.962	0.874	1	0.962	0.874	1	CLONAL	1	TRUE	1	0.315586959335485	2		404	896	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578284	7578297	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCAGACCTAAGAGC	CCAGACCTAAGAGC	-	novel	NA	P-0005864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	134	452	1	ENST00000269305.4:c.560-8_565del		p.X187_splice	ENST00000269305	NM_001126112.2	187		6/11	0.312130043444516	1	FACETS	0.899	0.817	0.984	0.899	0.817	0.984	CLONAL	1	TRUE	0	0.315586959335485	1		453	796	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0005865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	172	412	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	0.996	0.917	1			1	INDETERMINATE	1	TRUE	NA	0.423356379350169	2		412	816	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0005865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	302	556	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.344847657947193	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.423356379350169	1		556	1071	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554327	63554327	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	325	389	0	ENST00000307078.5:c.412T>C	p.Tyr138His	p.Y138H	ENST00000307078	NM_004655.3	138	Tac/Cac	2/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.423356379350169	2		389	1345	SUCCESS
APC	324	MSKCC	GRCh37	5	112175758	112175759	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0005865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	114	219	0	ENST00000257430.4:c.4468_4469del	p.His1490PhefsTer23	p.H1490Ffs*23	ENST00000257430	NM_000038.5	1489	ttACat/ttat	16/16	1	2	FACETS	0.96	0.867	1	0.96	0.867	1	CLONAL	1	TRUE	1	0.423356379350169	2		219	561	SUCCESS
APC	324	MSKCC	GRCh37	5	112173538	112173538	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	158	335	0	ENST00000257430.4:c.2247del	p.Leu749PhefsTer12	p.L749Ffs*12	ENST00000257430	NM_000038.5	749	ttG/tt	16/16	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.423356379350169	2		335	698	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591144	67591154	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ATACTTGATGT	ATACTTGATGT	C	novel	NA	P-0005865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	157	230	0	ENST00000274335.5:c.1737_1745+2delinsC		p.X579_splice	ENST00000274335		579		12/15	1	2	FACETS	0.975	0.894	1	0.975	0.894	1	CLONAL	1	TRUE	1	0.423356379350169	2		230	761	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720857	89720857	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs786201816	NA	P-0005869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	91	172	0	ENST00000371953.3:c.1008C>G	p.Tyr336Ter	p.Y336*	ENST00000371953	NM_000314.4	336	taC/taG	8/9	0.494494407677111	1	FACETS	0.949	0.853	1	0.949	0.853	1	CLONAL	1	TRUE	0	0.494494407677111	1		172	292	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566435	41566435	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	336	447	1	ENST00000263253.7:c.4312T>C	p.Cys1438Arg	p.C1438R	ENST00000263253	NM_001429.3	1438	Tgt/Cgt	27/31	0.494494407677111	2	FACETS	0.877	0.834	0.92	0.877	0.834	0.92	CLONAL	2	TRUE	0	0.494494407677111	2		448	775	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0005872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	37	412	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		412	715	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0005888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	298	316	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.176471764359414	3	FACETS	0.752	0.713	0.791	0.752	0.713	0.791	INDETERMINATE	2	TRUE	1	0.791627632332823	3		316	699	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0005888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	152	219	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.791627632332823	1	FACETS	0.955	0.898	1	0.955	0.898	1	CLONAL	1	TRUE	0	0.791627632332823	1		219	243	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0005888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	423	598	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.758554904494997	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.791627632332823	1		598	617	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243668558	243668558	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751275167	NA	P-0005888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	269	280	0	ENST00000263826.5:c.1433G>A	p.Arg478Gln	p.R478Q	ENST00000263826	NM_005465.4	478	cGa/cAa	13/13	0.235140618324047	1	FACETS	0.702	0.664	0.74	0.702	0.664	0.74	INDETERMINATE	1	TRUE	0	0.791627632332823	1		280	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577123	7577123	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876660333	NA	P-0005888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	508	450	1	ENST00000269305.4:c.815T>A	p.Val272Glu	p.V272E	ENST00000269305	NM_001126112.2	272	gTg/gAg	8/11	0.708369480882025	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.791627632332823	1		451	764	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030760	48030760	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	194	216	0	ENST00000234420.5:c.3374G>T	p.Gly1125Val	p.G1125V	ENST00000234420	NM_000179.2	1125	gGc/gTc	5/10	0.176471764359414	3	FACETS	1	0.989	1	0.663	0.619	0.708	INDETERMINATE	1	TRUE	1	0.791627632332823	3		216	516	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912309	29912309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	273	388	0	ENST00000376809.5:c.928G>A	p.Gly310Ser	p.G310S	ENST00000376809	NM_002116.7	310	Ggc/Agc	5/8	0.117498233386342	4	FACETS	1	0.993	1	0.731	0.688	0.775	INDETERMINATE	1	TRUE	2	0.791627632332823	4		388	845	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051619	30051619	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	397	362	0	ENST00000338641.4:c.553G>A	p.Glu185Lys	p.E185K	ENST00000338641	NM_000268.3	185	Gag/Aag	6/16	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.791627632332823	2		362	882	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183750	10183750	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	59	571	0	ENST00000256474.2:c.219G>C	p.Gln73His	p.Q73H	ENST00000256474	NM_000551.3	73	caG/caC	1/3	0.171492225397537	4	FACETS	0.948	0.814	1	0.474	0.407	0.547	CLONAL	1	TRUE	2	0.205256398124744	4		571	731	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129632	47129632	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	85	511	0	ENST00000409792.3:c.5248C>T	p.Gln1750Ter	p.Q1750*	ENST00000409792	NM_014159.6	1750	Cag/Tag	10/21	0.564937441727225	1	FACETS	0.85	0.763	0.941	0.85	0.763	0.941	CLONAL	1	TRUE	0	0.564937441727225	1		511	254	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207640	102207640	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	177	758	0	ENST00000263464.3:c.1622A>T	p.Asp541Val	p.D541V	ENST00000263464	NM_001165.4	541	gAt/gTt	9/9	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.564937441727225	2		758	576	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593603	55593606	+	protein_altering_variant	In_Frame_Del	DEL	TGGA	TGGA	C	novel	NA	P-0005891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	115	470	0	ENST00000288135.5:c.1669_1672delinsC	p.Trp557_Lys558delinsGln	p.W557_K558delinsQ	ENST00000288135	NM_000222.2	557	TGGAag/Cag	11/21	0.564937441727225	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.564937441727225	1		470	233	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0005903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	129	550	1	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.956	0.867	1	0.956	0.867	1	CLONAL	1	TRUE	1	0.3149042048429	2		551	857	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220649	1220649	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	573	624	0	ENST00000326873.7:c.667G>T	p.Glu223Ter	p.E223*	ENST00000326873	NM_000455.4	223	Gag/Tag	5/10	0.3149042048429	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	TRUE	0	0.3149042048429	3		624	1394	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439743	220439743	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367749891	NA	P-0005903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1418	282	922	0	ENST00000243786.2:c.596G>A	p.Arg199His	p.R199H	ENST00000243786	NM_002191.3	199	cGc/cAc	2/2	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.3149042048429	2		922	1700	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422552	225422552	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	60	188	0	ENST00000264414.4:c.88G>T	p.Val30Leu	p.V30L	ENST00000264414	NM_003590.4	30	Gta/Tta	2/16	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.3149042048429	2		188	375	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553680	106553680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	60	367	0	ENST00000369096.4:c.1645C>T	p.Leu549Phe	p.L549F	ENST00000369096	NM_001198.3	549	Ctc/Ttc	5/7	NA	2	FACETS	0.492	0.423	0.567			1	INDETERMINATE	1	TRUE	NA	0.3149042048429	2		367	775	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041596	42041596	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1399	253	912	1	ENST00000219905.7:c.5791G>T	p.Val1931Phe	p.V1931F	ENST00000219905	NM_001164273.1	1931	Gtt/Ttt	17/24	1	2	FACETS	0.973	0.907	1	0.973	0.907	1	CLONAL	1	TRUE	1	0.3149042048429	2		913	1652	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81957192	81957192	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1216454496	NA	P-0005903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	216	607	1	ENST00000359376.3:c.2410G>T	p.Gly804Trp	p.G804W	ENST00000359376	NM_002661.3	804	Ggg/Tgg	22/33	0.3149042048429	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.3149042048429	1		608	1077	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876618	59876618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	54	237	0	ENST00000259008.2:c.1183G>A	p.Ala395Thr	p.A395T	ENST00000259008	NM_032043.2	395	Gct/Act	9/20	0.300485686343443	3	FACETS	0.813	0.695	0.942	0.407	0.347	0.471	CLONAL	1	TRUE	1	0.3149042048429	3		237	488	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167550	24167550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	146	363	0	ENST00000263121.7:c.934G>T	p.Ala312Ser	p.A312S	ENST00000263121	NM_003073.3	312	Gca/Tca	7/9	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.3149042048429	2		363	811	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411395	63411395	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	197	285	0	ENST00000330258.3:c.1772G>T	p.Arg591Met	p.R591M	ENST00000330258	NM_152424.3	591	aGg/aTg	2/2	1	1	FACETS	0.857	0.798	0.918	1	0.993	1	CLONAL	2	TRUE	0	0.3149042048429	1		285	615	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051658	30051658	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555993345	NA	P-0005906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	210	472	0	ENST00000338641.4:c.592C>T	p.Arg198Ter	p.R198*	ENST00000338641	NM_000268.3	198	Cga/Tga	6/16	0.708070983582187	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.708070983582187	1		472	370	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288569	33288569	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	205	406	0	ENST00000374542.5:c.983G>C	p.Arg328Pro	p.R328P	ENST00000374542	NM_001141970.1	328	cGt/cCt	3/8	0.708070983582187	1	FACETS	0.972	0.916	1	0.972	0.916	1	CLONAL	1	TRUE	0	0.708070983582187	1		406	385	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0005910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	123	219	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	0.501965370026466	2		219	415	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0005910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	329	538	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.501965370026466	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.501965370026466	3		538	803	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0005910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	173	406	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.501965370026466	2		406	648	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0005910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	129	321	0	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	0.501965370026466	2		321	510	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0005910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	30	460	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	1	2	FACETS	0.155	0.124	0.19	0.155	0.124	0.19	SUBCLONAL	1	TRUE	1	0.501965370026466	2		460	771	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715678	30715678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039551	NA	P-0005910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	201	482	0	ENST00000295754.5:c.1336G>A	p.Asp446Asn	p.D446N	ENST00000295754	NM_003242.5	446	Gat/Aat	5/7	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.501965370026466	2		482	735	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903686	114903686	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	186	581	0	ENST00000543371.1:c.690C>G	p.Ile230Met	p.I230M	ENST00000543371	NM_001198531.1	230	atC/atG	7/14	0.501965370026466	1	FACETS	0.69	0.639	0.744	0.69	0.639	0.744	SUBCLONAL	1	TRUE	0	0.501965370026466	1		581	804	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160459	108160459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	197	501	0	ENST00000278616.4:c.4367G>A	p.Gly1456Asp	p.G1456D	ENST00000278616	NM_000051.3	1456	gGc/gAc	29/63	1	2	FACETS	0.94	0.872	1	0.94	0.872	1	CLONAL	1	TRUE	1	0.501965370026466	2		501	835	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37871571	37871571	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	46	494	0	ENST00000269571.5:c.1181C>A	p.Pro394Gln	p.P394Q	ENST00000269571		394	cCa/cAa	10/27	1	2	FACETS	0.229	0.192	0.27	0.229	0.192	0.27	SUBCLONAL	1	TRUE	1	0.501965370026466	2		494	801	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106394	27106398	+	frameshift_variant	Frame_Shift_Del	DEL	CCAAA	CCAAA	-	novel	NA	P-0005910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	128	340	1	ENST00000324856.7:c.6006_6010del	p.Lys2003ProfsTer28	p.K2003Pfs*28	ENST00000324856	NM_006015.4	2002	tCCAAA/t	20/20	1	2	FACETS	0.981	0.893	1	0.981	0.893	1	CLONAL	1	TRUE	1	0.501965370026466	2		341	520	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891330	151891330	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	186	409	0	ENST00000262189.6:c.4524del	p.Lys1508AsnfsTer55	p.K1508Nfs*55	ENST00000262189	NM_170606.2	1508	aaA/aa	30/59	0.501965370026466	2	FACETS	1	0.974	1	0.554	0.513	0.596	CLONAL	1	TRUE	0	0.501965370026466	2		409	669	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8252007	8252007	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	308	368	0	ENST00000335790.3:c.70T>A	p.Cys24Ser	p.C24S	ENST00000335790	NM_002315.2	24	Tgt/Agt	2/4	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.585254378748275	2		368	977	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0005929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	20310	673	9	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.160067469699231	176	FACETS	0.997	0.995	1			1	CLONAL	180	FALSE	NA	0.160067469699231	176		682	21096	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372184	55372184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs915105324	NA	P-0005929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	47	104	0	ENST00000297316.4:c.874G>A	p.Ala292Thr	p.A292T	ENST00000297316	NM_022454.3	292	Gcc/Acc	2/2	1	2	FACETS	0.94	0.814	1	1	0.982	1	CLONAL	5	FALSE	1	0.160067469699231	2		104	125	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591291	67591291	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	370	356	0	ENST00000274335.5:c.1789T>G	p.Trp597Gly	p.W597G	ENST00000274335		597	Tgg/Ggg	13/15	0.160067469699231	4	FACETS	0.973	0.926	1			1	CLONAL	6	FALSE	NA	0.160067469699231	4		356	919	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885344	111885344	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	207	582	0	ENST00000341259.2:c.1232C>A	p.Ala411Asp	p.A411D	ENST00000341259	NM_005475.2	411	gCc/gAc	6/8	1	2	FACETS	1	0.959	1	1	0.996	1	CLONAL	5	FALSE	1	0.160067469699231	2		582	502	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955058	17955058	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	156	453	1	ENST00000458235.1:c.169G>T	p.Ala57Ser	p.A57S	ENST00000458235	NM_000215.3	57	Gct/Tct	2/24	0.114619117096735	0	FACETS	1	0.939	1			1	CLONAL	4	FALSE	0	0.160067469699231	0		454	403	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345549	70345549	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	205	692	0	ENST00000374080.3:c.2408A>G	p.Asp803Gly	p.D803G	ENST00000374080		803	gAc/gGc	17/45	0.160067469699231	1	FACETS	0.932	0.869	0.996	1	0.995	1	CLONAL	4	FALSE	0	0.160067469699231	1		692	632	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0005946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	87	229	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.443047465736537	4	FACETS	1	0.893	1	0.503	0.446	0.564	CLONAL	1	TRUE	2	0.43945404658962	4		229	566	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11175499	11175499	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	151	551	0	ENST00000361445.4:c.7043G>T	p.Arg2348Leu	p.R2348L	ENST00000361445	NM_004958.3	2348	cGt/cTt	51/58	0.210702345223733	3	FACETS	1	0.947	1			1	INDETERMINATE	1	TRUE	NA	0.43945404658962	3		551	800	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101342	27101342	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	351	539	0	ENST00000324856.7:c.4624G>T	p.Glu1542Ter	p.E1542*	ENST00000324856	NM_006015.4	1542	Gaa/Taa	18/20	0.423181956281125	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	2	0.43945404658962	4		539	926	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543781	212543781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866138670	NA	P-0005946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	113	309	0	ENST00000342788.4:c.1618G>A	p.Asp540Asn	p.D540N	ENST00000342788	NM_005235.2	540	Gat/Aat	13/28	0.443047465736537	3	FACETS	0.98	0.884	1	0.49	0.442	0.541	CLONAL	1	TRUE	1	0.43945404658962	3		309	640	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479829	67479829	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	113	488	0	ENST00000327367.4:c.1136G>T	p.Gly379Val	p.G379V	ENST00000327367	NM_005902.3	379	gGc/gTc	8/9	0.10001490750926	4	FACETS	1	0.974	1	0.618	0.557	0.682	INDETERMINATE	1	TRUE	2	0.43945404658962	4		488	599	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72863735	72863735	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1156726263	NA	P-0005946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	293	574	0	ENST00000268489.5:c.3472G>A	p.Gly1158Arg	p.G1158R	ENST00000268489	NM_006885.3	1158	Gga/Aga	5/10	0.443047465736537	3	FACETS	0.841	0.793	0.89			1	CLONAL	2	TRUE	NA	0.43945404658962	3		574	967	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349940	15349940	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	95	405	0	ENST00000263377.2:c.3712G>C	p.Glu1238Gln	p.E1238Q	ENST00000263377	NM_058243.2	1238	Gag/Cag	18/20	0.443047465736537	3	FACETS	1	0.899	1			1	CLONAL	1	TRUE	NA	0.43945404658962	3		405	524	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937990	76937990	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	120	551	0	ENST00000373344.5:c.2758G>T	p.Gly920Cys	p.G920C	ENST00000373344	NM_000489.3	920	Ggt/Tgt	9/35	0.195559941706425	3	FACETS	0.864	0.78	0.952	0.288	0.26	0.318	INDETERMINATE	1	TRUE	0	0.43945404658962	3		551	771	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183725	10183725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs5030826	NA	P-0005954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	184	416	0	ENST00000256474.2:c.194C>T	p.Ser65Leu	p.S65L	ENST00000256474	NM_000551.3	65	tCg/tTg	1/3	0.207232445281096	4	FACETS	0.912	0.847	0.978			1	CLONAL	3	TRUE	NA	0.310417557445847	4		416	568	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164505	47164505	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	21	483	0	ENST00000409792.3:c.1621C>T	p.Arg541Ter	p.R541*	ENST00000409792	NM_014159.6	541	Cga/Tga	3/21	0.310417557445847	2	FACETS	0.739	0.573	0.931	0.37	0.286	0.466	CLONAL	1	TRUE	0	0.310417557445847	2		483	183	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513294	106513294	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	33	428	0	ENST00000359195.3:c.2198C>G	p.Thr733Ser	p.T733S	ENST00000359195	NM_002649.2	733	aCc/aGc	4/11	0.310417557445847	6	FACETS	0.907	0.739	1	0.302	0.246	0.365	CLONAL	1	TRUE	3	0.310417557445847	6		428	380	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794359	242794359	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	504	535	1	ENST00000334409.5:c.583G>A	p.Ala195Thr	p.A195T	ENST00000334409	NM_005018.2	195	Gcc/Acc	3/5	0.723925910415957	3	FACETS	0.961	0.925	0.996			1	CLONAL	2	TRUE	NA	0.738128064833243	3		536	973	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478803	57478803	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	190	347	0	ENST00000371085.3:c.389A>G	p.Tyr130Cys	p.Y130C	ENST00000371085	NM_000516.4	130	tAc/tGc	5/13	0.398871732532626	5	FACETS	1	0.976	1	0.378	0.349	0.408	INDETERMINATE	1	TRUE	2	0.738128064833243	5		347	956	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650870	48650870	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782126313	NA	P-0005970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	273	275	0	ENST00000376670.3:c.739C>T	p.Arg247Cys	p.R247C	ENST00000376670	NM_002049.3	247	Cgc/Tgc	4/6	0.738128064833243	3	FACETS	1	0.958	1			1	CLONAL	1	TRUE	NA	0.738128064833243	3		275	989	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0005971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	250	316	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.279912076846321	3	FACETS	1	0.99	1	0.651	0.61	0.693	INDETERMINATE	1	FALSE	1	0.53345038486564	3		316	912	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0005971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	66	405	0				ENST00000310581	NM_198253.2	-/1132			0.53345038486564	1	FACETS	0.864	0.762	0.97	0.864	0.762	0.97	CLONAL	1	FALSE	0	0.53345038486564	1		405	210	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771163	161771163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755627153	NA	P-0005971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	88	693	0	ENST00000366898.1:c.1366G>A	p.Val456Ile	p.V456I	ENST00000366898	NM_004562.2	456	Gtc/Atc	12/12	0.45466790961722	1	FACETS	0.401	0.356	0.45	0.401	0.356	0.45	SUBCLONAL	1	FALSE	0	0.53345038486564	1		693	603	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347309	89347310	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0005971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	106	1200	0	ENST00000301030.4:c.5640_5641delinsAA	p.Gly1881Ser	p.G1881S	ENST00000301030	NM_001256183.1	1880	gaGGgc/gaAAgc	9/13	0.433390590545396	1	FACETS	0.459	0.412	0.509	0.459	0.412	0.509	SUBCLONAL	1	FALSE	0	0.53345038486564	1		1200	635	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0005988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	261	437	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.923	0.871	0.974	1	0.996	1	CLONAL	4	TRUE	1	0.23	2		437	615	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226415	2226415	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs200251876	NA	P-0005988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	18	419	1	ENST00000398665.3:c.3895T>A	p.Ser1299Thr	p.S1299T	ENST00000398665	NM_032482.2	1299	Tcc/Acc	27/28	0.141331427336497	0	FACETS	0.349	0.262	0.452			1	SUBCLONAL	1	TRUE	0	0.23	0		420	345	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0006028-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	119	383	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	0.989	0.892	1	0.989	0.892	1	CLONAL	1	TRUE	1	0.27	2		383	891	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435300	110435302	+	inframe_deletion	In_Frame_Del	DEL	GGT	GGT	-	rs765493638	NA	P-0006028-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	15	106	0	ENST00000375856.3:c.3099_3101del	p.Pro1036del	p.P1036del	ENST00000375856	NM_003749.2	1033	ccACCg/ccg	1/2	1	2	FACETS	0.439	0.321	0.581	0.439	0.321	0.581	SUBCLONAL	1	TRUE	1	0.27	2		106	253	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665060	182665060	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006028-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	75	500	0	ENST00000292782.4:c.666G>T	p.Met222Ile	p.M222I	ENST00000292782	NM_020640.2	222	atG/atT	6/7	1	2	FACETS	0.433	0.378	0.493	0.433	0.378	0.493	SUBCLONAL	1	TRUE	1	0.27	2		500	1283	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860604	45860604	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006028-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1264	128	623	0	ENST00000391945.4:c.1403C>A	p.Pro468His	p.P468H	ENST00000391945	NM_000400.3	468	cCc/cAc	15/23	1	2	FACETS	0.681	0.615	0.751	0.681	0.615	0.751	SUBCLONAL	1	TRUE	1	0.27	2		623	1392	SUCCESS
AR	367	MSKCC	GRCh37	X	66765497	66765497	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006028-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	96	454	0	ENST00000374690.3:c.509C>T	p.Thr170Ile	p.T170I	ENST00000374690	NM_000044.3	170	aCt/aTt	1/8	1	2	FACETS	0.953	0.849	1	0.953	0.849	1	CLONAL	1	TRUE	1	0.27	2		454	746	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006038-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	120	407	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.16691614301842	2	FACETS	0.769	0.695	0.846	0.769	0.695	0.846	SUBCLONAL	2	TRUE	0	0.224289274420206	2		407	696	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0006038-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	155	622	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.224289274420206	1	FACETS	0.966	0.882	1	0.966	0.882	1	CLONAL	1	TRUE	0	0.224289274420206	1		624	1270	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436026	56436026	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771831816	NA	P-0006038-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	76	307	1	ENST00000407977.2:c.1111C>T	p.Arg371Ter	p.R371*	ENST00000407977		371	Cga/Tga	9/10	0.193824588022402	1	FACETS	0.969	0.85	1	0.969	0.85	1	CLONAL	1	TRUE	0	0.224289274420206	1		308	621	SUCCESS
H3C13	653604	MSKCC	GRCh37	1	149784860	149784860	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006038-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	53	269	0	ENST00000331491.1:c.377A>G	p.Gln126Arg	p.Q126R	ENST00000331491	NM_001123375.2	126	cAg/cGg	1/1	1	2	FACETS	0.744	0.634	0.865	0.744	0.634	0.865	SUBCLONAL	1	TRUE	1	0.224289274420206	2		269	635	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743298	162743298	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006038-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	45	426	2	ENST00000367921.3:c.1768G>A	p.Asp590Asn	p.D590N	ENST00000367921	NM_006182.2	590	Gac/Aac	14/18	1	2	FACETS	0.544	0.456	0.642	0.544	0.456	0.642	SUBCLONAL	1	TRUE	1	0.224289274420206	2		428	737	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949796	151949796	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006038-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	62	281	2	ENST00000262189.6:c.1304G>A	p.Cys435Tyr	p.C435Y	ENST00000262189	NM_170606.2	435	tGc/tAc	10/59	1	2	FACETS	0.918	0.793	1	0.918	0.793	1	CLONAL	1	TRUE	1	0.224289274420206	2		283	602	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008057	29008057	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139202898	NA	P-0006038-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	71	420	2	ENST00000282397.4:c.712C>T	p.Arg238Cys	p.R238C	ENST00000282397	NM_002019.4	238	Cgc/Tgc	6/30	1	2	FACETS	0.843	0.735	0.96	0.843	0.735	0.96	CLONAL	1	TRUE	1	0.224289274420206	2		422	751	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438262	110438262	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006038-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	25	100	0	ENST00000375856.3:c.139T>G	p.Phe47Val	p.F47V	ENST00000375856	NM_003749.2	47	Ttc/Gtc	1/2	1	2	FACETS	0.864	0.683	1	0.864	0.683	1	CLONAL	1	TRUE	1	0.224289274420206	2		100	258	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604650	48604650	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs377767367	NA	P-0006038-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	78	264	0	ENST00000342988.3:c.1472G>T	p.Gly491Val	p.G491V	ENST00000342988	NM_005359.5	491	gGt/gTt	12/12	0.224289274420206	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.224289274420206	1		264	580	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942751	44942751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763592177	NA	P-0006038-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	66	270	0	ENST00000377967.4:c.3331C>T	p.Arg1111Cys	p.R1111C	ENST00000377967	NM_021140.2	1111	Cgt/Tgt	23/29	1	1	FACETS	0.931	0.809	1	0.931	0.809	1	CLONAL	1	TRUE	0	0.224289274420206	1		270	561	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0006043-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	37	324	2	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.651	0.535	0.78	0.651	0.535	0.78	SUBCLONAL	1	FALSE	1	0.186761085282724	2		326	609	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006050-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	309	412	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.757	0.719	0.795	1	0.995	1	SUBCLONAL	2	TRUE	1	0.608510718668266	2		412	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0006050-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	52	502	1	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.608510718668266	1	FACETS	0.162	0.137	0.189	0.162	0.137	0.189	SUBCLONAL	1	TRUE	0	0.608510718668266	1		503	736	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555074	106555074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756685678	NA	P-0006050-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	372	399	0	ENST00000369096.4:c.2191G>A	p.Glu731Lys	p.E731K	ENST00000369096	NM_001198.3	731	Gag/Aag	7/7	0.188129745300301	4	FACETS	0.8	0.759	0.842	0.8	0.759	0.842	INDETERMINATE	2	TRUE	2	0.608510718668266	4		399	1229	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852242	128852242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140172891	NA	P-0006050-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	272	487	2	ENST00000249373.3:c.2314C>T	p.Arg772Cys	p.R772C	ENST00000249373	NM_005631.4	772	Cgc/Tgc	12/12	0.185886688317479	1	FACETS	0.681	0.64	0.722	0.681	0.64	0.722	INDETERMINATE	1	TRUE	0	0.608510718668266	1		489	914	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990331	81990331	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768299957	NA	P-0006050-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	393	642	0	ENST00000359376.3:c.3602G>A	p.Arg1201His	p.R1201H	ENST00000359376	NM_002661.3	1201	cGc/cAc	32/33	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.608510718668266	2		642	1217	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0006078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	192	547	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.3	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.36	1		547	844	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0006078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	138	546	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.36	2		546	746	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748480	43748480	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1395807781	NA	P-0006078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	213	857	1	ENST00000523873.1:c.434G>A	p.Arg145Gln	p.R145Q	ENST00000523873		145	cGa/cAa	6/8	1	2	FACETS	0.989	0.918	1	0.989	0.918	1	CLONAL	1	TRUE	1	0.36	2		858	1196	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404264	139404264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780251851	NA	P-0006078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	128	620	0	ENST00000277541.6:c.2890G>A	p.Val964Met	p.V964M	ENST00000277541	NM_017617.3	964	Gtg/Atg	18/34	1	2	FACETS	0.932	0.845	1	0.932	0.845	1	CLONAL	1	TRUE	1	0.36	2		620	763	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212457	5212457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	127	680	0	ENST00000357368.4:c.4660G>A	p.Ala1554Thr	p.A1554T	ENST00000357368	NM_002850.3	1554	Gcg/Acg	31/38	1	2	FACETS	0.89	0.806	0.978	0.89	0.806	0.978	CLONAL	1	TRUE	1	0.36	2		680	793	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645169	86645169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs191759701	NA	P-0006094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	66	387	2	ENST00000274376.6:c.1241G>A	p.Arg414Gln	p.R414Q	ENST00000274376	NM_002890.2	414	cGg/cAg	8/25	0.269500235997907	3	FACETS	0.828	0.718	0.946	0.414	0.359	0.473	CLONAL	1	TRUE	1	0.286228829981558	3		389	637	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38996925	38996925	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	73	457	0	ENST00000357387.3:c.452G>C	p.Arg151Thr	p.R151T	ENST00000357387	NM_152756.3	151	aGa/aCa	6/38	0.286228829981558	5	FACETS	0.794	0.693	0.904	0.265	0.231	0.302	CLONAL	1	TRUE	2	0.286228829981558	5		457	918	SUCCESS
APC	324	MSKCC	GRCh37	5	112163689	112163689	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	104	736	1	ENST00000257430.4:c.1612G>T	p.Glu538Ter	p.E538*	ENST00000257430	NM_000038.5	538	Gaa/Taa	13/16	0.269500235997907	3	FACETS	0.729	0.651	0.813	0.365	0.325	0.407	SUBCLONAL	1	TRUE	1	0.286228829981558	3		737	1139	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520098	106520098	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	69	336	0	ENST00000359195.3:c.2526G>C	p.Met842Ile	p.M842I	ENST00000359195	NM_002649.2	842	atG/atC	6/11	0.286228829981558	5	FACETS	1	0.938	1	0.226	0.197	0.258	CLONAL	1	TRUE	0	0.286228829981558	5		336	609	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412045	116412045	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0006094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	254	354	0	ENST00000397752.3:c.3028+2T>A		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.286228829981558	5	FACETS	0.94	0.889	0.991	0.94	0.889	0.991	CLONAL	5	TRUE	0	0.286228829981558	5		354	540	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426872	70426872	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	96	615	0	ENST00000373644.4:c.4532C>A	p.Pro1511Gln	p.P1511Q	ENST00000373644	NM_030625.2	1511	cCa/cAa	7/12	1	2	FACETS	0.9	0.802	1	0.9	0.802	1	CLONAL	1	TRUE	1	0.286228829981558	2		615	745	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995257	15995257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	111	651	0	ENST00000268712.3:c.2936G>C	p.Arg979Thr	p.R979T	ENST00000268712	NM_006311.3	979	aGa/aCa	22/46	0.269254576497271	2	FACETS	1	0.916	1	0.51	0.459	0.565	CLONAL	1	TRUE	0	0.286228829981558	2		651	760	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350782	15350782	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	77	674	0	ENST00000263377.2:c.3221C>A	p.Ser1074Ter	p.S1074*	ENST00000263377	NM_058243.2	1074	tCa/tAa	15/20	0.286228829981558	2	FACETS	0.868	0.762	0.981	0.434	0.381	0.491	CLONAL	1	TRUE	0	0.286228829981558	2		674	620	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937810	76937810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	126	919	0	ENST00000373344.5:c.2938G>A	p.Asp980Asn	p.D980N	ENST00000373344	NM_000489.3	980	Gat/Aat	9/35	0.286228829981558	2	FACETS	0.826	0.746	0.91	0.413	0.373	0.455	CLONAL	1	TRUE	0	0.286228829981558	2		919	1066	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938062	76938062	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	101	723	0	ENST00000373344.5:c.2686G>C	p.Asp896His	p.D896H	ENST00000373344	NM_000489.3	896	Gat/Cat	9/35	0.286228829981558	2	FACETS	0.881	0.787	0.981	0.441	0.393	0.491	CLONAL	1	TRUE	0	0.286228829981558	2		723	801	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938074	76938074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	98	692	0	ENST00000373344.5:c.2674G>A	p.Glu892Lys	p.E892K	ENST00000373344	NM_000489.3	892	Gaa/Aaa	9/35	0.286228829981558	2	FACETS	0.894	0.797	0.997	0.447	0.398	0.499	CLONAL	1	TRUE	0	0.286228829981558	2		692	766	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0006103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	210	401	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.410410919005794	3	FACETS	0.941	0.879	1	0.941	0.879	1	CLONAL	2	TRUE	1	0.410410919005794	3		401	655	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0006103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	111	591	1	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	1	2	FACETS	0.951	0.857	1	0.951	0.857	1	CLONAL	1	TRUE	1	0.410410919005794	2		592	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579533	7579533	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	403	572	1	ENST00000269305.4:c.154C>T	p.Gln52Ter	p.Q52*	ENST00000269305	NM_001126112.2	52	Caa/Taa	4/11	NA	2	FACETS	0.984	0.939	1			1	INDETERMINATE	2	TRUE	NA	0.410410919005794	2		573	998	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438576	52438584	+	frameshift_variant	Frame_Shift_Del	DEL	CACACCTGC	CACACCTGC	T	novel	NA	P-0006109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	76	413	0	ENST00000460680.1:c.1135_1143delinsA	p.Ala379ArgfsTer16	p.A379Rfs*16	ENST00000460680	NM_004656.3	379	GCAGGTGTG/A	12/17	0.285878964373448	1	FACETS	0.984	0.866	1	0.984	0.866	1	CLONAL	1	TRUE	0	0.285878964373448	1		413	463	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0006112-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	586	564	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.295753072958768	3	FACETS	1	0.982	1	1	0.997	1	CLONAL	4	TRUE	0	0.29	3		564	1128	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927714	131927714	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006112-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	31	336	0	ENST00000265335.6:c.1781T>A	p.Leu594His	p.L594H	ENST00000265335		594	cTt/cAt	11/25	0.295753072958768	3	FACETS	0.505	0.407	0.615			1	SUBCLONAL	1	TRUE	NA	0.29	3		336	485	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132465	11132465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006112-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	408	608	1	ENST00000358026.2:c.2681C>T	p.Thr894Met	p.T894M	ENST00000358026	NM_001128849.1	894	aCg/aTg	19/36	0.295753072958768	3	FACETS	0.955	0.911	1	1	0.995	1	CLONAL	3	TRUE	1	0.29	3		609	1124	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971007	21971018	+	inframe_deletion	In_Frame_Del	DEL	CAGGTCCACGGG	CAGGTCCACGGG	-	novel	NA	P-0006112-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	183	356	0	ENST00000304494.5:c.340_351del	p.Pro114_Leu117del	p.P114_L117del	ENST00000304494	NM_000077.4	114	CCCGTGGACCTG/-	2/3	0.295753072958768	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.29	2		356	551	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591971	48591987	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGCAAGGTATTGATTGT	AGCAAGGTATTGATTGT	-	novel	NA	P-0006112-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	33	368	0	ENST00000342988.3:c.1135_1139+12del		p.X379_splice	ENST00000342988	NM_005359.5	379		9/12	0.295753072958768	1	FACETS	0.433	0.353	0.525	0.433	0.353	0.525	SUBCLONAL	1	TRUE	0	0.29	1		368	449	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877388	28877396	+	frameshift_variant	Frame_Shift_Del	DEL	GTGGTCGTA	GTGGTCGTA	T	novel	NA	P-0006112-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	39	338	0	ENST00000282397.4:c.3925_3933delinsA	p.Tyr1309SerfsTer2	p.Y1309Sfs*2	ENST00000282397	NM_002019.4	1309	TACGACCAC/A	30/30	0.28589231067031	4	FACETS	0.457	0.378	0.546	0.152	0.126	0.182	SUBCLONAL	1	TRUE	1	0.29	4		338	759	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0006116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	57	411	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.14	2		411	724	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0006116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	76	477	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	1	2	FACETS	0.754	0.661	0.854	1	0.975	1	SUBCLONAL	2	TRUE	1	0.14	2		477	720	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348785	11348785	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	14	171	1	ENST00000332029.2:c.551C>T	p.Ala184Val	p.A184V	ENST00000332029	NM_003745.1	184	gCc/gTc	2/2	1	2	FACETS	0.769	0.556	1	0.769	0.556	1	CLONAL	1	TRUE	1	0.14	2		172	260	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397516436	NA	P-0006122-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	245	654	0	ENST00000269305.4:c.637C>G	p.Arg213Gly	p.R213G	ENST00000269305	NM_001126112.2	213	Cga/Gga	6/11	0.433288292690657	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.454031740275636	2		654	535	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219578	133219578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376530977	NA	P-0006122-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	124	324	0	ENST00000320574.5:c.4556G>A	p.Arg1519His	p.R1519H	ENST00000320574	NM_006231.2	1519	cGc/cAc	36/49	0.284194221056505	3	FACETS	1	0.942	1	0.69	0.632	0.748	CLONAL	2	TRUE	0	0.454031740275636	3		324	324	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970987	21971685	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGATGGCCCAGCTCCTCAGCCAGGTCCACGGGCAGACGGCCCCAGGCATCGCGCACGTCCAGCCGCGCCCCGGCCCGGTGCAGCACCACCAGCGTGTCCAGGAAGCCCTCCCGGGCAGCGTCGTGCACGGGTCGGGTGAGAGTGGCGGGGTCGGCGCAGTTGGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCTGCCCATCATCATGACCTGCCAGAGAGAACAGAATGGTCAGAGCCAGGGTGGGGGCCGGCATGACGGAAAGGAAGCTTGTGTAGAGCCCCCTCACCGCCAAGCAGACCCCCACACAAGCCCCAGGTGTCTAATTACCCCTACATTTGCTTCCAGTTTCCAATTTCCTTCTTGAGTTCTCTATCCATTCTTCAGTACACAATGAATTCCATTATATCCTCCGAACTTCTGCGGAGCTGTCGTCACAGGCAGAGAGCACTGTGAGGCACGGGCAAAATAGCAAAGGGGCAGGGACAGACTGACTTTTACTCCAGGCTAACTTCCTGTATTTCCCCTGAGATACAACTACTGAAATTTCTTCCTGAAATTATGTTAGGCCTGGAGATTTTTTTTTTTTTTTTTGTTCACTGCTGTATATCCAAGCGCAGAATGTGGTAATTGTTAAAAAGAGAAAACTTGTTTGTTTGTTAAAACAAATTCTCACAAAACTTTTAAG	CGATGGCCCAGCTCCTCAGCCAGGTCCACGGGCAGACGGCCCCAGGCATCGCGCACGTCCAGCCGCGCCCCGGCCCGGTGCAGCACCACCAGCGTGTCCAGGAAGCCCTCCCGGGCAGCGTCGTGCACGGGTCGGGTGAGAGTGGCGGGGTCGGCGCAGTTGGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCTGCCCATCATCATGACCTGCCAGAGAGAACAGAATGGTCAGAGCCAGGGTGGGGGCCGGCATGACGGAAAGGAAGCTTGTGTAGAGCCCCCTCACCGCCAAGCAGACCCCCACACAAGCCCCAGGTGTCTAATTACCCCTACATTTGCTTCCAGTTTCCAATTTCCTTCTTGAGTTCTCTATCCATTCTTCAGTACACAATGAATTCCATTATATCCTCCGAACTTCTGCGGAGCTGTCGTCACAGGCAGAGAGCACTGTGAGGCACGGGCAAAATAGCAAAGGGGCAGGGACAGACTGACTTTTACTCCAGGCTAACTTCCTGTATTTCCCCTGAGATACAACTACTGAAATTTCTTCCTGAAATTATGTTAGGCCTGGAGATTTTTTTTTTTTTTTTTGTTCACTGCTGTATATCCAAGCGCAGAATGTGGTAATTGTTAAAAAGAGAAAACTTGTTTGTTTGTTAAAACAAATTCTCACAAAACTTTTAAG	-	novel	NA	P-0006122-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	236	411	0	ENST00000304494.5:c.151-477_372del		p.X51_splice	ENST00000304494	NM_000077.4	51		2/3	0.433353517660598	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.454031740275636	2		411	494	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201844	66201844	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0006128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	41	326	0	ENST00000273854.3:c.2659-1G>A		p.X887_splice	ENST00000273854	NM_004439.5	887			1	2	FACETS	0.941	0.783	1	0.941	0.783	1	CLONAL	1	FALSE	1	0.177186882820623	2		326	492	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743859	40743859	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369430281	NA	P-0006128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	46	594	1	ENST00000373198.4:c.3136C>T	p.Arg1046Cys	p.R1046C	ENST00000373198	NM_133170.3	1046	Cgc/Tgc	23/32	1	2	FACETS	0.571	0.479	0.673	0.571	0.479	0.673	SUBCLONAL	1	FALSE	1	0.177186882820623	2		595	910	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712598	52712598	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	44	395	0	ENST00000394830.3:c.154G>T	p.Glu52Ter	p.E52*	ENST00000394830	NM_018313.4	52	Gaa/Taa	3/30	1	2	FACETS	0.717	0.602	0.844	0.717	0.602	0.844	SUBCLONAL	1	TRUE	1	0.288181113218248	2		395	426	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786489	135786489	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs118203491	NA	P-0006131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	104	441	0	ENST00000298552.3:c.1041G>A	p.Trp347Ter	p.W347*	ENST00000298552	NM_001162426.1	347	tgG/tgA	11/23	0.17701786764348	2	FACETS	1	0.982	1	0.734	0.66	0.811	CLONAL	1	TRUE	0	0.288181113218248	2		441	492	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775249	73775249	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	69	393	0	ENST00000254810.4:c.7C>G	p.Arg3Gly	p.R3G	ENST00000254810	NM_005324.3	3	Cga/Gga	2/4	1	2	FACETS	0.52	0.452	0.594	0.52	0.452	0.594	SUBCLONAL	1	TRUE	1	0.288181113218248	2		393	921	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101525	27101538	+	frameshift_variant	Frame_Shift_Del	DEL	AAGTCTCCATTCCT	AAGTCTCCATTCCT	-	novel	NA	P-0006131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	81	468	0	ENST00000324856.7:c.4807_4820del	p.Lys1603AlafsTer40	p.K1603Afs*40	ENST00000324856	NM_006015.4	1603	AAGTCTCCATTCCTg/g	18/20	1	2	FACETS	0.523	0.459	0.592	0.523	0.459	0.592	SUBCLONAL	1	TRUE	1	0.288181113218248	2		468	1075	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	31	412	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.12	2		412	477	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0006141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	47	436	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	1	2	FACETS	0.974	0.82	1	0.974	0.82	1	CLONAL	1	TRUE	1	0.12	2		436	804	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0006141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	20	384	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.539	0.411	0.691	0.539	0.411	0.691	SUBCLONAL	1	TRUE	1	0.12	2		384	618	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0006156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	234	666	2	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	0.474341139799314	3	FACETS	0.972	0.905	1	0.486	0.452	0.521	CLONAL	1	TRUE	1	0.470825495486172	3		668	1263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882025	NA	P-0006156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	412	559	0	ENST00000269305.4:c.646G>T	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ttg	6/11	0.356647376698539	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	0	0.470825495486172	3		559	695	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47735771	47735771	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0006156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	173	492	0	ENST00000449228.1:c.88+1G>C		p.X30_splice	ENST00000449228	NM_001127240.2	30			0.276515511458882	5	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.470825495486172	5		492	1040	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215308	123215308	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	295	587	0	ENST00000218089.9:c.2854G>C	p.Ala952Pro	p.A952P	ENST00000218089	NM_001042749.1	952	Gct/Cct	28/35	0.238893401486443	5	FACETS	0.96	0.903	1	0.64	0.602	0.678	INDETERMINATE	2	TRUE	2	0.470825495486172	5		587	1114	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502466	186502468	+	inframe_deletion	In_Frame_Del	DEL	TAT	TAT	-	rs755185062	NA	P-0006156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	229	526	0	ENST00000323963.5:c.193_195del	p.Ile65del	p.I65del	ENST00000323963		63	gcTATt/gct	3/11	0.474341139799314	3	FACETS	1	0.959	1	0.521	0.485	0.559	CLONAL	1	TRUE	1	0.470825495486172	3		526	1153	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0006175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	350	465	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.473473856549336	4	FACETS	0.974	0.924	1	0.974	0.924	1	CLONAL	2	TRUE	2	0.526033490868421	4		465	1042	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154748	2154748	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs369122420	NA	P-0006175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	250	589	0	ENST00000434045.2:c.473C>T	p.Pro158Leu	p.P158L	ENST00000434045	NM_001127598.1	158	cCg/cTg	4/5	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.526033490868421	2		589	927	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057811	27057811	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	347	816	0	ENST00000324856.7:c.1519C>T	p.Gln507Ter	p.Q507*	ENST00000324856	NM_006015.4	507	Caa/Taa	3/20	0.526033490868421	2	FACETS	0.848	0.801	0.897	0.424	0.4	0.449	CLONAL	1	TRUE	0	0.526033490868421	2		816	1555	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058093	27058093	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	42	70	0	ENST00000324856.7:c.1801C>T	p.Gln601Ter	p.Q601*	ENST00000324856	NM_006015.4	601	Cag/Tag	3/20	0.526033490868421	2	FACETS	0.845	0.714	0.986	0.422	0.357	0.493	CLONAL	1	TRUE	0	0.526033490868421	2		70	189	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793439	242793439	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	441	471	0	ENST00000334409.5:c.638C>A	p.Pro213His	p.P213H	ENST00000334409	NM_005018.2	213	cCc/cAc	5/5	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.526033490868421	2		471	757	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271223	153271223	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	128	393	0	ENST00000281708.4:c.555G>C	p.Lys185Asn	p.K185N	ENST00000281708	NM_033632.3	185	aaG/aaC	3/12	0.526033490868421	2	FACETS	0.858	0.781	0.939	0.429	0.39	0.47	CLONAL	1	TRUE	0	0.526033490868421	2		393	567	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931309	131931309	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	213	622	0	ENST00000265335.6:c.2014C>G	p.Gln672Glu	p.Q672E	ENST00000265335		672	Cag/Gag	13/25	0.526033490868421	3	FACETS	0.869	0.806	0.934	0.435	0.403	0.467	CLONAL	1	TRUE	1	0.526033490868421	3		622	1177	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406240	70406240	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	205	642	1	ENST00000373644.4:c.3754G>T	p.Glu1252Ter	p.E1252*	ENST00000373644	NM_030625.2	1252	Gag/Tag	4/12	0.526033490868421	3	FACETS	0.895	0.829	0.963	0.447	0.414	0.482	CLONAL	1	TRUE	1	0.526033490868421	3		643	1100	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180972	108180972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	130	381	0	ENST00000278616.4:c.5848G>A	p.Ala1950Thr	p.A1950T	ENST00000278616	NM_000051.3	1950	Gct/Act	39/63	0.526033490868421	3	FACETS	1	0.926	1	0.51	0.464	0.558	CLONAL	1	TRUE	1	0.526033490868421	3		381	612	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246147	46246147	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	141	430	0	ENST00000334344.6:c.4241G>A	p.Arg1414Lys	p.R1414K	ENST00000334344	NM_152641.2	1414	aGa/aAa	15/21	0.473473856549336	4	FACETS	0.924	0.842	1	0.462	0.421	0.506	CLONAL	1	TRUE	2	0.526033490868421	4		430	885	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110034	115110034	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	379	496	1	ENST00000257566.3:c.1844C>G	p.Ser615Cys	p.S615C	ENST00000257566	NM_016569.3	615	tCc/tGc	8/8	0.473473856549336	4	FACETS	0.89	0.845	0.936	0.89	0.845	0.936	CLONAL	2	TRUE	2	0.526033490868421	4		497	1235	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911829	32911829	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	290	949	1	ENST00000380152.3:c.3337G>T	p.Glu1113Ter	p.E1113*	ENST00000380152		1113	Gaa/Taa	11/27	0.526033490868421	2	FACETS	1	0.97	1	0.523	0.492	0.555	CLONAL	1	TRUE	0	0.526033490868421	2		950	1054	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059279	42059279	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1465	396	915	1	ENST00000219905.7:c.8999C>A	p.Ser3000Tyr	p.S3000Y	ENST00000219905	NM_001164273.1	3000	tCc/tAc	24/24	0.526033490868421	3	FACETS	1	0.964	1	0.341	0.322	0.359	CLONAL	1	TRUE	0	0.526033490868421	3		916	1861	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610376	10610376	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	537	627	0	ENST00000171111.5:c.334A>T	p.Thr112Ser	p.T112S	ENST00000171111	NM_203500.1	112	Acc/Tcc	2/6	0.526033490868421	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.526033490868421	2		627	985	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610380	10610380	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	549	631	0	ENST00000171111.5:c.330G>T	p.Met110Ile	p.M110I	ENST00000171111	NM_203500.1	110	atG/atT	2/6	0.526033490868421	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.526033490868421	2		631	999	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221299	1221300	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0006175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	503	600	0	ENST00000326873.7:c.823_824del	p.Pro275GlyfsTer9	p.P275Gfs*9	ENST00000326873	NM_000455.4	274	atCCcg/atcg	6/10	0.526033490868421	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.526033490868421	2		600	888	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0006184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	274	455	1	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.496166666218881	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.507653452860294	1		456	730	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161324	55161324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514550	NA	P-0006184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	159	478	1	ENST00000257290.5:c.3155C>T	p.Thr1052Met	p.T1052M	ENST00000257290	NM_006206.4	1052	aCg/aTg	23/23	NA	2	FACETS	0.797	0.731	0.865			1	INDETERMINATE	1	TRUE	NA	0.507653452860294	2		479	786	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266821	198266821	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	154	519	2	ENST00000335508.6:c.2111T>C	p.Ile704Thr	p.I704T	ENST00000335508	NM_012433.2	704	aTc/aCc	15/25	1	2	FACETS	0.837	0.767	0.909	0.837	0.767	0.909	CLONAL	1	TRUE	1	0.507653452860294	2		521	725	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272446	15272446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1235	415	715	0	ENST00000263388.2:c.5993G>A	p.Arg1998His	p.R1998H	ENST00000263388	NM_000435.2	1998	cGt/cAt	33/33	1	2	FACETS	0.991	0.941	1	0.991	0.941	1	CLONAL	1	TRUE	1	0.507653452860294	2		715	1650	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279510	1279510	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1295347738	NA	P-0121497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	406	445	1	ENST00000310581.5:c.2026C>A	p.Leu676Met	p.L676M	ENST00000310581	NM_198253.2	676	Ctg/Atg	5/16	0.254841307768573	5	FACETS	0.78	0.741	0.819			1	INDETERMINATE	2	NA	NA	0.769966372951803	5		446	1457	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662575	227662575	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	299	313	0	ENST00000305123.5:c.880C>A	p.Pro294Thr	p.P294T	ENST00000305123	NM_005544.2	294	Ccc/Acc	1/2	0.390085373216038	4	FACETS	1	0.99	1			1	INDETERMINATE	1	NA	NA	0.769966372951803	4		313	1107	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023646	27023646	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1210135390	NA	P-0006222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	117	582	7	ENST00000324856.7:c.752C>T	p.Pro251Leu	p.P251L	ENST00000324856	NM_006015.4	251	cCg/cTg	1/20	0.342796091969262	3	FACETS	1	0.945	1	0.535	0.482	0.59	CLONAL	1	FALSE	1	0.342796091969262	3		589	748	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139811068	139811068	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0006222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	85	753	0	ENST00000247668.2:c.678+1G>C		p.X226_splice	ENST00000247668	NM_021138.3	226			0.261323988191699	3	FACETS	1	0.977	1	0.707	0.628	0.79	CLONAL	1	FALSE	1	0.342796091969262	3		753	411	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342962	70342962	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	43	749	0	ENST00000374080.3:c.1503T>G	p.Asp501Glu	p.D501E	ENST00000374080		501	gaT/gaG	11/45	0.342796091969262	0	FACETS	0.746	0.63	0.872			1	SUBCLONAL	1	FALSE	0	0.342796091969262	0		749	221	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188196	10188196	+	splice_acceptor_variant	Splice_Site	DEL	A	A	-	novel	NA	P-0006222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	48	479	0	ENST00000256474.2:c.341-2del		p.X114_splice	ENST00000256474	NM_000551.3	114			0.282906541817183	3	FACETS	1	0.951	1	0.432	0.368	0.501	CLONAL	1	FALSE	0	0.342796091969262	3		479	253	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588836	52588836	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	69	718	0	ENST00000394830.3:c.4192del	p.Val1398LeufsTer34	p.V1398Lfs*34	ENST00000394830	NM_018313.4	1398	Gtt/tt	27/30	0.196819376776178	3	FACETS	0.786	0.691	0.887	0.524	0.46	0.591	INDETERMINATE	2	FALSE	0	0.342796091969262	3		718	300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578266	7578266	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs942158624	NA	P-0006257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	164	367	0	ENST00000269305.4:c.583A>T	p.Ile195Phe	p.I195F	ENST00000269305	NM_001126112.2	195	Atc/Ttc	6/11	0.243640824487233	2	FACETS	0.949	0.873	1	0.949	0.873	1	CLONAL	2	TRUE	0	0.246916398738072	2		367	700	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725183	49725183	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	46	313	0	ENST00000449682.2:c.242G>T	p.Arg81Leu	p.R81L	ENST00000449682	NM_020998.3	81	cGg/cTg	2/18	0.246916398738072	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.246916398738072	1		313	255	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106512981	106512981	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0006257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	22	482	1	ENST00000359195.3:c.1996-1G>T		p.X666_splice	ENST00000359195	NM_002649.2	666			0.246916398738072	3	FACETS	0.676	0.525	0.852	0.338	0.262	0.426	SUBCLONAL	1	TRUE	1	0.246916398738072	3		483	296	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272389	38272389	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	167	678	1	ENST00000425967.3:c.1978G>A	p.Val660Ile	p.V660I	ENST00000425967	NM_001174067.1	660	Gtc/Atc	15/19	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.246916398738072	NA		679	761	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933286	100933286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	285	973	0	ENST00000325455.5:c.2104G>A	p.Gly702Arg	p.G702R	ENST00000325455	NM_001202474.3	702	Gga/Aga	4/8	0.246916398738072	7	FACETS	1	0.974	1			1	CLONAL	5	TRUE	NA	0.246916398738072	7		973	711	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926888	112926888	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397507546	NA	P-0006257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	14	648	1	ENST00000351677.2:c.1508G>T	p.Gly503Val	p.G503V	ENST00000351677	NM_002834.3	503	gGg/gTg	13/16	1	2	FACETS	0.388	0.28	0.52	0.388	0.28	0.52	SUBCLONAL	1	TRUE	1	0.246916398738072	2		649	292	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562301	21562301	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	70	406	0	ENST00000382592.4:c.1618A>G	p.Met540Val	p.M540V	ENST00000382592	NM_014572.2	540	Atg/Gtg	4/8	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.246916398738072	2		406	567	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951169	48951169	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	55	546	0	ENST00000267163.4:c.1331A>T	p.Gln444Leu	p.Q444L	ENST00000267163	NM_000321.2	444	cAg/cTg	13/27	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.246916398738072	2		546	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0006275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	270	412	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.680231924643533	1	FACETS	0.981	0.932	1	0.981	0.932	1	CLONAL	1	TRUE	0	0.693906742524612	1		413	518	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0006275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	149	318	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	0.693906742524612	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.693906742524612	1		318	279	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727168	40727168	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761148007	NA	P-0006275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	576	396	1	ENST00000373198.4:c.3796G>A	p.Val1266Met	p.V1266M	ENST00000373198	NM_133170.3	1266	Gtg/Atg	28/32	0.232533391109213	6	FACETS	1	0.994	1			1	INDETERMINATE	3	TRUE	NA	0.693906742524612	6		397	1170	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117745	70117778	+	frameshift_variant	Frame_Shift_Del	DEL	GTGCATCCGCGAGGCGGTCAGCCAGGTGCTCAAA	GTGCATCCGCGAGGCGGTCAGCCAGGTGCTCAAA	-	novel	NA	P-0006275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	77	421	0	ENST00000245479.2:c.214_247del	p.Cys72AlafsTer27	p.C72Afs*27	ENST00000245479	NM_000346.3	71	gtGTGCATCCGCGAGGCGGTCAGCCAGGTGCTCAAA/gt	1/3	1	2	FACETS	0.215	0.188	0.245	0.215	0.188	0.245	SUBCLONAL	1	TRUE	1	0.693906742524612	2		421	1030	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006290-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	294	407	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.163976254185951	37	FACETS	0.986	0.95	1			1	CLONAL	35	TRUE	NA	0.163976254185951	37		407	402	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0006290-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	24	138	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.816	1	1	0.95	1	CLONAL	2	TRUE	1	0.163976254185951	2		138	142	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199854	108199854	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1565526758	NA	P-0006290-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	27	356	0	ENST00000278616.4:c.7196A>G	p.Gln2399Arg	p.Q2399R	ENST00000278616	NM_000051.3	2399	cAa/cGa	49/63	1	2	FACETS	1	0.907	1	1	0.961	1	CLONAL	2	TRUE	1	0.163976254185951	2		356	134	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491400	2491400	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006290-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	17	178	0	ENST00000355716.4:c.443A>G	p.Gln148Arg	p.Q148R	ENST00000355716	NM_003820.2	148	cAg/cGg	4/8	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.163976254185951	2		178	146	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439907	220439907	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006290-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	48	290	0	ENST00000243786.2:c.760G>T	p.Glu254Ter	p.E254*	ENST00000243786	NM_002191.3	254	Gag/Tag	2/2	1	2	FACETS	0.916	0.784	1	1	0.979	1	CLONAL	3	TRUE	1	0.163976254185951	2		290	213	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794961	242794961	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006290-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	21	261	0	ENST00000334409.5:c.248C>A	p.Pro83His	p.P83H	ENST00000334409	NM_005018.2	83	cCc/cAc	2/5	1	2	FACETS	0.771	0.599	0.97	1	0.922	1	CLONAL	2	TRUE	1	0.163976254185951	2		261	166	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631585	119631585	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006290-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	21	188	0	ENST00000316626.5:c.681G>T	p.Leu227Phe	p.L227F	ENST00000316626		227	ttG/ttT	6/12	1	2	FACETS	0.902	0.702	1	1	0.936	1	CLONAL	2	TRUE	1	0.163976254185951	2		188	142	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240682	55240682	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006290-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	35	180	0	ENST00000275493.2:c.1926G>T	p.Lys642Asn	p.K642N	ENST00000275493	NM_005228.3	642	aaG/aaT	17/28	1	2	FACETS	0.895	0.744	1	1	0.971	1	CLONAL	3	TRUE	1	0.163976254185951	2		180	159	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358975	81358975	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006290-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	26	184	0	ENST00000222390.5:c.986G>T	p.Trp329Leu	p.W329L	ENST00000222390	NM_000601.4	329	tGg/tTg	8/18	1	2	FACETS	0.911	0.728	1	1	0.948	1	CLONAL	2	TRUE	1	0.163976254185951	2		184	174	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89825095	89825095	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006290-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	32	216	0	ENST00000389301.3:c.2871G>T	p.Trp957Cys	p.W957C	ENST00000389301	NM_000135.2	957	tgG/tgT	30/43	0.163976254185951	1	FACETS	1	0.893	1	1	0.965	1	CLONAL	2	TRUE	0	0.163976254185951	1		216	159	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354789	40354789	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006290-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	38	236	0	ENST00000293328.3:c.2115G>T	p.Lys705Asn	p.K705N	ENST00000293328	NM_012448.3	705	aaG/aaT	17/19	0.163976254185951	1	FACETS	0.898	0.754	1	1	0.974	1	CLONAL	3	TRUE	0	0.163976254185951	1		236	158	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36253011	36253011	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs587776809	NA	P-0006290-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	17	100	0	ENST00000300305.3:c.352-1G>T		p.X118_splice	ENST00000300305		118			1	2	FACETS	1	0.777	1	1	0.931	1	CLONAL	2	TRUE	1	0.163976254185951	2		100	101	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655257	45655257	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006290-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	13	153	0	ENST00000407780.3:c.595G>T	p.Val199Leu	p.V199L	ENST00000407780	NM_001283052.1	199	Gtg/Ttg	4/7	1	2	FACETS	0.785	0.566	1	1	0.884	1	CLONAL	2	TRUE	1	0.163976254185951	2		153	101	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239902	53239902	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006290-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	47	267	0	ENST00000375401.3:c.1539G>T	p.Trp513Cys	p.W513C	ENST00000375401	NM_004187.3	513	tgG/tgT	11/26	0.163976254185951	0	FACETS	0.85	0.727	0.981			1	CLONAL	3	TRUE	0	0.163976254185951	0		267	188	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0006302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	15	654	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		654	444	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0006318-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	95	401	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.935	0.832	1	0.935	0.832	1	CLONAL	1	TRUE	1	0.28	2		401	726	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593586	55593588	+	inframe_deletion	In_Frame_Del	DEL	CCA	CCA	-	novel	NA	P-0006320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	748	520	0	ENST00000288135.5:c.1652_1654del	p.Pro551_Met552delinsLeu	p.P551_M552delinsL	ENST00000288135	NM_000222.2	551	cCCAtg/ctg	11/21	0.632925613755613	4	FACETS	0.927	0.901	0.953	0.927	0.901	0.953	CLONAL	3	TRUE	1	0.748071695799369	4		520	1257	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0006321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	182	443	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.488197603193979	3	FACETS	1	0.986	1	0.764	0.721	0.807	CLONAL	2	TRUE	0	0.688457267577432	3		443	310	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436117	51436117	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	53	273	0	ENST00000262662.1:c.77A>G	p.Gln26Arg	p.Q26R	ENST00000262662		26	cAa/cGa	3/4	0.201595522022874	3	FACETS	1	0.944	1			1	INDETERMINATE	1	TRUE	NA	0.688457267577432	3		273	176	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098390	11098414	+	frameshift_variant	Frame_Shift_Del	DEL	TTCCCCCGCAGCCAACGGGCCGCCC	TTCCCCCGCAGCCAACGGGCCGCCC	-	novel	NA	P-0006321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	79	417	0	ENST00000358026.2:c.917_941del	p.Gln306ArgfsTer12	p.Q306Rfs*12	ENST00000358026	NM_001128849.1	303	aTTCCCCCGCAGCCAACGGGCCGCCCt/at	6/36	0.593141695566562	2	FACETS	0.937	0.836	1	0.468	0.418	0.521	CLONAL	1	TRUE	0	0.688457267577432	2		417	245	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0006329-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	43	363	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	1	2	FACETS	0.466	0.389	0.551	0.466	0.389	0.551	SUBCLONAL	1	TRUE	1	0.32	2		363	577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28934577	NA	P-0006329-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	199	428	0	ENST00000269305.4:c.770T>C	p.Leu257Pro	p.L257P	ENST00000269305	NM_001126112.2	257	cTg/cCg	7/11	0.3	1	FACETS	0.965	0.893	1	0.965	0.893	1	CLONAL	1	TRUE	0	0.32	1		428	1083	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872498	136872498	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs104893624	NA	P-0006329-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1223	227	706	1	ENST00000241393.3:c.1000C>T	p.Arg334Ter	p.R334*	ENST00000241393	NM_003467.2	334	Cga/Tga	2/2	1	2	FACETS	0.978	0.909	1	0.978	0.909	1	CLONAL	1	TRUE	1	0.32	2		707	1450	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862107	68862107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501244	NA	P-0006329-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	80	435	0	ENST00000261769.5:c.2195G>A	p.Arg732Gln	p.R732Q	ENST00000261769	NM_004360.3	732	cGg/cAg	14/16	1	2	FACETS	0.523	0.459	0.592	0.523	0.459	0.592	SUBCLONAL	1	TRUE	1	0.32	2		435	956	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039629	47039629	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006329-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	374	192	0	ENST00000377604.3:c.1081C>T	p.Gln361Ter	p.Q361*	ENST00000377604	NM_001204468.1	361	Cag/Tag	11/24	0.211269403820836	2	FACETS	0.984	0.94	1			1	CLONAL	3	TRUE	NA	0.32	2		192	792	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932119	36932119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006329-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1455	173	592	0	ENST00000361632.4:c.2350C>T	p.Pro784Ser	p.P784S	ENST00000361632		784	Ccc/Tcc	16/16	1	2	FACETS	0.664	0.609	0.722	0.664	0.609	0.722	SUBCLONAL	1	TRUE	1	0.32	2		592	1628	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245391	153245391	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006329-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	111	320	0	ENST00000281708.4:c.1800T>G	p.Asp600Glu	p.D600E	ENST00000281708	NM_033632.3	600	gaT/gaG	11/12	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.32	2		320	610	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258954	153258954	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006329-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	100	329	0	ENST00000281708.4:c.861G>T	p.Glu287Asp	p.E287D	ENST00000281708	NM_033632.3	287	gaG/gaT	5/12	1	2	FACETS	0.926	0.828	1	0.926	0.828	1	CLONAL	1	TRUE	1	0.32	2		329	675	SUCCESS
APC	324	MSKCC	GRCh37	5	112137007	112137007	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1060503334	NA	P-0006329-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	47	349	1	ENST00000257430.4:c.761C>G	p.Ser254Ter	p.S254*	ENST00000257430	NM_000038.5	254	tCa/tGa	8/16	1	2	FACETS	0.53	0.447	0.622	0.53	0.447	0.622	SUBCLONAL	1	TRUE	1	0.32	2		350	554	SUCCESS
APC	324	MSKCC	GRCh37	5	112174394	112174394	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006329-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	83	307	0	ENST00000257430.4:c.3103C>T	p.Gln1035Ter	p.Q1035*	ENST00000257430	NM_000038.5	1035	Cag/Tag	16/16	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.32	2		307	519	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820303	139820303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774782158	NA	P-0006329-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1294	291	610	1	ENST00000247668.2:c.1456C>T	p.Arg486Trp	p.R486W	ENST00000247668	NM_021138.3	486	Cgg/Tgg	11/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.32	2		611	1585	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222760	5222760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199829286	NA	P-0006329-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	35	205	0	ENST00000357368.4:c.3043C>T	p.Arg1015Cys	p.R1015C	ENST00000357368	NM_002850.3	1015	Cgc/Tgc	18/38	1	2	FACETS	0.383	0.313	0.462	0.383	0.313	0.462	SUBCLONAL	1	TRUE	1	0.32	2		205	571	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0006355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	217	323	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.456118775552103	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.456118775552103	1		323	659	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974792	21974792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141798398	NA	P-0006355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	108	135	0	ENST00000304494.5:c.35C>T	p.Ser12Leu	p.S12L	ENST00000304494	NM_000077.4	12	tCg/tTg	1/3	0.21245443809154	1	FACETS	1	0.944	1	1	0.944	1	INDETERMINATE	1	TRUE	0	0.456118775552103	1		135	346	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929487	44929487	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	276	456	0	ENST00000377967.4:c.2587C>G	p.Gln863Glu	p.Q863E	ENST00000377967	NM_021140.2	863	Cag/Gag	17/29	NA	2	FACETS	1	0.967	1			1	INDETERMINATE	1	TRUE	NA	0.456118775552103	2		456	1157	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180867	106180867	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	270	358	1	ENST00000380013.4:c.3895A>G	p.Lys1299Glu	p.K1299E	ENST00000380013	NM_001127208.2	1299	Aag/Gag	7/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.456118775552103	2		359	985	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857152	9857152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369508378	NA	P-0006355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	175	352	0	ENST00000330684.3:c.4249C>T	p.Arg1417Trp	p.R1417W	ENST00000330684	NM_001134407.1	1417	Cgg/Tgg	13/13	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.456118775552103	2		352	760	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847399	68847399	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs886039685	NA	P-0006355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	176	305	0	ENST00000261769.5:c.1320+1G>C		p.X440_splice	ENST00000261769	NM_004360.3	440			0.456118775552103	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.456118775552103	1		305	489	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961875	15961875	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	175	281	0	ENST00000268712.3:c.5920G>T	p.Glu1974Ter	p.E1974*	ENST00000268712	NM_006311.3	1974	Gag/Tag	38/46	0.456118775552103	1	FACETS	0.968	0.896	1	0.968	0.896	1	CLONAL	1	TRUE	0	0.456118775552103	1		281	612	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366218	15366218	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	190	391	0	ENST00000263377.2:c.1937A>T	p.Asn646Ile	p.N646I	ENST00000263377	NM_058243.2	646	aAt/aTt	10/20	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.456118775552103	2		391	802	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57474036	57474036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750429818	NA	P-0006355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	181	224	0	ENST00000371085.3:c.253G>A	p.Asp85Asn	p.D85N	ENST00000371085	NM_000516.4	85	Gat/Aat	3/13	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.456118775552103	2		224	696	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502382	186502384	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1171371205	NA	P-0006355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1450	402	480	0	ENST00000323963.5:c.109_111del	p.Asp37del	p.D37del	ENST00000323963		35	ttTGAt/ttt	3/11	0.456118775552103	3	FACETS	1	0.99	1	0.584	0.554	0.616	CLONAL	1	TRUE	1	0.456118775552103	3		480	1852	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916935	178916947	+	protein_altering_variant	In_Frame_Del	DEL	CGTGAAGAAAAGA	CGTGAAGAAAAGA	G	novel	NA	P-0006355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	892	524	0	ENST00000263967.3:c.322_334delinsG	p.Arg108_Ile112delinsVal	p.R108_I112delinsV	ENST00000263967	NM_006218.2	108	CGTGAAGAAAAGAtc/Gtc	2/21	0.456118775552103	5	FACETS	0.901	0.875	0.927			1	CLONAL	4	TRUE	NA	0.456118775552103	5		524	1828	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	294	145	0				ENST00000310581	NM_198253.2	-/1132			0.58591699619751	4	FACETS	1	0.964	1	1	0.964	1	CLONAL	3	TRUE	1	0.58591699619751	4		145	524	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700232	117700232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146533107	NA	P-0006363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	111	373	1	ENST00000368508.3:c.2587C>T	p.Arg863Trp	p.R863W	ENST00000368508	NM_002944.2	863	Cgg/Tgg	17/43	1	2	FACETS	0.892	0.807	0.979	0.892	0.807	0.979	CLONAL	1	TRUE	1	0.58591699619751	2		374	425	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0006363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12227	3828	673	9	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.58591699619751	40	FACETS	0.987	0.971	1			1	CLONAL	10	TRUE	NA	0.58591699619751	40		682	16055	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612187	189612187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1051829008	NA	P-0006363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	84	392	2	ENST00000264731.3:c.1939C>T	p.Arg647Cys	p.R647C	ENST00000264731	NM_003722.4	647	Cgc/Tgc	14/14	1	2	FACETS	0.488	0.431	0.548	0.488	0.431	0.548	SUBCLONAL	1	TRUE	1	0.58591699619751	2		394	588	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs149840192	NA	P-0006363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4952	11103	547	0	ENST00000275493.2:c.866C>A	p.Ala289Asp	p.A289D	ENST00000275493	NM_005228.3	289	gCc/gAc	7/28	0.58591699619751	40	FACETS	0.988	0.981	0.994			1	CLONAL	29	TRUE	NA	0.58591699619751	40		547	16055	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508239	106508239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	179	206	0	ENST00000359195.3:c.233C>T	p.Ala78Val	p.A78V	ENST00000359195	NM_002649.2	78	gCg/gTg	2/11	0.579012052270472	4	FACETS	1	0.978	1	0.581	0.536	0.628	CLONAL	1	TRUE	2	0.58591699619751	4		206	834	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	426	412	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.528933379844376	4	FACETS	0.986	0.946	1	0.986	0.946	1	CLONAL	3	TRUE	1	0.528933379844376	4		412	833	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980849	40980849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs548511212	NA	P-0006371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	93	367	0	ENST00000373198.4:c.1637G>A	p.Arg546Gln	p.R546Q	ENST00000373198	NM_133170.3	546	cGg/cAg	10/32	0.270042605404054	1	FACETS	0.414	0.368	0.462	0.414	0.368	0.462	INDETERMINATE	1	TRUE	0	0.528933379844376	1		367	625	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578507	7578507	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	215	359	1	ENST00000269305.4:c.423C>A	p.Cys141Ter	p.C141*	ENST00000269305	NM_001126112.2	141	tgC/tgA	5/11	0.528933379844376	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.528933379844376	1		360	595	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974899	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	GCCAGCCAGTCAGCCGAAGGCTCCATGCTGCTCCCCGCCGCCGGCTCCATGCTGCTCCCCGCCGCCCGCTGCCTGCTCTCCCCCTCTCCGCAGCCGCCGAGCGCACGCGGTCCGCCCCACCCT	GCCAGCCAGTCAGCCGAAGGCTCCATGCTGCTCCCCGCCGCCGGCTCCATGCTGCTCCCCGCCGCCCGCTGCCTGCTCTCCCCCTCTCCGCAGCCGCCGAGCGCACGCGGTCCGCCCCACCCT	-	novel	NA	P-0006371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	122	126	0	ENST00000304494.5:c.-73_50del		p.*25*	ENST00000304494	NM_000077.4	?-17/156		1/3	NA	2	FACETS	0.754	0.692	0.817			1	INDETERMINATE	2	TRUE	NA	0.528933379844376	2		126	306	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193988	106193988	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0121456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	357	359	1	ENST00000380013.4:c.4450A>C	p.Asn1484His	p.N1484H	ENST00000380013	NM_001127208.2	1484	Aac/Cac	10/11	1	2	FACETS	0.983	0.937	1	0.983	0.937	1	CLONAL	1	NA	1	0.899971885350725	2		360	807	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38991050	38991050	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0121456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	265	239	0	ENST00000357387.3:c.583+1G>T		p.X195_splice	ENST00000357387	NM_152756.3	195			1	2	FACETS	0.948	0.896	1	0.948	0.896	1	CLONAL	1	NA	1	0.899971885350725	2		239	621	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585389	29585389	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0121456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	319	359	0	ENST00000356175.3:c.4138A>G	p.Ser1380Gly	p.S1380G	ENST00000356175	NM_000267.3	1380	Agc/Ggc	31/57	1	2	FACETS	0.839	0.795	0.883	0.839	0.795	0.883	CLONAL	1	NA	1	0.899971885350725	2		359	845	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246179	41246179	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0121456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	316	344	0	ENST00000357654.3:c.1369G>T	p.Glu457Ter	p.E457*	ENST00000357654	NM_007294.3	457	Gaa/Taa	10/23	1	2	FACETS	0.934	0.886	0.982	0.934	0.886	0.982	CLONAL	1	NA	1	0.899971885350725	2		344	752	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934082	39934082	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0121456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	344	219	0	ENST00000378444.4:c.517A>G	p.Ser173Gly	p.S173G	ENST00000378444	NM_001123385.1	173	Agc/Ggc	4/15	0.656784695157043	2	FACETS	0.975	0.928	1			1	CLONAL	1	NA	NA	0.899971885350725	2		219	784	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0006393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	52	550	1	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.734043758488725	7	FACETS	0.992	0.867	1			1	CLONAL	3	FALSE	NA	0.734043758488725	7		551	135	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25468912	25468912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780672407	NA	P-0006393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	20	389	0	ENST00000264709.3:c.1451G>A	p.Arg484Gln	p.R484Q	ENST00000264709	NM_175629.2	484	cGg/cAg	12/23	0.668512624320389	5	FACETS	0.938	0.744	1	0.626	0.496	0.765	CLONAL	2	FALSE	2	0.734043758488725	5		389	61	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942876	15942876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	30	651	0	ENST00000268712.3:c.6826G>A	p.Asp2276Asn	p.D2276N	ENST00000268712	NM_006311.3	2276	Gat/Aat	44/46	0.668512624320389	5	FACETS	0.965	0.801	1	0.643	0.534	0.759	CLONAL	2	FALSE	2	0.734043758488725	5		651	89	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0006397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	27	316	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.756	0.6	0.936	0.756	0.6	0.936	CLONAL	1	TRUE	1	0.12	2		316	595	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0006397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	41	345	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	1	2	FACETS	0.922	0.766	1	0.922	0.766	1	CLONAL	1	TRUE	1	0.12	2		345	741	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0006398-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	258	273	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.552949140200361	2		273	708	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0006398-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	113	493	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.534815566439513	1	FACETS	0.831	0.755	0.908	0.831	0.755	0.908	CLONAL	1	TRUE	0	0.552949140200361	1		495	356	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974678	21974678	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs587778189	NA	P-0006398-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	164	419	0	ENST00000304494.5:c.149A>G	p.Gln50Arg	p.Q50R	ENST00000304494	NM_000077.4	50	cAg/cGg	1/3	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.552949140200361	2		419	472	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223315	2223315	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006398-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	112	441	0	ENST00000326181.6:c.927C>A	p.Asp309Glu	p.D309E	ENST00000326181	NM_032271.2	309	gaC/gaA	10/21	0.285053885308765	1	FACETS	0.668	0.604	0.734	0.668	0.604	0.734	INDETERMINATE	1	TRUE	0	0.552949140200361	1		441	439	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022915	31022915	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1178321509	NA	P-0006398-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	99	514	0	ENST00000375687.4:c.2400T>G	p.Asp800Glu	p.D800E	ENST00000375687	NM_015338.5	800	gaT/gaG	13/13	0.328765643392062	1	FACETS	0.51	0.457	0.566	0.51	0.457	0.566	INDETERMINATE	1	TRUE	0	0.552949140200361	1		514	508	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907626	76907626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006398-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	159	612	0	ENST00000373344.5:c.4535G>A	p.Arg1512His	p.R1512H	ENST00000373344	NM_000489.3	1512	cGt/cAt	15/35	0.361863286221129	1	FACETS	0.517	0.474	0.562	0.517	0.474	0.562	SUBCLONAL	1	TRUE	0	0.552949140200361	1		612	805	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	59	412	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.228334627869843	4	FACETS	0.925	0.795	1			1	CLONAL	1	TRUE	NA	0.25	4		412	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0006399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	55	547	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.143026934906858	3	FACETS	0.952	0.815	1	0.317	0.271	0.368	INDETERMINATE	1	TRUE	0	0.25	3		547	520	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204511935	204511935	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	24	351	0	ENST00000367182.3:c.535G>A	p.Ala179Thr	p.A179T	ENST00000367182	NM_001278516.1	179	Gcc/Acc	8/11	0.131336713756143	4	FACETS	0.581	0.455	0.727	0.291	0.227	0.364	INDETERMINATE	1	TRUE	2	0.25	4		351	413	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214404	55214404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770290445	NA	P-0006399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	54	435	1	ENST00000275493.2:c.530C>T	p.Ser177Leu	p.S177L	ENST00000275493	NM_005228.3	177	tCg/tTg	4/28	1	2	FACETS	0.945	0.809	1	0.945	0.809	1	CLONAL	1	TRUE	1	0.25	2		436	457	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0006400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	68	538	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.861	0.753	0.977	0.861	0.753	0.977	CLONAL	1	TRUE	1	0.414491821573441	2		538	381	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298733	46298733	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1244681210	NA	P-0006400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	83	428	0	ENST00000334344.6:c.5380G>T	p.Glu1794Ter	p.E1794*	ENST00000334344	NM_152641.2	1794	Gaa/Taa	21/21	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.414491821573441	2		428	375	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348205	89348205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	142	666	3	ENST00000301030.4:c.4745G>A	p.Ser1582Asn	p.S1582N	ENST00000301030	NM_001256183.1	1582	aGc/aAc	9/13	1	2	FACETS	0.973	0.889	1	0.973	0.889	1	CLONAL	1	TRUE	1	0.414491821573441	2		669	704	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441970	40441970	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1406350203	NA	P-0006400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	141	660	1	ENST00000345506.4:c.215C>T	p.Ala72Val	p.A72V	ENST00000345506	NM_003152.3	72	gCg/gTg	4/20	1	2	FACETS	0.958	0.875	1	0.958	0.875	1	CLONAL	1	TRUE	1	0.414491821573441	2		661	710	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214581	5214581	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	102	503	0	ENST00000357368.4:c.4485G>C	p.Glu1495Asp	p.E1495D	ENST00000357368	NM_002850.3	1495	gaG/gaC	29/38	1	2	FACETS	0.893	0.801	0.99	0.893	0.801	0.99	CLONAL	1	TRUE	1	0.414491821573441	2		503	551	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248537	10248537	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	106	512	0	ENST00000340748.4:c.4216C>A	p.Gln1406Lys	p.Q1406K	ENST00000340748		1406	Cag/Aag	35/40	1	2	FACETS	0.829	0.745	0.918	0.829	0.745	0.918	CLONAL	1	TRUE	1	0.414491821573441	2		512	617	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913495	NA	P-0006400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	97	393	0	ENST00000371085.3:c.602G>T	p.Arg201Leu	p.R201L	ENST00000371085	NM_000516.4	201	cGt/cTt	8/13	1	2	FACETS	0.998	0.894	1	0.998	0.894	1	CLONAL	1	TRUE	1	0.414491821573441	2		393	469	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245325	46245338	+	frameshift_variant	Frame_Shift_Del	DEL	TACAAACTGTGCCC	TACAAACTGTGCCC	-	novel	NA	P-0006400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	74	474	1	ENST00000334344.6:c.3419_3432del	p.Val1140AspfsTer15	p.V1140Dfs*15	ENST00000334344	NM_152641.2	1140	gTACAAACTGTGCCC/g	15/21	1	2	FACETS	0.93	0.819	1	0.93	0.819	1	CLONAL	1	TRUE	1	0.414491821573441	2		475	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0006410-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	1295	595	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.827115255755343	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.827115255755343	2		595	1512	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814303	76814306	+	frameshift_variant	Frame_Shift_Del	DEL	ATAA	ATAA	-	novel	NA	P-0006410-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	417	262	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	0.827115255755343	1		262	539	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777134	9777134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1445282622	NA	P-0006410-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	342	605	0	ENST00000377346.4:c.898C>T	p.Arg300Cys	p.R300C	ENST00000377346	NM_005026.3	300	Cgt/Tgt	7/24	0.181858209117911	2	FACETS	0.762	0.722	0.803	0.381	0.361	0.402	INDETERMINATE	1	TRUE	0	0.827115255755343	2		605	1085	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935411	36935411	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006410-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	777	886	0	ENST00000361632.4:c.1316C>T	p.Ala439Val	p.A439V	ENST00000361632		439	gCc/gTc	10/16	0.181858209117911	2	FACETS	1	0.997	1	0.607	0.589	0.626	INDETERMINATE	1	TRUE	0	0.827115255755343	2		886	1547	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252156	226252156	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006410-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	33	38	0	ENST00000366813.1:c.104G>T	p.Gly35Val	p.G35V	ENST00000366813		35	gGg/gTg	1/3	0.181858209117911	2	FACETS	1	0.927	1	0.578	0.493	0.664	INDETERMINATE	1	TRUE	0	0.827115255755343	2		38	69	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549891	187549891	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006410-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	108	418	1	ENST00000441802.2:c.4350T>A	p.Asn1450Lys	p.N1450K	ENST00000441802	NM_005245.3	1450	aaT/aaA	8/27	0.364442462626618	1	FACETS	0.221	0.198	0.245	0.221	0.198	0.245	INDETERMINATE	1	TRUE	0	0.827115255755343	1		419	692	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004340	150004340	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs761243837	NA	P-0006410-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1210	83	703	0	ENST00000253339.5:c.1885T>C	p.Ser629Pro	p.S629P	ENST00000253339		629	Tct/Cct	3/7	1	2	FACETS	0.155	0.136	0.176	0.155	0.136	0.176	SUBCLONAL	1	TRUE	1	0.827115255755343	2		703	1293	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072508	5072508	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006410-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	72	253	0	ENST00000381652.3:c.1658A>T	p.Gln553Leu	p.Q553L	ENST00000381652	NM_004972.3	553	cAa/cTa	13/25	1	2	FACETS	0.343	0.3	0.39	0.343	0.3	0.39	SUBCLONAL	1	TRUE	1	0.827115255755343	2		253	507	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246890	10246890	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006410-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	50	400	0	ENST00000340748.4:c.4515C>G	p.Asn1505Lys	p.N1505K	ENST00000340748		1505	aaC/aaG	37/40	1	2	FACETS	0.174	0.147	0.204	0.174	0.147	0.204	SUBCLONAL	1	TRUE	1	0.827115255755343	2		400	693	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133522	55133536	+	inframe_deletion	In_Frame_Del	DEL	ACGGTCCCCGAGGCC	ACGGTCCCCGAGGCC	-	novel	NA	P-0006410-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	545	525	0	ENST00000257290.5:c.831_845del	p.Pro278_Val282del	p.P278_V282del	ENST00000257290	NM_006206.4	276	ACGGTCCCCGAGGCC/-	6/23	0.179755104043644	3	FACETS	0.792	0.762	0.822	0.528	0.508	0.548	INDETERMINATE	2	TRUE	0	0.827115255755343	3		525	1176	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	81	407	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.212337884443205	3	FACETS	0.93	0.818	1	0.465	0.409	0.526	CLONAL	1	FALSE	1	0.211637398388282	3		407	910	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0006417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	73	370	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.17254465295688	4	FACETS	0.816	0.712	0.93			1	CLONAL	1	FALSE	NA	0.211637398388282	4		370	1024	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448270	56448270	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0006417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	69	302	0	ENST00000407977.2:c.375+2T>C		p.X125_splice	ENST00000407977		125			0.123033767501481	3	FACETS	1	0.954	1	0.608	0.53	0.693	INDETERMINATE	1	FALSE	1	0.211637398388282	3		302	593	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073410	8073410	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2124	271	1143	0	ENST00000377482.5:c.1249A>G	p.Thr417Ala	p.T417A	ENST00000377482	NM_018948.3	417	Aca/Gca	4/4	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.211637398388282	NA		1143	2395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0006421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	166	622	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.165680517776954	3	FACETS	1	0.975	1	0.579	0.531	0.629	INDETERMINATE	1	TRUE	1	0.286850053313191	3		624	1143	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0006421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	86	391	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.286850053313191	1	FACETS	0.934	0.828	1	0.934	0.828	1	CLONAL	1	TRUE	0	0.286850053313191	1		391	550	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445074	89445074	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	71	449	0	ENST00000336596.2:c.1394G>T	p.Gly465Val	p.G465V	ENST00000336596	NM_005233.5	465	gGg/gTg	6/17	0.234046869818599	1	FACETS	0.64	0.558	0.728	0.64	0.558	0.728	SUBCLONAL	1	TRUE	0	0.286850053313191	1		449	663	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266679	142266679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146504354	NA	P-0006421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	298	463	0	ENST00000350721.4:c.3245G>A	p.Arg1082His	p.R1082H	ENST00000350721	NM_001184.3	1082	cGt/cAt	16/47	0.275777960543708	3	FACETS	0.933	0.881	0.985	0.933	0.881	0.985	CLONAL	3	TRUE	0	0.286850053313191	3		463	849	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973903	55973903	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0006421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	61	277	0	ENST00000263923.4:c.1412+1G>T		p.X471_splice	ENST00000263923	NM_002253.2	471			1	2	FACETS	0.989	0.856	1	0.989	0.856	1	CLONAL	1	TRUE	1	0.286850053313191	2		277	430	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117632257	117632257	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	58	448	0	ENST00000368508.3:c.6159G>T	p.Leu2053Phe	p.L2053F	ENST00000368508	NM_002944.2	2053	ttG/ttT	39/43	0.168805242109482	1	FACETS	0.525	0.45	0.606	0.525	0.45	0.606	INDETERMINATE	1	TRUE	0	0.286850053313191	1		448	660	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455144	50455144	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	215	295	0	ENST00000331340.3:c.691G>T	p.Gly231Cys	p.G231C	ENST00000331340	NM_006060.4	231	Ggc/Tgc	6/8	0.286850053313191	4	FACETS	0.953	0.89	1	0.953	0.89	1	CLONAL	3	TRUE	1	0.286850053313191	4		295	675	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117753	115117753	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765693432	NA	P-0006421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	71	484	0	ENST00000257566.3:c.682G>A	p.Ala228Thr	p.A228T	ENST00000257566	NM_016569.3	228	Gct/Act	3/8	0.168805242109482	1	FACETS	0.629	0.549	0.716	0.629	0.549	0.716	INDETERMINATE	1	TRUE	0	0.286850053313191	1		484	674	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411970	63411970	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	130	923	0	ENST00000330258.3:c.1197G>T	p.Glu399Asp	p.E399D	ENST00000330258	NM_152424.3	399	gaG/gaT	2/2	0.168805242109482	1	FACETS	0.655	0.592	0.721	0.655	0.592	0.721	INDETERMINATE	1	TRUE	0	0.286850053313191	1		923	1186	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939062	48939074	+	frameshift_variant	Frame_Shift_Del	DEL	TTTTATGAATTCT	TTTTATGAATTCT	-	novel	NA	P-0006421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	52	348	0	ENST00000267163.4:c.894_906del	p.Phe299LeufsTer4	p.F299Lfs*4	ENST00000267163	NM_000321.2	298	ccTTTTATGAATTCT/cc	9/27	1	2	FACETS	0.746	0.636	0.867	0.746	0.636	0.867	SUBCLONAL	1	TRUE	1	0.286850053313191	2		348	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577147	7577147	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	210	612	1	ENST00000269305.4:c.791del	p.Leu264HisfsTer81	p.L264Hfs*81	ENST00000269305	NM_001126112.2	264	cTa/ca	8/11	0.165680517776954	3	FACETS	0.773	0.717	0.831	0.773	0.717	0.831	INDETERMINATE	2	TRUE	1	0.286850053313191	3		613	1083	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525534	187525536	+	missense_variant	Missense_Mutation	TNP	CAC	CAC	AAA	novel	NA	P-0006421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	113	541	0	ENST00000441802.2:c.10543_10545delinsTTT	p.Val3515Phe	p.V3515F	ENST00000441802	NM_005245.3	3515	GTG/TTT	18/27	1	2	FACETS	0.992	0.893	1	0.992	0.893	1	CLONAL	1	TRUE	1	0.286850053313191	2		541	794	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0006436-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	127	370	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.839	0.764	0.916	0.839	0.764	0.916	CLONAL	1	TRUE	1	0.608056131101422	2		370	498	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720721	89720721	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs786204905	NA	P-0006436-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	13	91	0	ENST00000371953.3:c.875del	p.Asn292MetfsTer15	p.N292Mfs*15	ENST00000371953	NM_000314.4	291	gAa/ga	8/9	0.609817406357522	1	FACETS	0.48	0.351	0.629	0.48	0.351	0.629	SUBCLONAL	1	TRUE	0	0.608056131101422	1		91	62	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577569	7577569	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519981	NA	P-0006440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	95	612	0	ENST00000269305.4:c.712T>G	p.Cys238Gly	p.C238G	ENST00000269305	NM_001126112.2	238	Tgt/Ggt	7/11	1	2	FACETS	0.762	0.678	0.853	0.762	0.678	0.853	SUBCLONAL	1	TRUE	1	0.27	2		612	923	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442489	52442489	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1060503750	NA	P-0006452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	43	352	0	ENST00000460680.1:c.255+1G>A		p.X85_splice	ENST00000460680	NM_004656.3	85			0.196589593831265	1	FACETS	0.716	0.601	0.843	0.716	0.601	0.843	SUBCLONAL	1	TRUE	0	0.29	1		352	354	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162425	47162426	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0006452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	56	479	0	ENST00000409792.3:c.3700_3701del	p.Glu1234IlefsTer8	p.E1234Ifs*8	ENST00000409792	NM_014159.6	1234	GAa/a	3/21	0.196589593831265	1	FACETS	0.723	0.62	0.834	0.723	0.62	0.834	SUBCLONAL	1	TRUE	0	0.29	1		479	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0006455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	350	526	1	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.449031405444241	2	FACETS	0.922	0.878	0.967	0.922	0.878	0.967	CLONAL	2	TRUE	0	0.458893310514113	2		527	827	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0006455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1237	1527	589	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.458893310514113	10	FACETS	0.975	0.955	0.995			1	CLONAL	7	TRUE	NA	0.458893310514113	10		589	2764	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828914	72828914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147043604	NA	P-0006455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	80	712	1	ENST00000268489.5:c.7667C>T	p.Ala2556Val	p.A2556V	ENST00000268489	NM_006885.3	2556	gCg/gTg	9/10	0.413171922967578	3	FACETS	0.353	0.309	0.4	0.118	0.103	0.134	SUBCLONAL	1	TRUE	0	0.458893310514113	3		713	1216	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30668352	30668352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs538887974	NA	P-0006455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	85	680	2	ENST00000376406.3:c.6160C>T	p.Arg2054Trp	p.R2054W	ENST00000376406	NM_014641.2	2054	Cgg/Tgg	15/15	0.14016148371292	5	FACETS	0.669	0.59	0.754	0.167	0.147	0.189	INDETERMINATE	1	TRUE	1	0.458893310514113	5		682	935	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842337	68842337	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	134	471	1	ENST00000261769.5:c.398C>T	p.Ser133Phe	p.S133F	ENST00000261769	NM_004360.3	133	tCt/tTt	4/16	0.413171922967578	3	FACETS	0.98	0.891	1	0.327	0.297	0.358	CLONAL	1	TRUE	0	0.458893310514113	3		472	733	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244696	41244696	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	109	536	1	ENST00000357654.3:c.2852G>A	p.Arg951Lys	p.R951K	ENST00000357654	NM_007294.3	951	aGg/aAg	10/23	0.388794142120356	2	FACETS	0.752	0.676	0.831	0.376	0.338	0.416	SUBCLONAL	1	TRUE	0	0.458893310514113	2		537	632	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0006460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	211	375	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.200290294377638	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.212755829873436	2		377	936	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0006460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	166	476	2	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.192008224789456	2	FACETS	0.787	0.722	0.854	0.787	0.722	0.854	SUBCLONAL	2	TRUE	0	0.212755829873436	2		478	992	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0006460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	43	229	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.210331036155947	3	FACETS	0.92	0.77	1	0.46	0.385	0.544	CLONAL	1	TRUE	1	0.212755829873436	3		229	486	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380277	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913238	NA	P-0006460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	181	543	0	ENST00000311936.3:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	61	Caa/Aaa	3/5	0.210331036155947	3	FACETS	0.885	0.816	0.958	0.885	0.816	0.958	CLONAL	2	TRUE	1	0.212755829873436	3		543	1063	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176678824	176678824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	195	712	0	ENST00000439151.2:c.4735G>A	p.Gly1579Arg	p.G1579R	ENST00000439151	NM_022455.4	1579	Gga/Aga	12/23	0.212755829873436	3	FACETS	0.891	0.824	0.961			1	CLONAL	2	TRUE	NA	0.212755829873436	3		712	1138	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388640	31388640	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0006460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	204	607	2	ENST00000328111.2:c.1906-1G>T		p.X636_splice	ENST00000328111	NM_006892.3	636			0.138345512874417	4	FACETS	0.909	0.841	0.98	0.909	0.841	0.98	CLONAL	2	TRUE	2	0.212755829873436	4		609	1279	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0006464-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	236	401	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.988	0.93	1	0.988	0.93	1	CLONAL	1	TRUE	1	0.85	2		401	562	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272308	38272308	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs869320694	NA	P-0006464-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	308	494	0	ENST00000425967.3:c.2059A>G	p.Lys687Glu	p.K687E	ENST00000425967	NM_001174067.1	687	Aag/Gag	15/19	1	2	FACETS	0.913	0.865	0.961	0.913	0.865	0.961	CLONAL	1	TRUE	1	0.85	2		494	794	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0006474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	161	409	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.208053602533205	5	FACETS	1	0.945	1	1	0.945	1	CLONAL	5	TRUE	0	0.208053602533205	5		409	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913343	NA	P-0006474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	127	595	0	ENST00000269305.4:c.817C>A	p.Arg273Ser	p.R273S	ENST00000269305	NM_001126112.2	273	Cgt/Agt	8/11	0.20224420382458	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.208053602533205	2		595	536	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551932	150551932	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	79	282	0	ENST00000369026.2:c.75C>A	p.Ser25Arg	p.S25R	ENST00000369026	NM_021960.4	25	agC/agA	1/3	0.199798465516953	3	FACETS	0.902	0.796	1	0.902	0.796	1	CLONAL	2	TRUE	1	0.208053602533205	3		282	465	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845947	156845947	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	217	412	0	ENST00000524377.1:c.1577T>A	p.Leu526His	p.L526H	ENST00000524377	NM_002529.3	526	cTt/cAt	13/17	0.199798465516953	3	FACETS	1	0.953	1	1	0.992	1	CLONAL	3	TRUE	1	0.208053602533205	3		412	748	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736341	243736341	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	59	286	0	ENST00000263826.5:c.706C>A	p.His236Asn	p.H236N	ENST00000263826	NM_005465.4	236	Cat/Aat	8/13	0.199798465516953	3	FACETS	1	0.969	1	0.747	0.645	0.858	CLONAL	1	TRUE	1	0.208053602533205	3		286	419	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715668	30715668	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	41	352	0	ENST00000295754.5:c.1326C>G	p.Phe442Leu	p.F442L	ENST00000295754	NM_003242.5	442	ttC/ttG	5/7	0.194935061945509	3	FACETS	1	0.878	1	0.355	0.295	0.42	CLONAL	1	TRUE	0	0.208053602533205	3		352	409	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519938	NA	P-0006474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	82	223	0	ENST00000263967.3:c.1034A>C	p.Asn345Thr	p.N345T	ENST00000263967	NM_006218.2	345	aAt/aCt	5/21	0.194935061945509	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	3	TRUE	0	0.208053602533205	3		223	259	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900325	101900325	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	28	318	0	ENST00000374994.4:c.759G>T	p.Met253Ile	p.M253I	ENST00000374994	NM_004612.2	253	atG/atT	4/9	1	2	FACETS	0.821	0.657	1	0.821	0.657	1	CLONAL	1	TRUE	1	0.208053602533205	2		318	328	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100514	8100514	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	112	404	0	ENST00000346208.3:c.488C>A	p.Pro163Gln	p.P163Q	ENST00000346208		163	cCg/cAg	3/6	0.199798465516953	3	FACETS	0.895	0.806	0.989	0.895	0.806	0.989	CLONAL	2	TRUE	1	0.208053602533205	3		404	664	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573830	64573830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	39	256	2	ENST00000312049.6:c.923C>T	p.Ser308Leu	p.S308L	ENST00000312049	NM_130799.2	308	tCa/tTa	7/10	0.199798465516953	3	FACETS	1	0.929	1	0.62	0.515	0.735	CLONAL	1	TRUE	1	0.208053602533205	3		258	334	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216398	7216398	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	116	449	1	ENST00000380728.2:c.850G>T	p.Gly284Ter	p.G284*	ENST00000380728		284	Gga/Tga	10/11	0.20224420382458	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.208053602533205	2		450	504	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10244345	10244345	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	novel	NA	P-0006474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	112	441	0	ENST00000340748.4:c.4849T>C	p.Ter1617GlnextTer23	p.*1617Qext*23	ENST00000340748		1617	Tag/Cag	40/40	0.199798465516953	3	FACETS	0.974	0.878	1	0.974	0.878	1	CLONAL	2	TRUE	1	0.208053602533205	3		441	610	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561429	9561429	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	80	323	1	ENST00000353224.5:c.353G>T	p.Gly118Val	p.G118V	ENST00000353224	NM_177990.2	118	gGc/gTc	4/10	0.197416681659953	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.208053602533205	3		324	356	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545961	41545961	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	54	487	0	ENST00000263253.7:c.2576T>G	p.Ile859Ser	p.I859S	ENST00000263253	NM_001429.3	859	aTt/aGt	14/31	1	2	FACETS	0.927	0.792	1	0.927	0.792	1	CLONAL	1	TRUE	1	0.208053602533205	2		487	560	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006478-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	16	412	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.438556874659479	4	FACETS	0.205	0.151	0.271	0.103	0.075	0.136	SUBCLONAL	1	TRUE	2	0.432743683017915	4		412	516	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374932	45374932	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006478-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	32	544	0	ENST00000262160.6:c.911A>T	p.Asp304Val	p.D304V	ENST00000262160	NM_005901.5	304	gAc/gTc	8/11	0.168076728941954	4	FACETS	0.57	0.463	0.69	0.285	0.231	0.345	INDETERMINATE	1	TRUE	2	0.432743683017915	4		544	372	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0006479-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	12	219	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	NA	2	FACETS	0.795	0.58	1			1	INDETERMINATE	1	TRUE	NA	0.70229030268744	2		219	43	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212179	98212179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006479-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	11	1240	0	ENST00000331920.6:c.3493C>T	p.Leu1165Phe	p.L1165F	ENST00000331920	NM_000264.3	1165	Ctc/Ttc	21/24	1	2	FACETS	0.387	0.271	0.526	0.387	0.271	0.526	SUBCLONAL	1	TRUE	1	0.70229030268744	2		1240	81	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132912	64132912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200447389	NA	P-0006479-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	36	1032	0	ENST00000334205.4:c.1046C>T	p.Pro349Leu	p.P349L	ENST00000334205	NM_003942.2	349	cCa/cTa	9/17	0.591370943727668	4	FACETS	0.855	0.724	0.994	0.57	0.482	0.663	CLONAL	2	TRUE	1	0.70229030268744	4		1032	102	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557688	95557688	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006479-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	19	617	0	ENST00000393063.1:c.5379G>C	p.Glu1793Asp	p.E1793D	ENST00000393063	NM_030621.3	1793	gaG/gaC	26/28	0.70229030268744	3	FACETS	1	0.821	1	0.53	0.414	0.657	CLONAL	1	TRUE	1	0.70229030268744	3		617	69	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727920	41727920	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138094666	NA	P-0006479-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	20	1010	5	ENST00000301178.4:c.545C>T	p.Thr182Met	p.T182M	ENST00000301178	NM_021913.4	182	aCg/aTg	4/20	0.22000058630764	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.70229030268744	0		1015	54	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781440	135781440	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203542	NA	P-0006498-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	64	650	1	ENST00000298552.3:c.1525C>T	p.Arg509Ter	p.R509*	ENST00000298552	NM_001162426.1	509	Cga/Tga	15/23	0.340271927245613	1	FACETS	0.291	0.251	0.335	0.291	0.251	0.335	SUBCLONAL	1	TRUE	0	0.340271927245613	1		651	1071	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632379	215632379	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0006498-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	39	250	0	ENST00000260947.4:c.1396-1G>C		p.X466_splice	ENST00000260947	NM_000465.2	466			1	2	FACETS	0.78	0.649	0.924	0.78	0.649	0.924	CLONAL	1	TRUE	1	0.340271927245613	2		250	294	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856067	111856067	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1001185161	NA	P-0006498-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	162	183	1	ENST00000341259.2:c.118G>A	p.Glu40Lys	p.E40K	ENST00000341259	NM_005475.2	40	Gag/Aag	2/8	0.300308858830682	3	FACETS	0.784	0.721	0.849	0.784	0.721	0.849	SUBCLONAL	2	TRUE	1	0.340271927245613	3		184	711	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28971141	28971141	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006498-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	24	438	0	ENST00000282397.4:c.1616A>G	p.Asn539Ser	p.N539S	ENST00000282397	NM_002019.4	539	aAt/aGt	12/30	1	2	FACETS	0.316	0.247	0.396	0.316	0.247	0.396	SUBCLONAL	1	TRUE	1	0.340271927245613	2		438	446	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183814	10183821	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCAGCC	CCGCAGCC	-	novel	NA	P-0006498-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	91	177	0	ENST00000256474.2:c.284_291del	p.Pro95LeufsTer34	p.P95Lfs*34	ENST00000256474	NM_000551.3	95	CCGCAGCCc/c	1/3	0.335122056813538	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.340271927245613	1		177	395	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425896	49425896	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783685	NA	P-0006507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	112	604	0	ENST00000301067.7:c.12592C>T	p.Arg4198Ter	p.R4198*	ENST00000301067	NM_003482.3	4198	Cga/Tga	39/54	1	2	FACETS	0.914	0.821	1	0.914	0.821	1	CLONAL	1	TRUE	1	0.25	2		604	980	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553356	106553363	+	frameshift_variant	Frame_Shift_Del	DEL	CCGAGGCT	CCGAGGCT	G	novel	NA	P-0006507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	75	296	0	ENST00000369096.4:c.1321_1328delinsG	p.Pro441GlyfsTer63	p.P441Gfs*63	ENST00000369096	NM_001198.3	441	CCGAGGCTg/Gg	5/7	1	2	FACETS	0.863	0.756	0.979	0.863	0.756	0.979	CLONAL	1	TRUE	1	0.25	2		296	695	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913315	NA	P-0006508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	8	622	0	ENST00000326873.7:c.580G>A	p.Asp194Asn	p.D194N	ENST00000326873	NM_000455.4	194	Gac/Aac	4/10	1	2	FACETS	0.148	0.095	0.217	0.148	0.095	0.217	SUBCLONAL	1	TRUE	1	0.4032510584336	2		622	268	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0006511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	173	409	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	0.386509359729941	2		409	864	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459849	149459849	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	179	453	0	ENST00000286301.3:c.358G>C	p.Asp120His	p.D120H	ENST00000286301	NM_005211.3	120	Gac/Cac	4/22	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.386509359729941	2		453	894	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385306	4385306	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	164	460	0	ENST00000261254.3:c.331A>C	p.Lys111Gln	p.K111Q	ENST00000261254	NM_001759.3	111	Aaa/Caa	2/5	NA	2	FACETS	0.907	0.832	0.984			1	INDETERMINATE	1	TRUE	NA	0.386509359729941	2		460	936	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691039	NA	P-0006511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	174	416	0	ENST00000269305.4:c.919+1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.386509359729941	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.386509359729941	1		416	684	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974776	21974776	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	74	254	0	ENST00000304494.5:c.51del	p.Thr18ArgfsTer8	p.T18Rfs*8	ENST00000304494	NM_000077.4	17	gcC/gc	1/3	0.386509359729941	1	FACETS	0.835	0.735	0.941	0.835	0.735	0.941	CLONAL	1	TRUE	0	0.386509359729941	1		254	370	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332828	65332828	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	73	340	1	ENST00000342505.4:c.711G>T	p.Arg237Ser	p.R237S	ENST00000342505	NM_002227.2	237	agG/agT	7/25	0.150792783410478	5	FACETS	0.765	0.669	0.87			1	INDETERMINATE	1	TRUE	NA	0.408600893118018	5		341	753	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332843	65332843	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	63	335	2	ENST00000342505.4:c.696G>T	p.Arg232Ser	p.R232S	ENST00000342505	NM_002227.2	232	agG/agT	7/25	0.150792783410478	5	FACETS	0.702	0.607	0.807			1	INDETERMINATE	1	TRUE	NA	0.408600893118018	5		337	708	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578393	7578393	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876660821	NA	P-0006533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	51	285	1	ENST00000269305.4:c.537T>A	p.His179Gln	p.H179Q	ENST00000269305	NM_001126112.2	179	caT/caA	5/11	0.395857764777699	2	FACETS	0.877	0.775	0.978	0.877	0.775	0.978	CLONAL	2	FALSE	0	0.57598503451851	2		286	101	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0006533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	328	179	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.57598503451851	25	FACETS	0.983	0.96	1			1	CLONAL	24	FALSE	NA	0.57598503451851	25		179	368	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90976728	90976728	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	44	319	0	ENST00000265433.3:c.904C>G	p.Leu302Val	p.L302V	ENST00000265433	NM_002485.4	302	Ctt/Gtt	8/16	0.335435865298797	5	FACETS	1	0.876	1	0.683	0.585	0.786	INDETERMINATE	2	FALSE	2	0.57598503451851	5		319	139	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533552	533552	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	24	468	0	ENST00000451590.1:c.351G>T	p.Lys117Asn	p.K117N	ENST00000451590	NM_001130442.1	117	aaG/aaT	4/5	0.57598503451851	1	FACETS	0.263	0.206	0.327	0.263	0.206	0.327	SUBCLONAL	1	FALSE	0	0.57598503451851	1		468	226	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120692	115120692	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	124	463	1	ENST00000257566.3:c.314T>A	p.Val105Glu	p.V105E	ENST00000257566	NM_016569.3	105	gTg/gAg	1/8	0.393964655346279	5	FACETS	1	0.965	1	0.737	0.674	0.802	CLONAL	2	FALSE	2	0.57598503451851	5		464	363	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264821	46264821	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs764548730	NA	P-0006533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	72	643	0	ENST00000371998.3:c.1691A>G	p.Asn564Ser	p.N564S	ENST00000371998		564	aAt/aGt	12/23	0.227618967253543	5	FACETS	0.903	0.799	1	0.602	0.532	0.675	INDETERMINATE	2	FALSE	2	0.57598503451851	5		643	258	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0006541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	242	295	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.355953818413953	5	FACETS	1	0.988	1	0.8	0.753	0.848	INDETERMINATE	2	TRUE	2	0.636886016835265	5		295	619	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0006541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	162	384	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.624149545646922	4	FACETS	0.908	0.833	0.986	0.454	0.416	0.493	CLONAL	1	TRUE	2	0.636886016835265	4		384	917	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206647673	206647673	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0006541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	329	337	1	ENST00000367120.3:c.88-1G>A		p.X30_splice	ENST00000367120	NM_014002.3	30			0.624149545646922	4	FACETS	0.959	0.909	1	0.959	0.909	1	CLONAL	2	TRUE	2	0.636886016835265	4		338	882	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725042	89725042	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0006541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	360	342	0	ENST00000371953.3:c.1027-2A>T		p.X343_splice	ENST00000371953	NM_000314.4	343			0.636886016835265	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.636886016835265	2		342	497	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419837	41419837	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs267605939	NA	P-0006541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	233	379	0	ENST00000373198.4:c.484C>T	p.Gln162Ter	p.Q162*	ENST00000373198	NM_133170.3	162	Cag/Tag	3/32	0.624149545646922	4	FACETS	1	0.983	1	0.579	0.54	0.62	CLONAL	1	TRUE	2	0.636886016835265	4		379	1034	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476791	140476791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	320	489	0	ENST00000288602.6:c.1615C>T	p.His539Tyr	p.H539Y	ENST00000288602	NM_004333.4	539	Cac/Tac	13/18	0.355953818413953	5	FACETS	1	0.992	1	0.817	0.775	0.859	INDETERMINATE	2	TRUE	2	0.636886016835265	5		489	802	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187419	32187419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1727	239	518	0	ENST00000375023.3:c.1460G>A	p.Gly487Glu	p.G487E	ENST00000375023	NM_004557.3	487	gGa/gAa	8/30	0.636886016835265	6	FACETS	0.868	0.807	0.932	0.217	0.201	0.233	CLONAL	1	TRUE	2	0.636886016835265	6		518	1966	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439664	220439664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs992068119	NA	P-0006541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	785	581	2	ENST00000243786.2:c.517C>T	p.Pro173Ser	p.P173S	ENST00000243786	NM_002191.3	173	Ccc/Tcc	2/2	0.636886016835265	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	1	0.636886016835265	3		583	1445	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164307	47164307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	109	310	0	ENST00000409792.3:c.1819C>T	p.Pro607Ser	p.P607S	ENST00000409792	NM_014159.6	607	Cct/Tct	3/21	1	2	FACETS	0.943	0.855	1	0.943	0.855	1	CLONAL	1	TRUE	1	0.636886016835265	2		310	363	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102904	71102904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	175	378	0	ENST00000318789.4:c.303G>A	p.Met101Ile	p.M101I	ENST00000318789	NM_032682.5	101	atG/atA	8/21	1	2	FACETS	0.943	0.873	1	0.943	0.873	1	CLONAL	1	TRUE	1	0.636886016835265	2		378	583	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911572	134911572	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	258	438	0	ENST00000398015.3:c.2037C>A	p.Asn679Lys	p.N679K	ENST00000398015	NM_004441.4	679	aaC/aaA	11/16	0.603299439978753	4	FACETS	1	0.979	1	0.369	0.345	0.394	CLONAL	1	TRUE	1	0.636886016835265	4		438	1198	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554861	187554861	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	215	451	1	ENST00000441802.2:c.4300G>A	p.Gly1434Arg	p.G1434R	ENST00000441802	NM_005245.3	1434	Gga/Aga	7/27	0.636886016835265	3	FACETS	1	0.966	1	0.53	0.494	0.568	CLONAL	1	TRUE	1	0.636886016835265	3		452	839	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680877	30680877	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1953	344	557	0	ENST00000376406.3:c.842G>T	p.Gly281Val	p.G281V	ENST00000376406	NM_014641.2	281	gGg/gTg	5/15	0.636886016835265	6	FACETS	1	0.977	1	0.267	0.251	0.284	CLONAL	1	TRUE	2	0.636886016835265	6		557	2297	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641039	117641039	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1373810021	NA	P-0006541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	147	388	0	ENST00000368508.3:c.5932G>C	p.Ala1978Pro	p.A1978P	ENST00000368508	NM_002944.2	1978	Gca/Cca	36/43	NA	2	FACETS	1	0.953	1			1	INDETERMINATE	1	TRUE	NA	0.636886016835265	2		388	440	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2949769	2949769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376446854	NA	P-0006541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	481	405	2	ENST00000396946.4:c.3175G>A	p.Gly1059Ser	p.G1059S	ENST00000396946	NM_032415.4	1059	Ggc/Agc	24/25	0.355953818413953	5	FACETS	0.872	0.836	0.908	0.872	0.836	0.908	INDETERMINATE	3	TRUE	2	0.636886016835265	5		407	1129	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241632	55241632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	218	439	0	ENST00000275493.2:c.2080C>T	p.Pro694Ser	p.P694S	ENST00000275493	NM_005228.3	694	Ccc/Tcc	18/28	0.355953818413953	5	FACETS	1	0.991	1	0.492	0.458	0.528	INDETERMINATE	1	TRUE	2	0.636886016835265	5		439	906	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346575	81346575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	235	498	0	ENST00000222390.5:c.1378C>T	p.Pro460Ser	p.P460S	ENST00000222390	NM_000601.4	460	Cct/Tct	11/18	0.355953818413953	5	FACETS	1	0.981	1	0.742	0.697	0.789	INDETERMINATE	2	TRUE	2	0.636886016835265	5		498	648	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477794	140477794	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	169	353	0	ENST00000288602.6:c.1514T>A	p.Leu505His	p.L505H	ENST00000288602	NM_004333.4	505	cTc/cAc	12/18	0.355953818413953	5	FACETS	0.765	0.706	0.827	0.51	0.47	0.551	INDETERMINATE	2	TRUE	2	0.636886016835265	5		353	678	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915939	127915939	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	338	671	0	ENST00000373547.4:c.542G>A	p.Arg181Gln	p.R181Q	ENST00000373547	NM_002721.4	181	cGg/cAg	6/7	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.636886016835265	2		671	998	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137832	64137832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753090599	NA	P-0006541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	365	629	1	ENST00000334205.4:c.1933G>A	p.Glu645Lys	p.E645K	ENST00000334205	NM_003942.2	645	Gag/Aag	15/17	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.636886016835265	2		630	1084	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200425	67200425	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	186	304	0	ENST00000312629.5:c.619C>T	p.His207Tyr	p.H207Y	ENST00000312629	NM_003952.2	207	Cac/Tac	8/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.636886016835265	2		304	524	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514302	69514302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1255340343	NA	P-0006541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	218	431	1	ENST00000294312.3:c.379C>T	p.Arg127Cys	p.R127C	ENST00000294312	NM_005117.2	127	Cgc/Tgc	3/3	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.636886016835265	2		432	678	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119809	108119809	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	218	411	0	ENST00000278616.4:c.1215T>G	p.Asn405Lys	p.N405K	ENST00000278616	NM_000051.3	405	aaT/aaG	9/63	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.636886016835265	2		411	643	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444024	49444024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	191	328	0	ENST00000301067.7:c.3347C>T	p.Ser1116Phe	p.S1116F	ENST00000301067	NM_003482.3	1116	tCt/tTt	11/54	0.636886016835265	3	FACETS	0.929	0.86	1	0.465	0.43	0.501	CLONAL	1	TRUE	1	0.636886016835265	3		328	851	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859436	57859436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	337	692	2	ENST00000228682.2:c.581C>T	p.Pro194Leu	p.P194L	ENST00000228682	NM_005269.2	194	cCc/cTc	6/12	0.636886016835265	3	FACETS	1	0.945	1	0.5	0.472	0.529	CLONAL	1	TRUE	1	0.636886016835265	3		694	1394	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554305	81554305	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777252114	NA	P-0006541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	303	456	1	ENST00000298171.2:c.325C>T	p.Arg109Trp	p.R109W	ENST00000298171	NM_000369.2	109	Cgg/Tgg	4/10	0.636886016835265	3	FACETS	1	0.986	1	0.569	0.536	0.603	CLONAL	1	TRUE	1	0.636886016835265	3		457	1102	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003779	45003779	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	223	375	0	ENST00000558401.1:c.35T>C	p.Leu12Pro	p.L12P	ENST00000558401	NM_004048.2	12	cTa/cCa	1/4	0.636886016835265	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.636886016835265	1		375	426	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349080	11349080	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	133	265	0	ENST00000332029.2:c.256G>T	p.Val86Leu	p.V86L	ENST00000332029	NM_003745.1	86	Gtg/Ttg	2/2	0.636886016835265	3	FACETS	0.978	0.892	1	0.489	0.446	0.534	CLONAL	1	TRUE	1	0.636886016835265	3		265	563	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863648	68863648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782549	NA	P-0006541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	252	341	1	ENST00000261769.5:c.2387G>A	p.Arg796Gln	p.R796Q	ENST00000261769	NM_004360.3	796	cGg/cAg	15/16	0.636886016835265	2	FACETS	1	0.989	1	0.606	0.57	0.642	CLONAL	1	TRUE	0	0.636886016835265	2		342	653	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288726	15288726	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	38	86	0	ENST00000263388.2:c.4013G>C	p.Ser1338Thr	p.S1338T	ENST00000263388	NM_000435.2	1338	aGc/aCc	24/33	0.636886016835265	3	FACETS	0.915	0.766	1	0.457	0.383	0.538	CLONAL	1	TRUE	1	0.636886016835265	3		86	172	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538302	9538302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	443	483	0	ENST00000353224.5:c.1696C>T	p.His566Tyr	p.H566Y	ENST00000353224	NM_177990.2	566	Cac/Tac	7/10	0.624149545646922	4	FACETS	0.999	0.955	1	0.999	0.955	1	CLONAL	2	TRUE	2	0.636886016835265	4		483	1140	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714436	40714436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1228688924	NA	P-0006541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	499	414	0	ENST00000373198.4:c.3961G>A	p.Glu1321Lys	p.E1321K	ENST00000373198	NM_133170.3	1321	Gag/Aag	29/32	0.624149545646922	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	2	0.636886016835265	4		414	1115	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727065	40727065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866502487	NA	P-0006541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	399	359	0	ENST00000373198.4:c.3899C>T	p.Ala1300Val	p.A1300V	ENST00000373198	NM_133170.3	1300	gCc/gTc	28/32	0.624149545646922	4	FACETS	0.965	0.92	1	0.965	0.92	1	CLONAL	2	TRUE	2	0.636886016835265	4		359	1063	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159743	20159743	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	285	187	0	ENST00000379607.5:c.16G>T	p.Gly6Cys	p.G6C	ENST00000379607	NM_001412.3	6	Ggt/Tgt	1/7	0.58857441658033	2	FACETS	1	0.993	1			1	CLONAL	1	TRUE	NA	0.636886016835265	2		187	657	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912660	NA	P-0006544-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	880	785	0	ENST00000269305.4:c.839G>T	p.Arg280Ile	p.R280I	ENST00000269305	NM_001126112.2	280	aGa/aTa	8/11	0.698468256073571	2	FACETS	0.971	0.948	0.993	0.971	0.948	0.993	CLONAL	2	TRUE	0	0.698468256073571	2		785	1298	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020808	26020808	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs377197123	NA	P-0006544-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1216	1344	1282	0	ENST00000357647.3:c.91C>G	p.Pro31Ala	p.P31A	ENST00000357647	NM_003529.2	31	Ccg/Gcg	1/1	0.698468256073571	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.698468256073571	3		1282	2560	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936984	48937002	+	frameshift_variant	Frame_Shift_Del	DEL	GAACACCCAGGCGAGGTCA	GAACACCCAGGCGAGGTCA	-	novel	NA	P-0006544-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	771	631	0	ENST00000267163.4:c.757_775del	p.Pro253GlyfsTer5	p.P253Gfs*5	ENST00000267163	NM_000321.2	251	cGAACACCCAGGCGAGGTCAg/cg	8/27	0.683944944800381	3	FACETS	0.89	0.869	0.912	0.89	0.869	0.912	CLONAL	3	TRUE	0	0.698468256073571	3		631	1115	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0006545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	296	402	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.869597418337093	3	FACETS	1	0.964	1	0.514	0.485	0.544	CLONAL	1	TRUE	1	0.869597418337093	3		402	950	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252155	226252155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553260624	NA	P-0006545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	13	48	0	ENST00000366813.1:c.103G>A	p.Gly35Arg	p.G35R	ENST00000366813		35	Ggg/Agg	1/3	0.869597418337093	3	FACETS	0.875	0.646	1	0.438	0.323	0.567	CLONAL	1	TRUE	1	0.869597418337093	3		48	49	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082546	16082546	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1758	526	248	0	ENST00000281043.3:c.360C>A	p.Phe120Leu	p.F120L	ENST00000281043	NM_005378.4	120	ttC/ttA	2/3	0.869597418337093	15	FACETS	0.881	0.841	0.921			1	CLONAL	4	TRUE	NA	0.869597418337093	15		248	2284	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888839	76888839	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	336	200	1	ENST00000373344.5:c.4990G>T	p.Glu1664Ter	p.E1664*	ENST00000373344	NM_000489.3	1664	Gag/Tag	19/35	0.869597418337093	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.869597418337093	2		201	363	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578521	7578521	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	611	395	0	ENST00000269305.4:c.409del	p.Leu137TrpfsTer33	p.L137Wfs*33	ENST00000269305	NM_001126112.2	137	Ctg/tg	5/11	0.869597418337093	3	FACETS	0.978	0.947	1	0.978	0.947	1	CLONAL	2	TRUE	1	0.869597418337093	3		395	1031	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	109	407	0	ENST00000269305.4:c.517G>C	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ctg	5/11	1	2	FACETS	0.892	0.802	0.987	1	0.987	1	CLONAL	2	TRUE	1	0.18	2		407	679	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0006564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	34	324	1	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	1	2	FACETS	0.821	0.671	0.991	0.821	0.671	0.991	CLONAL	1	TRUE	1	0.18	2		325	460	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920447	114920447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	92	693	0	ENST00000543371.1:c.1388G>A	p.Cys463Tyr	p.C463Y	ENST00000543371	NM_001198531.1	463	tGc/tAc	13/14	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.18	2		693	1013	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241679	55241681	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	rs397517086	NA	P-0006606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	554	541	0	ENST00000275493.2:c.2127_2129del	p.Glu709_Thr710delinsAsp	p.E709_T710delinsD	ENST00000275493	NM_005228.3	709	gaAACt/gat	18/28	0.508437865873201	6	FACETS	0.963	0.928	0.998	0.963	0.928	0.998	CLONAL	4	TRUE	2	0.508437865873201	6		541	1141	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183564	185183564	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	196	410	0	ENST00000265026.3:c.1418A>G	p.Glu473Gly	p.E473G	ENST00000265026	NM_004721.4	473	gAg/gGg	9/14	0.508437865873201	3	FACETS	1	0.979	1	0.571	0.529	0.614	CLONAL	1	TRUE	1	0.508437865873201	3		410	847	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141565	11141565	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	125	364	1	ENST00000358026.2:c.3542A>G	p.His1181Arg	p.H1181R	ENST00000358026	NM_001128849.1	1181	cAc/cGc	25/36	0.508437865873201	3	FACETS	0.821	0.744	0.903	0.411	0.372	0.452	CLONAL	1	TRUE	1	0.508437865873201	3		365	751	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170455	108170455	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555104511	NA	P-0006610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	141	298	0	ENST00000278616.4:c.5020T>C	p.Cys1674Arg	p.C1674R	ENST00000278616	NM_000051.3	1674	Tgc/Cgc	34/63	0.263084460029201	3	FACETS	0.859	0.786	0.934	0.572	0.524	0.623	CLONAL	2	TRUE	0	0.342239465648902	3		298	562	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29002021	29002021	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766489043	NA	P-0006610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	76	310	1	ENST00000282397.4:c.1144C>T	p.Arg382Cys	p.R382C	ENST00000282397	NM_002019.4	382	Cgc/Tgc	9/30	0.305571422684743	3	FACETS	0.98	0.861	1	0.49	0.43	0.554	CLONAL	1	TRUE	1	0.342239465648902	3		311	531	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527895	103527895	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0006610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	127	412	0	ENST00000355739.4:c.3203C>G	p.Ser1068Ter	p.S1068*	ENST00000355739	NM_000123.3	1068	tCa/tGa	15/15	0.305571422684743	3	FACETS	1	0.975	1	0.609	0.552	0.668	CLONAL	1	TRUE	1	0.342239465648902	3		412	714	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444607	49444724	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTAGATGTGCCATGAAGAGTTACAGCTGTTCCAGAATAACAGAGTACTAACATCCCCTTACCTGGTGGCATCAGCTGAGGCGACAAGGATGGCTCCCCAGATGGGGACAACGGCAGC	ATTAGATGTGCCATGAAGAGTTACAGCTGTTCCAGAATAACAGAGTACTAACATCCCCTTACCTGGTGGCATCAGCTGAGGCGACAAGGATGGCTCCCCAGATGGGGACAACGGCAGC	-	novel	NA	P-0006610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	192	299	0	ENST00000301067.7:c.2742_2798-34del		p.X914_splice	ENST00000301067	NM_003482.3	914		10/54	0.291443817772586	4	FACETS	0.895	0.833	0.958			1	CLONAL	3	TRUE	NA	0.342239465648902	4		299	561	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006626-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	266	412	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.352644521058403	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.352644521058403	3		412	862	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0006626-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	358	474	0	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	0.348213953817118	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.352644521058403	2		474	977	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023380	27023381	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0006626-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	94	176	0	ENST00000324856.7:c.487_488del	p.Ala163ArgfsTer236	p.A163Rfs*236	ENST00000324856	NM_006015.4	162	gcCGcc/gccc	1/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.352644521058403	2		176	430	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0006649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	22	538	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.612	0.473	0.774	0.612	0.473	0.774	SUBCLONAL	1	TRUE	1	0.17	2		538	423	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0006649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	25	401	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.589	0.463	0.735	0.589	0.463	0.735	SUBCLONAL	1	TRUE	1	0.17	2		401	499	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630590	187630590	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3733415	NA	P-0006649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	31	508	2	ENST00000441802.2:c.392C>T	p.Ala131Val	p.A131V	ENST00000441802	NM_005245.3	131	gCg/gTg	2/27	1	2	FACETS	0.658	0.531	0.803	0.658	0.531	0.803	SUBCLONAL	1	TRUE	1	0.17	2		510	554	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511329	157511329	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	20	303	0	ENST00000346085.5:c.3851del	p.Gly1284GlufsTer2	p.G1284Efs*2	ENST00000346085	NM_020732.3	1283	Ggg/gg	15/20	1	2	FACETS	0.757	0.579	0.965	0.757	0.579	0.965	CLONAL	1	TRUE	1	0.17	2		303	311	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200476	67200476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777468878	NA	P-0006649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	26	426	1	ENST00000312629.5:c.670G>A	p.Ala224Thr	p.A224T	ENST00000312629	NM_003952.2	224	Gcc/Acc	8/15	1	2	FACETS	0.675	0.534	0.838	0.675	0.534	0.838	SUBCLONAL	1	TRUE	1	0.17	2		427	453	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082592	16082592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1003867645	NA	P-0006649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	15	103	0	ENST00000281043.3:c.406C>T	p.His136Tyr	p.H136Y	ENST00000281043	NM_005378.4	136	Cac/Tac	2/3	1	2	FACETS	0.751	0.55	0.993	0.751	0.55	0.993	CLONAL	1	TRUE	1	0.17	2		103	235	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104698	209104698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766985383	NA	P-0006649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	24	450	0	ENST00000345146.2:c.880G>A	p.Val294Met	p.V294M	ENST00000345146	NM_005896.2	294	Gtg/Atg	8/10	1	2	FACETS	0.609	0.476	0.762	0.609	0.476	0.762	SUBCLONAL	1	TRUE	1	0.17	2		450	464	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209108184	209108184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778401	NA	P-0006649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	29	479	0	ENST00000345146.2:c.665G>A	p.Arg222His	p.R222H	ENST00000345146	NM_005896.2	222	cGt/cAt	6/10	1	2	FACETS	0.767	0.615	0.94	0.767	0.615	0.94	CLONAL	1	TRUE	1	0.17	2		479	445	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629582	187629582	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748957825	NA	P-0006649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	28	451	1	ENST00000441802.2:c.1400C>T	p.Ala467Val	p.A467V	ENST00000441802	NM_005245.3	467	gCg/gTg	2/27	1	2	FACETS	0.676	0.54	0.833	0.676	0.54	0.833	SUBCLONAL	1	TRUE	1	0.17	2		452	487	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81927315	81927315	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	30	403	0	ENST00000359376.3:c.988T>C	p.Tyr330His	p.Y330H	ENST00000359376	NM_002661.3	330	Tac/Cac	12/33	1	2	FACETS	0.887	0.715	1	0.887	0.715	1	CLONAL	1	TRUE	1	0.17	2		403	398	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15967421	15967421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766158799	NA	P-0006649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	29	434	0	ENST00000268712.3:c.5182C>T	p.Arg1728Trp	p.R1728W	ENST00000268712	NM_006311.3	1728	Cgg/Tgg	35/46	1	2	FACETS	0.611	0.489	0.751	0.611	0.489	0.751	SUBCLONAL	1	TRUE	1	0.17	2		434	558	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435134	56435134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs184604359	NA	P-0006649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	20	357	2	ENST00000407977.2:c.2003G>A	p.Arg668Gln	p.R668Q	ENST00000407977		668	cGg/cAg	9/10	1	2	FACETS	0.659	0.503	0.842	0.659	0.503	0.842	SUBCLONAL	1	TRUE	1	0.17	2		359	357	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278055	18278055	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781265051	NA	P-0006649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	22	462	0	ENST00000222254.8:c.1675C>T	p.Arg559Cys	p.R559C	ENST00000222254	NM_005027.3	559	Cgc/Tgc	13/16	0.0824044114945349	0	FACETS	0.514	0.397	0.65			1	INDETERMINATE	1	TRUE	0	0.17	0		462	418	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290231	15290231	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	33	554	0	ENST00000263388.2:c.3404del	p.Gly1135ValfsTer137	p.G1135Vfs*137	ENST00000263388	NM_000435.2	1135	gGt/gt	21/33	0.0824044114945349	0	FACETS	0.609	0.495	0.738			1	INDETERMINATE	1	TRUE	0	0.17	0		554	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0006657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	402	528	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.408058178380299	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	TRUE	0	0.408058178380299	3		528	772	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0006657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	343	401	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.350507515700804	5	FACETS	1	0.991	1	0.817	0.774	0.861	CLONAL	2	TRUE	2	0.408058178380299	5		401	1106	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0006657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	285	365	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.343763993190033	2	FACETS	0.825	0.778	0.872	0.825	0.778	0.872	CLONAL	2	TRUE	0	0.408058178380299	2		365	847	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361214	66361214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375878596	NA	P-0006657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	50	493	0	ENST00000273854.3:c.958G>A	p.Gly320Ser	p.G320S	ENST00000273854	NM_004439.5	320	Ggc/Agc	4/18	1	2	FACETS	0.279	0.236	0.327	0.279	0.236	0.327	SUBCLONAL	1	TRUE	1	0.408058178380299	2		493	877	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801101	135801101	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs373855276	NA	P-0006657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	192	472	0	ENST00000298552.3:c.236A>G	p.Tyr79Cys	p.Y79C	ENST00000298552	NM_001162426.1	79	tAt/tGt	5/23	0.231419288689401	5	FACETS	1	0.989	1	0.47	0.434	0.508	INDETERMINATE	1	TRUE	2	0.408058178380299	5		472	1075	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858370	9858370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760522909	NA	P-0006657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	68	453	0	ENST00000330684.3:c.3031C>T	p.Arg1011Trp	p.R1011W	ENST00000330684	NM_001134407.1	1011	Cgg/Tgg	13/13	0.408058178380299	3	FACETS	0.528	0.459	0.603	0.264	0.229	0.302	SUBCLONAL	1	TRUE	1	0.408058178380299	3		453	760	SUCCESS
APC	324	MSKCC	GRCh37	5	112175755	112175755	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006669-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	116	284	0	ENST00000257430.4:c.4464del	p.Leu1488PhefsTer19	p.L1488Ffs*19	ENST00000257430	NM_000038.5	1488	ttA/tt	16/16	0.312989457810917	1	FACETS	0.43	0.388	0.474	0.43	0.388	0.474	INDETERMINATE	1	TRUE	0	0.621158679489837	1		284	599	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579321	7579322	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs587780067	NA	P-0006669-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	238	298	1	ENST00000269305.4:c.365_366del	p.Val122AspfsTer26	p.V122Dfs*26	ENST00000269305	NM_001126112.2	122	gTG/g	4/11	0.621158679489837	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.621158679489837	1		299	495	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099835	157099835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006669-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	237	395	1	ENST00000346085.5:c.772C>T	p.Gln258Ter	p.Q258*	ENST00000346085	NM_020732.3	258	Caa/Taa	1/20	1	2	FACETS	0.987	0.925	1	0.987	0.925	1	CLONAL	1	TRUE	1	0.621158679489837	2		396	773	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845780	151845780	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006669-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	305	396	0	ENST00000262189.6:c.13232G>A	p.Gly4411Glu	p.G4411E	ENST00000262189	NM_170606.2	4411	gGa/gAa	52/59	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.621158679489837	2		396	934	SUCCESS
APC	324	MSKCC	GRCh37	5	112174467	112174471	+	frameshift_variant	Frame_Shift_Del	DEL	AAATA	AAATA	-	rs1554084794	NA	P-0006669-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	239	332	0	ENST00000257430.4:c.3179_3183del	p.Ile1060ThrfsTer3	p.I1060Tfs*3	ENST00000257430	NM_000038.5	1059	gAAATA/g	16/16	0.312989457810917	1	FACETS	0.7	0.656	0.745	0.7	0.656	0.745	INDETERMINATE	1	TRUE	0	0.621158679489837	1		332	758	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098944	178098944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	288	212	0	ENST00000397062.3:c.101G>A	p.Arg34Gln	p.R34Q	ENST00000397062	NM_006164.4	34	cGa/cAa	2/5	0.662593092722898	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	3	TRUE	1	0.662593092722898	4		212	481	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	249	196	0	ENST00000397062.3:c.92G>A	p.Gly31Glu	p.G31E	ENST00000397062	NM_006164.4	31	gGa/gAa	2/5	0.662593092722898	4	FACETS	0.958	0.91	1	0.958	0.91	1	CLONAL	3	TRUE	1	0.662593092722898	4		196	435	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534285	534285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894226	NA	P-0006674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	545	293	0	ENST00000451590.1:c.38G>T	p.Gly13Val	p.G13V	ENST00000451590	NM_001130442.1	13	gGt/gTt	2/5	0.662593092722898	4	FACETS	0.959	0.926	0.991	0.959	0.926	0.991	CLONAL	3	TRUE	1	0.662593092722898	4		293	951	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0006674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	493	419	0	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	0.650082297259597	2	FACETS	0.995	0.963	1	0.995	0.963	1	CLONAL	2	TRUE	0	0.662593092722898	2		419	748	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17350566	17350566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201928318	NA	P-0006674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	194	284	1	ENST00000375499.3:c.544G>A	p.Gly182Arg	p.G182R	ENST00000375499	NM_003000.2	182	Ggg/Agg	6/8	0.528443315935415	4	FACETS	1	0.989	1	0.455	0.422	0.489	CLONAL	1	TRUE	1	0.662593092722898	4		285	713	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46543223	46543223	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0006674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	230	416	0	ENST00000262741.5:c.278C>G	p.Ser93Ter	p.S93*	ENST00000262741	NM_003629.3	93	tCa/tGa	3/10	0.528443315935415	4	FACETS	1	0.987	1	0.413	0.385	0.442	CLONAL	1	TRUE	1	0.662593092722898	4		416	932	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437669	52437669	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	590	595	0	ENST00000460680.1:c.1492G>C	p.Glu498Gln	p.E498Q	ENST00000460680	NM_004656.3	498	Gag/Cag	13/17	0.650082297259597	2	FACETS	0.984	0.955	1	0.984	0.955	1	CLONAL	2	TRUE	0	0.662593092722898	2		595	905	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503816	186503816	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1284	144	563	0	ENST00000323963.5:c.493G>C	p.Asp165His	p.D165H	ENST00000323963		165	Gat/Cat	5/11	0.329746380283204	6	FACETS	0.708	0.643	0.776	0.236	0.214	0.259	INDETERMINATE	1	TRUE	3	0.662593092722898	6		563	1428	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332882	153332882	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0006674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	132	231	0	ENST00000281708.4:c.74C>G	p.Ser25Ter	p.S25*	ENST00000281708	NM_033632.3	25	tCa/tGa	2/12	0.313643558998357	1	FACETS	0.798	0.734	0.862	0.798	0.734	0.862	INDETERMINATE	1	TRUE	0	0.662593092722898	1		231	334	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879199	151879199	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0006674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	496	469	1	ENST00000262189.6:c.5746A>T	p.Arg1916Ter	p.R1916*	ENST00000262189	NM_170606.2	1916	Aga/Tga	36/59	0.662593092722898	4	FACETS	1	0.994	1	0.78	0.749	0.81	CLONAL	2	TRUE	1	0.662593092722898	4		470	1064	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343567	118343567	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	210	252	0	ENST00000534358.1:c.1693C>G	p.Leu565Val	p.L565V	ENST00000534358	NM_005933.3	565	Ctg/Gtg	3/36	0.661826106842189	2	FACETS	1	0.992	1	0.72	0.678	0.763	CLONAL	1	TRUE	0	0.662593092722898	2		252	440	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349176	89349176	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	760	772	0	ENST00000301030.4:c.3774G>C	p.Glu1258Asp	p.E1258D	ENST00000301030	NM_001256183.1	1258	gaG/gaC	9/13	0.521162607685477	3	FACETS	0.926	0.897	0.956	0.926	0.897	0.956	CLONAL	2	TRUE	1	0.662593092722898	3		772	1649	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004865	16004865	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	288	294	0	ENST00000268712.3:c.2389G>C	p.Asp797His	p.D797H	ENST00000268712	NM_006311.3	797	Gat/Cat	20/46	0.650082297259597	2	FACETS	0.943	0.902	0.983	0.943	0.902	0.983	CLONAL	2	TRUE	0	0.662593092722898	2		294	461	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687486	37687486	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	207	226	0	ENST00000447079.4:c.4390C>G	p.Gln1464Glu	p.Q1464E	ENST00000447079	NM_015083.1	1464	Cag/Gag	14/14	0.662593092722898	3	FACETS	0.893	0.838	0.948	0.893	0.838	0.948	CLONAL	2	TRUE	1	0.662593092722898	3		226	466	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11114071	11114071	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	555	425	0	ENST00000358026.2:c.1999G>A	p.Glu667Lys	p.E667K	ENST00000358026	NM_001128849.1	667	Gag/Aag	13/36	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.662593092722898	NA		425	761	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916833	48916833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	188	200	0	ENST00000267163.4:c.363del	p.Asn123ThrfsTer2	p.N123Tfs*2	ENST00000267163	NM_000321.2	121	caG/ca	3/27	0.611052060074642	2	FACETS	0.773	0.726	0.82	0.773	0.726	0.82	SUBCLONAL	2	TRUE	0	0.662593092722898	2		200	367	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081624	143081625	+	stop_gained	Nonsense_Mutation	DNP	TC	TC	AG	novel	NA	P-0006674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	157	399	0	ENST00000262992.4:c.1449_1450delinsCT	p.Lys483_Lys484delinsAsnTer	p.K483_K484delinsN*	ENST00000262992	NM_001101669.1	483	aaGAag/aaCTag	15/24	0.313643558998357	1	FACETS	0.817	0.758	0.877	0.817	0.758	0.877	INDETERMINATE	1	TRUE	0	0.662593092722898	1		399	388	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0006679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	375	273	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.668260190598493	2	FACETS	0.988	0.952	1	0.988	0.952	1	CLONAL	2	TRUE	0	0.668260190598493	2		273	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578529	7578529	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs780442292	NA	P-0006679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	376	342	2	ENST00000269305.4:c.401T>G	p.Phe134Cys	p.F134C	ENST00000269305	NM_001126112.2	134	tTt/tGt	5/11	0.665381154835238	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.668260190598493	1		344	738	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851558	134851558	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs770155473	NA	P-0006679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	89	244	0	ENST00000398015.3:c.964G>A	p.Val322Ile	p.V322I	ENST00000398015	NM_004441.4	322	Gtc/Atc	5/16	0.34343004764355	2	FACETS	0.46	0.408	0.515	0.23	0.204	0.258	INDETERMINATE	1	TRUE	0	0.668260190598493	2		244	579	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325742	30325742	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	167	211	0	ENST00000322652.5:c.1940T>G	p.Ile647Arg	p.I647R	ENST00000322652	NM_015355.2	647	aTa/aGa	16/16	0.43704171348044	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.668260190598493	1		211	330	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223057	41223057	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730881494	NA	P-0006679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	404	487	0	ENST00000357654.3:c.4874A>G	p.Tyr1625Cys	p.Y1625C	ENST00000357654	NM_007294.3	1625	tAt/tGt	15/23	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.668260190598493	2		487	1138	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899179	78899179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760865448	NA	P-0006679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	213	227	0	ENST00000306801.3:c.2818G>A	p.Asp940Asn	p.D940N	ENST00000306801	NM_020761.2	940	Gac/Aac	24/34	0.665381154835238	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.668260190598493	1		227	414	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0006682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	65	219	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.200565768128595	6	FACETS	0.996	0.871	1	0.597	0.522	0.678	CLONAL	3	FALSE	1	0.200565768128595	6		219	304	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294284	11294284	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs757090752	NA	P-0006682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	79	340	0	ENST00000361445.4:c.2247C>G	p.Ile749Met	p.I749M	ENST00000361445	NM_004958.3	749	atC/atG	14/58	0.200565768128595	1	FACETS	0.848	0.749	0.952	1	0.981	1	CLONAL	2	FALSE	0	0.200565768128595	1		340	418	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506320	120506320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	98	379	1	ENST00000256646.2:c.1792G>A	p.Gly598Arg	p.G598R	ENST00000256646	NM_024408.3	598	Ggg/Agg	11/34	0.200565768128595	1	FACETS	1	0.943	1	1	0.988	1	CLONAL	2	FALSE	0	0.200565768128595	1		380	409	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746102	162746102	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs550210469	NA	P-0006682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	66	374	0	ENST00000367921.3:c.2225G>A	p.Arg742Gln	p.R742Q	ENST00000367921	NM_006182.2	742	cGg/cAg	16/18	0.200565768128595	4	FACETS	0.894	0.778	1	0.596	0.519	0.679	CLONAL	2	FALSE	1	0.200565768128595	4		374	442	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202152	67202152	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773369786	NA	P-0006682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	50	356	0	ENST00000312629.5:c.1255C>T	p.Arg419Trp	p.R419W	ENST00000312629	NM_003952.2	419	Cgg/Tgg	14/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.200565768128595	2		356	363	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748815	41748815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774958319	NA	P-0006682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	86	538	0	ENST00000301178.4:c.1340C>T	p.Ser447Leu	p.S447L	ENST00000301178	NM_021913.4	447	tCg/tTg	11/20	1	2	FACETS	0.897	0.797	1	1	0.983	1	CLONAL	2	FALSE	1	0.200565768128595	2		538	478	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855588	45855588	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	48	405	0	ENST00000391945.4:c.2069G>T	p.Arg690Leu	p.R690L	ENST00000391945	NM_000400.3	690	cGg/cTg	22/23	0.195200894294313	3	FACETS	0.921	0.783	1			1	CLONAL	2	FALSE	NA	0.200565768128595	3		405	286	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38978689	38978689	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	36	360	0	ENST00000357387.3:c.817C>G	p.Leu273Val	p.L273V	ENST00000357387	NM_152756.3	273	Ctc/Gtc	9/38	0.519215761431606	3	FACETS	0.278	0.227	0.334	0.139	0.113	0.167	SUBCLONAL	1	TRUE	1	0.519215761431606	3		360	629	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628341	86628341	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	125	268	0	ENST00000274376.6:c.710G>C	p.Gly237Ala	p.G237A	ENST00000274376	NM_002890.2	237	gGa/gCa	3/25	0.519215761431606	3	FACETS	1	0.984	1	0.685	0.624	0.747	CLONAL	1	TRUE	1	0.519215761431606	3		268	443	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287229	46287229	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0006688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	111	242	0	ENST00000334344.6:c.5174C>G	p.Ser1725Ter	p.S1725*	ENST00000334344	NM_152641.2	1725	tCa/tGa	19/21	0.357213908692507	2	FACETS	1	0.98	1	0.646	0.587	0.706	CLONAL	1	TRUE	0	0.519215761431606	2		242	331	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164730	36164730	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	108	386	1	ENST00000300305.3:c.1145C>T	p.Pro382Leu	p.P382L	ENST00000300305		382	cCg/cTg	8/8	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.519215761431606	2		387	397	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696430	47696430	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	371	401	0	ENST00000347630.2:c.393G>C	p.Trp131Cys	p.W131C	ENST00000347630	NM_001007230.1	131	tgG/tgC	6/11	0.705284498396446	4	FACETS	0.989	0.942	1	0.989	0.942	1	CLONAL	2	TRUE	2	0.713319278184342	4		401	901	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165507	118165507	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	263	262	0	ENST00000369448.3:c.17G>C	p.Ser6Thr	p.S6T	ENST00000369448	NM_017709.3	6	aGc/aCc	2/2	0.705284498396446	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	2	0.713319278184342	4		262	623	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372388	55372388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437921769	NA	P-0006692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	87	370	0	ENST00000297316.4:c.1078C>T	p.Arg360Cys	p.R360C	ENST00000297316	NM_022454.3	360	Cgc/Tgc	2/2	0.562360816213764	6	FACETS	0.558	0.493	0.629	0.14	0.123	0.158	SUBCLONAL	1	TRUE	2	0.713319278184342	6		370	1060	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380305	25380305	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0006692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	339	346	0	ENST00000311936.3:c.153T>A	p.Cys51Ter	p.C51*	ENST00000311936	NM_004985.3	51	tgT/tgA	3/5	0.705284498396446	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.713319278184342	4		346	807	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578252	7578299	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCTTCCACTCGGATAAGATGCTGAGGAGGGGCCAGACCTAAGAGCAA	TCCTTCCACTCGGATAAGATGCTGAGGAGGGGCCAGACCTAAGAGCAA	-	novel	NA	P-0006692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	341	489	2	ENST00000269305.4:c.560-10_597del		p.X187_splice	ENST00000269305	NM_001126112.2	187		6/11	0.713319278184342	2	FACETS	0.97	0.934	1	0.97	0.934	1	CLONAL	2	TRUE	0	0.713319278184342	2		491	493	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878816	151878816	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	838	504	0	ENST00000262189.6:c.6129del	p.Phe2043LeufsTer35	p.F2043Lfs*35	ENST00000262189	NM_170606.2	2043	ttT/tt	36/59	0.712171303953882	4	FACETS	0.939	0.92	0.957			1	CLONAL	4	TRUE	NA	0.713319278184342	4		504	1072	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185062	123185062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	11	756	1	ENST00000218089.9:c.1109G>A	p.Arg370Gln	p.R370Q	ENST00000218089	NM_001042749.1	370	cGg/cAg	12/35	0.184798108937487	1	FACETS	0.208	0.142	0.29	0.208	0.142	0.29	SUBCLONAL	1	TRUE	0	0.184798108937487	1		757	520	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939115	76939115	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	33	493	0	ENST00000373344.5:c.1633C>T	p.Gln545Ter	p.Q545*	ENST00000373344	NM_000489.3	545	Caa/Taa	9/35	0.184798108937487	1	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	0	0.184798108937487	1		493	284	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101662	27101663	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0006710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	78	522	0	ENST00000324856.7:c.4948_4949del	p.Gln1650AlafsTer47	p.Q1650Afs*47	ENST00000324856	NM_006015.4	1648	gcCAca/gcca	18/20	0.166574201063081	2	FACETS	0.807	0.711	0.91	0.807	0.711	0.91	CLONAL	2	TRUE	0	0.184798108937487	2		522	523	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577330	64577333	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	rs587776841	NA	P-0006710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	140	645	0	ENST00000312049.6:c.249_252del	p.Ile85SerfsTer33	p.I85Sfs*33	ENST00000312049	NM_130799.2	83	ctGTCT/ct	2/10	0.166574201063081	2	FACETS	0.917	0.836	1	0.917	0.836	1	CLONAL	2	TRUE	0	0.184798108937487	2		645	826	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165172	47165172	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	30	417	0	ENST00000409792.3:c.954del	p.Gly320ValfsTer20	p.G320Vfs*20	ENST00000409792	NM_014159.6	318	ttT/tt	3/21	0.166574201063081	2	FACETS	1	0.839	1	0.522	0.421	0.636	CLONAL	1	TRUE	0	0.184798108937487	2		417	311	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0006729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	50	397	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	0.947	0.803	1	0.947	0.803	1	CLONAL	1	TRUE	1	0.17	2		397	621	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0006729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	33	360	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.674	0.548	0.817	0.674	0.548	0.817	SUBCLONAL	1	TRUE	1	0.17	2		361	576	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181301	123181301	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	53	576	0	ENST00000218089.9:c.765G>C	p.Met255Ile	p.M255I	ENST00000218089	NM_001042749.1	255	atG/atC	9/35	1	2	FACETS	0.679	0.577	0.792	0.679	0.577	0.792	SUBCLONAL	1	TRUE	1	0.17	2		576	918	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	95	422	0	ENST00000269305.4:c.838del	p.Arg280GlufsTer65	p.R280Efs*65	ENST00000269305	NM_001126112.2	280	Aga/ga	8/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.17	2		422	918	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663434	29663440	+	frameshift_variant	Frame_Shift_Del	DEL	GATGGCA	GATGGCA	-	novel	NA	P-0006755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	263	418	0	ENST00000356175.3:c.6030_6036del	p.Met2010IlefsTer4	p.M2010Ifs*4	ENST00000356175	NM_000267.3	2009	gtGATGGCA/gt	40/57	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	FALSE	1	0.281308293586549	2		418	756	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	56	407	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.538833944133087	3	FACETS	0.904	0.793	1	0.904	0.793	1	CLONAL	2	TRUE	1	0.538833944133087	3		407	146	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0006763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	39	219	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	0.538833944133087	2		219	109	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934874	NA	P-0006763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	114	620	0	ENST00000269305.4:c.451C>G	p.Pro151Ala	p.P151A	ENST00000269305	NM_001126112.2	151	Ccc/Gcc	5/11	0.229907948153091	2	FACETS	1	0.986	1	0.748	0.684	0.812	INDETERMINATE	1	TRUE	0	0.538833944133087	2		620	283	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129241	152129241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	64	609	0	ENST00000206249.3:c.194C>T	p.Ala65Val	p.A65V	ENST00000206249	NM_000125.3	65	gCg/gTg	1/8	0.16359573130258	2	FACETS	0.828	0.723	0.939	0.414	0.361	0.47	INDETERMINATE	1	TRUE	0	0.538833944133087	2		609	287	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006194	22006194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	65	503	2	ENST00000276925.6:c.209C>T	p.Ala70Val	p.A70V	ENST00000276925	NM_004936.3	70	gCg/gTg	2/2	0.222044805187682	3	FACETS	1	0.966	1	0.654	0.575	0.738	INDETERMINATE	1	TRUE	1	0.538833944133087	3		505	234	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412569	63412569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	81	318	0	ENST00000330258.3:c.598G>A	p.Val200Ile	p.V200I	ENST00000330258	NM_152424.3	200	Gtc/Atc	2/2	0.469600757369151	2	FACETS	1	0.967	1			1	CLONAL	2	TRUE	NA	0.538833944133087	2		318	134	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0006769-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	394	595	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.656273627902024	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.656273627902024	2		595	565	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587157	189587157	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006769-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	83	458	0	ENST00000264731.3:c.1174A>G	p.Lys392Glu	p.K392E	ENST00000264731	NM_003722.4	392	Aaa/Gaa	9/14	0.154390101920377	5	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.656273627902024	5		458	348	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244280	153244280	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006769-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	139	287	1	ENST00000281708.4:c.1877C>A	p.Ala626Asp	p.A626D	ENST00000281708	NM_033632.3	626	gCt/gAt	12/12	0.656273627902024	2	FACETS	0.917	0.858	0.974	0.917	0.858	0.974	CLONAL	2	TRUE	0	0.656273627902024	2		288	231	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615110	43615110	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006769-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	175	623	0	ENST00000355710.3:c.2524G>C	p.Asp842His	p.D842H	ENST00000355710	NM_020975.4	842	Gat/Cat	14/20	0.61953887196634	3	FACETS	1	0.973	1	0.556	0.514	0.599	CLONAL	1	TRUE	1	0.656273627902024	3		623	637	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129654	11129654	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0006769-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	497	579	0	ENST00000358026.2:c.2460C>G	p.Tyr820Ter	p.Y820*	ENST00000358026	NM_001128849.1	820	taC/taG	17/36	0.62103792505871	5	FACETS	0.975	0.937	1			1	CLONAL	3	TRUE	NA	0.656273627902024	5		579	1028	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820008	36820008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373426288	NA	P-0006772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	215	366	0	ENST00000373129.3:c.580G>A	p.Val194Met	p.V194M	ENST00000373129	NM_032017.1	194	Gtg/Atg	7/12	0.303963743700007	4	FACETS	0.793	0.739	0.848	0.793	0.739	0.848	INDETERMINATE	2	TRUE	2	0.537520632164675	4		366	776	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248468	59248468	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	37	304	0	ENST00000371222.2:c.275C>A	p.Pro92Gln	p.P92Q	ENST00000371222	NM_002228.3	92	cCg/cAg	1/1	0.303963743700007	4	FACETS	0.328	0.27	0.394	0.164	0.135	0.197	INDETERMINATE	1	TRUE	2	0.537520632164675	4		304	645	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162932	47162932	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745925708	NA	P-0006772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	31	321	0	ENST00000409792.3:c.3194G>A	p.Arg1065His	p.R1065H	ENST00000409792	NM_014159.6	1065	cGt/cAt	3/21	0.537520632164675	3	FACETS	0.291	0.235	0.355	0.145	0.117	0.178	SUBCLONAL	1	TRUE	1	0.537520632164675	3		321	503	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557196	187557196	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	30	245	0	ENST00000441802.2:c.4166T>C	p.Leu1389Pro	p.L1389P	ENST00000441802	NM_005245.3	1389	cTt/cCt	6/27	1	2	FACETS	0.237	0.191	0.291	0.237	0.191	0.291	SUBCLONAL	1	TRUE	1	0.537520632164675	2		245	470	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023075	150023075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748057861	NA	P-0006772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	46	378	2	ENST00000253339.5:c.188G>A	p.Arg63Gln	p.R63Q	ENST00000253339		63	cGa/cAa	1/7	0.473030200126126	4	FACETS	0.292	0.245	0.345	0.146	0.122	0.173	SUBCLONAL	1	TRUE	2	0.537520632164675	4		380	900	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399389	139399389	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	26	297	0	ENST00000277541.6:c.4754T>C	p.Leu1585Pro	p.L1585P	ENST00000277541	NM_017617.3	1585	cTg/cCg	26/34	0.537520632164675	3	FACETS	0.232	0.183	0.289	0.116	0.091	0.145	SUBCLONAL	1	TRUE	1	0.537520632164675	3		297	529	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200958	108200958	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	30	203	0	ENST00000278616.4:c.7325A>G	p.Gln2442Arg	p.Q2442R	ENST00000278616	NM_000051.3	2442	cAg/cGg	50/63	0.537520632164675	4	FACETS	0.321	0.258	0.393	0.107	0.086	0.131	SUBCLONAL	1	TRUE	1	0.537520632164675	4		203	534	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	461439	461439	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	153	348	0	ENST00000399788.2:c.1081T>C	p.Tyr361His	p.Y361H	ENST00000399788	NM_001042603.1	361	Tat/Cat	9/28	0.537520632164675	4	FACETS	1	0.95	1	0.351	0.321	0.382	CLONAL	1	TRUE	1	0.537520632164675	4		348	831	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023111	1023111	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	210	349	0	ENST00000358495.3:c.1144A>C	p.Lys382Gln	p.K382Q	ENST00000358495	NM_134424.2	382	Aaa/Caa	11/12	0.537520632164675	4	FACETS	1	0.985	1	0.406	0.377	0.436	CLONAL	1	TRUE	1	0.537520632164675	4		349	986	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857835	57857835	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs749091656	NA	P-0006772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	72	478	0	ENST00000228682.2:c.154A>G	p.Ser52Gly	p.S52G	ENST00000228682	NM_005269.2	52	Agt/Ggt	3/12	NA	2	FACETS	0.332	0.289	0.378			1	INDETERMINATE	1	TRUE	NA	0.537520632164675	2		478	808	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004242	29004242	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766441216	NA	P-0006772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	127	296	1	ENST00000282397.4:c.1051C>T	p.Arg351Trp	p.R351W	ENST00000282397	NM_002019.4	351	Cgg/Tgg	8/30	0.537520632164675	3	FACETS	0.837	0.759	0.919	0.419	0.379	0.46	CLONAL	1	TRUE	1	0.537520632164675	3		297	716	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941741	48941741	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0006772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	15	149	0	ENST00000267163.4:c.1049+2T>C		p.X350_splice	ENST00000267163	NM_000321.2	350			0.537520632164675	3	FACETS	0.256	0.186	0.339	0.128	0.093	0.17	SUBCLONAL	1	TRUE	1	0.537520632164675	3		149	277	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061532	38061532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781269308	NA	P-0006772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	22	182	0	ENST00000250448.2:c.457G>A	p.Ala153Thr	p.A153T	ENST00000250448	NM_004496.3	153	Gcg/Acg	2/2	0.519453136180944	2	FACETS	0.283	0.219	0.357	0.142	0.109	0.179	SUBCLONAL	1	TRUE	0	0.537520632164675	2		182	289	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129586	2129586	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	40	363	0	ENST00000219476.3:c.3313A>G	p.Thr1105Ala	p.T1105A	ENST00000219476	NM_000548.3	1105	Acc/Gcc	29/42	0.537520632164675	3	FACETS	0.266	0.22	0.318	0.089	0.073	0.106	SUBCLONAL	1	TRUE	0	0.537520632164675	3		363	709	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519991	NA	P-0006772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	292	231	1	ENST00000269305.4:c.536A>C	p.His179Pro	p.H179P	ENST00000269305	NM_001126112.2	179	cAt/cCt	5/11	0.537520632164675	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	0	0.537520632164675	3		232	450	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945728	17945728	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	36	311	0	ENST00000458235.1:c.2132T>C	p.Phe711Ser	p.F711S	ENST00000458235	NM_000215.3	711	tTc/tCc	16/24	0.537520632164675	3	FACETS	0.269	0.221	0.324	0.135	0.11	0.162	SUBCLONAL	1	TRUE	1	0.537520632164675	3		311	631	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15840905	15840905	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	45	231	0	ENST00000307771.7:c.989A>G	p.His330Arg	p.H330R	ENST00000307771	NM_005089.3	330	cAt/cGt	11/11	0.537520632164675	2	FACETS	0.454	0.382	0.532	0.227	0.191	0.266	SUBCLONAL	1	TRUE	0	0.537520632164675	2		231	369	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0006772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	42	354	1	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.519453136180944	2	FACETS	0.347	0.29	0.411	0.174	0.145	0.206	SUBCLONAL	1	TRUE	0	0.537520632164675	2		355	450	SUCCESS
CBL	867	MSKCC	GRCh37	11	119145604	119145604	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	41	298	2	ENST00000264033.4:c.815del	p.Leu272Ter	p.L272*	ENST00000264033	NM_005188.3	270	gcT/gc	5/16	0.537520632164675	3	FACETS	0.258	0.214	0.308			1	SUBCLONAL	1	TRUE	NA	0.537520632164675	3		300	749	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390649	139390650	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs763016003	NA	P-0006772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	376	483	0	ENST00000277541.6:c.7541_7542del	p.Pro2514ArgfsTer4	p.P2514Rfs*4	ENST00000277541	NM_017617.3	2514	cCT/c	34/34	0.537520632164675	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.537520632164675	3		483	867	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491390	18491390	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1377942847	NA	P-0006772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	39	230	0	ENST00000266497.5:c.1309del	p.Ile437TyrfsTer5	p.I437Yfs*5	ENST00000266497		435	Aaa/aa	8/31	0.235332020336554	5	FACETS	0.51	0.422	0.608			1	INDETERMINATE	1	TRUE	NA	0.537520632164675	5		230	514	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0006773-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	44	324	2	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.921	0.771	1	0.921	0.771	1	CLONAL	1	TRUE	1	0.15	2		326	637	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913514	NA	P-0006773-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	40	392	0	ENST00000288135.5:c.2466T>A	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaA	17/21	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.15	2		392	486	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286196	66286196	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006773-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	37	434	0	ENST00000273854.3:c.1490G>C	p.Gly497Ala	p.G497A	ENST00000273854	NM_004439.5	497	gGa/gCa	6/18	1	2	FACETS	0.902	0.743	1	0.902	0.743	1	CLONAL	1	TRUE	1	0.15	2		434	547	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591247	67591247	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0006773-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	41	331	0	ENST00000274335.5:c.1746-1G>C		p.X582_splice	ENST00000274335		582			1	2	FACETS	0.964	0.802	1	0.964	0.802	1	CLONAL	1	TRUE	1	0.15	2		331	567	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445257	49445257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs539274614	NA	P-0006773-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	65	437	1	ENST00000301067.7:c.2209C>T	p.Arg737Trp	p.R737W	ENST00000301067	NM_003482.3	737	Cgg/Tgg	10/54	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.15	2		438	824	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0006780-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	43	201	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.658	0.553	0.775	0.658	0.553	0.775	SUBCLONAL	1	TRUE	1	0.38415240185135	2		201	340	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0006780-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	120	321	0	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.38415240185135	2		321	491	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534717	18534717	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006780-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	80	449	0	ENST00000266497.5:c.1775C>G	p.Ser592Cys	p.S592C	ENST00000266497		592	tCt/tGt	12/31	0.38415240185135	1	FACETS	0.58	0.511	0.654	0.58	0.511	0.654	SUBCLONAL	1	TRUE	0	0.38415240185135	1		449	580	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578502	7578502	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555526241	NA	P-0006780-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	159	523	0	ENST00000269305.4:c.428T>G	p.Val143Gly	p.V143G	ENST00000269305	NM_001126112.2	143	gTg/gGg	5/11	0.369180140144704	1	FACETS	0.929	0.853	1	0.929	0.853	1	CLONAL	1	TRUE	0	0.38415240185135	1		523	720	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39763596	39763596	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006780-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	126	433	1	ENST00000288319.7:c.856C>T	p.Gln286Ter	p.Q286*	ENST00000288319	NM_182918.3	286	Cag/Tag	8/10	0.38415240185135	1	FACETS	0.901	0.819	0.987	0.901	0.819	0.987	CLONAL	1	TRUE	0	0.38415240185135	1		434	588	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931643	39931643	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006780-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	217	557	2	ENST00000378444.4:c.2956G>A	p.Ala986Thr	p.A986T	ENST00000378444	NM_001123385.1	986	Gca/Aca	4/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.38415240185135	2		559	1059	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123199747	123199747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006780-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	163	568	0	ENST00000218089.9:c.2047G>A	p.Asp683Asn	p.D683N	ENST00000218089	NM_001042749.1	683	Gat/Aat	21/35	0.38415240185135	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.38415240185135	1		568	663	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717749	89717749	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006780-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	59	231	0	ENST00000371953.3:c.775del	p.His259ThrfsTer7	p.H259Tfs*7	ENST00000371953	NM_000314.4	258	ttC/tt	7/9	0.369180140144704	1	FACETS	0.919	0.798	1	0.919	0.798	1	CLONAL	1	TRUE	0	0.38415240185135	1		231	270	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006786-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	47	145	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.841	0.711	0.985	0.841	0.711	0.985	CLONAL	1	TRUE	1	0.25	2		145	447	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0006786-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	27	229	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.398	0.315	0.492	0.398	0.315	0.492	SUBCLONAL	1	TRUE	1	0.25	2		229	543	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556852	29556852	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0006786-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	125	279	0	ENST00000356175.3:c.2851-1G>A		p.X951_splice	ENST00000356175	NM_000267.3	951			1	2	FACETS	0.855	0.772	0.944	0.855	0.772	0.944	CLONAL	1	TRUE	1	0.25	2		279	1169	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419897	41419897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs577588058	NA	P-0006786-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	135	352	0	ENST00000373198.4:c.424G>A	p.Val142Ile	p.V142I	ENST00000373198	NM_133170.3	142	Gtc/Atc	3/32	1	2	FACETS	0.892	0.809	0.98	0.892	0.809	0.98	CLONAL	1	TRUE	1	0.25	2		352	1211	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006797-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	401	407	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.537903416147086	3	FACETS	0.997	0.952	1	0.997	0.952	1	CLONAL	2	TRUE	1	0.537903416147086	3		407	949	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0006805-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	106	381	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.879	0.788	0.976	0.879	0.788	0.976	CLONAL	1	TRUE	1	0.309925965195301	2		382	778	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0006805-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	168	353	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.309925965195301	2		353	774	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280062	66280062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006805-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	48	428	0	ENST00000273854.3:c.1627C>T	p.Arg543Cys	p.R543C	ENST00000273854	NM_004439.5	543	Cgt/Tgt	7/18	1	2	FACETS	0.362	0.305	0.425	0.362	0.305	0.425	SUBCLONAL	1	TRUE	1	0.309925965195301	2		428	856	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589639	67589639	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006805-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	27	266	1	ENST00000274335.5:c.1402G>T	p.Glu468Ter	p.E468*	ENST00000274335		468	Gaa/Taa	10/15	1	2	FACETS	0.396	0.314	0.489	0.396	0.314	0.489	SUBCLONAL	1	TRUE	1	0.309925965195301	2		267	440	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185163	123185163	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0006805-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	57	372	0	ENST00000218089.9:c.1117-2A>C		p.X373_splice	ENST00000218089	NM_001042749.1	373			1	2	FACETS	0.576	0.493	0.666	0.576	0.493	0.666	SUBCLONAL	1	TRUE	1	0.309925965195301	2		372	639	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217302	11217302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006807-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	474	336	1	ENST00000361445.4:c.4376C>A	p.Ala1459Asp	p.A1459D	ENST00000361445	NM_004958.3	1459	gCc/gAc	30/58	0.132172982697868	4	FACETS	1	0.992	1	1	0.992	1	INDETERMINATE	2	TRUE	2	0.828371455257294	4		337	944	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0006835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	43	299	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.129132761188487	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		299	662	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920452	114920452	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0006835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	73	566	0	ENST00000543371.1:c.1391+2T>C		p.X464_splice	ENST00000543371	NM_001198531.1	464			0.129132761188487	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		566	1226	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0006844-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	286	383	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.247020445203883	5	FACETS	0.939	0.882	0.996	0.939	0.882	0.996	CLONAL	3	TRUE	2	0.247020445203883	5		383	1127	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221123	5221123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769925793	NA	P-0006844-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	81	348	1	ENST00000357368.4:c.3343G>A	p.Ala1115Thr	p.A1115T	ENST00000357368	NM_002850.3	1115	Gcc/Acc	20/38	0.228485935387608	1	FACETS	0.907	0.799	1	0.907	0.799	1	CLONAL	1	TRUE	0	0.247020445203883	1		349	634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576863	7576863	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006844-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	148	320	0	ENST00000269305.4:c.983del	p.Phe328SerfsTer17	p.F328Sfs*17	ENST00000269305	NM_001126112.2	328	tTc/tc	9/11	0.247020445203883	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.247020445203883	1		320	742	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850272	128850272	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs777204354	NA	P-0006844-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	178	416	1	ENST00000249373.3:c.1535G>T	p.Arg512Leu	p.R512L	ENST00000249373	NM_005631.4	512	cGc/cTc	9/12	0.247020445203883	5	FACETS	0.857	0.788	0.928	0.571	0.525	0.619	CLONAL	2	TRUE	2	0.247020445203883	5		417	1153	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687512	29687512	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006844-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	60	286	0	ENST00000356175.3:c.8105A>G	p.Gln2702Arg	p.Q2702R	ENST00000356175	NM_000267.3	2702	cAa/cGa	56/57	0.247020445203883	3	FACETS	0.658	0.566	0.76	0.219	0.188	0.254	SUBCLONAL	1	TRUE	0	0.247020445203883	3		286	829	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21304092	21304092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1001709647	NA	P-0006844-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	150	404	0	ENST00000354336.3:c.871G>A	p.Val291Ile	p.V291I	ENST00000354336	NM_005207.3	291	Gtc/Atc	3/3	0.228485935387608	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.247020445203883	1		404	814	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0006853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	222	451	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.259679126389542	2	FACETS	0.783	0.73	0.838	0.783	0.73	0.838	SUBCLONAL	2	FALSE	0	0.318508685044731	2		452	890	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0006853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	103	268	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.259679126389542	2	FACETS	1	0.972	1	0.617	0.554	0.683	CLONAL	1	FALSE	0	0.318508685044731	2		268	524	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913237	NA	P-0006853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	260	270	0	ENST00000369535.4:c.35G>T	p.Gly12Val	p.G12V	ENST00000369535	NM_002524.4	12	gGt/gTt	2/7	0.318508685044731	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	FALSE	0	0.318508685044731	2		270	811	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133748277	133748277	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	202	350	0	ENST00000318560.5:c.938T>C	p.Ile313Thr	p.I313T	ENST00000318560	NM_005157.4	313	aTc/aCc	6/11	0.161697244510306	4	FACETS	0.917	0.851	0.986	0.917	0.851	0.986	INDETERMINATE	2	FALSE	2	0.318508685044731	4		350	912	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0006881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	36	273	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.675	0.552	0.813	0.675	0.552	0.813	SUBCLONAL	1	TRUE	1	0.13	2		273	821	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0006887-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	267	219	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.422818535089597	4	FACETS	0.919	0.869	0.97	0.689	0.652	0.728	CLONAL	3	TRUE	0	0.455242862481308	4		219	619	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0006887-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	276	391	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.428210339327688	3	FACETS	0.857	0.807	0.909	0.857	0.807	0.909	CLONAL	2	TRUE	1	0.455242862481308	3		391	868	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578281	7578281	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660254	NA	P-0006887-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	595	468	0	ENST00000269305.4:c.568C>A	p.Pro190Thr	p.P190T	ENST00000269305	NM_001126112.2	190	Cct/Act	6/11	0.455242862481308	3	FACETS	0.962	0.93	0.994			1	CLONAL	3	TRUE	NA	0.455242862481308	3		468	1112	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530163	212530163	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006887-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	53	467	0	ENST00000342788.4:c.1756G>T	p.Gly586Cys	p.G586C	ENST00000342788	NM_005235.2	586	Ggc/Tgc	15/28	0.428210339327688	3	FACETS	0.31	0.263	0.362	0.155	0.131	0.181	SUBCLONAL	1	TRUE	1	0.455242862481308	3		467	922	SUCCESS
ATR	545	MSKCC	GRCh37	3	142184010	142184010	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006887-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1212	177	559	0	ENST00000350721.4:c.6970A>G	p.Met2324Val	p.M2324V	ENST00000350721	NM_001184.3	2324	Atg/Gtg	41/47	0.422818535089597	4	FACETS	0.815	0.748	0.884	0.204	0.187	0.221	CLONAL	1	TRUE	0	0.455242862481308	4		559	1389	SUCCESS
APC	324	MSKCC	GRCh37	5	112128142	112128142	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0006887-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	135	363	0	ENST00000257430.4:c.646-1G>A		p.X216_splice	ENST00000257430	NM_000038.5	216			0.455242862481308	1	FACETS	0.858	0.784	0.935	0.858	0.784	0.935	CLONAL	1	TRUE	0	0.455242862481308	1		363	534	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609366	81609366	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1199376210	NA	P-0006887-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	277	685	1	ENST00000298171.2:c.964C>A	p.Leu322Ile	p.L322I	ENST00000298171	NM_000369.2	322	Ctc/Atc	10/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.455242862481308	2		686	1161	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	91	375	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.165821375069217	2	FACETS	1	0.923	1	0.524	0.466	0.587	CLONAL	1	FALSE	0	0.250016875347132	2		377	694	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226595555	226595555	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	75	440	0	ENST00000366794.5:c.76G>C	p.Glu26Gln	p.E26Q	ENST00000366794	NM_001618.3	26	Gag/Cag	1/23	1	2	FACETS	0.64	0.56	0.728	0.64	0.56	0.728	SUBCLONAL	1	FALSE	1	0.250016875347132	2		440	937	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937175	39937175	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	102	254	0	ENST00000378444.4:c.8C>T	p.Ser3Leu	p.S3L	ENST00000378444	NM_001123385.1	3	tCa/tTa	2/15	1	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	0	0.250016875347132	1		254	620	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248780	212248780	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	28	222	0	ENST00000342788.4:c.3487C>G	p.Leu1163Val	p.L1163V	ENST00000342788	NM_005235.2	1163	Ctg/Gtg	28/28	1	2	FACETS	0.593	0.473	0.728	0.593	0.473	0.728	SUBCLONAL	1	FALSE	1	0.250016875347132	2		222	378	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215617244	215617244	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	102	549	0	ENST00000260947.4:c.1604A>T	p.Asp535Val	p.D535V	ENST00000260947	NM_000465.2	535	gAt/gTt	7/11	1	2	FACETS	0.96	0.858	1	0.96	0.858	1	CLONAL	1	FALSE	1	0.250016875347132	2		549	850	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096124	71096124	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	130	311	1	ENST00000318789.4:c.633G>T	p.Gln211His	p.Q211H	ENST00000318789	NM_032682.5	211	caG/caT	10/21	0.165821375069217	2	FACETS	1	0.98	1	0.649	0.589	0.713	CLONAL	1	FALSE	0	0.250016875347132	2		312	801	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851787	134851787	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	169	459	0	ENST00000398015.3:c.1193C>G	p.Ala398Gly	p.A398G	ENST00000398015	NM_004441.4	398	gCc/gGc	5/16	0.165821375069217	2	FACETS	0.75	0.69	0.813	0.75	0.69	0.813	SUBCLONAL	2	FALSE	0	0.250016875347132	2		459	901	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960025	134960025	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	127	481	0	ENST00000398015.3:c.2382G>T	p.Glu794Asp	p.E794D	ENST00000398015	NM_004441.4	794	gaG/gaT	13/16	0.165821375069217	2	FACETS	1	0.967	1	0.574	0.519	0.631	CLONAL	1	FALSE	0	0.250016875347132	2		481	885	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519385	176519385	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	119	477	0	ENST00000292408.4:c.791G>T	p.Gly264Val	p.G264V	ENST00000292408	NM_213647.1	264	gGc/gTc	7/18	0.238060796243249	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	0	0.250016875347132	1		477	754	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675723	30675723	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1312	93	768	0	ENST00000376406.3:c.2633G>T	p.Gly878Val	p.G878V	ENST00000376406	NM_014641.2	878	gGg/gTg	8/15	1	2	FACETS	0.53	0.469	0.595	0.53	0.469	0.595	SUBCLONAL	1	FALSE	1	0.250016875347132	2		768	1405	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652159	36652159	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	56	408	0	ENST00000244741.5:c.281G>C	p.Arg94Pro	p.R94P	ENST00000244741	NM_000389.4	94	cGg/cCg	2/3	1	2	FACETS	0.601	0.514	0.697	0.601	0.514	0.697	SUBCLONAL	1	FALSE	1	0.250016875347132	2		408	745	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068124	94068124	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	184	785	0	ENST00000369303.4:c.838G>T	p.Gly280Cys	p.G280C	ENST00000369303	NM_004440.3	280	Ggc/Tgc	4/17	0.250016875347132	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	0	0.250016875347132	1		785	1077	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459486	50459486	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	97	500	0	ENST00000331340.3:c.775G>C	p.Glu259Gln	p.E259Q	ENST00000331340	NM_006060.4	259	Gag/Cag	7/8	1	2	FACETS	0.795	0.707	0.889	0.795	0.707	0.889	SUBCLONAL	1	FALSE	1	0.250016875347132	2		500	976	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372141	55372141	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs541569463	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	16	139	0	ENST00000297316.4:c.831G>T	p.Glu277Asp	p.E277D	ENST00000297316	NM_022454.3	277	gaG/gaT	2/2	1	2	FACETS	0.489	0.361	0.641	0.489	0.361	0.641	SUBCLONAL	1	FALSE	1	0.250016875347132	2		139	262	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376039	8376039	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	55	519	0	ENST00000356435.5:c.4558C>A	p.Pro1520Thr	p.P1520T	ENST00000356435		1520	Cct/Act	28/35	0.250016875347132	0	FACETS	0.518	0.442	0.601			1	SUBCLONAL	1	FALSE	0	0.250016875347132	0		519	637	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405020	70405020	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	65	503	0	ENST00000373644.4:c.2534A>T	p.His845Leu	p.H845L	ENST00000373644	NM_030625.2	845	cAt/cTt	4/12	1	2	FACETS	0.702	0.607	0.804	0.702	0.607	0.804	SUBCLONAL	1	FALSE	1	0.250016875347132	2		503	741	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	150	578	0	ENST00000267101.3:c.889G>C	p.Asp297His	p.D297H	ENST00000267101	NM_001982.3	297	Gat/Cat	8/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.250016875347132	2		578	937	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865122	57865122	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1427	299	951	0	ENST00000228682.2:c.2599C>A	p.Gln867Lys	p.Q867K	ENST00000228682	NM_005269.2	867	Cag/Aag	12/12	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	1	0.250016875347132	2		951	1726	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578211	28578211	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	125	559	0	ENST00000241453.7:c.2960A>T	p.Gln987Leu	p.Q987L	ENST00000241453	NM_004119.2	987	cAg/cTg	24/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.250016875347132	2		559	864	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32969038	32969038	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	97	662	0	ENST00000380152.3:c.9469G>C	p.Glu3157Gln	p.E3157Q	ENST00000380152		3157	Gag/Cag	25/27	1	2	FACETS	0.774	0.689	0.866	0.774	0.689	0.866	SUBCLONAL	1	FALSE	1	0.250016875347132	2		662	1002	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73340135	73340135	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs377447325	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	90	425	0	ENST00000377767.4:c.1945A>G	p.Ile649Val	p.I649V	ENST00000377767	NM_014953.3	649	Ata/Gta	15/21	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	FALSE	1	0.250016875347132	2		425	662	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437376	110437376	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs776945626	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	22	97	0	ENST00000375856.3:c.1025C>G	p.Ser342Trp	p.S342W	ENST00000375856	NM_003749.2	342	tCg/tGg	1/2	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	FALSE	1	0.250016875347132	2		97	127	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647047	23647047	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	104	559	0	ENST00000261584.4:c.820A>T	p.Thr274Ser	p.T274S	ENST00000261584	NM_024675.3	274	Act/Tct	4/13	0.165821375069217	2	FACETS	1	0.962	1	0.579	0.519	0.644	CLONAL	1	FALSE	0	0.250016875347132	2		559	718	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647305	23647305	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	110	450	1	ENST00000261584.4:c.562G>T	p.Ala188Ser	p.A188S	ENST00000261584	NM_024675.3	188	Gct/Tct	4/13	0.165821375069217	2	FACETS	1	0.982	1	0.719	0.647	0.794	CLONAL	1	FALSE	0	0.250016875347132	2		451	612	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830288	72830288	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	60	690	2	ENST00000268489.5:c.6293C>T	p.Ser2098Leu	p.S2098L	ENST00000268489	NM_006885.3	2098	tCg/tTg	9/10	0.165821375069217	2	FACETS	0.416	0.356	0.48	0.208	0.178	0.24	SUBCLONAL	1	FALSE	0	0.250016875347132	2		692	1155	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618422	37618422	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	136	530	0	ENST00000447079.4:c.98G>C	p.Arg33Thr	p.R33T	ENST00000447079	NM_015083.1	33	aGa/aCa	1/14	0.198617508729899	3	FACETS	1	0.98	1	0.648	0.588	0.71	CLONAL	1	FALSE	1	0.250016875347132	3		530	945	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805429	46805429	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1554	214	858	1	ENST00000290295.7:c.527G>T	p.Gly176Val	p.G176V	ENST00000290295	NM_006361.5	176	gGt/gTt	1/2	0.198617508729899	3	FACETS	1	0.97	1	0.545	0.504	0.587	CLONAL	1	FALSE	1	0.250016875347132	3		859	1768	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007222	62007222	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs756467709	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	132	487	0	ENST00000392795.3:c.460C>A	p.Gln154Lys	p.Q154K	ENST00000392795	NM_001039933.1	154	Cag/Aag	4/6	0.198617508729899	3	FACETS	1	0.97	1	0.585	0.53	0.643	CLONAL	1	FALSE	1	0.250016875347132	3		487	1016	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600046	10600046	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	126	381	0	ENST00000171111.5:c.1532-2A>G		p.X511_splice	ENST00000171111	NM_203500.1	511			0.198969118383593	2	FACETS	1	0.98	1	0.661	0.598	0.726	CLONAL	1	FALSE	0	0.250016875347132	2		381	763	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279935	18279935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	184	435	0	ENST00000222254.8:c.2018C>T	p.Thr673Met	p.T673M	ENST00000222254	NM_005027.3	673	aCg/aTg	16/16	0.198969118383593	2	FACETS	1	0.99	1	0.748	0.69	0.808	CLONAL	1	FALSE	0	0.250016875347132	2		435	984	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796856	42796856	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	202	610	0	ENST00000575354.2:c.3314C>G	p.Ser1105Ter	p.S1105*	ENST00000575354	NM_015125.3	1105	tCa/tGa	14/20	0.198969118383593	2	FACETS	1	0.99	1	0.742	0.687	0.799	CLONAL	1	FALSE	0	0.250016875347132	2		610	1089	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076903	41076903	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	132	640	0	ENST00000373198.4:c.1517G>T	p.Trp506Leu	p.W506L	ENST00000373198	NM_133170.3	506	tGg/tTg	9/32	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.250016875347132	2		640	927	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514546	41514546	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	110	488	1	ENST00000373198.4:c.115A>C	p.Ser39Arg	p.S39R	ENST00000373198	NM_133170.3	39	Agc/Cgc	2/32	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.250016875347132	2		489	764	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256423	46256423	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1266113034	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1277	232	971	0	ENST00000371998.3:c.651G>T	p.Met217Ile	p.M217I	ENST00000371998		217	atG/atT	7/23	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.250016875347132	2		971	1509	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321349	1321349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	82	532	0	ENST00000400841.2:c.406G>T	p.Val136Leu	p.V136L	ENST00000400841		136	Gtg/Ttg	4/6	1	1	FACETS	0.605	0.532	0.683	0.605	0.532	0.683	SUBCLONAL	1	FALSE	0	0.250016875347132	1		532	949	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152106	11152106	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	189	558	0	ENST00000358026.2:c.4390del	p.Asp1464ThrfsTer31	p.D1464Tfs*31	ENST00000358026	NM_001128849.1	1464	Gac/ac	31/36	0.198969118383593	2	FACETS	1	0.988	1	0.698	0.644	0.754	CLONAL	1	FALSE	0	0.250016875347132	2		558	1083	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148529793	148529794	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	C	novel	NA	P-0006895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	102	507	0	ENST00000320356.2:c.295_296delinsG	p.Lys99GlyfsTer3	p.K99Gfs*3	ENST00000320356	NM_004456.4	99	AAg/Gg	4/20	0.250016875347132	2	FACETS	0.959	0.857	1	0.479	0.428	0.534	CLONAL	1	FALSE	0	0.250016875347132	2		507	851	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0006896-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	238	549	1	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.328702628592837	2	FACETS	0.992	0.93	1	0.992	0.93	1	CLONAL	2	TRUE	0	0.328702628592837	2		550	730	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798449	45798449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1428261191	NA	P-0006896-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	232	640	0	ENST00000450313.1:c.562G>A	p.Glu188Lys	p.E188K	ENST00000450313	NM_012222.2	188	Gag/Aag	7/16	0.328702628592837	3	FACETS	0.997	0.932	1	0.997	0.932	1	CLONAL	2	TRUE	1	0.328702628592837	3		640	824	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920381	134920381	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006896-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	196	629	0	ENST00000398015.3:c.2196G>C	p.Met732Ile	p.M732I	ENST00000398015	NM_004441.4	732	atG/atC	12/16	0.328702628592837	2	FACETS	0.917	0.853	0.983	0.917	0.853	0.983	CLONAL	2	TRUE	0	0.328702628592837	2		629	650	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037969	49037969	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	rs587778868	NA	P-0006896-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	99	428	0	ENST00000267163.4:c.2209G>T	p.Glu737Ter	p.E737*	ENST00000267163	NM_000321.2	737	Gag/Tag	21/27	NA	2	FACETS	0.801	0.721	0.885			1	INDETERMINATE	2	TRUE	NA	0.328702628592837	2		428	376	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435612	110435612	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1240327417	NA	P-0006896-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	544	184	1	ENST00000375856.3:c.2789G>A	p.Arg930His	p.R930H	ENST00000375856	NM_003749.2	930	cGc/cAc	1/2	0.328702628592837	10	FACETS	0.994	0.969	1			1	CLONAL	11	TRUE	NA	0.328702628592837	10		185	701	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241417	105241417	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006896-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	225	512	0	ENST00000349310.3:c.563C>G	p.Ala188Gly	p.A188G	ENST00000349310	NM_001014432.1	188	gCc/gGc	7/15	0.328702628592837	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.328702628592837	2		512	607	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646717	23646717	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006896-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	130	582	0	ENST00000261584.4:c.1150G>T	p.Glu384Ter	p.E384*	ENST00000261584	NM_024675.3	384	Gaa/Taa	4/13	0.30871771902027	3	FACETS	0.824	0.75	0.9	0.824	0.75	0.9	CLONAL	2	TRUE	1	0.328702628592837	3		582	559	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387129	31387129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006896-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	170	398	0	ENST00000328111.2:c.1754C>T	p.Ala585Val	p.A585V	ENST00000328111	NM_006892.3	585	gCg/gTg	16/23	0.276984586794068	4	FACETS	0.96	0.885	1	0.96	0.885	1	CLONAL	2	TRUE	2	0.328702628592837	4		398	716	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755665	39755665	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006896-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	132	587	1	ENST00000288319.7:c.1100G>T	p.Arg367Leu	p.R367L	ENST00000288319	NM_182918.3	367	cGc/cTc	10/10	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.328702628592837	2		588	773	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739890	145739956	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CACGGTGGCAGGCCAGACACCTGCAAATGCAGGAGCGACAGCCGTCATACGCCAGCCCAGCCCTGGC	CACGGTGGCAGGCCAGACACCTGCAAATGCAGGAGCGACAGCCGTCATACGCCAGCCCAGCCCTGGC	-	novel	NA	P-0006896-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	92	497	0	ENST00000428558.2:c.1621-47_1640del		p.X541_splice	ENST00000428558	NM_004260.3	541		10/22	NA	2	FACETS	1	0.907	1			1	INDETERMINATE	1	TRUE	NA	0.328702628592837	2		497	549	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059204	27059210	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCCCC	CAGCCCC	-	novel	NA	P-0006896-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	134	562	0	ENST00000324856.7:c.1842_1848del	p.Ala615GlnfsTer2	p.A615Qfs*2	ENST00000324856	NM_006015.4	614	tCAGCCCCc/tc	4/20	0.328702628592837	3	FACETS	0.852	0.778	0.93	0.852	0.778	0.93	CLONAL	2	TRUE	1	0.328702628592837	3		562	557	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	301	145	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.865706888933843	2		145	692	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0006897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	860	556	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.865706888933843	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.865706888933843	1		556	1074	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812317	212812317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143662416	NA	P-0006897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	269	399	1	ENST00000342788.4:c.259G>A	p.Val87Met	p.V87M	ENST00000342788	NM_005235.2	87	Gtg/Atg	3/28	0.313591390542212	1	FACETS	0.32	0.3	0.341	0.32	0.3	0.341	INDETERMINATE	1	TRUE	0	0.865706888933843	1		400	1101	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519219	187519219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774367320	NA	P-0006897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	140	529	0	ENST00000441802.2:c.12164C>T	p.Pro4055Leu	p.P4055L	ENST00000441802	NM_005245.3	4055	cCg/cTg	23/27	0.865706888933843	1	FACETS	0.183	0.166	0.201	0.183	0.166	0.201	SUBCLONAL	1	TRUE	0	0.865706888933843	1		529	1000	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425662	49425662	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	108	432	0	ENST00000301067.7:c.12826G>T	p.Glu4276Ter	p.E4276*	ENST00000301067	NM_003482.3	4276	Gag/Tag	39/54	0.468198980192361	1	FACETS	0.158	0.141	0.176	0.158	0.141	0.176	INDETERMINATE	1	TRUE	0	0.865706888933843	1		432	894	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551052	41551052	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	890	591	0	ENST00000263253.7:c.3196T>A	p.Tyr1066Asn	p.Y1066N	ENST00000263253	NM_001429.3	1066	Tac/Aac	17/31	1	2	FACETS	0.963	0.934	0.993	0.963	0.934	0.993	CLONAL	1	TRUE	1	0.865706888933843	2		591	2135	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0006906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	253	316	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.235789913837104	5	FACETS	1	0.946	1	0.674	0.631	0.717	INDETERMINATE	2	TRUE	2	0.432099366556773	5		316	955	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0006906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	139	405	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.3901541564956	1	FACETS	0.794	0.725	0.866	0.794	0.725	0.866	SUBCLONAL	1	TRUE	0	0.432099366556773	1		405	635	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0006906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	345	440	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.397384796180843	2	FACETS	0.969	0.922	1	0.969	0.922	1	CLONAL	2	TRUE	0	0.432099366556773	2		440	824	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47607058	47607058	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	396	438	0	ENST00000263735.4:c.808G>T	p.Ala270Ser	p.A270S	ENST00000263735	NM_002354.2	270	Gct/Tct	7/9	0.370252340478123	3	FACETS	0.909	0.865	0.954	0.606	0.576	0.636	CLONAL	2	TRUE	0	0.432099366556773	3		438	1226	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686348	30686348	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	128	255	0	ENST00000295754.5:c.204G>T	p.Met68Ile	p.M68I	ENST00000295754	NM_003242.5	68	atG/atT	2/7	0.193915973190466	1	FACETS	0.68	0.617	0.746	0.68	0.617	0.746	INDETERMINATE	1	TRUE	0	0.432099366556773	1		255	683	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665383	138665383	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	107	332	0	ENST00000330315.3:c.182C>T	p.Ala61Val	p.A61V	ENST00000330315	NM_023067.3	61	gCg/gTg	1/1	0.193915973190466	1	FACETS	0.789	0.711	0.871	0.789	0.711	0.871	INDETERMINATE	1	TRUE	0	0.432099366556773	1		332	492	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332936	153332936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	141	220	0	ENST00000281708.4:c.20C>T	p.Ser7Phe	p.S7F	ENST00000281708	NM_033632.3	7	tCt/tTt	2/12	0.412632810754924	2	FACETS	1	0.979	1	0.611	0.56	0.664	CLONAL	1	TRUE	0	0.432099366556773	2		220	534	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405905	157405905	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774701560	NA	P-0006906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	60	301	4	ENST00000346085.5:c.2147C>T	p.Ala716Val	p.A716V	ENST00000346085	NM_020732.3	716	gCg/gTg	6/20	1	2	FACETS	0.435	0.374	0.501	0.435	0.374	0.501	SUBCLONAL	1	TRUE	1	0.432099366556773	2		305	639	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986830	36986830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	77	85	0	ENST00000354822.5:c.859C>T	p.Arg287Cys	p.R287C	ENST00000354822	NM_001079668.2	287	Cgc/Tgc	3/3	0.432305250296212	3	FACETS	0.843	0.75	0.94	0.843	0.75	0.94	CLONAL	2	TRUE	1	0.432099366556773	3		85	257	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438263	56438263	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	262	334	0	ENST00000407977.2:c.730del	p.Ala244ProfsTer175	p.A244Pfs*175	ENST00000407977		244	Gcc/cc	7/10	0.397384796180843	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.432099366556773	2		334	606	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0006915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	129	360	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.314224418274551	3	FACETS	0.98	0.898	1	0.653	0.599	0.709	CLONAL	2	TRUE	0	0.428677680647484	3		361	373	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0006915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	290	88	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.181165438451887	4	FACETS	0.996	0.939	1	0.996	0.939	1	INDETERMINATE	2	TRUE	2	0.428677680647484	4		88	970	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0006915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	200	483	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.181165438451887	4	FACETS	0.755	0.7	0.812	0.755	0.7	0.812	INDETERMINATE	2	TRUE	2	0.428677680647484	4		483	883	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692911	89692911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909241	NA	P-0006915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	120	349	0	ENST00000371953.3:c.395G>A	p.Gly132Asp	p.G132D	ENST00000371953	NM_000314.4	132	gGt/gAt	5/9	0.345035918107263	2	FACETS	1	0.981	1	0.651	0.592	0.712	CLONAL	1	TRUE	0	0.428677680647484	2		349	430	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187560928	187560928	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368776303	NA	P-0006915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	62	362	0	ENST00000441802.2:c.3590C>T	p.Thr1197Ile	p.T1197I	ENST00000441802	NM_005245.3	1197	aCa/aTa	4/27	0.358358937927605	3	FACETS	0.772	0.668	0.884	0.257	0.222	0.295	SUBCLONAL	1	TRUE	0	0.428677680647484	3		362	455	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753154	57753157	+	frameshift_variant	Frame_Shift_Del	DEL	TTTC	TTTC	-	novel	NA	P-0006915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	168	384	0	ENST00000274289.3:c.859_862del	p.Glu287LeufsTer5	p.E287Lfs*5	ENST00000274289	NM_006622.3	287	GAAAct/ct	7/14	0.314224418274551	3	FACETS	1	0.989	1	0.498	0.459	0.538	CLONAL	1	TRUE	0	0.428677680647484	3		384	637	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0006916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	154	528	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.156815742322183	3	FACETS	0.959	0.876	1	0.959	0.876	1	CLONAL	2	TRUE	1	0.16	3		528	1084	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25458581	25458581	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	85	363	0	ENST00000264709.3:c.2592G>A	p.Met864Ile	p.M864I	ENST00000264709	NM_175629.2	864	atG/atA	22/23	1	2	FACETS	0.909	0.801	1	0.909	0.801	1	CLONAL	1	TRUE	1	0.16	2		363	1169	SUCCESS
EED	8726	MSKCC	GRCh37	11	85968615	85968615	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1339838230	NA	P-0006916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	79	380	0	ENST00000263360.6:c.611A>G	p.Asn204Ser	p.N204S	ENST00000263360	NM_003797.3	204	aAt/aGt	6/12	1	2	FACETS	0.918	0.805	1	0.918	0.805	1	CLONAL	1	TRUE	1	0.16	2		380	1076	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426531	47426531	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0006916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	87	424	0	ENST00000377045.4:c.873+1G>T		p.X291_splice	ENST00000377045	NM_001654.4	291			0.3	2	FACETS	1	0.891	1			1	CLONAL	1	TRUE	NA	0.16	2		424	1077	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	263	407	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.487107867796827	2	FACETS	0.863	0.816	0.91	0.863	0.816	0.91	CLONAL	2	TRUE	0	0.519854871058394	2		407	586	SUCCESS
APC	324	MSKCC	GRCh37	5	112174784	112174784	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0006933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	101	449	1	ENST00000257430.4:c.3493A>T	p.Lys1165Ter	p.K1165*	ENST00000257430	NM_000038.5	1165	Aaa/Taa	16/16	1	2	FACETS	0.796	0.715	0.882	0.796	0.715	0.882	SUBCLONAL	1	TRUE	1	0.519854871058394	2		450	488	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99185133	99185133	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0006933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	239	398	2	ENST00000074304.5:c.2533+2T>C		p.X845_splice	ENST00000074304	NM_001134224.1	845			0.473927359823895	3	FACETS	0.924	0.868	0.98	0.924	0.868	0.98	CLONAL	2	TRUE	1	0.519854871058394	3		400	627	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813002	76813002	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	263	547	0	ENST00000373344.5:c.6619C>T	p.Leu2207Phe	p.L2207F	ENST00000373344	NM_000489.3	2207	Ctt/Ttt	30/35	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.519854871058394	2		547	836	SUCCESS
APC	324	MSKCC	GRCh37	5	112157627	112157628	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs1554080698	NA	P-0006933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	119	485	0	ENST00000257430.4:c.1354_1355del	p.Val452SerfsTer7	p.V452Sfs*7	ENST00000257430	NM_000038.5	449	gcTGtg/gctg	11/16	1	2	FACETS	0.886	0.803	0.972	0.886	0.803	0.972	CLONAL	1	TRUE	1	0.519854871058394	2		485	517	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14021950	14021950	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	123	371	0	ENST00000311895.7:c.650C>G	p.Ser217Cys	p.S217C	ENST00000311895	NM_005236.2	217	tCt/tGt	4/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.22	2		371	1016	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2199905	2199905	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	115	488	0	ENST00000398665.3:c.674C>T	p.Ser225Leu	p.S225L	ENST00000398665	NM_032482.2	225	tCa/tTa	8/28	1	2	FACETS	0.836	0.751	0.927	0.836	0.751	0.927	CLONAL	1	TRUE	1	0.22	2		488	1250	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412017	116412034	+	inframe_deletion	In_Frame_Del	DEL	TAGACTACCGAGCTACTT	TAGACTACCGAGCTACTT	-	novel	NA	P-0006941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	102	336	0	ENST00000397752.3:c.3003_3020del	p.Asp1002_Phe1007del	p.D1002_F1007del	ENST00000397752	NM_000245.2	1001	gTAGACTACCGAGCTACTTtt/gtt	14/21	0.243482402953299	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	0	0.22	1		336	812	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217274	66217274	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	70	341	0	ENST00000273854.3:c.2341C>A	p.Leu781Met	p.L781M	ENST00000273854	NM_004439.5	781	Ctg/Atg	14/18	0.644628369373195	2	FACETS	0.22	0.191	0.251	0.11	0.095	0.126	SUBCLONAL	1	TRUE	0	0.794173819037534	2		341	801	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599904	10599904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	401	472	0	ENST00000171111.5:c.1672G>A	p.Gly558Arg	p.G558R	ENST00000171111	NM_203500.1	558	Ggg/Agg	5/6	0.794173819037534	1	FACETS	0.985	0.95	1	0.985	0.95	1	CLONAL	1	TRUE	0	0.794173819037534	1		472	618	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422367	47422367	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0006950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	360	484	0	ENST00000377045.4:c.1A>G	p.Met1?	p.M1?	ENST00000377045	NM_001654.4	1	Atg/Gtg	2/16	0.210083247233453	1	FACETS	0.643	0.612	0.674	0.643	0.612	0.674	INDETERMINATE	1	TRUE	0	0.794173819037534	1		484	850	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0006959-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	175	622	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.280876595855899	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.284461756956602	1		624	943	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188197	10188197	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0006959-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	99	381	1	ENST00000256474.2:c.341-1G>T		p.X114_splice	ENST00000256474	NM_000551.3	114			0.284461756956602	1	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	0	0.284461756956602	1		382	590	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0006962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	82	454	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		454	896	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0006968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	334	375	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	0.991	0.958	1			1	INDETERMINATE	2	TRUE	NA	0.761067913412564	2		377	443	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0006968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	677	353	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.761067913412564	4	FACETS	0.95	0.923	0.977	0.95	0.923	0.977	CLONAL	3	TRUE	1	0.761067913412564	4		353	1099	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743865	40743865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758531464	NA	P-0006968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	272	471	0	ENST00000373198.4:c.3130G>A	p.Val1044Ile	p.V1044I	ENST00000373198	NM_133170.3	1044	Gtc/Atc	23/32	0.457997734601391	4	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.761067913412564	4		471	1092	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420289	49420289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768551828	NA	P-0006968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	266	497	2	ENST00000301067.7:c.15460C>T	p.Arg5154Trp	p.R5154W	ENST00000301067	NM_003482.3	5154	Cgg/Tgg	48/54	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.761067913412564	2		499	668	SUCCESS
APC	324	MSKCC	GRCh37	5	112154963	112154963	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660802	NA	P-0006968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	204	473	0	ENST00000257430.4:c.1234C>T	p.Gln412Ter	p.Q412*	ENST00000257430	NM_000038.5	412	Cag/Tag	10/16	0.761067913412564	1	FACETS	0.933	0.882	0.983	0.933	0.882	0.983	CLONAL	1	TRUE	0	0.761067913412564	1		473	356	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709139	117709139	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	217	419	0	ENST00000368508.3:c.1818G>T	p.Gln606His	p.Q606H	ENST00000368508	NM_002944.2	606	caG/caT	13/43	0.761067913412564	3	FACETS	0.861	0.802	0.923	0.431	0.401	0.462	CLONAL	1	TRUE	1	0.761067913412564	3		419	914	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920438	114920438	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	556	635	2	ENST00000543371.1:c.1379G>A	p.Cys460Tyr	p.C460Y	ENST00000543371	NM_001198531.1	460	tGc/tAc	13/14	0.122855530725321	4	FACETS	1	0.985	1	1	0.985	1	INDETERMINATE	2	TRUE	2	0.761067913412564	4		637	1232	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591807	48591807	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs377767339	NA	P-0006968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	214	423	0	ENST00000342988.3:c.970T>C	p.Cys324Arg	p.C324R	ENST00000342988	NM_005359.5	324	Tgt/Cgt	9/12	0.761067913412564	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.761067913412564	1		423	332	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0006969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	58	375	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.188682138798915	1	FACETS	0.796	0.684	0.919	0.796	0.684	0.919	CLONAL	1	TRUE	0	0.2046272753364	1		377	639	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983042	111983042	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs758371153	NA	P-0006969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1223	79	842	0	ENST00000368678.4:c.1505A>G	p.Lys502Arg	p.K502R	ENST00000368678		502	aAg/aGg	13/13	1	2	FACETS	0.593	0.519	0.673	0.593	0.519	0.673	SUBCLONAL	1	TRUE	1	0.2046272753364	2		842	1302	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724365	52724365	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	84	526	0	ENST00000322088.6:c.1497G>A	p.Met499Ile	p.M499I	ENST00000322088	NM_014225.5	499	atG/atA	12/15	0.2046272753364	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.2046272753364	1		526	694	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543542	9543542	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	93	586	2	ENST00000353224.5:c.1612A>T	p.Thr538Ser	p.T538S	ENST00000353224	NM_177990.2	538	Acc/Tcc	6/10	1	2	FACETS	0.913	0.81	1	0.913	0.81	1	CLONAL	1	TRUE	1	0.2046272753364	2		588	996	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325437	1325437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	116	522	0	ENST00000400841.2:c.238C>T	p.His80Tyr	p.H80Y	ENST00000400841		80	Cac/Tac	3/6	1	1	FACETS	0.989	0.89	1	0.989	0.89	1	CLONAL	1	TRUE	0	0.2046272753364	1		522	1029	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855952	76855952	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006970-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	387	303	0	ENST00000373344.5:c.5648G>A	p.Trp1883Ter	p.W1883*	ENST00000373344	NM_000489.3	1883	tGg/tAg	23/35	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.574126704521336	1		303	908	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692874	89692874	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786204930	NA	P-0006970-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	152	153	0	ENST00000371953.3:c.358G>A	p.Ala120Thr	p.A120T	ENST00000371953	NM_000314.4	120	Gca/Aca	5/9	0.548711782316075	1	FACETS	0.758	0.698	0.82	0.758	0.698	0.82	SUBCLONAL	1	TRUE	0	0.574126704521336	1		153	498	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577514	7577514	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006970-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	215	529	1	ENST00000269305.4:c.767C>A	p.Thr256Lys	p.T256K	ENST00000269305	NM_001126112.2	256	aCa/aAa	7/11	0.574126704521336	1	FACETS	0.737	0.687	0.787	0.737	0.687	0.787	SUBCLONAL	1	TRUE	0	0.574126704521336	1		530	725	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923093	48923094	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0006970-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	169	254	0	ENST00000267163.4:c.543_544del	p.Ser182TyrfsTer2	p.S182Yfs*2	ENST00000267163	NM_000321.2	181	ATa/a	6/27	0.429829305476717	1	FACETS	0.566	0.521	0.612	0.566	0.521	0.612	SUBCLONAL	1	TRUE	0	0.574126704521336	1		254	742	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0006978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	95	229	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.194425923861575	4	FACETS	0.901	0.813	0.99	0.901	0.813	0.99	INDETERMINATE	2	TRUE	2	0.618605167417995	4		229	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0006978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	155	296	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.577588137441594	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.618605167417995	1		296	265	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039610	180039610	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs202140363	NA	P-0006978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	125	342	1	ENST00000261937.6:c.3433C>T	p.Arg1145Cys	p.R1145C	ENST00000261937	NM_182925.4	1145	Cgc/Tgc	26/30	0.267389592875394	0	FACETS	0.499	0.458	0.54			1	INDETERMINATE	1	TRUE	0	0.618605167417995	0		343	309	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732969	30732969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893810	NA	P-0006978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	329	320	0	ENST00000295754.5:c.1582C>T	p.Arg528Cys	p.R528C	ENST00000295754	NM_003242.5	528	Cgt/Tgt	7/7	0.194425923861575	4	FACETS	0.976	0.926	1	0.976	0.926	1	INDETERMINATE	2	TRUE	2	0.618605167417995	4		320	882	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497874	25497874	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	86	363	0	ENST00000264709.3:c.575C>T	p.Ala192Val	p.A192V	ENST00000264709	NM_175629.2	192	gCg/gTg	6/23	1	2	FACETS	0.446	0.395	0.501	0.446	0.395	0.501	SUBCLONAL	1	TRUE	1	0.618605167417995	2		363	623	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851891	134851891	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs769821589	NA	P-0006978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	106	263	1	ENST00000398015.3:c.1297G>A	p.Ala433Thr	p.A433T	ENST00000398015	NM_004441.4	433	Gcc/Acc	5/16	0.194425923861575	4	FACETS	1	0.983	1	0.719	0.65	0.79	INDETERMINATE	1	TRUE	2	0.618605167417995	4		264	386	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980321	55980321	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	52	443	0	ENST00000263923.4:c.770A>C	p.Asp257Ala	p.D257A	ENST00000263923	NM_002253.2	257	gAc/gCc	6/30	0.341784798620108	0	FACETS	0.23	0.197	0.265			1	INDETERMINATE	1	TRUE	0	0.618605167417995	0		443	279	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361249	66361249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	73	299	0	ENST00000273854.3:c.923G>A	p.Gly308Glu	p.G308E	ENST00000273854	NM_004439.5	308	gGg/gAg	4/18	0.341784798620108	0	FACETS	0.291	0.257	0.328			1	INDETERMINATE	1	TRUE	0	0.618605167417995	0		299	309	SUCCESS
APC	324	MSKCC	GRCh37	5	112174466	112174466	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	112	358	0	ENST00000257430.4:c.3175G>T	p.Glu1059Ter	p.E1059*	ENST00000257430	NM_000038.5	1059	Gaa/Taa	16/16	1	2	FACETS	0.794	0.719	0.873	0.794	0.719	0.873	SUBCLONAL	1	TRUE	1	0.618605167417995	2		358	456	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279362	38279362	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	69	531	1	ENST00000425967.3:c.1127A>C	p.Asn376Thr	p.N376T	ENST00000425967	NM_001174067.1	376	aAc/aCc	9/19	0.194425923861575	4	FACETS	0.347	0.301	0.397	0.174	0.15	0.199	INDETERMINATE	1	TRUE	2	0.618605167417995	4		532	1040	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204764	94204764	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	44	308	0	ENST00000323929.3:c.821T>C	p.Leu274Pro	p.L274P	ENST00000323929	NM_005591.3	274	cTt/cCt	8/20	1	2	FACETS	0.34	0.285	0.4	0.34	0.285	0.4	SUBCLONAL	1	TRUE	1	0.618605167417995	2		308	419	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041266	47041266	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0006978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	209	456	0	ENST00000377604.3:c.1693+1G>C		p.X565_splice	ENST00000377604	NM_001204468.1	565			NA	2	FACETS	0.808	0.761	0.855			1	INDETERMINATE	2	TRUE	NA	0.618605167417995	2		456	418	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0006981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	76	396	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	0.695	0.608	0.788	0.695	0.608	0.788	SUBCLONAL	1	TRUE	1	0.254446133220842	2		396	860	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0006981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	1232	593	1	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.254446133220842	13	FACETS	1	0.984	1			1	CLONAL	11	TRUE	NA	0.254446133220842	13		594	2098	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609942	81609942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759709895	NA	P-0006981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	42	421	1	ENST00000298171.2:c.1540G>A	p.Val514Ile	p.V514I	ENST00000298171	NM_000369.2	514	Gtc/Atc	10/10	1	2	FACETS	0.525	0.437	0.622	0.525	0.437	0.622	SUBCLONAL	1	TRUE	1	0.254446133220842	2		422	629	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0006993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	164	409	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	0.433768318924531	2		409	765	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218500	1218500	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1131690951	NA	P-0006993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	144	463	0	ENST00000326873.7:c.374+1A>G		p.X125_splice	ENST00000326873	NM_000455.4	125			NA	2	FACETS	0.84	0.775	0.907			1	INDETERMINATE	2	TRUE	NA	0.433768318924531	2		463	395	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205032	128205032	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113166293	NA	P-0006993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	107	459	2	ENST00000341105.2:c.409C>T	p.Pro137Ser	p.P137S	ENST00000341105	NM_032638.4	137	Cca/Tca	3/6	0.433768318924531	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.433768318924531	1		461	347	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602563	10602563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	26	448	0	ENST00000171111.5:c.1015C>T	p.Leu339Phe	p.L339F	ENST00000171111	NM_203500.1	339	Ctc/Ttc	3/6	0.433768318924531	1	FACETS	0.306	0.242	0.378	0.306	0.242	0.378	SUBCLONAL	1	TRUE	0	0.433768318924531	1		448	307	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610136	10610136	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	57	605	0	ENST00000171111.5:c.574G>T	p.Glu192Ter	p.E192*	ENST00000171111	NM_203500.1	192	Gag/Tag	2/6	0.433768318924531	1	FACETS	0.406	0.348	0.469	0.406	0.348	0.469	SUBCLONAL	1	TRUE	0	0.433768318924531	1		605	507	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156715	20156715	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	173	258	0	ENST00000379607.5:c.42G>T	p.Arg14Ser	p.R14S	ENST00000379607	NM_001412.3	14	agG/agT	2/7	1	1	FACETS	0.868	0.811	0.924	1	0.993	1	CLONAL	2	TRUE	0	0.433768318924531	1		258	360	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045497	47045497	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0006993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	151	318	0	ENST00000377604.3:c.2464A>T	p.Arg822Ter	p.R822*	ENST00000377604	NM_001204468.1	822	Aga/Tga	22/24	1	1	FACETS	0.844	0.785	0.904	1	0.991	1	CLONAL	2	TRUE	0	0.433768318924531	1		318	323	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832404	72832404	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	195	715	1	ENST00000268489.5:c.4177del	p.Val1393CysfsTer32	p.V1393Cfs*32	ENST00000268489	NM_006885.3	1393	Gtg/tg	9/10	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.433768318924531	2		716	897	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127920568	127920568	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	174	460	0	ENST00000373547.4:c.331C>G	p.Arg111Gly	p.R111G	ENST00000373547	NM_002721.4	111	Cga/Gga	4/7	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.411960408507411	2		460	754	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692886	89692886	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	62	169	0	ENST00000371953.3:c.370T>A	p.Cys124Ser	p.C124S	ENST00000371953	NM_000314.4	124	Tgt/Agt	5/9	0.411960408507411	3	FACETS	1	0.964	1	0.66	0.575	0.75	CLONAL	1	TRUE	1	0.411960408507411	3		169	275	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492691	56492691	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	240	429	0	ENST00000407977.2:c.248T>C	p.Met83Thr	p.M83T	ENST00000407977		83	aTg/aCg	2/10	1	2	FACETS	0.994	0.931	1	0.994	0.931	1	CLONAL	1	TRUE	1	0.609899263241054	2		429	792	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0007028-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	437	339	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.63	2		339	1315	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007031-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	143	412	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.165590410818651	4	FACETS	1	0.923	1	1	0.923	1	CLONAL	2	TRUE	2	0.222369460062758	4		412	777	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459760	149459760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007031-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	106	424	1	ENST00000286301.3:c.447G>A	p.Met149Ile	p.M149I	ENST00000286301	NM_005211.3	149	atG/atA	4/22	0.185323191944923	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.222369460062758	1		425	814	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035298	42035298	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007031-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	111	644	0	ENST00000219905.7:c.5140A>G	p.Thr1714Ala	p.T1714A	ENST00000219905	NM_001164273.1	1714	Act/Gct	15/24	1	2	FACETS	0.811	0.727	0.901	0.811	0.727	0.901	CLONAL	1	TRUE	1	0.222369460062758	2		644	1231	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000366	42000366	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1379	81	527	0	ENST00000219905.7:c.2385G>A	p.Trp795Ter	p.W795*	ENST00000219905	NM_001164273.1	795	tgG/tgA	7/24	0.3	1	FACETS	0.529	0.463	0.599	0.529	0.463	0.599	SUBCLONAL	1	TRUE	0	0.19	1		527	1460	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0007074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	142	409	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.18757374099079	3	FACETS	0.95	0.865	1	0.475	0.432	0.52	INDETERMINATE	1	TRUE	1	0.379641270738481	3		409	937	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151921520	151921520	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	14	56	0	ENST00000262189.6:c.3158G>T	p.Trp1053Leu	p.W1053L	ENST00000262189	NM_170606.2	1053	tGg/tTg	19/59	1	2	FACETS	0.509	0.37	0.675	0.509	0.37	0.675	SUBCLONAL	1	TRUE	1	0.379641270738481	2		56	145	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954150	32954150	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	120	228	0	ENST00000380152.3:c.9124G>A	p.Asp3042Asn	p.D3042N	ENST00000380152		3042	Gat/Aat	24/27	1	2	FACETS	0.788	0.712	0.869	0.788	0.712	0.869	SUBCLONAL	1	TRUE	1	0.379641270738481	2		228	802	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602337	10602337	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	148	394	0	ENST00000171111.5:c.1241A>T	p.Asn414Ile	p.N414I	ENST00000171111	NM_203500.1	414	aAc/aTc	3/6	0.379641270738481	1	FACETS	0.956	0.875	1	0.956	0.875	1	CLONAL	1	TRUE	0	0.379641270738481	1		394	661	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966645	36966645	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	90	306	0	ENST00000358127.4:c.681del	p.Leu228CysfsTer50	p.L228Cfs*50	ENST00000358127	NM_001280556.1	227	gaC/ga	6/10	NA	2	FACETS	0.768	0.683	0.86			1	INDETERMINATE	1	TRUE	NA	0.379641270738481	2		306	617	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220643	1220662	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCCCGAGATTGCCAACGG	CCGCCCGAGATTGCCAACGG	GCGC	novel	NA	P-0007074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	87	329	0	ENST00000326873.7:c.661_680delinsGCGC	p.Pro221AlafsTer61	p.P221Afs*61	ENST00000326873	NM_000455.4	221	CCGCCCGAGATTGCCAACGGc/GCGCc	5/10	0.379641270738481	1	FACETS	0.785	0.698	0.878	0.785	0.698	0.878	SUBCLONAL	1	TRUE	0	0.379641270738481	1		329	473	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0007075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	71	273	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.19	2		273	697	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745588	162745588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754868982	NA	P-0007075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	88	300	0	ENST00000367921.3:c.2003G>A	p.Arg668His	p.R668H	ENST00000367921	NM_006182.2	668	cGc/cAc	15/18	1	2	FACETS	0.911	0.805	1	0.911	0.805	1	CLONAL	1	TRUE	1	0.19	2		300	1017	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0007091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	623	415	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.924742802568423	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.924742802568423	1		415	709	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923059	39923059	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	873	307	0	ENST00000378444.4:c.3649C>T	p.Arg1217Ter	p.R1217*	ENST00000378444	NM_001123385.1	1217	Cga/Tga	8/15	1	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.924742802568423	1		307	946	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981456	55981456	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	567	437	0	ENST00000263923.4:c.481C>A	p.Leu161Ile	p.L161I	ENST00000263923	NM_002253.2	161	Ctt/Att	4/30	0.924742802568423	1	FACETS	0.984	0.964	1	0.984	0.964	1	CLONAL	1	TRUE	0	0.924742802568423	1		437	670	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939014	131939014	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	403	259	0	ENST00000265335.6:c.2230G>A	p.Glu744Lys	p.E744K	ENST00000265335		744	Gag/Aag	14/25	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.924742802568423	2		259	844	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410108	139410108	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	549	346	0	ENST00000277541.6:c.1730A>G	p.Tyr577Cys	p.Y577C	ENST00000277541	NM_017617.3	577	tAc/tGc	11/34	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.924742802568423	2		346	1177	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881542	48881542	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	424	262	0	ENST00000267163.4:c.264G>T	p.Leu88Phe	p.L88F	ENST00000267163	NM_000321.2	88	ttG/ttT	2/27	0.924742802568423	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.924742802568423	1		262	490	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215920	41215920	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28897696	NA	P-0007091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	560	370	1	ENST00000357654.3:c.5123C>A	p.Ala1708Glu	p.A1708E	ENST00000357654	NM_007294.3	1708	gCg/gAg	17/23	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.924742802568423	2		371	1175	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	49	412	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.769	0.65	0.899	0.769	0.65	0.899	SUBCLONAL	1	TRUE	1	0.21	2		412	607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0007094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	107	493	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.21	2		495	1006	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0007094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	88	324	2	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.21	2		326	732	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0007094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	37	297	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.745	0.614	0.892	0.745	0.614	0.892	SUBCLONAL	1	TRUE	1	0.21	2		297	473	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101090	26101090	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0007094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	67	535	0	ENST00000435504.4:c.2T>C	p.Met1?	p.M1?	ENST00000435504		1	aTg/aCg	1/13	1	2	FACETS	0.713	0.618	0.816	0.713	0.618	0.816	SUBCLONAL	1	TRUE	1	0.21	2		535	895	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276250	15276250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747223569	NA	P-0007094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	109	549	2	ENST00000263388.2:c.5744G>A	p.Arg1915His	p.R1915H	ENST00000263388	NM_000435.2	1915	cGc/cAc	31/33	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.21	2		551	1004	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670707	86670707	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	130	267	0	ENST00000274376.6:c.1985C>A	p.Thr662Lys	p.T662K	ENST00000274376	NM_002890.2	662	aCa/aAa	15/25	1	2	FACETS	0.774	0.705	0.846	0.774	0.705	0.846	SUBCLONAL	1	NA	1	0.596996990001896	2		267	563	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814265	76814265	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	359	582	1	ENST00000373344.5:c.6379G>T	p.Val2127Leu	p.V2127L	ENST00000373344	NM_000489.3	2127	Gta/Tta	29/35	0.596996990001896	1	FACETS	0.968	0.921	1	0.968	0.921	1	CLONAL	1	NA	0	0.596996990001896	1		583	872	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007112-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	230	407	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.277544692399688	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.22	3		407	1089	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0007112-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	50	219	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.206195436934847	2	FACETS	0.816	0.692	0.952	0.408	0.346	0.476	CLONAL	1	TRUE	0	0.22	2		219	557	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0007112-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	114	365	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.884	0.794	0.98	0.884	0.794	0.98	CLONAL	1	TRUE	1	0.22	2		365	1172	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0007112-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	78	228	0	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.22	2		228	699	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984241	7984241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007112-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	82	360	2	ENST00000319144.4:c.488G>A	p.Arg163His	p.R163H	ENST00000319144	NM_001139.2	163	cGc/cAc	4/15	0.206195436934847	3	FACETS	0.915	0.806	1	0.458	0.403	0.517	CLONAL	1	TRUE	1	0.22	3		362	904	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054221	30054221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007112-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1185	147	452	0	ENST00000338641.4:c.643G>A	p.Glu215Lys	p.E215K	ENST00000338641	NM_000268.3	215	Gag/Aag	7/16	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.22	2		452	1332	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	177	407	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.32	2		407	857	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722927	49722927	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776261411	NA	P-0007138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	39	228	0	ENST00000449682.2:c.1400C>T	p.Pro467Leu	p.P467L	ENST00000449682	NM_020998.3	467	cCg/cTg	12/18	0.288266507234961	3	FACETS	0.978	0.815	1	0.489	0.407	0.58	CLONAL	1	TRUE	1	0.32	3		228	289	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307934	11307934	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	106	520	0	ENST00000361445.4:c.1058A>C	p.Lys353Thr	p.K353T	ENST00000361445	NM_004958.3	353	aAg/aCg	7/58	0.0842435641842969	3	FACETS	1	0.923	1			1	INDETERMINATE	1	TRUE	NA	0.32	3		520	743	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973019	25973019	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	71	464	0	ENST00000435504.4:c.1406T>A	p.Leu469His	p.L469H	ENST00000435504		469	cTc/cAc	12/13	0.298088417885657	1	FACETS	0.495	0.431	0.564	0.495	0.431	0.564	SUBCLONAL	1	TRUE	0	0.32	1		464	753	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271234	1271234	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	46	322	0	ENST00000310581.5:c.2468A>G	p.Lys823Arg	p.K823R	ENST00000310581	NM_198253.2	823	aAg/aGg	8/16	0.0700005546219251	3	FACETS	0.894	0.755	1			1	INDETERMINATE	1	TRUE	NA	0.32	3		322	373	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971181	13971181	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	83	386	0	ENST00000405192.2:c.748T>C	p.Phe250Leu	p.F250L	ENST00000405192	NM_001163147.1	250	Ttt/Ctt	8/12	0.193357182306363	3	FACETS	0.878	0.775	0.989	0.293	0.258	0.33	CLONAL	1	TRUE	0	0.32	3		386	685	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557603	21557603	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	59	485	0	ENST00000382592.4:c.2242A>G	p.Ile748Val	p.I748V	ENST00000382592	NM_014572.2	748	Atc/Gtc	5/8	0.298088417885657	7	FACETS	0.685	0.587	0.792			1	SUBCLONAL	1	TRUE	NA	0.32	7		485	969	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857998	9857998	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	70	525	0	ENST00000330684.3:c.3403T>G	p.Phe1135Val	p.F1135V	ENST00000330684	NM_001134407.1	1135	Ttt/Gtt	13/13	0.288266507234961	3	FACETS	0.954	0.833	1	0.477	0.416	0.542	CLONAL	1	TRUE	1	0.32	3		525	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577560	7577560	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	252	488	0	ENST00000269305.4:c.721T>A	p.Ser241Thr	p.S241T	ENST00000269305	NM_001126112.2	241	Tcc/Acc	7/11	0.127956986987824	4	FACETS	1	0.97	1			1	INDETERMINATE	3	TRUE	NA	0.32	4		488	662	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980892	40980892	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	40	339	0	ENST00000373198.4:c.1594A>G	p.Ser532Gly	p.S532G	ENST00000373198	NM_133170.3	532	Agt/Ggt	10/32	1	2	FACETS	0.441	0.366	0.525	0.441	0.366	0.525	SUBCLONAL	1	TRUE	1	0.32	2		339	567	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858237	27858238	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs763163035	NA	P-0007138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1775	179	852	0	ENST00000359303.2:c.333_334del	p.Ala112TyrfsTer11	p.A112Yfs*11	ENST00000359303	NM_003535.2	111	tgTGct/tgct	1/1	0.298088417885657	6	FACETS	0.939	0.862	1	0.235	0.215	0.255	CLONAL	1	TRUE	2	0.32	6		852	1954	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853361	151853361	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007139-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	378	406	0	ENST00000262189.6:c.11741A>G	p.Gln3914Arg	p.Q3914R	ENST00000262189	NM_170606.2	3914	cAg/cGg	45/59	0.372104983071755	4	FACETS	0.949	0.901	0.998	0.633	0.601	0.666	CLONAL	2	FALSE	1	0.458370966967412	4		406	1267	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371654	55371654	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007139-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	255	514	0	ENST00000297316.4:c.344G>A	p.Arg115Gln	p.R115Q	ENST00000297316	NM_022454.3	115	cGg/cAg	2/2	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	1	0.458370966967412	2		514	1089	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0007155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	309	409	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.619761466356517	4	FACETS	1	0.986	1			1	CLONAL	3	TRUE	NA	0.619761466356517	4		409	503	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696708	47696708	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	152	406	0	ENST00000347630.2:c.240C>G	p.Ser80Arg	p.S80R	ENST00000347630	NM_001007230.1	80	agC/agG	5/11	0.146138815270756	5	FACETS	1	0.982	1	0.803	0.743	0.864	INDETERMINATE	2	TRUE	2	0.619761466356517	5		406	393	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0007155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	571	175	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	0.619761466356517	2	FACETS	0.907	0.889	0.925	1	0.998	1	CLONAL	3	TRUE	0	0.619761466356517	2		175	677	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65316512	65316512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	40	317	1	ENST00000342505.4:c.1730G>A	p.Arg577Gln	p.R577Q	ENST00000342505	NM_002227.2	577	cGg/cAg	12/25	1	2	FACETS	0.171	0.141	0.204	0.171	0.141	0.204	SUBCLONAL	1	TRUE	1	0.619761466356517	2		318	754	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412310	63412337	+	frameshift_variant	Frame_Shift_Del	DEL	CTATGGGGCTCCTCTAGGCTACTGGCTT	CTATGGGGCTCCTCTAGGCTACTGGCTT	-	novel	NA	P-0007155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	39	546	0	ENST00000330258.3:c.830_857del	p.Glu277AlafsTer8	p.E277Afs*8	ENST00000330258	NM_152424.3	277	gAAGCCAGTAGCCTAGAGGAGCCCCATAGc/gc	2/2	0.346741507592202	1	FACETS	0.132	0.109	0.158	0.132	0.109	0.158	INDETERMINATE	1	TRUE	0	0.619761466356517	1		546	658	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0007165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	31	273	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.343	0.276	0.42	0.343	0.276	0.42	SUBCLONAL	1	TRUE	1	0.2	2		273	903	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934874	NA	P-0007165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	102	562	2	ENST00000269305.4:c.451C>A	p.Pro151Thr	p.P151T	ENST00000269305	NM_001126112.2	151	Ccc/Acc	5/11	1	2	FACETS	0.986	0.88	1	0.986	0.88	1	CLONAL	1	TRUE	1	0.2	2		564	1034	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211416	98211416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369966295	NA	P-0007165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	43	508	1	ENST00000331920.6:c.3739G>A	p.Ala1247Thr	p.A1247T	ENST00000331920	NM_000264.3	1247	Gcg/Acg	22/24	1	2	FACETS	0.515	0.429	0.611	0.515	0.429	0.611	SUBCLONAL	1	TRUE	1	0.2	2		509	835	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0007171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	36	565	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.415	0.339	0.5	0.415	0.339	0.5	SUBCLONAL	1	TRUE	1	0.18	2		565	964	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0007172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	240	580	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	0.497708227729876	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	0	0.497708227729876	1		580	678	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274102	10274102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	73	505	2	ENST00000330684.3:c.167G>A	p.Gly56Asp	p.G56D	ENST00000330684	NM_001134407.1	56	gGc/gAc	2/13	1	2	FACETS	0.453	0.396	0.514	0.453	0.396	0.514	SUBCLONAL	1	FALSE	1	0.497708227729876	2		507	648	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041486	14041486	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	183	367	0	ENST00000311895.7:c.2033A>G	p.Asn678Ser	p.N678S	ENST00000311895	NM_005236.2	678	aAt/aGt	11/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.497708227729876	2		367	700	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118696	11118696	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	58	692	0	ENST00000358026.2:c.2120T>C	p.Ile707Thr	p.I707T	ENST00000358026	NM_001128849.1	707	aTt/aCt	14/36	1	2	FACETS	0.268	0.229	0.311	0.268	0.229	0.311	SUBCLONAL	1	FALSE	1	0.497708227729876	2		692	869	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs748696421	NA	P-0007179-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	11	408	1	ENST00000397062.3:c.100C>T	p.Arg34Ter	p.R34*	ENST00000397062	NM_006164.4	34	Cga/Tga	2/5	0.14466139614358	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		409	402	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0007180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	125	229	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.394898448944359	3	FACETS	1	0.917	1	0.506	0.459	0.557	CLONAL	1	TRUE	1	0.415071416896242	3		229	718	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0007180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	159	406	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.415071416896242	3	FACETS	0.84	0.768	0.914	0.42	0.384	0.457	CLONAL	1	TRUE	1	0.415071416896242	3		406	1102	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0007180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	347	412	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	2	TRUE	NA	0.415071416896242	2		413	797	SUCCESS
APC	324	MSKCC	GRCh37	5	112175328	112175328	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	284	344	0	ENST00000257430.4:c.4037C>A	p.Ser1346Ter	p.S1346*	ENST00000257430	NM_000038.5	1346	tCa/tAa	16/16	0.415071416896242	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.415071416896242	3		344	786	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532546	63532546	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs368798367	NA	P-0007184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	92	386	0	ENST00000307078.5:c.2033T>C	p.Leu678Pro	p.L678P	ENST00000307078	NM_004655.3	678	cTg/cCg	8/11	1	2	FACETS	0.864	0.767	0.967	0.864	0.767	0.967	CLONAL	1	TRUE	1	0.27	2		386	789	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574002	7574002	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs375338359	NA	P-0007219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	97	602	0	ENST00000269305.4:c.1025G>C	p.Arg342Pro	p.R342P	ENST00000269305	NM_001126112.2	342	cGa/cCa	10/11	1	2	FACETS	0.814	0.724	0.909	0.814	0.724	0.909	CLONAL	1	TRUE	1	0.27	2		602	883	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0007236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	191	411	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.391570554244096	3	FACETS	0.805	0.75	0.861	0.805	0.75	0.861	CLONAL	2	TRUE	1	0.582375104312231	3		411	526	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045718	47045718	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	175	246	0	ENST00000377604.3:c.2599C>T	p.Gln867Ter	p.Q867*	ENST00000377604	NM_001204468.1	867	Cag/Tag	23/24	0.464090208256613	2	FACETS	0.969	0.912	1			1	CLONAL	2	TRUE	NA	0.582375104312231	2		246	310	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428527	78428527	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	37	470	0	ENST00000370768.2:c.1272G>C	p.Met424Ile	p.M424I	ENST00000370768	NM_003902.3	424	atG/atC	14/20	0.251675883240162	5	FACETS	0.323	0.265	0.388	0.108	0.088	0.13	INDETERMINATE	1	TRUE	2	0.582375104312231	5		470	737	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851274	156851274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751281792	NA	P-0007236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	59	444	0	ENST00000524377.1:c.2231G>A	p.Arg744His	p.R744H	ENST00000524377	NM_002529.3	744	cGt/cAt	17/17	0.226429973899106	5	FACETS	0.857	0.739	0.985	0.171	0.147	0.197	INDETERMINATE	1	TRUE	0	0.582375104312231	5		444	443	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991706	25991706	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	66	380	0	ENST00000435504.4:c.536A>G	p.Gln179Arg	p.Q179R	ENST00000435504		179	cAg/cGg	7/13	0.464090208256613	3	FACETS	0.443	0.384	0.507			1	SUBCLONAL	1	TRUE	NA	0.582375104312231	3		380	660	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702410	47702410	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs267607986	NA	P-0007236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	85	186	0	ENST00000233146.2:c.2005+1G>T		p.X669_splice	ENST00000233146	NM_000251.2	669			0.201029860810369	4	FACETS	0.799	0.715	0.887	0.799	0.715	0.887	INDETERMINATE	2	TRUE	2	0.582375104312231	4		186	289	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521670	89521670	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	45	495	1	ENST00000336596.2:c.2747C>A	p.Thr916Lys	p.T916K	ENST00000336596	NM_005233.5	916	aCa/aAa	16/17	NA	2	FACETS	0.463	0.39	0.542			1	INDETERMINATE	1	TRUE	NA	0.582375104312231	2		496	334	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131895051	131895051	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	88	254	0	ENST00000265335.6:c.205G>T	p.Asp69Tyr	p.D69Y	ENST00000265335		69	Gat/Tat	2/25	0.290307696197123	1	FACETS	0.475	0.423	0.53	0.475	0.423	0.53	INDETERMINATE	1	TRUE	0	0.582375104312231	1		254	451	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670945	30670945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	148	511	1	ENST00000376406.3:c.5801C>T	p.Thr1934Ile	p.T1934I	ENST00000376406	NM_014641.2	1934	aCa/aTa	12/15	0.31904089331986	5	FACETS	1	0.984	1	0.444	0.406	0.484	INDETERMINATE	1	TRUE	2	0.582375104312231	5		512	715	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509340	106509340	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	52	484	1	ENST00000359195.3:c.1334C>A	p.Ala445Asp	p.A445D	ENST00000359195	NM_002649.2	445	gCc/gAc	2/11	0.391570554244096	3	FACETS	0.398	0.338	0.463	0.199	0.169	0.232	SUBCLONAL	1	TRUE	1	0.582375104312231	3		485	580	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507340	8507340	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	25	536	0	ENST00000356435.5:c.1638C>A	p.Asn546Lys	p.N546K	ENST00000356435		546	aaC/aaA	11/35	0.582375104312231	0	FACETS	0.18	0.143	0.223			1	SUBCLONAL	1	TRUE	0	0.582375104312231	0		536	199	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250173	110250173	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	57	282	0	ENST00000374672.4:c.502G>T	p.Gly168Cys	p.G168C	ENST00000374672	NM_004235.4	168	Ggc/Tgc	3/5	0.290307696197123	1	FACETS	0.595	0.517	0.679	0.595	0.517	0.679	INDETERMINATE	1	TRUE	0	0.582375104312231	1		282	233	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425496	49425496	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	38	701	1	ENST00000301067.7:c.12992C>T	p.Pro4331Leu	p.P4331L	ENST00000301067	NM_003482.3	4331	cCc/cTc	39/54	0.218080772280778	2	FACETS	0.238	0.196	0.285	0.119	0.098	0.143	INDETERMINATE	1	TRUE	0	0.582375104312231	2		702	548	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39647351	39647351	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0007236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	74	507	1	ENST00000262039.4:c.2524-1G>T		p.X842_splice	ENST00000262039	NM_002647.2	842			0.582375104312231	1	FACETS	0.491	0.432	0.553	0.491	0.432	0.553	SUBCLONAL	1	TRUE	0	0.582375104312231	1		508	367	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144114	11144114	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	38	491	1	ENST00000358026.2:c.3695G>A	p.Gly1232Asp	p.G1232D	ENST00000358026	NM_001128849.1	1232	gGc/gAc	26/36	0.391570554244096	3	FACETS	0.296	0.244	0.354	0.148	0.122	0.177	SUBCLONAL	1	TRUE	1	0.582375104312231	3		492	569	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285135	15285135	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	156	432	0	ENST00000263388.2:c.4480G>T	p.Gly1494Cys	p.G1494C	ENST00000263388	NM_000435.2	1494	Ggc/Tgc	25/33	0.391570554244096	3	FACETS	0.901	0.835	0.967	0.901	0.835	0.967	CLONAL	2	TRUE	1	0.582375104312231	3		432	384	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044587	47044587	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	35	220	0	ENST00000377604.3:c.2084C>G	p.Ala695Gly	p.A695G	ENST00000377604	NM_001204468.1	695	gCc/gGc	18/24	0.464090208256613	2	FACETS	0.365	0.3	0.438			1	SUBCLONAL	1	TRUE	NA	0.582375104312231	2		220	329	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345913	70345913	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	35	259	0	ENST00000374080.3:c.2450G>T	p.Arg817Leu	p.R817L	ENST00000374080		817	cGc/cTc	18/45	0.464090208256613	2	FACETS	0.306	0.251	0.368			1	SUBCLONAL	1	TRUE	NA	0.582375104312231	2		259	393	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082361	16082361	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	29	413	0	ENST00000281043.3:c.179del	p.Pro60ArgfsTer71	p.P60Rfs*71	ENST00000281043	NM_005378.4	59	Ccc/cc	2/3	0.464090208256613	3	FACETS	0.402	0.323	0.491			1	SUBCLONAL	1	TRUE	NA	0.582375104312231	3		413	320	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0007240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	149	409	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.20244509027747	3	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	1	0.18	3		409	866	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039610	47039610	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0007240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	34	169	0	ENST00000377604.3:c.1063-1G>A		p.X355_splice	ENST00000377604	NM_001204468.1	355			1	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.18	1		169	266	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199854	108199854	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1565526758	NA	P-0007240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	74	356	0	ENST00000278616.4:c.7196A>G	p.Gln2399Arg	p.Q2399R	ENST00000278616	NM_000051.3	2399	cAa/cGa	49/63	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.18	2		356	806	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433955	149433955	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	53	468	3	ENST00000286301.3:c.2693C>A	p.Thr898Asn	p.T898N	ENST00000286301	NM_005211.3	898	aCc/aAc	21/22	0.20244509027747	3	FACETS	0.914	0.778	1	0.457	0.389	0.532	CLONAL	1	TRUE	1	0.18	3		471	702	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955516	90955516	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780093	NA	P-0007240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	78	409	0	ENST00000265433.3:c.2149A>G	p.Thr717Ala	p.T717A	ENST00000265433	NM_002485.4	717	Aca/Gca	14/16	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.18	2		409	807	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485983	8485983	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	47	549	0	ENST00000356435.5:c.2834C>A	p.Ala945Glu	p.A945E	ENST00000356435		945	gCa/gAa	17/35	1	2	FACETS	0.595	0.501	0.701	0.595	0.501	0.701	SUBCLONAL	1	TRUE	1	0.18	2		549	877	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519999	NA	P-0007240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	57	447	0	ENST00000269305.4:c.716A>G	p.Asn239Ser	p.N239S	ENST00000269305	NM_001126112.2	239	aAc/aGc	7/11	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.18	2		447	583	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805730	46805730	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1390422355	NA	P-0007240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	47	509	2	ENST00000290295.7:c.226G>T	p.Ala76Ser	p.A76S	ENST00000290295	NM_006361.5	76	Gct/Tct	1/2	1	2	FACETS	0.692	0.582	0.813	0.692	0.582	0.813	SUBCLONAL	1	TRUE	1	0.18	2		511	755	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292614	15292614	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0007240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	26	287	0	ENST00000263388.2:c.2567-2A>T		p.X856_splice	ENST00000263388	NM_000435.2	856			1	2	FACETS	0.666	0.526	0.826	0.666	0.526	0.826	SUBCLONAL	1	TRUE	1	0.18	2		287	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0007279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	77	375	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.34073651275576	1	FACETS	0.701	0.617	0.79	0.701	0.617	0.79	SUBCLONAL	1	TRUE	0	0.383578275049183	1		377	463	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0007279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	142	273	2	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.34073651275576	1	FACETS	0.862	0.787	0.94	0.862	0.787	0.94	CLONAL	1	TRUE	0	0.383578275049183	1		275	694	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0007279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	107	406	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.347219069535228	2	FACETS	1	0.982	1	0.713	0.645	0.784	CLONAL	1	TRUE	0	0.383578275049183	2		406	391	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665048	138665048	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	16	18	0	ENST00000330315.3:c.517G>T	p.Ala173Ser	p.A173S	ENST00000330315	NM_023067.3	173	Gca/Tca	1/1	1	2	FACETS	0.993	0.8	1	1	0.949	1	CLONAL	3	TRUE	1	0.383578275049183	2		18	28	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76764082	76764082	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs782233676	NA	P-0007279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	35	289	0	ENST00000373344.5:c.7226T>G	p.Leu2409Arg	p.L2409R	ENST00000373344	NM_000489.3	2409	cTt/cGt	35/35	0.12634169734938	2	FACETS	0.499	0.409	0.599			1	INDETERMINATE	1	TRUE	NA	0.383578275049183	2		289	366	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	213	407	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.279372533631709	3	FACETS	0.864	0.808	0.922	0.864	0.808	0.922	INDETERMINATE	2	TRUE	1	0.488394431509365	3		407	628	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0007287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	109	396	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.488394431509365	2		396	321	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161281	56161281	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	67	208	0	ENST00000399503.3:c.1150G>A	p.Glu384Lys	p.E384K	ENST00000399503	NM_005921.1	384	Gag/Aag	5/20	0.267511698462485	4	FACETS	1	0.972	1	0.719	0.631	0.812	INDETERMINATE	1	TRUE	2	0.488394431509365	4		208	284	SUCCESS
APC	324	MSKCC	GRCh37	5	112174412	112174412	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	67	280	0	ENST00000257430.4:c.3121C>T	p.Gln1041Ter	p.Q1041*	ENST00000257430	NM_000038.5	1041	Caa/Taa	16/16	NA	2	FACETS	1	0.945	1			1	INDETERMINATE	1	TRUE	NA	0.488394431509365	2		280	242	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480083	20480083	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	100	340	1	ENST00000346618.3:c.400C>T	p.Arg134Ter	p.R134*	ENST00000346618	NM_001949.4	134	Cga/Tga	2/7	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.488394431509365	2		341	319	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243362	46243362	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0007287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	94	341	0	ENST00000334344.6:c.1716-1G>C		p.X572_splice	ENST00000334344	NM_152641.2	572			0.279372533631709	3	FACETS	1	0.97	1	0.616	0.552	0.683	INDETERMINATE	1	TRUE	1	0.488394431509365	3		341	389	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110684	2110684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140910086	NA	P-0007287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	183	420	0	ENST00000219476.3:c.989C>T	p.Pro330Leu	p.P330L	ENST00000219476	NM_000548.3	330	cCg/cTg	11/42	0.363234765772511	4	FACETS	1	0.984	1			1	CLONAL	2	TRUE	NA	0.488394431509365	4		420	472	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916949	+	inframe_deletion	In_Frame_Del	DEL	AAGATC	AAGATC	-	novel	NA	P-0007287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	156	595	0	ENST00000263967.3:c.331_336del	p.Lys111_Ile112del	p.K111_I112del	ENST00000263967	NM_006218.2	111	AAGATC/-	2/21	0.279372533631709	3	FACETS	1	0.984	1	0.644	0.592	0.698	INDETERMINATE	1	TRUE	1	0.488394431509365	3		595	617	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191488	10191488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs5030818	NA	P-0007299-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	15	369	3	ENST00000256474.2:c.481C>T	p.Arg161Ter	p.R161*	ENST00000256474	NM_000551.3	161	Cga/Tga	3/3	0.154535451222328	2	FACETS	0.976	0.723	1	0.976	0.723	1	CLONAL	2	TRUE	0	0.156899106675519	2		372	98	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564327	86564327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007299-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	36	491	0	ENST00000274376.6:c.59G>A	p.Gly20Glu	p.G20E	ENST00000274376	NM_002890.2	20	gGa/gAa	1/25	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.156899106675519	2		491	371	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969143	93969143	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007299-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	17	827	0	ENST00000369303.4:c.1853A>G	p.Asn618Ser	p.N618S	ENST00000369303	NM_004440.3	618	aAt/aGt	10/17	1	2	FACETS	0.934	0.705	1	1	0.925	1	CLONAL	2	TRUE	1	0.156899106675519	2		827	116	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781382	135781382	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007299-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	59	807	0	ENST00000298552.3:c.1583del	p.Gly528AlafsTer4	p.G528Afs*4	ENST00000298552	NM_001162426.1	528	gGc/gc	15/23	0.154535451222328	2	FACETS	0.891	0.769	1	0.891	0.769	1	CLONAL	2	TRUE	0	0.156899106675519	2		807	422	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759968	133759968	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	60	461	0	ENST00000318560.5:c.2292del	p.Lys765ArgfsTer11	p.K765Rfs*11	ENST00000318560	NM_005157.4	764	cGg/cg	11/11	1	2	FACETS	0.15	0.128	0.174	0.15	0.128	0.174	SUBCLONAL	1	TRUE	1	0.682321222774145	2		461	1173	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	197	412	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.559454823859813	3	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	1	0.559454823859813	3		412	448	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123722	11123722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1263140481	NA	P-0007309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	229	485	1	ENST00000358026.2:c.2372C>T	p.Ala791Val	p.A791V	ENST00000358026	NM_001128849.1	791	gCg/gTg	16/36	0.442758480066527	2	FACETS	0.835	0.788	0.883	0.835	0.788	0.883	CLONAL	2	TRUE	0	0.559454823859813	2		486	490	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220691	1220691	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs878853247	NA	P-0007309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	176	376	0	ENST00000326873.7:c.709G>T	p.Asp237Tyr	p.D237Y	ENST00000326873	NM_000455.4	237	Gac/Tac	5/10	0.442758480066527	2	FACETS	1	0.991	1	0.733	0.683	0.784	CLONAL	1	TRUE	0	0.559454823859813	2		376	429	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56875696	56875696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	186	776	0	ENST00000308159.5:c.2300G>A	p.Ser767Asn	p.S767N	ENST00000308159	NM_014669.4	767	aGt/aAt	21/22	0.397742098134827	3	FACETS	0.882	0.814	0.952	0.441	0.407	0.476	CLONAL	1	TRUE	1	0.559454823859813	3		776	965	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602583	10602583	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	168	480	0	ENST00000171111.5:c.995del	p.Gly332AlafsTer68	p.G332Afs*68	ENST00000171111	NM_203500.1	332	gGc/gc	3/6	0.442758480066527	2	FACETS	0.848	0.792	0.905	0.848	0.792	0.905	CLONAL	2	TRUE	0	0.559454823859813	2		480	354	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	97	145	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.278094681873001	2		145	624	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120612013	120612014	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0007321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	20	19	0	ENST00000256646.2:c.7_8delinsTT	p.Ala3Phe	p.A3F	ENST00000256646	NM_024408.3	3	GCc/TTc	1/34	1	2	FACETS	0.953	0.735	1	0.953	0.735	1	CLONAL	1	TRUE	1	0.278094681873001	2		19	151	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423414	116423414	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913246	NA	P-0007321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1215	387	463	0	ENST00000397752.3:c.3689A>G	p.Tyr1230Cys	p.Y1230C	ENST00000397752	NM_000245.2	1230	tAt/tGt	19/21	0.278094681873001	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.278094681873001	4		463	1602	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374311	31374311	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1538	97	436	0	ENST00000328111.2:c.310C>T	p.Arg104Ter	p.R104*	ENST00000328111	NM_006892.3	104	Cga/Tga	5/23	1	2	FACETS	0.427	0.378	0.478	0.427	0.378	0.478	SUBCLONAL	1	TRUE	1	0.278094681873001	2		436	1635	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480495	57480495	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1422801076	NA	P-0007321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	134	281	0	ENST00000371085.3:c.490G>A	p.Glu164Lys	p.E164K	ENST00000371085	NM_000516.4	164	Gaa/Aaa	6/13	1	2	FACETS	0.876	0.794	0.962	0.876	0.794	0.962	CLONAL	1	TRUE	1	0.278094681873001	2		281	1100	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0007325-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	299	758	1	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	0.996	0.944	1	0.996	0.944	1	CLONAL	1	TRUE	1	0.814296857947088	2		759	737	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440879	52440909	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGCCGGGCCTTGTCTGTCCACTCCTCGTC	CCCGCCGGGCCTTGTCTGTCCACTCCTCGTC	-	novel	NA	P-0007325-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	413	473	0	ENST00000460680.1:c.595_625del	p.Asp199SerfsTer22	p.D199Sfs*22	ENST00000460680	NM_004656.3	199	GACGAGGAGTGGACAGACAAGGCCCGGCGGGtc/tc	8/17	0.808347040221958	2	FACETS	0.885	0.857	0.912	0.885	0.857	0.912	CLONAL	2	TRUE	0	0.814296857947088	2		473	573	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0007327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	286	401	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.256625163611976	3	FACETS	1	0.994	1	0.739	0.699	0.78	INDETERMINATE	1	TRUE	1	0.730912189370971	3		401	723	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415582	152415582	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	72	536	0	ENST00000206249.3:c.1432G>C	p.Val478Leu	p.V478L	ENST00000206249	NM_000125.3	478	Gtc/Ctc	7/8	1	2	FACETS	0.193	0.168	0.221	0.193	0.168	0.221	SUBCLONAL	1	TRUE	1	0.730912189370971	2		536	1019	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59770860	59770860	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0007327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	214	347	0	ENST00000259008.2:c.2506A>T	p.Arg836Ter	p.R836*	ENST00000259008	NM_032043.2	836	Aga/Tga	18/20	0.111627873378858	3	FACETS	1	0.981	1	0.567	0.529	0.606	INDETERMINATE	1	TRUE	1	0.730912189370971	3		347	705	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177026	56177026	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	185	241	0	ENST00000399503.3:c.2297del	p.Leu766TrpfsTer33	p.L766Wfs*33	ENST00000399503	NM_005921.1	766	Ttg/tg	13/20	0.256625163611976	3	FACETS	1	0.98	1	0.574	0.533	0.616	INDETERMINATE	1	TRUE	1	0.730912189370971	3		241	602	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0007330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	99	409	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.1600925010794	3	FACETS	1	0.97	1			1	CLONAL	2	TRUE	NA	0.1600925010794	3		409	544	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094351	27094351	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	68	463	0	ENST00000324856.7:c.3060del	p.Lys1021ArgfsTer18	p.K1021Rfs*18	ENST00000324856	NM_006015.4	1020	aGg/ag	11/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.1600925010794	2		463	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0007330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	74	526	1	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.1600925010794	2		527	719	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0007342-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	105	273	2	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.171241824168389	2	FACETS	0.837	0.751	0.928	0.837	0.751	0.928	CLONAL	2	FALSE	0	0.190739060958223	2		275	658	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382220	152382220	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007342-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	44	412	1	ENST00000206249.3:c.1330G>T	p.Glu444Ter	p.E444*	ENST00000206249	NM_000125.3	444	Gag/Tag	6/8	1	2	FACETS	0.837	0.702	0.988	0.837	0.702	0.988	CLONAL	1	FALSE	1	0.190739060958223	2		413	551	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249896	110249896	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007342-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	24	164	2	ENST00000374672.4:c.779C>A	p.Pro260Gln	p.P260Q	ENST00000374672	NM_004235.4	260	cCg/cAg	3/5	0.188678658931018	3	FACETS	1	0.914	1	0.679	0.535	0.843	CLONAL	1	FALSE	1	0.190739060958223	3		166	203	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118367047	118367047	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007342-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	138	440	0	ENST00000534358.1:c.5629G>A	p.Ala1877Thr	p.A1877T	ENST00000534358	NM_005933.3	1877	Gcg/Acg	20/36	0.188678658931018	3	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	FALSE	1	0.190739060958223	3		440	778	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859626	57859626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202128734	NA	P-0007342-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	93	612	2	ENST00000228682.2:c.680G>A	p.Arg227His	p.R227H	ENST00000228682	NM_005269.2	227	cGt/cAt	7/12	0.188678658931018	3	FACETS	1	0.891	1	0.502	0.445	0.564	CLONAL	1	FALSE	1	0.190739060958223	3		614	1063	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860787	45860787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760834335	NA	P-0007342-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	65	385	0	ENST00000391945.4:c.1322C>T	p.Ser441Leu	p.S441L	ENST00000391945	NM_000400.3	441	tCg/tTg	14/23	0.145864752948435	3	FACETS	1	0.959	1			1	CLONAL	1	FALSE	NA	0.190739060958223	3		385	584	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0007383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	168	248	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	0.945	0.875	1	0.945	0.875	1	CLONAL	1	TRUE	1	0.719955713627976	2		248	494	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877154	151877154	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs767365126	NA	P-0007383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	96	327	0	ENST00000262189.6:c.7207C>T	p.Arg2403Ter	p.R2403*	ENST00000262189	NM_170606.2	2403	Cga/Tga	37/59	0.682604078109207	3	FACETS	0.292	0.259	0.328	0.146	0.129	0.164	SUBCLONAL	1	TRUE	1	0.719955713627976	3		327	1240	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437846	52437846	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	579	542	0	ENST00000460680.1:c.1315G>C	p.Val439Leu	p.V439L	ENST00000460680	NM_004656.3	439	Gtg/Ctg	13/17	0.719955713627976	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.719955713627976	1		542	1014	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0007392-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	186	233	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		233	537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0007393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	236	474	0	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	0.253228438718343	1	FACETS	0.904	0.856	0.951	1	0.996	1	CLONAL	4	FALSE	0	0.262608415038269	1		474	432	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8525003	8525003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	120	375	1	ENST00000356435.5:c.601G>A	p.Asp201Asn	p.D201N	ENST00000356435		201	Gac/Aac	7/35	0.262608415038269	5	FACETS	1	0.968	1	0.392	0.353	0.433	CLONAL	1	FALSE	2	0.262608415038269	5		376	1084	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922182	100922182	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1716	185	519	0	ENST00000325455.5:c.2330A>T	p.Tyr777Phe	p.Y777F	ENST00000325455	NM_001202474.3	777	tAt/tTt	5/8	0.262608415038269	6	FACETS	1	0.973	1	0.377	0.346	0.409	CLONAL	1	FALSE	3	0.262608415038269	6		519	1901	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562696	21562696	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	17	156	0	ENST00000382592.4:c.1223C>G	p.Ser408Cys	p.S408C	ENST00000382592	NM_014572.2	408	tCc/tGc	4/8	0.262608415038269	7	FACETS	0.803	0.6	1			1	CLONAL	1	FALSE	NA	0.262608415038269	7		156	267	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0007407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	78	247	1				ENST00000310581	NM_198253.2	-/1132			0.108409580894561	5	FACETS	1	0.92	1	0.773	0.693	0.855	INDETERMINATE	3	TRUE	1	0.402726542944633	5		248	201	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641389	18641389	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1229278001	NA	P-0007407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	21	201	1	ENST00000266497.5:c.2393del	p.Asn798MetfsTer16	p.N798Mfs*16	ENST00000266497		796	ctA/ct	17/31	NA	2	FACETS	0.44	0.34	0.556			1	INDETERMINATE	1	TRUE	NA	0.402726542944633	2		202	237	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466381	120466381	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0007407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	119	412	0	ENST00000256646.2:c.4738A>T	p.Lys1580Ter	p.K1580*	ENST00000256646	NM_024408.3	1580	Aag/Tag	26/34	0.402726542944633	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.402726542944633	1		412	397	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657047	47657047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35717997	NA	P-0007407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	37	460	0	ENST00000233146.2:c.1243C>T	p.Pro415Ser	p.P415S	ENST00000233146	NM_000251.2	415	Cct/Tct	7/16	0.108409580894561	5	FACETS	0.585	0.482	0.701	0.146	0.12	0.176	INDETERMINATE	1	TRUE	1	0.402726542944633	5		460	504	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217262	66217262	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1219153956	NA	P-0007407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	112	351	1	ENST00000273854.3:c.2353T>A	p.Ser785Thr	p.S785T	ENST00000273854	NM_004439.5	785	Tct/Act	14/18	0.192106076840007	2	FACETS	1	0.98	1	0.662	0.6	0.727	INDETERMINATE	1	TRUE	0	0.402726542944633	2		352	420	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231757	66231757	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	96	366	0	ENST00000273854.3:c.1943G>T	p.Arg648Ile	p.R648I	ENST00000273854	NM_004439.5	648	aGa/aTa	11/18	0.192106076840007	2	FACETS	1	0.968	1	0.6	0.539	0.665	INDETERMINATE	1	TRUE	0	0.402726542944633	2		366	397	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402468	139402468	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	319	478	1	ENST00000277541.6:c.3449C>A	p.Ser1150Ter	p.S1150*	ENST00000277541	NM_017617.3	1150	tCa/tAa	21/34	0.39699201017531	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.402726542944633	3		479	595	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28931733	28931733	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs896353265	NA	P-0007407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	53	437	1	ENST00000282397.4:c.2206C>A	p.Gln736Lys	p.Q736K	ENST00000282397	NM_002019.4	736	Cag/Aag	15/30	0.394354537777452	1	FACETS	0.386	0.329	0.448	0.386	0.329	0.448	SUBCLONAL	1	TRUE	0	0.402726542944633	1		438	545	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110558	4110558	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	44	333	0	ENST00000262948.5:c.399C>G	p.Phe133Leu	p.F133L	ENST00000262948	NM_030662.3	133	ttC/ttG	3/11	0.273201164363349	0	FACETS	0.316	0.265	0.372			1	SUBCLONAL	1	TRUE	0	0.402726542944633	0		333	413	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879910	44879910	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	138	296	0	ENST00000377967.4:c.499A>C	p.Lys167Gln	p.K167Q	ENST00000377967	NM_021140.2	167	Aag/Cag	6/29	1	1	FACETS	0.791	0.73	0.853	1	0.989	1	SUBCLONAL	2	TRUE	0	0.402726542944633	1		296	346	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646578	23646581	+	frameshift_variant	Frame_Shift_Del	DEL	TGAA	TGAA	-	novel	NA	P-0007407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	69	269	0	ENST00000261584.4:c.1286_1289del	p.Ile429ArgfsTer22	p.I429Rfs*22	ENST00000261584	NM_024675.3	429	aTTCAg/ag	4/13	0.223950765601728	2	FACETS	1	0.958	1	0.603	0.531	0.68	INDETERMINATE	1	TRUE	0	0.402726542944633	2		269	284	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350086	81350086	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	178	459	0	ENST00000222390.5:c.1246del	p.Asp416ThrfsTer20	p.D416Tfs*20	ENST00000222390	NM_000601.4	416	Gac/ac	10/18	0.149930414169172	3	FACETS	1	0.99	1	0.743	0.686	0.801	INDETERMINATE	1	TRUE	1	0.402726542944633	3		459	715	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251017	99251018	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	A	novel	NA	P-0007407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	75	344	0	ENST00000268035.6:c.321_322delinsA	p.Gly108AlafsTer15	p.G108Afs*15	ENST00000268035	NM_000875.3	107	cgCGgc/cgAgc	2/21	0.178515808162423	2	FACETS	0.609	0.533	0.689	0.304	0.266	0.345	INDETERMINATE	1	TRUE	0	0.402726542944633	2		344	612	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0007415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	22	565	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.808858728310384	2	FACETS	0.08	0.061	0.101	0.04	0.03	0.051	SUBCLONAL	1	TRUE	0	0.813349734759381	2		565	680	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0007415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	394	316	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.813349734759381	4	FACETS	0.935	0.893	0.978	0.935	0.893	0.978	CLONAL	2	TRUE	2	0.813349734759381	4		316	939	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0007415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	120	233	0				ENST00000310581	NM_198253.2	-/1132			0.528538678941056	4	FACETS	1	0.971	1			1	CLONAL	1	TRUE	NA	0.813349734759381	4		233	457	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0007415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	414	365	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	0.807021659855696	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.813349734759381	2		365	509	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945028	151945028	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	16	28	0	ENST00000262189.6:c.2491A>G	p.Thr831Ala	p.T831A	ENST00000262189	NM_170606.2	831	Act/Gct	14/59	0.813349734759381	4	FACETS	0.927	0.7	1			1	CLONAL	1	TRUE	NA	0.813349734759381	4		28	77	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916852	48916852	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0007415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	152	194	0	ENST00000267163.4:c.380+2T>C		p.X127_splice	ENST00000267163	NM_000321.2	127			0.789094377941839	1	FACETS	0.981	0.926	1	0.981	0.926	1	CLONAL	1	TRUE	0	0.813349734759381	1		194	226	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0007420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	194	265	0	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	0.343822224965094	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.357962611497494	2		265	481	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742463	17742463	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	167	528	0	ENST00000250003.3:c.650del	p.Pro217ArgfsTer33	p.P217Rfs*33	ENST00000250003	NM_002478.4	215	ggC/gg	2/3	0.357962611497494	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.357962611497494	4		528	566	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233110	46233110	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0007420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	191	255	0	ENST00000334344.6:c.1331-2A>G		p.X444_splice	ENST00000334344	NM_152641.2	444			0.357962611497494	3	FACETS	1	0.942	1	1	0.942	1	CLONAL	3	TRUE	0	0.357962611497494	3		255	417	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677328	29677331	+	frameshift_variant	Frame_Shift_Del	DEL	TTCC	TTCC	GAA	novel	NA	P-0007420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	303	392	1	ENST00000356175.3:c.7386_7389delinsGAA	p.Ser2463AsnfsTer5	p.S2463Nfs*5	ENST00000356175	NM_000267.3	2462	ccTTCC/ccGAA	49/57	0.357962611497494	4	FACETS	0.979	0.933	1	0.979	0.933	1	CLONAL	4	TRUE	0	0.357962611497494	4		393	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0007426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	135	265	0	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	1	2	FACETS	0.732	0.668	0.798	0.732	0.668	0.798	SUBCLONAL	1	TRUE	1	0.66	2		265	559	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0007426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	39	369	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.215	0.178	0.257	0.215	0.178	0.257	SUBCLONAL	1	TRUE	1	0.66	2		369	549	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141874	108141874	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587781558	NA	P-0007426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	37	322	0	ENST00000278616.4:c.2921+1G>T		p.X974_splice	ENST00000278616	NM_000051.3	974			1	2	FACETS	0.232	0.191	0.278	0.232	0.191	0.278	SUBCLONAL	1	TRUE	1	0.66	2		322	484	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037400	12037400	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	83	514	0	ENST00000396373.4:c.1031A>C	p.Tyr344Ser	p.Y344S	ENST00000396373	NM_001987.4	344	tAc/tCc	6/8	1	2	FACETS	0.237	0.208	0.268	0.237	0.208	0.268	SUBCLONAL	1	TRUE	1	0.66	2		514	1062	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669547	88669547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56394626	NA	P-0007426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	33	343	1	ENST00000360948.2:c.1351G>A	p.Val451Ile	p.V451I	ENST00000360948	NM_001012338.2	451	Gtc/Atc	12/19	1	2	FACETS	0.156	0.126	0.19	0.156	0.126	0.19	SUBCLONAL	1	TRUE	1	0.66	2		344	641	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305384	65305384	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	48	282	0	ENST00000342505.4:c.2744G>A	p.Gly915Glu	p.G915E	ENST00000342505	NM_002227.2	915	gGa/gAa	20/25	1	2	FACETS	0.619	0.522	0.726	0.619	0.522	0.726	SUBCLONAL	1	TRUE	1	0.208517295382614	2		282	744	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305391	65305391	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	46	277	0	ENST00000342505.4:c.2737G>A	p.Glu913Lys	p.E913K	ENST00000342505	NM_002227.2	913	Gag/Aag	20/25	1	2	FACETS	0.618	0.519	0.728	0.618	0.519	0.728	SUBCLONAL	1	TRUE	1	0.208517295382614	2		277	714	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476761	140476761	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	24	198	0	ENST00000288602.6:c.1645G>C	p.Glu549Gln	p.E549Q	ENST00000288602	NM_004333.4	549	Gag/Cag	13/18	0.208517295382614	1	FACETS	0.509	0.399	0.637	0.509	0.399	0.637	SUBCLONAL	1	TRUE	0	0.208517295382614	1		198	405	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430284	47430284	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	44	249	0	ENST00000377045.4:c.1559T>C	p.Phe520Ser	p.F520S	ENST00000377045	NM_001654.4	520	tTt/tCt	15/16	0.138320286307038	0	FACETS	0.739	0.62	0.87			1	SUBCLONAL	1	TRUE	NA	0.208517295382614	0		249	452	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438545	52438545	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1553645146	NA	P-0007498-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	171	384	0	ENST00000460680.1:c.1174C>T	p.Gln392Ter	p.Q392*	ENST00000460680	NM_004656.3	392	Cag/Tag	12/17	0.307201158537362	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.307201158537362	1		384	767	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651459	52651459	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007498-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	209	763	0	ENST00000394830.3:c.1637T>G	p.Phe546Cys	p.F546C	ENST00000394830	NM_018313.4	546	tTt/tGt	15/30	0.307201158537362	1	FACETS	0.893	0.827	0.961	0.893	0.827	0.961	CLONAL	1	TRUE	0	0.307201158537362	1		763	1290	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054197	30054197	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007498-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	109	481	0	ENST00000338641.4:c.619del	p.Tyr207IlefsTer2	p.Y207Ifs*2	ENST00000338641	NM_000268.3	207	Tat/at	7/16	0.265273316228524	1	FACETS	0.625	0.56	0.694	0.625	0.56	0.694	SUBCLONAL	1	TRUE	0	0.307201158537362	1		481	961	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913517	NA	P-0007501-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	332	480	1	ENST00000288135.5:c.1676T>A	p.Val559Asp	p.V559D	ENST00000288135	NM_000222.2	559	gTt/gAt	11/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.605396440785808	2		481	1088	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0007507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	48	397	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.222776460569625	5	FACETS	0.963	0.825	1	0.963	0.825	1	CLONAL	3	TRUE	2	0.222776460569625	5		397	199	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577578	7577578	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	40	400	0	ENST00000269305.4:c.703A>G	p.Asn235Asp	p.N235D	ENST00000269305	NM_001126112.2	235	Aac/Gac	7/11	0.222776460569625	3	FACETS	1	0.921	1	1	0.921	1	CLONAL	2	TRUE	1	0.222776460569625	3		400	172	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0007507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	34	503	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	0.222776460569625	3	FACETS	1	0.923	1	0.626	0.514	0.751	CLONAL	1	TRUE	1	0.222776460569625	3		503	271	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007521-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	56	412	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	0.357491421162823	2		412	210	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0007521-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	22	237	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.303628147571999	1	FACETS	1	0.834	1	1	0.834	1	CLONAL	1	TRUE	0	0.357491421162823	1		237	95	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007695	45007705	+	frameshift_variant	Frame_Shift_Del	DEL	TCTGGGTTTCA	TCTGGGTTTCA	-	novel	NA	P-0007521-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	55	278	0	ENST00000558401.1:c.144_154del	p.Gly49IlefsTer4	p.G49Ifs*4	ENST00000558401	NM_004048.2	48	TCTGGGTTTCAt/t	2/4	1	2	FACETS	0.927	0.809	1	1	0.978	1	CLONAL	2	TRUE	1	0.357491421162823	2		278	166	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0007535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	296	564	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.362282378095454	2	FACETS	0.855	0.814	0.897	1	0.993	1	CLONAL	3	TRUE	0	0.39576650924718	2		564	583	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716212	52716212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555791268	NA	P-0007535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	94	328	0	ENST00000322088.6:c.656C>T	p.Ser219Leu	p.S219L	ENST00000322088	NM_014225.5	219	tCg/tTg	6/15	0.271404622794323	4	FACETS	0.861	0.772	0.955	0.861	0.772	0.955	CLONAL	2	TRUE	2	0.39576650924718	4		328	385	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100334	27100334	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	283	482	1	ENST00000324856.7:c.4046C>T	p.Pro1349Leu	p.P1349L	ENST00000324856	NM_006015.4	1349	cCt/cTt	17/20	0.39576650924718	5	FACETS	1	0.989	1	0.801	0.754	0.848	CLONAL	2	TRUE	2	0.39576650924718	5		483	949	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797977	42797977	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	36	513	0	ENST00000575354.2:c.4029C>A	p.Asp1343Glu	p.D1343E	ENST00000575354	NM_015125.3	1343	gaC/gaA	16/20	0.271404622794323	4	FACETS	0.404	0.331	0.486	0.202	0.165	0.243	SUBCLONAL	1	TRUE	2	0.39576650924718	4		513	628	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0007555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	65	565	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.71	0.614	0.814	0.71	0.614	0.814	SUBCLONAL	1	TRUE	1	0.223630989465021	2		565	819	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691003	NA	P-0007555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	160	438	0	ENST00000269305.4:c.96+1G>T		p.X32_splice	ENST00000269305	NM_001126112.2	32			NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.223630989465021	2		438	1003	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913527	NA	P-0007555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	198	327	0	ENST00000311936.3:c.436G>C	p.Ala146Pro	p.A146P	ENST00000311936	NM_004985.3	146	Gca/Cca	4/5	1	2	FACETS	0.934	0.865	1	1	0.993	1	CLONAL	2	TRUE	1	0.223630989465021	2		327	948	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0007556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	304	641	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.410710706754078	1	FACETS	0.786	0.741	0.831	0.786	0.741	0.831	SUBCLONAL	1	TRUE	0	0.550107063689064	1		642	1020	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637700	52637700	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	137	387	0	ENST00000394830.3:c.2616del	p.Phe872LeufsTer43	p.F872Lfs*43	ENST00000394830	NM_018313.4	872	ttT/tt	18/30	0.550107063689064	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.550107063689064	1		387	343	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074357	8074357	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	166	624	1	ENST00000377482.5:c.302A>T	p.Glu101Val	p.E101V	ENST00000377482	NM_018948.3	101	gAa/gTa	4/4	1	2	FACETS	0.489	0.448	0.532	0.489	0.448	0.532	SUBCLONAL	1	TRUE	1	0.550107063689064	2		625	1235	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059230	47059230	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs777018406	NA	P-0007556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	107	217	0	ENST00000409792.3:c.7432-1G>T		p.X2478_splice	ENST00000409792	NM_014159.6	2478			NA	2	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.550107063689064	2		217	342	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440175	49440175	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339434307	NA	P-0007556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	192	319	0	ENST00000301067.7:c.4451C>T	p.Ser1484Phe	p.S1484F	ENST00000301067	NM_003482.3	1484	tCc/tTc	16/54	NA	2	FACETS	0.923	0.856	0.993			1	INDETERMINATE	1	TRUE	NA	0.550107063689064	2		319	756	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21565442	21565442	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	66	597	0	ENST00000382592.4:c.444G>C	p.Gln148His	p.Q148H	ENST00000382592	NM_014572.2	148	caG/caC	3/8	0.211852669916669	1	FACETS	0.145	0.125	0.167	0.145	0.125	0.167	INDETERMINATE	1	TRUE	0	0.550107063689064	1		597	1202	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21565472	21565472	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	70	579	0	ENST00000382592.4:c.414G>C	p.Lys138Asn	p.K138N	ENST00000382592	NM_014572.2	138	aaG/aaC	3/8	0.211852669916669	1	FACETS	0.162	0.14	0.185	0.162	0.14	0.185	INDETERMINATE	1	TRUE	0	0.550107063689064	1		579	1140	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727517	66727517	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	327	364	0	ENST00000307102.5:c.233A>G	p.Asn78Ser	p.N78S	ENST00000307102	NM_002755.3	78	aAt/aGt	2/11	0.136476824834806	3	FACETS	0.776	0.734	0.818	0.776	0.734	0.818	INDETERMINATE	2	TRUE	1	0.550107063689064	3		364	977	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183742	10183742	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	336	313	0	ENST00000256474.2:c.213del	p.Ser72ProfsTer87	p.S72Pfs*87	ENST00000256474	NM_000551.3	71	Ccc/cc	1/3	NA	2	FACETS	0.982	0.939	1			1	INDETERMINATE	2	TRUE	NA	0.550107063689064	2		313	622	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332415	70332415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1419371452	NA	P-0007573-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	26	335	0	ENST00000373644.4:c.320G>A	p.Arg107Gln	p.R107Q	ENST00000373644	NM_030625.2	107	cGa/cAa	2/12	1	2	FACETS	0.222	0.175	0.276	0.222	0.175	0.276	SUBCLONAL	1	TRUE	1	0.521947370317368	2		335	449	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0007582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	7212	88	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.413948854506311	52	FACETS	1	0.999	1			1	CLONAL	51	TRUE	NA	0.413948854506311	52		88	7698	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639661	47639661	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750347	NA	P-0007582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	134	151	0	ENST00000233146.2:c.754C>T	p.Gln252Ter	p.Q252*	ENST00000233146	NM_000251.2	252	Cag/Tag	4/16	0.413948854506311	6	FACETS	1	0.958	1	0.219	0.199	0.241	CLONAL	1	TRUE	1	0.413948854506311	6		151	1079	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934727	49934727	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	270	87	0	ENST00000296474.3:c.2169G>C	p.Glu723Asp	p.E723D	ENST00000296474	NM_002447.2	723	gaG/gaC	7/20	0.324685545070903	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.413948854506311	4		87	790	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342702	87342702	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	123	144	0	ENST00000277120.3:c.987C>A	p.Tyr329Ter	p.Y329*	ENST00000277120		329	taC/taA	9/19	0.386150921511577	3	FACETS	1	0.969	1	0.388	0.351	0.426	CLONAL	1	TRUE	0	0.413948854506311	3		144	617	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254716	46254908	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGCAGTCTTGTAAAAAGTAAATGGCAATTTTATTTGATATATAAAAGTATTCTTTGTTTTGGAATGCTTTTATATTTAAGTTTCTGTCATCTATAGTTGCATGAAAATTTTCCTTTAGAACCACTAACTTTAGCGAAACTACAAGAGTTATATTTATGATCCATTATGTGGACCTAAACTAAGAAATTTATA	TGGCAGTCTTGTAAAAAGTAAATGGCAATTTTATTTGATATATAAAAGTATTCTTTGTTTTGGAATGCTTTTATATTTAAGTTTCTGTCATCTATAGTTGCATGAAAATTTTCCTTTAGAACCACTAACTTTAGCGAAACTACAAGAGTTATATTTATGATCCATTATGTGGACCTAAACTAAGAAATTTATA	-	novel	NA	P-0007582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	141	235	0	ENST00000334344.6:c.4907_4922+177del		p.X1636_splice	ENST00000334344	NM_152641.2	1636		16/21	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.413948854506311	2		235	508	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	59	145	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.94	1	1	0.982	1	CLONAL	2	TRUE	1	0.294813127916438	2		145	178	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0007589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	73	316	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.863	0.762	0.969	1	0.981	1	CLONAL	2	TRUE	1	0.294813127916438	2		316	287	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602799	10602799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	231	344	0	ENST00000171111.5:c.779G>A	p.Arg260Gln	p.R260Q	ENST00000171111	NM_203500.1	260	cGa/cAa	3/6	0.281380523656604	2	FACETS	0.951	0.895	1	1	0.993	1	CLONAL	3	TRUE	0	0.294813127916438	2		344	549	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791004	42791004	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	57	290	0	ENST00000575354.2:c.149A>G	p.Asp50Gly	p.D50G	ENST00000575354	NM_015125.3	50	gAc/gGc	2/20	1	2	FACETS	0.694	0.596	0.802	0.694	0.596	0.802	SUBCLONAL	1	TRUE	1	0.294813127916438	2		290	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0007598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	175	426	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.387308779451961	2	FACETS	1	0.99	1	0.736	0.681	0.792	CLONAL	1	TRUE	0	0.403241072907969	2		426	590	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226590079	226590079	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs768342881	NA	P-0007598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	85	407	0	ENST00000366794.5:c.122C>T	p.Ser41Leu	p.S41L	ENST00000366794	NM_001618.3	41	tCg/tTg	2/23	0.347356017194005	2	FACETS	1	0.914	1	0.517	0.459	0.577	CLONAL	1	TRUE	0	0.403241072907969	2		407	408	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847399	68847399	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0007598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	227	521	0	ENST00000261769.5:c.1320+1G>T		p.X440_splice	ENST00000261769	NM_004360.3	440			0.290390358650132	3	FACETS	0.968	0.913	1			1	CLONAL	3	TRUE	NA	0.403241072907969	3		521	466	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979319	40979319	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1217327426	NA	P-0007598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	79	359	1	ENST00000373198.4:c.1814C>T	p.Thr605Met	p.T605M	ENST00000373198	NM_133170.3	605	aCg/aTg	11/32	0.403241072907969	5	FACETS	0.927	0.816	1	0.232	0.204	0.262	CLONAL	1	TRUE	1	0.403241072907969	5		360	678	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024465	16024562	+	frameshift_variant	Frame_Shift_Del	DEL	TCCGGCCCTTACGGCGGCCCTGACTGTTGGCAGTCTTTCGCCCCCGGGGTGTGGCTTGCTCTCTTTCCTCAGTTTCTTCTGCTGTACCATCTATCTTG	TCCGGCCCTTACGGCGGCCCTGACTGTTGGCAGTCTTTCGCCCCCGGGGTGTGGCTTGCTCTCTTTCCTCAGTTTCTTCTGCTGTACCATCTATCTTG	-	novel	NA	P-0007598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	27	461	0	ENST00000268712.3:c.1656_1753del	p.Lys553HisfsTer20	p.K553Hfs*20	ENST00000268712	NM_006311.3	552	gaCAAGATAGATGGTACAGCAGAAGAAACTGAGGAAAGAGAGCAAGCCACACCCCGGGGGCGAAAGACTGCCAACAGTCAGGGCCGCCGTAAGGGCCGGAtc/gatc	16/46	0.387308779451961	2	FACETS	0.281	0.223	0.347	0.14	0.111	0.174	SUBCLONAL	1	TRUE	0	0.403241072907969	2		461	477	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	59	407	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.82	0.704	0.948	0.82	0.704	0.948	CLONAL	1	TRUE	1	0.17	2		407	846	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0007635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	81	535	1	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.17	2		536	932	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48586262	48586262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658694	NA	P-0007635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	44	396	0	ENST00000342988.3:c.931C>T	p.Gln311Ter	p.Q311*	ENST00000342988	NM_005359.5	311	Cag/Tag	8/12	1	2	FACETS	0.787	0.658	0.929	0.787	0.658	0.929	CLONAL	1	TRUE	1	0.17	2		396	658	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437511	56437511	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	47	314	0	ENST00000407977.2:c.951del	p.Glu318ArgfsTer101	p.E318Rfs*101	ENST00000407977		317	acA/ac	8/10	0.157751206996758	1	FACETS	0.836	0.705	0.982	0.836	0.705	0.982	CLONAL	1	TRUE	0	0.17	1		314	605	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191590	10191590	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs5030825	NA	P-0007639-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	39	375	0	ENST00000256474.2:c.583C>T	p.Gln195Ter	p.Q195*	ENST00000256474	NM_000551.3	195	Cag/Tag	3/3	NA	2	FACETS	1	0.896	1			1	INDETERMINATE	1	TRUE	NA	0.221839522580465	2		375	317	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786868	135786868	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs118203481	NA	P-0007639-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	24	425	0	ENST00000298552.3:c.1001C>A	p.Ser334Ter	p.S334*	ENST00000298552	NM_001162426.1	334	tCg/tAg	10/23	0.184946930354605	1	FACETS	0.661	0.519	0.824	0.661	0.519	0.824	SUBCLONAL	1	TRUE	0	0.221839522580465	1		425	291	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696683	47696683	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007639-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	25	492	0	ENST00000347630.2:c.265T>G	p.Leu89Val	p.L89V	ENST00000347630	NM_001007230.1	89	Tta/Gta	5/11	1	2	FACETS	0.64	0.505	0.796	0.64	0.505	0.796	SUBCLONAL	1	TRUE	1	0.221839522580465	2		492	352	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436420	52436423	+	frameshift_variant	Frame_Shift_Del	DEL	CTAG	CTAG	-	novel	NA	P-0007639-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	33	227	0	ENST00000460680.1:c.2071_2074del	p.Leu691TrpfsTer44	p.L691Wfs*44	ENST00000460680	NM_004656.3	691	CTAGtg/tg	17/17	0.205921990226155	1	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	0	0.221839522580465	1		227	228	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584584	52584591	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGTCCA	GGGGTCCA	-	novel	NA	P-0007639-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	22	420	0	ENST00000394830.3:c.4422_4429del	p.Gly1475CysfsTer31	p.G1475Cfs*31	ENST00000394830	NM_018313.4	1474	gcTGGACCCCct/gcct	29/30	0.205921990226155	1	FACETS	0.634	0.492	0.799	0.634	0.492	0.799	SUBCLONAL	1	TRUE	0	0.221839522580465	1		420	278	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0007654-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	268	273	2	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.424203431880964	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.424203431880964	2		275	605	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0007654-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	132	228	0	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	0.198085598153467	3	FACETS	1	0.98	1	0.638	0.581	0.698	INDETERMINATE	1	TRUE	1	0.424203431880964	3		228	591	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007654-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	155	300	0	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	0.198085598153467	3	FACETS	1	0.986	1	0.682	0.627	0.74	INDETERMINATE	1	TRUE	1	0.424203431880964	3		300	649	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784380	9784380	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007654-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	102	457	0	ENST00000377346.4:c.2765A>C	p.Lys922Thr	p.K922T	ENST00000377346	NM_005026.3	922	aAg/aCg	22/24	1	2	FACETS	0.61	0.545	0.678	0.61	0.545	0.678	SUBCLONAL	1	TRUE	1	0.424203431880964	2		457	789	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530147	212530147	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1287533544	NA	P-0007654-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	190	369	0	ENST00000342788.4:c.1772A>G	p.Glu591Gly	p.E591G	ENST00000342788	NM_005235.2	591	gAa/gGa	15/28	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.424203431880964	2		369	811	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397704	49397704	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007654-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	313	432	0	ENST00000418115.1:c.520G>C	p.Ala174Pro	p.A174P	ENST00000418115	NM_001664.2	174	Gct/Cct	5/5	0.424203431880964	3	FACETS	1	0.991	1	0.638	0.601	0.677	CLONAL	1	TRUE	1	0.424203431880964	3		432	1401	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281762	142281762	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007654-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	235	412	0	ENST00000350721.4:c.482G>A	p.Arg161Lys	p.R161K	ENST00000350721	NM_001184.3	161	aGa/aAa	4/47	0.424203431880964	3	FACETS	0.934	0.875	0.994	0.934	0.875	0.994	CLONAL	2	TRUE	1	0.424203431880964	3		412	719	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350147	81350147	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007654-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	86	428	0	ENST00000222390.5:c.1185T>A	p.Asn395Lys	p.N395K	ENST00000222390	NM_000601.4	395	aaT/aaA	10/18	0.424203431880964	3	FACETS	0.539	0.476	0.608	0.27	0.238	0.304	SUBCLONAL	1	TRUE	1	0.424203431880964	3		428	911	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865461	57865461	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007654-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	166	619	0	ENST00000228682.2:c.2938A>G	p.Arg980Gly	p.R980G	ENST00000228682	NM_005269.2	980	Agg/Ggg	12/12	1	2	FACETS	0.639	0.585	0.695	0.639	0.585	0.695	SUBCLONAL	1	TRUE	1	0.424203431880964	2		619	1225	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919686	28919686	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007654-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	72	315	0	ENST00000282397.4:c.2251A>C	p.Thr751Pro	p.T751P	ENST00000282397	NM_002019.4	751	Acc/Ccc	16/30	0.424203431880964	6	FACETS	0.509	0.443	0.581	0.085	0.073	0.097	SUBCLONAL	1	TRUE	0	0.424203431880964	6		315	1232	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0007663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	524	411	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.591730538561748	7	FACETS	0.941	0.902	0.981			1	CLONAL	3	TRUE	NA	0.591730538561748	7		411	1555	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125357	47125357	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	287	700	0	ENST00000409792.3:c.5913A>C	p.Glu1971Asp	p.E1971D	ENST00000409792	NM_014159.6	1971	gaA/gaC	12/21	0.591730538561748	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.591730538561748	1		700	675	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119721036	119721036	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	251	475	0	ENST00000316626.5:c.139G>T	p.Gly47Cys	p.G47C	ENST00000316626		47	Ggt/Tgt	2/12	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.591730538561748	2		475	744	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517413	157517413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370064281	NA	P-0007663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	188	389	1	ENST00000346085.5:c.3977G>A	p.Arg1326His	p.R1326H	ENST00000346085	NM_020732.3	1326	cGc/cAc	16/20	1	2	FACETS	0.956	0.887	1	0.956	0.887	1	CLONAL	1	TRUE	1	0.591730538561748	2		390	665	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584569	48584569	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	185	400	0	ENST00000342988.3:c.742C>T	p.Gln248Ter	p.Q248*	ENST00000342988	NM_005359.5	248	Cag/Tag	6/12	0.565539639146237	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.591730538561748	1		400	421	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	116	407	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.3	2	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.22	2		407	813	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979533	2979533	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	40	507	0	ENST00000396946.4:c.714G>C	p.Lys238Asn	p.K238N	ENST00000396946	NM_032415.4	238	aaG/aaC	6/25	0.3	0	FACETS	0.628	0.521	0.746			1	SUBCLONAL	1	TRUE	0	0.22	0		507	452	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0007696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	111	409	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.254461857797805	5	FACETS	1	0.959	1	1	0.959	1	CLONAL	4	TRUE	1	0.254461857797805	5		409	278	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0007696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	44	138	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.179094297285446	5	FACETS	0.905	0.764	1			1	CLONAL	2	TRUE	NA	0.254461857797805	5		138	264	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0007696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	92	488	0	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.242224531991552	2	FACETS	0.931	0.84	1	1	0.98	1	CLONAL	3	TRUE	0	0.254461857797805	2		488	259	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039610	47039610	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0007696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	17	169	0	ENST00000377604.3:c.1063-1G>A		p.X355_splice	ENST00000377604	NM_001204468.1	355			0.190351960084281	0	FACETS	0.83	0.64	1			1	CLONAL	2	TRUE	NA	0.254461857797805	0		169	60	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100845	27100845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs957501357	NA	P-0007696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	44	487	0	ENST00000324856.7:c.4127C>T	p.Thr1376Ile	p.T1376I	ENST00000324856	NM_006015.4	1376	aCa/aTa	18/20	1	2	FACETS	0.793	0.672	0.924	1	0.964	1	CLONAL	2	TRUE	1	0.254461857797805	2		487	218	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081511	143081511	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	14	316	0	ENST00000262992.4:c.1563G>T	p.Trp521Cys	p.W521C	ENST00000262992	NM_001101669.1	521	tgG/tgT	15/24	1	2	FACETS	0.622	0.451	0.827	0.622	0.451	0.827	SUBCLONAL	1	TRUE	1	0.254461857797805	2		316	177	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677879	117677879	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	51	519	1	ENST00000368508.3:c.4054A>T	p.Ile1352Leu	p.I1352L	ENST00000368508	NM_002944.2	1352	Ata/Tta	25/43	NA	2	FACETS	1	0.894	1			1	INDETERMINATE	2	TRUE	NA	0.254461857797805	2		520	192	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622184	162622184	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	15	370	0	ENST00000366898.1:c.513G>T	p.Gln171His	p.Q171H	ENST00000366898	NM_004562.2	171	caG/caT	4/12	0.24973884438329	4	FACETS	0.725	0.531	0.957	0.362	0.265	0.479	CLONAL	1	TRUE	2	0.254461857797805	4		370	204	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518344	8518344	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	79	252	0	ENST00000356435.5:c.1047G>T	p.Glu349Asp	p.E349D	ENST00000356435		349	gaG/gaT	10/35	0.254461857797805	5	FACETS	0.894	0.798	0.993	0.715	0.638	0.794	CLONAL	4	TRUE	0	0.254461857797805	5		252	240	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390479	118390479	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	62	396	0	ENST00000534358.1:c.11293G>T	p.Gly3765Cys	p.G3765C	ENST00000534358	NM_005933.3	3765	Ggc/Tgc	32/36	0.254461857797805	3	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	1	0.254461857797805	3		396	247	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112138	115112138	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	16	529	0	ENST00000257566.3:c.1602G>T	p.Met534Ile	p.M534I	ENST00000257566	NM_016569.3	534	atG/atT	7/8	0.151563002074487	1	FACETS	0.717	0.533	0.934	0.717	0.533	0.934	INDETERMINATE	1	TRUE	0	0.254461857797805	1		529	153	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274126	10274126	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	14	369	0	ENST00000330684.3:c.143A>T	p.Glu48Val	p.E48V	ENST00000330684	NM_001134407.1	48	gAg/gTg	2/13	1	2	FACETS	0.775	0.563	1	0.775	0.563	1	CLONAL	1	TRUE	1	0.254461857797805	2		369	142	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1627372	1627372	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	50	517	0	ENST00000344749.5:c.352G>T	p.Gly118Cys	p.G118C	ENST00000344749	NM_001136139.2	118	Ggc/Tgc	6/19	0.254461857797805	2	FACETS	0.954	0.82	1	0.954	0.82	1	CLONAL	2	TRUE	0	0.254461857797805	2		517	206	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296102	15296102	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	57	524	0	ENST00000263388.2:c.2262G>T	p.Met754Ile	p.M754I	ENST00000263388	NM_000435.2	754	atG/atT	14/33	0.254461857797805	2	FACETS	0.987	0.857	1	0.987	0.857	1	CLONAL	2	TRUE	0	0.254461857797805	2		524	227	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222282	2222283	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0007696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	63	442	1	ENST00000326181.6:c.566_567delinsTT	p.Arg189Leu	p.R189L	ENST00000326181	NM_032271.2	189	cGG/cTT	8/21	1	2	FACETS	1	0.911	1	1	0.981	1	CLONAL	2	TRUE	1	0.254461857797805	2		443	236	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	19	430	0	ENST00000269305.4:c.383del	p.Pro128LeufsTer42	p.P128Lfs*42	ENST00000269305	NM_001126112.2	128	cCt/ct	5/11	0.265407409450851	3	FACETS	0.865	0.669	1	0.432	0.334	0.543	INDETERMINATE	1	TRUE	1	0.627439872970913	3		430	92	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499619	18499619	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	42	718	1	ENST00000266497.5:c.1474C>T	p.Gln492Ter	p.Q492*	ENST00000266497		492	Cag/Tag	10/31	0.41467492482277	1	FACETS	0.604	0.514	0.701	0.604	0.514	0.701	SUBCLONAL	1	TRUE	0	0.627439872970913	1		719	152	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067452	37067452	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	53	476	0	ENST00000231790.2:c.1363A>G	p.Thr455Ala	p.T455A	ENST00000231790	NM_000249.3	455	Act/Gct	12/19	0.490035547057722	5	FACETS	0.965	0.838	1			1	CLONAL	2	TRUE	NA	0.627439872970913	5		476	170	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776898	76776898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	278	400	0	ENST00000373344.5:c.7054G>A	p.Asp2352Asn	p.D2352N	ENST00000373344	NM_000489.3	2352	Gat/Aat	33/35	0.622046795907123	2	FACETS	0.742	0.697	0.788			1	SUBCLONAL	1	TRUE	NA	0.747886294950211	2		400	1002	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0007744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	128	316	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	0.423136407170453	2		316	588	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	39	145	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	FALSE	1	0.222091996746001	2		145	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0007787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	57	440	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.222091996746001	1	FACETS	0.719	0.616	0.831	0.719	0.616	0.831	SUBCLONAL	1	FALSE	0	0.222091996746001	1		440	635	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094441	27094441	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	49	244	1	ENST00000324856.7:c.3149A>G	p.Asp1050Gly	p.D1050G	ENST00000324856	NM_006015.4	1050	gAc/gGc	11/20	0.179631056063112	1	FACETS	0.586	0.496	0.687	0.586	0.496	0.687	SUBCLONAL	1	FALSE	0	0.222091996746001	1		245	669	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951144	48951144	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	167	332	0	ENST00000267163.4:c.1306C>T	p.Gln436Ter	p.Q436*	ENST00000267163	NM_000321.2	436	Cag/Tag	13/27	0.222091996746001	3	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	FALSE	1	0.222091996746001	3		332	817	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103403	2103403	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	44	334	0	ENST00000219476.3:c.286G>T	p.Glu96Ter	p.E96*	ENST00000219476	NM_000548.3	96	Gag/Tag	4/42	0.222091996746001	0	FACETS	0.648	0.543	0.763			1	SUBCLONAL	1	FALSE	0	0.222091996746001	0		334	476	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0007788-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	161	383	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.258850574574498	4	FACETS	0.756	0.694	0.822	0.756	0.694	0.822	SUBCLONAL	2	TRUE	2	0.304838345869758	4		383	911	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0007788-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	46	229	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.298803160324858	2	FACETS	0.803	0.678	0.94	0.401	0.339	0.47	CLONAL	1	TRUE	0	0.304838345869758	2		229	376	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467197	25467197	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007788-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	124	405	0	ENST00000264709.3:c.1678G>T	p.Val560Leu	p.V560L	ENST00000264709	NM_175629.2	560	Gtg/Ttg	15/23	0.303149487990075	4	FACETS	0.93	0.844	1			1	CLONAL	2	TRUE	NA	0.304838345869758	4		405	571	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539493	187539493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007788-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	108	482	0	ENST00000441802.2:c.8247G>T	p.Glu2749Asp	p.E2749D	ENST00000441802	NM_005245.3	2749	gaG/gaT	10/27	1	2	FACETS	0.847	0.759	0.939	0.847	0.759	0.939	CLONAL	1	TRUE	1	0.304838345869758	2		482	837	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344679	70344679	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007788-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	209	549	2	ENST00000374080.3:c.2040del	p.Lys681SerfsTer30	p.K681Sfs*30	ENST00000374080		680	gaG/ga	14/45	0.258850574574498	4	FACETS	0.855	0.794	0.919	0.855	0.794	0.919	CLONAL	2	TRUE	2	0.304838345869758	4		551	1046	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489207	2489207	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007788-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	107	521	0	ENST00000355716.4:c.112G>C	p.Ala38Pro	p.A38P	ENST00000355716	NM_003820.2	38	Gct/Cct	2/8	0.304838345869758	3	FACETS	1	0.94	1	0.356	0.319	0.395	CLONAL	1	TRUE	0	0.304838345869758	3		521	758	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932152	36932152	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007788-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	130	664	0	ENST00000361632.4:c.2317A>G	p.Thr773Ala	p.T773A	ENST00000361632		773	Act/Gct	16/16	0.304838345869758	3	FACETS	1	0.954	1	0.362	0.328	0.398	CLONAL	1	TRUE	0	0.304838345869758	3		664	905	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46266444	46266444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007788-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	160	744	3	ENST00000371998.3:c.2429C>T	p.Ser810Phe	p.S810F	ENST00000371998		810	tCt/tTt	13/23	0.304838345869758	3	FACETS	0.959	0.877	1	0.479	0.438	0.523	CLONAL	1	TRUE	1	0.304838345869758	3		747	1262	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096065	11096068	+	frameshift_variant	Frame_Shift_Del	DEL	GGAC	GGAC	-	novel	NA	P-0007788-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	59	402	0	ENST00000358026.2:c.339_342del	p.Met113IlefsTer189	p.M113Ifs*189	ENST00000358026	NM_001128849.1	113	atGGAC/at	3/36	0.304838345869758	1	FACETS	0.758	0.654	0.87	0.758	0.654	0.87	SUBCLONAL	1	TRUE	0	0.304838345869758	1		402	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577562	7577563	+	missense_variant	Missense_Mutation	DNP	CT	CT	AA	novel	NA	P-0007788-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	248	487	0	ENST00000269305.4:c.718_719delinsTT	p.Ser240Phe	p.S240F	ENST00000269305	NM_001126112.2	240	AGt/TTt	7/11	0.304838345869758	3	FACETS	0.899	0.845	0.954	0.899	0.845	0.954	CLONAL	3	TRUE	0	0.304838345869758	3		487	695	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038275	30038275	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0007794-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	348	380	0	ENST00000338641.4:c.447+1G>A		p.X149_splice	ENST00000338641	NM_000268.3	149			0.52684453136681	2	FACETS	0.812	0.776	0.848	0.812	0.776	0.848	CLONAL	2	TRUE	0	0.642465430691425	2		380	667	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579356	7579366	+	frameshift_variant	Frame_Shift_Del	DEL	GACGGAAACCG	GACGGAAACCG	-	novel	NA	P-0007794-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	330	343	0	ENST00000269305.4:c.321_331del	p.Phe109LeufsTer36	p.F109Lfs*36	ENST00000269305	NM_001126112.2	107	taCGGTTTCCGTCtg/tatg	4/11	0.371034200101536	3	FACETS	1	0.992	1	0.769	0.736	0.803	INDETERMINATE	2	TRUE	0	0.642465430691425	3		343	588	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0007807-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	52	316	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.176288028012905	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		316	1079	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0007815-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	621	437	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.679966222043844	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.679966222043844	2		437	881	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520656	176520656	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs1465469681	NA	P-0007815-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	80	241	0	ENST00000292408.4:c.1399C>G	p.Leu467Val	p.L467V	ENST00000292408	NM_213647.1	467	Ctg/Gtg	11/18	1	2	FACETS	0.657	0.583	0.736	0.657	0.583	0.736	SUBCLONAL	1	TRUE	1	0.679966222043844	2		241	358	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020802	112020802	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007815-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	77	588	0	ENST00000368678.4:c.769G>C	p.Ala257Pro	p.A257P	ENST00000368678		257	Gct/Cct	8/13	0.679966222043844	2	FACETS	0.171	0.149	0.195	0.086	0.074	0.098	SUBCLONAL	1	TRUE	0	0.679966222043844	2		588	1322	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098944	178098944	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	56	322	0	ENST00000397062.3:c.101G>C	p.Arg34Pro	p.R34P	ENST00000397062	NM_006164.4	34	cGa/cCa	2/5	1	2	FACETS	0.981	0.84	1	0.981	0.84	1	CLONAL	1	TRUE	1	0.195794529293282	2		322	583	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18576974	18576974	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0007832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	29	248	0	ENST00000266497.5:c.2381+1G>A		p.X794_splice	ENST00000266497		794			1	2	FACETS	0.746	0.599	0.914	0.746	0.599	0.914	CLONAL	1	TRUE	1	0.195794529293282	2		248	397	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934194	48934194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	30	303	0	ENST00000267163.4:c.649C>T	p.Gln217Ter	p.Q217*	ENST00000267163	NM_000321.2	217	Cag/Tag	7/27	1	2	FACETS	0.719	0.579	0.878	0.719	0.579	0.878	SUBCLONAL	1	TRUE	1	0.195794529293282	2		303	426	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098846	178098846	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	77	584	0	ENST00000397062.3:c.199G>A	p.Glu67Lys	p.E67K	ENST00000397062	NM_006164.4	67	Gag/Aag	2/5	1	2	FACETS	0.939	0.823	1	0.939	0.823	1	CLONAL	1	TRUE	1	0.195794529293282	2		584	838	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649856	88649856	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	27	175	0	ENST00000372037.3:c.105G>A	p.Met35Ile	p.M35I	ENST00000372037	NM_004329.2	35	atG/atA	4/13	1	2	FACETS	0.87	0.693	1	0.87	0.693	1	CLONAL	1	TRUE	1	0.195794529293282	2		175	317	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88672116	88672116	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	41	259	0	ENST00000372037.3:c.650G>A	p.Gly217Asp	p.G217D	ENST00000372037	NM_004329.2	217	gGt/gAt	8/13	1	2	FACETS	0.899	0.749	1	0.899	0.749	1	CLONAL	1	TRUE	1	0.195794529293282	2		259	466	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289925	15289925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35031555	NA	P-0007832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	34	308	0	ENST00000263388.2:c.3629G>A	p.Arg1210His	p.R1210H	ENST00000263388	NM_000435.2	1210	cGc/cAc	22/33	1	2	FACETS	0.603	0.492	0.729	0.603	0.492	0.729	SUBCLONAL	1	TRUE	1	0.195794529293282	2		308	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578455	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0007832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	84	278	0	ENST00000269305.4:c.475_476del	p.Ala159HisfsTer21	p.A159Hfs*21	ENST00000269305	NM_001126112.2	159	GCc/c	5/11	1	2	FACETS	0.759	0.672	0.853	1	0.978	1	SUBCLONAL	2	TRUE	1	0.195794529293282	2		278	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0007866-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	111	375	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.221824362827139	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	2	TRUE	0	0.221824362827139	2		377	490	SUCCESS
APC	324	MSKCC	GRCh37	5	112163677	112163677	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0007866-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	64	491	0	ENST00000257430.4:c.1600A>T	p.Lys534Ter	p.K534*	ENST00000257430	NM_000038.5	534	Aaa/Taa	13/16	0.165988105159381	3	FACETS	0.995	0.862	1	0.498	0.431	0.571	CLONAL	1	TRUE	1	0.221824362827139	3		491	644	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0007866-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	35	209	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.165988105159381	3	FACETS	1	0.933	1	0.654	0.539	0.782	CLONAL	1	TRUE	1	0.221824362827139	3		209	268	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200723	128200723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007866-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	96	488	1	ENST00000341105.2:c.1082G>A	p.Arg361His	p.R361H	ENST00000341105	NM_032638.4	361	cGc/cAc	5/6	0.221824362827139	3	FACETS	0.965	0.858	1	0.483	0.429	0.54	CLONAL	1	TRUE	1	0.221824362827139	3		489	996	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910405	32910405	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0007866-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	42	567	0	ENST00000380152.3:c.1913T>A	p.Leu638Ter	p.L638*	ENST00000380152		638	tTa/tAa	11/27	0.221824362827139	3	FACETS	0.525	0.436	0.623	0.262	0.218	0.312	SUBCLONAL	1	TRUE	1	0.221824362827139	3		567	802	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735547	40735547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756810336	NA	P-0007866-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	297	315	0	ENST00000373198.4:c.3326G>A	p.Arg1109Gln	p.R1109Q	ENST00000373198	NM_133170.3	1109	cGg/cAg	25/32	0.221824362827139	8	FACETS	1	0.966	1	1	0.966	1	CLONAL	5	TRUE	3	0.221824362827139	8		315	865	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281149	46281149	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0007866-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1382	94	653	0	ENST00000371998.3:c.3947-1G>A		p.X1316_splice	ENST00000371998		1316			0.221824362827139	9	FACETS	1	0.902	1	0.146	0.129	0.164	CLONAL	1	TRUE	2	0.221824362827139	9		653	1476	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0007881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	22	335	1	ENST00000374080.3:c.3670C>T	p.Leu1224Phe	p.L1224F	ENST00000374080		1224	Ctc/Ttc	26/45	1	1	FACETS	0.565	0.437	0.713	0.565	0.437	0.713	SUBCLONAL	1	TRUE	0	0.18	1		336	394	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539042	23539042	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	34	445	0	ENST00000380871.4:c.397C>G	p.His133Asp	p.H133D	ENST00000380871	NM_006167.3	133	Cac/Gac	2/2	1	2	FACETS	0.781	0.637	0.942	0.781	0.637	0.942	CLONAL	1	TRUE	1	0.18	2		445	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0007887-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	136	353	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.476589321391195	1	FACETS	0.718	0.657	0.782	0.718	0.657	0.782	SUBCLONAL	1	TRUE	0	0.554140865321666	1		353	494	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0007887-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	138	369	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.554140865321666	2		369	462	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0007887-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	145	205	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	0.385564077992032	3	FACETS	1	0.983	1	0.79	0.736	0.844	CLONAL	2	TRUE	0	0.554140865321666	3		205	282	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604736	48604736	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007887-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	253	419	0	ENST00000342988.3:c.1558G>T	p.Glu520Ter	p.E520*	ENST00000342988	NM_005359.5	520	Gaa/Taa	12/12	0.451787156865448	2	FACETS	0.767	0.724	0.811	0.767	0.724	0.811	SUBCLONAL	2	TRUE	0	0.554140865321666	2		419	595	SUCCESS
ATR	545	MSKCC	GRCh37	3	142284970	142284970	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007887-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	73	428	0	ENST00000350721.4:c.285T>A	p.Ser95Arg	p.S95R	ENST00000350721	NM_001184.3	95	agT/agA	3/47	1	2	FACETS	0.608	0.534	0.688	0.608	0.534	0.688	SUBCLONAL	1	TRUE	1	0.554140865321666	2		428	433	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526167	189526167	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1274675449	NA	P-0007887-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	170	402	0	ENST00000264731.3:c.431C>T	p.Thr144Met	p.T144M	ENST00000264731	NM_003722.4	144	aCg/aTg	4/14	1	2	FACETS	0.733	0.675	0.794	0.733	0.675	0.794	SUBCLONAL	1	TRUE	1	0.554140865321666	2		402	837	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434463	49434463	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007887-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	105	325	0	ENST00000301067.7:c.7090A>C	p.Ser2364Arg	p.S2364R	ENST00000301067	NM_003482.3	2364	Agt/Cgt	31/54	1	2	FACETS	0.764	0.688	0.844	0.764	0.688	0.844	SUBCLONAL	1	TRUE	1	0.554140865321666	2		325	496	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56411570	56411570	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007887-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	199	494	0	ENST00000348428.3:c.1754A>G	p.Glu585Gly	p.E585G	ENST00000348428	NM_006785.3	585	gAa/gGa	15/17	0.451787156865448	2	FACETS	1	0.992	1	0.733	0.686	0.781	CLONAL	1	TRUE	0	0.554140865321666	2		494	490	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5286129	5286129	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007887-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	89	386	0	ENST00000357368.4:c.23G>C	p.Gly8Ala	p.G8A	ENST00000357368	NM_002850.3	8	gGc/gCc	2/38	1	2	FACETS	0.566	0.502	0.633	0.566	0.502	0.633	SUBCLONAL	1	TRUE	1	0.554140865321666	2		386	568	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172340	7172340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs181150880	NA	P-0007887-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	142	479	0	ENST00000302850.5:c.1229G>A	p.Arg410Gln	p.R410Q	ENST00000302850	NM_000208.2	410	cGg/cAg	5/22	1	2	FACETS	0.801	0.732	0.873	0.801	0.732	0.873	CLONAL	1	TRUE	1	0.554140865321666	2		479	640	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593613	55593613	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913521	NA	P-0007890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	654	488	0	ENST00000288135.5:c.1679T>A	p.Val560Asp	p.V560D	ENST00000288135	NM_000222.2	560	gTt/gAt	11/21	0.829503289071141	3	FACETS	0.954	0.924	0.984	0.954	0.924	0.984	CLONAL	2	TRUE	1	0.829503289071141	3		488	1169	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252077	226252077	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	17	80	0	ENST00000366813.1:c.25C>T	p.Arg9Cys	p.R9C	ENST00000366813		9	Cgc/Tgc	1/3	0.717525316579473	6	FACETS	0.327	0.244	0.427	0.065	0.048	0.086	SUBCLONAL	1	TRUE	1	0.829503289071141	6		80	333	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662959	52662959	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	608	431	1	ENST00000394830.3:c.1394C>T	p.Pro465Leu	p.P465L	ENST00000394830	NM_018313.4	465	cCc/cTc	13/30	0.829503289071141	3	FACETS	0.994	0.963	1	0.663	0.642	0.684	CLONAL	2	TRUE	0	0.829503289071141	3		432	1043	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144147	55144147	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	509	371	0	ENST00000257290.5:c.1976A>G	p.Asn659Ser	p.N659S	ENST00000257290	NM_006206.4	659	aAc/aGc	14/23	0.829503289071141	6	FACETS	0.856	0.822	0.892			1	CLONAL	3	TRUE	NA	0.829503289071141	6		371	1270	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161467	2161467	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	283	566	0	ENST00000434045.2:c.60G>T	p.Met20Ile	p.M20I	ENST00000434045	NM_001127598.1	20	atG/atT	2/5	0.325459049542178	5	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.829503289071141	5		566	1395	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161480	2161480	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	266	531	0	ENST00000434045.2:c.47A>G	p.Glu16Gly	p.E16G	ENST00000434045	NM_001127598.1	16	gAa/gGa	2/5	0.325459049542178	5	FACETS	1	0.975	1			1	INDETERMINATE	1	TRUE	NA	0.829503289071141	5		531	1330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0007905-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	218	556	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.788602617437351	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	FALSE	0	0.795123636405355	2		556	269	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136231	2136231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45517364	NA	P-0007905-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	115	534	0	ENST00000219476.3:c.4700G>A	p.Gly1567Asp	p.G1567D	ENST00000219476	NM_000548.3	1567	gGc/gAc	37/42	0.795123636405355	2	FACETS	0.933	0.879	0.984	0.933	0.879	0.984	CLONAL	2	FALSE	0	0.795123636405355	2		534	155	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107088	27107091	+	frameshift_variant	Frame_Shift_Del	DEL	GGCT	GGCT	-	novel	NA	P-0007905-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	147	361	0	ENST00000324856.7:c.6700_6703del	p.Ala2234ProfsTer32	p.A2234Pfs*32	ENST00000324856	NM_006015.4	2233	cgGGCT/cg	20/20	0.630836803869375	6	FACETS	1	0.982	1	0.808	0.746	0.872	CLONAL	2	FALSE	3	0.795123636405355	6		361	395	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051206	128051232	+	frameshift_variant	Frame_Shift_Del	DEL	GGGAACCGCTTCCTGAGGGTCGTTCCC	GGGAACCGCTTCCTGAGGGTCGTTCCC	A	novel	NA	P-0007905-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	97	807	0	ENST00000285398.2:c.91_117delinsT	p.Gly31PhefsTer9	p.G31Ffs*9	ENST00000285398	NM_000122.1	31	GGGAACGACCCTCAGGAAGCGGTTCCC/T	2/15	0.795123636405355	3	FACETS	0.881	0.792	0.975	0.441	0.396	0.488	CLONAL	1	FALSE	1	0.795123636405355	3		807	387	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295168	1295169	+	upstream_gene_variant	5'Flank	DNP	CG	CG	TC	novel	NA	P-0007905-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	58	195	0				ENST00000310581	NM_198253.2	-/1132			0.784359640451804	3	FACETS	0.962	0.861	1	0.962	0.861	1	CLONAL	2	FALSE	1	0.795123636405355	3		195	106	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0007921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	59	465	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.283625419286087	4	FACETS	1	0.871	1	0.508	0.436	0.588	CLONAL	1	TRUE	2	0.14	4		465	945	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022585	12022585	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	59	455	0	ENST00000396373.4:c.691G>C	p.Glu231Gln	p.E231Q	ENST00000396373	NM_001987.4	231	Gag/Cag	5/8	0.3	6	FACETS	0.849	0.73	0.979			1	CLONAL	2	TRUE	NA	0.14	6		455	635	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566575	41566575	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	23	346	0	ENST00000263253.7:c.4452G>T	p.Lys1484Asn	p.K1484N	ENST00000263253	NM_001429.3	1484	aaG/aaT	27/31	1	2	FACETS	0.733	0.571	0.923	0.733	0.571	0.923	CLONAL	1	TRUE	1	0.14	2		346	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579849	7579849	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	125	436	0	ENST00000269305.4:c.64del	p.Leu22TyrfsTer22	p.L22Yfs*22	ENST00000269305	NM_001126112.2	22	Cta/ta	2/11	0.185662581830952	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.201810654684579	1		436	843	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541725	120541725	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	71	645	0	ENST00000229340.5:c.132T>G	p.Asp44Glu	p.D44E	ENST00000229340	NM_006861.6	44	gaT/gaG	3/6	1	2	FACETS	0.578	0.503	0.66	0.578	0.503	0.66	SUBCLONAL	1	TRUE	1	0.201810654684579	2		645	1217	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10257130	10257130	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	54	331	0	ENST00000340748.4:c.2743del	p.Glu915ArgfsTer42	p.E915Rfs*42	ENST00000340748		915	Gag/ag	27/40	0.185662581830952	1	FACETS	0.63	0.537	0.732	0.63	0.537	0.732	SUBCLONAL	1	TRUE	0	0.201810654684579	1		331	764	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510563	38510563	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1578	87	382	0	ENST00000254066.5:c.817A>T	p.Ile273Phe	p.I273F	ENST00000254066	NM_000964.3	273	Atc/Ttc	7/9	0.492032100866334	13	FACETS	0.787	0.694	0.888			1	SUBCLONAL	1	TRUE	NA	0.492032100866334	13		382	1665	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265378	10265378	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	82	374	0	ENST00000340748.4:c.1668T>G	p.Phe556Leu	p.F556L	ENST00000340748		556	ttT/ttG	20/40	0.492032100866334	3	FACETS	0.839	0.742	0.942	0.42	0.371	0.471	CLONAL	1	TRUE	1	0.492032100866334	3		374	495	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929570	44929570	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0008010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	122	342	0	ENST00000377967.4:c.2670C>G	p.Tyr890Ter	p.Y890*	ENST00000377967	NM_021140.2	890	taC/taG	17/29	0.383774069150776	4	FACETS	1	0.939	1	0.525	0.475	0.577	CLONAL	1	TRUE	2	0.492032100866334	4		342	705	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0008018-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	283	758	1	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.791319250380081	2		759	625	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965689	25965689	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008018-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	347	489	0	ENST00000435504.4:c.3517A>C	p.Ser1173Arg	p.S1173R	ENST00000435504		1173	Agt/Cgt	13/13	1	2	FACETS	0.973	0.925	1	0.973	0.925	1	CLONAL	1	TRUE	1	0.791319250380081	2		489	901	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436379	52436392	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGACCCCTTGGC	GCTGACCCCTTGGC	-	novel	NA	P-0008018-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	257	476	0	ENST00000460680.1:c.2102_2115del	p.Arg701HisfsTer11	p.R701Hfs*11	ENST00000460680	NM_004656.3	701	cGCCAAGGGGTCAGC/c	17/17	0.791319250380081	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.791319250380081	1		476	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0008036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	385	454	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.508112063838116	3	FACETS	0.994	0.948	1	0.994	0.948	1	CLONAL	2	TRUE	1	0.508112063838116	3		454	956	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098944	178098944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	256	212	0	ENST00000397062.3:c.101G>A	p.Arg34Gln	p.R34Q	ENST00000397062	NM_006164.4	34	cGa/cAa	2/5	0.162988920892494	5	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.508112063838116	5		212	734	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578189	7578189	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0008036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	160	451	0	ENST00000269305.4:c.660T>G	p.Tyr220Ter	p.Y220*	ENST00000269305	NM_001126112.2	220	taT/taG	6/11	0.508112063838116	3	FACETS	0.854	0.783	0.928	0.427	0.391	0.464	CLONAL	1	TRUE	1	0.508112063838116	3		451	925	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480350	56480350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147905731	NA	P-0008036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	62	294	1	ENST00000267101.3:c.457G>A	p.Asp153Asn	p.D153N	ENST00000267101	NM_001982.3	153	Gat/Aat	4/28	0.508112063838116	3	FACETS	0.382	0.329	0.439	0.191	0.164	0.22	SUBCLONAL	1	TRUE	1	0.508112063838116	3		295	802	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577098	7577098	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	255	529	0	ENST00000269305.4:c.840A>T	p.Arg280Ser	p.R280S	ENST00000269305	NM_001126112.2	280	agA/agT	8/11	0.408333235101905	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.408333235101905	1		529	749	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15374341	15374341	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	59	408	0	ENST00000263377.2:c.1231G>A	p.Glu411Lys	p.E411K	ENST00000263377	NM_058243.2	411	Gag/Aag	7/20	0.297930031813095	5	FACETS	0.614	0.527	0.709			1	SUBCLONAL	1	TRUE	NA	0.408333235101905	5		408	759	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0008046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	71	409	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.814	0.709	0.928	0.814	0.709	0.928	CLONAL	1	TRUE	1	0.208078385318152	2		409	838	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219409	1219409	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	62	270	0	ENST00000326873.7:c.461A>T	p.His154Leu	p.H154L	ENST00000326873	NM_000455.4	154	cAc/cTc	3/10	NA	2	FACETS	0.974	0.841	1			1	INDETERMINATE	1	TRUE	NA	0.208078385318152	2		270	612	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076772	72076772	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1330	151	579	1	ENST00000357731.5:c.725T>A	p.Leu242Gln	p.L242Q	ENST00000357731	NM_173808.2	242	cTg/cAg	5/7	1	2	FACETS	0.98	0.893	1	0.98	0.893	1	CLONAL	1	TRUE	1	0.208078385318152	2		580	1481	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743316	162743316	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	330	331	0	ENST00000367921.3:c.1786G>A	p.Asp596Asn	p.D596N	ENST00000367921	NM_006182.2	596	Gat/Aat	14/18	0.208078385318152	4	FACETS	1	0.963	1	1	0.963	1	CLONAL	3	TRUE	1	0.208078385318152	4		331	1247	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696255	52696255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1246	100	382	0	ENST00000394830.3:c.422G>T	p.Trp141Leu	p.W141L	ENST00000394830	NM_018313.4	141	tGg/tTg	5/30	1	2	FACETS	0.714	0.636	0.798	0.714	0.636	0.798	SUBCLONAL	1	TRUE	1	0.208078385318152	2		382	1346	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998391	100998391	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	27	172	0	ENST00000325455.5:c.1411C>T	p.Gln471Ter	p.Q471*	ENST00000325455	NM_001202474.3	471	Cag/Tag	1/8	1	2	FACETS	1	0.818	1	1	0.818	1	CLONAL	1	TRUE	1	0.208078385318152	2		172	253	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597373	10597373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	104	425	0	ENST00000171111.5:c.1830G>A	p.Met610Ile	p.M610I	ENST00000171111	NM_203500.1	610	atG/atA	6/6	0.208078385318152	1	FACETS	0.938	0.838	1	0.938	0.838	1	CLONAL	1	TRUE	0	0.208078385318152	1		425	955	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0008050-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	68	316	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.733	0.639	0.835	0.733	0.639	0.835	SUBCLONAL	1	TRUE	1	0.351170959616527	2		316	528	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144891	47144891	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	99	503	1	ENST00000409792.3:c.4862G>T	p.Gly1621Val	p.G1621V	ENST00000409792	NM_014159.6	1621	gGa/gTa	7/21	0.513525800826004	1	FACETS	0.637	0.571	0.705	0.637	0.571	0.705	SUBCLONAL	1	TRUE	0	0.513525800826004	1		504	450	SUCCESS
APC	324	MSKCC	GRCh37	5	112155011	112155011	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	168	505	0	ENST00000257430.4:c.1282G>T	p.Glu428Ter	p.E428*	ENST00000257430	NM_000038.5	428	Gaa/Taa	10/16	0.513525800826004	5	FACETS	0.956	0.877	1	0.319	0.292	0.347	CLONAL	1	TRUE	2	0.513525800826004	5		505	1212	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468009	50468009	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	128	426	0	ENST00000331340.3:c.1244C>A	p.Thr415Asn	p.T415N	ENST00000331340	NM_006060.4	415	aCc/aAc	8/8	0.451598742113591	3	FACETS	0.913	0.829	1	0.457	0.414	0.501	CLONAL	1	TRUE	1	0.513525800826004	3		426	686	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845148	151845148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	149	554	0	ENST00000262189.6:c.13864G>A	p.Asp4622Asn	p.D4622N	ENST00000262189	NM_170606.2	4622	Gac/Aac	52/59	0.451598742113591	3	FACETS	0.728	0.664	0.795	0.364	0.332	0.398	SUBCLONAL	1	TRUE	1	0.513525800826004	3		554	1002	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41554444	41554444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	140	544	0	ENST00000263253.7:c.3530G>A	p.Cys1177Tyr	p.C1177Y	ENST00000263253	NM_001429.3	1177	tGc/tAc	19/31	0.204867025005971	0	FACETS	0.328	0.298	0.359			1	INDETERMINATE	1	TRUE	0	0.513525800826004	0		544	809	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950267	15950268	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0008065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	141	600	0	ENST00000268712.3:c.6676_6677del	p.Met2226GlyfsTer8	p.M2226Gfs*8	ENST00000268712	NM_006311.3	2226	ATg/g	42/46	1	2	FACETS	0.712	0.649	0.778	0.712	0.649	0.778	SUBCLONAL	1	TRUE	1	0.513525800826004	2		600	771	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191501	10191501	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	81	457	0	ENST00000256474.2:c.495del	p.Val166SerfsTer4	p.V166Sfs*4	ENST00000256474	NM_000551.3	165	gTt/gt	3/3	0.513525800826004	1	FACETS	0.554	0.491	0.622	0.554	0.491	0.622	SUBCLONAL	1	TRUE	0	0.513525800826004	1		457	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0008074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	348	507	0	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	0.757237353149525	1	FACETS	0.981	0.943	1	0.981	0.943	1	CLONAL	1	TRUE	0	0.786701282778904	1		507	547	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645032	67645032	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	375	537	0	ENST00000264010.4:c.297G>C	p.Gln99His	p.Q99H	ENST00000264010	NM_006565.3	99	caG/caC	3/12	0.786701282778904	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.786701282778904	1		537	550	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0008134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	110	228	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	1	2	FACETS	0.826	0.752	0.903	1	0.987	1	CLONAL	2	TRUE	1	0.413519493382975	2		228	322	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216125	7216125	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1267	314	458	0	ENST00000380728.2:c.934C>T	p.Arg312Trp	p.R312W	ENST00000380728		312	Cgg/Tgg	11/11	1	2	FACETS	0.961	0.904	1	0.961	0.904	1	CLONAL	1	TRUE	1	0.413519493382975	2		458	1581	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775242	73775242	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1278	214	274	0	ENST00000254810.4:c.14A>T	p.Lys5Met	p.K5M	ENST00000254810	NM_005324.3	5	aAg/aTg	2/4	0.281377441883335	5	FACETS	1	0.976	1	0.375	0.347	0.404	CLONAL	1	TRUE	2	0.413519493382975	5		274	1492	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627760	14627760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	257	380	1	ENST00000254322.2:c.310G>A	p.Glu104Lys	p.E104K	ENST00000254322	NM_006145.1	104	Gag/Aag	2/3	0.413519493382975	3	FACETS	1	0.968	1	0.529	0.494	0.565	CLONAL	1	TRUE	1	0.413519493382975	3		381	1418	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339535	70339535	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0008134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1229	489	382	0	ENST00000374080.3:c.205-1G>C		p.X69_splice	ENST00000374080		69			0.204250291757964	5	FACETS	1	0.99	1	0.744	0.71	0.778	INDETERMINATE	2	TRUE	2	0.413519493382975	5		382	1718	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655349	45655349	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs751702712	NA	P-0008146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	186	421	0	ENST00000407780.3:c.503A>G	p.Asn168Ser	p.N168S	ENST00000407780	NM_001283052.1	168	aAc/aGc	4/7	1	2	FACETS	0.884	0.818	0.952	0.884	0.818	0.952	CLONAL	1	TRUE	1	0.537365796911426	2		421	783	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437683	52437685	+	frameshift_variant	Frame_Shift_Del	DEL	GTA	GTA	T	novel	NA	P-0008146-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	207	434	0	ENST00000460680.1:c.1476_1478delinsA	p.Ser492ArgfsTer6	p.S492Rfs*6	ENST00000460680	NM_004656.3	492	agTACa/agAa	13/17	0.537365796911426	1	FACETS	0.928	0.867	0.991	0.928	0.867	0.991	CLONAL	1	TRUE	0	0.537365796911426	1		434	607	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0008165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	42	407	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.863	0.72	1	0.863	0.72	1	CLONAL	1	TRUE	1	0.18	2		407	541	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0008165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	60	755	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.18	2		755	661	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473756	67473756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906852	NA	P-0008165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	49	226	0	ENST00000327367.4:c.836G>A	p.Arg279Lys	p.R279K	ENST00000327367	NM_005902.3	279	aGg/aAg	6/9	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.18	2		226	479	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	279	473	0	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	0.316976561937657	18	FACETS	1	0.951	1			1	CLONAL	6	TRUE	NA	0.316976561937657	18		473	1024	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225338988	225338988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759758641	NA	P-0008178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	82	519	0	ENST00000264414.4:c.2281C>T	p.Arg761Cys	p.R761C	ENST00000264414	NM_003590.4	761	Cgc/Tgc	16/16	0.302879245198988	3	FACETS	1	0.973	1	0.454	0.402	0.509	CLONAL	1	TRUE	0	0.316976561937657	3		519	440	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939177	36939177	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	40	557	0	ENST00000361632.4:c.532G>C	p.Val178Leu	p.V178L	ENST00000361632		178	Gtg/Ctg	5/16	NA	2	FACETS	0.963	0.806	1			1	INDETERMINATE	1	TRUE	NA	0.316976561937657	2		557	262	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576120	88576120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147160868	NA	P-0008178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	54	405	0	ENST00000360948.2:c.1553G>A	p.Arg518His	p.R518H	ENST00000360948	NM_001012338.2	518	cGt/cAt	13/19	0.226149430352121	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.316976561937657	1		405	216	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296167	15296167	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	23	362	0	ENST00000263388.2:c.2197C>A	p.Leu733Met	p.L733M	ENST00000263388	NM_000435.2	733	Ctg/Atg	14/33	0.17842487283391	1	FACETS	0.86	0.678	1	0.86	0.678	1	INDETERMINATE	1	TRUE	0	0.316976561937657	1		362	142	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0008224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	44	407	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.806	0.677	0.948	0.806	0.677	0.948	CLONAL	1	TRUE	1	0.275635778564259	2		407	396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0008224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	90	622	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.20977006999347	1	FACETS	0.966	0.858	1	0.966	0.858	1	CLONAL	1	TRUE	0	0.275635778564259	1		624	583	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248369	212248369	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	60	351	0	ENST00000342788.4:c.3898C>A	p.Pro1300Thr	p.P1300T	ENST00000342788	NM_005235.2	1300	Cct/Act	28/28	1	2	FACETS	0.89	0.768	1	0.89	0.768	1	CLONAL	1	TRUE	1	0.275635778564259	2		351	489	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412361	63412361	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs781019812	NA	P-0008224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	73	304	0	ENST00000330258.3:c.806A>T	p.His269Leu	p.H269L	ENST00000330258	NM_152424.3	269	cAt/cTt	2/2	0.183822273421602	0	FACETS	1	0.952	1			1	CLONAL	1	TRUE	NA	0.275635778564259	0		304	331	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293119	91293119	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	50	274	0	ENST00000355112.3:c.623del	p.Leu208CysfsTer11	p.L208Cfs*11	ENST00000355112	NM_000057.2	207	gaT/ga	3/22	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.275635778564259	2		274	348	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	46	145	0				ENST00000310581	NM_198253.2	-/1132			0.739771937790038	3	FACETS	1	0.931	1	0.57	0.491	0.652	CLONAL	1	TRUE	1	0.853623540027224	3		145	135	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0008236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	442	316	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.851044834134351	3	FACETS	0.934	0.899	0.969	0.934	0.899	0.969	CLONAL	2	TRUE	1	0.853623540027224	3		316	791	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476745	140476745	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs878854675	NA	P-0008236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	258	371	0	ENST00000288602.6:c.1661T>C	p.Ile554Thr	p.I554T	ENST00000288602	NM_004333.4	554	aTa/aCa	13/18	0.851044834134351	3	FACETS	0.888	0.833	0.945	0.444	0.416	0.473	CLONAL	1	TRUE	1	0.853623540027224	3		371	971	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044421	5044421	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	577	442	0	ENST00000381652.3:c.369G>A	p.Trp123Ter	p.W123*	ENST00000381652	NM_004972.3	123	tgG/tgA	5/25	0.458260903902047	5	FACETS	1	0.989	1	0.713	0.686	0.741	INDETERMINATE	2	TRUE	2	0.853623540027224	5		442	1441	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77069983	77069983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768350096	NA	P-0008236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	229	342	0	ENST00000356341.3:c.557C>T	p.Pro186Leu	p.P186L	ENST00000356341	NM_002576.4	186	cCa/cTa	6/15	0.716039512299326	3	FACETS	0.877	0.819	0.937	0.438	0.409	0.469	CLONAL	1	TRUE	1	0.853623540027224	3		342	873	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008244-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	119	145	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.798612849417229	2		145	292	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0008244-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	258	411	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.952	0.897	1	0.952	0.897	1	CLONAL	1	TRUE	1	0.798612849417229	2		411	679	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799050	42799050	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008244-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	204	229	0	ENST00000575354.2:c.4534C>T	p.Arg1512Cys	p.R1512C	ENST00000575354	NM_015125.3	1512	Cgt/Tgt	20/20	0.798612849417229	1	FACETS	0.98	0.932	1	0.98	0.932	1	CLONAL	1	TRUE	0	0.798612849417229	1		229	313	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237594	16237594	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs1293292835	NA	P-0008244-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	131	146	0	ENST00000375759.3:c.1043-2A>T		p.X348_splice	ENST00000375759	NM_015001.2	348			0.724658367578437	1	FACETS	0.561	0.516	0.608	0.561	0.516	0.608	SUBCLONAL	1	TRUE	0	0.798612849417229	1		146	351	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023114	27023114	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008244-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	98	67	0	ENST00000324856.7:c.220C>T	p.Gln74Ter	p.Q74*	ENST00000324856	NM_006015.4	74	Cag/Tag	1/20	0.724658367578437	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.798612849417229	1		67	138	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647026	23647026	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs751882053	NA	P-0008244-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	195	312	0	ENST00000261584.4:c.841A>G	p.Ile281Val	p.I281V	ENST00000261584	NM_024675.3	281	Att/Gtt	4/13	1	2	FACETS	0.574	0.532	0.618	0.574	0.532	0.618	SUBCLONAL	1	TRUE	1	0.798612849417229	2		312	851	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0008259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	330	595	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.213004352063391	4	FACETS	0.994	0.941	1			1	CLONAL	3	TRUE	NA	0.2543613949691	4		595	1091	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	132	371	0	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	0.213504906862836	2	FACETS	0.858	0.781	0.938	0.858	0.781	0.938	CLONAL	2	TRUE	0	0.2543613949691	2		371	605	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247958	59247958	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	189	542	0	ENST00000371222.2:c.785A>G	p.Asn262Ser	p.N262S	ENST00000371222	NM_002228.3	262	aAc/aGc	1/1	0.213504906862836	2	FACETS	0.887	0.821	0.955	0.887	0.821	0.955	CLONAL	2	TRUE	0	0.2543613949691	2		542	838	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436320	110436320	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751461723	NA	P-0008259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	34	105	0	ENST00000375856.3:c.2081C>T	p.Ala694Val	p.A694V	ENST00000375856	NM_003749.2	694	gCc/gTc	1/2	0.2543613949691	6	FACETS	1	0.89	1	0.554	0.457	0.66	CLONAL	2	TRUE	2	0.2543613949691	6		105	182	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882964	89882964	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	28	203	0	ENST00000389301.3:c.60G>T	p.Arg20Ser	p.R20S	ENST00000389301	NM_000135.2	20	agG/agT	1/43	0.2543613949691	3	FACETS	0.896	0.718	1	0.448	0.359	0.549	CLONAL	1	TRUE	1	0.2543613949691	3		203	277	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0008267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	386	381	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.543312876946356	2	FACETS	0.932	0.893	0.972	0.932	0.893	0.972	CLONAL	2	FALSE	0	0.543312876946356	2		382	762	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0008267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	268	412	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.543312876946356	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	0	0.543312876946356	1		413	716	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0008267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	152	403	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.917	0.842	0.995	0.917	0.842	0.995	CLONAL	1	FALSE	1	0.543312876946356	2		403	610	SUCCESS
APC	324	MSKCC	GRCh37	5	112175328	112175328	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	144	344	0	ENST00000257430.4:c.4037C>A	p.Ser1346Ter	p.S1346*	ENST00000257430	NM_000038.5	1346	tCa/tAa	16/16	1	2	FACETS	0.898	0.823	0.977	0.898	0.823	0.977	CLONAL	1	FALSE	1	0.543312876946356	2		344	590	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609934	81609934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369995834	NA	P-0008267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	190	362	0	ENST00000298171.2:c.1532C>T	p.Thr511Met	p.T511M	ENST00000298171	NM_000369.2	511	aCg/aTg	10/10	0.160301948064156	0	FACETS	0.47	0.436	0.505			1	INDETERMINATE	1	FALSE	0	0.543312876946356	0		362	680	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0008283-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	181	316	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.19382554658076	4	FACETS	1	0.974	1	1	0.974	1	INDETERMINATE	2	TRUE	2	0.707148447138806	4		316	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0008283-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	364	641	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.707148447138806	2	FACETS	0.913	0.878	0.946	0.913	0.878	0.946	CLONAL	2	TRUE	0	0.707148447138806	2		642	564	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165236	47165236	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008283-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	21	380	0	ENST00000409792.3:c.890A>C	p.Lys297Thr	p.K297T	ENST00000409792	NM_014159.6	297	aAg/aCg	3/21	0.243609284285636	3	FACETS	0.203	0.155	0.258	0.101	0.077	0.129	INDETERMINATE	1	TRUE	1	0.707148447138806	3		380	397	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295313	1295313	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0008283-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	34	512	1				ENST00000310581	NM_198253.2	-/1132			0.253841240073192	2	FACETS	0.192	0.156	0.232	0.096	0.078	0.116	INDETERMINATE	1	TRUE	0	0.707148447138806	2		513	501	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0008292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	113	327	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	1	2	FACETS	0.738	0.663	0.818	0.738	0.663	0.818	SUBCLONAL	1	FALSE	1	0.305425352765165	2		327	1002	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338621	70338628	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTGAGC	TCTTGAGC	G	novel	NA	P-0008292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	120	474	0	ENST00000374080.3:c.17_24delinsG	p.Ile6SerfsTer7	p.I6Sfs*7	ENST00000374080		6	aTCTTGAGC/aG	1/45	1	2	FACETS	0.771	0.695	0.852	0.771	0.695	0.852	SUBCLONAL	1	FALSE	1	0.305425352765165	2		474	1019	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696294	52696294	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0008301-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	42	316	0	ENST00000394830.3:c.385-2A>T		p.X129_splice	ENST00000394830	NM_018313.4	129			1	2	FACETS	0.842	0.701	1	0.842	0.701	1	CLONAL	1	TRUE	1	0.12	2		316	831	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295257	1295257	+	upstream_gene_variant	5'Flank	SNP	C	C	T	rs1405879643	NA	P-0008301-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	26	207	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.843	0.666	1	0.843	0.666	1	CLONAL	1	TRUE	1	0.12	2		207	514	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652146	36652146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008301-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	52	253	0	ENST00000244741.5:c.268G>A	p.Gly90Arg	p.G90R	ENST00000244741	NM_000389.4	90	Gga/Aga	2/3	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.12	2		253	699	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022774	31022790	+	frameshift_variant	Frame_Shift_Del	DEL	CACTGGGGACCAGCCAT	CACTGGGGACCAGCCAT	-	novel	NA	P-0008301-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	39	205	0	ENST00000375687.4:c.2259_2275del	p.Thr754ProfsTer14	p.T754Pfs*14	ENST00000375687	NM_015338.5	753	ccCACTGGGGACCAGCCATgc/ccgc	13/13	1	2	FACETS	0.868	0.717	1	0.868	0.717	1	CLONAL	1	TRUE	1	0.12	2		205	749	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0008330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	314	528	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	1	2	FACETS	0.758	0.721	0.796	1	0.995	1	SUBCLONAL	2	TRUE	1	0.6	2		528	690	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627818	187627818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149283579	NA	P-0008330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	366	649	0	ENST00000441802.2:c.3164C>T	p.Thr1055Met	p.T1055M	ENST00000441802	NM_005245.3	1055	aCg/aTg	2/27	1	2	FACETS	0.81	0.766	0.854	0.81	0.766	0.854	CLONAL	1	TRUE	1	0.6	2		649	1507	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051246	128051246	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	41	450	0	ENST00000285398.2:c.77A>G	p.Glu26Gly	p.E26G	ENST00000285398	NM_000122.1	26	gAa/gGa	2/15	1	2	FACETS	0.622	0.517	0.74	0.622	0.517	0.74	SUBCLONAL	1	TRUE	1	0.2	2		450	659	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061221	38061232	+	inframe_deletion	In_Frame_Del	DEL	GTTCTCGAACAT	GTTCTCGAACAT	-	novel	NA	P-0008339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	32	343	0	ENST00000250448.2:c.757_768del	p.Met253_Asn256del	p.M253_N256del	ENST00000250448	NM_004496.3	253	ATGTTCGAGAAC/-	2/2	1	2	FACETS	0.796	0.646	0.965	0.796	0.646	0.965	CLONAL	1	TRUE	1	0.2	2		343	402	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0008340-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	23	114	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.525799536045746	1	FACETS	0.489	0.386	0.604	0.489	0.386	0.604	SUBCLONAL	1	TRUE	0	0.525799536045746	1		114	132	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0008340-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	244	420	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.525799536045746	1	FACETS	0.955	0.897	1	0.955	0.897	1	CLONAL	1	TRUE	0	0.525799536045746	1		420	716	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588848	69588848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs979866825	NA	P-0008340-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	256	607	0	ENST00000168712.1:c.388G>A	p.Gly130Ser	p.G130S	ENST00000168712	NM_002007.2	130	Ggc/Agc	2/3	1	2	FACETS	0.965	0.904	1	0.965	0.904	1	CLONAL	1	TRUE	1	0.525799536045746	2		607	1009	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217479	7217479	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0008340-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	365	648	1	ENST00000380728.2:c.318-1G>T		p.X106_splice	ENST00000380728		106			0.525799536045746	1	FACETS	0.894	0.848	0.94	0.894	0.848	0.94	CLONAL	1	TRUE	0	0.525799536045746	1		649	1145	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143232	24143233	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0008340-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	287	618	0	ENST00000263121.7:c.464_465delinsTT	p.Arg155Leu	p.R155L	ENST00000263121	NM_003073.3	155	cGC/cTT	4/9	1	2	FACETS	0.907	0.853	0.964	0.907	0.853	0.964	CLONAL	1	TRUE	1	0.525799536045746	2		618	1203	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425896	49425896	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783685	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	446	604	0	ENST00000301067.7:c.12592C>T	p.Arg4198Ter	p.R4198*	ENST00000301067	NM_003482.3	4198	Cga/Tga	39/54	0.3	3	FACETS	0.785	0.753	0.818			1	INDETERMINATE	2	TRUE	NA	0.84	3		604	960	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	406	565	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.933	0.89	0.976	0.933	0.89	0.976	CLONAL	1	TRUE	1	0.84	2		565	1036	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	474	792	4	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.862	0.824	0.899	0.862	0.824	0.899	CLONAL	1	TRUE	1	0.84	2		796	1310	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	228	390	2	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.846	0.793	0.899	0.846	0.793	0.899	CLONAL	1	TRUE	1	0.84	2		392	642	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	370	452	0	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	0.3	4	FACETS	0.929	0.886	0.973			1	INDETERMINATE	2	TRUE	NA	0.84	4		452	872	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023327	27023327	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	257	213	0	ENST00000324856.7:c.437del	p.Pro146GlnfsTer86	p.P146Qfs*86	ENST00000324856	NM_006015.4	145	Ccc/cc	1/20	1	2	FACETS	0.997	0.941	1	0.997	0.941	1	CLONAL	1	TRUE	1	0.84	2		213	614	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231437	46231437	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	455	542	4	ENST00000334344.6:c.1277C>T	p.Thr426Met	p.T426M	ENST00000334344	NM_152641.2	426	aCg/aTg	10/21	0.3	4	FACETS	0.848	0.811	0.886			1	INDETERMINATE	2	TRUE	NA	0.84	4		546	1175	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405111	139405111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201620358	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	349	501	1	ENST00000277541.6:c.2734C>T	p.Arg912Trp	p.R912W	ENST00000277541	NM_017617.3	912	Cgg/Tgg	17/34	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.84	2		502	787	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	295	371	1	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	0.3	3	FACETS	0.779	0.74	0.819			1	INDETERMINATE	2	TRUE	NA	0.84	3		372	640	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827732	72827732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241554729	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	440	870	2	ENST00000268489.5:c.8849G>A	p.Arg2950His	p.R2950H	ENST00000268489	NM_006885.3	2950	cGc/cAc	9/10	0.161338474467905	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.84	0		872	1016	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687472	37687472	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	215	276	0	ENST00000447079.4:c.4382del	p.Gly1461AlafsTer38	p.G1461Afs*38	ENST00000447079	NM_015083.1	1459	tGg/tg	14/14	0.3	3	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.84	3		276	562	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161405	185161405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	444	557	1	ENST00000265026.3:c.832C>T	p.Arg278Cys	p.R278C	ENST00000265026	NM_004721.4	278	Cgt/Tgt	4/14	0.237149759465274	3	FACETS	1	0.996	1	0.711	0.68	0.742	INDETERMINATE	1	TRUE	1	0.84	3		558	1056	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9787030	9787030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397518423	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	395	571	1	ENST00000377346.4:c.3061G>A	p.Glu1021Lys	p.E1021K	ENST00000377346	NM_005026.3	1021	Gaa/Aaa	24/24	1	2	FACETS	0.934	0.891	0.978	0.934	0.891	0.978	CLONAL	1	TRUE	1	0.84	2		572	1007	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289908	15289908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257835251	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	303	506	1	ENST00000263388.2:c.3646G>A	p.Ala1216Thr	p.A1216T	ENST00000263388	NM_000435.2	1216	Gcg/Acg	22/33	0.3	2	FACETS	0.97	0.919	1			1	INDETERMINATE	1	TRUE	NA	0.84	2		507	744	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101057	27101057	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	433	586	1	ENST00000324856.7:c.4339C>T	p.Pro1447Ser	p.P1447S	ENST00000324856	NM_006015.4	1447	Cca/Tca	18/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.84	2		587	994	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101294	27101294	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773815689	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	385	552	0	ENST00000324856.7:c.4576G>A	p.Val1526Met	p.V1526M	ENST00000324856	NM_006015.4	1526	Gtg/Atg	18/20	1	2	FACETS	0.987	0.941	1	0.987	0.941	1	CLONAL	1	TRUE	1	0.84	2		552	929	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416200	29416200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	355	624	1	ENST00000389048.3:c.4753G>A	p.Gly1585Ser	p.G1585S	ENST00000389048	NM_004304.4	1585	Ggc/Agc	29/29	0.3	2	FACETS	0.989	0.941	1			1	INDETERMINATE	1	TRUE	NA	0.84	2		625	855	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189287	99189287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760873847	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	176	292	0	ENST00000074304.5:c.2543G>A	p.Arg848Gln	p.R848Q	ENST00000074304	NM_001134224.1	848	cGg/cAg	24/26	1	2	FACETS	0.935	0.871	1	0.935	0.871	1	CLONAL	1	TRUE	1	0.84	2		292	448	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630588	187630588	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	615	610	6	ENST00000441802.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000441802	NM_005245.3	132	Cga/Tga	2/27	0.237149759465274	4	FACETS	0.986	0.951	1	0.986	0.951	1	INDETERMINATE	2	TRUE	2	0.84	4		616	1366	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505385	157505385	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	403	490	0	ENST00000346085.5:c.3366G>A	p.Trp1122Ter	p.W1122*	ENST00000346085	NM_020732.3	1122	tgG/tgA	13/20	0.3	3	FACETS	1	0.995	1			1	INDETERMINATE	1	TRUE	NA	0.84	3		490	992	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5073782	5073782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1168791735	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	316	370	0	ENST00000381652.3:c.1861G>A	p.Glu621Lys	p.E621K	ENST00000381652	NM_004972.3	621	Gag/Aag	14/25	0.3	2	FACETS	0.987	0.937	1			1	INDETERMINATE	1	TRUE	NA	0.84	2		370	762	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771903	135771903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	344	429	0	ENST00000298552.3:c.3214G>A	p.Ala1072Thr	p.A1072T	ENST00000298552	NM_001162426.1	1072	Gcc/Acc	23/23	1	2	FACETS	0.962	0.915	1	0.962	0.915	1	CLONAL	1	TRUE	1	0.84	2		429	851	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202552	67202552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373972783	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	509	639	0	ENST00000312629.5:c.1361C>T	p.Pro454Leu	p.P454L	ENST00000312629	NM_003952.2	454	cCg/cTg	15/15	0.3	3	FACETS	1	0.997	1			1	INDETERMINATE	1	TRUE	NA	0.84	3		639	1165	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375276	118375276	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782765039	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	341	497	0	ENST00000534358.1:c.8669G>A	p.Arg2890His	p.R2890H	ENST00000534358	NM_005933.3	2890	cGt/cAt	27/36	0.161338474467905	3	FACETS	1	0.994	1	0.666	0.633	0.7	INDETERMINATE	1	TRUE	1	0.84	3		497	865	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884756	111884756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148319611	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1286	127	1009	3	ENST00000341259.2:c.845G>A	p.Arg282Gln	p.R282Q	ENST00000341259	NM_005475.2	282	cGg/cAg	4/8	1	2	FACETS	0.214	0.193	0.236	0.214	0.193	0.236	SUBCLONAL	1	TRUE	1	0.84	2		1012	1413	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878064	48878064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886043138	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	212	283	0	ENST00000267163.4:c.16C>T	p.Pro6Ser	p.P6S	ENST00000267163	NM_000321.2	6	Ccc/Tcc	1/27	0.3	2	FACETS	0.945	0.886	1			1	INDETERMINATE	1	TRUE	NA	0.84	2		283	534	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341244	341244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773933232	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	330	570	2	ENST00000262320.3:c.2240C>T	p.Ala747Val	p.A747V	ENST00000262320	NM_003502.3	747	gCg/gTg	9/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.84	2		572	774	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	360013	360013	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1439391940	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	397	661	0	ENST00000262320.3:c.1076G>A	p.Ser359Asn	p.S359N	ENST00000262320	NM_003502.3	359	aGc/aAc	4/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.84	2		661	931	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822346	72822346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747616488	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	486	999	3	ENST00000268489.5:c.9829C>T	p.Pro3277Ser	p.P3277S	ENST00000268489	NM_006885.3	3277	Ccc/Tcc	10/10	0.161338474467905	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.84	0		1002	1197	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220015	5220015	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866165812	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	230	411	0	ENST00000357368.4:c.3700C>T	p.Arg1234Trp	p.R1234W	ENST00000357368	NM_002850.3	1234	Cgg/Tgg	22/38	0.10313576088329	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.84	0		411	594	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292490	15292490	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	384	597	2	ENST00000263388.2:c.2689G>A	p.Gly897Ser	p.G897S	ENST00000263388	NM_000435.2	897	Ggc/Agc	17/33	0.3	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.84	2		599	858	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274078	18274078	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	381	467	0	ENST00000222254.8:c.1296G>T	p.Gln432His	p.Q432H	ENST00000222254	NM_005027.3	432	caG/caT	11/16	0.3	2	FACETS	0.95	0.905	0.995			1	INDETERMINATE	1	TRUE	NA	0.84	2		467	955	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912858	50912858	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1306540639	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	458	788	2	ENST00000440232.2:c.2089G>A	p.Ala697Thr	p.A697T	ENST00000440232	NM_002691.3	697	Gcc/Acc	17/27	0.3	1	FACETS	0.629	0.603	0.655	0.629	0.603	0.655	INDETERMINATE	1	TRUE	0	0.84	1		790	1005	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31381363	31381363	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138596278	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	319	409	0	ENST00000328111.2:c.1088G>A	p.Arg363His	p.R363H	ENST00000328111	NM_006892.3	363	cGt/cAt	10/23	0.3	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.84	2		409	697	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564512	41564512	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555911075	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	404	517	1	ENST00000263253.7:c.3934C>T	p.Arg1312Ter	p.R1312*	ENST00000263253	NM_001429.3	1312	Cga/Tga	24/31	1	2	FACETS	0.917	0.875	0.96	0.917	0.875	0.96	CLONAL	1	TRUE	1	0.84	2		518	1049	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182928	123182928	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	556	360	1	ENST00000218089.9:c.893G>A	p.Arg298His	p.R298H	ENST00000218089	NM_001042749.1	298	cGt/cAt	10/35	0.3	2	FACETS	1	0.984	1	1	0.984	1	INDETERMINATE	2	TRUE	0	0.84	2		361	658	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705459	47705459	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	433	621	0	ENST00000233146.2:c.2260del	p.Thr754LeufsTer9	p.T754Lfs*9	ENST00000233146	NM_000251.2	753	ggA/gg	14/16	1	2	FACETS	0.996	0.953	1	0.996	0.953	1	CLONAL	1	TRUE	1	0.84	2		621	1035	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027087	71027087	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	259	378	0	ENST00000318789.4:c.1240del	p.Leu414Ter	p.L414*	ENST00000318789	NM_032682.5	414	Ctg/tg	15/21	0.3	2	FACETS	0.861	0.811	0.913			1	INDETERMINATE	1	TRUE	NA	0.84	2		378	716	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681752	78681752	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	295	558	0	ENST00000306801.3:c.463del	p.Val155CysfsTer47	p.V155Cfs*47	ENST00000306801	NM_020761.2	154	Ggg/gg	4/34	1	2	FACETS	0.913	0.864	0.963	0.913	0.864	0.963	CLONAL	1	TRUE	1	0.84	2		558	769	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427010	49427013	+	frameshift_variant	Frame_Shift_Del	DEL	CTGT	CTGT	-	rs1057519067	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	199	382	0	ENST00000301067.7:c.11475_11478del	p.Gln3826CysfsTer3	p.Q3826Cfs*3	ENST00000301067	NM_003482.3	3825	agACAG/ag	39/54	0.3	3	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.84	3		382	557	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651311	45651315	+	missense_variant	Missense_Mutation	ONP	CTCTC	CTCTC	TTTTT	novel	NA	P-0008345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	335	773	0	ENST00000407780.3:c.710_714delinsAAAAA	p.Gly237_Glu238delinsGluLys	p.G237_E238delinsEK	ENST00000407780	NM_001283052.1	237	gGAGAG/gAAAAA	5/7	0.3	2	FACETS	0.763	0.723	0.805			1	INDETERMINATE	1	TRUE	NA	0.84	2		773	1045	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0008355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	102	407	0	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	0.7	2		407	204	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524761	187524761	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	256	365	0	ENST00000441802.2:c.10919A>G	p.Asn3640Ser	p.N3640S	ENST00000441802	NM_005245.3	3640	aAc/aGc	19/27	0.213216403239581	4	FACETS	1	0.99	1	1	0.99	1	INDETERMINATE	2	TRUE	2	0.7	4		365	517	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223256	41223256	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs80358008	NA	P-0008355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	13	276	0	ENST00000357654.3:c.4676-1G>C		p.X1559_splice	ENST00000357654	NM_007294.3	1559			0.213216403239581	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.7	0		276	104	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435394	121435394	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0121558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	652	400	0	ENST00000257555.6:c.1427T>C	p.Leu476Pro	p.L476P	ENST00000257555		476	cTc/cCc	7/10	0.614093178305954	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	NA	1	0.614093178305954	3		400	1275	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099187	157099195	+	inframe_deletion	In_Frame_Del	DEL	GCGGCGGCA	GCGGCGGCA	-	rs769480864	NA	P-0008390-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	209	333	0	ENST00000346085.5:c.133_141del	p.Ala45_Ala47del	p.A45_A47del	ENST00000346085	NM_020732.3	42	GCGGCGGCA/-	1/20	0.789839173400653	3	FACETS	0.672	0.623	0.723	0.336	0.311	0.362	SUBCLONAL	1	TRUE	1	0.789839173400653	3		333	1098	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519980	NA	P-0008390-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	620	655	0	ENST00000269305.4:c.528C>G	p.Cys176Trp	p.C176W	ENST00000269305	NM_001126112.2	176	tgC/tgG	5/11	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	2	TRUE	NA	0.789839173400653	2		655	779	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061211	38061240	+	inframe_deletion	In_Frame_Del	DEL	AGTAGCAGCCGTTCTCGAACATGTTGCCGG	AGTAGCAGCCGTTCTCGAACATGTTGCCGG	-	novel	NA	P-0008390-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	225	274	0	ENST00000250448.2:c.749_778del	p.Ser250_Tyr259del	p.S250_Y259del	ENST00000250448	NM_004496.3	250	tCCGGCAACATGTTCGAGAACGGCTGCTACTtg/ttg	2/2	0.789839173400653	3	FACETS	0.79	0.736	0.846	0.395	0.368	0.423	SUBCLONAL	1	TRUE	1	0.789839173400653	3		274	1006	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237706	16237706	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008390-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	386	531	0	ENST00000375759.3:c.1153C>T	p.Gln385Ter	p.Q385*	ENST00000375759	NM_015001.2	385	Cag/Tag	5/15	NA	2	FACETS	0.776	0.737	0.816			1	INDETERMINATE	1	TRUE	NA	0.789839173400653	2		531	1259	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123667	11123667	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008390-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	458	465	0	ENST00000358026.2:c.2317C>A	p.Leu773Met	p.L773M	ENST00000358026	NM_001128849.1	773	Ctg/Atg	16/36	0.789839173400653	3	FACETS	0.989	0.943	1	0.494	0.471	0.518	CLONAL	1	TRUE	1	0.789839173400653	3		465	1636	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76777865	76777865	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008390-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	767	268	0	ENST00000373344.5:c.6851del	p.Gly2284AspfsTer2	p.G2284Dfs*2	ENST00000373344	NM_000489.3	2284	gGa/ga	32/35	0.665610245594857	2	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.789839173400653	2		268	944	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0008391-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	369	414	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	1	2	FACETS	0.921	0.876	0.967	0.921	0.876	0.967	CLONAL	1	TRUE	1	0.79	2		414	1014	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148972	119148972	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008391-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	54	480	0	ENST00000264033.4:c.1192C>G	p.His398Asp	p.H398D	ENST00000264033	NM_005188.3	398	Cac/Gac	8/16	1	2	FACETS	0.138	0.117	0.161	0.138	0.117	0.161	SUBCLONAL	1	TRUE	1	0.79	2		480	988	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845757	68845757	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587780784	NA	P-0008398-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	63	411	0	ENST00000261769.5:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000261769	NM_004360.3	335	Cga/Tga	7/16	1	2	FACETS	0.518	0.447	0.596	0.518	0.447	0.596	SUBCLONAL	1	FALSE	1	0.284390091609326	2		411	855	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259368	89259368	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008398-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	64	667	0	ENST00000336596.2:c.512T>C	p.Val171Ala	p.V171A	ENST00000336596	NM_005233.5	171	gTa/gCa	3/17	1	2	FACETS	0.379	0.326	0.436	0.379	0.326	0.436	SUBCLONAL	1	FALSE	1	0.284390091609326	2		667	1189	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184495	7184495	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1448475843	NA	P-0008398-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	63	343	0	ENST00000302850.5:c.806C>T	p.Pro269Leu	p.P269L	ENST00000302850	NM_000208.2	269	cCg/cTg	3/22	1	2	FACETS	0.398	0.343	0.459	0.398	0.343	0.459	SUBCLONAL	1	FALSE	1	0.284390091609326	2		343	1112	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873518	151873518	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008398-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	68	509	0	ENST00000262189.6:c.9020del	p.Gly3007GlufsTer25	p.G3007Efs*25	ENST00000262189	NM_170606.2	3007	gGa/ga	38/59	1	2	FACETS	0.414	0.359	0.475	0.414	0.359	0.475	SUBCLONAL	1	FALSE	1	0.284390091609326	2		509	1154	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	153	145	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.833801951300091	2		145	293	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0008403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	247	268	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.161974522123033	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.833801951300091	0		268	627	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0008403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	413	397	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.467172368812214	3	FACETS	0.861	0.826	0.897	0.861	0.826	0.897	INDETERMINATE	2	TRUE	1	0.833801951300091	3		397	815	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944629	40944629	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	136	177	0	ENST00000373198.4:c.1873C>T	p.Gln625Ter	p.Q625*	ENST00000373198	NM_133170.3	625	Cag/Tag	12/32	0.275316968141915	1	FACETS	0.478	0.439	0.518	0.478	0.439	0.518	INDETERMINATE	1	TRUE	0	0.833801951300091	1		177	398	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561352	9561352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773981325	NA	P-0008403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	288	407	0	ENST00000353224.5:c.430G>A	p.Glu144Lys	p.E144K	ENST00000353224	NM_177990.2	144	Gaa/Aaa	4/10	NA	2	FACETS	0.896	0.847	0.946			1	INDETERMINATE	1	TRUE	NA	0.833801951300091	2		407	771	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39644733	39644733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	307	477	0	ENST00000262039.4:c.2462C>T	p.Ser821Phe	p.S821F	ENST00000262039	NM_002647.2	821	tCc/tTc	23/25	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.833801951300091	2		477	675	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876208	35876208	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777033414	NA	P-0008403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	268	437	1	ENST00000303115.3:c.1000G>A	p.Glu334Lys	p.E334K	ENST00000303115	NM_002185.3	334	Gaa/Aaa	8/8	1	2	FACETS	0.978	0.924	1	0.978	0.924	1	CLONAL	1	TRUE	1	0.833801951300091	2		438	657	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36826860	36826860	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	383	536	0	ENST00000373129.3:c.74C>T	p.Ser25Phe	p.S25F	ENST00000373129	NM_032017.1	25	tCt/tTt	3/12	NA	2	FACETS	0.73	0.693	0.767			1	INDETERMINATE	1	TRUE	NA	0.833801951300091	2		536	1259	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085917	16085917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	136	281	0	ENST00000281043.3:c.1093C>T	p.Pro365Ser	p.P365S	ENST00000281043	NM_005378.4	365	Cca/Tca	3/3	NA	2	FACETS	0.836	0.769	0.906			1	INDETERMINATE	1	TRUE	NA	0.833801951300091	2		281	390	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652813	212652813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	218	565	0	ENST00000342788.4:c.493G>A	p.Asp165Asn	p.D165N	ENST00000342788	NM_005235.2	165	Gat/Aat	4/28	0.161974522123033	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.833801951300091	0		565	532	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440144	220440144	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	462	654	1	ENST00000243786.2:c.997G>A	p.Gly333Arg	p.G333R	ENST00000243786	NM_002191.3	333	Ggg/Agg	2/2	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.833801951300091	2		655	1030	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964893	55964893	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769138106	NA	P-0008403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	319	496	0	ENST00000263923.4:c.2344C>T	p.Leu782Phe	p.L782F	ENST00000263923	NM_002253.2	782	Ctt/Ttt	16/30	1	2	FACETS	0.991	0.941	1	0.991	0.941	1	CLONAL	1	TRUE	1	0.833801951300091	2		496	772	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178644	56178644	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	227	325	0	ENST00000399503.3:c.3617C>T	p.Pro1206Leu	p.P1206L	ENST00000399503	NM_005921.1	1206	cCt/cTt	14/20	1	2	FACETS	0.903	0.847	0.96	0.903	0.847	0.96	CLONAL	1	TRUE	1	0.833801951300091	2		325	603	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265323	152265323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866869178	NA	P-0008403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	190	328	0	ENST00000206249.3:c.776G>A	p.Arg259Gln	p.R259Q	ENST00000206249	NM_000125.3	259	cGa/cAa	4/8	1	2	FACETS	0.913	0.852	0.976	0.913	0.852	0.976	CLONAL	1	TRUE	1	0.833801951300091	2		328	499	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781165	161781165	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	298	515	0	ENST00000366898.1:c.1240A>G	p.Thr414Ala	p.T414A	ENST00000366898	NM_004562.2	414	Acc/Gcc	11/12	NA	2	FACETS	0.878	0.83	0.927			1	INDETERMINATE	1	TRUE	NA	0.833801951300091	2		515	814	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539056	23539056	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	253	412	1	ENST00000380871.4:c.383G>A	p.Arg128Gln	p.R128Q	ENST00000380871	NM_006167.3	128	cGa/cAa	2/2	1	2	FACETS	0.914	0.861	0.968	0.914	0.861	0.968	CLONAL	1	TRUE	1	0.833801951300091	2		413	664	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925412	114925412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs573425555	NA	P-0008403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	478	592	1	ENST00000543371.1:c.1490C>T	p.Pro497Leu	p.P497L	ENST00000543371	NM_001198531.1	497	cCg/cTg	14/14	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.833801951300091	2		593	1119	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134975	41134975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	582	721	0	ENST00000379561.5:c.653C>T	p.Ser218Phe	p.S218F	ENST00000379561	NM_002015.3	218	tCc/tTc	2/3	1	2	FACETS	0.961	0.925	0.998	0.961	0.925	0.998	CLONAL	1	TRUE	1	0.833801951300091	2		721	1452	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99486235	99486235	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	362	376	0	ENST00000268035.6:c.3541C>T	p.Pro1181Ser	p.P1181S	ENST00000268035	NM_000875.3	1181	Cct/Tct	19/21	NA	2	FACETS	0.982	0.935	1			1	INDETERMINATE	1	TRUE	NA	0.833801951300091	2		376	884	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877143	89877143	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141918444	NA	P-0008403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	308	479	0	ENST00000389301.3:c.494C>T	p.Ser165Phe	p.S165F	ENST00000389301	NM_000135.2	165	tCc/tTc	5/43	1	2	FACETS	0.951	0.901	1	0.951	0.901	1	CLONAL	1	TRUE	1	0.833801951300091	2		479	777	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272206	15272206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765403158	NA	P-0008403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	112	198	1	ENST00000263388.2:c.6233G>A	p.Arg2078Gln	p.R2078Q	ENST00000263388	NM_000435.2	2078	cGg/cAg	33/33	NA	2	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.833801951300091	2		199	255	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032793	30032794	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0008403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	369	459	0	ENST00000338641.4:c.168_169delinsTT	p.Arg57Ter	p.R57*	ENST00000338641	NM_000268.3	56	ctCCga/ctTTga	2/16	1	2	FACETS	0.969	0.923	1	0.969	0.923	1	CLONAL	1	TRUE	1	0.833801951300091	2		459	913	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0008426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	305	383	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.389736546683598	7	FACETS	1	0.971	1	0.828	0.785	0.872	CLONAL	4	TRUE	2	0.389736546683598	7		383	746	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106861	27106861	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	123	269	0	ENST00000324856.7:c.6472C>T	p.Arg2158Ter	p.R2158*	ENST00000324856	NM_006015.4	2158	Cga/Tga	20/20	0.171634894722137	2	FACETS	0.787	0.718	0.858	0.787	0.718	0.858	INDETERMINATE	2	TRUE	0	0.389736546683598	2		269	401	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374251	138374251	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	64	484	1	ENST00000289153.2:c.3193C>T	p.Arg1065Trp	p.R1065W	ENST00000289153	NM_006219.2	1065	Cgg/Tgg	22/22	0.389736546683598	3	FACETS	0.626	0.542	0.717	0.313	0.271	0.359	SUBCLONAL	1	TRUE	1	0.389736546683598	3		485	627	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692869	89692869	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	29	161	1	ENST00000371953.3:c.353A>T	p.His118Leu	p.H118L	ENST00000371953	NM_000314.4	118	cAt/cTt	5/9	0.389736546683598	1	FACETS	1	0.837	1	1	0.837	1	CLONAL	1	TRUE	0	0.389736546683598	1		162	117	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226223	2226223	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	165	509	0	ENST00000398665.3:c.3704del	p.Pro1235GlnfsTer92	p.P1235Qfs*92	ENST00000398665	NM_032482.2	1235	Cca/ca	27/28	0.190255399223082	2	FACETS	0.869	0.805	0.935	0.869	0.805	0.935	INDETERMINATE	2	TRUE	0	0.389736546683598	2		509	487	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0008428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	37	601	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.365368887138958	2	FACETS	0.17	0.139	0.205	0.085	0.069	0.103	SUBCLONAL	1	FALSE	0	0.486838790536287	2		601	894	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518010	8518010	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	60	709	0	ENST00000356435.5:c.1381C>T	p.Gln461Ter	p.Q461*	ENST00000356435		461	Caa/Taa	10/35	0.273032685826704	2	FACETS	0.211	0.181	0.244	0.106	0.09	0.122	INDETERMINATE	1	FALSE	0	0.486838790536287	2		709	1168	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034444	47034444	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	64	364	0	ENST00000377604.3:c.529G>T	p.Glu177Ter	p.E177*	ENST00000377604	NM_001204468.1	177	Gag/Tag	6/24	0.486838790536287	2	FACETS	0.373	0.323	0.429	0.187	0.161	0.215	SUBCLONAL	1	FALSE	0	0.486838790536287	2		364	704	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0008437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	269	170	0	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	0.821892374790403	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.821892374790403	1		170	358	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724631	162724631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371333028	NA	P-0008437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	666	354	0	ENST00000367921.3:c.403C>T	p.Arg135Cys	p.R135C	ENST00000367921	NM_006182.2	135	Cgt/Tgt	5/18	0.633498588595506	3	FACETS	1	0.997	1	0.812	0.791	0.832	CLONAL	2	TRUE	0	0.821892374790403	3		354	939	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578541	7578541	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1131691013	NA	P-0008437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	433	331	0	ENST00000269305.4:c.389T>C	p.Leu130Pro	p.L130P	ENST00000269305	NM_001126112.2	130	cTc/cCc	5/11	0.821892374790403	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.821892374790403	1		331	616	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	27	145	0				ENST00000310581	NM_198253.2	-/1132			0.279037177283049	3	FACETS	0.993	0.795	1	0.497	0.397	0.609	CLONAL	1	FALSE	1	0.279037177283049	3		145	222	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0008445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	47	295	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.279037177283049	3	FACETS	0.884	0.755	1	0.884	0.755	1	CLONAL	2	FALSE	1	0.279037177283049	3		295	217	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653860	89653860	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	19	224	0	ENST00000371953.3:c.158T>C	p.Val53Ala	p.V53A	ENST00000371953	NM_000314.4	53	gTa/gCa	2/9	0.279037177283049	1	FACETS	0.862	0.661	1	0.862	0.661	1	CLONAL	1	FALSE	0	0.279037177283049	1		224	136	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377213	118377213	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs200371479	NA	P-0008445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	34	318	0	ENST00000534358.1:c.10606C>A	p.Pro3536Thr	p.P3536T	ENST00000534358	NM_005933.3	3536	Ccc/Acc	27/36	1	2	FACETS	0.867	0.712	1	0.867	0.712	1	CLONAL	1	FALSE	1	0.279037177283049	2		318	281	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777900	3777900	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	103	475	0	ENST00000262367.5:c.7148C>T	p.Pro2383Leu	p.P2383L	ENST00000262367	NM_004380.2	2383	cCc/cTc	31/31	0.279037177283049	3	FACETS	0.955	0.854	1	0.477	0.427	0.532	CLONAL	1	FALSE	1	0.279037177283049	3		475	881	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546922	9546922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	37	214	0	ENST00000353224.5:c.1100C>T	p.Ser367Phe	p.S367F	ENST00000353224	NM_177990.2	367	tCc/tTc	5/10	0.279037177283049	3	FACETS	0.93	0.769	1	0.465	0.384	0.555	CLONAL	1	FALSE	1	0.279037177283049	3		214	325	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264865	46264865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	63	544	1	ENST00000371998.3:c.1735C>T	p.Pro579Ser	p.P579S	ENST00000371998		579	Cca/Tca	12/23	0.279037177283049	3	FACETS	0.98	0.849	1	0.49	0.424	0.561	CLONAL	1	FALSE	1	0.279037177283049	3		545	525	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0008482-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	84	536	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	0.189016781237851	1	FACETS	0.791	0.697	0.893	0.791	0.697	0.893	SUBCLONAL	1	TRUE	0	0.200051999476184	1		536	955	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138201237	138201237	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008482-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	183	287	0	ENST00000237289.4:c.1936C>T	p.Pro646Ser	p.P646S	ENST00000237289	NM_001270507.1	646	Ccc/Tcc	8/9	0.167496886850288	3	FACETS	0.958	0.887	1	1	0.989	1	CLONAL	3	TRUE	1	0.200051999476184	3		287	700	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325575	87325575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008482-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	56	412	0	ENST00000277120.3:c.452C>T	p.Thr151Ile	p.T151I	ENST00000277120		151	aCa/aTa	6/19	0.200051999476184	2	FACETS	0.786	0.673	0.911	0.393	0.336	0.456	CLONAL	1	TRUE	0	0.200051999476184	2		412	712	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332117	70332117	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057257286	NA	P-0008482-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	80	412	0	ENST00000373644.4:c.22A>G	p.Arg8Gly	p.R8G	ENST00000373644	NM_030625.2	8	Agg/Ggg	2/12	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.200051999476184	2		412	758	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888191	112888191	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008482-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	53	478	0	ENST00000351677.2:c.207G>C	p.Glu69Asp	p.E69D	ENST00000351677	NM_002834.3	69	gaG/gaC	3/16	1	2	FACETS	0.566	0.481	0.66	0.566	0.481	0.66	SUBCLONAL	1	TRUE	1	0.200051999476184	2		478	936	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29002020	29002020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs974445913	NA	P-0008482-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	42	316	0	ENST00000282397.4:c.1145G>A	p.Arg382His	p.R382H	ENST00000282397	NM_002019.4	382	cGc/cAc	9/30	1	2	FACETS	0.648	0.54	0.769	0.648	0.54	0.769	SUBCLONAL	1	TRUE	1	0.200051999476184	2		316	648	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987027	36987027	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008482-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	43	220	0	ENST00000354822.5:c.662G>A	p.Arg221His	p.R221H	ENST00000354822	NM_001079668.2	221	cGc/cAc	3/3	0.200051999476184	2	FACETS	1	0.905	1	0.558	0.468	0.658	CLONAL	1	TRUE	0	0.200051999476184	2		220	385	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556049	29556049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008482-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	29	265	0	ENST00000356175.3:c.2416G>A	p.Glu806Lys	p.E806K	ENST00000356175	NM_000267.3	806	Gaa/Aaa	21/57	0.200051999476184	1	FACETS	0.579	0.464	0.709	0.579	0.464	0.709	SUBCLONAL	1	TRUE	0	0.200051999476184	1		265	451	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0008490-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	33	407	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.82	1	1	0.82	1	CLONAL	1	TRUE	1	0.14	2		407	468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0008490-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	46	412	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.712	0.597	0.839	0.712	0.597	0.839	SUBCLONAL	1	TRUE	1	0.14	2		413	923	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494328	2494328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008490-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	55	294	0	ENST00000355716.4:c.719C>T	p.Ser240Phe	p.S240F	ENST00000355716	NM_003820.2	240	tCc/tTc	7/8	1	2	FACETS	0.853	0.728	0.991	0.853	0.728	0.991	CLONAL	1	TRUE	1	0.14	2		294	921	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228613024	228613024	+	start_lost	Translation_Start_Site	SNP	C	C	T	rs558923621	NA	P-0008490-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	80	427	0	ENST00000366696.1:c.3G>A	p.Met1?	p.M1?	ENST00000366696	NM_003493.2	1	atG/atA	1/1	1	2	FACETS	0.998	0.876	1	0.998	0.876	1	CLONAL	1	TRUE	1	0.14	2		427	1145	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086057	16086057	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008490-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	53	349	0	ENST00000281043.3:c.1233G>T	p.Leu411Phe	p.L411F	ENST00000281043	NM_005378.4	411	ttG/ttT	3/3	1	2	FACETS	0.816	0.694	0.951	0.816	0.694	0.951	CLONAL	1	TRUE	1	0.14	2		349	928	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181896	32181896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008490-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	54	407	0	ENST00000375023.3:c.2158G>A	p.Gly720Ser	p.G720S	ENST00000375023	NM_004557.3	720	Ggc/Agc	13/30	1	2	FACETS	0.745	0.634	0.868	0.745	0.634	0.868	SUBCLONAL	1	TRUE	1	0.14	2		407	1035	SUCCESS
MET	4233	MSKCC	GRCh37	7	116409732	116409732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008490-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	26	233	0	ENST00000397752.3:c.2617G>A	p.Glu873Lys	p.E873K	ENST00000397752	NM_000245.2	873	Gaa/Aaa	12/21	1	2	FACETS	1	0.799	1	1	0.799	1	CLONAL	1	TRUE	1	0.14	2		233	368	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481403	140481403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913357	NA	P-0008490-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	37	296	1	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	0.14	2		297	490	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534512	140534512	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008490-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	26	313	0	ENST00000288602.6:c.401C>T	p.Ser134Phe	p.S134F	ENST00000288602	NM_004333.4	134	tCt/tTt	3/18	1	2	FACETS	0.73	0.577	0.906	0.73	0.577	0.906	CLONAL	1	TRUE	1	0.14	2		313	509	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36846852	36846852	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008490-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	44	300	0	ENST00000358127.4:c.1087C>T	p.Pro363Ser	p.P363S	ENST00000358127	NM_001280556.1	363	Ccg/Tcg	9/10	1	2	FACETS	0.719	0.601	0.851	0.719	0.601	0.851	SUBCLONAL	1	TRUE	1	0.14	2		300	874	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249757	110249758	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0008490-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	34	263	0	ENST00000374672.4:c.917_918delinsTT	p.Pro306Leu	p.P306L	ENST00000374672	NM_004235.4	306	cCC/cTT	3/5	1	2	FACETS	0.798	0.65	0.964	0.798	0.65	0.964	CLONAL	1	TRUE	1	0.14	2		263	609	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944812	31944812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866971809	NA	P-0008490-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	54	355	2	ENST00000340398.3:c.289G>A	p.Glu97Lys	p.E97K	ENST00000340398	NM_001013699.2	97	Gaa/Aaa	1/1	1	2	FACETS	0.718	0.611	0.836	0.718	0.611	0.836	SUBCLONAL	1	TRUE	1	0.14	2		357	1074	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911275	32911275	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008490-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	37	549	0	ENST00000380152.3:c.2783T>C	p.Val928Ala	p.V928A	ENST00000380152		928	gTt/gCt	11/27	1	2	FACETS	0.766	0.63	0.919	0.766	0.63	0.919	CLONAL	1	TRUE	1	0.14	2		549	690	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504620	103504620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008490-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	32	297	0	ENST00000355739.4:c.241C>T	p.Pro81Ser	p.P81S	ENST00000355739	NM_000123.3	81	Cca/Tca	2/15	1	2	FACETS	1	0.82	1	1	0.82	1	CLONAL	1	TRUE	1	0.14	2		297	452	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95595906	95595906	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008490-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	24	340	0	ENST00000393063.1:c.637A>G	p.Lys213Glu	p.K213E	ENST00000393063	NM_030621.3	213	Aaa/Gaa	7/28	1	2	FACETS	0.736	0.576	0.921	0.736	0.576	0.921	CLONAL	1	TRUE	1	0.14	2		340	466	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312683	91312683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759330541	NA	P-0008490-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	81	407	0	ENST00000355112.3:c.2422C>T	p.Arg808Cys	p.R808C	ENST00000355112	NM_000057.2	808	Cgt/Tgt	12/22	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.14	2		407	910	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119111	70119111	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008490-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	16	114	0	ENST00000245479.2:c.683C>T	p.Ser228Leu	p.S228L	ENST00000245479	NM_000346.3	228	tCg/tTg	2/3	1	2	FACETS	0.808	0.597	1	0.808	0.597	1	CLONAL	1	TRUE	1	0.14	2		114	283	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101044	41101044	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143164081	NA	P-0008490-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	47	330	1	ENST00000373198.4:c.1312G>A	p.Glu438Lys	p.E438K	ENST00000373198	NM_133170.3	438	Gag/Aag	8/32	1	2	FACETS	0.844	0.71	0.992	0.844	0.71	0.992	CLONAL	1	TRUE	1	0.14	2		331	796	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456600	32456600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	60	68	0	ENST00000332351.3:c.292G>A	p.Gly98Ser	p.G98S	ENST00000332351	NM_024426.4	98	Ggc/Agc	1/10	0.85936040308304	3	FACETS	0.895	0.782	1	0.448	0.391	0.508	CLONAL	1	TRUE	1	0.85936040308304	3		68	223	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579355	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519997	NA	P-0008525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	236	471	0	ENST00000269305.4:c.332T>A	p.Leu111Gln	p.L111Q	ENST00000269305	NM_001126112.2	111	cTg/cAg	4/11	0.416510849220261	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.416510849220261	1		471	727	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264046	16264046	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1306	98	715	0	ENST00000375759.3:c.10416del	p.Leu3473CysfsTer18	p.L3473Cfs*18	ENST00000375759	NM_015001.2	3472	gTt/gt	12/15	0.416510849220261	2	FACETS	0.335	0.298	0.375	0.168	0.149	0.188	SUBCLONAL	1	TRUE	0	0.416510849220261	2		715	1404	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044473	12044473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	31	410	0	ENST00000353533.5:c.1098del	p.Phe366LeufsTer3	p.F366Lfs*3	ENST00000353533	NM_003010.3	366	Ttt/tt	11/11	0.416510849220261	1	FACETS	0.255	0.205	0.31	0.255	0.205	0.31	SUBCLONAL	1	TRUE	0	0.416510849220261	1		410	463	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0008534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	144	353	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.256606005496598	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.256606005496598	1		353	951	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256532	115256532	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	92	567	0	ENST00000369535.4:c.179G>T	p.Gly60Val	p.G60V	ENST00000369535	NM_002524.4	60	gGa/gTa	3/7	1	2	FACETS	0.78	0.692	0.875	0.78	0.692	0.875	SUBCLONAL	1	TRUE	1	0.256606005496598	2		567	919	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374269	138374269	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	76	635	1	ENST00000289153.2:c.3175T>G	p.Trp1059Gly	p.W1059G	ENST00000289153	NM_006219.2	1059	Tgg/Ggg	22/22	1	2	FACETS	0.551	0.482	0.626	0.551	0.482	0.626	SUBCLONAL	1	TRUE	1	0.256606005496598	2		636	1075	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944562	40944562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868189942	NA	P-0008534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	51	341	1	ENST00000373198.4:c.1940C>T	p.Ser647Leu	p.S647L	ENST00000373198	NM_133170.3	647	tCg/tTg	12/32	0.256606005496598	5	FACETS	0.686	0.582	0.802	0.172	0.145	0.201	SUBCLONAL	1	TRUE	1	0.256606005496598	5		342	802	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021734	71021734	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	116	660	0	ENST00000318789.4:c.1624del	p.Gln542LysfsTer57	p.Q542Kfs*57	ENST00000318789	NM_032682.5	542	Caa/aa	18/21	1	2	FACETS	0.75	0.674	0.83	0.75	0.674	0.83	SUBCLONAL	1	TRUE	1	0.256606005496598	2		660	1206	SUCCESS
APC	324	MSKCC	GRCh37	5	112174641	112174641	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	93	696	0	ENST00000257430.4:c.3350del	p.Ser1117LeufsTer9	p.S1117Lfs*9	ENST00000257430	NM_000038.5	1117	tCt/tt	16/16	1	2	FACETS	0.649	0.575	0.728	0.649	0.575	0.728	SUBCLONAL	1	TRUE	1	0.256606005496598	2		696	1117	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436009	110436009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767024195	NA	P-0008552-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	89	253	0	ENST00000375856.3:c.2392G>A	p.Val798Ile	p.V798I	ENST00000375856	NM_003749.2	798	Gtt/Att	1/2	0.884376889366269	3	FACETS	0.921	0.826	1	0.307	0.275	0.341	CLONAL	1	TRUE	0	0.884376889366269	3		253	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs28934577	NA	P-0008552-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	187	316	0	ENST00000269305.4:c.770T>G	p.Leu257Arg	p.L257R	ENST00000269305	NM_001126112.2	257	cTg/cGg	7/11	0.821658279742094	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.884376889366269	3		316	288	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576885	7576885	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0008552-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	42	401	0	ENST00000269305.4:c.961A>T	p.Lys321Ter	p.K321*	ENST00000269305	NM_001126112.2	321	Aaa/Taa	9/11	0.821658279742094	3	FACETS	0.958	0.816	1	0.479	0.408	0.555	CLONAL	1	TRUE	1	0.884376889366269	3		401	143	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460504	8460504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148300682	NA	P-0008552-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	70	408	1	ENST00000356435.5:c.3782C>T	p.Thr1261Met	p.T1261M	ENST00000356435		1261	aCg/aTg	22/35	0.884376889366269	3	FACETS	1	0.908	1	0.514	0.455	0.576	CLONAL	1	TRUE	1	0.884376889366269	3		409	222	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025543	1025543	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008552-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	185	503	0	ENST00000358495.3:c.832C>T	p.Arg278Ter	p.R278*	ENST00000358495	NM_134424.2	278	Cga/Tga	9/12	0.782830267264888	4	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.884376889366269	4		503	651	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65568283	65568283	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008552-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	62	296	0	ENST00000358664.4:c.44A>G	p.Gln15Arg	p.Q15R	ENST00000358664	NM_002382.4	15	cAa/cGa	2/5	0.771625282534822	4	FACETS	0.858	0.76	0.958	0.858	0.76	0.958	CLONAL	2	TRUE	2	0.884376889366269	4		296	154	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110085	8110085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199630207	NA	P-0008552-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	83	211	1	ENST00000585124.1:c.520G>A	p.Glu174Lys	p.E174K	ENST00000585124	NM_004217.3	174	Gag/Aag	6/9	0.821658279742094	3	FACETS	1	0.963	1	0.581	0.521	0.642	CLONAL	1	TRUE	1	0.884376889366269	3		212	233	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917797	29917797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748854412	NA	P-0008578-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	127	383	2	ENST00000389048.3:c.871C>T	p.Arg291Cys	p.R291C	ENST00000389048	NM_004304.4	291	Cgc/Tgc	3/29	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.29	2		385	631	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0008582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	77	412	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.301875759604405	1	FACETS	0.485	0.425	0.549	0.485	0.425	0.549	SUBCLONAL	1	TRUE	0	0.359809182742467	1		412	724	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0008582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	71	596	1	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	0.484	0.422	0.552	0.484	0.422	0.552	SUBCLONAL	1	TRUE	1	0.359809182742467	2		597	815	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278106	41278106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	138	563	1	ENST00000349496.5:c.1982G>A	p.Arg661Gln	p.R661Q	ENST00000349496	NM_001904.3	661	cGa/cAa	13/15	1	2	FACETS	0.604	0.548	0.664	0.604	0.548	0.664	SUBCLONAL	1	TRUE	1	0.359809182742467	2		564	1269	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918736	50918736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1422842883	NA	P-0008582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	82	563	0	ENST00000440232.2:c.2606C>T	p.Ser869Leu	p.S869L	ENST00000440232	NM_002691.3	869	tCg/tTg	21/27	1	2	FACETS	0.389	0.342	0.44	0.389	0.342	0.44	SUBCLONAL	1	TRUE	1	0.359809182742467	2		563	1171	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487277	56487277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035001455	NA	P-0008582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	84	353	1	ENST00000267101.3:c.1423C>T	p.Arg475Trp	p.R475W	ENST00000267101	NM_001982.3	475	Cgg/Tgg	12/28	1	2	FACETS	0.635	0.561	0.715	0.635	0.561	0.715	SUBCLONAL	1	TRUE	1	0.359809182742467	2		354	735	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577520	7577520	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	128	484	0	ENST00000269305.4:c.761T>A	p.Ile254Asn	p.I254N	ENST00000269305	NM_001126112.2	254	aTc/aAc	7/11	1	2	FACETS	0.753	0.682	0.828	0.753	0.682	0.828	SUBCLONAL	1	TRUE	1	0.359809182742467	2		484	945	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0008586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	35	654	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.3	2	FACETS	0.57	0.465	0.689			1	SUBCLONAL	1	TRUE	NA	0.14	2		654	877	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0008586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	45	360	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.76	0.637	0.897	0.76	0.637	0.897	SUBCLONAL	1	TRUE	1	0.14	2		361	846	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0008586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	36	538	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.226452120710096	3	FACETS	0.568	0.465	0.685	0.284	0.232	0.343	SUBCLONAL	1	TRUE	1	0.14	3		538	968	SUCCESS
APC	324	MSKCC	GRCh37	5	112175136	112175136	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	21	283	0	ENST00000257430.4:c.3845C>A	p.Ser1282Ter	p.S1282*	ENST00000257430	NM_000038.5	1282	tCa/tAa	16/16	1	2	FACETS	0.723	0.556	0.919	0.723	0.556	0.919	CLONAL	1	TRUE	1	0.14	2		283	415	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912149	114912149	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1295	97	956	3	ENST00000543371.1:c.1219C>T	p.Arg407Ter	p.R407*	ENST00000543371	NM_001198531.1	407	Cga/Tga	11/14	1	2	FACETS	0.995	0.884	1	0.995	0.884	1	CLONAL	1	TRUE	1	0.14	2		959	1392	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806227	1806227	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146114742	NA	P-0008586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	38	577	0	ENST00000260795.2:c.1246C>T	p.Arg416Cys	p.R416C	ENST00000260795		416	Cgc/Tgc	8/17	1	2	FACETS	0.939	0.775	1	0.939	0.775	1	CLONAL	1	TRUE	1	0.14	2		577	578	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911532	39911532	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	211	438	0	ENST00000378444.4:c.5098C>T	p.Gln1700Ter	p.Q1700*	ENST00000378444	NM_001123385.1	1700	Cag/Tag	15/15	0.297226383701803	2	FACETS	1	0.958	1			1	CLONAL	3	FALSE	NA	0.3	2		438	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579716	7579716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1192416464	NA	P-0008591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	435	957	1	ENST00000269305.4:c.80del	p.Pro27LeufsTer17	p.P27Lfs*17	ENST00000269305	NM_001126112.2	27	cCt/ct	3/11	0.811852642501211	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.811852642501211	1		958	629	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737819	145737819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750261857	NA	P-0008591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	133	572	0	ENST00000428558.2:c.3011G>A	p.Arg1004Gln	p.R1004Q	ENST00000428558	NM_004260.3	1004	cGg/cAg	18/22	0.811852642501211	3	FACETS	0.744	0.678	0.813	0.372	0.339	0.407	SUBCLONAL	1	TRUE	1	0.811852642501211	3		572	619	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0008644-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	120	407	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	0.919	0.832	1			1	INDETERMINATE	1	TRUE	NA	0.439712502995329	2		407	594	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0008644-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	135	240	0	ENST00000269305.4:c.559+1G>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.407243977385558	1	FACETS	0.871	0.795	0.95	0.871	0.795	0.95	CLONAL	1	TRUE	0	0.439712502995329	1		240	550	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938673	76938673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008644-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	153	610	1	ENST00000373344.5:c.2075C>T	p.Ser692Leu	p.S692L	ENST00000373344	NM_000489.3	692	tCa/tTa	9/35	0.319554360644666	0	FACETS	0.658	0.604	0.713			1	SUBCLONAL	1	TRUE	0	0.439712502995329	0		611	593	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742899	17742914	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGCTGGCGGACGTG	CCTGCTGGCGGACGTG	-	novel	NA	P-0008644-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	135	308	0	ENST00000250003.3:c.810_825del	p.Ala272SerfsTer59	p.A272Sfs*59	ENST00000250003	NM_002478.4	269	ctCCTGCTGGCGGACGTG/ct	3/3	1	2	FACETS	0.953	0.869	1	0.953	0.869	1	CLONAL	1	TRUE	1	0.439712502995329	2		308	644	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577559	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0008653-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	221	368	0	ENST00000269305.4:c.722_723delinsTT	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCC/tTT	7/11	0.538477689069781	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.538477689069781	1		368	533	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061334	38061334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008667-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	89	549	0	ENST00000250448.2:c.655C>A	p.Arg219Ser	p.R219S	ENST00000250448	NM_004496.3	219	Cgc/Agc	2/2	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.15	2		549	988	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864850	57864850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008667-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	65	723	1	ENST00000228682.2:c.2327C>T	p.Thr776Ile	p.T776I	ENST00000228682	NM_005269.2	776	aCc/aTc	12/12	1	2	FACETS	0.757	0.654	0.87	0.757	0.654	0.87	SUBCLONAL	1	TRUE	1	0.15	2		724	1145	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435312	49435312	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	29	296	0	ENST00000301067.7:c.6241G>A	p.Glu2081Lys	p.E2081K	ENST00000301067	NM_003482.3	2081	Gag/Aag	31/54	1	2	FACETS	0.244	0.196	0.3	0.244	0.196	0.3	SUBCLONAL	1	TRUE	1	0.579289543105817	2		296	410	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265579	198265579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	60	621	0	ENST00000335508.6:c.2578G>A	p.Glu860Lys	p.E860K	ENST00000335508	NM_012433.2	860	Gaa/Aaa	18/25	1	2	FACETS	0.312	0.268	0.359	0.312	0.268	0.359	SUBCLONAL	1	TRUE	1	0.579289543105817	2		621	665	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434413	140434413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775889922	NA	P-0008684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	65	582	1	ENST00000288602.6:c.2285C>T	p.Ala762Val	p.A762V	ENST00000288602	NM_004333.4	762	gCg/gTg	18/18	1	2	FACETS	0.265	0.229	0.305	0.265	0.229	0.305	SUBCLONAL	1	TRUE	1	0.579289543105817	2		583	846	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265441	198265441	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	45	529	0	ENST00000335508.6:c.2716G>A	p.Glu906Lys	p.E906K	ENST00000335508	NM_012433.2	906	Gag/Aag	18/25	1	2	FACETS	0.298	0.25	0.351	0.298	0.25	0.351	SUBCLONAL	1	TRUE	1	0.579289543105817	2		529	522	SUCCESS
ATR	545	MSKCC	GRCh37	3	142212050	142212050	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756650966	NA	P-0008684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	46	615	0	ENST00000350721.4:c.6002G>A	p.Arg2001Gln	p.R2001Q	ENST00000350721	NM_001184.3	2001	cGa/cAa	35/47	1	2	FACETS	0.244	0.204	0.287	0.244	0.204	0.287	SUBCLONAL	1	TRUE	1	0.579289543105817	2		615	652	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755698	57755698	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1283794284	NA	P-0008684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	47	456	0	ENST00000274289.3:c.89C>G	p.Ser30Trp	p.S30W	ENST00000274289	NM_006622.3	30	tCg/tGg	1/14	1	2	FACETS	0.281	0.236	0.33	0.281	0.236	0.33	SUBCLONAL	1	TRUE	1	0.579289543105817	2		456	578	SUCCESS
APC	324	MSKCC	GRCh37	5	112176739	112176739	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	32	472	0	ENST00000257430.4:c.5448G>C	p.Leu1816Phe	p.L1816F	ENST00000257430	NM_000038.5	1816	ttG/ttC	16/16	1	2	FACETS	0.201	0.162	0.245	0.201	0.162	0.245	SUBCLONAL	1	TRUE	1	0.579289543105817	2		472	550	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652213	36652213	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	35	373	0	ENST00000244741.5:c.335A>T	p.Asp112Val	p.D112V	ENST00000244741	NM_000389.4	112	gAc/gTc	2/3	0.272371731069055	3	FACETS	0.264	0.216	0.319	0.132	0.108	0.16	INDETERMINATE	1	TRUE	1	0.579289543105817	3		373	590	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860550	151860550	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0008684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	86	722	0	ENST00000262189.6:c.10112C>G	p.Ser3371Ter	p.S3371*	ENST00000262189	NM_170606.2	3371	tCa/tGa	43/59	1	2	FACETS	0.307	0.271	0.346	0.307	0.271	0.346	SUBCLONAL	1	TRUE	1	0.579289543105817	2		722	967	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371875	55371875	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	13	71	0	ENST00000297316.4:c.565C>A	p.Pro189Thr	p.P189T	ENST00000297316	NM_022454.3	189	Ccc/Acc	2/2	1	2	FACETS	0.416	0.299	0.554	0.416	0.299	0.554	SUBCLONAL	1	TRUE	1	0.579289543105817	2		71	108	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416189	416189	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	47	630	0	ENST00000399788.2:c.3997C>T	p.Arg1333Ter	p.R1333*	ENST00000399788	NM_001042603.1	1333	Cga/Tga	24/28	NA	2	FACETS	0.209	0.175	0.246			1	INDETERMINATE	1	TRUE	NA	0.579289543105817	2		630	777	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2114289	2114289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	111	689	0	ENST00000219476.3:c.1460C>T	p.Ser487Leu	p.S487L	ENST00000219476	NM_000548.3	487	tCa/tTa	15/42	1	2	FACETS	0.411	0.368	0.456	0.411	0.368	0.456	SUBCLONAL	1	TRUE	1	0.579289543105817	2		689	933	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778204	3778204	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	27	350	0	ENST00000262367.5:c.6844G>C	p.Asp2282His	p.D2282H	ENST00000262367	NM_004380.2	2282	Gac/Cac	31/31	1	2	FACETS	0.209	0.166	0.259	0.209	0.166	0.259	SUBCLONAL	1	TRUE	1	0.579289543105817	2		350	446	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390390	56390390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1279	108	1191	2	ENST00000348428.3:c.1129G>A	p.Asp377Asn	p.D377N	ENST00000348428	NM_006785.3	377	Gac/Aac	10/17	0.16513181666833	3	FACETS	0.347	0.31	0.386	0.173	0.155	0.193	INDETERMINATE	1	TRUE	1	0.579289543105817	3		1193	1387	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621023	1621023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1455	102	1151	0	ENST00000344749.5:c.1037G>A	p.Ser346Asn	p.S346N	ENST00000344749	NM_001136139.2	346	aGc/aAc	13/19	0.16513181666833	3	FACETS	0.292	0.259	0.326	0.146	0.129	0.163	INDETERMINATE	1	TRUE	1	0.579289543105817	3		1151	1557	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022616	31022616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	63	666	0	ENST00000375687.4:c.2101C>T	p.Pro701Ser	p.P701S	ENST00000375687	NM_015338.5	701	Cct/Tct	13/13	1	2	FACETS	0.22	0.19	0.254	0.22	0.19	0.254	SUBCLONAL	1	TRUE	1	0.579289543105817	2		666	987	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279766	46279766	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	55	534	0	ENST00000371998.3:c.3692G>C	p.Arg1231Thr	p.R1231T	ENST00000371998		1231	aGa/aCa	20/23	1	2	FACETS	0.236	0.201	0.275	0.236	0.201	0.275	SUBCLONAL	1	TRUE	1	0.579289543105817	2		534	803	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650445	48650445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	106	1038	1	ENST00000376670.3:c.415G>A	p.Glu139Lys	p.E139K	ENST00000376670	NM_002049.3	139	Gag/Aag	3/6	1	2	FACETS	0.285	0.255	0.318	0.285	0.255	0.318	SUBCLONAL	1	TRUE	1	0.579289543105817	2		1039	1283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0008691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	388	362	0	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	NA	2	FACETS	0.998	0.954	1			1	INDETERMINATE	2	TRUE	NA	0.469582537696901	2		362	828	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446807	49446807	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	159	402	0	ENST00000301067.7:c.1003C>G	p.Pro335Ala	p.P335A	ENST00000301067	NM_003482.3	335	Ccc/Gcc	8/54	0.425421688729869	5	FACETS	0.913	0.835	0.995			1	CLONAL	1	TRUE	NA	0.469582537696901	5		402	1264	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448509	49448509	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	168	392	0	ENST00000301067.7:c.202C>G	p.Leu68Val	p.L68V	ENST00000301067	NM_003482.3	68	Ctc/Gtc	3/54	0.425421688729869	5	FACETS	0.954	0.874	1			1	CLONAL	1	TRUE	NA	0.469582537696901	5		392	1279	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792770	33792770	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1457318927	NA	P-0008691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	43	87	0	ENST00000498907.2:c.551C>G	p.Pro184Arg	p.P184R	ENST00000498907	NM_004364.3	184	cCg/cGg	1/1	0.469582537696901	4	FACETS	0.928	0.781	1	0.464	0.39	0.545	CLONAL	1	TRUE	2	0.469582537696901	4		87	290	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0008705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	160	411	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.269463947367801	5	FACETS	0.982	0.901	1	0.655	0.601	0.711	CLONAL	2	TRUE	2	0.269463947367801	5		411	849	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612632	228612632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1265	128	950	1	ENST00000366696.1:c.395G>A	p.Arg132His	p.R132H	ENST00000366696	NM_003493.2	132	cGc/cAc	1/1	0.269463947367801	5	FACETS	0.958	0.865	1	0.319	0.288	0.352	CLONAL	1	TRUE	2	0.269463947367801	5		951	1393	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670404	88670404	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	108	418	0	ENST00000360948.2:c.1282G>C	p.Asp428His	p.D428H	ENST00000360948	NM_001012338.2	428	Gac/Cac	11/19	0.231766723818866	1	FACETS	0.953	0.856	1	0.953	0.856	1	CLONAL	1	TRUE	0	0.269463947367801	1		418	728	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372117	55372118	+	missense_variant	Missense_Mutation	DNP	CA	CA	AT	rs1563871910	NA	P-0008705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	14	147	0	ENST00000297316.4:c.807_808delinsAT	p.Met270Leu	p.M270L	ENST00000297316	NM_022454.3	269	ccCAtg/ccATtg	2/2	NA	2	FACETS	0.541	0.392	0.721			1	INDETERMINATE	1	TRUE	NA	0.269463947367801	2		147	192	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0008730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	111	407	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.156159345304492	1	FACETS	1	0.922	1	1	0.988	1	CLONAL	2	TRUE	0	0.156159345304492	1		407	638	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0008730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	19	401	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.422	0.319	0.545	0.422	0.319	0.545	SUBCLONAL	1	TRUE	1	0.156159345304492	2		401	576	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0008730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	42	365	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.643	0.535	0.763	0.643	0.535	0.763	SUBCLONAL	1	TRUE	1	0.156159345304492	2		365	837	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	138	660	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	1	0.971	1	1	0.991	1	CLONAL	2	TRUE	1	0.156159345304492	2		660	764	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11554273	NA	P-0008730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	71	557	0	ENST00000371085.3:c.601C>A	p.Arg201Ser	p.R201S	ENST00000371085	NM_000516.4	201	Cgt/Agt	8/13	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.156159345304492	2		557	831	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138431100	138431100	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	44	717	0	ENST00000289153.2:c.1349G>A	p.Gly450Glu	p.G450E	ENST00000289153	NM_006219.2	450	gGa/gAa	8/22	1	2	FACETS	0.659	0.551	0.78	0.659	0.551	0.78	SUBCLONAL	1	TRUE	1	0.156159345304492	2		717	855	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368213	45368213	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	244	542	1	ENST00000262160.6:c.1389C>A	p.Cys463Ter	p.C463*	ENST00000262160	NM_005901.5	463	tgC/tgA	11/11	0.156159345304492	2	FACETS	0.903	0.848	0.959	1	0.995	1	CLONAL	5	TRUE	0	0.156159345304492	2		543	692	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221229	1221229	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1223	115	989	0	ENST00000326873.7:c.752G>T	p.Gly251Val	p.G251V	ENST00000326873	NM_000455.4	251	gGt/gTt	6/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.156159345304492	2		989	1338	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540123	187540123	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	81	840	0	ENST00000441802.2:c.7617del	p.Arg2539SerfsTer4	p.R2539Sfs*4	ENST00000441802	NM_005245.3	2539	agA/ag	10/27	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.156159345304492	2		840	1027	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	343	145	0				ENST00000310581	NM_198253.2	-/1132			0.353114572315406	2	FACETS	0.796	0.755	0.837	0.398	0.377	0.419	INDETERMINATE	1	TRUE	0	0.911197843201285	2		145	946	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0008734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1262	78	451	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.862190579137035	1	FACETS	0.07	0.06	0.079	0.07	0.06	0.079	SUBCLONAL	1	TRUE	0	0.911197843201285	1		452	1340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	765	455	0	ENST00000269305.4:c.772G>C	p.Glu258Gln	p.E258Q	ENST00000269305	NM_001126112.2	258	Gaa/Caa	7/11	0.862190579137035	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.911197843201285	1		455	889	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610570	52610570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	611	662	2	ENST00000394830.3:c.3603G>A	p.Met1201Ile	p.M1201I	ENST00000394830	NM_018313.4	1201	atG/atA	23/30	0.460382593648818	1	FACETS	0.646	0.624	0.667	0.646	0.624	0.667	INDETERMINATE	1	TRUE	0	0.911197843201285	1		664	1131	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85741985	85741985	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1534	1307	1224	0	ENST00000370580.1:c.51G>C	p.Lys17Asn	p.K17N	ENST00000370580	NM_003921.4	17	aaG/aaC	1/3	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.911197843201285	2		1224	2841	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032825	48032825	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs753675331	NA	P-0008734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	314	571	0	ENST00000234420.5:c.3625C>G	p.Leu1209Val	p.L1209V	ENST00000234420	NM_000179.2	1209	Ctg/Gtg	7/10	0.476673560304053	1	FACETS	0.349	0.329	0.369	0.349	0.329	0.369	INDETERMINATE	1	TRUE	0	0.911197843201285	1		571	1075	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437315	52437315	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0008734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	720	621	0	ENST00000460680.1:c.1730-1G>T		p.X577_splice	ENST00000460680	NM_004656.3	577			0.460382593648818	1	FACETS	0.732	0.711	0.752	0.732	0.711	0.752	INDETERMINATE	1	TRUE	0	0.911197843201285	1		621	1176	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441431	52441431	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	413	667	2	ENST00000460680.1:c.421C>A	p.His141Asn	p.H141N	ENST00000460680	NM_004656.3	141	Cat/Aat	6/17	0.460382593648818	1	FACETS	0.364	0.346	0.382	0.364	0.346	0.382	INDETERMINATE	1	TRUE	0	0.911197843201285	1		669	1356	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610584	52610584	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	670	703	0	ENST00000394830.3:c.3589G>A	p.Glu1197Lys	p.E1197K	ENST00000394830	NM_018313.4	1197	Gaa/Aaa	23/30	0.460382593648818	1	FACETS	0.681	0.66	0.702	0.681	0.66	0.702	INDETERMINATE	1	TRUE	0	0.911197843201285	1		703	1176	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610608	52610608	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	690	711	1	ENST00000394830.3:c.3565G>A	p.Glu1189Lys	p.E1189K	ENST00000394830	NM_018313.4	1189	Gaa/Aaa	23/30	0.460382593648818	1	FACETS	0.669	0.649	0.69	0.669	0.649	0.69	INDETERMINATE	1	TRUE	0	0.911197843201285	1		712	1232	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526305	189526305	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	546	289	0	ENST00000264731.3:c.569C>G	p.Ala190Gly	p.A190G	ENST00000264731	NM_003722.4	190	gCc/gGc	4/14	0.604479345399856	3	FACETS	0.932	0.901	0.963	0.932	0.901	0.963	CLONAL	2	TRUE	1	0.911197843201285	3		289	936	SUCCESS
FIP1L1	81608	MSKCC	GRCh37	4	54280885	54280885	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	558	327	3	ENST00000358575.5:c.874C>A	p.Leu292Ile	p.L292I	ENST00000358575	NM_001134937.1	292	Cta/Ata	10/18	0.911197843201285	2	FACETS	0.997	0.981	1	0.997	0.981	1	CLONAL	2	TRUE	0	0.911197843201285	2		330	614	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18473935	18473935	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1444567095	NA	P-0008734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	544	562	0	ENST00000266497.5:c.1177C>G	p.Leu393Val	p.L393V	ENST00000266497		393	Cta/Gta	6/31	0.460382593648818	1	FACETS	0.675	0.652	0.698	0.675	0.652	0.698	INDETERMINATE	1	TRUE	0	0.911197843201285	1		562	963	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820792	3820792	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057520589	NA	P-0008734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	794	709	0	ENST00000262367.5:c.2659C>T	p.Gln887Ter	p.Q887*	ENST00000262367	NM_004380.2	887	Cag/Tag	14/31	0.523205359576769	1	FACETS	0.813	0.793	0.833	0.813	0.793	0.833	INDETERMINATE	1	TRUE	0	0.911197843201285	1		709	1167	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230827	53230827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	980	435	1	ENST00000375401.3:c.1966G>A	p.Glu656Lys	p.E656K	ENST00000375401	NM_004187.3	656	Gag/Aag	14/26	1	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.911197843201285	1		436	1040	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230843	53230843	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	923	410	0	ENST00000375401.3:c.1950G>T	p.Lys650Asn	p.K650N	ENST00000375401	NM_004187.3	650	aaG/aaT	14/26	1	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.911197843201285	1		410	983	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239625	53239625	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	930	385	0	ENST00000375401.3:c.1717C>T	p.Pro573Ser	p.P573S	ENST00000375401	NM_004187.3	573	Ccc/Tcc	12/26	1	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.911197843201285	1		385	1006	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239876	53239876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	1101	419	0	ENST00000375401.3:c.1565C>T	p.Ser522Phe	p.S522F	ENST00000375401	NM_004187.3	522	tCc/tTc	11/26	1	1	FACETS	1	0.999	1	1	0.999	1	CLONAL	1	TRUE	0	0.911197843201285	1		419	1152	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239987	53239987	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	1008	425	0	ENST00000375401.3:c.1454C>T	p.Ser485Phe	p.S485F	ENST00000375401	NM_004187.3	485	tCt/tTt	11/26	1	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.911197843201285	1		425	1080	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0008753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	475	538	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.376441050926379	4	FACETS	0.887	0.848	0.926			1	CLONAL	3	TRUE	NA	0.376441050926379	4		538	1306	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118951	70118951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	185	800	0	ENST00000245479.2:c.523C>T	p.Gln175Ter	p.Q175*	ENST00000245479	NM_000346.3	175	Cag/Tag	2/3	1	2	FACETS	0.995	0.918	1	0.995	0.918	1	CLONAL	1	TRUE	1	0.376441050926379	2		800	988	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266090	41266253	+	splice_donor_variant,coding_sequence_variant,intron_variant	In_Frame_Del	DEL	TTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTA	TTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTA	-	novel	NA	P-0008753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	260	664	0	ENST00000349496.5:c.90_241+12del		p.S29_D81del	ENST00000349496	NM_001904.3	29		3/15	0.323979029238402	3	FACETS	0.944	0.887	1	0.63	0.591	0.669	CLONAL	2	TRUE	0	0.376441050926379	3		664	869	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0008757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	284	353	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.342362299634244	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.342362299634244	2		353	737	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0008757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	289	88	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.191935053396345	5	FACETS	1	0.986	1	0.769	0.723	0.816	INDETERMINATE	2	TRUE	2	0.342362299634244	5		88	1108	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49929229	49929229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	249	854	1	ENST00000296474.3:c.3314C>T	p.Ala1105Val	p.A1105V	ENST00000296474	NM_002447.2	1105	gCc/gTc	15/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.342362299634244	2		855	1271	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242471	55242471	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	285	484	0	ENST00000275493.2:c.2241A>C	p.Leu747Phe	p.L747F	ENST00000275493	NM_005228.3	747	ttA/ttC	19/28	0.191935053396345	5	FACETS	1	0.986	1	0.77	0.724	0.817	INDETERMINATE	2	TRUE	2	0.342362299634244	5		484	1091	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241679	55241681	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	rs397517086	NA	P-0008765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	735	541	0	ENST00000275493.2:c.2127_2129del	p.Glu709_Thr710delinsAsp	p.E709_T710delinsD	ENST00000275493	NM_005228.3	709	gaAACt/gat	18/28	0.680171073914185	3	FACETS	0.991	0.96	1	0.991	0.96	1	CLONAL	2	TRUE	1	0.680171073914185	3		541	1461	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0008765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	197	228	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.680171073914185	2		228	493	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0008765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	281	401	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.895	0.843	0.949	0.895	0.843	0.949	CLONAL	1	TRUE	1	0.680171073914185	2		401	923	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920484	134920484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759860489	NA	P-0008765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	313	487	1	ENST00000398015.3:c.2299C>T	p.Arg767Cys	p.R767C	ENST00000398015	NM_004441.4	767	Cgc/Tgc	12/16	1	2	FACETS	0.933	0.882	0.986	0.933	0.882	0.986	CLONAL	1	TRUE	1	0.680171073914185	2		488	986	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391423	84391423	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	208	353	0	ENST00000321945.7:c.409C>G	p.Pro137Ala	p.P137A	ENST00000321945	NM_139076.2	137	Cca/Gca	5/9	1	2	FACETS	0.916	0.854	0.979	0.916	0.854	0.979	CLONAL	1	TRUE	1	0.680171073914185	2		353	668	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40491348	40491348	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	353	638	1	ENST00000264657.5:c.452T>A	p.Val151Asp	p.V151D	ENST00000264657	NM_139276.2	151	gTc/gAc	5/24	1	2	FACETS	0.942	0.893	0.991	0.942	0.893	0.991	CLONAL	1	TRUE	1	0.680171073914185	2		639	1102	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	28	145	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.959	0.767	1	0.959	0.767	1	CLONAL	1	TRUE	1	0.161747833510686	2		145	361	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423474	116423474	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913245	NA	P-0008772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	142	416	0	ENST00000397752.3:c.3749T>C	p.Met1250Thr	p.M1250T	ENST00000397752	NM_000245.2	1250	aTg/aCg	19/21	0.161747833510686	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.161747833510686	3		416	775	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148526903	148526903	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	42	568	0	ENST00000320356.2:c.401T>A	p.Met134Lys	p.M134K	ENST00000320356	NM_004456.4	134	aTg/aAg	5/20	0.161747833510686	3	FACETS	0.685	0.57	0.814	0.343	0.285	0.407	SUBCLONAL	1	TRUE	1	0.161747833510686	3		568	819	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860559	151860559	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	105	551	1	ENST00000262189.6:c.10103G>A	p.Gly3368Glu	p.G3368E	ENST00000262189	NM_170606.2	3368	gGg/gAg	43/59	0.161747833510686	3	FACETS	1	0.962	1	0.584	0.522	0.651	CLONAL	1	TRUE	1	0.161747833510686	3		552	1201	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0008787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	240	476	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			NA	2	FACETS	1	0.976	1			1	INDETERMINATE	2	TRUE	NA	0.407797977866033	2		476	553	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088703	27088703	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0008787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	193	518	0	ENST00000324856.7:c.2312T>A	p.Leu771Ter	p.L771*	ENST00000324856	NM_006015.4	771	tTa/tAa	7/20	0.395122380499591	3	FACETS	1	0.99	1	0.71	0.658	0.763	CLONAL	1	TRUE	1	0.407797977866033	3		518	803	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374364	138374364	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	125	347	0	ENST00000289153.2:c.3080C>G	p.Ser1027Cys	p.S1027C	ENST00000289153	NM_006219.2	1027	tCt/tGt	22/22	1	2	FACETS	0.79	0.722	0.86	1	0.988	1	SUBCLONAL	2	TRUE	1	0.407797977866033	2		347	388	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023200	27023229	+	inframe_deletion	In_Frame_Del	DEL	CTCGAACGGGAACGCGGGCCCTAGGCCCGC	CTCGAACGGGAACGCGGGCCCTAGGCCCGC	-	novel	NA	P-0008787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	90	214	0	ENST00000324856.7:c.307_336del	p.Ser103_Ala112del	p.S103_A112del	ENST00000324856	NM_006015.4	102	aaCTCGAACGGGAACGCGGGCCCTAGGCCCGCc/aac	1/20	0.395122380499591	3	FACETS	1	0.979	1	0.714	0.639	0.794	CLONAL	1	TRUE	1	0.407797977866033	3		214	372	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023683	27023686	+	frameshift_variant	Frame_Shift_Del	DEL	TTCG	TTCG	-	novel	NA	P-0008787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	248	487	0	ENST00000324856.7:c.790_793del	p.Ser264ProfsTer98	p.S264Pfs*98	ENST00000324856	NM_006015.4	263	tcTTCG/tc	1/20	0.395122380499591	3	FACETS	0.855	0.802	0.91	0.855	0.802	0.91	CLONAL	2	TRUE	1	0.407797977866033	3		487	856	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653848	89653849	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0008787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	175	383	0	ENST00000371953.3:c.148_149del	p.Ile50Ter	p.I50*	ENST00000371953	NM_000314.4	49	aAT/a	2/9	1	2	FACETS	1	0.956	1	1	0.993	1	CLONAL	2	TRUE	1	0.407797977866033	2		383	415	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0008790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	174	407	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.857	0.79	0.926	0.857	0.79	0.926	CLONAL	1	TRUE	1	0.497873694887908	2		407	816	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974732	21974732	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs878853650	NA	P-0008790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	158	442	0	ENST00000304494.5:c.95T>C	p.Leu32Pro	p.L32P	ENST00000304494	NM_000077.4	32	cTg/cCg	1/3	0.497873694887908	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.497873694887908	1		442	422	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715660	30715660	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	162	507	0	ENST00000295754.5:c.1318G>T	p.Glu440Ter	p.E440*	ENST00000295754	NM_003242.5	440	Gag/Tag	5/7	0.497873694887908	1	FACETS	0.889	0.82	0.959	0.889	0.82	0.959	CLONAL	1	TRUE	0	0.497873694887908	1		507	550	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622211	117622211	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs760646608	NA	P-0008790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	231	734	0	ENST00000368508.3:c.6659A>T	p.Asn2220Ile	p.N2220I	ENST00000368508	NM_002944.2	2220	aAt/aTt	42/43	0.497873694887908	1	FACETS	0.927	0.867	0.988	0.927	0.867	0.988	CLONAL	1	TRUE	0	0.497873694887908	1		734	752	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579700	7579703	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CAGA	CAGA	-	novel	NA	P-0008790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	168	623	0	ENST00000269305.4:c.93_96del	p.Leu32ProfsTer11	p.L32Pfs*11	ENST00000269305	NM_001126112.2	31	gtTCTG/gt	3/11	0.483338958678946	1	FACETS	0.78	0.719	0.842	0.78	0.719	0.842	SUBCLONAL	1	TRUE	0	0.497873694887908	1		623	650	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191507	10191507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs5030821	NA	P-0008799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	149	444	1	ENST00000256474.2:c.500G>A	p.Arg167Gln	p.R167Q	ENST00000256474	NM_000551.3	167	cGg/cAg	3/3	0.46258304653777	1	FACETS	0.884	0.812	0.959	0.884	0.812	0.959	CLONAL	1	TRUE	0	0.46258304653777	1		445	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0008811-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	58	375	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.259807152741198	3	FACETS	0.388	0.333	0.449	0.194	0.166	0.225	INDETERMINATE	1	TRUE	1	0.486670034620684	3		377	763	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333844	70333844	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs776152780	NA	P-0008811-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	335	457	0	ENST00000373644.4:c.1749G>C	p.Leu583Phe	p.L583F	ENST00000373644	NM_030625.2	583	ttG/ttC	2/12	0.486670034620684	2	FACETS	0.776	0.736	0.816	0.776	0.736	0.816	SUBCLONAL	2	TRUE	0	0.486670034620684	2		457	887	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0008815-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	373	595	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.285803416044453	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	0	0.359887993542434	3		595	773	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0008815-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	290	407	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.359887993542434	4	FACETS	0.865	0.816	0.914	1	0.992	1	CLONAL	3	TRUE	2	0.359887993542434	4		407	845	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209101894	209101894	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs375423243	NA	P-0008815-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	73	448	0	ENST00000345146.2:c.1155-1G>C		p.X385_splice	ENST00000345146	NM_005896.2	385			0.130540261525606	3	FACETS	0.869	0.761	0.985	0.29	0.253	0.329	INDETERMINATE	1	TRUE	0	0.359887993542434	3		448	551	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390071	89390071	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760135022	NA	P-0008815-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	58	414	0	ENST00000336596.2:c.820C>T	p.Arg274Ter	p.R274*	ENST00000336596	NM_005233.5	274	Cga/Tga	4/17	0.320516002619156	2	FACETS	0.518	0.445	0.598	0.259	0.222	0.299	SUBCLONAL	1	TRUE	0	0.359887993542434	2		414	622	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205229	61205229	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008815-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	160	588	0	ENST00000301761.2:c.169G>T	p.Glu57Ter	p.E57*	ENST00000301761	NM_017841.2	57	Gag/Tag	2/4	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.359887993542434	2		588	795	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858258	9858258	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008815-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	50	565	1	ENST00000330684.3:c.3143G>A	p.Ser1048Asn	p.S1048N	ENST00000330684	NM_001134407.1	1048	aGc/aAc	13/13	0.23393763764335	4	FACETS	0.567	0.48	0.662	0.189	0.16	0.221	SUBCLONAL	1	TRUE	1	0.359887993542434	4		566	667	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291807	15291807	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008815-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	41	494	0	ENST00000263388.2:c.2959A>G	p.Thr987Ala	p.T987A	ENST00000263388	NM_000435.2	987	Acc/Gcc	18/33	0.359887993542434	1	FACETS	0.474	0.395	0.561	0.474	0.395	0.561	SUBCLONAL	1	TRUE	0	0.359887993542434	1		494	394	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952092	76952092	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008815-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	88	898	1	ENST00000373344.5:c.343G>T	p.Asp115Tyr	p.D115Y	ENST00000373344	NM_000489.3	115	Gat/Tat	5/35	0.334509360644684	1	FACETS	0.409	0.361	0.46	0.409	0.361	0.46	SUBCLONAL	1	TRUE	0	0.359887993542434	1		899	981	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0008837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	598	409	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.350003631371	3	FACETS	1	0.996	1	0.794	0.769	0.818	INDETERMINATE	2	TRUE	0	0.683679171692643	3		409	986	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0008837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	335	417	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.683679171692643	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.683679171692643	1		417	571	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648258	206648258	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1553384828	NA	P-0008837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	135	448	0	ENST00000367120.3:c.279C>A	p.Ser93Arg	p.S93R	ENST00000367120	NM_014002.3	93	agC/agA	5/22	0.683679171692643	3	FACETS	0.515	0.468	0.566	0.258	0.234	0.283	SUBCLONAL	1	TRUE	1	0.683679171692643	3		448	1028	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972769	25972769	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	269	446	0	ENST00000435504.4:c.1656A>C	p.Lys552Asn	p.K552N	ENST00000435504		552	aaA/aaC	12/13	0.152562305058389	4	FACETS	1	0.989	1	0.414	0.388	0.44	INDETERMINATE	1	TRUE	1	0.683679171692643	4		446	1067	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361130	66361130	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	336	423	0	ENST00000273854.3:c.1042G>T	p.Asp348Tyr	p.D348Y	ENST00000273854	NM_004439.5	348	Gat/Tat	4/18	0.334247679779772	1	FACETS	0.81	0.77	0.85	0.81	0.77	0.85	INDETERMINATE	1	TRUE	0	0.683679171692643	1		423	799	SUCCESS
APC	324	MSKCC	GRCh37	5	112177095	112177095	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1346125460	NA	P-0008837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	212	568	0	ENST00000257430.4:c.5804A>T	p.Gln1935Leu	p.Q1935L	ENST00000257430	NM_000038.5	1935	cAg/cTg	16/16	0.447685875361294	1	FACETS	0.376	0.349	0.404	0.376	0.349	0.404	SUBCLONAL	1	TRUE	0	0.683679171692643	1		568	1085	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680734	30680734	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	152	448	0	ENST00000376406.3:c.985A>T	p.Ser329Cys	p.S329C	ENST00000376406	NM_014641.2	329	Agc/Tgc	5/15	0.683679171692643	3	FACETS	0.485	0.442	0.53	0.243	0.221	0.265	SUBCLONAL	1	TRUE	1	0.683679171692643	3		448	1230	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8526642	8526642	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	137	269	0	ENST00000356435.5:c.553G>T	p.Gly185Cys	p.G185C	ENST00000356435		185	Ggt/Tgt	6/35	0.683679171692643	1	FACETS	0.658	0.604	0.713	0.658	0.604	0.713	SUBCLONAL	1	TRUE	0	0.683679171692643	1		269	401	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891194	101891194	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	439	392	2	ENST00000374994.4:c.155G>T	p.Gly52Val	p.G52V	ENST00000374994	NM_004612.2	52	gGg/gTg	2/9	0.308999440701228	2	FACETS	1	0.996	1	0.707	0.678	0.736	INDETERMINATE	1	TRUE	0	0.683679171692643	2		394	908	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346976	73346976	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	330	309	0	ENST00000377767.4:c.1241G>T	p.Gly414Val	p.G414V	ENST00000377767	NM_014953.3	414	gGa/gTa	9/21	0.57792528688043	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.683679171692643	1		309	606	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2111880	2111880	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	103	353	0	ENST00000219476.3:c.1128C>G	p.Asp376Glu	p.D376E	ENST00000219476	NM_000548.3	376	gaC/gaG	12/42	0.530761468653796	1	FACETS	0.352	0.315	0.39	0.352	0.315	0.39	SUBCLONAL	1	TRUE	0	0.683679171692643	1		353	564	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820576	3820576	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	155	191	0	ENST00000262367.5:c.2875A>G	p.Thr959Ala	p.T959A	ENST00000262367	NM_004380.2	959	Aca/Gca	14/31	0.14682562310334	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.683679171692643	0		191	457	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993714	72993714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1266350809	NA	P-0008837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	180	462	1	ENST00000268489.5:c.331G>A	p.Glu111Lys	p.E111K	ENST00000268489	NM_006885.3	111	Gag/Aag	2/10	0.517072303061757	1	FACETS	0.451	0.417	0.487	0.451	0.417	0.487	SUBCLONAL	1	TRUE	0	0.683679171692643	1		463	768	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972475	81972475	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	231	705	0	ENST00000359376.3:c.3268T>A	p.Cys1090Ser	p.C1090S	ENST00000359376	NM_002661.3	1090	Tgt/Agt	29/33	0.517072303061757	1	FACETS	0.359	0.334	0.385	0.359	0.334	0.385	SUBCLONAL	1	TRUE	0	0.683679171692643	1		705	1240	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770089	56770089	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	141	393	0	ENST00000337432.4:c.85T>C	p.Ser29Pro	p.S29P	ENST00000337432	NM_058216.2	29	Tct/Cct	1/9	0.683679171692643	3	FACETS	0.45	0.408	0.493	0.225	0.204	0.247	SUBCLONAL	1	TRUE	1	0.683679171692643	3		393	1231	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897336	78897336	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs757484259	NA	P-0008837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	454	400	0	ENST00000306801.3:c.2671G>T	p.Asp891Tyr	p.D891Y	ENST00000306801	NM_020761.2	891	Gat/Tat	23/34	0.135555812447617	3	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.683679171692643	3		400	846	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212059	5212059	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770983463	NA	P-0008837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	103	364	0	ENST00000357368.4:c.4972G>A	p.Ala1658Thr	p.A1658T	ENST00000357368	NM_002850.3	1658	Gca/Aca	32/38	0.437624478459694	0	FACETS		NA	1			1	NA	1	TRUE	0	0.683679171692643	0		364	384	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781059	135781083	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTGTTTCCTTTTGCTTTCTTTAA	CTGTGTTTCCTTTTGCTTTCTTTAA	-	novel	NA	P-0008837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	417	622	0	ENST00000298552.3:c.1882_1906del	p.Leu628ArgfsTer17	p.L628Rfs*17	ENST00000298552	NM_001162426.1	628	TTAAAGAAAGCAAAAGGAAACACAGag/ag	15/23	0.308999440701228	2	FACETS	0.941	0.896	0.987	0.471	0.448	0.494	INDETERMINATE	1	TRUE	0	0.683679171692643	2		622	1296	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533104	63533104	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	558	397	0	ENST00000307078.5:c.1790del	p.Gly597GlufsTer92	p.G597Efs*92	ENST00000307078	NM_004655.3	597	gGa/ga	7/11	0.683679171692643	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.683679171692643	3		397	987	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0008849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	404	330	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.28686971459639	9	FACETS	0.927	0.884	0.97			1	CLONAL	6	TRUE	NA	0.28686971459639	9		330	1015	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242494	55242494	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	396	285	0	ENST00000275493.2:c.2264C>G	p.Ala755Gly	p.A755G	ENST00000275493	NM_005228.3	755	gCc/gGc	19/28	0.28686971459639	9	FACETS	0.988	0.944	1			1	CLONAL	6	TRUE	NA	0.28686971459639	9		285	933	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204513718	204513718	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	59	251	0	ENST00000367182.3:c.728A>T	p.Glu243Val	p.E243V	ENST00000367182	NM_001278516.1	243	gAg/gTg	9/11	0.28686971459639	2	FACETS	1	0.894	1	0.521	0.449	0.598	CLONAL	1	TRUE	0	0.28686971459639	2		251	395	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348996	70348996	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	116	561	0	ENST00000374080.3:c.3508C>G	p.Arg1170Gly	p.R1170G	ENST00000374080		1170	Cgg/Ggg	25/45	0.28686971459639	1	FACETS	0.966	0.872	1	0.966	0.872	1	CLONAL	1	TRUE	0	0.28686971459639	1		561	717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577132	7577132	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	140	474	0	ENST00000269305.4:c.806del	p.Ser269ThrfsTer76	p.S269Tfs*76	ENST00000269305	NM_001126112.2	269	aGc/ac	8/11	0.262599013908607	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.28686971459639	1		474	815	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437596	52437597	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0008849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	129	683	0	ENST00000460680.1:c.1564_1565del	p.Pro522CysfsTer14	p.P522Cfs*14	ENST00000460680	NM_004656.3	522	CCt/t	13/17	0.262599013908607	1	FACETS	0.904	0.82	0.993	0.904	0.82	0.993	CLONAL	1	TRUE	0	0.28686971459639	1		683	852	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0008858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	150	464	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.3	2	FACETS	0.851	0.783	0.922	0.851	0.783	0.922	CLONAL	2	TRUE	0	0.33	2		466	534	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101272	4101272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370799450	NA	P-0008858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	150	363	1	ENST00000262948.5:c.535C>T	p.Arg179Trp	p.R179W	ENST00000262948	NM_030662.3	179	Cgg/Tgg	5/11	0.228519737288184	3	FACETS	1	0.985	1	0.683	0.625	0.744	CLONAL	1	TRUE	1	0.33	3		364	775	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172027	32172027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1417982489	NA	P-0008858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	121	415	0	ENST00000375023.3:c.3005G>A	p.Arg1002His	p.R1002H	ENST00000375023	NM_004557.3	1002	cGc/cAc	19/30	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.33	2		415	519	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986886	36986886	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	47	116	0	ENST00000354822.5:c.803G>T	p.Gly268Val	p.G268V	ENST00000354822	NM_001079668.2	268	gGc/gTc	3/3	0.228519737288184	3	FACETS	1	0.869	1	0.514	0.435	0.599	CLONAL	1	TRUE	1	0.33	3		116	323	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028756	42028756	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	33	697	0	ENST00000219905.7:c.4294G>C	p.Val1432Leu	p.V1432L	ENST00000219905	NM_001164273.1	1432	Gtg/Ctg	13/24	1	2	FACETS	0.445	0.362	0.539	0.445	0.362	0.539	SUBCLONAL	1	TRUE	1	0.33	2		697	449	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831762	72831762	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	35	671	1	ENST00000268489.5:c.4819C>T	p.Gln1607Ter	p.Q1607*	ENST00000268489	NM_006885.3	1607	Cag/Tag	9/10	0.251691328614669	1	FACETS	0.366	0.299	0.441	0.366	0.299	0.441	SUBCLONAL	1	TRUE	0	0.33	1		672	484	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023242	27023333	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCACGGAGCCGCCCGGCGGCGGCGGTGGCGGCAGCAGCGATGGGGTGGGGGCGCCTCCTCACTCAGCCGCGGCCGCCTTGCCGCCCCCAG	CCTCACGGAGCCGCCCGGCGGCGGCGGTGGCGGCAGCAGCGATGGGGTGGGGGCGCCTCCTCACTCAGCCGCGGCCGCCTTGCCGCCCCCAG	-	novel	NA	P-0008858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	42	239	0	ENST00000324856.7:c.351_442del	p.Thr118ArgfsTer251	p.T118Rfs*251	ENST00000324856	NM_006015.4	116	aaCCTCACGGAGCCGCCCGGCGGCGGCGGTGGCGGCAGCAGCGATGGGGTGGGGGCGCCTCCTCACTCAGCCGCGGCCGCCTTGCCGCCCCCAGcc/aacc	1/20	1	2	FACETS	0.497	0.415	0.589	0.497	0.415	0.589	SUBCLONAL	1	TRUE	1	0.33	2		239	512	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660894	227660894	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs13306470	NA	P-0008863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	86	413	0	ENST00000305123.5:c.2561G>T	p.Arg854Leu	p.R854L	ENST00000305123	NM_005544.2	854	cGc/cTc	1/2	1	2	FACETS	0.552	0.487	0.622	0.552	0.487	0.622	SUBCLONAL	1	TRUE	1	0.293323174284083	2		413	1062	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11291387	11291387	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	148	432	0	ENST00000361445.4:c.2619G>T	p.Lys873Asn	p.K873N	ENST00000361445	NM_004958.3	873	aaG/aaT	17/58	0.168197364125364	2	FACETS	1	0.96	1	0.545	0.497	0.595	INDETERMINATE	1	TRUE	0	0.293323174284083	2		432	926	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085854	16085854	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	97	294	0	ENST00000281043.3:c.1030G>T	p.Ala344Ser	p.A344S	ENST00000281043	NM_005378.4	344	Gca/Tca	3/3	0.246036945989967	3	FACETS	0.775	0.69	0.867	0.388	0.345	0.434	SUBCLONAL	1	TRUE	1	0.293323174284083	3		294	978	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376544	118376544	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	80	340	1	ENST00000534358.1:c.9937G>C	p.Ala3313Pro	p.A3313P	ENST00000534358	NM_005933.3	3313	Gct/Cct	27/36	0.246036945989967	3	FACETS	0.606	0.532	0.686	0.303	0.266	0.343	SUBCLONAL	1	TRUE	1	0.293323174284083	3		341	1032	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544079	18544079	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	52	357	2	ENST00000266497.5:c.1896G>T	p.Trp632Cys	p.W632C	ENST00000266497		632	tgG/tgT	13/31	0.246036945989967	3	FACETS	0.966	0.824	1	0.483	0.412	0.56	CLONAL	1	TRUE	1	0.293323174284083	3		359	421	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644821	67644821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	84	333	0	ENST00000264010.4:c.86G>A	p.Arg29Gln	p.R29Q	ENST00000264010	NM_006565.3	29	cGg/cAg	3/12	0.18443191998271	3	FACETS	0.643	0.567	0.726	0.322	0.283	0.363	SUBCLONAL	1	TRUE	1	0.293323174284083	3		333	1021	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141487	11141487	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	175	473	0	ENST00000358026.2:c.3464G>T	p.Ser1155Ile	p.S1155I	ENST00000358026	NM_001128849.1	1155	aGc/aTc	25/36	0.168197364125364	2	FACETS	1	0.966	1	0.547	0.503	0.593	INDETERMINATE	1	TRUE	0	0.293323174284083	2		473	1091	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189862	66189862	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	55	459	0	ENST00000273854.3:c.3084del	p.Gln1029SerfsTer3	p.Q1029Sfs*3	ENST00000273854	NM_004439.5	1028	gtG/gt	18/18	1	2	FACETS	0.78	0.668	0.902	0.78	0.668	0.902	CLONAL	1	TRUE	1	0.293323174284083	2		459	481	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52685779	52685779	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	150	554	0	ENST00000394830.3:c.693del	p.Thr232ProfsTer21	p.T232Pfs*21	ENST00000394830	NM_018313.4	231	aaG/aa	7/30	0.168197364125364	2	FACETS	1	0.951	1	0.53	0.484	0.579	INDETERMINATE	1	TRUE	0	0.293323174284083	2		554	964	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578540	7578542	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0008863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	158	338	1	ENST00000269305.4:c.388_390del	p.Leu130del	p.L130del	ENST00000269305	NM_001126112.2	130	CTC/-	5/11	0.168197364125364	2	FACETS	1	0.947	1	0.523	0.478	0.57	INDETERMINATE	1	TRUE	0	0.293323174284083	2		339	1030	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0008868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	277	622	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.25035927893499	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	FALSE	0	0.25035927893499	2		624	937	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729094	66729099	+	inframe_deletion	In_Frame_Del	DEL	TGGAGA	TGGAGA	-	novel	NA	P-0008868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	209	433	0	ENST00000307102.5:c.303_308del	p.Glu102_Ile103del	p.E102_I103del	ENST00000307102	NM_002755.3	101	cTGGAGAtc/ctc	3/11	0.215553003561714	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	FALSE	2	0.25035927893499	4		433	996	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330619	65330619	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763659890	NA	P-0008868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	106	462	0	ENST00000342505.4:c.1027C>T	p.Arg343Trp	p.R343W	ENST00000342505	NM_002227.2	343	Cgg/Tgg	8/25	0.227121850201339	3	FACETS	1	0.897	1	0.501	0.448	0.557	CLONAL	1	FALSE	1	0.25035927893499	3		462	951	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961523	54961523	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	50	359	0	ENST00000312783.6:c.109T>A	p.Leu37Ile	p.L37I	ENST00000312783	NM_198436.1	37	Tta/Ata	4/10	0.215553003561714	4	FACETS	0.679	0.575	0.795	0.34	0.287	0.398	SUBCLONAL	1	FALSE	2	0.25035927893499	4		359	735	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755525	57755525	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	116	275	0	ENST00000274289.3:c.262C>A	p.Leu88Met	p.L88M	ENST00000274289	NM_006622.3	88	Ctg/Atg	1/14	0.533778075266943	3	FACETS	1	0.963	1	0.563	0.51	0.618	CLONAL	1	TRUE	1	0.533778075266943	3		275	489	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060679	38060679	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	515	716	0	ENST00000250448.2:c.1310T>A	p.Leu437Gln	p.L437Q	ENST00000250448	NM_004496.3	437	cTg/cAg	2/2	0.507448814738387	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.533778075266943	4		716	1389	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654516	29654516	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs876660141	NA	P-0008881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	465	526	0	ENST00000356175.3:c.5206-1G>C		p.X1736_splice	ENST00000356175	NM_000267.3	1736			0.533778075266943	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.533778075266943	3		526	700	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246311	41246311	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	336	732	0	ENST00000357654.3:c.1237T>A	p.Leu413Met	p.L413M	ENST00000357654	NM_007294.3	413	Ttg/Atg	10/23	0.533778075266943	3	FACETS	0.936	0.897	0.975	0.936	0.897	0.975	CLONAL	3	TRUE	0	0.533778075266943	3		732	568	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15975488	15975491	+	frameshift_variant	Frame_Shift_Del	DEL	CTTT	CTTT	-	novel	NA	P-0008881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	91	718	1	ENST00000268712.3:c.3863_3866del	p.Glu1288GlyfsTer8	p.E1288Gfs*8	ENST00000268712	NM_006311.3	1288	gAAAGg/gg	29/46	0.533778075266943	3	FACETS	0.894	0.797	0.997	0.447	0.398	0.499	CLONAL	1	TRUE	1	0.533778075266943	3		719	483	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061854	38061862	+	inframe_deletion	In_Frame_Del	DEL	GTTCATGGA	GTTCATGGA	-	novel	NA	P-0008881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	340	711	0	ENST00000250448.2:c.127_135del	p.Ser43_Asn45del	p.S43_N45del	ENST00000250448	NM_004496.3	43	TCCATGAAC/-	2/2	0.507448814738387	4	FACETS	0.789	0.746	0.832	0.789	0.746	0.832	SUBCLONAL	2	TRUE	2	0.533778075266943	4		711	1239	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060693	38060700	+	frameshift_variant	Frame_Shift_Del	DEL	CGTAGAGC	CGTAGAGC	-	novel	NA	P-0008881-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	533	730	0	ENST00000250448.2:c.1289_1296del	p.Gly430ValfsTer125	p.G430Vfs*125	ENST00000250448	NM_004496.3	430	gGCTCTACG/g	2/2	0.507448814738387	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	2	0.533778075266943	4		730	1406	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0008901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	188	283	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.473774545252677	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.473774545252677	3		283	470	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831831	72831831	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	328	942	0	ENST00000268489.5:c.4750C>T	p.Gln1584Ter	p.Q1584*	ENST00000268489	NM_006885.3	1584	Cag/Tag	9/10	0.473774545252677	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.473774545252677	1		942	853	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914395	32914395	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0008901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	330	1013	0	ENST00000380152.3:c.5903C>G	p.Ser1968Ter	p.S1968*	ENST00000380152		1968	tCa/tGa	11/27	0.473774545252677	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.473774545252677	1		1013	848	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656786	45656794	+	inframe_deletion	In_Frame_Del	DEL	CCTGGAATC	CCTGGAATC	-	novel	NA	P-0008901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	44	314	0	ENST00000407780.3:c.362_370del	p.Gly121_Gln123del	p.G121_Q123del	ENST00000407780	NM_001283052.1	121	gGATTCCAGGag/gag	3/7	1	2	FACETS	0.628	0.529	0.735	0.628	0.529	0.735	SUBCLONAL	1	TRUE	1	0.473774545252677	2		314	296	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913343	NA	P-0008915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1154	128	595	0	ENST00000269305.4:c.817C>A	p.Arg273Ser	p.R273S	ENST00000269305	NM_001126112.2	273	Cgt/Agt	8/11	0.176336826616773	1	FACETS	0.541	0.488	0.596	0.541	0.488	0.596	INDETERMINATE	1	TRUE	0	0.311844021018157	1		595	1282	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470497	25470497	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	85	402	0	ENST00000264709.3:c.977G>C	p.Arg326Pro	p.R326P	ENST00000264709	NM_175629.2	326	cGc/cCc	8/23	1	2	FACETS	0.496	0.437	0.56	0.496	0.437	0.56	SUBCLONAL	1	TRUE	1	0.311844021018157	2		402	1098	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251859	212251859	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	44	261	0	ENST00000342788.4:c.3200G>C	p.Arg1067Pro	p.R1067P	ENST00000342788	NM_005235.2	1067	cGa/cCa	27/28	1	2	FACETS	0.483	0.405	0.57	0.483	0.405	0.57	SUBCLONAL	1	TRUE	1	0.311844021018157	2		261	584	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967210	93967210	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	52	538	2	ENST00000369303.4:c.2142G>T	p.Met714Ile	p.M714I	ENST00000369303	NM_004440.3	714	atG/atT	12/17	1	2	FACETS	0.514	0.437	0.599	0.514	0.437	0.599	SUBCLONAL	1	TRUE	1	0.311844021018157	2		540	649	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974677	21974677	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1057519882	NA	P-0008915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	126	512	0	ENST00000304494.5:c.150G>T	p.Gln50His	p.Q50H	ENST00000304494	NM_000077.4	50	caG/caT	1/3	1	2	FACETS	0.678	0.612	0.748	0.678	0.612	0.748	SUBCLONAL	1	TRUE	1	0.311844021018157	2		512	1192	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620429	43620429	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	53	318	0	ENST00000355710.3:c.3038G>C	p.Arg1013Thr	p.R1013T	ENST00000355710	NM_020975.4	1013	aGa/aCa	18/20	1	2	FACETS	0.442	0.376	0.515	0.442	0.376	0.515	SUBCLONAL	1	TRUE	1	0.311844021018157	2		318	769	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139160	108139160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	51	461	0	ENST00000278616.4:c.2662G>A	p.Glu888Lys	p.E888K	ENST00000278616	NM_000051.3	888	Gaa/Aaa	18/63	1	2	FACETS	0.502	0.426	0.586	0.502	0.426	0.586	SUBCLONAL	1	TRUE	1	0.311844021018157	2		461	651	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226371	41226371	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	93	630	0	ENST00000357654.3:c.4652C>G	p.Ser1551Cys	p.S1551C	ENST00000357654	NM_007294.3	1551	tCt/tGt	14/23	1	2	FACETS	0.5	0.443	0.561	0.5	0.443	0.561	SUBCLONAL	1	TRUE	1	0.311844021018157	2		630	1194	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732266	74732269	+	frameshift_variant	Frame_Shift_Del	DEL	CTTC	CTTC	TTT	novel	NA	P-0008915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1498	119	748	0	ENST00000359995.5:c.640_643delinsAAA	p.Glu214LysfsTer18	p.E214Kfs*18	ENST00000359995	NM_001195427.1	214	GAAGag/AAAag	2/3	1	2	FACETS	0.472	0.424	0.523	0.472	0.424	0.523	SUBCLONAL	1	TRUE	1	0.311844021018157	2		748	1617	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453153	140453153	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913337	NA	P-0008926-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	24	346	0	ENST00000288602.6:c.1782T>A	p.Asp594Glu	p.D594E	ENST00000288602	NM_004333.4	594	gaT/gaA	15/18	1	2	FACETS	0.503	0.393	0.63	0.503	0.393	0.63	SUBCLONAL	1	TRUE	1	0.2	2		346	477	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608397	43608397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008926-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1611	158	918	1	ENST00000355710.3:c.1745C>T	p.Pro582Leu	p.P582L	ENST00000355710	NM_020975.4	582	cCt/cTt	9/20	1	2	FACETS	0.893	0.815	0.976	0.893	0.815	0.976	CLONAL	1	TRUE	1	0.2	2		919	1769	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008932-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	63	145	0				ENST00000310581	NM_198253.2	-/1132			0.151452554096161	2	FACETS	0.89	0.779	1	0.89	0.779	1	INDETERMINATE	2	TRUE	0	0.29	2		145	244	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0008932-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	434	894	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.3	5	FACETS	0.981	0.934	1	0.981	0.934	1	CLONAL	3	TRUE	2	0.29	5		894	1460	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412337	139412339	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0008932-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	121	383	0	ENST00000277541.6:c.1306_1308del	p.Phe436del	p.F436del	ENST00000277541	NM_017617.3	436	TTC/-	8/34	0.263882149502099	3	FACETS	1	0.932	1	0.686	0.624	0.751	CLONAL	2	TRUE	0	0.29	3		383	464	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543683	29543683	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008932-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	40	524	0	ENST00000389048.3:c.1480C>G	p.Leu494Val	p.L494V	ENST00000389048	NM_004304.4	494	Ctg/Gtg	7/29	1	2	FACETS	0.372	0.308	0.444	0.372	0.308	0.444	SUBCLONAL	1	TRUE	1	0.29	2		524	741	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629770	187629772	+	frameshift_variant	Frame_Shift_Del	DEL	ACT	ACT	CC	novel	NA	P-0008932-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	81	534	0	ENST00000441802.2:c.1210_1212delinsGG	p.Ser404GlyfsTer10	p.S404Gfs*10	ENST00000441802	NM_005245.3	404	AGT/GG	2/27	0.151452554096161	2	FACETS	1	0.93	1	0.537	0.474	0.604	INDETERMINATE	1	TRUE	0	0.29	2		534	520	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008939-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	84	145	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.957	0.849	1	0.957	0.849	1	CLONAL	1	TRUE	1	0.395584302185263	2		145	444	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480479	89480479	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008939-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	191	298	0	ENST00000336596.2:c.2316G>C	p.Glu772Asp	p.E772D	ENST00000336596	NM_005233.5	772	gaG/gaC	13/17	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.395584302185263	2		298	958	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496920	29496923	+	frameshift_variant	Frame_Shift_Del	DEL	TAAC	TAAC	-	novel	NA	P-0008939-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	159	321	0	ENST00000356175.3:c.492_495del	p.Thr165PhefsTer12	p.T165Ffs*12	ENST00000356175	NM_000267.3	164	tTAACt/tt	5/57	1	2	FACETS	0.856	0.784	0.931	0.856	0.784	0.931	CLONAL	1	TRUE	1	0.395584302185263	2		321	939	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553574	29553574	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008939-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	112	176	0	ENST00000356175.3:c.2124del	p.Cys709ValfsTer39	p.C709Vfs*39	ENST00000356175	NM_000267.3	708	tCc/tc	18/57	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.395584302185263	2		176	566	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0008952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	85	283	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.0788095763388375	3	FACETS	0.962	0.852	1	0.481	0.426	0.54	INDETERMINATE	1	TRUE	1	0.34	3		283	608	SUCCESS
REL	5966	MSKCC	GRCh37	2	61121646	61121646	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	39	362	1	ENST00000295025.8:c.268G>A	p.Glu90Lys	p.E90K	ENST00000295025	NM_002908.2	90	Gaa/Aaa	3/11	0.3	2	FACETS	0.39	0.323	0.466			1	SUBCLONAL	1	TRUE	NA	0.34	2		363	588	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924444	131924444	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs587780146	NA	P-0008952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	90	429	0	ENST00000265335.6:c.1117T>G	p.Ser373Ala	p.S373A	ENST00000265335		373	Tct/Gct	8/25	0.0788095763388375	3	FACETS	1	0.896	1	0.504	0.448	0.565	INDETERMINATE	1	TRUE	1	0.34	3		429	614	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268795	46268795	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	58	775	2	ENST00000371998.3:c.3080G>T	p.Arg1027Met	p.R1027M	ENST00000371998		1027	aGg/aTg	16/23	1	2	FACETS	0.31	0.265	0.359	0.31	0.265	0.359	SUBCLONAL	1	TRUE	1	0.34	2		777	1102	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0008978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	525	383	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.777472235205644	4	FACETS	0.838	0.804	0.873	0.838	0.804	0.873	CLONAL	2	TRUE	2	0.777472235205644	4		383	1432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0008978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	905	641	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.777472235205644	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.777472235205644	2		642	1133	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0009016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	29	316	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.645	0.515	0.793	0.645	0.515	0.793	SUBCLONAL	1	TRUE	1	0.125132219763187	2		316	719	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0009016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	34	476	2	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.664	0.541	0.805	0.664	0.541	0.805	SUBCLONAL	1	TRUE	1	0.125132219763187	2		478	818	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0009016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	110	303	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.125132219763187	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.125132219763187	2		303	784	SUCCESS
APC	324	MSKCC	GRCh37	5	112175852	112175852	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	84	371	1	ENST00000257430.4:c.4561G>T	p.Glu1521Ter	p.E1521*	ENST00000257430	NM_000038.5	1521	Gaa/Taa	16/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.125132219763187	2		372	929	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371722	55371722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	74	298	0	ENST00000297316.4:c.412C>T	p.Arg138Trp	p.R138W	ENST00000297316	NM_022454.3	138	Cgg/Tgg	2/2	1	2	FACETS	1	0.916	1	1	0.983	1	CLONAL	2	TRUE	1	0.125132219763187	2		298	559	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0009017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	108	283	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.617	0.554	0.683	0.617	0.554	0.683	SUBCLONAL	1	TRUE	1	0.491198824919893	2		283	713	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0009017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	299	327	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.426071442570041	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.491198824919893	1		327	850	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189835	66189835	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs55784741	NA	P-0009017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	240	429	0	ENST00000273854.3:c.3111G>T	p.Leu1037Phe	p.L1037F	ENST00000273854	NM_004439.5	1037	ttG/ttT	18/18	0.211639942282406	2	FACETS	0.846	0.789	0.905	0.423	0.394	0.453	INDETERMINATE	1	TRUE	0	0.491198824919893	2		429	1155	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029051	14029051	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1567247685	NA	P-0009017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	96	261	0	ENST00000311895.7:c.1262G>C	p.Arg421Thr	p.R421T	ENST00000311895	NM_005236.2	421	aGa/aCa	8/11	0.40012053205613	1	FACETS	0.41	0.365	0.458	0.41	0.365	0.458	SUBCLONAL	1	TRUE	0	0.491198824919893	1		261	719	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937951	36937951	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1238	173	467	0	ENST00000361632.4:c.885C>G	p.Cys295Trp	p.C295W	ENST00000361632		295	tgC/tgG	7/16	0.191850379048585	1	FACETS	0.377	0.345	0.409	0.377	0.345	0.409	INDETERMINATE	1	TRUE	0	0.491198824919893	1		467	1411	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939207	36939207	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs760685785	NA	P-0009017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1368	167	466	0	ENST00000361632.4:c.502C>T	p.Gln168Ter	p.Q168*	ENST00000361632		168	Cag/Tag	5/16	0.191850379048585	1	FACETS	0.334	0.306	0.364	0.334	0.306	0.364	INDETERMINATE	1	TRUE	0	0.491198824919893	1		466	1535	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830856	156830856	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	157	260	0	ENST00000524377.1:c.130G>T	p.Gly44Cys	p.G44C	ENST00000524377	NM_002529.3	44	Ggc/Tgc	1/17	0.491198824919893	2	FACETS	0.855	0.784	0.928	0.427	0.392	0.464	CLONAL	1	TRUE	0	0.491198824919893	2		260	748	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248749	212248749	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	166	247	0	ENST00000342788.4:c.3518C>G	p.Ser1173Cys	p.S1173C	ENST00000342788	NM_005235.2	1173	tCt/tGt	28/28	0.261016125139964	3	FACETS	0.895	0.822	0.971	0.447	0.411	0.486	INDETERMINATE	1	TRUE	1	0.491198824919893	3		247	941	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989584	212989584	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	239	374	0	ENST00000342788.4:c.127G>T	p.Glu43Ter	p.E43*	ENST00000342788	NM_005235.2	43	Gaa/Taa	2/28	1	2	FACETS	0.749	0.698	0.802	0.749	0.698	0.802	SUBCLONAL	1	TRUE	1	0.491198824919893	2		374	1299	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462411	89462411	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1310443133	NA	P-0009017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	49	236	1	ENST00000336596.2:c.1883G>A	p.Gly628Glu	p.G628E	ENST00000336596	NM_005233.5	628	gGa/gAa	10/17	1	2	FACETS	0.306	0.258	0.358	0.306	0.258	0.358	SUBCLONAL	1	TRUE	1	0.491198824919893	2		237	652	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612254	189612254	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	83	258	0	ENST00000264731.3:c.2006G>C	p.Arg669Pro	p.R669P	ENST00000264731	NM_003722.4	669	cGc/cCc	14/14	1	2	FACETS	0.345	0.303	0.39	0.345	0.303	0.39	SUBCLONAL	1	TRUE	1	0.491198824919893	2		258	980	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016357	150016357	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs746189857	NA	P-0009017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	215	281	1	ENST00000253339.5:c.349G>T	p.Asp117Tyr	p.D117Y	ENST00000253339		117	Gat/Tat	2/7	0.491198824919893	1	FACETS	0.884	0.825	0.945	0.884	0.825	0.945	CLONAL	1	TRUE	0	0.491198824919893	1		282	747	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508841	106508841	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	354	318	0	ENST00000359195.3:c.835G>T	p.Glu279Ter	p.E279*	ENST00000359195	NM_002649.2	279	Gag/Tag	2/11	0.361551631227461	1	FACETS	0.998	0.946	1	0.998	0.946	1	CLONAL	1	TRUE	0	0.491198824919893	1		318	1090	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829000	128829000	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	26	29	0	ENST00000249373.3:c.8C>A	p.Ala3Asp	p.A3D	ENST00000249373	NM_005631.4	3	gCt/gAt	1/12	0.361551631227461	1	FACETS	0.986	0.805	1	0.986	0.805	1	CLONAL	1	TRUE	0	0.491198824919893	1		29	81	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539108	23539108	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	380	422	1	ENST00000380871.4:c.331G>T	p.Gly111Cys	p.G111C	ENST00000380871	NM_006167.3	111	Ggc/Tgc	2/2	0.361551631227461	1	FACETS	0.887	0.842	0.933	0.887	0.842	0.933	CLONAL	1	TRUE	0	0.491198824919893	1		423	1316	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287372	38287372	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1195026291	NA	P-0009017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	111	350	0	ENST00000425967.3:c.285G>C	p.Gln95His	p.Q95H	ENST00000425967	NM_001174067.1	95	caG/caC	4/19	0.361551631227461	1	FACETS	0.335	0.3	0.372	0.335	0.3	0.372	SUBCLONAL	1	TRUE	0	0.491198824919893	1		350	1018	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331600	8331600	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	508	465	0	ENST00000356435.5:c.5516C>G	p.Pro1839Arg	p.P1839R	ENST00000356435		1839	cCc/cGc	33/35	0.491198824919893	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.491198824919893	1		465	1278	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891137	101891137	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1554698880	NA	P-0009017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	256	336	0	ENST00000374994.4:c.98C>T	p.Ala33Val	p.A33V	ENST00000374994	NM_004612.2	33	gCg/gTg	2/9	0.491198824919893	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.491198824919893	1		336	746	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524244	18524244	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	199	371	0	ENST00000266497.5:c.1756G>A	p.Glu586Lys	p.E586K	ENST00000266497		586	Gaa/Aaa	11/31	0.491198824919893	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.491198824919893	1		371	566	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524246	18524246	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs768013752	NA	P-0009017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	187	368	3	ENST00000266497.5:c.1757+1G>T		p.X586_splice	ENST00000266497		586			0.491198824919893	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.491198824919893	1		371	552	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873653	35873653	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	94	381	0	ENST00000216797.5:c.198G>C	p.Trp66Cys	p.W66C	ENST00000216797	NM_020529.2	66	tgG/tgC	1/6	NA	2	FACETS	0.347	0.307	0.389			1	INDETERMINATE	1	TRUE	NA	0.491198824919893	2		381	1104	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472420	88472420	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0009017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	139	299	0	ENST00000360948.2:c.2133+2T>A		p.X711_splice	ENST00000360948	NM_001012338.2	711			0.292094896856733	1	FACETS	0.501	0.455	0.548	0.501	0.455	0.548	INDETERMINATE	1	TRUE	0	0.491198824919893	1		299	853	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585438	29585438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	90	336	1	ENST00000356175.3:c.4187C>T	p.Ala1396Val	p.A1396V	ENST00000356175	NM_000267.3	1396	gCc/gTc	31/57	NA	2	FACETS	0.337	0.298	0.379			1	INDETERMINATE	1	TRUE	NA	0.491198824919893	2		337	1087	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78923309	78923309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	138	361	0	ENST00000306801.3:c.3332C>T	p.Ala1111Val	p.A1111V	ENST00000306801	NM_020761.2	1111	gCg/gTg	28/34	1	2	FACETS	0.492	0.446	0.54	0.492	0.446	0.54	SUBCLONAL	1	TRUE	1	0.491198824919893	2		361	1143	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60795994	60795994	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0009017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	81	284	0	ENST00000333681.4:c.586-2A>C		p.X196_splice	ENST00000333681		196			0.28066289034111	2	FACETS	0.376	0.33	0.425	0.188	0.165	0.213	INDETERMINATE	1	TRUE	0	0.491198824919893	2		284	878	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226416	2226416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751736857	NA	P-0009017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	83	359	0	ENST00000398665.3:c.3896C>T	p.Ser1299Phe	p.S1299F	ENST00000398665	NM_032482.2	1299	tCc/tTc	27/28	0.491198824919893	1	FACETS	0.306	0.27	0.346	0.306	0.27	0.346	SUBCLONAL	1	TRUE	0	0.491198824919893	1		359	832	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142878	7142878	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	332	337	1	ENST00000302850.5:c.2491G>T	p.Glu831Ter	p.E831*	ENST00000302850	NM_000208.2	831	Gag/Tag	12/22	0.491198824919893	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.491198824919893	1		338	855	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602374	10602374	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	417	446	0	ENST00000171111.5:c.1204C>T	p.Gln402Ter	p.Q402*	ENST00000171111	NM_203500.1	402	Cag/Tag	3/6	0.491198824919893	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.491198824919893	1		446	1130	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750381	39750381	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	112	355	0	ENST00000361337.2:c.1996A>G	p.Lys666Glu	p.K666E	ENST00000361337	NM_003286.2	666	Aaa/Gaa	19/21	0.261016125139964	3	FACETS	0.427	0.382	0.474	0.213	0.191	0.237	INDETERMINATE	1	TRUE	1	0.491198824919893	3		355	1331	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852417	42852417	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	229	330	0	ENST00000398585.3:c.669G>T	p.Arg223Ser	p.R223S	ENST00000398585	NM_001135099.1	223	agG/agT	6/14	0.491198824919893	1	FACETS	0.814	0.76	0.87	0.814	0.76	0.87	CLONAL	1	TRUE	0	0.491198824919893	1		330	864	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411331	63411331	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	288	210	0	ENST00000330258.3:c.1836G>T	p.Glu612Asp	p.E612D	ENST00000330258	NM_152424.3	612	gaG/gaT	2/2	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.491198824919893	1		210	642	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715664	18715664	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	291	332	0	ENST00000266497.5:c.3497del	p.Pro1166LeufsTer4	p.P1166Lfs*4	ENST00000266497		1165	ttC/tt	25/31	0.491198824919893	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.491198824919893	1		332	778	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243899	46243900	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0009017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	340	401	0	ENST00000334344.6:c.1996_1997del	p.Gln666AsnfsTer40	p.Q666Nfs*40	ENST00000334344	NM_152641.2	665	ACa/a	15/21	0.491198824919893	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.491198824919893	1		401	984	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713382	40713383	+	missense_variant	Missense_Mutation	DNP	CG	CG	GA	novel	NA	P-0009017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	197	359	0	ENST00000373198.4:c.4132_4133delinsTC	p.Arg1378Ser	p.R1378S	ENST00000373198	NM_133170.3	1378	CGa/TCa	30/32	0.261016125139964	3	FACETS	0.731	0.675	0.789	0.365	0.337	0.395	INDETERMINATE	1	TRUE	1	0.491198824919893	3		359	1367	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119666195	119666195	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	137	238	0	ENST00000316626.5:c.286C>G	p.Arg96Gly	p.R96G	ENST00000316626		96	Cga/Gga	3/12	0.608763992139343	5	FACETS	1	0.973	1	0.294	0.267	0.321	CLONAL	1	TRUE	1	0.608763992139343	5		238	733	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589630	67589630	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0009021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	323	338	0	ENST00000274335.5:c.1393A>T	p.Arg465Ter	p.R465*	ENST00000274335		465	Aga/Tga	10/15	0.608763992139343	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.608763992139343	2		338	463	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188392	32188392	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	185	266	0	ENST00000375023.3:c.949G>T	p.Glu317Ter	p.E317*	ENST00000375023	NM_004557.3	317	Gag/Tag	6/30	0.608763992139343	3	FACETS	0.938	0.867	1	0.469	0.433	0.506	CLONAL	1	TRUE	1	0.608763992139343	3		266	845	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139008	37139008	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	269	283	0	ENST00000373509.5:c.348C>A	p.Phe116Leu	p.F116L	ENST00000373509	NM_002648.3	116	ttC/ttA	4/6	0.608763992139343	3	FACETS	1	0.972	1	0.531	0.498	0.565	CLONAL	1	TRUE	1	0.608763992139343	3		283	1085	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710892	117710892	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1448	240	385	0	ENST00000368508.3:c.1380C>G	p.Ile460Met	p.I460M	ENST00000368508	NM_002944.2	460	atC/atG	12/43	0.608763992139343	5	FACETS	0.894	0.831	0.958	0.298	0.277	0.32	CLONAL	1	TRUE	2	0.608763992139343	5		385	1688	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371758	116371758	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs201980687	NA	P-0009021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1248	241	331	0	ENST00000397752.3:c.1237C>A	p.Arg413Ser	p.R413S	ENST00000397752	NM_000245.2	413	Cgt/Agt	3/21	0.579369377493593	5	FACETS	1	0.945	1	0.339	0.315	0.364	CLONAL	1	TRUE	2	0.608763992139343	5		331	1489	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211452	46211452	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0009021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	145	290	0	ENST00000334344.6:c.419-1G>C		p.X140_splice	ENST00000334344	NM_152641.2	140			0.608763992139343	3	FACETS	0.852	0.779	0.929	0.426	0.389	0.465	CLONAL	1	TRUE	1	0.608763992139343	3		290	729	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003303	42003303	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0009021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1259	414	600	0	ENST00000219905.7:c.2840C>G	p.Ser947Ter	p.S947*	ENST00000219905	NM_001164273.1	947	tCa/tGa	8/24	0.608763992139343	3	FACETS	1	0.98	1	0.53	0.503	0.558	CLONAL	1	TRUE	1	0.608763992139343	3		600	1673	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361137	70361137	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	267	309	1	ENST00000374080.3:c.6325C>T	p.Gln2109Ter	p.Q2109*	ENST00000374080		2109	Cag/Tag	43/45	0.608763992139343	3	FACETS	1	0.981	1	0.554	0.52	0.59	CLONAL	1	TRUE	1	0.608763992139343	3		310	1032	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577152	7577152	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	596	427	0	ENST00000269305.4:c.786del	p.Asn263IlefsTer82	p.N263Ifs*82	ENST00000269305	NM_001126112.2	262	ggT/gg	8/11	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.608763992139343	2		427	906	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47643522	47643522	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750245	NA	P-0009025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	102	615	0	ENST00000233146.2:c.1030C>T	p.Gln344Ter	p.Q344*	ENST00000233146	NM_000251.2	344	Cag/Tag	6/16	1	2	FACETS	0.827	0.738	0.923	0.827	0.738	0.923	CLONAL	1	TRUE	1	0.221564282146873	2		615	1113	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928685	49928685	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	159	687	1	ENST00000296474.3:c.3589G>A	p.Glu1197Lys	p.E1197K	ENST00000296474	NM_002447.2	1197	Gag/Aag	17/20	0.221564282146873	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.221564282146873	1		688	1242	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89176385	89176385	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	57	462	4	ENST00000336596.2:c.115C>T	p.Gln39Ter	p.Q39*	ENST00000336596	NM_005233.5	39	Caa/Taa	2/17	0.221564282146873	1	FACETS	0.563	0.482	0.652	0.563	0.482	0.652	SUBCLONAL	1	TRUE	0	0.221564282146873	1		466	813	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448627	89448627	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161663372	NA	P-0009025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	76	442	0	ENST00000336596.2:c.1591G>A	p.Asp531Asn	p.D531N	ENST00000336596	NM_005233.5	531	Gac/Aac	7/17	0.221564282146873	1	FACETS	0.73	0.639	0.828	0.73	0.639	0.828	SUBCLONAL	1	TRUE	0	0.221564282146873	1		442	836	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270137	66270137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520012	NA	P-0009025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	84	533	0	ENST00000273854.3:c.1745G>A	p.Gly582Glu	p.G582E	ENST00000273854	NM_004439.5	582	gGa/gAa	8/18	1	2	FACETS	0.743	0.654	0.838	0.743	0.654	0.838	SUBCLONAL	1	TRUE	1	0.221564282146873	2		533	1021	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523678	176523678	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	151	674	1	ENST00000292408.4:c.2089G>A	p.Glu697Lys	p.E697K	ENST00000292408	NM_213647.1	697	Gag/Aag	16/18	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.221564282146873	2		675	1281	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523713	176523714	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	92	592	3	ENST00000292408.4:c.2124_2125delinsAA	p.Met708_Asp709delinsIleAsn	p.M708_D709delinsIN	ENST00000292408	NM_213647.1	708	atGGac/atAAac	16/18	1	2	FACETS	0.772	0.684	0.866	0.772	0.684	0.866	SUBCLONAL	1	TRUE	1	0.221564282146873	2		595	1076	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524562	176524562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746179714	NA	P-0009025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	165	654	0	ENST00000292408.4:c.2294C>T	p.Ser765Phe	p.S765F	ENST00000292408	NM_213647.1	765	tCc/tTc	18/18	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.221564282146873	2		654	1304	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707784	176707785	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0009025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	114	565	0	ENST00000439151.2:c.5841_5842delinsTT	p.Arg1948Cys	p.R1948C	ENST00000439151	NM_022455.4	1947	ttCCgc/ttTTgc	18/23	1	2	FACETS	0.808	0.725	0.896	0.808	0.725	0.896	CLONAL	1	TRUE	1	0.221564282146873	2		565	1274	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394897	394897	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	89	381	0	ENST00000380956.4:c.293G>A	p.Arg98Gln	p.R98Q	ENST00000380956	NM_001195286.1	98	cGg/cAg	3/9	1	2	FACETS	0.879	0.778	0.987	0.879	0.778	0.987	CLONAL	1	TRUE	1	0.221564282146873	2		381	914	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168910	32168910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1220425760	NA	P-0009025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	105	614	1	ENST00000375023.3:c.4123G>A	p.Asp1375Asn	p.D1375N	ENST00000375023	NM_004557.3	1375	Gac/Aac	22/30	1	2	FACETS	0.781	0.698	0.871	0.781	0.698	0.871	SUBCLONAL	1	TRUE	1	0.221564282146873	2		615	1213	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638421	117638421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	45	412	1	ENST00000368508.3:c.6020C>T	p.Pro2007Leu	p.P2007L	ENST00000368508	NM_002944.2	2007	cCc/cTc	38/43	1	2	FACETS	0.615	0.515	0.725	0.615	0.515	0.725	SUBCLONAL	1	TRUE	1	0.221564282146873	2		413	661	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624371	140624371	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	19	146	0	ENST00000288602.6:c.133G>A	p.Glu45Lys	p.E45K	ENST00000288602	NM_004333.4	45	Gag/Aag	1/18	1	2	FACETS	0.496	0.376	0.637	0.496	0.376	0.637	SUBCLONAL	1	TRUE	1	0.221564282146873	2		146	346	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319955	8319955	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	144	382	0	ENST00000356435.5:c.5546G>A	p.Gly1849Glu	p.G1849E	ENST00000356435		1849	gGa/gAa	34/35	1	2	FACETS	0.841	0.768	0.917	1	0.989	1	CLONAL	2	TRUE	1	0.221564282146873	2		382	773	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317073	87317073	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0009025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	102	431	0	ENST00000277120.3:c.213-1G>A		p.X71_splice	ENST00000277120		71			1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.221564282146873	2		431	888	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339200	87339200	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1389555393	NA	P-0009025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	94	536	0	ENST00000277120.3:c.782G>A	p.Gly261Glu	p.G261E	ENST00000277120		261	gGg/gAg	8/19	1	2	FACETS	0.914	0.812	1	0.914	0.812	1	CLONAL	1	TRUE	1	0.221564282146873	2		536	928	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912248	97912248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269365165	NA	P-0009025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	114	582	0	ENST00000289081.3:c.643C>T	p.Leu215Phe	p.L215F	ENST00000289081	NM_000136.2	215	Ctc/Ttc	7/15	1	2	FACETS	0.959	0.862	1	0.959	0.862	1	CLONAL	1	TRUE	1	0.221564282146873	2		582	1073	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802668	135802668	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	84	444	0	ENST00000298552.3:c.130A>C	p.Thr44Pro	p.T44P	ENST00000298552	NM_001162426.1	44	Acc/Ccc	4/23	1	2	FACETS	0.935	0.825	1	0.935	0.825	1	CLONAL	1	TRUE	1	0.221564282146873	2		444	811	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114757	108114757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780629	NA	P-0009025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	87	438	1	ENST00000278616.4:c.574C>T	p.His192Tyr	p.H192Y	ENST00000278616	NM_000051.3	192	Cat/Tat	6/63	1	2	FACETS	0.778	0.687	0.876	0.778	0.687	0.876	SUBCLONAL	1	TRUE	1	0.221564282146873	2		439	1009	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28885802	28885802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	137	588	0	ENST00000282397.4:c.3560C>T	p.Pro1187Leu	p.P1187L	ENST00000282397	NM_002019.4	1187	cCt/cTt	27/30	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.221564282146873	2		588	1119	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911168	32911169	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0009025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	116	834	0	ENST00000380152.3:c.2676_2677delinsTT	p.Gln893Ter	p.Q893*	ENST00000380152		892	ttCCaa/ttTTaa	11/27	1	2	FACETS	0.826	0.743	0.916	0.826	0.743	0.916	CLONAL	1	TRUE	1	0.221564282146873	2		834	1267	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871250	35871250	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1305	111	612	0	ENST00000216797.5:c.923G>C	p.Cys308Ser	p.C308S	ENST00000216797	NM_020529.2	308	tGt/tCt	6/6	1	2	FACETS	0.708	0.634	0.787	0.708	0.634	0.787	SUBCLONAL	1	TRUE	1	0.221564282146873	2		612	1416	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423632	88423632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1478926904	NA	P-0009025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	83	364	0	ENST00000360948.2:c.2203C>T	p.Arg735Cys	p.R735C	ENST00000360948	NM_001012338.2	735	Cgc/Tgc	18/19	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.221564282146873	2		364	723	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829184	72829184	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1419	187	898	1	ENST00000268489.5:c.7397C>T	p.Thr2466Ile	p.T2466I	ENST00000268489	NM_006885.3	2466	aCt/aTt	9/10	0.221564282146873	1	FACETS	0.935	0.86	1	0.935	0.86	1	CLONAL	1	TRUE	0	0.221564282146873	1		899	1606	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348103	89348103	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1443	230	1118	2	ENST00000301030.4:c.4847G>A	p.Gly1616Glu	p.G1616E	ENST00000301030	NM_001256183.1	1616	gGa/gAa	9/13	0.221564282146873	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.221564282146873	1		1120	1673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0009025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1182	139	595	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.95	0.862	1	0.95	0.862	1	CLONAL	1	TRUE	1	0.221564282146873	2		595	1321	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884151	37884151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	142	594	0	ENST00000269571.5:c.3622C>T	p.His1208Tyr	p.H1208Y	ENST00000269571		1208	Cac/Tac	27/27	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.221564282146873	2		594	1172	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40498589	40498589	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	81	515	0	ENST00000264657.5:c.271C>T	p.Gln91Ter	p.Q91*	ENST00000264657	NM_139276.2	91	Cag/Tag	3/24	1	2	FACETS	0.783	0.688	0.885	0.783	0.688	0.885	SUBCLONAL	1	TRUE	1	0.221564282146873	2		515	934	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117740	70117740	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316632405	NA	P-0009025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	101	655	1	ENST00000245479.2:c.208C>T	p.Pro70Ser	p.P70S	ENST00000245479	NM_000346.3	70	Ccc/Tcc	1/3	1	2	FACETS	0.789	0.703	0.88	0.789	0.703	0.88	SUBCLONAL	1	TRUE	1	0.221564282146873	2		656	1156	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281275	15281275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	63	475	0	ENST00000263388.2:c.4981G>A	p.Gly1661Ser	p.G1661S	ENST00000263388	NM_000435.2	1661	Ggt/Agt	27/33	1	2	FACETS	0.694	0.598	0.797	0.694	0.598	0.797	SUBCLONAL	1	TRUE	1	0.221564282146873	2		475	820	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560980	9560980	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	62	545	0	ENST00000353224.5:c.802C>T	p.Pro268Ser	p.P268S	ENST00000353224	NM_177990.2	268	Cca/Tca	4/10	1	2	FACETS	0.658	0.567	0.758	0.658	0.567	0.758	SUBCLONAL	1	TRUE	1	0.221564282146873	2		545	850	SUCCESS
AR	367	MSKCC	GRCh37	X	66765647	66765647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	119	312	0	ENST00000374690.3:c.659C>T	p.Ser220Phe	p.S220F	ENST00000374690	NM_000044.3	220	tCc/tTc	1/8	1	1	FACETS	0.839	0.76	0.922	1	0.987	1	CLONAL	2	TRUE	0	0.221564282146873	1		312	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579366	7579369	+	frameshift_variant	Frame_Shift_Del	DEL	GTAG	GTAG	TAC	novel	NA	P-0009025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	67	481	0	ENST00000269305.4:c.318_321delinsGTA	p.Ser106ArgfsTer2	p.S106Rfs*2	ENST00000269305	NM_001126112.2	106	agCTAC/agGTA	4/11	1	2	FACETS	0.635	0.55	0.728	0.635	0.55	0.728	SUBCLONAL	1	TRUE	1	0.221564282146873	2		481	952	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0009027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	1273	547	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.703003748862285	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.703003748862285	2		547	1632	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0009050-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	17	470	1	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	1	2	FACETS	0.382	0.283	0.501	0.382	0.283	0.501	SUBCLONAL	1	TRUE	1	0.11	2		471	809	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0009055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	240	436	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.371145695326866	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.371145695326866	1		436	797	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0009055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	130	538	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.632	0.572	0.696	0.632	0.572	0.696	SUBCLONAL	1	TRUE	1	0.371145695326866	2		538	1108	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920331	134920331	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	244	457	0	ENST00000398015.3:c.2146T>G	p.Phe716Val	p.F716V	ENST00000398015	NM_004441.4	716	Ttc/Gtc	12/16	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.371145695326866	2		457	1116	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876392	35876392	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	72	257	0	ENST00000303115.3:c.1184A>G	p.Lys395Arg	p.K395R	ENST00000303115	NM_002185.3	395	aAg/aGg	8/8	1	2	FACETS	0.611	0.534	0.694	0.611	0.534	0.694	SUBCLONAL	1	TRUE	1	0.371145695326866	2		257	635	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827201	72827201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138835662	NA	P-0009055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	279	658	1	ENST00000268489.5:c.9380C>T	p.Pro3127Leu	p.P3127L	ENST00000268489	NM_006885.3	3127	cCg/cTg	9/10	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.371145695326866	NA		659	1386	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099371	27099374	+	frameshift_variant	Frame_Shift_Del	DEL	ATTC	ATTC	-	novel	NA	P-0009055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	259	397	0	ENST00000324856.7:c.3608_3611del	p.Asn1203ThrfsTer2	p.N1203Tfs*2	ENST00000324856	NM_006015.4	1203	aATTCc/ac	14/20	0.244513428105282	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.371145695326866	1		397	853	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591841	48591851	+	frameshift_variant	Frame_Shift_Del	DEL	TAGGAGAGACA	TAGGAGAGACA	-	novel	NA	P-0009055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	164	484	0	ENST00000342988.3:c.1005_1015del	p.Gly336Ter	p.G336*	ENST00000342988	NM_005359.5	335	gTAGGAGAGACA/g	9/12	0.358833461696825	1	FACETS	0.809	0.743	0.878	0.809	0.743	0.878	CLONAL	1	TRUE	0	0.371145695326866	1		484	890	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643389	52643397	+	inframe_deletion	In_Frame_Del	DEL	CGACGGTAG	CGACGGTAG	-	novel	NA	P-0009055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	396	501	0	ENST00000394830.3:c.2499_2507del	p.Tyr834_Arg836del	p.Y834_R836del	ENST00000394830	NM_018313.4	833	cgCTACCGTCGg/cgg	17/30	0.337386422599972	2	FACETS	0.889	0.846	0.933	0.889	0.846	0.933	CLONAL	2	TRUE	0	0.371145695326866	2		501	1200	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0009074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	382	758	1	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.678292729423185	2		759	1105	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131262	17131262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778587763	NA	P-0009074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1259	87	693	3	ENST00000285071.4:c.190G>A	p.Ala64Thr	p.A64T	ENST00000285071	NM_144997.5	64	Gca/Aca	4/14	1	2	FACETS	0.191	0.168	0.215	0.191	0.168	0.215	SUBCLONAL	1	TRUE	1	0.678292729423185	2		696	1346	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440870	52440887	+	inframe_deletion	In_Frame_Del	DEL	CCATGATGACCCGCCGGG	CCATGATGACCCGCCGGG	-	novel	NA	P-0009074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	288	512	0	ENST00000460680.1:c.617_634del	p.Ala206_Met211del	p.A206_M211del	ENST00000460680	NM_004656.3	206	gCCCGGCGGGTCATCATGGag/gag	8/17	0.67574639600006	1	FACETS	0.815	0.771	0.858	0.815	0.771	0.858	CLONAL	1	TRUE	0	0.678292729423185	1		512	689	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0009083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	179	426	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.155773799312596	2	FACETS	0.776	0.715	0.84	0.776	0.715	0.84	SUBCLONAL	2	TRUE	0	0.218173461337861	2		426	1057	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42788861	42788861	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	122	376	1	ENST00000575354.2:c.5A>G	p.Tyr2Cys	p.Y2C	ENST00000575354	NM_015125.3	2	tAt/tGt	1/20	0.218173461337861	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.218173461337861	1		377	924	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989483	7989483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769533529	NA	P-0009083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	50	313	1	ENST00000319144.4:c.203G>A	p.Arg68His	p.R68H	ENST00000319144	NM_001139.2	68	cGc/cAc	2/15	0.155773799312596	2	FACETS	0.564	0.477	0.66	0.282	0.238	0.33	SUBCLONAL	1	TRUE	0	0.218173461337861	2		314	813	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628521	187628521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	84	481	1	ENST00000441802.2:c.2461G>T	p.Glu821Ter	p.E821*	ENST00000441802	NM_005245.3	821	Gag/Tag	2/27	0.218173461337861	1	FACETS	0.551	0.485	0.623	0.551	0.485	0.623	SUBCLONAL	1	TRUE	0	0.218173461337861	1		482	1245	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265050	198265050	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	115	264	0	ENST00000335508.6:c.2827A>G	p.Lys943Glu	p.K943E	ENST00000335508	NM_012433.2	943	Aaa/Gaa	19/25	0.150660045418356	3	FACETS	1	0.97	1	0.6	0.54	0.664	CLONAL	1	TRUE	1	0.218173461337861	3		264	974	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215661784	215661784	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0009083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	128	491	0	ENST00000260947.4:c.215+1G>T		p.X72_splice	ENST00000260947	NM_000465.2	72			1	2	FACETS	0.919	0.83	1	0.919	0.83	1	CLONAL	1	TRUE	1	0.218173461337861	2		491	1277	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138407716	138407716	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0009083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	138	313	0	ENST00000289153.2:c.2136+1G>T		p.X712_splice	ENST00000289153	NM_006219.2	712			0.150660045418356	3	FACETS	1	0.978	1	0.628	0.57	0.689	CLONAL	1	TRUE	1	0.218173461337861	3		313	1117	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532683	187532683	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	69	416	0	ENST00000441802.2:c.9710C>A	p.Ala3237Asp	p.A3237D	ENST00000441802	NM_005245.3	3237	gCc/gAc	14/27	0.218173461337861	1	FACETS	0.5	0.433	0.572	0.5	0.433	0.572	SUBCLONAL	1	TRUE	0	0.218173461337861	1		416	1128	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874572	151874572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs553423994	NA	P-0009083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	52	288	0	ENST00000262189.6:c.7966G>A	p.Glu2656Lys	p.E2656K	ENST00000262189	NM_170606.2	2656	Gaa/Aaa	38/59	1	2	FACETS	0.493	0.418	0.576	0.493	0.418	0.576	SUBCLONAL	1	TRUE	1	0.218173461337861	2		288	966	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249877	110249877	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	41	158	0	ENST00000374672.4:c.798C>A	p.Tyr266Ter	p.Y266*	ENST00000374672	NM_004235.4	266	taC/taA	3/5	0.155773799312596	2	FACETS	0.895	0.746	1	0.447	0.373	0.53	CLONAL	1	TRUE	0	0.218173461337861	2		158	420	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405892	70405892	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	174	576	0	ENST00000373644.4:c.3406G>T	p.Gly1136Cys	p.G1136C	ENST00000373644	NM_030625.2	1136	Ggt/Tgt	4/12	0.218173461337861	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.218173461337861	1		576	1373	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996801	100996801	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1914	217	770	1	ENST00000325455.5:c.1726G>T	p.Gly576Cys	p.G576C	ENST00000325455	NM_001202474.3	576	Ggc/Tgc	2/8	1	2	FACETS	0.933	0.864	1	0.933	0.864	1	CLONAL	1	TRUE	1	0.218173461337861	2		771	2131	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620033	21620033	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1238	67	535	0	ENST00000382592.4:c.133A>G	p.Thr45Ala	p.T45A	ENST00000382592	NM_014572.2	45	Act/Gct	2/8	0.152542316073556	1	FACETS	0.419	0.363	0.481	0.419	0.363	0.481	SUBCLONAL	1	TRUE	0	0.218173461337861	1		535	1305	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936725	32936725	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs431825358	NA	P-0009083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	70	380	0	ENST00000380152.3:c.7871A>G	p.Tyr2624Cys	p.Y2624C	ENST00000380152		2624	tAt/tGt	17/27	0.152542316073556	1	FACETS	0.557	0.484	0.637	0.557	0.484	0.637	SUBCLONAL	1	TRUE	0	0.218173461337861	1		380	1026	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030410	49030410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	62	293	0	ENST00000267163.4:c.1885G>A	p.Glu629Lys	p.E629K	ENST00000267163	NM_000321.2	629	Gag/Aag	19/27	0.152542316073556	1	FACETS	0.609	0.524	0.701	0.609	0.524	0.701	SUBCLONAL	1	TRUE	0	0.218173461337861	1		293	832	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857223	9857223	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1440	121	613	0	ENST00000330684.3:c.4178C>A	p.Ser1393Tyr	p.S1393Y	ENST00000330684	NM_001134407.1	1393	tCc/tAc	13/13	0.218173461337861	1	FACETS	0.633	0.57	0.701	0.633	0.57	0.701	SUBCLONAL	1	TRUE	0	0.218173461337861	1		613	1561	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782278	56782278	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1597	118	628	2	ENST00000308159.5:c.119G>C	p.Gly40Ala	p.G40A	ENST00000308159	NM_014669.4	40	gGa/gCa	2/22	0.218173461337861	1	FACETS	0.562	0.505	0.623	0.562	0.505	0.623	SUBCLONAL	1	TRUE	0	0.218173461337861	1		630	1715	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942965	15942965	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1286959178	NA	P-0009083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	53	329	1	ENST00000268712.3:c.6737C>T	p.Ser2246Leu	p.S2246L	ENST00000268712	NM_006311.3	2246	tCa/tTa	44/46	0.155773799312596	2	FACETS	0.509	0.432	0.593	0.254	0.216	0.297	SUBCLONAL	1	TRUE	0	0.218173461337861	2		330	955	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216421	2216421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375109653	NA	P-0009083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	96	339	2	ENST00000398665.3:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000398665	NM_032482.2	689	Cgg/Tgg	20/28	0.218173461337861	1	FACETS	0.966	0.86	1	0.966	0.86	1	CLONAL	1	TRUE	0	0.218173461337861	1		341	812	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561186	9561186	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	73	416	0	ENST00000353224.5:c.596A>T	p.Tyr199Phe	p.Y199F	ENST00000353224	NM_177990.2	199	tAt/tTt	4/10	NA	2	FACETS	0.559	0.487	0.637			1	INDETERMINATE	1	TRUE	NA	0.218173461337861	2		416	1198	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600016	10600024	+	stop_gained	Nonsense_Mutation	ONP	ATAGATACA	ATAGATACA	CTAGACACC	novel	NA	P-0009083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	101	313	0	ENST00000171111.5:c.1552_1560delinsGGTGTCTAG	p.Cys518_Tyr520delinsGlyValTer	p.C518_Y520delinsGV*	ENST00000171111	NM_203500.1	518	TGTATCTAT/GGTGTCTAG	5/6	0.218173461337861	1	FACETS	0.957	0.854	1	0.957	0.854	1	CLONAL	1	TRUE	0	0.218173461337861	1		313	862	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	176	315	0	ENST00000257430.4:c.4199C>A	p.Ser1400Ter	p.S1400*	ENST00000257430	NM_000038.5	1400	tCg/tAg	16/16	0.488147265687528	1	FACETS	0.928	0.86	0.998	0.928	0.86	0.998	CLONAL	1	TRUE	0	0.497489509701035	1		315	573	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913514	NA	P-0009084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	168	392	0	ENST00000288135.5:c.2466T>A	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaA	17/21	1	2	FACETS	0.925	0.852	1	0.925	0.852	1	CLONAL	1	TRUE	1	0.497489509701035	2		392	730	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0009084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	130	304	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	0.914	0.832	0.999	0.914	0.832	0.999	CLONAL	1	TRUE	1	0.497489509701035	2		304	572	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593441	55593441	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs753212327	NA	P-0009084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	260	467	1	ENST00000288135.5:c.1598C>A	p.Ala533Asp	p.A533D	ENST00000288135	NM_000222.2	533	gCt/gAt	10/21	1	2	FACETS	0.94	0.88	1	0.94	0.88	1	CLONAL	1	TRUE	1	0.497489509701035	2		468	1112	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0009092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	36	214	0	ENST00000269305.4:c.559+1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			NA	2	FACETS	0.557	0.457	0.668			1	INDETERMINATE	1	TRUE	NA	0.28	2		214	462	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089776	27089776	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1553152166	NA	P-0009092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	12	120	0	ENST00000324856.7:c.2732G>T	p.Arg911Met	p.R911M	ENST00000324856	NM_006015.4	911	aGg/aTg	8/20	1	2	FACETS	0.433	0.304	0.591	0.433	0.304	0.591	SUBCLONAL	1	TRUE	1	0.28	2		120	198	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459131	120459131	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	60	358	1	ENST00000256646.2:c.6214C>T	p.Pro2072Ser	p.P2072S	ENST00000256646	NM_024408.3	2072	Cca/Tca	34/34	1	2	FACETS	0.493	0.424	0.569	0.493	0.424	0.569	SUBCLONAL	1	TRUE	1	0.28	2		359	869	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120469204	120469204	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	59	344	0	ENST00000256646.2:c.3923G>T	p.Cys1308Phe	p.C1308F	ENST00000256646	NM_024408.3	1308	tGt/tTt	24/34	1	2	FACETS	0.445	0.381	0.515	0.445	0.381	0.515	SUBCLONAL	1	TRUE	1	0.28	2		344	947	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248521	212248521	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1309	70	574	1	ENST00000342788.4:c.3746C>A	p.Pro1249His	p.P1249H	ENST00000342788	NM_005235.2	1249	cCt/cAt	28/28	1	2	FACETS	0.363	0.315	0.415	0.363	0.315	0.415	SUBCLONAL	1	TRUE	1	0.28	2		575	1379	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285253	212285253	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	57	415	0	ENST00000342788.4:c.3048G>T	p.Met1016Ile	p.M1016I	ENST00000342788	NM_005235.2	1016	atG/atT	25/28	1	2	FACETS	0.448	0.383	0.52	0.448	0.383	0.52	SUBCLONAL	1	TRUE	1	0.28	2		415	908	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968231	134968231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	77	446	0	ENST00000398015.3:c.2744C>T	p.Thr915Ile	p.T915I	ENST00000398015	NM_004441.4	915	aCc/aTc	15/16	1	2	FACETS	0.539	0.471	0.611	0.539	0.471	0.611	SUBCLONAL	1	TRUE	1	0.28	2		446	1021	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186501407	186501407	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs765785108	NA	P-0009092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1872	114	881	1	ENST00000323963.5:c.8G>T	p.Gly3Val	p.G3V	ENST00000323963		3	gGt/gTt	1/11	1	2	FACETS	0.41	0.367	0.456	0.41	0.367	0.456	SUBCLONAL	1	TRUE	1	0.28	2		882	1986	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948178	55948178	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1247088567	NA	P-0009092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1244	81	456	0	ENST00000263923.4:c.3793G>C	p.Ala1265Pro	p.A1265P	ENST00000263923	NM_002253.2	1265	Gcc/Ccc	29/30	0.11431904102103	3	FACETS	0.498	0.437	0.564	0.249	0.218	0.282	INDETERMINATE	1	TRUE	1	0.28	3		456	1325	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213888	66213888	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	68	497	0	ENST00000273854.3:c.2542G>T	p.Glu848Ter	p.E848*	ENST00000273854	NM_004439.5	848	Gaa/Taa	15/18	1	2	FACETS	0.418	0.362	0.479	0.418	0.362	0.479	SUBCLONAL	1	TRUE	1	0.28	2		497	1161	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171998	32171998	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	72	375	0	ENST00000375023.3:c.3034G>T	p.Asp1012Tyr	p.D1012Y	ENST00000375023	NM_004557.3	1012	Gac/Tac	19/30	0.11431904102103	3	FACETS	0.726	0.633	0.826	0.363	0.316	0.413	INDETERMINATE	1	TRUE	1	0.28	3		375	808	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946426	2946426	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	67	439	0	ENST00000396946.4:c.3311G>T	p.Arg1104Leu	p.R1104L	ENST00000396946	NM_032415.4	1104	cGg/cTg	25/25	1	2	FACETS	0.489	0.423	0.56	0.489	0.423	0.56	SUBCLONAL	1	TRUE	1	0.28	2		439	979	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395440	116395440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	101	459	0	ENST00000397752.3:c.1733G>A	p.Gly578Glu	p.G578E	ENST00000397752	NM_000245.2	578	gGg/gAg	6/21	1	2	FACETS	0.627	0.559	0.7	0.627	0.559	0.7	SUBCLONAL	1	TRUE	1	0.28	2		459	1150	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77070002	77070002	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	80	418	1	ENST00000356341.3:c.538G>T	p.Asp180Tyr	p.D180Y	ENST00000356341	NM_002576.4	180	Gat/Tat	6/15	1	2	FACETS	0.601	0.528	0.68	0.601	0.528	0.68	SUBCLONAL	1	TRUE	1	0.28	2		419	951	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160456	108160456	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1171	97	448	0	ENST00000278616.4:c.4364G>T	p.Ser1455Ile	p.S1455I	ENST00000278616	NM_000051.3	1455	aGt/aTt	29/63	1	2	FACETS	0.546	0.485	0.612	0.546	0.485	0.612	SUBCLONAL	1	TRUE	1	0.28	2		448	1268	SUCCESS
ATM	472	MSKCC	GRCh37	11	108183145	108183145	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	66	343	1	ENST00000278616.4:c.5926G>T	p.Ala1976Ser	p.A1976S	ENST00000278616	NM_000051.3	1976	Gca/Tca	40/63	1	2	FACETS	0.493	0.426	0.565	0.493	0.426	0.565	SUBCLONAL	1	TRUE	1	0.28	2		344	957	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205706	108205706	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	50	279	0	ENST00000278616.4:c.8021C>G	p.Thr2674Arg	p.T2674R	ENST00000278616	NM_000051.3	2674	aCa/aGa	55/63	1	2	FACETS	0.507	0.429	0.593	0.507	0.429	0.593	SUBCLONAL	1	TRUE	1	0.28	2		279	704	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435522	18435522	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	85	318	0	ENST00000266497.5:c.507A>G	p.Ile169Met	p.I169M	ENST00000266497		169	atA/atG	1/31	1	2	FACETS	0.761	0.672	0.856	0.761	0.672	0.856	SUBCLONAL	1	TRUE	1	0.28	2		318	798	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202852	133202852	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs778102693	NA	P-0009092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	94	393	0	ENST00000320574.5:c.6382G>T	p.Asp2128Tyr	p.D2128Y	ENST00000320574	NM_006231.2	2128	Gac/Tac	46/49	1	2	FACETS	0.804	0.715	0.9	0.804	0.715	0.9	CLONAL	1	TRUE	1	0.28	2		393	835	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012410	29012410	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	66	435	0	ENST00000282397.4:c.461T>G	p.Leu154Arg	p.L154R	ENST00000282397	NM_002019.4	154	cTc/cGc	4/30	1	2	FACETS	0.423	0.366	0.486	0.423	0.366	0.486	SUBCLONAL	1	TRUE	1	0.28	2		435	1114	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240223	41240223	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	16	135	0	ENST00000379561.5:c.127G>C	p.Ala43Pro	p.A43P	ENST00000379561	NM_002015.3	43	Gcg/Ccg	1/3	1	2	FACETS	0.404	0.298	0.53	0.404	0.298	0.53	SUBCLONAL	1	TRUE	1	0.28	2		135	283	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060907	38060907	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	35	362	0	ENST00000250448.2:c.1082G>T	p.Ser361Ile	p.S361I	ENST00000250448	NM_004496.3	361	aGc/aTc	2/2	1	2	FACETS	0.435	0.355	0.524	0.435	0.355	0.524	SUBCLONAL	1	TRUE	1	0.28	2		362	575	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042669	42042669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1614	138	778	2	ENST00000219905.7:c.6864G>T	p.Lys2288Asn	p.K2288N	ENST00000219905	NM_001164273.1	2288	aaG/aaT	17/24	1	2	FACETS	0.563	0.51	0.619	0.563	0.51	0.619	SUBCLONAL	1	TRUE	1	0.28	2		780	1752	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129625	2129625	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45496291	NA	P-0009092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	68	564	0	ENST00000219476.3:c.3352C>T	p.Gln1118Ter	p.Q1118*	ENST00000219476	NM_000548.3	1118	Cag/Tag	29/42	1	2	FACETS	0.404	0.35	0.463	0.404	0.35	0.463	SUBCLONAL	1	TRUE	1	0.28	2		564	1203	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687082	37687082	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	68	516	0	ENST00000447079.4:c.3986C>A	p.Ser1329Tyr	p.S1329Y	ENST00000447079	NM_015083.1	1329	tCc/tAc	14/14	1	2	FACETS	0.414	0.359	0.475	0.414	0.359	0.475	SUBCLONAL	1	TRUE	1	0.28	2		516	1172	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40451768	40451768	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0009092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1216	86	751	3	ENST00000345506.4:c.551-1G>T		p.X184_splice	ENST00000345506	NM_003152.3	184			0.3	1	FACETS	0.406	0.357	0.458	0.406	0.357	0.458	SUBCLONAL	1	TRUE	0	0.28	1		754	1302	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117590	4117590	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	41	312	0	ENST00000262948.5:c.130C>G	p.Leu44Val	p.L44V	ENST00000262948	NM_030662.3	44	Ctg/Gtg	2/11	1	2	FACETS	0.394	0.327	0.468	0.394	0.327	0.468	SUBCLONAL	1	TRUE	1	0.28	2		312	744	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268710	46268710	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1335	80	719	2	ENST00000371998.3:c.2995G>T	p.Gly999Cys	p.G999C	ENST00000371998		999	Ggc/Tgc	16/23	0.279003886667125	1	FACETS	0.347	0.304	0.394	0.347	0.304	0.394	SUBCLONAL	1	TRUE	0	0.28	1		721	1415	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875910	76875910	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1268	86	662	0	ENST00000373344.5:c.5225G>T	p.Arg1742Met	p.R1742M	ENST00000373344	NM_000489.3	1742	aGg/aTg	20/35	0.3	1	FACETS	0.39	0.344	0.44	0.39	0.344	0.44	SUBCLONAL	1	TRUE	0	0.28	1		662	1354	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167840	185167841	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0009092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	44	380	0	ENST00000265026.3:c.1164_1165del	p.Gln388HisfsTer5	p.Q388Hfs*5	ENST00000265026	NM_004721.4	388	cAG/c	6/14	1	2	FACETS	0.361	0.302	0.428	0.361	0.302	0.428	SUBCLONAL	1	TRUE	1	0.28	2		380	870	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231438	46231438	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	113	376	1	ENST00000334344.6:c.1279del	p.Glu427LysfsTer13	p.E427Kfs*13	ENST00000334344	NM_152641.2	426	acG/ac	10/21	1	2	FACETS	0.787	0.707	0.873	0.787	0.707	0.873	SUBCLONAL	1	TRUE	1	0.28	2		377	1025	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	132	407	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	TRUE	1	0.245162254489513	2		407	878	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039339	49039339	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0009093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	252	599	0	ENST00000267163.4:c.2326-2A>G		p.X776_splice	ENST00000267163	NM_000321.2	776			0.23483407019338	2	FACETS	0.888	0.831	0.948	0.888	0.831	0.948	CLONAL	2	TRUE	0	0.245162254489513	2		599	1157	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385183	41385183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1423243089	NA	P-0009093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	136	435	0	ENST00000373198.4:c.778C>T	p.Arg260Trp	p.R260W	ENST00000373198	NM_133170.3	260	Cgg/Tgg	6/32	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.245162254489513	2		435	775	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15364968	15364968	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	112	426	0	ENST00000263377.2:c.2153A>G	p.Glu718Gly	p.E718G	ENST00000263377	NM_058243.2	718	gAa/gGa	11/20	0.173459419751682	3	FACETS	1	0.973	1	0.624	0.561	0.691	CLONAL	1	TRUE	1	0.245162254489513	3		426	822	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0009099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	838	233	0				ENST00000310581	NM_198253.2	-/1132			0.76891102843385	10	FACETS	1	0.995	1	1	0.995	1	CLONAL	8	TRUE	2	0.76891102843385	10		233	1058	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0009099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	887	540	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	0.76891102843385	4	FACETS	1	0.993	1			1	CLONAL	4	TRUE	NA	0.76891102843385	4		540	1008	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188107	11188107	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	375	293	0	ENST00000361445.4:c.5987A>C	p.Lys1996Thr	p.K1996T	ENST00000361445	NM_004958.3	1996	aAg/aCg	43/58	0.76891102843385	5	FACETS	0.971	0.93	1	0.971	0.93	1	CLONAL	3	TRUE	2	0.76891102843385	5		293	721	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499670	8499670	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	222	298	0	ENST00000356435.5:c.2299G>C	p.Asp767His	p.D767H	ENST00000356435		767	Gat/Cat	14/35	0.330177508773708	5	FACETS	1	0.986	1	0.781	0.733	0.828	INDETERMINATE	2	TRUE	2	0.76891102843385	5		298	531	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760786	133760786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1330364358	NA	P-0009099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	185	406	1	ENST00000318560.5:c.3109G>A	p.Glu1037Lys	p.E1037K	ENST00000318560	NM_005157.4	1037	Gag/Aag	11/11	0.330177508773708	5	FACETS	1	0.952	1	0.685	0.638	0.733	INDETERMINATE	2	TRUE	2	0.76891102843385	5		407	504	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850801	63850801	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	348	518	1	ENST00000279873.7:c.1579G>T	p.Glu527Ter	p.E527*	ENST00000279873	NM_032199.2	527	Gag/Tag	10/10	0.76891102843385	2	FACETS	0.988	0.956	1	0.988	0.956	1	CLONAL	2	TRUE	0	0.76891102843385	2		519	458	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947585	48947585	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0009099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	222	341	0	ENST00000267163.4:c.1172C>G	p.Ser391Ter	p.S391*	ENST00000267163	NM_000321.2	391	tCa/tGa	12/27	NA	2	FACETS	0.975	0.935	1			1	INDETERMINATE	2	TRUE	NA	0.76891102843385	2		341	296	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061684	38061684	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1254047977	NA	P-0009099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	98	135	2	ENST00000250448.2:c.305C>A	p.Thr102Lys	p.T102K	ENST00000250448	NM_004496.3	102	aCg/aAg	2/2	0.761450845599611	4	FACETS	0.932	0.847	1	0.932	0.847	1	CLONAL	2	TRUE	2	0.76891102843385	4		137	242	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991815	72991815	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	205	698	0	ENST00000268489.5:c.2230C>T	p.His744Tyr	p.H744Y	ENST00000268489	NM_006885.3	744	Cat/Tat	2/10	0.276975316564213	3	FACETS	0.842	0.782	0.904	0.281	0.26	0.302	INDETERMINATE	1	TRUE	0	0.76891102843385	3		698	877	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346752	89346752	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	154	581	0	ENST00000301030.4:c.6198C>A	p.Phe2066Leu	p.F2066L	ENST00000301030	NM_001256183.1	2066	ttC/ttA	9/13	0.276975316564213	3	FACETS	0.854	0.785	0.927	0.285	0.261	0.309	INDETERMINATE	1	TRUE	0	0.76891102843385	3		581	649	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44935940	44935940	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0009099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	344	389	0	ENST00000377967.4:c.2703-2A>G		p.X901_splice	ENST00000377967	NM_021140.2	901			0.76891102843385	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.76891102843385	2		389	413	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044523	47044523	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	411	528	1	ENST00000377604.3:c.2020C>T	p.Gln674Ter	p.Q674*	ENST00000377604	NM_001204468.1	674	Cag/Tag	18/24	0.76891102843385	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.76891102843385	2		529	529	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426860	6426860	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	170	448	0	ENST00000356142.4:c.53G>C	p.Cys18Ser	p.C18S	ENST00000356142	NM_018890.3	18	tGc/tCc	2/7	1	2	FACETS	0.984	0.907	1	0.984	0.907	1	CLONAL	1	TRUE	1	0.465811417904239	2		448	742	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060844	38060844	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	171	562	1	ENST00000250448.2:c.1145A>T	p.His382Leu	p.H382L	ENST00000250448	NM_004496.3	382	cAc/cTc	2/2	0.465811417904239	3	FACETS	1	0.971	1	0.557	0.513	0.603	CLONAL	1	TRUE	1	0.465811417904239	3		563	812	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	115	145	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.454409665899249	2		145	366	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956220	55956220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190050670	NA	P-0009105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	311	402	0	ENST00000263923.4:c.3095G>A	p.Arg1032Gln	p.R1032Q	ENST00000263923	NM_002253.2	1032	cGa/cAa	23/30	0.454409665899249	3	FACETS	0.878	0.829	0.927	0.878	0.829	0.927	CLONAL	2	TRUE	1	0.454409665899249	3		402	957	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0009105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	116	419	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	0.364786776025485	3	FACETS	0.778	0.701	0.86	0.389	0.35	0.43	SUBCLONAL	1	TRUE	1	0.454409665899249	3		419	805	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218090	108218090	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	123	308	0	ENST00000278616.4:c.8669T>C	p.Leu2890Pro	p.L2890P	ENST00000278616	NM_000051.3	2890	cTa/cCa	59/63	0.337808889475836	2	FACETS	0.82	0.752	0.89	0.82	0.752	0.89	CLONAL	2	TRUE	0	0.454409665899249	2		308	330	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11205084	11205084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1282753680	NA	P-0009105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	159	535	0	ENST00000361445.4:c.4705G>A	p.Asp1569Asn	p.D1569N	ENST00000361445	NM_004958.3	1569	Gac/Aac	33/58	NA	2	FACETS	0.993	0.912	1			1	INDETERMINATE	1	TRUE	NA	0.454409665899249	2		535	705	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467059	25467059	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1396358001	NA	P-0009105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	200	379	0	ENST00000264709.3:c.1816C>T	p.Gln606Ter	p.Q606*	ENST00000264709	NM_175629.2	606	Cag/Tag	15/23	0.294324102235711	4	FACETS	1	0.991	1	0.747	0.693	0.803	CLONAL	1	TRUE	2	0.454409665899249	4		379	857	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272238	142272238	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	88	331	1	ENST00000350721.4:c.2636C>T	p.Ala879Val	p.A879V	ENST00000350721	NM_001184.3	879	gCc/gTc	13/47	0.364786776025485	3	FACETS	0.745	0.661	0.835	0.373	0.33	0.418	SUBCLONAL	1	TRUE	1	0.454409665899249	3		332	638	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38949889	38949889	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	337	394	0	ENST00000357387.3:c.4061C>T	p.Pro1354Leu	p.P1354L	ENST00000357387	NM_152756.3	1354	cCa/cTa	31/38	0.447832989112496	6	FACETS	1	0.989	1	0.851	0.808	0.894	CLONAL	3	TRUE	2	0.454409665899249	6		394	832	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177050	56177050	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	131	282	0	ENST00000399503.3:c.2320C>T	p.Pro774Ser	p.P774S	ENST00000399503	NM_005921.1	774	Cct/Tct	13/20	0.454409665899249	4	FACETS	0.934	0.854	1	0.934	0.854	1	CLONAL	2	TRUE	2	0.454409665899249	4		282	449	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589165	67589165	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	156	409	0	ENST00000274335.5:c.1153C>T	p.His385Tyr	p.H385Y	ENST00000274335		385	Cat/Tat	9/15	0.454409665899249	4	FACETS	1	0.987	1	0.717	0.659	0.779	CLONAL	1	TRUE	2	0.454409665899249	4		409	696	SUCCESS
APC	324	MSKCC	GRCh37	5	112175021	112175021	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs79122263	NA	P-0009105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	148	276	0	ENST00000257430.4:c.3730C>T	p.Gln1244Ter	p.Q1244*	ENST00000257430	NM_000038.5	1244	Caa/Taa	16/16	0.294324102235711	4	FACETS	1	0.986	1	0.706	0.646	0.768	CLONAL	1	TRUE	2	0.454409665899249	4		276	671	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032257	26032257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	248	273	0	ENST00000244661.2:c.32C>T	p.Ser11Phe	p.S11F	ENST00000244661	NM_003537.3	11	tCc/tTc	1/1	0.454409665899249	6	FACETS	0.85	0.794	0.909	0.567	0.529	0.606	CLONAL	2	TRUE	3	0.454409665899249	6		273	1225	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507354	8507354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	231	488	1	ENST00000356435.5:c.1624G>A	p.Asp542Asn	p.D542N	ENST00000356435		542	Gat/Aat	11/35	0.300852512136071	3	FACETS	0.802	0.75	0.855	0.802	0.75	0.855	CLONAL	2	TRUE	1	0.454409665899249	3		489	778	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8526630	8526630	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0009105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	41	245	0	ENST00000356435.5:c.565A>T	p.Arg189Ter	p.R189*	ENST00000356435		189	Aga/Tga	6/35	0.300852512136071	3	FACETS	0.661	0.552	0.781	0.331	0.276	0.391	SUBCLONAL	1	TRUE	1	0.454409665899249	3		245	335	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787758	135787758	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	127	452	0	ENST00000298552.3:c.824A>T	p.Tyr275Phe	p.Y275F	ENST00000298552	NM_001162426.1	275	tAt/tTt	9/23	0.300852512136071	3	FACETS	0.803	0.727	0.883	0.402	0.363	0.442	CLONAL	1	TRUE	1	0.454409665899249	3		452	854	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256237	123256237	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0009105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	149	333	0	ENST00000358487.5:c.1673-1G>A		p.X558_splice	ENST00000358487	NM_000141.4	558			0.255646529015528	3	FACETS	0.847	0.78	0.916	0.847	0.78	0.916	INDETERMINATE	2	TRUE	1	0.454409665899249	3		333	475	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981798	101981798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760222925	NA	P-0009105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	367	387	2	ENST00000282441.5:c.219G>A	p.Met73Ile	p.M73I	ENST00000282441	NM_001130145.2	73	atG/atA	1/9	0.337808889475836	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.454409665899249	2		389	801	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	461392	461392	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	85	486	0	ENST00000399788.2:c.1128T>A	p.Asp376Glu	p.D376E	ENST00000399788	NM_001042603.1	376	gaT/gaA	9/28	0.300852512136071	3	FACETS	0.731	0.647	0.821	0.366	0.323	0.411	SUBCLONAL	1	TRUE	1	0.454409665899249	3		486	628	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444788	49444788	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	149	413	0	ENST00000301067.7:c.2678C>T	p.Pro893Leu	p.P893L	ENST00000301067	NM_003482.3	893	cCc/cTc	10/54	0.300852512136071	3	FACETS	1	0.987	1	0.703	0.646	0.763	CLONAL	1	TRUE	1	0.454409665899249	3		413	572	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237640	133237640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	258	483	0	ENST00000320574.5:c.2975C>T	p.Ala992Val	p.A992V	ENST00000320574	NM_006231.2	992	gCc/gTc	25/49	0.300852512136071	3	FACETS	0.791	0.742	0.841	0.791	0.742	0.841	SUBCLONAL	2	TRUE	1	0.454409665899249	3		483	881	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608335	28608335	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	132	433	0	ENST00000241453.7:c.1721G>A	p.Ser574Asn	p.S574N	ENST00000241453	NM_004119.2	574	aGc/aAc	14/24	NA	2	FACETS	1	0.963	1			1	INDETERMINATE	1	TRUE	NA	0.454409665899249	2		433	526	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913149	32913149	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	283	823	1	ENST00000380152.3:c.4657A>T	p.Thr1553Ser	p.T1553S	ENST00000380152		1553	Act/Tct	11/27	0.300852512136071	3	FACETS	1	0.991	1	0.645	0.606	0.685	CLONAL	1	TRUE	1	0.454409665899249	3		824	1185	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744435	41744435	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	130	605	0	ENST00000301178.4:c.1055A>T	p.His352Leu	p.H352L	ENST00000301178	NM_021913.4	352	cAt/cTt	8/20	0.158649354115911	2	FACETS	0.584	0.529	0.643	0.292	0.264	0.322	INDETERMINATE	1	TRUE	0	0.454409665899249	2		605	979	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561090	9561090	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	128	320	0	ENST00000353224.5:c.692C>T	p.Ser231Leu	p.S231L	ENST00000353224	NM_177990.2	231	tCa/tTa	4/10	0.213921352712285	4	FACETS	0.779	0.709	0.851	0.779	0.709	0.851	INDETERMINATE	2	TRUE	2	0.454409665899249	4		320	526	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069315	30069315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	89	395	0	ENST00000338641.4:c.1180G>A	p.Glu394Lys	p.E394K	ENST00000338641	NM_000268.3	394	Gag/Aag	12/16	0.255646529015528	3	FACETS	0.722	0.64	0.809	0.361	0.32	0.405	INDETERMINATE	1	TRUE	1	0.454409665899249	3		395	666	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617551	100617551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	282	480	0	ENST00000308731.7:c.518G>A	p.Gly173Glu	p.G173E	ENST00000308731	NM_000061.2	173	gGa/gAa	6/19	0.454409665899249	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.454409665899249	1		480	680	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955541	48955541	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	142	371	0	ENST00000267163.4:c.1657del	p.Cys553ValfsTer58	p.C553Vfs*58	ENST00000267163	NM_000321.2	553	Tgt/gt	17/27	0.300852512136071	3	FACETS	0.799	0.733	0.867	0.799	0.733	0.867	SUBCLONAL	2	TRUE	1	0.454409665899249	3		371	480	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134905	41134905	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1268	208	811	0	ENST00000379561.5:c.723del	p.Glu242ArgfsTer91	p.E242Rfs*91	ENST00000379561	NM_002015.3	241	ccA/cc	2/3	0.300852512136071	3	FACETS	0.761	0.704	0.82	0.381	0.352	0.41	SUBCLONAL	1	TRUE	1	0.454409665899249	3		811	1476	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665159	29665207	+	splice_donor_variant,intron_variant	Splice_Site	DEL	TACCTGTTCCGCCCTCACTTCTCCCAAATATTTATGGTTCTCAAGTTGT	TACCTGTTCCGCCCTCACTTCTCCCAAATATTTATGGTTCTCAAGTTGT	-	novel	NA	P-0009105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	58	219	1	ENST00000356175.3:c.6756+2_6756+50del		p.X2252_splice	ENST00000356175	NM_000267.3	2252			0.434401549607798	3	FACETS	0.844	0.729	0.969	0.281	0.243	0.323	CLONAL	1	TRUE	0	0.454409665899249	3		220	371	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399226	139399227	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	120	311	0	ENST00000277541.6:c.4916_4917delinsTT	p.Ala1639Val	p.A1639V	ENST00000277541	NM_017617.3	1639	gCC/gTT	26/34	0.300852512136071	3	FACETS	1	0.973	1	0.599	0.543	0.658	CLONAL	1	TRUE	1	0.454409665899249	3		311	541	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296144	15296145	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	181	434	0	ENST00000263388.2:c.2219_2220delinsTT	p.Ser740Phe	p.S740F	ENST00000263388	NM_000435.2	740	tCC/tTT	14/33	0.158649354115911	2	FACETS	1	0.98	1	0.582	0.539	0.627	INDETERMINATE	1	TRUE	0	0.454409665899249	2		434	684	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66522053	66522054	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0009105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	186	135	0	ENST00000358598.2:c.708_708+1delinsAA		p.X236_splice	ENST00000358598	NM_212471.2	236		7/11	0.454409665899249	3	FACETS	1	0.944	1			1	CLONAL	3	TRUE	NA	0.454409665899249	3		135	334	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68934945	68934946	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	81	443	0	ENST00000487270.1:c.1014_1015delinsAA	p.Glu339Lys	p.E339K	ENST00000487270	NM_133509.3	338	aaGGag/aaAAag	10/11	0.300852512136071	3	FACETS	0.734	0.647	0.827	0.367	0.323	0.414	SUBCLONAL	1	TRUE	1	0.454409665899249	3		443	596	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031177	36031178	+	missense_variant	Missense_Mutation	DNP	GG	GG	CA	novel	NA	P-0009105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	215	465	1	ENST00000358208.4:c.1296_1297delinsCA	p.Ala433Thr	p.A433T	ENST00000358208		432	acGGct/acCAct	11/12	0.213921352712285	4	FACETS	0.762	0.709	0.817	0.762	0.709	0.817	INDETERMINATE	2	TRUE	2	0.454409665899249	4		466	903	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	177	145	0				ENST00000310581	NM_198253.2	-/1132			0.453186786510618	1	FACETS	0.819	0.772	0.865	0.819	0.772	0.865	INDETERMINATE	1	TRUE	0	0.845731641234241	1		145	295	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944629	40944629	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	135	177	0	ENST00000373198.4:c.1873C>T	p.Gln625Ter	p.Q625*	ENST00000373198	NM_133170.3	625	Cag/Tag	12/32	0.330457560818031	3	FACETS	1	0.972	1	0.566	0.52	0.614	INDETERMINATE	1	TRUE	1	0.845731641234241	3		177	401	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	936	372	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	0.618179087329839	4	FACETS	0.959	0.937	0.981	0.959	0.937	0.981	CLONAL	3	TRUE	1	0.845731641234241	4		372	1420	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561263	9561263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769939031	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	546	374	0	ENST00000353224.5:c.519G>A	p.Met173Ile	p.M173I	ENST00000353224	NM_177990.2	173	atG/atA	4/10	0.503678859293604	3	FACETS	0.867	0.836	0.897	0.867	0.836	0.897	INDETERMINATE	2	TRUE	1	0.845731641234241	3		374	1060	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247436	71247436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1358353721	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	362	376	1	ENST00000318789.4:c.97C>T	p.Arg33Trp	p.R33W	ENST00000318789	NM_032682.5	33	Cgg/Tgg	6/21	0.403911685870223	2	FACETS	0.976	0.93	1	0.488	0.465	0.512	INDETERMINATE	1	TRUE	0	0.845731641234241	2		377	877	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344107	118344107	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs727503777	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	454	289	1	ENST00000534358.1:c.2233C>T	p.Arg745Ter	p.R745*	ENST00000534358	NM_005933.3	745	Cga/Tga	3/36	0.268626756848796	4	FACETS	0.98	0.939	1	0.98	0.939	1	INDETERMINATE	2	TRUE	2	0.845731641234241	4		290	1011	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021727	71021727	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	822	603	0	ENST00000318789.4:c.1631G>A	p.Arg544Gln	p.R544Q	ENST00000318789	NM_032682.5	544	cGa/cAa	18/21	0.403911685870223	2	FACETS	1	0.998	1	0.723	0.704	0.742	INDETERMINATE	1	TRUE	0	0.845731641234241	2		603	1345	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670452	88670452	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143617169	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	399	478	0	ENST00000360948.2:c.1234G>A	p.Glu412Lys	p.E412K	ENST00000360948	NM_001012338.2	412	Gaa/Aaa	11/19	0.201507637062605	1	FACETS	0.563	0.537	0.589	0.563	0.537	0.589	INDETERMINATE	1	TRUE	0	0.845731641234241	1		478	967	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084111	47084111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	223	460	1	ENST00000409792.3:c.7178C>T	p.Pro2393Leu	p.P2393L	ENST00000409792	NM_014159.6	2393	cCc/cTc	17/21	0.403911685870223	2	FACETS	0.439	0.408	0.471	0.219	0.204	0.236	INDETERMINATE	1	TRUE	0	0.845731641234241	2		461	1202	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851420	156851420	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	269	273	0	ENST00000524377.1:c.2377G>A	p.Asp793Asn	p.D793N	ENST00000524377	NM_002529.3	793	Gat/Aat	17/17	1	2	FACETS	0.97	0.916	1	0.97	0.916	1	CLONAL	1	TRUE	1	0.845731641234241	2		273	656	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026923	48026923	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1553413197	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	416	585	0	ENST00000234420.5:c.1801C>G	p.Leu601Val	p.L601V	ENST00000234420	NM_000179.2	601	Ctc/Gtc	4/10	0.201507637062605	1	FACETS	0.478	0.455	0.5	0.478	0.455	0.5	INDETERMINATE	1	TRUE	0	0.845731641234241	1		585	1189	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095626	178095626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750553272	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	724	666	2	ENST00000397062.3:c.1705C>T	p.Arg569Cys	p.R569C	ENST00000397062	NM_006164.4	569	Cgt/Tgt	5/5	0.201507637062605	1	FACETS	0.646	0.625	0.667	0.646	0.625	0.667	INDETERMINATE	1	TRUE	0	0.845731641234241	1		668	1530	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723368	49723368	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	553	312	0	ENST00000449682.2:c.1175A>T	p.Tyr392Phe	p.Y392F	ENST00000449682	NM_020998.3	392	tAc/tTc	10/18	0.403911685870223	2	FACETS	0.767	0.744	0.791	0.767	0.744	0.791	INDETERMINATE	2	TRUE	0	0.845731641234241	2		312	852	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933692	49933692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750360885	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1284	380	762	0	ENST00000296474.3:c.2585C>T	p.Pro862Leu	p.P862L	ENST00000296474	NM_002447.2	862	cCa/cTa	10/20	0.403911685870223	2	FACETS	0.54	0.511	0.57	0.27	0.255	0.285	INDETERMINATE	1	TRUE	0	0.845731641234241	2		762	1664	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441265	52441265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	214	361	1	ENST00000460680.1:c.505C>T	p.His169Tyr	p.H169Y	ENST00000460680	NM_004656.3	169	Cac/Tac	7/17	0.403911685870223	2	FACETS	0.517	0.48	0.555	0.258	0.24	0.278	INDETERMINATE	1	TRUE	0	0.845731641234241	2		362	979	SUCCESS
APC	324	MSKCC	GRCh37	5	112179365	112179365	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	280	535	0	ENST00000257430.4:c.8074C>T	p.Pro2692Ser	p.P2692S	ENST00000257430	NM_000038.5	2692	Cca/Tca	16/16	0.453186786510618	1	FACETS	0.41	0.386	0.435	0.41	0.386	0.435	INDETERMINATE	1	TRUE	0	0.845731641234241	1		535	932	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068055	94068055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	1296	764	1	ENST00000369303.4:c.907G>A	p.Asp303Asn	p.D303N	ENST00000369303	NM_004440.3	303	Gat/Aat	4/17	0.845731641234241	2	FACETS	0.989	0.975	1	0.989	0.975	1	CLONAL	2	TRUE	0	0.845731641234241	2		765	1549	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976787	2976787	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1550	591	570	1	ENST00000396946.4:c.1225G>A	p.Glu409Lys	p.E409K	ENST00000396946	NM_032415.4	409	Gag/Aag	9/25	0.618179087329839	4	FACETS	1	0.994	1	0.402	0.385	0.419	CLONAL	1	TRUE	1	0.845731641234241	4		571	2141	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935611	13935611	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	908	330	0	ENST00000405192.2:c.1245G>A	p.Met415Ile	p.M415I	ENST00000405192	NM_001163147.1	415	atG/atA	12/12	0.618179087329839	4	FACETS	0.972	0.95	0.994	0.972	0.95	0.994	CLONAL	3	TRUE	1	0.845731641234241	4		330	1359	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027753	152027753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	1634	655	0	ENST00000262189.6:c.322C>T	p.Leu108Phe	p.L108F	ENST00000262189	NM_170606.2	108	Ctt/Ttt	3/59	0.618179087329839	4	FACETS	0.951	0.934	0.967	0.951	0.934	0.967	CLONAL	3	TRUE	1	0.845731641234241	4		655	2501	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346397	152346397	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2127	778	897	0	ENST00000359321.1:c.173T>C	p.Leu58Pro	p.L58P	ENST00000359321	NM_005431.1	58	cTt/cCt	3/3	0.618179087329839	4	FACETS	1	0.995	1	0.39	0.375	0.404	CLONAL	1	TRUE	1	0.845731641234241	4		897	2905	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738233	145738233	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762028333	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	456	321	0	ENST00000428558.2:c.2752G>A	p.Glu918Lys	p.E918K	ENST00000428558	NM_004260.3	918	Gag/Aag	16/22	0.422881951306874	4	FACETS	0.972	0.932	1	0.972	0.932	1	INDETERMINATE	2	TRUE	2	0.845731641234241	4		321	1024	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8733830	8733830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	107	259	1	ENST00000356435.5:c.14C>T	p.Ala5Val	p.A5V	ENST00000356435		5	gCc/gTc	1/35	0.453186786510618	1	FACETS	0.359	0.324	0.395	0.359	0.324	0.395	INDETERMINATE	1	TRUE	0	0.845731641234241	1		260	407	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606226	93606226	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	371	402	0	ENST00000375746.1:c.46T>A	p.Phe16Ile	p.F16I	ENST00000375746	NM_001174167.1	16	Ttt/Att	2/14	0.453186786510618	1	FACETS	0.724	0.694	0.755	0.724	0.694	0.755	INDETERMINATE	1	TRUE	0	0.845731641234241	1		402	699	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451338	70451338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	759	607	0	ENST00000373644.4:c.6178G>A	p.Gly2060Ser	p.G2060S	ENST00000373644	NM_030625.2	2060	Ggt/Agt	12/12	0.453186786510618	1	FACETS	0.799	0.777	0.822	0.799	0.777	0.822	INDETERMINATE	1	TRUE	0	0.845731641234241	1		607	1296	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149275	119149275	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	887	564	1	ENST00000264033.4:c.1283C>A	p.Pro428His	p.P428H	ENST00000264033	NM_005188.3	428	cCc/cAc	9/16	0.268626756848796	4	FACETS	1	0.994	1	1	0.994	1	INDETERMINATE	2	TRUE	2	0.845731641234241	4		565	1804	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443670	49443670	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	250	430	0	ENST00000301067.7:c.3701G>A	p.Gly1234Glu	p.G1234E	ENST00000301067	NM_003482.3	1234	gGg/gAg	11/54	0.396178069317436	1	FACETS	0.418	0.392	0.444	0.418	0.392	0.444	INDETERMINATE	1	TRUE	0	0.845731641234241	1		430	817	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865591	57865591	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	820	787	0	ENST00000228682.2:c.3068C>T	p.Pro1023Leu	p.P1023L	ENST00000228682	NM_005269.2	1023	cCt/cTt	12/12	0.453186786510618	1	FACETS	0.769	0.747	0.79	0.769	0.747	0.79	INDETERMINATE	1	TRUE	0	0.845731641234241	1		787	1456	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602426	28602426	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	478	345	0	ENST00000241453.7:c.1943-1G>A		p.X648_splice	ENST00000241453	NM_004119.2	648			0.446377459901802	3	FACETS	0.903	0.869	0.936	0.903	0.869	0.936	INDETERMINATE	2	TRUE	1	0.845731641234241	3		345	891	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041426	42041426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	829	842	0	ENST00000219905.7:c.5621C>T	p.Ser1874Phe	p.S1874F	ENST00000219905	NM_001164273.1	1874	tCt/tTt	17/24	0.201507637062605	1	FACETS	0.579	0.56	0.597	0.579	0.56	0.597	INDETERMINATE	1	TRUE	0	0.845731641234241	1		842	1955	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129652	2129652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373939435	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	730	512	0	ENST00000219476.3:c.3379C>T	p.Arg1127Trp	p.R1127W	ENST00000219476	NM_000548.3	1127	Cgg/Tgg	29/42	0.29733749402194	2	FACETS	1	0.998	1	0.702	0.682	0.722	INDETERMINATE	1	TRUE	0	0.845731641234241	2		512	1229	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943662	9943662	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560839364	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	226	367	0	ENST00000330684.3:c.1279G>A	p.Glu427Lys	p.E427K	ENST00000330684	NM_001134407.1	427	Gag/Aag	5/13	0.29733749402194	2	FACETS	0.603	0.562	0.644	0.301	0.281	0.322	INDETERMINATE	1	TRUE	0	0.845731641234241	2		367	887	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348936	11348936	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	137	195	0	ENST00000332029.2:c.400C>G	p.Arg134Gly	p.R134G	ENST00000332029	NM_003745.1	134	Cgc/Ggc	2/2	0.29733749402194	2	FACETS	0.627	0.573	0.682	0.313	0.286	0.341	INDETERMINATE	1	TRUE	0	0.845731641234241	2		195	517	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867272	68867272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781300	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	613	332	0	ENST00000261769.5:c.2519C>T	p.Ser840Phe	p.S840F	ENST00000261769	NM_004360.3	840	tCc/tTc	16/16	0.29733749402194	2	FACETS	1	0.997	1	0.729	0.707	0.751	INDETERMINATE	1	TRUE	0	0.845731641234241	2		332	994	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29497015	29497015	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs876659079	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	121	275	0	ENST00000356175.3:c.586G>A	p.Glu196Lys	p.E196K	ENST00000356175	NM_000267.3	196	Gaa/Aaa	5/57	0.466910356996186	1	FACETS	0.306	0.277	0.336	0.306	0.277	0.336	INDETERMINATE	1	TRUE	0	0.845731641234241	1		275	540	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10286241	10286241	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	638	616	1	ENST00000340748.4:c.575C>T	p.Ser192Phe	p.S192F	ENST00000340748		192	tCc/tTc	6/40	0.201507637062605	1	FACETS	0.645	0.623	0.667	0.645	0.623	0.667	INDETERMINATE	1	TRUE	0	0.845731641234241	1		617	1350	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296117	15296117	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	208	486	0	ENST00000263388.2:c.2247C>A	p.Cys749Ter	p.C749*	ENST00000263388	NM_000435.2	749	tgC/tgA	14/33	0.201507637062605	1	FACETS	0.281	0.26	0.302	0.281	0.26	0.302	INDETERMINATE	1	TRUE	0	0.845731641234241	1		486	1012	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31025064	31025064	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	464	274	0	ENST00000375687.4:c.4549C>T	p.Gln1517Ter	p.Q1517*	ENST00000375687	NM_015338.5	1517	Caa/Taa	13/13	0.503678859293604	3	FACETS	0.897	0.863	0.931	0.897	0.863	0.931	INDETERMINATE	2	TRUE	1	0.845731641234241	3		274	870	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368176	31368176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	802	526	1	ENST00000328111.2:c.47G>A	p.Gly16Glu	p.G16E	ENST00000328111	NM_006892.3	16	gGg/gAg	2/23	0.503678859293604	3	FACETS	0.906	0.88	0.932	0.906	0.88	0.932	INDETERMINATE	2	TRUE	1	0.845731641234241	3		527	1489	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527460	29527461	+	stop_gained	Nonsense_Mutation	DNP	AC	AC	TT	rs1555610854	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	343	334	0	ENST00000356175.3:c.909_910delinsTT	p.Arg304Ter	p.R304*	ENST00000356175	NM_000267.3	303	ctACga/ctTTga	9/57	0.466910356996186	1	FACETS	0.757	0.725	0.79	0.757	0.725	0.79	INDETERMINATE	1	TRUE	0	0.845731641234241	1		334	618	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339144	65339145	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	388	437	0	ENST00000342505.4:c.391_392delinsTT	p.Pro131Leu	p.P131L	ENST00000342505	NM_002227.2	131	CCa/TTa	5/25	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.845731641234241	2		437	916	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0009117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	36	375	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.430673083648391	1	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	0	0.430673083648391	1		377	121	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0009117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	20	273	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.852	0.662	1	0.852	0.662	1	CLONAL	1	TRUE	1	0.430673083648391	2		273	109	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147583	61147583	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1183761567	NA	P-0009117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	17	114	0	ENST00000295025.8:c.988A>G	p.Thr330Ala	p.T330A	ENST00000295025	NM_002908.2	330	Acc/Gcc	9/11	1	2	FACETS	0.255	0.19	0.333	0.255	0.19	0.333	SUBCLONAL	1	TRUE	1	0.430673083648391	2		114	309	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147587	61147587	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	30	125	0	ENST00000295025.8:c.992T>C	p.Leu331Ser	p.L331S	ENST00000295025	NM_002908.2	331	tTg/tCg	9/11	1	2	FACETS	0.389	0.314	0.475	0.389	0.314	0.475	SUBCLONAL	1	TRUE	1	0.430673083648391	2		125	358	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876449	35876449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2229232	NA	P-0009117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	26	261	0	ENST00000303115.3:c.1241C>T	p.Thr414Met	p.T414M	ENST00000303115	NM_002185.3	414	aCg/aTg	8/8	1	2	FACETS	0.816	0.654	0.996	0.816	0.654	0.996	CLONAL	1	TRUE	1	0.430673083648391	2		261	148	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041734	42041734	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	62	697	1	ENST00000219905.7:c.5929C>T	p.Gln1977Ter	p.Q1977*	ENST00000219905	NM_001164273.1	1977	Cag/Tag	17/24	0.269168611943363	1	FACETS	0.604	0.524	0.69	0.604	0.524	0.69	SUBCLONAL	1	TRUE	0	0.430673083648391	1		698	374	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221084	5221084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371881792	NA	P-0009117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	64	246	0	ENST00000357368.4:c.3382G>A	p.Val1128Ile	p.V1128I	ENST00000357368	NM_002850.3	1128	Gtc/Atc	20/38	0.373699293888596	3	FACETS	1	0.942	1	0.381	0.332	0.433	CLONAL	1	TRUE	0	0.430673083648391	3		246	316	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132464	11132468	+	stop_gained	Nonsense_Mutation	ONP	ACGCA	ACGCA	TAGCT	novel	NA	P-0009117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	28	377	0	ENST00000358026.2:c.2680_2684delinsTAGCT	p.Thr894_Gln895delinsTer	p.T894_Q895delins*	ENST00000358026	NM_001128849.1	894	ACGCAg/TAGCTg	19/36	0.373699293888596	3	FACETS	0.338	0.27	0.417	0.113	0.09	0.139	SUBCLONAL	1	TRUE	0	0.430673083648391	3		377	467	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030585	47030585	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	17	214	0	ENST00000377604.3:c.360T>A	p.Asp120Glu	p.D120E	ENST00000377604	NM_001204468.1	120	gaT/gaA	4/24	1	1	FACETS	0.227	0.169	0.296	0.227	0.169	0.296	SUBCLONAL	1	TRUE	0	0.430673083648391	1		214	273	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217354	123217354	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	21	288	0	ENST00000218089.9:c.3008T>G	p.Leu1003Arg	p.L1003R	ENST00000218089	NM_001042749.1	1003	cTg/cGg	29/35	1	1	FACETS	0.411	0.318	0.518	0.411	0.318	0.518	SUBCLONAL	1	TRUE	0	0.430673083648391	1		288	186	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0009121-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	52	375	2	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	FALSE	1	0.142805364995443	2		377	547	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554666	63554666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009121-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	34	301	0	ENST00000307078.5:c.73C>T	p.Pro25Ser	p.P25S	ENST00000307078	NM_004655.3	25	Cca/Tca	2/11	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	FALSE	1	0.142805364995443	2		301	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1555525585	NA	P-0009122-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	154	259	0	ENST00000269305.4:c.673-2A>G		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.534020615803832	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.534020615803832	1		259	392	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11999013	11999013	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0009122-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	185	305	0	ENST00000353533.5:c.513+2T>C		p.X171_splice	ENST00000353533	NM_003010.3	171			0.534020615803832	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.534020615803832	1		305	484	SUCCESS
ATR	545	MSKCC	GRCh37	3	142172040	142172040	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009122-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	343	461	0	ENST00000350721.4:c.7691A>G	p.Glu2564Gly	p.E2564G	ENST00000350721	NM_001184.3	2564	gAa/gGa	46/47	0.534020615803832	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.534020615803832	1		461	840	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0009149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	194	547	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.337082417419826	1	FACETS	0.939	0.869	1	0.939	0.869	1	CLONAL	1	TRUE	0	0.337082417419826	1		547	1019	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	146	490	0	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	0.33607063997515	1	FACETS	0.898	0.82	0.98	0.898	0.82	0.98	CLONAL	1	TRUE	0	0.337082417419826	1		490	802	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473779	67473779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906850	NA	P-0009149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	149	401	0	ENST00000327367.4:c.859C>T	p.Arg287Trp	p.R287W	ENST00000327367	NM_005902.3	287	Cgg/Tgg	6/9	0.337082417419826	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.337082417419826	1		401	610	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940012	76940012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs122445105	NA	P-0009149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	150	326	0	ENST00000373344.5:c.736C>T	p.Arg246Cys	p.R246C	ENST00000373344	NM_000489.3	246	Cgc/Tgc	9/35	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.337082417419826	1		326	581	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17350503	17350503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201517260	NA	P-0009149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	165	508	2	ENST00000375499.3:c.607G>A	p.Gly203Arg	p.G203R	ENST00000375499	NM_003000.2	203	Gga/Aga	6/8	0.33607063997515	1	FACETS	0.939	0.863	1	0.939	0.863	1	CLONAL	1	TRUE	0	0.337082417419826	1		510	867	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99823108	99823108	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757655058	NA	P-0009149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	59	486	0	ENST00000280892.6:c.104C>T	p.Pro35Leu	p.P35L	ENST00000280892	NM_001130678.1	35	cCg/cTg	2/7	0.33607063997515	1	FACETS	0.397	0.34	0.458	0.397	0.34	0.458	SUBCLONAL	1	TRUE	0	0.337082417419826	1		486	734	SUCCESS
APC	324	MSKCC	GRCh37	5	112175322	112175322	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	105	325	0	ENST00000257430.4:c.4031C>A	p.Ser1344Ter	p.S1344*	ENST00000257430	NM_000038.5	1344	tCa/tAa	16/16	0.337082417419826	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.337082417419826	1		325	483	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271216	38271216	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377620009	NA	P-0009149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	74	259	0	ENST00000425967.3:c.2492C>T	p.Pro831Leu	p.P831L	ENST00000425967	NM_001174067.1	831	cCg/cTg	19/19	0.337082417419826	1	FACETS	0.871	0.766	0.983	0.871	0.766	0.983	CLONAL	1	TRUE	0	0.337082417419826	1		259	419	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0009155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	475	303	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	NA	2	FACETS	0.877	0.845	0.908			1	INDETERMINATE	2	TRUE	NA	0.654220463715279	2		303	828	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115820	8115833	+	frameshift_variant	Frame_Shift_Del	DEL	GCTCGTTTAACCCG	GCTCGTTTAACCCG	-	novel	NA	P-0009155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1398	546	587	0	ENST00000346208.3:c.1168_1181del	p.Ser390ArgfsTer112	p.S390Rfs*112	ENST00000346208		389	aGCTCGTTTAACCCG/a	6/6	0.21965972421996	3	FACETS	1	0.992	1	0.57	0.545	0.595	INDETERMINATE	1	TRUE	1	0.654220463715279	3		587	1944	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0009164-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	92	397	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	1	2	FACETS	0.671	0.595	0.753	0.671	0.595	0.753	SUBCLONAL	1	FALSE	1	0.259081719685979	2		397	1058	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs967461896	NA	P-0009164-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	95	246	0	ENST00000269305.4:c.526T>A	p.Cys176Ser	p.C176S	ENST00000269305	NM_001126112.2	176	Tgc/Agc	5/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	1	0.259081719685979	2		246	661	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0009173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	129	654	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.895	0.81	0.984	1	0.988	1	CLONAL	2	TRUE	1	0.14	2		654	1030	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0009173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	50	381	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.644	0.544	0.755	0.644	0.544	0.755	SUBCLONAL	1	TRUE	1	0.14	2		382	1109	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	53	407	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.715	0.607	0.834	0.715	0.607	0.834	SUBCLONAL	1	TRUE	1	0.14	2		407	1059	SUCCESS
APC	324	MSKCC	GRCh37	5	112175876	112175876	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085992	NA	P-0009173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	63	424	0	ENST00000257430.4:c.4585C>T	p.Gln1529Ter	p.Q1529*	ENST00000257430	NM_000038.5	1529	Cag/Tag	16/16	1	2	FACETS	0.938	0.809	1	0.938	0.809	1	CLONAL	1	TRUE	1	0.14	2		424	960	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925700	114925700	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1003928208	NA	P-0009173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1390	103	746	0	ENST00000543371.1:c.1778C>T	p.Pro593Leu	p.P593L	ENST00000543371	NM_001198531.1	593	cCg/cTg	14/14	1	2	FACETS	0.986	0.879	1	0.986	0.879	1	CLONAL	1	TRUE	1	0.14	2		746	1493	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29701105	29701105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771006452	NA	P-0009173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	42	315	0	ENST00000356175.3:c.8389G>A	p.Ala2797Thr	p.A2797T	ENST00000356175	NM_000267.3	2797	Gca/Aca	57/57	1	2	FACETS	0.787	0.656	0.935	0.787	0.656	0.935	CLONAL	1	TRUE	1	0.14	2		315	762	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117738	70117750	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	TCCCCGTGTGCAT	TCCCCGTGTGCAT	GA	novel	NA	P-0009173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	50	523	0	ENST00000245479.2:c.206_218delinsGA	p.Phe69Ter	p.F69*	ENST00000245479	NM_000346.3	69	tTCCCCGTGTGCATc/tGAc	1/3	1	2	FACETS	0.751	0.635	0.88	0.751	0.635	0.88	SUBCLONAL	1	TRUE	1	0.14	2		523	951	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0009181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	242	246	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.350831901213053	5	FACETS	1	0.965	1			1	CLONAL	4	TRUE	NA	0.415331497713384	5		246	462	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371662	55371662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	59	241	0	ENST00000297316.4:c.352G>A	p.Val118Met	p.V118M	ENST00000297316	NM_022454.3	118	Gtg/Atg	2/2	0.244627805100275	3	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.415331497713384	3		241	256	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138778	64138778	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	153	388	0	ENST00000334205.4:c.2145G>C	p.Glu715Asp	p.E715D	ENST00000334205	NM_003942.2	715	gaG/gaC	17/17	0.415331497713384	6	FACETS	1	0.96	1			1	CLONAL	2	TRUE	NA	0.415331497713384	6		388	627	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881426	37881426	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	386	207	0	ENST00000269571.5:c.2618A>G	p.Asp873Gly	p.D873G	ENST00000269571		873	gAc/gGc	21/27	0.415331497713384	7	FACETS	1	0.985	1			1	CLONAL	6	TRUE	NA	0.415331497713384	7		207	606	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231802	36231802	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	458	406	1	ENST00000300305.3:c.582A>T	p.Lys194Asn	p.K194N	ENST00000300305		194	aaA/aaT	5/8	0.415331497713384	9	FACETS	1	0.99	1			1	CLONAL	4	TRUE	NA	0.415331497713384	9		407	1222	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063717	+	splice_donor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0009181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	144	124	0	ENST00000412916.2:c.165+1del		p.X55_splice	ENST00000412916		55			NA	2	FACETS	0.932	0.872	0.991			1	INDETERMINATE	3	TRUE	NA	0.415331497713384	2		124	248	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0009182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	125	376	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.622	0.562	0.684	0.622	0.562	0.684	SUBCLONAL	1	TRUE	1	0.474809885270328	2		376	847	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258511	16258511	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	118	282	0	ENST00000375759.3:c.5776C>T	p.Gln1926Ter	p.Q1926*	ENST00000375759	NM_015001.2	1926	Caa/Taa	11/15	1	2	FACETS	0.798	0.721	0.878	0.798	0.721	0.878	SUBCLONAL	1	TRUE	1	0.474809885270328	2		282	623	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667432	241667432	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs775639021	NA	P-0009182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1473	228	576	0	ENST00000366560.3:c.1018A>G	p.Asn340Asp	p.N340D	ENST00000366560	NM_000143.3	340	Aat/Gat	7/10	0.474809885270328	3	FACETS	0.699	0.648	0.751	0.349	0.324	0.376	SUBCLONAL	1	TRUE	1	0.474809885270328	3		576	1701	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243895	46243908	+	frameshift_variant	Frame_Shift_Del	DEL	TGCAACACAAATGT	TGCAACACAAATGT	-	novel	NA	P-0009182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	149	396	0	ENST00000334344.6:c.1989_2002del	p.Ala664PhefsTer38	p.A664Ffs*38	ENST00000334344	NM_152641.2	663	acTGCAACACAAATGTct/acct	15/21	1	2	FACETS	0.598	0.546	0.654	0.598	0.546	0.654	SUBCLONAL	1	TRUE	1	0.474809885270328	2		396	1049	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864359	162864361	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0009182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	131	325	0	ENST00000366898.1:c.152_154del	p.Arg51del	p.R51del	ENST00000366898	NM_004562.2	51	aGGAat/aat	2/12	1	2	FACETS	0.722	0.656	0.792	0.722	0.656	0.792	SUBCLONAL	1	TRUE	1	0.474809885270328	2		325	764	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0009183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	144	596	0	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.174202570843072	2		596	1270	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55270247	55270247	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	75	479	1	ENST00000275493.2:c.3200A>T	p.Gln1067Leu	p.Q1067L	ENST00000275493	NM_005228.3	1067	cAg/cTg	27/28	1	2	FACETS	0.854	0.746	0.971	0.854	0.746	0.971	CLONAL	1	TRUE	1	0.174202570843072	2		480	1008	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412331	139412331	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	55	449	0	ENST00000277541.6:c.1314C>G	p.Cys438Trp	p.C438W	ENST00000277541	NM_017617.3	438	tgC/tgG	8/34	1	2	FACETS	0.738	0.629	0.857	0.738	0.629	0.857	SUBCLONAL	1	TRUE	1	0.174202570843072	2		449	856	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412744	139412744	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	39	324	2	ENST00000277541.6:c.1100G>T	p.Gly367Val	p.G367V	ENST00000277541	NM_017617.3	367	gGt/gTt	7/34	1	2	FACETS	0.631	0.521	0.753	0.631	0.521	0.753	SUBCLONAL	1	TRUE	1	0.174202570843072	2		326	710	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445540	49445540	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	55	466	0	ENST00000301067.7:c.1926del	p.Pro643LeufsTer287	p.P643Lfs*287	ENST00000301067	NM_003482.3	642	tcA/tc	10/54	1	2	FACETS	0.677	0.577	0.787	0.677	0.577	0.787	SUBCLONAL	1	TRUE	1	0.174202570843072	2		466	933	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248099	110248099	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	120	465	0	ENST00000374672.4:c.1373G>T	p.Cys458Phe	p.C458F	ENST00000374672	NM_004235.4	458	tGc/tTc	5/5	1	2	FACETS	0.817	0.738	0.9	0.817	0.738	0.9	CLONAL	1	TRUE	1	0.388630611642556	2		465	756	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248103	110248103	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009190-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	123	463	0	ENST00000374672.4:c.1369C>G	p.Gln457Glu	p.Q457E	ENST00000374672	NM_004235.4	457	Cag/Gag	5/5	1	2	FACETS	0.829	0.75	0.912	0.829	0.75	0.912	CLONAL	1	TRUE	1	0.388630611642556	2		463	764	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0009203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	107	375	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.321071487569118	2	FACETS	0.921	0.835	1	0.921	0.835	1	CLONAL	2	TRUE	0	0.331980101279378	2		377	350	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	146	407	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.220822082864829	3	FACETS	0.874	0.801	0.949	0.874	0.801	0.949	CLONAL	2	TRUE	1	0.331980101279378	3		407	587	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277007	18277007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs146156161	NA	P-0009203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	169	292	0	ENST00000222254.8:c.1454A>G	p.Asn485Ser	p.N485S	ENST00000222254	NM_005027.3	485	aAt/aGt	12/16	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.331980101279378	2		292	681	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59861686	59861686	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0121582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	86	615	0	ENST00000259008.2:c.1573A>G	p.Ile525Val	p.I525V	ENST00000259008	NM_032043.2	525	Ata/Gta	11/20	0.451358482527201	5	FACETS	0.781	0.69	0.879	0.26	0.23	0.293	SUBCLONAL	1	NA	2	0.451358482527201	5		615	818	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258744	115258744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434596	NA	P-0009220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	42	341	0	ENST00000369535.4:c.38G>A	p.Gly13Asp	p.G13D	ENST00000369535	NM_002524.4	13	gGt/gAt	2/7	1	2	FACETS	0.45	0.375	0.535	0.45	0.375	0.535	SUBCLONAL	1	TRUE	1	0.25	2		341	746	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	75	145	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.959	1			1	INDETERMINATE	1	FALSE	NA	0.777310902570013	2		145	170	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0009245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	277	268	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.77694137308761	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	FALSE	2	0.777310902570013	4		268	608	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0009245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	339	397	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.788918417086738	4	FACETS	1	0.958	1			1	CLONAL	2	FALSE	NA	0.777310902570013	4		397	770	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041073	29041073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	128	350	0	ENST00000282397.4:c.355G>A	p.Glu119Lys	p.E119K	ENST00000282397	NM_002019.4	119	Gaa/Aaa	3/30	0.659868109063341	4	FACETS	1	0.96	1	0.365	0.332	0.399	CLONAL	1	FALSE	1	0.777310902570013	4		350	535	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587118	189587118	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761885185	NA	P-0009245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	120	345	0	ENST00000264731.3:c.1135C>T	p.Arg379Cys	p.R379C	ENST00000264731	NM_003722.4	379	Cgt/Tgt	9/14	NA	2	FACETS	1	0.941	1			1	INDETERMINATE	1	FALSE	NA	0.777310902570013	2		345	299	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0009245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	299	341	0	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	0.788918417086738	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	FALSE	2	0.777310902570013	4		341	680	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117645576	117645576	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	162	491	0	ENST00000368508.3:c.5560G>A	p.Asp1854Asn	p.D1854N	ENST00000368508	NM_002944.2	1854	Gat/Aat	34/43	0.221154420562142	5	FACETS	1	0.98	1	0.77	0.715	0.825	INDETERMINATE	2	FALSE	2	0.777310902570013	5		491	391	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070361	37070361	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	322	410	0	ENST00000231790.2:c.1496G>T	p.Arg499Met	p.R499M	ENST00000231790	NM_000249.3	499	aGg/aTg	13/19	0.788918417086738	4	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	FALSE	2	0.777310902570013	4		410	734	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165758	47165758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	367	459	0	ENST00000409792.3:c.368C>T	p.Thr123Ile	p.T123I	ENST00000409792	NM_014159.6	123	aCc/aTc	3/21	0.788918417086738	4	FACETS	0.966	0.92	1			1	CLONAL	2	FALSE	NA	0.777310902570013	4		459	869	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056989	180056989	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	294	467	0	ENST00000261937.6:c.630G>A	p.Trp210Ter	p.W210*	ENST00000261937	NM_182925.4	210	tgG/tgA	5/30	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	FALSE	NA	0.777310902570013	2		467	359	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673766	30673766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	488	343	0	ENST00000376406.3:c.3194C>T	p.Pro1065Leu	p.P1065L	ENST00000376406	NM_014641.2	1065	cCc/cTc	10/15	0.777310902570013	10	FACETS	0.917	0.88	0.955	0.917	0.88	0.955	CLONAL	5	FALSE	5	0.777310902570013	10		343	1125	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729784	41729784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866082326	NA	P-0009245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	228	520	0	ENST00000242208.4:c.745G>A	p.Glu249Lys	p.E249K	ENST00000242208	NM_002192.2	249	Gag/Aag	3/3	0.181582312493431	4	FACETS	0.896	0.841	0.951	0.896	0.841	0.951	INDETERMINATE	2	FALSE	2	0.777310902570013	4		520	582	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513177	106513177	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	223	254	0	ENST00000359195.3:c.2081T>A	p.Phe694Tyr	p.F694Y	ENST00000359195	NM_002649.2	694	tTt/tAt	4/11	0.524239806890354	6	FACETS	0.845	0.793	0.898	0.845	0.793	0.898	CLONAL	3	FALSE	3	0.777310902570013	6		254	578	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477861	140477861	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs397507474	NA	P-0009245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	206	315	0	ENST00000288602.6:c.1447A>G	p.Lys483Glu	p.K483E	ENST00000288602	NM_004333.4	483	Aaa/Gaa	12/18	0.524239806890354	6	FACETS	0.933	0.874	0.991	0.933	0.874	0.991	CLONAL	3	FALSE	3	0.777310902570013	6		315	484	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624537	93624537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237227040	NA	P-0009245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	157	390	0	ENST00000375746.1:c.628G>A	p.Glu210Lys	p.E210K	ENST00000375746	NM_001174167.1	210	Gaa/Aaa	4/14	NA	2	FACETS	1	0.938	1			1	INDETERMINATE	1	FALSE	NA	0.777310902570013	2		390	399	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771689	135771689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201867031	NA	P-0009245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	392	359	0	ENST00000298552.3:c.3428C>T	p.Pro1143Leu	p.P1143L	ENST00000298552	NM_001162426.1	1143	cCg/cTg	23/23	0.788918417086738	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	FALSE	2	0.777310902570013	4		359	877	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133208969	133208969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749342382	NA	P-0009245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	230	403	0	ENST00000320574.5:c.6262C>T	p.Pro2088Ser	p.P2088S	ENST00000320574	NM_006231.2	2088	Cct/Tct	45/49	0.559365511156234	4	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	FALSE	2	0.777310902570013	4		403	522	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907102	32907102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507269	NA	P-0009245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	292	281	0	ENST00000380152.3:c.1487C>T	p.Ser496Phe	p.S496F	ENST00000380152		496	tCt/tTt	10/27	0.659868109063341	4	FACETS	0.92	0.879	0.96	0.92	0.879	0.96	CLONAL	3	FALSE	1	0.777310902570013	4		281	484	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857299	9857299	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	139	364	0	ENST00000330684.3:c.4102C>T	p.Leu1368Phe	p.L1368F	ENST00000330684	NM_001134407.1	1368	Ctc/Ttc	13/13	NA	2	FACETS	1	0.929	1			1	INDETERMINATE	1	FALSE	NA	0.777310902570013	2		364	355	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068313	16068313	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	68	88	0	ENST00000268712.3:c.598C>T	p.Leu200Phe	p.L200F	ENST00000268712	NM_006311.3	200	Ctt/Ttt	5/46	0.656405804316934	6	FACETS	0.898	0.8	0.997	0.898	0.8	0.997	CLONAL	3	FALSE	3	0.777310902570013	6		88	166	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684077	29684077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750972729	NA	P-0009245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	168	326	1	ENST00000356175.3:c.7775C>T	p.Pro2592Leu	p.P2592L	ENST00000356175	NM_000267.3	2592	cCg/cTg	52/57	0.788918417086738	4	FACETS	0.902	0.838	0.966	0.902	0.838	0.966	CLONAL	2	FALSE	2	0.777310902570013	4		327	426	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325802	30325802	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	195	254	0	ENST00000322652.5:c.2000A>T	p.Asn667Ile	p.N667I	ENST00000322652	NM_015355.2	667	aAt/aTt	16/16	0.788918417086738	4	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	FALSE	2	0.777310902570013	4		254	443	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645606	215645607	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	189	294	0	ENST00000260947.4:c.991_992delinsTT	p.Pro331Phe	p.P331F	ENST00000260947	NM_000465.2	331	CCc/TTc	4/11	0.77694137308761	4	FACETS	0.859	0.801	0.918	0.859	0.801	0.918	CLONAL	2	FALSE	2	0.777310902570013	4		294	503	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120314	94120315	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	247	467	0	ENST00000369303.4:c.736_737delinsTT	p.Pro246Phe	p.P246F	ENST00000369303	NM_004440.3	246	CCc/TTc	3/17	0.221154420562142	5	FACETS	1	0.982	1	0.737	0.693	0.78	INDETERMINATE	2	FALSE	2	0.777310902570013	5		467	623	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218088	108218089	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0009245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	144	259	0	ENST00000278616.4:c.8667_8668delinsAA	p.Asp2889_Leu2890delinsGluIle	p.D2889_L2890delinsEI	ENST00000278616	NM_000051.3	2889	gaTCta/gaAAta	59/63	0.725872605389881	3	FACETS	0.88	0.834	0.923	0.88	0.834	0.923	CLONAL	3	FALSE	0	0.777310902570013	3		259	195	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032537	47032537	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009246-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	106	455	2	ENST00000377604.3:c.443A>G	p.Gln148Arg	p.Q148R	ENST00000377604	NM_001204468.1	148	cAg/cGg	5/24	1	2	FACETS	0.343	0.307	0.382	0.343	0.307	0.382	SUBCLONAL	1	TRUE	1	0.64	2		457	965	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	80	145	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.58	2		145	225	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0009264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	185	411	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	0.58	2		411	553	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860154	57860813	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAAGCCACACAAGTGCACGGTGAGGCACCAGTGTCCCAAGTCCAGGGTCTCTTCCTAAATCAGGGCTCTCCTTCAAGGTAGGGCCCAAGGCAGACTTTTGCTTTTATAAGTCCTTTCTTCCATAAACAAATATTAAAAATAATGTTTGTGTGACTGTGTTGGCATAAAGATGAATATGATGATATATATTAAAACACTCTTGGACCTAAAAGCTCATTTTTTTCCCCTTGATTTTAAAAGACATTAAAACAGGCCAGGCACGGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGAGCCAGGCAGATCACAAGGTCAGGAGTTCGAGACCAGCTTGGCCAATATTGGTGAAACCCTGTCTCTACTAAAAAATATAAAAATTAGCTGGGCGTGGTGATGGGCGCCTGTAGTCCCTGCTACTTGGGAGGATGAGGCAGAAGAATCACTTGAACCAAGGAGGTGGAGGTTGCAGTGAGCTGAGATGGCGCCACTGCACTCCAGCCTGGGCGACAGAGCAAAACTCCGCCTCAAAAAAAAAATTTTTTTTAAAAAAGACATTAAAACATGTTCGTGGGCCTCTTAAAGTATTGTTGGCCTTCAGTACTGTGCCTACTACTCTGCCTAATGGATAAACCCTGCATCAAGGACAACAGCCC	GAAGCCACACAAGTGCACGGTGAGGCACCAGTGTCCCAAGTCCAGGGTCTCTTCCTAAATCAGGGCTCTCCTTCAAGGTAGGGCCCAAGGCAGACTTTTGCTTTTATAAGTCCTTTCTTCCATAAACAAATATTAAAAATAATGTTTGTGTGACTGTGTTGGCATAAAGATGAATATGATGATATATATTAAAACACTCTTGGACCTAAAAGCTCATTTTTTTCCCCTTGATTTTAAAAGACATTAAAACAGGCCAGGCACGGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGAGCCAGGCAGATCACAAGGTCAGGAGTTCGAGACCAGCTTGGCCAATATTGGTGAAACCCTGTCTCTACTAAAAAATATAAAAATTAGCTGGGCGTGGTGATGGGCGCCTGTAGTCCCTGCTACTTGGGAGGATGAGGCAGAAGAATCACTTGAACCAAGGAGGTGGAGGTTGCAGTGAGCTGAGATGGCGCCACTGCACTCCAGCCTGGGCGACAGAGCAAAACTCCGCCTCAAAAAAAAAATTTTTTTTAAAAAAGACATTAAAACATGTTCGTGGGCCTCTTAAAGTATTGTTGGCCTTCAGTACTGTGCCTACTACTCTGCCTAATGGATAAACCCTGCATCAAGGACAACAGCCC	-	novel	NA	P-0009264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	127	733	0	ENST00000228682.2:c.895_913-302del		p.X299_splice	ENST00000228682	NM_005269.2	299		8/12	0.57460358826705	3	FACETS	0.526	0.475	0.579			1	SUBCLONAL	1	TRUE	NA	0.58	3		733	1075	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798370	42798370	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	100	503	0	ENST00000575354.2:c.4241del	p.Met1414ArgfsTer40	p.M1414Rfs*40	ENST00000575354	NM_015125.3	1414	aTg/ag	18/20	0.57460358826705	1	FACETS	0.576	0.518	0.637	0.576	0.518	0.637	SUBCLONAL	1	TRUE	0	0.58	1		503	425	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0009288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	57	412	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.481	0.41	0.558	0.481	0.41	0.558	SUBCLONAL	1	FALSE	1	0.198146238578959	2		412	1197	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0009288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	73	393	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			1	2	FACETS	0.802	0.7	0.913	0.802	0.7	0.913	CLONAL	1	FALSE	1	0.198146238578959	2		393	919	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966661	44966662	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0009288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	59	296	0	ENST00000377967.4:c.3886_3887del	p.Leu1296SerfsTer36	p.L1296Sfs*36	ENST00000377967	NM_021140.2	1295	tgTCtt/tgtt	27/29	1	1	FACETS	0.931	0.802	1	0.931	0.802	1	CLONAL	1	FALSE	0	0.198146238578959	1		296	576	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0009289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	298	412	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.250151215167843	3	FACETS	0.957	0.9	1	0.957	0.9	1	CLONAL	2	FALSE	1	0.307780803869489	3		412	1168	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612761	228612761	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1461	415	850	1	ENST00000366696.1:c.266C>A	p.Ala89Asp	p.A89D	ENST00000366696	NM_003493.2	89	gCc/gAc	1/1	0.307780803869489	5	FACETS	1	0.977	1	0.525	0.498	0.553	CLONAL	2	FALSE	1	0.307780803869489	5		851	1876	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661764	227661764	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	160	207	0	ENST00000305123.5:c.1691G>T	p.Ser564Ile	p.S564I	ENST00000305123	NM_005544.2	564	aGt/aTt	1/2	0.307780803869489	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	FALSE	1	0.307780803869489	3		207	541	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636977	176636977	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	238	340	0	ENST00000439151.2:c.1577G>T	p.Arg526Met	p.R526M	ENST00000439151	NM_022455.4	526	aGg/aTg	5/23	0.25765965444167	3	FACETS	0.998	0.933	1	0.998	0.933	1	CLONAL	2	FALSE	1	0.307780803869489	3		340	894	SUCCESS
ATM	472	MSKCC	GRCh37	11	108214050	108214050	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	186	364	0	ENST00000278616.4:c.8370A>T	p.Arg2790Ser	p.R2790S	ENST00000278616	NM_000051.3	2790	agA/agT	57/63	0.250151215167843	3	FACETS	1	0.98	1	0.589	0.543	0.638	CLONAL	1	FALSE	1	0.307780803869489	3		364	1183	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216560	108216560	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	406	431	1	ENST00000278616.4:c.8509G>A	p.Glu2837Lys	p.E2837K	ENST00000278616	NM_000051.3	2837	Gaa/Aaa	58/63	0.250151215167843	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	FALSE	1	0.307780803869489	3		432	1380	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861127	57861127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1283	201	619	0	ENST00000228682.2:c.924C>A	p.Cys308Ter	p.C308*	ENST00000228682	NM_005269.2	308	tgC/tgA	9/12	0.250151215167843	3	FACETS	1	0.937	1	0.508	0.469	0.548	CLONAL	1	FALSE	1	0.307780803869489	3		619	1484	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219321	1219321	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0009289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	237	379	0	ENST00000326873.7:c.375-2A>T		p.X125_splice	ENST00000326873	NM_000455.4	125			0.307780803869489	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	FALSE	0	0.307780803869489	2		379	689	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309774	30309774	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	95	273	0	ENST00000307677.4:c.248T>C	p.Met83Thr	p.M83T	ENST00000307677	NM_138578.1	83	aTg/aCg	2/3	0.208417178975946	2	FACETS	0.797	0.709	0.89	0.398	0.354	0.445	SUBCLONAL	1	FALSE	0	0.307780803869489	2		273	775	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368176	31368176	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	165	506	0	ENST00000328111.2:c.47G>T	p.Gly16Val	p.G16V	ENST00000328111	NM_006892.3	16	gGg/gTg	2/23	0.208417178975946	2	FACETS	0.95	0.871	1	0.475	0.435	0.516	CLONAL	1	FALSE	0	0.307780803869489	2		506	1129	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164462	36164463	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0009289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	44	137	0	ENST00000300305.3:c.1412_1413del	p.Arg471ProfsTer128	p.R471Pfs*128	ENST00000300305		471	cGC/c	8/8	1	2	FACETS	0.986	0.832	1	0.986	0.832	1	CLONAL	1	FALSE	1	0.307780803869489	2		137	290	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902729	50902729	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766784938	NA	P-0009301-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	135	619	1	ENST00000440232.2:c.304G>A	p.Asp102Asn	p.D102N	ENST00000440232	NM_002691.3	102	Gac/Aac	3/27	1	2	FACETS	0.744	0.675	0.817	0.744	0.675	0.817	SUBCLONAL	1	TRUE	1	0.321649458676493	2		620	1128	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120459	94120459	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	364	447	2	ENST00000369303.4:c.592G>T	p.Val198Phe	p.V198F	ENST00000369303	NM_004440.3	198	Gtc/Ttc	3/17	1	2	FACETS	0.969	0.917	1	0.969	0.917	1	CLONAL	1	TRUE	1	0.515405692278674	2		449	1458	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842344	151842344	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs749571160	NA	P-0009319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	226	277	0	ENST00000262189.6:c.14068C>T	p.Arg4690Ter	p.R4690*	ENST00000262189	NM_170606.2	4690	Cga/Tga	54/59	1	2	FACETS	0.886	0.825	0.948	0.886	0.825	0.948	CLONAL	1	TRUE	1	0.515405692278674	2		277	990	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0009327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	190	233	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.69135163871074	2		233	523	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0009327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1917	520	649	0	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.538879643676146	4	FACETS	1	0.979	1	0.522	0.498	0.547	CLONAL	1	TRUE	2	0.69135163871074	4		649	2437	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637445	176637445	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587784079	NA	P-0009327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	185	350	0	ENST00000439151.2:c.2048del	p.Lys683ArgfsTer2	p.K683Rfs*2	ENST00000439151	NM_022455.4	682	gAa/ga	5/23	1	2	FACETS	0.909	0.844	0.975	0.909	0.844	0.975	CLONAL	1	TRUE	1	0.69135163871074	2		350	589	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092848	27092849	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0009327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	283	414	0	ENST00000324856.7:c.2869_2870del	p.Asn957PhefsTer49	p.N957Ffs*49	ENST00000324856	NM_006015.4	957	AAt/t	9/20	1	2	FACETS	0.926	0.873	0.981	0.926	0.873	0.981	CLONAL	1	TRUE	1	0.69135163871074	2		414	884	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0009352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	197	353	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.3	1	FACETS	0.75	0.696	0.807	1	0.991	1	SUBCLONAL	2	TRUE	0	0.27	1		353	841	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0009352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	80	219	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.287754396925819	3	FACETS	1	0.972	1	0.684	0.603	0.769	CLONAL	1	TRUE	1	0.27	3		219	492	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999243	100999243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	155	633	0	ENST00000325455.5:c.559C>T	p.Arg187Trp	p.R187W	ENST00000325455	NM_001202474.3	187	Cgg/Tgg	1/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.27	2		633	1015	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941694	48941694	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0009360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	208	356	0	ENST00000267163.4:c.1004T>G	p.Leu335Ter	p.L335*	ENST00000267163	NM_000321.2	335	tTa/tGa	10/27	0.288635721730497	2	FACETS	0.803	0.747	0.86	0.803	0.747	0.86	CLONAL	2	TRUE	0	0.335067984996999	2		356	773	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890170	76890170	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	263	525	2	ENST00000373344.5:c.4724G>T	p.Cys1575Phe	p.C1575F	ENST00000373344	NM_000489.3	1575	tGc/tTc	17/35	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.335067984996999	2		527	1369	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0009361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	117	439	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	1	2	FACETS	0.603	0.542	0.668	0.603	0.542	0.668	SUBCLONAL	1	TRUE	1	0.305635101706793	2		439	1270	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533765	533765	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0009369-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1217	443	697	0	ENST00000451590.1:c.290+1G>T		p.X97_splice	ENST00000451590	NM_001130442.1	97			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		697	1660	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0009395-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	34	412	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.123103157423644	0	FACETS	0.532	0.433	0.644			1	SUBCLONAL	1	TRUE	0	0.16	0		412	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0009395-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	82	547	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.16	2		547	827	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223203	5223203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1416280955	NA	P-0009410-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	199	344	0	ENST00000357368.4:c.2600G>A	p.Arg867His	p.R867H	ENST00000357368	NM_002850.3	867	cGc/cAc	18/38	0.0995459256113047	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.91	0		344	457	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509411	46509411	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009410-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	344	393	0	ENST00000262741.5:c.1320C>A	p.His440Gln	p.H440Q	ENST00000262741	NM_003629.3	440	caC/caA	10/10	1	2	FACETS	0.947	0.902	0.993	0.947	0.902	0.993	CLONAL	1	TRUE	1	0.91	2		393	798	SUCCESS
APC	324	MSKCC	GRCh37	5	112174298	112174298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs564314108	NA	P-0009410-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	350	342	0	ENST00000257430.4:c.3007G>A	p.Asp1003Asn	p.D1003N	ENST00000257430	NM_000038.5	1003	Gac/Aac	16/16	1	2	FACETS	0.996	0.95	1	0.996	0.95	1	CLONAL	1	TRUE	1	0.91	2		342	772	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048168	180048168	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009410-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	220	347	0	ENST00000261937.6:c.2105C>A	p.Ala702Asp	p.A702D	ENST00000261937	NM_182925.4	702	gCc/gAc	14/30	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.91	2		347	469	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835930	151835930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770369091	NA	P-0009410-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	332	440	0	ENST00000262189.6:c.14594G>A	p.Gly4865Glu	p.G4865E	ENST00000262189	NM_170606.2	4865	gGa/gAa	58/59	1	2	FACETS	0.932	0.886	0.978	0.932	0.886	0.978	CLONAL	1	TRUE	1	0.91	2		440	783	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573211	41573231	+	inframe_deletion	In_Frame_Del	DEL	GGCCAGCATGCAGCGGACTGG	GGCCAGCATGCAGCGGACTGG	-	novel	NA	P-0009410-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	198	220	0	ENST00000263253.7:c.5496_5516del	p.Met1832_Gly1839delinsIle	p.M1832_G1839delinsI	ENST00000263253	NM_001429.3	1832	atGGCCAGCATGCAGCGGACTGGt/att	31/31	0.3	2	FACETS	1	0.955	1			1	INDETERMINATE	1	TRUE	NA	0.91	2		220	426	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372780	81372780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752123971	NA	P-0009416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	26	192	0	ENST00000222390.5:c.754G>A	p.Asp252Asn	p.D252N	ENST00000222390	NM_000601.4	252	Gac/Aac	7/18	0.941515465560838	1	FACETS	0.112	0.089	0.139	0.112	0.089	0.139	SUBCLONAL	1	TRUE	0	0.941515465560838	1		192	260	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103331	119103331	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	233	362	0	ENST00000264033.4:c.369G>A	p.Met123Ile	p.M123I	ENST00000264033	NM_005188.3	123	atG/atA	2/16	1	2	FACETS	0.885	0.833	0.938	0.885	0.833	0.938	CLONAL	1	TRUE	1	0.941515465560838	2		362	559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577592	7577602	+	frameshift_variant	Frame_Shift_Del	DEL	GTACAGTCAGA	GTACAGTCAGA	-	novel	NA	P-0009416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	103	208	0	ENST00000269305.4:c.679_689del	p.Ser227HisfsTer9	p.S227Hfs*9	ENST00000269305	NM_001126112.2	227	TCTGACTGTACc/c	7/11	0.92857126448805	1	FACETS	0.654	0.604	0.703	0.654	0.604	0.703	SUBCLONAL	1	TRUE	0	0.941515465560838	1		208	177	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0009426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	86	273	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.28401388450708	5	FACETS	1	0.969	1			1	CLONAL	2	FALSE	NA	0.28401388450708	5		273	346	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646188	215646188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	59	172	0	ENST00000260947.4:c.410G>A	p.Gly137Glu	p.G137E	ENST00000260947	NM_000465.2	137	gGa/gAa	4/11	0.28401388450708	6	FACETS	0.94	0.819	1	0.705	0.614	0.801	CLONAL	3	FALSE	2	0.28401388450708	6		172	231	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979609	55979609	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	55	300	0	ENST00000263923.4:c.838C>A	p.Gln280Lys	p.Q280K	ENST00000263923	NM_002253.2	280	Cag/Aag	7/30	0.179184866790899	4	FACETS	0.911	0.786	1	0.911	0.786	1	CLONAL	2	FALSE	2	0.28401388450708	4		300	273	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158419	106158419	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs751355910	NA	P-0009426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	60	194	0	ENST00000380013.4:c.3320C>A	p.Ser1107Ter	p.S1107*	ENST00000380013	NM_001127208.2	1107	tCa/tAa	3/11	0.28401388450708	5	FACETS	0.909	0.794	1	1	0.967	1	CLONAL	3	FALSE	3	0.28401388450708	5		194	221	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683698	162683698	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	24	207	0	ENST00000366898.1:c.271G>C	p.Ala91Pro	p.A91P	ENST00000366898	NM_004562.2	91	Gcg/Ccg	3/12	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	FALSE	1	0.28401388450708	2		207	148	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742501	145742501	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760851442	NA	P-0009426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	22	182	0	ENST00000428558.2:c.287G>A	p.Arg96Gln	p.R96Q	ENST00000428558	NM_004260.3	96	cGg/cAg	4/22	0.28401388450708	6	FACETS	0.789	0.617	0.984	0.526	0.411	0.656	CLONAL	2	FALSE	3	0.28401388450708	6		182	154	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986866	36986866	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	40	57	0	ENST00000354822.5:c.823C>A	p.Pro275Thr	p.P275T	ENST00000354822	NM_001079668.2	275	Ccg/Acg	3/3	0.281798840364428	4	FACETS	1	0.907	1	1	0.98	1	CLONAL	6	FALSE	2	0.28401388450708	4		57	59	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219414	1219414	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0009426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	33	149	0	ENST00000326873.7:c.464+2T>A		p.X155_splice	ENST00000326873	NM_000455.4	155			0.28401388450708	3	FACETS	0.951	0.799	1			1	CLONAL	3	FALSE	NA	0.28401388450708	3		149	93	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599874	10599874	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	59	276	0	ENST00000171111.5:c.1702G>T	p.Val568Phe	p.V568F	ENST00000171111	NM_203500.1	568	Gtc/Ttc	5/6	0.248042579437234	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	FALSE	0	0.28401388450708	2		276	190	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899091	40899091	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	18	296	0	ENST00000373198.4:c.2179C>A	p.Pro727Thr	p.P727T	ENST00000373198	NM_133170.3	727	Cca/Aca	14/32	0.28401388450708	1	FACETS	0.906	0.691	1	0.906	0.691	1	CLONAL	1	FALSE	0	0.28401388450708	1		296	120	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227920	123227920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	19	327	0	ENST00000218089.9:c.3631G>A	p.Val1211Ile	p.V1211I	ENST00000218089	NM_001042749.1	1211	Gtt/Att	33/35	NA	2	FACETS	0.527	0.4	0.675			1	INDETERMINATE	1	FALSE	NA	0.28401388450708	2		327	254	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0009433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	176	412	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.460109195773821	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.460109195773821	3		412	453	SUCCESS
APC	324	MSKCC	GRCh37	5	112173830	112173830	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	193	245	0	ENST00000257430.4:c.2539G>T	p.Glu847Ter	p.E847*	ENST00000257430	NM_000038.5	847	Gaa/Taa	16/16	0.460109195773821	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.460109195773821	3		245	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578260	7578260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204041	NA	P-0009433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	239	265	0	ENST00000269305.4:c.589G>A	p.Val197Met	p.V197M	ENST00000269305	NM_001126112.2	197	Gtg/Atg	6/11	NA	2	FACETS	1	0.956	1			1	INDETERMINATE	2	TRUE	NA	0.460109195773821	2		265	512	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539105	23539105	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	110	304	0	ENST00000380871.4:c.334G>T	p.Ala112Ser	p.A112S	ENST00000380871	NM_006167.3	112	Gcc/Tcc	2/2	0.460109195773821	3	FACETS	0.908	0.817	1	0.454	0.408	0.502	CLONAL	1	TRUE	1	0.460109195773821	3		304	648	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347080	89347080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs922813408	NA	P-0009433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	249	259	2	ENST00000301030.4:c.5870C>T	p.Ala1957Val	p.A1957V	ENST00000301030	NM_001256183.1	1957	gCg/gTg	9/13	0.272550559483908	5	FACETS	1	0.99	1	0.833	0.783	0.885	INDETERMINATE	2	TRUE	2	0.460109195773821	5		261	732	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410127	63410127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	187	283	0	ENST00000330258.3:c.3040G>C	p.Gly1014Arg	p.G1014R	ENST00000330258	NM_152424.3	1014	Ggg/Cgg	2/2	0.460109195773821	4	FACETS	0.754	0.698	0.812	0.754	0.698	0.812	SUBCLONAL	2	TRUE	2	0.460109195773821	4		283	787	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149246	119149246	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009435-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	250	494	0	ENST00000264033.4:c.1254C>A	p.Phe418Leu	p.F418L	ENST00000264033	NM_005188.3	418	ttC/ttA	9/16	0.293796628329113	2	FACETS	0.867	0.812	0.924	0.867	0.812	0.924	CLONAL	2	TRUE	0	0.293796628329113	2		494	981	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0009442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	159	409	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.774	0.709	0.842	0.774	0.709	0.842	SUBCLONAL	1	TRUE	1	0.43	2		409	956	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041007	47041007	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	58	164	0	ENST00000377604.3:c.1537G>T	p.Glu513Ter	p.E513*	ENST00000377604	NM_001204468.1	513	Gag/Tag	14/24	1	1	FACETS	0.547	0.472	0.629	0.547	0.472	0.629	SUBCLONAL	1	TRUE	0	0.43	1		164	387	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346609	225346609	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	64	328	0	ENST00000264414.4:c.2029G>T	p.Val677Phe	p.V677F	ENST00000264414	NM_003590.4	677	Gtt/Ttt	14/16	1	2	FACETS	0.29	0.25	0.334	0.29	0.25	0.334	SUBCLONAL	1	TRUE	1	0.43	2		328	1025	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55154995	55154995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	94	379	1	ENST00000257290.5:c.2704G>A	p.Asp902Asn	p.D902N	ENST00000257290	NM_006206.4	902	Gat/Aat	20/23	1	2	FACETS	0.375	0.333	0.421	0.375	0.333	0.421	SUBCLONAL	1	TRUE	1	0.43	2		380	1165	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405044	70405044	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	78	357	0	ENST00000373644.4:c.2558G>T	p.Gly853Val	p.G853V	ENST00000373644	NM_030625.2	853	gGt/gTt	4/12	1	2	FACETS	0.304	0.266	0.346	0.304	0.266	0.346	SUBCLONAL	1	TRUE	1	0.43	2		357	1192	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913338	28913338	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0009442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1303	84	456	0	ENST00000282397.4:c.2455A>T	p.Lys819Ter	p.K819*	ENST00000282397	NM_002019.4	819	Aag/Tag	17/30	1	2	FACETS	0.282	0.247	0.319	0.282	0.247	0.319	SUBCLONAL	1	TRUE	1	0.43	2		456	1387	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009454-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	155	145	0				ENST00000310581	NM_198253.2	-/1132			0.31542787692436	4	FACETS	1	0.962	1			1	CLONAL	3	TRUE	NA	0.390749377054327	4		145	349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0009454-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	83	178	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	0.337008268890365	2	FACETS	1	0.978	1	0.722	0.645	0.804	CLONAL	1	TRUE	0	0.390749377054327	2		178	294	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009454-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	263	372	0	ENST00000304494.5:c.143C>T	p.Pro48Leu	p.P48L	ENST00000304494	NM_000077.4	48	cCg/cTg	1/3	0.337008268890365	2	FACETS	0.947	0.892	1	0.947	0.892	1	CLONAL	2	TRUE	0	0.390749377054327	2		372	711	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430989	181430989	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1435482082	NA	P-0009454-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	88	264	1	ENST00000325404.1:c.841G>A	p.Ala281Thr	p.A281T	ENST00000325404	NM_003106.3	281	Gcc/Acc	1/1	0.370879867628491	3	FACETS	0.906	0.804	1	0.453	0.402	0.508	CLONAL	1	TRUE	1	0.390749377054327	3		265	594	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765753	41765753	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761731744	NA	P-0009454-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	71	192	0	ENST00000301178.4:c.2629G>A	p.Ala877Thr	p.A877T	ENST00000301178	NM_021913.4	877	Gct/Act	20/20	0.370879867628491	3	FACETS	1	0.925	1	0.539	0.472	0.61	CLONAL	1	TRUE	1	0.390749377054327	3		192	403	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693001	89693003	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0009454-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	131	217	0	ENST00000371953.3:c.486_488del	p.Asp162_Lys163delinsGlu	p.D162_K163delinsE	ENST00000371953	NM_000314.4	162	gACAaa/gaa	5/9	0.390749377054327	2	FACETS	0.851	0.78	0.924	0.851	0.78	0.924	CLONAL	2	TRUE	0	0.390749377054327	2		217	394	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0009514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	124	476	2	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.211539456632562	1	FACETS	0.985	0.89	1	0.985	0.89	1	CLONAL	1	TRUE	0	0.219476060858097	1		478	1021	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0009514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	31	587	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.258	0.207	0.316	0.258	0.207	0.316	SUBCLONAL	1	TRUE	1	0.219476060858097	2		587	1094	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0009514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	38	601	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.3	0.247	0.361	0.3	0.247	0.361	SUBCLONAL	1	TRUE	1	0.219476060858097	2		601	1153	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578528	7578528	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	102	505	0	ENST00000269305.4:c.402T>G	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	ttT/ttG	5/11	0.211539456632562	1	FACETS	0.829	0.74	0.924	0.829	0.74	0.924	CLONAL	1	TRUE	0	0.219476060858097	1		505	998	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032574	12032574	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	95	475	0	ENST00000353533.5:c.1010C>T	p.Ser337Phe	p.S337F	ENST00000353533	NM_003010.3	337	tCc/tTc	9/11	0.211539456632562	1	FACETS	0.874	0.777	0.977	0.874	0.777	0.977	CLONAL	1	TRUE	0	0.219476060858097	1		475	882	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0009523-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	383	547	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.339672444311674	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.352307515756926	2		547	977	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575150	48575150	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659844	NA	P-0009523-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	216	391	0	ENST00000342988.3:c.344G>A	p.Cys115Tyr	p.C115Y	ENST00000342988	NM_005359.5	115	tGt/tAt	3/12	0.352307515756926	2	FACETS	0.955	0.893	1	0.955	0.893	1	CLONAL	2	TRUE	0	0.352307515756926	2		391	642	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913396	NA	P-0009565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	363	485	0	ENST00000349496.5:c.95A>T	p.Asp32Val	p.D32V	ENST00000349496	NM_001904.3	32	gAc/gTc	3/15	0.301123452940591	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.315726893358428	3		485	1248	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456515	29456515	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1387	175	652	0	ENST00000389048.3:c.2403A>G	p.Ile801Met	p.I801M	ENST00000389048	NM_004304.4	801	atA/atG	14/29	0.301123452940591	3	FACETS	0.822	0.754	0.893	0.411	0.377	0.447	CLONAL	1	TRUE	1	0.315726893358428	3		652	1562	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333944	70333944	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	153	412	0	ENST00000373644.4:c.1849C>T	p.Gln617Ter	p.Q617*	ENST00000373644	NM_030625.2	617	Cag/Tag	2/12	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.315726893358428	2		412	953	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938499	76938501	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs1297294136	NA	P-0009565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	95	294	0	ENST00000373344.5:c.2247_2249del	p.Ser750del	p.S750del	ENST00000373344	NM_000489.3	749	tcTTCa/tca	9/35	1	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.315726893358428	1		294	359	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061227	38061241	+	inframe_deletion	In_Frame_Del	DEL	GAACATGTTGCCGGA	GAACATGTTGCCGGA	-	novel	NA	P-0009565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	100	383	0	ENST00000250448.2:c.748_762del	p.Ser250_Phe254del	p.S250_F254del	ENST00000250448	NM_004496.3	250	TCCGGCAACATGTTC/-	2/2	1	2	FACETS	0.794	0.709	0.884	0.794	0.709	0.884	SUBCLONAL	1	TRUE	1	0.315726893358428	2		383	798	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610427	10610427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	158	441	0	ENST00000171111.5:c.283G>A	p.Ala95Thr	p.A95T	ENST00000171111	NM_203500.1	95	Gcc/Acc	2/6	0.447640877724908	1	FACETS	0.953	0.878	1	0.953	0.878	1	CLONAL	1	TRUE	0	0.447640877724908	1		441	575	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0009590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	176	409	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA	2	FACETS	0.839	0.773	0.908			1	INDETERMINATE	1	TRUE	NA	0.447640877724908	2		409	937	SUCCESS
APC	324	MSKCC	GRCh37	5	112179437	112179437	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587778044	NA	P-0009590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	276	679	0	ENST00000257430.4:c.8146G>T	p.Val2716Leu	p.V2716L	ENST00000257430	NM_000038.5	2716	Gtg/Ttg	16/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.447640877724908	2		679	1173	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514425	125514425	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	158	470	1	ENST00000428830.2:c.1120G>T	p.Val374Phe	p.V374F	ENST00000428830	NM_001114121.2	374	Gtc/Ttc	11/14	1	2	FACETS	0.855	0.784	0.929	0.855	0.784	0.929	CLONAL	1	TRUE	1	0.447640877724908	2		471	826	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28885775	28885775	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	168	563	0	ENST00000282397.4:c.3587A>G	p.Glu1196Gly	p.E1196G	ENST00000282397	NM_002019.4	1196	gAa/gGa	27/30	1	2	FACETS	0.828	0.761	0.897	0.828	0.761	0.897	CLONAL	1	TRUE	1	0.447640877724908	2		563	907	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226101	2226101	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	211	511	0	ENST00000326181.6:c.1798G>T	p.Gly600Cys	p.G600C	ENST00000326181	NM_032271.2	600	Ggc/Tgc	19/21	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.447640877724908	2		511	937	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039648	47039648	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1556778373	NA	P-0009590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	180	566	0	ENST00000377604.3:c.1100A>C	p.His367Pro	p.H367P	ENST00000377604	NM_001204468.1	367	cAc/cCc	11/24	1	2	FACETS	0.959	0.885	1	0.959	0.885	1	CLONAL	1	TRUE	1	0.447640877724908	2		566	839	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123664	46123664	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	176	454	1	ENST00000334344.6:c.47del	p.Gly16AspfsTer42	p.G16Dfs*42	ENST00000334344	NM_152641.2	15	aaG/aa	1/21	0.408334282301391	1	FACETS	0.918	0.849	0.989	0.918	0.849	0.989	CLONAL	1	TRUE	0	0.447640877724908	1		455	665	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221222	1221226	+	frameshift_variant	Frame_Shift_Del	DEL	ACCAC	ACCAC	G	novel	NA	P-0009590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	206	668	0	ENST00000326873.7:c.745_749delinsG	p.Thr249GlyfsTer37	p.T249Gfs*37	ENST00000326873	NM_000455.4	249	ACCACg/Gg	6/10	0.447640877724908	1	FACETS	0.839	0.78	0.901	0.839	0.78	0.901	CLONAL	1	TRUE	0	0.447640877724908	1		668	851	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061222	38061246	+	protein_altering_variant	In_Frame_Del	DEL	TTCTCGAACATGTTGCCGGAGTCCG	TTCTCGAACATGTTGCCGGAGTCCG	C	novel	NA	P-0009603-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	72	279	0	ENST00000250448.2:c.743_767delinsG	p.Pro248_Asn256delinsArg	p.P248_N256delinsR	ENST00000250448	NM_004496.3	248	cCGGACTCCGGCAACATGTTCGAGAAc/cGc	2/2	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.17	2		279	706	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	102	145	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.560159491919245	2		145	314	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720833	89720836	+	frameshift_variant	Frame_Shift_Del	DEL	AAAT	AAAT	-	rs587782304	NA	P-0009634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	190	185	0	ENST00000371953.3:c.987_990del	p.Asn329LysfsTer14	p.N329Kfs*14	ENST00000371953	NM_000314.4	328	gcAAAT/gc	8/9	0.560159491919245	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.560159491919245	1		185	408	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873436	136873436	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1398	589	771	1	ENST00000241393.3:c.62A>G	p.Tyr21Cys	p.Y21C	ENST00000241393	NM_003467.2	21	tAt/tGt	2/2	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.560159491919245	2		772	1987	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294099	1294099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1268051204	NA	P-0009634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	228	405	0	ENST00000310581.5:c.902G>A	p.Arg301His	p.R301H	ENST00000310581	NM_198253.2	301	cGc/cAc	2/16	NA	2	FACETS	0.929	0.867	0.993			1	INDETERMINATE	1	TRUE	NA	0.560159491919245	2		405	876	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741843	40741843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	215	353	1	ENST00000392038.2:c.1129G>A	p.Ala377Thr	p.A377T	ENST00000392038	NM_001626.4	377	Gcc/Acc	11/14	1	2	FACETS	0.932	0.868	0.997	0.932	0.868	0.997	CLONAL	1	TRUE	1	0.560159491919245	2		354	824	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518445	204518445	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	22	489	2	ENST00000367182.3:c.1108G>T	p.Val370Phe	p.V370F	ENST00000367182	NM_001278516.1	370	Gtc/Ttc	11/11	1	2	FACETS	1	0.816	1	1	0.816	1	CLONAL	1	TRUE	1	0.21	2		491	199	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332010	81332010	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	18	515	0	ENST00000222390.5:c.2074G>T	p.Val692Phe	p.V692F	ENST00000222390	NM_000601.4	692	Gtt/Ttt	18/18	1	2	FACETS	0.82	0.62	1	0.82	0.62	1	CLONAL	1	TRUE	1	0.21	2		515	209	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350061	81350061	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	20	408	0	ENST00000222390.5:c.1271G>C	p.Arg424Pro	p.R424P	ENST00000222390	NM_000601.4	424	cGt/cCt	10/18	1	2	FACETS	0.92	0.707	1	0.92	0.707	1	CLONAL	1	TRUE	1	0.21	2		408	207	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779836	3779836	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	14	397	2	ENST00000262367.5:c.5212C>A	p.His1738Asn	p.H1738N	ENST00000262367	NM_004380.2	1738	Cat/Aat	31/31	0.283557961995414	1	FACETS	0.986	0.719	1	0.986	0.719	1	CLONAL	1	TRUE	0	0.21	1		399	121	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610498	10610498	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	22	385	0	ENST00000171111.5:c.212G>T	p.Arg71Leu	p.R71L	ENST00000171111	NM_203500.1	71	cGg/cTg	2/6	0.173334438408968	3	FACETS	1	0.846	1			1	CLONAL	2	TRUE	NA	0.21	3		385	106	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105568	11105568	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	54	386	1	ENST00000358026.2:c.1484G>A	p.Gly495Asp	p.G495D	ENST00000358026	NM_001128849.1	495	gGc/gAc	9/36	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.21	NA		387	162	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8339024	8339025	+	missense_variant	Missense_Mutation	DNP	TG	TG	CT	novel	NA	P-0009643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	16	312	0	ENST00000356435.5:c.5276_5277delinsAG	p.Pro1759Gln	p.P1759Q	ENST00000356435		1759	cCA/cAG	32/35	1	2	FACETS	0.952	0.708	1	0.952	0.708	1	CLONAL	1	TRUE	1	0.21	2		312	160	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486102	29486102	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0009646-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	276	427	0	ENST00000356175.3:c.279T>A	p.Cys93Ter	p.C93*	ENST00000356175	NM_000267.3	93	tgT/tgA	3/57	1	2	FACETS	0.775	0.732	0.819	1	0.994	1	SUBCLONAL	2	TRUE	1	0.492608175567271	2		427	723	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0009680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	69	353	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.207822972467312	3	FACETS	0.977	0.856	1	0.977	0.856	1	CLONAL	2	TRUE	1	0.207822972467312	3		353	375	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221956	1221956	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	68	579	1	ENST00000326873.7:c.871G>T	p.Glu291Ter	p.E291*	ENST00000326873	NM_000455.4	291	Gag/Tag	7/10	0.207822972467312	1	FACETS	0.934	0.819	1	1	0.98	1	CLONAL	2	TRUE	0	0.207822972467312	1		580	314	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178572	32178572	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	65	458	2	ENST00000375023.3:c.2822A>C	p.Asn941Thr	p.N941T	ENST00000375023	NM_004557.3	941	aAc/aCc	18/30	0.207822972467312	5	FACETS	1	0.916	1	1	0.916	1	CLONAL	2	TRUE	3	0.207822972467312	5		460	384	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022806	12022806	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1300993680	NA	P-0009680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	20	278	0	ENST00000396373.4:c.912C>G	p.Ile304Met	p.I304M	ENST00000396373	NM_001987.4	304	atC/atG	5/8	0.18180771079555	4	FACETS	0.662	0.506	0.846	0.331	0.253	0.423	SUBCLONAL	1	TRUE	2	0.207822972467312	4		278	351	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944785	31944785	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	26	361	0	ENST00000340398.3:c.316G>C	p.Asp106His	p.D106H	ENST00000340398	NM_001013699.2	106	Gat/Cat	1/1	0.18180771079555	4	FACETS	0.936	0.742	1	0.468	0.371	0.579	CLONAL	1	TRUE	2	0.207822972467312	4		361	323	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885848	59885848	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	68	454	1	ENST00000259008.2:c.898G>A	p.Glu300Lys	p.E300K	ENST00000259008	NM_032043.2	300	Gaa/Aaa	7/20	0.207822972467312	5	FACETS	0.862	0.751	0.981	0.431	0.375	0.491	CLONAL	2	TRUE	1	0.207822972467312	5		455	498	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727471	88727471	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	21	461	0	ENST00000360948.2:c.308C>G	p.Thr103Ser	p.T103S	ENST00000360948	NM_001012338.2	103	aCc/aGc	3/19	0.3264934970059	0	FACETS	0.114	0.087	0.145			1	SUBCLONAL	1	FALSE	0	0.500900329363808	0		461	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0009690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	299	375	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.566555671620276	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.584286088652822	1		377	620	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0009690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	116	360	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.368789538256225	1	FACETS	0.479	0.433	0.527	0.479	0.433	0.527	SUBCLONAL	1	TRUE	0	0.584286088652822	1		361	587	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728530	190728530	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	502	495	3	ENST00000441310.2:c.1918G>T	p.Glu640Ter	p.E640*	ENST00000441310	NM_000534.4	640	Gaa/Taa	10/13	0.526700659509875	3	FACETS	1	0.996	1	0.826	0.797	0.855	CLONAL	2	TRUE	0	0.584286088652822	3		498	896	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249468	153249468	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	321	521	0	ENST00000281708.4:c.1310G>T	p.Gly437Val	p.G437V	ENST00000281708	NM_033632.3	437	gGa/gTa	9/12	0.584286088652822	1	FACETS	0.99	0.939	1	0.99	0.939	1	CLONAL	1	TRUE	0	0.584286088652822	1		521	786	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0009690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	61	205	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	0.368789538256225	1	FACETS	0.302	0.26	0.346	0.302	0.26	0.346	SUBCLONAL	1	TRUE	0	0.584286088652822	1		205	490	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358367	91358367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779891	NA	P-0009690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	130	588	2	ENST00000355112.3:c.4112C>T	p.Thr1371Met	p.T1371M	ENST00000355112	NM_000057.2	1371	aCg/aTg	22/22	0.405165405047682	1	FACETS	0.322	0.292	0.355	0.322	0.292	0.355	SUBCLONAL	1	TRUE	0	0.584286088652822	1		590	977	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220648	2220648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376429748	NA	P-0009690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	303	640	2	ENST00000326181.6:c.265G>A	p.Ala89Thr	p.A89T	ENST00000326181	NM_032271.2	89	Gcc/Acc	5/21	0.320864556400729	1	FACETS	0.502	0.472	0.533	0.502	0.472	0.533	INDETERMINATE	1	TRUE	0	0.584286088652822	1		642	1463	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864694	37864694	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1256572460	NA	P-0009690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1562	174	647	1	ENST00000269571.5:c.346G>A	p.Val116Met	p.V116M	ENST00000269571		116	Gtg/Atg	3/27	0.336758554408355	3	FACETS	0.443	0.406	0.482	0.222	0.203	0.241	INDETERMINATE	1	TRUE	1	0.584286088652822	3		648	1736	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561138	9561138	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	103	487	0	ENST00000353224.5:c.644T>A	p.Leu215His	p.L215H	ENST00000353224	NM_177990.2	215	cTc/cAc	4/10	0.491174641624134	3	FACETS	0.482	0.43	0.536	0.241	0.215	0.268	SUBCLONAL	1	TRUE	1	0.584286088652822	3		487	946	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195709	123195709	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	215	394	0	ENST00000218089.9:c.1623A>C	p.Arg541Ser	p.R541S	ENST00000218089	NM_001042749.1	541	agA/agC	17/35	1	1	FACETS	0.651	0.607	0.697	0.651	0.607	0.697	SUBCLONAL	1	TRUE	0	0.584286088652822	1		394	800	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0009697-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	868	316	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.538519962410531	6	FACETS	0.941	0.914	0.969	0.941	0.914	0.969	CLONAL	4	TRUE	2	0.538519962410531	6		316	1778	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557239	187557239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs997211983	NA	P-0009697-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	273	749	0	ENST00000441802.2:c.4123C>T	p.His1375Tyr	p.H1375Y	ENST00000441802	NM_005245.3	1375	Cac/Tac	6/27	0.538519962410531	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.538519962410531	1		749	708	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176618925	176618925	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009697-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	322	1012	0	ENST00000439151.2:c.968T>C	p.Val323Ala	p.V323A	ENST00000439151	NM_022455.4	323	gTt/gCt	3/23	1	2	FACETS	0.867	0.818	0.918	0.867	0.818	0.918	CLONAL	1	TRUE	1	0.538519962410531	2		1012	1379	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628617	90628617	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1493	305	782	0	ENST00000330062.3:c.970T>G	p.Phe324Val	p.F324V	ENST00000330062	NM_002168.2	324	Ttt/Gtt	8/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.329755894116819	2		782	1798	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101427	27101430	+	frameshift_variant	Frame_Shift_Del	DEL	CTAA	CTAA	-	novel	NA	P-0009701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	191	637	0	ENST00000324856.7:c.4712_4715del	p.Asn1571ThrfsTer40	p.N1571Tfs*40	ENST00000324856	NM_006015.4	1570	tCTAAc/tc	18/20	0.329755894116819	1	FACETS	0.855	0.789	0.923	0.855	0.789	0.923	CLONAL	1	TRUE	0	0.329755894116819	1		637	1132	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970913	21970913	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	452	602	0	ENST00000304494.5:c.445G>T	p.Glu149Ter	p.E149*	ENST00000304494	NM_000077.4	149	Gaa/Taa	2/3	0.816935282644501	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.816935282644501	1		602	610	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533763	63533763	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777283610	NA	P-0009715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	452	544	0	ENST00000307078.5:c.1391C>T	p.Ser464Phe	p.S464F	ENST00000307078	NM_004655.3	464	tCc/tTc	6/11	0.255107401025458	4	FACETS	1	0.977	1	1	0.977	1	INDETERMINATE	2	TRUE	2	0.816935282644501	4		544	978	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380283	25380283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913528	NA	P-0009715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	654	626	1	ENST00000311936.3:c.175G>A	p.Ala59Thr	p.A59T	ENST00000311936	NM_004985.3	59	Gca/Aca	3/5	0.513344107912538	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.816935282644501	1		627	814	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413131	63413131	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	381	291	0	ENST00000330258.3:c.36G>T	p.Lys12Asn	p.K12N	ENST00000330258	NM_152424.3	12	aaG/aaT	2/2	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.816935282644501	1		291	461	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100977	27100977	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	612	594	0	ENST00000324856.7:c.4259A>T	p.Gln1420Leu	p.Q1420L	ENST00000324856	NM_006015.4	1420	cAg/cTg	18/20	0.605081727390337	3	FACETS	0.926	0.896	0.957	0.926	0.896	0.957	CLONAL	2	TRUE	1	0.816935282644501	3		594	1139	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301779	65301779	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0009715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	315	505	0	ENST00000342505.4:c.3258+2T>A		p.X1086_splice	ENST00000342505	NM_002227.2	1086			0.816935282644501	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.816935282644501	1		505	450	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256593	115256593	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	285	472	0	ENST00000369535.4:c.118T>G	p.Tyr40Asp	p.Y40D	ENST00000369535	NM_002524.4	40	Tac/Gac	3/7	0.816935282644501	1	FACETS	0.992	0.952	1	0.992	0.952	1	CLONAL	1	TRUE	0	0.816935282644501	1		472	416	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748442	162748442	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	206	636	0	ENST00000367921.3:c.2356G>C	p.Glu786Gln	p.E786Q	ENST00000367921	NM_006182.2	786	Gaa/Caa	17/18	0.452479650922935	1	FACETS	0.31	0.287	0.334	0.31	0.287	0.334	INDETERMINATE	1	TRUE	0	0.816935282644501	1		636	962	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136846	55136846	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	563	849	0	ENST00000257290.5:c.1168G>T	p.Gly390Cys	p.G390C	ENST00000257290	NM_006206.4	390	Ggc/Tgc	8/23	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.816935282644501	2		849	1373	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143043306	143043306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	449	733	1	ENST00000262992.4:c.2110G>A	p.Val704Met	p.V704M	ENST00000262992	NM_001101669.1	704	Gtg/Atg	19/24	0.816935282644501	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.816935282644501	1		734	641	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294033	1294033	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1777	596	805	4	ENST00000310581.5:c.968C>A	p.Pro323Gln	p.P323Q	ENST00000310581	NM_198253.2	323	cCg/cAg	2/16	0.816935282644501	4	FACETS	1	0.991	1	0.372	0.356	0.389	CLONAL	1	TRUE	1	0.816935282644501	4		809	2373	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052996	180052996	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	418	627	0	ENST00000261937.6:c.1294C>G	p.Pro432Ala	p.P432A	ENST00000261937	NM_182925.4	432	Ccc/Gcc	10/30	0.605081727390337	3	FACETS	1	0.982	1	0.532	0.506	0.558	CLONAL	1	TRUE	1	0.816935282644501	3		627	1354	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570395	87570395	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	494	789	1	ENST00000277120.3:c.2135G>T	p.Gly712Val	p.G712V	ENST00000277120		712	gGg/gTg	17/19	0.219661920612521	1	FACETS	0.631	0.606	0.657	0.631	0.606	0.657	INDETERMINATE	1	TRUE	0	0.816935282644501	1		790	1133	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750423	133750423	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	351	784	0	ENST00000318560.5:c.1254C>G	p.Ile418Met	p.I418M	ENST00000318560	NM_005157.4	418	atC/atG	7/11	0.219661920612521	1	FACETS	0.472	0.448	0.497	0.472	0.448	0.497	INDETERMINATE	1	TRUE	0	0.816935282644501	1		784	1076	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132834	64132834	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752611628	NA	P-0009715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	535	797	2	ENST00000334205.4:c.968G>A	p.Arg323His	p.R323H	ENST00000334205	NM_003942.2	323	cGc/cAc	9/17	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.816935282644501	2		799	1257	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212919	94212919	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	791	449	1	ENST00000323929.3:c.323G>T	p.Trp108Leu	p.W108L	ENST00000323929	NM_005591.3	108	tGg/tTg	5/20	0.776060860339347	4	FACETS	0.972	0.947	0.996			1	CLONAL	3	TRUE	NA	0.816935282644501	4		450	1207	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205250	46205250	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	697	770	1	ENST00000334344.6:c.334G>A	p.Glu112Lys	p.E112K	ENST00000334344	NM_152641.2	112	Gag/Aag	4/21	0.478975669710407	3	FACETS	0.843	0.816	0.871	0.843	0.816	0.871	INDETERMINATE	2	TRUE	1	0.816935282644501	3		771	1425	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864232	57864232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	512	891	1	ENST00000228682.2:c.1709C>T	p.Pro570Leu	p.P570L	ENST00000228682	NM_005269.2	570	cCa/cTa	12/12	0.478975669710407	3	FACETS	1	0.993	1	0.588	0.563	0.613	INDETERMINATE	1	TRUE	1	0.816935282644501	3		892	1502	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226318	133226318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572986717	NA	P-0009715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	325	752	1	ENST00000320574.5:c.3740C>T	p.Pro1247Leu	p.P1247L	ENST00000320574	NM_006231.2	1247	cCg/cTg	30/49	0.801148867492332	3	FACETS	0.834	0.787	0.882	0.278	0.262	0.294	CLONAL	1	TRUE	0	0.816935282644501	3		753	1344	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007791	45007791	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	380	570	0	ENST00000558401.1:c.238T>C	p.Trp80Arg	p.W80R	ENST00000558401	NM_004048.2	80	Tgg/Cgg	2/4	0.816935282644501	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.816935282644501	1		570	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577111	7577111	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786202082	NA	P-0009715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	613	755	2	ENST00000269305.4:c.827C>A	p.Ala276Asp	p.A276D	ENST00000269305	NM_001126112.2	276	gCc/gAc	8/11	0.785016762501207	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.816935282644501	1		757	790	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528438	29528438	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	592	571	4	ENST00000356175.3:c.1195G>T	p.Ala399Ser	p.A399S	ENST00000356175	NM_000267.3	399	Gct/Tct	11/57	0.255107401025458	4	FACETS	1	0.993	1	1	0.993	1	INDETERMINATE	2	TRUE	2	0.816935282644501	4		575	1190	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122892	7122892	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	416	653	0	ENST00000302850.5:c.3367G>T	p.Glu1123Ter	p.E1123*	ENST00000302850	NM_000208.2	1123	Gag/Tag	18/22	0.816935282644501	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.816935282644501	1		653	580	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912486	50912486	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	429	873	6	ENST00000440232.2:c.2000G>T	p.Arg667Leu	p.R667L	ENST00000440232	NM_002691.3	667	cGg/cTg	16/27	NA	2	FACETS	0.869	0.829	0.909			1	INDETERMINATE	1	TRUE	NA	0.816935282644501	2		879	1209	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40864900	40864900	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0009715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	583	671	0	ENST00000373198.4:c.2370-2A>G		p.X790_splice	ENST00000373198	NM_133170.3	790			0.528588482183986	4	FACETS	1	0.997	1	0.497	0.477	0.517	CLONAL	1	TRUE	1	0.816935282644501	4		671	1739	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877412	40877412	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	326	520	0	ENST00000373198.4:c.2284A>G	p.Asn762Asp	p.N762D	ENST00000373198	NM_133170.3	762	Aac/Gac	15/32	0.528588482183986	4	FACETS	1	0.986	1	0.377	0.356	0.399	CLONAL	1	TRUE	1	0.816935282644501	4		520	1282	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513788	41513788	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	147	565	0	ENST00000263253.7:c.692G>A	p.Gly231Glu	p.G231E	ENST00000263253	NM_001429.3	231	gGa/gAa	2/31	0.530488196927271	1	FACETS	0.287	0.262	0.313	0.287	0.262	0.313	SUBCLONAL	1	TRUE	0	0.816935282644501	1		565	741	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440756	56440756	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	429	486	0	ENST00000407977.2:c.462del	p.Leu155TrpfsTer3	p.L155Wfs*3	ENST00000407977		154	ccG/cc	5/10	0.255107401025458	4	FACETS	1	0.986	1	1	0.986	1	INDETERMINATE	2	TRUE	2	0.816935282644501	4		486	898	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912660	NA	P-0009753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	567	785	0	ENST00000269305.4:c.839G>T	p.Arg280Ile	p.R280I	ENST00000269305	NM_001126112.2	280	aGa/aTa	8/11	NA	2	FACETS	0.928	0.894	0.962			1	INDETERMINATE	2	TRUE	NA	0.514782810755349	2		785	1187	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519980	NA	P-0009759-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	54	655	0	ENST00000269305.4:c.528C>G	p.Cys176Trp	p.C176W	ENST00000269305	NM_001126112.2	176	tgC/tgG	5/11	0.260538187562847	1	FACETS	0.914	0.784	1	0.914	0.784	1	CLONAL	1	TRUE	0	0.28203570045647	1		655	360	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0009762-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	104	543	1	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	0.242305071530975	2	FACETS	0.932	0.833	1	0.466	0.416	0.519	CLONAL	1	TRUE	0	0.242305071530975	2		544	921	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191170	2191170	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009762-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	314	694	2	ENST00000398665.3:c.424G>T	p.Asp142Tyr	p.D142Y	ENST00000398665	NM_032482.2	142	Gac/Tac	5/28	0.242305071530975	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.242305071530975	2		696	1183	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486130	8486130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009762-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	112	544	0	ENST00000356435.5:c.2687C>T	p.Ser896Leu	p.S896L	ENST00000356435		896	tCa/tTa	17/35	1	2	FACETS	0.945	0.849	1	0.945	0.849	1	CLONAL	1	TRUE	1	0.242305071530975	2		544	978	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172518	108172518	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0009762-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	126	325	0	ENST00000278616.4:c.5319+2T>G		p.X1773_splice	ENST00000278616	NM_000051.3	1773			0.242305071530975	2	FACETS	0.889	0.808	0.974	0.889	0.808	0.974	CLONAL	2	TRUE	0	0.242305071530975	2		325	585	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380285	25380285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104894364	NA	P-0009762-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	192	435	1	ENST00000311936.3:c.173C>T	p.Thr58Ile	p.T58I	ENST00000311936	NM_004985.3	58	aCa/aTa	3/5	0.242305071530975	4	FACETS	0.906	0.837	0.978	0.906	0.837	0.978	CLONAL	2	TRUE	2	0.242305071530975	4		436	1086	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123691	11123691	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009762-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	56	496	0	ENST00000358026.2:c.2341A>T	p.Met781Leu	p.M781L	ENST00000358026	NM_001128849.1	781	Atg/Ttg	16/36	0.242305071530975	2	FACETS	0.546	0.467	0.634	0.273	0.233	0.317	SUBCLONAL	1	TRUE	0	0.242305071530975	2		496	846	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207029	1207029	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009762-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	171	362	0	ENST00000326873.7:c.118del	p.Arg40AlafsTer11	p.R40Afs*11	ENST00000326873	NM_000455.4	39	cgC/cg	1/10	0.242305071530975	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.242305071530975	2		362	655	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602692	10602692	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009762-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	180	513	0	ENST00000171111.5:c.886del	p.Arg296AlafsTer21	p.R296Afs*21	ENST00000171111	NM_203500.1	296	Cgc/gc	3/6	0.242305071530975	2	FACETS	0.886	0.818	0.957	0.886	0.818	0.957	CLONAL	2	TRUE	0	0.242305071530975	2		513	838	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578393	7578393	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876660821	NA	P-0009787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	93	285	1	ENST00000269305.4:c.537T>A	p.His179Gln	p.H179Q	ENST00000269305	NM_001126112.2	179	caT/caA	5/11	0.291643333946064	3	FACETS	0.917	0.824	1	0.611	0.549	0.676	CLONAL	2	FALSE	0	0.380788004788693	3		286	317	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0009817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	118	587	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.849	0.768	0.934	0.849	0.768	0.934	CLONAL	1	TRUE	1	0.457119809062924	2		587	608	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994278	21994278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	87	337	0	ENST00000579755.1:c.53C>T	p.Pro18Leu	p.P18L	ENST00000579755		18	cCg/cTg	1/3	0.255534041739409		FACETS		0.813	1				INDETERMINATE	1	TRUE	1	0.457119809062924	3		337	511	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696467	47696467	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	110	301	0	ENST00000347630.2:c.356G>A	p.Ser119Asn	p.S119N	ENST00000347630	NM_001007230.1	119	aGt/aAt	6/11	1	2	FACETS	0.869	0.783	0.959	0.869	0.783	0.959	CLONAL	1	TRUE	1	0.457119809062924	2		301	554	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0009833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	346	549	1	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.56169031373545	1	FACETS	0.964	0.916	1	0.964	0.916	1	CLONAL	1	TRUE	0	0.56169031373545	1		550	919	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039419	49039419	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	331	609	0	ENST00000267163.4:c.2406del	p.Asn803ThrfsTer7	p.N803Tfs*7	ENST00000267163	NM_000321.2	802	Ggg/gg	23/27	0.551451289337407	1	FACETS	0.972	0.922	1	0.972	0.922	1	CLONAL	1	TRUE	0	0.56169031373545	1		609	872	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965641	25965641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	423	514	0	ENST00000435504.4:c.3565G>A	p.Glu1189Lys	p.E1189K	ENST00000435504		1189	Gag/Aag	13/13	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.56169031373545	2		514	1236	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99136609	99136609	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1241900844	NA	P-0009833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	264	333	0	ENST00000074304.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000074304	NM_001134224.1	33	tCt/tGt	3/26	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.56169031373545	2		333	818	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499366	89499366	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs142030914	NA	P-0009833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	287	407	0	ENST00000336596.2:c.2536C>A	p.Pro846Thr	p.P846T	ENST00000336596	NM_005233.5	846	Ccc/Acc	15/17	0.56169031373545	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.56169031373545	1		407	724	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608586	189608586	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	1002	513	0	ENST00000264731.3:c.1661C>A	p.Ala554Glu	p.A554E	ENST00000264731	NM_003722.4	554	gCg/gAg	13/14	0.543076927714149	5	FACETS	1	0.996	1	0.833	0.811	0.856	CLONAL	3	TRUE	1	0.56169031373545	5		513	1972	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127411	55127411	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	302	542	0	ENST00000257290.5:c.199T>A	p.Ser67Thr	p.S67T	ENST00000257290	NM_006206.4	67	Tcc/Acc	3/23	0.252907870787309	3	FACETS	0.971	0.913	1	0.486	0.456	0.516	INDETERMINATE	1	TRUE	1	0.56169031373545	3		542	1418	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242768	66242768	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	393	513	2	ENST00000273854.3:c.1804G>T	p.Gly602Cys	p.G602C	ENST00000273854	NM_004439.5	602	Ggc/Tgc	9/18	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	1	TRUE	NA	0.56169031373545	2		515	963	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467504	66467504	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	121	488	0	ENST00000273854.3:c.765G>T	p.Leu255Phe	p.L255F	ENST00000273854	NM_004439.5	255	ttG/ttT	3/18	NA	2	FACETS	0.4	0.36	0.442			1	INDETERMINATE	1	TRUE	NA	0.56169031373545	2		488	1078	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264703	1264703	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	480	440	1	ENST00000310581.5:c.2659C>A	p.Leu887Met	p.L887M	ENST00000310581	NM_198253.2	887	Ctg/Atg	11/16	0.22274846800783	5	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.56169031373545	5		441	1275	SUCCESS
APC	324	MSKCC	GRCh37	5	112175642	112175642	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	75	614	0	ENST00000257430.4:c.4351G>C	p.Glu1451Gln	p.E1451Q	ENST00000257430	NM_000038.5	1451	Gaa/Caa	16/16	0.506125347155434	2	FACETS	0.222	0.193	0.253	0.111	0.096	0.127	SUBCLONAL	1	TRUE	0	0.56169031373545	2		614	1204	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725534	117725534	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	323	453	0	ENST00000368508.3:c.347C>G	p.Thr116Arg	p.T116R	ENST00000368508	NM_002944.2	116	aCa/aGa	5/43	0.56169031373545	1	FACETS	0.949	0.899	0.999	0.949	0.899	0.999	CLONAL	1	TRUE	0	0.56169031373545	1		453	872	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946210	13946210	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	299	307	0	ENST00000405192.2:c.886G>A	p.Glu296Lys	p.E296K	ENST00000405192	NM_001163147.1	296	Gag/Aag	10/12	0.308357934643761	3	FACETS	0.795	0.751	0.839	0.795	0.751	0.839	INDETERMINATE	2	TRUE	1	0.56169031373545	3		307	858	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81340833	81340833	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	458	465	0	ENST00000222390.5:c.1408G>A	p.Glu470Lys	p.E470K	ENST00000222390	NM_000601.4	470	Gaa/Aaa	12/18	0.308357934643761	3	FACETS	0.803	0.767	0.839	0.803	0.767	0.839	INDETERMINATE	2	TRUE	1	0.56169031373545	3		465	1301	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509367	106509367	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	522	527	1	ENST00000359195.3:c.1361C>A	p.Ser454Tyr	p.S454Y	ENST00000359195	NM_002649.2	454	tCc/tAc	2/11	0.308357934643761	3	FACETS	0.882	0.846	0.918	0.882	0.846	0.918	INDETERMINATE	2	TRUE	1	0.56169031373545	3		528	1350	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481408	140481408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867748453	NA	P-0009833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	417	446	1	ENST00000288602.6:c.1400C>T	p.Ser467Leu	p.S467L	ENST00000288602	NM_004333.4	467	tCa/tTa	11/18	0.308357934643761	3	FACETS	0.863	0.823	0.903	0.863	0.823	0.903	INDETERMINATE	2	TRUE	1	0.56169031373545	3		447	1102	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563512	87563512	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	151	312	0	ENST00000277120.3:c.1900G>C	p.Glu634Gln	p.E634Q	ENST00000277120		634	Gag/Cag	16/19	1	2	FACETS	0.826	0.757	0.897	0.826	0.757	0.897	CLONAL	1	TRUE	1	0.56169031373545	2		312	651	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101909971	101909971	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	216	436	0	ENST00000374994.4:c.1291C>G	p.Leu431Val	p.L431V	ENST00000374994	NM_004612.2	431	Ctt/Gtt	8/9	1	2	FACETS	0.876	0.816	0.938	0.876	0.816	0.938	CLONAL	1	TRUE	1	0.56169031373545	2		436	878	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596140	43596140	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	330	441	1	ENST00000355710.3:c.307C>A	p.His103Asn	p.H103N	ENST00000355710	NM_020975.4	103	Cat/Aat	2/20	0.252907870787309	3	FACETS	0.758	0.718	0.799	0.758	0.718	0.799	INDETERMINATE	2	TRUE	1	0.56169031373545	3		442	993	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596158	43596158	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	300	394	0	ENST00000355710.3:c.325C>A	p.Leu109Ile	p.L109I	ENST00000355710	NM_020975.4	109	Ctc/Atc	2/20	0.252907870787309	3	FACETS	1	0.994	1	0.745	0.704	0.788	INDETERMINATE	1	TRUE	1	0.56169031373545	3		394	918	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851998	63851998	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1198498194	NA	P-0009833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	204	252	0	ENST00000279873.7:c.2776C>T	p.His926Tyr	p.H926Y	ENST00000279873	NM_032199.2	926	Cat/Tat	10/10	0.252907870787309	3	FACETS	1	0.986	1	0.623	0.579	0.668	INDETERMINATE	1	TRUE	1	0.56169031373545	3		252	747	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999494	100999494	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	375	635	0	ENST00000325455.5:c.308C>A	p.Pro103His	p.P103H	ENST00000325455	NM_001202474.3	103	cCc/cAc	1/8	0.281542212322592	1	FACETS	0.843	0.801	0.886	0.843	0.801	0.886	INDETERMINATE	1	TRUE	0	0.56169031373545	1		635	1139	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793382	18793382	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	281	557	0	ENST00000266497.5:c.4079C>A	p.Ala1360Glu	p.A1360E	ENST00000266497		1360	gCg/gAg	30/31	0.182549024857436	1	FACETS	0.718	0.675	0.762	0.718	0.675	0.762	INDETERMINATE	1	TRUE	0	0.56169031373545	1		557	1002	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734074	58734074	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	471	720	0	ENST00000305921.3:c.1132G>C	p.Glu378Gln	p.E378Q	ENST00000305921	NM_003620.3	378	Gaa/Caa	5/6	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.56169031373545	2		720	1601	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118997	3118997	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	301	517	1	ENST00000078429.4:c.681G>T	p.Met227Ile	p.M227I	ENST00000078429	NM_002067.2	227	atG/atT	5/7	0.562229112521303	1	FACETS	0.955	0.904	1	0.955	0.904	1	CLONAL	1	TRUE	0	0.56169031373545	1		518	807	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610322	10610322	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	281	507	2	ENST00000171111.5:c.388C>A	p.Pro130Thr	p.P130T	ENST00000171111	NM_203500.1	130	Ccc/Acc	2/6	0.562229112521303	1	FACETS	0.995	0.94	1	0.995	0.94	1	CLONAL	1	TRUE	0	0.56169031373545	1		509	723	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258627	19258627	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	303	501	0	ENST00000162023.5:c.273G>T	p.Arg91Ser	p.R91S	ENST00000162023		91	agG/agT	8/13	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.56169031373545	2		501	1031	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44935994	44935994	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	49	758	0	ENST00000377967.4:c.2755C>T	p.Pro919Ser	p.P919S	ENST00000377967	NM_021140.2	919	Cca/Tca	18/29	1	2	FACETS	0.188	0.158	0.221	0.188	0.158	0.221	SUBCLONAL	1	TRUE	1	0.56169031373545	2		758	928	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936013	44936013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	51	791	0	ENST00000377967.4:c.2774C>T	p.Ser925Phe	p.S925F	ENST00000377967	NM_021140.2	925	tCt/tTt	18/29	1	2	FACETS	0.189	0.16	0.222	0.189	0.16	0.222	SUBCLONAL	1	TRUE	1	0.56169031373545	2		791	960	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936051	44936051	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	48	741	0	ENST00000377967.4:c.2812C>A	p.Pro938Thr	p.P938T	ENST00000377967	NM_021140.2	938	Cca/Aca	18/29	1	2	FACETS	0.184	0.155	0.217	0.184	0.155	0.217	SUBCLONAL	1	TRUE	1	0.56169031373545	2		741	928	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412461	63412461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1322854723	NA	P-0009833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	388	741	1	ENST00000330258.3:c.706G>A	p.Gly236Arg	p.G236R	ENST00000330258	NM_152424.3	236	Ggg/Agg	2/2	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.56169031373545	2		742	1379	SUCCESS
AR	367	MSKCC	GRCh37	X	66765239	66765239	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	153	339	0	ENST00000374690.3:c.251C>A	p.Pro84His	p.P84H	ENST00000374690	NM_000044.3	84	cCc/cAc	1/8	1	2	FACETS	0.874	0.803	0.949	0.874	0.803	0.949	CLONAL	1	TRUE	1	0.56169031373545	2		339	623	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258744	115258745	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0009833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	380	388	0	ENST00000369535.4:c.37_38delinsTT	p.Gly13Phe	p.G13F	ENST00000369535	NM_002524.4	13	GGt/TTt	2/7	0.313033918136132	2	FACETS	1	0.995	1	0.731	0.696	0.765	INDETERMINATE	1	TRUE	0	0.56169031373545	2		388	926	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777961	27777961	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2434	361	970	1	ENST00000369163.2:c.110A>T	p.Lys37Met	p.K37M	ENST00000369163	NM_003536.2	37	aAg/aTg	1/1	0.287241109478581	14	FACETS	1	0.99	1			1	CLONAL	2	FALSE	NA	0.287241109478581	14		971	2795	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714387	40714387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1441976520	NA	P-0009839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	76	383	0	ENST00000373198.4:c.4010G>A	p.Arg1337His	p.R1337H	ENST00000373198	NM_133170.3	1337	cGc/cAc	29/32	0.287241109478581	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	0	0.287241109478581	1		383	408	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973491	15973494	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	novel	NA	P-0009839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	106	351	0	ENST00000268712.3:c.4498_4501del	p.Asn1500GlufsTer21	p.N1500Efs*21	ENST00000268712	NM_006311.3	1500	AACAga/ga	31/46	0.233054775984183	3	FACETS	1	0.975	1	0.64	0.575	0.71	CLONAL	1	FALSE	1	0.287241109478581	3		351	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0009842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	109	622	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.185366193825546	1	FACETS	0.775	0.697	0.858	1	0.984	1	SUBCLONAL	2	TRUE	0	0.185366193825546	1		624	688	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366932	15366932	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	92	986	0	ENST00000263377.2:c.1694C>G	p.Ala565Gly	p.A565G	ENST00000263377	NM_058243.2	565	gCc/gGc	9/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.185366193825546	2		986	906	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087360	27087360	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0009842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	63	463	0	ENST00000324856.7:c.1934C>G	p.Ser645Ter	p.S645*	ENST00000324856	NM_006015.4	645	tCa/tGa	5/20	0.185366193825546	4	FACETS	1	0.956	1	0.632	0.547	0.726	CLONAL	1	TRUE	2	0.185366193825546	4		463	637	SUCCESS
APC	324	MSKCC	GRCh37	5	112175147	112175147	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	21	246	0	ENST00000257430.4:c.3856G>T	p.Glu1286Ter	p.E1286*	ENST00000257430	NM_000038.5	1286	Gaa/Taa	16/16	0.0938512471751822	4	FACETS	1	0.846	1	0.564	0.436	0.713	INDETERMINATE	1	TRUE	2	0.185366193825546	4		246	238	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528026	157528026	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	39	221	0	ENST00000346085.5:c.5751G>C	p.Lys1917Asn	p.K1917N	ENST00000346085	NM_020732.3	1917	aaG/aaC	20/20	0.173717017480539	4	FACETS	0.799	0.665	0.948	0.799	0.665	0.948	CLONAL	2	TRUE	2	0.185366193825546	4		221	312	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482816	67482816	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	54	491	0	ENST00000327367.4:c.1220T>C	p.Leu407Pro	p.L407P	ENST00000327367	NM_005902.3	407	cTt/cCt	9/9	1	2	FACETS	0.954	0.814	1	0.954	0.814	1	CLONAL	1	TRUE	1	0.185366193825546	2		491	611	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291576	15291576	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35769976	NA	P-0009842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	59	517	0	ENST00000263388.2:c.3058G>A	p.Ala1020Thr	p.A1020T	ENST00000263388	NM_000435.2	1020	Gcc/Acc	19/33	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.185366193825546	2		517	486	SUCCESS
ATM	472	MSKCC	GRCh37	11	108214065	108214074	+	frameshift_variant	Frame_Shift_Del	DEL	TTTCAGTGCC	TTTCAGTGCC	-	rs786202800	NA	P-0009842-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	54	430	0	ENST00000278616.4:c.8395_8404del	p.Phe2799LysfsTer4	p.F2799Kfs*4	ENST00000278616	NM_000051.3	2795	gaTTTCAGTGCC/ga	57/63	0.125848693313004	5	FACETS	1	0.912	1	0.366	0.312	0.425	CLONAL	1	TRUE	2	0.185366193825546	5		430	678	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520006	NA	P-0009851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	298	672	0	ENST00000269305.4:c.821T>C	p.Val274Ala	p.V274A	ENST00000269305	NM_001126112.2	274	gTt/gCt	8/11	0.415276620605269	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.415276620605269	1		672	993	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643504	52643504	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1384458457	NA	P-0009851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	177	532	0	ENST00000394830.3:c.2392A>G	p.Arg798Gly	p.R798G	ENST00000394830	NM_018313.4	798	Aga/Gga	17/30	1	2	FACETS	0.896	0.826	0.97	0.896	0.826	0.97	CLONAL	1	TRUE	1	0.415276620605269	2		532	951	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238332	98238332	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377566861	NA	P-0009851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	171	379	0	ENST00000331920.6:c.1712G>A	p.Arg571Gln	p.R571Q	ENST00000331920	NM_000264.3	571	cGg/cAg	12/24	1	2	FACETS	0.952	0.876	1	0.952	0.876	1	CLONAL	1	TRUE	1	0.415276620605269	2		379	865	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480542	50480542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559383300	NA	P-0009851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	97	488	0	ENST00000394963.4:c.412C>T	p.Arg138Cys	p.R138C	ENST00000394963	NM_003076.4	138	Cgt/Tgt	4/13	1	2	FACETS	0.533	0.475	0.596	0.533	0.475	0.596	SUBCLONAL	1	TRUE	1	0.415276620605269	2		488	876	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354464	40354464	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	224	605	0	ENST00000293328.3:c.2131T>G	p.Phe711Val	p.F711V	ENST00000293328	NM_012448.3	711	Ttt/Gtt	18/19	0.415276620605269	3	FACETS	1	0.963	1	0.528	0.491	0.567	CLONAL	1	TRUE	1	0.415276620605269	3		605	1234	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041534	42041534	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1236	356	841	0	ENST00000219905.7:c.5731del	p.Ser1911AlafsTer12	p.S1911Afs*12	ENST00000219905	NM_001164273.1	1910	cAa/ca	17/24	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.415276620605269	2		841	1592	SUCCESS
APC	324	MSKCC	GRCh37	5	112175464	112175468	+	frameshift_variant	Frame_Shift_Del	DEL	TTCAC	TTCAC	-	novel	NA	P-0009851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	266	394	0	ENST00000257430.4:c.4175_4179del	p.Ser1392Ter	p.S1392*	ENST00000257430	NM_000038.5	1391	agTTCACtt/agtt	16/16	0.415276620605269	2	FACETS	0.866	0.816	0.917	0.866	0.816	0.917	CLONAL	2	TRUE	0	0.415276620605269	2		394	740	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009852-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	42	145	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.534469387541625	2		145	148	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs149840192	NA	P-0009852-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1268	12596	547	0	ENST00000275493.2:c.866C>A	p.Ala289Asp	p.A289D	ENST00000275493	NM_005228.3	289	gCc/gAc	7/28	0.534469387541625	25	FACETS	1	0.999	1			1	CLONAL	24	TRUE	NA	0.534469387541625	25		547	13864	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0009852-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	288	596	0	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	1	2	FACETS	0.955	0.898	1	0.955	0.898	1	CLONAL	1	TRUE	1	0.534469387541625	2		596	1128	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348496	70348496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009852-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1301	360	572	0	ENST00000374080.3:c.3403C>T	p.Leu1135Phe	p.L1135F	ENST00000374080		1135	Ctc/Ttc	24/45	0.534469387541625	3	FACETS	1	0.965	1	0.514	0.486	0.543	CLONAL	1	TRUE	1	0.534469387541625	3		572	1661	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937379	76937379	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009852-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1204	260	494	1	ENST00000373344.5:c.3369C>A	p.Asn1123Lys	p.N1123K	ENST00000373344	NM_000489.3	1123	aaC/aaA	9/35	0.534469387541625	3	FACETS	0.842	0.787	0.899	0.421	0.393	0.45	CLONAL	1	TRUE	1	0.534469387541625	3		495	1464	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0009862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	43	219	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.895	0.749	1	0.895	0.749	1	CLONAL	1	TRUE	1	0.211225076410693	2		219	455	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0009862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	214	409	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.211225076410693	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.211225076410693	2		409	928	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0009862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	120	451	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.211225076410693	2		452	1021	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169724	11169724	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	103	491	0	ENST00000361445.4:c.7429G>A	p.Glu2477Lys	p.E2477K	ENST00000361445	NM_004958.3	2477	Gaa/Aaa	55/58	1	2	FACETS	0.977	0.873	1	0.977	0.873	1	CLONAL	1	TRUE	1	0.211225076410693	2		491	998	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570852	226570852	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	53	232	0	ENST00000366794.5:c.1044G>C	p.Leu348Phe	p.L348F	ENST00000366794	NM_001618.3	348	ttG/ttC	8/23	1	2	FACETS	0.876	0.747	1	0.876	0.747	1	CLONAL	1	TRUE	1	0.211225076410693	2		232	573	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099261	157099261	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	41	425	0	ENST00000346085.5:c.198C>A	p.Asn66Lys	p.N66K	ENST00000346085	NM_020732.3	66	aaC/aaA	1/20	1	2	FACETS	0.515	0.427	0.613	0.515	0.427	0.613	SUBCLONAL	1	TRUE	1	0.211225076410693	2		425	754	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984948	101984948	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	51	186	0	ENST00000282441.5:c.395T>G	p.Leu132Arg	p.L132R	ENST00000282441	NM_001130145.2	132	cTg/cGg	2/9	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.211225076410693	2		186	376	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231458	46231458	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	199	431	0	ENST00000334344.6:c.1298G>T	p.Cys433Phe	p.C433F	ENST00000334344	NM_152641.2	433	tGc/tTc	10/21	0.211225076410693	2	FACETS	0.972	0.901	1	0.972	0.901	1	CLONAL	2	TRUE	0	0.211225076410693	2		431	969	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506135	103506135	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375404851	NA	P-0009862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	77	348	4	ENST00000355739.4:c.293C>T	p.Ala98Val	p.A98V	ENST00000355739	NM_000123.3	98	gCg/gTg	3/15	1	2	FACETS	0.907	0.795	1	0.907	0.795	1	CLONAL	1	TRUE	1	0.211225076410693	2		352	804	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14628954	14628954	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	105	529	0	ENST00000254322.2:c.208G>C	p.Glu70Gln	p.E70Q	ENST00000254322	NM_006145.1	70	Gaa/Caa	1/3	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.211225076410693	2		529	985	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165101	47165111	+	frameshift_variant	Frame_Shift_Del	DEL	GAAAATTTTAA	GAAAATTTTAA	-	novel	NA	P-0009862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	165	362	0	ENST00000409792.3:c.1015_1025del	p.Leu339SerfsTer4	p.L339Sfs*4	ENST00000409792	NM_014159.6	339	TTAAAATTTTCa/a	3/21	1	2	FACETS	0.905	0.832	0.982	1	0.991	1	CLONAL	2	TRUE	1	0.211225076410693	2		362	863	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606120	81606120	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	122	575	0	ENST00000298171.2:c.791del	p.Pro264HisfsTer4	p.P264Hfs*4	ENST00000298171	NM_000369.2	264	Cca/ca	9/10	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.211225076410693	2		575	1040	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009893-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	481	407	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.700643503688243	4	FACETS	0.985	0.945	1			1	CLONAL	2	TRUE	NA	0.866725024941025	4		407	1052	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0009893-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	80	476	2	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.866725024941025	1	FACETS	0.333	0.296	0.372	0.333	0.296	0.372	SUBCLONAL	1	TRUE	0	0.866725024941025	1		478	314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578476	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTGCCGGGCGG	GGGTGCCGGGCGG	-	rs876659215	NA	P-0009893-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	557	350	0	ENST00000269305.4:c.454_466del	p.Pro152AlafsTer14	p.P152Afs*14	ENST00000269305	NM_001126112.2	152	CCGCCCGGCACCCgc/gc	5/11	0.861891170239083	2	FACETS	0.955	0.934	0.975	0.955	0.934	0.975	CLONAL	2	TRUE	0	0.866725024941025	2		350	673	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143324164	143324164	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009893-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	50	353	0	ENST00000262992.4:c.299C>T	p.Ser100Phe	p.S100F	ENST00000262992	NM_001101669.1	100	tCt/tTt	5/24	0.385834170677461	4	FACETS	0.302	0.255	0.353	0.075	0.063	0.089	INDETERMINATE	1	TRUE	0	0.866725024941025	4		353	714	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0009905-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	852	412	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.419733703365233	10	FACETS	0.948	0.925	0.97			1	CLONAL	9	TRUE	NA	0.419733703365233	10		412	1275	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0009905-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	283	598	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.419733703365233	2	FACETS	0.94	0.889	0.992	0.94	0.889	0.992	CLONAL	2	TRUE	0	0.419733703365233	2		598	717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574030	7574030	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009905-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	355	474	0	ENST00000269305.4:c.997del	p.Arg333ValfsTer12	p.R333Vfs*12	ENST00000269305	NM_001126112.2	333	Cgt/gt	10/11	0.419733703365233	3	FACETS	0.966	0.923	1	0.966	0.923	1	CLONAL	3	TRUE	0	0.419733703365233	3		474	706	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86658488	86658488	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009905-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	92	437	0	ENST00000274376.6:c.1453G>T	p.Gly485Cys	p.G485C	ENST00000274376	NM_002890.2	485	Ggc/Tgc	10/25	0.419733703365233	2	FACETS	1	0.961	1	0.58	0.519	0.644	CLONAL	1	TRUE	0	0.419733703365233	2		437	378	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164151	32164151	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009905-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	101	358	0	ENST00000375023.3:c.5248G>T	p.Ala1750Ser	p.A1750S	ENST00000375023	NM_004557.3	1750	Gcc/Tcc	29/30	0.419733703365233	3	FACETS	0.892	0.798	0.991	0.446	0.399	0.496	CLONAL	1	TRUE	1	0.419733703365233	3		358	653	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467910	50467910	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009905-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	87	255	0	ENST00000331340.3:c.1145T>C	p.Val382Ala	p.V382A	ENST00000331340	NM_006060.4	382	gTg/gCg	8/8	0.419733703365233	4	FACETS	0.974	0.864	1	0.487	0.432	0.546	CLONAL	1	TRUE	2	0.419733703365233	4		255	604	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427531	49427531	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780464972	NA	P-0009905-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	121	460	0	ENST00000301067.7:c.10957G>A	p.Gly3653Arg	p.G3653R	ENST00000301067	NM_003482.3	3653	Gga/Aga	39/54	0.419733703365233	3	FACETS	0.992	0.898	1	0.496	0.449	0.546	CLONAL	1	TRUE	1	0.419733703365233	3		460	703	SUCCESS
APC	324	MSKCC	GRCh37	5	112175630	112175630	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	220	663	1	ENST00000257430.4:c.4339C>T	p.Gln1447Ter	p.Q1447*	ENST00000257430	NM_000038.5	1447	Caa/Taa	16/16	0.544324234593578	1	FACETS	0.856	0.801	0.913	0.856	0.801	0.913	CLONAL	1	TRUE	0	0.549604691468885	1		664	678	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696438	47696438	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	245	558	0	ENST00000347630.2:c.385A>G	p.Lys129Glu	p.K129E	ENST00000347630	NM_001007230.1	129	Aaa/Gaa	6/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.549604691468885	2		558	770	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853028	151853028	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	161	238	0	ENST00000262189.6:c.11927del	p.Pro3976GlnfsTer11	p.P3976Qfs*11	ENST00000262189	NM_170606.2	3976	cCa/ca	46/59	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.549604691468885	2		238	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0009915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	162	379	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	0.664879712473812	1	FACETS	0.965	0.901	1	0.965	0.901	1	CLONAL	1	TRUE	0	0.664879712473812	1		379	337	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141128	55141128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	199	486	0	ENST00000257290.5:c.1774G>A	p.Gly592Arg	p.G592R	ENST00000257290	NM_006206.4	592	Gga/Aga	12/23	1	2	FACETS	0.969	0.902	1	0.969	0.902	1	CLONAL	1	TRUE	1	0.664879712473812	2		486	618	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528767	157528767	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	240	470	0	ENST00000346085.5:c.6492G>C	p.Glu2164Asp	p.E2164D	ENST00000346085	NM_020732.3	2164	gaG/gaC	20/20	1	2	FACETS	0.951	0.892	1	0.951	0.892	1	CLONAL	1	TRUE	1	0.664879712473812	2		470	759	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81340796	81340796	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0009915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	310	717	0	ENST00000222390.5:c.1444+1G>C		p.X482_splice	ENST00000222390	NM_000601.4	482			1	2	FACETS	0.995	0.941	1	0.995	0.941	1	CLONAL	1	TRUE	1	0.664879712473812	2		717	937	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830013	72830013	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0009915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	564	1041	0	ENST00000268489.5:c.6568A>T	p.Lys2190Ter	p.K2190*	ENST00000268489	NM_006885.3	2190	Aag/Tag	9/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.664879712473812	2		1041	1663	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532630	63532630	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	213	412	0	ENST00000307078.5:c.1949G>T	p.Arg650Leu	p.R650L	ENST00000307078	NM_004655.3	650	cGc/cTc	8/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.664879712473812	2		412	594	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665378	176665378	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	246	596	0	ENST00000439151.2:c.4065del	p.Leu1356TrpfsTer16	p.L1356Wfs*16	ENST00000439151	NM_022455.4	1354	ggC/gg	7/23	0.664879712473812	1	FACETS	0.874	0.825	0.924	0.874	0.825	0.924	CLONAL	1	TRUE	0	0.664879712473812	1		596	565	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271699	15271699	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	415	901	0	ENST00000263388.2:c.6740del	p.Pro2247HisfsTer82	p.P2247Hfs*82	ENST00000263388	NM_000435.2	2247	cCa/ca	33/33	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.664879712473812	2		901	1193	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	81	407	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	TRUE	1	0.15	2		407	885	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780068	NA	P-0009924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	51	373	0	ENST00000269305.4:c.472C>T	p.Arg158Cys	p.R158C	ENST00000269305	NM_001126112.2	158	Cgc/Tgc	5/11	1	2	FACETS	0.934	0.792	1	0.934	0.792	1	CLONAL	1	TRUE	1	0.15	2		373	728	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979371	93979371	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1192	77	723	0	ENST00000369303.4:c.1457G>T	p.Arg486Met	p.R486M	ENST00000369303	NM_004440.3	486	aGg/aTg	7/17	1	2	FACETS	0.809	0.708	0.919	0.809	0.708	0.919	CLONAL	1	TRUE	1	0.15	2		723	1269	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120509040	120509040	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	85	440	0	ENST00000256646.2:c.1526G>A	p.Cys509Tyr	p.C509Y	ENST00000256646	NM_024408.3	509	tGt/tAt	9/34	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.15	2		440	1070	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470925	25470925	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	83	561	0	ENST00000264709.3:c.836A>T	p.Asp279Val	p.D279V	ENST00000264709	NM_175629.2	279	gAt/gTt	7/23	1	2	FACETS	0.999	0.879	1	0.999	0.879	1	CLONAL	1	TRUE	1	0.15	2		561	1108	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656912	47656912	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	55	428	0	ENST00000233146.2:c.1108G>T	p.Ala370Ser	p.A370S	ENST00000233146	NM_000251.2	370	Gca/Tca	7/16	1	2	FACETS	0.743	0.633	0.864	0.743	0.633	0.864	SUBCLONAL	1	TRUE	1	0.15	2		428	987	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209108284	209108284	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	70	514	0	ENST00000345146.2:c.565A>T	p.Ile189Phe	p.I189F	ENST00000345146	NM_005896.2	189	Att/Ttt	6/10	1	2	FACETS	0.821	0.713	0.938	0.821	0.713	0.938	CLONAL	1	TRUE	1	0.15	2		514	1137	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161717	47161717	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	83	589	2	ENST00000409792.3:c.4409C>T	p.Pro1470Leu	p.P1470L	ENST00000409792	NM_014159.6	1470	cCa/cTa	3/21	1	2	FACETS	0.858	0.754	0.97	0.858	0.754	0.97	CLONAL	1	TRUE	1	0.15	2		591	1290	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164601	47164601	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0009924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	53	526	0	ENST00000409792.3:c.1525A>T	p.Lys509Ter	p.K509*	ENST00000409792	NM_014159.6	509	Aag/Tag	3/21	1	2	FACETS	0.685	0.582	0.799	0.685	0.582	0.799	SUBCLONAL	1	TRUE	1	0.15	2		526	1031	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564452	86564452	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	68	462	0	ENST00000274376.6:c.184G>T	p.Gly62Cys	p.G62C	ENST00000274376	NM_002890.2	62	Ggt/Tgt	1/25	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.15	2		462	889	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158719	26158719	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	21	144	0	ENST00000289316.2:c.322G>T	p.Ala108Ser	p.A108S	ENST00000289316	NM_138720.2	108	Gcc/Tcc	1/2	1	2	FACETS	1	0.842	1	1	0.842	1	CLONAL	1	TRUE	1	0.15	2		144	250	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526727	106526727	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	49	329	0	ENST00000359195.3:c.3020A>G	p.Gln1007Arg	p.Q1007R	ENST00000359195	NM_002649.2	1007	cAg/cGg	10/11	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.15	2		329	589	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100408	8100408	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1209	118	675	0	ENST00000346208.3:c.382G>T	p.Gly128Trp	p.G128W	ENST00000346208		128	Ggg/Tgg	3/6	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.15	2		675	1327	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50490728	50490728	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	102	477	0	ENST00000394963.4:c.1365G>T	p.Trp455Cys	p.W455C	ENST00000394963	NM_003076.4	455	tgG/tgT	11/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.15	2		477	1027	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680714	88680714	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs961685956	NA	P-0009924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	61	565	0	ENST00000360948.2:c.543G>T	p.Lys181Asn	p.K181N	ENST00000360948	NM_001012338.2	181	aaG/aaT	6/19	1	2	FACETS	0.806	0.693	0.93	0.806	0.693	0.93	CLONAL	1	TRUE	1	0.15	2		565	1009	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576054	29576054	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1226	90	601	1	ENST00000356175.3:c.4027A>T	p.Thr1343Ser	p.T1343S	ENST00000356175	NM_000267.3	1343	Act/Tct	30/57	1	2	FACETS	0.912	0.806	1	0.912	0.806	1	CLONAL	1	TRUE	1	0.15	2		602	1316	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4094482	4094482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879819202	NA	P-0009924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	53	455	1	ENST00000262948.5:c.1061C>T	p.Pro354Leu	p.P354L	ENST00000262948	NM_030662.3	354	cCa/cTa	10/11	1	2	FACETS	0.828	0.704	0.965	0.828	0.704	0.965	CLONAL	1	TRUE	1	0.15	2		456	853	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400147	139400148	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0009924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	70	540	0	ENST00000277541.6:c.4200_4201delinsTT	p.Gln1400_Gly1401delinsHisTrp	p.Q1400_G1401delinsHW	ENST00000277541	NM_017617.3	1400	caGGgg/caTTgg	25/34	1	2	FACETS	0.863	0.75	0.986	0.863	0.75	0.986	CLONAL	1	TRUE	1	0.15	2		540	1081	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696644	47696644	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519964	NA	P-0009939-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	36	644	0	ENST00000347630.2:c.304T>G	p.Phe102Val	p.F102V	ENST00000347630	NM_001007230.1	102	Ttc/Gtc	5/11	1	2	FACETS	0.9	0.74	1	0.9	0.74	1	CLONAL	1	TRUE	1	0.19	2		644	421	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221726	22221726	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009939-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	11	37	0	ENST00000215832.6:c.5C>T	p.Ala2Val	p.A2V	ENST00000215832	NM_002745.4	2	gCg/gTg	1/9	1	2	FACETS	0.965	0.671	1	0.965	0.671	1	CLONAL	1	TRUE	1	0.19	2		37	120	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0009957-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	150	411	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.156080654583942	3	FACETS	0.812	0.743	0.885	0.812	0.743	0.885	INDETERMINATE	2	TRUE	1	0.269667961659912	3		411	777	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781504	NA	P-0009957-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	78	374	0	ENST00000269305.4:c.314G>A	p.Gly105Asp	p.G105D	ENST00000269305	NM_001126112.2	105	gGc/gAc	4/11	1	2	FACETS	0.866	0.761	0.979	0.866	0.761	0.979	CLONAL	1	TRUE	1	0.269667961659912	2		374	668	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0009957-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	118	436	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.269667961659912	2		436	785	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161355	185161355	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009957-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	123	481	0	ENST00000265026.3:c.782C>G	p.Thr261Arg	p.T261R	ENST00000265026	NM_004721.4	261	aCa/aGa	4/14	NA	2	FACETS	0.942	0.851	1			1	INDETERMINATE	1	TRUE	NA	0.269667961659912	2		481	968	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009958-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	305	241	1	ENST00000397752.3:c.3028G>A	p.Asp1010Asn	p.D1010N	ENST00000397752	NM_000245.2	1010	Gat/Aat	14/21	0.688903634333	3	FACETS	1	0.994	1	0.734	0.695	0.774	CLONAL	1	TRUE	1	0.688903634333	3		242	811	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797786	42797786	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009958-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	59	402	0	ENST00000575354.2:c.3838G>A	p.Gly1280Arg	p.G1280R	ENST00000575354	NM_015125.3	1280	Ggg/Agg	16/20	1	2	FACETS	0.227	0.194	0.262	0.227	0.194	0.262	SUBCLONAL	1	TRUE	1	0.688903634333	2		402	756	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604754	48604754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009958-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	85	450	0	ENST00000342988.3:c.1576G>A	p.Glu526Lys	p.E526K	ENST00000342988	NM_005359.5	526	Gaa/Aaa	12/12	1	2	FACETS	0.297	0.261	0.334	0.297	0.261	0.334	SUBCLONAL	1	TRUE	1	0.688903634333	2		450	832	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924966	49924966	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009958-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	99	464	1	ENST00000296474.3:c.3977C>A	p.Ala1326Glu	p.A1326E	ENST00000296474	NM_002447.2	1326	gCa/gAa	20/20	1	2	FACETS	0.274	0.244	0.306	0.274	0.244	0.306	SUBCLONAL	1	TRUE	1	0.688903634333	2		465	1049	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522348	176522348	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009958-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	85	387	1	ENST00000292408.4:c.1537G>T	p.Asp513Tyr	p.D513Y	ENST00000292408	NM_213647.1	513	Gac/Tac	12/18	1	2	FACETS	0.342	0.302	0.385	0.342	0.302	0.385	SUBCLONAL	1	TRUE	1	0.688903634333	2		388	722	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772068	135772068	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009958-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	22	157	0	ENST00000298552.3:c.3049G>C	p.Glu1017Gln	p.E1017Q	ENST00000298552	NM_001162426.1	1017	Gag/Cag	23/23	1	2	FACETS	0.229	0.177	0.289	0.229	0.177	0.289	SUBCLONAL	1	TRUE	1	0.688903634333	2		157	279	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649842	88649842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009958-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	46	258	0	ENST00000372037.3:c.91C>T	p.His31Tyr	p.H31Y	ENST00000372037	NM_004329.2	31	Cat/Tat	4/13	1	2	FACETS	0.231	0.194	0.272	0.231	0.194	0.272	SUBCLONAL	1	TRUE	1	0.688903634333	2		258	577	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699288	18699288	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867629250	NA	P-0009958-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	97	432	0	ENST00000266497.5:c.3389G>A	p.Gly1130Glu	p.G1130E	ENST00000266497		1130	gGa/gAa	24/31	1	2	FACETS	0.255	0.226	0.286	0.255	0.226	0.286	SUBCLONAL	1	TRUE	1	0.688903634333	2		432	1104	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0009961-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	106	268	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.14994246069292	3	FACETS	1	0.958	1	0.565	0.507	0.627	INDETERMINATE	1	TRUE	1	0.301590027396693	3		268	716	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437262	52437262	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009961-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	172	650	0	ENST00000460680.1:c.1782del	p.Ser595ProfsTer22	p.S595Pfs*22	ENST00000460680	NM_004656.3	594	ggG/gg	14/17	0.301590027396693	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.301590027396693	1		650	804	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0009966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	95	401	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	0.365715015157073	2		401	424	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176145125	176145125	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	81	408	0	ENST00000367669.3:c.486G>C	p.Gln162His	p.Q162H	ENST00000367669	NM_022457.5	162	caG/caC	3/20	0.340592131559534	3	FACETS	0.787	0.693	0.887	0.393	0.346	0.444	SUBCLONAL	1	TRUE	1	0.365715015157073	3		408	666	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523100	176523100	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	150	386	0	ENST00000292408.4:c.1864G>C	p.Glu622Gln	p.E622Q	ENST00000292408	NM_213647.1	622	Gag/Cag	14/18	1	2	FACETS	0.696	0.634	0.76	0.696	0.634	0.76	SUBCLONAL	1	TRUE	1	0.365715015157073	2		386	1179	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2215902	2215902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1157927438	NA	P-0009966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1877	208	597	0	ENST00000326181.6:c.104G>A	p.Gly35Glu	p.G35E	ENST00000326181	NM_032271.2	35	gGa/gAa	3/21	0.365715015157073	3	FACETS	0.645	0.596	0.697	0.323	0.298	0.349	SUBCLONAL	1	TRUE	1	0.365715015157073	3		597	2085	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845585	68845585	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0009966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	161	298	0	ENST00000261769.5:c.833-2A>T		p.X278_splice	ENST00000261769	NM_004360.3	278			0.320101180918928	1	FACETS	0.928	0.853	1	0.928	0.853	1	CLONAL	1	TRUE	0	0.365715015157073	1		298	775	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0009982-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	286	550	1	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.453020731626951	2		551	1091	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589663	67589663	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587777709	NA	P-0009982-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	98	240	0	ENST00000274335.5:c.1425+1G>A		p.X475_splice	ENST00000274335		475			1	2	FACETS	0.888	0.796	0.986	0.888	0.796	0.986	CLONAL	1	TRUE	1	0.453020731626951	2		240	487	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760997	133760997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009982-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	325	429	0	ENST00000318560.5:c.3320G>A	p.Gly1107Asp	p.G1107D	ENST00000318560	NM_005157.4	1107	gGt/gAt	11/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.453020731626951	2		429	1355	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336068	73336068	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009982-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	155	331	0	ENST00000377767.4:c.2335A>T	p.Ile779Phe	p.I779F	ENST00000377767	NM_014953.3	779	Att/Ttt	17/21	1	2	FACETS	0.936	0.859	1	0.936	0.859	1	CLONAL	1	TRUE	1	0.453020731626951	2		331	731	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593468	55593468	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009986-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	311	623	0	ENST00000288135.5:c.1625T>C	p.Ile542Thr	p.I542T	ENST00000288135	NM_000222.2	542	aTt/aCt	10/21	0.666847177399002	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.666847177399002	1		623	601	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5029809	5029809	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009986-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	54	598	0	ENST00000381652.3:c.253T>C	p.Phe85Leu	p.F85L	ENST00000381652	NM_004972.3	85	Ttt/Ctt	4/25	0.288394339143405	3	FACETS	0.304	0.259	0.354	0.152	0.129	0.177	INDETERMINATE	1	TRUE	1	0.666847177399002	3		598	710	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578520	7578525	+	inframe_deletion	In_Frame_Del	DEL	AGTTGG	AGTTGG	-	novel	NA	P-0009986-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	529	588	0	ENST00000269305.4:c.405_410del	p.Cys135_Leu137delinsTrp	p.C135_L137delinsW	ENST00000269305	NM_001126112.2	135	tgCCAACTg/tgg	5/11	0.666847177399002	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.666847177399002	1		588	913	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249478	153249496	+	frameshift_variant	Frame_Shift_Del	DEL	TGATGTTGTCTCTCATTTG	TGATGTTGTCTCTCATTTG	-	novel	NA	P-0009986-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	202	516	0	ENST00000281708.4:c.1282_1300del	p.Gln428SerfsTer64	p.Q428Sfs*64	ENST00000281708	NM_033632.3	428	CAAATGAGAGACAACATCAtc/tc	9/12	0.666847177399002	1	FACETS	0.895	0.84	0.951	0.895	0.84	0.951	CLONAL	1	TRUE	0	0.666847177399002	1		516	451	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096124	71096124	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	191	311	1	ENST00000318789.4:c.633G>T	p.Gln211His	p.Q211H	ENST00000318789	NM_032682.5	211	caG/caT	10/21	0.741031552430547	2	FACETS	1	0.975	1	0.545	0.509	0.581	CLONAL	1	FALSE	0	0.738162884983194	2		312	475	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063628	67063628	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0009991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	281	263	0	ENST00000412916.2:c.79-2A>G		p.X27_splice	ENST00000412916		27			0.741031552430547	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	FALSE	0	0.738162884983194	2		263	332	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100676	27100983	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAAAAGACAATTTGTTAAGGTGATTCCCATGTTTTCTTGGAGTCTGTGTCCACCAAGCATCTGGTTGTAGCCATCTTGGCATCTGTGGGCTTTATGTCCCTGAGTGCAGAGTATTAACTTCCCCTCTGCTTGTCTCTGCCTTAGAATTACAAGCGGCCAATGGATGGCACATATGGCCCTCCTGCCAAGCGGCACGAAGGGGAGATGTACAGCGTGCCATACAGCACTGGGCAGGGGCAGCCTCAGCAGCAGCAGTTGCCCCCAGCCCAGCCCCAGCCTGCCAGCCAGCAACAAGCTGCCCAGCCTTC	CAAAAGACAATTTGTTAAGGTGATTCCCATGTTTTCTTGGAGTCTGTGTCCACCAAGCATCTGGTTGTAGCCATCTTGGCATCTGTGGGCTTTATGTCCCTGAGTGCAGAGTATTAACTTCCCCTCTGCTTGTCTCTGCCTTAGAATTACAAGCGGCCAATGGATGGCACATATGGCCCTCCTGCCAAGCGGCACGAAGGGGAGATGTACAGCGTGCCATACAGCACTGGGCAGGGGCAGCCTCAGCAGCAGCAGTTGCCCCCAGCCCAGCCCCAGCCTGCCAGCCAGCAACAAGCTGCCCAGCCTTC	-	novel	NA	P-0009991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	101	72	0	ENST00000324856.7:c.4102-143_4266del		p.X1368_splice	ENST00000324856	NM_006015.4	1368		18/20	0.538755831383624	6	FACETS	0.896	0.824	0.968	1	0.978	1	CLONAL	4	FALSE	3	0.738162884983194	6		72	189	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752729	128752731	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs1203089442	NA	P-0009991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	193	279	0	ENST00000377970.2:c.892_894del	p.Ser298del	p.S298del	ENST00000377970	NM_002467.4	297	cCTTct/cct	3/3	0.682549497319609	4	FACETS	1	0.991	1	0.735	0.684	0.788	CLONAL	1	FALSE	2	0.738162884983194	4		279	618	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595596	55595596	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001319-T05-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	369	429	0	ENST00000288135.5:c.2086G>T	p.Asp696Tyr	p.D696Y	ENST00000288135	NM_000222.2	696	Gat/Tat	14/21	1	2	FACETS	0.957	0.912	1	0.957	0.912	1	CLONAL	1	TRUE	1	0.838017035972166	2		429	920	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591300	67591330	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AATGAAAACACTGAAGAGTAAGTAGTTACTA	AATGAAAACACTGAAGAGTAAGTAGTTACTA	-	novel	NA	P-0001319-T05-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	86	359	0	ENST00000274335.5:c.1800_1814+16del		p.X600_splice	ENST00000274335		600		13/15	0.786289773918418	1	FACETS	0.263	0.234	0.295	0.263	0.234	0.295	SUBCLONAL	1	TRUE	0	0.838017035972166	1		359	453	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217858	7217858	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001319-T05-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	698	761	0	ENST00000380728.2:c.153del	p.Lys52ArgfsTer11	p.K52Rfs*11	ENST00000380728		51	agG/ag	3/11	0.838331488835775	1	FACETS	0.915	0.89	0.939	0.915	0.89	0.939	CLONAL	1	TRUE	0	0.838017035972166	1		761	1058	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39746938	39746938	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0001319-T05-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	55	367	0	ENST00000361337.2:c.1950+2T>C		p.X650_splice	ENST00000361337	NM_003286.2	650			1	2	FACETS	0.133	0.113	0.155	0.133	0.113	0.155	SUBCLONAL	1	TRUE	1	0.838017035972166	2		367	987	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0001347-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	160	194	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.16509651938961	2	FACETS	1	0.987	1	0.662	0.613	0.713	INDETERMINATE	1	TRUE	0	0.51829727402236	2		194	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0001347-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	428	637	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.51829727402236	2		637	1408	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0001347-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	156	445	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.223892754729222	0	FACETS	0.345	0.316	0.376			1	INDETERMINATE	1	TRUE	0	0.51829727402236	0		445	840	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933214	49933214	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001347-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1520	205	609	0	ENST00000296474.3:c.2896C>G	p.Leu966Val	p.L966V	ENST00000296474	NM_002447.2	966	Ctg/Gtg	12/20	0.16509651938961	2	FACETS	0.459	0.423	0.495	0.229	0.211	0.248	INDETERMINATE	1	TRUE	0	0.51829727402236	2		609	1725	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651523	52651523	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001347-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	77	416	0	ENST00000394830.3:c.1573A>G	p.Ile525Val	p.I525V	ENST00000394830	NM_018313.4	525	Atc/Gtc	15/30	0.16509651938961	2	FACETS	0.31	0.272	0.352	0.155	0.136	0.176	INDETERMINATE	1	TRUE	0	0.51829727402236	2		416	957	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38978730	38978730	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001347-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	261	271	0	ENST00000357387.3:c.776A>G	p.Asp259Gly	p.D259G	ENST00000357387	NM_152756.3	259	gAt/gGt	9/38	0.16509651938961	2	FACETS	1	0.992	1	0.668	0.628	0.708	INDETERMINATE	1	TRUE	0	0.51829727402236	2		271	754	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205322	46205322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001347-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	51	269	0	ENST00000334344.6:c.406C>T	p.His136Tyr	p.H136Y	ENST00000334344	NM_152641.2	136	Cac/Tac	4/21	1	2	FACETS	0.296	0.251	0.346	0.296	0.251	0.346	SUBCLONAL	1	TRUE	1	0.51829727402236	2		269	664	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435831	56435831	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1025275269	NA	P-0001347-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	239	266	0	ENST00000407977.2:c.1306C>T	p.Arg436Cys	p.R436C	ENST00000407977		436	Cgc/Tgc	9/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.51829727402236	2		266	877	SUCCESS
APC	324	MSKCC	GRCh37	5	112175606	112175606	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001347-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	191	423	0	ENST00000257430.4:c.4316del	p.Pro1439LeufsTer34	p.P1439Lfs*34	ENST00000257430	NM_000038.5	1439	Cct/ct	16/16	0.223892754729222	0	FACETS	0.344	0.318	0.371			1	INDETERMINATE	1	TRUE	0	0.51829727402236	0		423	1032	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907822	76907822	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001364-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	357	379	0	ENST00000373344.5:c.4339G>T	p.Glu1447Ter	p.E1447*	ENST00000373344	NM_000489.3	1447	Gag/Tag	15/35	0.326457255006525	3	FACETS	0.815	0.776	0.854	0.815	0.776	0.854	INDETERMINATE	2	TRUE	1	0.71232677734702	3		379	834	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944260	206944260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746523858	NA	P-0001364-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	243	399	2	ENST00000423557.1:c.370C>T	p.Arg124Trp	p.R124W	ENST00000423557	NM_000572.2	124	Cgg/Tgg	3/5	0.488007476961389	6	FACETS	1	0.989	1	0.426	0.397	0.456	CLONAL	1	TRUE	3	0.71232677734702	6		401	1295	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574693	64574693	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1114167472	NA	P-0001526-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	254	317	0	ENST00000312049.6:c.784-2A>G		p.X262_splice	ENST00000312049	NM_130799.2	262			0.68414209397359	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.68414209397359	1		317	466	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825407	134825407	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001526-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	79	440	0	ENST00000398015.3:c.923A>G	p.Tyr308Cys	p.Y308C	ENST00000398015	NM_004441.4	308	tAc/tGc	4/16	0.68414209397359	1	FACETS	0.29	0.255	0.327	0.29	0.255	0.327	SUBCLONAL	1	TRUE	0	0.68414209397359	1		440	524	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288180	33288180	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001526-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	126	292	0	ENST00000374542.5:c.1228G>T	p.Glu410Ter	p.E410*	ENST00000374542	NM_001141970.1	410	Gaa/Taa	4/8	0.68414209397359	1	FACETS	0.929	0.858	0.999	0.929	0.858	0.999	CLONAL	1	TRUE	0	0.68414209397359	1		292	261	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170590	108170590	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001526-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	39	392	0	ENST00000278616.4:c.5155A>G	p.Asn1719Asp	p.N1719D	ENST00000278616	NM_000051.3	1719	Aat/Gat	34/63	0.68414209397359	1	FACETS	0.354	0.296	0.417	0.354	0.296	0.417	SUBCLONAL	1	TRUE	0	0.68414209397359	1		392	212	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914394	32914394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555284455	NA	P-0001526-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	53	620	0	ENST00000380152.3:c.5902T>C	p.Ser1968Pro	p.S1968P	ENST00000380152		1968	Tca/Cca	11/27	1	2	FACETS	0.355	0.303	0.411	0.355	0.303	0.411	SUBCLONAL	1	TRUE	1	0.68414209397359	2		620	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0001627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	160	300	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.46117162364501	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.520797956510198	1		300	445	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952086	178952086	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	166	363	1	ENST00000263967.3:c.3141T>A	p.His1047Gln	p.H1047Q	ENST00000263967	NM_006218.2	1047	caT/caA	21/21	1	2	FACETS	0.884	0.814	0.957	0.884	0.814	0.957	CLONAL	1	TRUE	1	0.520797956510198	2		364	721	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293664	1293664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111952055	NA	P-0001627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	743	250	0	ENST00000310581.5:c.1337G>A	p.Arg446His	p.R446H	ENST00000310581	NM_198253.2	446	cGt/cAt	2/16	0.520797956510198	10	FACETS	1	0.995	1			1	CLONAL	9	TRUE	NA	0.520797956510198	10		250	931	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584497	48584497	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001627-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	37	225	0	ENST00000342988.3:c.670C>T	p.Gln224Ter	p.Q224*	ENST00000342988	NM_005359.5	224	Cag/Tag	6/12	0.475444950883169	1	FACETS	0.395	0.327	0.47	0.395	0.327	0.47	SUBCLONAL	1	TRUE	0	0.520797956510198	1		225	266	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0001688-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	384	210	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.494016537585571	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.494016537585571	2		210	740	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0001688-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	113	188	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	NA	2	FACETS	0.86	0.777	0.947			1	INDETERMINATE	1	TRUE	NA	0.494016537585571	2		188	532	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160227	22160227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001688-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	269	390	0	ENST00000215832.6:c.404G>A	p.Arg135Lys	p.R135K	ENST00000215832	NM_002745.4	135	aGa/aAa	3/9	0.494016537585571	2	FACETS	1	0.968	1	0.524	0.491	0.557	CLONAL	1	TRUE	0	0.494016537585571	2		390	1040	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150031	202150031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167464002	NA	P-0001688-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	385	283	0	ENST00000358485.4:c.1472G>A	p.Arg491Gln	p.R491Q	ENST00000358485	NM_001080125.1	491	cGa/cAa	8/9	0.494016537585571	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.494016537585571	2		283	731	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157758	106157758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001688-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	169	277	0	ENST00000380013.4:c.2659G>A	p.Glu887Lys	p.E887K	ENST00000380013	NM_001127208.2	887	Gag/Aag	3/11	1	2	FACETS	0.868	0.799	0.94	0.868	0.799	0.94	CLONAL	1	TRUE	1	0.494016537585571	2		277	788	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038431	180038431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001688-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	239	336	0	ENST00000261937.6:c.3586G>A	p.Glu1196Lys	p.E1196K	ENST00000261937	NM_182925.4	1196	Gag/Aag	27/30	0.494016537585571	2	FACETS	1	0.984	1	0.577	0.54	0.615	CLONAL	1	TRUE	0	0.494016537585571	2		336	838	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548886	29548886	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs953440640	NA	P-0001688-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	86	233	0	ENST00000356175.3:c.1660C>T	p.Gln554Ter	p.Q554*	ENST00000356175	NM_000267.3	554	Cag/Tag	15/57	1	2	FACETS	0.755	0.671	0.845	0.755	0.671	0.845	SUBCLONAL	1	TRUE	1	0.494016537585571	2		233	461	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612879	228612879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767647652	NA	P-0001688-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1649	383	500	0	ENST00000366696.1:c.148C>T	p.Arg50Cys	p.R50C	ENST00000366696	NM_003493.2	50	Cgc/Tgc	1/1	0.494016537585571	4	FACETS	1	0.988	1	0.57	0.539	0.602	CLONAL	1	TRUE	2	0.494016537585571	4		500	2032	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0002208-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	269	254	7	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.357120212063441	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.450052212865113	2		261	565	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197766	66197766	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002208-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	80	424	1	ENST00000273854.3:c.2933A>G	p.Lys978Arg	p.K978R	ENST00000273854	NM_004439.5	978	aAg/aGg	17/18	0.450052212865113	1	FACETS	0.685	0.607	0.769	0.685	0.607	0.769	SUBCLONAL	1	TRUE	0	0.450052212865113	1		425	402	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346184	152346190	+	frameshift_variant	Frame_Shift_Del	DEL	GTAAGAA	GTAAGAA	-	novel	NA	P-0002208-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	280	684	0	ENST00000359321.1:c.380_386del	p.Leu127HisfsTer5	p.L127Hfs*5	ENST00000359321	NM_005431.1	127	cTTCTTACa/ca	3/3	0.411341558733304	3	FACETS	0.869	0.819	0.92	0.869	0.819	0.92	CLONAL	2	TRUE	1	0.450052212865113	3		684	877	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0002512-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	435	595	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.245490745262897	3	FACETS	0.92	0.88	0.961			1	CLONAL	3	TRUE	NA	0.336078882039428	3		597	1095	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979436	2979436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs897102417	NA	P-0002512-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	133	440	1	ENST00000396946.4:c.811C>T	p.Arg271Trp	p.R271W	ENST00000396946	NM_032415.4	271	Cgg/Tgg	6/25	0.336078882039428	3	FACETS	0.862	0.782	0.948			1	CLONAL	1	TRUE	NA	0.336078882039428	3		441	1072	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604754	48604754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002512-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	113	408	0	ENST00000342988.3:c.1576G>A	p.Glu526Lys	p.E526K	ENST00000342988	NM_005359.5	526	Gaa/Aaa	12/12	0.336078882039428	1	FACETS	0.975	0.88	1	0.975	0.88	1	CLONAL	1	TRUE	0	0.336078882039428	1		408	574	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0002981-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	151	326	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.39254822793608	2		326	517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0002981-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	636	522	0	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	0.39254822793608	2	FACETS	1	0.971	1	1	0.998	1	CLONAL	3	TRUE	0	0.39254822793608	2		522	1078	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0002990-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	259	360	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.899	0.846	0.952	0.899	0.846	0.952	CLONAL	1	TRUE	1	0.808211987687518	2		360	713	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421807	49421808	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0002990-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	455	712	0	ENST00000301067.7:c.14499_14500del	p.Glu4834SerfsTer2	p.E4834Sfs*2	ENST00000301067	NM_003482.3	4833	ggGGaa/ggaa	46/54	1	2	FACETS	0.966	0.924	1	0.966	0.924	1	CLONAL	1	TRUE	1	0.808211987687518	2		712	1166	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0003135-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	132	552	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.319636663378155	3	FACETS	0.956	0.867	1	0.478	0.433	0.525	CLONAL	1	TRUE	1	0.319636663378155	3		552	1002	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70355083	70355083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779481901	NA	P-0003135-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	127	369	0	ENST00000374080.3:c.5005G>A	p.Asp1669Asn	p.D1669N	ENST00000374080		1669	Gat/Aat	36/45	1	1	FACETS	0.959	0.87	1	0.959	0.87	1	CLONAL	1	TRUE	0	0.319636663378155	1		369	696	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8497263	8497263	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs778423564	NA	P-0003135-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	40	368	0	ENST00000356435.5:c.2328A>C	p.Glu776Asp	p.E776D	ENST00000356435		776	gaA/gaC	15/35	1	2	FACETS	0.399	0.33	0.475	0.399	0.33	0.475	SUBCLONAL	1	TRUE	1	0.319636663378155	2		368	628	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913517	NA	P-0003416-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	393	430	0	ENST00000288135.5:c.1676T>A	p.Val559Asp	p.V559D	ENST00000288135	NM_000222.2	559	gTt/gAt	11/21	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.708357978415993	2		430	1007	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021203	31021203	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003416-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	73	470	0	ENST00000375687.4:c.1202C>T	p.Thr401Ile	p.T401I	ENST00000375687	NM_015338.5	401	aCc/aTc	12/13	1	2	FACETS	0.195	0.17	0.222	0.195	0.17	0.222	SUBCLONAL	1	TRUE	1	0.708357978415993	2		470	1057	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	123	260	0				ENST00000310581	NM_198253.2	-/1132			0.745072266953162	3	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.786066633307053	3		260	358	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057649	27057649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	408	615	0	ENST00000324856.7:c.1357C>T	p.Pro453Ser	p.P453S	ENST00000324856	NM_006015.4	453	Cct/Tct	3/20	0.786066633307053	4	FACETS	0.952	0.909	0.995	0.952	0.909	0.995	CLONAL	2	TRUE	2	0.786066633307053	4		615	974	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837973	156837973	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	285	631	1	ENST00000524377.1:c.506G>A	p.Gly169Glu	p.G169E	ENST00000524377	NM_002529.3	169	gGa/gAa	5/17	0.786066633307053	5	FACETS	0.853	0.804	0.904	0.569	0.536	0.603	CLONAL	2	TRUE	2	0.786066633307053	5		632	926	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849110	156849110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	481	693	0	ENST00000524377.1:c.2002G>A	p.Asp668Asn	p.D668N	ENST00000524377	NM_002529.3	668	Gat/Aat	15/17	0.786066633307053	5	FACETS	0.937	0.901	0.973	0.937	0.901	0.973	CLONAL	3	TRUE	2	0.786066633307053	5		693	949	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594221	55594221	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913512	NA	P-0003620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	308	477	0	ENST00000288135.5:c.1924A>G	p.Lys642Glu	p.K642E	ENST00000288135	NM_000222.2	642	Aaa/Gaa	13/21	0.786066633307053	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.786066633307053	3		477	519	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968136	55968136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747362899	NA	P-0003620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	183	589	1	ENST00000263923.4:c.2194G>A	p.Glu732Lys	p.E732K	ENST00000263923	NM_002253.2	732	Gaa/Aaa	15/30	0.786066633307053	3	FACETS	0.99	0.918	1	0.495	0.459	0.533	CLONAL	1	TRUE	1	0.786066633307053	3		590	655	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721094	176721094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	113	347	0	ENST00000439151.2:c.6725G>A	p.Gly2242Glu	p.G2242E	ENST00000439151	NM_022455.4	2242	gGa/gAa	23/23	0.786066633307053	3	FACETS	1	0.947	1	0.531	0.482	0.582	CLONAL	1	TRUE	1	0.786066633307053	3		347	377	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467732	50467732	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	125	539	0	ENST00000331340.3:c.967G>T	p.Gly323Trp	p.G323W	ENST00000331340	NM_006060.4	323	Ggg/Tgg	8/8	0.786066633307053	6	FACETS	0.748	0.676	0.825	0.187	0.169	0.207	SUBCLONAL	1	TRUE	2	0.786066633307053	6		539	1093	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515023	148515023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	167	619	0	ENST00000320356.2:c.1186G>A	p.Glu396Lys	p.E396K	ENST00000320356	NM_004456.4	396	Gag/Aag	10/20	0.786066633307053	3	FACETS	0.813	0.749	0.88	0.407	0.374	0.44	CLONAL	1	TRUE	1	0.786066633307053	3		619	728	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015115	37015115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	302	568	1	ENST00000358127.4:c.289G>A	p.Glu97Lys	p.E97K	ENST00000358127	NM_001280556.1	97	Gaa/Aaa	3/10	0.408720828668795	6	FACETS	1	0.952	1			1	INDETERMINATE	3	TRUE	NA	0.786066633307053	6		569	657	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412642	139412642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	429	581	0	ENST00000277541.6:c.1202C>T	p.Pro401Leu	p.P401L	ENST00000277541	NM_017617.3	401	cCc/cTc	7/34	0.781216363565498	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.786066633307053	2		581	535	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711914	89711914	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	293	405	0	ENST00000371953.3:c.532T>C	p.Tyr178His	p.Y178H	ENST00000371953	NM_000314.4	178	Tat/Cat	6/9	NA	2	FACETS	0.953	0.919	0.986			1	INDETERMINATE	2	TRUE	NA	0.786066633307053	2		405	391	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711935	89711935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	276	369	0	ENST00000371953.3:c.553C>T	p.His185Tyr	p.H185Y	ENST00000371953	NM_000314.4	185	Cat/Tat	6/9	NA	2	FACETS	0.957	0.922	0.99			1	INDETERMINATE	2	TRUE	NA	0.786066633307053	2		369	367	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575044	64575044	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894268	NA	P-0003620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	381	463	0	ENST00000312049.6:c.763G>A	p.Glu255Lys	p.E255K	ENST00000312049	NM_130799.2	255	Gag/Aag	4/10	0.750665239108453	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.786066633307053	4		463	861	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94211948	94211949	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0003620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	262	489	0	ENST00000323929.3:c.496_497delinsTT	p.Pro166Leu	p.P166L	ENST00000323929	NM_005591.3	166	CCg/TTg	6/20	0.750665239108453	4	FACETS	0.8	0.753	0.848	0.8	0.753	0.848	SUBCLONAL	2	TRUE	2	0.786066633307053	4		489	744	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376322	118376322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	429	864	0	ENST00000534358.1:c.9715C>T	p.Pro3239Ser	p.P3239S	ENST00000534358	NM_005933.3	3239	Ccc/Tcc	27/36	0.786066633307053	4	FACETS	0.911	0.871	0.952			1	CLONAL	2	TRUE	NA	0.786066633307053	4		864	1070	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715777	18715777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1203196085	NA	P-0003620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	343	503	2	ENST00000266497.5:c.3608G>A	p.Arg1203Lys	p.R1203K	ENST00000266497		1203	aGg/aAg	25/31	0.538999627415368	4	FACETS	1	0.994	1	0.826	0.79	0.862	CLONAL	2	TRUE	1	0.786066633307053	4		505	629	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145338	58145338	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555201372	NA	P-0003620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	440	478	1	ENST00000257904.6:c.163C>T	p.Arg55Cys	p.R55C	ENST00000257904	NM_000075.3	55	Cgt/Tgt	2/8	0.538999627415368	4	FACETS	0.849	0.817	0.881	0.849	0.817	0.881	CLONAL	3	TRUE	1	0.786066633307053	4		479	785	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984848	9984848	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	221	547	1	ENST00000330684.3:c.1117G>A	p.Glu373Lys	p.E373K	ENST00000330684	NM_001134407.1	373	Gaa/Aaa	4/13	0.443119561078709	5	FACETS	1	0.988	1	0.801	0.753	0.849	INDETERMINATE	2	TRUE	2	0.786066633307053	5		548	510	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110584	4110584	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519807	NA	P-0003620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	419	542	0	ENST00000262948.5:c.373T>A	p.Cys125Ser	p.C125S	ENST00000262948	NM_030662.3	125	Tgc/Agc	3/11	0.750665239108453	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.786066633307053	4		542	894	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546620	9546620	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764351685	NA	P-0003620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	310	579	1	ENST00000353224.5:c.1402G>A	p.Glu468Lys	p.E468K	ENST00000353224	NM_177990.2	468	Gag/Aag	5/10	0.513073951169939	6	FACETS	0.867	0.822	0.913	0.867	0.822	0.913	CLONAL	3	TRUE	3	0.786066633307053	6		580	780	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024038	31024038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1569336680	NA	P-0003620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	392	562	1	ENST00000375687.4:c.3523G>A	p.Glu1175Lys	p.E1175K	ENST00000375687	NM_015338.5	1175	Gag/Aag	13/13	0.513073951169939	6	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	3	0.786066633307053	6		563	801	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003693-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	52	260	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.21	2		260	394	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370786	225370786	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003693-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	138	395	0	ENST00000264414.4:c.1093C>G	p.Leu365Val	p.L365V	ENST00000264414	NM_003590.4	365	Ctc/Gtc	8/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.21	2		395	1198	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047906	180047906	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003693-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	44	422	1	ENST00000261937.6:c.2269G>A	p.Val757Ile	p.V757I	ENST00000261937	NM_182925.4	757	Gtc/Atc	15/30	1	2	FACETS	0.63	0.527	0.744	0.63	0.527	0.744	SUBCLONAL	1	TRUE	1	0.21	2		423	665	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273049	55273049	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003693-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	83	435	0	ENST00000275493.2:c.3372C>G	p.His1124Gln	p.H1124Q	ENST00000275493	NM_005228.3	1124	caC/caG	28/28	0.226947172213293	3	FACETS	0.921	0.811	1	0.461	0.405	0.52	CLONAL	1	TRUE	1	0.21	3		435	948	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135800973	135800973	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs118203372	NA	P-0003693-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	49	340	0	ENST00000298552.3:c.363+1G>A		p.X121_splice	ENST00000298552	NM_001162426.1	121			1	2	FACETS	0.657	0.555	0.77	0.657	0.555	0.77	SUBCLONAL	1	TRUE	1	0.21	2		340	710	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720650	89720650	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0003693-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	18	81	0	ENST00000371953.3:c.802-1G>C		p.X268_splice	ENST00000371953	NM_000314.4	268			0.175803422271508	1	FACETS	0.701	0.529	0.902	0.701	0.529	0.902	CLONAL	1	TRUE	0	0.21	1		81	219	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251576	212251576	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0003908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	533	109	248	0	ENST00000342788.4:c.3481+2T>A		p.X1161_splice	ENST00000342788	NM_005235.2	1161			0.3	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.16	3		248	642	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914637	39914644	+	frameshift_variant	Frame_Shift_Del	DEL	CATAAGTT	CATAAGTT	-	novel	NA	P-0003908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	612	45	346	0	ENST00000378444.4:c.4718_4725del	p.Glu1573GlyfsTer10	p.E1573Gfs*10	ENST00000378444	NM_001123385.1	1573	gAACTTATG/g	12/15	1	1	FACETS	0.788	0.661	0.929	0.788	0.661	0.929	CLONAL	1	TRUE	0	0.16	1		346	657	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	rs786202799	NA	P-0003916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	173	177	0	ENST00000269305.4:c.376-2A>T		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.813480149308638	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.81564764744778	2		177	212	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797111	45797111	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	202	338	0	ENST00000450313.1:c.1304A>G	p.His435Arg	p.H435R	ENST00000450313	NM_012222.2	435	cAc/cGc	13/16	0.767912813350605	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.81564764744778	3		338	309	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226558148	226558148	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	204	299	0	ENST00000366794.5:c.2141G>C	p.Ser714Thr	p.S714T	ENST00000366794	NM_001618.3	714	aGt/aCt	15/23	0.767912813350605	3	FACETS	0.992	0.938	1	0.992	0.938	1	CLONAL	2	TRUE	1	0.81564764744778	3		299	355	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965685	25965685	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	150	286	0	ENST00000435504.4:c.3521G>A	p.Ser1174Asn	p.S1174N	ENST00000435504		1174	aGc/aAc	13/13	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.81564764744778	2		286	324	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361136	66361136	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	85	207	0	ENST00000273854.3:c.1036G>T	p.Glu346Ter	p.E346*	ENST00000273854	NM_004439.5	346	Gag/Tag	4/18	0.807128977957533	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.81564764744778	1		207	121	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962967	2962967	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	137	193	0	ENST00000396946.4:c.1941A>T	p.Arg647Ser	p.R647S	ENST00000396946	NM_032415.4	647	agA/agT	16/25	0.81564764744778	3	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	1	0.81564764744778	3		193	232	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115844	8115844	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	210	359	0	ENST00000346208.3:c.1190C>A	p.Ser397Tyr	p.S397Y	ENST00000346208		397	tCc/tAc	6/6	0.784705015152684	2	FACETS	0.947	0.908	0.983	0.947	0.908	0.983	CLONAL	2	TRUE	0	0.81564764744778	2		359	272	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347601	118347601	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	118	281	0	ENST00000534358.1:c.3238G>T	p.Gly1080Cys	p.G1080C	ENST00000534358	NM_005933.3	1080	Ggc/Tgc	4/36	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.81564764744778	2		281	281	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431930	49431930	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	67	235	0	ENST00000301067.7:c.9209T>G	p.Leu3070Arg	p.L3070R	ENST00000301067	NM_003482.3	3070	cTg/cGg	34/54	1	2	FACETS	0.821	0.727	0.92	0.821	0.727	0.92	CLONAL	1	TRUE	1	0.81564764744778	2		235	200	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436366	49436366	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	92	349	0	ENST00000301067.7:c.5845C>T	p.Gln1949Ter	p.Q1949*	ENST00000301067	NM_003482.3	1949	Cag/Tag	27/54	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.81564764744778	2		349	218	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913663	32913663	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs80358743	NA	P-0003916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	122	172	0	ENST00000380152.3:c.5171T>C	p.Ile1724Thr	p.I1724T	ENST00000380152		1724	aTa/aCa	11/27	NA	2	FACETS	0.971	0.922	1			1	INDETERMINATE	2	TRUE	NA	0.81564764744778	2		172	154	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252726	10252726	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	87	246	0	ENST00000340748.4:c.3239C>T	p.Pro1080Leu	p.P1080L	ENST00000340748		1080	cCc/cTc	29/40	0.290466568539722	3	FACETS	0.944	0.845	1	0.315	0.281	0.35	INDETERMINATE	1	TRUE	0	0.81564764744778	3		246	318	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577518	7577518	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519995	NA	P-0003925-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	133	273	2	ENST00000269305.4:c.763A>T	p.Ile255Phe	p.I255F	ENST00000269305	NM_001126112.2	255	Atc/Ttc	7/11	0.627651804567028	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.627651804567028	1		275	269	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213922	66213922	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0003925-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	108	432	0	ENST00000273854.3:c.2509-1G>T		p.X837_splice	ENST00000273854	NM_004439.5	837			1	2	FACETS	0.407	0.365	0.452	0.407	0.365	0.452	SUBCLONAL	1	TRUE	1	0.627651804567028	2		432	845	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857382	68857382	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003925-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	129	366	0	ENST00000261769.5:c.2017C>T	p.Gln673Ter	p.Q673*	ENST00000261769	NM_004360.3	673	Cag/Tag	13/16	0.627651804567028	1	FACETS	0.63	0.575	0.686	0.63	0.575	0.686	SUBCLONAL	1	TRUE	0	0.627651804567028	1		366	448	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351422	70351422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003925-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	414	335	2	ENST00000374080.3:c.4070G>A	p.Arg1357His	p.R1357H	ENST00000374080		1357	cGc/cAc	29/45	1	1	FACETS	0.756	0.73	0.78	1	0.997	1	SUBCLONAL	2	TRUE	0	0.627651804567028	1		337	599	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0003946-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	145	397	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.924	0.85	1	0.924	0.85	1	CLONAL	1	TRUE	1	0.668987037207395	2		397	469	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056437	26056437	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003946-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	75	321	0	ENST00000343677.2:c.220G>C	p.Glu74Gln	p.E74Q	ENST00000343677	NM_005319.3	74	Gag/Cag	1/1	0.476809169171465	4	FACETS	0.45	0.394	0.511			1	SUBCLONAL	1	TRUE	NA	0.668987037207395	4		321	831	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442015	52442015	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003946-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	338	421	0	ENST00000460680.1:c.334del	p.Leu112Ter	p.L112*	ENST00000460680	NM_004656.3	112	Ctg/tg	5/17	0.668987037207395	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.668987037207395	1		421	669	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577497	7577497	+	splice_donor_variant	Splice_Site	SNP	A	A	C	rs876659076	NA	P-0004005-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	595	114	264	0	ENST00000269305.4:c.782+2T>G		p.X261_splice	ENST00000269305	NM_001126112.2	261			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		264	709	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164967	47164967	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004019-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	167	406	0	ENST00000409792.3:c.1159del	p.Thr387LeufsTer97	p.T387Lfs*97	ENST00000409792	NM_014159.6	387	Act/ct	3/21	0.454461330294323	2	FACETS	1	0.938	1	0.51	0.47	0.552	CLONAL	1	TRUE	0	0.454461330294323	2		406	720	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0004046-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	209	254	7	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.303474091717799	2	FACETS	0.987	0.921	1	0.987	0.921	1	CLONAL	2	TRUE	0	0.318336477113172	2		261	665	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189893	11189893	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004046-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	206	243	0	ENST00000361445.4:c.5616T>G	p.Asp1872Glu	p.D1872E	ENST00000361445	NM_004958.3	1872	gaT/gaG	40/58	0.303474091717799	2	FACETS	0.98	0.914	1	0.98	0.914	1	CLONAL	2	TRUE	0	0.318336477113172	2		243	660	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625126	69625126	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs782607197	NA	P-0004046-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	61	321	0	ENST00000334134.2:c.667T>C	p.Ser223Pro	p.S223P	ENST00000334134	NM_005247.2	223	Tct/Cct	3/3	0.318336477113172	1	FACETS	0.506	0.436	0.582	0.506	0.436	0.582	SUBCLONAL	1	TRUE	0	0.318336477113172	1		321	637	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30311657	30311657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004046-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20718	5761	269	2	ENST00000262643.3:c.511G>A	p.Asp171Asn	p.D171N	ENST00000262643	NM_001238.2	171	Gat/Aat	7/12	0.318336477113172	52	FACETS	1	0.995	1			1	CLONAL	12	TRUE	NA	0.318336477113172	52		271	26479	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312715	30312715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004046-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19419	5841	294	0	ENST00000262643.3:c.696G>A	p.Met232Ile	p.M232I	ENST00000262643	NM_001238.2	232	atG/atA	8/12	0.318336477113172	52	FACETS	1	0.987	1			1	CLONAL	13	TRUE	NA	0.318336477113172	52		294	25260	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313493	30313493	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004046-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22187	6860	446	1	ENST00000262643.3:c.1093G>A	p.Asp365Asn	p.D365N	ENST00000262643	NM_001238.2	365	Gac/Aac	11/12	0.318336477113172	52	FACETS	1	0.996	1			1	CLONAL	13	TRUE	NA	0.318336477113172	52		447	29047	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485959	8485959	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004046-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	93	439	0	ENST00000356435.5:c.2858A>G	p.Lys953Arg	p.K953R	ENST00000356435		953	aAg/aGg	17/35	0.318336477113172	1	FACETS	0.632	0.562	0.708	0.632	0.562	0.708	SUBCLONAL	1	TRUE	0	0.318336477113172	1		439	777	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313373	30313375	+	missense_variant	Missense_Mutation	TNP	GAG	GAG	AAA	novel	NA	P-0004046-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26274	5358	498	0	ENST00000262643.3:c.973_975delinsAAA	p.Glu325Lys	p.E325K	ENST00000262643	NM_001238.2	325	GAG/AAA	11/12	0.318336477113172	52	FACETS	0.953	0.939	0.968			1	CLONAL	10	TRUE	NA	0.318336477113172	52		498	31632	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0004183-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	235	210	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.965	0.903	1	0.965	0.903	1	CLONAL	1	TRUE	1	0.617413700182817	2		210	789	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004183-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	316	472	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.617413700182817	2		472	992	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988348	36988348	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs546402304	NA	P-0004183-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	100	174	1	ENST00000354822.5:c.305C>T	p.Ala102Val	p.A102V	ENST00000354822	NM_001079668.2	102	gCg/gTg	2/3	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.617413700182817	2		175	290	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0004709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	263	239	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.184769826454513	2	FACETS	1	0.992	1	0.665	0.627	0.703	INDETERMINATE	1	TRUE	0	0.576816223183856	2		240	686	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977852	134977852	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0004709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	248	756	0	ENST00000398015.3:c.2847-2A>G		p.X949_splice	ENST00000398015	NM_004441.4	949			NA	2	FACETS	0.921	0.873	0.968			1	INDETERMINATE	2	TRUE	NA	0.576816223183856	2		756	467	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022498	12022498	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs567885519	NA	P-0004709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	123	947	0	ENST00000396373.4:c.604C>T	p.Arg202Trp	p.R202W	ENST00000396373	NM_001987.4	202	Cgg/Tgg	5/8	NA	2	FACETS	0.595	0.538	0.654			1	INDETERMINATE	1	TRUE	NA	0.576816223183856	2		947	717	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220494	1220494	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519858	NA	P-0004709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	187	753	0	ENST00000326873.7:c.587G>T	p.Gly196Val	p.G196V	ENST00000326873	NM_000455.4	196	gGc/gTc	4/10	0.576816223183856	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.576816223183856	1		753	404	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602332	10602332	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	220	977	0	ENST00000171111.5:c.1246A>T	p.Ile416Phe	p.I416F	ENST00000171111	NM_203500.1	416	Atc/Ttc	3/6	0.576816223183856	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.576816223183856	1		977	480	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142886	30142886	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	194	666	0	ENST00000389048.3:c.640del	p.Arg214AlafsTer35	p.R214Afs*35	ENST00000389048	NM_004304.4	214	Cgc/gc	1/29	0.271431342749524	3	FACETS	0.824	0.769	0.88	0.824	0.769	0.88	INDETERMINATE	2	TRUE	1	0.576816223183856	3		666	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579513	7579519	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGTCT	TGGGTCT	-	novel	NA	P-0004709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	290	898	0	ENST00000269305.4:c.168_174del	p.Asp57ValfsTer64	p.D57Vfs*64	ENST00000269305	NM_001126112.2	56	gaAGACCCA/ga	4/11	0.560778706567601	2	FACETS	0.899	0.856	0.943	0.899	0.856	0.943	CLONAL	2	TRUE	0	0.576816223183856	2		898	559	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	656	464	0	ENST00000425967.3:c.1731C>G	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaG	13/19	0.720859964226185	2	FACETS	0.985	0.961	1	0.985	0.961	1	CLONAL	2	TRUE	0	0.757610667384514	2		464	879	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799129	42799129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139613152	NA	P-0004712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	44	294	0	ENST00000575354.2:c.4613C>T	p.Pro1538Leu	p.P1538L	ENST00000575354	NM_015125.3	1538	cCg/cTg	20/20	0.739126494117903	3	FACETS	0.219	0.183	0.259			1	SUBCLONAL	1	TRUE	NA	0.757610667384514	3		294	732	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891083	112891083	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397507520	NA	P-0004712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	310	505	0	ENST00000351677.2:c.417G>C	p.Glu139Asp	p.E139D	ENST00000351677	NM_002834.3	139	gaG/gaC	4/16	0.676151097347516	4	FACETS	0.995	0.936	1	0.332	0.312	0.352	CLONAL	1	TRUE	1	0.757610667384514	4		505	1446	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799291	42799291	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	22	161	0	ENST00000575354.2:c.4775C>A	p.Pro1592His	p.P1592H	ENST00000575354	NM_015125.3	1592	cCc/cAc	20/20	0.739126494117903	3	FACETS	0.194	0.15	0.246			1	SUBCLONAL	1	TRUE	NA	0.757610667384514	3		161	412	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939874	76939874	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	348	297	0	ENST00000373344.5:c.874C>T	p.Gln292Ter	p.Q292*	ENST00000373344	NM_000489.3	292	Cag/Tag	9/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.757610667384514	1		297	458	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs104886003	NA	P-0004720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	72	636	0	ENST00000263967.3:c.1633G>C	p.Glu545Gln	p.E545Q	ENST00000263967	NM_006218.2	545	Gag/Cag	10/21	1	2	FACETS	0.457	0.401	0.516	0.457	0.401	0.516	SUBCLONAL	1	TRUE	1	0.769212568188177	2		636	410	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259043	153259043	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	242	1075	0	ENST00000281708.4:c.772G>C	p.Asp258His	p.D258H	ENST00000281708	NM_033632.3	258	Gat/Cat	5/12	1	2	FACETS	0.92	0.864	0.977	0.92	0.864	0.977	CLONAL	1	TRUE	1	0.769212568188177	2		1075	684	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120666	94120666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	181	1512	1	ENST00000369303.4:c.385G>A	p.Glu129Lys	p.E129K	ENST00000369303	NM_004440.3	129	Gaa/Aaa	3/17	0.769212568188177	1	FACETS	0.454	0.42	0.489	0.454	0.42	0.489	SUBCLONAL	1	TRUE	0	0.769212568188177	1		1513	638	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856384	111856384	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	57	322	0	ENST00000341259.2:c.435C>G	p.Ile145Met	p.I145M	ENST00000341259	NM_005475.2	145	atC/atG	2/8	0.769212568188177	3	FACETS	0.537	0.463	0.618	0.269	0.231	0.309	SUBCLONAL	1	TRUE	1	0.769212568188177	3		322	382	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106696	2106696	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	178	1127	0	ENST00000219476.3:c.700G>C	p.Glu234Gln	p.E234Q	ENST00000219476	NM_000548.3	234	Gag/Cag	8/42	0.769212568188177	3	FACETS	0.624	0.574	0.676	0.312	0.287	0.338	SUBCLONAL	1	TRUE	1	0.769212568188177	3		1127	1027	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226520	1226520	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	461	1122	0	ENST00000326873.7:c.1176G>C	p.Met392Ile	p.M392I	ENST00000326873	NM_000455.4	392	atG/atC	9/10	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.769212568188177	2		1122	903	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214687	5214687	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762790087	NA	P-0004720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	157	1110	0	ENST00000357368.4:c.4379C>T	p.Ala1460Val	p.A1460V	ENST00000357368	NM_002850.3	1460	gCg/gTg	29/38	1	2	FACETS	0.614	0.564	0.666	0.614	0.564	0.666	SUBCLONAL	1	TRUE	1	0.769212568188177	2		1110	665	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426997	49426997	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	97	826	1	ENST00000301067.7:c.11491del	p.Gln3831SerfsTer50	p.Q3831Sfs*50	ENST00000301067	NM_003482.3	3831	Cag/ag	39/54	0.769212568188177	3	FACETS	0.514	0.458	0.573	0.257	0.229	0.287	SUBCLONAL	1	TRUE	1	0.769212568188177	3		827	680	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961964	41961964	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	163	1550	0	ENST00000219905.7:c.874del	p.Val292SerfsTer37	p.V292Sfs*37	ENST00000219905	NM_001164273.1	291	cGg/cg	2/24	1	2	FACETS	0.419	0.384	0.456	0.419	0.384	0.456	SUBCLONAL	1	TRUE	1	0.769212568188177	2		1550	1011	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578359	7578375	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCAGCTGCTCACCATCG	CCAGCTGCTCACCATCG	-	novel	NA	P-0004720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	211	760	0	ENST00000269305.4:c.555_559+12del		p.X185_splice	ENST00000269305	NM_001126112.2	185		5/11	0.769212568188177	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.769212568188177	1		760	319	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990481	69990481	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs201247895	NA	P-0004728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	318	271	0	ENST00000394351.3:c.440C>T	p.Thr147Met	p.T147M	ENST00000394351	NM_000248.3	147	aCg/aTg	4/9	1	2	FACETS	0.995	0.945	1	0.995	0.945	1	CLONAL	1	TRUE	1	0.822431717574697	2		271	777	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272308	38272308	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs869320694	NA	P-0004746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	810	547	0	ENST00000425967.3:c.2059A>G	p.Lys687Glu	p.K687E	ENST00000425967	NM_001174067.1	687	Aag/Gag	15/19	1	2	FACETS	0.945	0.916	0.974			1	CLONAL	5	TRUE	1	0.201999577688178	2		547	1697	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492769	56492769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1348	629	531	0	ENST00000407977.2:c.170C>T	p.Pro57Leu	p.P57L	ENST00000407977		57	cCc/cTc	2/10	0.201999577688178	7	FACETS	0.948	0.911	0.986	0.79	0.759	0.821	CLONAL	5	TRUE	1	0.201999577688178	7		531	1977	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775239	73775239	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1605	674	634	0	ENST00000254810.4:c.17A>C	p.Gln6Pro	p.Q6P	ENST00000254810	NM_005324.3	6	cAg/cCg	2/4	0.201999577688178	7	FACETS	1	0.992	1	0.734	0.706	0.763	CLONAL	4	TRUE	1	0.201999577688178	7		634	2279	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148875	119148875	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs397517076	NA	P-0004763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	32	244	0	ENST00000264033.4:c.1096-1G>T		p.X366_splice	ENST00000264033	NM_005188.3	366			0.167594626968714	4	FACETS	1	0.914	1	0.574	0.481	0.67	INDETERMINATE	2	TRUE	0	0.48	4		244	86	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594262	55594262	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519708	NA	P-0004763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	19	372	0	ENST00000288135.5:c.1965T>G	p.Asn655Lys	p.N655K	ENST00000288135	NM_000222.2	655	aaT/aaG	13/21	0.3	1	FACETS	0.97	0.762	1	0.97	0.762	1	CLONAL	1	TRUE	0	0.48	1		372	62	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599342	55599342	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	19	441	0	ENST00000288135.5:c.2468A>G	p.Tyr823Cys	p.Y823C	ENST00000288135	NM_000222.2	823	tAt/tGt	17/21	0.3	1	FACETS	0.557	0.429	0.703	0.557	0.429	0.703	SUBCLONAL	1	TRUE	0	0.48	1		441	108	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692961	89692961	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	36	311	0	ENST00000371953.3:c.445C>A	p.Gln149Lys	p.Q149K	ENST00000371953	NM_000314.4	149	Caa/Aaa	5/9	0.20566472946974	3	FACETS	0.869	0.734	1	0.869	0.734	1	INDETERMINATE	2	TRUE	1	0.48	3		311	107	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0004769-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	205	307	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	0.611800876545762	2		307	646	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119306	3119306	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004769-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	203	435	0	ENST00000078429.4:c.838G>C	p.Glu280Gln	p.E280Q	ENST00000078429	NM_002067.2	280	Gag/Cag	6/7	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.611800876545762	2		435	660	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557340	29557340	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0004778-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	65	275	0	ENST00000356175.3:c.3053T>A	p.Leu1018Ter	p.L1018*	ENST00000356175	NM_000267.3	1018	tTa/tAa	23/57	0.256942545382501	1	FACETS	0.944	0.821	1	0.944	0.821	1	CLONAL	1	TRUE	0	0.256942545382501	1		275	467	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0004793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	147	351	2	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.170405883156343	0	FACETS	0.601	0.555	0.647			1	INDETERMINATE	2	FALSE	0	0.396204220400952	0		353	373	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164627	47164627	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	189	322	0	ENST00000409792.3:c.1499C>G	p.Ser500Cys	p.S500C	ENST00000409792	NM_014159.6	500	tCt/tGt	3/21	NA	2	FACETS	0.984	0.918	1			1	INDETERMINATE	2	FALSE	NA	0.396204220400952	2		322	485	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945474	151945474	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0004793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	96	211	0	ENST00000262189.6:c.2045C>G	p.Ser682Ter	p.S682*	ENST00000262189	NM_170606.2	682	tCa/tGa	14/59	1	2	FACETS	0.757	0.682	0.835	1	0.983	1	SUBCLONAL	2	FALSE	1	0.396204220400952	2		211	320	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750945	128750945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	367	269	0	ENST00000377970.2:c.482C>T	p.Ser161Leu	p.S161L	ENST00000377970	NM_002467.4	161	tCa/tTa	2/3	1	2	FACETS	1	0.993	1	1	0.997	1	CLONAL	2	FALSE	1	0.396204220400952	2		269	757	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435775	49435775	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0004793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	259	327	0	ENST00000301067.7:c.6110-2A>G		p.X2037_splice	ENST00000301067	NM_003482.3	2037			0.20987144728126	3	FACETS	1	0.982	1			1	INDETERMINATE	2	FALSE	NA	0.396204220400952	3		327	708	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005479	42005479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746445154	NA	P-0004793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	261	484	4	ENST00000219905.7:c.3215G>A	p.Arg1072His	p.R1072H	ENST00000219905	NM_001164273.1	1072	cGc/cAc	9/24	1	2	FACETS	0.955	0.9	1	1	0.995	1	CLONAL	2	FALSE	1	0.396204220400952	2		488	690	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0004793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	224	296	0	ENST00000269305.4:c.673-1G>C		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.356830800178186	0	FACETS	0.641	0.61	0.672			1	SUBCLONAL	3	FALSE	0	0.396204220400952	0		296	355	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0004799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	65	158	0				ENST00000310581	NM_198253.2	-/1132			0.3	3	FACETS	1	0.956	1	0.624	0.542	0.712	CLONAL	1	TRUE	1	0.239663408911657	3		158	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0004799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	179	409	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.3	3	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	TRUE	1	0.239663408911657	3		409	832	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936983	48936983	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690863	NA	P-0004799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	140	485	0	ENST00000267163.4:c.751C>T	p.Arg251Ter	p.R251*	ENST00000267163	NM_000321.2	251	Cga/Tga	8/27	0.3	3	FACETS	1	0.921	1	1	0.921	1	CLONAL	2	TRUE	1	0.239663408911657	3		485	648	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039532	180039532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745459631	NA	P-0004799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	113	526	0	ENST00000261937.6:c.3511G>A	p.Asp1171Asn	p.D1171N	ENST00000261937	NM_182925.4	1171	Gac/Aac	26/30	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.239663408911657	2		526	860	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858267	9858267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	71	407	0	ENST00000330684.3:c.3134C>T	p.Ser1045Phe	p.S1045F	ENST00000330684	NM_001134407.1	1045	tCc/tTc	13/13	0.239663408911657	2	FACETS	1	0.893	1	0.513	0.447	0.583	CLONAL	1	TRUE	0	0.239663408911657	2		407	578	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163783	72163783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	68	683	0	ENST00000357731.5:c.575G>A	p.Gly192Glu	p.G192E	ENST00000357731	NM_173808.2	192	gGa/gAa	4/7	0.17331925633411	5	FACETS	0.764	0.666	0.87	0.509	0.444	0.58	SUBCLONAL	2	TRUE	2	0.239663408911657	5		683	505	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256503	115256503	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	75	384	0	ENST00000369535.4:c.208C>T	p.Gln70Ter	p.Q70*	ENST00000369535	NM_002524.4	70	Caa/Taa	3/7	0.17331925633411	5	FACETS	1	0.973	1	0.481	0.421	0.544	CLONAL	1	TRUE	2	0.239663408911657	5		384	590	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917784	29917784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754823963	NA	P-0004799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	70	534	0	ENST00000389048.3:c.884C>T	p.Ser295Phe	p.S295F	ENST00000389048	NM_004304.4	295	tCc/tTc	3/29	1	2	FACETS	0.602	0.523	0.688	0.602	0.523	0.688	SUBCLONAL	1	TRUE	1	0.239663408911657	2		534	970	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141587	202141587	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771150445	NA	P-0004799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	40	376	0	ENST00000358485.4:c.875G>A	p.Arg292Gln	p.R292Q	ENST00000358485	NM_001080125.1	292	cGg/cAg	7/9	1	2	FACETS	0.641	0.532	0.762	0.641	0.532	0.762	SUBCLONAL	1	TRUE	1	0.239663408911657	2		376	521	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155708	56155708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	80	303	0	ENST00000399503.3:c.800C>T	p.Pro267Leu	p.P267L	ENST00000399503	NM_005921.1	267	cCa/cTa	3/20	0.3	3	FACETS	0.95	0.835	1	0.475	0.417	0.537	CLONAL	1	TRUE	1	0.239663408911657	3		303	787	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502648	149502648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	85	325	0	ENST00000261799.4:c.2140G>A	p.Glu714Lys	p.E714K	ENST00000261799	NM_002609.3	714	Gag/Aag	15/23	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.239663408911657	2		325	622	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687422	117687422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	33	346	0	ENST00000368508.3:c.2629G>A	p.Ala877Thr	p.A877T	ENST00000368508	NM_002944.2	877	Gcc/Acc	18/43	1	2	FACETS	0.646	0.526	0.782	0.646	0.526	0.782	SUBCLONAL	1	TRUE	1	0.239663408911657	2		346	426	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489553	56489553	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1453938942	NA	P-0004799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	66	426	0	ENST00000267101.3:c.2018A>T	p.Asn673Ile	p.N673I	ENST00000267101	NM_001982.3	673	aAt/aTt	17/28	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.239663408911657	2		426	488	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039479	49039479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	141	379	0	ENST00000267163.4:c.2464C>T	p.Pro822Ser	p.P822S	ENST00000267163	NM_000321.2	822	Cca/Tca	23/27	0.3	3	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	1	0.239663408911657	3		379	642	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78829330	78829330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	192	380	0	ENST00000306801.3:c.1381C>T	p.Pro461Ser	p.P461S	ENST00000306801	NM_020761.2	461	Ccc/Tcc	12/34	0.229356722131524	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.239663408911657	2		380	708	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867639	78867639	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	92	426	0	ENST00000306801.3:c.2375C>T	p.Ser792Phe	p.S792F	ENST00000306801	NM_020761.2	792	tCc/tTc	20/34	0.229356722131524	2	FACETS	0.943	0.837	1	0.472	0.418	0.528	CLONAL	1	TRUE	0	0.239663408911657	2		426	814	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775485	39775485	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	126	326	0	ENST00000288319.7:c.535C>T	p.Leu179Phe	p.L179F	ENST00000288319	NM_182918.3	179	Ctc/Ttc	4/10	0.3	3	FACETS	1	0.985	1	0.741	0.671	0.814	CLONAL	1	TRUE	1	0.239663408911657	3		326	795	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412230	139412231	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0004799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	205	492	1	ENST00000277541.6:c.1414_1415delinsAA	p.Gly472Lys	p.G472K	ENST00000277541	NM_017617.3	472	GGg/AAg	8/34	0.239663408911657	5	FACETS	1	0.926	1	0.667	0.617	0.718	CLONAL	2	TRUE	2	0.239663408911657	5		493	1163	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004806-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	65	221	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.205653482526937	2		222	568	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869434	102869434	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004815-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	364	531	0	ENST00000307046.8:c.207G>C	p.Arg69Ser	p.R69S	ENST00000307046	NM_001111285.1	69	agG/agC	2/4	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.727985943004887	2		531	910	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003270	42003270	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004815-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	335	1132	0	ENST00000219905.7:c.2807A>G	p.Asp936Gly	p.D936G	ENST00000219905	NM_001164273.1	936	gAt/gGt	8/24	NA	2	FACETS	0.597	0.563	0.632			1	INDETERMINATE	1	TRUE	NA	0.727985943004887	2		1132	1542	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942040	17942040	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004815-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	228	686	0	ENST00000458235.1:c.2975T>C	p.Phe992Ser	p.F992S	ENST00000458235	NM_000215.3	992	tTc/tCc	21/24	0.342141633924762	3	FACETS	0.74	0.688	0.793	0.247	0.229	0.265	INDETERMINATE	1	TRUE	0	0.727985943004887	3		686	1155	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939373	76939373	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0004815-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	466	445	3	ENST00000373344.5:c.1375A>T	p.Lys459Ter	p.K459*	ENST00000373344	NM_000489.3	459	Aag/Tag	9/35	0.33580369761889	2	FACETS	1	0.997	1			1	INDETERMINATE	2	TRUE	NA	0.727985943004887	2		448	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0004818-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	310	254	7	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.619282759235042	1	FACETS	0.989	0.939	1	0.989	0.939	1	CLONAL	1	TRUE	0	0.619282759235042	1		261	699	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692901	89692901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786204929	NA	P-0004818-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	177	284	0	ENST00000371953.3:c.385G>A	p.Gly129Arg	p.G129R	ENST00000371953	NM_000314.4	129	Gga/Aga	5/9	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.619282759235042	2		284	553	SUCCESS
APC	324	MSKCC	GRCh37	5	112176623	112176623	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004818-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	69	413	0	ENST00000257430.4:c.5333del	p.Pro1778LeufsTer12	p.P1778Lfs*12	ENST00000257430	NM_000038.5	1778	Cct/ct	16/16	0.619282759235042	1	FACETS	0.276	0.24	0.314	0.276	0.24	0.314	SUBCLONAL	1	TRUE	0	0.619282759235042	1		413	558	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692982	89692982	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1554898210	NA	P-0004818-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	180	310	0	ENST00000371953.3:c.469del	p.Glu157LysfsTer2	p.E157Kfs*2	ENST00000371953	NM_000314.4	156	Ggg/gg	5/9	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.619282759235042	2		310	552	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004844-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	106	221	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.348938056455054	3	FACETS	1	0.979	1	0.669	0.603	0.739	CLONAL	1	TRUE	1	0.382662556553283	3		222	493	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0004844-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	78	277	1	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.356585214135904	3	FACETS	0.916	0.807	1	0.458	0.403	0.517	CLONAL	1	TRUE	1	0.382662556553283	3		278	530	SUCCESS
APC	324	MSKCC	GRCh37	5	112137081	112137081	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1554076225	NA	P-0004844-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	95	459	1	ENST00000257430.4:c.834+1G>A		p.X278_splice	ENST00000257430	NM_000038.5	278			0.356585214135904	3	FACETS	1	0.98	1	0.713	0.639	0.791	CLONAL	1	TRUE	1	0.382662556553283	3		460	415	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280384	1280384	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004844-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	158	429	0	ENST00000310581.5:c.1839G>T	p.Arg613Ser	p.R613S	ENST00000310581	NM_198253.2	613	agG/agT	4/16	0.356585214135904	3	FACETS	1	0.922	1	0.503	0.461	0.548	CLONAL	1	TRUE	1	0.382662556553283	3		429	977	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114917779	114917779	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0004844-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	118	449	0	ENST00000543371.1:c.1270-1G>A		p.X424_splice	ENST00000543371	NM_001198531.1	424			0.348938056455054	3	FACETS	0.928	0.837	1	0.464	0.418	0.512	CLONAL	1	TRUE	1	0.382662556553283	3		449	792	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488228	56488228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004844-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	306	452	0	ENST00000267101.3:c.1747C>T	p.Pro583Ser	p.P583S	ENST00000267101	NM_001982.3	583	Ccc/Tcc	15/28	0.348938056455054	3	FACETS	0.985	0.93	1	0.985	0.93	1	CLONAL	2	TRUE	1	0.382662556553283	3		452	967	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992375	72992375	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004844-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1324	218	751	0	ENST00000268489.5:c.1670C>T	p.Ser557Phe	p.S557F	ENST00000268489	NM_006885.3	557	tCc/tTc	2/10	0.348938056455054	3	FACETS	0.88	0.816	0.947	0.44	0.408	0.474	CLONAL	1	TRUE	1	0.382662556553283	3		751	1542	SUCCESS
AR	367	MSKCC	GRCh37	X	66943532	66943532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143040492	NA	P-0004844-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	300	276	1	ENST00000374690.3:c.2612C>T	p.Ala871Val	p.A871V	ENST00000374690	NM_000044.3	871	gCg/gTg	8/8	0.382662556553283	2	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.382662556553283	2		277	645	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	74	260	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.581551874208324	2		260	247	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0004853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	159	385	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.905	0.834	0.98	0.905	0.834	0.98	CLONAL	1	TRUE	1	0.581551874208324	2		385	604	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696387	47696387	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	202	456	2	ENST00000347630.2:c.436G>A	p.Ala146Thr	p.A146T	ENST00000347630	NM_001007230.1	146	Gcc/Acc	6/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.581551874208324	2		458	622	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410849	63410849	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	44	699	0	ENST00000330258.3:c.2318T>G	p.Leu773Arg	p.L773R	ENST00000330258	NM_152424.3	773	cTg/cGg	2/2	1	2	FACETS	0.174	0.145	0.207	0.174	0.145	0.207	SUBCLONAL	1	TRUE	1	0.581551874208324	2		699	868	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0004874-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	154	569	1	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.373236952899515	1	FACETS	0.825	0.757	0.896	0.825	0.757	0.896	CLONAL	1	TRUE	0	0.419000500441644	1		570	704	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147578	47147578	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004874-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	108	229	0	ENST00000409792.3:c.4748T>G	p.Val1583Gly	p.V1583G	ENST00000409792	NM_014159.6	1583	gTa/gGa	6/21	0.373236952899515	1	FACETS	0.914	0.825	1	0.914	0.825	1	CLONAL	1	TRUE	0	0.419000500441644	1		229	446	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675450	30675450	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004874-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	164	371	0	ENST00000376406.3:c.2906C>G	p.Pro969Arg	p.P969R	ENST00000376406	NM_014641.2	969	cCt/cGt	8/15	0.373236952899515	1	FACETS	0.987	0.91	1	0.987	0.91	1	CLONAL	1	TRUE	0	0.419000500441644	1		371	627	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951931	2951931	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0004874-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	62	268	0	ENST00000396946.4:c.3020-1G>A		p.X1007_splice	ENST00000396946	NM_032415.4	1007			1	2	FACETS	0.631	0.546	0.723	0.631	0.546	0.723	SUBCLONAL	1	TRUE	1	0.419000500441644	2		268	469	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573234	64573234	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004874-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	187	357	0	ENST00000312049.6:c.1058A>G	p.Tyr353Cys	p.Y353C	ENST00000312049	NM_130799.2	353	tAc/tGc	8/10	0.373236952899515	1	FACETS	0.931	0.862	1	0.931	0.862	1	CLONAL	1	TRUE	0	0.419000500441644	1		357	758	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100980	41100980	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868706902	NA	P-0004874-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	244	406	0	ENST00000373198.4:c.1376G>A	p.Arg459Gln	p.R459Q	ENST00000373198	NM_133170.3	459	cGg/cAg	8/32	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.419000500441644	2		406	964	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11177061	11177061	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004880-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	169	792	0	ENST00000361445.4:c.7016G>T	p.Arg2339Ile	p.R2339I	ENST00000361445	NM_004958.3	2339	aGa/aTa	50/58	1	2	FACETS	0.798	0.734	0.865	0.798	0.734	0.865	SUBCLONAL	1	TRUE	1	0.465868515095643	2		792	909	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582266	119582266	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004880-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	75	401	0	ENST00000316626.5:c.1135G>T	p.Glu379Ter	p.E379*	ENST00000316626		379	Gaa/Taa	10/12	0.447485949553582	3	FACETS	0.63	0.552	0.714	0.315	0.276	0.357	SUBCLONAL	1	TRUE	1	0.465868515095643	3		401	630	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570386	87570386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004880-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	103	627	0	ENST00000277120.3:c.2126G>A	p.Gly709Glu	p.G709E	ENST00000277120		709	gGg/gAg	17/19	1	2	FACETS	0.565	0.506	0.629	0.565	0.506	0.629	SUBCLONAL	1	TRUE	1	0.465868515095643	2		627	782	SUCCESS
RET	5979	MSKCC	GRCh37	10	43598057	43598057	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1194183394	NA	P-0004880-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	61	357	0	ENST00000355710.3:c.605T>C	p.Val202Ala	p.V202A	ENST00000355710	NM_020975.4	202	gTg/gCg	3/20	0.449117671680444	2	FACETS	0.557	0.481	0.639	0.279	0.24	0.32	SUBCLONAL	1	TRUE	0	0.465868515095643	2		357	470	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435930	56435930	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004880-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	85	356	0	ENST00000407977.2:c.1207C>A	p.Gln403Lys	p.Q403K	ENST00000407977		403	Cag/Aag	9/10	1	2	FACETS	0.816	0.725	0.913	0.816	0.725	0.913	CLONAL	1	TRUE	1	0.465868515095643	2		356	447	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095917	29095917	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780192	NA	P-0004880-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	168	539	0	ENST00000328354.6:c.917G>A	p.Gly306Glu	p.G306E	ENST00000328354	NM_007194.3	306	gGg/gAg	9/15	0.449117671680444	2	FACETS	1	0.973	1	0.56	0.516	0.605	CLONAL	1	TRUE	0	0.465868515095643	2		539	644	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0004883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	261	395	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.889620632908237	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	0	0.900413716171956	3		395	279	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112064	115112064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757023811	NA	P-0004883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	75	308	0	ENST00000257566.3:c.1676C>T	p.Thr559Met	p.T559M	ENST00000257566	NM_016569.3	559	aCg/aTg	7/8	0.867944987532794	3	FACETS	0.915	0.812	1	0.458	0.406	0.512	CLONAL	1	TRUE	1	0.900413716171956	3		308	264	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593580	55593606	+	splice_acceptor_variant,coding_sequence_variant	In_Frame_Del	DEL	AGAAACCCATGTATGAAGTACAGTGGA	AGAAACCCATGTATGAAGTACAGTGGA	-	rs121913234	NA	P-0004883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	86	290	0	ENST00000288135.5:c.1648_1674del		p.K550_K558del	ENST00000288135	NM_000222.2	550		11/21	0.620758175283962	4	FACETS	1	0.973	1	0.786	0.719	0.852	CLONAL	2	TRUE	1	0.900413716171956	4		290	154	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0004888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	96	423	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.192403274972844	3	FACETS	0.892	0.821	0.961			1	INDETERMINATE	4	TRUE	NA	0.38422273568217	3		423	167	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759890	133759890	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761082559	NA	P-0004888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	10	249	0	ENST00000318560.5:c.2213G>A	p.Arg738Gln	p.R738Q	ENST00000318560	NM_005157.4	738	cGg/cAg	11/11	0.263968980133108	6	FACETS	0.545	0.369	0.764			1	SUBCLONAL	1	TRUE	NA	0.38422273568217	6		249	169	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267433	7267433	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143919163	NA	P-0004888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	56	180	0	ENST00000302850.5:c.575G>A	p.Gly192Asp	p.G192D	ENST00000302850	NM_000208.2	192	gGc/gAc	2/22	0.210168925735511	2	FACETS	1	0.958	1	0.642	0.557	0.733	INDETERMINATE	1	TRUE	0	0.38422273568217	2		180	227	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577059	7577068	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTTTCTTG	CCCTTTCTTG	-	novel	NA	P-0004888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	43	221	0	ENST00000269305.4:c.870_879del	p.Lys291SerfsTer51	p.K291Sfs*51	ENST00000269305	NM_001126112.2	290	cgCAAGAAAGGG/cg	8/11	0.272823625401635	1	FACETS	1	0.927	1	1	0.977	1	CLONAL	2	TRUE	0	0.38422273568217	1		221	83	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0004891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	114	239	1	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	0.445840637397735	2		240	462	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165711	118165711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	120	216	0	ENST00000369448.3:c.221C>T	p.Ser74Phe	p.S74F	ENST00000369448	NM_017709.3	74	tCc/tTc	2/2	0.445840637397735	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.445840637397735	1		216	379	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117315	115117315	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	114	257	0	ENST00000257566.3:c.859G>A	p.Asp287Asn	p.D287N	ENST00000257566	NM_016569.3	287	Gat/Aat	4/8	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.445840637397735	2		257	489	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95579539	95579539	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	94	188	0	ENST00000393063.1:c.1930G>T	p.Asp644Tyr	p.D644Y	ENST00000393063	NM_030621.3	644	Gat/Tat	13/28	1	2	FACETS	0.956	0.855	1	0.956	0.855	1	CLONAL	1	TRUE	1	0.445840637397735	2		188	441	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220699	1220699	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137853082	NA	P-0004891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	121	249	0	ENST00000326873.7:c.717G>A	p.Trp239Ter	p.W239*	ENST00000326873	NM_000455.4	239	tgG/tgA	5/10	0.445840637397735	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.445840637397735	1		249	355	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600488	10600488	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	116	225	0	ENST00000171111.5:c.1367T>A	p.Met456Lys	p.M456K	ENST00000171111	NM_203500.1	456	aTg/aAg	4/6	0.445840637397735	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.445840637397735	1		225	376	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600525	10600525	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	121	203	0	ENST00000171111.5:c.1330G>T	p.Glu444Ter	p.E444*	ENST00000171111	NM_203500.1	444	Gag/Tag	4/6	0.445840637397735	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.445840637397735	1		203	362	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650785	48650785	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	137	391	0	ENST00000376670.3:c.654C>A	p.Asp218Glu	p.D218E	ENST00000376670	NM_002049.3	218	gaC/gaA	4/6	1	2	FACETS	0.94	0.857	1	0.94	0.857	1	CLONAL	1	TRUE	1	0.445840637397735	2		391	654	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652358	48652358	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	125	355	0	ENST00000376670.3:c.1029C>A	p.Ser343Arg	p.S343R	ENST00000376670	NM_002049.3	343	agC/agA	6/6	1	2	FACETS	0.987	0.897	1	0.987	0.897	1	CLONAL	1	TRUE	1	0.445840637397735	2		355	568	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339934	70339934	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	158	336	0	ENST00000374080.3:c.467C>A	p.Ala156Asp	p.A156D	ENST00000374080		156	gCt/gAt	4/45	1	2	FACETS	0.994	0.913	1	0.994	0.913	1	CLONAL	1	TRUE	1	0.445840637397735	2		336	713	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613615	100613615	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0004891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	132	319	0	ENST00000308731.7:c.964A>T	p.Lys322Ter	p.K322*	ENST00000308731	NM_000061.2	322	Aaa/Taa	11/19	1	2	FACETS	0.917	0.834	1	0.917	0.834	1	CLONAL	1	TRUE	1	0.445840637397735	2		319	646	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0004910-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	80	674	5	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.22	2		679	540	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0004910-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	20	553	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	1	2	FACETS	0.38	0.29	0.487	0.38	0.29	0.487	SUBCLONAL	1	TRUE	1	0.22	2		553	478	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245891	5245891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1045893958	NA	P-0004910-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	100	760	1	ENST00000357368.4:c.884G>A	p.Arg295Gln	p.R295Q	ENST00000357368	NM_002850.3	295	cGg/cAg	10/38	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.22	2		761	618	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519378	176519378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148292303	NA	P-0004910-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	23	492	0	ENST00000292408.4:c.784G>A	p.Val262Met	p.V262M	ENST00000292408	NM_213647.1	262	Gtg/Atg	7/18	1	2	FACETS	0.511	0.398	0.643	0.511	0.398	0.643	SUBCLONAL	1	TRUE	1	0.22	2		492	409	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827732	72827732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241554729	NA	P-0004910-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	30	821	0	ENST00000268489.5:c.8849G>A	p.Arg2950His	p.R2950H	ENST00000268489	NM_006885.3	2950	cGc/cAc	9/10	1	2	FACETS	0.475	0.382	0.582	0.475	0.382	0.582	SUBCLONAL	1	TRUE	1	0.22	2		821	574	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888736	76888736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004910-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	12	332	0	ENST00000373344.5:c.5093G>A	p.Arg1698Gln	p.R1698Q	ENST00000373344	NM_000489.3	1698	cGg/cAg	19/35	0.3	2	FACETS	0.613	0.431	0.835	0.306	0.215	0.418	SUBCLONAL	1	TRUE	0	0.22	2		332	178	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0004920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	255	158	0				ENST00000310581	NM_198253.2	-/1132			0.177160572300491	3	FACETS	1	0.99	1	0.638	0.599	0.677	INDETERMINATE	1	TRUE	1	0.711263873530546	3		158	762	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0004920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	645	544	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	NA	2	FACETS	0.976	0.95	1			1	INDETERMINATE	2	TRUE	NA	0.711263873530546	2		544	929	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120527	70120527	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0004920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	223	110	0	ENST00000245479.2:c.1529G>C	p.Ter510SerextTer49	p.*510Sext*49	ENST00000245479	NM_000346.3	510	tGa/tCa	3/3	0.38054642667468	1	FACETS	0.8	0.753	0.848	0.8	0.753	0.848	INDETERMINATE	1	TRUE	0	0.711263873530546	1		110	505	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057947	27057947	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0004920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	293	352	0	ENST00000324856.7:c.1655C>G	p.Ser552Ter	p.S552*	ENST00000324856	NM_006015.4	552	tCa/tGa	3/20	1	2	FACETS	0.968	0.914	1	0.968	0.914	1	CLONAL	1	TRUE	1	0.711263873530546	2		352	851	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77043802	77043802	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	330	493	0	ENST00000356341.3:c.1524G>C	p.Lys508Asn	p.K508N	ENST00000356341	NM_002576.4	508	aaG/aaC	14/15	0.252489885935468	1	FACETS	0.702	0.666	0.738	0.702	0.666	0.738	INDETERMINATE	1	TRUE	0	0.711263873530546	1		493	852	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187857	11187857	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519780	NA	P-0004920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	147	165	0	ENST00000361445.4:c.6040G>A	p.Glu2014Lys	p.E2014K	ENST00000361445	NM_004958.3	2014	Gag/Aag	44/58	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.711263873530546	2		165	382	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982389	25982389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	293	388	0	ENST00000435504.4:c.901C>T	p.Gln301Ter	p.Q301*	ENST00000435504		301	Caa/Taa	9/13	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.711263873530546	2		388	788	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994411	25994411	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1353470890	NA	P-0004920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	295	411	0	ENST00000435504.4:c.404-2A>G		p.X135_splice	ENST00000435504		135			1	2	FACETS	0.957	0.903	1	0.957	0.903	1	CLONAL	1	TRUE	1	0.711263873530546	2		411	867	SUCCESS
APC	324	MSKCC	GRCh37	5	112173992	112173992	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1114167559	NA	P-0004920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	183	284	1	ENST00000257430.4:c.2701C>T	p.Gln901Ter	p.Q901*	ENST00000257430	NM_000038.5	901	Cag/Tag	16/16	0.711263873530546	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.711263873530546	1		285	322	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869662	117869662	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	215	633	0	ENST00000297338.2:c.532G>C	p.Glu178Gln	p.E178Q	ENST00000297338	NM_006265.2	178	Gag/Cag	6/14	0.451718999163898	3	FACETS	0.596	0.552	0.641	0.298	0.276	0.321	SUBCLONAL	1	TRUE	1	0.711263873530546	3		633	1376	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77070044	77070044	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	165	319	0	ENST00000356341.3:c.496G>C	p.Glu166Gln	p.E166Q	ENST00000356341	NM_002576.4	166	Gag/Cag	6/15	0.252489885935468	1	FACETS	0.531	0.49	0.573	0.531	0.49	0.573	INDETERMINATE	1	TRUE	0	0.711263873530546	1		319	563	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491390	18491390	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1377942847	NA	P-0004920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	204	346	0	ENST00000266497.5:c.1309del	p.Ile437TyrfsTer5	p.I437Yfs*5	ENST00000266497		435	Aaa/aa	8/31	1	2	FACETS	0.869	0.81	0.93	0.869	0.81	0.93	CLONAL	1	TRUE	1	0.711263873530546	2		346	660	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0004964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	428	370	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.785437292771609	3	FACETS	0.954	0.917	0.992	0.954	0.917	0.992	CLONAL	2	TRUE	1	0.795389341936578	3		370	788	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0004964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	551	346	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.785437292771609	3	FACETS	0.964	0.931	0.997	0.964	0.931	0.997	CLONAL	2	TRUE	1	0.795389341936578	3		346	1004	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915115	131915115	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501980	NA	P-0004964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	198	403	1	ENST00000265335.6:c.472C>T	p.His158Tyr	p.H158Y	ENST00000265335		158	Cat/Tat	4/25	1	2	FACETS	0.886	0.826	0.947	0.886	0.826	0.947	CLONAL	1	TRUE	1	0.795389341936578	2		404	562	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436646	8436646	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	175	557	0	ENST00000356435.5:c.4032C>G	p.Asp1344Glu	p.D1344E	ENST00000356435		1344	gaC/gaG	24/35	0.199388982530434	4	FACETS	1	0.954	1			1	INDETERMINATE	1	TRUE	NA	0.795389341936578	4		557	755	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	441031	441031	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	572	611	0	ENST00000399788.2:c.1727A>T	p.Gln576Leu	p.Q576L	ENST00000399788	NM_001042603.1	576	cAg/cTg	13/28	0.281120645864339	5	FACETS	1	0.993	1			1	INDETERMINATE	3	TRUE	NA	0.795389341936578	5		611	966	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115111977	115111977	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	184	353	0	ENST00000257566.3:c.1763C>G	p.Ala588Gly	p.A588G	ENST00000257566	NM_016569.3	588	gCc/gGc	7/8	0.785437292771609	3	FACETS	0.904	0.837	0.974	0.452	0.418	0.487	CLONAL	1	TRUE	1	0.795389341936578	3		353	715	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476268	88476268	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	290	506	1	ENST00000360948.2:c.1864C>A	p.His622Asn	p.H622N	ENST00000360948	NM_001012338.2	622	Cat/Aat	15/19	1	2	FACETS	0.995	0.941	1	0.995	0.941	1	CLONAL	1	TRUE	1	0.795389341936578	2		507	733	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641136	23641136	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	316	503	0	ENST00000261584.4:c.2339G>T	p.Gly780Val	p.G780V	ENST00000261584	NM_024675.3	780	gGc/gTc	5/13	0.785437292771609	3	FACETS	1	0.965	1	0.515	0.486	0.544	CLONAL	1	TRUE	1	0.795389341936578	3		503	1079	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579592	7579592	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs879254212	NA	P-0004964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	225	372	0	ENST00000269305.4:c.97-2A>G		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.785437292771609	3	FACETS	1	0.967	1	0.528	0.493	0.563	CLONAL	1	TRUE	1	0.795389341936578	3		372	749	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39620695	39620695	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	248	562	1	ENST00000262039.4:c.2093G>A	p.Gly698Glu	p.G698E	ENST00000262039	NM_002647.2	698	gGa/gAa	19/25	1	2	FACETS	0.893	0.84	0.948	0.893	0.84	0.948	CLONAL	1	TRUE	1	0.795389341936578	2		563	698	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45423123	45423123	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	126	259	2	ENST00000262160.6:c.5C>A	p.Ser2Ter	p.S2*	ENST00000262160	NM_005901.5	2	tCg/tAg	2/11	1	2	FACETS	0.87	0.797	0.946	0.87	0.797	0.946	CLONAL	1	TRUE	1	0.795389341936578	2		261	364	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70355083	70355083	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1336	367	641	0	ENST00000374080.3:c.5005G>T	p.Asp1669Tyr	p.D1669Y	ENST00000374080		1669	Gat/Tat	36/45	0.743678881513502	4	FACETS	0.973	0.92	1	0.324	0.306	0.343	CLONAL	1	TRUE	1	0.795389341936578	4		641	1703	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0004968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	240	370	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.163391815013775	3	FACETS	0.91	0.853	0.968	0.91	0.853	0.968	INDETERMINATE	2	TRUE	1	0.424047698306168	3		370	754	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0004968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	191	648	1	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.958	0.886	1	0.958	0.886	1	CLONAL	1	TRUE	1	0.424047698306168	2		649	940	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435689	110435689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	48	260	1	ENST00000375856.3:c.2712G>A	p.Met904Ile	p.M904I	ENST00000375856	NM_003749.2	904	atG/atA	1/2	1	2	FACETS	0.444	0.375	0.52	0.444	0.375	0.52	SUBCLONAL	1	TRUE	1	0.424047698306168	2		261	510	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898765	134898765	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	232	714	0	ENST00000398015.3:c.1823G>T	p.Arg608Leu	p.R608L	ENST00000398015	NM_004441.4	608	cGg/cTg	10/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.424047698306168	2		714	1016	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441379	149441379	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779762340	NA	P-0004968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	236	516	1	ENST00000286301.3:c.1660G>A	p.Glu554Lys	p.E554K	ENST00000286301	NM_005211.3	554	Gag/Aag	12/22	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.424047698306168	2		517	909	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520054	106520054	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	202	513	0	ENST00000359195.3:c.2482A>T	p.Ile828Phe	p.I828F	ENST00000359195	NM_002649.2	828	Att/Ttt	6/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.424047698306168	2		513	757	SUCCESS
APC	324	MSKCC	GRCh37	5	112174113	112174114	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0004968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	146	583	0	ENST00000257430.4:c.2824_2825del	p.Asn942PhefsTer3	p.N942Ffs*3	ENST00000257430	NM_000038.5	941	gAA/g	16/16	1	2	FACETS	0.927	0.847	1	0.927	0.847	1	CLONAL	1	TRUE	1	0.424047698306168	2		583	743	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410716	63410716	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	410	432	0	ENST00000330258.3:c.2451del	p.Asp817GlufsTer50	p.D817Efs*50	ENST00000330258	NM_152424.3	817	gaT/ga	2/2	0.259108572813976	2	FACETS	0.871	0.837	0.905			1	CLONAL	3	TRUE	NA	0.424047698306168	2		432	740	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662725	227662725	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	98	466	0	ENST00000305123.5:c.730G>T	p.Val244Leu	p.V244L	ENST00000305123	NM_005544.2	244	Gtg/Ttg	1/2	0.234193568294504	3	FACETS	0.861	0.768	0.962	0.287	0.256	0.321	CLONAL	1	TRUE	0	0.306115144509413	3		466	857	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060776	38060776	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	109	834	2	ENST00000250448.2:c.1213C>A	p.Leu405Ile	p.L405I	ENST00000250448	NM_004496.3	405	Ctc/Atc	2/2	0.262144371490646	2	FACETS	1	0.95	1	0.546	0.491	0.604	CLONAL	1	TRUE	0	0.306115144509413	2		836	652	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609612	81609612	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	54	541	2	ENST00000298171.2:c.1210G>T	p.Glu404Ter	p.E404*	ENST00000298171	NM_000369.2	404	Gag/Tag	10/10	0.262144371490646	2	FACETS	0.681	0.582	0.789	0.341	0.291	0.395	SUBCLONAL	1	TRUE	0	0.306115144509413	2		543	518	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306781	41306781	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	41	284	0	ENST00000373198.4:c.878C>T	p.Ala293Val	p.A293V	ENST00000373198	NM_133170.3	293	gCt/gTt	7/32	0.306115144509413	3	FACETS	0.86	0.718	1	0.43	0.359	0.509	CLONAL	1	TRUE	1	0.306115144509413	3		284	359	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670491	134670491	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	50	439	0	ENST00000398015.3:c.403del	p.Leu135SerfsTer3	p.L135Sfs*3	ENST00000398015	NM_004441.4	134	taC/ta	3/16	0.251364687402179	2	FACETS	0.736	0.625	0.857	0.368	0.312	0.429	SUBCLONAL	1	TRUE	0	0.306115144509413	2		439	444	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004972-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	68	221	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.945	0.821	1	0.945	0.821	1	CLONAL	1	TRUE	1	0.16	2		222	899	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142966	47142966	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1559720382	NA	P-0004972-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	104	559	0	ENST00000409792.3:c.4997A>G	p.Tyr1666Cys	p.Y1666C	ENST00000409792	NM_014159.6	1666	tAt/tGt	8/21	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.16	2		559	1092	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222655	69222666	+	inframe_deletion	In_Frame_Del	DEL	GAGATATGTTGT	GAGATATGTTGT	-	novel	NA	P-0004972-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	73	716	0	ENST00000462284.1:c.630_641del	p.Ile211_Glu214del	p.I211_E214del	ENST00000462284	NM_002392.5	210	GAGATATGTTGT/-	8/11	1	2	FACETS	0.741	0.645	0.844	0.741	0.645	0.844	SUBCLONAL	1	TRUE	1	0.16	2		716	1232	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0004974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	107	618	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.337207919461708	1	FACETS	0.588	0.527	0.653	0.588	0.527	0.653	SUBCLONAL	1	TRUE	0	0.337207919461708	1		618	897	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849663	68849663	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587780113	NA	P-0004974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	155	372	0	ENST00000261769.5:c.1565+1G>A		p.X522_splice	ENST00000261769	NM_004360.3	522			0.337207919461708	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.337207919461708	1		372	716	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434352	49434352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748969699	NA	P-0004974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	191	480	0	ENST00000301067.7:c.7201C>T	p.Arg2401Cys	p.R2401C	ENST00000301067	NM_003482.3	2401	Cgc/Tgc	31/54	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.337207919461708	2		480	1100	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021828	71021828	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0004974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	109	263	0	ENST00000318789.4:c.1531-1G>A		p.X511_splice	ENST00000318789	NM_032682.5	511			1	2	FACETS	0.924	0.83	1	0.924	0.83	1	CLONAL	1	TRUE	1	0.337207919461708	2		263	700	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118895	115118895	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	111	313	0	ENST00000257566.3:c.446A>G	p.Tyr149Cys	p.Y149C	ENST00000257566	NM_016569.3	149	tAc/tGc	2/8	1	2	FACETS	0.858	0.772	0.95	0.858	0.772	0.95	CLONAL	1	TRUE	1	0.337207919461708	2		313	767	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023696	1023696	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	53	216	0	ENST00000358495.3:c.868G>C	p.Ala290Pro	p.A290P	ENST00000358495	NM_134424.2	290	Gcg/Ccg	10/12	0.325794191981857	5	FACETS	0.902	0.769	1			1	CLONAL	1	TRUE	NA	0.325794191981857	5		216	537	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634383	23634383	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	22	352	0	ENST00000261584.4:c.2903C>T	p.Ala968Val	p.A968V	ENST00000261584	NM_024675.3	968	gCt/gTt	9/13	1	2	FACETS	0.322	0.249	0.408	0.322	0.249	0.408	SUBCLONAL	1	TRUE	1	0.325794191981857	2		352	419	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0004998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	113	318	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.343358777339779	5	FACETS	0.963	0.877	1	0.723	0.658	0.79	CLONAL	3	TRUE	1	0.343358777339779	5		318	345	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749983	162749983	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	57	328	2	ENST00000367921.3:c.2515C>T	p.Arg839Cys	p.R839C	ENST00000367921	NM_006182.2	839	Cgt/Tgt	18/18	0.344745719750344	3	FACETS	0.886	0.762	1	0.295	0.254	0.341	CLONAL	1	TRUE	0	0.343358777339779	3		330	439	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130100	143130100	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	97	298	0	ENST00000262992.4:c.916C>G	p.Gln306Glu	p.Q306E	ENST00000262992	NM_001101669.1	306	Caa/Gaa	11/24	0.337468597406825	2	FACETS	0.867	0.781	0.955	0.867	0.781	0.955	CLONAL	2	TRUE	0	0.343358777339779	2		298	326	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225997	225997	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0004998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	10	54	0	ENST00000264932.6:c.457-1G>T		p.X153_splice	ENST00000264932	NM_004168.2	153			0.199228754740473	3	FACETS	0.682	0.466	0.949			1	INDETERMINATE	1	TRUE	NA	0.343358777339779	3		54	100	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788617	3788617	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	128	376	0	ENST00000262367.5:c.4337G>C	p.Arg1446Pro	p.R1446P	ENST00000262367	NM_004380.2	1446	cGc/cCc	26/31	0.303301214503837	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	0	0.343358777339779	2		376	357	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0004998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	130	442	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.227332585969744	3	FACETS	1	0.977	1	0.789	0.723	0.856	CLONAL	2	TRUE	0	0.343358777339779	3		442	375	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028662	12028662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	76	374	0	ENST00000353533.5:c.865G>T	p.Asp289Tyr	p.D289Y	ENST00000353533	NM_003010.3	289	Gat/Tat	8/11	0.227332585969744	3	FACETS	0.837	0.741	0.938	0.558	0.494	0.625	CLONAL	2	TRUE	0	0.343358777339779	3		374	310	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227982	53227982	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1556840029	NA	P-0004998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	41	273	0	ENST00000375401.3:c.2332C>T	p.Arg778Ter	p.R778*	ENST00000375401	NM_004187.3	778	Cga/Tga	16/26	1	1	FACETS	0.979	0.825	1	0.979	0.825	1	CLONAL	1	TRUE	0	0.343358777339779	1		273	202	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910336	29910343	+	frameshift_variant	Frame_Shift_Del	DEL	CGTCATGG	CGTCATGG	-	novel	NA	P-0004998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	87	354	0	ENST00000376809.5:c.8_15del	p.Val3AlafsTer93	p.V3Afs*93	ENST00000376809	NM_002116.7	2	gcCGTCATGGcg/gccg	1/8	0.343358777339779	9	FACETS	1	0.953	1	0.38	0.337	0.425	CLONAL	2	TRUE	3	0.343358777339779	9		354	490	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0005009-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	14	194	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.359	0.258	0.482	0.359	0.258	0.482	SUBCLONAL	1	TRUE	1	0.16	2		194	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579342	7579515	+	inframe_deletion	In_Frame_Del	DEL	ATGCAAGAAGCCCAGACGGAAACCGTAGCTGCCCTGGTAGGTTTTCTGGGAAGGGACAGAAGATGACAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTGCAGGGGCCACGGGGGGAGCAGCCTCTGGCATTCTGGGAGCTTCATCTGGACCTGG	ATGCAAGAAGCCCAGACGGAAACCGTAGCTGCCCTGGTAGGTTTTCTGGGAAGGGACAGAAGATGACAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTGCAGGGGCCACGGGGGGAGCAGCCTCTGGCATTCTGGGAGCTTCATCTGGACCTGG	-	novel	NA	P-0005009-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	146	450	0	ENST00000269305.4:c.172_345del	p.Pro58_His115del	p.P58_H115del	ENST00000269305	NM_001126112.2	58	CCAGGTCCAGATGAAGCTCCCAGAATGCCAGAGGCTGCTCCCCCCGTGGCCCCTGCACCAGCAGCTCCTACACCGGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTGTCATCTTCTGTCCCTTCCCAGAAAACCTACCAGGGCAGCTACGGTTTCCGTCTGGGCTTCTTGCAT/-	4/11	1	2	FACETS	0.83	0.756	0.907	1	0.989	1	CLONAL	2	TRUE	1	0.16	2		450	1100	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	168	260	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.894	0.829	0.96	0.894	0.829	0.96	CLONAL	1	TRUE	1	0.803033472069607	2		260	468	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165644	118165644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs538766512	NA	P-0005012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	339	270	0	ENST00000369448.3:c.154G>A	p.Val52Ile	p.V52I	ENST00000369448	NM_017709.3	52	Gtc/Atc	2/2	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.803033472069607	2		270	815	SUCCESS
APC	324	MSKCC	GRCh37	5	112179750	112179750	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200790804	NA	P-0005012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	327	268	0	ENST00000257430.4:c.8459C>T	p.Thr2820Ile	p.T2820I	ENST00000257430	NM_000038.5	2820	aCt/aTt	16/16	1	2	FACETS	0.946	0.897	0.995	0.946	0.897	0.995	CLONAL	1	TRUE	1	0.803033472069607	2		268	861	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994329	21994329	+	start_lost	Translation_Start_Site	SNP	A	A	C	novel	NA	P-0005012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	216	207	0	ENST00000579755.1:c.2T>G	p.Met1?	p.M1?	ENST00000579755		1	aTg/aGg	1/3	0.775608055650775		FACETS		0.956	1				CLONAL	1	TRUE	0	0.803033472069607	1		207	321	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916767	48916767	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs794727481	NA	P-0005012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	315	228	0	ENST00000267163.4:c.297G>A	p.Trp99Ter	p.W99*	ENST00000267163	NM_000321.2	99	tgG/tgA	3/27	0.729114205664923	1	FACETS	0.978	0.939	1	0.978	0.939	1	CLONAL	1	TRUE	0	0.803033472069607	1		228	480	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350146	89350146	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs575811373	NA	P-0005014-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	439	641	0	ENST00000301030.4:c.2804C>T	p.Ser935Leu	p.S935L	ENST00000301030	NM_001256183.1	935	tCg/tTg	9/13	0.113665636672154	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.78209812790009	0		641	1027	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696430	47696430	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005014-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	338	335	0	ENST00000347630.2:c.393G>C	p.Trp131Cys	p.W131C	ENST00000347630	NM_001007230.1	131	tgG/tgC	6/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.78209812790009	2		335	813	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827511	72827511	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005014-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	469	559	2	ENST00000268489.5:c.9070del	p.Thr3024GlnfsTer52	p.T3024Qfs*52	ENST00000268489	NM_006885.3	3024	Aca/ca	9/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.78209812790009	2		561	1198	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0005017-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	359	391	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.282756848530718	2	FACETS	0.947	0.898	0.997	0.947	0.898	0.997	CLONAL	2	TRUE	0	0.318523523511676	2		391	1190	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0005017-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	283	450	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	0.27128621108856	3	FACETS	1	0.941	1	0.667	0.627	0.707	CLONAL	2	TRUE	0	0.318523523511676	3		450	1030	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003313	143003313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754717740	NA	P-0005017-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	127	360	0	ENST00000262992.4:c.2513G>A	p.Arg838His	p.R838H	ENST00000262992	NM_001101669.1	838	cGt/cAt	23/24	1	2	FACETS	0.854	0.773	0.939	0.854	0.773	0.939	CLONAL	1	TRUE	1	0.318523523511676	2		360	934	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388043	81388043	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs754474625	NA	P-0005017-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	176	590	0	ENST00000222390.5:c.332A>T	p.Glu111Val	p.E111V	ENST00000222390	NM_000601.4	111	gAa/gTa	3/18	0.296847225340622	1	FACETS	0.971	0.894	1	0.971	0.894	1	CLONAL	1	TRUE	0	0.318523523511676	1		590	957	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0005019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	462	563	1	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	0.475705023213263	2	FACETS	0.917	0.879	0.954	0.917	0.879	0.954	CLONAL	2	TRUE	0	0.499441470888636	2		564	1009	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551835	150551835	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	142	177	1	ENST00000369026.2:c.172G>A	p.Gly58Ser	p.G58S	ENST00000369026	NM_021960.4	58	Ggc/Agc	1/3	0.46904908043488	3	FACETS	0.753	0.691	0.816	0.753	0.691	0.816	SUBCLONAL	2	TRUE	1	0.499441470888636	3		178	472	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987214	2987214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	240	402	1	ENST00000396946.4:c.215G>A	p.Arg72Gln	p.R72Q	ENST00000396946	NM_032415.4	72	cGa/cAa	3/25	0.274031161013612	5	FACETS	1	0.987	1			1	INDETERMINATE	2	TRUE	NA	0.499441470888636	5		403	704	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615083	43615083	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377767422	NA	P-0005019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	166	583	0	ENST00000355710.3:c.2497C>T	p.Arg833Cys	p.R833C	ENST00000355710	NM_020975.4	833	Cgc/Tgc	14/20	1	2	FACETS	0.789	0.726	0.856	0.789	0.726	0.856	SUBCLONAL	1	TRUE	1	0.499441470888636	2		583	842	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992187	72992187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1413049341	NA	P-0005019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	131	736	0	ENST00000268489.5:c.1858C>T	p.His620Tyr	p.H620Y	ENST00000268489	NM_006885.3	620	Cac/Tac	2/10	1	2	FACETS	0.405	0.366	0.446	0.405	0.366	0.446	SUBCLONAL	1	TRUE	1	0.499441470888636	2		736	1296	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032466	12032466	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	206	320	1	ENST00000353533.5:c.902C>A	p.Ala301Asp	p.A301D	ENST00000353533	NM_003010.3	301	gCc/gAc	9/11	0.475705023213263	2	FACETS	0.97	0.913	1	0.97	0.913	1	CLONAL	2	TRUE	0	0.499441470888636	2		321	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0005023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	205	395	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.656593413206471	1	FACETS	0.578	0.538	0.619	0.578	0.538	0.619	SUBCLONAL	1	TRUE	0	0.656593413206471	1		395	726	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0005023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	36	403	0	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	0.656593413206471	1	FACETS	0.165	0.135	0.198	0.165	0.135	0.198	SUBCLONAL	1	TRUE	0	0.656593413206471	1		403	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0005023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	157	471	3	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.656593413206471	1	FACETS	0.392	0.359	0.426	0.392	0.359	0.426	SUBCLONAL	1	TRUE	0	0.656593413206471	1		474	820	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539018	187539018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374444088	NA	P-0005023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	156	586	2	ENST00000441802.2:c.8722G>A	p.Val2908Ile	p.V2908I	ENST00000441802	NM_005245.3	2908	Gtc/Atc	10/27	1	2	FACETS	0.51	0.467	0.555	0.51	0.467	0.555	SUBCLONAL	1	TRUE	1	0.656593413206471	2		588	932	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45800101	45800101	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1060501338	NA	P-0005023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	207	407	1	ENST00000450313.1:c.119C>A	p.Ala40Asp	p.A40D	ENST00000450313	NM_012222.2	40	gCt/gAt	2/16	0.656593413206471	1	FACETS	0.637	0.594	0.681	0.637	0.594	0.681	SUBCLONAL	1	TRUE	0	0.656593413206471	1		408	665	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032802	48032802	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	280	520	0	ENST00000234420.5:c.3602T>C	p.Leu1201Pro	p.L1201P	ENST00000234420	NM_000179.2	1201	cTc/cCc	7/10	0.656593413206471	1	FACETS	0.998	0.947	1	0.998	0.947	1	CLONAL	1	TRUE	0	0.656593413206471	1		520	574	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668730	52668730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1394725381	NA	P-0005023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	35	505	1	ENST00000394830.3:c.1189C>T	p.Arg397Trp	p.R397W	ENST00000394830	NM_018313.4	397	Cgg/Tgg	12/30	0.53321070139169	1	FACETS	0.109	0.088	0.131	0.109	0.088	0.131	SUBCLONAL	1	TRUE	0	0.656593413206471	1		506	660	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920482	134920482	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	41	438	0	ENST00000398015.3:c.2297C>G	p.Ser766Cys	p.S766C	ENST00000398015	NM_004441.4	766	tCc/tGc	12/16	1	2	FACETS	0.175	0.145	0.209	0.175	0.145	0.209	SUBCLONAL	1	TRUE	1	0.656593413206471	2		438	712	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430303	181430303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	141	148	0	ENST00000325404.1:c.155C>T	p.Ser52Phe	p.S52F	ENST00000325404	NM_003106.3	52	tCc/tTc	1/1	1	2	FACETS	0.642	0.586	0.7	0.642	0.586	0.7	SUBCLONAL	1	TRUE	1	0.656593413206471	2		148	669	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288840	33288840	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1402930433	NA	P-0005023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	124	243	0	ENST00000374542.5:c.712C>T	p.Arg238Ter	p.R238*	ENST00000374542	NM_001141970.1	238	Cga/Tga	3/8	0.656593413206471	1	FACETS	0.671	0.613	0.731	0.671	0.613	0.731	SUBCLONAL	1	TRUE	0	0.656593413206471	1		243	378	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508536	106508536	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774529326	NA	P-0005023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	41	147	0	ENST00000359195.3:c.530G>A	p.Arg177His	p.R177H	ENST00000359195	NM_002649.2	177	cGc/cAc	2/11	NA	2	FACETS	0.315	0.262	0.373			1	INDETERMINATE	1	TRUE	NA	0.656593413206471	2		147	397	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853076	151853076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759319798	NA	P-0005023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	27	302	0	ENST00000262189.6:c.11879G>A	p.Arg3960Gln	p.R3960Q	ENST00000262189	NM_170606.2	3960	cGa/cAa	46/59	0.463520908130106	1	FACETS	0.155	0.123	0.191	0.155	0.123	0.191	SUBCLONAL	1	TRUE	0	0.656593413206471	1		302	357	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418237	139418237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768625801	NA	P-0005023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	57	328	0	ENST00000277541.6:c.335G>A	p.Arg112His	p.R112H	ENST00000277541	NM_017617.3	112	cGc/cAc	3/34	0.630781858303679	1	FACETS	0.129	0.11	0.15	0.129	0.11	0.15	SUBCLONAL	1	TRUE	0	0.656593413206471	1		328	902	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717733	89717733	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1554825235	NA	P-0005023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	80	259	0	ENST00000371953.3:c.758T>A	p.Ile253Asn	p.I253N	ENST00000371953	NM_000314.4	253	aTc/aAc	7/9	0.656593413206471	1	FACETS	0.507	0.45	0.567	0.507	0.45	0.567	SUBCLONAL	1	TRUE	0	0.656593413206471	1		259	323	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129658	2129658	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1028039505	NA	P-0005023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	223	370	0	ENST00000219476.3:c.3385C>T	p.Arg1129Cys	p.R1129C	ENST00000219476	NM_000548.3	1129	Cgt/Tgt	29/42	NA	2	FACETS	0.509	0.472	0.547			1	INDETERMINATE	1	TRUE	NA	0.656593413206471	2		370	1335	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832072	72832072	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	220	629	0	ENST00000268489.5:c.4509G>T	p.Gln1503His	p.Q1503H	ENST00000268489	NM_006885.3	1503	caG/caT	9/10	1	2	FACETS	0.66	0.614	0.708	0.66	0.614	0.708	SUBCLONAL	1	TRUE	1	0.656593413206471	2		629	1015	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989361	7989361	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs536446862	NA	P-0005023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	315	299	0	ENST00000319144.4:c.325G>C	p.Glu109Gln	p.E109Q	ENST00000319144	NM_001139.2	109	Gag/Cag	2/15	0.656593413206471	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.656593413206471	1		299	584	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266961	18266961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs534405273	NA	P-0005023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	91	115	0	ENST00000222254.8:c.272G>A	p.Arg91Gln	p.R91Q	ENST00000222254	NM_005027.3	91	cGg/cAg	2/16	0.359064461832393	1	FACETS	0.543	0.486	0.602	0.543	0.486	0.602	INDETERMINATE	1	TRUE	0	0.656593413206471	1		115	343	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653844	89653847	+	frameshift_variant	Frame_Shift_Del	DEL	AACA	AACA	-	novel	NA	P-0005023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	79	410	0	ENST00000371953.3:c.143_146del	p.Asn48IlefsTer5	p.N48Ifs*5	ENST00000371953	NM_000314.4	48	AACAat/at	2/9	0.656593413206471	1	FACETS	0.369	0.326	0.415	0.369	0.326	0.415	SUBCLONAL	1	TRUE	0	0.656593413206471	1		410	438	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910549	29910549	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45585732	NA	P-0005028-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	38	247	4	ENST00000376809.5:c.89G>A	p.Arg30Lys	p.R30K	ENST00000376809	NM_002116.7	30	aGg/aAg	2/8	0.494479157647468	2	FACETS	0.531	0.441	0.631	0.266	0.22	0.316	SUBCLONAL	1	TRUE	0	0.503587724048184	2		251	284	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349068	11349068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005028-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	37	270	0	ENST00000332029.2:c.268C>T	p.His90Tyr	p.H90Y	ENST00000332029	NM_003745.1	90	Cac/Tac	2/2	0.174601308495095	2	FACETS	0.289	0.237	0.346	0.144	0.118	0.173	INDETERMINATE	1	TRUE	0	0.503587724048184	2		270	509	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740566	58740640	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	AATAATAGCCTTCCAATTGGCCTTGTGCCTACTAATTCAACAAACACTGTCATGGACCAAAAAAATTTGAAGATG	AATAATAGCCTTCCAATTGGCCTTGTGCCTACTAATTCAACAAACACTGTCATGGACCAAAAAAATTTGAAGATG	TATCCTTAAAGTCAGGGCTTTAGCGCAATTTTCT	novel	NA	P-0005028-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	92	716	0	ENST00000305921.3:c.1471_1545delinsTATCCTTAAAGTCAGGGCTTTAGCGCAATTTTCT	p.Asn491TyrfsTer3	p.N491Yfs*3	ENST00000305921	NM_003620.3	491	AATAATAGCCTTCCAATTGGCCTTGTGCCTACTAATTCAACAAACACTGTCATGGACCAAAAAAATTTGAAGATG/TATCCTTAAAGTCAGGGCTTTAGCGCAATTTTCT	6/6	1	2	FACETS	0.335	0.296	0.376	0.335	0.296	0.376	SUBCLONAL	1	TRUE	1	0.503587724048184	2		716	1091	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0005058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	47	500	2	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		502	723	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923035	44923035	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	35	277	0	ENST00000377967.4:c.1896G>A	p.Trp632Ter	p.W632*	ENST00000377967	NM_021140.2	632	tgG/tgA	16/29	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		277	530	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244221	153244221	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	80	503	0	ENST00000281708.4:c.1936G>T	p.Val646Leu	p.V646L	ENST00000281708	NM_033632.3	646	Gta/Tta	12/12	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		503	1002	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0005061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	79	782	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.327232253243251	2	FACETS	1	0.979	1	0.723	0.648	0.8	CLONAL	1	TRUE	0	0.522966895843545	2		782	209	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519999	NA	P-0005061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	93	753	0	ENST00000269305.4:c.716A>G	p.Asn239Ser	p.N239S	ENST00000269305	NM_001126112.2	239	aAc/aGc	7/11	0.522966895843545	1	FACETS	0.837	0.77	0.901	1	0.988	1	CLONAL	2	TRUE	0	0.522966895843545	1		753	157	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863222	57863222	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	27	926	0	ENST00000228682.2:c.1317G>C	p.Gln439His	p.Q439H	ENST00000228682	NM_005269.2	439	caG/caC	11/12	0.230908748903842	2	FACETS	0.522	0.418	0.638	0.261	0.209	0.319	INDETERMINATE	1	TRUE	0	0.522966895843545	2		926	198	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383644	42383644	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs148797987	NA	P-0005061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	51	885	0	ENST00000221972.3:c.419C>A	p.Thr140Asn	p.T140N	ENST00000221972	NM_021601.3	140	aCc/aAc	3/5	0.522966895843545	6	FACETS	0.808	0.693	0.931			1	CLONAL	2	TRUE	NA	0.522966895843545	6		885	247	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573710	41573710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	38	862	0	ENST00000263253.7:c.5995G>A	p.Gly1999Arg	p.G1999R	ENST00000263253	NM_001429.3	1999	Gga/Aga	31/31	0.522966895843545	1	FACETS	0.74	0.623	0.866	0.74	0.623	0.866	SUBCLONAL	1	TRUE	0	0.522966895843545	1		862	145	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073882	8073888	+	frameshift_variant	Frame_Shift_Del	DEL	CTTGTTA	CTTGTTA	-	novel	NA	P-0005061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	67	1069	1	ENST00000377482.5:c.771_777del	p.Asn258GlnfsTer3	p.N258Qfs*3	ENST00000377482	NM_018948.3	257	ttTAACAAG/tt	4/4	0.390195197229977	1	FACETS	0.427	0.372	0.486	0.427	0.372	0.486	SUBCLONAL	1	TRUE	0	0.522966895843545	1		1070	443	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599333	55599333	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913682	NA	P-0005066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	806	373	0	ENST00000288135.5:c.2459A>T	p.Asp820Val	p.D820V	ENST00000288135	NM_000222.2	820	gAt/gTt	17/21	0.740223590903218	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.756903527354585	3		373	1436	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190585	11190585	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0005066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	266	389	1	ENST00000361445.4:c.5613+1G>T		p.X1871_splice	ENST00000361445	NM_004958.3	1871			0.756903527354585	1	FACETS	0.946	0.9	0.99	0.946	0.9	0.99	CLONAL	1	TRUE	0	0.756903527354585	1		390	462	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593606	55593614	+	protein_altering_variant	In_Frame_Del	DEL	AAGGTTGTT	AAGGTTGTT	TTG	novel	NA	P-0005066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	794	444	0	ENST00000288135.5:c.1672_1680delinsTTG	p.Lys558_Val560delinsLeu	p.K558_V560delinsL	ENST00000288135	NM_000222.2	558	AAGGTTGTT/TTG	11/21	0.740223590903218	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.756903527354585	3		444	1390	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0005067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	27	318	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.755	0.603	0.928	0.755	0.603	0.928	CLONAL	1	TRUE	1	0.26686638642462	2		318	268	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0005067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	37	731	0	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	1	2	FACETS	0.456	0.375	0.547	0.456	0.375	0.547	SUBCLONAL	1	TRUE	1	0.26686638642462	2		731	608	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692794	89692794	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121909238	NA	P-0005067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	9	354	0	ENST00000371953.3:c.278A>G	p.His93Arg	p.H93R	ENST00000371953	NM_000314.4	93	cAt/cGt	5/9	1	2	FACETS	0.263	0.174	0.378	0.263	0.174	0.378	SUBCLONAL	1	TRUE	1	0.26686638642462	2		354	256	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0005074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	475	476	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.52893546140856	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.52420031287493	2		476	886	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739747	145739747	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0005074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	166	395	0	ENST00000428558.2:c.1705-1G>T		p.X569_splice	ENST00000428558	NM_004260.3	569			NA	2	FACETS	0.951	0.877	1			1	INDETERMINATE	1	TRUE	NA	0.52420031287493	2		395	666	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094841	143094841	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	326	466	1	ENST00000262992.4:c.1303G>A	p.Ala435Thr	p.A435T	ENST00000262992	NM_001101669.1	435	Gca/Aca	14/24	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	2	TRUE	NA	0.52420031287493	2		467	600	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675644	30675644	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	278	496	0	ENST00000376406.3:c.2712A>T	p.Gln904His	p.Q904H	ENST00000376406	NM_014641.2	904	caA/caT	8/15	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.52420031287493	2		496	1048	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358924	81358924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766585116	NA	P-0005074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	157	336	0	ENST00000222390.5:c.1037G>A	p.Cys346Tyr	p.C346Y	ENST00000222390	NM_000601.4	346	tGc/tAc	8/18	0.52893546140856	4	FACETS	0.902	0.826	0.982	0.301	0.275	0.328	CLONAL	1	TRUE	1	0.52420031287493	4		336	1012	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358937	81358937	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	168	378	0	ENST00000222390.5:c.1024G>A	p.Glu342Lys	p.E342K	ENST00000222390	NM_000601.4	342	Gaa/Aaa	8/18	0.52893546140856	4	FACETS	0.904	0.83	0.981	0.301	0.276	0.327	CLONAL	1	TRUE	1	0.52420031287493	4		378	1081	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4094485	4094485	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	231	430	0	ENST00000262948.5:c.1058A>T	p.Asn353Ile	p.N353I	ENST00000262948	NM_030662.3	353	aAc/aTc	10/11	0.52893546140856	2	FACETS	1	0.98	1	0.557	0.521	0.594	CLONAL	1	TRUE	0	0.52420031287493	2		430	791	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434913	49434913	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	316	307	1	ENST00000301067.7:c.6640del	p.Ala2214ProfsTer50	p.A2214Pfs*50	ENST00000301067	NM_003482.3	2214	Gcc/cc	31/54	0.52893546140856	3	FACETS	0.819	0.775	0.864	0.546	0.516	0.576	CLONAL	2	TRUE	0	0.52420031287493	3		308	929	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	209	221	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.307492270511407	3	FACETS	0.956	0.89	1	0.956	0.89	1	CLONAL	2	FALSE	1	0.307492270511407	3		222	820	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587780070	NA	P-0005075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	246	279	1	ENST00000269305.4:c.535C>G	p.His179Asp	p.H179D	ENST00000269305	NM_001126112.2	179	Cat/Gat	5/11	0.307492270511407	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	FALSE	0	0.307492270511407	2		280	798	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478590	57478590	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	223	349	1	ENST00000371085.3:c.262A>G	p.Lys88Glu	p.K88E	ENST00000371085	NM_000516.4	88	Aag/Gag	4/13	0.280476514373302	4	FACETS	0.969	0.902	1	0.969	0.902	1	CLONAL	2	FALSE	2	0.307492270511407	4		350	979	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942837	44942842	+	inframe_deletion	In_Frame_Del	DEL	AGGGAG	AGGGAG	-	novel	NA	P-0005075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	261	296	0	ENST00000377967.4:c.3417_3422del	p.Gly1140_Ser1141del	p.G1140_S1141del	ENST00000377967	NM_021140.2	1139	ccAGGGAGc/ccc	23/29	0.255546245072415	2	FACETS	0.994	0.941	1			1	CLONAL	3	FALSE	NA	0.307492270511407	2		296	569	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715368	61715368	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	11	614	3	ENST00000401558.2:c.2245C>T	p.Arg749Ter	p.R749*	ENST00000401558	NM_003400.3	749	Cga/Tga	19/25	0.249193855986345	5	FACETS	0.329	0.226	0.457			1	SUBCLONAL	1	TRUE	NA	0.249193855986345	5		617	369	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	109	221	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.148537949134067	1	FACETS	1	0.917	1	1	0.917	1	INDETERMINATE	1	TRUE	0	0.283179976667475	1		222	647	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0005102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	184	688	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	0.283179976667475	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.283179976667475	1		688	839	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979407	2979407	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	202	718	2	ENST00000396946.4:c.840C>A	p.Asn280Lys	p.N280K	ENST00000396946	NM_032415.4	280	aaC/aaA	6/25	0.131834951357251	4	FACETS	0.817	0.756	0.879	0.817	0.756	0.879	INDETERMINATE	2	TRUE	2	0.283179976667475	4		720	1121	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457304	67457304	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	247	717	0	ENST00000327367.4:c.278G>T	p.Arg93Leu	p.R93L	ENST00000327367	NM_005902.3	93	cGa/cTa	2/9	0.283179976667475	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.283179976667475	1		717	1174	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368214	45368214	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	127	607	0	ENST00000262160.6:c.1388G>T	p.Cys463Phe	p.C463F	ENST00000262160	NM_005901.5	463	tGc/tTc	11/11	0.283179976667475	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.283179976667475	1		607	710	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041703	47041716	+	frameshift_variant	Frame_Shift_Del	DEL	ACAAGACCAAGACA	ACAAGACCAAGACA	-	novel	NA	P-0005102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	154	498	0	ENST00000377604.3:c.1928_1941del	p.His643ArgfsTer25	p.H643Rfs*25	ENST00000377604	NM_001204468.1	643	cACAAGACCAAGACA/c	17/24	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.283179976667475	1		498	646	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0005104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	188	544	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.266074469465701	2	FACETS	0.875	0.813	0.94	0.875	0.813	0.94	CLONAL	2	TRUE	0	0.343632932192888	2		544	625	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098953	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	50	256	0	ENST00000397062.3:c.92G>C	p.Gly31Ala	p.G31A	ENST00000397062	NM_006164.4	31	gGa/gCa	2/5	0.343632932192888	3	FACETS	0.932	0.793	1	0.466	0.396	0.542	CLONAL	1	TRUE	1	0.343632932192888	3		256	366	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067386	37067386	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs63750443	NA	P-0005104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	103	376	0	ENST00000231790.2:c.1297G>C	p.Glu433Gln	p.E433Q	ENST00000231790	NM_000249.3	433	Gaa/Caa	12/19	0.343632932192888	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.343632932192888	1		376	365	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336376	80336376	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	35	306	0	ENST00000286548.4:c.943G>C	p.Asp315His	p.D315H	ENST00000286548	NM_002072.3	315	Gac/Cac	7/7	1	2	FACETS	0.681	0.56	0.816	0.681	0.56	0.816	SUBCLONAL	1	TRUE	1	0.343632932192888	2		306	299	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692902	89692902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909218	NA	P-0005104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	93	259	0	ENST00000371953.3:c.386G>A	p.Gly129Glu	p.G129E	ENST00000371953	NM_000314.4	129	gGa/gAa	5/9	0.343632932192888	1	FACETS	0.8	0.722	0.882	1	0.984	1	SUBCLONAL	2	TRUE	0	0.343632932192888	1		259	280	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813343	102813343	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0005104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	109	403	0	ENST00000307046.8:c.346A>T	p.Lys116Ter	p.K116*	ENST00000307046	NM_001111285.1	116	Aag/Tag	3/4	0.175234320752075	4	FACETS	1	0.976	1	0.641	0.576	0.709	INDETERMINATE	1	TRUE	2	0.343632932192888	4		403	665	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560382	95560382	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	70	277	0	ENST00000393063.1:c.5207G>T	p.Arg1736Leu	p.R1736L	ENST00000393063	NM_030621.3	1736	cGg/cTg	25/28	0.343632932192888	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.343632932192888	1		277	270	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778653	3778653	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	86	297	0	ENST00000262367.5:c.6395G>T	p.Gly2132Val	p.G2132V	ENST00000262367	NM_004380.2	2132	gGc/gTc	31/31	1	2	FACETS	0.886	0.785	0.993	0.886	0.785	0.993	CLONAL	1	TRUE	1	0.343632932192888	2		297	565	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299866	15299866	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1163542868	NA	P-0005104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	216	392	1	ENST00000263388.2:c.1312G>A	p.Gly438Arg	p.G438R	ENST00000263388	NM_000435.2	438	Ggg/Agg	8/33	1	2	FACETS	0.818	0.763	0.875	1	0.993	1	CLONAL	2	TRUE	1	0.343632932192888	2		393	768	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974809	21974809	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	49	67	0	ENST00000304494.5:c.18del	p.Ser7AlafsTer19	p.S7Afs*19	ENST00000304494	NM_000077.4	6	ggG/gg	1/3	0.266074469465701	2	FACETS	0.844	0.727	0.967	0.844	0.727	0.967	CLONAL	2	TRUE	0	0.343632932192888	2		67	169	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0005112-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	109	397	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.886	0.801	0.975	0.886	0.801	0.975	CLONAL	1	TRUE	1	0.555252600465085	2		397	443	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142016	108142016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555085052	NA	P-0005112-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	109	262	0	ENST00000278616.4:c.2960G>A	p.Cys987Tyr	p.C987Y	ENST00000278616	NM_000051.3	987	tGt/tAt	20/63	1	2	FACETS	0.85	0.767	0.936	0.85	0.767	0.936	CLONAL	1	TRUE	1	0.555252600465085	2		262	462	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439206	52439206	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005112-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	157	359	1	ENST00000460680.1:c.1036del	p.Val346PhefsTer16	p.V346Ffs*16	ENST00000460680	NM_004656.3	346	Gtt/tt	11/17	0.520048811345003	1	FACETS	0.86	0.794	0.927	0.86	0.794	0.927	CLONAL	1	TRUE	0	0.555252600465085	1		360	475	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058631	72058631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	551	677	0	ENST00000357731.5:c.809G>A	p.Gly270Glu	p.G270E	ENST00000357731	NM_173808.2	270	gGa/gAa	6/7	0.895725989423335	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.895725989423335	1		677	649	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0005118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	698	311	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	0.895725989423335	3	FACETS	1	0.986	1			1	CLONAL	2	TRUE	NA	0.895725989423335	3		311	1104	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149899	202149899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1249963205	NA	P-0005118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	320	366	1	ENST00000358485.4:c.1340C>T	p.Pro447Leu	p.P447L	ENST00000358485	NM_001080125.1	447	cCt/cTt	8/9	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.895725989423335	2		367	660	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725076	49725076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	582	580	2	ENST00000449682.2:c.268C>T	p.His90Tyr	p.H90Y	ENST00000449682	NM_020998.3	90	Cat/Tat	3/18	NA	2	FACETS	0.974	0.938	1			1	INDETERMINATE	1	TRUE	NA	0.895725989423335	2		582	1334	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259262	89259262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770780950	NA	P-0005118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	402	375	0	ENST00000336596.2:c.406C>T	p.Arg136Ter	p.R136*	ENST00000336596	NM_005233.5	136	Cga/Tga	3/17	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.895725989423335	2		375	860	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967348	134967348	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	396	348	0	ENST00000398015.3:c.2687C>T	p.Ala896Val	p.A896V	ENST00000398015	NM_004441.4	896	gCc/gTc	14/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.895725989423335	2		348	849	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156829	106156829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	426	428	0	ENST00000380013.4:c.1730C>T	p.Ser577Phe	p.S577F	ENST00000380013	NM_001127208.2	577	tCc/tTc	3/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.895725989423335	2		428	890	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0005118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	123	283	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.895725989423335	2		283	259	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658469	117658469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	200	279	0	ENST00000368508.3:c.5114C>T	p.Ser1705Leu	p.S1705L	ENST00000368508	NM_002944.2	1705	tCa/tTa	31/43	NA	2	FACETS	0.926	0.867	0.986			1	INDETERMINATE	1	TRUE	NA	0.895725989423335	2		279	482	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877987	151877987	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs887554056	NA	P-0005118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	670	298	0	ENST00000262189.6:c.6958C>T	p.His2320Tyr	p.H2320Y	ENST00000262189	NM_170606.2	2320	Cat/Tat	36/59	0.895725989423335	3	FACETS	0.991	0.962	1	0.991	0.962	1	CLONAL	2	TRUE	1	0.895725989423335	3		298	1093	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949069	151949069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776295921	NA	P-0005118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	754	405	0	ENST00000262189.6:c.1576C>T	p.Arg526Cys	p.R526C	ENST00000262189	NM_170606.2	526	Cgt/Tgt	11/59	0.895725989423335	3	FACETS	0.981	0.954	1	0.981	0.954	1	CLONAL	2	TRUE	1	0.895725989423335	3		405	1243	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451525	70451525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	384	560	0	ENST00000373644.4:c.6365C>T	p.Pro2122Leu	p.P2122L	ENST00000373644	NM_030625.2	2122	cCt/cTt	12/12	0.166015729823874	1	FACETS	0.524	0.5	0.549	0.524	0.5	0.549	INDETERMINATE	1	TRUE	0	0.895725989423335	1		560	903	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195673	102195673	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	601	816	0	ENST00000263464.3:c.433C>T	p.Pro145Ser	p.P145S	ENST00000263464	NM_001165.4	145	Cct/Tct	2/9	0.895725989423335	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.895725989423335	1		816	734	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959073	28959073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761475937	NA	P-0005118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	428	518	1	ENST00000282397.4:c.2065G>A	p.Glu689Lys	p.E689K	ENST00000282397	NM_002019.4	689	Gag/Aag	14/30	1	2	FACETS	0.972	0.93	1	0.972	0.93	1	CLONAL	1	TRUE	1	0.895725989423335	2		519	983	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609925	81609925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772490052	NA	P-0005118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	350	332	0	ENST00000298171.2:c.1523C>T	p.Ser508Leu	p.S508L	ENST00000298171	NM_000369.2	508	tCg/tTg	10/10	1	2	FACETS	0.924	0.879	0.969	0.924	0.879	0.969	CLONAL	1	TRUE	1	0.895725989423335	2		332	846	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81939102	81939102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	414	641	0	ENST00000359376.3:c.1457C>T	p.Ser486Phe	p.S486F	ENST00000359376	NM_002661.3	486	tCc/tTc	15/33	0.166015729823874	1	FACETS	0.534	0.51	0.558	0.534	0.51	0.558	INDETERMINATE	1	TRUE	0	0.895725989423335	1		641	956	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31015936	31015936	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	243	304	0	ENST00000375687.4:c.258T>A	p.Asp86Glu	p.D86E	ENST00000375687	NM_015338.5	86	gaT/gaA	5/13	1	2	FACETS	0.945	0.891	1	0.945	0.891	1	CLONAL	1	TRUE	1	0.895725989423335	2		304	574	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156735	20156735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	400	395	0	ENST00000379607.5:c.22G>A	p.Gly8Arg	p.G8R	ENST00000379607	NM_001412.3	8	Gga/Aga	2/7	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.895725989423335	1		395	446	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0005131-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	339	229	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.680644263796643	3	FACETS	0.994	0.964	1			1	CLONAL	3	TRUE	NA	0.71829647068923	3		229	430	SUCCESS
FIP1L1	81608	MSKCC	GRCh37	4	54280802	54280802	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005131-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	225	268	0	ENST00000358575.5:c.791C>G	p.Ser264Cys	p.S264C	ENST00000358575	NM_001134937.1	264	tCt/tGt	10/18	1	2	FACETS	0.971	0.91	1	0.971	0.91	1	CLONAL	1	TRUE	1	0.71829647068923	2		268	645	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579350	7579350	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587781642	NA	P-0005131-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	254	371	0	ENST00000269305.4:c.337T>G	p.Phe113Val	p.F113V	ENST00000269305	NM_001126112.2	113	Ttc/Gtc	4/11	0.71829647068923	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.71829647068923	1		371	443	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057775	27057775	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005131-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	392	534	0	ENST00000324856.7:c.1483C>G	p.His495Asp	p.H495D	ENST00000324856	NM_006015.4	495	Cat/Gat	3/20	1	2	FACETS	0.908	0.864	0.953	0.908	0.864	0.953	CLONAL	1	TRUE	1	0.71829647068923	2		534	1202	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782166	135782167	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	G	novel	NA	P-0005131-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	37	315	0	ENST00000298552.3:c.1389_1390delinsC	p.Leu463PhefsTer69	p.L463Ffs*69	ENST00000298552	NM_001162426.1	463	ttAGgt/ttCgt	14/23	0.71829647068923	1	FACETS	0.13	0.107	0.157	0.13	0.107	0.157	SUBCLONAL	1	TRUE	0	0.71829647068923	1		315	506	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023863	27023933	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCGCCGGCAAGGGCCCGGCGGACATGGCCTCGCAGTGTTGGGGGGCTGCGGCGGCGGCAGCTGCGGCGG	GGGCGCCGGCAAGGGCCCGGCGGACATGGCCTCGCAGTGTTGGGGGGCTGCGGCGGCGGCAGCTGCGGCGG	-	novel	NA	P-0005131-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	103	137	0	ENST00000324856.7:c.969_1039del	p.Ala325ArgfsTer51	p.A325Rfs*51	ENST00000324856	NM_006015.4	323	ggGGGCGCCGGCAAGGGCCCGGCGGACATGGCCTCGCAGTGTTGGGGGGCTGCGGCGGCGGCAGCTGCGGCGGcg/ggcg	1/20	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.71829647068923	2		137	278	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244760	41244760	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	168	594	1	ENST00000357654.3:c.2788C>T	p.Pro930Ser	p.P930S	ENST00000357654	NM_007294.3	930	Cct/Tct	10/23	1	2	FACETS	0.966	0.892	1	0.966	0.892	1	CLONAL	1	TRUE	1	0.57	2		595	610	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	19	221	1	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		222	366	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0005147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	25	300	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.512876934555474	3	FACETS	0.413	0.326	0.511	0.206	0.163	0.256	SUBCLONAL	1	TRUE	1	0.633267791028705	3		300	252	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56381323	56381323	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	66	450	0	ENST00000348428.3:c.967A>C	p.Asn323His	p.N323H	ENST00000348428	NM_006785.3	323	Aat/Cat	8/17	0.218552533608053	4	FACETS	0.373	0.323	0.428	0.187	0.161	0.214	INDETERMINATE	1	TRUE	2	0.633267791028705	4		450	912	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0005148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	424	386	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.874	0.834	0.916	0.874	0.834	0.916	CLONAL	1	TRUE	1	0.786029813433165	2		386	1234	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0005148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	234	342	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	1	2	FACETS	0.45	0.419	0.483	0.45	0.419	0.483	SUBCLONAL	1	TRUE	1	0.786029813433165	2		342	1323	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546761	9546761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768724288	NA	P-0005148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	165	227	0	ENST00000353224.5:c.1261G>A	p.Asp421Asn	p.D421N	ENST00000353224	NM_177990.2	421	Gac/Aac	5/10	1	2	FACETS	0.525	0.483	0.57	0.525	0.483	0.57	SUBCLONAL	1	TRUE	1	0.786029813433165	2		227	799	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445005	89445005	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112239794	NA	P-0005148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	115	235	0	ENST00000336596.2:c.1325C>T	p.Thr442Met	p.T442M	ENST00000336596	NM_005233.5	442	aCg/aTg	6/17	0.397605154977931	1	FACETS	0.394	0.357	0.432	0.394	0.357	0.432	INDETERMINATE	1	TRUE	0	0.786029813433165	1		235	451	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069966	5069966	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	193	262	0	ENST00000381652.3:c.1555G>C	p.Asp519His	p.D519H	ENST00000381652	NM_004972.3	519	Gat/Cat	12/25	0.52454809989549	1	FACETS	0.477	0.443	0.511	0.477	0.443	0.511	SUBCLONAL	1	TRUE	0	0.786029813433165	1		262	625	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5070046	5070046	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	140	155	0	ENST00000381652.3:c.1635G>C	p.Leu545Phe	p.L545F	ENST00000381652	NM_004972.3	545	ttG/ttC	12/25	0.52454809989549	1	FACETS	0.438	0.401	0.476	0.438	0.401	0.476	SUBCLONAL	1	TRUE	0	0.786029813433165	1		155	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121912666	NA	P-0005148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	561	535	0	ENST00000269305.4:c.659A>C	p.Tyr220Ser	p.Y220S	ENST00000269305	NM_001126112.2	220	tAt/tCt	6/11	0.738100654788311	1	FACETS	0.983	0.953	1	0.983	0.953	1	CLONAL	1	TRUE	0	0.786029813433165	1		535	881	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485759	57485759	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	211	325	0	ENST00000371085.3:c.1060G>A	p.Asp354Asn	p.D354N	ENST00000371085	NM_000516.4	354	Gat/Aat	13/13	1	2	FACETS	0.445	0.413	0.479	0.445	0.413	0.479	SUBCLONAL	1	TRUE	1	0.786029813433165	2		325	1206	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0005150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	47	173	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		174	244	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	235	320	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.44	2		320	456	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	95	125	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.96	0.872	1	1	0.988	1	CLONAL	2	TRUE	1	0.44	2		125	225	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112154	115112154	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	105	455	4	ENST00000257566.3:c.1586del	p.Gly529AlafsTer103	p.G529Afs*103	ENST00000257566	NM_016569.3	529	gGc/gc	7/8	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.44	2		459	438	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	115	468	0	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	1	2	FACETS	0.9	0.813	0.991	0.9	0.813	0.991	CLONAL	1	TRUE	1	0.44	2		468	581	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	22	93	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.787	0.618	0.978	0.787	0.618	0.978	CLONAL	1	TRUE	1	0.44	2		93	127	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	67	271	0	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.995	0.872	1	0.995	0.872	1	CLONAL	1	TRUE	1	0.44	2		271	306	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	62	234	0	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	0.918	0.799	1	0.918	0.799	1	CLONAL	1	TRUE	1	0.44	2		234	307	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638491	176638491	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784096	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	97	361	0	ENST00000439151.2:c.3091C>T	p.Arg1031Ter	p.R1031*	ENST00000439151	NM_022455.4	1031	Cga/Tga	5/23	0.265710447032288	1	FACETS	0.759	0.68	0.842	0.759	0.68	0.842	SUBCLONAL	1	TRUE	0	0.44	1		361	453	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287520	33287520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141395832	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	48	228	0	ENST00000374542.5:c.1577G>A	p.Arg526His	p.R526H	ENST00000374542	NM_001141970.1	526	cGc/cAc	6/8	1	2	FACETS	0.615	0.521	0.716	0.615	0.521	0.716	SUBCLONAL	1	TRUE	1	0.44	2		228	355	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	32	280	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.301	0.243	0.365	0.301	0.243	0.365	SUBCLONAL	1	TRUE	1	0.44	2		280	484	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834552	156834552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540521894	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	81	434	2	ENST00000524377.1:c.320C>T	p.Ala107Val	p.A107V	ENST00000524377	NM_002529.3	107	gCg/gTg	3/17	1	2	FACETS	0.923	0.818	1	0.923	0.818	1	CLONAL	1	TRUE	1	0.44	2		436	399	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	15	65	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	0.141554915639714	0	FACETS	0.466	0.347	0.603			1	INDETERMINATE	1	TRUE	0	0.44	0		65	82	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333266	70333266	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	57	417	0	ENST00000373644.4:c.1171G>A	p.Glu391Lys	p.E391K	ENST00000373644	NM_030625.2	391	Gag/Aag	2/12	1	2	FACETS	0.623	0.536	0.717	0.623	0.536	0.717	SUBCLONAL	1	TRUE	1	0.44	2		417	416	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032045	26032045	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	165	826	0	ENST00000244661.2:c.244G>C	p.Asp82His	p.D82H	ENST00000244661	NM_003537.3	82	Gat/Cat	1/1	0.182728280544451	4	FACETS	1	0.969	1	0.556	0.51	0.604	INDETERMINATE	1	TRUE	2	0.44	4		826	971	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073525	8073525	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	133	700	0	ENST00000377482.5:c.1134C>A	p.Cys378Ter	p.C378*	ENST00000377482	NM_018948.3	378	tgC/tgA	4/4	0.265710447032288	1	FACETS	0.731	0.666	0.8	0.731	0.666	0.8	SUBCLONAL	1	TRUE	0	0.44	1		700	645	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777020	9777020	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs796730337	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	103	431	0	ENST00000377346.4:c.784A>G	p.Ile262Val	p.I262V	ENST00000377346	NM_005026.3	262	Atc/Gtc	7/24	0.265710447032288	1	FACETS	0.936	0.845	1	0.936	0.845	1	CLONAL	1	TRUE	0	0.44	1		431	390	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46715676	46715676	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	112	381	0	ENST00000371975.4:c.95C>A	p.Pro32His	p.P32H	ENST00000371975	NM_003579.3	32	cCt/cAt	3/18	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.44	2		381	474	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439853	51439853	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1557609882	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	36	100	0	ENST00000262662.1:c.418G>A	p.Ala140Thr	p.A140T	ENST00000262662		140	Gcc/Acc	4/4	1	2	FACETS	0.779	0.646	0.925	0.779	0.646	0.925	CLONAL	1	TRUE	1	0.44	2		100	210	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907654	111907654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141962978	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	107	460	0	ENST00000393256.3:c.428G>A	p.Arg143His	p.R143H	ENST00000393256	NM_006538.4	143	cGc/cAc	3/4	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.44	2		460	418	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719073	190719073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369839744	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	97	191	2	ENST00000441310.2:c.1075G>A	p.Val359Ile	p.V359I	ENST00000441310	NM_000534.4	359	Gtt/Att	9/13	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.44	2		193	427	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691881	30691881	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	62	277	1	ENST00000295754.5:c.383A>G	p.Lys128Arg	p.K128R	ENST00000295754	NM_003242.5	128	aAg/aGg	3/7	0.3	3	FACETS	0.828	0.718	0.948	0.276	0.239	0.316	CLONAL	1	TRUE	0	0.44	3		278	415	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162317	47162317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752087228	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	70	244	1	ENST00000409792.3:c.3809C>T	p.Thr1270Met	p.T1270M	ENST00000409792	NM_014159.6	1270	aCg/aTg	3/21	NA	2	FACETS	1	0.924	1			1	INDETERMINATE	1	TRUE	NA	0.44	2		245	298	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928374	69928374	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1170368454	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	105	301	0	ENST00000352241.4:c.194G>A	p.Arg65His	p.R65H	ENST00000352241	NM_198159.2	65	cGt/cAt	2/10	1	2	FACETS	0.929	0.835	1	0.929	0.835	1	CLONAL	1	TRUE	1	0.44	2		301	514	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967276	134967276	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs534330476	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	100	404	0	ENST00000398015.3:c.2615C>T	p.Ala872Val	p.A872V	ENST00000398015	NM_004441.4	872	gCg/gTg	14/16	1	2	FACETS	0.971	0.872	1	0.971	0.872	1	CLONAL	1	TRUE	1	0.44	2		404	468	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158313	106158313	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	113	375	0	ENST00000380013.4:c.3214G>A	p.Ala1072Thr	p.A1072T	ENST00000380013	NM_001127208.2	1072	Gca/Aca	3/11	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.44	2		375	511	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963022	38963022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763305312	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	97	269	1	ENST00000357387.3:c.1522C>T	p.Arg508Trp	p.R508W	ENST00000357387	NM_152756.3	508	Cgg/Tgg	17/38	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.44	2		270	422	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590986	67590986	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	58	146	0	ENST00000274335.5:c.1579A>G	p.Asn527Asp	p.N527D	ENST00000274335		527	Aat/Gat	12/15	1	2	FACETS	0.864	0.748	0.989	0.864	0.748	0.989	CLONAL	1	TRUE	1	0.44	2		146	305	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467700	50467700	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	80	415	0	ENST00000331340.3:c.935A>G	p.Asp312Gly	p.D312G	ENST00000331340	NM_006060.4	312	gAc/gGc	8/8	1	2	FACETS	0.758	0.669	0.852	0.758	0.669	0.852	SUBCLONAL	1	TRUE	1	0.44	2		415	480	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239932	98239932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	86	263	0	ENST00000331920.6:c.1400G>A	p.Gly467Asp	p.G467D	ENST00000331920	NM_000264.3	467	gGt/gAt	10/24	1	2	FACETS	0.933	0.83	1	0.933	0.83	1	CLONAL	1	TRUE	1	0.44	2		263	419	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900273	101900273	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	60	362	0	ENST00000374994.4:c.707C>A	p.Ser236Tyr	p.S236Y	ENST00000374994	NM_004612.2	236	tCt/tAt	4/9	1	2	FACETS	0.678	0.587	0.778	0.678	0.587	0.778	SUBCLONAL	1	TRUE	1	0.44	2		362	402	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801065	135801065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs118203361	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	75	427	1	ENST00000298552.3:c.272C>T	p.Ser91Leu	p.S91L	ENST00000298552	NM_001162426.1	91	tCg/tTg	5/23	1	2	FACETS	0.842	0.741	0.949	0.842	0.741	0.949	CLONAL	1	TRUE	1	0.44	2		428	405	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412238	139412238	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	38	494	1	ENST00000277541.6:c.1407C>G	p.Asp469Glu	p.D469E	ENST00000277541	NM_017617.3	469	gaC/gaG	8/34	1	2	FACETS	0.315	0.259	0.376	0.315	0.259	0.376	SUBCLONAL	1	TRUE	1	0.44	2		495	549	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564426	139564426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	32	341	1	ENST00000308874.7:c.374G>A	p.Cys125Tyr	p.C125Y	ENST00000308874		125	tGc/tAc	6/10	1	2	FACETS	0.453	0.368	0.548	0.453	0.368	0.548	SUBCLONAL	1	TRUE	1	0.44	2		342	321	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	464407	464407	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	69	266	0	ENST00000399788.2:c.787A>C	p.Thr263Pro	p.T263P	ENST00000399788	NM_001042603.1	263	Acc/Ccc	7/28	1	2	FACETS	0.767	0.671	0.87	0.767	0.671	0.87	SUBCLONAL	1	TRUE	1	0.44	2		266	409	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425796	49425796	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1165766760	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	67	211	0	ENST00000301067.7:c.12692T>G	p.Leu4231Arg	p.L4231R	ENST00000301067	NM_003482.3	4231	cTg/cGg	39/54	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.44	2		211	286	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915013	32915013	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	134	646	0	ENST00000380152.3:c.6521T>G	p.Val2174Gly	p.V2174G	ENST00000380152		2174	gTt/gGt	11/27	1	2	FACETS	0.873	0.794	0.955	0.873	0.794	0.955	CLONAL	1	TRUE	1	0.44	2		646	698	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336137	73336137	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	140	388	2	ENST00000377767.4:c.2266T>C	p.Ser756Pro	p.S756P	ENST00000377767	NM_014953.3	756	Tct/Cct	17/21	0.182728280544451	4	FACETS	0.8	0.731	0.871	0.8	0.731	0.871	INDETERMINATE	2	TRUE	2	0.44	4		390	573	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435010	110435010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	13	143	0	ENST00000375856.3:c.3391C>T	p.Arg1131Cys	p.R1131C	ENST00000375856	NM_003749.2	1131	Cgc/Tgc	1/2	0.182728280544451	4	FACETS	0.372	0.265	0.502	0.186	0.132	0.251	INDETERMINATE	1	TRUE	2	0.44	4		143	229	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99491810	99491810	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886044448	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	40	370	1	ENST00000268035.6:c.3595G>A	p.Gly1199Arg	p.G1199R	ENST00000268035	NM_000875.3	1199	Ggg/Agg	20/21	1	2	FACETS	0.378	0.314	0.45	0.378	0.314	0.45	SUBCLONAL	1	TRUE	1	0.44	2		371	481	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032245	10032245	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	36	299	0	ENST00000330684.3:c.578A>G	p.Asn193Ser	p.N193S	ENST00000330684	NM_001134407.1	193	aAc/aGc	3/13	0.141554915639714	0	FACETS	0.325	0.268	0.388			1	INDETERMINATE	1	TRUE	0	0.44	0		299	282	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641370	23641370	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	85	676	0	ENST00000261584.4:c.2105T>C	p.Ile702Thr	p.I702T	ENST00000261584	NM_024675.3	702	aTa/aCa	5/13	0.141554915639714	0	FACETS	0.469	0.416	0.526			1	INDETERMINATE	1	TRUE	0	0.44	0		676	461	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993653	72993653	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	126	645	1	ENST00000268489.5:c.392G>T	p.Gly131Val	p.G131V	ENST00000268489	NM_006885.3	131	gGg/gTg	2/10	0.283271529469497	0	FACETS	0.579	0.526	0.634			1	SUBCLONAL	1	TRUE	0	0.44	0		646	554	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348128	89348128	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	80	950	1	ENST00000301030.4:c.4822A>T	p.Met1608Leu	p.M1608L	ENST00000301030	NM_001256183.1	1608	Atg/Ttg	9/13	1	2	FACETS	0.614	0.541	0.693	0.614	0.541	0.693	SUBCLONAL	1	TRUE	1	0.44	2		951	592	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348580	89348580	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	54	1083	0	ENST00000301030.4:c.4370A>T	p.Lys1457Ile	p.K1457I	ENST00000301030	NM_001256183.1	1457	aAa/aTa	9/13	1	2	FACETS	0.358	0.305	0.416	0.358	0.305	0.416	SUBCLONAL	1	TRUE	1	0.44	2		1083	686	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15938195	15938195	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	116	485	0	ENST00000268712.3:c.7019C>A	p.Pro2340His	p.P2340H	ENST00000268712	NM_006311.3	2340	cCt/cAt	45/46	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.44	2		485	521	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676141	29676141	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1567623401	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	14	197	0	ENST00000356175.3:c.7130A>G	p.Tyr2377Cys	p.Y2377C	ENST00000356175	NM_000267.3	2377	tAc/tGc	48/57	1	2	FACETS	0.241	0.174	0.323	0.241	0.174	0.323	SUBCLONAL	1	TRUE	1	0.44	2		197	264	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428299	33428299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368914740	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	104	387	1	ENST00000345365.6:c.824G>A	p.Arg275Gln	p.R275Q	ENST00000345365	NM_002878.3	275	cGg/cAg	9/10	1	2	FACETS	0.882	0.792	0.976	0.882	0.792	0.976	CLONAL	1	TRUE	1	0.44	2		388	536	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618703	37618703	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	140	568	0	ENST00000447079.4:c.379C>T	p.Gln127Ter	p.Q127*	ENST00000447079	NM_015083.1	127	Cag/Tag	1/14	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.44	2		568	593	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687283	37687283	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	33	397	1	ENST00000447079.4:c.4187A>G	p.Gln1396Arg	p.Q1396R	ENST00000447079	NM_015083.1	1396	cAg/cGg	14/14	1	2	FACETS	0.304	0.247	0.369	0.304	0.247	0.369	SUBCLONAL	1	TRUE	1	0.44	2		398	493	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40376865	40376865	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	98	637	0	ENST00000293328.3:c.307A>G	p.Met103Val	p.M103V	ENST00000293328	NM_012448.3	103	Atg/Gtg	4/19	0.3	0	FACETS	0.497	0.445	0.552			1	SUBCLONAL	1	TRUE	0	0.44	0		637	502	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223087	41223087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555580805	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	102	484	0	ENST00000357654.3:c.4844C>T	p.Ala1615Val	p.A1615V	ENST00000357654	NM_007294.3	1615	gCt/gTt	15/23	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.44	2		484	442	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619371	1619371	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1287548803	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	149	546	1	ENST00000344749.5:c.1270G>A	p.Ala424Thr	p.A424T	ENST00000344749	NM_001136139.2	424	Gcg/Acg	15/19	0.141554915639714	0	FACETS	0.766	0.705	0.829			1	INDETERMINATE	1	TRUE	0	0.44	0		547	495	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217034	2217034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368118931	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	101	456	0	ENST00000398665.3:c.2489C>T	p.Pro830Leu	p.P830L	ENST00000398665	NM_032482.2	830	cCg/cTg	21/28	0.141554915639714	0	FACETS	0.633	0.57	0.699			1	INDETERMINATE	1	TRUE	0	0.44	0		456	406	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265274	10265274	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	81	317	0	ENST00000340748.4:c.1772C>T	p.Thr591Met	p.T591M	ENST00000340748		591	aCg/aTg	20/40	0.141554915639714	0	FACETS	0.565	0.501	0.632			1	INDETERMINATE	1	TRUE	0	0.44	0		317	365	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291890	15291890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	78	403	0	ENST00000263388.2:c.2876G>A	p.Cys959Tyr	p.C959Y	ENST00000263388	NM_000435.2	959	tGc/tAc	18/33	0.141554915639714	0	FACETS	0.591	0.523	0.662			1	INDETERMINATE	1	TRUE	0	0.44	0		403	336	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012773	36012773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	21	267	1	ENST00000358208.4:c.217G>A	p.Val73Ile	p.V73I	ENST00000358208		73	Gtc/Atc	2/12	1	2	FACETS	0.316	0.243	0.401	0.316	0.243	0.401	SUBCLONAL	1	TRUE	1	0.44	2		268	302	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573608	41573608	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	76	370	0	ENST00000263253.7:c.5893A>G	p.Met1965Val	p.M1965V	ENST00000263253	NM_001429.3	1965	Atg/Gtg	31/31	1	2	FACETS	0.83	0.732	0.935	0.83	0.732	0.935	CLONAL	1	TRUE	1	0.44	2		370	416	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574133	41574133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367685222	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	131	307	0	ENST00000263253.7:c.6418G>A	p.Val2140Ile	p.V2140I	ENST00000263253	NM_001429.3	2140	Gtt/Att	31/31	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.44	2		307	445	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256341	46256341	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	91	619	0	ENST00000371998.3:c.574del	p.Ser192AlafsTer9	p.S192Afs*9	ENST00000371998		190	cAa/ca	7/23	0.293047131038968	0	FACETS	0.415	0.369	0.464			1	SUBCLONAL	1	TRUE	0	0.44	0		619	558	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591259	67591259	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	37	313	0	ENST00000274335.5:c.1761del	p.Gly588ValfsTer7	p.G588Vfs*7	ENST00000274335		586	cAa/ca	13/15	1	2	FACETS	0.329	0.271	0.394	0.329	0.271	0.394	SUBCLONAL	1	TRUE	1	0.44	2		313	511	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930282	39930282	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	131	354	0	ENST00000378444.4:c.3182del	p.Lys1061SerfsTer52	p.K1061Sfs*52	ENST00000378444	NM_001123385.1	1061	aAg/ag	6/15	1	1	FACETS	0.851	0.787	0.914	1	0.99	1	CLONAL	2	TRUE	0	0.44	1		354	273	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012359	29012359	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	97	308	0	ENST00000282397.4:c.512del	p.Lys171SerfsTer7	p.K171Sfs*7	ENST00000282397	NM_002019.4	171	aAg/ag	4/30	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.44	2		308	421	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907421	32907421	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359306	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	92	277	3	ENST00000380152.3:c.1813del	p.Ile605TyrfsTer9	p.I605Yfs*9	ENST00000380152		602	ggA/gg	10/27	1	2	FACETS	0.853	0.761	0.951	0.853	0.761	0.951	CLONAL	1	TRUE	1	0.44	2		280	490	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038923	12038925	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	101	351	0	ENST00000396373.4:c.1218_1220del	p.Ile407del	p.I407del	ENST00000396373	NM_001987.4	406	ATT/-	7/8	0.3	5	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.44	5		351	529	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073616	8073616	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	122	681	0	ENST00000377482.5:c.1043del	p.Pro348ArgfsTer104	p.P348Rfs*104	ENST00000377482	NM_018948.3	348	cCg/cg	4/4	0.265710447032288	1	FACETS	0.703	0.637	0.773	0.703	0.637	0.773	SUBCLONAL	1	TRUE	0	0.44	1		681	615	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924551	131924551	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	96	321	0	ENST00000265335.6:c.1228del	p.Thr410LeufsTer5	p.T410Lfs*5	ENST00000265335		408	gcA/gc	8/25	1	2	FACETS	0.838	0.749	0.931	0.838	0.749	0.931	CLONAL	1	TRUE	1	0.44	2		321	521	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41203123	41203123	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs80357886	NA	P-0005151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	67	276	0	ENST00000357654.3:c.5289del	p.Leu1764Ter	p.L1764*	ENST00000357654	NM_007294.3	1763	ggG/gg	20/23	1	2	FACETS	0.875	0.765	0.992	0.875	0.765	0.992	CLONAL	1	TRUE	1	0.44	2		276	348	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281604	198281604	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	297	251	0	ENST00000335508.6:c.527C>A	p.Ala176Asp	p.A176D	ENST00000335508	NM_012433.2	176	gCt/gAt	6/25	1	2	FACETS	0.95	0.901	0.999	0.95	0.901	0.999	CLONAL	1	TRUE	1	0.925288615145247	2		251	676	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0005186-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	467	525	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.838403959849444	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.838403959849444	2		526	553	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998600	100998600	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005186-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	131	394	0	ENST00000325455.5:c.1202C>T	p.Pro401Leu	p.P401L	ENST00000325455	NM_001202474.3	401	cCg/cTg	1/8	0.838403959849444	5	FACETS	0.645	0.584	0.71	0.161	0.146	0.178	SUBCLONAL	1	TRUE	1	0.838403959849444	5		394	1093	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299908	15299908	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1381959540	NA	P-0005186-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	246	413	0	ENST00000263388.2:c.1270A>G	p.Thr424Ala	p.T424A	ENST00000263388	NM_000435.2	424	Act/Gct	8/33	0.746054428382797	3	FACETS	1	0.967	1	0.524	0.491	0.557	CLONAL	1	TRUE	1	0.838403959849444	3		413	795	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598082	52598082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	55	427	0	ENST00000394830.3:c.3784G>A	p.Glu1262Lys	p.E1262K	ENST00000394830	NM_018313.4	1262	Gaa/Aaa	24/30	0.426819682501775	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.426819682501775	1		427	168	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57567456	57567456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1439469695	NA	P-0005202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	98	449	0	ENST00000316660.6:c.47G>A	p.Arg16Gln	p.R16Q	ENST00000316660	NM_021127.2	16	cGg/cAg	1/2	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.426819682501775	2		449	382	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266105	41266619	+	splice_donor_variant,splice_acceptor_variant,stop_lost,protein_altering_variant,intron_variant	Splice_Site	DEL	AATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTT	AATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTT	-	novel	NA	P-0005202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	54	440	0	ENST00000349496.5:c.102_416del		p.X34_splice	ENST00000349496	NM_001904.3	34	ggAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTg/ggg	3-4/15	0.426819682501775	1	FACETS	0.985	0.854	1	0.985	0.854	1	CLONAL	1	TRUE	0	0.426819682501775	1		440	202	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950048	44950048	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	79	250	0	ENST00000377967.4:c.3817del	p.Leu1273PhefsTer19	p.L1273Ffs*19	ENST00000377967	NM_021140.2	1273	Ctt/tt	26/29	1	1	FACETS	0.818	0.737	0.9	1	0.983	1	CLONAL	2	TRUE	0	0.426819682501775	1		250	178	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0005223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	205	383	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.292591646365171	4	FACETS	0.959	0.89	1			1	CLONAL	2	FALSE	NA	0.3	4		383	926	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680532	241680532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201878591	NA	P-0005235-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	81	415	1	ENST00000366560.3:c.217G>A	p.Val73Met	p.V73M	ENST00000366560	NM_000143.3	73	Gtg/Atg	2/10	0.218262788357155	2	FACETS	0.711	0.626	0.803	0.356	0.313	0.402	SUBCLONAL	1	FALSE	0	0.3	2		416	759	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436219	110436219	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005235-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	35	191	0	ENST00000375856.3:c.2182A>G	p.Lys728Glu	p.K728E	ENST00000375856	NM_003749.2	728	Aag/Gag	1/2	0.3	1	FACETS	0.471	0.386	0.567	0.471	0.386	0.567	SUBCLONAL	1	FALSE	0	0.3	1		191	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0005267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	32	476	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	0.775	0.629	0.941	0.775	0.629	0.941	CLONAL	1	FALSE	1	0.183523169450639	2		476	450	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120527	70120527	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0005267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	40	110	0	ENST00000245479.2:c.1529G>C	p.Ter510SerextTer49	p.*510Sext*49	ENST00000245479	NM_000346.3	510	tGa/tCa	3/3	1	2	FACETS	1	0.891	1	1	0.971	1	CLONAL	2	FALSE	1	0.183523169450639	2		110	202	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341947	8341947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159863	NA	P-0005267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	35	142	0	ENST00000356435.5:c.4693G>A	p.Val1565Ile	p.V1565I	ENST00000356435		1565	Gtc/Atc	29/35	1	2	FACETS	0.691	0.565	0.833	0.691	0.565	0.833	SUBCLONAL	1	FALSE	1	0.183523169450639	2		142	552	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846080	68846080	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555515726	NA	P-0005267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	40	243	0	ENST00000261769.5:c.1051C>T	p.Gln351Ter	p.Q351*	ENST00000261769	NM_004360.3	351	Caa/Taa	8/16	0.172935952798127	0	FACETS	0.76	0.632	0.904			1	CLONAL	1	FALSE	0	0.183523169450639	0		243	468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577077	7577077	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs748891343	NA	P-0005267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	32	206	0	ENST00000269305.4:c.861G>C	p.Glu287Asp	p.E287D	ENST00000269305	NM_001126112.2	287	gaG/gaC	8/11	1	2	FACETS	0.756	0.613	0.918	0.756	0.613	0.918	CLONAL	1	FALSE	1	0.183523169450639	2		206	461	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921160	50921160	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1568643585	NA	P-0005267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	26	260	0	ENST00000440232.2:c.3280C>T	p.Gln1094Ter	p.Q1094*	ENST00000440232	NM_002691.3	1094	Cag/Tag	27/27	0.172935952798127	0	FACETS	0.592	0.468	0.733			1	SUBCLONAL	1	FALSE	0	0.183523169450639	0		260	391	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118932	115118934	+	frameshift_variant	Frame_Shift_Del	DEL	TAA	TAA	AT	novel	NA	P-0005267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	49	148	0	ENST00000257566.3:c.407_409delinsAT	p.Phe136TyrfsTer3	p.F136Yfs*3	ENST00000257566	NM_016569.3	136	tTTAaa/tATaa	2/8	0.183523169450639	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	0	0.183523169450639	1		148	365	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890116	76890116	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005270-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	41	385	1	ENST00000373344.5:c.4778C>T	p.Ala1593Val	p.A1593V	ENST00000373344	NM_000489.3	1593	gCc/gTc	17/35	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		386	223	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913250	NA	P-0005304-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	1401	361	2	ENST00000369535.4:c.34G>A	p.Gly12Ser	p.G12S	ENST00000369535	NM_002524.4	12	Ggt/Agt	2/7	0.443093967181213	9	FACETS	1	0.995	1			1	CLONAL	8	TRUE	NA	0.443093967181213	9		363	1955	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259185	89259185	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005304-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	52	427	1	ENST00000336596.2:c.329C>T	p.Pro110Leu	p.P110L	ENST00000336596	NM_005233.5	110	cCa/cTa	3/17	1	2	FACETS	0.278	0.235	0.324	0.278	0.235	0.324	SUBCLONAL	1	TRUE	1	0.443093967181213	2		428	845	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11181391	11181391	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	67	600	0	ENST00000361445.4:c.6845A>C	p.Gln2282Pro	p.Q2282P	ENST00000361445	NM_004958.3	2282	cAg/cCg	49/58	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.203426136802421	2		600	588	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612753	228612753	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1257	219	933	0	ENST00000366696.1:c.274G>T	p.Ala92Ser	p.A92S	ENST00000366696	NM_003493.2	92	Gcg/Tcg	1/1	0.203426136802421	3	FACETS	0.804	0.745	0.864	0.804	0.745	0.864	CLONAL	2	TRUE	1	0.203426136802421	3		933	1476	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118817	61118817	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0005309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	118	327	0	ENST00000295025.8:c.11-1G>T		p.X4_splice	ENST00000295025	NM_002908.2	4			0.203426136802421	7	FACETS	0.932	0.843	1	0.699	0.632	0.769	CLONAL	3	TRUE	3	0.203426136802421	7		327	626	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578362	212578362	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	81	325	0	ENST00000342788.4:c.895G>T	p.Val299Leu	p.V299L	ENST00000342788	NM_005235.2	299	Gta/Tta	8/28	0.203426136802421	4	FACETS	0.978	0.864	1	0.978	0.864	1	CLONAL	2	TRUE	2	0.203426136802421	4		325	490	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021715	71021715	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	117	486	0	ENST00000318789.4:c.1643A>G	p.Lys548Arg	p.K548R	ENST00000318789	NM_032682.5	548	aAg/aGg	18/21	0.203426136802421	2	FACETS	0.829	0.748	0.914	0.829	0.748	0.914	CLONAL	2	TRUE	0	0.203426136802421	2		486	694	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391031	89391031	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	42	570	1	ENST00000336596.2:c.1097G>T	p.Cys366Phe	p.C366F	ENST00000336596	NM_005233.5	366	tGt/tTt	5/17	0.203426136802421	2	FACETS	0.724	0.604	0.858	0.362	0.302	0.429	SUBCLONAL	1	TRUE	0	0.203426136802421	2		571	570	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920381	134920381	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	58	589	0	ENST00000398015.3:c.2196G>T	p.Met732Ile	p.M732I	ENST00000398015	NM_004441.4	732	atG/atT	12/16	0.188609411444268	3	FACETS	0.94	0.807	1	0.47	0.403	0.543	CLONAL	1	TRUE	1	0.203426136802421	3		589	668	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293614	1293614	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	52	291	1	ENST00000310581.5:c.1387G>T	p.Gly463Cys	p.G463C	ENST00000310581	NM_198253.2	463	Ggc/Tgc	2/16	0.203426136802421	5	FACETS	1	0.877	1	0.259	0.22	0.302	CLONAL	1	TRUE	1	0.203426136802421	5		292	644	SUCCESS
APC	324	MSKCC	GRCh37	5	112137039	112137039	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	112	528	1	ENST00000257430.4:c.793G>T	p.Gly265Ter	p.G265*	ENST00000257430	NM_000038.5	265	Gga/Tga	8/16	0.203426136802421	2	FACETS	0.985	0.889	1	0.985	0.889	1	CLONAL	2	TRUE	0	0.203426136802421	2		529	559	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181887	32181887	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	93	352	0	ENST00000375023.3:c.2167G>T	p.Gly723Ter	p.G723*	ENST00000375023	NM_004557.3	723	Gga/Tga	13/30	0.203426136802421	5	FACETS	1	0.96	1	0.775	0.692	0.864	CLONAL	2	TRUE	2	0.203426136802421	5		352	513	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287387	33287387	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	129	398	0	ENST00000374542.5:c.1710G>T	p.Glu570Asp	p.E570D	ENST00000374542	NM_001141970.1	570	gaG/gaT	6/8	0.203426136802421	5	FACETS	1	0.978	1	0.83	0.754	0.909	CLONAL	2	TRUE	2	0.203426136802421	5		398	665	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265378	152265378	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	59	371	0	ENST00000206249.3:c.831G>T	p.Arg277Ser	p.R277S	ENST00000206249	NM_000125.3	277	agG/agT	4/8	0.203426136802421	2	FACETS	1	0.967	1	0.721	0.623	0.828	CLONAL	1	TRUE	0	0.203426136802421	2		371	402	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527949	157527949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764671385	NA	P-0005309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	80	287	2	ENST00000346085.5:c.5674G>A	p.Ala1892Thr	p.A1892T	ENST00000346085	NM_020732.3	1892	Gca/Aca	20/20	0.203426136802421	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.203426136802421	2		289	346	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949089	151949089	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	48	435	1	ENST00000262189.6:c.1556A>T	p.His519Leu	p.H519L	ENST00000262189	NM_170606.2	519	cAc/cTc	11/59	0.203426136802421	4	FACETS	0.835	0.705	0.979	0.278	0.235	0.327	CLONAL	1	TRUE	1	0.203426136802421	4		436	680	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636774	8636774	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	55	398	0	ENST00000356435.5:c.135C>A	p.Cys45Ter	p.C45*	ENST00000356435		45	tgC/tgA	2/35	0.203426136802421	1	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	0	0.203426136802421	1		398	459	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006017	22006017	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	84	398	0	ENST00000276925.6:c.386C>A	p.Ala129Glu	p.A129E	ENST00000276925	NM_004936.3	129	gCa/gAa	2/2	0.187515349188848	3	FACETS	1	0.973	1	0.454	0.401	0.511	CLONAL	1	TRUE	0	0.203426136802421	3		398	668	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966544	36966544	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0005309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	113	363	0	ENST00000358127.4:c.780+2T>C		p.X260_splice	ENST00000358127	NM_001280556.1	260			0.187515349188848	3	FACETS	1	0.968	1	0.78	0.705	0.859	CLONAL	2	TRUE	0	0.203426136802421	3		363	523	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772055	135772055	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	16	125	1	ENST00000298552.3:c.3062C>T	p.Pro1021Leu	p.P1021L	ENST00000298552	NM_001162426.1	1021	cCc/cTc	23/23	0.187515349188848	3	FACETS	1	0.796	1	0.361	0.268	0.471	CLONAL	1	TRUE	0	0.203426136802421	3		126	160	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125523721	125523721	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	47	342	1	ENST00000428830.2:c.1314G>T	p.Leu438Phe	p.L438F	ENST00000428830	NM_001114121.2	438	ttG/ttT	12/14	0.188609411444268	3	FACETS	0.929	0.783	1	0.464	0.391	0.545	CLONAL	1	TRUE	1	0.203426136802421	3		343	548	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619197	23619197	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	178	510	1	ENST00000261584.4:c.3338G>T	p.Gly1113Val	p.G1113V	ENST00000261584	NM_024675.3	1113	gGg/gTg	12/13	0.203426136802421	5	FACETS	1	0.935	1	1	0.935	1	CLONAL	3	TRUE	2	0.203426136802421	5		511	751	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602413	10602413	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	161	521	0	ENST00000171111.5:c.1165G>T	p.Asp389Tyr	p.D389Y	ENST00000171111	NM_203500.1	389	Gac/Tac	3/6	0.203426136802421	2	FACETS	0.999	0.918	1	0.999	0.918	1	CLONAL	2	TRUE	0	0.203426136802421	2		521	792	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610648	10610648	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	94	275	0	ENST00000171111.5:c.62C>A	p.Ser21Ter	p.S21*	ENST00000171111	NM_203500.1	21	tCa/tAa	2/6	0.203426136802421	2	FACETS	0.989	0.885	1	0.989	0.885	1	CLONAL	2	TRUE	0	0.203426136802421	2		275	467	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918966	76918966	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	137	339	0	ENST00000373344.5:c.4025G>C	p.Arg1342Pro	p.R1342P	ENST00000373344	NM_000489.3	1342	cGg/cCg	12/35	0.203426136802421	2	FACETS	1	0.94	1			1	CLONAL	3	TRUE	NA	0.203426136802421	2		339	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577070	7577070	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	116	514	0	ENST00000269305.4:c.868del	p.Arg290AlafsTer55	p.R290Afs*55	ENST00000269305	NM_001126112.2	290	Cgc/gc	8/11	0.203426136802421	4	FACETS	0.98	0.885	1	0.98	0.885	1	CLONAL	2	TRUE	2	0.203426136802421	4		514	700	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439627	140439628	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0005309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	67	230	0	ENST00000288602.6:c.2111_2112del	p.Arg704ThrfsTer11	p.R704Tfs*11	ENST00000288602	NM_004333.4	704	aGA/a	17/18	0.203426136802421	4	FACETS	0.858	0.752	0.971	0.858	0.752	0.971	CLONAL	3	TRUE	1	0.203426136802421	4		230	308	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105624	11105628	+	frameshift_variant	Frame_Shift_Del	DEL	GAGCA	GAGCA	-	novel	NA	P-0005309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	178	540	1	ENST00000358026.2:c.1542_1546del	p.Gln515GlufsTer17	p.Q515Efs*17	ENST00000358026	NM_001128849.1	514	GAGCAg/g	9/36	0.203426136802421	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.203426136802421	2		541	831	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286235	66286235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746116670	NA	P-0005323-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	539	532	5	ENST00000273854.3:c.1451G>A	p.Ser484Asn	p.S484N	ENST00000273854	NM_004439.5	484	aGc/aAc	6/18	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.73188259627789	2		537	1410	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710819	117710819	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1422557855	NA	P-0005323-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	876	772	6	ENST00000368508.3:c.1453T>C	p.Ser485Pro	p.S485P	ENST00000368508	NM_002944.2	485	Tct/Cct	12/43	0.73188259627789	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.73188259627789	3		778	1629	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450405	50450405	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005323-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	195	371	2	ENST00000331340.3:c.589G>T	p.Val197Phe	p.V197F	ENST00000331340	NM_006060.4	197	Gtt/Ttt	5/8	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.73188259627789	2		373	522	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950085	44950085	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	38	644	0	ENST00000377967.4:c.3854A>T	p.Asp1285Val	p.D1285V	ENST00000377967	NM_021140.2	1285	gAt/gTt	26/29	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		644	209	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576883	7576883	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	76	501	0	ENST00000269305.4:c.963del	p.Lys321AsnfsTer24	p.K321Nfs*24	ENST00000269305	NM_001126112.2	321	aaA/aa	9/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.2	2		501	634	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174395	11174395	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	162	499	0	ENST00000361445.4:c.7280T>G	p.Leu2427Arg	p.L2427R	ENST00000361445	NM_004958.3	2427	cTg/cGg	53/58	0.460389948208592	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	0	0.460389948208592	1		499	468	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0005360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	347	385	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.567733326818768	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.567733326818768	3		385	721	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	125	472	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.422864174183225	3	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.567733326818768	3		472	386	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061261	38061264	+	missense_variant	Missense_Mutation	ONP	TAGG	TAGG	GAGC	novel	NA	P-0005360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	491	473	0	ENST00000250448.2:c.725_728delinsGCTC	p.Ser242_Tyr243delinsCysSer	p.S242_Y243delinsCS	ENST00000250448	NM_004496.3	242	tCCTAc/tGCTCc	2/2	0.567733326818768	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	1	0.567733326818768	4		473	866	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628763	187628763	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	33	417	0	ENST00000441802.2:c.2219A>C	p.Asn740Thr	p.N740T	ENST00000441802	NM_005245.3	740	aAc/aCc	2/27	0.214925288092103	4	FACETS	0.406	0.33	0.491			1	INDETERMINATE	1	TRUE	NA	0.567733326818768	4		417	449	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637724	176637724	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	56	378	0	ENST00000439151.2:c.2324A>T	p.Gln775Leu	p.Q775L	ENST00000439151	NM_022455.4	775	cAa/cTa	5/23	0.492327937717643	4	FACETS	0.603	0.517	0.697	0.301	0.258	0.349	SUBCLONAL	1	TRUE	2	0.567733326818768	4		378	513	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382214	152382214	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	212	418	0	ENST00000206249.3:c.1324G>C	p.Gly442Arg	p.G442R	ENST00000206249	NM_000125.3	442	Gga/Cga	6/8	0.422864174183225	3	FACETS	1	0.992	1			1	CLONAL	1	TRUE	NA	0.567733326818768	3		418	640	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575049	64575049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs386134259	NA	P-0005360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	214	397	1	ENST00000312049.6:c.758C>T	p.Ser253Leu	p.S253L	ENST00000312049	NM_130799.2	253	tCg/tTg	4/10	0.567733326818768	3	FACETS	0.93	0.883	0.976	1	0.993	1	CLONAL	3	TRUE	1	0.567733326818768	3		398	347	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184583	7184583	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	61	181	0	ENST00000302850.5:c.718del	p.Leu240TrpfsTer42	p.L240Wfs*42	ENST00000302850	NM_000208.2	240	Ctg/tg	3/22	0.567733326818768	3	FACETS	0.908	0.789	1	0.454	0.394	0.517	CLONAL	1	TRUE	1	0.567733326818768	3		181	304	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	2109	221	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.472010092947107	10	FACETS	1	0.996	1			1	CLONAL	9	TRUE	NA	0.472010092947107	10		222	2807	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	90	260	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.472010092947107	2		260	364	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466019	69466019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	295	561	0	ENST00000227507.2:c.857C>T	p.Thr286Ile	p.T286I	ENST00000227507	NM_053056.2	286	aCa/aTa	5/5	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.472010092947107	2		561	1135	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004199	29004199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757138085	NA	P-0005364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	171	454	1	ENST00000282397.4:c.1094C>T	p.Pro365Leu	p.P365L	ENST00000282397	NM_002019.4	365	cCg/cTg	8/30	0.472010092947107	3	FACETS	0.811	0.745	0.88	0.406	0.372	0.44	CLONAL	1	TRUE	1	0.472010092947107	3		455	1104	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829671	72829671	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1380	461	802	1	ENST00000268489.5:c.6910C>T	p.Gln2304Ter	p.Q2304*	ENST00000268489	NM_006885.3	2304	Cag/Tag	9/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.472010092947107	2		803	1841	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950108	44950121	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGTAAGTCTTTTC	AAGTAAGTCTTTTC	-	novel	NA	P-0005364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	263	512	0	ENST00000377967.4:c.3877_3878+12del		p.X1293_splice	ENST00000377967	NM_021140.2	1293		26/29	0.472010092947107	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.472010092947107	1		512	838	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188115	108188115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555114568	NA	P-0005399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	193	363	0	ENST00000278616.4:c.6214G>A	p.Gly2072Arg	p.G2072R	ENST00000278616	NM_000051.3	2072	Gga/Aga	43/63	0.295180946293258	2	FACETS	1	0.991	1	0.747	0.694	0.802	CLONAL	1	TRUE	0	0.38	2		363	680	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057800	180057800	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0005399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	51	209	0	ENST00000261937.6:c.156-1G>C		p.X52_splice	ENST00000261937	NM_182925.4	52			0.295180946293258	3	FACETS	0.781	0.665	0.907			1	CLONAL	1	TRUE	NA	0.38	3		209	409	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680572	30680572	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	79	399	0	ENST00000376406.3:c.1147G>T	p.Gly383Cys	p.G383C	ENST00000376406	NM_014641.2	383	Ggc/Tgc	5/15	0.108614715371023	4	FACETS	0.779	0.684	0.88	0.389	0.342	0.44	INDETERMINATE	1	TRUE	2	0.38	4		399	737	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0005404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	100	318	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.932	0.842	1	0.932	0.842	1	CLONAL	1	TRUE	1	0.66	2		318	325	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46725752	46725752	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	362	433	1	ENST00000371975.4:c.388G>T	p.Asp130Tyr	p.D130Y	ENST00000371975	NM_003579.3	130	Gac/Tac	5/18	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.66	2		434	1063	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266611	198266611	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs755415626	NA	P-0005404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	196	313	0	ENST00000335508.6:c.2225G>A	p.Gly742Asp	p.G742D	ENST00000335508	NM_012433.2	742	gGt/gAt	16/25	1	2	FACETS	0.919	0.855	0.985	0.919	0.855	0.985	CLONAL	1	TRUE	1	0.66	2		313	646	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896463	151896463	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	182	344	0	ENST00000262189.6:c.4174C>T	p.Gln1392Ter	p.Q1392*	ENST00000262189	NM_170606.2	1392	Cag/Tag	27/59	1	2	FACETS	0.93	0.863	0.999	0.93	0.863	0.999	CLONAL	1	TRUE	1	0.66	2		344	593	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198885	67198885	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1426	92	561	0	ENST00000312629.5:c.356A>C	p.Glu119Ala	p.E119A	ENST00000312629	NM_003952.2	119	gAg/gCg	5/15	1	2	FACETS	0.184	0.162	0.207	0.184	0.162	0.207	SUBCLONAL	1	TRUE	1	0.66	2		561	1518	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685250	86685250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773025020	NA	P-0005429-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	106	259	0	ENST00000274376.6:c.2966C>T	p.Thr989Met	p.T989M	ENST00000274376	NM_002890.2	989	aCg/aTg	24/25	1	2	FACETS	0.827	0.744	0.914	0.827	0.744	0.914	CLONAL	1	TRUE	1	0.468758892456066	2		259	547	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857322	68857322	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0005429-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	146	209	0	ENST00000261769.5:c.1957A>T	p.Lys653Ter	p.K653*	ENST00000261769	NM_004360.3	653	Aag/Tag	13/16	0.468758892456066	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.468758892456066	1		209	423	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12043155	12043155	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0005429-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	129	282	2	ENST00000353533.5:c.1041-1G>T		p.X347_splice	ENST00000353533	NM_003010.3	347			0.468758892456066	1	FACETS	0.815	0.743	0.89	0.815	0.743	0.89	CLONAL	1	TRUE	0	0.468758892456066	1		284	517	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029431	16029435	+	frameshift_variant	Frame_Shift_Del	DEL	TTTCT	TTTCT	-	novel	NA	P-0005429-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	128	269	0	ENST00000268712.3:c.1595_1599del	p.Lys532ArgfsTer2	p.K532Rfs*2	ENST00000268712	NM_006311.3	532	aAGAAA/a	15/46	0.468758892456066	1	FACETS	0.882	0.805	0.962	0.882	0.805	0.962	CLONAL	1	TRUE	0	0.468758892456066	1		269	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0005436-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	62	346	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.278336251802982	0	FACETS	0.883	0.778	0.993			1	CLONAL	2	FALSE	0	0.278336251802982	0		346	182	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434891	56434891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005436-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	82	546	0	ENST00000407977.2:c.2246C>T	p.Ser749Phe	p.S749F	ENST00000407977		749	tCt/tTt	9/10	0.278336251802982	1	FACETS	0.957	0.855	1	1	0.985	1	CLONAL	2	FALSE	0	0.278336251802982	1		546	265	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0005454-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	245	254	7	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.706670188911009	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.706670188911009	1		261	432	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746132	162746132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1374086542	NA	P-0005454-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	333	352	0	ENST00000367921.3:c.2255G>A	p.Arg752His	p.R752H	ENST00000367921	NM_006182.2	752	cGc/cAc	16/18	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.706670188911009	2		352	886	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0005457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	869	570	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.621317716468319	3	FACETS	0.953	0.94	0.965	1	0.998	1	CLONAL	4	FALSE	0	0.618738025498944	3		570	965	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998862	100998862	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767505462	NA	P-0005457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	230	618	0	ENST00000325455.5:c.940G>A	p.Ala314Thr	p.A314T	ENST00000325455	NM_001202474.3	314	Gcc/Acc	1/8	0.33071236143361	4	FACETS	1	0.984	1			1	INDETERMINATE	1	FALSE	NA	0.618738025498944	4		618	1019	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415870	49415870	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	1358	473	0	ENST00000301067.7:c.16477A>G	p.Lys5493Glu	p.K5493E	ENST00000301067	NM_003482.3	5493	Aaa/Gaa	53/54	0.618738025498944	8	FACETS	1	0.995	1	1	0.995	1	CLONAL	5	FALSE	3	0.618738025498944	8		473	2384	SUCCESS
ATR	545	MSKCC	GRCh37	3	142238539	142238544	+	inframe_deletion	In_Frame_Del	DEL	CCCGAA	CCCGAA	-	novel	NA	P-0005457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	397	346	0	ENST00000350721.4:c.4349_4354del	p.Val1450_Arg1451del	p.V1450_R1451del	ENST00000350721	NM_001184.3	1450	gTTCGGGaa/gaa	24/47	0.538251505682698	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	3	FALSE	1	0.618738025498944	4		346	688	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0005482-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	213	354	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.218681272314048	4	FACETS	0.984	0.917	1			1	CLONAL	3	TRUE	NA	0.236615970119147	4		354	754	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099379	157099379	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005482-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	29	219	0	ENST00000346085.5:c.316C>A	p.Leu106Ile	p.L106I	ENST00000346085	NM_020732.3	106	Cta/Ata	1/20	0.236615970119147	3	FACETS	0.627	0.503	0.769	0.209	0.167	0.257	SUBCLONAL	1	TRUE	0	0.236615970119147	3		219	437	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0005484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	511	529	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.459055224318496	8	FACETS	1	0.971	1	1	0.971	1	CLONAL	6	TRUE	2	0.459055224318496	8		529	877	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0005484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	319	609	0	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	0.44287931241466	2	FACETS	0.96	0.912	1	0.96	0.912	1	CLONAL	2	TRUE	0	0.459055224318496	2		609	724	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670376	134670376	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	103	354	0	ENST00000398015.3:c.287G>T	p.Cys96Phe	p.C96F	ENST00000398015	NM_004441.4	96	tGc/tTc	3/16	1	2	FACETS	0.905	0.813	1	0.905	0.813	1	CLONAL	1	TRUE	1	0.459055224318496	2		354	496	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435273	18435273	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	92	347	1	ENST00000266497.5:c.258G>T	p.Leu86Phe	p.L86F	ENST00000266497		86	ttG/ttT	1/31	0.459055224318496	8	FACETS	0.967	0.858	1	0.161	0.143	0.181	CLONAL	1	TRUE	2	0.459055224318496	8		348	985	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918545	44918545	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	131	536	2	ENST00000377967.4:c.1028del	p.Cys343LeufsTer16	p.C343Lfs*16	ENST00000377967	NM_021140.2	343	tGt/tt	12/29	0.450406940083596	3	FACETS	0.862	0.782	0.946	0.431	0.391	0.473	CLONAL	1	TRUE	1	0.459055224318496	3		538	814	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0005492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	348	544	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.46326181853686	2	FACETS	0.903	0.86	0.946	0.903	0.86	0.946	CLONAL	2	TRUE	0	0.486822209452432	2		544	792	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098944	178098944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	94	298	0	ENST00000397062.3:c.101G>A	p.Arg34Gln	p.R34Q	ENST00000397062	NM_006164.4	34	cGa/cAa	2/5	0.486822209452432	3	FACETS	0.955	0.853	1	0.477	0.426	0.532	CLONAL	1	TRUE	1	0.486822209452432	3		298	503	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725042	89725042	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0005492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	296	387	0	ENST00000371953.3:c.1027-2A>T		p.X343_splice	ENST00000371953	NM_000314.4	343			0.486822209452432	3	FACETS	0.92	0.876	0.963	0.92	0.876	0.963	CLONAL	3	TRUE	0	0.486822209452432	3		387	548	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885761	23885761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	174	657	0	ENST00000374561.5:c.157G>A	p.Glu53Lys	p.E53K	ENST00000374561	NM_002167.4	53	Gaa/Aaa	1/3	1	2	FACETS	0.732	0.674	0.793	0.732	0.674	0.793	SUBCLONAL	1	TRUE	1	0.486822209452432	2		657	976	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964923	25964923	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	134	439	0	ENST00000435504.4:c.4283G>T	p.Cys1428Phe	p.C1428F	ENST00000435504		1428	tGc/tTc	13/13	0.486822209452432	3	FACETS	0.911	0.829	0.998	0.456	0.414	0.499	CLONAL	1	TRUE	1	0.486822209452432	3		439	751	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426761	212426761	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	250	388	0	ENST00000342788.4:c.2354G>T	p.Gly785Val	p.G785V	ENST00000342788	NM_005235.2	785	gGt/gTt	20/28	0.247085441280961	3	FACETS	1	0.961	1			1	INDETERMINATE	2	TRUE	NA	0.486822209452432	3		388	623	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712591	52712591	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	239	416	0	ENST00000394830.3:c.161A>G	p.Tyr54Cys	p.Y54C	ENST00000394830	NM_018313.4	54	tAt/tGt	3/30	0.454884705621931	2	FACETS	0.889	0.838	0.941	0.889	0.838	0.941	CLONAL	2	TRUE	0	0.486822209452432	2		416	552	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020742	26020742	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1265	227	674	0	ENST00000357647.3:c.25C>G	p.Arg9Gly	p.R9G	ENST00000357647	NM_003529.2	9	Cgg/Ggg	1/1	0.485859607192055	4	FACETS	0.929	0.863	0.998	0.232	0.215	0.25	CLONAL	1	TRUE	0	0.486822209452432	4		674	1492	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524663	106524663	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs745386444	NA	P-0005492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	584	347	1	ENST00000359195.3:c.2824C>A	p.Leu942Ile	p.L942I	ENST00000359195	NM_002649.2	942	Ctt/Att	9/11	0.486822209452432	5	FACETS	0.946	0.918	0.973			1	CLONAL	5	TRUE	NA	0.486822209452432	5		348	878	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852745	63852745	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	162	142	0	ENST00000279873.7:c.3523C>T	p.Pro1175Ser	p.P1175S	ENST00000279873	NM_032199.2	1175	Cca/Tca	10/10	0.486822209452432	3	FACETS	0.926	0.867	0.984	0.926	0.867	0.984	CLONAL	3	TRUE	0	0.486822209452432	3		142	298	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279562	123279562	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121918499	NA	P-0005492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	364	491	0	ENST00000358487.5:c.870G>C	p.Trp290Cys	p.W290C	ENST00000358487	NM_000141.4	290	tgG/tgC	7/18	0.486822209452432	3	FACETS	0.851	0.814	0.889	0.851	0.814	0.889	CLONAL	3	TRUE	0	0.486822209452432	3		491	728	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916158	9916158	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	283	425	0	ENST00000330684.3:c.2131A>C	p.Lys711Gln	p.K711Q	ENST00000330684	NM_001134407.1	711	Aaa/Caa	10/13	0.373132177518851	4	FACETS	0.935	0.887	0.984	0.935	0.887	0.984	CLONAL	3	TRUE	1	0.486822209452432	4		425	616	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733232	40733232	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	208	366	0	ENST00000373198.4:c.3574A>T	p.Ser1192Cys	p.S1192C	ENST00000373198	NM_133170.3	1192	Agc/Tgc	26/32	0.455182595199303	3	FACETS	0.987	0.924	1	0.987	0.924	1	CLONAL	2	TRUE	1	0.486822209452432	3		366	538	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531904	41531904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	109	369	0	ENST00000263253.7:c.1616C>T	p.Ser539Phe	p.S539F	ENST00000263253	NM_001429.3	539	tCt/tTt	7/31	0.278848133467385	3	FACETS	0.991	0.893	1	0.33	0.297	0.365	INDETERMINATE	1	TRUE	0	0.486822209452432	3		369	562	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	245	221	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.19912827393436	5	FACETS	0.914	0.859	0.971			1	CLONAL	5	TRUE	NA	0.19912827393436	5		222	699	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846291	156846291	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760764097	NA	P-0005518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	87	544	0	ENST00000524377.1:c.1732G>A	p.Val578Ile	p.V578I	ENST00000524377	NM_002529.3	578	Gtc/Atc	14/17	0.19912827393436	3	FACETS	0.772	0.681	0.87	0.386	0.34	0.435	SUBCLONAL	1	TRUE	1	0.19912827393436	3		544	1245	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467144	25467144	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	91	536	0	ENST00000264709.3:c.1731G>C	p.Lys577Asn	p.K577N	ENST00000264709	NM_175629.2	577	aaG/aaC	15/23	0.19912827393436	2	FACETS	0.927	0.821	1	0.463	0.41	0.52	CLONAL	1	TRUE	0	0.19912827393436	2		536	986	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578281	7578281	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660254	NA	P-0005518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	186	477	0	ENST00000269305.4:c.568C>A	p.Pro190Thr	p.P190T	ENST00000269305	NM_001126112.2	190	Cct/Act	6/11	0.19912827393436	2	FACETS	0.886	0.818	0.958	0.886	0.818	0.958	CLONAL	2	TRUE	0	0.19912827393436	2		477	1054	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827922	40827922	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	101	584	0	ENST00000373198.4:c.2506G>T	p.Asp836Tyr	p.D836Y	ENST00000373198	NM_133170.3	836	Gat/Tat	17/32	0.19912827393436	3	FACETS	1	0.925	1	0.523	0.466	0.584	CLONAL	1	TRUE	1	0.19912827393436	3		584	1066	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101211	27101211	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005520-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	22	621	0	ENST00000324856.7:c.4493G>A	p.Trp1498Ter	p.W1498*	ENST00000324856	NM_006015.4	1498	tGg/tAg	18/20	0.31181201582941	2	FACETS	1	0.862	1	0.56	0.444	0.689	CLONAL	1	TRUE	0	0.426879177740287	2		621	92	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43815015	43815015	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005520-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	17	611	0	ENST00000372470.3:c.1550T>G	p.Phe517Cys	p.F517C	ENST00000372470	NM_005373.2	517	tTt/tGt	10/12	0.31181201582941	2	FACETS	0.983	0.749	1	0.492	0.374	0.624	CLONAL	1	TRUE	0	0.426879177740287	2		611	81	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0005528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	404	500	2	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	0.510781575264512	2	FACETS	0.975	0.934	1	0.975	0.934	1	CLONAL	2	TRUE	0	0.510781575264512	2		502	811	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21565435	21565435	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1217575272	NA	P-0005528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1581	123	551	2	ENST00000382592.4:c.451C>T	p.Arg151Trp	p.R151W	ENST00000382592	NM_014572.2	151	Cgg/Tgg	3/8	0.510781575264512	3	FACETS	0.355	0.319	0.393	0.118	0.106	0.131	SUBCLONAL	1	TRUE	0	0.510781575264512	3		553	1704	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004625	150004625	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	203	611	1	ENST00000253339.5:c.1600G>A	p.Glu534Lys	p.E534K	ENST00000253339		534	Gag/Aag	3/7	0.392137171649549	4	FACETS	1	0.954	1	0.521	0.482	0.561	CLONAL	1	TRUE	2	0.510781575264512	4		612	1153	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039419	49039419	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	58	571	0	ENST00000267163.4:c.2404G>C	p.Gly802Arg	p.G802R	ENST00000267163	NM_000321.2	802	Ggg/Cgg	23/27	0.510781575264512	3	FACETS	0.259	0.221	0.3	0.086	0.073	0.1	SUBCLONAL	1	TRUE	0	0.510781575264512	3		571	1102	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245882	41245882	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs587783041	NA	P-0005528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	123	544	0	ENST00000357654.3:c.1666A>C	p.Lys556Gln	p.K556Q	ENST00000357654	NM_007294.3	556	Aaa/Caa	10/23	0.505076313759294	3	FACETS	0.998	0.905	1	0.333	0.301	0.365	CLONAL	1	TRUE	0	0.510781575264512	3		544	606	SUCCESS
APC	324	MSKCC	GRCh37	5	112175350	112175351	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0005528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	180	331	0	ENST00000257430.4:c.4059_4060del	p.Glu1353AspfsTer21	p.E1353Dfs*21	ENST00000257430	NM_000038.5	1353	gaATtt/gatt	16/16	0.502721682155194	2	FACETS	0.911	0.852	0.97	0.911	0.852	0.97	CLONAL	2	TRUE	0	0.510781575264512	2		331	387	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0005597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	62	370	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.141562090398391	4	FACETS	0.646	0.557	0.744	0.323	0.278	0.372	INDETERMINATE	1	TRUE	2	0.28626411859073	4		370	862	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0005597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	28	625	2	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.216066243453786	3	FACETS	0.244	0.194	0.302	0.122	0.097	0.151	SUBCLONAL	1	TRUE	1	0.28626411859073	3		627	917	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	34	705	0	ENST00000342988.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000342988	NM_005359.5	356	cCt/cTt	9/12	0.216066243453786	3	FACETS	0.27	0.219	0.328	0.135	0.109	0.164	SUBCLONAL	1	TRUE	1	0.28626411859073	3		705	1005	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0005597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	31	262	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.192692293119465	4	FACETS	0.558	0.451	0.68	0.279	0.225	0.34	SUBCLONAL	1	TRUE	2	0.28626411859073	4		262	499	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125496704	125496704	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	78	600	1	ENST00000428830.2:c.41C>A	p.Thr14Asn	p.T14N	ENST00000428830	NM_001114121.2	14	aCc/aAc	2/14	0.181637494594929	3	FACETS	0.531	0.465	0.603			1	SUBCLONAL	1	TRUE	NA	0.28626411859073	3		601	1173	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0005599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	337	496	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.413304792205163	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.413304792205163	2		496	757	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	42	260	0				ENST00000310581	NM_198253.2	-/1132			0.247604397419661	3	FACETS	0.647	0.541	0.766			1	SUBCLONAL	1	TRUE	NA	0.339501548586574	3		260	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	136	320	0	ENST00000269305.4:c.542G>C	p.Arg181Pro	p.R181P	ENST00000269305	NM_001126112.2	181	cGc/cCc	5/11	0.173463343278685	2	FACETS	1	0.984	1	0.688	0.628	0.751	INDETERMINATE	1	TRUE	0	0.339501548586574	2		320	582	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100988	27100988	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	89	495	0	ENST00000324856.7:c.4270C>G	p.Gln1424Glu	p.Q1424E	ENST00000324856	NM_006015.4	1424	Cag/Gag	18/20	0.204560122685866	3	FACETS	0.686	0.607	0.771	0.343	0.303	0.386	SUBCLONAL	1	TRUE	1	0.339501548586574	3		495	894	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101186	27101186	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	92	603	0	ENST00000324856.7:c.4468G>A	p.Glu1490Lys	p.E1490K	ENST00000324856	NM_006015.4	1490	Gag/Aag	18/20	0.204560122685866	3	FACETS	0.555	0.491	0.623	0.277	0.245	0.312	SUBCLONAL	1	TRUE	1	0.339501548586574	3		603	1143	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102121	27102121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	106	643	0	ENST00000324856.7:c.5047G>A	p.Glu1683Lys	p.E1683K	ENST00000324856	NM_006015.4	1683	Gag/Aag	19/20	0.204560122685866	3	FACETS	0.618	0.552	0.688	0.309	0.276	0.344	SUBCLONAL	1	TRUE	1	0.339501548586574	3		643	1182	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106248	27106248	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	93	436	0	ENST00000324856.7:c.5859G>C	p.Lys1953Asn	p.K1953N	ENST00000324856	NM_006015.4	1953	aaG/aaC	20/20	0.204560122685866	3	FACETS	0.732	0.65	0.819	0.366	0.325	0.41	SUBCLONAL	1	TRUE	1	0.339501548586574	3		436	876	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128028984	128028984	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	174	539	0	ENST00000285398.2:c.1873C>G	p.Gln625Glu	p.Q625E	ENST00000285398	NM_000122.1	625	Cag/Gag	12/15	0.266568622757734	3	FACETS	1	0.954	1	0.527	0.484	0.572	CLONAL	1	TRUE	1	0.339501548586574	3		539	1138	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702616	52702616	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	106	394	0	ENST00000394830.3:c.282G>C	p.Leu94Phe	p.L94F	ENST00000394830	NM_018313.4	94	ttG/ttC	4/30	0.204560122685866	3	FACETS	1	0.98	1	0.694	0.625	0.768	CLONAL	1	TRUE	1	0.339501548586574	3		394	526	SUCCESS
APC	324	MSKCC	GRCh37	5	112178983	112178983	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	52	333	0	ENST00000257430.4:c.7692G>C	p.Trp2564Cys	p.W2564C	ENST00000257430	NM_000038.5	2564	tgG/tgC	16/16	1	2	FACETS	0.546	0.465	0.635	0.546	0.465	0.635	SUBCLONAL	1	TRUE	1	0.339501548586574	2		333	561	SUCCESS
APC	324	MSKCC	GRCh37	5	112179300	112179300	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	98	461	0	ENST00000257430.4:c.8009G>C	p.Arg2670Thr	p.R2670T	ENST00000257430	NM_000038.5	2670	aGa/aCa	16/16	1	2	FACETS	0.79	0.705	0.88	0.79	0.705	0.88	SUBCLONAL	1	TRUE	1	0.339501548586574	2		461	731	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505128	149505128	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	120	609	0	ENST00000261799.4:c.1687G>C	p.Glu563Gln	p.E563Q	ENST00000261799	NM_002609.3	563	Gag/Cag	12/23	1	2	FACETS	0.652	0.587	0.72	0.652	0.587	0.72	SUBCLONAL	1	TRUE	1	0.339501548586574	2		609	1085	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250824	26250824	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1194	422	1065	3	ENST00000446824.2:c.10A>T	p.Thr4Ser	p.T4S	ENST00000446824	NM_021018.2	4	Acg/Tcg	1/1	0.218420526525904	3	FACETS	0.9	0.855	0.945	0.6	0.57	0.63	CLONAL	2	TRUE	0	0.339501548586574	3		1068	1616	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835883	151835883	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	101	347	0	ENST00000262189.6:c.14641G>C	p.Glu4881Gln	p.E4881Q	ENST00000262189	NM_170606.2	4881	Gag/Cag	58/59	0.191894593215752	5	FACETS	1	0.965	1	0.395	0.353	0.44	INDETERMINATE	1	TRUE	2	0.339501548586574	5		347	757	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456699	32456699	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	27	181	0	ENST00000332351.3:c.193G>T	p.Glu65Ter	p.E65*	ENST00000332351	NM_024426.4	65	Gag/Tag	1/10	0.204560122685866	3	FACETS	0.594	0.474	0.732	0.297	0.237	0.366	SUBCLONAL	1	TRUE	1	0.339501548586574	3		181	313	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136198	64136198	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	222	589	0	ENST00000334205.4:c.1357G>T	p.Glu453Ter	p.E453*	ENST00000334205	NM_003942.2	453	Gaa/Taa	12/17	0.204560122685866	3	FACETS	0.757	0.704	0.811	0.757	0.704	0.811	SUBCLONAL	2	TRUE	1	0.339501548586574	3		589	1011	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871879	12871879	+	stop_lost	Nonstop_Mutation	SNP	A	A	C	novel	NA	P-0005600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	62	113	0	ENST00000228872.4:c.596A>C	p.Ter199SerextTer60	p.*199Sext*60	ENST00000228872	NM_004064.3	199	tAa/tCa	2/3	0.23382980093724	2	FACETS	1	0.962	1	0.65	0.566	0.739	CLONAL	1	TRUE	0	0.339501548586574	2		113	281	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562277	21562277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	82	613	0	ENST00000382592.4:c.1642C>T	p.Pro548Ser	p.P548S	ENST00000382592	NM_014572.2	548	Ccc/Tcc	4/8	1	2	FACETS	0.475	0.418	0.537	0.475	0.418	0.537	SUBCLONAL	1	TRUE	1	0.339501548586574	2		613	1016	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907194	32907194	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	49	525	0	ENST00000380152.3:c.1579C>G	p.Pro527Ala	p.P527A	ENST00000380152		527	Cca/Gca	10/27	1	2	FACETS	0.476	0.403	0.557	0.476	0.403	0.557	SUBCLONAL	1	TRUE	1	0.339501548586574	2		525	606	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929086	32929086	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs80358941	NA	P-0005600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	86	1019	0	ENST00000380152.3:c.7096C>G	p.Leu2366Val	p.L2366V	ENST00000380152		2366	Ctg/Gtg	14/27	1	2	FACETS	0.424	0.374	0.479	0.424	0.374	0.479	SUBCLONAL	1	TRUE	1	0.339501548586574	2		1019	1194	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645462	67645462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	56	405	0	ENST00000264010.4:c.727G>A	p.Glu243Lys	p.E243K	ENST00000264010	NM_006565.3	243	Gag/Aag	3/12	0.339501548586574	5	FACETS	0.541	0.462	0.627	0.135	0.115	0.157	SUBCLONAL	1	TRUE	1	0.339501548586574	5		405	921	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131449	17131449	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0005600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	60	294	0	ENST00000285071.4:c.3G>A	p.Met1?	p.M1?	ENST00000285071	NM_144997.5	1	atG/atA	4/14	0.173463343278685	2	FACETS	0.584	0.503	0.673	0.292	0.251	0.337	INDETERMINATE	1	TRUE	0	0.339501548586574	2		294	605	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512332	38512332	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1229	101	474	0	ENST00000254066.5:c.1243G>C	p.Glu415Gln	p.E415Q	ENST00000254066	NM_000964.3	415	Gag/Cag	9/9	0.339501548586574	7	FACETS	0.827	0.737	0.924			1	CLONAL	1	TRUE	NA	0.339501548586574	7		474	1330	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624791	9624791	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	50	362	0	ENST00000353224.5:c.186C>G	p.Ile62Met	p.I62M	ENST00000353224	NM_177990.2	62	atC/atG	3/10	0.339501548586574	3	FACETS	0.526	0.445	0.615	0.263	0.222	0.308	SUBCLONAL	1	TRUE	1	0.339501548586574	3		362	655	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225362540	225362540	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	30	408	0	ENST00000264414.4:c.1637G>C	p.Arg546Pro	p.R546P	ENST00000264414	NM_003590.4	546	cGa/cCa	12/16	0.132064580755252	3	FACETS	0.415	0.334	0.508			1	INDETERMINATE	1	TRUE	NA	0.339501548586574	3		408	498	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005600-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	25	260	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.54	0.426	0.672	0.54	0.426	0.672	SUBCLONAL	1	FALSE	1	0.262066687475487	2		260	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005600-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	80	320	0	ENST00000269305.4:c.542G>C	p.Arg181Pro	p.R181P	ENST00000269305	NM_001126112.2	181	cGc/cCc	5/11	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	FALSE	1	0.262066687475487	2		320	562	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100988	27100988	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005600-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	48	495	0	ENST00000324856.7:c.4270C>G	p.Gln1424Glu	p.Q1424E	ENST00000324856	NM_006015.4	1424	Cag/Gag	18/20	0.187421385538539	1	FACETS	0.457	0.386	0.537	0.457	0.386	0.537	SUBCLONAL	1	FALSE	0	0.262066687475487	1		495	696	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101186	27101186	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005600-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	63	603	0	ENST00000324856.7:c.4468G>A	p.Glu1490Lys	p.E1490K	ENST00000324856	NM_006015.4	1490	Gag/Aag	18/20	0.187421385538539	1	FACETS	0.571	0.493	0.656	0.571	0.493	0.656	SUBCLONAL	1	FALSE	0	0.262066687475487	1		603	732	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102121	27102121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005600-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	47	643	0	ENST00000324856.7:c.5047G>A	p.Glu1683Lys	p.E1683K	ENST00000324856	NM_006015.4	1683	Gag/Aag	19/20	0.187421385538539	1	FACETS	0.367	0.308	0.432	0.367	0.308	0.432	SUBCLONAL	1	FALSE	0	0.262066687475487	1		643	850	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106248	27106248	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005600-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	54	436	0	ENST00000324856.7:c.5859G>C	p.Lys1953Asn	p.K1953N	ENST00000324856	NM_006015.4	1953	aaG/aaC	20/20	0.187421385538539	1	FACETS	0.499	0.425	0.58	0.499	0.425	0.58	SUBCLONAL	1	FALSE	0	0.262066687475487	1		436	718	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128028984	128028984	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005600-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	83	539	0	ENST00000285398.2:c.1873C>G	p.Gln625Glu	p.Q625E	ENST00000285398	NM_000122.1	625	Cag/Gag	12/15	1	2	FACETS	0.658	0.58	0.743	0.658	0.58	0.743	SUBCLONAL	1	FALSE	1	0.262066687475487	2		539	962	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702616	52702616	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005600-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	122	394	0	ENST00000394830.3:c.282G>C	p.Leu94Phe	p.L94F	ENST00000394830	NM_018313.4	94	ttG/ttC	4/30	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.262066687475487	2		394	827	SUCCESS
APC	324	MSKCC	GRCh37	5	112178983	112178983	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005600-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	47	333	0	ENST00000257430.4:c.7692G>C	p.Trp2564Cys	p.W2564C	ENST00000257430	NM_000038.5	2564	tgG/tgC	16/16	0.103266225789495	0	FACETS	0.391	0.329	0.46			1	INDETERMINATE	1	FALSE	0	0.262066687475487	0		333	677	SUCCESS
APC	324	MSKCC	GRCh37	5	112179300	112179300	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005600-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	51	461	0	ENST00000257430.4:c.8009G>C	p.Arg2670Thr	p.R2670T	ENST00000257430	NM_000038.5	2670	aGa/aCa	16/16	0.103266225789495	0	FACETS	0.36	0.305	0.421			1	INDETERMINATE	1	FALSE	0	0.262066687475487	0		461	798	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505128	149505128	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005600-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	72	609	0	ENST00000261799.4:c.1687G>C	p.Glu563Gln	p.E563Q	ENST00000261799	NM_002609.3	563	Gag/Cag	12/23	0.103266225789495	0	FACETS	0.49	0.427	0.558			1	INDETERMINATE	1	FALSE	0	0.262066687475487	0		609	827	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250824	26250824	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005600-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	308	1065	3	ENST00000446824.2:c.10A>T	p.Thr4Ser	p.T4S	ENST00000446824	NM_021018.2	4	Acg/Tcg	1/1	0.24709250707564	2	FACETS	0.952	0.897	1	0.952	0.897	1	CLONAL	2	FALSE	0	0.262066687475487	2		1068	1234	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835883	151835883	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005600-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	40	347	0	ENST00000262189.6:c.14641G>C	p.Glu4881Gln	p.E4881Q	ENST00000262189	NM_170606.2	4881	Gag/Cag	58/59	1	2	FACETS	0.409	0.338	0.487	0.409	0.338	0.487	SUBCLONAL	1	FALSE	1	0.262066687475487	2		347	747	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456699	32456699	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005600-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	15	181	0	ENST00000332351.3:c.193G>T	p.Glu65Ter	p.E65*	ENST00000332351	NM_024426.4	65	Gag/Tag	1/10	1	2	FACETS	0.392	0.286	0.52	0.392	0.286	0.52	SUBCLONAL	1	FALSE	1	0.262066687475487	2		181	292	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136198	64136198	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005600-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	114	589	0	ENST00000334205.4:c.1357G>T	p.Glu453Ter	p.E453*	ENST00000334205	NM_003942.2	453	Gaa/Taa	12/17	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.262066687475487	2		589	700	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871879	12871879	+	stop_lost	Nonstop_Mutation	SNP	A	A	C	novel	NA	P-0005600-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	70	113	0	ENST00000228872.4:c.596A>C	p.Ter199SerextTer60	p.*199Sext*60	ENST00000228872	NM_004064.3	199	tAa/tCa	2/3	0.234898763809898	4	FACETS	0.971	0.853	1			1	CLONAL	2	FALSE	NA	0.262066687475487	4		113	347	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562277	21562277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005600-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	38	613	0	ENST00000382592.4:c.1642C>T	p.Pro548Ser	p.P548S	ENST00000382592	NM_014572.2	548	Ccc/Tcc	4/8	0.244456012455985	1	FACETS	0.422	0.348	0.505	0.422	0.348	0.505	SUBCLONAL	1	FALSE	0	0.262066687475487	1		613	597	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907194	32907194	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005600-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	69	525	0	ENST00000380152.3:c.1579C>G	p.Pro527Ala	p.P527A	ENST00000380152		527	Cca/Gca	10/27	0.244456012455985	1	FACETS	0.428	0.371	0.49	0.428	0.371	0.49	SUBCLONAL	1	FALSE	0	0.262066687475487	1		525	1069	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929086	32929086	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs80358941	NA	P-0005600-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1362	97	1019	0	ENST00000380152.3:c.7096C>G	p.Leu2366Val	p.L2366V	ENST00000380152		2366	Ctg/Gtg	14/27	0.244456012455985	1	FACETS	0.441	0.391	0.494	0.441	0.391	0.494	SUBCLONAL	1	FALSE	0	0.262066687475487	1		1019	1459	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645462	67645462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005600-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	75	405	0	ENST00000264010.4:c.727G>A	p.Glu243Lys	p.E243K	ENST00000264010	NM_006565.3	243	Gag/Aag	3/12	0.179700231603499	1	FACETS	0.624	0.546	0.708	0.624	0.546	0.708	SUBCLONAL	1	FALSE	0	0.262066687475487	1		405	797	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131449	17131449	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0005600-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	32	294	0	ENST00000285071.4:c.3G>A	p.Met1?	p.M1?	ENST00000285071	NM_144997.5	1	atG/atA	4/14	1	2	FACETS	0.531	0.43	0.645	0.531	0.43	0.645	SUBCLONAL	1	FALSE	1	0.262066687475487	2		294	460	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512332	38512332	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005600-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	46	474	0	ENST00000254066.5:c.1243G>C	p.Glu415Gln	p.E415Q	ENST00000254066	NM_000964.3	415	Gag/Cag	9/9	NA	2	FACETS	0.544	0.457	0.641			1	INDETERMINATE	1	FALSE	NA	0.262066687475487	2		474	645	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624791	9624791	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005600-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	62	362	0	ENST00000353224.5:c.186C>G	p.Ile62Met	p.I62M	ENST00000353224	NM_177990.2	62	atC/atG	3/10	1	2	FACETS	0.782	0.675	0.898	0.782	0.675	0.898	SUBCLONAL	1	FALSE	1	0.262066687475487	2		362	605	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783259	9783259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	134	651	3	ENST00000377346.4:c.2503G>A	p.Ala835Thr	p.A835T	ENST00000377346	NM_005026.3	835	Gcc/Acc	20/24	1	2	FACETS	0.791	0.717	0.869	0.791	0.717	0.869	SUBCLONAL	1	TRUE	1	0.319370974304741	2		654	1061	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692919	89692919	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782360	NA	P-0005602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	16	388	0	ENST00000371953.3:c.403A>G	p.Ile135Val	p.I135V	ENST00000371953	NM_000314.4	135	Ata/Gta	5/9	0.22210937721575	2	FACETS	0.441	0.327	0.578	0.221	0.163	0.289	SUBCLONAL	1	TRUE	0	0.319370974304741	2		388	227	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250793	26250793	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1843	153	1274	0	ENST00000446824.2:c.41G>C	p.Gly14Ala	p.G14A	ENST00000446824	NM_021018.2	14	gGc/gCc	1/1	0.319370974304741	3	FACETS	0.557	0.507	0.61	0.278	0.253	0.305	SUBCLONAL	1	TRUE	1	0.319370974304741	3		1274	1996	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115712	8115875	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAGAACAGCTCGTTTAACCCGGCCGCCCTCTCCAGACACATGTCCTCCCTGAGCCACATCTCG	CCCTGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAGAACAGCTCGTTTAACCCGGCCGCCCTCTCCAGACACATGTCCTCCCTGAGCCACATCTCG	-	novel	NA	P-0005602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	78	801	0	ENST00000346208.3:c.1062_1225del	p.Thr355GlnfsTer97	p.T355Qfs*97	ENST00000346208		353	cCCCTGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAGAACAGCTCGTTTAACCCGGCCGCCCTCTCCAGACACATGTCCTCCCTGAGCCACATCTCG/c	6/6	NA	2	FACETS	0.596	0.523	0.675			1	INDETERMINATE	1	TRUE	NA	0.319370974304741	2		801	820	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45423125	45423125	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0005607-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	13	256	0	ENST00000262160.6:c.3G>A	p.Met1?	p.M1?	ENST00000262160	NM_005901.5	1	atG/atA	2/11	1	2	FACETS	0.192	0.137	0.26	0.192	0.137	0.26	SUBCLONAL	1	TRUE	1	0.617959163033361	2		256	219	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0005610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	46	43	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	0.291341191938392	6	FACETS	1	0.935	1	1	0.966	1	CLONAL	6	TRUE	1	0.291341191938392	6		43	77	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740713	58740713	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs751126916	NA	P-0005610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	570	1528	1	ENST00000305921.3:c.1618G>T	p.Glu540Ter	p.E540*	ENST00000305921	NM_003620.3	540	Gag/Tag	6/6	0.291341191938392	6	FACETS	1	0.968	1	1	0.996	1	CLONAL	6	TRUE	1	0.291341191938392	6		1529	1030	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16235857	16235857	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs752245407	NA	P-0005626-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	84	454	0	ENST00000375759.3:c.923G>C	p.Arg308Pro	p.R308P	ENST00000375759	NM_015001.2	308	cGa/cCa	4/15	0.775486684239513	1	FACETS	0.217	0.191	0.244	0.217	0.191	0.244	SUBCLONAL	1	TRUE	0	0.79707997981005	1		454	585	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593590	55593595	+	inframe_deletion	In_Frame_Del	DEL	GTATGA	GTATGA	-	novel	NA	P-0005626-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	469	584	0	ENST00000288135.5:c.1656_1661del	p.Met552_Glu554delinsIle	p.M552_E554delinsI	ENST00000288135	NM_000222.2	552	atGTATGAa/ata	11/21	1	2	FACETS	0.881	0.842	0.92	0.881	0.842	0.92	CLONAL	1	TRUE	1	0.79707997981005	2		584	1336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0005634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	300	552	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.358029356882762	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.368630572244441	2		552	785	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0005634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	170	381	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.282107066376573	2	FACETS	0.816	0.755	0.879	0.816	0.755	0.879	CLONAL	2	TRUE	0	0.368630572244441	2		381	565	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0005634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	154	277	1	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.345263272685188	3	FACETS	0.934	0.86	1	0.934	0.86	1	CLONAL	2	TRUE	1	0.368630572244441	3		278	530	SUCCESS
APC	324	MSKCC	GRCh37	5	112173947	112173947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs755806668	NA	P-0005634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	96	350	0	ENST00000257430.4:c.2656C>T	p.Gln886Ter	p.Q886*	ENST00000257430	NM_000038.5	886	Cag/Tag	16/16	0.345263272685188	3	FACETS	0.857	0.763	0.956	0.428	0.381	0.478	CLONAL	1	TRUE	1	0.368630572244441	3		350	720	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245411	153245411	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	245	376	0	ENST00000281708.4:c.1780C>T	p.Leu594Phe	p.L594F	ENST00000281708	NM_033632.3	594	Ctt/Ttt	11/12	0.368630572244441	2	FACETS	0.985	0.926	1	0.985	0.926	1	CLONAL	2	TRUE	0	0.368630572244441	2		376	675	SUCCESS
APC	324	MSKCC	GRCh37	5	112176245	112176245	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	157	487	0	ENST00000257430.4:c.4954T>C	p.Ser1652Pro	p.S1652P	ENST00000257430	NM_000038.5	1652	Tcc/Ccc	16/16	0.345263272685188	3	FACETS	1	0.947	1	0.523	0.478	0.569	CLONAL	1	TRUE	1	0.368630572244441	3		487	965	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562462	176562462	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	146	408	0	ENST00000439151.2:c.358G>C	p.Gly120Arg	p.G120R	ENST00000439151	NM_022455.4	120	Ggt/Cgt	2/23	0.355310049672797	4	FACETS	0.969	0.883	1	0.323	0.294	0.354	CLONAL	1	TRUE	1	0.368630572244441	4		408	1119	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968293	2968293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	204	473	1	ENST00000396946.4:c.1693G>A	p.Ala565Thr	p.A565T	ENST00000396946	NM_032415.4	565	Gcc/Acc	13/25	0.368630572244441	4	FACETS	0.918	0.853	0.985	0.918	0.853	0.985	CLONAL	2	TRUE	2	0.368630572244441	4		474	825	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103261	119103261	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0005634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	239	546	0	ENST00000264033.4:c.299C>G	p.Ser100Ter	p.S100*	ENST00000264033	NM_005188.3	100	tCa/tGa	2/16	0.368630572244441	4	FACETS	0.949	0.887	1	0.633	0.591	0.675	CLONAL	2	TRUE	1	0.368630572244441	4		546	935	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0005637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	77	688	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	0.253453013008659	3	FACETS	1	0.907	1	0.677	0.605	0.752	INDETERMINATE	2	TRUE	0	0.425686322693111	3		688	216	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503793	186503793	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	407	677	0	ENST00000323963.5:c.470T>G	p.Val157Gly	p.V157G	ENST00000323963		157	gTt/gGt	5/11	0.425686322693111	6	FACETS	0.893	0.849	0.937	0.669	0.637	0.703	CLONAL	3	TRUE	2	0.425686322693111	6		677	1322	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	49	260	0				ENST00000310581	NM_198253.2	-/1132			0.34171171575841	3	FACETS	1	0.924	1	1	0.974	1	CLONAL	3	TRUE	1	0.369472802284994	3		260	98	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0005650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	40	264	1	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.369472802284994	2	FACETS	0.887	0.755	1	0.887	0.755	1	CLONAL	2	TRUE	0	0.369472802284994	2		265	122	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247436	71247436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1358353721	NA	P-0005650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	28	173	1	ENST00000318789.4:c.97C>T	p.Arg33Trp	p.R33W	ENST00000318789	NM_032682.5	33	Cgg/Tgg	6/21	0.301577868449678	1	FACETS	0.951	0.772	1	0.951	0.772	1	CLONAL	1	TRUE	0	0.369472802284994	1		174	130	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482437	56482437	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	11	181	0	ENST00000267101.3:c.985A>G	p.Lys329Glu	p.K329E	ENST00000267101	NM_001982.3	329	Aaa/Gaa	8/28	0.239494377148144	3	FACETS	1	0.796	1	0.588	0.415	0.792	CLONAL	1	TRUE	1	0.369472802284994	3		181	60	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405951	49405951	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	11	313	0	ENST00000418115.1:c.187C>A	p.Gln63Lys	p.Q63K	ENST00000418115	NM_001664.2	63	Cag/Aag	3/5	0.301577868449678	1	FACETS	0.552	0.386	0.752	0.552	0.386	0.752	SUBCLONAL	1	TRUE	0	0.369472802284994	1		313	88	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0005700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	114	540	1	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	1	2	FACETS	0.933	0.84	1	0.933	0.84	1	CLONAL	1	TRUE	1	0.313179946403342	2		541	780	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0005700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	114	559	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.313179946403342	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.313179946403342	1		559	444	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600417	10600417	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	164	695	1	ENST00000171111.5:c.1438G>T	p.Gly480Trp	p.G480W	ENST00000171111	NM_203500.1	480	Ggg/Tgg	4/6	0.313179946403342	2	FACETS	0.94	0.868	1	0.94	0.868	1	CLONAL	2	TRUE	0	0.313179946403342	2		696	557	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25458647	25458647	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	104	617	0	ENST00000264709.3:c.2526G>T	p.Gln842His	p.Q842H	ENST00000264709	NM_175629.2	842	caG/caT	22/23	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.313179946403342	2		617	560	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448470	49448470	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	120	562	0	ENST00000301067.7:c.241G>T	p.Glu81Ter	p.E81*	ENST00000301067	NM_003482.3	81	Gag/Tag	3/54	0.229245345358418	3	FACETS	1	0.985	1	0.745	0.675	0.819	CLONAL	1	TRUE	1	0.313179946403342	3		562	595	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220428	1220428	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	138	700	0	ENST00000326873.7:c.521A>T	p.His174Leu	p.H174L	ENST00000326873	NM_000455.4	174	cAc/cTc	4/10	0.313179946403342	1	FACETS	0.92	0.846	0.996	1	0.991	1	CLONAL	2	TRUE	0	0.313179946403342	1		700	404	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894228	NA	P-0005718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	89	488	0	ENST00000451590.1:c.37G>C	p.Gly13Arg	p.G13R	ENST00000451590	NM_001130442.1	13	Ggt/Cgt	2/5	1	2	FACETS	0.828	0.735	0.927	1	0.982	1	CLONAL	2	TRUE	1	0.18	2		488	597	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732318	74732318	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	104	712	0	ENST00000359995.5:c.591G>C	p.Lys197Asn	p.K197N	ENST00000359995	NM_001195427.1	197	aaG/aaC	2/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.18	2		712	901	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984928	55984928	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	28	490	0	ENST00000263923.4:c.201G>C	p.Gln67His	p.Q67H	ENST00000263923	NM_002253.2	67	caG/caC	3/30	1	2	FACETS	0.608	0.485	0.749	0.608	0.485	0.749	SUBCLONAL	1	TRUE	1	0.18	2		490	512	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532735	187532735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	53	542	1	ENST00000441802.2:c.9658G>A	p.Val3220Ile	p.V3220I	ENST00000441802	NM_005245.3	3220	Gtt/Att	14/27	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.18	2		543	567	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851141	151851141	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0005718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	33	600	0	ENST00000262189.6:c.12230C>G	p.Ser4077Ter	p.S4077*	ENST00000262189	NM_170606.2	4077	tCa/tGa	48/59	1	2	FACETS	0.623	0.506	0.755	0.623	0.506	0.755	SUBCLONAL	1	TRUE	1	0.18	2		600	589	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431975	49431975	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	31	525	1	ENST00000301067.7:c.9164C>A	p.Pro3055His	p.P3055H	ENST00000301067	NM_003482.3	3055	cCt/cAt	34/54	1	2	FACETS	0.65	0.525	0.792	0.65	0.525	0.792	SUBCLONAL	1	TRUE	1	0.18	2		526	530	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89806439	89806439	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	62	593	0	ENST00000389301.3:c.3897G>T	p.Lys1299Asn	p.K1299N	ENST00000389301	NM_000135.2	1299	aaG/aaT	39/43	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.18	2		593	550	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578509	7578509	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519978	NA	P-0005718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	82	607	0	ENST00000269305.4:c.421T>G	p.Cys141Gly	p.C141G	ENST00000269305	NM_001126112.2	141	Tgc/Ggc	5/11	1	2	FACETS	0.771	0.68	0.867	1	0.978	1	SUBCLONAL	2	TRUE	1	0.18	2		607	591	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427024	49427031	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGGGGG	CCTGGGGG	-	novel	NA	P-0005718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	27	455	0	ENST00000301067.7:c.11457_11464del	p.Gln3821SerfsTer188	p.Q3821Sfs*188	ENST00000301067	NM_003482.3	3819	ggCCCCCAGGgc/gggc	39/54	1	2	FACETS	0.685	0.544	0.846	0.685	0.544	0.846	SUBCLONAL	1	TRUE	1	0.18	2		455	438	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285572	46285572	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005727-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	239	933	1	ENST00000334344.6:c.4932G>T	p.Gln1644His	p.Q1644H	ENST00000334344	NM_152641.2	1644	caG/caT	17/21	0.674655658184156	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.674655658184156	1		934	451	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2115632	2115632	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs397515093	NA	P-0005727-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	286	1163	1	ENST00000219476.3:c.1712T>C	p.Leu571Pro	p.L571P	ENST00000219476	NM_000548.3	571	cTt/cCt	16/42	0.674655658184156	1	FACETS	0.994	0.945	1	0.994	0.945	1	CLONAL	1	TRUE	0	0.674655658184156	1		1164	565	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546847	9546847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	168	389	0	ENST00000353224.5:c.1175C>T	p.Ser392Leu	p.S392L	ENST00000353224	NM_177990.2	392	tCg/tTg	5/10	0.396164435693043	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.586226395918411	1		389	400	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0005733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	723	409	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.586226395918411	7	FACETS	0.956	0.936	0.975	0.956	0.936	0.975	CLONAL	7	TRUE	0	0.586226395918411	7		409	909	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254623	16254623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749814808	NA	P-0005733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	183	694	2	ENST00000375759.3:c.1888C>T	p.Arg630Cys	p.R630C	ENST00000375759	NM_015001.2	630	Cgt/Tgt	11/15	1	2	FACETS	0.747	0.69	0.806	0.747	0.69	0.806	SUBCLONAL	1	TRUE	1	0.586226395918411	2		696	836	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159128	143159128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	176	516	0	ENST00000262992.4:c.725C>T	p.Pro242Leu	p.P242L	ENST00000262992	NM_001101669.1	242	cCc/cTc	10/24	NA	2	FACETS	0.952	0.881	1			1	INDETERMINATE	1	TRUE	NA	0.586226395918411	2		516	631	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500561	149500561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	81	383	0	ENST00000261799.4:c.2476G>A	p.Asp826Asn	p.D826N	ENST00000261799	NM_002609.3	826	Gac/Aac	18/23	0.352503835726851	1	FACETS	0.364	0.321	0.41	0.364	0.321	0.41	SUBCLONAL	1	TRUE	0	0.586226395918411	1		383	536	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781200	135781200	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1299279813	NA	P-0005733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	566	860	0	ENST00000298552.3:c.1765C>T	p.Pro589Ser	p.P589S	ENST00000298552	NM_001162426.1	589	Cca/Tca	15/23	0.586226395918411	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.586226395918411	1		860	1044	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274723	123274723	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1441011501	NA	P-0005733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	240	563	1	ENST00000358487.5:c.1195C>T	p.Arg399Ter	p.R399*	ENST00000358487	NM_000141.4	399	Cga/Tga	9/18	1	2	FACETS	0.972	0.91	1	0.972	0.91	1	CLONAL	1	TRUE	1	0.586226395918411	2		564	842	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135623	64135623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	318	580	0	ENST00000334205.4:c.1091C>T	p.Pro364Leu	p.P364L	ENST00000334205	NM_003942.2	364	cCc/cTc	10/17	1	2	FACETS	0.988	0.933	1	0.988	0.933	1	CLONAL	1	TRUE	1	0.586226395918411	2		580	1098	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577469	64577469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs794728616	NA	P-0005733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	212	534	0	ENST00000312049.6:c.113C>T	p.Ser38Phe	p.S38F	ENST00000312049	NM_130799.2	38	tCc/tTc	2/10	1	2	FACETS	0.911	0.848	0.975	0.911	0.848	0.975	CLONAL	1	TRUE	1	0.586226395918411	2		534	794	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989562	85989562	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs767548896	NA	P-0005733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	192	522	1	ENST00000263360.6:c.1321C>T	p.Arg441Ter	p.R441*	ENST00000263360	NM_003797.3	441	Cga/Tga	12/12	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.586226395918411	2		523	591	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118782	115118782	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	289	535	0	ENST00000257566.3:c.559C>T	p.His187Tyr	p.H187Y	ENST00000257566	NM_016569.3	187	Cac/Tac	2/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.586226395918411	2		535	850	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219905	133219905	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	252	528	0	ENST00000320574.5:c.4456C>T	p.His1486Tyr	p.H1486Y	ENST00000320574	NM_006231.2	1486	Cat/Tat	35/49	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.586226395918411	2		528	795	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914811	32914811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	384	941	2	ENST00000380152.3:c.6319C>T	p.Pro2107Ser	p.P2107S	ENST00000380152		2107	Cct/Tct	11/27	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.586226395918411	2		943	1234	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042616	42042616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	362	783	0	ENST00000219905.7:c.6811C>T	p.Gln2271Ter	p.Q2271*	ENST00000219905	NM_001164273.1	2271	Cag/Tag	17/24	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.586226395918411	2		783	969	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892232	9892232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	260	521	0	ENST00000330684.3:c.2258G>A	p.Gly753Glu	p.G753E	ENST00000330684	NM_001134407.1	753	gGg/gAg	11/13	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.586226395918411	2		521	848	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419965	41419965	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	443	509	1	ENST00000373198.4:c.356C>T	p.Ala119Val	p.A119V	ENST00000373198	NM_133170.3	119	gCc/gTc	3/32	0.532109482552215	5	FACETS	0.919	0.876	0.964	0.613	0.584	0.643	CLONAL	2	TRUE	2	0.586226395918411	5		510	1545	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354585	70354585	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	243	614	0	ENST00000374080.3:c.4750G>A	p.Asp1584Asn	p.D1584N	ENST00000374080		1584	Gac/Aac	35/45	1	2	FACETS	0.902	0.844	0.962	0.902	0.844	0.962	CLONAL	1	TRUE	1	0.586226395918411	2		614	919	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888754	76888754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	231	766	1	ENST00000373344.5:c.5075G>A	p.Gly1692Glu	p.G1692E	ENST00000373344	NM_000489.3	1692	gGa/gAa	19/35	1	2	FACETS	0.775	0.723	0.829	0.775	0.723	0.829	SUBCLONAL	1	TRUE	1	0.586226395918411	2		767	1017	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853077	151853077	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005733-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	109	293	0	ENST00000262189.6:c.11878C>T	p.Arg3960Ter	p.R3960*	ENST00000262189	NM_170606.2	3960	Cga/Tga	46/59	0.586226395918411	3	FACETS	0.763	0.687	0.844			1	SUBCLONAL	1	TRUE	NA	0.586226395918411	3		293	630	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624297	89624297	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs797044910	NA	P-0005735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	172	262	0	ENST00000371953.3:c.71A>G	p.Asp24Gly	p.D24G	ENST00000371953	NM_000314.4	24	gAc/gGc	1/9	0.431057845777726	3	FACETS	0.794	0.734	0.856	0.794	0.734	0.856	SUBCLONAL	2	TRUE	1	0.431057845777726	3		262	611	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250365	110250365	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	535	823	0	ENST00000374672.4:c.310G>T	p.Asp104Tyr	p.D104Y	ENST00000374672	NM_004235.4	104	Gac/Tac	3/5	0.431057845777726	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.431057845777726	2		823	1177	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104359255	104359255	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	99	576	0	ENST00000369902.3:c.976C>T	p.Pro326Ser	p.P326S	ENST00000369902	NM_016169.3	326	Cca/Tca	8/12	0.431057845777726	3	FACETS	0.67	0.598	0.748	0.335	0.299	0.374	SUBCLONAL	1	TRUE	1	0.431057845777726	3		576	833	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218426	133218426	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	51	350	0	ENST00000320574.5:c.5185C>A	p.Leu1729Met	p.L1729M	ENST00000320574	NM_006231.2	1729	Ctg/Atg	39/49	0.431057845777726	2	FACETS	0.533	0.454	0.62	0.266	0.227	0.31	SUBCLONAL	1	TRUE	0	0.431057845777726	2		350	444	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983722	15983722	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	129	226	1	ENST00000268712.3:c.3400G>A	p.Gly1134Ser	p.G1134S	ENST00000268712	NM_006311.3	1134	Ggt/Agt	25/46	0.385951580826224	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.431057845777726	2		227	290	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246474	10246474	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1461695373	NA	P-0005735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	50	558	0	ENST00000340748.4:c.4663C>T	p.Arg1555Cys	p.R1555C	ENST00000340748		1555	Cgc/Tgc	38/40	0.280316087737356	4	FACETS	0.354	0.299	0.415	0.177	0.149	0.208	SUBCLONAL	1	TRUE	2	0.431057845777726	4		558	938	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357233	70357233	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	22	420	0	ENST00000374080.3:c.5748G>C	p.Gln1916His	p.Q1916H	ENST00000374080		1916	caG/caC	39/45	0.368776877325412	1	FACETS	0.202	0.156	0.255	0.202	0.156	0.255	SUBCLONAL	1	TRUE	0	0.431057845777726	1		420	397	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591118	67591245	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATCCAGCTGAGAAAGACGAGAGACCAATACTTGATGTAAGTATTTGAAATGGAATCCTATACATGAATAATTGGTGATTGCTACAATTCAGGATGAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTC	ATCCAGCTGAGAAAGACGAGAGACCAATACTTGATGTAAGTATTTGAAATGGAATCCTATACATGAATAATTGGTGATTGCTACAATTCAGGATGAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTC	-	novel	NA	P-0005735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	103	353	1	ENST00000274335.5:c.1712_1746-2del		p.X571_splice	ENST00000274335		571		12/15	0.431057845777726	3	FACETS	0.981	0.88	1	0.491	0.44	0.544	CLONAL	1	TRUE	1	0.431057845777726	3		354	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577003	7577039	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTCCTGCTTGCTTACCTCGCTTAGTGCTCCCTGGGG	TGTCCTGCTTGCTTACCTCGCTTAGTGCTCCCTGGGG	-	novel	NA	P-0005735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	227	379	0	ENST00000269305.4:c.899_919+16del		p.X300_splice	ENST00000269305	NM_001126112.2	300		8/11	0.385951580826224	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.431057845777726	2		379	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0005744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	188	495	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.256189287568123	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.256189287568123	1		495	1013	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051637	30051637	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	88	666	0	ENST00000338641.4:c.571T>G	p.Trp191Gly	p.W191G	ENST00000338641	NM_000268.3	191	Tgg/Ggg	6/16	0.256189287568123	1	FACETS	0.876	0.776	0.982	0.876	0.776	0.982	CLONAL	1	TRUE	0	0.256189287568123	1		666	684	SUCCESS
ATR	545	MSKCC	GRCh37	3	142212054	142212054	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	53	600	0	ENST00000350721.4:c.5998G>T	p.Gly2000Cys	p.G2000C	ENST00000350721	NM_001184.3	2000	Ggt/Tgt	35/47	1	2	FACETS	0.726	0.619	0.843	0.726	0.619	0.843	SUBCLONAL	1	TRUE	1	0.256189287568123	2		600	570	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0005769-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	259	158	0				ENST00000310581	NM_198253.2	-/1132			0.455334480064303	7	FACETS	0.89	0.835	0.946	0.668	0.626	0.71	CLONAL	3	TRUE	3	0.455334480064303	7		158	911	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0005769-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	356	531	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.455334480064303	8	FACETS	1	0.967	1	1	0.967	1	CLONAL	6	TRUE	2	0.455334480064303	8		531	611	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711911	89711911	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005769-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	62	403	0	ENST00000371953.3:c.529T>G	p.Tyr177Asp	p.Y177D	ENST00000371953	NM_000314.4	177	Tat/Gat	6/9	1	2	FACETS	0.952	0.83	1	0.952	0.83	1	CLONAL	1	TRUE	1	0.455334480064303	2		403	286	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794751	42794751	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005769-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	131	594	0	ENST00000575354.2:c.1831C>T	p.Pro611Ser	p.P611S	ENST00000575354	NM_015125.3	611	Cca/Tca	10/20	0.455334480064303	3	FACETS	1	0.975	1	0.597	0.543	0.652	CLONAL	1	TRUE	1	0.455334480064303	3		594	592	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878307	151878308	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0005769-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	212	512	0	ENST00000262189.6:c.6637_6638delinsAA	p.Gly2213Lys	p.G2213K	ENST00000262189	NM_170606.2	2213	GGa/AAa	36/59	0.455334480064303	8	FACETS	1	0.956	1	0.346	0.321	0.372	CLONAL	2	TRUE	2	0.455334480064303	8		512	1060	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0005784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	129	385	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.837	0.758	0.92	0.837	0.758	0.92	CLONAL	1	TRUE	1	0.330495758663263	2		385	933	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184038	123184038	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	109	504	0	ENST00000218089.9:c.896A>G	p.Asp299Gly	p.D299G	ENST00000218089	NM_001042749.1	299	gAt/gGt	11/35	NA	2	FACETS	0.644	0.577	0.715			1	INDETERMINATE	1	TRUE	NA	0.330495758663263	2		504	1024	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0005799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	201	566	0	ENST00000269305.4:c.375+1del		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.336624672885739	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.336624672885739	2		566	553	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46727002	46727002	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	109	829	1	ENST00000371975.4:c.836G>T	p.Arg279Leu	p.R279L	ENST00000371975	NM_003579.3	279	cGc/cTc	8/18	0.259145277830057	4	FACETS	0.923	0.827	1			1	CLONAL	1	TRUE	NA	0.336624672885739	4		830	938	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268994	142268994	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	75	625	1	ENST00000350721.4:c.2956G>A	p.Asp986Asn	p.D986N	ENST00000350721	NM_001184.3	986	Gat/Aat	14/47	0.336624672885739	6	FACETS	0.654	0.571	0.744	0.164	0.142	0.186	SUBCLONAL	1	TRUE	2	0.336624672885739	6		626	1140	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550585	29550585	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1131691080	NA	P-0005799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	110	423	0	ENST00000356175.3:c.1845G>T	p.Lys615Asn	p.K615N	ENST00000356175	NM_000267.3	615	aaG/aaT	16/57	0.336624672885739	2	FACETS	0.984	0.895	1	0.984	0.895	1	CLONAL	2	TRUE	0	0.336624672885739	2		423	332	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054675	13054686	+	inframe_deletion	In_Frame_Del	DEL	AGGAGGAAGATG	AGGAGGAAGATG	-	rs778508102	NA	P-0005799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1717	112	1386	0	ENST00000316448.5:c.1214_1225del	p.Glu405_Asp408del	p.E405_D408del	ENST00000316448	NM_004343.3	401	aAGGAGGAAGATGag/aag	9/9	0.336624672885739	3	FACETS	0.425	0.38	0.473	0.213	0.19	0.237	SUBCLONAL	1	TRUE	1	0.336624672885739	3		1386	1829	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005807-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	193	221	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.272190921434165	4	FACETS	1	0.989	1			1	CLONAL	1	TRUE	NA	0.272190921434165	4		222	1282	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0005807-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	44	254	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.272190921434165	1	FACETS	0.671	0.564	0.79	0.671	0.564	0.79	SUBCLONAL	1	TRUE	0	0.272190921434165	1		254	416	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457271	67457271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005807-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	111	550	0	ENST00000327367.4:c.245G>A	p.Gly82Glu	p.G82E	ENST00000327367	NM_005902.3	82	gGg/gAg	2/9	1	2	FACETS	0.954	0.857	1	0.954	0.857	1	CLONAL	1	TRUE	1	0.272190921434165	2		550	855	SUCCESS
APC	324	MSKCC	GRCh37	5	112176167	112176167	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005807-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	157	614	1	ENST00000257430.4:c.4879del	p.Gln1627LysfsTer23	p.Q1627Kfs*23	ENST00000257430	NM_000038.5	1626	Ccc/cc	16/16	0.166163286107554	2	FACETS	1	0.946	1	0.522	0.478	0.57	CLONAL	1	TRUE	0	0.272190921434165	2		615	1104	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664577	29664577	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005811-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	190	651	0	ENST00000356175.3:c.6556G>T	p.Glu2186Ter	p.E2186*	ENST00000356175	NM_000267.3	2186	Gaa/Taa	42/57	1	2	FACETS	0.766	0.708	0.826	0.766	0.708	0.826	SUBCLONAL	1	TRUE	1	0.508956237669838	2		651	975	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71050149	71050150	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	AT	novel	NA	P-0005811-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	140	470	3	ENST00000318789.4:c.1035_1036delinsAT	p.Met345_Gln346delinsIleTer	p.M345_Q346delinsI*	ENST00000318789	NM_032682.5	345	atGCag/atATag	13/21	1	2	FACETS	0.762	0.695	0.832	0.762	0.695	0.832	SUBCLONAL	1	TRUE	1	0.508956237669838	2		473	722	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	248	221	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.478101864208744	6	FACETS	0.926	0.874	0.978			1	CLONAL	4	FALSE	NA	0.478101864208744	6		222	548	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0005821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	76	425	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	0.484960973307563	1	FACETS	0.812	0.735	0.889	1	0.983	1	CLONAL	2	FALSE	0	0.478101864208744	1		425	149	SUCCESS
APC	324	MSKCC	GRCh37	5	112103088	112103088	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0005821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	82	379	0	ENST00000257430.4:c.422+1G>A		p.X141_splice	ENST00000257430	NM_000038.5	141			0.484960973307563	1	FACETS	0.754	0.683	0.826	1	0.983	1	SUBCLONAL	2	FALSE	0	0.478101864208744	1		379	173	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643771	52643771	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	108	473	0	ENST00000394830.3:c.2125del	p.Ile709PhefsTer5	p.I709Ffs*5	ENST00000394830	NM_018313.4	709	Att/tt	17/30	0.484960973307563	1	FACETS	0.8	0.735	0.864	1	0.988	1	SUBCLONAL	2	FALSE	0	0.478101864208744	1		473	215	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0005845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	739	240	386	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.196562059468375	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.259762903122561	4		386	979	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820602	3820602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749011678	NA	P-0005845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	654	40	383	0	ENST00000262367.5:c.2849C>T	p.Thr950Met	p.T950M	ENST00000262367	NM_004380.2	950	aCg/aTg	14/31	0.259762903122561	3	FACETS	0.501	0.415	0.598	0.167	0.138	0.2	SUBCLONAL	1	TRUE	0	0.259762903122561	3		383	694	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937729	76937729	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	919	62	561	0	ENST00000373344.5:c.3019C>T	p.Gln1007Ter	p.Q1007*	ENST00000373344	NM_000489.3	1007	Caa/Taa	9/35	0.233855796406245	2	FACETS	0.487	0.419	0.561	0.243	0.209	0.281	SUBCLONAL	1	TRUE	0	0.259762903122561	2		561	981	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0005849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	97	239	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.499775046399795	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.499775046399795	1		240	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0005849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	366	572	1	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.476780596180614	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.499775046399795	1		573	1058	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494680	2494680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1255646168	NA	P-0005849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1288	86	503	1	ENST00000355716.4:c.820C>T	p.Pro274Ser	p.P274S	ENST00000355716	NM_003820.2	274	Ccc/Tcc	8/8	0.374174401625285	3	FACETS	0.313	0.276	0.354	0.157	0.138	0.177	SUBCLONAL	1	TRUE	1	0.499775046399795	3		504	1374	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348185	348185	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	216	406	2	ENST00000262320.3:c.1321G>T	p.Ala441Ser	p.A441S	ENST00000262320	NM_003502.3	441	Gcc/Tcc	6/11	1	2	FACETS	0.983	0.916	1	0.983	0.916	1	CLONAL	1	TRUE	1	0.499775046399795	2		408	879	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647164	2647164	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	276	520	2	ENST00000342085.4:c.1442G>T	p.Gly481Val	p.G481V	ENST00000342085	NM_002613.4	481	gGa/gTa	13/14	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.499775046399795	2		522	1090	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207020	1207020	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs137853079	NA	P-0005849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	277	491	0	ENST00000326873.7:c.108C>G	p.Tyr36Ter	p.Y36*	ENST00000326873	NM_000455.4	36	taC/taG	1/10	0.499775046399795	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.499775046399795	1		491	818	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610343	10610343	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	360	562	0	ENST00000171111.5:c.367G>T	p.Val123Leu	p.V123L	ENST00000171111	NM_203500.1	123	Gtg/Ttg	2/6	0.499775046399795	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.499775046399795	1		562	977	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546799	9546799	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	317	544	0	ENST00000353224.5:c.1223C>A	p.Ser408Tyr	p.S408Y	ENST00000353224	NM_177990.2	408	tCc/tAc	5/10	0.499775046399795	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.499775046399795	1		544	817	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468103	50468104	+	missense_variant	Missense_Mutation	DNP	GG	GG	TC	novel	NA	P-0005849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	252	399	1	ENST00000331340.3:c.1338_1339delinsTC	p.Gln446_Asp447delinsHisHis	p.Q446_D447delinsHH	ENST00000331340	NM_006060.4	446	caGGac/caTCac	8/8	1	2	FACETS	0.986	0.923	1	0.986	0.923	1	CLONAL	1	TRUE	1	0.499775046399795	2		400	1023	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0005853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	989	552	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.566111495623352	3	FACETS	0.857	0.838	0.875	0.857	0.838	0.875	CLONAL	3	TRUE	0	0.74287930204274	3		552	1421	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31372633	31372633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149520896	NA	P-0005853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3351	604	872	0	ENST00000328111.2:c.274C>T	p.Arg92Trp	p.R92W	ENST00000328111	NM_006892.3	92	Cgg/Tgg	4/23	0.74287930204274	9	FACETS	1	0.996	1	0.211	0.202	0.221	CLONAL	1	TRUE	2	0.74287930204274	9		872	3955	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870804	12870804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779193240	NA	P-0005853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	156	295	0	ENST00000228872.4:c.31C>T	p.Pro11Ser	p.P11S	ENST00000228872	NM_004064.3	11	Cct/Tct	1/3	0.74287930204274	3	FACETS	0.826	0.759	0.897	0.413	0.379	0.449	CLONAL	1	TRUE	1	0.74287930204274	3		295	697	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008200	29008200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1014160326	NA	P-0005853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	574	687	2	ENST00000282397.4:c.671G>A	p.Arg224Gln	p.R224Q	ENST00000282397	NM_002019.4	224	cGa/cAa	5/30	0.613467044663654	2	FACETS	0.812	0.787	0.838	0.812	0.787	0.838	CLONAL	2	TRUE	0	0.74287930204274	2		689	951	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615691	1615691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141432924	NA	P-0005853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1396	777	1337	4	ENST00000344749.5:c.1580G>A	p.Arg527Gln	p.R527Q	ENST00000344749	NM_001136139.2	527	cGg/cAg	17/19	0.603356056936334	3	FACETS	1	0.997	1	0.44	0.425	0.456	CLONAL	1	TRUE	0	0.74287930204274	3		1341	2173	SUCCESS
APC	324	MSKCC	GRCh37	5	112175419	112175420	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0005853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	705	530	0	ENST00000257430.4:c.4129_4130del	p.Val1377SerfsTer8	p.V1377Sfs*8	ENST00000257430	NM_000038.5	1376	taTGtt/tatt	16/16	0.74287930204274	3	FACETS	0.855	0.833	0.876	0.855	0.833	0.876	CLONAL	3	TRUE	0	0.74287930204274	3		530	1015	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	105	260	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.867475938418212	2		260	198	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266107	41266107	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	229	782	0	ENST00000349496.5:c.104T>G	p.Ile35Ser	p.I35S	ENST00000349496	NM_001904.3	35	aTc/aGc	3/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.867475938418212	2		782	509	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564705	55564705	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	221	675	0	ENST00000288135.5:c.593A>G	p.Glu198Gly	p.E198G	ENST00000288135	NM_000222.2	198	gAa/gGa	3/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.867475938418212	2		675	493	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38960607	38960607	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	166	609	0	ENST00000357387.3:c.1744A>G	p.Lys582Glu	p.K582E	ENST00000357387	NM_152756.3	582	Aag/Gag	20/38	0.121417997061132	4	FACETS	0.814	0.755	0.874	0.814	0.755	0.874	INDETERMINATE	2	TRUE	2	0.867475938418212	4		609	439	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475207	475207	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	201	908	2	ENST00000399788.2:c.430A>T	p.Ser144Cys	p.S144C	ENST00000399788	NM_001042603.1	144	Agt/Tgt	4/28	NA	2	FACETS	1	0.972	1			1	INDETERMINATE	1	TRUE	NA	0.867475938418212	2		910	437	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098806	178098829	+	inframe_deletion	In_Frame_Del	DEL	GTCTCTTCATCTAGTTGTAACTGA	GTCTCTTCATCTAGTTGTAACTGA	-	novel	NA	P-0005854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	227	838	1	ENST00000397062.3:c.216_239del	p.Gln73_Thr80del	p.Q73_T80del	ENST00000397062	NM_006164.4	72	gcTCAGTTACAACTAGATGAAGAGACa/gca	2/5	0.651953880643448	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.867475938418212	1		839	277	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375227	15375227	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	56	395	0	ENST00000263377.2:c.1200G>C	p.Met400Ile	p.M400I	ENST00000263377	NM_058243.2	400	atG/atC	6/20	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	FALSE	1	0.272040603077635	2		395	411	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200380	138200380	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	111	302	0	ENST00000237289.4:c.1798G>C	p.Asp600His	p.D600H	ENST00000237289	NM_001270507.1	600	Gac/Cac	7/9	0.144119123330327	3	FACETS	1	0.977	1	0.634	0.573	0.699	INDETERMINATE	1	TRUE	1	0.4390553291057	3		302	486	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599876	10599879	+	frameshift_variant	Frame_Shift_Del	DEL	TAGA	TAGA	-	novel	NA	P-0005871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	297	599	0	ENST00000171111.5:c.1697_1700del	p.Ile566ThrfsTer28	p.I566Tfs*28	ENST00000171111	NM_203500.1	566	aTCTAc/ac	5/6	0.4390553291057	2	FACETS	0.892	0.845	0.941	0.892	0.845	0.941	CLONAL	2	TRUE	0	0.4390553291057	2		599	758	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879601	37879602	+	missense_variant	Missense_Mutation	DNP	TT	TT	AG	novel	NA	P-0005871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	174	296	0	ENST00000269571.5:c.1976_1977delinsAG	p.Val659Glu	p.V659E	ENST00000269571		659	gTT/gAG	17/27	0.334866510662116	3	FACETS	0.836	0.774	0.9	0.836	0.774	0.9	CLONAL	2	TRUE	1	0.4390553291057	3		296	578	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005874-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	95	260	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		260	480	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499710	18499710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	30	364	1	ENST00000266497.5:c.1565C>T	p.Pro522Leu	p.P522L	ENST00000266497		522	cCt/cTt	10/31	0.231105682465123	7	FACETS	1	0.848	1	0.212	0.171	0.259	CLONAL	1	TRUE	2	0.231105682465123	7		365	386	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015336	176015336	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	26	339	0	ENST00000367669.3:c.1402A>G	p.Thr468Ala	p.T468A	ENST00000367669	NM_022457.5	468	Acc/Gcc	12/20	0.213668864111901	4	FACETS	0.727	0.576	0.901	0.242	0.192	0.301	CLONAL	1	TRUE	1	0.231105682465123	4		339	381	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754961	29754961	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	86	417	0	ENST00000389048.3:c.974C>A	p.Thr325Asn	p.T325N	ENST00000389048	NM_004304.4	325	aCc/aAc	4/29	0.213668864111901	4	FACETS	1	0.971	1	0.439	0.388	0.493	CLONAL	1	TRUE	1	0.231105682465123	4		417	696	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660222	227660222	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs769228929	NA	P-0005889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	70	438	0	ENST00000305123.5:c.3233G>T	p.Ser1078Ile	p.S1078I	ENST00000305123	NM_005544.2	1078	aGt/aTt	1/2	0.231105682465123	3	FACETS	0.988	0.861	1	0.494	0.43	0.563	CLONAL	1	TRUE	1	0.231105682465123	3		438	684	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459762	149459762	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	126	533	0	ENST00000286301.3:c.445A>G	p.Met149Val	p.M149V	ENST00000286301	NM_005211.3	149	Atg/Gtg	4/22	0.231105682465123	2	FACETS	1	0.975	1	0.612	0.554	0.673	CLONAL	1	TRUE	0	0.231105682465123	2		533	891	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517484	176517484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754036845	NA	P-0005889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	141	571	1	ENST00000292408.4:c.185G>A	p.Arg62His	p.R62H	ENST00000292408	NM_213647.1	62	cGt/cAt	3/18	0.231105682465123	2	FACETS	1	0.983	1	0.674	0.614	0.738	CLONAL	1	TRUE	0	0.231105682465123	2		572	905	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227987	55227987	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	49	507	0	ENST00000275493.2:c.1454G>A	p.Gly485Asp	p.G485D	ENST00000275493	NM_005228.3	485	gGt/gAt	12/28	0.168575032757752	4	FACETS	1	0.858	1	0.507	0.429	0.592	CLONAL	1	TRUE	2	0.231105682465123	4		507	515	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437772	49437772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	67	365	0	ENST00000301067.7:c.5198C>T	p.Ala1733Val	p.A1733V	ENST00000301067	NM_003482.3	1733	gCt/gTt	22/54	0.168575032757752	4	FACETS	1	0.947	1	0.589	0.512	0.673	CLONAL	1	TRUE	2	0.231105682465123	4		365	606	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95584002	95584002	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	23	238	2	ENST00000393063.1:c.1466C>A	p.Pro489His	p.P489H	ENST00000393063	NM_030621.3	489	cCt/cAt	10/28	1	2	FACETS	0.851	0.666	1	0.851	0.666	1	CLONAL	1	TRUE	1	0.231105682465123	2		240	234	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089935	16089935	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	50	355	0	ENST00000268712.3:c.175C>A	p.Gln59Lys	p.Q59K	ENST00000268712	NM_006311.3	59	Caa/Aaa	3/46	1	2	FACETS	0.977	0.83	1	0.977	0.83	1	CLONAL	1	TRUE	1	0.231105682465123	2		355	443	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349580	15349580	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	69	432	0	ENST00000263377.2:c.3994G>T	p.Glu1332Ter	p.E1332*	ENST00000263377	NM_058243.2	1332	Gag/Tag	19/20	0.231105682465123	3	FACETS	0.942	0.82	1	0.471	0.41	0.538	CLONAL	1	TRUE	1	0.231105682465123	3		432	707	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358569	67358571	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0005889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	85	667	0	ENST00000327367.4:c.82_84del	p.Glu28del	p.E28del	ENST00000327367	NM_005902.3	26	cAGGag/cag	1/9	1	2	FACETS	0.663	0.584	0.748	0.663	0.584	0.748	SUBCLONAL	1	TRUE	1	0.231105682465123	2		667	1110	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405652	70405652	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	62	478	1	ENST00000373644.4:c.3171del	p.Lys1057AsnfsTer25	p.K1057Nfs*25	ENST00000373644	NM_030625.2	1056	Aaa/aa	4/12	0.231105682465123	3	FACETS	1	0.961	1	0.661	0.572	0.756	CLONAL	1	TRUE	1	0.231105682465123	3		479	453	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058535	72058535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1300841328	NA	P-0005899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1394	464	737	0	ENST00000357731.5:c.905A>G	p.Lys302Arg	p.K302R	ENST00000357731	NM_173808.2	302	aAg/aGg	6/7	0.317267126729919	3	FACETS	0.825	0.786	0.865	0.825	0.786	0.865	CLONAL	2	TRUE	1	0.356438056211622	3		737	1858	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248599	212248599	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	147	416	0	ENST00000342788.4:c.3668A>C	p.Lys1223Thr	p.K1223T	ENST00000342788	NM_005235.2	1223	aAg/aCg	28/28	0.317267126729919	3	FACETS	0.931	0.849	1	0.465	0.424	0.509	CLONAL	1	TRUE	1	0.356438056211622	3		416	1044	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970840	55970840	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	132	478	0	ENST00000263923.4:c.1957C>T	p.His653Tyr	p.H653Y	ENST00000263923	NM_002253.2	653	Cat/Tat	13/30	0.310443724723339	2	FACETS	0.801	0.726	0.879	0.4	0.363	0.44	CLONAL	1	TRUE	0	0.356438056211622	2		478	925	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799344	88799344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761609264	NA	P-0005899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	82	482	0	ENST00000360948.2:c.41G>A	p.Arg14Gln	p.R14Q	ENST00000360948	NM_001012338.2	14	cGg/cAg	2/19	0.350382301203571	3	FACETS	0.488	0.429	0.552	0.244	0.214	0.276	SUBCLONAL	1	TRUE	1	0.356438056211622	3		482	1110	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56878430	56878430	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771046738	NA	P-0005899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1201	188	591	0	ENST00000308159.5:c.2369G>A	p.Arg790His	p.R790H	ENST00000308159	NM_014669.4	790	cGc/cAc	22/22	0.310443724723339	2	FACETS	0.759	0.7	0.822	0.38	0.35	0.411	SUBCLONAL	1	TRUE	0	0.356438056211622	2		591	1389	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885570	111885606	+	frameshift_variant	Frame_Shift_Del	DEL	GTGCGGCGCCGCCTGTGATGTCCGGCTCTCCAGCTAC	GTGCGGCGCCGCCTGTGATGTCCGGCTCTCCAGCTAC	-	novel	NA	P-0005899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1718	250	804	0	ENST00000341259.2:c.1350_1386del	p.Cys450TrpfsTer2	p.C450Wfs*2	ENST00000341259	NM_005475.2	449	gaGTGCGGCGCCGCCTGTGATGTCCGGCTCTCCAGCTAC/ga	7/8	0.317267126729919	3	FACETS	0.84	0.782	0.9	0.42	0.391	0.45	CLONAL	1	TRUE	1	0.356438056211622	3		804	1968	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578423	7579121	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CATGTGCTGTGACTGCTTGTAGATGGCCATGGCGCGGACGCGGGTGCCGGGCGGGGGTGTGGAATCAACCCACAGCTGCACAGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAAGCAACTGGAAGACGGCAGCAAAGAAACAAACATGCGTAAGCACCTCCTGCAACCCACTAGCGAGCTAGAGAGAGTTGGCGTCTACACCTCAGGAGCTTTTCTTTTTTTTTTTTTTTTTTGAGATAGGGTCTTGCTCTGTCACTCAGGCTGGAGCACAGTGGTGTGATCACAGCTCACTGCAGCCTCCATCTCCTGGCCTCAAGTGATCTTCCCACCTCAGCCTCCTAAGTGGCTGGGACTATAGGTGTGCACCACCATGCCTGGCTAATTTTTTGTATTTTTTTGTAGAGACGAGGTTTCATCATGTTACCCAGGCTGGTCTTGAACTCCTGGGCTCAGGTGATCTGCCTGCCTTGGCCTCTTTGAGAGTGCTGGGATTGCAGGTGTGAGCCACCAAGCCTGGTCAGGAGCTTATTTTCAAAAGCCAAGGAATACACGTGGATGAAGAAAAAGAAAAGTTCTGCATCCCCAGGAGAGATGCTGAGGGTGTGATGGGATGGATAAAAGCCCA	CATGTGCTGTGACTGCTTGTAGATGGCCATGGCGCGGACGCGGGTGCCGGGCGGGGGTGTGGAATCAACCCACAGCTGCACAGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAAGCAACTGGAAGACGGCAGCAAAGAAACAAACATGCGTAAGCACCTCCTGCAACCCACTAGCGAGCTAGAGAGAGTTGGCGTCTACACCTCAGGAGCTTTTCTTTTTTTTTTTTTTTTTTGAGATAGGGTCTTGCTCTGTCACTCAGGCTGGAGCACAGTGGTGTGATCACAGCTCACTGCAGCCTCCATCTCCTGGCCTCAAGTGATCTTCCCACCTCAGCCTCCTAAGTGGCTGGGACTATAGGTGTGCACCACCATGCCTGGCTAATTTTTTGTATTTTTTTGTAGAGACGAGGTTTCATCATGTTACCCAGGCTGGTCTTGAACTCCTGGGCTCAGGTGATCTGCCTGCCTTGGCCTCTTTGAGAGTGCTGGGATTGCAGGTGTGAGCCACCAAGCCTGGTCAGGAGCTTATTTTCAAAAGCCAAGGAATACACGTGGATGAAGAAAAAGAAAAGTTCTGCATCCCCAGGAGAGATGCTGAGGGTGTGATGGGATGGATAAAAGCCCA	-	novel	NA	P-0005899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	213	344	1	ENST00000269305.4:c.375+191_507del		p.X125_splice	ENST00000269305	NM_001126112.2	125		5/11	0.310443724723339	2	FACETS	0.845	0.788	0.903	0.845	0.788	0.903	CLONAL	2	TRUE	0	0.356438056211622	2		345	707	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799113	45799118	+	inframe_deletion	In_Frame_Del	DEL	TCTTGG	TCTTGG	-	novel	NA	P-0005899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	162	468	0	ENST00000450313.1:c.315_320del	p.Asp105_Gln106del	p.D105_Q106del	ENST00000450313	NM_012222.2	105	gaCCAAGAg/gag	3/16	0.317267126729919	3	FACETS	0.865	0.792	0.942	0.433	0.396	0.471	CLONAL	1	TRUE	1	0.356438056211622	3		468	1238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0005930-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	347	254	7	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.674966621378324	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.674966621378324	4		261	806	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0005930-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	608	595	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.674966621378324	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	2	0.674966621378324	4		597	1409	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094468	27094470	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs767284798	NA	P-0005930-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	180	292	0	ENST00000324856.7:c.3178_3180del	p.Glu1060del	p.E1060del	ENST00000324856	NM_006015.4	1059	aAGGag/aag	11/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.674966621378324	2		292	490	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989562	212989562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755026855	NA	P-0005930-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	210	423	0	ENST00000342788.4:c.149G>A	p.Arg50His	p.R50H	ENST00000342788	NM_005235.2	50	cGc/cAc	2/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.674966621378324	2		423	564	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830919	72830919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005930-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1475	217	832	2	ENST00000268489.5:c.5662G>A	p.Glu1888Lys	p.E1888K	ENST00000268489	NM_006885.3	1888	Gaa/Aaa	9/10	0.443619017624021	5	FACETS	0.765	0.708	0.824			1	SUBCLONAL	1	TRUE	NA	0.674966621378324	5		834	1692	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183771	10183771	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	145	445	0	ENST00000256474.2:c.240T>G	p.Ser80Arg	p.S80R	ENST00000256474	NM_000551.3	80	agT/agG	1/3	0.535178794390927	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.535178794390927	1		445	357	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143129613	143129613	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	64	456	0	ENST00000262992.4:c.1037T>A	p.Leu346Gln	p.L346Q	ENST00000262992	NM_001101669.1	346	cTg/cAg	12/24	1	2	FACETS	0.938	0.821	1	0.938	0.821	1	CLONAL	1	TRUE	1	0.535178794390927	2		456	255	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675415	30675415	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	133	508	0	ENST00000376406.3:c.2941T>G	p.Ser981Ala	p.S981A	ENST00000376406	NM_014641.2	981	Tca/Gca	8/15	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.535178794390927	2		508	465	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39661099	39661099	+	stop_lost	Nonstop_Mutation	SNP	T	T	G	novel	NA	P-0005934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	61	532	0	ENST00000262039.4:c.2662T>G	p.Ter888GlyextTer4	p.*888Gext*4	ENST00000262039	NM_002647.2	888	Tga/Gga	25/25	0.133633431805578	0	FACETS	0.404	0.352	0.46			1	INDETERMINATE	1	TRUE	0	0.535178794390927	0		532	262	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651509	52651509	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	93	500	0	ENST00000394830.3:c.1587del	p.Val530PhefsTer39	p.V530Ffs*39	ENST00000394830	NM_018313.4	529	gtT/gt	15/30	0.535178794390927	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.535178794390927	1		500	231	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147497	47147497	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	103	604	0	ENST00000409792.3:c.4829del	p.Lys1610ArgfsTer5	p.K1610Rfs*5	ENST00000409792	NM_014159.6	1610	aAg/ag	6/21	0.535178794390927	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.535178794390927	1		604	247	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005935-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	25	260	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		260	409	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005939-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	31	260	0				ENST00000310581	NM_198253.2	-/1132			0.148068191710175	3	FACETS	0.859	0.732	0.984	0.859	0.732	0.984	INDETERMINATE	2	TRUE	1	0.860452047688856	3		260	60	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0005939-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	83	326	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.315684751910113	4	FACETS	1	0.953	1	1	0.953	1	INDETERMINATE	2	TRUE	2	0.860452047688856	4		326	166	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075591	8075591	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005939-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	91	541	2	ENST00000377482.5:c.89G>A	p.Arg30Lys	p.R30K	ENST00000377482	NM_018948.3	30	aGg/aAg	2/4	0.860452047688856	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.860452047688856	1		543	100	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416368	29416368	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779663817	NA	P-0005939-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	47	491	0	ENST00000389048.3:c.4585G>A	p.Asp1529Asn	p.D1529N	ENST00000389048	NM_004304.4	1529	Gac/Aac	29/29	NA	2	FACETS	0.719	0.619	0.824			1	INDETERMINATE	1	TRUE	NA	0.860452047688856	2		491	152	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204642	128204642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005939-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	85	474	0	ENST00000341105.2:c.799C>T	p.Pro267Ser	p.P267S	ENST00000341105	NM_032638.4	267	Ccc/Tcc	3/6	0.355854359428296	4	FACETS	0.879	0.793	0.967			1	INDETERMINATE	2	TRUE	NA	0.860452047688856	4		474	209	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416797	121416797	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005939-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	34	613	1	ENST00000257555.6:c.226G>T	p.Asp76Tyr	p.D76Y	ENST00000257555		76	Gac/Tac	1/10	0.217698160272844	4	FACETS	1	0.852	1	0.514	0.427	0.609	INDETERMINATE	1	TRUE	2	0.860452047688856	4		614	143	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791984	42791984	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005939-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	127	525	0	ENST00000575354.2:c.788C>G	p.Ala263Gly	p.A263G	ENST00000575354	NM_015125.3	263	gCc/gGc	6/20	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.860452047688856	2		525	135	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0005943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	199	318	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.358219618202561	5	FACETS	0.879	0.825	0.933	0.879	0.825	0.933	INDETERMINATE	3	TRUE	2	0.741661103213658	5		318	430	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106058	8106058	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	444	362	0	ENST00000346208.3:c.878T>A	p.Met293Lys	p.M293K	ENST00000346208		293	aTg/aAg	4/6	0.741661103213658	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.741661103213658	3		362	811	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	337	776	0	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	0.741661103213658	2	FACETS	1	0.98	1	0.53	0.503	0.557	CLONAL	1	TRUE	0	0.741661103213658	2		776	858	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143509	108143509	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	447	656	1	ENST00000278616.4:c.3214G>A	p.Glu1072Lys	p.E1072K	ENST00000278616	NM_000051.3	1072	Gaa/Aaa	22/63	0.741661103213658	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.741661103213658	3		657	809	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023696	27023696	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	247	561	0	ENST00000324856.7:c.802C>T	p.Gln268Ter	p.Q268*	ENST00000324856	NM_006015.4	268	Cag/Tag	1/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.741661103213658	2		561	619	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255133	16255133	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	278	588	0	ENST00000375759.3:c.2398G>T	p.Glu800Ter	p.E800*	ENST00000375759	NM_015001.2	800	Gag/Tag	11/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.741661103213658	2		588	700	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178143	56178143	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0005943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	197	408	0	ENST00000399503.3:c.3116C>G	p.Ser1039Ter	p.S1039*	ENST00000399503	NM_005921.1	1039	tCa/tGa	14/20	0.741661103213658	3	FACETS	1	0.954	1	0.517	0.48	0.555	CLONAL	1	TRUE	1	0.741661103213658	3		408	704	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178646	56178646	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	381	408	0	ENST00000399503.3:c.3619C>T	p.Gln1207Ter	p.Q1207*	ENST00000399503	NM_005921.1	1207	Cag/Tag	14/20	0.741661103213658	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.741661103213658	3		408	673	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250743	26250743	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1415	391	1033	0	ENST00000446824.2:c.91C>G	p.Pro31Ala	p.P31A	ENST00000446824	NM_021018.2	31	Cca/Gca	1/1	0.741661103213658	5	FACETS	1	0.992	1	0.247	0.233	0.26	CLONAL	1	TRUE	0	0.741661103213658	5		1033	1806	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55270250	55270250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374501041	NA	P-0005943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	214	592	1	ENST00000275493.2:c.3203G>A	p.Arg1068Gln	p.R1068Q	ENST00000275493	NM_005228.3	1068	cGa/cAa	27/28	0.741661103213658	3	FACETS	0.95	0.884	1	0.475	0.442	0.509	CLONAL	1	TRUE	1	0.741661103213658	3		593	833	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851415	151851415	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	539	656	0	ENST00000262189.6:c.12076G>T	p.Glu4026Ter	p.E4026*	ENST00000262189	NM_170606.2	4026	Gag/Tag	47/59	0.741661103213658	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.741661103213658	3		656	949	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752653	128752653	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	348	451	0	ENST00000377970.2:c.814G>T	p.Glu272Ter	p.E272*	ENST00000377970	NM_002467.4	272	Gaa/Taa	3/3	0.741661103213658	3	FACETS	0.935	0.893	0.977	0.935	0.893	0.977	CLONAL	2	TRUE	1	0.741661103213658	3		451	688	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571841	64571841	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	912	954	0	ENST00000312049.6:c.1798C>G	p.Leu600Val	p.L600V	ENST00000312049	NM_130799.2	600	Ctg/Gtg	10/10	0.312641515836616	6	FACETS	0.952	0.927	0.977			1	INDETERMINATE	4	TRUE	NA	0.741661103213658	6		954	1604	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481859	56481859	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	315	594	0	ENST00000267101.3:c.787C>G	p.Leu263Val	p.L263V	ENST00000267101	NM_001982.3	263	Ctt/Gtt	7/28	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.741661103213658	2		594	753	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626775	28626775	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	229	570	0	ENST00000241453.7:c.521G>C	p.Arg174Thr	p.R174T	ENST00000241453	NM_004119.2	174	aGa/aCa	5/24	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.741661103213658	2		570	558	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091121	29091121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	314	435	2	ENST00000328354.6:c.1369G>A	p.Glu457Lys	p.E457K	ENST00000328354	NM_007194.3	457	Gag/Aag	12/15	0.661480284851868	4	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	2	0.741661103213658	4		437	730	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091814	29091814	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	251	394	0	ENST00000328354.6:c.1143G>A	p.Met381Ile	p.M381I	ENST00000328354	NM_007194.3	381	atG/atA	11/15	0.661480284851868	4	FACETS	0.914	0.861	0.968	0.914	0.861	0.968	CLONAL	2	TRUE	2	0.741661103213658	4		394	645	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179189	123179189	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	494	619	0	ENST00000218089.9:c.638G>A	p.Arg213Lys	p.R213K	ENST00000218089	NM_001042749.1	213	aGa/aAa	8/35	0.741661103213658	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.741661103213658	3		619	878	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	120	260	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.56	2		260	419	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217299	11217299	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519779	NA	P-0005952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	155	440	1	ENST00000361445.4:c.4379T>C	p.Leu1460Pro	p.L1460P	ENST00000361445	NM_004958.3	1460	cTt/cCt	30/58	0.3	2	FACETS	0.626	0.573	0.681			1	INDETERMINATE	1	TRUE	NA	0.56	2		441	885	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134414	41134414	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1897	148	634	0	ENST00000379561.5:c.1214A>G	p.Tyr405Cys	p.Y405C	ENST00000379561	NM_002015.3	405	tAc/tGc	2/3	1	2	FACETS	0.258	0.235	0.284	0.258	0.235	0.284	SUBCLONAL	1	TRUE	1	0.56	2		634	2045	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945725	17945725	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	158	337	0	ENST00000458235.1:c.2135G>T	p.Gly712Val	p.G712V	ENST00000458235	NM_000215.3	712	gGc/gTc	16/24	0.164347940892293	0	FACETS	0.344	0.315	0.373			1	INDETERMINATE	1	TRUE	0	0.56	0		337	722	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696294	52696294	+	splice_acceptor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0005952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	128	287	0	ENST00000394830.3:c.385-2del		p.X129_splice	ENST00000394830	NM_018313.4	129			0.572671261769437	1	FACETS	0.866	0.793	0.941	0.866	0.793	0.941	CLONAL	1	TRUE	0	0.56	1		287	380	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188294	10188309	+	frameshift_variant	Frame_Shift_Del	DEL	CTATTTTTGCCAATAT	CTATTTTTGCCAATAT	-	novel	NA	P-0005952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	223	404	0	ENST00000256474.2:c.438_453del	p.Ile147HisfsTer7	p.I147Hfs*7	ENST00000256474	NM_000551.3	146	cCTATTTTTGCCAATATc/cc	2/3	0.572671261769437	1	FACETS	0.982	0.921	1	0.982	0.921	1	CLONAL	1	TRUE	0	0.56	1		404	584	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0005971-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	263	531	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.562958589477524	4	FACETS	1	0.99	1	0.416	0.391	0.442	CLONAL	1	TRUE	1	0.930215424577478	4		531	874	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910549	29910549	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45585732	NA	P-0005971-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	37	247	4	ENST00000376809.5:c.89G>A	p.Arg30Lys	p.R30K	ENST00000376809	NM_002116.7	30	aGg/aAg	2/8	0.930215424577478	4	FACETS	0.344	0.283	0.411	0.172	0.141	0.206	SUBCLONAL	1	TRUE	2	0.930215424577478	4		251	447	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0005971-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	199	283	0				ENST00000310581	NM_198253.2	-/1132			0.664882233606654	3	FACETS	0.845	0.796	0.893	0.845	0.796	0.893	CLONAL	2	TRUE	1	0.930215424577478	3		283	371	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347309	89347309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005971-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	580	1002	1	ENST00000301030.4:c.5641G>A	p.Gly1881Ser	p.G1881S	ENST00000301030	NM_001256183.1	1881	Ggc/Agc	9/13	0.495388360178982	1	FACETS	0.706	0.684	0.728	0.706	0.684	0.728	INDETERMINATE	1	TRUE	0	0.930215424577478	1		1003	945	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916957	178916957	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005971-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	290	851	0	ENST00000263967.3:c.344G>C	p.Arg115Pro	p.R115P	ENST00000263967	NM_006218.2	115	cGa/cCa	2/21	0.484615588934377	1	FACETS	0.36	0.339	0.381	0.36	0.339	0.381	INDETERMINATE	1	TRUE	0	0.930215424577478	1		851	927	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593603	55593603	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913235	NA	P-0005973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	28	186	0	ENST00000288135.5:c.1669T>C	p.Trp557Arg	p.W557R	ENST00000288135	NM_000222.2	557	Tgg/Cgg	11/21	0.485611160264459	2	FACETS	0.314	0.251	0.386	0.157	0.125	0.193	SUBCLONAL	1	TRUE	0	0.544960884922582	2		186	327	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858341	89858341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	64	381	0	ENST00000389301.3:c.1219C>T	p.Leu407Phe	p.L407F	ENST00000389301	NM_000135.2	407	Ctt/Ttt	13/43	NA	2	FACETS	0.354	0.306	0.406			1	INDETERMINATE	1	TRUE	NA	0.544960884922582	2		381	664	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278049	18278049	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs372272045	NA	P-0005973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	102	524	1	ENST00000222254.8:c.1669G>C	p.Asp557His	p.D557H	ENST00000222254	NM_005027.3	557	Gac/Cac	13/16	0.516636763918326	3	FACETS	0.461	0.411	0.514	0.23	0.205	0.257	SUBCLONAL	1	TRUE	1	0.544960884922582	3		525	1034	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0005980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	268	608	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.727272934493214	3	FACETS	0.995	0.945	1	0.995	0.945	1	CLONAL	2	TRUE	1	0.727272934493214	3		608	505	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519767	137519767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	58	172	0	ENST00000367739.4:c.871G>A	p.Val291Ile	p.V291I	ENST00000367739	NM_000416.2	291	Gta/Ata	7/7	0.727272934493214	4	FACETS	0.81	0.7	0.929			1	CLONAL	1	TRUE	NA	0.727272934493214	4		172	340	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249690	110249690	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	105	481	0	ENST00000374672.4:c.985G>T	p.Asp329Tyr	p.D329Y	ENST00000374672	NM_004235.4	329	Gac/Tac	3/5	1	2	FACETS	0.953	0.865	1	0.953	0.865	1	CLONAL	1	TRUE	1	0.727272934493214	2		481	303	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99491805	99491805	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	94	473	0	ENST00000268035.6:c.3590C>A	p.Ser1197Tyr	p.S1197Y	ENST00000268035	NM_000875.3	1197	tCc/tAc	20/21	0.121042936675488	4	FACETS	1	0.962	1			1	INDETERMINATE	1	TRUE	NA	0.727272934493214	4		473	385	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164317	47164317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	164	400	0	ENST00000409792.3:c.1809del	p.Asn604IlefsTer18	p.N604Ifs*18	ENST00000409792	NM_014159.6	603	atT/at	3/21	0.727272934493214	2	FACETS	0.826	0.777	0.874	0.826	0.777	0.874	CLONAL	2	TRUE	0	0.727272934493214	2		400	273	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077427	30077427	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0005990-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	47	257	0	ENST00000338641.4:c.1575-1G>A		p.X525_splice	ENST00000338641	NM_000268.3	525			1	2	FACETS	0.601	0.506	0.705	0.601	0.506	0.705	SUBCLONAL	1	TRUE	1	0.26	2		257	602	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005990-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1299	120	580	0	ENST00000269305.4:c.641del	p.His214LeufsTer33	p.H214Lfs*33	ENST00000269305	NM_001126112.2	214	cAt/ct	6/11	1	2	FACETS	0.651	0.585	0.72	0.651	0.585	0.72	SUBCLONAL	1	TRUE	1	0.26	2		580	1419	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426671	47426671	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005990-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	63	270	0	ENST00000377045.4:c.916C>A	p.Pro306Thr	p.P306T	ENST00000377045	NM_001654.4	306	Cca/Aca	10/16	1	1	FACETS	0.596	0.515	0.685	0.596	0.515	0.685	SUBCLONAL	1	TRUE	0	0.26	1		270	707	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0006002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	87	383	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.178711265907805	3	FACETS	1	0.978	1	0.742	0.658	0.831	CLONAL	1	TRUE	1	0.231712026925525	3		383	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578415	7578415	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	74	397	0	ENST00000269305.4:c.515T>A	p.Val172Asp	p.V172D	ENST00000269305	NM_001126112.2	172	gTt/gAt	5/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.231712026925525	2		397	426	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241677	55241677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504256	NA	P-0006003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	865	392	0	ENST00000275493.2:c.2125G>A	p.Glu709Lys	p.E709K	ENST00000275493	NM_005228.3	709	Gaa/Aaa	18/28	0.634500083621587	6	FACETS	1	0.995	1	0.845	0.82	0.87	CLONAL	3	TRUE	2	0.634500083621587	6		392	1831	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0006003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	831	349	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.634500083621587	6	FACETS	1	0.996	1	0.868	0.842	0.894	CLONAL	3	TRUE	2	0.634500083621587	6		349	1711	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913384	NA	P-0006003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	525	189	0	ENST00000304494.5:c.262G>T	p.Glu88Ter	p.E88*	ENST00000304494	NM_000077.4	88	Gag/Tag	2/3	0.612273559869007	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	4	TRUE	0	0.634500083621587	4		189	663	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802688	135802688	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750441497	NA	P-0006003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	211	322	0	ENST00000298552.3:c.110G>A	p.Arg37His	p.R37H	ENST00000298552	NM_001162426.1	37	cGt/cAt	4/23	0.612273559869007	4	FACETS	1	0.981	1	0.288	0.267	0.309	CLONAL	1	TRUE	0	0.634500083621587	4		322	945	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532741	187532741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388615666	NA	P-0006003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	249	457	0	ENST00000441802.2:c.9652G>A	p.Val3218Ile	p.V3218I	ENST00000441802	NM_005245.3	3218	Gta/Ata	14/27	1	2	FACETS	0.991	0.93	1	0.991	0.93	1	CLONAL	1	TRUE	1	0.634500083621587	2		457	792	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370958	55370958	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	219	445	1	ENST00000297316.4:c.260C>T	p.Ala87Val	p.A87V	ENST00000297316	NM_022454.3	87	gCg/gTg	1/2	0.6300518451864	4	FACETS	0.989	0.919	1	0.33	0.306	0.354	CLONAL	1	TRUE	1	0.634500083621587	4		446	1141	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25368457	25368457	+	intron_variant	Intron	SNP	A	A	C	novel	NA	P-0006003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	148	273	0	ENST00000311936.3:c.451-5612T>G		p.*151*	ENST00000311936	NM_004985.3	163/189			0.575362901763318	3	FACETS	0.938	0.859	1	0.469	0.429	0.51	CLONAL	1	TRUE	1	0.634500083621587	3		273	655	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254611	10254611	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	174	356	0	ENST00000340748.4:c.2899G>C	p.Asp967His	p.D967H	ENST00000340748		967	Gac/Cac	28/40	0.624083815273304	2	FACETS	0.828	0.766	0.894	0.414	0.383	0.447	CLONAL	1	TRUE	0	0.634500083621587	2		356	662	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	27	221	1	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		222	502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0006027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	74	637	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		637	883	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121912580	NA	P-0006027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	15	451	0	ENST00000342988.3:c.1157G>T	p.Gly386Val	p.G386V	ENST00000342988	NM_005359.5	386	gGt/gTt	10/12	0.183093545386918	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		451	577	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0006029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	71	385	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.17	2		385	759	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061204	38061204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	34	220	0	ENST00000250448.2:c.785G>A	p.Arg262His	p.R262H	ENST00000250448	NM_004496.3	262	cGc/cAc	2/2	1	2	FACETS	0.803	0.656	0.97	0.803	0.656	0.97	CLONAL	1	TRUE	1	0.17	2		220	498	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0006029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	94	239	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.938	1	1	0.987	1	CLONAL	2	TRUE	1	0.17	2		239	515	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878187	48878187	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0006029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	19	212	0	ENST00000267163.4:c.137+2T>A		p.X46_splice	ENST00000267163	NM_000321.2	46			1	2	FACETS	0.79	0.6	1	0.79	0.6	1	CLONAL	1	TRUE	1	0.17	2		212	283	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266442	55266442	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	49	448	0	ENST00000275493.2:c.2734T>G	p.Ser912Ala	p.S912A	ENST00000275493	NM_005228.3	912	Tcc/Gcc	23/28	0.163310699569192	3	FACETS	0.643	0.543	0.755	0.322	0.271	0.378	SUBCLONAL	1	TRUE	1	0.17	3		448	972	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859302	151859701	+	frameshift_variant	Frame_Shift_Del	DEL	GATGACTTTTTATTTTTCAACAAGTGTTTCAGAAGTTCATTCCCTGAGTCTCCTTTGGCAGCAGGGGCCCCAGCAGAATGGGGAGGACTCTGTGCTGAGGAGACAGGACAGGCTACAGCGTTTCCTTCTACCTTACTACCATTCTGTTCCTCCAATTTAGGCTCCTCTTGGCCTGGGCAGGACTCTGTCTCAGCCTTTTCCAGTTTTATCTCTTCTGTTTTGGCAGGGGTTTCCATGGAGAGCTTGTCTACTTCTGAATTTGCATACGTCTGTTGATTTGGAGTTGCTTGTGAGAAATCACTATTGGGCAGTTTGTTCTCTAATTCTGTACATAGCTGGCCTGCTGCCATATTGGGAGTGGATGGGCCGACTGGTTCCACCGACTCTTGGTCGGCTTGTT	GATGACTTTTTATTTTTCAACAAGTGTTTCAGAAGTTCATTCCCTGAGTCTCCTTTGGCAGCAGGGGCCCCAGCAGAATGGGGAGGACTCTGTGCTGAGGAGACAGGACAGGCTACAGCGTTTCCTTCTACCTTACTACCATTCTGTTCCTCCAATTTAGGCTCCTCTTGGCCTGGGCAGGACTCTGTCTCAGCCTTTTCCAGTTTTATCTCTTCTGTTTTGGCAGGGGTTTCCATGGAGAGCTTGTCTACTTCTGAATTTGCATACGTCTGTTGATTTGGAGTTGCTTGTGAGAAATCACTATTGGGCAGTTTGTTCTCTAATTCTGTACATAGCTGGCCTGCTGCCATATTGGGAGTGGATGGGCCGACTGGTTCCACCGACTCTTGGTCGGCTTGTT	-	novel	NA	P-0006029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	63	274	0	ENST00000262189.6:c.10961_11360del	p.Gln3654LeufsTer4	p.Q3654Lfs*4	ENST00000262189	NM_170606.2	3654	cAACAAGCCGACCAAGAGTCGGTGGAACCAGTCGGCCCATCCACTCCCAATATGGCAGCAGGCCAGCTATGTACAGAATTAGAGAACAAACTGCCCAATAGTGATTTCTCACAAGCAACTCCAAATCAACAGACGTATGCAAATTCAGAAGTAGACAAGCTCTCCATGGAAACCCCTGCCAAAACAGAAGAGATAAAACTGGAAAAGGCTGAGACAGAGTCCTGCCCAGGCCAAGAGGAGCCTAAATTGGAGGAACAGAATGGTAGTAAGGTAGAAGGAAACGCTGTAGCCTGTCCTGTCTCCTCAGCACAGAGTCCTCCCCATTCTGCTGGGGCCCCTGCTGCCAAAGGAGACTCAGGGAATGAACTTCTGAAACACTTGTTGAAAAATAAAAAGTCATCt/ct	43/59	0.163310699569192	3	FACETS	1	0.875	1	0.507	0.438	0.583	CLONAL	1	TRUE	1	0.17	3		274	793	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477842	140477850	+	inframe_deletion	In_Frame_Del	DEL	GCTGTCACA	GCTGTCACA	-	novel	NA	P-0006029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	80	406	1	ENST00000288602.6:c.1458_1466del	p.Asn486_Ala489delinsLys	p.N486_A489delinsK	ENST00000288602	NM_004333.4	486	aaTGTGACAGCa/aaa	12/18	0.163310699569192	3	FACETS	1	0.943	1	0.564	0.495	0.638	CLONAL	1	TRUE	1	0.17	3		407	905	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0006037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	561	552	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.653603816285019	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.653603816285019	2		552	788	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0006037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	158	275	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.653603816285019	2		275	353	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439526	220439526	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	330	480	0	ENST00000243786.2:c.379A>G	p.Thr127Ala	p.T127A	ENST00000243786	NM_002191.3	127	Act/Gct	2/2	1	2	FACETS	0.986	0.934	1	0.986	0.934	1	CLONAL	1	TRUE	1	0.653603816285019	2		480	1024	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944379	76944379	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	194	208	0	ENST00000373344.5:c.526C>T	p.Gln176Ter	p.Q176*	ENST00000373344	NM_000489.3	176	Caa/Taa	7/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.653603816285019	1		208	278	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006052-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	91	261	0	ENST00000397752.3:c.3028G>T	p.Asp1010Tyr	p.D1010Y	ENST00000397752	NM_000245.2	1010	Gat/Tat	14/21	0.30318472989119	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	2	TRUE	0	0.31	2		261	293	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1555525429	NA	P-0006052-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	424	441	0	ENST00000269305.4:c.782+1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			NA	2	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.31	2		441	1160	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341980	8341980	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0006052-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	31	237	0	ENST00000356435.5:c.4662-2A>G		p.X1554_splice	ENST00000356435		1554			0.294158520344387	3	FACETS	0.828	0.672	1	0.276	0.224	0.335	CLONAL	1	TRUE	0	0.31	3		237	279	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118339	17118345	+	frameshift_variant	Frame_Shift_Del	DEL	CCACATC	CCACATC	-	novel	NA	P-0006052-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	213	508	0	ENST00000285071.4:c.1492_1498del	p.Asp498TrpfsTer13	p.D498Wfs*13	ENST00000285071	NM_144997.5	498	GATGTGGtg/tg	13/14	0.234499654940743	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.31	1		508	969	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2969709	2969709	+	splice_acceptor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0006052-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	223	491	0	ENST00000396946.4:c.1571-1del		p.X524_splice	ENST00000396946	NM_032415.4	524			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.31	2		491	1210	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29563024	29563024	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006052-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	98	460	0	ENST00000356175.3:c.3960del	p.Val1321TrpfsTer6	p.V1321Wfs*6	ENST00000356175	NM_000267.3	1320	gAa/ga	29/57	0.234499654940743	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.31	1		460	487	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0006067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	129	194	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.287816225056284	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	1	0.287816225056284	3		194	472	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441204	52441204	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	103	499	0	ENST00000460680.1:c.566A>T	p.Tyr189Phe	p.Y189F	ENST00000460680	NM_004656.3	189	tAc/tTc	7/17	0.287816225056284	3	FACETS	0.935	0.835	1	0.467	0.417	0.52	CLONAL	1	TRUE	1	0.287816225056284	3		499	876	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870837	12870837	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	84	323	0	ENST00000228872.4:c.64G>T	p.Glu22Ter	p.E22*	ENST00000228872	NM_004064.3	22	Gag/Tag	1/3	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.287816225056284	2		323	470	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178466	56178473	+	frameshift_variant	Frame_Shift_Del	DEL	GTAACTTT	GTAACTTT	A	novel	NA	P-0006067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	105	605	0	ENST00000399503.3:c.3439_3446delinsA	p.Val1147IlefsTer23	p.V1147Ifs*23	ENST00000399503	NM_005921.1	1147	GTAACTTTt/At	14/20	1	2	FACETS	0.895	0.802	0.995	0.895	0.802	0.995	CLONAL	1	TRUE	1	0.287816225056284	2		605	815	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	94	221	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.819	0.729	0.915	0.819	0.729	0.915	CLONAL	1	TRUE	1	0.343030474206323	2		222	669	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0006076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	101	648	1	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.769	0.687	0.856	0.769	0.687	0.856	SUBCLONAL	1	TRUE	1	0.343030474206323	2		649	766	SUCCESS
APC	324	MSKCC	GRCh37	5	112170822	112170822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1114167575	NA	P-0006076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	121	667	0	ENST00000257430.4:c.1918C>T	p.Arg640Trp	p.R640W	ENST00000257430	NM_000038.5	640	Cgg/Tgg	15/16	1	2	FACETS	0.946	0.855	1	0.946	0.855	1	CLONAL	1	TRUE	1	0.343030474206323	2		667	746	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114799786	114799786	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0006076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	160	724	0	ENST00000543371.1:c.453T>A	p.Tyr151Ter	p.Y151*	ENST00000543371	NM_001198531.1	151	taT/taA	5/14	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.343030474206323	2		724	860	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438663	49438663	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	146	506	0	ENST00000301067.7:c.4827C>A	p.His1609Gln	p.H1609Q	ENST00000301067	NM_003482.3	1609	caC/caA	19/54	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.343030474206323	2		506	687	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627356	37627356	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1035682276	NA	P-0006076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	138	745	0	ENST00000447079.4:c.1271C>A	p.Pro424His	p.P424H	ENST00000447079	NM_015083.1	424	cCt/cAt	2/14	1	2	FACETS	0.999	0.91	1	0.999	0.91	1	CLONAL	1	TRUE	1	0.343030474206323	2		745	805	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430385	47430385	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs947894890	NA	P-0006076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	161	705	1	ENST00000377045.4:c.1660C>T	p.Arg554Trp	p.R554W	ENST00000377045	NM_001654.4	554	Cgg/Tgg	15/16	0.140985943659778	0	FACETS	0.715	0.656	0.776			1	INDETERMINATE	1	TRUE	0	0.343030474206323	0		706	863	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645300	67645300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	135	573	0	ENST00000264010.4:c.566del	p.Pro189LeufsTer33	p.P189Lfs*33	ENST00000264010	NM_006565.3	189	Cct/ct	3/12	0.323162251848896	3	FACETS	1	0.969	1	0.573	0.521	0.628	CLONAL	1	TRUE	1	0.343030474206323	3		573	804	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584801	48584823	+	frameshift_variant	Frame_Shift_Del	DEL	TATGCCGCCCCATCCCGGACATT	TATGCCGCCCCATCCCGGACATT	-	novel	NA	P-0006076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	38	568	0	ENST00000342988.3:c.879_901del	p.Met294LeufsTer6	p.M294Lfs*6	ENST00000342988	NM_005359.5	293	ccTATGCCGCCCCATCCCGGACATTac/ccac	7/12	0.343030474206323	1	FACETS	0.324	0.267	0.387	0.324	0.267	0.387	SUBCLONAL	1	TRUE	0	0.343030474206323	1		568	567	SUCCESS
APC	324	MSKCC	GRCh37	5	112174182	112174185	+	frameshift_variant	Frame_Shift_Del	DEL	TAAA	TAAA	-	novel	NA	P-0006076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	133	608	0	ENST00000257430.4:c.2893_2896del	p.Asn965ValfsTer14	p.N965Vfs*14	ENST00000257430	NM_000038.5	964	tTAAAt/tt	16/16	1	2	FACETS	0.955	0.868	1	0.955	0.868	1	CLONAL	1	TRUE	1	0.343030474206323	2		608	812	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412233	139412233	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs753964476	NA	P-0006077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	460	590	0	ENST00000277541.6:c.1412T>C	p.Ile471Thr	p.I471T	ENST00000277541	NM_017617.3	471	aTt/aCt	8/34	0.666852686617768	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.666852686617768	1		590	873	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675391	241675391	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1471	363	501	1	ENST00000366560.3:c.431G>C	p.Gly144Ala	p.G144A	ENST00000366560	NM_000143.3	144	gGa/gCa	4/10	0.244381099277349	6	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.666852686617768	6		502	1834	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164794	106164794	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1022416496	NA	P-0006077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	740	422	0	ENST00000380013.4:c.3662G>A	p.Cys1221Tyr	p.C1221Y	ENST00000380013	NM_001127208.2	1221	tGt/tAt	6/11	0.666852686617768	2	FACETS	0.968	0.943	0.994	0.968	0.943	0.994	CLONAL	2	TRUE	0	0.666852686617768	2		422	1146	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041170	180041170	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	390	576	0	ENST00000261937.6:c.3229C>G	p.Pro1077Ala	p.P1077A	ENST00000261937	NM_182925.4	1077	Ccc/Gcc	24/30	1	2	FACETS	0.997	0.949	1	0.997	0.949	1	CLONAL	1	TRUE	1	0.666852686617768	2		576	1173	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578378	7578395	+	inframe_deletion	In_Frame_Del	DEL	ATCTGAGCAGCGCTCATG	ATCTGAGCAGCGCTCATG	-	novel	NA	P-0006077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	656	369	2	ENST00000269305.4:c.535_552del	p.His179_Asp184del	p.H179_D184del	ENST00000269305	NM_001126112.2	179	CATGAGCGCTGCTCAGAT/-	5/11	0.666852686617768	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.666852686617768	2		371	967	SUCCESS
APC	324	MSKCC	GRCh37	5	112173968	112173968	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs199740875	NA	P-0006084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	227	333	1	ENST00000257430.4:c.2677G>T	p.Glu893Ter	p.E893*	ENST00000257430	NM_000038.5	893	Gaa/Taa	16/16	0.639174286700344	2	FACETS	0.987	0.939	1	0.987	0.939	1	CLONAL	2	TRUE	0	0.639174286700344	2		334	360	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221995	1221995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201090	NA	P-0006084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	455	593	1	ENST00000326873.7:c.910C>T	p.Arg304Trp	p.R304W	ENST00000326873	NM_000455.4	304	Cgg/Tgg	7/10	0.639174286700344	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.639174286700344	2		594	667	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235442	235442	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	309	414	0	ENST00000264932.6:c.1248C>A	p.Asn416Lys	p.N416K	ENST00000264932	NM_004168.2	416	aaC/aaA	9/15	0.639174286700344	5	FACETS	0.815	0.768	0.863	0.543	0.512	0.575	CLONAL	2	TRUE	2	0.639174286700344	5		414	1162	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37876039	37876039	+	splice_acceptor_variant	In_Frame_Del	SNP	G	G	T	novel	NA	P-0006084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	472	595	0	ENST00000269571.5:c.1899-1G>T		p.C634_S649del	ENST00000269571		634			0.594590391683306	4	FACETS	0.995	0.952	1	0.995	0.952	1	CLONAL	2	TRUE	2	0.639174286700344	4		595	1217	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144059	11144059	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	544	623	1	ENST00000358026.2:c.3640A>T	p.Ile1214Phe	p.I1214F	ENST00000358026	NM_001128849.1	1214	Atc/Ttc	26/36	0.639174286700344	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.639174286700344	2		624	851	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986863	36986872	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGGCACCC	GCGGGCACCC	-	novel	NA	P-0006084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	149	120	0	ENST00000354822.5:c.817_826del	p.Gly273SerfsTer19	p.G273Sfs*19	ENST00000354822	NM_001079668.2	273	GGGTGCCCGCag/ag	3/3	0.639174286700344	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.639174286700344	3		120	257	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098980	178098982	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	novel	NA	P-0006084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	128	229	0	ENST00000397062.3:c.63_65del	p.Asp21_Ile22delinsGlu	p.D21_I22delinsE	ENST00000397062	NM_006164.4	21	gaCATa/gaa	2/5	0.639174286700344	3	FACETS	0.861	0.792	0.93	0.861	0.792	0.93	CLONAL	2	TRUE	1	0.639174286700344	3		229	307	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339175	65339175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180823763	NA	P-0006108-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	43	353	0	ENST00000342505.4:c.361G>A	p.Asp121Asn	p.D121N	ENST00000342505	NM_002227.2	121	Gac/Aac	5/25	1	2	FACETS	0.956	0.799	1	0.956	0.799	1	CLONAL	1	TRUE	1	0.15	2		353	600	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495537	56495537	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006108-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	64	374	0	ENST00000267101.3:c.3727C>G	p.Leu1243Val	p.L1243V	ENST00000267101	NM_001982.3	1243	Ctc/Gtc	28/28	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.15	2		374	699	SUCCESS
APC	324	MSKCC	GRCh37	5	112173626	112173626	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006113-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	290	407	0	ENST00000257430.4:c.2335T>G	p.Leu779Val	p.L779V	ENST00000257430	NM_000038.5	779	Tta/Gta	16/16	0.396556130107882	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.396556130107882	3		407	794	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0006114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	189	531	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.883	0.816	0.951	0.883	0.816	0.951	CLONAL	1	TRUE	1	0.487776300181345	2		531	878	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779782	3779782	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	220	300	0	ENST00000262367.5:c.5266C>T	p.Gln1756Ter	p.Q1756*	ENST00000262367	NM_004380.2	1756	Cag/Tag	31/31	1	2	FACETS	0.92	0.856	0.985	0.92	0.856	0.985	CLONAL	1	TRUE	1	0.487776300181345	2		300	981	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129620	47129623	+	frameshift_variant	Frame_Shift_Del	DEL	AGGT	AGGT	-	novel	NA	P-0006114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	318	387	0	ENST00000409792.3:c.5257_5260del	p.Thr1753ValfsTer14	p.T1753Vfs*14	ENST00000409792	NM_014159.6	1753	ACCTgt/gt	10/21	1	2	FACETS	0.882	0.83	0.934	0.882	0.83	0.934	CLONAL	1	TRUE	1	0.487776300181345	2		387	1479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0006127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	233	552	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.228069117342479	2	FACETS	0.848	0.792	0.907	0.848	0.792	0.907	CLONAL	2	TRUE	0	0.29	2		552	947	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541181	187541181	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1350200944	NA	P-0006127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	69	439	0	ENST00000441802.2:c.6559T>C	p.Tyr2187His	p.Y2187H	ENST00000441802	NM_005245.3	2187	Tac/Cac	10/27	1	2	FACETS	0.667	0.581	0.761	0.667	0.581	0.761	SUBCLONAL	1	TRUE	1	0.29	2		439	713	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541193	187541193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	79	493	0	ENST00000441802.2:c.6547G>A	p.Glu2183Lys	p.E2183K	ENST00000441802	NM_005245.3	2183	Gaa/Aaa	10/27	1	2	FACETS	0.71	0.624	0.803	0.71	0.624	0.803	SUBCLONAL	1	TRUE	1	0.29	2		493	767	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541310	187541310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	144	618	0	ENST00000441802.2:c.6430G>A	p.Asp2144Asn	p.D2144N	ENST00000441802	NM_005245.3	2144	Gac/Aac	10/27	1	2	FACETS	0.925	0.842	1	0.925	0.842	1	CLONAL	1	TRUE	1	0.29	2		618	1074	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226486	1226486	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1218	77	876	1	ENST00000326873.7:c.1142G>T	p.Gly381Val	p.G381V	ENST00000326873	NM_000455.4	381	gGa/gTa	9/10	0.215237147025311	3	FACETS	0.47	0.41	0.534			1	SUBCLONAL	1	TRUE	NA	0.29	3		877	1295	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650319	48650319	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	161	371	0	ENST00000376670.3:c.289G>C	p.Ala97Pro	p.A97P	ENST00000376670	NM_002049.3	97	Gcc/Ccc	3/6	0.282443517486231	2	FACETS	0.842	0.775	0.912			1	CLONAL	2	TRUE	NA	0.29	2		371	659	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541569	187541589	+	inframe_deletion	In_Frame_Del	DEL	ATGTTCCTCTGTCACTTCTAC	ATGTTCCTCTGTCACTTCTAC	-	novel	NA	P-0006127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	115	534	0	ENST00000441802.2:c.6151_6171del	p.Val2051_His2057del	p.V2051_H2057del	ENST00000441802	NM_005245.3	2051	GTAGAAGTGACAGAGGAACAT/-	10/27	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.29	2		534	740	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411888	116411907	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTCTCTGTTTTAAGATCTG	TCTCTCTGTTTTAAGATCTG	-	novel	NA	P-0006127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	188	334	0	ENST00000397752.3:c.2888-15_2892del		p.X963_splice	ENST00000397752	NM_000245.2	963		14/21	0.215237147025311	3	FACETS	1	0.96	1			1	CLONAL	3	TRUE	NA	0.29	3		334	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	143	522	0	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	0.21935658074932	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.21935658074932	2		522	550	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729094	66729099	+	inframe_deletion	In_Frame_Del	DEL	TGGAGA	TGGAGA	-	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	77	440	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	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.21935658074932	2		440	685	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971138	21971138	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs760640852	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	40	102	0	ENST00000304494.5:c.220G>T	p.Asp74Tyr	p.D74Y	ENST00000304494	NM_000077.4	74	Gac/Tac	2/3	0.21935658074932	2	FACETS	0.894	0.758	1	1	0.951	1	CLONAL	3	TRUE	0	0.21935658074932	2		102	136	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163373	47163373	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	67	339	0	ENST00000409792.3:c.2753C>G	p.Ser918Ter	p.S918*	ENST00000409792	NM_014159.6	918	tCa/tGa	3/21	0.165362407023499	2	FACETS	1	0.94	1	0.572	0.498	0.652	CLONAL	1	TRUE	0	0.21935658074932	2		339	534	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119789	70119789	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	52	468	0	ENST00000245479.2:c.791G>C	p.Arg264Thr	p.R264T	ENST00000245479	NM_000346.3	264	aGa/aCa	3/3	0.21935658074932	3	FACETS	0.899	0.765	1	0.45	0.382	0.524	CLONAL	1	TRUE	1	0.21935658074932	3		468	585	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344314	118344314	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	29	226	0	ENST00000534358.1:c.2440C>T	p.Gln814Ter	p.Q814*	ENST00000534358	NM_005933.3	814	Cag/Tag	3/36	0.197447041318138	3	FACETS	0.878	0.706	1	0.439	0.353	0.537	CLONAL	1	TRUE	1	0.21935658074932	3		226	334	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097687	27097687	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	71	454	0	ENST00000324856.7:c.3276G>C	p.Leu1092Phe	p.L1092F	ENST00000324856	NM_006015.4	1092	ttG/ttC	12/20	0.218518591976082	3	FACETS	0.916	0.799	1	0.458	0.399	0.522	CLONAL	1	TRUE	1	0.21935658074932	3		454	784	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259249	16259249	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	33	266	0	ENST00000375759.3:c.6514G>C	p.Glu2172Gln	p.E2172Q	ENST00000375759	NM_015001.2	2172	Gag/Cag	11/15	0.218518591976082	3	FACETS	1	0.854	1	0.527	0.43	0.635	CLONAL	1	TRUE	1	0.21935658074932	3		266	317	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874596	155874596	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	89	517	0	ENST00000368323.3:c.164-1G>A		p.X55_splice	ENST00000368323	NM_006912.5	55			0.21935658074932	4	FACETS	0.9	0.796	1	0.45	0.398	0.506	CLONAL	1	TRUE	2	0.21935658074932	4		517	1099	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956187	175956187	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	121	483	0	ENST00000367669.3:c.2025G>T	p.Leu675Phe	p.L675F	ENST00000367669	NM_022457.5	675	ttG/ttT	18/20	0.21935658074932	4	FACETS	1	0.983	1	0.717	0.647	0.791	CLONAL	1	TRUE	2	0.21935658074932	4		483	938	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736256	243736256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	72	452	0	ENST00000263826.5:c.791C>T	p.Ser264Phe	p.S264F	ENST00000263826	NM_005465.4	264	tCc/tTc	8/13	0.21935658074932	4	FACETS	0.968	0.844	1	0.484	0.422	0.551	CLONAL	1	TRUE	2	0.21935658074932	4		452	827	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455312	29455312	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	38	257	0	ENST00000389048.3:c.2490G>A	p.Met830Ile	p.M830I	ENST00000389048	NM_004304.4	830	atG/atA	15/29	NA	2	FACETS	1	0.867	1			1	INDETERMINATE	1	TRUE	NA	0.21935658074932	2		257	329	SUCCESS
ALK	238	MSKCC	GRCh37	2	29541192	29541192	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	64	506	1	ENST00000389048.3:c.1625C>A	p.Pro542Gln	p.P542Q	ENST00000389048	NM_004304.4	542	cCg/cAg	8/29	NA	2	FACETS	0.799	0.691	0.917			1	INDETERMINATE	1	TRUE	NA	0.21935658074932	2		507	730	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47643501	47643501	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs63750778	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	79	565	0	ENST00000233146.2:c.1009C>G	p.Gln337Glu	p.Q337E	ENST00000233146	NM_000251.2	337	Caa/Gaa	6/16	0.218518591976082	3	FACETS	0.945	0.83	1	0.472	0.415	0.535	CLONAL	1	TRUE	1	0.21935658074932	3		565	846	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738248	190738248	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	45	253	0	ENST00000441310.2:c.2500G>C	p.Glu834Gln	p.E834Q	ENST00000441310	NM_000534.4	834	Gaa/Caa	12/13	0.203218279274449	4	FACETS	0.807	0.677	0.951	0.403	0.338	0.476	CLONAL	1	TRUE	2	0.21935658074932	4		253	620	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149928	202149928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	48	427	0	ENST00000358485.4:c.1369G>A	p.Asp457Asn	p.D457N	ENST00000358485	NM_001080125.1	457	Gac/Aac	8/9	0.203218279274449	4	FACETS	0.762	0.643	0.894	0.381	0.321	0.447	SUBCLONAL	1	TRUE	2	0.21935658074932	4		427	700	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932898	49932898	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	75	589	0	ENST00000296474.3:c.3046G>C	p.Asp1016His	p.D1016H	ENST00000296474	NM_002447.2	1016	Gac/Cac	13/20	0.165362407023499	2	FACETS	1	0.93	1	0.545	0.478	0.618	CLONAL	1	TRUE	0	0.21935658074932	2		589	627	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940549	49940549	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1208496017	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	54	565	1	ENST00000296474.3:c.494C>T	p.Ser165Leu	p.S165L	ENST00000296474	NM_002447.2	165	tCa/tTa	1/20	0.165362407023499	2	FACETS	0.826	0.705	0.959	0.413	0.352	0.48	CLONAL	1	TRUE	0	0.21935658074932	2		566	596	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391177	89391177	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	69	282	0	ENST00000336596.2:c.1243G>T	p.Val415Leu	p.V415L	ENST00000336596	NM_005233.5	415	Gtg/Ttg	5/17	0.165362407023499	2	FACETS	1	0.972	1	0.723	0.632	0.821	CLONAL	1	TRUE	0	0.21935658074932	2		282	435	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880945	134880945	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	87	451	0	ENST00000398015.3:c.1508T>C	p.Val503Ala	p.V503A	ENST00000398015	NM_004441.4	503	gTg/gCg	7/16	0.134101855921524	3	FACETS	0.758	0.672	0.849			1	SUBCLONAL	2	TRUE	NA	0.21935658074932	3		451	581	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911617	134911617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1208037312	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	61	373	0	ENST00000398015.3:c.2082G>A	p.Met694Ile	p.M694I	ENST00000398015	NM_004441.4	694	atG/atA	11/16	0.134101855921524	3	FACETS	1	0.897	1			1	CLONAL	1	TRUE	NA	0.21935658074932	3		373	589	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951994	178951994	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	97	433	0	ENST00000263967.3:c.3049G>C	p.Asp1017His	p.D1017H	ENST00000263967	NM_006218.2	1017	Gat/Cat	21/21	0.1830910769094	4	FACETS	1	0.97	1	0.63	0.561	0.704	CLONAL	1	TRUE	2	0.21935658074932	4		433	856	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503747	186503747	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	153	624	0	ENST00000323963.5:c.424C>G	p.Arg142Gly	p.R142G	ENST00000323963		142	Cga/Gga	5/11	0.1830910769094	4	FACETS	0.772	0.705	0.843	0.772	0.705	0.843	SUBCLONAL	2	TRUE	2	0.21935658074932	4		624	1101	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497194	149497194	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	139	360	1	ENST00000261799.4:c.3124C>A	p.Pro1042Thr	p.P1042T	ENST00000261799	NM_002609.3	1042	Ccc/Acc	22/23	0.21935658074932	2	FACETS	0.889	0.815	0.966	1	0.984	1	CLONAL	3	TRUE	0	0.21935658074932	2		361	475	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032171	26032171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	184	671	0	ENST00000244661.2:c.118C>T	p.His40Tyr	p.H40Y	ENST00000244661	NM_003537.3	40	Cac/Tac	1/1	0.198989006199055	3	FACETS	1	0.944	1	0.685	0.632	0.74	CLONAL	2	TRUE	0	0.21935658074932	3		671	906	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206891	162206891	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	50	379	0	ENST00000366898.1:c.784G>C	p.Asp262His	p.D262H	ENST00000366898	NM_004562.2	262	Gac/Cac	7/12	0.21935658074932	3	FACETS	0.827	0.701	0.965	0.413	0.35	0.483	CLONAL	1	TRUE	1	0.21935658074932	3		379	612	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14017058	14017058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1435454184	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	57	354	0	ENST00000405192.2:c.229G>A	p.Glu77Lys	p.E77K	ENST00000405192	NM_001163147.1	77	Gaa/Aaa	5/12	0.203218279274449	4	FACETS	0.854	0.731	0.988	0.427	0.365	0.494	CLONAL	1	TRUE	2	0.21935658074932	4		354	742	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450274	50450274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	48	451	0	ENST00000331340.3:c.458C>T	p.Ser153Leu	p.S153L	ENST00000331340	NM_006060.4	153	tCa/tTa	5/8	0.203218279274449	4	FACETS	0.74	0.624	0.868	0.37	0.312	0.434	SUBCLONAL	1	TRUE	2	0.21935658074932	4		451	721	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381564	81381564	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	96	372	0	ENST00000222390.5:c.497G>T	p.Ser166Ile	p.S166I	ENST00000222390	NM_000601.4	166	aGc/aTc	5/18	0.1830910769094	4	FACETS	0.76	0.677	0.848	0.76	0.677	0.848	SUBCLONAL	2	TRUE	2	0.21935658074932	4		372	702	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619249	43619249	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	44	380	0	ENST00000355710.3:c.2932G>C	p.Glu978Gln	p.E978Q	ENST00000355710	NM_020975.4	978	Gag/Cag	17/20	0.165362407023499	2	FACETS	0.906	0.76	1	0.453	0.38	0.533	CLONAL	1	TRUE	0	0.21935658074932	2		380	443	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161487	2161487	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1290587925	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	45	532	0	ENST00000434045.2:c.40G>A	p.Glu14Lys	p.E14K	ENST00000434045	NM_001127598.1	14	Gag/Aag	2/5	1	2	FACETS	0.886	0.745	1	0.886	0.745	1	CLONAL	1	TRUE	1	0.21935658074932	2		532	463	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195876	102195876	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	104	627	0	ENST00000263464.3:c.636G>C	p.Leu212Phe	p.L212F	ENST00000263464	NM_001165.4	212	ttG/ttC	2/9	0.197447041318138	3	FACETS	0.988	0.883	1	0.494	0.441	0.55	CLONAL	1	TRUE	1	0.21935658074932	3		627	1065	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344204	118344204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	37	334	0	ENST00000534358.1:c.2330C>T	p.Ser777Phe	p.S777F	ENST00000534358	NM_005933.3	777	tCt/tTt	3/36	0.197447041318138	3	FACETS	0.683	0.562	0.819	0.342	0.281	0.41	SUBCLONAL	1	TRUE	1	0.21935658074932	3		334	548	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644406	18644406	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	111	472	2	ENST00000266497.5:c.2584G>T	p.Gly862Cys	p.G862C	ENST00000266497		862	Ggc/Tgc	18/31	NA	2	FACETS	0.775	0.698	0.856			1	INDETERMINATE	2	TRUE	NA	0.21935658074932	2		474	653	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495711	56495711	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	57	325	0	ENST00000267101.3:c.3901C>G	p.Gln1301Glu	p.Q1301E	ENST00000267101	NM_001982.3	1301	Cag/Gag	28/28	0.21935658074932	4	FACETS	1	0.934	1	0.579	0.497	0.669	CLONAL	1	TRUE	2	0.21935658074932	4		325	547	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884834	111884834	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs181079548	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	82	569	1	ENST00000341259.2:c.923G>A	p.Arg308Gln	p.R308Q	ENST00000341259	NM_005475.2	308	cGa/cAa	4/8	0.21935658074932	4	FACETS	0.977	0.86	1	0.489	0.43	0.552	CLONAL	1	TRUE	2	0.21935658074932	4		570	933	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32932056	32932056	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	46	391	0	ENST00000380152.3:c.7795G>C	p.Glu2599Gln	p.E2599Q	ENST00000380152		2599	Gaa/Caa	16/27	0.175610628465182	2	FACETS	0.648	0.545	0.763	0.324	0.272	0.382	SUBCLONAL	1	TRUE	0	0.21935658074932	2		391	647	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527662	103527662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	87	345	0	ENST00000355739.4:c.2970G>T	p.Gln990His	p.Q990H	ENST00000355739	NM_000123.3	990	caG/caT	15/15	0.21935658074932	3	FACETS	1	0.978	1	0.743	0.659	0.833	CLONAL	1	TRUE	1	0.21935658074932	3		345	592	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007752	45007752	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	87	411	1	ENST00000558401.1:c.199G>T	p.Glu67Ter	p.E67*	ENST00000558401	NM_004048.2	67	Gaa/Taa	2/4	1	2	FACETS	0.951	0.841	1	0.951	0.841	1	CLONAL	1	TRUE	1	0.21935658074932	2		412	834	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129378	2129378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368095502	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	37	484	1	ENST00000219476.3:c.3233G>A	p.Arg1078Gln	p.R1078Q	ENST00000219476	NM_000548.3	1078	cGg/cAg	28/42	1	2	FACETS	0.671	0.552	0.803	0.671	0.552	0.803	SUBCLONAL	1	TRUE	1	0.21935658074932	2		485	503	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923342	9923342	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397514557	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	69	566	0	ENST00000330684.3:c.1945C>G	p.Leu649Val	p.L649V	ENST00000330684	NM_001134407.1	649	Ctg/Gtg	9/13	1	2	FACETS	0.997	0.868	1	0.997	0.868	1	CLONAL	1	TRUE	1	0.21935658074932	2		566	631	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029521	14029521	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	42	281	1	ENST00000311895.7:c.1732G>T	p.Val578Leu	p.V578L	ENST00000311895	NM_005236.2	578	Gtg/Ttg	8/11	0.21935658074932	3	FACETS	1	0.876	1			1	CLONAL	1	TRUE	NA	0.21935658074932	3		282	402	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56875633	56875633	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs751390416	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	78	494	0	ENST00000308159.5:c.2237C>G	p.Ser746Ter	p.S746*	ENST00000308159	NM_014669.4	746	tCa/tGa	21/22	1	2	FACETS	0.849	0.745	0.961	0.849	0.745	0.961	CLONAL	1	TRUE	1	0.21935658074932	2		494	838	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346246	89346246	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	88	384	0	ENST00000301030.4:c.6704C>A	p.Pro2235Gln	p.P2235Q	ENST00000301030	NM_001256183.1	2235	cCg/cAg	9/13	1	2	FACETS	0.841	0.748	0.94	1	0.983	1	CLONAL	2	TRUE	1	0.21935658074932	2		384	477	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347050	89347050	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	80	573	0	ENST00000301030.4:c.5900C>T	p.Ser1967Phe	p.S1967F	ENST00000301030	NM_001256183.1	1967	tCt/tTt	9/13	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.21935658074932	2		573	642	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011209	12011209	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	43	311	0	ENST00000353533.5:c.616G>T	p.Gly206Cys	p.G206C	ENST00000353533	NM_003010.3	206	Ggc/Tgc	5/11	0.21935658074932	2	FACETS	0.834	0.698	0.985	0.417	0.349	0.493	CLONAL	1	TRUE	0	0.21935658074932	2		311	470	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965093	15965093	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	42	261	0	ENST00000268712.3:c.5503G>C	p.Asp1835His	p.D1835H	ENST00000268712	NM_006311.3	1835	Gat/Cat	37/46	0.21935658074932	2	FACETS	0.927	0.775	1	0.464	0.387	0.548	CLONAL	1	TRUE	0	0.21935658074932	2		261	413	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353809	40353809	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	100	577	1	ENST00000293328.3:c.2311G>T	p.Glu771Ter	p.E771*	ENST00000293328	NM_012448.3	771	Gag/Tag	19/19	0.21935658074932	3	FACETS	1	0.93	1	0.529	0.471	0.59	CLONAL	1	TRUE	1	0.21935658074932	3		578	957	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245326	41245326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357051	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	64	490	0	ENST00000357654.3:c.2222C>T	p.Ser741Phe	p.S741F	ENST00000357654	NM_007294.3	741	tCt/tTt	10/23	0.21935658074932	3	FACETS	0.788	0.681	0.904	0.394	0.34	0.452	CLONAL	1	TRUE	1	0.21935658074932	3		490	822	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733240	74733240	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	66	402	0	ENST00000359995.5:c.3G>A	p.Met1?	p.M1?	ENST00000359995	NM_001195427.1	1	atG/atA	1/3	0.21935658074932	3	FACETS	1	0.889	1	0.514	0.445	0.588	CLONAL	1	TRUE	1	0.21935658074932	3		402	650	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584530	48584530	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	112	409	1	ENST00000342988.3:c.703G>A	p.Glu235Lys	p.E235K	ENST00000342988	NM_005359.5	235	Gaa/Aaa	6/12	0.21935658074932	2	FACETS	0.915	0.826	1	0.915	0.826	1	CLONAL	2	TRUE	0	0.21935658074932	2		410	558	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597387	10597387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150193881	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	39	451	0	ENST00000171111.5:c.1816G>A	p.Val606Met	p.V606M	ENST00000171111	NM_203500.1	606	Gtg/Atg	6/6	0.197447041318138	3	FACETS	0.547	0.452	0.653	0.273	0.226	0.327	SUBCLONAL	1	TRUE	1	0.21935658074932	3		451	722	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054544	13054544	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	89	743	0	ENST00000316448.5:c.1071G>A	p.Met357Ile	p.M357I	ENST00000316448	NM_004343.3	357	atG/atA	9/9	0.197447041318138	3	FACETS	0.827	0.731	0.93	0.413	0.365	0.465	CLONAL	1	TRUE	1	0.21935658074932	3		743	1089	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054665	13054665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150264068	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	98	829	0	ENST00000316448.5:c.1192G>A	p.Glu398Lys	p.E398K	ENST00000316448	NM_004343.3	398	Gag/Aag	9/9	0.197447041318138	3	FACETS	0.896	0.797	1	0.448	0.398	0.501	CLONAL	1	TRUE	1	0.21935658074932	3		829	1107	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292577	15292577	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	65	418	2	ENST00000263388.2:c.2602G>T	p.Val868Leu	p.V868L	ENST00000263388	NM_000435.2	868	Gtg/Ttg	17/33	0.175610628465182	2	FACETS	1	0.968	1	0.696	0.605	0.793	CLONAL	1	TRUE	0	0.21935658074932	2		420	426	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624805	9624805	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	41	326	0	ENST00000353224.5:c.172T>A	p.Cys58Ser	p.C58S	ENST00000353224	NM_177990.2	58	Tgc/Agc	3/10	1	2	FACETS	0.799	0.665	0.947	0.799	0.665	0.947	CLONAL	1	TRUE	1	0.21935658074932	2		326	468	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899042	40899042	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	92	572	1	ENST00000373198.4:c.2228C>A	p.Thr743Asn	p.T743N	ENST00000373198	NM_133170.3	743	aCc/aAc	14/32	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.21935658074932	2		573	727	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41554419	41554419	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	129	437	0	ENST00000263253.7:c.3505G>C	p.Glu1169Gln	p.E1169Q	ENST00000263253	NM_001429.3	1169	Gag/Cag	19/31	NA	2	FACETS	0.87	0.79	0.953			1	INDETERMINATE	2	TRUE	NA	0.21935658074932	2		437	676	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41554476	41554476	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	128	441	0	ENST00000263253.7:c.3562G>C	p.Asp1188His	p.D1188H	ENST00000263253	NM_001429.3	1188	Gat/Cat	19/31	NA	2	FACETS	0.883	0.802	0.968			1	INDETERMINATE	2	TRUE	NA	0.21935658074932	2		441	661	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41554499	41554499	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	104	362	0	ENST00000263253.7:c.3585G>C	p.Gln1195His	p.Q1195H	ENST00000263253	NM_001429.3	1195	caG/caC	19/31	NA	2	FACETS	0.888	0.798	0.983			1	INDETERMINATE	2	TRUE	NA	0.21935658074932	2		362	534	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0006151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	2376	386	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.302415393113567	22	FACETS	0.975	0.962	0.988			1	CLONAL	19	TRUE	NA	0.33	22		386	3342	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782620	NA	P-0006151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	188	572	2	ENST00000269305.4:c.427G>A	p.Val143Met	p.V143M	ENST00000269305	NM_001126112.2	143	Gtg/Atg	5/11	0.205831081705847	2	FACETS	1	0.99	1	0.733	0.679	0.789	CLONAL	1	TRUE	0	0.33	2		574	777	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161293455	161293455	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	64	446	0	ENST00000367975.2:c.72C>G	p.Ile24Met	p.I24M	ENST00000367975	NM_003001.3	24	atC/atG	2/6	0.302415393113567	4	FACETS	0.453	0.39	0.521	0.151	0.13	0.174	SUBCLONAL	1	TRUE	1	0.33	4		446	1140	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212615430	212615430	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0006151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	68	495	0	ENST00000342788.4:c.557-1G>T		p.X186_splice	ENST00000342788	NM_005235.2	186			0.302415393113567	3	FACETS	0.758	0.66	0.865	0.379	0.33	0.433	SUBCLONAL	1	TRUE	1	0.33	3		495	633	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590660	189590660	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	53	425	0	ENST00000264731.3:c.1225G>C	p.Glu409Gln	p.E409Q	ENST00000264731	NM_003722.4	409	Gag/Cag	10/14	0.158591806201948	5	FACETS	0.688	0.586	0.801	0.229	0.195	0.267	INDETERMINATE	1	TRUE	2	0.33	5		425	698	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165783	108165783	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1060501627	NA	P-0006151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	54	444	0	ENST00000278616.4:c.4906C>G	p.Gln1636Glu	p.Q1636E	ENST00000278616	NM_000051.3	1636	Cag/Gag	32/63	0.302415393113567	3	FACETS	0.504	0.429	0.586	0.252	0.214	0.293	SUBCLONAL	1	TRUE	1	0.33	3		444	757	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	141	260	0				ENST00000310581	NM_198253.2	-/1132			0.251511747750647	3	FACETS	0.966	0.909	1	0.966	0.909	1	INDETERMINATE	3	FALSE	0	0.595816494209077	3		260	212	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0006157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	359	307	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.607052660977071	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	FALSE	0	0.595816494209077	3		307	449	SUCCESS
ALK	238	MSKCC	GRCh37	2	29448345	29448345	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	90	777	0	ENST00000389048.3:c.3154T>A	p.Phe1052Ile	p.F1052I	ENST00000389048	NM_004304.4	1052	Ttc/Atc	19/29	0.364644266017568	0	FACETS	0.471	0.424	0.52			1	SUBCLONAL	1	FALSE	0	0.595816494209077	0		777	259	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117645576	117645576	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	122	679	0	ENST00000368508.3:c.5560G>A	p.Asp1854Asn	p.D1854N	ENST00000368508	NM_002944.2	1854	Gat/Aat	34/43	0.307287808048764	0	FACETS	0.49	0.448	0.532			1	INDETERMINATE	1	FALSE	0	0.595816494209077	0		679	338	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715647	18715647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	92	401	0	ENST00000266497.5:c.3478G>A	p.Glu1160Lys	p.E1160K	ENST00000266497		1160	Gaa/Aaa	25/31	0.581099238794938	1	FACETS	0.907	0.821	0.996	0.907	0.821	0.996	CLONAL	1	FALSE	0	0.595816494209077	1		401	239	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907453	32907453	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	46	491	0	ENST00000380152.3:c.1838T>C	p.Leu613Pro	p.L613P	ENST00000380152		613	cTa/cCa	10/27	NA	2	FACETS	0.349	0.294	0.409			1	INDETERMINATE	1	FALSE	NA	0.595816494209077	2		491	443	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244104	5244104	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1387246320	NA	P-0006157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	138	659	0	ENST00000357368.4:c.1378T>C	p.Tyr460His	p.Y460H	ENST00000357368	NM_002850.3	460	Tac/Cac	11/38	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.595816494209077	2		659	346	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791256	42791256	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	132	412	1	ENST00000575354.2:c.316C>T	p.Pro106Ser	p.P106S	ENST00000575354	NM_015125.3	106	Cca/Tca	3/20	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	FALSE	NA	0.595816494209077	2		413	302	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867041	45867041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	87	317	0	ENST00000391945.4:c.1078G>A	p.Gly360Ser	p.G360S	ENST00000391945	NM_000400.3	360	Ggc/Agc	11/23	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	FALSE	NA	0.595816494209077	2		317	212	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553332	41553332	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	155	584	0	ENST00000263253.7:c.3421T>A	p.Tyr1141Asn	p.Y1141N	ENST00000263253	NM_001429.3	1141	Tac/Aac	18/31	0.197475972870459	3	FACETS	1	0.989	1	0.747	0.69	0.805	INDETERMINATE	1	FALSE	1	0.595816494209077	3		584	452	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564575	41564575	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754552219	NA	P-0006157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	148	590	0	ENST00000263253.7:c.3997G>A	p.Val1333Met	p.V1333M	ENST00000263253	NM_001429.3	1333	Gtg/Atg	24/31	0.197475972870459	3	FACETS	0.792	0.731	0.854	0.792	0.731	0.854	INDETERMINATE	2	FALSE	1	0.595816494209077	3		590	407	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	174	260	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.791	0.739	0.843			1	INDETERMINATE	2	TRUE	NA	0.582039730011884	2		260	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0006160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	300	254	7	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.579409482548378	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.582039730011884	2		261	465	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0006160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	274	385	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.580766313262434	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.582039730011884	3		385	598	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215330	142215330	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	146	417	0	ENST00000350721.4:c.5771G>T	p.Trp1924Leu	p.W1924L	ENST00000350721	NM_001184.3	1924	tGg/tTg	34/47	0.580766313262434	3	FACETS	0.83	0.759	0.905	0.415	0.379	0.453	CLONAL	1	TRUE	1	0.582039730011884	3		417	780	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579566	7579566	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	271	334	0	ENST00000269305.4:c.121G>C	p.Asp41His	p.D41H	ENST00000269305	NM_001126112.2	41	Gat/Cat	4/11	0.579409482548378	2	FACETS	0.972	0.926	1	0.972	0.926	1	CLONAL	2	TRUE	0	0.582039730011884	2		334	479	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035169	30035169	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	595	448	0	ENST00000338641.4:c.331C>T	p.Gln111Ter	p.Q111*	ENST00000338641	NM_000268.3	111	Cag/Tag	3/16	0.582039730011884	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.582039730011884	3		448	821	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	22	221	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.415	0.32	0.527	0.415	0.32	0.527	SUBCLONAL	1	TRUE	1	0.13	2		222	815	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202158	67202158	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	50	302	0	ENST00000312629.5:c.1261C>T	p.Pro421Ser	p.P421S	ENST00000312629	NM_003952.2	421	Ccc/Tcc	14/15	1	2	FACETS	0.815	0.689	0.954	0.815	0.689	0.954	CLONAL	1	TRUE	1	0.13	2		302	944	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578453	7578455	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	novel	NA	P-0006165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	65	331	0	ENST00000269305.4:c.475_477del	p.Ala159del	p.A159del	ENST00000269305	NM_001126112.2	159	GCC/-	5/11	0.3	2	FACETS	0.857	0.74	0.984			1	CLONAL	1	TRUE	NA	0.13	2		331	1167	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0006167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	91	355	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.338402528210024	2		355	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579536	7579536	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567556930	NA	P-0006167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	135	555	1	ENST00000269305.4:c.151G>T	p.Glu51Ter	p.E51*	ENST00000269305	NM_001126112.2	51	Gaa/Taa	4/11	0.338402528210024	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.338402528210024	1		556	501	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913250	NA	P-0006167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	117	466	0	ENST00000369535.4:c.34G>C	p.Gly12Arg	p.G12R	ENST00000369535	NM_002524.4	12	Ggt/Cgt	2/7	0.338402528210024	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.338402528210024	1		466	501	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042066	14042066	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	71	493	0	ENST00000311895.7:c.2613G>C	p.Lys871Asn	p.K871N	ENST00000311895	NM_005236.2	871	aaG/aaC	11/11	0.291439513886617	1	FACETS	0.512	0.446	0.583	0.512	0.446	0.583	SUBCLONAL	1	TRUE	0	0.338402528210024	1		493	681	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688691	47688691	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	45	530	0	ENST00000347630.2:c.609C>G	p.Cys203Trp	p.C203W	ENST00000347630	NM_001007230.1	203	tgC/tgG	7/11	0.338402528210024	1	FACETS	0.296	0.248	0.35	0.296	0.248	0.35	SUBCLONAL	1	TRUE	0	0.338402528210024	1		530	746	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119712	70119768	+	inframe_deletion	In_Frame_Del	DEL	CACCACCCCCAAAACCGACGTGCAGCCGGGCAAGGCTGACCTGAAGCGAGAGGGGCG	CACCACCCCCAAAACCGACGTGCAGCCGGGCAAGGCTGACCTGAAGCGAGAGGGGCG	-	novel	NA	P-0006167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	73	557	0	ENST00000245479.2:c.715_771del	p.Thr239_Arg257del	p.T239_R257del	ENST00000245479	NM_000346.3	238	ccCACCACCCCCAAAACCGACGTGCAGCCGGGCAAGGCTGACCTGAAGCGAGAGGGGCGc/ccc	3/3	0.279018844553271	4	FACETS	0.566	0.494	0.645			1	SUBCLONAL	1	TRUE	NA	0.338402528210024	4		557	1020	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593380	67593380	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	117	403	0	ENST00000274335.5:c.2128del	p.Leu710SerfsTer5	p.L710Sfs*5	ENST00000274335		709	tCc/tc	15/15	0.193551238892623	3	FACETS	1	0.944	1	0.533	0.481	0.589	INDETERMINATE	1	TRUE	1	0.338402528210024	3		403	758	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591139	67591140	+	missense_variant	Missense_Mutation	DNP	GA	GA	CC	novel	NA	P-0006167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	119	408	0	ENST00000274335.5:c.1732_1733delinsCC	p.Asp578Pro	p.D578P	ENST00000274335		578	GAc/CCc	12/15	0.193551238892623	3	FACETS	1	0.947	1	0.537	0.484	0.592	INDETERMINATE	1	TRUE	1	0.338402528210024	3		408	766	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0006195-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	471	572	1	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.763479180515566	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.774020323034453	2		573	591	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664819	138664819	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006195-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	67	66	2	ENST00000330315.3:c.746C>A	p.Ala249Glu	p.A249E	ENST00000330315	NM_023067.3	249	gCg/gAg	1/1	0.317684726272358	6	FACETS	0.985	0.893	1	1	0.977	1	INDETERMINATE	4	TRUE	3	0.774020323034453	6		68	112	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627732	187627732	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006195-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	597	527	0	ENST00000441802.2:c.3250A>G	p.Ile1084Val	p.I1084V	ENST00000441802	NM_005245.3	1084	Ata/Gta	2/27	0.774020323034453	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.774020323034453	3		527	1013	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628340	86628340	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006195-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	375	365	0	ENST00000274376.6:c.709G>T	p.Gly237Ter	p.G237*	ENST00000274376	NM_002890.2	237	Gga/Tga	3/25	0.774020323034453	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.774020323034453	2		365	454	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339890	116339890	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006195-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	592	505	0	ENST00000397752.3:c.752A>C	p.His251Pro	p.H251P	ENST00000397752	NM_000245.2	251	cAt/cCt	2/21	0.771802972080857	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.774020323034453	3		505	1025	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889069	76889069	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006195-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	237	516	0	ENST00000373344.5:c.4941T>A	p.Asp1647Glu	p.D1647E	ENST00000373344	NM_000489.3	1647	gaT/gaA	18/35	0.774020323034453	3	FACETS	0.773	0.721	0.827	0.386	0.36	0.414	SUBCLONAL	1	TRUE	1	0.774020323034453	3		516	1099	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050846	49050846	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006195-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	230	247	0	ENST00000267163.4:c.2531del	p.Lys844SerfsTer5	p.K844Sfs*5	ENST00000267163	NM_000321.2	844	Aag/ag	25/27	0.774020323034453	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.774020323034453	2		247	296	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0006199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	165	239	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.137071302164467	3	FACETS	0.8	0.735	0.868	0.8	0.735	0.868	INDETERMINATE	2	TRUE	1	0.27	3		240	867	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777894	NA	P-0006199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	114	535	0	ENST00000361445.4:c.6644C>T	p.Ser2215Phe	p.S2215F	ENST00000361445	NM_004958.3	2215	tCt/tTt	47/58	0.255729111711692	1	FACETS	0.901	0.811	0.996	0.901	0.811	0.996	CLONAL	1	TRUE	0	0.27	1		535	811	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038416	180038416	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	248	616	0	ENST00000261937.6:c.3601C>G	p.Gln1201Glu	p.Q1201E	ENST00000261937	NM_182925.4	1201	Cag/Gag	27/30	0.228513106131141	4	FACETS	0.991	0.926	1			1	CLONAL	2	TRUE	NA	0.27	4		616	1177	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546599	9546599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	137	483	0	ENST00000353224.5:c.1423G>A	p.Val475Ile	p.V475I	ENST00000353224	NM_177990.2	475	Gtt/Att	5/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.27	2		483	848	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409901	63409901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	257	383	1	ENST00000330258.3:c.3266G>A	p.Arg1089Lys	p.R1089K	ENST00000330258	NM_152424.3	1089	aGg/aAg	2/2	0.3	2	FACETS	0.884	0.832	0.937			1	CLONAL	3	TRUE	NA	0.27	2		384	718	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164211	47164228	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	CGGACTTAAAAATAGGCA	CGGACTTAAAAATAGGCA	-	novel	NA	P-0006199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	158	284	0	ENST00000409792.3:c.1898_1915del	p.Leu633_Glu639delinsTer	p.L633_E639delins*	ENST00000409792	NM_014159.6	633	tTGCCTATTTTTAAGTCCGaa/taa	3/21	NA	2	FACETS	1	0.952	1			1	INDETERMINATE	2	TRUE	NA	0.27	2		284	560	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100762	8100762	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	82	344	0	ENST00000346208.3:c.737del	p.Gly246AlafsTer19	p.G246Afs*19	ENST00000346208		246	Ggc/gc	3/6	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.27	2		344	607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691039	NA	P-0006202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	520	387	1	ENST00000269305.4:c.919+1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			1	2	FACETS	0.924	0.896	0.951	1	0.998	1	CLONAL	2	TRUE	1	0.743463021180862	2		388	757	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851645	134851645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1395878132	NA	P-0006202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	318	468	0	ENST00000398015.3:c.1051C>T	p.Arg351Trp	p.R351W	ENST00000398015	NM_004441.4	351	Cgg/Tgg	5/16	1	2	FACETS	0.915	0.866	0.965	0.915	0.866	0.965	CLONAL	1	TRUE	1	0.743463021180862	2		468	935	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572404	41572404	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs139310551	NA	P-0006202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	307	494	0	ENST00000263253.7:c.4933C>T	p.Arg1645Ter	p.R1645*	ENST00000263253	NM_001429.3	1645	Cga/Tga	30/31	1	2	FACETS	0.772	0.728	0.817	0.772	0.728	0.817	SUBCLONAL	1	TRUE	1	0.743463021180862	2		494	1070	SUCCESS
APC	324	MSKCC	GRCh37	5	112111435	112111435	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0006202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	92	248	0	ENST00000257430.4:c.531+1G>T		p.X177_splice	ENST00000257430	NM_000038.5	177			0.743463021180862	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.743463021180862	1		248	155	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265561	152265561	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	186	320	0	ENST00000206249.3:c.1014T>G	p.Ser338Arg	p.S338R	ENST00000206249	NM_000125.3	338	agT/agG	4/8	0.126786821086676	4	FACETS	0.803	0.747	0.861	0.803	0.747	0.861	INDETERMINATE	2	TRUE	2	0.743463021180862	4		320	543	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636264	87636264	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	437	588	0	ENST00000277120.3:c.2429C>G	p.Pro810Arg	p.P810R	ENST00000277120		810	cCc/cGc	19/19	1	2	FACETS	0.975	0.931	1	0.975	0.931	1	CLONAL	1	TRUE	1	0.743463021180862	2		588	1206	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981646	101981646	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	43	58	0	ENST00000282441.5:c.67C>A	p.Pro23Thr	p.P23T	ENST00000282441	NM_001130145.2	23	Ccc/Acc	1/9	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.743463021180862	2		58	107	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944967	31944967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	363	519	0	ENST00000340398.3:c.134C>T	p.Thr45Ile	p.T45I	ENST00000340398	NM_001013699.2	45	aCc/aTc	1/1	0.202583235965397	1	FACETS	0.559	0.53	0.588	0.559	0.53	0.588	INDETERMINATE	1	TRUE	0	0.743463021180862	1		519	1098	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608074	28608074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	266	597	0	ENST00000241453.7:c.1892G>A	p.Gly631Glu	p.G631E	ENST00000241453	NM_004119.2	631	gGa/gAa	15/24	NA	2	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.743463021180862	2		597	701	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039340	49039340	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0006202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	206	391	0	ENST00000267163.4:c.2326-1G>A		p.X776_splice	ENST00000267163	NM_000321.2	776			0.202583235965397	1	FACETS	0.63	0.589	0.671	0.63	0.589	0.671	INDETERMINATE	1	TRUE	0	0.743463021180862	1		391	553	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961751	41961751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	292	727	0	ENST00000219905.7:c.659G>A	p.Gly220Asp	p.G220D	ENST00000219905	NM_001164273.1	220	gGc/gAc	2/24	1	2	FACETS	0.959	0.906	1	0.959	0.906	1	CLONAL	1	TRUE	1	0.743463021180862	2		727	819	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954211	48954211	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	181	368	0	ENST00000267163.4:c.1415del	p.Asn472IlefsTer6	p.N472Ifs*6	ENST00000267163	NM_000321.2	471	cAa/ca	15/27	0.202583235965397	1	FACETS	0.543	0.504	0.584	0.543	0.504	0.584	INDETERMINATE	1	TRUE	0	0.743463021180862	1		368	563	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	482	221	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.858289460341916	3	FACETS	0.97	0.936	1	0.97	0.936	1	CLONAL	2	TRUE	1	0.858289460341916	3		222	827	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821962	72821962	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs140577707	NA	P-0006208-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	631	493	0	ENST00000268489.5:c.10213C>G	p.Pro3405Ala	p.P3405A	ENST00000268489	NM_006885.3	3405	Ccc/Gcc	10/10	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.9	2		493	1219	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	70	386	0	ENST00000295754.5:c.1583G>T	p.Arg528Leu	p.R528L	ENST00000295754	NM_003242.5	528	cGt/cTt	7/7	1	2	FACETS	0.813	0.707	0.928	0.813	0.707	0.928	CLONAL	1	TRUE	1	0.2	2		386	861	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574000	7574000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	164	484	0	ENST00000269305.4:c.1027G>T	p.Glu343Ter	p.E343*	ENST00000269305	NM_001126112.2	343	Gag/Tag	10/11	0.186345252102836	4	FACETS	0.903	0.839	0.968	0.903	0.839	0.968	INDETERMINATE	2	TRUE	2	0.839322218643865	4		484	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0006229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	163	430	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.186345252102836	4	FACETS	0.942	0.877	1	0.942	0.877	1	INDETERMINATE	2	TRUE	2	0.839322218643865	4		430	379	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149218	119149218	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs727504426	NA	P-0006229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	131	398	1	ENST00000264033.4:c.1228-2A>G		p.X410_splice	ENST00000264033	NM_005188.3	410			0.303653885291742	4	FACETS	1	0.987	1	0.738	0.677	0.801	INDETERMINATE	1	TRUE	2	0.839322218643865	4		399	389	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888157	112888157	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs751437780	NA	P-0006229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	165	398	0	ENST00000351677.2:c.173A>G	p.Asn58Ser	p.N58S	ENST00000351677	NM_002834.3	58	aAc/aGc	3/16	0.683645419690358	3	FACETS	1	0.991	1	0.831	0.79	0.869	CLONAL	2	TRUE	0	0.839322218643865	3		398	224	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10267066	10267066	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0006229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	26	255	0	ENST00000340748.4:c.1351+1G>T		p.X451_splice	ENST00000340748		451			0.798853044253399	4	FACETS	0.316	0.25	0.391	0.158	0.125	0.196	SUBCLONAL	1	TRUE	2	0.839322218643865	4		255	361	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383732	15383732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	202	442	1	ENST00000263377.2:c.179C>T	p.Thr60Ile	p.T60I	ENST00000263377	NM_058243.2	60	aCc/aTc	2/20	0.798853044253399	4	FACETS	0.984	0.923	1	0.984	0.923	1	CLONAL	2	TRUE	2	0.839322218643865	4		443	450	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143054	7143054	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006238-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	297	241	0	ENST00000302850.5:c.2315T>A	p.Val772Glu	p.V772E	ENST00000302850	NM_000208.2	772	gTg/gAg	12/22	1	2	FACETS	0.939	0.887	0.992	0.939	0.887	0.992	CLONAL	1	TRUE	1	0.728823145754574	2		241	868	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0006241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	71	476	2	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.919	0.801	1	0.919	0.801	1	CLONAL	1	TRUE	1	0.222043968901397	2		478	696	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023754	27023754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	81	403	0	ENST00000324856.7:c.860C>T	p.Pro287Leu	p.P287L	ENST00000324856	NM_006015.4	287	cCc/cTc	1/20	1	2	FACETS	0.832	0.732	0.94	0.832	0.732	0.94	CLONAL	1	TRUE	1	0.222043968901397	2		403	877	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664504	29664504	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0006241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	78	476	0	ENST00000356175.3:c.6483C>G	p.Tyr2161Ter	p.Y2161*	ENST00000356175	NM_000267.3	2161	taC/taG	42/57	1	2	FACETS	0.86	0.755	0.974	0.86	0.755	0.974	CLONAL	1	TRUE	1	0.222043968901397	2		476	817	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922096	39922096	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	130	854	0	ENST00000378444.4:c.4076G>A	p.Gly1359Glu	p.G1359E	ENST00000378444	NM_001123385.1	1359	gGg/gAg	9/15	0.222043968901397	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.222043968901397	1		854	965	SUCCESS
AR	367	MSKCC	GRCh37	X	66905879	66905879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	69	702	0	ENST00000374690.3:c.1796G>A	p.Arg599Lys	p.R599K	ENST00000374690	NM_000044.3	599	aGa/aAa	3/8	0.222043968901397	1	FACETS	0.845	0.736	0.963	0.845	0.736	0.963	CLONAL	1	TRUE	0	0.222043968901397	1		702	654	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720650	89720650	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1257124719	NA	P-0006248-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	14	97	0	ENST00000371953.3:c.802-1G>A		p.X268_splice	ENST00000371953	NM_000314.4	268			0.274846819507746	1	FACETS	0.526	0.382	0.7	0.526	0.382	0.7	SUBCLONAL	1	TRUE	0	0.274846819507746	1		97	167	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256365	46256365	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773838233	NA	P-0006248-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	359	724	0	ENST00000371998.3:c.593G>A	p.Arg198His	p.R198H	ENST00000371998		198	cGt/cAt	7/23	1	2	FACETS	1	0.95	1	1	0.996	1	CLONAL	2	TRUE	1	0.274846819507746	2		724	1302	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115720	8115815	+	inframe_deletion	In_Frame_Del	DEL	ATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAG	ATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAG	-	novel	NA	P-0006248-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	62	500	0	ENST00000346208.3:c.1067_1162del	p.Met356_Lys387del	p.M356_K387del	ENST00000346208		356	ATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAG/-	6/6	1	2	FACETS	0.544	0.468	0.626	0.544	0.468	0.626	SUBCLONAL	1	TRUE	1	0.274846819507746	2		500	830	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	402	221	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.622060527224872	2	FACETS	0.849	0.818	0.879	0.849	0.818	0.879	CLONAL	2	TRUE	0	0.746805257202203	2		222	634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0006273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	442	395	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.631730222117874	2	FACETS	0.886	0.856	0.915	0.886	0.856	0.915	CLONAL	2	TRUE	0	0.746805257202203	2		395	668	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776783	NA	P-0006273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	291	183	0	ENST00000267163.4:c.1215+1G>A		p.X405_splice	ENST00000267163	NM_000321.2	405			0.572583381513267	3	FACETS	1	0.993	1	0.805	0.772	0.838	CLONAL	2	TRUE	0	0.746805257202203	3		183	443	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142954	47142954	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	187	328	0	ENST00000409792.3:c.5009G>T	p.Arg1670Ile	p.R1670I	ENST00000409792	NM_014159.6	1670	aGa/aTa	8/21	1	2	FACETS	0.769	0.714	0.826	0.769	0.714	0.826	SUBCLONAL	1	TRUE	1	0.746805257202203	2		328	651	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131184	55131184	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	228	387	0	ENST00000257290.5:c.727G>C	p.Val243Leu	p.V243L	ENST00000257290	NM_006206.4	243	Gtt/Ctt	5/23	1	2	FACETS	0.739	0.69	0.789	0.739	0.69	0.789	SUBCLONAL	1	TRUE	1	0.746805257202203	2		387	826	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900997	3900997	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	186	344	0	ENST00000262367.5:c.99G>T	p.Leu33Phe	p.L33F	ENST00000262367	NM_004380.2	33	ttG/ttT	2/31	1	2	FACETS	0.784	0.728	0.843	0.784	0.728	0.843	SUBCLONAL	1	TRUE	1	0.746805257202203	2		344	635	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992240	72992240	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs964926619	NA	P-0006273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	262	518	0	ENST00000268489.5:c.1805C>T	p.Ala602Val	p.A602V	ENST00000268489	NM_006885.3	602	gCa/gTa	2/10	1	2	FACETS	0.775	0.728	0.824	0.775	0.728	0.824	SUBCLONAL	1	TRUE	1	0.746805257202203	2		518	905	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969426	44969426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	345	517	0	ENST00000377967.4:c.4108G>T	p.Glu1370Ter	p.E1370*	ENST00000377967	NM_021140.2	1370	Gaa/Taa	28/29	0.667101166622908	1	FACETS	0.783	0.747	0.82	0.783	0.747	0.82	SUBCLONAL	1	TRUE	0	0.746805257202203	1		517	739	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593603	55593603	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913235	NA	P-0006293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	187	186	0	ENST00000288135.5:c.1669T>C	p.Trp557Arg	p.W557R	ENST00000288135	NM_000222.2	557	Tgg/Cgg	11/21	1	2	FACETS	0.942	0.876	1	0.942	0.876	1	CLONAL	1	TRUE	1	0.707409794067941	2		186	561	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910549	29910549	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45585732	NA	P-0006293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	17	247	4	ENST00000376809.5:c.89G>A	p.Arg30Lys	p.R30K	ENST00000376809	NM_002116.7	30	aGg/aAg	2/8	1	2	FACETS	0.31	0.233	0.401	0.31	0.233	0.401	SUBCLONAL	1	TRUE	1	0.707409794067941	2		251	155	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41023254	41023254	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	237	249	1	ENST00000267868.3:c.898T>A	p.Leu300Met	p.L300M	ENST00000267868	NM_002875.4	300	Ttg/Atg	10/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.707409794067941	2		250	667	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339769	116340321	+	frameshift_variant	Frame_Shift_Del	DEL	TTGCATTCGATATCAGTGAGAAGGCTAAAGGAAACGAAAGATGGTTTTATGTTTTTGACGGACCAGTCCTACATTGATGTTTTACCTGAGTTCAGAGATTCTTACCCCATTAAGTATGTCCATGCCTTTGAAAGCAACAATTTTATTTACTTCTTGACGGTCCAAAGGGAAACTCTAGATGCTCAGACTTTTCACACAAGAATAATCAGGTTCTGTTCCATAAACTCTGGATTGCATTCCTACATGGAAATGCCTCTGGAGTGTATTCTCACAGAAAAGAGAAAAAAGAGATCCACAAAGAAGGAAGTGTTTAATATACTTCAGGCTGCGTATGTCAGCAAGCCTGGGGCCCAGCTTGCTAGACAAATAGGAGCCAGCCTGAATGATGACATTCTTTTCGGGGTGTTCGCACAAAGCAAGCCAGATTCTGCCGAACCAATGGATCGATCTGCCATGTGTGCATTCCCTATCAAATATGTCAACGACTTCTTCAACAAGATCGTCAACAAAAACAATGTGAGATGTCTCCAGCATTTTTACGGACCCAATCATG	TTGCATTCGATATCAGTGAGAAGGCTAAAGGAAACGAAAGATGGTTTTATGTTTTTGACGGACCAGTCCTACATTGATGTTTTACCTGAGTTCAGAGATTCTTACCCCATTAAGTATGTCCATGCCTTTGAAAGCAACAATTTTATTTACTTCTTGACGGTCCAAAGGGAAACTCTAGATGCTCAGACTTTTCACACAAGAATAATCAGGTTCTGTTCCATAAACTCTGGATTGCATTCCTACATGGAAATGCCTCTGGAGTGTATTCTCACAGAAAAGAGAAAAAAGAGATCCACAAAGAAGGAAGTGTTTAATATACTTCAGGCTGCGTATGTCAGCAAGCCTGGGGCCCAGCTTGCTAGACAAATAGGAGCCAGCCTGAATGATGACATTCTTTTCGGGGTGTTCGCACAAAGCAAGCCAGATTCTGCCGAACCAATGGATCGATCTGCCATGTGTGCATTCCCTATCAAATATGTCAACGACTTCTTCAACAAGATCGTCAACAAAAACAATGTGAGATGTCTCCAGCATTTTTACGGACCCAATCATG	-	novel	NA	P-0006293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	77	249	0	ENST00000397752.3:c.631_1183del	p.Leu211SerfsTer9	p.L211Sfs*9	ENST00000397752	NM_000245.2	211	TTGCATTCGATATCAGTGAGAAGGCTAAAGGAAACGAAAGATGGTTTTATGTTTTTGACGGACCAGTCCTACATTGATGTTTTACCTGAGTTCAGAGATTCTTACCCCATTAAGTATGTCCATGCCTTTGAAAGCAACAATTTTATTTACTTCTTGACGGTCCAAAGGGAAACTCTAGATGCTCAGACTTTTCACACAAGAATAATCAGGTTCTGTTCCATAAACTCTGGATTGCATTCCTACATGGAAATGCCTCTGGAGTGTATTCTCACAGAAAAGAGAAAAAAGAGATCCACAAAGAAGGAAGTGTTTAATATACTTCAGGCTGCGTATGTCAGCAAGCCTGGGGCCCAGCTTGCTAGACAAATAGGAGCCAGCCTGAATGATGACATTCTTTTCGGGGTGTTCGCACAAAGCAAGCCAGATTCTGCCGAACCAATGGATCGATCTGCCATGTGTGCATTCCCTATCAAATATGTCAACGACTTCTTCAACAAGATCGTCAACAAAAACAATGTGAGATGTCTCCAGCATTTTTACGGACCCAATCATGag/ag	2/21	1	2	FACETS	0.377	0.331	0.426	0.377	0.331	0.426	SUBCLONAL	1	TRUE	1	0.707409794067941	2		249	578	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544718	65544718	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	26	202	0	ENST00000358664.4:c.208del	p.Tyr70IlefsTer100	p.Y70Ifs*100	ENST00000358664	NM_002382.4	70	Tat/at	4/5	0.707409794067941	1	FACETS	0.129	0.102	0.16	0.129	0.102	0.16	SUBCLONAL	1	TRUE	0	0.707409794067941	1		202	369	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432664	29432664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113994087	NA	P-0121462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	732	445	0	ENST00000389048.3:c.3824G>A	p.Arg1275Gln	p.R1275Q	ENST00000389048	NM_004304.4	1275	cGa/cAa	25/29	0.851071013583411	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	NA	1	0.851071013583411	4		445	1037	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006322-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	21	221	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.549	0.421	0.7	0.549	0.421	0.7	SUBCLONAL	1	TRUE	1	0.12	2		222	637	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573561	48573561	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006322-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	60	354	0	ENST00000342988.3:c.145G>T	p.Glu49Ter	p.E49*	ENST00000342988	NM_005359.5	49	Gag/Tag	2/12	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.12	2		354	829	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0006327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	435	674	5	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	0.927753609876228	2	FACETS	1	0.962	1	0.502	0.481	0.523	CLONAL	1	TRUE	0	0.930111368640126	2		679	932	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562226	95562226	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	267	599	0	ENST00000393063.1:c.5031C>G	p.Phe1677Leu	p.F1677L	ENST00000393063	NM_030621.3	1677	ttC/ttG	24/28	1	2	FACETS	0.981	0.929	1	0.981	0.929	1	CLONAL	1	TRUE	1	0.930111368640126	2		599	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0006331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	388	254	7	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.586671467534313	2	FACETS	0.939	0.901	0.976	0.939	0.901	0.976	CLONAL	2	TRUE	0	0.60238381041585	2		261	686	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0006331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	575	307	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.60238381041585	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	2	0.60238381041585	4		307	1510	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543605	9543605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1159424856	NA	P-0006331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1840	354	414	0	ENST00000353224.5:c.1549G>A	p.Asp517Asn	p.D517N	ENST00000353224	NM_177990.2	517	Gat/Aat	6/10	0.60238381041585	5	FACETS	1	0.959	1	0.255	0.24	0.27	CLONAL	1	TRUE	1	0.60238381041585	5		414	2194	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776164	135776164	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	270	422	0	ENST00000298552.3:c.2563C>A	p.Leu855Ile	p.L855I	ENST00000298552	NM_001162426.1	855	Ctt/Att	20/23	0.60238381041585	3	FACETS	0.912	0.854	0.971	0.304	0.284	0.324	CLONAL	1	TRUE	0	0.60238381041585	3		422	1279	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914218	32914218	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs80358798	NA	P-0006331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2529	499	736	0	ENST00000380152.3:c.5726A>G	p.Asp1909Gly	p.D1909G	ENST00000380152		1909	gAt/gGt	11/27	0.60238381041585	4	FACETS	0.877	0.835	0.92			1	CLONAL	1	TRUE	NA	0.60238381041585	4		736	3028	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370829	55370829	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006336-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	162	315	0	ENST00000297316.4:c.131T>G	p.Val44Gly	p.V44G	ENST00000297316	NM_022454.3	44	gTg/gGg	1/2	1	2	FACETS	0.885	0.819	0.952	0.885	0.819	0.952	CLONAL	1	TRUE	1	0.784143118709651	2		315	467	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428365	33428365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060502963	NA	P-0006336-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	337	428	0	ENST00000345365.6:c.758G>A	p.Arg253Gln	p.R253Q	ENST00000345365	NM_002878.3	253	cGa/cAa	9/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.784143118709651	2		428	806	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870864	12870864	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006336-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	378	264	0	ENST00000228872.4:c.92del	p.Asn31ThrfsTer11	p.N31Tfs*11	ENST00000228872	NM_004064.3	31	Aac/ac	1/3	0.781802393171999	2	FACETS	0.996	0.967	1	0.996	0.967	1	CLONAL	2	TRUE	0	0.784143118709651	2		264	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0006360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	68	386	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.214383934578894	1	FACETS	0.592	0.514	0.676	0.592	0.514	0.676	SUBCLONAL	1	TRUE	0	0.284014697249451	1		386	694	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0006360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	31	165	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.284014697249451	1	FACETS	0.696	0.565	0.843	0.696	0.565	0.843	SUBCLONAL	1	TRUE	0	0.284014697249451	1		165	269	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842679	68842682	+	protein_altering_variant	In_Frame_Del	DEL	TATT	TATT	A	novel	NA	P-0006360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	111	564	1	ENST00000261769.5:c.615_618delinsA	p.Phe205_Ile206delinsLeu	p.F205_I206delinsL	ENST00000261769	NM_004360.3	205	ttTATT/ttA	5/16	1	2	FACETS	0.755	0.677	0.838	0.755	0.677	0.838	SUBCLONAL	1	TRUE	1	0.284014697249451	2		565	1035	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	99	370	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	0.18	2		370	1018	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	58	260	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.915	0.785	1	0.915	0.785	1	CLONAL	1	TRUE	1	0.18	2		260	704	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940494	29940494	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1524	105	598	0	ENST00000389048.3:c.737C>G	p.Thr246Ser	p.T246S	ENST00000389048	NM_004304.4	246	aCc/aGc	2/29	1	2	FACETS	0.716	0.639	0.799	0.716	0.639	0.799	SUBCLONAL	1	TRUE	1	0.18	2		598	1629	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439554	220439554	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1591	102	491	0	ENST00000243786.2:c.407G>T	p.Gly136Val	p.G136V	ENST00000243786	NM_002191.3	136	gGg/gTg	2/2	1	2	FACETS	0.669	0.596	0.748	0.669	0.596	0.748	SUBCLONAL	1	TRUE	1	0.18	2		491	1693	SUCCESS
ATM	472	MSKCC	GRCh37	11	108154953	108154953	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs730881364	NA	P-0006364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	30	178	0	ENST00000278616.4:c.3747-1G>C		p.X1249_splice	ENST00000278616	NM_000051.3	1249			0.3	2	FACETS	0.756	0.609	0.923			1	CLONAL	1	TRUE	NA	0.18	2		178	441	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040679	47040679	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	88	262	2	ENST00000377604.3:c.1314C>A	p.Tyr438Ter	p.Y438*	ENST00000377604	NM_001204468.1	438	taC/taA	13/24	1	1	FACETS	0.954	0.843	1	0.954	0.843	1	CLONAL	1	TRUE	0	0.18	1		264	933	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0006411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6	49	43	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	0.865114581843146	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.928710075154576	1		43	55	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	466	470	0	ENST00000269305.4:c.472C>G	p.Arg158Gly	p.R158G	ENST00000269305	NM_001126112.2	158	Cgc/Ggc	5/11	0.90244566310008	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.928710075154576	1		470	522	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52692286	52692286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	290	475	1	ENST00000394830.3:c.574G>A	p.Ala192Thr	p.A192T	ENST00000394830	NM_018313.4	192	Gcc/Acc	6/30	1	2	FACETS	0.56	0.527	0.594	0.56	0.527	0.594	SUBCLONAL	1	TRUE	1	0.928710075154576	2		476	1115	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136847	55136847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	20157	522	6	ENST00000257290.5:c.1169G>A	p.Gly390Asp	p.G390D	ENST00000257290	NM_006206.4	390	gGc/gAc	8/23	0.928710075154576	17	FACETS	1	0.999	1			1	CLONAL	16	TRUE	NA	0.928710075154576	17		528	20991	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912657	NA	P-0006412-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	568	674	0	ENST00000269305.4:c.814G>C	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ctg	8/11	0.532605475206493	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.544241196857632	2		674	1030	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390166	89390166	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006412-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	54	452	0	ENST00000336596.2:c.915G>C	p.Arg305Ser	p.R305S	ENST00000336596	NM_005233.5	305	agG/agC	4/17	0.53296229313754	2	FACETS	0.375	0.32	0.435	0.188	0.16	0.218	SUBCLONAL	1	TRUE	0	0.544241196857632	2		452	529	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037973	49037973	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0006412-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	229	372	0	ENST00000267163.4:c.2211+2T>A		p.X737_splice	ENST00000267163	NM_000321.2	737			0.53296229313754	2	FACETS	0.941	0.89	0.993	0.941	0.89	0.993	CLONAL	2	TRUE	0	0.544241196857632	2		372	447	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442054	52442054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	218	590	0	ENST00000460680.1:c.295G>A	p.Val99Met	p.V99M	ENST00000460680	NM_004656.3	99	Gtg/Atg	5/17	1	2	FACETS	0.923	0.861	0.986	0.923	0.861	0.986	CLONAL	1	TRUE	1	0.628991913713671	2		590	751	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067836	30067836	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315499	NA	P-0006419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	163	541	3	ENST00000338641.4:c.1021C>T	p.Arg341Ter	p.R341*	ENST00000338641	NM_000268.3	341	Cga/Tga	11/16	0.578209209059424	1	FACETS	0.935	0.87	1	0.935	0.87	1	CLONAL	1	TRUE	0	0.628991913713671	1		544	380	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156735	20156735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	105	395	0	ENST00000379607.5:c.22G>A	p.Gly8Arg	p.G8R	ENST00000379607	NM_001412.3	8	Gga/Aga	2/7	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.372833031490733	2		395	542	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0006444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	290	447	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.355968160388752	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.372833031490733	3		447	820	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7174633	7174633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs72549237	NA	P-0121569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	365	657	3	ENST00000302850.5:c.1084G>A	p.Val362Ile	p.V362I	ENST00000302850	NM_000208.2	362	Gtc/Atc	4/22	1	2	FACETS	0.998	0.952	1	0.998	0.952	1	CLONAL	1	NA	1	0.893130468241066	2		660	819	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282115	38282115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554562012	NA	P-0121569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	57	598	0	ENST00000425967.3:c.941C>T	p.Pro314Leu	p.P314L	ENST00000425967	NM_001174067.1	314	cCg/cTg	8/19	1	2	FACETS	0.201	0.172	0.232	0.201	0.172	0.232	SUBCLONAL	1	NA	1	0.893130468241066	2		598	636	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0006463-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	357	500	2	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	0.773294477428181	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.773294477428181	1		502	563	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533548	533548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006463-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	456	473	0	ENST00000451590.1:c.355G>A	p.Asp119Asn	p.D119N	ENST00000451590	NM_001130442.1	119	Gac/Aac	4/5	1	2	FACETS	0.999	0.955	1	0.999	0.955	1	CLONAL	1	TRUE	1	0.773294477428181	2		473	1181	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190824	11190824	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006463-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	179	187	0	ENST00000361445.4:c.5375C>G	p.Ala1792Gly	p.A1792G	ENST00000361445	NM_004958.3	1792	gCg/gGg	39/58	1	2	FACETS	0.981	0.913	1	0.981	0.913	1	CLONAL	1	TRUE	1	0.773294477428181	2		187	472	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509206	106509206	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006463-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	497	528	0	ENST00000359195.3:c.1200C>A	p.Ser400Arg	p.S400R	ENST00000359195	NM_002649.2	400	agC/agA	2/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.773294477428181	2		528	1249	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196024	67196024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1315522473	NA	P-0006463-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	400	386	0	ENST00000312629.5:c.8C>T	p.Ala3Val	p.A3V	ENST00000312629	NM_003952.2	3	gCc/gTc	1/15	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.773294477428181	2		386	938	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420090	49420090	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006463-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	481	519	0	ENST00000301067.7:c.15659G>C	p.Arg5220Pro	p.R5220P	ENST00000301067	NM_003482.3	5220	cGc/cCc	48/54	1	2	FACETS	0.997	0.955	1	0.997	0.955	1	CLONAL	1	TRUE	1	0.773294477428181	2		519	1248	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918710	44918710	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006463-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	326	349	4	ENST00000377967.4:c.1193A>T	p.Gln398Leu	p.Q398L	ENST00000377967	NM_021140.2	398	cAg/cTg	12/29	NA	2	FACETS	0.972	0.922	1			1	INDETERMINATE	1	TRUE	NA	0.773294477428181	2		353	867	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006469-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	125	221	1	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	0.537222091995281	2		222	437	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0006469-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	458	559	1	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.537222091995281	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.537222091995281	3		560	1072	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006469-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	203	705	0	ENST00000342988.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000342988	NM_005359.5	356	cCt/cTt	9/12	0.537222091995281	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.537222091995281	1		705	495	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0006469-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	143	305	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	0.537222091995281	3	FACETS	1	0.918	1	0.503	0.459	0.548	CLONAL	1	TRUE	1	0.537222091995281	3		305	672	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411576	63411576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006469-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	657	373	0	ENST00000330258.3:c.1591C>T	p.Arg531Ter	p.R531*	ENST00000330258	NM_152424.3	531	Cga/Tga	2/2	0.484501868723739	2	FACETS	0.879	0.856	0.901			1	CLONAL	3	TRUE	NA	0.537222091995281	2		373	928	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444408	50444408	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006469-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	148	306	0	ENST00000331340.3:c.338C>A	p.Pro113His	p.P113H	ENST00000331340	NM_006060.4	113	cCt/cAt	4/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.537222091995281	2		306	478	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45422959	45422959	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006469-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	177	510	3	ENST00000262160.6:c.169C>T	p.Arg57Ter	p.R57*	ENST00000262160	NM_005901.5	57	Cga/Tga	2/11	0.537222091995281	1	FACETS	0.688	0.635	0.741	0.688	0.635	0.741	SUBCLONAL	1	TRUE	0	0.537222091995281	1		513	701	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163443	32163443	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	675	786	3	ENST00000375023.3:c.5783C>A	p.Ala1928Glu	p.A1928E	ENST00000375023	NM_004557.3	1928	gCg/gAg	30/30	0.884137400679407	2	FACETS	0.859	0.828	0.891	0.43	0.414	0.446	CLONAL	1	TRUE	0	0.884137400679407	2		789	1777	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579355	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519997	NA	P-0006484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	580	670	1	ENST00000269305.4:c.332T>G	p.Leu111Arg	p.L111R	ENST00000269305	NM_001126112.2	111	cTg/cGg	4/11	0.884137400679407	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.884137400679407	1		671	729	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101081	41101081	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	238	675	0	ENST00000373198.4:c.1275G>C	p.Gln425His	p.Q425H	ENST00000373198	NM_133170.3	425	caG/caC	8/32	1	2	FACETS	0.404	0.376	0.433	0.404	0.376	0.433	SUBCLONAL	1	TRUE	1	0.884137400679407	2		675	1333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1555525585	NA	P-0006493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	354	392	0	ENST00000269305.4:c.673-2A>G		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.714626189170648	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.713277526499138	2		392	490	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162742015	162742015	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	269	645	0	ENST00000367921.3:c.1706T>G	p.Leu569Arg	p.L569R	ENST00000367921	NM_006182.2	569	cTg/cGg	13/18	0.668080500722924	3	FACETS	0.842	0.789	0.897			1	CLONAL	1	TRUE	NA	0.713277526499138	3		645	1215	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523012	25523012	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	328	706	0	ENST00000264709.3:c.173C>T	p.Pro58Leu	p.P58L	ENST00000264709	NM_175629.2	58	cCc/cTc	3/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.713277526499138	2		706	887	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722099	176722099	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	200	468	0	ENST00000439151.2:c.7730T>G	p.Val2577Gly	p.V2577G	ENST00000439151	NM_022455.4	2577	gTg/gGg	23/23	0.714626189170648	2	FACETS	0.987	0.921	1	0.494	0.46	0.528	CLONAL	1	TRUE	0	0.713277526499138	2		468	568	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925649	114925649	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	954	1127	1	ENST00000543371.1:c.1727C>A	p.Ser576Ter	p.S576*	ENST00000543371	NM_001198531.1	576	tCg/tAg	14/14	0.714626189170648	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.713277526499138	3		1128	1787	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161426	2161426	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	277	749	0	ENST00000434045.2:c.101T>C	p.Ile34Thr	p.I34T	ENST00000434045	NM_001127598.1	34	aTa/aCa	2/5	1	2	FACETS	0.978	0.922	1	0.978	0.922	1	CLONAL	1	TRUE	1	0.713277526499138	2		749	794	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476412	88476412	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	446	295	0	ENST00000360948.2:c.1720C>G	p.Leu574Val	p.L574V	ENST00000360948	NM_001012338.2	574	Ctg/Gtg	15/19	0.714626189170648	3	FACETS	1	0.981	1			1	CLONAL	3	TRUE	NA	0.713277526499138	3		295	560	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0006497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	106	318	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.395563533443459	1	FACETS	0.395	0.356	0.435	0.395	0.356	0.435	INDETERMINATE	1	TRUE	0	0.78069251514241	1		318	419	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063312	67063312	+	start_lost	Translation_Start_Site	SNP	T	T	A	novel	NA	P-0006497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	314	282	0	ENST00000412916.2:c.2T>A	p.Met1?	p.M1?	ENST00000412916		1	aTg/aAg	1/6	0.78069251514241	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.78069251514241	1		282	392	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161191	56161209	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTGTATTCATCTGCTAT	TTCTGTATTCATCTGCTAT	-	novel	NA	P-0006497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	284	515	0	ENST00000399503.3:c.1062_1080del	p.Phe354LeufsTer2	p.F354Lfs*2	ENST00000399503	NM_005921.1	354	TTCTGTATTCATCTGCTATtt/tt	5/20	0.78069251514241	1	FACETS	0.96	0.918	1	0.96	0.918	1	CLONAL	1	TRUE	0	0.78069251514241	1		515	462	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16052760	16052770	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCACCCTTTG	CTCACCCTTTG	-	novel	NA	P-0006497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	261	538	0	ENST00000268712.3:c.904_909+5del		p.X302_splice	ENST00000268712	NM_006311.3	302		9/46	0.78069251514241	1	FACETS	0.968	0.924	1	0.968	0.924	1	CLONAL	1	TRUE	0	0.78069251514241	1		538	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574014	7574025	+	inframe_deletion	In_Frame_Del	DEL	AAGCGCTCACGC	AAGCGCTCACGC	-	novel	NA	P-0006497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	412	776	0	ENST00000269305.4:c.1002_1013del	p.Arg335_Phe338del	p.R335_F338del	ENST00000269305	NM_001126112.2	334	ggGCGTGAGCGCTTc/ggc	10/11	0.78069251514241	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.78069251514241	1		776	585	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	341	221	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.618652945929338	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.618652945929338	2		222	543	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	363	260	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.618652945929338	2		260	983	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860903	45860903	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	435	612	1	ENST00000391945.4:c.1292C>A	p.Pro431His	p.P431H	ENST00000391945	NM_000400.3	431	cCc/cAc	13/23	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.618652945929338	2		613	1390	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397742	49397742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552757	NA	P-0006535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	645	563	0	ENST00000418115.1:c.482C>T	p.Ala161Val	p.A161V	ENST00000418115	NM_001664.2	161	gCa/gTa	5/5	0.618652945929338	3	FACETS	0.998	0.964	1	0.998	0.964	1	CLONAL	2	TRUE	1	0.618652945929338	3		563	1368	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563213	21563213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	433	432	0	ENST00000382592.4:c.706G>A	p.Gly236Ser	p.G236S	ENST00000382592	NM_014572.2	236	Ggt/Agt	4/8	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.618652945929338	2		432	1214	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039371	47039371	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	384	543	0	ENST00000377604.3:c.994C>G	p.Arg332Gly	p.R332G	ENST00000377604	NM_001204468.1	332	Cgc/Ggc	10/24	NA	2	FACETS	0.967	0.918	1			1	INDETERMINATE	1	TRUE	NA	0.618652945929338	2		543	1284	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912660	NA	P-0006544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	271	434	0	ENST00000269305.4:c.839G>T	p.Arg280Ile	p.R280I	ENST00000269305	NM_001126112.2	280	aGa/aTa	8/11	0.220342736714988	2	FACETS	0.84	0.787	0.895	0.84	0.787	0.895	CLONAL	2	TRUE	0	0.251844696120594	2		434	1281	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020808	26020808	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs377197123	NA	P-0006544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1763	416	722	0	ENST00000357647.3:c.91C>G	p.Pro31Ala	p.P31A	ENST00000357647	NM_003529.2	31	Ccg/Gcg	1/1	0.251844696120594	3	FACETS	0.854	0.809	0.899	0.854	0.809	0.899	CLONAL	2	TRUE	1	0.251844696120594	3		722	2179	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936984	48937002	+	frameshift_variant	Frame_Shift_Del	DEL	GAACACCCAGGCGAGGTCA	GAACACCCAGGCGAGGTCA	-	novel	NA	P-0006544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	236	365	0	ENST00000267163.4:c.757_775del	p.Pro253GlyfsTer5	p.P253Gfs*5	ENST00000267163	NM_000321.2	251	cGAACACCCAGGCGAGGTCAg/cg	8/27	0.2183053296816	3	FACETS	1	0.981	1	0.754	0.704	0.805	CLONAL	2	TRUE	0	0.251844696120594	3		365	933	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223347	53223347	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	130	246	0	ENST00000375401.3:c.4012G>T	p.Glu1338Ter	p.E1338*	ENST00000375401	NM_004187.3	1338	Gag/Tag	23/26	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.501112657780839	1		246	290	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183799	10183799	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs869025623	NA	P-0006550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	108	228	0	ENST00000256474.2:c.269del	p.Asn90ThrfsTer69	p.N90Tfs*69	ENST00000256474	NM_000551.3	90	Aac/ac	1/3	0.501112657780839	1	FACETS	0.95	0.862	1	0.95	0.862	1	CLONAL	1	TRUE	0	0.501112657780839	1		228	340	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	199	221	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.202550629048347	3	FACETS	1	0.976	1	0.567	0.524	0.612	CLONAL	1	FALSE	1	0.292377971228606	3		222	1376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0006559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	248	595	1	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.294396141019049	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	0	0.292377971228606	1		596	1092	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306569	41306569	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	158	595	1	ENST00000373198.4:c.1090C>T	p.Arg364Ter	p.R364*	ENST00000373198	NM_133170.3	364	Cga/Tga	7/32	0.261428500819306	1	FACETS	0.776	0.71	0.846	0.776	0.71	0.846	SUBCLONAL	1	FALSE	0	0.292377971228606	1		596	1189	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11177096	11177096	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1273	281	761	0	ENST00000361445.4:c.6981G>C	p.Met2327Ile	p.M2327I	ENST00000361445	NM_004958.3	2327	atG/atC	50/58	0.196234128315721	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	0	0.292377971228606	1		761	1554	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293209	212293209	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0006559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	188	296	0	ENST00000342788.4:c.2644-1G>T		p.X882_splice	ENST00000342788	NM_005235.2	882			0.294396141019049	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	0	0.292377971228606	1		296	776	SUCCESS
APC	324	MSKCC	GRCh37	5	112174152	112174152	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0006559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	192	511	0	ENST00000257430.4:c.2861T>G	p.Leu954Ter	p.L954*	ENST00000257430	NM_000038.5	954	tTa/tGa	16/16	0.294396141019049	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	0	0.292377971228606	1		511	991	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391185	139391185	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	76	252	0	ENST00000277541.6:c.7006A>G	p.Ser2336Gly	p.S2336G	ENST00000277541	NM_017617.3	2336	Agc/Ggc	34/34	1	2	FACETS	0.909	0.796	1	0.909	0.796	1	CLONAL	1	TRUE	1	0.2	2		252	836	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851713	63851713	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1342574091	NA	P-0006565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	93	307	0	ENST00000279873.7:c.2491T>C	p.Phe831Leu	p.F831L	ENST00000279873	NM_032199.2	831	Ttc/Ctc	10/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.2	2		307	786	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47108584	47108584	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	34	268	0	ENST00000409792.3:c.6085del	p.Ser2029ValfsTer118	p.S2029Vfs*118	ENST00000409792	NM_014159.6	2029	Agt/gt	13/21	0.225649217201113	1	FACETS	0.7	0.572	0.845	0.7	0.572	0.845	SUBCLONAL	1	TRUE	0	0.2	1		268	437	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30061032	30061032	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	57	309	0	ENST00000338641.4:c.866del	p.Lys289SerfsTer7	p.K289Sfs*7	ENST00000338641	NM_000268.3	288	tcA/tc	9/16	0.186732630697402	1	FACETS	0.752	0.644	0.87	0.752	0.644	0.87	SUBCLONAL	1	TRUE	0	0.2	1		309	682	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020632	37020632	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0006574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	38	262	0	ENST00000358127.4:c.212+1G>A		p.X71_splice	ENST00000358127	NM_001280556.1	71			1	2	FACETS	1	0.844	1	1	0.844	1	CLONAL	1	TRUE	1	0.22	2		262	339	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619305	37619305	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0006574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	49	223	0	ENST00000447079.4:c.981T>G	p.Tyr327Ter	p.Y327*	ENST00000447079	NM_015083.1	327	taT/taG	1/14	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.22	2		223	323	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696448	47696448	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	29	351	0	ENST00000347630.2:c.375T>G	p.Phe125Leu	p.F125L	ENST00000347630	NM_001007230.1	125	ttT/ttG	6/11	1	2	FACETS	0.62	0.497	0.76	0.62	0.497	0.76	SUBCLONAL	1	TRUE	1	0.22	2		351	425	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649112	37649112	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	59	408	0	ENST00000447079.4:c.2218del	p.Gln740LysfsTer13	p.Q740Kfs*13	ENST00000447079	NM_015083.1	739	ggC/gg	4/14	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.22	2		408	534	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480403	89480403	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	72	405	0	ENST00000336596.2:c.2240T>A	p.Leu747His	p.L747H	ENST00000336596	NM_005233.5	747	cTc/cAc	13/17	0.135723062092842	3	FACETS	1	0.973	1	0.494	0.431	0.562	CLONAL	1	TRUE	0	0.14	3		405	743	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671846	30671846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	75	482	0	ENST00000376406.3:c.5114C>T	p.Thr1705Ile	p.T1705I	ENST00000376406	NM_014641.2	1705	aCc/aTc	10/15	0.135723062092842	5	FACETS	1	0.959	1	0.415	0.362	0.472	CLONAL	1	TRUE	2	0.14	5		482	1041	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152041	11152041	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	106	344	1	ENST00000358026.2:c.4325C>A	p.Ser1442Ter	p.S1442*	ENST00000358026	NM_001128849.1	1442	tCa/tAa	31/36	0.135723062092842	3	FACETS	1	0.959	1	0.757	0.679	0.84	CLONAL	2	TRUE	0	0.14	3		345	713	SUCCESS
AR	367	MSKCC	GRCh37	X	66941674	66941674	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0006582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	99	504	1	ENST00000374690.3:c.2319-1G>A		p.X773_splice	ENST00000374690	NM_000044.3	773			0.135723062092842	3	FACETS	0.824	0.735	0.92	0.549	0.49	0.613	CLONAL	2	TRUE	0	0.14	3		505	918	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221983	1222003	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	ATCCGGCAGATCCGGCAGCAC	ATCCGGCAGATCCGGCAGCAC	GGAT	novel	NA	P-0006582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	122	452	0	ENST00000326873.7:c.898_918delinsGGAT	p.Ile300GlyfsTer2	p.I300Gfs*2	ENST00000326873	NM_000455.4	300	ATCCGGCAGATCCGGCAGCAC/GGAT	7/10	0.135723062092842	3	FACETS	1	0.948	1	0.717	0.648	0.79	CLONAL	2	TRUE	0	0.14	3		452	867	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0006588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	106	386	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.912	0.816	1	0.912	0.816	1	CLONAL	1	TRUE	1	0.24	2		386	969	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259654	11259654	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1205998733	NA	P-0006599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	50	367	0	ENST00000361445.4:c.4051G>A	p.Ala1351Thr	p.A1351T	ENST00000361445	NM_004958.3	1351	Gct/Act	27/58	0.369525417699257	1	FACETS	0.416	0.353	0.486	0.416	0.353	0.486	SUBCLONAL	1	TRUE	0	0.369525417699257	1		367	530	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65311203	65311203	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	181	372	0	ENST00000342505.4:c.2108G>T	p.Ser703Ile	p.S703I	ENST00000342505	NM_002227.2	703	aGc/aTc	15/25	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.369525417699257	2		372	680	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176085816	176085816	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	92	380	0	ENST00000367669.3:c.970A>G	p.Ser324Gly	p.S324G	ENST00000367669	NM_022457.5	324	Agt/Ggt	9/20	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.369525417699257	2		380	479	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427765	72427765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	36	204	0	ENST00000477973.2:c.725G>A	p.Arg242Lys	p.R242K	ENST00000477973	NM_012234.5	242	aGg/aAg	4/4	1	2	FACETS	0.447	0.367	0.536	0.447	0.367	0.536	SUBCLONAL	1	TRUE	1	0.369525417699257	2		204	436	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404281	139404281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	64	365	1	ENST00000277541.6:c.2873C>T	p.Ala958Val	p.A958V	ENST00000277541	NM_017617.3	958	gCc/gTc	18/34	1	2	FACETS	0.405	0.35	0.465	0.405	0.35	0.465	SUBCLONAL	1	TRUE	1	0.369525417699257	2		366	855	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241679	55241681	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	rs397517086	NA	P-0006606-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	789	800	0	ENST00000275493.2:c.2127_2129del	p.Glu709_Thr710delinsAsp	p.E709_T710delinsD	ENST00000275493	NM_005228.3	709	gaAACt/gat	18/28	0.606660161538707	4	FACETS	0.88	0.854	0.905	0.88	0.854	0.905	CLONAL	3	TRUE	1	0.70946674518856	4		800	1441	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183564	185183564	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006606-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	144	781	0	ENST00000265026.3:c.1418A>G	p.Glu473Gly	p.E473G	ENST00000265026	NM_004721.4	473	gAg/gGg	9/14	0.332504112990098	2	FACETS	0.507	0.462	0.553	0.253	0.231	0.277	INDETERMINATE	1	TRUE	0	0.70946674518856	2		781	801	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141565	11141565	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006606-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	133	772	0	ENST00000358026.2:c.3542A>G	p.His1181Arg	p.H1181R	ENST00000358026	NM_001128849.1	1181	cAc/cGc	25/36	0.379868275912077	1	FACETS	0.331	0.301	0.363	0.331	0.301	0.363	INDETERMINATE	1	TRUE	0	0.70946674518856	1		772	731	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353834	68353834	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006606-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	157	736	0	ENST00000487270.1:c.669A>T	p.Gln223His	p.Q223H	ENST00000487270	NM_133509.3	223	caA/caT	7/11	0.680478799566823	2	FACETS	0.512	0.469	0.557	0.256	0.234	0.279	SUBCLONAL	1	TRUE	0	0.70946674518856	2		736	864	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0006615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	400	268	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.572408407637878	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.572408407637878	2		268	643	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604778	48604778	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767383	NA	P-0006615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	345	259	1	ENST00000342988.3:c.1600C>T	p.Gln534Ter	p.Q534*	ENST00000342988	NM_005359.5	534	Cag/Tag	12/12	0.552407057036393	2	FACETS	0.951	0.909	0.992	0.951	0.909	0.992	CLONAL	2	TRUE	0	0.572408407637878	2		260	634	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670788	134670788	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	179	195	0	ENST00000398015.3:c.699C>A	p.Asp233Glu	p.D233E	ENST00000398015	NM_004441.4	233	gaC/gaA	3/16	0.42811865562563	4	FACETS	0.818	0.758	0.88	0.818	0.758	0.88	CLONAL	2	TRUE	2	0.572408407637878	4		195	601	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354424	354427	+	frameshift_variant	Frame_Shift_Del	DEL	CGGC	CGGC	-	novel	NA	P-0006615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	375	298	1	ENST00000262320.3:c.1131_1134del	p.Pro378ArgfsTer35	p.P378Rfs*35	ENST00000262320	NM_003502.3	377	gtGCCG/gt	5/11	0.572408407637878	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.572408407637878	2		299	608	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577054	7577054	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	406	304	0	ENST00000269305.4:c.884del	p.Pro295LeufsTer50	p.P295Lfs*50	ENST00000269305	NM_001126112.2	295	cCt/ct	8/11	0.572408407637878	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.572408407637878	2		304	688	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0006616-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	121	570	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	0.224761590063287	2		570	904	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0006616-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	88	531	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	FALSE	1	0.224761590063287	2		531	767	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499710	18499710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006616-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	37	364	1	ENST00000266497.5:c.1565C>T	p.Pro522Leu	p.P522L	ENST00000266497		522	cCt/cTt	10/31	1	2	FACETS	0.516	0.424	0.619	0.516	0.424	0.619	SUBCLONAL	1	FALSE	1	0.224761590063287	2		365	638	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405654	139405654	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006616-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	57	218	0	ENST00000277541.6:c.2537A>C	p.Gln846Pro	p.Q846P	ENST00000277541	NM_017617.3	846	cAa/cCa	16/34	0.224761590063287	1	FACETS	0.91	0.781	1	0.91	0.781	1	CLONAL	1	FALSE	0	0.224761590063287	1		218	495	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298776	15298776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755398328	NA	P-0006616-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	87	333	1	ENST00000263388.2:c.1522G>A	p.Val508Met	p.V508M	ENST00000263388	NM_000435.2	508	Gtg/Atg	10/33	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	FALSE	1	0.224761590063287	2		334	688	SUCCESS
AXL	558	MSKCC	GRCh37	19	41759587	41759587	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006616-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	46	395	0	ENST00000301178.4:c.2010C>G	p.His670Gln	p.H670Q	ENST00000301178	NM_021913.4	670	caC/caG	17/20	1	2	FACETS	0.465	0.39	0.548	0.465	0.39	0.548	SUBCLONAL	1	FALSE	1	0.224761590063287	2		395	881	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006617-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	35	370	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.597	0.488	0.72	0.597	0.488	0.72	SUBCLONAL	1	TRUE	1	0.2	2		370	586	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0006617-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	100	295	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.190146157354182	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.2	1		295	852	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0006617-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	41	358	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.619	0.515	0.736	0.619	0.515	0.736	SUBCLONAL	1	TRUE	1	0.2	2		358	662	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0006620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	153	254	7	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.200173690726216	2	FACETS	0.754	0.69	0.821	0.754	0.69	0.821	SUBCLONAL	2	TRUE	0	0.229497279212514	2		261	884	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0006620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	64	366	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	0.229497279212514	1	FACETS	0.524	0.452	0.602	0.524	0.452	0.602	SUBCLONAL	1	TRUE	0	0.229497279212514	1		366	942	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285817	87285817	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	152	473	0	ENST00000277120.3:c.154A>T	p.Ile52Phe	p.I52F	ENST00000277120		52	Atc/Ttc	2/19	0.229497279212514	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.229497279212514	1		473	1143	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674272	86674276	+	frameshift_variant	Frame_Shift_Del	DEL	ATGAA	ATGAA	-	novel	NA	P-0006620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	38	305	0	ENST00000274376.6:c.2405_2409del	p.Met802SerfsTer26	p.M802Sfs*26	ENST00000274376	NM_002890.2	802	ATGAAa/a	18/25	0.229497279212514	1	FACETS	0.392	0.323	0.47	0.392	0.323	0.47	SUBCLONAL	1	TRUE	0	0.229497279212514	1		305	748	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564081	139564081	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200217167	NA	P-0006625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	249	720	1	ENST00000308874.7:c.221G>A	p.Arg74His	p.R74H	ENST00000308874		74	cGc/cAc	5/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.459956405456528	2		721	956	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636064	28636064	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	278	489	0	ENST00000241453.7:c.308G>T	p.Cys103Phe	p.C103F	ENST00000241453	NM_004119.2	103	tGt/tTt	3/24	1	2	FACETS	0.929	0.871	0.989	0.929	0.871	0.989	CLONAL	1	TRUE	1	0.459956405456528	2		489	1301	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858738	9858738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149698593	NA	P-0006625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	200	410	0	ENST00000330684.3:c.2663C>T	p.Thr888Met	p.T888M	ENST00000330684	NM_001134407.1	888	aCg/aTg	13/13	1	2	FACETS	0.942	0.874	1	0.942	0.874	1	CLONAL	1	TRUE	1	0.459956405456528	2		410	923	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424167	49424168	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0006625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	146	417	2	ENST00000301067.7:c.13894_13895delinsTT	p.Pro4632Leu	p.P4632L	ENST00000301067	NM_003482.3	4632	CCa/TTa	42/54	1	2	FACETS	0.75	0.684	0.818	0.75	0.684	0.818	SUBCLONAL	1	TRUE	1	0.459956405456528	2		419	847	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913315	NA	P-0006663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	95	410	0	ENST00000326873.7:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000326873	NM_000455.4	194	Gac/Tac	4/10	0.153219988927886	2	FACETS	0.912	0.812	1	0.912	0.812	1	CLONAL	2	TRUE	0	0.153219988927886	2		410	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782144	NA	P-0006663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	98	382	0	ENST00000269305.4:c.473G>C	p.Arg158Pro	p.R158P	ENST00000269305	NM_001126112.2	158	cGc/cCc	5/11	0.148118401495661	2	FACETS	0.924	0.825	1	0.924	0.825	1	CLONAL	2	TRUE	0	0.153219988927886	2		382	692	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732727	204732727	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	109	366	0	ENST00000302823.3:c.62C>A	p.Pro21His	p.P21H	ENST00000302823	NM_005214.4	21	cCc/cAc	1/4	0.153219988927886	3	FACETS	0.918	0.824	1	0.918	0.824	1	CLONAL	2	TRUE	1	0.153219988927886	3		366	834	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285182	212285182	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	71	356	0	ENST00000342788.4:c.3119G>C	p.Arg1040Thr	p.R1040T	ENST00000342788	NM_005235.2	1040	aGa/aCa	25/28	0.153219988927886	3	FACETS	0.889	0.777	1	0.889	0.777	1	CLONAL	2	TRUE	1	0.153219988927886	3		356	561	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632276	215632276	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	65	515	0	ENST00000260947.4:c.1498G>C	p.Asp500His	p.D500H	ENST00000260947	NM_000465.2	500	Gat/Cat	6/11	0.153219988927886	3	FACETS	1	0.909	1	0.533	0.461	0.611	CLONAL	1	TRUE	1	0.153219988927886	3		515	857	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928295	69928295	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	115	320	1	ENST00000352241.4:c.115G>T	p.Glu39Ter	p.E39*	ENST00000352241	NM_198159.2	39	Gag/Tag	2/10	0.148118401495661	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	2	TRUE	0	0.153219988927886	2		321	742	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391084	89391084	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	135	412	0	ENST00000336596.2:c.1150C>A	p.Pro384Thr	p.P384T	ENST00000336596	NM_005233.5	384	Cct/Act	5/17	0.148118401495661	2	FACETS	0.996	0.905	1	0.996	0.905	1	CLONAL	2	TRUE	0	0.153219988927886	2		412	885	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141119	55141119	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	57	370	0	ENST00000257290.5:c.1765C>A	p.Pro589Thr	p.P589T	ENST00000257290	NM_006206.4	589	Cca/Aca	12/23	0.148118401495661	2	FACETS	1	0.897	1	0.529	0.453	0.612	CLONAL	1	TRUE	0	0.153219988927886	2		370	703	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146561	55146561	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs763727620	NA	P-0006663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	65	424	0	ENST00000257290.5:c.2235G>T	p.Met745Ile	p.M745I	ENST00000257290	NM_006206.4	745	atG/atT	16/23	0.148118401495661	2	FACETS	1	0.885	1	0.512	0.443	0.588	CLONAL	1	TRUE	0	0.153219988927886	2		424	828	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504379	149504379	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1420457092	NA	P-0006663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	117	392	0	ENST00000261799.4:c.1823C>A	p.Ser608Tyr	p.S608Y	ENST00000261799	NM_002609.3	608	tCt/tAt	13/23	0.148118401495661	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	0	0.153219988927886	2		392	720	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680106	30680106	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs756858990	NA	P-0006663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	140	511	0	ENST00000376406.3:c.1613T>C	p.Ile538Thr	p.I538T	ENST00000376406	NM_014641.2	538	aTa/aCa	5/15	0.153219988927886	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.153219988927886	3		511	853	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704571	117704571	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	69	441	0	ENST00000368508.3:c.2405A>G	p.Tyr802Cys	p.Y802C	ENST00000368508	NM_002944.2	802	tAc/tGc	16/43	0.153219988927886	3	FACETS	1	0.947	1	0.589	0.512	0.673	CLONAL	1	TRUE	1	0.153219988927886	3		441	823	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341190	8341190	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	61	457	1	ENST00000356435.5:c.5026G>A	p.Val1676Ile	p.V1676I	ENST00000356435		1676	Gtt/Att	30/35	0.153219988927886	2	FACETS	1	0.89	1	0.519	0.447	0.598	CLONAL	1	TRUE	0	0.153219988927886	2		458	767	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331797	68331797	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	77	523	0	ENST00000487270.1:c.393G>T	p.Met131Ile	p.M131I	ENST00000487270	NM_133509.3	131	atG/atT	5/11	0.153219988927886	3	FACETS	0.876	0.766	0.995	0.438	0.383	0.498	CLONAL	1	TRUE	1	0.153219988927886	3		523	1235	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779649	3779649	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	111	390	1	ENST00000262367.5:c.5399G>T	p.Arg1800Leu	p.R1800L	ENST00000262367	NM_004380.2	1800	cGg/cTg	31/31	0.153219988927886	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	1	0.153219988927886	3		391	705	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10271060	10271060	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs370592431	NA	P-0006663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	87	357	0	ENST00000340748.4:c.995C>T	p.Pro332Leu	p.P332L	ENST00000340748		332	cCa/cTa	13/40	0.153219988927886	2	FACETS	0.872	0.773	0.979	0.872	0.773	0.979	CLONAL	2	TRUE	0	0.153219988927886	2		357	651	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134270	11134270	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	117	386	0	ENST00000358026.2:c.2936G>T	p.Arg979Leu	p.R979L	ENST00000358026	NM_001128849.1	979	cGa/cTa	20/36	0.153219988927886	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.153219988927886	2		386	669	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943652	17943652	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	156	454	0	ENST00000458235.1:c.2437G>T	p.Asp813Tyr	p.D813Y	ENST00000458235	NM_000215.3	813	Gac/Tac	18/24	0.153219988927886	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.153219988927886	2		454	921	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100992	41100992	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	125	409	0	ENST00000373198.4:c.1364T>C	p.Phe455Ser	p.F455S	ENST00000373198	NM_133170.3	455	tTc/tCc	8/32	0.153219988927886	3	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	1	0.153219988927886	3		409	840	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41740116	41740116	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0006663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	14	97	0	ENST00000242208.4:c.-143-1G>T		p.X48_splice	ENST00000242208	NM_002192.2	48			0.153219988927886	3	FACETS	1	0.85	1	0.647	0.47	0.859	CLONAL	1	TRUE	1	0.153219988927886	3		97	152	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006672-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	70	260	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.306922331709301	2		260	391	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0006672-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	64	189	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.306922331709301	2		189	344	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888211	112888211	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121918465	NA	P-0006672-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	52	434	0	ENST00000351677.2:c.227A>G	p.Glu76Gly	p.E76G	ENST00000351677	NM_002834.3	76	gAg/gGg	3/16	1	2	FACETS	0.555	0.472	0.646	0.555	0.472	0.646	SUBCLONAL	1	TRUE	1	0.306922331709301	2		434	611	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684326	29684326	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201367	NA	P-0006672-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	89	355	1	ENST00000356175.3:c.7846C>T	p.Arg2616Ter	p.R2616*	ENST00000356175	NM_000267.3	2616	Cga/Tga	53/57	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.306922331709301	2		356	578	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505026	149505026	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006672-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	126	244	0	ENST00000261799.4:c.1789C>T	p.Arg597Trp	p.R597W	ENST00000261799	NM_002609.3	597	Cgg/Tgg	12/23	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.306922331709301	2		244	706	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953107	81953107	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006672-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	216	590	0	ENST00000359376.3:c.2073G>T	p.Lys691Asn	p.K691N	ENST00000359376	NM_002661.3	691	aaG/aaT	20/33	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.306922331709301	2		590	1369	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	68	370	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.398915824402761	3	FACETS	0.903	0.789	1	0.452	0.394	0.514	CLONAL	1	TRUE	1	0.41278804375995	3		370	440	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0006693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	304	254	7	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.365997762650463	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.41278804375995	2		261	712	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0006693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	163	341	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	0.41278804375995	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	0	0.41278804375995	2		341	395	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0006693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	243	317	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.41278804375995	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	0	0.41278804375995	3		317	446	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420688	49420688	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783695	NA	P-0006693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	121	257	0	ENST00000301067.7:c.15061C>T	p.Arg5021Ter	p.R5021*	ENST00000301067	NM_003482.3	5021	Cga/Tga	48/54	0.398915824402761	3	FACETS	0.998	0.902	1	0.499	0.451	0.549	CLONAL	1	TRUE	1	0.41278804375995	3		257	709	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660124	12660124	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	90	458	0	ENST00000251849.4:c.97G>C	p.Val33Leu	p.V33L	ENST00000251849	NM_002880.3	33	Gtt/Ctt	2/17	0.32836896677903	4	FACETS	0.77	0.683	0.864	0.385	0.341	0.432	SUBCLONAL	1	TRUE	2	0.41278804375995	4		458	800	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956965	2956965	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142828146	NA	P-0006693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	314	365	0	ENST00000396946.4:c.2662C>T	p.Arg888Cys	p.R888C	ENST00000396946	NM_032415.4	888	Cgt/Tgt	20/25	0.32836896677903	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.41278804375995	4		365	1038	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006697-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	226	260	0				ENST00000310581	NM_198253.2	-/1132			0.209141035071617	5	FACETS	1	0.954	1	1	0.954	1	INDETERMINATE	3	FALSE	2	0.402559496770083	5		260	589	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473780	67473780	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730880214	NA	P-0006697-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	111	256	1	ENST00000327367.4:c.860G>A	p.Arg287Gln	p.R287Q	ENST00000327367	NM_005902.3	287	cGg/cAg	6/9	0.174688912114987	3	FACETS	0.919	0.827	1	0.306	0.275	0.339	INDETERMINATE	1	FALSE	0	0.402559496770083	3		257	721	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806089	1806089	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913479	NA	P-0006697-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	211	406	0	ENST00000260795.2:c.1108G>T	p.Gly370Cys	p.G370C	ENST00000260795		370	Ggc/Tgc	8/17	0.209141035071617	5	FACETS	1	0.99	1	0.465	0.431	0.5	INDETERMINATE	1	FALSE	2	0.402559496770083	5		406	1206	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226825	142226825	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006697-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	231	309	2	ENST00000350721.4:c.4979C>A	p.Ser1660Ter	p.S1660*	ENST00000350721	NM_001184.3	1660	tCa/tAa	28/47	0.402559496770083	5	FACETS	1	0.975	1			1	CLONAL	3	FALSE	NA	0.402559496770083	5		311	574	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404754	404754	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006697-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	197	373	0	ENST00000399788.2:c.4440C>G	p.Phe1480Leu	p.F1480L	ENST00000399788	NM_001042603.1	1480	ttC/ttG	26/28	0.209141035071617	5	FACETS	0.981	0.91	1	0.654	0.607	0.703	INDETERMINATE	2	FALSE	2	0.402559496770083	5		373	800	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058951	42058951	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006697-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	267	536	0	ENST00000219905.7:c.8671C>G	p.Gln2891Glu	p.Q2891E	ENST00000219905	NM_001164273.1	2891	Caa/Gaa	24/24	0.174688912114987	3	FACETS	1	0.993	1	0.498	0.467	0.53	INDETERMINATE	1	FALSE	0	0.402559496770083	3		536	1066	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949156	44949156	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006697-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	244	199	0	ENST00000377967.4:c.3717G>T	p.Trp1239Cys	p.W1239C	ENST00000377967	NM_021140.2	1239	tgG/tgT	25/29	0.402559496770083	2	FACETS	1	0.954	1			1	CLONAL	3	FALSE	NA	0.402559496770083	2		199	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0006700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	50	395	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.156797508939517	1	FACETS	0.837	0.714	0.971	0.837	0.714	0.971	INDETERMINATE	1	TRUE	0	0.31201722265353	1		395	323	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937695	36937695	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	54	616	0	ENST00000361632.4:c.1043A>G	p.Asp348Gly	p.D348G	ENST00000361632		348	gAc/gGc	8/16	1	2	FACETS	0.911	0.781	1	0.911	0.781	1	CLONAL	1	TRUE	1	0.31201722265353	2		616	380	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748001	72748001	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0006700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	26	732	0	ENST00000357731.5:c.176+1G>A		p.X59_splice	ENST00000357731	NM_173808.2	59			1	2	FACETS	0.337	0.266	0.418	0.337	0.266	0.418	SUBCLONAL	1	TRUE	1	0.31201722265353	2		732	495	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012322	176012322	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	60	551	0	ENST00000367669.3:c.1612G>A	p.Val538Met	p.V538M	ENST00000367669	NM_022457.5	538	Gtg/Atg	14/20	0.31201722265353	3	FACETS	1	0.944	1	0.59	0.51	0.675	CLONAL	1	TRUE	1	0.31201722265353	3		551	377	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215884	98215884	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	31	372	0	ENST00000331920.6:c.3325G>C	p.Gly1109Arg	p.G1109R	ENST00000331920	NM_000264.3	1109	Ggc/Cgc	20/24	0.258626125865799	2	FACETS	0.707	0.574	0.857	0.354	0.287	0.429	SUBCLONAL	1	TRUE	0	0.31201722265353	2		372	281	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21565425	21565425	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	52	630	0	ENST00000382592.4:c.461A>C	p.Lys154Thr	p.K154T	ENST00000382592	NM_014572.2	154	aAg/aCg	3/8	0.268112428343613	3	FACETS	0.815	0.694	0.946	0.407	0.347	0.473	CLONAL	1	TRUE	1	0.31201722265353	3		630	473	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434788	99434788	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	24	424	0	ENST00000268035.6:c.875A>G	p.Asp292Gly	p.D292G	ENST00000268035	NM_000875.3	292	gAc/gGc	3/21	0.156797508939517	1	FACETS	0.47	0.369	0.586	0.47	0.369	0.586	INDETERMINATE	1	TRUE	0	0.31201722265353	1		424	276	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99452063	99452063	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	58	447	1	ENST00000268035.6:c.1397C>A	p.Thr466Lys	p.T466K	ENST00000268035	NM_000875.3	466	aCg/aAg	6/21	0.156797508939517	1	FACETS	1	0.915	1	1	0.915	1	INDETERMINATE	1	TRUE	0	0.31201722265353	1		448	291	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900479	3900479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759312345	NA	P-0006700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	33	665	1	ENST00000262367.5:c.617C>T	p.Ala206Val	p.A206V	ENST00000262367	NM_004380.2	206	gCg/gTg	2/31	0.31201722265353	1	FACETS	0.438	0.356	0.529	0.438	0.356	0.529	SUBCLONAL	1	TRUE	0	0.31201722265353	1		666	408	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832028	72832028	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs770545151	NA	P-0006700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	68	766	0	ENST00000268489.5:c.4553G>T	p.Gly1518Val	p.G1518V	ENST00000268489	NM_006885.3	1518	gGc/gTc	9/10	0.30600802568187	0	FACETS	0.666	0.581	0.758			1	SUBCLONAL	1	TRUE	0	0.31201722265353	0		766	450	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266939	18266939	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773024898	NA	P-0006700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	38	148	0	ENST00000222254.8:c.250G>A	p.Ala84Thr	p.A84T	ENST00000222254	NM_005027.3	84	Gcc/Acc	2/16	0.258626125865799	2	FACETS	0.776	0.651	0.91	0.776	0.651	0.91	CLONAL	2	TRUE	0	0.31201722265353	2		148	157	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0006701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	182	268	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.460784513366214	4	FACETS	1	0.986	1	0.434	0.401	0.469	CLONAL	1	TRUE	1	0.481669137238731	4		268	860	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0006701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	68	229	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.447334853738628	3	FACETS	1	0.907	1	0.521	0.457	0.59	CLONAL	1	TRUE	1	0.481669137238731	3		229	336	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0006701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	243	405	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	0.447334853738628	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	1	0.481669137238731	3		405	620	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166812	32166812	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs917534864	NA	P-0006701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	80	344	0	ENST00000375023.3:c.4426C>T	p.Arg1476Ter	p.R1476*	ENST00000375023	NM_004557.3	1476	Cga/Tga	24/30	0.19451432348272	5	FACETS	0.541	0.475	0.612	0.18	0.158	0.204	INDETERMINATE	1	TRUE	2	0.481669137238731	5		344	1058	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171645	32171645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	193	296	0	ENST00000375023.3:c.3133G>A	p.Val1045Met	p.V1045M	ENST00000375023	NM_004557.3	1045	Gtg/Atg	20/30	0.19451432348272	5	FACETS	1	0.952	1	0.688	0.639	0.738	INDETERMINATE	2	TRUE	2	0.481669137238731	5		296	669	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0006706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	200	254	7	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.20466143377108	2	FACETS	0.898	0.836	0.961	0.898	0.836	0.961	INDETERMINATE	2	TRUE	0	0.343301676323152	2		261	649	SUCCESS
APC	324	MSKCC	GRCh37	5	112175174	112175174	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	76	259	0	ENST00000257430.4:c.3883G>T	p.Glu1295Ter	p.E1295*	ENST00000257430	NM_000038.5	1295	Gaa/Taa	16/16	0.249060908809516	3	FACETS	0.935	0.821	1	0.467	0.41	0.529	CLONAL	1	TRUE	1	0.343301676323152	3		259	555	SUCCESS
APC	324	MSKCC	GRCh37	5	112175340	112175340	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	123	354	0	ENST00000257430.4:c.4049A>C	p.Lys1350Thr	p.K1350T	ENST00000257430	NM_000038.5	1350	aAa/aCa	16/16	0.249060908809516	3	FACETS	1	0.964	1	0.567	0.513	0.623	CLONAL	1	TRUE	1	0.343301676323152	3		354	741	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184978	32184978	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	310	547	1	ENST00000375023.3:c.1690G>T	p.Gly564Trp	p.G564W	ENST00000375023	NM_004557.3	564	Ggg/Tgg	10/30	0.235061895124696	3	FACETS	1	0.968	1	0.691	0.652	0.73	CLONAL	2	TRUE	0	0.343301676323152	3		548	1021	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940411	13940411	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	83	479	0	ENST00000405192.2:c.1095A>T	p.Lys365Asn	p.K365N	ENST00000405192	NM_001163147.1	365	aaA/aaT	11/12	0.343301676323152	5	FACETS	0.638	0.561	0.721	0.16	0.14	0.181	SUBCLONAL	1	TRUE	1	0.343301676323152	5		479	1148	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856596	111856596	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	120	139	0	ENST00000341259.2:c.647G>A	p.Arg216His	p.R216H	ENST00000341259	NM_005475.2	216	cGc/cAc	2/8	1	2	FACETS	0.99	0.905	1	1	0.99	1	CLONAL	2	TRUE	1	0.343301676323152	2		139	353	SUCCESS
APC	324	MSKCC	GRCh37	5	112175328	112175335	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCCAGG	CAGCCAGG	-	novel	NA	P-0006706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	119	378	0	ENST00000257430.4:c.4039_4046del	p.Ala1347GlnfsTer4	p.A1347Qfs*4	ENST00000257430	NM_000038.5	1346	tCAGCCAGG/t	16/16	0.249060908809516	3	FACETS	1	0.947	1	0.536	0.484	0.591	CLONAL	1	TRUE	1	0.343301676323152	3		378	758	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0006721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	201	570	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.273261807811792	2	FACETS	1	0.989	1	0.664	0.618	0.712	CLONAL	1	TRUE	0	0.42491234698373	2		570	712	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775569	39775569	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	210	448	0	ENST00000288319.7:c.451G>C	p.Gly151Arg	p.G151R	ENST00000288319	NM_182918.3	151	Ggc/Cgc	4/10	0.261428140828731	2	FACETS	0.912	0.854	0.971	0.912	0.854	0.971	CLONAL	2	TRUE	0	0.42491234698373	2		448	542	SUCCESS
APC	324	MSKCC	GRCh37	5	112175498	112175498	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	175	437	0	ENST00000257430.4:c.4207del	p.Ser1403AlafsTer12	p.S1403Afs*12	ENST00000257430	NM_000038.5	1403	Agc/gc	16/16	0.321869126790951	3	FACETS	1	0.965	1	0.708	0.658	0.759	CLONAL	2	TRUE	0	0.42491234698373	3		437	470	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967012	25967013	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCAGTTCCAGTGTGGGGCCCTTT	novel	NA	P-0006721-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	80	503	0	ENST00000435504.4:c.2193_2194insAAAGGGCCCCACACTGGAACTGG	p.Ala732LysfsTer75	p.A732Kfs*75	ENST00000435504		731	-/AAAGGGCCCCACACTGGAACTGG	13/13	0.385453695677706	5	FACETS	0.811	0.713	0.916	0.27	0.237	0.306	CLONAL	1	TRUE	2	0.42491234698373	5		503	760	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0006736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	38	254	7	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.15519861769259	2	FACETS	1	0.897	1	0.562	0.464	0.67	CLONAL	1	TRUE	0	0.15519861769259	2		261	436	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576096	88576096	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	47	569	1	ENST00000360948.2:c.1577C>A	p.Pro526Gln	p.P526Q	ENST00000360948	NM_001012338.2	526	cCg/cAg	13/19	1	2	FACETS	0.897	0.756	1	0.897	0.756	1	CLONAL	1	TRUE	1	0.15519861769259	2		570	675	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71161741	71161741	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	81	582	2	ENST00000318789.4:c.228G>T	p.Gln76His	p.Q76H	ENST00000318789	NM_032682.5	76	caG/caT	7/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.15519861769259	2		584	710	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0006744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	349	430	1	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.569462336956309	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.569462336956309	2		431	598	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0006744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	124	255	0	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	0.527897444856177	3	FACETS	0.978	0.888	1	0.489	0.444	0.536	CLONAL	1	TRUE	1	0.569462336956309	3		255	572	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472663	88472663	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	70	261	0	ENST00000360948.2:c.1892C>A	p.Ala631Asp	p.A631D	ENST00000360948	NM_001012338.2	631	gCc/gAc	16/19	1	2	FACETS	0.897	0.791	1	0.897	0.791	1	CLONAL	1	TRUE	1	0.569462336956309	2		261	274	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352556	89352556	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	79	509	0	ENST00000301030.4:c.783G>C	p.Gln261His	p.Q261H	ENST00000301030	NM_001256183.1	261	caG/caC	8/13	0.527897444856177	3	FACETS	0.346	0.303	0.392	0.173	0.151	0.196	SUBCLONAL	1	TRUE	1	0.569462336956309	3		509	1031	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740840	58740840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149137187	NA	P-0006744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1691	278	722	0	ENST00000305921.3:c.1745G>A	p.Arg582His	p.R582H	ENST00000305921	NM_003620.3	582	cGc/cAc	6/6	0.43445213209628	5	FACETS	0.919	0.86	0.981	0.306	0.286	0.327	CLONAL	1	TRUE	2	0.569462336956309	5		722	1969	SUCCESS
APC	324	MSKCC	GRCh37	5	112173451	112173451	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	326	396	2	ENST00000257430.4:c.2162del	p.Gly721GlufsTer6	p.G721Efs*6	ENST00000257430	NM_000038.5	720	atG/at	16/16	0.527897444856177	3	FACETS	0.865	0.821	0.91	0.865	0.821	0.91	CLONAL	2	TRUE	1	0.569462336956309	3		398	850	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0006771-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	65	366	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.235983774166085	1	FACETS	0.902	0.783	1	0.902	0.783	1	CLONAL	1	TRUE	0	0.243928679728675	1		366	519	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561423	9561423	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201131316	NA	P-0006771-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	135	362	1	ENST00000353224.5:c.359C>T	p.Ala120Val	p.A120V	ENST00000353224	NM_177990.2	120	gCg/gTg	4/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.243928679728675	2		363	767	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546065	29546065	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1135402815	NA	P-0006771-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	57	375	1	ENST00000356175.3:c.1570G>T	p.Glu524Ter	p.E524*	ENST00000356175	NM_000267.3	524	Gaa/Taa	14/57	0.235983774166085	1	FACETS	0.644	0.552	0.745	0.644	0.552	0.745	SUBCLONAL	1	TRUE	0	0.243928679728675	1		376	637	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675622	86675622	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0006771-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	49	244	0	ENST00000274376.6:c.2558C>G	p.Ser853Ter	p.S853*	ENST00000274376	NM_002890.2	853	tCa/tGa	19/25	1	2	FACETS	0.875	0.742	1	0.875	0.742	1	CLONAL	1	TRUE	1	0.243928679728675	2		244	459	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546099	29546099	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006771-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	53	350	0	ENST00000356175.3:c.1604A>T	p.Gln535Leu	p.Q535L	ENST00000356175	NM_000267.3	535	cAg/cTg	14/57	0.235983774166085	1	FACETS	0.642	0.547	0.747	0.642	0.547	0.747	SUBCLONAL	1	TRUE	0	0.243928679728675	1		350	594	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006778-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	93	221	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.747	0.665	0.835	0.747	0.665	0.835	SUBCLONAL	1	FALSE	1	0.39142429265493	2		222	636	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0006778-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	105	254	7	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.196402640320019	2	FACETS	1	0.978	1	0.656	0.592	0.723	INDETERMINATE	1	FALSE	0	0.39142429265493	2		261	409	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743777	46743777	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1356611440	NA	P-0006778-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	54	557	0	ENST00000371975.4:c.2067G>C	p.Gln689His	p.Q689H	ENST00000371975	NM_003579.3	689	caG/caC	18/18	1	2	FACETS	0.428	0.365	0.498	0.428	0.365	0.498	SUBCLONAL	1	FALSE	1	0.39142429265493	2		557	644	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119779	70119779	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1555629290	NA	P-0006778-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	149	637	0	ENST00000245479.2:c.781G>T	p.Glu261Ter	p.E261*	ENST00000245479	NM_000346.3	261	Gag/Tag	3/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.39142429265493	2		637	625	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266028	41266420	+	splice_donor_variant,coding_sequence_variant,intron_variant	In_Frame_Del	DEL	GAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGT	GAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGT	-	novel	NA	P-0006778-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	106	460	0	ENST00000349496.5:c.29_242-21del		p.E9_D81del	ENST00000349496	NM_001904.3	9		3/15	0.196402640320019	2	FACETS	0.9	0.808	0.996	0.45	0.404	0.498	INDETERMINATE	1	FALSE	0	0.39142429265493	2		460	602	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0006787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	218	385	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.303429686502767	5	FACETS	0.922	0.864	0.98	0.922	0.864	0.98	CLONAL	3	TRUE	2	0.471550952689224	5		385	571	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0006787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	119	254	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.303429686502767	5	FACETS	0.994	0.912	1	0.994	0.912	1	CLONAL	3	TRUE	2	0.471550952689224	5		254	289	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204515931	204515931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	590	541	0	ENST00000367182.3:c.829G>A	p.Glu277Lys	p.E277K	ENST00000367182	NM_001278516.1	277	Gaa/Aaa	10/11	0.471550952689224	7	FACETS	0.935	0.903	0.968	0.935	0.903	0.968	CLONAL	5	TRUE	2	0.471550952689224	7		541	1166	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497952	25497952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	108	239	0	ENST00000264709.3:c.497C>T	p.Ser166Phe	p.S166F	ENST00000264709	NM_175629.2	166	tCc/tTc	6/23	0.475298526730312	4	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.471550952689224	4		239	518	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215595214	215595214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752870879	NA	P-0006787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	158	359	0	ENST00000260947.4:c.1922G>A	p.Arg641Gln	p.R641Q	ENST00000260947	NM_000465.2	641	cGa/cAa	10/11	0.475298526730312	4	FACETS	0.841	0.78	0.902	1	0.986	1	CLONAL	3	TRUE	2	0.471550952689224	4		359	391	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504987	186504987	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1980299	NA	P-0006787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	440	638	2	ENST00000323963.5:c.843T>A	p.Asn281Lys	p.N281K	ENST00000323963		281	aaT/aaA	8/11	0.303429686502767	5	FACETS	0.852	0.814	0.892	0.852	0.814	0.892	CLONAL	3	TRUE	2	0.471550952689224	5		640	1246	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807856	1807856	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	234	545	0	ENST00000260795.2:c.1915G>T	p.Ala639Ser	p.A639S	ENST00000260795		639	Gcc/Tcc	13/17	0.360585153139628	5	FACETS	0.996	0.937	1			1	CLONAL	3	TRUE	NA	0.471550952689224	5		545	567	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138603	55138603	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61735621	NA	P-0006787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	78	431	1	ENST00000257290.5:c.1280C>T	p.Ser427Leu	p.S427L	ENST00000257290	NM_006206.4	427	tCa/tTa	9/23	NA	2	FACETS	1	0.946	1			1	INDETERMINATE	1	TRUE	NA	0.471550952689224	2		432	298	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245420	153245420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	265	406	1	ENST00000281708.4:c.1771G>A	p.Asp591Asn	p.D591N	ENST00000281708	NM_033632.3	591	Gac/Aac	11/12	0.303429686502767	5	FACETS	0.984	0.929	1	0.984	0.929	1	CLONAL	3	TRUE	2	0.471550952689224	5		407	650	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840069	27840069	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	371	817	1	ENST00000328488.2:c.25C>T	p.Arg9Cys	p.R9C	ENST00000328488	NM_003533.2	9	Cgc/Tgc	1/1	0.471550952689224	7	FACETS	0.891	0.845	0.938	0.669	0.634	0.704	CLONAL	3	TRUE	3	0.471550952689224	7		818	1282	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117870635	117870635	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	463	651	0	ENST00000297338.2:c.437G>C	p.Arg146Thr	p.R146T	ENST00000297338	NM_006265.2	146	aGa/aCa	5/14	0.471550952689224	5	FACETS	0.974	0.933	1	0.974	0.933	1	CLONAL	3	TRUE	2	0.471550952689224	5		651	1147	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770065	56770065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752608224	NA	P-0006787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	24	508	0	ENST00000337432.4:c.61C>T	p.Pro21Ser	p.P21S	ENST00000337432	NM_058216.2	21	Cca/Tca	1/9	0.475298526730312	3	FACETS	0.345	0.27	0.431	0.115	0.09	0.144	SUBCLONAL	1	TRUE	0	0.471550952689224	3		508	365	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168931	11168931	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	88	376	0	ENST00000358026.2:c.4521C>A	p.Ser1507Arg	p.S1507R	ENST00000358026	NM_001128849.1	1507	agC/agA	32/36	0.475298526730312	4	FACETS	1	0.973	1	0.657	0.585	0.733	CLONAL	1	TRUE	2	0.471550952689224	4		376	418	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034483	123034483	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	44	486	0	ENST00000355640.3:c.1240C>G	p.Leu414Val	p.L414V	ENST00000355640		414	Cta/Gta	6/7	0.47049538615851	2	FACETS	0.562	0.473	0.66	0.281	0.236	0.33	SUBCLONAL	1	TRUE	0	0.471550952689224	2		486	332	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120378	94120378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	128	617	0	ENST00000369303.4:c.673del	p.Ser225ProfsTer3	p.S225Pfs*3	ENST00000369303	NM_004440.3	225	Tcc/cc	3/17	0.475298526730312	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.471550952689224	1		617	316	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923087	39923087	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	171	362	0	ENST00000378444.4:c.3621del	p.Lys1207AsnfsTer31	p.K1207Nfs*31	ENST00000378444	NM_001123385.1	1207	aaA/aa	8/15	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.258022740747249	1		362	830	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027599	48027599	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	29	244	0	ENST00000234420.5:c.2477A>G	p.His826Arg	p.H826R	ENST00000234420	NM_000179.2	826	cAt/cGt	4/10	1	2	FACETS	0.494	0.396	0.606	0.494	0.396	0.606	SUBCLONAL	1	TRUE	1	0.258022740747249	2		244	455	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87322770	87322770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781137734	NA	P-0006790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	45	357	0	ENST00000277120.3:c.371G>A	p.Arg124Gln	p.R124Q	ENST00000277120		124	cGa/cAa	5/19	1	2	FACETS	0.404	0.338	0.477	0.404	0.338	0.477	SUBCLONAL	1	TRUE	1	0.258022740747249	2		357	864	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577150	7577150	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	146	498	0	ENST00000269305.4:c.788del	p.Asn263IlefsTer82	p.N263Ifs*82	ENST00000269305	NM_001126112.2	263	aAt/at	8/11	0.142535792939171	1	FACETS	0.765	0.696	0.837	0.765	0.696	0.837	INDETERMINATE	1	TRUE	0	0.258022740747249	1		498	1289	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398280	25398281	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0006790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	152	430	1	ENST00000311936.3:c.38_39delinsTT	p.Gly13Val	p.G13V	ENST00000311936	NM_004985.3	13	gGC/gTT	2/5	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.258022740747249	2		431	949	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510819	120510819	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs782540275	NA	P-0006791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	465	443	0	ENST00000256646.2:c.1145A>G	p.Asn382Ser	p.N382S	ENST00000256646	NM_024408.3	382	aAt/aGt	7/34	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.923259087940371	2		443	992	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	256	260	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		260	576	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211804	123211806	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TAG	TAG	-	novel	NA	P-0006792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	512	435	1	ENST00000218089.9:c.2674-1_2675del		p.X892_splice	ENST00000218089	NM_001042749.1	892			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		436	703	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	12	221	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.214827524832613	3	FACETS	0.798	0.563	1	0.399	0.281	0.543	CLONAL	1	TRUE	1	0.214827524832613	3		222	155	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0006817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	21	228	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.172956176787206	3	FACETS	1	0.918	1	0.741	0.576	0.93	CLONAL	1	TRUE	1	0.214827524832613	3		229	146	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553539	106553539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762241140	NA	P-0006817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	20	144	2	ENST00000369096.4:c.1504G>A	p.Ala502Thr	p.A502T	ENST00000369096	NM_001198.3	502	Gcc/Acc	5/7	0.214827524832613	6	FACETS	1	0.871	1			1	CLONAL	1	TRUE	NA	0.214827524832613	6		146	218	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006852-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	199	260	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.767	0.722	0.812	1	0.993	1	SUBCLONAL	2	TRUE	1	0.675795620020291	2		260	384	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0006852-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	420	531	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	0.994	1	CLONAL	1	TRUE	1	0.675795620020291	2		531	980	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699242	117699242	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006852-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	351	378	0	ENST00000369458.3:c.399C>G	p.Ile133Met	p.I133M	ENST00000369458	NM_024626.3	133	atC/atG	3/6	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.675795620020291	2		378	845	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147570	47147570	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006852-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	250	277	1	ENST00000409792.3:c.4756C>G	p.His1586Asp	p.H1586D	ENST00000409792	NM_014159.6	1586	Cat/Gat	6/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.675795620020291	2		278	677	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949096	44949096	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006852-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	467	256	0	ENST00000377967.4:c.3657G>C	p.Trp1219Cys	p.W1219C	ENST00000377967	NM_021140.2	1219	tgG/tgC	25/29	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.675795620020291	1		256	628	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587781702	NA	P-0006854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	251	370	0	ENST00000269305.4:c.920-1G>C		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.759885438415427	1	FACETS	0.979	0.933	1	0.979	0.933	1	CLONAL	1	TRUE	0	0.774243056326662	1		370	406	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0006854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	435	194	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.743701780325791	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	1	0.774243056326662	4		194	655	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	228	291	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.774243056326662	2		291	563	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0006910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	1676	469	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.677922549077687	6	FACETS	1	0.998	1			1	CLONAL	6	TRUE	NA	0.854156463336646	6		469	1744	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031815	10031815	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs397518465	NA	P-0006910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	117	165	0	ENST00000330684.3:c.1007+1G>A		p.X336_splice	ENST00000330684	NM_001134407.1	336			0.75904449521554	1	FACETS	0.662	0.611	0.714	0.662	0.611	0.714	SUBCLONAL	1	TRUE	0	0.854156463336646	1		165	237	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061463	38061463	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	543	275	0	ENST00000250448.2:c.526A>G	p.Ile176Val	p.I176V	ENST00000250448	NM_004496.3	176	Atc/Gtc	2/2	0.854156463336646	7	FACETS	1	0.991	1			1	CLONAL	3	TRUE	NA	0.854156463336646	7		275	1215	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142990	30142990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316424431	NA	P-0006910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	17	333	2	ENST00000389048.3:c.536G>A	p.Arg179His	p.R179H	ENST00000389048	NM_004304.4	179	cGc/cAc	1/29	0.854156463336646	1	FACETS	0.069	0.051	0.091	0.069	0.051	0.091	SUBCLONAL	1	TRUE	0	0.854156463336646	1		335	330	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859846	151859846	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0006910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	274	324	0	ENST00000262189.6:c.10816A>T	p.Arg3606Ter	p.R3606*	ENST00000262189	NM_170606.2	3606	Aga/Tga	43/59	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.854156463336646	2		324	614	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120854	115120854	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	439	233	0	ENST00000257566.3:c.152del	p.Ala51GlyfsTer37	p.A51Gfs*37	ENST00000257566	NM_016569.3	51	gCg/gg	1/8	0.854156463336646	6	FACETS	0.979	0.938	1			1	CLONAL	3	TRUE	NA	0.854156463336646	6		233	948	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847253	68847253	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	354	369	0	ENST00000261769.5:c.1175del	p.Val392GlufsTer5	p.V392Efs*5	ENST00000261769	NM_004360.3	392	gTa/ga	9/16	0.854156463336646	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.854156463336646	1		369	415	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156737	20156737	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	458	426	0	ENST00000379607.5:c.20A>G	p.Lys7Arg	p.K7R	ENST00000379607	NM_001412.3	7	aAa/aGa	2/7	0.8475299380796	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.8475299380796	2		426	539	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0006923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	154	346	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	1	2	FACETS	1	0.915	1	1	0.991	1	CLONAL	2	TRUE	1	0.172693043655423	2		346	892	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212487	133212487	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	98	346	0	ENST00000320574.5:c.5802C>G	p.His1934Gln	p.H1934Q	ENST00000320574	NM_006231.2	1934	caC/caG	42/49	0.172693043655423	2	FACETS	1	0.974	1	0.655	0.583	0.731	CLONAL	1	TRUE	0	0.172693043655423	2		346	867	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339942	70339942	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1243	103	521	0	ENST00000374080.3:c.475C>A	p.Leu159Ile	p.L159I	ENST00000374080		159	Ctc/Atc	4/45	1	2	FACETS	0.886	0.79	0.989	0.886	0.79	0.989	CLONAL	1	TRUE	1	0.172693043655423	2		521	1346	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188196	10188196	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs869025637	NA	P-0006935-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	226	318	0	ENST00000256474.2:c.341-2A>G		p.X114_splice	ENST00000256474	NM_000551.3	114			0.501277173845327	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.510129558267091	1		318	630	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223788	53223789	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0006935-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	291	234	0	ENST00000375401.3:c.3570_3571del	p.Cys1190TrpfsTer13	p.C1190Wfs*13	ENST00000375401	NM_004187.3	1190	tgTGgg/tggg	23/26	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.510129558267091	1		234	648	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598116	52598119	+	protein_altering_variant	In_Frame_Del	DEL	CTTC	CTTC	A	novel	NA	P-0006935-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	191	420	0	ENST00000394830.3:c.3747_3750delinsT	p.Leu1249_Lys1250delinsPhe	p.L1249_K1250delinsF	ENST00000394830	NM_018313.4	1249	ttGAAG/ttT	24/30	0.501277173845327	1	FACETS	0.824	0.765	0.885	0.824	0.765	0.885	CLONAL	1	TRUE	0	0.510129558267091	1		420	677	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0006938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	82	531	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.779	0.69	0.873	1	0.979	1	SUBCLONAL	2	FALSE	1	0.238192267845056	2		531	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0006942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	42	373	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.674	0.561	0.801	0.674	0.561	0.801	SUBCLONAL	1	TRUE	1	0.14	2		373	890	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968580	55968580	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs767881241	NA	P-0006942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	56	603	1	ENST00000263923.4:c.2083C>A	p.Pro695Thr	p.P695T	ENST00000263923	NM_002253.2	695	Cct/Act	14/30	1	2	FACETS	0.851	0.727	0.988	0.851	0.727	0.988	CLONAL	1	TRUE	1	0.14	2		604	940	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509624	106509624	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	64	680	0	ENST00000359195.3:c.1618G>T	p.Gly540Trp	p.G540W	ENST00000359195	NM_002649.2	540	Ggg/Tgg	2/11	1	2	FACETS	0.917	0.792	1	0.917	0.792	1	CLONAL	1	TRUE	1	0.14	2		680	997	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066888	77066888	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0006942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	45	413	0	ENST00000356341.3:c.598-1G>T		p.X200_splice	ENST00000356341	NM_002576.4	200			1	2	FACETS	0.903	0.757	1	0.903	0.757	1	CLONAL	1	TRUE	1	0.14	2		413	712	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954237	32954237	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	55	644	0	ENST00000380152.3:c.9211G>T	p.Glu3071Ter	p.E3071*	ENST00000380152		3071	Gag/Tag	24/27	1	2	FACETS	0.734	0.626	0.854	0.734	0.626	0.854	SUBCLONAL	1	TRUE	1	0.14	2		644	1070	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553501	29553501	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	54	575	0	ENST00000356175.3:c.2050C>T	p.Gln684Ter	p.Q684*	ENST00000356175	NM_000267.3	684	Cag/Tag	18/57	1	2	FACETS	0.793	0.675	0.923	0.793	0.675	0.923	CLONAL	1	TRUE	1	0.14	2		575	973	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132477	11132477	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	52	650	0	ENST00000358026.2:c.2693A>G	p.Asn898Ser	p.N898S	ENST00000358026	NM_001128849.1	898	aAc/aGc	19/36	1	2	FACETS	0.815	0.691	0.951	0.815	0.691	0.951	CLONAL	1	TRUE	1	0.14	2		650	912	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31025100	31025100	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	62	534	0	ENST00000375687.4:c.4585G>A	p.Gly1529Arg	p.G1529R	ENST00000375687	NM_015338.5	1529	Gga/Aga	13/13	1	2	FACETS	0.989	0.852	1	0.989	0.852	1	CLONAL	1	TRUE	1	0.14	2		534	896	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034416	47034416	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0006942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	69	590	0	ENST00000377604.3:c.503-2A>T		p.X168_splice	ENST00000377604	NM_001204468.1	168			0.0987990269068554	0	FACETS	1	0.908	1			1	CLONAL	1	TRUE	0	0.14	0		590	803	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102196257	102196259	+	missense_variant	Missense_Mutation	TNP	GAG	GAG	AAA	novel	NA	P-0006942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1357	94	812	0	ENST00000263464.3:c.914_916delinsAAA	p.Gly305_Asp306delinsGluAsn	p.G305_D306delinsEN	ENST00000263464	NM_001165.4	305	gGAGat/gAAAat	3/9	1	2	FACETS	0.925	0.82	1	0.925	0.82	1	CLONAL	1	TRUE	1	0.14	2		812	1451	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476318	88476318	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	317	494	0	ENST00000360948.2:c.1814G>T	p.Gly605Val	p.G605V	ENST00000360948	NM_001012338.2	605	gGa/gTa	15/19	1	2	FACETS	0.948	0.895	1	0.948	0.895	1	CLONAL	1	TRUE	1	0.621057002748003	2		494	1077	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578433	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555526101	NA	P-0006976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	336	415	0	ENST00000269305.4:c.497C>G	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	166	tCa/tGa	5/11	0.621057002748003	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.621057002748003	1		415	685	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092812	27092812	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	341	511	0	ENST00000324856.7:c.2833G>T	p.Gly945Ter	p.G945*	ENST00000324856	NM_006015.4	945	Gga/Tga	9/20	0.280109781397807	1	FACETS	0.683	0.647	0.72	0.683	0.647	0.72	INDETERMINATE	1	TRUE	0	0.621057002748003	1		511	1108	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430334	78430334	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	142	367	0	ENST00000370768.2:c.834A>G	p.Ile278Met	p.I278M	ENST00000370768	NM_003902.3	278	atA/atG	10/20	0.280109781397807	1	FACETS	0.351	0.319	0.384	0.351	0.319	0.384	INDETERMINATE	1	TRUE	0	0.621057002748003	1		367	899	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012883	176012883	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1174	229	555	0	ENST00000367669.3:c.1493G>T	p.Trp498Leu	p.W498L	ENST00000367669	NM_022457.5	498	tGg/tTg	13/20	0.310037669301295	2	FACETS	0.526	0.488	0.564	0.263	0.244	0.282	INDETERMINATE	1	TRUE	0	0.621057002748003	2		555	1403	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662389	227662389	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	229	403	0	ENST00000305123.5:c.1066G>C	p.Ala356Pro	p.A356P	ENST00000305123	NM_005544.2	356	Gcc/Ccc	1/2	1	2	FACETS	0.827	0.772	0.883	0.827	0.772	0.883	CLONAL	1	TRUE	1	0.621057002748003	2		403	892	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119721078	119721078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	252	363	0	ENST00000316626.5:c.97G>A	p.Asp33Asn	p.D33N	ENST00000316626		33	Gac/Aac	2/12	NA	2	FACETS	0.894	0.838	0.951			1	INDETERMINATE	1	TRUE	NA	0.621057002748003	2		363	908	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549835	187549835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	318	396	1	ENST00000441802.2:c.4406C>T	p.Thr1469Ile	p.T1469I	ENST00000441802	NM_005245.3	1469	aCa/aTa	8/27	0.410195585469781	1	FACETS	0.797	0.755	0.84	0.797	0.755	0.84	SUBCLONAL	1	TRUE	0	0.621057002748003	1		397	886	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729984	41729984	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs766987359	NA	P-0006976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	433	768	2	ENST00000242208.4:c.545C>A	p.Pro182Gln	p.P182Q	ENST00000242208	NM_002192.2	182	cCg/cAg	3/3	1	2	FACETS	0.859	0.817	0.902	0.859	0.817	0.902	CLONAL	1	TRUE	1	0.621057002748003	2		770	1623	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246213	46246213	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	347	525	0	ENST00000334344.6:c.4307A>C	p.Asn1436Thr	p.N1436T	ENST00000334344	NM_152641.2	1436	aAt/aCt	15/21	1	2	FACETS	0.86	0.813	0.907	0.86	0.813	0.907	CLONAL	1	TRUE	1	0.621057002748003	2		525	1300	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438726	49438726	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	324	515	0	ENST00000301067.7:c.4764A>T	p.Glu1588Asp	p.E1588D	ENST00000301067	NM_003482.3	1588	gaA/gaT	19/54	1	2	FACETS	0.898	0.848	0.949	0.898	0.848	0.949	CLONAL	1	TRUE	1	0.621057002748003	2		515	1162	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857547	57857547	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	362	537	1	ENST00000228682.2:c.73C>T	p.Gln25Ter	p.Q25*	ENST00000228682	NM_005269.2	25	Cag/Tag	2/12	1	2	FACETS	0.975	0.924	1	0.975	0.924	1	CLONAL	1	TRUE	1	0.621057002748003	2		538	1196	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41011093	41011093	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	387	562	0	ENST00000267868.3:c.526G>A	p.Glu176Lys	p.E176K	ENST00000267868	NM_002875.4	176	Gag/Aag	6/10	1	2	FACETS	0.912	0.866	0.96	0.912	0.866	0.96	CLONAL	1	TRUE	1	0.621057002748003	2		562	1366	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792773	33792773	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1222448862	NA	P-0006976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	60	92	0	ENST00000498907.2:c.548C>A	p.Pro183Gln	p.P183Q	ENST00000498907	NM_004364.3	183	cCg/cAg	1/1	1	2	FACETS	0.981	0.859	1	0.981	0.859	1	CLONAL	1	TRUE	1	0.621057002748003	2		92	197	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374361	138374362	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0006976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	93	283	0	ENST00000289153.2:c.3082_3083del	p.Leu1028CysfsTer6	p.L1028Cfs*6	ENST00000289153	NM_006219.2	1028	CTt/t	22/22	0.472234628515976	4	FACETS	0.425	0.377	0.477	0.142	0.125	0.159	SUBCLONAL	1	TRUE	1	0.621057002748003	4		283	1142	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11181302	11181302	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0006976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	137	446	0	ENST00000361445.4:c.6933+1del		p.X2311_splice	ENST00000361445	NM_004958.3	2311			0.410195585469781	1	FACETS	0.365	0.332	0.4	0.365	0.332	0.4	SUBCLONAL	1	TRUE	0	0.621057002748003	1		446	834	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879885	37879885	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	338	478	4	ENST00000269571.5:c.2180G>C	p.Gly727Ala	p.G727A	ENST00000269571		727	gGa/gCa	18/27	0.660504868401856	3	FACETS	1	0.989	1			1	CLONAL	1	FALSE	NA	0.660504868401856	3		482	1160	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257388	16257388	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	124	412	0	ENST00000375759.3:c.4653A>T	p.Glu1551Asp	p.E1551D	ENST00000375759	NM_015001.2	1551	gaA/gaT	11/15	1	2	FACETS	0.49	0.443	0.539	0.49	0.443	0.539	SUBCLONAL	1	FALSE	1	0.660504868401856	2		412	766	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873092	134873092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	157	479	4	ENST00000398015.3:c.1396G>A	p.Asp466Asn	p.D466N	ENST00000398015	NM_004441.4	466	Gac/Aac	6/16	1	2	FACETS	0.504	0.461	0.548	0.504	0.461	0.548	SUBCLONAL	1	FALSE	1	0.660504868401856	2		483	944	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141060	55141060	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	136	442	0	ENST00000257290.5:c.1706G>T	p.Gly569Val	p.G569V	ENST00000257290	NM_006206.4	569	gGa/gTa	12/23	1	2	FACETS	0.436	0.396	0.478	0.436	0.396	0.478	SUBCLONAL	1	FALSE	1	0.660504868401856	2		442	945	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808343	99808343	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	72	250	0	ENST00000280892.6:c.346G>T	p.Asp116Tyr	p.D116Y	ENST00000280892	NM_001130678.1	116	Gat/Tat	5/7	1	2	FACETS	0.409	0.358	0.464	0.409	0.358	0.464	SUBCLONAL	1	FALSE	1	0.660504868401856	2		250	533	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510308	187510308	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs778375461	NA	P-0006979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	290	328	1	ENST00000441802.2:c.13205A>C	p.Asn4402Thr	p.N4402T	ENST00000441802	NM_005245.3	4402	aAc/aCc	27/27	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.660504868401856	2		329	756	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170121	32170121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	125	387	0	ENST00000375023.3:c.3487C>T	p.His1163Tyr	p.H1163Y	ENST00000375023	NM_004557.3	1163	Cac/Tac	21/30	1	2	FACETS	0.535	0.485	0.588	0.535	0.485	0.588	SUBCLONAL	1	FALSE	1	0.660504868401856	2		387	707	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183157	32183157	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs562471310	NA	P-0006979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	242	386	3	ENST00000375023.3:c.1867C>G	p.Leu623Val	p.L623V	ENST00000375023	NM_004557.3	623	Ctc/Gtc	12/30	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.660504868401856	2		389	686	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100310	8100310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	152	448	3	ENST00000346208.3:c.284C>T	p.Pro95Leu	p.P95L	ENST00000346208		95	cCc/cTc	3/6	1	2	FACETS	0.545	0.498	0.593	0.545	0.498	0.593	SUBCLONAL	1	FALSE	1	0.660504868401856	2		451	845	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332922	70332922	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	141	555	1	ENST00000373644.4:c.827G>T	p.Arg276Leu	p.R276L	ENST00000373644	NM_030625.2	276	cGa/cTa	2/12	1	2	FACETS	0.432	0.393	0.473	0.432	0.393	0.473	SUBCLONAL	1	FALSE	1	0.660504868401856	2		556	988	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588108	69588108	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	127	507	0	ENST00000168712.1:c.590T>C	p.Met197Thr	p.M197T	ENST00000168712	NM_002007.2	197	aTg/aCg	3/3	1	2	FACETS	0.481	0.435	0.528	0.481	0.435	0.528	SUBCLONAL	1	FALSE	1	0.660504868401856	2		507	800	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114168	115114168	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	172	519	0	ENST00000257566.3:c.1049C>A	p.Ala350Asp	p.A350D	ENST00000257566	NM_016569.3	350	gCc/gAc	6/8	1	2	FACETS	0.502	0.461	0.544	0.502	0.461	0.544	SUBCLONAL	1	FALSE	1	0.660504868401856	2		519	1038	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862876	9862876	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1064795647	NA	P-0006979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	189	412	0	ENST00000330684.3:c.2427C>A	p.Ser809Arg	p.S809R	ENST00000330684	NM_001134407.1	809	agC/agA	12/13	0.22574998247265	4	FACETS	0.697	0.642	0.754			1	INDETERMINATE	1	FALSE	NA	0.660504868401856	4		412	1364	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs786201057	NA	P-0006979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	132	326	1	ENST00000269305.4:c.374C>A	p.Thr125Lys	p.T125K	ENST00000269305	NM_001126112.2	125	aCg/aAg	4/11	0.660504868401856	2	FACETS	0.724	0.66	0.791	0.362	0.33	0.396	SUBCLONAL	1	FALSE	0	0.660504868401856	2		327	552	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15952238	15952238	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	204	486	0	ENST00000268712.3:c.6457C>T	p.Pro2153Ser	p.P2153S	ENST00000268712	NM_006311.3	2153	Ccc/Tcc	41/46	0.22574998247265	4	FACETS	0.792	0.733	0.854			1	INDETERMINATE	1	FALSE	NA	0.660504868401856	4		486	1295	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879838	37879838	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	321	459	4	ENST00000269571.5:c.2133G>C	p.Gln711His	p.Q711H	ENST00000269571		711	caG/caC	18/27	0.660504868401856	3	FACETS	1	0.992	1			1	CLONAL	1	FALSE	NA	0.660504868401856	3		463	1028	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63537617	63537617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502160	NA	P-0006979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	127	544	0	ENST00000307078.5:c.1015C>T	p.Arg339Cys	p.R339C	ENST00000307078	NM_004655.3	339	Cgc/Tgc	4/11	1	2	FACETS	0.364	0.329	0.401	0.364	0.329	0.401	SUBCLONAL	1	FALSE	1	0.660504868401856	2		544	1057	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220415	1220415	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913323	NA	P-0006979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	135	462	2	ENST00000326873.7:c.508C>T	p.Gln170Ter	p.Q170*	ENST00000326873	NM_000455.4	170	Cag/Tag	4/10	0.660504868401856	1	FACETS	0.447	0.408	0.489	0.447	0.408	0.489	SUBCLONAL	1	FALSE	0	0.660504868401856	1		464	612	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610382	10610382	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	138	484	0	ENST00000171111.5:c.328A>G	p.Met110Val	p.M110V	ENST00000171111	NM_203500.1	110	Atg/Gtg	2/6	0.660504868401856	1	FACETS	0.439	0.4	0.479	0.439	0.4	0.479	SUBCLONAL	1	FALSE	0	0.660504868401856	1		484	638	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719050	52719050	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs777655260	NA	P-0006979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	181	419	1	ENST00000322088.6:c.826C>A	p.Pro276Thr	p.P276T	ENST00000322088	NM_014225.5	276	Cct/Act	7/15	0.660504868401856	2	FACETS	0.73	0.675	0.787	0.365	0.337	0.394	SUBCLONAL	1	FALSE	0	0.660504868401856	2		420	751	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101834	11101835	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AT	novel	NA	P-0006979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	126	455	0	ENST00000358026.2:c.1254_1255delinsAT	p.Glu419Ter	p.E419*	ENST00000358026	NM_001128849.1	418	caGGag/caATag	8/36	0.660504868401856	1	FACETS	0.42	0.381	0.46	0.42	0.381	0.46	SUBCLONAL	1	FALSE	0	0.660504868401856	1		455	609	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178632	108178632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766901049	NA	P-0006982-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	34	304	0	ENST00000278616.4:c.5683C>T	p.His1895Tyr	p.H1895Y	ENST00000278616	NM_000051.3	1895	Cac/Tac	38/63	0.133313603658202	3	FACETS	0.527	0.429	0.637	0.263	0.214	0.319	INDETERMINATE	1	TRUE	1	0.26	3		304	561	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272413	15272413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372627766	NA	P-0006982-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	22	570	0	ENST00000263388.2:c.6026G>A	p.Arg2009Gln	p.R2009Q	ENST00000263388	NM_000435.2	2009	cGg/cAg	33/33	0.133313603658202	0	FACETS	0.374	0.289	0.472			1	INDETERMINATE	1	TRUE	0	0.26	0		570	335	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750956	128750956	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	125	410	2	ENST00000377970.2:c.493G>T	p.Ala165Ser	p.A165S	ENST00000377970	NM_002467.4	165	Gcc/Tcc	2/3	0.27791352784222	4	FACETS	0.828	0.752	0.907	0.828	0.752	0.907	CLONAL	2	TRUE	2	0.365427058463803	4		412	564	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533836	533836	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	106	569	0	ENST00000451590.1:c.220A>C	p.Thr74Pro	p.T74P	ENST00000451590	NM_001130442.1	74	Acc/Ccc	3/5	0.365427058463803	3	FACETS	0.932	0.836	1	0.466	0.418	0.517	CLONAL	1	TRUE	1	0.365427058463803	3		569	736	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343114	118343114	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	151	408	2	ENST00000534358.1:c.1240G>T	p.Val414Phe	p.V414F	ENST00000534358	NM_005933.3	414	Gtc/Ttc	3/36	0.354445441089869	2	FACETS	0.879	0.81	0.95	0.879	0.81	0.95	CLONAL	2	TRUE	0	0.365427058463803	2		410	470	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148902	119148902	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	151	426	0	ENST00000264033.4:c.1124del	p.Gly375AlafsTer17	p.G375Afs*17	ENST00000264033	NM_005188.3	374	atG/at	8/16	0.354445441089869	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.365427058463803	2		426	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0006990-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	306	295	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.442752857128966	2	FACETS	0.945	0.897	0.995	0.945	0.897	0.995	CLONAL	2	TRUE	0	0.442752857128966	2		295	731	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612269	189612269	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs34713855	NA	P-0006990-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	77	165	0	ENST00000264731.3:c.2021G>T	p.Arg674Leu	p.R674L	ENST00000264731	NM_003722.4	674	cGc/cTc	14/14	0.408044298555524	3	FACETS	0.715	0.628	0.808	0.358	0.314	0.404	SUBCLONAL	1	TRUE	1	0.442752857128966	3		165	594	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361223	66361223	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006990-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	255	256	0	ENST00000273854.3:c.949C>G	p.Gln317Glu	p.Q317E	ENST00000273854	NM_004439.5	317	Cag/Gag	4/18	0.442752857128966	2	FACETS	0.853	0.804	0.904	0.853	0.804	0.904	CLONAL	2	TRUE	0	0.442752857128966	2		256	675	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993075	90993075	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006990-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	80	106	0	ENST00000265433.3:c.367T>C	p.Ser123Pro	p.S123P	ENST00000265433	NM_002485.4	123	Tct/Cct	4/16	0.442752857128966	8	FACETS	1	0.943	1	0.187	0.164	0.212	CLONAL	1	TRUE	2	0.442752857128966	8		106	749	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878848	117878848	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006990-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1960	123	312	0	ENST00000297338.2:c.121G>C	p.Val41Leu	p.V41L	ENST00000297338	NM_006265.2	41	Gtg/Ctg	2/14	0.442752857128966	8	FACETS	0.621	0.559	0.688	0.104	0.093	0.115	SUBCLONAL	1	TRUE	2	0.442752857128966	8		312	2083	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78933911	78933911	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006990-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	164	304	0	ENST00000306801.3:c.3511A>T	p.Ser1171Cys	p.S1171C	ENST00000306801	NM_020761.2	1171	Agt/Tgt	30/34	0.442752857128966	6	FACETS	1	0.985	1	0.266	0.243	0.289	CLONAL	1	TRUE	1	0.442752857128966	6		304	1051	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040930	47040930	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006990-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	34	274	0	ENST00000377604.3:c.1460G>C	p.Gly487Ala	p.G487A	ENST00000377604	NM_001204468.1	487	gGg/gCg	14/24	0.442752857128966	2	FACETS	0.279	0.227	0.338	0.14	0.113	0.169	SUBCLONAL	1	TRUE	0	0.442752857128966	2		274	550	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177763	56177763	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006990-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	100	254	0	ENST00000399503.3:c.2739del	p.Gly914AspfsTer7	p.G914Dfs*7	ENST00000399503	NM_005921.1	912	ggA/gg	14/20	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.442752857128966	NA		254	568	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989355	7989361	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTCTC	GGGTCTC	-	novel	NA	P-0006990-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	112	271	0	ENST00000319144.4:c.325_331del	p.Glu109TrpfsTer86	p.E109Wfs*86	ENST00000319144	NM_001139.2	109	GAGACCCtg/tg	2/15	0.442752857128966	2	FACETS	1	0.905	1	0.501	0.452	0.552	CLONAL	1	TRUE	0	0.442752857128966	2		271	505	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989365	7989369	+	frameshift_variant	Frame_Shift_Del	DEL	GCCAT	GCCAT	-	novel	NA	P-0006990-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	105	278	0	ENST00000319144.4:c.317_321del	p.Asp106ValfsTer17	p.D106Vfs*17	ENST00000319144	NM_001139.2	106	gATGGC/g	2/15	0.442752857128966	2	FACETS	0.878	0.79	0.972	0.439	0.395	0.486	CLONAL	1	TRUE	0	0.442752857128966	2		278	540	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117861226	117861229	+	frameshift_variant	Frame_Shift_Del	DEL	TTCT	TTCT	-	novel	NA	P-0006990-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1827	114	287	0	ENST00000297338.2:c.1660_1663del	p.Arg554AspfsTer57	p.R554Dfs*57	ENST00000297338	NM_006265.2	554	AGAAga/ga	13/14	0.442752857128966	8	FACETS	0.618	0.553	0.687	0.103	0.092	0.115	SUBCLONAL	1	TRUE	2	0.442752857128966	8		287	1941	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0006995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	400	478	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	NA	2	FACETS	0.924	0.891	0.955			1	INDETERMINATE	2	TRUE	NA	0.720487252934301	2		478	601	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242483	55242506	+	inframe_deletion	In_Frame_Del	DEL	ATCTCCGAAAGCCAACAAGGAAAT	ATCTCCGAAAGCCAACAAGGAAAT	-	rs727504232	NA	P-0006995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	1479	386	1	ENST00000275493.2:c.2253_2276del	p.Ser752_Ile759del	p.S752_I759del	ENST00000275493	NM_005228.3	751	acATCTCCGAAAGCCAACAAGGAAATc/acc	19/28	0.720487252934301	11	FACETS	1	0.995	1	0.807	0.791	0.823	CLONAL	7	TRUE	2	0.720487252934301	11		387	2397	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900250	101900250	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	31	409	0	ENST00000374994.4:c.684A>T	p.Glu228Asp	p.E228D	ENST00000374994	NM_004612.2	228	gaA/gaT	4/9	0.410449581751972	1	FACETS	0.096	0.077	0.117	0.096	0.077	0.117	INDETERMINATE	1	TRUE	0	0.720487252934301	1		409	576	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041266	47041266	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0006995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	261	472	0	ENST00000377604.3:c.1693+1G>T		p.X565_splice	ENST00000377604	NM_001204468.1	565			0.649318610178598	1	FACETS	0.832	0.788	0.877	0.832	0.788	0.877	CLONAL	1	TRUE	0	0.720487252934301	1		472	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0006996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	539	552	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.560742586815483	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	TRUE	0	0.562845605032241	3		552	818	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146540	185146540	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs139333467	NA	P-0006996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	130	338	0	ENST00000265026.3:c.171C>G	p.Ile57Met	p.I57M	ENST00000265026	NM_004721.4	57	atC/atG	2/14	0.341868548499078	5	FACETS	0.912	0.827	1	0.304	0.275	0.334	CLONAL	1	TRUE	2	0.562845605032241	5		338	934	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467509	66467509	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	324	441	0	ENST00000273854.3:c.760C>A	p.Gln254Lys	p.Q254K	ENST00000273854	NM_004439.5	254	Caa/Aaa	3/18	0.425927147266459	4	FACETS	0.911	0.862	0.96			1	CLONAL	2	TRUE	NA	0.562845605032241	4		441	988	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400005	139400005	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1479377696	NA	P-0006996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	148	344	1	ENST00000277541.6:c.4343C>T	p.Ala1448Val	p.A1448V	ENST00000277541	NM_017617.3	1448	gCg/gTg	25/34	0.552110943975458	3	FACETS	0.953	0.872	1	0.318	0.29	0.346	CLONAL	1	TRUE	0	0.562845605032241	3		345	707	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560947	9560947	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	184	357	0	ENST00000353224.5:c.835C>G	p.Gln279Glu	p.Q279E	ENST00000353224	NM_177990.2	279	Cag/Gag	4/10	0.566195827591085	3	FACETS	0.952	0.879	1			1	CLONAL	1	TRUE	NA	0.562845605032241	3		357	880	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504056	123504056	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1362460627	NA	P-0006996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	293	300	1	ENST00000371139.4:c.232C>T	p.Arg78Trp	p.R78W	ENST00000371139	NM_001114937.2	78	Cgg/Tgg	3/4	0.504629895477894	5	FACETS	1	0.992	1			1	CLONAL	1	TRUE	NA	0.562845605032241	5		301	1422	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606196	47606199	+	splice_region_variant,intron_variant	Splice_Region	DEL	GAGT	GAGT	-	novel	NA	P-0006996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	138	284	0	ENST00000263735.4:c.657+3_657+6del		p.X219_splice	ENST00000263735	NM_002354.2	219			0.381350691997496	5	FACETS	0.945	0.859	1	0.315	0.286	0.345	CLONAL	1	TRUE	2	0.562845605032241	5		284	957	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0007004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	196	356	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.382061826756645	2		356	760	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220717	1220717	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587782018	NA	P-0007004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	154	695	0	ENST00000326873.7:c.734+1G>T		p.X245_splice	ENST00000326873	NM_000455.4	245			0.382061826756645	1	FACETS	0.769	0.711	0.828	1	0.99	1	SUBCLONAL	2	TRUE	0	0.382061826756645	1		695	424	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71064719	71064719	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	128	717	0	ENST00000318789.4:c.955G>C	p.Asp319His	p.D319H	ENST00000318789	NM_032682.5	319	Gat/Cat	12/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.382061826756645	2		717	628	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486233	8486233	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	177	923	0	ENST00000356435.5:c.2584C>G	p.Arg862Gly	p.R862G	ENST00000356435		862	Cgc/Ggc	17/35	0.225867067419356	1	FACETS	1	0.979	1	1	0.979	1	INDETERMINATE	1	TRUE	0	0.382061826756645	1		923	646	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518067	8518067	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	144	831	0	ENST00000356435.5:c.1324G>T	p.Glu442Ter	p.E442*	ENST00000356435		442	Gaa/Taa	10/35	0.225867067419356	1	FACETS	1	0.933	1	1	0.933	1	INDETERMINATE	1	TRUE	0	0.382061826756645	1		831	597	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007484	62007484	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	184	1229	0	ENST00000392795.3:c.383A>G	p.Asn128Ser	p.N128S	ENST00000392795	NM_001039933.1	128	aAc/aGc	3/6	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.382061826756645	2		1229	846	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426638	47426638	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	135	1229	0	ENST00000377045.4:c.883G>T	p.Gly295Trp	p.G295W	ENST00000377045	NM_001654.4	295	Ggg/Tgg	10/16	0.255177227465427	1	FACETS	0.64	0.581	0.702	0.64	0.581	0.702	SUBCLONAL	1	TRUE	0	0.382061826756645	1		1229	893	SUCCESS
APC	324	MSKCC	GRCh37	5	112173494	112173494	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs559313229	NA	P-0007012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	43	332	0	ENST00000257430.4:c.2203G>C	p.Ala735Pro	p.A735P	ENST00000257430	NM_000038.5	735	Gcg/Ccg	16/16	0.301559134653572	2	FACETS	0.306	0.255	0.363	0.153	0.127	0.182	SUBCLONAL	1	TRUE	0	0.356466492440815	2		332	788	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	185	299	0	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	0.301559134653572	2	FACETS	1	0.99	1	0.745	0.69	0.801	CLONAL	1	TRUE	0	0.356466492440815	2		299	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057520007	NA	P-0007012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	489	575	2	ENST00000269305.4:c.614A>C	p.Tyr205Ser	p.Y205S	ENST00000269305	NM_001126112.2	205	tAt/tCt	6/11	0.356466492440815	2	FACETS	0.987	0.944	1	0.987	0.944	1	CLONAL	2	TRUE	0	0.356466492440815	2		577	1390	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054378	13054378	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1835	140	780	0	ENST00000316448.5:c.988T>G	p.Phe330Val	p.F330V	ENST00000316448	NM_004343.3	330	Ttc/Gtc	8/9	0.166403300399817	2	FACETS	0.398	0.36	0.437	0.199	0.18	0.219	INDETERMINATE	1	TRUE	0	0.356466492440815	2		780	1975	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285027	15285028	+	missense_variant	Missense_Mutation	DNP	CG	CG	AA	novel	NA	P-0007012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	93	517	1	ENST00000263388.2:c.4587_4588delinsTT	p.Asp1530Tyr	p.D1530Y	ENST00000263388	NM_000435.2	1529	gcCGac/gcTTac	25/33	0.166403300399817	2	FACETS	0.484	0.429	0.544	0.242	0.214	0.272	INDETERMINATE	1	TRUE	0	0.356466492440815	2		518	1077	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288735	15288735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	48	113	0	ENST00000263388.2:c.4004G>A	p.Ser1335Asn	p.S1335N	ENST00000263388	NM_000435.2	1335	aGc/aAc	24/33	0.166403300399817	2	FACETS	0.866	0.736	1	0.433	0.368	0.504	INDETERMINATE	1	TRUE	0	0.356466492440815	2		113	311	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794685	42794685	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767618694	NA	P-0007012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	107	491	1	ENST00000575354.2:c.1765C>T	p.Arg589Trp	p.R589W	ENST00000575354	NM_015125.3	589	Cgg/Tgg	10/20	0.232007218699553	1	FACETS	0.466	0.417	0.518	0.466	0.417	0.518	SUBCLONAL	1	TRUE	0	0.356466492440815	1		492	1059	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938769	76938769	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	85	187	0	ENST00000373344.5:c.1979A>C	p.Lys660Thr	p.K660T	ENST00000373344	NM_000489.3	660	aAg/aCg	9/35	0.190283940147799	2	FACETS	0.933	0.827	1			1	INDETERMINATE	1	TRUE	NA	0.356466492440815	2		187	511	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126114	2126116	+	inframe_deletion	In_Frame_Del	DEL	GTG	GTG	-	novel	NA	P-0007012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	286	605	0	ENST00000219476.3:c.2687_2689del	p.Trp896del	p.W896del	ENST00000219476	NM_000548.3	895	atGTGg/atg	24/42	0.356466492440815	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.356466492440815	1		605	1221	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910617	29910617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199474377	NA	P-0007021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	137	414	0	ENST00000376809.5:c.157G>A	p.Asp53Asn	p.D53N	ENST00000376809	NM_002116.7	53	Gac/Aac	2/8	0.424566546621884	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.424566546621884	1		414	502	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740432	58740432	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs775750934	NA	P-0007021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1335	357	935	0	ENST00000305921.3:c.1337C>G	p.Ser446Ter	p.S446*	ENST00000305921	NM_003620.3	446	tCa/tGa	6/6	1	2	FACETS	0.994	0.939	1	0.994	0.939	1	CLONAL	1	TRUE	1	0.424566546621884	2		935	1692	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0007036-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	231	385	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	0.495805055808938	2		385	840	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0007064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	445	373	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.95	0.906	0.995	0.95	0.906	0.995	CLONAL	1	TRUE	1	0.672809301481657	2		373	1392	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645367	215645367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	416	409	0	ENST00000260947.4:c.1231C>T	p.Pro411Ser	p.P411S	ENST00000260947	NM_000465.2	411	Ccc/Tcc	4/11	1	2	FACETS	0.943	0.898	0.989	0.943	0.898	0.989	CLONAL	1	TRUE	1	0.672809301481657	2		409	1311	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0007067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	394	570	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.3	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	FALSE	0	0.3	2		570	1253	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644775	67644775	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1402646118	NA	P-0007067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	335	442	0	ENST00000264010.4:c.40G>A	p.Glu14Lys	p.E14K	ENST00000264010	NM_006565.3	14	Gaa/Aaa	3/12	0.3	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	FALSE	1	0.3	3		442	1247	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271291	1271291	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1442845192	NA	P-0007067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2079	433	493	1	ENST00000310581.5:c.2411G>T	p.Gly804Val	p.G804V	ENST00000310581	NM_198253.2	804	gGc/gTc	8/16	0.3	7	FACETS	1	0.954	1			1	CLONAL	2	FALSE	NA	0.3	7		494	2512	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68934953	68934953	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	192	346	0	ENST00000487270.1:c.1022G>T	p.Gly341Val	p.G341V	ENST00000487270	NM_133509.3	341	gGc/gTc	10/11	0.3	3	FACETS	0.962	0.892	1	0.962	0.892	1	CLONAL	2	FALSE	1	0.3	3		346	765	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14021913	14021913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	139	318	0	ENST00000311895.7:c.613G>A	p.Glu205Lys	p.E205K	ENST00000311895	NM_005236.2	205	Gaa/Aaa	4/11	NA	2	FACETS	1	0.974	1			1	INDETERMINATE	2	FALSE	NA	0.3	2		318	405	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435132	56435132	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	178	366	0	ENST00000407977.2:c.2005C>G	p.Pro669Ala	p.P669A	ENST00000407977		669	Ccc/Gcc	9/10	0.3	3	FACETS	1	0.977	1	0.58	0.534	0.629	CLONAL	1	FALSE	1	0.3	3		366	1176	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610505	10610505	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	417	396	0	ENST00000171111.5:c.205G>T	p.Glu69Ter	p.E69*	ENST00000171111	NM_203500.1	69	Gag/Tag	2/6	0.293333639297775	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	FALSE	0	0.3	2		396	1318	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024572	31024572	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	329	335	1	ENST00000375687.4:c.4057A>T	p.Arg1353Trp	p.R1353W	ENST00000375687	NM_015338.5	1353	Agg/Tgg	13/13	0.3	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	FALSE	0	0.3	2		336	931	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105240257	105240315	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CGTTGGCGTACTCCATGACAAAGCAGAGGCGGTCGTGGGTCTGGAAAGAGTACTTCAGG	CGTTGGCGTACTCCATGACAAAGCAGAGGCGGTCGTGGGTCTGGAAAGAGTACTTCAGG	-	novel	NA	P-0007067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1376	83	450	0	ENST00000349310.3:c.636_694del	p.Leu213GlyfsTer24	p.L213Gfs*24	ENST00000349310	NM_001014432.1	212	gcCCTGAAGTACTCTTTCCAGACCCACGACCGCCTCTGCTTTGTCATGGAGTACGCCAACGgg/gcgg	9/15	0.3	3	FACETS	0.436	0.383	0.494	0.218	0.191	0.247	SUBCLONAL	1	FALSE	1	0.3	3		450	1459	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0007093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	35	318	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.328	0.269	0.395	0.328	0.269	0.395	SUBCLONAL	1	TRUE	1	0.487266726929021	2		318	438	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0007093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	5541	407	29	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.487266726929021	14	FACETS	1	0.998	1			1	CLONAL	15	TRUE	NA	0.487266726929021	14		436	5907	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591092	67591092	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	229	263	0	ENST00000274335.5:c.1685G>C	p.Arg562Pro	p.R562P	ENST00000274335		562	cGt/cCt	12/15	0.495973877044047	2	FACETS	1	0.978	1	0.552	0.515	0.589	CLONAL	1	TRUE	0	0.487266726929021	2		263	852	SUCCESS
APC	324	MSKCC	GRCh37	5	112174688	112174688	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	282	410	2	ENST00000257430.4:c.3397G>C	p.Asp1133His	p.D1133H	ENST00000257430	NM_000038.5	1133	Gat/Cat	16/16	0.495973877044047	2	FACETS	1	0.985	1	0.567	0.533	0.602	CLONAL	1	TRUE	0	0.487266726929021	2		412	1020	SUCCESS
APC	324	MSKCC	GRCh37	5	112174888	112174888	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	240	311	0	ENST00000257430.4:c.3597G>C	p.Lys1199Asn	p.K1199N	ENST00000257430	NM_000038.5	1199	aaG/aaC	16/16	0.495973877044047	2	FACETS	1	0.985	1	0.586	0.549	0.625	CLONAL	1	TRUE	0	0.487266726929021	2		311	840	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576857	7576857	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	541	308	2	ENST00000269305.4:c.989T>C	p.Leu330Pro	p.L330P	ENST00000269305	NM_001126112.2	330	cTt/cCt	9/11	0.495973877044047	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.487266726929021	2		310	945	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490395	29490395	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0007093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	402	221	0	ENST00000356175.3:c.479+1G>C		p.X160_splice	ENST00000356175	NM_000267.3	160			0.480999266027707	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	3	TRUE	0	0.487266726929021	3		221	681	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0007099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	112	381	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.98	0.882	1	0.98	0.882	1	CLONAL	1	TRUE	1	0.309601161193285	2		381	738	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540652	NA	P-0007099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	156	428	0	ENST00000269305.4:c.743G>C	p.Arg248Pro	p.R248P	ENST00000269305	NM_001126112.2	248	cGg/cCg	7/11	0.275703510462091	1	FACETS	0.946	0.867	1	0.946	0.867	1	CLONAL	1	TRUE	0	0.309601161193285	1		428	900	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220382	1220382	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	135	349	0	ENST00000326873.7:c.475C>T	p.Gln159Ter	p.Q159*	ENST00000326873	NM_000455.4	159	Cag/Tag	4/10	0.306436231317016	1	FACETS	0.901	0.819	0.987	0.901	0.819	0.987	CLONAL	1	TRUE	0	0.309601161193285	1		349	818	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602584	10602584	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1208201314	NA	P-0007099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	149	283	0	ENST00000171111.5:c.994G>T	p.Gly332Cys	p.G332C	ENST00000171111	NM_203500.1	332	Ggc/Tgc	3/6	0.306436231317016	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.309601161193285	1		283	755	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023492	27023492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	185	1518	4	ENST00000324856.7:c.598C>T	p.Gln200Ter	p.Q200*	ENST00000324856	NM_006015.4	200	Cag/Tag	1/20	0.275703510462091	1	FACETS	0.985	0.909	1	0.985	0.909	1	CLONAL	1	TRUE	0	0.309601161193285	1		1522	1025	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259427	89259427	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	202	460	0	ENST00000336596.2:c.571G>T	p.Ala191Ser	p.A191S	ENST00000336596	NM_005233.5	191	Gcc/Tcc	3/17	0.275703510462091	1	FACETS	0.852	0.788	0.919	0.852	0.788	0.919	CLONAL	1	TRUE	0	0.309601161193285	1		460	1294	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971046	55971046	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	160	397	1	ENST00000263923.4:c.1751A>T	p.Tyr584Phe	p.Y584F	ENST00000263923	NM_002253.2	584	tAc/tTc	13/30	1	2	FACETS	0.858	0.785	0.934	0.858	0.785	0.934	CLONAL	1	TRUE	1	0.309601161193285	2		398	1205	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755707	57755707	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	109	211	0	ENST00000274289.3:c.80G>T	p.Gly27Val	p.G27V	ENST00000274289	NM_006622.3	27	gGa/gTa	1/14	1	2	FACETS	0.899	0.807	0.997	0.899	0.807	0.997	CLONAL	1	TRUE	1	0.309601161193285	2		211	783	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190315	32190315	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	97	214	1	ENST00000375023.3:c.424C>T	p.Gln142Ter	p.Q142*	ENST00000375023	NM_004557.3	142	Cag/Tag	3/30	0.275703510462091	1	FACETS	0.877	0.783	0.976	0.877	0.783	0.976	CLONAL	1	TRUE	0	0.309601161193285	1		215	604	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120458	70120458	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	361	388	0	ENST00000245479.2:c.1460C>T	p.Pro487Leu	p.P487L	ENST00000245479	NM_000346.3	487	cCt/cTt	3/3	0.309601161193285	2	FACETS	0.932	0.883	0.982	0.932	0.883	0.982	CLONAL	2	TRUE	0	0.309601161193285	2		388	1251	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424426	47424426	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	155	403	1	ENST00000377045.4:c.346C>A	p.Leu116Ile	p.L116I	ENST00000377045	NM_001654.4	116	Ctt/Att	5/16	1	2	FACETS	0.776	0.709	0.847	0.776	0.709	0.847	SUBCLONAL	1	TRUE	1	0.309601161193285	2		404	1290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0007104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	472	471	3	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.904845392005627	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.905842876942408	1		474	569	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138672	55138672	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9925	5455	364	2	ENST00000257290.5:c.1349G>T	p.Cys450Phe	p.C450F	ENST00000257290	NM_006206.4	450	tGc/tTc	9/23	0.905842876942408	15	FACETS	1	0.998	1			1	CLONAL	5	TRUE	NA	0.905842876942408	15		366	15380	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138677	55138677	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1204540280	NA	P-0007104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9483	5168	349	0	ENST00000257290.5:c.1354G>T	p.Asp452Tyr	p.D452Y	ENST00000257290	NM_006206.4	452	Gat/Tat	9/23	0.905842876942408	15	FACETS	1	0.998	1			1	CLONAL	5	TRUE	NA	0.905842876942408	15		349	14651	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371942	55371942	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	95	132	0	ENST00000297316.4:c.632C>T	p.Ala211Val	p.A211V	ENST00000297316	NM_022454.3	211	gCg/gTg	2/2	0.243129815199131	6	FACETS	0.855	0.768	0.945			1	INDETERMINATE	2	TRUE	NA	0.905842876942408	6		132	345	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0007120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	1057	570	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA	2	FACETS	1	0.997	1			1	INDETERMINATE	3	TRUE	NA	0.506256623930969	2		570	1303	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0007120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	548	559	1	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.506256623930969	1	FACETS	1	0.991	1	1	0.998	1	CLONAL	2	TRUE	0	0.506256623930969	1		560	771	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591898	48591898	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	931	594	0	ENST00000342988.3:c.1061T>G	p.Val354Gly	p.V354G	ENST00000342988	NM_005359.5	354	gTg/gGg	9/12	0.506256623930969	2	FACETS	1	0.996	1	1	0.998	1	CLONAL	3	TRUE	0	0.506256623930969	2		594	1164	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0007120-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	565	570	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.506256623930969	2		570	1061	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0007120-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	291	559	1	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.506256623930969	1	FACETS	0.964	0.909	1	0.964	0.909	1	CLONAL	1	TRUE	0	0.506256623930969	1		560	891	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591898	48591898	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007120-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	490	594	0	ENST00000342988.3:c.1061T>G	p.Val354Gly	p.V354G	ENST00000342988	NM_005359.5	354	gTg/gGg	9/12	0.506256623930969	2	FACETS	0.928	0.892	0.964	0.928	0.892	0.964	CLONAL	2	TRUE	0	0.506256623930969	2		594	1043	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579356	7579359	+	frameshift_variant	Frame_Shift_Del	DEL	GACG	GACG	-	novel	NA	P-0007127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	327	697	0	ENST00000269305.4:c.328_331del	p.Arg110TrpfsTer12	p.R110Wfs*12	ENST00000269305	NM_001126112.2	110	CGTCtg/tg	4/11	0.589372876185413	2	FACETS	0.94	0.9	0.979	0.94	0.9	0.979	CLONAL	2	TRUE	0	0.622565349281193	2		697	559	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138201288	138201288	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773168508	NA	P-0007127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	125	556	1	ENST00000237289.4:c.1987G>A	p.Gly663Ser	p.G663S	ENST00000237289	NM_001270507.1	663	Ggc/Agc	8/9	0.12449663310942	4	FACETS	1	0.978	1	0.625	0.569	0.684	INDETERMINATE	1	TRUE	2	0.622565349281193	4		557	521	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136771	2136771	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	307	859	0	ENST00000219476.3:c.4888G>C	p.Val1630Leu	p.V1630L	ENST00000219476	NM_000548.3	1630	Gtg/Ctg	38/42	NA	2	FACETS	0.827	0.788	0.867			1	INDETERMINATE	2	TRUE	NA	0.622565349281193	2		859	596	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587424	29587424	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	61	547	0	ENST00000356175.3:c.4405G>A	p.Asp1469Asn	p.D1469N	ENST00000356175	NM_000267.3	1469	Gat/Aat	33/57	0.622565349281193	7	FACETS	0.526	0.452	0.607	0.075	0.064	0.087	SUBCLONAL	1	TRUE	0	0.622565349281193	7		547	952	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	146	221	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.508120360828857	4	FACETS	0.879	0.814	0.945	0.586	0.543	0.63	INDETERMINATE	2	TRUE	1	0.933230964627305	4		222	344	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0007128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	184	385	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.52700908475891	5	FACETS	1	0.987	1	0.813	0.761	0.865	INDETERMINATE	2	TRUE	2	0.933230964627305	5		385	388	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0007128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	130	265	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.661509012778233	4	FACETS	0.866	0.798	0.935	0.866	0.798	0.935	CLONAL	2	TRUE	2	0.933230964627305	4		265	311	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133805	55133805	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376626935	NA	P-0007128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	135	532	2	ENST00000257290.5:c.1018C>T	p.Arg340Trp	p.R340W	ENST00000257290	NM_006206.4	340	Cgg/Tgg	7/23	0.828279389319232	3	FACETS	1	0.97	1	0.558	0.513	0.605	CLONAL	1	TRUE	1	0.933230964627305	3		534	380	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921774	111921774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150291943	NA	P-0007128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	47	450	0	ENST00000393256.3:c.563G>A	p.Arg188His	p.R188H	ENST00000393256	NM_006538.4	188	cGt/cAt	4/4	0.933230964627305	4	FACETS	0.301	0.253	0.354			1	SUBCLONAL	1	TRUE	NA	0.933230964627305	4		450	647	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748522	43748522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150806902	NA	P-0007128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	235	674	4	ENST00000523873.1:c.476G>A	p.Arg159Gln	p.R159Q	ENST00000523873		159	cGg/cAg	6/8	0.933230964627305	3	FACETS	0.787	0.735	0.84	0.393	0.367	0.42	SUBCLONAL	1	TRUE	1	0.933230964627305	3		678	939	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188049	151188049	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519950	NA	P-0007128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	75	643	0	ENST00000262187.5:c.104A>G	p.Tyr35Cys	p.Y35C	ENST00000262187	NM_005614.3	35	tAc/tGc	2/8	0.828279389319232	3	FACETS	0.821	0.727	0.92	0.411	0.363	0.46	CLONAL	1	TRUE	1	0.933230964627305	3		643	287	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971157	21971157	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	12	136	0	ENST00000579755.1:c.244C>T	p.Arg82Cys	p.R82C	ENST00000579755		82	Cgc/Tgc	2/3	0.719385353867618	4	FACETS	0.222	0.156	0.304	0.111	0.078	0.152	SUBCLONAL	1	TRUE	2	0.933230964627305	4		136	224	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710564	114710564	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	276	735	2	ENST00000543371.1:c.49G>A	p.Glu17Lys	p.E17K	ENST00000543371	NM_001198531.1	17	Gaa/Aaa	1/14	0.508120360828857	4	FACETS	1	0.972	1	0.353	0.331	0.376	INDETERMINATE	1	TRUE	1	0.933230964627305	4		737	1079	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133238173	133238173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	226	557	0	ENST00000320574.5:c.2804G>A	p.Gly935Glu	p.G935E	ENST00000320574	NM_006231.2	935	gGg/gAg	24/49	0.508120360828857	4	FACETS	0.904	0.85	0.958	0.603	0.567	0.639	INDETERMINATE	2	TRUE	1	0.933230964627305	4		557	518	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743921	41743921	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	150	528	0	ENST00000301178.4:c.856C>A	p.Gln286Lys	p.Q286K	ENST00000301178	NM_021913.4	286	Caa/Aaa	7/20	0.508120360828857	4	FACETS	0.813	0.744	0.886	0.271	0.248	0.296	INDETERMINATE	1	TRUE	1	0.933230964627305	4		528	764	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0007136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	353	525	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.471532397799075	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.471532397799075	1		526	930	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0007136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	164	338	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.197739029458103	2	FACETS	1	0.959	1	0.532	0.49	0.575	INDETERMINATE	1	TRUE	0	0.471532397799075	2		338	654	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0007136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	68	218	1	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	0.370886948017372	1	FACETS	0.755	0.663	0.852	0.755	0.663	0.852	SUBCLONAL	1	TRUE	0	0.471532397799075	1		219	292	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672519	30672519	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	357	514	1	ENST00000376406.3:c.4441T>A	p.Ser1481Thr	p.S1481T	ENST00000376406	NM_014641.2	1481	Tcc/Acc	10/15	0.104747379026939	3	FACETS	0.863	0.819	0.908	0.575	0.546	0.606	INDETERMINATE	2	TRUE	0	0.471532397799075	3		515	1084	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981660	101981660	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	12	32	0	ENST00000282441.5:c.81G>C	p.Gln27His	p.Q27H	ENST00000282441	NM_001130145.2	27	caG/caC	1/9	1	2	FACETS	0.727	0.521	0.97	0.727	0.521	0.97	CLONAL	1	TRUE	1	0.471532397799075	2		32	70	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218347	133218347	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760235113	NA	P-0007136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	312	420	0	ENST00000320574.5:c.5264G>A	p.Gly1755Glu	p.G1755E	ENST00000320574	NM_006231.2	1755	gGg/gAg	39/49	0.197739029458103	2	FACETS	0.822	0.779	0.866	0.822	0.779	0.866	INDETERMINATE	2	TRUE	0	0.471532397799075	2		420	805	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857538	9857538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778951185	NA	P-0007136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	63	292	0	ENST00000330684.3:c.3863G>A	p.Arg1288His	p.R1288H	ENST00000330684	NM_001134407.1	1288	cGt/cAt	13/13	0.197739029458103	2	FACETS	0.503	0.435	0.577	0.252	0.217	0.289	INDETERMINATE	1	TRUE	0	0.471532397799075	2		292	531	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792869	33792869	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	223	141	0	ENST00000498907.2:c.452G>C	p.Gly151Ala	p.G151A	ENST00000498907	NM_004364.3	151	gGg/gCg	1/1	0.141100181224845	3	FACETS	0.841	0.786	0.897	0.841	0.786	0.897	INDETERMINATE	2	TRUE	1	0.471532397799075	3		141	695	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412109	63412109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1157288902	NA	P-0007136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1399	458	804	1	ENST00000330258.3:c.1058G>A	p.Arg353Gln	p.R353Q	ENST00000330258	NM_152424.3	353	cGa/cAa	2/2	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.471532397799075	2		805	1857	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	359	260	0				ENST00000310581	NM_198253.2	-/1132			0.379635785144278	3	FACETS	1	0.984	1	1	0.996	1	CLONAL	4	TRUE	0	0.38697904207516	3		260	534	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0007157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	9	385	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.106	0.07	0.153	0.106	0.07	0.153	SUBCLONAL	1	TRUE	1	0.38697904207516	2		385	438	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913396	NA	P-0007157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	219	414	0	ENST00000349496.5:c.95A>G	p.Asp32Gly	p.D32G	ENST00000349496	NM_001904.3	32	gAc/gGc	3/15	1	2	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	1	0.38697904207516	2		414	483	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098965	178098965	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	68	198	0	ENST00000397062.3:c.80A>C	p.Asp27Ala	p.D27A	ENST00000397062	NM_006164.4	27	gAt/gCt	2/5	1	2	FACETS	0.825	0.729	0.925	1	0.979	1	CLONAL	2	TRUE	1	0.38697904207516	2		198	213	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155446	106155446	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	203	469	0	ENST00000380013.4:c.347A>C	p.Gln116Pro	p.Q116P	ENST00000380013	NM_001127208.2	116	cAa/cCa	3/11	1	2	FACETS	0.97	0.906	1	1	0.994	1	CLONAL	2	TRUE	1	0.38697904207516	2		469	541	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104268933	104268933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	174	461	0	ENST00000369902.3:c.190G>A	p.Gly64Ser	p.G64S	ENST00000369902	NM_016169.3	64	Ggc/Agc	2/12	1	2	FACETS	0.8	0.741	0.861	1	0.991	1	SUBCLONAL	2	TRUE	1	0.38697904207516	2		461	562	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107083	27107083	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	187	190	0	ENST00000324856.7:c.6694del	p.Arg2232GlyfsTer35	p.R2232Gfs*35	ENST00000324856	NM_006015.4	2232	Cgg/gg	20/20	1	2	FACETS	0.933	0.869	0.998	1	0.993	1	CLONAL	2	TRUE	1	0.38697904207516	2		190	518	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339072	225339072	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	305	255	0	ENST00000264414.4:c.2197C>T	p.Arg733Ter	p.R733*	ENST00000264414	NM_003590.4	733	Cga/Tga	16/16	NA	2	FACETS	0.974	0.947	0.999			1	INDETERMINATE	2	TRUE	NA	0.872139679509437	2		255	359	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145705	11145705	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1204091534	NA	P-0007160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	275	443	0	ENST00000358026.2:c.4067G>A	p.Arg1356Gln	p.R1356Q	ENST00000358026	NM_001128849.1	1356	cGg/cAg	29/36	0.770032985193534	4	FACETS	0.972	0.911	1	0.486	0.455	0.517	CLONAL	1	TRUE	2	0.872139679509437	4		443	1215	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56409103	56409106	+	frameshift_variant	Frame_Shift_Del	DEL	GTAA	GTAA	-	novel	NA	P-0007160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	212	299	0	ENST00000348428.3:c.1612_1615del	p.Lys538ValfsTer10	p.K538Vfs*10	ENST00000348428	NM_006785.3	537	gGTAAg/gg	14/17	0.770032985193534	4	FACETS	1	0.962	1	0.525	0.489	0.564	CLONAL	1	TRUE	2	0.872139679509437	4		299	866	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577032	7577032	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs786202055	NA	P-0007160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	207	309	0	ENST00000269305.4:c.906del	p.Ser303AlafsTer42	p.S303Afs*42	ENST00000269305	NM_001126112.2	302	ggG/gg	8/11	0.869183150132093	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.872139679509437	1		309	261	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549439	187549439	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	419	304	0	ENST00000441802.2:c.4679del	p.Pro1560ArgfsTer25	p.P1560Rfs*25	ENST00000441802	NM_005245.3	1560	cCg/cg	9/27	0.85740456871565	2	FACETS	0.959	0.935	0.981	0.959	0.935	0.981	CLONAL	2	TRUE	0	0.872139679509437	2		304	501	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207519	102207521	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0007160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	253	442	0	ENST00000263464.3:c.1611_1613del	p.Glu537del	p.E537del	ENST00000263464	NM_001165.4	536	acAGAa/aca	8/9	0.872139679509437	3	FACETS	0.878	0.823	0.935	0.439	0.411	0.468	CLONAL	1	TRUE	1	0.872139679509437	3		442	949	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910549	29910549	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45585732	NA	P-0007166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	19	247	4	ENST00000376809.5:c.89G>A	p.Arg30Lys	p.R30K	ENST00000376809	NM_002116.7	30	aGg/aAg	2/8	1	2	FACETS	0.808	0.613	1	0.808	0.613	1	CLONAL	1	TRUE	1	0.14	2		251	336	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0007170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	337	239	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.249503558566571	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	3	TRUE	0	0.280778641994902	3		240	908	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0007170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	178	572	1	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.280778641994902	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.280778641994902	1		573	859	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248481	212248481	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1217	170	608	1	ENST00000342788.4:c.3786C>A	p.Tyr1262Ter	p.Y1262*	ENST00000342788	NM_005235.2	1262	taC/taA	28/28	0.280778641994902	3	FACETS	0.996	0.913	1	0.498	0.456	0.541	CLONAL	1	TRUE	1	0.280778641994902	3		609	1387	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504347	8504347	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs758284103	NA	P-0007170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	136	477	0	ENST00000356435.5:c.1736G>T	p.Ser579Ile	p.S579I	ENST00000356435		579	aGc/aTc	12/35	0.280778641994902	1	FACETS	0.879	0.799	0.964	0.879	0.799	0.964	CLONAL	1	TRUE	0	0.280778641994902	1		477	947	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219437	133219437	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	147	589	0	ENST00000320574.5:c.4697G>T	p.Arg1566Ile	p.R1566I	ENST00000320574	NM_006231.2	1566	aGa/aTa	36/49	0.270083075484673	2	FACETS	1	0.938	1	0.517	0.472	0.565	CLONAL	1	TRUE	0	0.280778641994902	2		589	1012	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457600	67457600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	95	328	0	ENST00000327367.4:c.410C>T	p.Pro137Leu	p.P137L	ENST00000327367	NM_005902.3	137	cCt/cTt	3/9	0.175136794922875	3	FACETS	1	0.924	1	0.349	0.31	0.39	CLONAL	1	TRUE	0	0.280778641994902	3		328	737	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410352	63410352	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	196	627	0	ENST00000330258.3:c.2815G>T	p.Glu939Ter	p.E939*	ENST00000330258	NM_152424.3	939	Gaa/Taa	2/2	0.280778641994902	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.280778641994902	1		627	1029	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15365032	15365033	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0007170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	243	474	0	ENST00000263377.2:c.2088_2089delinsTT	p.Lys696_Gly697delinsAsnCys	p.K696_G697delinsNC	ENST00000263377	NM_058243.2	696	aaGGgc/aaTTgc	11/20	0.278567765614764	2	FACETS	0.962	0.9	1	0.962	0.9	1	CLONAL	2	TRUE	0	0.280778641994902	2		474	900	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0007173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	42	43	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	0.590747391612838	4	FACETS	1	0.894	1	1	0.894	1	CLONAL	2	FALSE	2	0.651428251175658	4		43	102	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0007173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	315	510	1	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.651428251175658	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	FALSE	0	0.651428251175658	2		511	459	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0007183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	187	271	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.899	0.839	0.961	0.899	0.839	0.961	CLONAL	1	TRUE	1	0.871771450373271	2		271	477	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562623	95562623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	156	199	0	ENST00000393063.1:c.4634C>T	p.Ser1545Phe	p.S1545F	ENST00000393063	NM_030621.3	1545	tCt/tTt	24/28	1	2	FACETS	0.487	0.447	0.529	0.487	0.447	0.529	SUBCLONAL	1	TRUE	1	0.871771450373271	2		199	735	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213924	2213924	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs373677359	NA	P-0007183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1287	399	230	0	ENST00000326181.6:c.3G>A	p.Met1?	p.M1?	ENST00000326181	NM_032271.2	1	atG/atA	2/21	0.871771450373271	4	FACETS	1	0.962	1	0.339	0.321	0.357	CLONAL	1	TRUE	1	0.871771450373271	4		230	1686	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871758	12871758	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0007183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	184	95	0	ENST00000228872.4:c.476-1G>C		p.X159_splice	ENST00000228872	NM_004064.3	159			NA	2	FACETS	0.902	0.864	0.937			1	INDETERMINATE	2	TRUE	NA	0.871771450373271	2		95	234	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932358	36932358	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	662	453	0	ENST00000361632.4:c.2111A>G	p.Lys704Arg	p.K704R	ENST00000361632		704	aAg/aGg	16/16	NA	2	FACETS	0.987	0.953	1			1	INDETERMINATE	1	TRUE	NA	0.871771450373271	2		453	1538	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226589926	226589926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	311	161	0	ENST00000366794.5:c.275G>A	p.Gly92Glu	p.G92E	ENST00000366794	NM_001618.3	92	gGa/gAa	2/23	0.604236459330896	5	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.871771450373271	5		161	1299	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137450	202137450	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	377	278	0	ENST00000358485.4:c.678C>G	p.Ile226Met	p.I226M	ENST00000358485	NM_001080125.1	226	atC/atG	4/9	1	2	FACETS	0.958	0.913	1	0.958	0.913	1	CLONAL	1	TRUE	1	0.871771450373271	2		278	903	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578349	212578349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1484791833	NA	P-0007183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	217	191	0	ENST00000342788.4:c.908C>T	p.Ser303Phe	p.S303F	ENST00000342788	NM_005235.2	303	tCt/tTt	8/28	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.871771450373271	2		191	486	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650419	12650419	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	210	196	0	ENST00000251849.4:c.427C>T	p.Arg143Trp	p.R143W	ENST00000251849	NM_002880.3	143	Cgg/Tgg	5/17	1	2	FACETS	0.96	0.9	1	0.96	0.9	1	CLONAL	1	TRUE	1	0.871771450373271	2		196	502	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55962480	55962480	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	169	262	0	ENST00000263923.4:c.2644C>G	p.Leu882Val	p.L882V	ENST00000263923	NM_002253.2	882	Ctc/Gtc	19/30	1	2	FACETS	0.443	0.407	0.48	0.443	0.407	0.48	SUBCLONAL	1	TRUE	1	0.871771450373271	2		262	875	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737588	145737588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749717457	NA	P-0007183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	155	251	0	ENST00000428558.2:c.3175G>A	p.Val1059Met	p.V1059M	ENST00000428558	NM_004260.3	1059	Gtg/Atg	19/22	1	2	FACETS	0.421	0.385	0.458	0.421	0.385	0.458	SUBCLONAL	1	TRUE	1	0.871771450373271	2		251	845	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127920586	127920586	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	164	424	0	ENST00000373547.4:c.313G>C	p.Asp105His	p.D105H	ENST00000373547	NM_002721.4	105	Gat/Cat	4/7	1	2	FACETS	0.282	0.258	0.307	0.282	0.258	0.307	SUBCLONAL	1	TRUE	1	0.871771450373271	2		424	1334	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925606	114925606	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs529966412	NA	P-0007183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	612	473	0	ENST00000543371.1:c.1684G>T	p.Ala562Ser	p.A562S	ENST00000543371	NM_001198531.1	562	Gct/Tct	14/14	1	2	FACETS	0.928	0.894	0.963	0.928	0.894	0.963	CLONAL	1	TRUE	1	0.871771450373271	2		473	1513	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742515	17742515	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768652299	NA	P-0007183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	402	261	0	ENST00000250003.3:c.697G>A	p.Glu233Lys	p.E233K	ENST00000250003	NM_002478.4	233	Gag/Aag	2/3	1	2	FACETS	0.96	0.916	1	0.96	0.916	1	CLONAL	1	TRUE	1	0.871771450373271	2		261	961	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142446	119142446	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs267602720	NA	P-0007183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	221	168	0	ENST00000264033.4:c.445C>T	p.Arg149Ter	p.R149*	ENST00000264033	NM_005188.3	149	Cga/Tga	3/16	0.868779877855853	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.871771450373271	1		168	277	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264275	30264275	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1299892734	NA	P-0007183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	37	10	0	ENST00000322652.5:c.10C>T	p.Gln4Ter	p.Q4*	ENST00000322652	NM_015355.2	4	Cag/Tag	1/16	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.871771450373271	2		10	66	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955130	17955130	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs565783591	NA	P-0007183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	364	234	0	ENST00000458235.1:c.97C>T	p.Arg33Trp	p.R33W	ENST00000458235	NM_000215.3	33	Cgg/Tgg	2/24	1	2	FACETS	0.93	0.885	0.975	0.93	0.885	0.975	CLONAL	1	TRUE	1	0.871771450373271	2		234	898	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39935769	39935769	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	461	321	1	ENST00000378444.4:c.103G>T	p.Asp35Tyr	p.D35Y	ENST00000378444	NM_001123385.1	35	Gat/Tat	3/15	1	2	FACETS	0.905	0.867	0.945	0.905	0.867	0.945	CLONAL	1	TRUE	1	0.871771450373271	2		322	1168	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950082	44950082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	319	352	0	ENST00000377967.4:c.3851C>T	p.Ser1284Leu	p.S1284L	ENST00000377967	NM_021140.2	1284	tCa/tTa	26/29	1	2	FACETS	0.992	0.942	1	0.992	0.942	1	CLONAL	1	TRUE	1	0.871771450373271	2		352	738	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411831	63411831	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	572	459	0	ENST00000330258.3:c.1336C>T	p.Pro446Ser	p.P446S	ENST00000330258	NM_152424.3	446	Cct/Tct	2/2	1	2	FACETS	0.948	0.912	0.985	0.948	0.912	0.985	CLONAL	1	TRUE	1	0.871771450373271	2		459	1384	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0007203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	52	318	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.993	0.844	1	0.993	0.844	1	CLONAL	1	TRUE	1	0.15	2		318	698	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0007203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	25	343	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	1	2	FACETS	0.439	0.344	0.548	0.439	0.344	0.548	SUBCLONAL	1	TRUE	1	0.15	2		343	760	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440916	52440916	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007208-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	160	424	0	ENST00000460680.1:c.588G>A	p.Trp196Ter	p.W196*	ENST00000460680	NM_004656.3	196	tgG/tgA	8/17	1	2	FACETS	0.878	0.807	0.95	0.878	0.807	0.95	CLONAL	1	TRUE	1	0.549992442108215	2		424	663	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288883	15288883	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007208-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	104	258	0	ENST00000263388.2:c.3856T>A	p.Cys1286Ser	p.C1286S	ENST00000263388	NM_000435.2	1286	Tgc/Agc	24/33	1	2	FACETS	0.977	0.882	1	0.977	0.882	1	CLONAL	1	TRUE	1	0.549992442108215	2		258	387	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443746	52443746	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007208-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	154	356	0	ENST00000460680.1:c.51del	p.Leu18SerfsTer54	p.L18Sfs*54	ENST00000460680	NM_004656.3	17	ctG/ct	2/17	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.549992442108215	2		356	538	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021383	42021383	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	202	580	0	ENST00000219905.7:c.3680del	p.Pro1227GlnfsTer9	p.P1227Qfs*9	ENST00000219905	NM_001164273.1	1227	Cca/ca	11/24	1	2	FACETS	0.816	0.758	0.876	0.816	0.758	0.876	CLONAL	1	TRUE	1	0.609115276753058	2		580	813	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	97	260	0				ENST00000310581	NM_198253.2	-/1132			0.144057617092684	4	FACETS	0.839	0.749	0.935	0.839	0.749	0.935	CLONAL	2	TRUE	2	0.218007720583116	4		260	646	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543605	9543605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1159424856	NA	P-0007220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	165	414	0	ENST00000353224.5:c.1549G>A	p.Asp517Asn	p.D517N	ENST00000353224	NM_177990.2	517	Gat/Aat	6/10	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.218007720583116	2		414	1080	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0007220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	205	375	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.76	0.703	0.818	1	0.991	1	SUBCLONAL	2	TRUE	1	0.218007720583116	2		375	1238	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133979	41133979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149675484	NA	P-0007220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1333	95	597	3	ENST00000379561.5:c.1649C>T	p.Ser550Leu	p.S550L	ENST00000379561	NM_002015.3	550	tCg/tTg	2/3	0.218007720583116	2	FACETS	0.61	0.541	0.685	0.305	0.27	0.343	SUBCLONAL	1	TRUE	0	0.218007720583116	2		600	1428	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106024	27106024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369894428	NA	P-0007220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	44	217	0	ENST00000324856.7:c.5635C>T	p.Arg1879Trp	p.R1879W	ENST00000324856	NM_006015.4	1879	Cgg/Tgg	20/20	1	2	FACETS	0.676	0.566	0.798	0.676	0.566	0.798	SUBCLONAL	1	TRUE	1	0.218007720583116	2		217	597	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468004	120468004	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1174	91	457	1	ENST00000256646.2:c.4435C>T	p.Gln1479Ter	p.Q1479*	ENST00000256646	NM_024408.3	1479	Cag/Tag	25/34	1	2	FACETS	0.66	0.584	0.742	0.66	0.584	0.742	SUBCLONAL	1	TRUE	1	0.218007720583116	2		458	1265	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199873	128199873	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780263343	NA	P-0007220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	51	284	1	ENST00000341105.2:c.1432G>A	p.Ala478Thr	p.A478T	ENST00000341105	NM_032638.4	478	Gcc/Acc	6/6	0.218007720583116	3	FACETS	0.585	0.496	0.684	0.292	0.248	0.342	SUBCLONAL	1	TRUE	1	0.218007720583116	3		285	887	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55963852	55963852	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs766711473	NA	P-0007220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	77	392	0	ENST00000263923.4:c.2591C>G	p.Thr864Arg	p.T864R	ENST00000263923	NM_002253.2	864	aCa/aGa	18/30	1	2	FACETS	0.624	0.546	0.709	0.624	0.546	0.709	SUBCLONAL	1	TRUE	1	0.218007720583116	2		392	1132	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959301	38959301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465345926	NA	P-0007220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	121	343	0	ENST00000357387.3:c.2174C>T	p.Thr725Ile	p.T725I	ENST00000357387	NM_152756.3	725	aCt/aTt	22/38	0.144057617092684	4	FACETS	1	0.983	1	0.732	0.66	0.807	CLONAL	1	TRUE	2	0.218007720583116	4		343	924	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197061	106197119	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGATGCTTCCAGCTCTTAACCATGATAGAACTGCTTGTGTCCAAGGAGGCTTACACA	AAAGATGCTTCCAGCTCTTAACCATGATAGAACTGCTTGTGTCCAAGGAGGCTTACACA	-	novel	NA	P-0007220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	110	290	0	ENST00000380013.4:c.5396_5454del	p.Lys1799IlefsTer3	p.K1799Ifs*3	ENST00000380013	NM_001127208.2	1798	tcAAAGATGCTTCCAGCTCTTAACCATGATAGAACTGCTTGTGTCCAAGGAGGCTTACACAaa/tcaa	11/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.218007720583116	2		290	831	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578524	+	frameshift_variant	Frame_Shift_Del	DEL	GCACAGGGCAGGTCTTGGCCAGTTG	GCACAGGGCAGGTCTTGGCCAGTTG	-	novel	NA	P-0007220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	128	433	0	ENST00000269305.4:c.406_430del	p.Gln136SerfsTer26	p.Q136Sfs*26	ENST00000269305	NM_001126112.2	136	CAACTGGCCAAGACCTGCCCTGTGCag/ag	5/11	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.218007720583116	2		433	1172	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206646599	206646599	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	425	450	0	ENST00000367120.3:c.29A>T	p.His10Leu	p.H10L	ENST00000367120	NM_014002.3	10	cAc/cTc	3/22	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.773951301738749	2		450	1070	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153252022	153252022	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0007235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	37	328	0	ENST00000281708.4:c.986-2A>C		p.X329_splice	ENST00000281708	NM_033632.3	329			0.773951301738749	1	FACETS	0.221	0.183	0.263	0.221	0.183	0.263	SUBCLONAL	1	TRUE	0	0.773951301738749	1		328	265	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258954	153258954	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	14	384	0	ENST00000281708.4:c.861G>C	p.Glu287Asp	p.E287D	ENST00000281708	NM_033632.3	287	gaG/gaC	5/12	0.773951301738749	1	FACETS	0.086	0.062	0.115	0.086	0.062	0.115	SUBCLONAL	1	TRUE	0	0.773951301738749	1		384	258	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589664	67589664	+	splice_donor_variant	Splice_Site	SNP	T	T	G	rs1554051075	NA	P-0007235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	26	206	0	ENST00000274335.5:c.1425+2T>G		p.X475_splice	ENST00000274335		475			0.773951301738749	1	FACETS	0.213	0.17	0.262	0.213	0.17	0.262	SUBCLONAL	1	TRUE	0	0.773951301738749	1		206	193	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913035	32913035	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0007235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1451	98	853	0	ENST00000380152.3:c.4543A>T	p.Lys1515Ter	p.K1515*	ENST00000380152		1515	Aag/Tag	11/27	NA	2	FACETS	0.163	0.145	0.183			1	INDETERMINATE	1	TRUE	NA	0.773951301738749	2		853	1549	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913388	32913388	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1252	81	829	1	ENST00000380152.3:c.4896T>A	p.Ser1632Arg	p.S1632R	ENST00000380152		1632	agT/agA	11/27	NA	2	FACETS	0.157	0.137	0.178			1	INDETERMINATE	1	TRUE	NA	0.773951301738749	2		830	1333	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913404	32913404	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs886040553	NA	P-0007235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1281	85	821	0	ENST00000380152.3:c.4912A>G	p.Lys1638Glu	p.K1638E	ENST00000380152		1638	Aaa/Gaa	11/27	NA	2	FACETS	0.161	0.141	0.182			1	INDETERMINATE	1	TRUE	NA	0.773951301738749	2		821	1366	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914197	32914197	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	323	754	0	ENST00000380152.3:c.5705A>C	p.Asp1902Ala	p.D1902A	ENST00000380152		1902	gAt/gCt	11/27	NA	2	FACETS	0.974	0.923	1			1	INDETERMINATE	1	TRUE	NA	0.773951301738749	2		754	857	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041659	42041659	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	642	710	0	ENST00000219905.7:c.5854C>T	p.Gln1952Ter	p.Q1952*	ENST00000219905	NM_001164273.1	1952	Caa/Taa	17/24	0.774866741335407	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.773951301738749	1		710	990	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0007298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	108	552	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.254448050446807	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	FALSE	0	0.253326629099622	1		552	700	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72863677	72863677	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0007298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	106	702	1	ENST00000268489.5:c.3529+1G>A		p.X1177_splice	ENST00000268489	NM_006885.3	1177			0.146482907463023	3	FACETS	0.763	0.682	0.85	0.381	0.341	0.425	INDETERMINATE	1	FALSE	1	0.253326629099622	3		703	1236	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097692	27097694	+	inframe_deletion	In_Frame_Del	DEL	AGC	AGC	-	novel	NA	P-0007298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	259	625	0	ENST00000324856.7:c.3283_3285del	p.Gln1095del	p.Q1095del	ENST00000324856	NM_006015.4	1094	aAGCag/aag	12/20	NA	2	FACETS	0.887	0.831	0.946			1	INDETERMINATE	2	FALSE	NA	0.253326629099622	2		625	1152	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0007301-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	65	582	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.586848425646307	2	FACETS	0.803	0.723	0.882	0.803	0.723	0.882	CLONAL	2	TRUE	0	0.67485942958746	2		582	120	SUCCESS
EED	8726	MSKCC	GRCh37	11	85966317	85966317	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007301-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	28	467	0	ENST00000263360.6:c.414del	p.Tyr138Ter	p.Y138*	ENST00000263360	NM_003797.3	138	taC/ta	4/12	0.617725987762263	1	FACETS	0.723	0.599	0.854	0.723	0.599	0.854	SUBCLONAL	1	TRUE	0	0.67485942958746	1		467	76	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576913	7576913	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567546373	NA	P-0007307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	271	367	0	ENST00000269305.4:c.933del	p.Asn311LysfsTer34	p.N311Kfs*34	ENST00000269305	NM_001126112.2	311	aaC/aa	9/11	0.314026200070532	0	FACETS	0.884	0.838	0.931			1	CLONAL	2	FALSE	0	0.346082322101072	0		367	579	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	20	278	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.263	0.2	0.337	0.263	0.2	0.337	SUBCLONAL	1	TRUE	1	0.22	2		278	692	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818256	43818256	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	85	500	2	ENST00000372470.3:c.1721C>A	p.Ser574Tyr	p.S574Y	ENST00000372470	NM_005373.2	574	tCc/tAc	12/12	1	2	FACETS	0.623	0.548	0.703	0.623	0.548	0.703	SUBCLONAL	1	TRUE	1	0.22	2		502	1241	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129739	47129739	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0007328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	74	262	0	ENST00000409792.3:c.5143-2A>T		p.X1715_splice	ENST00000409792	NM_014159.6	1715			1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.22	2		262	619	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974387	93974387	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1239	95	560	0	ENST00000369303.4:c.1667T>A	p.Ile556Asn	p.I556N	ENST00000369303	NM_004440.3	556	aTt/aAt	8/17	1	2	FACETS	0.647	0.574	0.726	0.647	0.574	0.726	SUBCLONAL	1	TRUE	1	0.22	2		560	1334	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439718	140439718	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	40	215	0	ENST00000288602.6:c.2021T>A	p.Leu674Gln	p.L674Q	ENST00000288602	NM_004333.4	674	cTg/cAg	17/18	1	2	FACETS	0.77	0.64	0.916	0.77	0.64	0.916	CLONAL	1	TRUE	1	0.22	2		215	472	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974756	21974756	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894097	NA	P-0007328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	48	230	0	ENST00000304494.5:c.71G>C	p.Arg24Pro	p.R24P	ENST00000304494	NM_000077.4	24	cGg/cCg	1/3	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.22	2		230	390	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123260375	123260375	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	64	433	0	ENST00000358487.5:c.1526A>T	p.Lys509Met	p.K509M	ENST00000358487	NM_000141.4	509	aAg/aTg	11/18	1	2	FACETS	0.558	0.481	0.641	0.558	0.481	0.641	SUBCLONAL	1	TRUE	1	0.22	2		433	1043	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246476	46246476	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1271	125	496	1	ENST00000334344.6:c.4570A>T	p.Arg1524Trp	p.R1524W	ENST00000334344	NM_152641.2	1524	Agg/Tgg	15/21	0.109743959199941	3	FACETS	0.904	0.815	0.998	0.452	0.407	0.499	INDETERMINATE	1	TRUE	1	0.22	3		497	1396	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012466	29012466	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	70	290	0	ENST00000282397.4:c.405C>G	p.Phe135Leu	p.F135L	ENST00000282397	NM_002019.4	135	ttC/ttG	4/30	1	2	FACETS	0.954	0.832	1	0.954	0.832	1	CLONAL	1	TRUE	1	0.22	2		290	667	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632723	23632723	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	103	401	0	ENST00000261584.4:c.3073G>T	p.Ala1025Ser	p.A1025S	ENST00000261584	NM_024675.3	1025	Gct/Tct	10/13	1	2	FACETS	0.996	0.89	1	0.996	0.89	1	CLONAL	1	TRUE	1	0.22	2		401	940	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577135	7577149	+	inframe_deletion	In_Frame_Del	DEL	TTCCGTCCCAGTAGA	TTCCGTCCCAGTAGA	-	novel	NA	P-0007328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	157	519	0	ENST00000269305.4:c.789_803del	p.Leu264_Asn268del	p.L264_N268del	ENST00000269305	NM_001126112.2	263	aaTCTACTGGGACGGAAc/aac	8/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.22	2		519	1239	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991343	41991344	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0007328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1389	92	633	0	ENST00000219905.7:c.2174_2175del	p.Pro725ArgfsTer19	p.P725Rfs*19	ENST00000219905	NM_001164273.1	725	cCT/c	5/24	1	2	FACETS	0.565	0.5	0.635	0.565	0.5	0.635	SUBCLONAL	1	TRUE	1	0.22	2		633	1481	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170475	11170475	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	86	466	0	ENST00000358026.2:c.4779del	p.Gln1594ArgfsTer34	p.Q1594Rfs*34	ENST00000358026	NM_001128849.1	1593	cGg/cg	34/36	1	2	FACETS	0.783	0.691	0.882	0.783	0.691	0.882	SUBCLONAL	1	TRUE	1	0.22	2		466	998	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007336-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	96	221	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.431982695616139	2		222	325	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0007336-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	120	436	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.420815335969223	1	FACETS	0.951	0.865	1	0.951	0.865	1	CLONAL	1	TRUE	0	0.431982695616139	1		436	458	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0007336-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	69	439	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	1	2	FACETS	0.983	0.863	1	0.983	0.863	1	CLONAL	1	TRUE	1	0.431982695616139	2		439	325	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0007336-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	106	533	0	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	0.431982695616139	1	FACETS	0.992	0.897	1	0.992	0.897	1	CLONAL	1	TRUE	0	0.431982695616139	1		533	388	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923706	131923706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007336-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	63	589	0	ENST00000265335.6:c.976C>T	p.His326Tyr	p.H326Y	ENST00000265335		326	Cat/Tat	7/25	1	2	FACETS	0.982	0.857	1	0.982	0.857	1	CLONAL	1	TRUE	1	0.431982695616139	2		589	297	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	108	260	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.708300091269866	2		260	240	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916623	178916623	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1051397	NA	P-0007337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	323	745	1	ENST00000263967.3:c.10C>T	p.Arg4Ter	p.R4*	ENST00000263967	NM_006218.2	4	Cga/Tga	2/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.708300091269866	2		746	885	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170135	32170135	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	42	508	0	ENST00000375023.3:c.3473G>C	p.Arg1158Pro	p.R1158P	ENST00000375023	NM_004557.3	1158	cGa/cCa	21/30	1	2	FACETS	0.18	0.149	0.214	0.18	0.149	0.214	SUBCLONAL	1	TRUE	1	0.708300091269866	2		508	660	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520087	106520087	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774448553	NA	P-0007337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	139	357	0	ENST00000359195.3:c.2515C>T	p.Arg839Cys	p.R839C	ENST00000359195	NM_002649.2	839	Cgc/Tgc	6/11	0.704044179074483	3	FACETS	0.889	0.812	0.969	0.444	0.406	0.485	CLONAL	1	TRUE	1	0.708300091269866	3		357	598	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711916	89711916	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs104894184	NA	P-0007337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	295	469	0	ENST00000371953.3:c.534T>G	p.Tyr178Ter	p.Y178*	ENST00000371953	NM_000314.4	178	taT/taG	6/9	0.708300091269866	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.708300091269866	1		469	459	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926909	112926909	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	175	460	0	ENST00000351677.2:c.1529A>T	p.Gln510Leu	p.Q510L	ENST00000351677	NM_002834.3	510	cAg/cTg	13/16	NA	2	FACETS	0.784	0.725	0.845			1	INDETERMINATE	1	TRUE	NA	0.708300091269866	2		460	630	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858117	9858117	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	346	647	0	ENST00000330684.3:c.3284C>A	p.Pro1095His	p.P1095H	ENST00000330684	NM_001134407.1	1095	cCc/cAc	13/13	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.708300091269866	2		647	927	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111855951	111855951	+	start_lost	Translation_Start_Site	SNP	T	T	G	novel	NA	P-0007340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1575	252	681	0	ENST00000341259.2:c.2T>G	p.Met1?	p.M1?	ENST00000341259	NM_005475.2	1	aTg/aGg	2/8	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.240742493562849	NA		681	1827	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733218	74733218	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2485	181	778	2	ENST00000359995.5:c.25G>A	p.Asp9Asn	p.D9N	ENST00000359995	NM_001195427.1	9	Gat/Aat	1/3	0.240742493562849	9	FACETS	1	0.945	1	0.173	0.158	0.189	CLONAL	1	TRUE	3	0.240742493562849	9		780	2666	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572904	41572904	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1335	212	623	0	ENST00000263253.7:c.5189C>A	p.Ser1730Tyr	p.S1730Y	ENST00000263253	NM_001429.3	1730	tCt/tAt	31/31	0.240742493562849	3	FACETS	1	0.986	1	0.425	0.393	0.458	CLONAL	1	TRUE	0	0.240742493562849	3		623	1547	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40447674	40447674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1439727336	NA	P-0007344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	262	714	0	ENST00000345506.4:c.413C>T	p.Ser138Phe	p.S138F	ENST00000345506	NM_003152.3	138	tCc/tTc	6/20	0.620106567955357	4	FACETS	1	0.956	1	0.513	0.48	0.547	CLONAL	1	TRUE	2	0.717652999200368	4		714	1222	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0007345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	280	356	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.233622230825576	4	FACETS	0.99	0.932	1	0.99	0.932	1	CLONAL	3	TRUE	1	0.266613350512699	4		356	896	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794899	242794899	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	25	374	1	ENST00000334409.5:c.310C>A	p.Arg104Ser	p.R104S	ENST00000334409	NM_005018.2	104	Cgt/Agt	2/5	1	2	FACETS	0.384	0.302	0.479	0.384	0.302	0.479	SUBCLONAL	1	TRUE	1	0.266613350512699	2		375	488	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180384	94180384	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0007345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	66	345	0	ENST00000323929.3:c.1783+1G>T		p.X595_splice	ENST00000323929	NM_005591.3	595			0.266613350512699	3	FACETS	1	0.892	1	0.515	0.447	0.588	CLONAL	1	TRUE	1	0.266613350512699	3		345	545	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444486	49444486	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	63	213	0	ENST00000301067.7:c.2885G>T	p.Gly962Val	p.G962V	ENST00000301067	NM_003482.3	962	gGt/gTt	11/54	0.233622230825576	4	FACETS	1	0.97	1	0.488	0.423	0.557	CLONAL	1	TRUE	1	0.266613350512699	4		213	409	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760727	59760727	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	105	516	0	ENST00000259008.2:c.3680A>T	p.His1227Leu	p.H1227L	ENST00000259008	NM_032043.2	1227	cAt/cTt	20/20	0.228785796385816	3	FACETS	0.926	0.828	1	0.463	0.414	0.515	CLONAL	1	TRUE	1	0.266613350512699	3		516	964	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298770	15298770	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	34	362	0	ENST00000263388.2:c.1528G>T	p.Glu510Ter	p.E510*	ENST00000263388	NM_000435.2	510	Gaa/Taa	10/33	NA	2	FACETS	0.609	0.497	0.734			1	INDETERMINATE	1	TRUE	NA	0.266613350512699	2		362	419	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344011	70344011	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	58	273	0	ENST00000374080.3:c.1747G>T	p.Asp583Tyr	p.D583Y	ENST00000374080		583	Gac/Tac	13/45	0.193675779864399	2	FACETS	0.848	0.729	0.977			1	CLONAL	1	TRUE	NA	0.266613350512699	2		273	513	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190670474	190670475	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	T	novel	NA	P-0007345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	34	349	0	ENST00000441310.2:c.412_413delinsT	p.Gly138PhefsTer6	p.G138Ffs*6	ENST00000441310	NM_000534.4	138	GGt/Tt	4/13	0.193675779864399	4	FACETS	0.612	0.499	0.739			1	SUBCLONAL	1	TRUE	NA	0.266613350512699	4		349	528	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593587	55593598	+	inframe_deletion	In_Frame_Del	DEL	CATGTATGAAGT	CATGTATGAAGT	-	novel	NA	P-0007374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	87	557	0	ENST00000288135.5:c.1653_1664del	p.Met552_Val555del	p.M552_V555del	ENST00000288135	NM_000222.2	551	ccCATGTATGAAGTa/cca	11/21	1	2	FACETS	0.96	0.852	1	0.96	0.852	1	CLONAL	1	TRUE	1	0.335097757977203	2		557	541	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	53	260	0				ENST00000310581	NM_198253.2	-/1132			0.224929701053975	3	FACETS	0.854	0.733	0.985	0.854	0.733	0.985	CLONAL	2	TRUE	1	0.224929701053975	3		260	307	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0007388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	98	525	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.224929701053975	1	FACETS	0.955	0.851	1	0.955	0.851	1	CLONAL	1	TRUE	0	0.224929701053975	1		526	810	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307229	65307229	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	37	419	0	ENST00000342505.4:c.2459T>A	p.Leu820Gln	p.L820Q	ENST00000342505	NM_002227.2	820	cTg/cAg	18/25	1	2	FACETS	0.513	0.422	0.616	0.513	0.422	0.616	SUBCLONAL	1	TRUE	1	0.224929701053975	2		419	641	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637669	52637669	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751492205	NA	P-0007388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	42	463	1	ENST00000394830.3:c.2647G>A	p.Gly883Arg	p.G883R	ENST00000394830	NM_018313.4	883	Gga/Aga	18/30	0.167945593578293	2	FACETS	0.481	0.4	0.572	0.241	0.2	0.286	SUBCLONAL	1	TRUE	0	0.224929701053975	2		464	776	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678785	52678785	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	48	353	0	ENST00000394830.3:c.834A>C	p.Lys278Asn	p.K278N	ENST00000394830	NM_018313.4	278	aaA/aaC	9/30	0.167945593578293	2	FACETS	0.761	0.643	0.891	0.38	0.321	0.446	SUBCLONAL	1	TRUE	0	0.224929701053975	2		353	561	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968544	55968544	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	53	435	0	ENST00000263923.4:c.2119C>A	p.Leu707Ile	p.L707I	ENST00000263923	NM_002253.2	707	Ctt/Att	14/30	1	2	FACETS	0.74	0.63	0.86	0.74	0.63	0.86	SUBCLONAL	1	TRUE	1	0.224929701053975	2		435	637	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956546	93956546	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	66	585	4	ENST00000369303.4:c.2690C>A	p.Pro897Gln	p.P897Q	ENST00000369303	NM_004440.3	897	cCa/cAa	15/17	1	2	FACETS	0.682	0.59	0.781	0.682	0.59	0.781	SUBCLONAL	1	TRUE	1	0.224929701053975	2		589	861	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412628	139412628	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	91	313	1	ENST00000277541.6:c.1216G>A	p.Gly406Ser	p.G406S	ENST00000277541	NM_017617.3	406	Ggc/Agc	7/34	1	2	FACETS	0.846	0.755	0.943	1	0.983	1	CLONAL	2	TRUE	1	0.224929701053975	2		314	478	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2111872	2111872	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	26	353	0	ENST00000219476.3:c.1120A>T	p.Thr374Ser	p.T374S	ENST00000219476	NM_000548.3	374	Acc/Tcc	12/42	0.224929701053975	2	FACETS	0.447	0.353	0.555	0.224	0.176	0.278	SUBCLONAL	1	TRUE	0	0.224929701053975	2		353	517	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985836	60985836	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0007388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	50	405	0	ENST00000333681.4:c.64A>T	p.Lys22Ter	p.K22*	ENST00000333681		22	Aag/Tag	2/3	0.224929701053975	1	FACETS	0.56	0.474	0.654	0.56	0.474	0.654	SUBCLONAL	1	TRUE	0	0.224929701053975	1		405	705	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613645	100613645	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	43	499	0	ENST00000308731.7:c.934G>C	p.Ala312Pro	p.A312P	ENST00000308731	NM_000061.2	312	Gct/Cct	11/19	1	2	FACETS	0.488	0.407	0.579	0.488	0.407	0.579	SUBCLONAL	1	TRUE	1	0.224929701053975	2		499	783	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579411	7579441	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCCAGGAGGGGGCTGGTGCAGGGGCCGCC	GGGCCAGGAGGGGGCTGGTGCAGGGGCCGCC	-	novel	NA	P-0007388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	58	289	0	ENST00000269305.4:c.246_276del	p.Ala83CysfsTer30	p.A83Cfs*30	ENST00000269305	NM_001126112.2	82	ccGGCGGCCCCTGCACCAGCCCCCTCCTGGCCC/cc	4/11	0.224929701053975	1	FACETS	0.903	0.777	1	0.903	0.777	1	CLONAL	1	TRUE	0	0.224929701053975	1		289	507	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0007394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	250	397	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	0.93	0.873	0.988	0.93	0.873	0.988	CLONAL	1	TRUE	1	0.703050466379552	2		397	765	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443604	52443623	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CCACTTGCACCCCCTTGACA	CCACTTGCACCCCCTTGACA	-	novel	NA	P-0007394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	251	278	0	ENST00000460680.1:c.69_88del	p.Val24GlyfsTer38	p.V24Gfs*38	ENST00000460680	NM_004656.3	23	ggTGTCAAGGGGGTGCAAGTGGag/ggag	3/17	0.647186660321888	2	FACETS	1	0.993	1	0.681	0.644	0.718	CLONAL	1	TRUE	0	0.703050466379552	2		278	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0007398-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	590	552	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.701053567799189	2	FACETS		NA	1	1	0.998	1	NA	3	TRUE	0	0.694573041459891	2		552	653	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0007398-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1284	270	358	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.701053567799189	4	FACETS	0.848	0.793	0.904			1	CLONAL	1	TRUE	NA	0.694573041459891	4		358	1554	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36265239	36265239	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007398-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	245	406	0	ENST00000300305.3:c.80C>T	p.Pro27Leu	p.P27L	ENST00000300305		27	cCt/cTt	2/8	0.701053567799189	3	FACETS	1	0.943	1			1	CLONAL	1	TRUE	NA	0.694573041459891	3		406	943	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735467	40735467	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776642212	NA	P-0007398-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	436	429	1	ENST00000373198.4:c.3406C>T	p.Arg1136Cys	p.R1136C	ENST00000373198	NM_133170.3	1136	Cgt/Tgt	25/32	0.658861817102712	3	FACETS	0.892	0.855	0.93			1	CLONAL	2	TRUE	NA	0.694573041459891	3		430	948	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163898	152163898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007398-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	306	391	1	ENST00000206249.3:c.619G>A	p.Ala207Thr	p.A207T	ENST00000206249	NM_000125.3	207	Gcc/Acc	2/8	0.701053567799189	3	FACETS	1	0.992	1	0.631	0.596	0.667	CLONAL	1	TRUE	1	0.694573041459891	3		392	940	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371718	55371718	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007398-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	1186	264	0	ENST00000297316.4:c.408G>C	p.Lys136Asn	p.K136N	ENST00000297316	NM_022454.3	136	aaG/aaC	2/2	0.694573041459891	8	FACETS	0.966	0.953	0.978			1	CLONAL	8	TRUE	NA	0.694573041459891	8		264	1363	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	47	221	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.385	0.323	0.453	0.385	0.323	0.453	SUBCLONAL	1	TRUE	1	0.26	2		222	939	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1023835002	NA	P-0007408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	74	320	0	ENST00000558401.1:c.1A>G	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Gtg	1/4	1	2	FACETS	0.698	0.61	0.794	0.698	0.61	0.794	SUBCLONAL	1	TRUE	1	0.26	2		320	815	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404399	139404399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1478316908	NA	P-0007408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	45	348	0	ENST00000277541.6:c.2755G>A	p.Gly919Arg	p.G919R	ENST00000277541	NM_017617.3	919	Ggg/Agg	18/34	1	2	FACETS	0.47	0.394	0.555	0.47	0.394	0.555	SUBCLONAL	1	TRUE	1	0.26	2		348	736	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034441	47034441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	80	469	1	ENST00000377604.3:c.526G>A	p.Val176Ile	p.V176I	ENST00000377604	NM_001204468.1	176	Gtc/Atc	6/24	1	2	FACETS	0.574	0.503	0.649	0.574	0.503	0.649	SUBCLONAL	1	TRUE	1	0.26	2		470	1073	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0007412-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	8	254	7	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.237000935571833	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		261	224	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349618	89349618	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007412-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	71	756	0	ENST00000301030.4:c.3332A>G	p.Lys1111Arg	p.K1111R	ENST00000301030	NM_001256183.1	1111	aAa/aGa	9/13	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		756	844	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0007417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	134	318	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	0.931	1	CLONAL	1	TRUE	1	0.268722583797704	2		318	968	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99452106	99452106	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	124	278	0	ENST00000268035.6:c.1440G>T	p.Arg480Ser	p.R480S	ENST00000268035	NM_000875.3	480	agG/agT	6/21	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.268722583797704	2		278	891	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587782272	NA	P-0007421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	85	297	0	ENST00000269305.4:c.994-1G>C		p.X332_splice	ENST00000269305	NM_001126112.2	332			1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.147674649181766	2		297	923	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945200	44945201	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0007421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	115	254	0	ENST00000377967.4:c.3526_3527del	p.Val1176SerfsTer3	p.V1176Sfs*3	ENST00000377967	NM_021140.2	1175	gGT/g	24/29	1	1	FACETS	1	0.914	1	1	0.989	1	CLONAL	2	FALSE	0	0.147674649181766	1		254	711	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007502-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	219	370	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.24367803215935	3	FACETS	0.952	0.886	1			1	CLONAL	2	TRUE	NA	0.248584919911657	3		370	1040	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577544	7577544	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587780074	NA	P-0007502-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	110	357	0	ENST00000269305.4:c.737T>C	p.Met246Thr	p.M246T	ENST00000269305	NM_001126112.2	246	aTg/aCg	7/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.248584919911657	2		357	824	SUCCESS
FH	2271	MSKCC	GRCh37	1	241665841	241665841	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587778362	NA	P-0007506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	377	375	0	ENST00000366560.3:c.1138A>G	p.Met380Val	p.M380V	ENST00000366560	NM_000143.3	380	Atg/Gtg	8/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.89	2		375	802	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729671	162729671	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376303676	NA	P-0007506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	244	416	0	ENST00000367921.3:c.757G>A	p.Gly253Ser	p.G253S	ENST00000367921	NM_006182.2	253	Ggc/Agc	8/18	1	2	FACETS	0.689	0.646	0.733	0.689	0.646	0.733	SUBCLONAL	1	TRUE	1	0.89	2		416	796	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	456	370	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.450843136990909	3	FACETS	0.891	0.856	0.926			1	CLONAL	3	TRUE	NA	0.455310943851018	3		370	920	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0007511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	166	552	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.458014074532855	3	FACETS	1	0.97	1	0.556	0.511	0.603	CLONAL	1	TRUE	1	0.455310943851018	3		552	805	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0007511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	330	574	0	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	0.458014074532855	3	FACETS	0.877	0.831	0.925	0.877	0.831	0.925	CLONAL	2	TRUE	1	0.455310943851018	3		574	1014	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0007511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	138	306	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.458014074532855	3	FACETS	1	0.973	1	0.581	0.53	0.635	CLONAL	1	TRUE	1	0.455310943851018	3		306	640	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796958	78796958	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	54	349	0	ENST00000306801.3:c.1071G>A	p.Met357Ile	p.M357I	ENST00000306801	NM_020761.2	357	atG/atA	9/34	0.458014074532855	3	FACETS	0.309	0.263	0.36	0.154	0.131	0.18	SUBCLONAL	1	TRUE	1	0.455310943851018	3		349	943	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804266	43804266	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	133	427	0	ENST00000372470.3:c.266C>A	p.Thr89Asn	p.T89N	ENST00000372470	NM_005373.2	89	aCc/aAc	3/12	0.458014074532855	3	FACETS	0.748	0.678	0.821	0.374	0.339	0.411	SUBCLONAL	1	TRUE	1	0.455310943851018	3		427	959	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101737	71101737	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0007511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	197	486	0	ENST00000318789.4:c.461T>A	p.Leu154Ter	p.L154*	ENST00000318789	NM_032682.5	154	tTg/tAg	9/21	0.458014074532855	3	FACETS	0.991	0.917	1	0.495	0.458	0.534	CLONAL	1	TRUE	1	0.455310943851018	3		486	1072	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733355	40733355	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	217	192	0	ENST00000373198.4:c.3451C>T	p.Gln1151Ter	p.Q1151*	ENST00000373198	NM_133170.3	1151	Caa/Taa	26/32	0.455310943851018	6	FACETS	0.979	0.916	1	0.979	0.916	1	CLONAL	3	TRUE	3	0.455310943851018	6		192	620	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938947	76938947	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	536	676	1	ENST00000373344.5:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000373344	NM_000489.3	601	Aaa/Gaa	9/35	0.455310943851018	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.455310943851018	2		677	1156	SUCCESS
APC	324	MSKCC	GRCh37	5	112175622	112175622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	271	503	0	ENST00000257430.4:c.4333del	p.Thr1445GlnfsTer28	p.T1445Qfs*28	ENST00000257430	NM_000038.5	1444	cAa/ca	16/16	0.458014074532855	3	FACETS	1	0.993	1	0.73	0.685	0.776	CLONAL	1	TRUE	1	0.455310943851018	3		503	1001	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168809	56168809	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007536-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	135	367	0	ENST00000399503.3:c.1663G>C	p.Asp555His	p.D555H	ENST00000399503	NM_005921.1	555	Gat/Cat	9/20	0.278562634603073	4	FACETS	1	0.978	1	0.615	0.56	0.672	INDETERMINATE	1	TRUE	2	0.486244058402511	4		367	671	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0007545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	23	229	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.169	0.131	0.213	0.169	0.131	0.213	SUBCLONAL	1	TRUE	1	0.613109016510706	2		229	443	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0007545-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	153	449	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.134139613886818	4	FACETS	0.813	0.743	0.887	0.407	0.371	0.444	INDETERMINATE	1	TRUE	2	0.613109016510706	4		449	990	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0007549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	179	300	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.226870685962951	2	FACETS	0.754	0.696	0.814	0.754	0.696	0.814	SUBCLONAL	2	TRUE	0	0.291750399229506	2		300	814	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546626	9546626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751328296	NA	P-0007549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	248	554	0	ENST00000353224.5:c.1396G>A	p.Ala466Thr	p.A466T	ENST00000353224	NM_177990.2	466	Gcc/Acc	5/10	0.211452981022938	3	FACETS	1	0.992	1	0.72	0.672	0.77	CLONAL	1	TRUE	1	0.291750399229506	3		554	1353	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45800084	45800084	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	197	551	0	ENST00000450313.1:c.136G>T	p.Ala46Ser	p.A46S	ENST00000450313	NM_012222.2	46	Gcc/Tcc	2/16	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.291750399229506	2		551	1326	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035147	37035147	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs63751012	NA	P-0007549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	31	140	0	ENST00000231790.2:c.109G>C	p.Glu37Gln	p.E37Q	ENST00000231790	NM_000249.3	37	Gag/Cag	1/19	1	2	FACETS	0.631	0.511	0.766	0.631	0.511	0.766	SUBCLONAL	1	TRUE	1	0.291750399229506	2		140	337	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448601	89448601	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	122	472	0	ENST00000336596.2:c.1565G>T	p.Arg522Leu	p.R522L	ENST00000336596	NM_005233.5	522	cGc/cTc	7/17	1	2	FACETS	0.82	0.74	0.905	0.82	0.74	0.905	CLONAL	1	TRUE	1	0.291750399229506	2		472	1020	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898825	134898825	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0007549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	147	335	0	ENST00000398015.3:c.1882+1G>T		p.X628_splice	ENST00000398015	NM_004441.4	628			NA	2	FACETS	1	0.967	1			1	INDETERMINATE	1	TRUE	NA	0.291750399229506	2		335	901	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157414	106157414	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	105	327	0	ENST00000380013.4:c.2315A>T	p.Glu772Val	p.E772V	ENST00000380013	NM_001127208.2	772	gAa/gTa	3/11	1	2	FACETS	0.883	0.791	0.981	0.883	0.791	0.981	CLONAL	1	TRUE	1	0.291750399229506	2		327	815	SUCCESS
APC	324	MSKCC	GRCh37	5	112173451	112173451	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	43	464	0	ENST00000257430.4:c.2160G>T	p.Met720Ile	p.M720I	ENST00000257430	NM_000038.5	720	atG/atT	16/16	0.16791420514788	2	FACETS	0.353	0.295	0.419	0.177	0.147	0.21	INDETERMINATE	1	TRUE	0	0.291750399229506	2		464	834	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694659	176694659	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	116	534	0	ENST00000439151.2:c.5243G>T	p.Cys1748Phe	p.C1748F	ENST00000439151	NM_022455.4	1748	tGt/tTt	15/23	0.16791420514788	2	FACETS	0.632	0.568	0.701	0.316	0.284	0.351	INDETERMINATE	1	TRUE	0	0.291750399229506	2		534	1258	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401525	401525	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	47	348	1	ENST00000380956.4:c.847G>A	p.Asp283Asn	p.D283N	ENST00000380956	NM_001195286.1	283	Gac/Aac	7/9	NA	2	FACETS	0.36	0.303	0.424			1	INDETERMINATE	1	TRUE	NA	0.291750399229506	2		349	894	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6048631	6048631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780048	NA	P-0007549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	66	451	0	ENST00000265849.7:c.20C>T	p.Ser7Leu	p.S7L	ENST00000265849	NM_000535.5	7	tCg/tTg	1/15	0.211452981022938	3	FACETS	0.493	0.427	0.566	0.247	0.213	0.283	SUBCLONAL	1	TRUE	1	0.291750399229506	3		451	1051	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467717	50467717	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	122	482	0	ENST00000331340.3:c.952G>C	p.Ala318Pro	p.A318P	ENST00000331340	NM_006060.4	318	Gcc/Ccc	8/8	0.211452981022938	3	FACETS	0.853	0.769	0.941	0.426	0.384	0.471	CLONAL	1	TRUE	1	0.291750399229506	3		482	1124	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335653	81335653	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	104	442	0	ENST00000222390.5:c.1707G>C	p.Gln569His	p.Q569H	ENST00000222390	NM_000601.4	569	caG/caC	15/18	0.211452981022938	3	FACETS	0.659	0.588	0.735	0.33	0.294	0.368	SUBCLONAL	1	TRUE	1	0.291750399229506	3		442	1239	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140507759	140507759	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0007549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	98	295	1	ENST00000288602.6:c.711+1G>A		p.X237_splice	ENST00000288602	NM_004333.4	237			0.276591373770987	3	FACETS	0.803	0.715	0.897			1	CLONAL	1	TRUE	NA	0.291750399229506	3		296	959	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515124	148515124	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	208	533	0	ENST00000320356.2:c.1085G>T	p.Arg362Leu	p.R362L	ENST00000320356	NM_004456.4	362	cGg/cTg	10/20	0.276591373770987	3	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.291750399229506	3		533	1237	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271672	38271672	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	76	458	0	ENST00000425967.3:c.2277G>C	p.Glu759Asp	p.E759D	ENST00000425967	NM_001174067.1	759	gaG/gaC	17/19	1	2	FACETS	0.461	0.403	0.524	0.461	0.403	0.524	SUBCLONAL	1	TRUE	1	0.291750399229506	2		458	1130	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123003	5123003	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs952575429	NA	P-0007549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	201	334	1	ENST00000381652.3:c.3060-1G>T		p.X1020_splice	ENST00000381652	NM_004972.3	1020			0.239851933590704	2	FACETS	0.916	0.852	0.983	0.916	0.852	0.983	CLONAL	2	TRUE	0	0.291750399229506	2		335	752	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243857	46243857	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	271	316	0	ENST00000334344.6:c.1951C>T	p.Gln651Ter	p.Q651*	ENST00000334344	NM_152641.2	651	Cag/Tag	15/21	0.282818697166658	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.291750399229506	2		316	879	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582004	95582004	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	71	249	0	ENST00000393063.1:c.1907G>C	p.Arg636Thr	p.R636T	ENST00000393063	NM_030621.3	636	aGa/aCa	12/28	0.291750399229506	3	FACETS	0.724	0.631	0.825	0.362	0.315	0.413	SUBCLONAL	1	TRUE	1	0.291750399229506	3		249	770	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135010	11135010	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	234	386	1	ENST00000358026.2:c.2977G>T	p.Glu993Ter	p.E993*	ENST00000358026	NM_001128849.1	993	Gag/Tag	21/36	0.239851933590704	2	FACETS	0.946	0.884	1	0.946	0.884	1	CLONAL	2	TRUE	0	0.291750399229506	2		387	848	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0007562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	445	570	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.552763476692041	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.564735434338323	1		570	1037	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953730	48953730	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs3092891	NA	P-0007562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	119	293	1	ENST00000267163.4:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000267163	NM_000321.2	445	Cga/Tga	14/27	NA	2	FACETS	0.535	0.483	0.59			1	INDETERMINATE	1	TRUE	NA	0.564735434338323	2		294	788	SUCCESS
APC	324	MSKCC	GRCh37	5	112179737	112179737	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	193	278	1	ENST00000257430.4:c.8446C>T	p.Arg2816Ter	p.R2816*	ENST00000257430	NM_000038.5	2816	Cga/Tga	16/16	1	2	FACETS	0.995	0.924	1	0.995	0.924	1	CLONAL	1	TRUE	1	0.564735434338323	2		279	687	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722141	176722141	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	218	247	0	ENST00000439151.2:c.7772C>T	p.Ala2591Val	p.A2591V	ENST00000439151	NM_022455.4	2591	gCa/gTa	23/23	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.564735434338323	2		247	739	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271314	26271314	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1410	694	970	0	ENST00000305910.3:c.299A>G	p.Tyr100Cys	p.Y100C	ENST00000305910	NM_003534.2	100	tAc/tGc	1/1	0.288195997799404	1	FACETS	0.838	0.807	0.87	0.838	0.807	0.87	INDETERMINATE	1	TRUE	0	0.564735434338323	1		970	2104	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954915	2954915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752709289	NA	P-0007562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	342	384	1	ENST00000396946.4:c.2795G>A	p.Arg932Gln	p.R932Q	ENST00000396946	NM_032415.4	932	cGg/cAg	21/25	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.564735434338323	2		385	1046	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223555	55223555	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749132706	NA	P-0007562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	328	410	1	ENST00000275493.2:c.922G>A	p.Val308Ile	p.V308I	ENST00000275493	NM_005228.3	308	Gtc/Atc	8/28	0.157051006201777	6	FACETS	0.808	0.761	0.856			1	INDETERMINATE	2	TRUE	NA	0.564735434338323	6		411	1531	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148516750	148516750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	179	268	0	ENST00000320356.2:c.937C>T	p.Arg313Trp	p.R313W	ENST00000320356	NM_004456.4	313	Cgg/Tgg	9/20	0.552763476692041	1	FACETS	0.972	0.905	1	0.972	0.905	1	CLONAL	1	TRUE	0	0.564735434338323	1		268	468	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212182	98212182	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371346118	NA	P-0007562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1418	99	403	0	ENST00000331920.6:c.3490G>A	p.Val1164Ile	p.V1164I	ENST00000331920	NM_000264.3	1164	Gtt/Att	21/24	0.363370209311304	4	FACETS	0.362	0.321	0.405			1	SUBCLONAL	1	TRUE	NA	0.564735434338323	4		403	1517	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127817	64127817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	156	159	0	ENST00000334205.4:c.310G>A	p.Ala104Thr	p.A104T	ENST00000334205	NM_003942.2	104	Gct/Act	3/17	0.288195997799404	1	FACETS	0.796	0.734	0.86	0.796	0.734	0.86	INDETERMINATE	1	TRUE	0	0.564735434338323	1		159	498	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033971	49033971	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1566235515	NA	P-0007562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	371	276	0	ENST00000267163.4:c.2106+2T>C		p.X702_splice	ENST00000267163	NM_000321.2	702			NA	2	FACETS	0.778	0.742	0.815			1	INDETERMINATE	2	TRUE	NA	0.564735434338323	2		276	844	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022899	33022899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868208266	NA	P-0007562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1274	342	715	0	ENST00000300177.4:c.8G>A	p.Arg3His	p.R3H	ENST00000300177	NM_001191322.1	3	cGc/cAc	2/2	0.288195997799404	1	FACETS	0.538	0.507	0.569	0.538	0.507	0.569	INDETERMINATE	1	TRUE	0	0.564735434338323	1		715	1616	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	338166	338166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376835130	NA	P-0007562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1489	451	532	4	ENST00000262320.3:c.2545G>A	p.Val849Ile	p.V849I	ENST00000262320	NM_003502.3	849	Gtc/Atc	11/11	0.157051006201777	6	FACETS	0.877	0.834	0.92			1	INDETERMINATE	2	TRUE	NA	0.564735434338323	6		536	1940	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907651	76907651	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	610	777	2	ENST00000373344.5:c.4510C>T	p.Arg1504Ter	p.R1504*	ENST00000373344	NM_000489.3	1504	Cga/Tga	15/35	0.564735434338323	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.564735434338323	1		779	1424	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630266	100630266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368549990	NA	P-0007562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	370	389	0	ENST00000308731.7:c.7G>A	p.Ala3Thr	p.A3T	ENST00000308731	NM_000061.2	3	Gca/Aca	2/19	0.564735434338323	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.564735434338323	1		389	867	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0007583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	615	239	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.4938136177239	5	FACETS	1	0.99	1	1	0.99	1	CLONAL	5	TRUE	0	0.4938136177239	5		240	842	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0007583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	292	436	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.165332872880569	5	FACETS	1	0.988	1			1	INDETERMINATE	3	TRUE	NA	0.4938136177239	5		436	609	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573650	48573650	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	63	165	1	ENST00000342988.3:c.234G>T	p.Leu78Phe	p.L78F	ENST00000342988	NM_005359.5	78	ttG/ttT	2/12	NA	2	FACETS	0.828	0.722	0.942			1	INDETERMINATE	1	TRUE	NA	0.4938136177239	2		166	308	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411395	63411395	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	268	397	0	ENST00000330258.3:c.1772G>T	p.Arg591Met	p.R591M	ENST00000330258	NM_152424.3	591	aGg/aTg	2/2	0.195430742450417	5	FACETS	0.98	0.92	1	0.653	0.613	0.694	INDETERMINATE	2	TRUE	2	0.4938136177239	5		397	964	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075649	8075649	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	169	436	0	ENST00000377482.5:c.31A>T	p.Ile11Phe	p.I11F	ENST00000377482	NM_018948.3	11	Atc/Ttc	2/4	0.467376672719551	3	FACETS	1	0.973	1	0.564	0.519	0.61	CLONAL	1	TRUE	1	0.4938136177239	3		436	757	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628722	187628722	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	209	301	0	ENST00000441802.2:c.2260T>A	p.Tyr754Asn	p.Y754N	ENST00000441802	NM_005245.3	754	Tat/Aat	2/27	0.467376672719551	3	FACETS	0.773	0.72	0.826	0.773	0.72	0.826	SUBCLONAL	2	TRUE	1	0.4938136177239	3		301	683	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515388	149515388	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	173	207	0	ENST00000261799.4:c.94G>T	p.Gly32Cys	p.G32C	ENST00000261799	NM_002609.3	32	Ggc/Tgc	3/23	0.385779590908971	2	FACETS	0.77	0.716	0.825	0.77	0.716	0.825	SUBCLONAL	2	TRUE	0	0.4938136177239	2		207	455	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519536	137519536	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	317	332	0	ENST00000367739.4:c.1102G>T	p.Gly368Cys	p.G368C	ENST00000367739	NM_000416.2	368	Ggc/Tgc	7/7	0.4938136177239	3	FACETS	1	0.992	1	0.815	0.776	0.854	CLONAL	2	TRUE	0	0.4938136177239	3		332	655	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226047	133226047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753426630	NA	P-0007583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	212	298	0	ENST00000320574.5:c.3850C>T	p.Arg1284Trp	p.R1284W	ENST00000320574	NM_006231.2	1284	Cgg/Tgg	31/49	0.467376672719551	3	FACETS	0.759	0.708	0.812	0.759	0.708	0.812	SUBCLONAL	2	TRUE	1	0.4938136177239	3		298	705	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855903	45855903	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	272	260	0	ENST00000391945.4:c.1907G>T	p.Arg636Leu	p.R636L	ENST00000391945	NM_000400.3	636	cGg/cTg	21/23	0.445178054631118	4	FACETS	1	0.99	1	0.814	0.769	0.859	CLONAL	2	TRUE	1	0.4938136177239	4		260	674	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411815	63411815	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	362	539	0	ENST00000330258.3:c.1352G>T	p.Gly451Val	p.G451V	ENST00000330258	NM_152424.3	451	gGg/gTg	2/2	0.195430742450417	5	FACETS	0.957	0.907	1	0.638	0.604	0.673	INDETERMINATE	2	TRUE	2	0.4938136177239	5		539	1333	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209103865	209103867	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0007583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	275	358	0	ENST00000345146.2:c.1082_1084del	p.Glu361del	p.E361del	ENST00000345146	NM_005896.2	361	gAAGtc/gtc	9/10	0.414493625522789	4	FACETS	0.864	0.817	0.911	0.864	0.817	0.911	CLONAL	3	TRUE	1	0.4938136177239	4		358	642	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069277	30069277	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	211	232	0	ENST00000338641.4:c.1142del	p.Ala381ValfsTer45	p.A381Vfs*45	ENST00000338641	NM_000268.3	381	gCt/gt	12/16	0.322437119801552	3	FACETS	1	0.982	1	0.743	0.698	0.789	CLONAL	2	TRUE	0	0.4938136177239	3		232	478	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151181826	151181826	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	251	453	0	ENST00000262187.5:c.189del	p.Gln64LysfsTer13	p.Q64Kfs*13	ENST00000262187	NM_005614.3	63	ggG/gg	3/8	0.399458547427967	4	FACETS	0.845	0.792	0.899	0.845	0.792	0.899	CLONAL	2	TRUE	2	0.4938136177239	4		453	899	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0007588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	47	277	1	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.642	0.543	0.751	0.642	0.543	0.751	SUBCLONAL	1	TRUE	1	0.374250294939084	2		278	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0007588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	208	525	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.374250294939084	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.374250294939084	1		526	870	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390120	89390120	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	116	468	0	ENST00000336596.2:c.869G>T	p.Cys290Phe	p.C290F	ENST00000336596	NM_005233.5	290	tGc/tTc	4/17	1	2	FACETS	0.834	0.752	0.921	0.834	0.752	0.921	CLONAL	1	TRUE	1	0.374250294939084	2		468	743	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763431	59763431	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs754224663	NA	P-0007588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	99	444	0	ENST00000259008.2:c.2671G>C	p.Val891Leu	p.V891L	ENST00000259008	NM_032043.2	891	Gtt/Ctt	19/20	1	2	FACETS	0.879	0.786	0.977	0.879	0.786	0.977	CLONAL	1	TRUE	1	0.374250294939084	2		444	602	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374941	45374941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	156	498	0	ENST00000262160.6:c.902G>A	p.Gly301Asp	p.G301D	ENST00000262160	NM_005901.5	301	gGc/gAc	8/11	0.374250294939084	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.374250294939084	1		498	649	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0007597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	1055	574	0	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	0.600429323281505	2	FACETS	0.993	0.97	1	0.993	0.97	1	CLONAL	2	TRUE	0	0.603434428074902	2		574	1760	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309819	65309819	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1519	184	455	0	ENST00000342505.4:c.2331G>C	p.Trp777Cys	p.W777C	ENST00000342505	NM_002227.2	777	tgG/tgC	17/25	0.603862614345315	3	FACETS	0.466	0.428	0.506	0.233	0.214	0.253	SUBCLONAL	1	TRUE	1	0.603434428074902	3		455	1703	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163494	47163494	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	282	433	0	ENST00000409792.3:c.2632G>T	p.Gly878Cys	p.G878C	ENST00000409792	NM_014159.6	878	Ggt/Tgt	3/21	0.532547145556321	3	FACETS	1	0.993	1	0.821	0.783	0.859	CLONAL	2	TRUE	0	0.603434428074902	3		433	494	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457260	89457260	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	85	450	0	ENST00000336596.2:c.1741C>T	p.Leu581Phe	p.L581F	ENST00000336596	NM_005233.5	581	Ctt/Ttt	9/17	0.532547145556321	3	FACETS	0.654	0.579	0.734	0.218	0.193	0.245	SUBCLONAL	1	TRUE	0	0.603434428074902	3		450	561	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528647	89528647	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	205	362	0	ENST00000336596.2:c.2947G>T	p.Val983Leu	p.V983L	ENST00000336596	NM_005233.5	983	Gtg/Ttg	17/17	0.532547145556321	3	FACETS	1	0.958	1	0.348	0.323	0.374	CLONAL	1	TRUE	0	0.603434428074902	3		362	847	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391537	84391537	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	63	226	0	ENST00000321945.7:c.295T>C	p.Trp99Arg	p.W99R	ENST00000321945	NM_139076.2	99	Tgg/Cgg	5/9	1	2	FACETS	0.863	0.755	0.976	0.863	0.755	0.976	CLONAL	1	TRUE	1	0.603434428074902	2		226	242	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687360	117687360	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866590541	NA	P-0007597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	70	541	0	ENST00000368508.3:c.2691G>C	p.Trp897Cys	p.W897C	ENST00000368508	NM_002944.2	897	tgG/tgC	18/43	0.375112461026488	1	FACETS	0.298	0.26	0.339	0.298	0.26	0.339	SUBCLONAL	1	TRUE	0	0.603434428074902	1		541	543	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528780	8528780	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0007597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	90	352	0	ENST00000356435.5:c.353-1G>C		p.X118_splice	ENST00000356435		118			0.563958554805055	1	FACETS	0.481	0.429	0.536	0.481	0.429	0.536	SUBCLONAL	1	TRUE	0	0.603434428074902	1		352	433	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0007597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	2715	356	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.603434428074902	17	FACETS	1	0.997	1			1	CLONAL	16	TRUE	NA	0.603434428074902	17		356	3073	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120954	115120954	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	1018	401	0	ENST00000257566.3:c.52C>A	p.His18Asn	p.H18N	ENST00000257566	NM_016569.3	18	Cat/Aat	1/8	0.416020641515058	3	FACETS	0.93	0.909	0.951	0.93	0.909	0.951	CLONAL	3	TRUE	0	0.603434428074902	3		401	1574	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061520	38061520	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs370464225	NA	P-0007597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1445	183	291	1	ENST00000250448.2:c.469G>T	p.Gly157Cys	p.G157C	ENST00000250448	NM_004496.3	157	Ggc/Tgc	2/2	0.603434428074902	6	FACETS	0.822	0.756	0.892			1	CLONAL	1	TRUE	NA	0.603434428074902	6		292	1628	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094931	11094931	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs563079629	NA	P-0007597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1793	239	496	0	ENST00000358026.2:c.104C>T	p.Ser35Leu	p.S35L	ENST00000358026	NM_001128849.1	35	tCg/tTg	2/36	0.603862614345315	3	FACETS	0.507	0.471	0.545	0.254	0.235	0.273	SUBCLONAL	1	TRUE	1	0.603434428074902	3		496	2032	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408893	41408893	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1376	675	512	0	ENST00000373198.4:c.533C>A	p.Ala178Asp	p.A178D	ENST00000373198	NM_133170.3	178	gCc/gAc	4/32	0.603862614345315	4	FACETS	0.874	0.842	0.908	0.874	0.842	0.908	CLONAL	2	TRUE	2	0.603434428074902	4		512	2051	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929232	44929232	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	341	379	0	ENST00000377967.4:c.2332C>A	p.Pro778Thr	p.P778T	ENST00000377967	NM_021140.2	778	Cct/Act	17/29	0.568225108575548	2	FACETS	1	0.99	1			1	CLONAL	1	TRUE	NA	0.603434428074902	2		379	970	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929551	44929551	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0007597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	251	317	0	ENST00000377967.4:c.2651C>G	p.Ser884Ter	p.S884*	ENST00000377967	NM_021140.2	884	tCa/tGa	17/29	0.568225108575548	2	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.603434428074902	2		317	657	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041636	47041636	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	888	260	0	ENST00000377604.3:c.1861C>T	p.Gln621Ter	p.Q621*	ENST00000377604	NM_001204468.1	621	Cag/Tag	17/24	0.568225108575548	2	FACETS	1	0.998	1			1	CLONAL	2	TRUE	NA	0.603434428074902	2		260	1242	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0007600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	31	318	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	TRUE	1	0.28	2		318	212	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	117	221	1	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	0.28	2		222	808	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0007600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	54	373	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.294081792371528	1	FACETS	0.298	0.253	0.347	0.298	0.253	0.347	SUBCLONAL	1	TRUE	0	0.28	1		373	1115	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277880	41277880	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	155	746	0	ENST00000349496.5:c.1844C>A	p.Ala615Glu	p.A615E	ENST00000349496	NM_001904.3	615	gCa/gAa	12/15	1	2	FACETS	0.903	0.825	0.985	0.903	0.825	0.985	CLONAL	1	TRUE	1	0.28	2		746	1226	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272302	15272302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	89	489	0	ENST00000263388.2:c.6137C>A	p.Pro2046Gln	p.P2046Q	ENST00000263388	NM_000435.2	2046	cCa/cAa	33/33	1	2	FACETS	0.929	0.824	1	0.929	0.824	1	CLONAL	1	TRUE	1	0.28	2		489	684	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89851344	89851344	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	62	393	0	ENST00000389301.3:c.1388A>G	p.His463Arg	p.H463R	ENST00000389301	NM_000135.2	463	cAt/cGt	15/43	0.3	2	FACETS	1	0.941	1			1	CLONAL	2	TRUE	NA	0.13	2		393	412	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945263	54945263	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0007625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	92	272	0	ENST00000312783.6:c.1163C>G	p.Ser388Ter	p.S388*	ENST00000312783	NM_198436.1	388	tCa/tGa	10/10	0.3	3	FACETS	0.954	0.857	1			1	CLONAL	5	TRUE	NA	0.13	3		272	316	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0007626-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	154	192	1	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	0.358269427645254	4	FACETS	0.993	0.92	1	0.993	0.92	1	CLONAL	3	TRUE	1	0.358269427645254	4		193	392	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0007626-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	144	561	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	0.322877527760229	3	FACETS	0.942	0.858	1	0.471	0.429	0.515	CLONAL	1	TRUE	1	0.358269427645254	3		561	1006	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775653	9775653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007626-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	98	344	0	ENST00000377346.4:c.196G>A	p.Glu66Lys	p.E66K	ENST00000377346	NM_005026.3	66	Gag/Aag	4/24	0.322877527760229	3	FACETS	0.977	0.873	1	0.489	0.436	0.544	CLONAL	1	TRUE	1	0.358269427645254	3		344	660	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120496243	120496243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782306821	NA	P-0007626-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	127	422	2	ENST00000256646.2:c.2288C>T	p.Ser763Leu	p.S763L	ENST00000256646	NM_024408.3	763	tCg/tTg	14/34	0.358269427645254	2	FACETS	0.928	0.841	1	0.464	0.42	0.51	CLONAL	1	TRUE	0	0.358269427645254	2		424	764	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978974	25978974	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1206861877	NA	P-0007626-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	125	491	1	ENST00000435504.4:c.949G>C	p.Asp317His	p.D317H	ENST00000435504		317	Gat/Cat	10/13	0.358269427645254	4	FACETS	0.889	0.803	0.98	0.296	0.267	0.327	CLONAL	1	TRUE	1	0.358269427645254	4		492	1066	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370822	225370822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1265558901	NA	P-0007626-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	95	373	0	ENST00000264414.4:c.1057G>A	p.Asp353Asn	p.D353N	ENST00000264414	NM_003590.4	353	Gat/Aat	8/16	0.356934558831919	4	FACETS	0.987	0.879	1	0.247	0.219	0.276	CLONAL	1	TRUE	0	0.358269427645254	4		373	730	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489571	56489571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007626-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	269	492	0	ENST00000267101.3:c.2036G>A	p.Arg679Gln	p.R679Q	ENST00000267101	NM_001982.3	679	cGa/cAa	17/28	0.205858833613907	5	FACETS	1	0.985	1	0.764	0.717	0.812	INDETERMINATE	2	TRUE	2	0.358269427645254	5		492	1007	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807953	3807953	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755945995	NA	P-0007626-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	231	393	0	ENST00000262367.5:c.3466G>A	p.Asp1156Asn	p.D1156N	ENST00000262367	NM_004380.2	1156	Gac/Aac	18/31	0.358269427645254	5	FACETS	1	0.96	1	0.52	0.485	0.556	CLONAL	2	TRUE	1	0.358269427645254	5		393	953	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171462	123171462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007626-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	408	500	0	ENST00000218089.9:c.374C>T	p.Ser125Leu	p.S125L	ENST00000218089	NM_001042749.1	125	tCa/tTa	6/35	0.338298028093948	5	FACETS	0.996	0.949	1			1	CLONAL	3	TRUE	NA	0.358269427645254	5		500	1172	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775120	73775147	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGACCTACCTGTAGCGATGAGGCTTCTT	CGACCTACCTGTAGCGATGAGGCTTCTT	-	novel	NA	P-0007626-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	72	443	0	ENST00000254810.4:c.109_128+8del		p.X37_splice	ENST00000254810	NM_005324.3	37		2/4	0.331850708355721	4	FACETS	0.635	0.553	0.723	0.212	0.184	0.241	SUBCLONAL	1	TRUE	1	0.358269427645254	4		443	860	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0007627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	757	210	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.585347840356929	6	FACETS	0.967	0.947	0.986			1	CLONAL	6	TRUE	NA	0.585347840356929	6		210	968	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099851	27099851	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	307	270	0	ENST00000324856.7:c.3730C>G	p.Pro1244Ala	p.P1244A	ENST00000324856	NM_006015.4	1244	Ccc/Gcc	15/20	NA	2	FACETS	0.98	0.937	1			1	INDETERMINATE	2	TRUE	NA	0.585347840356929	2		270	535	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151868348	151868348	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0007627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	503	332	1	ENST00000262189.6:c.9453+1G>A		p.X3151_splice	ENST00000262189	NM_170606.2	3151			0.561629827864351	4	FACETS	0.925	0.89	0.959	0.925	0.89	0.959	CLONAL	3	TRUE	1	0.585347840356929	4		333	982	SUCCESS
ATM	472	MSKCC	GRCh37	11	108213948	108213948	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0007627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	239	248	0	ENST00000278616.4:c.8269-1G>A		p.X2757_splice	ENST00000278616	NM_000051.3	2757			0.577852591034125	3	FACETS	0.965	0.91	1	0.965	0.91	1	CLONAL	2	TRUE	1	0.585347840356929	3		248	547	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699369	47699369	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	455	497	0	ENST00000347630.2:c.139G>T	p.Glu47Ter	p.E47*	ENST00000347630	NM_001007230.1	47	Gaa/Taa	4/11	0.557567439302949	2	FACETS	0.979	0.943	1	0.979	0.943	1	CLONAL	2	TRUE	0	0.585347840356929	2		497	794	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528172	29528173	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0007627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	372	331	0	ENST00000356175.3:c.1181_1182del	p.Phe394Ter	p.F394*	ENST00000356175	NM_000267.3	394	TTt/t	10/57	0.557567439302949	2	FACETS	0.964	0.925	1	0.964	0.925	1	CLONAL	2	TRUE	0	0.585347840356929	2		331	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0007634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	67	262	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	FALSE	1	0.200336794499658	2		262	663	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641151	117641151	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	63	476	1	ENST00000368508.3:c.5820C>A	p.Phe1940Leu	p.F1940L	ENST00000368508	NM_002944.2	1940	ttC/ttA	36/43	1	2	FACETS	0.536	0.461	0.617	0.536	0.461	0.617	SUBCLONAL	1	FALSE	1	0.200336794499658	2		477	1174	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242769	98242769	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	68	252	0	ENST00000331920.6:c.848A>G	p.Asn283Ser	p.N283S	ENST00000331920	NM_000264.3	283	aAt/aGt	6/24	1	2	FACETS	0.896	0.778	1	0.896	0.778	1	CLONAL	1	FALSE	1	0.200336794499658	2		252	758	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039182	49039182	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587778642	NA	P-0007634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	40	294	0	ENST00000267163.4:c.2260G>C	p.Val754Leu	p.V754L	ENST00000267163	NM_000321.2	754	Gta/Cta	22/27	1	2	FACETS	0.659	0.546	0.785	0.659	0.546	0.785	SUBCLONAL	1	FALSE	1	0.200336794499658	2		294	606	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95599669	95599669	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	43	298	0	ENST00000393063.1:c.127A>G	p.Thr43Ala	p.T43A	ENST00000393063	NM_030621.3	43	Acg/Gcg	3/28	1	2	FACETS	0.569	0.474	0.674	0.569	0.474	0.674	SUBCLONAL	1	FALSE	1	0.200336794499658	2		298	755	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021190	31021190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369058266	NA	P-0007634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	69	282	1	ENST00000375687.4:c.1189C>T	p.Arg397Cys	p.R397C	ENST00000375687	NM_015338.5	397	Cgt/Tgt	12/13	1	2	FACETS	0.95	0.827	1	0.95	0.827	1	CLONAL	1	FALSE	1	0.200336794499658	2		283	725	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095949	11095949	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	48	221	0	ENST00000358026.2:c.225del	p.Met76TrpfsTer18	p.M76Wfs*18	ENST00000358026	NM_001128849.1	75	Ccc/cc	3/36	1	2	FACETS	0.805	0.68	0.944	0.805	0.68	0.944	CLONAL	1	FALSE	1	0.200336794499658	2		221	595	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0007643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	186	307	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	0.337742227390702	2		307	1017	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0007643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	270	292	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	0.337742227390702	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.337742227390702	2		292	796	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254872	16254872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761290842	NA	P-0007643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	136	280	0	ENST00000375759.3:c.2137C>T	p.Arg713Trp	p.R713W	ENST00000375759	NM_015001.2	713	Cgg/Tgg	11/15	1	2	FACETS	0.947	0.862	1	0.947	0.862	1	CLONAL	1	TRUE	1	0.337742227390702	2		280	850	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261574	142261574	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	123	285	0	ENST00000350721.4:c.3383T>C	p.Leu1128Ser	p.L1128S	ENST00000350721	NM_001184.3	1128	tTg/tCg	17/47	1	2	FACETS	0.892	0.806	0.982	0.892	0.806	0.982	CLONAL	1	TRUE	1	0.337742227390702	2		285	817	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55962438	55962438	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	144	303	1	ENST00000263923.4:c.2686C>T	p.Leu896Phe	p.L896F	ENST00000263923	NM_002253.2	896	Ctc/Ttc	19/30	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.337742227390702	2		304	826	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418448	49418448	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	99	178	0	ENST00000301067.7:c.15965G>T	p.Gly5322Val	p.G5322V	ENST00000301067	NM_003482.3	5322	gGg/gTg	50/54	0.195180331031941	3	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.337742227390702	3		178	538	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972517	81972517	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1385319449	NA	P-0007643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	139	424	0	ENST00000359376.3:c.3310G>T	p.Val1104Leu	p.V1104L	ENST00000359376	NM_002661.3	1104	Gtg/Ttg	29/33	0.127507283489354	3	FACETS	0.878	0.798	0.962	0.293	0.266	0.321	INDETERMINATE	1	TRUE	0	0.337742227390702	3		424	1096	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568631	41568631	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	146	278	0	ENST00000263253.7:c.4584del	p.Lys1528AsnfsTer13	p.K1528Nfs*13	ENST00000263253	NM_001429.3	1527	agA/ag	28/31	1	2	FACETS	0.997	0.91	1	0.997	0.91	1	CLONAL	1	TRUE	1	0.337742227390702	2		278	867	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647458	117647462	+	frameshift_variant	Frame_Shift_Del	DEL	CTGAA	CTGAA	-	novel	NA	P-0007643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	145	448	0	ENST00000368508.3:c.5482_5486del	p.Phe1828SerfsTer6	p.F1828Sfs*6	ENST00000368508	NM_002944.2	1828	TTCAGa/a	33/43	1	2	FACETS	0.903	0.823	0.987	0.903	0.823	0.987	CLONAL	1	TRUE	1	0.337742227390702	2		448	951	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428511	78428511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408536007	NA	P-0007655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	11	485	1	ENST00000370768.2:c.1288C>T	p.Arg430Cys	p.R430C	ENST00000370768	NM_003902.3	430	Cgt/Tgt	14/20	1	2	FACETS	0.361	0.248	0.503	0.361	0.248	0.503	SUBCLONAL	1	TRUE	1	0.15	2		486	406	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467596	66467596	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007672-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	61	458	1	ENST00000273854.3:c.673T>A	p.Ser225Thr	p.S225T	ENST00000273854	NM_004439.5	225	Tct/Act	3/18	1	2	FACETS	0.846	0.735	0.965	1	0.976	1	CLONAL	2	TRUE	1	0.231766465819479	2		459	311	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	97	370	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.114926519231425	5	FACETS	0.917	0.818	1	0.611	0.545	0.681	INDETERMINATE	2	TRUE	2	0.224993196639492	5		370	629	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910549	29910549	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45585732	NA	P-0007678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	21	247	4	ENST00000376809.5:c.89G>A	p.Arg30Lys	p.R30K	ENST00000376809	NM_002116.7	30	aGg/aAg	2/8	0.199480504367357	4	FACETS	0.945	0.738	1	0.945	0.738	1	CLONAL	2	TRUE	2	0.224993196639492	4		251	121	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0007678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	89	488	4	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.172587527319951	3	FACETS	1	0.958	1	0.587	0.52	0.658	CLONAL	1	TRUE	1	0.224993196639492	3		492	750	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306741	41306741	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	52	423	0	ENST00000373198.4:c.918G>T	p.Trp306Cys	p.W306C	ENST00000373198	NM_133170.3	306	tgG/tgT	7/32	1	2	FACETS	0.763	0.649	0.888	0.763	0.649	0.888	SUBCLONAL	1	TRUE	1	0.224993196639492	2		423	606	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631129	69631129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs281860303	NA	P-0007678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	44	755	3	ENST00000334134.2:c.283C>T	p.Arg95Trp	p.R95W	ENST00000334134	NM_005247.2	95	Cgg/Tgg	2/3	0.172587527319951	3	FACETS	0.547	0.457	0.647	0.274	0.228	0.324	SUBCLONAL	1	TRUE	1	0.224993196639492	3		758	795	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0007681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1362	223	342	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.708902774510645	5	FACETS	0.819	0.76	0.881	0.205	0.19	0.221	CLONAL	1	TRUE	1	0.708902774510645	5		342	1585	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0007681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	669	395	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.708902774510645	5	FACETS	1	0.994	1	0.831	0.806	0.857	CLONAL	3	TRUE	1	0.708902774510645	5		395	1171	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460417	149460417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756076440	NA	P-0007681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	231	355	0	ENST00000286301.3:c.220G>A	p.Ala74Thr	p.A74T	ENST00000286301	NM_005211.3	74	Gct/Act	3/22	0.682402898301406	4	FACETS	0.898	0.836	0.963	0.225	0.209	0.241	CLONAL	1	TRUE	0	0.708902774510645	4		355	1240	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800978	243800978	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	346	413	0	ENST00000263826.5:c.496C>T	p.Arg166Ter	p.R166*	ENST00000263826	NM_005465.4	166	Cga/Tga	5/13	0.681796150700681	3	FACETS	0.919	0.868	0.971	0.459	0.434	0.486	CLONAL	1	TRUE	1	0.708902774510645	3		413	1439	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7119479	7119479	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369102740	NA	P-0007681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	237	382	1	ENST00000302850.5:c.3775G>A	p.Asp1259Asn	p.D1259N	ENST00000302850	NM_000208.2	1259	Gac/Aac	21/22	0.173307714184841	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.708902774510645	0		383	705	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0007749-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	240	552	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.58831411054974	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.58831411054974	1		552	501	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176671220	176671220	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007749-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	147	611	0	ENST00000439151.2:c.4327A>C	p.Asn1443His	p.N1443H	ENST00000439151	NM_022455.4	1443	Aat/Cat	9/23	1	2	FACETS	0.466	0.425	0.51	0.466	0.425	0.51	SUBCLONAL	1	TRUE	1	0.58831411054974	2		611	1072	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0007758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	190	423	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.442129241935702	3	FACETS	0.821	0.763	0.881	0.821	0.763	0.881	CLONAL	2	TRUE	1	0.442129241935702	3		423	639	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844151	68844151	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	175	423	2	ENST00000261769.5:c.739G>T	p.Glu247Ter	p.E247*	ENST00000261769	NM_004360.3	247	Gag/Tag	6/16	0.442129241935702	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.442129241935702	1		425	616	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217869	7217869	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	241	745	0	ENST00000380728.2:c.142C>T	p.Gln48Ter	p.Q48*	ENST00000380728		48	Cag/Tag	3/11	0.442129241935702	1	FACETS	0.915	0.856	0.976	0.915	0.856	0.976	CLONAL	1	TRUE	0	0.442129241935702	1		745	928	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11999013	11999013	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0007758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	101	321	0	ENST00000353533.5:c.513+2T>C		p.X171_splice	ENST00000353533	NM_003010.3	171			0.442129241935702	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.442129241935702	1		321	324	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0007786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	21	177	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.723	0.555	0.919	0.723	0.555	0.919	CLONAL	1	TRUE	1	0.13	2		177	447	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0007786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	37	324	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.726	0.597	0.872	0.726	0.597	0.872	SUBCLONAL	1	TRUE	1	0.13	2		324	784	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696689	47696689	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519972	NA	P-0007786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	43	373	0	ENST00000347630.2:c.259T>A	p.Tyr87Asn	p.Y87N	ENST00000347630	NM_001007230.1	87	Tac/Aac	5/11	1	2	FACETS	0.87	0.726	1	0.87	0.726	1	CLONAL	1	TRUE	1	0.13	2		373	760	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521400	187521400	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	40	284	0	ENST00000441802.2:c.11755A>T	p.Asn3919Tyr	p.N3919Y	ENST00000441802	NM_005245.3	3919	Aat/Tat	22/27	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.13	2		284	598	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061481	38061481	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	24	254	0	ENST00000250448.2:c.508A>G	p.Lys170Glu	p.K170E	ENST00000250448	NM_004496.3	170	Aag/Gag	2/2	1	2	FACETS	0.828	0.648	1	0.828	0.648	1	CLONAL	1	TRUE	1	0.13	2		254	446	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0007788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	69	395	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.258850574574498	4	FACETS	0.849	0.744	0.96	0.849	0.744	0.96	CLONAL	2	TRUE	2	0.304838345869758	4		395	348	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0007788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	27	229	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.298803160324858	2	FACETS	0.877	0.703	1	0.438	0.351	0.537	CLONAL	1	TRUE	0	0.304838345869758	2		229	202	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0007788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	20	385	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.298803160324858	2	FACETS	0.457	0.35	0.583	0.229	0.175	0.292	SUBCLONAL	1	TRUE	0	0.304838345869758	2		385	287	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094465	27094465	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	26	369	3	ENST00000324856.7:c.3173T>C	p.Val1058Ala	p.V1058A	ENST00000324856	NM_006015.4	1058	gTg/gCg	11/20	0.304838345869758	3	FACETS	0.587	0.465	0.726	0.196	0.155	0.242	SUBCLONAL	1	TRUE	0	0.304838345869758	3		372	335	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467197	25467197	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	33	405	0	ENST00000264709.3:c.1678G>T	p.Val560Leu	p.V560L	ENST00000264709	NM_175629.2	560	Gtg/Ttg	15/23	0.303149487990075	4	FACETS	1	0.836	1			1	CLONAL	1	TRUE	NA	0.304838345869758	4		405	276	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539493	187539493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	63	482	0	ENST00000441802.2:c.8247G>T	p.Glu2749Asp	p.E2749D	ENST00000441802	NM_005245.3	2749	gaG/gaT	10/27	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.304838345869758	2		482	382	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001288	150001288	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs766443146	NA	P-0007788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	12	521	0	ENST00000253339.5:c.2316C>G	p.Phe772Leu	p.F772L	ENST00000253339		772	ttC/ttG	4/7	0.304838345869758	3	FACETS	0.388	0.272	0.53	0.129	0.09	0.177	SUBCLONAL	1	TRUE	0	0.304838345869758	3		521	234	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513024	106513024	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	18	368	0	ENST00000359195.3:c.2038T>C	p.Phe680Leu	p.F680L	ENST00000359195	NM_002649.2	680	Ttt/Ctt	3/11	0.258850574574498	4	FACETS	0.463	0.348	0.599	0.231	0.174	0.3	SUBCLONAL	1	TRUE	2	0.304838345869758	4		368	333	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344644	70344644	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	42	638	0	ENST00000374080.3:c.2005G>C	p.Asp669His	p.D669H	ENST00000374080		669	Gac/Cac	14/45	0.258850574574498	4	FACETS	0.993	0.832	1	0.497	0.416	0.586	CLONAL	1	TRUE	2	0.304838345869758	4		638	362	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344679	70344679	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	65	549	2	ENST00000374080.3:c.2040del	p.Lys681SerfsTer30	p.K681Sfs*30	ENST00000374080		680	gaG/ga	14/45	0.258850574574498	4	FACETS	0.788	0.687	0.896	0.788	0.687	0.896	SUBCLONAL	2	TRUE	2	0.304838345869758	4		551	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577562	7577563	+	missense_variant	Missense_Mutation	DNP	CT	CT	AA	novel	NA	P-0007788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	73	487	0	ENST00000269305.4:c.718_719delinsTT	p.Ser240Phe	p.S240F	ENST00000269305	NM_001126112.2	240	AGt/TTt	7/11	0.304838345869758	3	FACETS	1	0.938	1	0.727	0.644	0.814	CLONAL	2	TRUE	0	0.304838345869758	3		487	253	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	41	260	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.845	0.724	0.972	0.845	0.724	0.972	CLONAL	1	TRUE	1	0.873763769477582	2		260	111	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468511	89468511	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	144	576	1	ENST00000336596.2:c.2045T>A	p.Ile682Asn	p.I682N	ENST00000336596	NM_005233.5	682	aTc/aAc	11/17	1	2	FACETS	0.953	0.881	1	0.953	0.881	1	CLONAL	1	TRUE	1	0.873763769477582	2		577	346	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415115	116415115	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	215	648	1	ENST00000397752.3:c.3209T>C	p.Val1070Ala	p.V1070A	ENST00000397752	NM_000245.2	1070	gTg/gCg	15/21	0.543790576394807	4	FACETS	1	0.984	1	0.392	0.365	0.419	CLONAL	1	TRUE	1	0.873763769477582	4		649	785	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981649	101981649	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	10	49	0	ENST00000282441.5:c.70C>G	p.Pro24Ala	p.P24A	ENST00000282441	NM_001130145.2	24	Ccg/Gcg	1/9	1	2	FACETS	0.654	0.462	0.871	0.654	0.462	0.871	SUBCLONAL	1	TRUE	1	0.873763769477582	2		49	35	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983334	149983334	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	93	413	0	ENST00000253339.5:c.2924del	p.Ala975ValfsTer22	p.A975Vfs*22	ENST00000253339		975	gCt/gt	7/7	1	2	FACETS	0.887	0.803	0.973	0.887	0.803	0.973	CLONAL	1	TRUE	1	0.873763769477582	2		413	240	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0007805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	365	381	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.99	0.943	1	0.99	0.943	1	CLONAL	1	TRUE	1	0.853667313407669	2		381	864	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679366	29679366	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs866445127	NA	P-0007805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	421	384	1	ENST00000356175.3:c.7486C>T	p.Arg2496Ter	p.R2496*	ENST00000356175	NM_000267.3	2496	Cga/Tga	50/57	0.844830211549763	1	FACETS	0.833	0.802	0.862	0.833	0.802	0.862	CLONAL	1	TRUE	0	0.853667313407669	1		385	679	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627215	12627215	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2654	1218	388	0	ENST00000251849.4:c.1501C>T	p.Gln501Ter	p.Q501*	ENST00000251849	NM_002880.3	501	Cag/Tag	14/17	NA	2	FACETS	0.737	0.716	0.758			1	INDETERMINATE	1	TRUE	NA	0.853667313407669	2		388	3872	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589819	55589819	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	165	419	1	ENST00000288135.5:c.1301C>A	p.Pro434Gln	p.P434Q	ENST00000288135	NM_000222.2	434	cCa/cAa	8/21	1	2	FACETS	0.34	0.311	0.37	0.34	0.311	0.37	SUBCLONAL	1	TRUE	1	0.853667313407669	2		420	1137	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460585	149460585	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	203	214	2	ENST00000286301.3:c.52C>T	p.Gln18Ter	p.Q18*	ENST00000286301	NM_005211.3	18	Cag/Tag	3/22	0.853667313407669	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.853667313407669	1		216	269	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5465553	5465553	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	563	564	0	ENST00000381577.3:c.737C>G	p.Ala246Gly	p.A246G	ENST00000381577	NM_014143.3	246	gCc/gGc	5/7	0.853667313407669	1	FACETS	0.981	0.954	1	0.981	0.954	1	CLONAL	1	TRUE	0	0.853667313407669	1		564	771	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918210	50918210	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	413	478	0	ENST00000440232.2:c.2527C>G	p.Leu843Val	p.L843V	ENST00000440232	NM_002691.3	843	Ctg/Gtg	20/27	1	2	FACETS	0.957	0.914	1	0.957	0.914	1	CLONAL	1	TRUE	1	0.853667313407669	2		478	1011	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44910953	44910953	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0007805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	640	264	0	ENST00000377967.4:c.655-1G>A		p.X219_splice	ENST00000377967	NM_021140.2	219			1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.853667313407669	1		264	745	SUCCESS
AR	367	MSKCC	GRCh37	X	66765163	66765163	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	52	99	0	ENST00000374690.3:c.175C>T	p.Gln59Ter	p.Q59*	ENST00000374690	NM_000044.3	59	Cag/Tag	1/8	1	1	FACETS	0.358	0.309	0.41	0.358	0.309	0.41	SUBCLONAL	1	TRUE	0	0.853667313407669	1		99	195	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220440	123220440	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1569520709	NA	P-0007805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	609	291	2	ENST00000218089.9:c.3097C>T	p.Arg1033Ter	p.R1033*	ENST00000218089	NM_001042749.1	1033	Cga/Tga	30/35	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.853667313407669	1		293	715	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027861	48027861	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	363	423	0	ENST00000234420.5:c.2739del	p.Asp913GlufsTer32	p.D913Efs*32	ENST00000234420	NM_000179.2	913	gaT/ga	4/10	1	2	FACETS	0.936	0.891	0.981	0.936	0.891	0.981	CLONAL	1	TRUE	1	0.853667313407669	2		423	909	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680798	30680809	+	inframe_deletion	In_Frame_Del	DEL	GCTGTCATCATC	GCTGTCATCATC	-	novel	NA	P-0007805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	405	456	0	ENST00000376406.3:c.910_921del	p.Asp304_Ser307del	p.D304_S307del	ENST00000376406	NM_014641.2	304	GATGATGACAGC/-	5/15	0.466138047723935	1	FACETS	0.707	0.678	0.736	0.707	0.678	0.736	INDETERMINATE	1	TRUE	0	0.853667313407669	1		456	769	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579383	7579383	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	339	380	0	ENST00000269305.4:c.304del	p.Thr102ProfsTer21	p.T102Pfs*21	ENST00000269305	NM_001126112.2	102	Acc/cc	4/11	0.844830211549763	1	FACETS	0.944	0.911	0.977	0.944	0.911	0.977	CLONAL	1	TRUE	0	0.853667313407669	1		380	482	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860908	151860908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	147	212	0	ENST00000262189.6:c.9754C>T	p.Arg3252Cys	p.R3252C	ENST00000262189	NM_170606.2	3252	Cgt/Tgt	43/59	0.369898532490116	6	FACETS	0.937	0.861	1	0.937	0.861	1	CLONAL	3	TRUE	3	0.369898532490116	6		212	492	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184559	11184559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	228	521	0	ENST00000361445.4:c.6658C>T	p.Leu2220Phe	p.L2220F	ENST00000361445	NM_004958.3	2220	Ctc/Ttc	47/58	0.235779057332101	2	FACETS	0.858	0.803	0.915	0.858	0.803	0.915	CLONAL	2	TRUE	0	0.369898532490116	2		521	718	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183782	10183782	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	123	331	0	ENST00000256474.2:c.251T>A	p.Val84Glu	p.V84E	ENST00000256474	NM_000551.3	84	gTg/gAg	1/3	0.344877857224587	2	FACETS	0.929	0.85	1	0.929	0.85	1	CLONAL	2	TRUE	0	0.369898532490116	2		331	358	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441220	52441220	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	155	410	0	ENST00000460680.1:c.550G>C	p.Asp184His	p.D184H	ENST00000460680	NM_004656.3	184	Gat/Cat	7/17	0.344877857224587	2	FACETS	0.893	0.825	0.964	0.893	0.825	0.964	CLONAL	2	TRUE	0	0.369898532490116	2		410	469	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52676063	52676063	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0007834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	180	328	1	ENST00000394830.3:c.996-2A>G		p.X332_splice	ENST00000394830	NM_018313.4	332			0.344877857224587	2	FACETS	0.966	0.898	1	0.966	0.898	1	CLONAL	2	TRUE	0	0.369898532490116	2		329	504	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226093	2226093	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	111	533	0	ENST00000326181.6:c.1790G>T	p.Gly597Val	p.G597V	ENST00000326181	NM_032271.2	597	gGc/gTc	19/21	0.353685639903385	3	FACETS	0.939	0.845	1	0.47	0.422	0.52	CLONAL	1	TRUE	1	0.369898532490116	3		533	757	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857503	68857503	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	138	335	0	ENST00000261769.5:c.2138T>A	p.Ile713Asn	p.I713N	ENST00000261769	NM_004360.3	713	aTt/aAt	13/16	0.353685639903385	3	FACETS	0.949	0.87	1	0.949	0.87	1	CLONAL	2	TRUE	1	0.369898532490116	3		335	466	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0007839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	35	194	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.26735433533768	5	FACETS	0.941	0.772	1	0.235	0.193	0.283	CLONAL	1	TRUE	1	0.26735433533768	5		194	390	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061701	38061701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	48	124	0	ENST00000250448.2:c.288G>A	p.Met96Ile	p.M96I	ENST00000250448	NM_004496.3	96	atG/atA	2/2	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.26735433533768	2		124	269	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0007869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	351	525	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.592402004133899	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.592402004133899	2		526	558	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56867142	56867142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756496678	NA	P-0007869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	313	627	4	ENST00000308159.5:c.1361C>T	p.Thr454Met	p.T454M	ENST00000308159	NM_014669.4	454	aCg/aTg	13/22	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.592402004133899	2		631	747	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132500	11132500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs898406635	NA	P-0007869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	375	377	0	ENST00000358026.2:c.2716C>T	p.Arg906Cys	p.R906C	ENST00000358026	NM_001128849.1	906	Cgc/Tgc	19/36	0.269851748953331	6	FACETS	0.974	0.933	1	0.649	0.622	0.677	INDETERMINATE	4	TRUE	0	0.592402004133899	6		377	710	SUCCESS
APC	324	MSKCC	GRCh37	5	112175450	112175457	+	frameshift_variant	Frame_Shift_Del	DEL	TGTACTTC	TGTACTTC	-	novel	NA	P-0007869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	188	296	0	ENST00000257430.4:c.4162_4169del	p.Thr1388GlnfsTer4	p.T1388Qfs*4	ENST00000257430	NM_000038.5	1387	TGTACTTCt/t	16/16	0.591081495731518	2	FACETS	0.889	0.836	0.942	0.889	0.836	0.942	CLONAL	2	TRUE	0	0.592402004133899	2		296	357	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0007872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	455	570	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.375602429840937	1	FACETS	0.805	0.772	0.839	1	0.997	1	CLONAL	2	TRUE	0	0.428787525009641	1		570	1035	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589561	67589585	+	frameshift_variant	Frame_Shift_Del	DEL	ATTGAAGCTGTAGGGAAAAAATTAC	ATTGAAGCTGTAGGGAAAAAATTAC	-	novel	NA	P-0007872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	84	432	0	ENST00000274335.5:c.1326_1350del	p.Ile442MetfsTer30	p.I442Mfs*30	ENST00000274335		442	ATTGAAGCTGTAGGGAAAAAATTACat/at	10/15	1	2	FACETS	0.51	0.45	0.575	0.51	0.45	0.575	SUBCLONAL	1	TRUE	1	0.428787525009641	2		432	768	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0007873-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	55	356	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.110796213973234	3	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	1	0.06	3		356	785	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0007873-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	25	385	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.06	2		385	708	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579377	+	frameshift_variant	Frame_Shift_Del	DEL	CCTG	CCTG	-	novel	NA	P-0007873-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	32	357	0	ENST00000269305.4:c.310_313del	p.Gln104AlafsTer18	p.Q104Afs*18	ENST00000269305	NM_001126112.2	104	CAGGgc/gc	4/11	1	2	FACETS	1	0.845	1	1	0.961	1	CLONAL	2	TRUE	1	0.06	2		357	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578397	7578397	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007877-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	29	231	0	ENST00000269305.4:c.533del	p.His178ProfsTer69	p.H178Pfs*69	ENST00000269305	NM_001126112.2	178	cAc/cc	5/11	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		231	354	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0007904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	261	449	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.575535465058622	3	FACETS	1	0.983	1	0.568	0.532	0.605	CLONAL	1	TRUE	1	0.575535465058622	3		449	1028	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578537	7578537	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	24	396	0	ENST00000269305.4:c.393C>G	p.Asn131Lys	p.N131K	ENST00000269305	NM_001126112.2	131	aaC/aaG	5/11	1	2	FACETS	0.126	0.098	0.159	0.126	0.098	0.159	SUBCLONAL	1	TRUE	1	0.575535465058622	2		396	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	72	418	0	ENST00000269305.4:c.745del	p.Arg249GlyfsTer96	p.R249Gfs*96	ENST00000269305	NM_001126112.2	249	Agg/gg	7/11	1	2	FACETS	0.352	0.307	0.401	0.352	0.307	0.401	SUBCLONAL	1	TRUE	1	0.575535465058622	2		418	710	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	282	221	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.299953383867527	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	TRUE	1	0.32	4		222	746	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578412	7578412	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519747	NA	P-0007906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	94	286	0	ENST00000269305.4:c.518T>G	p.Val173Gly	p.V173G	ENST00000269305	NM_001126112.2	173	gTg/gGg	5/11	0.189991731382657	3	FACETS	1	0.959	1	0.75	0.675	0.827	INDETERMINATE	2	TRUE	0	0.32	3		286	303	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732911	30732911	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0007906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	91	255	0	ENST00000295754.5:c.1526del		p.X509_splice	ENST00000295754	NM_003242.5	509			0.299953383867527	3	FACETS	0.934	0.837	1	0.934	0.837	1	CLONAL	2	TRUE	1	0.32	3		255	353	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0007910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	422	613	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	0.871846774670192	2	FACETS	0.962	0.939	0.984	0.962	0.939	0.984	CLONAL	2	TRUE	0	0.871846774670192	2		613	503	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913514	NA	P-0007910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	197	512	0	ENST00000288135.5:c.2466T>G	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaG	17/21	0.871846774670192	2	FACETS	1	0.966	1	0.522	0.489	0.555	CLONAL	1	TRUE	0	0.871846774670192	2		512	433	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0007910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	196	608	3	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	0.871846774670192	3	FACETS	0.707	0.655	0.761	0.354	0.327	0.381	SUBCLONAL	1	TRUE	1	0.871846774670192	3		611	913	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435168	56435168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766439784	NA	P-0007910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	118	283	1	ENST00000407977.2:c.1969C>T	p.Arg657Trp	p.R657W	ENST00000407977		657	Cgg/Tgg	9/10	0.838906911904687	4	FACETS	0.877	0.793	0.964	0.438	0.396	0.482	CLONAL	1	TRUE	2	0.871846774670192	4		284	578	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0007967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	768	613	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	0.819551951144378	3	FACETS	0.976	0.949	1	0.976	0.949	1	CLONAL	2	TRUE	1	0.819551951144378	3		613	1353	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229610	98229610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779296683	NA	P-0007967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	660	431	1	ENST00000331920.6:c.2348G>A	p.Arg783Gln	p.R783Q	ENST00000331920	NM_000264.3	783	cGg/cAg	15/24	0.819551951144378	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.819551951144378	3		432	1122	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0007970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	30	158	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.955	0.768	1	0.955	0.768	1	CLONAL	1	TRUE	1	0.14	2		158	449	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0007970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	46	531	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.14	2		531	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577102	7577102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793881	NA	P-0007970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	67	400	2	ENST00000269305.4:c.836G>A	p.Gly279Glu	p.G279E	ENST00000269305	NM_001126112.2	279	gGg/gAg	8/11	1	2	FACETS	0.877	0.76	1	0.877	0.76	1	CLONAL	1	TRUE	1	0.14	2		402	1091	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076815	72076815	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	64	313	0	ENST00000357731.5:c.682C>T	p.Gln228Ter	p.Q228*	ENST00000357731	NM_173808.2	228	Cag/Tag	5/7	1	2	FACETS	0.976	0.843	1	0.976	0.843	1	CLONAL	1	TRUE	1	0.14	2		313	937	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84384745	84384745	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	27	212	0	ENST00000321945.7:c.698T>C	p.Val233Ala	p.V233A	ENST00000321945	NM_139076.2	233	gTg/gCg	8/9	1	2	FACETS	0.999	0.795	1	0.999	0.795	1	CLONAL	1	TRUE	1	0.14	2		212	386	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971210	13971210	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	61	326	0	ENST00000405192.2:c.719C>T	p.Thr240Ile	p.T240I	ENST00000405192	NM_001163147.1	240	aCc/aTc	8/12	1	2	FACETS	0.861	0.74	0.993	0.861	0.74	0.993	CLONAL	1	TRUE	1	0.14	2		326	1012	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879201	151879201	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	72	454	0	ENST00000262189.6:c.5744C>T	p.Ser1915Phe	p.S1915F	ENST00000262189	NM_170606.2	1915	tCc/tTc	36/59	1	2	FACETS	0.995	0.867	1	0.995	0.867	1	CLONAL	1	TRUE	1	0.14	2		454	1034	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971068	21971068	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	23	220	0	ENST00000304494.5:c.290T>G	p.Leu97Arg	p.L97R	ENST00000304494	NM_000077.4	97	cTg/cGg	2/3	1	2	FACETS	0.742	0.577	0.933	0.742	0.577	0.933	CLONAL	1	TRUE	1	0.14	2		220	443	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419049	419049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	60	414	0	ENST00000399788.2:c.3298G>A	p.Glu1100Lys	p.E1100K	ENST00000399788	NM_001042603.1	1100	Gaa/Aaa	22/28	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.14	2		414	829	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15967454	15967454	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1204491653	NA	P-0007970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	66	387	0	ENST00000268712.3:c.5149G>A	p.Glu1717Lys	p.E1717K	ENST00000268712	NM_006311.3	1717	Gaa/Aaa	35/46	1	2	FACETS	0.82	0.709	0.941	0.82	0.709	0.941	CLONAL	1	TRUE	1	0.14	2		387	1150	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520257	9520257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	45	261	0	ENST00000353224.5:c.2012C>T	p.Ser671Leu	p.S671L	ENST00000353224	NM_177990.2	671	tCa/tTa	10/10	1	2	FACETS	0.938	0.787	1	0.938	0.787	1	CLONAL	1	TRUE	1	0.14	2		261	685	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410948	63410948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	33	228	0	ENST00000330258.3:c.2219C>T	p.Ser740Phe	p.S740F	ENST00000330258	NM_152424.3	740	tCt/tTt	2/2	1	1	FACETS	0.837	0.68	1	0.837	0.68	1	CLONAL	1	TRUE	0	0.14	1		228	524	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	429	370	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.458645249054442	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.458645249054442	3		370	960	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0007973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	169	385	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	0.458645249054442	2		385	688	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	120	278	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	0.458645249054442	2		278	508	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0007973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	155	445	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	0.967	0.887	1	0.967	0.887	1	CLONAL	1	TRUE	1	0.458645249054442	2		445	699	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482854	67482854	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1206533102	NA	P-0007973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	114	347	0	ENST00000327367.4:c.1258C>T	p.Arg420Cys	p.R420C	ENST00000327367	NM_005902.3	420	Cgc/Tgc	9/9	1	2	FACETS	0.949	0.858	1	0.949	0.858	1	CLONAL	1	TRUE	1	0.458645249054442	2		347	524	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0007988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	49	385	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	0.377582129379004	2		385	211	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974899	15974899	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	42	616	1	ENST00000268712.3:c.3976C>T	p.Arg1326Ter	p.R1326*	ENST00000268712	NM_006311.3	1326	Cga/Tga	30/46	0.377582129379004	1	FACETS	0.722	0.607	0.847	0.722	0.607	0.847	SUBCLONAL	1	TRUE	0	0.377582129379004	1		617	250	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841213	15841213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765274095	NA	P-0007988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	160	397	1	ENST00000307771.7:c.1297C>T	p.Arg433Cys	p.R433C	ENST00000307771	NM_005089.3	433	Cgc/Tgc	11/11	0.279363253773391	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.377582129379004	1		398	685	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0007991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	127	158	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		158	331	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30730004	30730004	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs727503475	NA	P-0008004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	33	171	0	ENST00000295754.5:c.1524+1G>A		p.X508_splice	ENST00000295754	NM_003242.5	508			0.153743788054306	1	FACETS	0.752	0.612	0.91	0.752	0.612	0.91	CLONAL	1	TRUE	0	0.176218233233124	1		171	454	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219351	1219358	+	frameshift_variant	Frame_Shift_Del	DEL	GGCATGCA	GGCATGCA	-	novel	NA	P-0008004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	75	376	0	ENST00000326873.7:c.405_412del	p.Met136AsnfsTer24	p.M136Nfs*24	ENST00000326873	NM_000455.4	135	GGCATGCAg/g	3/10	0.153743788054306	1	FACETS	0.898	0.786	1	0.898	0.786	1	CLONAL	1	TRUE	0	0.176218233233124	1		376	864	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	71	260	0				ENST00000310581	NM_198253.2	-/1132			0.38425909192935	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	0	0.42268059400391	2		260	161	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0008009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	438	307	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.42268059400391	5	FACETS	0.949	0.911	0.988			1	CLONAL	4	TRUE	NA	0.42268059400391	5		307	892	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922293	100922293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149186732	NA	P-0008009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	195	682	0	ENST00000325455.5:c.2219G>A	p.Arg740Gln	p.R740Q	ENST00000325455	NM_001202474.3	740	cGa/cAa	5/8	0.38425909192935	2	FACETS	0.812	0.757	0.869	0.812	0.757	0.869	CLONAL	2	TRUE	0	0.42268059400391	2		682	568	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273258	198273258	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	160	399	1	ENST00000335508.6:c.952C>T	p.Arg318Ter	p.R318*	ENST00000335508	NM_012433.2	318	Cga/Tga	8/25	0.42268059400391	3	FACETS	1	0.971	1	0.561	0.515	0.61	CLONAL	1	TRUE	1	0.42268059400391	3		400	817	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911568	134911568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	125	326	0	ENST00000398015.3:c.2033C>T	p.Pro678Leu	p.P678L	ENST00000398015	NM_004441.4	678	cCt/cTt	11/16	0.394057284488954	4	FACETS	1	0.926	1	0.514	0.465	0.565	CLONAL	1	TRUE	2	0.42268059400391	4		326	819	SUCCESS
ATR	545	MSKCC	GRCh37	3	142254972	142254972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	121	307	0	ENST00000350721.4:c.3797C>T	p.Ala1266Val	p.A1266V	ENST00000350721	NM_001184.3	1266	gCc/gTc	20/47	0.394057284488954	4	FACETS	0.797	0.724	0.874	0.797	0.724	0.874	SUBCLONAL	2	TRUE	2	0.42268059400391	4		307	511	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945009	31945009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	374	588	0	ENST00000340398.3:c.92C>T	p.Pro31Leu	p.P31L	ENST00000340398	NM_001013699.2	31	cCc/cTc	1/1	0.350954796095834	4	FACETS	0.979	0.929	1	0.979	0.929	1	CLONAL	2	TRUE	2	0.42268059400391	4		588	1286	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857547	9857547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367543132	NA	P-0008009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	82	312	0	ENST00000330684.3:c.3854G>A	p.Arg1285Lys	p.R1285K	ENST00000330684	NM_001134407.1	1285	aGg/aAg	13/13	0.357192109510141	3	FACETS	0.888	0.785	0.999	0.444	0.392	0.5	CLONAL	1	TRUE	1	0.42268059400391	3		312	529	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78599546	78599546	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	279	418	1	ENST00000306801.3:c.218C>T	p.Pro73Leu	p.P73L	ENST00000306801	NM_020761.2	73	cCc/cTc	2/34	0.350954796095834	4	FACETS	0.991	0.932	1	0.991	0.932	1	CLONAL	2	TRUE	2	0.42268059400391	4		419	948	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042172	42042173	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0008009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	330	971	2	ENST00000219905.7:c.6367_6368delinsTT	p.Pro2123Leu	p.P2123L	ENST00000219905	NM_001164273.1	2123	CCa/TTa	17/24	0.350954796095834	4	FACETS	0.892	0.843	0.943	0.892	0.843	0.943	CLONAL	2	TRUE	2	0.42268059400391	4		973	1245	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0008013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	129	221	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.361280038089899	3	FACETS	1	0.95	1	0.536	0.486	0.589	CLONAL	1	TRUE	1	0.361280038089899	3		222	786	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0008013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	81	254	7	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.361280038089899	2		261	331	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582302	119582302	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	73	426	0	ENST00000316626.5:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000316626		367	Cga/Tga	10/12	0.361280038089899	3	FACETS	0.509	0.444	0.58	0.255	0.222	0.29	SUBCLONAL	1	TRUE	1	0.361280038089899	3		426	937	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625168	69625168	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs374453035	NA	P-0008013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	84	489	1	ENST00000334134.2:c.625C>T	p.Arg209Ter	p.R209*	ENST00000334134	NM_005247.2	209	Cga/Tga	3/3	0.361280038089899	4	FACETS	0.889	0.785	1	0.296	0.261	0.334	CLONAL	1	TRUE	1	0.361280038089899	4		490	712	SUCCESS
AR	367	MSKCC	GRCh37	X	66765122	66765122	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	118	252	0	ENST00000374690.3:c.134C>T	p.Ala45Val	p.A45V	ENST00000374690	NM_000044.3	45	gCg/gTg	1/8	0.152341522245214	2	FACETS	1	0.929	1			1	INDETERMINATE	2	TRUE	NA	0.361280038089899	2		252	321	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0008029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	49	356	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.845	0.716	0.987	0.845	0.716	0.987	CLONAL	1	TRUE	1	0.24	2		356	483	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728826	190728826	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	28	225	1	ENST00000441310.2:c.2214G>T	p.Met738Ile	p.M738I	ENST00000441310	NM_000534.4	738	atG/atT	10/13	1	2	FACETS	0.56	0.447	0.688	0.56	0.447	0.688	SUBCLONAL	1	TRUE	1	0.24	2		226	417	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006198	22006198	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs779655098	NA	P-0008029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	26	290	0	ENST00000276925.6:c.205G>T	p.Gly69Cys	p.G69C	ENST00000276925	NM_004936.3	69	Ggc/Tgc	2/2	1	2	FACETS	0.602	0.477	0.745	0.602	0.477	0.745	SUBCLONAL	1	TRUE	1	0.24	2		290	360	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186756	108186756	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs774993357	NA	P-0008029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	51	473	0	ENST00000278616.4:c.6114C>G	p.His2038Gln	p.H2038Q	ENST00000278616	NM_000051.3	2038	caC/caG	42/63	0.17439235385073	1	FACETS	0.565	0.479	0.659	0.565	0.479	0.659	SUBCLONAL	1	TRUE	0	0.24	1		473	662	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143043283	143043283	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	118	596	0	ENST00000262992.4:c.2133A>C	p.Arg711Ser	p.R711S	ENST00000262992	NM_001101669.1	711	agA/agC	19/24	0.428213303496759	3	FACETS	0.871	0.802	0.94	0.871	0.802	0.94	INDETERMINATE	2	TRUE	1	0.755838548589062	3		596	247	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0008056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	13	529	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.216298444660468	5	FACETS	0.664	0.476	0.888	0.221	0.158	0.296	INDETERMINATE	1	TRUE	2	0.55	5		529	130	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361160	70361160	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs79912241	NA	P-0008056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	46	441	0	ENST00000374080.3:c.6348C>A	p.His2116Gln	p.H2116Q	ENST00000374080		2116	caC/caA	43/45	1	1	FACETS	0.709	0.607	0.818	0.709	0.607	0.818	SUBCLONAL	1	TRUE	0	0.55	1		441	171	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0008064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	456	340	1	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.372030094526263	3	FACETS	0.905	0.868	0.942	0.905	0.868	0.942	CLONAL	3	TRUE	0	0.41386024845282	3		341	980	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879390	151879390	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	198	489	0	ENST00000262189.6:c.5555C>G	p.Ala1852Gly	p.A1852G	ENST00000262189	NM_170606.2	1852	gCt/gGt	36/59	0.41386024845282	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.41386024845282	1		489	713	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258042	123258042	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519798	NA	P-0008064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	80	569	0	ENST00000358487.5:c.1639A>G	p.Ile547Val	p.I547V	ENST00000358487	NM_000141.4	547	Atc/Gtc	12/18	0.299684149158434	1	FACETS	0.533	0.47	0.601	0.533	0.47	0.601	SUBCLONAL	1	TRUE	0	0.41386024845282	1		569	575	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005581	42005581	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	200	775	0	ENST00000219905.7:c.3317G>C	p.Arg1106Pro	p.R1106P	ENST00000219905	NM_001164273.1	1106	cGa/cCa	9/24	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.41386024845282	2		775	954	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0008079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	350	570	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.492240909903645	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.492240909903645	1		570	1010	SUCCESS
APC	324	MSKCC	GRCh37	5	112173830	112173830	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	120	342	0	ENST00000257430.4:c.2539G>T	p.Glu847Ter	p.E847*	ENST00000257430	NM_000038.5	847	Gaa/Taa	16/16	0.492240909903645	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.492240909903645	1		342	354	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771821	135771821	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660132	NA	P-0008079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	116	621	0	ENST00000298552.3:c.3296A>G	p.Lys1099Arg	p.K1099R	ENST00000298552	NM_001162426.1	1099	aAg/aGg	23/23	0.280221793149668	1	FACETS	0.364	0.327	0.403	0.364	0.327	0.403	INDETERMINATE	1	TRUE	0	0.492240909903645	1		621	977	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857396	68857396	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	85	460	0	ENST00000261769.5:c.2031A>C	p.Gln677His	p.Q677H	ENST00000261769	NM_004360.3	677	caA/caC	13/16	1	2	FACETS	0.418	0.368	0.47	0.418	0.368	0.47	SUBCLONAL	1	TRUE	1	0.492240909903645	2		460	827	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604715	48604715	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	186	414	0	ENST00000342988.3:c.1537T>C	p.Tyr513His	p.Y513H	ENST00000342988	NM_005359.5	513	Tac/Cac	12/12	0.492240909903645	1	FACETS	0.991	0.921	1	0.991	0.921	1	CLONAL	1	TRUE	0	0.492240909903645	1		414	575	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251528	10251528	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	87	472	0	ENST00000340748.4:c.3404A>C	p.Lys1135Thr	p.K1135T	ENST00000340748		1135	aAg/aCg	31/40	0.206630240605803	3	FACETS	0.395	0.349	0.446	0.132	0.116	0.149	INDETERMINATE	1	TRUE	0	0.492240909903645	3		472	1114	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042300	42042301	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs866465268	NA	P-0008079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	77	856	1	ENST00000219905.7:c.6499_6500del	p.Leu2167GlyfsTer27	p.L2167Gfs*27	ENST00000219905	NM_001164273.1	2165	gaCTct/gact	17/24	0.356527797043109	1	FACETS	0.308	0.27	0.349	0.308	0.27	0.349	SUBCLONAL	1	TRUE	0	0.492240909903645	1		857	766	SUCCESS
AR	367	MSKCC	GRCh37	X	66943543	66943543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852581	NA	P-0008098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	134	335	1	ENST00000374690.3:c.2623C>T	p.His875Tyr	p.H875Y	ENST00000374690	NM_000044.3	875	Cat/Tat	8/8	0.515883814977451	2	FACETS	0.448	0.406	0.493			1	SUBCLONAL	1	TRUE	NA	0.515883814977451	2		336	1159	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935319	36935319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748675453	NA	P-0008098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	282	677	0	ENST00000361632.4:c.1408G>A	p.Ala470Thr	p.A470T	ENST00000361632		470	Gcg/Acg	10/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.515883814977451	2		677	1004	SUCCESS
APC	324	MSKCC	GRCh37	5	112154678	112154678	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	219	377	0	ENST00000257430.4:c.949T>C	p.Ser317Pro	p.S317P	ENST00000257430	NM_000038.5	317	Tca/Cca	10/16	NA	2	FACETS	0.809	0.759	0.858			1	INDETERMINATE	2	TRUE	NA	0.515883814977451	2		377	525	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696689	47696689	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	259	638	0	ENST00000347630.2:c.259T>G	p.Tyr87Asp	p.Y87D	ENST00000347630	NM_001007230.1	87	Tac/Gac	5/11	1	2	FACETS	0.912	0.854	0.972	0.912	0.854	0.972	CLONAL	1	TRUE	1	0.515883814977451	2		638	1101	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103355	2103410	+	frameshift_variant	Frame_Shift_Del	DEL	GCACTCTGGAAGGCGGTCGCGGATCTGTTGCAGCCGGAGCGGCCGCTGGAGGCCCG	GCACTCTGGAAGGCGGTCGCGGATCTGTTGCAGCCGGAGCGGCCGCTGGAGGCCCG	-	novel	NA	P-0008098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	120	388	0	ENST00000219476.3:c.242_297del	p.Leu81ArgfsTer26	p.L81Rfs*26	ENST00000219476	NM_000548.3	80	GCACTCTGGAAGGCGGTCGCGGATCTGTTGCAGCCGGAGCGGCCGCTGGAGGCCCGg/g	4/42	0.457923663627494	4	FACETS	0.642	0.578	0.709	0.214	0.192	0.237	SUBCLONAL	1	TRUE	1	0.515883814977451	4		388	1099	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0008102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	548	552	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.613702908164302	2		552	1269	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244232	153244232	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	349	639	0	ENST00000281708.4:c.1925A>G	p.Asp642Gly	p.D642G	ENST00000281708	NM_033632.3	642	gAt/gGt	12/12	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.613702908164302	NA		639	1263	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418250	139418250	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	622	584	0	ENST00000277541.6:c.322A>G	p.Thr108Ala	p.T108A	ENST00000277541	NM_017617.3	108	Acc/Gcc	3/34	1	2	FACETS	0.751	0.725	0.778	1	0.997	1	SUBCLONAL	2	TRUE	1	0.613702908164302	2		584	1349	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0008128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	9	318	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.106	0.069	0.153	0.106	0.069	0.153	SUBCLONAL	1	TRUE	1	0.482682925593945	2		318	352	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0008128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	235	381	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.482682925593945	3	FACETS	0.817	0.765	0.87	0.817	0.765	0.87	CLONAL	2	TRUE	1	0.482682925593945	3		381	740	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903763	114903763	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	298	655	1	ENST00000543371.1:c.767C>T	p.Pro256Leu	p.P256L	ENST00000543371	NM_001198531.1	256	cCg/cTg	7/14	1	2	FACETS	0.989	0.93	1	0.989	0.93	1	CLONAL	1	TRUE	1	0.482682925593945	2		656	1249	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325956	30325956	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	198	456	0	ENST00000322652.5:c.2154A>C	p.Lys718Asn	p.K718N	ENST00000322652	NM_015355.2	718	aaA/aaC	16/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.482682925593945	2		456	772	SUCCESS
APC	324	MSKCC	GRCh37	5	112175580	112175592	+	frameshift_variant	Frame_Shift_Del	DEL	CCATGCCACCAAG	CCATGCCACCAAG	-	novel	NA	P-0008128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	182	392	0	ENST00000257430.4:c.4290_4302del	p.Met1431GlufsTer38	p.M1431Efs*38	ENST00000257430	NM_000038.5	1430	aCCATGCCACCAAGc/ac	16/16	1	2	FACETS	0.899	0.83	0.97	0.899	0.83	0.97	CLONAL	1	TRUE	1	0.482682925593945	2		392	839	SUCCESS
APC	324	MSKCC	GRCh37	5	112151281	112151281	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	150	314	0	ENST00000257430.4:c.926del	p.Gly309GlufsTer27	p.G309Efs*27	ENST00000257430	NM_000038.5	308	ctG/ct	9/16	1	2	FACETS	0.884	0.81	0.962	0.884	0.81	0.962	CLONAL	1	TRUE	1	0.482682925593945	2		314	703	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0008131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	506	386	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.66356034357974	7	FACETS	0.891	0.853	0.93			1	CLONAL	3	TRUE	NA	0.66356034357974	7		386	1517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0008131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	958	500	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.66356034357974	4	FACETS	0.989	0.971	1	0.989	0.971	1	CLONAL	4	TRUE	0	0.66356034357974	4		500	1214	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439900	220439900	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	256	519	1	ENST00000243786.2:c.753G>T	p.Arg251Ser	p.R251S	ENST00000243786	NM_002191.3	251	agG/agT	2/2	0.66356034357974	3	FACETS	0.953	0.892	1	0.477	0.446	0.508	CLONAL	1	TRUE	1	0.66356034357974	3		520	1078	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167708	185167708	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	545	577	0	ENST00000265026.3:c.1031G>C	p.Trp344Ser	p.W344S	ENST00000265026	NM_004721.4	344	tGg/tCg	6/14	0.66356034357974	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.66356034357974	4		577	1359	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188638	32188638	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	396	377	0	ENST00000375023.3:c.817T>A	p.Cys273Ser	p.C273S	ENST00000375023	NM_004557.3	273	Tgt/Agt	5/30	0.66356034357974	5	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.66356034357974	5		377	1020	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099508	157099508	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	121	267	0	ENST00000346085.5:c.445C>T	p.Gln149Ter	p.Q149*	ENST00000346085	NM_020732.3	149	Cag/Tag	1/20	0.66356034357974	3	FACETS	1	0.938	1	0.52	0.473	0.569	CLONAL	1	TRUE	1	0.66356034357974	3		267	467	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099492	157099494	+	inframe_deletion	In_Frame_Del	DEL	GGG	GGG	-	novel	NA	P-0008131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	130	299	0	ENST00000346085.5:c.429_431del	p.Gly146del	p.G146del	ENST00000346085	NM_020732.3	143	gcGGGc/gcc	1/20	0.66356034357974	3	FACETS	1	0.915	1	0.502	0.457	0.548	CLONAL	1	TRUE	1	0.66356034357974	3		299	520	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566817	212566817	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	77	307	0	ENST00000342788.4:c.1364C>A	p.Ala455Glu	p.A455E	ENST00000342788	NM_005235.2	455	gCa/gAa	12/28	1	2	FACETS	0.891	0.781	1	0.891	0.781	1	CLONAL	1	TRUE	1	0.219102414057762	2		307	789	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355298	81355298	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	106	324	0	ENST00000222390.5:c.1076G>T	p.Gly359Val	p.G359V	ENST00000222390	NM_000601.4	359	gGg/gTg	9/18	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.219102414057762	2		324	800	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993072	90993072	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	44	185	0	ENST00000265433.3:c.370G>C	p.Gly124Arg	p.G124R	ENST00000265433	NM_002485.4	124	Ggg/Cgg	4/16	1	2	FACETS	0.781	0.655	0.921	0.781	0.655	0.921	CLONAL	1	TRUE	1	0.219102414057762	2		185	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578476	7578476	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	89	252	0	ENST00000269305.4:c.454C>A	p.Pro152Thr	p.P152T	ENST00000269305	NM_001126112.2	152	Ccg/Acg	5/11	0.180445773121275	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.219102414057762	1		252	609	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266835	18266835	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	39	126	0	ENST00000222254.8:c.146G>C	p.Arg49Pro	p.R49P	ENST00000222254	NM_005027.3	49	cGc/cCc	2/16	0.216225509269597	1	FACETS	0.93	0.773	1	0.93	0.773	1	CLONAL	1	TRUE	0	0.219102414057762	1		126	341	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651210	45651210	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	71	253	0	ENST00000407780.3:c.815C>A	p.Ala272Asp	p.A272D	ENST00000407780	NM_001283052.1	272	gCc/gAc	5/7	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.219102414057762	2		253	632	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650778	48650778	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	109	409	2	ENST00000376670.3:c.647G>T	p.Arg216Leu	p.R216L	ENST00000376670	NM_002049.3	216	cGg/cTg	4/6	0.18597757836936	1	FACETS	0.869	0.778	0.965	0.869	0.778	0.965	CLONAL	1	TRUE	0	0.219102414057762	1		411	1020	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579312	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0008135-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	312	274	0	ENST00000269305.4:c.375_375+1delinsAA		p.X125_splice	ENST00000269305	NM_001126112.2	125		4/11	0.502575216314433	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	TRUE	0	0.524755927917458	3		274	495	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361252	66361252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008135-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	76	278	0	ENST00000273854.3:c.920C>T	p.Pro307Leu	p.P307L	ENST00000273854	NM_004439.5	307	cCt/cTt	4/18	0.524755927917458	2	FACETS	0.724	0.638	0.815	0.362	0.319	0.408	SUBCLONAL	1	TRUE	0	0.524755927917458	2		278	400	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998904	100998904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008135-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	281	456	0	ENST00000325455.5:c.898G>A	p.Val300Met	p.V300M	ENST00000325455	NM_001202474.3	300	Gtg/Atg	1/8	0.483758448380949	5	FACETS	0.991	0.932	1			1	CLONAL	2	TRUE	NA	0.524755927917458	5		456	966	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0008136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	46	221	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.882	0.741	1	0.882	0.741	1	CLONAL	1	TRUE	1	0.16	2		222	652	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	57	657	0	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.16	2		657	710	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011200	12011200	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	29	479	0	ENST00000353533.5:c.607G>T	p.Glu203Ter	p.E203*	ENST00000353533	NM_003010.3	203	Gaa/Taa	5/11	1	2	FACETS	0.718	0.575	0.881	0.718	0.575	0.881	SUBCLONAL	1	TRUE	1	0.16	2		479	505	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212492	5212492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	42	591	0	ENST00000357368.4:c.4625G>A	p.Ser1542Asn	p.S1542N	ENST00000357368	NM_002850.3	1542	aGt/aAt	31/38	1	2	FACETS	0.77	0.641	0.913	0.77	0.641	0.913	CLONAL	1	TRUE	1	0.16	2		591	682	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578175	7578233	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ACCTCAGGCGGCTCATAGGGCACCACCACACTATGTCGAAAAGTGTTTCTGTCATCCAA	ACCTCAGGCGGCTCATAGGGCACCACCACACTATGTCGAAAAGTGTTTCTGTCATCCAA	-	novel	NA	P-0008136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	63	762	0	ENST00000269305.4:c.616_672+2del		p.X206_splice	ENST00000269305	NM_001126112.2	206		6/11	1	2	FACETS	0.854	0.737	0.982	0.854	0.737	0.982	CLONAL	1	TRUE	1	0.16	2		762	922	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022913	27022938	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGCCGCCGCCAGCAGCCTGGGCAA	CCCGCCGCCGCCAGCAGCCTGGGCAA	-	rs797045262	NA	P-0008137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	16	37	0	ENST00000324856.7:c.31_56del	p.Ser11AlafsTer91	p.S11Afs*91	ENST00000324856	NM_006015.4	7	CCCGCCGCCGCCAGCAGCCTGGGCAAc/c	1/20	0.236592611354986	1	FACETS	1	0.785	1	1	0.785	1	CLONAL	1	TRUE	0	0.236592611354986	1		37	113	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183873	10183873	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0008137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	36	194	0	ENST00000256474.2:c.340+2T>A		p.X114_splice	ENST00000256474	NM_000551.3	114			0.236592611354986	1	FACETS	0.796	0.656	0.952	0.796	0.656	0.952	CLONAL	1	TRUE	0	0.236592611354986	1		194	337	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474041	29474041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs78723472	NA	P-0008137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1568	212	744	1	ENST00000389048.3:c.2134G>A	p.Val712Met	p.V712M	ENST00000389048	NM_004304.4	712	Gtg/Atg	12/29	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.236592611354986	2		745	1780	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987021	36987021	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	29	208	0	ENST00000354822.5:c.668A>T	p.His223Leu	p.H223L	ENST00000354822	NM_001079668.2	223	cAc/cTc	3/3	0.610123581927783	1	FACETS	0.182	0.146	0.223	0.182	0.146	0.223	SUBCLONAL	1	TRUE	0	0.610123581927783	1		208	363	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241677	55241677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504256	NA	P-0008145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	108	392	0	ENST00000275493.2:c.2125G>A	p.Glu709Lys	p.E709K	ENST00000275493	NM_005228.3	709	Gaa/Aaa	18/28	0.199505155793555	3	FACETS	1	0.982	1	0.728	0.654	0.806	CLONAL	1	TRUE	1	0.242582060571252	3		392	686	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0008145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	103	349	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.199505155793555	3	FACETS	0.78	0.7	0.866	0.78	0.7	0.866	SUBCLONAL	2	TRUE	1	0.242582060571252	3		349	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0008145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	69	240	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.242582060571252	2		240	416	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077427	30077427	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0008145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	33	146	0	ENST00000338641.4:c.1575-1G>C		p.X525_splice	ENST00000338641	NM_000268.3	525			0.237914520630876	1	FACETS	0.876	0.716	1	0.876	0.716	1	CLONAL	1	TRUE	0	0.242582060571252	1		146	273	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202283	133202283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764457707	NA	P-0008145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	64	310	0	ENST00000320574.5:c.6605C>T	p.Thr2202Met	p.T2202M	ENST00000320574	NM_006231.2	2202	aCg/aTg	47/49	0.195761421624277	2	FACETS	0.907	0.785	1	0.453	0.392	0.519	CLONAL	1	TRUE	0	0.242582060571252	2		310	582	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106663	2106663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	36	373	0	ENST00000219476.3:c.667G>A	p.Asp223Asn	p.D223N	ENST00000219476	NM_000548.3	223	Gac/Aac	8/42	0.242582060571252	2	FACETS	0.455	0.373	0.548	0.228	0.186	0.274	SUBCLONAL	1	TRUE	0	0.242582060571252	2		373	652	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533478	63533478	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1060502126	NA	P-0008145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	38	276	0	ENST00000307078.5:c.1676C>G	p.Ser559Cys	p.S559C	ENST00000307078	NM_004655.3	559	tCc/tGc	6/11	1	2	FACETS	0.579	0.478	0.692	0.579	0.478	0.692	SUBCLONAL	1	TRUE	1	0.242582060571252	2		276	541	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0008175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	34	254	7	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.267578866534264	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.19	1		261	270	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0008175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	82	529	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.944	0.831	1	0.944	0.831	1	CLONAL	1	TRUE	1	0.19	2		529	914	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295773	212295773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1299031105	NA	P-0008175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	62	625	1	ENST00000342788.4:c.2540G>A	p.Arg847His	p.R847H	ENST00000342788	NM_005235.2	847	cGt/cAt	21/28	0.152426251953481	3	FACETS	0.653	0.562	0.752	0.326	0.281	0.376	SUBCLONAL	1	TRUE	1	0.19	3		626	1095	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581338	48581339	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0008175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	64	385	0	ENST00000342988.3:c.642_643del	p.Pro215GlnfsTer19	p.P215Qfs*19	ENST00000342988	NM_005359.5	214	ttTCcc/ttcc	5/12	1	2	FACETS	0.877	0.758	1	0.877	0.758	1	CLONAL	1	TRUE	1	0.19	2		385	768	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0008184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	62	370	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.935	0.807	1	0.935	0.807	1	CLONAL	1	TRUE	1	0.19	2		370	698	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750945	128750945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	28	269	0	ENST00000377970.2:c.482C>T	p.Ser161Leu	p.S161L	ENST00000377970	NM_002467.4	161	tCa/tTa	2/3	1	2	FACETS	0.659	0.526	0.811	0.659	0.526	0.811	SUBCLONAL	1	TRUE	1	0.19	2		269	447	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16001793	16001793	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0008184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	63	387	0	ENST00000268712.3:c.2708C>G	p.Ser903Ter	p.S903*	ENST00000268712	NM_006311.3	903	tCa/tGa	21/46	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.19	2		387	638	SUCCESS
ATR	545	MSKCC	GRCh37	3	142253951	142253951	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	38	382	0	ENST00000350721.4:c.3916A>C	p.Ser1306Arg	p.S1306R	ENST00000350721	NM_001184.3	1306	Agc/Cgc	21/47	1	2	FACETS	0.587	0.483	0.702	0.587	0.483	0.702	SUBCLONAL	1	TRUE	1	0.19	2		382	682	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982491	25982491	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	32	304	2	ENST00000435504.4:c.799G>T	p.Ala267Ser	p.A267S	ENST00000435504		267	Gct/Tct	9/13	1	2	FACETS	0.603	0.488	0.733	0.603	0.488	0.733	SUBCLONAL	1	TRUE	1	0.19	2		306	559	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710983	117710983	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	35	154	0	ENST00000368508.3:c.1289G>A	p.Gly430Asp	p.G430D	ENST00000368508	NM_002944.2	430	gGc/gAc	12/43	1	2	FACETS	0.758	0.625	0.905	1	0.95	1	CLONAL	2	TRUE	1	0.19	2		154	243	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453150	140453150	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913341	NA	P-0008184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	61	316	0	ENST00000288602.6:c.1785T>G	p.Phe595Leu	p.F595L	ENST00000288602	NM_004333.4	595	ttT/ttG	15/18	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.19	2		316	542	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751197	128751197	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	31	233	0	ENST00000377970.2:c.734C>T	p.Ser245Phe	p.S245F	ENST00000377970	NM_002467.4	245	tCc/tTc	2/3	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.19	2		233	309	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907164	101907164	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	48	272	1	ENST00000374994.4:c.1124C>A	p.Thr375Lys	p.T375K	ENST00000374994	NM_004612.2	375	aCa/aAa	6/9	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.19	2		273	383	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0008189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	136	158	0				ENST00000310581	NM_198253.2	-/1132			0.323096699656237	3	FACETS	0.757	0.697	0.819	0.757	0.697	0.819	INDETERMINATE	2	FALSE	1	0.643144348892666	3		158	369	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0008189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	271	531	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.27188812459102	4	FACETS	0.904	0.852	0.957	0.904	0.852	0.957	INDETERMINATE	2	FALSE	2	0.643144348892666	4		531	766	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584522	189584522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	43	493	0	ENST00000264731.3:c.818C>T	p.Ala273Val	p.A273V	ENST00000264731	NM_003722.4	273	gCc/gTc	6/14	0.243587630762943	1	FACETS	0.12	0.1	0.143	0.12	0.1	0.143	INDETERMINATE	1	FALSE	0	0.643144348892666	1		493	755	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391718	139391718	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	261	304	0	ENST00000277541.6:c.6473T>G	p.Val2158Gly	p.V2158G	ENST00000277541	NM_017617.3	2158	gTc/gGc	34/34	0.643144348892666	2	FACETS	0.888	0.845	0.931	0.888	0.845	0.931	CLONAL	2	FALSE	0	0.643144348892666	2		304	457	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347234	89347234	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008212-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	446	438	0	ENST00000301030.4:c.5716G>T	p.Ala1906Ser	p.A1906S	ENST00000301030	NM_001256183.1	1906	Gcc/Tcc	9/13	1	2	FACETS	0.976	0.935	1	0.976	0.935	1	CLONAL	1	TRUE	1	0.866065660074334	2		438	1055	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579592	7579592	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0008241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	376	321	0	ENST00000269305.4:c.97-2A>T		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.605052518680961	2	FACETS	0.96	0.922	0.997	0.96	0.922	0.997	CLONAL	2	TRUE	0	0.621975387221529	2		321	630	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41219712	41219712	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	177	356	0	ENST00000357654.3:c.4987A>G	p.Met1663Val	p.M1663V	ENST00000357654	NM_007294.3	1663	Atg/Gtg	16/23	1	2	FACETS	0.704	0.649	0.76	0.704	0.649	0.76	SUBCLONAL	1	TRUE	1	0.621975387221529	2		356	809	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562398	95562398	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	74	270	0	ENST00000393063.1:c.4859G>T	p.Ser1620Ile	p.S1620I	ENST00000393063	NM_030621.3	1620	aGc/aTc	24/28	1	2	FACETS	0.519	0.455	0.588	0.519	0.455	0.588	SUBCLONAL	1	TRUE	1	0.5	2		270	570	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86667971	86667971	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770599456	NA	P-0008265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	137	563	0	ENST00000274376.6:c.1735C>T	p.Arg579Trp	p.R579W	ENST00000274376	NM_002890.2	579	Cgg/Tgg	13/25	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		563	1021	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023028	150023028	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	242	620	0	ENST00000253339.5:c.235C>G	p.Gln79Glu	p.Q79E	ENST00000253339		79	Cag/Gag	1/7	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.719112611519917	2		620	616	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199963	108199963	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1160508407	NA	P-0008291-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	139	282	0	ENST00000278616.4:c.7305C>A	p.Asn2435Lys	p.N2435K	ENST00000278616	NM_000051.3	2435	aaC/aaA	49/63	0.175823273443954	3	FACETS	1	0.919	1	0.672	0.612	0.734	CLONAL	2	TRUE	0	0.207050716833903	3		282	735	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0008302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	123	158	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.374326502247806	2		158	585	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508490	106508490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	51	64	0	ENST00000359195.3:c.484G>A	p.Val162Ile	p.V162I	ENST00000359195	NM_002649.2	162	Gtc/Atc	2/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.374326502247806	2		64	187	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620673	52620674	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0008302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	122	252	0	ENST00000394830.3:c.3079_3080del	p.Asp1028Ter	p.D1028*	ENST00000394830	NM_018313.4	1027	CGa/a	21/30	0.374326502247806	1	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	0	0.374326502247806	1		252	529	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188224	10188224	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	239	423	0	ENST00000256474.2:c.369del	p.Thr124HisfsTer35	p.T124Hfs*35	ENST00000256474	NM_000551.3	123	Ggg/gg	2/3	0.374326502247806	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.374326502247806	1		423	917	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610382	10610382	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	62	484	0	ENST00000171111.5:c.328A>G	p.Met110Val	p.M110V	ENST00000171111	NM_203500.1	110	Atg/Gtg	2/6	0.194067431121323	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.194067431121323	1		484	526	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0008307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	40	490	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	0.194067431121323	1	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	0	0.194067431121323	1		490	332	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044922	47044922	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	50	206	0	ENST00000377604.3:c.2248G>T	p.Glu750Ter	p.E750*	ENST00000377604	NM_001204468.1	750	Gag/Tag	20/24	0.185506322109425	0	FACETS	0.714	0.609	0.826			1	SUBCLONAL	2	TRUE	NA	0.194067431121323	0		206	291	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276919	123276919	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	70	584	0	ENST00000358487.5:c.998C>T	p.Thr333Ile	p.T333I	ENST00000358487	NM_000141.4	333	aCt/aTt	8/18	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.194067431121323	2		584	626	SUCCESS
EED	8726	MSKCC	GRCh37	11	85961491	85961491	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0008307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	45	357	0	ENST00000263360.6:c.267+1G>T		p.X89_splice	ENST00000263360	NM_003797.3	89			1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.194067431121323	2		357	369	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138543	2138543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371543182	NA	P-0008307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	54	535	0	ENST00000219476.3:c.5356C>T	p.Pro1786Ser	p.P1786S	ENST00000219476	NM_000548.3	1786	Cct/Tct	42/42	1	2	FACETS	0.755	0.644	0.878	0.755	0.644	0.878	SUBCLONAL	1	TRUE	1	0.194067431121323	2		535	737	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857496	9857496	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008307-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	43	377	0	ENST00000330684.3:c.3905T>A	p.Leu1302Gln	p.L1302Q	ENST00000330684	NM_001134407.1	1302	cTa/cAa	13/13	1	2	FACETS	0.914	0.765	1	0.914	0.765	1	CLONAL	1	TRUE	1	0.194067431121323	2		377	485	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0008310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	103	342	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.225230742740066	5	FACETS	1	0.924	1	0.348	0.31	0.388	CLONAL	1	TRUE	2	0.225230742740066	5		342	1172	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0008310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	222	395	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.225230742740066	5	FACETS	1	0.982	1	0.777	0.722	0.833	CLONAL	2	TRUE	2	0.225230742740066	5		395	1132	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0008310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	49	395	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.132236436573462	0	FACETS	0.664	0.562	0.775			1	INDETERMINATE	1	TRUE	0	0.225230742740066	0		395	508	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604653	48604653	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	45	297	0	ENST00000342988.3:c.1475T>G	p.Val492Gly	p.V492G	ENST00000342988	NM_005359.5	492	gTt/gGt	12/12	0.225230742740066	1	FACETS	0.657	0.551	0.773	0.657	0.551	0.773	SUBCLONAL	1	TRUE	0	0.225230742740066	1		297	540	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0008316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	80	318	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.402709321738129	5	FACETS	0.972	0.88	1	0.972	0.88	1	CLONAL	4	TRUE	1	0.402709321738129	5		318	164	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519896	NA	P-0008316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	50	480	1	ENST00000281708.4:c.1514G>T	p.Arg505Leu	p.R505L	ENST00000281708	NM_033632.3	505	cGc/cTc	10/12	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.402709321738129	2		481	230	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287380	38287380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	32	465	0	ENST00000425967.3:c.277G>A	p.Asp93Asn	p.D93N	ENST00000425967	NM_001174067.1	93	Gat/Aat	4/19	0.176219187188948	1	FACETS	0.747	0.613	0.894	0.747	0.613	0.894	INDETERMINATE	1	TRUE	0	0.402709321738129	1		465	170	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104353781	104353781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369465986	NA	P-0008316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	46	486	0	ENST00000369902.3:c.715C>T	p.Arg239Trp	p.R239W	ENST00000369902	NM_016169.3	239	Cgg/Tgg	6/12	0.309382548767101	4	FACETS	1	0.957	1			1	CLONAL	1	TRUE	NA	0.402709321738129	4		486	229	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058751	42058751	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	70	631	0	ENST00000219905.7:c.8471C>T	p.Thr2824Ile	p.T2824I	ENST00000219905	NM_001164273.1	2824	aCt/aTt	24/24	0.154283358955626	0	FACETS	0.855	0.755	0.959			1	INDETERMINATE	1	TRUE	0	0.402709321738129	0		631	243	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304202	91304202	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	41	535	0	ENST00000355112.3:c.1599G>C	p.Gln533His	p.Q533H	ENST00000355112	NM_000057.2	533	caG/caC	7/22	0.282108083711202	1	FACETS	0.767	0.645	0.899	0.767	0.645	0.899	SUBCLONAL	1	TRUE	0	0.402709321738129	1		535	212	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136278	2136278	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039446	NA	P-0008316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	50	530	2	ENST00000219476.3:c.4747G>A	p.Glu1583Lys	p.E1583K	ENST00000219476	NM_000548.3	1583	Gag/Aag	37/42	0.176219187188948	1	FACETS	1	0.941	1	1	0.941	1	INDETERMINATE	1	TRUE	0	0.402709321738129	1		532	169	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934515	9934515	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	46	596	0	ENST00000330684.3:c.1640C>T	p.Ser547Phe	p.S547F	ENST00000330684	NM_001134407.1	547	tCt/tTt	7/13	0.176219187188948	1	FACETS	1	0.946	1	1	0.946	1	INDETERMINATE	1	TRUE	0	0.402709321738129	1		596	149	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1161557773	NA	P-0008316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	97	642	0	ENST00000308159.5:c.43C>A	p.Gln15Lys	p.Q15K	ENST00000308159	NM_014669.4	15	Cag/Aag	2/22	0.176219187188948	1	FACETS	1	0.972	1	1	0.972	1	INDETERMINATE	1	TRUE	0	0.402709321738129	1		642	316	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770039	56770039	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764394130	NA	P-0008316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	33	453	1	ENST00000337432.4:c.35G>A	p.Arg12Gln	p.R12Q	ENST00000337432	NM_058216.2	12	cGg/cAg	1/9	0.154283358955626	0	FACETS	0.499	0.41	0.598			1	INDETERMINATE	1	TRUE	0	0.402709321738129	0		454	196	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78858886	78858886	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765318427	NA	P-0008316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	42	537	1	ENST00000306801.3:c.1921G>A	p.Asp641Asn	p.D641N	ENST00000306801	NM_020761.2	641	Gac/Aac	17/34	0.260505112494149	5	FACETS	1	0.956	1	0.481	0.405	0.564	CLONAL	1	TRUE	2	0.402709321738129	5		538	232	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624974	9624974	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0008316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	10	272	0	ENST00000353224.5:c.3G>A	p.Met1?	p.M1?	ENST00000353224	NM_177990.2	1	atG/atA	3/10	0.176219187188948	1	FACETS	0.793	0.552	1	0.793	0.552	1	INDETERMINATE	1	TRUE	0	0.402709321738129	1		272	50	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446760	49446760	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	47	462	0	ENST00000301067.7:c.1050del	p.His350GlnfsTer52	p.H350Qfs*52	ENST00000301067	NM_003482.3	350	caC/ca	8/54	0.227701064032245	3	FACETS	1	0.942	1	0.612	0.522	0.71	INDETERMINATE	1	TRUE	1	0.402709321738129	3		462	229	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846405	128846406	+	missense_variant	Missense_Mutation	DNP	TG	TG	GT	novel	NA	P-0008316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	12	473	0	ENST00000249373.3:c.1241_1242delinsGT	p.Val414Gly	p.V414G	ENST00000249373	NM_005631.4	414	gTG/gGT	6/12	0.410725574535515	1	FACETS	0.476	0.338	0.642	0.476	0.338	0.642	SUBCLONAL	1	TRUE	0	0.402709321738129	1		473	100	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0008322-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	164	254	7	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.563156440639997	1	FACETS	0.825	0.764	0.887	0.825	0.764	0.887	CLONAL	1	TRUE	0	0.606352080633797	1		261	457	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163634	47163634	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008322-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	150	316	0	ENST00000409792.3:c.2492C>A	p.Ser831Ter	p.S831*	ENST00000409792	NM_014159.6	831	tCa/tAa	3/21	0.555451987015808	1	FACETS	0.853	0.789	0.92	0.853	0.789	0.92	CLONAL	1	TRUE	0	0.606352080633797	1		316	404	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225899	53225899	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008322-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	293	199	0	ENST00000375401.3:c.2950G>T	p.Glu984Ter	p.E984*	ENST00000375401	NM_004187.3	984	Gag/Tag	19/26	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.606352080633797	1		199	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0008340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	950	525	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.525799536045746	1	FACETS	0.968	0.947	0.989	1	0.999	1	CLONAL	2	TRUE	0	0.525799536045746	1		526	1376	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0008340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	43	143	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.525799536045746	1	FACETS	0.709	0.603	0.823	0.709	0.603	0.823	SUBCLONAL	1	TRUE	0	0.525799536045746	1		143	170	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217479	7217479	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0008340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	1196	648	1	ENST00000380728.2:c.318-1G>T		p.X106_splice	ENST00000380728		106			0.525799536045746	1	FACETS	0.955	0.936	0.974	1	0.999	1	CLONAL	2	TRUE	0	0.525799536045746	1		649	1756	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794715	42794715	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201902940	NA	P-0008340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	136	468	0	ENST00000575354.2:c.1795C>T	p.Arg599Trp	p.R599W	ENST00000575354	NM_015125.3	599	Cgg/Tgg	10/20	1	2	FACETS	0.762	0.694	0.833	0.762	0.694	0.833	SUBCLONAL	1	TRUE	1	0.525799536045746	2		468	679	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0008346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	432	210	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.476818005753711	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	TRUE	0	0.476490525571713	3		210	735	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873192	71873192	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs759861079	NA	P-0008346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	301	987	4	ENST00000357731.5:c.1002C>A	p.Tyr334Ter	p.Y334*	ENST00000357731	NM_173808.2	334	taC/taA	7/7	0.476490525571713	2	FACETS	0.954	0.898	1	0.477	0.449	0.506	CLONAL	1	TRUE	0	0.476490525571713	2		991	1324	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211169	55211169	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	72	427	0	ENST00000275493.2:c.412A>G	p.Arg138Gly	p.R138G	ENST00000275493	NM_005228.3	138	Aga/Gga	3/28	0.476490525571713	2	FACETS	0.54	0.472	0.613	0.27	0.236	0.307	SUBCLONAL	1	TRUE	0	0.476490525571713	2		427	560	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884952	111884952	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1281832778	NA	P-0008346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	457	711	0	ENST00000341259.2:c.950T>C	p.Met317Thr	p.M317T	ENST00000341259	NM_005475.2	317	aTg/aCg	5/8	0.476818005753711	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	2	0.476490525571713	4		711	1413	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796768	42796768	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	140	480	0	ENST00000575354.2:c.3226C>A	p.Pro1076Thr	p.P1076T	ENST00000575354	NM_015125.3	1076	Ccc/Acc	14/20	0.455973932248197	1	FACETS	0.834	0.763	0.907	0.834	0.763	0.907	CLONAL	1	TRUE	0	0.476490525571713	1		480	537	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061137	38061161	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCCCGCTTCCGCTCCCGCCCCCG	GCCCCCGCTTCCGCTCCCGCCCCCG	-	novel	NA	P-0008346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	53	110	0	ENST00000250448.2:c.828_852del	p.Gly277AlafsTer36	p.G277Afs*36	ENST00000250448	NM_004496.3	276	ggCGGGGGCGGGAGCGGAAGCGGGGGC/gg	2/2	0.476818005753711	4	FACETS	1	0.96	1	0.676	0.582	0.776	CLONAL	1	TRUE	2	0.476490525571713	4		110	243	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954334	48954335	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	rs587778832	NA	P-0008346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	241	448	0	ENST00000267163.4:c.1456_1457del	p.Leu486IlefsTer6	p.L486Ifs*6	ENST00000267163	NM_000321.2	485	tcTTta/tcta	16/27	0.476490525571713	2	FACETS	0.77	0.723	0.817	0.77	0.723	0.817	SUBCLONAL	2	TRUE	0	0.476490525571713	2		448	657	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004609	16004609	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	321	555	0	ENST00000268712.3:c.2645del	p.Thr882SerfsTer27	p.T882Sfs*27	ENST00000268712	NM_006311.3	882	aCg/ag	20/46	0.476490525571713	2	FACETS	0.904	0.859	0.95	0.904	0.859	0.95	CLONAL	2	TRUE	0	0.476490525571713	2		555	745	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579403	7579410	+	frameshift_variant	Frame_Shift_Del	DEL	GATGACAG	GATGACAG	-	novel	NA	P-0008346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	203	437	0	ENST00000269305.4:c.277_284del	p.Leu93PhefsTer53	p.L93Ffs*53	ENST00000269305	NM_001126112.2	93	CTGTCATCt/t	4/11	0.476490525571713	2	FACETS	1	0.991	1	0.722	0.674	0.771	CLONAL	1	TRUE	0	0.476490525571713	2		437	590	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156731	20156731	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	612	758	1	ENST00000379607.5:c.26G>T	p.Gly9Val	p.G9V	ENST00000379607	NM_001412.3	9	gGt/gTt	2/7	0.886413020826809	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.886413020826809	1		759	668	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092813	27092814	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0008354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	345	699	0	ENST00000324856.7:c.2834_2835del	p.Gly945AlafsTer61	p.G945Afs*61	ENST00000324856	NM_006015.4	945	gGA/g	9/20	1	2	FACETS	0.955	0.909	1	0.955	0.909	1	CLONAL	1	TRUE	1	0.886413020826809	2		699	815	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0008372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	161	426	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.971	0.892	1	0.971	0.892	1	CLONAL	1	TRUE	1	0.420247920802442	2		426	789	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466799	25466799	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751562376	NA	P-0008372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	234	425	0	ENST00000264709.3:c.1904G>A	p.Arg635Gln	p.R635Q	ENST00000264709	NM_175629.2	635	cGg/cAg	16/23	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.420247920802442	2		425	976	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	114	260	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.976	0.895	1			1	INDETERMINATE	1	TRUE	NA	0.898596190055208	2		260	260	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0008388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	385	326	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.949	0.905	0.993	0.949	0.905	0.993	CLONAL	1	TRUE	1	0.898596190055208	2		326	903	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849844	151849844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	77	521	0	ENST00000262189.6:c.12472G>A	p.Val4158Met	p.V4158M	ENST00000262189	NM_170606.2	4158	Gtg/Atg	49/59	0.602048822630775	3	FACETS	0.225	0.197	0.256	0.113	0.098	0.128	SUBCLONAL	1	TRUE	1	0.898596190055208	3		521	1103	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991707	72991715	+	inframe_deletion	In_Frame_Del	DEL	CCGCAGCCA	CCGCAGCCA	-	rs767895847	NA	P-0008388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	248	420	0	ENST00000268489.5:c.2330_2338del	p.Val777_Ala779del	p.V777_A779del	ENST00000268489	NM_006885.3	777	gTGGCTGCGGcg/gcg	2/10	0.898596190055208	1	FACETS	0.652	0.618	0.686	0.652	0.618	0.686	SUBCLONAL	1	TRUE	0	0.898596190055208	1		420	466	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325894	65325894	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	66	478	2	ENST00000342505.4:c.1228G>A	p.Asp410Asn	p.D410N	ENST00000342505	NM_002227.2	410	Gat/Aat	9/25	0.898596190055208	1	FACETS	0.177	0.154	0.203	0.177	0.154	0.203	SUBCLONAL	1	TRUE	0	0.898596190055208	1		480	456	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091334	193091334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	35	316	0	ENST00000367435.3:c.4G>A	p.Ala2Thr	p.A2T	ENST00000367435	NM_024529.4	2	Gcg/Acg	1/17	1	2	FACETS	0.158	0.129	0.191	0.158	0.129	0.191	SUBCLONAL	1	TRUE	1	0.898596190055208	2		316	493	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645807	215645807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	106	651	1	ENST00000260947.4:c.791G>A	p.Gly264Asp	p.G264D	ENST00000260947	NM_000465.2	264	gGc/gAc	4/11	1	2	FACETS	0.213	0.19	0.237	0.213	0.19	0.237	SUBCLONAL	1	TRUE	1	0.898596190055208	2		652	1110	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050397	37050397	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs267607765	NA	P-0008388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	114	638	0	ENST00000231790.2:c.545+1G>A		p.X182_splice	ENST00000231790	NM_000249.3	182			0.263552608037669	1	FACETS	0.144	0.129	0.16	0.144	0.129	0.16	INDETERMINATE	1	TRUE	0	0.898596190055208	1		638	970	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200074	128200074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	71	627	1	ENST00000341105.2:c.1231G>A	p.Ala411Thr	p.A411T	ENST00000341105	NM_032638.4	411	Gcg/Acg	6/6	1	2	FACETS	0.179	0.156	0.205	0.179	0.156	0.205	SUBCLONAL	1	TRUE	1	0.898596190055208	2		628	881	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670306	134670306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	77	541	0	ENST00000398015.3:c.217C>T	p.Leu73Phe	p.L73F	ENST00000398015	NM_004441.4	73	Ctc/Ttc	3/16	1	2	FACETS	0.216	0.189	0.245	0.216	0.189	0.245	SUBCLONAL	1	TRUE	1	0.898596190055208	2		541	794	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526173	189526173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	55	603	0	ENST00000264731.3:c.437C>T	p.Pro146Leu	p.P146L	ENST00000264731	NM_003722.4	146	cCc/cTc	4/14	1	2	FACETS	0.136	0.116	0.159	0.136	0.116	0.159	SUBCLONAL	1	TRUE	1	0.898596190055208	2		603	899	SUCCESS
APC	324	MSKCC	GRCh37	5	112173660	112173660	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	107	535	0	ENST00000257430.4:c.2369G>A	p.Arg790Lys	p.R790K	ENST00000257430	NM_000038.5	790	aGa/aAa	16/16	0.112321961573951	5	FACETS	0.527	0.472	0.587	0.176	0.157	0.196	INDETERMINATE	1	TRUE	2	0.898596190055208	5		535	1060	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504362	149504362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	53	518	0	ENST00000261799.4:c.1840G>A	p.Val614Met	p.V614M	ENST00000261799	NM_002609.3	614	Gtg/Atg	13/23	1	2	FACETS	0.163	0.139	0.191	0.163	0.139	0.191	SUBCLONAL	1	TRUE	1	0.898596190055208	2		518	722	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622239	162622239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55654276	NA	P-0008388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	91	512	0	ENST00000366898.1:c.458C>T	p.Pro153Leu	p.P153L	ENST00000366898	NM_004562.2	153	cCc/cTc	4/12	1	2	FACETS	0.191	0.169	0.215	0.191	0.169	0.215	SUBCLONAL	1	TRUE	1	0.898596190055208	2		512	1060	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959088	2959088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	46	515	0	ENST00000396946.4:c.2428G>A	p.Asp810Asn	p.D810N	ENST00000396946	NM_032415.4	810	Gac/Aac	18/25	NA	2	FACETS	0.151	0.126	0.178			1	INDETERMINATE	1	TRUE	NA	0.898596190055208	2		515	680	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97888854	97888854	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	88	681	0	ENST00000289081.3:c.853G>A	p.Ala285Thr	p.A285T	ENST00000289081	NM_000136.2	285	Gcc/Acc	9/15	1	2	FACETS	0.197	0.174	0.222	0.197	0.174	0.222	SUBCLONAL	1	TRUE	1	0.898596190055208	2		681	994	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215820	98215820	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	64	474	0	ENST00000331920.6:c.3389C>T	p.Ala1130Val	p.A1130V	ENST00000331920	NM_000264.3	1130	gCc/gTc	20/24	1	2	FACETS	0.209	0.18	0.24	0.209	0.18	0.24	SUBCLONAL	1	TRUE	1	0.898596190055208	2		474	682	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023096	1023096	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	112	654	1	ENST00000358495.3:c.1159G>A	p.Asp387Asn	p.D387N	ENST00000358495	NM_134424.2	387	Gac/Aac	11/12	1	2	FACETS	0.234	0.209	0.26	0.234	0.209	0.26	SUBCLONAL	1	TRUE	1	0.898596190055208	2		655	1066	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230581	46230581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	105	815	0	ENST00000334344.6:c.830G>A	p.Gly277Asp	p.G277D	ENST00000334344	NM_152641.2	277	gGc/gAc	8/21	1	2	FACETS	0.199	0.177	0.222	0.199	0.177	0.222	SUBCLONAL	1	TRUE	1	0.898596190055208	2		815	1176	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504614	103504614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767355056	NA	P-0008388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	118	591	0	ENST00000355739.4:c.235G>A	p.Asp79Asn	p.D79N	ENST00000355739	NM_000123.3	79	Gat/Aat	2/15	1	2	FACETS	0.222	0.199	0.246	0.222	0.199	0.246	SUBCLONAL	1	TRUE	1	0.898596190055208	2		591	1184	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842663	68842663	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555515266	NA	P-0008388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	121	909	0	ENST00000261769.5:c.599C>T	p.Pro200Leu	p.P200L	ENST00000261769	NM_004360.3	200	cCc/cTc	5/16	0.796834381368054	1	FACETS	0.196	0.176	0.216	0.196	0.176	0.216	SUBCLONAL	1	TRUE	0	0.898596190055208	1		909	758	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81954852	81954852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	76	939	0	ENST00000359376.3:c.2285C>T	p.Pro762Leu	p.P762L	ENST00000359376	NM_002661.3	762	cCc/cTc	21/33	0.898596190055208	1	FACETS	0.132	0.115	0.15	0.132	0.115	0.15	SUBCLONAL	1	TRUE	0	0.898596190055208	1		939	706	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370301	40370301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1408	144	1260	0	ENST00000293328.3:c.1037C>T	p.Thr346Ile	p.T346I	ENST00000293328	NM_012448.3	346	aCc/aTc	9/19	1	2	FACETS	0.207	0.187	0.227	0.207	0.187	0.227	SUBCLONAL	1	TRUE	1	0.898596190055208	2		1260	1552	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246823	41246823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	115	676	0	ENST00000357654.3:c.725G>A	p.Ser242Asn	p.S242N	ENST00000357654	NM_007294.3	242	aGt/aAt	10/23	1	2	FACETS	0.239	0.214	0.265	0.239	0.214	0.265	SUBCLONAL	1	TRUE	1	0.898596190055208	2		676	1073	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584393	39584393	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	105	594	0	ENST00000262039.4:c.1058G>A	p.Gly353Glu	p.G353E	ENST00000262039	NM_002647.2	353	gGa/gAa	10/25	1	2	FACETS	0.202	0.18	0.225	0.202	0.18	0.225	SUBCLONAL	1	TRUE	1	0.898596190055208	2		594	1159	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4097300	4097300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	58	472	0	ENST00000262948.5:c.961C>T	p.Leu321Phe	p.L321F	ENST00000262948	NM_030662.3	321	Ctc/Ttc	8/11	1	2	FACETS	0.151	0.129	0.175	0.151	0.129	0.175	SUBCLONAL	1	TRUE	1	0.898596190055208	2		472	854	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520246	9520246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	100	518	0	ENST00000353224.5:c.2023G>A	p.Gly675Arg	p.G675R	ENST00000353224	NM_177990.2	675	Gga/Aga	10/10	1	2	FACETS	0.248	0.221	0.277	0.248	0.221	0.277	SUBCLONAL	1	TRUE	1	0.898596190055208	2		518	897	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1331454	1331454	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	46	622	1	ENST00000400841.2:c.74G>A	p.Gly25Glu	p.G25E	ENST00000400841		25	gGa/gAa	1/6	0.897937032508384	1	FACETS	0.088	0.074	0.104	0.088	0.074	0.104	SUBCLONAL	1	TRUE	0	0.898596190055208	1		623	639	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040965	47040965	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781843473	NA	P-0008388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	80	542	1	ENST00000377604.3:c.1495G>A	p.Ala499Thr	p.A499T	ENST00000377604	NM_001204468.1	499	Gcc/Acc	14/24	0.856514487162481	1	FACETS	0.208	0.184	0.234	0.208	0.184	0.234	SUBCLONAL	1	TRUE	0	0.898596190055208	1		543	471	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794714	42794714	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	336	557	1	ENST00000575354.2:c.1795del	p.Arg599GlyfsTer129	p.R599Gfs*129	ENST00000575354	NM_015125.3	598	ttC/tt	10/20	0.796834381368054	1	FACETS	0.974	0.944	1	0.974	0.944	1	CLONAL	1	TRUE	0	0.898596190055208	1		558	423	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518692	176518692	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1349255606	NA	P-0008397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	148	241	0	ENST00000292408.4:c.610C>A	p.His204Asn	p.H204N	ENST00000292408	NM_213647.1	204	Cat/Aat	6/18	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.640850932356007	2		241	452	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393428	139393428	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	297	331	0	ENST00000277541.6:c.6103G>C	p.Ala2035Pro	p.A2035P	ENST00000277541	NM_017617.3	2035	Gcc/Ccc	33/34	1	2	FACETS	0.756	0.719	0.794	1	0.995	1	SUBCLONAL	2	TRUE	1	0.640850932356007	2		331	613	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437536	56437536	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	248	349	0	ENST00000407977.2:c.926G>T	p.Cys309Phe	p.C309F	ENST00000407977		309	tGc/tTc	8/10	0.640850932356007	3	FACETS	0.908	0.849	0.97	0.454	0.424	0.485	CLONAL	1	TRUE	1	0.640850932356007	3		349	1125	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0008429-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	188	370	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.765	0.708	0.825	0.765	0.708	0.825	SUBCLONAL	1	TRUE	1	0.545836657352623	2		370	900	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0008429-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	248	277	1	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	NA	2	FACETS	0.759	0.715	0.803			1	INDETERMINATE	2	TRUE	NA	0.545836657352623	2		278	599	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046958	128046958	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs772883177	NA	P-0008429-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	311	542	2	ENST00000285398.2:c.777A>T	p.Glu259Asp	p.E259D	ENST00000285398	NM_000122.1	259	gaA/gaT	6/15	1	2	FACETS	0.884	0.833	0.937	0.884	0.833	0.937	CLONAL	1	TRUE	1	0.545836657352623	2		544	1289	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929285	32929285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1364927725	NA	P-0008429-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1319	950	956	1	ENST00000380152.3:c.7295G>A	p.Arg2432Lys	p.R2432K	ENST00000380152		2432	aGa/aAa	14/27	0.473588404048466	3	FACETS	0.976	0.948	1	0.976	0.948	1	CLONAL	2	TRUE	1	0.545836657352623	3		957	2269	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858728	9858728	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008429-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	197	503	0	ENST00000330684.3:c.2673G>T	p.Gln891His	p.Q891H	ENST00000330684	NM_001134407.1	891	caG/caT	13/13	1	2	FACETS	0.734	0.679	0.79	0.734	0.679	0.79	SUBCLONAL	1	TRUE	1	0.545836657352623	2		503	984	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222852	5222852	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776974729	NA	P-0008429-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	138	313	0	ENST00000357368.4:c.2951C>T	p.Pro984Leu	p.P984L	ENST00000357368	NM_002850.3	984	cCg/cTg	18/38	1	2	FACETS	0.879	0.804	0.958	0.879	0.804	0.958	CLONAL	1	TRUE	1	0.545836657352623	2		313	575	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0008478-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	339	385	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.265759292841207	4	FACETS	1	0.951	1	1	0.951	1	CLONAL	4	FALSE	0	0.264902346424061	4		385	809	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846065	68846065	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008478-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	115	560	0	ENST00000261769.5:c.1036C>T	p.Gln346Ter	p.Q346*	ENST00000261769	NM_004360.3	346	Caa/Taa	8/16	0.265759292841207	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	0	0.264902346424061	1		560	565	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443345	187443347	+	inframe_deletion	In_Frame_Del	DEL	CGA	CGA	-	novel	NA	P-0008478-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	234	409	0	ENST00000232014.4:c.1779_1781del	p.Arg594del	p.R594del	ENST00000232014	NM_001130845.1	593	acTCGa/aca	8/10	0.265759292841207	4	FACETS	1	0.982	1	0.839	0.787	0.892	CLONAL	3	FALSE	0	0.264902346424061	4		409	666	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231437	46231437	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	213	647	1	ENST00000334344.6:c.1277C>T	p.Thr426Met	p.T426M	ENST00000334344	NM_152641.2	426	aCg/aTg	10/21	0.257497902535892	4	FACETS	0.818	0.76	0.879	0.818	0.76	0.879	CLONAL	2	TRUE	2	0.314484417419088	4		648	1088	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0008524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2202	718	643	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	0.314484417419088	19	FACETS	0.957	0.921	0.995			1	CLONAL	6	TRUE	NA	0.314484417419088	19		643	2920	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	194	483	0	ENST00000335508.6:c.1874G>T	p.Arg625Leu	p.R625L	ENST00000335508	NM_012433.2	625	cGt/cTt	14/25	0.314484417419088	4	FACETS	0.925	0.856	0.995	0.925	0.856	0.995	CLONAL	2	TRUE	2	0.314484417419088	4		483	877	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517403	176517403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	50	352	0	ENST00000292408.4:c.104C>T	p.Ala35Val	p.A35V	ENST00000292408	NM_213647.1	35	gCt/gTt	3/18	0.185816694679795	4	FACETS	1	0.938	1	0.601	0.512	0.697	INDETERMINATE	1	TRUE	2	0.314484417419088	4		352	348	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239843	98239843	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1398130707	NA	P-0008524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	229	678	0	ENST00000331920.6:c.1489G>A	p.Ala497Thr	p.A497T	ENST00000331920	NM_000264.3	497	Gct/Act	10/24	0.128951505571405	4	FACETS	0.994	0.927	1	0.994	0.927	1	INDETERMINATE	2	TRUE	2	0.314484417419088	4		678	963	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137524714	137524716	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs587776858	NA	P-0008524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	250	746	0	ENST00000367739.4:c.653_655del	p.Glu218del	p.E218del	ENST00000367739	NM_000416.2	218	gAAGga/gga	5/7	0.307900069072573	2	FACETS	0.857	0.802	0.912	0.857	0.802	0.912	CLONAL	2	TRUE	0	0.314484417419088	2		746	928	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0008553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	42	356	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.734	0.611	0.871	0.734	0.611	0.871	SUBCLONAL	1	TRUE	1	0.16	2		356	715	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0008553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	13	389	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	1	2	FACETS	0.374	0.266	0.508	0.374	0.266	0.508	SUBCLONAL	1	TRUE	1	0.16	2		389	434	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439563	51439563	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0008553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	38	483	0	ENST00000262662.1:c.130-2A>T		p.X44_splice	ENST00000262662		44			1	2	FACETS	0.772	0.637	0.924	0.772	0.637	0.924	CLONAL	1	TRUE	1	0.16	2		483	615	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321281	65321281	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	40	533	0	ENST00000342505.4:c.1559G>T	p.Gly520Val	p.G520V	ENST00000342505	NM_002227.2	520	gGa/gTa	11/25	1	2	FACETS	0.683	0.566	0.814	0.683	0.566	0.814	SUBCLONAL	1	TRUE	1	0.16	2		533	732	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281569	198281569	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	50	663	0	ENST00000335508.6:c.562G>T	p.Ala188Ser	p.A188S	ENST00000335508	NM_012433.2	188	Gca/Tca	6/25	1	2	FACETS	0.638	0.54	0.748	0.638	0.54	0.748	SUBCLONAL	1	TRUE	1	0.16	2		663	979	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281939	142281939	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	36	331	0	ENST00000350721.4:c.305G>A	p.Trp102Ter	p.W102*	ENST00000350721	NM_001184.3	102	tGg/tAg	4/47	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.16	2		331	393	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492945	8492945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759831182	NA	P-0008553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	67	562	0	ENST00000356435.5:c.2384C>T	p.Ser795Phe	p.S795F	ENST00000356435		795	tCc/tTc	16/35	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.16	2		562	817	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399281	139399281	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	64	539	0	ENST00000277541.6:c.4862G>T	p.Gly1621Val	p.G1621V	ENST00000277541	NM_017617.3	1621	gGc/gTc	26/34	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.16	2		539	756	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871131	12871131	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	24	263	2	ENST00000228872.4:c.361del	p.Ala121LeufsTer24	p.A121Lfs*24	ENST00000228872	NM_004064.3	120	Ggg/gg	1/3	1	2	FACETS	0.721	0.565	0.902	0.721	0.565	0.902	CLONAL	1	TRUE	1	0.16	2		265	416	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247045	53247045	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0008554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1214	385	703	0	ENST00000375401.3:c.455T>A	p.Leu152Ter	p.L152*	ENST00000375401	NM_004187.3	152	tTg/tAg	4/26	0.382569354333696	4	FACETS	0.814	0.771	0.857	0.814	0.771	0.857	CLONAL	2	TRUE	2	0.420249018417829	4		703	1599	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0008559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	116	423	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.979	0.89	1	0.979	0.89	1	CLONAL	1	TRUE	1	0.562710216325902	2		423	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	253	509	0	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	0.536580097204115	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.562710216325902	1		509	646	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519861	29519861	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	44	451	0	ENST00000389048.3:c.1710G>C	p.Glu570Asp	p.E570D	ENST00000389048	NM_004304.4	570	gaG/gaC	9/29	1	2	FACETS	0.226	0.189	0.268	0.226	0.189	0.268	SUBCLONAL	1	TRUE	1	0.562710216325902	2		451	691	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0008589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	463	210	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.36792368280183	6	FACETS	0.935	0.898	0.973	0.935	0.898	0.973	CLONAL	4	TRUE	2	0.521261221447878	6		210	970	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226566888	226566888	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	701	484	0	ENST00000366794.5:c.1700A>T	p.Asn567Ile	p.N567I	ENST00000366794	NM_001618.3	567	aAc/aTc	12/23	0.488764390354682	5	FACETS	0.978	0.944	1	0.978	0.944	1	CLONAL	3	TRUE	2	0.521261221447878	5		484	1634	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0008595-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	42	194	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.761	0.642	0.889	0.761	0.642	0.889	SUBCLONAL	1	TRUE	1	0.544022044431159	2		194	203	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092809	27092809	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008595-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	128	455	1	ENST00000324856.7:c.2830C>T	p.Gln944Ter	p.Q944*	ENST00000324856	NM_006015.4	944	Cag/Tag	9/20	1	2	FACETS	0.846	0.77	0.926	0.846	0.77	0.926	CLONAL	1	TRUE	1	0.544022044431159	2		456	556	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205055	128205055	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0008595-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	77	326	0	ENST00000341105.2:c.386C>G	p.Ser129Ter	p.S129*	ENST00000341105	NM_032638.4	129	tCa/tGa	3/6	1	2	FACETS	0.552	0.485	0.623	0.552	0.485	0.623	SUBCLONAL	1	TRUE	1	0.544022044431159	2		326	513	SUCCESS
ATR	545	MSKCC	GRCh37	3	142171996	142171996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008595-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	106	545	2	ENST00000350721.4:c.7735G>A	p.Glu2579Lys	p.E2579K	ENST00000350721	NM_001184.3	2579	Gaa/Aaa	46/47	1	2	FACETS	0.718	0.645	0.794	0.718	0.645	0.794	SUBCLONAL	1	TRUE	1	0.544022044431159	2		547	543	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189448	56189448	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008595-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	96	410	1	ENST00000399503.3:c.4480C>T	p.Gln1494Ter	p.Q1494*	ENST00000399503	NM_005921.1	1494	Cag/Tag	20/20	1	2	FACETS	0.83	0.744	0.921	0.83	0.744	0.921	CLONAL	1	TRUE	1	0.544022044431159	2		411	425	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163768	32163768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008595-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	73	284	0	ENST00000375023.3:c.5458G>A	p.Glu1820Lys	p.E1820K	ENST00000375023	NM_004557.3	1820	Gaa/Aaa	30/30	1	2	FACETS	0.604	0.53	0.684	0.604	0.53	0.684	SUBCLONAL	1	TRUE	1	0.544022044431159	2		284	444	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163848	32163848	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008595-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	50	177	0	ENST00000375023.3:c.5378G>C	p.Arg1793Pro	p.R1793P	ENST00000375023	NM_004557.3	1793	cGa/cCa	30/30	1	2	FACETS	0.615	0.525	0.712	0.615	0.525	0.712	SUBCLONAL	1	TRUE	1	0.544022044431159	2		177	299	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420075	420075	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008595-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	139	523	0	ENST00000399788.2:c.3192G>C	p.Lys1064Asn	p.K1064N	ENST00000399788	NM_001042603.1	1064	aaG/aaC	21/28	1	2	FACETS	0.702	0.64	0.767	0.702	0.64	0.767	SUBCLONAL	1	TRUE	1	0.544022044431159	2		523	728	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570416	95570416	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008595-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	42	215	0	ENST00000393063.1:c.3317C>G	p.Ser1106Cys	p.S1106C	ENST00000393063	NM_030621.3	1106	tCt/tGt	22/28	1	2	FACETS	0.553	0.465	0.651	0.553	0.465	0.651	SUBCLONAL	1	TRUE	1	0.544022044431159	2		215	279	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858783	9858783	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008595-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	54	252	0	ENST00000330684.3:c.2618G>C	p.Gly873Ala	p.G873A	ENST00000330684	NM_001134407.1	873	gGa/gCa	13/13	1	2	FACETS	0.717	0.617	0.824	0.717	0.617	0.824	SUBCLONAL	1	TRUE	1	0.544022044431159	2		252	277	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863554	68863554	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	G	rs113067020	NA	P-0008595-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	158	398	0	ENST00000261769.5:c.2296-3A>G		p.X766_splice	ENST00000261769	NM_004360.3	766			0.45384135686413	1	FACETS	0.952	0.881	1	0.952	0.881	1	CLONAL	1	TRUE	0	0.544022044431159	1		398	444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0008650-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	209	316	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.286570595465196	2	FACETS	0.934	0.869	1	0.934	0.869	1	CLONAL	2	TRUE	0	0.286570595465196	2		316	781	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028898	47028898	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0008650-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	164	131	0	ENST00000377604.3:c.201+1G>T		p.X67_splice	ENST00000377604	NM_001204468.1	67			0.286570595465196	2	FACETS	1	0.947	1			1	CLONAL	3	TRUE	NA	0.286570595465196	2		131	374	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974765	21974765	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1329324238	NA	P-0008650-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	60	195	0	ENST00000304494.5:c.62C>A	p.Ala21Asp	p.A21D	ENST00000304494	NM_000077.4	21	gCc/gAc	1/3	1	2	FACETS	0.775	0.668	0.892	0.775	0.668	0.892	SUBCLONAL	1	TRUE	1	0.286570595465196	2		195	540	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412039	116412045	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	AGAAGGT	AGAAGGT	-	novel	NA	P-0008650-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	72	223	0	ENST00000397752.3:c.3025_3028+3del		p.X1009_splice	ENST00000397752	NM_000245.2	1009		14/21	0.255086310566791	2	FACETS	1	0.975	1	0.743	0.654	0.838	CLONAL	1	TRUE	0	0.286570595465196	2		223	338	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911477	134911477	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1341771878	NA	P-0008678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	476	340	0	ENST00000398015.3:c.1942G>T	p.Val648Leu	p.V648L	ENST00000398015	NM_004441.4	648	Gtg/Ttg	11/16	0.797720565440739	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.797720565440739	3		340	833	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707743	176707743	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	701	561	0	ENST00000439151.2:c.5800C>G	p.Gln1934Glu	p.Q1934E	ENST00000439151	NM_022455.4	1934	Cag/Gag	18/23	0.796244660242522	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.797720565440739	3		561	1226	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	401	282	0	ENST00000397752.3:c.3028G>C	p.Asp1010His	p.D1010H	ENST00000397752	NM_000245.2	1010	Gat/Cat	14/21	0.797720565440739	3	FACETS	0.971	0.946	0.994	0.971	0.946	0.994	CLONAL	3	TRUE	0	0.797720565440739	3		282	483	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544756	65544756	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0008678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	396	321	0	ENST00000358664.4:c.172-2A>T		p.X58_splice	ENST00000358664	NM_002382.4	58			0.790409493229109	2	FACETS	0.979	0.951	1	0.979	0.951	1	CLONAL	2	TRUE	0	0.797720565440739	2		321	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0008678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	586	454	0	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	0.778478915564758	2	FACETS	0.936	0.912	0.959	0.936	0.912	0.959	CLONAL	2	TRUE	0	0.797720565440739	2		454	785	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216586	2216586	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	200	528	0	ENST00000398665.3:c.2230G>T	p.Asp744Tyr	p.D744Y	ENST00000398665	NM_032482.2	744	Gac/Tac	20/28	0.778478915564758	2	FACETS	0.598	0.555	0.643	0.299	0.277	0.322	SUBCLONAL	1	TRUE	0	0.797720565440739	2		528	838	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045157	47045157	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	843	600	1	ENST00000377604.3:c.2398G>T	p.Glu800Ter	p.E800*	ENST00000377604	NM_001204468.1	800	Gag/Tag	21/24	0.797720565440739	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.797720565440739	3		601	1469	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305301	65305301	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	649	880	0	ENST00000342505.4:c.2827del	p.Ile943SerfsTer33	p.I943Sfs*33	ENST00000342505	NM_002227.2	943	Atc/tc	20/25	0.495399950406842	3	FACETS	0.779	0.752	0.806	0.779	0.752	0.806	SUBCLONAL	2	TRUE	1	0.797720565440739	3		880	1461	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0008679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	81	385	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	FALSE	1	0.799297324274977	2		385	180	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519938	NA	P-0008679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	42	402	0	ENST00000263967.3:c.1034A>T	p.Asn345Ile	p.N345I	ENST00000263967	NM_006218.2	345	aAt/aTt	5/21	1	2	FACETS	0.653	0.554	0.758	0.653	0.554	0.758	SUBCLONAL	1	FALSE	1	0.799297324274977	2		402	161	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061204	38061204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	77	220	0	ENST00000250448.2:c.785G>A	p.Arg262His	p.R262H	ENST00000250448	NM_004496.3	262	cGc/cAc	2/2	1	2	FACETS	0.529	0.468	0.595	0.529	0.468	0.595	SUBCLONAL	1	FALSE	1	0.799297324274977	2		220	364	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913315	NA	P-0008679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	15	608	1	ENST00000326873.7:c.580G>A	p.Asp194Asn	p.D194N	ENST00000326873	NM_000455.4	194	Gac/Aac	4/10	1	2	FACETS	0.069	0.05	0.093	0.069	0.05	0.093	SUBCLONAL	1	FALSE	1	0.799297324274977	2		609	542	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437431	121437431	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0008679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	72	260	0	ENST00000257555.6:c.1768+1G>A		p.X590_splice	ENST00000257555		590			1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	FALSE	1	0.799297324274977	2		260	170	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119234	3119234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775040372	NA	P-0008679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	12	775	2	ENST00000078429.4:c.766C>T	p.Arg256Trp	p.R256W	ENST00000078429	NM_002067.2	256	Cgg/Tgg	6/7	1	2	FACETS	0.053	0.037	0.074	0.053	0.037	0.074	SUBCLONAL	1	FALSE	1	0.799297324274977	2		777	563	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0008683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	12	318	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.459	0.322	0.628	0.459	0.322	0.628	SUBCLONAL	1	TRUE	1	0.21	2		318	249	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469669	NA	P-0008683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	87	345	0	ENST00000374080.3:c.130G>A	p.Gly44Ser	p.G44S	ENST00000374080		44	Ggt/Agt	2/45	1	2	FACETS	0.798	0.705	0.899	0.798	0.705	0.899	SUBCLONAL	1	TRUE	1	0.21	2		345	1038	SUCCESS
APC	324	MSKCC	GRCh37	5	112175240	112175240	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	60	296	0	ENST00000257430.4:c.3949G>T	p.Glu1317Ter	p.E1317*	ENST00000257430	NM_000038.5	1317	Gaa/Taa	16/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.21	2		296	428	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs770248150	NA	P-0008683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	65	526	0	ENST00000311936.3:c.351A>T	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaT	4/5	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.21	2		526	496	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993730	90993730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778998026	NA	P-0008686-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	129	283	0	ENST00000265433.3:c.193G>A	p.Val65Ile	p.V65I	ENST00000265433	NM_002485.4	65	Gta/Ata	3/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.728247982645635	2		283	329	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0008724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	255	559	1	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.804	0.753	0.856	0.804	0.753	0.856	CLONAL	1	TRUE	1	0.627723829697169	2		560	1011	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023904	27023904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1232964733	NA	P-0008724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	88	132	0	ENST00000324856.7:c.1015del	p.Ala339LeufsTer24	p.A339Lfs*24	ENST00000324856	NM_006015.4	337	tGg/tg	1/20	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.627723829697169	2		132	272	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0008724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	699	379	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.323448108733954	3	FACETS	0.963	0.938	0.987			1	INDETERMINATE	3	TRUE	NA	0.627723829697169	3		379	1013	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521615	89521615	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	110	301	0	ENST00000336596.2:c.2692C>T	p.Pro898Ser	p.P898S	ENST00000336596	NM_005233.5	898	Cca/Tca	16/17	0.604316960286858	2	FACETS	0.733	0.662	0.808	0.367	0.331	0.404	SUBCLONAL	1	TRUE	0	0.627723829697169	2		301	478	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532540	187532540	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	147	442	0	ENST00000441802.2:c.9853G>C	p.Gly3285Arg	p.G3285R	ENST00000441802	NM_005245.3	3285	Ggg/Cgg	14/27	1	2	FACETS	0.915	0.841	0.991	0.915	0.841	0.991	CLONAL	1	TRUE	1	0.627723829697169	2		442	512	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279865	46279865	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1460	216	474	0	ENST00000371998.3:c.3791A>C	p.Gln1264Pro	p.Q1264P	ENST00000371998		1264	cAa/cCa	20/23	0.627723829697169	4	FACETS	0.668	0.619	0.72	0.334	0.309	0.36	SUBCLONAL	1	TRUE	2	0.627723829697169	4		474	1676	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0008748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	169	529	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.249858178503348	4	FACETS	1	0.971	1	0.743	0.684	0.804	CLONAL	2	TRUE	1	0.234647341114718	4		529	798	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786201059	NA	P-0008748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	260	721	0	ENST00000269305.4:c.856G>C	p.Glu286Gln	p.E286Q	ENST00000269305	NM_001126112.2	286	Gaa/Caa	8/11	0.202593602803342	2	FACETS	0.926	0.866	0.987	0.926	0.866	0.987	CLONAL	2	TRUE	0	0.234647341114718	2		721	1197	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112555	2112555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	153	761	1	ENST00000219476.3:c.1315G>A	p.Asp439Asn	p.D439N	ENST00000219476	NM_000548.3	439	Gac/Aac	13/42	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.234647341114718	2		762	1297	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322752	30322752	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	85	551	0	ENST00000322652.5:c.1765C>T	p.Pro589Ser	p.P589S	ENST00000322652	NM_015355.2	589	Cct/Tct	14/16	0.187245262028595	3	FACETS	0.953	0.842	1	0.318	0.28	0.358	CLONAL	1	TRUE	0	0.234647341114718	3		551	849	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0008754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	51	221	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.809	0.685	0.946	0.809	0.685	0.946	CLONAL	1	TRUE	1	0.12	2		222	1051	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0008754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	74	569	1	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.12	2		570	1187	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272143	38272143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257312391	NA	P-0008754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	42	387	0	ENST00000425967.3:c.2075G>A	p.Arg692Gln	p.R692Q	ENST00000425967	NM_001174067.1	692	cGa/cAa	16/19	1	2	FACETS	0.882	0.734	1	0.882	0.734	1	CLONAL	1	TRUE	1	0.12	2		387	794	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409101	4409101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1487732338	NA	P-0008754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	67	469	0	ENST00000261254.3:c.796C>T	p.Arg266Cys	p.R266C	ENST00000261254	NM_001759.3	266	Cgt/Tgt	5/5	0.3	2	FACETS	0.999	0.865	1			1	CLONAL	1	TRUE	NA	0.12	2		469	1118	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795794	42795794	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	65	511	0	ENST00000575354.2:c.2786del	p.Pro929LeufsTer17	p.P929Lfs*17	ENST00000575354	NM_015125.3	928	gCc/gc	11/20	1	2	FACETS	0.865	0.747	0.994	0.865	0.747	0.994	CLONAL	1	TRUE	1	0.12	2		511	1252	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259013	16259013	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	221	496	0	ENST00000375759.3:c.6278T>C	p.Leu2093Pro	p.L2093P	ENST00000375759	NM_015001.2	2093	cTg/cCg	11/15	0.222215762779724	3	FACETS	1	0.988	1	0.634	0.591	0.679	INDETERMINATE	1	TRUE	1	0.515484195867513	3		496	850	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218910	193218910	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	91	378	0	ENST00000367435.3:c.1468C>G	p.Gln490Glu	p.Q490E	ENST00000367435	NM_024529.4	490	Cag/Gag	16/17	0.438629725593998	4	FACETS	0.901	0.801	1	0.3	0.267	0.336	CLONAL	1	TRUE	1	0.515484195867513	4		378	594	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149304	61149304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	126	370	0	ENST00000295025.8:c.1494G>A	p.Met498Ile	p.M498I	ENST00000295025	NM_002908.2	498	atG/atA	11/11	0.497414732817456	3	FACETS	0.906	0.821	0.994	0.453	0.41	0.497	CLONAL	1	TRUE	1	0.515484195867513	3		370	679	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540679	187540679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746997376	NA	P-0008763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	242	555	0	ENST00000441802.2:c.7061G>A	p.Arg2354Gln	p.R2354Q	ENST00000441802	NM_005245.3	2354	cGg/cAg	10/27	0.497414732817456	3	FACETS	0.979	0.914	1	0.49	0.457	0.524	CLONAL	1	TRUE	1	0.515484195867513	3		555	1206	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506247	148506247	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	295	408	0	ENST00000320356.2:c.2111T>G	p.Val704Gly	p.V704G	ENST00000320356	NM_004456.4	704	gTt/gGt	19/20	0.427642314527851	4	FACETS	0.927	0.874	0.98	0.927	0.874	0.98	CLONAL	2	TRUE	2	0.515484195867513	4		408	936	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680760	88680760	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	1534	387	0	ENST00000360948.2:c.497G>T	p.Cys166Phe	p.C166F	ENST00000360948	NM_001012338.2	166	tGt/tTt	6/19	0.515484195867513	10	FACETS	1	0.996	1			1	CLONAL	8	TRUE	NA	0.515484195867513	10		387	2182	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0008763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	488	476	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.476282591798784	2	FACETS	0.99	0.953	1	0.99	0.953	1	CLONAL	2	TRUE	0	0.515484195867513	2		476	956	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602323	10602323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	389	440	0	ENST00000171111.5:c.1255G>T	p.Gly419Trp	p.G419W	ENST00000171111	NM_203500.1	419	Ggg/Tgg	3/6	0.278440583057442	4	FACETS	1	0.984	1	1	0.984	1	INDETERMINATE	2	TRUE	2	0.515484195867513	4		440	1068	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105618	11105618	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	250	359	1	ENST00000358026.2:c.1534G>T	p.Glu512Ter	p.E512*	ENST00000358026	NM_001128849.1	512	Gag/Tag	9/36	0.278440583057442	4	FACETS	0.791	0.741	0.843	0.791	0.741	0.843	INDETERMINATE	2	TRUE	2	0.515484195867513	4		360	929	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480471	57480472	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0008763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	181	216	0	ENST00000371085.3:c.466_467delinsAT	p.Asp156Ile	p.D156I	ENST00000371085	NM_000516.4	156	GAt/ATt	6/13	0.427642314527851	4	FACETS	0.861	0.798	0.926	0.861	0.798	0.926	CLONAL	2	TRUE	2	0.515484195867513	4		216	618	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755560	39755560	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	164	459	0	ENST00000288319.7:c.1205A>G	p.His402Arg	p.H402R	ENST00000288319	NM_182918.3	402	cAc/cGc	10/10	0.497414732817456	3	FACETS	0.859	0.788	0.932	0.429	0.394	0.466	CLONAL	1	TRUE	1	0.515484195867513	3		459	932	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524486	44524486	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	122	307	0	ENST00000291552.4:c.71T>C	p.Ile24Thr	p.I24T	ENST00000291552	NM_006758.2	24	aTt/aCt	2/8	0.497414732817456	3	FACETS	0.903	0.818	0.993	0.452	0.409	0.497	CLONAL	1	TRUE	1	0.515484195867513	3		307	659	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145749	11145752	+	frameshift_variant	Frame_Shift_Del	DEL	TCCC	TCCC	GA	novel	NA	P-0008763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	326	514	0	ENST00000358026.2:c.4111_4114delinsGA	p.Ser1371GlufsTer28	p.S1371Efs*28	ENST00000358026	NM_001128849.1	1371	TCCCgc/GAgc	29/36	0.278440583057442	4	FACETS	0.918	0.868	0.969	0.918	0.868	0.969	INDETERMINATE	2	TRUE	2	0.515484195867513	4		514	1044	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207019	1207023	+	frameshift_variant	Frame_Shift_Del	DEL	ACCAG	ACCAG	-	novel	NA	P-0008763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	307	313	0	ENST00000326873.7:c.107_111del	p.Tyr36SerfsTer125	p.Y36Sfs*125	ENST00000326873	NM_000455.4	36	tACCAG/t	1/10	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.515484195867513	NA		313	596	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0008788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	75	381	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.238822156827161	5	FACETS	0.993	0.869	1	0.497	0.434	0.564	CLONAL	1	TRUE	3	0.238822156827161	5		381	859	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954198	48954198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123331	NA	P-0008788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	346	363	0	ENST00000267163.4:c.1399C>T	p.Arg467Ter	p.R467*	ENST00000267163	NM_000321.2	467	Cga/Tga	15/27	0.238822156827161	5	FACETS	1	0.989	1	0.698	0.661	0.735	CLONAL	3	TRUE	0	0.238822156827161	5		363	1128	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577524	7577524	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	56	335	0	ENST00000269305.4:c.757A>C	p.Thr253Pro	p.T253P	ENST00000269305	NM_001126112.2	253	Acc/Ccc	7/11	0.238822156827161	1	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	0	0.238822156827161	1		335	411	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40738973	40738973	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	37	290	0	ENST00000373198.4:c.3311G>T	p.Ser1104Ile	p.S1104I	ENST00000373198	NM_133170.3	1104	aGt/aTt	24/32	0.238822156827161	5	FACETS	0.746	0.614	0.894	0.249	0.204	0.298	SUBCLONAL	1	TRUE	2	0.238822156827161	5		290	564	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482552	56482552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	138	381	0	ENST00000267101.3:c.1009G>A	p.Gly337Arg	p.G337R	ENST00000267101	NM_001982.3	337	Ggg/Agg	9/28	0.238822156827161	5	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	3	0.238822156827161	5		381	729	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830652	72830652	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	142	940	0	ENST00000268489.5:c.5929G>C	p.Gly1977Arg	p.G1977R	ENST00000268489	NM_006885.3	1977	Gga/Cga	9/10	0.238822156827161	2	FACETS	0.977	0.888	1	0.489	0.444	0.536	CLONAL	1	TRUE	0	0.238822156827161	2		940	1217	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214696	5214696	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369756620	NA	P-0008788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	43	387	0	ENST00000357368.4:c.4370G>A	p.Cys1457Tyr	p.C1457Y	ENST00000357368	NM_002850.3	1457	tGt/tAt	29/38	0.238822156827161	1	FACETS	0.638	0.534	0.754	0.638	0.534	0.754	SUBCLONAL	1	TRUE	0	0.238822156827161	1		387	497	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087932	27087933	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0008788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	154	396	0	ENST00000324856.7:c.2219_2220del	p.Ser740TyrfsTer76	p.S740Yfs*76	ENST00000324856	NM_006015.4	740	tCC/t	6/20	0.238822156827161	5	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	3	0.238822156827161	5		396	824	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0008792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	67	318	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.533630563494653	5	FACETS	0.759	0.659	0.866	0.253	0.219	0.289	SUBCLONAL	1	TRUE	2	0.533630563494653	5		318	596	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0008792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	432	430	1	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.111874345296161	5	FACETS	1	0.992	1			1	INDETERMINATE	4	TRUE	NA	0.533630563494653	5		431	665	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782006	NA	P-0008792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	65	665	1	ENST00000269305.4:c.859G>A	p.Glu287Lys	p.E287K	ENST00000269305	NM_001126112.2	287	Gag/Aag	8/11	0.111874345296161	5	FACETS	0.451	0.39	0.518			1	INDETERMINATE	1	TRUE	NA	0.533630563494653	5		666	972	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022297	31022297	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	420	749	0	ENST00000375687.4:c.1786del	p.Arg596GlyfsTer107	p.R596Gfs*107	ENST00000375687	NM_015338.5	594	tgC/tg	13/13	0.533630563494653	3	FACETS	0.962	0.919	1	0.962	0.919	1	CLONAL	2	TRUE	1	0.533630563494653	3		749	1036	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643707	52643707	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs764372541	NA	P-0008792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	122	396	0	ENST00000394830.3:c.2189T>C	p.Met730Thr	p.M730T	ENST00000394830	NM_018313.4	730	aTg/aCg	17/30	0.533630563494653	2	FACETS	1	0.976	1	0.597	0.545	0.651	CLONAL	1	TRUE	0	0.533630563494653	2		396	383	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196871	106196871	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	265	559	0	ENST00000380013.4:c.5204G>A	p.Gly1735Glu	p.G1735E	ENST00000380013	NM_001127208.2	1735	gGa/gAa	11/11	0.501106467941938	4	FACETS	0.932	0.877	0.989	0.932	0.877	0.989	CLONAL	2	TRUE	2	0.533630563494653	4		559	817	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915715	131915715	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	342	572	0	ENST00000265335.6:c.713A>T	p.Lys238Met	p.K238M	ENST00000265335		238	aAg/aTg	5/25	0.533630563494653	3	FACETS	0.942	0.895	0.989	0.942	0.895	0.989	CLONAL	2	TRUE	1	0.533630563494653	3		572	862	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737084	145737084	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	259	549	0	ENST00000428558.2:c.3482C>G	p.Ala1161Gly	p.A1161G	ENST00000428558	NM_004260.3	1161	gCc/gGc	21/22	0.533630563494653	6	FACETS	0.994	0.932	1	0.497	0.466	0.529	CLONAL	2	TRUE	2	0.533630563494653	6		549	1009	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484375	8484375	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	77	365	1	ENST00000356435.5:c.3157C>G	p.Leu1053Val	p.L1053V	ENST00000356435		1053	Ctt/Gtt	19/35	0.533630563494653	5	FACETS	0.623	0.546	0.706	0.125	0.109	0.142	SUBCLONAL	1	TRUE	0	0.533630563494653	5		366	834	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519909	66519909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	357	484	1	ENST00000358598.2:c.392C>T	p.Ala131Val	p.A131V	ENST00000358598	NM_212471.2	131	gCc/gTc	4/11	0.26199035655979	5	FACETS	1	0.991	1	0.8	0.76	0.841	INDETERMINATE	2	TRUE	2	0.533630563494653	5		485	1004	SUCCESS
AR	367	MSKCC	GRCh37	X	66943665	66943665	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	242	442	0	ENST00000374690.3:c.2745C>G	p.Ile915Met	p.I915M	ENST00000374690	NM_000044.3	915	atC/atG	8/8	0.462489317615792	2	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.533630563494653	2		442	777	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175757	24175757	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0008797-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	168	693	0	ENST00000263121.7:c.987-2A>T		p.X329_splice	ENST00000263121	NM_003073.3	329			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		693	779	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054254	30054254	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1555994854	NA	P-0008797-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	290	906	1	ENST00000338641.4:c.675+1G>A		p.X225_splice	ENST00000338641	NM_000268.3	225			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		907	1152	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349903	89349926	+	inframe_deletion	In_Frame_Del	DEL	TCGGGGCCATCCTTCTTCTCCTTC	TCGGGGCCATCCTTCTTCTCCTTC	-	novel	NA	P-0008798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1990	241	1123	0	ENST00000301030.4:c.3024_3047del	p.Glu1008_Pro1015del	p.E1008_P1015del	ENST00000301030	NM_001256183.1	1008	gaGAAGGAGAAGAAGGATGGCCCCGAt/gat	9/13	1	2	FACETS	0.8	0.744	0.859	0.8	0.744	0.859	SUBCLONAL	1	TRUE	1	0.27	2		1123	2231	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076967	41076967	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008814-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	18	420	0	ENST00000373198.4:c.1453C>A	p.Pro485Thr	p.P485T	ENST00000373198	NM_133170.3	485	Cca/Aca	9/32	0.265280284341447	3	FACETS	0.329	0.248	0.424	0.11	0.082	0.142	INDETERMINATE	1	TRUE	0	0.647444580316049	3		420	224	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30061040	30061040	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008814-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	78	471	0	ENST00000338641.4:c.872G>C	p.Arg291Pro	p.R291P	ENST00000338641	NM_000268.3	291	cGt/cCt	9/16	0.621525918856112	2	FACETS	0.811	0.72	0.907	0.406	0.36	0.454	CLONAL	1	TRUE	0	0.647444580316049	2		471	297	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760887	133760888	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0008814-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	32	689	0	ENST00000318560.5:c.3212_3213del	p.Val1071GlyfsTer22	p.V1071Gfs*22	ENST00000318560	NM_005157.4	1070	taTGtg/tatg	11/11	0.609184121804212	3	FACETS	0.269	0.218	0.327	0.09	0.072	0.109	SUBCLONAL	1	TRUE	0	0.647444580316049	3		689	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0008835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	27	431	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.842	0.668	1	0.842	0.668	1	CLONAL	1	TRUE	1	0.11	2		433	583	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639857	93639857	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	27	359	0	ENST00000375746.1:c.1186G>T	p.Val396Leu	p.V396L	ENST00000375746	NM_001174167.1	396	Gtg/Ttg	10/14	1	2	FACETS	0.984	0.781	1	0.984	0.781	1	CLONAL	1	TRUE	1	0.11	2		359	499	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870264	44870264	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	18	327	1	ENST00000377967.4:c.443G>T	p.Trp148Leu	p.W148L	ENST00000377967	NM_021140.2	148	tGg/tTg	5/29	1	1	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	0	0.11	1		328	259	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197864	123197864	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	15	275	0	ENST00000218089.9:c.1988A>G	p.Asp663Gly	p.D663G	ENST00000218089	NM_001042749.1	663	gAt/gGt	20/35	1	1	FACETS	1	0.774	1	1	0.774	1	CLONAL	1	TRUE	0	0.11	1		275	242	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922789	44922790	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0008835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	26	252	0	ENST00000377967.4:c.1650_1651del	p.Pro551Ter	p.P551*	ENST00000377967	NM_021140.2	550	gtGCct/gtct	16/29	1	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	0	0.11	1		252	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0008839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	71	403	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.13	2		403	1042	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0008848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	376	239	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.103118136251775	5	FACETS	0.855	0.816	0.894			1	INDETERMINATE	3	TRUE	NA	0.749115254187636	5		240	831	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120612013	120612014	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0008848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	10	40	2	ENST00000256646.2:c.7_8delinsTT	p.Ala3Phe	p.A3F	ENST00000256646	NM_024408.3	3	GCc/TTc	1/34	1	2	FACETS	0.234	0.159	0.327	0.234	0.159	0.327	SUBCLONAL	1	TRUE	1	0.749115254187636	2		42	114	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253911	NA	P-0008848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	261	193	1	ENST00000269305.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000269305	NM_001126112.2	180	Gag/Aag	5/11	0.726069741197595	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.749115254187636	1		194	434	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584491	52584491	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	439	393	0	ENST00000394830.3:c.4522G>C	p.Glu1508Gln	p.E1508Q	ENST00000394830	NM_018313.4	1508	Gaa/Caa	29/30	1	2	FACETS	0.935	0.893	0.979	0.935	0.893	0.979	CLONAL	1	TRUE	1	0.749115254187636	2		393	1253	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204938	128204938	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	1022	466	0	ENST00000341105.2:c.503C>A	p.Ser168Tyr	p.S168Y	ENST00000341105	NM_032638.4	168	tCc/tAc	3/6	0.600762461327397	5	FACETS	1	0.995	1			1	CLONAL	3	TRUE	NA	0.749115254187636	5		466	1803	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900045	151900045	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	501	408	0	ENST00000262189.6:c.4066G>C	p.Glu1356Gln	p.E1356Q	ENST00000262189	NM_170606.2	1356	Gaa/Caa	26/59	0.739878778960627	3	FACETS	0.917	0.883	0.952			1	CLONAL	2	TRUE	NA	0.749115254187636	3		408	1002	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0008861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	1168	570	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.982736217082479	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.982736217082479	1		570	1187	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0008878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	111	520	1	ENST00000269305.4:c.994-1G>T		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.168180752197911	1	FACETS	0.769	0.691	0.852	0.769	0.691	0.852	INDETERMINATE	1	TRUE	0	0.3	1		521	818	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0008878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	309	381	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.3	3	FACETS	1	0.987	1	0.762	0.719	0.806	CLONAL	2	TRUE	0	0.3	3		381	1036	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999088	100999088	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	233	565	0	ENST00000325455.5:c.714G>C	p.Lys238Asn	p.K238N	ENST00000325455	NM_001202474.3	238	aaG/aaC	1/8	0.284130596860317	4	FACETS	0.759	0.706	0.814	0.759	0.706	0.814	SUBCLONAL	2	TRUE	2	0.3	4		565	1330	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576091	29576091	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	163	687	0	ENST00000356175.3:c.4064C>A	p.Ser1355Ter	p.S1355*	ENST00000356175	NM_000267.3	1355	tCa/tAa	30/57	1	2	FACETS	0.793	0.726	0.864	0.793	0.726	0.864	SUBCLONAL	1	TRUE	1	0.3	2		687	1370	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4123808	4123808	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1325938060	NA	P-0008878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	64	482	1	ENST00000262948.5:c.65C>T	p.Pro22Leu	p.P22L	ENST00000262948	NM_030662.3	22	cCa/cTa	1/11	1	2	FACETS	0.568	0.491	0.652	0.568	0.491	0.652	SUBCLONAL	1	TRUE	1	0.3	2		483	751	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308405	30308405	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	108	571	0	ENST00000262643.3:c.419T>G	p.Leu140Arg	p.L140R	ENST00000262643	NM_001238.2	140	cTg/cGg	6/12	1	2	FACETS	0.62	0.555	0.69	0.62	0.555	0.69	SUBCLONAL	1	TRUE	1	0.3	2		571	1161	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0008922-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	302	221	1	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		222	1016	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0008922-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	37	495	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		495	1024	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207021	1207021	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913324	NA	P-0008922-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	105	186	0	ENST00000326873.7:c.109C>T	p.Gln37Ter	p.Q37*	ENST00000326873	NM_000455.4	37	Cag/Tag	1/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		186	441	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610359	10610359	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008922-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	176	198	0	ENST00000171111.5:c.351G>T	p.Glu117Asp	p.E117D	ENST00000171111	NM_203500.1	117	gaG/gaT	2/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		198	644	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980354	55980354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008922-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	140	267	0	ENST00000263923.4:c.737G>A	p.Cys246Tyr	p.C246Y	ENST00000263923	NM_002253.2	246	tGt/tAt	6/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		267	1101	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672658	30672658	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008922-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	191	335	0	ENST00000376406.3:c.4302G>T	p.Arg1434Ser	p.R1434S	ENST00000376406	NM_014641.2	1434	agG/agT	10/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		335	974	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81399248	81399248	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008922-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	139	193	2	ENST00000222390.5:c.40C>A	p.His14Asn	p.H14N	ENST00000222390	NM_000601.4	14	Cat/Aat	1/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		195	817	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554329	63554329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008922-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	221	324	1	ENST00000307078.5:c.410G>A	p.Arg137Lys	p.R137K	ENST00000307078	NM_004655.3	137	aGg/aAg	2/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		325	1332	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0008944-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	208	488	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.271288671251193	3	FACETS	0.846	0.786	0.907	0.846	0.786	0.907	CLONAL	2	TRUE	1	0.338744321020865	3		488	849	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0008944-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	185	448	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.29032697948722	2	FACETS	0.863	0.8	0.927	0.863	0.8	0.927	CLONAL	2	TRUE	0	0.338744321020865	2		448	633	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72866458	72866458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1195327191	NA	P-0008944-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	40	514	1	ENST00000325599.8:c.805C>T	p.Arg269Cys	p.R269C	ENST00000325599	NM_018130.2	269	Cgt/Tgt	7/11	0.29032697948722	2	FACETS	0.33	0.273	0.394	0.165	0.136	0.197	SUBCLONAL	1	TRUE	0	0.338744321020865	2		515	715	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467403	66467403	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008944-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	151	312	0	ENST00000273854.3:c.866G>T	p.Cys289Phe	p.C289F	ENST00000273854	NM_004439.5	289	tGc/tTc	3/18	0.29032697948722	2	FACETS	0.986	0.91	1	0.986	0.91	1	CLONAL	2	TRUE	0	0.338744321020865	2		312	452	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753381	57753381	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008944-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	75	438	0	ENST00000274289.3:c.743C>T	p.Ser248Phe	p.S248F	ENST00000274289	NM_006622.3	248	tCt/tTt	6/14	0.335391471900734	1	FACETS	0.634	0.556	0.718	0.634	0.556	0.718	SUBCLONAL	1	TRUE	0	0.338744321020865	1		438	580	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417827	32417827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008944-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	75	425	1	ENST00000332351.3:c.1225C>A	p.Gln409Lys	p.Q409K	ENST00000332351	NM_024426.4	409	Cag/Aag	7/10	1	2	FACETS	0.624	0.546	0.707	0.624	0.546	0.707	SUBCLONAL	1	TRUE	1	0.338744321020865	2		426	710	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588157	69588157	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008944-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	266	753	0	ENST00000168712.1:c.541C>G	p.Leu181Val	p.L181V	ENST00000168712	NM_002007.2	181	Ctg/Gtg	3/3	1	2	FACETS	0.768	0.72	0.816	1	0.993	1	SUBCLONAL	2	TRUE	1	0.338744321020865	2		753	1023	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885148	111885148	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1042844452	NA	P-0008944-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	277	696	0	ENST00000341259.2:c.1036G>A	p.Gly346Arg	p.G346R	ENST00000341259	NM_005475.2	346	Ggg/Agg	6/8	0.314747700947743	2	FACETS	0.864	0.813	0.917	0.864	0.813	0.917	CLONAL	2	TRUE	0	0.338744321020865	2		696	946	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104319	2104319	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008944-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	148	546	0	ENST00000219476.3:c.359G>T	p.Arg120Ile	p.R120I	ENST00000219476	NM_000548.3	120	aGa/aTa	5/42	0.228832414783352	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.338744321020865	1		546	719	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600324	10600324	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008944-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	120	483	2	ENST00000171111.5:c.1531G>T	p.Gly511Cys	p.G511C	ENST00000171111	NM_203500.1	511	Ggc/Tgc	4/6	0.338744321020865	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.338744321020865	1		485	568	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035154	30035154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008944-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	226	615	0	ENST00000338641.4:c.316G>A	p.Glu106Lys	p.E106K	ENST00000338641	NM_000268.3	106	Gaa/Aaa	3/16	0.29032697948722	2	FACETS	0.794	0.741	0.849	0.794	0.741	0.849	SUBCLONAL	2	TRUE	0	0.338744321020865	2		615	840	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467825	66467825	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008959-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	115	519	1	ENST00000273854.3:c.444G>T	p.Lys148Asn	p.K148N	ENST00000273854	NM_004439.5	148	aaG/aaT	3/18	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.718229080260167	2		520	272	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0008967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	75	221	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.3	3	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	3		222	1007	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0008967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	38	625	2	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		627	828	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866376	42866376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777667088	NA	P-0008967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	46	354	0	ENST00000398585.3:c.256G>A	p.Val86Met	p.V86M	ENST00000398585	NM_001135099.1	86	Gtg/Atg	3/14	0.134253460742922	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		354	535	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740730	145740730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767811680	NA	P-0008967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	27	336	1	ENST00000428558.2:c.1370G>A	p.Gly457Glu	p.G457E	ENST00000428558	NM_004260.3	457	gGg/gAg	7/22	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		337	447	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	21	458	0	ENST00000358026.2:c.2729C>G	p.Thr910Arg	p.T910R	ENST00000358026	NM_001128849.1	910	aCg/aGg	19/36	0.3	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		458	412	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0008969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	84	370	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.541961517543158	8	FACETS	0.969	0.867	1			1	CLONAL	3	TRUE	NA	0.541961517543158	8		370	280	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964869	55964869	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	21	347	0	ENST00000263923.4:c.2368A>C	p.Lys790Gln	p.K790Q	ENST00000263923	NM_002253.2	790	Aag/Cag	16/30	0.139827153459854	3	FACETS	0.752	0.586	0.94	0.251	0.195	0.314	INDETERMINATE	1	TRUE	0	0.541961517543158	3		347	131	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740626	58740626	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0008969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	38	709	0	ENST00000305921.3:c.1531A>T	p.Lys511Ter	p.K511*	ENST00000305921	NM_003620.3	511	Aaa/Taa	6/6	0.541961517543158	3	FACETS	0.829	0.691	0.979	0.414	0.345	0.49	CLONAL	1	TRUE	1	0.541961517543158	3		709	215	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626928	14626928	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	87	658	2	ENST00000254322.2:c.847G>T	p.Val283Phe	p.V283F	ENST00000254322	NM_006145.1	283	Gtc/Ttc	3/3	0.541961517543158	4	FACETS	0.81	0.718	0.909	0.405	0.359	0.455	CLONAL	1	TRUE	2	0.541961517543158	4		660	611	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268669	46268669	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	49	559	0	ENST00000371998.3:c.2954G>T	p.Arg985Met	p.R985M	ENST00000371998		985	aGg/aTg	16/23	0.541961517543158	3	FACETS	1	0.932	1	0.575	0.493	0.662	CLONAL	1	TRUE	1	0.541961517543158	3		559	200	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918553	44918553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	27	270	0	ENST00000377967.4:c.1036C>T	p.Gln346Ter	p.Q346*	ENST00000377967	NM_021140.2	346	Caa/Taa	12/29	0.450037570300318	2	FACETS	1	0.934	1			1	CLONAL	1	TRUE	NA	0.541961517543158	2		270	74	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014133	14014138	+	inframe_deletion	In_Frame_Del	DEL	CGGGCT	CGGGCT	-	novel	NA	P-0008969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	74	339	0	ENST00000311895.7:c.114_119del	p.Leu39_Gly40del	p.L39_G40del	ENST00000311895	NM_005236.2	37	cgCGGGCTc/cgc	1/11	0.541961517543158	3	FACETS	1	0.932	1	0.541	0.477	0.608	CLONAL	1	TRUE	1	0.541961517543158	3		339	321	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288958	33288959	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0008969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	42	215	0	ENST00000374542.5:c.593_594del	p.Tyr198CysfsTer19	p.Y198Cfs*19	ENST00000374542	NM_001141970.1	198	tAT/t	3/8	0.369985699990388	4	FACETS	0.833	0.699	0.979	0.416	0.349	0.49	CLONAL	1	TRUE	2	0.541961517543158	4		215	287	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555525857	NA	P-0008971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	157	441	0	ENST00000269305.4:c.596G>A	p.Gly199Glu	p.G199E	ENST00000269305	NM_001126112.2	199	gGa/gAa	6/11	0.699953912835869	1	FACETS	0.808	0.751	0.866	0.808	0.751	0.866	CLONAL	1	TRUE	0	0.699953912835869	1		441	361	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039669	47039669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	228	290	0	ENST00000377604.3:c.1121G>T	p.Gly374Val	p.G374V	ENST00000377604	NM_001204468.1	374	gGc/gTc	11/24	0.650932178734612	2	FACETS	0.847	0.817	0.875			1	CLONAL	3	TRUE	NA	0.64078249440153	2		290	280	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729101	66729101	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	41	462	0	ENST00000307102.5:c.309C>G	p.Ile103Met	p.I103M	ENST00000307102	NM_002755.3	103	atC/atG	3/11	0.636727575010865	2	FACETS	1	0.964	1	0.719	0.622	0.817	CLONAL	1	TRUE	0	0.64078249440153	2		462	89	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220707	1220707	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	632	419	0	ENST00000326873.7:c.725G>T	p.Gly242Val	p.G242V	ENST00000326873	NM_000455.4	242	gGg/gTg	5/10	0.64078249440153	7	FACETS	1	0.983	1	1	0.983	1	CLONAL	6	TRUE	1	0.64078249440153	7		419	847	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973802	131973802	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	29	363	2	ENST00000265335.6:c.3505G>T	p.Ala1169Ser	p.A1169S	ENST00000265335		1169	Gcc/Tcc	23/25	0.620143116666126	5	FACETS	0.915	0.753	1			1	CLONAL	2	TRUE	NA	0.64078249440153	5		365	97	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538982	23538982	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs774732037	NA	P-0008976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	266	520	0	ENST00000380871.4:c.457G>C	p.Glu153Gln	p.E153Q	ENST00000380871	NM_006167.3	153	Gaa/Caa	2/2	0.622166924147651	3	FACETS	0.937	0.887	0.988	0.937	0.887	0.988	CLONAL	2	TRUE	1	0.64078249440153	3		520	585	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245080	53245080	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	111	351	0	ENST00000375401.3:c.860C>A	p.Ser287Ter	p.S287*	ENST00000375401	NM_004187.3	287	tCg/tAg	7/26	0.650932178734612	2	FACETS	0.855	0.812	0.894			1	CLONAL	3	TRUE	NA	0.64078249440153	2		351	135	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169476	11169483	+	frameshift_variant	Frame_Shift_Del	DEL	AACCACAA	AACCACAA	-	novel	NA	P-0008976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	199	520	0	ENST00000358026.2:c.4642_4649del	p.Asn1548ValfsTer30	p.N1548Vfs*30	ENST00000358026	NM_001128849.1	1548	AACCACAAg/g	33/36	0.64078249440153	7	FACETS	0.979	0.935	1	0.84	0.801	0.876	CLONAL	6	TRUE	0	0.64078249440153	7		520	275	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602922	10602923	+	missense_variant	Missense_Mutation	DNP	TC	TC	GA	novel	NA	P-0008976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	433	385	0	ENST00000171111.5:c.655_656inv	p.Glu219Ser	p.E219S	ENST00000171111	NM_203500.1	219	GAg/TCg	3/6	0.64078249440153	8	FACETS	1	0.975	1			1	CLONAL	7	TRUE	NA	0.64078249440153	8		385	562	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009018-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	80	260	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.19	2		260	690	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188197	10188197	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0009018-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	241	527	0	ENST00000256474.2:c.341-1G>T		p.X114_splice	ENST00000256474	NM_000551.3	114			1	2	FACETS	1	0.98	1	1	0.995	1	CLONAL	2	TRUE	1	0.19	2		527	1126	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436305	52436305	+	stop_lost	Nonstop_Mutation	SNP	C	C	A	novel	NA	P-0009018-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	171	573	0	ENST00000460680.1:c.2189G>T	p.Ter730LeuextTer205	p.*730Lext*205	ENST00000460680	NM_004656.3	730	tGa/tTa	17/17	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.19	2		573	1349	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972101	55972101	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009018-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	87	481	0	ENST00000263923.4:c.1543A>G	p.Ser515Gly	p.S515G	ENST00000263923	NM_002253.2	515	Agt/Ggt	12/30	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.19	2		481	799	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624275	89624275	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204910	NA	P-0009022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	52	335	1	ENST00000371953.3:c.49C>T	p.Gln17Ter	p.Q17*	ENST00000371953	NM_000314.4	17	Caa/Taa	1/9	1	2	FACETS	1	0.946	1	1	0.979	1	CLONAL	2	TRUE	1	0.15	2		336	282	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344032	70344032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	35	936	1	ENST00000374080.3:c.1768C>T	p.Arg590Trp	p.R590W	ENST00000374080		590	Cgg/Tgg	13/45	0.251924449537549	1	FACETS	0.821	0.672	0.988	0.821	0.672	0.988	CLONAL	1	TRUE	0	0.15	1		937	526	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332689	65332689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	20	711	0	ENST00000342505.4:c.850G>A	p.Glu284Lys	p.E284K	ENST00000342505	NM_002227.2	284	Gaa/Aaa	7/25	1	2	FACETS	0.739	0.564	0.943	0.739	0.564	0.943	CLONAL	1	TRUE	1	0.15	2		711	361	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97863997	97863997	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs863224610	NA	P-0009022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	35	517	0	ENST00000289081.3:c.1669C>G	p.Gln557Glu	p.Q557E	ENST00000289081	NM_000136.2	557	Caa/Gaa	15/15	1	2	FACETS	0.913	0.748	1	0.913	0.748	1	CLONAL	1	TRUE	1	0.15	2		517	511	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109770	115109770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	50	543	0	ENST00000257566.3:c.2108C>T	p.Ser703Phe	p.S703F	ENST00000257566	NM_016569.3	703	tCc/tTc	8/8	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.15	2		543	587	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606131	81606131	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	34	763	0	ENST00000298171.2:c.801G>C	p.Leu267Phe	p.L267F	ENST00000298171	NM_000369.2	267	ttG/ttC	9/10	1	2	FACETS	0.863	0.705	1	0.863	0.705	1	CLONAL	1	TRUE	1	0.15	2		763	525	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771344	68771344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555509646	NA	P-0009022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	26	288	3	ENST00000261769.5:c.26C>T	p.Ser9Leu	p.S9L	ENST00000261769	NM_004360.3	9	tCg/tTg	1/16	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.15	2		291	292	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349036	89349036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	42	1001	0	ENST00000301030.4:c.3914C>T	p.Ser1305Phe	p.S1305F	ENST00000301030	NM_001256183.1	1305	tCt/tTt	9/13	1	2	FACETS	0.876	0.73	1	0.876	0.73	1	CLONAL	1	TRUE	1	0.15	2		1001	639	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912290	29912290	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	37	513	0	ENST00000376809.5:c.909del	p.Gln303HisfsTer19	p.Q303Hfs*19	ENST00000376809	NM_002116.7	303	caG/ca	5/8	0.173570397979832	4	FACETS	1	0.94	1	0.68	0.561	0.813	CLONAL	1	TRUE	2	0.15	4		513	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0009056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1243	82	431	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.952	0.836	1	0.952	0.836	1	CLONAL	1	TRUE	1	0.13	2		433	1325	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016264	150016264	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	148	468	1	ENST00000253339.5:c.442C>T	p.Arg148Ter	p.R148*	ENST00000253339		148	Cga/Tga	2/7	1	2	FACETS	0.46	0.42	0.502	0.46	0.42	0.502	SUBCLONAL	1	TRUE	1	0.793227997550561	2		469	811	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115733	108115733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	54	212	0	ENST00000278616.4:c.881G>A	p.Gly294Glu	p.G294E	ENST00000278616	NM_000051.3	294	gGa/gAa	7/63	0.793227997550561	2	FACETS	0.285	0.244	0.331	0.143	0.122	0.166	SUBCLONAL	1	TRUE	0	0.793227997550561	2		212	477	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105237106	105237106	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	126	575	0	ENST00000349310.3:c.1339A>T	p.Ile447Phe	p.I447F	ENST00000349310	NM_001014432.1	447	Atc/Ttc	14/15	0.506792714886605	1	FACETS	0.344	0.312	0.376	0.344	0.312	0.376	SUBCLONAL	1	TRUE	0	0.793227997550561	1		575	558	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867689	45867689	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	135	596	0	ENST00000391945.4:c.711C>G	p.His237Gln	p.H237Q	ENST00000391945	NM_000400.3	237	caC/caG	8/23	0.472776469429616	3	FACETS	0.596	0.542	0.653	0.199	0.18	0.218	INDETERMINATE	1	TRUE	0	0.793227997550561	3		596	798	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579547	7579547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567557016	NA	P-0009060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	314	399	0	ENST00000269305.4:c.140del	p.Pro47ArgfsTer76	p.P47Rfs*76	ENST00000269305	NM_001126112.2	47	cCg/cg	4/11	0.775432266137628	2	FACETS	0.878	0.845	0.91	0.878	0.845	0.91	CLONAL	2	TRUE	0	0.793227997550561	2		399	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0009065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	258	254	7	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.41657740517118	3	FACETS	1	0.991	1	0.828	0.785	0.872	CLONAL	2	TRUE	0	0.487131927970174	3		261	530	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880169	151880169	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	111	342	0	ENST00000262189.6:c.5155C>T	p.Gln1719Ter	p.Q1719*	ENST00000262189	NM_170606.2	1719	Cag/Tag	35/59	1	2	FACETS	0.637	0.572	0.705	0.637	0.572	0.705	SUBCLONAL	1	TRUE	1	0.466703951198318	2		342	747	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880175	151880175	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1277391709	NA	P-0009085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	104	332	0	ENST00000262189.6:c.5149A>G	p.Lys1717Glu	p.K1717E	ENST00000262189	NM_170606.2	1717	Aaa/Gaa	35/59	1	2	FACETS	0.614	0.55	0.682	0.614	0.55	0.682	SUBCLONAL	1	TRUE	1	0.466703951198318	2		332	726	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061249	38061249	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	131	334	0	ENST00000250448.2:c.740A>T	p.His247Leu	p.H247L	ENST00000250448	NM_004496.3	247	cAc/cTc	2/2	1	2	FACETS	0.659	0.598	0.723	0.659	0.598	0.723	SUBCLONAL	1	TRUE	1	0.466703951198318	2		334	852	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0009111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	87	337	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.240698331258006	2	FACETS	0.835	0.748	0.926	0.835	0.748	0.926	CLONAL	2	TRUE	0	0.342697072838116	2		337	304	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0009111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	232	608	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.342697072838116	5	FACETS	0.835	0.781	0.891	0.835	0.781	0.891	CLONAL	3	TRUE	2	0.342697072838116	5		608	818	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604665	48604665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660045	NA	P-0009111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	42	213	0	ENST00000342988.3:c.1487G>A	p.Arg496His	p.R496H	ENST00000342988	NM_005359.5	496	cGt/cAt	12/12	0.342697072838116	1	FACETS	0.673	0.564	0.792	0.673	0.564	0.792	SUBCLONAL	1	TRUE	0	0.342697072838116	1		213	302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0009112-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	33	570	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.735	0.599	0.889	0.735	0.599	0.889	SUBCLONAL	1	TRUE	1	0.22	2		570	408	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0009112-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	46	210	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.22	2		210	284	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665453	176665454	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009112-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	22	290	1	ENST00000439151.2:c.4137_4138delinsAA	p.Glu1380Lys	p.E1380K	ENST00000439151	NM_022455.4	1379	ccGGaa/ccAAaa	7/23	1	2	FACETS	0.59	0.457	0.745	0.59	0.457	0.745	SUBCLONAL	1	TRUE	1	0.22	2		291	339	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55974019	55974019	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	39	333	0	ENST00000263923.4:c.1297G>T	p.Asp433Tyr	p.D433Y	ENST00000263923	NM_002253.2	433	Gat/Tat	10/30	0.602762152795619	4	FACETS	0.603	0.501	0.716	0.301	0.25	0.358	SUBCLONAL	1	TRUE	2	0.602762152795619	4		333	344	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562300	176562300	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs993486328	NA	P-0009147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	56	493	0	ENST00000439151.2:c.196C>G	p.Pro66Ala	p.P66A	ENST00000439151	NM_022455.4	66	Cca/Gca	2/23	NA	2	FACETS	0.537	0.462	0.618			1	INDETERMINATE	1	TRUE	NA	0.602762152795619	2		493	346	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972439	81972439	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	96	866	1	ENST00000359376.3:c.3232C>T	p.Arg1078Ter	p.R1078*	ENST00000359376	NM_002661.3	1078	Cga/Tga	29/33	0.602762152795619	3	FACETS	0.621	0.553	0.692	0.207	0.184	0.231	SUBCLONAL	1	TRUE	0	0.602762152795619	3		867	668	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0009163-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	133	356	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.946	0.859	1	0.946	0.859	1	CLONAL	1	TRUE	1	0.333976138585482	2		356	842	SUCCESS
APC	324	MSKCC	GRCh37	5	112175419	112175419	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0009163-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	218	337	0	ENST00000257430.4:c.4128T>A	p.Tyr1376Ter	p.Y1376*	ENST00000257430	NM_000038.5	1376	taT/taA	16/16	0.308448803392652	2	FACETS	0.868	0.81	0.928	0.868	0.81	0.928	CLONAL	2	TRUE	0	0.333976138585482	2		337	752	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244139	153244139	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009163-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	164	461	0	ENST00000281708.4:c.2018G>C	p.Trp673Ser	p.W673S	ENST00000281708	NM_033632.3	673	tGg/tCg	12/12	NA	2	FACETS	0.844	0.773	0.918			1	INDETERMINATE	1	TRUE	NA	0.333976138585482	2		461	1164	SUCCESS
ATM	472	MSKCC	GRCh37	11	108128333	108128333	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs754267376	NA	P-0009163-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	85	267	0	ENST00000278616.4:c.2376G>C	p.Lys792Asn	p.K792N	ENST00000278616	NM_000051.3	792	aaG/aaC	15/63	1	2	FACETS	0.716	0.633	0.805	0.716	0.633	0.805	SUBCLONAL	1	TRUE	1	0.333976138585482	2		267	711	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216531	108216531	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434216	NA	P-0009163-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	145	513	0	ENST00000278616.4:c.8480T>G	p.Phe2827Cys	p.F2827C	ENST00000278616	NM_000051.3	2827	tTt/tGt	58/63	1	2	FACETS	0.831	0.757	0.909	0.831	0.757	0.909	CLONAL	1	TRUE	1	0.333976138585482	2		513	1045	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39772564	39772564	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009163-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	62	286	0	ENST00000288319.7:c.677G>A	p.Gly226Asp	p.G226D	ENST00000288319	NM_182918.3	226	gGt/gAt	6/10	1	2	FACETS	0.575	0.496	0.66	0.575	0.496	0.66	SUBCLONAL	1	TRUE	1	0.333976138585482	2		286	646	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354072	15354080	+	inframe_deletion	In_Frame_Del	DEL	CTGCAGCTG	CTGCAGCTG	-	rs1195422874	NA	P-0009163-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	44	131	0	ENST00000263377.2:c.2800_2808del	p.Gln934_Gln936del	p.Q934_Q936del	ENST00000263377	NM_058243.2	934	CAGCTGCAG/-	14/20	1	2	FACETS	0.706	0.594	0.83	0.706	0.594	0.83	SUBCLONAL	1	TRUE	1	0.333976138585482	2		131	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0009172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	162	495	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.256520319666863	1	FACETS	0.779	0.713	0.849	0.779	0.713	0.849	SUBCLONAL	1	TRUE	0	0.28	1		495	1277	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0009172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	131	383	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	1	2	FACETS	0.854	0.773	0.939	0.854	0.773	0.939	CLONAL	1	TRUE	1	0.28	2		383	1096	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579494	7579494	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1555526721	NA	P-0009184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	693	449	0	ENST00000269305.4:c.193A>T	p.Arg65Ter	p.R65*	ENST00000269305	NM_001126112.2	65	Aga/Tga	4/11	0.894163898495397	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.905518014989389	2		449	746	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225395	26225395	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1482691981	NA	P-0009184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	751	907	0	ENST00000360408.1:c.13A>G	p.Lys5Glu	p.K5E	ENST00000360408	NM_003532.2	5	Aag/Gag	1/1	0.309453776336513	3	FACETS	1	0.997	1	0.681	0.658	0.703	INDETERMINATE	1	TRUE	1	0.905518014989389	3		907	1770	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982053	93982053	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	589	656	0	ENST00000369303.4:c.1412G>C	p.Gly471Ala	p.G471A	ENST00000369303	NM_004440.3	471	gGa/gCa	6/17	1	2	FACETS	0.967	0.931	1	0.967	0.931	1	CLONAL	1	TRUE	1	0.905518014989389	2		656	1346	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395153	139395153	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	827	606	0	ENST00000277541.6:c.5785G>T	p.Glu1929Ter	p.E1929*	ENST00000277541	NM_017617.3	1929	Gag/Tag	31/34	NA	2	FACETS	0.978	0.963	0.991			1	INDETERMINATE	2	TRUE	NA	0.905518014989389	2		606	934	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486838	56486838	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs201880960	NA	P-0009184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	883	551	1	ENST00000267101.3:c.1252A>G	p.Ile418Val	p.I418V	ENST00000267101	NM_001982.3	418	Att/Gtt	11/28	0.829102024168997	3	FACETS	0.949	0.924	0.973	0.949	0.924	0.973	CLONAL	2	TRUE	1	0.905518014989389	3		552	1493	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975669	26975669	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	1273	659	1	ENST00000381527.3:c.1177A>T	p.Ser393Cys	p.S393C	ENST00000381527	NM_001260.1	393	Agc/Tgc	12/13	NA	2	FACETS	0.991	0.98	1			1	INDETERMINATE	2	TRUE	NA	0.905518014989389	2		660	1418	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916850	48916850	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	391	251	0	ENST00000267163.4:c.380G>T	p.Ser127Ile	p.S127I	ENST00000267163	NM_000321.2	127	aGt/aTt	3/27	0.905518014989389	2	FACETS	0.988	0.968	1	0.988	0.968	1	CLONAL	2	TRUE	0	0.905518014989389	2		251	437	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060968	38060968	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	261	333	0	ENST00000250448.2:c.1021A>T	p.Thr341Ser	p.T341S	ENST00000250448	NM_004496.3	341	Acg/Tcg	2/2	0.905518014989389	3	FACETS	0.981	0.921	1	0.49	0.46	0.521	CLONAL	1	TRUE	1	0.905518014989389	3		333	854	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934602	9934602	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs397518470	NA	P-0009184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	362	548	2	ENST00000330684.3:c.1553G>T	p.Arg518Leu	p.R518L	ENST00000330684	NM_001134407.1	518	cGt/cTt	7/13	NA	2	FACETS	0.895	0.852	0.939			1	INDETERMINATE	1	TRUE	NA	0.905518014989389	2		550	893	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029227	14029227	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1234590300	NA	P-0009184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	632	619	0	ENST00000311895.7:c.1438A>G	p.Thr480Ala	p.T480A	ENST00000311895	NM_005236.2	480	Acc/Gcc	8/11	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.905518014989389	2		619	1361	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210740	2210740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	828	593	0	ENST00000398665.3:c.1237C>T	p.Arg413Cys	p.R413C	ENST00000398665	NM_032482.2	413	Cgc/Tgc	14/28	0.897043203371821	3	FACETS	0.989	0.963	1	0.989	0.963	1	CLONAL	2	TRUE	1	0.905518014989389	3		593	1343	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7293823	7293823	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	221	157	0	ENST00000302850.5:c.80G>T	p.Gly27Val	p.G27V	ENST00000302850	NM_000208.2	27	gGc/gTc	1/22	0.897043203371821	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.905518014989389	3		157	336	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792431	33792431	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	434	745	0	ENST00000498907.2:c.890G>T	p.Arg297Leu	p.R297L	ENST00000498907	NM_004364.3	297	cGc/cTc	1/1	0.415642194097095	3	FACETS	0.901	0.858	0.945			1	INDETERMINATE	1	TRUE	NA	0.905518014989389	3		745	1546	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565524	41565524	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	498	583	0	ENST00000263253.7:c.4190A>C	p.Tyr1397Ser	p.Y1397S	ENST00000263253	NM_001429.3	1397	tAc/tCc	26/31	1	2	FACETS	0.954	0.916	0.993	0.954	0.916	0.993	CLONAL	1	TRUE	1	0.905518014989389	2		583	1153	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225914	53225914	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	403	638	1	ENST00000375401.3:c.2935A>G	p.Ile979Val	p.I979V	ENST00000375401	NM_004187.3	979	Att/Gtt	19/26	0.348634534357904	3	FACETS	0.886	0.841	0.931			1	INDETERMINATE	1	TRUE	NA	0.905518014989389	3		639	1460	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835669	68835670	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0009184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	544	673	0	ENST00000261769.5:c.260_261delinsCT	p.Arg87Thr	p.R87T	ENST00000261769	NM_004360.3	87	aGG/aCT	3/16	NA	2	FACETS	0.948	0.912	0.985			1	INDETERMINATE	1	TRUE	NA	0.905518014989389	2		673	1267	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0009198-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	98	531	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.13752726890701	3	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	1	0.221174844406054	3		531	472	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048602	180048602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778453271	NA	P-0009198-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	79	195	2	ENST00000261937.6:c.1960G>A	p.Glu654Lys	p.E654K	ENST00000261937	NM_182925.4	654	Gaa/Aaa	13/30	0.221174844406054	3	FACETS	0.979	0.866	1	0.979	0.866	1	CLONAL	2	TRUE	1	0.221174844406054	3		197	405	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106504	27106504	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009198-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	116	449	1	ENST00000324856.7:c.6115C>T	p.Gln2039Ter	p.Q2039*	ENST00000324856	NM_006015.4	2039	Caa/Taa	20/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.221174844406054	2		450	996	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162528	47162528	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009198-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	38	269	0	ENST00000409792.3:c.3598G>T	p.Glu1200Ter	p.E1200*	ENST00000409792	NM_014159.6	1200	Gaa/Taa	3/21	1	2	FACETS	0.883	0.731	1	0.883	0.731	1	CLONAL	1	TRUE	1	0.221174844406054	2		269	389	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164943	47164943	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0009198-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	43	261	0	ENST00000409792.3:c.1183A>T	p.Arg395Ter	p.R395*	ENST00000409792	NM_014159.6	395	Aga/Tga	3/21	1	2	FACETS	0.892	0.747	1	0.892	0.747	1	CLONAL	1	TRUE	1	0.221174844406054	2		261	436	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061406	38061406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009198-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	78	242	0	ENST00000250448.2:c.583G>A	p.Glu195Lys	p.E195K	ENST00000250448	NM_004496.3	195	Gag/Aag	2/2	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.221174844406054	2		242	518	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	54	260	0				ENST00000310581	NM_198253.2	-/1132			0.332159458637683	3	FACETS	0.924	0.805	1	0.924	0.805	1	CLONAL	2	TRUE	1	0.424001370038737	3		260	167	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519938	NA	P-0009201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	91	301	0	ENST00000263967.3:c.1034A>C	p.Asn345Thr	p.N345T	ENST00000263967	NM_006218.2	345	aAt/aCt	5/21	0.35877141470212	4	FACETS	0.876	0.784	0.971	0.876	0.784	0.971	CLONAL	2	TRUE	2	0.424001370038737	4		301	349	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104359285	104359285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746448939	NA	P-0009201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	156	283	1	ENST00000369902.3:c.1006G>A	p.Ala336Thr	p.A336T	ENST00000369902	NM_016169.3	336	Gcc/Acc	8/12	0.424001370038737	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.424001370038737	2		284	320	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410441	63410441	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	159	274	0	ENST00000330258.3:c.2726C>G	p.Ser909Cys	p.S909C	ENST00000330258	NM_152424.3	909	tCc/tGc	2/2	0.271333994109245	2	FACETS	0.996	0.939	1			1	CLONAL	3	TRUE	NA	0.424001370038737	2		274	251	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647638	23647639	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs1555461870	NA	P-0009201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	113	272	0	ENST00000261584.4:c.228_229del	p.Ile76MetfsTer4	p.I76Mfs*4	ENST00000261584	NM_024675.3	76	atATgt/atgt	4/13	0.276208898045576	4	FACETS	1	0.912	1	1	0.912	1	CLONAL	2	TRUE	2	0.424001370038737	4		272	378	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0009216-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	343	326	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.985	1	1	0.996	1	CLONAL	2	TRUE	1	0.390544742000237	2		326	808	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782329	NA	P-0009216-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	902	313	1	ENST00000269305.4:c.746G>C	p.Arg249Thr	p.R249T	ENST00000269305	NM_001126112.2	249	aGg/aCg	7/11	0.390544742000237	2	FACETS	1	0.998	1	1	0.999	1	CLONAL	4	TRUE	0	0.390544742000237	2		314	1042	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939793	76939793	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0009216-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	652	318	1	ENST00000373344.5:c.955A>T	p.Lys319Ter	p.K319*	ENST00000373344	NM_000489.3	319	Aag/Tag	9/35	1	1	FACETS	0.979	0.954	1	1	0.998	1	CLONAL	3	TRUE	0	0.390544742000237	1		319	915	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574000	7574000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009221-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	229	484	0	ENST00000269305.4:c.1027G>T	p.Glu343Ter	p.E343*	ENST00000269305	NM_001126112.2	343	Gag/Tag	10/11	0.356482866397276	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.356482866397276	1		484	913	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226549731	226549731	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009221-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	79	497	0	ENST00000366794.5:c.2902G>C	p.Asp968His	p.D968H	ENST00000366794	NM_001618.3	968	Gac/Cac	22/23	1	2	FACETS	0.405	0.355	0.459	0.405	0.355	0.459	SUBCLONAL	1	TRUE	1	0.356482866397276	2		497	1094	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37141715	37141715	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009221-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	69	380	0	ENST00000373509.5:c.790C>T	p.Gln264Ter	p.Q264*	ENST00000373509	NM_002648.3	264	Cag/Tag	6/6	1	2	FACETS	0.561	0.488	0.64	0.561	0.488	0.64	SUBCLONAL	1	TRUE	1	0.356482866397276	2		380	690	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5078403	5078403	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	24	293	0	ENST00000381652.3:c.2090T>G	p.Leu697Arg	p.L697R	ENST00000381652	NM_004972.3	697	cTt/cGt	16/25	0.440414489122663	3	FACETS	0.307	0.241	0.383			1	INDETERMINATE	1	TRUE	NA	0.756729966437337	3		293	285	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	227	329	1	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	0.557399793888338	6	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.756729966437337	6		330	1345	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089554	27089554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	112	414	2	ENST00000324856.7:c.2510C>T	p.Ala837Val	p.A837V	ENST00000324856	NM_006015.4	837	gCc/gTc	8/20	0.756729966437337	4	FACETS	0.537	0.482	0.595	0.179	0.16	0.199	SUBCLONAL	1	TRUE	1	0.756729966437337	4		416	969	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305328	65305328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	278	583	0	ENST00000342505.4:c.2800C>T	p.His934Tyr	p.H934Y	ENST00000342505	NM_002227.2	934	Cat/Tat	20/25	0.756729966437337	4	FACETS	1	0.94	1	0.334	0.313	0.356	CLONAL	1	TRUE	1	0.756729966437337	4		583	1288	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666608	206666608	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	195	341	0	ENST00000367120.3:c.1942G>T	p.Glu648Ter	p.E648*	ENST00000367120	NM_014002.3	648	Gag/Tag	20/22	0.6819200032561	5	FACETS	0.895	0.827	0.967	0.298	0.275	0.323	CLONAL	1	TRUE	2	0.756729966437337	5		341	1229	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719588	61719588	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	101	377	0	ENST00000401558.2:c.1595G>C	p.Arg532Thr	p.R532T	ENST00000401558	NM_003400.3	532	aGa/aCa	15/25	0.756729966437337	5	FACETS	0.794	0.71	0.883	0.265	0.236	0.295	SUBCLONAL	1	TRUE	2	0.756729966437337	5		377	718	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152080	55152080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	77	388	0	ENST00000257290.5:c.2512G>A	p.Gly838Ser	p.G838S	ENST00000257290	NM_006206.4	838	Ggc/Agc	18/23	0.318683964996862	4	FACETS	0.728	0.641	0.821	0.364	0.32	0.411	INDETERMINATE	1	TRUE	2	0.756729966437337	4		388	491	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997485	149997485	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	94	333	0	ENST00000253339.5:c.2794G>C	p.Asp932His	p.D932H	ENST00000253339		932	Gat/Cat	6/7	0.756729966437337	4	FACETS	0.779	0.695	0.869	0.26	0.231	0.29	SUBCLONAL	1	TRUE	1	0.756729966437337	4		333	560	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374320	81374320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	130	326	0	ENST00000222390.5:c.742G>A	p.Glu248Lys	p.E248K	ENST00000222390	NM_000601.4	248	Gaa/Aaa	6/18	0.756729966437337	6	FACETS	0.758	0.69	0.828	0.379	0.345	0.414	SUBCLONAL	2	TRUE	2	0.756729966437337	6		326	570	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118367074	118367074	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	42	265	0	ENST00000534358.1:c.5656A>T	p.Ser1886Cys	p.S1886C	ENST00000534358	NM_005933.3	1886	Agt/Tgt	20/36	0.756729966437337	5	FACETS	0.316	0.262	0.375	0.079	0.065	0.094	SUBCLONAL	1	TRUE	1	0.756729966437337	5		265	751	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444726	49444726	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	114	286	0	ENST00000301067.7:c.2740G>T	p.Glu914Ter	p.E914*	ENST00000301067	NM_003482.3	914	Gag/Tag	10/54	0.557399793888338	6	FACETS	0.613	0.55	0.68			1	SUBCLONAL	1	TRUE	NA	0.756729966437337	6		286	1236	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756598	756598	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1199294016	NA	P-0009253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2650	217	391	0	ENST00000314574.4:c.230C>T	p.Ser77Leu	p.S77L	ENST00000314574	NM_005433.3	77	tCa/tTa	2/12	0.756729966437337	18	FACETS	1	0.989	1			1	CLONAL	1	TRUE	NA	0.756729966437337	18		391	2867	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799281	42799281	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	82	135	0	ENST00000575354.2:c.4765G>C	p.Glu1589Gln	p.E1589Q	ENST00000575354	NM_015125.3	1589	Gag/Cag	20/20	0.756729966437337	4	FACETS	0.765	0.676	0.859	0.255	0.225	0.287	SUBCLONAL	1	TRUE	1	0.756729966437337	4		135	498	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578264	7578265	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0009253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	399	459	1	ENST00000269305.4:c.584_585delinsAA	p.Ile195Lys	p.I195K	ENST00000269305	NM_001126112.2	195	aTC/aAA	6/11	0.756729966437337	4	FACETS	0.911	0.869	0.953	0.607	0.579	0.636	CLONAL	2	TRUE	1	0.756729966437337	4		460	1017	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0009256-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	175	239	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.231620622797942	3	FACETS	0.988	0.915	1			1	CLONAL	2	TRUE	NA	0.345549628671008	3		240	601	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220400	1220400	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1359582062	NA	P-0009256-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	261	430	0	ENST00000326873.7:c.493G>T	p.Glu165Ter	p.E165*	ENST00000326873	NM_000455.4	165	Gag/Tag	4/10	NA	2	FACETS	1	0.963	1			1	INDETERMINATE	2	TRUE	NA	0.345549628671008	2		430	733	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218084	108218084	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs760955058	NA	P-0009256-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	72	246	0	ENST00000278616.4:c.8663T>C	p.Ile2888Thr	p.I2888T	ENST00000278616	NM_000051.3	2888	aTa/aCa	59/63	0.345549628671008	3	FACETS	0.989	0.866	1	0.495	0.433	0.561	CLONAL	1	TRUE	1	0.345549628671008	3		246	494	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468494	89468494	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009256-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	122	356	0	ENST00000336596.2:c.2028G>T	p.Gln676His	p.Q676H	ENST00000336596	NM_005233.5	676	caG/caT	11/17	1	2	FACETS	0.965	0.873	1	0.965	0.873	1	CLONAL	1	TRUE	1	0.345549628671008	2		356	732	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971126	13971126	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0009256-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	131	168	0	ENST00000405192.2:c.802+1G>T		p.X268_splice	ENST00000405192	NM_001163147.1	268			0.278675824302576	4	FACETS	0.972	0.886	1	0.972	0.886	1	CLONAL	2	TRUE	2	0.345549628671008	4		168	525	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760981	133760981	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009256-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	301	410	0	ENST00000318560.5:c.3304G>T	p.Ala1102Ser	p.A1102S	ENST00000318560	NM_005157.4	1102	Gcg/Tcg	11/11	0.278675824302576	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	2	0.345549628671008	4		410	1132	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612054	43612054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009256-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	386	597	0	ENST00000355710.3:c.2159C>T	p.Pro720Leu	p.P720L	ENST00000355710	NM_020975.4	720	cCt/cTt	12/20	0.345549628671008	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.345549628671008	3		597	1268	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199763	108199763	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009256-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	171	234	0	ENST00000278616.4:c.7105G>T	p.Gly2369Ter	p.G2369*	ENST00000278616	NM_000051.3	2369	Gga/Tga	49/63	0.345549628671008	3	FACETS	0.999	0.924	1	0.999	0.924	1	CLONAL	2	TRUE	1	0.345549628671008	3		234	581	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900321	3900321	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs750216784	NA	P-0009256-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	261	364	0	ENST00000262367.5:c.775G>T	p.Ala259Ser	p.A259S	ENST00000262367	NM_004380.2	259	Gca/Tca	2/31	0.345549628671008	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.345549628671008	3		364	864	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412676	63412676	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009256-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	166	395	0	ENST00000330258.3:c.491A>T	p.Lys164Met	p.K164M	ENST00000330258	NM_152424.3	164	aAg/aTg	2/2	0.278675824302576	4	FACETS	1	0.971	1	0.563	0.516	0.612	CLONAL	1	TRUE	2	0.345549628671008	4		395	1148	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0009265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	65	239	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.321539572460132	1	FACETS	0.953	0.831	1	0.953	0.831	1	CLONAL	1	TRUE	0	0.321539572460132	1		240	356	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0009265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	55	358	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	NA	2	FACETS	0.734	0.629	0.849			1	INDETERMINATE	1	TRUE	NA	0.321539572460132	2		358	466	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346338	73346338	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	77	450	1	ENST00000377767.4:c.1462G>T	p.Asp488Tyr	p.D488Y	ENST00000377767	NM_014953.3	488	Gat/Tat	10/21	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.321539572460132	2		451	416	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0009274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	658	239	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.426938070947186	2	FACETS	0.765	0.744	0.786	0.765	0.744	0.786	INDETERMINATE	2	TRUE	0	0.855542798914662	2		240	1005	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45864886	45864886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200043231	NA	P-0009274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	212	415	0	ENST00000391945.4:c.1133G>A	p.Arg378His	p.R378H	ENST00000391945	NM_000400.3	378	cGc/cAc	12/23	0.855542798914662	1	FACETS	0.483	0.452	0.515	0.483	0.452	0.515	SUBCLONAL	1	TRUE	0	0.855542798914662	1		415	587	SUCCESS
APC	324	MSKCC	GRCh37	5	112170772	112170772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765557332	NA	P-0009274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	265	421	0	ENST00000257430.4:c.1868G>A	p.Arg623Gln	p.R623Q	ENST00000257430	NM_000038.5	623	cGg/cAg	15/16	1	2	FACETS	0.484	0.453	0.516	0.484	0.453	0.516	SUBCLONAL	1	TRUE	1	0.855542798914662	2		421	1280	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747127	40747127	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	192	303	1	ENST00000373198.4:c.2955G>T	p.Glu985Asp	p.E985D	ENST00000373198	NM_133170.3	985	gaG/gaT	22/32	0.426938070947186	2	FACETS	0.47	0.434	0.507	0.235	0.217	0.254	INDETERMINATE	1	TRUE	0	0.855542798914662	2		304	955	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0009291-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	46	415	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.238043313743907	1	FACETS	0.895	0.758	1	0.895	0.758	1	CLONAL	1	TRUE	0	0.29	1		415	303	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500317	99500317	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009291-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	103	589	0	ENST00000268035.6:c.3750G>C	p.Gln1250His	p.Q1250H	ENST00000268035	NM_000875.3	1250	caG/caC	21/21	0.303523810665699	5	FACETS	0.829	0.743	0.919			1	CLONAL	2	TRUE	NA	0.29	5		589	615	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183694	10183709	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGCCGGGCGGCCGC	GAGGCCGGGCGGCCGC	-	novel	NA	P-0009291-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	34	442	0	ENST00000256474.2:c.164_179del	p.Glu55GlyfsTer7	p.E55Gfs*7	ENST00000256474	NM_000551.3	55	GAGGCCGGGCGGCCGCgg/gg	1/3	0.238043313743907	1	FACETS	0.502	0.411	0.606	0.502	0.411	0.606	SUBCLONAL	1	TRUE	0	0.29	1		442	399	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0009316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	36	318	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.732	0.607	0.868	0.732	0.607	0.868	SUBCLONAL	1	TRUE	1	0.48706223771419	2		318	202	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0009316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	51	143	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.437882328362349	3	FACETS	1	0.937	1	0.742	0.651	0.835	CLONAL	2	TRUE	0	0.48706223771419	3		143	117	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699360	47699360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	91	411	0	ENST00000347630.2:c.148G>A	p.Glu50Lys	p.E50K	ENST00000347630	NM_001007230.1	50	Gaa/Aaa	4/11	1	2	FACETS	0.668	0.595	0.747	0.668	0.595	0.747	SUBCLONAL	1	TRUE	1	0.48706223771419	2		411	559	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372518	55372518	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	146	301	1	ENST00000297316.4:c.1208G>T	p.Ser403Ile	p.S403I	ENST00000297316	NM_022454.3	403	aGc/aTc	2/2	1	2	FACETS	0.875	0.801	0.953	0.875	0.801	0.953	CLONAL	1	TRUE	1	0.48706223771419	2		302	685	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0009316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	90	340	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	1	2	FACETS	0.917	0.819	1	0.917	0.819	1	CLONAL	1	TRUE	1	0.48706223771419	2		340	403	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101387	27101394	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTCTGC	CCCTCTGC	-	novel	NA	P-0009316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	116	308	0	ENST00000324856.7:c.4673_4680del	p.Ser1558CysfsTer11	p.S1558Cfs*11	ENST00000324856	NM_006015.4	1557	CCCTCTGCc/c	18/20	1	2	FACETS	0.89	0.806	0.979	0.89	0.806	0.979	CLONAL	1	TRUE	1	0.48706223771419	2		308	535	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602692	10602692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1278385562	NA	P-0009316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	173	333	0	ENST00000171111.5:c.886C>T	p.Arg296Cys	p.R296C	ENST00000171111	NM_203500.1	296	Cgc/Tgc	3/6	1	2	FACETS	0.896	0.826	0.969	0.896	0.826	0.969	CLONAL	1	TRUE	1	0.48706223771419	2		333	793	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630626	158630626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912678	NA	P-0009316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	117	508	0	ENST00000263640.3:c.617G>A	p.Arg206His	p.R206H	ENST00000263640	NM_001105.4	206	cGc/cAc	6/11	1	2	FACETS	0.676	0.61	0.745	0.676	0.61	0.745	SUBCLONAL	1	TRUE	1	0.48706223771419	2		508	711	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741533	145741533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781105713	NA	P-0009316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	174	388	0	ENST00000428558.2:c.970C>T	p.Pro324Ser	p.P324S	ENST00000428558	NM_004260.3	324	Ccc/Tcc	5/22	1	2	FACETS	0.837	0.771	0.905	0.837	0.771	0.905	CLONAL	1	TRUE	1	0.48706223771419	2		388	854	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112440	115112440	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1033763029	NA	P-0009316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	113	237	0	ENST00000257566.3:c.1300G>A	p.Asp434Asn	p.D434N	ENST00000257566	NM_016569.3	434	Gac/Aac	7/8	1	2	FACETS	0.838	0.756	0.923	0.838	0.756	0.923	CLONAL	1	TRUE	1	0.48706223771419	2		237	554	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564698	86564698	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	94	310	1	ENST00000274376.6:c.434del	p.Pro145LeufsTer29	p.P145Lfs*29	ENST00000274376	NM_002890.2	144	Ccc/cc	1/25	1	2	FACETS	0.749	0.669	0.835	0.749	0.669	0.835	SUBCLONAL	1	TRUE	1	0.48706223771419	2		311	515	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0009320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	132	158	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.95	0.872	1	0.95	0.872	1	CLONAL	1	TRUE	1	0.729320967277762	2		158	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0009320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	338	329	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.719877180642165	1	FACETS	0.972	0.93	1	0.972	0.93	1	CLONAL	1	TRUE	0	0.729320967277762	1		329	606	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685281	89685281	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1060500116	NA	P-0009320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	226	241	0	ENST00000371953.3:c.176C>G	p.Ser59Ter	p.S59*	ENST00000371953	NM_000314.4	59	tCa/tGa	3/9	0.729320967277762	1	FACETS	0.956	0.905	1	0.956	0.905	1	CLONAL	1	TRUE	0	0.729320967277762	1		241	412	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041888	42041888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773937278	NA	P-0009320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	519	573	0	ENST00000219905.7:c.6083G>A	p.Arg2028Lys	p.R2028K	ENST00000219905	NM_001164273.1	2028	aGg/aAg	17/24	1	2	FACETS	0.956	0.916	0.997	0.956	0.916	0.997	CLONAL	1	TRUE	1	0.729320967277762	2		573	1488	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039441	49039441	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	377	382	0	ENST00000267163.4:c.2426del	p.Leu809ArgfsTer17	p.L809Rfs*17	ENST00000267163	NM_000321.2	809	cTg/cg	23/27	0.719877180642165	1	FACETS	0.985	0.945	1	0.985	0.945	1	CLONAL	1	TRUE	0	0.729320967277762	1		382	667	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056214	27056214	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	96	263	1	ENST00000324856.7:c.1210C>T	p.Gln404Ter	p.Q404*	ENST00000324856	NM_006015.4	404	Caa/Taa	2/20	0.240102249440941	2	FACETS	1	0.898	1	0.504	0.449	0.563	CLONAL	1	TRUE	0	0.240102249440941	2		264	793	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509407	46509407	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs776413265	NA	P-0009343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	126	354	0	ENST00000262741.5:c.1324G>T	p.Asp442Tyr	p.D442Y	ENST00000262741	NM_003629.3	442	Gac/Tac	10/10	0.240102249440941	2	FACETS	0.984	0.889	1	0.492	0.444	0.542	CLONAL	1	TRUE	0	0.240102249440941	2		354	1067	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445247	29445247	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	124	391	0	ENST00000389048.3:c.3478G>C	p.Asp1160His	p.D1160H	ENST00000389048	NM_004304.4	1160	Gac/Cac	22/29	0.231282285720201	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.240102249440941	1		391	900	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39567804	39567804	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	114	313	0	ENST00000262039.4:c.560T>C	p.Met187Thr	p.M187T	ENST00000262039	NM_002647.2	187	aTg/aCg	5/25	0.231282285720201	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.240102249440941	1		313	807	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929498	44929498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	95	243	0	ENST00000377967.4:c.2598G>A	p.Met866Ile	p.M866I	ENST00000377967	NM_021140.2	866	atG/atA	17/29	1	1	FACETS	0.924	0.822	1	0.924	0.822	1	CLONAL	1	TRUE	0	0.240102249440941	1		243	754	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948714	55948714	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	107	398	0	ENST00000263923.4:c.3751del	p.Val1251Ter	p.V1251*	ENST00000263923	NM_002253.2	1251	Gta/ta	28/30	1	2	FACETS	0.801	0.716	0.891	0.801	0.716	0.891	CLONAL	1	TRUE	1	0.240102249440941	2		398	1113	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs786202525	NA	P-0009343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	72	244	0	ENST00000269305.4:c.532del	p.His178ThrfsTer69	p.H178Tfs*69	ENST00000269305	NM_001126112.2	178	Cac/ac	5/11	0.231282285720201	1	FACETS	0.946	0.827	1	0.946	0.827	1	CLONAL	1	TRUE	0	0.240102249440941	1		244	558	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0009355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	33	531	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.351	0.284	0.426	0.351	0.284	0.426	SUBCLONAL	1	FALSE	1	0.228429721890735	2		531	824	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0009355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	25	300	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	1	2	FACETS	0.551	0.434	0.686	0.551	0.434	0.686	SUBCLONAL	1	FALSE	1	0.228429721890735	2		300	397	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223203	5223203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1416280955	NA	P-0009355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	22	295	0	ENST00000357368.4:c.2600G>A	p.Arg867His	p.R867H	ENST00000357368	NM_002850.3	867	cGc/cAc	18/38	1	2	FACETS	0.47	0.363	0.594	0.47	0.363	0.594	SUBCLONAL	1	FALSE	1	0.228429721890735	2		295	410	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0009362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	68	265	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.745	0.649	0.849	0.745	0.649	0.849	SUBCLONAL	1	TRUE	1	0.341041879415309	2		265	535	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0009362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	71	214	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	1	2	FACETS	0.79	0.691	0.897	0.79	0.691	0.897	SUBCLONAL	1	TRUE	1	0.341041879415309	2		214	527	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0009362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	184	259	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.341041879415309	2	FACETS	0.882	0.818	0.947	0.882	0.818	0.947	CLONAL	2	TRUE	0	0.341041879415309	2		259	612	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980849	40980849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs548511212	NA	P-0009362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	292	327	0	ENST00000373198.4:c.1637G>A	p.Arg546Gln	p.R546Q	ENST00000373198	NM_133170.3	546	cGg/cAg	10/32	0.282658281177958	5	FACETS	0.886	0.835	0.938	0.886	0.835	0.938	CLONAL	3	TRUE	2	0.341041879415309	5		327	974	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259729	16259729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758740337	NA	P-0009362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	141	334	0	ENST00000375759.3:c.6994C>T	p.Arg2332Cys	p.R2332C	ENST00000375759	NM_015001.2	2332	Cgc/Tgc	11/15	1	2	FACETS	0.923	0.84	1	0.923	0.84	1	CLONAL	1	TRUE	1	0.341041879415309	2		334	896	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958190	2958190	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753952757	NA	P-0009362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	167	334	0	ENST00000396946.4:c.2542C>T	p.Arg848Cys	p.R848C	ENST00000396946	NM_032415.4	848	Cgc/Tgc	19/25	0.341041879415309	3	FACETS	0.792	0.729	0.857	0.792	0.729	0.857	SUBCLONAL	2	TRUE	1	0.341041879415309	3		334	724	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467763	50467763	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	72	279	0	ENST00000331340.3:c.998C>T	p.Thr333Met	p.T333M	ENST00000331340	NM_006060.4	333	aCg/aTg	8/8	0.341041879415309	3	FACETS	0.899	0.786	1	0.449	0.393	0.51	CLONAL	1	TRUE	1	0.341041879415309	3		279	550	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678541	88678541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145157285	NA	P-0009362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	61	220	0	ENST00000360948.2:c.995C>T	p.Thr332Met	p.T332M	ENST00000360948	NM_001012338.2	332	aCg/aTg	9/19	1	2	FACETS	0.906	0.784	1	0.906	0.784	1	CLONAL	1	TRUE	1	0.341041879415309	2		220	395	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584605	48584612	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TACCATCA	TACCATCA	-	novel	NA	P-0009362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	36	297	0	ENST00000342988.3:c.780_787del	p.Tyr260Ter	p.Y260*	ENST00000342988	NM_005359.5	260	TACCATCAt/t	6/12	0.341041879415309	1	FACETS	0.347	0.284	0.417	0.347	0.284	0.417	SUBCLONAL	1	TRUE	0	0.341041879415309	1		297	505	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	83	221	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.254244582585746	3	FACETS	1	0.92	1			1	CLONAL	2	TRUE	NA	0.254244582585746	3		222	353	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952100	178952100	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	27	433	1	ENST00000263967.3:c.3155C>A	p.Thr1052Lys	p.T1052K	ENST00000263967	NM_006218.2	1052	aCa/aAa	21/21	0.196496382539818	3	FACETS	1	0.917	1	0.654	0.525	0.799	CLONAL	1	TRUE	1	0.254244582585746	3		434	183	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0009398-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	293	326	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.613543000323869	2		326	825	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0009398-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	660	570	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.613543000323869	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.613543000323869	2		570	1029	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76856035	76856035	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0009398-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	305	241	1	ENST00000373344.5:c.5567-2A>G		p.X1856_splice	ENST00000373344	NM_000489.3	1856			1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.613543000323869	1		242	462	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979329	93979329	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	29	628	0	ENST00000369303.4:c.1499C>G	p.Ala500Gly	p.A500G	ENST00000369303	NM_004440.3	500	gCc/gGc	7/17	0.287773309901391	5	FACETS	0.499	0.4	0.613	0.166	0.133	0.205	SUBCLONAL	1	FALSE	2	0.340126657186799	5		628	516	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409175	4409175	+	stop_lost	Nonstop_Mutation	SNP	A	A	T	novel	NA	P-0009400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	11	288	0	ENST00000261254.3:c.870A>T	p.Ter290CysextTer13	p.*290Cext*13	ENST00000261254	NM_001759.3	290	tgA/tgT	5/5	0.340126657186799	7	FACETS	0.647	0.447	0.894	0.162	0.111	0.224	SUBCLONAL	1	FALSE	3	0.340126657186799	7		288	185	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793433	42793433	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	23	261	0	ENST00000575354.2:c.1235C>G	p.Ala412Gly	p.A412G	ENST00000575354	NM_015125.3	412	gCc/gGc	8/20	0.340126657186799	8	FACETS	0.955	0.746	1			1	CLONAL	1	FALSE	NA	0.340126657186799	8		261	286	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867502	45867502	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161399233	NA	P-0009400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	19	384	0	ENST00000391945.4:c.806C>T	p.Thr269Met	p.T269M	ENST00000391945	NM_000400.3	269	aCg/aTg	9/23	0.310714584711726	4	FACETS	0.865	0.661	1			1	CLONAL	1	FALSE	NA	0.340126657186799	4		384	173	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0009436-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	137	158	0				ENST00000310581	NM_198253.2	-/1132			0.205434715193007	1	FACETS	0.7	0.645	0.756	0.7	0.645	0.756	INDETERMINATE	1	TRUE	0	0.710583054024745	1		158	355	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0009436-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	322	386	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.695803890970375	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.710583054024745	1		386	527	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984813	55984813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200544155	NA	P-0009436-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	504	420	1	ENST00000263923.4:c.316C>T	p.Arg106Trp	p.R106W	ENST00000263923	NM_002253.2	106	Cgg/Tgg	3/30	0.206879629169178	2	FACETS	1	0.995	1	0.621	0.596	0.646	INDETERMINATE	1	TRUE	0	0.710583054024745	2		421	1142	SUCCESS
EED	8726	MSKCC	GRCh37	11	85979591	85979591	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009436-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	300	209	0	ENST00000263360.6:c.954G>C	p.Leu318Phe	p.L318F	ENST00000263360	NM_003797.3	318	ttG/ttC	9/12	1	2	FACETS	0.952	0.899	1	0.952	0.899	1	CLONAL	1	TRUE	1	0.710583054024745	2		209	887	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943370	17943370	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009436-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	434	390	0	ENST00000458235.1:c.2638A>G	p.Ser880Gly	p.S880G	ENST00000458235	NM_000215.3	880	Agt/Ggt	19/24	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.710583054024745	2		390	1175	SUCCESS
APC	324	MSKCC	GRCh37	5	112175360	112175360	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	178	208	0	ENST00000257430.4:c.4069G>T	p.Gly1357Ter	p.G1357*	ENST00000257430	NM_000038.5	1357	Gga/Tga	16/16	0.326019537827603	2	FACETS	0.992	0.921	1	0.992	0.921	1	CLONAL	2	TRUE	0	0.329171299007499	2		208	545	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795030	242795030	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	344	491	1	ENST00000334409.5:c.179C>A	p.Ser60Ter	p.S60*	ENST00000334409	NM_005018.2	60	tCg/tAg	2/5	0.209741382398973	4	FACETS	0.975	0.922	1	0.975	0.922	1	CLONAL	2	TRUE	2	0.329171299007499	4		492	1424	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864403	162864403	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148990138	NA	P-0009445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	158	323	1	ENST00000366898.1:c.110C>T	p.Pro37Leu	p.P37L	ENST00000366898	NM_004562.2	37	cCg/cTg	2/12	0.31872956721244	3	FACETS	1	0.986	1	0.678	0.622	0.737	CLONAL	1	TRUE	1	0.329171299007499	3		324	824	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1206952	1206952	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	122	199	0	ENST00000326873.7:c.40G>C	p.Glu14Gln	p.E14Q	ENST00000326873	NM_000455.4	14	Gag/Cag	1/10	0.329171299007499	3	FACETS	0.899	0.818	0.984	0.899	0.818	0.984	CLONAL	2	TRUE	1	0.329171299007499	3		199	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579469	7579469	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	131	246	0	ENST00000269305.4:c.218del	p.Val73GlyfsTer50	p.V73Gfs*50	ENST00000269305	NM_001126112.2	73	gTg/gg	4/11	0.326019537827603	2	FACETS	0.761	0.694	0.831	0.761	0.694	0.831	SUBCLONAL	2	TRUE	0	0.329171299007499	2		246	523	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	49	260	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.896	0.774	1	1	0.98	1	CLONAL	3	FALSE	1	0.235222203674486	2		260	155	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0009449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19582	1231	237	0	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.235222203674486	189	FACETS	0.964	0.932	0.996			1	CLONAL	12	FALSE	NA	0.235222203674486	189		237	20813	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722719	49722719	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	24	23	0	ENST00000449682.2:c.1520C>T	p.Pro507Leu	p.P507L	ENST00000449682	NM_020998.3	507	cCc/cTc	13/18	0.196006693439242	1	FACETS	0.9	0.761	1	1	0.968	1	CLONAL	5	FALSE	0	0.235222203674486	1		23	40	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937494	178937494	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	153	263	0	ENST00000263967.3:c.1882C>G	p.Leu628Val	p.L628V	ENST00000263967	NM_006218.2	628	Ctt/Gtt	12/21	1	2	FACETS	1	0.937	1	1	0.994	1	CLONAL	3	FALSE	1	0.235222203674486	2		263	427	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024767	31024767	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1302458782	NA	P-0009449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	156	317	1	ENST00000375687.4:c.4252G>T	p.Gly1418Trp	p.G1418W	ENST00000375687	NM_015338.5	1418	Ggg/Tgg	13/13	0.235222203674486	4	FACETS	0.885	0.814	0.959	0.885	0.814	0.959	CLONAL	3	FALSE	1	0.235222203674486	4		318	617	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	71	260	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.62651240668538	2		260	188	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729925	41729925	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	249	745	0	ENST00000242208.4:c.604A>T	p.Ser202Cys	p.S202C	ENST00000242208	NM_002192.2	202	Agt/Tgt	3/3	0.590564695527455	3	FACETS	0.85	0.794	0.908	0.425	0.397	0.454	CLONAL	1	TRUE	1	0.62651240668538	3		745	1228	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380017	116380017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752842662	NA	P-0009453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	226	524	0	ENST00000397752.3:c.1406G>A	p.Arg469Gln	p.R469Q	ENST00000397752	NM_000245.2	469	cGa/cAa	4/21	0.590564695527455	3	FACETS	0.978	0.911	1	0.489	0.455	0.523	CLONAL	1	TRUE	1	0.62651240668538	3		524	969	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998607	100998607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778889652	NA	P-0009453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	202	535	1	ENST00000325455.5:c.1195C>T	p.Arg399Cys	p.R399C	ENST00000325455	NM_001202474.3	399	Cgc/Tgc	1/8	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.62651240668538	2		536	624	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0009474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	742	570	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.523346763425953	3	FACETS	0.989	0.961	1			1	CLONAL	3	TRUE	NA	0.519607393047093	3		570	1213	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0009474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	623	317	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.523346763425953	3	FACETS	0.939	0.91	0.968	0.939	0.91	0.968	CLONAL	3	TRUE	0	0.519607393047093	3		317	1072	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151564	55151564	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	150	401	0	ENST00000257290.5:c.2350G>C	p.Asp784His	p.D784H	ENST00000257290	NM_006206.4	784	Gat/Cat	17/23	0.505383500889854	2	FACETS	0.773	0.707	0.841	0.386	0.353	0.421	SUBCLONAL	1	TRUE	0	0.519607393047093	2		401	747	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638885	176638885	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	481	378	1	ENST00000439151.2:c.3485G>A	p.Arg1162His	p.R1162H	ENST00000439151	NM_022455.4	1162	cGt/cAt	5/23	0.523346763425953	4	FACETS	0.891	0.851	0.932			1	CLONAL	2	TRUE	NA	0.519607393047093	4		379	1578	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973698	15973698	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	455	314	0	ENST00000268712.3:c.4294C>G	p.Arg1432Gly	p.R1432G	ENST00000268712	NM_006311.3	1432	Cgg/Ggg	31/46	0.523346763425953	3	FACETS	1	0.976	1	0.685	0.656	0.715	CLONAL	2	TRUE	0	0.519607393047093	3		314	1073	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0009478-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	84	318	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.481051438706969	4	FACETS	1	0.977	1	0.47	0.418	0.525	CLONAL	1	TRUE	1	0.481051438706969	4		318	367	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707660	176707660	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009478-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	290	257	2	ENST00000439151.2:c.5717G>T	p.Gly1906Val	p.G1906V	ENST00000439151	NM_022455.4	1906	gGg/gTg	18/23	0.481051438706969	3	FACETS	1	0.957	1	0.676	0.639	0.713	CLONAL	2	TRUE	0	0.481051438706969	3		259	738	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910350	29910350	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009478-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	67	355	1	ENST00000376809.5:c.20G>A	p.Arg7Gln	p.R7Q	ENST00000376809	NM_002116.7	7	cGa/cAa	1/8	0.481051438706969	3	FACETS	0.3	0.26	0.345	0.15	0.13	0.173	SUBCLONAL	1	TRUE	1	0.481051438706969	3		356	1150	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099179	157099179	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009478-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	37	194	0	ENST00000346085.5:c.116C>G	p.Ser39Cys	p.S39C	ENST00000346085	NM_020732.3	39	tCc/tGc	1/20	0.481051438706969	3	FACETS	0.28	0.23	0.337	0.14	0.115	0.169	SUBCLONAL	1	TRUE	1	0.481051438706969	3		194	681	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738518	145738518	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368611522	NA	P-0009478-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	46	121	0	ENST00000428558.2:c.2467G>A	p.Glu823Lys	p.E823K	ENST00000428558	NM_004260.3	823	Gaa/Aaa	16/22	0.481051438706969	4	FACETS	0.573	0.483	0.673	0.191	0.161	0.225	SUBCLONAL	1	TRUE	1	0.481051438706969	4		121	494	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873724	35873724	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs999467784	NA	P-0009478-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	200	412	0	ENST00000216797.5:c.127G>C	p.Glu43Gln	p.E43Q	ENST00000216797	NM_020529.2	43	Gag/Cag	1/6	0.103748358189648	5	FACETS	1	0.985	1	0.311	0.288	0.336	INDETERMINATE	1	TRUE	1	0.481051438706969	5		412	1149	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735464	40735464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009478-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	162	361	0	ENST00000373198.4:c.3409G>A	p.Glu1137Lys	p.E1137K	ENST00000373198	NM_133170.3	1137	Gag/Aag	25/32	0.292987424752715	5	FACETS	0.939	0.859	1	0.313	0.286	0.341	CLONAL	1	TRUE	2	0.481051438706969	5		361	1235	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961505	54961505	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009478-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	70	199	0	ENST00000312783.6:c.127C>T	p.Gln43Ter	p.Q43*	ENST00000312783	NM_198436.1	43	Cag/Tag	4/10	0.292987424752715	5	FACETS	0.684	0.596	0.78	0.228	0.198	0.26	SUBCLONAL	1	TRUE	2	0.481051438706969	5		199	732	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148648	20148648	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009478-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	54	338	0	ENST00000379607.5:c.415G>T	p.Glu139Ter	p.E139*	ENST00000379607	NM_001412.3	139	Gaa/Taa	6/7	0.200923216743067	3	FACETS	0.399	0.34	0.464			1	INDETERMINATE	1	TRUE	NA	0.481051438706969	3		338	698	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156693	20156693	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009478-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	89	434	1	ENST00000379607.5:c.64G>C	p.Glu22Gln	p.E22Q	ENST00000379607	NM_001412.3	22	Gaa/Caa	2/7	0.200923216743067	3	FACETS	0.415	0.366	0.467			1	INDETERMINATE	1	TRUE	NA	0.481051438706969	3		435	1107	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907663	76907663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009478-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	67	674	0	ENST00000373344.5:c.4498G>A	p.Glu1500Lys	p.E1500K	ENST00000373344	NM_000489.3	1500	Gag/Aag	15/35	0.306318388618793	1	FACETS	0.185	0.16	0.213	0.185	0.16	0.213	SUBCLONAL	1	TRUE	0	0.481051438706969	1		674	1142	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443468	49443469	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0009478-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	155	187	0	ENST00000301067.7:c.3902_3903del	p.Lys1301ThrfsTer23	p.K1301Tfs*23	ENST00000301067	NM_003482.3	1301	aAA/a	11/54	0.481051438706969	2	FACETS	1	0.978	1	0.589	0.542	0.637	CLONAL	1	TRUE	0	0.481051438706969	2		187	547	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860750	151860752	+	frameshift_variant	Frame_Shift_Del	DEL	AAA	AAA	T	novel	NA	P-0009478-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	392	290	0	ENST00000262189.6:c.9910_9912delinsA	p.Phe3304ThrfsTer21	p.F3304Tfs*21	ENST00000262189	NM_170606.2	3304	TTT/A	43/59	1	2	FACETS	1	0.979	1	1	0.997	1	CLONAL	2	TRUE	1	0.481051438706969	2		290	787	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241679	55241681	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	rs397517086	NA	P-0009481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	197	800	0	ENST00000275493.2:c.2127_2129del	p.Glu709_Thr710delinsAsp	p.E709_T710delinsD	ENST00000275493	NM_005228.3	709	gaAACt/gat	18/28	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.31	2		800	953	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150545	157150545	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	56	189	0	ENST00000346085.5:c.1727C>G	p.Pro576Arg	p.P576R	ENST00000346085	NM_020732.3	576	cCt/cGt	2/20	0.196060733876177	1	FACETS	0.756	0.649	0.871	0.756	0.649	0.871	SUBCLONAL	1	TRUE	0	0.31	1		189	404	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186757	108186757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs864622251	NA	P-0009481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	223	474	0	ENST00000278616.4:c.6115G>A	p.Glu2039Lys	p.E2039K	ENST00000278616	NM_000051.3	2039	Gaa/Aaa	42/63	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.31	2		474	1093	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911472	101911472	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	40	282	0	ENST00000374994.4:c.1397del	p.Val466GlufsTer6	p.V466Efs*6	ENST00000374994	NM_004612.2	466	gTa/ga	9/9	0.3	1	FACETS	0.472	0.392	0.561	0.472	0.392	0.561	SUBCLONAL	1	TRUE	0	0.31	1		282	462	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912049	76912049	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0009481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	240	517	0	ENST00000373344.5:c.4214+1del		p.X1405_splice	ENST00000373344	NM_000489.3	1405			1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.31	2		517	1219	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360516	118360516	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009482-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	291	469	0	ENST00000534358.1:c.4489G>T	p.Glu1497Ter	p.E1497*	ENST00000534358	NM_005933.3	1497	Gag/Tag	12/36	0.335358898178451	3	FACETS	1	0.989	1	0.792	0.748	0.836	CLONAL	2	TRUE	0	0.368584199872343	3		469	787	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	50	221	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.608	0.514	0.711	0.608	0.514	0.711	SUBCLONAL	1	TRUE	1	0.19	2		222	866	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0009487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	49	471	3	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	NA	2	FACETS	0.986	0.835	1			1	INDETERMINATE	1	TRUE	NA	0.19	2		474	523	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143993	11143993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568509370	NA	P-0009487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	85	253	0	ENST00000358026.2:c.3574C>T	p.Arg1192Cys	p.R1192C	ENST00000358026	NM_001128849.1	1192	Cgc/Tgc	26/36	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.19	2		253	636	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587167	212587167	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	163	348	0	ENST00000342788.4:c.834T>A	p.Asn278Lys	p.N278K	ENST00000342788	NM_005235.2	278	aaT/aaA	7/28	0.134801473801252	3	FACETS	0.786	0.72	0.856	0.786	0.72	0.856	SUBCLONAL	2	TRUE	1	0.19	3		348	1195	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0009490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	351	306	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	0.554971049974584	3	FACETS	0.915	0.879	0.949			1	CLONAL	3	TRUE	NA	0.61041510052087	3		306	547	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289678	33289678	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	66	229	0	ENST00000374542.5:c.25G>T	p.Val9Leu	p.V9L	ENST00000374542	NM_001141970.1	9	Gtg/Ttg	2/8	0.351975904211286	5	FACETS	0.827	0.719	0.943	0.276	0.239	0.315	INDETERMINATE	1	TRUE	2	0.61041510052087	5		229	501	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0009505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	804	608	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.447542861713398	3	FACETS	0.885	0.858	0.912			1	CLONAL	3	TRUE	NA	0.447542861713398	3		608	1656	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198396	108198396	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	174	460	0	ENST00000278616.4:c.7000T>G	p.Tyr2334Asp	p.Y2334D	ENST00000278616	NM_000051.3	2334	Tac/Gac	48/63	0.443197001120272	1	FACETS	0.872	0.806	0.941	0.872	0.806	0.941	CLONAL	1	TRUE	0	0.447542861713398	1		460	692	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219344	1219344	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	462	619	0	ENST00000326873.7:c.396del	p.Cys132TrpfsTer29	p.C132Wfs*29	ENST00000326873	NM_000455.4	132	tgC/tg	3/10	0.4208319620825	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.447542861713398	2		619	1008	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0009507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	148	326	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.15847396876333	5	FACETS	0.895	0.826	0.966	1	0.98	1	INDETERMINATE	4	TRUE	2	0.29	5		326	409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0009507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	252	313	0	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	0.3	9	FACETS	1	0.987	1			1	CLONAL	11	TRUE	NA	0.29	9		313	306	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939418	76939418	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	162	370	0	ENST00000373344.5:c.1330C>T	p.Arg444Ter	p.R444*	ENST00000373344	NM_000489.3	444	Cga/Tga	9/35	0.3	2	FACETS	1	0.952	1	1	0.994	1	CLONAL	4	TRUE	0	0.29	2		370	275	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046362	128046362	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs753495508	NA	P-0009507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	60	460	0	ENST00000285398.2:c.901T>G	p.Ser301Ala	p.S301A	ENST00000285398	NM_000122.1	301	Tct/Gct	7/15	0.3	1	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	0	0.29	1		460	349	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144122	11144122	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	62	493	1	ENST00000358026.2:c.3703G>T	p.Asp1235Tyr	p.D1235Y	ENST00000358026	NM_001128849.1	1235	Gac/Tac	26/36	0.08278616166348	0	FACETS	0.703	0.616	0.794			1	INDETERMINATE	2	TRUE	0	0.29	0		494	216	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541967	187541967	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	85	505	0	ENST00000441802.2:c.5773del	p.Glu1925ArgfsTer20	p.E1925Rfs*20	ENST00000441802	NM_005245.3	1925	Gag/ag	10/27	0.3	1	FACETS	1	0.932	1	1	0.987	1	CLONAL	2	TRUE	0	0.29	1		505	239	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009516-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	8	515	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	0.169986620119874	1	FACETS	0.204	0.13	0.299	0.204	0.13	0.299	SUBCLONAL	1	FALSE	0	0.23580982148725	1		515	294	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0009520-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	21	143	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.458119762079247	5	FACETS	0.83	0.66	1	0.553	0.44	0.677	INDETERMINATE	2	FALSE	2	0.814854605159771	5		143	69	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009530-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	177	221	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.263282423354562	3	FACETS	0.871	0.804	0.941	0.871	0.804	0.941	CLONAL	2	TRUE	1	0.283117423975192	3		222	819	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93973599	93973599	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750462795	NA	P-0009530-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1291	374	667	0	ENST00000369303.4:c.1777G>A	p.Asp593Asn	p.D593N	ENST00000369303	NM_004440.3	593	Gat/Aat	9/17	0.283117423975192	3	FACETS	0.906	0.857	0.955	0.906	0.857	0.955	CLONAL	2	TRUE	1	0.283117423975192	3		667	1665	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400212	139400212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764123906	NA	P-0009530-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	61	344	0	ENST00000277541.6:c.4136C>T	p.Thr1379Met	p.T1379M	ENST00000277541	NM_017617.3	1379	aCg/aTg	25/34	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.283117423975192	2		344	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578538	7578538	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1131691037	NA	P-0009530-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	208	386	0	ENST00000269305.4:c.392A>T	p.Asn131Ile	p.N131I	ENST00000269305	NM_001126112.2	131	aAc/aTc	5/11	NA	2	FACETS	1	0.968	1			1	INDETERMINATE	2	TRUE	NA	0.283117423975192	2		386	691	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943345	17943345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009530-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	103	471	0	ENST00000458235.1:c.2663G>A	p.Gly888Asp	p.G888D	ENST00000458235	NM_000215.3	888	gGt/gAt	19/24	0.283117423975192	3	FACETS	0.982	0.878	1			1	CLONAL	1	TRUE	NA	0.283117423975192	3		471	846	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0009558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	102	531	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		531	734	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685315	89685315	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1554897280	NA	P-0009564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	112	325	0	ENST00000371953.3:c.209+1G>T		p.X70_splice	ENST00000371953	NM_000314.4	70			0.630782594126034	1	FACETS	0.914	0.837	0.992	0.914	0.837	0.992	CLONAL	1	TRUE	0	0.630782594126034	1		325	266	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0009564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	354	523	0	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	0.630782594126034	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.630782594126034	1		523	708	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8105965	8105965	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	276	297	0	ENST00000346208.3:c.785A>T	p.Glu262Val	p.E262V	ENST00000346208		262	gAg/gTg	4/6	0.62537341488942	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.630782594126034	1		297	541	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658553	206658553	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009590-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	62	383	0	ENST00000367120.3:c.1526G>T	p.Cys509Phe	p.C509F	ENST00000367120	NM_014002.3	509	tGc/tTc	15/22	0.160484183868342	3	FACETS	0.774	0.667	0.89	0.387	0.333	0.445	SUBCLONAL	1	TRUE	1	0.24	3		383	748	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794444	242794444	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009590-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	40	492	0	ENST00000334409.5:c.498C>G	p.Phe166Leu	p.F166L	ENST00000334409	NM_005018.2	166	ttC/ttG	3/5	1	2	FACETS	0.426	0.352	0.508	0.426	0.352	0.508	SUBCLONAL	1	TRUE	1	0.24	2		492	783	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200374	138200374	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009590-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	26	245	1	ENST00000237289.4:c.1792C>T	p.Pro598Ser	p.P598S	ENST00000237289	NM_001270507.1	598	Cct/Tct	7/9	1	2	FACETS	0.45	0.356	0.559	0.45	0.356	0.559	SUBCLONAL	1	TRUE	1	0.24	2		246	481	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778535	3778535	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009590-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	78	691	0	ENST00000262367.5:c.6513G>C	p.Leu2171Phe	p.L2171F	ENST00000262367	NM_004380.2	2171	ttG/ttC	31/31	1	2	FACETS	0.635	0.557	0.72	0.635	0.557	0.72	SUBCLONAL	1	TRUE	1	0.24	2		691	1023	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221229	1221229	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009590-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	229	676	1	ENST00000326873.7:c.752G>T	p.Gly251Val	p.G251V	ENST00000326873	NM_000455.4	251	gGt/gTt	6/10	NA	2	FACETS	0.816	0.76	0.875			1	INDETERMINATE	2	TRUE	NA	0.24	2		677	1169	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602872	10602872	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009590-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	116	477	1	ENST00000171111.5:c.706G>T	p.Asp236Tyr	p.D236Y	ENST00000171111	NM_203500.1	236	Gac/Tac	3/6	0.17348717497036	2	FACETS	1	0.972	1	0.61	0.55	0.674	CLONAL	1	TRUE	0	0.24	2		478	792	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953319	17953319	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009590-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	40	357	1	ENST00000458235.1:c.667C>T	p.Arg223Cys	p.R223C	ENST00000458235	NM_000215.3	223	Cgc/Tgc	6/24	0.17348717497036	2	FACETS	0.559	0.464	0.666	0.28	0.232	0.333	SUBCLONAL	1	TRUE	0	0.24	2		358	596	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2206769	2206777	+	inframe_deletion	In_Frame_Del	DEL	TTCAGAATA	TTCAGAATA	-	novel	NA	P-0009590-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	210	655	0	ENST00000398665.3:c.829_837del	p.Phe277_Ile279del	p.F277_I279del	ENST00000398665	NM_032482.2	277	TTCAGAATA/-	10/28	0.17348717497036	2	FACETS	1	0.987	1	0.65	0.602	0.7	CLONAL	1	TRUE	0	0.24	2		655	1346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0009598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	223	510	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.295950681714073	1	FACETS	0.834	0.777	0.891	1	0.993	1	CLONAL	2	TRUE	0	0.27	1		510	857	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057302	30057302	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315496	NA	P-0009598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	125	344	0	ENST00000338641.4:c.784C>T	p.Arg262Ter	p.R262*	ENST00000338641	NM_000268.3	262	Cga/Tga	8/16	0.295950681714073	1	FACETS	0.761	0.692	0.833	1	0.986	1	SUBCLONAL	2	TRUE	0	0.27	1		344	526	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654634	29654634	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	58	452	0	ENST00000356175.3:c.5323G>T	p.Glu1775Ter	p.E1775*	ENST00000356175	NM_000267.3	1775	Gag/Tag	37/57	0.282748329523936	2	FACETS	0.544	0.466	0.629	0.272	0.233	0.315	SUBCLONAL	1	TRUE	0	0.27	2		452	790	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143033	47143033	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	180	454	0	ENST00000409792.3:c.4930G>T	p.Gly1644Ter	p.G1644*	ENST00000409792	NM_014159.6	1644	Gga/Tga	8/21	0.532109566193378	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.532109566193378	1		454	464	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440393	52440393	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0009606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	97	225	1	ENST00000460680.1:c.660-1G>A		p.X220_splice	ENST00000460680	NM_004656.3	220			0.532109566193378	1	FACETS	0.926	0.837	1	0.926	0.837	1	CLONAL	1	TRUE	0	0.532109566193378	1		226	289	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866987936	NA	P-0009606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	86	281	1	ENST00000281708.4:c.1436G>T	p.Arg479Leu	p.R479L	ENST00000281708	NM_033632.3	479	cGa/cTa	10/12	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.532109566193378	2		282	310	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175437	108175437	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0009606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	153	422	0	ENST00000278616.4:c.5532C>G	p.Tyr1844Ter	p.Y1844*	ENST00000278616	NM_000051.3	1844	taC/taG	37/63	0.532109566193378	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.532109566193378	1		422	386	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051615	30051615	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	184	517	0	ENST00000338641.4:c.549G>A	p.Met183Ile	p.M183I	ENST00000338641	NM_000268.3	183	atG/atA	6/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.532109566193378	2		517	665	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0009635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	225	426	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.477728693060244	3	FACETS	0.92	0.856	0.988	0.46	0.428	0.494	CLONAL	1	TRUE	1	0.477728693060244	3		426	1268	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913517	NA	P-0009648-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	4093	605	0	ENST00000288135.5:c.1676T>C	p.Val559Ala	p.V559A	ENST00000288135	NM_000222.2	559	gTt/gCt	11/21	0.873760718722156	14	FACETS	1	0.999	1			1	CLONAL	13	TRUE	NA	0.873760718722156	14		605	4370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0009661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	55	552	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.336	0.286	0.39	0.336	0.286	0.39	SUBCLONAL	1	TRUE	1	0.330740102284966	2		552	991	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0009661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	272	386	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.330740102284966	3	FACETS	0.808	0.758	0.86	0.808	0.758	0.86	CLONAL	2	TRUE	1	0.330740102284966	3		386	1186	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210075	55210075	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1314	401	576	0	ENST00000275493.2:c.185T>G	p.Leu62Arg	p.L62R	ENST00000275493	NM_005228.3	62	cTt/cGt	2/28	0.330740102284966	3	FACETS	0.824	0.781	0.867	0.824	0.781	0.867	CLONAL	2	TRUE	1	0.330740102284966	3		576	1715	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578250	7578250	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1131691011	NA	P-0009661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	124	507	0	ENST00000269305.4:c.599del	p.Asn200IlefsTer47	p.N200Ifs*47	ENST00000269305	NM_001126112.2	200	aAt/at	6/11	1	2	FACETS	0.608	0.548	0.671	0.608	0.548	0.671	SUBCLONAL	1	TRUE	1	0.330740102284966	2		507	1233	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921808	111921808	+	stop_lost	Nonstop_Mutation	SNP	A	A	T	novel	NA	P-0009661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	49	344	0	ENST00000393256.3:c.597A>T	p.Ter199CysextTer70	p.*199Cext*70	ENST00000393256	NM_006538.4	199	tgA/tgT	4/4	1	2	FACETS	0.339	0.286	0.398	0.339	0.286	0.398	SUBCLONAL	1	TRUE	1	0.330740102284966	2		344	873	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0009682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	50	381	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.839	0.709	0.983	1	0.968	1	CLONAL	2	TRUE	1	0.06	2		381	993	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268881	98268881	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	26	193	0	ENST00000331920.6:c.202G>A	p.Gly68Arg	p.G68R	ENST00000331920	NM_000264.3	68	Ggg/Agg	2/24	1	2	FACETS	0.863	0.682	1	1	0.942	1	CLONAL	2	TRUE	1	0.06	2		193	502	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220717	1220717	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs587782018	NA	P-0009682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	68	355	0	ENST00000326873.7:c.734+1G>C		p.X245_splice	ENST00000326873	NM_000455.4	245			1	2	FACETS	1	0.953	1	1	0.983	1	CLONAL	2	TRUE	1	0.06	2		355	929	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0009691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	127	648	2	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.168660969318574	2		650	1181	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073323	8073323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1573	140	839	0	ENST00000377482.5:c.1336G>T	p.Asp446Tyr	p.D446Y	ENST00000377482	NM_018948.3	446	Gat/Tat	4/4	1	2	FACETS	0.969	0.879	1	0.969	0.879	1	CLONAL	1	TRUE	1	0.168660969318574	2		839	1713	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796865	45796865	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782263	NA	P-0009691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	39	351	0	ENST00000450313.1:c.1465G>T	p.Ala489Ser	p.A489S	ENST00000450313	NM_012222.2	489	Gcc/Tcc	14/16	1	2	FACETS	0.599	0.495	0.716	0.599	0.495	0.716	SUBCLONAL	1	TRUE	1	0.168660969318574	2		351	772	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798613	45798613	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	42	362	0	ENST00000450313.1:c.481G>T	p.Asp161Tyr	p.D161Y	ENST00000450313	NM_012222.2	161	Gac/Tac	6/16	1	2	FACETS	0.699	0.582	0.83	0.699	0.582	0.83	SUBCLONAL	1	TRUE	1	0.168660969318574	2		362	712	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153657	55153657	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1325	146	665	0	ENST00000257290.5:c.2623C>A	p.Leu875Met	p.L875M	ENST00000257290	NM_006206.4	875	Ctg/Atg	19/23	0.168660969318574	3	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.168660969318574	3		665	1471	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593669	55593669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	167	448	2	ENST00000288135.5:c.1735G>T	p.Asp579Tyr	p.D579Y	ENST00000288135	NM_000222.2	579	Gat/Tat	11/21	0.168660969318574	3	FACETS	1	0.934	1			1	CLONAL	2	TRUE	NA	0.168660969318574	3		450	1052	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946329	55946329	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	33	256	0	ENST00000263923.4:c.3850G>C	p.Gly1284Arg	p.G1284R	ENST00000263923	NM_002253.2	1284	Gga/Cga	30/30	0.168660969318574	3	FACETS	0.747	0.607	0.905			1	CLONAL	1	TRUE	NA	0.168660969318574	3		256	568	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242776	66242776	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	119	446	0	ENST00000273854.3:c.1796G>T	p.Cys599Phe	p.C599F	ENST00000273854	NM_004439.5	599	tGc/tTc	9/18	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.168660969318574	2		446	1012	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729968	41729968	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1379	154	899	0	ENST00000242208.4:c.561C>A	p.Asp187Glu	p.D187E	ENST00000242208	NM_002192.2	187	gaC/gaA	3/3	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.168660969318574	2		899	1533	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459467	50459467	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	91	390	0	ENST00000331340.3:c.756C>G	p.Asp252Glu	p.D252E	ENST00000331340	NM_006060.4	252	gaC/gaG	7/8	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.168660969318574	2		390	901	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492867	8492867	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	143	440	0	ENST00000356435.5:c.2462G>T	p.Gly821Val	p.G821V	ENST00000356435		821	gGg/gTg	16/35	1	2	FACETS	0.844	0.769	0.924	1	0.989	1	CLONAL	2	TRUE	1	0.168660969318574	2		440	1004	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518363	8518363	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	96	343	0	ENST00000356435.5:c.1028G>T	p.Trp343Leu	p.W343L	ENST00000356435		343	tGg/tTg	10/35	1	2	FACETS	0.901	0.803	1	1	0.985	1	CLONAL	2	TRUE	1	0.168660969318574	2		343	632	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451003	70451003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	42	424	1	ENST00000373644.4:c.5843C>T	p.Ser1948Phe	p.S1948F	ENST00000373644	NM_030625.2	1948	tCt/tTt	12/12	1	2	FACETS	0.639	0.531	0.758	0.639	0.531	0.758	SUBCLONAL	1	TRUE	1	0.168660969318574	2		425	780	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416218	416218	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs368037236	NA	P-0009691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1263	113	577	1	ENST00000399788.2:c.3968G>T	p.Arg1323Leu	p.R1323L	ENST00000399788	NM_001042603.1	1323	cGg/cTg	24/28	0.168660969318574	3	FACETS	1	0.934	1			1	CLONAL	1	TRUE	NA	0.168660969318574	3		578	1376	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117759	115117759	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	87	562	1	ENST00000257566.3:c.676G>T	p.Asp226Tyr	p.D226Y	ENST00000257566	NM_016569.3	226	Gat/Tat	3/8	1	2	FACETS	0.931	0.822	1	0.931	0.822	1	CLONAL	1	TRUE	1	0.168660969318574	2		563	1108	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36989288	36989288	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	153	580	1	ENST00000354822.5:c.47C>A	p.Ala16Glu	p.A16E	ENST00000354822	NM_001079668.2	16	gCg/gAg	1/3	1	2	FACETS	0.858	0.784	0.936	1	0.99	1	CLONAL	2	TRUE	1	0.168660969318574	2		581	1057	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023013	33023013	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	69	765	0	ENST00000300177.4:c.122A>C	p.His41Pro	p.H41P	ENST00000300177	NM_001191322.1	41	cAc/cCc	2/2	0.168660969318574	1	FACETS	0.685	0.595	0.784	0.685	0.595	0.784	SUBCLONAL	1	TRUE	0	0.168660969318574	1		765	1093	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273974	10273974	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	123	640	0	ENST00000330684.3:c.295G>C	p.Val99Leu	p.V99L	ENST00000330684	NM_001134407.1	99	Gtg/Ctg	2/13	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.168660969318574	2		640	1052	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645032	67645032	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	60	499	1	ENST00000264010.4:c.297G>T	p.Gln99His	p.Q99H	ENST00000264010	NM_006565.3	99	caG/caT	3/12	1	2	FACETS	0.759	0.652	0.877	0.759	0.652	0.877	SUBCLONAL	1	TRUE	1	0.168660969318574	2		500	937	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923738	72923738	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	70	772	0	ENST00000268489.5:c.3340C>G	p.Arg1114Gly	p.R1114G	ENST00000268489	NM_006885.3	1114	Cga/Gga	4/10	1	2	FACETS	0.654	0.568	0.748	0.654	0.568	0.748	SUBCLONAL	1	TRUE	1	0.168660969318574	2		772	1269	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220488	1220488	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913316	NA	P-0009691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	94	444	0	ENST00000326873.7:c.581A>T	p.Asp194Val	p.D194V	ENST00000326873	NM_000455.4	194	gAc/gTc	4/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.168660969318574	2		444	884	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523275	9523275	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	132	659	0	ENST00000353224.5:c.1962G>T	p.Arg654Ser	p.R654S	ENST00000353224	NM_177990.2	654	agG/agT	9/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.168660969318574	2		659	1165	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714387	40714387	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	78	428	0	ENST00000373198.4:c.4010G>T	p.Arg1337Leu	p.R1337L	ENST00000373198	NM_133170.3	1337	cGc/cTc	29/32	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.168660969318574	2		428	852	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0009698-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	40	381	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.691	0.572	0.823	0.691	0.572	0.823	SUBCLONAL	1	TRUE	1	0.16	2		381	724	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239902	41239902	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009698-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	24	139	0	ENST00000379561.5:c.448C>T	p.Arg150Cys	p.R150C	ENST00000379561	NM_002015.3	150	Cgc/Tgc	1/3	1	2	FACETS	1	0.801	1	1	0.801	1	CLONAL	1	TRUE	1	0.16	2		139	294	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039140	49039140	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009698-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	41	265	0	ENST00000267163.4:c.2218A>G	p.Lys740Glu	p.K740E	ENST00000267163	NM_000321.2	740	Aaa/Gaa	22/27	1	2	FACETS	0.839	0.697	0.996	0.839	0.697	0.996	CLONAL	1	TRUE	1	0.16	2		265	611	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306545	41306545	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009698-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	64	380	0	ENST00000373198.4:c.1114C>A	p.Pro372Thr	p.P372T	ENST00000373198	NM_133170.3	372	Ccg/Acg	7/32	1	2	FACETS	0.86	0.743	0.988	0.86	0.743	0.988	CLONAL	1	TRUE	1	0.16	2		380	930	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0009725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	201	271	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.197354464456817	2	FACETS	0.776	0.723	0.83	0.776	0.723	0.83	INDETERMINATE	2	TRUE	0	0.41455162035275	2		271	625	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0009725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	286	544	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.364271888307614	1	FACETS	0.979	0.921	1	0.979	0.921	1	CLONAL	1	TRUE	0	0.41455162035275	1		544	1117	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082526	16082526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	71	250	0	ENST00000281043.3:c.340G>A	p.Asp114Asn	p.D114N	ENST00000281043	NM_005378.4	114	Gac/Aac	2/3	0.41455162035275	1	FACETS	0.521	0.455	0.592	0.521	0.455	0.592	SUBCLONAL	1	TRUE	0	0.41455162035275	1		250	521	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437747	52437747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1419	315	725	0	ENST00000460680.1:c.1414G>A	p.Gly472Arg	p.G472R	ENST00000460680	NM_004656.3	472	Ggg/Agg	13/17	1	2	FACETS	0.876	0.824	0.93	0.876	0.824	0.93	CLONAL	1	TRUE	1	0.41455162035275	2		725	1734	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429022	47429022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	274	522	0	ENST00000377045.4:c.1385C>T	p.Pro462Leu	p.P462L	ENST00000377045	NM_001654.4	462	cCc/cTc	13/16	1	2	FACETS	0.924	0.866	0.985	0.924	0.866	0.985	CLONAL	1	TRUE	1	0.41455162035275	2		522	1430	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0009735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	59	552	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.105676094198791	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.666733797737965	0		552	885	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216545	108216545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779872	NA	P-0009735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	393	452	0	ENST00000278616.4:c.8494C>T	p.Arg2832Cys	p.R2832C	ENST00000278616	NM_000051.3	2832	Cgt/Tgt	58/63	0.666733797737965	1	FACETS	0.918	0.878	0.959	0.918	0.878	0.959	CLONAL	1	TRUE	0	0.666733797737965	1		452	856	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845580	151845580	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1287135873	NA	P-0009735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	327	262	0	ENST00000262189.6:c.13432C>T	p.Arg4478Ter	p.R4478*	ENST00000262189	NM_170606.2	4478	Cga/Tga	52/59	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.666733797737965	2		262	972	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420190	49420190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775954885	NA	P-0009735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	170	325	2	ENST00000301067.7:c.15559G>A	p.Ala5187Thr	p.A5187T	ENST00000301067	NM_003482.3	5187	Gcc/Acc	48/54	0.309563880499328	1	FACETS	0.406	0.374	0.44	0.406	0.374	0.44	INDETERMINATE	1	TRUE	0	0.666733797737965	1		327	837	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306677	41306677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs724159835	NA	P-0009735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	116	347	0	ENST00000373198.4:c.982C>T	p.Arg328Cys	p.R328C	ENST00000373198	NM_133170.3	328	Cgc/Tgc	7/32	1	2	FACETS	0.35	0.315	0.388	0.35	0.315	0.388	SUBCLONAL	1	TRUE	1	0.666733797737965	2		347	993	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032551	47032551	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1198280152	NA	P-0009735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	262	237	0	ENST00000377604.3:c.457G>A	p.Gly153Ser	p.G153S	ENST00000377604	NM_001204468.1	153	Ggc/Agc	5/24	1	1	FACETS	0.693	0.652	0.735	0.693	0.652	0.735	SUBCLONAL	1	TRUE	0	0.666733797737965	1		237	756	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656262	18656262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774333984	NA	P-0009735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	57	366	0	ENST00000266497.5:c.2941C>T	p.Arg981Cys	p.R981C	ENST00000266497		981	Cgc/Tgc	21/31	0.309563880499328	1	FACETS	0.129	0.11	0.149	0.129	0.11	0.149	INDETERMINATE	1	TRUE	0	0.666733797737965	1		366	887	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462643	29462643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs187200776	NA	P-0009735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	191	461	0	ENST00000389048.3:c.2258G>A	p.Arg753Gln	p.R753Q	ENST00000389048	NM_004304.4	753	cGg/cAg	13/29	0.666733797737965	1	FACETS	0.44	0.407	0.474	0.44	0.407	0.474	SUBCLONAL	1	TRUE	0	0.666733797737965	1		461	868	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526314	189526314	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	26	146	0	ENST00000264731.3:c.578C>T	p.Thr193Met	p.T193M	ENST00000264731	NM_003722.4	193	aCg/aTg	4/14	0.666733797737965	1	FACETS	0.176	0.139	0.218	0.176	0.139	0.218	SUBCLONAL	1	TRUE	0	0.666733797737965	1		146	295	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975385	13975385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	47	225	0	ENST00000405192.2:c.502C>T	p.His168Tyr	p.H168Y	ENST00000405192	NM_001163147.1	168	Cac/Tac	7/12	1	2	FACETS	0.179	0.15	0.211	0.179	0.15	0.211	SUBCLONAL	1	TRUE	1	0.666733797737965	2		225	788	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845229	151845229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	51	218	0	ENST00000262189.6:c.13783C>T	p.Arg4595Cys	p.R4595C	ENST00000262189	NM_170606.2	4595	Cgc/Tgc	52/59	1	2	FACETS	0.188	0.159	0.22	0.188	0.159	0.22	SUBCLONAL	1	TRUE	1	0.666733797737965	2		218	814	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156011	119156011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143034856	NA	P-0009735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	256	438	1	ENST00000264033.4:c.1676G>A	p.Arg559Gln	p.R559Q	ENST00000264033	NM_005188.3	559	cGa/cAa	11/16	0.666733797737965	1	FACETS	0.5	0.468	0.533	0.5	0.468	0.533	SUBCLONAL	1	TRUE	0	0.666733797737965	1		439	1024	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95577662	95577662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1270	92	504	0	ENST00000393063.1:c.2248C>T	p.Pro750Ser	p.P750S	ENST00000393063	NM_030621.3	750	Cca/Tca	15/28	0.344565254175344	1	FACETS	0.135	0.119	0.152	0.135	0.119	0.152	INDETERMINATE	1	TRUE	0	0.666733797737965	1		504	1362	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217623	7217623	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	237	509	1	ENST00000380728.2:c.304C>T	p.Arg102Ter	p.R102*	ENST00000380728		102	Cga/Tga	4/11	0.105676094198791	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.666733797737965	0		510	1433	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246061	41246061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28897677	NA	P-0009735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	131	291	0	ENST00000357654.3:c.1487G>A	p.Arg496His	p.R496H	ENST00000357654	NM_007294.3	496	cGt/cAt	10/23	NA	2	FACETS	0.42	0.381	0.462			1	INDETERMINATE	1	TRUE	NA	0.666733797737965	2		291	935	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136107	11136107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749947536	NA	P-0009735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	199	438	0	ENST00000358026.2:c.3091G>A	p.Gly1031Ser	p.G1031S	ENST00000358026	NM_001128849.1	1031	Ggc/Agc	22/36	1	2	FACETS	0.526	0.486	0.567	0.526	0.486	0.567	SUBCLONAL	1	TRUE	1	0.666733797737965	2		438	1135	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902197	50902197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765969481	NA	P-0009735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1729	94	701	0	ENST00000440232.2:c.89G>A	p.Arg30Gln	p.R30Q	ENST00000440232	NM_002691.3	30	cGg/cAg	2/27	1	2	FACETS	0.155	0.137	0.174	0.155	0.137	0.174	SUBCLONAL	1	TRUE	1	0.666733797737965	2		701	1823	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841277	15841277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746617360	NA	P-0009735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	63	165	0	ENST00000307771.7:c.1361G>A	p.Arg454Gln	p.R454Q	ENST00000307771	NM_005089.3	454	cGg/cAg	11/11	1	1	FACETS	0.227	0.196	0.26	0.227	0.196	0.26	SUBCLONAL	1	TRUE	0	0.666733797737965	1		165	555	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921580	39921580	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	77	187	0	ENST00000378444.4:c.4240C>T	p.Gln1414Ter	p.Q1414*	ENST00000378444	NM_001123385.1	1414	Cag/Tag	10/15	1	1	FACETS	0.192	0.168	0.218	0.192	0.168	0.218	SUBCLONAL	1	TRUE	0	0.666733797737965	1		187	801	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932711	39932711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	314	331	0	ENST00000378444.4:c.1888G>A	p.Glu630Lys	p.E630K	ENST00000378444	NM_001123385.1	630	Gag/Aag	4/15	1	1	FACETS	0.653	0.618	0.69	0.653	0.618	0.69	SUBCLONAL	1	TRUE	0	0.666733797737965	1		331	961	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148526849	148526849	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	57	393	0	ENST00000320356.2:c.455del	p.Asn152IlefsTer15	p.N152Ifs*15	ENST00000320356	NM_004456.4	152	aAt/at	5/20	1	2	FACETS	0.152	0.13	0.177	0.152	0.13	0.177	SUBCLONAL	1	TRUE	1	0.666733797737965	2		393	1122	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0009739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	253	624	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.120528052441029	3	FACETS	0.846	0.797	0.897	0.846	0.797	0.897	INDETERMINATE	3	TRUE	0	0.353066143817764	3		624	664	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36989307	36989307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	105	473	0	ENST00000354822.5:c.28C>T	p.Arg10Trp	p.R10W	ENST00000354822	NM_001079668.2	10	Cgg/Tgg	1/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.353066143817764	2		473	480	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587404	29587404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564989006	NA	P-0009739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	96	425	0	ENST00000356175.3:c.4385C>T	p.Ala1462Val	p.A1462V	ENST00000356175	NM_000267.3	1462	gCa/gTa	33/57	0.120528052441029	3	FACETS	0.922	0.822	1	0.307	0.274	0.343	INDETERMINATE	1	TRUE	0	0.353066143817764	3		425	694	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298128	15298128	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	97	409	0	ENST00000263388.2:c.1628A>T	p.Asp543Val	p.D543V	ENST00000263388	NM_000435.2	543	gAt/gTt	11/33	0.171248984843186	2	FACETS	1	0.964	1	0.588	0.527	0.653	INDETERMINATE	1	TRUE	0	0.353066143817764	2		409	467	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748443	40748443	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	136	647	0	ENST00000392038.2:c.439G>A	p.Val147Met	p.V147M	ENST00000392038	NM_001626.4	147	Gtg/Atg	5/14	1	2	FACETS	0.939	0.851	1	0.939	0.851	1	CLONAL	1	TRUE	1	0.23891055394922	2		647	1213	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411874	116411902	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	ACAAGCTCTTTCTTTCTCTCTGTTTTAAG	ACAAGCTCTTTCTTTCTCTCTGTTTTAAG	-	novel	NA	P-0009742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	153	246	0	ENST00000397752.3:c.2888-28_2888del		p.X963_splice	ENST00000397752	NM_000245.2	963			0.23891055394922	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.23891055394922	2		246	527	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0009751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	189	354	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.214224845873774	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.214224845873774	2		354	783	SUCCESS
APC	324	MSKCC	GRCh37	5	112175772	112175772	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	50	301	0	ENST00000257430.4:c.4483del	p.Ser1495ValfsTer12	p.S1495Vfs*12	ENST00000257430	NM_000038.5	1494	gAa/ga	16/16	1	2	FACETS	0.864	0.733	1	0.864	0.733	1	CLONAL	1	TRUE	1	0.214224845873774	2		301	540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579317	7579317	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs730881997	NA	P-0009751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	134	325	0	ENST00000269305.4:c.370T>G	p.Cys124Gly	p.C124G	ENST00000269305	NM_001126112.2	124	Tgc/Ggc	4/11	0.214224845873774	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	0	0.214224845873774	2		325	615	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459687	40459687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1206	138	784	2	ENST00000345506.4:c.1852C>T	p.Arg618Cys	p.R618C	ENST00000345506	NM_003152.3	618	Cgc/Tgc	16/20	0.214224845873774	2	FACETS	0.959	0.87	1	0.479	0.435	0.527	CLONAL	1	TRUE	0	0.214224845873774	2		786	1344	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593466	48593466	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	68	371	0	ENST00000342988.3:c.1217C>A	p.Ala406Glu	p.A406E	ENST00000342988	NM_005359.5	406	gCg/gAg	10/12	0.214224845873774	1	FACETS	0.908	0.79	1	0.908	0.79	1	CLONAL	1	TRUE	0	0.214224845873774	1		371	624	SUCCESS
APC	324	MSKCC	GRCh37	5	112173902	112173902	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1554084299	NA	P-0009751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	56	290	0	ENST00000257430.4:c.2612del	p.Gly871GlufsTer45	p.G871Efs*45	ENST00000257430	NM_000038.5	871	Gga/ga	16/16	1	2	FACETS	0.776	0.664	0.898	0.776	0.664	0.898	SUBCLONAL	1	TRUE	1	0.214224845873774	2		290	674	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0009754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	70	552	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.277385246362661	2		552	406	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	41	260	0				ENST00000310581	NM_198253.2	-/1132			0.155020629634443	3	FACETS	0.829	0.698	0.971	0.829	0.698	0.971	INDETERMINATE	2	FALSE	1	0.277385246362661	3		260	203	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925131	81925131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1382212475	NA	P-0009754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	36	889	0	ENST00000359376.3:c.922G>A	p.Ala308Thr	p.A308T	ENST00000359376	NM_002661.3	308	Gcg/Acg	11/33	0.277385246362661	1	FACETS	0.324	0.265	0.39	0.324	0.265	0.39	SUBCLONAL	1	FALSE	0	0.277385246362661	1		889	690	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391922	139391932	+	frameshift_variant	Frame_Shift_Del	DEL	GTGATGTCCCG	GTGATGTCCCG	-	novel	NA	P-0009754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	63	918	0	ENST00000277541.6:c.6259_6269del	p.Arg2087GlyfsTer177	p.R2087Gfs*177	ENST00000277541	NM_017617.3	2087	CGGGACATCACg/g	34/34	1	2	FACETS	0.931	0.807	1	0.931	0.807	1	CLONAL	1	FALSE	1	0.277385246362661	2		918	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203436	NA	P-0009763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	55	328	0	ENST00000269305.4:c.487T>C	p.Tyr163His	p.Y163H	ENST00000269305	NM_001126112.2	163	Tac/Cac	5/11	1	2	FACETS	0.806	0.688	0.935	0.806	0.688	0.935	CLONAL	1	TRUE	1	0.198690084646965	2		328	687	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005552	150005553	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0009763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	102	400	0	ENST00000253339.5:c.672_673del	p.Gln225SerfsTer4	p.Q225Sfs*4	ENST00000253339		224	gtTCaa/gtaa	3/7	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.198690084646965	2		400	817	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090624	71090624	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009815-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	126	434	0	ENST00000318789.4:c.724G>T	p.Glu242Ter	p.E242*	ENST00000318789	NM_032682.5	242	Gaa/Taa	11/21	0.266720910760624	2	FACETS	0.596	0.541	0.653	0.298	0.27	0.327	INDETERMINATE	1	TRUE	0	0.70579430801297	2		434	599	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574366	95574366	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009815-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	34	393	0	ENST00000393063.1:c.2501C>T	p.Ser834Phe	p.S834F	ENST00000393063	NM_030621.3	834	tCt/tTt	17/28	0.384168732346175	3	FACETS	0.218	0.177	0.264	0.073	0.059	0.088	INDETERMINATE	1	TRUE	0	0.70579430801297	3		393	598	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553622	29553622	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009815-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	91	401	0	ENST00000356175.3:c.2171A>G	p.Asp724Gly	p.D724G	ENST00000356175	NM_000267.3	724	gAt/gGt	18/57	0.447455316143101	5	FACETS	0.6	0.532	0.673			1	SUBCLONAL	1	TRUE	NA	0.70579430801297	5		401	885	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291501	10291501	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009815-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	55	761	0	ENST00000340748.4:c.178C>G	p.Gln60Glu	p.Q60E	ENST00000340748		60	Cag/Gag	3/40	1	2	FACETS	0.186	0.158	0.216	0.186	0.158	0.216	SUBCLONAL	1	TRUE	1	0.70579430801297	2		761	839	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29497012	29497192	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGGGTAAGTTTAAATGTATAATATATCTGAAAAAAATCACTGGGTCAAAAACTAGTATCATGAATGTACTAATTATATTAATTGTGCTGAACTAGAACACCAAACTGGATTTTATAATGACATTTCCTTGTGAAATAACCAGTAATACAAATGGGTAATTATTTTTCAATCTTTGAAAAT	AAGGGTAAGTTTAAATGTATAATATATCTGAAAAAAATCACTGGGTCAAAAACTAGTATCATGAATGTACTAATTATATTAATTGTGCTGAACTAGAACACCAAACTGGATTTTATAATGACATTTCCTTGTGAAATAACCAGTAATACAAATGGGTAATTATTTTTCAATCTTTGAAAAT	-	novel	NA	P-0009815-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	124	253	0	ENST00000356175.3:c.585_586+179del		p.X195_splice	ENST00000356175	NM_000267.3	195		5/57	0.447455316143101	5	FACETS	1	0.928	1			1	CLONAL	1	TRUE	NA	0.70579430801297	5		253	703	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578372	7578373	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AT	AT	C	novel	NA	P-0009815-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	98	279	0	ENST00000269305.4:c.557_558delinsG	p.Asp186GlyfsTer61	p.D186Gfs*61	ENST00000269305	NM_001126112.2	186	gAT/gG	5/11	0.70579430801297	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.70579430801297	1		279	164	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0009816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	131	531	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.928	0.841	1	0.928	0.841	1	CLONAL	1	TRUE	1	0.313127133363662	2		531	902	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224209	98224209	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	68	397	0	ENST00000331920.6:c.2632G>C	p.Asp878His	p.D878H	ENST00000331920	NM_000264.3	878	Gac/Cac	16/24	0.313127133363662	1	FACETS	0.471	0.409	0.539	0.471	0.409	0.539	SUBCLONAL	1	TRUE	0	0.313127133363662	1		397	777	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996803	100996803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1470	138	781	1	ENST00000325455.5:c.1724C>T	p.Ser575Leu	p.S575L	ENST00000325455	NM_001202474.3	575	tCa/tTa	2/8	0.229985873423779	1	FACETS	0.462	0.419	0.508	0.462	0.419	0.508	SUBCLONAL	1	TRUE	0	0.313127133363662	1		782	1608	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	68	221	1	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	0.21	2		222	490	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296442	15296442	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	87	780	0	ENST00000263388.2:c.2000G>T	p.Gly667Val	p.G667V	ENST00000263388	NM_000435.2	667	gGc/gTc	13/33	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.21	2		780	781	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954604	17954604	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	54	609	0	ENST00000458235.1:c.290T>C	p.Val97Ala	p.V97A	ENST00000458235	NM_000215.3	97	gTc/gCc	3/24	1	2	FACETS	0.905	0.773	1	0.905	0.773	1	CLONAL	1	TRUE	1	0.21	2		609	568	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258525	19258525	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs563992764	NA	P-0009823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	98	911	0	ENST00000162023.5:c.375G>T	p.Leu125Phe	p.L125F	ENST00000162023		125	ttG/ttT	8/13	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.21	2		911	885	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0009841-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	39	385	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.879	0.729	1	0.879	0.729	1	CLONAL	1	TRUE	1	0.23	2		385	386	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163606	32163606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532094081	NA	P-0009841-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	21	331	0	ENST00000375023.3:c.5620G>A	p.Gly1874Arg	p.G1874R	ENST00000375023	NM_004557.3	1874	Gga/Aga	30/30	1	2	FACETS	0.484	0.372	0.615	0.484	0.372	0.615	SUBCLONAL	1	TRUE	1	0.23	2		331	377	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738828	145738828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201883228	NA	P-0009841-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	52	235	3	ENST00000428558.2:c.2237C>T	p.Ala746Val	p.A746V	ENST00000428558	NM_004260.3	746	gCg/gTg	14/22	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.23	2		238	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578485	7578485	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1064793929	NA	P-0009841-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	78	484	0	ENST00000269305.4:c.445del	p.Ser149ProfsTer21	p.S149Pfs*21	ENST00000269305	NM_001126112.2	149	Tcc/cc	5/11	1	2	FACETS	0.922	0.809	1	0.922	0.809	1	CLONAL	1	TRUE	1	0.23	2		484	736	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113344	209113344	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009844-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	81	408	0	ENST00000345146.2:c.163C>T	p.Gln55Ter	p.Q55*	ENST00000345146	NM_005896.2	55	Caa/Taa	4/10	0.148108989677654	4	FACETS	0.879	0.786	0.977	0.879	0.786	0.977	INDETERMINATE	2	TRUE	2	0.56215648020121	4		408	256	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459884	149459884	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009844-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	17	305	0	ENST00000286301.3:c.323G>A	p.Trp108Ter	p.W108*	ENST00000286301	NM_005211.3	108	tGg/tAg	4/22	1	2	FACETS	0.535	0.404	0.686	0.535	0.404	0.686	SUBCLONAL	1	TRUE	1	0.56215648020121	2		305	113	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436809	52436809	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	344	514	1	ENST00000460680.1:c.1969A>T	p.Arg657Trp	p.R657W	ENST00000460680	NM_004656.3	657	Agg/Tgg	15/17	0.633700355524246	1	FACETS	0.891	0.848	0.935	0.891	0.848	0.935	CLONAL	1	TRUE	0	0.653631502066157	1		515	795	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401731	401731	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	220	301	0	ENST00000380956.4:c.1053G>C	p.Glu351Asp	p.E351D	ENST00000380956	NM_001195286.1	351	gaG/gaC	7/9	1	2	FACETS	0.88	0.821	0.94	0.88	0.821	0.94	CLONAL	1	TRUE	1	0.653631502066157	2		301	765	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112996	2112996	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45494392	NA	P-0009853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	247	330	0	ENST00000219476.3:c.1385G>A	p.Arg462His	p.R462H	ENST00000219476	NM_000548.3	462	cGc/cAc	14/42	1	2	FACETS	0.993	0.932	1	0.993	0.932	1	CLONAL	1	TRUE	1	0.653631502066157	2		330	761	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663810	29663810	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	312	420	0	ENST00000356175.3:c.6242A>C	p.Tyr2081Ser	p.Y2081S	ENST00000356175	NM_000267.3	2081	tAc/tCc	41/57	1	2	FACETS	0.914	0.863	0.967	0.914	0.863	0.967	CLONAL	1	TRUE	1	0.653631502066157	2		420	1044	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46740384	46740632	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGTCTGTAAGGATGGTGATAGTAGTCATAGTAGGGGTGGGTCATGGAACGAGATCTTCAGGACCATCTTGTTCCTTAGTGCCTCTCTTTGGCCTTTCTGCCTCTAGCAGTAGCCAAGCTATGGGCCCAGAAGTGAGTCTTTTATTCTTCTGTTCTCCCTCCCCTTCTCTCCACCCCATTCCCTCAAACCATTCTTACTGTGCCATCTGGACACCTGTTCAGTACATCCTTTTCACAGGACACCTGCTT	CTGTCTGTAAGGATGGTGATAGTAGTCATAGTAGGGGTGGGTCATGGAACGAGATCTTCAGGACCATCTTGTTCCTTAGTGCCTCTCTTTGGCCTTTCTGCCTCTAGCAGTAGCCAAGCTATGGGCCCAGAAGTGAGTCTTTTATTCTTCTGTTCTCCCTCCCCTTCTCTCCACCCCATTCCCTCAAACCATTCTTACTGTGCCATCTGGACACCTGTTCAGTACATCCTTTTCACAGGACACCTGCTT	-	novel	NA	P-0009853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	158	323	0	ENST00000371975.4:c.1865_1869+244del		p.X622_splice	ENST00000371975	NM_003579.3	622		16/18	1	2	FACETS	0.652	0.598	0.707	0.652	0.598	0.707	SUBCLONAL	1	TRUE	1	0.653631502066157	2		323	742	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969448	44969450	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0009853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	358	271	0	ENST00000377967.4:c.4131_4133del	p.Gln1377_Tyr1378delinsHis	p.Q1377_Y1378delinsH	ENST00000377967	NM_021140.2	1377	cAGTac/cac	28/29	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.653631502066157	1		271	625	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597452	10597452	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	167	491	0	ENST00000171111.5:c.1751A>G	p.Tyr584Cys	p.Y584C	ENST00000171111	NM_203500.1	584	tAc/tGc	6/6	0.17813870592103	2	FACETS	1	0.987	1	0.711	0.653	0.772	CLONAL	1	FALSE	0	0.249279769601084	2		491	942	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248700	59248700	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	156	467	0	ENST00000371222.2:c.43A>G	p.Asn15Asp	p.N15D	ENST00000371222	NM_002228.3	15	Aac/Gac	1/1	0.249279769601084	4	FACETS	1	0.986	1			1	CLONAL	1	FALSE	NA	0.249279769601084	4		467	1099	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414881	78414881	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	59	456	0	ENST00000370768.2:c.1885A>G	p.Thr629Ala	p.T629A	ENST00000370768	NM_003902.3	629	Aca/Gca	19/20	0.128313700941589	4	FACETS	0.646	0.554	0.746	0.323	0.277	0.373	INDETERMINATE	1	FALSE	2	0.249279769601084	4		456	916	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588167	67588167	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	92	272	0	ENST00000274335.5:c.997T>C	p.Trp333Arg	p.W333R	ENST00000274335		333	Tgg/Cgg	7/15	0.17813870592103	2	FACETS	1	0.979	1	0.734	0.654	0.818	CLONAL	1	FALSE	0	0.249279769601084	2		272	503	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857011	9857011	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	302	565	0	ENST00000330684.3:c.4390G>A	p.Val1464Ile	p.V1464I	ENST00000330684	NM_001134407.1	1464	Gtt/Att	13/13	0.234887448181746	4	FACETS	1	0.99	1	0.824	0.776	0.874	CLONAL	2	FALSE	1	0.249279769601084	4		565	1224	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs730882026	NA	P-0009857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	198	395	1	ENST00000269305.4:c.707A>C	p.Tyr236Ser	p.Y236S	ENST00000269305	NM_001126112.2	236	tAc/tCc	7/11	0.166012244046356	3	FACETS	1	0.97	1	0.723	0.67	0.777	CLONAL	2	FALSE	0	0.249279769601084	3		396	824	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430202	181430202	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	34	98	0	ENST00000325404.1:c.59del	p.Gly20AlafsTer26	p.G20Afs*26	ENST00000325404	NM_003106.3	18	tcG/tc	1/1	0.249279769601084	5	FACETS	0.901	0.742	1	0.601	0.495	0.717	CLONAL	2	FALSE	2	0.249279769601084	5		98	208	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0009860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	113	370	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.859	0.771	0.951	0.859	0.771	0.951	CLONAL	1	TRUE	1	0.272191058301514	2		370	967	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0009860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	130	337	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.272191058301514	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.272191058301514	1		337	765	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591888	48591888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519739	NA	P-0009860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	138	504	3	ENST00000342988.3:c.1051G>A	p.Asp351Asn	p.D351N	ENST00000342988	NM_005359.5	351	Gat/Aat	9/12	0.272191058301514	1	FACETS	0.896	0.814	0.982	0.896	0.814	0.982	CLONAL	1	TRUE	0	0.272191058301514	1		507	978	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0009861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	209	395	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	0.915	0.85	0.983	1	0.993	1	CLONAL	2	TRUE	1	0.232771719956579	2		395	981	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0009861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	147	391	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.232771719956579	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.232771719956579	1		391	789	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0009869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	61	531	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.479	0.411	0.553	0.479	0.411	0.553	SUBCLONAL	1	TRUE	1	0.22	2		531	1158	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0009895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	333	239	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.887	0.842	0.932	0.887	0.842	0.932	CLONAL	1	TRUE	1	0.888952973451523	2		240	845	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602257	10602257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	241	355	0	ENST00000171111.5:c.1321G>T	p.Glu441Ter	p.E441*	ENST00000171111	NM_203500.1	441	Gag/Tag	3/6	0.888952973451523	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.888952973451523	1		355	290	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220400	1220400	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1359582062	NA	P-0009895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	369	430	0	ENST00000326873.7:c.493G>T	p.Glu165Ter	p.E165*	ENST00000326873	NM_000455.4	165	Gag/Tag	4/10	0.888952973451523	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.888952973451523	1		430	449	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143984	11143984	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	240	355	0	ENST00000358026.2:c.3565C>G	p.Arg1189Gly	p.R1189G	ENST00000358026	NM_001128849.1	1189	Cga/Gga	26/36	0.888952973451523	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.888952973451523	1		355	300	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971093	21971093	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	170	177	0	ENST00000304494.5:c.265G>T	p.Gly89Cys	p.G89C	ENST00000304494	NM_000077.4	89	Ggc/Tgc	2/3	0.888952973451523	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.888952973451523	1		177	205	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498018	29498018	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	489	591	0	ENST00000389048.3:c.1988A>T	p.Glu663Val	p.E663V	ENST00000389048	NM_004304.4	663	gAg/gTg	11/29	1	2	FACETS	0.937	0.899	0.976	0.937	0.899	0.976	CLONAL	1	TRUE	1	0.888952973451523	2		591	1174	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959025	2959025	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	224	356	0	ENST00000396946.4:c.2491A>T	p.Thr831Ser	p.T831S	ENST00000396946	NM_032415.4	831	Acc/Tcc	18/25	1	2	FACETS	0.905	0.85	0.961	0.905	0.85	0.961	CLONAL	1	TRUE	1	0.888952973451523	2		356	557	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333705	70333705	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1474368532	NA	P-0009895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	373	523	2	ENST00000373644.4:c.1610G>T	p.Gly537Val	p.G537V	ENST00000373644	NM_030625.2	537	gGt/gTt	2/12	1	2	FACETS	0.982	0.936	1	0.982	0.936	1	CLONAL	1	TRUE	1	0.888952973451523	2		525	855	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051379	13051379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	519	678	1	ENST00000316448.5:c.727C>T	p.Pro243Ser	p.P243S	ENST00000316448	NM_004343.3	243	Cct/Tct	6/9	0.888952973451523	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.888952973451523	1		679	622	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040995	47040995	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	335	233	0	ENST00000377604.3:c.1525C>T	p.Gln509Ter	p.Q509*	ENST00000377604	NM_001204468.1	509	Caa/Taa	14/24	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.888952973451523	1		233	375	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419971	41419971	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	373	468	0	ENST00000373198.4:c.350del	p.Pro117GlnfsTer4	p.P117Qfs*4	ENST00000373198	NM_133170.3	117	cCa/ca	3/32	NA	2	FACETS	0.995	0.95	1			1	INDETERMINATE	1	TRUE	NA	0.888952973451523	2		468	843	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30061031	30061031	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0009896-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	304	593	0	ENST00000338641.4:c.863C>G	p.Ser288Ter	p.S288*	ENST00000338641	NM_000268.3	288	tCa/tGa	9/16	0.553028716806666	2	FACETS	0.941	0.897	0.984	0.941	0.897	0.984	CLONAL	2	TRUE	0	0.566992106598643	2		593	570	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0009904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	11	509	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.349	0.24	0.486	0.349	0.24	0.486	SUBCLONAL	1	TRUE	1	0.13	2		509	485	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136874	55136874	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	36	663	0	ENST00000257290.5:c.1196A>C	p.Glu399Ala	p.E399A	ENST00000257290	NM_006206.4	399	gAa/gCa	8/23	1	2	FACETS	0.925	0.759	1	0.925	0.759	1	CLONAL	1	TRUE	1	0.13	2		663	599	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134526	41134526	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	49	905	2	ENST00000379561.5:c.1102C>A	p.Pro368Thr	p.P368T	ENST00000379561	NM_002015.3	368	Ccc/Acc	2/3	1	2	FACETS	0.906	0.765	1	0.906	0.765	1	CLONAL	1	TRUE	1	0.13	2		907	832	SUCCESS
ATM	472	MSKCC	GRCh37	11	108159738	108159738	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	44	492	0	ENST00000278616.4:c.4145del	p.Pro1382HisfsTer4	p.P1382Hfs*4	ENST00000278616	NM_000051.3	1382	Cca/ca	28/63	1	2	FACETS	0.808	0.678	0.951	1	0.963	1	CLONAL	2	TRUE	1	0.13	2		492	419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009922-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	216	369	0	ENST00000269305.4:c.383del	p.Pro128LeufsTer42	p.P128Lfs*42	ENST00000269305	NM_001126112.2	128	cCt/ct	5/11	0.419721664296384	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.419721664296384	1		369	741	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096642	178096642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009922-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	192	349	0	ENST00000397062.3:c.689C>T	p.Ser230Leu	p.S230L	ENST00000397062	NM_006164.4	230	tCa/tTa	5/5	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.419721664296384	2		349	847	SUCCESS
APC	324	MSKCC	GRCh37	5	112151271	112151271	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009922-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	207	403	0	ENST00000257430.4:c.914C>G	p.Thr305Arg	p.T305R	ENST00000257430	NM_000038.5	305	aCa/aGa	9/16	1	2	FACETS	0.979	0.908	1	0.979	0.908	1	CLONAL	1	TRUE	1	0.419721664296384	2		403	1008	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864446	162864446	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009922-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	190	419	0	ENST00000366898.1:c.67A>G	p.Ile23Val	p.I23V	ENST00000366898	NM_004562.2	23	Atc/Gtc	2/12	1	2	FACETS	0.897	0.829	0.968	0.897	0.829	0.968	CLONAL	1	TRUE	1	0.419721664296384	2		419	1009	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363812	118363812	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009922-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	250	393	0	ENST00000534358.1:c.5045G>C	p.Ser1682Thr	p.S1682T	ENST00000534358	NM_005933.3	1682	aGt/aCt	16/36	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.419721664296384	2		393	998	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244784	41244784	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555588988	NA	P-0009922-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	312	533	0	ENST00000357654.3:c.2764A>G	p.Thr922Ala	p.T922A	ENST00000357654	NM_007294.3	922	Aca/Gca	10/23	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.419721664296384	2		533	1208	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761133	59761133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768065626	NA	P-0009922-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	259	473	1	ENST00000259008.2:c.3274C>T	p.Pro1092Ser	p.P1092S	ENST00000259008	NM_032043.2	1092	Ccg/Tcg	20/20	0.178573886965019	3	FACETS	1	0.992	1	0.711	0.666	0.757	INDETERMINATE	1	TRUE	1	0.419721664296384	3		474	1050	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266706	18266706	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009922-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	141	243	0	ENST00000222254.8:c.17G>C	p.Gly6Ala	p.G6A	ENST00000222254	NM_005027.3	6	gGc/gCc	2/16	0.419721664296384	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.419721664296384	1		243	491	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0009934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	84	318	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.488896299004373	2	FACETS	0.676	0.6	0.758	0.338	0.3	0.379	SUBCLONAL	1	TRUE	0	0.547095543650467	2		318	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577126	7577126	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	405	500	0	ENST00000269305.4:c.812A>T	p.Glu271Val	p.E271V	ENST00000269305	NM_001126112.2	271	gAg/gTg	8/11	0.547095543650467	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.547095543650467	1		500	908	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711969	89711978	+	frameshift_variant	Frame_Shift_Del	DEL	ACAAGATGAT	ACAAGATGAT	-	novel	NA	P-0009934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	213	282	0	ENST00000371953.3:c.587_596del	p.His196ArgfsTer22	p.H196Rfs*22	ENST00000371953	NM_000314.4	196	cACAAGATGATg/cg	6/9	0.547095543650467	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.547095543650467	1		282	520	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659201	86659210	+	stop_gained	Nonsense_Mutation	DEL	TAGAGGGTAG	TAGAGGGTAG	AAGT	novel	NA	P-0009934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	90	434	0	ENST00000274376.6:c.1490_1499delinsAAGT	p.Leu497_Ser500delinsTer	p.L497_S500delins*	ENST00000274376	NM_002890.2	497	tTAGAGGGTAGt/tAAGTt	11/25	0.273693529323051	1	FACETS	0.275	0.243	0.309	0.275	0.243	0.309	INDETERMINATE	1	TRUE	0	0.547095543650467	1		434	869	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913514	NA	P-0009938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	297	512	0	ENST00000288135.5:c.2466T>G	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaG	17/21	1	2	FACETS	0.98	0.925	1	0.98	0.925	1	CLONAL	1	TRUE	1	0.648663280817399	2		512	934	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593608	55593628	+	inframe_deletion	In_Frame_Del	DEL	GGTTGTTGAGGAGATAAATGG	GGTTGTTGAGGAGATAAATGG	-	novel	NA	P-0009938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	347	538	0	ENST00000288135.5:c.1674_1694del	p.Val559_Gly565del	p.V559_G565del	ENST00000288135	NM_000222.2	558	aaGGTTGTTGAGGAGATAAATGGa/aaa	11/21	1	2	FACETS	0.931	0.882	0.981	0.931	0.882	0.981	CLONAL	1	TRUE	1	0.648663280817399	2		538	1149	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221319	1221319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913322	NA	P-0009942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	14	353	0	ENST00000326873.7:c.842C>T	p.Pro281Leu	p.P281L	ENST00000326873	NM_000455.4	281	cCg/cTg	6/10	1	2	FACETS	0.343	0.247	0.461	0.343	0.247	0.461	SUBCLONAL	1	TRUE	1	0.17	2		353	480	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	41	158	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.220334693896794	2		158	315	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	43	194	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	0.220334693896794	2		194	275	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491716	120491716	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	42	394	0	ENST00000256646.2:c.2513C>T	p.Ser838Phe	p.S838F	ENST00000256646	NM_024408.3	838	tCc/tTc	16/34	1	2	FACETS	0.482	0.401	0.572	0.482	0.401	0.572	SUBCLONAL	1	TRUE	1	0.220334693896794	2		394	791	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666650	206666650	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	70	414	0	ENST00000367120.3:c.1984C>T	p.Gln662Ter	p.Q662*	ENST00000367120	NM_014002.3	662	Cag/Tag	20/22	1	2	FACETS	0.592	0.514	0.677	0.592	0.514	0.677	SUBCLONAL	1	TRUE	1	0.220334693896794	2		414	1073	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966508	25966508	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764952565	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	93	526	0	ENST00000435504.4:c.2698C>T	p.Pro900Ser	p.P900S	ENST00000435504		900	Cct/Tct	13/13	1	2	FACETS	0.687	0.609	0.772	0.687	0.609	0.772	SUBCLONAL	1	TRUE	1	0.220334693896794	2		526	1228	SUCCESS
ALK	238	MSKCC	GRCh37	2	29473971	29473971	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	68	371	0	ENST00000389048.3:c.2204G>A	p.Ser735Asn	p.S735N	ENST00000389048	NM_004304.4	735	aGc/aAc	12/29	1	2	FACETS	0.703	0.61	0.804	0.703	0.61	0.804	SUBCLONAL	1	TRUE	1	0.220334693896794	2		371	878	SUCCESS
ALK	238	MSKCC	GRCh37	2	29473990	29473990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	81	419	2	ENST00000389048.3:c.2185C>T	p.Pro729Ser	p.P729S	ENST00000389048	NM_004304.4	729	Cca/Tca	12/29	1	2	FACETS	0.768	0.675	0.869	0.768	0.675	0.869	SUBCLONAL	1	TRUE	1	0.220334693896794	2		421	957	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630683	158630683	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146610930	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	138	566	2	ENST00000263640.3:c.560C>T	p.Ser187Leu	p.S187L	ENST00000263640	NM_001105.4	187	tCg/tTg	6/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.220334693896794	2		568	1133	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286748	212286748	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	47	343	0	ENST00000342788.4:c.2948G>A	p.Arg983Lys	p.R983K	ENST00000342788	NM_005235.2	983	aGa/aAa	24/28	1	2	FACETS	0.864	0.729	1	0.864	0.729	1	CLONAL	1	TRUE	1	0.220334693896794	2		343	494	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058699	47058699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	59	349	0	ENST00000409792.3:c.7579C>T	p.Pro2527Ser	p.P2527S	ENST00000409792	NM_014159.6	2527	Cct/Tct	21/21	1	2	FACETS	0.633	0.543	0.731	0.633	0.543	0.731	SUBCLONAL	1	TRUE	1	0.220334693896794	2		349	846	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612176	189612176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	98	392	1	ENST00000264731.3:c.1928G>A	p.Arg643Gln	p.R643Q	ENST00000264731	NM_003722.4	643	cGa/cAa	14/14	1	2	FACETS	0.797	0.709	0.891	0.797	0.709	0.891	SUBCLONAL	1	TRUE	1	0.220334693896794	2		393	1116	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976627	55976627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	106	421	0	ENST00000263923.4:c.1198C>T	p.Leu400Phe	p.L400F	ENST00000263923	NM_002253.2	400	Ctt/Ttt	9/30	1	2	FACETS	0.991	0.887	1	0.991	0.887	1	CLONAL	1	TRUE	1	0.220334693896794	2		421	971	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196318	106196318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	120	375	2	ENST00000380013.4:c.4651C>T	p.His1551Tyr	p.H1551Y	ENST00000380013	NM_001127208.2	1551	Cac/Tac	11/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.220334693896794	2		377	976	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499034	149499034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs921756253	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	52	346	0	ENST00000261799.4:c.2794G>A	p.Glu932Lys	p.E932K	ENST00000261799	NM_002609.3	932	Gag/Aag	20/23	1	2	FACETS	0.573	0.486	0.668	0.573	0.486	0.668	SUBCLONAL	1	TRUE	1	0.220334693896794	2		346	824	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517948	176517948	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	70	391	1	ENST00000292408.4:c.446G>A	p.Trp149Ter	p.W149*	ENST00000292408	NM_213647.1	149	tGg/tAg	5/18	1	2	FACETS	0.661	0.575	0.755	0.661	0.575	0.755	SUBCLONAL	1	TRUE	1	0.220334693896794	2		392	961	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523082	176523082	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	91	395	0	ENST00000292408.4:c.1846C>G	p.Arg616Gly	p.R616G	ENST00000292408	NM_213647.1	616	Cgc/Ggc	14/18	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.220334693896794	2		395	818	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180040050	180040050	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	69	572	0	ENST00000261937.6:c.3392G>A	p.Gly1131Asp	p.G1131D	ENST00000261937	NM_182925.4	1131	gGc/gAc	25/30	1	2	FACETS	0.539	0.467	0.616	0.539	0.467	0.616	SUBCLONAL	1	TRUE	1	0.220334693896794	2		572	1163	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672653	30672653	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1191236258	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	222	492	0	ENST00000376406.3:c.4307G>C	p.Arg1436Thr	p.R1436T	ENST00000376406	NM_014641.2	1436	aGg/aCg	10/15	0.220334693896794	3	FACETS	0.843	0.783	0.905	0.843	0.783	0.905	CLONAL	2	TRUE	1	0.220334693896794	3		492	1327	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956597	93956597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1227	82	597	0	ENST00000369303.4:c.2639G>A	p.Arg880Lys	p.R880K	ENST00000369303	NM_004440.3	880	aGg/aAg	15/17	1	2	FACETS	0.569	0.499	0.644	0.569	0.499	0.644	SUBCLONAL	1	TRUE	1	0.220334693896794	2		597	1309	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93973599	93973599	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750462795	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	66	667	0	ENST00000369303.4:c.1777G>A	p.Asp593Asn	p.D593N	ENST00000369303	NM_004440.3	593	Gat/Aat	9/17	1	2	FACETS	0.735	0.637	0.842	0.735	0.637	0.842	SUBCLONAL	1	TRUE	1	0.220334693896794	2		667	815	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662582	117662582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	98	398	0	ENST00000368508.3:c.4883G>A	p.Gly1628Glu	p.G1628E	ENST00000368508	NM_002944.2	1628	gGa/gAa	29/43	0.184934194824627	1	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	0	0.220334693896794	1		398	768	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781201	161781201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55830907	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	148	480	0	ENST00000366898.1:c.1204C>T	p.Arg402Cys	p.R402C	ENST00000366898	NM_004562.2	402	Cgt/Tgt	11/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.220334693896794	2		480	1030	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951913	2951913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	88	303	0	ENST00000396946.4:c.3037G>A	p.Glu1013Lys	p.E1013K	ENST00000396946	NM_032415.4	1013	Gag/Aag	23/25	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.220334693896794	2		303	744	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	24	453	1	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	1	2	FACETS	0.27	0.21	0.339	0.27	0.21	0.339	SUBCLONAL	1	TRUE	1	0.220334693896794	2		454	807	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739911	41739911	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1241	98	569	1	ENST00000242208.4:c.62C>T	p.Ser21Phe	p.S21F	ENST00000242208	NM_002192.2	21	tCc/tTc	2/3	1	2	FACETS	0.664	0.59	0.744	0.664	0.59	0.744	SUBCLONAL	1	TRUE	1	0.220334693896794	2		570	1339	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508470	106508470	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	46	93	0	ENST00000359195.3:c.464C>G	p.Thr155Arg	p.T155R	ENST00000359195	NM_002649.2	155	aCg/aGg	2/11	0.152675552640992	4	FACETS	1	0.954	1	0.692	0.585	0.81	CLONAL	1	TRUE	2	0.220334693896794	4		93	368	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509236	106509236	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	138	401	0	ENST00000359195.3:c.1230G>A	p.Trp410Ter	p.W410*	ENST00000359195	NM_002649.2	410	tgG/tgA	2/11	0.152675552640992	4	FACETS	1	0.981	1	0.66	0.599	0.724	CLONAL	1	TRUE	2	0.220334693896794	4		401	1158	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513378	106513378	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1290751197	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	82	372	0	ENST00000359195.3:c.2282C>T	p.Ser761Phe	p.S761F	ENST00000359195	NM_002649.2	761	tCc/tTc	4/11	0.152675552640992	4	FACETS	0.965	0.849	1	0.483	0.424	0.545	CLONAL	1	TRUE	2	0.220334693896794	4		372	941	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965810	90965810	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	48	368	0	ENST00000265433.3:c.1507A>T	p.Asn503Tyr	p.N503Y	ENST00000265433	NM_002485.4	503	Aat/Tat	11/16	0.152675552640992	4	FACETS	0.762	0.643	0.894	0.381	0.321	0.447	SUBCLONAL	1	TRUE	2	0.220334693896794	4		368	698	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868510	117868510	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	122	328	0	ENST00000297338.2:c.832C>T	p.Pro278Ser	p.P278S	ENST00000297338	NM_006265.2	278	Cct/Tct	8/14	0.152675552640992	4	FACETS	0.88	0.796	0.969	0.88	0.796	0.969	CLONAL	2	TRUE	2	0.220334693896794	4		328	768	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341196	8341196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	98	472	0	ENST00000356435.5:c.5020C>T	p.Arg1674Cys	p.R1674C	ENST00000356435		1674	Cgc/Tgc	30/35	0.192535024384088	2	FACETS	1	0.979	1	0.716	0.64	0.797	CLONAL	1	TRUE	0	0.220334693896794	2		472	621	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341794	8341794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	75	531	1	ENST00000356435.5:c.4846G>A	p.Gly1616Arg	p.G1616R	ENST00000356435		1616	Gga/Aga	29/35	0.192535024384088	2	FACETS	0.926	0.811	1	0.463	0.405	0.526	CLONAL	1	TRUE	0	0.220334693896794	2		532	735	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971047	21971047	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	58	131	0	ENST00000304494.5:c.311T>G	p.Leu104Arg	p.L104R	ENST00000304494	NM_000077.4	104	cTg/cGg	2/3	0.192535024384088	2	FACETS	1	0.967	1	0.727	0.628	0.835	CLONAL	1	TRUE	0	0.220334693896794	2		131	362	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417634	139417634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749786734	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	65	325	1	ENST00000277541.6:c.410C>T	p.Ser137Leu	p.S137L	ENST00000277541	NM_017617.3	137	tCg/tTg	4/34	0.192535024384088	2	FACETS	0.661	0.571	0.758	0.33	0.285	0.379	SUBCLONAL	1	TRUE	0	0.220334693896794	2		326	893	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851285	63851285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	77	316	1	ENST00000279873.7:c.2063C>T	p.Ser688Phe	p.S688F	ENST00000279873	NM_032199.2	688	tCc/tTc	10/10	0.135059644560521	1	FACETS	0.87	0.763	0.985	0.87	0.763	0.985	CLONAL	1	TRUE	0	0.220334693896794	1		317	715	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94170374	94170374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	74	412	0	ENST00000323929.3:c.1895C>T	p.Ser632Phe	p.S632F	ENST00000323929	NM_005591.3	632	tCc/tTc	17/20	0.220334693896794	1	FACETS	0.937	0.82	1	0.937	0.82	1	CLONAL	1	TRUE	0	0.220334693896794	1		412	638	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920734	100920734	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	67	654	0	ENST00000325455.5:c.2414C>T	p.Pro805Leu	p.P805L	ENST00000325455	NM_001202474.3	805	cCa/cTa	6/8	0.220334693896794	1	FACETS	0.644	0.559	0.737	0.644	0.559	0.737	SUBCLONAL	1	TRUE	0	0.220334693896794	1		654	840	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573894	18573894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759658584	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	39	370	0	ENST00000266497.5:c.2212C>T	p.Arg738Cys	p.R738C	ENST00000266497		738	Cgt/Tgt	15/31	1	2	FACETS	0.556	0.459	0.664	0.556	0.459	0.664	SUBCLONAL	1	TRUE	1	0.220334693896794	2		370	637	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641477	18641477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375375394	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	47	430	1	ENST00000266497.5:c.2476G>A	p.Asp826Asn	p.D826N	ENST00000266497		826	Gat/Aat	17/31	1	2	FACETS	0.653	0.55	0.767	0.653	0.55	0.767	SUBCLONAL	1	TRUE	1	0.220334693896794	2		431	653	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420268	49420268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757664799	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	76	389	1	ENST00000301067.7:c.15481G>A	p.Glu5161Lys	p.E5161K	ENST00000301067	NM_003482.3	5161	Gag/Aag	48/54	1	2	FACETS	0.63	0.551	0.716	0.63	0.551	0.716	SUBCLONAL	1	TRUE	1	0.220334693896794	2		390	1095	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858600	57858600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756282060	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1267	102	577	1	ENST00000228682.2:c.338G>A	p.Arg113Gln	p.R113Q	ENST00000228682	NM_005269.2	113	cGa/cAa	4/12	1	2	FACETS	0.676	0.603	0.755	0.676	0.603	0.755	SUBCLONAL	1	TRUE	1	0.220334693896794	2		578	1369	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865804	57865804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267603606	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	107	664	0	ENST00000228682.2:c.3281C>T	p.Ser1094Phe	p.S1094F	ENST00000228682	NM_005269.2	1094	tCc/tTc	12/12	1	2	FACETS	0.741	0.663	0.825	0.741	0.663	0.825	SUBCLONAL	1	TRUE	1	0.220334693896794	2		664	1310	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112884162	112884162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	68	326	0	ENST00000351677.2:c.97C>T	p.Pro33Ser	p.P33S	ENST00000351677	NM_002834.3	33	Cct/Tct	2/16	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.220334693896794	2		326	563	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924381	112924381	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779236638	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	43	310	0	ENST00000351677.2:c.1327C>T	p.His443Tyr	p.H443Y	ENST00000351677	NM_002834.3	443	Cac/Tac	11/16	1	2	FACETS	0.494	0.412	0.586	0.494	0.412	0.586	SUBCLONAL	1	TRUE	1	0.220334693896794	2		310	790	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623828	28623828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	48	449	1	ENST00000241453.7:c.826C>T	p.His276Tyr	p.H276Y	ENST00000241453	NM_004119.2	276	Cat/Tat	7/24	0.184934194824627	1	FACETS	0.587	0.496	0.689	0.587	0.496	0.689	SUBCLONAL	1	TRUE	0	0.220334693896794	1		450	660	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355835	73355835	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776781574	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	33	119	0	ENST00000377767.4:c.136C>T	p.Pro46Ser	p.P46S	ENST00000377767	NM_014953.3	46	Ccg/Tcg	1/21	0.184934194824627	1	FACETS	0.82	0.669	0.989	0.82	0.669	0.989	CLONAL	1	TRUE	0	0.220334693896794	1		119	325	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524595	103524595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756972065	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	62	397	0	ENST00000355739.4:c.2726C>T	p.Pro909Leu	p.P909L	ENST00000355739	NM_000123.3	909	cCt/cTt	13/15	0.184934194824627	1	FACETS	0.648	0.558	0.745	0.648	0.558	0.745	SUBCLONAL	1	TRUE	0	0.220334693896794	1		397	773	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988410	41988410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	97	676	0	ENST00000219905.7:c.1202C>T	p.Thr401Ile	p.T401I	ENST00000219905	NM_001164273.1	401	aCt/aTt	3/24	1	2	FACETS	0.849	0.755	0.949	0.849	0.755	0.949	CLONAL	1	TRUE	1	0.220334693896794	2		676	1037	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058882	42058882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1379	103	676	1	ENST00000219905.7:c.8602C>T	p.Pro2868Ser	p.P2868S	ENST00000219905	NM_001164273.1	2868	Cct/Tct	24/24	1	2	FACETS	0.631	0.562	0.704	0.631	0.562	0.704	SUBCLONAL	1	TRUE	1	0.220334693896794	2		677	1482	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483930	88483930	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	175	467	0	ENST00000360948.2:c.1640G>A	p.Gly547Glu	p.G547E	ENST00000360948	NM_001012338.2	547	gGa/gAa	14/19	0.220334693896794	3	FACETS	0.797	0.733	0.864	0.797	0.733	0.864	SUBCLONAL	2	TRUE	1	0.220334693896794	3		467	1106	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032197	10032197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774932381	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	47	358	0	ENST00000330684.3:c.626C>T	p.Ser209Phe	p.S209F	ENST00000330684	NM_001134407.1	209	tCc/tTc	3/13	0.220334693896794	1	FACETS	0.482	0.405	0.567	0.482	0.405	0.567	SUBCLONAL	1	TRUE	0	0.220334693896794	1		358	788	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993237	72993237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567606533	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1340	89	645	2	ENST00000268489.5:c.808G>A	p.Asp270Asn	p.D270N	ENST00000268489	NM_006885.3	270	Gat/Aat	2/10	0.220334693896794	1	FACETS	0.503	0.444	0.567	0.503	0.444	0.567	SUBCLONAL	1	TRUE	0	0.220334693896794	1		647	1429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	131	478	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.220334693896794	2		478	907	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556061	29556061	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	83	265	0	ENST00000356175.3:c.2428A>T	p.Lys810Ter	p.K810*	ENST00000356175	NM_000267.3	810	Aag/Tag	21/57	0.184934194824627	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.220334693896794	1		265	631	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576027	29576027	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs878853892	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	91	443	1	ENST00000356175.3:c.4000G>T	p.Glu1334Ter	p.E1334*	ENST00000356175	NM_000267.3	1334	Gaa/Taa	30/57	0.184934194824627	1	FACETS	0.965	0.856	1	0.965	0.856	1	CLONAL	1	TRUE	0	0.220334693896794	1		444	762	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585377	29585377	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	100	372	0	ENST00000356175.3:c.4126T>C	p.Phe1376Leu	p.F1376L	ENST00000356175	NM_000267.3	1376	Ttc/Ctc	31/57	0.184934194824627	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.220334693896794	1		372	780	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56809867	56809867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555605068	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	79	479	0	ENST00000337432.4:c.988C>T	p.Pro330Ser	p.P330S	ENST00000337432	NM_058216.2	330	Ccc/Tcc	8/9	0.184934194824627	1	FACETS	0.958	0.843	1	0.958	0.843	1	CLONAL	1	TRUE	0	0.220334693896794	1		479	666	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897378	78897378	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769393175	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	130	421	1	ENST00000306801.3:c.2713C>T	p.Arg905Trp	p.R905W	ENST00000306801	NM_020761.2	905	Cgg/Tgg	23/34	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.220334693896794	2		422	1032	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414893	56414893	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	182	585	0	ENST00000348428.3:c.2294C>T	p.Pro765Leu	p.P765L	ENST00000348428	NM_006785.3	765	cCt/cTt	17/17	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.220334693896794	2		585	1340	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210674	2210674	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	62	426	0	ENST00000398665.3:c.1171C>T	p.Pro391Ser	p.P391S	ENST00000398665	NM_032482.2	391	Ccc/Tcc	14/28	0.15836179497787	3	FACETS	0.534	0.459	0.615			1	SUBCLONAL	1	TRUE	NA	0.220334693896794	3		426	1171	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105576	11105576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	131	423	1	ENST00000358026.2:c.1492C>T	p.Gln498Ter	p.Q498*	ENST00000358026	NM_001128849.1	498	Cag/Tag	9/36	0.099842338385032	4	FACETS	1	0.982	1	0.678	0.614	0.746	INDETERMINATE	1	TRUE	2	0.220334693896794	4		424	1070	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289672	15289672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	156	505	0	ENST00000263388.2:c.3799C>T	p.Pro1267Ser	p.P1267S	ENST00000263388	NM_000435.2	1267	Cct/Tct	23/33	0.099842338385032	4	FACETS	1	0.987	1	0.724	0.662	0.79	INDETERMINATE	1	TRUE	2	0.220334693896794	4		505	1193	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523270	9523270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367986819	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	128	545	1	ENST00000353224.5:c.1967G>A	p.Arg656Gln	p.R656Q	ENST00000353224	NM_177990.2	656	cGg/cAg	9/10	1	2	FACETS	0.882	0.796	0.972	0.882	0.796	0.972	CLONAL	1	TRUE	1	0.220334693896794	2		546	1318	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525120	9525120	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	136	417	0	ENST00000353224.5:c.1765T>G	p.Phe589Val	p.F589V	ENST00000353224	NM_177990.2	589	Ttc/Gtc	8/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.220334693896794	2		417	1064	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560982	9560982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	78	411	0	ENST00000353224.5:c.800G>A	p.Arg267Lys	p.R267K	ENST00000353224	NM_177990.2	267	aGg/aAg	4/10	1	2	FACETS	0.641	0.561	0.727	0.641	0.561	0.727	SUBCLONAL	1	TRUE	1	0.220334693896794	2		411	1105	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710603	40710603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	40	308	0	ENST00000373198.4:c.4248G>A	p.Met1416Ile	p.M1416I	ENST00000373198	NM_133170.3	1416	atG/atA	31/32	1	2	FACETS	0.489	0.405	0.583	0.489	0.405	0.583	SUBCLONAL	1	TRUE	1	0.220334693896794	2		308	743	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790165	40790165	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	28	177	0	ENST00000373198.4:c.2566G>A	p.Glu856Lys	p.E856K	ENST00000373198	NM_133170.3	856	Gag/Aag	18/32	1	2	FACETS	0.586	0.467	0.721	0.586	0.467	0.721	SUBCLONAL	1	TRUE	1	0.220334693896794	2		177	434	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420082	41420082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	79	248	0	ENST00000373198.4:c.239C>T	p.Ser80Phe	p.S80F	ENST00000373198	NM_133170.3	80	tCt/tTt	3/32	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.220334693896794	2		248	678	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755481	39755481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	62	420	0	ENST00000288319.7:c.1284G>A	p.Met428Ile	p.M428I	ENST00000288319	NM_182918.3	428	atG/atA	10/10	0.135059644560521	1	FACETS	0.48	0.413	0.553	0.48	0.413	0.553	SUBCLONAL	1	TRUE	0	0.220334693896794	1		420	1044	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949167	44949167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	48	261	0	ENST00000377967.4:c.3728C>T	p.Pro1243Leu	p.P1243L	ENST00000377967	NM_021140.2	1243	cCa/cTa	25/29	1	1	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	0	0.220334693896794	1		261	364	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411779	63411779	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	84	346	0	ENST00000330258.3:c.1388C>T	p.Ser463Phe	p.S463F	ENST00000330258	NM_152424.3	463	tCc/tTc	2/2	1	1	FACETS	0.996	0.88	1	0.996	0.88	1	CLONAL	1	TRUE	0	0.220334693896794	1		346	681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121912666	NA	P-0009951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	100	535	0	ENST00000269305.4:c.659A>C	p.Tyr220Ser	p.Y220S	ENST00000269305	NM_001126112.2	220	tAt/tCt	6/11	0.213104879852597	1	FACETS	0.917	0.818	1	0.917	0.818	1	CLONAL	1	TRUE	0	0.213104879852597	1		535	914	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341941	8341941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	53	342	0	ENST00000356435.5:c.4699G>A	p.Asp1567Asn	p.D1567N	ENST00000356435		1567	Gat/Aat	29/35	0.213104879852597	1	FACETS	0.708	0.603	0.823	0.708	0.603	0.823	SUBCLONAL	1	TRUE	0	0.213104879852597	1		342	628	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521739	89521739	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	41	265	0	ENST00000336596.2:c.2816C>G	p.Ser939Cys	p.S939C	ENST00000336596	NM_005233.5	939	tCt/tGt	16/17	0.213104879852597	1	FACETS	0.66	0.549	0.783	0.66	0.549	0.783	SUBCLONAL	1	TRUE	0	0.213104879852597	1		265	521	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056402	180056402	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	50	334	0	ENST00000261937.6:c.842A>G	p.Glu281Gly	p.E281G	ENST00000261937	NM_182925.4	281	gAg/gGg	7/30	0.213104879852597	1	FACETS	0.857	0.728	0.999	0.857	0.728	0.999	CLONAL	1	TRUE	0	0.213104879852597	1		334	489	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793539	89793539	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	85	309	0	ENST00000336032.3:c.608T>C	p.Ile203Thr	p.I203T	ENST00000336032	NM_006813.2	203	aTa/aCa	2/2	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.213104879852597	2		309	760	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984107	2984107	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	50	241	0	ENST00000396946.4:c.423G>C	p.Gln141His	p.Q141H	ENST00000396946	NM_032415.4	141	caG/caC	5/25	0.202183858963399	3	FACETS	1	0.937	1	0.401	0.34	0.467	CLONAL	1	TRUE	0	0.213104879852597	3		241	432	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589540	69589540	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1174143141	NA	P-0009951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	33	123	0	ENST00000168712.1:c.313G>A	p.Gly105Ser	p.G105S	ENST00000168712	NM_002007.2	105	Ggc/Agc	1/3	0.199977763962515	3	FACETS	1	0.886	1			1	CLONAL	1	TRUE	NA	0.213104879852597	3		123	306	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992208	11992208	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	77	378	0	ENST00000396373.4:c.298G>C	p.Glu100Gln	p.E100Q	ENST00000396373	NM_001987.4	100	Gag/Cag	3/8	0.0815668501774665	4	FACETS	1	0.953	1	0.592	0.519	0.67	INDETERMINATE	1	TRUE	2	0.213104879852597	4		378	741	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937380	32937380	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	56	398	0	ENST00000380152.3:c.8041A>C	p.Thr2681Pro	p.T2681P	ENST00000380152		2681	Aca/Cca	18/27	1	2	FACETS	0.75	0.641	0.869	0.75	0.641	0.869	SUBCLONAL	1	TRUE	1	0.213104879852597	2		398	701	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992178	72992178	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	164	684	0	ENST00000268489.5:c.1867G>T	p.Ala623Ser	p.A623S	ENST00000268489	NM_006885.3	623	Gct/Tct	2/10	0.213104879852597	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.213104879852597	1		684	1059	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575055	48575055	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0009951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	56	358	1	ENST00000342988.3:c.250-1G>T		p.X84_splice	ENST00000342988	NM_005359.5	84			1	2	FACETS	0.793	0.678	0.918	0.793	0.678	0.918	CLONAL	1	TRUE	1	0.213104879852597	2		359	663	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024858	31024858	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	76	560	0	ENST00000375687.4:c.4343A>T	p.Gln1448Leu	p.Q1448L	ENST00000375687	NM_015338.5	1448	cAa/cTa	13/13	0.213104879852597	3	FACETS	0.727	0.636	0.826			1	SUBCLONAL	1	TRUE	NA	0.213104879852597	3		560	1085	SUCCESS
AR	367	MSKCC	GRCh37	X	66765796	66765796	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	107	310	1	ENST00000374690.3:c.808G>T	p.Ala270Ser	p.A270S	ENST00000374690	NM_000044.3	270	Gcc/Tcc	1/8	1	1	FACETS	0.801	0.721	0.886	1	0.985	1	CLONAL	2	TRUE	0	0.213104879852597	1		311	560	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498386	89498386	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	53	377	0	ENST00000336596.2:c.2360del	p.Pro787GlnfsTer10	p.P787Qfs*10	ENST00000336596	NM_005233.5	786	atC/at	14/17	0.213104879852597	1	FACETS	0.871	0.744	1	0.871	0.744	1	CLONAL	1	TRUE	0	0.213104879852597	1		377	510	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076932	41076932	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	109	449	0	ENST00000373198.4:c.1488del	p.Phe498LeufsTer103	p.F498Lfs*103	ENST00000373198	NM_133170.3	496	ggG/gg	9/32	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.213104879852597	2		449	746	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89828356	89828357	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AT	novel	NA	P-0009951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	43	387	0	ENST00000389301.3:c.2852_2852+1delinsAT		p.X951_splice	ENST00000389301	NM_000135.2	951		29/43	0.213104879852597	1	FACETS	0.513	0.428	0.607	0.513	0.428	0.607	SUBCLONAL	1	TRUE	0	0.213104879852597	1		387	703	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0009956-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	162	370	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.256775073822008	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.256775073822008	2		370	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009956-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	148	472	1	ENST00000269305.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	336	Gag/Tag	10/11	0.256775073822008	1	FACETS	0.962	0.878	1	0.962	0.878	1	CLONAL	1	TRUE	0	0.256775073822008	1		473	1044	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974681	21974681	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009956-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	169	446	0	ENST00000304494.5:c.146T>A	p.Ile49Asn	p.I49N	ENST00000304494	NM_000077.4	49	aTc/aAc	1/3	0.256775073822008	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.256775073822008	1		446	1010	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127665	64127665	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1291878532	NA	P-0009968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	175	341	2	ENST00000334205.4:c.158C>T	p.Ala53Val	p.A53V	ENST00000334205	NM_003942.2	53	gCg/gTg	3/17	1	2	FACETS	0.945	0.88	1	1	0.995	1	CLONAL	4	TRUE	1	0.22	2		343	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0000282-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	927	751	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.621679517135917	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.636077702231875	2		753	1431	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729601	41729601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000282-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	1392	730	8	ENST00000242208.4:c.928C>T	p.Arg310Trp	p.R310W	ENST00000242208	NM_002192.2	310	Cgg/Tgg	3/3	0.595910158777557	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	1	0.636077702231875	4		738	2375	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710664	114710664	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000282-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1239	1186	724	8	ENST00000543371.1:c.149A>G	p.Asn50Ser	p.N50S	ENST00000543371	NM_001198531.1	50	aAt/aGt	1/14	0.204166139725574	5	FACETS	1	0.977	1			1	INDETERMINATE	3	TRUE	NA	0.636077702231875	5		732	2425	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0000444-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	40	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.275349273272013	5	FACETS	0.581	0.481	0.692			1	SUBCLONAL	1	TRUE	NA	0.275349273272013	5		249	707	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971070	21971072	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0000444-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	74	300	0	ENST00000304494.5:c.286_288del	p.Val96del	p.V96del	ENST00000304494	NM_000077.4	96	GTG/-	2/3	0.242227761814185	2	FACETS	1	0.952	1	0.587	0.515	0.663	CLONAL	1	TRUE	0	0.275349273272013	2		300	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578460	+	inframe_deletion	In_Frame_Del	DEL	CGCGGA	CGCGGA	-	novel	NA	P-0000444-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	166	474	0	ENST00000269305.4:c.470_475del	p.Val157_Arg158del	p.V157_R158del	ENST00000269305	NM_001126112.2	157	gTCCGCGcc/gcc	5/11	NA	2	FACETS	0.802	0.738	0.868			1	INDETERMINATE	2	TRUE	NA	0.275349273272013	2		474	752	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335121	65335121	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000444-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	94	527	0	ENST00000342505.4:c.520C>T	p.Arg174Ter	p.R174*	ENST00000342505	NM_002227.2	174	Cga/Tga	6/25	0.214420040840839	1	FACETS	0.75	0.667	0.839	0.75	0.667	0.839	SUBCLONAL	1	TRUE	0	0.275349273272013	1		527	785	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851558	134851558	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs770155473	NA	P-0000444-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	57	393	0	ENST00000398015.3:c.964G>A	p.Val322Ile	p.V322I	ENST00000398015	NM_004441.4	322	Gtc/Atc	5/16	NA	2	FACETS	0.718	0.615	0.829			1	INDETERMINATE	1	TRUE	NA	0.275349273272013	2		393	577	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733513	85733513	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1401934631	NA	P-0000444-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1280	175	919	0	ENST00000370580.1:c.499T>C	p.Ser167Pro	p.S167P	ENST00000370580	NM_003921.4	167	Tct/Cct	3/3	0.214420040840839	1	FACETS	0.753	0.691	0.818	0.753	0.691	0.818	SUBCLONAL	1	TRUE	0	0.275349273272013	1		919	1455	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165306	32165306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747002761	NA	P-0000444-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	124	597	0	ENST00000375023.3:c.4822G>A	p.Ala1608Thr	p.A1608T	ENST00000375023	NM_004557.3	1608	Gca/Aca	27/30	0.232726574298099	2	FACETS	0.976	0.882	1	0.488	0.441	0.538	CLONAL	1	TRUE	0	0.275349273272013	2		597	923	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771855	135771855	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000444-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	89	588	0	ENST00000298552.3:c.3262C>G	p.Leu1088Val	p.L1088V	ENST00000298552	NM_001162426.1	1088	Ctg/Gtg	23/23	0.242227761814185	2	FACETS	0.668	0.591	0.751	0.334	0.295	0.376	SUBCLONAL	1	TRUE	0	0.275349273272013	2		588	968	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999611	100999611	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs750407171	NA	P-0000444-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1257	313	931	0	ENST00000325455.5:c.191G>T	p.Cys64Phe	p.C64F	ENST00000325455	NM_001202474.3	64	tGc/tTc	1/8	0.245153534704267	3	FACETS	0.824	0.775	0.874	0.824	0.775	0.874	CLONAL	2	TRUE	1	0.275349273272013	3		931	1570	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49430906	49430906	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0000444-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	50	274	0	ENST00000301067.7:c.10231+2T>C		p.X3411_splice	ENST00000301067	NM_003482.3	3411			1	2	FACETS	0.74	0.628	0.862	0.74	0.628	0.862	SUBCLONAL	1	TRUE	1	0.275349273272013	2		274	491	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907344	32907344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000444-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	82	409	1	ENST00000380152.3:c.1729G>A	p.Ala577Thr	p.A577T	ENST00000380152		577	Gca/Aca	10/27	0.275349273272013	3	FACETS	0.701	0.617	0.792			1	SUBCLONAL	1	TRUE	NA	0.275349273272013	3		410	966	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0000839-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	1295	368	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.909146819173762	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.922671915454163	2		368	1402	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0000839-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	225	481	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.129562403013664	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.922671915454163	0		481	455	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618601	37618601	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000842-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	244	412	0	ENST00000447079.4:c.277C>T	p.Arg93Ter	p.R93*	ENST00000447079	NM_015083.1	93	Cga/Tga	1/14	0.705952848527445	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.705952848527445	2		412	320	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0000978-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	158	649	2	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.446626477677021	2	FACETS	1	0.981	1	0.605	0.558	0.654	CLONAL	1	TRUE	0	0.498070129240876	2		651	524	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385183	41385183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1423243089	NA	P-0000978-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	147	657	5	ENST00000373198.4:c.778C>T	p.Arg260Trp	p.R260W	ENST00000373198	NM_133170.3	260	Cgg/Tgg	6/32	0.240460045805285	4	FACETS	0.845	0.771	0.924	0.423	0.385	0.462	INDETERMINATE	1	TRUE	2	0.498070129240876	4		662	1046	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739353	46739353	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000978-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	248	679	0	ENST00000371975.4:c.1544A>G	p.Lys515Arg	p.K515R	ENST00000371975	NM_003579.3	515	aAa/aGa	14/18	0.240460045805285	4	FACETS	0.865	0.811	0.921	0.865	0.811	0.921	INDETERMINATE	2	TRUE	2	0.498070129240876	4		679	862	SUCCESS
APC	324	MSKCC	GRCh37	5	112175106	112175106	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs863225348	NA	P-0000978-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	66	293	0	ENST00000257430.4:c.3815C>G	p.Ser1272Ter	p.S1272*	ENST00000257430	NM_000038.5	1272	tCa/tGa	16/16	0.281814876732954	1	FACETS	0.657	0.575	0.744	0.657	0.575	0.744	INDETERMINATE	1	TRUE	0	0.498070129240876	1		293	303	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943734	9943734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000978-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	162	503	1	ENST00000330684.3:c.1207G>A	p.Asp403Asn	p.D403N	ENST00000330684	NM_001134407.1	403	Gac/Aac	5/13	0.240460045805285	4	FACETS	1	0.977	1	0.588	0.54	0.639	INDETERMINATE	1	TRUE	2	0.498070129240876	4		504	828	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561156	9561156	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000978-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	134	462	0	ENST00000353224.5:c.626C>A	p.Pro209Gln	p.P209Q	ENST00000353224	NM_177990.2	209	cCa/cAa	4/10	NA	2	FACETS	0.62	0.563	0.68			1	INDETERMINATE	1	TRUE	NA	0.498070129240876	2		462	868	SUCCESS
APC	324	MSKCC	GRCh37	5	112175783	112175786	+	frameshift_variant	Frame_Shift_Del	DEL	GATG	GATG	-	novel	NA	P-0000978-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	106	385	0	ENST00000257430.4:c.4495_4498del	p.Gly1499PhefsTer7	p.G1499Ffs*7	ENST00000257430	NM_000038.5	1498	GATGga/ga	16/16	0.281814876732954	1	FACETS	0.679	0.611	0.749	0.679	0.611	0.749	INDETERMINATE	1	TRUE	0	0.498070129240876	1		385	471	SUCCESS
APC	324	MSKCC	GRCh37	5	112175729	112175777	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGTTCTTCCAGATGCTGATACTTTATTACATTTTGCCACGGAAAGTA	CAGGTTCTTCCAGATGCTGATACTTTATTACATTTTGCCACGGAAAGTA	-	novel	NA	P-0000978-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	101	451	0	ENST00000257430.4:c.4439_4487del	p.Gln1480LeufsTer11	p.Q1480Lfs*11	ENST00000257430	NM_000038.5	1480	CAGGTTCTTCCAGATGCTGATACTTTATTACATTTTGCCACGGAAAGTAct/ct	16/16	0.281814876732954	1	FACETS	0.655	0.588	0.725	0.655	0.588	0.725	INDETERMINATE	1	TRUE	0	0.498070129240876	1		451	465	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411887	116411901	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TTCTCTCTGTTTTAA	TTCTCTCTGTTTTAA	-	novel	NA	P-0000978-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	204	314	0	ENST00000397752.3:c.2888-16_2888-2del		p.X963_splice	ENST00000397752	NM_000245.2	963			0.451748642496535	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.498070129240876	2		314	387	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0001495-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	96	484	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.383	0.341	0.427	0.383	0.341	0.427	SUBCLONAL	1	TRUE	1	0.740388890207357	2		484	677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0001495-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	565	423	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	NA	2	FACETS	0.996	0.97	1			1	INDETERMINATE	2	TRUE	NA	0.740388890207357	2		424	766	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268156	153268156	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001495-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	319	448	2	ENST00000281708.4:c.652C>T	p.Gln218Ter	p.Q218*	ENST00000281708	NM_033632.3	218	Caa/Taa	4/12	0.740388890207357	1	FACETS	0.925	0.883	0.966	0.925	0.883	0.966	CLONAL	1	TRUE	0	0.740388890207357	1		450	587	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373919	118373919	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001495-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	679	552	0	ENST00000534358.1:c.7312G>A	p.Glu2438Lys	p.E2438K	ENST00000534358	NM_005933.3	2438	Gaa/Aaa	27/36	0.740388890207357	3	FACETS	0.948	0.918	0.979	0.948	0.918	0.979	CLONAL	2	TRUE	1	0.740388890207357	3		552	1325	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9787087	9787087	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001495-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	264	323	2	ENST00000377346.4:c.3120del	p.Asp1041ThrfsTer28	p.D1041Tfs*28	ENST00000377346	NM_005026.3	1040	Aaa/aa	24/24	0.283886818667892	3	FACETS	0.905	0.848	0.963	0.452	0.424	0.482	INDETERMINATE	1	TRUE	1	0.740388890207357	3		325	1080	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373928	118373928	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001495-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	710	553	0	ENST00000534358.1:c.7323del	p.Glu2442LysfsTer14	p.E2442Kfs*14	ENST00000534358	NM_005933.3	2441	Aaa/aa	27/36	0.740388890207357	3	FACETS	0.968	0.938	0.998	0.968	0.938	0.998	CLONAL	2	TRUE	1	0.740388890207357	3		553	1357	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185770	32185770	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0001495-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	94	359	0	ENST00000375023.3:c.1624+2T>A		p.X542_splice	ENST00000375023	NM_004557.3	542			1	2	FACETS	0.375	0.333	0.419	0.375	0.333	0.419	SUBCLONAL	1	TRUE	1	0.740388890207357	2		359	678	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99180089	99180089	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001495-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	66	310	0	ENST00000074304.5:c.2032T>G	p.Phe678Val	p.F678V	ENST00000074304	NM_001134224.1	678	Ttc/Gtc	19/26	0.667195784616351	3	FACETS	0.303	0.263	0.348			1	SUBCLONAL	1	TRUE	NA	0.740388890207357	3		310	805	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376012	8376012	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001495-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	83	533	0	ENST00000356435.5:c.4585A>C	p.Thr1529Pro	p.T1529P	ENST00000356435		1529	Aca/Cca	28/35	0.731439941451186	2	FACETS	0.248	0.218	0.28	0.124	0.109	0.14	SUBCLONAL	1	TRUE	0	0.740388890207357	2		533	905	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352784	118352784	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001495-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	66	348	0	ENST00000534358.1:c.3989A>C	p.Lys1330Thr	p.K1330T	ENST00000534358	NM_005933.3	1330	aAg/aCg	7/36	0.740388890207357	3	FACETS	0.265	0.229	0.304	0.133	0.114	0.152	SUBCLONAL	1	TRUE	1	0.740388890207357	3		348	921	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054594	13054594	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs775075852	NA	P-0001495-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1842	207	809	1	ENST00000316448.5:c.1121A>G	p.Lys374Arg	p.K374R	ENST00000316448	NM_004343.3	374	aAg/aGg	9/9	0.667195784616351	3	FACETS	0.374	0.345	0.404			1	SUBCLONAL	1	TRUE	NA	0.740388890207357	3		810	2049	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958090	54958090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370497957	NA	P-0001495-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	108	492	0	ENST00000312783.6:c.517G>A	p.Gly173Arg	p.G173R	ENST00000312783	NM_198436.1	173	Gga/Aga	6/10	1	2	FACETS	0.302	0.271	0.336	0.302	0.271	0.336	SUBCLONAL	1	TRUE	1	0.740388890207357	2		492	965	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445110	49445112	+	frameshift_variant	Frame_Shift_Del	DEL	GCT	GCT	CC	novel	NA	P-0001495-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	39	188	0	ENST00000301067.7:c.2354_2356delinsGG	p.Glu785GlyfsTer145	p.E785Gfs*145	ENST00000301067	NM_003482.3	785	gAGCca/gGGca	10/54	1	2	FACETS	0.229	0.189	0.272	0.229	0.189	0.272	SUBCLONAL	1	TRUE	1	0.740388890207357	2		188	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0001795-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	391	775	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.503016829887932	2	FACETS	0.969	0.928	1	0.969	0.928	1	CLONAL	2	TRUE	0	0.538843118095704	2		775	749	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371708	225371708	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001795-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	141	367	0	ENST00000264414.4:c.896T>G	p.Met299Arg	p.M299R	ENST00000264414	NM_003590.4	299	aTg/aGg	7/16	0.458843685200727	4	FACETS	0.855	0.785	0.927	0.855	0.785	0.927	CLONAL	2	TRUE	2	0.538843118095704	4		367	471	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868068	56868068	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001795-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	215	702	0	ENST00000308159.5:c.1566C>A	p.Cys522Ter	p.C522*	ENST00000308159	NM_014669.4	522	tgC/tgA	14/22	NA	2	FACETS	0.902	0.839	0.966			1	INDETERMINATE	1	TRUE	NA	0.538843118095704	2		702	885	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56401613	56401613	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001795-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	156	733	0	ENST00000348428.3:c.1475C>G	p.Thr492Arg	p.T492R	ENST00000348428	NM_006785.3	492	aCg/aGg	12/17	NA	2	FACETS	0.786	0.721	0.853			1	INDETERMINATE	1	TRUE	NA	0.538843118095704	2		733	737	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120173	70120173	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002461-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	91	200	0	ENST00000245479.2:c.1177del	p.Gln393SerfsTer10	p.Q393Sfs*10	ENST00000245479	NM_000346.3	392	tCc/tc	3/3	0.253753480146232	2	FACETS	0.987	0.886	1	0.987	0.886	1	CLONAL	2	TRUE	0	0.29	2		200	318	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333734	70333734	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002461-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	100	535	0	ENST00000373644.4:c.1639C>A	p.Gln547Lys	p.Q547K	ENST00000373644	NM_030625.2	547	Cag/Aag	2/12	0.287618736515599	3	FACETS	0.85	0.758	0.948	0.425	0.379	0.474	CLONAL	1	TRUE	1	0.29	3		535	929	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492779	56492786	+	frameshift_variant	Frame_Shift_Del	DEL	TCAAGGGG	TCAAGGGG	-	novel	NA	P-0002461-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	174	416	0	ENST00000407977.2:c.153_160del	p.Pro52AsnfsTer20	p.P52Nfs*20	ENST00000407977		51	atCCCCTTGAaa/ataa	2/10	0.253753480146232	2	FACETS	0.893	0.825	0.963	0.893	0.825	0.963	CLONAL	2	TRUE	0	0.29	2		416	672	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432664	29432664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113994087	NA	P-0121427-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	362	184	0	ENST00000389048.3:c.3824G>A	p.Arg1275Gln	p.R1275Q	ENST00000389048	NM_004304.4	1275	cGa/cAa	25/29	0.664932936346262	3	FACETS	0.896	0.863	0.927	0.896	0.863	0.927	CLONAL	3	NA	0	0.664932936346262	3		184	540	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997395	149997395	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0121427-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	36	209	0	ENST00000253339.5:c.2883+1G>T		p.X961_splice	ENST00000253339		961			0.664932936346262	3	FACETS	0.237	0.194	0.286	0.119	0.097	0.143	SUBCLONAL	1	NA	1	0.664932936346262	3		209	608	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859437	151859437	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121427-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	60	194	0	ENST00000262189.6:c.11225G>T	p.Ser3742Ile	p.S3742I	ENST00000262189	NM_170606.2	3742	aGt/aTt	43/59	0.62259058689886	4	FACETS	0.469	0.404	0.541	0.235	0.202	0.271	SUBCLONAL	1	NA	2	0.664932936346262	4		194	640	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995230	15995230	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs576257941	NA	P-0121427-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	47	210	1	ENST00000268712.3:c.2963G>T	p.Arg988Ile	p.R988I	ENST00000268712	NM_006311.3	988	aGa/aTa	22/46	0.453835025277462	6	FACETS	0.4	0.336	0.471	0.133	0.112	0.157	SUBCLONAL	1	NA	3	0.664932936346262	6		211	823	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0003738-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	45	291	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.138	0.115	0.163	0.138	0.115	0.163	SUBCLONAL	1	TRUE	1	0.84	2		291	778	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715708	30715708	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003738-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	38	281	0	ENST00000295754.5:c.1366G>A	p.Glu456Lys	p.E456K	ENST00000295754	NM_003242.5	456	Gaa/Aaa	5/7	1	2	FACETS	0.131	0.107	0.157	0.131	0.107	0.157	SUBCLONAL	1	TRUE	1	0.84	2		281	693	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042451	42042451	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003738-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1429	125	676	0	ENST00000219905.7:c.6646C>T	p.Gln2216Ter	p.Q2216*	ENST00000219905	NM_001164273.1	2216	Cag/Tag	17/24	1	2	FACETS	0.192	0.172	0.212	0.192	0.172	0.212	SUBCLONAL	1	TRUE	1	0.84	2		676	1554	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435734	56435734	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003738-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	40	173	0	ENST00000407977.2:c.1403C>T	p.Ser468Leu	p.S468L	ENST00000407977		468	tCa/tTa	9/10	1	2	FACETS	0.219	0.182	0.261	0.219	0.182	0.261	SUBCLONAL	1	TRUE	1	0.84	2		173	434	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057193	30057193	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003738-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	55	302	0	ENST00000338641.4:c.676-1G>A		p.X226_splice	ENST00000338641	NM_000268.3	226			1	2	FACETS	0.197	0.168	0.229	0.197	0.168	0.229	SUBCLONAL	1	TRUE	1	0.84	2		302	665	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577095	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519984	NA	P-0003762-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	503	573	1	ENST00000269305.4:c.843C>A	p.Asp281Glu	p.D281E	ENST00000269305	NM_001126112.2	281	gaC/gaA	8/11	0.395355742856559	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	3	TRUE	0	0.395355742856559	3		574	1015	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652411	206652411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781909564	NA	P-0003762-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	459	407	0	ENST00000367120.3:c.1118C>T	p.Thr373Met	p.T373M	ENST00000367120	NM_014002.3	373	aCg/aTg	10/22	0.395355742856559	7	FACETS	0.892	0.852	0.932	0.714	0.682	0.746	CLONAL	4	TRUE	2	0.395355742856559	7		407	1294	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162722912	162722912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003762-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1513	129	513	1	ENST00000367921.3:c.110C>T	p.Ser37Leu	p.S37L	ENST00000367921	NM_006182.2	37	tCa/tTa	4/18	0.395355742856559	7	FACETS	0.79	0.713	0.872	0.158	0.142	0.175	SUBCLONAL	1	TRUE	2	0.395355742856559	7		514	1642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0003913-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	250	333	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.642194044291619	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.642194044291619	1		333	484	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664385	29664385	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs747100254	NA	P-0003913-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	237	375	0	ENST00000356175.3:c.6365-1G>A		p.X2122_splice	ENST00000356175	NM_000267.3	2122			0.642194044291619	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.642194044291619	1		375	455	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259419	11259421	+	inframe_deletion	In_Frame_Del	DEL	CAG	CAG	-	novel	NA	P-0003913-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	274	422	0	ENST00000361445.4:c.4147_4149del	p.Leu1383del	p.L1383del	ENST00000361445	NM_004958.3	1383	CTG/-	28/58	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.642194044291619	2		422	731	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0003932-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	146	330	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.591039111379558	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.591039111379558	1		330	319	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325437	1325437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003932-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	122	434	0	ENST00000400841.2:c.238C>T	p.His80Tyr	p.H80Y	ENST00000400841		80	Cac/Tac	3/6	NA	2	FACETS	0.878	0.799	0.961			1	INDETERMINATE	1	TRUE	NA	0.591039111379558	2		434	470	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945648	206945648	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs570050304	NA	P-0003932-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	140	437	0	ENST00000423557.1:c.133C>T	p.Arg45Ter	p.R45*	ENST00000423557	NM_000572.2	45	Cga/Tga	1/5	1	2	FACETS	0.855	0.783	0.931	0.855	0.783	0.931	CLONAL	1	TRUE	1	0.591039111379558	2		437	554	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628074	187628074	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003932-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	429	544	0	ENST00000441802.2:c.2908G>T	p.Gly970Ter	p.G970*	ENST00000441802	NM_005245.3	970	Gga/Tga	2/27	NA	2	FACETS	0.968	0.931	1			1	INDETERMINATE	2	TRUE	NA	0.591039111379558	2		544	750	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042169	6042169	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003932-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	207	434	0	ENST00000265849.7:c.452G>T	p.Arg151Leu	p.R151L	ENST00000265849	NM_000535.5	151	cGc/cTc	5/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.591039111379558	2		434	622	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334725	81334725	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003932-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	353	552	0	ENST00000222390.5:c.1991T>A	p.Ile664Asn	p.I664N	ENST00000222390	NM_000601.4	664	aTt/aAt	17/18	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.591039111379558	2		552	1156	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151871316	151871316	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1237156948	NA	P-0003932-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	226	409	0	ENST00000262189.6:c.9274A>G	p.Ile3092Val	p.I3092V	ENST00000262189	NM_170606.2	3092	Att/Gtt	39/59	1	2	FACETS	0.987	0.922	1	0.987	0.922	1	CLONAL	1	TRUE	1	0.591039111379558	2		409	775	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563399	87563399	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003932-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	155	320	0	ENST00000277120.3:c.1787A>G	p.Asn596Ser	p.N596S	ENST00000277120		596	aAt/aGt	16/19	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.591039111379558	2		320	491	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241978	133241978	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003932-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	172	472	0	ENST00000320574.5:c.2378G>C	p.Arg793Pro	p.R793P	ENST00000320574	NM_006231.2	793	cGc/cCc	21/49	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.591039111379558	2		472	566	SUCCESS
AR	367	MSKCC	GRCh37	X	66765362	66765362	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003932-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	145	604	0	ENST00000374690.3:c.374G>T	p.Cys125Phe	p.C125F	ENST00000374690	NM_000044.3	125	tGc/tTc	1/8	0.339374268783242	1	FACETS	0.641	0.588	0.696	0.641	0.588	0.696	INDETERMINATE	1	TRUE	0	0.591039111379558	1		604	539	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76812927	76812927	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003932-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	220	492	0	ENST00000373344.5:c.6694C>T	p.Pro2232Ser	p.P2232S	ENST00000373344	NM_000489.3	2232	Cca/Tca	30/35	0.339374268783242	1	FACETS	0.612	0.57	0.655	0.612	0.57	0.655	INDETERMINATE	1	TRUE	0	0.591039111379558	1		492	857	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939048	76939048	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0003932-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	330	488	0	ENST00000373344.5:c.1700C>G	p.Ser567Ter	p.S567*	ENST00000373344	NM_000489.3	567	tCa/tGa	9/35	0.339374268783242	1	FACETS	0.822	0.779	0.866	0.822	0.779	0.866	INDETERMINATE	1	TRUE	0	0.591039111379558	1		488	957	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203436	NA	P-0003939-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	80	333	0	ENST00000269305.4:c.487T>C	p.Tyr163His	p.Y163H	ENST00000269305	NM_001126112.2	163	Tac/Cac	5/11	0.3	1	FACETS	0.973	0.86	1	0.973	0.86	1	CLONAL	1	FALSE	0	0.3	1		333	466	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551457	150551457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003939-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1404	392	710	1	ENST00000369026.2:c.550C>T	p.Arg184Trp	p.R184W	ENST00000369026	NM_021960.4	184	Cgg/Tgg	1/3	0.218464236582966	3	FACETS	0.837	0.793	0.882	0.837	0.793	0.882	CLONAL	2	FALSE	1	0.3	3		711	1796	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973802	131973802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003939-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	85	289	0	ENST00000265335.6:c.3505G>A	p.Ala1169Thr	p.A1169T	ENST00000265335		1169	Gcc/Acc	23/25	1	2	FACETS	0.777	0.687	0.874	0.777	0.687	0.874	SUBCLONAL	1	FALSE	1	0.3	2		289	729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0003942-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	176	432	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.225989616535008	3	FACETS	0.858	0.798	0.919	0.858	0.798	0.919	CLONAL	3	FALSE	0	0.348334438435067	3		432	461	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003942-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	82	382	3	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	0.348334438435067	5	FACETS	1	0.911	1			1	CLONAL	1	FALSE	NA	0.348334438435067	5		385	690	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441252	52441252	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003942-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	273	558	0	ENST00000460680.1:c.518A>G	p.Tyr173Cys	p.Y173C	ENST00000460680	NM_004656.3	173	tAt/tGt	7/17	0.27003521529714	5	FACETS	1	0.981	1			1	CLONAL	3	FALSE	NA	0.348334438435067	5		558	731	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66777425	66777425	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003942-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	130	575	0	ENST00000307102.5:c.791C>G	p.Pro264Arg	p.P264R	ENST00000307102	NM_002755.3	264	cCt/cGt	7/11	0.348334438435067	3	FACETS	0.778	0.709	0.851	0.519	0.472	0.567	SUBCLONAL	2	FALSE	0	0.348334438435067	3		575	563	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533682	63533682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794048	NA	P-0003942-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	363	556	2	ENST00000307078.5:c.1472C>T	p.Ala491Val	p.A491V	ENST00000307078	NM_004655.3	491	gCc/gTc	6/11	0.348334438435067	3	FACETS	0.885	0.847	0.924	1	0.993	1	CLONAL	4	FALSE	0	0.348334438435067	3		558	691	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004002-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	306	233	0	ENST00000269305.4:c.517G>C	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ctg	5/11	0.449515493742755	5	FACETS	0.929	0.896	0.96	1	0.992	1	CLONAL	6	TRUE	0	0.449515493742755	5		233	409	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913527	NA	P-0004002-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	836	309	0	ENST00000311936.3:c.436G>C	p.Ala146Pro	p.A146P	ENST00000311936	NM_004985.3	146	Gca/Cca	4/5	0.449515493742755	6	FACETS	1	0.978	1			1	CLONAL	5	TRUE	NA	0.449515493742755	6		309	1406	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117639351	117639351	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004002-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	60	397	0	ENST00000368508.3:c.6005G>A	p.Ser2002Asn	p.S2002N	ENST00000368508	NM_002944.2	2002	aGc/aAc	37/43	0.124690045941589	4	FACETS	0.441	0.378	0.509	0.22	0.189	0.255	INDETERMINATE	1	TRUE	2	0.449515493742755	4		397	878	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807297	3807297	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0004002-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	79	252	0	ENST00000262367.5:c.3690T>G	p.Tyr1230Ter	p.Y1230*	ENST00000262367	NM_004380.2	1230	taT/taG	19/31	0.207378834056608	3	FACETS	0.79	0.696	0.89	0.263	0.232	0.297	INDETERMINATE	1	TRUE	0	0.449515493742755	3		252	545	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371684	55371684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004007-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	42	329	0	ENST00000297316.4:c.374G>A	p.Arg125His	p.R125H	ENST00000297316	NM_022454.3	125	cGc/cAc	2/2	0.142450958103471	0	FACETS	0.424	0.353	0.503			1	SUBCLONAL	1	FALSE	0	0.232299150022702	0		329	655	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0004007-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1279	124	305	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.232299150022702	1	FACETS	0.673	0.606	0.743	0.673	0.606	0.743	SUBCLONAL	1	FALSE	0	0.232299150022702	1		305	1403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0004007-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	99	392	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	1	2	FACETS	0.997	0.889	1	0.997	0.889	1	CLONAL	1	FALSE	1	0.232299150022702	2		392	855	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913355	NA	P-0004007-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	115	458	0	ENST00000288602.6:c.1406G>A	p.Gly469Glu	p.G469E	ENST00000288602	NM_004333.4	469	gGa/gAa	11/18	NA	2	FACETS	0.849	0.763	0.941			1	INDETERMINATE	1	FALSE	NA	0.232299150022702	2		458	1166	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405041	405041	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1169247876	NA	P-0004007-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	86	468	0	ENST00000380956.4:c.1123G>A	p.Gly375Ser	p.G375S	ENST00000380956	NM_001195286.1	375	Ggc/Agc	8/9	NA	2	FACETS	0.611	0.538	0.689			1	INDETERMINATE	1	FALSE	NA	0.232299150022702	2		468	1212	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276844	123276844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004007-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	53	443	1	ENST00000358487.5:c.1073C>T	p.Thr358Ile	p.T358I	ENST00000358487	NM_000141.4	358	aCa/aTa	8/18	0.232299150022702	1	FACETS	0.392	0.332	0.457	0.392	0.332	0.457	SUBCLONAL	1	FALSE	0	0.232299150022702	1		444	1030	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358684	67358684	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004007-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	131	427	0	ENST00000327367.4:c.192C>A	p.Cys64Ter	p.C64*	ENST00000327367	NM_005902.3	64	tgC/tgA	1/9	0.23183134910669	1	FACETS	0.929	0.841	1	0.929	0.841	1	CLONAL	1	FALSE	0	0.232299150022702	1		427	1073	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0004046-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	258	375	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.277812325252457	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.290986933891408	2		378	776	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0004046-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	24	338	0	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	0.277812325252457	2	FACETS	0.168	0.131	0.212	0.084	0.065	0.106	SUBCLONAL	1	TRUE	0	0.290986933891408	2		338	979	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189893	11189893	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004046-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	182	244	0	ENST00000361445.4:c.5616T>G	p.Asp1872Glu	p.D1872E	ENST00000361445	NM_004958.3	1872	gaT/gaG	40/58	1	2	FACETS	0.883	0.818	0.951	1	0.992	1	CLONAL	2	TRUE	1	0.290986933891408	2		244	708	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625126	69625126	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs782607197	NA	P-0004046-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	99	429	0	ENST00000334134.2:c.667T>C	p.Ser223Pro	p.S223P	ENST00000334134	NM_005247.2	223	Tct/Cct	3/3	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.290986933891408	NA		429	1001	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257822	133257822	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs370268888	NA	P-0004046-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1206	147	477	0	ENST00000320574.5:c.106G>T	p.Glu36Ter	p.E36*	ENST00000320574	NM_006231.2	36	Gaa/Taa	2/49	1	2	FACETS	0.747	0.68	0.818	0.747	0.68	0.818	SUBCLONAL	1	TRUE	1	0.290986933891408	2		477	1353	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678392	88678392	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004046-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1262	176	745	0	ENST00000360948.2:c.1144A>C	p.Asn382His	p.N382H	ENST00000360948	NM_001012338.2	382	Aac/Cac	9/19	1	2	FACETS	0.841	0.772	0.913	0.841	0.772	0.913	CLONAL	1	TRUE	1	0.290986933891408	2		745	1438	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39638006	39638006	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004046-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	60	309	1	ENST00000262039.4:c.2423A>G	p.His808Arg	p.H808R	ENST00000262039	NM_002647.2	808	cAc/cGc	22/25	0.277812325252457	2	FACETS	0.569	0.489	0.656	0.284	0.244	0.328	SUBCLONAL	1	TRUE	0	0.290986933891408	2		310	725	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30311657	30311657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004046-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12627	2051	479	0	ENST00000262643.3:c.511G>A	p.Asp171Asn	p.D171N	ENST00000262643	NM_001238.2	171	Gat/Aat	7/12	0.290986933891408	35	FACETS	0.929	0.906	0.952			1	CLONAL	6	TRUE	NA	0.290986933891408	35		479	14678	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312715	30312715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004046-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12929	2152	500	0	ENST00000262643.3:c.696G>A	p.Met232Ile	p.M232I	ENST00000262643	NM_001238.2	232	atG/atA	8/12	0.290986933891408	35	FACETS	0.948	0.926	0.971			1	CLONAL	6	TRUE	NA	0.290986933891408	35		500	15081	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313373	30313373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1286644454	NA	P-0004046-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14334	2505	486	0	ENST00000262643.3:c.973G>A	p.Glu325Lys	p.E325K	ENST00000262643	NM_001238.2	325	Gag/Aag	11/12	0.290986933891408	35	FACETS	0.989	0.967	1			1	CLONAL	6	TRUE	NA	0.290986933891408	35		486	16839	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313493	30313493	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004046-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11688	2306	397	0	ENST00000262643.3:c.1093G>A	p.Asp365Asn	p.D365N	ENST00000262643	NM_001238.2	365	Gac/Aac	11/12	0.290986933891408	35	FACETS	0.939	0.917	0.96			1	CLONAL	7	TRUE	NA	0.290986933891408	35		397	13994	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0004690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	299	591	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.41261024864227	2	FACETS	0.928	0.878	0.978	0.928	0.878	0.978	CLONAL	2	TRUE	0	0.418999463407696	2		591	769	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857449	9857449	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774419037	NA	P-0004690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	183	433	2	ENST00000330684.3:c.3952C>T	p.Arg1318Trp	p.R1318W	ENST00000330684	NM_001134407.1	1318	Cgg/Tgg	13/13	0.37866606314063	4	FACETS	0.848	0.785	0.913	0.848	0.785	0.913	CLONAL	2	TRUE	2	0.418999463407696	4		435	731	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101092	41101092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs724159837	NA	P-0004690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	170	380	1	ENST00000373198.4:c.1264C>T	p.Leu422Phe	p.L422F	ENST00000373198	NM_133170.3	422	Ctc/Ttc	8/32	0.418999463407696	7	FACETS	0.998	0.919	1	0.399	0.367	0.433	CLONAL	2	TRUE	2	0.418999463407696	7		381	832	SUCCESS
APC	324	MSKCC	GRCh37	5	112174043	112174044	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0004690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	192	497	0	ENST00000257430.4:c.2756_2757del	p.Arg919LysfsTer4	p.R919Kfs*4	ENST00000257430	NM_000038.5	918	GAg/g	16/16	0.41261024864227	2	FACETS	0.791	0.737	0.848	0.791	0.737	0.848	SUBCLONAL	2	TRUE	0	0.418999463407696	2		497	579	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0004693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	61	295	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.21223892393122	2		295	561	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0004693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	177	386	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.167398676638067	2	FACETS	0.809	0.745	0.876	0.809	0.745	0.876	CLONAL	2	TRUE	0	0.21223892393122	2		386	1031	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220644	1220644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1167609100	NA	P-0004693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	130	524	0	ENST00000326873.7:c.662C>T	p.Pro221Leu	p.P221L	ENST00000326873	NM_000455.4	221	cCg/cTg	5/10	1	2	FACETS	0.866	0.787	0.95	1	0.988	1	CLONAL	2	TRUE	1	0.21223892393122	2		524	707	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746077	162746077	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	111	415	1	ENST00000367921.3:c.2200A>G	p.Asn734Asp	p.N734D	ENST00000367921	NM_006182.2	734	Aac/Gac	16/18	0.167398676638067	2	FACETS	1	0.97	1	0.606	0.544	0.672	CLONAL	1	TRUE	0	0.21223892393122	2		416	863	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390976	89390976	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	80	521	0	ENST00000336596.2:c.1042C>A	p.Pro348Thr	p.P348T	ENST00000336596	NM_005233.5	348	Ccc/Acc	5/17	1	2	FACETS	0.76	0.667	0.86	0.76	0.667	0.86	SUBCLONAL	1	TRUE	1	0.21223892393122	2		521	992	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524675	106524675	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	46	349	1	ENST00000359195.3:c.2836G>A	p.Asp946Asn	p.D946N	ENST00000359195	NM_002649.2	946	Gac/Aac	9/11	1	2	FACETS	0.542	0.455	0.638	0.542	0.455	0.638	SUBCLONAL	1	TRUE	1	0.21223892393122	2		350	800	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137241	64137241	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	60	463	1	ENST00000334205.4:c.1673G>T	p.Arg558Leu	p.R558L	ENST00000334205	NM_003942.2	558	cGg/cTg	14/17	1	2	FACETS	0.777	0.668	0.895	0.777	0.668	0.895	SUBCLONAL	1	TRUE	1	0.21223892393122	2		464	728	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103393	77103393	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1184	117	543	0	ENST00000356341.3:c.173T>C	p.Ile58Thr	p.I58T	ENST00000356341	NM_002576.4	58	aTt/aCt	2/15	1	2	FACETS	0.847	0.762	0.939	0.847	0.762	0.939	CLONAL	1	TRUE	1	0.21223892393122	2		543	1301	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524687	103524687	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	57	487	0	ENST00000355739.4:c.2818G>T	p.Val940Leu	p.V940L	ENST00000355739	NM_000123.3	940	Gtg/Ttg	13/15	1	2	FACETS	0.579	0.495	0.672	0.579	0.495	0.672	SUBCLONAL	1	TRUE	1	0.21223892393122	2		487	927	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615730	100615730	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	55	467	1	ENST00000308731.7:c.602C>T	p.Pro201Leu	p.P201L	ENST00000308731	NM_000061.2	201	cCa/cTa	8/19	0.21223892393122	1	FACETS	0.48	0.409	0.558	0.48	0.409	0.558	SUBCLONAL	1	TRUE	0	0.21223892393122	1		468	965	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591892	48591892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767345	NA	P-0004705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	113	442	0	ENST00000342988.3:c.1055G>A	p.Gly352Glu	p.G352E	ENST00000342988	NM_005359.5	352	gGa/gAa	9/12	0.367416933223557	1	FACETS	0.94	0.85	1	0.94	0.85	1	CLONAL	1	TRUE	0	0.367416933223557	1		442	534	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099376	157099376	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1162476911	NA	P-0004705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	100	216	0	ENST00000346085.5:c.313G>A	p.Ala105Thr	p.A105T	ENST00000346085	NM_020732.3	105	Gca/Aca	1/20	0.367416933223557	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.367416933223557	1		216	317	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533916	63533916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1399215718	NA	P-0004705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	59	234	1	ENST00000307078.5:c.1238C>T	p.Ser413Leu	p.S413L	ENST00000307078	NM_004655.3	413	tCg/tTg	6/11	0.159232577362093	3	FACETS	1	0.912	1	0.537	0.464	0.615	INDETERMINATE	1	TRUE	1	0.367416933223557	3		235	354	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356498	70356498	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	159	351	0	ENST00000374080.3:c.5393A>T	p.Lys1798Met	p.K1798M	ENST00000374080		1798	aAg/aTg	37/45	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.367416933223557	2		351	724	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037953	49037974	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCTCATGCTGTTCAGGAGGTA	TCCTCATGCTGTTCAGGAGGTA	-	novel	NA	P-0004705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	206	414	0	ENST00000267163.4:c.2193_2211+3del		p.X731_splice	ENST00000267163	NM_000321.2	731		21/27	0.367416933223557	3	FACETS	0.869	0.814	0.925	0.869	0.814	0.925	CLONAL	3	TRUE	0	0.367416933223557	3		414	509	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0004714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	186	343	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.291277794316077	2		343	1039	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578419	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587781845	NA	P-0004714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	78	270	0	ENST00000269305.4:c.511G>T	p.Glu171Ter	p.E171*	ENST00000269305	NM_001126112.2	171	Gag/Tag	5/11	0.260916669556248	1	FACETS	0.756	0.665	0.854	0.756	0.665	0.854	SUBCLONAL	1	TRUE	0	0.291277794316077	1		270	605	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851396	156851396	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	55	298	1	ENST00000524377.1:c.2353G>A	p.Ala785Thr	p.A785T	ENST00000524377	NM_002529.3	785	Gcc/Acc	17/17	1	2	FACETS	0.561	0.479	0.651	0.561	0.479	0.651	SUBCLONAL	1	TRUE	1	0.291277794316077	2		299	673	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462324	89462324	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	40	299	0	ENST00000336596.2:c.1796C>A	p.Pro599Gln	p.P599Q	ENST00000336596	NM_005233.5	599	cCa/cAa	10/17	1	2	FACETS	0.367	0.304	0.437	0.367	0.304	0.437	SUBCLONAL	1	TRUE	1	0.291277794316077	2		299	749	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979502	2979502	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	134	331	0	ENST00000396946.4:c.745C>A	p.Gln249Lys	p.Q249K	ENST00000396946	NM_032415.4	249	Cag/Aag	6/25	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.291277794316077	2		331	899	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845134	128845134	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	151	363	0	ENST00000249373.3:c.628G>T	p.Val210Leu	p.V210L	ENST00000249373	NM_005631.4	210	Gtg/Ttg	3/12	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.291277794316077	2		363	953	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491401	18491401	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	143	301	0	ENST00000266497.5:c.1314C>G	p.Cys438Trp	p.C438W	ENST00000266497		438	tgC/tgG	8/31	1	2	FACETS	0.958	0.872	1	0.958	0.872	1	CLONAL	1	TRUE	1	0.291277794316077	2		301	1025	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337680	73337680	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	138	302	0	ENST00000377767.4:c.2036A>C	p.His679Pro	p.H679P	ENST00000377767	NM_014953.3	679	cAt/cCt	16/21	0.291277794316077	1	FACETS	0.815	0.741	0.894	0.815	0.741	0.894	CLONAL	1	TRUE	0	0.291277794316077	1		302	993	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817756	3817756	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	152	404	0	ENST00000262367.5:c.3215C>T	p.Ser1072Phe	p.S1072F	ENST00000262367	NM_004380.2	1072	tCt/tTt	16/31	1	2	FACETS	0.977	0.892	1	0.977	0.892	1	CLONAL	1	TRUE	1	0.291277794316077	2		404	1068	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33430537	33430537	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	63	355	0	ENST00000345365.6:c.603G>T	p.Lys201Asn	p.K201N	ENST00000345365	NM_002878.3	201	aaG/aaT	7/10	0.291277794316077	3	FACETS	0.455	0.392	0.525	0.228	0.196	0.263	SUBCLONAL	1	TRUE	1	0.291277794316077	3		355	1088	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40738973	40738973	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	43	259	0	ENST00000373198.4:c.3311G>T	p.Ser1104Ile	p.S1104I	ENST00000373198	NM_133170.3	1104	aGt/aTt	24/32	0.156593157802864	3	FACETS	0.523	0.436	0.619	0.261	0.218	0.31	INDETERMINATE	1	TRUE	1	0.291277794316077	3		259	647	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180958	32180959	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0004714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	94	315	0	ENST00000375023.3:c.2391_2392delinsAA	p.Phe797_Gln798delinsLeuLys	p.F797_Q798delinsLK	ENST00000375023	NM_004557.3	797	ttCCag/ttAAag	15/30	1	2	FACETS	0.861	0.766	0.962	0.861	0.766	0.962	CLONAL	1	TRUE	1	0.291277794316077	2		315	750	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0004724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	177	484	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.362433334674925	3	FACETS	1	0.988	1	0.707	0.652	0.764	CLONAL	1	TRUE	1	0.362433334674925	3		484	816	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0004724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	346	672	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.362433334674925	3	FACETS	0.988	0.941	1	0.988	0.941	1	CLONAL	3	TRUE	0	0.362433334674925	3		672	761	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445404	49445404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371076182	NA	P-0004724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	64	590	0	ENST00000301067.7:c.2062C>T	p.Arg688Cys	p.R688C	ENST00000301067	NM_003482.3	688	Cgc/Tgc	10/54	0.362433334674925	4	FACETS	0.803	0.696	0.92	0.402	0.348	0.46	CLONAL	1	TRUE	2	0.362433334674925	4		590	599	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337611	73337611	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	63	632	0	ENST00000377767.4:c.2105T>C	p.Leu702Pro	p.L702P	ENST00000377767	NM_014953.3	702	cTt/cCt	16/21	0.265948811092996	4	FACETS	0.448	0.386	0.516	0.224	0.193	0.258	SUBCLONAL	1	TRUE	2	0.362433334674925	4		632	1057	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984462	72984462	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	64	875	0	ENST00000268489.5:c.3122A>C	p.Lys1041Thr	p.K1041T	ENST00000268489	NM_006885.3	1041	aAg/aCg	3/10	0.362433334674925	2	FACETS	0.428	0.369	0.491	0.214	0.184	0.246	SUBCLONAL	1	TRUE	0	0.362433334674925	2		875	826	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720825	89720825	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	162	80	302	0	ENST00000371953.3:c.976G>C	p.Asp326His	p.D326H	ENST00000371953	NM_000314.4	326	Gac/Cac	8/9	0.466424173213606	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.48650623807688	1		302	242	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385324	4385324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	253	93	545	0	ENST00000261254.3:c.349C>T	p.Pro117Ser	p.P117S	ENST00000261254	NM_001759.3	117	Ccg/Tcg	2/5	NA	2	FACETS	1	0.952	1			1	INDETERMINATE	1	TRUE	NA	0.48650623807688	2		545	346	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923160	48923160	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776789	NA	P-0004731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	285	105	332	0	ENST00000267163.4:c.607+1G>A		p.X203_splice	ENST00000267163	NM_000321.2	203			0.472341738253405	1	FACETS	0.838	0.757	0.922	0.838	0.757	0.922	CLONAL	1	TRUE	0	0.48650623807688	1		332	390	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574193	41574193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	UNKNOWN	NA	NA	NA	MSK-IMPACT	NA	NA	180	58	677	2	ENST00000263253.7:c.6478G>A	p.Gly2160Arg	p.G2160R	ENST00000263253	NM_001429.3	2160	Ggg/Agg	31/31	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.48650623807688	2		679	238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0004739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	125	749	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.219490963778938	1	FACETS	0.844	0.763	0.929	0.844	0.763	0.929	CLONAL	1	TRUE	0	0.280580850699951	1		750	908	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0004739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	271	519	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	0.280580850699951	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.280580850699951	4		519	1080	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199431	11199431	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	127	628	0	ENST00000361445.4:c.5060A>T	p.His1687Leu	p.H1687L	ENST00000361445	NM_004958.3	1687	cAt/cTt	36/58	1	2	FACETS	0.813	0.734	0.895	0.813	0.734	0.895	CLONAL	1	TRUE	1	0.280580850699951	2		628	1114	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0004748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	69	154	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.955	0.851	1	1	0.986	1	CLONAL	3	TRUE	1	0.283385588349677	2		154	170	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0004758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	90	365	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	0.957	0.848	1	0.957	0.848	1	CLONAL	1	TRUE	1	0.24	2		365	784	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482369	56482369	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	83	383	0	ENST00000267101.3:c.917C>G	p.Pro306Arg	p.P306R	ENST00000267101	NM_001982.3	306	cCt/cGt	8/28	1	2	FACETS	0.887	0.782	0.999	0.887	0.782	0.999	CLONAL	1	TRUE	1	0.24	2		383	780	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726677	41726677	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	74	344	0	ENST00000301178.4:c.222G>C	p.Gln74His	p.Q74H	ENST00000301178	NM_021913.4	74	caG/caC	2/20	0.26312759673788	1	FACETS	0.686	0.6	0.779	0.686	0.6	0.779	SUBCLONAL	1	TRUE	0	0.24	1		344	791	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554254	29554475	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAAGAGTGATGGCACTGCTGAGGCGCATTGAGCATCCCACTGCAGGAAACACTGAGGTATGCCCTTAGCAACAGAAACACCCCTCCCAGGCGCCCACCCTCAATTTGGAAGCCTCTTGTTACATATGTGTGATCAGGAATAGCTTTTGAAGTAAATCCAAGATACGTGCATATTACAAGTATAATATCTGAGTATTTAATATACATCAAGTTTGAAACTTGG	AAAGAGTGATGGCACTGCTGAGGCGCATTGAGCATCCCACTGCAGGAAACACTGAGGTATGCCCTTAGCAACAGAAACACCCCTCCCAGGCGCCCACCCTCAATTTGGAAGCCTCTTGTTACATATGTGTGATCAGGAATAGCTTTTGAAGTAAATCCAAGATACGTGCATATTACAAGTATAATATCTGAGTATTTAATATACATCAAGTTTGAAACTTGG	-	novel	NA	P-0004758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	79	304	0	ENST00000356175.3:c.2270_2326-66del		p.X757_splice	ENST00000356175	NM_000267.3	757		19/57	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.24	2		304	648	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713606	30713606	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	211	287	0	ENST00000295754.5:c.931G>T	p.Glu311Ter	p.E311*	ENST00000295754	NM_003242.5	311	Gag/Tag	4/7	0.517689548032322	1	FACETS	0.962	0.899	1	0.962	0.899	1	CLONAL	1	TRUE	0	0.517689548032322	1		287	628	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069342	30069342	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	260	612	0	ENST00000338641.4:c.1207G>C	p.Ala403Pro	p.A403P	ENST00000338641	NM_000268.3	403	Gca/Cca	12/16	1	2	FACETS	0.885	0.829	0.943	0.885	0.829	0.943	CLONAL	1	TRUE	1	0.517689548032322	2		612	1135	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045772	143045772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145209328	NA	P-0004780-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	165	330	0	ENST00000262992.4:c.1862C>T	p.Thr621Met	p.T621M	ENST00000262992	NM_001101669.1	621	aCg/aTg	17/24	0.510037439092013	1	FACETS	0.855	0.792	0.921	0.855	0.792	0.921	CLONAL	1	TRUE	0	0.559210980469678	1		330	497	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363489	40363489	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749442938	NA	P-0004780-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	170	438	0	ENST00000397332.2:c.740G>A	p.Arg247His	p.R247H	ENST00000397332	NM_001033082.2	247	cGt/cAt	3/3	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.559210980469678	2		438	598	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890141	76890148	+	frameshift_variant	Frame_Shift_Del	DEL	ATTTCTTT	ATTTCTTT	-	novel	NA	P-0004780-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	514	285	0	ENST00000373344.5:c.4746_4753del	p.Lys1583SerfsTer15	p.K1583Sfs*15	ENST00000373344	NM_000489.3	1582	acAAAGAAATct/acct	17/35	0.559210980469678	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.559210980469678	2		285	767	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579473	7579474	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	T	novel	NA	P-0004782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	131	164	0	ENST00000269305.4:c.213_214delinsA	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	71	ccCCcc/ccAcc	4/11	0.446947180755769	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.446947180755769	1		164	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0004795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	94	514	0	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.170637218130421	2	FACETS	0.87	0.776	0.97	0.87	0.776	0.97	CLONAL	2	TRUE	0	0.192190055936066	2		514	562	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521769	89521769	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	73	413	0	ENST00000336596.2:c.2846A>T	p.Asp949Val	p.D949V	ENST00000336596	NM_005233.5	949	gAt/gTt	16/17	0.170637218130421	2	FACETS	0.852	0.747	0.963	0.852	0.747	0.963	CLONAL	2	TRUE	0	0.192190055936066	2		413	446	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177433	56177433	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	132	579	0	ENST00000399503.3:c.2406G>T	p.Leu802Phe	p.L802F	ENST00000399503	NM_005921.1	802	ttG/ttT	14/20	0.167233680856305	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.192190055936066	3		579	645	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268090	55268090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745490627	NA	P-0004795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	80	570	1	ENST00000275493.2:c.2930G>A	p.Arg977His	p.R977H	ENST00000275493	NM_005228.3	977	cGc/cAc	24/28	0.192190055936066	4	FACETS	1	0.976	1	0.748	0.659	0.845	CLONAL	1	TRUE	2	0.192190055936066	4		571	663	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612120	43612120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773256580	NA	P-0004795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	52	808	2	ENST00000355710.3:c.2225C>T	p.Thr742Met	p.T742M	ENST00000355710	NM_020975.4	742	aCg/aTg	12/20	0.192190055936066	3	FACETS	0.764	0.649	0.891			1	SUBCLONAL	1	TRUE	NA	0.192190055936066	3		810	776	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007672	45007672	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0004795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	97	477	0	ENST00000558401.1:c.119C>G	p.Ser40Ter	p.S40*	ENST00000558401	NM_004048.2	40	tCa/tGa	2/4	0.170637218130421	2	FACETS	0.945	0.845	1	0.945	0.845	1	CLONAL	2	TRUE	0	0.192190055936066	2		477	534	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647728	2647728	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1272589968	NA	P-0004795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	77	716	0	ENST00000342085.4:c.1631G>A	p.Arg544Lys	p.R544K	ENST00000342085	NM_002613.4	544	aGg/aAg	14/14	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.192190055936066	2		716	653	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134499	30134499	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs955881745	NA	P-0004795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	23	335	0	ENST00000263025.4:c.32G>T	p.Gly11Val	p.G11V	ENST00000263025	NM_002746.2	11	gGc/gTc	1/9	1	2	FACETS	0.883	0.69	1	0.883	0.69	1	CLONAL	1	TRUE	1	0.192190055936066	2		335	271	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604655	48604655	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121912578	NA	P-0004795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	39	488	0	ENST00000342988.3:c.1477G>C	p.Asp493His	p.D493H	ENST00000342988	NM_005359.5	493	Gat/Cat	12/12	0.192190055936066	1	FACETS	0.861	0.714	1	0.861	0.714	1	CLONAL	1	TRUE	0	0.192190055936066	1		488	426	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439962	56439962	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	90	632	0	ENST00000407977.2:c.630del	p.Phe210LeufsTer2	p.F210Lfs*2	ENST00000407977		210	ttT/tt	6/10	1	2	FACETS	0.838	0.745	0.936	1	0.983	1	CLONAL	2	TRUE	1	0.192190055936066	2		632	559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0004821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	464	303	0	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	0.657818086448274	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.657818086448274	1		303	894	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087452	27087452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	442	326	0	ENST00000324856.7:c.2026C>T	p.Pro676Ser	p.P676S	ENST00000324856	NM_006015.4	676	Cca/Tca	5/20	NA	2	FACETS	1	0.963	1			1	INDETERMINATE	1	TRUE	NA	0.657818086448274	2		326	1330	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705494	47705494	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	507	328	0	ENST00000233146.2:c.2294C>G	p.Ala765Gly	p.A765G	ENST00000233146	NM_000251.2	765	gCt/gGt	14/16	1	2	FACETS	0.938	0.897	0.979	0.938	0.897	0.979	CLONAL	1	TRUE	1	0.657818086448274	2		328	1644	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162867	47162867	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	506	273	0	ENST00000409792.3:c.3259T>G	p.Ser1087Ala	p.S1087A	ENST00000409792	NM_014159.6	1087	Tct/Gct	3/21	0.657818086448274	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.657818086448274	1		273	996	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403554	138403554	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2030	522	360	0	ENST00000289153.2:c.2228A>G	p.His743Arg	p.H743R	ENST00000289153	NM_006219.2	743	cAt/cGt	15/22	0.570811805523464	4	FACETS	1	0.975	1	0.344	0.328	0.36	CLONAL	1	TRUE	1	0.657818086448274	4		360	2552	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339364	116339364	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	71	287	0	ENST00000397752.3:c.226G>T	p.Glu76Ter	p.E76*	ENST00000397752	NM_000245.2	76	Gaa/Taa	2/21	0.657818086448274	1	FACETS	0.152	0.131	0.173	0.152	0.131	0.173	SUBCLONAL	1	TRUE	0	0.657818086448274	1		287	956	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692994	89692994	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	319	192	0	ENST00000371953.3:c.478A>G	p.Thr160Ala	p.T160A	ENST00000371953	NM_000314.4	160	Acc/Gcc	5/9	0.657818086448274	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.657818086448274	1		192	602	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348880	89348880	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	578	383	2	ENST00000301030.4:c.4070C>A	p.Ser1357Tyr	p.S1357Y	ENST00000301030	NM_001256183.1	1357	tCc/tAc	9/13	0.657818086448274	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.657818086448274	1		385	1054	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938271	36938271	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	83	373	0	ENST00000361632.4:c.690del	p.Met231CysfsTer32	p.M231Cfs*32	ENST00000361632		230	ccC/cc	6/16	NA	2	FACETS	0.203	0.178	0.23			1	INDETERMINATE	1	TRUE	NA	0.657818086448274	2		373	1243	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019450	42019466	+	frameshift_variant	Frame_Shift_Del	DEL	ATCCAGAACCAGTTTAT	ATCCAGAACCAGTTTAT	-	novel	NA	P-0004821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	499	409	0	ENST00000219905.7:c.3507_3523del	p.Glu1170HisfsTer6	p.E1170Hfs*6	ENST00000219905	NM_001164273.1	1168	gATCCAGAACCAGTTTAT/g	10/24	0.657818086448274	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.657818086448274	1		409	1014	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817819	3817819	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1249	601	377	0	ENST00000262367.5:c.3152del	p.Lys1051ArgfsTer5	p.K1051Rfs*5	ENST00000262367	NM_004380.2	1051	aAg/ag	16/31	0.270522597394843	3	FACETS	1	0.996	1			1	INDETERMINATE	1	TRUE	NA	0.657818086448274	3		377	1850	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0004823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	208	785	4	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.592791906988732	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.592791906988732	1		789	419	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0004823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	72	499	2	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.592791906988732	1	FACETS	0.784	0.696	0.875	0.784	0.696	0.875	SUBCLONAL	1	TRUE	0	0.592791906988732	1		501	218	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0004823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	163	305	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.465913209907602	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.592791906988732	1		305	266	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953890	55953890	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	15	331	0	ENST00000263923.4:c.3546G>T	p.Glu1182Asp	p.E1182D	ENST00000263923	NM_002253.2	1182	gaG/gaT	27/30	0.398393186676606	2	FACETS	0.177	0.129	0.235	0.088	0.064	0.118	SUBCLONAL	1	TRUE	0	0.592791906988732	2		331	286	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411291	63411291	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1408150272	NA	P-0004823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	308	413	0	ENST00000330258.3:c.1876C>T	p.Arg626Ter	p.R626*	ENST00000330258	NM_152424.3	626	Cga/Tga	2/2	0.172953942187056	3	FACETS	1	0.99	1	0.76	0.724	0.796	INDETERMINATE	2	TRUE	0	0.592791906988732	3		413	591	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411695	63411695	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370645786	NA	P-0004823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	108	420	1	ENST00000330258.3:c.1472G>A	p.Arg491His	p.R491H	ENST00000330258	NM_152424.3	491	cGc/cAc	2/2	0.172953942187056	3	FACETS	1	0.932	1	0.347	0.313	0.382	INDETERMINATE	1	TRUE	0	0.592791906988732	3		421	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578213	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs864309495	NA	P-0004829-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	253	471	1	ENST00000269305.4:c.636del	p.Arg213AspfsTer34	p.R213Dfs*34	ENST00000269305	NM_001126112.2	212	ttT/tt	6/11	0.607816392529693	2	FACETS	0.899	0.855	0.943	0.899	0.855	0.943	CLONAL	2	FALSE	0	0.628055793586063	2		472	448	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630180	187630180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004829-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	136	321	0	ENST00000441802.2:c.802G>A	p.Asp268Asn	p.D268N	ENST00000441802	NM_005245.3	268	Gac/Aac	2/27	0.612188660284118	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	FALSE	0	0.628055793586063	2		321	216	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457998	69457998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866931401	NA	P-0004829-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	123	352	0	ENST00000227507.2:c.398G>A	p.Arg133Gln	p.R133Q	ENST00000227507	NM_053056.2	133	cGg/cAg	2/5	0.628055793586063	5	FACETS	1	0.917	1	0.338	0.306	0.372	CLONAL	1	FALSE	2	0.628055793586063	5		352	750	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412174	139412646	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTTTCCCGCCCTGGCCCCGGCCGACGCACCGGGCATGCAGATGCACTGGAACTCCCCAATCTGGTCCAGGCAGGTGGCGTCGTTCTGGCACGGGTTCGAGACGCACTCGTTGACGTCGATCTCGCATCGGGGGCCCGTGTAGCCCTGCAGACACTGGCACTCGAAGGAGCCCAGCGTGTTGATGCACTTGCCCGCATGCTCGCAGGGGTTGGCACCTGGCGAGGGCACACGGGTGAGAGGCTGCTCCAGGCACCCTGGCCCCTGCAACACCTCACTGCACACCACCCCCATCGGACTGGCAGGGTCCCATCCCCCATCTAACTGGGCACCCCCTGAAGCCAGAATCGACTTCTCATCGGTTCTGGGGCCAGGCTGCCACCCCCACCTGGCCGCACCCCCTGTGCTGGCACCTACCCAGCGAGCACTCATCCACGTCCTGGCTGCAGGCCGGGCCCGTGTACCCCGAGGGGCA	GGTTTCCCGCCCTGGCCCCGGCCGACGCACCGGGCATGCAGATGCACTGGAACTCCCCAATCTGGTCCAGGCAGGTGGCGTCGTTCTGGCACGGGTTCGAGACGCACTCGTTGACGTCGATCTCGCATCGGGGGCCCGTGTAGCCCTGCAGACACTGGCACTCGAAGGAGCCCAGCGTGTTGATGCACTTGCCCGCATGCTCGCAGGGGTTGGCACCTGGCGAGGGCACACGGGTGAGAGGCTGCTCCAGGCACCCTGGCCCCTGCAACACCTCACTGCACACCACCCCCATCGGACTGGCAGGGTCCCATCCCCCATCTAACTGGGCACCCCCTGAAGCCAGAATCGACTTCTCATCGGTTCTGGGGCCAGGCTGCCACCCCCACCTGGCCGCACCCCCTGTGCTGGCACCTACCCAGCGAGCACTCATCCACGTCCTGGCTGCAGGCCGGGCCCGTGTACCCCGAGGGGCA	-	novel	NA	P-0004829-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	150	273	1	ENST00000277541.6:c.1198_1441+30del		p.X400_splice	ENST00000277541	NM_017617.3	400		7-8/34	0.419193733001554	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	FALSE	2	0.628055793586063	4		274	369	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953720	48953750	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTGTTTGTAGCGATACAAACTTGGAGTTCGC	TTGTTTGTAGCGATACAAACTTGGAGTTCGC	-	novel	NA	P-0004829-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	130	239	0	ENST00000267163.4:c.1333-6_1357del		p.X445_splice	ENST00000267163	NM_000321.2	445		14/27	0.591629103772334	2	FACETS	0.937	0.874	0.998	0.937	0.874	0.998	CLONAL	2	FALSE	0	0.628055793586063	2		239	221	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527606	29527606	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004829-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	140	369	0	ENST00000356175.3:c.1055del	p.Asp352ValfsTer24	p.D352Vfs*24	ENST00000356175	NM_000267.3	352	gAt/gt	9/57	0.607816392529693	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	FALSE	0	0.628055793586063	2		369	213	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0004838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	208	286	1	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	0.994	1	CLONAL	2	TRUE	1	0.23	2		287	851	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0004838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	21	182	1	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	0.567	0.437	0.719	0.567	0.437	0.719	SUBCLONAL	1	TRUE	1	0.23	2		183	322	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0004838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	59	451	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.643	0.552	0.743	0.643	0.552	0.743	SUBCLONAL	1	TRUE	1	0.23	2		452	798	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0004839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	239	266	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.922	0.862	0.984	0.922	0.862	0.984	CLONAL	1	TRUE	1	0.564591377142926	2		266	918	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584593	48584593	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	268	535	0	ENST00000342988.3:c.766C>T	p.Gln256Ter	p.Q256*	ENST00000342988	NM_005359.5	256	Cag/Tag	6/12	0.554565216212176	1	FACETS	0.987	0.932	1	0.987	0.932	1	CLONAL	1	TRUE	0	0.564591377142926	1		535	690	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29913010	29913010	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs112569059	NA	P-0004839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	235	490	0	ENST00000376809.5:c.1046-1G>C		p.X349_splice	ENST00000376809	NM_002116.7	349			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.564591377142926	2		490	817	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32905124	32905127	+	frameshift_variant	Frame_Shift_Del	DEL	GACA	GACA	-	rs80359659	NA	P-0004839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	235	554	0	ENST00000380152.3:c.755_758del	p.Asp252ValfsTer24	p.D252Vfs*24	ENST00000380152		250	gtGACA/gt	9/27	1	2	FACETS	0.856	0.8	0.915	0.856	0.8	0.915	CLONAL	1	TRUE	1	0.564591377142926	2		554	972	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668637	52668653	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGCATTTTAATTTGC	TGGGCATTTTAATTTGC	-	novel	NA	P-0004839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	298	652	0	ENST00000394830.3:c.1266_1282del	p.Gln422HisfsTer16	p.Q422Hfs*16	ENST00000394830	NM_018313.4	422	caGCAAATTAAAATGCCCAta/cata	12/30	0.521764742072344	1	FACETS	0.868	0.82	0.917	0.868	0.82	0.917	CLONAL	1	TRUE	0	0.564591377142926	1		652	873	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0004851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	278	541	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	0.614067624822744	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.614067624822744	1		541	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0004851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	212	514	0	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.614067624822744	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.614067624822744	1		514	475	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974721	21974721	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	123	379	0	ENST00000304494.5:c.106del	p.Ala36ArgfsTer17	p.A36Rfs*17	ENST00000304494	NM_000077.4	36	Gcg/cg	1/3	0.562847799018917	1	FACETS	0.778	0.711	0.846	0.778	0.711	0.846	SUBCLONAL	1	TRUE	0	0.614067624822744	1		379	357	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056402	26056402	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	188	331	0	ENST00000343677.2:c.255G>C	p.Lys85Asn	p.K85N	ENST00000343677	NM_005319.3	85	aaG/aaC	1/1	0.614067624822744	3	FACETS	1	0.948	1	0.515	0.477	0.555	CLONAL	1	TRUE	1	0.614067624822744	3		331	777	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230752	53230752	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	363	357	0	ENST00000375401.3:c.2041C>T	p.Arg681Ter	p.R681*	ENST00000375401	NM_004187.3	681	Cga/Tga	14/26	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.614067624822744	1		357	558	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400827	72400827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	271	957	0	ENST00000357731.5:c.344C>A	p.Pro115Gln	p.P115Q	ENST00000357731	NM_173808.2	115	cCa/cAa	2/7	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.614067624822744	2		957	744	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881518	111881518	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	243	472	0	ENST00000393256.3:c.196C>T	p.Pro66Ser	p.P66S	ENST00000393256	NM_006538.4	66	Cca/Tca	2/4	0.171471910648334	3	FACETS	1	0.992	1	0.69	0.647	0.733	INDETERMINATE	1	TRUE	1	0.614067624822744	3		472	750	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113307	209113307	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1465733605	NA	P-0004851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	197	565	0	ENST00000345146.2:c.200A>G	p.His67Arg	p.H67R	ENST00000345146	NM_005896.2	67	cAt/cGt	4/10	1	2	FACETS	0.953	0.887	1	0.953	0.887	1	CLONAL	1	TRUE	1	0.614067624822744	2		565	673	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056291	180056291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199942873	NA	P-0004851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	305	695	0	ENST00000261937.6:c.953G>A	p.Arg318Gln	p.R318Q	ENST00000261937	NM_182925.4	318	cGa/cAa	7/30	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.614067624822744	2		695	962	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526712	106526712	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	148	336	0	ENST00000359195.3:c.3005C>A	p.Thr1002Lys	p.T1002K	ENST00000359195	NM_002649.2	1002	aCa/aAa	10/11	1	2	FACETS	0.876	0.805	0.951	0.876	0.805	0.951	CLONAL	1	TRUE	1	0.614067624822744	2		336	550	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371821	116371821	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	155	543	0	ENST00000397752.3:c.1300T>A	p.Phe434Ile	p.F434I	ENST00000397752	NM_000245.2	434	Ttc/Atc	3/21	1	2	FACETS	0.954	0.879	1	0.954	0.879	1	CLONAL	1	TRUE	1	0.614067624822744	2		543	529	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945093	151945093	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	54	376	0	ENST00000262189.6:c.2426G>T	p.Gly809Val	p.G809V	ENST00000262189	NM_170606.2	809	gGa/gTa	14/59	1	2	FACETS	0.456	0.39	0.527	0.456	0.39	0.527	SUBCLONAL	1	TRUE	1	0.614067624822744	2		376	386	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883981	37883981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1357550606	NA	P-0004851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	204	447	0	ENST00000269571.5:c.3452C>T	p.Ser1151Leu	p.S1151L	ENST00000269571		1151	tCg/tTg	27/27	0.249347631035372	1	FACETS	0.78	0.728	0.833	0.78	0.728	0.833	INDETERMINATE	1	TRUE	0	0.614067624822744	1		447	590	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038563	47038563	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0004851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	288	397	0	ENST00000377604.3:c.724+1G>C		p.X242_splice	ENST00000377604	NM_001204468.1	242			1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.614067624822744	1		397	444	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14028655	14028655	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	37	389	0	ENST00000405192.2:c.23A>T	p.Gln8Leu	p.Q8L	ENST00000405192	NM_001163147.1	8	cAa/cTa	2/12	1	2	FACETS	0.451	0.37	0.541	0.451	0.37	0.541	SUBCLONAL	1	TRUE	1	0.23	2		389	714	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868419	117868419	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	203	535	0	ENST00000297338.2:c.923C>T	p.Pro308Leu	p.P308L	ENST00000297338	NM_006265.2	308	cCt/cTt	8/14	0.3	3	FACETS	0.969	0.898	1	0.969	0.898	1	CLONAL	2	TRUE	1	0.23	3		535	1016	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100358	8100358	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	63	576	0	ENST00000346208.3:c.332C>A	p.Pro111His	p.P111H	ENST00000346208		111	cCc/cAc	3/6	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.23	2		576	506	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220699	1220699	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	78	453	0	ENST00000326873.7:c.717G>T	p.Trp239Cys	p.W239C	ENST00000326873	NM_000455.4	239	tgG/tgT	5/10	NA	2	FACETS	0.85	0.751	0.955			1	INDETERMINATE	2	TRUE	NA	0.23	2		453	399	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610321	10610321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	80	514	1	ENST00000171111.5:c.389C>T	p.Pro130Leu	p.P130L	ENST00000171111	NM_203500.1	130	cCc/cTc	2/6	0.237229535317377	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.23	1		515	472	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811726	102811726	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	100	457	0	ENST00000307046.8:c.458del	p.Pro153GlnfsTer49	p.P153Qfs*49	ENST00000307046	NM_001111285.1	153	cCa/ca	4/4	0.3	3	FACETS	1	0.968	1			1	CLONAL	1	TRUE	NA	0.23	3		457	791	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165746	108165751	+	inframe_deletion	In_Frame_Del	DEL	ACATAA	ACATAA	-	novel	NA	P-0004858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	67	438	0	ENST00000278616.4:c.4870_4875del	p.His1624_Lys1625del	p.H1624_K1625del	ENST00000278616	NM_000051.3	1623	ctACATAAa/cta	32/63	1	2	FACETS	0.659	0.571	0.755	0.659	0.571	0.755	SUBCLONAL	1	TRUE	1	0.23	2		438	884	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	54	291	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.289218617260055	1	FACETS	0.878	0.754	1	0.878	0.754	1	CLONAL	1	TRUE	0	0.326755996740106	1		291	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876659802	NA	P-0004864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	44	730	1	ENST00000269305.4:c.833C>A	p.Pro278His	p.P278H	ENST00000269305	NM_001126112.2	278	cCt/cAt	8/11	0.326755996740106	1	FACETS	0.841	0.71	0.983	0.841	0.71	0.983	CLONAL	1	TRUE	0	0.326755996740106	1		731	268	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	149	291	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.989	0.911	1	0.989	0.911	1	CLONAL	1	TRUE	1	0.647866743081588	2		291	465	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0004872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	89	154	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	0.647866743081588	2		154	264	SUCCESS
APC	324	MSKCC	GRCh37	5	112174868	112174868	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085128	NA	P-0004872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	211	449	0	ENST00000257430.4:c.3577C>T	p.Gln1193Ter	p.Q1193*	ENST00000257430	NM_000038.5	1193	Cag/Tag	16/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.647866743081588	2		449	639	SUCCESS
APC	324	MSKCC	GRCh37	5	112175198	112175198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	126	262	1	ENST00000257430.4:c.3907C>T	p.Gln1303Ter	p.Q1303*	ENST00000257430	NM_000038.5	1303	Caa/Taa	16/16	1	2	FACETS	0.958	0.875	1	0.958	0.875	1	CLONAL	1	TRUE	1	0.647866743081588	2		263	406	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912188	114912188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	374	607	0	ENST00000543371.1:c.1258C>T	p.Arg420Trp	p.R420W	ENST00000543371	NM_001198531.1	420	Cgg/Tgg	11/14	1	2	FACETS	0.995	0.945	1	0.995	0.945	1	CLONAL	1	TRUE	1	0.647866743081588	2		607	1160	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186769	108186769	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767939328	NA	P-0004872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	171	421	2	ENST00000278616.4:c.6127G>A	p.Gly2043Ser	p.G2043S	ENST00000278616	NM_000051.3	2043	Ggc/Agc	42/63	1	2	FACETS	0.716	0.66	0.774	0.716	0.66	0.774	SUBCLONAL	1	TRUE	1	0.647866743081588	2		423	737	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885901	111885901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs79819500	NA	P-0004872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	374	624	0	ENST00000341259.2:c.1523G>A	p.Arg508Gln	p.R508Q	ENST00000341259	NM_005475.2	508	cGg/cAg	8/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.647866743081588	2		624	1108	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609825	81609825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760771267	NA	P-0004872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	184	315	0	ENST00000298171.2:c.1423C>T	p.Leu475Phe	p.L475F	ENST00000298171	NM_000369.2	475	Ctc/Ttc	10/10	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.647866743081588	2		315	560	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870948	12870948	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	229	413	0	ENST00000228872.4:c.176del	p.Lys59SerfsTer12	p.K59Sfs*12	ENST00000228872	NM_004064.3	59	Aag/ag	1/3	1	2	FACETS	0.922	0.862	0.983	0.922	0.862	0.983	CLONAL	1	TRUE	1	0.647866743081588	2		413	767	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	39	246	0				ENST00000310581	NM_198253.2	-/1132			0.158479732710833	3	FACETS	1	0.953	1	0.741	0.616	0.879	CLONAL	1	TRUE	1	0.17	3		246	336	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0004876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	69	536	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.871	0.757	0.995	0.871	0.757	0.995	CLONAL	1	TRUE	1	0.17	2		536	932	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865272	57865272	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	93	736	0	ENST00000228682.2:c.2749G>T	p.Asp917Tyr	p.D917Y	ENST00000228682	NM_005269.2	917	Gat/Tat	12/12	1	2	FACETS	0.888	0.787	0.997	0.888	0.787	0.997	CLONAL	1	TRUE	1	0.17	2		736	1232	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335818	73335818	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs904553704	NA	P-0004876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	54	379	0	ENST00000377767.4:c.2477A>G	p.Tyr826Cys	p.Y826C	ENST00000377767	NM_014953.3	826	tAt/tGt	18/21	1	2	FACETS	0.945	0.806	1	0.945	0.806	1	CLONAL	1	TRUE	1	0.17	2		379	672	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054015	42054015	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	113	703	0	ENST00000219905.7:c.7477A>G	p.Asn2493Asp	p.N2493D	ENST00000219905	NM_001164273.1	2493	Aat/Gat	21/24	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.17	2		703	1241	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103416	2103416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375824753	NA	P-0004876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	57	511	1	ENST00000219476.3:c.299C>T	p.Ala100Val	p.A100V	ENST00000219476	NM_000548.3	100	gCg/gTg	4/42	1	2	FACETS	0.879	0.753	1	0.879	0.753	1	CLONAL	1	TRUE	1	0.17	2		512	763	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16056711	16056711	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0004876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	58	394	0	ENST00000268712.3:c.733-2A>G		p.X245_splice	ENST00000268712	NM_006311.3	245			0.158479732710833	1	FACETS	0.891	0.764	1	0.891	0.764	1	CLONAL	1	TRUE	0	0.17	1		394	701	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733170	74733170	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	66	561	0	ENST00000359995.5:c.73A>T	p.Thr25Ser	p.T25S	ENST00000359995	NM_001195427.1	25	Acc/Tcc	1/3	1	2	FACETS	0.824	0.714	0.945	0.824	0.714	0.945	CLONAL	1	TRUE	1	0.17	2		561	942	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197056	123197056	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0004876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	32	270	0	ENST00000218089.9:c.1821+1G>T		p.X607_splice	ENST00000218089	NM_001042749.1	607			1	1	FACETS	0.725	0.588	0.881	0.725	0.588	0.881	SUBCLONAL	1	TRUE	0	0.17	1		270	475	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092967	27092980	+	frameshift_variant	Frame_Shift_Del	DEL	GATGATGGGCCTTG	GATGATGGGCCTTG	-	novel	NA	P-0004876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	71	506	0	ENST00000324856.7:c.2899_2912del	p.Met967GlyfsTer35	p.M967Gfs*35	ENST00000324856	NM_006015.4	966	gaGATGATGGGCCTTGgg/gagg	10/20	1	2	FACETS	0.93	0.81	1	0.93	0.81	1	CLONAL	1	TRUE	1	0.17	2		506	898	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162335	47162342	+	frameshift_variant	Frame_Shift_Del	DEL	TGAGAGAA	TGAGAGAA	-	novel	NA	P-0004876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	46	337	0	ENST00000409792.3:c.3784_3791del	p.Phe1262ArgfsTer11	p.F1262Rfs*11	ENST00000409792	NM_014159.6	1262	TTCTCTCAa/a	3/21	1	2	FACETS	0.843	0.709	0.992	0.843	0.709	0.992	CLONAL	1	TRUE	1	0.17	2		337	642	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106999	27106999	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	45	352	0	ENST00000324856.7:c.6610del	p.Ala2204ProfsTer27	p.A2204Pfs*27	ENST00000324856	NM_006015.4	2204	Gcc/cc	20/20	1	2	FACETS	0.855	0.718	1	0.855	0.718	1	CLONAL	1	TRUE	1	0.17	2		352	619	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0004895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	137	484	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	1	0.974	1			1	INDETERMINATE	2	TRUE	NA	0.398059526630222	2		484	308	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579415	7579415	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	75	305	0	ENST00000269305.4:c.272G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tGg/tAg	4/11	0.361383856246922	2	FACETS	0.986	0.883	1	0.986	0.883	1	CLONAL	2	TRUE	0	0.398059526630222	2		305	191	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974732	21974732	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	160	235	0	ENST00000304494.5:c.95T>A	p.Leu32Gln	p.L32Q	ENST00000304494	NM_000077.4	32	cTg/cAg	1/3	0.196541418069496	4	FACETS	0.912	0.853	0.971	1	0.986	1	INDETERMINATE	4	TRUE	1	0.398059526630222	4		235	308	SUCCESS
ATR	545	MSKCC	GRCh37	3	142254979	142254979	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	43	223	0	ENST00000350721.4:c.3790A>T	p.Ile1264Leu	p.I1264L	ENST00000350721	NM_001184.3	1264	Ata/Tta	20/47	0.273412155744195	4	FACETS	1	0.852	1	0.507	0.426	0.595	CLONAL	1	TRUE	2	0.398059526630222	4		223	298	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164100	108164100	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	50	233	0	ENST00000278616.4:c.4672A>G	p.Thr1558Ala	p.T1558A	ENST00000278616	NM_000051.3	1558	Acg/Gcg	31/63	1	2	FACETS	0.642	0.544	0.75	0.642	0.544	0.75	SUBCLONAL	1	TRUE	1	0.25	2		233	623	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569894	95569894	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	82	398	0	ENST00000393063.1:c.3839G>T	p.Ser1280Ile	p.S1280I	ENST00000393063	NM_030621.3	1280	aGc/aTc	22/28	1	2	FACETS	0.883	0.778	0.996	0.883	0.778	0.996	CLONAL	1	TRUE	1	0.25	2		398	743	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566430	41566430	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	88	353	0	ENST00000263253.7:c.4307G>C	p.Trp1436Ser	p.W1436S	ENST00000263253	NM_001429.3	1436	tGg/tCg	27/31	1	2	FACETS	0.756	0.669	0.85	0.756	0.669	0.85	SUBCLONAL	1	TRUE	1	0.25	2		353	931	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578226	7578229	+	frameshift_variant	Frame_Shift_Del	DEL	TCAT	TCAT	-	novel	NA	P-0004902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	115	385	0	ENST00000269305.4:c.620_623del	p.Asp207AlafsTer39	p.D207Afs*39	ENST00000269305	NM_001126112.2	207	gATGAc/gc	6/11	0.3	1	FACETS	0.783	0.704	0.867	0.783	0.704	0.867	SUBCLONAL	1	TRUE	0	0.25	1		385	1028	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0004913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	236	419	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.327421332338387	2	FACETS	0.781	0.737	0.825	0.781	0.737	0.825	INDETERMINATE	2	TRUE	0	0.598352357983322	2		419	505	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936083	178936083	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519927	NA	P-0004913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	122	181	0	ENST00000263967.3:c.1625A>C	p.Glu542Ala	p.E542A	ENST00000263967	NM_006218.2	542	gAa/gCa	10/21	0.327421332338387	2	FACETS	0.784	0.723	0.846	0.784	0.723	0.846	INDETERMINATE	2	TRUE	0	0.598352357983322	2		181	260	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056000	180056000	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0004913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	47	456	0	ENST00000261937.6:c.986-1G>T		p.X329_splice	ENST00000261937	NM_182925.4	329			0.348465899914665	3	FACETS	0.275	0.232	0.324	0.138	0.116	0.162	INDETERMINATE	1	TRUE	1	0.598352357983322	3		456	741	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075288	16075288	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	90	305	0	ENST00000268712.3:c.264T>G	p.Ser88Arg	p.S88R	ENST00000268712	NM_006311.3	88	agT/agG	4/46	0.408922560662137	1	FACETS	0.459	0.409	0.512	0.459	0.409	0.512	SUBCLONAL	1	TRUE	0	0.598352357983322	1		305	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0004922-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	617	488	0	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	0.509850490077655	2	FACETS	1	0.997	1	1	0.998	1	CLONAL	3	TRUE	0	0.509850490077655	2		488	736	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498415	89498415	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004922-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	531	460	0	ENST00000336596.2:c.2387T>A	p.Ile796Lys	p.I796K	ENST00000336596	NM_005233.5	796	aTa/aAa	14/17	0.509850490077655	7	FACETS	0.946	0.912	0.979			1	CLONAL	5	TRUE	NA	0.509850490077655	7		460	1002	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514559	149514559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004922-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	379	504	0	ENST00000261799.4:c.385C>T	p.Pro129Ser	p.P129S	ENST00000261799	NM_002609.3	129	Cct/Tct	4/23	0.509850490077655	2	FACETS	1	0.995	1	1	0.997	1	CLONAL	3	TRUE	0	0.509850490077655	2		504	451	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061733	38061733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004922-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	98	234	0	ENST00000250448.2:c.256C>T	p.Pro86Ser	p.P86S	ENST00000250448	NM_004496.3	86	Ccg/Tcg	2/2	0.509850490077655	3	FACETS	1	0.981	1	0.703	0.634	0.776	CLONAL	1	TRUE	1	0.509850490077655	3		234	343	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300492	11300493	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0004922-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	212	531	0	ENST00000361445.4:c.1653_1654delinsTT	p.Leu552Phe	p.L552F	ENST00000361445	NM_004958.3	551	ccCCtt/ccTTtt	11/58	0.509850490077655	4	FACETS	1	0.978	1	0.565	0.524	0.607	CLONAL	1	TRUE	2	0.509850490077655	4		531	1112	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0004929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	164	484	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.837	0.773	0.904	1	0.991	1	CLONAL	2	TRUE	1	0.347215988220766	2		484	564	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453146	140453146	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913369	NA	P-0004929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	61	341	0	ENST00000288602.6:c.1789C>G	p.Leu597Val	p.L597V	ENST00000288602	NM_004333.4	597	Cta/Gta	15/18	1	2	FACETS	0.721	0.623	0.828	0.721	0.623	0.828	SUBCLONAL	1	TRUE	1	0.347215988220766	2		341	487	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619228	23619228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201657283	NA	P-0004929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	92	564	0	ENST00000261584.4:c.3307G>A	p.Val1103Met	p.V1103M	ENST00000261584	NM_024675.3	1103	Gtg/Atg	12/13	1	2	FACETS	0.686	0.609	0.768	0.686	0.609	0.768	SUBCLONAL	1	TRUE	1	0.347215988220766	2		564	773	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56411573	56411573	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	101	662	0	ENST00000348428.3:c.1757T>G	p.Leu586Arg	p.L586R	ENST00000348428	NM_006785.3	586	cTt/cGt	15/17	0.294938641477078	1	FACETS	0.724	0.648	0.805	0.724	0.648	0.805	SUBCLONAL	1	TRUE	0	0.347215988220766	1		662	664	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339931	70339931	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	159	738	0	ENST00000374080.3:c.464G>C	p.Arg155Pro	p.R155P	ENST00000374080		155	cGg/cCg	4/45	0.347215988220766	1	FACETS	0.887	0.814	0.964	0.887	0.814	0.964	CLONAL	1	TRUE	0	0.347215988220766	1		738	853	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578376	7578379	+	frameshift_variant	Frame_Shift_Del	DEL	CTAT	CTAT	-	novel	NA	P-0004929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	84	317	0	ENST00000269305.4:c.551_554del	p.Asp184AlafsTer62	p.D184Afs*62	ENST00000269305	NM_001126112.2	184	gATAGc/gc	5/11	0.294938641477078	1	FACETS	0.875	0.776	0.98	0.875	0.776	0.98	CLONAL	1	TRUE	0	0.347215988220766	1		317	457	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572579	64572615	+	protein_altering_variant	In_Frame_Del	DEL	CCCTCCTCCCATTTGCAGATGCCGTCGTAGAATCGCA	CCCTCCTCCCATTTGCAGATGCCGTCGTAGAATCGCA	T	novel	NA	P-0004929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	84	477	0	ENST00000312049.6:c.1241_1277delinsA	p.Leu414_Gly426delinsHis	p.L414_G426delinsH	ENST00000312049	NM_130799.2	414	cTGCGATTCTACGACGGCATCTGCAAATGGGAGGAGGGc/cAc	9/10	1	2	FACETS	0.734	0.649	0.826	0.734	0.649	0.826	SUBCLONAL	1	TRUE	1	0.347215988220766	2		477	659	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998989	100998989	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0121603-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	336	493	0	ENST00000325455.5:c.813A>T	p.Glu271Asp	p.E271D	ENST00000325455	NM_001202474.3	271	gaA/gaT	1/8	0.762208231127942	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	NA	0	0.762208231127942	1		493	538	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0004936-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	44	207	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.238533539142507	2		207	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0004936-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	262	749	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.238533539142507	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.238533539142507	2		750	922	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244616	46244616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004936-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	34	478	0	ENST00000334344.6:c.2710C>T	p.Gln904Ter	p.Q904*	ENST00000334344	NM_152641.2	904	Cag/Tag	15/21	0.238533539142507	2	FACETS	0.42	0.342	0.509	0.21	0.171	0.255	SUBCLONAL	1	TRUE	0	0.238533539142507	2		478	678	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182631	38182631	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004936-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	46	457	0	ENST00000396334.3:c.784C>G	p.Gln262Glu	p.Q262E	ENST00000396334	NM_002468.4	262	Cag/Gag	5/5	0.238533539142507	1	FACETS	0.609	0.512	0.716	0.609	0.512	0.716	SUBCLONAL	1	TRUE	0	0.238533539142507	1		457	558	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331997	81331997	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004936-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	170	582	2	ENST00000222390.5:c.2087G>T	p.Gly696Val	p.G696V	ENST00000222390	NM_000601.4	696	gGa/gTa	18/18	0.238533539142507	3	FACETS	0.933	0.859	1	0.933	0.859	1	CLONAL	2	TRUE	1	0.238533539142507	3		584	855	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125006	46125006	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004936-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	195	439	0	ENST00000334344.6:c.193G>T	p.Glu65Ter	p.E65*	ENST00000334344	NM_152641.2	65	Gag/Tag	3/21	0.238533539142507	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.238533539142507	2		439	723	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547874	41547874	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0004936-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	86	490	0	ENST00000263253.7:c.2855C>G	p.Ser952Ter	p.S952*	ENST00000263253	NM_001429.3	952	tCa/tGa	15/31	0.238533539142507	3	FACETS	1	0.928	1	0.534	0.472	0.6	CLONAL	1	TRUE	1	0.238533539142507	3		490	756	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573321	55573321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004945-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	117	544	0	ENST00000288135.5:c.983G>A	p.Gly328Glu	p.G328E	ENST00000288135	NM_000222.2	328	gGa/gAa	6/21	0.134972078003521	4	FACETS	1	0.983	1	0.731	0.66	0.805	INDETERMINATE	1	TRUE	2	0.328032813072621	4		544	648	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721532	176721532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373116626	NA	P-0004945-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	92	297	1	ENST00000439151.2:c.7163C>T	p.Pro2388Leu	p.P2388L	ENST00000439151	NM_022455.4	2388	cCg/cTg	23/23	0.197581597959885	4	FACETS	1	0.978	1	0.716	0.638	0.799	CLONAL	1	TRUE	2	0.328032813072621	4		298	520	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653141	29653150	+	frameshift_variant	Frame_Shift_Del	DEL	GAAACTGGCT	GAAACTGGCT	-	novel	NA	P-0004945-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	164	350	0	ENST00000356175.3:c.5078_5087del	p.Lys1693SerfsTer3	p.K1693Sfs*3	ENST00000356175	NM_000267.3	1692	ggGAAACTGGCT/gg	36/57	0.328032813072621	3	FACETS	1	0.983	1	0.807	0.747	0.868	CLONAL	2	TRUE	0	0.328032813072621	3		350	481	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576899	7576912	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGAGGAGCTGGT	GGAGAGGAGCTGGT	-	novel	NA	P-0004945-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	209	395	0	ENST00000269305.4:c.934_947del	p.Thr312ProfsTer20	p.T312Pfs*20	ENST00000269305	NM_001126112.2	312	ACCAGCTCCTCTCCc/c	9/11	0.328032813072621	3	FACETS	1	0.972	1	0.72	0.671	0.77	CLONAL	2	TRUE	0	0.328032813072621	3		395	687	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484595	57484595	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs797045203	NA	P-0004995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	63	152	0	ENST00000371085.3:c.679C>A	p.Gln227Lys	p.Q227K	ENST00000371085	NM_000516.4	227	Cag/Aag	9/13	0.287690544744861	7	FACETS	0.827	0.717	0.946			1	CLONAL	2	TRUE	NA	0.287690544744861	7		152	455	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520166	176520166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs911440999	NA	P-0004995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	64	224	0	ENST00000292408.4:c.1085C>T	p.Ala362Val	p.A362V	ENST00000292408	NM_213647.1	362	gCg/gTg	9/18	0.287690544744861	3	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	1	0.287690544744861	3		224	233	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41242982	41242982	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	45	284	0	ENST00000357654.3:c.4164G>C	p.Gln1388His	p.Q1388H	ENST00000357654	NM_007294.3	1388	caG/caC	11/23	0.287690544744861	3	FACETS	0.929	0.783	1	0.465	0.391	0.546	CLONAL	1	TRUE	1	0.287690544744861	3		284	385	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0005016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	41	484	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.851	0.709	1	0.851	0.709	1	CLONAL	1	TRUE	1	0.21	2		484	459	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0005016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	20	154	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.661	0.506	0.843	0.661	0.506	0.843	SUBCLONAL	1	TRUE	1	0.21	2		154	288	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0005016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	64	293	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	1	2	FACETS	0.856	0.745	0.975	1	0.977	1	CLONAL	2	TRUE	1	0.21	2		293	356	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467646	66467646	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	41	252	1	ENST00000273854.3:c.623del	p.Lys208ArgfsTer60	p.K208Rfs*60	ENST00000273854	NM_004439.5	208	aAg/ag	3/18	1	2	FACETS	0.862	0.718	1	0.862	0.718	1	CLONAL	1	TRUE	1	0.21	2		253	453	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs80338963	NA	P-0005016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	47	275	0	ENST00000342988.3:c.1081C>A	p.Arg361Ser	p.R361S	ENST00000342988	NM_005359.5	361	Cgc/Agc	9/12	0.241490144011455	1	FACETS	0.869	0.734	1	0.869	0.734	1	CLONAL	1	TRUE	0	0.21	1		275	461	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112029177	112029177	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	53	482	0	ENST00000368678.4:c.391G>A	p.Gly131Ser	p.G131S	ENST00000368678		131	Ggt/Agt	5/13	0.241490144011455	1	FACETS	0.674	0.574	0.784	0.674	0.574	0.784	SUBCLONAL	1	TRUE	0	0.21	1		482	670	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120013	70120013	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	16	52	1	ENST00000245479.2:c.1015C>T	p.Gln339Ter	p.Q339*	ENST00000245479	NM_000346.3	339	Cag/Tag	3/3	1	2	FACETS	1	0.854	1	1	0.936	1	CLONAL	2	TRUE	1	0.21	2		53	64	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368203	45368203	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	55	278	0	ENST00000262160.6:c.1399del	p.Ser467HisfsTer13	p.S467Hfs*13	ENST00000262160	NM_005901.5	467	Tca/ca	11/11	0.241490144011455	1	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	0	0.21	1		278	438	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	86	291	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	0.229672922818637	2		291	694	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971194	21971194	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs561034503	NA	P-0005020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	54	218	1	ENST00000304494.5:c.164G>T	p.Gly55Val	p.G55V	ENST00000304494	NM_000077.4	55	gGc/gTc	2/3	0.229672922818637	1	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	0	0.229672922818637	1		219	398	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0005026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	36	154	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.153474336176896	4	FACETS	0.486	0.398	0.585	0.243	0.199	0.293	INDETERMINATE	1	TRUE	2	0.26	4		154	718	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469632	25469632	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	77	419	1	ENST00000264709.3:c.1136G>T	p.Arg379Leu	p.R379L	ENST00000264709	NM_175629.2	379	cGc/cTc	10/23	1	2	FACETS	0.631	0.553	0.716	0.631	0.553	0.716	SUBCLONAL	1	TRUE	1	0.26	2		420	938	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519920	NA	P-0005026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	68	256	0	ENST00000397062.3:c.85G>C	p.Asp29His	p.D29H	ENST00000397062	NM_006164.4	29	Gat/Cat	2/5	1	2	FACETS	0.743	0.646	0.848	0.743	0.646	0.848	SUBCLONAL	1	TRUE	1	0.26	2		256	704	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331733	8331733	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	65	316	0	ENST00000356435.5:c.5383G>T	p.Gly1795Cys	p.G1795C	ENST00000356435		1795	Ggc/Tgc	33/35	1	2	FACETS	0.758	0.656	0.867	0.758	0.656	0.867	SUBCLONAL	1	TRUE	1	0.26	2		316	660	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226280	133226280	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	93	469	0	ENST00000320574.5:c.3778G>T	p.Ala1260Ser	p.A1260S	ENST00000320574	NM_006231.2	1260	Gcc/Tcc	30/49	1	2	FACETS	0.687	0.609	0.771	0.687	0.609	0.771	SUBCLONAL	1	TRUE	1	0.26	2		469	1041	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557844	21557844	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	80	456	0	ENST00000382592.4:c.2001G>T	p.Met667Ile	p.M667I	ENST00000382592	NM_014572.2	667	atG/atT	5/8	1	2	FACETS	0.575	0.504	0.651	0.575	0.504	0.651	SUBCLONAL	1	TRUE	1	0.26	2		456	1071	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0005026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	134	569	1	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	1	2	FACETS	0.903	0.818	0.992	0.903	0.818	0.992	CLONAL	1	TRUE	1	0.26	2		570	1142	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016154	31016154	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1269	96	532	1	ENST00000375687.4:c.400G>T	p.Ala134Ser	p.A134S	ENST00000375687	NM_015338.5	134	Gca/Tca	6/13	1	2	FACETS	0.541	0.48	0.606	0.541	0.48	0.606	SUBCLONAL	1	TRUE	1	0.26	2		533	1365	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790089	40790089	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	49	346	0	ENST00000373198.4:c.2642G>T	p.Arg881Leu	p.R881L	ENST00000373198	NM_133170.3	881	cGg/cTg	18/32	1	2	FACETS	0.453	0.382	0.531	0.453	0.382	0.531	SUBCLONAL	1	TRUE	1	0.26	2		346	832	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	32	246	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.28	2		246	176	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951166	48951166	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1060503079	NA	P-0005033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	20	485	0	ENST00000267163.4:c.1328C>A	p.Ser443Ter	p.S443*	ENST00000267163	NM_000321.2	443	tCa/tAa	13/27	0.176704673639021	3	FACETS	0.857	0.659	1	0.429	0.329	0.544	CLONAL	1	TRUE	1	0.28	3		485	190	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023803	27023803	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	38	399	0	ENST00000324856.7:c.909C>A	p.Ser303Arg	p.S303R	ENST00000324856	NM_006015.4	303	agC/agA	1/20	1	2	FACETS	0.805	0.668	0.958	0.805	0.668	0.958	CLONAL	1	TRUE	1	0.28	2		399	337	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593645	215593645	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	15	464	0	ENST00000260947.4:c.2089G>T	p.Ala697Ser	p.A697S	ENST00000260947	NM_000465.2	697	Gca/Tca	11/11	1	2	FACETS	0.864	0.638	1	0.864	0.638	1	CLONAL	1	TRUE	1	0.28	2		464	124	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675583	30675583	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	52	926	0	ENST00000376406.3:c.2773A>C	p.Asn925His	p.N925H	ENST00000376406	NM_014641.2	925	Aac/Cac	8/15	0.238157316125579	4	FACETS	0.918	0.782	1	0.459	0.391	0.534	CLONAL	1	TRUE	2	0.28	4		926	518	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343712	118343712	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	16	422	0	ENST00000534358.1:c.1838G>C	p.Arg613Pro	p.R613P	ENST00000534358	NM_005933.3	613	cGa/cCa	3/36	1	2	FACETS	0.767	0.571	0.998	0.767	0.571	0.998	CLONAL	1	TRUE	1	0.28	2		422	149	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942733	44942733	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	17	403	0	ENST00000377967.4:c.3313A>C	p.Lys1105Gln	p.K1105Q	ENST00000377967	NM_021140.2	1105	Aaa/Caa	23/29	0.3	2	FACETS	0.941	0.709	1	0.471	0.354	0.606	CLONAL	1	TRUE	0	0.28	2		403	129	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0005034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	2256	343	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.697634051525494	11	FACETS	1	0.996	1			1	CLONAL	9	TRUE	NA	0.697634051525494	11		343	2911	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0005034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2278	446	420	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.697634051525494	11	FACETS	0.971	0.922	1			1	CLONAL	2	TRUE	NA	0.697634051525494	11		420	2724	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0005034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	503	668	0	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	0.697634051525494	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.697634051525494	2		668	682	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12653551	12653551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140884322	NA	P-0005034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	105	544	0	ENST00000251849.4:c.218G>A	p.Arg73Gln	p.R73Q	ENST00000251849	NM_002880.3	73	cGa/cAa	3/17	0.651741497573239	3	FACETS	0.462	0.413	0.514	0.154	0.137	0.172	SUBCLONAL	1	TRUE	0	0.697634051525494	3		544	879	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371684	55371684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	192	329	0	ENST00000297316.4:c.374G>A	p.Arg125His	p.R125H	ENST00000297316	NM_022454.3	125	cGc/cAc	2/2	0.639375006225267	3	FACETS	1	0.983	1	0.395	0.367	0.424	CLONAL	1	TRUE	0	0.697634051525494	3		329	626	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830292	72830292	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	99	660	0	ENST00000268489.5:c.6289T>G	p.Phe2097Val	p.F2097V	ENST00000268489	NM_006885.3	2097	Ttc/Gtc	9/10	0.697634051525494	2	FACETS	0.387	0.345	0.431	0.193	0.172	0.216	SUBCLONAL	1	TRUE	0	0.697634051525494	2		660	734	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0005050-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	280	345	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.808476071985026	2		345	674	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060816	38060816	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005050-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	578	734	0	ENST00000250448.2:c.1173C>A	p.Asp391Glu	p.D391E	ENST00000250448	NM_004496.3	391	gaC/gaA	2/2	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.808476071985026	2		734	1307	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29107980	29107980	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1179425981	NA	P-0005050-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	275	583	0	ENST00000328354.6:c.709G>A	p.Ala237Thr	p.A237T	ENST00000328354	NM_007194.3	237	Gct/Act	6/15	1	2	FACETS	0.987	0.933	1	0.987	0.933	1	CLONAL	1	TRUE	1	0.808476071985026	2		583	689	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0005073-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	73	419	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	NA	2	FACETS	1	0.926	1			1	INDETERMINATE	1	TRUE	NA	0.572501357117928	2		419	241	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0005079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	46	419	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		419	502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578505	7578505	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	92	352	0	ENST00000269305.4:c.425del	p.Pro142LeufsTer28	p.P142Lfs*28	ENST00000269305	NM_001126112.2	142	cCt/ct	5/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.171985190742049	2		352	726	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584505	187584505	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0005107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	85	358	0	ENST00000441802.2:c.3528C>G	p.Tyr1176Ter	p.Y1176*	ENST00000441802	NM_005245.3	1176	taC/taG	3/27	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.171985190742049	2		358	882	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717629	89717629	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1554825165	NA	P-0005107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	76	317	0	ENST00000371953.3:c.654C>A	p.Cys218Ter	p.C218*	ENST00000371953	NM_000314.4	218	tgC/tgA	7/9	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.171985190742049	2		317	650	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448453	49448453	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	42	292	0	ENST00000301067.7:c.258G>T	p.Glu86Asp	p.E86D	ENST00000301067	NM_003482.3	86	gaG/gaT	3/54	1	2	FACETS	0.74	0.616	0.878	0.74	0.616	0.878	SUBCLONAL	1	TRUE	1	0.171985190742049	2		292	660	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992763	72992763	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	64	463	0	ENST00000268489.5:c.1282A>T	p.Thr428Ser	p.T428S	ENST00000268489	NM_006885.3	428	Acc/Tcc	2/10	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.171985190742049	2		463	616	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56376691	56376691	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0005115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	220	441	1	ENST00000348428.3:c.731T>A	p.Leu244Ter	p.L244*	ENST00000348428	NM_006785.3	244	tTg/tAg	5/17	1	2	FACETS	0.959	0.899	1	0.959	0.899	1	CLONAL	1	TRUE	1	0.769586537580115	2		442	596	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399491	139399514	+	inframe_deletion	In_Frame_Del	DEL	CTGTTGCAGCCCTGGTCGCAGTGC	CTGTTGCAGCCCTGGTCGCAGTGC	-	novel	NA	P-0005115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	390	260	0	ENST00000277541.6:c.4629_4652del	p.His1544_Ser1551del	p.H1544_S1551del	ENST00000277541	NM_017617.3	1543	ggGCACTGCGACCAGGGCTGCAACAGc/ggc	26/34	0.767045492830458	2	FACETS	0.942	0.912	0.971	0.942	0.912	0.971	CLONAL	2	TRUE	0	0.769586537580115	2		260	538	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579350	7579350	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587781642	NA	P-0005131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	217	492	0	ENST00000269305.4:c.337T>G	p.Phe113Val	p.F113V	ENST00000269305	NM_001126112.2	113	Ttc/Gtc	4/11	0.321953004062367	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.321953004062367	1		492	1016	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0005131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	189	158	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.321953004062367	4	FACETS	1	0.96	1			1	CLONAL	3	TRUE	NA	0.321953004062367	4		158	497	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188196	10188196	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs869025637	NA	P-0005134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	122	376	0	ENST00000256474.2:c.341-2A>G		p.X114_splice	ENST00000256474	NM_000551.3	114			0.249624450049553	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.386398208365062	1		376	503	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846194	128846194	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1268449742	NA	P-0005134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	126	464	1	ENST00000249373.3:c.1124T>A	p.Ile375Asn	p.I375N	ENST00000249373	NM_005631.4	375	aTc/aAc	5/12	1	2	FACETS	0.891	0.808	0.979	0.891	0.808	0.979	CLONAL	1	TRUE	1	0.386398208365062	2		465	732	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684014	29684014	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	71	467	0	ENST00000356175.3:c.7712A>G	p.His2571Arg	p.H2571R	ENST00000356175	NM_000267.3	2571	cAt/cGt	52/57	1	2	FACETS	0.365	0.317	0.416	0.365	0.317	0.416	SUBCLONAL	1	TRUE	1	0.386398208365062	2		467	1008	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860547	151860547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	178	464	0	ENST00000262189.6:c.10115del	p.Asn3372MetfsTer12	p.N3372Mfs*12	ENST00000262189	NM_170606.2	3372	aAt/at	43/59	1	2	FACETS	0.971	0.895	1	0.971	0.895	1	CLONAL	1	TRUE	1	0.386398208365062	2		464	949	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117026	193117038	+	frameshift_variant	Frame_Shift_Del	DEL	TCAATCTGTAAAA	TCAATCTGTAAAA	-	novel	NA	P-0005134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	106	417	1	ENST00000367435.3:c.759_771del	p.Gln254ProfsTer61	p.Q254Pfs*61	ENST00000367435	NM_024529.4	253	ctTCAATCTGTAAAA/ct	8/17	1	2	FACETS	0.659	0.59	0.732	0.659	0.59	0.732	SUBCLONAL	1	TRUE	1	0.386398208365062	2		418	833	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172440	108172442	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	novel	NA	P-0005134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	159	502	0	ENST00000278616.4:c.5243_5245del	p.Ser1748_Phe1749delinsIle	p.S1748_F1749delinsI	ENST00000278616	NM_000051.3	1748	aGTTtc/atc	35/63	1	2	FACETS	0.822	0.753	0.895	0.822	0.753	0.895	CLONAL	1	TRUE	1	0.386398208365062	2		502	1001	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005135-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	48	246	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		246	514	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441431	52441431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	85	440	1	ENST00000460680.1:c.421C>T	p.His141Tyr	p.H141Y	ENST00000460680	NM_004656.3	141	Cat/Tat	6/17	NA	2	FACETS	0.92	0.819	1			1	INDETERMINATE	1	TRUE	NA	0.496633411260046	2		441	372	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859549	151859549	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	90	436	1	ENST00000262189.6:c.11113G>C	p.Asp3705His	p.D3705H	ENST00000262189	NM_170606.2	3705	Gac/Cac	43/59	1	2	FACETS	0.718	0.639	0.801	0.718	0.639	0.801	SUBCLONAL	1	TRUE	1	0.496633411260046	2		437	505	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005696	42005696	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0005140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	78	309	0	ENST00000219905.7:c.3430+2T>C		p.X1144_splice	ENST00000219905	NM_001164273.1	1144			0.111778579773726	0	FACETS	0.456	0.403	0.511			1	INDETERMINATE	1	TRUE	0	0.496633411260046	0		309	347	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094904	11094904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	94	478	1	ENST00000358026.2:c.77C>T	p.Ala26Val	p.A26V	ENST00000358026	NM_001128849.1	26	gCc/gTc	2/36	1	2	FACETS	0.978	0.877	1	0.978	0.877	1	CLONAL	1	TRUE	1	0.496633411260046	2		479	387	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0005144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	47	207	0				ENST00000310581	NM_198253.2	-/1132			0.418104444544805	0	FACETS	0.538	0.469	0.609			1	SUBCLONAL	2	TRUE	0	0.444872804838859	0		207	109	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741994	162741994	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	272	474	0	ENST00000367921.3:c.1685T>G	p.Leu562Arg	p.L562R	ENST00000367921	NM_006182.2	562	cTc/cGc	13/18	0.25882195948985	6	FACETS	1	0.967	1			1	INDETERMINATE	2	TRUE	NA	0.444872804838859	6		474	1105	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390968	89390968	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	187	432	2	ENST00000336596.2:c.1034G>T	p.Trp345Leu	p.W345L	ENST00000336596	NM_005233.5	345	tGg/tTg	5/17	0.412174461449722	4	FACETS	0.779	0.721	0.839	0.779	0.721	0.839	SUBCLONAL	2	TRUE	2	0.444872804838859	4		434	780	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218084	108218084	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs760955058	NA	P-0005144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	151	305	0	ENST00000278616.4:c.8663T>C	p.Ile2888Thr	p.I2888T	ENST00000278616	NM_000051.3	2888	aTa/aCa	59/63	0.368716131519554	2	FACETS	0.864	0.799	0.93	0.864	0.799	0.93	CLONAL	2	TRUE	0	0.444872804838859	2		305	393	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443861	18443861	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	141	327	0	ENST00000266497.5:c.834T>A	p.Phe278Leu	p.F278L	ENST00000266497		278	ttT/ttA	3/31	0.207686153031911	4	FACETS	0.948	0.87	1	0.948	0.87	1	INDETERMINATE	2	TRUE	2	0.444872804838859	4		327	483	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641453	18641453	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	202	410	0	ENST00000266497.5:c.2452T>A	p.Phe818Ile	p.F818I	ENST00000266497		818	Ttc/Atc	17/31	0.207686153031911	4	FACETS	0.933	0.868	1	0.933	0.868	1	INDETERMINATE	2	TRUE	2	0.444872804838859	4		410	703	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727098	40727098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	242	544	0	ENST00000373198.4:c.3866C>T	p.Ser1289Phe	p.S1289F	ENST00000373198	NM_133170.3	1289	tCc/tTc	28/32	0.323965555530898	3	FACETS	1	0.985	1			1	CLONAL	2	TRUE	NA	0.444872804838859	3		544	584	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0005154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	23	419	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.599	0.466	0.754	0.599	0.466	0.754	SUBCLONAL	1	TRUE	1	0.162288629698507	2		419	473	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0005154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	29	154	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	0.162288629698507	2		154	286	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405890	49405890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	55	579	0	ENST00000418115.1:c.248G>A	p.Cys83Tyr	p.C83Y	ENST00000418115	NM_001664.2	83	tGt/tAt	3/5	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.162288629698507	2		579	512	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839742	27839742	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	50	1148	0	ENST00000328488.2:c.352G>A	p.Val118Ile	p.V118I	ENST00000328488	NM_003533.2	118	Gtc/Atc	1/1	1	2	FACETS	0.818	0.693	0.957	0.818	0.693	0.957	CLONAL	1	TRUE	1	0.162288629698507	2		1148	753	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647389	117647389	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	76	676	0	ENST00000368508.3:c.5555G>T	p.Gly1852Val	p.G1852V	ENST00000368508	NM_002944.2	1852	gGa/gTa	33/43	0.162288629698507	0	FACETS	1	0.97	1			1	CLONAL	1	TRUE	0	0.162288629698507	0		676	574	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840603	36840603	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs966082163	NA	P-0005154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	20	271	0	ENST00000358127.4:c.1130G>A	p.Arg377Gln	p.R377Q	ENST00000358127	NM_001280556.1	377	cGa/cAa	10/10	1	2	FACETS	0.974	0.746	1	0.974	0.746	1	CLONAL	1	TRUE	1	0.162288629698507	2		271	253	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575374	64575374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs794728621	NA	P-0005154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	51	253	0	ENST00000312049.6:c.643G>A	p.Val215Met	p.V215M	ENST00000312049	NM_130799.2	215	Gtg/Atg	3/10	1	2	FACETS	1	0.905	1	1	0.977	1	CLONAL	2	TRUE	1	0.162288629698507	2		253	292	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	463358	463358	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	56	520	0	ENST00000399788.2:c.913G>A	p.Glu305Lys	p.E305K	ENST00000399788	NM_001042603.1	305	Gaa/Aaa	8/28	0.162288629698507	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.162288629698507	1		520	462	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431328	121431328	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	11	184	0	ENST00000257555.6:c.532A>G	p.Thr178Ala	p.T178A	ENST00000257555		178	Acc/Gcc	3/10	1	2	FACETS	0.721	0.499	0.997	0.721	0.499	0.997	CLONAL	1	TRUE	1	0.162288629698507	2		184	188	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562325	21562325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	24	248	1	ENST00000382592.4:c.1594G>A	p.Asp532Asn	p.D532N	ENST00000382592	NM_014572.2	532	Gac/Aac	4/8	NA	2	FACETS	1	0.889	1			1	INDETERMINATE	1	TRUE	NA	0.162288629698507	2		249	242	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56878521	56878521	+	stop_lost	Nonstop_Mutation	SNP	A	A	C	novel	NA	P-0005154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	28	591	0	ENST00000308159.5:c.2460A>C	p.Ter820TyrextTer50	p.*820Yext*50	ENST00000308159	NM_014669.4	820	taA/taC	22/22	0.162288629698507	0	FACETS	0.623	0.497	0.767			1	SUBCLONAL	1	TRUE	0	0.162288629698507	0		591	464	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827486	72827486	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs367676710	NA	P-0005154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	37	819	0	ENST00000268489.5:c.9095A>C	p.Lys3032Thr	p.K3032T	ENST00000268489	NM_006885.3	3032	aAg/aCg	9/10	0.162288629698507	0	FACETS	0.582	0.479	0.699			1	SUBCLONAL	1	TRUE	0	0.162288629698507	0		819	656	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022397	31022397	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0005154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	16	188	0	ENST00000375687.4:c.1882A>T	p.Arg628Ter	p.R628*	ENST00000375687	NM_015338.5	628	Aga/Tga	13/13	0.162288629698507	3	FACETS	0.772	0.571	1	0.386	0.285	0.507	CLONAL	1	TRUE	1	0.162288629698507	3		188	276	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200089	123200089	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	41	567	2	ENST00000218089.9:c.2161G>T	p.Glu721Ter	p.E721*	ENST00000218089	NM_001042749.1	721	Gaa/Taa	22/35	0.15427957461661	0	FACETS	0.787	0.655	0.934			1	CLONAL	1	TRUE	0	0.162288629698507	0		569	538	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0005154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	33	395	0	ENST00000346208.3:c.1221_1222del	p.Pro408LeufsTer98	p.P408Lfs*98	ENST00000346208		407	tCG/t	6/6	0.162288629698507	5	FACETS	0.986	0.802	1	0.246	0.2	0.299	CLONAL	1	TRUE	1	0.162288629698507	5		395	513	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578414	7578414	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	127	292	0	ENST00000269305.4:c.516del	p.Val173Ter	p.V173*	ENST00000269305	NM_001126112.2	172	gtT/gt	5/11	0.212375654556667	2	FACETS	1	0.983	1	0.692	0.628	0.758	CLONAL	1	TRUE	0	0.30815201433651	2		292	596	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506296	120506296	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	110	373	0	ENST00000256646.2:c.1816G>T	p.Asp606Tyr	p.D606Y	ENST00000256646	NM_024408.3	606	Gac/Tac	11/34	0.276101042686302	4	FACETS	0.819	0.733	0.909	0.409	0.366	0.455	CLONAL	1	TRUE	2	0.30815201433651	4		373	1141	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243553	46243553	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	131	314	0	ENST00000334344.6:c.1906C>G	p.Pro636Ala	p.P636A	ENST00000334344	NM_152641.2	636	Cct/Gct	14/21	0.30815201433651	7	FACETS	0.827	0.75	0.908			1	CLONAL	2	TRUE	NA	0.30815201433651	7		314	910	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039174	49039174	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	195	460	0	ENST00000267163.4:c.2252C>G	p.Ser751Cys	p.S751C	ENST00000267163	NM_000321.2	751	tCt/tGt	22/27	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.30815201433651	2		460	927	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514772	44514772	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	180	373	0	ENST00000291552.4:c.475G>A	p.Glu159Lys	p.E159K	ENST00000291552	NM_006758.2	159	Gag/Aag	6/8	0.30815201433651	3	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.30815201433651	3		373	1135	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934335	39934335	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	85	535	0	ENST00000378444.4:c.264C>G	p.Ile88Met	p.I88M	ENST00000378444	NM_001123385.1	88	atC/atG	4/15	NA	2	FACETS	0.539	0.475	0.608			1	INDETERMINATE	1	TRUE	NA	0.30815201433651	2		535	1023	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0005178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	331	399	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.426789435532833	5	FACETS	0.848	0.804	0.893	0.848	0.804	0.893	CLONAL	3	TRUE	2	0.491957315927481	5		400	919	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0005178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	76	375	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.333578291838234	2	FACETS	1	0.978	1	0.725	0.648	0.805	CLONAL	1	TRUE	0	0.491957315927481	2		378	213	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0005178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	870	569	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.491957315927481	15	FACETS	0.967	0.943	0.991			1	CLONAL	11	TRUE	NA	0.491957315927481	15		569	1396	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883547	37883547	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0005178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	82	387	0	ENST00000269571.5:c.3160-1G>C		p.X1054_splice	ENST00000269571		1054			0.491957315927481	9	FACETS	0.897	0.789	1			1	CLONAL	1	TRUE	NA	0.491957315927481	9		387	1011	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919051	50919051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144111108	NA	P-0005178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	30	634	2	ENST00000440232.2:c.2788G>A	p.Ala930Thr	p.A930T	ENST00000440232	NM_002691.3	930	Gcc/Acc	22/27	0.491957315927481	1	FACETS	0.222	0.179	0.272	0.222	0.179	0.272	SUBCLONAL	1	TRUE	0	0.491957315927481	1		636	414	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0005181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	138	484	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.289160877815406	3	FACETS	1	0.916	1	0.503	0.458	0.549	INDETERMINATE	1	TRUE	1	0.495907750497848	3		484	691	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0005181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	191	353	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.495907750497848	3	FACETS	0.808	0.751	0.866	0.808	0.751	0.866	CLONAL	2	TRUE	1	0.495907750497848	3		353	595	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566890	212566890	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	54	298	0	ENST00000342788.4:c.1291G>A	p.Gly431Ser	p.G431S	ENST00000342788	NM_005235.2	431	Ggc/Agc	12/28	1	2	FACETS	0.476	0.407	0.551	0.476	0.407	0.551	SUBCLONAL	1	TRUE	1	0.495907750497848	2		298	458	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685308	89685308	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876660634	NA	P-0005181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	32	286	0	ENST00000371953.3:c.203A>G	p.Tyr68Cys	p.Y68C	ENST00000371953	NM_000314.4	68	tAc/tGc	3/9	0.495907750497848	3	FACETS	0.418	0.339	0.507	0.209	0.169	0.254	SUBCLONAL	1	TRUE	1	0.495907750497848	3		286	385	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420229	49420229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	280	482	2	ENST00000301067.7:c.15520C>T	p.Arg5174Trp	p.R5174W	ENST00000301067	NM_003482.3	5174	Cgg/Tgg	48/54	1	2	FACETS	0.884	0.83	0.941	0.884	0.83	0.941	CLONAL	1	TRUE	1	0.495907750497848	2		484	1277	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226132	2226132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1662	273	589	0	ENST00000326181.6:c.1829C>T	p.Thr610Met	p.T610M	ENST00000326181	NM_032271.2	610	aCg/aTg	19/21	1	2	FACETS	0.569	0.532	0.608	0.569	0.532	0.608	SUBCLONAL	1	TRUE	1	0.495907750497848	2		589	1935	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836984	89836984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199938598	NA	P-0005181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1471	169	528	0	ENST00000389301.3:c.2210C>T	p.Ala737Val	p.A737V	ENST00000389301	NM_000135.2	737	gCt/gTt	24/43	1	2	FACETS	0.416	0.38	0.453	0.416	0.38	0.453	SUBCLONAL	1	TRUE	1	0.495907750497848	2		528	1640	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0005183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	130	399	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.58	2		400	435	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	35	246	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	0.595	0.496	0.702	0.595	0.496	0.702	INDETERMINATE	1	TRUE	0	0.58	1		246	144	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148727	20148727	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0005183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	80	501	0	ENST00000379607.5:c.338-2A>T		p.X113_splice	ENST00000379607	NM_001412.3	113			0.3	2	FACETS	0.732	0.648	0.82			1	INDETERMINATE	1	TRUE	NA	0.58	2		501	377	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831172	72831221	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGATGTAGAAAGGGAAGAGGAGGTGCTGCTGCTGCTGTAGTTGCAGCA	GGGGATGTAGAAAGGGAAGAGGAGGTGCTGCTGCTGCTGTAGTTGCAGCA	-	novel	NA	P-0005183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	122	697	0	ENST00000268489.5:c.5360_5409del	p.Leu1787GlnfsTer3	p.L1787Qfs*3	ENST00000268489	NM_006885.3	1787	cTGCTGCAACTACAGCAGCAGCAGCACCTCCTCTTCCCTTTCTACATCCCC/c	9/10	0.3	1	FACETS	0.593	0.538	0.649	0.593	0.538	0.649	INDETERMINATE	1	TRUE	0	0.58	1		697	504	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866546	117866551	+	inframe_deletion	In_Frame_Del	DEL	CTGTCT	CTGTCT	-	novel	NA	P-0005183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	178	965	0	ENST00000297338.2:c.1094_1099del	p.Glu365_Thr366del	p.E365_T366del	ENST00000297338	NM_006265.2	365	gAGACAGga/gga	9/14	0.121342987292782	3	FACETS	1	0.986	1	0.644	0.596	0.693	INDETERMINATE	1	TRUE	1	0.58	3		965	615	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0005191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	273	325	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.296297239699986	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	3	TRUE	0	0.29	3		325	706	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0005191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	156	398	0	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	0.257537084205	2	FACETS	0.924	0.851	1	0.924	0.851	1	CLONAL	2	TRUE	0	0.29	2		398	582	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170840	99170840	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1442257080	NA	P-0005191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	64	443	0	ENST00000074304.5:c.1469C>T	p.Ser490Leu	p.S490L	ENST00000074304	NM_001134224.1	490	tCg/tTg	16/26	0.165765324569436	2	FACETS	0.691	0.598	0.792	0.345	0.299	0.396	INDETERMINATE	1	TRUE	0	0.29	2		443	639	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812230	212812230	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	59	377	0	ENST00000342788.4:c.346G>T	p.Ala116Ser	p.A116S	ENST00000342788	NM_005235.2	116	Gcc/Tcc	3/28	0.165765324569436	2	FACETS	0.575	0.494	0.663	0.287	0.247	0.332	INDETERMINATE	1	TRUE	0	0.29	2		377	708	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022108	5022108	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	123	441	0	ENST00000381652.3:c.121G>C	p.Val41Leu	p.V41L	ENST00000381652	NM_004972.3	41	Gtg/Ctg	3/25	0.296297239699986	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.29	1		441	622	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341944	8341944	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs954644962	NA	P-0005191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	97	319	0	ENST00000356435.5:c.4696A>G	p.Ile1566Val	p.I1566V	ENST00000356435		1566	Ata/Gta	29/35	0.296297239699986	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.29	1		319	442	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8501045	8501045	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	72	276	0	ENST00000356435.5:c.1837C>A	p.Pro613Thr	p.P613T	ENST00000356435		613	Cct/Act	13/35	0.296297239699986	1	FACETS	0.956	0.838	1	0.956	0.838	1	CLONAL	1	TRUE	0	0.29	1		276	444	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998186	100998186	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	58	324	0	ENST00000325455.5:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000325455	NM_001202474.3	539	cCg/cGg	1/8	0.208775435427594	3	FACETS	0.985	0.848	1	0.492	0.424	0.567	CLONAL	1	TRUE	1	0.29	3		324	465	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129062	2129062	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149808366	NA	P-0005191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	51	360	0	ENST00000219476.3:c.2996G>C	p.Ser999Thr	p.S999T	ENST00000219476	NM_000548.3	999	aGc/aCc	27/42	1	2	FACETS	0.694	0.59	0.808	0.694	0.59	0.808	SUBCLONAL	1	TRUE	1	0.29	2		360	507	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007883	45007919	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAAGATAGTTAAGTGGGGTAAGTCTTACATTCTTTTG	CAAGATAGTTAAGTGGGGTAAGTCTTACATTCTTTTG	-	novel	NA	P-0005191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	65	272	0	ENST00000558401.1:c.330_346+20del		p.X110_splice	ENST00000558401	NM_004048.2	110		2/4	0.296297239699986	1	FACETS	0.924	0.804	1	0.924	0.804	1	CLONAL	1	TRUE	0	0.29	1		272	415	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796944	45796944	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	62	430	0	ENST00000450313.1:c.1386del	p.Gln463ArgfsTer4	p.Q463Rfs*4	ENST00000450313	NM_012222.2	462	ggG/gg	14/16	1	2	FACETS	0.68	0.587	0.781	0.68	0.587	0.781	SUBCLONAL	1	TRUE	1	0.29	2		430	629	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038773	47038773	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	54	325	0	ENST00000377604.3:c.782del	p.Gly261ValfsTer5	p.G261Vfs*5	ENST00000377604	NM_001204468.1	260	ctG/ct	9/24	0.296297239699986	1	FACETS	0.937	0.804	1	0.937	0.804	1	CLONAL	1	TRUE	0	0.29	1		325	340	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857510	9857510	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	28	305	1	ENST00000330684.3:c.3891del	p.Asp1297GlufsTer6	p.D1297Efs*6	ENST00000330684	NM_001134407.1	1297	gaC/ga	13/13	1	2	FACETS	0.438	0.349	0.539	0.438	0.349	0.539	SUBCLONAL	1	TRUE	1	0.29	2		306	441	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519886	NA	P-0005198-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	148	481	0	ENST00000349496.5:c.97T>C	p.Ser33Pro	p.S33P	ENST00000349496	NM_001904.3	33	Tct/Cct	3/15	1	2	FACETS	0.939	0.863	1	0.939	0.863	1	CLONAL	1	TRUE	1	0.621930425865316	2		481	507	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040945	47040945	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005198-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	163	399	0	ENST00000377604.3:c.1475C>A	p.Ser492Ter	p.S492*	ENST00000377604	NM_001204468.1	492	tCg/tAg	14/24	0.198805264772382	1	FACETS	0.688	0.636	0.742	0.688	0.636	0.742	INDETERMINATE	1	TRUE	0	0.621930425865316	1		399	525	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357700	70357700	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005198-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	167	624	0	ENST00000374080.3:c.5952del	p.Val1985Ter	p.V1985*	ENST00000374080		1984	cTt/ct	41/45	0.198805264772382	1	FACETS	0.64	0.591	0.691	0.64	0.591	0.691	INDETERMINATE	1	TRUE	0	0.621930425865316	1		624	578	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242486	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATCT	AATTAAGAGAAGCAACATCT	TC	rs121913424	NA	P-0005198-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	115	365	0	ENST00000275493.2:c.2237_2256delinsTC	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCT/gTC	19/28	1	2	FACETS	0.75	0.679	0.824	0.75	0.679	0.824	SUBCLONAL	1	TRUE	1	0.621930425865316	2		365	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576662	7576870	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAAATATATATTATGGTATAAGTTGGTGTTCTGAAGTTAGTTAGCTACAACCAGGAGCCATTGTCTTTGAGGCATCACTGCCCCCTGATGGCAAATGCCCCAATTGCAGGTAAAACAGTCAAGAAGAAAACGGCATTTTGAGTGTTAGACTGGAAACTTTCCACTTGATAAGAGGTCCCAAGACTTAGTACCTGAAGGGTGAAATATTC	AAAATATATATTATGGTATAAGTTGGTGTTCTGAAGTTAGTTAGCTACAACCAGGAGCCATTGTCTTTGAGGCATCACTGCCCCCTGATGGCAAATGCCCCAATTGCAGGTAAAACAGTCAAGAAGAAAACGGCATTTTGAGTGTTAGACTGGAAACTTTCCACTTGATAAGAGGTCCCAAGACTTAGTACCTGAAGGGTGAAATATTC	-	novel	NA	P-0005206-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	66	274	0	ENST00000269305.4:c.976_993+191del		p.X326_splice	ENST00000269305	NM_001126112.2	326		9/11	1	2	FACETS	0.814	0.71	0.926	1	0.976	1	CLONAL	2	TRUE	1	0.199677205823454	2		274	406	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096724	178096724	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005206-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	37	183	0	ENST00000397062.3:c.607del	p.Glu203LysfsTer18	p.E203Kfs*18	ENST00000397062	NM_006164.4	203	Gaa/aa	5/5	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.199677205823454	2		183	328	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0005212-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	132	154	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.551383467419632	4	FACETS	0.993	0.912	1	0.993	0.912	1	CLONAL	2	TRUE	2	0.551383467419632	4		154	374	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434745	49434745	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777903880	NA	P-0005212-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	42	193	0	ENST00000301067.7:c.6808G>A	p.Glu2270Lys	p.E2270K	ENST00000301067	NM_003482.3	2270	Gag/Aag	31/54	0.522319071692341	3	FACETS	1	0.921	1	0.572	0.484	0.665	CLONAL	1	TRUE	1	0.551383467419632	3		193	170	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098953	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005212-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	131	241	0	ENST00000397062.3:c.92G>C	p.Gly31Ala	p.G31A	ENST00000397062	NM_006164.4	31	gGa/gCa	2/5	0.473798501026394	3	FACETS	1	0.98	1	0.777	0.72	0.834	CLONAL	2	TRUE	0	0.551383467419632	3		241	260	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664886	138664886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005212-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	14	56	0	ENST00000330315.3:c.679G>A	p.Ala227Thr	p.A227T	ENST00000330315	NM_023067.3	227	Gca/Aca	1/1	0.551383467419632	4	FACETS	1	0.871	1	0.668	0.496	0.862	CLONAL	1	TRUE	2	0.551383467419632	4		56	59	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916845	178916845	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005212-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	219	697	0	ENST00000263967.3:c.232G>A	p.Glu78Lys	p.E78K	ENST00000263967	NM_006218.2	78	Gaa/Aaa	2/21	0.551383467419632	4	FACETS	0.892	0.827	0.959	0.446	0.413	0.48	CLONAL	1	TRUE	2	0.551383467419632	4		697	1382	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244100	153244100	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005212-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	200	286	0	ENST00000281708.4:c.2057T>A	p.Val686Asp	p.V686D	ENST00000281708	NM_033632.3	686	gTt/gAt	12/12	0.551383467419632	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.551383467419632	2		286	324	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273086	55273086	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005212-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	188	374	0	ENST00000275493.2:c.3409G>T	p.Glu1137Ter	p.E1137*	ENST00000275493	NM_005228.3	1137	Gag/Tag	28/28	0.551383467419632	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	0	0.551383467419632	2		374	339	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420183	49420183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005212-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	232	405	0	ENST00000301067.7:c.15566G>A	p.Gly5189Glu	p.G5189E	ENST00000301067	NM_003482.3	5189	gGa/gAa	48/54	0.522319071692341	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.551383467419632	3		405	486	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444166	49444166	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005212-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	114	356	0	ENST00000301067.7:c.3205G>T	p.Glu1069Ter	p.E1069*	ENST00000301067	NM_003482.3	1069	Gag/Tag	11/54	0.522319071692341	3	FACETS	1	0.943	1	0.53	0.479	0.583	CLONAL	1	TRUE	1	0.551383467419632	3		356	498	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482368	56482368	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005212-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	236	395	0	ENST00000267101.3:c.916C>T	p.Pro306Ser	p.P306S	ENST00000267101	NM_001982.3	306	Cct/Tct	8/28	0.522319071692341	3	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	1	0.551383467419632	3		395	546	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858928	57858928	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005212-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	191	589	0	ENST00000228682.2:c.424C>T	p.Gln142Ter	p.Q142*	ENST00000228682	NM_005269.2	142	Caa/Taa	5/12	0.522319071692341	3	FACETS	1	0.978	1	0.568	0.526	0.611	CLONAL	1	TRUE	1	0.551383467419632	3		589	778	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114241	115114241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005212-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	102	372	0	ENST00000257566.3:c.976G>A	p.Asp326Asn	p.D326N	ENST00000257566	NM_016569.3	326	Gat/Aat	6/8	0.522319071692341	3	FACETS	1	0.959	1	0.562	0.506	0.621	CLONAL	1	TRUE	1	0.551383467419632	3		372	420	SUCCESS
BLM	641	MSKCC	GRCh37	15	91308618	91308618	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005212-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	81	405	0	ENST00000355112.3:c.2167C>T	p.Gln723Ter	p.Q723*	ENST00000355112	NM_000057.2	723	Caa/Taa	9/22	1	2	FACETS	0.675	0.598	0.758	0.675	0.598	0.758	SUBCLONAL	1	TRUE	1	0.551383467419632	2		405	435	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131719	2131719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746588726	NA	P-0005212-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	83	558	0	ENST00000219476.3:c.3734G>A	p.Arg1245Gln	p.R1245Q	ENST00000219476	NM_000548.3	1245	cGg/cAg	31/42	0.551383467419632	1	FACETS	0.811	0.725	0.9	0.811	0.725	0.9	CLONAL	1	TRUE	0	0.551383467419632	1		558	269	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56401549	56401549	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005212-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	167	478	0	ENST00000348428.3:c.1411G>A	p.Asp471Asn	p.D471N	ENST00000348428	NM_006785.3	471	Gat/Aat	12/17	0.522319071692341	3	FACETS	0.92	0.846	0.997	0.46	0.423	0.499	CLONAL	1	TRUE	1	0.551383467419632	3		478	840	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1206916	1206916	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005212-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	57	246	0	ENST00000326873.7:c.4G>C	p.Glu2Gln	p.E2Q	ENST00000326873	NM_000455.4	2	Gag/Cag	1/10	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.551383467419632	NA		246	232	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0005221-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	23	286	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.284637520993229	3	FACETS	0.987	0.787	1	0.987	0.787	1	CLONAL	2	FALSE	1	0.282878397770555	3		286	94	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114901060	114901060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs190966900	NA	P-0005221-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	15	617	1	ENST00000543371.1:c.670G>A	p.Val224Ile	p.V224I	ENST00000543371	NM_001198531.1	224	Gta/Ata	6/14	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.282878397770555	NA		618	123	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377211	118377211	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005221-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	26	524	0	ENST00000534358.1:c.10604G>A	p.Gly3535Asp	p.G3535D	ENST00000534358	NM_005933.3	3535	gGt/gAt	27/36	0.282878397770555	5	FACETS	1	0.858	1	0.721	0.581	0.876	CLONAL	2	FALSE	2	0.282878397770555	5		524	121	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0005239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	40	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.107365531762354	3	FACETS	0.885	0.735	1	0.443	0.367	0.526	INDETERMINATE	1	TRUE	1	0.2	3		249	497	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989487	212989487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765191737	NA	P-0005239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	41	405	1	ENST00000342788.4:c.224C>T	p.Ser75Phe	p.S75F	ENST00000342788	NM_005235.2	75	tCc/tTc	2/28	1	2	FACETS	0.504	0.419	0.6	0.504	0.419	0.6	SUBCLONAL	1	TRUE	1	0.2	2		406	813	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683535	182683535	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	60	233	0	ENST00000292782.4:c.10T>A	p.Leu4Met	p.L4M	ENST00000292782	NM_020640.2	4	Ttg/Atg	2/7	0.107365531762354	3	FACETS	1	0.935	1	0.575	0.495	0.662	INDETERMINATE	1	TRUE	1	0.2	3		233	574	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180040078	180040078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	106	420	0	ENST00000261937.6:c.3364G>A	p.Glu1122Lys	p.E1122K	ENST00000261937	NM_182925.4	1122	Gag/Aag	25/30	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.2	2		420	991	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130352	2130352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773951533	NA	P-0005244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	32	392	1	ENST00000219476.3:c.3584C>T	p.Ala1195Val	p.A1195V	ENST00000219476	NM_000548.3	1195	gCg/gTg	30/42	0.822171373052854	1	FACETS	0.072	0.058	0.088	0.072	0.058	0.088	SUBCLONAL	1	TRUE	0	0.822171373052854	1		393	639	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0005244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	612	474	21	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	0.807621746005051	1	FACETS	0.982	0.955	1	0.982	0.955	1	CLONAL	1	TRUE	0	0.822171373052854	1		495	893	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958497	175958497	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0005244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	398	445	0	ENST00000367669.3:c.1847+1G>A		p.X616_splice	ENST00000367669	NM_022457.5	616			0.822171373052854	1	FACETS	0.958	0.925	0.991	0.958	0.925	0.991	CLONAL	1	TRUE	0	0.822171373052854	1		445	595	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933240	49933240	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143096514	NA	P-0005244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	92	661	0	ENST00000296474.3:c.2870C>T	p.Thr957Met	p.T957M	ENST00000296474	NM_002447.2	957	aCg/aTg	12/20	0.822171373052854	1	FACETS	0.139	0.123	0.157	0.139	0.123	0.157	SUBCLONAL	1	TRUE	0	0.822171373052854	1		661	946	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149452913	149452913	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	695	537	1	ENST00000286301.3:c.1033C>A	p.His345Asn	p.H345N	ENST00000286301	NM_005211.3	345	Cac/Aac	7/22	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.822171373052854	2		538	1633	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288600	33288600	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs779014832	NA	P-0005244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	451	326	2	ENST00000374542.5:c.952C>T	p.Arg318Ter	p.R318*	ENST00000374542	NM_001141970.1	318	Cga/Tga	3/8	0.822171373052854	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.822171373052854	1		328	613	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152357858	152357858	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs750903875	NA	P-0005244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	665	629	1	ENST00000359321.1:c.49C>T	p.Arg17Ter	p.R17*	ENST00000359321	NM_005431.1	17	Cga/Tga	2/3	1	2	FACETS	0.989	0.954	1	0.989	0.954	1	CLONAL	1	TRUE	1	0.822171373052854	2		630	1635	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563167	21563167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371775408	NA	P-0005244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	106	346	0	ENST00000382592.4:c.752C>T	p.Ala251Val	p.A251V	ENST00000382592	NM_014572.2	251	gCg/gTg	4/8	1	2	FACETS	0.249	0.222	0.277	0.249	0.222	0.277	SUBCLONAL	1	TRUE	1	0.822171373052854	2		346	1036	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103409	2103409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372321790	NA	P-0005244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	498	465	0	ENST00000219476.3:c.292C>T	p.Arg98Trp	p.R98W	ENST00000219476	NM_000548.3	98	Cgg/Tgg	4/42	0.822171373052854	1	FACETS	0.799	0.77	0.827	0.799	0.77	0.827	SUBCLONAL	1	TRUE	0	0.822171373052854	1		465	893	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510581	38510581	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	739	488	0	ENST00000254066.5:c.835C>A	p.Pro279Thr	p.P279T	ENST00000254066	NM_000964.3	279	Ccc/Acc	7/9	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.822171373052854	2		488	1697	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443599	52443601	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0005256-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	233	153	0	ENST00000460680.1:c.91_93del	p.Glu31del	p.E31del	ENST00000460680	NM_004656.3	31	GAG/-	3/17	0.524129830785327	2	FACETS	0.881	0.835	0.927	0.881	0.835	0.927	CLONAL	2	TRUE	0	0.624915999159074	2		153	423	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778096	135778096	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203671	NA	P-0005256-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	282	225	0	ENST00000298552.3:c.2287C>T	p.Gln763Ter	p.Q763*	ENST00000298552	NM_001162426.1	763	Cag/Tag	18/23	0.524129830785327	2	FACETS	0.912	0.869	0.954	0.912	0.869	0.954	CLONAL	2	TRUE	0	0.624915999159074	2		225	495	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954652	17954652	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005256-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	180	194	0	ENST00000458235.1:c.242G>T	p.Trp81Leu	p.W81L	ENST00000458235	NM_000215.3	81	tGg/tTg	3/24	0.339711187519697	5	FACETS	1	0.974	1	0.731	0.679	0.783	INDETERMINATE	2	TRUE	2	0.624915999159074	5		194	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0005259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	83	749	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.628	0.552	0.709	0.628	0.552	0.709	SUBCLONAL	1	TRUE	1	0.25	2		750	1058	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0005259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	102	569	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	1	2	FACETS	0.94	0.84	1	0.94	0.84	1	CLONAL	1	TRUE	1	0.25	2		569	868	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715678	30715678	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	76	572	1	ENST00000295754.5:c.1336G>T	p.Asp446Tyr	p.D446Y	ENST00000295754	NM_003242.5	446	Gat/Tat	5/7	1	2	FACETS	0.67	0.587	0.761	0.67	0.587	0.761	SUBCLONAL	1	TRUE	1	0.25	2		573	907	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589762	28589762	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	132	706	0	ENST00000241453.7:c.2618C>T	p.Ser873Leu	p.S873L	ENST00000241453	NM_004119.2	873	tCa/tTa	21/24	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.25	2		706	1020	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680491	241680491	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs755343833	NA	P-0005272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	342	330	0	ENST00000366560.3:c.258A>C	p.Glu86Asp	p.E86D	ENST00000366560	NM_000143.3	86	gaA/gaC	2/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.920373721261554	2		330	733	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665641	86665641	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005291-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	406	286	0	ENST00000274376.6:c.1622T>G	p.Phe541Cys	p.F541C	ENST00000274376	NM_002890.2	541	tTt/tGt	12/25	0.689507361543124	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.690302123809463	2		286	515	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0005299-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	634	785	4	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.791174870140474	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	FALSE	0	0.813992281125833	2		789	753	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913384	NA	P-0005299-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	143	247	0	ENST00000304494.5:c.262G>T	p.Glu88Ter	p.E88*	ENST00000304494	NM_000077.4	88	Gag/Tag	2/3	0.813992281125833	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	0	0.813992281125833	1		247	204	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71064784	71064784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757909648	NA	P-0005299-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	734	445	0	ENST00000318789.4:c.890C>T	p.Pro297Leu	p.P297L	ENST00000318789	NM_032682.5	297	cCc/cTc	12/21	0.567766764059051	4	FACETS	0.939	0.914	0.964	0.939	0.914	0.964	CLONAL	3	FALSE	1	0.813992281125833	4		445	1161	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0005300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	192	375	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.310442349459796	2	FACETS	0.935	0.877	0.994	0.935	0.877	0.994	CLONAL	2	TRUE	0	0.504407457226428	2		378	407	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741868	17741868	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1466899825	NA	P-0005300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	35	71	1	ENST00000250003.3:c.539C>T	p.Ala180Val	p.A180V	ENST00000250003	NM_002478.4	180	gCg/gTg	1/3	0.432498675478059	2	FACETS	1	0.954	1	0.723	0.611	0.84	CLONAL	1	TRUE	0	0.504407457226428	2		72	96	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532623	46532623	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	144	559	0	ENST00000262741.5:c.455T>G	p.Leu152Arg	p.L152R	ENST00000262741	NM_003629.3	152	cTt/cGt	4/10	0.432498675478059	2	FACETS	0.797	0.729	0.869	0.399	0.364	0.435	SUBCLONAL	1	TRUE	0	0.504407457226428	2		559	716	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830850	156830850	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs995918945	NA	P-0005300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	82	415	0	ENST00000524377.1:c.124C>T	p.Pro42Ser	p.P42S	ENST00000524377	NM_002529.3	42	Ccc/Tcc	1/17	1	2	FACETS	0.869	0.772	0.972	0.869	0.772	0.972	CLONAL	1	TRUE	1	0.504407457226428	2		415	374	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274521	198274521	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	53	607	0	ENST00000335508.6:c.877T>C	p.Trp293Arg	p.W293R	ENST00000335508	NM_012433.2	293	Tgg/Cgg	7/25	0.206465151193018	3	FACETS	0.407	0.346	0.473	0.136	0.115	0.158	INDETERMINATE	1	TRUE	0	0.504407457226428	3		607	647	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440379	52440379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	168	331	0	ENST00000460680.1:c.673G>A	p.Asp225Asn	p.D225N	ENST00000460680	NM_004656.3	225	Gac/Aac	9/17	0.38620518513523	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.38620518513523	1		331	485	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867657	78867657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	65	609	0	ENST00000306801.3:c.2393C>T	p.Ser798Phe	p.S798F	ENST00000306801	NM_020761.2	798	tCc/tTc	20/34	0.312109070791598	1	FACETS	0.372	0.321	0.426	0.372	0.321	0.426	SUBCLONAL	1	TRUE	0	0.38620518513523	1		609	731	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432664	29432664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113994087	NA	P-0121533-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	440	184	0	ENST00000389048.3:c.3824G>A	p.Arg1275Gln	p.R1275Q	ENST00000389048	NM_004304.4	1275	cGa/cAa	25/29	0.85956629811149	3	FACETS	0.893	0.85	0.937	0.447	0.425	0.469	CLONAL	1	NA	1	0.902871787419958	3		184	1584	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196701	67196701	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121533-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	39	175	0	ENST00000312629.5:c.230G>T	p.Gly77Val	p.G77V	ENST00000312629	NM_003952.2	77	gGc/gTc	3/15	1	2	FACETS	0.278	0.231	0.33	0.278	0.231	0.33	SUBCLONAL	1	NA	1	0.902871787419958	2		175	311	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042083	14042083	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121533-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	369	340	0	ENST00000311895.7:c.2630C>A	p.Ala877Glu	p.A877E	ENST00000311895	NM_005236.2	877	gCa/gAa	11/11	1	2	FACETS	0.972	0.927	1	0.972	0.927	1	CLONAL	1	NA	1	0.902871787419958	2		340	841	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110669	2110669	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0005325-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	286	512	0	ENST00000219476.3:c.976-2A>G		p.X326_splice	ENST00000219476	NM_000548.3	326			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		512	777	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0005328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	164	574	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.241469454849232	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.241469454849232	1		574	1033	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643943	52643943	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	28	256	0	ENST00000394830.3:c.1953del	p.Lys651AsnfsTer5	p.K651Nfs*5	ENST00000394830	NM_018313.4	651	aaA/aa	17/30	0.241469454849232	1	FACETS	0.957	0.77	1	0.957	0.77	1	CLONAL	1	TRUE	0	0.241469454849232	1		256	213	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718999	190718999	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147084726	NA	P-0005328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	26	310	0	ENST00000441310.2:c.1001C>T	p.Thr334Met	p.T334M	ENST00000441310	NM_000534.4	334	aCg/aTg	9/13	1	2	FACETS	0.81	0.643	0.999	0.81	0.643	0.999	CLONAL	1	TRUE	1	0.241469454849232	2		310	266	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591246	67591246	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0005328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	139	380	1	ENST00000274335.5:c.1746-2A>T		p.X582_splice	ENST00000274335		582			1	2	FACETS	0.814	0.742	0.889	1	0.988	1	CLONAL	2	TRUE	1	0.241469454849232	2		381	707	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191469	10191469	+	splice_acceptor_variant	Splice_Site	DEL	A	A	-	novel	NA	P-0005328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	50	316	0	ENST00000256474.2:c.464-2del		p.X155_splice	ENST00000256474	NM_000551.3	155			0.241469454849232	1	FACETS	0.739	0.627	0.861	0.739	0.627	0.861	SUBCLONAL	1	TRUE	0	0.241469454849232	1		316	493	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692916	89692931	+	frameshift_variant	Frame_Shift_Del	DEL	ATGATATGTGCATATT	ATGATATGTGCATATT	-	novel	NA	P-0005328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	25	375	0	ENST00000371953.3:c.400_415del	p.Met134TyrfsTer8	p.M134Yfs*8	ENST00000371953	NM_000314.4	134	ATGATATGTGCATATTta/ta	5/9	1	2	FACETS	0.459	0.361	0.572	0.459	0.361	0.572	SUBCLONAL	1	TRUE	1	0.241469454849232	2		375	451	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0005345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	288	377	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.671398799353376	2		377	839	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0005352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	156	207	0				ENST00000310581	NM_198253.2	-/1132			0.729856104335835	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.729856104335835	1		207	239	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0005352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	462	386	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	0.729856104335835	2		386	1211	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186501402	186501402	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0005352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2043	773	888	1	ENST00000323963.5:c.3G>A	p.Met1?	p.M1?	ENST00000323963		1	atG/atA	1/11	0.404992373993345	4	FACETS	1	0.996	1	0.651	0.627	0.675	INDETERMINATE	1	TRUE	2	0.729856104335835	4		889	2816	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043370	6043370	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	121	88	0	ENST00000265849.7:c.304G>A	p.Glu102Lys	p.E102K	ENST00000265849	NM_000535.5	102	Gaa/Aaa	4/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.729856104335835	2		88	253	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945054	151945054	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	72	218	0	ENST00000262189.6:c.2465A>G	p.Lys822Arg	p.K822R	ENST00000262189	NM_170606.2	822	aAa/aGa	14/59	1	2	FACETS	0.405	0.355	0.459	0.405	0.355	0.459	SUBCLONAL	1	TRUE	1	0.729856104335835	2		218	487	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138133	64138133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762396567	NA	P-0005352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	346	366	1	ENST00000334205.4:c.2056C>T	p.Arg686Trp	p.R686W	ENST00000334205	NM_003942.2	686	Cgg/Tgg	16/17	0.729856104335835	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.729856104335835	1		367	559	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121834	2121834	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	231	309	0	ENST00000219476.3:c.1996C>T	p.Pro666Ser	p.P666S	ENST00000219476	NM_000548.3	666	Ccc/Tcc	19/42	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.729856104335835	2		309	617	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976980	7976980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	420	426	7	ENST00000319144.4:c.1750G>A	p.Gly584Ser	p.G584S	ENST00000319144	NM_001139.2	584	Ggc/Agc	13/15	0.729856104335835	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.729856104335835	1		433	680	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512320	38512320	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	448	421	1	ENST00000254066.5:c.1231C>T	p.Gln411Ter	p.Q411*	ENST00000254066	NM_000964.3	411	Cag/Tag	9/9	0.729856104335835	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.729856104335835	1		422	712	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546769	9546769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	269	309	0	ENST00000353224.5:c.1253C>T	p.Ser418Phe	p.S418F	ENST00000353224	NM_177990.2	418	tCc/tTc	5/10	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.729856104335835	2		309	734	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994051	21994203	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCTAGAGACGAATTATCTGTTTACGAAATCACACCAAACAAAACAAGTGCCGAATGCGCCCCGGACTTTTCGAGGGCCTTTCCTACCTGGTCTTCTAGGAAGCGGCTGCTGCCCTAGACGCTGGCTCCTCAGTAGCATCAGCACGAGGGCCA	GGCTAGAGACGAATTATCTGTTTACGAAATCACACCAAACAAAACAAGTGCCGAATGCGCCCCGGACTTTTCGAGGGCCTTTCCTACCTGGTCTTCTAGGAAGCGGCTGCTGCCCTAGACGCTGGCTCCTCAGTAGCATCAGCACGAGGGCCA	-	novel	NA	P-0005352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	119	159	2	ENST00000579755.1:c.128_193+87del		p.X43_splice	ENST00000579755		43		1/3	1		FACETS		0.739	0.886				CLONAL	1	TRUE	1	0.729856104335835	2		161	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	292	448	1	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.226723408287265	2	FACETS	0.671	0.631	0.711	0.335	0.315	0.356	INDETERMINATE	1	TRUE	0	0.834205974668106	2		449	1044	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271974	18271974	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	65	152	0	ENST00000222254.8:c.577G>C	p.Glu193Gln	p.E193Q	ENST00000222254	NM_005027.3	193	Gag/Cag	5/16	0.139804317589665	3	FACETS	0.515	0.448	0.587	0.172	0.149	0.196	INDETERMINATE	1	TRUE	0	0.834205974668106	3		152	429	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005369-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	93	246	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.997	0.905	1	0.997	0.905	1	CLONAL	1	TRUE	1	0.86	2		246	217	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0005369-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	353	386	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.994	0.946	1	0.994	0.946	1	CLONAL	1	TRUE	1	0.86	2		386	826	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846137	68846137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005369-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	302	386	1	ENST00000261769.5:c.1108G>A	p.Asp370Asn	p.D370N	ENST00000261769	NM_004360.3	370	Gat/Aat	8/16	1	2	FACETS	0.882	0.835	0.93	0.882	0.835	0.93	CLONAL	1	TRUE	1	0.86	2		387	796	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185053	123185053	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005369-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	593	313	0	ENST00000218089.9:c.1100T>G	p.Phe367Cys	p.F367C	ENST00000218089	NM_001042749.1	367	tTt/tGt	12/35	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.86	1		313	708	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992195	11992209	+	inframe_deletion	In_Frame_Del	DEL	GCTGCTGACCAAAGA	GCTGCTGACCAAAGA	-	novel	NA	P-0005369-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	336	393	0	ENST00000396373.4:c.286_300del	p.Leu96_Glu100del	p.L96_E100del	ENST00000396373	NM_001987.4	95	ctGCTGCTGACCAAAGAg/ctg	3/8	0.184889666873233	4	FACETS	0.831	0.789	0.874	0.831	0.789	0.874	INDETERMINATE	2	TRUE	2	0.86	4		393	874	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924772	49924772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs533872004	NA	P-0005371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	241	643	1	ENST00000296474.3:c.4171C>T	p.Arg1391Trp	p.R1391W	ENST00000296474	NM_002447.2	1391	Cgg/Tgg	20/20	1	2	FACETS	0.872	0.814	0.933	0.872	0.814	0.933	CLONAL	1	TRUE	1	0.462676927941117	2		644	1194	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268739	98268739	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	235	435	1	ENST00000331920.6:c.344G>T	p.Gly115Val	p.G115V	ENST00000331920	NM_000264.3	115	gGa/gTa	2/24	0.401545955181777	1	FACETS	0.875	0.818	0.934	0.875	0.818	0.934	CLONAL	1	TRUE	0	0.462676927941117	1		436	892	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0005381-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	97	375	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.530770657650279	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.641926744595553	1		378	171	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0005381-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	149	516	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.448658089016487	1	FACETS	0.888	0.823	0.954	0.888	0.823	0.954	CLONAL	1	TRUE	0	0.641926744595553	1		516	355	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0005381-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	198	533	1	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	NA	2	FACETS	0.852	0.803	0.9			1	INDETERMINATE	2	TRUE	NA	0.641926744595553	2		534	362	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0005381-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	42	280	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.173184957413481	2	FACETS	0.719	0.608	0.838	0.359	0.304	0.419	INDETERMINATE	1	TRUE	0	0.641926744595553	2		280	182	SUCCESS
APC	324	MSKCC	GRCh37	5	112174835	112174835	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0005381-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	92	342	0	ENST00000257430.4:c.3544A>T	p.Lys1182Ter	p.K1182*	ENST00000257430	NM_000038.5	1182	Aaa/Taa	16/16	0.173184957413481	2	FACETS	1	0.974	1	0.615	0.557	0.675	INDETERMINATE	1	TRUE	0	0.641926744595553	2		342	233	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41526008	41526008	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0005381-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	173	261	1	ENST00000263253.7:c.1282+1G>A		p.X428_splice	ENST00000263253	NM_001429.3	428			0.591266692303262	2	FACETS	0.834	0.783	0.886	0.834	0.783	0.886	CLONAL	2	TRUE	0	0.641926744595553	2		262	323	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16040667	16040717	+	inframe_deletion	In_Frame_Del	DEL	GGCTTTATAATTCTCATTTTTCTTGGTTAAATAGTAATACAAAACACAATC	GGCTTTATAATTCTCATTTTTCTTGGTTAAATAGTAATACAAAACACAATC	-	novel	NA	P-0005381-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	65	321	1	ENST00000268712.3:c.1417_1467del	p.Asp473_Ala489del	p.D473_A489del	ENST00000268712	NM_006311.3	473	GATTGTGTTTTGTATTACTATTTAACCAAGAAAAATGAGAATTATAAAGCC/-	14/46	0.410156565321018	1	FACETS	0.354	0.308	0.404	0.354	0.308	0.404	SUBCLONAL	1	TRUE	0	0.641926744595553	1		322	388	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457242	25457242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147001633	NA	P-0005388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	161	703	0	ENST00000264709.3:c.2645G>A	p.Arg882His	p.R882H	ENST00000264709	NM_175629.2	882	cGc/cAc	23/23	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		703	658	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197149	106197149	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	79	826	0	ENST00000380013.4:c.5482del	p.Gln1828SerfsTer5	p.Q1828Sfs*5	ENST00000380013	NM_001127208.2	1828	Cag/ag	11/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		826	533	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0005404-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	83	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.897	0.797	1	0.897	0.797	1	CLONAL	1	TRUE	1	0.52	2		249	356	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46725752	46725752	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005404-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	122	346	0	ENST00000371975.4:c.388G>T	p.Asp130Tyr	p.D130Y	ENST00000371975	NM_003579.3	130	Gac/Tac	5/18	0.121402750817494	0	FACETS	0.496	0.451	0.543			1	INDETERMINATE	1	TRUE	0	0.52	0		346	454	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266611	198266611	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs755415626	NA	P-0005404-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	84	229	0	ENST00000335508.6:c.2225G>A	p.Gly742Asp	p.G742D	ENST00000335508	NM_012433.2	742	gGt/gAt	16/25	1	2	FACETS	0.885	0.788	0.988	0.885	0.788	0.988	CLONAL	1	TRUE	1	0.52	2		229	365	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896463	151896463	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005404-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	108	257	0	ENST00000262189.6:c.4174C>T	p.Gln1392Ter	p.Q1392*	ENST00000262189	NM_170606.2	1392	Cag/Tag	27/59	1	2	FACETS	0.931	0.841	1	0.931	0.841	1	CLONAL	1	TRUE	1	0.52	2		257	446	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005424-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	66	246	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.964	0.856	1	0.964	0.856	1	CLONAL	1	TRUE	1	0.805058461063494	2		246	170	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0005424-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	129	141	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.839	0.769	0.911	0.839	0.769	0.911	CLONAL	1	TRUE	1	0.805058461063494	2		141	382	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397710	49397710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005424-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	328	282	0	ENST00000418115.1:c.514G>A	p.Glu172Lys	p.E172K	ENST00000418115	NM_001664.2	172	Gaa/Aaa	5/5	1	2	FACETS	0.945	0.897	0.994	0.945	0.897	0.994	CLONAL	1	TRUE	1	0.805058461063494	2		282	862	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803208	1803208	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005424-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	338	213	0	ENST00000260795.2:c.560C>G	p.Ser187Cys	p.S187C	ENST00000260795		187	tCc/tGc	4/17	1	2	FACETS	0.926	0.879	0.974	0.926	0.879	0.974	CLONAL	1	TRUE	1	0.805058461063494	2		213	907	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0005477-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	320	207	0				ENST00000310581	NM_198253.2	-/1132			0.384268911965332	3	FACETS	1	0.993	1	0.653	0.619	0.688	INDETERMINATE	1	TRUE	1	0.822839150948557	3		207	840	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685286	89685286	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005477-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	76	221	0	ENST00000371953.3:c.181C>A	p.His61Asn	p.H61N	ENST00000371953	NM_000314.4	61	Cat/Aat	3/9	0.822839150948557	1	FACETS	0.471	0.419	0.524	0.471	0.419	0.524	SUBCLONAL	1	TRUE	0	0.822839150948557	1		221	231	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432278	49432278	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005477-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1592	87	689	0	ENST00000301067.7:c.8861G>C	p.Gly2954Ala	p.G2954A	ENST00000301067	NM_003482.3	2954	gGt/gCt	34/54	NA	2	FACETS	0.126	0.111	0.143			1	INDETERMINATE	1	TRUE	NA	0.822839150948557	2		689	1679	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939910	76939910	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs797045408	NA	P-0005477-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	80	648	0	ENST00000373344.5:c.838T>C	p.Cys280Arg	p.C280R	ENST00000373344	NM_000489.3	280	Tgt/Cgt	9/35	NA	2	FACETS	0.179	0.156	0.203			1	INDETERMINATE	1	TRUE	NA	0.822839150948557	2		648	1089	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	321	455	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.911273052530735	2		455	636	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172064	99172064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	277	258	0	ENST00000074304.5:c.1630C>T	p.Arg544Cys	p.R544C	ENST00000074304	NM_001134224.1	544	Cgt/Tgt	17/26	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.911273052530735	2		258	588	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231689	66231689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	247	333	1	ENST00000273854.3:c.2011G>A	p.Glu671Lys	p.E671K	ENST00000273854	NM_004439.5	671	Gaa/Aaa	11/18	0.197522328230251	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.911273052530735	0		334	581	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797247	135797284	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	TGTAATGAGAACGCAAAAAGGAGACGAAGTTGCAAGGG	TGTAATGAGAACGCAAAAAGGAGACGAAGTTGCAAGGG	-	novel	NA	P-0005495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	76	317	0	ENST00000298552.3:c.585_622del	p.Tyr195Ter	p.Y195*	ENST00000298552	NM_001162426.1	195	taCCCTTGCAACTTCGTCTCCTTTTTGCGTTCTCATTACAgt/tagt	7/23	0.911273052530735	1	FACETS	0.213	0.187	0.24	0.213	0.187	0.24	SUBCLONAL	1	TRUE	0	0.911273052530735	1		317	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540652	NA	P-0005496-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	443	410	0	ENST00000269305.4:c.743G>C	p.Arg248Pro	p.R248P	ENST00000269305	NM_001126112.2	248	cGg/cCg	7/11	0.808407846725151	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.811464786652867	1		410	603	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876145	35876145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005496-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	431	413	0	ENST00000303115.3:c.937G>A	p.Asp313Asn	p.D313N	ENST00000303115	NM_002185.3	313	Gac/Aac	8/8	1	2	FACETS	0.991	0.947	1	0.991	0.947	1	CLONAL	1	TRUE	1	0.811464786652867	2		413	1072	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937904	36937904	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005496-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2233	577	675	0	ENST00000361632.4:c.932G>T	p.Arg311Leu	p.R311L	ENST00000361632		311	cGc/cTc	7/16	0.746869909289095	5	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.811464786652867	5		675	2810	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436314	52436314	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005496-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	444	448	1	ENST00000460680.1:c.2180A>T	p.Lys727Met	p.K727M	ENST00000460680	NM_004656.3	727	aAg/aTg	17/17	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.811464786652867	NA		449	654	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55569934	55569934	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005496-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	278	418	0	ENST00000288135.5:c.801C>A	p.Phe267Leu	p.F267L	ENST00000288135	NM_000222.2	267	ttC/ttA	5/21	0.796210702224802	3	FACETS	0.838	0.786	0.89	0.419	0.393	0.445	CLONAL	1	TRUE	1	0.811464786652867	3		418	1150	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391625	139391625	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005496-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	727	395	0	ENST00000277541.6:c.6566G>A	p.Cys2189Tyr	p.C2189Y	ENST00000277541	NM_017617.3	2189	tGc/tAc	34/34	0.811464786652867	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.811464786652867	2		395	867	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16021212	16021212	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005496-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	332	387	0	ENST00000268712.3:c.2045A>T	p.His682Leu	p.H682L	ENST00000268712	NM_006311.3	682	cAt/cTt	18/46	0.808407846725151	1	FACETS	0.941	0.903	0.977	0.941	0.903	0.977	CLONAL	1	TRUE	0	0.811464786652867	1		387	517	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593603	55593603	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913235	NA	P-0005505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	409	644	0	ENST00000288135.5:c.1669T>A	p.Trp557Arg	p.W557R	ENST00000288135	NM_000222.2	557	Tgg/Agg	11/21	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.620097299556648	2		644	1200	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551842	150551843	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0005505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	87	150	0	ENST00000369026.2:c.164_165del	p.Ala55GlyfsTer54	p.A55Gfs*54	ENST00000369026	NM_021960.4	55	gCG/g	1/3	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.620097299556648	2		150	278	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070931	30070931	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0005514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	193	562	2	ENST00000338641.4:c.1446+1G>A		p.X482_splice	ENST00000338641	NM_000268.3	482			1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		564	627	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077464	30077465	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	TT	novel	NA	P-0005514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	162	495	2	ENST00000338641.4:c.1611_1612delinsTT	p.Glu537_Gln538delinsAspTer	p.E537_Q538delinsD*	ENST00000338641	NM_000268.3	537	gaGCag/gaTTag	15/16	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		497	621	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0005561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	120	377	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	0.189202656511904	4	FACETS	0.785	0.715	0.857	0.785	0.715	0.857	INDETERMINATE	2	TRUE	2	0.606602268945854	4		377	405	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0005568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	96	266	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.281648212169565	1	FACETS	0.677	0.602	0.757	0.677	0.602	0.757	SUBCLONAL	1	TRUE	0	0.281648212169565	1		266	865	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578448	7578448	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1064795691	NA	P-0005568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	104	411	0	ENST00000269305.4:c.482C>A	p.Ala161Asp	p.A161D	ENST00000269305	NM_001126112.2	161	gCc/gAc	5/11	1	2	FACETS	0.976	0.874	1	0.976	0.874	1	CLONAL	1	TRUE	1	0.281648212169565	2		411	757	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187947	32187947	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771104755	NA	P-0005568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	64	491	1	ENST00000375023.3:c.1274C>T	p.Ser425Leu	p.S425L	ENST00000375023	NM_004557.3	425	tCg/tTg	7/30	0.258066113671637	1	FACETS	0.373	0.322	0.429	0.373	0.322	0.429	SUBCLONAL	1	TRUE	0	0.281648212169565	1		492	1046	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591933	48591933	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060500733	NA	P-0005568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	151	371	0	ENST00000342988.3:c.1096C>T	p.Gln366Ter	p.Q366*	ENST00000342988	NM_005359.5	366	Caa/Taa	9/12	0.281648212169565	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.281648212169565	1		371	862	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220504	1220544	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTAGGCACGTGCTAGGGGGGGCCCTGGGGCGCCCCCTCCC	GGTAGGCACGTGCTAGGGGGGGCCCTGGGGCGCCCCCTCCC	-	novel	NA	P-0005568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	104	341	0	ENST00000326873.7:c.597+2_598-34del		p.X199_splice	ENST00000326873	NM_000455.4	199		4/10	0.258066113671637	1	FACETS	0.926	0.83	1	0.926	0.83	1	CLONAL	1	TRUE	0	0.281648212169565	1		341	685	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0005571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	74	580	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.69646040293577	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.69646040293577	1		580	107	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0005577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	85	516	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.17693449970987	3	FACETS	1	0.958	1	0.587	0.52	0.658	INDETERMINATE	1	TRUE	1	0.308600196137985	3		516	542	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0005577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	89	431	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.207319627427091	2	FACETS	1	0.971	1	0.639	0.57	0.713	CLONAL	1	TRUE	0	0.308600196137985	2		431	451	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591132	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	rs1057519842	NA	P-0005577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	90	272	0	ENST00000274335.5:c.1727_1729del	p.Thr576del	p.T576del	ENST00000274335		575	aaGACg/aag	12/15	0.20545053966745	4	FACETS	1	0.978	1	0.713	0.635	0.797	CLONAL	1	TRUE	2	0.308600196137985	4		272	535	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107258	193107258	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	71	325	0	ENST00000367435.3:c.467G>A	p.Arg156His	p.R156H	ENST00000367435	NM_024529.4	156	cGt/cAt	6/17	0.176326073695541	3	FACETS	0.844	0.737	0.96	0.422	0.368	0.48	INDETERMINATE	1	TRUE	1	0.308600196137985	3		325	629	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0005580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	134	343	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.195470197180063	3	FACETS	0.938	0.853	1	0.938	0.853	1	CLONAL	2	TRUE	1	0.205274502604214	3		343	767	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117764	108117772	+	inframe_deletion	In_Frame_Del	DEL	TATAGGAAG	TATAGGAAG	-	novel	NA	P-0005580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	48	417	0	ENST00000278616.4:c.977_985del	p.Ile326_Ser328del	p.I326_S328del	ENST00000278616	NM_000051.3	325	caTATAGGAAGt/cat	8/63	0.190828635251213	3	FACETS	0.705	0.595	0.828	0.235	0.198	0.276	SUBCLONAL	1	TRUE	0	0.205274502604214	3		417	731	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	45	246	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.234222950787939	2		246	358	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433896	49433896	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	38	340	1	ENST00000301067.7:c.7657C>T	p.Gln2553Ter	p.Q2553*	ENST00000301067	NM_003482.3	2553	Cag/Tag	31/54	0.191807912863871	4	FACETS	1	0.942	1	0.674	0.56	0.801	CLONAL	1	TRUE	2	0.234222950787939	4		341	297	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119789	70119789	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	82	477	0	ENST00000245479.2:c.791G>C	p.Arg264Thr	p.R264T	ENST00000245479	NM_000346.3	264	aGa/aCa	3/3	0.234222950787939	3	FACETS	1	0.973	1	0.459	0.405	0.517	CLONAL	1	TRUE	0	0.234222950787939	3		477	568	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0005587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	8	208	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	0.103074537584943	4	FACETS	0.261	0.167	0.383	0.131	0.083	0.192	INDETERMINATE	1	TRUE	2	0.234222950787939	4		208	323	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174917	11174917	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	57	393	0	ENST00000361445.4:c.7117G>C	p.Glu2373Gln	p.E2373Q	ENST00000361445	NM_004958.3	2373	Gag/Cag	52/58	NA	2	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.234222950787939	2		393	331	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11273585	11273585	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	34	311	0	ENST00000361445.4:c.3156C>G	p.Ile1052Met	p.I1052M	ENST00000361445	NM_004958.3	1052	atC/atG	21/58	NA	2	FACETS	0.891	0.729	1			1	INDETERMINATE	1	TRUE	NA	0.234222950787939	2		311	326	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11273594	11273594	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	33	287	0	ENST00000361445.4:c.3147G>C	p.Gln1049His	p.Q1049H	ENST00000361445	NM_004958.3	1049	caG/caC	21/58	NA	2	FACETS	0.955	0.781	1			1	INDETERMINATE	1	TRUE	NA	0.234222950787939	2		287	295	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721100	61721100	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	76	454	0	ENST00000401558.2:c.1174C>G	p.Pro392Ala	p.P392A	ENST00000401558	NM_003400.3	392	Ccg/Gcg	12/25	0.146977828794273	3	FACETS	0.82	0.722	0.925	0.82	0.722	0.925	CLONAL	2	TRUE	1	0.234222950787939	3		454	442	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280750	41280750	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	80	388	0	ENST00000349496.5:c.2263G>C	p.Asp755His	p.D755H	ENST00000349496	NM_001904.3	755	Gat/Cat	15/15	0.103074537584943	4	FACETS	0.974	0.861	1	0.974	0.861	1	INDETERMINATE	2	TRUE	2	0.234222950787939	4		388	433	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103792	47103792	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	51	474	0	ENST00000409792.3:c.6154C>G	p.Pro2052Ala	p.P2052A	ENST00000409792	NM_014159.6	2052	Cct/Gct	14/21	0.103074537584943	4	FACETS	1	0.934	1	0.592	0.504	0.689	INDETERMINATE	1	TRUE	2	0.234222950787939	4		474	454	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014160	70014160	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	141	838	0	ENST00000394351.3:c.1021C>G	p.Leu341Val	p.L341V	ENST00000394351	NM_000248.3	341	Ctc/Gtc	9/9	0.103074537584943	4	FACETS	0.848	0.773	0.928	0.848	0.773	0.928	INDETERMINATE	2	TRUE	2	0.234222950787939	4		838	876	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518306	187518306	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	17	83	0	ENST00000441802.2:c.12388G>C	p.Glu4130Gln	p.E4130Q	ENST00000441802	NM_005245.3	4130	Gag/Cag	25/27	0.234222950787939	3	FACETS	1	0.844	1			1	CLONAL	2	TRUE	NA	0.234222950787939	3		83	71	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539252	187539252	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	73	390	0	ENST00000441802.2:c.8488C>T	p.Gln2830Ter	p.Q2830*	ENST00000441802	NM_005245.3	2830	Cag/Tag	10/27	0.234222950787939	3	FACETS	0.86	0.755	0.971			1	CLONAL	2	TRUE	NA	0.234222950787939	3		390	405	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183005	32183005	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	24	353	0	ENST00000375023.3:c.2019G>C	p.Gln673His	p.Q673H	ENST00000375023	NM_004557.3	673	caG/caC	12/30	0.153878544298846	1	FACETS	1	0.798	1	1	0.798	1	CLONAL	1	TRUE	0	0.234222950787939	1		353	179	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183067	32183067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	32	551	0	ENST00000375023.3:c.1957G>A	p.Asp653Asn	p.D653N	ENST00000375023	NM_004557.3	653	Gat/Aat	12/30	0.153878544298846	1	FACETS	0.89	0.726	1	0.89	0.726	1	CLONAL	1	TRUE	0	0.234222950787939	1		551	271	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43738986	43738986	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0005587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	149	418	0	ENST00000523873.1:c.3G>A	p.Met1?	p.M1?	ENST00000523873		1	atG/atA	1/8	0.234222950787939	5	FACETS	0.908	0.829	0.991	0.605	0.552	0.661	CLONAL	2	TRUE	2	0.234222950787939	5		418	947	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907119	101907119	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	142	398	0	ENST00000374994.4:c.1079C>A	p.Ser360Ter	p.S360*	ENST00000374994	NM_004612.2	360	tCa/tAa	6/9	0.193225123835485	3	FACETS	0.878	0.805	0.954	0.878	0.805	0.954	CLONAL	3	TRUE	0	0.234222950787939	3		398	514	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433945	49433945	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	38	305	0	ENST00000301067.7:c.7608C>A	p.Phe2536Leu	p.F2536L	ENST00000301067	NM_003482.3	2536	ttC/ttA	31/54	0.191807912863871	4	FACETS	0.821	0.683	0.972	0.821	0.683	0.972	CLONAL	2	TRUE	2	0.234222950787939	4		305	244	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486842	56486842	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	105	457	0	ENST00000267101.3:c.1256G>C	p.Gly419Ala	p.G419A	ENST00000267101	NM_001982.3	419	gGa/gCa	11/28	NA	2	FACETS	0.908	0.823	0.996			1	INDETERMINATE	3	TRUE	NA	0.234222950787939	2		457	329	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133737	2133737	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	52	535	0	ENST00000219476.3:c.3925C>T	p.Pro1309Ser	p.P1309S	ENST00000219476	NM_000548.3	1309	Cct/Tct	33/42	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.234222950787939	2		535	436	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844155	68844155	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	53	410	0	ENST00000261769.5:c.743T>A	p.Ile248Asn	p.I248N	ENST00000261769	NM_004360.3	248	aTt/aAt	6/16	0.234222950787939	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.234222950787939	1		410	295	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983772	15983772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	112	311	0	ENST00000268712.3:c.3350C>T	p.Ser1117Leu	p.S1117L	ENST00000268712	NM_006311.3	1117	tCa/tTa	25/46	0.234222950787939	2	FACETS	0.924	0.84	1	1	0.983	1	CLONAL	3	TRUE	0	0.234222950787939	2		311	345	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883959	37883959	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138611862	NA	P-0005587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	41	208	0	ENST00000269571.5:c.3430G>A	p.Asp1144Asn	p.D1144N	ENST00000269571		1144	Gat/Aat	27/27	0.234222950787939	2	FACETS	0.858	0.73	0.994	1	0.947	1	CLONAL	3	TRUE	0	0.234222950787939	2		208	136	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942782	44942782	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs766711516	NA	P-0005587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	21	315	0	ENST00000377967.4:c.3362A>C	p.His1121Pro	p.H1121P	ENST00000377967	NM_021140.2	1121	cAt/cCt	23/29	0.234222950787939	2	FACETS	0.476	0.366	0.604			1	SUBCLONAL	1	TRUE	NA	0.234222950787939	2		315	377	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0005604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	343	207	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.794017088002031	2		207	820	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397780	116397780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	359	700	0	ENST00000397752.3:c.2054G>A	p.Gly685Glu	p.G685E	ENST00000397752	NM_000245.2	685	gGg/gAg	8/21	1	2	FACETS	0.972	0.925	1	0.972	0.925	1	CLONAL	1	TRUE	1	0.794017088002031	2		700	930	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717679	89717679	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	70	426	0	ENST00000371953.3:c.704A>G	p.Glu235Gly	p.E235G	ENST00000371953	NM_000314.4	235	gAa/gGa	7/9	0.709721666179346	1	FACETS	0.143	0.124	0.163	0.143	0.124	0.163	SUBCLONAL	1	TRUE	0	0.794017088002031	1		426	745	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205335	46205335	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0005604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	273	370	1	ENST00000334344.6:c.418+1G>A		p.X140_splice	ENST00000334344	NM_152641.2	140			0.794017088002031	1	FACETS	0.903	0.862	0.945	0.903	0.862	0.945	CLONAL	1	TRUE	0	0.794017088002031	1		371	459	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797831	42797831	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1250417352	NA	P-0005604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	446	495	0	ENST00000575354.2:c.3883C>T	p.Pro1295Ser	p.P1295S	ENST00000575354	NM_015125.3	1295	Ccg/Tcg	16/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.794017088002031	2		495	1057	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577106	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0005604-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	662	798	0	ENST00000269305.4:c.832_833delinsTT	p.Pro278Phe	p.P278F	ENST00000269305	NM_001126112.2	278	CCt/TTt	8/11	0.794017088002031	1	FACETS	0.994	0.966	1	0.994	0.966	1	CLONAL	1	TRUE	0	0.794017088002031	1		798	1012	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0005605-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	615	577	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	0.433441889631396	5	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	2	0.433441889631396	5		577	1497	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0005605-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	264	390	1	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.33851480950669	3	FACETS	0.854	0.802	0.906	0.854	0.802	0.906	CLONAL	2	TRUE	1	0.433441889631396	3		391	868	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0005614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	78	749	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.18258248893883	4	FACETS	1	0.951	1	0.58	0.51	0.655	INDETERMINATE	1	TRUE	2	0.326761113724619	4		750	546	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265590	198265590	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	69	428	1	ENST00000335508.6:c.2567A>T	p.Asp856Val	p.D856V	ENST00000335508	NM_012433.2	856	gAt/gTt	18/25	0.218732921095512	4	FACETS	0.974	0.849	1	0.487	0.424	0.555	CLONAL	1	TRUE	2	0.326761113724619	4		429	575	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658308	18658308	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	167	481	0	ENST00000266497.5:c.3113A>G	p.Asn1038Ser	p.N1038S	ENST00000266497		1038	aAt/aGt	22/31	NA	2	FACETS	0.909	0.84	0.98			1	INDETERMINATE	2	TRUE	NA	0.326761113724619	2		481	562	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005615-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	154	246	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.54712422340014	2		246	464	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0005615-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	184	375	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.258133699384353	1	FACETS	0.712	0.66	0.766	0.712	0.66	0.766	INDETERMINATE	1	TRUE	0	0.54712422340014	1		378	686	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0005615-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	56	93	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.54712422340014	1	FACETS	0.86	0.751	0.974	0.86	0.751	0.974	CLONAL	1	TRUE	0	0.54712422340014	1		93	173	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0005615-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	201	299	2	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	0.303904358546754	3	FACETS	0.777	0.725	0.831	0.777	0.725	0.831	INDETERMINATE	2	TRUE	1	0.54712422340014	3		301	602	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720857	89720857	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs786201816	NA	P-0005615-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	17	180	0	ENST00000371953.3:c.1008C>G	p.Tyr336Ter	p.Y336*	ENST00000371953	NM_000314.4	336	taC/taG	8/9	0.54712422340014	1	FACETS	0.137	0.102	0.179	0.137	0.102	0.179	SUBCLONAL	1	TRUE	0	0.54712422340014	1		180	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572981	7572984	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	novel	NA	P-0005615-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	38	330	0	ENST00000269305.4:c.1125_1128del	p.Ser376ProfsTer45	p.S376Pfs*45	ENST00000269305	NM_001126112.2	375	caGTCT/ca	11/11	0.258133699384353	1	FACETS	0.138	0.113	0.166	0.138	0.113	0.166	INDETERMINATE	1	TRUE	0	0.54712422340014	1		330	732	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141586	202141586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760898260	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	275	480	2	ENST00000358485.4:c.874C>T	p.Arg292Trp	p.R292W	ENST00000358485	NM_001080125.1	292	Cgg/Tgg	7/9	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.548271038610447	2		482	810	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46215271	46215271	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	150	445	0	ENST00000334344.6:c.705+1G>A		p.X235_splice	ENST00000334344	NM_152641.2	235			1	2	FACETS	0.884	0.811	0.96	0.884	0.811	0.96	CLONAL	1	TRUE	1	0.548271038610447	2		445	619	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	154	215	0	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	0.429163259037021	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.548271038610447	1		215	338	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	136	252	0				ENST00000310581	NM_198253.2	-/1132			0.159418699443584	3	FACETS	1	0.984	1	0.664	0.608	0.722	INDETERMINATE	1	TRUE	1	0.548271038610447	3		252	476	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076812	72076812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	184	452	0	ENST00000357731.5:c.685G>A	p.Glu229Lys	p.E229K	ENST00000357731	NM_173808.2	229	Gaa/Aaa	5/7	1	2	FACETS	0.936	0.867	1	0.936	0.867	1	CLONAL	1	TRUE	1	0.548271038610447	2		452	717	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648217	206648217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149591181	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	251	484	1	ENST00000367120.3:c.238C>T	p.Arg80Trp	p.R80W	ENST00000367120	NM_014002.3	80	Cgg/Tgg	5/22	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.548271038610447	2		485	880	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944353	206944353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	219	509	1	ENST00000423557.1:c.277G>A	p.Glu93Lys	p.E93K	ENST00000423557	NM_000572.2	93	Gag/Aag	3/5	1	2	FACETS	0.937	0.873	1	0.937	0.873	1	CLONAL	1	TRUE	1	0.548271038610447	2		510	853	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716044	243716044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	163	389	1	ENST00000263826.5:c.1150G>A	p.Asp384Asn	p.D384N	ENST00000263826	NM_005465.4	384	Gat/Aat	10/13	1	2	FACETS	0.996	0.918	1	0.996	0.918	1	CLONAL	1	TRUE	1	0.548271038610447	2		390	597	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149979	202149979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1182826593	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	199	449	1	ENST00000358485.4:c.1420C>T	p.Pro474Ser	p.P474S	ENST00000358485	NM_001080125.1	474	Cct/Tct	8/9	1	2	FACETS	0.869	0.807	0.934	0.869	0.807	0.934	CLONAL	1	TRUE	1	0.548271038610447	2		450	835	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098937	47098937	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867188953	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	159	357	0	ENST00000409792.3:c.6337C>T	p.Arg2113Cys	p.R2113C	ENST00000409792	NM_014159.6	2113	Cgc/Tgc	15/21	1	2	FACETS	0.988	0.91	1	0.988	0.91	1	CLONAL	1	TRUE	1	0.548271038610447	2		357	587	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164393	47164393	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	211	405	0	ENST00000409792.3:c.1733T>A	p.Leu578Ter	p.L578*	ENST00000409792	NM_014159.6	578	tTa/tAa	3/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.548271038610447	2		405	708	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928499	69928499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	200	424	0	ENST00000352241.4:c.319C>T	p.Pro107Ser	p.P107S	ENST00000352241	NM_198159.2	107	Ccc/Tcc	2/10	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.548271038610447	2		424	728	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468522	89468522	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	172	414	0	ENST00000336596.2:c.2056G>C	p.Glu686Gln	p.E686Q	ENST00000336596	NM_005233.5	686	Gaa/Caa	11/17	1	2	FACETS	0.962	0.889	1	0.962	0.889	1	CLONAL	1	TRUE	1	0.548271038610447	2		414	652	SUCCESS
ATR	545	MSKCC	GRCh37	3	142204079	142204079	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	187	445	0	ENST00000350721.4:c.6124C>T	p.Leu2042Phe	p.L2042F	ENST00000350721	NM_001184.3	2042	Ctt/Ttt	36/47	1	2	FACETS	0.919	0.852	0.989	0.919	0.852	0.989	CLONAL	1	TRUE	1	0.548271038610447	2		445	742	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502485	186502485	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	201	447	0	ENST00000323963.5:c.208G>A	p.Gly70Arg	p.G70R	ENST00000323963		70	Ggg/Agg	3/11	1	2	FACETS	0.991	0.921	1	0.991	0.921	1	CLONAL	1	TRUE	1	0.548271038610447	2		447	740	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526217	189526217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1320669467	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	212	517	0	ENST00000264731.3:c.481C>T	p.Pro161Ser	p.P161S	ENST00000264731	NM_003722.4	161	Cca/Tca	4/14	1	2	FACETS	0.945	0.88	1	0.945	0.88	1	CLONAL	1	TRUE	1	0.548271038610447	2		517	818	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665394	176665394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	229	498	0	ENST00000439151.2:c.4078G>A	p.Glu1360Lys	p.E1360K	ENST00000439151	NM_022455.4	1360	Gaa/Aaa	7/23	0.124399401647688	1	FACETS	0.75	0.701	0.801	0.75	0.701	0.801	INDETERMINATE	1	TRUE	0	0.548271038610447	1		498	808	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180040101	180040101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909652	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	185	486	0	ENST00000261937.6:c.3341C>T	p.Pro1114Leu	p.P1114L	ENST00000261937	NM_182925.4	1114	cCg/cTg	25/30	0.124399401647688	1	FACETS	0.642	0.594	0.692	0.642	0.594	0.692	INDETERMINATE	1	TRUE	0	0.548271038610447	1		486	763	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005438	150005438	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1437806382	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	210	512	0	ENST00000253339.5:c.787C>T	p.Pro263Ser	p.P263S	ENST00000253339		263	Cca/Tca	3/7	1	2	FACETS	0.921	0.857	0.987	0.921	0.857	0.987	CLONAL	1	TRUE	1	0.548271038610447	2		512	832	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976759	2976759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	263	603	1	ENST00000396946.4:c.1253G>A	p.Arg418Lys	p.R418K	ENST00000396946	NM_032415.4	418	aGg/aAg	9/25	1	2	FACETS	0.991	0.93	1	0.991	0.93	1	CLONAL	1	TRUE	1	0.548271038610447	2		604	968	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935526	13935526	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	117	267	0	ENST00000405192.2:c.1330A>C	p.Asn444His	p.N444H	ENST00000405192	NM_001163147.1	444	Aac/Cac	12/12	1	2	FACETS	0.864	0.783	0.948	0.864	0.783	0.948	CLONAL	1	TRUE	1	0.548271038610447	2		267	494	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508955	106508955	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759136884	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	147	304	0	ENST00000359195.3:c.949G>A	p.Glu317Lys	p.E317K	ENST00000359195	NM_002649.2	317	Gag/Aag	2/11	1	2	FACETS	0.979	0.898	1	0.979	0.898	1	CLONAL	1	TRUE	1	0.548271038610447	2		304	548	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738990	145738990	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs985482776	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	258	355	0	ENST00000428558.2:c.2165C>T	p.Thr722Ile	p.T722I	ENST00000428558	NM_004260.3	722	aCc/aTc	13/22	0.159418699443584	3	FACETS	1	0.992	1	0.71	0.666	0.754	INDETERMINATE	1	TRUE	1	0.548271038610447	3		355	845	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507300	8507300	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	212	508	1	ENST00000356435.5:c.1677+1G>A		p.X559_splice	ENST00000356435		559			NA	2	FACETS	1	0.952	1			1	INDETERMINATE	1	TRUE	NA	0.548271038610447	2		509	753	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020670	37020670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	161	369	1	ENST00000358127.4:c.175C>T	p.Arg59Trp	p.R59W	ENST00000358127	NM_001280556.1	59	Cgg/Tgg	2/10	1	2	FACETS	0.989	0.911	1	0.989	0.911	1	CLONAL	1	TRUE	1	0.548271038610447	2		370	594	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570274	87570274	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	221	390	0	ENST00000277120.3:c.2014A>G	p.Ile672Val	p.I672V	ENST00000277120		672	Ata/Gta	17/19	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.548271038610447	2		390	705	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636258	87636258	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	274	589	1	ENST00000277120.3:c.2423G>A	p.Arg808Gln	p.R808Q	ENST00000277120		808	cGa/cAa	19/19	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.548271038610447	2		590	950	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401823	139401823	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	327	527	0	ENST00000277541.6:c.3577C>T	p.Gln1193Ter	p.Q1193*	ENST00000277541	NM_017617.3	1193	Cag/Tag	22/34	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.548271038610447	2		527	1029	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417305	139417305	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	155	249	0	ENST00000277541.6:c.739C>T	p.Pro247Ser	p.P247S	ENST00000277541	NM_017617.3	247	Cca/Tca	4/34	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.548271038610447	2		249	547	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276835	123276835	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	252	555	1	ENST00000358487.5:c.1082C>T	p.Pro361Leu	p.P361L	ENST00000358487	NM_000141.4	361	cCa/cTa	8/18	1	2	FACETS	0.973	0.911	1	0.973	0.911	1	CLONAL	1	TRUE	1	0.548271038610447	2		556	945	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444987	49444987	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	166	202	0	ENST00000301067.7:c.2479C>T	p.Gln827Ter	p.Q827*	ENST00000301067	NM_003482.3	827	Caa/Taa	10/54	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.548271038610447	2		202	488	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864591	57864591	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	316	740	1	ENST00000228682.2:c.2068C>T	p.Pro690Ser	p.P690S	ENST00000228682	NM_005269.2	690	Ccc/Tcc	12/12	1	2	FACETS	0.971	0.916	1	0.971	0.916	1	CLONAL	1	TRUE	1	0.548271038610447	2		741	1187	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881519	48881519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	185	487	1	ENST00000267163.4:c.241G>A	p.Val81Ile	p.V81I	ENST00000267163	NM_000321.2	81	Gtt/Att	2/27	1	2	FACETS	0.982	0.91	1	0.982	0.91	1	CLONAL	1	TRUE	1	0.548271038610447	2		488	687	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49054172	49054172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	166	419	0	ENST00000267163.4:c.2752G>A	p.Asp918Asn	p.D918N	ENST00000267163	NM_000321.2	918	Gat/Aat	27/27	1	2	FACETS	0.781	0.719	0.846	0.781	0.719	0.846	SUBCLONAL	1	TRUE	1	0.548271038610447	2		419	775	SUCCESS
BLM	641	MSKCC	GRCh37	15	91295130	91295130	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	171	415	0	ENST00000355112.3:c.913C>T	p.Pro305Ser	p.P305S	ENST00000355112	NM_000057.2	305	Cca/Tca	4/22	0.548271038610447	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.548271038610447	1		415	453	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23652456	23652456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150390726	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	181	462	0	ENST00000261584.4:c.23C>T	p.Pro8Leu	p.P8L	ENST00000261584	NM_024675.3	8	cCc/cTc	1/13	1	2	FACETS	0.947	0.877	1	0.947	0.877	1	CLONAL	1	TRUE	1	0.548271038610447	2		462	697	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56878418	56878418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374875893	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	259	605	1	ENST00000308159.5:c.2357G>A	p.Arg786Gln	p.R786Q	ENST00000308159	NM_014669.4	786	cGa/cAa	22/22	1	2	FACETS	0.938	0.879	0.999	0.938	0.879	0.999	CLONAL	1	TRUE	1	0.548271038610447	2		606	1007	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828822	72828822	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	349	845	1	ENST00000268489.5:c.7759C>T	p.Gln2587Ter	p.Q2587*	ENST00000268489	NM_006885.3	2587	Cag/Tag	9/10	0.124399401647688	1	FACETS	0.775	0.734	0.817	0.775	0.734	0.817	INDETERMINATE	1	TRUE	0	0.548271038610447	1		846	1192	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578502	7578502	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	491	550	0	ENST00000269305.4:c.428T>C	p.Val143Ala	p.V143A	ENST00000269305	NM_001126112.2	143	gTg/gCg	5/11	NA	2	FACETS	0.987	0.951	1			1	INDETERMINATE	2	TRUE	NA	0.548271038610447	2		550	907	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560188	29560188	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772745260	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	175	400	0	ENST00000356175.3:c.3665C>T	p.Pro1222Leu	p.P1222L	ENST00000356175	NM_000267.3	1222	cCt/cTt	27/57	1	2	FACETS	0.939	0.868	1	0.939	0.868	1	CLONAL	1	TRUE	1	0.548271038610447	2		400	680	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222868	5222868	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1028304582	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	162	219	0	ENST00000357368.4:c.2935C>G	p.Arg979Gly	p.R979G	ENST00000357368	NM_002850.3	979	Cga/Gga	18/38	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.548271038610447	2		219	523	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755511	39755511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	225	487	0	ENST00000288319.7:c.1254G>A	p.Met418Ile	p.M418I	ENST00000288319	NM_182918.3	418	atG/atA	10/10	0.124399401647688	1	FACETS	0.774	0.723	0.826	0.774	0.723	0.826	INDETERMINATE	1	TRUE	0	0.548271038610447	1		487	770	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424299	47424299	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	208	458	0	ENST00000377045.4:c.303+1G>T		p.X101_splice	ENST00000377045	NM_001654.4	101			0.291743574606708	1	FACETS	0.797	0.743	0.853	0.797	0.743	0.853	INDETERMINATE	1	TRUE	0	0.548271038610447	1		458	691	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413030	63413030	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	520	758	0	ENST00000330258.3:c.137C>T	p.Ser46Leu	p.S46L	ENST00000330258	NM_152424.3	46	tCa/tTa	2/2	0.109675735902903	5	FACETS	0.891	0.855	0.927	0.668	0.641	0.696	INDETERMINATE	3	TRUE	1	0.548271038610447	5		758	1293	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776372	76776372	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	342	534	1	ENST00000373344.5:c.7094C>G	p.Ser2365Ter	p.S2365*	ENST00000373344	NM_000489.3	2365	tCa/tGa	34/35	0.109675735902903	5	FACETS	1	0.989	1	0.576	0.546	0.606	INDETERMINATE	2	TRUE	1	0.548271038610447	5		535	987	SUCCESS
BTK	695	MSKCC	GRCh37	X	100629541	100629541	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs930891306	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	258	617	0	ENST00000308731.7:c.223C>G	p.Pro75Ala	p.P75A	ENST00000308731	NM_000061.2	75	Cca/Gca	3/19	0.109675735902903	5	FACETS	0.783	0.733	0.835	0.392	0.366	0.418	INDETERMINATE	2	TRUE	1	0.548271038610447	5		617	1095	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205268	46205283	+	frameshift_variant	Frame_Shift_Del	DEL	CCAAAGCCACAGCTTC	CCAAAGCCACAGCTTC	-	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	232	547	0	ENST00000334344.6:c.353_368del	p.Pro118LeufsTer92	p.P118Lfs*92	ENST00000334344	NM_152641.2	118	CCAAAGCCACAGCTTCct/ct	4/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.548271038610447	2		547	785	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577605	64577605	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	32	47	0	ENST00000312049.6:c.-23-1G>A		p.X8_splice	ENST00000312049	NM_130799.2	8			1	2	FACETS	0.957	0.792	1	0.957	0.792	1	CLONAL	1	TRUE	1	0.548271038610447	2		47	122	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204623	128204624	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	197	542	0	ENST00000341105.2:c.817_818delinsAA	p.Gly273Lys	p.G273K	ENST00000341105	NM_032638.4	273	GGa/AAa	3/6	1	2	FACETS	0.885	0.821	0.951	0.885	0.821	0.951	CLONAL	1	TRUE	1	0.548271038610447	2		542	812	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555019	106555020	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	188	359	0	ENST00000369096.4:c.2136_2137delinsAA	p.Ala713Thr	p.A713T	ENST00000369096	NM_001198.3	712	gcGGcc/gcAAcc	7/7	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.548271038610447	2		359	683	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413267	139413269	+	stop_gained	Nonsense_Mutation	TNP	CAG	CAG	AAT	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	242	510	0	ENST00000277541.6:c.873_875delinsATT	p.Tyr291_Cys292delinsTer	p.Y291_C292delins*	ENST00000277541	NM_017617.3	291	taCTGt/taATTt	6/34	1	2	FACETS	0.961	0.899	1	0.961	0.899	1	CLONAL	1	TRUE	1	0.548271038610447	2		510	919	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448729	49448730	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	232	495	0	ENST00000301067.7:c.129_130delinsTT	p.Leu44Phe	p.L44F	ENST00000301067	NM_003482.3	43	gtCCtt/gtTTtt	2/54	1	2	FACETS	0.956	0.893	1	0.956	0.893	1	CLONAL	1	TRUE	1	0.548271038610447	2		495	885	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924288	11924289	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	30	67	0	ENST00000353533.5:c.85_86delinsTT	p.Pro29Leu	p.P29L	ENST00000353533	NM_003010.3	29	CCa/TTa	1/11	1	2	FACETS	0.782	0.639	0.938	0.782	0.639	0.938	CLONAL	1	TRUE	1	0.548271038610447	2		67	140	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522193	157522194	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0005619-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	172	335	2	ENST00000346085.5:c.4465_4466delinsTT	p.Pro1489Phe	p.P1489F	ENST00000346085	NM_020732.3	1489	CCt/TTt	18/20	1	2	FACETS	0.891	0.822	0.962	0.891	0.822	0.962	CLONAL	1	TRUE	1	0.548271038610447	2		337	704	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751183	57751183	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005630-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	33	395	0	ENST00000274289.3:c.1684C>T	p.Pro562Ser	p.P562S	ENST00000274289	NM_006622.3	562	Cct/Tct	12/14	1	2	FACETS	0.488	0.397	0.592	0.488	0.397	0.592	SUBCLONAL	1	TRUE	1	0.24	2		395	563	SUCCESS
APC	324	MSKCC	GRCh37	5	112175925	112175925	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs863225356	NA	P-0005630-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	59	351	0	ENST00000257430.4:c.4634C>G	p.Ser1545Ter	p.S1545*	ENST00000257430	NM_000038.5	1545	tCa/tGa	16/16	1	2	FACETS	0.91	0.784	1	0.91	0.784	1	CLONAL	1	TRUE	1	0.24	2		351	540	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805714	46805714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005630-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	100	656	0	ENST00000290295.7:c.242G>A	p.Gly81Asp	p.G81D	ENST00000290295	NM_006361.5	81	gGt/gAt	1/2	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.24	2		656	653	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176342	24176342	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1410970733	NA	P-0005630-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	36	455	0	ENST00000263121.7:c.1133T>C	p.Leu378Pro	p.L378P	ENST00000263121	NM_003073.3	378	cTt/cCt	9/9	1	2	FACETS	0.611	0.502	0.734	0.611	0.502	0.734	SUBCLONAL	1	TRUE	1	0.24	2		455	491	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970927	21970927	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501274	NA	P-0005639-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	109	513	1	ENST00000304494.5:c.431G>A	p.Arg144His	p.R144H	ENST00000304494	NM_000077.4	144	cGc/cAc	2/3	0.3	4	FACETS	1	0.934	1			1	CLONAL	2	TRUE	NA	0.31	4		514	442	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518049	176518049	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs566495475	NA	P-0005639-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	152	632	0	ENST00000292408.4:c.547C>T	p.Arg183Cys	p.R183C	ENST00000292408	NM_213647.1	183	Cgc/Tgc	5/18	0.250756505581796	3	FACETS	0.923	0.853	0.994	1	0.988	1	CLONAL	3	TRUE	1	0.31	3		632	409	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667868	37667868	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005639-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	70	522	0	ENST00000447079.4:c.2753A>G	p.Asp918Gly	p.D918G	ENST00000447079	NM_015083.1	918	gAt/gGt	8/14	0.195291347297573	3	FACETS	0.756	0.664	0.854	0.756	0.664	0.854	SUBCLONAL	2	TRUE	1	0.31	3		522	345	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649069	37649070	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0005639-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	95	534	0	ENST00000447079.4:c.2175_2176del	p.Asp725GlufsTer3	p.D725Efs*3	ENST00000447079	NM_015083.1	725	gAC/g	4/14	0.195291347297573	3	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	1	0.31	3		534	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0005648-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	120	468	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	0.344445611432035	3	FACETS	0.883	0.804	0.963			1	CLONAL	2	TRUE	NA	0.418346499972769	3		468	393	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553402	41553402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005648-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	139	522	0	ENST00000263253.7:c.3491G>A	p.Cys1164Tyr	p.C1164Y	ENST00000263253	NM_001429.3	1164	tGt/tAt	18/31	0.294977588108219	3	FACETS	1	0.957	1	0.707	0.651	0.764	CLONAL	2	TRUE	0	0.418346499972769	3		522	379	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074378	8074378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1392840731	NA	P-0005648-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	155	915	0	ENST00000377482.5:c.281C>T	p.Pro94Leu	p.P94L	ENST00000377482	NM_018948.3	94	cCt/cTt	4/4	0.00191126052680213	3	FACETS	1	0.949	1			1	INDETERMINATE	1	TRUE	NA	0.418346499972769	3		915	853	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671558	30671558	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005648-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	268	706	3	ENST00000376406.3:c.5402C>A	p.Pro1801Gln	p.P1801Q	ENST00000376406	NM_014641.2	1801	cCg/cAg	10/15	0.418346499972769	3	FACETS	1	0.985	1	0.752	0.709	0.795	CLONAL	2	TRUE	0	0.418346499972769	3		709	687	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371806	55371806	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005648-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	22	74	0	ENST00000297316.4:c.496G>A	p.Ala166Thr	p.A166T	ENST00000297316	NM_022454.3	166	Gcg/Acg	2/2	0.418346499972769	8	FACETS	1	0.893	1			1	CLONAL	1	TRUE	NA	0.418346499972769	8		74	187	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104352359	104352359	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005648-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	34	600	0	ENST00000369902.3:c.475G>T	p.Asp159Tyr	p.D159Y	ENST00000369902	NM_016169.3	159	Gac/Tac	4/12	0.301917150205799	2	FACETS	0.375	0.306	0.452	0.187	0.153	0.226	SUBCLONAL	1	TRUE	0	0.418346499972769	2		600	434	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395732	45395732	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1267982516	NA	P-0005648-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	43	485	0	ENST00000262160.6:c.402G>A	p.Trp134Ter	p.W134*	ENST00000262160	NM_005901.5	134	tgG/tgA	4/11	1	2	FACETS	0.794	0.669	0.93	0.794	0.669	0.93	CLONAL	1	TRUE	1	0.418346499972769	2		485	259	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309813	65309813	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0121532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	171	503	0	ENST00000342505.4:c.2337T>G	p.Phe779Leu	p.F779L	ENST00000342505	NM_002227.2	779	ttT/ttG	17/25	0.461161147544789	3	FACETS	1	0.953	1	0.524	0.483	0.568	CLONAL	1	NA	1	0.461161147544789	3		503	870	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0005681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	353	411	3	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.855699436692182	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.855699436692182	1		414	429	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376021	8376021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	435	591	3	ENST00000356435.5:c.4576G>T	p.Glu1526Ter	p.E1526*	ENST00000356435		1526	Gaa/Taa	28/35	1	2	FACETS	0.903	0.863	0.944	0.903	0.863	0.944	CLONAL	1	TRUE	1	0.855699436692182	2		594	1126	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027248	49027248	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0005681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	212	306	1	ENST00000267163.4:c.1814+1G>A		p.X605_splice	ENST00000267163	NM_000321.2	605			0.855699436692182	1	FACETS	0.964	0.922	1	0.964	0.922	1	CLONAL	1	TRUE	0	0.855699436692182	1		307	294	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576118	88576118	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	495	562	2	ENST00000360948.2:c.1555C>A	p.Gln519Lys	p.Q519K	ENST00000360948	NM_001012338.2	519	Cag/Aag	13/19	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.855699436692182	2		564	1142	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068426	16068426	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	35	297	1	ENST00000268712.3:c.485G>T	p.Gly162Val	p.G162V	ENST00000268712	NM_006311.3	162	gGg/gTg	5/46	0.855699436692182	1	FACETS	0.153	0.126	0.184	0.153	0.126	0.184	SUBCLONAL	1	TRUE	0	0.855699436692182	1		298	305	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792721	33792721	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	174	136	0	ENST00000498907.2:c.600C>G	p.His200Gln	p.H200Q	ENST00000498907	NM_004364.3	200	caC/caG	1/1	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.855699436692182	2		136	401	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0005695-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	315	599	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.16763163430933	2	FACETS	1	0.987	1	0.564	0.535	0.595	INDETERMINATE	1	TRUE	0	0.666761899394321	2		599	837	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578177	7578177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs267605076	NA	P-0005695-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	330	491	2	ENST00000269305.4:c.672G>T	p.Glu224Asp	p.E224D	ENST00000269305	NM_001126112.2	224	gaG/gaT	6/11	0.666761899394321	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.666761899394321	1		493	544	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936083	178936083	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519927	NA	P-0005695-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	223	181	0	ENST00000263967.3:c.1625A>C	p.Glu542Ala	p.E542A	ENST00000263967	NM_006218.2	542	gAa/gCa	10/21	0.228151575108571	3	FACETS	0.757	0.71	0.805	0.757	0.71	0.805	INDETERMINATE	2	TRUE	1	0.666761899394321	3		181	589	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853037	151853037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005695-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	25	378	1	ENST00000262189.6:c.11918C>T	p.Ala3973Val	p.A3973V	ENST00000262189	NM_170606.2	3973	gCc/gTc	46/59	0.172508569157699	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.666761899394321	0		379	479	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913471	NA	P-0005702-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	38	666	0	ENST00000269571.5:c.2329G>C	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ctg	20/27	0.3	3	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	3		666	406	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057744	180057744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138831198	NA	P-0005711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	118	422	0	ENST00000261937.6:c.211G>A	p.Gly71Arg	p.G71R	ENST00000261937	NM_182925.4	71	Gga/Aga	3/30	0.485064529044386	1	FACETS	0.544	0.492	0.6	0.544	0.492	0.6	SUBCLONAL	1	TRUE	0	0.485064529044386	1		422	677	SUCCESS
AR	367	MSKCC	GRCh37	X	66937465	66937465	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs1569314508	NA	P-0005711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	175	184	0	ENST00000374690.3:c.2318+1G>C		p.X773_splice	ENST00000374690	NM_000044.3	773			1	1	FACETS	0.831	0.779	0.882	1	0.993	1	CLONAL	2	TRUE	0	0.485064529044386	1		184	329	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577591	7577596	+	inframe_deletion	In_Frame_Del	DEL	GGTACA	GGTACA	-	novel	NA	P-0005711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	172	455	0	ENST00000269305.4:c.685_690del	p.Cys229_Thr230del	p.C229_T230del	ENST00000269305	NM_001126112.2	229	TGTACC/-	7/11	0.485064529044386	1	FACETS	0.91	0.842	0.981	0.91	0.842	0.981	CLONAL	1	TRUE	0	0.485064529044386	1		455	590	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220640	1220640	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690940	NA	P-0005723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	620	599	0	ENST00000326873.7:c.658C>T	p.Gln220Ter	p.Q220*	ENST00000326873	NM_000455.4	220	Cag/Tag	5/10	0.314410568586022	4	FACETS	1	0.986	1			1	CLONAL	3	TRUE	NA	0.314410568586022	4		599	1647	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702542	52702542	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	126	582	0	ENST00000394830.3:c.356T>C	p.Leu119Pro	p.L119P	ENST00000394830	NM_018313.4	119	cTt/cCt	4/30	0.308540946092531	1	FACETS	0.761	0.688	0.837	0.761	0.688	0.837	SUBCLONAL	1	TRUE	0	0.314410568586022	1		582	888	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753888	133753888	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	484	827	0	ENST00000318560.5:c.1357G>C	p.Glu453Gln	p.E453Q	ENST00000318560	NM_005157.4	453	Gag/Cag	8/11	0.304248938072133	2	FACETS	0.947	0.905	0.991	0.947	0.905	0.991	CLONAL	2	TRUE	0	0.314410568586022	2		827	1625	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720741	89720741	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs371387815	NA	P-0005723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	24	109	0	ENST00000371953.3:c.892C>T	p.Gln298Ter	p.Q298*	ENST00000371953	NM_000314.4	298	Caa/Taa	8/9	0.304248938072133	2	FACETS	0.816	0.645	1	0.408	0.322	0.506	CLONAL	1	TRUE	0	0.314410568586022	2		109	187	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444804	49444804	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	567	745	0	ENST00000301067.7:c.2662G>A	p.Glu888Lys	p.E888K	ENST00000301067	NM_003482.3	888	Gaa/Aaa	10/54	0.223733725743386	3	FACETS	0.851	0.817	0.886			1	CLONAL	3	TRUE	NA	0.314410568586022	3		745	1635	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037944	49037944	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	186	687	0	ENST00000267163.4:c.2184C>A	p.Tyr728Ter	p.Y728*	ENST00000267163	NM_000321.2	728	taC/taA	21/27	0.290522275188126	1	FACETS	0.955	0.881	1	0.955	0.881	1	CLONAL	1	TRUE	0	0.314410568586022	1		687	1044	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011168	12011171	+	frameshift_variant	Frame_Shift_Del	DEL	TATA	TATA	-	novel	NA	P-0005723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	174	521	0	ENST00000353533.5:c.577_580del	p.Tyr193ValfsTer3	p.Y193Vfs*3	ENST00000353533	NM_003010.3	192	gTATAt/gt	5/11	0.23307414870005	3	FACETS	0.938	0.866	1	0.625	0.577	0.675	CLONAL	2	TRUE	0	0.314410568586022	3		521	683	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871756	12871765	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAGATTCTTC	TAGATTCTTC	-	novel	NA	P-0005723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	200	279	0	ENST00000228872.4:c.476-1_484del		p.X159_splice	ENST00000228872	NM_004064.3	159		2/3	0.312670450050514	3	FACETS	0.934	0.868	1	0.623	0.578	0.669	CLONAL	2	TRUE	0	0.314410568586022	3		279	788	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602952	55602952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1237984655	NA	P-0005729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	69	287	0	ENST00000288135.5:c.2662C>T	p.Arg888Trp	p.R888W	ENST00000288135	NM_000222.2	888	Cgg/Tgg	19/21	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.18	2		287	754	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871001	12871001	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	81	331	0	ENST00000228872.4:c.228G>A	p.Trp76Ter	p.W76*	ENST00000228872	NM_004064.3	76	tgG/tgA	1/3	0.105103317604015	3	FACETS	1	0.949	1	0.574	0.505	0.649	INDETERMINATE	1	TRUE	1	0.18	3		331	854	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727443	66727443	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	63	391	0	ENST00000307102.5:c.159T>A	p.Phe53Leu	p.F53L	ENST00000307102	NM_002755.3	53	ttT/ttA	2/11	1	2	FACETS	0.731	0.631	0.841	0.731	0.631	0.841	SUBCLONAL	1	TRUE	1	0.18	2		391	957	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985344	60985344	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	84	420	0	ENST00000333681.4:c.556C>G	p.His186Asp	p.H186D	ENST00000333681		186	Cac/Gac	2/3	1	2	FACETS	0.92	0.81	1	0.92	0.81	1	CLONAL	1	TRUE	1	0.18	2		420	1015	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985629	60985629	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	11	66	0	ENST00000333681.4:c.271C>T	p.Pro91Ser	p.P91S	ENST00000333681		91	Cct/Tct	2/3	1	2	FACETS	1	0.795	1	1	0.795	1	CLONAL	1	TRUE	1	0.18	2		66	102	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985715	60985715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747696230	NA	P-0005729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	16	79	0	ENST00000333681.4:c.185C>T	p.Ser62Phe	p.S62F	ENST00000333681		62	tCc/tTc	2/3	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.18	2		79	141	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733590	85733591	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0005729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	112	543	0	ENST00000370580.1:c.421_422del	p.Ser141Ter	p.S141*	ENST00000370580	NM_003921.4	141	AGt/t	3/3	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.18	2		543	1235	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871012	12871015	+	missense_variant	Missense_Mutation	ONP	AGAA	AGAA	TGAG	novel	NA	P-0005729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	67	320	0	ENST00000228872.4:c.239_242delinsTGAG	p.Glu80_Lys81delinsValArg	p.E80_K81delinsVR	ENST00000228872	NM_004064.3	80	gAGAAg/gTGAGg	1/3	0.105103317604015	3	FACETS	0.993	0.862	1	0.497	0.431	0.568	INDETERMINATE	1	TRUE	1	0.18	3		320	817	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985530	60985533	+	missense_variant	Missense_Mutation	ONP	AGGG	AGGG	CGGC	novel	NA	P-0005729-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	49	333	0	ENST00000333681.4:c.367_370delinsGCCG	p.Pro123_Phe124delinsAlaVal	p.P123_F124delinsAV	ENST00000333681		123	CCCTtc/GCCGtc	2/3	1	2	FACETS	0.851	0.719	0.995	0.851	0.719	0.995	CLONAL	1	TRUE	1	0.18	2		333	640	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197151	106197151	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	59	569	0	ENST00000380013.4:c.5484G>C	p.Gln1828His	p.Q1828H	ENST00000380013	NM_001127208.2	1828	caG/caC	11/11	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.195955525971591	2		569	589	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205828	108205828	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	56	487	0	ENST00000278616.4:c.8143C>T	p.Leu2715Phe	p.L2715F	ENST00000278616	NM_000051.3	2715	Ctt/Ttt	55/63	NA	2	FACETS	1	0.923	1			1	INDETERMINATE	1	TRUE	NA	0.195955525971591	2		487	511	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649451	23649451	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs1440838364	NA	P-0005761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	84	596	0	ENST00000261584.4:c.49-1G>C		p.X17_splice	ENST00000261584	NM_024675.3	17			NA	2	FACETS	1	0.952	1			1	INDETERMINATE	1	TRUE	NA	0.195955525971591	2		596	744	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117870592	117870607	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AAAATCATTTTCTTGT	AAAATCATTTTCTTGT	-	novel	NA	P-0005761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	79	633	0	ENST00000297338.2:c.465_480del	p.Gln156ValfsTer10	p.Q156Vfs*10	ENST00000297338	NM_006265.2	155	ttACAAGAAAATGATTTT/tt	5/14	0.200801622620584	3	FACETS	0.883	0.774	1	0.441	0.387	0.5	CLONAL	1	TRUE	1	0.195955525971591	3		633	1003	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061225	38061238	+	protein_altering_variant	In_Frame_Del	DEL	TCGAACATGTTGCC	TCGAACATGTTGCC	GA	novel	NA	P-0005761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	117	557	0	ENST00000250448.2:c.751_764delinsTC	p.Gly251_Glu255delinsSer	p.G251_E255delinsS	ENST00000250448	NM_004496.3	251	GGCAACATGTTCGAg/TCg	2/2	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.195955525971591	2		557	1109	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0005766-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	85	375	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.955	0.848	1	1	0.984	1	CLONAL	2	TRUE	1	0.21	2		378	424	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570318	95570318	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0005766-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	32	309	1	ENST00000393063.1:c.3415A>T	p.Arg1139Ter	p.R1139*	ENST00000393063	NM_030621.3	1139	Aga/Tga	22/28	1	2	FACETS	0.696	0.564	0.844	0.696	0.564	0.844	SUBCLONAL	1	TRUE	1	0.21	2		310	438	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533550	63533550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005766-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	65	689	0	ENST00000307078.5:c.1604C>A	p.Ala535Asp	p.A535D	ENST00000307078	NM_004655.3	535	gCc/gAc	6/11	1	2	FACETS	0.747	0.646	0.856	0.747	0.646	0.856	SUBCLONAL	1	TRUE	1	0.21	2		689	829	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030067	36030067	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005766-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	38	584	0	ENST00000358208.4:c.1102G>A	p.Asp368Asn	p.D368N	ENST00000358208		368	Gac/Aac	9/12	1	2	FACETS	0.553	0.456	0.661	0.553	0.456	0.661	SUBCLONAL	1	TRUE	1	0.21	2		584	655	SUCCESS
APC	324	MSKCC	GRCh37	5	112162696	112162892	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATATTCTCATTGATTGAGTTTTTTTTTCCTAGTATTTAAGTTACCAACTTGGTACCAGTTTGTTTTATTTTAGATGATTGTCTTTTTCCTCTTGCCCTTTTTAAATTAGGGGGACTACAGGCCATTGCAGAATTATTGCAAGTGGACTGTGAAATGTATGGGCTTACTAATGACCACTACAGTATTACACTAAGACG	ATATTCTCATTGATTGAGTTTTTTTTTCCTAGTATTTAAGTTACCAACTTGGTACCAGTTTGTTTTATTTTAGATGATTGTCTTTTTCCTCTTGCCCTTTTTAAATTAGGGGGACTACAGGCCATTGCAGAATTATTGCAAGTGGACTGTGAAATGTATGGGCTTACTAATGACCACTACAGTATTACACTAAGACG	-	novel	NA	P-0005766-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	30	48	0	ENST00000257430.4:c.1409-105_1500del		p.X470_splice	ENST00000257430	NM_000038.5	470		12/16	1	2	FACETS	1	0.908	1	1	0.973	1	CLONAL	4	TRUE	1	0.21	2		48	64	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	145	455	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.657419974947126	1	FACETS	0.476	0.436	0.518	0.476	0.436	0.518	SUBCLONAL	1	TRUE	0	0.657419974947126	1		455	622	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206806	162206806	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	154	459	0	ENST00000366898.1:c.869T>A	p.Val290Glu	p.V290E	ENST00000366898	NM_004562.2	290	gTg/gAg	7/12	0.657419974947126	1	FACETS	0.491	0.451	0.533	0.491	0.451	0.533	SUBCLONAL	1	TRUE	0	0.657419974947126	1		459	640	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564084	139564084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759831503	NA	P-0005785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	190	623	2	ENST00000308874.7:c.224G>A	p.Arg75His	p.R75H	ENST00000308874		75	cGc/cAc	5/10	0.657419974947126	1	FACETS	0.513	0.475	0.552	0.513	0.475	0.552	SUBCLONAL	1	TRUE	0	0.657419974947126	1		625	757	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115943	8115964	+	frameshift_variant	Frame_Shift_Del	DEL	TTGGACCACACCACCCCTCCAG	TTGGACCACACCACCCCTCCAG	-	novel	NA	P-0005785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	166	316	0	ENST00000346208.3:c.1289_1310del	p.Phe430SerfsTer38	p.F430Sfs*38	ENST00000346208		430	tTTGGACCACACCACCCCTCCAGc/tc	6/6	0.332309815449976	1	FACETS	0.692	0.641	0.744	0.692	0.641	0.744	INDETERMINATE	1	TRUE	0	0.657419974947126	1		316	490	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	67	291	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.886	0.771	1	0.886	0.771	1	CLONAL	1	TRUE	1	0.283307507099996	2		291	534	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0005788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	154	785	4	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.283307507099996	2		789	989	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537965	212537965	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	53	397	1	ENST00000342788.4:c.1640A>C	p.Glu547Ala	p.E547A	ENST00000342788	NM_005235.2	547	gAg/gCg	14/28	1	2	FACETS	0.554	0.472	0.645	0.554	0.472	0.645	SUBCLONAL	1	TRUE	1	0.283307507099996	2		398	675	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78865638	78865638	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0005788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	43	340	0	ENST00000306801.3:c.2101+1G>T		p.X701_splice	ENST00000306801	NM_020761.2	701			1	2	FACETS	0.564	0.472	0.667	0.564	0.472	0.667	SUBCLONAL	1	TRUE	1	0.283307507099996	2		340	538	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932171	39932171	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555918056	NA	P-0005788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	112	375	0	ENST00000378444.4:c.2428C>T	p.Arg810Ter	p.R810*	ENST00000378444	NM_001123385.1	810	Cga/Tga	4/15	1	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.283307507099996	1		375	594	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120523	70120533	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	CCTTGAGGAGG	CCTTGAGGAGG	-	novel	NA	P-0005788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	356	95	0	ENST00000245479.2:c.1528_*8del		p.*510*	ENST00000245479	NM_000346.3	509		3/3	1	2	FACETS	1	0.985	1	1	0.997	1	CLONAL	3	TRUE	1	0.283307507099996	2		95	779	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005789-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	135	246	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.8	2		246	321	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0005789-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	193	411	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	0.8	2		411	468	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562657	29562660	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs1064794276	NA	P-0005789-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	153	361	0	ENST00000356175.3:c.3739_3742del	p.Phe1247IlefsTer18	p.F1247Ifs*18	ENST00000356175	NM_000267.3	1246	cTGTTt/ct	28/57	1	2	FACETS	0.523	0.479	0.568	0.523	0.479	0.568	SUBCLONAL	1	TRUE	1	0.8	2		361	732	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0005789-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	132	329	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.652	0.595	0.711	0.652	0.595	0.711	SUBCLONAL	1	TRUE	1	0.8	2		329	506	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236215	108236215	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs730881332	NA	P-0005800-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	189	971	0	ENST00000278616.4:c.9151G>C	p.Gly3051Arg	p.G3051R	ENST00000278616	NM_000051.3	3051	Gga/Cga	63/63	0.309012339397447	2	FACETS	0.937	0.87	1	0.937	0.87	1	CLONAL	2	TRUE	0	0.309012339397447	2		971	653	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696431	47696431	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519969	NA	P-0005804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	128	383	0	ENST00000347630.2:c.392G>C	p.Trp131Ser	p.W131S	ENST00000347630	NM_001007230.1	131	tGg/tCg	6/11	1	2	FACETS	0.946	0.859	1	0.946	0.859	1	CLONAL	1	TRUE	1	0.407716063292726	2		383	664	SUCCESS
APC	324	MSKCC	GRCh37	5	112175193	112175193	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1064794042	NA	P-0005804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	12	207	0	ENST00000257430.4:c.3904del	p.Leu1302CysfsTer3	p.L1302Cfs*3	ENST00000257430	NM_000038.5	1301	aCc/ac	16/16	0.407716063292726	1	FACETS	0.201	0.141	0.275	0.201	0.141	0.275	SUBCLONAL	1	TRUE	0	0.407716063292726	1		207	233	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604628	55604628	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs139000082	NA	P-0005819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	288	516	0	ENST00000288135.5:c.2836C>T	p.Arg946Ter	p.R946*	ENST00000288135	NM_000222.2	946	Cga/Tga	21/21	0.488402225315638	3	FACETS	0.903	0.853	0.953	0.903	0.853	0.953	CLONAL	2	TRUE	1	0.512641267957993	3		516	782	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245132	46245132	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0005819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	227	364	0	ENST00000334344.6:c.3226A>T	p.Lys1076Ter	p.K1076*	ENST00000334344	NM_152641.2	1076	Aag/Tag	15/21	NA	2	FACETS	0.906	0.853	0.958			1	INDETERMINATE	2	TRUE	NA	0.512641267957993	2		364	489	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435357	110435357	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	229	251	0	ENST00000375856.3:c.3044C>T	p.Pro1015Leu	p.P1015L	ENST00000375856	NM_003749.2	1015	cCg/cTg	1/2	0.321766003335228	5	FACETS	1	0.982	1	0.754	0.706	0.803	CLONAL	2	TRUE	2	0.512641267957993	5		251	699	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221956	1221956	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	414	604	0	ENST00000326873.7:c.871G>T	p.Glu291Ter	p.E291*	ENST00000326873	NM_000455.4	291	Gag/Tag	7/10	0.439184671695421	2	FACETS	0.833	0.796	0.87	0.833	0.796	0.87	CLONAL	2	TRUE	0	0.512641267957993	2		604	970	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641478	47641478	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1286	236	741	0	ENST00000233146.2:c.863A>T	p.Gln288Leu	p.Q288L	ENST00000233146	NM_000251.2	288	cAg/cTg	5/16	1	2	FACETS	0.525	0.489	0.564	0.525	0.489	0.564	SUBCLONAL	1	TRUE	1	0.590153056327213	2		741	1522	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148507476	148507476	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	575	488	0	ENST00000320356.2:c.1978G>C	p.Gly660Arg	p.G660R	ENST00000320356	NM_004456.4	660	Ggg/Cgg	17/20	0.590153056327213	2	FACETS	0.976	0.944	1	0.976	0.944	1	CLONAL	2	TRUE	0	0.590153056327213	2		488	998	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117630048	117630048	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	26	598	0	ENST00000368508.3:c.6478C>T	p.Gln2160Ter	p.Q2160*	ENST00000368508	NM_002944.2	2160	Cag/Tag	41/43	NA	2	FACETS	0.521	0.417	0.637			1	INDETERMINATE	1	TRUE	NA	0.631918610526794	2		598	158	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344788	65344788	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	59	742	0	ENST00000342505.4:c.249G>C	p.Glu83Asp	p.E83D	ENST00000342505	NM_002227.2	83	gaG/gaC	4/25	0.639525853839435	4	FACETS	1	0.872	1			1	CLONAL	1	TRUE	NA	0.631918610526794	4		742	303	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564794	86564794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	81	795	1	ENST00000274376.6:c.526C>T	p.Pro176Ser	p.P176S	ENST00000274376	NM_002890.2	176	Cct/Tct	1/25	0.631918610526794	6	FACETS	0.961	0.855	1	0.48	0.427	0.536	CLONAL	2	TRUE	2	0.631918610526794	6		796	302	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520253	176520253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375466821	NA	P-0005832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	77	403	0	ENST00000292408.4:c.1172G>A	p.Arg391Gln	p.R391Q	ENST00000292408	NM_213647.1	391	cGa/cAa	9/18	0.639525853839435	4	FACETS	0.872	0.79	0.955	0.872	0.79	0.955	CLONAL	3	TRUE	1	0.631918610526794	4		403	152	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362561	118362561	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	59	584	0	ENST00000534358.1:c.4922A>C	p.Lys1641Thr	p.K1641T	ENST00000534358	NM_005933.3	1641	aAa/aCa	15/36	0.639525853839435	4	FACETS	1	0.936	1	0.378	0.328	0.431	CLONAL	1	TRUE	1	0.631918610526794	4		584	269	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544706	65544706	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	90	594	0	ENST00000358664.4:c.220A>G	p.Met74Val	p.M74V	ENST00000358664	NM_002382.4	74	Atg/Gtg	4/5	0.631918610526794	6	FACETS	0.858	0.767	0.953	0.572	0.511	0.636	CLONAL	2	TRUE	3	0.631918610526794	6		594	376	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988919	41988919	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	68	887	0	ENST00000219905.7:c.1711G>C	p.Asp571His	p.D571H	ENST00000219905	NM_001164273.1	571	Gat/Cat	3/24	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.631918610526794	2		887	192	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857925	9857925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs534440095	NA	P-0005832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	33	516	1	ENST00000330684.3:c.3476G>A	p.Arg1159His	p.R1159H	ENST00000330684	NM_001134407.1	1159	cGc/cAc	13/13	0.376487501869572	1	FACETS	0.59	0.491	0.698	0.59	0.491	0.698	INDETERMINATE	1	TRUE	0	0.631918610526794	1		517	121	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993389	72993389	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0005832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	55	852	0	ENST00000268489.5:c.656C>G	p.Ser219Ter	p.S219*	ENST00000268489	NM_006885.3	219	tCa/tGa	2/10	0.220343872056303	4	FACETS	0.891	0.766	1	0.445	0.383	0.512	INDETERMINATE	1	TRUE	2	0.631918610526794	4		852	319	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383106	42383106	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	61	725	0	ENST00000221972.3:c.126G>C	p.Leu42Phe	p.L42F	ENST00000221972	NM_021601.3	42	ttG/ttC	2/5	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.631918610526794	NA		725	290	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931616	39931616	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	23	561	0	ENST00000378444.4:c.2983C>A	p.Gln995Lys	p.Q995K	ENST00000378444	NM_001123385.1	995	Caa/Aaa	4/15	0.446652535507407	5	FACETS	0.565	0.442	0.707			1	SUBCLONAL	1	TRUE	NA	0.631918610526794	5		561	251	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944328	76944328	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	16	715	0	ENST00000373344.5:c.577C>T	p.Gln193Ter	p.Q193*	ENST00000373344	NM_000489.3	193	Caa/Taa	7/35	0.63628781436434	3	FACETS	0.242	0.179	0.318			1	SUBCLONAL	1	TRUE	NA	0.631918610526794	3		715	275	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440875	52440875	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1383276496	NA	P-0005843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	473	648	0	ENST00000460680.1:c.629T>C	p.Ile210Thr	p.I210T	ENST00000460680	NM_004656.3	210	aTc/aCc	8/17	0.534268051362844	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.534268051362844	1		648	1204	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52649438	52649438	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	443	594	0	ENST00000394830.3:c.1853T>G	p.Leu618Arg	p.L618R	ENST00000394830	NM_018313.4	618	cTc/cGc	16/30	0.534268051362844	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.534268051362844	1		594	1094	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211469	46211469	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	298	437	0	ENST00000334344.6:c.435T>A	p.Ser145Arg	p.S145R	ENST00000334344	NM_152641.2	145	agT/agA	5/21	1	2	FACETS	0.989	0.931	1	0.989	0.931	1	CLONAL	1	TRUE	1	0.534268051362844	2		437	1128	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032830	30032830	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	403	629	0	ENST00000338641.4:c.206del	p.Lys69ArgfsTer54	p.K69Rfs*54	ENST00000338641	NM_000268.3	69	Aag/ag	2/16	0.534268051362844	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.534268051362844	1		629	1082	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	112	291	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.853	0.766	0.945	1	0.986	1	CLONAL	2	TRUE	1	0.14	2		291	938	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0005847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	44	516	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.572	0.477	0.677	0.572	0.477	0.677	SUBCLONAL	1	TRUE	1	0.14	2		516	1099	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650322	12650322	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs397516822	NA	P-0005847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	88	609	0	ENST00000251849.4:c.524A>G	p.His175Arg	p.H175R	ENST00000251849	NM_002880.3	175	cAc/cGc	5/17	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.14	2		609	1052	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650571	18650571	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	93	571	0	ENST00000266497.5:c.2782C>T	p.Gln928Ter	p.Q928*	ENST00000266497		928	Cag/Tag	20/31	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.14	2		571	1053	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120244	70120244	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	98	590	0	ENST00000245479.2:c.1246C>T	p.Gln416Ter	p.Q416*	ENST00000245479	NM_000346.3	416	Caa/Taa	3/3	1	2	FACETS	0.766	0.682	0.855	1	0.981	1	SUBCLONAL	2	TRUE	1	0.14	2		590	914	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223039	1223052	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGACACCAAGGA	CCAGACACCAAGGA	-	novel	NA	P-0005847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	72	503	0	ENST00000326873.7:c.978_991del	p.Asp327ValfsTer28	p.D327Vfs*28	ENST00000326873	NM_000455.4	326	CCAGACACCAAGGAc/c	8/10	0.189269280523751	1	FACETS	0.856	0.748	0.971	1	0.979	1	CLONAL	2	TRUE	0	0.14	1		503	559	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193121531	193121531	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	29	391	0	ENST00000367435.3:c.929A>G	p.Asp310Gly	p.D310G	ENST00000367435	NM_024529.4	310	gAc/gGc	10/17	1	2	FACETS	0.178	0.142	0.218	0.178	0.142	0.218	SUBCLONAL	1	TRUE	1	0.808283142951663	2		391	404	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005886-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	308	246	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.8	0.765	0.834			1	INDETERMINATE	2	FALSE	NA	0.743520429839168	2		246	518	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0005886-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	312	352	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.743520429839168	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	0	0.743520429839168	1		352	505	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858907	57858907	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005886-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	227	507	0	ENST00000228682.2:c.403T>A	p.Phe135Ile	p.F135I	ENST00000228682	NM_005269.2	135	Ttc/Atc	5/12	0.743520429839168	15	FACETS	1	0.974	1			1	CLONAL	3	FALSE	NA	0.743520429839168	15		507	1088	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117766	115117766	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005886-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	263	232	0	ENST00000257566.3:c.669C>A	p.Phe223Leu	p.F223L	ENST00000257566	NM_016569.3	223	ttC/ttA	3/8	1	2	FACETS	0.821	0.771	0.871	0.821	0.771	0.871	CLONAL	1	FALSE	1	0.743520429839168	2		232	862	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2105495	2105495	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005886-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	252	262	2	ENST00000219476.3:c.574G>T	p.Asp192Tyr	p.D192Y	ENST00000219476	NM_000548.3	192	Gac/Tac	6/42	0.127086747101389	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.743520429839168	0		264	653	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0005895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	1962	343	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.717125855572244	14	FACETS	0.98	0.968	0.992			1	CLONAL	12	TRUE	NA	0.717125855572244	14		343	2467	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226595555	226595555	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	233	395	0	ENST00000366794.5:c.76G>T	p.Glu26Ter	p.E26*	ENST00000366794	NM_001618.3	26	Gag/Tag	1/23	0.719988363794698	5	FACETS	1	0.973	1	0.271	0.252	0.291	CLONAL	1	TRUE	1	0.717125855572244	5		395	1244	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022423	12022423	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	374	632	0	ENST00000396373.4:c.529G>C	p.Glu177Gln	p.E177Q	ENST00000396373	NM_001987.4	177	Gaa/Caa	5/8	0.719988363794698	4	FACETS	1	0.993	1			1	CLONAL	1	TRUE	NA	0.717125855572244	4		632	1394	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78858943	78858943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	91	365	0	ENST00000306801.3:c.1978C>T	p.Arg660Trp	p.R660W	ENST00000306801	NM_020761.2	660	Cgg/Tgg	17/34	0.719988363794698	4	FACETS	0.56	0.497	0.628	0.187	0.165	0.21	SUBCLONAL	1	TRUE	1	0.717125855572244	4		365	778	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1327782	1327782	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	209	348	0	ENST00000400841.2:c.99G>C	p.Gln33His	p.Q33H	ENST00000400841		33	caG/caC	2/6	0.404958663293715	4	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.717125855572244	4		348	786	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576920	7576936	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCAGTGCTAGGAAAGA	GGCAGTGCTAGGAAAGA	-	novel	NA	P-0005895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	359	296	0	ENST00000269305.4:c.920-10_926del		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	0.659950727661389	4	FACETS	0.901	0.872	0.929	0.901	0.872	0.929	CLONAL	4	TRUE	0	0.717125855572244	4		296	477	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	37	246	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.243534256675649	2		246	271	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0005928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	205	334	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	0.243534256675649	5	FACETS	1	0.978	1	0.835	0.778	0.894	CLONAL	3	TRUE	1	0.243534256675649	5		334	688	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522662	176522662	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs555513735	NA	P-0005928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	82	538	0	ENST00000292408.4:c.1759C>T	p.Pro587Ser	p.P587S	ENST00000292408	NM_213647.1	587	Cca/Tca	13/18	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.243534256675649	2		538	668	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17124889	17124889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748031634	NA	P-0005928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	62	444	2	ENST00000285071.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000285071	NM_144997.5	278	cCg/cTg	8/14	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.243534256675649	2		446	500	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594221	55594221	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913512	NA	P-0005928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	48	344	0	ENST00000288135.5:c.1924A>G	p.Lys642Glu	p.K642E	ENST00000288135	NM_000222.2	642	Aaa/Gaa	13/21	0.235137298931873	3	FACETS	1	0.851	1	0.502	0.425	0.587	CLONAL	1	TRUE	1	0.243534256675649	3		344	440	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933474	36933474	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	394	703	1	ENST00000361632.4:c.1813C>A	p.Gln605Lys	p.Q605K	ENST00000361632		605	Cag/Aag	13/16	0.243534256675649	5	FACETS	0.981	0.934	1	0.981	0.934	1	CLONAL	4	TRUE	1	0.243534256675649	5		704	1126	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139534	47139534	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	89	434	0	ENST00000409792.3:c.5053T>A	p.Cys1685Ser	p.C1685S	ENST00000409792	NM_014159.6	1685	Tgc/Agc	9/21	0.236227838241324	4	FACETS	0.786	0.698	0.88	0.786	0.698	0.88	SUBCLONAL	2	TRUE	2	0.243534256675649	4		434	578	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279477	1279477	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	67	510	0	ENST00000310581.5:c.2059C>T	p.His687Tyr	p.H687Y	ENST00000310581	NM_198253.2	687	Cac/Tac	5/16	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.243534256675649	2		510	494	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120377	94120377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	53	632	0	ENST00000369303.4:c.674C>T	p.Ser225Phe	p.S225F	ENST00000369303	NM_004440.3	225	tCc/tTc	3/17	NA	2	FACETS	0.772	0.658	0.896			1	INDETERMINATE	1	TRUE	NA	0.243534256675649	2		632	564	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104352345	104352345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	80	427	2	ENST00000369902.3:c.461C>T	p.Thr154Ile	p.T154I	ENST00000369902	NM_016169.3	154	aCc/aTc	4/12	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.243534256675649	2		429	580	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998507	100998507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	40	315	0	ENST00000325455.5:c.1295C>T	p.Ser432Phe	p.S432F	ENST00000325455	NM_001202474.3	432	tCc/tTc	1/8	1	2	FACETS	0.807	0.671	0.958	0.807	0.671	0.958	CLONAL	1	TRUE	1	0.243534256675649	2		315	407	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205756	108205756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531980488	NA	P-0005928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	46	356	0	ENST00000278616.4:c.8071C>T	p.Arg2691Cys	p.R2691C	ENST00000278616	NM_000051.3	2691	Cgc/Tgc	55/63	0.115863335341744	3	FACETS	1	0.901	1			1	INDETERMINATE	1	TRUE	NA	0.243534256675649	3		356	388	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111965605	111965605	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	15	105	0	ENST00000375549.3:c.391C>A	p.Leu131Ile	p.L131I	ENST00000375549	NM_003002.3	131	Ctt/Att	4/4	0.115863335341744	3	FACETS	1	0.778	1			1	INDETERMINATE	1	TRUE	NA	0.243534256675649	3		105	130	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374532	118374532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	64	417	1	ENST00000534358.1:c.7925C>T	p.Ser2642Phe	p.S2642F	ENST00000534358	NM_005933.3	2642	tCc/tTc	27/36	0.115863335341744	3	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.243534256675649	3		418	461	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989597	15989597	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	53	304	0	ENST00000268712.3:c.3176A>T	p.Gln1059Leu	p.Q1059L	ENST00000268712	NM_006311.3	1059	cAg/cTg	23/46	1	2	FACETS	0.829	0.707	0.962	0.829	0.707	0.962	CLONAL	1	TRUE	1	0.243534256675649	2		304	525	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016158	31016158	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	94	510	1	ENST00000375687.4:c.404C>T	p.Ser135Phe	p.S135F	ENST00000375687	NM_015338.5	135	tCc/tTc	6/13	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.243534256675649	2		511	706	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420074	41420074	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457746024	NA	P-0005928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	62	404	0	ENST00000373198.4:c.247G>A	p.Ala83Thr	p.A83T	ENST00000373198	NM_133170.3	83	Gcc/Acc	3/32	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.243534256675649	2		404	450	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650403	48650403	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782411113	NA	P-0005928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	111	304	0	ENST00000376670.3:c.373G>A	p.Asp125Asn	p.D125N	ENST00000376670	NM_002049.3	125	Gat/Aat	3/6	1	1	FACETS	1	0.916	1	1	0.989	1	CLONAL	2	TRUE	0	0.243534256675649	1		304	396	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569869	95569870	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0005928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	85	519	0	ENST00000393063.1:c.3863_3864delinsAA	p.Arg1288Lys	p.R1288K	ENST00000393063	NM_030621.3	1288	aGG/aAA	22/28	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.243534256675649	2		519	683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0005941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	452	638	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.668097969614144	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.708010832032381	2		638	603	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40738998	40738998	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	486	465	0	ENST00000373198.4:c.3286G>T	p.Ala1096Ser	p.A1096S	ENST00000373198	NM_133170.3	1096	Gct/Tct	24/32	0.708010832032381	6	FACETS	1	0.993	1	0.683	0.657	0.709	CLONAL	3	TRUE	1	0.708010832032381	6		465	971	SUCCESS
APC	324	MSKCC	GRCh37	5	112174574	112174574	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	82	597	4	ENST00000257430.4:c.3283C>T	p.Gln1095Ter	p.Q1095*	ENST00000257430	NM_000038.5	1095	Cag/Tag	16/16	0.308775320756519	2	FACETS	0.486	0.429	0.545	0.243	0.214	0.273	INDETERMINATE	1	TRUE	0	0.708010832032381	2		601	477	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399161	139399161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1163223024	NA	P-0005941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	15	392	0	ENST00000277541.6:c.4982G>A	p.Arg1661Gln	p.R1661Q	ENST00000277541	NM_017617.3	1661	cGg/cAg	26/34	0.668097969614144	2	FACETS	0.141	0.103	0.188	0.071	0.051	0.094	SUBCLONAL	1	TRUE	0	0.708010832032381	2		392	300	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333069	70333069	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	28	626	0	ENST00000373644.4:c.974C>G	p.Ser325Cys	p.S325C	ENST00000373644	NM_030625.2	325	tCt/tGt	2/12	0.67326852776834	2	FACETS	0.169	0.135	0.209	0.085	0.067	0.105	SUBCLONAL	1	TRUE	0	0.708010832032381	2		626	467	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473625	67473625	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	204	575	0	ENST00000327367.4:c.705C>G	p.Ile235Met	p.I235M	ENST00000327367	NM_005902.3	235	atC/atG	6/9	1	2	FACETS	0.939	0.876	1	0.939	0.876	1	CLONAL	1	TRUE	1	0.708010832032381	2		575	614	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032306	10032306	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	78	396	0	ENST00000330684.3:c.517G>C	p.Val173Leu	p.V173L	ENST00000330684	NM_001134407.1	173	Gtg/Ctg	3/13	0.255717868487385	3	FACETS	0.88	0.779	0.986	0.293	0.259	0.329	INDETERMINATE	1	TRUE	0	0.708010832032381	3		396	339	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593519	48593519	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	120	383	0	ENST00000342988.3:c.1270G>C	p.Asp424His	p.D424H	ENST00000342988	NM_005359.5	424	Gat/Cat	10/12	0.708010832032381	1	FACETS	0.897	0.828	0.967	0.897	0.828	0.967	CLONAL	1	TRUE	0	0.708010832032381	1		383	244	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	409	246	0				ENST00000310581	NM_198253.2	-/1132			0.433011956134567	4	FACETS	0.991	0.959	1			1	INDETERMINATE	3	TRUE	NA	0.901748832434234	4		246	580	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789684	3789684	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	115	641	0	ENST00000262367.5:c.4175G>A	p.Arg1392Gln	p.R1392Q	ENST00000262367	NM_004380.2	1392	cGa/cAa	25/31	0.700100691601948	1	FACETS	0.237	0.214	0.261	0.237	0.214	0.261	SUBCLONAL	1	TRUE	0	0.901748832434234	1		641	591	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518619	204518619	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754846508	NA	P-0005966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	621	533	0	ENST00000367182.3:c.1282G>A	p.Glu428Lys	p.E428K	ENST00000367182	NM_001278516.1	428	Gag/Aag	11/11	0.299701500379008	3	FACETS	0.973	0.943	1	0.649	0.629	0.668	INDETERMINATE	2	TRUE	0	0.901748832434234	3		533	1027	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390537	139390537	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1289429344	NA	P-0005966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	156	705	1	ENST00000277541.6:c.7654G>A	p.Glu2552Lys	p.E2552K	ENST00000277541	NM_017617.3	2552	Gag/Aag	34/34	0.901748832434234	1	FACETS	0.3	0.275	0.325	0.3	0.275	0.325	SUBCLONAL	1	TRUE	0	0.901748832434234	1		706	634	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158261	106158261	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	130	627	0	ENST00000380013.4:c.3165del	p.Val1056LeufsTer10	p.V1056Lfs*10	ENST00000380013	NM_001127208.2	1054	gtA/gt	3/11	NA	2	FACETS	0.478	0.435	0.523			1	INDETERMINATE	1	TRUE	NA	0.901748832434234	2		627	603	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970972	21970972	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005992-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	46	419	0	ENST00000304494.5:c.386A>G	p.Tyr129Cys	p.Y129C	ENST00000304494	NM_000077.4	129	tAc/tGc	2/3	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		419	887	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0005993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	455	426	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.536275952607504	2	FACETS	0.933	0.896	0.969	0.933	0.896	0.969	CLONAL	2	TRUE	0	0.542094516095203	2		426	900	SUCCESS
AR	367	MSKCC	GRCh37	X	66766357	66766389	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	-	rs746853821	NA	P-0005993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	70	42	0	ENST00000374690.3:c.1388_1420del	p.Gly463_Gly473del	p.G463_G473del	ENST00000374690	NM_000044.3	457	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC/-	1/8	0.542094516095203	2	FACETS	1	0.974	1			1	CLONAL	1	TRUE	NA	0.542094516095203	2		42	188	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98244463	98244463	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	53	315	0	ENST00000331920.6:c.607T>C	p.Cys203Arg	p.C203R	ENST00000331920	NM_000264.3	203	Tgt/Cgt	4/24	1	2	FACETS	0.281	0.239	0.328	0.281	0.239	0.328	SUBCLONAL	1	TRUE	1	0.542094516095203	2		315	695	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347664	118347664	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886041856	NA	P-0005993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	243	518	1	ENST00000534358.1:c.3301C>T	p.Arg1101Ter	p.R1101*	ENST00000534358	NM_005933.3	1101	Cga/Tga	4/36	1	2	FACETS	0.885	0.827	0.945	0.885	0.827	0.945	CLONAL	1	TRUE	1	0.542094516095203	2		519	1013	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728676	190728678	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs777263508	NA	P-0005993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	284	473	0	ENST00000441310.2:c.2067_2069del	p.Arg690del	p.R690del	ENST00000441310	NM_000534.4	688	aaAAGa/aaa	10/13	1	2	FACETS	0.88	0.827	0.935	0.88	0.827	0.935	CLONAL	1	TRUE	1	0.542094516095203	2		473	1190	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0005994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	81	207	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.851	0.749	0.96	0.851	0.749	0.96	CLONAL	1	FALSE	1	0.265613650321504	2		207	717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578476	7578476	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	182	410	0	ENST00000269305.4:c.454C>A	p.Pro152Thr	p.P152T	ENST00000269305	NM_001126112.2	152	Ccg/Acg	5/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.265613650321504	2		410	1221	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39772534	39772534	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	60	304	0	ENST00000288319.7:c.707T>C	p.Val236Ala	p.V236A	ENST00000288319	NM_182918.3	236	gTa/gCa	6/10	1	2	FACETS	0.447	0.384	0.517	0.447	0.384	0.517	SUBCLONAL	1	FALSE	1	0.265613650321504	2		304	1010	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966779	44966779	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	47	207	0	ENST00000377967.4:c.4003G>T	p.Glu1335Ter	p.E1335*	ENST00000377967	NM_021140.2	1335	Gaa/Taa	27/29	1	1	FACETS	0.513	0.432	0.603	0.513	0.432	0.603	SUBCLONAL	1	FALSE	0	0.265613650321504	1		207	598	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234522	41234522	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006001-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	75	472	0	ENST00000357654.3:c.4256A>G	p.Glu1419Gly	p.E1419G	ENST00000357654	NM_007294.3	1419	gAa/gGa	12/23	0.726420674096283	2	FACETS	0.274	0.24	0.311	0.137	0.12	0.156	SUBCLONAL	1	TRUE	0	0.726420674096283	2		472	753	SUCCESS
EED	8726	MSKCC	GRCh37	11	85987679	85988037	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTGTAATTGACCTGTGCTATAAAACACTTAAAGTCTCTGGGTGTCAGAGTATCTAGAGCTGAACTTGGTTTAACTTGAAAGAGAAATGTTGACTTCCAAAATGAATATTTCAGACAATGTGATTCTTTTGTATTATCGAATTCTGTTGATAATCAGATTTCTTGTCCTTAAGTATGGTCATTGACTGTAAATATAAATGAATGTACATCACTGTACTTGATAGATGGATTAACCAGGTTCTAAGAGCTGTGAATTCCAAAACAATAGAAAAGCCTTGTTTTTACTTTGTAAGATTCAGTTCCTCATTAACATTTCTTTTTCTCATTTCTCTCTCTGTTTTAGTCTTGTGAAAATGCCA	TTTGTAATTGACCTGTGCTATAAAACACTTAAAGTCTCTGGGTGTCAGAGTATCTAGAGCTGAACTTGGTTTAACTTGAAAGAGAAATGTTGACTTCCAAAATGAATATTTCAGACAATGTGATTCTTTTGTATTATCGAATTCTGTTGATAATCAGATTTCTTGTCCTTAAGTATGGTCATTGACTGTAAATATAAATGAATGTACATCACTGTACTTGATAGATGGATTAACCAGGTTCTAAGAGCTGTGAATTCCAAAACAATAGAAAAGCCTTGTTTTTACTTTGTAAGATTCAGTTCCTCATTAACATTTCTTTTTCTCATTTCTCTCTCTGTTTTAGTCTTGTGAAAATGCCA	-	novel	NA	P-0006001-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1	159	1	0	ENST00000263360.6:c.967-341_984del		p.X323_splice	ENST00000263360	NM_003797.3	323		10/12	0.638241125818179	1	FACETS		NA	1	1	0.995	1	NA	2	TRUE	0	0.726420674096283	1		1	160	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	1318	484	0	ENST00000269305.4:c.880del	p.Glu294SerfsTer51	p.E294Sfs*51	ENST00000269305	NM_001126112.2	294	Gag/ag	8/11	0.843095006567314	1	FACETS	0.996	0.979	1	0.996	0.979	1	CLONAL	1	TRUE	0	0.843095006567314	1		484	1815	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435871	49435871	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0006025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1783	1256	554	2	ENST00000301067.7:c.6109+1G>A		p.X2037_splice	ENST00000301067	NM_003482.3	2037			1	2	FACETS	0.98	0.955	1	0.98	0.955	1	CLONAL	1	TRUE	1	0.843095006567314	2		556	3039	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50490680	50490680	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2044	1481	497	0	ENST00000394963.4:c.1317G>C	p.Glu439Asp	p.E439D	ENST00000394963	NM_003076.4	439	gaG/gaC	11/13	1	2	FACETS	0.997	0.973	1	0.997	0.973	1	CLONAL	1	TRUE	1	0.843095006567314	2		497	3525	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916747	48916747	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690915	NA	P-0006025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	1016	341	0	ENST00000267163.4:c.277C>T	p.Gln93Ter	p.Q93*	ENST00000267163	NM_000321.2	93	Caa/Taa	3/27	0.843095006567314	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.843095006567314	1		341	1385	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576158	88576158	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2140	822	466	1	ENST00000360948.2:c.1515G>T	p.Met505Ile	p.M505I	ENST00000360948	NM_001012338.2	505	atG/atT	13/19	1	2	FACETS	0.658	0.635	0.682	0.658	0.635	0.682	SUBCLONAL	1	TRUE	1	0.843095006567314	2		467	2962	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023360	31023360	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1859	856	388	1	ENST00000375687.4:c.2845G>C	p.Gly949Arg	p.G949R	ENST00000375687	NM_015338.5	949	Ggt/Cgt	13/13	1	2	FACETS	0.748	0.723	0.773	0.748	0.723	0.773	SUBCLONAL	1	TRUE	1	0.843095006567314	2		389	2715	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937764	76937764	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2806	290	538	0	ENST00000373344.5:c.2984C>T	p.Pro995Leu	p.P995L	ENST00000373344	NM_000489.3	995	cCt/cTt	9/35	0.233051452774386	1	FACETS	0.129	0.12	0.138	0.129	0.12	0.138	INDETERMINATE	1	TRUE	0	0.843095006567314	1		538	3096	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577061	7577064	+	frameshift_variant	Frame_Shift_Del	DEL	CTTT	CTTT	-	novel	NA	P-0006030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	63	447	0	ENST00000269305.4:c.874_877del	p.Lys292GlyfsTer52	p.K292Gfs*52	ENST00000269305	NM_001126112.2	292	AAAGgg/gg	8/11	0.181580040134225	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.236270660775286	1		447	427	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156719	20156719	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	112	291	0	ENST00000379607.5:c.38G>C	p.Arg13Pro	p.R13P	ENST00000379607	NM_001412.3	13	cGc/cCc	2/7	0.730776971184506	1	FACETS	0.973	0.9	1	0.973	0.9	1	CLONAL	1	TRUE	0	0.730776971184506	1		291	200	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799553	72799553	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs764319736	NA	P-0006053-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	28	470	0	ENST00000325599.8:c.1616T>C	p.Ile539Thr	p.I539T	ENST00000325599	NM_018130.2	539	aTa/aCa	11/11	1	2	FACETS	0.843	0.689	1	0.843	0.689	1	CLONAL	1	TRUE	1	0.632696341261883	2		470	105	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871250	35871250	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006053-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	75	559	2	ENST00000216797.5:c.923G>C	p.Cys308Ser	p.C308S	ENST00000216797	NM_020529.2	308	tGt/tCt	6/6	0.632696341261883	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.632696341261883	1		561	154	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348620	89348620	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006053-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	134	862	0	ENST00000301030.4:c.4330G>T	p.Glu1444Ter	p.E1444*	ENST00000301030	NM_001256183.1	1444	Gaa/Taa	9/13	0.632696341261883	3	FACETS	1	0.958	1	0.539	0.492	0.588	CLONAL	1	TRUE	1	0.632696341261883	3		862	517	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475359	40475359	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006053-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	123	555	0	ENST00000264657.5:c.1667G>C	p.Gly556Ala	p.G556A	ENST00000264657	NM_139276.2	556	gGc/gCc	19/24	0.359291978727596	5	FACETS	1	0.978	1	0.802	0.736	0.869	INDETERMINATE	2	TRUE	2	0.632696341261883	5		555	315	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321310	1321310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006053-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	35	381	0	ENST00000400841.2:c.445G>A	p.Glu149Lys	p.E149K	ENST00000400841		149	Gag/Aag	4/6	1	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.632696341261883	1		381	68	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0006057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	31	419	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		419	909	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579350	7579350	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587781642	NA	P-0006057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	88	492	0	ENST00000269305.4:c.337T>G	p.Phe113Val	p.F113V	ENST00000269305	NM_001126112.2	113	Ttc/Gtc	4/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		492	925	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690847	89690847	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776667	NA	P-0006058-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	164	323	0	ENST00000371953.3:c.253+1G>A		p.X85_splice	ENST00000371953	NM_000314.4	85			NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.470880508555499	2		323	514	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294156	1294156	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006058-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	93	508	2	ENST00000310581.5:c.845C>T	p.Ala282Val	p.A282V	ENST00000310581	NM_198253.2	282	gCc/gTc	2/16	0.276582174253764	1	FACETS	0.733	0.656	0.814	0.733	0.656	0.814	INDETERMINATE	1	TRUE	0	0.470880508555499	1		510	412	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974785	21974785	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006058-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	43	209	0	ENST00000304494.5:c.42C>G	p.Asp14Glu	p.D14E	ENST00000304494	NM_000077.4	14	gaC/gaG	1/3	1	2	FACETS	0.798	0.673	0.932	0.798	0.673	0.932	CLONAL	1	TRUE	1	0.470880508555499	2		209	229	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0006063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	15019	286	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.45981851698612	54	FACETS	1	0.999	1			1	CLONAL	55	TRUE	NA	0.45981851698612	54		287	15269	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551245	29551245	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	423	706	2	ENST00000389048.3:c.1385C>A	p.Ala462Asp	p.A462D	ENST00000389048	NM_004304.4	462	gCc/gAc	6/29	0.454283026029056	4	FACETS	0.985	0.938	1	0.492	0.469	0.516	CLONAL	2	TRUE	0	0.45981851698612	4		708	1364	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467847	50467847	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	302	493	0	ENST00000331340.3:c.1082C>A	p.Ser361Tyr	p.S361Y	ENST00000331340	NM_006060.4	361	tCc/tAc	8/8	0.45981851698612	3	FACETS	0.829	0.783	0.877	0.553	0.522	0.585	CLONAL	2	TRUE	0	0.45981851698612	3		493	974	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291008	15291008	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs974250630	NA	P-0006063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1171	282	903	1	ENST00000263388.2:c.3202C>T	p.His1068Tyr	p.H1068Y	ENST00000263388	NM_000435.2	1068	Cac/Tac	20/33	0.455970047916363	3	FACETS	1	0.963	1	0.346	0.324	0.369	CLONAL	1	TRUE	0	0.45981851698612	3		904	1453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	rs879253905	NA	P-0006063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	945	762	0	ENST00000269305.4:c.785del	p.Gly262ValfsTer83	p.G262Vfs*83	ENST00000269305	NM_001126112.2	262	gGt/gt	8/11	0.454283026029056	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	4	TRUE	0	0.45981851698612	4		762	1465	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	145	316	0	ENST00000397752.3:c.3028G>C	p.Asp1010His	p.D1010H	ENST00000397752	NM_000245.2	1010	Gat/Cat	14/21	0.203689630525828	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	TRUE	1	0.203689630525828	4		316	495	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755587	57755587	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	113	492	0	ENST00000274289.3:c.200C>G	p.Pro67Arg	p.P67R	ENST00000274289	NM_006622.3	67	cCg/cGg	1/14	0.161616962387153	3	FACETS	0.991	0.894	1	0.991	0.894	1	CLONAL	2	TRUE	1	0.203689630525828	3		492	617	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0006073-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	121	286	1	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	0.18	2		287	925	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006073-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	44	291	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.53	0.442	0.627	0.53	0.442	0.627	SUBCLONAL	1	TRUE	1	0.18	2		291	923	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0006073-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	32	404	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.317	0.256	0.387	0.317	0.256	0.387	SUBCLONAL	1	TRUE	1	0.18	2		405	1121	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641430	47641430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs34136999	NA	P-0006091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1465	433	815	3	ENST00000233146.2:c.815C>T	p.Ala272Val	p.A272V	ENST00000233146	NM_000251.2	272	gCg/gTg	5/16	0.635188414810478	3	FACETS	0.946	0.899	0.995	0.473	0.449	0.498	CLONAL	1	TRUE	1	0.635188414810478	3		818	1898	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61725909	61725909	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	233	535	0	ENST00000401558.2:c.658C>G	p.Pro220Ala	p.P220A	ENST00000401558	NM_003400.3	220	Cca/Gca	9/25	0.635188414810478	3	FACETS	0.852	0.794	0.913	0.426	0.397	0.457	CLONAL	1	TRUE	1	0.635188414810478	3		535	1134	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081641	143081641	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	587	578	0	ENST00000262992.4:c.1433C>A	p.Pro478Gln	p.P478Q	ENST00000262992	NM_001101669.1	478	cCa/cAa	15/24	0.635188414810478	2	FACETS	0.985	0.955	1	0.985	0.955	1	CLONAL	2	TRUE	0	0.635188414810478	2		578	938	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446187	49446187	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	308	300	0	ENST00000301067.7:c.1279G>C	p.Glu427Gln	p.E427Q	ENST00000301067	NM_003482.3	427	Gag/Cag	10/54	0.635188414810478	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.635188414810478	2		300	452	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431338	121431338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	41	463	0	ENST00000257555.6:c.542G>A	p.Gly181Glu	p.G181E	ENST00000257555		181	gGg/gAg	3/10	0.635188414810478	2	FACETS	0.167	0.138	0.199	0.083	0.069	0.1	SUBCLONAL	1	TRUE	0	0.635188414810478	2		463	775	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514815	103514815	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	457	489	0	ENST00000355739.4:c.1316G>C	p.Gly439Ala	p.G439A	ENST00000355739	NM_000123.3	439	gGa/gCa	8/15	0.635188414810478	2	FACETS	0.924	0.89	0.957	0.924	0.89	0.957	CLONAL	2	TRUE	0	0.635188414810478	2		489	779	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76954064	76954064	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	408	784	0	ENST00000373344.5:c.187G>T	p.Glu63Ter	p.E63*	ENST00000373344	NM_000489.3	63	Gag/Tag	3/35	1	2	FACETS	0.976	0.929	1	0.976	0.929	1	CLONAL	1	TRUE	1	0.635188414810478	2		784	1316	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522166	157522174	+	inframe_deletion	In_Frame_Del	DEL	GGCCCTGGC	GGCCCTGGC	-	novel	NA	P-0006091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1238	441	470	0	ENST00000346085.5:c.4444_4452del	p.Gly1482_Pro1484del	p.G1482_P1484del	ENST00000346085	NM_020732.3	1480	GGCCCTGGC/-	18/20	0.595049552513288	4	FACETS	1	0.995	1	0.676	0.643	0.71	CLONAL	1	TRUE	2	0.635188414810478	4		470	1679	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578470	7578482	+	frameshift_variant	Frame_Shift_Del	DEL	CGGGCGGGGGTGT	CGGGCGGGGGTGT	-	rs1064792930	NA	P-0006091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	690	607	0	ENST00000269305.4:c.448_460del	p.Thr150AlafsTer16	p.T150Afs*16	ENST00000269305	NM_001126112.2	150	ACACCCCCGCCCGgc/gc	5/11	0.635188414810478	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.635188414810478	2		607	1039	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578466	7578466	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786202752	NA	P-0006102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	371	630	0	ENST00000269305.4:c.464C>A	p.Thr155Asn	p.T155N	ENST00000269305	NM_001126112.2	155	aCc/aAc	5/11	0.784721321686133	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.784721321686133	1		630	563	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424401	49424401	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1239520880	NA	P-0006102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	267	642	0	ENST00000301067.7:c.13822T>A	p.Ser4608Thr	p.S4608T	ENST00000301067	NM_003482.3	4608	Tcc/Acc	41/54	1	2	FACETS	0.856	0.806	0.907	0.856	0.806	0.907	CLONAL	1	TRUE	1	0.784721321686133	2		642	795	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	63	484	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.759	0.656	0.871	0.759	0.656	0.871	SUBCLONAL	1	TRUE	1	0.250917911860088	2		484	662	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0006106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	65	525	1	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.250917911860088	1	FACETS	0.688	0.596	0.787	0.688	0.596	0.787	SUBCLONAL	1	TRUE	0	0.250917911860088	1		526	659	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971107	21971107	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	71	242	0	ENST00000304494.5:c.251A>T	p.Asp84Val	p.D84V	ENST00000304494	NM_000077.4	84	gAc/gTc	2/3	0.187373573118011	2	FACETS	0.751	0.659	0.849	0.751	0.659	0.849	SUBCLONAL	2	TRUE	0	0.250917911860088	2		242	377	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	200	484	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.265680435074094	4	FACETS	1	0.982	1	0.781	0.725	0.838	CLONAL	2	TRUE	1	0.273197579662878	4		484	796	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0006125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	156	661	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.189883909109579	3	FACETS	0.964	0.886	1	0.643	0.59	0.698	CLONAL	2	TRUE	0	0.273197579662878	3		663	673	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096394	178096394	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	44	510	0	ENST00000397062.3:c.937C>G	p.Leu313Val	p.L313V	ENST00000397062	NM_006164.4	313	Cta/Gta	5/5	0.273197579662878	5	FACETS	0.566	0.473	0.67			1	SUBCLONAL	1	TRUE	NA	0.273197579662878	5		510	802	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268780	98268780	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	55	660	0	ENST00000331920.6:c.303C>G	p.Phe101Leu	p.F101L	ENST00000331920	NM_000264.3	101	ttC/ttG	2/24	0.186697080065337	3	FACETS	0.452	0.385	0.525	0.151	0.128	0.175	SUBCLONAL	1	TRUE	0	0.273197579662878	3		660	1013	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165758	108165758	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	61	643	0	ENST00000278616.4:c.4881G>C	p.Gln1627His	p.Q1627H	ENST00000278616	NM_000051.3	1627	caG/caC	32/63	0.273517250024385	4	FACETS	0.808	0.696	0.93	0.269	0.232	0.31	CLONAL	1	TRUE	1	0.273197579662878	4		643	704	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0006134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	141	328	2	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.235358966240522	1	FACETS	0.86	0.783	0.942	0.86	0.783	0.942	CLONAL	1	FALSE	0	0.288793887761441	1		330	971	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449926	29449926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568177600	NA	P-0006134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	85	352	0	ENST00000389048.3:c.2929G>A	p.Gly977Arg	p.G977R	ENST00000389048	NM_004304.4	977	Ggg/Agg	18/29	1	2	FACETS	0.496	0.436	0.559	0.496	0.436	0.559	SUBCLONAL	1	FALSE	1	0.288793887761441	2		352	1188	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144062	55144062	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0006134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	125	351	0	ENST00000257290.5:c.1892-1G>T		p.X631_splice	ENST00000257290	NM_006206.4	631			0.113975061588376	0	FACETS	0.586	0.53	0.646			1	INDETERMINATE	1	FALSE	0	0.288793887761441	0		351	1050	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069025	5069025	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	53	228	0	ENST00000381652.3:c.1330G>T	p.Glu444Ter	p.E444*	ENST00000381652	NM_004972.3	444	Gaa/Taa	11/25	0.243331324525022	0	FACETS	0.355	0.302	0.413			1	SUBCLONAL	1	FALSE	0	0.288793887761441	0		228	736	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858056	45858056	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	608	449	1	ENST00000391945.4:c.1597G>A	p.Asp533Asn	p.D533N	ENST00000391945	NM_000400.3	533	Gat/Aat	17/23	0.274246715976455	4	FACETS	1	0.982	1			1	CLONAL	3	FALSE	NA	0.288793887761441	4		450	1747	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15808637	15808637	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006134-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	60	183	0	ENST00000307771.7:c.19A>G	p.Met7Val	p.M7V	ENST00000307771	NM_005089.3	7	Atg/Gtg	1/11	1	1	FACETS	0.594	0.511	0.683	0.594	0.511	0.683	SUBCLONAL	1	FALSE	0	0.288793887761441	1		183	599	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0006138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	193	749	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.234461992235784	2		750	1211	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0006138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	86	499	2	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.746	0.659	0.841	0.746	0.659	0.841	SUBCLONAL	1	TRUE	1	0.234461992235784	2		501	983	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275492	38275492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	110	370	0	ENST00000425967.3:c.1541C>T	p.Pro514Leu	p.P514L	ENST00000425967	NM_001174067.1	514	cCc/cTc	12/19	0.234461992235784	1	FACETS	0.977	0.877	1	0.977	0.877	1	CLONAL	1	TRUE	0	0.234461992235784	1		370	848	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465638	8465638	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	74	436	0	ENST00000356435.5:c.3542G>T	p.Arg1181Leu	p.R1181L	ENST00000356435		1181	cGt/cTt	21/35	0.189739358509724	1	FACETS	0.615	0.537	0.699	0.615	0.537	0.699	SUBCLONAL	1	TRUE	0	0.234461992235784	1		436	906	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	156	484	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.433622863430019	3	FACETS	1	0.959	1	0.537	0.492	0.584	CLONAL	1	TRUE	1	0.433622863430019	3		484	815	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057520007	NA	P-0006144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	97	542	1	ENST00000269305.4:c.614A>T	p.Tyr205Phe	p.Y205F	ENST00000269305	NM_001126112.2	205	tAt/tTt	6/11	1	2	FACETS	0.395	0.351	0.442	0.395	0.351	0.442	SUBCLONAL	1	TRUE	1	0.433622863430019	2		543	1133	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391151	89391151	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	35	382	0	ENST00000336596.2:c.1217C>G	p.Thr406Ser	p.T406S	ENST00000336596	NM_005233.5	406	aCc/aGc	5/17	1	2	FACETS	0.248	0.203	0.3	0.248	0.203	0.3	SUBCLONAL	1	TRUE	1	0.433622863430019	2		382	650	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971032	21971040	+	inframe_deletion	In_Frame_Del	DEL	GCATCGCGC	GCATCGCGC	-	novel	NA	P-0006144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	42	292	0	ENST00000304494.5:c.318_326del	p.Arg107_Ala109del	p.R107_A109del	ENST00000304494	NM_000077.4	106	gtGCGCGATGCc/gtc	2/3	0.229156347170983	1	FACETS	0.317	0.264	0.375	0.317	0.264	0.375	INDETERMINATE	1	TRUE	0	0.433622863430019	1		292	479	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0006154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	121	207	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.39598067977993	2		207	582	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436414	52436414	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	107	397	1	ENST00000460680.1:c.2080C>T	p.Gln694Ter	p.Q694*	ENST00000460680	NM_004656.3	694	Cag/Tag	17/17	0.393721933887107	1	FACETS	0.829	0.746	0.915	0.829	0.746	0.915	CLONAL	1	TRUE	0	0.39598067977993	1		398	523	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983017	149983017	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757876116	NA	P-0006154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	208	546	0	ENST00000253339.5:c.3241C>T	p.Arg1081Ter	p.R1081*	ENST00000253339		1081	Cga/Tga	7/7	0.387217398700312	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.39598067977993	1		546	842	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549161	21549161	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	256	723	1	ENST00000382592.4:c.3115G>T	p.Glu1039Ter	p.E1039*	ENST00000382592	NM_014572.2	1039	Gaa/Taa	8/8	0.395541819776	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.39598067977993	1		724	1014	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0006161-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	59	368	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.674	0.579	0.778	0.674	0.579	0.778	SUBCLONAL	1	TRUE	1	0.241974124027679	2		368	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0006161-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	114	589	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	NA	2	FACETS	0.713	0.64	0.791			1	INDETERMINATE	1	TRUE	NA	0.241974124027679	2		589	1321	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610715	52610715	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0006161-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	46	335	0	ENST00000394830.3:c.3459-1G>A		p.X1153_splice	ENST00000394830	NM_018313.4	1153			1	2	FACETS	0.557	0.468	0.656	0.557	0.468	0.656	SUBCLONAL	1	TRUE	1	0.241974124027679	2		335	682	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406628	70406628	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006161-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1246	100	550	0	ENST00000373644.4:c.4142G>C	p.Gly1381Ala	p.G1381A	ENST00000373644	NM_030625.2	1381	gGa/gCa	4/12	0.155536641763817	3	FACETS	0.688	0.613	0.77	0.344	0.306	0.385	SUBCLONAL	1	TRUE	1	0.241974124027679	3		550	1346	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434857	110434857	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006161-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	86	425	0	ENST00000375856.3:c.3544C>G	p.Leu1182Val	p.L1182V	ENST00000375856	NM_003749.2	1182	Ctc/Gtc	1/2	0.234156976853257	1	FACETS	0.679	0.6	0.765	0.679	0.6	0.765	SUBCLONAL	1	TRUE	0	0.241974124027679	1		425	920	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436963	110436963	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006161-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	11	46	0	ENST00000375856.3:c.1438C>G	p.Arg480Gly	p.R480G	ENST00000375856	NM_003749.2	480	Cgg/Ggg	1/2	0.234156976853257	1	FACETS	1	0.709	1	1	0.709	1	CLONAL	1	TRUE	0	0.241974124027679	1		46	79	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964909	15964909	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006161-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	121	566	0	ENST00000268712.3:c.5687C>G	p.Ser1896Cys	p.S1896C	ENST00000268712	NM_006311.3	1896	tCt/tGt	37/46	0.241974124027679	1	FACETS	0.79	0.712	0.873	0.79	0.712	0.873	SUBCLONAL	1	TRUE	0	0.241974124027679	1		566	1113	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0006171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1962	138	420	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.549375496260566	5	FACETS	0.436	0.395	0.48	0.109	0.098	0.12	SUBCLONAL	1	TRUE	1	0.549375496260566	5		420	2100	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0006171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	983	519	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	0.549375496260566	5	FACETS	0.882	0.859	0.905	0.882	0.859	0.905	CLONAL	4	TRUE	1	0.549375496260566	5		519	1850	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0006172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	127	286	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.25559736922712	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.25559736922712	1		287	649	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430425	181430425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1313	145	550	0	ENST00000325404.1:c.277G>A	p.Glu93Lys	p.E93K	ENST00000325404	NM_003106.3	93	Gag/Aag	1/1	0.175430976416856	1	FACETS	0.679	0.617	0.744	0.679	0.617	0.744	SUBCLONAL	1	TRUE	0	0.25559736922712	1		550	1458	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220494	1220494	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519858	NA	P-0006172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	143	432	2	ENST00000326873.7:c.587G>T	p.Gly196Val	p.G196V	ENST00000326873	NM_000455.4	196	gGc/gTc	4/10	0.25559736922712	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.25559736922712	1		434	956	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630162	187630162	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	145	294	1	ENST00000441802.2:c.820G>T	p.Ala274Ser	p.A274S	ENST00000441802	NM_005245.3	274	Gca/Tca	2/27	0.25559736922712	1	FACETS	0.788	0.721	0.857	1	0.988	1	SUBCLONAL	2	TRUE	0	0.25559736922712	1		295	628	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212842	94212842	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	60	328	0	ENST00000323929.3:c.400G>T	p.Gly134Trp	p.G134W	ENST00000323929	NM_005591.3	134	Ggg/Tgg	5/20	0.175430976416856	1	FACETS	0.559	0.48	0.644	0.559	0.48	0.644	SUBCLONAL	1	TRUE	0	0.25559736922712	1		328	733	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602320	10602320	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1482163272	NA	P-0006172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	237	460	2	ENST00000171111.5:c.1258del	p.Val420SerfsTer38	p.V420Sfs*38	ENST00000171111	NM_203500.1	420	Gtc/tc	3/6	0.25559736922712	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.25559736922712	1		462	1229	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	15	246	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.752	0.551	0.993	0.752	0.551	0.993	CLONAL	1	TRUE	1	0.19	2		246	210	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0006178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	53	261	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	0.19	2		261	532	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106414	27106414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	33	470	0	ENST00000324856.7:c.6025C>T	p.Leu2009Phe	p.L2009F	ENST00000324856	NM_006015.4	2009	Ctc/Ttc	20/20	1	2	FACETS	0.934	0.761	1	0.934	0.761	1	CLONAL	1	TRUE	1	0.19	2		470	372	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999792	100999792	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	78	736	0	ENST00000325455.5:c.10C>G	p.Leu4Val	p.L4V	ENST00000325455	NM_001202474.3	4	Ctg/Gtg	1/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.19	2		736	593	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216725	2216725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200144638	NA	P-0006178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	33	428	1	ENST00000398665.3:c.2369C>T	p.Thr790Met	p.T790M	ENST00000398665	NM_032482.2	790	aCg/aTg	20/28	1	2	FACETS	0.902	0.735	1	0.902	0.735	1	CLONAL	1	TRUE	1	0.19	2		429	385	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0006191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	82	286	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.788	0.695	0.889	0.788	0.695	0.889	SUBCLONAL	1	TRUE	1	0.288481607322699	2		287	721	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782318	9782318	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	113	474	0	ENST00000377346.4:c.2251T>A	p.Phe751Ile	p.F751I	ENST00000377346	NM_005026.3	751	Ttc/Atc	18/24	1	2	FACETS	0.868	0.78	0.961	0.868	0.78	0.961	CLONAL	1	TRUE	1	0.288481607322699	2		474	903	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444447	50444447	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	58	201	0	ENST00000331340.3:c.377G>T	p.Cys126Phe	p.C126F	ENST00000331340	NM_006060.4	126	tGc/tTc	4/8	1	2	FACETS	0.951	0.819	1	0.951	0.819	1	CLONAL	1	TRUE	1	0.288481607322699	2		201	423	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108259	8108259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006200-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1344	163	639	1	ENST00000585124.1:c.965C>T	p.Ser322Leu	p.S322L	ENST00000585124	NM_004217.3	322	tCa/tTa	9/9	0.102335611337849	3	FACETS	1	0.987	1	0.721	0.659	0.786	CLONAL	1	FALSE	1	0.16226257664425	3		640	1507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578433	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006206-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	257	474	0	ENST00000269305.4:c.497C>A	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	166	tCa/tAa	5/11	0.566658312400896	1	FACETS	0.991	0.934	1	0.991	0.934	1	CLONAL	1	TRUE	0	0.566658312400896	1		474	656	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256687	16256740	+	inframe_deletion	In_Frame_Del	DEL	GAACAGATGGCAGATATGGCCAAAATAAAACTATCTGTCTTGAATTCTGAAGAT	GAACAGATGGCAGATATGGCCAAAATAAAACTATCTGTCTTGAATTCTGAAGAT	-	novel	NA	P-0006206-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	175	324	0	ENST00000375759.3:c.3956_4009del	p.Gln1319_Glu1336del	p.Q1319_E1336del	ENST00000375759	NM_015001.2	1318	GAACAGATGGCAGATATGGCCAAAATAAAACTATCTGTCTTGAATTCTGAAGAT/-	11/15	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.566658312400896	2		324	594	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591104	67591115	+	inframe_deletion	In_Frame_Del	DEL	TTAAACCAGACC	TTAAACCAGACC	-	novel	NA	P-0121560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	267	437	0	ENST00000274335.5:c.1700_1711del	p.Lys567_Leu570del	p.K567_L570del	ENST00000274335		566	aTTAAACCAGACCtt/att	12/15	0.490421025600257	4	FACETS	0.858	0.809	0.908			1	CLONAL	2	NA	NA	0.77456594612373	4		437	713	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445273	29445273	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs113994091	NA	P-0121560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	74	459	0	ENST00000389048.3:c.3452C>T	p.Thr1151Met	p.T1151M	ENST00000389048	NM_004304.4	1151	aCg/aTg	22/29	0.77456594612373	3	FACETS	0.592	0.52	0.669	0.296	0.26	0.335	SUBCLONAL	1	NA	1	0.77456594612373	3		459	448	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540703	187540703	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	259	650	0	ENST00000441802.2:c.7037G>T	p.Arg2346Ile	p.R2346I	ENST00000441802	NM_005245.3	2346	aGa/aTa	10/27	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	NA	1	0.77456594612373	2		650	615	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495478	56495478	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0121560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	106	645	0	ENST00000267101.3:c.3668A>C	p.Glu1223Ala	p.E1223A	ENST00000267101	NM_001982.3	1223	gAg/gCg	28/28	0.77456594612373	3	FACETS	0.417	0.373	0.464	0.209	0.186	0.232	SUBCLONAL	1	NA	1	0.77456594612373	3		645	910	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2185891	2185891	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0121560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	79	696	0	ENST00000398665.3:c.163A>G	p.Met55Val	p.M55V	ENST00000398665	NM_032482.2	55	Atg/Gtg	3/28	1	2	FACETS	0.255	0.224	0.289	0.255	0.224	0.289	SUBCLONAL	1	NA	1	0.77456594612373	2		696	800	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0006227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	674	368	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.355151413822337	11	FACETS	0.98	0.951	1			1	CLONAL	9	TRUE	NA	0.355151413822337	11		368	1118	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0006227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	60	352	1	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.355151413822337	1	FACETS	0.605	0.523	0.695	0.605	0.523	0.695	SUBCLONAL	1	TRUE	0	0.355151413822337	1		353	459	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0006227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	68	562	1	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	1	2	FACETS	0.669	0.583	0.763	0.669	0.583	0.763	SUBCLONAL	1	TRUE	1	0.355151413822337	2		563	572	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862208	68862208	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0006227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	33	396	0	ENST00000261769.5:c.2295+1G>A		p.X765_splice	ENST00000261769	NM_004360.3	765			0.355151413822337	1	FACETS	0.503	0.41	0.606	0.503	0.41	0.606	SUBCLONAL	1	TRUE	0	0.355151413822337	1		396	304	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122676	108122676	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	23	503	1	ENST00000278616.4:c.1720G>A	p.Glu574Lys	p.E574K	ENST00000278616	NM_000051.3	574	Gaa/Aaa	11/63	1	2	FACETS	0.453	0.353	0.568	0.453	0.353	0.568	SUBCLONAL	1	TRUE	1	0.355151413822337	2		504	286	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15836709	15836709	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0006227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	74	874	0	ENST00000307771.7:c.772-1G>C		p.X258_splice	ENST00000307771	NM_005089.3	258			0.355151413822337	1	FACETS	0.763	0.671	0.862	0.763	0.671	0.862	SUBCLONAL	1	TRUE	0	0.355151413822337	1		874	449	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112100	115112101	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	C	novel	NA	P-0006227-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	157	698	0	ENST00000257566.3:c.1639_1640delinsG	p.Ser547ValfsTer85	p.S547Vfs*85	ENST00000257566	NM_016569.3	547	TCt/Gt	7/8	1	2	FACETS	0.811	0.742	0.884	0.811	0.742	0.884	CLONAL	1	TRUE	1	0.355151413822337	2		698	1090	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030577	48030577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369042519	NA	P-0006235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	91	372	0	ENST00000234420.5:c.3191C>T	p.Ala1064Val	p.A1064V	ENST00000234420	NM_000179.2	1064	gCt/gTt	5/10	0.166614307018196	4	FACETS	1	0.967	1	0.613	0.545	0.684	INDETERMINATE	1	TRUE	2	0.39879558959016	4		372	521	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436887	52436887	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	50	296	1	ENST00000460680.1:c.1891G>T	p.Glu631Ter	p.E631*	ENST00000460680	NM_004656.3	631	Gag/Tag	15/17	0.385942255111156	1	FACETS	0.951	0.817	1	0.951	0.817	1	CLONAL	1	TRUE	0	0.39879558959016	1		297	211	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022465	12022465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	775	658	0	ENST00000396373.4:c.571C>T	p.Arg191Trp	p.R191W	ENST00000396373	NM_001987.4	191	Cgg/Tgg	5/8	0.188715818554523	4	FACETS	0.961	0.931	0.992	1	0.998	1	CLONAL	5	TRUE	2	0.238569044229145	4		658	1674	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191546	10191546	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	29	657	2	ENST00000256474.2:c.539T>A	p.Ile180Asn	p.I180N	ENST00000256474	NM_000551.3	180	aTc/aAc	3/3	1	2	FACETS	1	0.821	1	1	0.821	1	CLONAL	1	TRUE	1	0.13	2		659	435	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162336	47162336	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	18	440	0	ENST00000409792.3:c.3790C>T	p.Gln1264Ter	p.Q1264*	ENST00000409792	NM_014159.6	1264	Caa/Taa	3/21	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.13	2		440	222	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668799	52668799	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	26	509	0	ENST00000394830.3:c.1120G>T	p.Glu374Ter	p.E374*	ENST00000394830	NM_018313.4	374	Gaa/Taa	12/30	1	2	FACETS	1	0.827	1	1	0.827	1	CLONAL	1	TRUE	1	0.13	2		509	381	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275758	38275758	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	35	670	0	ENST00000425967.3:c.1511T>A	p.Leu504Gln	p.L504Q	ENST00000425967	NM_001174067.1	504	cTg/cAg	11/19	1	2	FACETS	0.907	0.741	1	0.907	0.741	1	CLONAL	1	TRUE	1	0.13	2		670	594	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28903860	28903860	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	21	461	0	ENST00000282397.4:c.2599G>A	p.Ala867Thr	p.A867T	ENST00000282397	NM_002019.4	867	Gcc/Acc	19/30	1	2	FACETS	0.777	0.597	0.987	0.777	0.597	0.987	CLONAL	1	TRUE	1	0.13	2		461	416	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942542	17942542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375807308	NA	P-0006252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	34	584	0	ENST00000458235.1:c.2746C>T	p.Arg916Trp	p.R916W	ENST00000458235	NM_000215.3	916	Cgg/Tgg	20/24	1	2	FACETS	0.978	0.798	1	0.978	0.798	1	CLONAL	1	TRUE	1	0.13	2		584	535	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	288	246	0				ENST00000310581	NM_198253.2	-/1132			0.483770219366529	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.523461919702841	3		246	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0006253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	139	775	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.478824560452426	1	FACETS	0.778	0.713	0.846	0.778	0.713	0.846	SUBCLONAL	1	TRUE	0	0.523461919702841	1		775	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577077	7577077	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs748891343	NA	P-0006253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	138	756	0	ENST00000269305.4:c.861G>C	p.Glu287Asp	p.E287D	ENST00000269305	NM_001126112.2	287	gaG/gaC	8/11	0.478824560452426	1	FACETS	0.808	0.74	0.878	0.808	0.74	0.878	CLONAL	1	TRUE	0	0.523461919702841	1		756	482	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652020	36652020	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1407742055	NA	P-0006253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	205	574	1	ENST00000244741.5:c.142C>T	p.Arg48Ter	p.R48*	ENST00000244741	NM_000389.4	48	Cga/Tga	2/3	0.216922464215054	3	FACETS	0.912	0.853	0.972	0.912	0.853	0.972	INDETERMINATE	2	TRUE	1	0.523461919702841	3		575	542	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949758	151949758	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	101	716	1	ENST00000262189.6:c.1342C>T	p.Gln448Ter	p.Q448*	ENST00000262189	NM_170606.2	448	Cag/Tag	10/59	1	2	FACETS	0.9	0.809	0.994	0.9	0.809	0.994	CLONAL	1	TRUE	1	0.523461919702841	2		717	429	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174452	11174452	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs931743029	NA	P-0006253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	154	778	2	ENST00000361445.4:c.7223G>A	p.Arg2408Gln	p.R2408Q	ENST00000361445	NM_004958.3	2408	cGa/cAa	53/58	0.295540416276405	1	FACETS	0.759	0.698	0.823	0.759	0.698	0.823	INDETERMINATE	1	TRUE	0	0.523461919702841	1		780	572	SUCCESS
APC	324	MSKCC	GRCh37	5	112175147	112175147	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	36	383	0	ENST00000257430.4:c.3856G>C	p.Glu1286Gln	p.E1286Q	ENST00000257430	NM_000038.5	1286	Gaa/Caa	16/16	0.507585542220446	1	FACETS	0.747	0.625	0.877	0.747	0.625	0.877	SUBCLONAL	1	TRUE	0	0.523461919702841	1		383	136	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203493	108203493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140263969	NA	P-0006253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	61	568	0	ENST00000278616.4:c.7793G>A	p.Arg2598Gln	p.R2598Q	ENST00000278616	NM_000051.3	2598	cGa/cAa	53/63	1	2	FACETS	0.683	0.593	0.781	0.683	0.593	0.781	SUBCLONAL	1	TRUE	1	0.523461919702841	2		568	341	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549137	21549137	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	154	830	0	ENST00000382592.4:c.3139G>C	p.Asp1047His	p.D1047H	ENST00000382592	NM_014572.2	1047	Gat/Cat	8/8	NA	2	FACETS	0.946	0.869	1			1	INDETERMINATE	1	TRUE	NA	0.523461919702841	2		830	622	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039501	49039501	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0006253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	92	664	0	ENST00000267163.4:c.2486C>G	p.Ser829Ter	p.S829*	ENST00000267163	NM_000321.2	829	tCa/tGa	23/27	0.507585542220446	1	FACETS	0.707	0.633	0.784	0.707	0.633	0.784	SUBCLONAL	1	TRUE	0	0.523461919702841	1		664	367	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2137898	2137898	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	133	721	0	ENST00000219476.3:c.5024C>G	p.Pro1675Arg	p.P1675R	ENST00000219476	NM_000548.3	1675	cCg/cGg	39/42	0.523461919702841	1	FACETS	0.877	0.803	0.952	0.877	0.803	0.952	CLONAL	1	TRUE	0	0.523461919702841	1		721	428	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0006262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	27	154	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.813	1	1	0.813	1	CLONAL	1	TRUE	1	0.14	2		154	377	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510333	187510333	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	25	372	0	ENST00000441802.2:c.13180C>G	p.Leu4394Val	p.L4394V	ENST00000441802	NM_005245.3	4394	Ctg/Gtg	27/27	1	2	FACETS	0.848	0.668	1	0.848	0.668	1	CLONAL	1	TRUE	1	0.14	2		372	421	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250442	110250444	+	inframe_deletion	In_Frame_Del	DEL	CCG	CCG	-	novel	NA	P-0006262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	30	426	0	ENST00000374672.4:c.231_233del	p.Gly78del	p.G78del	ENST00000374672	NM_004235.4	77	ggCGGa/gga	3/5	1	2	FACETS	0.895	0.72	1	0.895	0.72	1	CLONAL	1	TRUE	1	0.14	2		426	479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574014	7574014	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	82	673	0	ENST00000269305.4:c.1013del	p.Phe338SerfsTer7	p.F338Sfs*7	ENST00000269305	NM_001126112.2	338	tTc/tc	10/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.14	2		673	788	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751902	57751902	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	47	398	0	ENST00000274289.3:c.1335T>G	p.Ile445Met	p.I445M	ENST00000274289	NM_006622.3	445	atT/atG	10/14	0.259893492298962	4	FACETS	0.502	0.422	0.591	0.251	0.211	0.296	SUBCLONAL	1	TRUE	2	0.259893492298962	4		398	907	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579541	7579541	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	39	392	1	ENST00000269305.4:c.146A>T	p.Asp49Val	p.D49V	ENST00000269305	NM_001126112.2	49	gAt/gTt	4/11	0.148811413837715	0	FACETS	0.577	0.479	0.686			1	INDETERMINATE	1	TRUE	0	0.259893492298962	0		393	385	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006294-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	69	291	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.145574851164788	4	FACETS	1	0.959	1	0.629	0.548	0.716	CLONAL	1	TRUE	2	0.233801250212756	4		291	579	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120298	94120298	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006294-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	66	258	0	ENST00000369303.4:c.753T>A	p.Ser251Arg	p.S251R	ENST00000369303	NM_004440.3	251	agT/agA	3/17	1	2	FACETS	0.661	0.572	0.758	0.661	0.572	0.758	SUBCLONAL	1	TRUE	1	0.233801250212756	2		258	854	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425494	49425494	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006294-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	49	322	0	ENST00000301067.7:c.12994A>G	p.Thr4332Ala	p.T4332A	ENST00000301067	NM_003482.3	4332	Act/Gct	39/54	0.145574851164788	4	FACETS	0.588	0.497	0.69	0.294	0.248	0.345	SUBCLONAL	1	TRUE	2	0.233801250212756	4		322	879	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543382	65543382	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0006294-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	75	212	0	ENST00000358664.4:c.296-1G>T		p.X99_splice	ENST00000358664	NM_002382.4	99			0.233801250212756	2	FACETS	1	0.927	1	0.54	0.473	0.612	CLONAL	1	TRUE	0	0.233801250212756	2		212	594	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593667	55593669	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	rs1060502543	NA	P-0006295-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	113	279	0	ENST00000288135.5:c.1735_1737del	p.Asp579del	p.D579del	ENST00000288135	NM_000222.2	578	tATGat/tat	11/21	1	2	FACETS	0.856	0.776	0.938	0.856	0.776	0.938	CLONAL	1	TRUE	1	0.647221074180763	2		279	408	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828077	72828077	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006295-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	393	345	0	ENST00000268489.5:c.8504G>C	p.Cys2835Ser	p.C2835S	ENST00000268489	NM_006885.3	2835	tGt/tCt	9/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.647221074180763	2		345	1194	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775804	9775804	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	166	132	0	ENST00000377346.4:c.347A>G	p.Gln116Arg	p.Q116R	ENST00000377346	NM_005026.3	116	cAg/cGg	4/24	0.285336632985437	5	FACETS	0.904	0.843	0.965	0.904	0.843	0.965	INDETERMINATE	3	TRUE	2	0.705824829742738	5		132	357	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161414	55161414	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	242	228	0	ENST00000257290.5:c.3245A>G	p.Asp1082Gly	p.D1082G	ENST00000257290	NM_006206.4	1082	gAc/gGc	23/23	0.672355646323267	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.705824829742738	3		228	450	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539348	187539348	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	124	169	1	ENST00000441802.2:c.8392C>T	p.Gln2798Ter	p.Q2798*	ENST00000441802	NM_005245.3	2798	Caa/Taa	10/27	0.672355646323267	3	FACETS	0.772	0.709	0.836	0.772	0.709	0.836	SUBCLONAL	2	TRUE	1	0.705824829742738	3		170	308	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294577	1294577	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	52	68	0	ENST00000310581.5:c.424C>G	p.Arg142Gly	p.R142G	ENST00000310581	NM_198253.2	142	Cgc/Ggc	2/16	0.604865465470657	3	FACETS	1	0.954	1			1	CLONAL	1	TRUE	NA	0.705824829742738	3		68	161	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117629990	117629990	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	77	131	0	ENST00000368508.3:c.6536G>T	p.Arg2179Ile	p.R2179I	ENST00000368508	NM_002944.2	2179	aGa/aTa	41/43	0.662560673751475	3	FACETS	0.908	0.804	1	0.454	0.402	0.509	CLONAL	1	TRUE	1	0.705824829742738	3		131	325	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711876	89711876	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	10	131	0	ENST00000371953.3:c.494G>A	p.Gly165Glu	p.G165E	ENST00000371953	NM_000314.4	165	gGa/gAa	6/9	1	2	FACETS	0.149	0.101	0.21	0.149	0.101	0.21	SUBCLONAL	1	TRUE	1	0.705824829742738	2		131	190	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123324023	123324023	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	100	232	0	ENST00000358487.5:c.447C>A	p.Asn149Lys	p.N149K	ENST00000358487	NM_000141.4	149	aaC/aaA	4/18	1	2	FACETS	0.838	0.757	0.923	0.838	0.757	0.923	CLONAL	1	TRUE	1	0.705824829742738	2		232	338	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422892	49422892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751383638	NA	P-0006296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	145	165	0	ENST00000301067.7:c.14203C>T	p.Arg4735Trp	p.R4735W	ENST00000301067	NM_003482.3	4735	Cgg/Tgg	44/54	0.705824829742738	4	FACETS	1	0.957	1	0.268	0.245	0.292	CLONAL	1	TRUE	0	0.705824829742738	4		165	654	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440042	49440042	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0006296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	613	232	1	ENST00000301067.7:c.4583+1G>T		p.X1528_splice	ENST00000301067	NM_003482.3	1528			0.705824829742738	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	4	TRUE	0	0.705824829742738	4		233	724	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869478	102869478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	350	130	0	ENST00000307046.8:c.163G>A	p.Gly55Arg	p.G55R	ENST00000307046	NM_001111285.1	55	Ggg/Agg	2/4	0.705824829742738	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	4	TRUE	0	0.705824829742738	4		130	401	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027133	49027133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853292	NA	P-0006296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	137	173	0	ENST00000267163.4:c.1700C>T	p.Ser567Leu	p.S567L	ENST00000267163	NM_000321.2	567	tCa/tTa	18/27	0.705824829742738	2	FACETS	0.92	0.864	0.974	0.92	0.864	0.974	CLONAL	2	TRUE	0	0.705824829742738	2		173	211	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81971470	81971470	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	184	192	0	ENST00000359376.3:c.3160G>C	p.Glu1054Gln	p.E1054Q	ENST00000359376	NM_002661.3	1054	Gag/Cag	28/33	0.705824829742738	3	FACETS	1	0.962	1	0.529	0.49	0.569	CLONAL	1	TRUE	1	0.705824829742738	3		192	667	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16001704	16001704	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	79	182	0	ENST00000268712.3:c.2797C>T	p.Arg933Ter	p.R933*	ENST00000268712	NM_006311.3	933	Cga/Tga	21/46	0.690552267056744	3	FACETS	1	0.902	1	0.339	0.301	0.379	CLONAL	1	TRUE	0	0.705824829742738	3		182	298	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770635	40770635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	88	121	0	ENST00000373198.4:c.2747C>T	p.Pro916Leu	p.P916L	ENST00000373198	NM_133170.3	916	cCa/cTa	19/32	0.705824829742738	3	FACETS	0.95	0.849	1	0.475	0.424	0.529	CLONAL	1	TRUE	1	0.705824829742738	3		121	355	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930889	39930889	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0006296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	191	245	0	ENST00000378444.4:c.3051+1G>T		p.X1017_splice	ENST00000378444	NM_001123385.1	1017			0.705824829742738	5	FACETS	0.775	0.719	0.833	0.517	0.479	0.555	SUBCLONAL	2	TRUE	2	0.705824829742738	5		245	719	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938756	76938756	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	177	202	0	ENST00000373344.5:c.1992G>T	p.Leu664Phe	p.L664F	ENST00000373344	NM_000489.3	664	ttG/ttT	9/35	0.683532490103984	4	FACETS	0.76	0.704	0.817	0.507	0.469	0.545	SUBCLONAL	2	TRUE	1	0.705824829742738	4		202	563	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938784	76938784	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	164	194	0	ENST00000373344.5:c.1964G>T	p.Arg655Ile	p.R655I	ENST00000373344	NM_000489.3	655	aGa/aTa	9/35	0.683532490103984	4	FACETS	1	0.988	1	0.469	0.433	0.507	CLONAL	1	TRUE	1	0.705824829742738	4		194	563	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610077	81610078	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	C	novel	NA	P-0006296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	100	171	0	ENST00000298171.2:c.1675_1676delinsC	p.Gly559GlnfsTer2	p.G559Qfs*2	ENST00000298171	NM_000369.2	559	GGa/Ca	10/10	0.705824829742738	6	FACETS	0.898	0.802	1	0.224	0.2	0.25	CLONAL	1	TRUE	2	0.705824829742738	6		171	761	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0006300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	73	207	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.992	0.878	1			1	INDETERMINATE	1	TRUE	NA	0.551253304814961	2		207	267	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0006300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	91	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.246473276447613	4	FACETS	0.816	0.732	0.903	0.408	0.366	0.452	INDETERMINATE	2	TRUE	0	0.551253304814961	4		249	314	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442781	442781	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	39	173	0	ENST00000399788.2:c.1525C>T	p.His509Tyr	p.H509Y	ENST00000399788	NM_001042603.1	509	Cat/Tat	12/28	1	2	FACETS	0.349	0.29	0.416	0.349	0.29	0.416	SUBCLONAL	1	TRUE	1	0.551253304814961	2		173	405	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966955	25966955	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	63	186	0	ENST00000435504.4:c.2251C>T	p.Gln751Ter	p.Q751*	ENST00000435504		751	Cag/Tag	13/13	1	2	FACETS	0.43	0.372	0.492	0.43	0.372	0.492	SUBCLONAL	1	TRUE	1	0.551253304814961	2		186	532	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967008	25967008	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	54	179	0	ENST00000435504.4:c.2198G>A	p.Gly733Glu	p.G733E	ENST00000435504		733	gGa/gAa	13/13	1	2	FACETS	0.433	0.371	0.502	0.433	0.371	0.502	SUBCLONAL	1	TRUE	1	0.551253304814961	2		179	452	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96931022	96931022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	14	76	0	ENST00000258439.3:c.98C>T	p.Ser33Leu	p.S33L	ENST00000258439	NM_001193304.2	33	tCg/tTg	2/4	1	2	FACETS	0.334	0.242	0.444	0.334	0.242	0.444	SUBCLONAL	1	TRUE	1	0.551253304814961	2		76	152	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426027	138426027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1379286326	NA	P-0006300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	41	168	0	ENST00000289153.2:c.1504C>T	p.Pro502Ser	p.P502S	ENST00000289153	NM_006219.2	502	Cct/Tct	9/22	0.246473276447613	4	FACETS	0.406	0.338	0.483	0.102	0.084	0.121	INDETERMINATE	1	TRUE	0	0.551253304814961	4		168	568	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058719	180058719	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	50	194	0	ENST00000261937.6:c.118G>T	p.Val40Phe	p.V40F	ENST00000261937	NM_182925.4	40	Gtc/Ttc	2/30	1	2	FACETS	0.452	0.385	0.526	0.452	0.385	0.526	SUBCLONAL	1	TRUE	1	0.551253304814961	2		194	401	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910587	29910587	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	37	125	0	ENST00000376809.5:c.127G>C	p.Glu43Gln	p.E43Q	ENST00000376809	NM_002116.7	43	Gag/Cag	2/8	0.551253304814961	3	FACETS	0.544	0.449	0.648	0.272	0.224	0.324	SUBCLONAL	1	TRUE	1	0.551253304814961	3		125	315	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120882	94120882	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867992353	NA	P-0006300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	85	241	0	ENST00000369303.4:c.169G>A	p.Glu57Lys	p.E57K	ENST00000369303	NM_004440.3	57	Gaa/Aaa	3/17	1	2	FACETS	0.555	0.491	0.622	0.555	0.491	0.622	SUBCLONAL	1	TRUE	1	0.551253304814961	2		241	556	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509142	106509142	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	59	179	0	ENST00000359195.3:c.1136T>G	p.Leu379Arg	p.L379R	ENST00000359195	NM_002649.2	379	cTc/cGc	2/11	1	2	FACETS	0.42	0.361	0.483	0.42	0.361	0.483	SUBCLONAL	1	TRUE	1	0.551253304814961	2		179	510	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945702	151945702	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0006300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	12	41	0	ENST00000262189.6:c.1817C>G	p.Ser606Ter	p.S606*	ENST00000262189	NM_170606.2	606	tCa/tGa	14/59	0.551253304814961	1	FACETS	0.471	0.337	0.627	0.471	0.337	0.627	SUBCLONAL	1	TRUE	0	0.551253304814961	1		41	67	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77051792	77051792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	237	221	0	ENST00000356341.3:c.1015G>A	p.Glu339Lys	p.E339K	ENST00000356341	NM_002576.4	339	Gag/Aag	11/15	0.0840189537623219	3	FACETS	0.864	0.811	0.917			1	INDETERMINATE	2	TRUE	NA	0.551253304814961	3		221	635	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242027	105242027	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	47	240	0	ENST00000349310.3:c.397G>C	p.Glu133Gln	p.E133Q	ENST00000349310	NM_001014432.1	133	Gag/Cag	6/15	1	2	FACETS	0.349	0.295	0.41	0.349	0.295	0.41	SUBCLONAL	1	TRUE	1	0.551253304814961	2		240	488	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929432	81929432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775728338	NA	P-0006300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	266	290	0	ENST00000359376.3:c.1093G>A	p.Asp365Asn	p.D365N	ENST00000359376	NM_002661.3	365	Gat/Aat	13/33	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.551253304814961	2		290	733	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474351	40474351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780466766	NA	P-0006300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	194	285	2	ENST00000264657.5:c.2050G>A	p.Gly684Arg	p.G684R	ENST00000264657	NM_139276.2	684	Gga/Aga	21/24	1	2	FACETS	0.954	0.885	1	0.954	0.885	1	CLONAL	1	TRUE	1	0.551253304814961	2		287	738	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611804	1611804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1343124101	NA	P-0006300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	106	355	0	ENST00000344749.5:c.1858G>A	p.Glu620Lys	p.E620K	ENST00000344749	NM_001136139.2	620	Gag/Aag	19/19	1	2	FACETS	0.619	0.556	0.686	0.619	0.556	0.686	SUBCLONAL	1	TRUE	1	0.551253304814961	2		355	621	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245892	5245892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1423516878	NA	P-0006300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	140	252	0	ENST00000357368.4:c.883C>T	p.Arg295Trp	p.R295W	ENST00000357368	NM_002850.3	295	Cgg/Tgg	10/38	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.551253304814961	2		252	422	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791036	42791036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373786775	NA	P-0006300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	43	138	0	ENST00000575354.2:c.181C>T	p.Pro61Ser	p.P61S	ENST00000575354	NM_015125.3	61	Cct/Tct	2/20	1	2	FACETS	0.553	0.465	0.649	0.553	0.465	0.649	SUBCLONAL	1	TRUE	1	0.551253304814961	2		138	282	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568590	41568590	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	58	256	0	ENST00000263253.7:c.4540G>A	p.Glu1514Lys	p.E1514K	ENST00000263253	NM_001429.3	1514	Gaa/Aaa	28/31	1	2	FACETS	0.31	0.266	0.358	0.31	0.266	0.358	SUBCLONAL	1	TRUE	1	0.551253304814961	2		256	679	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0006308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	82	286	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.476101767038931	3	FACETS	0.928	0.832	1	0.928	0.832	1	CLONAL	2	TRUE	1	0.475569820333916	3		287	230	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220578	1220578	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0006308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	55	317	0	ENST00000326873.7:c.598-2A>T		p.X200_splice	ENST00000326873	NM_000455.4	200			0.441208934038829	1	FACETS	0.864	0.75	0.985	0.864	0.75	0.985	CLONAL	1	TRUE	0	0.475569820333916	1		317	204	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979195	93979195	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	33	545	0	ENST00000369303.4:c.1633G>C	p.Ala545Pro	p.A545P	ENST00000369303	NM_004440.3	545	Gct/Cct	7/17	NA	2	FACETS	0.625	0.513	0.75			1	INDETERMINATE	1	TRUE	NA	0.475569820333916	2		545	222	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101895021	101895021	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	17	308	1	ENST00000374994.4:c.574G>T	p.Gly192Cys	p.G192C	ENST00000374994	NM_004612.2	192	Ggt/Tgt	3/9	0.475417337630751	1	FACETS	0.524	0.396	0.671	0.524	0.396	0.671	SUBCLONAL	1	TRUE	0	0.475569820333916	1		309	104	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998897	100998897	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	99	627	0	ENST00000325455.5:c.905A>G	p.Asp302Gly	p.D302G	ENST00000325455	NM_001202474.3	302	gAt/gGt	1/8	0.135845101554641	4	FACETS	0.88	0.793	0.97	0.88	0.793	0.97	INDETERMINATE	2	TRUE	2	0.475569820333916	4		627	349	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223232	41223232	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	54	359	0	ENST00000357654.3:c.4699G>T	p.Gly1567Ter	p.G1567*	ENST00000357654	NM_007294.3	1567	Gga/Tga	15/23	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.475569820333916	2		359	214	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602286	10602286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	80	412	0	ENST00000171111.5:c.1292C>T	p.Ser431Phe	p.S431F	ENST00000171111	NM_203500.1	431	tCc/tTc	3/6	0.437521571352298	1	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	0	0.475569820333916	1		412	253	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797363	42797363	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	70	454	0	ENST00000575354.2:c.3725C>G	p.Thr1242Arg	p.T1242R	ENST00000575354	NM_015125.3	1242	aCg/aGg	15/20	1	2	FACETS	0.834	0.732	0.943	0.834	0.732	0.943	CLONAL	1	TRUE	1	0.475569820333916	2		454	353	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902632	50902632	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	102	615	0	ENST00000440232.2:c.207G>T	p.Gln69His	p.Q69H	ENST00000440232	NM_002691.3	69	caG/caT	3/27	1	2	FACETS	0.97	0.873	1	0.97	0.873	1	CLONAL	1	TRUE	1	0.475569820333916	2		615	442	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845423	42845423	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	42	302	0	ENST00000398585.3:c.839C>G	p.Ala280Gly	p.A280G	ENST00000398585	NM_001135099.1	280	gCc/gGc	9/14	1	2	FACETS	0.721	0.607	0.846	0.721	0.607	0.846	SUBCLONAL	1	TRUE	1	0.475569820333916	2		302	245	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317445	1317445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780018008	NA	P-0006308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	82	445	0	ENST00000400841.2:c.620C>T	p.Thr207Ile	p.T207I	ENST00000400841		207	aCa/aTa	5/6	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.475569820333916	2		445	322	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940108	49940108	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	99	553	0	ENST00000296474.3:c.935del	p.Pro312GlnfsTer26	p.P312Qfs*26	ENST00000296474	NM_002447.2	312	cCa/ca	1/20	0.437521571352298	1	FACETS	0.925	0.834	1	0.925	0.834	1	CLONAL	1	TRUE	0	0.475569820333916	1		553	343	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0006316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	257	661	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.737358506744521	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.737358506744521	1		663	407	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0006316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	403	325	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.494456331892246	4	FACETS	0.945	0.909	0.98			1	CLONAL	3	TRUE	NA	0.737358506744521	4		325	670	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554630	63554630	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555583747	NA	P-0006316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	88	328	0	ENST00000307078.5:c.109C>T	p.Gln37Ter	p.Q37*	ENST00000307078	NM_004655.3	37	Cag/Tag	2/11	0.491956174941786	1	FACETS	0.367	0.326	0.409	0.367	0.326	0.409	SUBCLONAL	1	TRUE	0	0.737358506744521	1		328	411	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992807	72992807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	136	924	2	ENST00000268489.5:c.1238C>A	p.Thr413Asn	p.T413N	ENST00000268489	NM_006885.3	413	aCc/aAc	2/10	0.737358506744521	3	FACETS	0.385	0.349	0.423	0.193	0.174	0.212	SUBCLONAL	1	TRUE	1	0.737358506744521	3		926	1311	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044962	47044962	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	350	713	0	ENST00000377604.3:c.2288T>C	p.Leu763Pro	p.L763P	ENST00000377604	NM_001204468.1	763	cTc/cCc	20/24	0.560551723971135	1	FACETS	0.764	0.728	0.801	0.764	0.728	0.801	SUBCLONAL	1	TRUE	0	0.737358506744521	1		713	784	SUCCESS
APC	324	MSKCC	GRCh37	5	112175112	112175139	+	frameshift_variant	Frame_Shift_Del	DEL	GTAGTTCATTATCATCTTTGTCATCAGC	GTAGTTCATTATCATCTTTGTCATCAGC	-	novel	NA	P-0006316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	107	259	0	ENST00000257430.4:c.3821_3848del	p.Cys1274LeufsTer5	p.C1274Lfs*5	ENST00000257430	NM_000038.5	1274	tGTAGTTCATTATCATCTTTGTCATCAGCt/tt	16/16	0.326361373375953	5	FACETS	0.967	0.879	1	0.645	0.586	0.706	INDETERMINATE	2	TRUE	2	0.737358506744521	5		259	316	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118701	115118701	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	259	590	0	ENST00000257566.3:c.640del	p.Ser214GlnfsTer29	p.S214Qfs*29	ENST00000257566	NM_016569.3	214	Tca/ca	2/8	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.737358506744521	2		590	687	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0006324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	77	261	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.945	0.832	1	0.945	0.832	1	CLONAL	1	TRUE	1	0.354358755676743	2		261	460	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	114	837	2	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	1	2	FACETS	0.814	0.733	0.9	0.814	0.733	0.9	CLONAL	1	TRUE	1	0.354358755676743	2		839	790	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464547	25464547	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs758402405	NA	P-0006324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	108	500	0	ENST00000264709.3:c.1966C>T	p.Gln656Ter	p.Q656*	ENST00000264709	NM_175629.2	656	Cag/Tag	17/23	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.354358755676743	2		500	595	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916553	39916553	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	108	633	0	ENST00000378444.4:c.4450G>C	p.Glu1484Gln	p.E1484Q	ENST00000378444	NM_001123385.1	1484	Gag/Cag	11/15	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.354358755676743	2		633	579	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0006333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	133	523	0	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	0.500647372646305	3	FACETS	0.948	0.862	1	0.474	0.431	0.519	CLONAL	1	TRUE	1	0.500647372646305	3		523	701	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999006	100999006	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1333528332	NA	P-0006333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	86	589	0	ENST00000325455.5:c.796G>A	p.Ala266Thr	p.A266T	ENST00000325455	NM_001202474.3	266	Gcc/Acc	1/8	1	2	FACETS	0.968	0.863	1	0.968	0.863	1	CLONAL	1	TRUE	1	0.500647372646305	2		589	355	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445499	49445499	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772870804	NA	P-0006333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	114	490	1	ENST00000301067.7:c.1967del	p.Leu656ArgfsTer274	p.L656Rfs*274	ENST00000301067	NM_003482.3	656	cTg/cg	10/54	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.500647372646305	2		491	437	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183809	10183809	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1553619440	NA	P-0006334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	29	239	0	ENST00000256474.2:c.278G>T	p.Gly93Val	p.G93V	ENST00000256474	NM_000551.3	93	gGc/gTc	1/3	1	2	FACETS	0.851	0.683	1	0.851	0.683	1	CLONAL	1	TRUE	1	0.17	2		239	401	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143042	47143042	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	38	501	0	ENST00000409792.3:c.4921A>T	p.Thr1641Ser	p.T1641S	ENST00000409792	NM_014159.6	1641	Act/Tct	8/21	1	2	FACETS	0.661	0.545	0.792	0.661	0.545	0.792	SUBCLONAL	1	TRUE	1	0.17	2		501	676	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440305	52440324	+	frameshift_variant	Frame_Shift_Del	DEL	CTTCAGCACATGCAGCCTGG	CTTCAGCACATGCAGCCTGG	-	novel	NA	P-0006334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	32	463	0	ENST00000460680.1:c.728_747del	p.Ala243GlyfsTer34	p.A243Gfs*34	ENST00000460680	NM_004656.3	243	gCCAGGCTGCATGTGCTGAAG/g	9/17	1	2	FACETS	0.655	0.53	0.796	0.655	0.53	0.796	SUBCLONAL	1	TRUE	1	0.17	2		463	575	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073739	8073739	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1361059014	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	818	589	0	ENST00000377482.5:c.920C>T	p.Ser307Leu	p.S307L	ENST00000377482	NM_018948.3	307	tCg/tTg	4/4	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.862410119276592	2		589	1755	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303175	11303175	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	473	350	0	ENST00000361445.4:c.1408C>T	p.His470Tyr	p.H470Y	ENST00000361445	NM_004958.3	470	Cat/Tat	9/58	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.862410119276592	2		350	1065	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841527	156841527	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	756	451	0	ENST00000524377.1:c.830C>T	p.Ser277Phe	p.S277F	ENST00000524377	NM_002529.3	277	tCt/tTt	7/17	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.862410119276592	2		451	1745	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212522526	212522526	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1646	213	435	0	ENST00000342788.4:c.1899C>A	p.Cys633Ter	p.C633*	ENST00000342788	NM_005235.2	633	tgC/tgA	16/28	0.862410119276592	3	FACETS	0.38	0.352	0.41	0.19	0.176	0.205	SUBCLONAL	1	TRUE	1	0.862410119276592	3		435	1859	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412982	49412982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	653	481	0	ENST00000418115.1:c.41G>A	p.Gly14Glu	p.G14E	ENST00000418115	NM_001664.2	14	gGa/gAa	2/5	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.862410119276592	2		481	1441	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940454	49940455	+	stop_gained	Nonsense_Mutation	DNP	AA	AA	TC	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1491	1090	633	0	ENST00000296474.3:c.588_589delinsGA	p.Tyr196_Phe197delinsTer	p.Y196_F197delins*	ENST00000296474	NM_002447.2	196	taTTtc/taGAtc	1/20	0.811294693150531	1	FACETS	0.557	0.542	0.573	0.557	0.542	0.573	SUBCLONAL	1	TRUE	0	0.862410119276592	1		633	2581	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70005623	70005623	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	482	349	0	ENST00000394351.3:c.652T>C	p.Phe218Leu	p.F218L	ENST00000394351	NM_000248.3	218	Ttt/Ctt	7/9	1	2	FACETS	0.996	0.956	1	0.996	0.956	1	CLONAL	1	TRUE	1	0.862410119276592	2		349	1122	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119666195	119666195	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1163587458	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	326	282	0	ENST00000316626.5:c.286C>T	p.Arg96Ter	p.R96*	ENST00000316626		96	Cga/Tga	3/12	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.862410119276592	2		282	752	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189585721	189585721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	398	286	0	ENST00000264731.3:c.982G>A	p.Glu328Lys	p.E328K	ENST00000264731	NM_003722.4	328	Gaa/Aaa	7/14	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.862410119276592	2		286	887	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189611995	189611995	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	365	211	0	ENST00000264731.3:c.1747G>A	p.Asp583Asn	p.D583N	ENST00000264731	NM_003722.4	583	Gat/Aat	14/14	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.862410119276592	2		211	824	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332741	153332741	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	506	340	2	ENST00000281708.4:c.215C>T	p.Ser72Phe	p.S72F	ENST00000281708	NM_033632.3	72	tCc/tTc	2/12	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.862410119276592	2		342	1121	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873598	35873598	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	405	305	0	ENST00000303115.3:c.554G>A	p.Ser185Asn	p.S185N	ENST00000303115	NM_002185.3	185	aGc/aAc	5/8	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.862410119276592	2		305	847	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591043	67591043	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	474	283	0	ENST00000274335.5:c.1636G>T	p.Glu546Ter	p.E546*	ENST00000274335		546	Gaa/Taa	12/15	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.862410119276592	2		283	1000	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696647	176696647	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	454	349	0	ENST00000439151.2:c.5348A>G	p.Asn1783Ser	p.N1783S	ENST00000439151	NM_022455.4	1783	aAc/aGc	16/23	1	2	FACETS	0.98	0.939	1	0.98	0.939	1	CLONAL	1	TRUE	1	0.862410119276592	2		349	1074	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187419	32187419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2051	909	498	0	ENST00000375023.3:c.1460G>A	p.Gly487Glu	p.G487E	ENST00000375023	NM_004557.3	487	gGa/gAa	8/30	0.862410119276592	3	FACETS	1	0.981	1	0.51	0.493	0.527	CLONAL	1	TRUE	1	0.862410119276592	3		498	2960	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188847	32188847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1705	786	411	0	ENST00000375023.3:c.707G>A	p.Gly236Glu	p.G236E	ENST00000375023	NM_004557.3	236	gGa/gAa	4/30	0.862410119276592	3	FACETS	1	0.987	1	0.524	0.505	0.542	CLONAL	1	TRUE	1	0.862410119276592	3		411	2491	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641174	117641174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	825	629	1	ENST00000368508.3:c.5797G>A	p.Glu1933Lys	p.E1933K	ENST00000368508	NM_002944.2	1933	Gag/Aag	36/43	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.862410119276592	2		630	1726	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663565	117663565	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	469	393	0	ENST00000368508.3:c.4667G>A	p.Gly1556Glu	p.G1556E	ENST00000368508	NM_002944.2	1556	gGa/gAa	28/43	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.862410119276592	2		393	1061	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714396	117714396	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	507	416	2	ENST00000368508.3:c.1253C>T	p.Ser418Leu	p.S418L	ENST00000368508	NM_002944.2	418	tCa/tTa	11/43	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.862410119276592	2		418	1148	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715890	117715890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371206741	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	449	437	0	ENST00000368508.3:c.868G>A	p.Glu290Lys	p.E290K	ENST00000368508	NM_002944.2	290	Gaa/Aaa	9/43	1	2	FACETS	0.955	0.914	0.997	0.955	0.914	0.997	CLONAL	1	TRUE	1	0.862410119276592	2		437	1090	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129499	152129499	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	271	118	1	ENST00000206249.3:c.452G>A	p.Arg151Lys	p.R151K	ENST00000206249	NM_000125.3	151	aGg/aAg	1/8	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.862410119276592	2		119	478	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683748	162683748	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	715	383	0	ENST00000366898.1:c.221G>A	p.Trp74Ter	p.W74*	ENST00000366898	NM_004562.2	74	tGg/tAg	3/12	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.862410119276592	2		383	1574	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975495	13975495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1003578447	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	341	219	0	ENST00000405192.2:c.392G>A	p.Gly131Glu	p.G131E	ENST00000405192	NM_001163147.1	131	gGa/gAa	7/12	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.862410119276592	2		219	772	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450300	50450300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	913	441	0	ENST00000331340.3:c.484C>T	p.Arg162Trp	p.R162W	ENST00000331340	NM_006060.4	162	Cgg/Tgg	5/8	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.862410119276592	2		441	1927	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372394	55372394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	691	400	0	ENST00000297316.4:c.1084G>A	p.Glu362Lys	p.E362K	ENST00000297316	NM_022454.3	362	Gaa/Aaa	2/2	1	2	FACETS	0.984	0.95	1	0.984	0.95	1	CLONAL	1	TRUE	1	0.862410119276592	2		400	1628	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971016	21971016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878853648	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	644	261	0	ENST00000579755.1:c.385C>T	p.Arg129Cys	p.R129C	ENST00000579755		129	Cgt/Tgt	2/3	0.862410119276592	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.862410119276592	1		261	743	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971018	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	642	260	0	ENST00000304494.5:c.340_341delinsTT	p.Pro114Phe	p.P114F	ENST00000304494	NM_000077.4	114	CCc/TTc	2/3	0.862410119276592				0.997	1				CLONAL	1	TRUE	0	0.862410119276592	1		260	740	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317295	87317295	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	465	420	0	ENST00000277120.3:c.320C>T	p.Ala107Val	p.A107V	ENST00000277120		107	gCt/gTt	4/19	1	2	FACETS	0.992	0.951	1	0.992	0.951	1	CLONAL	1	TRUE	1	0.862410119276592	2		420	1087	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720658	89720658	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	121	102	0	ENST00000371953.3:c.809T>C	p.Met270Thr	p.M270T	ENST00000371953	NM_000314.4	270	aTg/aCg	8/9	0.853410145773669	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.862410119276592	1		102	141	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514083	125514083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs539323916	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	919	551	1	ENST00000428830.2:c.1021G>A	p.Gly341Arg	p.G341R	ENST00000428830	NM_001114121.2	341	Ggg/Agg	10/14	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.862410119276592	2		552	1974	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246137	46246137	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	405	345	0	ENST00000334344.6:c.4231C>T	p.Gln1411Ter	p.Q1411*	ENST00000334344	NM_152641.2	1411	Caa/Taa	15/21	1	2	FACETS	0.991	0.947	1	0.991	0.947	1	CLONAL	1	TRUE	1	0.862410119276592	2		345	948	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433373	49433373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771966959	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	409	166	1	ENST00000301067.7:c.8074C>T	p.Arg2692Trp	p.R2692W	ENST00000301067	NM_003482.3	2692	Cgg/Tgg	32/54	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.862410119276592	2		167	919	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445370	49445370	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	831	403	0	ENST00000301067.7:c.2096C>T	p.Ser699Phe	p.S699F	ENST00000301067	NM_003482.3	699	tCc/tTc	10/54	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.862410119276592	2		403	1813	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857557	57857557	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	1022	565	0	ENST00000228682.2:c.83C>T	p.Pro28Leu	p.P28L	ENST00000228682	NM_005269.2	28	cCc/cTc	2/12	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.862410119276592	2		565	2150	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133238150	133238150	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	787	508	0	ENST00000320574.5:c.2827C>T	p.Pro943Ser	p.P943S	ENST00000320574	NM_006231.2	943	Cca/Tca	24/49	NA	2	FACETS	0.957	0.925	0.988			1	INDETERMINATE	1	TRUE	NA	0.862410119276592	2		508	1908	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944627	32944627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55763607	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	618	528	0	ENST00000380152.3:c.8420C>T	p.Ser2807Leu	p.S2807L	ENST00000380152		2807	tCg/tTg	19/27	1	2	FACETS	0.903	0.869	0.937	0.903	0.869	0.937	CLONAL	1	TRUE	1	0.862410119276592	2		528	1588	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515211	103515211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759628522	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	422	403	0	ENST00000355739.4:c.1712C>T	p.Pro571Leu	p.P571L	ENST00000355739	NM_000123.3	571	cCg/cTg	8/15	1	2	FACETS	0.889	0.849	0.93	0.889	0.849	0.93	CLONAL	1	TRUE	1	0.862410119276592	2		403	1101	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436921	110436921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	389	102	0	ENST00000375856.3:c.1480G>A	p.Asp494Asn	p.D494N	ENST00000375856	NM_003749.2	494	Gac/Aac	1/2	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.862410119276592	2		102	737	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544745	65544747	+	missense_variant	Missense_Mutation	TNP	CCC	CCC	TTT	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	491	327	0	ENST00000358664.4:c.179_181delinsAAA	p.Arg60_Ala61delinsGlnThr	p.R60_A61delinsQT	ENST00000358664	NM_002382.4	60	cGGGcc/cAAAcc	4/5	1	2	FACETS	0.899	0.862	0.937	0.899	0.862	0.937	CLONAL	1	TRUE	1	0.862410119276592	2		327	1266	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058882	42058882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	786	693	0	ENST00000219905.7:c.8602C>T	p.Pro2868Ser	p.P2868S	ENST00000219905	NM_001164273.1	2868	Cct/Tct	24/24	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.862410119276592	2		693	1763	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831500	72831500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1174151260	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1233	963	670	1	ENST00000268489.5:c.5081G>A	p.Gly1694Glu	p.G1694E	ENST00000268489	NM_006885.3	1694	gGg/gAg	9/10	0.102755152012329	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.862410119276592	0		671	2196	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81939038	81939038	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	981	681	0	ENST00000359376.3:c.1393G>A	p.Asp465Asn	p.D465N	ENST00000359376	NM_002661.3	465	Gat/Aat	15/33	0.102755152012329	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.862410119276592	0		681	2131	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81941368	81941368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs968560555	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	796	525	0	ENST00000359376.3:c.1546G>A	p.Glu516Lys	p.E516K	ENST00000359376	NM_002661.3	516	Gaa/Aaa	16/33	0.102755152012329	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.862410119276592	0		525	1771	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348164	89348165	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1640	1301	653	1	ENST00000301030.4:c.4785_4786delinsAA	p.Glu1596Lys	p.E1596K	ENST00000301030	NM_001256183.1	1595	gaGGag/gaAAag	9/13	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.862410119276592	2		654	2941	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348806	89348806	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2174	1687	918	0	ENST00000301030.4:c.4144G>A	p.Glu1382Lys	p.E1382K	ENST00000301030	NM_001256183.1	1382	Gag/Aag	9/13	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.862410119276592	2		918	3861	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592318	29592318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	1084	403	0	ENST00000356175.3:c.4733C>T	p.Ser1578Phe	p.S1578F	ENST00000356175	NM_000267.3	1578	tCc/tTc	35/57	0.862410119276592	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.862410119276592	2		403	1194	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436050	56436050	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761926947	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	1322	392	0	ENST00000407977.2:c.1087C>T	p.Arg363Trp	p.R363W	ENST00000407977		363	Cgg/Tgg	9/10	0.862410119276592	3	FACETS	0.999	0.978	1	0.999	0.978	1	CLONAL	2	TRUE	1	0.862410119276592	3		392	2197	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39575933	39575933	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	494	344	0	ENST00000262039.4:c.866A>T	p.Asn289Ile	p.N289I	ENST00000262039	NM_002647.2	289	aAt/aTt	8/25	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.862410119276592	2		344	1097	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098498	11098498	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	552	287	0	ENST00000358026.2:c.1016C>T	p.Pro339Leu	p.P339L	ENST00000358026	NM_001128849.1	339	cCc/cTc	6/36	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.862410119276592	2		287	1166	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39708792	39708792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	375	327	0	ENST00000361337.2:c.403C>T	p.Pro135Ser	p.P135S	ENST00000361337	NM_003286.2	135	Cca/Tca	6/21	0.862410119276592	3	FACETS	0.862	0.817	0.908	0.431	0.408	0.454	CLONAL	1	TRUE	1	0.862410119276592	3		327	1444	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733217	40733217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	855	315	0	ENST00000373198.4:c.3589G>A	p.Glu1197Lys	p.E1197K	ENST00000373198	NM_133170.3	1197	Gaa/Aaa	26/32	0.862410119276592	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.862410119276592	3		315	1409	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739115	40739115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	1084	310	0	ENST00000373198.4:c.3169G>A	p.Glu1057Lys	p.E1057K	ENST00000373198	NM_133170.3	1057	Gag/Aag	24/32	0.862410119276592	3	FACETS	0.999	0.976	1	0.999	0.976	1	CLONAL	2	TRUE	1	0.862410119276592	3		310	1800	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790168	40790168	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745346735	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	328	193	0	ENST00000373198.4:c.2563G>A	p.Gly855Arg	p.G855R	ENST00000373198	NM_133170.3	855	Ggg/Agg	18/32	0.862410119276592	3	FACETS	1	0.969	1	0.517	0.489	0.546	CLONAL	1	TRUE	1	0.862410119276592	3		193	1053	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306568	41306568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	1092	388	1	ENST00000373198.4:c.1091G>A	p.Arg364Gln	p.R364Q	ENST00000373198	NM_133170.3	364	cGa/cAa	7/32	0.862410119276592	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.862410119276592	3		389	1785	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306689	41306689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868376470	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	1151	403	1	ENST00000373198.4:c.970G>A	p.Glu324Lys	p.E324K	ENST00000373198	NM_133170.3	324	Gaa/Aaa	7/32	0.862410119276592	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.862410119276592	3		404	1893	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092940	29092940	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	501	454	0	ENST00000328354.6:c.1044A>T	p.Leu348Phe	p.L348F	ENST00000328354	NM_007194.3	348	ttA/ttT	10/15	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.862410119276592	2		454	1087	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050689	30050689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	418	329	0	ENST00000338641.4:c.491C>T	p.Ala164Val	p.A164V	ENST00000338641	NM_000268.3	164	gCc/gTc	5/16	1	2	FACETS	0.943	0.901	0.985	0.943	0.901	0.985	CLONAL	1	TRUE	1	0.862410119276592	2		329	1028	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933732	39933732	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1332	1057	506	0	ENST00000378444.4:c.867G>A	p.Trp289Ter	p.W289*	ENST00000378444	NM_001123385.1	289	tgG/tgA	4/15	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.862410119276592	2		506	2389	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045732	47045734	+	missense_variant	Missense_Mutation	TNP	GAA	GAA	TAG	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	759	479	0	ENST00000377604.3:c.2613_2615delinsTAG	p.Trp871_Lys872delinsCysArg	p.W871_K872delinsCR	ENST00000377604	NM_001204468.1	871	tgGAAa/tgTAGa	23/24	NA	2	FACETS	0.931	0.9	0.962			1	INDETERMINATE	1	TRUE	NA	0.862410119276592	2		479	1891	SUCCESS
AR	367	MSKCC	GRCh37	X	66905852	66905852	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	538	440	0	ENST00000374690.3:c.1769G>A	p.Gly590Glu	p.G590E	ENST00000374690	NM_000044.3	590	gGg/gAg	3/8	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.862410119276592	2		440	1207	SUCCESS
AR	367	MSKCC	GRCh37	X	66937343	66937343	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	799	524	0	ENST00000374690.3:c.2197G>A	p.Asp733Asn	p.D733N	ENST00000374690	NM_000044.3	733	Gac/Aac	5/8	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.862410119276592	2		524	1704	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344077	70344077	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	805	668	1	ENST00000374080.3:c.1813C>T	p.Arg605Ter	p.R605*	ENST00000374080		605	Cga/Tga	13/45	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.862410119276592	2		669	1832	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344158	70344158	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	525	466	0	ENST00000374080.3:c.1894C>T	p.Arg632Trp	p.R632W	ENST00000374080		632	Cgg/Tgg	13/45	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.862410119276592	2		466	1185	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76777866	76777866	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	454	392	0	ENST00000373344.5:c.6850G>A	p.Gly2284Arg	p.G2284R	ENST00000373344	NM_000489.3	2284	Gga/Aga	32/35	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.862410119276592	2		392	995	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937819	76937819	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	646	600	0	ENST00000373344.5:c.2929A>G	p.Thr977Ala	p.T977A	ENST00000373344	NM_000489.3	977	Act/Gct	9/35	NA	2	FACETS	0.972	0.937	1			1	INDETERMINATE	1	TRUE	NA	0.862410119276592	2		600	1541	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164893	123164893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	833	661	0	ENST00000218089.9:c.206G>A	p.Arg69Gln	p.R69Q	ENST00000218089	NM_001042749.1	69	cGa/cAa	5/35	NA	2	FACETS	1	0.972	1			1	INDETERMINATE	1	TRUE	NA	0.862410119276592	2		661	1925	SUCCESS
APC	324	MSKCC	GRCh37	5	112176863	112176863	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1270783041	NA	P-0006342-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	71	342	0	ENST00000257430.4:c.5572C>T	p.Arg1858Ter	p.R1858*	ENST00000257430	NM_000038.5	1858	Cga/Tga	16/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.22911722228001	2		342	441	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0006343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	78	286	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.3	3	FACETS	1	0.932	1	0.544	0.478	0.614	CLONAL	1	TRUE	1	0.27	3		287	603	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428534	72428534	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	32	238	0	ENST00000477973.2:c.470A>C	p.Gln157Pro	p.Q157P	ENST00000477973	NM_012234.5	157	cAa/cCa	2/4	1	2	FACETS	0.506	0.411	0.615	0.506	0.411	0.615	SUBCLONAL	1	TRUE	1	0.27	2		238	468	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140703	55140703	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	49	320	0	ENST00000257290.5:c.1564C>G	p.Arg522Gly	p.R522G	ENST00000257290	NM_006206.4	522	Cgt/Ggt	11/23	NA	2	FACETS	0.503	0.425	0.59			1	INDETERMINATE	1	TRUE	NA	0.27	2		320	721	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355312	81355312	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	40	423	0	ENST00000222390.5:c.1062C>G	p.Cys354Trp	p.C354W	ENST00000222390	NM_000601.4	354	tgC/tgG	9/18	1	2	FACETS	0.462	0.383	0.551	0.462	0.383	0.551	SUBCLONAL	1	TRUE	1	0.27	2		423	641	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856085	151856085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1047176280	NA	P-0006343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	59	388	0	ENST00000262189.6:c.11533G>A	p.Glu3845Lys	p.E3845K	ENST00000262189	NM_170606.2	3845	Gaa/Aaa	44/59	1	2	FACETS	0.577	0.496	0.667	0.577	0.496	0.667	SUBCLONAL	1	TRUE	1	0.27	2		388	757	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2111926	2111926	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	75	458	0	ENST00000219476.3:c.1174G>T	p.Glu392Ter	p.E392*	ENST00000219476	NM_000548.3	392	Gag/Tag	12/42	1	2	FACETS	0.665	0.582	0.755	0.665	0.582	0.755	SUBCLONAL	1	TRUE	1	0.27	2		458	835	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0006349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	180	426	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.735760860383886	2		426	478	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0006349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	345	525	1	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.724130037355359	1	FACETS	0.958	0.917	0.998	0.958	0.917	0.998	CLONAL	1	TRUE	0	0.735760860383886	1		526	619	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913351	NA	P-0006349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	215	319	1	ENST00000288602.6:c.1397G>T	p.Gly466Val	p.G466V	ENST00000288602	NM_004333.4	466	gGa/gTa	11/18	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.735760860383886	2		320	568	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666385	206666385	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199747005	NA	P-0006349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	285	267	0	ENST00000367120.3:c.1865G>T	p.Arg622Leu	p.R622L	ENST00000367120	NM_014002.3	622	cGc/cTc	19/22	1		FACETS		0.871	0.977				CLONAL	1	TRUE	1	0.735760860383886	2		267	839	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212252700	212252700	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	184	248	0	ENST00000342788.4:c.3153C>A	p.Ser1051Arg	p.S1051R	ENST00000342788	NM_005235.2	1051	agC/agA	26/28	1	2	FACETS	0.871	0.809	0.935	0.871	0.809	0.935	CLONAL	1	TRUE	1	0.735760860383886	2		248	574	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543781	212543781	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	239	220	1	ENST00000342788.4:c.1618G>T	p.Asp540Tyr	p.D540Y	ENST00000342788	NM_005235.2	540	Gat/Tat	13/28	1	2	FACETS	0.977	0.917	1	0.977	0.917	1	CLONAL	1	TRUE	1	0.735760860383886	2		221	665	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778027	27778027	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs767895248	NA	P-0006349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	530	623	0	ENST00000369163.2:c.176C>G	p.Thr59Ser	p.T59S	ENST00000369163	NM_003536.2	59	aCc/aGc	1/1	1	2	FACETS	0.906	0.868	0.945	0.906	0.868	0.945	CLONAL	1	TRUE	1	0.735760860383886	2		623	1590	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517405	157517405	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	311	331	0	ENST00000346085.5:c.3969G>T	p.Met1323Ile	p.M1323I	ENST00000346085	NM_020732.3	1323	atG/atT	16/20	1	2	FACETS	0.997	0.944	1	0.997	0.944	1	CLONAL	1	TRUE	1	0.735760860383886	2		331	848	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386579	81386579	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	145	264	0	ENST00000222390.5:c.408C>A	p.Tyr136Ter	p.Y136*	ENST00000222390	NM_000601.4	136	taC/taA	4/18	1	2	FACETS	0.932	0.858	1	0.932	0.858	1	CLONAL	1	TRUE	1	0.735760860383886	2		264	423	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924399	112924399	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	261	233	0	ENST00000351677.2:c.1345A>T	p.Ile449Phe	p.I449F	ENST00000351677	NM_002834.3	449	Atc/Ttc	11/16	1	2	FACETS	0.924	0.869	0.979	0.924	0.869	0.979	CLONAL	1	TRUE	1	0.735760860383886	2		233	768	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857443	68857443	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	274	255	0	ENST00000261769.5:c.2078G>T	p.Gly693Val	p.G693V	ENST00000261769	NM_004360.3	693	gGc/gTc	13/16	0.724130037355359	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.735760860383886	1		255	470	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41199690	41199690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1303996018	NA	P-0006349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	339	384	1	ENST00000357654.3:c.5437G>A	p.Asp1813Asn	p.D1813N	ENST00000357654	NM_007294.3	1813	Gat/Aat	22/23	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.735760860383886	2		385	887	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719287	52719287	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	343	344	0	ENST00000322088.6:c.953G>C	p.Arg318Pro	p.R318P	ENST00000322088	NM_014225.5	318	cGg/cCg	8/15	1	2	FACETS	0.954	0.905	1	0.954	0.905	1	CLONAL	1	TRUE	1	0.735760860383886	2		344	977	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069267	30069267	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	301	261	0	ENST00000338641.4:c.1132G>T	p.Glu378Ter	p.E378*	ENST00000338641	NM_000268.3	378	Gag/Tag	12/16	0.671406397863306	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.735760860383886	1		261	511	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272221	142272226	+	inframe_deletion	In_Frame_Del	DEL	CCAAAT	CCAAAT	-	novel	NA	P-0006349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	182	277	0	ENST00000350721.4:c.2648_2653del	p.Asp883_Leu884del	p.D883_L884del	ENST00000350721	NM_001184.3	883	gATTTGGta/gta	13/47	1	2	FACETS	0.83	0.77	0.892	0.83	0.77	0.892	CLONAL	1	TRUE	1	0.735760860383886	2		277	596	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649676	206649676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764259024	NA	P-0006350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	532	259	2	ENST00000367120.3:c.511G>A	p.Val171Ile	p.V171I	ENST00000367120	NM_014002.3	171	Gtc/Atc	6/22	0.659110146164307	4	FACETS	0.901	0.871	0.931	0.901	0.871	0.931	CLONAL	3	TRUE	1	0.764938731243578	4		261	908	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	447	291	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.6131653459788	3	FACETS	0.951	0.911	0.991	0.951	0.911	0.991	CLONAL	2	TRUE	1	0.6131653459788	3		291	1002	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	424	551	1	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	0.947	0.902	0.994	0.947	0.902	0.994	CLONAL	1	TRUE	1	0.6131653459788	2		552	1460	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498248	498248	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	85	126	0	ENST00000399788.2:c.10G>A	p.Val4Met	p.V4M	ENST00000399788	NM_001042603.1	4	Gtg/Atg	1/28	NA	2	FACETS	0.84	0.749	0.935			1	INDETERMINATE	1	TRUE	NA	0.6131653459788	2		126	330	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265908	41266236	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	In_Frame_Del	DEL	TTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACA	TTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACA	-	novel	NA	P-0006359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	36	47	0	ENST00000349496.5:c.14-109_233del		p.A5_Q79del	ENST00000349496	NM_001904.3	5		3/15	0.6131653459788	2	FACETS	0.917	0.797	1	0.917	0.797	1	CLONAL	2	TRUE	0	0.6131653459788	2		47	64	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118931	70118948	+	inframe_deletion	In_Frame_Del	DEL	ACCACCCGGATTACAAGT	ACCACCCGGATTACAAGT	-	novel	NA	P-0006359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	390	447	0	ENST00000245479.2:c.507_524del	p.His169_Tyr174del	p.H169_Y174del	ENST00000245479	NM_000346.3	168	gACCACCCGGATTACAAGTac/gac	2/3	0.605841338699237	3	FACETS	1	0.961	1	0.508	0.482	0.536	CLONAL	1	TRUE	1	0.6131653459788	3		447	1635	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0006362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	61	645	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	1	2	FACETS	0.961	0.826	1	0.961	0.826	1	CLONAL	1	TRUE	1	0.13	2		645	977	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0006362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	40	570	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.623	0.515	0.744	0.623	0.515	0.744	SUBCLONAL	1	TRUE	1	0.13	2		570	988	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953914	55953914	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	46	470	0	ENST00000263923.4:c.3522C>A	p.Asp1174Glu	p.D1174E	ENST00000263923	NM_002253.2	1174	gaC/gaA	27/30	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.13	2		470	576	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878863	151878863	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1563288201	NA	P-0006362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	51	636	1	ENST00000262189.6:c.6082C>T	p.Arg2028Ter	p.R2028*	ENST00000262189	NM_170606.2	2028	Cga/Tga	36/59	1	2	FACETS	0.964	0.817	1	0.964	0.817	1	CLONAL	1	TRUE	1	0.13	2		637	814	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374913	118374913	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	67	876	0	ENST00000534358.1:c.8306A>G	p.His2769Arg	p.H2769R	ENST00000534358	NM_005933.3	2769	cAt/cGt	27/36	1	2	FACETS	0.918	0.795	1	0.918	0.795	1	CLONAL	1	TRUE	1	0.13	2		876	1123	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575091	48575091	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0006362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	51	783	0	ENST00000342988.3:c.285T>G	p.Tyr95Ter	p.Y95*	ENST00000342988	NM_005359.5	95	taT/taG	3/12	1	2	FACETS	0.774	0.655	0.905	0.774	0.655	0.905	CLONAL	1	TRUE	1	0.13	2		783	1014	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172365	7172365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144929085	NA	P-0006362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	76	656	3	ENST00000302850.5:c.1204G>A	p.Ala402Thr	p.A402T	ENST00000302850	NM_000208.2	402	Gct/Act	5/22	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.13	2		659	969	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123691	11123691	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	48	653	0	ENST00000358026.2:c.2341A>G	p.Met781Val	p.M781V	ENST00000358026	NM_001128849.1	781	Atg/Gtg	16/36	1	2	FACETS	0.995	0.839	1	0.995	0.839	1	CLONAL	1	TRUE	1	0.13	2		653	742	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0006396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	213	411	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.968	0.908	1	1	0.994	1	CLONAL	2	TRUE	1	0.424855570910213	2		411	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587781525	NA	P-0006396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	368	513	0	ENST00000269305.4:c.842A>G	p.Asp281Gly	p.D281G	ENST00000269305	NM_001126112.2	281	gAc/gGc	8/11	1	2	FACETS	1	0.953	1	1	0.997	1	CLONAL	2	TRUE	1	0.424855570910213	2		513	866	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0006396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	394	555	2	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	1	2	FACETS	0.979	0.935	1	1	0.997	1	CLONAL	2	TRUE	1	0.424855570910213	2		557	947	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874448	76874448	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0006396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	188	227	0	ENST00000373344.5:c.5274T>G	p.Tyr1758Ter	p.Y1758*	ENST00000373344	NM_000489.3	1758	taT/taG	21/35	0.334659728903354	0	FACETS		NA	1			1	NA	3	TRUE	NA	0.424855570910213	0		227	245	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0006415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	75	426	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.917	0.817	1	0.917	0.817	1	CLONAL	1	TRUE	1	0.739965498022197	2		426	221	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959007	2959007	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs1554271741	NA	P-0006415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	93	469	0	ENST00000396946.4:c.2509C>T	p.Arg837Ter	p.R837*	ENST00000396946	NM_032415.4	837	Cga/Tga	18/25	1	2	FACETS	0.967	0.873	1	0.967	0.873	1	CLONAL	1	TRUE	1	0.739965498022197	2		469	260	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404589	8404589	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0006415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	142	605	0	ENST00000356435.5:c.4158C>G	p.Tyr1386Ter	p.Y1386*	ENST00000356435		1386	taC/taG	25/35	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.739965498022197	2		605	359	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692896	89692896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123322	NA	P-0006415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	61	366	0	ENST00000371953.3:c.380G>A	p.Gly127Glu	p.G127E	ENST00000371953	NM_000314.4	127	gGa/gAa	5/9	0.739965498022197	1	FACETS	0.962	0.865	1	0.962	0.865	1	CLONAL	1	TRUE	0	0.739965498022197	1		366	108	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584802	48584805	+	frameshift_variant	Frame_Shift_Del	DEL	ATGC	ATGC	GG	novel	NA	P-0006415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	94	588	0	ENST00000342988.3:c.880_883delinsGG	p.Met294GlyfsTer13	p.M294Gfs*13	ENST00000342988	NM_005359.5	294	ATGCcg/GGcg	7/12	0.739965498022197	1	FACETS	0.97	0.892	1	0.97	0.892	1	CLONAL	1	TRUE	0	0.739965498022197	1		588	165	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0006423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	734	399	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.785654368660924	2	FACETS	0.949	0.928	0.97	0.949	0.928	0.97	CLONAL	2	TRUE	0	0.785654368660924	2		400	984	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439260	52439260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760860535	NA	P-0006423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	621	413	0	ENST00000460680.1:c.982C>T	p.Pro328Ser	p.P328S	ENST00000460680	NM_004656.3	328	Cct/Tct	11/17	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.785654368660924	2		413	1456	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280068	66280068	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	367	492	0	ENST00000273854.3:c.1621C>T	p.Arg541Ter	p.R541*	ENST00000273854	NM_004439.5	541	Cga/Tga	7/18	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.785654368660924	2		492	933	SUCCESS
APC	324	MSKCC	GRCh37	5	112116491	112116491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	241	323	1	ENST00000257430.4:c.536C>T	p.Ser179Phe	p.S179F	ENST00000257430	NM_000038.5	179	tCc/tTc	6/16	1	2	FACETS	0.932	0.876	0.99	0.932	0.876	0.99	CLONAL	1	TRUE	1	0.785654368660924	2		324	658	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172067	32172067	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1382	820	647	0	ENST00000375023.3:c.2965G>C	p.Gly989Arg	p.G989R	ENST00000375023	NM_004557.3	989	Gga/Cga	19/30	1	2	FACETS	0.948	0.917	0.979	0.948	0.917	0.979	CLONAL	1	TRUE	1	0.785654368660924	2		647	2202	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118339515	118339515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	373	426	1	ENST00000534358.1:c.458C>T	p.Ser153Leu	p.S153L	ENST00000534358	NM_005933.3	153	tCa/tTa	2/36	0.776979085622267	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.785654368660924	1		427	545	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602362	28602362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	562	555	0	ENST00000241453.7:c.2006G>A	p.Gly669Glu	p.G669E	ENST00000241453	NM_004119.2	669	gGa/gAa	16/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.785654368660924	2		555	1419	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32968940	32968940	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28897759	NA	P-0006423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	341	447	0	ENST00000380152.3:c.9371A>G	p.Asn3124Ser	p.N3124S	ENST00000380152		3124	aAc/aGc	25/27	1	2	FACETS	0.973	0.924	1	0.973	0.924	1	CLONAL	1	TRUE	1	0.785654368660924	2		447	892	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419913	41419913	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	651	612	0	ENST00000373198.4:c.408G>A	p.Trp136Ter	p.W136*	ENST00000373198	NM_133170.3	136	tgG/tgA	3/32	1	2	FACETS	0.934	0.9	0.969	0.934	0.9	0.969	CLONAL	1	TRUE	1	0.785654368660924	2		612	1774	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5064861	5064897	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTTTTTCTTTTCTCTGCTTAGGAAATTGAACTTAGC	TCTTTTTCTTTTCTCTGCTTAGGAAATTGAACTTAGC	-	novel	NA	P-0006423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	182	154	0	ENST00000381652.3:c.1057-20_1073del		p.X353_splice	ENST00000381652	NM_004972.3	353		9/25	0.782114995098558	1	FACETS	0.957	0.904	1	0.957	0.904	1	CLONAL	1	TRUE	0	0.785654368660924	1		154	294	SUCCESS
BLM	641	MSKCC	GRCh37	15	91308637	91308638	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0006423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	259	398	0	ENST00000355112.3:c.2186_2187delinsTT	p.Ser729Phe	p.S729F	ENST00000355112	NM_000057.2	729	tCC/tTT	9/22	1	2	FACETS	0.753	0.707	0.8	0.753	0.707	0.8	SUBCLONAL	1	TRUE	1	0.785654368660924	2		398	876	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947827	178947827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	397	585	1	ENST00000263967.3:c.2702G>T	p.Cys901Phe	p.C901F	ENST00000263967	NM_006218.2	901	tGt/tTt	19/21	0.407170636096271	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.407170636096271	3		586	1159	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601863	43601863	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	332	628	0	ENST00000355710.3:c.907G>A	p.Val303Met	p.V303M	ENST00000355710	NM_020975.4	303	Gtg/Atg	5/20	0.13581150503112	0	FACETS	0.642	0.611	0.674			1	INDETERMINATE	2	TRUE	0	0.407170636096271	0		628	753	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0006431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	258	314	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	0.407170636096271	1	FACETS	1	0.981	1	1	0.996	1	CLONAL	2	TRUE	0	0.407170636096271	1		314	474	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61711074	61711074	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs755621083	NA	P-0006431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	221	424	0	ENST00000401558.2:c.2675C>T	p.Thr892Met	p.T892M	ENST00000401558	NM_003400.3	892	aCg/aTg	21/25	1	2	FACETS	0.9	0.843	0.958	1	0.994	1	CLONAL	2	TRUE	1	0.407170636096271	2		424	603	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130391	29130391	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs775320614	NA	P-0006431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	224	332	0	ENST00000328354.6:c.319G>A	p.Glu107Lys	p.E107K	ENST00000328354	NM_007194.3	107	Gaa/Aaa	2/15	0.407170636096271	0	FACETS		NA	1			1	NA	3	TRUE	0	0.407170636096271	0		332	291	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	309	291	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.328533374096185	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.461341300785208	3		291	800	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0006433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	226	375	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.461341300785208	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.461341300785208	1		378	643	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165843	47165843	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	336	568	0	ENST00000409792.3:c.283G>T	p.Glu95Ter	p.E95*	ENST00000409792	NM_014159.6	95	Gaa/Taa	3/21	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.461341300785208	2		568	1196	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603148	48603148	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0006433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	202	281	1	ENST00000342988.3:c.1447+2T>G		p.X483_splice	ENST00000342988	NM_005359.5	483			0.461341300785208	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.461341300785208	1		282	653	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023232	27023233	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	A	novel	NA	P-0006433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	226	206	0	ENST00000324856.7:c.338_339delinsA	p.Leu113GlnfsTer119	p.L113Qfs*119	ENST00000324856	NM_006015.4	113	cTG/cA	1/20	0.412909036505369	2	FACETS	0.833	0.782	0.885	0.833	0.782	0.885	CLONAL	2	TRUE	0	0.461341300785208	2		206	588	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	150	484	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.38600541817572	3	FACETS	0.933	0.859	1	0.933	0.859	1	CLONAL	2	TRUE	1	0.38600541817572	3		484	497	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0006457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	66	265	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.585	0.507	0.668	0.585	0.507	0.668	SUBCLONAL	1	TRUE	1	0.38600541817572	2		265	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780071	NA	P-0006457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	148	347	0	ENST00000269305.4:c.580C>T	p.Leu194Phe	p.L194F	ENST00000269305	NM_001126112.2	194	Ctt/Ttt	6/11	0.357577865700567	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.38600541817572	1		347	601	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946181	55946181	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	156	352	0	ENST00000263923.4:c.3998G>C	p.Gly1333Ala	p.G1333A	ENST00000263923	NM_002253.2	1333	gGa/gCa	30/30	0.38600541817572	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.38600541817572	1		352	558	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955522	48955522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	108	337	1	ENST00000267163.4:c.1638G>A	p.Met546Ile	p.M546I	ENST00000267163	NM_000321.2	546	atG/atA	17/27	1	2	FACETS	0.847	0.761	0.937	0.847	0.761	0.937	CLONAL	1	TRUE	1	0.38600541817572	2		338	661	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724945	162724946	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	TT	novel	NA	P-0006457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	89	305	0	ENST00000367921.3:c.418-1_418delinsTT		p.X140_splice	ENST00000367921	NM_006182.2	140		6/18	1	2	FACETS	0.91	0.809	1	0.91	0.809	1	CLONAL	1	TRUE	1	0.38600541817572	2		305	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0006458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	394	376	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.410368092857637	3	FACETS	1	0.993	1	0.802	0.765	0.839	CLONAL	2	FALSE	0	0.410368092857637	3		376	962	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729610	162729610	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	60	278	0	ENST00000367921.3:c.696G>C	p.Leu232Phe	p.L232F	ENST00000367921	NM_006182.2	232	ttG/ttC	8/18	0.410368092857637	6	FACETS	0.609	0.523	0.703	0.203	0.174	0.235	SUBCLONAL	1	FALSE	3	0.410368092857637	6		278	874	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638779	176638779	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	73	418	0	ENST00000439151.2:c.3379C>G	p.Leu1127Val	p.L1127V	ENST00000439151	NM_022455.4	1127	Ctc/Gtc	5/23	0.243926513871421	3	FACETS	0.806	0.706	0.913	0.269	0.235	0.305	INDETERMINATE	1	FALSE	0	0.410368092857637	3		418	532	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860054	57860054	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201621277	NA	P-0006458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1423	149	608	2	ENST00000228682.2:c.794G>A	p.Arg265Gln	p.R265Q	ENST00000228682	NM_005269.2	265	cGg/cAg	8/12	0.410368092857637	5	FACETS	0.746	0.679	0.817	0.249	0.226	0.273	SUBCLONAL	1	FALSE	2	0.410368092857637	5		610	1572	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480484	57480484	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	179	357	0	ENST00000371085.3:c.479G>C	p.Arg160Pro	p.R160P	ENST00000371085	NM_000516.4	160	cGt/cCt	6/13	0.410368092857637	7	FACETS	1	0.989	1	0.364	0.335	0.395	CLONAL	1	FALSE	3	0.410368092857637	7		357	1213	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598073	55598324	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGAGGATGACGAGTTGGCCCTAGACTTAGAAGACTTGCTGAGCTTTTCTTACCAGGTGGCAAAGGGCATGGCTTTCCTCGCCTCCAAGAATGTAAGTGGGAGTGATTCTCTAAAGAGTTTTGTGTTTTGTTTTTTTGATTTTTTTTTTTTTTTTTTTTTTTTTGAGAACAGAGCATTTTAGAGCCATAGTTAAAATGCAGAATGTCATTTTGAAGTGTGGTAACCAAAAGCAGAGGAAATTTAGTTTCTTC	TGGAGGATGACGAGTTGGCCCTAGACTTAGAAGACTTGCTGAGCTTTTCTTACCAGGTGGCAAAGGGCATGGCTTTCCTCGCCTCCAAGAATGTAAGTGGGAGTGATTCTCTAAAGAGTTTTGTGTTTTGTTTTTTTGATTTTTTTTTTTTTTTTTTTTTTTTTGAGAACAGAGCATTTTAGAGCCATAGTTAAAATGCAGAATGTCATTTTGAAGTGTGGTAACCAAAAGCAGAGGAAATTTAGTTTCTTC	-	novel	NA	P-0006458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	60	552	0	ENST00000288135.5:c.2270_2361+160del		p.X757_splice	ENST00000288135	NM_000222.2	757		16/21	0.340814120067464	3	FACETS	0.377	0.324	0.435	0.126	0.108	0.145	SUBCLONAL	1	FALSE	0	0.410368092857637	3		552	935	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383340	42383342	+	frameshift_variant	Frame_Shift_Del	DEL	CAC	CAC	AT	novel	NA	P-0006458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1861	135	546	2	ENST00000221972.3:c.360_362delinsAT	p.Thr121SerfsTer71	p.T121Sfs*71	ENST00000221972	NM_021601.3	120	ggCACc/ggATc	2/5	0.410368092857637	5	FACETS	0.533	0.482	0.587	0.133	0.12	0.147	SUBCLONAL	1	FALSE	1	0.410368092857637	5		548	1996	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061334	38061334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006461-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	185	536	1	ENST00000250448.2:c.655C>T	p.Arg219Cys	p.R219C	ENST00000250448	NM_004496.3	219	Cgc/Tgc	2/2	1	2	FACETS	0.942	0.869	1	0.942	0.869	1	CLONAL	1	TRUE	1	0.38092424317909	2		537	1031	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105997	27105997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006461-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	76	227	0	ENST00000324856.7:c.5608C>T	p.Pro1870Ser	p.P1870S	ENST00000324856	NM_006015.4	1870	Cct/Tct	20/20	0.38092424317909	1	FACETS	0.833	0.734	0.937	0.833	0.734	0.937	CLONAL	1	TRUE	0	0.38092424317909	1		227	388	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168752	32168752	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006461-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	170	556	0	ENST00000375023.3:c.4171C>A	p.Arg1391Ser	p.R1391S	ENST00000375023	NM_004557.3	1391	Cgc/Agc	23/30	1	2	FACETS	0.974	0.896	1	0.974	0.896	1	CLONAL	1	TRUE	1	0.38092424317909	2		556	916	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169083	32169083	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1056526093	NA	P-0006461-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	150	445	1	ENST00000375023.3:c.3950G>A	p.Arg1317Gln	p.R1317Q	ENST00000375023	NM_004557.3	1317	cGg/cAg	22/30	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.38092424317909	2		446	752	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209203	98209203	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006461-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	44	285	0	ENST00000331920.6:c.4335C>G	p.Ser1445Arg	p.S1445R	ENST00000331920	NM_000264.3	1445	agC/agG	23/24	1	2	FACETS	0.414	0.347	0.489	0.414	0.347	0.489	SUBCLONAL	1	TRUE	1	0.38092424317909	2		285	558	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934581	9934581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006461-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	184	511	0	ENST00000330684.3:c.1574C>T	p.Ser525Phe	p.S525F	ENST00000330684	NM_001134407.1	525	tCt/tTt	7/13	NA	2	FACETS	0.853	0.786	0.922			1	INDETERMINATE	1	TRUE	NA	0.38092424317909	2		511	1133	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610522	10610522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006461-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	139	488	0	ENST00000171111.5:c.188C>T	p.Ala63Val	p.A63V	ENST00000171111	NM_203500.1	63	gCc/gTc	2/6	1	2	FACETS	0.937	0.854	1	0.937	0.854	1	CLONAL	1	TRUE	1	0.38092424317909	2		488	779	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915083	32915084	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs80359605	NA	P-0006461-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	287	788	0	ENST00000380152.3:c.6591_6592del	p.Glu2198AsnfsTer4	p.E2198Nfs*4	ENST00000380152		2197	acTGaa/acaa	11/27	0.355081807325594	1	FACETS	0.923	0.866	0.981	0.923	0.866	0.981	CLONAL	1	TRUE	0	0.38092424317909	1		788	1322	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061010	38061021	+	inframe_deletion	In_Frame_Del	DEL	CGGGGGCCGGCG	CGGGGGCCGGCG	-	novel	NA	P-0006461-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	58	179	0	ENST00000250448.2:c.968_979del	p.Ala323_Pro326del	p.A323_P326del	ENST00000250448	NM_004496.3	323	gCGCCGGCCCCCGgg/ggg	2/2	1	2	FACETS	0.973	0.842	1	0.973	0.842	1	CLONAL	1	TRUE	1	0.38092424317909	2		179	313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0006477-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	20	672	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.258971969083593	4	FACETS	1	0.82	1	0.535	0.414	0.673	CLONAL	1	TRUE	2	0.412806242752568	4		672	128	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619838	21619838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746455173	NA	P-0006477-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	47	474	1	ENST00000382592.4:c.328G>A	p.Ala110Thr	p.A110T	ENST00000382592	NM_014572.2	110	Gca/Aca	2/8	0.413632641637226	3	FACETS	1	0.889	1	1	0.889	1	CLONAL	2	TRUE	1	0.412806242752568	3		475	133	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561120	9561120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	106	739	0	ENST00000353224.5:c.662G>A	p.Arg221Lys	p.R221K	ENST00000353224	NM_177990.2	221	aGa/aAa	4/10	0.838470166817098	3	FACETS	1	0.915	1	0.505	0.457	0.555	CLONAL	1	TRUE	1	0.838470166817098	3		739	355	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801777	3801777	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	123	906	0	ENST00000262367.5:c.3729G>C	p.Glu1243Asp	p.E1243D	ENST00000262367	NM_004380.2	1243	gaG/gaC	20/31	0.198315990866337	1	FACETS	0.596	0.548	0.644	0.596	0.548	0.644	INDETERMINATE	1	TRUE	0	0.838470166817098	1		906	286	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10283842	10283842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568861011	NA	P-0006480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	101	1028	0	ENST00000340748.4:c.644G>A	p.Arg215Lys	p.R215K	ENST00000340748		215	aGa/aAa	8/40	0.198315990866337	1	FACETS	0.585	0.533	0.638	0.585	0.533	0.638	INDETERMINATE	1	TRUE	0	0.838470166817098	1		1028	239	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206816	36206816	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	66	553	0	ENST00000300305.3:c.696del	p.Arg233AlafsTer4	p.R233Afs*4	ENST00000300305		232	cgG/cg	6/8	0.838470166817098	1	FACETS	0.809	0.732	0.884	0.809	0.732	0.884	CLONAL	1	TRUE	0	0.838470166817098	1		553	113	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0006539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	400	597	2	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.204867157922729	1	FACETS	1	0.987	1	1	0.987	1	INDETERMINATE	1	TRUE	0	0.527016305583365	1		599	1027	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183788	10183788	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882034	NA	P-0006539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	217	353	0	ENST00000256474.2:c.257C>G	p.Pro86Arg	p.P86R	ENST00000256474	NM_000551.3	86	cCc/cGc	1/3	0.527016305583365	1	FACETS	0.842	0.786	0.9	0.842	0.786	0.9	CLONAL	1	TRUE	0	0.527016305583365	1		353	720	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712520	52712520	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	244	593	1	ENST00000394830.3:c.232C>T	p.Arg78Ter	p.R78*	ENST00000394830	NM_018313.4	78	Cga/Tga	3/30	0.527016305583365	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.527016305583365	1		594	651	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797297	135797297	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs118203403	NA	P-0006539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	171	527	0	ENST00000298552.3:c.572T>A	p.Leu191His	p.L191H	ENST00000298552	NM_001162426.1	191	cTt/cAt	7/23	0.527016305583365	1	FACETS	0.966	0.896	1	0.966	0.896	1	CLONAL	1	TRUE	0	0.527016305583365	1		527	495	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285879	46285879	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	161	452	0	ENST00000334344.6:c.5147A>C	p.Lys1716Thr	p.K1716T	ENST00000334344	NM_152641.2	1716	aAg/aCg	18/21	1	2	FACETS	0.998	0.92	1	0.998	0.92	1	CLONAL	1	TRUE	1	0.527016305583365	2		452	612	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158152	47158152	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	234	573	0	ENST00000409792.3:c.4547G>C	p.Cys1516Ser	p.C1516S	ENST00000409792	NM_014159.6	1516	tGt/tCt	4/21	0.471745325833516	1	FACETS	0.793	0.74	0.847	0.793	0.74	0.847	SUBCLONAL	1	TRUE	0	0.471745325833516	1		573	956	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668715	52668715	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	337	602	0	ENST00000394830.3:c.1204C>T	p.Gln402Ter	p.Q402*	ENST00000394830	NM_018313.4	402	Cag/Tag	12/30	0.471745325833516	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.471745325833516	1		602	990	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665017	138665017	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	76	70	0	ENST00000330315.3:c.548C>A	p.Ala183Asp	p.A183D	ENST00000330315	NM_023067.3	183	gCc/gAc	1/1	0.437743578645321	3	FACETS	0.957	0.855	1	0.957	0.855	1	CLONAL	2	TRUE	1	0.471745325833516	3		70	208	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197464	106197464	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	415	693	0	ENST00000380013.4:c.5797G>T	p.Glu1933Ter	p.E1933*	ENST00000380013	NM_001127208.2	1933	Gaa/Taa	11/11	0.471745325833516	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.471745325833516	1		693	1262	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187372	32187372	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	214	519	0	ENST00000375023.3:c.1507C>G	p.Pro503Ala	p.P503A	ENST00000375023	NM_004557.3	503	Cca/Gca	8/30	1	2	FACETS	0.865	0.803	0.929	0.865	0.803	0.929	CLONAL	1	TRUE	1	0.471745325833516	2		519	1049	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271732	38271732	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	315	685	0	ENST00000425967.3:c.2217A>C	p.Glu739Asp	p.E739D	ENST00000425967	NM_001174067.1	739	gaA/gaC	17/19	1	2	FACETS	0.986	0.929	1	0.986	0.929	1	CLONAL	1	TRUE	1	0.471745325833516	2		685	1355	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103520561	103520561	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	272	543	0	ENST00000355739.4:c.2632C>G	p.Leu878Val	p.L878V	ENST00000355739	NM_000123.3	878	Ctc/Gtc	12/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.471745325833516	2		543	1126	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514799	44514799	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	258	427	0	ENST00000291552.4:c.448T>A	p.Phe150Ile	p.F150I	ENST00000291552	NM_006758.2	150	Ttc/Atc	6/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.471745325833516	2		427	1034	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231130	53231130	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	305	328	0	ENST00000375401.3:c.1772G>T	p.Gly591Val	p.G591V	ENST00000375401	NM_004187.3	591	gGa/gTa	13/26	1	1	FACETS	0.794	0.756	0.833	1	0.995	1	SUBCLONAL	2	TRUE	0	0.471745325833516	1		328	622	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188239	10188241	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0006542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	317	545	0	ENST00000256474.2:c.384_386del	p.Leu129del	p.L129del	ENST00000256474	NM_000551.3	128	CTT/-	2/3	0.471745325833516	1	FACETS	0.941	0.889	0.995	0.941	0.889	0.995	CLONAL	1	TRUE	0	0.471745325833516	1		545	1091	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0006551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	48	419	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.712	0.605	0.828	0.712	0.605	0.828	SUBCLONAL	1	TRUE	1	0.433705652387631	2		419	311	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862076	68862076	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0006551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	61	489	0	ENST00000261769.5:c.2165-1G>A		p.X722_splice	ENST00000261769	NM_004360.3	722			0.349011865019642	1	FACETS	0.819	0.713	0.931	0.819	0.713	0.931	CLONAL	1	TRUE	0	0.433705652387631	1		489	269	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152443	56152446	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	novel	NA	P-0006551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	29	351	0	ENST00000399503.3:c.502_505del	p.Glu168LeufsTer16	p.E168Lfs*16	ENST00000399503	NM_005921.1	167	AAAGaa/aa	2/20	1	2	FACETS	0.64	0.517	0.777	0.64	0.517	0.777	SUBCLONAL	1	TRUE	1	0.433705652387631	2		351	209	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	147	411	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.946	0.873	1	0.946	0.873	1	CLONAL	1	TRUE	1	0.77515171888205	2		411	401	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692790	89692790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	94	285	0	ENST00000371953.3:c.274G>A	p.Asp92Asn	p.D92N	ENST00000371953	NM_000314.4	92	Gac/Aac	5/9	1	2	FACETS	0.99	0.896	1	0.99	0.896	1	CLONAL	1	TRUE	1	0.77515171888205	2		285	245	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254918	16254918	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	171	550	0	ENST00000375759.3:c.2183C>T	p.Pro728Leu	p.P728L	ENST00000375759	NM_015001.2	728	cCt/cTt	11/15	0.77515171888205	1	FACETS	0.91	0.856	0.963	0.91	0.856	0.963	CLONAL	1	TRUE	0	0.77515171888205	1		550	297	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226549216	226549216	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	154	513	0	ENST00000366794.5:c.2990T>C	p.Val997Ala	p.V997A	ENST00000366794	NM_001618.3	997	gTa/gCa	23/23	1	2	FACETS	0.901	0.832	0.971	0.901	0.832	0.971	CLONAL	1	TRUE	1	0.77515171888205	2		513	441	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226574082	226574082	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	210	698	0	ENST00000366794.5:c.779A>G	p.Asp260Gly	p.D260G	ENST00000366794	NM_001618.3	260	gAc/gGc	6/23	1	2	FACETS	0.966	0.904	1	0.966	0.904	1	CLONAL	1	TRUE	1	0.77515171888205	2		698	561	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637344	47637344	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63751426	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	204	985	0	ENST00000233146.2:c.478C>T	p.Gln160Ter	p.Q160*	ENST00000233146	NM_000251.2	160	Cag/Tag	3/16	1	2	FACETS	0.945	0.883	1	0.945	0.883	1	CLONAL	1	TRUE	1	0.77515171888205	2		985	557	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690198	47690198	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553365723	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	144	643	1	ENST00000233146.2:c.1415C>T	p.Pro472Leu	p.P472L	ENST00000233146	NM_000251.2	472	cCt/cTt	9/16	1	2	FACETS	0.844	0.777	0.914	0.844	0.777	0.914	CLONAL	1	TRUE	1	0.77515171888205	2		644	440	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146565	55146565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	192	689	1	ENST00000257290.5:c.2239G>A	p.Glu747Lys	p.E747K	ENST00000257290	NM_006206.4	747	Gaa/Aaa	16/23	0.170725409651606	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.77515171888205	0		690	488	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55569969	55569969	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	197	696	0	ENST00000288135.5:c.836C>T	p.Ser279Leu	p.S279L	ENST00000288135	NM_000222.2	279	tCa/tTa	5/21	0.170725409651606	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.77515171888205	0		696	508	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593466	55593466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	137	651	1	ENST00000288135.5:c.1623G>A	p.Met541Ile	p.M541I	ENST00000288135	NM_000222.2	541	atG/atA	10/21	0.170725409651606	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.77515171888205	0		652	410	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602896	55602896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	139	490	2	ENST00000288135.5:c.2606C>T	p.Pro869Leu	p.P869L	ENST00000288135	NM_000222.2	869	cCc/cTc	19/21	0.170725409651606	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.77515171888205	0		492	373	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332619	153332619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	146	639	1	ENST00000281708.4:c.337G>A	p.Glu113Lys	p.E113K	ENST00000281708	NM_033632.3	113	Gag/Aag	2/12	1	2	FACETS	0.908	0.837	0.98	0.908	0.837	0.98	CLONAL	1	TRUE	1	0.77515171888205	2		640	415	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588933	67588933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	134	320	0	ENST00000274335.5:c.1024G>A	p.Glu342Lys	p.E342K	ENST00000274335		342	Gaa/Aaa	8/15	0.12273136837786	4	FACETS	0.843	0.775	0.912	0.843	0.775	0.912	INDETERMINATE	2	TRUE	2	0.77515171888205	4		320	364	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045670	26045670	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	415	1096	0	ENST00000540144.1:c.32C>T	p.Ser11Phe	p.S11F	ENST00000540144	NM_003531.2	11	tCt/tTt	1/1	0.321026913689521	4	FACETS	0.894	0.853	0.935			1	INDETERMINATE	2	TRUE	NA	0.77515171888205	4		1096	1063	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729733	41729733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	264	868	0	ENST00000242208.4:c.796G>A	p.Glu266Lys	p.E266K	ENST00000242208	NM_002192.2	266	Gag/Aag	3/3	0.136525773740249	3	FACETS	0.773	0.731	0.816	0.773	0.731	0.816	INDETERMINATE	2	TRUE	1	0.77515171888205	3		868	611	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340052	116340052	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	86	347	0	ENST00000397752.3:c.914A>C	p.Lys305Thr	p.K305T	ENST00000397752	NM_000245.2	305	aAa/aCa	2/21	0.769373689460463	2	FACETS	0.986	0.889	1	0.493	0.444	0.543	CLONAL	1	TRUE	0	0.77515171888205	2		347	225	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843351	128843351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	267	630	1	ENST00000249373.3:c.458C>T	p.Pro153Leu	p.P153L	ENST00000249373	NM_005631.4	153	cCc/cTc	2/12	0.769373689460463	2	FACETS	1	0.981	1	0.542	0.512	0.572	CLONAL	1	TRUE	0	0.77515171888205	2		631	636	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875082	151875082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	79	253	0	ENST00000262189.6:c.7456G>A	p.Gly2486Arg	p.G2486R	ENST00000262189	NM_170606.2	2486	Gga/Aga	38/59	0.769373689460463	2	FACETS	1	0.938	1	0.531	0.477	0.586	CLONAL	1	TRUE	0	0.77515171888205	2		253	192	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389279	8389279	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758084050	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	149	793	5	ENST00000356435.5:c.4339C>T	p.Arg1447Trp	p.R1447W	ENST00000356435		1447	Cgg/Tgg	26/35	0.77515171888205	1	FACETS	0.752	0.699	0.805	0.752	0.699	0.805	SUBCLONAL	1	TRUE	0	0.77515171888205	1		798	313	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98244316	98244316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	175	581	2	ENST00000331920.6:c.661G>A	p.Glu221Lys	p.E221K	ENST00000331920	NM_000264.3	221	Gaa/Aaa	5/24	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.77515171888205	2		583	443	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248108	98248108	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	170	642	0	ENST00000331920.6:c.443G>A	p.Gly148Glu	p.G148E	ENST00000331920	NM_000264.3	148	gGa/gAa	3/24	1	2	FACETS	0.954	0.885	1	0.954	0.885	1	CLONAL	1	TRUE	1	0.77515171888205	2		642	460	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104375044	104375044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	251	521	1	ENST00000369902.3:c.1042G>A	p.Glu348Lys	p.E348K	ENST00000369902	NM_016169.3	348	Gaa/Aaa	9/12	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.77515171888205	2		522	608	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154827	2154827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	185	729	0	ENST00000434045.2:c.394G>A	p.Asp132Asn	p.D132N	ENST00000434045	NM_001127598.1	132	Gac/Aac	4/5	1	2	FACETS	0.887	0.825	0.951	0.887	0.825	0.951	CLONAL	1	TRUE	1	0.77515171888205	2		729	538	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307552	118307552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	218	384	0	ENST00000534358.1:c.325G>A	p.Gly109Ser	p.G109S	ENST00000534358	NM_005933.3	109	Ggc/Agc	1/36	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.77515171888205	2		384	549	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372474	118372474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	194	834	0	ENST00000534358.1:c.6407C>T	p.Ser2136Phe	p.S2136F	ENST00000534358	NM_005933.3	2136	tCc/tTc	26/36	1	2	FACETS	0.792	0.737	0.849	0.792	0.737	0.849	SUBCLONAL	1	TRUE	1	0.77515171888205	2		834	632	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435212	49435212	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	126	254	0	ENST00000301067.7:c.6341G>A	p.Gly2114Asp	p.G2114D	ENST00000301067	NM_003482.3	2114	gGc/gAc	31/54	0.112057069985721	4	FACETS	0.902	0.828	0.976	0.902	0.828	0.976	INDETERMINATE	2	TRUE	2	0.77515171888205	4		254	320	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445260	49445260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs552543556	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	227	654	0	ENST00000301067.7:c.2206C>T	p.Pro736Ser	p.P736S	ENST00000301067	NM_003482.3	736	Ccc/Tcc	10/54	0.112057069985721	4	FACETS	1	0.992	1	0.747	0.699	0.796	INDETERMINATE	1	TRUE	2	0.77515171888205	4		654	696	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426743	121426743	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555211426	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	254	838	1	ENST00000257555.6:c.434C>T	p.Ser145Phe	p.S145F	ENST00000257555		145	tCc/tTc	2/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.77515171888205	2		839	633	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557564	21557564	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	152	757	0	ENST00000382592.4:c.2281G>A	p.Glu761Lys	p.E761K	ENST00000382592	NM_014572.2	761	Gag/Aag	5/8	0.137290297741028	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.77515171888205	0		757	422	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872018	35872018	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	286	1027	0	ENST00000216797.5:c.595G>A	p.Val199Met	p.V199M	ENST00000216797	NM_020529.2	199	Gtg/Atg	4/6	1	2	FACETS	0.821	0.774	0.869	0.821	0.774	0.869	CLONAL	1	TRUE	1	0.77515171888205	2		1027	899	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987016	36987016	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	103	390	0	ENST00000354822.5:c.673G>C	p.Ala225Pro	p.A225P	ENST00000354822	NM_001079668.2	225	Gcc/Ccc	3/3	1	2	FACETS	0.818	0.74	0.898	0.818	0.74	0.898	CLONAL	1	TRUE	1	0.77515171888205	2		390	325	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679793	88679793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	175	677	0	ENST00000360948.2:c.670G>A	p.Gly224Ser	p.G224S	ENST00000360948	NM_001012338.2	224	Ggt/Agt	7/19	1	2	FACETS	0.875	0.812	0.94	0.875	0.812	0.94	CLONAL	1	TRUE	1	0.77515171888205	2		677	516	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120548	2120548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1318655892	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	220	629	0	ENST00000219476.3:c.1808C>T	p.Thr603Ile	p.T603I	ENST00000219476	NM_000548.3	603	aCc/aTc	17/42	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.77515171888205	2		629	567	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89862352	89862352	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	232	710	1	ENST00000389301.3:c.968C>T	p.Thr323Ile	p.T323I	ENST00000389301	NM_000135.2	323	aCc/aTc	11/43	NA	2	FACETS	0.981	0.922	1			1	INDETERMINATE	1	TRUE	NA	0.77515171888205	2		711	610	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459613	40459613	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	231	787	0	ENST00000345506.4:c.1778C>A	p.Ala593Asp	p.A593D	ENST00000345506	NM_003152.3	593	gCc/gAc	16/20	1	2	FACETS	0.753	0.704	0.803	0.753	0.704	0.803	SUBCLONAL	1	TRUE	1	0.77515171888205	2		787	792	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244181	41244181	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	172	602	1	ENST00000357654.3:c.3367G>A	p.Asp1123Asn	p.D1123N	ENST00000357654	NM_007294.3	1123	Gat/Aat	10/23	1	2	FACETS	0.997	0.927	1	0.997	0.927	1	CLONAL	1	TRUE	1	0.77515171888205	2		603	445	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985652	60985652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375594294	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	79	94	0	ENST00000333681.4:c.248G>A	p.Gly83Glu	p.G83E	ENST00000333681		83	gGg/gAg	2/3	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.77515171888205	2		94	173	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211622	5211622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	136	516	0	ENST00000357368.4:c.5213C>T	p.Ala1738Val	p.A1738V	ENST00000357368	NM_002850.3	1738	gCc/gTc	33/38	1	2	FACETS	0.967	0.89	1	0.967	0.89	1	CLONAL	1	TRUE	1	0.77515171888205	2		516	363	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260236	10260236	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs963570572	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	165	579	0	ENST00000340748.4:c.2431C>T	p.Pro811Ser	p.P811S	ENST00000340748		811	Cct/Tct	25/40	1	2	FACETS	0.803	0.743	0.866	0.803	0.743	0.866	CLONAL	1	TRUE	1	0.77515171888205	2		579	530	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291085	10291085	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	133	568	0	ENST00000340748.4:c.386C>T	p.Pro129Leu	p.P129L	ENST00000340748		129	cCc/cTc	4/40	1	2	FACETS	0.766	0.701	0.833	0.766	0.701	0.833	SUBCLONAL	1	TRUE	1	0.77515171888205	2		568	448	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520159	9520159	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1484691555	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	194	648	0	ENST00000353224.5:c.2110G>A	p.Gly704Ser	p.G704S	ENST00000353224	NM_177990.2	704	Ggt/Agt	10/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.77515171888205	2		648	446	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023142	31023142	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	167	535	0	ENST00000375687.4:c.2627G>A	p.Arg876Lys	p.R876K	ENST00000375687	NM_015338.5	876	aGg/aAg	13/13	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.77515171888205	2		535	403	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764361	39764361	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368736293	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	87	283	0	ENST00000288319.7:c.751C>T	p.Pro251Ser	p.P251S	ENST00000288319	NM_182918.3	251	Cca/Tca	7/10	0.170725409651606	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.77515171888205	0		283	225	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527391	41527391	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	138	493	0	ENST00000263253.7:c.1283-1G>A		p.X428_splice	ENST00000263253	NM_001429.3	428			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.77515171888205	2		493	340	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325362	1325362	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1271369285	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	156	661	0	ENST00000400841.2:c.313C>T	p.Pro105Ser	p.P105S	ENST00000400841		105	Ccc/Tcc	3/6	0.560018547530088	1	FACETS	0.736	0.685	0.787	0.736	0.685	0.787	SUBCLONAL	1	TRUE	0	0.77515171888205	1		661	335	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211886	123211886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	299	967	0	ENST00000218089.9:c.2753C>T	p.Thr918Ile	p.T918I	ENST00000218089	NM_001042749.1	918	aCc/aTc	27/35	0.560018547530088	1	FACETS	0.827	0.788	0.867	0.827	0.788	0.867	CLONAL	1	TRUE	0	0.77515171888205	1		967	571	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796554	42796555	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0006554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	205	431	0	ENST00000575354.2:c.3112_3113del	p.Val1038SerfsTer112	p.V1038Sfs*112	ENST00000575354	NM_015125.3	1037	tcTGta/tcta	13/20	0.77515171888205	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.77515171888205	1		431	290	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	131	246	0				ENST00000310581	NM_198253.2	-/1132			0.3	5	FACETS	0.904	0.826	0.985	0.904	0.826	0.985	CLONAL	3	FALSE	2	0.3	5		246	467	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484248	120484248	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	163	656	0	ENST00000256646.2:c.2882G>A	p.Gly961Glu	p.G961E	ENST00000256646	NM_024408.3	961	gGa/gAa	18/34	0.281581476453482	3	FACETS	0.981	0.904	1	0.981	0.904	1	CLONAL	2	FALSE	1	0.3	3		656	637	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226053	226053	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782076	NA	P-0006555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	35	76	0	ENST00000264932.6:c.512G>A	p.Arg171His	p.R171H	ENST00000264932	NM_004168.2	171	cGt/cAt	5/15	0.3	5	FACETS	1	0.93	1	0.823	0.687	0.97	CLONAL	2	FALSE	2	0.3	5		76	137	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158376	108158376	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	22	508	0	ENST00000278616.4:c.4043T>G	p.Leu1348Trp	p.L1348W	ENST00000278616	NM_000051.3	1348	tTg/tGg	27/63	0.282799334753842	2	FACETS	0.339	0.262	0.429	0.169	0.131	0.215	SUBCLONAL	1	FALSE	0	0.3	2		508	433	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096120	178096120	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	219	349	0	ENST00000397062.3:c.1211T>C	p.Val404Ala	p.V404A	ENST00000397062	NM_006164.4	404	gTa/gCa	5/5	0.618998709438223	3	FACETS	1	0.985	1	0.598	0.558	0.639	CLONAL	1	TRUE	1	0.615860526582437	3		349	778	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645366	215645366	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	225	475	0	ENST00000260947.4:c.1232C>T	p.Pro411Leu	p.P411L	ENST00000260947	NM_000465.2	411	cCc/cTc	4/11	0.538560228253179	4	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.615860526582437	4		475	1046	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155489	47155489	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	121	285	0	ENST00000409792.3:c.4592C>G	p.Ser1531Cys	p.S1531C	ENST00000409792	NM_014159.6	1531	tCt/tGt	5/21	0.618998709438223	3	FACETS	0.894	0.81	0.981	0.447	0.405	0.491	CLONAL	1	TRUE	1	0.615860526582437	3		285	575	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493986	56493986	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs373276051	NA	P-0006567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3266	248	372	2	ENST00000267101.3:c.3158G>C	p.Gly1053Ala	p.G1053A	ENST00000267101	NM_001982.3	1053	gGa/gCa	26/28	0.615860526582437	19	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.615860526582437	19		374	3514	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830889	72830889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373169704	NA	P-0006567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	340	723	0	ENST00000268489.5:c.5692G>A	p.Gly1898Arg	p.G1898R	ENST00000268489	NM_006885.3	1898	Ggg/Agg	9/10	0.342532341048622	3	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.615860526582437	3		723	1215	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	101	291	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.0894112382113823	4	FACETS	0.872	0.779	0.97	0.872	0.779	0.97	INDETERMINATE	2	FALSE	2	0.190876784189683	4		291	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0006580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	96	580	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.190876784189683	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	0	0.190876784189683	1		580	653	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0006580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	44	187	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	0.190876784189683	1	FACETS	0.802	0.677	0.938	1	0.964	1	CLONAL	2	FALSE	0	0.190876784189683	1		187	260	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435423	110435423	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	75	333	0	ENST00000375856.3:c.2978C>A	p.Ala993Asp	p.A993D	ENST00000375856	NM_003749.2	993	gCc/gAc	1/2	0.112524089216536	4	FACETS	0.785	0.688	0.889	0.785	0.688	0.889	INDETERMINATE	2	FALSE	2	0.190876784189683	4		333	596	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125857	47125857	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	35	118	0	ENST00000409792.3:c.5413G>T	p.Glu1805Ter	p.E1805*	ENST00000409792	NM_014159.6	1805	Gaa/Taa	12/21	0.223309390301524	1	FACETS	0.947	0.779	1	0.947	0.779	1	CLONAL	1	TRUE	0	0.223309390301524	1		118	294	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401386	139401386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561646185	NA	P-0006598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	70	300	0	ENST00000277541.6:c.3683C>T	p.Pro1228Leu	p.P1228L	ENST00000277541	NM_017617.3	1228	cCc/cTc	23/34	1	2	FACETS	0.913	0.795	1	0.913	0.795	1	CLONAL	1	TRUE	1	0.223309390301524	2		300	687	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440819	52440888	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAACAGGGCAGGCACAGGGCCCTTACCCTGCAGTGGCGAGGCCGATACGCTCCATGATGACCCGCCGGGC	GAACAGGGCAGGCACAGGGCCCTTACCCTGCAGTGGCGAGGCCGATACGCTCCATGATGACCCGCCGGGC	-	novel	NA	P-0006598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	63	389	0	ENST00000460680.1:c.616_659+26del		p.X206_splice	ENST00000460680	NM_004656.3	206		8/17	0.223309390301524	1	FACETS	0.57	0.491	0.655	0.57	0.491	0.655	SUBCLONAL	1	TRUE	0	0.223309390301524	1		389	880	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794812	242794812	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	53	407	0	ENST00000334409.5:c.397C>G	p.Gln133Glu	p.Q133E	ENST00000334409	NM_005018.2	133	Cag/Gag	2/5	0.788306926816695	3	FACETS	0.274	0.233	0.319	0.137	0.116	0.16	SUBCLONAL	1	FALSE	1	0.788306926816695	3		407	685	SUCCESS
AR	367	MSKCC	GRCh37	X	66765876	66765876	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	121	358	0	ENST00000374690.3:c.888C>G	p.Asp296Glu	p.D296E	ENST00000374690	NM_000044.3	296	gaC/gaG	1/8	0.788306926816695	2	FACETS	0.41	0.37	0.452			1	SUBCLONAL	1	FALSE	NA	0.788306926816695	2		358	749	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183773	10183773	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193922608	NA	P-0006619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	35	369	1	ENST00000256474.2:c.242C>A	p.Pro81Gln	p.P81Q	ENST00000256474	NM_000551.3	81	cCg/cAg	1/3	1	2	FACETS	0.794	0.649	0.957	0.794	0.649	0.957	CLONAL	1	TRUE	1	0.14	2		370	630	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117730760	117730760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	94	623	0	ENST00000368508.3:c.274G>A	p.Glu92Lys	p.E92K	ENST00000368508	NM_002944.2	92	Gaa/Aaa	4/43	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.14	2		623	1189	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0006620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	21	378	1	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		379	980	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146733	185146733	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	86	429	1	ENST00000265026.3:c.364A>T	p.Arg122Trp	p.R122W	ENST00000265026	NM_004721.4	122	Agg/Tgg	2/14	0.267260727803279	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		430	1247	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006623-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	71	484	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.172364373449166	4	FACETS	0.839	0.735	0.95	0.839	0.735	0.95	CLONAL	2	FALSE	2	0.240848171690198	4		484	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0006623-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	96	404	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.166112074675393	2	FACETS	1	0.979	1	0.718	0.641	0.799	CLONAL	1	FALSE	0	0.240848171690198	2		405	555	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106747	27106747	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006623-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	60	324	0	ENST00000324856.7:c.6358G>T	p.Glu2120Ter	p.E2120*	ENST00000324856	NM_006015.4	2120	Gaa/Taa	20/20	0.203120819642603	3	FACETS	1	0.883	1	0.513	0.442	0.59	CLONAL	1	FALSE	1	0.240848171690198	3		324	544	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626680	12626680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751232720	NA	P-0006623-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	80	392	0	ENST00000251849.4:c.1609G>A	p.Val537Ile	p.V537I	ENST00000251849	NM_002880.3	537	Gta/Ata	15/17	0.192350277407725	2	FACETS	1	0.976	1	0.725	0.641	0.815	CLONAL	1	FALSE	0	0.240848171690198	2		392	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0006629-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	28	423	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		424	922	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727454	66727454	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519909	NA	P-0006629-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	27	370	0	ENST00000307102.5:c.170A>C	p.Lys57Thr	p.K57T	ENST00000307102	NM_002755.3	57	aAg/aCg	2/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		370	1114	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0006635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	26	485	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.565869268985337	1	FACETS	0.103	0.081	0.129	0.103	0.081	0.129	SUBCLONAL	1	TRUE	0	0.565869268985337	1		485	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579352	7579352	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	265	481	0	ENST00000269305.4:c.335del	p.Gly112AlafsTer11	p.G112Afs*11	ENST00000269305	NM_001126112.2	112	gGc/gc	4/11	0.565869268985337	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.565869268985337	1		481	633	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0006636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	112	645	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.286773346340361	3	FACETS	1	0.982	1	0.739	0.664	0.819	CLONAL	1	TRUE	1	0.17	3		645	967	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0006636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	83	403	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	1	2	FACETS	0.941	0.828	1	0.941	0.828	1	CLONAL	1	TRUE	1	0.17	2		403	1038	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473722	67473722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs794727798	NA	P-0006636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	148	412	1	ENST00000327367.4:c.802C>T	p.Arg268Cys	p.R268C	ENST00000327367	NM_005902.3	268	Cgc/Tgc	6/9	1	2	FACETS	0.777	0.709	0.85	1	0.988	1	SUBCLONAL	2	TRUE	1	0.17	2		413	1120	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825358	134825358	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	159	435	0	ENST00000398015.3:c.874C>G	p.Arg292Gly	p.R292G	ENST00000398015	NM_004441.4	292	Cgc/Ggc	4/16	1	2	FACETS	0.892	0.817	0.972	1	0.991	1	CLONAL	2	TRUE	1	0.17	2		435	1048	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191540	10191540	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs5030822	NA	P-0006639-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	258	516	2	ENST00000256474.2:c.533T>C	p.Leu178Pro	p.L178P	ENST00000256474	NM_000551.3	178	cTg/cCg	3/3	0.515498760884519	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.515498760884519	1		518	581	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712541	52712543	+	frameshift_variant	Frame_Shift_Del	DEL	GCT	GCT	CA	novel	NA	P-0006639-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	68	536	0	ENST00000394830.3:c.209_211delinsTG	p.Glu70ValfsTer25	p.E70Vfs*25	ENST00000394830	NM_018313.4	70	gAGCtc/gTGtc	3/30	0.515498760884519	1	FACETS	0.405	0.353	0.461	0.405	0.353	0.461	SUBCLONAL	1	TRUE	0	0.515498760884519	1		536	484	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134741	41134746	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCAT	GGCCAT	A	novel	NA	P-0006639-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	248	704	0	ENST00000379561.5:c.882_887delinsT	p.Lys294AsnfsTer10	p.K294Nfs*10	ENST00000379561	NM_002015.3	294	aaATGGCCt/aaTt	2/3	1	2	FACETS	0.909	0.85	0.969	0.909	0.85	0.969	CLONAL	1	TRUE	1	0.515498760884519	2		704	1059	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209103952	209103952	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	93	361	0	ENST00000345146.2:c.997A>G	p.Ile333Val	p.I333V	ENST00000345146	NM_005896.2	333	Att/Gtt	9/10	1	2	FACETS	0.959	0.852	1	0.959	0.852	1	CLONAL	1	TRUE	1	0.257312285687285	2		361	754	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169256	32169256	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	123	391	0	ENST00000375023.3:c.3777C>A	p.Cys1259Ter	p.C1259*	ENST00000375023	NM_004557.3	1259	tgC/tgA	22/30	0.144094329603939	5	FACETS	1	0.976	1	0.418	0.377	0.461	INDETERMINATE	1	TRUE	2	0.257312285687285	5		391	1057	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334768	81334768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	175	515	0	ENST00000222390.5:c.1948G>A	p.Val650Met	p.V650M	ENST00000222390	NM_000601.4	650	Gtg/Atg	17/18	0.229381018274908	5	FACETS	0.828	0.762	0.898	0.552	0.508	0.599	CLONAL	2	TRUE	2	0.257312285687285	5		515	1138	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370870	55370870	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	219	370	1	ENST00000297316.4:c.172G>T	p.Ala58Ser	p.A58S	ENST00000297316	NM_022454.3	58	Gcc/Tcc	1/2	0.257312285687285	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.257312285687285	3		371	916	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097835	8097835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	51	422	1	ENST00000346208.3:c.217C>T	p.Gln73Ter	p.Q73*	ENST00000346208		73	Cag/Tag	2/6	1	2	FACETS	0.407	0.344	0.476	0.407	0.344	0.476	SUBCLONAL	1	TRUE	1	0.257312285687285	2		423	975	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090304	77090304	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	311	452	0	ENST00000356341.3:c.421A>G	p.Lys141Glu	p.K141E	ENST00000356341	NM_002576.4	141	Aaa/Gaa	4/15	1	2	FACETS	0.846	0.796	0.897	1	0.995	1	CLONAL	2	TRUE	1	0.257312285687285	2		452	1429	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160372	108160372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	68	376	0	ENST00000278616.4:c.4280C>T	p.Ala1427Val	p.A1427V	ENST00000278616	NM_000051.3	1427	gCt/gTt	29/63	1	2	FACETS	0.555	0.481	0.635	0.555	0.481	0.635	SUBCLONAL	1	TRUE	1	0.257312285687285	2		376	953	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426453	49426453	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1284	88	596	1	ENST00000301067.7:c.12035C>T	p.Pro4012Leu	p.P4012L	ENST00000301067	NM_003482.3	4012	cCt/cTt	39/54	1	2	FACETS	0.499	0.44	0.562	0.499	0.44	0.562	SUBCLONAL	1	TRUE	1	0.257312285687285	2		597	1372	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434604	49434604	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	58	396	0	ENST00000301067.7:c.6949G>C	p.Gly2317Arg	p.G2317R	ENST00000301067	NM_003482.3	2317	Ggt/Cgt	31/54	1	2	FACETS	0.531	0.455	0.614	0.531	0.455	0.614	SUBCLONAL	1	TRUE	1	0.257312285687285	2		396	849	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779226	3779226	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	70	268	0	ENST00000262367.5:c.5822A>T	p.Gln1941Leu	p.Q1941L	ENST00000262367	NM_004380.2	1941	cAg/cTg	31/31	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.257312285687285	2		268	542	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578440	7578440	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0006642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	120	470	0	ENST00000269305.4:c.490A>T	p.Lys164Ter	p.K164*	ENST00000269305	NM_001126112.2	164	Aag/Tag	5/11	1	2	FACETS	0.969	0.873	1	0.969	0.873	1	CLONAL	1	TRUE	1	0.257312285687285	2		470	963	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33446604	33446604	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	166	490	2	ENST00000345365.6:c.29C>A	p.Pro10His	p.P10H	ENST00000345365	NM_002878.3	10	cCt/cAt	1/10	0.191766294208301	4	FACETS	1	0.984	1	0.647	0.593	0.704	CLONAL	1	TRUE	2	0.257312285687285	4		492	1254	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885864	59885864	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	181	451	1	ENST00000259008.2:c.882A>T	p.Arg294Ser	p.R294S	ENST00000259008	NM_032043.2	294	agA/agT	7/20	0.191766294208301	4	FACETS	0.79	0.727	0.855	0.79	0.727	0.855	SUBCLONAL	2	TRUE	2	0.257312285687285	4		452	1120	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56409159	56409159	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	84	604	0	ENST00000348428.3:c.1666G>C	p.Glu556Gln	p.E556Q	ENST00000348428	NM_006785.3	556	Gag/Cag	14/17	1	2	FACETS	0.513	0.451	0.58	0.513	0.451	0.58	SUBCLONAL	1	TRUE	1	0.257312285687285	2		604	1273	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944546	40944546	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0006642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1188	77	470	0	ENST00000373198.4:c.1956T>A	p.Tyr652Ter	p.Y652*	ENST00000373198	NM_133170.3	652	taT/taA	12/32	0.178196639930209	4	FACETS	0.595	0.52	0.676	0.198	0.173	0.226	SUBCLONAL	1	TRUE	1	0.257312285687285	4		470	1265	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543885	41543885	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs778286798	NA	P-0006642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1152	70	534	0	ENST00000263253.7:c.2176G>T	p.Val726Leu	p.V726L	ENST00000263253	NM_001429.3	726	Gta/Tta	12/31	1	2	FACETS	0.445	0.386	0.509	0.445	0.386	0.509	SUBCLONAL	1	TRUE	1	0.257312285687285	2		534	1222	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922919	39922919	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	93	539	0	ENST00000378444.4:c.3789G>T	p.Glu1263Asp	p.E1263D	ENST00000378444	NM_001123385.1	1263	gaG/gaT	8/15	0.188799555525135	1	FACETS	0.541	0.479	0.607	0.541	0.479	0.607	SUBCLONAL	1	TRUE	0	0.257312285687285	1		539	1164	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041261	47041261	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	79	536	0	ENST00000377604.3:c.1689G>T	p.Gln563His	p.Q563H	ENST00000377604	NM_001204468.1	563	caG/caT	15/24	0.188799555525135	1	FACETS	0.479	0.42	0.544	0.479	0.42	0.544	SUBCLONAL	1	TRUE	0	0.257312285687285	1		536	1116	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411363	63411363	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	60	541	0	ENST00000330258.3:c.1804G>T	p.Glu602Ter	p.E602*	ENST00000330258	NM_152424.3	602	Gag/Tag	2/2	1	2	FACETS	0.414	0.355	0.478	0.414	0.355	0.478	SUBCLONAL	1	TRUE	1	0.257312285687285	2		541	1127	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615565	100615565	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	75	554	0	ENST00000308731.7:c.767A>G	p.Asp256Gly	p.D256G	ENST00000308731	NM_000061.2	256	gAt/gGt	8/19	1	2	FACETS	0.479	0.418	0.546	0.479	0.418	0.546	SUBCLONAL	1	TRUE	1	0.257312285687285	2		554	1216	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460533	8460533	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	81	461	0	ENST00000356435.5:c.3753del	p.Ser1252GlnfsTer16	p.S1252Qfs*16	ENST00000356435		1251	gtG/gt	22/35	0.257312285687285	1	FACETS	0.602	0.529	0.681	0.602	0.529	0.681	SUBCLONAL	1	TRUE	0	0.257312285687285	1		461	911	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0006661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	176	286	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.327713556670702	6	FACETS	0.898	0.834	0.963			1	CLONAL	4	TRUE	NA	0.327713556670702	6		287	495	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0006661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	31	275	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	1	2	FACETS	0.951	0.775	1	0.951	0.775	1	CLONAL	1	TRUE	1	0.327713556670702	2		275	199	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0006661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	132	400	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.315956995444609	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.327713556670702	2		400	371	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	62	418	0	ENST00000304494.5:c.143C>T	p.Pro48Leu	p.P48L	ENST00000304494	NM_000077.4	48	cCg/cTg	1/3	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.327713556670702	2		418	318	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604694	48604694	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	67	428	0	ENST00000342988.3:c.1516del	p.Val506Ter	p.V506*	ENST00000342988	NM_005359.5	506	Gtg/tg	12/12	0.327713556670702	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.327713556670702	1		428	316	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0006678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	111	411	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.273364855711341	3	FACETS	1	0.983	1	0.705	0.641	0.771	INDETERMINATE	1	TRUE	1	0.61	3		411	337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0006678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	8	426	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	1	2	FACETS	0.089	0.057	0.131	0.089	0.057	0.131	SUBCLONAL	1	TRUE	1	0.61	2		426	294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0006678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	173	749	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.61	2		750	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577563	7577563	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1567549584	NA	P-0006678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	86	359	0	ENST00000269305.4:c.718A>G	p.Ser240Gly	p.S240G	ENST00000269305	NM_001126112.2	240	Agt/Ggt	7/11	1	2	FACETS	0.868	0.775	0.965	0.868	0.775	0.965	CLONAL	1	TRUE	1	0.61	2		359	325	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577577	7577577	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs144340710	NA	P-0006678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	84	329	0	ENST00000269305.4:c.704A>G	p.Asn235Ser	p.N235S	ENST00000269305	NM_001126112.2	235	aAc/aGc	7/11	1	2	FACETS	0.888	0.793	0.989	0.888	0.793	0.989	CLONAL	1	TRUE	1	0.61	2		329	310	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006717-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	142	291	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	0.477729006788029	2		291	547	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006717-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	134	492	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	0.881	0.802	0.962	0.881	0.802	0.962	CLONAL	1	TRUE	1	0.477729006788029	2		492	637	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760421	133760421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368347512	NA	P-0006717-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	145	363	1	ENST00000318560.5:c.2744C>T	p.Ser915Leu	p.S915L	ENST00000318560	NM_005157.4	915	tCg/tTg	11/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.477729006788029	2		364	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0006732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	70	749	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.262116244473255	1	FACETS	0.722	0.633	0.819	0.722	0.633	0.819	SUBCLONAL	1	TRUE	0	0.381536323495883	1		750	411	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097630	27097630	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	51	576	0	ENST00000324856.7:c.3219G>A	p.Trp1073Ter	p.W1073*	ENST00000324856	NM_006015.4	1073	tgG/tgA	12/20	1	2	FACETS	0.514	0.437	0.599	0.514	0.437	0.599	SUBCLONAL	1	TRUE	1	0.381536323495883	2		576	520	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420160	420160	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746956221	NA	P-0006732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	42	502	1	ENST00000399788.2:c.3107G>A	p.Arg1036His	p.R1036H	ENST00000399788	NM_001042603.1	1036	cGt/cAt	21/28	NA	2	FACETS	0.493	0.411	0.583			1	INDETERMINATE	1	TRUE	NA	0.381536323495883	2		503	447	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493467	56493467	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	55	546	0	ENST00000267101.3:c.2875A>G	p.Lys959Glu	p.K959E	ENST00000267101	NM_001982.3	959	Aaa/Gaa	24/28	0.244324423560049	3	FACETS	0.821	0.704	0.948	0.411	0.352	0.474	CLONAL	1	TRUE	1	0.381536323495883	3		546	418	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	121	484	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.220621131660833	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.26	1		484	785	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89478256	89478256	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1460422282	NA	P-0006747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	134	306	0	ENST00000336596.2:c.2075G>T	p.Ser692Ile	p.S692I	ENST00000336596	NM_005233.5	692	aGt/aTt	12/17	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.26	2		306	908	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748152	41748152	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587778606	NA	P-0006747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	44	253	0	ENST00000226382.2:c.617C>A	p.Pro206His	p.P206H	ENST00000226382	NM_003924.3	206	cCc/cAc	3/3	0.116200245357411	0	FACETS	0.548	0.46	0.646			1	INDETERMINATE	1	TRUE	0	0.26	0		253	457	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864204	57864204	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	110	538	0	ENST00000228682.2:c.1681C>A	p.Leu561Met	p.L561M	ENST00000228682	NM_005269.2	561	Ctg/Atg	12/12	1	2	FACETS	0.781	0.7	0.867	0.781	0.7	0.867	SUBCLONAL	1	TRUE	1	0.26	2		538	1084	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943818	9943818	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	36	184	0	ENST00000330684.3:c.1123G>T	p.Val375Leu	p.V375L	ENST00000330684	NM_001134407.1	375	Gtg/Ttg	5/13	1	2	FACETS	0.798	0.657	0.955	0.798	0.657	0.955	CLONAL	1	TRUE	1	0.26	2		184	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578463	7578463	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371524413	NA	P-0006747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	87	375	0	ENST00000269305.4:c.467G>C	p.Arg156Pro	p.R156P	ENST00000269305	NM_001126112.2	156	cGc/cCc	5/11	0.166690754466559	0	FACETS	0.83	0.735	0.93			1	CLONAL	1	TRUE	0	0.26	0		375	597	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446054	49446056	+	inframe_deletion	In_Frame_Del	DEL	GGT	GGT	-	novel	NA	P-0006747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	105	559	1	ENST00000301067.7:c.1410_1412del	p.Pro471del	p.P471del	ENST00000301067	NM_003482.3	470	ccACCt/cct	10/54	1	2	FACETS	0.705	0.63	0.785	0.705	0.63	0.785	SUBCLONAL	1	TRUE	1	0.26	2		560	1146	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907724	111907724	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	307	408	0	ENST00000393256.3:c.498G>C	p.Arg166Ser	p.R166S	ENST00000393256	NM_006538.4	166	agG/agC	3/4	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.499583206951658	2		408	1192	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732250	74732250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1431153603	NA	P-0006756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	390	547	0	ENST00000359995.5:c.659C>T	p.Ser220Phe	p.S220F	ENST00000359995	NM_001195427.1	220	tCc/tTc	2/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.499583206951658	2		547	1502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	304	436	0	ENST00000269305.4:c.569del	p.Pro190LeufsTer57	p.P190Lfs*57	ENST00000269305	NM_001126112.2	190	cCt/ct	6/11	0.499583206951658	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.499583206951658	1		436	813	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0006759-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	116	284	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.771	0.698	0.848	0.771	0.698	0.848	SUBCLONAL	1	TRUE	1	0.569792864725416	2		284	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0006759-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	356	403	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.569792864725416	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.569792864725416	1		403	715	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934988	49934988	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006759-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1522	106	757	0	ENST00000296474.3:c.2011G>C	p.Asp671His	p.D671H	ENST00000296474	NM_002447.2	671	Gac/Cac	6/20	0.564194118047582	2	FACETS	0.229	0.204	0.255	0.114	0.102	0.128	SUBCLONAL	1	TRUE	0	0.569792864725416	2		757	1628	SUCCESS
APC	324	MSKCC	GRCh37	5	112090687	112090687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006759-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	58	362	0	ENST00000257430.4:c.100C>T	p.Leu34Phe	p.L34F	ENST00000257430	NM_000038.5	34	Ctt/Ttt	2/16	1	2	FACETS	0.259	0.222	0.3	0.259	0.222	0.3	SUBCLONAL	1	TRUE	1	0.569792864725416	2		362	785	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87322806	87322806	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144037140	NA	P-0006759-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	113	347	2	ENST00000277120.3:c.407G>A	p.Arg136His	p.R136H	ENST00000277120		136	cGt/cAt	5/19	0.205840978709603	2	FACETS	0.565	0.509	0.624	0.283	0.254	0.312	INDETERMINATE	1	TRUE	0	0.569792864725416	2		349	702	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549395	21549395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143631255	NA	P-0006759-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	117	229	0	ENST00000382592.4:c.2881C>T	p.Arg961Trp	p.R961W	ENST00000382592	NM_014572.2	961	Cgg/Tgg	8/8	0.569792864725416	3	FACETS	0.811	0.732	0.893	0.405	0.366	0.447	CLONAL	1	TRUE	1	0.569792864725416	3		229	651	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592632	28592632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006759-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	118	551	0	ENST00000241453.7:c.2513G>A	p.Ser838Asn	p.S838N	ENST00000241453	NM_004119.2	838	aGt/aAt	20/24	0.569792864725416	3	FACETS	0.416	0.374	0.461	0.208	0.187	0.231	SUBCLONAL	1	TRUE	1	0.569792864725416	3		551	1279	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691039	NA	P-0006766-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	294	515	0	ENST00000269305.4:c.919+1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			NA	2	FACETS	0.983	0.94	1			1	INDETERMINATE	2	TRUE	NA	0.607730279022648	2		515	492	SUCCESS
APC	324	MSKCC	GRCh37	5	112116485	112116485	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs752152148	NA	P-0006766-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	297	370	0	ENST00000257430.4:c.532-2A>T		p.X178_splice	ENST00000257430	NM_000038.5	178			0.607730279022648	3	FACETS	0.93	0.891	0.967	0.93	0.891	0.967	CLONAL	3	TRUE	0	0.607730279022648	3		370	457	SUCCESS
AR	367	MSKCC	GRCh37	X	66765159	66765185	+	inframe_deletion	In_Frame_Del	DEL	GCAGCAGCAGCAGCAGCAGCAGCAGCA	GCAGCAGCAGCAGCAGCAGCAGCAGCA	-	rs3032358	NA	P-0006766-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	58	364	0	ENST00000374690.3:c.213_239del	p.Gln72_Gln80del	p.Q72_Q80del	ENST00000374690	NM_000044.3	57	ctGCAGCAGCAGCAGCAGCAGCAGCAGCAg/ctg	1/8	0.607730279022648	2	FACETS	0.565	0.488	0.648	0.282	0.244	0.324	SUBCLONAL	1	TRUE	0	0.607730279022648	2		364	338	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0006770-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	357	538	2	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.692926246557881	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.692926246557881	1		540	545	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775687	9775687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006770-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	345	438	0	ENST00000377346.4:c.230C>T	p.Ala77Val	p.A77V	ENST00000377346	NM_005026.3	77	gCg/gTg	4/24	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.692926246557881	2		438	995	SUCCESS
APC	324	MSKCC	GRCh37	5	112175358	112175358	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006770-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	182	210	0	ENST00000257430.4:c.4067C>A	p.Ser1356Ter	p.S1356*	ENST00000257430	NM_000038.5	1356	tCa/tAa	16/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.692926246557881	2		210	462	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911436	39911436	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006770-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	60	248	0	ENST00000378444.4:c.5194G>T	p.Glu1732Ter	p.E1732*	ENST00000378444	NM_001123385.1	1732	Gaa/Taa	15/15	0.653510442130135	2	FACETS	0.167	0.143	0.193			1	SUBCLONAL	1	TRUE	NA	0.692926246557881	2		248	1040	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554728	63554729	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0006770-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	164	184	0	ENST00000307078.5:c.10_11del	p.Ala4TyrfsTer15	p.A4Yfs*15	ENST00000307078	NM_004655.3	4	GCt/t	2/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.692926246557881	2		184	406	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374241	138374245	+	frameshift_variant	Frame_Shift_Del	DEL	TAGTC	TAGTC	-	novel	NA	P-0006770-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	58	362	0	ENST00000289153.2:c.3199_3203del	p.Asp1067GlnfsTer?	p.D1067Qfs*?	ENST00000289153	NM_006219.2	1067	GACTAc/c	22/22	0.258251545936393	2	FACETS	0.242	0.207	0.28	0.121	0.103	0.14	INDETERMINATE	1	TRUE	0	0.692926246557881	2		362	692	SUCCESS
APC	324	MSKCC	GRCh37	5	112174520	112174533	+	frameshift_variant	Frame_Shift_Del	DEL	GTTTATACTGAGAG	GTTTATACTGAGAG	-	novel	NA	P-0006770-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	154	310	0	ENST00000257430.4:c.3229_3242del	p.Val1077HisfsTer2	p.V1077Hfs*2	ENST00000257430	NM_000038.5	1077	GTTTATACTGAGAGc/c	16/16	1	2	FACETS	0.896	0.826	0.968	0.896	0.826	0.968	CLONAL	1	TRUE	1	0.692926246557881	2		310	496	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0006775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	83	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.363052860612745	3	FACETS	1	0.925	1	0.527	0.468	0.59	CLONAL	1	TRUE	1	0.496208618717173	3		249	396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782329	NA	P-0006775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	219	499	0	ENST00000269305.4:c.746G>C	p.Arg249Thr	p.R249T	ENST00000269305	NM_001126112.2	249	aGg/aCg	7/11	0.492901982213938	1	FACETS	0.977	0.914	1	0.977	0.914	1	CLONAL	1	TRUE	0	0.496208618717173	1		499	679	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519920	NA	P-0006775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	204	214	1	ENST00000397062.3:c.85G>T	p.Asp29Tyr	p.D29Y	ENST00000397062	NM_006164.4	29	Gat/Tat	2/5	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.496208618717173	2		215	575	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645919	215645919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	146	563	0	ENST00000260947.4:c.679G>A	p.Gly227Ser	p.G227S	ENST00000260947	NM_000465.2	227	Ggt/Agt	4/11	NA	2	FACETS	0.786	0.718	0.856			1	INDETERMINATE	1	TRUE	NA	0.496208618717173	2		563	749	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629441	187629441	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	184	346	0	ENST00000441802.2:c.1541A>G	p.His514Arg	p.H514R	ENST00000441802	NM_005245.3	514	cAt/cGt	2/27	0.239865248273195	1	FACETS	0.936	0.869	1	0.936	0.869	1	INDETERMINATE	1	TRUE	0	0.496208618717173	1		346	596	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346079	89346079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	61	101	0	ENST00000301030.4:c.6871G>A	p.Glu2291Lys	p.E2291K	ENST00000301030	NM_001256183.1	2291	Gag/Aag	9/13	0.107097234133986	5	FACETS	0.882	0.779	0.989			1	INDETERMINATE	3	TRUE	NA	0.496208618717173	5		101	162	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547032	9547032	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0006775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	33	136	0	ENST00000353224.5:c.991-1G>A		p.X331_splice	ENST00000353224	NM_177990.2	331			1	2	FACETS	0.943	0.781	1	0.943	0.781	1	CLONAL	1	TRUE	1	0.496208618717173	2		136	141	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940087	76940087	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0006775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	64	164	0	ENST00000373344.5:c.663-2A>T		p.X221_splice	ENST00000373344	NM_000489.3	221			0.404931840786756	0	FACETS	0.537	0.471	0.607			1	SUBCLONAL	1	TRUE	NA	0.496208618717173	0		164	242	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205008	123205008	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	56	144	0	ENST00000218089.9:c.2368A>G	p.Ile790Val	p.I790V	ENST00000218089	NM_001042749.1	790	Att/Gtt	25/35	0.404931840786756	0	FACETS	0.539	0.468	0.614			1	SUBCLONAL	1	TRUE	NA	0.496208618717173	0		144	211	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0006776-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	27	145	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.814	1	1	0.814	1	CLONAL	1	TRUE	1	0.12	2		145	439	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0006785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	368	591	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.60353271808666	2	FACETS	0.906	0.869	0.942	0.906	0.869	0.942	CLONAL	2	TRUE	0	0.644832025655674	2		591	630	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602619	10602619	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1239985410	NA	P-0006785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	313	524	0	ENST00000171111.5:c.959G>T	p.Arg320Leu	p.R320L	ENST00000171111	NM_203500.1	320	cGg/cTg	3/6	0.605279868023032	3	FACETS	0.958	0.911	1	0.958	0.911	1	CLONAL	2	TRUE	1	0.644832025655674	3		524	670	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873137	71873137	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	167	559	1	ENST00000357731.5:c.1057C>A	p.Leu353Ile	p.L353I	ENST00000357731	NM_173808.2	353	Cta/Ata	7/7	0.60944932321399	3	FACETS	1	0.978	1	0.579	0.535	0.625	CLONAL	1	TRUE	1	0.644832025655674	3		560	591	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965056	25965056	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1004952488	NA	P-0006785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	265	615	0	ENST00000435504.4:c.4150G>A	p.Val1384Ile	p.V1384I	ENST00000435504		1384	Gtt/Att	13/13	0.605279868023032	3	FACETS	0.822	0.776	0.869	0.822	0.776	0.869	CLONAL	2	TRUE	1	0.644832025655674	3		615	661	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278153	142278153	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	126	433	1	ENST00000350721.4:c.1672G>T	p.Asp558Tyr	p.D558Y	ENST00000350721	NM_001184.3	558	Gac/Tac	7/47	0.644832025655674	3	FACETS	0.916	0.833	1	0.458	0.416	0.502	CLONAL	1	TRUE	1	0.644832025655674	3		434	564	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157495171	157495171	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	179	492	0	ENST00000346085.5:c.3055C>A	p.Pro1019Thr	p.P1019T	ENST00000346085	NM_020732.3	1019	Cct/Act	11/20	0.644832025655674	3	FACETS	1	0.933	1	0.505	0.467	0.545	CLONAL	1	TRUE	1	0.644832025655674	3		492	727	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372210	55372210	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	133	202	0	ENST00000297316.4:c.900G>T	p.Met300Ile	p.M300I	ENST00000297316	NM_022454.3	300	atG/atT	2/2	0.626422539893556	5	FACETS	1	0.976	1	0.771	0.709	0.834	CLONAL	2	TRUE	2	0.644832025655674	5		202	351	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609784	28609784	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	560	404	0	ENST00000241453.7:c.1445T>A	p.Val482Asp	p.V482D	ENST00000241453	NM_004119.2	482	gTc/gAc	12/24	0.590832774385998	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	4	TRUE	0	0.644832025655674	4		404	713	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860657	3860657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	201	566	1	ENST00000262367.5:c.922C>T	p.Pro308Ser	p.P308S	ENST00000262367	NM_004380.2	308	Ccc/Tcc	3/31	0.644832025655674	3	FACETS	1	0.96	1	0.524	0.486	0.562	CLONAL	1	TRUE	1	0.644832025655674	3		567	787	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420477	49420477	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	241	412	0	ENST00000301067.7:c.15272del	p.Lys5091SerfsTer56	p.K5091Sfs*56	ENST00000301067	NM_003482.3	5091	aAg/ag	48/54	0.293728926594856	5	FACETS	1	0.979	1	0.728	0.684	0.773	INDETERMINATE	2	TRUE	2	0.644832025655674	5		412	673	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099103	27099103	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	211	612	0	ENST00000324856.7:c.3524del	p.Pro1175HisfsTer5	p.P1175Hfs*5	ENST00000324856	NM_006015.4	1173	atC/at	13/20	0.293728926594856	5	FACETS	0.769	0.716	0.824	0.513	0.477	0.55	INDETERMINATE	2	TRUE	2	0.644832025655674	5		612	837	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0006793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	380	783	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.280068259801317	3	FACETS	0.888	0.841	0.935	0.888	0.841	0.935	CLONAL	2	TRUE	1	0.33236808582292	3		783	1502	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0006793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	207	393	0	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	0.285015043324488	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	0	0.33236808582292	2		393	618	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870952	12870952	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	200	597	1	ENST00000228872.4:c.179G>A	p.Trp60Ter	p.W60*	ENST00000228872	NM_004064.3	60	tGg/tAg	1/3	0.33236808582292	3	FACETS	1	0.986	1	0.642	0.594	0.692	CLONAL	1	TRUE	1	0.33236808582292	3		598	1093	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518020	187518020	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755404071	NA	P-0006793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	179	495	2	ENST00000441802.2:c.12674C>T	p.Thr4225Met	p.T4225M	ENST00000441802	NM_005245.3	4225	aCg/aTg	25/27	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.33236808582292	2		497	936	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101327	27101327	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	390	648	0	ENST00000324856.7:c.4609C>T	p.Gln1537Ter	p.Q1537*	ENST00000324856	NM_006015.4	1537	Cag/Tag	18/20	0.33236808582292	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.33236808582292	3		648	1263	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630396	47630396	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs200632093	NA	P-0006793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	257	568	0	ENST00000233146.2:c.66C>G	p.Phe22Leu	p.F22L	ENST00000233146	NM_000251.2	22	ttC/ttG	1/16	0.33236808582292	3	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	1	0.33236808582292	3		568	900	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728779	190728779	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	223	399	0	ENST00000441310.2:c.2167G>T	p.Glu723Ter	p.E723*	ENST00000441310	NM_000534.4	723	Gaa/Taa	10/13	0.33236808582292	3	FACETS	0.93	0.868	0.995	0.93	0.868	0.995	CLONAL	2	TRUE	1	0.33236808582292	3		399	841	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295792	212295792	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	270	651	1	ENST00000342788.4:c.2521C>T	p.His841Tyr	p.H841Y	ENST00000342788	NM_005235.2	841	Cat/Tat	21/28	0.33236808582292	3	FACETS	0.862	0.809	0.917	0.862	0.809	0.917	CLONAL	2	TRUE	1	0.33236808582292	3		652	1099	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646195	215646195	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	171	291	1	ENST00000260947.4:c.403G>T	p.Asp135Tyr	p.D135Y	ENST00000260947	NM_000465.2	135	Gat/Tat	4/11	0.33236808582292	3	FACETS	0.952	0.88	1	0.952	0.88	1	CLONAL	2	TRUE	1	0.33236808582292	3		292	630	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440045	220440045	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1256	163	794	1	ENST00000243786.2:c.898C>A	p.Pro300Thr	p.P300T	ENST00000243786	NM_002191.3	300	Cca/Aca	2/2	0.33236808582292	3	FACETS	0.806	0.737	0.878	0.403	0.368	0.439	CLONAL	1	TRUE	1	0.33236808582292	3		795	1419	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390065	89390065	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0006793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	220	467	0	ENST00000336596.2:c.815-1G>T		p.X272_splice	ENST00000336596	NM_005233.5	272			0.299969181265134	2	FACETS	0.84	0.784	0.898	0.84	0.784	0.898	CLONAL	2	TRUE	0	0.33236808582292	2		467	788	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390221	89390221	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs531563474	NA	P-0006793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	214	532	0	ENST00000336596.2:c.970C>G	p.Arg324Gly	p.R324G	ENST00000336596	NM_005233.5	324	Cga/Gga	4/17	0.299969181265134	2	FACETS	0.755	0.703	0.809	0.755	0.703	0.809	SUBCLONAL	2	TRUE	0	0.33236808582292	2		532	853	SUCCESS
ATR	545	MSKCC	GRCh37	3	142204114	142204114	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	117	454	3	ENST00000350721.4:c.6089C>A	p.Ala2030Glu	p.A2030E	ENST00000350721	NM_001184.3	2030	gCg/gAg	36/47	0.280068259801317	3	FACETS	1	0.928	1	0.518	0.467	0.572	CLONAL	1	TRUE	1	0.33236808582292	3		457	793	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609749	117609749	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	252	582	0	ENST00000368508.3:c.6950A>G	p.Gln2317Arg	p.Q2317R	ENST00000368508	NM_002944.2	2317	cAa/cGa	43/43	0.299969181265134	2	FACETS	0.801	0.75	0.853	0.801	0.75	0.853	CLONAL	2	TRUE	0	0.33236808582292	2		582	947	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026817	6026817	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	76	191	0	ENST00000265849.7:c.1579A>T	p.Arg527Trp	p.R527W	ENST00000265849	NM_000535.5	527	Agg/Tgg	11/15	0.252888202684651	4	FACETS	0.907	0.802	1	0.907	0.802	1	CLONAL	2	TRUE	2	0.33236808582292	4		191	336	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339742	116339742	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	152	520	0	ENST00000397752.3:c.604A>G	p.Asn202Asp	p.N202D	ENST00000397752	NM_000245.2	202	Aat/Gat	2/21	0.292214081533335	3	FACETS	0.916	0.836	1	0.458	0.418	0.5	CLONAL	1	TRUE	1	0.33236808582292	3		520	1165	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	463372	463372	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	320	663	1	ENST00000399788.2:c.899G>T	p.Gly300Val	p.G300V	ENST00000399788	NM_001042603.1	300	gGt/gTt	8/28	0.33236808582292	3	FACETS	0.838	0.79	0.887	0.838	0.79	0.887	CLONAL	2	TRUE	1	0.33236808582292	3		664	1340	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420870	49420870	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370465399	NA	P-0006793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	357	604	2	ENST00000301067.7:c.14879G>A	p.Arg4960Gln	p.R4960Q	ENST00000301067	NM_003482.3	4960	cGa/cAa	48/54	0.33236808582292	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.33236808582292	3		606	1210	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919668	28919668	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	311	583	0	ENST00000282397.4:c.2269C>A	p.Leu757Met	p.L757M	ENST00000282397	NM_002019.4	757	Ctg/Atg	16/30	0.299969181265134	2	FACETS	0.824	0.778	0.872	0.824	0.778	0.872	CLONAL	2	TRUE	0	0.33236808582292	2		583	1135	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910950	32910950	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	450	880	2	ENST00000380152.3:c.2458G>T	p.Asp820Tyr	p.D820Y	ENST00000380152		820	Gat/Tat	11/27	0.299969181265134	2	FACETS	0.846	0.806	0.886	0.846	0.806	0.886	CLONAL	2	TRUE	0	0.33236808582292	2		882	1601	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023262	33023262	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1242	311	925	1	ENST00000300177.4:c.371C>A	p.Ser124Tyr	p.S124Y	ENST00000300177	NM_001191322.1	124	tCt/tAt	2/2	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.33236808582292	2		926	1553	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647734	2647734	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	319	679	0	ENST00000342085.4:c.1637G>C	p.Arg546Pro	p.R546P	ENST00000342085	NM_002613.4	546	cGa/cCa	14/14	0.299969181265134	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.33236808582292	2		679	935	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604707	48604707	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	114	633	0	ENST00000342988.3:c.1529G>C	p.Gly510Ala	p.G510A	ENST00000342988	NM_005359.5	510	gGa/gCa	12/12	0.327122040700728	1	FACETS	0.651	0.585	0.72	0.651	0.585	0.72	SUBCLONAL	1	TRUE	0	0.33236808582292	1		633	879	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221243	1221243	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1057520606	NA	P-0006793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	448	703	1	ENST00000326873.7:c.766G>T	p.Glu256Ter	p.E256*	ENST00000326873	NM_000455.4	256	Gaa/Taa	6/10	0.285015043324488	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.33236808582292	2		704	1334	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219979	5219979	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	278	598	0	ENST00000357368.4:c.3736G>T	p.Val1246Leu	p.V1246L	ENST00000357368	NM_002850.3	1246	Gtg/Ttg	22/38	0.285015043324488	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.33236808582292	2		598	795	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713421	40713421	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	237	578	1	ENST00000373198.4:c.4094C>A	p.Thr1365Lys	p.T1365K	ENST00000373198	NM_133170.3	1365	aCg/aAg	30/32	0.252888202684651	4	FACETS	0.881	0.822	0.942	0.881	0.822	0.942	CLONAL	2	TRUE	2	0.33236808582292	4		579	1078	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933895	39933895	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1290	127	805	0	ENST00000378444.4:c.704C>A	p.Ser235Tyr	p.S235Y	ENST00000378444	NM_001123385.1	235	tCt/tAt	4/15	0.148222336613336	2	FACETS	0.539	0.487	0.595	0.27	0.243	0.298	INDETERMINATE	1	TRUE	0	0.33236808582292	2		805	1417	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357736	70357736	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	135	791	1	ENST00000374080.3:c.5987G>T	p.Ser1996Ile	p.S1996I	ENST00000374080		1996	aGt/aTt	41/45	0.148222336613336	2	FACETS	0.636	0.576	0.699	0.318	0.288	0.35	INDETERMINATE	1	TRUE	0	0.33236808582292	2		792	1278	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195724	123195724	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1394	115	783	0	ENST00000218089.9:c.1638G>T	p.Arg546Ser	p.R546S	ENST00000218089	NM_001042749.1	546	agG/agT	17/35	0.148222336613336	2	FACETS	0.459	0.411	0.509	0.229	0.205	0.255	INDETERMINATE	1	TRUE	0	0.33236808582292	2		783	1509	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0006813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	64	215	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.639	0.555	0.73	0.639	0.555	0.73	SUBCLONAL	1	TRUE	1	0.4584107387898	2		215	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0006813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	490	672	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.4584107387898	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.4584107387898	2		672	994	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0006813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	120	177	1	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	1	2	FACETS	0.955	0.866	1	0.955	0.866	1	CLONAL	1	TRUE	1	0.4584107387898	2		178	548	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0006813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	27	213	0	ENST00000311936.3:c.34_35delinsTT	p.Gly12Phe	p.G12F	ENST00000311936	NM_004985.3	12	GGt/TTt	2/5	0.162427237381051	4	FACETS	0.335	0.266	0.414			1	INDETERMINATE	1	TRUE	NA	0.4584107387898	4		213	513	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332740	65332740	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	135	232	0	ENST00000342505.4:c.799A>G	p.Lys267Glu	p.K267E	ENST00000342505	NM_002227.2	267	Aag/Gag	7/25	1	2	FACETS	0.995	0.908	1	0.995	0.908	1	CLONAL	1	TRUE	1	0.4584107387898	2		232	592	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739895	41739895	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	271	335	0	ENST00000242208.4:c.78del	p.Glu27ArgfsTer37	p.E27Rfs*37	ENST00000242208	NM_002192.2	26	tcC/tc	2/3	0.4584107387898	3	FACETS	1	0.962	1	0.519	0.485	0.553	CLONAL	1	TRUE	1	0.4584107387898	3		335	1401	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0006815-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	134	365	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.32432501996631	2	FACETS	1	0.965	1	0.552	0.505	0.601	CLONAL	1	TRUE	0	0.526621667944819	2		365	461	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584590	52584590	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006815-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	133	398	0	ENST00000394830.3:c.4423G>A	p.Gly1475Arg	p.G1475R	ENST00000394830	NM_018313.4	1475	Gga/Aga	29/30	0.143743965822398	5	FACETS	0.765	0.697	0.836	0.51	0.465	0.557	INDETERMINATE	2	TRUE	2	0.526621667944819	5		398	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0006823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	190	785	4	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.248255395186467	4	FACETS	0.989	0.923	1	1	0.989	1	CLONAL	4	FALSE	1	0.248255395186467	4		789	483	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644817	67644817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772369151	NA	P-0006823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	24	362	1	ENST00000264010.4:c.82C>T	p.Arg28Cys	p.R28C	ENST00000264010	NM_006565.3	28	Cgc/Tgc	3/12	0.197702378291868	3	FACETS	0.542	0.424	0.678	0.271	0.212	0.339	SUBCLONAL	1	FALSE	1	0.248255395186467	3		363	401	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0006828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	301	352	1	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.201435631504614	3	FACETS	0.933	0.88	0.988	0.933	0.88	0.988	CLONAL	3	TRUE	0	0.228135455947622	3		353	1050	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	57	484	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.228135455947622	1	FACETS	0.851	0.738	0.973	1	0.975	1	CLONAL	2	TRUE	0	0.228135455947622	1		484	260	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732960	30732960	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	268	381	0	ENST00000295754.5:c.1573C>A	p.Pro525Thr	p.P525T	ENST00000295754	NM_003242.5	525	Cca/Aca	7/7	0.201435631504614	3	FACETS	0.882	0.828	0.938	0.882	0.828	0.938	CLONAL	3	TRUE	0	0.228135455947622	3		381	989	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945494	17945494	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	81	464	0	ENST00000458235.1:c.2236G>C	p.Ala746Pro	p.A746P	ENST00000458235	NM_000215.3	746	Gcc/Ccc	17/24	0.228135455947622	3	FACETS	0.737	0.647	0.833	0.368	0.323	0.417	SUBCLONAL	1	TRUE	1	0.228135455947622	3		464	1074	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436050	56436050	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	255	401	0	ENST00000407977.2:c.1087del	p.Arg363GlyfsTer56	p.R363Gfs*56	ENST00000407977		363	Cgg/gg	9/10	0.201435631504614	3	FACETS	0.879	0.824	0.936	0.879	0.824	0.936	CLONAL	3	TRUE	0	0.228135455947622	3		401	944	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0006831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	278	352	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.540175653792261	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.540175653792261	1		352	607	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	358	425	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	0.540175653792261	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.540175653792261	1		425	811	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164611	36164611	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	194	424	0	ENST00000300305.3:c.1264G>A	p.Glu422Lys	p.E422K	ENST00000300305		422	Gag/Aag	8/8	1	2	FACETS	0.754	0.697	0.812	0.754	0.697	0.812	SUBCLONAL	1	TRUE	1	0.540175653792261	2		424	953	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579321	7579322	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs587780067	NA	P-0006831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	357	247	1	ENST00000269305.4:c.365_366del	p.Val122AspfsTer26	p.V122Dfs*26	ENST00000269305	NM_001126112.2	122	gTG/g	4/11	0.540175653792261	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.540175653792261	1		248	804	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47600989	47600989	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0006831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	436	567	0	ENST00000263735.4:c.227C>G	p.Ser76Ter	p.S76*	ENST00000263735	NM_002354.2	76	tCa/tGa	3/9	0.540175653792261	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.540175653792261	1		567	937	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140775	55140775	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	161	473	0	ENST00000257290.5:c.1636G>A	p.Val546Ile	p.V546I	ENST00000257290	NM_006206.4	546	Gtt/Att	11/23	0.540175653792261	1	FACETS	0.535	0.491	0.581	0.535	0.491	0.581	SUBCLONAL	1	TRUE	0	0.540175653792261	1		473	813	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527547	157527547	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370789207	NA	P-0006831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	456	554	3	ENST00000346085.5:c.5272G>A	p.Asp1758Asn	p.D1758N	ENST00000346085	NM_020732.3	1758	Gat/Aat	20/20	0.540175653792261	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.540175653792261	1		557	1056	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562710	29562710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863224660	NA	P-0006831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	379	503	1	ENST00000356175.3:c.3790G>A	p.Glu1264Lys	p.E1264K	ENST00000356175	NM_000267.3	1264	Gaa/Aaa	28/57	0.41767427667303	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.540175653792261	1		504	912	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796331	42796331	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	427	553	0	ENST00000575354.2:c.2980C>T	p.Gln994Ter	p.Q994*	ENST00000575354	NM_015125.3	994	Cag/Tag	12/20	0.540175653792261	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.540175653792261	1		553	974	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578206	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs886039484	NA	P-0006837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	209	505	0	ENST00000269305.4:c.643A>C	p.Ser215Arg	p.S215R	ENST00000269305	NM_001126112.2	215	Agt/Cgt	6/11	0.328120244754624	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.328120244754624	1		505	762	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006841-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	146	291	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.273043048927193	4	FACETS		NA	1			1	NA	NA	FALSE	2	NA	4		291	1005	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0006841-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	41	439	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		440	659	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517201	NA	P-0006841-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	36	307	0	ENST00000263967.3:c.1637A>C	p.Gln546Pro	p.Q546P	ENST00000263967	NM_006218.2	546	cAg/cCg	10/21	0.143115277440328	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		307	565	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81941320	81941320	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762012909	NA	P-0006841-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	58	625	1	ENST00000359376.3:c.1498G>A	p.Asp500Asn	p.D500N	ENST00000359376	NM_002661.3	500	Gat/Aat	16/33	0.273043048927193	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		626	530	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39729988	39729988	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006841-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	68	379	0	ENST00000361337.2:c.1303A>G	p.Ile435Val	p.I435V	ENST00000361337	NM_003286.2	435	Atc/Gtc	13/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		379	632	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577027	7577027	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	247	351	0	ENST00000269305.4:c.911del	p.Thr304IlefsTer41	p.T304Ifs*41	ENST00000269305	NM_001126112.2	304	aCt/at	8/11	NA	2	FACETS	0.988	0.944	1			1	INDETERMINATE	2	TRUE	NA	0.679440855370915	2		351	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0006860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	244	404	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.572052000181369	1	FACETS	0.978	0.922	1	0.978	0.922	1	CLONAL	1	TRUE	0	0.610400518122214	1		405	568	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519938	NA	P-0006860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	178	211	0	ENST00000263967.3:c.1034A>T	p.Asn345Ile	p.N345I	ENST00000263967	NM_006218.2	345	aAt/aTt	5/21	0.610400518122214	3	FACETS	0.998	0.921	1	0.499	0.46	0.539	CLONAL	1	TRUE	1	0.610400518122214	3		211	763	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0006860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	174	273	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.593139522075671	2	FACETS	0.95	0.879	1	0.475	0.439	0.512	CLONAL	1	TRUE	0	0.610400518122214	2		273	600	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0006860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	218	323	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.88	0.82	0.941	0.88	0.82	0.941	CLONAL	1	TRUE	1	0.610400518122214	2		323	812	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125785	47125785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	160	235	1	ENST00000409792.3:c.5485C>T	p.Gln1829Ter	p.Q1829*	ENST00000409792	NM_014159.6	1829	Cag/Tag	12/21	0.519765715067797	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.610400518122214	1		236	360	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352373	70352373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	260	581	2	ENST00000374080.3:c.4400G>A	p.Arg1467Gln	p.R1467Q	ENST00000374080		1467	cGa/cAa	31/45	1	2	FACETS	0.863	0.809	0.918	0.863	0.809	0.918	CLONAL	1	TRUE	1	0.610400518122214	2		583	987	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341585	89341585	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	58	267	0	ENST00000301030.4:c.7485del	p.Ser2496ProfsTer6	p.S2496Pfs*6	ENST00000301030	NM_001256183.1	2495	ccC/cc	10/13	1	2	FACETS	0.437	0.376	0.503	0.437	0.376	0.503	SUBCLONAL	1	TRUE	1	0.610400518122214	2		267	435	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662980	52662980	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	243	268	0	ENST00000394830.3:c.1373del	p.Asn458MetfsTer17	p.N458Mfs*17	ENST00000394830	NM_018313.4	458	aAt/at	13/30	0.519765715067797	1	FACETS	0.947	0.892	1	0.947	0.892	1	CLONAL	1	TRUE	0	0.610400518122214	1		268	584	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646267	23646267	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	133	506	2	ENST00000261584.4:c.1600T>C	p.Ser534Pro	p.S534P	ENST00000261584	NM_024675.3	534	Tct/Cct	4/13	NA	2	FACETS	0.299	0.27	0.329			1	INDETERMINATE	1	TRUE	NA	0.784561189736602	2		508	1135	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782275	56782275	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1227243689	NA	P-0006882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2460	249	544	0	ENST00000308159.5:c.116C>T	p.Ala39Val	p.A39V	ENST00000308159	NM_014669.4	39	gCg/gTg	2/22	0.664639983950643	3	FACETS	0.326	0.303	0.35			1	SUBCLONAL	1	TRUE	NA	0.784561189736602	3		544	2709	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899241	78899241	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	49	297	0	ENST00000306801.3:c.2880C>A	p.Cys960Ter	p.C960*	ENST00000306801	NM_020761.2	960	tgC/tgA	24/34	0.784561189736602	3	FACETS	0.2	0.169	0.235	0.1	0.084	0.118	SUBCLONAL	1	TRUE	1	0.784561189736602	3		297	869	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	157	484	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.333625279160468	2		484	796	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129385	152129385	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	91	322	0	ENST00000206249.3:c.338C>T	p.Pro113Leu	p.P113L	ENST00000206249	NM_000125.3	113	cCg/cTg	1/8	0.223308192771148	3	FACETS	0.741	0.657	0.831	0.371	0.328	0.416	SUBCLONAL	1	TRUE	1	0.333625279160468	3		322	859	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953894	55953894	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	90	343	0	ENST00000263923.4:c.3542C>A	p.Ser1181Ter	p.S1181*	ENST00000263923	NM_002253.2	1181	tCa/tAa	27/30	NA	2	FACETS	0.714	0.633	0.8			1	INDETERMINATE	1	TRUE	NA	0.333625279160468	2		343	756	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566520	41566520	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	145	557	0	ENST00000263253.7:c.4397G>A	p.Trp1466Ter	p.W1466*	ENST00000263253	NM_001429.3	1466	tGg/tAg	27/31	1	2	FACETS	0.664	0.604	0.727	0.664	0.604	0.727	SUBCLONAL	1	TRUE	1	0.333625279160468	2		557	1309	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266029	41266287	+	splice_donor_variant,coding_sequence_variant,intron_variant	In_Frame_Del	DEL	AGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGC	AGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGC	-	novel	NA	P-0006890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	45	390	0	ENST00000349496.5:c.30_241+47del		p.E9_D81del	ENST00000349496	NM_001904.3	9		3/15	0.181200824667435	2	FACETS	0.341	0.286	0.403	0.171	0.143	0.202	INDETERMINATE	1	TRUE	0	0.333625279160468	2		390	790	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499626	18499626	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	181	429	0	ENST00000266497.5:c.1481T>A	p.Ile494Asn	p.I494N	ENST00000266497		494	aTc/aAc	10/31	0.176948968190253	5	FACETS	1	0.969	1			1	INDETERMINATE	2	TRUE	NA	0.49456422549064	5		429	589	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604673	48604673	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060500738	NA	P-0006894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	93	287	0	ENST00000342988.3:c.1495T>C	p.Cys499Arg	p.C499R	ENST00000342988	NM_005359.5	499	Tgc/Cgc	12/12	0.49456422549064	1	FACETS	0.928	0.835	1	0.928	0.835	1	CLONAL	1	TRUE	0	0.49456422549064	1		287	305	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183872	10183872	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs730882032	NA	P-0006904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	10	175	0	ENST00000256474.2:c.340+1G>A		p.X114_splice	ENST00000256474	NM_000551.3	114			1	2	FACETS	1	0.734	1	1	0.734	1	CLONAL	1	TRUE	1	0.21	2		175	88	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098916	47098916	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	34	320	0	ENST00000409792.3:c.6358del	p.Glu2120AsnfsTer27	p.E2120Nfs*27	ENST00000409792	NM_014159.6	2120	Gaa/aa	15/21	1	2	FACETS	0.878	0.718	1	0.878	0.718	1	CLONAL	1	TRUE	1	0.21	2		320	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0006909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	328	672	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.612556283170331	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.612556283170331	1		672	652	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0006909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	376	467	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.577412153508565	2	FACETS	0.853	0.816	0.889	0.853	0.816	0.889	CLONAL	2	TRUE	0	0.612556283170331	2		467	720	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121913370	NA	P-0006909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	149	249	0	ENST00000288602.6:c.1742A>G	p.Asn581Ser	p.N581S	ENST00000288602	NM_004333.4	581	aAt/aGt	15/18	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.612556283170331	2		249	469	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920600	96920600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777665433	NA	P-0006909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	226	409	0	ENST00000258439.3:c.380G>A	p.Arg127His	p.R127H	ENST00000258439	NM_001193304.2	127	cGt/cAt	3/4	1	2	FACETS	0.951	0.889	1	0.951	0.889	1	CLONAL	1	TRUE	1	0.612556283170331	2		409	776	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530101	212530101	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	72	483	0	ENST00000342788.4:c.1818G>T	p.Lys606Asn	p.K606N	ENST00000342788	NM_005235.2	606	aaG/aaT	15/28	1	2	FACETS	0.305	0.265	0.347	0.305	0.265	0.347	SUBCLONAL	1	TRUE	1	0.612556283170331	2		483	772	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266586	41266586	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	343	473	0	ENST00000349496.5:c.383C>T	p.Pro128Leu	p.P128L	ENST00000349496	NM_001904.3	128	cCa/cTa	4/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.612556283170331	2		473	1019	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163887	152163887	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	71	468	0	ENST00000206249.3:c.608A>T	p.Glu203Val	p.E203V	ENST00000206249	NM_000125.3	203	gAg/gTg	2/8	1	2	FACETS	0.272	0.237	0.311	0.272	0.237	0.311	SUBCLONAL	1	TRUE	1	0.612556283170331	2		468	851	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884618	111884618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149554298	NA	P-0006909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	249	695	1	ENST00000341259.2:c.794G>A	p.Arg265Gln	p.R265Q	ENST00000341259	NM_005475.2	265	cGg/cAg	3/8	1	2	FACETS	0.774	0.723	0.825	0.774	0.723	0.825	SUBCLONAL	1	TRUE	1	0.612556283170331	2		696	1051	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691931	30691931	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006911-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	65	235	0	ENST00000295754.5:c.433G>T	p.Asp145Tyr	p.D145Y	ENST00000295754	NM_003242.5	145	Gac/Tac	3/7	0.277467164548818	1	FACETS	0.632	0.547	0.723	0.632	0.547	0.723	SUBCLONAL	1	TRUE	0	0.277457626381457	1		235	639	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845622	68845622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006911-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	128	385	0	ENST00000261769.5:c.868G>A	p.Asp290Asn	p.D290N	ENST00000261769	NM_004360.3	290	Gac/Aac	7/16	1	2	FACETS	0.841	0.761	0.926	0.841	0.761	0.926	CLONAL	1	TRUE	1	0.277457626381457	2		385	1097	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023811	27023811	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1470097993	NA	P-0006911-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	69	315	0	ENST00000324856.7:c.920del	p.Gly307AlafsTer56	p.G307Afs*56	ENST00000324856	NM_006015.4	306	cGg/cg	1/20	1	2	FACETS	0.623	0.542	0.712	0.623	0.542	0.712	SUBCLONAL	1	TRUE	1	0.277457626381457	2		315	798	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	196	246	0				ENST00000310581	NM_198253.2	-/1132			0.674520297687162	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	1	0.674520297687162	4		246	310	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686796	117686796	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759586931	NA	P-0006927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	24	496	2	ENST00000368508.3:c.2921C>T	p.Ala974Val	p.A974V	ENST00000368508	NM_002944.2	974	gCg/gTg	19/43	0.212207933419508	1	FACETS	0.433	0.345	0.529	0.433	0.345	0.529	INDETERMINATE	1	TRUE	0	0.674520297687162	1		498	109	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0006927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	170	422	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	NA	2	FACETS	0.93	0.878	0.981			1	INDETERMINATE	2	TRUE	NA	0.674520297687162	2		422	271	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954353	48954353	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	55	343	0	ENST00000267163.4:c.1474G>T	p.Glu492Ter	p.E492*	ENST00000267163	NM_000321.2	492	Gag/Tag	16/27	0.665362548488137	2	FACETS	0.906	0.814	0.994	0.906	0.814	0.994	CLONAL	2	TRUE	0	0.674520297687162	2		343	90	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920597	96920597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779277417	NA	P-0006927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	89	435	0	ENST00000258439.3:c.383G>A	p.Arg128His	p.R128H	ENST00000258439	NM_001193304.2	128	cGc/cAc	3/4	1	2	FACETS	0.851	0.763	0.943	0.851	0.763	0.943	CLONAL	1	TRUE	1	0.674520297687162	2		435	310	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409453	80409453	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	11	242	0	ENST00000286548.4:c.661G>C	p.Glu221Gln	p.E221Q	ENST00000286548	NM_002072.3	221	Gaa/Caa	5/7	1	2	FACETS	0.429	0.301	0.583	0.429	0.301	0.583	SUBCLONAL	1	TRUE	1	0.674520297687162	2		242	76	SUCCESS
BLM	641	MSKCC	GRCh37	15	91298109	91298109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759626611	NA	P-0006927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	50	463	0	ENST00000355112.3:c.1028C>T	p.Ser343Leu	p.S343L	ENST00000355112	NM_000057.2	343	tCa/tTa	5/22	0.672164208819478	2	FACETS	0.815	0.702	0.934	0.407	0.351	0.467	CLONAL	1	TRUE	0	0.674520297687162	2		463	182	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727831	78727831	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	102	540	0	ENST00000306801.3:c.676C>A	p.His226Asn	p.H226N	ENST00000306801	NM_020761.2	226	Cac/Aac	6/34	1	2	FACETS	0.847	0.765	0.933	0.847	0.765	0.933	CLONAL	1	TRUE	1	0.674520297687162	2		540	357	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044719	47044719	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	103	236	0	ENST00000377604.3:c.2119C>T	p.Gln707Ter	p.Q707*	ENST00000377604	NM_001204468.1	707	Cag/Tag	19/24	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.674520297687162	1		236	153	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057661	27057661	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	106	798	0	ENST00000324856.7:c.1369del	p.Gln457LysfsTer162	p.Q457Kfs*162	ENST00000324856	NM_006015.4	457	Caa/aa	3/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.674520297687162	2		798	303	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44921908	44921908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778421870	NA	P-0006963-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	202	398	0	ENST00000377967.4:c.1442G>A	p.Arg481His	p.R481H	ENST00000377967	NM_021140.2	481	cGc/cAc	15/29	1	2	FACETS	0.801	0.743	0.861	0.801	0.743	0.861	CLONAL	1	TRUE	1	0.545941960219118	2		398	924	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255142	16255145	+	frameshift_variant	Frame_Shift_Del	DEL	GAGA	GAGA	-	novel	NA	P-0006963-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	284	410	0	ENST00000375759.3:c.2415_2418del	p.Glu805AspfsTer3	p.E805Dfs*3	ENST00000375759	NM_015001.2	803	GAGAga/ga	11/15	NA	2	FACETS	0.843	0.792	0.896			1	INDETERMINATE	1	TRUE	NA	0.545941960219118	2		410	1234	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075394	8075394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006963-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	367	549	0	ENST00000377482.5:c.176C>T	p.Ser59Phe	p.S59F	ENST00000377482	NM_018948.3	59	tCt/tTt	3/4	NA	2	FACETS	0.915	0.866	0.964			1	INDETERMINATE	1	TRUE	NA	0.545941960219118	2		549	1470	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118365075	118365075	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs886041896	NA	P-0006963-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	249	401	0	ENST00000534358.1:c.5251A>T	p.Lys1751Ter	p.K1751*	ENST00000534358	NM_005933.3	1751	Aaa/Taa	17/36	0.544807351080685	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.545941960219118	1		401	629	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650391	48650391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200509606	NA	P-0006963-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	264	533	1	ENST00000376670.3:c.361G>A	p.Val121Met	p.V121M	ENST00000376670	NM_002049.3	121	Gtg/Atg	3/6	1	2	FACETS	0.99	0.929	1	0.99	0.929	1	CLONAL	1	TRUE	1	0.545941960219118	2		534	977	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264106	16264113	+	frameshift_variant	Frame_Shift_Del	DEL	CCCAGAGA	CCCAGAGA	-	novel	NA	P-0006963-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	230	416	0	ENST00000375759.3:c.10478_10485del	p.Gln3493ArgfsTer23	p.Q3493Rfs*23	ENST00000375759	NM_015001.2	3492	tCCCAGAGA/t	12/15	NA	2	FACETS	0.854	0.796	0.913			1	INDETERMINATE	1	TRUE	NA	0.545941960219118	2		416	987	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098809	178098811	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0006963-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	328	434	0	ENST00000397062.3:c.234_236del	p.Glu79del	p.E79del	ENST00000397062	NM_006164.4	78	gaAGAg/gag	2/5	1	2	FACETS	0.887	0.837	0.938	0.887	0.837	0.938	CLONAL	1	TRUE	1	0.545941960219118	2		434	1355	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0006971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	329	484	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.63259392226257	2		484	1008	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443591	52443617	+	inframe_deletion	In_Frame_Del	DEL	TCGTAGATCTCCTCCACTTGCACCCCC	TCGTAGATCTCCTCCACTTGCACCCCC	-	novel	NA	P-0006971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	190	455	0	ENST00000460680.1:c.75_101del	p.Lys25_Asp34delinsAsn	p.K25_D34delinsN	ENST00000460680	NM_004656.3	25	aaGGGGGTGCAAGTGGAGGAGATCTACGAc/aac	3/17	0.63259392226257	1	FACETS	0.74	0.689	0.792	0.74	0.689	0.792	SUBCLONAL	1	TRUE	0	0.63259392226257	1		455	555	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857896	9857896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369878342	NA	P-0006974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	165	458	0	ENST00000330684.3:c.3505C>T	p.Arg1169Trp	p.R1169W	ENST00000330684	NM_001134407.1	1169	Cgg/Tgg	13/13	0.407067734787393	3	FACETS	1	0.959	1	0.535	0.491	0.581	CLONAL	1	TRUE	1	0.407067734787393	3		458	912	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274911	41274911	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs868651538	NA	P-0006974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	485	469	1	ENST00000349496.5:c.1161T>A	p.Asn387Lys	p.N387K	ENST00000349496	NM_001904.3	387	aaT/aaA	8/15	0.360309694606758	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	0	0.407067734787393	3		470	948	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277955	41277955	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	562	644	0	ENST00000349496.5:c.1919T>G	p.Leu640Arg	p.L640R	ENST00000349496	NM_001904.3	640	cTg/cGg	12/15	0.360309694606758	3	FACETS	0.921	0.887	0.955	0.921	0.887	0.955	CLONAL	3	TRUE	0	0.407067734787393	3		644	1203	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	319	513	0	ENST00000263967.3:c.3132T>G	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaG	21/21	0.233588128924496	3	FACETS	0.877	0.829	0.927	0.877	0.829	0.927	INDETERMINATE	2	TRUE	1	0.407067734787393	3		513	1075	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119894	70119936	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCCAACGGCCACCCGGGGGTGCCGGCCACGCACGGCCAGGT	CGCCCAACGGCCACCCGGGGGTGCCGGCCACGCACGGCCAGGT	-	novel	NA	P-0006974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	276	533	0	ENST00000245479.2:c.897_939del	p.Asn301ThrfsTer68	p.N301Tfs*68	ENST00000245479	NM_000346.3	299	cCGCCCAACGGCCACCCGGGGGTGCCGGCCACGCACGGCCAGGTc/cc	3/3	0.407067734787393	2	FACETS	0.954	0.901	1	0.954	0.901	1	CLONAL	2	TRUE	0	0.407067734787393	2		533	711	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690578	88690578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1021707498	NA	P-0006975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	296	470	2	ENST00000360948.2:c.452G>A	p.Ser151Asn	p.S151N	ENST00000360948	NM_001012338.2	151	aGt/aAt	5/19	0.780708495171444	4	FACETS	0.85	0.804	0.898	0.567	0.536	0.598	CLONAL	2	TRUE	1	0.770069903039263	4		472	800	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0006980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	648	286	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.285840756221533	9	FACETS	0.996	0.968	1	1	0.995	1	CLONAL	9	FALSE	1	0.285840756221533	9		287	1012	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916957	178916957	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200018596	NA	P-0006980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1447	350	670	0	ENST00000263967.3:c.344G>T	p.Arg115Leu	p.R115L	ENST00000263967	NM_006218.2	115	cGa/cTa	2/21	0.285840756221533	8	FACETS	0.844	0.796	0.893	0.362	0.341	0.383	CLONAL	3	FALSE	1	0.285840756221533	8		670	1797	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099403	157099429	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAGCAGCAACAG	CAGCAGCAGCAGCAGCAGCAGCAACAG	-	rs910569810	NA	P-0006980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	141	200	0	ENST00000346085.5:c.360_386del	p.Gln123_Gln131del	p.Q123_Q131del	ENST00000346085	NM_020732.3	114	CAGCAGCAGCAGCAGCAGCAGCAACAG/-	1/20	0.253481535985799	3	FACETS	0.864	0.794	0.936	1	0.984	1	CLONAL	3	FALSE	1	0.285840756221533	3		200	435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0006984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	207	751	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.201483741198401	2	FACETS	0.968	0.9	1	0.968	0.9	1	CLONAL	2	FALSE	0	0.239382099867398	2		753	893	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673738	37673758	+	inframe_deletion	In_Frame_Del	DEL	CAAACTGCCCTACTTCAACAC	CAAACTGCCCTACTTCAACAC	-	novel	NA	P-0006984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	103	438	0	ENST00000447079.4:c.2894_2914del	p.Lys965_Thr971del	p.K965_T971del	ENST00000447079	NM_015083.1	964	atCAAACTGCCCTACTTCAACACc/atc	10/14	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.239382099867398	2		438	727	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0007001-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	297	423	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.260216267623618	3	FACETS	0.992	0.936	1	0.661	0.624	0.7	CLONAL	2	TRUE	0	0.377863331393799	3		424	942	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0007001-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	355	722	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	0.24270971232465	5	FACETS	1	0.979	1	0.712	0.673	0.751	CLONAL	2	TRUE	2	0.377863331393799	5		722	1379	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472523	88472523	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1419472052	NA	P-0007001-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	96	634	0	ENST00000360948.2:c.2032C>T	p.Arg678Ter	p.R678*	ENST00000360948	NM_001012338.2	678	Cga/Tga	16/19	0.160089244333141	2	FACETS	0.474	0.421	0.531	0.237	0.21	0.266	INDETERMINATE	1	TRUE	0	0.377863331393799	2		634	1071	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0007006-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	318	932	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.338692434173156	2	FACETS	0.956	0.907	1	0.956	0.907	1	CLONAL	2	TRUE	0	0.412498785423062	2		934	806	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653796	89653798	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs1554893765	NA	P-0007006-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	82	364	0	ENST00000371953.3:c.97_99del	p.Ile33del	p.I33del	ENST00000371953	NM_000314.4	32	ATT/-	2/9	0.187379835456147	1	FACETS	0.928	0.825	1	0.928	0.825	1	INDETERMINATE	1	TRUE	0	0.412498785423062	1		364	340	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572252	41572254	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0007006-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	91	344	0	ENST00000263253.7:c.4785_4787del	p.Phe1596del	p.F1596del	ENST00000263253	NM_001429.3	1594	gTCTtc/gtc	30/31	0.187379835456147	1	FACETS	0.893	0.799	0.993	0.893	0.799	0.993	INDETERMINATE	1	TRUE	0	0.412498785423062	1		344	392	SUCCESS
APC	324	MSKCC	GRCh37	5	112164620	112164620	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007006-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	67	401	0	ENST00000257430.4:c.1694A>T	p.Glu565Val	p.E565V	ENST00000257430	NM_000038.5	565	gAa/gTa	14/16	0.187379835456147	1	FACETS	0.594	0.518	0.676	0.594	0.518	0.676	INDETERMINATE	1	TRUE	0	0.412498785423062	1		401	434	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0007015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	636	207	0				ENST00000310581	NM_198253.2	-/1132			0.563774868341362	5	FACETS	1	0.991	1	1	0.991	1	CLONAL	4	TRUE	1	0.563760294178087	5		207	991	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0007015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	77	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.563760294178087	5	FACETS	0.773	0.679	0.875	0.258	0.226	0.292	SUBCLONAL	1	TRUE	2	0.563760294178087	5		249	652	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0007015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	783	785	4	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.223710006370241	4	FACETS	0.927	0.903	0.949			1	INDETERMINATE	4	TRUE	NA	0.563760294178087	4		789	1172	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129655	11129655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	532	477	1	ENST00000358026.2:c.2461G>A	p.Glu821Lys	p.E821K	ENST00000358026	NM_001128849.1	821	Gag/Aag	17/36	0.563774868341362	3	FACETS	0.979	0.941	1	0.979	0.941	1	CLONAL	2	TRUE	1	0.563760294178087	3		478	1235	SUCCESS
H3C13	653604	MSKCC	GRCh37	1	149785218	149785218	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1429145694	NA	P-0007015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	29	29	0	ENST00000331491.1:c.19A>G	p.Thr7Ala	p.T7A	ENST00000331491	NM_001123375.2	7	Act/Gct	1/1	0.563774868341362	3	FACETS	0.758	0.627	0.897	0.758	0.627	0.897	SUBCLONAL	2	TRUE	1	0.563760294178087	3		29	87	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193202123	193202123	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	85	165	0	ENST00000367435.3:c.1155A>T	p.Lys385Asn	p.K385N	ENST00000367435	NM_024529.4	385	aaA/aaT	14/17	0.563774868341362	3	FACETS	0.632	0.559	0.709	0.316	0.279	0.355	SUBCLONAL	1	TRUE	1	0.563760294178087	3		165	612	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149616	202149616	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	201	314	0	ENST00000358485.4:c.1057G>A	p.Glu353Lys	p.E353K	ENST00000358485	NM_001080125.1	353	Gag/Aag	8/9	0.563774868341362	3	FACETS	1	0.975	1	0.553	0.514	0.594	CLONAL	1	TRUE	1	0.563760294178087	3		314	826	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158685	26158685	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs747681852	NA	P-0007015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	12	27	0	ENST00000289316.2:c.288G>T	p.Gln96His	p.Q96H	ENST00000289316	NM_138720.2	96	caG/caT	1/2	0.563774868341362	3	FACETS	0.84	0.603	1	0.42	0.301	0.559	CLONAL	1	TRUE	1	0.563760294178087	3		27	65	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672089	30672089	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	128	424	0	ENST00000376406.3:c.4871C>G	p.Ser1624Cys	p.S1624C	ENST00000376406	NM_014641.2	1624	tCc/tGc	10/15	0.563774868341362	3	FACETS	0.639	0.578	0.703	0.319	0.289	0.352	SUBCLONAL	1	TRUE	1	0.563760294178087	3		424	911	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413167	139413167	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	829	474	0	ENST00000277541.6:c.975C>A	p.Asn325Lys	p.N325K	ENST00000277541	NM_017617.3	325	aaC/aaA	6/34	0.557494971271977	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.563760294178087	3		474	1201	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420210	49420210	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	468	422	0	ENST00000301067.7:c.15539T>G	p.Val5180Gly	p.V5180G	ENST00000301067	NM_003482.3	5180	gTg/gGg	48/54	0.563774868341362	3	FACETS	0.956	0.916	0.996	0.956	0.916	0.996	CLONAL	2	TRUE	1	0.563760294178087	3		422	1113	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480419	50480419	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	106	202	0	ENST00000394963.4:c.381G>C	p.Lys127Asn	p.K127N	ENST00000394963	NM_003076.4	127	aaG/aaC	3/13	0.563774868341362	3	FACETS	0.798	0.717	0.884	0.399	0.358	0.442	SUBCLONAL	1	TRUE	1	0.563760294178087	3		202	604	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037915	49037915	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	343	315	1	ENST00000267163.4:c.2155C>T	p.Leu719Phe	p.L719F	ENST00000267163	NM_000321.2	719	Ctt/Ttt	21/27	0.563774868341362	3	FACETS	0.785	0.744	0.826	0.785	0.744	0.826	SUBCLONAL	2	TRUE	1	0.563760294178087	3		316	994	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860619	45860619	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	657	612	1	ENST00000391945.4:c.1388C>T	p.Pro463Leu	p.P463L	ENST00000391945	NM_000400.3	463	cCg/cTg	15/23	0.520926587984307	4	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.563760294178087	4		613	1689	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912919	50912919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	219	636	0	ENST00000440232.2:c.2150C>T	p.Ser717Leu	p.S717L	ENST00000440232	NM_002691.3	717	tCa/tTa	17/27	0.212260009763911	3	FACETS	0.822	0.764	0.883			1	INDETERMINATE	1	TRUE	NA	0.563760294178087	3		636	1211	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087896	27087902	+	frameshift_variant	Frame_Shift_Del	DEL	CACCCAG	CACCCAG	-	novel	NA	P-0007015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	460	362	0	ENST00000324856.7:c.2183_2189del	p.Pro728LeufsTer12	p.P728Lfs*12	ENST00000324856	NM_006015.4	728	cCACCCAGt/ct	6/20	0.563774868341362	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.563760294178087	3		362	1018	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0007036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	367	785	4	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.584181957595658	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.584181957595658	1		789	761	SUCCESS
APC	324	MSKCC	GRCh37	5	112175246	112175246	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1057517558	NA	P-0007036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	323	341	0	ENST00000257430.4:c.3956del	p.Pro1319LeufsTer2	p.P1319Lfs*2	ENST00000257430	NM_000038.5	1319	Cct/ct	16/16	0.584181957595658	2	FACETS	0.994	0.952	1	0.994	0.952	1	CLONAL	2	TRUE	0	0.584181957595658	2		341	556	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86667996	86667996	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs894219060	NA	P-0007036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	174	350	0	ENST00000274376.6:c.1760A>G	p.Asn587Ser	p.N587S	ENST00000274376	NM_002890.2	587	aAt/aGt	13/25	0.584181957595658	2	FACETS	1	0.986	1	0.622	0.578	0.667	CLONAL	1	TRUE	0	0.584181957595658	2		350	479	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534226	534226	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	483	533	0	ENST00000451590.1:c.97G>T	p.Asp33Tyr	p.D33Y	ENST00000451590	NM_001130442.1	33	Gac/Tac	2/5	0.485696183440617	3	FACETS	0.894	0.857	0.932	0.894	0.857	0.932	CLONAL	2	TRUE	1	0.584181957595658	3		533	1195	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40739786	40739786	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1017033490	NA	P-0007036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	294	396	3	ENST00000392038.2:c.1439G>A	p.Arg480His	p.R480H	ENST00000392038	NM_001626.4	480	cGc/cAc	14/14	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.584181957595658	2		399	866	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574725	41574725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1569122710	NA	P-0007036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	385	628	1	ENST00000263253.7:c.7010C>T	p.Pro2337Leu	p.P2337L	ENST00000263253	NM_001429.3	2337	cCa/cTa	31/31	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.584181957595658	2		629	1230	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134598	2134598	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45517340	NA	P-0007059-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	428	262	0	ENST00000219476.3:c.4375C>T	p.Arg1459Ter	p.R1459*	ENST00000219476	NM_000548.3	1459	Cga/Tga	34/42	0.699574029113988	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.699574029113988	2		262	600	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984062	7984062	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007059-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	210	295	0	ENST00000319144.4:c.564C>G	p.Ile188Met	p.I188M	ENST00000319144	NM_001139.2	188	atC/atG	5/15	0.699574029113988	1	FACETS	0.954	0.9	1	0.954	0.9	1	CLONAL	1	TRUE	0	0.699574029113988	1		295	409	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	161	291	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.145497748203753	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.177101823561429	4		291	870	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971177	21971177	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913382	NA	P-0007060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	19	120	0	ENST00000304494.5:c.181G>T	p.Glu61Ter	p.E61*	ENST00000304494	NM_000077.4	61	Gag/Tag	2/3	0.167358878136942	2	FACETS	0.858	0.653	1	0.429	0.326	0.55	CLONAL	1	TRUE	0	0.177101823561429	2		120	250	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0007060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	223	638	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.177101823561429	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.177101823561429	2		638	1060	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024573	14024573	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373570729	NA	P-0007060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	77	238	0	ENST00000311895.7:c.799C>T	p.Arg267Cys	p.R267C	ENST00000311895	NM_005236.2	267	Cgc/Tgc	5/11	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.177101823561429	2		238	773	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699513	117699513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	54	216	2	ENST00000369458.3:c.128C>T	p.Ala43Val	p.A43V	ENST00000369458	NM_024626.3	43	gCc/gTc	3/6	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.177101823561429	2		218	609	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274897	41274897	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	122	282	0	ENST00000349496.5:c.1147T>C	p.Trp383Arg	p.W383R	ENST00000349496	NM_001904.3	383	Tgg/Cgg	8/15	1	2	FACETS	0.885	0.801	0.975	1	0.988	1	CLONAL	2	TRUE	1	0.177101823561429	2		282	778	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936072	44936072	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0007060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	201	220	0	ENST00000377967.4:c.2832+1G>T		p.X944_splice	ENST00000377967	NM_021140.2	944			0.176017978723836	2	FACETS	0.973	0.904	1			1	CLONAL	3	TRUE	NA	0.177101823561429	2		220	778	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044603	47044610	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTGTGTT	GGTGTGTT	-	novel	NA	P-0007060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	162	197	0	ENST00000377604.3:c.2100+2_2100+9del		p.X700_splice	ENST00000377604	NM_001204468.1	700		18/24	0.176017978723836	2	FACETS	0.953	0.878	1			1	CLONAL	3	TRUE	NA	0.177101823561429	2		197	640	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0007097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	76	284	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.406686421049398	2		284	275	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0007097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	135	419	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.406686421049398	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.406686421049398	3		419	378	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0007097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	322	533	1	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	0.406686421049398	5	FACETS	0.95	0.909	0.989			1	CLONAL	5	TRUE	NA	0.406686421049398	5		534	537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0007097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	189	454	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.350302100189088	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.406686421049398	2		454	407	SUCCESS
APC	324	MSKCC	GRCh37	5	112175525	112175525	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	44	329	0	ENST00000257430.4:c.4234G>T	p.Gly1412Ter	p.G1412*	ENST00000257430	NM_000038.5	1412	Gga/Tga	16/16	NA	2	FACETS	0.917	0.776	1			1	INDETERMINATE	1	TRUE	NA	0.406686421049398	2		329	236	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729603	41729603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	96	564	0	ENST00000242208.4:c.926G>A	p.Arg309Gln	p.R309Q	ENST00000242208	NM_002192.2	309	cGg/cAg	3/3	0.285402505030721	5	FACETS	0.968	0.862	1	0.323	0.287	0.361	CLONAL	1	TRUE	2	0.406686421049398	5		564	785	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337660	73337660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	36	312	0	ENST00000377767.4:c.2056G>A	p.Ala686Thr	p.A686T	ENST00000377767	NM_014953.3	686	Gct/Act	16/21	0.406686421049398	7	FACETS	0.569	0.466	0.684	0.142	0.116	0.171	SUBCLONAL	1	TRUE	3	0.406686421049398	7		312	628	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841258	15841258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763087055	NA	P-0007097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	117	473	0	ENST00000307771.7:c.1342C>T	p.Arg448Cys	p.R448C	ENST00000307771	NM_005089.3	448	Cgc/Tgc	11/11	0.251717354329678	4	FACETS	1	0.937	1			1	CLONAL	1	TRUE	NA	0.406686421049398	4		473	770	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0007100-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	70	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.962	0.843	1	0.962	0.843	1	CLONAL	1	TRUE	1	0.368275259096652	2		249	395	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55269434	55269434	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1420042114	NA	P-0007100-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	164	383	0	ENST00000275493.2:c.3121A>G	p.Thr1041Ala	p.T1041A	ENST00000275493	NM_005228.3	1041	Acc/Gcc	26/28	1	2	FACETS	0.913	0.838	0.992	0.913	0.838	0.992	CLONAL	1	TRUE	1	0.368275259096652	2		383	975	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142524	119142524	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007100-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	122	383	2	ENST00000264033.4:c.523C>T	p.Gln175Ter	p.Q175*	ENST00000264033	NM_005188.3	175	Cag/Tag	3/16	1	2	FACETS	0.833	0.753	0.918	0.833	0.753	0.918	CLONAL	1	TRUE	1	0.368275259096652	2		385	795	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112555	115112555	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007100-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	286	282	0	ENST00000257566.3:c.1185del	p.Ser396ProfsTer236	p.S396Pfs*236	ENST00000257566	NM_016569.3	395	atC/at	7/8	0.368275259096652	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.368275259096652	2		282	657	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849643	68849649	+	frameshift_variant	Frame_Shift_Del	DEL	TTTATGG	TTTATGG	-	novel	NA	P-0007100-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	132	378	0	ENST00000261769.5:c.1546_1552del	p.Phe516AsnfsTer4	p.F516Nfs*4	ENST00000261769	NM_004360.3	516	TTTATGGaa/aa	10/16	0.368275259096652	1	FACETS	0.851	0.774	0.932	0.851	0.774	0.932	CLONAL	1	TRUE	0	0.368275259096652	1		378	687	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	43	484	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.673	0.561	0.798	0.673	0.561	0.798	SUBCLONAL	1	TRUE	1	0.15	2		484	852	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0007116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	42	439	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.735	0.612	0.872	0.735	0.612	0.872	SUBCLONAL	1	TRUE	1	0.15	2		440	762	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573506	41573506	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	513	587	3	ENST00000263253.7:c.5791C>T	p.Gln1931Ter	p.Q1931*	ENST00000263253	NM_001429.3	1931	Cag/Tag	31/31	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.856640786825896	2		590	1187	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0007142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	47	261	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.205892165758341	3	FACETS	1	0.934	1	0.606	0.511	0.709	CLONAL	1	TRUE	1	0.18	3		261	470	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814938	139814938	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	30	696	0	ENST00000247668.2:c.931C>T	p.Gln311Ter	p.Q311*	ENST00000247668	NM_021138.3	311	Caa/Taa	8/11	0.127348009802343	1	FACETS	0.685	0.551	0.836	0.685	0.551	0.836	SUBCLONAL	1	TRUE	0	0.18	1		696	443	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205765	108205765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555127157	NA	P-0007142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	28	379	0	ENST00000278616.4:c.8080G>A	p.Gly2694Arg	p.G2694R	ENST00000278616	NM_000051.3	2694	Gga/Aga	55/63	1	2	FACETS	0.812	0.649	0.998	0.812	0.649	0.998	CLONAL	1	TRUE	1	0.18	2		379	383	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919665	28919665	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	27	491	0	ENST00000282397.4:c.2272G>A	p.Glu758Lys	p.E758K	ENST00000282397	NM_002019.4	758	Gag/Aag	16/30	1	2	FACETS	0.709	0.564	0.876	0.709	0.564	0.876	SUBCLONAL	1	TRUE	1	0.18	2		491	423	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500376	99500376	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	28	546	0	ENST00000268035.6:c.3809T>G	p.Met1270Arg	p.M1270R	ENST00000268035	NM_000875.3	1270	aTg/aGg	21/21	1	2	FACETS	0.852	0.681	1	0.852	0.681	1	CLONAL	1	TRUE	1	0.18	2		546	365	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476301	88476301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	183	463	0	ENST00000360948.2:c.1831G>A	p.Asp611Asn	p.D611N	ENST00000360948	NM_001012338.2	611	Gac/Aac	15/19	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.25	2		463	1040	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298200	123298200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	90	379	0	ENST00000358487.5:c.654G>A	p.Met218Ile	p.M218I	ENST00000358487	NM_000141.4	218	atG/atA	6/18	1	2	FACETS	0.922	0.817	1	0.922	0.817	1	CLONAL	1	TRUE	1	0.25	2		379	781	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777859	27777859	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1404	225	1553	2	ENST00000369163.2:c.8G>T	p.Arg3Leu	p.R3L	ENST00000369163	NM_003536.2	3	cGt/cTt	1/1	1	2	FACETS	0.895	0.831	0.962	0.895	0.831	0.962	CLONAL	1	TRUE	1	0.308645495647069	2		1555	1629	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779649	3779649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	221	817	1	ENST00000262367.5:c.5399G>A	p.Arg1800Gln	p.R1800Q	ENST00000262367	NM_004380.2	1800	cGg/cAg	31/31	0.262039663566506	2	FACETS	0.858	0.8	0.917	0.858	0.8	0.917	CLONAL	2	TRUE	0	0.308645495647069	2		818	835	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	154	864	0	ENST00000269305.4:c.329del	p.Arg110LeufsTer13	p.R110Lfs*13	ENST00000269305	NM_001126112.2	110	cGt/ct	4/11	0.22481334878778	1	FACETS	0.809	0.739	0.882	0.809	0.739	0.882	CLONAL	1	TRUE	0	0.308645495647069	1		864	1043	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797942	45797944	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0007159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	143	1057	0	ENST00000450313.1:c.827_829del	p.Gly276del	p.G276del	ENST00000450313	NM_012222.2	276	gGAGat/gat	10/16	1	2	FACETS	0.77	0.7	0.843	0.77	0.7	0.843	SUBCLONAL	1	TRUE	1	0.308645495647069	2		1057	1204	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0007162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	235	295	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.3	3	FACETS	0.949	0.887	1	0.949	0.887	1	CLONAL	2	TRUE	1	0.33	3		295	874	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0007162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	119	346	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	1	2	FACETS	0.977	0.883	1	0.977	0.883	1	CLONAL	1	TRUE	1	0.33	2		346	738	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0007162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	115	519	2	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.774	0.697	0.857	0.774	0.697	0.857	SUBCLONAL	1	TRUE	1	0.33	2		521	900	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048131	180048131	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	48	368	1	ENST00000261937.6:c.2142C>A	p.Asp714Glu	p.D714E	ENST00000261937	NM_182925.4	714	gaC/gaA	14/30	1	2	FACETS	0.382	0.322	0.449	0.382	0.322	0.449	SUBCLONAL	1	TRUE	1	0.33	2		369	761	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863224683	NA	P-0007162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	260	378	0	ENST00000269305.4:c.388C>T	p.Leu130Phe	p.L130F	ENST00000269305	NM_001126112.2	130	Ctc/Ttc	5/11	0.297389245529118	2	FACETS	0.859	0.806	0.913	0.859	0.806	0.913	CLONAL	2	TRUE	0	0.33	2		378	917	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979435	2979435	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	131	409	0	ENST00000396946.4:c.812G>A	p.Arg271Gln	p.R271Q	ENST00000396946	NM_032415.4	271	cGg/cAg	6/25	0.27787315596361	4	FACETS	0.86	0.778	0.946	0.287	0.259	0.316	CLONAL	1	TRUE	1	0.33	4		409	1228	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0007178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	158	375	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.179505124379848	3	FACETS	0.974	0.897	1	0.649	0.598	0.703	INDETERMINATE	2	FALSE	0	0.322609999247234	3		378	584	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446317	29446317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768123237	NA	P-0007178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1222	152	512	2	ENST00000389048.3:c.3250C>T	p.Arg1084Cys	p.R1084C	ENST00000389048	NM_004304.4	1084	Cgc/Tgc	20/29	0.285741612874817	3	FACETS	0.796	0.726	0.871	0.398	0.363	0.436	SUBCLONAL	1	FALSE	1	0.322609999247234	3		514	1374	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390198	89390198	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	67	328	0	ENST00000336596.2:c.947A>C	p.Asp316Ala	p.D316A	ENST00000336596	NM_005233.5	316	gAc/gCc	4/17	NA	2	FACETS	0.535	0.464	0.612			1	INDETERMINATE	1	FALSE	NA	0.322609999247234	2		328	776	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627271	37627271	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	164	387	0	ENST00000447079.4:c.1186G>T	p.Gly396Ter	p.G396*	ENST00000447079	NM_015083.1	396	Gga/Tga	2/14	0.228675402291142	4	FACETS	0.77	0.707	0.836	0.77	0.707	0.836	SUBCLONAL	2	FALSE	2	0.322609999247234	4		387	873	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699374	47699374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	195	380	0	ENST00000347630.2:c.134G>T	p.Arg45Leu	p.R45L	ENST00000347630	NM_001007230.1	45	cGg/cTg	4/11	0.163064871601227	4	FACETS	0.772	0.714	0.833	0.772	0.714	0.833	INDETERMINATE	2	FALSE	2	0.322609999247234	4		380	1035	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984166	2984166	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	48	116	0	ENST00000396946.4:c.364del	p.Glu122LysfsTer10	p.E122Kfs*10	ENST00000396946	NM_032415.4	122	Gaa/aa	5/25	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	FALSE	1	0.322609999247234	2		116	272	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71161689	71161689	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	112	301	0	ENST00000318789.4:c.280del	p.Gln94ArgfsTer8	p.Q94Rfs*8	ENST00000318789	NM_032682.5	94	Cag/ag	7/21	0.228675402291142	4	FACETS	1	0.976	1	0.641	0.577	0.709	CLONAL	1	FALSE	2	0.322609999247234	4		301	716	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209106719	209106719	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	234	473	0	ENST00000345146.2:c.849A>C	p.Gln283His	p.Q283H	ENST00000345146	NM_005896.2	283	caA/caC	7/10	0.364881531850139	3	FACETS	1	0.99	1	0.679	0.633	0.727	CLONAL	1	TRUE	1	0.364881531850139	3		473	1117	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178158	142178158	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	61	372	0	ENST00000350721.4:c.7260A>T	p.Lys2420Asn	p.K2420N	ENST00000350721	NM_001184.3	2420	aaA/aaT	43/47	1	2	FACETS	0.53	0.457	0.61	0.53	0.457	0.61	SUBCLONAL	1	TRUE	1	0.364881531850139	2		372	631	SUCCESS
APC	324	MSKCC	GRCh37	5	112174268	112174268	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0007185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	185	547	0	ENST00000257430.4:c.2977A>T	p.Lys993Ter	p.K993*	ENST00000257430	NM_000038.5	993	Aag/Tag	16/16	0.364881531850139	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.364881531850139	1		547	737	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638915	176638915	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1354	125	552	0	ENST00000439151.2:c.3515A>C	p.Lys1172Thr	p.K1172T	ENST00000439151	NM_022455.4	1172	aAg/aCg	5/23	0.313321384138324	4	FACETS	0.632	0.57	0.698	0.316	0.285	0.349	SUBCLONAL	1	TRUE	2	0.364881531850139	4		552	1479	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332799	152332799	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	227	580	0	ENST00000206249.3:c.1105G>T	p.Asp369Tyr	p.D369Y	ENST00000206249	NM_000125.3	369	Gat/Tat	5/8	0.230014918721312	4	FACETS	1	0.991	1	0.709	0.659	0.76	CLONAL	1	TRUE	2	0.364881531850139	4		580	1198	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683641	162683641	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	135	538	0	ENST00000366898.1:c.328T>A	p.Ser110Thr	p.S110T	ENST00000366898	NM_004562.2	110	Tca/Aca	3/12	0.230014918721312	4	FACETS	0.888	0.806	0.976	0.444	0.403	0.488	CLONAL	1	TRUE	2	0.364881531850139	4		538	1137	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740417	145740417	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1307	113	460	0	ENST00000428558.2:c.1523A>C	p.Lys508Thr	p.K508T	ENST00000428558	NM_004260.3	508	aAg/aCg	9/22	0.364881531850139	6	FACETS	0.754	0.676	0.838	0.151	0.135	0.168	SUBCLONAL	1	TRUE	1	0.364881531850139	6		460	1420	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447842	49447842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1280814073	NA	P-0007185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	124	451	0	ENST00000301067.7:c.592G>A	p.Ala198Thr	p.A198T	ENST00000301067	NM_003482.3	198	Gcg/Acg	5/54	0.344836158847722	2	FACETS	0.658	0.594	0.726	0.329	0.297	0.363	SUBCLONAL	1	TRUE	0	0.364881531850139	2		451	1033	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023366	31023366	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	124	404	0	ENST00000375687.4:c.2851G>C	p.Asp951His	p.D951H	ENST00000375687	NM_015338.5	951	Gat/Cat	13/13	0.248655108056803	5	FACETS	0.948	0.856	1	0.316	0.285	0.349	CLONAL	1	TRUE	2	0.364881531850139	5		404	1109	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945293	54945293	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	52	215	0	ENST00000312783.6:c.1133T>G	p.Leu378Arg	p.L378R	ENST00000312783	NM_198436.1	378	cTt/cGt	10/10	0.248655108056803	5	FACETS	0.76	0.647	0.885	0.253	0.215	0.295	SUBCLONAL	1	TRUE	2	0.364881531850139	5		215	580	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579427	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGGCTG	GGGGGCTG	-	novel	NA	P-0007185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	377	521	0	ENST00000269305.4:c.260_267del	p.Pro87LeufsTer59	p.P87Lfs*59	ENST00000269305	NM_001126112.2	87	cCAGCCCCC/c	4/11	0.344836158847722	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.364881531850139	2		521	968	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925597	114925597	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1535	292	853	3	ENST00000543371.1:c.1679del	p.Pro560GlnfsTer42	p.P560Qfs*42	ENST00000543371	NM_001198531.1	559	Ccc/cc	14/14	0.148229773193055	2	FACETS	0.876	0.821	0.933	0.438	0.41	0.467	INDETERMINATE	1	TRUE	0	0.364881531850139	2		856	1827	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940384	49940384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749581478	NA	P-0007223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	656	832	0	ENST00000296474.3:c.659G>A	p.Arg220His	p.R220H	ENST00000296474	NM_002447.2	220	cGt/cAt	1/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.806080040759653	2		832	1599	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577256	64577266	+	frameshift_variant	Frame_Shift_Del	DEL	TCTCGAGGATA	TCTCGAGGATA	-	novel	NA	P-0007223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	530	725	4	ENST00000312049.6:c.316_326del	p.Tyr106ArgfsTer7	p.Y106Rfs*7	ENST00000312049	NM_130799.2	106	TATCCTCGAGAa/a	2/10	0.806080040759653	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.806080040759653	1		729	784	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	43	246	0				ENST00000310581	NM_198253.2	-/1132			0.855006949372871	1	FACETS	0.559	0.483	0.637	0.559	0.483	0.637	SUBCLONAL	1	TRUE	0	0.855006949372871	1		246	103	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0007224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	736	551	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	0.691820679944593	6	FACETS	1	0.986	1			1	CLONAL	5	TRUE	NA	0.855006949372871	6		551	925	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549464	21549464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	150	193	0	ENST00000382592.4:c.2812G>A	p.Val938Met	p.V938M	ENST00000382592	NM_014572.2	938	Gtg/Atg	8/8	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.855006949372871	2		193	236	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929602	44929602	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	245	426	0	ENST00000377967.4:c.2702G>C	p.Arg901Thr	p.R901T	ENST00000377967	NM_021140.2	901	aGg/aCg	17/29	0.187684378201882	2	FACETS	1	0.989	1	0.593	0.561	0.625	INDETERMINATE	1	TRUE	0	0.855006949372871	2		426	483	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197903	123197903	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0007224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	269	510	1	ENST00000218089.9:c.2025+2T>A		p.X675_splice	ENST00000218089	NM_001042749.1	675			0.187684378201882	2	FACETS	1	0.991	1	0.61	0.579	0.64	INDETERMINATE	1	TRUE	0	0.855006949372871	2		511	516	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0007275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	231	253	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	0.720286667467599	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.720286667467599	1		253	371	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0007275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	269	295	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	0.942	0.887	0.998	0.942	0.887	0.998	CLONAL	1	TRUE	1	0.720286667467599	2		295	793	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087961	27087961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	282	400	0	ENST00000324856.7:c.2248C>T	p.Arg750Ter	p.R750*	ENST00000324856	NM_006015.4	750	Cga/Tga	6/20	0.720286667467599	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.720286667467599	1		400	452	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729154	66729154	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519731	NA	P-0007275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	336	454	0	ENST00000307102.5:c.362G>C	p.Cys121Ser	p.C121S	ENST00000307102	NM_002755.3	121	tGc/tCc	3/11	1	2	FACETS	0.938	0.889	0.988	0.938	0.889	0.988	CLONAL	1	TRUE	1	0.720286667467599	2		454	995	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847282	68847282	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	415	626	1	ENST00000261769.5:c.1204G>T	p.Asp402Tyr	p.D402Y	ENST00000261769	NM_004360.3	402	Gat/Tat	9/16	1	2	FACETS	0.927	0.883	0.972	0.927	0.883	0.972	CLONAL	1	TRUE	1	0.720286667467599	2		627	1243	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044472	47044472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556781457	NA	P-0007275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	445	285	1	ENST00000377604.3:c.1969C>T	p.Arg657Cys	p.R657C	ENST00000377604	NM_001204468.1	657	Cgc/Tgc	18/24	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.720286667467599	1		286	644	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068390	26068393	+	frameshift_variant	Frame_Shift_Del	DEL	TTTC	TTTC	-	novel	NA	P-0007275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	249	575	0	ENST00000435504.4:c.97_100del	p.Glu33PhefsTer10	p.E33Ffs*10	ENST00000435504		33	GAAAtt/tt	2/13	1	2	FACETS	0.954	0.896	1	0.954	0.896	1	CLONAL	1	TRUE	1	0.720286667467599	2		575	725	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678454	88678468	+	inframe_deletion	In_Frame_Del	DEL	CCCTCGGAAATCTCT	CCCTCGGAAATCTCT	-	novel	NA	P-0007275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	420	667	0	ENST00000360948.2:c.1068_1082del	p.Glu357_Gly361del	p.E357_G361del	ENST00000360948	NM_001012338.2	356	ggAGAGATTTCCGAGGGc/ggc	9/19	1	2	FACETS	0.903	0.861	0.947	0.903	0.861	0.947	CLONAL	1	TRUE	1	0.720286667467599	2		667	1291	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522198	157522198	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	233	345	0	ENST00000346085.5:c.4472del	p.Pro1491GlnfsTer3	p.P1491Qfs*3	ENST00000346085	NM_020732.3	1490	taC/ta	18/20	0.110925120101626	3	FACETS	1	0.989	1	0.632	0.592	0.673	INDETERMINATE	1	TRUE	1	0.720286667467599	3		345	696	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0007304-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	74	286	1	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		287	1054	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0007314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	186	207	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		207	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0007315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	223	554	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.39734150088355	2	FACETS	0.858	0.803	0.914	0.858	0.803	0.914	CLONAL	2	TRUE	0	0.39734150088355	2		554	654	SUCCESS
APC	324	MSKCC	GRCh37	5	112174814	112174814	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085081	NA	P-0007315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	176	465	0	ENST00000257430.4:c.3523C>T	p.Gln1175Ter	p.Q1175*	ENST00000257430	NM_000038.5	1175	Cag/Tag	16/16	0.39734150088355	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	1	0.39734150088355	3		465	519	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708054	117708054	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	143	459	1	ENST00000368508.3:c.2123C>T	p.Ser708Leu	p.S708L	ENST00000368508	NM_002944.2	708	tCa/tTa	14/43	0.39734150088355	3	FACETS	1	0.986	1	0.71	0.649	0.772	CLONAL	1	TRUE	1	0.39734150088355	3		460	608	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807902	3807902	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	102	479	2	ENST00000262367.5:c.3517C>T	p.Arg1173Ter	p.R1173*	ENST00000262367	NM_004380.2	1173	Cga/Tga	18/31	0.33726006622394	3	FACETS	1	0.913	1	0.51	0.457	0.567	CLONAL	1	TRUE	1	0.39734150088355	3		481	603	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	106	291	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	0.417208735895719	2		291	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0007338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	188	328	2	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.318765743189969	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.417208735895719	1		330	535	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670813	134670813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765851482	NA	P-0007338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	45	231	0	ENST00000398015.3:c.724G>A	p.Gly242Arg	p.G242R	ENST00000398015	NM_004441.4	242	Ggg/Agg	3/16	0.166472281057848	1	FACETS	0.545	0.46	0.638	0.545	0.46	0.638	INDETERMINATE	1	TRUE	0	0.417208735895719	1		231	313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882025	NA	P-0007348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	65	492	0	ENST00000269305.4:c.646G>C	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ctg	6/11	0.151328652548256	2	FACETS	0.924	0.801	1	0.462	0.4	0.529	CLONAL	1	FALSE	0	0.241345968937012	2		492	583	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61749745	61749745	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0007348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	39	418	0	ENST00000401558.2:c.301+1G>C		p.X101_splice	ENST00000401558	NM_003400.3	101			1	2	FACETS	0.676	0.56	0.805	0.676	0.56	0.805	SUBCLONAL	1	FALSE	1	0.241345968937012	2		418	478	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641493	23641493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs71379822	NA	P-0007348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	37	474	0	ENST00000261584.4:c.1982C>T	p.Pro661Leu	p.P661L	ENST00000261584	NM_024675.3	661	cCt/cTt	5/13	1	2	FACETS	0.571	0.47	0.684	0.571	0.47	0.684	SUBCLONAL	1	FALSE	1	0.241345968937012	2		474	537	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0007364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	206	419	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.946	0.88	1	0.946	0.88	1	CLONAL	1	TRUE	1	0.569101596262815	2		419	765	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243999	53243999	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	286	452	4	ENST00000375401.3:c.994C>T	p.Arg332Ter	p.R332*	ENST00000375401	NM_004187.3	332	Cga/Tga	8/26	0.569101596262815	1	FACETS	0.916	0.865	0.968	0.916	0.865	0.968	CLONAL	1	TRUE	0	0.569101596262815	1		456	785	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912188	114912188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	333	607	0	ENST00000543371.1:c.1258C>T	p.Arg420Trp	p.R420W	ENST00000543371	NM_001198531.1	420	Cgg/Tgg	11/14	0.425133324963209	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.425133324963209	2		607	742	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0007380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	118	288	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.425133324963209	2	FACETS	0.89	0.814	0.967	0.89	0.814	0.967	CLONAL	2	TRUE	0	0.425133324963209	2		288	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs28934577	NA	P-0007380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	163	285	0	ENST00000269305.4:c.770T>G	p.Leu257Arg	p.L257R	ENST00000269305	NM_001126112.2	257	cTg/cGg	7/11	0.425133324963209	2	FACETS	0.996	0.926	1	0.996	0.926	1	CLONAL	2	TRUE	0	0.425133324963209	2		285	385	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248657	59248657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762323939	NA	P-0007380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	93	400	1	ENST00000371222.2:c.86G>A	p.Ser29Asn	p.S29N	ENST00000371222	NM_002228.3	29	aGt/aAt	1/1	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.425133324963209	2		401	410	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022357	12022357	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0007380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	126	550	0	ENST00000396373.4:c.464-1G>A		p.X155_splice	ENST00000396373	NM_001987.4	155			0.425133324963209	2	FACETS	0.925	0.839	1	0.462	0.419	0.507	CLONAL	1	TRUE	0	0.425133324963209	2		550	641	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808929	3808929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	85	359	0	ENST00000262367.5:c.3295G>A	p.Glu1099Lys	p.E1099K	ENST00000262367	NM_004380.2	1099	Gaa/Aaa	17/31	0.405073491358148	3	FACETS	0.86	0.761	0.965	0.43	0.38	0.483	CLONAL	1	TRUE	1	0.425133324963209	3		359	564	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527441	29527441	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	34	260	0	ENST00000356175.3:c.890A>C	p.Lys297Thr	p.K297T	ENST00000356175	NM_000267.3	297	aAg/aCg	9/57	0.405073491358148	3	FACETS	0.882	0.726	1	0.441	0.363	0.527	CLONAL	1	TRUE	1	0.425133324963209	3		260	220	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0007381-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	551	638	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.50873441037025	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.50873441037025	2		638	1029	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516851	187516851	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007381-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	45	284	0	ENST00000441802.2:c.13130A>T	p.Asp4377Val	p.D4377V	ENST00000441802	NM_005245.3	4377	gAt/gTt	26/27	0.325425519707951	1	FACETS	0.291	0.245	0.343	0.291	0.245	0.343	SUBCLONAL	1	TRUE	0	0.50873441037025	1		284	453	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628224	187628224	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007381-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	58	361	0	ENST00000441802.2:c.2758G>A	p.Val920Ile	p.V920I	ENST00000441802	NM_005245.3	920	Gtt/Att	2/27	0.325425519707951	1	FACETS	0.39	0.336	0.449	0.39	0.336	0.449	SUBCLONAL	1	TRUE	0	0.50873441037025	1		361	436	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963132	38963132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167728976	NA	P-0007381-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	51	336	0	ENST00000357387.3:c.1412C>T	p.Ala471Val	p.A471V	ENST00000357387	NM_152756.3	471	gCa/gTa	17/38	0.325425519707951	1	FACETS	0.484	0.413	0.56	0.484	0.413	0.56	SUBCLONAL	1	TRUE	0	0.50873441037025	1		336	309	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227868	55227868	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007381-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4535	5010	385	0	ENST00000275493.2:c.1335A>G	p.Ile445Met	p.I445M	ENST00000275493	NM_005228.3	445	atA/atG	12/28	0.50873441037025	44	FACETS	1	0.992	1			1	CLONAL	24	TRUE	NA	0.50873441037025	44		385	9545	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348215	348215	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1407100371	NA	P-0007381-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	45	266	0	ENST00000262320.3:c.1291C>T	p.Pro431Ser	p.P431S	ENST00000262320	NM_003502.3	431	Ccc/Tcc	6/11	NA	2	FACETS	0.274	0.229	0.323			1	INDETERMINATE	1	TRUE	NA	0.50873441037025	2		266	646	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412898	49412898	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519954	NA	P-0007386-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	447	755	0	ENST00000418115.1:c.125A>G	p.Tyr42Cys	p.Y42C	ENST00000418115	NM_001664.2	42	tAt/tGt	2/5	0.290123298411938	2	FACETS	0.879	0.837	0.921	0.879	0.837	0.921	CLONAL	2	TRUE	0	0.32	2		755	1590	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740128	162740128	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007386-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	85	482	0	ENST00000367921.3:c.1330A>C	p.Ser444Arg	p.S444R	ENST00000367921	NM_006182.2	444	Agc/Cgc	12/18	0.268501690534294	3	FACETS	0.547	0.482	0.617	0.273	0.241	0.309	SUBCLONAL	1	TRUE	1	0.32	3		482	1127	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606788	43606788	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007386-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	280	587	0	ENST00000355710.3:c.1397T>C	p.Phe466Ser	p.F466S	ENST00000355710	NM_020975.4	466	tTt/tCt	7/20	0.250705015784127	2	FACETS	0.808	0.759	0.858	0.808	0.759	0.858	CLONAL	2	TRUE	0	0.32	2		587	1083	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578496	7578496	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587782197	NA	P-0007386-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	315	519	2	ENST00000269305.4:c.434T>A	p.Leu145Gln	p.L145Q	ENST00000269305	NM_001126112.2	145	cTg/cAg	5/11	0.279434752701462	2	FACETS	0.893	0.843	0.944	0.893	0.843	0.944	CLONAL	2	TRUE	0	0.32	2		521	1102	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546725	9546725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210292896	NA	P-0007386-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	278	392	1	ENST00000353224.5:c.1297C>T	p.Arg433Trp	p.R433W	ENST00000353224	NM_177990.2	433	Cgg/Tgg	5/10	0.270011915238726	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.32	4		393	1035	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528971	157528972	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0007386-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	193	295	0	ENST00000346085.5:c.6700_6701del	p.Leu2234GlyfsTer7	p.L2234Gfs*7	ENST00000346085	NM_020732.3	2232	aaCTct/aact	20/20	0.279434752701462	2	FACETS	0.874	0.812	0.938	0.874	0.812	0.938	CLONAL	2	TRUE	0	0.32	2		295	690	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0007398-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	105	265	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.31470803200863	6	FACETS	1	0.945	1	0.538	0.484	0.595	CLONAL	2	TRUE	2	0.31470803200863	6		265	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0007398-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	171	423	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.31470803200863	2	FACETS	0.919	0.857	0.982	1	0.99	1	CLONAL	3	TRUE	0	0.31470803200863	2		424	394	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735467	40735467	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776642212	NA	P-0007398-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	235	342	1	ENST00000373198.4:c.3406C>T	p.Arg1136Cys	p.R1136C	ENST00000373198	NM_133170.3	1136	Cgt/Tgt	25/32	0.31470803200863	5	FACETS	0.978	0.916	1	0.978	0.916	1	CLONAL	3	TRUE	2	0.31470803200863	5		343	749	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591254	67591254	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007398-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	83	252	0	ENST00000274335.5:c.1752G>T	p.Leu584Phe	p.L584F	ENST00000274335		584	ttG/ttT	13/15	0.252445112483648	5	FACETS	1	0.966	1	0.814	0.725	0.907	CLONAL	2	TRUE	2	0.31470803200863	5		252	318	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163898	152163898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007398-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	165	321	0	ENST00000206249.3:c.619G>A	p.Ala207Thr	p.A207T	ENST00000206249	NM_000125.3	207	Gcc/Acc	2/8	0.31470803200863	5	FACETS	1	0.934	1	1	0.99	1	CLONAL	3	TRUE	3	0.31470803200863	5		321	509	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371718	55371718	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007398-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	548	279	0	ENST00000297316.4:c.408G>C	p.Lys136Asn	p.K136N	ENST00000297316	NM_022454.3	136	aaG/aaC	2/2	0.31470803200863	15	FACETS	0.974	0.944	1			1	CLONAL	13	TRUE	NA	0.31470803200863	15		279	838	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0007399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	46	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.477060706335701	5	FACETS	0.885	0.747	1	0.295	0.249	0.346	CLONAL	1	TRUE	2	0.477060706335701	5		249	374	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191488	10191488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs5030818	NA	P-0007399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	371	224	0	ENST00000256474.2:c.481C>T	p.Arg161Ter	p.R161*	ENST00000256474	NM_000551.3	161	Cga/Tga	3/3	0.477060706335701	3	FACETS	0.928	0.889	0.967	0.928	0.889	0.967	CLONAL	3	TRUE	0	0.477060706335701	3		224	692	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552837	106552837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1399614609	NA	P-0007399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	258	465	2	ENST00000369096.4:c.802C>T	p.Arg268Cys	p.R268C	ENST00000369096	NM_001198.3	268	Cgt/Tgt	5/7	1	2	FACETS	0.982	0.919	1	0.982	0.919	1	CLONAL	1	TRUE	1	0.477060706335701	2		467	1102	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806171	1806171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542210035	NA	P-0007402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	184	503	1	ENST00000260795.2:c.1190G>A	p.Arg397His	p.R397H	ENST00000260795		397	cGc/cAc	8/17	NA	2	FACETS	0.77	0.712	0.83			1	INDETERMINATE	1	TRUE	NA	0.604521154207356	2		504	791	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696450	47696450	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	278	366	0	ENST00000347630.2:c.373T>G	p.Phe125Val	p.F125V	ENST00000347630	NM_001007230.1	125	Ttt/Gtt	6/11	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.604521154207356	2		366	725	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444377	49444377	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1057519595	NA	P-0007402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	119	258	1	ENST00000301067.7:c.2994del	p.Met999Ter	p.M999*	ENST00000301067	NM_003482.3	998	ccT/cc	11/54	1	2	FACETS	0.841	0.764	0.922	0.841	0.764	0.922	CLONAL	1	TRUE	1	0.604521154207356	2		259	468	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	194	291	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.219913832729783	4	FACETS	1	0.976	1	0.741	0.688	0.795	CLONAL	2	TRUE	1	0.345503339692025	4		291	680	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0007405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	69	154	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.345503339692025	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	2	TRUE	0	0.345503339692025	2		154	196	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591888	48591888	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	258	472	0	ENST00000342988.3:c.1051G>T	p.Asp351Tyr	p.D351Y	ENST00000342988	NM_005359.5	351	Gat/Tat	9/12	0.345503339692025	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.345503339692025	2		472	661	SUCCESS
APC	324	MSKCC	GRCh37	5	112174112	112174112	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	133	341	0	ENST00000257430.4:c.2821G>T	p.Glu941Ter	p.E941*	ENST00000257430	NM_000038.5	941	Gaa/Taa	16/16	0.234736272680782	4	FACETS	0.972	0.887	1	0.972	0.887	1	CLONAL	2	TRUE	2	0.345503339692025	4		341	533	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096319	178096319	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	246	337	0	ENST00000397062.3:c.1012G>T	p.Glu338Ter	p.E338*	ENST00000397062	NM_006164.4	338	Gaa/Taa	5/5	0.219913832729783	4	FACETS	0.838	0.786	0.891	0.838	0.786	0.891	CLONAL	3	TRUE	1	0.345503339692025	4		337	762	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155022	55155022	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	98	363	0	ENST00000257290.5:c.2731A>T	p.Ser911Cys	p.S911C	ENST00000257290	NM_006206.4	911	Agt/Tgt	20/23	0.34208615481659	3	FACETS	0.889	0.793	0.992	0.445	0.396	0.496	CLONAL	1	TRUE	1	0.345503339692025	3		363	748	SUCCESS
APC	324	MSKCC	GRCh37	5	112176023	112176024	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs863225359	NA	P-0007405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	145	255	0	ENST00000257430.4:c.4733_4734del	p.Cys1578TyrfsTer12	p.C1578Yfs*12	ENST00000257430	NM_000038.5	1578	TGt/t	16/16	0.234736272680782	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.345503339692025	4		255	492	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0007419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	25	649	2	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.712	0.56	0.889	0.712	0.56	0.889	SUBCLONAL	1	TRUE	1	0.13	2		651	540	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	22	484	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.695	0.537	0.879	0.695	0.537	0.879	SUBCLONAL	1	TRUE	1	0.13	2		484	487	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674233	86674233	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1463885690	NA	P-0007419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	20	288	1	ENST00000274376.6:c.2365C>T	p.Arg789Ter	p.R789*	ENST00000274376	NM_002890.2	789	Cga/Tga	18/25	1	2	FACETS	0.825	0.63	1	0.825	0.63	1	CLONAL	1	TRUE	1	0.13	2		289	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	rs786202799	NA	P-0007428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	249	263	1	ENST00000269305.4:c.376-2A>T		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.381085317679256	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.381085317679256	1		264	922	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098804	178098804	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1570	506	584	0	ENST00000397062.3:c.241G>C	p.Gly81Arg	p.G81R	ENST00000397062	NM_006164.4	81	Ggt/Cgt	2/5	0.161726920677754	3	FACETS	0.761	0.727	0.797	0.761	0.727	0.797	INDETERMINATE	2	TRUE	1	0.381085317679256	3		584	2076	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188309	10188309	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	236	403	0	ENST00000256474.2:c.452T>A	p.Ile151Asn	p.I151N	ENST00000256474	NM_000551.3	151	aTc/aAc	2/3	0.381085317679256	1	FACETS	0.949	0.886	1	0.949	0.886	1	CLONAL	1	TRUE	0	0.381085317679256	1		403	1056	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347144	89347144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765986335	NA	P-0007428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1410	311	598	0	ENST00000301030.4:c.5806G>A	p.Glu1936Lys	p.E1936K	ENST00000301030	NM_001256183.1	1936	Gag/Aag	9/13	1	2	FACETS	0.948	0.891	1	0.948	0.891	1	CLONAL	1	TRUE	1	0.381085317679256	2		598	1721	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610705	52610705	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	127	379	0	ENST00000394830.3:c.3468del	p.Val1157TyrfsTer36	p.V1157Yfs*36	ENST00000394830	NM_018313.4	1156	aaA/aa	23/30	0.381085317679256	1	FACETS	0.771	0.699	0.846	0.771	0.699	0.846	SUBCLONAL	1	TRUE	0	0.381085317679256	1		379	700	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0007485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	46	208	1	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	1	2	FACETS	0.96	0.806	1	0.96	0.806	1	CLONAL	1	TRUE	1	0.12	2		209	799	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868216	37868216	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	54	201	0	ENST00000269571.5:c.937C>G	p.Leu313Val	p.L313V	ENST00000269571		313	Ctc/Gtc	8/27	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.12	2		201	830	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0007509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	207	333	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.334763691623118	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.350248269690211	1		333	932	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0007509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	670	426	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.350248269690211	4	FACETS	0.992	0.96	1	0.992	0.96	1	CLONAL	4	TRUE	0	0.350248269690211	4		426	1302	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778016	135778016	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	195	316	0	ENST00000298552.3:c.2367C>G	p.Phe789Leu	p.F789L	ENST00000298552	NM_001162426.1	789	ttC/ttG	18/23	0.350248269690211	2	FACETS	1	0.946	1	0.514	0.475	0.555	CLONAL	1	TRUE	0	0.350248269690211	2		316	1083	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	397	484	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.992	0.947	1	0.992	0.947	1	CLONAL	1	TRUE	1	0.835574750985246	2		484	958	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0007513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	399	419	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.976	0.931	1	0.976	0.931	1	CLONAL	1	TRUE	1	0.835574750985246	2		419	979	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593667	55593669	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	rs1060502543	NA	P-0007513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	433	279	0	ENST00000288135.5:c.1735_1737del	p.Asp579del	p.D579del	ENST00000288135	NM_000222.2	578	tATGat/tat	11/21	NA	2	FACETS	0.938	0.896	0.98			1	INDETERMINATE	1	TRUE	NA	0.835574750985246	2		279	1105	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0007532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	57	286	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.3	1	FACETS	0.722	0.618	0.836	0.722	0.618	0.836	SUBCLONAL	1	TRUE	0	0.18	1		287	798	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89815102	89815102	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	93	352	0	ENST00000389301.3:c.3313T>A	p.Cys1105Ser	p.C1105S	ENST00000389301	NM_000135.2	1105	Tgc/Agc	33/43	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.18	2		352	980	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127566	55127566	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0007532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	49	189	0	ENST00000257290.5:c.354C>G	p.Tyr118Ter	p.Y118*	ENST00000257290	NM_006206.4	118	taC/taG	3/23	1	2	FACETS	0.999	0.846	1	0.999	0.846	1	CLONAL	1	TRUE	1	0.18	2		189	545	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372205	55372205	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	17	113	0	ENST00000297316.4:c.895G>T	p.Ala299Ser	p.A299S	ENST00000297316	NM_022454.3	299	Gcg/Tcg	2/2	1	2	FACETS	0.649	0.484	0.845	0.649	0.484	0.845	SUBCLONAL	1	TRUE	1	0.18	2		113	291	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98241298	98241298	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	106	404	0	ENST00000331920.6:c.1199A>T	p.Gln400Leu	p.Q400L	ENST00000331920	NM_000264.3	400	cAg/cTg	8/24	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.18	2		404	1146	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045016	47045016	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	53	367	0	ENST00000377604.3:c.2342C>A	p.Ser781Ter	p.S781*	ENST00000377604	NM_001204468.1	781	tCa/tAa	20/24	1	2	FACETS	0.745	0.634	0.868	0.745	0.634	0.868	SUBCLONAL	1	TRUE	1	0.18	2		367	790	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044554	47044554	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	84	395	0	ENST00000377604.3:c.2052del	p.Arg684SerfsTer20	p.R684Sfs*20	ENST00000377604	NM_001204468.1	684	aGg/ag	18/24	1	2	FACETS	0.947	0.834	1	0.947	0.834	1	CLONAL	1	TRUE	1	0.18	2		395	986	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0007541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	86	375	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.32324814577326	1	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	0	0.33375898152061	1		378	424	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0007541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	97	353	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.745	0.664	0.832	0.745	0.664	0.832	SUBCLONAL	1	TRUE	1	0.33375898152061	2		354	780	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871182	12871182	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1328655695	NA	P-0007541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	25	123	1	ENST00000228872.4:c.410del	p.Pro137ArgfsTer8	p.P137Rfs*8	ENST00000228872	NM_004064.3	137	Ccg/cg	1/3	1	2	FACETS	0.713	0.565	0.881	0.713	0.565	0.881	SUBCLONAL	1	TRUE	1	0.33375898152061	2		124	210	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884864	134884864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257672576	NA	P-0007541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	191	495	3	ENST00000398015.3:c.1640C>T	p.Ala547Val	p.A547V	ENST00000398015	NM_004441.4	547	gCg/gTg	8/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.33375898152061	2		498	987	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842372	68842372	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	206	593	0	ENST00000261769.5:c.433T>A	p.Ser145Thr	p.S145T	ENST00000261769	NM_004360.3	145	Tcc/Acc	4/16	0.141451310903586	3	FACETS	1	0.967	1	0.539	0.499	0.581	INDETERMINATE	1	TRUE	1	0.33375898152061	3		593	1336	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188983	11188983	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1152	103	1037	1	ENST00000361445.4:c.5740G>T	p.Gly1914Cys	p.G1914C	ENST00000361445	NM_004958.3	1914	Ggt/Tgt	41/58	1	2	FACETS	0.912	0.813	1	0.912	0.813	1	CLONAL	1	TRUE	1	0.18	2		1038	1255	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023832	27023832	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	93	622	3	ENST00000324856.7:c.938G>T	p.Gly313Val	p.G313V	ENST00000324856	NM_006015.4	313	gGg/gTg	1/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.18	2		625	788	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748120	41748120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759792321	NA	P-0007542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	23	231	1	ENST00000226382.2:c.649G>A	p.Gly217Arg	p.G217R	ENST00000226382	NM_003924.3	217	Ggg/Agg	3/3	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.18	2		232	205	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125058	46125058	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	54	712	0	ENST00000334344.6:c.245G>C	p.Cys82Ser	p.C82S	ENST00000334344	NM_152641.2	82	tGt/tCt	3/21	1	2	FACETS	0.556	0.473	0.648	0.556	0.473	0.648	SUBCLONAL	1	TRUE	1	0.18	2		712	1079	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861936	57861936	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1363	107	1311	0	ENST00000228682.2:c.1237G>T	p.Glu413Ter	p.E413*	ENST00000228682	NM_005269.2	413	Gag/Tag	10/12	1	2	FACETS	0.809	0.723	0.901	0.809	0.723	0.901	CLONAL	1	TRUE	1	0.18	2		1311	1470	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99452055	99452055	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	51	760	0	ENST00000268035.6:c.1389G>T	p.Glu463Asp	p.E463D	ENST00000268035	NM_000875.3	463	gaG/gaT	6/21	1	2	FACETS	0.587	0.497	0.686	0.587	0.497	0.686	SUBCLONAL	1	TRUE	1	0.18	2		760	966	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863593	68863593	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	112	873	1	ENST00000261769.5:c.2332G>T	p.Ala778Ser	p.A778S	ENST00000261769	NM_004360.3	778	Gct/Tct	15/16	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.18	2		874	1075	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0007542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	92	649	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.18	2		649	827	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556886	29556886	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	56	510	1	ENST00000356175.3:c.2884G>T	p.Glu962Ter	p.E962*	ENST00000356175	NM_000267.3	962	Gaa/Taa	22/57	1	2	FACETS	0.842	0.72	0.976	0.842	0.72	0.976	CLONAL	1	TRUE	1	0.18	2		511	739	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030598	47030598	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	106	783	0	ENST00000377604.3:c.373G>T	p.Glu125Ter	p.E125*	ENST00000377604	NM_001204468.1	125	Gag/Tag	4/24	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.18	2		783	799	SUCCESS
AR	367	MSKCC	GRCh37	X	66943642	66943642	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1402	207	1258	0	ENST00000374690.3:c.2722C>A	p.Leu908Ile	p.L908I	ENST00000374690	NM_000044.3	908	Ctt/Att	8/8	0.15888578860614	0	FACETS	1	0.98	1			1	CLONAL	1	TRUE	0	0.18	0		1258	1609	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851071	63851071	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	45	388	0	ENST00000279873.7:c.1851del	p.Ala618ProfsTer11	p.A618Pfs*11	ENST00000279873	NM_032199.2	617	Ccc/cc	10/10	1	2	FACETS	0.978	0.822	1	0.978	0.822	1	CLONAL	1	TRUE	1	0.18	2		388	511	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	316	291	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.571910437812586	2		291	1063	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0007548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	458	785	4	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.571910437812586	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.571910437812586	1		789	1096	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954198	48954198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123331	NA	P-0007548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	396	607	0	ENST00000267163.4:c.1399C>T	p.Arg467Ter	p.R467*	ENST00000267163	NM_000321.2	467	Cga/Tga	15/27	0.571910437812586	2	FACETS	0.802	0.767	0.838	0.802	0.767	0.838	CLONAL	2	TRUE	0	0.571910437812586	2		607	863	SUCCESS
APC	324	MSKCC	GRCh37	5	112177788	112177788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752091655	NA	P-0007548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	225	386	0	ENST00000257430.4:c.6497G>A	p.Arg2166Gln	p.R2166Q	ENST00000257430	NM_000038.5	2166	cGa/cAa	16/16	0.272994084693883	1	FACETS	0.874	0.819	0.93	0.874	0.819	0.93	INDETERMINATE	1	TRUE	0	0.571910437812586	1		386	643	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026303	48026303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	156	522	2	ENST00000234420.5:c.1181C>T	p.Ser394Phe	p.S394F	ENST00000234420	NM_000179.2	394	tCt/tTt	4/10	0.272994084693883	1	FACETS	0.471	0.431	0.512	0.471	0.431	0.512	INDETERMINATE	1	TRUE	0	0.571910437812586	1		524	827	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277619	142277619	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0007548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	97	302	0	ENST00000350721.4:c.1733-1G>A		p.X578_splice	ENST00000350721	NM_001184.3	578			0.272994084693883	1	FACETS	0.505	0.452	0.56	0.505	0.452	0.56	INDETERMINATE	1	TRUE	0	0.571910437812586	1		302	480	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198252	185198252	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	307	499	0	ENST00000265026.3:c.2734G>C	p.Ala912Pro	p.A912P	ENST00000265026	NM_004721.4	912	Gcc/Ccc	13/14	0.272994084693883	1	FACETS	0.889	0.841	0.938	0.889	0.841	0.938	INDETERMINATE	1	TRUE	0	0.571910437812586	1		499	862	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508082	106508082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	126	296	1	ENST00000359195.3:c.76C>T	p.Arg26Cys	p.R26C	ENST00000359195	NM_002649.2	26	Cgc/Tgc	2/11	1	2	FACETS	0.864	0.786	0.945	0.864	0.786	0.945	CLONAL	1	TRUE	1	0.571910437812586	2		297	510	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	88	246	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.682689059354022	2		246	249	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685314	89685315	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TG	TG	-	rs1564826836	NA	P-0007551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	89	203	0	ENST00000371953.3:c.209+1_209+2del		p.X70_splice	ENST00000371953	NM_000314.4	70		3/9	0.682689059354022	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.682689059354022	1		203	170	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0007551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	52	436	0	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	0.682689059354022	1	FACETS	0.301	0.257	0.349	0.301	0.257	0.349	SUBCLONAL	1	TRUE	0	0.682689059354022	1		436	333	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170558	7170558	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	27	263	0	ENST00000302850.5:c.1473C>G	p.Asp491Glu	p.D491E	ENST00000302850	NM_000208.2	491	gaC/gaG	6/22	0.648138358958384	2	FACETS	0.313	0.249	0.384	0.156	0.124	0.192	SUBCLONAL	1	TRUE	0	0.682689059354022	2		263	253	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246590	46246590	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	52	173	0	ENST00000334344.6:c.4685del	p.Pro1562GlnfsTer4	p.P1562Qfs*4	ENST00000334344	NM_152641.2	1562	Cca/ca	15/21	1	2	FACETS	0.946	0.822	1	0.946	0.822	1	CLONAL	1	TRUE	1	0.682689059354022	2		173	161	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782177	NA	P-0007576-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	259	490	0	ENST00000269305.4:c.644G>T	p.Ser215Ile	p.S215I	ENST00000269305	NM_001126112.2	215	aGt/aTt	6/11	0.419357180968659	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.419357180968659	1		490	755	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857896	9857896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369878342	NA	P-0007576-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	122	458	0	ENST00000330684.3:c.3505C>T	p.Arg1169Trp	p.R1169W	ENST00000330684	NM_001134407.1	1169	Cgg/Tgg	13/13	1	2	FACETS	0.976	0.885	1	0.976	0.885	1	CLONAL	1	TRUE	1	0.419357180968659	2		458	596	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054349	42054351	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0007576-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	143	520	0	ENST00000219905.7:c.7537_7539del	p.Lys2513del	p.K2513del	ENST00000219905	NM_001164273.1	2511	ctGAAg/ctg	22/24	1	2	FACETS	0.788	0.719	0.862	0.788	0.719	0.862	SUBCLONAL	1	TRUE	1	0.419357180968659	2		520	865	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0007586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	251	751	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.493817553009224	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.493817553009224	2		753	447	SUCCESS
APC	324	MSKCC	GRCh37	5	112175524	112175524	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	59	245	0	ENST00000257430.4:c.4233del	p.Ser1411ArgfsTer4	p.S1411Rfs*4	ENST00000257430	NM_000038.5	1411	agT/ag	16/16	0.266887431710239	2	FACETS	0.542	0.467	0.623	0.271	0.233	0.312	INDETERMINATE	1	TRUE	0	0.493817553009224	2		245	441	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0007586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	114	252	1	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	0.266887431710239	2	FACETS	1	0.979	1	0.632	0.575	0.692	INDETERMINATE	1	TRUE	0	0.493817553009224	2		253	365	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521721	89521721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372594677	NA	P-0007586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	132	333	2	ENST00000336596.2:c.2798C>T	p.Thr933Met	p.T933M	ENST00000336596	NM_005233.5	933	aCg/aTg	16/17	0.493817553009224	3	FACETS	0.904	0.822	0.991	0.452	0.411	0.496	CLONAL	1	TRUE	1	0.493817553009224	3		335	737	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0007619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	190	399	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.240820524043227	3	FACETS	0.875	0.809	0.944			1	CLONAL	2	TRUE	NA	0.240820524043227	3		400	1010	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0007619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	166	352	1	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.188631538605545	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.240820524043227	2		353	576	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220371	1220371	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0007619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	184	241	0	ENST00000326873.7:c.465-1G>T		p.X155_splice	ENST00000326873	NM_000455.4	155			0.240820524043227	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.240820524043227	2		241	637	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471091	25471091	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	117	285	0	ENST00000264709.3:c.670A>G	p.Met224Val	p.M224V	ENST00000264709	NM_175629.2	224	Atg/Gtg	7/23	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.240820524043227	2		285	872	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451773	29451773	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	114	299	0	ENST00000389048.3:c.2792G>T	p.Gly931Val	p.G931V	ENST00000389048	NM_004304.4	931	gGt/gTt	16/29	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.240820524043227	2		299	869	SUCCESS
APC	324	MSKCC	GRCh37	5	112173893	112173893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	104	210	0	ENST00000257430.4:c.2602G>A	p.Glu868Lys	p.E868K	ENST00000257430	NM_000038.5	868	Gaa/Aaa	16/16	0.240820524043227	3	FACETS	1	0.973	1	0.631	0.565	0.701	CLONAL	1	TRUE	1	0.240820524043227	3		210	767	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508350	106508350	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	24	82	0	ENST00000359195.3:c.344T>G	p.Val115Gly	p.V115G	ENST00000359195	NM_002649.2	115	gTg/gGg	2/11	0.240820524043227	3	FACETS	0.866	0.681	1	0.433	0.34	0.539	CLONAL	1	TRUE	1	0.240820524043227	3		82	258	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347239	89347239	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1381795153	NA	P-0007619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	133	349	0	ENST00000301030.4:c.5711A>G	p.Glu1904Gly	p.E1904G	ENST00000301030	NM_001256183.1	1904	gAa/gGa	9/13	0.218598461534527	3	FACETS	1	0.966	1	0.568	0.515	0.625	CLONAL	1	TRUE	1	0.240820524043227	3		349	1089	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602647	10602647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	154	266	0	ENST00000171111.5:c.931C>T	p.His311Tyr	p.H311Y	ENST00000171111	NM_203500.1	311	Cac/Tac	3/6	0.240820524043227	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.240820524043227	2		266	595	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100988	41100988	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	77	195	0	ENST00000373198.4:c.1368G>A	p.Met456Ile	p.M456I	ENST00000373198	NM_133170.3	456	atG/atA	8/32	0.240820524043227	4	FACETS	1	0.935	1	0.551	0.483	0.624	CLONAL	1	TRUE	2	0.240820524043227	4		195	720	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717615	89717615	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909227	NA	P-0007622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	59	284	0	ENST00000371953.3:c.640C>T	p.Gln214Ter	p.Q214*	ENST00000371953	NM_000314.4	214	Cag/Tag	7/9	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.16	2		284	513	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719711	190719711	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	38	357	0	ENST00000441310.2:c.1713C>G	p.Ile571Met	p.I571M	ENST00000441310	NM_000534.4	571	atC/atG	9/13	1	2	FACETS	0.723	0.596	0.865	0.723	0.596	0.865	SUBCLONAL	1	TRUE	1	0.16	2		357	657	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839850	27839850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	106	745	1	ENST00000328488.2:c.244G>A	p.Asp82Asn	p.D82N	ENST00000328488	NM_003533.2	82	Gat/Aat	1/1	0.233303676210228	1	FACETS	0.848	0.76	0.94	1	0.985	1	CLONAL	2	TRUE	0	0.16	1		746	719	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372109	55372109	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	17	102	0	ENST00000297316.4:c.799G>A	p.Ala267Thr	p.A267T	ENST00000297316	NM_022454.3	267	Gcc/Acc	2/2	1	2	FACETS	1	0.831	1	1	0.831	1	CLONAL	1	TRUE	1	0.16	2		102	185	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131787	2131787	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	65	198	0	ENST00000219476.3:c.3802C>G	p.Arg1268Gly	p.R1268G	ENST00000219476	NM_000548.3	1268	Cgc/Ggc	31/42	0.179520421837557	3	FACETS	0.936	0.813	1	0.936	0.813	1	CLONAL	2	TRUE	1	0.16	3		198	469	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045736	47045736	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	62	165	0	ENST00000377604.3:c.2617G>C	p.Glu873Gln	p.E873Q	ENST00000377604	NM_001204468.1	873	Gag/Cag	23/24	1	1	FACETS	0.914	0.798	1	1	0.984	1	CLONAL	3	TRUE	0	0.16	1		165	260	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786767	3786767	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587783495	NA	P-0007623-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	48	456	4	ENST00000262367.5:c.4444T>G	p.Tyr1482Asp	p.Y1482D	ENST00000262367	NM_004380.2	1482	Tac/Gac	27/31	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		460	897	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0007629-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	79	345	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	0.216464317287352	1	FACETS	0.353	0.311	0.397	0.353	0.311	0.397	INDETERMINATE	1	TRUE	0	0.617043628451762	1		345	502	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204864	NA	P-0007629-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	156	278	0	ENST00000371953.3:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000371953	NM_000314.4	171	Cag/Tag	6/9	0.617043628451762	1	FACETS	0.923	0.856	0.99	0.923	0.856	0.99	CLONAL	1	TRUE	0	0.617043628451762	1		278	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0007629-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	178	454	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.617043628451762	1	FACETS	0.978	0.913	1	0.978	0.913	1	CLONAL	1	TRUE	0	0.617043628451762	1		454	408	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11293481	11293481	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007629-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	128	335	0	ENST00000361445.4:c.2395C>G	p.Leu799Val	p.L799V	ENST00000361445	NM_004958.3	799	Ctg/Gtg	15/58	0.216464317287352	1	FACETS	0.509	0.463	0.557	0.509	0.463	0.557	INDETERMINATE	1	TRUE	0	0.617043628451762	1		335	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0007632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	133	932	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.268197402407357	2		934	814	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	53	484	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.892	0.762	1	0.892	0.762	1	CLONAL	1	TRUE	1	0.268197402407357	2		484	443	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0007632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	47	419	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.268197402407357	2		419	304	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446027	49446027	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	70	468	0	ENST00000301067.7:c.1439del	p.Pro480LeufsTer450	p.P480Lfs*450	ENST00000301067	NM_003482.3	480	cCt/ct	10/54	1	2	FACETS	0.705	0.614	0.804	0.705	0.614	0.804	SUBCLONAL	1	TRUE	1	0.268197402407357	2		468	740	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973772	131973772	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0007632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	17	328	0	ENST00000265335.6:c.3476-1G>A		p.X1159_splice	ENST00000265335		1159			0.268197402407357	1	FACETS	0.384	0.286	0.5	0.384	0.286	0.5	SUBCLONAL	1	TRUE	0	0.268197402407357	1		328	286	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221846	55221846	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0007632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	130	524	0	ENST00000275493.2:c.889+1G>A		p.X297_splice	ENST00000275493	NM_005228.3	297			1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.268197402407357	2		524	845	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923394	36923394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759191217	NA	P-0007632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	90	379	2	ENST00000358127.4:c.868G>A	p.Gly290Arg	p.G290R	ENST00000358127	NM_001280556.1	290	Ggg/Agg	7/10	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.268197402407357	2		381	610	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265579	41266277	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	In_Frame_Del	DEL	GTCATTAAATCTTTAGTTACTGAATTGGGGCTCTGCTTCGTTGCCATTAAGCCAGTCTGGCTGAGATCCCCCTGCTTTCCTCTCTCCCTGCTTACTTGTCAGGCTACCTTTTGCTCCATTTTCTGCTCACTCCTCCTAATGGCTTGGTGAAATAGCAAACAAGCCACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAA	GTCATTAAATCTTTAGTTACTGAATTGGGGCTCTGCTTCGTTGCCATTAAGCCAGTCTGGCTGAGATCCCCCTGCTTTCCTCTCTCCCTGCTTACTTGTCAGGCTACCTTTTGCTCCATTTTCTGCTCACTCCTCCTAATGGCTTGGTGAAATAGCAAACAAGCCACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAA	-	novel	NA	P-0007632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	58	399	0	ENST00000349496.5:c.13+11_241+37del		p.A5_D81del	ENST00000349496	NM_001904.3	5		3/15	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.268197402407357	2		399	398	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220542	98220542	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007640-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	569	298	0	ENST00000331920.6:c.2921T>G	p.Phe974Cys	p.F974C	ENST00000331920	NM_000264.3	974	tTc/tGc	18/24	0.649432999310976	4	FACETS	1	0.975	1			1	CLONAL	3	TRUE	NA	0.650344486739155	4		298	954	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217251	7217251	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007640-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	405	473	0	ENST00000380728.2:c.454C>T	p.Gln152Ter	p.Q152*	ENST00000380728		152	Caa/Taa	6/11	1	2	FACETS	0.908	0.863	0.953	0.908	0.863	0.953	CLONAL	1	TRUE	1	0.650344486739155	2		473	1372	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257879	16257879	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	56	149	0	ENST00000375759.3:c.5144T>A	p.Met1715Lys	p.M1715K	ENST00000375759	NM_015001.2	1715	aTg/aAg	11/15	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.251754725022115	2		149	406	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437668	52437674	+	frameshift_variant	Frame_Shift_Del	DEL	TCAGAGG	TCAGAGG	-	novel	NA	P-0007642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	228	367	0	ENST00000460680.1:c.1487_1493del	p.Ala496GlyfsTer73	p.A496Gfs*73	ENST00000460680	NM_004656.3	496	gCCTCTGAg/gg	13/17	0.251754725022115	2	FACETS	0.959	0.895	1	0.959	0.895	1	CLONAL	2	TRUE	0	0.251754725022115	2		367	944	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0007657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	98	284	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.769	0.688	0.855	1	0.982	1	SUBCLONAL	2	TRUE	1	0.218586826891807	2		284	583	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578207	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0007657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	129	414	0	ENST00000269305.4:c.642_643del	p.His214GlnfsTer7	p.H214Qfs*7	ENST00000269305	NM_001126112.2	214	caTAgt/cagt	6/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.218586826891807	2		414	872	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0007657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	76	305	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.218586826891807	2	FACETS	0.925	0.816	1	0.925	0.816	1	CLONAL	2	TRUE	0	0.218586826891807	2		305	376	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481627	56481627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1429784531	NA	P-0007657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	198	431	0	ENST00000267101.3:c.662C>T	p.Pro221Leu	p.P221L	ENST00000267101	NM_001982.3	221	cCc/cTc	6/28	0.218586826891807	2	FACETS	0.965	0.894	1	0.965	0.894	1	CLONAL	2	TRUE	0	0.218586826891807	2		431	939	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807896	1807896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	48	299	0	ENST00000260795.2:c.1955C>T	p.Thr652Ile	p.T652I	ENST00000260795		652	aCc/aTc	13/17	1	2	FACETS	0.884	0.747	1	0.884	0.747	1	CLONAL	1	TRUE	1	0.218586826891807	2		299	497	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17124931	17124940	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GCCTTCAGGA	GCCTTCAGGA	-	novel	NA	P-0007657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	29	246	0	ENST00000285071.4:c.782_791del	p.Leu261ArgfsTer6	p.L261Rfs*6	ENST00000285071	NM_144997.5	261	cTCCTGAAGGCg/cg	8/14	1	2	FACETS	0.616	0.494	0.755	0.616	0.494	0.755	SUBCLONAL	1	TRUE	1	0.218586826891807	2		246	431	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085918	16085918	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs150742977	NA	P-0007660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	108	316	0	ENST00000281043.3:c.1094C>A	p.Pro365Gln	p.P365Q	ENST00000281043	NM_005378.4	365	cCa/cAa	3/3	0.58383691057167	3	FACETS	1	0.972	1	0.602	0.545	0.662	CLONAL	1	TRUE	1	0.58383691057167	3		316	397	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459319	120459319	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0007660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	30	109	0	ENST00000256646.2:c.6028-2A>G		p.X2010_splice	ENST00000256646	NM_024408.3	2010			NA	2	FACETS	0.791	0.648	0.946			1	INDETERMINATE	1	TRUE	NA	0.58383691057167	2		109	130	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946225	81946225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1325870340	NA	P-0007660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	282	828	0	ENST00000359376.3:c.1958G>A	p.Arg653His	p.R653H	ENST00000359376	NM_002661.3	653	cGc/cAc	19/33	NA	2	FACETS	0.85	0.798	0.902			1	INDETERMINATE	1	TRUE	NA	0.58383691057167	2		828	1137	SUCCESS
YES1	7525	MSKCC	GRCh37	18	742935	742935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780838371	NA	P-0007660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	277	652	0	ENST00000314574.4:c.1043C>T	p.Thr348Ile	p.T348I	ENST00000314574	NM_005433.3	348	aCt/aTt	8/12	0.58383691057167	3	FACETS	0.961	0.902	1	0.481	0.451	0.512	CLONAL	1	TRUE	1	0.58383691057167	3		652	1275	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	418	246	0				ENST00000310581	NM_198253.2	-/1132			0.565265343225013	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	1	0.565265343225013	4		246	742	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0007666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	226	261	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.565265343225013	3	FACETS	0.885	0.823	0.949	0.442	0.411	0.475	CLONAL	1	TRUE	1	0.565265343225013	3		261	1159	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627941	187627941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	364	821	0	ENST00000441802.2:c.3041C>T	p.Ser1014Phe	p.S1014F	ENST00000441802	NM_005245.3	1014	tCt/tTt	2/27	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.565265343225013	2		821	1260	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981679	101981679	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773573203	NA	P-0007666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	41	70	0	ENST00000282441.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000282441	NM_001130145.2	34	Ggg/Agg	1/9	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.565265343225013	2		70	131	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005287	29005287	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	223	499	0	ENST00000282397.4:c.974C>T	p.Ser325Leu	p.S325L	ENST00000282397	NM_002019.4	325	tCa/tTa	7/30	NA	2	FACETS	0.937	0.874	1			1	INDETERMINATE	1	TRUE	NA	0.565265343225013	2		499	842	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973821	15973821	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	232	498	0	ENST00000268712.3:c.4171G>C	p.Asp1391His	p.D1391H	ENST00000268712	NM_006311.3	1391	Gac/Cac	31/46	1	2	FACETS	0.971	0.908	1	0.971	0.908	1	CLONAL	1	TRUE	1	0.565265343225013	2		498	845	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054418	13054418	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	270	843	2	ENST00000316448.5:c.1028G>T	p.Gly343Val	p.G343V	ENST00000316448	NM_004343.3	343	gGc/gTc	8/9	1	2	FACETS	0.76	0.712	0.809	0.76	0.712	0.809	SUBCLONAL	1	TRUE	1	0.565265343225013	2		845	1257	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246390	53246390	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007667-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	227	489	1	ENST00000375401.3:c.592C>T	p.Arg198Ter	p.R198*	ENST00000375401	NM_004187.3	198	Cga/Tga	5/26	0.241712453285338	0	FACETS	0.762	0.716	0.809			1	INDETERMINATE	1	TRUE	NA	0.510095914451474	0		490	572	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131930653	131930653	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007667-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	166	645	0	ENST00000265335.6:c.1886T>A	p.Leu629Gln	p.L629Q	ENST00000265335		629	cTg/cAg	12/25	0.200681561603132	0	FACETS	0.44	0.405	0.477			1	INDETERMINATE	1	TRUE	0	0.510095914451474	0		645	724	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134744	41134744	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007667-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	368	1123	1	ENST00000379561.5:c.884G>A	p.Trp295Ter	p.W295*	ENST00000379561	NM_002015.3	295	tGg/tAg	2/3	0.510095914451474	1	FACETS	0.971	0.922	1	0.971	0.922	1	CLONAL	1	TRUE	0	0.510095914451474	1		1124	1107	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90992976	90992985	+	frameshift_variant	Frame_Shift_Del	DEL	TCACTGATAC	TCACTGATAC	-	novel	NA	P-0007667-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	137	573	0	ENST00000265433.3:c.457_466del	p.Val153LysfsTer17	p.V153Kfs*17	ENST00000265433	NM_002485.4	153	GTATCAGTGAaa/aa	4/16	0.478234630585468	1	FACETS	0.864	0.792	0.939	0.864	0.792	0.939	CLONAL	1	TRUE	0	0.510095914451474	1		573	463	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0007676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	54	475	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.16079891183404	2		475	581	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398220	25398220	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	85	510	0	ENST00000311936.3:c.99T>G	p.Asp33Glu	p.D33E	ENST00000311936	NM_004985.3	33	gaT/gaG	2/5	0.143345557020605	4	FACETS	0.933	0.825	1	0.933	0.825	1	CLONAL	2	TRUE	2	0.16079891183404	4		510	658	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857796	57857796	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1418545492	NA	P-0007676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	115	695	0	ENST00000228682.2:c.115C>T	p.Pro39Ser	p.P39S	ENST00000228682	NM_005269.2	39	Ccc/Tcc	3/12	0.153404737927215	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	0	0.16079891183404	2		695	682	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220494	1220494	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519858	NA	P-0007695-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	58	432	2	ENST00000326873.7:c.587G>T	p.Gly196Val	p.G196V	ENST00000326873	NM_000455.4	196	gGc/gTc	4/10	0.153356000373758	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		434	684	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0007695-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	32	485	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.153356000373758	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		485	625	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729820	47729820	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0007695-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2333	247	558	0	ENST00000449228.1:c.568+1G>C		p.X190_splice	ENST00000449228	NM_001127240.2	190			0.12343086342961	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		558	2580	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600043	10600050	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCCTAAAG	GCCTAAAG	-	novel	NA	P-0007695-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	28	353	0	ENST00000171111.5:c.1532-6_1533del		p.X511_splice	ENST00000171111	NM_203500.1	511		5/6	0.153356000373758	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		353	490	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0007747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	55	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.892	0.769	1	1	0.975	1	CLONAL	2	TRUE	1	0.212672541573944	2		249	290	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0007747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	38	43	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	0.212672541573944	5	FACETS	1	0.907	1	1	0.967	1	CLONAL	6	TRUE	1	0.212672541573944	5		43	74	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630626	158630626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912678	NA	P-0007747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	234	775	0	ENST00000263640.3:c.617G>A	p.Arg206His	p.R206H	ENST00000263640	NM_001105.4	206	cGc/cAc	6/11	0.118456666738048	0	FACETS	0.974	0.916	1			1	INDETERMINATE	3	TRUE	0	0.212672541573944	0		775	593	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224754	123224754	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	137	936	1	ENST00000218089.9:c.3518A>T	p.Gln1173Leu	p.Q1173L	ENST00000218089	NM_001042749.1	1173	cAa/cTa	32/35	0.184181637233223	0	FACETS	1	0.956	1			1	CLONAL	2	TRUE	0	0.212672541573944	0		937	475	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782082	NA	P-0007750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	276	446	15	ENST00000269305.4:c.745A>T	p.Arg249Trp	p.R249W	ENST00000269305	NM_001126112.2	249	Agg/Tgg	7/11	0.55223696599053	2	FACETS	0.752	0.715	0.788	0.752	0.715	0.788	SUBCLONAL	2	TRUE	0	0.721361209476462	2		461	509	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98003010	98003010	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	25	585	0	ENST00000289081.3:c.266T>A	p.Ile89Asn	p.I89N	ENST00000289081	NM_000136.2	89	aTt/aAt	4/15	0.421559452376516	3	FACETS	0.261	0.205	0.324	0.13	0.102	0.162	INDETERMINATE	1	TRUE	1	0.721361209476462	3		585	362	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900866	3900881	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCCTCGTAGAAGCT	CCTCCTCGTAGAAGCT	-	novel	NA	P-0007750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	230	526	8	ENST00000262367.5:c.215_230del	p.Glu72AlafsTer10	p.E72Afs*10	ENST00000262367	NM_004380.2	72	gAGCTTCTACGAGGAGGc/gc	2/31	0.299961196229562	3	FACETS	0.76	0.714	0.806	0.76	0.714	0.806	INDETERMINATE	2	TRUE	1	0.721361209476462	3		534	571	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	118	246	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.634950206659008	2		246	321	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148930	119148930	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs387906664	NA	P-0007756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	17	384	0	ENST00000264033.4:c.1150T>C	p.Cys384Arg	p.C384R	ENST00000264033	NM_005188.3	384	Tgt/Cgt	8/16	0.182161913951875	1	FACETS	0.045	0.033	0.06	0.045	0.033	0.06	INDETERMINATE	1	TRUE	0	0.634950206659008	1		384	809	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911144	40911144	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1173	244	576	2	ENST00000373198.4:c.2161C>A	p.Arg721Ser	p.R721S	ENST00000373198	NM_133170.3	721	Cgt/Agt	13/32	0.306582726366751	3	FACETS	0.715	0.666	0.765	0.238	0.222	0.255	INDETERMINATE	1	TRUE	0	0.634950206659008	3		578	1417	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591105	67591107	+	inframe_deletion	In_Frame_Del	DEL	TAA	TAA	-	novel	NA	P-0007756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	245	306	0	ENST00000274335.5:c.1698_1700del	p.Lys567del	p.K567del	ENST00000274335		566	atTAAa/ata	12/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.634950206659008	2		306	735	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589848	212589848	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007781-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	38	367	0	ENST00000342788.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000342788	NM_005235.2	232	Cga/Tga	6/28	0.190708576175696	4	FACETS	1	0.921	1	0.604	0.5	0.72	CLONAL	1	TRUE	2	0.196004969606308	4		367	384	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971120	55971120	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007781-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	78	447	1	ENST00000263923.4:c.1677G>T	p.Met559Ile	p.M559I	ENST00000263923	NM_002253.2	559	atG/atT	13/30	0.196004969606308	3	FACETS	0.883	0.782	0.989	1	0.971	1	CLONAL	3	TRUE	1	0.196004969606308	3		448	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007781-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	43	388	0	ENST00000269305.4:c.503A>C	p.His168Pro	p.H168P	ENST00000269305	NM_001126112.2	168	cAc/cCc	5/11	0.185736951266373	3	FACETS	0.811	0.682	0.952	0.811	0.682	0.952	CLONAL	2	TRUE	1	0.196004969606308	3		388	297	SUCCESS
APC	324	MSKCC	GRCh37	5	112175533	112175903	+	frameshift_variant	Frame_Shift_Del	DEL	AAGTGGCATTATAAGCCCCAGTGATCTTCCAGATAGCCCTGGACAAACCATGCCACCAAGCAGAAGTAAAACACCTCCACCACCTCCTCAAACAGCTCAAACCAAGCGAGAAGTACCTAAAAATAAAGCACCTACTGCTGAAAAGAGAGAGAGTGGACCTAAGCAAGCTGCAGTAAATGCTGCAGTTCAGAGGGTCCAGGTTCTTCCAGATGCTGATACTTTATTACATTTTGCCACGGAAAGTACTCCAGATGGATTTTCTTGTTCATCCAGCCTGAGTGCTCTGAGCCTCGATGAGCCATTTATACAGAAAGATGTGGAATTAAGAATAATGCCTCCAGTTCAGGAAAATGACAATGGGAATGAAACAG	AAGTGGCATTATAAGCCCCAGTGATCTTCCAGATAGCCCTGGACAAACCATGCCACCAAGCAGAAGTAAAACACCTCCACCACCTCCTCAAACAGCTCAAACCAAGCGAGAAGTACCTAAAAATAAAGCACCTACTGCTGAAAAGAGAGAGAGTGGACCTAAGCAAGCTGCAGTAAATGCTGCAGTTCAGAGGGTCCAGGTTCTTCCAGATGCTGATACTTTATTACATTTTGCCACGGAAAGTACTCCAGATGGATTTTCTTGTTCATCCAGCCTGAGTGCTCTGAGCCTCGATGAGCCATTTATACAGAAAGATGTGGAATTAAGAATAATGCCTCCAGTTCAGGAAAATGACAATGGGAATGAAACAG	-	novel	NA	P-0007781-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	94	435	0	ENST00000257430.4:c.4244_4614del	p.Ser1415IlefsTer5	p.S1415Ifs*5	ENST00000257430	NM_000038.5	1414	gtAAGTGGCATTATAAGCCCCAGTGATCTTCCAGATAGCCCTGGACAAACCATGCCACCAAGCAGAAGTAAAACACCTCCACCACCTCCTCAAACAGCTCAAACCAAGCGAGAAGTACCTAAAAATAAAGCACCTACTGCTGAAAAGAGAGAGAGTGGACCTAAGCAAGCTGCAGTAAATGCTGCAGTTCAGAGGGTCCAGGTTCTTCCAGATGCTGATACTTTATTACATTTTGCCACGGAAAGTACTCCAGATGGATTTTCTTGTTCATCCAGCCTGAGTGCTCTGAGCCTCGATGAGCCATTTATACAGAAAGATGTGGAATTAAGAATAATGCCTCCAGTTCAGGAAAATGACAATGGGAATGAAACAGaa/gtaa	16/16	0.196004969606308	4	FACETS	1	0.962	1	0.864	0.776	0.955	CLONAL	3	TRUE	0	0.196004969606308	4		435	332	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604754	48604754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	100	372	1	ENST00000342988.3:c.1576G>A	p.Glu526Lys	p.E526K	ENST00000342988	NM_005359.5	526	Gaa/Aaa	12/12	1	2	FACETS	0.917	0.818	1	0.917	0.818	1	CLONAL	1	TRUE	1	0.233225300853864	2		373	935	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578433	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	57	474	0	ENST00000269305.4:c.497C>A	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	166	tCa/tAa	5/11	0.219404078725875	1	FACETS	0.867	0.745	1	0.867	0.745	1	CLONAL	1	TRUE	0	0.233225300853864	1		474	498	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719466	190719466	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	93	302	0	ENST00000441310.2:c.1468T>C	p.Ser490Pro	p.S490P	ENST00000441310	NM_000534.4	490	Tct/Cct	9/13	0.177457650115277	3	FACETS	0.974	0.865	1			1	CLONAL	1	TRUE	NA	0.233225300853864	3		302	914	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660891	227660891	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	90	370	0	ENST00000305123.5:c.2564T>C	p.Leu855Pro	p.L855P	ENST00000305123	NM_005544.2	855	cTg/cCg	1/2	0.233225300853864	4	FACETS	1	0.945	1	0.556	0.492	0.624	CLONAL	1	TRUE	2	0.233225300853864	4		370	856	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738807	145738807	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540601452	NA	P-0007784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	29	192	0	ENST00000428558.2:c.2258G>A	p.Arg753Gln	p.R753Q	ENST00000428558	NM_004260.3	753	cGg/cAg	14/22	0.233225300853864	5	FACETS	0.689	0.552	0.846	0.172	0.138	0.212	SUBCLONAL	1	TRUE	1	0.233225300853864	5		192	487	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0007841-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	355	324	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.216534037546778	6	FACETS	1	0.981	1	0.807	0.764	0.852	CLONAL	3	TRUE	2	0.216534037546778	6		324	1455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253911	NA	P-0007841-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	104	244	0	ENST00000269305.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000269305	NM_001126112.2	180	Gag/Aag	5/11	0.160098309117042	2	FACETS	1	0.972	1	0.624	0.558	0.693	CLONAL	1	TRUE	0	0.216534037546778	2		244	770	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330484	65330484	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007841-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	61	369	0	ENST00000342505.4:c.1162G>A	p.Asp388Asn	p.D388N	ENST00000342505	NM_002227.2	388	Gac/Aac	8/25	0.216534037546778	3	FACETS	0.918	0.791	1	0.459	0.395	0.529	CLONAL	1	TRUE	1	0.216534037546778	3		369	680	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136148	11136148	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007841-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1382	78	423	0	ENST00000358026.2:c.3132G>C	p.Lys1044Asn	p.K1044N	ENST00000358026	NM_001128849.1	1044	aaG/aaC	22/36	0.216534037546778	3	FACETS	0.547	0.478	0.621	0.273	0.239	0.311	SUBCLONAL	1	TRUE	1	0.216534037546778	3		423	1460	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0007850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	38	419	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	0.23	2		419	310	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720833	89720836	+	frameshift_variant	Frame_Shift_Del	DEL	AAAT	AAAT	-	rs587782304	NA	P-0007850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	25	184	0	ENST00000371953.3:c.987_990del	p.Asn329LysfsTer14	p.N329Kfs*14	ENST00000371953	NM_000314.4	328	gcAAAT/gc	8/9	0.175026179873925	3	FACETS	0.958	0.758	1	0.479	0.379	0.594	CLONAL	1	TRUE	1	0.23	3		184	253	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711885	89711885	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	59	317	0	ENST00000371953.3:c.504del	p.Ser170ValfsTer13	p.S170Vfs*13	ENST00000371953	NM_000314.4	168	aTt/at	6/9	0.175026179873925	3	FACETS	0.836	0.724	0.958	0.836	0.724	0.958	CLONAL	2	TRUE	1	0.23	3		317	342	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	209	291	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	0.939	1	CLONAL	1	TRUE	1	0.53910451615873	2		291	768	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0007865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	191	404	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.538670444760781	1	FACETS	0.91	0.847	0.974	0.91	0.847	0.974	CLONAL	1	TRUE	0	0.53910451615873	1		405	569	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575183	48575183	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	220	305	0	ENST00000342988.3:c.377T>C	p.Val126Ala	p.V126A	ENST00000342988	NM_005359.5	126	gTc/gCc	3/12	0.519686833319277	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.53910451615873	1		305	547	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189844	11189844	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	167	373	0	ENST00000361445.4:c.5665T>G	p.Phe1889Val	p.F1889V	ENST00000361445	NM_004958.3	1889	Ttc/Gtc	40/58	0.306009045451605	3	FACETS	0.945	0.873	1	0.945	0.873	1	CLONAL	2	TRUE	1	0.359542511723668	3		373	580	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612897	228612897	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	172	646	1	ENST00000366696.1:c.130C>T	p.Pro44Ser	p.P44S	ENST00000366696	NM_003493.2	44	Ccc/Tcc	1/1	0.359542511723668	6	FACETS	0.969	0.892	1	0.484	0.446	0.524	CLONAL	2	TRUE	2	0.359542511723668	6		647	849	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61712993	61712993	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1197531120	NA	P-0007888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	109	521	1	ENST00000401558.2:c.2418A>G	p.Ile806Met	p.I806M	ENST00000401558	NM_003400.3	806	atA/atG	20/25	0.359542511723668	3	FACETS	0.988	0.888	1	0.494	0.444	0.547	CLONAL	1	TRUE	1	0.359542511723668	3		522	724	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007064	152007064	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0007888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	100	477	0	ENST00000262189.6:c.836C>G	p.Ser279Ter	p.S279*	ENST00000262189	NM_170606.2	279	tCa/tGa	6/59	1	2	FACETS	0.926	0.828	1	0.926	0.828	1	CLONAL	1	TRUE	1	0.359542511723668	2		477	601	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521315	8521315	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	56	296	0	ENST00000356435.5:c.923T>C	p.Leu308Pro	p.L308P	ENST00000356435		308	cTg/cCg	9/35	1	2	FACETS	0.858	0.738	0.988	0.858	0.738	0.988	CLONAL	1	TRUE	1	0.359542511723668	2		296	363	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609055	43609055	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	87	580	1	ENST00000355710.3:c.1811C>A	p.Ala604Asp	p.A604D	ENST00000355710	NM_020975.4	604	gCt/gAt	10/20	NA	2	FACETS	1	0.89	1			1	INDETERMINATE	1	TRUE	NA	0.359542511723668	2		581	483	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99452063	99452063	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1273841068	NA	P-0007888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	162	448	0	ENST00000268035.6:c.1397C>T	p.Thr466Met	p.T466M	ENST00000268035	NM_000875.3	466	aCg/aTg	6/21	0.359542511723668	4	FACETS	0.983	0.906	1	0.656	0.604	0.709	CLONAL	2	TRUE	1	0.359542511723668	4		448	623	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243370	46243370	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	95	446	0	ENST00000334344.6:c.1725del	p.Pro576GlnfsTer5	p.P576Qfs*5	ENST00000334344	NM_152641.2	575	Ttt/tt	14/21	NA	2	FACETS	0.995	0.889	1			1	INDETERMINATE	1	TRUE	NA	0.359542511723668	2		446	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0007893-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	453	375	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.602434057178313	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.602434057178313	2		378	730	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726417	46726417	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007893-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	225	302	0	ENST00000371975.4:c.496G>A	p.Glu166Lys	p.E166K	ENST00000371975	NM_003579.3	166	Gag/Aag	7/18	NA	2	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.602434057178313	2		302	679	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658497	117658497	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007893-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	139	215	0	ENST00000368508.3:c.5086T>C	p.Tyr1696His	p.Y1696H	ENST00000368508	NM_002944.2	1696	Tac/Cac	31/43	1	2	FACETS	0.93	0.852	1	0.93	0.852	1	CLONAL	1	TRUE	1	0.602434057178313	2		215	496	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946355	2946355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372251654	NA	P-0007893-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	352	464	0	ENST00000396946.4:c.3382G>A	p.Val1128Ile	p.V1128I	ENST00000396946	NM_032415.4	1128	Gta/Ata	25/25	0.602434057178313	3	FACETS	1	0.973	1	0.523	0.494	0.552	CLONAL	1	TRUE	1	0.602434057178313	3		464	1455	SUCCESS
EED	8726	MSKCC	GRCh37	11	85975279	85975279	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007893-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	291	501	0	ENST00000263360.6:c.700G>C	p.Gly234Arg	p.G234R	ENST00000263360	NM_003797.3	234	Ggg/Cgg	7/12	1	2	FACETS	0.867	0.816	0.92	0.867	0.816	0.92	CLONAL	1	TRUE	1	0.602434057178313	2		501	1114	SUCCESS
APC	324	MSKCC	GRCh37	5	112151251	112151252	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs397515735	NA	P-0007893-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	341	511	0	ENST00000257430.4:c.896_897del	p.Ser299CysfsTer27	p.S299Cfs*27	ENST00000257430	NM_000038.5	298	caCTct/cact	9/16	0.602434057178313	1	FACETS	0.934	0.888	0.981	0.934	0.888	0.981	CLONAL	1	TRUE	0	0.602434057178313	1		511	847	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	77	246	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.907	0.812	1			1	INDETERMINATE	1	TRUE	NA	0.832511705977621	2		246	204	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	162	369	1	ENST00000269305.4:c.166G>T	p.Glu56Ter	p.E56*	ENST00000269305	NM_001126112.2	56	Gaa/Taa	4/11	1	2	FACETS	0.867	0.803	0.932	0.867	0.803	0.932	CLONAL	1	TRUE	1	0.832511705977621	2		370	449	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0007897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7784	704	748	1	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.832511705977621	24	FACETS	1	0.967	1			1	CLONAL	2	TRUE	NA	0.832511705977621	24		749	8488	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154836	2154836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1383314827	NA	P-0007897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	223	518	0	ENST00000434045.2:c.385C>T	p.Arg129Cys	p.R129C	ENST00000434045	NM_001127598.1	129	Cgc/Tgc	4/5	1	2	FACETS	0.962	0.903	1	0.962	0.903	1	CLONAL	1	TRUE	1	0.832511705977621	2		518	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0007909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	83	375	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.362021717057972	4	FACETS	1	0.936	1	1	0.985	1	INDETERMINATE	3	FALSE	2	0.603883046003847	4		378	143	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0007909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	77	454	5	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.603883046003847	3	FACETS	0.858	0.784	0.93	0.858	0.784	0.93	CLONAL	3	FALSE	0	0.603883046003847	3		459	129	SUCCESS
APC	324	MSKCC	GRCh37	5	112178606	112178606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1311878041	NA	P-0007909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	97	585	1	ENST00000257430.4:c.7315C>T	p.Arg2439Cys	p.R2439C	ENST00000257430	NM_000038.5	2439	Cgc/Tgc	16/16	0.603883046003847	3	FACETS	1	0.979	1	0.815	0.75	0.879	CLONAL	2	FALSE	0	0.603883046003847	3		586	171	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728481	190728481	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs567568410	NA	P-0007909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	16	303	0	ENST00000441310.2:c.1869G>C	p.Lys623Asn	p.K623N	ENST00000441310	NM_000534.4	623	aaG/aaC	10/13	0.301695341708218	4	FACETS	1	0.831	1	0.378	0.285	0.483	INDETERMINATE	1	FALSE	1	0.603883046003847	4		303	75	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430708	181430708	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	10	366	1	ENST00000325404.1:c.560A>T	p.Asn187Ile	p.N187I	ENST00000325404	NM_003106.3	187	aAt/aTt	1/1	0.301695341708218	4	FACETS	0.287	0.194	0.404	0.096	0.064	0.135	INDETERMINATE	1	FALSE	1	0.603883046003847	4		367	185	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477157	67477157	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	85	638	0	ENST00000327367.4:c.964C>T	p.Gln322Ter	p.Q322*	ENST00000327367	NM_005902.3	322	Cag/Tag	7/9	0.457278931394525	3	FACETS	0.818	0.736	0.902	0.545	0.491	0.601	CLONAL	2	FALSE	0	0.603883046003847	3		638	224	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136178	11136178	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	43	568	0	ENST00000358026.2:c.3162C>G	p.His1054Gln	p.H1054Q	ENST00000358026	NM_001128849.1	1054	caC/caG	22/36	0.450701371955534	4	FACETS	0.822	0.692	0.964	0.411	0.346	0.482	CLONAL	1	FALSE	2	0.603883046003847	4		568	278	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200489	138201187	+	splice_donor_variant,intron_variant	Splice_Site	DEL	GTGAGTGAAGTGGTTGACTTCCTAACACAGCGGCTGCTGTCCAGAAGGGGTTTTGTTCCTGACCTTTAAGAAAAAAAGCCCATGTAGGCAGTCAGGCAGAACTGTCAGGACCTACCGTGCTTTTCTACCAGCTTGTGCAGGGGACAGTCACGGTGGCCCTGCCAGCCGCCCATGGAGGCAAAAGGCACTGCGTGATTACAGCAGCTCCTAATATCACATTCCAAAAACCAGAGTGCCCTGTAGACAGAGCTCATGGGATGTGCTTTTACTAGACCATTCAGGTCTGGCATATCTAAGAGAGTCTAAGTTTAAACTAGACTTATTTTGCAACTTAGATATAACAGAACAATCTTAAAATCTGAAGAGTAGTAACTGGAGAGAAGGAAGTCTCTGTTGACACTGTAAGGAAACAGATGTGGTTTGGAAATCTCTCATTGGAAAGAAGGGTGATCAGGTAATGCCTGCTCCTTGCCTGTTCCTGTGAGCAATCAGTGCTTCAAGTTCAAAATGAGAGATTGGTAAAGCCAAAGATGTTTCCATAATAGGGATGTTATTTCTTTTGCTGAATTTATAGACTTAAACATATACATATATATATTTCTATACATTTAAGGCTGGCCTAATCTGTATTTGGAACCCATTTATTTCTCTACTGTCAGCATCTCTGTATCGGTGGGGTGACCCCTATGTGGTACTAAC	GTGAGTGAAGTGGTTGACTTCCTAACACAGCGGCTGCTGTCCAGAAGGGGTTTTGTTCCTGACCTTTAAGAAAAAAAGCCCATGTAGGCAGTCAGGCAGAACTGTCAGGACCTACCGTGCTTTTCTACCAGCTTGTGCAGGGGACAGTCACGGTGGCCCTGCCAGCCGCCCATGGAGGCAAAAGGCACTGCGTGATTACAGCAGCTCCTAATATCACATTCCAAAAACCAGAGTGCCCTGTAGACAGAGCTCATGGGATGTGCTTTTACTAGACCATTCAGGTCTGGCATATCTAAGAGAGTCTAAGTTTAAACTAGACTTATTTTGCAACTTAGATATAACAGAACAATCTTAAAATCTGAAGAGTAGTAACTGGAGAGAAGGAAGTCTCTGTTGACACTGTAAGGAAACAGATGTGGTTTGGAAATCTCTCATTGGAAAGAAGGGTGATCAGGTAATGCCTGCTCCTTGCCTGTTCCTGTGAGCAATCAGTGCTTCAAGTTCAAAATGAGAGATTGGTAAAGCCAAAGATGTTTCCATAATAGGGATGTTATTTCTTTTGCTGAATTTATAGACTTAAACATATACATATATATATTTCTATACATTTAAGGCTGGCCTAATCTGTATTTGGAACCCATTTATTTCTCTACTGTCAGCATCTCTGTATCGGTGGGGTGACCCCTATGTGGTACTAAC	-	novel	NA	P-0007909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	14	289	0	ENST00000237289.4:c.1906+1_1907-21del		p.X636_splice	ENST00000237289	NM_001270507.1	636			0.506285176098741	3	FACETS	0.349	0.253	0.464	0.174	0.126	0.232	SUBCLONAL	1	FALSE	1	0.603883046003847	3		289	173	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519975	NA	P-0007912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	172	438	0	ENST00000269305.4:c.403T>C	p.Cys135Arg	p.C135R	ENST00000269305	NM_001126112.2	135	Tgc/Cgc	5/11	0.664291929235427	1	FACETS	0.977	0.914	1	0.977	0.914	1	CLONAL	1	TRUE	0	0.664291929235427	1		438	354	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457264	67457264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750707381	NA	P-0007912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	151	363	1	ENST00000327367.4:c.238C>T	p.Arg80Trp	p.R80W	ENST00000327367	NM_005902.3	80	Cgg/Tgg	2/9	0.664291929235427	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.664291929235427	1		364	301	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109987	115109987	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs769814877	NA	P-0007912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	114	376	0	ENST00000257566.3:c.1891C>G	p.Leu631Val	p.L631V	ENST00000257566	NM_016569.3	631	Ctg/Gtg	8/8	0.413172264722893	1	FACETS	0.855	0.784	0.928	0.855	0.784	0.928	CLONAL	1	TRUE	0	0.664291929235427	1		376	268	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298118	123298118	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	102	556	0	ENST00000358487.5:c.736C>A	p.Leu246Met	p.L246M	ENST00000358487	NM_000141.4	246	Ctg/Atg	6/18	NA	2	FACETS	0.437	0.391	0.486			1	INDETERMINATE	1	TRUE	NA	0.664291929235427	2		556	703	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900269	32900269	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555280950	NA	P-0007912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	212	479	1	ENST00000380152.3:c.457C>A	p.Pro153Thr	p.P153T	ENST00000380152		153	Cca/Aca	5/27	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.664291929235427	2		480	612	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95583972	95583972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	86	377	0	ENST00000393063.1:c.1496G>A	p.Arg499Lys	p.R499K	ENST00000393063	NM_030621.3	499	aGa/aAa	10/28	NA	2	FACETS	0.642	0.572	0.717			1	INDETERMINATE	1	TRUE	NA	0.664291929235427	2		377	403	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229584	5229584	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	21	169	0	ENST00000357368.4:c.2267A>G	p.Tyr756Cys	p.Y756C	ENST00000357368	NM_002850.3	756	tAc/tGc	15/38	0.664291929235427	1	FACETS	0.332	0.259	0.416	0.332	0.259	0.416	SUBCLONAL	1	TRUE	0	0.664291929235427	1		169	127	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0007925-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	67	207	0				ENST00000310581	NM_198253.2	-/1132			0.397454029354757	3	FACETS	1	0.933	1	0.553	0.483	0.627	CLONAL	1	TRUE	1	0.421581984002663	3		207	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0007925-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	128	405	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	0.397454029354757	3	FACETS	0.777	0.709	0.848	0.777	0.709	0.848	SUBCLONAL	2	TRUE	1	0.421581984002663	3		405	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0007925-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	42	261	0	ENST00000269305.4:c.673-1G>C		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.397454029354757	3	FACETS	0.794	0.666	0.934	0.397	0.333	0.467	CLONAL	1	TRUE	1	0.421581984002663	3		261	304	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677849	117677849	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007925-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	80	396	0	ENST00000368508.3:c.4084G>T	p.Ala1362Ser	p.A1362S	ENST00000368508	NM_002944.2	1362	Gca/Tca	25/43	1	2	FACETS	0.879	0.777	0.987	0.879	0.777	0.987	CLONAL	1	TRUE	1	0.421581984002663	2		396	432	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134510	30134510	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007925-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	34	379	0	ENST00000263025.4:c.21G>T	p.Gln7His	p.Q7H	ENST00000263025	NM_002746.2	7	caG/caT	1/9	0.139164165595792	5	FACETS	0.887	0.727	1	0.222	0.181	0.267	INDETERMINATE	1	TRUE	1	0.421581984002663	5		379	297	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	15	484	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.134670218369652	4	FACETS	0.504	0.367	0.669	0.252	0.183	0.335	SUBCLONAL	1	TRUE	2	0.19	4		484	373	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0007931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	21	360	1				ENST00000310581	NM_198253.2	-/1132			0.305705047834593	2	FACETS	0.957	0.757	1			1	CLONAL	3	TRUE	NA	0.19	2		361	77	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514495	NA	P-0007931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	14	401	0	ENST00000269305.4:c.542G>A	p.Arg181His	p.R181H	ENST00000269305	NM_001126112.2	181	cGc/cAc	5/11	1	2	FACETS	1	0.734	1	1	0.734	1	CLONAL	1	TRUE	1	0.19	2		401	146	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490834	56490834	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759458720	NA	P-0007931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	13	445	0	ENST00000267101.3:c.2280G>A	p.Met760Ile	p.M760I	ENST00000267101	NM_001982.3	760	atG/atA	20/28	0.134670218369652	4	FACETS	0.646	0.461	0.873	0.323	0.23	0.437	SUBCLONAL	1	TRUE	2	0.19	4		445	252	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437575	56437575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1459309530	NA	P-0007931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	19	565	0	ENST00000407977.2:c.887G>A	p.Arg296His	p.R296H	ENST00000407977		296	cGt/cAt	8/10	0.134670218369652	0	FACETS	0.681	0.518	0.871			1	SUBCLONAL	1	TRUE	0	0.19	0		565	238	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612346	1612346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769011342	NA	P-0007931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	31	1057	4	ENST00000344749.5:c.1673G>A	p.Arg558His	p.R558H	ENST00000344749	NM_001136139.2	558	cGc/cAc	18/19	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.19	2		1061	283	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807561	36807561	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	12	432	0	ENST00000373129.3:c.1103A>G	p.Glu368Gly	p.E368G	ENST00000373129	NM_032017.1	368	gAg/gGg	12/12	0.305705047834593	2	FACETS	0.859	0.606	1			1	CLONAL	1	TRUE	NA	0.19	2		432	147	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552821	226552821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182639036	NA	P-0007931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	14	586	1	ENST00000366794.5:c.2540G>A	p.Arg847His	p.R847H	ENST00000366794	NM_001618.3	847	cGt/cAt	19/23	0.134670218369652	3	FACETS	0.667	0.482	0.891	0.333	0.241	0.446	SUBCLONAL	1	TRUE	1	0.19	3		587	242	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656969	47656969	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779075	NA	P-0007931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	16	721	0	ENST00000233146.2:c.1165C>T	p.Arg389Ter	p.R389*	ENST00000233146	NM_000251.2	389	Cga/Tga	7/16	1	2	FACETS	0.556	0.41	0.73	0.556	0.41	0.73	SUBCLONAL	1	TRUE	1	0.19	2		721	303	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630312	187630312	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765758588	NA	P-0007931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	21	544	2	ENST00000441802.2:c.670G>A	p.Ala224Thr	p.A224T	ENST00000441802	NM_005245.3	224	Gct/Act	2/27	0.134670218369652	3	FACETS	0.773	0.596	0.981	0.387	0.298	0.491	CLONAL	1	TRUE	1	0.19	3		546	313	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294277	1294277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	10	283	3	ENST00000310581.5:c.724G>A	p.Ala242Thr	p.A242T	ENST00000310581	NM_198253.2	242	Gct/Act	2/16	0.305705047834593	2	FACETS	1	0.746	1			1	CLONAL	1	TRUE	NA	0.19	2		286	95	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041242	112041242	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	33	969	2	ENST00000368678.4:c.13C>T	p.Gln5Ter	p.Q5*	ENST00000368678		5	Caa/Taa	3/13	0.305705047834593	2	FACETS	0.814	0.662	0.984			1	CLONAL	1	TRUE	NA	0.19	2		971	427	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508284	106508284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	13	193	0	ENST00000359195.3:c.278C>T	p.Pro93Leu	p.P93L	ENST00000359195	NM_002649.2	93	cCg/cTg	2/11	0.261841419767788	4	FACETS	1	0.827	1	0.617	0.443	0.826	CLONAL	1	TRUE	2	0.19	4		193	132	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867262	68867262	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	19	593	0	ENST00000261769.5:c.2509G>T	p.Gly837Ter	p.G837*	ENST00000261769	NM_004360.3	837	Gga/Tga	16/16	0.134670218369652	0	FACETS	0.596	0.452	0.764			1	SUBCLONAL	1	TRUE	0	0.19	0		593	272	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805041	89805041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772505725	NA	P-0007931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	16	726	1	ENST00000389301.3:c.4336G>A	p.Ala1446Thr	p.A1446T	ENST00000389301	NM_000135.2	1446	Gct/Act	43/43	0.134670218369652	0	FACETS	0.604	0.447	0.79			1	SUBCLONAL	1	TRUE	0	0.19	0		727	226	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40456578	40456578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1204224434	NA	P-0007931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	20	960	2	ENST00000345506.4:c.1288C>T	p.Arg430Trp	p.R430W	ENST00000345506	NM_003152.3	430	Cgg/Tgg	12/20	0.134670218369652	0	FACETS	0.44	0.335	0.562			1	SUBCLONAL	1	TRUE	0	0.19	0		962	388	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40457680	40457680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	22	946	2	ENST00000345506.4:c.1433C>T	p.Ala478Val	p.A478V	ENST00000345506	NM_003152.3	478	gCc/gTc	13/20	0.134670218369652	0	FACETS	0.496	0.384	0.627			1	SUBCLONAL	1	TRUE	0	0.19	0		948	378	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227057	2227057	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	13	223	1	ENST00000398665.3:c.4537G>A	p.Ala1513Thr	p.A1513T	ENST00000398665	NM_032482.2	1513	Gct/Act	27/28	1	2	FACETS	0.752	0.544	0.998	1	0.878	1	CLONAL	2	TRUE	1	0.19	2		224	91	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117439	4117439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202220799	NA	P-0007931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	20	539	1	ENST00000262948.5:c.281C>T	p.Ser94Leu	p.S94L	ENST00000262948	NM_030662.3	94	tCg/tTg	2/11	1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	1	0.19	2		540	193	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389134	31389134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377397627	NA	P-0007931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	20	671	0	ENST00000328111.2:c.2047C>T	p.Arg683Cys	p.R683C	ENST00000328111	NM_006892.3	683	Cgc/Tgc	19/23	0.134670218369652	3	FACETS	0.781	0.598	0.996	0.391	0.299	0.498	CLONAL	1	TRUE	1	0.19	3		671	295	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070875	30070875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776109136	NA	P-0007931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	15	686	1	ENST00000338641.4:c.1391C>T	p.Ala464Val	p.A464V	ENST00000338641	NM_000268.3	464	gCg/gTg	13/16	1	2	FACETS	0.583	0.426	0.771	0.583	0.426	0.771	SUBCLONAL	1	TRUE	1	0.19	2		687	271	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545993	41545993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	17	777	3	ENST00000263253.7:c.2608C>T	p.Pro870Ser	p.P870S	ENST00000263253	NM_001429.3	870	Cca/Tca	14/31	1	2	FACETS	0.581	0.433	0.757	0.581	0.433	0.757	SUBCLONAL	1	TRUE	1	0.19	2		780	308	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874051	151874052	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0007931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	22	897	0	ENST00000262189.6:c.8486_8487del	p.Pro2829GlnfsTer3	p.P2829Qfs*3	ENST00000262189	NM_170606.2	2829	cCA/c	38/59	1	2	FACETS	0.633	0.49	0.799	0.633	0.49	0.799	SUBCLONAL	1	TRUE	1	0.19	2		897	366	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578204	7578204	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520001	NA	P-0007965-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	35	578	0	ENST00000269305.4:c.645T>G	p.Ser215Arg	p.S215R	ENST00000269305	NM_001126112.2	215	agT/agG	6/11	1	2	FACETS	0.507	0.414	0.613	0.507	0.414	0.613	SUBCLONAL	1	TRUE	1	0.14	2		578	986	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577144	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs879253942	NA	P-0007965-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	62	519	0	ENST00000269305.4:c.794T>C	p.Leu265Pro	p.L265P	ENST00000269305	NM_001126112.2	265	cTg/cCg	8/11	1	2	FACETS	0.982	0.846	1	0.982	0.846	1	CLONAL	1	TRUE	1	0.14	2		519	902	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610547	215610547	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007965-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	50	512	0	ENST00000260947.4:c.1709T>G	p.Leu570Arg	p.L570R	ENST00000260947	NM_000465.2	570	cTt/cGt	8/11	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.14	2		512	704	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449516	187449516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs551620719	NA	P-0007965-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	90	356	0	ENST00000232014.4:c.364C>T	p.Arg122Trp	p.R122W	ENST00000232014	NM_001130845.1	122	Cgg/Tgg	4/10	1	2	FACETS	0.951	0.844	1	1	0.985	1	CLONAL	2	TRUE	1	0.14	2		356	676	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061211	38061240	+	inframe_deletion	In_Frame_Del	DEL	AGTAGCAGCCGTTCTCGAACATGTTGCCGG	AGTAGCAGCCGTTCTCGAACATGTTGCCGG	-	novel	NA	P-0007965-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	28	342	0	ENST00000250448.2:c.749_778del	p.Ser250_Tyr259del	p.S250_Y259del	ENST00000250448	NM_004496.3	250	tCCGGCAACATGTTCGAGAACGGCTGCTACTtg/ttg	2/2	1	2	FACETS	1	0.82	1	1	0.82	1	CLONAL	1	TRUE	1	0.14	2		342	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0007974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	272	504	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.759774917131975	1	FACETS	0.961	0.916	1	0.961	0.916	1	CLONAL	1	TRUE	0	0.759774917131975	1		504	462	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325778	30325778	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	316	245	0	ENST00000322652.5:c.1976A>G	p.His659Arg	p.H659R	ENST00000322652	NM_015355.2	659	cAt/cGt	16/16	0.634322267681022	3	FACETS	1	0.987	1			1	CLONAL	2	TRUE	NA	0.759774917131975	3		245	532	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685315	89685315	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1554897280	NA	P-0008006-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	139	337	0	ENST00000371953.3:c.209+1G>A		p.X70_splice	ENST00000371953	NM_000314.4	70			0.3	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.25	2		337	460	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028636	12028636	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008006-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	96	524	0	ENST00000353533.5:c.839C>A	p.Ser280Ter	p.S280*	ENST00000353533	NM_003010.3	280	tCa/tAa	8/11	0.27638703463372	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.25	1		524	537	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496965	29496965	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0008015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	255	333	2	ENST00000356175.3:c.536T>A	p.Leu179Ter	p.L179*	ENST00000356175	NM_000267.3	179	tTg/tAg	5/57	1	2	FACETS	0.734	0.689	0.779	0.734	0.689	0.779	SUBCLONAL	1	TRUE	1	0.885190043601718	2		335	785	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29662010	29662010	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1567615902	NA	P-0008015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	266	374	0	ENST00000356175.3:c.5904C>G	p.Tyr1968Ter	p.Y1968*	ENST00000356175	NM_000267.3	1968	taC/taG	39/57	1	2	FACETS	0.988	0.935	1	0.988	0.935	1	CLONAL	1	TRUE	1	0.885190043601718	2		374	608	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933631	39933641	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGTGACCGC	CTGGTGACCGC	-	novel	NA	P-0008015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	289	184	0	ENST00000378444.4:c.958_968del	p.Ala320TrpfsTer57	p.A320Wfs*57	ENST00000378444	NM_001123385.1	320	GCGGTCACCAGt/t	4/15	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.885190043601718	1		184	343	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0008040-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	64	286	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		287	729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579315	7579316	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0008040-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	41	305	0	ENST00000269305.4:c.371_372del	p.Cys124TyrfsTer24	p.C124Yfs*24	ENST00000269305	NM_001126112.2	124	tGC/t	4/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		305	628	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202996	16202996	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747427891	NA	P-0008049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	37	361	0	ENST00000375759.3:c.704G>A	p.Arg235Gln	p.R235Q	ENST00000375759	NM_015001.2	235	cGg/cAg	3/15	1	2	FACETS	0.239	0.197	0.287	0.239	0.197	0.287	SUBCLONAL	1	TRUE	1	0.548540553683749	2		361	564	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936831	32936831	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs81002873	NA	P-0008049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	294	495	0	ENST00000380152.3:c.7976+1G>A		p.X2659_splice	ENST00000380152		2659			0.374315420136436	4	FACETS	0.89	0.839	0.941			1	CLONAL	2	TRUE	NA	0.548540553683749	4		495	933	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846037	68846037	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0008049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	115	672	0	ENST00000261769.5:c.1009-1G>A		p.X337_splice	ENST00000261769	NM_004360.3	337			1	2	FACETS	0.519	0.467	0.574	0.519	0.467	0.574	SUBCLONAL	1	TRUE	1	0.548540553683749	2		672	808	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991902	72991902	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	190	1002	2	ENST00000268489.5:c.2143C>T	p.Arg715Ter	p.R715*	ENST00000268489	NM_006885.3	715	Cga/Tga	2/10	1	2	FACETS	0.654	0.603	0.706	0.654	0.603	0.706	SUBCLONAL	1	TRUE	1	0.548540553683749	2		1004	1060	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941462	48941699	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTACCTCACTTTTAGATAGACCTTATTTATATTGCATGCGAACTCAGTGTATATTACAAAATTAAATGTATATTATACAAAAATTCTTTAATGAAATCTGTGCCTCTGTGTGCTGAGAGATGTAATGACATGTAAAGGATAATTGTCAGTGACTTTTTTCTTTCAAGGTTGAAAATCTTTCTAAACGATACGAAGAAATTTATCTTAAAAATAAAGATCTAGATGCAAGATTATTTT	TGTACCTCACTTTTAGATAGACCTTATTTATATTGCATGCGAACTCAGTGTATATTACAAAATTAAATGTATATTATACAAAAATTCTTTAATGAAATCTGTGCCTCTGTGTGCTGAGAGATGTAATGACATGTAAAGGATAATTGTCAGTGACTTTTTTCTTTCAAGGTTGAAAATCTTTCTAAACGATACGAAGAAATTTATCTTAAAAATAAAGATCTAGATGCAAGATTATTTT	-	novel	NA	P-0008049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	39	33	0	ENST00000267163.4:c.940-166_1011del		p.X314_splice	ENST00000267163	NM_000321.2	314		10/27	0.384385087799972	3	FACETS	0.915	0.803	1	1	0.964	1	CLONAL	3	TRUE	1	0.548540553683749	3		33	66	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109975	115109978	+	frameshift_variant	Frame_Shift_Del	DEL	GCAT	GCAT	-	novel	NA	P-0008049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	68	342	0	ENST00000257566.3:c.1900_1903del	p.Met634AlafsTer254	p.M634Afs*254	ENST00000257566	NM_016569.3	634	ATGCgc/gc	8/8	0.141826664526236	3	FACETS	0.812	0.71	0.922	0.271	0.236	0.308	INDETERMINATE	1	TRUE	0	0.548540553683749	3		342	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0008052-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	242	538	2	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.569734359359718	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.569734359359718	1		540	577	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730915	40730915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753788938	NA	P-0008052-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	141	260	0	ENST00000373198.4:c.3620G>A	p.Arg1207His	p.R1207H	ENST00000373198	NM_133170.3	1207	cGt/cAt	27/32	1	2	FACETS	0.98	0.899	1	0.98	0.899	1	CLONAL	1	TRUE	1	0.569734359359718	2		260	505	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0008059-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	16	484	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		484	197	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0008059-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	22	293	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		293	137	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0008059-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	13	330	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		330	98	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0008075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	135	932	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.277718844413061	2		934	965	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0008075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	62	400	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	0.277718844413061	2		401	406	SUCCESS
APC	324	MSKCC	GRCh37	5	112175476	112175476	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	49	326	0	ENST00000257430.4:c.4188del	p.Phe1396LeufsTer19	p.F1396Lfs*19	ENST00000257430	NM_000038.5	1395	agT/ag	16/16	1	2	FACETS	0.969	0.824	1	0.969	0.824	1	CLONAL	1	TRUE	1	0.277718844413061	2		326	364	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117848	70117848	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0008075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	215	332	0	ENST00000245479.2:c.316A>T	p.Lys106Ter	p.K106*	ENST00000245479	NM_000346.3	106	Aag/Tag	1/3	0.277718844413061	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	1	0.277718844413061	4		332	596	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579505	7579505	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	69	348	0	ENST00000269305.4:c.182del	p.Asp61ValfsTer62	p.D61Vfs*62	ENST00000269305	NM_001126112.2	61	gAt/gt	4/11	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.277718844413061	2		348	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0008077-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	60	458	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.184704491321429	4	FACETS	1	0.917	1	0.721	0.624	0.825	CLONAL	2	TRUE	1	0.184704491321429	4		458	356	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243484	46243484	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008077-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	63	357	0	ENST00000334344.6:c.1837C>T	p.Gln613Ter	p.Q613*	ENST00000334344	NM_152641.2	613	Cag/Tag	14/21	0.184704491321429	6	FACETS	1	0.939	1	0.846	0.739	0.96	CLONAL	3	TRUE	2	0.184704491321429	6		357	276	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741454	145741454	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008077-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	54	502	2	ENST00000428558.2:c.1049G>T	p.Arg350Met	p.R350M	ENST00000428558	NM_004260.3	350	aGg/aTg	5/22	0.184704491321429	6	FACETS	0.92	0.792	1	0.92	0.792	1	CLONAL	3	TRUE	3	0.184704491321429	6		504	290	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741492	17741492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008077-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	11	310	0	ENST00000250003.3:c.163G>A	p.Ala55Thr	p.A55T	ENST00000250003	NM_002478.4	55	Gcg/Acg	1/3	0.184704491321429	1	FACETS	0.901	0.626	1	0.901	0.626	1	CLONAL	1	TRUE	0	0.184704491321429	1		310	120	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467176	99467176	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008077-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	27	495	0	ENST00000268035.6:c.2557C>A	p.Pro853Thr	p.P853T	ENST00000268035	NM_000875.3	853	Ccg/Acg	12/21	0.184704491321429	7	FACETS	1	0.906	1	0.315	0.251	0.389	CLONAL	1	TRUE	3	0.184704491321429	7		495	339	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667601	29667601	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008077-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	94	387	0	ENST00000356175.3:c.6937G>C	p.Gly2313Arg	p.G2313R	ENST00000356175	NM_000267.3	2313	Ggt/Cgt	46/57	0.184704491321429	4	FACETS	1	0.911	1	1	0.911	1	CLONAL	3	TRUE	1	0.184704491321429	4		387	395	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868166	45868166	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1463343405	NA	P-0008077-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	43	383	0	ENST00000391945.4:c.524A>G	p.Tyr175Cys	p.Y175C	ENST00000391945	NM_000400.3	175	tAc/tGc	7/23	0.184704491321429	1	FACETS	1	0.902	1	1	0.973	1	CLONAL	2	TRUE	0	0.184704491321429	1		383	194	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0008083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	113	208	1	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	0.41526033148749	3	FACETS	1	0.981	1	0.663	0.602	0.725	CLONAL	1	TRUE	1	0.618326205482228	3		209	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0008083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	211	485	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.58472760202075	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.618326205482228	2		485	334	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006194	22006194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	22	457	0	ENST00000276925.6:c.209C>T	p.Ala70Val	p.A70V	ENST00000276925	NM_004936.3	70	gCg/gTg	2/2	0.58472760202075	2	FACETS	0.244	0.189	0.307	0.122	0.094	0.154	SUBCLONAL	1	TRUE	0	0.618326205482228	2		457	292	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275068	41275068	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	34	601	0	ENST00000349496.5:c.1234G>C	p.Asp412His	p.D412H	ENST00000349496	NM_001904.3	412	Gat/Cat	9/15	0.58472760202075	2	FACETS	0.47	0.386	0.563	0.235	0.193	0.282	SUBCLONAL	1	TRUE	0	0.618326205482228	2		601	234	SUCCESS
APC	324	MSKCC	GRCh37	5	112164585	112164585	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398123116	NA	P-0008083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	36	427	0	ENST00000257430.4:c.1659G>A	p.Trp553Ter	p.W553*	ENST00000257430	NM_000038.5	553	tgG/tgA	14/16	0.618326205482228	1	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	0	0.618326205482228	1		427	78	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045946	26045946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	164	1309	3	ENST00000540144.1:c.308G>T	p.Gly103Val	p.G103V	ENST00000540144	NM_003531.2	103	gGa/gTa	1/1	0.618326205482228	3	FACETS	1	0.931	1	0.506	0.466	0.548	CLONAL	1	TRUE	1	0.618326205482228	3		1312	686	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2952986	2952986	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747477589	NA	P-0008083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	378	474	0	ENST00000396946.4:c.2954C>G	p.Ala985Gly	p.A985G	ENST00000396946	NM_032415.4	985	gCc/gGc	22/25	0.41526033148749	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.618326205482228	3		474	713	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249029	55249029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs483352806	NA	P-0008083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	38	525	1	ENST00000275493.2:c.2327G>A	p.Arg776His	p.R776H	ENST00000275493	NM_005228.3	776	cGc/cAc	20/28	0.41526033148749	3	FACETS	0.392	0.324	0.468	0.196	0.162	0.234	SUBCLONAL	1	TRUE	1	0.618326205482228	3		526	410	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501331	140501331	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	36	367	0	ENST00000288602.6:c.741T>A	p.Phe247Leu	p.F247L	ENST00000288602	NM_004333.4	247	ttT/ttA	6/18	1	2	FACETS	0.82	0.686	0.964	0.82	0.686	0.964	CLONAL	1	TRUE	1	0.618326205482228	2		367	142	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920396	114920396	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	228	811	0	ENST00000543371.1:c.1337A>C	p.Lys446Thr	p.K446T	ENST00000543371	NM_001198531.1	446	aAg/aCg	13/14	0.195038617483296	4	FACETS	0.932	0.874	0.992	0.932	0.874	0.992	INDETERMINATE	2	TRUE	2	0.618326205482228	4		811	640	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052630	42052630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372072518	NA	P-0008083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	175	1106	2	ENST00000219905.7:c.7301G>A	p.Arg2434Gln	p.R2434Q	ENST00000219905	NM_001164273.1	2434	cGg/cAg	20/24	0.616381850995315	1	FACETS	0.54	0.499	0.583	0.54	0.499	0.583	SUBCLONAL	1	TRUE	0	0.618326205482228	1		1108	724	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646234	23646234	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs180177103	NA	P-0008083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	233	822	1	ENST00000261584.4:c.1633G>T	p.Glu545Ter	p.E545*	ENST00000261584	NM_024675.3	545	Gaa/Taa	4/13	0.618326205482228	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.618326205482228	2		823	346	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581186	48581204	+	frameshift_variant	Frame_Shift_Del	DEL	CATGACTTTGAGGGACAGC	CATGACTTTGAGGGACAGC	-	novel	NA	P-0008083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	102	426	0	ENST00000342988.3:c.493_511del	p.Asp165ArgfsTer31	p.D165Rfs*31	ENST00000342988	NM_005359.5	164	CATGACTTTGAGGGACAGCca/ca	5/12	0.58472760202075	2	FACETS	0.846	0.777	0.914	0.846	0.777	0.914	CLONAL	2	TRUE	0	0.618326205482228	2		426	195	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827998	72828017	+	frameshift_variant	Frame_Shift_Del	DEL	TATTCCCGTTGCACTGTCGT	TATTCCCGTTGCACTGTCGT	-	novel	NA	P-0008083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	114	1272	1	ENST00000268489.5:c.8564_8583del	p.Asn2855SerfsTer3	p.N2855Sfs*3	ENST00000268489	NM_006885.3	2855	aACGACAGTGCAACGGGAATA/a	9/10	0.618326205482228	2	FACETS	0.505	0.455	0.558	0.253	0.227	0.279	SUBCLONAL	1	TRUE	0	0.618326205482228	2		1273	730	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415537	152415537	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519714	NA	P-0008104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	99	610	0	ENST00000206249.3:c.1387T>C	p.Ser463Pro	p.S463P	ENST00000206249	NM_000125.3	463	Tcc/Ccc	7/8	0.208396817504667	3	FACETS	0.805	0.718	0.898	0.268	0.239	0.3	CLONAL	1	TRUE	0	0.322244641864473	3		610	886	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933485	100933510	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TACAGAGAAGAAAAAAAAGAAATTCA	TACAGAGAAGAAAAAAAAGAAATTCA	-	novel	NA	P-0008124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	28	234	0	ENST00000325455.5:c.1907-27_1907-2del		p.X636_splice	ENST00000325455	NM_001202474.3	636			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		234	331	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176470	123176470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008139-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	127	427	0	ENST00000218089.9:c.437G>A	p.Arg146Gln	p.R146Q	ENST00000218089	NM_001042749.1	146	cGa/cAa	7/35	0.454845752132832	2	FACETS	0.999	0.93	1			1	CLONAL	2	TRUE	NA	0.586060136514036	2		427	217	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0008153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	276	370	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.802522923609933	2		370	662	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0008153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	486	918	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.802522923609933	2		918	1185	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0008153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	217	419	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.945	0.886	1	0.945	0.886	1	CLONAL	1	TRUE	1	0.802522923609933	2		419	572	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0008153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	328	580	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	1	TRUE	NA	0.802522923609933	2		580	786	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132522	11132522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778175819	NA	P-0008153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	354	487	1	ENST00000358026.2:c.2738C>T	p.Pro913Leu	p.P913L	ENST00000358026	NM_001128849.1	913	cCg/cTg	19/36	0.776570828702696	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.802522923609933	1		488	471	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55524194	55524194	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	247	543	0	ENST00000288135.5:c.13C>A	p.Arg5Ser	p.R5S	ENST00000288135	NM_000222.2	5	Cgc/Agc	1/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.802522923609933	2		543	589	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841049	15841049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	513	818	0	ENST00000307771.7:c.1133G>A	p.Arg378Gln	p.R378Q	ENST00000307771	NM_005089.3	378	cGg/cAg	11/11	NA	2	FACETS	1	0.963	1			1	INDETERMINATE	1	TRUE	NA	0.802522923609933	2		818	1273	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022914	27022942	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCCGCCGCCAGCAGCCTGGGCAACCCG	CCGCCGCCGCCAGCAGCCTGGGCAACCCG	-	novel	NA	P-0008153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	13	27	0	ENST00000324856.7:c.31_59del	p.Ser11AlafsTer90	p.S11Afs*90	ENST00000324856	NM_006015.4	7	cCCGCCGCCGCCAGCAGCCTGGGCAACCCG/c	1/20	1	2	FACETS	0.623	0.458	0.81	0.623	0.458	0.81	SUBCLONAL	1	TRUE	1	0.802522923609933	2		27	52	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692965	89692980	+	frameshift_variant	Frame_Shift_Del	DEL	AGGCCCTAGATTTCTA	AGGCCCTAGATTTCTA	-	novel	NA	P-0008153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	177	295	0	ENST00000371953.3:c.449_464del	p.Glu150ValfsTer4	p.E150Vfs*4	ENST00000371953	NM_000314.4	150	gAGGCCCTAGATTTCTAt/gt	5/9	0.802522923609933	3	FACETS	0.969	0.897	1			1	CLONAL	1	TRUE	NA	0.802522923609933	3		295	638	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371799	55371820	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCCGCGCTGGGCCCCGAG	GGCGGCCGCGCTGGGCCCCGAG	-	novel	NA	P-0008153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	48	53	0	ENST00000297316.4:c.499_520del	p.Leu167TrpfsTer213	p.L167Wfs*213	ENST00000297316	NM_022454.3	163	caGGCGGCCGCGCTGGGCCCCGAG/ca	2/2	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.802522923609933	2		53	113	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654704	67654706	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	novel	NA	P-0008153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	239	414	0	ENST00000264010.4:c.1191_1193del	p.His397_Met398delinsGln	p.H397_M398delinsQ	ENST00000264010	NM_006565.3	397	caCATg/cag	6/12	1	2	FACETS	0.898	0.844	0.954	0.898	0.844	0.954	CLONAL	1	TRUE	1	0.802522923609933	2		414	663	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092847	27092864	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAATTCTGCAGGTAAGTG	CAATTCTGCAGGTAAGTG	-	novel	NA	P-0008153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	261	443	0	ENST00000324856.7:c.2869_2878+8del		p.X957_splice	ENST00000324856	NM_006015.4	957		9/20	1	2	FACETS	0.948	0.894	1	0.948	0.894	1	CLONAL	1	TRUE	1	0.802522923609933	2		443	686	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155721	56155722	+	stop_gained	Nonsense_Mutation	DNP	AA	AA	GT	novel	NA	P-0008153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	373	313	0	ENST00000399503.3:c.813_814delinsGT	p.Lys272Ter	p.K272*	ENST00000399503	NM_005921.1	271	agAAaa/agGTaa	3/20	0.802522923609933	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.802522923609933	2		313	444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0008172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	261	932	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.195770057323571	2	FACETS	1	0.99	1	0.644	0.603	0.687	INDETERMINATE	1	TRUE	0	0.337323208097884	2		934	1201	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0008172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	214	484	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.214770549326019	4	FACETS	1	0.988	1	0.655	0.607	0.704	CLONAL	1	TRUE	2	0.337323208097884	4		484	1296	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732404	74732404	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1256	318	587	0	ENST00000359995.5:c.505T>A	p.Ser169Thr	p.S169T	ENST00000359995	NM_001195427.1	169	Tcc/Acc	2/3	0.506875114806193	3	FACETS	0.999	0.941	1	0.5	0.47	0.53	CLONAL	1	TRUE	1	0.506875114806193	3		587	1574	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069321	30069357	+	frameshift_variant	Frame_Shift_Del	DEL	AAACTTCTGGCCCAGAAGGCCGCAGAGGCTGAGCAGG	AAACTTCTGGCCCAGAAGGCCGCAGAGGCTGAGCAGG	-	novel	NA	P-0008177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	192	348	0	ENST00000338641.4:c.1189_1225del	p.Leu397CysfsTer17	p.L397Cfs*17	ENST00000338641	NM_000268.3	396	AAACTTCTGGCCCAGAAGGCCGCAGAGGCTGAGCAGGaa/aa	12/16	0.506875114806193	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.506875114806193	1		348	562	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0008187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	346	422	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.638826862969368	2	FACETS	0.876	0.839	0.912	0.876	0.839	0.912	CLONAL	2	TRUE	0	0.659755805530302	2		422	599	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481620	56481620	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	87	468	0	ENST00000267101.3:c.655T>C	p.Phe219Leu	p.F219L	ENST00000267101	NM_001982.3	219	Ttt/Ctt	6/28	1	2	FACETS	0.282	0.249	0.318	0.282	0.249	0.318	SUBCLONAL	1	TRUE	1	0.659755805530302	2		468	934	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956164	55956164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780209077	NA	P-0008187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	296	512	1	ENST00000263923.4:c.3151C>T	p.Arg1051Trp	p.R1051W	ENST00000263923	NM_002253.2	1051	Cgg/Tgg	23/30	0.638826862969368	2	FACETS	0.94	0.886	0.994	0.47	0.443	0.497	CLONAL	1	TRUE	0	0.659755805530302	2		513	955	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120532	94120532	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	351	685	0	ENST00000369303.4:c.519G>T	p.Glu173Asp	p.E173D	ENST00000369303	NM_004440.3	173	gaG/gaT	3/17	0.659755805530302	3	FACETS	0.965	0.912	1	0.482	0.456	0.51	CLONAL	1	TRUE	1	0.659755805530302	3		685	1467	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041440	47041440	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	263	252	0	ENST00000377604.3:c.1784A>T	p.Gln595Leu	p.Q595L	ENST00000377604	NM_001204468.1	595	cAg/cTg	16/24	0.659755805530302	2	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.659755805530302	2		252	707	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573498	48573498	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	267	470	0	ENST00000342988.3:c.82del	p.Gln28LysfsTer17	p.Q28Kfs*17	ENST00000342988	NM_005359.5	28	Caa/aa	2/12	0.624688362360264	1	FACETS	0.905	0.857	0.955	0.905	0.857	0.955	CLONAL	1	TRUE	0	0.659755805530302	1		470	599	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0008233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	87	148	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.829716941842302	1	FACETS	0.916	0.846	0.983	0.916	0.846	0.983	CLONAL	1	TRUE	0	0.829716941842302	1		148	134	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45800144	45800144	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	433	574	0	ENST00000450313.1:c.76C>T	p.His26Tyr	p.H26Y	ENST00000450313	NM_012222.2	26	Cac/Tac	2/16	NA	2	FACETS	0.956	0.914	0.999			1	INDETERMINATE	1	TRUE	NA	0.829716941842302	2		574	1092	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99823074	99823074	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	281	348	0	ENST00000280892.6:c.138G>C	p.Gln46His	p.Q46H	ENST00000280892	NM_001130678.1	46	caG/caC	2/7	0.809838148302119	1	FACETS	0.95	0.911	0.989	0.95	0.911	0.989	CLONAL	1	TRUE	0	0.829716941842302	1		348	417	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250806	26250806	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2014	628	726	0	ENST00000446824.2:c.28A>G	p.Lys10Glu	p.K10E	ENST00000446824	NM_021018.2	10	Aag/Gag	1/1	0.659446074547775	4	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.829716941842302	4		726	2642	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183022	32183022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	251	371	0	ENST00000375023.3:c.2002C>T	p.His668Tyr	p.H668Y	ENST00000375023	NM_004557.3	668	Cac/Tac	12/30	0.829716941842302	5	FACETS	0.993	0.927	1	0.248	0.231	0.266	CLONAL	1	TRUE	1	0.829716941842302	5		371	1368	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609958	43609958	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	735	1096	0	ENST00000355710.3:c.1910T>C	p.Val637Ala	p.V637A	ENST00000355710	NM_020975.4	637	gTg/gCg	11/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.829716941842302	2		1096	1746	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480335	56480335	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	280	365	0	ENST00000267101.3:c.442T>C	p.Tyr148His	p.Y148H	ENST00000267101	NM_001982.3	148	Tat/Cat	4/28	NA	2	FACETS	0.925	0.873	0.976			1	INDETERMINATE	1	TRUE	NA	0.829716941842302	2		365	730	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0008245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	219	484	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.234004317695848	4	FACETS	0.778	0.723	0.835	0.778	0.723	0.835	SUBCLONAL	2	TRUE	2	0.347998723514967	4		484	1090	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440713	56440713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779337229	NA	P-0008245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	185	987	1	ENST00000407977.2:c.505G>A	p.Ala169Thr	p.A169T	ENST00000407977		169	Gct/Act	5/10	0.108338287140316	4	FACETS	1	0.968	1	1	0.968	1	INDETERMINATE	2	TRUE	2	0.347998723514967	4		988	665	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11554273	NA	P-0008245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	123	916	0	ENST00000371085.3:c.601C>A	p.Arg201Ser	p.R201S	ENST00000371085	NM_000516.4	201	Cgt/Agt	8/13	1	2	FACETS	0.887	0.802	0.976	0.887	0.802	0.976	CLONAL	1	TRUE	1	0.347998723514967	2		916	797	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265040	198265040	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	234	886	0	ENST00000335508.6:c.2837A>C	p.Lys946Thr	p.K946T	ENST00000335508	NM_012433.2	946	aAa/aCa	19/25	0.234004317695848	4	FACETS	0.853	0.796	0.913	0.853	0.796	0.913	CLONAL	2	TRUE	2	0.347998723514967	4		886	1062	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448355	56448366	+	inframe_deletion	In_Frame_Del	DEL	TGTCGTCATCAC	TGTCGTCATCAC	-	novel	NA	P-0008245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	180	809	1	ENST00000407977.2:c.281_292del	p.Ser94_Asp97del	p.S94_D97del	ENST00000407977		94	aGTGATGACGACAat/aat	3/10	0.108338287140316	4	FACETS	0.981	0.907	1	0.981	0.907	1	INDETERMINATE	2	TRUE	2	0.347998723514967	4		810	711	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119759	70119778	+	frameshift_variant	Frame_Shift_Del	DEL	GAGAGGGGCGCCCCTTGCCA	GAGAGGGGCGCCCCTTGCCA	-	novel	NA	P-0008245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	260	932	0	ENST00000245479.2:c.764_783del	p.Glu255GlyfsTer34	p.E255Gfs*34	ENST00000245479	NM_000346.3	254	cGAGAGGGGCGCCCCTTGCCA/c	3/3	0.347998723514967	5	FACETS	1	0.956	1			1	CLONAL	3	TRUE	NA	0.347998723514967	5		932	744	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	172	246	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.995	0.926	1			1	INDETERMINATE	1	TRUE	NA	0.811301795773645	2		246	426	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220274	55220274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4359	1431	447	1	ENST00000275493.2:c.664C>T	p.Arg222Cys	p.R222C	ENST00000275493	NM_005228.3	222	Cgc/Tgc	6/28	0.811301795773645	14	FACETS	0.894	0.869	0.919			1	CLONAL	4	TRUE	NA	0.811301795773645	14		448	5790	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589626	67589626	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0008258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	241	358	0	ENST00000274335.5:c.1389T>G	p.Tyr463Ter	p.Y463*	ENST00000274335		463	taT/taG	10/15	1	2	FACETS	0.968	0.91	1	0.968	0.91	1	CLONAL	1	TRUE	1	0.811301795773645	2		358	614	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588144	67588145	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0008258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	275	304	0	ENST00000274335.5:c.976_977del	p.Met326ValfsTer6	p.M326Vfs*6	ENST00000274335		325	aAT/a	7/15	1	2	FACETS	0.919	0.867	0.971	0.919	0.867	0.971	CLONAL	1	TRUE	1	0.811301795773645	2		304	738	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0008261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	344	286	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.367161027724711	2	FACETS	1	0.995	1	0.664	0.634	0.693	INDETERMINATE	1	TRUE	0	0.784192962814474	2		287	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578177	7578177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs267605076	NA	P-0008261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	733	491	2	ENST00000269305.4:c.672G>T	p.Glu224Asp	p.E224D	ENST00000269305	NM_001126112.2	224	gaG/gaT	6/11	0.741623187310696	2	FACETS	0.915	0.893	0.936	0.915	0.893	0.936	CLONAL	2	TRUE	0	0.784192962814474	2		493	1022	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664819	138664819	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	44	45	0	ENST00000330315.3:c.746C>A	p.Ala249Glu	p.A249E	ENST00000330315	NM_023067.3	249	gCg/gAg	1/1	0.784192962814474	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.784192962814474	1		45	56	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120873	94120873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	583	1770	1	ENST00000369303.4:c.178G>T	p.Gly60Cys	p.G60C	ENST00000369303	NM_004440.3	60	Ggt/Tgt	3/17	0.784192962814474	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.784192962814474	1		1771	823	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539078	187539078	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	594	543	0	ENST00000441802.2:c.8662G>T	p.Val2888Phe	p.V2888F	ENST00000441802	NM_005245.3	2888	Gtt/Ttt	10/27	0.784192962814474	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.784192962814474	1		543	821	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971053	21971053	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137854598	NA	P-0008261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	125	239	0	ENST00000304494.5:c.305C>T	p.Ala102Val	p.A102V	ENST00000304494	NM_000077.4	102	gCg/gTg	2/3	0.784192962814474	1	FACETS	0.818	0.758	0.877	0.818	0.758	0.877	CLONAL	1	TRUE	0	0.784192962814474	1		239	237	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254639	46254639	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	599	464	0	ENST00000334344.6:c.4829C>G	p.Ser1610Cys	p.S1610C	ENST00000334344	NM_152641.2	1610	tCt/tGt	16/21	0.677745667836333	1	FACETS	0.898	0.87	0.927	0.898	0.87	0.927	CLONAL	1	TRUE	0	0.784192962814474	1		464	1034	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913233	32913233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368952892	NA	P-0008261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	588	707	1	ENST00000380152.3:c.4741G>A	p.Glu1581Lys	p.E1581K	ENST00000380152		1581	Gag/Aag	11/27	0.784192962814474	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.784192962814474	1		708	906	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934798	9934798	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs757713617	NA	P-0008261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	293	572	0	ENST00000330684.3:c.1492G>T	p.Gly498Cys	p.G498C	ENST00000330684	NM_001134407.1	498	Ggt/Tgt	6/13	0.487452289335217	1	FACETS	0.405	0.381	0.43	0.405	0.381	0.43	SUBCLONAL	1	TRUE	0	0.784192962814474	1		572	1122	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141502	11141502	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	402	436	0	ENST00000358026.2:c.3479G>T	p.Gly1160Val	p.G1160V	ENST00000358026	NM_001128849.1	1160	gGg/gTg	25/36	0.383403690840572	1	FACETS	0.747	0.715	0.779	0.747	0.715	0.779	INDETERMINATE	1	TRUE	0	0.784192962814474	1		436	834	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527919	103527934	+	frameshift_variant	Frame_Shift_Del	DEL	CAGATTCTAAAGGAAA	CAGATTCTAAAGGAAA	-	novel	NA	P-0008261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	68	359	0	ENST00000355739.4:c.3227_3242del	p.Ser1076Ter	p.S1076*	ENST00000355739	NM_000123.3	1076	tCAGATTCTAAAGGAAAg/tg	15/15	0.784192962814474	1	FACETS	0.211	0.183	0.24	0.211	0.183	0.24	SUBCLONAL	1	TRUE	0	0.784192962814474	1		359	500	SUCCESS
APC	324	MSKCC	GRCh37	5	112175755	112175755	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	172	235	0	ENST00000257430.4:c.4464del	p.Leu1488PhefsTer19	p.L1488Ffs*19	ENST00000257430	NM_000038.5	1488	ttA/tt	16/16	0.776358734035805	1	FACETS	0.695	0.648	0.742	0.695	0.648	0.742	SUBCLONAL	1	TRUE	0	0.776358734035805	1		235	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578207	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0008288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	822	414	0	ENST00000269305.4:c.642_643del	p.His214GlnfsTer7	p.H214Qfs*7	ENST00000269305	NM_001126112.2	214	caTAgt/cagt	6/11	0.753194152201639	2	FACETS	0.93	0.91	0.951	0.93	0.91	0.951	CLONAL	2	TRUE	0	0.776358734035805	2		414	1138	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131945032	131945035	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	rs587780154	NA	P-0008288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	146	312	0	ENST00000265335.6:c.2983_2986del	p.Glu995ArgfsTer2	p.E995Rfs*2	ENST00000265335		994	AAAGaa/aa	19/25	1	2	FACETS	0.36	0.328	0.394	0.36	0.328	0.394	SUBCLONAL	1	TRUE	1	0.776358734035805	2		312	1045	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0008318-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	25	785	4	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		789	895	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842472	68842472	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0008318-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	36	398	1	ENST00000261769.5:c.531+2T>A		p.X177_splice	ENST00000261769	NM_004360.3	177			1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		399	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579321	7579322	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs587780067	NA	P-0008324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	267	247	1	ENST00000269305.4:c.365_366del	p.Val122AspfsTer26	p.V122Dfs*26	ENST00000269305	NM_001126112.2	122	gTG/g	4/11	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.722697234868779	2		248	663	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266134	41266136	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs587776850	NA	P-0008324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	438	321	1	ENST00000349496.5:c.133_135del	p.Ser45del	p.S45del	ENST00000349496	NM_001904.3	44	cCTTct/cct	3/15	0.157734891000876	3	FACETS	1	0.996	1	0.749	0.716	0.782	INDETERMINATE	1	TRUE	1	0.722697234868779	3		322	1102	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475061	40475063	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0008324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	526	558	0	ENST00000264657.5:c.1847_1849del	p.Glu616del	p.E616del	ENST00000264657	NM_139276.2	616	gAAGga/gga	20/24	1	2	FACETS	0.996	0.955	1	0.996	0.955	1	CLONAL	1	TRUE	1	0.722697234868779	2		558	1461	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426120	47426120	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	568	524	0	ENST00000377045.4:c.640T>C	p.Ser214Pro	p.S214P	ENST00000377045	NM_001654.4	214	Tcc/Ccc	7/16	0.1984866125392	1	FACETS	0.826	0.796	0.857	0.826	0.796	0.857	INDETERMINATE	1	TRUE	0	0.722697234868779	1		524	1215	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578537	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs879254214	NA	P-0008324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	294	287	0	ENST00000269305.4:c.393_395del	p.Asn131del	p.N131del	ENST00000269305	NM_001126112.2	131	aaCAAg/aag	5/11	NA	2	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.722697234868779	2		287	766	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333991	70333993	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	rs903550402	NA	P-0008324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	84	239	2	ENST00000373644.4:c.1902_1904del	p.Val635del	p.V635del	ENST00000373644	NM_030625.2	632	tcTGTt/tct	2/12	NA	2	FACETS	0.417	0.369	0.469			1	INDETERMINATE	1	TRUE	NA	0.722697234868779	2		241	557	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439874	52439874	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	277	360	1	ENST00000460680.1:c.838C>T	p.Gln280Ter	p.Q280*	ENST00000460680	NM_004656.3	280	Cag/Tag	10/17	0.722697234868779	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.722697234868779	1		361	487	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845621	63845621	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	340	269	0	ENST00000279873.7:c.1360G>C	p.Glu454Gln	p.E454Q	ENST00000279873	NM_032199.2	454	Gaa/Caa	9/10	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.722697234868779	2		269	846	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870835	12870835	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1229515408	NA	P-0008324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	195	137	0	ENST00000228872.4:c.62C>T	p.Ala21Val	p.A21V	ENST00000228872	NM_004064.3	21	gCg/gTg	1/3	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.722697234868779	2		137	536	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39629539	39629539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	225	382	0	ENST00000262039.4:c.2233C>T	p.His745Tyr	p.H745Y	ENST00000262039	NM_002647.2	745	Cac/Tac	21/25	1	2	FACETS	0.517	0.481	0.555	0.517	0.481	0.555	SUBCLONAL	1	TRUE	1	0.722697234868779	2		382	1204	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871245	35871246	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs1229730339	NA	P-0008324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1225	918	498	0	ENST00000216797.5:c.927_928del	p.Phe310TrpfsTer30	p.F310Wfs*30	ENST00000216797	NM_020529.2	309	gtGTtt/gttt	6/6	0.558768730143333	3	FACETS	0.807	0.783	0.831			1	CLONAL	2	TRUE	NA	0.722697234868779	3		498	2143	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313265	65313267	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs1339036568	NA	P-0008324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	456	609	0	ENST00000342505.4:c.1847_1849del	p.Lys616del	p.K616del	ENST00000342505	NM_002227.2	616	aAGAta/ata	13/25	0.165062598070517	4	FACETS	1	0.996	1	0.743	0.709	0.778	INDETERMINATE	1	TRUE	2	0.722697234868779	4		609	1463	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845627	63845627	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	275	245	0	ENST00000279873.7:c.1366del	p.Glu456LysfsTer23	p.E456Kfs*23	ENST00000279873	NM_032199.2	456	Gaa/aa	9/10	NA	2	FACETS	0.956	0.901	1			1	INDETERMINATE	1	TRUE	NA	0.722697234868779	2		245	796	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691941	30691943	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs1274930605	NA	P-0008324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	246	254	0	ENST00000295754.5:c.446_448del	p.Phe149del	p.F149del	ENST00000295754	NM_003242.5	148	aTCTtc/atc	3/7	0.157734891000876	3	FACETS	1	0.991	1	0.664	0.624	0.705	INDETERMINATE	1	TRUE	1	0.722697234868779	3		254	698	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713896	30713899	+	frameshift_variant	Frame_Shift_Del	DEL	TCTG	TCTG	-	novel	NA	P-0008324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	256	274	0	ENST00000295754.5:c.1226_1229del	p.Ser409TrpfsTer21	p.S409Wfs*21	ENST00000295754	NM_003242.5	407	acTCTG/ac	4/7	0.157734891000876	3	FACETS	1	0.99	1	0.631	0.593	0.67	INDETERMINATE	1	TRUE	1	0.722697234868779	3		274	764	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913514	NA	P-0008342-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	309	435	0	ENST00000288135.5:c.2466T>A	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaA	17/21	0.375289338233537	5	FACETS	0.918	0.876	0.959	1	0.991	1	CLONAL	5	TRUE	1	0.375289338233537	5		435	561	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372087	45372087	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008342-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	65	397	0	ENST00000262160.6:c.1082A>G	p.Asn361Ser	p.N361S	ENST00000262160	NM_005901.5	361	aAt/aGt	9/11	1	2	FACETS	0.916	0.798	1	0.916	0.798	1	CLONAL	1	TRUE	1	0.375289338233537	2		397	378	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254887	16254887	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	64	381	0	ENST00000375759.3:c.2152G>T	p.Glu718Ter	p.E718*	ENST00000375759	NM_015001.2	718	Gag/Tag	11/15	1	2	FACETS	0.831	0.72	0.952	0.831	0.72	0.952	CLONAL	1	TRUE	1	0.252068923054608	2		381	611	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332892	65332892	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0008348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	18	249	0	ENST00000342505.4:c.648-1G>T		p.X216_splice	ENST00000342505	NM_002227.2	216			1	2	FACETS	0.965	0.732	1	0.965	0.732	1	CLONAL	1	TRUE	1	0.252068923054608	2		249	148	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144146	11144146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	138	305	0	ENST00000358026.2:c.3727C>T	p.Arg1243Trp	p.R1243W	ENST00000358026	NM_001128849.1	1243	Cgg/Tgg	26/36	0.10692302151234	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.69	0		305	346	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843447	3843447	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783461	NA	P-0008352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	181	390	0	ENST00000262367.5:c.1156C>T	p.Arg386Ter	p.R386*	ENST00000262367	NM_004380.2	386	Cga/Tga	4/31	0.10692302151234	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.69	0		390	503	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896563	78896563	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	103	395	0	ENST00000306801.3:c.2560T>G	p.Ser854Ala	p.S854A	ENST00000306801	NM_020761.2	854	Tcc/Gcc	22/34	0.10692302151234	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.69	0		395	361	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0008377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	244	395	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.28756670991096	3	FACETS	0.983	0.924	1			1	CLONAL	2	TRUE	NA	0.439363745113227	3		395	689	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916937	+	inframe_deletion	In_Frame_Del	DEL	GGCAACCGT	GGCAACCGT	-	novel	NA	P-0008377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	192	789	0	ENST00000263967.3:c.317_325del	p.Gly106_Arg108del	p.G106_R108del	ENST00000263967	NM_006218.2	106	GGCAACCGT/-	2/21	1	2	FACETS	0.828	0.765	0.893	0.828	0.765	0.893	CLONAL	1	TRUE	1	0.439363745113227	2		789	1056	SUCCESS
APC	324	MSKCC	GRCh37	5	112175720	112175720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	140	372	0	ENST00000257430.4:c.4429C>T	p.Gln1477Ter	p.Q1477*	ENST00000257430	NM_000038.5	1477	Cag/Tag	16/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.439363745113227	2		372	573	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467824	99467824	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142608976	NA	P-0008377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	144	494	0	ENST00000268035.6:c.2693C>T	p.Pro898Leu	p.P898L	ENST00000268035	NM_000875.3	898	cCg/cTg	13/21	1	2	FACETS	0.917	0.838	0.999	0.917	0.838	0.999	CLONAL	1	TRUE	1	0.439363745113227	2		494	715	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81922869	81922869	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs962152757	NA	P-0008377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	287	775	0	ENST00000359376.3:c.858T>G	p.Phe286Leu	p.F286L	ENST00000359376	NM_002661.3	286	ttT/ttG	10/33	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.439363745113227	2		775	1266	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983583	7983583	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	33	417	0	ENST00000319144.4:c.724A>T	p.Ile242Phe	p.I242F	ENST00000319144	NM_001139.2	242	Att/Ttt	6/15	0.435080416001554	1	FACETS	0.195	0.158	0.237	0.195	0.158	0.237	SUBCLONAL	1	TRUE	0	0.439363745113227	1		417	600	SUCCESS
APC	324	MSKCC	GRCh37	5	112173571	112173571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	143	359	0	ENST00000257430.4:c.2280del	p.Glu761LysfsTer4	p.E761Kfs*4	ENST00000257430	NM_000038.5	760	ctA/ct	16/16	1	2	FACETS	0.957	0.875	1	0.957	0.875	1	CLONAL	1	TRUE	1	0.439363745113227	2		359	680	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670129	86670130	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0008377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	92	328	0	ENST00000274376.6:c.1927_1928del	p.Val643LeufsTer2	p.V643Lfs*2	ENST00000274376	NM_002890.2	642	ttTGtc/tttc	14/25	0.43155337187816	1	FACETS	0.923	0.827	1	0.923	0.827	1	CLONAL	1	TRUE	0	0.439363745113227	1		328	354	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151262	202151265	+	frameshift_variant	Frame_Shift_Del	DEL	AGAT	AGAT	-	novel	NA	P-0008377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	146	713	0	ENST00000358485.4:c.1562_1565del	p.Gln521ArgfsTer8	p.Q521Rfs*8	ENST00000358485	NM_001080125.1	521	cAGATg/cg	9/9	1	2	FACETS	0.518	0.471	0.567	0.518	0.471	0.567	SUBCLONAL	1	TRUE	1	0.439363745113227	2		713	1284	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0008394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	47	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.180388915238969	3	FACETS	1	0.919	1	0.569	0.482	0.664	CLONAL	1	TRUE	1	0.262541857823538	3		249	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0008394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	94	397	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.262541857823538	2		397	530	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663346	227663346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024227751	NA	P-0008394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	28	188	0	ENST00000305123.5:c.109G>A	p.Glu37Lys	p.E37K	ENST00000305123	NM_005544.2	37	Gag/Aag	1/2	1	2	FACETS	0.961	0.772	1	0.961	0.772	1	CLONAL	1	TRUE	1	0.262541857823538	2		188	222	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690565	88690565	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0008394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	50	395	0	ENST00000360948.2:c.464+1del		p.X155_splice	ENST00000360948	NM_001012338.2	155			0.262541857823538	1	FACETS	0.449	0.38	0.525	0.449	0.38	0.525	SUBCLONAL	1	TRUE	0	0.262541857823538	1		395	737	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057519990	NA	P-0008407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	57	620	0	ENST00000269305.4:c.796G>T	p.Gly266Ter	p.G266*	ENST00000269305	NM_001126112.2	266	Gga/Tga	8/11	NA	2	FACETS	0.618	0.528	0.717			1	INDETERMINATE	1	TRUE	NA	0.17	2		620	1085	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0008416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	267	411	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	0.72	2		411	675	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	241	255	2	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.72	2		257	647	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413070	139413072	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0008416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	183	373	0	ENST00000277541.6:c.1070_1072del	p.Phe357del	p.F357del	ENST00000277541	NM_017617.3	357	tTCTac/tac	6/34	1	2	FACETS	0.673	0.623	0.726	0.673	0.623	0.726	SUBCLONAL	1	TRUE	1	0.72	2		373	755	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0008416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	263	536	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	0.689	0.646	0.734	0.689	0.646	0.734	SUBCLONAL	1	TRUE	1	0.72	2		536	1060	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428562	78428562	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	201	404	1	ENST00000370768.2:c.1237C>T	p.Gln413Ter	p.Q413*	ENST00000370768	NM_003902.3	413	Cag/Tag	14/20	0.729388112972894	1	FACETS	0.849	0.797	0.9	0.849	0.797	0.9	CLONAL	1	TRUE	0	0.72	1		405	421	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417142	417143	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0008416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	193	266	0	ENST00000399788.2:c.3407_3408del	p.Lys1136ArgfsTer3	p.K1136Rfs*3	ENST00000399788	NM_001042603.1	1136	aAA/a	23/28	0.729388112972894	2	FACETS	0.757	0.703	0.813			1	SUBCLONAL	1	TRUE	NA	0.72	2		266	708	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023482	31023483	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0008416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	174	296	0	ENST00000375687.4:c.2967_2968del	p.Glu990SerfsTer7	p.E990Sfs*7	ENST00000375687	NM_015338.5	989	tcTGaa/tcaa	13/13	1	2	FACETS	0.689	0.637	0.744	0.689	0.637	0.744	SUBCLONAL	1	TRUE	1	0.72	2		296	701	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088689	27088689	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	205	478	0	ENST00000324856.7:c.2298G>T	p.Gln766His	p.Q766H	ENST00000324856	NM_006015.4	766	caG/caT	7/20	0.492967768437959	3	FACETS	1	0.952	1	0.517	0.479	0.556	CLONAL	1	TRUE	1	0.50020066675918	3		478	991	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439677	51439677	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	160	315	0	ENST00000262662.1:c.242G>T	p.Gly81Val	p.G81V	ENST00000262662		81	gGt/gTt	4/4	0.492967768437959	3	FACETS	1	0.949	1	0.523	0.48	0.567	CLONAL	1	TRUE	1	0.50020066675918	3		315	765	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841515	156841515	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	147	310	0	ENST00000524377.1:c.818G>T	p.Arg273Leu	p.R273L	ENST00000524377	NM_002529.3	273	cGg/cTg	7/17	1	2	FACETS	0.97	0.889	1	0.97	0.889	1	CLONAL	1	TRUE	1	0.50020066675918	2		310	606	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984842	55984842	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	362	436	2	ENST00000263923.4:c.287A>T	p.Asn96Ile	p.N96I	ENST00000263923	NM_002253.2	96	aAt/aTt	3/30	0.443565976688585	3	FACETS	0.973	0.926	1	0.973	0.926	1	CLONAL	2	TRUE	1	0.50020066675918	3		438	930	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295307	1295307	+	upstream_gene_variant	5'Flank	SNP	G	G	C	novel	NA	P-0008419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	171	369	0				ENST00000310581	NM_198253.2	-/1132			0.477693770467466	4	FACETS	1	0.949	1			1	CLONAL	1	TRUE	NA	0.50020066675918	4		369	984	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175951	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1392778905	NA	P-0008419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	247	307	1	ENST00000257430.4:c.4660G>T	p.Glu1554Ter	p.E1554*	ENST00000257430	NM_000038.5	1554	Gaa/Taa	16/16	0.50020066675918	2	FACETS	0.903	0.852	0.953	0.903	0.852	0.953	CLONAL	2	TRUE	0	0.50020066675918	2		308	547	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460486	149460486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	394	374	0	ENST00000286301.3:c.151G>A	p.Asp51Asn	p.D51N	ENST00000286301	NM_005211.3	51	Gat/Aat	3/22	0.50020066675918	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.50020066675918	2		374	750	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289657	33289657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	270	262	0	ENST00000374542.5:c.46G>A	p.Asp16Asn	p.D16N	ENST00000374542	NM_001141970.1	16	Gat/Aat	2/8	0.50020066675918	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.50020066675918	4		262	750	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346098	152346098	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	447	618	0	ENST00000359321.1:c.472G>T	p.Asp158Tyr	p.D158Y	ENST00000359321	NM_005431.1	158	Gac/Tac	3/3	0.50020066675918	4	FACETS	0.974	0.929	1	0.974	0.929	1	CLONAL	2	TRUE	2	0.50020066675918	4		618	1377	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711916	89711916	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs104894184	NA	P-0008419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	168	387	0	ENST00000371953.3:c.534T>G	p.Tyr178Ter	p.Y178*	ENST00000371953	NM_000314.4	178	taT/taG	6/9	0.50020066675918	2	FACETS	1	0.952	1	0.522	0.481	0.563	CLONAL	1	TRUE	0	0.50020066675918	2		387	644	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437211	49437211	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	346	314	2	ENST00000301067.7:c.5468G>T	p.Gly1823Val	p.G1823V	ENST00000301067	NM_003482.3	1823	gGa/gTa	24/54	0.492967768437959	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.50020066675918	3		316	789	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914484	32914484	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397507819	NA	P-0008419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	186	600	0	ENST00000380152.3:c.5992C>T	p.Gln1998Ter	p.Q1998*	ENST00000380152		1998	Caa/Taa	11/27	1	2	FACETS	0.956	0.885	1	0.956	0.885	1	CLONAL	1	TRUE	1	0.50020066675918	2		600	778	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134795	41134795	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	307	556	0	ENST00000379561.5:c.833A>T	p.Gln278Leu	p.Q278L	ENST00000379561	NM_002015.3	278	cAg/cTg	2/3	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.50020066675918	2		556	1032	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121804	2121804	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	306	352	0	ENST00000219476.3:c.1966G>T	p.Glu656Ter	p.E656*	ENST00000219476	NM_000548.3	656	Gag/Tag	19/42	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	2	TRUE	NA	0.50020066675918	2		352	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0008419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	731	454	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.364187111511417	4	FACETS	1	0.978	1			1	CLONAL	4	TRUE	NA	0.50020066675918	4		454	1092	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761488	59761488	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	587	270	0	ENST00000259008.2:c.2919C>A	p.Phe973Leu	p.F973L	ENST00000259008	NM_032043.2	973	ttC/ttA	20/20	0.50020066675918	6	FACETS	0.954	0.929	0.979			1	CLONAL	6	TRUE	NA	0.50020066675918	6		270	820	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584377	39584377	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	515	357	0	ENST00000262039.4:c.1042G>T	p.Ala348Ser	p.A348S	ENST00000262039	NM_002647.2	348	Gcc/Tcc	10/25	0.50020066675918	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	0	0.50020066675918	3		357	840	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222800	5222800	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	261	159	0	ENST00000357368.4:c.3003G>T	p.Lys1001Asn	p.K1001N	ENST00000357368	NM_002850.3	1001	aaG/aaT	18/38	0.50020066675918	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.50020066675918	3		159	402	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0008429-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	78	484	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.494221992225678	2		484	311	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0008429-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	79	280	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.472143020051142	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.494221992225678	1		280	191	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046958	128046958	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs772883177	NA	P-0008429-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	79	488	3	ENST00000285398.2:c.777A>T	p.Glu259Asp	p.E259D	ENST00000285398	NM_000122.1	259	gaA/gaT	6/15	1	2	FACETS	0.866	0.767	0.971	0.866	0.767	0.971	CLONAL	1	TRUE	1	0.494221992225678	2		491	369	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431427	121431427	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008429-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	161	383	0	ENST00000257555.6:c.631C>A	p.Gln211Lys	p.Q211K	ENST00000257555		211	Cag/Aag	3/10	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.494221992225678	2		383	615	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929285	32929285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1364927725	NA	P-0008429-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	257	858	0	ENST00000380152.3:c.7295G>A	p.Arg2432Lys	p.R2432K	ENST00000380152		2432	aGa/aAa	14/27	0.424410114837556	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.494221992225678	3		858	605	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858728	9858728	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008429-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	67	450	0	ENST00000330684.3:c.2673G>T	p.Gln891His	p.Q891H	ENST00000330684	NM_001134407.1	891	caG/caT	13/13	1	2	FACETS	0.886	0.776	1	0.886	0.776	1	CLONAL	1	TRUE	1	0.494221992225678	2		450	306	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222852	5222852	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776974729	NA	P-0008429-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	90	189	0	ENST00000357368.4:c.2951C>T	p.Pro984Leu	p.P984L	ENST00000357368	NM_002850.3	984	cCg/cTg	18/38	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.494221992225678	2		189	323	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0008438-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	119	325	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.981	0.888	1	0.981	0.888	1	CLONAL	1	TRUE	1	0.404470198158354	2		325	600	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988309	36988309	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776709	NA	P-0008438-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	50	127	0	ENST00000354822.5:c.344del	p.Gly115AlafsTer10	p.G115Afs*10	ENST00000354822	NM_001079668.2	115	gGc/gc	2/3	0.374135331912953	1	FACETS	0.897	0.769	1	0.897	0.769	1	CLONAL	1	TRUE	0	0.404470198158354	1		127	220	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599312	55599312	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008438-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	111	371	0	ENST00000288135.5:c.2438T>C	p.Leu813Pro	p.L813P	ENST00000288135	NM_000222.2	813	cTa/cCa	17/21	1	2	FACETS	0.85	0.765	0.939	0.85	0.765	0.939	CLONAL	1	TRUE	1	0.404470198158354	2		371	646	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876659675	NA	P-0008441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	263	433	0	ENST00000269305.4:c.764T>G	p.Ile255Ser	p.I255S	ENST00000269305	NM_001126112.2	255	aTc/aGc	7/11	0.749855219189869	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.784947158318735	1		433	386	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0008442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	99	343	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.561825951076931	3	FACETS	0.986	0.885	1	0.493	0.442	0.546	CLONAL	1	TRUE	1	0.561825951076931	3		343	458	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0008442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	138	158	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.511077668523594	3	FACETS	0.915	0.844	0.987	0.915	0.844	0.987	CLONAL	2	TRUE	1	0.561825951076931	3		158	344	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151168674	151168674	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	183	552	1	ENST00000262187.5:c.293T>C	p.Val98Ala	p.V98A	ENST00000262187	NM_005614.3	98	gTt/gCt	5/8	0.488566399613867	5	FACETS	0.872	0.803	0.945			1	CLONAL	1	TRUE	NA	0.561825951076931	5		553	1376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519990	NA	P-0008442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	167	380	0	ENST00000269305.4:c.796G>C	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Cga	8/11	0.559130425936849	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.561825951076931	1		380	375	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48921973	48921974	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0008442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	80	328	0	ENST00000267163.4:c.518_519del	p.Tyr173PhefsTer11	p.Y173Ffs*11	ENST00000267163	NM_000321.2	171	ctTAta/ctta	5/27	0.561230002705559	1	FACETS	0.531	0.47	0.595	0.531	0.47	0.595	SUBCLONAL	1	TRUE	0	0.561825951076931	1		328	386	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0008461-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	262	352	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.840725972963638	1	FACETS	0.989	0.959	1	0.989	0.959	1	CLONAL	1	TRUE	0	0.926638884602083	1		352	307	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931463	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622007	NA	P-0008461-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	382	288	1	ENST00000374690.3:c.2105T>A	p.Leu702His	p.L702H	ENST00000374690	NM_000044.3	702	cTc/cAc	4/8	0.774467574451065	2	FACETS	0.954	0.911	0.998			1	CLONAL	1	TRUE	NA	0.926638884602083	2		289	864	SUCCESS
AR	367	MSKCC	GRCh37	X	66943543	66943543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852581	NA	P-0008461-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	851	299	0	ENST00000374690.3:c.2623C>T	p.His875Tyr	p.H875Y	ENST00000374690	NM_000044.3	875	Cat/Tat	8/8	0.774467574451065	2	FACETS	1	0.998	1			1	CLONAL	2	TRUE	NA	0.926638884602083	2		299	889	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884912	151884915	+	frameshift_variant	Frame_Shift_Del	DEL	GAGG	GAGG	-	novel	NA	P-0008461-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	220	331	0	ENST00000262189.6:c.4678_4681del	p.Pro1560SerfsTer2	p.P1560Sfs*2	ENST00000262189	NM_170606.2	1560	CCTCtc/tc	32/59	1	2	FACETS	0.859	0.806	0.912	0.859	0.806	0.912	CLONAL	1	TRUE	1	0.926638884602083	2		331	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008461-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	183	262	0	ENST00000269305.4:c.548del	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/ta	5/11	0.926638884602083	1	FACETS	0.977	0.941	1	0.977	0.941	1	CLONAL	1	TRUE	0	0.926638884602083	1		262	217	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993222	72993226	+	frameshift_variant	Frame_Shift_Del	DEL	AGAGC	AGAGC	-	novel	NA	P-0008461-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	533	683	1	ENST00000268489.5:c.819_823del	p.Leu274TrpfsTer29	p.L274Wfs*29	ENST00000268489	NM_006885.3	273	gtGCTCTat/gtat	2/10	0.926638884602083	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.926638884602083	1		684	608	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0008476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	287	468	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.299355326138516	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.333654392778585	3		468	929	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0008476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	232	431	1	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.299355326138516	3	FACETS	0.991	0.926	1	0.991	0.926	1	CLONAL	2	TRUE	1	0.333654392778585	3		432	819	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0008476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	384	617	1	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.249438233683195	3	FACETS	1	0.992	1	0.794	0.755	0.834	CLONAL	2	TRUE	0	0.333654392778585	3		618	1127	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540406	187540406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	35	224	0	ENST00000441802.2:c.7334G>A	p.Gly2445Glu	p.G2445E	ENST00000441802	NM_005245.3	2445	gGg/gAg	10/27	0.249438233683195	3	FACETS	0.48	0.393	0.578	0.16	0.131	0.193	SUBCLONAL	1	TRUE	0	0.333654392778585	3		224	510	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515369	149515369	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754766440	NA	P-0008476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	68	310	1	ENST00000261799.4:c.113C>T	p.Pro38Leu	p.P38L	ENST00000261799	NM_002609.3	38	cCg/cTg	3/23	0.299355326138516	3	FACETS	0.679	0.59	0.776	0.34	0.295	0.388	SUBCLONAL	1	TRUE	1	0.333654392778585	3		311	700	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734200	58734200	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0008476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1675	153	766	0	ENST00000305921.3:c.1258A>T	p.Lys420Ter	p.K420*	ENST00000305921	NM_003620.3	420	Aag/Tag	5/6	0.333654392778585	5	FACETS	0.753	0.686	0.824	0.251	0.228	0.275	SUBCLONAL	1	TRUE	2	0.333654392778585	5		766	1828	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220449	1220449	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	100	567	0	ENST00000326873.7:c.542A>C	p.Asn181Thr	p.N181T	ENST00000326873	NM_000455.4	181	aAc/aCc	4/10	0.262176261374837	2	FACETS	0.729	0.651	0.813	0.365	0.325	0.407	SUBCLONAL	1	TRUE	0	0.333654392778585	2		567	822	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172365	7172365	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs144929085	NA	P-0008476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	229	540	0	ENST00000302850.5:c.1204G>T	p.Ala402Ser	p.A402S	ENST00000302850	NM_000208.2	402	Gct/Tct	5/22	0.262176261374837	2	FACETS	0.832	0.777	0.888	0.832	0.777	0.888	CLONAL	2	TRUE	0	0.333654392778585	2		540	825	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0008514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	8773	343	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.515525322040184	24	FACETS	1	0.999	1			1	CLONAL	24	TRUE	NA	0.515525322040184	24		343	9364	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587782272	NA	P-0008514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	433	514	0	ENST00000269305.4:c.994-1G>C		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.439135919522311	3	FACETS	0.908	0.867	0.95	0.908	0.867	0.95	CLONAL	2	TRUE	1	0.515525322040184	3		514	1163	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259521	55259521	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	8822	534	1	ENST00000275493.2:c.2579A>T	p.Lys860Ile	p.K860I	ENST00000275493	NM_005228.3	860	aAa/aTa	21/28	0.515525322040184	24	FACETS	1	0.999	1			1	CLONAL	24	TRUE	NA	0.515525322040184	24		535	9387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578284	7578284	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	186	467	0	ENST00000269305.4:c.565del	p.Ala189ProfsTer58	p.A189Pfs*58	ENST00000269305	NM_001126112.2	189	Gcc/cc	6/11	0.439135919522311	3	FACETS	0.818	0.755	0.885	0.409	0.377	0.443	CLONAL	1	TRUE	1	0.515525322040184	3		467	1109	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0008519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	13	154	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.86	0.612	1	0.86	0.612	1	CLONAL	1	TRUE	1	0.11	2		154	275	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0008519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	29	592	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	0.502	0.401	0.619	0.502	0.401	0.619	SUBCLONAL	1	TRUE	1	0.11	2		592	1050	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577544	7577544	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587780074	NA	P-0008519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	64	561	0	ENST00000269305.4:c.737T>A	p.Met246Lys	p.M246K	ENST00000269305	NM_001126112.2	246	aTg/aAg	7/11	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.11	2		561	1103	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799017	42799017	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008547-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	69	588	0	ENST00000575354.2:c.4501T>G	p.Phe1501Val	p.F1501V	ENST00000575354	NM_015125.3	1501	Ttt/Gtt	20/20	1	2	FACETS	0.25	0.217	0.286	0.25	0.217	0.286	SUBCLONAL	1	TRUE	1	0.819382735064982	2		588	673	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0008560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	41	145	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.223666582934846	1	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	0	0.223666582934846	1		145	286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0008560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	84	293	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.175071797771686	2	FACETS	0.756	0.669	0.847	0.756	0.669	0.847	SUBCLONAL	2	TRUE	0	0.223666582934846	2		293	497	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0008560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	40	205	1	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	0.123082533137724	3	FACETS	1	0.928	1	0.612	0.51	0.724	INDETERMINATE	1	TRUE	1	0.223666582934846	3		206	325	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672306	30672306	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	65	525	1	ENST00000376406.3:c.4654A>T	p.Thr1552Ser	p.T1552S	ENST00000376406	NM_014641.2	1552	Aca/Tca	10/15	1	2	FACETS	0.795	0.688	0.911	0.795	0.688	0.911	CLONAL	1	TRUE	1	0.223666582934846	2		526	731	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032597	47032597	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0008560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	58	451	0	ENST00000377604.3:c.502+1G>A		p.X168_splice	ENST00000377604	NM_001204468.1	168			1	2	FACETS	0.664	0.569	0.768	0.664	0.569	0.768	SUBCLONAL	1	TRUE	1	0.223666582934846	2		451	781	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250023	53250023	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	115	633	1	ENST00000375401.3:c.226G>C	p.Glu76Gln	p.E76Q	ENST00000375401	NM_004187.3	76	Gag/Cag	2/26	1	2	FACETS	0.938	0.843	1	0.938	0.843	1	CLONAL	1	TRUE	1	0.223666582934846	2		634	1096	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0008565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	169	346	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	1	2	FACETS	0.866	0.801	0.933	0.866	0.801	0.933	CLONAL	1	TRUE	1	0.710826814413597	2		346	549	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0008565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	286	330	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.710826814413597	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.710826814413597	1		330	418	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0008565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	201	370	1	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	1	2	FACETS	0.877	0.817	0.938	0.877	0.817	0.938	CLONAL	1	TRUE	1	0.710826814413597	2		371	645	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55603364	55603364	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	100	428	1	ENST00000288135.5:c.2720G>T	p.Trp907Leu	p.W907L	ENST00000288135	NM_000222.2	907	tGg/tTg	20/21	0.394965937031749	1	FACETS	0.398	0.357	0.441	0.398	0.357	0.441	INDETERMINATE	1	TRUE	0	0.710826814413597	1		429	456	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286196	66286196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	33	579	1	ENST00000273854.3:c.1490G>A	p.Gly497Glu	p.G497E	ENST00000273854	NM_004439.5	497	gGa/gAa	6/18	0.394965937031749	1	FACETS	0.105	0.085	0.128	0.105	0.085	0.128	INDETERMINATE	1	TRUE	0	0.710826814413597	1		580	569	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180049827	180049827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	45	387	0	ENST00000261937.6:c.1561C>A	p.Leu521Met	p.L521M	ENST00000261937	NM_182925.4	521	Ctg/Atg	12/30	0.104797990975287	6	FACETS	0.382	0.32	0.452			1	INDETERMINATE	1	TRUE	NA	0.710826814413597	6		387	802	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401642	401642	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210576093	NA	P-0008565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	185	278	0	ENST00000380956.4:c.964G>A	p.Asp322Asn	p.D322N	ENST00000380956	NM_001195286.1	322	Gac/Aac	7/9	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.710826814413597	2		278	486	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730075	41730075	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748897120	NA	P-0008565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1423	717	973	0	ENST00000242208.4:c.454C>T	p.Arg152Cys	p.R152C	ENST00000242208	NM_002192.2	152	Cgt/Tgt	3/3	0.39271252178158	3	FACETS	1	0.996	1	0.639	0.616	0.662	INDETERMINATE	1	TRUE	1	0.710826814413597	3		973	2140	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451272	70451272	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	161	481	1	ENST00000373644.4:c.6112C>T	p.Arg2038Cys	p.R2038C	ENST00000373644	NM_030625.2	2038	Cgt/Tgt	12/12	0.446778847923289	1	FACETS	0.394	0.362	0.428	0.394	0.362	0.428	SUBCLONAL	1	TRUE	0	0.710826814413597	1		482	741	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885577	111885577	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1416067054	NA	P-0008565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	352	883	1	ENST00000341259.2:c.1354G>A	p.Ala452Thr	p.A452T	ENST00000341259	NM_005475.2	452	Gcc/Acc	7/8	0.327216522981637	1	FACETS	0.469	0.444	0.496	0.469	0.444	0.496	INDETERMINATE	1	TRUE	0	0.710826814413597	1		884	1360	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820836	3820836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747877878	NA	P-0008565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	246	383	0	ENST00000262367.5:c.2615C>T	p.Thr872Met	p.T872M	ENST00000262367	NM_004380.2	872	aCg/aTg	14/31	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.710826814413597	2		383	634	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030608	47030608	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	115	495	0	ENST00000377604.3:c.383G>C	p.Ser128Thr	p.S128T	ENST00000377604	NM_001204468.1	128	aGt/aCt	4/24	0.42050834064262	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.710826814413597	0		495	464	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120413	70120413	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	604	726	0	ENST00000245479.2:c.1415del	p.Ala472ValfsTer51	p.A472Vfs*51	ENST00000245479	NM_000346.3	472	gCt/gt	3/3	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.710826814413597	2		726	1363	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0008590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	217	286	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.427245292987944	3	FACETS	0.853	0.796	0.911	0.853	0.796	0.911	CLONAL	2	TRUE	1	0.426860827511885	3		287	723	SUCCESS
APC	324	MSKCC	GRCh37	5	112154998	112154998	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	386	501	2	ENST00000257430.4:c.1269G>A	p.Trp423Ter	p.W423*	ENST00000257430	NM_000038.5	423	tgG/tgA	10/16	0.196600500566087	5	FACETS	0.971	0.929	1	0.777	0.743	0.81	INDETERMINATE	4	TRUE	0	0.426860827511885	5		503	764	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604673	55604673	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773828910	NA	P-0008590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	298	398	0	ENST00000288135.5:c.2881G>A	p.Gly961Ser	p.G961S	ENST00000288135	NM_000222.2	961	Ggc/Agc	21/21	0.426860827511885	2	FACETS	0.983	0.932	1	0.983	0.932	1	CLONAL	2	TRUE	0	0.426860827511885	2		398	710	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184800	32184800	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	81	413	0	ENST00000375023.3:c.1783A>G	p.Ser595Gly	p.S595G	ENST00000375023	NM_004557.3	595	Agt/Ggt	11/30	0.173301748023006	5	FACETS	1	0.967	1	0.423	0.374	0.476	INDETERMINATE	1	TRUE	2	0.426860827511885	5		413	490	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615186	43615186	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	20	279	0	ENST00000355710.3:c.2600A>C	p.Glu867Ala	p.E867A	ENST00000355710	NM_020975.4	867	gAg/gCg	14/20	0.427245292987944	3	FACETS	0.348	0.266	0.444	0.174	0.133	0.222	SUBCLONAL	1	TRUE	1	0.426860827511885	3		279	327	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433511	49433511	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779506886	NA	P-0008590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	229	680	1	ENST00000301067.7:c.8042G>A	p.Arg2681Gln	p.R2681Q	ENST00000301067	NM_003482.3	2681	cGg/cAg	31/54	0.427245292987944	3	FACETS	1	0.986	1	0.611	0.569	0.655	CLONAL	1	TRUE	1	0.426860827511885	3		681	1065	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562963	21562963	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	53	427	0	ENST00000382592.4:c.956A>G	p.Lys319Arg	p.K319R	ENST00000382592	NM_014572.2	319	aAg/aGg	4/8	0.427245292987944	4	FACETS	0.485	0.412	0.564	0.162	0.137	0.188	SUBCLONAL	1	TRUE	1	0.426860827511885	4		427	731	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424743	47424743	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	157	685	0	ENST00000377045.4:c.551G>A	p.Gly184Asp	p.G184D	ENST00000377045	NM_001654.4	184	gGt/gAt	6/16	0.173301748023006	5	FACETS	0.974	0.89	1	0.325	0.296	0.354	INDETERMINATE	1	TRUE	2	0.426860827511885	5		685	1239	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0008647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	244	352	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.452038775994622	2	FACETS	0.929	0.876	0.983	0.929	0.876	0.983	CLONAL	2	TRUE	0	0.459940544987059	2		352	571	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222733	5222733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202163446	NA	P-0008647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	162	242	0	ENST00000357368.4:c.3070C>T	p.Pro1024Ser	p.P1024S	ENST00000357368	NM_002850.3	1024	Ccc/Tcc	18/38	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.459940544987059	2		242	660	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106696	2106696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1462	379	541	1	ENST00000219476.3:c.700G>A	p.Glu234Lys	p.E234K	ENST00000219476	NM_000548.3	234	Gag/Aag	8/42	1	2	FACETS	0.895	0.847	0.945	0.895	0.847	0.945	CLONAL	1	TRUE	1	0.459940544987059	2		542	1841	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814539	43814539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	227	430	0	ENST00000372470.3:c.1334G>A	p.Arg445Gln	p.R445Q	ENST00000372470	NM_005373.2	445	cGa/cAa	9/12	0.385202888970834	1	FACETS	0.829	0.773	0.886	0.829	0.773	0.886	CLONAL	1	TRUE	0	0.459940544987059	1		430	917	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89880961	89880961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	339	605	0	ENST00000389301.3:c.250G>A	p.Glu84Lys	p.E84K	ENST00000389301	NM_000135.2	84	Gag/Aag	3/43	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.459940544987059	2		605	1311	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589599	67589604	+	inframe_deletion	In_Frame_Del	DEL	TCAGTT	TCAGTT	-	novel	NA	P-0008647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	140	353	0	ENST00000274335.5:c.1365_1370del	p.Phe456_Gln457del	p.F456_Q457del	ENST00000274335		454	acTCAGTTt/act	10/15	1	2	FACETS	0.847	0.772	0.924	0.847	0.772	0.924	CLONAL	1	TRUE	1	0.459940544987059	2		353	719	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161298278	161298278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1348	243	436	0	ENST00000367975.2:c.170C>T	p.Thr57Ile	p.T57I	ENST00000367975	NM_003001.3	57	aCt/aTt	3/6	0.460592362434247	3	FACETS	0.817	0.761	0.875	0.408	0.38	0.438	CLONAL	1	TRUE	1	0.459940544987059	3		436	1591	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226589975	226589975	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1237	268	395	1	ENST00000366794.5:c.226G>T	p.Glu76Ter	p.E76*	ENST00000366794	NM_001618.3	76	Gag/Tag	2/23	0.450398183015869	3	FACETS	0.952	0.891	1	0.476	0.445	0.508	CLONAL	1	TRUE	1	0.459940544987059	3		396	1505	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27016043	27016043	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1454	154	903	0	ENST00000335756.4:c.319G>C	p.Glu107Gln	p.E107Q	ENST00000335756	NM_001809.3	107	Gag/Cag	4/5	1	2	FACETS	0.416	0.379	0.456	0.416	0.379	0.456	SUBCLONAL	1	TRUE	1	0.459940544987059	2		903	1608	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158626884	158626884	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	203	658	0	ENST00000263640.3:c.786C>G	p.Ile262Met	p.I262M	ENST00000263640	NM_001105.4	262	atC/atG	7/11	1	2	FACETS	0.88	0.816	0.947	0.88	0.816	0.947	CLONAL	1	TRUE	1	0.459940544987059	2		658	1003	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096733	178096733	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	88	225	0	ENST00000397062.3:c.598C>G	p.Leu200Val	p.L200V	ENST00000397062	NM_006164.4	200	Ctt/Gtt	5/5	1	2	FACETS	0.802	0.713	0.896	0.802	0.713	0.896	CLONAL	1	TRUE	1	0.459940544987059	2		225	477	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35857155	35857155	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	160	384	0	ENST00000303115.3:c.76C>G	p.Gln26Glu	p.Q26E	ENST00000303115	NM_002185.3	26	Caa/Gaa	1/8	1	2	FACETS	0.98	0.901	1	0.98	0.901	1	CLONAL	1	TRUE	1	0.459940544987059	2		384	710	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179462	56179462	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1189714200	NA	P-0008647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	119	364	0	ENST00000399503.3:c.3775C>G	p.Gln1259Glu	p.Q1259E	ENST00000399503	NM_005921.1	1259	Cag/Gag	15/20	1	2	FACETS	0.755	0.683	0.832	0.755	0.683	0.832	SUBCLONAL	1	TRUE	1	0.459940544987059	2		364	685	SUCCESS
APC	324	MSKCC	GRCh37	5	112176824	112176824	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	182	468	3	ENST00000257430.4:c.5533C>A	p.His1845Asn	p.H1845N	ENST00000257430	NM_000038.5	1845	Cat/Aat	16/16	0.460592362434247	1	FACETS	0.759	0.701	0.819	0.759	0.701	0.819	SUBCLONAL	1	TRUE	0	0.459940544987059	1		471	803	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911475	131911475	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786201699	NA	P-0008647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	122	291	0	ENST00000265335.6:c.220C>G	p.Gln74Glu	p.Q74E	ENST00000265335		74	Caa/Gaa	3/25	1	2	FACETS	0.826	0.749	0.908	0.826	0.749	0.908	CLONAL	1	TRUE	1	0.459940544987059	2		291	642	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509485	149509485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1223	113	481	0	ENST00000261799.4:c.1414G>A	p.Glu472Lys	p.E472K	ENST00000261799	NM_002609.3	472	Gag/Aag	10/23	1	2	FACETS	0.368	0.33	0.409	0.368	0.33	0.409	SUBCLONAL	1	TRUE	1	0.459940544987059	2		481	1336	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722042	176722042	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	216	303	0	ENST00000439151.2:c.7673G>C	p.Arg2558Thr	p.R2558T	ENST00000439151	NM_022455.4	2558	aGa/aCa	23/23	1	2	FACETS	0.924	0.859	0.992	0.924	0.859	0.992	CLONAL	1	TRUE	1	0.459940544987059	2		303	1016	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481446	20481446	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	102	290	0	ENST00000346618.3:c.515C>G	p.Ser172Cys	p.S172C	ENST00000346618	NM_001949.4	172	tCt/tGt	3/7	0.327669705596505	3	FACETS	0.847	0.759	0.941			1	CLONAL	1	TRUE	NA	0.459940544987059	3		290	644	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100145	157100145	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	44	78	0	ENST00000346085.5:c.1082C>G	p.Ser361Trp	p.S361W	ENST00000346085	NM_020732.3	361	tCg/tGg	1/20	0.385202888970834	1	FACETS	0.872	0.743	1	0.872	0.743	1	CLONAL	1	TRUE	0	0.459940544987059	1		78	169	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878044	151878044	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	127	325	0	ENST00000262189.6:c.6901C>T	p.Gln2301Ter	p.Q2301*	ENST00000262189	NM_170606.2	2301	Cag/Tag	36/59	1	2	FACETS	0.965	0.878	1	0.965	0.878	1	CLONAL	1	TRUE	1	0.459940544987059	2		325	572	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719975	18719975	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	110	343	0	ENST00000266497.5:c.3872C>T	p.Ser1291Leu	p.S1291L	ENST00000266497		1291	tCa/tTa	27/31	NA	2	FACETS	0.951	0.858	1			1	INDETERMINATE	1	TRUE	NA	0.459940544987059	2		343	503	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771344	68771344	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	196	250	1	ENST00000261769.5:c.26C>A	p.Ser9Ter	p.S9*	ENST00000261769	NM_004360.3	9	tCg/tAg	1/16	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.459940544987059	2		251	668	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108663	8108663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	294	441	0	ENST00000585124.1:c.732G>A	p.Met244Ile	p.M244I	ENST00000585124	NM_004217.3	244	atG/atA	8/9	0.349546429040984	1	FACETS	0.888	0.836	0.942	0.888	0.836	0.942	CLONAL	1	TRUE	0	0.459940544987059	1		441	1108	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553702	29553702	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	65	214	0	ENST00000356175.3:c.2251G>T	p.Gly751Ter	p.G751*	ENST00000356175	NM_000267.3	751	Gga/Tga	18/57	0.349546429040984	1	FACETS	0.728	0.636	0.825	0.728	0.636	0.825	SUBCLONAL	1	TRUE	0	0.459940544987059	1		214	299	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775161	73775161	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1765	443	688	0	ENST00000254810.4:c.95C>G	p.Ser32Cys	p.S32C	ENST00000254810	NM_005324.3	32	tCt/tGt	2/4	1	2	FACETS	0.872	0.829	0.917	0.872	0.829	0.917	CLONAL	1	TRUE	1	0.459940544987059	2		688	2208	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2199905	2199905	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0008647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1238	299	622	0	ENST00000398665.3:c.674C>G	p.Ser225Ter	p.S225*	ENST00000398665	NM_032482.2	225	tCa/tGa	8/28	1	2	FACETS	0.846	0.795	0.899	0.846	0.795	0.899	CLONAL	1	TRUE	1	0.459940544987059	2		622	1537	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344869	70344869	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1493	275	711	1	ENST00000374080.3:c.2099C>T	p.Ser700Phe	p.S700F	ENST00000374080		700	tCc/tTc	15/45	0.34867629380394	1	FACETS	0.521	0.487	0.556	0.521	0.487	0.556	SUBCLONAL	1	TRUE	0	0.459940544987059	1		712	1768	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0008650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	29	286	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		286	798	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0008666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	689	421	1	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	0.469315469169385	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	FALSE	0	0.464911846683761	3		422	1188	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564308	86564308	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	48	354	0	ENST00000274376.6:c.40G>T	p.Val14Leu	p.V14L	ENST00000274376	NM_002890.2	14	Gta/Tta	1/25	1	2	FACETS	0.23	0.194	0.271	0.23	0.194	0.271	SUBCLONAL	1	FALSE	1	0.464911846683761	2		354	897	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060604	38060604	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3265	682	1009	1	ENST00000250448.2:c.1385G>C	p.Gly462Ala	p.G462A	ENST00000250448	NM_004496.3	462	gGt/gCt	2/2	0.464911846683761	6	FACETS	1	0.997	1			1	CLONAL	1	FALSE	NA	0.464911846683761	6		1010	3947	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267688	7267688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140762552	NA	P-0008666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	66	388	0	ENST00000302850.5:c.320C>T	p.Thr107Met	p.T107M	ENST00000302850	NM_000208.2	107	aCg/aTg	2/22	0.43951614140253	2	FACETS	0.333	0.288	0.382	0.167	0.144	0.191	SUBCLONAL	1	FALSE	0	0.464911846683761	2		388	852	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0008694-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	52	154	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.911	0.782	1	0.911	0.782	1	CLONAL	1	TRUE	1	0.421146916266073	2		154	271	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0008694-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	77	497	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.639	0.562	0.722	0.639	0.562	0.722	SUBCLONAL	1	TRUE	1	0.421146916266073	2		497	572	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907476	32907476	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008694-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	49	572	0	ENST00000380152.3:c.1861G>A	p.Glu621Lys	p.E621K	ENST00000380152		621	Gaa/Aaa	10/27	0.3346609545395	3	FACETS	0.314	0.265	0.369	0.157	0.132	0.185	SUBCLONAL	1	TRUE	1	0.421146916266073	3		572	896	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841345	15841345	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008694-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	260	1084	1	ENST00000307771.7:c.1429C>T	p.Gln477Ter	p.Q477*	ENST00000307771	NM_005089.3	477	Cag/Tag	11/11	0.16077893494997	0	FACETS	0.508	0.474	0.542			1	INDETERMINATE	1	TRUE	0	0.421146916266073	0		1085	1408	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023401	27023401	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008694-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	169	615	0	ENST00000324856.7:c.508del	p.His170ThrfsTer62	p.H170Tfs*62	ENST00000324856	NM_006015.4	169	ttC/tt	1/20	0.415397343226478	1	FACETS	0.876	0.808	0.948	0.876	0.808	0.948	CLONAL	1	TRUE	0	0.421146916266073	1		615	723	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0008735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	748	286	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.83072486084465	5	FACETS	0.973	0.95	0.996	0.973	0.95	0.996	CLONAL	4	TRUE	1	0.839825406061879	5		287	1034	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0008735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	533	592	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.839825406061879	2		592	620	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206941988	206941988	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376415487	NA	P-0008735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	152	289	0	ENST00000423557.1:c.530G>A	p.Arg177Gln	p.R177Q	ENST00000423557	NM_000572.2	177	cGa/cAa	5/5	0.839825406061879	3	FACETS	0.838	0.77	0.91	0.419	0.385	0.455	CLONAL	1	TRUE	1	0.839825406061879	3		289	613	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266570	41266570	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	302	353	0	ENST00000349496.5:c.367C>T	p.Gln123Ter	p.Q123*	ENST00000349496	NM_001904.3	123	Cag/Tag	4/15	0.820427166529242	4	FACETS	0.995	0.936	1	0.497	0.468	0.528	CLONAL	1	TRUE	2	0.839825406061879	4		353	1330	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448592	89448592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543425684	NA	P-0008735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	163	529	0	ENST00000336596.2:c.1556C>T	p.Thr519Met	p.T519M	ENST00000336596	NM_005233.5	519	aCg/aTg	7/17	0.839825406061879	3	FACETS	0.492	0.45	0.535	0.246	0.225	0.268	SUBCLONAL	1	TRUE	1	0.839825406061879	3		529	1121	SUCCESS
APC	324	MSKCC	GRCh37	5	112173965	112173965	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1561578889	NA	P-0008735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	221	262	1	ENST00000257430.4:c.2674G>T	p.Glu892Ter	p.E892*	ENST00000257430	NM_000038.5	892	Gaa/Taa	16/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.839825406061879	2		263	487	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866540	117866540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3440	436	984	0	ENST00000297338.2:c.1105G>A	p.Val369Ile	p.V369I	ENST00000297338	NM_006265.2	369	Gta/Ata	9/14	0.839825406061879	8	FACETS	0.943	0.893	0.994	0.189	0.178	0.199	CLONAL	1	TRUE	3	0.839825406061879	8		984	3876	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32968926	32968926	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555289562	NA	P-0008735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	425	546	0	ENST00000380152.3:c.9357A>C	p.Leu3119Phe	p.L3119F	ENST00000380152		3119	ttA/ttC	25/27	0.496379677914355	6	FACETS	0.906	0.863	0.951	0.604	0.575	0.634	INDETERMINATE	2	TRUE	3	0.839825406061879	6		546	1496	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0008735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	291	421	2	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.871	0.823	0.919	0.871	0.823	0.919	CLONAL	1	TRUE	1	0.839825406061879	2		423	796	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0008735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	1013	783	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.839825406061879	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.839825406061879	2		783	1153	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0008744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	1234	343	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.295933605770329	10	FACETS	0.984	0.961	1	0.984	0.961	1	CLONAL	8	FALSE	2	0.295933605770329	10		343	2314	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102094475	102094475	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	116	490	0	ENST00000282441.5:c.1155C>A	p.Phe385Leu	p.F385L	ENST00000282441	NM_001130145.2	385	ttC/ttA	7/9	0.295933605770329	3	FACETS	1	0.905	1	0.503	0.452	0.556	CLONAL	1	FALSE	1	0.295933605770329	3		490	895	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133211	30133211	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1361	209	909	3	ENST00000263025.4:c.287G>A	p.Arg96His	p.R96H	ENST00000263025	NM_002746.2	96	cGc/cAc	2/9	0.295933605770329	3	FACETS	1	0.949	1	0.516	0.478	0.557	CLONAL	1	FALSE	1	0.295933605770329	3		912	1570	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2199926	2199926	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	142	733	0	ENST00000398665.3:c.695T>A	p.Ile232Asn	p.I232N	ENST00000398665	NM_032482.2	232	aTc/aAc	8/28	1	2	FACETS	0.889	0.809	0.974	0.889	0.809	0.974	CLONAL	1	FALSE	1	0.295933605770329	2		733	1079	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0008747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	431	749	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.507572830822107	1	FACETS	0.999	0.952	1	0.999	0.952	1	CLONAL	1	TRUE	0	0.507572830822107	1		750	1269	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380277	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913238	NA	P-0008747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	289	547	0	ENST00000311936.3:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	61	Caa/Aaa	3/5	NA	2	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.507572830822107	2		547	1055	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508826	106508826	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1462539802	NA	P-0008747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	157	436	1	ENST00000359195.3:c.820G>A	p.Val274Ile	p.V274I	ENST00000359195	NM_002649.2	274	Gtc/Atc	2/11	0.25621143026862	1	FACETS	0.436	0.398	0.475	0.436	0.398	0.475	INDETERMINATE	1	TRUE	0	0.507572830822107	1		437	1060	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456881	32456881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs948132360	NA	P-0008747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	62	136	0	ENST00000332351.3:c.11C>T	p.Pro4Leu	p.P4L	ENST00000332351	NM_024426.4	4	cCg/cTg	1/10	0.221343973071518	1	FACETS	0.701	0.612	0.796	0.701	0.612	0.796	INDETERMINATE	1	TRUE	0	0.507572830822107	1		136	260	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149330	61149330	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	97	425	0	ENST00000295025.8:c.1520G>C	p.Gly507Ala	p.G507A	ENST00000295025	NM_002908.2	507	gGa/gCa	11/11	0.278318689940178	3	FACETS	0.859	0.765	0.96	0.43	0.382	0.48	CLONAL	1	FALSE	1	0.278318689940178	3		425	924	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436617	52436617	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0008750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	217	457	1	ENST00000460680.1:c.2056+1G>A		p.X686_splice	ENST00000460680	NM_004656.3	686			0.137359008077011	1	FACETS	0.896	0.836	0.958	1	0.993	1	INDETERMINATE	2	FALSE	0	0.278318689940178	1		458	749	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958408	90958408	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	93	468	0	ENST00000265433.3:c.2030A>G	p.Asp677Gly	p.D677G	ENST00000265433	NM_002485.4	677	gAt/gGt	13/16	0.278318689940178	3	FACETS	0.83	0.737	0.93	0.415	0.368	0.465	CLONAL	1	FALSE	1	0.278318689940178	3		468	917	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110086	115110086	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	57	275	0	ENST00000257566.3:c.1792G>T	p.Gly598Ter	p.G598*	ENST00000257566	NM_016569.3	598	Gga/Tga	8/8	0.248082955771034	4	FACETS	0.93	0.798	1	0.465	0.399	0.537	CLONAL	1	FALSE	2	0.278318689940178	4		275	563	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008760-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	247	383	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	0.839	0.788	0.891	0.839	0.788	0.891	CLONAL	1	TRUE	1	0.818734385151957	2		383	719	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008760-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	18	378	0	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	1	2	FACETS	0.061	0.045	0.08	0.061	0.045	0.08	SUBCLONAL	1	TRUE	1	0.818734385151957	2		378	720	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056427	26056427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs182693914	NA	P-0008760-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	25	278	0	ENST00000343677.2:c.230A>G	p.Asn77Ser	p.N77S	ENST00000343677	NM_005319.3	77	aAc/aGc	1/1	1	2	FACETS	0.125	0.098	0.156	0.125	0.098	0.156	SUBCLONAL	1	TRUE	1	0.818734385151957	2		278	490	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927411	178927411	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008760-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	183	598	0	ENST00000263967.3:c.1174T>C	p.Tyr392His	p.Y392H	ENST00000263967	NM_006218.2	392	Tac/Cac	7/21	1	2	FACETS	0.982	0.916	1	0.982	0.916	1	CLONAL	1	TRUE	1	0.818734385151957	2		598	455	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842439	68842439	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs864622655	NA	P-0008760-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	186	583	3	ENST00000261769.5:c.504del	p.Gly169AlafsTer46	p.G169Afs*46	ENST00000261769	NM_004360.3	167	gAa/ga	4/16	0.796614633855085	1	FACETS	0.889	0.84	0.936	0.889	0.84	0.936	CLONAL	1	TRUE	0	0.818734385151957	1		586	302	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070630	67070642	+	frameshift_variant	Frame_Shift_Del	DEL	ATGTCGACTTAGA	ATGTCGACTTAGA	-	novel	NA	P-0008760-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	244	574	0	ENST00000412916.2:c.255_267del	p.Tyr85Ter	p.Y85*	ENST00000412916		85	tATGTCGACTTAGAa/ta	3/6	0.796614633855085	1	FACETS	0.972	0.93	1	0.972	0.93	1	CLONAL	1	TRUE	0	0.818734385151957	1		574	362	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158119	47158119	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	198	496	0	ENST00000409792.3:c.4580T>C	p.Ile1527Thr	p.I1527T	ENST00000409792	NM_014159.6	1527	aTt/aCt	4/21	1	2	FACETS	0.911	0.845	0.98	0.911	0.845	0.98	CLONAL	1	TRUE	1	0.485426331485303	2		496	895	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431140	49431140	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	183	367	0	ENST00000301067.7:c.9999G>C	p.Gln3333His	p.Q3333H	ENST00000301067	NM_003482.3	3333	caG/caC	34/54	1	2	FACETS	0.913	0.844	0.985	0.913	0.844	0.985	CLONAL	1	TRUE	1	0.485426331485303	2		367	826	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500321	99500321	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	241	442	0	ENST00000268035.6:c.3754A>G	p.Asn1252Asp	p.N1252D	ENST00000268035	NM_000875.3	1252	Aac/Gac	21/21	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.485426331485303	2		442	929	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602587	10602587	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	196	321	0	ENST00000171111.5:c.991G>C	p.Ala331Pro	p.A331P	ENST00000171111	NM_203500.1	331	Gcg/Ccg	3/6	0.485426331485303	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.485426331485303	1		321	537	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814285	76814285	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	149	592	0	ENST00000373344.5:c.6359G>C	p.Gly2120Ala	p.G2120A	ENST00000373344	NM_000489.3	2120	gGa/gCa	29/35	1	2	FACETS	0.867	0.794	0.943	0.867	0.794	0.943	CLONAL	1	TRUE	1	0.485426331485303	2		592	708	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0008778-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	195	254	0	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.230522956111889	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.274732602186914	2		254	690	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226271	2226271	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008778-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	71	384	0	ENST00000326181.6:c.1884G>T	p.Trp628Cys	p.W628C	ENST00000326181	NM_032271.2	628	tgG/tgT	20/21	0.27337684559041	4	FACETS	0.656	0.571	0.749			1	SUBCLONAL	1	TRUE	NA	0.274732602186914	4		384	1004	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946247	55946247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008800-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	58	328	0	ENST00000263923.4:c.3932C>T	p.Ser1311Phe	p.S1311F	ENST00000263923	NM_002253.2	1311	tCc/tTc	30/30	0.295716913022836	3	FACETS	0.53	0.454	0.613	0.265	0.227	0.307	SUBCLONAL	1	FALSE	1	0.3	3		328	839	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250820	26250820	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008800-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	114	507	0	ENST00000446824.2:c.14A>G	p.Lys5Arg	p.K5R	ENST00000446824	NM_021018.2	5	aAg/aGg	1/1	0.263221679157924	3	FACETS	0.792	0.712	0.878	0.396	0.356	0.439	SUBCLONAL	1	FALSE	1	0.3	3		507	1103	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907705	76907705	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008800-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	72	265	0	ENST00000373344.5:c.4456G>T	p.Asp1486Tyr	p.D1486Y	ENST00000373344	NM_000489.3	1486	Gat/Tat	15/35	0.174643883761587	2	FACETS	0.648	0.565	0.737			1	INDETERMINATE	1	FALSE	NA	0.3	2		265	741	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0008809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	115	592	1	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.173712404635429	1	FACETS	0.867	0.78	0.959	0.867	0.78	0.959	CLONAL	1	TRUE	0	0.240409188036526	1		593	971	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578210	7578210	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008812-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	482	745	0	ENST00000269305.4:c.639del	p.His214IlefsTer33	p.H214Ifs*33	ENST00000269305	NM_001126112.2	213	cgA/cg	6/11	0.348103194972844	3	FACETS	1	0.994	1	0.799	0.768	0.83	CLONAL	2	TRUE	0	0.519986487657369	3		745	974	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220516	123220516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008816-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	61	711	0	ENST00000218089.9:c.3173C>T	p.Ser1058Leu	p.S1058L	ENST00000218089	NM_001042749.1	1058	tCa/tTa	30/35	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		711	971	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586056	29586056	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1135402857	NA	P-0008831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	207	356	0	ENST00000356175.3:c.4276C>T	p.Gln1426Ter	p.Q1426*	ENST00000356175	NM_000267.3	1426	Cag/Tag	32/57	0.728277984963903	1	FACETS	0.831	0.781	0.881	0.831	0.781	0.881	CLONAL	1	TRUE	0	0.728277984963903	1		356	435	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180882	106180882	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	475	543	0	ENST00000380013.4:c.3911del	p.Lys1304ArgfsTer59	p.K1304Rfs*59	ENST00000380013	NM_001127208.2	1304	Aag/ag	7/11	0.728277984963903	1	FACETS	0.99	0.954	1	0.99	0.954	1	CLONAL	1	TRUE	0	0.728277984963903	1		543	838	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0008841-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	64	325	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.924	0.798	1	0.924	0.798	1	CLONAL	1	TRUE	1	0.15	2		325	924	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0008841-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	54	215	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	TRUE	1	0.15	2		215	720	SUCCESS
APC	324	MSKCC	GRCh37	5	112175766	112175766	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008841-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	61	282	0	ENST00000257430.4:c.4476del	p.Thr1493ArgfsTer14	p.T1493Rfs*14	ENST00000257430	NM_000038.5	1492	gCc/gc	16/16	1	2	FACETS	0.965	0.83	1	0.965	0.83	1	CLONAL	1	TRUE	1	0.15	2		282	843	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138172	64138172	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008841-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	107	348	0	ENST00000334205.4:c.2095C>T	p.Arg699Cys	p.R699C	ENST00000334205	NM_003942.2	699	Cgc/Tgc	16/17	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.15	2		348	1067	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0008846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	226	672	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.293206735983203	2	FACETS	1	0.94	1	0.504	0.47	0.539	INDETERMINATE	1	TRUE	0	0.507579084503202	2		672	883	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0008855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	138	337	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	1	2	FACETS	0.742	0.676	0.812	0.742	0.676	0.812	SUBCLONAL	1	TRUE	1	0.503030694542021	2		337	739	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0008859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	27	386	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		386	771	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057520005	NA	P-0008874-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	96	732	0	ENST00000269305.4:c.820G>T	p.Val274Phe	p.V274F	ENST00000269305	NM_001126112.2	274	Gtt/Ttt	8/11	0.174670482960865	3	FACETS	0.902	0.803	1	0.451	0.401	0.504	CLONAL	1	TRUE	1	0.29	3		732	840	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597488	10597488	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008874-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	59	506	0	ENST00000171111.5:c.1715A>G	p.Tyr572Cys	p.Y572C	ENST00000171111	NM_203500.1	572	tAt/tGt	6/6	0.186910703322369	0	FACETS	0.471	0.405	0.543			1	SUBCLONAL	1	TRUE	0	0.29	0		506	613	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288924	212288924	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008874-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	93	586	0	ENST00000342788.4:c.2822A>T	p.Gln941Leu	p.Q941L	ENST00000342788	NM_005235.2	941	cAg/cTg	23/28	0.141894598688324	4	FACETS	0.84	0.745	0.941	0.42	0.372	0.471	INDETERMINATE	1	TRUE	2	0.29	4		586	985	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643705	52643705	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008874-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	41	421	0	ENST00000394830.3:c.2191A>T	p.Met731Leu	p.M731L	ENST00000394830	NM_018313.4	731	Atg/Ttg	17/30	0.174670482960865	3	FACETS	0.514	0.427	0.611	0.257	0.213	0.306	SUBCLONAL	1	TRUE	1	0.29	3		421	630	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643715	52643715	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008874-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	43	439	0	ENST00000394830.3:c.2181C>G	p.Asp727Glu	p.D727E	ENST00000394830	NM_018313.4	727	gaC/gaG	17/30	0.174670482960865	3	FACETS	0.49	0.409	0.58	0.245	0.204	0.29	SUBCLONAL	1	TRUE	1	0.29	3		439	693	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586470	189586470	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008874-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	88	395	0	ENST00000264731.3:c.1094C>A	p.Ser365Ter	p.S365*	ENST00000264731	NM_003722.4	365	tCg/tAg	8/14	0.174670482960865	3	FACETS	1	0.905	1	0.512	0.453	0.574	CLONAL	1	TRUE	1	0.29	3		395	679	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043656	6043656	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs769554577	NA	P-0008874-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	38	432	0	ENST00000265849.7:c.197T>C	p.Ile66Thr	p.I66T	ENST00000265849	NM_000535.5	66	aTt/aCt	3/15	0.141894598688324	4	FACETS	0.533	0.44	0.638	0.267	0.22	0.319	INDETERMINATE	1	TRUE	2	0.29	4		432	634	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509312	106509312	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008874-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	95	586	2	ENST00000359195.3:c.1306G>T	p.Gly436Cys	p.G436C	ENST00000359195	NM_002649.2	436	Ggt/Tgt	2/11	0.17097661808977	4	FACETS	0.719	0.638	0.805	0.359	0.319	0.403	INDETERMINATE	1	TRUE	2	0.29	4		588	1176	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376690	31376690	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008874-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	89	478	0	ENST00000328111.2:c.685G>T	p.Val229Leu	p.V229L	ENST00000328111	NM_006892.3	229	Gtg/Ttg	7/23	0.159521028051125	3	FACETS	1	0.896	1	0.506	0.448	0.567	INDETERMINATE	1	TRUE	1	0.29	3		478	695	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221264	1221267	+	frameshift_variant	Frame_Shift_Del	DEL	TTGT	TTGT	-	rs121913320	NA	P-0008874-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	44	776	0	ENST00000326873.7:c.790_793del	p.Phe264ArgfsTer22	p.F264Rfs*22	ENST00000326873	NM_000455.4	263	TTGTtt/tt	6/10	0.186910703322369	0	FACETS	0.307	0.257	0.363			1	SUBCLONAL	1	TRUE	0	0.29	0		776	701	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515225	106515226	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0008874-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	65	494	0	ENST00000359195.3:c.2368_2369delinsTT	p.Gly790Leu	p.G790L	ENST00000359195	NM_002649.2	790	GGa/TTa	5/11	0.17097661808977	4	FACETS	0.685	0.593	0.786	0.343	0.296	0.393	INDETERMINATE	1	TRUE	2	0.29	4		494	844	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0008876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	196	286	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.921	0.853	0.993	0.921	0.853	0.993	CLONAL	1	TRUE	1	0.426246437350581	2		287	998	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76949316	76949316	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1210	288	617	0	ENST00000373344.5:c.481G>T	p.Gly161Ter	p.G161*	ENST00000373344	NM_000489.3	161	Gga/Tga	6/35	0.426246437350581	1	FACETS	0.71	0.666	0.755	0.71	0.666	0.755	SUBCLONAL	1	TRUE	0	0.426246437350581	1		617	1498	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207065	1207065	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	182	382	0	ENST00000326873.7:c.157del	p.Asp53ThrfsTer11	p.D53Tfs*11	ENST00000326873	NM_000455.4	51	atG/at	1/10	0.410674307521664	1	FACETS	0.848	0.784	0.915	0.848	0.784	0.915	CLONAL	1	TRUE	0	0.426246437350581	1		382	792	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984794	55984794	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761016513	NA	P-0008876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	294	478	0	ENST00000263923.4:c.335C>T	p.Ser112Leu	p.S112L	ENST00000263923	NM_002253.2	112	tCg/tTg	3/30	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.426246437350581	2		478	1229	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602584	10602584	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1208201314	NA	P-0008876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	200	310	1	ENST00000171111.5:c.994G>T	p.Gly332Cys	p.G332C	ENST00000171111	NM_203500.1	332	Ggc/Tgc	3/6	0.410674307521664	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.426246437350581	1		311	689	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971151	55971151	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	131	191	0	ENST00000263923.4:c.1646G>A	p.Arg549Lys	p.R549K	ENST00000263923	NM_002253.2	549	aGg/aAg	13/30	1	2	FACETS	0.976	0.888	1	0.976	0.888	1	CLONAL	1	TRUE	1	0.426246437350581	2		191	630	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231715	66231715	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	214	459	0	ENST00000273854.3:c.1985C>A	p.Ala662Asp	p.A662D	ENST00000273854	NM_004439.5	662	gCt/gAt	11/18	1	2	FACETS	0.976	0.907	1	0.976	0.907	1	CLONAL	1	TRUE	1	0.426246437350581	2		459	1029	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293920	1293920	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	391	346	1	ENST00000310581.5:c.1081G>T	p.Val361Leu	p.V361L	ENST00000310581	NM_198253.2	361	Gtg/Ttg	2/16	0.397585673190514	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.426246437350581	3		347	1075	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976808	2976808	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0008876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	232	537	0	ENST00000396946.4:c.1204A>T	p.Lys402Ter	p.K402*	ENST00000396946	NM_032415.4	402	Aag/Tag	9/25	1	2	FACETS	0.788	0.733	0.845	0.788	0.733	0.845	SUBCLONAL	1	TRUE	1	0.426246437350581	2		537	1382	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334737	81334737	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs772967560	NA	P-0008876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	236	483	0	ENST00000222390.5:c.1979G>T	p.Gly660Val	p.G660V	ENST00000222390	NM_000601.4	660	gGg/gTg	17/18	1	2	FACETS	0.911	0.849	0.976	0.911	0.849	0.976	CLONAL	1	TRUE	1	0.426246437350581	2		483	1215	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123080	5123080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	212	471	0	ENST00000381652.3:c.3136G>A	p.Glu1046Lys	p.E1046K	ENST00000381652	NM_004972.3	1046	Gaa/Aaa	23/25	0.410674307521664	1	FACETS	0.962	0.895	1	0.962	0.895	1	CLONAL	1	TRUE	0	0.426246437350581	1		471	814	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333123	70333123	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	272	470	1	ENST00000373644.4:c.1028C>A	p.Pro343Gln	p.P343Q	ENST00000373644	NM_030625.2	343	cCa/cAa	2/12	0.398506139248468	2	FACETS	0.955	0.895	1	0.478	0.447	0.509	CLONAL	1	TRUE	0	0.426246437350581	2		471	1336	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205552	61205552	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	263	481	0	ENST00000301761.2:c.337A>T	p.Ser113Cys	p.S113C	ENST00000301761	NM_017841.2	113	Agt/Tgt	3/4	1	2	FACETS	0.99	0.926	1	0.99	0.926	1	CLONAL	1	TRUE	1	0.426246437350581	2		481	1247	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435967	49435967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	256	438	0	ENST00000301067.7:c.6014G>A	p.Arg2005His	p.R2005H	ENST00000301067	NM_003482.3	2005	cGc/cAc	28/54	1	2	FACETS	0.959	0.897	1	0.959	0.897	1	CLONAL	1	TRUE	1	0.426246437350581	2		438	1252	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264353	30264353	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	86	138	3	ENST00000322652.5:c.88G>T	p.Ala30Ser	p.A30S	ENST00000322652	NM_015355.2	30	Gcg/Tcg	1/16	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.426246437350581	2		141	369	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650619	48650619	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1335908216	NA	P-0008876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	290	480	1	ENST00000376670.3:c.589C>A	p.Pro197Thr	p.P197T	ENST00000376670	NM_002049.3	197	Cct/Act	3/6	1	2	FACETS	0.987	0.927	1	0.987	0.927	1	CLONAL	1	TRUE	1	0.426246437350581	2		481	1378	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101952	11101965	+	frameshift_variant	Frame_Shift_Del	DEL	AAGCAGCAGAAGAT	AAGCAGCAGAAGAT	-	novel	NA	P-0008876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	131	333	0	ENST00000358026.2:c.1372_1385del	p.Lys458ArgfsTer16	p.K458Rfs*16	ENST00000358026	NM_001128849.1	458	AAGCAGCAGAAGATc/c	8/36	0.410674307521664	1	FACETS	0.853	0.777	0.932	0.853	0.777	0.932	CLONAL	1	TRUE	0	0.426246437350581	1		333	567	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331843	68331844	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0008876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	188	383	0	ENST00000487270.1:c.440_441del	p.Phe147Ter	p.F147*	ENST00000487270	NM_133509.3	147	TTt/t	5/11	0.410674307521664	1	FACETS	0.737	0.681	0.795	0.737	0.681	0.795	SUBCLONAL	1	TRUE	0	0.426246437350581	1		383	942	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0008902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	423	749	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.349709167306542	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.383716253613774	2		750	1096	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665752	29665755	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1555535032	NA	P-0008902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	228	516	0	ENST00000356175.3:c.6789_6792del	p.Tyr2264ThrfsTer5	p.Y2264Tfs*5	ENST00000356175	NM_000267.3	2263	ACTTac/ac	45/57	0.349709167306542	2	FACETS	0.884	0.828	0.941	0.884	0.828	0.941	CLONAL	2	TRUE	0	0.383716253613774	2		516	672	SUCCESS
APC	324	MSKCC	GRCh37	5	112164642	112164642	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	75	318	0	ENST00000257430.4:c.1716G>C	p.Leu572Phe	p.L572F	ENST00000257430	NM_000038.5	572	ttG/ttC	14/16	1	2	FACETS	0.758	0.665	0.857	0.758	0.665	0.857	SUBCLONAL	1	TRUE	1	0.383716253613774	2		318	516	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406614	70406614	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0008902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	115	599	0	ENST00000373644.4:c.4128T>A	p.Cys1376Ter	p.C1376*	ENST00000373644	NM_030625.2	1376	tgT/tgA	4/12	0.383716253613774	4	FACETS	0.689	0.619	0.764			1	SUBCLONAL	1	TRUE	NA	0.383716253613774	4		599	1203	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590546	95590546	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	107	396	0	ENST00000393063.1:c.1363G>T	p.Val455Phe	p.V455F	ENST00000393063	NM_030621.3	455	Gtt/Ttt	9/28	0.349709167306542	2	FACETS	0.939	0.844	1	0.469	0.422	0.52	CLONAL	1	TRUE	0	0.383716253613774	2		396	594	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0008906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	169	286	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.421213210033466	3	FACETS	0.931	0.87	0.991	1	0.99	1	CLONAL	3	TRUE	1	0.421213210033466	3		287	348	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	19	293	2	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	0.276723411984319	1	FACETS	0.306	0.232	0.391	0.306	0.232	0.391	SUBCLONAL	1	TRUE	0	0.421213210033466	1		295	233	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs17849781	NA	P-0008906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	372	445	0	ENST00000269305.4:c.832C>G	p.Pro278Ala	p.P278A	ENST00000269305	NM_001126112.2	278	Cct/Gct	8/11	0.421213210033466	2	FACETS	0.957	0.911	1	0.957	0.911	1	CLONAL	2	TRUE	0	0.421213210033466	2		445	923	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681726	30681726	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	166	366	0	ENST00000376406.3:c.371C>A	p.Ala124Asp	p.A124D	ENST00000376406	NM_014641.2	124	gCt/gAt	3/15	0.271725862731778	4	FACETS	1	0.96	1	0.538	0.493	0.585	CLONAL	1	TRUE	2	0.421213210033466	4		366	1041	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271160	38271160	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008906-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	88	152	0	ENST00000425967.3:c.2548C>A	p.Leu850Ile	p.L850I	ENST00000425967	NM_001174067.1	850	Ctc/Atc	19/19	0.421213210033466	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.421213210033466	1		152	314	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560494	65560494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008914-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	297	708	0	ENST00000358664.4:c.103C>T	p.Arg35Cys	p.R35C	ENST00000358664	NM_002382.4	35	Cgt/Tgt	3/5	0.709865971727944	1	FACETS	0.961	0.916	1	0.961	0.916	1	CLONAL	1	TRUE	0	0.720343136625166	1		708	549	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0008917-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	1598	343	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.19352190302794	23	FACETS	0.998	0.981	1			1	CLONAL	21	TRUE	NA	0.19352190302794	23		343	2389	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0008917-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2188	279	420	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.19352190302794	23	FACETS	0.886	0.828	0.946			1	CLONAL	4	TRUE	NA	0.19352190302794	23		420	2467	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0008917-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	61	481	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.188118038096738	2	FACETS	0.928	0.8	1	0.464	0.4	0.534	CLONAL	1	TRUE	0	0.19352190302794	2		481	679	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001390	150001390	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008917-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	50	526	0	ENST00000253339.5:c.2214G>C	p.Lys738Asn	p.K738N	ENST00000253339		738	aaG/aaC	4/7	0.19352190302794	2	FACETS	0.603	0.51	0.706	0.301	0.255	0.353	SUBCLONAL	1	TRUE	0	0.19352190302794	2		526	857	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739088	145739088	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008917-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	69	249	0	ENST00000428558.2:c.2067G>T	p.Leu689Phe	p.L689F	ENST00000428558	NM_004260.3	689	ttG/ttT	13/22	0.19352190302794	3	FACETS	1	0.953	1	0.605	0.527	0.69	CLONAL	1	TRUE	1	0.19352190302794	3		249	646	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145349	58145349	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008917-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	51	341	0	ENST00000257904.6:c.152T>C	p.Ile51Thr	p.I51T	ENST00000257904	NM_000075.3	51	aTc/aCc	2/8	0.19352190302794	3	FACETS	0.732	0.62	0.855	0.366	0.31	0.428	SUBCLONAL	1	TRUE	1	0.19352190302794	3		341	790	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78931503	78931503	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008917-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	68	407	0	ENST00000306801.3:c.3450G>A	p.Trp1150Ter	p.W1150*	ENST00000306801	NM_020761.2	1150	tgG/tgA	29/34	0.19352190302794	3	FACETS	0.906	0.786	1	0.453	0.393	0.518	CLONAL	1	TRUE	1	0.19352190302794	3		407	851	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188143	11188167	+	frameshift_variant	Frame_Shift_Del	DEL	GTGGTAGACTTAGAAGCCACTGTCA	GTGGTAGACTTAGAAGCCACTGTCA	-	novel	NA	P-0008917-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	53	308	0	ENST00000361445.4:c.5927_5951del	p.Leu1976ArgfsTer12	p.L1976Rfs*12	ENST00000361445	NM_004958.3	1976	cTGACAGTGGCTTCTAAGTCTACCACg/cg	43/58	0.126930127813399	4	FACETS	0.831	0.707	0.967	0.415	0.353	0.484	CLONAL	1	TRUE	2	0.19352190302794	4		308	787	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0008920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	216	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.868	0.814	0.923	1	0.995	1	CLONAL	3	FALSE	1	0.3	2		249	553	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0008920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	371	421	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	NA	2	FACETS	0.935	0.891	0.979			1	INDETERMINATE	3	FALSE	NA	0.3	2		421	882	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110035	115110035	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs763473739	NA	P-0008920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	223	349	0	ENST00000257566.3:c.1843T>G	p.Ser615Ala	p.S615A	ENST00000257566	NM_016569.3	615	Tcc/Gcc	8/8	0.3	6	FACETS	0.962	0.902	1			1	CLONAL	4	FALSE	NA	0.3	6		349	618	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061231	38061231	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	873	420	0	ENST00000250448.2:c.758T>G	p.Met253Arg	p.M253R	ENST00000250448	NM_004496.3	253	aTg/aGg	2/2	0.3	19	FACETS	1	0.99	1			1	CLONAL	11	FALSE	NA	0.3	19		420	1800	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0008922-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	39	291	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.266359726273099	3	FACETS	0.3	0.247	0.359	0.15	0.123	0.18	SUBCLONAL	1	TRUE	1	0.35052976563946	3		291	873	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207021	1207021	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913324	NA	P-0008922-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	23	352	1	ENST00000326873.7:c.109C>T	p.Gln37Ter	p.Q37*	ENST00000326873	NM_000455.4	37	Cag/Tag	1/10	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.35052976563946	NA		353	404	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610359	10610359	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008922-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	34	198	0	ENST00000171111.5:c.351G>T	p.Glu117Asp	p.E117D	ENST00000171111	NM_203500.1	117	gaG/gaT	2/6	0.308778753896342	2	FACETS	0.333	0.271	0.403	0.167	0.135	0.202	SUBCLONAL	1	TRUE	0	0.35052976563946	2		198	582	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	68	246	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.985	0.868	1	0.985	0.868	1	CLONAL	1	TRUE	1	0.556874149062572	2		246	248	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447841	49447841	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748834953	NA	P-0008927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	97	292	1	ENST00000301067.7:c.593C>T	p.Ala198Val	p.A198V	ENST00000301067	NM_003482.3	198	gCg/gTg	5/54	NA	2	FACETS	0.848	0.761	0.939			1	INDETERMINATE	1	TRUE	NA	0.556874149062572	2		293	411	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221710	55221710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10727	578	303	0	ENST00000275493.2:c.754C>T	p.Arg252Cys	p.R252C	ENST00000275493	NM_005228.3	252	Cgc/Tgc	7/28	0.556874149062572	53	FACETS	0.93	0.886	0.976			1	CLONAL	3	TRUE	NA	0.556874149062572	53		303	11305	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs149840192	NA	P-0008927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15677	2415	595	2	ENST00000275493.2:c.866C>A	p.Ala289Asp	p.A289D	ENST00000275493	NM_005228.3	289	gCc/gAc	7/28	0.556874149062572	53	FACETS	1	0.994	1			1	CLONAL	7	TRUE	NA	0.556874149062572	53		597	18092	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937620	17937620	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778211961	NA	P-0008927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	132	521	1	ENST00000458235.1:c.3307C>T	p.Arg1103Trp	p.R1103W	ENST00000458235	NM_000215.3	1103	Cgg/Tgg	24/24	0.556874149062572	3	FACETS	0.989	0.9	1	0.494	0.45	0.541	CLONAL	1	TRUE	1	0.556874149062572	3		522	613	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251644	212251644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368679346	NA	P-0008956-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	217	432	1	ENST00000342788.4:c.3415C>T	p.Arg1139Trp	p.R1139W	ENST00000342788	NM_005235.2	1139	Cgg/Tgg	27/28	1	2	FACETS	0.975	0.909	1	1	0.994	1	CLONAL	2	TRUE	1	0.272135737029571	2		433	818	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793431	242793431	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376257658	NA	P-0008956-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	71	393	0	ENST00000334409.5:c.646G>A	p.Val216Met	p.V216M	ENST00000334409	NM_005018.2	216	Gtg/Atg	5/5	0.166728115611652	1	FACETS	0.681	0.594	0.775	0.681	0.594	0.775	SUBCLONAL	1	TRUE	0	0.272135737029571	1		393	662	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678799	52678799	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008956-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	78	297	0	ENST00000394830.3:c.820A>C	p.Asn274His	p.N274H	ENST00000394830	NM_018313.4	274	Aat/Cat	9/30	0.166728115611652	1	FACETS	0.992	0.875	1	0.992	0.875	1	CLONAL	1	TRUE	0	0.272135737029571	1		297	499	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499407	89499407	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008956-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	88	353	0	ENST00000336596.2:c.2577C>G	p.Asp859Glu	p.D859E	ENST00000336596	NM_005233.5	859	gaC/gaG	15/17	1	2	FACETS	0.872	0.772	0.978	0.872	0.772	0.978	CLONAL	1	TRUE	1	0.272135737029571	2		353	742	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340222	116340222	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008956-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	99	322	0	ENST00000397752.3:c.1084A>C	p.Met362Leu	p.M362L	ENST00000397752	NM_000245.2	362	Atg/Ctg	2/21	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.272135737029571	2		322	686	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435451	18435451	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008956-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	88	395	0	ENST00000266497.5:c.436C>G	p.Pro146Ala	p.P146A	ENST00000266497		146	Cca/Gca	1/31	0.197288358078296	3	FACETS	0.931	0.824	1	0.466	0.412	0.523	CLONAL	1	TRUE	1	0.272135737029571	3		395	789	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422733	49422733	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008956-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	95	423	0	ENST00000301067.7:c.14260G>C	p.Asp4754His	p.D4754H	ENST00000301067	NM_003482.3	4754	Gat/Cat	45/54	0.197288358078296	3	FACETS	1	0.901	1	0.507	0.451	0.566	CLONAL	1	TRUE	1	0.272135737029571	3		423	783	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16052787	16052787	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008956-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	103	422	0	ENST00000268712.3:c.887G>T	p.Arg296Ile	p.R296I	ENST00000268712	NM_006311.3	296	aGa/aTa	9/46	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.272135737029571	2		422	616	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411202	63411202	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008956-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	79	561	0	ENST00000330258.3:c.1965G>T	p.Gln655His	p.Q655H	ENST00000330258	NM_152424.3	655	caG/caT	2/2	0.272135737029571	1	FACETS	0.774	0.681	0.874	0.774	0.681	0.874	SUBCLONAL	1	TRUE	0	0.272135737029571	1		561	648	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893330	32893330	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs398122733	NA	P-0008956-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	135	610	0	ENST00000380152.3:c.186del	p.Phe62LeufsTer18	p.F62Lfs*18	ENST00000380152		62	Ttt/tt	3/27	0.170570434500263	1	FACETS	0.776	0.704	0.853	0.776	0.704	0.853	SUBCLONAL	1	TRUE	0	0.272135737029571	1		610	1104	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554780	106554790	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGTAGGTCTG	CTGTAGGTCTG	-	novel	NA	P-0008956-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	46	165	0	ENST00000369096.4:c.1903-5_1908del		p.X635_splice	ENST00000369096	NM_001198.3	635		7/7	0.272135737029571	5	FACETS	1	0.909	1			1	CLONAL	1	TRUE	NA	0.272135737029571	5		165	427	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0008957-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	91	402	0	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	1	2	FACETS	0.854	0.758	0.956	0.854	0.758	0.956	CLONAL	1	TRUE	1	0.29	2		402	735	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350470	15350470	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs779348570	NA	P-0008957-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	58	209	0	ENST00000263377.2:c.3445C>T	p.Arg1149Trp	p.R1149W	ENST00000263377	NM_058243.2	1149	Cgg/Tgg	16/20	0.295421405329858	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.29	1		209	273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520008	NA	P-0008957-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	332	466	0	ENST00000269305.4:c.613T>C	p.Tyr205His	p.Y205H	ENST00000269305	NM_001126112.2	205	Tat/Cat	6/11	0.294645319327048	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.29	2		466	1020	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162735826	162735826	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008957-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	132	491	0	ENST00000367921.3:c.1135A>T	p.Thr379Ser	p.T379S	ENST00000367921	NM_006182.2	379	Acc/Tcc	10/18	1	2	FACETS	0.997	0.905	1	0.997	0.905	1	CLONAL	1	TRUE	1	0.29	2		491	913	SUCCESS
BLM	641	MSKCC	GRCh37	15	91341566	91341566	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008957-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	168	340	2	ENST00000355112.3:c.3357G>T	p.Leu1119Phe	p.L1119F	ENST00000355112	NM_000057.2	1119	ttG/ttT	17/22	0.294645319327048	2	FACETS	0.798	0.735	0.863	0.798	0.735	0.863	SUBCLONAL	2	TRUE	0	0.29	2		342	726	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934946	9934946	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008957-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	70	298	0	ENST00000330684.3:c.1344G>T	p.Glu448Asp	p.E448D	ENST00000330684	NM_001134407.1	448	gaG/gaT	6/13	1	2	FACETS	0.96	0.839	1	0.96	0.839	1	CLONAL	1	TRUE	1	0.29	2		298	503	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805642	46805642	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008957-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	181	605	0	ENST00000290295.7:c.314C>A	p.Thr105Asn	p.T105N	ENST00000290295	NM_006361.5	105	aCc/aAc	1/2	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.29	2		605	1036	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219384	1219384	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0008957-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	133	385	0	ENST00000326873.7:c.436A>T	p.Lys146Ter	p.K146*	ENST00000326873	NM_000455.4	146	Aag/Tag	3/10	0.295421405329858	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.29	1		385	622	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717661	89717684	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	CAGGACCCACACGACGGGAAGACA	CAGGACCCACACGACGGGAAGACA	-	novel	NA	P-0008957-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	46	313	0	ENST00000371953.3:c.686_709del	p.Ser229_Lys237delinsTer	p.S229_K237delins*	ENST00000371953	NM_000314.4	229	tCAGGACCCACACGACGGGAAGACAag/tag	7/9	0.262046254159057	2	FACETS	0.61	0.514	0.717	0.305	0.257	0.359	SUBCLONAL	1	TRUE	0	0.29	2		313	520	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39613900	39613901	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0008957-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	90	457	0	ENST00000262039.4:c.1818_1819delinsTT	p.Glu607Ter	p.E607*	ENST00000262039	NM_002647.2	606	ccGGaa/ccTTaa	16/25	1	2	FACETS	0.728	0.645	0.817	0.728	0.645	0.817	SUBCLONAL	1	TRUE	1	0.29	2		457	853	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0008999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	553	399	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.63981379179514	2	FACETS	0.947	0.916	0.977	0.947	0.916	0.977	CLONAL	2	TRUE	0	0.63981379179514	2		400	913	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	157	246	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.63981379179514	2		246	400	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149450022	149450022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	188	284	0	ENST00000286301.3:c.1195C>T	p.Arg399Ter	p.R399*	ENST00000286301	NM_005211.3	399	Cga/Tga	8/22	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.63981379179514	2		284	573	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99185086	99185086	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	357	529	0	ENST00000074304.5:c.2488T>G	p.Leu830Val	p.L830V	ENST00000074304	NM_001134224.1	830	Tta/Gta	23/26	1	2	FACETS	0.979	0.928	1	0.979	0.928	1	CLONAL	1	TRUE	1	0.63981379179514	2		529	1140	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795129	242795129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	171	244	0	ENST00000334409.5:c.80C>T	p.Ser27Phe	p.S27F	ENST00000334409	NM_005018.2	27	tCc/tTc	2/5	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.63981379179514	2		244	512	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52649448	52649448	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	263	356	0	ENST00000394830.3:c.1843G>A	p.Glu615Lys	p.E615K	ENST00000394830	NM_018313.4	615	Gag/Aag	16/30	1	2	FACETS	0.986	0.927	1	0.986	0.927	1	CLONAL	1	TRUE	1	0.63981379179514	2		356	834	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435903	110435903	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	70	80	0	ENST00000375856.3:c.2498T>C	p.Ile833Thr	p.I833T	ENST00000375856	NM_003749.2	833	aTc/aCc	1/2	1	2	FACETS	0.986	0.873	1	0.986	0.873	1	CLONAL	1	TRUE	1	0.63981379179514	2		80	222	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610125	81610125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757875222	NA	P-0008999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	236	407	1	ENST00000298171.2:c.1723G>A	p.Glu575Lys	p.E575K	ENST00000298171	NM_000369.2	575	Gag/Aag	10/10	1	2	FACETS	0.853	0.797	0.91	0.853	0.797	0.91	CLONAL	1	TRUE	1	0.63981379179514	2		408	865	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126502	2126502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	327	441	0	ENST00000219476.3:c.2753C>T	p.Ser918Phe	p.S918F	ENST00000219476	NM_000548.3	918	tCc/tTc	25/42	1	2	FACETS	0.971	0.918	1	0.971	0.918	1	CLONAL	1	TRUE	1	0.63981379179514	2		441	1053	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47700145	47700145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752686914	NA	P-0008999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	565	335	0	ENST00000347630.2:c.28C>T	p.Pro10Ser	p.P10S	ENST00000347630	NM_001007230.1	10	Ccg/Tcg	3/11	0.330026392955636	3	FACETS	1	0.991	1	0.717	0.692	0.742	INDETERMINATE	2	TRUE	0	0.63981379179514	3		335	1084	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748895	41748895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138883984	NA	P-0008999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	352	507	0	ENST00000301178.4:c.1420C>T	p.Arg474Trp	p.R474W	ENST00000301178	NM_021913.4	474	Cgg/Tgg	11/20	1	2	FACETS	0.999	0.948	1	0.999	0.948	1	CLONAL	1	TRUE	1	0.63981379179514	2		507	1101	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828014	3828015	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0008999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	186	375	0	ENST00000262367.5:c.2110_2111delinsTT	p.Pro704Leu	p.P704L	ENST00000262367	NM_004380.2	704	CCa/TTa	10/31	1	2	FACETS	0.755	0.699	0.813	0.755	0.699	0.813	SUBCLONAL	1	TRUE	1	0.63981379179514	2		375	770	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0009011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	100	362	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.472786622406877	1	FACETS	0.705	0.636	0.778	0.705	0.636	0.778	SUBCLONAL	1	TRUE	0	0.557325777282701	1		362	367	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs864622237	NA	P-0009011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	103	328	0	ENST00000269305.4:c.700T>A	p.Tyr234Asn	p.Y234N	ENST00000269305	NM_001126112.2	234	Tac/Aac	7/11	0.477651903037849	1	FACETS	0.942	0.856	1	0.942	0.856	1	CLONAL	1	TRUE	0	0.557325777282701	1		328	283	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951923	178951923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	92	348	0	ENST00000263967.3:c.2978A>G	p.Gln993Arg	p.Q993R	ENST00000263967	NM_006218.2	993	cAg/cGg	21/21	0.477651903037849	1	FACETS	0.842	0.758	0.928	0.842	0.758	0.928	CLONAL	1	TRUE	0	0.557325777282701	1		348	283	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978402	2978402	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	91	404	0	ENST00000396946.4:c.928A>C	p.Lys310Gln	p.K310Q	ENST00000396946	NM_032415.4	310	Aag/Cag	7/25	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.557325777282701	2		404	297	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450657	70450657	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	105	443	0	ENST00000373644.4:c.5497C>G	p.Leu1833Val	p.L1833V	ENST00000373644	NM_030625.2	1833	Ctg/Gtg	12/12	1	2	FACETS	0.864	0.779	0.953	0.864	0.779	0.953	CLONAL	1	TRUE	1	0.557325777282701	2		443	436	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041046	29041046	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	84	317	0	ENST00000282397.4:c.382A>T	p.Ile128Phe	p.I128F	ENST00000282397	NM_002019.4	128	Att/Ttt	3/30	1	2	FACETS	0.928	0.827	1	0.928	0.827	1	CLONAL	1	TRUE	1	0.557325777282701	2		317	325	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81960695	81960695	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	119	528	0	ENST00000359376.3:c.2426G>C	p.Gly809Ala	p.G809A	ENST00000359376	NM_002661.3	809	gGa/gCa	23/33	0.557325777282701	1	FACETS	0.868	0.792	0.946	0.868	0.792	0.946	CLONAL	1	TRUE	0	0.557325777282701	1		528	355	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0009020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	100	484	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.146731661149814	1	FACETS	0.759	0.679	0.843	1	0.982	1	SUBCLONAL	2	TRUE	0	0.204410232508103	1		484	579	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469592	25469592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	66	482	0	ENST00000264709.3:c.1176G>T	p.Glu392Asp	p.E392D	ENST00000264709	NM_175629.2	392	gaG/gaT	10/23	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.204410232508103	2		482	487	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968200	134968200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143309901	NA	P-0009020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	57	455	2	ENST00000398015.3:c.2713C>T	p.Arg905Cys	p.R905C	ENST00000398015	NM_004441.4	905	Cgc/Tgc	15/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.204410232508103	2		457	422	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575430	67575430	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	47	319	0	ENST00000274335.5:c.503A>G	p.Asp168Gly	p.D168G	ENST00000274335		168	gAt/gGt	4/15	0.204410232508103	5	FACETS	1	0.922	1			1	CLONAL	1	TRUE	NA	0.204410232508103	5		319	519	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497286	149497286	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	23	435	0	ENST00000261799.4:c.3032C>A	p.Ala1011Asp	p.A1011D	ENST00000261799	NM_002609.3	1011	gCc/gAc	22/23	1	2	FACETS	0.507	0.394	0.638	0.507	0.394	0.638	SUBCLONAL	1	TRUE	1	0.204410232508103	2		435	444	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500798	149500798	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	34	474	1	ENST00000261799.4:c.2432C>A	p.Ala811Asp	p.A811D	ENST00000261799	NM_002609.3	811	gCc/gAc	17/23	1	2	FACETS	0.748	0.611	0.902	0.748	0.611	0.902	CLONAL	1	TRUE	1	0.204410232508103	2		475	445	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245495	46245495	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	31	247	1	ENST00000334344.6:c.3589G>T	p.Ala1197Ser	p.A1197S	ENST00000334344	NM_152641.2	1197	Gct/Tct	15/21	0.146731661149814	1	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	0	0.204410232508103	1		248	258	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993483	72993483	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	36	647	0	ENST00000268489.5:c.562G>T	p.Ala188Ser	p.A188S	ENST00000268489	NM_006885.3	188	Gca/Tca	2/10	0.204410232508103	0	FACETS	0.575	0.473	0.691			1	SUBCLONAL	1	TRUE	0	0.204410232508103	0		647	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577563	7577563	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1567549584	NA	P-0009020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	51	359	0	ENST00000269305.4:c.718A>G	p.Ser240Gly	p.S240G	ENST00000269305	NM_001126112.2	240	Agt/Ggt	7/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.204410232508103	2		359	392	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533361	29533361	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	28	311	0	ENST00000356175.3:c.1364G>T	p.Gly455Val	p.G455V	ENST00000356175	NM_000267.3	455	gGa/gTa	12/57	1	2	FACETS	0.87	0.696	1	0.87	0.696	1	CLONAL	1	TRUE	1	0.204410232508103	2		311	315	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756815	756815	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	35	406	2	ENST00000314574.4:c.13A>G	p.Lys5Glu	p.K5E	ENST00000314574	NM_005433.3	5	Aaa/Gaa	2/12	1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	1	0.204410232508103	2		408	341	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220326	5220326	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	18	422	0	ENST00000357368.4:c.3494G>T	p.Arg1165Leu	p.R1165L	ENST00000357368	NM_002850.3	1165	cGt/cTt	21/38	0.204410232508103	0	FACETS	0.497	0.374	0.642			1	SUBCLONAL	1	TRUE	0	0.204410232508103	0		422	282	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518136	187518145	+	frameshift_variant	Frame_Shift_Del	DEL	AACGATTCCA	AACGATTCCA	-	novel	NA	P-0009020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	43	499	0	ENST00000441802.2:c.12549_12558del	p.Ile4183MetfsTer20	p.I4183Mfs*20	ENST00000441802	NM_005245.3	4183	atTGGAATCGTT/at	25/27	1	2	FACETS	0.867	0.726	1	0.867	0.726	1	CLONAL	1	TRUE	1	0.204410232508103	2		499	485	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670307	134670307	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009024-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	52	434	2	ENST00000398015.3:c.218T>C	p.Leu73Pro	p.L73P	ENST00000398015	NM_004441.4	73	cTc/cCc	3/16	1	2	FACETS	0.155	0.131	0.181	0.155	0.131	0.181	SUBCLONAL	1	TRUE	1	0.71572794887511	2		436	937	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0009046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	352	411	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	0.69847176631526	2		411	866	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839769	42839769	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	302	437	0	ENST00000398585.3:c.1470G>C	p.Trp490Cys	p.W490C	ENST00000398585	NM_001135099.1	490	tgG/tgC	13/14	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.69847176631526	2		437	829	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888862	76888862	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0009046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	480	256	1	ENST00000373344.5:c.4967T>G	p.Leu1656Ter	p.L1656*	ENST00000373344	NM_000489.3	1656	tTa/tGa	19/35	1	1	FACETS		NA	1	1	0.998	1	NA	2	TRUE	0	0.69847176631526	1		257	572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578377	7578377	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	374	211	0	ENST00000269305.4:c.553del	p.Ser185AlafsTer62	p.S185Afs*62	ENST00000269305	NM_001126112.2	185	Agc/gc	5/11	0.69847176631526	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.69847176631526	2		211	435	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	153	291	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.233795952796953	3	FACETS	1	0.986	1	0.696	0.637	0.757	CLONAL	1	TRUE	1	0.321093755046399	3		291	795	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0009062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	456	932	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.198062407484864	4	FACETS	1	0.981	1	0.784	0.749	0.818	CLONAL	3	TRUE	0	0.321093755046399	4		934	1197	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604787	48604787	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519741	NA	P-0009062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	184	347	0	ENST00000342988.3:c.1609G>T	p.Asp537Tyr	p.D537Y	ENST00000342988	NM_005359.5	537	Gac/Tac	12/12	0.189562262126087	2	FACETS	0.805	0.745	0.866	0.805	0.745	0.866	INDETERMINATE	2	TRUE	0	0.321093755046399	2		347	712	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0009062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	107	293	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	0.321093755046399	2	FACETS	0.944	0.855	1	0.944	0.855	1	CLONAL	2	TRUE	0	0.321093755046399	2		293	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0009080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	380	331	1	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.739476765808842	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.739476765808842	1		332	571	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55963919	55963919	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs41469552	NA	P-0009080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	372	323	2	ENST00000263923.4:c.2524C>A	p.Arg842Ser	p.R842S	ENST00000263923	NM_002253.2	842	Cgt/Agt	18/30	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.739476765808842	2		325	995	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509894	187509894	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1056427147	NA	P-0009080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	261	286	0	ENST00000441802.2:c.13619A>G	p.Tyr4540Cys	p.Y4540C	ENST00000441802	NM_005245.3	4540	tAc/tGc	27/27	1	2	FACETS	0.954	0.898	1	0.954	0.898	1	CLONAL	1	TRUE	1	0.739476765808842	2		286	740	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654769	29654769	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786203570	NA	P-0009080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	302	295	0	ENST00000356175.3:c.5458C>T	p.Gln1820Ter	p.Q1820*	ENST00000356175	NM_000267.3	1820	Caa/Taa	37/57	0.739476765808842	1	FACETS	0.994	0.95	1	0.994	0.95	1	CLONAL	1	TRUE	0	0.739476765808842	1		295	518	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41525924	41525924	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	962	402	0	ENST00000263253.7:c.1199T>G	p.Ile400Ser	p.I400S	ENST00000263253	NM_001429.3	400	aTt/aGt	5/31	0.506171048048928	4	FACETS	0.909	0.886	0.932	0.909	0.886	0.932	CLONAL	3	TRUE	1	0.739476765808842	4		402	1660	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059229	47059237	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTGCAGGC	TCTGCAGGC	-	novel	NA	P-0009080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	262	186	0	ENST00000409792.3:c.7432-8_7432del		p.X2478_splice	ENST00000409792	NM_014159.6	2478		20/21	0.679501026967399	2	FACETS	0.769	0.731	0.806	0.769	0.731	0.806	SUBCLONAL	2	TRUE	0	0.739476765808842	2		186	461	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0009096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	181	343	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.129061624839641	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	1	0.16256478248133	3		343	1151	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045030	47045030	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0009096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	154	161	0	ENST00000377604.3:c.2355+1G>A		p.X785_splice	ENST00000377604	NM_001204468.1	785			0.12272615377309	2	FACETS	1	0.95	1			1	CLONAL	3	TRUE	NA	0.16256478248133	2		161	604	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0009100-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	231	799	0	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	0.457402064530262	1	FACETS	0.497	0.463	0.532	0.497	0.463	0.532	SUBCLONAL	1	FALSE	0	0.617173071008012	1		799	1042	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121912580	NA	P-0009100-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	143	370	1	ENST00000342988.3:c.1157G>T	p.Gly386Val	p.G386V	ENST00000342988	NM_005359.5	386	gGt/gTt	10/12	0.445438885341812	3	FACETS	0.864	0.789	0.942			1	CLONAL	1	FALSE	NA	0.617173071008012	3		371	702	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577529	7577529	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs730882027	NA	P-0009100-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	69	315	0	ENST00000269305.4:c.752T>A	p.Ile251Asn	p.I251N	ENST00000269305	NM_001126112.2	251	aTc/aAc	7/11	0.604676541453616	5	FACETS	0.346	0.3	0.396			1	SUBCLONAL	1	FALSE	NA	0.617173071008012	5		315	1244	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0009114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	79	749	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.268583300579311	1	FACETS	0.903	0.795	1	0.903	0.795	1	CLONAL	1	TRUE	0	0.268583300579311	1		750	564	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396746	139396746	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	39	139	0	ENST00000277541.6:c.5362G>A	p.Gly1788Ser	p.G1788S	ENST00000277541	NM_017617.3	1788	Ggc/Agc	28/34	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.268583300579311	2		139	214	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944243	81944243	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759496244	NA	P-0009114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	88	443	0	ENST00000359376.3:c.1852C>T	p.Arg618Cys	p.R618C	ENST00000359376	NM_002661.3	618	Cgc/Tgc	18/33	0.268583300579311	1	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	0	0.268583300579311	1		443	564	SUCCESS
APC	324	MSKCC	GRCh37	5	112175351	112175364	+	frameshift_variant	Frame_Shift_Del	DEL	TTTTCTTCAGGAGC	TTTTCTTCAGGAGC	-	novel	NA	P-0009114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	43	168	0	ENST00000257430.4:c.4060_4073del	p.Phe1354GlufsTer16	p.F1354Efs*16	ENST00000257430	NM_000038.5	1354	TTTTCTTCAGGAGCg/g	16/16	1	2	FACETS	0.936	0.786	1	0.936	0.786	1	CLONAL	1	TRUE	1	0.268583300579311	2		168	342	SUCCESS
APC	324	MSKCC	GRCh37	5	112170677	112170679	+	stop_gained	Nonsense_Mutation	TNP	CTT	CTT	ATA	novel	NA	P-0009114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	57	282	0	ENST00000257430.4:c.1773_1775delinsATA	p.Leu592Ter	p.L592*	ENST00000257430	NM_000038.5	591	gcCTTa/gcATAa	15/16	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.268583300579311	2		282	424	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0009143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	381	353	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.644399224740204	3	FACETS	0.967	0.934	0.998	1	0.997	1	CLONAL	3	TRUE	1	0.644399224740204	3		353	539	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578189	7578189	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0009143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	868	523	0	ENST00000269305.4:c.660T>G	p.Tyr220Ter	p.Y220*	ENST00000269305	NM_001126112.2	220	taT/taG	6/11	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	2	TRUE	NA	0.644399224740204	2		523	1335	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0009143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1279	798	918	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.632793610568627	4	FACETS	0.98	0.948	1	0.98	0.948	1	CLONAL	2	TRUE	2	0.644399224740204	4		918	2077	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023622	27023622	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	727	346	1	ENST00000324856.7:c.728C>G	p.Ala243Gly	p.A243G	ENST00000324856	NM_006015.4	243	gCg/gGg	1/20	0.644399224740204	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	1	0.644399224740204	4		347	1159	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057705	27057705	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	1582	735	2	ENST00000324856.7:c.1413C>A	p.Tyr471Ter	p.Y471*	ENST00000324856	NM_006015.4	471	taC/taA	3/20	0.644399224740204	4	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	1	0.644399224740204	4		737	2588	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519815	29519815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs75158395	NA	P-0009143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1384	363	450	0	ENST00000389048.3:c.1756G>A	p.Ala586Thr	p.A586T	ENST00000389048	NM_004304.4	586	Gcc/Acc	9/29	0.644399224740204	4	FACETS	1	0.977	1	0.353	0.334	0.374	CLONAL	1	TRUE	1	0.644399224740204	4		450	1747	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176715876	176715876	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2149	832	620	0	ENST00000439151.2:c.6208T>G	p.Cys2070Gly	p.C2070G	ENST00000439151	NM_022455.4	2070	Tgc/Ggc	21/23	0.644399224740204	6	FACETS	0.991	0.957	1			1	CLONAL	2	TRUE	NA	0.644399224740204	6		620	2981	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239436	123239436	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	679	468	0	ENST00000358487.5:c.2401G>T	p.Asp801Tyr	p.D801Y	ENST00000358487	NM_000141.4	801	Gac/Tac	18/18	0.644399224740204	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.644399224740204	3		468	1386	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447416	49447416	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs201994402	NA	P-0009143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	380	323	0	ENST00000301067.7:c.682C>G	p.Arg228Gly	p.R228G	ENST00000301067	NM_003482.3	228	Cgc/Ggc	6/54	0.255230627074313	3	FACETS	0.816	0.778	0.855			1	INDETERMINATE	2	TRUE	NA	0.644399224740204	3		323	955	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72863715	72863715	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	954	736	0	ENST00000268489.5:c.3492del	p.Asp1165IlefsTer22	p.D1165Ifs*22	ENST00000268489	NM_006885.3	1164	gcT/gc	5/10	0.644399224740204	2	FACETS	0.964	0.941	0.987	0.964	0.941	0.987	CLONAL	2	TRUE	0	0.644399224740204	2		736	1535	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0009151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	35	370	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	0.193642975170881	3	FACETS	1	0.834	1	0.507	0.417	0.607	CLONAL	1	TRUE	1	0.26	3		370	300	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0009151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	47	531	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	0.193642975170881	3	FACETS	1	0.913	1	0.56	0.474	0.654	CLONAL	1	TRUE	1	0.26	3		531	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0009158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	242	352	1	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.410613069235082	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.410613069235082	1		353	890	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948121	55948121	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0009158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	199	411	0	ENST00000263923.4:c.3848+2T>G		p.X1283_splice	ENST00000263923	NM_002253.2	1283			1	2	FACETS	0.985	0.912	1	0.985	0.912	1	CLONAL	1	TRUE	1	0.410613069235082	2		411	984	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945089	151945089	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	22	128	0	ENST00000262189.6:c.2430C>A	p.Asn810Lys	p.N810K	ENST00000262189	NM_170606.2	810	aaC/aaA	14/59	1	2	FACETS	0.425	0.33	0.535	0.425	0.33	0.535	SUBCLONAL	1	TRUE	1	0.410613069235082	2		128	252	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421894	49421894	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	260	375	0	ENST00000301067.7:c.14413G>T	p.Glu4805Ter	p.E4805*	ENST00000301067	NM_003482.3	4805	Gag/Tag	46/54	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.410613069235082	2		375	1100	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915170	32915170	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	349	874	1	ENST00000380152.3:c.6678A>T	p.Glu2226Asp	p.E2226D	ENST00000380152		2226	gaA/gaT	11/27	0.410613069235082	1	FACETS	0.923	0.873	0.975	0.923	0.873	0.975	CLONAL	1	TRUE	0	0.410613069235082	1		875	1463	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984783	11984783	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	137	280	0	ENST00000353533.5:c.329G>T	p.Arg110Leu	p.R110L	ENST00000353533	NM_003010.3	110	cGa/cTa	3/11	0.410613069235082	1	FACETS	0.859	0.784	0.938	0.859	0.784	0.938	CLONAL	1	TRUE	0	0.410613069235082	1		280	617	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168992	11168992	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	285	455	2	ENST00000358026.2:c.4582G>T	p.Glu1528Ter	p.E1528*	ENST00000358026	NM_001128849.1	1528	Gag/Tag	32/36	0.410613069235082	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.410613069235082	1		457	991	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520225	9520225	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	231	448	0	ENST00000353224.5:c.2044G>T	p.Val682Leu	p.V682L	ENST00000353224	NM_177990.2	682	Gtg/Ttg	10/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.410613069235082	2		448	1080	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747141	40747141	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0009158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	181	388	0	ENST00000373198.4:c.2942-1G>T		p.X981_splice	ENST00000373198	NM_133170.3	981			1	2	FACETS	0.95	0.876	1	0.95	0.876	1	CLONAL	1	TRUE	1	0.410613069235082	2		388	928	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411017	63411017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751217981	NA	P-0009158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	262	316	1	ENST00000330258.3:c.2150G>A	p.Cys717Tyr	p.C717Y	ENST00000330258	NM_152424.3	717	tGc/tAc	2/2	1	1	FACETS	0.764	0.72	0.808	1	0.994	1	SUBCLONAL	2	TRUE	0	0.410613069235082	1		317	664	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220498	123220498	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	354	382	0	ENST00000218089.9:c.3155G>T	p.Gly1052Val	p.G1052V	ENST00000218089	NM_001042749.1	1052	gGt/gTt	30/35	1	1	FACETS	0.815	0.776	0.854	1	0.996	1	CLONAL	2	TRUE	0	0.410613069235082	1		382	841	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0009161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	319	286	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.240945386014194	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	3	TRUE	0	0.240945386014194	3		287	982	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0009161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	60	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.209540819632082	3	FACETS	1	0.882	1	0.342	0.294	0.394	CLONAL	1	TRUE	0	0.240945386014194	3		249	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0009161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	112	562	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.240945386014194	1	FACETS	0.947	0.852	1	0.947	0.852	1	CLONAL	1	TRUE	0	0.240945386014194	1		562	863	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577599	7577599	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	52	309	0	ENST00000269305.4:c.682G>C	p.Asp228His	p.D228H	ENST00000269305	NM_001126112.2	228	Gac/Cac	7/11	0.240945386014194	1	FACETS	0.793	0.675	0.921	0.793	0.675	0.921	CLONAL	1	TRUE	0	0.240945386014194	1		309	479	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263941	104263941	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1227379293	NA	P-0009161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	17	124	0	ENST00000369902.3:c.32G>A	p.Gly11Asp	p.G11D	ENST00000369902	NM_016169.3	11	gGc/gAc	1/12	1	2	FACETS	0.53	0.396	0.69	0.53	0.396	0.69	SUBCLONAL	1	TRUE	1	0.240945386014194	2		124	266	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584497	48584497	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	93	213	0	ENST00000342988.3:c.670C>T	p.Gln224Ter	p.Q224*	ENST00000342988	NM_005359.5	224	Cag/Tag	6/12	0.240945386014194	1	FACETS	0.751	0.671	0.835	1	0.981	1	SUBCLONAL	2	TRUE	0	0.240945386014194	1		213	452	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445400	29445400	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	96	485	1	ENST00000389048.3:c.3433C>A	p.Leu1145Met	p.L1145M	ENST00000389048	NM_004304.4	1145	Ctg/Atg	21/29	1	2	FACETS	0.971	0.864	1	0.971	0.864	1	CLONAL	1	TRUE	1	0.240945386014194	2		486	821	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61722634	61722634	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	145	420	0	ENST00000401558.2:c.1003C>G	p.Gln335Glu	p.Q335E	ENST00000401558	NM_003400.3	335	Caa/Gaa	11/25	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.240945386014194	2		420	886	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579545	7579545	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	77	359	0	ENST00000269305.4:c.142G>C	p.Asp48His	p.D48H	ENST00000269305	NM_001126112.2	48	Gac/Cac	4/11	0.240945386014194	1	FACETS	0.953	0.837	1	0.953	0.837	1	CLONAL	1	TRUE	0	0.240945386014194	1		359	590	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534390	63534390	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	118	398	0	ENST00000307078.5:c.1131G>C	p.Arg377Ser	p.R377S	ENST00000307078	NM_004655.3	377	agG/agC	5/11	0.240945386014194	3	FACETS	1	0.975	1	0.624	0.563	0.69	CLONAL	1	TRUE	1	0.240945386014194	3		398	879	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500764	8500765	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0009161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	142	295	0	ENST00000356435.5:c.2117_2118delinsAA	p.Thr706Lys	p.T706K	ENST00000356435		706	aCC/aAA	13/35	0.209540819632082	3	FACETS	1	0.965	1	0.736	0.673	0.801	CLONAL	2	TRUE	0	0.240945386014194	3		295	598	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0009196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	18	305	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.573	0.43	0.742	0.573	0.43	0.742	SUBCLONAL	1	TRUE	1	0.15	2		305	419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0009196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	46	267	0	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	1	2	FACETS	0.851	0.715	1	0.851	0.715	1	CLONAL	1	TRUE	1	0.15	2		267	721	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220717	1220717	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587782018	NA	P-0009196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	48	216	1	ENST00000326873.7:c.734+1G>T		p.X245_splice	ENST00000326873	NM_000455.4	245			1	2	FACETS	1	0.844	1	1	0.844	1	CLONAL	1	TRUE	1	0.15	2		217	640	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267367	198267367	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	45	331	1	ENST00000335508.6:c.1990G>T	p.Gly664Cys	p.G664C	ENST00000335508	NM_012433.2	664	Ggt/Tgt	14/25	1	2	FACETS	0.778	0.652	0.918	0.778	0.652	0.918	CLONAL	1	TRUE	1	0.15	2		332	771	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643549	52643549	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	56	284	0	ENST00000394830.3:c.2347C>T	p.His783Tyr	p.H783Y	ENST00000394830	NM_018313.4	783	Cac/Tac	17/30	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.15	2		284	684	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851726	134851726	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	46	259	0	ENST00000398015.3:c.1132G>T	p.Glu378Ter	p.E378*	ENST00000398015	NM_004441.4	378	Gag/Tag	5/16	1	2	FACETS	0.963	0.81	1	0.963	0.81	1	CLONAL	1	TRUE	1	0.15	2		259	637	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55597504	55597504	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	35	319	2	ENST00000288135.5:c.2152A>T	p.Thr718Ser	p.T718S	ENST00000288135	NM_000222.2	718	Act/Tct	15/21	1	2	FACETS	0.682	0.558	0.823	0.682	0.558	0.823	SUBCLONAL	1	TRUE	1	0.15	2		321	684	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675196	30675196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs551577509	NA	P-0009196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	66	371	0	ENST00000376406.3:c.3049G>A	p.Ala1017Thr	p.A1017T	ENST00000376406	NM_014641.2	1017	Gct/Act	9/15	1	2	FACETS	0.918	0.794	1	0.918	0.794	1	CLONAL	1	TRUE	1	0.15	2		371	959	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126332	5126332	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0009196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	19	178	0	ENST00000381652.3:c.3178-1G>C		p.X1060_splice	ENST00000381652	NM_004972.3	1060			1	2	FACETS	0.911	0.692	1	0.911	0.692	1	CLONAL	1	TRUE	1	0.15	2		178	278	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597430	10597430	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	86	331	0	ENST00000171111.5:c.1773G>A	p.Trp591Ter	p.W591*	ENST00000171111	NM_203500.1	591	tgG/tgA	6/6	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.15	2		331	1007	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411212	63411212	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0009196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	56	379	1	ENST00000330258.3:c.1955T>A	p.Leu652Ter	p.L652*	ENST00000330258	NM_152424.3	652	tTa/tAa	2/2	0.118373231258137	0	FACETS	0.716	0.611	0.83			1	SUBCLONAL	1	TRUE	0	0.15	0		380	887	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0009204-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	495	404	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.783356707548589	2	FACETS	0.957	0.931	0.983	0.957	0.931	0.983	CLONAL	2	TRUE	0	0.783356707548589	2		405	660	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	77	207	0				ENST00000310581	NM_198253.2	-/1132			0.250137528954127	3	FACETS	1	0.943	1			1	CLONAL	1	TRUE	NA	0.250137528954127	3		207	614	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	190	418	0	ENST00000304494.5:c.143C>T	p.Pro48Leu	p.P48L	ENST00000304494	NM_000077.4	48	cCg/cTg	1/3	0.250137528954127	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.250137528954127	1		418	1027	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36824418	36824418	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	61	348	0	ENST00000373129.3:c.118C>G	p.Arg40Gly	p.R40G	ENST00000373129	NM_032017.1	40	Cgt/Ggt	4/12	1	2	FACETS	0.486	0.418	0.561	0.486	0.418	0.561	SUBCLONAL	1	TRUE	1	0.250137528954127	2		348	1003	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941125	36941125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375879178	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	165	599	1	ENST00000361632.4:c.214G>A	p.Gly72Arg	p.G72R	ENST00000361632		72	Ggg/Agg	3/16	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.250137528954127	2		600	1307	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754791	29754791	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	97	351	0	ENST00000389048.3:c.1144G>A	p.Gly382Arg	p.G382R	ENST00000389048	NM_004304.4	382	Ggg/Agg	4/29	1	2	FACETS	0.876	0.78	0.979	0.876	0.78	0.979	CLONAL	1	TRUE	1	0.250137528954127	2		351	885	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99162507	99162507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780563566	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	125	400	0	ENST00000074304.5:c.1025G>A	p.Arg342Lys	p.R342K	ENST00000074304	NM_001134224.1	342	aGg/aAg	12/26	1	2	FACETS	0.948	0.857	1	0.948	0.857	1	CLONAL	1	TRUE	1	0.250137528954127	2		400	1054	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578332	212578332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	91	358	0	ENST00000342788.4:c.925C>T	p.Pro309Ser	p.P309S	ENST00000342788	NM_005235.2	309	Cct/Tct	8/28	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.250137528954127	2		358	686	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440145	220440145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	168	567	1	ENST00000243786.2:c.998G>A	p.Gly333Glu	p.G333E	ENST00000243786	NM_002191.3	333	gGg/gAg	2/2	1	2	FACETS	0.99	0.907	1	0.99	0.907	1	CLONAL	1	TRUE	1	0.250137528954127	2		568	1357	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732969	30732969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893810	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	108	287	0	ENST00000295754.5:c.1582C>T	p.Arg528Cys	p.R528C	ENST00000295754	NM_003242.5	528	Cgt/Tgt	7/7	0.240929711746849	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.250137528954127	1		287	706	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807357	1807357	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	133	439	0	ENST00000260795.2:c.1606A>G	p.Lys536Glu	p.K536E	ENST00000260795		536	Aaa/Gaa	11/17	1	2	FACETS	0.943	0.854	1	0.943	0.854	1	CLONAL	1	TRUE	1	0.250137528954127	2		439	1128	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156475	106156475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	150	439	1	ENST00000380013.4:c.1376C>T	p.Pro459Leu	p.P459L	ENST00000380013	NM_001127208.2	459	cCt/cTt	3/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.250137528954127	2		440	1141	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196303	106196303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1238625315	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	50	378	1	ENST00000380013.4:c.4636C>T	p.Gln1546Ter	p.Q1546*	ENST00000380013	NM_001127208.2	1546	Cag/Tag	11/11	1	2	FACETS	0.426	0.36	0.499	0.426	0.36	0.499	SUBCLONAL	1	TRUE	1	0.250137528954127	2		379	938	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279500	1279500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	243	412	0	ENST00000310581.5:c.2036C>T	p.Ser679Phe	p.S679F	ENST00000310581	NM_198253.2	679	tCt/tTt	5/16	0.250137528954127	3	FACETS	1	0.969	1			1	CLONAL	2	TRUE	NA	0.250137528954127	3		412	1030	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751556	57751556	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	65	364	1	ENST00000274289.3:c.1435C>A	p.Leu479Ile	p.L479I	ENST00000274289	NM_006622.3	479	Ctt/Att	11/14	1	2	FACETS	0.569	0.492	0.653	0.569	0.492	0.653	SUBCLONAL	1	TRUE	1	0.250137528954127	2		365	914	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287216	33287217	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	49	406	1	ENST00000374542.5:c.1880_1881delinsTT	p.Pro627Leu	p.P627L	ENST00000374542	NM_001141970.1	627	cCC/cTT	6/8	0.240929711746849	1	FACETS	0.39	0.329	0.457	0.39	0.329	0.457	SUBCLONAL	1	TRUE	0	0.250137528954127	1		407	880	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287309	33287310	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	110	388	0	ENST00000374542.5:c.1787_1788delinsTT	p.Pro596Leu	p.P596L	ENST00000374542	NM_001141970.1	596	cCC/cTT	6/8	0.240929711746849	1	FACETS	0.82	0.736	0.91	0.82	0.736	0.91	CLONAL	1	TRUE	0	0.250137528954127	1		388	938	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622266	117622266	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	127	475	0	ENST00000368508.3:c.6604C>T	p.Pro2202Ser	p.P2202S	ENST00000368508	NM_002944.2	2202	Ccc/Tcc	42/43	0.250137528954127	1	FACETS	0.884	0.8	0.973	0.884	0.8	0.973	CLONAL	1	TRUE	0	0.250137528954127	1		475	1005	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946092	13946092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	126	296	0	ENST00000405192.2:c.1004G>A	p.Gly335Asp	p.G335D	ENST00000405192	NM_001163147.1	335	gGt/gAt	10/12	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.250137528954127	2		296	924	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729949	41729949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1165688714	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1467	210	635	0	ENST00000242208.4:c.580G>A	p.Glu194Lys	p.E194K	ENST00000242208	NM_002192.2	194	Gaa/Aaa	3/3	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.250137528954127	2		635	1677	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55229300	55229300	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	125	477	0	ENST00000275493.2:c.1607T>A	p.Val536Glu	p.V536E	ENST00000275493	NM_005228.3	536	gTg/gAg	13/28	1	2	FACETS	0.856	0.773	0.945	0.856	0.773	0.945	CLONAL	1	TRUE	1	0.250137528954127	2		477	1167	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522569	106522569	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746783339	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	105	383	0	ENST00000359195.3:c.2546G>A	p.Arg849Gln	p.R849Q	ENST00000359195	NM_002649.2	849	cGa/cAa	7/11	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.250137528954127	2		383	834	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148529748	148529748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	61	326	0	ENST00000320356.2:c.341C>T	p.Ser114Phe	p.S114F	ENST00000320356	NM_004456.4	114	tCt/tTt	4/20	1	2	FACETS	0.607	0.522	0.699	0.607	0.522	0.699	SUBCLONAL	1	TRUE	1	0.250137528954127	2		326	804	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471012	8471012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	108	425	0	ENST00000356435.5:c.3487G>A	p.Glu1163Lys	p.E1163K	ENST00000356435		1163	Gaa/Aaa	20/35	0.250137528954127	1	FACETS	0.904	0.811	1	0.904	0.811	1	CLONAL	1	TRUE	0	0.250137528954127	1		425	836	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93629456	93629456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	57	365	0	ENST00000375746.1:c.890C>T	p.Ser297Phe	p.S297F	ENST00000375746	NM_001174167.1	297	tCc/tTc	7/14	0.19218368650234	2	FACETS	0.456	0.39	0.529	0.228	0.195	0.265	SUBCLONAL	1	TRUE	0	0.250137528954127	2		365	999	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97897654	97897654	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143181565	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	196	436	0	ENST00000289081.3:c.817G>A	p.Glu273Lys	p.E273K	ENST00000289081	NM_000136.2	273	Gaa/Aaa	8/15	0.19218368650234	2	FACETS	0.755	0.698	0.814	0.755	0.698	0.814	SUBCLONAL	2	TRUE	0	0.250137528954127	2		436	1038	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759415	133759416	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	225	558	1	ENST00000318560.5:c.1738_1739delinsTT	p.Pro580Leu	p.P580L	ENST00000318560	NM_005157.4	580	CCg/TTg	11/11	0.19218368650234	2	FACETS	1	0.99	1	0.709	0.659	0.761	CLONAL	1	TRUE	0	0.250137528954127	2		559	1269	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413088	139413088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	192	456	0	ENST00000277541.6:c.1054G>A	p.Asp352Asn	p.D352N	ENST00000277541	NM_017617.3	352	Gac/Aac	6/34	0.16438255788277	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.250137528954127	1		456	1047	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332628	70332628	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457729740	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	79	394	0	ENST00000373644.4:c.533C>T	p.Pro178Leu	p.P178L	ENST00000373644	NM_030625.2	178	cCc/cTc	2/12	1	2	FACETS	0.703	0.617	0.795	0.703	0.617	0.795	SUBCLONAL	1	TRUE	1	0.250137528954127	2		394	899	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575026	64575026	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs1057520733	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	80	243	0	ENST00000312049.6:c.781C>T	p.Gln261Ter	p.Q261*	ENST00000312049	NM_130799.2	261	Cag/Tag	4/10	1	2	FACETS	0.877	0.772	0.991	0.877	0.772	0.991	CLONAL	1	TRUE	1	0.250137528954127	2		243	729	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94169019	94169019	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	124	368	0	ENST00000323929.3:c.1973C>T	p.Thr658Ile	p.T658I	ENST00000323929	NM_005591.3	658	aCc/aTc	18/20	1	2	FACETS	0.864	0.78	0.954	0.864	0.78	0.954	CLONAL	1	TRUE	1	0.250137528954127	2		368	1147	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195555	102195556	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1487	193	683	3	ENST00000263464.3:c.315_316delinsAA	p.Glu106Lys	p.E106K	ENST00000263464	NM_001165.4	105	ttGGaa/ttAAaa	2/9	1	2	FACETS	0.919	0.846	0.994	0.919	0.846	0.994	CLONAL	1	TRUE	1	0.250137528954127	2		686	1680	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343451	118343451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	114	276	0	ENST00000534358.1:c.1577G>A	p.Arg526Lys	p.R526K	ENST00000534358	NM_005933.3	526	aGg/aAg	3/36	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.250137528954127	2		276	890	SUCCESS
CBL	867	MSKCC	GRCh37	11	119145638	119145638	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	138	387	0	ENST00000264033.4:c.844C>T	p.Gln282Ter	p.Q282*	ENST00000264033	NM_005188.3	282	Cag/Tag	5/16	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.250137528954127	2		387	1046	SUCCESS
CBL	867	MSKCC	GRCh37	11	119146837	119146837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	87	367	0	ENST00000264033.4:c.1000G>A	p.Glu334Lys	p.E334K	ENST00000264033	NM_005188.3	334	Gaa/Aaa	6/16	1	2	FACETS	0.77	0.681	0.867	0.77	0.681	0.867	SUBCLONAL	1	TRUE	1	0.250137528954127	2		367	903	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170253	119170253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763756632	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	116	361	1	ENST00000264033.4:c.2483C>T	p.Pro828Leu	p.P828L	ENST00000264033	NM_005188.3	828	cCg/cTg	16/16	1	2	FACETS	0.844	0.759	0.934	0.844	0.759	0.934	CLONAL	1	TRUE	1	0.250137528954127	2		362	1099	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170256	119170256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374672276	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	116	358	0	ENST00000264033.4:c.2486G>A	p.Arg829Gln	p.R829Q	ENST00000264033	NM_005188.3	829	cGg/cAg	16/16	1	2	FACETS	0.846	0.761	0.937	0.846	0.761	0.937	CLONAL	1	TRUE	1	0.250137528954127	2		358	1096	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425412	49425412	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	60	453	0	ENST00000301067.7:c.13076C>G	p.Ser4359Ter	p.S4359*	ENST00000301067	NM_003482.3	4359	tCa/tGa	39/54	1	2	FACETS	0.456	0.391	0.526	0.456	0.391	0.526	SUBCLONAL	1	TRUE	1	0.250137528954127	2		453	1053	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56474138	56474139	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	58	351	0	ENST00000267101.3:c.54_55delinsAA	p.Gly19Ser	p.G19S	ENST00000267101	NM_001982.3	18	cgGGgc/cgAAgc	1/28	1	2	FACETS	0.507	0.434	0.587	0.507	0.434	0.587	SUBCLONAL	1	TRUE	1	0.250137528954127	2		351	915	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233073	69233073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	51	325	1	ENST00000462284.1:c.938C>T	p.Ser313Leu	p.S313L	ENST00000462284	NM_002392.5	313	tCa/tTa	11/11	1	2	FACETS	0.574	0.486	0.67	0.574	0.486	0.67	SUBCLONAL	1	TRUE	1	0.250137528954127	2		326	711	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434481	110434481	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1482272496	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	54	265	0	ENST00000375856.3:c.3920G>A	p.Gly1307Glu	p.G1307E	ENST00000375856	NM_003749.2	1307	gGg/gAg	1/2	1	2	FACETS	0.626	0.533	0.727	0.626	0.533	0.727	SUBCLONAL	1	TRUE	1	0.250137528954127	2		265	690	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610644	81610644	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1265	74	493	0	ENST00000298171.2:c.2242A>G	p.Thr748Ala	p.T748A	ENST00000298171	NM_000369.2	748	Acc/Gcc	10/10	1	2	FACETS	0.442	0.385	0.504	0.442	0.385	0.504	SUBCLONAL	1	TRUE	1	0.250137528954127	2		493	1339	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772227	68772227	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	146	442	1	ENST00000261769.5:c.76G>A	p.Glu26Lys	p.E26K	ENST00000261769	NM_004360.3	26	Gag/Aag	2/16	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.250137528954127	2		443	1153	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81957181	81957182	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	117	477	0	ENST00000359376.3:c.2399_2400delinsTT	p.Ser800Phe	p.S800F	ENST00000359376	NM_002661.3	800	tCC/tTT	22/33	1	2	FACETS	0.787	0.708	0.872	0.787	0.708	0.872	SUBCLONAL	1	TRUE	1	0.250137528954127	2		477	1188	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341317	89341317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555523386	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	44	174	0	ENST00000301030.4:c.7618C>T	p.Arg2540Trp	p.R2540W	ENST00000301030	NM_001256183.1	2540	Cgg/Tgg	11/13	1	2	FACETS	0.928	0.78	1	0.928	0.78	1	CLONAL	1	TRUE	1	0.250137528954127	2		174	379	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805693	89805693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149775657	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	133	402	1	ENST00000389301.3:c.4015C>T	p.Leu1339Phe	p.L1339F	ENST00000389301	NM_000135.2	1339	Ctc/Ttc	41/43	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.250137528954127	2		403	1051	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578479	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	211	352	0	ENST00000269305.4:c.451_452delinsTT	p.Pro151Phe	p.P151F	ENST00000269305	NM_001126112.2	151	CCc/TTc	5/11	NA	2	FACETS	0.824	0.765	0.885			1	INDETERMINATE	2	TRUE	NA	0.250137528954127	2		352	1024	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110596	8110596	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465361269	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	143	372	0	ENST00000585124.1:c.296G>A	p.Ser99Asn	p.S99N	ENST00000585124	NM_004217.3	99	aGc/aAc	5/9	NA	2	FACETS	1	0.935	1			1	INDETERMINATE	1	TRUE	NA	0.250137528954127	2		372	1106	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325889	30325889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	112	485	0	ENST00000322652.5:c.2087C>T	p.Pro696Leu	p.P696L	ENST00000322652	NM_015355.2	696	cCt/cTt	16/16	1	2	FACETS	0.862	0.774	0.956	0.862	0.774	0.956	CLONAL	1	TRUE	1	0.250137528954127	2		485	1039	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805372	46805372	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1173	154	571	0	ENST00000290295.7:c.584G>A	p.Trp195Ter	p.W195*	ENST00000290295	NM_006361.5	195	tGg/tAg	1/2	1	2	FACETS	0.928	0.847	1	0.928	0.847	1	CLONAL	1	TRUE	1	0.250137528954127	2		571	1327	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117630	70117630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	126	384	3	ENST00000245479.2:c.98C>T	p.Ser33Leu	p.S33L	ENST00000245479	NM_000346.3	33	tCg/tTg	1/3	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.250137528954127	2		387	866	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857751	78857752	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	101	281	0	ENST00000306801.3:c.1821_1822delinsTT	p.Leu608Phe	p.L608F	ENST00000306801	NM_020761.2	607	ctCCtc/ctTTtc	16/34	1	2	FACETS	0.953	0.851	1	0.953	0.851	1	CLONAL	1	TRUE	1	0.250137528954127	2		281	847	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217876	2217876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	117	394	0	ENST00000398665.3:c.2650C>T	p.Pro884Ser	p.P884S	ENST00000398665	NM_032482.2	884	Ccc/Tcc	22/28	1	2	FACETS	0.956	0.86	1	0.956	0.86	1	CLONAL	1	TRUE	1	0.250137528954127	2		394	979	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208356	5208356	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1257575436	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	129	444	0	ENST00000357368.4:c.5534C>T	p.Pro1845Leu	p.P1845L	ENST00000357368	NM_002850.3	1845	cCg/cTg	36/38	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.250137528954127	2		444	1029	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117187	7117188	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	69	446	1	ENST00000302850.5:c.4028_4029delinsAA	p.Arg1343Gln	p.R1343Q	ENST00000302850	NM_000208.2	1343	cGG/cAA	22/22	1	2	FACETS	0.48	0.416	0.549	0.48	0.416	0.549	SUBCLONAL	1	TRUE	1	0.250137528954127	2		447	1149	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098365	11098365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs970190031	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	68	394	0	ENST00000358026.2:c.883C>T	p.Pro295Ser	p.P295S	ENST00000358026	NM_001128849.1	295	Ccc/Tcc	6/36	1	2	FACETS	0.534	0.463	0.611	0.534	0.463	0.611	SUBCLONAL	1	TRUE	1	0.250137528954127	2		394	1018	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291900	15291900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745954040	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	79	451	0	ENST00000263388.2:c.2866G>A	p.Gly956Arg	p.G956R	ENST00000263388	NM_000435.2	956	Gga/Aga	18/33	1	2	FACETS	0.643	0.564	0.728	0.643	0.564	0.728	SUBCLONAL	1	TRUE	1	0.250137528954127	2		451	983	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794481	42794481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	129	515	0	ENST00000575354.2:c.1561C>T	p.Pro521Ser	p.P521S	ENST00000575354	NM_015125.3	521	Cct/Tct	10/20	1	2	FACETS	0.817	0.739	0.9	0.817	0.739	0.9	CLONAL	1	TRUE	1	0.250137528954127	2		515	1262	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797380	42797380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746056115	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	60	395	0	ENST00000575354.2:c.3742C>T	p.Pro1248Ser	p.P1248S	ENST00000575354	NM_015125.3	1248	Cca/Tca	15/20	1	2	FACETS	0.534	0.458	0.616	0.534	0.458	0.616	SUBCLONAL	1	TRUE	1	0.250137528954127	2		395	899	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101129	41101130	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	67	280	1	ENST00000373198.4:c.1226_1227delinsTT	p.Pro409Leu	p.P409L	ENST00000373198	NM_133170.3	409	cCC/cTT	8/32	1	2	FACETS	0.76	0.66	0.869	0.76	0.66	0.869	SUBCLONAL	1	TRUE	1	0.250137528954127	2		281	705	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608911	100608911	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	146	266	0	ENST00000308731.7:c.1697C>A	p.Pro566Gln	p.P566Q	ENST00000308731	NM_000061.2	566	cCg/cAg	17/19	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.250137528954127	1		266	703	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913396	NA	P-0009242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	346	362	0	ENST00000349496.5:c.95A>G	p.Asp32Gly	p.D32G	ENST00000349496	NM_001904.3	32	gAc/gGc	3/15	1	2	FACETS	1	0.988	1	1	0.997	1	CLONAL	2	TRUE	1	0.4	2		362	777	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006641	62006641	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149266494	NA	P-0009242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	45	391	0	ENST00000392795.3:c.638C>T	p.Thr213Met	p.T213M	ENST00000392795	NM_001039933.1	213	aCg/aTg	6/6	1	2	FACETS	0.275	0.23	0.325	0.275	0.23	0.325	SUBCLONAL	1	TRUE	1	0.4	2		391	817	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0009248-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	186	484	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.173832558179819	4	FACETS	0.935	0.866	1	0.935	0.866	1	CLONAL	3	TRUE	1	0.222413844163734	4		484	729	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696190	52696190	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009248-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1342	153	574	1	ENST00000394830.3:c.487G>A	p.Asp163Asn	p.D163N	ENST00000394830	NM_018313.4	163	Gat/Aat	5/30	1	2	FACETS	0.92	0.839	1	0.92	0.839	1	CLONAL	1	TRUE	1	0.222413844163734	2		575	1495	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28599030	28599030	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009248-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	74	429	1	ENST00000241453.7:c.2258C>T	p.Ser753Leu	p.S753L	ENST00000241453	NM_004119.2	753	tCa/tTa	18/24	1	2	FACETS	0.823	0.719	0.935	0.823	0.719	0.935	CLONAL	1	TRUE	1	0.222413844163734	2		430	809	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853848	59853848	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009248-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	112	550	0	ENST00000259008.2:c.2011G>C	p.Glu671Gln	p.E671Q	ENST00000259008	NM_032043.2	671	Gag/Cag	14/20	1	2	FACETS	0.792	0.71	0.88	0.792	0.71	0.88	SUBCLONAL	1	TRUE	1	0.222413844163734	2		550	1271	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288748	33288748	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009251-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	339	352	0	ENST00000374542.5:c.804C>G	p.Asn268Lys	p.N268K	ENST00000374542	NM_001141970.1	268	aaC/aaG	3/8	0.70514403976872	2	FACETS	0.987	0.951	1	0.987	0.951	1	CLONAL	2	TRUE	0	0.70514403976872	2		352	487	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0009267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1297	156	484	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	FALSE	1	0.201595303469821	2		484	1453	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0009267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	73	145	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.201595303469821	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	0	0.201595303469821	1		145	579	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0009267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	256	370	1	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.868	0.811	0.928	1	0.994	1	CLONAL	2	FALSE	1	0.201595303469821	2		371	1463	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105718	27105718	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	137	359	1	ENST00000324856.7:c.5329G>T	p.Glu1777Ter	p.E1777*	ENST00000324856	NM_006015.4	1777	Gaa/Taa	20/20	0.148947355908428	1	FACETS	0.934	0.847	1	0.934	0.847	1	CLONAL	1	FALSE	0	0.201595303469821	1		360	1309	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	116	246	0				ENST00000310581	NM_198253.2	-/1132			0.16433766214577	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.178256381516714	3		246	577	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0009268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	64	266	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.602	0.519	0.692	0.602	0.519	0.692	SUBCLONAL	1	TRUE	1	0.178256381516714	2		266	1193	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0009268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1272	134	425	1	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.150458695751997	1	FACETS	0.974	0.882	1	0.974	0.882	1	CLONAL	1	TRUE	0	0.178256381516714	1		426	1406	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916836	178916836	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1829	166	679	0	ENST00000263967.3:c.223C>G	p.Gln75Glu	p.Q75E	ENST00000263967	NM_006218.2	75	Caa/Gaa	2/21	0.16433766214577	3	FACETS	1	0.928	1	0.508	0.465	0.555	CLONAL	1	TRUE	1	0.178256381516714	3		679	1995	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934194	48934194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	159	355	1	ENST00000267163.4:c.649C>T	p.Gln217Ter	p.Q217*	ENST00000267163	NM_000321.2	217	Cag/Tag	7/27	0.178256381516714	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.178256381516714	2		356	856	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120478182	120478182	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	127	324	0	ENST00000256646.2:c.3568G>A	p.Glu1190Lys	p.E1190K	ENST00000256646	NM_024408.3	1190	Gag/Aag	22/34	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.178256381516714	2		324	1217	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059348	42059348	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1885	186	653	1	ENST00000219905.7:c.9068C>T	p.Ser3023Leu	p.S3023L	ENST00000219905	NM_001164273.1	3023	tCa/tTa	24/24	0.178256381516714	1	FACETS	0.918	0.844	0.996	0.918	0.844	0.996	CLONAL	1	TRUE	0	0.178256381516714	1		654	2071	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610349	10610349	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	137	378	0	ENST00000171111.5:c.361G>T	p.Glu121Ter	p.E121*	ENST00000171111	NM_203500.1	121	Gag/Tag	2/6	0.150458695751997	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.178256381516714	1		378	1265	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026164	36026164	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1435	150	436	0	ENST00000358208.4:c.766C>G	p.Gln256Glu	p.Q256E	ENST00000358208		256	Cag/Gag	7/12	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.178256381516714	2		436	1585	SUCCESS
AR	367	MSKCC	GRCh37	X	66765461	66765461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1261	102	369	0	ENST00000374690.3:c.473C>T	p.Ser158Leu	p.S158L	ENST00000374690	NM_000044.3	158	tCa/tTa	1/8	0.150458695751997	1	FACETS	0.765	0.681	0.854	0.765	0.681	0.854	SUBCLONAL	1	TRUE	0	0.178256381516714	1		369	1363	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041683	47041683	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1563	152	539	0	ENST00000377604.3:c.1908del	p.Glu638ArgfsTer66	p.E638Rfs*66	ENST00000377604	NM_001204468.1	636	ggC/gg	17/24	0.150458695751997	1	FACETS	0.906	0.825	0.991	0.906	0.825	0.991	CLONAL	1	TRUE	0	0.178256381516714	1		539	1715	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0009293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	26	481	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.170276138469447	2	FACETS	0.259	0.204	0.322	0.129	0.102	0.161	INDETERMINATE	1	TRUE	0	0.342107768513294	2		481	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577084	7577084	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121912667	NA	P-0009293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	122	392	0	ENST00000269305.4:c.854A>T	p.Glu285Val	p.E285V	ENST00000269305	NM_001126112.2	285	gAg/gTg	8/11	0.342107768513294	1	FACETS	0.972	0.881	1	0.972	0.881	1	CLONAL	1	TRUE	0	0.342107768513294	1		392	608	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250386	110250386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752786911	NA	P-0009293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	28	421	0	ENST00000374672.4:c.289G>A	p.Glu97Lys	p.E97K	ENST00000374672	NM_004235.4	97	Gag/Aag	3/5	0.342107768513294	1	FACETS	0.247	0.196	0.304	0.247	0.196	0.304	SUBCLONAL	1	TRUE	0	0.342107768513294	1		421	550	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435246	110435246	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	59	122	0	ENST00000375856.3:c.3155C>T	p.Thr1052Ile	p.T1052I	ENST00000375856	NM_003749.2	1052	aCc/aTc	1/2	NA	2	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.342107768513294	2		122	241	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258508	16258508	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	42	242	0	ENST00000375759.3:c.5773G>C	p.Glu1925Gln	p.E1925Q	ENST00000375759	NM_015001.2	1925	Gag/Cag	11/15	1	2	FACETS	0.485	0.405	0.575	0.485	0.405	0.575	SUBCLONAL	1	TRUE	1	0.342107768513294	2		242	506	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164240	47164240	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	137	273	0	ENST00000409792.3:c.1886A>T	p.Lys629Met	p.K629M	ENST00000409792	NM_014159.6	629	aAg/aTg	3/21	0.254578983801416	1	FACETS	0.753	0.69	0.817	1	0.988	1	SUBCLONAL	2	TRUE	0	0.342107768513294	1		273	441	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498522	89498522	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	19	277	0	ENST00000336596.2:c.2494G>C	p.Asp832His	p.D832H	ENST00000336596	NM_005233.5	832	Gat/Cat	14/17	1	2	FACETS	0.455	0.346	0.583	0.455	0.346	0.583	SUBCLONAL	1	TRUE	1	0.342107768513294	2		277	244	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156130	106156130	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	83	318	0	ENST00000380013.4:c.1031C>A	p.Thr344Lys	p.T344K	ENST00000380013	NM_001127208.2	344	aCa/aAa	3/11	1	2	FACETS	0.885	0.783	0.995	0.885	0.783	0.995	CLONAL	1	TRUE	1	0.342107768513294	2		318	548	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157600	106157600	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	65	390	0	ENST00000380013.4:c.2501G>C	p.Cys834Ser	p.C834S	ENST00000380013	NM_001127208.2	834	tGt/tCt	3/11	1	2	FACETS	0.699	0.606	0.799	0.699	0.606	0.799	SUBCLONAL	1	TRUE	1	0.342107768513294	2		390	544	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535351	187535351	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	74	347	0	ENST00000441802.2:c.9223G>T	p.Asp3075Tyr	p.D3075Y	ENST00000441802	NM_005245.3	3075	Gac/Tac	12/27	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.342107768513294	2		347	400	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453149	140453149	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913361	NA	P-0009293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	110	261	0	ENST00000288602.6:c.1786G>C	p.Gly596Arg	p.G596R	ENST00000288602	NM_004333.4	596	Ggt/Cgt	15/18	0.235742273363891	3	FACETS	1	0.908	1	0.668	0.605	0.732	CLONAL	2	TRUE	0	0.342107768513294	3		261	376	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471044	8471044	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	83	364	0	ENST00000356435.5:c.3455G>T	p.Gly1152Val	p.G1152V	ENST00000356435		1152	gGg/gTg	20/35	0.342107768513294	1	FACETS	0.94	0.834	1	0.94	0.834	1	CLONAL	1	TRUE	0	0.342107768513294	1		364	428	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431831	49431831	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	19	209	0	ENST00000301067.7:c.9308C>G	p.Ala3103Gly	p.A3103G	ENST00000301067	NM_003482.3	3103	gCt/gGt	34/54	0.342107768513294	1	FACETS	0.242	0.183	0.312	0.242	0.183	0.312	SUBCLONAL	1	TRUE	0	0.342107768513294	1		209	380	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110087	115110087	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	17	153	0	ENST00000257566.3:c.1791C>A	p.Phe597Leu	p.F597L	ENST00000257566	NM_016569.3	597	ttC/ttA	8/8	0.342107768513294	1	FACETS	0.246	0.183	0.321	0.246	0.183	0.321	SUBCLONAL	1	TRUE	0	0.342107768513294	1		153	335	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437494	110437494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	30	290	0	ENST00000375856.3:c.907C>T	p.Arg303Cys	p.R303C	ENST00000375856	NM_003749.2	303	Cgc/Tgc	1/2	NA	2	FACETS	0.377	0.303	0.461			1	INDETERMINATE	1	TRUE	NA	0.342107768513294	2		290	465	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548914	29548914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	19	205	0	ENST00000356175.3:c.1688C>T	p.Pro563Leu	p.P563L	ENST00000356175	NM_000267.3	563	cCt/cTt	15/57	0.342107768513294	3	FACETS	0.496	0.377	0.636			1	SUBCLONAL	1	TRUE	NA	0.342107768513294	3		205	262	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661899	29661899	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	114	361	0	ENST00000356175.3:c.5793G>C	p.Trp1931Cys	p.W1931C	ENST00000356175	NM_000267.3	1931	tgG/tgC	39/57	0.342107768513294	3	FACETS	0.82	0.742	0.901			1	CLONAL	2	TRUE	NA	0.342107768513294	3		361	476	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868185	37868185	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	141	315	0	ENST00000269571.5:c.906C>G	p.Asn302Lys	p.N302K	ENST00000269571		302	aaC/aaG	8/27	0.342107768513294	3	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.342107768513294	3		315	757	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760959	59760959	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	130	409	0	ENST00000259008.2:c.3448G>T	p.Ala1150Ser	p.A1150S	ENST00000259008	NM_032043.2	1150	Gct/Tct	20/20	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.342107768513294	2		409	534	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719044	52719044	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	253	312	2	ENST00000322088.6:c.820G>T	p.Val274Leu	p.V274L	ENST00000322088	NM_014225.5	274	Gtg/Ttg	7/15	0.342107768513294	4	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.342107768513294	4		314	801	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795341	39795341	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	100	300	0	ENST00000288319.7:c.379G>C	p.Val127Leu	p.V127L	ENST00000288319	NM_182918.3	127	Gtg/Ctg	3/10	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.342107768513294	2		300	559	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394760	45394761	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0009293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	67	369	0	ENST00000262160.6:c.588_589del	p.Thr197SerfsTer8	p.T197Sfs*8	ENST00000262160	NM_005901.5	196	taTAct/tact	5/11	0.342107768513294	1	FACETS	0.89	0.777	1	0.89	0.777	1	CLONAL	1	TRUE	0	0.342107768513294	1		369	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0009295-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	400	525	1	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.602508672329291	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.602508672329291	2		526	626	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162688917	162688917	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009295-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	422	411	0	ENST00000367921.3:c.64A>G	p.Lys22Glu	p.K22E	ENST00000367921	NM_006182.2	22	Aaa/Gaa	3/18	0.520387513495149	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.602508672329291	4		411	1099	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637579	52637579	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009295-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	641	612	1	ENST00000394830.3:c.2737G>T	p.Glu913Ter	p.E913*	ENST00000394830	NM_018313.4	913	Gaa/Taa	18/30	0.602508672329291	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.602508672329291	2		613	1044	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69788784	69788784	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs750693668	NA	P-0009295-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	230	408	0	ENST00000352241.4:c.36A>C	p.Glu12Asp	p.E12D	ENST00000352241	NM_198159.2	12	gaA/gaC	1/10	0.602508672329291	2	FACETS	0.963	0.9	1	0.481	0.45	0.514	CLONAL	1	TRUE	0	0.602508672329291	2		408	793	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188201	142188201	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009295-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	164	381	0	ENST00000350721.4:c.6530G>A	p.Trp2177Ter	p.W2177*	ENST00000350721	NM_001184.3	2177	tGg/tAg	38/47	0.602508672329291	5	FACETS	0.822	0.753	0.895	0.274	0.251	0.299	CLONAL	1	TRUE	2	0.602508672329291	5		381	1261	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514427	149514427	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009295-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	691	522	0	ENST00000261799.4:c.517T>G	p.Tyr173Asp	p.Y173D	ENST00000261799	NM_002609.3	173	Tat/Gat	4/23	0.602508672329291	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.602508672329291	3		522	961	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431430	49431430	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs886049479	NA	P-0009295-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	385	406	0	ENST00000301067.7:c.9709G>T	p.Glu3237Ter	p.E3237*	ENST00000301067	NM_003482.3	3237	Gag/Tag	34/54	0.602508672329291	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.602508672329291	3		406	804	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274024	10274024	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009295-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	233	472	0	ENST00000330684.3:c.245T>C	p.Leu82Pro	p.L82P	ENST00000330684	NM_001134407.1	82	cTc/cCc	2/13	0.520387513495149	4	FACETS	1	0.937	1	0.503	0.469	0.54	CLONAL	1	TRUE	2	0.602508672329291	4		472	1231	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313454	30313454	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1304746106	NA	P-0009295-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	504	504	1	ENST00000262643.3:c.1054G>T	p.Val352Phe	p.V352F	ENST00000262643	NM_001238.2	352	Gtc/Ttc	11/12	0.520387513495149	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.602508672329291	4		505	1286	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	31	291	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.519	0.418	0.634	0.519	0.418	0.634	SUBCLONAL	1	TRUE	1	0.15	2		291	797	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0009305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	19	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.754	0.572	0.969	0.754	0.572	0.969	CLONAL	1	TRUE	1	0.15	2		249	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0009305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	26	295	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	1	0.15	2		295	319	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0009305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	37	284	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.754	0.62	0.905	0.754	0.62	0.905	CLONAL	1	TRUE	1	0.15	2		284	654	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	19	255	2	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.475	0.359	0.613	0.475	0.359	0.613	SUBCLONAL	1	TRUE	1	0.15	2		257	533	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0009305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	72	370	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.15	2		370	884	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730831	40730831	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372700928	NA	P-0009305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	44	311	0	ENST00000373198.4:c.3704G>A	p.Arg1235His	p.R1235H	ENST00000373198	NM_133170.3	1235	cGc/cAc	27/32	1	2	FACETS	0.978	0.819	1	0.978	0.819	1	CLONAL	1	TRUE	1	0.15	2		311	600	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0009306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	38	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.211153360123889	4	FACETS	0.767	0.635	0.913	0.383	0.317	0.457	INDETERMINATE	1	TRUE	2	0.394928935033022	4		249	350	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0009306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	168	427	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	0.394928935033022	2		427	745	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913351	NA	P-0009313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	299	319	1	ENST00000288602.6:c.1397G>T	p.Gly466Val	p.G466V	ENST00000288602	NM_004333.4	466	gGa/gTa	11/18	0.343948938484546	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	1	0.343948938484546	3		320	998	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0009313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	133	331	1	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.243063393151022	1	FACETS	0.899	0.818	0.985	0.899	0.818	0.985	CLONAL	1	TRUE	0	0.343948938484546	1		332	712	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292570	15292570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	46	241	0	ENST00000263388.2:c.2609C>T	p.Ser870Phe	p.S870F	ENST00000263388	NM_000435.2	870	tCc/tTc	17/33	1	2	FACETS	0.343	0.288	0.405	0.343	0.288	0.405	SUBCLONAL	1	TRUE	1	0.343948938484546	2		241	779	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239450	123239450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	66	319	0	ENST00000358487.5:c.2387C>T	p.Ser796Phe	p.S796F	ENST00000358487	NM_000141.4	796	tCt/tTt	18/18	1	2	FACETS	0.406	0.351	0.465	0.406	0.351	0.465	SUBCLONAL	1	TRUE	1	0.343948938484546	2		319	946	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190834	11190834	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	21	124	0	ENST00000361445.4:c.5365G>A	p.Ala1789Thr	p.A1789T	ENST00000361445	NM_004958.3	1789	Gcc/Acc	39/58	1	2	FACETS	0.391	0.301	0.496	0.391	0.301	0.496	SUBCLONAL	1	TRUE	1	0.343948938484546	2		124	312	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120548069	120548069	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	13	28	0	ENST00000256646.2:c.298G>T	p.Asp100Tyr	p.D100Y	ENST00000256646	NM_024408.3	100	Gac/Tac	3/34	0.283595267535323	4	FACETS	1	0.857	1	0.446	0.323	0.589	CLONAL	1	TRUE	1	0.343948938484546	4		28	76	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157996	106157996	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	39	188	0	ENST00000380013.4:c.2897A>T	p.Gln966Leu	p.Q966L	ENST00000380013	NM_001127208.2	966	cAg/cTg	3/11	0.165910620614727	2	FACETS	0.415	0.344	0.496	0.208	0.172	0.248	INDETERMINATE	1	TRUE	0	0.343948938484546	2		188	546	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915684	131915684	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	178	366	0	ENST00000265335.6:c.682A>T	p.Thr228Ser	p.T228S	ENST00000265335		228	Aca/Tca	5/25	0.131289939264289	4	FACETS	0.799	0.737	0.864	0.799	0.737	0.864	INDETERMINATE	2	TRUE	2	0.343948938484546	4		366	870	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515373	149515373	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	126	240	0	ENST00000261799.4:c.109C>A	p.Pro37Thr	p.P37T	ENST00000261799	NM_002609.3	37	Ccc/Acc	3/23	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.343948938484546	2		240	731	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066438	94066438	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	89	383	0	ENST00000369303.4:c.1321G>T	p.Ala441Ser	p.A441S	ENST00000369303	NM_004440.3	441	Gca/Tca	5/17	0.310001207680201	1	FACETS	0.453	0.401	0.51	0.453	0.401	0.51	SUBCLONAL	1	TRUE	0	0.343948938484546	1		383	945	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951921	2951921	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	98	219	2	ENST00000396946.4:c.3029C>A	p.Thr1010Lys	p.T1010K	ENST00000396946	NM_032415.4	1010	aCa/aAa	23/25	0.343948938484546	6	FACETS	0.903	0.804	1	0.181	0.16	0.202	CLONAL	1	TRUE	1	0.343948938484546	6		221	1065	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128030	64128030	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs949665366	NA	P-0009313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	125	312	0	ENST00000334205.4:c.428G>T	p.Gly143Val	p.G143V	ENST00000334205	NM_003942.2	143	gGt/gTt	4/17	1	2	FACETS	0.733	0.662	0.807	0.733	0.662	0.807	SUBCLONAL	1	TRUE	1	0.343948938484546	2		312	992	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243830	46243830	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	55	230	0	ENST00000334344.6:c.1924G>T	p.Gly642Ter	p.G642*	ENST00000334344	NM_152641.2	642	Gga/Tga	15/21	1	2	FACETS	0.523	0.447	0.607	0.523	0.447	0.607	SUBCLONAL	1	TRUE	1	0.343948938484546	2		230	611	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961408	41961408	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	313	513	0	ENST00000219905.7:c.316C>T	p.Pro106Ser	p.P106S	ENST00000219905	NM_001164273.1	106	Cct/Tct	2/24	0.343948938484546	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.343948938484546	1		513	1372	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724551	724551	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	23	82	0	ENST00000314574.4:c.1505A>T	p.His502Leu	p.H502L	ENST00000314574	NM_005433.3	502	cAt/cTt	12/12	1	2	FACETS	0.456	0.356	0.572	0.456	0.356	0.572	SUBCLONAL	1	TRUE	1	0.343948938484546	2		82	293	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39647352	39647352	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	147	402	0	ENST00000262039.4:c.2524G>T	p.Val842Phe	p.V842F	ENST00000262039	NM_002647.2	842	Gtt/Ttt	24/25	1	2	FACETS	0.937	0.855	1	0.937	0.855	1	CLONAL	1	TRUE	1	0.343948938484546	2		402	912	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937660	76937660	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0009313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	55	464	0	ENST00000373344.5:c.3088A>T	p.Lys1030Ter	p.K1030*	ENST00000373344	NM_000489.3	1030	Aag/Tag	9/35	0.209999027747727	1	FACETS	0.278	0.237	0.324	0.278	0.237	0.324	SUBCLONAL	1	TRUE	0	0.343948938484546	1		464	952	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716080	243716080	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	365	326	0	ENST00000263826.5:c.1114del	p.Asp372MetfsTer10	p.D372Mfs*10	ENST00000263826	NM_005465.4	372	Gat/at	10/13	0.283595267535323	4	FACETS	1	0.992	1	0.815	0.774	0.858	CLONAL	2	TRUE	1	0.343948938484546	4		326	1166	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983875	2983875	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1547	281	359	0	ENST00000396946.4:c.655del	p.Val219SerfsTer2	p.V219Sfs*2	ENST00000396946	NM_032415.4	219	Gtc/tc	5/25	0.343948938484546	6	FACETS	0.754	0.706	0.804	0.302	0.282	0.322	SUBCLONAL	2	TRUE	1	0.343948938484546	6		359	1828	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837917	156837918	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0009313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	73	325	1	ENST00000524377.1:c.450_451delinsAA	p.His151Asn	p.H151N	ENST00000524377	NM_002529.3	150	ctGCac/ctAAac	5/17	0.283595267535323	4	FACETS	0.529	0.461	0.602	0.176	0.153	0.201	SUBCLONAL	1	TRUE	1	0.343948938484546	4		326	1079	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988436	41988436	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009323-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	302	632	1	ENST00000219905.7:c.1228G>T	p.Glu410Ter	p.E410*	ENST00000219905	NM_001164273.1	410	Gag/Tag	3/24	0.292282084638906	2	FACETS	0.982	0.927	1	0.982	0.927	1	CLONAL	2	TRUE	0	0.338782217142396	2		633	908	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609940	43609946	+	protein_altering_variant	In_Frame_Del	DEL	ACGAGCT	ACGAGCT	C	novel	NA	P-0009323-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	444	648	0	ENST00000355710.3:c.1892_1898delinsC	p.Asp631_Leu633delinsAla	p.D631_L633delinsA	ENST00000355710	NM_020975.4	631	gACGAGCTg/gCg	11/20	0.338782217142396	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.338782217142396	2		648	1204	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0009339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	572	404	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.51582331715877	3	FACETS	1	0.981	1			1	CLONAL	3	TRUE	NA	0.51582331715877	3		405	914	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443695	29443695	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs863225281	NA	P-0009339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	124	249	0	ENST00000389048.3:c.3522C>G	p.Phe1174Leu	p.F1174L	ENST00000389048	NM_004304.4	1174	ttC/ttG	23/29	0.51582331715877	6	FACETS	0.881	0.795	0.972			1	CLONAL	1	TRUE	NA	0.51582331715877	6		249	1109	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183770	10183770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs5030805	NA	P-0009348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	58	240	0	ENST00000256474.2:c.239G>A	p.Ser80Asn	p.S80N	ENST00000256474	NM_000551.3	80	aGt/aAt	1/3	0.311907446882443	1	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	0	0.311907446882443	1		240	310	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158112	47158112	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0009348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	128	545	0	ENST00000409792.3:c.4586+1G>A		p.X1529_splice	ENST00000409792	NM_014159.6	1529			0.311907446882443	1	FACETS	0.921	0.836	1	0.921	0.836	1	CLONAL	1	TRUE	0	0.311907446882443	1		545	752	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643538	52643538	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	80	449	0	ENST00000394830.3:c.2358del	p.Phe786LeufsTer5	p.F786Lfs*5	ENST00000394830	NM_018313.4	786	ttT/tt	17/30	0.311907446882443	1	FACETS	0.665	0.586	0.75	0.665	0.586	0.75	SUBCLONAL	1	TRUE	0	0.311907446882443	1		449	651	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911508	101911509	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0009348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	120	418	0	ENST00000374994.4:c.1433_1434del	p.Asn478ArgfsTer4	p.N478Rfs*4	ENST00000374994	NM_004612.2	478	aAT/a	9/9	0.311907446882443	1	FACETS	0.915	0.827	1	0.915	0.827	1	CLONAL	1	TRUE	0	0.311907446882443	1		418	710	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0009351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	19	580	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.826	1	1	0.826	1	CLONAL	1	TRUE	1	0.381856297997981	2		580	92	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0009351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	14	487	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.381856297997981	1	FACETS	0.742	0.546	0.969	0.742	0.546	0.969	CLONAL	1	TRUE	0	0.381856297997981	1		487	80	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904947	101904947	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	18	342	1	ENST00000374994.4:c.935G>T	p.Gly312Val	p.G312V	ENST00000374994	NM_004612.2	312	gGt/gTt	5/9	0.362719340177398	2	FACETS	1	0.882	1	0.629	0.485	0.789	CLONAL	1	TRUE	0	0.381856297997981	2		343	75	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976873	55976873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750983015	NA	P-0009351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	12	492	0	ENST00000263923.4:c.1039C>T	p.Arg347Cys	p.R347C	ENST00000263923	NM_002253.2	347	Cgt/Tgt	8/30	1	2	FACETS	0.861	0.616	1	0.861	0.616	1	CLONAL	1	TRUE	1	0.381856297997981	2		492	73	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0009394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	208	375	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.456839096313531	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.47632367886049	2		378	409	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163817	72163817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	72	414	1	ENST00000357731.5:c.541C>T	p.Pro181Ser	p.P181S	ENST00000357731	NM_173808.2	181	Cca/Tca	4/7	0.437929098971246	2	FACETS	0.385	0.335	0.438	0.192	0.167	0.219	SUBCLONAL	1	TRUE	0	0.47632367886049	2		415	786	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156781	106156781	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	141	337	0	ENST00000380013.4:c.1682A>G	p.Lys561Arg	p.K561R	ENST00000380013	NM_001127208.2	561	aAa/aGa	3/11	0.422557547274768	2	FACETS	1	0.919	1	0.503	0.459	0.547	CLONAL	1	TRUE	0	0.47632367886049	2		337	589	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294069	1294069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs974018889	NA	P-0009394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	77	327	0	ENST00000310581.5:c.932C>T	p.Ser311Leu	p.S311L	ENST00000310581	NM_198253.2	311	tCg/tTg	2/16	0.47632367886049	1	FACETS	0.669	0.591	0.752	0.669	0.591	0.752	SUBCLONAL	1	TRUE	0	0.47632367886049	1		327	368	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112884112	112884112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	111	240	0	ENST00000351677.2:c.47C>T	p.Ala16Val	p.A16V	ENST00000351677	NM_002834.3	16	gCa/gTa	2/16	NA	2	FACETS	1	0.944	1			1	INDETERMINATE	1	TRUE	NA	0.47632367886049	2		240	439	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0009406-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	275	419	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.281538307505337	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.281538307505337	3		419	981	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181413	185181413	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009406-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	136	491	0	ENST00000265026.3:c.1354G>C	p.Glu452Gln	p.E452Q	ENST00000265026	NM_004721.4	452	Gaa/Caa	8/14	0.281538307505337	3	FACETS	0.978	0.887	1	0.489	0.443	0.537	CLONAL	1	TRUE	1	0.281538307505337	3		491	1127	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181440	185181440	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009406-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	111	427	0	ENST00000265026.3:c.1381G>C	p.Glu461Gln	p.E461Q	ENST00000265026	NM_004721.4	461	Gag/Cag	8/14	0.281538307505337	3	FACETS	0.939	0.843	1	0.469	0.421	0.521	CLONAL	1	TRUE	1	0.281538307505337	3		427	958	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874919	151874919	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009406-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	220	457	0	ENST00000262189.6:c.7619A>T	p.His2540Leu	p.H2540L	ENST00000262189	NM_170606.2	2540	cAt/cTt	38/59	0.275440086041259	2	FACETS	0.872	0.812	0.934	0.872	0.812	0.934	CLONAL	2	TRUE	0	0.281538307505337	2		457	896	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405802	70405802	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009406-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	72	319	0	ENST00000373644.4:c.3316A>G	p.Ser1106Gly	p.S1106G	ENST00000373644	NM_030625.2	1106	Agc/Ggc	4/12	0.190109831068883	1	FACETS	0.611	0.533	0.695	0.611	0.533	0.695	SUBCLONAL	1	TRUE	0	0.281538307505337	1		319	719	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102056760	102056760	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009406-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	108	306	0	ENST00000282441.5:c.700G>C	p.Asp234His	p.D234H	ENST00000282441	NM_001130145.2	234	Gat/Cat	4/9	0.281538307505337	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.281538307505337	1		306	598	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188181	108188181	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009406-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	98	321	0	ENST00000278616.4:c.6280G>A	p.Glu2094Lys	p.E2094K	ENST00000278616	NM_000051.3	2094	Gaa/Aaa	43/63	0.281538307505337	1	FACETS	0.91	0.813	1	0.91	0.813	1	CLONAL	1	TRUE	0	0.281538307505337	1		321	657	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188190	108188190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009406-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	98	302	0	ENST00000278616.4:c.6289G>A	p.Glu2097Lys	p.E2097K	ENST00000278616	NM_000051.3	2097	Gaa/Aaa	43/63	0.281538307505337	1	FACETS	0.932	0.832	1	0.932	0.832	1	CLONAL	1	TRUE	0	0.281538307505337	1		302	642	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923137	48923137	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009406-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	62	241	0	ENST00000267163.4:c.585G>A	p.Trp195Ter	p.W195*	ENST00000267163	NM_000321.2	195	tgG/tgA	6/27	0.281538307505337	1	FACETS	0.956	0.829	1	0.956	0.829	1	CLONAL	1	TRUE	0	0.281538307505337	1		241	396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0009406-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	189	397	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.281538307505337	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.281538307505337	1		397	1031	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874913	151874913	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009406-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	203	456	0	ENST00000262189.6:c.7625del	p.Ser2542TyrfsTer20	p.S2542Yfs*20	ENST00000262189	NM_170606.2	2542	tCa/ta	38/59	0.275440086041259	2	FACETS	0.78	0.724	0.839	0.78	0.724	0.839	SUBCLONAL	2	TRUE	0	0.281538307505337	2		456	924	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0009412-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	160	261	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.727	0.667	0.789	0.727	0.667	0.789	SUBCLONAL	1	TRUE	1	0.520517304779575	2		261	846	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624239	89624272	+	frameshift_variant	Frame_Shift_Del	DEL	ATCAAAGAGATCGTTAGCAGAAACAAAAGGAGAT	ATCAAAGAGATCGTTAGCAGAAACAAAAGGAGAT	-	novel	NA	P-0009412-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	80	78	0	ENST00000371953.3:c.18_51del	p.Glu7ArgfsTer6	p.E7Rfs*6	ENST00000371953	NM_000314.4	5	ATCAAAGAGATCGTTAGCAGAAACAAAAGGAGATat/at	1/9	0.511231363982073	1	FACETS	0.984	0.881	1	0.984	0.881	1	CLONAL	1	TRUE	0	0.520517304779575	1		78	231	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	58	291	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.283395812576206	2		291	373	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907053	101907053	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	56	318	0	ENST00000374994.4:c.1013A>T	p.Asn338Ile	p.N338I	ENST00000374994	NM_004612.2	338	aAt/aTt	6/9	0.283395812576206	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.283395812576206	1		318	271	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0009419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	50	397	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	1	2	FACETS	0.843	0.713	0.986	0.843	0.713	0.986	CLONAL	1	TRUE	1	0.15	2		397	791	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971000	21971000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	24	214	0	ENST00000304494.5:c.358G>T	p.Glu120Ter	p.E120*	ENST00000304494	NM_000077.4	120	Gag/Tag	2/3	1	2	FACETS	0.711	0.556	0.89	0.711	0.556	0.89	SUBCLONAL	1	TRUE	1	0.15	2		214	450	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599868	10599868	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	55	327	1	ENST00000171111.5:c.1708G>T	p.Gly570Ter	p.G570*	ENST00000171111	NM_203500.1	570	Gga/Tga	5/6	1	2	FACETS	0.992	0.847	1	0.992	0.847	1	CLONAL	1	TRUE	1	0.15	2		328	739	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045016	47045016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556782040	NA	P-0009419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	31	200	0	ENST00000377604.3:c.2342C>T	p.Ser781Leu	p.S781L	ENST00000377604	NM_001204468.1	781	tCa/tTa	20/24	1	1	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	0	0.15	1		200	338	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435782	149435782	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	38	362	0	ENST00000286301.3:c.2442T>A	p.Asn814Lys	p.N814K	ENST00000286301	NM_005211.3	814	aaT/aaA	18/22	1	2	FACETS	0.685	0.564	0.82	0.685	0.564	0.82	SUBCLONAL	1	TRUE	1	0.15	2		362	740	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265479	152265479	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766779326	NA	P-0009419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	34	242	0	ENST00000206249.3:c.932C>T	p.Thr311Met	p.T311M	ENST00000206249	NM_000125.3	311	aCg/aTg	4/8	1	2	FACETS	0.944	0.771	1	0.944	0.771	1	CLONAL	1	TRUE	1	0.15	2		242	480	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121575	108121575	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	30	380	0	ENST00000278616.4:c.1383A>T	p.Glu461Asp	p.E461D	ENST00000278616	NM_000051.3	461	gaA/gaT	10/63	1	2	FACETS	0.717	0.576	0.877	0.717	0.576	0.877	SUBCLONAL	1	TRUE	1	0.15	2		380	558	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029573	14029573	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	17	149	0	ENST00000311895.7:c.1784G>T	p.Arg595Met	p.R595M	ENST00000311895	NM_005236.2	595	aGg/aTg	8/11	1	2	FACETS	0.691	0.515	0.901	0.691	0.515	0.901	SUBCLONAL	1	TRUE	1	0.15	2		149	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579370	7579370	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567555883	NA	P-0009419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	39	304	0	ENST00000269305.4:c.317G>T	p.Ser106Ile	p.S106I	ENST00000269305	NM_001126112.2	106	aGc/aTc	4/11	1	2	FACETS	0.784	0.649	0.937	0.784	0.649	0.937	CLONAL	1	TRUE	1	0.15	2		304	663	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484597	57484597	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs137854533	NA	P-0009419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	13	175	0	ENST00000371085.3:c.681G>T	p.Gln227His	p.Q227H	ENST00000371085	NM_000516.4	227	caG/caT	9/13	1	2	FACETS	0.45	0.32	0.61	0.45	0.32	0.61	SUBCLONAL	1	TRUE	1	0.15	2		175	385	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649559	48649559	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	33	261	0	ENST00000376670.3:c.43C>A	p.Leu15Ile	p.L15I	ENST00000376670	NM_002049.3	15	Ctc/Atc	2/6	1	1	FACETS	0.958	0.78	1	0.958	0.78	1	CLONAL	1	TRUE	0	0.15	1		261	425	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611216	100611216	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	23	150	0	ENST00000308731.7:c.1390T>A	p.Cys464Ser	p.C464S	ENST00000308731	NM_000061.2	464	Tgc/Agc	15/19	1	1	FACETS	0.946	0.738	1	0.946	0.738	1	CLONAL	1	TRUE	0	0.15	1		150	300	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938089	76938092	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	novel	NA	P-0009456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	30	196	0	ENST00000373344.5:c.2656_2659del	p.Glu886LeufsTer18	p.E886Lfs*18	ENST00000373344	NM_000489.3	886	GAGAct/ct	9/35	1	1	FACETS	0.193	0.156	0.236	0.193	0.156	0.236	SUBCLONAL	1	TRUE	0	0.7	1		196	288	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467512	66467512	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009463-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	95	329	0	ENST00000273854.3:c.757T>A	p.Ser253Thr	p.S253T	ENST00000273854	NM_004439.5	253	Tcc/Acc	3/18	0.263233238677596	4	FACETS	0.96	0.853	1	0.48	0.426	0.537	CLONAL	1	TRUE	2	0.263233238677596	4		329	950	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350581	15350581	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009463-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	60	297	0	ENST00000263377.2:c.3334G>C	p.Glu1112Gln	p.E1112Q	ENST00000263377	NM_058243.2	1112	Gag/Cag	16/20	0.263233238677596	4	FACETS	0.861	0.741	0.992	0.43	0.37	0.496	CLONAL	1	TRUE	2	0.263233238677596	4		297	669	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0009466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	231	775	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.251676996787305	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.251676996787305	1		775	1177	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602290	10602290	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	143	291	1	ENST00000171111.5:c.1288G>T	p.Gly430Cys	p.G430C	ENST00000171111	NM_203500.1	430	Ggc/Tgc	3/6	0.251676996787305	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.251676996787305	1		292	742	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420049	49420049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1240	186	413	0	ENST00000301067.7:c.15700G>A	p.Glu5234Lys	p.E5234K	ENST00000301067	NM_003482.3	5234	Gag/Aag	48/54	0.194502250855346	3	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.251676996787305	3		413	1426	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023895	27023895	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	35	135	0	ENST00000324856.7:c.1001C>G	p.Ser334Trp	p.S334W	ENST00000324856	NM_006015.4	334	tCg/tGg	1/20	1	2	FACETS	0.659	0.54	0.792	0.659	0.54	0.792	SUBCLONAL	1	TRUE	1	0.251676996787305	2		135	422	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885466	23885466	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1525	123	487	0	ENST00000374561.5:c.345G>T	p.Arg115Ser	p.R115S	ENST00000374561	NM_002167.4	115	agG/agT	2/3	1	2	FACETS	0.593	0.534	0.656	0.593	0.534	0.656	SUBCLONAL	1	TRUE	1	0.251676996787305	2		487	1648	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631122	69631122	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	230	476	0	ENST00000334134.2:c.290T>A	p.Leu97Gln	p.L97Q	ENST00000334134	NM_005247.2	97	cTg/cAg	2/3	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.251676996787305	2		476	1291	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443689	49443689	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	184	357	0	ENST00000301067.7:c.3682G>T	p.Gly1228Cys	p.G1228C	ENST00000301067	NM_003482.3	1228	Ggc/Tgc	11/54	0.194502250855346	3	FACETS	1	0.989	1			1	CLONAL	1	TRUE	NA	0.251676996787305	3		357	1139	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73352337	73352337	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1446	237	473	0	ENST00000377767.4:c.568C>T	p.Pro190Ser	p.P190S	ENST00000377767	NM_014953.3	190	Cca/Tca	3/21	0.119239581919762	4	FACETS	1	0.99	1	0.7	0.651	0.751	INDETERMINATE	1	TRUE	2	0.251676996787305	4		473	1683	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207058	1207069	+	inframe_deletion	In_Frame_Del	DEL	ACCTGATGGGGG	ACCTGATGGGGG	-	rs1131690916	NA	P-0009466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	116	330	0	ENST00000326873.7:c.151_162del	p.Met51_Leu54del	p.M51_L54del	ENST00000326873	NM_000455.4	49	tACCTGATGGGGGac/tac	1/10	0.251676996787305	1	FACETS	0.935	0.842	1	0.935	0.842	1	CLONAL	1	TRUE	0	0.251676996787305	1		330	862	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0009480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	96	328	0	ENST00000269305.4:c.375+1G>T		p.X125_splice	ENST00000269305	NM_001126112.2	125			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		328	523	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	76	291	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.14	2		291	922	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755470	39755470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	210	437	3	ENST00000288319.7:c.1295C>T	p.Ala432Val	p.A432V	ENST00000288319	NM_182918.3	432	gCg/gTg	10/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.29	2		440	1059	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618691	37618692	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0009556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	150	577	1	ENST00000447079.4:c.367_368del	p.Leu123LysfsTer3	p.L123Kfs*3	ENST00000447079	NM_015083.1	123	CTa/a	1/14	1	2	FACETS	0.826	0.753	0.903	0.826	0.753	0.903	CLONAL	1	TRUE	1	0.29	2		578	1252	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618979	37618982	+	stop_gained	Nonsense_Mutation	ONP	AGAT	AGAT	TGAG	novel	NA	P-0009556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	82	316	0	ENST00000447079.4:c.655_658delinsTGAG	p.Arg219_Ser220delinsTer	p.R219_S220delins*	ENST00000447079	NM_015083.1	219	AGATcc/TGAGcc	1/14	1	2	FACETS	0.762	0.672	0.859	0.762	0.672	0.859	SUBCLONAL	1	TRUE	1	0.29	2		316	742	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0009560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	308	475	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	0.723746302792131	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.723746302792131	2		475	420	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413951	139413951	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	469	651	0	ENST00000277541.6:c.809del	p.Gly270ValfsTer7	p.G270Vfs*7	ENST00000277541	NM_017617.3	270	gGt/gt	5/34	0.723746302792131	3	FACETS	0.97	0.933	1	0.97	0.933	1	CLONAL	2	TRUE	1	0.723746302792131	3		651	910	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258163	16258163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144013241	NA	P-0009560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	271	448	0	ENST00000375759.3:c.5428C>T	p.Pro1810Ser	p.P1810S	ENST00000375759	NM_015001.2	1810	Cca/Tca	11/15	0.597049303688537	4	FACETS	0.974	0.92	1	0.974	0.92	1	CLONAL	2	TRUE	2	0.723746302792131	4		448	663	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332672	153332672	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1382361753	NA	P-0009560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	187	683	0	ENST00000281708.4:c.284A>G	p.Gln95Arg	p.Q95R	ENST00000281708	NM_033632.3	95	cAa/cGa	2/12	0.161827840110248	2	FACETS	0.801	0.743	0.861	0.401	0.371	0.431	INDETERMINATE	1	TRUE	0	0.723746302792131	2		683	645	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282734	1282734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	190	373	1	ENST00000310581.5:c.1579G>A	p.Gly527Ser	p.G527S	ENST00000310581	NM_198253.2	527	Ggc/Agc	3/16	0.723746302792131	7	FACETS	0.838	0.775	0.903	0.335	0.31	0.362	CLONAL	2	TRUE	2	0.723746302792131	7		374	880	SUCCESS
ATM	472	MSKCC	GRCh37	11	108213992	108213992	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	152	364	0	ENST00000278616.4:c.8312C>A	p.Thr2771Lys	p.T2771K	ENST00000278616	NM_000051.3	2771	aCa/aAa	57/63	0.723746302792131	3	FACETS	0.947	0.87	1	0.474	0.435	0.514	CLONAL	1	TRUE	1	0.723746302792131	3		364	604	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589385	28589385	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	331	558	5	ENST00000241453.7:c.2662C>A	p.Pro888Thr	p.P888T	ENST00000241453	NM_004119.2	888	Cct/Act	22/24	NA	2	FACETS	0.965	0.93	0.999			1	INDETERMINATE	2	TRUE	NA	0.723746302792131	2		563	474	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89355052	89355052	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	448	859	0	ENST00000301030.4:c.628A>T	p.Asn210Tyr	p.N210Y	ENST00000301030	NM_001256183.1	210	Aac/Tac	7/13	0.300496361373888	3	FACETS	0.931	0.894	0.969	0.931	0.894	0.969	INDETERMINATE	2	TRUE	1	0.723746302792131	3		859	905	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0009587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	121	207	0				ENST00000310581	NM_198253.2	-/1132			0.360210288939877	1	FACETS	0.594	0.544	0.645	0.594	0.544	0.645	INDETERMINATE	1	TRUE	0	0.782264640541701	1		207	317	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0009587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3831	12945	748	1	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.782264640541701	22	FACETS	1	0.999	1			1	CLONAL	17	TRUE	NA	0.782264640541701	22		749	16776	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0009587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13865	2941	604	5	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.782264640541701	22	FACETS	0.987	0.967	1			1	CLONAL	4	TRUE	NA	0.782264640541701	22		609	16806	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523007	25523007	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0009587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	408	638	1	ENST00000264709.3:c.177+1G>A		p.X59_splice	ENST00000264709	NM_175629.2	59			1	2	FACETS	0.895	0.852	0.937	0.895	0.852	0.937	CLONAL	1	TRUE	1	0.782264640541701	2		639	1166	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508856	106508856	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376958957	NA	P-0009587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	252	336	1	ENST00000359195.3:c.850G>A	p.Glu284Lys	p.E284K	ENST00000359195	NM_002649.2	284	Gaa/Aaa	2/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.782264640541701	2		337	614	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682563	37682563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1446971298	NA	P-0009587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	241	365	0	ENST00000447079.4:c.3754G>A	p.Ala1252Thr	p.A1252T	ENST00000447079	NM_015083.1	1252	Gca/Aca	13/14	1	2	FACETS	0.976	0.918	1	0.976	0.918	1	CLONAL	1	TRUE	1	0.782264640541701	2		365	631	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0009596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	126	427	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.422956960845998	2		427	589	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279564	123279564	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121918501	NA	P-0009596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	309	443	0	ENST00000358487.5:c.868T>C	p.Trp290Arg	p.W290R	ENST00000358487	NM_000141.4	290	Tgg/Cgg	7/18	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.422956960845998	2		443	1028	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467924	50467924	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	106	289	0	ENST00000331340.3:c.1159G>C	p.Glu387Gln	p.E387Q	ENST00000331340	NM_006060.4	387	Gag/Cag	8/8	0.484270284505372	4	FACETS	0.985	0.884	1	0.328	0.294	0.364	CLONAL	1	TRUE	1	0.505884697780975	4		289	641	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679408	29679408	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	197	393	0	ENST00000356175.3:c.7528C>G	p.Gln2510Glu	p.Q2510E	ENST00000356175	NM_000267.3	2510	Cag/Gag	50/57	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.505884697780975	2		393	718	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922364	178922364	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	393	382	0	ENST00000263967.3:c.1133G>T	p.Cys378Phe	p.C378F	ENST00000263967	NM_006218.2	378	tGt/tTt	6/21	0.505884697780975	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.505884697780975	2		382	768	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134230	2134230	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs148527903	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	163	377	2	ENST00000219476.3:c.4007C>T	p.Ser1336Leu	p.S1336L	ENST00000219476	NM_000548.3	1336	tCg/tTg	34/42	0.505884697780975	3	FACETS	0.959	0.881	1	0.479	0.44	0.52	CLONAL	1	TRUE	1	0.505884697780975	3		379	842	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522416	176522416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519792	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	196	321	0	ENST00000292408.4:c.1605C>A	p.Asn535Lys	p.N535K	ENST00000292408	NM_213647.1	535	aaC/aaA	12/18	0.505884697780975	3	FACETS	1	0.979	1	0.572	0.53	0.615	CLONAL	1	TRUE	1	0.505884697780975	3		321	849	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814569	43814569	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	162	403	0	ENST00000372470.3:c.1364C>G	p.Ser455Cys	p.S455C	ENST00000372470	NM_005373.2	455	tCt/tGt	9/12	0.505884697780975	3	FACETS	0.923	0.848	1	0.462	0.424	0.502	CLONAL	1	TRUE	1	0.505884697780975	3		403	869	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175942	176175942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs964768927	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	12	23	0	ENST00000367669.3:c.173C>T	p.Ser58Leu	p.S58L	ENST00000367669	NM_022457.5	58	tCg/tTg	1/20	0.505884697780975	6	FACETS	0.757	0.544	1	0.505	0.363	0.671	CLONAL	2	TRUE	3	0.505884697780975	6		23	63	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466805	25466805	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	429	435	0	ENST00000264709.3:c.1898C>A	p.Pro633His	p.P633H	ENST00000264709	NM_175629.2	633	cCc/cAc	16/23	0.505366331987823	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.505884697780975	4		435	1210	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728766	190728766	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	133	305	0	ENST00000441310.2:c.2154A>C	p.Leu718Phe	p.L718F	ENST00000441310	NM_000534.4	718	ttA/ttC	10/13	0.505366331987823	4	FACETS	0.91	0.826	0.998	0.455	0.413	0.499	CLONAL	1	TRUE	2	0.505884697780975	4		305	870	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209106780	209106780	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	180	455	1	ENST00000345146.2:c.788G>T	p.Gly263Val	p.G263V	ENST00000345146	NM_005896.2	263	gGa/gTa	7/10	0.505884697780975	2	FACETS	0.876	0.809	0.946	0.438	0.404	0.473	CLONAL	1	TRUE	0	0.505884697780975	2		456	812	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138409908	138409908	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1674	218	469	0	ENST00000289153.2:c.1970C>G	p.Ser657Cys	p.S657C	ENST00000289153	NM_006219.2	657	tCt/tGt	13/22	0.505884697780975	6	FACETS	0.916	0.849	0.987			1	CLONAL	1	TRUE	NA	0.505884697780975	6		469	1892	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138423286	138423286	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1501	201	497	0	ENST00000289153.2:c.1580C>T	p.Ser527Leu	p.S527L	ENST00000289153	NM_006219.2	527	tCa/tTa	10/22	0.505884697780975	6	FACETS	0.939	0.867	1			1	CLONAL	1	TRUE	NA	0.505884697780975	6		497	1702	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226829	142226829	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	183	424	0	ENST00000350721.4:c.4975G>T	p.Glu1659Ter	p.E1659*	ENST00000350721	NM_001184.3	1659	Gaa/Taa	28/47	0.505884697780975	2	FACETS	1	0.964	1	0.533	0.493	0.573	CLONAL	1	TRUE	0	0.505884697780975	2		424	679	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629511	187629511	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	175	390	0	ENST00000441802.2:c.1471G>C	p.Asp491His	p.D491H	ENST00000441802	NM_005245.3	491	Gat/Cat	2/27	1	2	FACETS	0.966	0.892	1	0.966	0.892	1	CLONAL	1	TRUE	1	0.505884697780975	2		390	716	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178610	56178610	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs759009214	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	319	333	0	ENST00000399503.3:c.3583A>G	p.Met1195Val	p.M1195V	ENST00000399503	NM_005921.1	1195	Atg/Gtg	14/20	0.505366331987823	4	FACETS	0.996	0.943	1	0.996	0.943	1	CLONAL	2	TRUE	2	0.505884697780975	4		333	953	SUCCESS
APC	324	MSKCC	GRCh37	5	112174929	112174929	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554085199	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	166	344	0	ENST00000257430.4:c.3638C>T	p.Ser1213Leu	p.S1213L	ENST00000257430	NM_000038.5	1213	tCa/tTa	16/16	0.505884697780975	3	FACETS	0.985	0.905	1	0.492	0.452	0.534	CLONAL	1	TRUE	1	0.505884697780975	3		344	835	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672780	30672780	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1276	274	565	0	ENST00000376406.3:c.4180G>A	p.Gly1394Arg	p.G1394R	ENST00000376406	NM_014641.2	1394	Gga/Aga	10/15	0.505366331987823	4	FACETS	1	0.968	1	0.526	0.492	0.561	CLONAL	1	TRUE	2	0.505884697780975	4		565	1550	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519599	137519599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	217	533	1	ENST00000367739.4:c.1039G>A	p.Glu347Lys	p.E347K	ENST00000367739	NM_000416.2	347	Gaa/Aaa	7/7	0.505884697780975	2	FACETS	1	0.936	1	0.502	0.468	0.538	CLONAL	1	TRUE	0	0.505884697780975	2		534	854	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508841	106508841	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	164	368	0	ENST00000359195.3:c.835G>C	p.Glu279Gln	p.E279Q	ENST00000359195	NM_002649.2	279	Gag/Cag	2/11	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.505884697780975	2		368	632	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151871283	151871283	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	203	422	0	ENST00000262189.6:c.9307G>A	p.Ala3103Thr	p.A3103T	ENST00000262189	NM_170606.2	3103	Gcc/Acc	39/59	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.505884697780975	2		422	786	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878871	151878871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1483929906	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	188	349	0	ENST00000262189.6:c.6074C>T	p.Ser2025Leu	p.S2025L	ENST00000262189	NM_170606.2	2025	tCa/tTa	36/59	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.505884697780975	2		349	701	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606202	93606202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	135	343	0	ENST00000375746.1:c.22G>A	p.Asp8Asn	p.D8N	ENST00000375746	NM_001174167.1	8	Gac/Aac	2/14	1	2	FACETS	0.862	0.786	0.942	0.862	0.786	0.942	CLONAL	1	TRUE	1	0.505884697780975	2		343	619	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753929	133753929	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	165	377	1	ENST00000318560.5:c.1398G>C	p.Glu466Asp	p.E466D	ENST00000318560	NM_005157.4	466	gaG/gaC	8/11	1	2	FACETS	0.987	0.909	1	0.987	0.909	1	CLONAL	1	TRUE	1	0.505884697780975	2		378	661	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760670	133760670	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1009628344	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	218	423	1	ENST00000318560.5:c.2993C>T	p.Ser998Phe	p.S998F	ENST00000318560	NM_005157.4	998	tCt/tTt	11/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.505884697780975	2		424	824	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772611	135772611	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	292	682	0	ENST00000298552.3:c.2935G>C	p.Glu979Gln	p.E979Q	ENST00000298552	NM_001162426.1	979	Gaa/Caa	22/23	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.505884697780975	2		682	1151	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620362	43620362	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	148	277	0	ENST00000355710.3:c.2971G>T	p.Glu991Ter	p.E991*	ENST00000355710	NM_020975.4	991	Gag/Tag	18/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.505884697780975	2		277	531	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577476	64577476	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	179	438	0	ENST00000312049.6:c.106C>T	p.Leu36Phe	p.L36F	ENST00000312049	NM_130799.2	36	Ctc/Ttc	2/10	0.505884697780975	3	FACETS	0.995	0.918	1	0.498	0.459	0.538	CLONAL	1	TRUE	1	0.505884697780975	3		438	891	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173658	108173658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	147	385	0	ENST00000278616.4:c.5398G>A	p.Glu1800Lys	p.E1800K	ENST00000278616	NM_000051.3	1800	Gaa/Aaa	36/63	0.505884697780975	3	FACETS	0.832	0.76	0.908	0.416	0.38	0.454	CLONAL	1	TRUE	1	0.505884697780975	3		385	875	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375233	118375233	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	168	385	0	ENST00000534358.1:c.8626G>C	p.Glu2876Gln	p.E2876Q	ENST00000534358	NM_005933.3	2876	Gaa/Caa	27/36	0.505884697780975	3	FACETS	0.924	0.849	1	0.462	0.424	0.501	CLONAL	1	TRUE	1	0.505884697780975	3		385	901	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254641	46254641	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	189	503	1	ENST00000334344.6:c.4831C>A	p.Gln1611Lys	p.Q1611K	ENST00000334344	NM_152641.2	1611	Cag/Aag	16/21	0.505884697780975	3	FACETS	0.88	0.812	0.95	0.44	0.406	0.475	CLONAL	1	TRUE	1	0.505884697780975	3		504	1064	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864313	57864313	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1361	255	592	1	ENST00000228682.2:c.1790G>A	p.Arg597Lys	p.R597K	ENST00000228682	NM_005269.2	597	aGa/aAa	12/12	0.505366331987823	4	FACETS	0.939	0.877	1	0.47	0.438	0.503	CLONAL	1	TRUE	2	0.505884697780975	4		593	1616	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28971181	28971181	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	136	349	0	ENST00000282397.4:c.1576G>A	p.Asp526Asn	p.D526N	ENST00000282397	NM_002019.4	526	Gac/Aac	12/30	0.505884697780975	2	FACETS	0.822	0.749	0.898	0.411	0.374	0.449	CLONAL	1	TRUE	0	0.505884697780975	2		349	654	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961099	41961099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	189	481	0	ENST00000219905.7:c.7G>A	p.Glu3Lys	p.E3K	ENST00000219905	NM_001164273.1	3	Gag/Aag	2/24	0.505884697780975	3	FACETS	0.849	0.783	0.917	0.424	0.391	0.459	CLONAL	1	TRUE	1	0.505884697780975	3		481	1103	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029338	14029338	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150291286	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	241	481	0	ENST00000311895.7:c.1549G>A	p.Glu517Lys	p.E517K	ENST00000311895	NM_005236.2	517	Gaa/Aaa	8/11	0.505884697780975	3	FACETS	1	0.956	1	0.515	0.481	0.551	CLONAL	1	TRUE	1	0.505884697780975	3		481	1158	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122397	17122397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	199	500	0	ENST00000285071.4:c.998C>T	p.Ser333Leu	p.S333L	ENST00000285071	NM_144997.5	333	tCa/tTa	9/14	1	2	FACETS	0.987	0.916	1	0.987	0.916	1	CLONAL	1	TRUE	1	0.505884697780975	2		500	797	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553697	29553697	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs778344080	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	129	281	0	ENST00000356175.3:c.2246C>G	p.Ser749Ter	p.S749*	ENST00000356175	NM_000267.3	749	tCa/tGa	18/57	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.505884697780975	2		281	501	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679291	29679291	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555536340	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	176	414	0	ENST00000356175.3:c.7411C>T	p.Gln2471Ter	p.Q2471*	ENST00000356175	NM_000267.3	2471	Cag/Tag	50/57	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.505884697780975	2		414	690	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222277	2222277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	175	372	0	ENST00000398665.3:c.3109C>T	p.Pro1037Ser	p.P1037S	ENST00000398665	NM_032482.2	1037	Cct/Tct	24/28	1	2	FACETS	0.974	0.9	1	0.974	0.9	1	CLONAL	1	TRUE	1	0.505884697780975	2		372	710	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764328	39764328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747584221	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	143	330	0	ENST00000288319.7:c.784G>A	p.Gly262Ser	p.G262S	ENST00000288319	NM_182918.3	262	Ggt/Agt	7/10	0.505884697780975	3	FACETS	1	0.939	1	0.517	0.472	0.564	CLONAL	1	TRUE	1	0.505884697780975	3		330	685	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817464	39817464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	212	436	0	ENST00000288319.7:c.99G>A	p.Met33Ile	p.M33I	ENST00000288319	NM_182918.3	33	atG/atA	2/10	0.505884697780975	3	FACETS	1	0.953	1	0.517	0.48	0.555	CLONAL	1	TRUE	1	0.505884697780975	3		436	1016	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221638	22221638	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	82	164	0	ENST00000215832.6:c.93C>G	p.Ile31Met	p.I31M	ENST00000215832	NM_002745.4	31	atC/atG	1/9	0.505884697780975	2	FACETS	0.908	0.807	1	0.454	0.403	0.508	CLONAL	1	TRUE	0	0.505884697780975	2		164	357	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938499	76938499	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	182	417	1	ENST00000373344.5:c.2249C>A	p.Ser750Ter	p.S750*	ENST00000373344	NM_000489.3	750	tCa/tAa	9/35	0.505884697780975	3	FACETS	0.932	0.86	1	0.466	0.43	0.504	CLONAL	1	TRUE	1	0.505884697780975	3		418	967	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179161	123179161	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	227	453	0	ENST00000218089.9:c.610C>T	p.Leu204Phe	p.L204F	ENST00000218089	NM_001042749.1	204	Ctt/Ttt	8/35	0.505884697780975	3	FACETS	1	0.968	1	0.533	0.497	0.571	CLONAL	1	TRUE	1	0.505884697780975	3		453	1054	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123499661	123499661	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1290371898	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	245	583	0	ENST00000371139.4:c.188C>T	p.Ser63Phe	p.S63F	ENST00000371139	NM_001114937.2	63	tCt/tTt	2/4	0.505884697780975	3	FACETS	0.982	0.916	1	0.491	0.458	0.525	CLONAL	1	TRUE	1	0.505884697780975	3		583	1236	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100903	27100915	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGCAGGGGCAG	TGGGCAGGGGCAG	-	novel	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	180	448	0	ENST00000324856.7:c.4185_4197del	p.Gly1396LeufsTer81	p.G1396Lfs*81	ENST00000324856	NM_006015.4	1395	acTGGGCAGGGGCAG/ac	18/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.505884697780975	2		448	678	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958520	175958521	+	missense_variant	Missense_Mutation	DNP	TC	TC	CA	novel	NA	P-0009602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1645	184	484	0	ENST00000367669.3:c.1824_1825delinsTG	p.Ser609Gly	p.S609G	ENST00000367669	NM_022457.5	608	gtGAgt/gtTGgt	16/20	0.505884697780975	6	FACETS	0.8	0.735	0.868	0.267	0.245	0.29	SUBCLONAL	1	TRUE	3	0.505884697780975	6		484	1829	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0009608-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	96	324	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	0.884	0.787	0.988	1	0.984	1	CLONAL	2	TRUE	1	0.13	2		324	835	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0009608-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	43	649	2	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.97	0.81	1	0.97	0.81	1	CLONAL	1	TRUE	1	0.13	2		651	682	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508614	106508614	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377001952	NA	P-0009608-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	27	310	0	ENST00000359195.3:c.608C>T	p.Thr203Met	p.T203M	ENST00000359195	NM_002649.2	203	aCg/aTg	2/11	1	2	FACETS	0.778	0.617	0.962	0.778	0.617	0.962	CLONAL	1	TRUE	1	0.13	2		310	534	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135023	2135023	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs144062721	NA	P-0009608-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	58	607	0	ENST00000219476.3:c.4565A>G	p.Asn1522Ser	p.N1522S	ENST00000219476	NM_000548.3	1522	aAt/aGt	35/42	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.13	2		607	875	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0009612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	120	207	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.751	0.69	0.814			1	INDETERMINATE	2	TRUE	NA	0.546908044656784	2		207	292	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781324	3781326	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs587783502	NA	P-0009612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	180	390	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	0.546908044656784	2		390	636	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470554	25470554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759380437	NA	P-0009612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	189	412	0	ENST00000264709.3:c.920C>T	p.Pro307Leu	p.P307L	ENST00000264709	NM_175629.2	307	cCa/cTa	8/23	0.185956239790277	3	FACETS	1	0.989	1	0.678	0.629	0.728	INDETERMINATE	1	TRUE	1	0.546908044656784	3		412	649	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711875	89711875	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587782603	NA	P-0009612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	165	297	0	ENST00000371953.3:c.493G>A	p.Gly165Arg	p.G165R	ENST00000371953	NM_000314.4	165	Gga/Aga	6/9	0.257097325299043	1	FACETS	1	0.978	1	1	0.978	1	INDETERMINATE	1	TRUE	0	0.546908044656784	1		297	389	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222317	2222317	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009612-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	174	355	0	ENST00000398665.3:c.3149C>G	p.Thr1050Ser	p.T1050S	ENST00000398665	NM_032482.2	1050	aCc/aGc	24/28	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.546908044656784	2		355	634	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0009624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	129	286	1	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		287	1042	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0009624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	213	397	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		397	1072	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157454269	157454269	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554301237	NA	P-0009624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	148	460	0	ENST00000346085.5:c.2479G>T	p.Gly827Ter	p.G827*	ENST00000346085	NM_020732.3	827	Gga/Tga	8/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		460	1068	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220597	1220597	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	112	380	0	ENST00000326873.7:c.616del	p.Ala206ArgfsTer81	p.A206Rfs*81	ENST00000326873	NM_000455.4	205	gcG/gc	5/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		380	927	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	243	661	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.486952247242487	2		663	944	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098393	11098393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	205	405	1	ENST00000358026.2:c.911C>T	p.Pro304Leu	p.P304L	ENST00000358026	NM_001128849.1	304	cCc/cTc	6/36	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.486952247242487	2		406	797	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350094	81350094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1315332617	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	256	424	0	ENST00000222390.5:c.1238C>T	p.Ser413Leu	p.S413L	ENST00000222390	NM_000601.4	413	tCa/tTa	10/18	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.486952247242487	2		424	916	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459558	50459558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	138	258	0	ENST00000331340.3:c.847C>T	p.Leu283Phe	p.L283F	ENST00000331340	NM_006060.4	283	Ctt/Ttt	7/8	1	2	FACETS	0.891	0.813	0.972	0.891	0.813	0.972	CLONAL	1	TRUE	1	0.486952247242487	2		258	636	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924381	131924381	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1341798216	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	101	117	0	ENST00000265335.6:c.1054C>T	p.Arg352Cys	p.R352C	ENST00000265335		352	Cgt/Tgt	8/25	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.486952247242487	2		117	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577537	7577538	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	160	372	2	ENST00000269305.4:c.743_744delinsAA	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGG/cAA	7/11	1	2	FACETS	0.825	0.757	0.895	0.825	0.757	0.895	CLONAL	1	TRUE	1	0.486952247242487	2		374	797	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73351584	73351584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	188	375	0	ENST00000377767.4:c.628C>T	p.Arg210Cys	p.R210C	ENST00000377767	NM_014953.3	210	Cgt/Tgt	4/21	1	2	FACETS	0.863	0.798	0.93	0.863	0.798	0.93	CLONAL	1	TRUE	1	0.486952247242487	2		375	895	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209103871	209103871	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	246	444	1	ENST00000345146.2:c.1078G>A	p.Glu360Lys	p.E360K	ENST00000345146	NM_005896.2	360	Gaa/Aaa	9/10	1	2	FACETS	0.998	0.934	1	0.998	0.934	1	CLONAL	1	TRUE	1	0.486952247242487	2		445	1012	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509849	106509849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426277818	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	239	450	0	ENST00000359195.3:c.1843G>A	p.Glu615Lys	p.E615K	ENST00000359195	NM_002649.2	615	Gaa/Aaa	2/11	1	2	FACETS	0.96	0.897	1	0.96	0.897	1	CLONAL	1	TRUE	1	0.486952247242487	2		450	1022	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256666	16256666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	153	301	0	ENST00000375759.3:c.3931C>T	p.Pro1311Ser	p.P1311S	ENST00000375759	NM_015001.2	1311	Cct/Tct	11/15	1	2	FACETS	0.991	0.91	1	0.991	0.91	1	CLONAL	1	TRUE	1	0.486952247242487	2		301	634	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462882	120462882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	149	280	0	ENST00000256646.2:c.5449G>A	p.Asp1817Asn	p.D1817N	ENST00000256646	NM_024408.3	1817	Gat/Aat	30/34	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.486952247242487	2		280	610	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068357	26068357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	176	358	1	ENST00000435504.4:c.133G>A	p.Glu45Lys	p.E45K	ENST00000435504		45	Gaa/Aaa	2/13	1	2	FACETS	0.939	0.866	1	0.939	0.866	1	CLONAL	1	TRUE	1	0.486952247242487	2		359	770	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898711	134898711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	195	420	0	ENST00000398015.3:c.1769G>A	p.Gly590Glu	p.G590E	ENST00000398015	NM_004441.4	590	gGg/gAg	10/16	1	2	FACETS	0.915	0.848	0.985	0.915	0.848	0.985	CLONAL	1	TRUE	1	0.486952247242487	2		420	875	SUCCESS
ATR	545	MSKCC	GRCh37	3	142184073	142184073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	148	295	0	ENST00000350721.4:c.6907C>T	p.Leu2303Phe	p.L2303F	ENST00000350721	NM_001184.3	2303	Ctt/Ttt	41/47	1	2	FACETS	0.929	0.851	1	0.929	0.851	1	CLONAL	1	TRUE	1	0.486952247242487	2		295	654	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808882	1808882	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748492376	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	216	551	3	ENST00000260795.2:c.2314C>T	p.Pro772Ser	p.P772S	ENST00000260795		772	Ccg/Tcg	17/17	1	2	FACETS	0.967	0.9	1	0.967	0.9	1	CLONAL	1	TRUE	1	0.486952247242487	2		554	917	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955558	55955558	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	255	521	0	ENST00000263923.4:c.3387T>A	p.Asp1129Glu	p.D1129E	ENST00000263923	NM_002253.2	1129	gaT/gaA	25/30	1	2	FACETS	0.985	0.922	1	0.985	0.922	1	CLONAL	1	TRUE	1	0.486952247242487	2		521	1063	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094790	143094790	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	123	311	0	ENST00000262992.4:c.1354G>A	p.Glu452Lys	p.E452K	ENST00000262992	NM_001101669.1	452	Gaa/Aaa	14/24	1	2	FACETS	0.787	0.713	0.864	0.787	0.713	0.864	SUBCLONAL	1	TRUE	1	0.486952247242487	2		311	642	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114319	143114319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758982158	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	189	365	1	ENST00000262992.4:c.1102G>A	p.Ala368Thr	p.A368T	ENST00000262992	NM_001101669.1	368	Gcc/Acc	13/24	1	2	FACETS	0.984	0.911	1	0.984	0.911	1	CLONAL	1	TRUE	1	0.486952247242487	2		366	789	SUCCESS
APC	324	MSKCC	GRCh37	5	112090642	112090642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	219	396	0	ENST00000257430.4:c.55G>A	p.Glu19Lys	p.E19K	ENST00000257430	NM_000038.5	19	Gag/Aag	2/16	1	2	FACETS	0.995	0.927	1	0.995	0.927	1	CLONAL	1	TRUE	1	0.486952247242487	2		396	904	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068019	94068019	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	283	504	0	ENST00000369303.4:c.943G>C	p.Gly315Arg	p.G315R	ENST00000369303	NM_004440.3	315	Ggg/Cgg	4/17	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.486952247242487	2		504	1148	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111995704	111995704	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	252	506	1	ENST00000368678.4:c.1394C>A	p.Pro465Gln	p.P465Q	ENST00000368678		465	cCa/cAa	12/13	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.486952247242487	2		507	1034	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729265	41729265	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	293	567	0	ENST00000242208.4:c.1264G>A	p.Glu422Lys	p.E422K	ENST00000242208	NM_002192.2	422	Gag/Aag	3/3	1	2	FACETS	0.927	0.871	0.985	0.927	0.871	0.985	CLONAL	1	TRUE	1	0.486952247242487	2		567	1298	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508079	106508079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	113	191	0	ENST00000359195.3:c.73C>T	p.Pro25Ser	p.P25S	ENST00000359195	NM_002649.2	25	Ccg/Tcg	2/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.486952247242487	2		191	414	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514459	148514459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	251	366	0	ENST00000320356.2:c.1265C>T	p.Pro422Leu	p.P422L	ENST00000320356	NM_004456.4	422	cCa/cTa	11/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.486952247242487	2		366	1004	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878448	151878448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	174	377	0	ENST00000262189.6:c.6497C>T	p.Pro2166Leu	p.P2166L	ENST00000262189	NM_170606.2	2166	cCc/cTc	36/59	1	2	FACETS	0.842	0.776	0.911	0.842	0.776	0.911	CLONAL	1	TRUE	1	0.486952247242487	2		377	849	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492974	8492974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	142	285	0	ENST00000356435.5:c.2355G>A	p.Met785Ile	p.M785I	ENST00000356435		785	atG/atA	16/35	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.486952247242487	2		285	557	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507308	8507308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	195	428	2	ENST00000356435.5:c.1670G>A	p.Gly557Glu	p.G557E	ENST00000356435		557	gGa/gAa	11/35	1	2	FACETS	0.93	0.862	1	0.93	0.862	1	CLONAL	1	TRUE	1	0.486952247242487	2		430	861	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915925	127915925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	304	566	0	ENST00000373547.4:c.556C>T	p.Pro186Ser	p.P186S	ENST00000373547	NM_002721.4	186	Cct/Tct	6/7	0.471112060639965	2	FACETS	1	0.965	1	0.517	0.487	0.548	CLONAL	1	TRUE	0	0.486952247242487	2		566	1207	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730217	133730217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	408	341	0	ENST00000318560.5:c.283C>T	p.His95Tyr	p.H95Y	ENST00000318560	NM_005157.4	95	Cac/Tac	3/11	0.471112060639965	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.486952247242487	2		341	796	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730241	133730241	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	180	368	0	ENST00000318560.5:c.307C>T	p.Gln103Ter	p.Q103*	ENST00000318560	NM_005157.4	103	Caa/Taa	3/11	0.471112060639965	2	FACETS	0.859	0.792	0.927	0.429	0.396	0.464	CLONAL	1	TRUE	0	0.486952247242487	2		368	861	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139411837	139411837	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	353	360	0	ENST00000277541.6:c.1442G>A	p.Gly481Asp	p.G481D	ENST00000277541	NM_017617.3	481	gGc/gAc	9/34	0.471112060639965	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.486952247242487	2		360	711	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70442648	70442648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	267	376	2	ENST00000373644.4:c.4970C>T	p.Pro1657Leu	p.P1657L	ENST00000373644	NM_030625.2	1657	cCc/cTc	10/12	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.486952247242487	2		378	1009	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435247	18435247	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs775419502	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	216	389	0	ENST00000266497.5:c.232T>A	p.Leu78Ile	p.L78I	ENST00000266497		78	Tta/Ata	1/31	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.486952247242487	2		389	886	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243866	46243866	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	206	294	1	ENST00000334344.6:c.1960C>T	p.Pro654Ser	p.P654S	ENST00000334344	NM_152641.2	654	Cct/Tct	15/21	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.486952247242487	2		295	779	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431837	49431837	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1271758887	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	94	220	0	ENST00000301067.7:c.9302C>T	p.Pro3101Leu	p.P3101L	ENST00000301067	NM_003482.3	3101	cCc/cTc	34/54	1	2	FACETS	0.904	0.809	1	0.904	0.809	1	CLONAL	1	TRUE	1	0.486952247242487	2		220	427	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588656	28588656	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367849862	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	233	414	0	ENST00000241453.7:c.2792G>A	p.Arg931Lys	p.R931K	ENST00000241453	NM_004119.2	931	aGg/aAg	23/24	1	2	FACETS	0.89	0.83	0.952	0.89	0.83	0.952	CLONAL	1	TRUE	1	0.486952247242487	2		414	1075	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727414	66727414	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	192	293	0	ENST00000307102.5:c.130G>A	p.Glu44Lys	p.E44K	ENST00000307102	NM_002755.3	44	Gag/Aag	2/11	1	2	FACETS	0.977	0.905	1	0.977	0.905	1	CLONAL	1	TRUE	1	0.486952247242487	2		293	807	SUCCESS
BLM	641	MSKCC	GRCh37	15	91333880	91333880	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	195	302	0	ENST00000355112.3:c.2825T>C	p.Val942Ala	p.V942A	ENST00000355112	NM_000057.2	942	gTt/gCt	15/22	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.486952247242487	2		302	746	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807365	3807365	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	179	347	0	ENST00000262367.5:c.3622C>T	p.Pro1208Ser	p.P1208S	ENST00000262367	NM_004380.2	1208	Cca/Tca	19/31	1	2	FACETS	0.895	0.827	0.967	0.895	0.827	0.967	CLONAL	1	TRUE	1	0.486952247242487	2		347	821	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858642	9858642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	231	490	0	ENST00000330684.3:c.2759G>A	p.Arg920Lys	p.R920K	ENST00000330684	NM_001134407.1	920	aGa/aAa	13/13	1	2	FACETS	0.985	0.919	1	0.985	0.919	1	CLONAL	1	TRUE	1	0.486952247242487	2		490	963	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274180	10274180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567354651	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	98	257	0	ENST00000330684.3:c.89G>A	p.Gly30Asp	p.G30D	ENST00000330684	NM_001134407.1	30	gGt/gAt	2/13	1	2	FACETS	0.818	0.733	0.908	0.818	0.733	0.908	CLONAL	1	TRUE	1	0.486952247242487	2		257	492	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346903	89346903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1190073937	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	141	308	0	ENST00000301030.4:c.6047C>T	p.Pro2016Leu	p.P2016L	ENST00000301030	NM_001256183.1	2016	cCc/cTc	9/13	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.486952247242487	2		308	460	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836333	89836333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747545118	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	217	356	0	ENST00000389301.3:c.2416C>T	p.Pro806Ser	p.P806S	ENST00000389301	NM_000135.2	806	Cct/Tct	26/43	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.486952247242487	2		356	741	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653001	29653001	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs865781825	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	287	486	1	ENST00000356175.3:c.4936C>T	p.Pro1646Ser	p.P1646S	ENST00000356175	NM_000267.3	1646	Cct/Tct	36/57	1	2	FACETS	0.973	0.915	1	0.973	0.915	1	CLONAL	1	TRUE	1	0.486952247242487	2		487	1211	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677858	47677858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	173	329	0	ENST00000347630.2:c.1007C>T	p.Ser336Phe	p.S336F	ENST00000347630	NM_001007230.1	336	tCt/tTt	11/11	1	2	FACETS	0.976	0.901	1	0.976	0.901	1	CLONAL	1	TRUE	1	0.486952247242487	2		329	728	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637978	39637978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1406322792	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	200	355	0	ENST00000262039.4:c.2395C>T	p.Arg799Cys	p.R799C	ENST00000262039	NM_002647.2	799	Cgt/Tgt	22/25	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.486952247242487	2		355	807	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56411576	56411576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	220	541	0	ENST00000348428.3:c.1760C>T	p.Pro587Leu	p.P587L	ENST00000348428	NM_006785.3	587	cCa/cTa	15/17	1	2	FACETS	0.908	0.845	0.973	0.908	0.845	0.973	CLONAL	1	TRUE	1	0.486952247242487	2		541	995	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621917	1621917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1215598833	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	226	544	0	ENST00000344749.5:c.875C>T	p.Ser292Phe	p.S292F	ENST00000344749	NM_001136139.2	292	tCc/tTc	11/19	1	2	FACETS	0.994	0.927	1	0.994	0.927	1	CLONAL	1	TRUE	1	0.486952247242487	2		544	934	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302906	15302906	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28933697	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	145	278	0	ENST00000263388.2:c.544C>T	p.Arg182Cys	p.R182C	ENST00000263388	NM_000435.2	182	Cgc/Tgc	4/33	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.486952247242487	2		278	579	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349918	15349918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293348757	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	144	235	0	ENST00000263377.2:c.3734C>T	p.Ala1245Val	p.A1245V	ENST00000263377	NM_058243.2	1245	gCc/gTc	18/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.486952247242487	2		235	516	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727958	41727958	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	137	331	0	ENST00000301178.4:c.583C>T	p.Pro195Ser	p.P195S	ENST00000301178	NM_021913.4	195	Cca/Tca	4/20	1	2	FACETS	0.959	0.875	1	0.959	0.875	1	CLONAL	1	TRUE	1	0.486952247242487	2		331	587	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758303	41758303	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	226	523	0	ENST00000301178.4:c.1759G>A	p.Val587Ile	p.V587I	ENST00000301178	NM_021913.4	587	Gtc/Atc	15/20	1	2	FACETS	0.985	0.919	1	0.985	0.919	1	CLONAL	1	TRUE	1	0.486952247242487	2		523	942	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39706232	39706232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375933660	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	223	372	1	ENST00000361337.2:c.290C>T	p.Ser97Phe	p.S97F	ENST00000361337	NM_003286.2	97	tCt/tTt	5/21	1	2	FACETS	0.974	0.908	1	0.974	0.908	1	CLONAL	1	TRUE	1	0.486952247242487	2		373	940	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41562638	41562638	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764929476	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	212	361	1	ENST00000263253.7:c.3842G>A	p.Arg1281Gln	p.R1281Q	ENST00000263253	NM_001429.3	1281	cGa/cAa	23/31	1	2	FACETS	0.96	0.893	1	0.96	0.893	1	CLONAL	1	TRUE	1	0.486952247242487	2		362	907	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933346	39933346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1176327750	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	262	561	0	ENST00000378444.4:c.1253G>A	p.Arg418Lys	p.R418K	ENST00000378444	NM_001123385.1	418	aGa/aAa	4/15	1	2	FACETS	0.909	0.851	0.969	0.909	0.851	0.969	CLONAL	1	TRUE	1	0.486952247242487	2		561	1184	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424498	47424498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	211	436	1	ENST00000377045.4:c.418G>A	p.Val140Ile	p.V140I	ENST00000377045	NM_001654.4	140	Gtc/Atc	5/16	1	2	FACETS	0.935	0.869	1	0.935	0.869	1	CLONAL	1	TRUE	1	0.486952247242487	2		437	927	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424746	47424746	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	255	481	0	ENST00000377045.4:c.554C>T	p.Pro185Leu	p.P185L	ENST00000377045	NM_001654.4	185	cCc/cTc	6/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.486952247242487	2		481	984	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361204	70361204	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1212501146	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	253	440	1	ENST00000374080.3:c.6392C>T	p.Pro2131Leu	p.P2131L	ENST00000374080		2131	cCc/cTc	43/45	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.486952247242487	2		441	984	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220477	123220477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1372684971	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	307	501	0	ENST00000218089.9:c.3134G>A	p.Arg1045Gln	p.R1045Q	ENST00000218089	NM_001042749.1	1045	cGa/cAa	30/35	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.486952247242487	2		501	1166	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218586	98218587	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TA	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	199	386	0	ENST00000331920.6:c.3277_3278delinsTA	p.Gly1093Ter	p.G1093*	ENST00000331920	NM_000264.3	1093	GGa/TAa	19/24	0.486952247242487	1	FACETS	0.934	0.869	1	0.934	0.869	1	CLONAL	1	TRUE	0	0.486952247242487	1		386	662	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351871	89351872	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1205	337	683	0	ENST00000301030.4:c.1078_1079delinsTT	p.Pro360Leu	p.P360L	ENST00000301030	NM_001256183.1	360	CCg/TTg	9/13	1	2	FACETS	0.898	0.847	0.95	0.898	0.847	0.95	CLONAL	1	TRUE	1	0.486952247242487	2		683	1542	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985553	2985554	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	183	426	0	ENST00000396946.4:c.257_258delinsAA	p.Arg86Lys	p.R86K	ENST00000396946	NM_032415.4	86	aGG/aAA	4/25	1	2	FACETS	0.926	0.856	0.998	0.926	0.856	0.998	CLONAL	1	TRUE	1	0.486952247242487	2		426	812	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226545	2226546	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	135	376	0	ENST00000398665.3:c.4025_4026delinsTT	p.Pro1342Leu	p.P1342L	ENST00000398665	NM_032482.2	1342	cCC/cTT	27/28	1	2	FACETS	0.907	0.828	0.991	0.907	0.828	0.991	CLONAL	1	TRUE	1	0.486952247242487	2		376	611	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159753	20159754	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	116	305	0	ENST00000379607.5:c.5_6delinsTT	p.Pro2Leu	p.P2L	ENST00000379607	NM_001412.3	2	cCC/cTT	1/7	1	2	FACETS	0.922	0.834	1	0.922	0.834	1	CLONAL	1	TRUE	1	0.486952247242487	2		305	517	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661079	227661080	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	144	376	0	ENST00000305123.5:c.2375_2376delinsTT	p.Ser792Phe	p.S792F	ENST00000305123	NM_005544.2	792	tCC/tTT	1/2	1	2	FACETS	0.942	0.862	1	0.942	0.862	1	CLONAL	1	TRUE	1	0.486952247242487	2		376	628	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976860	55976861	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	210	432	0	ENST00000263923.4:c.1051_1052delinsTT	p.Pro351Phe	p.P351F	ENST00000263923	NM_002253.2	351	CCt/TTt	8/30	1	2	FACETS	0.919	0.853	0.986	0.919	0.853	0.986	CLONAL	1	TRUE	1	0.486952247242487	2		432	939	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375003	118375004	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	130	273	0	ENST00000534358.1:c.8396_8397delinsTT	p.Ser2799Phe	p.S2799F	ENST00000534358	NM_005933.3	2799	tCC/tTT	27/36	1	2	FACETS	0.824	0.749	0.902	0.824	0.749	0.902	CLONAL	1	TRUE	1	0.486952247242487	2		273	648	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446463	49446464	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	104	219	0	ENST00000301067.7:c.1141_1142delinsTT	p.Pro381Phe	p.P381F	ENST00000301067	NM_003482.3	381	CCc/TTc	9/54	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.486952247242487	2		219	418	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968828	15968829	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	177	330	0	ENST00000268712.3:c.4921_4922delinsTT	p.Pro1641Leu	p.P1641L	ENST00000268712	NM_006311.3	1641	CCa/TTa	33/46	1	2	FACETS	0.862	0.795	0.932	0.862	0.795	0.932	CLONAL	1	TRUE	1	0.486952247242487	2		330	843	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983287	15983288	+	missense_variant	Missense_Mutation	DNP	AG	AG	TA	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	220	412	0	ENST00000268712.3:c.3491_3492delinsTA	p.Ser1164Leu	p.S1164L	ENST00000268712	NM_006311.3	1164	tCT/tTA	26/46	1	2	FACETS	0.997	0.929	1	0.997	0.929	1	CLONAL	1	TRUE	1	0.486952247242487	2		412	906	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871865	35871866	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	237	479	0	ENST00000216797.5:c.640_641delinsTT	p.Pro214Phe	p.P214F	ENST00000216797	NM_020529.2	214	CCc/TTc	5/6	1	2	FACETS	0.869	0.811	0.93	0.869	0.811	0.93	CLONAL	1	TRUE	1	0.486952247242487	2		479	1120	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104268943	104268944	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	242	508	0	ENST00000369902.3:c.200_201delinsTT	p.Pro67Leu	p.P67L	ENST00000369902	NM_016169.3	67	cCC/cTT	2/12	1	2	FACETS	0.97	0.906	1	0.97	0.906	1	CLONAL	1	TRUE	1	0.486952247242487	2		508	1025	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40477071	40477072	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009625-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	179	491	1	ENST00000264657.5:c.1373_1374delinsTT	p.Ser458Phe	p.S458F	ENST00000264657	NM_139276.2	458	tCC/tTT	16/24	1	2	FACETS	0.793	0.731	0.858	0.793	0.731	0.858	SUBCLONAL	1	TRUE	1	0.486952247242487	2		492	927	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591888	48591888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519739	NA	P-0009631-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	270	545	0	ENST00000342988.3:c.1051G>A	p.Asp351Asn	p.D351N	ENST00000342988	NM_005359.5	351	Gat/Aat	9/12	0.466498750274529	1	FACETS	0.986	0.927	1	0.986	0.927	1	CLONAL	1	TRUE	0	0.468606776308176	1		545	895	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578192	7578192	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009631-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	315	579	0	ENST00000269305.4:c.657del	p.Tyr220MetfsTer27	p.Y220Mfs*27	ENST00000269305	NM_001126112.2	219	ccC/cc	6/11	0.466498750274529	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.468606776308176	1		579	978	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250172	110250172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393858212	NA	P-0009631-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	55	265	0	ENST00000374672.4:c.503G>A	p.Gly168Asp	p.G168D	ENST00000374672	NM_004235.4	168	gGc/gAc	3/5	1	2	FACETS	0.599	0.514	0.691	0.599	0.514	0.691	SUBCLONAL	1	TRUE	1	0.468606776308176	2		265	392	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512392	38512392	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009631-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	660	340	0	ENST00000254066.5:c.1303G>A	p.Gly435Ser	p.G435S	ENST00000254066	NM_000964.3	435	Ggt/Agt	9/9	0.462531550746099	5	FACETS	1	0.994	1			1	CLONAL	4	TRUE	NA	0.468606776308176	5		340	1102	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0009637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	34	538	2	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.257447791812902	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.257447791812902	1		540	158	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944512	40944512	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	16	494	0	ENST00000373198.4:c.1990T>G	p.Phe664Val	p.F664V	ENST00000373198	NM_133170.3	664	Ttt/Gtt	12/32	1	2	FACETS	0.6	0.445	0.785	0.6	0.445	0.785	SUBCLONAL	1	TRUE	1	0.257447791812902	2		494	207	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748042	72748042	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	30	853	0	ENST00000357731.5:c.136G>A	p.Asp46Asn	p.D46N	ENST00000357731	NM_173808.2	46	Gac/Aac	1/7	0.257447791812902	1	FACETS	0.71	0.574	0.863	0.71	0.574	0.863	SUBCLONAL	1	TRUE	0	0.257447791812902	1		853	286	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443618	29443618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200585833	NA	P-0009637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	31	465	1	ENST00000389048.3:c.3599C>T	p.Ala1200Val	p.A1200V	ENST00000389048	NM_004304.4	1200	gCg/gTg	23/29	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.257447791812902	2		466	186	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0009640-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	145	463	1	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	0.374761214810666	2		464	626	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0009641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	272	562	1	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.465602647695915	2		563	1125	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	150	455	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.465602647695915	2	FACETS	1	0.946	1	0.52	0.477	0.565	CLONAL	1	TRUE	0	0.465602647695915	2		455	619	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0009641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	133	354	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.435565464708985	3	FACETS	0.965	0.877	1	0.482	0.438	0.528	CLONAL	1	TRUE	1	0.465602647695915	3		354	730	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057520007	NA	P-0009641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	459	542	1	ENST00000269305.4:c.614A>T	p.Tyr205Phe	p.Y205F	ENST00000269305	NM_001126112.2	205	tAt/tTt	6/11	0.465602647695915	2	FACETS	0.958	0.918	0.998	0.958	0.918	0.998	CLONAL	2	TRUE	0	0.465602647695915	2		543	1029	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871776	12871776	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0009641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	219	201	0	ENST00000228872.4:c.493A>T	p.Lys165Ter	p.K165*	ENST00000228872	NM_004064.3	165	Aaa/Taa	2/3	0.435565464708985	3	FACETS	0.979	0.918	1	0.979	0.918	1	CLONAL	2	TRUE	1	0.465602647695915	3		201	592	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241952	133241952	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	160	423	0	ENST00000320574.5:c.2404G>C	p.Asp802His	p.D802H	ENST00000320574	NM_006231.2	802	Gac/Cac	21/49	1	2	FACETS	0.797	0.731	0.866	0.797	0.731	0.866	SUBCLONAL	1	TRUE	1	0.465602647695915	2		423	862	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244953	133244953	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	225	559	0	ENST00000320574.5:c.2162G>C	p.Arg721Thr	p.R721T	ENST00000320574	NM_006231.2	721	aGa/aCa	19/49	1	2	FACETS	0.986	0.919	1	0.986	0.919	1	CLONAL	1	TRUE	1	0.465602647695915	2		559	980	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2114332	2114332	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	1128	559	0	ENST00000219476.3:c.1503C>A	p.Asp501Glu	p.D501E	ENST00000219476	NM_000548.3	501	gaC/gaA	15/42	0.465602647695915	7	FACETS	1	0.982	1	1	0.982	1	CLONAL	5	TRUE	2	0.465602647695915	7		559	2080	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	34	291	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		291	1141	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0009693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	40	439	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		440	981	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559089	29559089	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1131691089	NA	P-0009702-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	56	70	0	ENST00000356175.3:c.3198-2A>G		p.X1066_splice	ENST00000356175	NM_000267.3	1066			0.233229327912654	2	FACETS	0.834	0.726	0.947	1	0.957	1	CLONAL	3	TRUE	0	0.233229327912654	2		70	192	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858938	243858938	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009702-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	83	650	0	ENST00000263826.5:c.127C>T	p.Gln43Ter	p.Q43*	ENST00000263826	NM_005465.4	43	Caa/Taa	2/13	1	2	FACETS	0.634	0.558	0.717	0.634	0.558	0.717	SUBCLONAL	1	TRUE	1	0.233229327912654	2		650	1122	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40740972	40740972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009702-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	112	669	0	ENST00000392038.2:c.1346C>T	p.Thr449Ile	p.T449I	ENST00000392038	NM_001626.4	449	aCa/aTa	13/14	1	2	FACETS	0.828	0.743	0.919	0.828	0.743	0.919	CLONAL	1	TRUE	1	0.233229327912654	2		669	1160	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656829	45656829	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009702-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	71	438	0	ENST00000407780.3:c.327G>C	p.Gln109His	p.Q109H	ENST00000407780	NM_001283052.1	109	caG/caC	3/7	1	2	FACETS	0.823	0.717	0.937	0.823	0.717	0.937	CLONAL	1	TRUE	1	0.233229327912654	2		438	740	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074313	30074313	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0009702-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	55	295	0	ENST00000338641.4:c.1574+1G>A		p.X525_splice	ENST00000338641	NM_000268.3	525			1	2	FACETS	0.853	0.73	0.988	0.853	0.73	0.988	CLONAL	1	TRUE	1	0.233229327912654	2		295	553	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0009711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	42	207	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.894	0.746	1	0.894	0.746	1	CLONAL	1	TRUE	1	0.178884525663933	2		207	525	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0009711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6864	510	604	5	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.178884525663933	35	FACETS	1	0.964	1			1	CLONAL	3	TRUE	NA	0.178884525663933	35		609	7374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0009711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	98	376	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	1	2	FACETS	0.98	0.872	1	0.98	0.872	1	CLONAL	1	TRUE	1	0.178884525663933	2		376	1118	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857178	9857178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763219483	NA	P-0009711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1640	139	627	0	ENST00000330684.3:c.4223C>T	p.Thr1408Met	p.T1408M	ENST00000330684	NM_001134407.1	1408	aCg/aTg	13/13	1	2	FACETS	0.874	0.792	0.96	0.874	0.792	0.96	CLONAL	1	TRUE	1	0.178884525663933	2		627	1779	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	100	291	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.212249504606515	3	FACETS	1	0.979	1	0.703	0.629	0.782	CLONAL	1	TRUE	1	0.245290874825393	3		291	651	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0009765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	88	785	4	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.206833525705495	1	FACETS	0.771	0.683	0.867	0.771	0.683	0.867	SUBCLONAL	1	TRUE	0	0.245290874825393	1		789	816	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252155	226252155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	37	63	0	ENST00000366813.1:c.103G>T	p.Gly35Trp	p.G35W	ENST00000366813		35	Ggg/Tgg	1/3	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.585815923686312	2		63	117	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721265	176721267	+	missense_variant	Missense_Mutation	TNP	TCG	TCG	AGC	novel	NA	P-0009799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	148	242	0	ENST00000439151.2:c.6896_6898delinsAGC	p.Leu2299_Ala2300delinsGlnPro	p.L2299_A2300delinsQP	ENST00000439151	NM_022455.4	2299	cTCGct/cAGCct	23/23	1	2	FACETS	0.858	0.787	0.931	0.858	0.787	0.931	CLONAL	1	TRUE	1	0.585815923686312	2		242	589	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	105	291	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.851	0.762	0.947	0.851	0.762	0.947	CLONAL	1	TRUE	1	0.271661112655763	2		291	908	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149995	202149995	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	204	539	2	ENST00000358485.4:c.1436G>A	p.Trp479Ter	p.W479*	ENST00000358485	NM_001080125.1	479	tGg/tAg	8/9	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.271661112655763	2		541	1290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578188	7578188	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201592	NA	P-0009827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	214	688	0	ENST00000269305.4:c.661G>T	p.Glu221Ter	p.E221*	ENST00000269305	NM_001126112.2	221	Gag/Tag	6/11	0.271661112655763	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.271661112655763	1		688	1257	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632035	1632035	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0009827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1267	210	755	1	ENST00000344749.5:c.298+2T>C		p.X100_splice	ENST00000344749	NM_001136139.2	100			1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.271661112655763	2		756	1477	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0009855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	611	386	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.632583121725816	2	FACETS	0.968	0.938	0.997	0.968	0.938	0.997	CLONAL	2	FALSE	0	0.632583121725816	2		386	998	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748309	41748309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs894529129	NA	P-0009855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	239	350	0	ENST00000226382.2:c.460C>T	p.Arg154Cys	p.R154C	ENST00000226382	NM_003924.3	154	Cgc/Tgc	3/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.632583121725816	2		350	708	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362576	118362576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	304	468	0	ENST00000534358.1:c.4937C>T	p.Ser1646Phe	p.S1646F	ENST00000534358	NM_005933.3	1646	tCt/tTt	15/36	0.607376076788103	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	0	0.632583121725816	1		468	648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0009872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	603	785	4	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.486476298270111	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.486476298270111	2		789	1164	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0009872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	183	592	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.486476298270111	1	FACETS	0.868	0.804	0.933	0.868	0.804	0.933	CLONAL	1	TRUE	0	0.486476298270111	1		592	656	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508083	106508083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339698935	NA	P-0009872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	169	223	0	ENST00000359195.3:c.77G>A	p.Arg26His	p.R26H	ENST00000359195	NM_002649.2	26	cGc/cAc	2/11	0.486476298270111	3	FACETS	0.785	0.726	0.846	0.524	0.484	0.564	SUBCLONAL	2	TRUE	0	0.486476298270111	3		223	550	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745453	162745453	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	353	356	1	ENST00000367921.3:c.1868T>C	p.Leu623Pro	p.L623P	ENST00000367921	NM_006182.2	623	cTt/cCt	15/18	0.486476298270111	3	FACETS	0.921	0.874	0.968	0.921	0.874	0.968	CLONAL	2	TRUE	1	0.486476298270111	3		357	980	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511177	148511177	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	649	330	0	ENST00000320356.2:c.1725G>T	p.Gln575His	p.Q575H	ENST00000320356	NM_004456.4	575	caG/caT	15/20	0.486476298270111	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.486476298270111	3		330	1061	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	76	291	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.713	0.624	0.81	0.713	0.624	0.81	SUBCLONAL	1	TRUE	1	0.22	2		291	969	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980850	40980850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752620539	NA	P-0009899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	132	705	0	ENST00000373198.4:c.1636C>T	p.Arg546Trp	p.R546W	ENST00000373198	NM_133170.3	546	Cgg/Tgg	10/32	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.22	2		705	1095	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015040	37015040	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756345939	NA	P-0009899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	94	626	2	ENST00000358127.4:c.364C>T	p.Arg122Trp	p.R122W	ENST00000358127	NM_001280556.1	122	Cgg/Tgg	3/10	1	2	FACETS	0.769	0.682	0.862	0.769	0.682	0.862	SUBCLONAL	1	TRUE	1	0.22	2		628	1111	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72873620	72873620	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772128613	NA	P-0009901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	140	569	0	ENST00000325599.8:c.682G>A	p.Ala228Thr	p.A228T	ENST00000325599	NM_018130.2	228	Gcc/Acc	6/11	0.260756165098618	3	FACETS	0.975	0.886	1	0.487	0.443	0.535	CLONAL	1	TRUE	1	0.260756165098618	3		569	1245	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725504	117725504	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009917-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	74	421	0	ENST00000368508.3:c.377G>A	p.Gly126Glu	p.G126E	ENST00000368508	NM_002944.2	126	gGa/gAa	5/43	0.311486454889387	4	FACETS	0.736	0.643	0.836	0.368	0.321	0.418	SUBCLONAL	1	TRUE	2	0.362473853105039	4		421	756	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339500	81339500	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009917-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	123	625	0	ENST00000222390.5:c.1504C>G	p.Arg502Gly	p.R502G	ENST00000222390	NM_000601.4	502	Cga/Gga	13/18	0.295217995842479	4	FACETS	0.736	0.664	0.813	0.245	0.221	0.271	SUBCLONAL	1	TRUE	1	0.362473853105039	4		625	1256	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932239	39932239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376056253	NA	P-0009917-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	92	772	1	ENST00000378444.4:c.2360C>T	p.Pro787Leu	p.P787L	ENST00000378444	NM_001123385.1	787	cCg/cTg	4/15	0.354600797217326	2	FACETS	0.488	0.432	0.547	0.244	0.216	0.274	SUBCLONAL	1	TRUE	0	0.362473853105039	2		773	1041	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0009927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	73	439	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.17	2		440	762	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727455	66727455	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs869025608	NA	P-0009927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	59	453	0	ENST00000307102.5:c.171G>T	p.Lys57Asn	p.K57N	ENST00000307102	NM_002755.3	57	aaG/aaT	2/11	1	2	FACETS	0.939	0.807	1	0.939	0.807	1	CLONAL	1	TRUE	1	0.17	2		453	739	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44921977	44921977	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	87	611	0	ENST00000377967.4:c.1511T>C	p.Leu504Ser	p.L504S	ENST00000377967	NM_021140.2	504	tTa/tCa	15/29	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.17	2		611	1001	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0009930-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	22	261	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		261	677	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0009936-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	74	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.485	0.427	0.548	0.485	0.427	0.548	SUBCLONAL	1	TRUE	1	0.779812050964219	2		249	391	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510153	187510153	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367799188	NA	P-0009936-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	125	549	0	ENST00000441802.2:c.13360G>A	p.Glu4454Lys	p.E4454K	ENST00000441802	NM_005245.3	4454	Gaa/Aaa	27/27	1	2	FACETS	0.423	0.383	0.465	0.423	0.383	0.465	SUBCLONAL	1	TRUE	1	0.779812050964219	2		549	758	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467924	50467924	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009936-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	51	289	0	ENST00000331340.3:c.1159G>C	p.Glu387Gln	p.E387Q	ENST00000331340	NM_006060.4	387	Gag/Cag	8/8	1	2	FACETS	0.461	0.394	0.532	0.461	0.394	0.532	SUBCLONAL	1	TRUE	1	0.779812050964219	2		289	284	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117039	193117039	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009936-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	86	411	4	ENST00000367435.3:c.772G>T	p.Ala258Ser	p.A258S	ENST00000367435	NM_024529.4	258	Gcc/Tcc	8/17	0.761899438263126	3	FACETS	0.291	0.257	0.328	0.146	0.128	0.164	SUBCLONAL	1	TRUE	1	0.779812050964219	3		415	1053	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138409957	138409957	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009936-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	123	378	0	ENST00000289153.2:c.1921C>T	p.Gln641Ter	p.Q641*	ENST00000289153	NM_006219.2	641	Caa/Taa	13/22	1	2	FACETS	0.502	0.454	0.551	0.502	0.454	0.551	SUBCLONAL	1	TRUE	1	0.779812050964219	2		378	629	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607577	43607577	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009936-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	106	314	0	ENST00000355710.3:c.1553C>G	p.Ser518Cys	p.S518C	ENST00000355710	NM_020975.4	518	tCc/tGc	8/20	0.248535000510811	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.779812050964219	0		314	370	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117323	115117323	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009936-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	391	477	0	ENST00000257566.3:c.851A>G	p.Tyr284Cys	p.Y284C	ENST00000257566	NM_016569.3	284	tAc/tGc	4/8	0.780110763455836	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.779812050964219	1		477	533	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786183	3786183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009936-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	178	494	0	ENST00000262367.5:c.4582G>A	p.Glu1528Lys	p.E1528K	ENST00000262367	NM_004380.2	1528	Gaa/Aaa	28/31	1	2	FACETS	0.667	0.617	0.719	0.667	0.617	0.719	SUBCLONAL	1	TRUE	1	0.779812050964219	2		494	684	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995180	15995180	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009936-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	263	434	0	ENST00000268712.3:c.3013del	p.Glu1005LysfsTer10	p.E1005Kfs*10	ENST00000268712	NM_006311.3	1005	Gaa/aa	22/46	0.733981110718008	1	FACETS	0.897	0.853	0.939	0.897	0.853	0.939	CLONAL	1	TRUE	0	0.779812050964219	1		434	459	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913492	NA	P-0009944-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	186	383	0	ENST00000286548.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000286548	NM_002072.3	209	cAa/cTa	5/7	0.621094847930009	1	FACETS	0.954	0.891	1	0.954	0.891	1	CLONAL	1	TRUE	0	0.621094847930009	1		383	433	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267749	198267751	+	inframe_deletion	In_Frame_Del	DEL	ACC	ACC	-	novel	NA	P-0009944-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	246	408	0	ENST00000335508.6:c.1728_1730del	p.Val577del	p.V577del	ENST00000335508	NM_012433.2	576	gtGGTc/gtc	13/25	1	2	FACETS	0.9	0.843	0.959	0.9	0.843	0.959	CLONAL	1	TRUE	1	0.621094847930009	2		408	880	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772709	135772709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	228	653	1	ENST00000298552.3:c.2837G>A	p.Ser946Asn	p.S946N	ENST00000298552	NM_001162426.1	946	aGc/aAc	22/23	0.175976217629399	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.175976217629399	2		654	1113	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649827	88649827	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	46	247	0	ENST00000372037.3:c.76C>G	p.Leu26Val	p.L26V	ENST00000372037	NM_004329.2	26	Ctg/Gtg	4/13	0.175976217629399	2	FACETS	1	0.958	1	0.722	0.61	0.845	CLONAL	1	TRUE	0	0.175976217629399	2		247	362	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239624	53239624	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1367	173	623	0	ENST00000375401.3:c.1718C>G	p.Pro573Arg	p.P573R	ENST00000375401	NM_004187.3	573	cCc/cGc	12/26	0.175976217629399	5	FACETS	0.807	0.74	0.877			1	CLONAL	2	TRUE	NA	0.175976217629399	5		623	1540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579469	7579476	+	frameshift_variant	Frame_Shift_Del	DEL	ACGGGGGG	ACGGGGGG	-	novel	NA	P-0009946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	74	338	0	ENST00000269305.4:c.211_218del	p.Pro71GlyfsTer75	p.P71Gfs*75	ENST00000269305	NM_001126112.2	71	CCCCCCGTg/g	4/11	0.175976217629399	2	FACETS	1	0.974	1	0.733	0.642	0.83	CLONAL	1	TRUE	0	0.175976217629399	2		338	574	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0009954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1283	318	751	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.526199177898237	3	FACETS	0.954	0.898	1	0.477	0.449	0.506	CLONAL	1	TRUE	1	0.526199177898237	3		753	1601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0009954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	370	375	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.526199177898237	3	FACETS	0.981	0.935	1	0.981	0.935	1	CLONAL	2	TRUE	1	0.526199177898237	3		378	905	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0009954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	1042	533	1	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	0.526199177898237	7	FACETS	0.984	0.962	1	0.984	0.962	1	CLONAL	6	TRUE	1	0.526199177898237	7		534	1554	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120360	94120360	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs749418654	NA	P-0009954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	603	891	2	ENST00000369303.4:c.691C>T	p.Arg231Ter	p.R231*	ENST00000369303	NM_004440.3	231	Cga/Tga	3/17	0.526199177898237	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.526199177898237	3		893	1427	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371782	55371782	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	41	76	1	ENST00000297316.4:c.472G>A	p.Gly158Ser	p.G158S	ENST00000297316	NM_022454.3	158	Ggc/Agc	2/2	0.526199177898237	4	FACETS	0.812	0.679	0.957	0.271	0.226	0.319	CLONAL	1	TRUE	1	0.526199177898237	4		77	293	SUCCESS
APC	324	MSKCC	GRCh37	5	112157640	112157655	+	frameshift_variant	Frame_Shift_Del	DEL	ATGAAACTTTCATTTG	ATGAAACTTTCATTTG	-	novel	NA	P-0009954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	374	601	1	ENST00000257430.4:c.1365_1380del	p.Leu456SerfsTer6	p.L456Sfs*6	ENST00000257430	NM_000038.5	454	ATGAAACTTTCATTTGat/at	11/16	0.526199177898237	3	FACETS	0.874	0.832	0.917	0.874	0.832	0.917	CLONAL	2	TRUE	1	0.526199177898237	3		602	1027	SUCCESS
APC	324	MSKCC	GRCh37	5	112175751	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	A	novel	NA	P-0009954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	151	477	0	ENST00000257430.4:c.4460_4461delinsA	p.Thr1487AsnfsTer20	p.T1487Nfs*20	ENST00000257430	NM_000038.5	1487	aCT/aA	16/16	0.526199177898237	3	FACETS	0.806	0.737	0.879	0.403	0.368	0.44	CLONAL	1	TRUE	1	0.526199177898237	3		477	899	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910337	29910337	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs41541013	NA	P-0009970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1222	301	471	1	ENST00000376809.5:c.7G>T	p.Val3Phe	p.V3F	ENST00000376809	NM_002116.7	3	Gtc/Ttc	1/8	0.18124274709088	3	FACETS	0.645	0.606	0.685	0.322	0.303	0.343	INDETERMINATE	1	TRUE	1	0.884107593100211	3		472	1523	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528381	157528381	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	196	405	1	ENST00000346085.5:c.6106G>A	p.Asp2036Asn	p.D2036N	ENST00000346085	NM_020732.3	2036	Gac/Aac	20/20	1	2	FACETS	0.367	0.339	0.396	0.367	0.339	0.396	SUBCLONAL	1	TRUE	1	0.884107593100211	2		406	1209	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	27	246	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.76	0.608	0.931	0.76	0.608	0.931	CLONAL	1	TRUE	1	0.34	2		246	209	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0009973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	118	959	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.34	2		959	554	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578191	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs530941076	NA	P-0009973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	174	1093	0	ENST00000269305.4:c.658T>G	p.Tyr220Asp	p.Y220D	ENST00000269305	NM_001126112.2	220	Tat/Gat	6/11	0.297001932927932	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.34	1		1093	574	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711935	89711935	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	104	727	2	ENST00000371953.3:c.553del	p.His185IlefsTer14	p.H185Ifs*14	ENST00000371953	NM_000314.4	185	Cat/at	6/9	0.289670779508037	2	FACETS	0.797	0.719	0.877	0.797	0.719	0.877	SUBCLONAL	2	TRUE	0	0.34	2		729	384	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686796	117686796	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759586931	NA	P-0009987-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	1177	496	2	ENST00000368508.3:c.2921C>T	p.Ala974Val	p.A974V	ENST00000368508	NM_002944.2	974	gCg/gTg	19/43	0.768986268908702	6	FACETS	0.99	0.968	1	0.99	0.968	1	CLONAL	4	TRUE	2	0.768986268908702	6		498	1961	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579331	7579331	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009989-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	258	457	0	ENST00000269305.4:c.356C>G	p.Ala119Gly	p.A119G	ENST00000269305	NM_001126112.2	119	gCc/gGc	4/11	0.696826497231874	1	FACETS	0.879	0.832	0.926	0.879	0.832	0.926	CLONAL	1	TRUE	0	0.696826497231874	1		457	549	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182681838	182681838	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0009989-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	289	412	0	ENST00000292782.4:c.221-1G>T		p.X74_splice	ENST00000292782	NM_020640.2	74			1	2	FACETS	0.925	0.872	0.978	0.925	0.872	0.978	CLONAL	1	TRUE	1	0.696826497231874	2		412	897	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216555	108216555	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009989-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	399	703	1	ENST00000278616.4:c.8504G>T	p.Cys2835Phe	p.C2835F	ENST00000278616	NM_000051.3	2835	tGc/tTc	58/63	1	2	FACETS	0.978	0.931	1	0.978	0.931	1	CLONAL	1	TRUE	1	0.696826497231874	2		704	1171	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37871752	37871752	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009989-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	71	542	0	ENST00000269571.5:c.1276C>A	p.Gln426Lys	p.Q426K	ENST00000269571		426	Cag/Aag	11/27	1	2	FACETS	0.17	0.147	0.194	0.17	0.147	0.194	SUBCLONAL	1	TRUE	1	0.696826497231874	2		542	1202	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217873	7217873	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009989-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	605	855	0	ENST00000380728.2:c.138del	p.Glu47AsnfsTer16	p.E47Nfs*16	ENST00000380728		46	gaA/ga	3/11	0.696826497231874	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.696826497231874	1		855	1059	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49413010	49413010	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519952	NA	P-0000076-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1400	152	323	3	ENST00000418115.1:c.13C>T	p.Arg5Trp	p.R5W	ENST00000418115	NM_001664.2	5	Cgg/Tgg	2/5	1	2	FACETS	0.979	0.892	1	0.979	0.892	1	CLONAL	1	TRUE	1	0.2	2		326	1552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519975	NA	P-0000076-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	140	267	0	ENST00000269305.4:c.403T>G	p.Cys135Gly	p.C135G	ENST00000269305	NM_001126112.2	135	Tgc/Ggc	5/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.2	2		267	1234	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945275	54945275	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs918964104	NA	P-0000076-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	57	207	0	ENST00000312783.6:c.1151C>G	p.Thr384Arg	p.T384R	ENST00000312783	NM_198436.1	384	aCa/aGa	10/10	1	2	FACETS	0.695	0.595	0.805	0.695	0.595	0.805	SUBCLONAL	1	TRUE	1	0.2	2		207	820	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777894	NA	P-0000208-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	104	601	0	ENST00000361445.4:c.6644C>T	p.Ser2215Phe	p.S2215F	ENST00000361445	NM_004958.3	2215	tCt/tTt	47/58	0.233903292392395	4	FACETS	0.844	0.761	0.931			1	INDETERMINATE	2	TRUE	NA	0.415019596683308	4		601	420	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509386	46509386	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000208-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	130	644	0	ENST00000262741.5:c.1345G>A	p.Ala449Thr	p.A449T	ENST00000262741	NM_003629.3	449	Gcc/Acc	10/10	0.169295622537175	5	FACETS	1	0.913	1			1	INDETERMINATE	2	TRUE	NA	0.415019596683308	5		644	508	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617517	158617517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000208-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	189	771	0	ENST00000263640.3:c.1139G>A	p.Arg380His	p.R380H	ENST00000263640	NM_001105.4	380	cGc/cAc	9/11	0.417416956024096	4	FACETS	0.952	0.883	1	0.952	0.883	1	CLONAL	2	TRUE	2	0.415019596683308	4		771	677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579576	7579577	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	C	novel	NA	P-0000249-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	26	295	0	ENST00000269305.4:c.110_111delinsG	p.Ser37CysfsTer7	p.S37Cfs*7	ENST00000269305	NM_001126112.2	37	tCC/tG	4/11	0.300994360020044	3	FACETS	0.866	0.69	1	0.433	0.345	0.533	CLONAL	1	TRUE	1	0.33	3		295	212	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000258-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	118	225	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.947	0.869	1	0.947	0.869	1	CLONAL	1	TRUE	1	0.9	2		225	277	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288590	33288590	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000258-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	195	247	0	ENST00000374542.5:c.962G>A	p.Gly321Asp	p.G321D	ENST00000374542	NM_001141970.1	321	gGc/gAc	3/8	1	2	FACETS	0.974	0.912	1	0.974	0.912	1	CLONAL	1	TRUE	1	0.9	2		247	445	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912102	127912102	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000258-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	361	683	0	ENST00000373547.4:c.768G>A	p.Trp256Ter	p.W256*	ENST00000373547	NM_002721.4	256	tgG/tgA	7/7	1	2	FACETS	0.718	0.681	0.756	0.718	0.681	0.756	SUBCLONAL	1	TRUE	1	0.9	2		683	1117	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795804	42795804	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000258-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	38	285	0	ENST00000575354.2:c.2793G>T	p.Met931Ile	p.M931I	ENST00000575354	NM_015125.3	931	atG/atT	11/20	1	2	FACETS	0.152	0.125	0.183	0.152	0.125	0.183	SUBCLONAL	1	TRUE	1	0.9	2		285	554	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000657-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	132	225	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.992	0.913	1	0.992	0.913	1	CLONAL	1	TRUE	1	0.775601578258065	2		225	343	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0000657-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	65	92	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.775601578258065	1	FACETS	0.808	0.725	0.891	0.808	0.725	0.891	CLONAL	1	TRUE	0	0.775601578258065	1		92	127	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs139236063	NA	P-0000657-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10761	5453	417	1	ENST00000275493.2:c.1793G>C	p.Gly598Ala	p.G598A	ENST00000275493	NM_005228.3	598	gGa/gCa	15/28	0.775601578258065	27	FACETS	1	0.997	1			1	CLONAL	9	TRUE	NA	0.775601578258065	27		418	16214	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508692	106508692	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000657-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	245	334	0	ENST00000359195.3:c.686C>G	p.Thr229Ser	p.T229S	ENST00000359195	NM_002649.2	229	aCc/aGc	2/11	0.775601578258065	3	FACETS	0.985	0.922	1	0.493	0.461	0.525	CLONAL	1	TRUE	1	0.775601578258065	3		334	890	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782177	NA	P-0000681-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	215	546	0	ENST00000269305.4:c.644G>T	p.Ser215Ile	p.S215I	ENST00000269305	NM_001126112.2	215	aGt/aTt	6/11	0.214568369362971	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.342599272238482	1		546	983	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797759	45797759	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0000681-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	85	485	1	ENST00000450313.1:c.934-1G>T		p.X312_splice	ENST00000450313	NM_012222.2	312			1	2	FACETS	0.624	0.551	0.703	0.624	0.551	0.703	SUBCLONAL	1	TRUE	1	0.342599272238482	2		486	795	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635608	47635608	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1330621664	NA	P-0000681-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	154	367	0	ENST00000233146.2:c.280C>G	p.Leu94Val	p.L94V	ENST00000233146	NM_000251.2	94	Ctg/Gtg	2/16	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.342599272238482	2		367	887	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732725	204732725	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000681-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	95	470	1	ENST00000302823.3:c.60G>T	p.Trp20Cys	p.W20C	ENST00000302823	NM_005214.4	20	tgG/tgT	1/4	0.148433297217581	0	FACETS	0.438	0.389	0.49			1	INDETERMINATE	1	TRUE	0	0.342599272238482	0		471	833	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468414	89468414	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000681-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	196	319	2	ENST00000336596.2:c.1948G>T	p.Val650Leu	p.V650L	ENST00000336596	NM_005233.5	650	Gtg/Ttg	11/17	0.275288051164894	2	FACETS	0.904	0.841	0.968	0.904	0.841	0.968	CLONAL	2	TRUE	0	0.342599272238482	2		321	633	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679595	86679595	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000681-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	198	269	0	ENST00000274376.6:c.2756C>T	p.Ser919Leu	p.S919L	ENST00000274376	NM_002890.2	919	tCa/tTa	21/25	0.210091611913643	3	FACETS	0.936	0.876	0.997			1	CLONAL	3	TRUE	NA	0.342599272238482	3		269	482	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150533	157150533	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000681-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	92	311	0	ENST00000346085.5:c.1715G>C	p.Gly572Ala	p.G572A	ENST00000346085	NM_020732.3	572	gGa/gCa	2/20	0.275288051164894	2	FACETS	1	0.956	1	0.569	0.508	0.634	CLONAL	1	TRUE	0	0.342599272238482	2		311	472	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0000681-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	134	497	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.342599272238482	3	FACETS	0.976	0.886	1	0.488	0.443	0.536	CLONAL	1	TRUE	1	0.342599272238482	3		497	939	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398067	4398067	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000681-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	139	519	1	ENST00000261254.3:c.631A>T	p.Ile211Phe	p.I211F	ENST00000261254	NM_001759.3	211	Atc/Ttc	4/5	0.305722142389718	1	FACETS	0.88	0.802	0.962	0.88	0.802	0.962	CLONAL	1	TRUE	0	0.342599272238482	1		520	764	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440412	49440412	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000681-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	102	338	0	ENST00000301067.7:c.4398G>T	p.Lys1466Asn	p.K1466N	ENST00000301067	NM_003482.3	1466	aaG/aaT	15/54	1	2	FACETS	0.902	0.808	1	0.902	0.808	1	CLONAL	1	TRUE	1	0.342599272238482	2		338	660	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222326	2222326	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000681-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	57	498	0	ENST00000326181.6:c.610G>A	p.Glu204Lys	p.E204K	ENST00000326181	NM_032271.2	204	Gag/Aag	8/21	1	2	FACETS	0.521	0.446	0.602	0.521	0.446	0.602	SUBCLONAL	1	TRUE	1	0.342599272238482	2		498	639	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7168073	7168073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754537233	NA	P-0000681-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	83	463	0	ENST00000302850.5:c.1516C>T	p.Arg506Trp	p.R506W	ENST00000302850	NM_000208.2	506	Cgg/Tgg	7/22	1	2	FACETS	0.584	0.514	0.658	0.584	0.514	0.658	SUBCLONAL	1	TRUE	1	0.342599272238482	2		463	830	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164775	36164775	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867474432	NA	P-0000681-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	147	482	0	ENST00000300305.3:c.1100G>A	p.Gly367Asp	p.G367D	ENST00000300305		367	gGc/gAc	8/8	1	2	FACETS	0.988	0.902	1	0.988	0.902	1	CLONAL	1	TRUE	1	0.342599272238482	2		482	869	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039611	47039611	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000681-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	123	390	1	ENST00000377604.3:c.1063G>T	p.Glu355Ter	p.E355*	ENST00000377604	NM_001204468.1	355	Gag/Tag	11/24	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.342599272238482	2		391	688	SUCCESS
AR	367	MSKCC	GRCh37	X	66765309	66765309	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0000681-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	164	632	0	ENST00000374690.3:c.321C>G	p.Tyr107Ter	p.Y107*	ENST00000374690	NM_000044.3	107	taC/taG	1/8	1	2	FACETS	0.927	0.85	1	0.927	0.85	1	CLONAL	1	TRUE	1	0.342599272238482	2		632	1033	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341596	70341596	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs773615925	NA	P-0000681-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	157	559	0	ENST00000374080.3:c.1031C>A	p.Thr344Asn	p.T344N	ENST00000374080		344	aCt/aAt	7/45	1	2	FACETS	0.805	0.736	0.878	0.805	0.736	0.878	CLONAL	1	TRUE	1	0.342599272238482	2		559	1138	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940319	49940319	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000681-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	110	694	0	ENST00000296474.3:c.724C>G	p.Leu242Val	p.L242V	ENST00000296474	NM_002447.2	242	Ctt/Gtt	1/20	0.275288051164894	2	FACETS	0.523	0.468	0.581	0.261	0.234	0.291	SUBCLONAL	1	TRUE	0	0.342599272238482	2		694	1228	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504938	186504938	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000681-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1268	188	617	0	ENST00000323963.5:c.794G>A	p.Cys265Tyr	p.C265Y	ENST00000323963		265	tGt/tAt	8/11	0.342599272238482	3	FACETS	0.883	0.813	0.956	0.441	0.406	0.478	CLONAL	1	TRUE	1	0.342599272238482	3		617	1456	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504944	186504944	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0000681-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1281	200	638	0	ENST00000323963.5:c.800T>A	p.Leu267Ter	p.L267*	ENST00000323963		267	tTg/tAg	8/11	0.342599272238482	3	FACETS	0.923	0.853	0.997	0.462	0.426	0.499	CLONAL	1	TRUE	1	0.342599272238482	3		638	1481	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134652	41134652	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000681-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	91	743	0	ENST00000379561.5:c.976G>C	p.Gly326Arg	p.G326R	ENST00000379561	NM_002015.3	326	Ggg/Cgg	2/3	0.221516235288882	1	FACETS	0.37	0.327	0.416	0.37	0.327	0.416	SUBCLONAL	1	TRUE	0	0.342599272238482	1		743	1191	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81979806	81979806	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000681-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	99	683	0	ENST00000359376.3:c.3508G>T	p.Gly1170Trp	p.G1170W	ENST00000359376	NM_002661.3	1170	Ggg/Tgg	31/33	1	2	FACETS	0.526	0.468	0.588	0.526	0.468	0.588	SUBCLONAL	1	TRUE	1	0.342599272238482	2		683	1098	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58725406	58725406	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0000681-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	195	671	0	ENST00000305921.3:c.980C>G	p.Ser327Ter	p.S327*	ENST00000305921	NM_003620.3	327	tCa/tGa	4/6	1	2	FACETS	0.946	0.874	1	0.946	0.874	1	CLONAL	1	TRUE	1	0.342599272238482	2		671	1203	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412610	63412610	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000681-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	114	446	0	ENST00000330258.3:c.557G>T	p.Gly186Val	p.G186V	ENST00000330258	NM_152424.3	186	gGg/gTg	2/2	1	2	FACETS	0.892	0.804	0.986	0.892	0.804	0.986	CLONAL	1	TRUE	1	0.342599272238482	2		446	746	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857648	59857649	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0000681-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	99	438	0	ENST00000259008.2:c.1908_1909delinsCT	p.Glu636_Ala637delinsAspSer	p.E636_A637delinsDS	ENST00000259008	NM_032043.2	636	gaGGct/gaCTct	13/20	1	2	FACETS	0.727	0.649	0.81	0.727	0.649	0.81	SUBCLONAL	1	TRUE	1	0.342599272238482	2		438	795	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0000690-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	67	213	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.245804306425033	3	FACETS	0.868	0.759	0.984	0.868	0.759	0.984	CLONAL	2	TRUE	1	0.254395905362685	3		213	342	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0000690-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	74	354	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.254395905362685	2		354	478	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448571	89448571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000690-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	78	484	0	ENST00000336596.2:c.1535G>A	p.Arg512Gln	p.R512Q	ENST00000336596	NM_005233.5	512	cGa/cAa	7/17	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.254395905362685	2		484	589	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001242-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	34	426	0	ENST00000269305.4:c.736del	p.Met246Ter	p.M246*	ENST00000269305	NM_001126112.2	246	Atg/tg	7/11	0.653761353656262	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.653761353656262	1		426	59	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670327	134670327	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373140258	NA	P-0001242-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	33	427	0	ENST00000398015.3:c.238C>T	p.Arg80Trp	p.R80W	ENST00000398015	NM_004441.4	80	Cgg/Tgg	3/16	0.653761353656262	4	FACETS	1	0.861	1	0.35	0.289	0.417	CLONAL	1	TRUE	1	0.653761353656262	4		427	159	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0001747-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	792	534	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.628931429544888	2	FACETS	0.927	0.903	0.95	0.927	0.903	0.95	CLONAL	2	TRUE	0	0.690770623153425	2		535	1237	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989475	85989475	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001747-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	170	477	0	ENST00000263360.6:c.1234G>A	p.Ala412Thr	p.A412T	ENST00000263360	NM_003797.3	412	Gct/Act	12/12	0.360541730011576	2	FACETS	0.498	0.458	0.54	0.249	0.229	0.27	INDETERMINATE	1	TRUE	0	0.690770623153425	2		477	988	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371676	55371683	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGCTGC	GCGGCTGC	-	novel	NA	P-0001747-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1413	180	457	0	ENST00000297316.4:c.369_376del	p.Leu124AlafsTer35	p.L124Afs*35	ENST00000297316	NM_022454.3	122	gaGCGGCTGCgc/gagc	2/2	0.338650521916084	5	FACETS	0.666	0.612	0.723	0.222	0.204	0.241	INDETERMINATE	1	TRUE	2	0.690770623153425	5		457	1593	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371727	55371729	+	inframe_deletion	In_Frame_Del	DEL	GCG	GCG	-	novel	NA	P-0001747-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	142	329	0	ENST00000297316.4:c.423_425del	p.Arg142del	p.R142del	ENST00000297316	NM_022454.3	139	ccGCGg/ccg	2/2	0.338650521916084	5	FACETS	0.694	0.63	0.76	0.231	0.21	0.254	INDETERMINATE	1	TRUE	2	0.690770623153425	5		329	1207	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371821	55371823	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	novel	NA	P-0001747-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	32	64	0	ENST00000297316.4:c.514_516del	p.Gly172del	p.G172del	ENST00000297316	NM_022454.3	171	GGC/-	2/2	0.338650521916084	5	FACETS	0.824	0.673	0.992	0.275	0.224	0.331	INDETERMINATE	1	TRUE	2	0.690770623153425	5		64	229	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619118	43619118	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0001747-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	147	388	0	ENST00000355710.3:c.2802-1G>A		p.X934_splice	ENST00000355710	NM_020975.4	934			NA	2	FACETS	0.502	0.458	0.548			1	INDETERMINATE	1	TRUE	NA	0.690770623153425	2		388	848	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619192	43619192	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778658	NA	P-0001747-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	52	412	0	ENST00000355710.3:c.2875C>T	p.Arg959Trp	p.R959W	ENST00000355710	NM_020975.4	959	Cgg/Tgg	17/20	NA	2	FACETS	0.159	0.134	0.186			1	INDETERMINATE	1	TRUE	NA	0.690770623153425	2		412	947	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0001843-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	226	330	0				ENST00000310581	NM_198253.2	-/1132			0.305056889977169	1	FACETS	0.644	0.606	0.682	0.644	0.606	0.682	INDETERMINATE	1	FALSE	0	0.816439164466634	1		330	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0001843-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	636	519	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	NA	2	FACETS	0.952	0.93	0.973			1	INDETERMINATE	2	FALSE	NA	0.816439164466634	2		519	818	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711984	89711984	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001843-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	257	213	0	ENST00000371953.3:c.604del	p.Thr202LeufsTer19	p.T202Lfs*19	ENST00000371953	NM_000314.4	201	gAa/ga	6/9	0.816439164466634	1	FACETS	0.97	0.928	1	0.97	0.928	1	CLONAL	1	FALSE	0	0.816439164466634	1		213	384	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157419	106157419	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs756025246	NA	P-0001843-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	298	400	0	ENST00000380013.4:c.2320T>C	p.Ser774Pro	p.S774P	ENST00000380013	NM_001127208.2	774	Tca/Cca	3/11	0.356159416636437	1	FACETS	0.535	0.506	0.565	0.535	0.506	0.565	INDETERMINATE	1	FALSE	0	0.816439164466634	1		400	807	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057600	180057600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1267101992	NA	P-0001843-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	449	713	3	ENST00000261937.6:c.355C>T	p.Arg119Cys	p.R119C	ENST00000261937	NM_182925.4	119	Cgc/Tgc	3/30	NA	2	FACETS	1	0.958	1			1	INDETERMINATE	1	FALSE	NA	0.816439164466634	2		716	1099	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367798	15367798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144627512	NA	P-0001843-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	320	444	1	ENST00000263377.2:c.1528C>T	p.Arg510Trp	p.R510W	ENST00000263377	NM_058243.2	510	Cgg/Tgg	8/20	0.816439164466634	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	0	0.816439164466634	1		445	452	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050971	49050985	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGATGGAAGGTAGGA	AGATGGAAGGTAGGA	-	novel	NA	P-0001843-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	230	295	0	ENST00000267163.4:c.2656_2663+7del		p.X886_splice	ENST00000267163	NM_000321.2	886		25/27	0.793814857239092	1	FACETS	0.811	0.769	0.853	0.811	0.769	0.853	CLONAL	1	FALSE	0	0.816439164466634	1		295	411	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223973	2223973	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002071-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	589	661	0	ENST00000326181.6:c.1187A>G	p.Gln396Arg	p.Q396R	ENST00000326181	NM_032271.2	396	cAg/cGg	13/21	0.58746993380369	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	2	0.711703989748419	4		661	1306	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0002091-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	263	536	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.284498580820485	6	FACETS	1	0.984	1	0.888	0.838	0.939	CLONAL	4	TRUE	1	0.284498580820485	6		536	653	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0002091-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	47	401	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.284498580820485	6	FACETS	0.799	0.673	0.938	0.16	0.134	0.188	CLONAL	1	TRUE	1	0.284498580820485	6		401	649	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404534	70404534	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002091-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	88	567	0	ENST00000373644.4:c.2048A>C	p.Gln683Pro	p.Q683P	ENST00000373644	NM_030625.2	683	cAa/cCa	4/12	0.284498580820485	3	FACETS	0.96	0.85	1	0.48	0.425	0.539	CLONAL	1	TRUE	1	0.284498580820485	3		567	736	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941628	48941628	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0002091-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	285	400	0	ENST00000267163.4:c.940-2A>G		p.X314_splice	ENST00000267163	NM_000321.2	314			0.284498580820485	4	FACETS	0.904	0.855	0.953	0.904	0.855	0.953	CLONAL	4	TRUE	0	0.284498580820485	4		400	712	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577113	7577113	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555525279	NA	P-0002091-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	286	467	0	ENST00000269305.4:c.825T>G	p.Cys275Trp	p.C275W	ENST00000269305	NM_001126112.2	275	tgT/tgG	8/11	0.284498580820485	4	FACETS	0.957	0.906	1	0.957	0.906	1	CLONAL	4	TRUE	0	0.284498580820485	4		467	675	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969926	81969926	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002091-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	163	585	2	ENST00000359376.3:c.2995C>A	p.Pro999Thr	p.P999T	ENST00000359376	NM_002661.3	999	Ccc/Acc	27/33	0.284498580820485	1	FACETS	0.879	0.811	0.949	1	0.991	1	CLONAL	2	TRUE	0	0.284498580820485	1		587	559	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195151	123195151	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002091-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	75	595	2	ENST00000218089.9:c.1494G>T	p.Met498Ile	p.M498I	ENST00000218089	NM_001042749.1	498	atG/atT	16/35	0.146760365467784	4	FACETS	0.73	0.638	0.829	0.365	0.319	0.415	INDETERMINATE	1	TRUE	2	0.284498580820485	4		597	928	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015045	27015045	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002091-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	76	522	0	ENST00000335756.4:c.148del	p.Glu50ArgfsTer12	p.E50Rfs*12	ENST00000335756	NM_001809.3	49	aaG/aa	2/5	0.284498580820485	3	FACETS	0.923	0.81	1			1	CLONAL	1	TRUE	NA	0.284498580820485	3		522	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0002208-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	307	386	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.495539157690223	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.495539157690223	3		386	652	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197766	66197766	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002208-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	103	343	0	ENST00000273854.3:c.2933A>G	p.Lys978Arg	p.K978R	ENST00000273854	NM_004439.5	978	aAg/aGg	17/18	0.344564621616619	3	FACETS	1	0.942	1	0.357	0.32	0.395	CLONAL	1	TRUE	0	0.495539157690223	3		343	485	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958195	2958195	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002208-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	64	384	0	ENST00000396946.4:c.2537T>A	p.Leu846Gln	p.L846Q	ENST00000396946	NM_032415.4	846	cTg/cAg	19/25	0.495539157690223	3	FACETS	0.348	0.301	0.401	0.174	0.15	0.201	SUBCLONAL	1	TRUE	1	0.495539157690223	3		384	925	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95595810	95595810	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002208-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	53	269	0	ENST00000393063.1:c.733A>G	p.Arg245Gly	p.R245G	ENST00000393063	NM_030621.3	245	Agg/Ggg	7/28	0.495539157690223	3	FACETS	0.434	0.37	0.505	0.145	0.123	0.169	SUBCLONAL	1	TRUE	0	0.495539157690223	3		269	615	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724244	52724244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002208-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	72	357	0	ENST00000322088.6:c.1376G>A	p.Arg459His	p.R459H	ENST00000322088	NM_014225.5	459	cGc/cAc	12/15	0.495539157690223	3	FACETS	0.443	0.386	0.505			1	SUBCLONAL	1	TRUE	NA	0.495539157690223	3		357	818	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346184	152346190	+	frameshift_variant	Frame_Shift_Del	DEL	GTAAGAA	GTAAGAA	-	novel	NA	P-0002208-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	573	592	1	ENST00000359321.1:c.380_386del	p.Leu127HisfsTer5	p.L127Hfs*5	ENST00000359321	NM_005431.1	127	cTTCTTACa/ca	3/3	0.30568381243527	6	FACETS	1	0.977	1	0.768	0.738	0.798	CLONAL	3	TRUE	2	0.495539157690223	6		593	1499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782664	NA	P-0002513-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	519	494	0	ENST00000269305.4:c.711G>C	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atC	7/11	0.632113275783741	8	FACETS	0.945	0.931	0.958	1	0.998	1	CLONAL	9	FALSE	1	0.632113275783741	8		494	559	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878227	151878227	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002513-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	158	403	0	ENST00000262189.6:c.6718A>G	p.Arg2240Gly	p.R2240G	ENST00000262189	NM_170606.2	2240	Aga/Gga	36/59	0.632113275783741	5	FACETS	0.859	0.797	0.921	0.859	0.797	0.921	CLONAL	3	FALSE	2	0.632113275783741	5		403	378	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122461	17122461	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002513-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	135	617	0	ENST00000285071.4:c.934G>C	p.Val312Leu	p.V312L	ENST00000285071	NM_144997.5	312	Gtg/Ctg	9/14	0.632113275783741	8	FACETS	1	0.984	1	0.2	0.181	0.22	CLONAL	1	FALSE	1	0.632113275783741	8		617	883	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890106	76890106	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002513-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	188	685	0	ENST00000373344.5:c.4788G>C	p.Met1596Ile	p.M1596I	ENST00000373344	NM_000489.3	1596	atG/atC	17/35	0.333019883302845	3	FACETS	0.833	0.777	0.889	0.555	0.518	0.593	INDETERMINATE	2	FALSE	0	0.632113275783741	3		685	470	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423407	116423407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913671	NA	P-0002707-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	473	335	0	ENST00000397752.3:c.3682G>A	p.Asp1228Asn	p.D1228N	ENST00000397752	NM_000245.2	1228	Gac/Aac	19/21	0.436619617900326	4	FACETS	1	0.992	1	0.777	0.743	0.811	CLONAL	2	TRUE	1	0.436619617900326	4		335	1336	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0002756-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	170	446	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.441899041274098	3	FACETS	0.825	0.766	0.885	0.825	0.766	0.885	CLONAL	2	TRUE	1	0.583564776231062	3		446	456	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519925	NA	P-0002756-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	151	302	0	ENST00000263967.3:c.1357G>C	p.Glu453Gln	p.E453Q	ENST00000263967	NM_006218.2	453	Gaa/Caa	8/21	0.441899041274098	3	FACETS	0.996	0.913	1	0.498	0.456	0.541	CLONAL	1	TRUE	1	0.583564776231062	3		302	671	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114276	115114276	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0002756-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	110	295	0	ENST00000257566.3:c.942-1G>C		p.X314_splice	ENST00000257566	NM_016569.3	314			1	2	FACETS	0.769	0.695	0.848	0.769	0.695	0.848	SUBCLONAL	1	TRUE	1	0.583564776231062	2		295	490	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021383	42021383	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002756-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	237	556	0	ENST00000219905.7:c.3679C>A	p.Pro1227Thr	p.P1227T	ENST00000219905	NM_001164273.1	1227	Cca/Aca	11/24	1	2	FACETS	0.789	0.737	0.844	0.789	0.737	0.844	SUBCLONAL	1	TRUE	1	0.583564776231062	2		556	1029	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0002883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	321	595	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.308046352404801	2	FACETS	0.988	0.934	1	0.988	0.934	1	CLONAL	2	TRUE	0	0.308046352404801	2		596	1055	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500891	8500891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	247	492	0	ENST00000356435.5:c.1991G>A	p.Gly664Glu	p.G664E	ENST00000356435		664	gGa/gAa	13/35	0.235759392514094	4	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	2	0.308046352404801	4		492	1027	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608087	28608087	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs997265952	NA	P-0002883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	295	557	4	ENST00000241453.7:c.1879G>A	p.Ala627Thr	p.A627T	ENST00000241453	NM_004119.2	627	Gca/Aca	15/24	0.301112717258686	4	FACETS	0.897	0.843	0.953	0.897	0.843	0.953	CLONAL	2	TRUE	2	0.308046352404801	4		561	1396	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944897	131944897	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1129482	NA	P-0002883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	57	381	0	ENST00000265335.6:c.2918A>T	p.Lys973Met	p.K973M	ENST00000265335		973	aAg/aTg	18/25	0.204405103182933	4	FACETS	0.562	0.48	0.651	0.281	0.24	0.326	SUBCLONAL	1	TRUE	2	0.308046352404801	4		381	862	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250689	26250689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1319	409	814	2	ENST00000446824.2:c.145C>T	p.Leu49Phe	p.L49F	ENST00000446824	NM_021018.2	49	Ctc/Ttc	1/1	0.301112717258686	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	2	0.308046352404801	4		816	1728	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019523	42019523	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1557	100	753	0	ENST00000219905.7:c.3576A>C	p.Glu1192Asp	p.E1192D	ENST00000219905	NM_001164273.1	1192	gaA/gaC	10/24	0.235759392514094	4	FACETS	0.513	0.456	0.574	0.256	0.228	0.287	SUBCLONAL	1	TRUE	2	0.308046352404801	4		753	1657	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822742	72822742	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	88	775	0	ENST00000268489.5:c.9433A>C	p.Thr3145Pro	p.T3145P	ENST00000268489	NM_006885.3	3145	Acg/Ccg	10/10	0.308046352404801	2	FACETS	0.468	0.413	0.528	0.234	0.206	0.264	SUBCLONAL	1	TRUE	0	0.308046352404801	2		775	1220	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912781	50912781	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002883-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	60	533	0	ENST00000440232.2:c.2012A>T	p.Lys671Met	p.K671M	ENST00000440232	NM_002691.3	671	aAg/aTg	17/27	0.308046352404801	3	FACETS	0.401	0.344	0.464	0.201	0.172	0.232	SUBCLONAL	1	TRUE	1	0.308046352404801	3		533	1121	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003941-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	107	213	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	0.409009724205594	2		213	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520006	NA	P-0003941-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	301	691	0	ENST00000269305.4:c.821T>C	p.Val274Ala	p.V274A	ENST00000269305	NM_001126112.2	274	gTt/gCt	8/11	0.409009724205594	1	FACETS	0.871	0.827	0.916	1	0.996	1	CLONAL	2	TRUE	0	0.409009724205594	1		691	672	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508404	106508404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003941-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	70	265	0	ENST00000359195.3:c.398G>A	p.Gly133Asp	p.G133D	ENST00000359195	NM_002649.2	133	gGc/gAc	2/11	1	2	FACETS	0.906	0.794	1	0.906	0.794	1	CLONAL	1	TRUE	1	0.409009724205594	2		265	378	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0003959-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	338	283	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	0.48034742811286	4	FACETS	0.825	0.781	0.87	0.55	0.52	0.58	CLONAL	2	TRUE	1	0.572068025053185	4		283	1126	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167772	56167772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003959-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	307	229	0	ENST00000399503.3:c.1337G>A	p.Cys446Tyr	p.C446Y	ENST00000399503	NM_005921.1	446	tGc/tAc	7/20	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.572068025053185	2		229	722	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0003981-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	426	531	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.451455884644475	2	FACETS	0.967	0.926	1	0.967	0.926	1	CLONAL	2	TRUE	0	0.490239903846871	2		531	899	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0003981-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	147	344	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.697	0.637	0.761	0.697	0.637	0.761	SUBCLONAL	1	TRUE	1	0.490239903846871	2		344	860	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476748	140476748	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003981-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	61	398	0	ENST00000288602.6:c.1658T>G	p.Leu553Arg	p.L553R	ENST00000288602	NM_004333.4	553	cTt/cGt	13/18	0.451455884644475	2	FACETS	0.304	0.261	0.35	0.152	0.13	0.175	SUBCLONAL	1	TRUE	0	0.490239903846871	2		398	819	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59770854	59770854	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003981-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	164	487	0	ENST00000259008.2:c.2512G>C	p.Asp838His	p.D838H	ENST00000259008	NM_032043.2	838	Gat/Cat	18/20	0.458069392260745	2	FACETS	0.819	0.753	0.888	0.409	0.376	0.444	CLONAL	1	TRUE	0	0.490239903846871	2		487	817	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288385	15288385	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003981-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	174	340	0	ENST00000263388.2:c.4354C>G	p.Leu1452Val	p.L1452V	ENST00000263388	NM_000435.2	1452	Ctc/Gtc	24/33	0.490239903846871	2	FACETS	0.866	0.807	0.925	0.866	0.807	0.925	CLONAL	2	TRUE	0	0.490239903846871	2		340	410	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003985-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	57	213	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.378394910020853	3	FACETS	0.963	0.841	1	0.963	0.841	1	CLONAL	2	TRUE	1	0.378394910020853	3		213	186	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870929	12870929	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003985-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	182	323	0	ENST00000228872.4:c.157del	p.Glu53LysfsTer18	p.E53Kfs*18	ENST00000228872	NM_004064.3	52	atG/at	1/3	0.378394910020853	5	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.378394910020853	5		323	1156	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003994-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	51	213	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.547708762588913	4	FACETS	1	0.858	1	0.501	0.429	0.579	CLONAL	1	FALSE	2	0.564880264324306	4		213	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1064795203	NA	P-0003994-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	188	298	0	ENST00000269305.4:c.532C>G	p.His178Asp	p.H178D	ENST00000269305	NM_001126112.2	178	Cac/Gac	5/11	0.564880264324306	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	4	FALSE	0	0.564880264324306	4		298	251	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380279	25380279	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs727503108	NA	P-0003994-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	822	440	0	ENST00000311936.3:c.179G>T	p.Gly60Val	p.G60V	ENST00000311936	NM_004985.3	60	gGt/gTt	3/5	0.564880264324306	8	FACETS	1	0.991	1			1	CLONAL	6	FALSE	NA	0.564880264324306	8		440	1266	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0004007-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	168	477	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.274695482686846	3	FACETS	0.755	0.695	0.817			1	SUBCLONAL	2	TRUE	NA	0.341069078596841	3		477	764	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0004007-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	67	392	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.341069078596841	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.341069078596841	1		392	294	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913355	NA	P-0004007-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	112	458	0	ENST00000288602.6:c.1406G>A	p.Gly469Glu	p.G469E	ENST00000288602	NM_004333.4	469	gGa/gAa	11/18	0.341069078596841	3	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.341069078596841	3		458	546	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371684	55371684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004007-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	18	329	0	ENST00000297316.4:c.374G>A	p.Arg125His	p.R125H	ENST00000297316	NM_022454.3	125	cGc/cAc	2/2	0.341069078596841	1	FACETS	0.376	0.283	0.485	0.376	0.283	0.485	SUBCLONAL	1	TRUE	0	0.341069078596841	1		329	233	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405041	405041	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1169247876	NA	P-0004007-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	69	468	0	ENST00000380956.4:c.1123G>A	p.Gly375Ser	p.G375S	ENST00000380956	NM_001195286.1	375	Ggc/Agc	8/9	0.200329186328783	3	FACETS	1	0.905	1			1	INDETERMINATE	1	TRUE	NA	0.341069078596841	3		468	454	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276844	123276844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004007-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	40	443	1	ENST00000358487.5:c.1073C>T	p.Thr358Ile	p.T358I	ENST00000358487	NM_000141.4	358	aCa/aTa	8/18	0.341069078596841	1	FACETS	0.537	0.447	0.637	0.537	0.447	0.637	SUBCLONAL	1	TRUE	0	0.341069078596841	1		444	362	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358684	67358684	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004007-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	121	427	0	ENST00000327367.4:c.192C>A	p.Cys64Ter	p.C64*	ENST00000327367	NM_005902.3	64	tgC/tgA	1/9	0.341069078596841	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.341069078596841	1		427	449	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0004361-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	215	379	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.253695097146324	3	FACETS	1	0.967	1			1	CLONAL	3	TRUE	NA	0.347524013150528	3		379	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0004361-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	67	323	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	0.347524013150528	4	FACETS	0.802	0.702	0.908	0.802	0.702	0.908	CLONAL	2	TRUE	2	0.347524013150528	4		323	324	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190670377	190670377	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0004361-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	84	282	0	ENST00000441310.2:c.316-1G>T		p.X106_splice	ENST00000441310	NM_000534.4	106			0.347524013150528	3	FACETS	1	0.919	1	1	0.919	1	CLONAL	2	TRUE	1	0.347524013150528	3		282	275	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003281	42003281	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0004361-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	197	542	1	ENST00000219905.7:c.2818A>T	p.Lys940Ter	p.K940*	ENST00000219905	NM_001164273.1	940	Aag/Tag	8/24	0.347524013150528	3	FACETS	1	0.982	1	0.77	0.718	0.824	CLONAL	2	TRUE	0	0.347524013150528	3		543	576	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679129	88679129	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0004361-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	113	281	0	ENST00000360948.2:c.907+1G>T		p.X303_splice	ENST00000360948	NM_001012338.2	303			0.347524013150528	3	FACETS	1	0.932	1	1	0.932	1	CLONAL	3	TRUE	0	0.347524013150528	3		281	250	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727529	88727529	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004361-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	71	245	1	ENST00000360948.2:c.250C>T	p.His84Tyr	p.H84Y	ENST00000360948	NM_001012338.2	84	Cac/Tac	3/19	0.347524013150528	3	FACETS	1	0.96	1	0.791	0.704	0.882	CLONAL	2	TRUE	0	0.347524013150528	3		246	202	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774132	56774132	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1188093917	NA	P-0004361-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	99	453	0	ENST00000337432.4:c.483G>T	p.Glu161Asp	p.E161D	ENST00000337432	NM_058216.2	161	gaG/gaT	3/9	0.347524013150528	4	FACETS	1	0.967	1	0.605	0.541	0.674	CLONAL	1	TRUE	2	0.347524013150528	4		453	634	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840006	27840006	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004361-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	137	519	0	ENST00000328488.2:c.88G>T	p.Ala30Ser	p.A30S	ENST00000328488	NM_003533.2	30	Gct/Tct	1/1	0.347524013150528	12	FACETS	0.902	0.818	0.99			1	CLONAL	2	TRUE	NA	0.347524013150528	12		519	1197	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115728	8115728	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004361-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	48	410	1	ENST00000346208.3:c.1074G>T	p.Lys358Asn	p.K358N	ENST00000346208		358	aaG/aaT	6/6	NA	2	FACETS	0.729	0.618	0.85			1	INDETERMINATE	1	TRUE	NA	0.347524013150528	2		411	379	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861837	57861837	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs759838377	NA	P-0004361-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	98	525	0	ENST00000228682.2:c.1138C>T	p.Arg380Ter	p.R380*	ENST00000228682	NM_005269.2	380	Cga/Tga	10/12	0.269752123781222	3	FACETS	1	0.913	1	0.342	0.305	0.381	CLONAL	1	TRUE	0	0.347524013150528	3		525	646	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386370	31386370	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004361-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	55	333	1	ENST00000328111.2:c.1595G>T	p.Cys532Phe	p.C532F	ENST00000328111	NM_006892.3	532	tGt/tTt	15/23	0.347524013150528	4	FACETS	1	0.863	1	0.503	0.431	0.581	CLONAL	1	TRUE	2	0.347524013150528	4		334	424	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937374	76937374	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004361-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	13	283	0	ENST00000373344.5:c.3374C>A	p.Ser1125Tyr	p.S1125Y	ENST00000373344	NM_000489.3	1125	tCt/tAt	9/35	1	2	FACETS	0.318	0.227	0.43	0.318	0.227	0.43	SUBCLONAL	1	TRUE	1	0.347524013150528	2		283	235	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191772	123191772	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004361-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	87	409	0	ENST00000218089.9:c.1361A>G	p.Gln454Arg	p.Q454R	ENST00000218089	NM_001042749.1	454	cAa/cGa	15/35	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.347524013150528	2		409	498	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269101	142269101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146041880	NA	P-0004577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	15	668	1	ENST00000350721.4:c.2849C>T	p.Pro950Leu	p.P950L	ENST00000350721	NM_001184.3	950	cCg/cTg	14/47	0.438565881539691	3	FACETS	0.668	0.493	0.873	0.223	0.164	0.291	SUBCLONAL	1	TRUE	0	0.465574840315212	3		669	119	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0004580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	361	254	1	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.49206025655049	5	FACETS	0.899	0.86	0.937	0.899	0.86	0.937	CLONAL	4	TRUE	1	0.533335001278103	5		255	678	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510128	149510128	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	109	378	0	ENST00000261799.4:c.1341C>G	p.Ile447Met	p.I447M	ENST00000261799	NM_002609.3	447	atC/atG	9/23	0.110384741327554	4	FACETS	1	0.978	1	0.657	0.593	0.724	INDETERMINATE	1	TRUE	2	0.533335001278103	4		378	477	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165273	32165273	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs755664291	NA	P-0004580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	121	394	0	ENST00000375023.3:c.4855C>G	p.Leu1619Val	p.L1619V	ENST00000375023	NM_004557.3	1619	Ctg/Gtg	27/30	0.322037509958148	5	FACETS	1	0.945	1	0.355	0.321	0.391	CLONAL	1	TRUE	2	0.533335001278103	5		394	767	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781488	135781488	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	191	769	0	ENST00000298552.3:c.1477G>C	p.Glu493Gln	p.E493Q	ENST00000298552	NM_001162426.1	493	Gag/Cag	15/23	0.533335001278103	3	FACETS	1	0.935	1	0.506	0.468	0.545	CLONAL	1	TRUE	1	0.533335001278103	3		769	897	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139794048	139794048	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	57	664	0	ENST00000247668.2:c.191C>G	p.Ser64Cys	p.S64C	ENST00000247668	NM_021138.3	64	tCt/tGt	3/11	0.533335001278103	3	FACETS	0.309	0.264	0.359	0.155	0.132	0.18	SUBCLONAL	1	TRUE	1	0.533335001278103	3		664	875	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852095	63852095	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	67	289	0	ENST00000279873.7:c.2873C>A	p.Ser958Ter	p.S958*	ENST00000279873	NM_032199.2	958	tCa/tAa	10/10	1	2	FACETS	0.681	0.595	0.773	0.681	0.595	0.773	SUBCLONAL	1	TRUE	1	0.533335001278103	2		289	369	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589513	69589513	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	rs1001068009	NA	P-0004580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	34	87	0	ENST00000168712.1:c.340A>T	p.Ser114Cys	p.S114C	ENST00000168712	NM_002007.2	114	Agc/Tgc	1/3	0.533335001278103	4	FACETS	1	0.892	1			1	CLONAL	1	TRUE	NA	0.533335001278103	4		87	176	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103453	77103453	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	127	603	0	ENST00000356341.3:c.113C>G	p.Ser38Cys	p.S38C	ENST00000356341	NM_002576.4	38	tCt/tGt	2/15	NA	2	FACETS	0.889	0.809	0.972			1	INDETERMINATE	1	TRUE	NA	0.533335001278103	2		603	536	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422616	49422616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	112	385	0	ENST00000301067.7:c.14377G>A	p.Ala4793Thr	p.A4793T	ENST00000301067	NM_003482.3	4793	Gcc/Acc	45/54	0.533335001278103	3	FACETS	0.953	0.86	1	0.477	0.43	0.526	CLONAL	1	TRUE	1	0.533335001278103	3		385	558	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008078	29008078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	80	362	0	ENST00000282397.4:c.691G>A	p.Asp231Asn	p.D231N	ENST00000282397	NM_002019.4	231	Gat/Aat	6/30	0.533335001278103	4	FACETS	0.796	0.701	0.897	0.265	0.233	0.299	SUBCLONAL	1	TRUE	1	0.533335001278103	4		362	578	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972816	32972816	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs431825279	NA	P-0004580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	91	449	0	ENST00000380152.3:c.10166C>T	p.Ser3389Phe	p.S3389F	ENST00000380152		3389	tCt/tTt	27/27	0.533335001278103	5	FACETS	0.674	0.598	0.756			1	SUBCLONAL	1	TRUE	NA	0.533335001278103	5		449	911	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646234	23646234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs180177103	NA	P-0004580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	140	608	0	ENST00000261584.4:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000261584	NM_024675.3	545	Gaa/Aaa	4/13	0.322037509958148	5	FACETS	1	0.97	1	0.382	0.348	0.418	CLONAL	1	TRUE	2	0.533335001278103	5		608	825	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81922876	81922876	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	112	574	0	ENST00000359376.3:c.865G>A	p.Glu289Lys	p.E289K	ENST00000359376	NM_002661.3	289	Gag/Aag	10/33	0.509792125575012	2	FACETS	0.855	0.773	0.941	0.428	0.386	0.471	CLONAL	1	TRUE	0	0.533335001278103	2		574	491	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732266	74732266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1227	163	681	1	ENST00000359995.5:c.643G>A	p.Glu215Lys	p.E215K	ENST00000359995	NM_001195427.1	215	Gag/Aag	2/3	0.533335001278103	5	FACETS	0.792	0.724	0.862	0.264	0.241	0.288	SUBCLONAL	1	TRUE	2	0.533335001278103	5		682	1390	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790123	40790123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757562149	NA	P-0004580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	46	256	1	ENST00000373198.4:c.2608C>T	p.Arg870Cys	p.R870C	ENST00000373198	NM_133170.3	870	Cgc/Tgc	18/32	0.284151262342001	5	FACETS	0.872	0.737	1	0.291	0.245	0.34	INDETERMINATE	1	TRUE	2	0.533335001278103	5		257	356	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833960	44833960	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	34	617	0	ENST00000377967.4:c.384G>C	p.Lys128Asn	p.K128N	ENST00000377967	NM_021140.2	128	aaG/aaC	4/29	NA	2	FACETS	0.212	0.172	0.256			1	INDETERMINATE	1	TRUE	NA	0.533335001278103	2		617	602	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422380	47422380	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1048525052	NA	P-0004580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	142	549	1	ENST00000377045.4:c.14G>A	p.Arg5Gln	p.R5Q	ENST00000377045	NM_001654.4	5	cGg/cAg	2/16	NA	2	FACETS	1	0.95	1			1	INDETERMINATE	1	TRUE	NA	0.533335001278103	2		550	507	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54948551	54949166	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTCTATGAATAACTCTCTTCGAATGACAGTAAGACAGGGCATTTGCCAATTCTGTTATATACTGTTAAAACAATATTGAAAGCCTATGTTTTAGATTTTATATAACACAAGTTAATATTAGACATCTCTTCCGAAAGGAACACAACATAGATTTAACATGGTTTGCAGGTTTTGGCCAGGCACAGTGGCTCACACCTATAATCCCAACACTTTGGGGGACTGAGGTGGGAGGATCACTTGAGCCCAGGGGTTCAAGACCAGCCTGGGAAACATAGCAAGACTCCATCTCTACAAAAATTTAAAAATTAGCTGAGCGTGATGGTGCATGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGGATTGCTTGAGACCAGGAGGTCAAAGCTGCAGTGAGCCATGATCACACTTCAGCCTGGGTGACAGAAGGAGACCCTGTCTCAAAAAGGAAAAGACAAAACAAAAAATACATTTTGCAGGTTTTAAAGCAAGGATTGTAGAAATTATATAGGAGTCTACACACACACACACACACACACACACACACACACATCAACTGAACCAATTTATAGTGGTTAGCATGAAGTGAAATTACCCAATGCTTAGTCATC	TCTCTATGAATAACTCTCTTCGAATGACAGTAAGACAGGGCATTTGCCAATTCTGTTATATACTGTTAAAACAATATTGAAAGCCTATGTTTTAGATTTTATATAACACAAGTTAATATTAGACATCTCTTCCGAAAGGAACACAACATAGATTTAACATGGTTTGCAGGTTTTGGCCAGGCACAGTGGCTCACACCTATAATCCCAACACTTTGGGGGACTGAGGTGGGAGGATCACTTGAGCCCAGGGGTTCAAGACCAGCCTGGGAAACATAGCAAGACTCCATCTCTACAAAAATTTAAAAATTAGCTGAGCGTGATGGTGCATGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGGATTGCTTGAGACCAGGAGGTCAAAGCTGCAGTGAGCCATGATCACACTTCAGCCTGGGTGACAGAAGGAGACCCTGTCTCAAAAAGGAAAAGACAAAACAAAAAATACATTTTGCAGGTTTTAAAGCAAGGATTGTAGAAATTATATAGGAGTCTACACACACACACACACACACACACACACACACACATCAACTGAACCAATTTATAGTGGTTAGCATGAAGTGAAATTACCCAATGCTTAGTCATC	-	novel	NA	P-0004580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1322	428	502	0	ENST00000312783.6:c.706-554_767del		p.X236_splice	ENST00000312783	NM_198436.1	236		8/10	0.533335001278103	13	FACETS	0.902	0.857	0.947			1	CLONAL	4	TRUE	NA	0.533335001278103	13		502	1750	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577125	7577131	+	frameshift_variant	Frame_Shift_Del	DEL	CTCAAAG	CTCAAAG	-	novel	NA	P-0004580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	235	559	0	ENST00000269305.4:c.807_813del	p.Ser269ArgfsTer74	p.S269Rfs*74	ENST00000269305	NM_001126112.2	269	agCTTTGAG/ag	8/11	0.500203069120322	2	FACETS	0.928	0.877	0.979	0.928	0.877	0.979	CLONAL	2	TRUE	0	0.533335001278103	2		559	475	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160680	56160689	+	frameshift_variant	Frame_Shift_Del	DEL	ACTGCAGCAG	ACTGCAGCAG	-	novel	NA	P-0004580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	181	462	0	ENST00000399503.3:c.955_964del	p.Leu319Ter	p.L319*	ENST00000399503	NM_005921.1	318	ttACTGCAGCAG/tt	4/20	0.252284707823738	4	FACETS	0.995	0.925	1	0.995	0.925	1	INDETERMINATE	2	TRUE	2	0.533335001278103	4		462	523	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015097	27015097	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004685-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	150	455	1	ENST00000335756.4:c.199T>C	p.Phe67Leu	p.F67L	ENST00000335756	NM_001809.3	67	Ttc/Ctc	2/5	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.460677946722152	2		456	603	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938089	76938092	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	novel	NA	P-0004685-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	136	187	0	ENST00000373344.5:c.2656_2659del	p.Glu886LeufsTer18	p.E886Lfs*18	ENST00000373344	NM_000489.3	886	GAGAct/ct	9/35	1	1	FACETS	0.797	0.739	0.856	1	0.99	1	SUBCLONAL	2	TRUE	0	0.460677946722152	1		187	285	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113113	+	missense_variant	Missense_Mutation	DNP	CG	CG	AT	novel	NA	P-0004685-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	122	368	0	ENST00000345146.2:c.394_395delinsAT	p.Arg132Ile	p.R132I	ENST00000345146	NM_005896.2	132	CGt/ATt	4/10	1	2	FACETS	0.994	0.902	1	0.994	0.902	1	CLONAL	1	TRUE	1	0.460677946722152	2		368	533	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0004691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	130	262	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	0.222693264671531	2		262	894	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004702-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	22	387	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.111660239971822	3	FACETS	0.609	0.47	0.771	0.305	0.235	0.386	SUBCLONAL	1	TRUE	1	0.14	3		387	552	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0004702-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	12	194	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.542	0.38	0.743	0.542	0.38	0.743	SUBCLONAL	1	TRUE	1	0.14	2		194	316	SUCCESS
AR	367	MSKCC	GRCh37	X	66943543	66943543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852581	NA	P-0004704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	229	262	0	ENST00000374690.3:c.2623C>T	p.His875Tyr	p.H875Y	ENST00000374690	NM_000044.3	875	Cat/Tat	8/8	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.659827264765573	1		262	335	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190670454	190670454	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	200	457	0	ENST00000441310.2:c.392C>T	p.Ser131Phe	p.S131F	ENST00000441310	NM_000534.4	131	tCt/tTt	4/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.659827264765573	2		457	559	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872477	35872477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	165	500	0	ENST00000216797.5:c.426del	p.Arg143GlufsTer21	p.R143Efs*21	ENST00000216797	NM_020529.2	142	ttT/tt	3/6	NA	2	FACETS	0.937	0.866	1			1	INDETERMINATE	1	TRUE	NA	0.659827264765573	2		500	534	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620611	52620611	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	181	355	0	ENST00000394830.3:c.3142del	p.Ile1048LeufsTer86	p.I1048Lfs*86	ENST00000394830	NM_018313.4	1048	Att/tt	21/30	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.659827264765573	2		355	454	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0004706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	117	323	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	1	2	FACETS	0.763	0.693	0.834	0.763	0.693	0.834	SUBCLONAL	1	TRUE	1	0.755772172681421	2		323	406	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0004706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	191	395	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	0.959	0.894	1	0.959	0.894	1	CLONAL	1	TRUE	1	0.755772172681421	2		395	527	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240780	55240780	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150423237	NA	P-0004706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	181	468	0	ENST00000275493.2:c.2024G>A	p.Arg675Gln	p.R675Q	ENST00000275493	NM_005228.3	675	cGg/cAg	17/28	1	2	FACETS	0.882	0.819	0.946	0.882	0.819	0.946	CLONAL	1	TRUE	1	0.755772172681421	2		468	543	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	401951	401951	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	225	630	0	ENST00000399788.2:c.4840A>G	p.Asn1614Asp	p.N1614D	ENST00000399788	NM_001042603.1	1614	Aac/Gac	27/28	NA	2	FACETS	0.887	0.831	0.945			1	INDETERMINATE	1	TRUE	NA	0.755772172681421	2		630	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0004722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	492	553	3	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.793982134608141	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.793982134608141	2		556	584	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469065	25469065	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	209	487	0	ENST00000264709.3:c.1393C>G	p.Pro465Ala	p.P465A	ENST00000264709	NM_175629.2	465	Ccc/Gcc	11/23	0.793982134608141	4	FACETS	0.962	0.893	1	0.481	0.446	0.517	CLONAL	1	TRUE	2	0.793982134608141	4		487	982	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0004725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	40	595	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.112830057494639	0	FACETS	0.534	0.444	0.635			1	INDETERMINATE	1	TRUE	0	0.26	0		596	426	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99136554	99136554	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	38	343	0	ENST00000074304.5:c.43C>A	p.Arg15Ser	p.R15S	ENST00000074304	NM_001134224.1	15	Cgt/Agt	3/26	1	2	FACETS	0.5	0.412	0.598	0.5	0.412	0.598	SUBCLONAL	1	TRUE	1	0.26	2		343	585	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0004741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	185	213	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.286965725962538	5	FACETS	0.894	0.832	0.957	0.894	0.832	0.957	CLONAL	4	TRUE	1	0.286965725962538	5		213	516	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885835	23885835	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	112	704	0	ENST00000374561.5:c.83G>C	p.Arg28Pro	p.R28P	ENST00000374561	NM_002167.4	28	cGa/cCa	1/3	1	2	FACETS	0.928	0.834	1	0.928	0.834	1	CLONAL	1	TRUE	1	0.286965725962538	2		704	841	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309827	65309827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	108	530	0	ENST00000342505.4:c.2323G>A	p.Asp775Asn	p.D775N	ENST00000342505	NM_002227.2	775	Gac/Aac	17/25	0.289623823362757	4	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.286965725962538	4		530	682	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310572	65310572	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	165	352	0	ENST00000342505.4:c.2116G>A	p.Glu706Lys	p.E706K	ENST00000342505	NM_002227.2	706	Gag/Aag	16/25	0.289623823362757	4	FACETS	1	0.928	1			1	CLONAL	3	TRUE	NA	0.286965725962538	4		352	492	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226574083	226574083	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs955943944	NA	P-0004741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	81	601	0	ENST00000366794.5:c.778G>A	p.Asp260Asn	p.D260N	ENST00000366794	NM_001618.3	260	Gac/Aac	6/23	0.238913443825382	0	FACETS	0.716	0.632	0.806			1	SUBCLONAL	1	TRUE	0	0.286965725962538	0		601	562	SUCCESS
REL	5966	MSKCC	GRCh37	2	61121646	61121646	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	108	386	0	ENST00000295025.8:c.268G>A	p.Glu90Lys	p.E90K	ENST00000295025	NM_002908.2	90	Gaa/Aaa	3/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.286965725962538	2		386	695	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610579	215610579	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs767208318	NA	P-0004741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	108	382	0	ENST00000260947.4:c.1678-1G>T		p.X560_splice	ENST00000260947	NM_000465.2	560			0.289623823362757	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.286965725962538	1		382	471	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204626	128204626	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	77	583	0	ENST00000341105.2:c.815G>T	p.Gly272Val	p.G272V	ENST00000341105	NM_032638.4	272	gGg/gTg	3/6	0.289623823362757	3	FACETS	1	0.897	1			1	CLONAL	1	TRUE	NA	0.286965725962538	3		583	600	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55524236	55524236	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	107	525	0	ENST00000288135.5:c.55C>G	p.Arg19Gly	p.R19G	ENST00000288135	NM_000222.2	19	Cgc/Ggc	1/21	0.148496428521545	0	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	0	0.286965725962538	0		525	462	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729782	41729782	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	152	722	0	ENST00000242208.4:c.747G>C	p.Glu249Asp	p.E249D	ENST00000242208	NM_002192.2	249	gaG/gaC	3/3	0.246038910303604	4	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.286965725962538	4		722	931	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989440	85989440	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0004741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	114	382	0	ENST00000263360.6:c.1200-1G>C		p.X400_splice	ENST00000263360	NM_003797.3	400			0.289623823362757	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.286965725962538	1		382	475	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690579	88690579	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	28	399	0	ENST00000360948.2:c.451A>T	p.Ser151Cys	p.S151C	ENST00000360948	NM_001012338.2	151	Agt/Tgt	5/19	0.281969176812348	0	FACETS	0.366	0.292	0.45			1	SUBCLONAL	1	TRUE	0	0.286965725962538	0		399	380	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576048	29576048	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854559	NA	P-0004741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	114	591	1	ENST00000356175.3:c.4021C>T	p.Gln1341Ter	p.Q1341*	ENST00000356175	NM_000267.3	1341	Cag/Tag	30/57	0.281969176812348	0	FACETS	1	0.949	1			1	CLONAL	1	TRUE	0	0.286965725962538	0		592	527	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732950	74732950	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0004741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	177	392	0	ENST00000359995.5:c.293C>G	p.Ser98Ter	p.S98*	ENST00000359995	NM_001195427.1	98	tCa/tGa	1/3	0.289623823362757	5	FACETS	0.929	0.86	1	0.697	0.645	0.751	CLONAL	3	TRUE	1	0.286965725962538	5		392	633	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420311	49420460	+	inframe_deletion	In_Frame_Del	DEL	CAGCTCTTGCTCACAGGGCCCCTTGATCTTATGCATTGGACACAGCATGGTCTTGTCCTTGAAGAACATGCACTTGGCACGGATGGCACAAGCAAAATGGTAGACATTGGGGCAACGCATGCGATTGCAGCTGCTGGTGGCACCAGTTCG	CAGCTCTTGCTCACAGGGCCCCTTGATCTTATGCATTGGACACAGCATGGTCTTGTCCTTGAAGAACATGCACTTGGCACGGATGGCACAAGCAAAATGGTAGACATTGGGGCAACGCATGCGATTGCAGCTGCTGGTGGCACCAGTTCG	-	novel	NA	P-0004741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	117	588	0	ENST00000301067.7:c.15289_15438del	p.Arg5097_Leu5146del	p.R5097_L5146del	ENST00000301067	NM_003482.3	5097	CGAACTGGTGCCACCAGCAGCTGCAATCGCATGCGTTGCCCCAATGTCTACCATTTTGCTTGTGCCATCCGTGCCAAGTGCATGTTCTTCAAGGACAAGACCATGCTGTGTCCAATGCATAAGATCAAGGGGCCCTGTGAGCAAGAGCTG/-	48/54	0.170460977974735	1	FACETS	1	0.958	1	1	0.958	1	INDETERMINATE	1	TRUE	0	0.286965725962538	1		588	629	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428425	72428425	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	173	506	0	ENST00000477973.2:c.577del	p.Asn195IlefsTer13	p.N195Ifs*13	ENST00000477973	NM_012234.5	193	aaG/aa	2/4	0.289623823362757	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.286965725962538	1		506	716	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131463	202131463	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	73	290	0	ENST00000358485.4:c.431A>T	p.Glu144Val	p.E144V	ENST00000358485	NM_001080125.1	144	gAg/gTg	2/9	0.273134370438668	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		290	550	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0004759-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	194	358	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.669725891948576	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.669725891948576	1		358	272	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604682	48604684	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0004759-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	336	402	0	ENST00000342988.3:c.1505_1507del	p.Arg502del	p.R502del	ENST00000342988	NM_005359.5	502	AGG/-	12/12	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	2	TRUE	NA	0.669725891948576	2		402	501	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549139	87549139	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	243	325	0	ENST00000277120.3:c.1696G>A	p.Gly566Arg	p.G566R	ENST00000277120		566	Gga/Aga	15/19	0.496118463161166	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.496118463161166	3		325	562	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578313	7578425	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGAGGCCTGGGGACCCTGGGCAACCAGCCCTGTCGTCTCTCCAGCCCCAGCTGCTCACCATCGCTATCTGAGCAGCGCTCATGGTGGGGGCAGCGCCTCACAACCTCCGTCAT	AGAGGCCTGGGGACCCTGGGCAACCAGCCCTGTCGTCTCTCCAGCCCCAGCTGCTCACCATCGCTATCTGAGCAGCGCTCATGGTGGGGGCAGCGCCTCACAACCTCCGTCAT	-	novel	NA	P-0004775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	453	260	0	ENST00000269305.4:c.505_560-24del		p.X169_splice	ENST00000269305	NM_001126112.2	169		5/11	0.496118463161166	2	FACETS	0.861	0.832	0.89	1	0.996	1	CLONAL	3	TRUE	0	0.496118463161166	2		260	707	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056053	26056067	+	inframe_deletion	In_Frame_Del	DEL	CCTTGGGCTTAGCGG	CCTTGGGCTTAGCGG	-	rs756916945	NA	P-0004775-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	96	194	0	ENST00000343677.2:c.590_604del	p.Ala197_Lys201del	p.A197_K201del	ENST00000343677	NM_005319.3	197	gCCGCTAAGCCCAAGGtt/gtt	1/1	0.496118463161166	3	FACETS	0.877	0.783	0.976	0.438	0.391	0.488	CLONAL	1	TRUE	1	0.496118463161166	3		194	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0004777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	152	316	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.152365593949219	2	FACETS	0.927	0.85	1	0.927	0.85	1	CLONAL	2	TRUE	0	0.240064696136843	2		316	683	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750482	41750482	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs559227588	NA	P-0004777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	36	335	0	ENST00000226382.2:c.146C>A	p.Thr49Asn	p.T49N	ENST00000226382	NM_003924.3	49	aCc/aAc	1/3	0.183755808825733	1	FACETS	0.447	0.367	0.538	0.447	0.367	0.538	SUBCLONAL	1	TRUE	0	0.240064696136843	1		335	590	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143326466	143326466	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	24	190	1	ENST00000262992.4:c.148C>A	p.Leu50Ile	p.L50I	ENST00000262992	NM_001101669.1	50	Ctc/Atc	4/24	0.183755808825733	1	FACETS	0.42	0.329	0.526	0.42	0.329	0.526	SUBCLONAL	1	TRUE	0	0.240064696136843	1		191	419	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126424	5126424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs780942191	NA	P-0004777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	17	243	0	ENST00000381652.3:c.3269G>C	p.Arg1090Thr	p.R1090T	ENST00000381652	NM_004972.3	1090	aGa/aCa	24/25	0.228605156162341	1	FACETS	0.659	0.494	0.854	0.659	0.494	0.854	SUBCLONAL	1	TRUE	0	0.240064696136843	1		243	189	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871890	12871890	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0004777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	41	126	0	ENST00000228872.4:c.*8+2T>C			ENST00000228872	NM_004064.3	-/198			0.228605156162341	1	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	0	0.240064696136843	1		126	281	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916753	48916753	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1555282775	NA	P-0004777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	17	282	2	ENST00000267163.4:c.283A>T	p.Lys95Ter	p.K95*	ENST00000267163	NM_000321.2	95	Aaa/Taa	3/27	0.240064696136843	1	FACETS	0.434	0.324	0.565	0.434	0.324	0.565	SUBCLONAL	1	TRUE	0	0.240064696136843	1		284	287	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749415085	NA	P-0004781-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	149	511	0	ENST00000263967.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000263967	NM_006218.2	38	Cgt/Tgt	2/21	0.228377509608302	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.228377509608302	1		511	1020	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0004781-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	50	344	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.228377509608302	3	FACETS	0.621	0.525	0.726	0.207	0.175	0.242	SUBCLONAL	1	TRUE	0	0.228377509608302	3		344	786	SUCCESS
APC	324	MSKCC	GRCh37	5	112175593	112175611	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAAGTAAAACACCTCCA	CAGAAGTAAAACACCTCCA	-	novel	NA	P-0004781-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	106	418	0	ENST00000257430.4:c.4303_4321del	p.Arg1435HisfsTer32	p.R1435Hfs*32	ENST00000257430	NM_000038.5	1434	agCAGAAGTAAAACACCTCCA/ag	16/16	0.120807477656454	4	FACETS	1	0.966	1	0.597	0.534	0.664	INDETERMINATE	1	TRUE	2	0.228377509608302	4		418	955	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579483	7579484	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0004781-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	115	276	0	ENST00000269305.4:c.203_204del	p.Glu68GlyfsTer80	p.E68Gfs*80	ENST00000269305	NM_001126112.2	68	gAG/g	4/11	0.228377509608302	3	FACETS	1	0.983	1	0.746	0.672	0.824	CLONAL	1	TRUE	1	0.228377509608302	3		276	752	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599332	55599332	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519710	NA	P-0004784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	605	254	0	ENST00000288135.5:c.2458G>T	p.Asp820Tyr	p.D820Y	ENST00000288135	NM_000222.2	820	Gat/Tat	17/21	0.822904048659947	2	FACETS	0.956	0.937	0.974	0.956	0.937	0.974	CLONAL	2	TRUE	0	0.88141941227041	2		254	718	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033823	49033838	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GTGTATCGGCTAGCCT	GTGTATCGGCTAGCCT	-	novel	NA	P-0004784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	224	197	0	ENST00000267163.4:c.1961-1_1975del		p.X654_splice	ENST00000267163	NM_000321.2	654		20/27	0.88141941227041	1	FACETS	0.997	0.959	1	0.997	0.959	1	CLONAL	1	TRUE	0	0.88141941227041	1		197	285	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593582	55593598	+	protein_altering_variant,splice_region_variant	In_Frame_Del	DEL	AAACCCATGTATGAAGT	AAACCCATGTATGAAGT	CA	novel	NA	P-0004784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	541	295	0	ENST00000288135.5:c.1648_1664delinsCA	p.Lys550_Val555delinsGln	p.K550_V555delinsQ	ENST00000288135	NM_000222.2	550	AAACCCATGTATGAAGTa/CAa	11/21	0.822904048659947	2	FACETS	0.94	0.919	0.96	0.94	0.919	0.96	CLONAL	2	TRUE	0	0.88141941227041	2		295	653	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409987	63409987	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004794-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	242	530	0	ENST00000330258.3:c.3180C>A	p.Cys1060Ter	p.C1060*	ENST00000330258	NM_152424.3	1060	tgC/tgA	2/2	0.164172130106573	0	FACETS	0.298	0.278	0.318			1	INDETERMINATE	1	TRUE	0	0.641768002279685	0		530	907	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145639	61145639	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004794-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	235	460	0	ENST00000295025.8:c.753del	p.Ala252LeufsTer6	p.A252Lfs*6	ENST00000295025	NM_002908.2	251	Aaa/aa	7/11	1	2	FACETS	0.945	0.885	1	0.945	0.885	1	CLONAL	1	TRUE	1	0.641768002279685	2		460	775	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0004803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	68	287	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.907	0.795	1	0.907	0.795	1	CLONAL	1	TRUE	1	0.479129602536512	2		287	313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0004803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	223	386	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.479129602536512	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.479129602536512	1		386	569	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0004803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	70	294	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	0.360134785846534	3	FACETS	0.951	0.833	1	0.475	0.416	0.538	CLONAL	1	TRUE	1	0.479129602536512	3		294	381	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593505	48593505	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	74	282	0	ENST00000342988.3:c.1256G>T	p.Gly419Val	p.G419V	ENST00000342988	NM_005359.5	419	gGg/gTg	10/12	0.479129602536512	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.479129602536512	1		282	202	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445111	89445111	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	36	244	0	ENST00000336596.2:c.1431G>T	p.Lys477Asn	p.K477N	ENST00000336596	NM_005233.5	477	aaG/aaT	6/17	1	2	FACETS	0.771	0.64	0.914	0.771	0.64	0.914	CLONAL	1	TRUE	1	0.479129602536512	2		244	195	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356149	66356149	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs142589245	NA	P-0004803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	157	333	0	ENST00000273854.3:c.1348T>G	p.Leu450Val	p.L450V	ENST00000273854	NM_004439.5	450	Ttg/Gtg	5/18	0.233723740395471	2	FACETS	0.803	0.744	0.863	0.803	0.744	0.863	INDETERMINATE	2	TRUE	0	0.479129602536512	2		333	408	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40738998	40738998	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	269	276	1	ENST00000373198.4:c.3286G>T	p.Ala1096Ser	p.A1096S	ENST00000373198	NM_133170.3	1096	Gct/Tct	24/32	0.28365745512109	5	FACETS	1	0.961	1	0.687	0.645	0.729	INDETERMINATE	2	TRUE	2	0.479129602536512	5		277	937	SUCCESS
APC	324	MSKCC	GRCh37	5	112175749	112175749	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004803-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	118	281	0	ENST00000257430.4:c.4458del	p.Asp1486GlufsTer21	p.D1486Efs*21	ENST00000257430	NM_000038.5	1486	gaT/ga	16/16	0.360134785846534	3	FACETS	0.791	0.72	0.864	0.791	0.72	0.864	SUBCLONAL	2	TRUE	1	0.479129602536512	3		281	386	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004812-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	173	225	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.748358788510179	2		225	411	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913499	NA	P-0004812-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	177	338	0	ENST00000345146.2:c.394C>A	p.Arg132Ser	p.R132S	ENST00000345146	NM_005896.2	132	Cgt/Agt	4/10	1	2	FACETS	0.919	0.853	0.986	0.919	0.853	0.986	CLONAL	1	TRUE	1	0.748358788510179	2		338	515	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791794	42791794	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004812-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	318	378	0	ENST00000575354.2:c.680A>T	p.Asn227Ile	p.N227I	ENST00000575354	NM_015125.3	227	aAc/aTc	5/20	0.748358788510179	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.748358788510179	1		378	504	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802662	135802662	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004812-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	297	380	0	ENST00000298552.3:c.136del	p.Val46TrpfsTer16	p.V46Wfs*16	ENST00000298552	NM_001162426.1	46	Gtg/tg	4/23	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.748358788510179	2		380	753	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191493	10191493	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs5030622	NA	P-0004813-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	244	670	0	ENST00000256474.2:c.486C>A	p.Cys162Ter	p.C162*	ENST00000256474	NM_000551.3	162	tgC/tgA	3/3	0.584371459859356	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.584371459859356	1		670	569	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147552	47147552	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057518410	NA	P-0004813-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	157	470	0	ENST00000409792.3:c.4774C>T	p.Arg1592Ter	p.R1592*	ENST00000409792	NM_014159.6	1592	Cga/Tga	6/21	0.584371459859356	1	FACETS	0.985	0.914	1	0.985	0.914	1	CLONAL	1	TRUE	0	0.584371459859356	1		470	386	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845145	151845145	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004813-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	343	930	1	ENST00000262189.6:c.13867C>A	p.Leu4623Met	p.L4623M	ENST00000262189	NM_170606.2	4623	Ctg/Atg	52/59	1	2	FACETS	0.993	0.94	1	0.993	0.94	1	CLONAL	1	TRUE	1	0.584371459859356	2		931	1182	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243870	53243870	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0004813-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	424	605	0	ENST00000375401.3:c.1122+1G>A		p.X374_splice	ENST00000375401	NM_004187.3	374			1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.584371459859356	1		605	708	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566749	212566749	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	105	446	0	ENST00000342788.4:c.1432T>G	p.Phe478Val	p.F478V	ENST00000342788	NM_005235.2	478	Ttc/Gtc	12/28	1	2	FACETS	0.279	0.249	0.31	0.279	0.249	0.31	SUBCLONAL	1	TRUE	1	0.837916918138889	2		446	899	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457676	149457676	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	130	488	0	ENST00000286301.3:c.728A>G	p.Lys243Arg	p.K243R	ENST00000286301	NM_005211.3	243	aAg/aGg	5/22	1	2	FACETS	0.402	0.365	0.442	0.402	0.365	0.442	SUBCLONAL	1	TRUE	1	0.837916918138889	2		488	771	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781122	161781122	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1283	137	475	3	ENST00000366898.1:c.1283del	p.Asn428MetfsTer7	p.N428Mfs*7	ENST00000366898	NM_004562.2	428	aAt/at	11/12	0.384491614520574	5	FACETS	0.52	0.471	0.571			1	INDETERMINATE	1	TRUE	NA	0.837916918138889	5		478	1420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691025	NA	P-0004822-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	535	456	0	ENST00000269305.4:c.785G>T	p.Gly262Val	p.G262V	ENST00000269305	NM_001126112.2	262	gGt/gTt	8/11	0.710301746732332	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.732098456189853	2		456	727	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607131	189607131	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	164	333	0	ENST00000264731.3:c.1510C>G	p.Pro504Ala	p.P504A	ENST00000264731	NM_003722.4	504	Ccc/Gcc	12/14	1	2	FACETS	0.991	0.923	1	0.991	0.923	1	CLONAL	1	TRUE	1	0.899618619405991	2		333	368	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467694	50467694	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	402	414	0	ENST00000331340.3:c.929T>C	p.Val310Ala	p.V310A	ENST00000331340	NM_006060.4	310	gTg/gCg	8/8	0.858352305335961	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.899618619405991	3		414	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0004846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	64	386	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.852	0.741	0.971	0.852	0.741	0.971	CLONAL	1	TRUE	1	0.387319523480383	2		386	388	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0004846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	40	330	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.387319523480383	2		330	185	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224307	55224307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1164954595	NA	P-0004846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	121	307	0	ENST00000275493.2:c.1088C>T	p.Thr363Ile	p.T363I	ENST00000275493	NM_005228.3	363	aCc/aTc	9/28	0.38731952529636	3	FACETS	1	0.942	1	0.528	0.478	0.581	CLONAL	1	TRUE	1	0.387319523480383	3		307	706	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857505	57857505	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2564	260	469	0	ENST00000228682.2:c.31A>G	p.Ser11Gly	p.S11G	ENST00000228682	NM_005269.2	11	Agt/Ggt	2/12	0.387319523480383	21	FACETS	1	0.978	1			1	CLONAL	2	TRUE	NA	0.387319523480383	21		469	2824	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610115	28610115	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	121	391	0	ENST00000241453.7:c.1375T>A	p.Leu459Ile	p.L459I	ENST00000241453	NM_004119.2	459	Tta/Ata	11/24	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.387319523480383	2		391	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578177	7578177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	38	341	0	ENST00000269305.4:c.672G>C	p.Glu224Asp	p.E224D	ENST00000269305	NM_001126112.2	224	gaG/gaC	6/11	1	2	FACETS	0.406	0.335	0.485	0.406	0.335	0.485	SUBCLONAL	1	TRUE	1	0.387319523480383	2		341	483	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0004856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	107	381	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.889	0.8	0.983	0.889	0.8	0.983	CLONAL	1	TRUE	1	0.431516226776382	2		381	558	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0004856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	140	260	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.430054924097278	2	FACETS	1	0.964	1	0.55	0.503	0.599	CLONAL	1	TRUE	0	0.431516226776382	2		260	590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577507	7577507	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	140	380	1	ENST00000269305.4:c.774A>T	p.Glu258Asp	p.E258D	ENST00000269305	NM_001126112.2	258	gaA/gaT	7/11	0.431516226776382	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.431516226776382	1		381	465	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553588	106553588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753673199	NA	P-0004856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	84	303	0	ENST00000369096.4:c.1553C>T	p.Thr518Met	p.T518M	ENST00000369096	NM_001198.3	518	aCg/aTg	5/7	0.431516226776382	1	FACETS	0.937	0.835	1	0.937	0.835	1	CLONAL	1	TRUE	0	0.431516226776382	1		303	326	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974778	21974786	+	inframe_deletion	In_Frame_Del	DEL	CCAGCCAGT	CCAGCCAGT	-	novel	NA	P-0004856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	51	175	0	ENST00000304494.5:c.41_49del	p.Asp14_Leu16del	p.D14_L16del	ENST00000304494	NM_000077.4	14	gACTGGCTGGcc/gcc	1/3	0.431516226776382	1	FACETS	0.854	0.735	0.982	0.854	0.735	0.982	CLONAL	1	TRUE	0	0.431516226776382	1		175	217	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0004861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	792	354	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.691675605399049	4	FACETS	1	0.997	1	1	0.997	1	CLONAL	4	TRUE	0	0.691675605399049	4		354	910	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625120	69625120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782246758	NA	P-0004861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	160	404	0	ENST00000334134.2:c.673G>A	p.Val225Ile	p.V225I	ENST00000334134	NM_005247.2	225	Gtt/Att	3/3	0.691675605399049	4	FACETS	1	0.961	1	0.359	0.329	0.389	CLONAL	1	TRUE	1	0.691675605399049	4		404	727	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226573315	226573315	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	448	442	1	ENST00000366794.5:c.901C>A	p.Gln301Lys	p.Q301K	ENST00000366794	NM_001618.3	301	Cag/Aag	7/23	0.599227247320818	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.691675605399049	4		443	1024	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142990	47142990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	592	496	0	ENST00000409792.3:c.4973C>T	p.Ser1658Leu	p.S1658L	ENST00000409792	NM_014159.6	1658	tCa/tTa	8/21	0.691675605399049	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.691675605399049	2		496	753	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015170	71015170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1185427456	NA	P-0004861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	417	373	2	ENST00000318789.4:c.1760C>T	p.Thr587Ile	p.T587I	ENST00000318789	NM_032682.5	587	aCc/aTc	20/21	0.691675605399049	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.691675605399049	2		375	565	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467859	66467859	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	713	481	1	ENST00000273854.3:c.410G>A	p.Cys137Tyr	p.C137Y	ENST00000273854	NM_004439.5	137	tGc/tAc	3/18	0.691675605399049	4	FACETS	0.868	0.841	0.894	0.868	0.841	0.894	CLONAL	3	TRUE	1	0.691675605399049	4		482	1340	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298229	123298229	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	240	312	0	ENST00000358487.5:c.625G>A	p.Val209Ile	p.V209I	ENST00000358487	NM_000141.4	209	Gta/Ata	6/18	0.691675605399049	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.691675605399049	3		312	453	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440200	49440201	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0004861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	172	413	0	ENST00000301067.7:c.4425_4426del	p.Ser1476LeufsTer14	p.S1476Lfs*14	ENST00000301067	NM_003482.3	1475	gtGTcc/gtcc	16/54	0.691675605399049	3	FACETS	0.881	0.812	0.952	0.44	0.406	0.476	CLONAL	1	TRUE	1	0.691675605399049	3		413	760	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0004862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	142	287	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.239583048028305	3	FACETS	0.792	0.725	0.86	0.792	0.725	0.86	INDETERMINATE	2	TRUE	1	0.404587138152965	3		287	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0004862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	324	334	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.404587138152965	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.404587138152965	2		334	717	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0004862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	288	450	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.404587138152965	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.404587138152965	2		450	693	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660408	227660408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747700323	NA	P-0004862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	181	298	0	ENST00000305123.5:c.3047G>A	p.Arg1016Gln	p.R1016Q	ENST00000305123	NM_005544.2	1016	cGa/cAa	1/2	0.17608608867584	3	FACETS	0.854	0.791	0.918			1	INDETERMINATE	2	TRUE	NA	0.404587138152965	3		298	630	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878142	48878142	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	127	150	0	ENST00000267163.4:c.94G>A	p.Asp32Asn	p.D32N	ENST00000267163	NM_000321.2	32	Gac/Aac	1/27	0.404587138152965	5	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	3	0.404587138152965	5		150	415	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108583	8108583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	80	461	0	ENST00000585124.1:c.812C>T	p.Pro271Leu	p.P271L	ENST00000585124	NM_004217.3	271	cCa/cTa	8/9	0.404587138152965	2	FACETS	0.534	0.469	0.603	0.267	0.234	0.302	SUBCLONAL	1	TRUE	0	0.404587138152965	2		461	741	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262213	10262213	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1336324296	NA	P-0004862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	72	361	0	ENST00000340748.4:c.2078A>G	p.Asn693Ser	p.N693S	ENST00000340748		693	aAt/aGt	23/40	0.223977756543236	3	FACETS	0.556	0.485	0.633	0.185	0.161	0.211	INDETERMINATE	1	TRUE	0	0.404587138152965	3		361	769	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0004896-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	137	446	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	0.62320889171686	2		446	387	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004896-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	246	176	0	ENST00000206249.3:c.1607T>A	p.Leu536His	p.L536H	ENST00000206249	NM_000125.3	536	cTc/cAc	8/8	0.62320889171686	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.62320889171686	1		176	480	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0004909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	72	388	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.12	2		389	1117	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057520005	NA	P-0004909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1173	43	437	0	ENST00000269305.4:c.820G>C	p.Val274Leu	p.V274L	ENST00000269305	NM_001126112.2	274	Gtt/Ctt	8/11	1	2	FACETS	0.589	0.491	0.7	0.589	0.491	0.7	SUBCLONAL	1	TRUE	1	0.12	2		437	1216	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120612018	120612018	+	start_lost	Translation_Start_Site	SNP	C	C	T	rs56159748	NA	P-0004909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	15	34	0	ENST00000256646.2:c.3G>A	p.Met1?	p.M1?	ENST00000256646	NM_024408.3	1	atG/atA	1/34	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.12	2		34	176	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466824	57466824	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	33	232	0	ENST00000371085.3:c.43G>T	p.Glu15Ter	p.E15*	ENST00000371085	NM_000516.4	15	Gag/Tag	1/13	0.3	2	FACETS	0.849	0.689	1			1	CLONAL	1	TRUE	NA	0.12	2		232	648	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0004927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	4194	478	5	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.769675452968741	17	FACETS	0.999	0.991	1			1	CLONAL	15	TRUE	NA	0.769675452968741	17		483	4927	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0004927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5599	271	401	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.769675452968741	17	FACETS	0.812	0.756	0.871			1	CLONAL	1	TRUE	NA	0.769675452968741	17		401	5870	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367288	50367288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775793261	NA	P-0004927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1962	251	371	2	ENST00000331340.3:c.95C>T	p.Pro32Leu	p.P32L	ENST00000331340	NM_006060.4	32	cCg/cTg	3/8	0.769675452968741	9	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.769675452968741	9		373	2213	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992637	72992637	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	358	450	1	ENST00000268489.5:c.1408G>T	p.Glu470Ter	p.E470*	ENST00000268489	NM_006885.3	470	Gaa/Taa	2/10	0.500264188903905	4	FACETS	1	0.995	1	0.73	0.692	0.768	CLONAL	1	TRUE	2	0.769675452968741	4		451	1128	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44527560	44527560	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0004927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	239	420	0	ENST00000291552.4:c.44+1G>A		p.X15_splice	ENST00000291552	NM_006758.2	15			0.769675452968741	3	FACETS	0.98	0.916	1	0.49	0.458	0.523	CLONAL	1	TRUE	1	0.769675452968741	3		420	878	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433625	49433626	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0004931-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	138	506	3	ENST00000301067.7:c.7927_7928del	p.Glu2643LysfsTer11	p.E2643Kfs*11	ENST00000301067	NM_003482.3	2643	GAa/a	31/54	1	2	FACETS	0.759	0.695	0.825	0.759	0.695	0.825	SUBCLONAL	1	TRUE	1	0.73	2		509	498	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0004939-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	15	511	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.371681087771157	5	FACETS	0.361	0.263	0.478	0.12	0.087	0.16	SUBCLONAL	1	TRUE	2	0.543137775570511	5		511	278	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913136	44913136	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004939-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	26	901	1	ENST00000377967.4:c.811C>T	p.Gln271Ter	p.Q271*	ENST00000377967	NM_021140.2	271	Cag/Tag	10/29	0.310834454312112	4	FACETS	0.403	0.319	0.499			1	INDETERMINATE	1	TRUE	NA	0.543137775570511	4		902	367	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662539	227662539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004939-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	12	382	0	ENST00000305123.5:c.916G>A	p.Glu306Lys	p.E306K	ENST00000305123	NM_005544.2	306	Gag/Aag	1/2	0.441012719551026	4	FACETS	0.334	0.235	0.456			1	SUBCLONAL	1	TRUE	NA	0.543137775570511	4		382	204	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268401	46268401	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004939-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	29	967	0	ENST00000371998.3:c.2788A>G	p.Met930Val	p.M930V	ENST00000371998		930	Atg/Gtg	15/23	NA	2	FACETS	0.25	0.2	0.307			1	INDETERMINATE	1	TRUE	NA	0.543137775570511	2		967	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578206	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs886039484	NA	P-0004942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	218	470	0	ENST00000269305.4:c.643A>G	p.Ser215Gly	p.S215G	ENST00000269305	NM_001126112.2	215	Agt/Ggt	6/11	0.6196775180366	3	FACETS	0.932	0.889	0.974	0.932	0.889	0.974	CLONAL	3	TRUE	0	0.641642481189729	3		470	321	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952513	38952513	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	54	232	0	ENST00000357387.3:c.2912T>C	p.Val971Ala	p.V971A	ENST00000357387	NM_152756.3	971	gTa/gCa	30/38	NA	2	FACETS	0.94	0.817	1			1	INDETERMINATE	1	TRUE	NA	0.641642481189729	2		232	179	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836338	89836338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	82	620	1	ENST00000389301.3:c.2411G>A	p.Gly804Asp	p.G804D	ENST00000389301	NM_000135.2	804	gGt/gAt	26/43	1	2	FACETS	0.897	0.8	0.998	0.897	0.8	0.998	CLONAL	1	TRUE	1	0.641642481189729	2		621	285	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589557	67589598	+	inframe_deletion	In_Frame_Del	DEL	TAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACAC	TAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACAC	-	novel	NA	P-0004942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	141	342	0	ENST00000274335.5:c.1321_1362del	p.Asn441_Thr454del	p.N441_T454del	ENST00000274335		440	gaTAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACACt/gat	10/15	0.554492225912444	3	FACETS	0.892	0.838	0.944	0.892	0.838	0.944	CLONAL	3	TRUE	0	0.641642481189729	3		342	217	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562746	29562746	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs199474742	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	177	400	0	ENST00000356175.3:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000356175	NM_000267.3	1276	Cga/Tga	28/57	0.158420570364687	5	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.503424209749999	5		400	959	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272525	15272525	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	143	306	0	ENST00000263388.2:c.5914G>A	p.Glu1972Lys	p.E1972K	ENST00000263388	NM_000435.2	1972	Gag/Aag	33/33	0.164426131963043	2	FACETS	0.853	0.79	0.917	0.853	0.79	0.917	INDETERMINATE	2	TRUE	0	0.503424209749999	2		306	333	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551574	150551574	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1325605187	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	230	468	0	ENST00000369026.2:c.433G>C	p.Glu145Gln	p.E145Q	ENST00000369026	NM_021960.4	145	Gag/Cag	1/3	0.354661184081644	4	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.503424209749999	4		468	1167	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176153772	176153772	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	200	402	0	ENST00000367669.3:c.464T>G	p.Phe155Cys	p.F155C	ENST00000367669	NM_022457.5	155	tTt/tGt	2/20	1	2	FACETS	0.926	0.859	0.995	0.926	0.859	0.995	CLONAL	1	TRUE	1	0.503424209749999	2		402	858	SUCCESS
ALK	238	MSKCC	GRCh37	2	29473981	29473981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768366852	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	130	476	3	ENST00000389048.3:c.2194G>A	p.Asp732Asn	p.D732N	ENST00000389048	NM_004304.4	732	Gac/Aac	12/29	0.164426131963043	2	FACETS	0.852	0.776	0.932	0.426	0.388	0.466	INDETERMINATE	1	TRUE	0	0.503424209749999	2		479	606	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268439	198268439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	268	513	0	ENST00000335508.6:c.1589C>T	p.Pro530Leu	p.P530L	ENST00000335508	NM_012433.2	530	cCt/cTt	12/25	0.471783523973244	3	FACETS	1	0.938	1	0.501	0.469	0.534	CLONAL	1	TRUE	1	0.503424209749999	3		513	1330	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248486	212248486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1178525913	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	388	568	1	ENST00000342788.4:c.3781G>A	p.Glu1261Lys	p.E1261K	ENST00000342788	NM_005235.2	1261	Gag/Aag	28/28	0.471783523973244	3	FACETS	0.875	0.833	0.918	0.875	0.833	0.918	CLONAL	2	TRUE	1	0.503424209749999	3		569	1102	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713741	30713741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199660234	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	292	369	0	ENST00000295754.5:c.1066C>T	p.Arg356Trp	p.R356W	ENST00000295754	NM_003242.5	356	Cgg/Tgg	4/7	0.503424209749999	3	FACETS	0.996	0.943	1	0.996	0.943	1	CLONAL	2	TRUE	1	0.503424209749999	3		369	729	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940894	49940894	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	207	878	0	ENST00000296474.3:c.149C>T	p.Ser50Phe	p.S50F	ENST00000296474	NM_002447.2	50	tCc/tTc	1/20	NA	2	FACETS	0.837	0.776	0.899			1	INDETERMINATE	1	TRUE	NA	0.503424209749999	2		878	983	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279534	1279534	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	93	603	0	ENST00000310581.5:c.2002G>T	p.Glu668Ter	p.E668*	ENST00000310581	NM_198253.2	668	Gag/Tag	5/16	0.307867263352038	0	FACETS	0.492	0.441	0.546			1	SUBCLONAL	1	TRUE	0	0.503424209749999	0		603	373	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401718	401718	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	123	458	0	ENST00000380956.4:c.1040C>T	p.Pro347Leu	p.P347L	ENST00000380956	NM_001195286.1	347	cCc/cTc	7/9	NA	2	FACETS	0.694	0.628	0.763			1	INDETERMINATE	1	TRUE	NA	0.503424209749999	2		458	704	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979378	93979378	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	218	465	1	ENST00000369303.4:c.1450G>A	p.Asp484Asn	p.D484N	ENST00000369303	NM_004440.3	484	Gat/Aat	7/17	NA	2	FACETS	0.92	0.857	0.986			1	INDETERMINATE	1	TRUE	NA	0.503424209749999	2		466	941	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686267	117686267	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	216	423	0	ENST00000368508.3:c.3074G>A	p.Gly1025Glu	p.G1025E	ENST00000368508	NM_002944.2	1025	gGa/gAa	20/43	0.158420570364687	5	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.503424209749999	5		423	1092	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431584	6431584	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	105	223	0	ENST00000356142.4:c.137T>G	p.Val46Gly	p.V46G	ENST00000356142	NM_018890.3	46	gTa/gGa	3/7	0.163088813244264	2	FACETS	0.79	0.71	0.874	0.395	0.355	0.437	INDETERMINATE	1	TRUE	0	0.503424209749999	2		223	528	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340234	116340234	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	210	387	0	ENST00000397752.3:c.1096C>T	p.Pro366Ser	p.P366S	ENST00000397752	NM_000245.2	366	Cct/Tct	2/21	0.471783523973244	3	FACETS	0.97	0.9	1	0.485	0.45	0.521	CLONAL	1	TRUE	1	0.503424209749999	3		387	1077	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879526	151879526	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	288	424	0	ENST00000262189.6:c.5419C>G	p.Gln1807Glu	p.Q1807E	ENST00000262189	NM_170606.2	1807	Cag/Gag	36/59	0.471783523973244	3	FACETS	0.857	0.808	0.906	0.857	0.808	0.906	CLONAL	2	TRUE	1	0.503424209749999	3		424	836	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636727	8636727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159852	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	636	298	1	ENST00000356435.5:c.182G>A	p.Gly61Glu	p.G61E	ENST00000356435		61	gGa/gAa	2/35	0.503424209749999	5	FACETS	0.954	0.928	0.979	0.954	0.928	0.979	CLONAL	5	TRUE	0	0.503424209749999	5		299	930	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238434	98238434	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	33	383	1	ENST00000331920.6:c.1610C>T	p.Thr537Ile	p.T537I	ENST00000331920	NM_000264.3	537	aCc/aTc	12/24	0.253166458082867	1	FACETS	0.201	0.163	0.243	0.201	0.163	0.243	INDETERMINATE	1	TRUE	0	0.503424209749999	1		384	489	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911535	114911535	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	571	654	2	ENST00000543371.1:c.1053G>C	p.Lys351Asn	p.K351N	ENST00000543371	NM_001198531.1	351	aaG/aaC	10/14	0.493076705156385	2	FACETS	0.979	0.945	1	0.979	0.945	1	CLONAL	2	TRUE	0	0.503424209749999	2		656	1158	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137244	64137244	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774562817	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	328	594	0	ENST00000334205.4:c.1676C>T	p.Pro559Leu	p.P559L	ENST00000334205	NM_003942.2	559	cCg/cTg	14/17	0.313770511336547	3	FACETS	0.907	0.86	0.955	0.907	0.86	0.955	CLONAL	2	TRUE	1	0.503424209749999	3		594	899	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975759	26975759	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1175776547	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	161	410	0	ENST00000381527.3:c.1267C>T	p.Gln423Ter	p.Q423*	ENST00000381527	NM_001260.1	423	Cag/Tag	12/13	0.151894809728337	0	FACETS	0.457	0.42	0.495			1	INDETERMINATE	1	TRUE	0	0.503424209749999	0		410	695	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623828	28623828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	144	399	1	ENST00000241453.7:c.826C>T	p.His276Tyr	p.H276Y	ENST00000241453	NM_004119.2	276	Cat/Tat	7/24	0.151894809728337	0	FACETS	0.416	0.38	0.453			1	INDETERMINATE	1	TRUE	0	0.503424209749999	0		400	683	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28908249	28908249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	150	526	0	ENST00000282397.4:c.2506G>A	p.Gly836Arg	p.G836R	ENST00000282397	NM_002019.4	836	Ggg/Agg	18/30	0.151894809728337	0	FACETS	0.414	0.379	0.45			1	INDETERMINATE	1	TRUE	0	0.503424209749999	0		526	715	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961309	41961309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	306	741	0	ENST00000219905.7:c.217G>A	p.Gly73Ser	p.G73S	ENST00000219905	NM_001164273.1	73	Ggt/Agt	2/24	0.151894809728337	0	FACETS	0.467	0.439	0.495			1	INDETERMINATE	1	TRUE	0	0.503424209749999	0		741	1294	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858424	9858424	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	229	531	0	ENST00000330684.3:c.2977C>T	p.Pro993Ser	p.P993S	ENST00000330684	NM_001134407.1	993	Cct/Tct	13/13	0.304122626835559	3	FACETS	1	0.976	1			1	CLONAL	1	TRUE	NA	0.503424209749999	3		531	1036	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23640971	23640971	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660357	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	260	352	0	ENST00000261584.4:c.2504C>T	p.Ser835Phe	p.S835F	ENST00000261584	NM_024675.3	835	tCc/tTc	5/13	0.503424209749999	2	FACETS	0.946	0.896	0.996	0.946	0.896	0.996	CLONAL	2	TRUE	0	0.503424209749999	2		352	546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579361	7579361	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1064796722	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	423	568	0	ENST00000269305.4:c.326T>C	p.Phe109Ser	p.F109S	ENST00000269305	NM_001126112.2	109	tTc/tCc	4/11	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.503424209749999	2		568	718	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652981	29652981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	532	507	2	ENST00000356175.3:c.4916C>T	p.Ser1639Phe	p.S1639F	ENST00000356175	NM_000267.3	1639	tCt/tTt	36/57	0.158420570364687	5	FACETS	0.943	0.906	0.981			1	INDETERMINATE	3	TRUE	NA	0.503424209749999	5		509	1311	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883621	37883621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748800582	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	316	604	0	ENST00000269571.5:c.3233C>T	p.Ser1078Phe	p.S1078F	ENST00000269571		1078	tCc/tTc	26/27	NA	2	FACETS	0.882	0.838	0.926			1	INDETERMINATE	2	TRUE	NA	0.503424209749999	2		604	712	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120370	70120370	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555629443	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	529	761	0	ENST00000245479.2:c.1372C>T	p.Gln458Ter	p.Q458*	ENST00000245479	NM_000346.3	458	Cag/Tag	3/3	0.255544416673746	4	FACETS	1	0.987	1	1	0.987	1	INDETERMINATE	2	TRUE	2	0.503424209749999	4		761	1482	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56411674	56411674	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	277	763	0	ENST00000348428.3:c.1858T>C	p.Tyr620His	p.Y620H	ENST00000348428	NM_006785.3	620	Tac/Cac	15/17	0.163088813244264	2	FACETS	0.791	0.741	0.842	0.395	0.37	0.421	INDETERMINATE	1	TRUE	0	0.503424209749999	2		763	1392	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798881	42798881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	105	522	0	ENST00000575354.2:c.4453C>T	p.Pro1485Ser	p.P1485S	ENST00000575354	NM_015125.3	1485	Ccg/Tcg	19/20	0.16801990722463	5	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.503424209749999	5		522	597	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961538	54961538	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1338142196	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	342	396	0	ENST00000312783.6:c.94C>T	p.Pro32Ser	p.P32S	ENST00000312783	NM_198436.1	32	Cct/Tct	4/10	0.16801990722463	5	FACETS	0.891	0.846	0.936			1	INDETERMINATE	3	TRUE	NA	0.503424209749999	5		396	892	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44948986	44948986	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	342	148	1	ENST00000377967.4:c.3549-2A>G		p.X1183_splice	ENST00000377967	NM_021140.2	1183			0.417153213929357	2	FACETS	0.908	0.874	0.94			1	CLONAL	3	TRUE	NA	0.503424209749999	2		149	499	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617642	100617642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	286	325	1	ENST00000308731.7:c.427C>T	p.His143Tyr	p.H143Y	ENST00000308731	NM_000061.2	143	Cac/Tac	6/19	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.503424209749999	1		326	576	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938711	76938720	+	frameshift_variant	Frame_Shift_Del	DEL	TTCATCTGAA	TTCATCTGAA	-	novel	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	396	245	0	ENST00000373344.5:c.2028_2037del	p.Asn676LysfsTer17	p.N676Kfs*17	ENST00000373344	NM_000489.3	676	aaTTCAGATGAA/aa	9/35	0.417153213929357	2	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.503424209749999	2		245	662	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527360	187527361	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0004952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	74	193	0	ENST00000441802.2:c.10213_10214delinsAA	p.Gly3405Asn	p.G3405N	ENST00000441802	NM_005245.3	3405	GGt/AAt	17/27	0.230314335804408	1	FACETS	0.703	0.621	0.79	0.703	0.621	0.79	INDETERMINATE	1	TRUE	0	0.503424209749999	1		193	313	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0004955-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	84	591	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	FALSE	1	0.230805350070503	2		591	693	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0004955-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	76	546	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.741	0.648	0.841	0.741	0.648	0.841	SUBCLONAL	1	FALSE	1	0.230805350070503	2		546	889	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982497	25982497	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0004955-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	89	346	1	ENST00000435504.4:c.793A>T	p.Lys265Ter	p.K265*	ENST00000435504		265	Aaa/Taa	9/13	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	FALSE	1	0.230805350070503	2		347	749	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878718	151878718	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004955-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	95	386	0	ENST00000262189.6:c.6227C>G	p.Ala2076Gly	p.A2076G	ENST00000262189	NM_170606.2	2076	gCt/gGt	36/59	1	2	FACETS	0.876	0.778	0.98	0.876	0.778	0.98	CLONAL	1	FALSE	1	0.230805350070503	2		386	940	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0004980-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	26	534	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	0.873	0.691	1	0.873	0.691	1	CLONAL	1	TRUE	1	0.13	2		535	458	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355057	15355057	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1401989162	NA	P-0004989-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	43	560	0	ENST00000263377.2:c.2566G>A	p.Val856Met	p.V856M	ENST00000263377	NM_058243.2	856	Gtg/Atg	13/20	0.126564159981923	3	FACETS	1	0.84	1	0.501	0.42	0.592	CLONAL	1	FALSE	1	0.210641776098469	3		560	450	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741694	17741694	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005006-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	868	340	0	ENST00000250003.3:c.365T>G	p.Leu122Arg	p.L122R	ENST00000250003	NM_002478.4	122	cTg/cGg	1/3	NA	2	FACETS	1	0.998	1			1	INDETERMINATE	2	TRUE	NA	0.880962229212291	2		340	931	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245341	153245349	+	inframe_deletion	In_Frame_Del	DEL	AATGTTTGT	AATGTTTGT	-	novel	NA	P-0005006-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	182	253	0	ENST00000281708.4:c.1842_1850del	p.Thr616_Gln618del	p.T616_Q618del	ENST00000281708	NM_033632.3	614	ttACAAACATTg/ttg	11/12	1	2	FACETS	0.904	0.843	0.966	0.904	0.843	0.966	CLONAL	1	TRUE	1	0.880962229212291	2		253	457	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46597600	46597614	+	protein_altering_variant	In_Frame_Del	DEL	CCATACTCCACACCG	CCATACTCCACACCG	ATT	novel	NA	P-0005006-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	402	409	1	ENST00000262741.5:c.11_25delinsAAT	p.Thr4_Asp9delinsLysTyr	p.T4_D9delinsKY	ENST00000262741	NM_003629.3	4	aCGGTGTGGAGTATGGac/aAATac	1/10	1	2	FACETS	0.918	0.876	0.96	0.918	0.876	0.96	CLONAL	1	TRUE	1	0.880962229212291	2		410	994	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0005010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	144	534	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.162391872256183	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.162391872256183	3		535	867	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120396	94120396	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	84	351	0	ENST00000369303.4:c.655G>A	p.Val219Met	p.V219M	ENST00000369303	NM_004440.3	219	Gtg/Atg	3/17	0.162391872256183	6	FACETS	0.759	0.669	0.856	0.506	0.446	0.571	SUBCLONAL	2	TRUE	3	0.162391872256183	6		351	903	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59886000	59886000	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	29	180	0	ENST00000259008.2:c.746G>C	p.Gly249Ala	p.G249A	ENST00000259008	NM_032043.2	249	gGg/gCg	7/20	0.162391872256183	4	FACETS	1	0.833	1	0.522	0.418	0.639	CLONAL	1	TRUE	2	0.162391872256183	4		180	398	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0005011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	42	348	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.926	0.775	1	0.926	0.775	1	CLONAL	1	TRUE	1	0.220600616060662	2		348	411	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0005011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	52	345	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.175086375896305	4	FACETS	1	0.96	1	0.698	0.596	0.81	CLONAL	1	TRUE	2	0.220600616060662	4		345	412	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0005011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	94	548	1	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.220600616060662	2	FACETS	0.793	0.708	0.884	0.793	0.708	0.884	SUBCLONAL	2	TRUE	0	0.220600616060662	2		549	537	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63810716	63810716	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	35	222	0	ENST00000279873.7:c.803T>C	p.Val268Ala	p.V268A	ENST00000279873	NM_032199.2	268	gTt/gCt	5/10	1	2	FACETS	0.752	0.616	0.904	0.752	0.616	0.904	CLONAL	1	TRUE	1	0.220600616060662	2		222	422	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99454671	99454671	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs749713600	NA	P-0005011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	46	217	0	ENST00000268035.6:c.1589+1G>A		p.X530_splice	ENST00000268035	NM_000875.3	530			1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.220600616060662	2		217	413	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443695	29443695	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs863225281	NA	P-0121445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	312	529	0	ENST00000389048.3:c.3522C>A	p.Phe1174Leu	p.F1174L	ENST00000389048	NM_004304.4	1174	ttC/ttA	23/29	0.45781239376585	4	FACETS	0.948	0.895	1	0.948	0.895	1	CLONAL	2	NA	2	0.45781239376585	4		529	1048	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829778	76829778	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	284	776	0	ENST00000373344.5:c.6263G>T	p.Gly2088Val	p.G2088V	ENST00000373344	NM_000489.3	2088	gGt/gTt	28/35	0.407671047468512	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	NA	0	0.45781239376585	1		776	921	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0005027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	125	548	1	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.481676835431054	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.478768843857907	1		549	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578490	7578490	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1453167097	NA	P-0005027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	287	474	0	ENST00000269305.4:c.440T>G	p.Val147Gly	p.V147G	ENST00000269305	NM_001126112.2	147	gTt/gGt	5/11	0.306203799133246	3	FACETS	0.867	0.824	0.91	0.867	0.824	0.91	CLONAL	3	TRUE	0	0.478768843857907	3		474	571	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511629	46511629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	34	566	0	ENST00000262741.5:c.1148G>A	p.Arg383His	p.R383H	ENST00000262741	NM_003629.3	383	cGt/cAt	9/10	1	2	FACETS	0.24	0.195	0.29	0.24	0.195	0.29	SUBCLONAL	1	TRUE	1	0.478768843857907	2		566	592	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465530	8465530	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs375972549	NA	P-0005027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	55	576	0	ENST00000356435.5:c.3650A>G	p.Lys1217Arg	p.K1217R	ENST00000356435		1217	aAg/aGg	21/35	0.481676835431054	1	FACETS	0.408	0.35	0.472	0.408	0.35	0.472	SUBCLONAL	1	TRUE	0	0.478768843857907	1		576	428	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174395	11174395	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1085307113	NA	P-0005044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	108	459	0	ENST00000361445.4:c.7280T>A	p.Leu2427Gln	p.L2427Q	ENST00000361445	NM_004958.3	2427	cTg/cAg	53/58	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.26	2		459	651	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188207	10188207	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1559428056	NA	P-0005044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	80	372	0	ENST00000256474.2:c.350G>A	p.Trp117Ter	p.W117*	ENST00000256474	NM_000551.3	117	tGg/tAg	2/3	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.26	2		372	615	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729997	41729997	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	84	682	0	ENST00000242208.4:c.532C>T	p.Gln178Ter	p.Q178*	ENST00000242208	NM_002192.2	178	Cag/Tag	3/3	1	2	FACETS	0.579	0.51	0.654	0.579	0.51	0.654	SUBCLONAL	1	TRUE	1	0.26	2		682	1116	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740620	145740620	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	74	458	0	ENST00000428558.2:c.1397C>G	p.Pro466Arg	p.P466R	ENST00000428558	NM_004260.3	466	cCg/cGg	8/22	1	2	FACETS	0.697	0.609	0.792	0.697	0.609	0.792	SUBCLONAL	1	TRUE	1	0.26	2		458	817	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953292	17953292	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	94	409	0	ENST00000458235.1:c.694C>A	p.His232Asn	p.H232N	ENST00000458235	NM_000215.3	232	Cac/Aac	6/24	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.26	2		409	629	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0005053-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	19	446	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.317	0.239	0.408	0.317	0.239	0.408	SUBCLONAL	1	FALSE	1	0.247768777441255	2		446	484	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0005053-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	80	330	0				ENST00000310581	NM_198253.2	-/1132			0.213643177766902	1	FACETS	0.818	0.72	0.923	0.818	0.72	0.923	CLONAL	1	FALSE	0	0.247768777441255	1		330	692	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978946	25978946	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005053-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	63	547	1	ENST00000435504.4:c.977C>T	p.Ala326Val	p.A326V	ENST00000435504		326	gCc/gTc	10/13	1	2	FACETS	0.523	0.451	0.602	0.523	0.451	0.602	SUBCLONAL	1	FALSE	1	0.247768777441255	2		548	972	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164097	47164097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764219907	NA	P-0005053-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	82	395	0	ENST00000409792.3:c.2029C>T	p.Pro677Ser	p.P677S	ENST00000409792	NM_014159.6	677	Cct/Tct	3/21	1	2	FACETS	0.842	0.742	0.95	0.842	0.742	0.95	CLONAL	1	FALSE	1	0.247768777441255	2		395	786	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587167	189587167	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1209841422	NA	P-0005053-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	71	493	0	ENST00000264731.3:c.1184C>T	p.Ser395Phe	p.S395F	ENST00000264731	NM_003722.4	395	tCc/tTc	9/14	1	2	FACETS	0.748	0.652	0.852	0.748	0.652	0.852	SUBCLONAL	1	FALSE	1	0.247768777441255	2		493	766	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629997	187629997	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1312806008	NA	P-0005053-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	49	440	0	ENST00000441802.2:c.985C>T	p.Pro329Ser	p.P329S	ENST00000441802	NM_005245.3	329	Cct/Tct	2/27	0.213643177766902	1	FACETS	0.444	0.375	0.521	0.444	0.375	0.521	SUBCLONAL	1	FALSE	0	0.247768777441255	1		440	780	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718277	117718277	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1298952570	NA	P-0005053-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	80	401	0	ENST00000368508.3:c.580C>T	p.Pro194Ser	p.P194S	ENST00000368508	NM_002944.2	194	Cct/Tct	7/43	0.247768777441255	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	FALSE	0	0.247768777441255	1		401	546	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8501020	8501020	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005053-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	54	455	0	ENST00000356435.5:c.1862C>T	p.Pro621Leu	p.P621L	ENST00000356435		621	cCa/cTa	13/35	0.247768777441255	1	FACETS	0.654	0.558	0.759	0.654	0.558	0.759	SUBCLONAL	1	FALSE	0	0.247768777441255	1		455	584	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77054927	77054927	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005053-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	124	610	0	ENST00000356341.3:c.935T>A	p.Ile312Asn	p.I312N	ENST00000356341	NM_002576.4	312	aTt/aAt	10/15	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	FALSE	1	0.247768777441255	2		610	994	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225356	2225356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005053-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	59	500	2	ENST00000326181.6:c.1441C>T	p.Pro481Ser	p.P481S	ENST00000326181	NM_032271.2	481	Ccg/Tcg	16/21	0.124925926899247	0	FACETS	0.412	0.353	0.476			1	INDETERMINATE	1	FALSE	0	0.247768777441255	0		502	870	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923172	39923172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005053-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	166	333	0	ENST00000378444.4:c.3536C>T	p.Ser1179Phe	p.S1179F	ENST00000378444	NM_001123385.1	1179	tCc/tTc	8/15	1	1	FACETS	0.762	0.701	0.826	1	0.989	1	SUBCLONAL	2	FALSE	0	0.247768777441255	1		333	770	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356356	70356356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005053-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	132	274	0	ENST00000374080.3:c.5251C>T	p.Pro1751Ser	p.P1751S	ENST00000374080		1751	Ccg/Tcg	37/45	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	0	0.247768777441255	1		274	715	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729104	66729109	+	inframe_deletion	In_Frame_Del	DEL	ACCCGC	ACCCGC	-	novel	NA	P-0005053-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	186	610	0	ENST00000307102.5:c.313_318del	p.Pro105_Ala106del	p.P105_A106del	ENST00000307102	NM_002755.3	104	aaACCCGCa/aaa	3/11	0.202896044009137	2	FACETS	1	0.981	1	0.602	0.554	0.651	CLONAL	1	FALSE	0	0.247768777441255	2		610	1248	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0005059-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	63	536	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	1	2	FACETS	0.722	0.622	0.83	0.722	0.622	0.83	SUBCLONAL	1	FALSE	1	0.165681827079867	2		536	1054	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0005059-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	35	401	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	1	2	FACETS	0.394	0.321	0.477	0.394	0.321	0.477	SUBCLONAL	1	FALSE	1	0.165681827079867	2		401	1072	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0005059-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	65	414	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	0.165681827079867	1	FACETS	0.989	0.856	1	0.989	0.856	1	CLONAL	1	FALSE	0	0.165681827079867	1		414	728	SUCCESS
APC	324	MSKCC	GRCh37	5	112174901	112174901	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005059-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	102	495	0	ENST00000257430.4:c.3610C>T	p.Gln1204Ter	p.Q1204*	ENST00000257430	NM_000038.5	1204	Caa/Taa	16/16	0.165681827079867	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	0	0.165681827079867	1		495	1017	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717751	89717751	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005059-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	57	244	0	ENST00000371953.3:c.776A>C	p.His259Pro	p.H259P	ENST00000371953	NM_000314.4	259	cAc/cCc	7/9	0.165681827079867	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	FALSE	0	0.165681827079867	1		244	558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0005065-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	635	534	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.292937470414719	5	FACETS	1	0.996	1			1	CLONAL	5	TRUE	NA	0.484727765258612	5		535	823	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518464	204518464	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777416962	NA	P-0005065-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	144	429	0	ENST00000367182.3:c.1127C>T	p.Ala376Val	p.A376V	ENST00000367182	NM_001278516.1	376	gCg/gTg	11/11	0.484727765258612	8	FACETS	0.834	0.761	0.911			1	CLONAL	2	TRUE	NA	0.484727765258612	8		429	874	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244137	153244137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140856583	NA	P-0005065-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	96	448	0	ENST00000281708.4:c.2020C>T	p.Arg674Trp	p.R674W	ENST00000281708	NM_033632.3	674	Cgg/Tgg	12/12	0.486545872864767	3	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.484727765258612	3		448	391	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138409841	138409841	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0005065-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	124	387	0	ENST00000289153.2:c.2036+1G>C		p.X679_splice	ENST00000289153	NM_006219.2	679			0.484727765258612	5	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.484727765258612	5		387	610	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940111	49940111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005065-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	57	546	0	ENST00000296474.3:c.932C>A	p.Ala311Asp	p.A311D	ENST00000296474	NM_002447.2	311	gCc/gAc	1/20	0.265745204014806	3	FACETS	0.462	0.395	0.534			1	INDETERMINATE	1	TRUE	NA	0.484727765258612	3		546	633	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851908	63851908	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005065-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	70	296	0	ENST00000279873.7:c.2686G>T	p.Ala896Ser	p.A896S	ENST00000279873	NM_032199.2	896	Gca/Tca	10/10	0.486545872864767	5	FACETS	0.938	0.819	1	0.313	0.273	0.356	CLONAL	1	TRUE	2	0.484727765258612	5		296	532	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127994	64127994	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005065-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	47	335	0	ENST00000334205.4:c.392A>G	p.Gln131Arg	p.Q131R	ENST00000334205	NM_003942.2	131	cAg/cGg	4/17	0.486545872864767	5	FACETS	0.662	0.558	0.776	0.221	0.186	0.259	SUBCLONAL	1	TRUE	2	0.484727765258612	5		335	506	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869492	102869492	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005065-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	72	346	0	ENST00000307046.8:c.149C>G	p.Pro50Arg	p.P50R	ENST00000307046	NM_001111285.1	50	cCg/cGg	2/4	0.484727765258612	5	FACETS	0.655	0.572	0.746			1	SUBCLONAL	1	TRUE	NA	0.484727765258612	5		346	783	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636138	87636174	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTCTCATCCTATCTTTGATCTCCATCCAGGTGATAGA	GTCTCATCCTATCTTTGATCTCCATCCAGGTGATAGA	-	novel	NA	P-0005065-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	50	249	0	ENST00000277120.3:c.2332-27_2341del		p.X778_splice	ENST00000277120		778		19/19	0.328492151744078	3	FACETS	0.816	0.696	0.946	0.408	0.348	0.473	CLONAL	1	TRUE	1	0.484727765258612	3		249	314	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	77	225	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		225	236	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	42	213	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.249934879838625	3	FACETS	1	0.928	1	0.602	0.505	0.709	CLONAL	1	TRUE	1	0.25	3		213	314	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	40	225	0				ENST00000310581	NM_198253.2	-/1132			0.301993609903994	1	FACETS	0.809	0.674	0.959	0.809	0.674	0.959	CLONAL	1	TRUE	0	0.25	1		225	346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	72	595	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.301993609903994	3	FACETS	1	0.878	1	0.502	0.439	0.571	CLONAL	1	TRUE	1	0.25	3		596	645	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	21	511	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.301993609903994	3	FACETS	0.274	0.21	0.349	0.137	0.105	0.175	SUBCLONAL	1	TRUE	1	0.25	3		511	690	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781386	135781386	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203549	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	65	796	2	ENST00000298552.3:c.1579C>T	p.Gln527Ter	p.Q527*	ENST00000298552	NM_001162426.1	527	Cag/Tag	15/23	0.249934879838625	3	FACETS	0.7	0.605	0.803	0.35	0.302	0.402	SUBCLONAL	1	TRUE	1	0.25	3		798	836	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691003	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	26	489	1	ENST00000269305.4:c.96+1G>T		p.X32_splice	ENST00000269305	NM_001126112.2	32			0.301993609903994	3	FACETS	0.47	0.371	0.584	0.235	0.185	0.292	SUBCLONAL	1	TRUE	1	0.25	3		490	498	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860557	45860557	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	82	650	0	ENST00000391945.4:c.1450A>G	p.Thr484Ala	p.T484A	ENST00000391945	NM_000400.3	484	Acg/Gcg	15/23	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.25	2		650	655	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879888	37879888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	130	581	1	ENST00000269571.5:c.2183C>T	p.Ser728Phe	p.S728F	ENST00000269571		728	tCt/tTt	18/27	0.301993609903994	3	FACETS	1	0.984	1	0.716	0.649	0.786	CLONAL	1	TRUE	1	0.25	3		582	817	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16203095	16203095	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	63	465	1	ENST00000375759.3:c.803C>T	p.Ser268Phe	p.S268F	ENST00000375759	NM_015001.2	268	tCc/tTc	3/15	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.25	2		466	424	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085773	16085773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	274	567	0	ENST00000281043.3:c.949G>A	p.Glu317Lys	p.E317K	ENST00000281043	NM_005378.4	317	Gag/Aag	3/3	0.301993609903994	3	FACETS	0.873	0.82	0.926	1	0.991	1	CLONAL	3	TRUE	1	0.25	3		567	942	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966832	25966832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	142	502	0	ENST00000435504.4:c.2374G>A	p.Val792Ile	p.V792I	ENST00000435504		792	Gtc/Atc	13/13	0.301993609903994	3	FACETS	1	0.917	1	1	0.917	1	CLONAL	2	TRUE	1	0.25	3		502	637	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646225	215646225	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553622720	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	21	208	0	ENST00000260947.4:c.373G>A	p.Glu125Lys	p.E125K	ENST00000260947	NM_000465.2	125	Gaa/Aaa	4/11	1	2	FACETS	0.844	0.653	1	0.844	0.653	1	CLONAL	1	TRUE	1	0.25	2		208	199	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053523	37053523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	44	586	1	ENST00000231790.2:c.610G>A	p.Val204Ile	p.V204I	ENST00000231790	NM_000249.3	204	Gtt/Att	8/19	0.249934879838625	3	FACETS	0.669	0.56	0.79	0.334	0.28	0.395	SUBCLONAL	1	TRUE	1	0.25	3		587	592	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713670	52713670	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	58	556	0	ENST00000394830.3:c.58G>A	p.Asp20Asn	p.D20N	ENST00000394830	NM_018313.4	20	Gat/Aat	2/30	0.249934879838625	3	FACETS	0.74	0.635	0.856	0.37	0.317	0.428	SUBCLONAL	1	TRUE	1	0.25	3		556	705	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455618	189455618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	82	517	0	ENST00000264731.3:c.152G>A	p.Ser51Asn	p.S51N	ENST00000264731	NM_003722.4	51	aGt/aAt	2/14	0.249934879838625	3	FACETS	1	0.977	1	0.731	0.646	0.821	CLONAL	1	TRUE	1	0.25	3		517	505	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608648	189608648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	46	520	0	ENST00000264731.3:c.1723C>T	p.Gln575Ter	p.Q575*	ENST00000264731	NM_003722.4	575	Cag/Tag	13/14	0.249934879838625	3	FACETS	0.726	0.611	0.854	0.363	0.305	0.427	SUBCLONAL	1	TRUE	1	0.25	3		520	570	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247165	153247165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	41	444	0	ENST00000281708.4:c.1637C>T	p.Ser546Leu	p.S546L	ENST00000281708	NM_033632.3	546	tCa/tTa	10/12	0.24263675369685	3	FACETS	0.643	0.535	0.763			1	SUBCLONAL	1	TRUE	NA	0.25	3		444	574	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525019	187525019	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768202106	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	52	435	0	ENST00000441802.2:c.10661C>T	p.Ser3554Phe	p.S3554F	ENST00000441802	NM_005245.3	3554	tCt/tTt	19/27	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.25	2		435	406	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534380	187534380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	49	589	1	ENST00000441802.2:c.9346G>A	p.Glu3116Lys	p.E3116K	ENST00000441802	NM_005245.3	3116	Gaa/Aaa	13/27	1	2	FACETS	0.696	0.589	0.814	0.696	0.589	0.814	SUBCLONAL	1	TRUE	1	0.25	2		590	563	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754354	57754354	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	46	389	2	ENST00000274289.3:c.497C>T	p.Ser166Leu	p.S166L	ENST00000274289	NM_006622.3	166	tCa/tTa	4/14	0.301993609903994	3	FACETS	0.99	0.836	1	0.495	0.418	0.581	CLONAL	1	TRUE	1	0.25	3		391	418	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20488404	20488404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	47	658	1	ENST00000346618.3:c.1060G>A	p.Glu354Lys	p.E354K	ENST00000346618	NM_001949.4	354	Gag/Aag	6/7	NA	2	FACETS	0.649	0.547	0.762			1	INDETERMINATE	1	TRUE	NA	0.25	2		659	579	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778251	27778251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761484168	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1557	158	1026	2	ENST00000369163.2:c.400G>A	p.Glu134Lys	p.E134K	ENST00000369163	NM_003536.2	134	Gag/Aag	1/1	0.301993609903994	7	FACETS	1	0.977	1	0.299	0.273	0.327	CLONAL	1	TRUE	3	0.25	7		1028	1715	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524698	106524698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	75	375	0	ENST00000359195.3:c.2859G>A	p.Met953Ile	p.M953I	ENST00000359195	NM_002649.2	953	atG/atA	9/11	0.301993609903994	3	FACETS	0.807	0.711	0.91	0.807	0.711	0.91	CLONAL	2	TRUE	1	0.25	3		375	418	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820231	139820231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144092600	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	75	813	1	ENST00000247668.2:c.1384G>A	p.Asp462Asn	p.D462N	ENST00000247668	NM_021138.3	462	Gac/Aac	11/11	0.249934879838625	3	FACETS	0.727	0.635	0.826	0.363	0.317	0.413	SUBCLONAL	1	TRUE	1	0.25	3		814	929	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123245044	123245044	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	38	426	0	ENST00000358487.5:c.2060G>A	p.Trp687Ter	p.W687*	ENST00000358487	NM_000141.4	687	tGg/tAg	16/18	1	2	FACETS	0.822	0.68	0.979	0.822	0.68	0.979	CLONAL	1	TRUE	1	0.25	2		426	370	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577290	64577290	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886039413	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	111	701	0	ENST00000312049.6:c.292C>T	p.Arg98Ter	p.R98*	ENST00000312049	NM_130799.2	98	Cga/Tga	2/10	0.24263675369685	3	FACETS	1	0.971	1			1	CLONAL	1	TRUE	NA	0.25	3		701	817	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218086	108218086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781814	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	60	425	0	ENST00000278616.4:c.8665G>A	p.Asp2889Asn	p.D2889N	ENST00000278616	NM_000051.3	2889	Gat/Aat	59/63	0.258280301197035	3	FACETS	1	0.902	1	0.528	0.456	0.607	CLONAL	1	TRUE	1	0.25	3		425	511	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038894	12038894	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	131	505	2	ENST00000396373.4:c.1187G>A	p.Arg396Lys	p.R396K	ENST00000396373	NM_001987.4	396	aGa/aAa	7/8	0.295815926259552	4	FACETS	0.995	0.905	1	0.995	0.905	1	CLONAL	2	TRUE	2	0.25	4		507	658	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481620	56481620	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	115	695	0	ENST00000267101.3:c.655T>C	p.Phe219Leu	p.F219L	ENST00000267101	NM_001982.3	219	Ttt/Ctt	6/28	0.258280301197035	3	FACETS	0.908	0.821	1	0.908	0.821	1	CLONAL	2	TRUE	1	0.25	3		695	570	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975751	26975751	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	45	540	0	ENST00000381527.3:c.1259C>T	p.Ser420Leu	p.S420L	ENST00000381527	NM_001260.1	420	tCa/tTa	12/13	1	2	FACETS	0.717	0.603	0.844	0.717	0.603	0.844	SUBCLONAL	1	TRUE	1	0.25	2		540	502	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961442	41961442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	97	839	1	ENST00000219905.7:c.350C>T	p.Ser117Leu	p.S117L	ENST00000219905	NM_001164273.1	117	tCa/tTa	2/24	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.25	2		840	773	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108813	2108813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770137362	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	66	646	0	ENST00000219476.3:c.914G>A	p.Gly305Glu	p.G305E	ENST00000219476	NM_000548.3	305	gGa/gAa	10/42	NA	2	FACETS	0.78	0.676	0.892			1	INDETERMINATE	1	TRUE	NA	0.25	2		646	677	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14021950	14021950	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424124466	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	34	573	0	ENST00000311895.7:c.650C>T	p.Ser217Phe	p.S217F	ENST00000311895	NM_005236.2	217	tCt/tTt	4/11	1	2	FACETS	0.522	0.426	0.631	0.522	0.426	0.631	SUBCLONAL	1	TRUE	1	0.25	2		573	521	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33446619	33446619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	49	551	0	ENST00000345365.6:c.14G>A	p.Arg5Lys	p.R5K	ENST00000345365	NM_002878.3	5	aGg/aAg	1/10	0.301993609903994	3	FACETS	0.487	0.411	0.571	0.243	0.205	0.286	SUBCLONAL	1	TRUE	1	0.25	3		551	906	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246515	41246515	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	75	663	0	ENST00000357654.3:c.1033G>C	p.Asp345His	p.D345H	ENST00000357654	NM_007294.3	345	Gat/Cat	10/23	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.25	2		663	536	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554172	63554172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762082964	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	69	594	0	ENST00000307078.5:c.567G>A	p.Met189Ile	p.M189I	ENST00000307078	NM_004655.3	189	atG/atA	2/11	0.301993609903994	3	FACETS	1	0.917	1	0.535	0.466	0.61	CLONAL	1	TRUE	1	0.25	3		594	580	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591826	48591826	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs281875324	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	60	641	0	ENST00000342988.3:c.989A>G	p.Glu330Gly	p.E330G	ENST00000342988	NM_005359.5	330	gAa/gGa	9/12	0.249934879838625	3	FACETS	0.975	0.84	1	0.487	0.42	0.561	CLONAL	1	TRUE	1	0.25	3		641	554	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366186	15366186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	101	755	0	ENST00000263377.2:c.1969G>A	p.Glu657Lys	p.E657K	ENST00000263377	NM_058243.2	657	Gag/Aag	10/20	1	2	FACETS	0.767	0.684	0.855	0.767	0.684	0.855	SUBCLONAL	1	TRUE	1	0.25	2		755	1054	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793002	33793002	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	15	86	0	ENST00000498907.2:c.319G>C	p.Asp107His	p.D107H	ENST00000498907	NM_004364.3	107	Gac/Cac	1/1	1	2	FACETS	0.938	0.692	1	0.938	0.692	1	CLONAL	1	TRUE	1	0.25	2		86	128	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950005	44950005	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	82	381	0	ENST00000377967.4:c.3774G>A	p.Trp1258Ter	p.W1258*	ENST00000377967	NM_021140.2	1258	tgG/tgA	26/29	0.301993609903994	2	FACETS	0.775	0.687	0.869			1	SUBCLONAL	2	TRUE	NA	0.25	2		381	423	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247213	153247233	+	inframe_deletion	In_Frame_Del	DEL	GTCTCTGGATCCCACACCTTT	GTCTCTGGATCCCACACCTTT	-	novel	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	66	623	1	ENST00000281708.4:c.1569_1589del	p.Lys524_Thr530del	p.K524_T530del	ENST00000281708	NM_033632.3	523	gtAAAGGTGTGGGATCCAGAGACt/gtt	10/12	0.24263675369685	3	FACETS	0.784	0.679	0.897			1	SUBCLONAL	1	TRUE	NA	0.25	3		624	758	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577494	64577513	+	frameshift_variant	Frame_Shift_Del	DEL	CTCGGCCCAGCTCGGCAGCA	CTCGGCCCAGCTCGGCAGCA	-	novel	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	43	374	0	ENST00000312049.6:c.69_88del	p.Phe23LeufsTer87	p.F23Lfs*87	ENST00000312049	NM_130799.2	23	ttTGCTGCCGAGCTGGGCCGAGag/ttag	2/10	0.24263675369685	3	FACETS	0.59	0.493	0.698			1	SUBCLONAL	1	TRUE	NA	0.25	3		374	656	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665051	138665074	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCTCCGGCCCCGAAGAGCCCCT	CGCCTCCGGCCCCGAAGAGCCCCT	AG	novel	NA	P-0005087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	30	83	0	ENST00000330315.3:c.491_514delinsCT	p.Lys164ThrfsTer100	p.K164Tfs*100	ENST00000330315	NM_023067.3	164	aAGGGGCTCTTCGGGGCCGGAGGCGcc/aCTcc	1/1	0.249934879838625	3	FACETS	1	0.892	1	1	0.892	1	CLONAL	2	TRUE	1	0.25	3		83	120	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228402	228402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764534044	NA	P-0005093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	321	485	1	ENST00000264932.6:c.724G>A	p.Gly242Arg	p.G242R	ENST00000264932	NM_004168.2	242	Ggg/Agg	6/15	0.588741834672807	1	FACETS	0.717	0.678	0.757	0.717	0.678	0.757	SUBCLONAL	1	FALSE	0	0.588741834672807	1		486	1073	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441477	52441477	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0005093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	273	434	0	ENST00000460680.1:c.376-1G>A		p.X126_splice	ENST00000460680	NM_004656.3	126			0.588741834672807	1	FACETS	0.91	0.859	0.962	0.91	0.859	0.962	CLONAL	1	FALSE	0	0.588741834672807	1		434	719	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148991	119148991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs192712314	NA	P-0005096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	23	502	4	ENST00000264033.4:c.1211G>A	p.Cys404Tyr	p.C404Y	ENST00000264033	NM_005188.3	404	tGt/tAt	8/16	1	2	FACETS	0.158	0.123	0.2	0.158	0.123	0.2	SUBCLONAL	1	FALSE	1	0.66903581777147	2		506	434	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064413	30064413	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	156	581	0	ENST00000338641.4:c.979del	p.Glu327ArgfsTer19	p.E327Rfs*19	ENST00000338641	NM_000268.3	326	aGg/ag	10/16	0.66903581777147	1	FACETS	0.907	0.844	0.971	0.907	0.844	0.971	CLONAL	1	FALSE	0	0.66903581777147	1		581	342	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0005097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	82	413	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.135328242711623	5	FACETS	0.971	0.861	1	0.486	0.43	0.544	INDETERMINATE	2	TRUE	1	0.306599213790132	5		413	402	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013737	12013737	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	59	506	0	ENST00000353533.5:c.679C>G	p.His227Asp	p.H227D	ENST00000353533	NM_003010.3	227	Cac/Gac	6/11	0.135328242711623	5	FACETS	0.982	0.852	1	0.491	0.426	0.561	INDETERMINATE	2	TRUE	1	0.306599213790132	5		506	286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0005098-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1698	154	491	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	1	2	FACETS	0.978	0.891	1	0.978	0.891	1	CLONAL	1	TRUE	1	0.17	2		491	1852	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477202	67477202	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	53	240	0	ENST00000327367.4:c.1009G>C	p.Gly337Arg	p.G337R	ENST00000327367	NM_005902.3	337	Gga/Cga	7/9	1	2	FACETS	0.915	0.786	1	0.915	0.786	1	CLONAL	1	TRUE	1	0.413652248650853	2		240	280	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0005120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	17	179	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.588	0.446	0.75	0.588	0.446	0.75	SUBCLONAL	1	TRUE	1	0.602673296239713	2		179	96	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0005120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	23	213	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.681	0.54	0.839	0.681	0.54	0.839	SUBCLONAL	1	TRUE	1	0.602673296239713	2		213	112	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819820	170819820	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	56	518	0	ENST00000296930.5:c.459G>T	p.Gln153His	p.Q153H	ENST00000296930	NM_002520.6	153	caG/caT	5/11	1	2	FACETS	0.701	0.606	0.803	0.701	0.606	0.803	SUBCLONAL	1	TRUE	1	0.602673296239713	2		518	265	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415547	152415547	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	148	502	0	ENST00000206249.3:c.1397T>A	p.Leu466Gln	p.L466Q	ENST00000206249	NM_000125.3	466	cTg/cAg	7/8	0.189225123261486	3	FACETS	1	0.982	1	0.624	0.574	0.676	INDETERMINATE	1	TRUE	1	0.602673296239713	3		502	512	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856050	68856050	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	103	489	1	ENST00000261769.5:c.1859del	p.Pro620LeufsTer11	p.P620Lfs*11	ENST00000261769	NM_004360.3	620	Cct/ct	12/16	0.603558906451605	1	FACETS	0.975	0.889	1	0.975	0.889	1	CLONAL	1	TRUE	0	0.602673296239713	1		490	245	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578419	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587781845	NA	P-0005124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	468	346	1	ENST00000269305.4:c.511G>T	p.Glu171Ter	p.E171*	ENST00000269305	NM_001126112.2	171	Gag/Tag	5/11	0.490659124419492	3	FACETS	0.994	0.958	1	0.994	0.958	1	CLONAL	3	TRUE	0	0.490659124419492	3		347	797	SUCCESS
APC	324	MSKCC	GRCh37	5	112175536	112175536	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	358	446	0	ENST00000257430.4:c.4245del	p.Ser1415ArgfsTer4	p.S1415Rfs*4	ENST00000257430	NM_000038.5	1415	agT/ag	16/16	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.490659124419492	2		446	647	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46714199	46714199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1271019876	NA	P-0005124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	105	484	1	ENST00000371975.4:c.19C>T	p.Pro7Ser	p.P7S	ENST00000371975	NM_003579.3	7	Ccc/Tcc	2/18	0.490659124419492	3	FACETS	0.525	0.469	0.584	0.262	0.234	0.292	SUBCLONAL	1	TRUE	1	0.490659124419492	3		485	1016	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668619	52668619	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	415	604	1	ENST00000394830.3:c.1300C>T	p.Arg434Ter	p.R434*	ENST00000394830	NM_018313.4	434	Cga/Tga	12/30	0.247153454585218	5	FACETS	0.836	0.797	0.876			1	INDETERMINATE	3	TRUE	NA	0.490659124419492	5		605	1171	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671882	30671882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374561704	NA	P-0005124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	192	642	0	ENST00000376406.3:c.5078C>T	p.Pro1693Leu	p.P1693L	ENST00000376406	NM_014641.2	1693	cCg/cTg	10/15	0.490659124419492	3	FACETS	0.907	0.839	0.979	0.454	0.419	0.49	CLONAL	1	TRUE	1	0.490659124419492	3		642	1074	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622269	117622269	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	110	572	0	ENST00000368508.3:c.6601G>T	p.Glu2201Ter	p.E2201*	ENST00000368508	NM_002944.2	2201	Gaa/Taa	42/43	NA	2	FACETS	0.5	0.448	0.555			1	INDETERMINATE	1	TRUE	NA	0.490659124419492	2		572	897	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012561	36012561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1452	149	498	0	ENST00000358208.4:c.5G>A	p.Gly2Asp	p.G2D	ENST00000358208		2	gGt/gAt	2/12	0.490659124419492	6	FACETS	0.752	0.684	0.823	0.15	0.136	0.165	SUBCLONAL	1	TRUE	1	0.490659124419492	6		498	1601	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593405	48593405	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	86	290	0	ENST00000342988.3:c.1156G>C	p.Gly386Arg	p.G386R	ENST00000342988	NM_005359.5	386	Ggt/Cgt	10/12	0.812802637124901	1	FACETS	0.897	0.825	0.967	0.897	0.825	0.967	CLONAL	1	TRUE	0	0.812802637124901	1		290	140	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319907	8319907	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	112	321	0	ENST00000356435.5:c.5594G>C	p.Arg1865Thr	p.R1865T	ENST00000356435		1865	aGa/aCa	34/35	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.812802637124901	2		321	270	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0005165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	79	388	1	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	0.335381149649536	2		389	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0005165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	102	523	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.335381149649536	1	FACETS	0.868	0.779	0.963	0.868	0.779	0.963	CLONAL	1	TRUE	0	0.335381149649536	1		523	583	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845813	151845813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	61	432	1	ENST00000262189.6:c.13199G>A	p.Arg4400Gln	p.R4400Q	ENST00000262189	NM_170606.2	4400	cGg/cAg	52/59	1	2	FACETS	0.988	0.857	1	0.988	0.857	1	CLONAL	1	TRUE	1	0.335381149649536	2		433	368	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555999	226555999	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	54	278	0	ENST00000366794.5:c.2178C>G	p.Asp726Glu	p.D726E	ENST00000366794	NM_001618.3	726	gaC/gaG	16/23	1	2	FACETS	0.979	0.841	1	0.979	0.841	1	CLONAL	1	TRUE	1	0.335381149649536	2		278	329	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090829	5090829	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	39	517	0	ENST00000381652.3:c.2977G>T	p.Gly993Ter	p.G993*	ENST00000381652	NM_004972.3	993	Gga/Tga	22/25	0.335381149649536	1	FACETS	0.544	0.452	0.646	0.544	0.452	0.646	SUBCLONAL	1	TRUE	0	0.335381149649536	1		517	356	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231089	98231089	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	60	272	0	ENST00000331920.6:c.2194C>G	p.Leu732Val	p.L732V	ENST00000331920	NM_000264.3	732	Ctc/Gtc	14/24	1	2	FACETS	0.852	0.736	0.977	0.852	0.736	0.977	CLONAL	1	TRUE	1	0.335381149649536	2		272	420	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132421	11132422	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0005165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	144	509	1	ENST00000358026.2:c.2639_2640del	p.Val880GlyfsTer64	p.V880Gfs*64	ENST00000358026	NM_001128849.1	879	atTGtg/attg	19/36	0.335381149649536	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.335381149649536	1		510	627	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060869	38060870	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0005165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	79	311	0	ENST00000250448.2:c.1119_1120del	p.His374ProfsTer40	p.H374Pfs*40	ENST00000250448	NM_004496.3	373	tcTCac/tcac	2/2	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.335381149649536	2		311	459	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846036	68846037	+	splice_acceptor_variant	Splice_Site	DEL	AG	AG	-	rs786201045	NA	P-0005165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	40	452	0	ENST00000261769.5:c.1009_1010del		p.X337_splice	ENST00000261769	NM_004360.3	337			0.304223129172221	1	FACETS	0.767	0.641	0.904	0.767	0.641	0.904	CLONAL	1	TRUE	0	0.335381149649536	1		452	259	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880219	37880235	+	missense_variant	Missense_Mutation	ONP	TTGAGGGAAAACACATC	TTGAGGGAAAACACATC	GCCCAAAGCCAACAAAG	novel	NA	P-0005165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	185	539	0	ENST00000269571.5:c.2263_2279delinsGCCCAAAGCCAACAAAG	p.Leu755_Thr759delinsAlaGlnSerGlnGln	p.L755_T759delinsAQSQQ	ENST00000269571		755	TTGAGGGAAAACACATCc/GCCCAAAGCCAACAAAGc	19/27	0.335381149649536	3	FACETS	1	0.94	1			1	CLONAL	2	TRUE	NA	0.335381149649536	3		539	635	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087503	27087503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	44	327	0	ENST00000324856.7:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000324856	NM_006015.4	693	Cga/Tga	5/20	1	2	FACETS	0.941	0.788	1	0.941	0.788	1	CLONAL	1	TRUE	1	0.14	2		327	668	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412898	49412898	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519954	NA	P-0005168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	91	555	0	ENST00000418115.1:c.125A>G	p.Tyr42Cys	p.Y42C	ENST00000418115	NM_001664.2	42	tAt/tGt	2/5	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.14	2		555	1165	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477149	67477149	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057524771	NA	P-0005168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	43	406	0	ENST00000327367.4:c.956A>G	p.Asn319Ser	p.N319S	ENST00000327367	NM_005902.3	319	aAc/aGc	7/9	1	2	FACETS	0.784	0.654	0.928	0.784	0.654	0.928	CLONAL	1	TRUE	1	0.14	2		406	784	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230438	46230438	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	314	381	0	ENST00000334344.6:c.772G>T	p.Glu258Ter	p.E258*	ENST00000334344	NM_152641.2	258	Gaa/Taa	7/21	0.297022486803485	3	FACETS	0.886	0.839	0.933	0.886	0.839	0.933	CLONAL	3	TRUE	0	0.325109217450888	3		381	845	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128036909	128036909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	238	540	0	ENST00000285398.2:c.1570G>A	p.Ala524Thr	p.A524T	ENST00000285398	NM_000122.1	524	Gca/Aca	10/15	0.17769498105959	5	FACETS	1	0.959	1	0.691	0.645	0.739	INDETERMINATE	2	TRUE	2	0.325109217450888	5		540	1050	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530972	187530972	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1187011117	NA	P-0005173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	321	418	0	ENST00000441802.2:c.10051G>C	p.Glu3351Gln	p.E3351Q	ENST00000441802	NM_005245.3	3351	Gag/Cag	15/27	0.297022486803485	3	FACETS	0.948	0.9	0.997	0.948	0.9	0.997	CLONAL	3	TRUE	0	0.325109217450888	3		418	807	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730035	41730035	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	271	699	0	ENST00000242208.4:c.494A>G	p.Asn165Ser	p.N165S	ENST00000242208	NM_002192.2	165	aAc/aGc	3/3	0.325109217450888	4	FACETS	0.877	0.822	0.934	0.877	0.822	0.934	CLONAL	2	TRUE	2	0.325109217450888	4		699	1259	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435026	110435026	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs749040670	NA	P-0005173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	59	150	0	ENST00000375856.3:c.3375G>T	p.Gln1125His	p.Q1125H	ENST00000375856	NM_003749.2	1125	caG/caT	1/2	1	2	FACETS	0.84	0.725	0.965	0.84	0.725	0.965	CLONAL	1	TRUE	1	0.325109217450888	2		150	432	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807355	3807355	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	89	470	0	ENST00000262367.5:c.3632T>C	p.Leu1211Ser	p.L1211S	ENST00000262367	NM_004380.2	1211	tTg/tCg	19/31	NA	2	FACETS	0.756	0.67	0.848			1	INDETERMINATE	1	TRUE	NA	0.325109217450888	2		470	724	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14031657	14031657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	123	448	0	ENST00000311895.7:c.1846G>A	p.Glu616Lys	p.E616K	ENST00000311895	NM_005236.2	616	Gaa/Aaa	9/11	NA	2	FACETS	0.83	0.75	0.914			1	INDETERMINATE	1	TRUE	NA	0.325109217450888	2		448	912	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0005173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	159	318	0	ENST00000269305.4:c.394A>T	p.Lys132Ter	p.K132*	ENST00000269305	NM_001126112.2	132	Aag/Tag	5/11	0.25759039627354	2	FACETS	0.892	0.823	0.964	0.892	0.823	0.964	CLONAL	2	TRUE	0	0.325109217450888	2		318	548	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030599	47030599	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	111	428	0	ENST00000377604.3:c.374A>T	p.Glu125Val	p.E125V	ENST00000377604	NM_001204468.1	125	gAg/gTg	4/24	0.126981636098687	1	FACETS	0.638	0.573	0.707	0.638	0.573	0.707	INDETERMINATE	1	TRUE	0	0.325109217450888	1		428	896	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044850	47044850	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	72	287	0	ENST00000377604.3:c.2176C>T	p.Arg726Ter	p.R726*	ENST00000377604	NM_001204468.1	726	Cga/Tga	20/24	0.126981636098687	1	FACETS	0.66	0.577	0.749	0.66	0.577	0.749	INDETERMINATE	1	TRUE	0	0.325109217450888	1		287	562	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410458	63410458	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	126	632	0	ENST00000330258.3:c.2709G>T	p.Glu903Asp	p.E903D	ENST00000330258	NM_152424.3	903	gaG/gaT	2/2	0.126981636098687	1	FACETS	0.784	0.71	0.862	0.784	0.71	0.862	INDETERMINATE	1	TRUE	0	0.325109217450888	1		632	828	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938442	76938442	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	101	516	0	ENST00000373344.5:c.2306C>G	p.Thr769Ser	p.T769S	ENST00000373344	NM_000489.3	769	aCt/aGt	9/35	0.126981636098687	1	FACETS	0.637	0.569	0.709	0.637	0.569	0.709	INDETERMINATE	1	TRUE	0	0.325109217450888	1		516	817	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465633	8465634	+	stop_gained	Nonsense_Mutation	DNP	CA	CA	AT	novel	NA	P-0005173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	114	484	0	ENST00000356435.5:c.3546_3547delinsAT	p.Tyr1182_Gly1183delinsTer	p.Y1182_G1183delins*	ENST00000356435		1182	taTGgg/taATgg	21/35	0.325109217450888	1	FACETS	0.918	0.828	1	0.918	0.828	1	CLONAL	1	TRUE	0	0.325109217450888	1		484	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0005174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	70	305	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.173191459265927	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.173191459265927	1		305	560	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206706	36206706	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0005174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	52	199	0	ENST00000300305.3:c.805+1G>A		p.X269_splice	ENST00000300305		269			0.173191459265927	1	FACETS	0.788	0.674	0.912	1	0.968	1	CLONAL	2	TRUE	0	0.173191459265927	1		199	348	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916918	178916920	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	novel	NA	P-0005174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	233	842	1	ENST00000263967.3:c.305_307del	p.Ile102_Glu103delinsLys	p.I102_E103delinsK	ENST00000263967	NM_006218.2	102	aTTGaa/aaa	2/21	0.173191459265927	5	FACETS	0.953	0.888	1	0.953	0.888	1	CLONAL	3	TRUE	2	0.173191459265927	5		843	1185	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0005177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	103	323	0	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	0.581956524866606	2		323	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005205-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	144	507	1	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.200951510215818	1	FACETS	0.787	0.718	0.859	1	0.988	1	SUBCLONAL	2	TRUE	0	0.200951510215818	1		508	819	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953587	32953587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886040798	NA	P-0005205-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	94	413	0	ENST00000380152.3:c.8888C>T	p.Ser2963Leu	p.S2963L	ENST00000380152		2963	tCa/tTa	22/27	0.200951510215818	3	FACETS	0.83	0.736	0.93			1	CLONAL	1	TRUE	NA	0.200951510215818	3		413	1241	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587777894	NA	P-0005214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	183	519	0	ENST00000361445.4:c.6644C>A	p.Ser2215Tyr	p.S2215Y	ENST00000361445	NM_004958.3	2215	tCt/tAt	47/58	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		519	709	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864458	151864458	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	91	293	0	ENST00000262189.6:c.9523T>C	p.Ser3175Pro	p.S3175P	ENST00000262189	NM_170606.2	3175	Tca/Cca	42/59	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		293	371	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574000	7574000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	451	858	0	ENST00000269305.4:c.1027G>T	p.Glu343Ter	p.E343*	ENST00000269305	NM_001126112.2	343	Gag/Tag	10/11	0.846307859997476	4	FACETS	0.978	0.964	0.991			1	CLONAL	4	TRUE	NA	0.927769324387506	4		858	479	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251583	212251583	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	69	342	0	ENST00000342788.4:c.3476A>C	p.Lys1159Thr	p.K1159T	ENST00000342788	NM_005235.2	1159	aAa/aCa	27/28	0.159498001427007	4	FACETS	0.779	0.693	0.868	0.779	0.693	0.868	INDETERMINATE	2	TRUE	2	0.927769324387506	4		342	184	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212184	98212184	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs864622120	NA	P-0005224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	128	776	0	ENST00000331920.6:c.3488G>T	p.Gly1163Val	p.G1163V	ENST00000331920	NM_000264.3	1163	gGc/gTc	21/24	0.89020934016245	2	FACETS	1	0.949	1	0.517	0.478	0.556	CLONAL	1	TRUE	0	0.927769324387506	2		776	267	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410669	32410669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	219	641	0	ENST00000332351.3:c.1489G>A	p.Asp497Asn	p.D497N	ENST00000332351	NM_024426.4	497	Gat/Aat	10/10	0.243236537399733	5	FACETS	1	0.982	1	1	0.982	1	INDETERMINATE	3	TRUE	2	0.927769324387506	5		641	350	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347035	89347035	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	135	766	0	ENST00000301030.4:c.5915G>C	p.Ser1972Thr	p.S1972T	ENST00000301030	NM_001256183.1	1972	aGc/aCc	9/13	0.641023867414819	1	FACETS	0.555	0.514	0.596	0.555	0.514	0.596	SUBCLONAL	1	TRUE	0	0.927769324387506	1		766	281	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023958	31023958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555465153	NA	P-0005224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	141	623	1	ENST00000375687.4:c.3443G>A	p.Arg1148His	p.R1148H	ENST00000375687	NM_015338.5	1148	cGc/cAc	13/13	0.645075086910959	4	FACETS	1	0.987	1	0.476	0.438	0.516	CLONAL	1	TRUE	1	0.927769324387506	4		624	410	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176176047	176176049	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0005224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	90	500	0	ENST00000367669.3:c.66_68del	p.Ser23del	p.S23del	ENST00000367669	NM_022457.5	22	tcCTCg/tcg	1/20	0.927769324387506	4	FACETS	0.86	0.767	0.958	0.287	0.255	0.32	CLONAL	1	TRUE	1	0.927769324387506	4		500	435	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245026	133245026	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs5744800	NA	P-0005245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	13	443	0	ENST00000320574.5:c.2089C>G	p.Pro697Ala	p.P697A	ENST00000320574	NM_006231.2	697	Ccc/Gcc	19/49	0.206564868199229	0	FACETS	0.445	0.317	0.6			1	SUBCLONAL	1	TRUE	0	0.21	0		443	220	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355537	15355537	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	27	556	0	ENST00000263377.2:c.2195G>A	p.Gly732Glu	p.G732E	ENST00000263377	NM_058243.2	732	gGg/gAg	12/20	0.3	2	FACETS	0.731	0.582	0.901			1	CLONAL	1	TRUE	NA	0.21	2		556	352	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222339	2222339	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	15	399	0	ENST00000326181.6:c.623G>T	p.Arg208Leu	p.R208L	ENST00000326181	NM_032271.2	208	cGa/cTa	8/21	0.311254460240062	0	FACETS	0.482	0.353	0.638			1	SUBCLONAL	1	TRUE	0	0.21	0		399	234	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121266	29121266	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730881701	NA	P-0005245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	54	638	0	ENST00000328354.6:c.409C>T	p.Arg137Ter	p.R137*	ENST00000328354	NM_007194.3	137	Cga/Tga	3/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.21	2		638	363	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549436	187549439	+	frameshift_variant	Frame_Shift_Del	DEL	CACG	CACG	-	novel	NA	P-0005245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	23	493	0	ENST00000441802.2:c.4679_4682del	p.Pro1560ArgfsTer24	p.P1560Rfs*24	ENST00000441802	NM_005245.3	1560	cCGTGg/cg	9/27	0.206564868199229	0	FACETS	0.709	0.555	0.887			1	SUBCLONAL	1	TRUE	0	0.21	0		493	244	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942733	44942733	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	29	256	0	ENST00000377967.4:c.3315del	p.Lys1105AsnfsTer15	p.K1105Nfs*15	ENST00000377967	NM_021140.2	1105	Aaa/aa	23/29	0.3	2	FACETS	1	0.915	1	0.633	0.511	0.77	CLONAL	1	TRUE	0	0.21	2		256	218	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0005249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	121	518	2	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.272758373176877	3	FACETS	0.984	0.928	1	1	0.993	1	CLONAL	7	TRUE	1	0.24	3		520	164	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0005249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	71	463	3	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.272758373176877	3	FACETS	1	0.941	1	1	0.98	1	CLONAL	3	TRUE	1	0.24	3		466	202	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937537	76937537	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	58	218	0	ENST00000373344.5:c.3211G>T	p.Gly1071Ter	p.G1071*	ENST00000373344	NM_000489.3	1071	Gga/Tga	9/35	0.112542296351265	2	FACETS	1	0.916	1			1	INDETERMINATE	5	TRUE	NA	0.24	2		218	95	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0005255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	318	591	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.835949443274575	2		591	725	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876193	35876193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	298	790	1	ENST00000303115.3:c.985C>T	p.Pro329Ser	p.P329S	ENST00000303115	NM_002185.3	329	Cct/Tct	8/8	1	2	FACETS	0.925	0.875	0.975	0.925	0.875	0.975	CLONAL	1	TRUE	1	0.835949443274575	2		791	771	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052720	42052720	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	277	772	1	ENST00000219905.7:c.7391T>C	p.Leu2464Pro	p.L2464P	ENST00000219905	NM_001164273.1	2464	cTt/cCt	20/24	0.4015206568965	1	FACETS	0.489	0.461	0.517	0.489	0.461	0.517	INDETERMINATE	1	TRUE	0	0.835949443274575	1		773	789	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912048	127912048	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	500	996	1	ENST00000373547.4:c.822del	p.Phe274LeufsTer4	p.F274Lfs*4	ENST00000373547	NM_002721.4	274	ttC/tt	7/7	0.835949443274575	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.835949443274575	1		997	661	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845753	68845753	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	303	681	0	ENST00000261769.5:c.1000del	p.Asp334ThrfsTer22	p.D334Tfs*22	ENST00000261769	NM_004360.3	333	ctG/ct	7/16	1	2	FACETS	0.98	0.928	1	0.98	0.928	1	CLONAL	1	TRUE	1	0.835949443274575	2		681	740	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463242	25463242	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	181	667	0	ENST00000264709.3:c.2251T>G	p.Phe751Val	p.F751V	ENST00000264709	NM_175629.2	751	Ttc/Gtc	19/23	1	2	FACETS	0.942	0.869	1	0.942	0.869	1	CLONAL	1	TRUE	1	0.400098571425276	2		667	960	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903755	41903755	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	180	525	0	ENST00000372991.4:c.802A>G	p.Lys268Glu	p.K268E	ENST00000372991	NM_001760.3	268	Aaa/Gaa	5/5	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.400098571425276	2		525	814	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432764	432764	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0005262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	88	461	0	ENST00000399788.2:c.2150+2T>C		p.X717_splice	ENST00000399788	NM_001042603.1	717			1	2	FACETS	0.644	0.571	0.722	0.644	0.571	0.722	SUBCLONAL	1	TRUE	1	0.400098571425276	2		461	683	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005268-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	162	387	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.47691765663025	2	FACETS	1	0.945	1	0.516	0.475	0.558	CLONAL	1	TRUE	0	0.503328214774336	2		387	624	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0005268-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	501	388	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.503328214774336	6	FACETS	0.913	0.877	0.949	0.913	0.877	0.949	CLONAL	4	TRUE	2	0.503328214774336	6		389	1094	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191513	10191513	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1131690962	NA	P-0005271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	94	503	0	ENST00000256474.2:c.506T>C	p.Leu169Pro	p.L169P	ENST00000256474	NM_000551.3	169	cTa/cCa	3/3	0.26539237064408	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.26539237064408	1		503	569	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952086	178952086	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519932	NA	P-0005271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	64	562	0	ENST00000263967.3:c.3141T>G	p.His1047Gln	p.H1047Q	ENST00000263967	NM_006218.2	1047	caT/caG	21/21	1	2	FACETS	0.488	0.421	0.561	0.488	0.421	0.561	SUBCLONAL	1	TRUE	1	0.26539237064408	2		562	988	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713816	30713816	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0005271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	92	397	0	ENST00000295754.5:c.1141A>T	p.Lys381Ter	p.K381*	ENST00000295754	NM_003242.5	381	Aag/Tag	4/7	0.26539237064408	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.26539237064408	1		397	551	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125873	47125873	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0005271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	28	162	0	ENST00000409792.3:c.5398-1G>C		p.X1800_splice	ENST00000409792	NM_014159.6	1800			0.26539237064408	1	FACETS	0.934	0.752	1	0.934	0.752	1	CLONAL	1	TRUE	0	0.26539237064408	1		162	196	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653865	89653865	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	114	393	0	ENST00000371953.3:c.163A>T	p.Arg55Trp	p.R55W	ENST00000371953	NM_000314.4	55	Agg/Tgg	2/9	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.26539237064408	2		393	766	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061243	38061243	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1416489774	NA	P-0005271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	79	498	0	ENST00000250448.2:c.746A>G	p.Asp249Gly	p.D249G	ENST00000250448	NM_004496.3	249	gAc/gGc	2/2	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.26539237064408	2		498	486	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225339	2225339	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	69	575	0	ENST00000326181.6:c.1424T>C	p.Ile475Thr	p.I475T	ENST00000326181	NM_032271.2	475	aTc/aCc	16/21	0.26539237064408	1	FACETS	0.838	0.731	0.954	0.838	0.731	0.954	CLONAL	1	TRUE	0	0.26539237064408	1		575	538	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595873	52595873	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	132	628	0	ENST00000394830.3:c.4042del	p.Gln1348AsnfsTer32	p.Q1348Nfs*32	ENST00000394830	NM_018313.4	1348	Caa/aa	26/30	0.26539237064408	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.26539237064408	1		628	677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0005274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	368	531	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.548690739794031	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.587525498295051	2		531	601	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082389	16082389	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	32	519	0	ENST00000281043.3:c.203C>G	p.Ala68Gly	p.A68G	ENST00000281043	NM_005378.4	68	gCg/gGg	2/3	0.169367789225123	2	FACETS	0.243	0.197	0.295	0.122	0.098	0.148	INDETERMINATE	1	TRUE	0	0.587525498295051	2		519	448	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425256	49425256	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	185	571	0	ENST00000301067.7:c.13232C>G	p.Ser4411Cys	p.S4411C	ENST00000301067	NM_003482.3	4411	tCc/tGc	39/54	0.150209512177493	5	FACETS	0.911	0.845	0.98	0.608	0.563	0.653	INDETERMINATE	2	TRUE	2	0.587525498295051	5		571	650	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341311	89341311	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	28	202	0	ENST00000301030.4:c.7624G>T	p.Ala2542Ser	p.A2542S	ENST00000301030	NM_001256183.1	2542	Gcc/Tcc	11/13	0.587525498295051	3	FACETS	0.455	0.365	0.557	0.228	0.182	0.279	SUBCLONAL	1	TRUE	1	0.587525498295051	3		202	271	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49419980	49420007	+	frameshift_variant	Frame_Shift_Del	DEL	CAGTGAAGACCAGGTCCTCCAGGCCCTG	CAGTGAAGACCAGGTCCTCCAGGCCCTG	-	novel	NA	P-0005274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	209	507	0	ENST00000301067.7:c.15742_15769del	p.Gln5248ThrfsTer18	p.Q5248Tfs*18	ENST00000301067	NM_003482.3	5248	CAGGGCCTGGAGGACCTGGTCTTCACTGac/ac	48/54	0.150209512177493	5	FACETS	0.902	0.84	0.966	0.601	0.56	0.644	INDETERMINATE	2	TRUE	2	0.587525498295051	5		507	742	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627602	14627604	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	novel	NA	P-0005274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	153	562	0	ENST00000254322.2:c.466_468del	p.Ala156del	p.A156del	ENST00000254322	NM_006145.1	156	GCC/-	2/3	0.289122204535159	3	FACETS	0.868	0.795	0.944	0.434	0.397	0.472	INDETERMINATE	1	TRUE	1	0.587525498295051	3		562	776	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0005279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	116	278	0	ENST00000269305.4:c.559+1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.332266521216613	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.332266521216613	1		278	511	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0005279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1892	163	717	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	0.147050972956888	3	FACETS	0.557	0.508	0.608	0.278	0.254	0.304	INDETERMINATE	1	TRUE	1	0.332266521216613	3		717	2055	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0005279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	72	499	3	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	1	2	FACETS	0.65	0.567	0.739	0.65	0.567	0.739	SUBCLONAL	1	TRUE	1	0.332266521216613	2		502	667	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419837	41419837	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs267605939	NA	P-0005279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	63	401	0	ENST00000373198.4:c.484C>T	p.Gln162Ter	p.Q162*	ENST00000373198	NM_133170.3	162	Cag/Tag	3/32	1	2	FACETS	0.464	0.4	0.534	0.464	0.4	0.534	SUBCLONAL	1	TRUE	1	0.332266521216613	2		401	817	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120467958	120467958	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	186	590	0	ENST00000256646.2:c.4481T>G	p.Phe1494Cys	p.F1494C	ENST00000256646	NM_024408.3	1494	tTt/tGt	25/34	0.332266521216613	1	FACETS	0.852	0.786	0.921	0.852	0.786	0.921	CLONAL	1	TRUE	0	0.332266521216613	1		590	1096	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245515	153245515	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	189	474	0	ENST00000281708.4:c.1676T>C	p.Leu559Pro	p.L559P	ENST00000281708	NM_033632.3	559	cTt/cCt	11/12	0.332266521216613	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.332266521216613	1		474	912	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900245	101900245	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502042	NA	P-0005279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	231	455	0	ENST00000374994.4:c.679G>A	p.Glu227Lys	p.E227K	ENST00000374994	NM_004612.2	227	Gaa/Aaa	4/9	0.31564580752366	2	FACETS	1	0.991	1	0.712	0.664	0.762	CLONAL	1	TRUE	0	0.332266521216613	2		455	976	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981884	101981884	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	58	445	0	ENST00000282441.5:c.305A>G	p.Lys102Arg	p.K102R	ENST00000282441	NM_001130145.2	102	aAa/aGa	1/9	1	2	FACETS	0.399	0.341	0.461	0.399	0.341	0.461	SUBCLONAL	1	TRUE	1	0.332266521216613	2		445	876	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444749	49444749	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	46	514	0	ENST00000301067.7:c.2717C>T	p.Pro906Leu	p.P906L	ENST00000301067	NM_003482.3	906	cCa/cTa	10/54	1	2	FACETS	0.306	0.256	0.361	0.306	0.256	0.361	SUBCLONAL	1	TRUE	1	0.332266521216613	2		514	905	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278181	15278181	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	122	560	0	ENST00000263388.2:c.5241C>A	p.Cys1747Ter	p.C1747*	ENST00000263388	NM_000435.2	1747	tgC/tgA	29/33	0.332266521216613	1	FACETS	0.693	0.626	0.764	0.693	0.626	0.764	SUBCLONAL	1	TRUE	0	0.332266521216613	1		560	884	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569744	41569744	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760998327	NA	P-0005279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	130	605	0	ENST00000263253.7:c.4735G>A	p.Asp1579Asn	p.D1579N	ENST00000263253	NM_001429.3	1579	Gac/Aac	29/31	1	2	FACETS	0.729	0.66	0.802	0.729	0.66	0.802	SUBCLONAL	1	TRUE	1	0.332266521216613	2		605	1073	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432664	29432664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113994087	NA	P-0121548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	341	675	2	ENST00000389048.3:c.3824G>A	p.Arg1275Gln	p.R1275Q	ENST00000389048	NM_004304.4	1275	cGa/cAa	25/29	0.406151559412253	6	FACETS	1	0.989	1	0.577	0.547	0.607	INDETERMINATE	2	NA	2	0.811625575933189	6		677	955	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245201	41245201	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0121548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	220	683	1	ENST00000357654.3:c.2347A>C	p.Ile783Leu	p.I783L	ENST00000357654	NM_007294.3	783	Atc/Ctc	10/23	0.691577453235531	4	FACETS	1	0.96	1	0.522	0.486	0.56	CLONAL	1	NA	2	0.811625575933189	4		684	940	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940000	76940000	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1311466929	NA	P-0121548-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	254	385	0	ENST00000373344.5:c.748C>T	p.Arg250Ter	p.R250*	ENST00000373344	NM_000489.3	250	Cga/Tga	9/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	NA	0	0.811625575933189	1		385	317	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	94	543	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	0.96	0.856	1			1	INDETERMINATE	1	TRUE	NA	0.339954335954104	2		543	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0005288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	64	278	0	ENST00000269305.4:c.559+1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.313789885620966	1	FACETS	0.933	0.813	1	0.933	0.813	1	CLONAL	1	TRUE	0	0.339954335954104	1		278	335	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094339	193094339	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	78	328	0	ENST00000367435.3:c.229C>G	p.Arg77Gly	p.R77G	ENST00000367435	NM_024529.4	77	Cgt/Ggt	2/17	1	2	FACETS	0.927	0.817	1	0.927	0.817	1	CLONAL	1	TRUE	1	0.339954335954104	2		328	495	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584607	48584607	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	121	471	0	ENST00000342988.3:c.781del	p.His261IlefsTer75	p.H261Ifs*75	ENST00000342988	NM_005359.5	260	taC/ta	6/12	0.339954335954104	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.339954335954104	1		471	525	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0005289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	61	379	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	0.400924798897205	2		379	242	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0005289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	45	365	0	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	1	2	FACETS	0.928	0.786	1	0.928	0.786	1	CLONAL	1	TRUE	1	0.400924798897205	2		365	242	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958549	175958549	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	55	473	1	ENST00000367669.3:c.1796G>T	p.Arg599Leu	p.R599L	ENST00000367669	NM_022457.5	599	cGt/cTt	16/20	0.400924798897205	3	FACETS	1	0.933	1	0.572	0.493	0.657	CLONAL	1	TRUE	1	0.400924798897205	3		474	288	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196261	106196261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	46	312	0	ENST00000380013.4:c.4594C>T	p.Gln1532Ter	p.Q1532*	ENST00000380013	NM_001127208.2	1532	Cag/Tag	11/11	0.120258526320266	4	FACETS	1	0.956	1	0.69	0.586	0.802	INDETERMINATE	1	TRUE	2	0.400924798897205	4		312	233	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172085	32172085	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	48	487	0	ENST00000375023.3:c.2947T>C	p.Cys983Arg	p.C983R	ENST00000375023	NM_004557.3	983	Tgt/Cgt	19/30	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.400924798897205	2		487	219	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149298	119149298	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	59	409	0	ENST00000264033.4:c.1306C>G	p.Pro436Ala	p.P436A	ENST00000264033	NM_005188.3	436	Cct/Gct	9/16	0.400924798897205	3	FACETS	1	0.951	1	0.607	0.526	0.693	CLONAL	1	TRUE	1	0.400924798897205	3		409	291	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149364	119149364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	48	309	0	ENST00000264033.4:c.1372G>A	p.Asp458Asn	p.D458N	ENST00000264033	NM_005188.3	458	Gat/Aat	9/16	0.400924798897205	3	FACETS	1	0.946	1	0.622	0.531	0.72	CLONAL	1	TRUE	1	0.400924798897205	3		309	231	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433226	49433226	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	38	387	0	ENST00000301067.7:c.8221G>T	p.Gly2741Trp	p.G2741W	ENST00000301067	NM_003482.3	2741	Ggg/Tgg	32/54	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.400924798897205	2		387	175	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134585	41134585	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	50	514	0	ENST00000379561.5:c.1043A>T	p.Tyr348Phe	p.Y348F	ENST00000379561	NM_002015.3	348	tAc/tTc	2/3	0.162040826812474	1	FACETS	0.717	0.613	0.83	0.717	0.613	0.83	INDETERMINATE	1	TRUE	0	0.400924798897205	1		514	278	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572440	41572440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	53	473	0	ENST00000263253.7:c.4969G>A	p.Glu1657Lys	p.E1657K	ENST00000263253	NM_001429.3	1657	Gag/Aag	30/31	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.400924798897205	2		473	217	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579366	7579366	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0005292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	27	698	0	ENST00000269305.4:c.321C>G	p.Tyr107Ter	p.Y107*	ENST00000269305	NM_001126112.2	107	taC/taG	4/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		698	652	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0005335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	231	287	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.499153188134228	4	FACETS	0.936	0.876	0.998			1	CLONAL	2	TRUE	NA	0.499153188134228	4		287	741	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0005335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	202	458	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.499153188134228	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.499153188134228	2		458	351	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678508	88678508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs183806623	NA	P-0005335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	88	303	0	ENST00000360948.2:c.1028G>A	p.Arg343Gln	p.R343Q	ENST00000360948	NM_001012338.2	343	cGg/cAg	9/19	0.345045424466085	1	FACETS	0.952	0.854	1	0.952	0.854	1	CLONAL	1	TRUE	0	0.499153188134228	1		303	278	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462059	120462059	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1458372923	NA	P-0005335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	110	323	0	ENST00000256646.2:c.5657G>A	p.Arg1886His	p.R1886H	ENST00000256646	NM_024408.3	1886	cGc/cAc	31/34	0.499153188134228	7	FACETS	1	0.913	1	0.204	0.183	0.227	CLONAL	1	TRUE	2	0.499153188134228	7		323	971	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755660	39755660	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	117	399	1	ENST00000288319.7:c.1105C>T	p.Leu369Phe	p.L369F	ENST00000288319	NM_182918.3	369	Ctc/Ttc	10/10	0.290768847140707	3	FACETS	1	0.983	1	0.694	0.631	0.76	INDETERMINATE	1	TRUE	1	0.499153188134228	3		400	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0005339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	476	595	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.833330427607547	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	FALSE	0	0.833330427607547	2		596	533	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375621	118375621	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	147	235	0	ENST00000534358.1:c.9014A>T	p.Asp3005Val	p.D3005V	ENST00000534358	NM_005933.3	3005	gAc/gTc	27/36	0.833330427607547	3	FACETS	0.986	0.906	1	0.493	0.453	0.534	CLONAL	1	FALSE	1	0.833330427607547	3		235	507	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727150	40727150	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	199	310	0	ENST00000373198.4:c.3814C>G	p.Leu1272Val	p.L1272V	ENST00000373198	NM_133170.3	1272	Cta/Gta	28/32	0.695125516927907	4	FACETS	0.97	0.899	1	0.485	0.449	0.522	CLONAL	1	FALSE	2	0.833330427607547	4		310	903	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0005343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	47	428	3	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.175873299858051	5	FACETS	0.654	0.55	0.77	0.218	0.183	0.257	SUBCLONAL	1	TRUE	2	0.21	5		431	900	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0005343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	57	595	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.175873299858051	3	FACETS	0.825	0.707	0.955	0.413	0.353	0.478	CLONAL	1	TRUE	1	0.21	3		596	727	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0005363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	200	345	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.235847481750663	4	FACETS	1	0.98	1	0.772	0.716	0.829	CLONAL	2	TRUE	1	0.252579494023893	4		345	857	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11210283	11210283	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	44	302	4	ENST00000361445.4:c.4470G>C	p.Trp1490Cys	p.W1490C	ENST00000361445	NM_004958.3	1490	tgG/tgC	31/58	1	2	FACETS	0.63	0.528	0.743	0.63	0.528	0.743	SUBCLONAL	1	TRUE	1	0.252579494023893	2		306	553	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973162	25973162	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	68	462	0	ENST00000435504.4:c.1263A>T	p.Arg421Ser	p.R421S	ENST00000435504		421	agA/agT	12/13	0.16734589729707	2	FACETS	0.802	0.698	0.916	0.401	0.349	0.458	CLONAL	1	TRUE	0	0.252579494023893	2		462	671	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432895	432895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	87	399	1	ENST00000399788.2:c.2021G>A	p.Arg674Gln	p.R674Q	ENST00000399788	NM_001042603.1	674	cGg/cAg	15/28	NA	2	FACETS	0.862	0.763	0.969			1	INDETERMINATE	1	TRUE	NA	0.252579494023893	2		400	799	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578247	7578247	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0005363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	135	467	2	ENST00000269305.4:c.602T>A	p.Leu201Ter	p.L201*	ENST00000269305	NM_001126112.2	201	tTg/tAg	6/11	0.16734589729707	2	FACETS	1	0.977	1	0.613	0.557	0.672	CLONAL	1	TRUE	0	0.252579494023893	2		469	872	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	23	448	4	ENST00000263121.7:c.1130G>T	p.Arg377Leu	p.R377L	ENST00000263121	NM_003073.3	377	cGt/cTt	9/9	0.16734589729707	2	FACETS	0.23	0.178	0.29	0.115	0.089	0.145	SUBCLONAL	1	TRUE	0	0.252579494023893	2		452	792	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936995	48936995	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778842	NA	P-0005378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	612	718	1	ENST00000267163.4:c.763C>T	p.Arg255Ter	p.R255*	ENST00000267163	NM_000321.2	255	Cga/Tga	8/27	0.391035941703986	3	FACETS	0.852	0.821	0.884	0.852	0.821	0.884	CLONAL	3	TRUE	0	0.391035941703986	3		719	1464	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863224683	NA	P-0005378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	277	264	0	ENST00000269305.4:c.388C>T	p.Leu130Phe	p.L130F	ENST00000269305	NM_001126112.2	130	Ctc/Ttc	5/11	0.292698078215125	2	FACETS	0.869	0.819	0.92	0.869	0.819	0.92	CLONAL	2	TRUE	0	0.391035941703986	2		264	815	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499590	149499590	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	611	983	1	ENST00000261799.4:c.2683G>T	p.Glu895Ter	p.E895*	ENST00000261799	NM_002609.3	895	Gag/Tag	19/23	0.357317220802107	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.391035941703986	2		984	1513	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55087043	55087043	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	181	464	0	ENST00000275493.2:c.73C>G	p.Leu25Val	p.L25V	ENST00000275493	NM_005228.3	25	Ctg/Gtg	1/28	0.267130935773461	3	FACETS	1	0.988	1	0.682	0.63	0.736	CLONAL	1	TRUE	1	0.391035941703986	3		464	811	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133729485	133729485	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	318	579	0	ENST00000318560.5:c.114G>C	p.Glu38Asp	p.E38D	ENST00000318560	NM_005157.4	38	gaG/gaC	2/11	0.391035941703986	3	FACETS	0.827	0.78	0.874	0.827	0.78	0.874	CLONAL	2	TRUE	1	0.391035941703986	3		579	1176	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795885	42795886	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	A	novel	NA	P-0005378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	259	795	3	ENST00000575354.2:c.2874_2875delinsA	p.Ser961AlafsTer6	p.S961Afs*6	ENST00000575354	NM_015125.3	958	caGCcc/caAcc	11/20	0.391035941703986	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.391035941703986	1		798	877	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233628	233628	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	69	158	0	ENST00000264932.6:c.932G>T	p.Cys311Phe	p.C311F	ENST00000264932	NM_004168.2	311	tGt/tTt	8/15	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.76	2		158	181	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287328	46287328	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0005379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	52	324	0	ENST00000334344.6:c.5271+2T>A		p.X1757_splice	ENST00000334344	NM_152641.2	1757			1	2	FACETS	0.421	0.36	0.487	0.421	0.36	0.487	SUBCLONAL	1	TRUE	1	0.76	2		324	325	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579717	7579717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs922736614	NA	P-0005379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	77	401	1	ENST00000269305.4:c.79C>T	p.Pro27Ser	p.P27S	ENST00000269305	NM_001126112.2	27	Cct/Tct	3/11	1	2	FACETS	0.302	0.265	0.343	0.302	0.265	0.343	SUBCLONAL	1	TRUE	1	0.76	2		402	670	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0005395-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	387	819	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.469987957101865	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.469987957101865	1		819	1091	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151240	202151240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005395-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	724	561	1	ENST00000358485.4:c.1540G>A	p.Asp514Asn	p.D514N	ENST00000358485	NM_001080125.1	514	Gac/Aac	9/9	NA	2	FACETS	0.998	0.965	1			1	INDETERMINATE	2	TRUE	NA	0.469987957101865	2		562	1544	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584521	189584521	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1218025384	NA	P-0005395-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1880	348	492	0	ENST00000264731.3:c.817G>T	p.Ala273Ser	p.A273S	ENST00000264731	NM_003722.4	273	Gcc/Tcc	6/14	0.469987957101865	4	FACETS	0.977	0.921	1	0.489	0.46	0.518	CLONAL	1	TRUE	2	0.469987957101865	4		492	2228	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982782	90982782	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0005395-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	279	213	0	ENST00000265433.3:c.706A>T	p.Lys236Ter	p.K236*	ENST00000265433	NM_002485.4	236	Aag/Tag	7/16	0.469987957101865	4	FACETS	0.823	0.774	0.874	0.823	0.774	0.874	CLONAL	2	TRUE	2	0.469987957101865	4		213	1060	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139818386	139818400	+	protein_altering_variant	In_Frame_Del	DEL	GTCCCTCTTCTTTGT	GTCCCTCTTCTTTGT	CATTCG	novel	NA	P-0005395-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1679	342	695	0	ENST00000247668.2:c.1221_1235delinsCATTCG	p.Ser408_Val412delinsIleArg	p.S408_V412delinsIR	ENST00000247668	NM_021138.3	407	ctGTCCCTCTTCTTTGTg/ctCATTCGg	10/11	0.19400113215857	5	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.469987957101865	5		695	2021	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169376	11169376	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005398-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	159	640	0	ENST00000361445.4:c.7499T>A	p.Ile2500Asn	p.I2500N	ENST00000361445	NM_004958.3	2500	aTt/aAt	56/58	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		640	755	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0005416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	401	348	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	TRUE	1	0.513650842824664	2		348	1508	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1625	429	283	2	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.447627093179231	4	FACETS	1	0.992	1			1	CLONAL	1	TRUE	NA	0.513650842824664	4		285	2054	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061465	38061465	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1197	452	347	0	ENST00000250448.2:c.524A>G	p.Tyr175Cys	p.Y175C	ENST00000250448	NM_004496.3	175	tAc/tGc	2/2	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.513650842824664	2		347	1649	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857716	59857716	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1576	536	447	0	ENST00000259008.2:c.1841C>A	p.Ser614Tyr	p.S614Y	ENST00000259008	NM_032043.2	614	tCt/tAt	13/20	1	2	FACETS	0.988	0.945	1	0.988	0.945	1	CLONAL	1	TRUE	1	0.513650842824664	2		447	2112	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519988	NA	P-0005419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	324	349	0	ENST00000269305.4:c.808T>C	p.Phe270Leu	p.F270L	ENST00000269305	NM_001126112.2	270	Ttt/Ctt	8/11	0.400933311291876	3	FACETS	0.99	0.944	1			1	CLONAL	3	TRUE	NA	0.400933311291876	3		349	653	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37092022	37092022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	66	340	0	ENST00000231790.2:c.2149G>A	p.Glu717Lys	p.E717K	ENST00000231790	NM_000249.3	717	Gaa/Aaa	19/19	0.296372666235291	4	FACETS	0.932	0.81	1	0.233	0.202	0.266	CLONAL	1	TRUE	0	0.400933311291876	4		340	495	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046347	128046347	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1291272894	NA	P-0005419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	141	306	0	ENST00000285398.2:c.916A>G	p.Ile306Val	p.I306V	ENST00000285398	NM_000122.1	306	Atc/Gtc	7/15	0.400933311291876	3	FACETS	0.942	0.866	1	0.942	0.866	1	CLONAL	2	TRUE	1	0.400933311291876	3		306	448	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212252715	212252715	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	27	174	0	ENST00000342788.4:c.3138T>A	p.Ser1046Arg	p.S1046R	ENST00000342788	NM_005235.2	1046	agT/agA	26/28	NA	2	FACETS	0.663	0.531	0.812			1	INDETERMINATE	1	TRUE	NA	0.400933311291876	2		174	203	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530154	212530154	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	27	255	0	ENST00000342788.4:c.1765T>A	p.Cys589Ser	p.C589S	ENST00000342788	NM_005235.2	589	Tgt/Agt	15/28	NA	2	FACETS	0.376	0.299	0.464			1	INDETERMINATE	1	TRUE	NA	0.400933311291876	2		255	358	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215674233	215674233	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs864622206	NA	P-0005419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	31	249	0	ENST00000260947.4:c.61C>G	p.Arg21Gly	p.R21G	ENST00000260947	NM_000465.2	21	Cgt/Ggt	1/11	0.400933311291876	3	FACETS	0.33	0.266	0.402	0.165	0.133	0.201	SUBCLONAL	1	TRUE	1	0.400933311291876	3		249	563	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715597	30715597	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	156	242	0	ENST00000295754.5:c.1255G>A	p.Val419Met	p.V419M	ENST00000295754	NM_003242.5	419	Gtg/Atg	5/7	0.296372666235291	4	FACETS	0.925	0.857	0.993	0.694	0.643	0.745	CLONAL	3	TRUE	0	0.400933311291876	4		242	393	SUCCESS
ATR	545	MSKCC	GRCh37	3	142212018	142212018	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	29	285	0	ENST00000350721.4:c.6034G>C	p.Glu2012Gln	p.E2012Q	ENST00000350721	NM_001184.3	2012	Gaa/Caa	35/47	NA	2	FACETS	0.415	0.333	0.507			1	INDETERMINATE	1	TRUE	NA	0.400933311291876	2		285	349	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595547	55595547	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	54	297	0	ENST00000288135.5:c.2037G>C	p.Leu679Phe	p.L679F	ENST00000288135	NM_000222.2	679	ttG/ttC	14/21	1	2	FACETS	0.724	0.621	0.836	0.724	0.621	0.836	SUBCLONAL	1	TRUE	1	0.400933311291876	2		297	372	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984794	55984794	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761016513	NA	P-0005419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	23	295	0	ENST00000263923.4:c.335C>T	p.Ser112Leu	p.S112L	ENST00000263923	NM_002253.2	112	tCg/tTg	3/30	1	2	FACETS	0.285	0.222	0.359	0.285	0.222	0.359	SUBCLONAL	1	TRUE	1	0.400933311291876	2		295	402	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628371	86628371	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	51	192	0	ENST00000274376.6:c.740C>A	p.Ser247Tyr	p.S247Y	ENST00000274376	NM_002890.2	247	tCt/tAt	3/25	0.400933311291876	4	FACETS	0.78	0.664	0.907	0.195	0.166	0.227	CLONAL	1	TRUE	0	0.400933311291876	4		192	457	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225585	26225585	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1372	507	642	0	ENST00000360408.1:c.203T>A	p.Phe68Tyr	p.F68Y	ENST00000360408	NM_003532.2	68	tTt/tAt	1/1	0.400933311291876	8	FACETS	0.988	0.944	1			1	CLONAL	3	TRUE	NA	0.400933311291876	8		642	1879	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741499	145741499	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs915387235	NA	P-0005419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	70	226	1	ENST00000428558.2:c.1004G>A	p.Gly335Asp	p.G335D	ENST00000428558	NM_004260.3	335	gGc/gAc	5/22	0.400933311291876	6	FACETS	1	0.954	1			1	CLONAL	1	TRUE	NA	0.400933311291876	6		227	521	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435563	18435563	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	20	232	0	ENST00000266497.5:c.548C>T	p.Ser183Leu	p.S183L	ENST00000266497		183	tCa/tTa	1/31	0.284233841938854	0	FACETS	0.228	0.174	0.291			1	SUBCLONAL	1	TRUE	0	0.400933311291876	0		232	262	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519189	103519189	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	22	156	0	ENST00000355739.4:c.2527C>G	p.Gln843Glu	p.Q843E	ENST00000355739	NM_000123.3	843	Caa/Gaa	11/15	0.266856959195146	3	FACETS	0.433	0.336	0.546	0.144	0.112	0.182	SUBCLONAL	1	TRUE	0	0.400933311291876	3		156	304	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104379	2104379	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	25	266	0	ENST00000219476.3:c.419T>A	p.Leu140Gln	p.L140Q	ENST00000219476	NM_000548.3	140	cTg/cAg	5/42	NA	2	FACETS	0.269	0.211	0.335			1	INDETERMINATE	1	TRUE	NA	0.400933311291876	2		266	464	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822034	72822034	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149197237	NA	P-0005419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	19	249	0	ENST00000268489.5:c.10141C>T	p.Arg3381Trp	p.R3381W	ENST00000268489	NM_006885.3	3381	Cgg/Tgg	10/10	0.284233841938854	0	FACETS	0.218	0.165	0.279			1	SUBCLONAL	1	TRUE	0	0.400933311291876	0		249	261	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652533	48652533	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	20	136	0	ENST00000376670.3:c.1204A>T	p.Thr402Ser	p.T402S	ENST00000376670	NM_002049.3	402	Acc/Tcc	6/6	0.379781399752023	1	FACETS	0.6	0.464	0.755	0.6	0.464	0.755	SUBCLONAL	1	TRUE	0	0.400933311291876	1		136	133	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487579	56487581	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0005419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	273	270	0	ENST00000267101.3:c.1515_1517del	p.Ser506del	p.S506del	ENST00000267101	NM_001982.3	504	tgCTCc/tgc	13/28	0.400933311291876	5	FACETS	1	0.983	1	1	0.994	1	CLONAL	4	TRUE	2	0.400933311291876	5		270	507	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25462032	25462032	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	98	310	0	ENST00000264709.3:c.2375del	p.Arg792ProfsTer10	p.R792Pfs*10	ENST00000264709	NM_175629.2	792	cGc/cc	20/23	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.400933311291876	2		310	420	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509597	29509614	+	inframe_deletion	In_Frame_Del	DEL	CCACTACAAATCATTCTC	CCACTACAAATCATTCTC	-	novel	NA	P-0005419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	163	284	0	ENST00000356175.3:c.803_820del	p.Pro268_Leu273del	p.P268_L273del	ENST00000356175	NM_000267.3	268	CCACTACAAATCATTCTC/-	8/57	0.400933311291876	3	FACETS	1	0.981	1			1	CLONAL	2	TRUE	NA	0.400933311291876	3		284	417	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589149	67589151	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	novel	NA	P-0005419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	313	154	0	ENST00000274335.5:c.1138_1140del	p.Leu380del	p.L380del	ENST00000274335		379	aaATTa/aaa	9/15	0.400933311291876	4	FACETS	0.921	0.884	0.957	1	0.992	1	CLONAL	5	TRUE	0	0.400933311291876	4		154	475	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0005432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	18	287	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.644	0.483	0.836	0.644	0.483	0.836	SUBCLONAL	1	TRUE	1	0.11	2		287	508	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0005432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	18	194	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.943	0.709	1	0.943	0.709	1	CLONAL	1	TRUE	1	0.11	2		194	347	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244091	153244091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	34	425	1	ENST00000281708.4:c.2066G>A	p.Arg689Gln	p.R689Q	ENST00000281708	NM_033632.3	689	cGg/cAg	12/12	1	2	FACETS	0.92	0.75	1	0.92	0.75	1	CLONAL	1	TRUE	1	0.11	2		426	672	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127916221	127916221	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	74	841	0	ENST00000373547.4:c.423C>A	p.Tyr141Ter	p.Y141*	ENST00000373547	NM_002721.4	141	taC/taA	5/7	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.11	2		841	1102	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0005444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	66	546	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.197323104025919	2	FACETS	0.346	0.301	0.396	0.173	0.15	0.198	INDETERMINATE	1	TRUE	0	0.695573646476096	2		546	548	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	150	225	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.948	0.876	1	1	0.992	1	CLONAL	2	FALSE	1	0.386920480792484	2		225	409	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625249	69625249	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781935233	NA	P-0005459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	374	702	0	ENST00000334134.2:c.544G>A	p.Val182Met	p.V182M	ENST00000334134	NM_005247.2	182	Gtg/Atg	3/3	1	2	FACETS	1	0.952	1	1	0.997	1	CLONAL	2	FALSE	1	0.386920480792484	2		702	967	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117846	108117846	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	179	338	0	ENST00000278616.4:c.1057T>C	p.Cys353Arg	p.C353R	ENST00000278616	NM_000051.3	353	Tgt/Cgt	8/63	1	2	FACETS	0.891	0.828	0.956	1	0.992	1	CLONAL	2	FALSE	1	0.386920480792484	2		338	519	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474431	40474431	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs193922721	NA	P-0005459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	503	940	0	ENST00000264657.5:c.1970A>G	p.Tyr657Cys	p.Y657C	ENST00000264657	NM_139276.2	657	tAt/tGt	21/24	1	2	FACETS	0.916	0.877	0.956	1	0.997	1	CLONAL	2	FALSE	1	0.386920480792484	2		940	1419	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-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	80	185	0	ENST00000269305.4:c.709_782+90del		p.X237_splice	ENST00000269305	NM_001126112.2	237		7/11	0.367980740515875	0	FACETS	0.919	0.839	0.996			1	CLONAL	2	FALSE	0	0.386920480792484	0		185	138	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0005460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	194	595	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.310202513292548	2		596	1144	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696644	47696644	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519964	NA	P-0005460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	160	697	0	ENST00000347630.2:c.304T>G	p.Phe102Val	p.F102V	ENST00000347630	NM_001007230.1	102	Ttc/Gtc	5/11	1	2	FACETS	0.942	0.862	1	0.942	0.862	1	CLONAL	1	TRUE	1	0.310202513292548	2		697	1095	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459922	99459922	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	74	436	0	ENST00000268035.6:c.2018A>G	p.Tyr673Cys	p.Y673C	ENST00000268035	NM_000875.3	673	tAt/tGt	10/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		436	725	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391234	139391238	+	frameshift_variant	Frame_Shift_Del	DEL	CACCA	CACCA	-	novel	NA	P-0005462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	66	439	0	ENST00000277541.6:c.6953_6957del	p.Met2318ThrfsTer34	p.M2318Tfs*34	ENST00000277541	NM_017617.3	2318	aTGGTG/a	34/34	0.137915321002497	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		439	516	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0005467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	278	478	5	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.245955835277585	3	FACETS	0.833	0.784	0.884	0.833	0.784	0.884	CLONAL	3	TRUE	0	0.25596969328552	3		483	980	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0005476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	343	429	1	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.619194507058277	2	FACETS	0.989	0.949	1	0.989	0.949	1	CLONAL	2	TRUE	0	0.619194507058277	2		430	560	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099108	27099108	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	166	420	0	ENST00000324856.7:c.3524C>A	p.Pro1175Gln	p.P1175Q	ENST00000324856	NM_006015.4	1175	cCa/cAa	13/20	1	2	FACETS	0.966	0.893	1	0.966	0.893	1	CLONAL	1	TRUE	1	0.619194507058277	2		420	555	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661867	227661867	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	93	213	2	ENST00000305123.5:c.1588A>G	p.Thr530Ala	p.T530A	ENST00000305123	NM_005544.2	530	Aca/Gca	1/2	0.119328864178899	0	FACETS	0.417	0.376	0.46			1	INDETERMINATE	1	TRUE	0	0.619194507058277	0		215	274	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979471	55979471	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	230	328	0	ENST00000263923.4:c.976G>T	p.Glu326Ter	p.E326*	ENST00000263923	NM_002253.2	326	Gaa/Taa	7/30	0.616375328447116	2	FACETS	0.924	0.876	0.971	0.924	0.876	0.971	CLONAL	2	TRUE	0	0.619194507058277	2		328	402	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176618958	176618958	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	193	502	2	ENST00000439151.2:c.1001G>T	p.Arg334Leu	p.R334L	ENST00000439151	NM_022455.4	334	cGc/cTc	3/23	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.619194507058277	2		504	620	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517998	8517998	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	125	462	0	ENST00000356435.5:c.1393A>G	p.Asn465Asp	p.N465D	ENST00000356435		465	Aac/Gac	10/35	0.619194507058277	1	FACETS	0.891	0.818	0.964	0.891	0.818	0.964	CLONAL	1	TRUE	0	0.619194507058277	1		462	313	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8527350	8527350	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	80	293	0	ENST00000356435.5:c.545C>A	p.Ser182Tyr	p.S182Y	ENST00000356435		182	tCt/tAt	5/35	0.619194507058277	1	FACETS	0.756	0.676	0.839	0.756	0.676	0.839	SUBCLONAL	1	TRUE	0	0.619194507058277	1		293	236	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0005476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	91	198	2	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.619194507058277	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.619194507058277	1		200	187	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218566	98218566	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	262	348	0	ENST00000331920.6:c.3298G>T	p.Val1100Phe	p.V1100F	ENST00000331920	NM_000264.3	1100	Gtt/Ttt	19/24	0.617788694766357	2	FACETS	0.996	0.95	1	0.996	0.95	1	CLONAL	2	TRUE	0	0.619194507058277	2		348	425	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944914	31944914	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	131	261	0	ENST00000340398.3:c.187C>G	p.Arg63Gly	p.R63G	ENST00000340398	NM_001013699.2	63	Cgg/Ggg	1/1	0.529147117681346	5	FACETS	0.758	0.692	0.828	0.379	0.346	0.414	SUBCLONAL	2	TRUE	1	0.619194507058277	5		261	538	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858999	57859000	+	missense_variant	Missense_Mutation	DNP	CC	CC	GA	novel	NA	P-0005476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	413	614	0	ENST00000228682.2:c.495_496delinsGA	p.Ile165_Pro166delinsMetThr	p.I165_P166delinsMT	ENST00000228682	NM_005269.2	165	atCCca/atGAca	5/12	0.619194507058277	3	FACETS	0.902	0.862	0.943	0.902	0.862	0.943	CLONAL	2	TRUE	1	0.619194507058277	3		614	968	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120828	115120828	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs756033342	NA	P-0005476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	268	302	0	ENST00000257566.3:c.178C>A	p.Leu60Met	p.L60M	ENST00000257566	NM_016569.3	60	Ctg/Atg	1/8	0.619194507058277	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.619194507058277	3		302	468	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235975	133235975	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	399	412	1	ENST00000320574.5:c.3181G>A	p.Ala1061Thr	p.A1061T	ENST00000320574	NM_006231.2	1061	Gcc/Acc	26/49	0.619194507058277	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.619194507058277	2		413	613	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914274	32914274	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	198	729	0	ENST00000380152.3:c.5782G>C	p.Glu1928Gln	p.E1928Q	ENST00000380152		1928	Gaa/Caa	11/27	0.619194507058277	2	FACETS	0.97	0.903	1	0.485	0.451	0.52	CLONAL	1	TRUE	0	0.619194507058277	2		729	659	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515386	103515386	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	208	320	0	ENST00000355739.4:c.1887G>T	p.Gln629His	p.Q629H	ENST00000355739	NM_000123.3	629	caG/caT	8/15	0.619194507058277	2	FACETS	0.901	0.851	0.95	0.901	0.851	0.95	CLONAL	2	TRUE	0	0.619194507058277	2		320	373	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212208	5212208	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	322	367	0	ENST00000357368.4:c.4823G>C	p.Arg1608Pro	p.R1608P	ENST00000357368	NM_002850.3	1608	cGg/cCg	32/38	0.563612752843189	3	FACETS	0.952	0.906	0.999	0.952	0.906	0.999	CLONAL	2	TRUE	1	0.619194507058277	3		367	715	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0005531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	882	735	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.422426615486065	3	FACETS	0.986	0.967	1			1	INDETERMINATE	3	TRUE	NA	0.732714330397813	3		735	1112	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400966	72400966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	244	1001	0	ENST00000357731.5:c.205G>A	p.Gly69Ser	p.G69S	ENST00000357731	NM_173808.2	69	Ggt/Agt	2/7	0.579174307877266	4	FACETS	0.928	0.866	0.992	0.464	0.433	0.496	CLONAL	1	TRUE	2	0.732714330397813	4		1001	1244	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763965	76763965	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	102	864	0	ENST00000373344.5:c.7343C>A	p.Pro2448His	p.P2448H	ENST00000373344	NM_000489.3	2448	cCt/cAt	35/35	0.266303503123464	1	FACETS	0.296	0.265	0.329	0.296	0.265	0.329	INDETERMINATE	1	TRUE	0	0.732714330397813	1		864	596	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005578-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	112	225	0				ENST00000310581	NM_198253.2	-/1132			0.364758495316638	3	FACETS	1	0.984	1	0.742	0.671	0.816	CLONAL	1	TRUE	1	0.382863087203092	3		225	470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0005578-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	679	366	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.382863087203092	4	FACETS	1	0.995	1			1	CLONAL	4	TRUE	NA	0.382863087203092	4		366	1112	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118354937	118354937	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005578-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	226	262	0	ENST00000534358.1:c.4126A>T	p.Thr1376Ser	p.T1376S	ENST00000534358	NM_005933.3	1376	Act/Tct	9/36	0.319900058269617	2	FACETS	0.969	0.909	1	0.969	0.909	1	CLONAL	2	TRUE	0	0.382863087203092	2		262	609	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500479	149500490	+	inframe_deletion	In_Frame_Del	DEL	CGCATGATGTCT	CGCATGATGTCT	-	novel	NA	P-0005578-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	94	367	0	ENST00000261799.4:c.2547_2558del	p.Ile851_Asp854del	p.I851_D854del	ENST00000261799	NM_002609.3	849	cgAGACATCATGCGg/cgg	18/23	1	2	FACETS	0.626	0.556	0.7	0.626	0.556	0.7	SUBCLONAL	1	TRUE	1	0.382863087203092	2		367	785	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443757	52443757	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1208026193	NA	P-0005581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	123	301	0	ENST00000460680.1:c.40C>T	p.Leu14Phe	p.L14F	ENST00000460680	NM_004656.3	14	Ctc/Ttc	2/17	0.32879495914943	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.32879495914943	1		301	512	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208027	5208027	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	114	536	0	ENST00000357368.4:c.5684T>C	p.Ile1895Thr	p.I1895T	ENST00000357368	NM_002850.3	1895	aTc/aCc	37/38	0.32879495914943	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.32879495914943	1		536	446	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624840	9624840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1184049921	NA	P-0005581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	58	424	0	ENST00000353224.5:c.137C>T	p.Thr46Met	p.T46M	ENST00000353224	NM_177990.2	46	aCg/aTg	3/10	0.32879495914943	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.32879495914943	1		424	236	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	58	225	0				ENST00000310581	NM_198253.2	-/1132			0.3	3	FACETS	0.887	0.76	1			1	CLONAL	1	TRUE	NA	0.13	3		225	1071	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0005586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	64	539	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	1	2	FACETS	0.913	0.788	1	0.913	0.788	1	CLONAL	1	TRUE	1	0.13	2		539	1078	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023151	27023179	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	-	novel	NA	P-0005586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	97	75	0	ENST00000324856.7:c.267_295del	p.Ser90ProfsTer11	p.S90Pfs*11	ENST00000324856	NM_006015.4	86	gGCGGAGCCGGCAGCGGCGGCGGGCCCGGC/g	1/20	1	2	FACETS	1	0.963	1	1	0.988	1	CLONAL	2	TRUE	1	0.13	2		75	634	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253377	226253377	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	17	191	0	ENST00000366813.1:c.149G>T	p.Arg50Leu	p.R50L	ENST00000366813		50	cGt/cTt	2/3	1	2	FACETS	0.937	0.7	1	0.937	0.7	1	CLONAL	1	TRUE	1	0.13	2		191	279	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671286	30671286	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	87	334	0	ENST00000376406.3:c.5591G>C	p.Arg1864Thr	p.R1864T	ENST00000376406	NM_014641.2	1864	aGa/aCa	11/15	1	2	FACETS	0.752	0.665	0.846	1	0.978	1	SUBCLONAL	2	TRUE	1	0.13	2		334	890	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112602	115112602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs865915137	NA	P-0005586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	58	265	0	ENST00000257566.3:c.1138G>A	p.Glu380Lys	p.E380K	ENST00000257566	NM_016569.3	380	Gag/Aag	7/8	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.13	2		265	890	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112614	115112614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	49	220	1	ENST00000257566.3:c.1126G>A	p.Asp376Asn	p.D376N	ENST00000257566	NM_016569.3	376	Gac/Aac	7/8	1	2	FACETS	0.932	0.787	1	0.932	0.787	1	CLONAL	1	TRUE	1	0.13	2		221	809	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0005591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	97	511	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.18	2		511	786	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0005591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	25	454	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.391	0.306	0.488	0.391	0.306	0.488	SUBCLONAL	1	TRUE	1	0.18	2		454	711	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49929216	49929216	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	369	847	2	ENST00000296474.3:c.3327C>G	p.Ile1109Met	p.I1109M	ENST00000296474	NM_002447.2	1109	atC/atG	15/20	0.193049218964995	1	FACETS	1	0.965	1	1	0.965	1	INDETERMINATE	1	TRUE	0	0.397405035109718	1		849	1454	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189850	66189850	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs777006749	NA	P-0005594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	89	452	1	ENST00000273854.3:c.3096C>A	p.Asn1032Lys	p.N1032K	ENST00000273854	NM_004439.5	1032	aaC/aaA	18/18	0.229702593052243	3	FACETS	0.457	0.403	0.514	0.228	0.201	0.257	INDETERMINATE	1	TRUE	1	0.397405035109718	3		453	1176	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982101	93982101	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	143	586	0	ENST00000369303.4:c.1364T>A	p.Leu455Gln	p.L455Q	ENST00000369303	NM_004440.3	455	cTg/cAg	6/17	0.193049218964995	1	FACETS	0.446	0.405	0.489	0.446	0.405	0.489	INDETERMINATE	1	TRUE	0	0.397405035109718	1		586	1294	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864368	162864368	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	115	436	1	ENST00000366898.1:c.145G>T	p.Glu49Ter	p.E49*	ENST00000366898	NM_004562.2	49	Gag/Tag	2/12	0.193049218964995	1	FACETS	0.55	0.495	0.608	0.55	0.495	0.608	INDETERMINATE	1	TRUE	0	0.397405035109718	1		437	843	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515198	106515198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146675267	NA	P-0005594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	150	357	1	ENST00000359195.3:c.2341G>A	p.Glu781Lys	p.E781K	ENST00000359195	NM_002649.2	781	Gaa/Aaa	5/11	1	2	FACETS	0.87	0.795	0.948	0.87	0.795	0.948	CLONAL	1	TRUE	1	0.397405035109718	2		358	868	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499811	8499811	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372425454	NA	P-0005594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1256	82	476	0	ENST00000356435.5:c.2158G>A	p.Val720Ile	p.V720I	ENST00000356435		720	Gta/Ata	14/35	0.397405035109718	3	FACETS	0.37	0.324	0.419	0.185	0.162	0.21	SUBCLONAL	1	TRUE	1	0.397405035109718	3		476	1338	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006017	22006017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253220031	NA	P-0005594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1332	128	506	4	ENST00000276925.6:c.386C>T	p.Ala129Val	p.A129V	ENST00000276925	NM_004936.3	129	gCa/gTa	2/2	0.397405035109718	3	FACETS	0.529	0.477	0.584	0.264	0.238	0.292	SUBCLONAL	1	TRUE	1	0.397405035109718	3		510	1460	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989482	85989482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	213	432	1	ENST00000263360.6:c.1241G>A	p.Arg414Gln	p.R414Q	ENST00000263360	NM_003797.3	414	cGa/cAa	12/12	0.397405035109718	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.397405035109718	1		433	780	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40458310	40458310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs532878442	NA	P-0005594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	73	398	0	ENST00000345506.4:c.1525G>A	p.Glu509Lys	p.E509K	ENST00000345506	NM_003152.3	509	Gag/Aag	14/20	0.252868378247008	1	FACETS	0.483	0.422	0.548	0.483	0.422	0.548	SUBCLONAL	1	TRUE	0	0.397405035109718	1		398	610	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411063	63411063	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	223	544	0	ENST00000330258.3:c.2104G>T	p.Glu702Ter	p.E702*	ENST00000330258	NM_152424.3	702	Gag/Tag	2/2	0.382953217140921	1	FACETS	0.89	0.829	0.954	0.89	0.829	0.954	CLONAL	1	TRUE	0	0.397405035109718	1		544	1010	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088678	27088679	+	missense_variant	Missense_Mutation	DNP	AG	AG	TT	novel	NA	P-0005594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	108	532	0	ENST00000324856.7:c.2287_2288delinsTT	p.Ser763Phe	p.S763F	ENST00000324856	NM_006015.4	763	AGt/TTt	7/20	1	2	FACETS	0.441	0.394	0.491	0.441	0.394	0.491	SUBCLONAL	1	TRUE	1	0.397405035109718	2		532	1232	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	175	330	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.708	0.654	0.763	0.708	0.654	0.763	SUBCLONAL	1	TRUE	1	0.744920458753491	2		330	664	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	49	484	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.424	0.361	0.493	0.424	0.361	0.493	SUBCLONAL	1	TRUE	1	0.744920458753491	2		484	310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	419	786	2	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	1	2	FACETS	0.944	0.9	0.988	0.944	0.9	0.988	CLONAL	1	TRUE	1	0.744920458753491	2		788	1192	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913355	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	9	493	0	ENST00000288602.6:c.1406G>T	p.Gly469Val	p.G469V	ENST00000288602	NM_004333.4	469	gGa/gTa	11/18	1	2	FACETS	0.145	0.095	0.207	0.145	0.095	0.207	SUBCLONAL	1	TRUE	1	0.744920458753491	2		493	167	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864656	37864656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs950730453	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	401	850	0	ENST00000269571.5:c.308G>A	p.Arg103Gln	p.R103Q	ENST00000269571		103	cGa/cAa	3/27	1	2	FACETS	0.882	0.84	0.926	0.882	0.84	0.926	CLONAL	1	TRUE	1	0.744920458753491	2		850	1220	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856356	45856356	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	373	872	0	ENST00000391945.4:c.1816G>C	p.Glu606Gln	p.E606Q	ENST00000391945	NM_000400.3	606	Gag/Cag	19/23	0.122248697453305	4	FACETS	0.789	0.749	0.829	0.789	0.749	0.829	INDETERMINATE	2	TRUE	2	0.744920458753491	4		872	1108	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812261	43812261	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	217	622	0	ENST00000372470.3:c.1126C>T	p.His376Tyr	p.H376Y	ENST00000372470	NM_005373.2	376	Cac/Tac	7/12	1	2	FACETS	0.844	0.789	0.901	0.844	0.789	0.901	CLONAL	1	TRUE	1	0.744920458753491	2		622	690	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120478170	120478170	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	192	566	1	ENST00000256646.2:c.3580C>T	p.Gln1194Ter	p.Q1194*	ENST00000256646	NM_024408.3	1194	Cag/Tag	22/34	1	2	FACETS	0.893	0.832	0.957	0.893	0.832	0.957	CLONAL	1	TRUE	1	0.744920458753491	2		567	577	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551334	150551334	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	336	914	1	ENST00000369026.2:c.673G>A	p.Glu225Lys	p.E225K	ENST00000369026	NM_021960.4	225	Gag/Aag	1/3	1	2	FACETS	0.735	0.694	0.776	0.735	0.694	0.776	SUBCLONAL	1	TRUE	1	0.744920458753491	2		915	1228	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25536793	25536793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	484	822	2	ENST00000264709.3:c.61G>A	p.Glu21Lys	p.E21K	ENST00000264709	NM_175629.2	21	Gag/Aag	2/23	1	2	FACETS	0.925	0.885	0.966	0.925	0.885	0.966	CLONAL	1	TRUE	1	0.744920458753491	2		824	1405	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662433	227662433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751685762	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	125	444	1	ENST00000305123.5:c.1022C>T	p.Ser341Leu	p.S341L	ENST00000305123	NM_005544.2	341	tCg/tTg	1/2	1	2	FACETS	0.679	0.618	0.743	0.679	0.618	0.743	SUBCLONAL	1	TRUE	1	0.744920458753491	2		445	494	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528627	89528627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	142	571	0	ENST00000336596.2:c.2927C>T	p.Ser976Leu	p.S976L	ENST00000336596	NM_005233.5	976	tCa/tTa	17/17	1	2	FACETS	0.863	0.793	0.934	0.863	0.793	0.934	CLONAL	1	TRUE	1	0.744920458753491	2		571	442	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157173	106157173	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	99	448	2	ENST00000380013.4:c.2074G>A	p.Glu692Lys	p.E692K	ENST00000380013	NM_001127208.2	692	Gaa/Aaa	3/11	1	2	FACETS	0.949	0.86	1	0.949	0.86	1	CLONAL	1	TRUE	1	0.744920458753491	2		450	280	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532702	187532702	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	133	693	1	ENST00000441802.2:c.9691G>A	p.Glu3231Lys	p.E3231K	ENST00000441802	NM_005245.3	3231	Gag/Aag	14/27	1	2	FACETS	0.867	0.795	0.941	0.867	0.795	0.941	CLONAL	1	TRUE	1	0.744920458753491	2		694	412	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903779	41903779	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	341	725	1	ENST00000372991.4:c.778C>T	p.Gln260Ter	p.Q260*	ENST00000372991	NM_001760.3	260	Cag/Tag	5/5	1	2	FACETS	0.889	0.842	0.936	0.889	0.842	0.936	CLONAL	1	TRUE	1	0.744920458753491	2		726	1030	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004728	150004728	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	130	583	1	ENST00000253339.5:c.1497A>T	p.Lys499Asn	p.K499N	ENST00000253339		499	aaA/aaT	3/7	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.744920458753491	2		584	333	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129213	152129213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	426	944	2	ENST00000206249.3:c.166G>A	p.Glu56Lys	p.E56K	ENST00000206249	NM_000125.3	56	Gag/Aag	1/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.744920458753491	2		946	1118	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100532	157100532	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	358	448	0	ENST00000346085.5:c.1469G>A	p.Trp490Ter	p.W490*	ENST00000346085	NM_020732.3	490	tGg/tAg	1/20	1	2	FACETS	0.908	0.862	0.955	0.908	0.862	0.955	CLONAL	1	TRUE	1	0.744920458753491	2		448	1058	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157495181	157495181	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867250266	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	247	594	0	ENST00000346085.5:c.3065C>T	p.Ser1022Phe	p.S1022F	ENST00000346085	NM_020732.3	1022	tCc/tTc	11/20	1	2	FACETS	0.958	0.901	1	0.958	0.901	1	CLONAL	1	TRUE	1	0.744920458753491	2		594	692	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431631	6431631	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	71	336	0	ENST00000356142.4:c.184G>A	p.Glu62Lys	p.E62K	ENST00000356142	NM_018890.3	62	Gaa/Aaa	3/7	1	2	FACETS	0.934	0.831	1	0.934	0.831	1	CLONAL	1	TRUE	1	0.744920458753491	2		336	204	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339409	116339409	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	85	353	0	ENST00000397752.3:c.271G>A	p.Glu91Lys	p.E91K	ENST00000397752	NM_000245.2	91	Gaa/Aaa	2/21	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.744920458753491	2		353	225	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80646085	80646085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	68	147	0	ENST00000286548.4:c.67G>A	p.Asp23Asn	p.D23N	ENST00000286548	NM_002072.3	23	Gac/Aac	1/7	1	2	FACETS	0.982	0.871	1	0.982	0.871	1	CLONAL	1	TRUE	1	0.744920458753491	2		147	186	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263941	104263941	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1227379293	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	112	166	0	ENST00000369902.3:c.32G>A	p.Gly11Asp	p.G11D	ENST00000369902	NM_016169.3	11	gGc/gAc	1/12	1	2	FACETS	0.976	0.89	1	0.976	0.89	1	CLONAL	1	TRUE	1	0.744920458753491	2		166	308	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534285	534285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894226	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	402	661	0	ENST00000451590.1:c.38G>A	p.Gly13Asp	p.G13D	ENST00000451590	NM_001130442.1	13	gGt/gAt	2/5	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.744920458753491	2		661	906	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243472	46243472	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	82	681	0	ENST00000334344.6:c.1825C>T	p.Gln609Ter	p.Q609*	ENST00000334344	NM_152641.2	609	Cag/Tag	14/21	1	2	FACETS	0.957	0.859	1	0.957	0.859	1	CLONAL	1	TRUE	1	0.744920458753491	2		681	230	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355074	73355074	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763490458	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	70	430	0	ENST00000377767.4:c.296G>A	p.Arg99Lys	p.R99K	ENST00000377767	NM_014953.3	99	aGa/aAa	2/21	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.744920458753491	2		430	187	SUCCESS
BLM	641	MSKCC	GRCh37	15	91295100	91295100	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146096923	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	66	522	0	ENST00000355112.3:c.883G>A	p.Asp295Asn	p.D295N	ENST00000355112	NM_000057.2	295	Gat/Aat	4/22	0.130928597962176	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.744920458753491	0		522	197	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857944	9857944	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267604687	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	68	525	0	ENST00000330684.3:c.3457G>A	p.Asp1153Asn	p.D1153N	ENST00000330684	NM_001134407.1	1153	Gat/Aat	13/13	0.122248697453305	4	FACETS	0.557	0.485	0.635	0.278	0.242	0.318	INDETERMINATE	1	TRUE	2	0.744920458753491	4		525	572	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14016009	14016009	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	60	463	0	ENST00000311895.7:c.329C>T	p.Thr110Ile	p.T110I	ENST00000311895	NM_005236.2	110	aCa/aTa	2/11	0.122248697453305	4	FACETS	1	0.973	1	0.744	0.652	0.839	INDETERMINATE	1	TRUE	2	0.744920458753491	4		463	189	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653079	29653079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	45	550	0	ENST00000356175.3:c.5014C>T	p.His1672Tyr	p.H1672Y	ENST00000356175	NM_000267.3	1672	Cat/Tat	36/57	1	2	FACETS	0.257	0.216	0.303	0.257	0.216	0.303	SUBCLONAL	1	TRUE	1	0.744920458753491	2		550	470	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626772	14626772	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	248	1050	2	ENST00000254322.2:c.1003G>A	p.Glu335Lys	p.E335K	ENST00000254322	NM_006145.1	335	Gag/Aag	3/3	0.122248697453305	4	FACETS	0.781	0.733	0.829	0.781	0.733	0.829	INDETERMINATE	2	TRUE	2	0.744920458753491	4		1052	744	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937611	17937611	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	397	1020	1	ENST00000458235.1:c.3316G>A	p.Glu1106Lys	p.E1106K	ENST00000458235	NM_000215.3	1106	Gag/Aag	24/24	0.122248697453305	4	FACETS	1	0.995	1	0.712	0.676	0.747	INDETERMINATE	1	TRUE	2	0.744920458753491	4		1021	1307	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36421175	36421175	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	128	411	0	ENST00000300305.3:c.22G>A	p.Glu8Lys	p.E8K	ENST00000300305		8	Gag/Aag	1/8	1	2	FACETS	0.909	0.833	0.988	0.909	0.833	0.988	CLONAL	1	TRUE	1	0.744920458753491	2		411	378	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922785	44922785	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	377	423	0	ENST00000377967.4:c.1646G>A	p.Arg549Lys	p.R549K	ENST00000377967	NM_021140.2	549	aGa/aAa	16/29	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.744920458753491	1		423	520	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942733	44942733	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	118	401	1	ENST00000377967.4:c.3313A>T	p.Lys1105Ter	p.K1105*	ENST00000377967	NM_021140.2	1105	Aaa/Taa	23/29	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.744920458753491	1		402	156	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023875	27023875	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	157	190	0	ENST00000324856.7:c.983del	p.Gly328AlafsTer35	p.G328Afs*35	ENST00000324856	NM_006015.4	327	aaG/aa	1/20	1	2	FACETS	0.818	0.755	0.884	0.818	0.755	0.884	CLONAL	1	TRUE	1	0.744920458753491	2		190	515	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950398	38950398	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	37	466	0	ENST00000357387.3:c.3552del	p.Lys1184AsnfsTer20	p.K1184Nfs*20	ENST00000357387	NM_152756.3	1184	aaA/aa	31/38	1	2	FACETS	0.526	0.438	0.621	0.526	0.438	0.621	SUBCLONAL	1	TRUE	1	0.744920458753491	2		466	189	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005631-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	49	414	0	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	0.41291126207724	3	FACETS	0.922	0.797	1			1	CLONAL	2	TRUE	NA	0.410581310033488	3		414	156	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430906	181430906	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005631-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	23	536	1	ENST00000325404.1:c.758C>T	p.Pro253Leu	p.P253L	ENST00000325404	NM_003106.3	253	cCt/cTt	1/1	0.41291126207724	3	FACETS	0.888	0.7	1			1	CLONAL	1	TRUE	NA	0.410581310033488	3		537	152	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923712	131923712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005631-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	16	443	0	ENST00000265335.6:c.982G>A	p.Glu328Lys	p.E328K	ENST00000265335		328	Gaa/Aaa	7/25	0.314659846301441	4	FACETS	0.785	0.585	1	0.393	0.292	0.511	CLONAL	1	TRUE	2	0.410581310033488	4		443	140	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577586	7577586	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587781589	NA	P-0005631-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	36	443	0	ENST00000269305.4:c.695T>G	p.Ile232Ser	p.I232S	ENST00000269305	NM_001126112.2	232	aTc/aGc	7/11	0.41291126207724	3	FACETS	0.859	0.722	1	0.859	0.722	1	CLONAL	2	TRUE	1	0.410581310033488	3		443	123	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38955767	38955767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1489359552	NA	P-0005632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	426	419	0	ENST00000357387.3:c.2539C>T	p.Leu847Phe	p.L847F	ENST00000357387	NM_152756.3	847	Ctc/Ttc	26/38	0.651898230796329	5	FACETS	0.924	0.884	0.963	0.924	0.884	0.963	CLONAL	3	FALSE	2	0.651898230796329	5		419	933	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0005670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	90	345	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	FALSE	1	0.265386051170614	2		345	607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0005670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	149	399	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	FALSE	1	0.265386051170614	2		399	908	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524215	18524215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769408892	NA	P-0005670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	90	510	2	ENST00000266497.5:c.1727C>T	p.Ala576Val	p.A576V	ENST00000266497		576	gCg/gTg	11/31	1	2	FACETS	0.81	0.718	0.909	0.81	0.718	0.909	CLONAL	1	FALSE	1	0.265386051170614	2		512	837	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008501	70008501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147148433	NA	P-0005670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	57	349	0	ENST00000394351.3:c.788G>A	p.Arg263His	p.R263H	ENST00000394351	NM_000248.3	263	cGc/cAc	8/9	1	2	FACETS	0.524	0.449	0.608	0.524	0.449	0.608	SUBCLONAL	1	FALSE	1	0.265386051170614	2		349	819	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205200	46205200	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0005670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	89	316	0	ENST00000334344.6:c.285-1G>C		p.X95_splice	ENST00000334344	NM_152641.2	95			1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	FALSE	1	0.265386051170614	2		316	631	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984702	11984702	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	33	125	0	ENST00000353533.5:c.248C>A	p.Ser83Ter	p.S83*	ENST00000353533	NM_003010.3	83	tCa/tAa	3/11	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	FALSE	1	0.265386051170614	2		125	233	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395668	31395668	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	55	361	0	ENST00000328111.2:c.2521C>A	p.His841Asn	p.H841N	ENST00000328111	NM_006892.3	841	Cac/Aac	23/23	1	2	FACETS	0.476	0.406	0.554	0.476	0.406	0.554	SUBCLONAL	1	FALSE	1	0.265386051170614	2		361	870	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	85	225	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.407464970440405	2		225	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0005671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	44	565	0	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	0.407464970440405	1	FACETS	0.236	0.197	0.28	0.236	0.197	0.28	SUBCLONAL	1	TRUE	0	0.407464970440405	1		565	728	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966913	25966913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	81	396	0	ENST00000435504.4:c.2293C>T	p.Pro765Ser	p.P765S	ENST00000435504		765	Cct/Tct	13/13	1	2	FACETS	0.444	0.39	0.502	0.444	0.39	0.502	SUBCLONAL	1	TRUE	1	0.407464970440405	2		396	896	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885834	111885847	+	frameshift_variant	Frame_Shift_Del	DEL	TCAGAGTCCCTTCC	TCAGAGTCCCTTCC	-	novel	NA	P-0005671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	251	781	1	ENST00000341259.2:c.1459_1472del	p.Glu487LeufsTer11	p.E487Lfs*11	ENST00000341259	NM_005475.2	486	TCAGAGTCCCTTCCt/t	8/8	1	2	FACETS	0.951	0.888	1	0.951	0.888	1	CLONAL	1	TRUE	1	0.407464970440405	2		782	1295	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101331	27101331	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	74	401	0	ENST00000324856.7:c.4615del	p.Ala1539ProfsTer26	p.A1539Pfs*26	ENST00000324856	NM_006015.4	1538	aGg/ag	18/20	0.144959930129378	0	FACETS	0.293	0.256	0.333			1	INDETERMINATE	1	TRUE	0	0.407464970440405	0		401	735	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343390	118343390	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	140	296	0	ENST00000534358.1:c.1516del	p.Thr506ProfsTer61	p.T506Pfs*61	ENST00000534358	NM_005933.3	506	Acc/cc	3/36	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.407464970440405	2		296	651	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107088	27107094	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTGCC	GGCTGCC	CG	novel	NA	P-0005671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	53	229	0	ENST00000324856.7:c.6699_6705delinsCG	p.Ala2235ArgfsTer41	p.A2235Rfs*41	ENST00000324856	NM_006015.4	2233	cgGGCTGCC/cgCG	20/20	0.144959930129378	0	FACETS	0.357	0.305	0.414			1	INDETERMINATE	1	TRUE	0	0.407464970440405	0		229	432	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0005672-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	71	345	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		345	567	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912580	NA	P-0005675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	16	352	0	ENST00000342988.3:c.1157G>A	p.Gly386Asp	p.G386D	ENST00000342988	NM_005359.5	386	gGt/gAt	10/12	0.450752127363408	1	FACETS	0.092	0.067	0.122	0.092	0.067	0.122	SUBCLONAL	1	TRUE	0	0.450752127363408	1		352	597	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258625	16258625	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	36	306	0	ENST00000375759.3:c.5890G>T	p.Glu1964Ter	p.E1964*	ENST00000375759	NM_015001.2	1964	Gag/Tag	11/15	0.360190497945025	1	FACETS	0.243	0.199	0.292	0.243	0.199	0.292	SUBCLONAL	1	TRUE	0	0.450752127363408	1		306	509	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465294	120465294	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	205	470	0	ENST00000256646.2:c.4967A>C	p.Gln1656Pro	p.Q1656P	ENST00000256646	NM_024408.3	1656	cAg/cCg	27/34	1	2	FACETS	0.996	0.925	1	0.996	0.925	1	CLONAL	1	TRUE	1	0.450752127363408	2		470	913	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949078	151949078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	66	438	0	ENST00000262189.6:c.1567G>A	p.Glu523Lys	p.E523K	ENST00000262189	NM_170606.2	523	Gag/Aag	11/59	0.228490510513212	3	FACETS	0.352	0.305	0.405	0.118	0.101	0.135	INDETERMINATE	1	TRUE	0	0.450752127363408	3		438	1018	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856113	68856113	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782750	NA	P-0005675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	192	445	1	ENST00000261769.5:c.1921C>T	p.Gln641Ter	p.Q641*	ENST00000261769	NM_004360.3	641	Cag/Tag	12/16	0.450752127363408	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.450752127363408	1		446	628	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115830	8115837	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGGCCG	CCCGGCCG	-	novel	NA	P-0005691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	130	758	0	ENST00000346208.3:c.1179_1186del	p.Ala394LeufsTer110	p.A394Lfs*110	ENST00000346208		392	aaCCCGGCCGcc/aacc	6/6	1	2	FACETS	0.945	0.856	1	0.945	0.856	1	CLONAL	1	TRUE	1	0.2860769316329	2		758	962	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129857	55129857	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	51	519	0	ENST00000257290.5:c.391C>A	p.Leu131Ile	p.L131I	ENST00000257290	NM_006206.4	131	Cta/Ata	4/23	1	2	FACETS	0.684	0.582	0.797	0.684	0.582	0.797	SUBCLONAL	1	TRUE	1	0.2860769316329	2		519	521	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611108	100611108	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	86	788	2	ENST00000308731.7:c.1498G>T	p.Glu500Ter	p.E500*	ENST00000308731	NM_000061.2	500	Gag/Tag	15/19	0.2860769316329	1	FACETS	0.838	0.742	0.94	0.838	0.742	0.94	CLONAL	1	TRUE	0	0.2860769316329	1		790	615	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56867144	56867144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs908131101	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	104	514	0	ENST00000308159.5:c.1363G>A	p.Val455Met	p.V455M	ENST00000308159	NM_014669.4	455	Gtg/Atg	13/22	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.239289723687257	2		514	736	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400334	139400334	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	24	85	0	ENST00000277541.6:c.4015-1G>A		p.X1339_splice	ENST00000277541	NM_017617.3	1339			0.239289723687257	2	FACETS	0.993	0.795	1	0.993	0.795	1	CLONAL	2	TRUE	0	0.239289723687257	2		85	101	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578502	7578502	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	119	404	0	ENST00000269305.4:c.428T>C	p.Val143Ala	p.V143A	ENST00000269305	NM_001126112.2	143	gTg/gCg	5/11	0.239289723687257	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	2	TRUE	0	0.239289723687257	2		404	495	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202852	16202852	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	78	356	0	ENST00000375759.3:c.560G>T	p.Arg187Leu	p.R187L	ENST00000375759	NM_015001.2	187	cGg/cTg	3/15	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.239289723687257	2		356	650	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510233	120510233	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	80	314	1	ENST00000256646.2:c.1276C>T	p.Pro426Ser	p.P426S	ENST00000256646	NM_024408.3	426	Cct/Tct	8/34	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.239289723687257	2		315	649	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243708851	243708851	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	49	390	0	ENST00000263826.5:c.1212C>A	p.Phe404Leu	p.F404L	ENST00000263826	NM_005465.4	404	ttC/ttA	11/13	1	2	FACETS	0.692	0.585	0.809	0.692	0.585	0.809	SUBCLONAL	1	TRUE	1	0.239289723687257	2		390	592	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27016127	27016127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	81	471	0	ENST00000335756.4:c.403C>G	p.Leu135Val	p.L135V	ENST00000335756	NM_001809.3	135	Ctt/Gtt	4/5	1	2	FACETS	0.948	0.835	1	0.948	0.835	1	CLONAL	1	TRUE	1	0.239289723687257	2		471	714	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551237	29551237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553411110	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	62	384	1	ENST00000389048.3:c.1393G>A	p.Glu465Lys	p.E465K	ENST00000389048	NM_004304.4	465	Gaa/Aaa	6/29	1	2	FACETS	0.958	0.828	1	0.958	0.828	1	CLONAL	1	TRUE	1	0.239289723687257	2		385	541	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010547	48010547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761033647	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	44	221	0	ENST00000234420.5:c.175C>T	p.Pro59Ser	p.P59S	ENST00000234420	NM_000179.2	59	Ccc/Tcc	1/10	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.239289723687257	2		221	301	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713624	52713624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	101	436	0	ENST00000394830.3:c.104G>A	p.Arg35Lys	p.R35K	ENST00000394830	NM_018313.4	35	aGg/aAg	2/30	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.239289723687257	2		436	713	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268500	142268500	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	65	273	0	ENST00000350721.4:c.2992C>A	p.Leu998Ile	p.L998I	ENST00000350721	NM_001184.3	998	Cta/Ata	15/47	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.239289723687257	2		273	412	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972909	55972909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	83	369	1	ENST00000263923.4:c.1481G>A	p.Gly494Glu	p.G494E	ENST00000263923	NM_002253.2	494	gGa/gAa	11/30	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.239289723687257	2		370	587	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540740	187540740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	74	398	0	ENST00000441802.2:c.7000C>T	p.His2334Tyr	p.H2334Y	ENST00000441802	NM_005245.3	2334	Cat/Tat	10/27	1	2	FACETS	0.994	0.871	1	0.994	0.871	1	CLONAL	1	TRUE	1	0.239289723687257	2		398	622	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520274	176520274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1562071377	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	39	200	1	ENST00000292408.4:c.1193G>A	p.Arg398Gln	p.R398Q	ENST00000292408	NM_213647.1	398	cGg/cAg	9/18	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.239289723687257	2		201	281	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524564	176524564	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779686518	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	63	442	0	ENST00000292408.4:c.2296C>T	p.Pro766Ser	p.P766S	ENST00000292408	NM_213647.1	766	Ccc/Tcc	18/18	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.239289723687257	2		442	520	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683581	162683581	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	61	307	0	ENST00000366898.1:c.388G>C	p.Asp130His	p.D130H	ENST00000366898	NM_004562.2	130	Gac/Cac	3/12	0.136675871556245	3	FACETS	1	0.947	1	0.6	0.518	0.688	INDETERMINATE	1	TRUE	1	0.239289723687257	3		307	476	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508937	106508937	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	60	258	0	ENST00000359195.3:c.931C>T	p.Pro311Ser	p.P311S	ENST00000359195	NM_002649.2	311	Cca/Tca	2/11	0.136675871556245	3	FACETS	1	0.947	1	0.602	0.52	0.692	INDETERMINATE	1	TRUE	1	0.239289723687257	3		258	466	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397511	116397511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	92	414	2	ENST00000397752.3:c.1883C>T	p.Pro628Leu	p.P628L	ENST00000397752	NM_000245.2	628	cCt/cTt	7/21	0.136675871556245	3	FACETS	1	0.97	1	0.639	0.568	0.714	INDETERMINATE	1	TRUE	1	0.239289723687257	3		416	674	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965596	90965596	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	82	453	0	ENST00000265433.3:c.1721T>C	p.Leu574Ser	p.L574S	ENST00000265433	NM_002485.4	574	tTa/tCa	11/16	0.136675871556245	3	FACETS	0.883	0.777	0.997	0.442	0.388	0.499	INDETERMINATE	1	TRUE	1	0.239289723687257	3		453	869	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218696	98218696	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1060502285	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	84	212	0	ENST00000331920.6:c.3169-1G>A		p.X1057_splice	ENST00000331920	NM_000264.3	1057			0.239289723687257	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.239289723687257	2		212	299	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900209	101900209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	176	453	0	ENST00000374994.4:c.643C>T	p.Arg215Ter	p.R215*	ENST00000374994	NM_004612.2	215	Cga/Tga	4/9	0.239289723687257	2	FACETS	0.933	0.861	1	0.933	0.861	1	CLONAL	2	TRUE	0	0.239289723687257	2		453	788	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615113	43615113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755837568	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	82	467	2	ENST00000355710.3:c.2527G>A	p.Glu843Lys	p.E843K	ENST00000355710	NM_020975.4	843	Gag/Aag	14/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.239289723687257	2		469	563	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572213	64572213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	87	336	0	ENST00000312049.6:c.1426C>T	p.Arg476Trp	p.R476W	ENST00000312049	NM_130799.2	476	Cgg/Tgg	10/10	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.239289723687257	2		336	687	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245102	46245102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	58	341	0	ENST00000334344.6:c.3196C>T	p.Pro1066Ser	p.P1066S	ENST00000334344	NM_152641.2	1066	Ccg/Tcg	15/21	0.136675871556245	3	FACETS	1	0.898	1	0.527	0.453	0.607	INDETERMINATE	1	TRUE	1	0.239289723687257	3		341	515	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253136	133253136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	58	326	0	ENST00000320574.5:c.905G>A	p.Gly302Asp	p.G302D	ENST00000320574	NM_006231.2	302	gGc/gAc	9/49	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.239289723687257	2		326	395	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563093	21563093	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	82	285	1	ENST00000382592.4:c.826C>T	p.Gln276Ter	p.Q276*	ENST00000382592	NM_014572.2	276	Cag/Tag	4/8	0.142197577046377	3	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.239289723687257	3		286	608	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988574	36988574	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs766700164	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	89	528	0	ENST00000354822.5:c.79C>T	p.Arg27Cys	p.R27C	ENST00000354822	NM_001079668.2	27	Cgc/Tgc	2/3	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.239289723687257	2		528	670	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42002997	42002997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	120	622	0	ENST00000219905.7:c.2534C>T	p.Ser845Phe	p.S845F	ENST00000219905	NM_001164273.1	845	tCt/tTt	8/24	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.239289723687257	2		622	825	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348752	89348752	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	115	645	1	ENST00000301030.4:c.4198G>A	p.Asp1400Asn	p.D1400N	ENST00000301030	NM_001256183.1	1400	Gat/Aat	9/13	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.239289723687257	2		646	930	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110126	8110126	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	51	284	0	ENST00000585124.1:c.479G>A	p.Gly160Glu	p.G160E	ENST00000585124	NM_004217.3	160	gGg/gAg	6/9	0.239289723687257	2	FACETS	1	0.936	1	0.592	0.505	0.687	CLONAL	1	TRUE	0	0.239289723687257	2		284	360	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191030	2191030	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	66	350	0	ENST00000398665.3:c.284C>T	p.Pro95Leu	p.P95L	ENST00000398665	NM_032482.2	95	cCc/cTc	5/28	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.239289723687257	2		350	440	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955096	17955096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201650430	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	62	343	0	ENST00000458235.1:c.131C>T	p.Ser44Phe	p.S44F	ENST00000458235	NM_000215.3	44	tCc/tTc	2/24	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.239289723687257	2		343	467	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902277	50902277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1281656236	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	106	590	1	ENST00000440232.2:c.169G>A	p.Glu57Lys	p.E57K	ENST00000440232	NM_002691.3	57	Gag/Aag	2/27	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.239289723687257	2		591	784	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909463	50909463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568626065	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	88	487	1	ENST00000440232.2:c.1267C>T	p.Arg423Cys	p.R423C	ENST00000440232	NM_002691.3	423	Cgt/Tgt	11/27	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.239289723687257	2		488	568	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770597	40770597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761441812	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	74	327	0	ENST00000373198.4:c.2785G>A	p.Asp929Asn	p.D929N	ENST00000373198	NM_133170.3	929	Gat/Aat	19/32	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.239289723687257	2		327	445	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877453	40877453	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	61	359	0	ENST00000373198.4:c.2243C>A	p.Thr748Asn	p.T748N	ENST00000373198	NM_133170.3	748	aCc/aAc	15/32	1	2	FACETS	0.906	0.782	1	0.906	0.782	1	CLONAL	1	TRUE	1	0.239289723687257	2		359	563	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546029	41546029	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	72	406	0	ENST00000263253.7:c.2644C>T	p.Pro882Ser	p.P882S	ENST00000263253	NM_001429.3	882	Cca/Tca	14/31	1	2	FACETS	0.91	0.795	1	0.91	0.795	1	CLONAL	1	TRUE	1	0.239289723687257	2		406	661	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038130	128038130	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	104	360	0	ENST00000285398.2:c.1420del	p.Asp474MetfsTer7	p.D474Mfs*7	ENST00000285398	NM_000122.1	474	Gat/at	9/15	1	2	FACETS	0.757	0.68	0.839	1	0.983	1	SUBCLONAL	2	TRUE	1	0.239289723687257	2		360	574	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702576	52702578	+	frameshift_variant	Frame_Shift_Del	DEL	CAT	CAT	TA	novel	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	92	375	0	ENST00000394830.3:c.320_322delinsTA	p.Asp107ValfsTer6	p.D107Vfs*6	ENST00000394830	NM_018313.4	107	gATGat/gTAat	4/30	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.239289723687257	2		375	558	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	54	214	0				ENST00000310581	NM_198253.2	-/1132			0.136675871556245	3	FACETS	0.987	0.844	1	0.493	0.422	0.572	INDETERMINATE	1	TRUE	1	0.239289723687257	3		214	512	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985472	2985473	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0005703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	71	423	0	ENST00000396946.4:c.338_339delinsAA	p.Arg113Gln	p.R113Q	ENST00000396946	NM_032415.4	113	cGG/cAA	4/25	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.239289723687257	2		423	563	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012220	16012220	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	119	401	0	ENST00000268712.3:c.2062C>T	p.Arg688Ter	p.R688*	ENST00000268712	NM_006311.3	688	Cga/Tga	19/46	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.401049300752796	2		401	561	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0005712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	150	334	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.403748807358722	1	FACETS	0.908	0.833	0.986	0.908	0.833	0.986	CLONAL	1	TRUE	0	0.42506416289286	1		334	612	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592087	67592087	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	167	556	1	ENST00000274335.5:c.1903G>T	p.Glu635Ter	p.E635*	ENST00000274335		635	Gaa/Taa	14/15	0.403748807358722	1	FACETS	0.961	0.886	1	0.961	0.886	1	CLONAL	1	TRUE	0	0.42506416289286	1		557	644	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972801	32972801	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358397	NA	P-0005712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	117	400	1	ENST00000380152.3:c.10151G>A	p.Arg3384Gln	p.R3384Q	ENST00000380152		3384	cGa/cAa	27/27	NA	2	FACETS	0.829	0.749	0.914			1	INDETERMINATE	1	TRUE	NA	0.42506416289286	2		401	664	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878132	151878154	+	frameshift_variant	Frame_Shift_Del	DEL	TGTATCAGGTGGCCTTACCAACG	TGTATCAGGTGGCCTTACCAACG	-	novel	NA	P-0005712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	111	451	0	ENST00000262189.6:c.6791_6813del	p.Pro2264LeufsTer6	p.P2264Lfs*6	ENST00000262189	NM_170606.2	2264	cCGTTGGTAAGGCCACCTGATACA/c	36/59	0.403748807358722	1	FACETS	0.881	0.796	0.969	0.881	0.796	0.969	CLONAL	1	TRUE	0	0.42506416289286	1		451	467	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0005713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	112	468	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.551007726041199	2	FACETS	0.963	0.889	1	0.963	0.889	1	CLONAL	2	TRUE	0	0.551007726041199	2		468	211	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871182	12871182	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1328655695	NA	P-0005713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	51	211	0	ENST00000228872.4:c.410del	p.Pro137ArgfsTer8	p.P137Rfs*8	ENST00000228872	NM_004064.3	137	Ccg/cg	1/3	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.551007726041199	2		211	174	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155241	185155241	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	189	470	1	ENST00000265026.3:c.482G>C	p.Trp161Ser	p.W161S	ENST00000265026	NM_004721.4	161	tGg/tCg	3/14	0.551007726041199	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.551007726041199	3		471	390	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506669	103506669	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs188898060	NA	P-0005713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	98	413	0	ENST00000355739.4:c.412C>T	p.Arg138Ter	p.R138*	ENST00000355739	NM_000123.3	138	Cga/Tga	4/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.551007726041199	2		413	298	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0005752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	113	338	0	ENST00000397752.3:c.3028+1G>C		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.147126191037334	2	FACETS	0.901	0.814	0.994	1	0.98	1	CLONAL	3	TRUE	0	0.147126191037334	2		338	568	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891367	101891367	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	79	356	1	ENST00000374994.4:c.328G>T	p.Glu110Ter	p.E110*	ENST00000374994	NM_004612.2	110	Gaa/Taa	2/9	0.147126191037334	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	2	TRUE	0	0.147126191037334	2		357	537	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985466	60985466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1387	81	798	0	ENST00000333681.4:c.434G>A	p.Gly145Glu	p.G145E	ENST00000333681		145	gGg/gAg	2/3	1	2	FACETS	0.75	0.658	0.85	0.75	0.658	0.85	SUBCLONAL	1	TRUE	1	0.147126191037334	2		798	1468	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215358	123215358	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	144	313	1	ENST00000218089.9:c.2904A>T	p.Glu968Asp	p.E968D	ENST00000218089	NM_001042749.1	968	gaA/gaT	28/35	0.147126191037334	2	FACETS	1	0.959	1			1	CLONAL	3	TRUE	NA	0.147126191037334	2		314	605	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0005753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	26	345	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		345	1229	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0005756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	252	213	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.901143814614148	2		213	483	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637574	176637574	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774810620	NA	P-0005756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	665	348	2	ENST00000439151.2:c.2174C>T	p.Thr725Met	p.T725M	ENST00000439151	NM_022455.4	725	aCg/aTg	5/23	0.466835591800969	2	FACETS	0.797	0.777	0.816	0.797	0.777	0.816	INDETERMINATE	2	TRUE	0	0.901143814614148	2		350	926	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577129	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519986	NA	P-0005756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	637	532	0	ENST00000269305.4:c.809T>G	p.Phe270Cys	p.F270C	ENST00000269305	NM_001126112.2	270	tTt/tGt	8/11	0.901143814614148	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.901143814614148	1		532	758	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0005772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	316	446	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.474182092553496	6	FACETS	1	0.984	1	1	0.984	1	CLONAL	5	TRUE	1	0.474182092553496	6		446	495	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0005772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	86	895	2	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	1	2	FACETS	0.965	0.86	1	0.965	0.86	1	CLONAL	1	TRUE	1	0.474182092553496	2		897	376	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907712	111907712	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0005772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	165	1156	0	ENST00000393256.3:c.486C>G	p.Tyr162Ter	p.Y162*	ENST00000393256	NM_006538.4	162	taC/taG	3/4	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.474182092553496	2		1156	591	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645088	86645088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	68	602	0	ENST00000274376.6:c.1160C>T	p.Ser387Leu	p.S387L	ENST00000274376	NM_002890.2	387	tCa/tTa	8/25	1	2	FACETS	0.775	0.678	0.879	0.775	0.678	0.879	SUBCLONAL	1	TRUE	1	0.474182092553496	2		602	370	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119998	70119998	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	26	168	0	ENST00000245479.2:c.1000G>A	p.Val334Met	p.V334M	ENST00000245479	NM_000346.3	334	Gtg/Atg	3/3	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.474182092553496	2		168	75	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191158	2191158	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	127	1283	3	ENST00000398665.3:c.412G>T	p.Glu138Ter	p.E138*	ENST00000398665	NM_032482.2	138	Gag/Tag	5/28	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.474182092553496	2		1286	507	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524146	187524146	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368616927	NA	P-0005781-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	241	606	1	ENST00000441802.2:c.11393C>T	p.Pro3798Leu	p.P3798L	ENST00000441802	NM_005245.3	3798	cCg/cTg	20/27	NA	2	FACETS	0.93	0.872	0.99			1	INDETERMINATE	1	FALSE	NA	0.680830531741932	2		607	761	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575422	64575422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005781-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	336	576	0	ENST00000312049.6:c.595C>T	p.His199Tyr	p.H199Y	ENST00000312049	NM_130799.2	199	Cac/Tac	3/10	0.609830230410132	1	FACETS	0.907	0.864	0.95	0.907	0.864	0.95	CLONAL	1	FALSE	0	0.680830531741932	1		576	718	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12043188	12043188	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005781-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	355	645	0	ENST00000353533.5:c.1073A>G	p.Tyr358Cys	p.Y358C	ENST00000353533	NM_003010.3	358	tAt/tGt	10/11	0.650094628411896	1	FACETS	0.988	0.945	1	0.988	0.945	1	CLONAL	1	FALSE	0	0.680830531741932	1		645	696	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115944	8115953	+	frameshift_variant	Frame_Shift_Del	DEL	TGGACCACAC	TGGACCACAC	-	novel	NA	P-0005781-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	314	332	0	ENST00000346208.3:c.1290_1299del	p.Gly431ThrfsTer41	p.G431Tfs*41	ENST00000346208		430	ttTGGACCACAC/tt	6/6	0.229585519781822	1	FACETS	0.747	0.707	0.786	0.747	0.707	0.786	INDETERMINATE	1	FALSE	0	0.680830531741932	1		332	815	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188297	10188297	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs869025653	NA	P-0005794-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	22	614	0	ENST00000256474.2:c.444del	p.Phe148LeufsTer11	p.F148Lfs*11	ENST00000256474	NM_000551.3	147	aTt/at	2/3	0.165415036233045	1	FACETS	1	0.848	1	1	0.949	1	CLONAL	2	FALSE	0	0.165415036233045	1		614	111	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52663005	52663007	+	inframe_deletion	In_Frame_Del	DEL	ACT	ACT	-	novel	NA	P-0005794-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	44	468	0	ENST00000394830.3:c.1346_1348del	p.Glu449_Cys450delinsGly	p.E449_C450delinsG	ENST00000394830	NM_018313.4	449	gAGTgt/ggt	13/30	0.165415036233045	0	FACETS	0.874	0.739	1			1	CLONAL	2	FALSE	0	0.165415036233045	0		468	254	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0005796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	34	348	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.21	2		348	294	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	22	543	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.935	0.728	1	0.935	0.728	1	CLONAL	1	TRUE	1	0.21	2		543	224	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0005796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	19	501	2	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.653	0.496	0.838	0.653	0.496	0.838	SUBCLONAL	1	TRUE	1	0.21	2		503	277	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238416	98238416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150284288	NA	P-0005796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	40	555	1	ENST00000331920.6:c.1628G>A	p.Arg543His	p.R543H	ENST00000331920	NM_000264.3	543	cGc/cAc	12/24	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.21	2		556	355	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226130	53226130	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	42	323	0	ENST00000375401.3:c.2719A>T	p.Arg907Trp	p.R907W	ENST00000375401	NM_004187.3	907	Agg/Tgg	19/26	1	1	FACETS	0.796	0.67	0.932	1	0.962	1	CLONAL	2	TRUE	0	0.21	1		323	225	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40468872	40468872	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005802-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	319	874	0	ENST00000264657.5:c.2192del	p.Leu731Ter	p.L731*	ENST00000264657	NM_139276.2	731	tTa/ta	23/24	0.576197373802551	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.576197373802551	1		874	787	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061192	38061192	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005802-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	156	287	0	ENST00000250448.2:c.797del	p.Phe266SerfsTer55	p.F266Sfs*55	ENST00000250448	NM_004496.3	266	tTc/tc	2/2	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.576197373802551	2		287	487	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0005827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	18	213	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.496	0.373	0.643	0.496	0.373	0.643	SUBCLONAL	1	TRUE	1	0.19	2		213	382	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0005827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	82	379	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	0.19	2		379	612	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015329	176015329	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	37	458	0	ENST00000367669.3:c.1409A>T	p.Asn470Ile	p.N470I	ENST00000367669	NM_022457.5	470	aAt/aTt	12/20	1	2	FACETS	0.601	0.494	0.721	0.601	0.494	0.721	SUBCLONAL	1	TRUE	1	0.19	2		458	648	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463206	25463206	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	59	690	0	ENST00000264709.3:c.2287G>T	p.Val763Phe	p.V763F	ENST00000264709	NM_175629.2	763	Gtt/Ttt	19/23	0.3	2	FACETS	0.869	0.746	1			1	CLONAL	1	TRUE	NA	0.19	2		690	715	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967042	25967042	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	37	501	0	ENST00000435504.4:c.2164G>A	p.Glu722Lys	p.E722K	ENST00000435504		722	Gaa/Aaa	13/13	0.3	2	FACETS	0.773	0.636	0.925			1	CLONAL	1	TRUE	NA	0.19	2		501	504	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026838	71026838	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs138415721	NA	P-0005827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	32	480	0	ENST00000318789.4:c.1384G>T	p.Ala462Ser	p.A462S	ENST00000318789	NM_032682.5	462	Gca/Tca	16/21	1	2	FACETS	0.596	0.483	0.725	0.596	0.483	0.725	SUBCLONAL	1	TRUE	1	0.19	2		480	565	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146703	185146703	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	92	617	1	ENST00000265026.3:c.334G>T	p.Gly112Ter	p.G112*	ENST00000265026	NM_004721.4	112	Gga/Tga	2/14	1	2	FACETS	0.782	0.696	0.874	1	0.981	1	SUBCLONAL	2	TRUE	1	0.19	2		618	619	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730025	41730025	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	68	996	0	ENST00000242208.4:c.504G>T	p.Arg168Ser	p.R168S	ENST00000242208	NM_002192.2	168	agG/agT	3/3	1	2	FACETS	0.685	0.594	0.784	0.685	0.594	0.784	SUBCLONAL	1	TRUE	1	0.19	2		996	1045	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201921	102201921	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	57	1034	0	ENST00000263464.3:c.1273G>C	p.Asp425His	p.D425H	ENST00000263464	NM_001165.4	425	Gat/Cat	6/9	1	2	FACETS	0.537	0.459	0.623	0.537	0.459	0.623	SUBCLONAL	1	TRUE	1	0.19	2		1034	1117	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95578517	95578517	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	39	433	0	ENST00000393063.1:c.2108A>T	p.His703Leu	p.H703L	ENST00000393063	NM_030621.3	703	cAc/cTc	14/28	1	2	FACETS	0.786	0.651	0.938	0.786	0.651	0.938	CLONAL	1	TRUE	1	0.19	2		433	522	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835584	68835584	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	17	500	0	ENST00000261769.5:c.175G>C	p.Asp59His	p.D59H	ENST00000261769	NM_004360.3	59	Gat/Cat	3/16	0.276822442601146	1	FACETS	0.498	0.371	0.65	0.498	0.371	0.65	SUBCLONAL	1	TRUE	0	0.19	1		500	325	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119827	70119827	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	87	677	0	ENST00000245479.2:c.829G>T	p.Glu277Ter	p.E277*	ENST00000245479	NM_000346.3	277	Gag/Tag	3/3	1	2	FACETS	0.844	0.745	0.95	0.844	0.745	0.95	CLONAL	1	TRUE	1	0.19	2		677	1085	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120253	70120253	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1179	182	783	1	ENST00000245479.2:c.1255G>T	p.Ala419Ser	p.A419S	ENST00000245479	NM_000346.3	419	Gcc/Tcc	3/3	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.19	2		784	1361	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604787	48604787	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	20	538	0	ENST00000342988.3:c.1609G>C	p.Asp537His	p.D537H	ENST00000342988	NM_005359.5	537	Gac/Cac	12/12	0.108892917579475	0	FACETS	0.419	0.32	0.536			1	INDETERMINATE	1	TRUE	0	0.19	0		538	407	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602381	10602381	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	105	750	1	ENST00000171111.5:c.1197G>A	p.Met399Ile	p.M399I	ENST00000171111	NM_203500.1	399	atG/atA	3/6	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.19	2		751	919	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931753	39931753	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	59	793	0	ENST00000378444.4:c.2846C>A	p.Ser949Ter	p.S949*	ENST00000378444	NM_001123385.1	949	tCa/tAa	4/15	0.3	2	FACETS	0.785	0.674	0.907			1	CLONAL	1	TRUE	NA	0.19	2		793	791	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933638	39933638	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs750773978	NA	P-0005827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	86	707	0	ENST00000378444.4:c.961G>T	p.Val321Phe	p.V321F	ENST00000378444	NM_001123385.1	321	Gtc/Ttc	4/15	0.3	2	FACETS	1	0.92	1			1	CLONAL	1	TRUE	NA	0.19	2		707	860	SUCCESS
BTK	695	MSKCC	GRCh37	X	100629546	100629546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	51	800	0	ENST00000308731.7:c.218C>T	p.Pro73Leu	p.P73L	ENST00000308731	NM_000061.2	73	cCt/cTt	3/19	0.3	1	FACETS	0.688	0.584	0.803	0.688	0.584	0.803	SUBCLONAL	1	TRUE	0	0.19	1		800	706	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391034	89391035	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0005827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	43	679	0	ENST00000336596.2:c.1100_1101delinsAT	p.Gly367Asp	p.G367D	ENST00000336596	NM_005233.5	367	gGG/gAT	5/17	1	2	FACETS	0.681	0.568	0.806	0.681	0.568	0.806	SUBCLONAL	1	TRUE	1	0.19	2		679	665	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45649972	45649973	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0005827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	28	354	2	ENST00000407780.3:c.863-1_863delinsTT		p.X288_splice	ENST00000407780	NM_001283052.1	288		6/7	1	2	FACETS	0.693	0.554	0.853	0.693	0.554	0.853	SUBCLONAL	1	TRUE	1	0.19	2		356	425	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160488	108160488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730881369	NA	P-0005829-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	92	645	1	ENST00000278616.4:c.4396C>T	p.Arg1466Ter	p.R1466*	ENST00000278616	NM_000051.3	1466	Cga/Tga	29/63	NA	2	FACETS	1	0.959	1			1	INDETERMINATE	2	TRUE	NA	0.531978175561616	2		646	161	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572450	41572450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005829-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	50	876	0	ENST00000263253.7:c.4979C>T	p.Thr1660Met	p.T1660M	ENST00000263253	NM_001429.3	1660	aCg/aTg	30/31	0.531978175561616	2	FACETS	0.81	0.695	0.934	0.405	0.347	0.467	CLONAL	1	TRUE	0	0.531978175561616	2		876	232	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0005833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	142	413	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.510517559569448	1	FACETS	0.942	0.866	1	0.942	0.866	1	CLONAL	1	TRUE	0	0.510517559569448	1		413	440	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0005833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	144	497	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.2584441764509	3	FACETS	1	0.981	1	0.627	0.574	0.681	INDETERMINATE	1	TRUE	1	0.510517559569448	3		497	565	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913255	NA	P-0005833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	416	599	0	ENST00000369535.4:c.183A>C	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caC	3/7	0.510517559569448	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.510517559569448	3		599	908	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562378	21562378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772963885	NA	P-0005833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	89	465	0	ENST00000382592.4:c.1541C>T	p.Pro514Leu	p.P514L	ENST00000382592	NM_014572.2	514	cCg/cTg	4/8	0.510517559569448	6	FACETS	0.837	0.741	0.94	0.209	0.185	0.235	CLONAL	1	TRUE	2	0.510517559569448	6		465	842	SUCCESS
APC	324	MSKCC	GRCh37	5	112175184	112175194	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCTAATACC	CTGCTAATACC	-	novel	NA	P-0005833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	91	324	0	ENST00000257430.4:c.3897_3907del	p.Thr1301SerfsTer10	p.T1301Sfs*10	ENST00000257430	NM_000038.5	1298	tCTGCTAATACC/t	16/16	0.2584441764509	3	FACETS	0.817	0.735	0.901	0.817	0.735	0.901	INDETERMINATE	2	TRUE	1	0.510517559569448	3		324	274	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17359604	17359604	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	65	613	0	ENST00000375499.3:c.237T>G	p.Ile79Met	p.I79M	ENST00000375499	NM_003000.2	79	atT/atG	3/8	1	2	FACETS	0.441	0.381	0.507	0.441	0.381	0.507	SUBCLONAL	1	TRUE	1	0.25	2		613	1178	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495621	56495621	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	92	489	0	ENST00000267101.3:c.3811G>T	p.Gly1271Cys	p.G1271C	ENST00000267101	NM_001982.3	1271	Ggt/Tgt	28/28	1	2	FACETS	0.821	0.729	0.921	0.821	0.729	0.921	CLONAL	1	TRUE	1	0.25	2		489	896	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191565	10191572	+	frameshift_variant	Frame_Shift_Del	DEL	AGATCTGG	AGATCTGG	-	novel	NA	P-0005837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	104	590	2	ENST00000256474.2:c.559_566del	p.Asp187ArgfsTer66	p.D187Rfs*66	ENST00000256474	NM_000551.3	186	gaAGATCTGGaa/gaaa	3/3	1	2	FACETS	0.995	0.891	1	0.995	0.891	1	CLONAL	1	TRUE	1	0.25	2		592	836	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0005850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	272	379	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.97	0.912	1	0.97	0.912	1	CLONAL	1	TRUE	1	0.595138348764204	2		379	942	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519922	NA	P-0005850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	369	829	0	ENST00000397062.3:c.235G>A	p.Glu79Lys	p.E79K	ENST00000397062	NM_006164.4	79	Gag/Aag	2/5	1	2	FACETS	0.917	0.869	0.966	0.917	0.869	0.966	CLONAL	1	TRUE	1	0.595138348764204	2		829	1352	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088788	27088788	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	192	786	0	ENST00000324856.7:c.2397G>T	p.Gln799His	p.Q799H	ENST00000324856	NM_006015.4	799	caG/caT	7/20	0.3704522256447	1	FACETS	0.719	0.669	0.772	0.719	0.669	0.772	SUBCLONAL	1	TRUE	0	0.595138348764204	1		786	630	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376262	225376262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	151	478	0	ENST00000264414.4:c.692C>T	p.Ser231Leu	p.S231L	ENST00000264414	NM_003590.4	231	tCa/tTa	6/16	1	2	FACETS	0.793	0.727	0.861	0.793	0.727	0.861	SUBCLONAL	1	TRUE	1	0.595138348764204	2		478	640	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702594	52702594	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	345	617	0	ENST00000394830.3:c.304A>G	p.Lys102Glu	p.K102E	ENST00000394830	NM_018313.4	102	Aaa/Gaa	4/30	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.595138348764204	2		617	1050	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167747	56167747	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	222	649	2	ENST00000399503.3:c.1312G>T	p.Glu438Ter	p.E438*	ENST00000399503	NM_005921.1	438	Gaa/Taa	7/20	0.368027160648535	1	FACETS	0.741	0.693	0.791	0.741	0.693	0.791	SUBCLONAL	1	TRUE	0	0.595138348764204	1		651	707	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576505	67576505	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	234	586	0	ENST00000274335.5:c.784A>G	p.Arg262Gly	p.R262G	ENST00000274335		262	Aga/Gga	5/15	0.368027160648535	1	FACETS	0.74	0.693	0.789	0.74	0.693	0.789	SUBCLONAL	1	TRUE	0	0.595138348764204	1		586	746	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589273	67589273	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	105	468	0	ENST00000274335.5:c.1261G>T	p.Asp421Tyr	p.D421Y	ENST00000274335		421	Gat/Tat	9/15	0.368027160648535	1	FACETS	0.369	0.331	0.409	0.369	0.331	0.409	SUBCLONAL	1	TRUE	0	0.595138348764204	1		468	672	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963973	2963973	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	272	917	0	ENST00000396946.4:c.1834G>T	p.Gly612Ter	p.G612*	ENST00000396946	NM_032415.4	612	Gga/Tga	15/25	1	2	FACETS	0.905	0.85	0.961	0.905	0.85	0.961	CLONAL	1	TRUE	1	0.595138348764204	2		917	1010	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26911754	26911754	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	418	862	0	ENST00000381527.3:c.179C>G	p.Ser60Cys	p.S60C	ENST00000381527	NM_001260.1	60	tCt/tGt	2/13	0.595138348764204	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.595138348764204	1		862	954	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348481	56348481	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	527	1153	1	ENST00000348428.3:c.289G>T	p.Gly97Cys	p.G97C	ENST00000348428	NM_006785.3	97	Ggt/Tgt	2/17	0.595138348764204	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.595138348764204	1		1154	1160	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1646417	1646417	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	347	747	0	ENST00000344749.5:c.82C>G	p.Leu28Val	p.L28V	ENST00000344749	NM_001136139.2	28	Ctg/Gtg	3/19	0.479624031648842	1	FACETS	0.847	0.804	0.891	0.847	0.804	0.891	CLONAL	1	TRUE	0	0.595138348764204	1		747	967	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961591	54961591	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0005850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	155	340	0	ENST00000312783.6:c.43-2A>C		p.X15_splice	ENST00000312783	NM_198436.1	15			0.164074411685634	0	FACETS	0.395	0.363	0.427			1	INDETERMINATE	1	TRUE	0	0.595138348764204	0		340	534	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661997	29661997	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	293	646	2	ENST00000356175.3:c.5895del	p.Lys1965AsnfsTer26	p.K1965Nfs*26	ENST00000356175	NM_000267.3	1964	gAa/ga	39/57	0.584966531810884	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.595138348764204	1		648	687	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0005917-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	112	491	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	1	2	FACETS	0.952	0.856	1	0.952	0.856	1	CLONAL	1	TRUE	1	0.306083886959716	2		491	769	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467937	66467937	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005917-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	133	482	0	ENST00000273854.3:c.332A>C	p.Asn111Thr	p.N111T	ENST00000273854	NM_004439.5	111	aAc/aCc	3/18	1	2	FACETS	0.949	0.861	1	0.949	0.861	1	CLONAL	1	TRUE	1	0.306083886959716	2		482	916	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577042	7577043	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0005917-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	88	400	0	ENST00000269305.4:c.895_896del	p.Leu299AlafsTer6	p.L299Afs*6	ENST00000269305	NM_001126112.2	299	CTg/g	8/11	1	2	FACETS	0.89	0.789	0.998	0.89	0.789	0.998	CLONAL	1	TRUE	1	0.306083886959716	2		400	646	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594221	55594221	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913512	NA	P-0005923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	1140	335	0	ENST00000288135.5:c.1924A>G	p.Lys642Glu	p.K642E	ENST00000288135	NM_000222.2	642	Aaa/Gaa	13/21	0.308616505977239	15	FACETS	1	0.986	1			1	CLONAL	12	TRUE	NA	0.308616505977239	15		335	1832	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207077	1207077	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs121913319	NA	P-0005927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	234	606	0	ENST00000326873.7:c.169del	p.Glu57LysfsTer7	p.E57Kfs*7	ENST00000326873	NM_000455.4	55	ctG/ct	1/10	0.406252718960371	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.406252718960371	1		606	853	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105819	27105819	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	113	535	0	ENST00000324856.7:c.5430C>G	p.Asp1810Glu	p.D1810E	ENST00000324856	NM_006015.4	1810	gaC/gaG	20/20	1	2	FACETS	0.491	0.441	0.545	0.491	0.441	0.545	SUBCLONAL	1	TRUE	1	0.406252718960371	2		535	1132	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532671	187532671	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	185	502	0	ENST00000441802.2:c.9722A>T	p.Glu3241Val	p.E3241V	ENST00000441802	NM_005245.3	3241	gAg/gTg	14/27	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.406252718960371	2		502	902	SUCCESS
CBL	867	MSKCC	GRCh37	11	119146796	119146796	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	168	497	0	ENST00000264033.4:c.959A>G	p.His320Arg	p.H320R	ENST00000264033	NM_005188.3	320	cAc/cGc	6/16	1	2	FACETS	0.94	0.864	1	0.94	0.864	1	CLONAL	1	TRUE	1	0.406252718960371	2		497	880	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181319	123181319	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	198	609	0	ENST00000218089.9:c.783T>A	p.Asn261Lys	p.N261K	ENST00000218089	NM_001042749.1	261	aaT/aaA	9/35	1	2	FACETS	0.983	0.91	1	0.983	0.91	1	CLONAL	1	TRUE	1	0.406252718960371	2		609	992	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186638	108186638	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	389	337	0	ENST00000278616.4:c.6095G>C	p.Arg2032Thr	p.R2032T	ENST00000278616	NM_000051.3	2032	aGa/aCa	41/63	0.61846884634463	4	FACETS	0.857	0.822	0.893	0.857	0.822	0.893	CLONAL	3	TRUE	1	0.709362232866159	4		337	729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0005956-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	275	458	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.513586507139413	2		458	1059	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276891	15276891	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005957-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	63	382	2	ENST00000263388.2:c.5374C>G	p.Pro1792Ala	p.P1792A	ENST00000263388	NM_000435.2	1792	Ccg/Gcg	30/33	0.173210363207362	2	FACETS	0.535	0.462	0.614	0.267	0.231	0.307	INDETERMINATE	1	TRUE	0	0.35	2		384	673	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278152	15278152	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005957-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	169	618	1	ENST00000263388.2:c.5270C>T	p.Ala1757Val	p.A1757V	ENST00000263388	NM_000435.2	1757	gCt/gTt	29/33	0.173210363207362	2	FACETS	0.82	0.753	0.891	0.41	0.376	0.446	INDETERMINATE	1	TRUE	0	0.35	2		619	1177	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266088	41266099	+	inframe_deletion	In_Frame_Del	DEL	TCTTACCTGGAC	TCTTACCTGGAC	-	novel	NA	P-0005957-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	180	494	0	ENST00000349496.5:c.88_99del	p.Tyr30_Ser33del	p.Y30_S33del	ENST00000349496	NM_001904.3	29	TCTTACCTGGAC/-	3/15	1	2	FACETS	0.909	0.837	0.984	0.909	0.837	0.984	CLONAL	1	TRUE	1	0.35	2		494	1132	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934265	48934314	+	splice_donor_variant,intron_variant	Splice_Site	DEL	TAAGTATTTAATTTATGCCCCTTTTACTTTCTCATTCAGCAGTTGCTTAT	TAAGTATTTAATTTATGCCCCTTTTACTTTCTCATTCAGCAGTTGCTTAT	-	novel	NA	P-0005957-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	71	256	0	ENST00000267163.4:c.718+3_718+52del		p.X240_splice	ENST00000267163	NM_000321.2	240			0.298173597096087	1	FACETS	0.651	0.569	0.739	0.651	0.569	0.739	SUBCLONAL	1	TRUE	0	0.35	1		256	514	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0005974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	299	339	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.245542142159052	3	FACETS	0.81	0.765	0.855			1	INDETERMINATE	2	TRUE	NA	0.542650909544401	3		339	865	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0005974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	193	477	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	0.542650909544401	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.542650909544401	1		477	517	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188164	11188164	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587777893	NA	P-0005974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	126	357	0	ENST00000361445.4:c.5930C>A	p.Thr1977Lys	p.T1977K	ENST00000361445	NM_004958.3	1977	aCa/aAa	43/58	NA	2	FACETS	0.883	0.803	0.966			1	INDETERMINATE	1	TRUE	NA	0.542650909544401	2		357	526	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434990	49434990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs541122919	NA	P-0005974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	110	213	0	ENST00000301067.7:c.6563G>A	p.Arg2188His	p.R2188H	ENST00000301067	NM_003482.3	2188	cGc/cAc	31/54	1	2	FACETS	0.979	0.887	1	0.979	0.887	1	CLONAL	1	TRUE	1	0.542650909544401	2		213	414	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	protein_altering_variant	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	CCT	novel	NA	P-0005974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	113	380	0	ENST00000275493.2:c.2236_2250delinsCCT	p.Glu746_Ala750delinsPro	p.E746_A750delinsP	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/CCT	19/28	0.162938693147487	6	FACETS	0.926	0.832	1			1	INDETERMINATE	1	TRUE	NA	0.542650909544401	6		380	938	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872556	35872556	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005986-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	208	565	0	ENST00000216797.5:c.347A>G	p.His116Arg	p.H116R	ENST00000216797	NM_020529.2	116	cAc/cGc	3/6	0.366791083730459	3	FACETS	1	0.992	1	0.738	0.689	0.788	CLONAL	1	TRUE	1	0.582440515815874	3		565	625	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003749	45003749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368160918	NA	P-0005986-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	197	373	0	ENST00000558401.1:c.5C>T	p.Ser2Phe	p.S2F	ENST00000558401	NM_004048.2	2	tCt/tTt	1/4	0.287988571431165	4	FACETS	1	0.961	1			1	INDETERMINATE	2	TRUE	NA	0.582440515815874	4		373	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578440	7578440	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs879254249	NA	P-0005999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	22	428	0	ENST00000269305.4:c.490A>G	p.Lys164Glu	p.K164E	ENST00000269305	NM_001126112.2	164	Aag/Gag	5/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		428	709	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0006007-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	39	446	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.28	2		446	218	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0006007-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	112	366	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.28	2		366	536	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432623	49432623	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555191147	NA	P-0006007-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	85	559	0	ENST00000301067.7:c.8516C>G	p.Ser2839Ter	p.S2839*	ENST00000301067	NM_003482.3	2839	tCa/tGa	34/54	1	2	FACETS	0.898	0.794	1	0.898	0.794	1	CLONAL	1	TRUE	1	0.28	2		559	676	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980903	40980903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs906977293	NA	P-0006007-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	26	280	0	ENST00000373198.4:c.1583C>T	p.Ser528Leu	p.S528L	ENST00000373198	NM_133170.3	528	tCg/tTg	10/32	0.299968376167449	1	FACETS	0.671	0.534	0.827	0.671	0.534	0.827	SUBCLONAL	1	TRUE	0	0.28	1		280	238	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546102	41546102	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006007-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	36	284	0	ENST00000263253.7:c.2717C>G	p.Ser906Cys	p.S906C	ENST00000263253	NM_001429.3	906	tCt/tGt	14/31	1	2	FACETS	0.789	0.65	0.943	0.789	0.65	0.943	CLONAL	1	TRUE	1	0.28	2		284	326	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325378	1325378	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006007-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	61	478	0	ENST00000400841.2:c.297C>G	p.Ile99Met	p.I99M	ENST00000400841		99	atC/atG	3/6	0.299968376167449	1	FACETS	0.824	0.712	0.944	0.824	0.712	0.944	CLONAL	1	TRUE	0	0.28	1		478	455	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878876	151878876	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006007-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	53	360	0	ENST00000262189.6:c.6069del	p.Asp2024ThrfsTer8	p.D2024Tfs*8	ENST00000262189	NM_170606.2	2023	ccT/cc	36/59	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.28	2		360	319	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325467	1325467	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121573-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	134	400	0	ENST00000400841.2:c.208C>A	p.Gln70Lys	p.Q70K	ENST00000400841		70	Cag/Aag	3/6	1	2	FACETS	0.942	0.858	1	0.942	0.858	1	CLONAL	1	NA	1	0.431159192933567	2		400	660	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0006014-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	248	553	3	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.498512384579151	1	FACETS	0.92	0.863	0.978	0.92	0.863	0.978	CLONAL	1	TRUE	0	0.498512384579151	1		556	812	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0006014-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	123	363	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	1	2	FACETS	0.928	0.843	1	0.928	0.843	1	CLONAL	1	TRUE	1	0.498512384579151	2		363	532	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263882	133263882	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006014-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	45	277	0	ENST00000320574.5:c.20G>T	p.Gly7Val	p.G7V	ENST00000320574	NM_006231.2	7	gGg/gTg	1/49	0.24685937330167	1	FACETS	0.304	0.255	0.357	0.304	0.255	0.357	INDETERMINATE	1	TRUE	0	0.498512384579151	1		277	446	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879794	37879794	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006014-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	660	341	1	ENST00000269571.5:c.2089G>T	p.Val697Leu	p.V697L	ENST00000269571		697	Gtg/Ttg	18/27	0.498512384579151	5	FACETS	0.929	0.899	0.958			1	CLONAL	4	TRUE	NA	0.498512384579151	5		342	1246	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444561	49444564	+	frameshift_variant	Frame_Shift_Del	DEL	GGAG	GGAG	-	novel	NA	P-0006014-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	94	322	0	ENST00000301067.7:c.2807_2810del	p.Pro936LeufsTer21	p.P936Lfs*21	ENST00000301067	NM_003482.3	936	cCTCCt/ct	11/54	0.24685937330167	1	FACETS	0.527	0.47	0.588	0.527	0.47	0.588	INDETERMINATE	1	TRUE	0	0.498512384579151	1		322	537	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894228	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	75	330	0	ENST00000451590.1:c.37G>C	p.Gly13Arg	p.G13R	ENST00000451590	NM_001130442.1	13	Ggt/Cgt	2/5	1	2	FACETS	0.261	0.228	0.296	0.261	0.228	0.296	SUBCLONAL	1	TRUE	1	0.841565255254868	2		330	683	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478922	56478922	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	434	437	1	ENST00000267101.3:c.378C>A	p.Asn126Lys	p.N126K	ENST00000267101	NM_001982.3	126	aaC/aaA	3/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.841565255254868	2		438	978	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	54	323	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	1	2	FACETS	0.186	0.158	0.216	0.186	0.158	0.216	SUBCLONAL	1	TRUE	1	0.841565255254868	2		323	691	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339680	116339680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	152	239	0	ENST00000397752.3:c.542G>A	p.Gly181Glu	p.G181E	ENST00000397752	NM_000245.2	181	gGa/gAa	2/21	1	2	FACETS	0.892	0.825	0.96	0.892	0.825	0.96	CLONAL	1	TRUE	1	0.841565255254868	2		239	405	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199857	108199857	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	56	277	0	ENST00000278616.4:c.7199G>C	p.Arg2400Thr	p.R2400T	ENST00000278616	NM_000051.3	2400	aGa/aCa	49/63	1	2	FACETS	0.315	0.27	0.363	0.315	0.27	0.363	SUBCLONAL	1	TRUE	1	0.841565255254868	2		277	423	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073494	8073494	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756319881	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	515	696	1	ENST00000377482.5:c.1165G>A	p.Val389Ile	p.V389I	ENST00000377482	NM_018948.3	389	Gtt/Att	4/4	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.841565255254868	2		697	1180	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257989	16257989	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	310	301	0	ENST00000375759.3:c.5254G>A	p.Glu1752Lys	p.E1752K	ENST00000375759	NM_015001.2	1752	Gag/Aag	11/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.841565255254868	2		301	700	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082790	16082790	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	69	54	0	ENST00000281043.3:c.604C>T	p.Pro202Ser	p.P202S	ENST00000281043	NM_005378.4	202	Cca/Tca	2/3	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.841565255254868	2		54	125	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52677265	52677265	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs374515597	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	222	370	0	ENST00000394830.3:c.994C>G	p.Arg332Gly	p.R332G	ENST00000394830	NM_018313.4	332	Cgt/Ggt	10/30	1	2	FACETS	0.879	0.824	0.935	0.879	0.824	0.935	CLONAL	1	TRUE	1	0.841565255254868	2		370	600	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84390222	84390222	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	143	255	0	ENST00000321945.7:c.559A>G	p.Met187Val	p.M187V	ENST00000321945	NM_139076.2	187	Atg/Gtg	6/9	1	2	FACETS	0.977	0.903	1	0.977	0.903	1	CLONAL	1	TRUE	1	0.841565255254868	2		255	348	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245442	153245442	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	150	320	0	ENST00000281708.4:c.1749A>C	p.Leu583Phe	p.L583F	ENST00000281708	NM_033632.3	583	ttA/ttC	11/12	1	2	FACETS	0.996	0.923	1	0.996	0.923	1	CLONAL	1	TRUE	1	0.841565255254868	2		320	358	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247208	153247208	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	217	360	0	ENST00000281708.4:c.1594A>C	p.Thr532Pro	p.T532P	ENST00000281708	NM_033632.3	532	Acc/Ccc	10/12	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.841565255254868	2		360	504	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247241	153247241	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	233	389	0	ENST00000281708.4:c.1561T>G	p.Phe521Val	p.F521V	ENST00000281708	NM_033632.3	521	Ttt/Gtt	10/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.841565255254868	2		389	526	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752365	57752365	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	130	282	0	ENST00000274289.3:c.1208A>C	p.Lys403Thr	p.K403T	ENST00000274289	NM_006622.3	403	aAa/aCa	9/14	1	2	FACETS	0.798	0.732	0.867	0.798	0.732	0.867	SUBCLONAL	1	TRUE	1	0.841565255254868	2		282	387	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982096	93982096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1484017296	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	238	462	1	ENST00000369303.4:c.1369C>T	p.Arg457Trp	p.R457W	ENST00000369303	NM_004440.3	457	Cgg/Tgg	6/17	1	2	FACETS	0.868	0.815	0.921	0.868	0.815	0.921	CLONAL	1	TRUE	1	0.841565255254868	2		463	652	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100550	157100550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1420609905	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	286	259	0	ENST00000346085.5:c.1487G>A	p.Arg496Lys	p.R496K	ENST00000346085	NM_020732.3	496	aGg/aAg	1/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.841565255254868	2		259	645	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97887445	97887445	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	191	356	0	ENST00000289081.3:c.919G>T	p.Gly307Trp	p.G307W	ENST00000289081	NM_000136.2	307	Ggg/Tgg	10/15	1	2	FACETS	0.97	0.906	1	0.97	0.906	1	CLONAL	1	TRUE	1	0.841565255254868	2		356	468	SUCCESS
EED	8726	MSKCC	GRCh37	11	85975268	85975268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	219	415	0	ENST00000263360.6:c.689G>A	p.Gly230Glu	p.G230E	ENST00000263360	NM_003797.3	230	gGa/gAa	7/12	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.841565255254868	2		415	487	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198467	108198467	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753951063	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	26	286	1	ENST00000278616.4:c.7071G>A	p.Met2357Ile	p.M2357I	ENST00000278616	NM_000051.3	2357	atG/atA	48/63	1	2	FACETS	0.18	0.142	0.223	0.18	0.142	0.223	SUBCLONAL	1	TRUE	1	0.841565255254868	2		287	344	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374549	118374549	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	53	372	0	ENST00000534358.1:c.7942A>C	p.Ile2648Leu	p.I2648L	ENST00000534358	NM_005933.3	2648	Att/Ctt	27/36	1	2	FACETS	0.217	0.185	0.253	0.217	0.185	0.253	SUBCLONAL	1	TRUE	1	0.841565255254868	2		372	580	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125036	46125036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	189	311	0	ENST00000334344.6:c.223G>A	p.Glu75Lys	p.E75K	ENST00000334344	NM_152641.2	75	Gag/Aag	3/21	1	2	FACETS	0.956	0.892	1	0.956	0.892	1	CLONAL	1	TRUE	1	0.841565255254868	2		311	470	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914851	32914851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507845	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	292	572	0	ENST00000380152.3:c.6359C>T	p.Ser2120Leu	p.S2120L	ENST00000380152		2120	tCa/tTa	11/27	1	2	FACETS	0.883	0.835	0.932	0.883	0.835	0.932	CLONAL	1	TRUE	1	0.841565255254868	2		572	786	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954351	48954351	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587778848	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	107	188	0	ENST00000267163.4:c.1472T>C	p.Leu491Pro	p.L491P	ENST00000267163	NM_000321.2	491	cTt/cCt	16/27	0.841565255254868	1	FACETS	0.932	0.87	0.991	0.932	0.87	0.991	CLONAL	1	TRUE	0	0.841565255254868	1		188	158	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003429	42003429	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	501	598	0	ENST00000219905.7:c.2966C>G	p.Ser989Cys	p.S989C	ENST00000219905	NM_001164273.1	989	tCt/tGt	8/24	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.841565255254868	2		598	1081	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304065	91304065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1477193473	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	47	417	0	ENST00000355112.3:c.1462G>A	p.Glu488Lys	p.E488K	ENST00000355112	NM_000057.2	488	Gaa/Aaa	7/22	1	2	FACETS	0.216	0.182	0.253	0.216	0.182	0.253	SUBCLONAL	1	TRUE	1	0.841565255254868	2		417	518	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556111	29556111	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	92	156	0	ENST00000356175.3:c.2478A>G	p.Ile826Met	p.I826M	ENST00000356175	NM_000267.3	826	atA/atG	21/57	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.841565255254868	2		156	204	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576112	29576112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540108477	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	174	360	0	ENST00000356175.3:c.4085G>A	p.Arg1362Gln	p.R1362Q	ENST00000356175	NM_000267.3	1362	cGa/cAa	30/57	1	2	FACETS	0.885	0.823	0.949	0.885	0.823	0.949	CLONAL	1	TRUE	1	0.841565255254868	2		360	467	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38504676	38504676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	282	348	0	ENST00000254066.5:c.287C>T	p.Ser96Leu	p.S96L	ENST00000254066	NM_000964.3	96	tCa/tTa	3/9	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.841565255254868	2		348	667	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41228517	41228517	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	187	353	1	ENST00000357654.3:c.4472C>T	p.Pro1491Leu	p.P1491L	ENST00000357654	NM_007294.3	1491	cCa/cTa	13/23	1	2	FACETS	0.972	0.908	1	0.972	0.908	1	CLONAL	1	TRUE	1	0.841565255254868	2		354	457	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051159	13051159	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199565419	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	515	587	1	ENST00000316448.5:c.595G>A	p.Asp199Asn	p.D199N	ENST00000316448	NM_004343.3	199	Gat/Aat	5/9	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.841565255254868	2		588	1157	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627600	14627600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	419	431	0	ENST00000254322.2:c.470G>A	p.Arg157Gln	p.R157Q	ENST00000254322	NM_006145.1	157	cGa/cAa	2/3	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.841565255254868	2		431	849	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743954	41743954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	433	489	0	ENST00000301178.4:c.889G>A	p.Gly297Ser	p.G297S	ENST00000301178	NM_021913.4	297	Ggc/Agc	7/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.841565255254868	2		489	979	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867584	45867584	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	305	357	0	ENST00000391945.4:c.724G>T	p.Val242Phe	p.V242F	ENST00000391945	NM_000400.3	242	Gtc/Ttc	9/23	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.841565255254868	2		357	657	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224615	123224615	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	182	250	0	ENST00000218089.9:c.3467+1G>T		p.X1156_splice	ENST00000218089	NM_001042749.1	1156			1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.841565255254868	1		250	223	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105844	27105867	+	inframe_deletion	In_Frame_Del	DEL	AAGAATGATCCATTTGTGGTGGAC	AAGAATGATCCATTTGTGGTGGAC	-	novel	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	281	448	0	ENST00000324856.7:c.5455_5478del	p.Lys1819_Asp1826del	p.K1819_D1826del	ENST00000324856	NM_006015.4	1819	AAGAATGATCCATTTGTGGTGGAC/-	20/20	1	2	FACETS	0.919	0.868	0.97	0.919	0.868	0.97	CLONAL	1	TRUE	1	0.841565255254868	2		448	727	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70360789	70360793	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	AAGGT	AAGGT	-	novel	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	55	158	0	ENST00000373644.4:c.1968_1968+4del		p.X656_splice	ENST00000373644	NM_030625.2	656		3/12	1	2	FACETS	0.591	0.512	0.676	0.591	0.512	0.676	SUBCLONAL	1	TRUE	1	0.841565255254868	2		158	221	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569702	41569711	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGGCAACA	AGGGGCAACA	-	novel	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	228	532	1	ENST00000263253.7:c.4695_4704del	p.Gly1566ArgfsTer29	p.G1566Rfs*29	ENST00000263253	NM_001429.3	1565	AGGGGCAACAag/ag	29/31	1	2	FACETS	0.747	0.699	0.797	0.747	0.699	0.797	SUBCLONAL	1	TRUE	1	0.841565255254868	2		533	725	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368453	225368467	+	inframe_deletion	In_Frame_Del	DEL	ATAACGTTCAAATAC	ATAACGTTCAAATAC	-	novel	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	25	273	0	ENST00000264414.4:c.1279_1293del	p.Val427_Tyr431del	p.V427_Y431del	ENST00000264414	NM_003590.4	427	GTATTTGAACGTTAT/-	9/16	0.662522762297636	1	FACETS	0.138	0.109	0.172	0.138	0.109	0.172	SUBCLONAL	1	TRUE	0	0.841565255254868	1		273	249	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564565	86564588	+	inframe_deletion	In_Frame_Del	DEL	TGCTGGCGTGGCCGGTGCTGCTGT	TGCTGGCGTGGCCGGTGCTGCTGT	-	rs768241743	NA	P-0006015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	189	367	0	ENST00000274376.6:c.303_326del	p.Val102_Gly109del	p.V102_G109del	ENST00000274376	NM_002890.2	99	gcTGCTGGCGTGGCCGGTGCTGCTGTt/gct	1/25	1	2	FACETS	0.765	0.711	0.82	0.765	0.711	0.82	SUBCLONAL	1	TRUE	1	0.841565255254868	2		367	587	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0006021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	41	379	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	0.25	2		379	230	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044898	47044898	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	22	907	0	ENST00000377604.3:c.2224C>T	p.Gln742Ter	p.Q742*	ENST00000377604	NM_001204468.1	742	Cag/Tag	20/24	NA	2	FACETS	0.85	0.681	1			1	INDETERMINATE	3	TRUE	NA	0.25	2		907	69	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103520589	103520589	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs773661355	NA	P-0006021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	23	1311	0	ENST00000355739.4:c.2660A>G	p.Glu887Gly	p.E887G	ENST00000355739	NM_000123.3	887	gAa/gGa	12/15	1	2	FACETS	0.939	0.736	1	0.939	0.736	1	CLONAL	1	TRUE	1	0.25	2		1311	196	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774134	66774134	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	21	1664	2	ENST00000307102.5:c.610A>T	p.Ile204Phe	p.I204F	ENST00000307102	NM_002755.3	204	Atc/Ttc	6/11	1	2	FACETS	0.747	0.577	0.943	0.747	0.577	0.943	CLONAL	1	TRUE	1	0.25	2		1666	225	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779870	3779870	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	22	1463	3	ENST00000262367.5:c.5178C>A	p.Tyr1726Ter	p.Y1726*	ENST00000262367	NM_004380.2	1726	taC/taA	31/31	1	2	FACETS	1	0.781	1	1	0.781	1	CLONAL	1	TRUE	1	0.25	2		1466	176	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220640	1220640	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690940	NA	P-0006071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	272	673	1	ENST00000326873.7:c.658C>T	p.Gln220Ter	p.Q220*	ENST00000326873	NM_000455.4	220	Cag/Tag	5/10	0.764777800248991	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.764777800248991	1		674	435	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592144	55592144	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	553	595	0	ENST00000288135.5:c.1468G>C	p.Glu490Gln	p.E490Q	ENST00000288135	NM_000222.2	490	Gaa/Caa	9/21	0.66259282382679	3	FACETS	0.971	0.938	1	0.971	0.938	1	CLONAL	2	TRUE	1	0.764777800248991	3		595	1029	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286224	66286224	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	547	574	0	ENST00000273854.3:c.1462T>A	p.Ser488Thr	p.S488T	ENST00000273854	NM_004439.5	488	Tct/Act	6/18	0.764777800248991	2	FACETS	0.956	0.93	0.981	0.956	0.93	0.981	CLONAL	2	TRUE	0	0.764777800248991	2		574	748	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874567	35874567	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1294534112	NA	P-0006071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	453	577	0	ENST00000303115.3:c.723C>G	p.Ile241Met	p.I241M	ENST00000303115	NM_002185.3	241	atC/atG	6/8	0.749454951784084	2	FACETS	0.946	0.918	0.974	0.946	0.918	0.974	CLONAL	2	TRUE	0	0.764777800248991	2		577	626	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335732	81335732	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	476	364	0	ENST00000222390.5:c.1628A>G	p.Asp543Gly	p.D543G	ENST00000222390	NM_000601.4	543	gAt/gGt	15/18	0.68609606786629	4	FACETS	0.988	0.956	1			1	CLONAL	3	TRUE	NA	0.764777800248991	4		364	741	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971012	21971012	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1477500164	NA	P-0006071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	212	373	0	ENST00000304494.5:c.346G>T	p.Asp116Tyr	p.D116Y	ENST00000304494	NM_000077.4	116	Gac/Tac	2/3	0.534451231124961	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.764777800248991	1		373	328	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37006501	37006501	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	660	562	0	ENST00000358127.4:c.444C>A	p.Asn148Lys	p.N148K	ENST00000358127	NM_001280556.1	148	aaC/aaA	4/10	0.764777800248991	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.764777800248991	3		562	784	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148972	119148972	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	500	526	0	ENST00000264033.4:c.1192C>A	p.His398Asn	p.H398N	ENST00000264033	NM_005188.3	398	Cac/Aac	8/16	0.764777800248991	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.764777800248991	2		526	640	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937076	48937076	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	376	425	1	ENST00000267163.4:c.844G>T	p.Glu282Ter	p.E282*	ENST00000267163	NM_000321.2	282	Gaa/Taa	8/27	0.764777800248991	2	FACETS	0.989	0.958	1	0.989	0.958	1	CLONAL	2	TRUE	0	0.764777800248991	2		426	497	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987037	36987037	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs745996705	NA	P-0006071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	288	324	0	ENST00000354822.5:c.652G>T	p.Ala218Ser	p.A218S	ENST00000354822	NM_001079668.2	218	Gcg/Tcg	3/3	0.738162472139113	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.764777800248991	4		324	616	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420224	88420224	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	169	583	1	ENST00000360948.2:c.2462A>T	p.Tyr821Phe	p.Y821F	ENST00000360948	NM_001012338.2	821	tAc/tTc	19/19	NA	2	FACETS	0.863	0.8	0.928			1	INDETERMINATE	1	TRUE	NA	0.764777800248991	2		584	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578517	7578517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750600586	NA	P-0006071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	569	621	0	ENST00000269305.4:c.413C>T	p.Ala138Val	p.A138V	ENST00000269305	NM_001126112.2	138	gCc/gTc	5/11	0.764777800248991	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.764777800248991	2		621	723	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585423	29585423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	516	562	0	ENST00000356175.3:c.4172G>A	p.Arg1391Lys	p.R1391K	ENST00000356175	NM_000267.3	1391	aGa/aAa	31/57	0.382690158261905	2	FACETS	1	0.985	1	1	0.985	1	INDETERMINATE	2	TRUE	0	0.764777800248991	2		562	665	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591889	48591892	+	missense_variant	Missense_Mutation	ONP	ATGG	ATGG	TTTT	novel	NA	P-0006071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	465	643	0	ENST00000342988.3:c.1052_1055delinsTTTT	p.Asp351_Gly352delinsValLeu	p.D351_G352delinsVL	ENST00000342988	NM_005359.5	351	gATGGa/gTTTTa	9/12	0.764777800248991	2	FACETS	0.94	0.912	0.967	0.94	0.912	0.967	CLONAL	2	TRUE	0	0.764777800248991	2		643	647	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600335	10600335	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	486	591	0	ENST00000171111.5:c.1520G>T	p.Arg507Leu	p.R507L	ENST00000171111	NM_203500.1	507	cGa/cTa	4/6	0.764777800248991	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.764777800248991	2		591	632	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100054	11100054	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	516	646	0	ENST00000358026.2:c.1180G>C	p.Gly394Arg	p.G394R	ENST00000358026	NM_001128849.1	394	Ggg/Cgg	7/36	0.764777800248991	2	FACETS	0.985	0.959	1	0.985	0.959	1	CLONAL	2	TRUE	0	0.764777800248991	2		646	685	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561124	9561124	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	349	420	0	ENST00000353224.5:c.658C>T	p.Gln220Ter	p.Q220*	ENST00000353224	NM_177990.2	220	Cag/Tag	4/10	NA	2	FACETS	0.959	0.926	0.99			1	INDETERMINATE	2	TRUE	NA	0.764777800248991	2		420	476	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55124922	55124922	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0006071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	511	549	0	ENST00000257290.5:c.-12-2A>T		p.X4_splice	ENST00000257290	NM_006206.4	4			0.66259282382679	3	FACETS	0.961	0.926	0.996	0.961	0.926	0.996	CLONAL	2	TRUE	1	0.764777800248991	3		549	961	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031970	26031970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	77	1279	0	ENST00000244661.2:c.319G>A	p.Asp107Asn	p.D107N	ENST00000244661	NM_003537.3	107	Gac/Aac	1/1	0.420204641384619	5	FACETS	0.414	0.362	0.471	0.138	0.12	0.157	SUBCLONAL	1	TRUE	2	0.564730823186154	5		1279	1216	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	133	672	0	ENST00000206249.3:c.1607T>C	p.Leu536Pro	p.L536P	ENST00000206249	NM_000125.3	536	cTc/cCc	8/8	0.564730823186154	3	FACETS	1	0.974	1	0.586	0.535	0.639	CLONAL	1	TRUE	1	0.564730823186154	3		672	515	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577102	7577102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793881	NA	P-0006074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	401	901	3	ENST00000269305.4:c.836G>A	p.Gly279Glu	p.G279E	ENST00000269305	NM_001126112.2	279	gGg/gAg	8/11	0.325930596200856	3	FACETS	0.927	0.892	0.961			1	INDETERMINATE	3	TRUE	NA	0.564730823186154	3		904	655	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090479	71090479	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	147	679	1	ENST00000318789.4:c.869G>C	p.Ser290Thr	p.S290T	ENST00000318789	NM_032682.5	290	aGt/aCt	11/21	0.564730823186154	3	FACETS	1	0.987	1	0.468	0.431	0.507	CLONAL	1	TRUE	0	0.564730823186154	3		680	475	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032007	26032007	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	141	1381	0	ENST00000244661.2:c.282G>T	p.Gln94His	p.Q94H	ENST00000244661	NM_003537.3	94	caG/caT	1/1	0.420204641384619	5	FACETS	0.678	0.616	0.744	0.226	0.205	0.248	SUBCLONAL	1	TRUE	2	0.564730823186154	5		1381	1360	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197265	26197265	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs892619198	NA	P-0006074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1310	366	1651	0	ENST00000356476.2:c.214G>C	p.Val72Leu	p.V72L	ENST00000356476		72	Gtc/Ctc	1/1	0.420204641384619	5	FACETS	1	0.994	1	0.476	0.45	0.503	CLONAL	1	TRUE	2	0.564730823186154	5		1651	1676	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63553976	63553976	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	63	768	0	ENST00000307078.5:c.763C>G	p.Leu255Val	p.L255V	ENST00000307078	NM_004655.3	255	Ctg/Gtg	2/11	0.564730823186154	4	FACETS	0.395	0.341	0.455	0.099	0.085	0.114	SUBCLONAL	1	TRUE	0	0.564730823186154	4		768	883	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593607	55593615	+	inframe_deletion	In_Frame_Del	DEL	AGGTTGTTG	AGGTTGTTG	-	novel	NA	P-0006104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	426	704	0	ENST00000288135.5:c.1676_1684del	p.Val559_Glu561del	p.V559_E561del	ENST00000288135	NM_000222.2	558	aAGGTTGTTGag/aag	11/21	1	2	FACETS	0.876	0.836	0.915	0.876	0.836	0.915	CLONAL	1	TRUE	1	0.889410723493865	2		704	1094	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692901	89692901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786204929	NA	P-0006104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	285	348	0	ENST00000371953.3:c.385G>A	p.Gly129Arg	p.G129R	ENST00000371953	NM_000314.4	129	Gga/Aga	5/9	0.889410723493865	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.889410723493865	1		348	334	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599334	55599334	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	420	574	0	ENST00000288135.5:c.2460T>G	p.Asp820Glu	p.D820E	ENST00000288135	NM_000222.2	820	gaT/gaG	17/21	1	2	FACETS	0.959	0.917	1	0.959	0.917	1	CLONAL	1	TRUE	1	0.889410723493865	2		574	985	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041029	42041029	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	314	1093	1	ENST00000219905.7:c.5407C>T	p.His1803Tyr	p.H1803Y	ENST00000219905	NM_001164273.1	1803	Cac/Tac	16/24	0.889410723493865	1	FACETS	0.39	0.368	0.412	0.39	0.368	0.412	SUBCLONAL	1	TRUE	0	0.889410723493865	1		1094	1006	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0006105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	178	536	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.235940678189429	4	FACETS	0.876	0.808	0.947	0.876	0.808	0.947	CLONAL	2	TRUE	2	0.314003126256167	4		536	850	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0006105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	129	401	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.235940678189429	4	FACETS	0.981	0.887	1	0.49	0.443	0.54	CLONAL	1	TRUE	2	0.314003126256167	4		401	1101	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266112	41266112	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913228	NA	P-0006105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	77	592	0	ENST00000349496.5:c.109T>G	p.Ser37Ala	p.S37A	ENST00000349496	NM_001904.3	37	Tct/Gct	3/15	1	2	FACETS	0.89	0.783	1	0.89	0.783	1	CLONAL	1	TRUE	1	0.314003126256167	2		592	551	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057800	180057800	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0006105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	66	359	0	ENST00000261937.6:c.156-1G>A		p.X52_splice	ENST00000261937	NM_182925.4	52			0.311198359654106	3	FACETS	1	0.881	1	0.507	0.441	0.578	CLONAL	1	TRUE	1	0.314003126256167	3		359	480	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720850	89720850	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1206321984	NA	P-0006105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	53	273	0	ENST00000371953.3:c.1001A>G	p.Asn334Ser	p.N334S	ENST00000371953	NM_000314.4	334	aAc/aGc	8/9	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.314003126256167	2		273	263	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786719	3786719	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	211	672	1	ENST00000262367.5:c.4492C>T	p.Arg1498Ter	p.R1498*	ENST00000262367	NM_004380.2	1498	Cga/Tga	27/31	0.39191601444858	3	FACETS	0.94	0.871	1	0.47	0.435	0.506	CLONAL	1	TRUE	1	0.438008201402251	3		673	1250	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0006129-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	16	440	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		440	503	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	74	287	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.200404286863656	1	FACETS	0.553	0.483	0.628	0.553	0.483	0.628	SUBCLONAL	1	TRUE	0	0.284893734288731	1		287	806	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0006136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	108	531	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.176071340941276	1	FACETS	0.652	0.584	0.725	0.652	0.584	0.725	SUBCLONAL	1	TRUE	0	0.284893734288731	1		531	997	SUCCESS
APC	324	MSKCC	GRCh37	5	112170777	112170780	+	frameshift_variant	Frame_Shift_Del	DEL	CAGA	CAGA	-	rs878853420	NA	P-0006136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	94	530	0	ENST00000257430.4:c.1875_1878del	p.Asn627LeufsTer2	p.N627Lfs*2	ENST00000257430	NM_000038.5	625	CAGAca/ca	15/16	1	2	FACETS	0.546	0.484	0.612	0.546	0.484	0.612	SUBCLONAL	1	TRUE	1	0.284893734288731	2		530	1209	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575080	48575080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	81	447	0	ENST00000342988.3:c.274C>T	p.His92Tyr	p.H92Y	ENST00000342988	NM_005359.5	92	Cat/Tat	3/12	1	2	FACETS	0.601	0.528	0.68	0.601	0.528	0.68	SUBCLONAL	1	TRUE	1	0.284893734288731	2		447	946	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66468014	66468014	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	41	272	1	ENST00000273854.3:c.255G>T	p.Glu85Asp	p.E85D	ENST00000273854	NM_004439.5	85	gaG/gaT	3/18	0.176071340941276	1	FACETS	0.507	0.422	0.601	0.507	0.422	0.601	SUBCLONAL	1	TRUE	0	0.284893734288731	1		273	487	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0006152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	188	345	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.308239721816388	3	FACETS	1	0.99	1	0.736	0.68	0.795	CLONAL	1	TRUE	1	0.308239721816388	3		345	956	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0006152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	50	595	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.836	0.711	0.972	0.836	0.711	0.972	CLONAL	1	TRUE	1	0.308239721816388	2		596	388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0006152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	60	451	1	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	0.912	0.788	1	0.912	0.788	1	CLONAL	1	TRUE	1	0.308239721816388	2		452	427	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468032	50468032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757907717	NA	P-0006152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	102	377	1	ENST00000331340.3:c.1267C>T	p.Arg423Cys	p.R423C	ENST00000331340	NM_006060.4	423	Cgc/Tgc	8/8	0.308239721816388	3	FACETS	1	0.971	1	0.622	0.557	0.691	CLONAL	1	TRUE	1	0.308239721816388	3		378	614	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151855984	151855984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	57	472	1	ENST00000262189.6:c.11634G>A	p.Met3878Ile	p.M3878I	ENST00000262189	NM_170606.2	3878	atG/atA	44/59	0.308239721816388	3	FACETS	0.463	0.396	0.537	0.232	0.198	0.269	SUBCLONAL	1	TRUE	1	0.308239721816388	3		473	921	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864273	57864273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	51	607	0	ENST00000228682.2:c.1750G>A	p.Ala584Thr	p.A584T	ENST00000228682	NM_005269.2	584	Gcc/Acc	12/12	1	2	FACETS	0.606	0.515	0.706	0.606	0.515	0.706	SUBCLONAL	1	TRUE	1	0.308239721816388	2		607	546	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975615	26975615	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	74	389	2	ENST00000381527.3:c.1123C>T	p.Gln375Ter	p.Q375*	ENST00000381527	NM_001260.1	375	Cag/Tag	12/13	NA	2	FACETS	0.66	0.578	0.75			1	INDETERMINATE	1	TRUE	NA	0.308239721816388	2		391	727	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435061	110435061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	49	203	0	ENST00000375856.3:c.3340G>A	p.Val1114Met	p.V1114M	ENST00000375856	NM_003749.2	1114	Gtg/Atg	1/2	0.308239721816388	6	FACETS	1	0.917	1			1	CLONAL	1	TRUE	NA	0.308239721816388	6		203	456	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99491888	99491888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752140857	NA	P-0006152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	146	519	0	ENST00000268035.6:c.3673G>A	p.Val1225Ile	p.V1225I	ENST00000268035	NM_000875.3	1225	Gtc/Atc	20/21	1	2	FACETS	0.897	0.824	0.973	1	0.991	1	CLONAL	2	TRUE	1	0.308239721816388	2		519	528	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548932	29548932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	19	209	0	ENST00000356175.3:c.1706C>T	p.Thr569Ile	p.T569I	ENST00000356175	NM_000267.3	569	aCa/aTa	15/57	0.17212669237865	3	FACETS	0.381	0.289	0.491	0.191	0.144	0.246	INDETERMINATE	1	TRUE	1	0.308239721816388	3		209	373	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770623	40770623	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	91	374	0	ENST00000373198.4:c.2759C>A	p.Thr920Lys	p.T920K	ENST00000373198	NM_133170.3	920	aCa/aAa	19/32	0.308239721816388	3	FACETS	1	0.977	1	0.698	0.622	0.779	CLONAL	1	TRUE	1	0.308239721816388	3		374	488	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412680	63412680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762389559	NA	P-0006152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	49	520	0	ENST00000330258.3:c.487C>T	p.Pro163Ser	p.P163S	ENST00000330258	NM_152424.3	163	Ccc/Tcc	2/2	0.243524592847829	0	FACETS	0.53	0.45	0.618			1	SUBCLONAL	1	TRUE	0	0.308239721816388	0		520	415	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939403	76939403	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	115	542	0	ENST00000373344.5:c.1345C>T	p.Pro449Ser	p.P449S	ENST00000373344	NM_000489.3	449	Cct/Tct	9/35	0.20727167437097	1	FACETS	0.77	0.693	0.851	0.77	0.693	0.851	SUBCLONAL	1	TRUE	0	0.308239721816388	1		542	820	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519069	66519069	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0006179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	98	483	0	ENST00000358598.2:c.348+2T>C		p.X116_splice	ENST00000358598	NM_212471.2	116			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		483	550	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	967	435	0	ENST00000269305.4:c.472C>G	p.Arg158Gly	p.R158G	ENST00000269305	NM_001126112.2	158	Cgc/Ggc	5/11	0.888912168742829	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	FALSE	0	0.888912168742829	2		435	1054	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133814	55133814	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	2358	494	2	ENST00000257290.5:c.1027C>T	p.Pro343Ser	p.P343S	ENST00000257290	NM_006206.4	343	Cca/Tca	7/23	0.888912168742829	5	FACETS	1	0.993	1			1	CLONAL	4	FALSE	NA	0.888912168742829	5		496	3072	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252155	226252155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553260624	NA	P-0006182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	56	59	0	ENST00000366813.1:c.103G>A	p.Gly35Arg	p.G35R	ENST00000366813		35	Ggg/Agg	1/3	0.519076427026102	4	FACETS	1	0.964	1	0.443	0.386	0.503	INDETERMINATE	1	FALSE	1	0.888912168742829	4		59	179	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939666	76939669	+	frameshift_variant	Frame_Shift_Del	DEL	TCAA	TCAA	-	novel	NA	P-0006182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	562	295	0	ENST00000373344.5:c.1079_1082del	p.Ile360ArgfsTer6	p.I360Rfs*6	ENST00000373344	NM_000489.3	360	aTTGAg/ag	9/35	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	FALSE	0	0.888912168742829	1		295	662	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224525	123224526	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0006182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	767	357	0	ENST00000218089.9:c.3383_3384del	p.Glu1128AlafsTer7	p.E1128Afs*7	ENST00000218089	NM_001042749.1	1126	atGAga/atga	31/35	1	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	0	0.888912168742829	1		357	955	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520503	176520503	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138256705	NA	P-0006187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	116	418	1	ENST00000292408.4:c.1348G>A	p.Val450Met	p.V450M	ENST00000292408	NM_213647.1	450	Gtg/Atg	10/18	0.124791017577588	4	FACETS	1	0.98	1	0.673	0.608	0.741	INDETERMINATE	1	TRUE	2	0.416880900370722	4		419	586	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953076	2953076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	41	379	2	ENST00000396946.4:c.2864G>A	p.Gly955Asp	p.G955D	ENST00000396946	NM_032415.4	955	gGc/gAc	22/25	0.416880900370722	5	FACETS	0.489	0.406	0.581	0.163	0.135	0.194	SUBCLONAL	1	TRUE	2	0.416880900370722	5		381	654	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0006198-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	331	536	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.444583618960171	6	FACETS	1	0.984	1	0.737	0.696	0.779	CLONAL	2	TRUE	3	0.444583618960171	6		536	1273	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499393	89499393	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006198-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	97	510	1	ENST00000336596.2:c.2563C>T	p.Gln855Ter	p.Q855*	ENST00000336596	NM_005233.5	855	Cag/Tag	15/17	0.413132290631729	1	FACETS	0.741	0.664	0.822	0.741	0.664	0.822	SUBCLONAL	1	TRUE	0	0.444583618960171	1		511	458	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0006210-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1311	202	262	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.23	2		262	1513	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057627	180057627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756234174	NA	P-0006210-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1295	148	787	0	ENST00000261937.6:c.328G>A	p.Val110Ile	p.V110I	ENST00000261937	NM_182925.4	110	Gtc/Atc	3/30	1	2	FACETS	0.892	0.812	0.976	0.892	0.812	0.976	CLONAL	1	TRUE	1	0.23	2		787	1443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0006210-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	65	316	0	ENST00000269305.4:c.97-1G>C		p.X33_splice	ENST00000269305	NM_001126112.2	33			1	2	FACETS	0.952	0.825	1	0.952	0.825	1	CLONAL	1	TRUE	1	0.23	2		316	594	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360597	70360597	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006210-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	112	503	0	ENST00000374080.3:c.6157C>T	p.Gln2053Ter	p.Q2053*	ENST00000374080		2053	Cag/Tag	42/45	1	2	FACETS	0.978	0.878	1	0.978	0.878	1	CLONAL	1	TRUE	1	0.23	2		503	996	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	367	399	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.372757468724736	3	FACETS	0.914	0.867	0.961			1	CLONAL	2	TRUE	NA	0.4	3		399	1205	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131505	202131505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	65	311	0	ENST00000358485.4:c.473C>T	p.Ser158Phe	p.S158F	ENST00000358485	NM_001080125.1	158	tCt/tTt	2/9	1	2	FACETS	0.535	0.463	0.612	0.535	0.463	0.612	SUBCLONAL	1	TRUE	1	0.4	2		311	608	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162123	47162123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1216047088	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	133	268	0	ENST00000409792.3:c.4003C>T	p.Arg1335Cys	p.R1335C	ENST00000409792	NM_014159.6	1335	Cgt/Tgt	3/21	0.105805218381449	3	FACETS	1	0.982	1	0.661	0.602	0.722	INDETERMINATE	1	TRUE	1	0.4	3		268	604	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932906	49932906	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759642387	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	423	773	0	ENST00000296474.3:c.3038C>T	p.Ser1013Leu	p.S1013L	ENST00000296474	NM_002447.2	1013	tCg/tTg	13/20	0.105805218381449	3	FACETS	0.899	0.856	0.943	0.899	0.856	0.943	INDETERMINATE	2	TRUE	1	0.4	3		773	1412	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259595	89259595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	92	241	0	ENST00000336596.2:c.739G>A	p.Glu247Lys	p.E247K	ENST00000336596	NM_005233.5	247	Gaa/Aaa	3/17	0.173913998605087	0	FACETS	0.701	0.627	0.778			1	INDETERMINATE	1	TRUE	0	0.4	0		241	394	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199957	128199957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370164300	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	260	527	1	ENST00000341105.2:c.1348G>A	p.Gly450Arg	p.G450R	ENST00000341105	NM_032638.4	450	Gga/Aga	6/6	0.173913998605087	0	FACETS	1	0.961	1			1	INDETERMINATE	1	TRUE	0	0.4	0		528	759	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952049	178952049	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1242945375	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	286	444	0	ENST00000263967.3:c.3104C>T	p.Ala1035Val	p.A1035V	ENST00000263967	NM_006218.2	1035	gCt/gTt	21/21	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.4	2		444	987	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973959	55973959	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	158	385	0	ENST00000263923.4:c.1357C>T	p.Pro453Ser	p.P453S	ENST00000263923	NM_002253.2	453	Ccg/Tcg	10/30	0.267810789505335	0	FACETS	0.692	0.636	0.75			1	SUBCLONAL	1	TRUE	0	0.4	0		385	685	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278776	1278776	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	219	385	0	ENST00000310581.5:c.2266C>G	p.Arg756Gly	p.R756G	ENST00000310581	NM_198253.2	756	Cgc/Ggc	6/16	0.173913998605087	0	FACETS	1	0.955	1			1	INDETERMINATE	1	TRUE	0	0.4	0		385	640	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576482	67576482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768144572	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	214	373	0	ENST00000274335.5:c.761C>T	p.Ser254Phe	p.S254F	ENST00000274335		254	tCc/tTc	5/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.4	2		373	881	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722431	176722431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	317	443	0	ENST00000439151.2:c.8062C>T	p.His2688Tyr	p.H2688Y	ENST00000439151	NM_022455.4	2688	Cac/Tac	23/23	0.372757468724736	2	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.4	2		443	1248	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043372	180043373	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	180	466	0	ENST00000261937.6:c.3213_3214delinsAA	p.Gly1072Ser	p.G1072S	ENST00000261937	NM_182925.4	1071	aaGGgc/aaAAgc	23/30	0.372757468724736	0	FACETS	0.823	0.762	0.886			1	CLONAL	1	TRUE	0	0.4	0		466	656	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168620	32168620	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777423381	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	289	547	0	ENST00000375023.3:c.4303C>T	p.His1435Tyr	p.H1435Y	ENST00000375023	NM_004557.3	1435	Cat/Tat	23/30	0.372757468724736	2	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.4	2		547	1211	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638312	117638312	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	64	412	0	ENST00000368508.3:c.6129G>A	p.Met2043Ile	p.M2043I	ENST00000368508	NM_002944.2	2043	atG/atA	38/43	0.372757468724736	0	FACETS	0.283	0.245	0.325			1	SUBCLONAL	1	TRUE	0	0.4	0		412	678	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	302	377	1	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.4	2		378	1246	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346589	81346589	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	274	532	0	ENST00000222390.5:c.1364G>A	p.Gly455Glu	p.G455E	ENST00000222390	NM_000601.4	455	gGa/gAa	11/18	0.173913998605087	0	FACETS	0.755	0.709	0.802			1	INDETERMINATE	1	TRUE	0	0.4	0		532	1089	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439727	140439727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507485	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	87	227	0	ENST00000288602.6:c.2012G>A	p.Arg671Gln	p.R671Q	ENST00000288602	NM_004333.4	671	cGa/cAa	17/18	1	2	FACETS	0.975	0.868	1	0.975	0.868	1	CLONAL	1	TRUE	1	0.4	2		227	446	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949173	151949173	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	258	282	0	ENST00000262189.6:c.1472G>A	p.Trp491Ter	p.W491*	ENST00000262189	NM_170606.2	491	tGg/tAg	11/59	0.372757468724736	3	FACETS	0.977	0.919	1	0.977	0.919	1	CLONAL	2	TRUE	1	0.4	3		282	792	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008947	152008947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	379	526	0	ENST00000262189.6:c.675G>A	p.Trp225Ter	p.W225*	ENST00000262189	NM_170606.2	225	tgG/tgA	5/59	0.372757468724736	3	FACETS	0.867	0.822	0.912	0.867	0.822	0.912	CLONAL	2	TRUE	1	0.4	3		526	1312	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457309	5457309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781724241	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	197	307	0	ENST00000381577.3:c.283G>A	p.Gly95Arg	p.G95R	ENST00000381577	NM_014143.3	95	Gga/Aga	3/7	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.4	2		307	878	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971149	21971149	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786202575	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	127	156	0	ENST00000304494.5:c.209C>T	p.Pro70Leu	p.P70L	ENST00000304494	NM_000077.4	70	cCc/cTc	2/3	1	2	FACETS	0.91	0.834	0.987	1	0.99	1	CLONAL	2	TRUE	1	0.4	2		156	349	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923443	36923444	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	256	492	0	ENST00000358127.4:c.818_819delinsAA	p.Gly273Glu	p.G273E	ENST00000358127	NM_001280556.1	273	gGG/gAA	7/10	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.4	2		492	856	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211527	98211527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	278	422	2	ENST00000331920.6:c.3628C>T	p.Pro1210Ser	p.P1210S	ENST00000331920	NM_000264.3	1210	Ccg/Tcg	22/24	1	2	FACETS	0.77	0.724	0.816	1	0.994	1	SUBCLONAL	2	TRUE	1	0.4	2		424	903	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606773	43606773	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	172	552	2	ENST00000355710.3:c.1382C>T	p.Thr461Ile	p.T461I	ENST00000355710	NM_020975.4	461	aCc/aTc	7/20	0.267810789505335	0	FACETS	0.769	0.71	0.83			1	SUBCLONAL	1	TRUE	0	0.4	0		554	671	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610149	43610149	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1199456015	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	216	626	0	ENST00000355710.3:c.2101G>A	p.Glu701Lys	p.E701K	ENST00000355710	NM_020975.4	701	Gag/Aag	11/20	0.267810789505335	0	FACETS	0.804	0.749	0.86			1	CLONAL	1	TRUE	0	0.4	0		626	806	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710645	114710645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	304	741	0	ENST00000543371.1:c.130G>T	p.Val44Phe	p.V44F	ENST00000543371	NM_001198531.1	44	Gtc/Ttc	1/14	0.173913998605087	0	FACETS	0.72	0.678	0.764			1	INDETERMINATE	1	TRUE	0	0.4	0		741	1266	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199820	108199820	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	80	357	0	ENST00000278616.4:c.7162C>T	p.Leu2388Phe	p.L2388F	ENST00000278616	NM_000051.3	2388	Ctc/Ttc	49/63	0.105805218381449	3	FACETS	0.602	0.529	0.68	0.301	0.264	0.34	INDETERMINATE	1	TRUE	1	0.4	3		357	798	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432886	432886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	319	493	0	ENST00000399788.2:c.2030C>T	p.Ser677Leu	p.S677L	ENST00000399788	NM_001042603.1	677	tCa/tTa	15/28	0.372757468724736	4	FACETS	0.923	0.871	0.977			1	CLONAL	2	TRUE	NA	0.4	4		493	1209	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245141	46245141	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	199	368	0	ENST00000334344.6:c.3235C>T	p.Leu1079Phe	p.L1079F	ENST00000334344	NM_152641.2	1079	Ctc/Ttc	15/21	0.372757468724736	3	FACETS	1	0.99	1			1	CLONAL	1	TRUE	NA	0.4	3		368	830	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494845	56494845	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1395403428	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	205	280	0	ENST00000267101.3:c.3202G>A	p.Glu1068Lys	p.E1068K	ENST00000267101	NM_001982.3	1068	Gag/Aag	27/28	0.267810789505335	4	FACETS	1	0.99	1	0.72	0.668	0.775	CLONAL	1	TRUE	2	0.4	4		280	996	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233093	69233094	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	235	370	0	ENST00000462284.1:c.958_959delinsTT	p.Pro320Phe	p.P320F	ENST00000462284	NM_002392.5	320	CCc/TTc	11/11	0.267810789505335	4	FACETS	0.821	0.766	0.877	0.821	0.766	0.877	CLONAL	2	TRUE	2	0.4	4		370	1002	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563352	21563353	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	266	604	0	ENST00000382592.4:c.566_567delinsTT	p.Thr189Ile	p.T189I	ENST00000382592	NM_014572.2	189	aCC/aTT	4/8	0.372757468724736	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.4	1		604	1011	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954210	48954210	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1354030520	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	233	392	0	ENST00000267163.4:c.1411C>T	p.Gln471Ter	p.Q471*	ENST00000267163	NM_000321.2	471	Caa/Taa	15/27	0.372757468724736	2	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.4	2		392	840	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434943	110434943	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs986125580	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	288	497	0	ENST00000375856.3:c.3458C>T	p.Ser1153Phe	p.S1153F	ENST00000375856	NM_003749.2	1153	tCc/tTc	1/2	0.372757468724736	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.4	1		497	1003	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029332	14029332	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866657450	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	295	571	0	ENST00000311895.7:c.1543C>T	p.Arg515Cys	p.R515C	ENST00000311895	NM_005236.2	515	Cgt/Tgt	8/11	0.372757468724736	2	FACETS	1	0.989	1			1	CLONAL	1	TRUE	NA	0.4	2		571	1219	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821812	72821812	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	369	828	0	ENST00000268489.5:c.10363C>T	p.Pro3455Ser	p.P3455S	ENST00000268489	NM_006885.3	3455	Ccc/Tcc	10/10	0.372757468724736	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.4	1		828	1146	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346132	89346132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	133	247	0	ENST00000301030.4:c.6818G>A	p.Gly2273Asp	p.G2273D	ENST00000301030	NM_001256183.1	2273	gGc/gAc	9/13	0.372757468724736	2	FACETS	0.757	0.693	0.823			1	SUBCLONAL	2	TRUE	NA	0.4	2		247	439	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348103	89348103	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	462	947	1	ENST00000301030.4:c.4847G>A	p.Gly1616Glu	p.G1616E	ENST00000301030	NM_001256183.1	1616	gGa/gAa	9/13	0.372757468724736	2	FACETS	1	0.996	1			1	CLONAL	1	TRUE	NA	0.4	2		948	1541	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7218356	7218356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1250	461	495	1	ENST00000380728.2:c.16G>A	p.Glu6Lys	p.E6K	ENST00000380728		6	Gag/Aag	2/11	0.372757468724736	3	FACETS	0.808	0.77	0.847			1	CLONAL	2	TRUE	NA	0.4	3		496	1711	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	392	482	0	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.372757468724736	3	FACETS	0.932	0.886	0.979			1	CLONAL	2	TRUE	NA	0.4	3		482	1262	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989406	7989406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs8077661	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	277	452	0	ENST00000319144.4:c.280G>A	p.Gly94Ser	p.G94S	ENST00000319144	NM_001139.2	94	Ggc/Agc	2/15	0.372757468724736	3	FACETS	0.803	0.754	0.853			1	CLONAL	2	TRUE	NA	0.4	3		452	1035	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16041488	16041488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	325	458	2	ENST00000268712.3:c.1391C>T	p.Ser464Leu	p.S464L	ENST00000268712	NM_006311.3	464	tCa/tTa	13/46	0.372757468724736	3	FACETS	0.776	0.732	0.82	0.776	0.732	0.82	SUBCLONAL	2	TRUE	1	0.4	3		460	1257	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049724	16049724	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	483	532	0	ENST00000268712.3:c.1048C>T	p.Arg350Ter	p.R350*	ENST00000268712	NM_006311.3	350	Cga/Tga	10/46	0.372757468724736	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	1	0.4	3		532	1214	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654530	29654530	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	295	359	0	ENST00000356175.3:c.5219C>T	p.Ala1740Val	p.A1740V	ENST00000356175	NM_000267.3	1740	gCt/gTt	37/57	0.372757468724736	3	FACETS	1	0.993	1	0.696	0.654	0.739	CLONAL	1	TRUE	1	0.4	3		359	1272	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243979	41243980	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	202	348	0	ENST00000357654.3:c.3568_3569delinsTT	p.Pro1190Phe	p.P1190F	ENST00000357654	NM_007294.3	1190	CCt/TTt	10/23	0.372757468724736	2	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.4	2		348	867	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245648	41245648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357056	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	219	371	0	ENST00000357654.3:c.1900C>T	p.Pro634Ser	p.P634S	ENST00000357654	NM_007294.3	634	Cct/Tct	10/23	0.372757468724736	2	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.4	2		371	977	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621930	1621930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	366	670	2	ENST00000344749.5:c.862C>T	p.Pro288Ser	p.P288S	ENST00000344749	NM_001136139.2	288	Cca/Tca	11/19	0.372757468724736	2	FACETS	0.763	0.723	0.802			1	SUBCLONAL	2	TRUE	NA	0.4	2		672	1200	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284961	15284962	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	189	512	0	ENST00000263388.2:c.4653_4654delinsTT	p.Gln1552Ter	p.Q1552*	ENST00000263388	NM_000435.2	1551	ggCCag/ggTTag	25/33	0.372757468724736	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.4	1		512	704	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349555	15349555	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	137	275	0	ENST00000263377.2:c.4019C>T	p.Ala1340Val	p.A1340V	ENST00000263377	NM_058243.2	1340	gCc/gTc	19/20	0.372757468724736	1	FACETS	0.93	0.85	1	0.93	0.85	1	CLONAL	1	TRUE	0	0.4	1		275	589	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866306	42866307	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	126	238	0	ENST00000398585.3:c.325_326delinsTT	p.Pro109Leu	p.P109L	ENST00000398585	NM_001135099.1	109	CCa/TTa	3/14	0.173913998605087	0	FACETS	0.813	0.741	0.888			1	INDETERMINATE	1	TRUE	0	0.4	0		238	465	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411411	63411411	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	113	263	0	ENST00000330258.3:c.1756C>T	p.Arg586Ter	p.R586*	ENST00000330258	NM_152424.3	586	Cga/Tga	2/2	0.372757468724736	0	FACETS	0.909	0.826	0.995			1	CLONAL	1	TRUE	0	0.4	0		263	373	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611882	100611882	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	355	327	0	ENST00000308731.7:c.1239T>A	p.Phe413Leu	p.F413L	ENST00000308731	NM_000061.2	413	ttT/ttA	14/19	1	1	FACETS	1	0.98	1	1	0.997	1	CLONAL	2	TRUE	0	0.4	1		327	681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782620	NA	P-0006217-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	146	447	1	ENST00000269305.4:c.427G>A	p.Val143Met	p.V143M	ENST00000269305	NM_001126112.2	143	Gtg/Atg	5/11	0.499687675530765	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.495037428874806	1		448	341	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910549	29910549	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45585732	NA	P-0006217-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	22	120	2	ENST00000376809.5:c.89G>A	p.Arg30Lys	p.R30K	ENST00000376809	NM_002116.7	30	aGg/aAg	2/8	0.495037428874806	5	FACETS	0.622	0.483	0.782	0.124	0.096	0.157	SUBCLONAL	1	TRUE	0	0.495037428874806	5		122	249	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514047	69514047	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006217-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	39	510	0	ENST00000294312.3:c.634C>T	p.Pro212Ser	p.P212S	ENST00000294312	NM_005117.2	212	Ccc/Tcc	3/3	0.499687675530765	1	FACETS	0.507	0.423	0.598	0.507	0.423	0.598	SUBCLONAL	1	TRUE	0	0.495037428874806	1		510	234	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	202	543	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.386970408664104	4	FACETS	0.951	0.886	1	0.951	0.886	1	CLONAL	2	TRUE	2	0.483177183040393	4		543	652	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0006225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	488	819	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.433624284147856	2	FACETS	0.958	0.92	0.996	0.958	0.92	0.996	CLONAL	2	TRUE	0	0.483177183040393	2		819	1054	SUCCESS
APC	324	MSKCC	GRCh37	5	112175595	112175595	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	400	544	0	ENST00000257430.4:c.4304del	p.Arg1435LysfsTer38	p.R1435Kfs*38	ENST00000257430	NM_000038.5	1435	aGa/aa	16/16	0.416264641628328	3	FACETS	0.845	0.809	0.881	0.845	0.809	0.881	CLONAL	3	TRUE	0	0.483177183040393	3		544	811	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120612013	120612014	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0006225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	19	63	1	ENST00000256646.2:c.7_8delinsTT	p.Ala3Phe	p.A3F	ENST00000256646	NM_024408.3	3	GCc/TTc	1/34	0.473030220683263	4	FACETS	0.821	0.629	1	0.274	0.209	0.348	CLONAL	1	TRUE	1	0.483177183040393	4		64	142	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998492	100998492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	142	250	0	ENST00000325455.5:c.1310C>T	p.Ala437Val	p.A437V	ENST00000325455	NM_001202474.3	437	gCg/gTg	1/8	0.436496431888099	2	FACETS	1	0.95	1	0.526	0.481	0.572	CLONAL	1	TRUE	0	0.483177183040393	2		250	559	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50483983	50484303	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGCTAACTAGCTTCATCCCCTATACTTTGGTTCCCTGCAGCCTCCCCAGTTTAAATTAGACCCCCGCCTAGCTCGACTCCTGGGCATCCATACCCAGACTCGTCCAGTGATCATCCAAGCACTGTGGCAATATATTAAGACACATAAGCTCCAGGACCCTCACGAGCGGGAGTTTGTCATCTGTGACAAGTACCTGCAGCAGGTAAGTAATGGACCCATTCTTTTGCTAGAATCCATTAGAACACTAGTTATGCTCAAACTGCTAACCTCGTGCTTCTCCCCTTTGCTACAGATCTTTGAGTCTCAACGTATGAAGTTTT	CAGCTAACTAGCTTCATCCCCTATACTTTGGTTCCCTGCAGCCTCCCCAGTTTAAATTAGACCCCCGCCTAGCTCGACTCCTGGGCATCCATACCCAGACTCGTCCAGTGATCATCCAAGCACTGTGGCAATATATTAAGACACATAAGCTCCAGGACCCTCACGAGCGGGAGTTTGTCATCTGTGACAAGTACCTGCAGCAGGTAAGTAATGGACCCATTCTTTTGCTAGAATCCATTAGAACACTAGTTATGCTCAAACTGCTAACCTCGTGCTTCTCCCCTTTGCTACAGATCTTTGAGTCTCAACGTATGAAGTTTT	-	novel	NA	P-0006225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	61	214	0	ENST00000394963.4:c.874-38_1066del		p.X292_splice	ENST00000394963	NM_003076.4	292		8-9/13	0.325493777696551	5	FACETS	0.836	0.722	0.96			1	CLONAL	1	TRUE	NA	0.483177183040393	5		214	521	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631837	90631837	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	310	524	0	ENST00000330062.3:c.516G>T	p.Arg172Ser	p.R172S	ENST00000330062	NM_002168.2	172	agG/agT	4/11	0.115852481134351	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.695596080417619	0		524	782	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879337	151879337	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	276	483	0	ENST00000262189.6:c.5608C>T	p.Gln1870Ter	p.Q1870*	ENST00000262189	NM_170606.2	1870	Cag/Tag	36/59	1	2	FACETS	0.902	0.849	0.956	0.902	0.849	0.956	CLONAL	1	TRUE	1	0.695596080417619	2		483	880	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0006306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	125	402	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.40847591696959	2		402	580	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0006306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	130	719	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.888	0.806	0.973	0.888	0.806	0.973	CLONAL	1	TRUE	1	0.40847591696959	2		719	717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs967461896	NA	P-0006306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	124	380	1	ENST00000269305.4:c.526T>A	p.Cys176Ser	p.C176S	ENST00000269305	NM_001126112.2	176	Tgc/Agc	5/11	0.40847591696959	1	FACETS	0.938	0.853	1	0.938	0.853	1	CLONAL	1	TRUE	0	0.40847591696959	1		381	515	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3841994	3841994	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	155	506	0	ENST00000262367.5:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000262367	NM_004380.2	440	Cga/Tga	5/31	1	2	FACETS	0.866	0.793	0.943	0.866	0.793	0.943	CLONAL	1	TRUE	1	0.40847591696959	2		506	876	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068381	16068381	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	15	37	0	ENST00000268712.3:c.530C>A	p.Ser177Ter	p.S177*	ENST00000268712	NM_006311.3	177	tCa/tAa	5/46	0.40847591696959	1	FACETS	1	0.772	1	1	0.772	1	CLONAL	1	TRUE	0	0.40847591696959	1		37	57	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435051	49435051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	79	241	0	ENST00000301067.7:c.6502C>T	p.Pro2168Ser	p.P2168S	ENST00000301067	NM_003482.3	2168	Ccc/Tcc	31/54	0.188987930328567	2	FACETS	1	0.967	1	0.643	0.566	0.726	CLONAL	1	TRUE	0	0.204776035983357	2		241	600	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0006314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	108	540	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	1	2	FACETS	0.781	0.702	0.865	1	0.984	1	SUBCLONAL	2	TRUE	1	0.204776035983357	2		540	675	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0006314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	34	567	2	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	1	2	FACETS	0.368	0.299	0.446	0.368	0.299	0.446	SUBCLONAL	1	TRUE	1	0.204776035983357	2		569	903	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176618906	176618906	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1232661858	NA	P-0006314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	94	366	0	ENST00000439151.2:c.949A>G	p.Thr317Ala	p.T317A	ENST00000439151	NM_022455.4	317	Acg/Gcg	3/23	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.204776035983357	2		366	796	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991910	72991910	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	69	453	0	ENST00000268489.5:c.2135G>T	p.Arg712Leu	p.R712L	ENST00000268489	NM_006885.3	712	cGg/cTg	2/10	1	2	FACETS	0.588	0.51	0.672	0.588	0.51	0.672	SUBCLONAL	1	TRUE	1	0.204776035983357	2		453	1147	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30323856	30323856	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	69	375	0	ENST00000322652.5:c.1834G>A	p.Glu612Lys	p.E612K	ENST00000322652	NM_015355.2	612	Gaa/Aaa	15/16	1	2	FACETS	0.854	0.743	0.975	0.854	0.743	0.975	CLONAL	1	TRUE	1	0.204776035983357	2		375	789	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713367	40713367	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	98	296	0	ENST00000373198.4:c.4148A>T	p.Gln1383Leu	p.Q1383L	ENST00000373198	NM_133170.3	1383	cAg/cTg	30/32	0.14485213157086	3	FACETS	1	0.974	1	0.658	0.586	0.734	CLONAL	1	TRUE	1	0.204776035983357	3		296	802	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573790	41573790	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs755035922	NA	P-0006314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	100	366	0	ENST00000263253.7:c.6075G>T	p.Leu2025Phe	p.L2025F	ENST00000263253	NM_001429.3	2025	ttG/ttT	31/31	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.204776035983357	2		366	864	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938428	76938428	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	18	203	0	ENST00000373344.5:c.2320del	p.Asp774MetfsTer29	p.D774Mfs*29	ENST00000373344	NM_000489.3	774	Gat/at	9/35	0.204776035983357	0	FACETS	0.532	0.4	0.686			1	SUBCLONAL	1	TRUE	NA	0.204776035983357	0		203	263	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519818	29519818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772496459	NA	P-0006323-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	99	386	0	ENST00000389048.3:c.1753G>A	p.Ala585Thr	p.A585T	ENST00000389048	NM_004304.4	585	Gcc/Acc	9/29	0.939959958629024	1	FACETS	0.534	0.488	0.581	0.534	0.488	0.581	SUBCLONAL	1	TRUE	0	0.939959958629024	1		386	209	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175504	108175504	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006323-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	234	308	0	ENST00000278616.4:c.5599C>G	p.Gln1867Glu	p.Q1867E	ENST00000278616	NM_000051.3	1867	Cag/Gag	37/63	0.939959958629024	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.939959958629024	1		308	258	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	44	287	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.261059712190696	2		287	296	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0006326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	46	345	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.235042816755761	1	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	0	0.261059712190696	1		345	295	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0006326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	54	396	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	0.261059712190696	2		396	397	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0006344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	97	388	1	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	0.701792601778948	2		389	198	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913400	NA	P-0006344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	82	429	0	ENST00000349496.5:c.98C>A	p.Ser33Tyr	p.S33Y	ENST00000349496	NM_001904.3	33	tCt/tAt	3/15	1	2	FACETS	0.913	0.816	1	0.913	0.816	1	CLONAL	1	TRUE	1	0.701792601778948	2		429	256	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243048	105243048	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519804	NA	P-0006344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	301	496	0	ENST00000349310.3:c.235C>A	p.Gln79Lys	p.Q79K	ENST00000349310	NM_001014432.1	79	Cag/Aag	5/15	0.701792601778948	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.701792601778948	2		496	365	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107095	27107096	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0006344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	59	224	0	ENST00000324856.7:c.6711_6712del	p.Leu2238AlafsTer39	p.L2238Afs*39	ENST00000324856	NM_006015.4	2236	CGc/c	20/20	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.701792601778948	2		224	161	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399351	139399351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779195962	NA	P-0006344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	8	354	1	ENST00000277541.6:c.4792C>T	p.Arg1598Cys	p.R1598C	ENST00000277541	NM_017617.3	1598	Cgc/Tgc	26/34	1	2	FACETS	0.09	0.057	0.132	0.09	0.057	0.132	SUBCLONAL	1	TRUE	1	0.701792601778948	2		355	253	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617397	43617397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	11	455	0	ENST00000355710.3:c.2734C>T	p.Arg912Trp	p.R912W	ENST00000355710	NM_020975.4	912	Cgg/Tgg	16/20	1	2	FACETS	0.143	0.098	0.199	0.143	0.098	0.199	SUBCLONAL	1	TRUE	1	0.701792601778948	2		455	219	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099084	27099088	+	frameshift_variant	Frame_Shift_Del	DEL	CCACA	CCACA	-	novel	NA	P-0006344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	131	486	1	ENST00000324856.7:c.3506_3510del	p.Pro1169GlnfsTer22	p.P1169Qfs*22	ENST00000324856	NM_006015.4	1167	tCCACA/t	13/20	1	2	FACETS	0.915	0.838	0.994	0.915	0.838	0.994	CLONAL	1	TRUE	1	0.701792601778948	2		487	408	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645140	67645140	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	127	398	0	ENST00000264010.4:c.409del	p.Ala137LeufsTer17	p.A137Lfs*17	ENST00000264010	NM_006565.3	135	caG/ca	3/12	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.701792601778948	2		398	286	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649676	206649676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764259024	NA	P-0006350-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	672	318	0	ENST00000367120.3:c.511G>A	p.Val171Ile	p.V171I	ENST00000367120	NM_014002.3	171	Gtc/Atc	6/22	0.904209537200414	4	FACETS	0.92	0.895	0.945	0.92	0.895	0.945	CLONAL	3	TRUE	1	0.904209537200414	4		318	1025	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923160	48923160	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776789	NA	P-0006369-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	256	258	0	ENST00000267163.4:c.607+1G>A		p.X203_splice	ENST00000267163	NM_000321.2	203			0.826069248767863	2	FACETS	0.975	0.943	1	0.975	0.943	1	CLONAL	2	TRUE	0	0.846925975766259	2		258	310	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782124	135782124	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006369-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	84	437	0	ENST00000298552.3:c.1432G>C	p.Glu478Gln	p.E478Q	ENST00000298552	NM_001162426.1	478	Gaa/Caa	14/23	0.779201539639404	3	FACETS	0.362	0.319	0.408	0.181	0.159	0.204	SUBCLONAL	1	TRUE	1	0.846925975766259	3		437	780	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795265	42795265	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006369-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	66	398	0	ENST00000575354.2:c.2345C>A	p.Ala782Asp	p.A782D	ENST00000575354	NM_015125.3	782	gCc/gAc	10/20	0.779201539639404	3	FACETS	0.358	0.31	0.409	0.179	0.155	0.205	SUBCLONAL	1	TRUE	1	0.846925975766259	3		398	620	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15818059	15818059	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006369-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	375	323	0	ENST00000307771.7:c.186G>C	p.Lys62Asn	p.K62N	ENST00000307771	NM_005089.3	62	aaG/aaC	3/11	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.846925975766259	1		323	450	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105685	27105685	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	195	497	1	ENST00000324856.7:c.5296G>T	p.Glu1766Ter	p.E1766*	ENST00000324856	NM_006015.4	1766	Gaa/Taa	20/20	0.572656138728787	1	FACETS	0.909	0.85	0.97	0.909	0.85	0.97	CLONAL	1	TRUE	0	0.605339219581715	1		498	494	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287893	33287893	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	187	472	0	ENST00000374542.5:c.1360G>T	p.Glu454Ter	p.E454*	ENST00000374542	NM_001141970.1	454	Gaa/Taa	5/8	0.605339219581715	1	FACETS	0.845	0.787	0.904	0.845	0.787	0.904	CLONAL	1	TRUE	0	0.605339219581715	1		472	510	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288804	33288804	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	245	244	0	ENST00000374542.5:c.748G>T	p.Gly250Cys	p.G250C	ENST00000374542	NM_001141970.1	250	Ggc/Tgc	3/8	0.605339219581715	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.605339219581715	1		244	461	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692982	89692982	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	103	239	0	ENST00000371953.3:c.466G>T	p.Gly156Trp	p.G156W	ENST00000371953	NM_000314.4	156	Ggg/Tgg	5/9	0.572656138728787	1	FACETS	0.934	0.851	1	0.934	0.851	1	CLONAL	1	TRUE	0	0.605339219581715	1		239	254	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533503	533503	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	415	437	0	ENST00000451590.1:c.400G>T	p.Ala134Ser	p.A134S	ENST00000451590	NM_001130442.1	134	Gcc/Tcc	4/5	0.572656138728787	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.605339219581715	1		437	785	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575044	64575044	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	385	358	0	ENST00000312049.6:c.763G>T	p.Glu255Ter	p.E255*	ENST00000312049	NM_130799.2	255	Gag/Tag	4/10	0.572656138728787	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.605339219581715	1		358	732	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627730	14627730	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	200	540	1	ENST00000254322.2:c.340A>G	p.Thr114Ala	p.T114A	ENST00000254322	NM_006145.1	114	Acc/Gcc	2/3	1	2	FACETS	0.538	0.497	0.58	0.538	0.497	0.58	SUBCLONAL	1	TRUE	1	0.605339219581715	2		541	1228	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741239	40741239	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	351	435	0	ENST00000392038.2:c.1194C>A	p.Ser398Arg	p.S398R	ENST00000392038	NM_001626.4	398	agC/agA	12/14	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.605339219581715	2		435	1019	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246427	53246427	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	384	308	2	ENST00000375401.3:c.555G>T	p.Glu185Asp	p.E185D	ENST00000375401	NM_004187.3	185	gaG/gaT	5/26	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.605339219581715	1		310	668	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0006390-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	428	413	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.628336055272201	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.636360195868084	1		413	888	SUCCESS
APC	324	MSKCC	GRCh37	5	112174096	112174096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs137854575	NA	P-0006390-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	240	529	0	ENST00000257430.4:c.2805C>A	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	taC/taA	16/16	0.636360195868084	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.636360195868084	1		529	480	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641487	23641487	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1462734899	NA	P-0006390-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	337	472	1	ENST00000261584.4:c.1988G>A	p.Arg663His	p.R663H	ENST00000261584	NM_024675.3	663	cGc/cAc	5/13	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.636360195868084	2		473	1041	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0006395-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	41	319	2	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		321	814	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881414	37881414	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1131692237	NA	P-0006456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	186	410	0	ENST00000269571.5:c.2606T>G	p.Leu869Arg	p.L869R	ENST00000269571		869	cTg/cGg	21/27	0.155265519391037	3	FACETS	1	0.991	1	0.746	0.696	0.797	INDETERMINATE	1	TRUE	1	0.722284772094099	3		410	470	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112630	115112630	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	132	266	0	ENST00000257566.3:c.1110del	p.Ser371AlafsTer261	p.S371Afs*261	ENST00000257566	NM_016569.3	370	ccC/cc	7/8	0.393498906427064	1	FACETS	0.695	0.64	0.751	0.695	0.64	0.751	INDETERMINATE	1	TRUE	0	0.722284772094099	1		266	336	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259178	36259179	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0006456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	287	477	0	ENST00000300305.3:c.312_313delinsTT	p.His105Tyr	p.H105Y	ENST00000300305		104	acGCac/acTTac	3/8	1	2	FACETS	0.974	0.919	1	0.974	0.919	1	CLONAL	1	TRUE	1	0.722284772094099	2		477	816	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0006471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	244	427	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.252566752337849	3	FACETS	1	0.978	1	0.73	0.684	0.777	CLONAL	2	TRUE	0	0.32	3		427	808	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858476	27858476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766861086	NA	P-0006471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1248	107	807	0	ENST00000359303.2:c.95C>T	p.Ala32Val	p.A32V	ENST00000359303	NM_003535.2	32	gCg/gTg	1/1	0.206791055723739	5	FACETS	0.73	0.653	0.813	0.243	0.217	0.271	SUBCLONAL	1	TRUE	2	0.32	5		807	1355	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027208	49027229	+	frameshift_variant	Frame_Shift_Del	DEL	TTAATCTTCCTCTCCAGAATAA	TTAATCTTCCTCTCCAGAATAA	-	novel	NA	P-0006471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	83	347	0	ENST00000267163.4:c.1776_1797del	p.Asn593ThrfsTer11	p.N593Tfs*11	ENST00000267163	NM_000321.2	592	cTTAATCTTCCTCTCCAGAATAAt/ct	18/27	0.2352307449613	2	FACETS	1	0.971	1	0.652	0.578	0.729	CLONAL	1	TRUE	0	0.32	2		347	398	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	87	225	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.534242809963321	2		225	289	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0006476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	288	345	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.534242809963321	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.534242809963321	3		345	647	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0006476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	339	531	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.393525011116957	3	FACETS	1	0.989	1	0.746	0.71	0.781	CLONAL	2	TRUE	0	0.534242809963321	3		531	719	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862896	9862896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1198247451	NA	P-0006476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	86	759	0	ENST00000330684.3:c.2407G>A	p.Glu803Lys	p.E803K	ENST00000330684	NM_001134407.1	803	Gag/Aag	12/13	1	2	FACETS	0.759	0.675	0.848	0.759	0.675	0.848	SUBCLONAL	1	TRUE	1	0.534242809963321	2		759	424	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145431	58145431	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11547328	NA	P-0006476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	289	577	1	ENST00000257904.6:c.70C>T	p.Arg24Cys	p.R24C	ENST00000257904	NM_000075.3	24	Cgt/Tgt	2/8	0.534242809963321	3	FACETS	0.865	0.818	0.914	0.577	0.545	0.61	CLONAL	2	TRUE	0	0.534242809963321	3		578	792	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858184	9858184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	109	821	0	ENST00000330684.3:c.3217G>A	p.Glu1073Lys	p.E1073K	ENST00000330684	NM_001134407.1	1073	Gaa/Aaa	13/13	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.534242809963321	2		821	401	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699300	117699300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	96	721	1	ENST00000369458.3:c.341C>T	p.Ser114Phe	p.S114F	ENST00000369458	NM_024626.3	114	tCt/tTt	3/6	0.534242809963321	3	FACETS	0.843	0.754	0.938	0.422	0.377	0.469	CLONAL	1	TRUE	1	0.534242809963321	3		722	540	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713694	30713694	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	217	508	0	ENST00000295754.5:c.1019A>G	p.His340Arg	p.H340R	ENST00000295754	NM_003242.5	340	cAt/cGt	4/7	0.340428041510117	5	FACETS	1	0.962	1	0.617	0.581	0.654	CLONAL	3	TRUE	0	0.534242809963321	5		508	474	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012382	152012382	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	62	572	2	ENST00000262189.6:c.431C>T	p.Ser144Phe	p.S144F	ENST00000262189	NM_170606.2	144	tCc/tTc	4/59	0.534242809963321	3	FACETS	0.455	0.392	0.522	0.227	0.196	0.261	SUBCLONAL	1	TRUE	1	0.534242809963321	3		574	647	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608446	28608446	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	158	636	2	ENST00000241453.7:c.1696T>A	p.Tyr566Asn	p.Y566N	ENST00000241453	NM_004119.2	566	Tac/Aac	13/24	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.534242809963321	2		638	489	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950860	32950860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373203204	NA	P-0006476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	222	830	0	ENST00000380152.3:c.8686C>T	p.Arg2896Cys	p.R2896C	ENST00000380152		2896	Cgt/Tgt	21/27	0.326691528334273	5	FACETS	0.97	0.905	1	0.646	0.603	0.691	CLONAL	2	TRUE	2	0.534242809963321	5		830	772	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916198	9916198	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	56	663	0	ENST00000330684.3:c.2091C>G	p.Asn697Lys	p.N697K	ENST00000330684	NM_001134407.1	697	aaC/aaG	10/13	1	2	FACETS	0.556	0.478	0.64	0.556	0.478	0.64	SUBCLONAL	1	TRUE	1	0.534242809963321	2		663	377	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273456	5273456	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1054506328	NA	P-0006476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	58	646	0	ENST00000357368.4:c.376C>T	p.Arg126Ter	p.R126*	ENST00000357368	NM_002850.3	126	Cga/Tga	4/38	0.534242809963321	3	FACETS	0.644	0.555	0.741	0.322	0.277	0.371	SUBCLONAL	1	TRUE	1	0.534242809963321	3		646	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0006512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	409	404	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.281462181711757	3	FACETS	0.988	0.942	1	0.988	0.942	1	CLONAL	3	FALSE	0	0.286887826724775	3		405	1100	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0006512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	128	351	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.93	0.848	1	1	0.99	1	CLONAL	2	FALSE	1	0.286887826724775	2		351	480	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0006512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	34	394	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.149906917541768	3	FACETS	0.411	0.335	0.498	0.206	0.167	0.249	INDETERMINATE	1	FALSE	1	0.286887826724775	3		394	659	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0006512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	29	292	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.642	0.516	0.784	0.642	0.516	0.784	SUBCLONAL	1	FALSE	1	0.286887826724775	2		292	315	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439858	220439858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	142	587	0	ENST00000243786.2:c.711G>A	p.Met237Ile	p.M237I	ENST00000243786	NM_002191.3	237	atG/atA	2/2	0.228267356853846	4	FACETS	0.99	0.9	1			1	CLONAL	1	FALSE	NA	0.286887826724775	4		587	1287	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048668	180048668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1158883745	NA	P-0006512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	55	322	2	ENST00000261937.6:c.1894C>T	p.Arg632Cys	p.R632C	ENST00000261937	NM_182925.4	632	Cgc/Tgc	13/30	NA	2	FACETS	0.617	0.528	0.716			1	INDETERMINATE	1	FALSE	NA	0.286887826724775	2		324	621	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352801	118352801	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	69	224	0	ENST00000534358.1:c.4006G>C	p.Glu1336Gln	p.E1336Q	ENST00000534358	NM_005933.3	1336	Gaa/Caa	7/36	0.286887826724775	2	FACETS	1	0.938	1	0.561	0.49	0.636	CLONAL	1	FALSE	0	0.286887826724775	2		224	429	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325846	30325846	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763509688	NA	P-0006512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	130	278	1	ENST00000322652.5:c.2044C>T	p.Arg682Cys	p.R682C	ENST00000322652	NM_015355.2	682	Cgt/Tgt	16/16	0.286887826724775	3	FACETS	0.991	0.903	1	0.991	0.903	1	CLONAL	2	FALSE	1	0.286887826724775	3		279	523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0006519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	111	540	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.359570055590049	2		540	432	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971107	21971107	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	36	302	0	ENST00000304494.5:c.251A>G	p.Asp84Gly	p.D84G	ENST00000304494	NM_000077.4	84	gAc/gGc	2/3	1	2	FACETS	0.612	0.505	0.732	0.612	0.505	0.732	SUBCLONAL	1	TRUE	1	0.359570055590049	2		302	327	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412326	139412326	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	40	612	0	ENST00000277541.6:c.1319G>T	p.Cys440Phe	p.C440F	ENST00000277541	NM_017617.3	440	tGt/tTt	8/34	1	2	FACETS	0.443	0.368	0.527	0.443	0.368	0.527	SUBCLONAL	1	TRUE	1	0.359570055590049	2		612	502	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220067	133220067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	84	699	1	ENST00000320574.5:c.4370G>A	p.Gly1457Asp	p.G1457D	ENST00000320574	NM_006231.2	1457	gGc/gAc	34/49	0.181223870642573	1	FACETS	0.803	0.712	0.9	0.803	0.712	0.9	INDETERMINATE	1	TRUE	0	0.359570055590049	1		700	477	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942868	15942868	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	56	576	0	ENST00000268712.3:c.6834A>C	p.Lys2278Asn	p.K2278N	ENST00000268712	NM_006311.3	2278	aaA/aaC	44/46	0.35523144831037	3	FACETS	0.543	0.464	0.629			1	SUBCLONAL	1	TRUE	NA	0.359570055590049	3		576	677	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944502	40944502	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	37	671	0	ENST00000373198.4:c.2000A>G	p.Glu667Gly	p.E667G	ENST00000373198	NM_133170.3	667	gAg/gGg	12/32	0.359570055590049	3	FACETS	0.329	0.27	0.396	0.165	0.135	0.198	SUBCLONAL	1	TRUE	1	0.359570055590049	3		671	737	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419834	41419834	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0006519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	30	468	0	ENST00000373198.4:c.486+1G>T		p.X162_splice	ENST00000373198	NM_133170.3	162			0.359570055590049	3	FACETS	0.338	0.272	0.414	0.169	0.136	0.207	SUBCLONAL	1	TRUE	1	0.359570055590049	3		468	582	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0006537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	504	915	1	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.932701110591899	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.932701110591899	1		916	557	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456520	189456520	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1177278893	NA	P-0006537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	424	1217	0	ENST00000264731.3:c.281A>T	p.Asp94Val	p.D94V	ENST00000264731	NM_003722.4	94	gAc/gTc	3/14	0.932701110591899	2	FACETS	1	0.978	1	0.515	0.494	0.537	CLONAL	1	TRUE	0	0.932701110591899	2		1217	882	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297963	15297984	+	frameshift_variant	Frame_Shift_Del	DEL	AGGCATTTGCCGCCATGGCGGC	AGGCATTTGCCGCCATGGCGGC	-	novel	NA	P-0006537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	567	1164	1	ENST00000263388.2:c.1772_1793del	p.Cys591Ter	p.C591*	ENST00000263388	NM_000435.2	591	tGCCGCCATGGCGGCAAATGCCTa/ta	11/33	1	2	FACETS	0.984	0.948	1	0.984	0.948	1	CLONAL	1	TRUE	1	0.932701110591899	2		1165	1235	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459561	50459561	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006537-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	329	697	0	ENST00000331340.3:c.850+1del		p.G284fs	ENST00000331340	NM_006060.4	284	Ggg/gg	7/8	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.932701110591899	2		697	703	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0006546-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	436	463	3	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.486383580422442	1	FACETS	0.748	0.723	0.773	0.748	0.723	0.773	INDETERMINATE	1	TRUE	0	0.937794510074603	1		466	660	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951087	48951088	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs1131690889	NA	P-0006546-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	302	478	0	ENST00000267163.4:c.1251_1252del	p.Arg418SerfsTer9	p.R418Sfs*9	ENST00000267163	NM_000321.2	417	AAa/a	13/27	0.937794510074603	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.937794510074603	1		478	329	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0006546-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	991	422	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.937794510074603	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.937794510074603	2		422	1019	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230432	46230432	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006546-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	501	553	0	ENST00000334344.6:c.766T>G	p.Ser256Ala	p.S256A	ENST00000334344	NM_152641.2	256	Tct/Gct	7/21	0.210759632405407	1	FACETS	0.487	0.467	0.507	0.487	0.467	0.507	INDETERMINATE	1	TRUE	0	0.937794510074603	1		553	1165	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857663	78857663	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006546-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	371	486	0	ENST00000306801.3:c.1733C>G	p.Ala578Gly	p.A578G	ENST00000306801	NM_020761.2	578	gCc/gGc	16/34	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.937794510074603	2		486	783	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778806	76778807	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0006546-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	828	534	0	ENST00000373344.5:c.6772_6773del	p.Leu2258GlyfsTer10	p.L2258Gfs*10	ENST00000373344	NM_000489.3	2258	TTg/g	31/35	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.937794510074603	1		534	906	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940531	49940531	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006546-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1272	97	766	0	ENST00000296474.3:c.512C>A	p.Pro171His	p.P171H	ENST00000296474	NM_002447.2	171	cCc/cAc	1/20	1	2	FACETS	0.151	0.134	0.17	0.151	0.134	0.17	SUBCLONAL	1	TRUE	1	0.937794510074603	2		766	1369	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144893	47144893	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006547-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	136	619	0	ENST00000409792.3:c.4860A>T	p.Lys1620Asn	p.K1620N	ENST00000409792	NM_014159.6	1620	aaA/aaT	7/21	0.103388056087535	3	FACETS	0.901	0.821	0.985			1	CLONAL	4	TRUE	NA	0.119521584271901	3		619	669	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436617	52436617	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0006547-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	289	657	0	ENST00000460680.1:c.2056+1G>C		p.X686_splice	ENST00000460680	NM_004656.3	686			0.103388056087535	3	FACETS	0.99	0.941	1			1	CLONAL	9	TRUE	NA	0.119521584271901	3		657	575	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930726	32930726	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006547-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	152	541	0	ENST00000380152.3:c.7597T>C	p.Ser2533Pro	p.S2533P	ENST00000380152		2533	Tct/Cct	15/27	0.119953631751908	0	FACETS	0.907	0.833	0.984			1	CLONAL	4	TRUE	0	0.119521584271901	0		541	617	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47088090	47088102	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGACTTGGCTG	GAAGACTTGGCTG	-	novel	NA	P-0006547-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	85	590	0	ENST00000409792.3:c.6973_6985del	p.Gln2325SerfsTer24	p.Q2325Sfs*24	ENST00000409792	NM_014159.6	2325	CAGCCAAGTCTTCag/ag	16/21	0.103388056087535	3	FACETS	0.859	0.76	0.964			1	CLONAL	3	TRUE	NA	0.119521584271901	3		590	585	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858645	57858645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006552-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	118	399	0	ENST00000228682.2:c.383C>T	p.Thr128Ile	p.T128I	ENST00000228682	NM_005269.2	128	aCc/aTc	4/12	0.260277567429741	3	FACETS	1	0.956	1	0.55	0.497	0.607	CLONAL	1	TRUE	1	0.361116636407609	3		399	701	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164928	47164928	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	147	279	0	ENST00000409792.3:c.1198C>T	p.Arg400Ter	p.R400*	ENST00000409792	NM_014159.6	400	Cga/Tga	3/21	0.2374540855032	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	0	0.3	2		279	486	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637653	52637653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	237	476	1	ENST00000394830.3:c.2663C>T	p.Ser888Leu	p.S888L	ENST00000394830	NM_018313.4	888	tCa/tTa	18/30	0.2374540855032	2	FACETS	0.961	0.899	1	0.961	0.899	1	CLONAL	2	TRUE	0	0.3	2		477	822	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098804	178098804	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	210	464	0	ENST00000397062.3:c.241G>C	p.Gly81Arg	p.G81R	ENST00000397062	NM_006164.4	81	Ggt/Cgt	2/5	0.3	3	FACETS	0.907	0.843	0.972	0.907	0.843	0.972	CLONAL	2	TRUE	1	0.3	3		464	888	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715340	117715340	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	67	314	0	ENST00000368508.3:c.1149C>A	p.Phe383Leu	p.F383L	ENST00000368508	NM_002944.2	383	ttC/ttA	10/43	0.3	1	FACETS	0.729	0.634	0.831	0.729	0.634	0.831	SUBCLONAL	1	TRUE	0	0.3	1		314	521	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522066	157522066	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	130	331	0	ENST00000346085.5:c.4338G>T	p.Gln1446His	p.Q1446H	ENST00000346085	NM_020732.3	1446	caG/caT	18/20	1	2	FACETS	0.984	0.892	1	0.984	0.892	1	CLONAL	1	TRUE	1	0.3	2		331	881	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66518954	66518954	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	197	451	0	ENST00000358598.2:c.235G>T	p.Glu79Ter	p.E79*	ENST00000358598	NM_212471.2	79	Gag/Tag	3/11	0.3	3	FACETS	0.966	0.896	1	0.966	0.896	1	CLONAL	2	TRUE	1	0.3	3		451	782	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214592	5214592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369295620	NA	P-0006557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	104	448	1	ENST00000357368.4:c.4474C>T	p.Arg1492Trp	p.R1492W	ENST00000357368	NM_002850.3	1492	Cgg/Tgg	29/38	0.3	3	FACETS	0.673	0.601	0.751	0.337	0.3	0.376	SUBCLONAL	1	TRUE	1	0.3	3		449	1184	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944464	40944464	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1366	201	610	1	ENST00000373198.4:c.2038A>T	p.Thr680Ser	p.T680S	ENST00000373198	NM_133170.3	680	Aca/Tca	12/32	0.203894152972408	5	FACETS	1	0.984	1	0.413	0.381	0.447	CLONAL	1	TRUE	2	0.3	5		611	1567	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183805	10183808	+	frameshift_variant	Frame_Shift_Del	DEL	GACG	GACG	-	novel	NA	P-0006557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	126	249	0	ENST00000256474.2:c.275_278del	p.Asp92AlafsTer66	p.D92Afs*66	ENST00000256474	NM_000551.3	92	GACGgc/gc	1/3	0.2374540855032	2	FACETS	0.861	0.784	0.94	0.861	0.784	0.94	CLONAL	2	TRUE	0	0.3	2		249	488	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	340	287	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.103702207513108	4	FACETS	1	0.98	1	1	0.995	1	INDETERMINATE	3	TRUE	2	0.205494797262504	4		287	1237	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970971	21970971	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	179	460	0	ENST00000304494.5:c.387C>A	p.Tyr129Ter	p.Y129*	ENST00000304494	NM_000077.4	129	taC/taA	2/3	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.205494797262504	2		460	1216	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	285	225	0				ENST00000310581	NM_198253.2	-/1132			0.509033270560796	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.509033270560796	3		225	684	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0006590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	147	345	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.168836203363872	1	FACETS	0.906	0.834	0.981	0.906	0.834	0.981	INDETERMINATE	1	TRUE	0	0.509033270560796	1		345	475	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0006590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	58	386	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.509033270560796	1	FACETS	0.336	0.288	0.387	0.336	0.288	0.387	SUBCLONAL	1	TRUE	0	0.509033270560796	1		386	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0006590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	86	381	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	0.509033270560796	1	FACETS	0.326	0.288	0.367	0.326	0.288	0.367	SUBCLONAL	1	TRUE	0	0.509033270560796	1		381	773	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029169	26029169	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	38	345	1	ENST00000435504.4:c.181C>T	p.His61Tyr	p.H61Y	ENST00000435504		61	Cac/Tac	4/13	1	2	FACETS	0.22	0.181	0.263	0.22	0.181	0.263	SUBCLONAL	1	TRUE	1	0.509033270560796	2		346	680	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037445	12037445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	85	402	3	ENST00000396373.4:c.1076G>A	p.Arg359Gln	p.R359Q	ENST00000396373	NM_001987.4	359	cGa/cAa	6/8	1	2	FACETS	0.361	0.319	0.408	0.361	0.319	0.408	SUBCLONAL	1	TRUE	1	0.509033270560796	2		405	924	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0006595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	288	819	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.858000005150408	1	FACETS	0.424	0.4	0.449	0.424	0.4	0.449	SUBCLONAL	1	TRUE	0	0.885419870994196	1		819	855	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0006595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	41	578	1	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	0.858000005150408	1	FACETS	0.066	0.055	0.079	0.066	0.055	0.079	SUBCLONAL	1	TRUE	0	0.885419870994196	1		579	779	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248586	59248586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs996081434	NA	P-0006595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	613	576	0	ENST00000371222.2:c.157C>T	p.Leu53Phe	p.L53F	ENST00000371222	NM_002228.3	53	Ctc/Ttc	1/1	1	2	FACETS	0.916	0.882	0.95	0.916	0.882	0.95	CLONAL	1	TRUE	1	0.885419870994196	2		576	1512	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575089	64575089	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs868087064	NA	P-0006595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	544	517	1	ENST00000312049.6:c.718G>T	p.Val240Leu	p.V240L	ENST00000312049	NM_130799.2	240	Gtg/Ttg	4/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.885419870994196	2		518	1215	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59793346	59793346	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	286	534	0	ENST00000259008.2:c.2458C>G	p.Gln820Glu	p.Q820E	ENST00000259008	NM_032043.2	820	Caa/Gaa	17/20	1	2	FACETS	0.466	0.437	0.496	0.466	0.437	0.496	SUBCLONAL	1	TRUE	1	0.885419870994196	2		534	1385	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248614	59248631	+	inframe_deletion	In_Frame_Del	DEL	GGCCAGGTTCAGGGTCAT	GGCCAGGTTCAGGGTCAT	-	novel	NA	P-0006595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	650	591	0	ENST00000371222.2:c.112_129del	p.Met38_Ala43del	p.M38_A43del	ENST00000371222	NM_002228.3	38	ATGACCCTGAACCTGGCC/-	1/1	1	2	FACETS	0.971	0.937	1	0.971	0.937	1	CLONAL	1	TRUE	1	0.885419870994196	2		591	1512	SUCCESS
APC	324	MSKCC	GRCh37	5	112177113	112177116	+	frameshift_variant	Frame_Shift_Del	DEL	CAGA	CAGA	-	rs864622228	NA	P-0006595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	517	544	0	ENST00000257430.4:c.5826_5829del	p.Asp1942GlufsTer27	p.D1942Efs*27	ENST00000257430	NM_000038.5	1941	cCAGAc/cc	16/16	0.858000005150408	1	FACETS	0.893	0.867	0.918	0.893	0.867	0.918	CLONAL	1	TRUE	0	0.885419870994196	1		544	729	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958555	38958555	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	46	380	0	ENST00000357387.3:c.2410C>G	p.Leu804Val	p.L804V	ENST00000357387	NM_152756.3	804	Ctc/Gtc	24/38	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.21	2		380	425	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536918	120536918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1367775509	NA	P-0006597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1264	142	586	1	ENST00000229340.5:c.268G>A	p.Val90Ile	p.V90I	ENST00000229340	NM_006861.6	90	Gtc/Atc	4/6	1	2	FACETS	0.962	0.874	1	0.962	0.874	1	CLONAL	1	TRUE	1	0.21	2		587	1406	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191583	10191584	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0006597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	99	463	0	ENST00000256474.2:c.577_578del	p.Asn193CysfsTer62	p.N193Cfs*62	ENST00000256474	NM_000551.3	192	ccAAat/ccat	3/3	0.159772955096518	1	FACETS	0.942	0.84	1	0.942	0.84	1	CLONAL	1	TRUE	0	0.21	1		463	896	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0006609-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	567	348	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.638667558439786	4	FACETS	1	0.983	1	1	0.998	1	CLONAL	4	TRUE	1	0.638667558439786	4		348	721	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006609-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	182	387	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	0.984	0.914	1	0.984	0.914	1	CLONAL	1	TRUE	1	0.638667558439786	2		387	579	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0006613-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	21	260	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.14875694812045	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		260	530	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006633-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	156	225	0				ENST00000310581	NM_198253.2	-/1132			0.218729830692863	3	FACETS	1	0.986	1	0.66	0.608	0.713	INDETERMINATE	1	TRUE	1	0.586772353937586	3		225	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577115	7577115	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519983	NA	P-0006633-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	394	468	0	ENST00000269305.4:c.823T>C	p.Cys275Arg	p.C275R	ENST00000269305	NM_001126112.2	275	Tgt/Cgt	8/11	0.586772353937586	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.586772353937586	1		468	730	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916703	178916703	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006633-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	227	644	0	ENST00000263967.3:c.90G>T	p.Met30Ile	p.M30I	ENST00000263967	NM_006218.2	30	atG/atT	2/21	0.218729830692863	3	FACETS	1	0.987	1	0.614	0.573	0.656	INDETERMINATE	1	TRUE	1	0.586772353937586	3		644	815	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740416	58740416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777279856	NA	P-0006633-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	532	610	1	ENST00000305921.3:c.1321C>T	p.Arg441Cys	p.R441C	ENST00000305921	NM_003620.3	441	Cgt/Tgt	6/6	0.288651895039259	6	FACETS	0.902	0.869	0.936	0.902	0.869	0.936	INDETERMINATE	4	TRUE	2	0.586772353937586	6		611	1092	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106184	2106226	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTGCTCCCTGCAGGATGATCTGTCTGCTGTGCGTCCGGACCGC	GTGCTCCCTGCAGGATGATCTGTCTGCTGTGCGTCCGGACCGC	CG	novel	NA	P-0006633-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	288	459	0	ENST00000219476.3:c.600-13_629delinsCG		p.X200_splice	ENST00000219476	NM_000548.3	200		7/42	0.447913550502497	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.586772353937586	1		459	581	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602664	55602664	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs1057519713	NA	P-0006638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	329	346	0	ENST00000288135.5:c.2485G>C	p.Ala829Pro	p.A829P	ENST00000288135	NM_000222.2	829	Gct/Cct	18/21	1	2	FACETS	0.975	0.927	1	0.975	0.927	1	CLONAL	1	TRUE	1	0.895447682922184	2		346	754	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593607	55593615	+	inframe_deletion	In_Frame_Del	DEL	AGGTTGTTG	AGGTTGTTG	-	novel	NA	P-0006638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	388	704	0	ENST00000288135.5:c.1676_1684del	p.Val559_Glu561del	p.V559_E561del	ENST00000288135	NM_000222.2	558	aAGGTTGTTGag/aag	11/21	1	2	FACETS	0.884	0.843	0.926	0.884	0.843	0.926	CLONAL	1	TRUE	1	0.895447682922184	2		704	980	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265533	198265533	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1211158121	NA	P-0006638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	273	501	0	ENST00000335508.6:c.2624T>C	p.Ile875Thr	p.I875T	ENST00000335508	NM_012433.2	875	aTt/aCt	18/25	1	2	FACETS	0.94	0.888	0.991	0.94	0.888	0.991	CLONAL	1	TRUE	1	0.895447682922184	2		501	649	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210741	2210741	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	552	505	4	ENST00000398665.3:c.1238G>A	p.Arg413His	p.R413H	ENST00000398665	NM_032482.2	413	cGc/cAc	14/28	1	2	FACETS	0.984	0.947	1	0.984	0.947	1	CLONAL	1	TRUE	1	0.895447682922184	2		509	1253	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877352	40877352	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006638-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	374	380	1	ENST00000373198.4:c.2344G>T	p.Gly782Cys	p.G782C	ENST00000373198	NM_133170.3	782	Ggc/Tgc	15/32	1	2	FACETS	0.927	0.884	0.971	0.927	0.884	0.971	CLONAL	1	TRUE	1	0.895447682922184	2		381	901	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0006641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	1170	877	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.244960048919317	13	FACETS	0.981	0.959	1	0.981	0.959	1	CLONAL	11	TRUE	2	0.244960048919317	13		878	2077	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278049	18278049	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs372272045	NA	P-0006641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	210	377	2	ENST00000222254.8:c.1669G>T	p.Asp557Tyr	p.D557Y	ENST00000222254	NM_005027.3	557	Gac/Tac	13/16	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.244960048919317	2		379	1199	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143192	30143192	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500227	NA	P-0006641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	102	265	1	ENST00000389048.3:c.334G>A	p.Ala112Thr	p.A112T	ENST00000389048	NM_004304.4	112	Gcc/Acc	1/29	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.244960048919317	2		266	709	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436137	116436137	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	72	303	0	ENST00000397752.3:c.4132G>T	p.Glu1378Ter	p.E1378*	ENST00000397752	NM_000245.2	1378	Gag/Tag	21/21	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.244960048919317	2		303	554	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565575	41565575	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	188	434	0	ENST00000263253.7:c.4241A>G	p.Tyr1414Cys	p.Y1414C	ENST00000263253	NM_001429.3	1414	tAt/tGt	26/31	1	2	FACETS	1	0.978	1	1	0.994	1	CLONAL	2	TRUE	1	0.244960048919317	2		434	675	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0006643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	231	531	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.195108951008205	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.294662968611176	1		531	906	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0006643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	143	546	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	0.974	1	CLONAL	1	TRUE	1	0.294662968611176	2		546	824	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751132	57751132	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs771454331	NA	P-0006643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	305	355	0	ENST00000274289.3:c.1735A>G	p.Met579Val	p.M579V	ENST00000274289	NM_006622.3	579	Atg/Gtg	12/14	0.294662968611176	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.294662968611176	2		355	881	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508281	106508281	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	60	244	0	ENST00000359195.3:c.275G>T	p.Gly92Val	p.G92V	ENST00000359195	NM_002649.2	92	gGa/gTa	2/11	0.238091157622367	1	FACETS	0.806	0.696	0.924	0.806	0.696	0.924	CLONAL	1	TRUE	0	0.294662968611176	1		244	431	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675692	30675695	+	frameshift_variant	Frame_Shift_Del	DEL	CTCC	CTCC	-	rs1402588124	NA	P-0006643-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1918	137	534	0	ENST00000376406.3:c.2661_2664del	p.Glu888ValfsTer2	p.E888Vfs*2	ENST00000376406	NM_014641.2	887	agGGAG/ag	8/15	0.294662968611176	6	FACETS	0.719	0.651	0.792	0.144	0.13	0.159	SUBCLONAL	1	TRUE	1	0.294662968611176	6		534	2055	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225367699	225367699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006653-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	36	511	1	ENST00000264414.4:c.1468C>T	p.His490Tyr	p.H490Y	ENST00000264414	NM_003590.4	490	Cat/Tat	10/16	1	2	FACETS	0.817	0.672	0.978	0.817	0.672	0.978	CLONAL	1	TRUE	1	0.221548054130746	2		512	398	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136862	55136862	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006653-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	79	622	0	ENST00000257290.5:c.1184T>G	p.Val395Gly	p.V395G	ENST00000257290	NM_006206.4	395	gTa/gGa	8/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.221548054130746	2		622	538	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822270	72822270	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006653-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1640	499	724	0	ENST00000268489.5:c.9905del	p.Leu3302CysfsTer51	p.L3302Cfs*51	ENST00000268489	NM_006885.3	3302	tTg/tg	10/10	0.221548054130746	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.221548054130746	3		724	2139	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696230	52696230	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006653-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	90	525	0	ENST00000394830.3:c.447del	p.Asn149LysfsTer25	p.N149Kfs*25	ENST00000394830	NM_018313.4	149	aaT/aa	5/30	0.221548054130746	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.221548054130746	1		525	684	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098908	47098908	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006653-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	109	437	0	ENST00000409792.3:c.6366del	p.Lys2123SerfsTer24	p.K2123Sfs*24	ENST00000409792	NM_014159.6	2122	cgG/cg	15/21	0.221548054130746	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.221548054130746	1		437	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0006696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	350	528	1	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.78527632661623	2	FACETS	0.975	0.945	1	0.975	0.945	1	CLONAL	2	TRUE	0	0.799146042966104	2		529	449	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272421	11272421	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	123	356	0	ENST00000361445.4:c.3509G>C	p.Arg1170Pro	p.R1170P	ENST00000361445	NM_004958.3	1170	cGc/cCc	23/58	0.799146042966104	4	FACETS	0.934	0.847	1	0.467	0.423	0.513	CLONAL	1	TRUE	2	0.799146042966104	4		356	593	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098846	178098846	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	151	510	0	ENST00000397062.3:c.199G>A	p.Glu67Lys	p.E67K	ENST00000397062	NM_006164.4	67	Gag/Aag	2/5	0.799146042966104	3	FACETS	1	0.964	1	0.541	0.498	0.585	CLONAL	1	TRUE	1	0.799146042966104	3		510	489	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056024	26056024	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs750505144	NA	P-0006696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	145	193	0	ENST00000343677.2:c.633G>C	p.Lys211Asn	p.K211N	ENST00000343677	NM_005319.3	211	aaG/aaC	1/1	0.594255288960401	4	FACETS	1	0.982	1	0.78	0.727	0.833	CLONAL	2	TRUE	1	0.799146042966104	4		193	279	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250737	26250737	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	646	826	0	ENST00000446824.2:c.97A>G	p.Thr33Ala	p.T33A	ENST00000446824	NM_021018.2	33	Acc/Gcc	1/1	0.594255288960401	4	FACETS	1	0.996	1	0.822	0.796	0.848	CLONAL	2	TRUE	1	0.799146042966104	4		826	1180	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120231	94120231	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	254	496	0	ENST00000369303.4:c.820G>T	p.Asp274Tyr	p.D274Y	ENST00000369303	NM_004440.3	274	Gac/Tac	3/17	0.486015496426474	4	FACETS	0.859	0.816	0.9	0.859	0.816	0.9	CLONAL	3	TRUE	1	0.799146042966104	4		496	444	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997697	149997697	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs145871963	NA	P-0006696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	75	323	0	ENST00000253339.5:c.2770C>T	p.Arg924Ter	p.R924*	ENST00000253339		924	Cga/Tga	5/7	0.799146042966104	3	FACETS	0.915	0.811	1	0.458	0.405	0.513	CLONAL	1	TRUE	1	0.799146042966104	3		323	287	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962921	2962921	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	335	355	0	ENST00000396946.4:c.1987G>T	p.Gly663Trp	p.G663W	ENST00000396946	NM_032415.4	663	Ggg/Tgg	16/25	0.744660355715946	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.799146042966104	4		355	722	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729560	41729560	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	406	667	4	ENST00000242208.4:c.969G>T	p.Lys323Asn	p.K323N	ENST00000242208	NM_002192.2	323	aaG/aaT	3/3	0.744660355715946	4	FACETS	0.945	0.903	0.988	0.945	0.903	0.988	CLONAL	2	TRUE	2	0.799146042966104	4		671	967	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350077	81350077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	215	384	0	ENST00000222390.5:c.1255A>T	p.Met419Leu	p.M419L	ENST00000222390	NM_000601.4	419	Atg/Ttg	10/18	0.744660355715946	4	FACETS	0.974	0.915	1	0.974	0.915	1	CLONAL	2	TRUE	2	0.799146042966104	4		384	497	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380138	116380138	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	158	488	2	ENST00000397752.3:c.1527G>T	p.Lys509Asn	p.K509N	ENST00000397752	NM_000245.2	509	aaG/aaT	4/21	0.744660355715946	4	FACETS	0.885	0.82	0.95	0.885	0.82	0.95	CLONAL	2	TRUE	2	0.799146042966104	4		490	402	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412237	139412237	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1564199455	NA	P-0006696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	207	424	0	ENST00000277541.6:c.1408C>G	p.Gln470Glu	p.Q470E	ENST00000277541	NM_017617.3	470	Cag/Gag	8/34	0.799146042966104	3	FACETS	1	0.969	1	0.534	0.497	0.571	CLONAL	1	TRUE	1	0.799146042966104	3		424	679	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18648994	18648994	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0006696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	147	261	0	ENST00000266497.5:c.2671-2A>T		p.X891_splice	ENST00000266497		891			0.744660355715946	4	FACETS	0.997	0.924	1	0.997	0.924	1	CLONAL	2	TRUE	2	0.799146042966104	4		261	332	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061257	38061257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	429	423	0	ENST00000250448.2:c.732G>C	p.Trp244Cys	p.W244C	ENST00000250448	NM_004496.3	244	tgG/tgC	2/2	0.744660355715946	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.799146042966104	4		423	923	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030403	49030403	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	192	287	0	ENST00000267163.4:c.1880del	p.Asn627MetfsTer16	p.N627Mfs*16	ENST00000267163	NM_000321.2	626	gcA/gc	19/27	0.78527632661623	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.799146042966104	2		287	213	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0006723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	186	717	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	0.97	0.894	1	0.97	0.894	1	CLONAL	1	TRUE	1	0.32	2		717	1199	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0006723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	145	388	1	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	0.32	2		389	721	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591825	48591825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767342	NA	P-0006723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	96	443	0	ENST00000342988.3:c.988G>A	p.Glu330Lys	p.E330K	ENST00000342988	NM_005359.5	330	Gaa/Aaa	9/12	0.3	1	FACETS	0.89	0.795	0.991	0.89	0.795	0.991	CLONAL	1	TRUE	0	0.32	1		443	566	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696716	47696716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	99	404	1	ENST00000347630.2:c.232G>A	p.Glu78Lys	p.E78K	ENST00000347630	NM_001007230.1	78	Gaa/Aaa	5/11	1	2	FACETS	0.844	0.754	0.94	0.844	0.754	0.94	CLONAL	1	TRUE	1	0.32	2		405	733	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550806	150550806	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs142581495	NA	P-0006723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	79	267	0	ENST00000369026.2:c.850G>C	p.Glu284Gln	p.E284Q	ENST00000369026	NM_021960.4	284	Gaa/Caa	2/3	0.3	3	FACETS	0.865	0.761	0.977	0.433	0.38	0.489	CLONAL	1	TRUE	1	0.32	3		267	662	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518761	176518761	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	76	410	0	ENST00000292408.4:c.679G>C	p.Glu227Gln	p.E227Q	ENST00000292408	NM_213647.1	227	Gag/Cag	6/18	0.3	3	FACETS	0.715	0.626	0.81	0.357	0.313	0.405	SUBCLONAL	1	TRUE	1	0.32	3		410	771	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793517	89793517	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	88	308	0	ENST00000336032.3:c.586C>G	p.His196Asp	p.H196D	ENST00000336032	NM_006813.2	196	Cat/Gat	2/2	0.3	3	FACETS	1	0.895	1	0.505	0.447	0.566	CLONAL	1	TRUE	1	0.32	3		308	632	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292938	91292938	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	104	289	0	ENST00000355112.3:c.440C>T	p.Ser147Phe	p.S147F	ENST00000355112	NM_000057.2	147	tCt/tTt	3/22	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.32	2		289	585	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827361	72827361	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	399	657	0	ENST00000268489.5:c.9220C>T	p.Gln3074Ter	p.Q3074*	ENST00000268489	NM_006885.3	3074	Cag/Tag	9/10	0.3	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.32	2		657	1139	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862165	68862165	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	241	447	0	ENST00000261769.5:c.2253del	p.Asn751LysfsTer19	p.N751Kfs*19	ENST00000261769	NM_004360.3	751	aaC/aa	14/16	0.3	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	0	0.32	2		447	753	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0006740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	194	479	1	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.422525255415635	1	FACETS	0.846	0.784	0.911	0.846	0.784	0.911	CLONAL	1	TRUE	0	0.422525255415635	1		480	856	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524660	103524660	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	63	410	0	ENST00000355739.4:c.2791G>T	p.Ala931Ser	p.A931S	ENST00000355739	NM_000123.3	931	Gct/Tct	13/15	1	2	FACETS	0.36	0.31	0.414	0.36	0.31	0.414	SUBCLONAL	1	TRUE	1	0.422525255415635	2		410	829	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226540	1226540	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	102	427	0	ENST00000326873.7:c.1196A>C	p.Gln399Pro	p.Q399P	ENST00000326873	NM_000455.4	399	cAg/cCg	9/10	0.252893203133182	1	FACETS	0.399	0.356	0.445	0.399	0.356	0.445	INDETERMINATE	1	TRUE	0	0.422525255415635	1		427	955	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012726	36012726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006740-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	244	110	0	ENST00000358208.4:c.170C>T	p.Ala57Val	p.A57V	ENST00000358208		57	gCg/gTg	2/12	0.422525255415635	4	FACETS	0.973	0.917	1	0.973	0.917	1	CLONAL	3	TRUE	1	0.422525255415635	4		110	563	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967350	134967350	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs61736108	NA	P-0006757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	55	514	0	ENST00000398015.3:c.2689G>A	p.Val897Met	p.V897M	ENST00000398015	NM_004441.4	897	Gtg/Atg	14/16	1	2	FACETS	0.719	0.615	0.832	0.719	0.615	0.832	SUBCLONAL	1	FALSE	1	0.3	2		514	510	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0006765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	104	381	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.15	2		381	1271	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0006765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	107	257	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.15	2		257	984	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942166	81942166	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1915	115	577	1	ENST00000359376.3:c.1703C>A	p.Thr568Asn	p.T568N	ENST00000359376	NM_002661.3	568	aCc/aAc	17/33	1	2	FACETS	0.755	0.677	0.839	0.755	0.677	0.839	SUBCLONAL	1	TRUE	1	0.15	2		578	2030	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817489	39817489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763409220	NA	P-0006765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1384	89	411	0	ENST00000288319.7:c.74C>T	p.Thr25Met	p.T25M	ENST00000288319	NM_182918.3	25	aCg/aTg	2/10	1	2	FACETS	0.806	0.711	0.907	0.806	0.711	0.907	CLONAL	1	TRUE	1	0.15	2		411	1473	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0006783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	43	379	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.73	0.61	0.864	0.73	0.61	0.864	SUBCLONAL	1	TRUE	1	0.19	2		379	620	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057002	180057002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	67	475	1	ENST00000261937.6:c.617G>A	p.Cys206Tyr	p.C206Y	ENST00000261937	NM_182925.4	206	tGc/tAc	5/30	1	2	FACETS	0.742	0.643	0.85	0.742	0.643	0.85	SUBCLONAL	1	TRUE	1	0.19	2		476	950	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340378	8340378	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	67	420	0	ENST00000356435.5:c.5218G>T	p.Val1740Phe	p.V1740F	ENST00000356435		1740	Gtt/Ttt	31/35	1	2	FACETS	0.83	0.719	0.95	0.83	0.719	0.95	CLONAL	1	TRUE	1	0.19	2		420	850	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111447	8111447	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	75	375	1	ENST00000346208.3:c.933G>T	p.Arg311Ser	p.R311S	ENST00000346208		311	agG/agT	5/6	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.19	2		376	786	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619416	1619416	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	89	441	1	ENST00000344749.5:c.1225G>T	p.Val409Leu	p.V409L	ENST00000344749	NM_001136139.2	409	Gtg/Ttg	15/19	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.19	2		442	851	SUCCESS
AR	367	MSKCC	GRCh37	X	66863233	66863233	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	56	461	0	ENST00000374690.3:c.1752C>A	p.Phe584Leu	p.F584L	ENST00000374690	NM_000044.3	584	ttC/ttA	2/8	1	2	FACETS	0.688	0.588	0.798	0.688	0.588	0.798	SUBCLONAL	1	TRUE	1	0.19	2		461	857	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0006786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	47	213	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.44	0.372	0.514	0.44	0.372	0.514	SUBCLONAL	1	TRUE	1	0.545294955756681	2		213	392	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	123	225	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.545294955756681	2		225	437	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591116	67591116	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	121	359	2	ENST00000274335.5:c.1709T>C	p.Leu570Pro	p.L570P	ENST00000274335		570	cTt/cCt	12/15	1	2	FACETS	0.544	0.491	0.6	0.544	0.491	0.6	SUBCLONAL	1	TRUE	1	0.545294955756681	2		361	816	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556852	29556852	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0006786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	171	321	1	ENST00000356175.3:c.2851-1G>A		p.X951_splice	ENST00000356175	NM_000267.3	951			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.545294955756681	2		322	604	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419897	41419897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs577588058	NA	P-0006786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	296	428	3	ENST00000373198.4:c.424G>A	p.Val142Ile	p.V142I	ENST00000373198	NM_133170.3	142	Gtc/Atc	3/32	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.545294955756681	2		431	972	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335503	73335503	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs373059317	NA	P-0006804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	226	398	0	ENST00000377767.4:c.2668G>A	p.Glu890Lys	p.E890K	ENST00000377767	NM_014953.3	890	Gag/Aag	19/21	1	2	FACETS	0.992	0.93	1	0.992	0.93	1	CLONAL	1	TRUE	1	0.736178404795824	2		398	619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0006805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	126	404	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.435	0.392	0.48	0.435	0.392	0.48	SUBCLONAL	1	TRUE	1	0.466920399057744	2		405	1241	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0006805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	46	309	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.257	0.215	0.303	0.257	0.215	0.303	SUBCLONAL	1	TRUE	1	0.466920399057744	2		310	768	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0006808-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	311	249	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	NA	2	FACETS	0.908	0.86	0.956			1	INDETERMINATE	2	TRUE	NA	0.430837693013286	2		249	795	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162475188	162475188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006808-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	357	343	1	ENST00000366898.1:c.553G>A	p.Asp185Asn	p.D185N	ENST00000366898	NM_004562.2	185	Gat/Aat	5/12	0.4252475341409	3	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.430837693013286	3		344	839	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891209	101891209	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006808-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	209	308	0	ENST00000374994.4:c.170C>G	p.Ser57Cys	p.S57C	ENST00000374994	NM_004612.2	57	tCt/tGt	2/9	0.415566781489022	2	FACETS	1	0.992	1	0.744	0.694	0.795	CLONAL	1	TRUE	0	0.430837693013286	2		308	652	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657313	29657313	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0006808-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	107	216	0	ENST00000356175.3:c.5547-1G>T		p.X1849_splice	ENST00000356175	NM_000267.3	1849			0.396528852636748	2	FACETS	1	0.983	1	0.716	0.649	0.785	CLONAL	1	TRUE	0	0.430837693013286	2		216	347	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867660	78867660	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006808-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	402	350	0	ENST00000306801.3:c.2396T>A	p.Leu799His	p.L799H	ENST00000306801	NM_020761.2	799	cTc/cAc	20/34	0.430837693013286	3	FACETS	0.777	0.738	0.817	0.518	0.492	0.545	SUBCLONAL	2	TRUE	0	0.430837693013286	3		350	1459	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979283	40979283	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006808-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	270	291	0	ENST00000373198.4:c.1850G>T	p.Arg617Leu	p.R617L	ENST00000373198	NM_133170.3	617	cGg/cTg	11/32	0.189873510553398	5	FACETS	1	0.973	1	0.709	0.666	0.753	INDETERMINATE	2	TRUE	2	0.430837693013286	5		291	970	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675550	86675554	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGTTA	AGTTA	-	novel	NA	P-0006808-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	47	169	0	ENST00000274376.6:c.2489_2493del		p.X830_splice	ENST00000274376	NM_002890.2	830		19/25	0.28767724836153	2	FACETS	1	0.959	1	0.682	0.586	0.783	CLONAL	1	TRUE	0	0.430837693013286	2		169	160	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717619	89717633	+	inframe_deletion	In_Frame_Del	DEL	TTGTGGTCTGCCAGC	TTGTGGTCTGCCAGC	-	novel	NA	P-0006808-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	216	214	0	ENST00000371953.3:c.645_659del	p.Phe215_Gln219del	p.F215_Q219del	ENST00000371953	NM_000314.4	215	tTTGTGGTCTGCCAGCta/tta	7/9	0.339427020454262	3	FACETS	1	0.989	1	0.817	0.768	0.867	CLONAL	2	TRUE	0	0.430837693013286	3		214	497	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	94	543	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	0.815	0.727	0.908			1	INDETERMINATE	1	TRUE	NA	0.417934734050676	2		543	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0006821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	82	440	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	1	2	FACETS	0.66	0.582	0.742	0.66	0.582	0.742	SUBCLONAL	1	TRUE	1	0.417934734050676	2		440	595	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0006821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	86	292	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.299540622930744	2	FACETS	1	0.963	1	0.595	0.53	0.662	CLONAL	1	TRUE	0	0.417934734050676	2		292	346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876659675	NA	P-0006821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	171	513	1	ENST00000269305.4:c.764T>A	p.Ile255Asn	p.I255N	ENST00000269305	NM_001126112.2	255	aTc/aAc	7/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.417934734050676	2		514	623	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436039	116436039	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs768188910	NA	P-0006821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	283	547	2	ENST00000397752.3:c.4034T>C	p.Ile1345Thr	p.I1345T	ENST00000397752	NM_000245.2	1345	aTt/aCt	21/21	0.128827139589502	5	FACETS	1	0.983	1	0.743	0.699	0.788	INDETERMINATE	2	TRUE	2	0.417934734050676	5		549	989	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961502	54961502	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006821-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	53	370	0	ENST00000312783.6:c.130G>T	p.Ala44Ser	p.A44S	ENST00000312783	NM_198436.1	44	Gct/Tct	4/10	0.369967189751047	3	FACETS	0.399	0.339	0.465			1	SUBCLONAL	1	TRUE	NA	0.417934734050676	3		370	768	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0006844-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	217	478	5	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.170629870797406	4	FACETS	1	0.969	1	0.717	0.665	0.77	CLONAL	2	FALSE	1	0.207422940699557	4		483	1175	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221123	5221123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769925793	NA	P-0006844-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	65	408	0	ENST00000357368.4:c.3343G>A	p.Ala1115Thr	p.A1115T	ENST00000357368	NM_002850.3	1115	Gcc/Acc	20/38	0.203814118244647	1	FACETS	0.722	0.625	0.828	0.722	0.625	0.828	SUBCLONAL	1	FALSE	0	0.207422940699557	1		408	778	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576863	7576863	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006844-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	141	415	0	ENST00000269305.4:c.983del	p.Phe328SerfsTer17	p.F328Sfs*17	ENST00000269305	NM_001126112.2	328	tTc/tc	9/11	0.203814118244647	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	0	0.207422940699557	1		415	964	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850272	128850272	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs777204354	NA	P-0006844-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1311	126	477	2	ENST00000249373.3:c.1535G>T	p.Arg512Leu	p.R512L	ENST00000249373	NM_005631.4	512	cGc/cTc	9/12	0.170629870797406	4	FACETS	1	0.919	1	0.34	0.307	0.376	CLONAL	1	FALSE	1	0.207422940699557	4		479	1437	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687512	29687512	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006844-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	46	403	0	ENST00000356175.3:c.8105A>G	p.Gln2702Arg	p.Q2702R	ENST00000356175	NM_000267.3	2702	cAa/cGa	56/57	0.158020237332913	3	FACETS	0.547	0.459	0.645	0.182	0.153	0.215	SUBCLONAL	1	FALSE	0	0.207422940699557	3		403	895	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21304092	21304092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1001709647	NA	P-0006844-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	102	520	0	ENST00000354336.3:c.871G>A	p.Val291Ile	p.V291I	ENST00000354336	NM_005207.3	291	Gtc/Atc	3/3	1	2	FACETS	0.859	0.766	0.958	0.859	0.766	0.958	CLONAL	1	FALSE	1	0.207422940699557	2		520	1145	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461167	120461167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs983208690	NA	P-0006844-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	58	342	0	ENST00000256646.2:c.5791C>T	p.Arg1931Cys	p.R1931C	ENST00000256646	NM_024408.3	1931	Cgc/Tgc	32/34	1	2	FACETS	0.685	0.587	0.792	0.685	0.587	0.792	SUBCLONAL	1	FALSE	1	0.207422940699557	2		342	817	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	89	225	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.983	0.882	1			1	INDETERMINATE	1	TRUE	NA	0.613628689880979	2		225	295	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0006846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20374	555	409	0	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.613628689880979	37	FACETS	1	0.963	1			1	CLONAL	1	TRUE	NA	0.613628689880979	37		409	20929	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344009	70344009	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs772155788	NA	P-0006846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	279	529	0	ENST00000374080.3:c.1745C>T	p.Thr582Met	p.T582M	ENST00000374080		582	aCg/aTg	13/45	1	2	FACETS	0.894	0.841	0.949	0.894	0.841	0.949	CLONAL	1	TRUE	1	0.613628689880979	2		529	1017	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223587	55223587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14073	11014	369	5	ENST00000275493.2:c.954G>A	p.Met318Ile	p.M318I	ENST00000275493	NM_005228.3	318	atG/atA	8/28	0.613628689880979	37	FACETS	0.988	0.979	0.997			1	CLONAL	17	TRUE	NA	0.613628689880979	37		374	25087	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791986	42791986	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006846-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	231	431	0	ENST00000575354.2:c.790C>A	p.His264Asn	p.H264N	ENST00000575354	NM_015125.3	264	Cac/Aac	6/20	0.59797071161254	3	FACETS	0.942	0.879	1	0.471	0.439	0.504	CLONAL	1	TRUE	1	0.613628689880979	3		431	1044	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	97	225	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.945	1			1	INDETERMINATE	1	TRUE	NA	0.522252182092909	2		225	346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0006848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	346	422	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.499812012606856	2	FACETS	0.871	0.83	0.912	0.871	0.83	0.912	CLONAL	2	TRUE	0	0.522252182092909	2		422	761	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999579	100999579	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs147067970	NA	P-0006848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	62	618	3	ENST00000325455.5:c.223C>A	p.Gln75Lys	p.Q75K	ENST00000325455	NM_001202474.3	75	Cag/Aag	1/8	0.522252182092909	1	FACETS	0.18	0.155	0.208	0.18	0.155	0.208	SUBCLONAL	1	TRUE	0	0.522252182092909	1		621	973	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684326	29684326	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201367	NA	P-0006848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	430	463	0	ENST00000356175.3:c.7846C>T	p.Arg2616Ter	p.R2616*	ENST00000356175	NM_000267.3	2616	Cga/Tga	53/57	0.499812012606856	2	FACETS	0.874	0.837	0.911	0.874	0.837	0.911	CLONAL	2	TRUE	0	0.522252182092909	2		463	942	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717663	89717663	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554825186	NA	P-0006848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	275	398	0	ENST00000371953.3:c.688G>T	p.Gly230Ter	p.G230*	ENST00000371953	NM_000314.4	230	Gga/Tga	7/9	0.522252182092909	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.522252182092909	1		398	728	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345319	70345319	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	78	476	2	ENST00000374080.3:c.2345T>C	p.Leu782Pro	p.L782P	ENST00000374080		782	cTg/cCg	16/45	1	2	FACETS	0.251	0.22	0.286	0.251	0.22	0.286	SUBCLONAL	1	TRUE	1	0.522252182092909	2		478	1188	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456495	189456498	+	frameshift_variant	Frame_Shift_Del	DEL	ACAA	ACAA	-	novel	NA	P-0006848-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	244	466	0	ENST00000264731.3:c.260_263del	p.Asn87ArgfsTer16	p.N87Rfs*16	ENST00000264731	NM_003722.4	86	ACAAac/ac	3/14	1	2	FACETS	0.819	0.765	0.875	0.819	0.765	0.875	CLONAL	1	TRUE	1	0.522252182092909	2		466	1141	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913492	NA	P-0006850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	174	323	0	ENST00000286548.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000286548	NM_002072.3	209	cAa/cTa	5/7	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.584764164531601	2		323	452	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0006858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	25	213	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.546	0.431	0.679	0.546	0.431	0.679	SUBCLONAL	1	TRUE	1	0.27	2		213	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	151	202	0	ENST00000269305.4:c.528C>A	p.Cys176Ter	p.C176*	ENST00000269305	NM_001126112.2	176	tgC/tgA	5/11	0.496617201692033	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.496617201692033	1		202	403	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985451	2985451	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0006864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	67	234	0	ENST00000396946.4:c.358+2T>C		p.X120_splice	ENST00000396946	NM_032415.4	120			0.464176153820962	4	FACETS	0.34	0.294	0.39	0.113	0.098	0.13	SUBCLONAL	1	TRUE	1	0.496617201692033	4		234	1189	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0006880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	273	399	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.281575440427859	2	FACETS	0.957	0.9	1	0.957	0.9	1	CLONAL	2	TRUE	0	0.319217496913476	2		399	894	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205052	128205052	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	83	423	0	ENST00000341105.2:c.389C>A	p.Ala130Asp	p.A130D	ENST00000341105	NM_032638.4	130	gCt/gAt	3/6	0.185005477880869	4	FACETS	0.655	0.577	0.74	0.328	0.288	0.37	INDETERMINATE	1	TRUE	2	0.319217496913476	4		423	1047	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670720	134670720	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	113	377	0	ENST00000398015.3:c.631A>G	p.Thr211Ala	p.T211A	ENST00000398015	NM_004441.4	211	Aca/Gca	3/16	0.185005477880869	4	FACETS	1	0.959	1	0.563	0.506	0.623	INDETERMINATE	1	TRUE	2	0.319217496913476	4		377	830	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633631	69633631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554981422	NA	P-0006880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	55	63	0	ENST00000334134.2:c.71G>A	p.Arg24Gln	p.R24Q	ENST00000334134	NM_005247.2	24	cGg/cAg	1/3	0.319217496913476	12	FACETS	0.898	0.776	1			1	CLONAL	4	TRUE	NA	0.319217496913476	12		63	249	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412637	63412637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779222316	NA	P-0006880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	196	470	0	ENST00000330258.3:c.530G>A	p.Arg177His	p.R177H	ENST00000330258	NM_152424.3	177	cGc/cAc	2/2	0.277534974092456	2	FACETS	0.847	0.787	0.909	0.847	0.787	0.909	CLONAL	2	TRUE	0	0.319217496913476	2		470	725	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0006883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	399	342	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	0.421781343026767	4	FACETS	0.966	0.923	1	0.725	0.692	0.758	CLONAL	3	TRUE	0	0.421781343026767	4		342	928	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-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	113	291	0	ENST00000269305.4:c.991_993+4del		p.X331_splice	ENST00000269305	NM_001126112.2	331		9/11	0.283966178997756	1	FACETS	0.76	0.687	0.838	0.76	0.687	0.838	SUBCLONAL	1	TRUE	0	0.421781343026767	1		291	556	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782144	NA	P-0006892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	639	451	0	ENST00000269305.4:c.473G>C	p.Arg158Pro	p.R158P	ENST00000269305	NM_001126112.2	158	cGc/cCc	5/11	0.766769174397717	3	FACETS	0.968	0.947	0.988	0.968	0.947	0.988	CLONAL	3	TRUE	0	0.766769174397717	3		451	794	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673595	30673595	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	359	881	0	ENST00000376406.3:c.3365C>G	p.Ser1122Cys	p.S1122C	ENST00000376406	NM_014641.2	1122	tCt/tGt	10/15	0.766769174397717	3	FACETS	0.929	0.879	0.979	0.464	0.439	0.49	CLONAL	1	TRUE	1	0.766769174397717	3		881	1395	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047227	77047227	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	261	563	0	ENST00000356341.3:c.1317G>C	p.Lys439Asn	p.K439N	ENST00000356341	NM_002576.4	439	aaG/aaC	13/15	NA	2	FACETS	0.974	0.918	1			1	INDETERMINATE	1	TRUE	NA	0.766769174397717	2		563	699	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350779	89350779	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1567578679	NA	P-0006919-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	69	689	0	ENST00000301030.4:c.2171C>A	p.Thr724Lys	p.T724K	ENST00000301030	NM_001256183.1	724	aCa/aAa	9/13	0.387646433395607	1	FACETS	0.238	0.206	0.272	0.238	0.206	0.272	SUBCLONAL	1	TRUE	0	0.387646433395607	1		689	1208	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0006948-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	189	531	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.217826903809933	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.280761384079223	1		531	1013	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467946	66467946	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs767139493	NA	P-0006948-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	70	448	0	ENST00000273854.3:c.323A>T	p.Asn108Ile	p.N108I	ENST00000273854	NM_004439.5	108	aAt/aTt	3/18	1	2	FACETS	0.516	0.448	0.589	0.516	0.448	0.589	SUBCLONAL	1	TRUE	1	0.280761384079223	2		448	967	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372244	55372244	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006948-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	20	182	0	ENST00000297316.4:c.934C>G	p.Gln312Glu	p.Q312E	ENST00000297316	NM_022454.3	312	Cag/Gag	2/2	1	2	FACETS	0.366	0.279	0.468	0.366	0.279	0.468	SUBCLONAL	1	TRUE	1	0.280761384079223	2		182	389	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0006954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	75	641	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.465	0.407	0.528	0.465	0.407	0.528	SUBCLONAL	1	TRUE	1	0.3898549579399	2		641	827	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497358	149497358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35731372	NA	P-0006954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	108	540	0	ENST00000261799.4:c.2960G>A	p.Arg987Gln	p.R987Q	ENST00000261799	NM_002609.3	987	cGg/cAg	22/23	1	2	FACETS	0.841	0.756	0.931	0.841	0.756	0.931	CLONAL	1	TRUE	1	0.3898549579399	2		540	659	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878948	151878948	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	86	482	0	ENST00000262189.6:c.5997A>G	p.Ile1999Met	p.I1999M	ENST00000262189	NM_170606.2	1999	atA/atG	36/59	1	2	FACETS	0.729	0.646	0.818	0.729	0.646	0.818	SUBCLONAL	1	TRUE	1	0.3898549579399	2		482	605	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431971	121431971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	103	493	0	ENST00000257555.6:c.718G>A	p.Glu240Lys	p.E240K	ENST00000257555		240	Gaa/Aaa	4/10	1	2	FACETS	0.755	0.676	0.839	0.755	0.676	0.839	SUBCLONAL	1	TRUE	1	0.3898549579399	2		493	700	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916266	9916266	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	117	447	0	ENST00000330684.3:c.2023G>T	p.Asp675Tyr	p.D675Y	ENST00000330684	NM_001134407.1	675	Gac/Tac	10/13	1	2	FACETS	0.933	0.843	1	0.933	0.843	1	CLONAL	1	TRUE	1	0.3898549579399	2		447	643	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868282	37868282	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	66	511	1	ENST00000269571.5:c.1003A>T	p.Ser335Cys	p.S335C	ENST00000269571		335	Agc/Tgc	8/27	1	2	FACETS	0.523	0.454	0.599	0.523	0.454	0.599	SUBCLONAL	1	TRUE	1	0.3898549579399	2		512	647	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222987	1222987	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	72	338	0	ENST00000326873.7:c.924G>T	p.Trp308Cys	p.W308C	ENST00000326873	NM_000455.4	308	tgG/tgT	8/10	0.320356670510201	1	FACETS	0.757	0.664	0.855	0.757	0.664	0.855	SUBCLONAL	1	TRUE	0	0.3898549579399	1		338	393	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602370	10602370	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	143	534	0	ENST00000171111.5:c.1208G>A	p.Trp403Ter	p.W403*	ENST00000171111	NM_203500.1	403	tGg/tAg	3/6	0.320356670510201	1	FACETS	0.759	0.693	0.829	0.759	0.693	0.829	SUBCLONAL	1	TRUE	0	0.3898549579399	1		534	778	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0006964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	543	536	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.35568902713739	6	FACETS	1	0.99	1	0.861	0.828	0.894	CLONAL	4	TRUE	1	0.35568902713739	6		536	1214	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579386	7579386	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0006964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	283	678	0	ENST00000269305.4:c.301A>T	p.Lys101Ter	p.K101*	ENST00000269305	NM_001126112.2	101	Aaa/Taa	4/11	0.292914560479892	2	FACETS	0.929	0.876	0.984	0.929	0.876	0.984	CLONAL	2	TRUE	0	0.35568902713739	2		678	856	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047527	49047527	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587778850	NA	P-0006970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	53	202	0	ENST00000267163.4:c.2520+1G>A		p.X840_splice	ENST00000267163	NM_000321.2	840			0.146272242604308	3	FACETS	0.965	0.825	1	0.965	0.825	1	CLONAL	2	TRUE	1	0.146272242604308	3		202	403	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855952	76855952	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	132	219	1	ENST00000373344.5:c.5648G>A	p.Trp1883Ter	p.W1883*	ENST00000373344	NM_000489.3	1883	tGg/tAg	23/35	0.146272242604308	2	FACETS	0.901	0.822	0.982			1	CLONAL	4	TRUE	NA	0.146272242604308	2		220	501	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692874	89692874	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786204930	NA	P-0006970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	58	127	0	ENST00000371953.3:c.358G>A	p.Ala120Thr	p.A120T	ENST00000371953	NM_000314.4	120	Gca/Aca	5/9	0.146272242604308	2	FACETS	0.872	0.755	0.998	1	0.96	1	CLONAL	3	TRUE	0	0.146272242604308	2		127	303	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106767	2106767	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	117	674	0	ENST00000219476.3:c.771G>A	p.Trp257Ter	p.W257*	ENST00000219476	NM_000548.3	257	tgG/tgA	8/42	0.146272242604308	1	FACETS	0.816	0.735	0.902	1	0.986	1	CLONAL	2	TRUE	0	0.146272242604308	1		674	908	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577514	7577514	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	171	539	1	ENST00000269305.4:c.767C>A	p.Thr256Lys	p.T256K	ENST00000269305	NM_001126112.2	256	aCa/aAa	7/11	0.115834551961373	3	FACETS	1	0.982	1	0.83	0.763	0.9	CLONAL	2	TRUE	0	0.146272242604308	3		540	1008	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0006973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	140	330	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.951	0.88	1	1	0.992	1	CLONAL	2	TRUE	1	0.457015323244559	2		330	322	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0006973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	202	445	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.457015323244559	2		445	595	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0006973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	374	546	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.417738518533455	4	FACETS	0.99	0.945	1	0.99	0.945	1	CLONAL	3	TRUE	1	0.457015323244559	4		546	803	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880494	155880494	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778233462	NA	P-0006973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1533	331	577	0	ENST00000368323.3:c.59G>A	p.Arg20Gln	p.R20Q	ENST00000368323	NM_006912.5	20	cGg/cAg	2/6	0.457015323244559	8	FACETS	0.921	0.868	0.977			1	CLONAL	2	TRUE	NA	0.457015323244559	8		577	1864	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293572	1293572	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	161	477	0	ENST00000310581.5:c.1429C>T	p.Leu477Phe	p.L477F	ENST00000310581	NM_198253.2	477	Ctc/Ttc	2/16	1	2	FACETS	0.769	0.712	0.828	1	0.99	1	SUBCLONAL	2	TRUE	1	0.457015323244559	2		477	458	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830859	3830859	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	381	457	0	ENST00000262367.5:c.1697C>T	p.Ser566Phe	p.S566F	ENST00000262367	NM_004380.2	566	tCc/tTc	8/31	0.456753587096274	4	FACETS	1	0.959	1			1	CLONAL	3	TRUE	NA	0.457015323244559	4		457	807	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934606	9934606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	209	500	1	ENST00000330684.3:c.1549G>A	p.Glu517Lys	p.E517K	ENST00000330684	NM_001134407.1	517	Gaa/Aaa	7/13	0.123581953482138	5	FACETS	1	0.934	1			1	INDETERMINATE	2	TRUE	NA	0.457015323244559	5		501	768	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436145	56436145	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1194	63	597	0	ENST00000407977.2:c.992C>G	p.Ser331Cys	p.S331C	ENST00000407977		331	tCt/tGt	9/10	0.457015323244559	5	FACETS	0.37	0.318	0.426	0.123	0.106	0.142	SUBCLONAL	1	TRUE	2	0.457015323244559	5		597	1257	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56363618	56363618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	251	334	0	ENST00000348428.3:c.397C>T	p.Pro133Ser	p.P133S	ENST00000348428	NM_006785.3	133	Cca/Tca	3/17	0.457015323244559	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.457015323244559	3		334	402	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626903	14626903	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	769	773	1	ENST00000254322.2:c.872C>T	p.Pro291Leu	p.P291L	ENST00000254322	NM_006145.1	291	cCt/cTt	3/3	0.457015323244559	3	FACETS	0.929	0.901	0.956	1	0.997	1	CLONAL	3	TRUE	1	0.457015323244559	3		774	1484	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910852	114910852	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	184	769	2	ENST00000543371.1:c.973del	p.Gln325ArgfsTer26	p.Q325Rfs*26	ENST00000543371	NM_001198531.1	324	tCc/tc	9/14	0.178897610847371	3	FACETS	0.885	0.816	0.957	0.442	0.408	0.479	INDETERMINATE	1	TRUE	1	0.457015323244559	3		771	1118	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102881	71102882	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0006973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	323	477	0	ENST00000318789.4:c.325_326delinsTT	p.Pro109Phe	p.P109F	ENST00000318789	NM_032682.5	109	CCc/TTc	8/21	0.413011744565816	6	FACETS	0.881	0.837	0.925	0.881	0.837	0.925	CLONAL	4	TRUE	2	0.457015323244559	6		477	768	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0007026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	65	386	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.733	0.635	0.84	0.733	0.635	0.84	SUBCLONAL	1	TRUE	1	0.241281518703748	2		386	735	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0007026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	446	393	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.241281518703748	4	FACETS	1	0.98	1	1	0.996	1	CLONAL	4	TRUE	1	0.241281518703748	4		393	1101	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795067	242795067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	152	346	0	ENST00000334409.5:c.142G>A	p.Asp48Asn	p.D48N	ENST00000334409	NM_005018.2	48	Gac/Aac	2/5	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.241281518703748	2		346	1248	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668799	52668799	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	47	244	0	ENST00000394830.3:c.1120G>C	p.Glu374Gln	p.E374Q	ENST00000394830	NM_018313.4	374	Gaa/Caa	12/30	0.198622535785937	1	FACETS	0.451	0.379	0.53	0.451	0.379	0.53	SUBCLONAL	1	TRUE	0	0.241281518703748	1		244	760	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141523	11141523	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	64	331	0	ENST00000358026.2:c.3500C>G	p.Ser1167Trp	p.S1167W	ENST00000358026	NM_001128849.1	1167	tCg/tGg	25/36	1	2	FACETS	0.548	0.473	0.63	0.548	0.473	0.63	SUBCLONAL	1	TRUE	1	0.241281518703748	2		331	968	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035972	47035972	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1171	130	439	0	ENST00000377604.3:c.650G>A	p.Trp217Ter	p.W217*	ENST00000377604	NM_001204468.1	217	tGg/tAg	7/24	0.198622535785937	1	FACETS	0.728	0.659	0.802	0.728	0.659	0.802	SUBCLONAL	1	TRUE	0	0.241281518703748	1		439	1301	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472559	88472559	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	149	587	1	ENST00000360948.2:c.1996G>T	p.Gly666Cys	p.G666C	ENST00000360948	NM_001012338.2	666	Ggt/Tgt	16/19	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.220826474973237	2		588	1167	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220649	1220649	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	114	483	0	ENST00000326873.7:c.667G>T	p.Glu223Ter	p.E223*	ENST00000326873	NM_000455.4	223	Gag/Tag	5/10	0.220826474973237	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.220826474973237	1		483	825	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602354	10602354	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	264	585	0	ENST00000171111.5:c.1224del	p.Met409Ter	p.M409*	ENST00000171111	NM_203500.1	408	ccC/cc	3/6	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	2	TRUE	NA	0.220826474973237	2		585	1107	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285249	212285249	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	80	398	1	ENST00000342788.4:c.3052G>T	p.Asp1018Tyr	p.D1018Y	ENST00000342788	NM_005235.2	1018	Gat/Tat	25/28	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.220826474973237	2		399	588	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950233	38950233	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	21	277	0	ENST00000357387.3:c.3717G>C	p.Glu1239Asp	p.E1239D	ENST00000357387	NM_152756.3	1239	gaG/gaC	31/38	0.112027680618988	4	FACETS	0.572	0.439	0.727	0.286	0.219	0.364	INDETERMINATE	1	TRUE	2	0.220826474973237	4		277	406	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38957801	38957801	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	56	330	0	ENST00000357387.3:c.2452C>G	p.Leu818Val	p.L818V	ENST00000357387	NM_152756.3	818	Ctg/Gtg	25/38	0.112027680618988	4	FACETS	0.765	0.654	0.888	0.383	0.327	0.444	INDETERMINATE	1	TRUE	2	0.220826474973237	4		330	809	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629138	86629138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	59	329	0	ENST00000274376.6:c.883G>A	p.Asp295Asn	p.D295N	ENST00000274376	NM_002890.2	295	Gac/Aac	4/25	0.168586925053473	1	FACETS	0.945	0.814	1	0.945	0.814	1	CLONAL	1	TRUE	0	0.220826474973237	1		329	503	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158692	26158692	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	10	48	0	ENST00000289316.2:c.295G>A	p.Val99Met	p.V99M	ENST00000289316	NM_138720.2	99	Gtg/Atg	1/2	1	2	FACETS	0.974	0.666	1	0.974	0.666	1	CLONAL	1	TRUE	1	0.220826474973237	2		48	93	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878241	151878241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	91	394	1	ENST00000262189.6:c.6704G>A	p.Arg2235Lys	p.R2235K	ENST00000262189	NM_170606.2	2235	aGg/aAg	36/59	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.220826474973237	2		395	811	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608325	28608325	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	52	389	0	ENST00000241453.7:c.1731G>C	p.Gln577His	p.Q577H	ENST00000241453	NM_004119.2	577	caG/caC	14/24	0.220826474973237	1	FACETS	0.533	0.453	0.622	0.533	0.453	0.622	SUBCLONAL	1	TRUE	0	0.220826474973237	1		389	786	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89851291	89851291	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	315	612	0	ENST00000389301.3:c.1441G>T	p.Val481Leu	p.V481L	ENST00000389301	NM_000135.2	481	Gtg/Ttg	15/43	0.214303858963592	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.220826474973237	2		612	1259	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257435	19257435	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	184	589	0	ENST00000162023.5:c.698A>T	p.Gln233Leu	p.Q233L	ENST00000162023		233	cAg/cTg	11/13	0.220826474973237	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.220826474973237	1		589	1113	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272078	142272078	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	46	262	0	ENST00000350721.4:c.2796del	p.Ile933SerfsTer6	p.I933Sfs*6	ENST00000350721	NM_001184.3	932	ccC/cc	13/47	1	2	FACETS	0.9	0.758	1	0.9	0.758	1	CLONAL	1	TRUE	1	0.220826474973237	2		262	463	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578471	7578471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	267	444	0	ENST00000269305.4:c.459del	p.Gly154AlafsTer16	p.G154Afs*16	ENST00000269305	NM_001126112.2	153	ccC/cc	5/11	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.220826474973237	2		444	987	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0007045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	161	213	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.362743531938639	6	FACETS	1	0.961	1	1	0.961	1	CLONAL	3	TRUE	3	0.591298847093208	6		213	377	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256550	115256550	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	123	352	0	ENST00000369535.4:c.161A>G	p.Asp54Gly	p.D54G	ENST00000369535	NM_002524.4	54	gAc/gGc	3/7	0.468203863126311	4	FACETS	0.676	0.61	0.745	0.338	0.305	0.373	SUBCLONAL	1	TRUE	2	0.591298847093208	4		352	980	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593545	215593545	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	207	305	0	ENST00000260947.4:c.2189A>T	p.Gln730Leu	p.Q730L	ENST00000260947	NM_000465.2	730	cAg/cTg	11/11	0.591298847093208	3	FACETS	1	0.984	1	0.594	0.552	0.636	CLONAL	1	TRUE	1	0.591298847093208	3		305	764	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95577791	95577791	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	220	481	1	ENST00000393063.1:c.2119G>T	p.Glu707Ter	p.E707*	ENST00000393063	NM_030621.3	707	Gaa/Taa	15/28	0.591298847093208	3	FACETS	0.997	0.928	1	0.499	0.464	0.534	CLONAL	1	TRUE	1	0.591298847093208	3		482	967	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654569	29654569	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1316	218	366	0	ENST00000356175.3:c.5258G>A	p.Gly1753Glu	p.G1753E	ENST00000356175	NM_000267.3	1753	gGg/gAg	37/57	0.591298847093208	5	FACETS	0.907	0.841	0.976			1	CLONAL	1	TRUE	NA	0.591298847093208	5		366	1534	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618489	37618489	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3118	1448	412	0	ENST00000447079.4:c.165G>C	p.Leu55Phe	p.L55F	ENST00000447079	NM_015083.1	55	ttG/ttC	1/14	0.591298847093208	14	FACETS	0.976	0.95	1			1	CLONAL	5	TRUE	NA	0.591298847093208	14		412	4566	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817802	3817809	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTCACT	CTTTCACT	-	novel	NA	P-0007045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1574	191	510	1	ENST00000262367.5:c.3162_3169del	p.Glu1054AspfsTer4	p.E1054Dfs*4	ENST00000262367	NM_004380.2	1054	gaAGTGAAAGta/gata	16/31	0.591298847093208	4	FACETS	0.582	0.536	0.631	0.194	0.178	0.211	SUBCLONAL	1	TRUE	1	0.591298847093208	4		511	1765	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579438	7579439	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	rs1131691010	NA	P-0007045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	424	391	0	ENST00000269305.4:c.248_249del	p.Ala83GlyfsTer65	p.A83Gfs*65	ENST00000269305	NM_001126112.2	83	gCG/g	4/11	0.591298847093208	2	FACETS	0.978	0.941	1	0.978	0.941	1	CLONAL	2	TRUE	0	0.591298847093208	2		391	733	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519988	NA	P-0007054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	264	480	0	ENST00000269305.4:c.808T>G	p.Phe270Val	p.F270V	ENST00000269305	NM_001126112.2	270	Ttt/Gtt	8/11	0.273491359561991	2	FACETS	0.965	0.91	1	1	0.993	1	CLONAL	3	TRUE	0	0.273491359561991	2		480	667	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880219	37880220	+	missense_variant	Missense_Mutation	DNP	TT	TT	GC	novel	NA	P-0007054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	240	604	1	ENST00000269571.5:c.2263_2264delinsGC	p.Leu755Ala	p.L755A	ENST00000269571		755	TTg/GCg	19/27	0.245291325048872	3	FACETS	0.941	0.883	1			1	CLONAL	3	TRUE	NA	0.273491359561991	3		605	707	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0007061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	87	186	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.217429912771993	2		186	595	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442095	52442095	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0007061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	158	231	2	ENST00000460680.1:c.256-2A>T		p.X86_splice	ENST00000460680	NM_004656.3	86			0.217429912771993	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	FALSE	0	0.217429912771993	2		233	713	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509541	46509541	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	38	222	0	ENST00000262741.5:c.1190C>T	p.Ala397Val	p.A397V	ENST00000262741	NM_003629.3	397	gCc/gTc	10/10	1	2	FACETS	0.259	0.214	0.311	0.259	0.214	0.311	SUBCLONAL	1	TRUE	1	0.437400447296114	2		222	670	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521483	46521483	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs968243629	NA	P-0007068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1255	104	426	2	ENST00000262741.5:c.925C>T	p.Arg309Ter	p.R309*	ENST00000262741	NM_003629.3	309	Cga/Tga	7/10	1	2	FACETS	0.35	0.312	0.391	0.35	0.312	0.391	SUBCLONAL	1	TRUE	1	0.437400447296114	2		428	1359	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140756	55140756	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	139	341	0	ENST00000257290.5:c.1617C>G	p.Ile539Met	p.I539M	ENST00000257290	NM_006206.4	539	atC/atG	11/23	0.231395414370169	1	FACETS	0.577	0.525	0.632	0.577	0.525	0.632	INDETERMINATE	1	TRUE	0	0.437400447296114	1		341	860	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659321	86659321	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	207	299	1	ENST00000274376.6:c.1610G>T	p.Arg537Met	p.R537M	ENST00000274376	NM_002890.2	537	aGg/aTg	11/25	0.437400447296114	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.437400447296114	1		300	651	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8733827	8733827	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	186	333	0	ENST00000356435.5:c.17G>T	p.Arg6Met	p.R6M	ENST00000356435		6	aGg/aTg	1/35	0.437400447296114	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.437400447296114	1		333	634	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129400	64129400	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	383	329	3	ENST00000334205.4:c.832T>A	p.Cys278Ser	p.C278S	ENST00000334205	NM_003942.2	278	Tgt/Agt	8/17	0.186099679884865	2	FACETS	0.899	0.857	0.942	0.899	0.857	0.942	INDETERMINATE	2	TRUE	0	0.437400447296114	2		332	974	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420065	420065	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	288	353	0	ENST00000399788.2:c.3202C>G	p.His1068Asp	p.H1068D	ENST00000399788	NM_001042603.1	1068	Cat/Gat	21/28	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.437400447296114	2		353	1175	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577138	7577138	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587780075	NA	P-0007068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	400	395	0	ENST00000269305.4:c.800G>C	p.Arg267Pro	p.R267P	ENST00000269305	NM_001126112.2	267	cGg/cCg	8/11	0.346913190408566	2	FACETS	0.916	0.874	0.959	0.916	0.874	0.959	CLONAL	2	TRUE	0	0.437400447296114	2		395	998	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411990	63411990	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	278	258	0	ENST00000330258.3:c.1177G>C	p.Glu393Gln	p.E393Q	ENST00000330258	NM_152424.3	393	Gaa/Caa	2/2	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.437400447296114	1		258	675	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007070-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	78	301	1	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	0.325830652502178	2	FACETS	1	0.976	1	0.721	0.639	0.808	CLONAL	1	TRUE	0	0.325830652502178	2		302	332	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325170	123325170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371358242	NA	P-0007070-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	79	326	0	ENST00000358487.5:c.158C>T	p.Ala53Val	p.A53V	ENST00000358487	NM_000141.4	53	gCg/gTg	3/18	1	2	FACETS	0.794	0.699	0.896	0.794	0.699	0.896	SUBCLONAL	1	TRUE	1	0.325830652502178	2		326	611	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs863224499	NA	P-0007070-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	229	495	2	ENST00000269305.4:c.672+1G>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.27021915913144	3	FACETS	1	0.966	1	0.701	0.656	0.748	CLONAL	2	TRUE	0	0.325830652502178	3		497	777	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867303	45867303	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776223836	NA	P-0007070-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	150	209	0	ENST00000391945.4:c.890C>T	p.Ala297Val	p.A297V	ENST00000391945	NM_000400.3	297	gCc/gTc	10/23	0.325830652502178	4	FACETS	0.879	0.806	0.956	0.879	0.806	0.956	CLONAL	2	TRUE	2	0.325830652502178	4		209	694	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	60	225	0				ENST00000310581	NM_198253.2	-/1132			0.329897627703371	4	FACETS	0.845	0.735	0.963	0.845	0.735	0.963	CLONAL	2	TRUE	2	0.348031180685428	4		225	275	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230707	46230707	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	241	384	0	ENST00000334344.6:c.956C>T	p.Ser319Phe	p.S319F	ENST00000334344	NM_152641.2	319	tCt/tTt	8/21	0.311210138245924	4	FACETS	0.993	0.929	1			1	CLONAL	2	TRUE	NA	0.348031180685428	4		384	940	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023323	33023323	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1216	236	539	1	ENST00000300177.4:c.432C>G	p.Cys144Trp	p.C144W	ENST00000300177	NM_001191322.1	144	tgC/tgG	2/2	0.320679105347844	3	FACETS	1	0.975	1	0.548	0.51	0.588	CLONAL	1	TRUE	1	0.348031180685428	3		540	1452	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831239	3831239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	130	320	0	ENST00000262367.5:c.1642G>A	p.Glu548Lys	p.E548K	ENST00000262367	NM_004380.2	548	Gaa/Aaa	7/31	0.348031180685428	3	FACETS	1	0.912	1	0.503	0.456	0.553	CLONAL	1	TRUE	1	0.348031180685428	3		320	872	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0007071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	244	293	0	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	0.161404268487656	3	FACETS	1	0.962	1			1	INDETERMINATE	3	TRUE	NA	0.348031180685428	3		293	536	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610405	10610405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	199	354	0	ENST00000171111.5:c.305C>T	p.Ser102Leu	p.S102L	ENST00000171111	NM_203500.1	102	tCa/tTa	2/6	0.348031180685428	2	FACETS	0.948	0.884	1	0.948	0.884	1	CLONAL	2	TRUE	0	0.348031180685428	2		354	603	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354945	70354945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	91	413	0	ENST00000374080.3:c.4867G>C	p.Glu1623Gln	p.E1623Q	ENST00000374080		1623	Gag/Cag	36/45	0.348031180685428	3	FACETS	0.741	0.657	0.83	0.37	0.328	0.415	SUBCLONAL	1	TRUE	1	0.348031180685428	3		413	829	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	26	386	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	0.119	0.093	0.148			1	INDETERMINATE	1	TRUE	NA	0.59015752410557	2		386	742	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073422	8073422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1462	394	610	1	ENST00000377482.5:c.1237G>A	p.Glu413Lys	p.E413K	ENST00000377482	NM_018948.3	413	Gaa/Aaa	4/4	0.59015752410557	2	FACETS	0.719	0.682	0.758	0.36	0.341	0.379	SUBCLONAL	1	TRUE	0	0.59015752410557	2		611	1856	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777652	9777652	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	52	347	0	ENST00000377346.4:c.988G>A	p.Gly330Ser	p.G330S	ENST00000377346	NM_005026.3	330	Ggc/Agc	8/24	0.59015752410557	2	FACETS	0.186	0.157	0.217	0.093	0.078	0.109	SUBCLONAL	1	TRUE	0	0.59015752410557	2		347	948	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11181324	11181324	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	213	316	0	ENST00000361445.4:c.6912G>A	p.Trp2304Ter	p.W2304*	ENST00000361445	NM_004958.3	2304	tgG/tgA	49/58	0.59015752410557	2	FACETS	0.718	0.667	0.771	0.359	0.333	0.386	SUBCLONAL	1	TRUE	0	0.59015752410557	2		316	1005	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182065	11182065	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	255	284	0	ENST00000361445.4:c.6781C>T	p.Leu2261Phe	p.L2261F	ENST00000361445	NM_004958.3	2261	Ctc/Ttc	48/58	0.59015752410557	2	FACETS	0.874	0.819	0.931	0.437	0.409	0.466	CLONAL	1	TRUE	0	0.59015752410557	2		284	989	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254590	16254590	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1192	98	456	0	ENST00000375759.3:c.1855G>A	p.Glu619Lys	p.E619K	ENST00000375759	NM_015001.2	619	Gaa/Aaa	11/15	0.59015752410557	2	FACETS	0.257	0.229	0.288	0.129	0.114	0.144	SUBCLONAL	1	TRUE	0	0.59015752410557	2		456	1290	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263913	16263913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1486750640	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	239	366	0	ENST00000375759.3:c.10282C>T	p.Pro3428Ser	p.P3428S	ENST00000375759	NM_015001.2	3428	Ccg/Tcg	12/15	0.59015752410557	2	FACETS	0.7	0.653	0.749	0.35	0.326	0.375	SUBCLONAL	1	TRUE	0	0.59015752410557	2		366	1157	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100115	27100115	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs947871708	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	278	328	0	ENST00000324856.7:c.3911C>T	p.Ala1304Val	p.A1304V	ENST00000324856	NM_006015.4	1304	gCc/gTc	16/20	0.59015752410557	2	FACETS	0.839	0.788	0.892	0.419	0.394	0.446	CLONAL	1	TRUE	0	0.59015752410557	2		328	1123	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932200	36932200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1254567031	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	324	463	0	ENST00000361632.4:c.2269G>A	p.Gly757Ser	p.G757S	ENST00000361632		757	Ggc/Agc	16/16	NA	2	FACETS	0.816	0.769	0.863			1	INDETERMINATE	1	TRUE	NA	0.59015752410557	2		463	1346	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46543281	46543281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	196	382	0	ENST00000262741.5:c.220G>A	p.Glu74Lys	p.E74K	ENST00000262741	NM_003629.3	74	Gag/Aag	3/10	0.59015752410557	2	FACETS	0.605	0.559	0.652	0.302	0.279	0.326	SUBCLONAL	1	TRUE	0	0.59015752410557	2		382	1098	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247782	59247782	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	356	492	2	ENST00000371222.2:c.961C>T	p.Gln321Ter	p.Q321*	ENST00000371222	NM_002228.3	321	Caa/Taa	1/1	0.59015752410557	2	FACETS	0.795	0.752	0.84	0.398	0.376	0.42	SUBCLONAL	1	TRUE	0	0.59015752410557	2		494	1517	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325897	65325897	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	230	248	1	ENST00000342505.4:c.1225G>A	p.Val409Ile	p.V409I	ENST00000342505	NM_002227.2	409	Gta/Ata	9/25	0.59015752410557	2	FACETS	0.769	0.717	0.822	0.384	0.358	0.412	SUBCLONAL	1	TRUE	0	0.59015752410557	2		249	1014	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434595	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	75	298	0	ENST00000369535.4:c.37G>A	p.Gly13Ser	p.G13S	ENST00000369535	NM_002524.4	13	Ggt/Agt	2/7	0.59015752410557	2	FACETS	0.256	0.224	0.292	0.128	0.112	0.146	SUBCLONAL	1	TRUE	0	0.59015752410557	2		298	992	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695712	117695712	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	207	437	1	ENST00000369458.3:c.724+1G>A		p.X242_splice	ENST00000369458	NM_024626.3	242			0.59015752410557	2	FACETS	0.666	0.618	0.716	0.333	0.309	0.358	SUBCLONAL	1	TRUE	0	0.59015752410557	2		438	1053	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551831	150551831	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	66	83	0	ENST00000369026.2:c.176G>A	p.Gly59Glu	p.G59E	ENST00000369026	NM_021960.4	59	gGa/gAa	1/3	0.59015752410557	2	FACETS	0.844	0.741	0.953	0.422	0.37	0.477	CLONAL	1	TRUE	0	0.59015752410557	2		83	265	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731226	162731226	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	66	274	0	ENST00000367921.3:c.1081G>A	p.Glu361Lys	p.E361K	ENST00000367921	NM_006182.2	361	Gag/Aag	9/18	0.59015752410557	2	FACETS	0.236	0.204	0.271	0.118	0.102	0.136	SUBCLONAL	1	TRUE	0	0.59015752410557	2		274	946	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658574	206658574	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	75	294	0	ENST00000367120.3:c.1547C>T	p.Thr516Ile	p.T516I	ENST00000367120	NM_014002.3	516	aCc/aTc	15/22	0.59015752410557	2	FACETS	0.244	0.213	0.278	0.122	0.106	0.139	SUBCLONAL	1	TRUE	0	0.59015752410557	2		294	1041	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253472	226253472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	40	175	0	ENST00000366813.1:c.244G>A	p.Asp82Asn	p.D82N	ENST00000366813		82	Gat/Aat	2/3	0.59015752410557	2	FACETS	0.231	0.191	0.275	0.115	0.095	0.138	SUBCLONAL	1	TRUE	0	0.59015752410557	2		175	587	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675293	241675293	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	260	364	0	ENST00000366560.3:c.529C>T	p.Pro177Ser	p.P177S	ENST00000366560	NM_000143.3	177	Ccc/Tcc	4/10	0.59015752410557	2	FACETS	0.764	0.715	0.815	0.382	0.357	0.408	SUBCLONAL	1	TRUE	0	0.59015752410557	2		364	1153	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085638	16085638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	73	266	0	ENST00000281043.3:c.814G>A	p.Asp272Asn	p.D272N	ENST00000281043	NM_005378.4	272	Gat/Aat	3/3	0.59015752410557	2	FACETS	0.274	0.239	0.312	0.137	0.119	0.156	SUBCLONAL	1	TRUE	0	0.59015752410557	2		266	902	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25462035	25462035	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	85	341	0	ENST00000264709.3:c.2372C>T	p.Ala791Val	p.A791V	ENST00000264709	NM_175629.2	791	gCc/gTc	20/23	0.59015752410557	2	FACETS	0.263	0.232	0.297	0.132	0.116	0.149	SUBCLONAL	1	TRUE	0	0.59015752410557	2		341	1094	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25990512	25990512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	236	394	0	ENST00000435504.4:c.715G>A	p.Glu239Lys	p.E239K	ENST00000435504		239	Gaa/Aaa	8/13	0.59015752410557	2	FACETS	0.717	0.669	0.767	0.359	0.334	0.384	SUBCLONAL	1	TRUE	0	0.59015752410557	2		394	1115	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707933	47707933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	247	349	0	ENST00000233146.2:c.2557G>A	p.Glu853Lys	p.E853K	ENST00000233146	NM_000251.2	853	Gag/Aag	15/16	0.59015752410557	2	FACETS	0.761	0.711	0.812	0.38	0.355	0.406	SUBCLONAL	1	TRUE	0	0.59015752410557	2		349	1100	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033952	48033952	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374649126	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	61	279	0	ENST00000234420.5:c.4036G>A	p.Asp1346Asn	p.D1346N	ENST00000234420	NM_000179.2	1346	Gat/Aat	10/10	0.59015752410557	2	FACETS	0.267	0.23	0.308	0.134	0.115	0.154	SUBCLONAL	1	TRUE	0	0.59015752410557	2		279	774	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721145	61721145	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	264	387	0	ENST00000401558.2:c.1129G>A	p.Ala377Thr	p.A377T	ENST00000401558	NM_003400.3	377	Gct/Act	12/25	0.59015752410557	2	FACETS	0.791	0.741	0.842	0.396	0.37	0.421	SUBCLONAL	1	TRUE	0	0.59015752410557	2		387	1131	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051163	128051163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	66	337	1	ENST00000285398.2:c.160G>A	p.Asp54Asn	p.D54N	ENST00000285398	NM_000122.1	54	Gat/Aat	2/15	0.59015752410557	2	FACETS	0.197	0.17	0.227	0.099	0.085	0.114	SUBCLONAL	1	TRUE	0	0.59015752410557	2		338	1134	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578314	212578314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	54	362	0	ENST00000342788.4:c.943G>A	p.Val315Ile	p.V315I	ENST00000342788	NM_005235.2	315	Gta/Ata	8/28	0.59015752410557	2	FACETS	0.199	0.169	0.232	0.099	0.084	0.116	SUBCLONAL	1	TRUE	0	0.59015752410557	2		362	920	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439632	220439632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	275	445	0	ENST00000243786.2:c.485C>T	p.Pro162Leu	p.P162L	ENST00000243786	NM_002191.3	162	cCc/cTc	2/2	0.59015752410557	2	FACETS	0.74	0.693	0.787	0.37	0.346	0.394	SUBCLONAL	1	TRUE	0	0.59015752410557	2		445	1260	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067228	37067228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	90	354	0	ENST00000231790.2:c.1139C>T	p.Ala380Val	p.A380V	ENST00000231790	NM_000249.3	380	gCc/gTc	12/19	0.587850199540583	2	FACETS	0.273	0.241	0.307	0.136	0.12	0.154	SUBCLONAL	1	TRUE	0	0.59015752410557	2		354	1118	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180399	38180399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1263307618	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	202	292	0	ENST00000396334.3:c.247C>T	p.Pro83Ser	p.P83S	ENST00000396334	NM_002468.4	83	Ccc/Tcc	1/5	0.587850199540583	2	FACETS	0.715	0.663	0.769	0.358	0.331	0.385	SUBCLONAL	1	TRUE	0	0.59015752410557	2		292	957	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162103	47162103	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	63	280	0	ENST00000409792.3:c.4023G>A	p.Trp1341Ter	p.W1341*	ENST00000409792	NM_014159.6	1341	tgG/tgA	3/21	0.587850199540583	2	FACETS	0.225	0.194	0.259	0.112	0.097	0.13	SUBCLONAL	1	TRUE	0	0.59015752410557	2		280	949	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162267	47162267	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	75	336	0	ENST00000409792.3:c.3859C>T	p.Gln1287Ter	p.Q1287*	ENST00000409792	NM_014159.6	1287	Cag/Tag	3/21	0.587850199540583	2	FACETS	0.225	0.196	0.256	0.112	0.098	0.128	SUBCLONAL	1	TRUE	0	0.59015752410557	2		336	1131	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428228	72428228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	66	425	0	ENST00000477973.2:c.664G>A	p.Ala222Thr	p.A222T	ENST00000477973	NM_012234.5	222	Gct/Act	3/4	0.587850199540583	2	FACETS	0.178	0.153	0.204	0.089	0.076	0.102	SUBCLONAL	1	TRUE	0	0.59015752410557	2		425	1259	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447268	187447268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	170	217	0	ENST00000232014.4:c.925G>A	p.Glu309Lys	p.E309K	ENST00000232014	NM_001130845.1	309	Gaa/Aaa	5/10	0.59015752410557	2	FACETS	0.703	0.647	0.761	0.351	0.323	0.381	SUBCLONAL	1	TRUE	0	0.59015752410557	2		217	820	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447321	187447321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746322343	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	160	217	1	ENST00000232014.4:c.872C>T	p.Ala291Val	p.A291V	ENST00000232014	NM_001130845.1	291	gCc/gTc	5/10	0.59015752410557	2	FACETS	0.749	0.688	0.812	0.374	0.344	0.406	SUBCLONAL	1	TRUE	0	0.59015752410557	2		218	724	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456471	189456471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1157	62	427	0	ENST00000264731.3:c.232G>A	p.Asp78Asn	p.D78N	ENST00000264731	NM_003722.4	78	Gat/Aat	3/14	0.59015752410557	2	FACETS	0.172	0.148	0.199	0.086	0.074	0.1	SUBCLONAL	1	TRUE	0	0.59015752410557	2		427	1219	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565892	55565892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1490	233	375	0	ENST00000288135.5:c.716C>T	p.Ser239Phe	p.S239F	ENST00000288135	NM_000222.2	239	tCt/tTt	4/21	0.543107076737482	4	FACETS	0.729	0.677	0.783	0.364	0.338	0.392	SUBCLONAL	1	TRUE	2	0.59015752410557	4		375	1723	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958882	55958882	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs762149605	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	179	262	0	ENST00000263923.4:c.2972-1G>A		p.X991_splice	ENST00000263923	NM_002253.2	991			0.543107076737482	4	FACETS	0.778	0.716	0.843	0.389	0.358	0.422	SUBCLONAL	1	TRUE	2	0.59015752410557	4		262	1240	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201797	66201797	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1436	222	290	0	ENST00000273854.3:c.2705A>T	p.Asp902Val	p.D902V	ENST00000273854	NM_004439.5	902	gAt/gTt	16/18	0.543107076737482	4	FACETS	0.722	0.669	0.776	0.361	0.334	0.388	SUBCLONAL	1	TRUE	2	0.59015752410557	4		290	1658	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467532	66467532	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1640	303	335	0	ENST00000273854.3:c.737C>T	p.Thr246Ile	p.T246I	ENST00000273854	NM_004439.5	246	aCc/aTc	3/18	0.543107076737482	4	FACETS	0.84	0.789	0.894	0.42	0.394	0.447	CLONAL	1	TRUE	2	0.59015752410557	4		335	1943	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193739	106193739	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	122	161	0	ENST00000380013.4:c.4201G>A	p.Glu1401Lys	p.E1401K	ENST00000380013	NM_001127208.2	1401	Gaa/Aaa	10/11	0.59015752410557	2	FACETS	0.73	0.663	0.801	0.365	0.331	0.401	SUBCLONAL	1	TRUE	0	0.59015752410557	2		161	566	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264595	1264595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	62	363	0	ENST00000310581.5:c.2767C>T	p.Pro923Ser	p.P923S	ENST00000310581	NM_198253.2	923	Ccg/Tcg	11/16	0.515433342863587	2	FACETS	0.178	0.153	0.206	0.089	0.076	0.103	SUBCLONAL	1	TRUE	0	0.59015752410557	2		363	1179	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294252	1294252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	32	181	1	ENST00000310581.5:c.749C>T	p.Pro250Leu	p.P250L	ENST00000310581	NM_198253.2	250	cCc/cTc	2/16	0.515433342863587	2	FACETS	0.209	0.169	0.254	0.104	0.084	0.127	SUBCLONAL	1	TRUE	0	0.59015752410557	2		182	519	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967523	38967523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	235	337	0	ENST00000357387.3:c.1067G>A	p.Gly356Glu	p.G356E	ENST00000357387	NM_152756.3	356	gGg/gAg	13/38	0.59015752410557	2	FACETS	0.8	0.747	0.855	0.4	0.373	0.428	SUBCLONAL	1	TRUE	0	0.59015752410557	2		337	995	SUCCESS
APC	324	MSKCC	GRCh37	5	112178985	112178985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	51	289	0	ENST00000257430.4:c.7694G>A	p.Arg2565Lys	p.R2565K	ENST00000257430	NM_000038.5	2565	aGa/aAa	16/16	0.59015752410557	2	FACETS	0.197	0.166	0.23	0.098	0.083	0.115	SUBCLONAL	1	TRUE	0	0.59015752410557	2		289	879	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939102	131939102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	215	417	0	ENST00000265335.6:c.2318C>T	p.Thr773Ile	p.T773I	ENST00000265335		773	aCa/aTa	14/25	0.59015752410557	2	FACETS	0.731	0.679	0.784	0.365	0.339	0.392	SUBCLONAL	1	TRUE	0	0.59015752410557	2		417	997	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459662	149459662	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	248	330	0	ENST00000286301.3:c.545G>A	p.Gly182Asp	p.G182D	ENST00000286301	NM_005211.3	182	gGt/gAt	4/22	0.59015752410557	2	FACETS	0.822	0.769	0.877	0.411	0.384	0.439	CLONAL	1	TRUE	0	0.59015752410557	2		330	1022	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562768	176562768	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	84	382	0	ENST00000439151.2:c.664G>A	p.Val222Ile	p.V222I	ENST00000439151	NM_022455.4	222	Gtc/Atc	2/23	0.59015752410557	2	FACETS	0.242	0.213	0.273	0.121	0.106	0.137	SUBCLONAL	1	TRUE	0	0.59015752410557	2		382	1177	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721306	176721306	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	168	229	0	ENST00000439151.2:c.6937C>T	p.Gln2313Ter	p.Q2313*	ENST00000439151	NM_022455.4	2313	Cag/Tag	23/23	0.59015752410557	2	FACETS	0.797	0.735	0.862	0.399	0.367	0.431	SUBCLONAL	1	TRUE	0	0.59015752410557	2		229	714	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163642	32163642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	42	158	0	ENST00000375023.3:c.5584C>T	p.Arg1862Trp	p.R1862W	ENST00000375023	NM_004557.3	1862	Cgg/Tgg	30/30	0.59015752410557	2	FACETS	0.241	0.201	0.286	0.121	0.1	0.143	SUBCLONAL	1	TRUE	0	0.59015752410557	2		158	590	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178554	32178554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759200326	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	109	306	0	ENST00000375023.3:c.2840C>T	p.Ala947Val	p.A947V	ENST00000375023	NM_004557.3	947	gCc/gTc	18/30	0.59015752410557	2	FACETS	0.405	0.363	0.45	0.203	0.181	0.225	SUBCLONAL	1	TRUE	0	0.59015752410557	2		306	911	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184998	32184998	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	66	324	1	ENST00000375023.3:c.1670G>A	p.Ser557Asn	p.S557N	ENST00000375023	NM_004557.3	557	aGc/aAc	10/30	0.59015752410557	2	FACETS	0.199	0.172	0.229	0.099	0.086	0.115	SUBCLONAL	1	TRUE	0	0.59015752410557	2		325	1125	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288602	33288602	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	427	204	0	ENST00000374542.5:c.950T>C	p.Phe317Ser	p.F317S	ENST00000374542	NM_001141970.1	317	tTc/tCc	3/8	0.59015752410557	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.59015752410557	2		204	708	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89791095	89791095	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381565761	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	12	28	0	ENST00000336032.3:c.482G>A	p.Ser161Asn	p.S161N	ENST00000336032	NM_006813.2	161	aGc/aAc	1/2	0.59015752410557	2	FACETS	0.363	0.257	0.491	0.182	0.128	0.246	SUBCLONAL	1	TRUE	0	0.59015752410557	2		28	112	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017543	112017543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1258	361	477	0	ENST00000368678.4:c.970G>A	p.Val324Ile	p.V324I	ENST00000368678		324	Gtc/Atc	9/13	0.59015752410557	2	FACETS	0.756	0.714	0.798	0.378	0.357	0.399	SUBCLONAL	1	TRUE	0	0.59015752410557	2		477	1619	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199930	138199930	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	68	167	0	ENST00000237289.4:c.1348C>T	p.Pro450Ser	p.P450S	ENST00000237289	NM_001270507.1	450	Cct/Tct	7/9	0.59015752410557	2	FACETS	0.406	0.353	0.463	0.203	0.176	0.232	SUBCLONAL	1	TRUE	0	0.59015752410557	2		167	568	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005291	150005291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	85	372	0	ENST00000253339.5:c.934C>T	p.Pro312Ser	p.P312S	ENST00000253339		312	Cct/Tct	3/7	0.59015752410557	2	FACETS	0.243	0.214	0.275	0.122	0.107	0.138	SUBCLONAL	1	TRUE	0	0.59015752410557	2		372	1185	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005641	150005641	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768880668	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	189	290	0	ENST00000253339.5:c.584G>A	p.Gly195Glu	p.G195E	ENST00000253339		195	gGa/gAa	3/7	0.59015752410557	2	FACETS	0.72	0.666	0.777	0.36	0.333	0.389	SUBCLONAL	1	TRUE	0	0.59015752410557	2		290	889	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016329	150016329	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	279	427	0	ENST00000253339.5:c.377C>T	p.Thr126Ile	p.T126I	ENST00000253339		126	aCt/aTt	2/7	0.59015752410557	2	FACETS	0.774	0.727	0.824	0.387	0.363	0.412	SUBCLONAL	1	TRUE	0	0.59015752410557	2		427	1221	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099892	157099892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	54	340	0	ENST00000346085.5:c.829C>T	p.Pro277Ser	p.P277S	ENST00000346085	NM_020732.3	277	Ccc/Tcc	1/20	0.59015752410557	2	FACETS	0.198	0.168	0.23	0.099	0.084	0.115	SUBCLONAL	1	TRUE	0	0.59015752410557	2		340	926	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157256607	157256607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	63	385	0	ENST00000346085.5:c.1934C>T	p.Ser645Phe	p.S645F	ENST00000346085	NM_020732.3	645	tCt/tTt	5/20	0.59015752410557	2	FACETS	0.193	0.166	0.223	0.097	0.083	0.112	SUBCLONAL	1	TRUE	0	0.59015752410557	2		385	1105	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55219020	55219020	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1335854310	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1505	272	360	0	ENST00000275493.2:c.593G>A	p.Ser198Asn	p.S198N	ENST00000275493	NM_005228.3	198	aGc/aAc	5/28	0.543107076737482	4	FACETS	0.825	0.771	0.881	0.412	0.385	0.441	CLONAL	1	TRUE	2	0.59015752410557	4		360	1777	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55260472	55260472	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1741	292	424	0	ENST00000275493.2:c.2639G>A	p.Trp880Ter	p.W880*	ENST00000275493	NM_005228.3	880	tGg/tAg	22/28	0.543107076737482	4	FACETS	0.774	0.725	0.825	0.387	0.362	0.413	SUBCLONAL	1	TRUE	2	0.59015752410557	4		424	2033	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411666	116411666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1395	261	377	0	ENST00000397752.3:c.2845C>T	p.Leu949Phe	p.L949F	ENST00000397752	NM_000245.2	949	Ctt/Ttt	13/21	0.543107076737482	4	FACETS	0.849	0.793	0.908	0.425	0.396	0.454	CLONAL	1	TRUE	2	0.59015752410557	4		377	1656	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435757	116435757	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1572	224	321	0	ENST00000397752.3:c.3847C>T	p.Pro1283Ser	p.P1283S	ENST00000397752	NM_000245.2	1283	Cct/Tct	20/21	0.543107076737482	4	FACETS	0.672	0.623	0.723	0.336	0.311	0.362	SUBCLONAL	1	TRUE	2	0.59015752410557	4		321	1796	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849987	151849987	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1255	234	308	1	ENST00000262189.6:c.12329C>T	p.Pro4110Leu	p.P4110L	ENST00000262189	NM_170606.2	4110	cCt/cTt	49/59	0.504048546631562	4	FACETS	0.847	0.788	0.908	0.423	0.394	0.454	CLONAL	1	TRUE	2	0.59015752410557	4		309	1489	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851388	151851388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1584	98	359	0	ENST00000262189.6:c.12103C>T	p.Pro4035Ser	p.P4035S	ENST00000262189	NM_170606.2	4035	Ccc/Tcc	47/59	0.504048546631562	4	FACETS	0.314	0.279	0.352	0.157	0.139	0.176	SUBCLONAL	1	TRUE	2	0.59015752410557	4		359	1682	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851460	151851460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1563167589	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1658	179	408	0	ENST00000262189.6:c.12031G>A	p.Val4011Ile	p.V4011I	ENST00000262189	NM_170606.2	4011	Gtt/Att	47/59	0.504048546631562	4	FACETS	0.525	0.482	0.571	0.263	0.241	0.286	SUBCLONAL	1	TRUE	2	0.59015752410557	4		408	1837	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271525	38271525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	77	373	0	ENST00000425967.3:c.2296G>A	p.Asp766Asn	p.D766N	ENST00000425967	NM_001174067.1	766	Gac/Aac	18/19	0.59015752410557	2	FACETS	0.265	0.232	0.301	0.133	0.116	0.151	SUBCLONAL	1	TRUE	0	0.59015752410557	2		373	984	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371953	55371953	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	99	108	0	ENST00000297316.4:c.643G>A	p.Asp215Asn	p.D215N	ENST00000297316	NM_022454.3	215	Gac/Aac	2/2	0.59015752410557	2	FACETS	0.869	0.782	0.96	0.435	0.391	0.48	CLONAL	1	TRUE	0	0.59015752410557	2		108	386	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864306	117864306	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	97	425	0	ENST00000297338.2:c.1351C>T	p.Leu451Phe	p.L451F	ENST00000297338	NM_006265.2	451	Ctc/Ttc	11/14	0.59015752410557	2	FACETS	0.288	0.256	0.322	0.144	0.128	0.161	SUBCLONAL	1	TRUE	0	0.59015752410557	2		425	1142	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866494	117866494	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1185	106	434	0	ENST00000297338.2:c.1151G>A	p.Arg384Lys	p.R384K	ENST00000297338	NM_006265.2	384	aGa/aAa	9/14	0.59015752410557	2	FACETS	0.278	0.248	0.31	0.139	0.124	0.155	SUBCLONAL	1	TRUE	0	0.59015752410557	2		434	1291	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044467	5044467	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1175492497	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1914	190	427	1	ENST00000381652.3:c.415G>A	p.Gly139Ser	p.G139S	ENST00000381652	NM_004972.3	139	Ggt/Agt	5/25	0.447508880770108	4	FACETS	0.487	0.447	0.528			1	SUBCLONAL	1	TRUE	NA	0.59015752410557	4		428	2104	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486206	8486206	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426671700	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	273	358	0	ENST00000356435.5:c.2611C>T	p.Leu871Phe	p.L871F	ENST00000356435		871	Ctt/Ttt	17/35	NA	2	FACETS	0.819	0.768	0.871			1	INDETERMINATE	1	TRUE	NA	0.59015752410557	2		358	1130	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412545	80412545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	206	324	0	ENST00000286548.4:c.496C>T	p.Arg166Cys	p.R166C	ENST00000286548	NM_002072.3	166	Cgc/Tgc	4/7	0.59015752410557	2	FACETS	0.698	0.648	0.751	0.349	0.324	0.376	SUBCLONAL	1	TRUE	0	0.59015752410557	2		324	1000	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93607731	93607731	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	213	281	0	ENST00000375746.1:c.433C>T	p.Gln145Ter	p.Q145*	ENST00000375746	NM_001174167.1	145	Cag/Tag	3/14	0.59015752410557	2	FACETS	0.814	0.757	0.872	0.407	0.378	0.436	CLONAL	1	TRUE	0	0.59015752410557	2		281	887	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915850	127915850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1444	119	511	0	ENST00000373547.4:c.631G>A	p.Gly211Arg	p.G211R	ENST00000373547	NM_002721.4	211	Gga/Aga	6/7	0.59015752410557	2	FACETS	0.258	0.232	0.286	0.129	0.116	0.143	SUBCLONAL	1	TRUE	0	0.59015752410557	2		511	1563	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133729468	133729468	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	193	260	0	ENST00000318560.5:c.97G>A	p.Val33Ile	p.V33I	ENST00000318560	NM_005157.4	33	Gta/Ata	2/11	0.59015752410557	2	FACETS	0.742	0.687	0.799	0.371	0.343	0.4	SUBCLONAL	1	TRUE	0	0.59015752410557	2		260	881	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760607	133760607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778015	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	291	373	0	ENST00000318560.5:c.2930G>A	p.Ser977Asn	p.S977N	ENST00000318560	NM_005157.4	977	aGc/aAc	11/11	0.59015752410557	2	FACETS	0.809	0.76	0.859	0.405	0.38	0.43	CLONAL	1	TRUE	0	0.59015752410557	2		373	1219	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786050	135786050	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	227	272	0	ENST00000298552.3:c.1171C>T	p.Pro391Ser	p.P391S	ENST00000298552	NM_001162426.1	391	Cca/Tca	12/23	0.59015752410557	2	FACETS	0.785	0.732	0.84	0.392	0.366	0.42	SUBCLONAL	1	TRUE	0	0.59015752410557	2		272	980	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391776	139391776	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	39	196	0	ENST00000277541.6:c.6415C>T	p.Leu2139Phe	p.L2139F	ENST00000277541	NM_017617.3	2139	Ctc/Ttc	34/34	0.59015752410557	2	FACETS	0.207	0.171	0.247	0.103	0.085	0.124	SUBCLONAL	1	TRUE	0	0.59015752410557	2		196	639	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139411838	139411838	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	227	285	0	ENST00000277541.6:c.1442-1G>A		p.X481_splice	ENST00000277541	NM_017617.3	481			0.59015752410557	2	FACETS	0.806	0.751	0.862	0.403	0.375	0.431	CLONAL	1	TRUE	0	0.59015752410557	2		285	955	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139804421	139804421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	266	440	1	ENST00000247668.2:c.578G>A	p.Gly193Asp	p.G193D	ENST00000247668	NM_021138.3	193	gGc/gAc	6/11	0.59015752410557	2	FACETS	0.703	0.658	0.75	0.352	0.329	0.375	SUBCLONAL	1	TRUE	0	0.59015752410557	2		441	1282	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759891	63759891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	123	377	0	ENST00000279873.7:c.544C>T	p.Pro182Ser	p.P182S	ENST00000279873	NM_032199.2	182	Ccc/Tcc	4/10	0.59015752410557	2	FACETS	0.369	0.333	0.407	0.184	0.166	0.204	SUBCLONAL	1	TRUE	0	0.59015752410557	2		377	1130	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405299	70405299	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	65	335	0	ENST00000373644.4:c.2813G>A	p.Arg938Lys	p.R938K	ENST00000373644	NM_030625.2	938	aGa/aAa	4/12	0.59015752410557	2	FACETS	0.2	0.172	0.23	0.1	0.086	0.115	SUBCLONAL	1	TRUE	0	0.59015752410557	2		335	1104	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405848	70405848	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	284	420	0	ENST00000373644.4:c.3362G>A	p.Gly1121Asp	p.G1121D	ENST00000373644	NM_030625.2	1121	gGc/gAc	4/12	0.59015752410557	2	FACETS	0.725	0.681	0.771	0.363	0.34	0.386	SUBCLONAL	1	TRUE	0	0.59015752410557	2		420	1327	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70412263	70412263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	69	405	0	ENST00000373644.4:c.4373G>A	p.Gly1458Asp	p.G1458D	ENST00000373644	NM_030625.2	1458	gGt/gAt	6/12	0.59015752410557	2	FACETS	0.192	0.166	0.22	0.096	0.083	0.11	SUBCLONAL	1	TRUE	0	0.59015752410557	2		405	1217	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685281	89685281	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	321	247	0	ENST00000371953.3:c.176C>A	p.Ser59Ter	p.S59*	ENST00000371953	NM_000314.4	59	tCa/tAa	3/9	0.59015752410557	2	FACETS	0.925	0.883	0.966	0.925	0.883	0.966	CLONAL	2	TRUE	0	0.59015752410557	2		247	588	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276956	123276956	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	79	267	0	ENST00000358487.5:c.961G>A	p.Asp321Asn	p.D321N	ENST00000358487	NM_000141.4	321	Gac/Aac	8/18	0.59015752410557	2	FACETS	0.291	0.255	0.329	0.145	0.127	0.165	SUBCLONAL	1	TRUE	0	0.59015752410557	2		267	921	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572261	64572261	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs104894267	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	643	358	1	ENST00000312049.6:c.1378C>T	p.Arg460Ter	p.R460*	ENST00000312049	NM_130799.2	460	Cga/Tga	10/10	0.59015752410557	2	FACETS	0.997	0.967	1	0.997	0.967	1	CLONAL	2	TRUE	0	0.59015752410557	2		359	1093	SUCCESS
EED	8726	MSKCC	GRCh37	11	85968612	85968612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	71	404	0	ENST00000263360.6:c.608C>T	p.Pro203Leu	p.P203L	ENST00000263360	NM_003797.3	203	cCa/cTa	6/12	0.59015752410557	2	FACETS	0.204	0.177	0.233	0.102	0.088	0.117	SUBCLONAL	1	TRUE	0	0.59015752410557	2		404	1179	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100531	102100531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	293	341	0	ENST00000282441.5:c.1375G>A	p.Glu459Lys	p.E459K	ENST00000282441	NM_001130145.2	459	Gaa/Aaa	9/9	0.59015752410557	2	FACETS	0.796	0.748	0.845	0.398	0.374	0.423	SUBCLONAL	1	TRUE	0	0.59015752410557	2		341	1248	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201099	108201099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759728261	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	188	281	2	ENST00000278616.4:c.7466C>T	p.Ser2489Phe	p.S2489F	ENST00000278616	NM_000051.3	2489	tCc/tTc	50/63	0.59015752410557	2	FACETS	0.716	0.662	0.772	0.358	0.331	0.386	SUBCLONAL	1	TRUE	0	0.59015752410557	2		283	890	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343369	118343369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	79	297	0	ENST00000534358.1:c.1495C>T	p.Leu499Phe	p.L499F	ENST00000534358	NM_005933.3	499	Ctt/Ttt	3/36	0.59015752410557	2	FACETS	0.296	0.26	0.336	0.148	0.13	0.168	SUBCLONAL	1	TRUE	0	0.59015752410557	2		297	904	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344620	118344620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	326	474	1	ENST00000534358.1:c.2746G>A	p.Val916Ile	p.V916I	ENST00000534358	NM_005933.3	916	Gtt/Att	3/36	0.59015752410557	2	FACETS	0.825	0.778	0.873	0.413	0.389	0.437	CLONAL	1	TRUE	0	0.59015752410557	2		475	1339	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348826	118348826	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	83	368	2	ENST00000534358.1:c.3479G>A	p.Gly1160Asp	p.G1160D	ENST00000534358	NM_005933.3	1160	gGc/gAc	5/36	0.59015752410557	2	FACETS	0.241	0.212	0.273	0.121	0.106	0.137	SUBCLONAL	1	TRUE	0	0.59015752410557	2		370	1165	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170204	119170204	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	57	256	0	ENST00000264033.4:c.2435-1G>A		p.X812_splice	ENST00000264033	NM_005188.3	812			0.59015752410557	2	FACETS	0.233	0.199	0.271	0.117	0.099	0.136	SUBCLONAL	1	TRUE	0	0.59015752410557	2		256	828	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475252	475252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1359	219	381	0	ENST00000399788.2:c.385G>A	p.Gly129Ser	p.G129S	ENST00000399788	NM_001042603.1	129	Ggt/Agt	4/28	0.59015752410557	4	FACETS	0.748	0.693	0.805			1	SUBCLONAL	1	TRUE	NA	0.59015752410557	4		381	1578	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	493269	493269	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1734	290	462	2	ENST00000399788.2:c.294G>A	p.Trp98Ter	p.W98*	ENST00000399788	NM_001042603.1	98	tgG/tgA	3/28	0.59015752410557	4	FACETS	0.772	0.723	0.823			1	SUBCLONAL	1	TRUE	NA	0.59015752410557	4		464	2024	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446891	18446891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1381	204	434	0	ENST00000266497.5:c.976C>T	p.Gln326Ter	p.Q326*	ENST00000266497		326	Cag/Tag	4/31	0.543107076737482	4	FACETS	0.694	0.641	0.749	0.347	0.32	0.375	SUBCLONAL	1	TRUE	2	0.59015752410557	4		434	1585	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715756	18715756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs950782237	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1494	230	376	0	ENST00000266497.5:c.3587C>T	p.Ser1196Phe	p.S1196F	ENST00000266497		1196	tCc/tTc	25/31	0.543107076737482	4	FACETS	0.719	0.668	0.772	0.359	0.334	0.386	SUBCLONAL	1	TRUE	2	0.59015752410557	4		376	1724	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380271	25380271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1716	250	400	0	ENST00000311936.3:c.187G>A	p.Glu63Lys	p.E63K	ENST00000311936	NM_004985.3	63	Gag/Aag	3/5	0.543107076737482	4	FACETS	0.685	0.638	0.734	0.343	0.319	0.367	SUBCLONAL	1	TRUE	2	0.59015752410557	4		400	1966	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246458	46246458	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1675	233	422	1	ENST00000334344.6:c.4552C>T	p.Pro1518Ser	p.P1518S	ENST00000334344	NM_152641.2	1518	Cca/Tca	15/21	0.543107076737482	4	FACETS	0.658	0.611	0.707	0.329	0.305	0.354	SUBCLONAL	1	TRUE	2	0.59015752410557	4		423	1908	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254671	46254671	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1983	117	433	0	ENST00000334344.6:c.4861C>T	p.Pro1621Ser	p.P1621S	ENST00000334344	NM_152641.2	1621	Cct/Tct	16/21	0.543107076737482	4	FACETS	0.3	0.269	0.334	0.15	0.134	0.167	SUBCLONAL	1	TRUE	2	0.59015752410557	4		433	2100	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298802	46298802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1504	238	384	1	ENST00000334344.6:c.5449G>A	p.Glu1817Lys	p.E1817K	ENST00000334344	NM_152641.2	1817	Gaa/Aaa	21/21	0.543107076737482	4	FACETS	0.736	0.685	0.79	0.368	0.342	0.395	SUBCLONAL	1	TRUE	2	0.59015752410557	4		385	1742	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435468	121435468	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs371807951	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1423	87	311	1	ENST00000257555.6:c.1501G>A	p.Ala501Thr	p.A501T	ENST00000257555		501	Gcc/Acc	7/10	0.543107076737482	4	FACETS	0.31	0.273	0.351	0.155	0.136	0.176	SUBCLONAL	1	TRUE	2	0.59015752410557	4		312	1510	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237629	133237629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1216797884	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1577	94	400	0	ENST00000320574.5:c.2986G>A	p.Gly996Ser	p.G996S	ENST00000320574	NM_006231.2	996	Ggc/Agc	25/49	0.543107076737482	4	FACETS	0.303	0.268	0.341	0.152	0.134	0.171	SUBCLONAL	1	TRUE	2	0.59015752410557	4		400	1671	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245240	133245240	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1271	147	292	2	ENST00000320574.5:c.2007G>A	p.Trp669Ter	p.W669*	ENST00000320574	NM_006231.2	669	tgG/tgA	18/49	0.543107076737482	4	FACETS	0.559	0.508	0.612	0.279	0.254	0.306	SUBCLONAL	1	TRUE	2	0.59015752410557	4		294	1418	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563318	21563318	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1365	227	359	0	ENST00000382592.4:c.601C>T	p.Pro201Ser	p.P201S	ENST00000382592	NM_014572.2	201	Ccc/Tcc	4/8	0.543107076737482	4	FACETS	0.768	0.713	0.826	0.384	0.356	0.413	SUBCLONAL	1	TRUE	2	0.59015752410557	4		359	1592	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913575	32913575	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs938190132	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1983	205	518	2	ENST00000380152.3:c.5083G>A	p.Glu1695Lys	p.E1695K	ENST00000380152		1695	Gaa/Aaa	11/27	0.543107076737482	4	FACETS	0.505	0.466	0.546	0.252	0.233	0.273	SUBCLONAL	1	TRUE	2	0.59015752410557	4		520	2188	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134768	41134768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1952	339	479	0	ENST00000379561.5:c.860G>A	p.Ser287Asn	p.S287N	ENST00000379561	NM_002015.3	287	aGc/aAc	2/3	0.543107076737482	4	FACETS	0.797	0.751	0.846	0.399	0.375	0.423	SUBCLONAL	1	TRUE	2	0.59015752410557	4		479	2291	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435114	110435114	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763264747	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	47	195	0	ENST00000375856.3:c.3287C>T	p.Ala1096Val	p.A1096V	ENST00000375856	NM_003749.2	1096	gCc/gTc	1/2	0.59015752410557	4	FACETS	0.274	0.23	0.323	0.137	0.115	0.162	SUBCLONAL	1	TRUE	2	0.59015752410557	4		195	924	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435772	110435772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	47	46	0	ENST00000375856.3:c.2629C>T	p.Pro877Ser	p.P877S	ENST00000375856	NM_003749.2	877	Ccg/Tcg	1/2	0.59015752410557	4	FACETS	0.928	0.788	1	0.464	0.394	0.54	CLONAL	1	TRUE	2	0.59015752410557	4		46	273	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987226	36987226	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	92	135	0	ENST00000354822.5:c.464-1G>A		p.X155_splice	ENST00000354822	NM_001079668.2	155			0.543107076737482	4	FACETS	0.71	0.631	0.795	0.355	0.315	0.398	SUBCLONAL	1	TRUE	2	0.59015752410557	4		135	698	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061147	38061147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	20	66	0	ENST00000250448.2:c.842G>A	p.Gly281Glu	p.G281E	ENST00000250448	NM_004496.3	281	gGa/gAa	2/2	0.543107076737482	4	FACETS	0.304	0.232	0.389	0.152	0.116	0.195	SUBCLONAL	1	TRUE	2	0.59015752410557	4		66	354	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042196	42042196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770346689	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1225	350	543	0	ENST00000219905.7:c.6391C>T	p.Pro2131Ser	p.P2131S	ENST00000219905	NM_001164273.1	2131	Cca/Tca	17/24	0.59015752410557	2	FACETS	0.753	0.711	0.796	0.377	0.355	0.398	SUBCLONAL	1	TRUE	0	0.59015752410557	2		543	1575	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358542	67358542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	47	272	0	ENST00000327367.4:c.50G>A	p.Gly17Asp	p.G17D	ENST00000327367	NM_005902.3	17	gGc/gAc	1/9	0.59015752410557	2	FACETS	0.179	0.15	0.21	0.089	0.075	0.105	SUBCLONAL	1	TRUE	0	0.59015752410557	2		272	892	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996200	73996200	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757435411	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	154	200	0	ENST00000318443.5:c.934G>A	p.Ala312Thr	p.A312T	ENST00000318443	NM_001024736.1	312	Gcc/Acc	5/10	0.59015752410557	2	FACETS	0.791	0.726	0.858	0.395	0.363	0.429	SUBCLONAL	1	TRUE	0	0.59015752410557	2		200	660	SUCCESS
BLM	641	MSKCC	GRCh37	15	91334051	91334051	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	46	290	0	ENST00000355112.3:c.2996C>T	p.Thr999Ile	p.T999I	ENST00000355112	NM_000057.2	999	aCc/aTc	15/22	0.59015752410557	2	FACETS	0.17	0.142	0.201	0.085	0.071	0.101	SUBCLONAL	1	TRUE	0	0.59015752410557	2		290	918	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434697	99434697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747099881	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	255	315	0	ENST00000268035.6:c.784C>T	p.Pro262Ser	p.P262S	ENST00000268035	NM_000875.3	262	Cct/Tct	3/21	0.59015752410557	2	FACETS	0.875	0.819	0.931	0.437	0.409	0.466	CLONAL	1	TRUE	0	0.59015752410557	2		315	988	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467859	99467859	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	73	358	0	ENST00000268035.6:c.2728C>T	p.Leu910Phe	p.L910F	ENST00000268035	NM_000875.3	910	Ctc/Ttc	13/21	0.59015752410557	2	FACETS	0.221	0.192	0.252	0.111	0.096	0.126	SUBCLONAL	1	TRUE	0	0.59015752410557	2		358	1119	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339439	339439	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs773799650	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	114	344	0	ENST00000262320.3:c.2462+1G>A		p.X821_splice	ENST00000262320	NM_003502.3	821			0.59015752410557	2	FACETS	0.42	0.377	0.465	0.21	0.188	0.233	SUBCLONAL	1	TRUE	0	0.59015752410557	2		344	920	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106696	2106696	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs397515018	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	717	377	2	ENST00000219476.3:c.700G>T	p.Glu234Ter	p.E234*	ENST00000219476	NM_000548.3	234	Gag/Tag	8/42	0.59015752410557	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.59015752410557	2		379	1204	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226342	2226342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	79	320	0	ENST00000326181.6:c.1955C>T	p.Ser652Phe	p.S652F	ENST00000326181	NM_032271.2	652	tCc/tTc	20/21	0.59015752410557	2	FACETS	0.26	0.227	0.295	0.13	0.113	0.148	SUBCLONAL	1	TRUE	0	0.59015752410557	2		320	1031	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647222	2647222	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	131	393	1	ENST00000342085.4:c.1500G>A	p.Trp500Ter	p.W500*	ENST00000342085	NM_002613.4	500	tgG/tgA	13/14	0.59015752410557	2	FACETS	0.369	0.334	0.406	0.185	0.167	0.203	SUBCLONAL	1	TRUE	0	0.59015752410557	2		394	1203	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779058	3779058	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758101123	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	43	209	0	ENST00000262367.5:c.5990C>T	p.Pro1997Leu	p.P1997L	ENST00000262367	NM_004380.2	1997	cCc/cTc	31/31	0.59015752410557	2	FACETS	0.211	0.176	0.25	0.106	0.088	0.125	SUBCLONAL	1	TRUE	0	0.59015752410557	2		209	690	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779196	3779196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	94	151	0	ENST00000262367.5:c.5852C>T	p.Pro1951Leu	p.P1951L	ENST00000262367	NM_004380.2	1951	cCc/cTc	31/31	0.59015752410557	2	FACETS	0.645	0.576	0.718	0.322	0.288	0.359	SUBCLONAL	1	TRUE	0	0.59015752410557	2		151	494	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274027	10274027	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	54	382	0	ENST00000330684.3:c.242G>A	p.Ser81Asn	p.S81N	ENST00000330684	NM_001134407.1	81	aGc/aAc	2/13	0.59015752410557	2	FACETS	0.177	0.151	0.207	0.089	0.075	0.104	SUBCLONAL	1	TRUE	0	0.59015752410557	2		382	1032	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660553	67660553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1308	91	445	2	ENST00000264010.4:c.1453C>T	p.His485Tyr	p.H485Y	ENST00000264010	NM_006565.3	485	Cat/Tat	8/12	0.59015752410557	2	FACETS	0.22	0.195	0.248	0.11	0.097	0.124	SUBCLONAL	1	TRUE	0	0.59015752410557	2		447	1399	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821152	72821152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141983735	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1288	81	445	0	ENST00000268489.5:c.11023C>T	p.Pro3675Ser	p.P3675S	ENST00000268489	NM_006885.3	3675	Ccg/Tcg	10/10	0.59015752410557	2	FACETS	0.201	0.176	0.227	0.1	0.088	0.114	SUBCLONAL	1	TRUE	0	0.59015752410557	2		445	1369	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822541	72822541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs570446390	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	70	380	0	ENST00000268489.5:c.9634C>T	p.Pro3212Ser	p.P3212S	ENST00000268489	NM_006885.3	3212	Ccg/Tcg	10/10	0.59015752410557	2	FACETS	0.203	0.176	0.232	0.102	0.088	0.117	SUBCLONAL	1	TRUE	0	0.59015752410557	2		380	1168	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992732	72992732	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200794923	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	311	461	1	ENST00000268489.5:c.1313C>T	p.Ala438Val	p.A438V	ENST00000268489	NM_006885.3	438	gCg/gTg	2/10	0.59015752410557	2	FACETS	0.736	0.693	0.781	0.368	0.346	0.391	SUBCLONAL	1	TRUE	0	0.59015752410557	2		462	1432	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348158	89348158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1460	93	536	0	ENST00000301030.4:c.4792C>T	p.His1598Tyr	p.H1598Y	ENST00000301030	NM_001256183.1	1598	Cac/Tac	9/13	0.59015752410557	2	FACETS	0.203	0.179	0.228	0.101	0.089	0.114	SUBCLONAL	1	TRUE	0	0.59015752410557	2		536	1553	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371683	89371683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1483035114	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1202	99	367	2	ENST00000301030.4:c.157G>A	p.Glu53Lys	p.E53K	ENST00000301030	NM_001256183.1	53	Gag/Aag	4/13	0.59015752410557	2	FACETS	0.258	0.229	0.289	0.129	0.114	0.145	SUBCLONAL	1	TRUE	0	0.59015752410557	2		369	1301	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974943	15974943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1562	252	406	0	ENST00000268712.3:c.3932G>A	p.Gly1311Asp	p.G1311D	ENST00000268712	NM_006311.3	1311	gGc/gAc	30/46	0.59015752410557	4	FACETS	0.749	0.698	0.802	0.374	0.349	0.401	SUBCLONAL	1	TRUE	2	0.59015752410557	4		406	1814	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649105	37649105	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs570432132	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1451	253	310	1	ENST00000447079.4:c.2210C>T	p.Thr737Ile	p.T737I	ENST00000447079	NM_015083.1	737	aCc/aTc	4/14	0.59015752410557	4	FACETS	0.8	0.746	0.856	0.4	0.373	0.428	SUBCLONAL	1	TRUE	2	0.59015752410557	4		311	1704	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686947	37686947	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1563	101	354	1	ENST00000447079.4:c.3851G>A	p.Gly1284Asp	p.G1284D	ENST00000447079	NM_015083.1	1284	gGc/gAc	14/14	0.59015752410557	4	FACETS	0.327	0.291	0.366	0.164	0.145	0.183	SUBCLONAL	1	TRUE	2	0.59015752410557	4		355	1664	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868262	37868262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763793826	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1455	224	329	0	ENST00000269571.5:c.983C>T	p.Thr328Ile	p.T328I	ENST00000269571		328	aCa/aTa	8/27	0.59015752410557	4	FACETS	0.719	0.667	0.773	0.359	0.333	0.387	SUBCLONAL	1	TRUE	2	0.59015752410557	4		329	1679	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37882913	37882913	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs112493843	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1271	210	341	1	ENST00000269571.5:c.2970+1G>A		p.X990_splice	ENST00000269571		990			0.59015752410557	4	FACETS	0.764	0.707	0.823	0.382	0.353	0.412	SUBCLONAL	1	TRUE	2	0.59015752410557	4		342	1481	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883770	37883770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747888253	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1618	284	399	0	ENST00000269571.5:c.3382G>A	p.Val1128Ile	p.V1128I	ENST00000269571		1128	Gtt/Att	26/27	0.59015752410557	4	FACETS	0.805	0.753	0.858	0.402	0.376	0.429	CLONAL	1	TRUE	2	0.59015752410557	4		399	1902	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354430	40354430	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2042	382	533	0	ENST00000293328.3:c.2165G>A	p.Ser722Asn	p.S722N	ENST00000293328	NM_012448.3	722	aGc/aAc	18/19	0.59015752410557	4	FACETS	0.849	0.802	0.897	0.425	0.401	0.449	CLONAL	1	TRUE	2	0.59015752410557	4		533	2424	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688819	47688819	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1315	91	239	0	ENST00000347630.2:c.481G>A	p.Val161Met	p.V161M	ENST00000347630	NM_001007230.1	161	Gtg/Atg	7/11	0.59015752410557	4	FACETS	0.349	0.308	0.392	0.174	0.154	0.196	SUBCLONAL	1	TRUE	2	0.59015752410557	4		239	1406	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533467	63533467	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1231	203	264	0	ENST00000307078.5:c.1687G>A	p.Glu563Lys	p.E563K	ENST00000307078	NM_004655.3	563	Gaa/Aaa	6/11	0.59015752410557	4	FACETS	0.763	0.705	0.823	0.381	0.352	0.412	SUBCLONAL	1	TRUE	2	0.59015752410557	4		264	1434	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733208	74733208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1542	88	370	0	ENST00000359995.5:c.35G>A	p.Gly12Asp	p.G12D	ENST00000359995	NM_001195427.1	12	gGt/gAt	1/3	0.59015752410557	4	FACETS	0.291	0.256	0.328	0.145	0.128	0.164	SUBCLONAL	1	TRUE	2	0.59015752410557	4		370	1630	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39575854	39575854	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	197	256	0	ENST00000262039.4:c.787G>A	p.Glu263Lys	p.E263K	ENST00000262039	NM_002647.2	263	Gag/Aag	8/25	0.59015752410557	2	FACETS	0.818	0.759	0.879	0.409	0.379	0.44	CLONAL	1	TRUE	0	0.59015752410557	2		256	816	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211782	2211782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868591504	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	104	417	0	ENST00000398665.3:c.1498G>A	p.Ala500Thr	p.A500T	ENST00000398665	NM_032482.2	500	Gca/Aca	16/28	0.59015752410557	2	FACETS	0.261	0.233	0.292	0.131	0.116	0.146	SUBCLONAL	1	TRUE	0	0.59015752410557	2		417	1349	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248549	10248549	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	266	339	1	ENST00000340748.4:c.4204G>A	p.Gly1402Ser	p.G1402S	ENST00000340748		1402	Ggc/Agc	35/40	0.59015752410557	2	FACETS	0.809	0.758	0.861	0.405	0.379	0.431	CLONAL	1	TRUE	0	0.59015752410557	2		340	1114	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290896	15290896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1828	278	457	1	ENST00000263388.2:c.3314G>A	p.Gly1105Asp	p.G1105D	ENST00000263388	NM_000435.2	1105	gGc/gAc	20/33	0.543107076737482	4	FACETS	0.711	0.665	0.76	0.356	0.332	0.38	SUBCLONAL	1	TRUE	2	0.59015752410557	4		458	2106	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375214	15375214	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	158	168	0	ENST00000263377.2:c.1212+1G>A		p.X404_splice	ENST00000263377	NM_058243.2	404			0.543107076737482	4	FACETS	0.83	0.76	0.904	0.415	0.38	0.452	CLONAL	1	TRUE	2	0.59015752410557	4		168	1026	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942055	17942055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1238	206	325	1	ENST00000458235.1:c.2960G>A	p.Gly987Asp	p.G987D	ENST00000458235	NM_000215.3	987	gGc/gAc	21/24	0.543107076737482	4	FACETS	0.769	0.711	0.829	0.384	0.355	0.415	SUBCLONAL	1	TRUE	2	0.59015752410557	4		326	1444	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952226	17952226	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1360733708	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	179	230	0	ENST00000458235.1:c.1114G>A	p.Val372Met	p.V372M	ENST00000458235	NM_000215.3	372	Gtg/Atg	8/24	0.543107076737482	4	FACETS	0.755	0.694	0.818	0.377	0.347	0.409	SUBCLONAL	1	TRUE	2	0.59015752410557	4		230	1278	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257615	19257615	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139889780	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1406	234	320	0	ENST00000162023.5:c.611C>T	p.Thr204Met	p.T204M	ENST00000162023		204	aCg/aTg	10/13	0.543107076737482	4	FACETS	0.769	0.715	0.825	0.384	0.357	0.413	SUBCLONAL	1	TRUE	2	0.59015752410557	4		320	1640	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030049	36030049	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs984277412	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1516	109	312	0	ENST00000358208.4:c.1084C>T	p.Arg362Trp	p.R362W	ENST00000358208		362	Cgg/Tgg	9/12	0.543107076737482	4	FACETS	0.361	0.323	0.403	0.181	0.161	0.202	SUBCLONAL	1	TRUE	2	0.59015752410557	4		312	1625	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485137	57485137	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1185	91	251	0	ENST00000371085.3:c.970+1G>A		p.X324_splice	ENST00000371085	NM_000516.4	324			0.543107076737482	4	FACETS	0.384	0.34	0.432	0.192	0.17	0.216	SUBCLONAL	1	TRUE	2	0.59015752410557	4		251	1276	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41489045	41489045	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	271	322	0	ENST00000263253.7:c.37G>A	p.Ala13Thr	p.A13T	ENST00000263253	NM_001429.3	13	Gcc/Acc	1/31	0.587850199540583	2	FACETS	0.808	0.758	0.86	0.404	0.379	0.43	CLONAL	1	TRUE	0	0.59015752410557	2		322	1136	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536175	41536175	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	236	356	0	ENST00000263253.7:c.1792G>A	p.Ala598Thr	p.A598T	ENST00000263253	NM_001429.3	598	Gct/Act	9/31	0.587850199540583	2	FACETS	0.703	0.655	0.752	0.351	0.327	0.376	SUBCLONAL	1	TRUE	0	0.59015752410557	2		356	1138	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574035	41574035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	172	251	1	ENST00000263253.7:c.6320C>T	p.Pro2107Leu	p.P2107L	ENST00000263253	NM_001429.3	2107	cCc/cTc	31/31	0.587850199540583	2	FACETS	0.815	0.752	0.881	0.408	0.376	0.441	CLONAL	1	TRUE	0	0.59015752410557	2		252	715	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929053	44929053	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1224090700	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1305	207	512	0	ENST00000377967.4:c.2153G>A	p.Ser718Asn	p.S718N	ENST00000377967	NM_021140.2	718	aGc/aAc	17/29	0.59015752410557	2	FACETS	0.464	0.429	0.5	0.232	0.214	0.25	SUBCLONAL	1	TRUE	0	0.59015752410557	2		512	1512	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044898	47044898	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	204	907	0	ENST00000377604.3:c.2224C>T	p.Gln742Ter	p.Q742*	ENST00000377604	NM_001204468.1	742	Cag/Tag	20/24	0.59015752410557	2	FACETS	0.666	0.617	0.717	0.333	0.308	0.359	SUBCLONAL	1	TRUE	0	0.59015752410557	2		907	1038	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410019	63410019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	238	381	0	ENST00000330258.3:c.3148G>A	p.Asp1050Asn	p.D1050N	ENST00000330258	NM_152424.3	1050	Gat/Aat	2/2	0.59015752410557	2	FACETS	0.703	0.656	0.752	0.352	0.328	0.376	SUBCLONAL	1	TRUE	0	0.59015752410557	2		381	1147	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356132	70356132	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1343	92	433	0	ENST00000374080.3:c.5027G>A	p.Gly1676Asp	p.G1676D	ENST00000374080		1676	gGt/gAt	37/45	0.59015752410557	2	FACETS	0.217	0.192	0.245	0.109	0.096	0.123	SUBCLONAL	1	TRUE	0	0.59015752410557	2		433	1435	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357681	70357681	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781207905	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1389	89	454	0	ENST00000374080.3:c.5932C>T	p.Pro1978Ser	p.P1978S	ENST00000374080		1978	Cct/Tct	41/45	0.59015752410557	2	FACETS	0.204	0.18	0.23	0.102	0.09	0.115	SUBCLONAL	1	TRUE	0	0.59015752410557	2		454	1478	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940464	76940464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1380	94	533	1	ENST00000373344.5:c.629G>A	p.Ser210Asn	p.S210N	ENST00000373344	NM_000489.3	210	aGc/aAc	8/35	0.59015752410557	2	FACETS	0.216	0.191	0.243	0.108	0.095	0.122	SUBCLONAL	1	TRUE	0	0.59015752410557	2		534	1474	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551492	150551494	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	rs759789515	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	591	416	7	ENST00000369026.2:c.513_515del	p.Glu171del	p.E171del	ENST00000369026	NM_021960.4	171	gaGGAc/gac	1/3	0.59015752410557	2	FACETS	0.91	0.88	0.941	0.91	0.88	0.941	CLONAL	2	TRUE	0	0.59015752410557	2		423	1100	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519505	137519506	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs780346130	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	233	327	1	ENST00000367739.4:c.1132_1133del	p.Ser378PhefsTer6	p.S378Ffs*6	ENST00000367739	NM_000416.2	378	AGt/t	7/7	0.59015752410557	2	FACETS	0.79	0.737	0.844	0.395	0.368	0.422	SUBCLONAL	1	TRUE	0	0.59015752410557	2		328	1000	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870952	12870975	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	GGAATTTCGATTTTCAGAATCACA	GGAATTTCGATTTTCAGAATCACA	-	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	435	274	0	ENST00000228872.4:c.179_202del	p.Trp60_Lys68delinsTer	p.W60_K68delins*	ENST00000228872	NM_004064.3	60	tGGAATTTCGATTTTCAGAATCACAaa/taa	1/3	0.543107076737482	4	FACETS	0.859	0.819	0.9	0.859	0.819	0.9	CLONAL	2	TRUE	2	0.59015752410557	4		274	1364	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823845	3823863	+	frameshift_variant	Frame_Shift_Del	DEL	CTGAGCGGGCGCCTGGGCC	CTGAGCGGGCGCCTGGGCC	-	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	590	294	1	ENST00000262367.5:c.2352_2370del	p.Met784IlefsTer17	p.M784Ifs*17	ENST00000262367	NM_004380.2	784	atGGCCCAGGCGCCCGCTCAG/at	13/31	0.59015752410557	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.59015752410557	2		295	995	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007076-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	31	258	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	0.59015752410557	2	FACETS	0.223	0.179	0.271	0.111	0.089	0.136	SUBCLONAL	1	TRUE	0	0.59015752410557	2		258	472	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838040	156838040	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0007105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	77	543	0	ENST00000524377.1:c.573T>A	p.Cys191Ter	p.C191*	ENST00000524377	NM_002529.3	191	tgT/tgA	5/17	0.270509568843796	3	FACETS	0.801	0.703	0.908	0.401	0.351	0.454	CLONAL	1	TRUE	1	0.282241231647069	3		543	777	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247243	153247243	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	299	555	1	ENST00000281708.4:c.1559A>T	p.Asp520Val	p.D520V	ENST00000281708	NM_033632.3	520	gAt/gTt	10/12	0.265857068971464	2	FACETS	0.938	0.883	0.993	0.938	0.883	0.993	CLONAL	2	TRUE	0	0.282241231647069	2		556	1130	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216542	7216542	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	175	652	0	ENST00000380728.2:c.793T>G	p.Phe265Val	p.F265V	ENST00000380728		265	Ttc/Gtc	9/11	0.265857068971464	2	FACETS	1	0.94	1	0.513	0.471	0.557	CLONAL	1	TRUE	0	0.282241231647069	2		652	1208	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0007123-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	114	379	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.255912947880277	2		379	805	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220717	1220717	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587782018	NA	P-0007123-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	107	307	0	ENST00000326873.7:c.734+1G>T		p.X245_splice	ENST00000326873	NM_000455.4	245			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.255912947880277	2		307	567	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602286	10602286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007123-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	158	348	1	ENST00000171111.5:c.1292C>T	p.Ser431Phe	p.S431F	ENST00000171111	NM_203500.1	431	tCc/tTc	3/6	1	2	FACETS	0.837	0.768	0.908	1	0.99	1	CLONAL	2	TRUE	1	0.255912947880277	2		349	738	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168735	56168735	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs781158252	NA	P-0007123-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	98	287	1	ENST00000399503.3:c.1589G>T	p.Gly530Val	p.G530V	ENST00000399503	NM_005921.1	530	gGa/gTa	9/20	1	2	FACETS	0.787	0.701	0.879	0.787	0.701	0.879	SUBCLONAL	1	TRUE	1	0.255912947880277	2		288	973	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143350325	143350325	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0007123-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	67	174	0	ENST00000262992.4:c.136+1G>T		p.X46_splice	ENST00000262992	NM_001101669.1	46			0.183101292548508	2	FACETS	0.9	0.782	1	0.45	0.391	0.514	CLONAL	1	TRUE	0	0.255912947880277	2		174	582	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480158	20480158	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007123-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	113	320	0	ENST00000346618.3:c.475G>T	p.Ala159Ser	p.A159S	ENST00000346618	NM_001949.4	159	Gct/Tct	2/7	1	2	FACETS	0.982	0.883	1	0.982	0.883	1	CLONAL	1	TRUE	1	0.255912947880277	2		320	899	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900306	101900306	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007123-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	114	343	0	ENST00000374994.4:c.740A>T	p.Glu247Val	p.E247V	ENST00000374994	NM_004612.2	247	gAg/gTg	4/9	1	2	FACETS	0.904	0.813	1	0.904	0.813	1	CLONAL	1	TRUE	1	0.255912947880277	2		343	985	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422949	49422949	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs759084640	NA	P-0007123-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	80	443	1	ENST00000301067.7:c.14146G>T	p.Gly4716Trp	p.G4716W	ENST00000301067	NM_003482.3	4716	Ggg/Tgg	44/54	1	2	FACETS	0.657	0.577	0.744	0.657	0.577	0.744	SUBCLONAL	1	TRUE	1	0.255912947880277	2		444	951	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352698	70352698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007123-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	78	397	0	ENST00000374080.3:c.4419G>A	p.Met1473Ile	p.M1473I	ENST00000374080		1473	atG/atA	32/45	1	2	FACETS	0.746	0.655	0.845	0.746	0.655	0.845	SUBCLONAL	1	TRUE	1	0.255912947880277	2		397	817	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578206	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs886039484	NA	P-0007126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	994	470	0	ENST00000269305.4:c.643A>G	p.Ser215Gly	p.S215G	ENST00000269305	NM_001126112.2	215	Agt/Ggt	6/11	0.713833746633441	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.713833746633441	3		470	1184	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0007126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	364	346	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	0.713376582638351	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.713833746633441	2		346	507	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158626924	158626924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760152551	NA	P-0007126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	131	535	2	ENST00000263640.3:c.746C>T	p.Thr249Met	p.T249M	ENST00000263640	NM_001105.4	249	aCg/aTg	7/11	0.713833746633441	3	FACETS	0.386	0.349	0.425	0.193	0.174	0.213	SUBCLONAL	1	TRUE	1	0.713833746633441	3		537	1291	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169106	32169106	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	140	427	0	ENST00000375023.3:c.3927C>G	p.Asp1309Glu	p.D1309E	ENST00000375023	NM_004557.3	1309	gaC/gaG	22/30	0.713833746633441	3	FACETS	0.508	0.462	0.557	0.254	0.231	0.279	SUBCLONAL	1	TRUE	1	0.713833746633441	3		427	1047	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926270	112926270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918457	NA	P-0007126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	186	484	0	ENST00000351677.2:c.1403C>T	p.Thr468Met	p.T468M	ENST00000351677	NM_002834.3	468	aCg/aTg	12/16	0.404476002849993	3	FACETS	0.682	0.629	0.737	0.341	0.314	0.369	INDETERMINATE	1	TRUE	1	0.713833746633441	3		484	1037	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926893	112926893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	252	391	2	ENST00000351677.2:c.1513G>A	p.Val505Ile	p.V505I	ENST00000351677	NM_002834.3	505	Gtc/Atc	13/16	0.404476002849993	3	FACETS	1	0.993	1	0.735	0.692	0.778	INDETERMINATE	1	TRUE	1	0.713833746633441	3		393	652	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557552	95557552	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1447120867	NA	P-0007126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	44	401	1	ENST00000393063.1:c.5515C>T	p.Arg1839Trp	p.R1839W	ENST00000393063	NM_030621.3	1839	Cgg/Tgg	26/28	0.404476002849993	3	FACETS	0.218	0.182	0.258	0.109	0.091	0.129	INDETERMINATE	1	TRUE	1	0.713833746633441	3		402	768	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41525902	41525902	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	334	374	0	ENST00000263253.7:c.1177T>A	p.Cys393Ser	p.C393S	ENST00000263253	NM_001429.3	393	Tgt/Agt	5/31	0.713833746633441	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.713833746633441	2		374	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0007132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	253	278	0	ENST00000269305.4:c.559+1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.555536919547553	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.555536919547553	2		278	424	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564516	55564516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1174814949	NA	P-0007132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	182	297	1	ENST00000288135.5:c.404G>A	p.Arg135His	p.R135H	ENST00000288135	NM_000222.2	135	cGc/cAc	3/21	0.227197791246416	3	FACETS	1	0.966	1	0.539	0.498	0.581	INDETERMINATE	1	TRUE	1	0.555536919547553	3		298	777	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261103	16261103	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	103	241	0	ENST00000375759.3:c.8368A>T	p.Met2790Leu	p.M2790L	ENST00000375759	NM_015001.2	2790	Atg/Ttg	11/15	1	2	FACETS	0.849	0.764	0.937	0.849	0.764	0.937	CLONAL	1	TRUE	1	0.555536919547553	2		241	437	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295789	212295789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1240072004	NA	P-0007132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	351	397	0	ENST00000342788.4:c.2524C>T	p.Arg842Trp	p.R842W	ENST00000342788	NM_005235.2	842	Cgg/Tgg	21/28	0.365960255631181	4	FACETS	0.8	0.758	0.844	0.8	0.758	0.844	SUBCLONAL	2	TRUE	2	0.555536919547553	4		397	1228	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437585	52437585	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	537	649	0	ENST00000460680.1:c.1576C>T	p.His526Tyr	p.H526Y	ENST00000460680	NM_004656.3	526	Cac/Tac	13/17	0.280274969273382	5	FACETS	1	0.995	1	0.818	0.784	0.851	INDETERMINATE	2	TRUE	2	0.555536919547553	5		649	1445	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971324	13971324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752431857	NA	P-0007132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1568	271	411	1	ENST00000405192.2:c.605C>T	p.Thr202Met	p.T202M	ENST00000405192	NM_001163147.1	202	aCg/aTg	8/12	0.555536919547553	5	FACETS	0.973	0.909	1	0.324	0.303	0.347	CLONAL	1	TRUE	2	0.555536919547553	5		412	1839	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476733	140476733	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1278812236	NA	P-0007132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	182	409	0	ENST00000288602.6:c.1673G>A	p.Arg558Gln	p.R558Q	ENST00000288602	NM_004333.4	558	cGa/cAa	13/18	0.536667812453977	4	FACETS	0.963	0.888	1	0.241	0.222	0.261	CLONAL	1	TRUE	0	0.555536919547553	4		409	1058	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100271	8100271	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	304	293	0	ENST00000346208.3:c.245G>T	p.Ser82Ile	p.S82I	ENST00000346208		82	aGc/aTc	3/6	0.555536919547553	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	0	0.555536919547553	3		293	452	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52663030	52663032	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	novel	NA	P-0007132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	207	271	0	ENST00000394830.3:c.1321_1323del	p.Glu441del	p.E441del	ENST00000394830	NM_018313.4	441	GAA/-	13/30	0.280274969273382	5	FACETS	1	0.973	1	0.721	0.672	0.77	INDETERMINATE	2	TRUE	2	0.555536919547553	5		271	632	SUCCESS
APC	324	MSKCC	GRCh37	5	112164629	112164630	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0007132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	304	356	0	ENST00000257430.4:c.1706_1707del	p.Val569GlufsTer11	p.V569Efs*11	ENST00000257430	NM_000038.5	568	aGT/a	14/16	0.555536919547553	3	FACETS	0.895	0.848	0.943	0.895	0.848	0.943	CLONAL	2	TRUE	1	0.555536919547553	3		356	781	SUCCESS
APC	324	MSKCC	GRCh37	5	112175487	112175487	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	154	320	0	ENST00000257430.4:c.4196del	p.Arg1399LeufsTer16	p.R1399Lfs*16	ENST00000257430	NM_000038.5	1399	cGt/ct	16/16	0.555536919547553	3	FACETS	0.704	0.644	0.768	0.352	0.322	0.384	SUBCLONAL	1	TRUE	1	0.555536919547553	3		320	1006	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	100	225	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.31398089394225	2		225	534	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0007151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	153	348	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	NA	2	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.31398089394225	2		348	902	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0007151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	175	345	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.31398089394225	3	FACETS	0.896	0.827	0.967	0.896	0.827	0.967	CLONAL	2	TRUE	1	0.31398089394225	3		345	720	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755599	57755599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	120	292	1	ENST00000274289.3:c.188C>T	p.Ser63Leu	p.S63L	ENST00000274289	NM_006622.3	63	tCg/tTg	1/14	1	2	FACETS	0.919	0.829	1	0.919	0.829	1	CLONAL	1	TRUE	1	0.31398089394225	2		293	832	SUCCESS
AR	367	MSKCC	GRCh37	X	66766501	66766501	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	49	464	0	ENST00000374690.3:c.1513C>G	p.Pro505Ala	p.P505A	ENST00000374690	NM_000044.3	505	Cct/Gct	1/8	0.759457791409814	1	FACETS	0.368	0.314	0.425	0.368	0.314	0.425	SUBCLONAL	1	TRUE	0	0.74	1		464	227	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519988	NA	P-0007161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	135	349	0	ENST00000269305.4:c.808T>C	p.Phe270Leu	p.F270L	ENST00000269305	NM_001126112.2	270	Ttt/Ctt	8/11	0.500813403087711	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.551129635881401	1		349	345	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144515	58144515	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	105	389	0	ENST00000257904.6:c.556C>G	p.Leu186Val	p.L186V	ENST00000257904	NM_000075.3	186	Ctt/Gtt	5/8	0.500813403087711	1	FACETS	0.752	0.68	0.827	0.752	0.68	0.827	SUBCLONAL	1	TRUE	0	0.551129635881401	1		389	367	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148529796	148529796	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	297	405	0	ENST00000320356.2:c.293T>C	p.Leu98Ser	p.L98S	ENST00000320356	NM_004456.4	98	tTa/tCa	4/20	0.46364964430105	1	FACETS	0.966	0.91	1	0.966	0.91	1	CLONAL	1	TRUE	0	0.46364964430105	1		405	1019	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385246	4385246	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	638	448	0	ENST00000261254.3:c.271G>T	p.Val91Phe	p.V91F	ENST00000261254	NM_001759.3	91	Gtc/Ttc	2/5	NA	2	FACETS	0.883	0.851	0.915			1	INDETERMINATE	2	TRUE	NA	0.46364964430105	2		448	1559	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210789	133210789	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	248	609	0	ENST00000320574.5:c.5987T>C	p.Phe1996Ser	p.F1996S	ENST00000320574	NM_006231.2	1996	tTc/tCc	43/49	0.291902214842826	1	FACETS	0.566	0.528	0.606	0.566	0.528	0.606	SUBCLONAL	1	TRUE	0	0.46364964430105	1		609	1451	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608095	28608095	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1202	214	575	0	ENST00000241453.7:c.1871T>G	p.Val624Gly	p.V624G	ENST00000241453	NM_004119.2	624	gTg/gGg	15/24	0.163454231940469	2	FACETS	0.652	0.604	0.702	0.326	0.302	0.351	INDETERMINATE	1	TRUE	0	0.46364964430105	2		575	1416	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346848	73346848	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	128	314	0	ENST00000377767.4:c.1369T>C	p.Trp457Arg	p.W457R	ENST00000377767	NM_014953.3	457	Tgg/Cgg	9/21	0.32798236888304	0	FACETS	0.407	0.369	0.447			1	SUBCLONAL	1	TRUE	0	0.46364964430105	0		314	727	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226383	2226383	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	167	436	0	ENST00000326181.6:c.1996A>C	p.Lys666Gln	p.K666Q	ENST00000326181	NM_032271.2	666	Aag/Cag	20/21	0.179709989259401	0	FACETS	0.384	0.353	0.418			1	INDETERMINATE	1	TRUE	0	0.46364964430105	0		436	1005	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41219643	41219643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555579648	NA	P-0007176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	162	393	0	ENST00000357654.3:c.5056C>T	p.His1686Tyr	p.H1686Y	ENST00000357654	NM_007294.3	1686	Cat/Tat	16/23	0.195623361116198	3	FACETS	0.7	0.641	0.763	0.35	0.32	0.382	INDETERMINATE	1	TRUE	1	0.46364964430105	3		393	1229	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383156	42383156	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2808	307	688	0	ENST00000221972.3:c.176G>A	p.Ser59Asn	p.S59N	ENST00000221972	NM_021601.3	59	aGc/aAc	2/5	0.46364964430105	5	FACETS	0.721	0.675	0.768			1	SUBCLONAL	1	TRUE	NA	0.46364964430105	5		688	3115	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264427	46264427	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2046	412	781	0	ENST00000371998.3:c.1474A>G	p.Ile492Val	p.I492V	ENST00000371998		492	Ata/Gta	11/23	0.119055479341023	3	FACETS	0.891	0.844	0.939			1	INDETERMINATE	1	TRUE	NA	0.46364964430105	3		781	2458	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845291	76845304	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTTGTAGCTCACC	ATTTGTAGCTCACC	-	novel	NA	P-0007176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	156	265	0	ENST00000373344.5:c.6217_6217+13del		p.X2073_splice	ENST00000373344	NM_000489.3	2073		27/35	1	1	FACETS	0.957	0.882	1	0.957	0.882	1	CLONAL	1	TRUE	0	0.46364964430105	1		265	540	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845285	76845314	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGAAATATTTGTAGCTCACCTTTATAAATA	AGAAATATTTGTAGCTCACCTTTATAAATA	TGAAGATTTTCTTG	novel	NA	P-0007176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	160	290	0	ENST00000373344.5:c.6207_6217+19delinsCAAGAAAATCTTCA		p.X2069_splice	ENST00000373344	NM_000489.3	2069		27/35	1	1	FACETS	0.885	0.815	0.957	0.885	0.815	0.957	CLONAL	1	TRUE	0	0.46364964430105	1		290	599	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	115	543	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	0.271552983010581	2		543	762	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0007179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	59	309	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.517	0.443	0.597	0.517	0.443	0.597	SUBCLONAL	1	TRUE	1	0.271552983010581	2		310	841	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576870	7576870	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs876659384	NA	P-0007179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	138	411	0	ENST00000269305.4:c.976G>T	p.Glu326Ter	p.E326*	ENST00000269305	NM_001126112.2	326	Gaa/Taa	9/11	0.271552983010581	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.271552983010581	1		411	771	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971101	21971101	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	14	182	0	ENST00000579755.1:c.300C>A	p.Cys100Ter	p.C100*	ENST00000579755		100	tgC/tgA	2/3	0.271552983010581	1	FACETS	0.356	0.257	0.476	0.356	0.257	0.476	SUBCLONAL	1	TRUE	0	0.271552983010581	1		182	250	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023159	27023159	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	61	51	0	ENST00000324856.7:c.265G>C	p.Gly89Arg	p.G89R	ENST00000324856	NM_006015.4	89	Ggc/Cgc	1/20	0.211832473505502	1	FACETS	1	0.958	1	1	0.983	1	CLONAL	2	TRUE	0	0.271552983010581	1		51	161	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971075	21971075	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007179-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	15	197	0	ENST00000304494.5:c.283G>A	p.Val95Met	p.V95M	ENST00000304494	NM_000077.4	95	Gtg/Atg	2/3	0.271552983010581				0.232	0.422				SUBCLONAL	1	TRUE	0	0.271552983010581	1		197	300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882025	NA	P-0007182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	120	564	0	ENST00000269305.4:c.646G>T	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ttg	6/11	0.766280289921346	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.766277860263818	1		564	177	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426036	138426036	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	365	319	0	ENST00000289153.2:c.1495A>G	p.Lys499Glu	p.K499E	ENST00000289153	NM_006219.2	499	Aaa/Gaa	9/22	0.766280289921346	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	1	0.766277860263818	4		319	537	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998483	100998483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	47	165	0	ENST00000325455.5:c.1319C>T	p.Thr440Met	p.T440M	ENST00000325455	NM_001202474.3	440	aCg/aTg	1/8	0.668204400284531	5	FACETS	1	0.887	1	0.35	0.298	0.407	CLONAL	1	TRUE	2	0.766277860263818	5		165	251	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0007204-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	22	194	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		194	218	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0007204-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	48	534	1	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		535	1036	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650532	48650532	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007204-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	58	438	0	ENST00000376670.3:c.502T>G	p.Phe168Val	p.F168V	ENST00000376670	NM_002049.3	168	Ttt/Gtt	3/6	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		438	1053	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	42	287	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.244593198540423	1	FACETS	0.806	0.675	0.951	0.806	0.675	0.951	CLONAL	1	TRUE	0	0.255882604185555	1		287	355	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0007207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	108	404	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.255882604185555	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.255882604185555	1		405	677	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0007207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	101	349	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.255882604185555	2		349	738	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0007207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	50	293	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.92	0.782	1	0.92	0.782	1	CLONAL	1	TRUE	1	0.255882604185555	2		293	425	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956132	175956132	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	78	342	0	ENST00000367669.3:c.2080G>C	p.Asp694His	p.D694H	ENST00000367669	NM_022457.5	694	Gat/Cat	18/20	0.196403299029168	4	FACETS	1	0.966	1	0.427	0.375	0.482	CLONAL	1	TRUE	1	0.255882604185555	4		342	598	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670719	67670719	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	124	412	0	ENST00000264010.4:c.1964C>A	p.Pro655His	p.P655H	ENST00000264010	NM_006565.3	655	cCc/cAc	11/12	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.255882604185555	2		412	882	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366129	15366129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1468704458	NA	P-0007207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	101	329	0	ENST00000263377.2:c.2026C>T	p.Arg676Trp	p.R676W	ENST00000263377	NM_058243.2	676	Cgg/Tgg	10/20	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.255882604185555	2		329	756	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349925	70349925	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	124	471	0	ENST00000374080.3:c.3908A>G	p.Asp1303Gly	p.D1303G	ENST00000374080		1303	gAc/gGc	28/45	0.255882604185555	3	FACETS	0.918	0.828	1	0.459	0.414	0.507	CLONAL	1	TRUE	1	0.255882604185555	3		471	1191	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0007216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	337	719	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.292614116269436	2	FACETS	0.827	0.787	0.867	0.827	0.787	0.867	INDETERMINATE	2	TRUE	0	0.529221286264506	2		719	770	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0007216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	214	446	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.27615849282865	3	FACETS	1	0.977	1	0.719	0.676	0.763	INDETERMINATE	2	TRUE	0	0.529221286264506	3		446	474	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0007216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	216	349	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	0.879	0.818	0.942	0.879	0.818	0.942	CLONAL	1	TRUE	1	0.529221286264506	2		349	929	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0007216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	403	531	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.529221286264506	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.529221286264506	1		531	927	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0007216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	257	624	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.529221286264506	2		624	952	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106072	8106072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	202	349	0	ENST00000346208.3:c.892C>T	p.Arg298Trp	p.R298W	ENST00000346208		298	Cgg/Tgg	4/6	1	2	FACETS	0.934	0.868	1	0.934	0.868	1	CLONAL	1	TRUE	1	0.529221286264506	2		349	817	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932130	36932130	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	83	609	0	ENST00000361632.4:c.2339T>C	p.Leu780Pro	p.L780P	ENST00000361632		780	cTc/cCc	16/16	0.312897568504569	1	FACETS	0.222	0.195	0.251	0.222	0.195	0.251	INDETERMINATE	1	TRUE	0	0.529221286264506	1		609	1041	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47166034	47166034	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	40	206	0	ENST00000409792.3:c.92A>C	p.Lys31Thr	p.K31T	ENST00000409792	NM_014159.6	31	aAg/aCg	3/21	0.312897568504569	1	FACETS	0.355	0.296	0.42	0.355	0.296	0.42	INDETERMINATE	1	TRUE	0	0.529221286264506	1		206	313	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513289	149513289	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	62	383	0	ENST00000261799.4:c.794T>C	p.Leu265Pro	p.L265P	ENST00000261799	NM_002609.3	265	cTc/cCc	6/23	1	2	FACETS	0.305	0.262	0.351	0.305	0.262	0.351	SUBCLONAL	1	TRUE	1	0.529221286264506	2		383	769	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450293	50450293	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	161	516	0	ENST00000331340.3:c.477C>A	p.Asn159Lys	p.N159K	ENST00000331340	NM_006060.4	159	aaC/aaA	5/8	0.322270992207992	1	FACETS	0.466	0.427	0.507	0.466	0.427	0.507	SUBCLONAL	1	TRUE	0	0.529221286264506	1		516	960	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602575	10602575	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	43	444	0	ENST00000171111.5:c.1003T>G	p.Phe335Val	p.F335V	ENST00000171111	NM_203500.1	335	Ttc/Gtc	3/6	0.34376293394199	1	FACETS	0.144	0.119	0.171	0.144	0.119	0.171	SUBCLONAL	1	TRUE	0	0.529221286264506	1		444	832	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0007233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	137	385	1	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.45545498833776	2		386	476	SUCCESS
ATM	472	MSKCC	GRCh37	11	108181016	108181016	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs786202728	NA	P-0007233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	25	318	0	ENST00000278616.4:c.5892G>C	p.Lys1964Asn	p.K1964N	ENST00000278616	NM_000051.3	1964	aaG/aaC	39/63	1	2	FACETS	0.638	0.507	0.786	0.638	0.507	0.786	SUBCLONAL	1	FALSE	1	0.45545498833776	2		318	172	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226243	2226243	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	99	516	1	ENST00000398665.3:c.3723G>T	p.Trp1241Cys	p.W1241C	ENST00000398665	NM_032482.2	1241	tgG/tgT	27/28	0.240336475958099	2	FACETS	0.717	0.642	0.798	0.359	0.321	0.399	INDETERMINATE	1	FALSE	0	0.45545498833776	2		517	606	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878846	117878849	+	frameshift_variant	Frame_Shift_Del	DEL	CACG	CACG	-	novel	NA	P-0007233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	66	681	0	ENST00000297338.2:c.120_123del	p.Ser40ArgfsTer9	p.S40Rfs*9	ENST00000297338	NM_006265.2	40	agCGTG/ag	2/14	1	2	FACETS	0.914	0.8	1	0.914	0.8	1	CLONAL	1	FALSE	1	0.45545498833776	2		681	317	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727451	66727451	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519729	NA	P-0007234-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	454	519	1	ENST00000307102.5:c.167A>C	p.Gln56Pro	p.Q56P	ENST00000307102	NM_002755.3	56	cAg/cCg	2/11	1	2	FACETS	0.825	0.788	0.863	0.825	0.788	0.863	CLONAL	1	TRUE	1	0.817824642053677	2		520	1346	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220622	1220622	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690923	NA	P-0007234-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	934	392	3	ENST00000326873.7:c.640C>T	p.Gln214Ter	p.Q214*	ENST00000326873	NM_000455.4	214	Cag/Tag	5/10	0.75992250647013	2	FACETS	0.92	0.901	0.937	0.92	0.901	0.937	CLONAL	2	TRUE	0	0.817824642053677	2		395	1242	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406220	70406220	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007234-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	368	412	0	ENST00000373644.4:c.3734A>T	p.Gln1245Leu	p.Q1245L	ENST00000373644	NM_030625.2	1245	cAg/cTg	4/12	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.817824642053677	2		412	868	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431428	49431428	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007234-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	425	448	0	ENST00000301067.7:c.9711G>T	p.Glu3237Asp	p.E3237D	ENST00000301067	NM_003482.3	3237	gaG/gaT	34/54	1	2	FACETS	0.919	0.877	0.961	0.919	0.877	0.961	CLONAL	1	TRUE	1	0.817824642053677	2		448	1131	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602620	10602692	+	frameshift_variant	Frame_Shift_Del	DEL	GGCAGGGCATCACCTGCGTGGGCTTGTGCAGGGTGAGCTCCTCGAAGATCTTGACCAGGTAGTCCTTGCAGCG	GGCAGGGCATCACCTGCGTGGGCTTGTGCAGGGTGAGCTCCTCGAAGATCTTGACCAGGTAGTCCTTGCAGCG	AGC	novel	NA	P-0007234-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	609	367	0	ENST00000171111.5:c.886_958delinsGCT	p.Arg296AlafsTer9	p.R296Afs*9	ENST00000171111	NM_203500.1	296	CGCTGCAAGGACTACCTGGTCAAGATCTTCGAGGAGCTCACCCTGCACAAGCCCACGCAGGTGATGCCCTGCCgg/GCTgg	3/6	0.75992250647013	2	FACETS	0.809	0.785	0.831	0.809	0.785	0.831	CLONAL	2	TRUE	0	0.817824642053677	2		367	921	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539675	187539675	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	150	353	0	ENST00000441802.2:c.8065G>T	p.Val2689Phe	p.V2689F	ENST00000441802	NM_005245.3	2689	Gtc/Ttc	10/27	1	2	FACETS	0.879	0.814	0.946	0.879	0.814	0.946	CLONAL	1	TRUE	1	0.91	2		353	375	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222982	1222982	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs727504172	NA	P-0007239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	125	165	0	ENST00000326873.7:c.921-2A>T		p.X307_splice	ENST00000326873	NM_000455.4	307			0.926397378884503	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.91	1		165	143	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600464	10600464	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	220	367	0	ENST00000171111.5:c.1391G>T	p.Gly464Val	p.G464V	ENST00000171111	NM_203500.1	464	gGc/gTc	4/6	0.926397378884503	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.91	1		367	241	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411420	63411420	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	135	366	0	ENST00000330258.3:c.1747G>T	p.Ala583Ser	p.A583S	ENST00000330258	NM_152424.3	583	Gca/Tca	2/2	0.926397378884503	1	FACETS	0.7	0.653	0.746	0.7	0.653	0.746	SUBCLONAL	1	TRUE	0	0.91	1		366	231	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	309	543	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.132305455988874	4	FACETS	0.996	0.937	1	0.996	0.937	1	INDETERMINATE	2	FALSE	2	0.3	4		543	1345	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0007272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	370	450	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	0.846	0.802	0.892	1	0.996	1	CLONAL	2	FALSE	1	0.3	2		450	1457	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749415085	NA	P-0007272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1973	432	511	0	ENST00000263967.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000263967	NM_006218.2	38	Cgt/Tgt	2/21	0.161433856579396	3	FACETS	1	0.994	1	0.689	0.653	0.725	INDETERMINATE	1	FALSE	1	0.3	3		511	2405	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922301	178922301	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	203	340	0	ENST00000263967.3:c.1070G>T	p.Arg357Leu	p.R357L	ENST00000263967	NM_006218.2	357	cGa/cTa	6/21	0.161433856579396	3	FACETS	0.752	0.697	0.809	0.752	0.697	0.809	INDETERMINATE	2	FALSE	1	0.3	3		340	1035	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953114	81953114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764736362	NA	P-0007272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	87	624	1	ENST00000359376.3:c.2080C>T	p.Arg694Cys	p.R694C	ENST00000359376	NM_002661.3	694	Cgc/Tgc	20/33	0.123988058869048	0	FACETS	0.332	0.292	0.374			1	INDETERMINATE	1	FALSE	0	0.3	0		625	1224	SUCCESS
APC	324	MSKCC	GRCh37	5	112175872	112175872	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	244	315	0	ENST00000257430.4:c.4581del	p.Val1528PhefsTer37	p.V1528Ffs*37	ENST00000257430	NM_000038.5	1527	ccA/cc	16/16	1	2	FACETS	0.828	0.774	0.884	1	0.993	1	CLONAL	2	FALSE	1	0.3	2		315	982	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	312	507	1	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.620938120078915	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.695593290119784	1		508	580	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401442	401442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	21	157	0	ENST00000380956.4:c.764G>A	p.Cys255Tyr	p.C255Y	ENST00000380956	NM_001195286.1	255	tGc/tAc	7/9	0.335098586423577	3	FACETS	0.259	0.199	0.329	0.13	0.099	0.165	INDETERMINATE	1	TRUE	1	0.695593290119784	3		157	314	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305399	65305399	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	252	351	0	ENST00000342505.4:c.2729T>C	p.Leu910Pro	p.L910P	ENST00000342505	NM_002227.2	910	cTg/cCg	20/25	1	2	FACETS	0.953	0.889	1	0.953	0.889	1	CLONAL	1	TRUE	1	0.386170970964735	2		351	1370	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985853	60985853	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	252	389	0	ENST00000333681.4:c.47T>A	p.Met16Lys	p.M16K	ENST00000333681		16	aTg/aAg	2/3	1	2	FACETS	0.95	0.887	1	0.95	0.887	1	CLONAL	1	TRUE	1	0.386170970964735	2		389	1374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0007357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	443	358	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			NA	2	FACETS	0.898	0.864	0.932			1	INDETERMINATE	3	TRUE	NA	0.404535944909581	2		358	813	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218844	133218844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	103	567	0	ENST00000320574.5:c.5092G>A	p.Glu1698Lys	p.E1698K	ENST00000320574	NM_006231.2	1698	Gag/Aag	38/49	0.263884604674706	1	FACETS	0.69	0.619	0.765	0.69	0.619	0.765	SUBCLONAL	1	TRUE	0	0.404535944909581	1		567	589	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0007357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	70	468	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.826	0.723	0.936	0.826	0.723	0.936	CLONAL	1	TRUE	1	0.404535944909581	2		468	419	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899272	78899272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368064754	NA	P-0007357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	165	364	1	ENST00000306801.3:c.2911G>A	p.Val971Ile	p.V971I	ENST00000306801	NM_020761.2	971	Gtc/Atc	24/34	0.404535944909581	1	FACETS	1	0.944	1	1	0.993	1	CLONAL	2	TRUE	0	0.404535944909581	1		365	322	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197530	106197530	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	157	682	0	ENST00000380013.4:c.5863G>T	p.Glu1955Ter	p.E1955*	ENST00000380013	NM_001127208.2	1955	Gag/Tag	11/11	0.404019682759416	2	FACETS	0.907	0.831	0.986	0.453	0.415	0.493	CLONAL	1	TRUE	0	0.404535944909581	2		682	856	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158382	108158382	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781785	NA	P-0007357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	223	546	1	ENST00000278616.4:c.4049C>T	p.Thr1350Met	p.T1350M	ENST00000278616	NM_000051.3	1350	aCg/aTg	27/63	0.404535944909581	2	FACETS	0.808	0.756	0.862	0.808	0.756	0.862	CLONAL	2	TRUE	0	0.404535944909581	2		547	682	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355941	73355941	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	189	570	1	ENST00000377767.4:c.30G>T	p.Lys10Asn	p.K10N	ENST00000377767	NM_014953.3	10	aaG/aaT	1/21	0.404535944909581	5	FACETS	1	0.981	1	0.399	0.367	0.431	CLONAL	1	TRUE	2	0.404535944909581	5		571	1255	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857275	9857275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426934537	NA	P-0007357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	106	611	2	ENST00000330684.3:c.4126C>T	p.Arg1376Cys	p.R1376C	ENST00000330684	NM_001134407.1	1376	Cgc/Tgc	13/13	0.217449905974887	0	FACETS	0.511	0.459	0.566			1	INDETERMINATE	1	TRUE	0	0.404535944909581	0		613	611	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0007363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	196	366	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.197421533897759	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.197421533897759	2		366	880	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045639	26045639	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs753541483	NA	P-0007363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1299	160	590	0	ENST00000540144.1:c.1A>G	p.Met1?	p.M1?	ENST00000540144	NM_003531.2	1	Atg/Gtg	1/1	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.197421533897759	2		590	1459	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989446	85989446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	38	368	0	ENST00000263360.6:c.1205C>T	p.Thr402Ile	p.T402I	ENST00000263360	NM_003797.3	402	aCa/aTa	12/12	1	2	FACETS	0.912	0.755	1	0.912	0.755	1	CLONAL	1	TRUE	1	0.197421533897759	2		368	422	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44894228	44894228	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	41	438	0	ENST00000377967.4:c.617A>C	p.Glu206Ala	p.E206A	ENST00000377967	NM_021140.2	206	gAa/gCa	7/29	0.197421533897759	1	FACETS	0.877	0.731	1	0.877	0.731	1	CLONAL	1	TRUE	0	0.197421533897759	1		438	427	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44894178	44894220	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TTTTCAGTTAGCTTTGGTTGACTGTAATCCCTGCACTTTGTCC	TTTTCAGTTAGCTTTGGTTGACTGTAATCCCTGCACTTTGTCC	AA	novel	NA	P-0007363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	38	526	0	ENST00000377967.4:c.567_609delinsAA	p.His189GlnfsTer4	p.H189Qfs*4	ENST00000377967	NM_021140.2	189	caTTTTCAGTTAGCTTTGGTTGACTGTAATCCCTGCACTTTGTCC/caAA	7/29	0.197421533897759	1	FACETS	0.669	0.552	0.799	0.669	0.552	0.799	SUBCLONAL	1	TRUE	0	0.197421533897759	1		526	519	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968916	15968916	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	100	284	0	ENST00000268712.3:c.4834A>G	p.Thr1612Ala	p.T1612A	ENST00000268712	NM_006311.3	1612	Aca/Gca	33/46	1	2	FACETS	0.916	0.822	1	0.916	0.822	1	CLONAL	1	TRUE	1	0.44278222319608	2		284	493	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911651	32911661	+	frameshift_variant	Frame_Shift_Del	DEL	AGATAATCAAA	AGATAATCAAA	-	novel	NA	P-0007366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	121	376	1	ENST00000380152.3:c.3162_3172del	p.Asp1054GlufsTer9	p.D1054Efs*9	ENST00000380152		1053	ttAGATAATCAAAag/ttag	11/27	0.44278222319608	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.44278222319608	1		377	401	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225940	2225940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	182	445	0	ENST00000326181.6:c.1732G>A	p.Glu578Lys	p.E578K	ENST00000326181	NM_032271.2	578	Gag/Aag	18/21	0.860740541518783	2	FACETS	1	0.982	1	0.567	0.531	0.603	CLONAL	1	TRUE	0	0.860740541518783	2		445	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579476	7579524	+	frameshift_variant	Frame_Shift_Del	DEL	GAGCAGCCTCTGGCATTCTGGGAGCTTCATCTGGACCTGGGTCTTCAGT	GAGCAGCCTCTGGCATTCTGGGAGCTTCATCTGGACCTGGGTCTTCAGT	-	novel	NA	P-0007370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	219	435	0	ENST00000269305.4:c.163_211del	p.Thr55ProfsTer52	p.T55Pfs*52	ENST00000269305	NM_001126112.2	55	ACTGAAGACCCAGGTCCAGATGAAGCTCCCAGAATGCCAGAGGCTGCTCcc/cc	4/11	0.860740541518783	2	FACETS	0.96	0.927	0.991	0.96	0.927	0.991	CLONAL	2	TRUE	0	0.860740541518783	2		435	265	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0007396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	58	254	1	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.801	0.687	0.925	0.801	0.687	0.925	CLONAL	1	TRUE	1	0.21	2		255	690	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948136	178948136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	66	275	0	ENST00000263967.3:c.2908G>A	p.Glu970Lys	p.E970K	ENST00000263967	NM_006218.2	970	Gaa/Aaa	20/21	1	2	FACETS	0.89	0.772	1	0.89	0.772	1	CLONAL	1	TRUE	1	0.21	2		275	706	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115380	115115400	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCACCTTTTTTCTCTTCGGC	CTCACCTTTTTTCTCTTCGGC	-	novel	NA	P-0007396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	77	406	0	ENST00000257566.3:c.926_941+5del		p.X309_splice	ENST00000257566	NM_016569.3	309		5/8	1	2	FACETS	0.736	0.645	0.835	0.736	0.645	0.835	SUBCLONAL	1	TRUE	1	0.21	2		406	996	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371708	225371708	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007411-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	250	383	0	ENST00000264414.4:c.896T>G	p.Met299Arg	p.M299R	ENST00000264414	NM_003590.4	299	aTg/aGg	7/16	0.278961989475338	3	FACETS	1	0.975	1	0.542	0.507	0.578	INDETERMINATE	1	TRUE	1	0.571682119850198	3		383	1037	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685307	89685307	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123317	NA	P-0007411-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	195	317	0	ENST00000371953.3:c.202T>C	p.Tyr68His	p.Y68H	ENST00000371953	NM_000314.4	68	Tac/Cac	3/9	0.278961989475338	3	FACETS	0.755	0.703	0.808	0.755	0.703	0.808	INDETERMINATE	2	TRUE	1	0.571682119850198	3		317	581	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032039	26032039	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007411-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	367	898	0	ENST00000244661.2:c.250C>A	p.Arg84Ser	p.R84S	ENST00000244661	NM_003537.3	84	Cgc/Agc	1/1	0.214931563828395	4	FACETS	1	0.994	1	0.675	0.639	0.712	INDETERMINATE	1	TRUE	2	0.571682119850198	4		898	1494	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391128	89391128	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007411-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	186	355	0	ENST00000336596.2:c.1194C>A	p.Asp398Glu	p.D398E	ENST00000336596	NM_005233.5	398	gaC/gaA	5/17	0.278961989475338	3	FACETS	1	0.969	1	0.543	0.503	0.585	INDETERMINATE	1	TRUE	1	0.571682119850198	3		355	770	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	147	287	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.158766171172163	3	FACETS	0.889	0.81	0.972	0.889	0.81	0.972	CLONAL	2	FALSE	1	0.158766171172163	3		287	1124	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0007487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	74	445	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.158766171172163	3	FACETS	0.971	0.848	1	0.486	0.424	0.553	CLONAL	1	FALSE	1	0.158766171172163	3		445	1036	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0007487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	90	440	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.158766171172163	2	FACETS	0.935	0.831	1	0.935	0.831	1	CLONAL	2	FALSE	0	0.158766171172163	2		440	606	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076758	72076758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1274	159	540	0	ENST00000357731.5:c.739G>A	p.Gly247Ser	p.G247S	ENST00000357731	NM_173808.2	247	Ggt/Agt	5/7	0.114739713511244	3	FACETS	0.754	0.689	0.823			1	SUBCLONAL	2	FALSE	NA	0.158766171172163	3		540	1433	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218998	193218998	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	129	264	0	ENST00000367435.3:c.1556A>T	p.Asp519Val	p.D519V	ENST00000367435	NM_024529.4	519	gAc/gTc	16/17	0.158766171172163	5	FACETS	0.941	0.852	1	0.627	0.568	0.691	CLONAL	2	FALSE	2	0.158766171172163	5		264	1069	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800963	243800963	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	189	430	1	ENST00000263826.5:c.511G>T	p.Gly171Ter	p.G171*	ENST00000263826	NM_005465.4	171	Gga/Tga	5/13	0.158766171172163	5	FACETS	1	0.943	1	0.685	0.631	0.742	CLONAL	2	FALSE	2	0.158766171172163	5		431	1434	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89176380	89176380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	55	312	0	ENST00000336596.2:c.110C>T	p.Thr37Ile	p.T37I	ENST00000336596	NM_005233.5	37	aCa/aTa	2/17	1	2	FACETS	0.694	0.592	0.807	0.694	0.592	0.807	SUBCLONAL	1	FALSE	1	0.158766171172163	2		312	998	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339554	81339554	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs571102402	NA	P-0007487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1231	135	402	0	ENST00000222390.5:c.1450G>T	p.Val484Leu	p.V484L	ENST00000222390	NM_000601.4	484	Gta/Tta	13/18	0.158766171172163	6	FACETS	0.82	0.743	0.902	0.547	0.495	0.601	CLONAL	2	FALSE	3	0.158766171172163	6		402	1366	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242310	98242310	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	67	313	0	ENST00000331920.6:c.1008C>A	p.His336Gln	p.H336Q	ENST00000331920	NM_000264.3	336	caC/caA	7/24	1	2	FACETS	0.847	0.734	0.971	0.847	0.734	0.971	CLONAL	1	FALSE	1	0.158766171172163	2		313	996	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132861	64132861	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751393577	NA	P-0007487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	327	438	1	ENST00000334205.4:c.995C>T	p.Ala332Val	p.A332V	ENST00000334205	NM_003942.2	332	gCg/gTg	9/17	0.158766171172163	3	FACETS	1	0.982	1	1	0.995	1	CLONAL	3	FALSE	1	0.158766171172163	3		439	1354	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137809	64137809	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	284	437	0	ENST00000334205.4:c.1910G>T	p.Gly637Val	p.G637V	ENST00000334205	NM_003942.2	637	gGg/gTg	15/17	0.158766171172163	3	FACETS	1	0.952	1	1	0.993	1	CLONAL	3	FALSE	1	0.158766171172163	3		437	1267	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457998	69457998	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs866931401	NA	P-0007487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	224	258	0	ENST00000227507.2:c.398G>T	p.Arg133Leu	p.R133L	ENST00000227507	NM_053056.2	133	cGg/cTg	2/5	0.158766171172163	6	FACETS	1	0.979	1			1	CLONAL	3	FALSE	NA	0.158766171172163	6		258	1102	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657373	29657373	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1567613630	NA	P-0007487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1229	144	368	0	ENST00000356175.3:c.5606G>T	p.Gly1869Val	p.G1869V	ENST00000356175	NM_000267.3	1869	gGc/gTc	38/57	0.114906721807522	4	FACETS	0.765	0.696	0.839	0.765	0.696	0.839	SUBCLONAL	2	FALSE	2	0.158766171172163	4		368	1373	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619428	1619428	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757623802	NA	P-0007487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	93	382	0	ENST00000344749.5:c.1213C>T	p.Arg405Cys	p.R405C	ENST00000344749	NM_001136139.2	405	Cgc/Tgc	15/19	0.158766171172163	2	FACETS	1	0.937	1	0.542	0.481	0.608	CLONAL	1	FALSE	0	0.158766171172163	2		382	1080	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007800	45007801	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0007487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	70	261	0	ENST00000558401.1:c.248_249del	p.Tyr83SerfsTer6	p.Y83Sfs*6	ENST00000558401	NM_004048.2	83	TAt/t	2/4	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	FALSE	1	0.158766171172163	2		261	841	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993615	90993615	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1554568272	NA	P-0007487-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	51	268	0	ENST00000265433.3:c.308G>T	p.Gly103Val	p.G103V	ENST00000265433	NM_002485.4	103	gGa/gTa	3/16	0.114906721807522	4	FACETS	0.759	0.643	0.887	0.379	0.321	0.444	SUBCLONAL	1	FALSE	2	0.158766171172163	4		268	981	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007494-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	54	543	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.0977127428483827	3	FACETS	0.87	0.742	1	0.87	0.742	1	CLONAL	2	FALSE	1	0.0977127428483827	3		543	666	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795082	242795082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368829632	NA	P-0007494-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	47	328	0	ENST00000334409.5:c.127G>A	p.Val43Met	p.V43M	ENST00000334409	NM_005018.2	43	Gtg/Atg	2/5	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.0977127428483827	2		328	673	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991139	41991139	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007494-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	60	458	0	ENST00000219905.7:c.2092G>A	p.Gly698Ser	p.G698S	ENST00000219905	NM_001164273.1	698	Ggt/Agt	4/24	0.0911908064550298	2	FACETS	1	0.96	1	0.673	0.578	0.777	CLONAL	1	FALSE	0	0.0977127428483827	2		458	912	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482861	67482861	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567005581	NA	P-0007494-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	87	241	0	ENST00000327367.4:c.1265C>A	p.Ser422Tyr	p.S422Y	ENST00000327367	NM_005902.3	422	tCc/tAc	9/9	0.0911908064550298	2	FACETS	1	0.946	1	1	0.982	1	CLONAL	3	FALSE	0	0.0977127428483827	2		241	534	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913529	39913542	+	frameshift_variant	Frame_Shift_Del	DEL	AAGTCCCAAGTGCC	AAGTCCCAAGTGCC	-	novel	NA	P-0007494-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	86	323	0	ENST00000378444.4:c.4786_4799del	p.Gly1596LeufsTer7	p.G1596Lfs*7	ENST00000378444	NM_001123385.1	1596	GGCACTTGGGACTTc/c	13/15	1	1	FACETS	1	0.96	1	1	0.987	1	CLONAL	2	FALSE	0	0.0977127428483827	1		323	699	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0007497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	55	388	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.281139227165966	2		389	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0007497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	98	411	0	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.210640961525038	3	FACETS	1	0.961	1	0.757	0.682	0.836	CLONAL	2	TRUE	0	0.281139227165966	3		411	350	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651960	36651960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763967941	NA	P-0007497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	51	262	0	ENST00000244741.5:c.82G>A	p.Glu28Lys	p.E28K	ENST00000244741	NM_000389.4	28	Gag/Aag	2/3	0.294294732569146	4	FACETS	1	0.899	1	1	0.899	1	CLONAL	2	TRUE	2	0.281139227165966	4		262	220	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913468	32913468	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	360	739	0	ENST00000380152.3:c.4976C>G	p.Ser1659Cys	p.S1659C	ENST00000380152		1659	tCc/tGc	11/27	0.281139227165966	14	FACETS	0.964	0.913	1			1	CLONAL	5	TRUE	NA	0.281139227165966	14		739	1427	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915261	32915261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1566235374	NA	P-0007497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	323	713	0	ENST00000380152.3:c.6769C>T	p.Pro2257Ser	p.P2257S	ENST00000380152		2257	Ccc/Tcc	11/27	0.281139227165966	14	FACETS	1	0.95	1			1	CLONAL	5	TRUE	NA	0.281139227165966	14		713	1227	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343540	343540	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	37	474	0	ENST00000262320.3:c.2134C>T	p.Arg712Ter	p.R712*	ENST00000262320	NM_003502.3	712	Cga/Tga	8/11	0.272031652669933	3	FACETS	1	0.889	1	0.55	0.455	0.654	CLONAL	1	TRUE	1	0.281139227165966	3		474	273	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867370	68867370	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	22	389	0	ENST00000261769.5:c.2617G>A	p.Ala873Thr	p.A873T	ENST00000261769	NM_004360.3	873	Gct/Act	16/16	0.272031652669933	3	FACETS	0.609	0.472	0.768	0.305	0.236	0.384	SUBCLONAL	1	TRUE	1	0.281139227165966	3		389	293	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490259	29490259	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	64	495	0	ENST00000356175.3:c.344C>T	p.Pro115Leu	p.P115L	ENST00000356175	NM_000267.3	115	cCa/cTa	4/57	0.210640961525038	3	FACETS	1	0.951	1	0.402	0.349	0.459	CLONAL	1	TRUE	0	0.281139227165966	3		495	431	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0007500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	72	719	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.16	2		719	734	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167813	56167813	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	45	443	0	ENST00000399503.3:c.1378G>C	p.Glu460Gln	p.E460Q	ENST00000399503	NM_005921.1	460	Gaa/Caa	7/20	0.503024919938176	2	FACETS	0.233	0.195	0.276	0.117	0.097	0.138	SUBCLONAL	1	TRUE	0	0.50983179802988	2		443	757	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514569	103514569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	75	281	0	ENST00000355739.4:c.1070C>T	p.Ser357Leu	p.S357L	ENST00000355739	NM_000123.3	357	tCa/tTa	8/15	0.499570952811449	2	FACETS	0.588	0.517	0.665	0.294	0.258	0.333	SUBCLONAL	1	TRUE	0	0.50983179802988	2		281	500	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383631	15383631	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	40	284	0	ENST00000263377.2:c.280C>T	p.Leu94Phe	p.L94F	ENST00000263377	NM_058243.2	94	Ctc/Ttc	2/20	0.499570952811449	2	FACETS	0.275	0.228	0.327	0.137	0.114	0.164	SUBCLONAL	1	TRUE	0	0.50983179802988	2		284	571	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578424	7578427	+	frameshift_variant	Frame_Shift_Del	DEL	ATGT	ATGT	-	novel	NA	P-0007518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	356	273	0	ENST00000269305.4:c.503_506del	p.His168ArgfsTer5	p.H168Rfs*5	ENST00000269305	NM_001126112.2	168	cACATg/cg	5/11	0.482859816798688	3	FACETS	0.938	0.899	0.976	0.938	0.899	0.976	CLONAL	3	TRUE	0	0.50983179802988	3		273	623	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0007543-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	140	446	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.437459395521214	4	FACETS	0.803	0.734	0.874	0.535	0.489	0.583	CLONAL	2	TRUE	1	0.437459395521214	4		446	573	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259433	89259433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007543-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	241	718	0	ENST00000336596.2:c.577G>A	p.Val193Met	p.V193M	ENST00000336596	NM_005233.5	193	Gtg/Atg	3/17	NA	2	FACETS	0.832	0.776	0.891			1	INDETERMINATE	1	TRUE	NA	0.437459395521214	2		718	1324	SUCCESS
AXL	558	MSKCC	GRCh37	19	41736934	41736934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768702995	NA	P-0007543-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	172	444	0	ENST00000301178.4:c.649C>T	p.Arg217Cys	p.R217C	ENST00000301178	NM_021913.4	217	Cgc/Tgc	5/20	1	2	FACETS	0.911	0.839	0.986	0.911	0.839	0.986	CLONAL	1	TRUE	1	0.437459395521214	2		444	863	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016149	31016149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370054224	NA	P-0007543-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	240	734	0	ENST00000375687.4:c.395C>T	p.Ser132Leu	p.S132L	ENST00000375687	NM_015338.5	132	tCg/tTg	6/13	1	2	FACETS	0.894	0.834	0.957	0.894	0.834	0.957	CLONAL	1	TRUE	1	0.437459395521214	2		734	1227	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711894	89711894	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786204865	NA	P-0007566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	224	342	0	ENST00000371953.3:c.512A>G	p.Gln171Arg	p.Q171R	ENST00000371953	NM_000314.4	171	cAg/cGg	6/9	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.598835683690932	2		342	709	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342743	87342743	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	238	358	0	ENST00000277120.3:c.1028A>G	p.His343Arg	p.H343R	ENST00000277120		343	cAc/cGc	9/19	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.598835683690932	2		358	738	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845610	68845618	+	inframe_deletion	In_Frame_Del	DEL	GCCACAGAC	GCCACAGAC	-	novel	NA	P-0007566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	204	366	0	ENST00000261769.5:c.858_866del	p.Thr287_Ala289del	p.T287_A289del	ENST00000261769	NM_004360.3	286	GCCACAGAC/-	7/16	0.598835683690932	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.598835683690932	1		366	456	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720809	89720809	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	82	174	1	ENST00000371953.3:c.961del	p.Thr321GlnfsTer23	p.T321Qfs*23	ENST00000371953	NM_000314.4	320	ttA/tt	8/9	1	2	FACETS	0.958	0.854	1	0.958	0.854	1	CLONAL	1	TRUE	1	0.598835683690932	2		175	286	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007578-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	128	225	0				ENST00000310581	NM_198253.2	-/1132			0.309633837042189	5	FACETS	1	0.948	1	0.698	0.64	0.757	INDETERMINATE	2	TRUE	2	0.677421580356466	5		225	364	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0007578-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	161	319	2	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.430777419622009	3	FACETS	1	0.94	1	0.512	0.472	0.554	CLONAL	1	TRUE	1	0.677421580356466	3		321	621	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782329	NA	P-0007578-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	237	209	2	ENST00000269305.4:c.746G>C	p.Arg249Thr	p.R249T	ENST00000269305	NM_001126112.2	249	aGg/aCg	7/11	0.576021225452274	2	FACETS	0.847	0.804	0.89	0.847	0.804	0.89	CLONAL	2	TRUE	0	0.677421580356466	2		211	413	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145430	58145430	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894340	NA	P-0007578-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	251	202	1	ENST00000257904.6:c.71G>T	p.Arg24Leu	p.R24L	ENST00000257904	NM_000075.3	24	cGt/cTt	2/8	0.303882266622642	4	FACETS	0.924	0.869	0.979	0.924	0.869	0.979	INDETERMINATE	2	TRUE	2	0.677421580356466	4		203	673	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344011	70344011	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007578-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	412	247	1	ENST00000374080.3:c.1747G>T	p.Asp583Tyr	p.D583Y	ENST00000374080		583	Gac/Tac	13/45	0.540305431401891	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.677421580356466	2		248	542	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436684	8436684	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1294993838	NA	P-0007578-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	498	257	0	ENST00000356435.5:c.3994G>T	p.Ala1332Ser	p.A1332S	ENST00000356435		1332	Gct/Tct	24/35	0.677421580356466	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	0	0.677421580356466	3		257	646	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431339	49431339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007578-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	98	85	0	ENST00000301067.7:c.9800C>T	p.Ser3267Leu	p.S3267L	ENST00000301067	NM_003482.3	3267	tCa/tTa	34/54	0.365158257890261	4	FACETS	0.831	0.751	0.913			1	INDETERMINATE	2	TRUE	NA	0.677421580356466	4		85	292	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862746	9862746	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007578-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	64	233	0	ENST00000330684.3:c.2557T>A	p.Cys853Ser	p.C853S	ENST00000330684	NM_001134407.1	853	Tgc/Agc	12/13	0.365158257890261	4	FACETS	0.481	0.416	0.552			1	INDETERMINATE	1	TRUE	NA	0.677421580356466	4		233	659	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33430271	33430271	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0007578-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	356	345	0	ENST00000345365.6:c.738+2T>C		p.X246_splice	ENST00000345365	NM_002878.3	246			0.303882266622642	4	FACETS	0.944	0.897	0.991	0.944	0.897	0.991	INDETERMINATE	2	TRUE	2	0.677421580356466	4		345	934	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207181	1207181	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007578-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	251	208	0	ENST00000326873.7:c.269A>T	p.Asn90Ile	p.N90I	ENST00000326873	NM_000455.4	90	aAc/aTc	1/10	0.309633837042189	5	FACETS	1	0.97	1	0.699	0.658	0.742	INDETERMINATE	2	TRUE	2	0.677421580356466	5		208	712	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0007624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	25	522	1	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	1	2	FACETS	0.269	0.211	0.336	0.269	0.211	0.336	SUBCLONAL	1	FALSE	1	0.3	2		523	619	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0007624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	21	330	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.143	0.109	0.183	0.143	0.109	0.183	SUBCLONAL	1	FALSE	1	0.3	2		330	981	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593387	48593387	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0007630-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	219	252	0	ENST00000342988.3:c.1140-2A>T		p.X380_splice	ENST00000342988	NM_005359.5	380			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		252	539	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	189	225	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.94	0.879	1	0.94	0.879	1	CLONAL	1	TRUE	1	0.893395357128332	2		225	450	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0007649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	330	546	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.893395357128332	1	FACETS	0.962	0.931	0.991	0.962	0.931	0.991	CLONAL	1	TRUE	0	0.893395357128332	1		546	425	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962834	2962834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778151	NA	P-0007649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	86	304	0	ENST00000396946.4:c.2074G>A	p.Val692Met	p.V692M	ENST00000396946	NM_032415.4	692	Gtg/Atg	16/25	1	2	FACETS	0.222	0.196	0.25	0.222	0.196	0.25	SUBCLONAL	1	TRUE	1	0.893395357128332	2		304	868	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138061	64138061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	92	284	1	ENST00000334205.4:c.1984C>T	p.Arg662Trp	p.R662W	ENST00000334205	NM_003942.2	662	Cgg/Tgg	16/17	1	2	FACETS	0.227	0.201	0.255	0.227	0.201	0.255	SUBCLONAL	1	TRUE	1	0.893395357128332	2		285	907	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922940	39922941	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0007649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	105	261	0	ENST00000378444.4:c.3767_3768del	p.Lys1256ThrfsTer20	p.K1256Tfs*20	ENST00000378444	NM_001123385.1	1256	aAA/a	8/15	1	1	FACETS	0.216	0.194	0.24	0.216	0.194	0.24	SUBCLONAL	1	TRUE	0	0.893395357128332	1		261	601	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0007650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	18	334	2	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	0.457	0.345	0.589	0.457	0.345	0.589	SUBCLONAL	1	TRUE	1	0.364586159632516	2		336	216	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913492	NA	P-0007650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	8	323	0	ENST00000286548.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000286548	NM_002072.3	209	cAa/cTa	5/7	1	2	FACETS	0.219	0.141	0.321	0.219	0.141	0.321	SUBCLONAL	1	TRUE	1	0.364586159632516	2		323	200	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610581	10610583	+	frameshift_variant	Frame_Shift_Del	DEL	CGT	CGT	A	novel	NA	P-0007665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	11	457	0	ENST00000171111.5:c.127_129delinsT	p.Thr43SerfsTer35	p.T43Sfs*35	ENST00000171111	NM_203500.1	43	ACG/T	2/6	0.0974390620318837	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		457	127	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418345	139418345	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007677-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	111	523	0	ENST00000277541.6:c.227T>A	p.Val76Glu	p.V76E	ENST00000277541	NM_017617.3	76	gTg/gAg	3/34	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.627663769474265	2		523	343	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0007686-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	208	345	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.486305898356017	4	FACETS	0.817	0.761	0.874	0.817	0.761	0.874	CLONAL	2	TRUE	2	0.569298258595724	4		345	702	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0007686-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	674	334	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.330195144212831	4	FACETS	0.877	0.853	0.902	0.877	0.853	0.902	INDETERMINATE	4	TRUE	0	0.569298258595724	4		334	1059	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0007686-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	302	351	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.55337772229007	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.569298258595724	2		351	524	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650063	206650063	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007686-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1206	80	283	1	ENST00000367120.3:c.583C>A	p.Gln195Lys	p.Q195K	ENST00000367120	NM_014002.3	195	Caa/Aaa	7/22	0.486305898356017	4	FACETS	0.343	0.3	0.389	0.171	0.15	0.195	SUBCLONAL	1	TRUE	2	0.569298258595724	4		284	1286	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858566	27858566	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007686-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	275	491	0	ENST00000359303.2:c.5C>A	p.Ala2Asp	p.A2D	ENST00000359303	NM_003535.2	2	gCc/gAc	1/1	0.323852766475052	4	FACETS	1	0.99	1	0.637	0.597	0.678	INDETERMINATE	1	TRUE	2	0.569298258595724	4		491	1190	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0007690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	306	395	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	0.276045702374783	2	FACETS	0.786	0.746	0.826	0.786	0.746	0.826	INDETERMINATE	2	TRUE	0	0.569940059331222	2		395	683	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437503	52437522	+	frameshift_variant	Frame_Shift_Del	DEL	AGATCACGGACAGCACGGTT	AGATCACGGACAGCACGGTT	-	novel	NA	P-0007690-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	448	674	0	ENST00000460680.1:c.1639_1658del	p.Asn547GlyfsTer13	p.N547Gfs*13	ENST00000460680	NM_004656.3	547	AACCGTGCTGTCCGTGATCTg/g	13/17	0.539725817353254	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.569940059331222	2		674	783	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0007693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	32	567	2	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	1	2	FACETS	0.125	0.101	0.153	0.125	0.101	0.153	SUBCLONAL	1	TRUE	1	0.68620438195545	2		569	744	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0007693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	242	522	1	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.68620438195545	2		523	519	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711902	89711902	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	339	455	0	ENST00000371953.3:c.520T>C	p.Tyr174His	p.Y174H	ENST00000371953	NM_000314.4	174	Tat/Cat	6/9	0.68620438195545	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.68620438195545	1		455	495	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432028	121432028	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778074427	NA	P-0007693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	229	590	0	ENST00000257555.6:c.775G>A	p.Val259Ile	p.V259I	ENST00000257555		259	Gtc/Atc	4/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.68620438195545	2		590	569	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533390	29533390	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs267604791	NA	P-0007693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	193	221	0	ENST00000356175.3:c.1392+1G>A		p.X464_splice	ENST00000356175	NM_000267.3	464			1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.68620438195545	2		221	468	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652851	29652851	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007693-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	239	424	0	ENST00000356175.3:c.4786C>T	p.Gln1596Ter	p.Q1596*	ENST00000356175	NM_000267.3	1596	Caa/Taa	36/57	1	2	FACETS	0.827	0.774	0.882	0.827	0.774	0.882	CLONAL	1	TRUE	1	0.68620438195545	2		424	842	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0007705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	66	456	0	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	0.289507106931974	0	FACETS	0.422	0.366	0.482			1	SUBCLONAL	1	TRUE	0	0.368626018036069	0		456	536	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797845	45797845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782727	NA	P-0007746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	49	358	0	ENST00000450313.1:c.926G>A	p.Arg309His	p.R309H	ENST00000450313	NM_012222.2	309	cGc/cAc	10/16	1	2	FACETS	0.829	0.7	0.973	0.829	0.7	0.973	CLONAL	1	TRUE	1	0.13	2		358	909	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573505	48573506	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0007746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	55	421	0	ENST00000342988.3:c.94_95del	p.Ser32Ter	p.S32*	ENST00000342988	NM_005359.5	30	gGA/g	2/12	1	2	FACETS	0.78	0.665	0.907	0.78	0.665	0.907	CLONAL	1	TRUE	1	0.13	2		421	1085	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535450	66535450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	14	136	0	ENST00000273854.3:c.11C>T	p.Ser4Leu	p.S4L	ENST00000273854	NM_004439.5	4	tCg/tTg	1/18	1	2	FACETS	0.804	0.58	1	0.804	0.58	1	CLONAL	1	TRUE	1	0.13	2		136	268	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11297958	11297958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs566273004	NA	P-0007746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	39	358	0	ENST00000361445.4:c.2150G>A	p.Arg717Gln	p.R717Q	ENST00000361445	NM_004958.3	717	cGa/cAa	13/58	1	2	FACETS	0.821	0.678	0.981	0.821	0.678	0.981	CLONAL	1	TRUE	1	0.13	2		358	731	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044408	128044408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373790042	NA	P-0007746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	55	426	0	ENST00000285398.2:c.1213G>A	p.Val405Ile	p.V405I	ENST00000285398	NM_000122.1	405	Gtt/Att	8/15	1	2	FACETS	0.953	0.813	1	0.953	0.813	1	CLONAL	1	TRUE	1	0.13	2		426	888	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606743	43606743	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774092678	NA	P-0007746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	46	398	0	ENST00000355710.3:c.1352C>T	p.Thr451Met	p.T451M	ENST00000355710	NM_020975.4	451	aCg/aTg	7/20	1	2	FACETS	0.775	0.65	0.914	0.775	0.65	0.914	CLONAL	1	TRUE	1	0.13	2		398	913	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562996	21562996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	33	342	0	ENST00000382592.4:c.923C>T	p.Ala308Val	p.A308V	ENST00000382592	NM_014572.2	308	gCc/gTc	4/8	1	2	FACETS	0.827	0.672	1	0.827	0.672	1	CLONAL	1	TRUE	1	0.13	2		342	614	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0007748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	63	735	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.483017173898692	3	FACETS	1	0.911	1	0.529	0.461	0.602	CLONAL	1	FALSE	1	0.483017173898692	3		735	306	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909864	100909864	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	40	544	0	ENST00000325455.5:c.2785C>T	p.Leu929Phe	p.L929F	ENST00000325455	NM_001202474.3	929	Ctc/Ttc	8/8	0.483017173898692	3	FACETS	0.791	0.661	0.933	0.395	0.33	0.467	CLONAL	1	FALSE	1	0.483017173898692	3		544	260	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0007771-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	486	735	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.750043115204945	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.750043115204945	2		735	614	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227855	55227855	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007771-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	304	334	0	ENST00000275493.2:c.1322T>G	p.Val441Gly	p.V441G	ENST00000275493	NM_005228.3	441	gTc/gGc	12/28	0.750043115204945	6	FACETS	1	0.988	1	0.461	0.435	0.486	CLONAL	2	TRUE	1	0.750043115204945	6		334	880	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195296	102195296	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238807475	NA	P-0007771-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	242	742	1	ENST00000263464.3:c.56C>T	p.Thr19Met	p.T19M	ENST00000263464	NM_001165.4	19	aCg/aTg	2/9	0.750043115204945	3	FACETS	0.828	0.774	0.885	0.414	0.387	0.443	CLONAL	1	TRUE	1	0.750043115204945	3		743	1071	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350291	15350291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1233820799	NA	P-0007771-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	495	432	1	ENST00000263377.2:c.3488G>A	p.Arg1163Gln	p.R1163Q	ENST00000263377	NM_058243.2	1163	cGg/cAg	17/20	0.750043115204945	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.750043115204945	3		433	559	SUCCESS
APC	324	MSKCC	GRCh37	5	112164587	112164587	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007771-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	278	257	0	ENST00000257430.4:c.1661del	p.Arg554GlnfsTer4	p.R554Qfs*4	ENST00000257430	NM_000038.5	554	cGa/ca	14/16	0.750043115204945	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.750043115204945	2		257	348	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0007774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	293	365	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.660370172864729	1	FACETS	0.777	0.735	0.82	0.777	0.735	0.82	SUBCLONAL	1	TRUE	0	0.660370172864729	1		365	765	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	193	233	0	ENST00000269305.4:c.542G>C	p.Arg181Pro	p.R181P	ENST00000269305	NM_001126112.2	181	cGc/cCc	5/11	0.660370172864729	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.660370172864729	1		233	353	SUCCESS
APC	324	MSKCC	GRCh37	5	112175174	112175174	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	67	151	0	ENST00000257430.4:c.3883G>T	p.Glu1295Ter	p.E1295*	ENST00000257430	NM_000038.5	1295	Gaa/Taa	16/16	1	2	FACETS	0.793	0.697	0.894	0.793	0.697	0.894	SUBCLONAL	1	TRUE	1	0.660370172864729	2		151	256	SUCCESS
APC	324	MSKCC	GRCh37	5	112174814	112174814	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085081	NA	P-0007774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	159	386	0	ENST00000257430.4:c.3523C>T	p.Gln1175Ter	p.Q1175*	ENST00000257430	NM_000038.5	1175	Cag/Tag	16/16	1	2	FACETS	0.839	0.773	0.907	0.839	0.773	0.907	CLONAL	1	TRUE	1	0.660370172864729	2		386	574	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936349	49936349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755080567	NA	P-0007774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	540	655	2	ENST00000296474.3:c.1499G>A	p.Arg500Gln	p.R500Q	ENST00000296474	NM_002447.2	500	cGg/cAg	3/20	1	2	FACETS	0.988	0.947	1	0.988	0.947	1	CLONAL	1	TRUE	1	0.660370172864729	2		657	1655	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003272	42003272	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0007774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	402	705	0	ENST00000219905.7:c.2809A>T	p.Lys937Ter	p.K937*	ENST00000219905	NM_001164273.1	937	Aag/Tag	8/24	0.660370172864729	1	FACETS	0.964	0.923	1	0.964	0.923	1	CLONAL	1	TRUE	0	0.660370172864729	1		705	846	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388036	31388036	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs768347895	NA	P-0007774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2110	227	473	0	ENST00000328111.2:c.1837G>T	p.Val613Phe	p.V613F	ENST00000328111	NM_006892.3	613	Gtt/Ttt	17/23	0.660370172864729	5	FACETS	0.586	0.543	0.631	0.195	0.181	0.211	SUBCLONAL	1	TRUE	2	0.660370172864729	5		473	2337	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	GA	novel	NA	P-0007774-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	154	344	0	ENST00000311936.3:c.34_35delinsTC	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	GGt/TCt	2/5	1	2	FACETS	0.799	0.734	0.865	0.799	0.734	0.865	SUBCLONAL	1	TRUE	1	0.660370172864729	2		344	584	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377118	118377118	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	62	436	0	ENST00000534358.1:c.10511T>C	p.Leu3504Ser	p.L3504S	ENST00000534358	NM_005933.3	3504	tTa/tCa	27/36	1	2	FACETS	0.418	0.36	0.482	0.418	0.36	0.482	SUBCLONAL	1	TRUE	1	0.332740121145596	2		436	891	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	401	287	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.338898258165052	5	FACETS	0.998	0.95	1	0.998	0.95	1	CLONAL	3	TRUE	2	0.338898258165052	5		287	1192	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0007838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	159	339	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.2480968466568	2	FACETS	0.768	0.707	0.831	0.768	0.707	0.831	SUBCLONAL	2	TRUE	0	0.338898258165052	2		339	611	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910333	29910333	+	start_lost	Translation_Start_Site	SNP	G	G	T	novel	NA	P-0007838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	83	548	0	ENST00000376809.5:c.3G>T	p.Met1?	p.M1?	ENST00000376809	NM_002116.7	1	atG/atT	1/8	0.306619271474996	4	FACETS	0.618	0.544	0.698	0.206	0.181	0.233	SUBCLONAL	1	TRUE	1	0.338898258165052	4		548	1061	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133845	41133845	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1205	161	659	0	ENST00000379561.5:c.1783C>T	p.Gln595Ter	p.Q595*	ENST00000379561	NM_002015.3	595	Cag/Tag	2/3	0.338898258165052	3	FACETS	0.813	0.744	0.887	0.271	0.248	0.296	CLONAL	1	TRUE	0	0.338898258165052	3		659	1366	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729820	47729820	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0007838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	159	408	0	ENST00000449228.1:c.568+1G>A		p.X190_splice	ENST00000449228	NM_001127240.2	190			0.338898258165052	4	FACETS	0.756	0.693	0.821	0.756	0.693	0.821	SUBCLONAL	2	TRUE	2	0.338898258165052	4		408	831	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89871723	89872081	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGGATGCTTCCATCTGTTCACAAAGGCAGCACAGATTCCTGAAGAGCCACGATCCCACAGCATGCATGTCGGGATGGCTGGAGACACACACAGAGGCAGACGTAAGGCTCAACTAAATCCCATCATCAGGGGATTGAGTTGAGCCATATGTCCCAATTTTTTTTTTGAGACAGTTTTTTGCTGTCACTGAGGCTGGAGTGCAGTGGCGCAATCAGTCACTGCACCCTCGACCTCCCAGGCTCAAGCAATCCTTCCACCTCAGCCTCCTGAGTAGTTGGGACAACAGGCGCATACCACCACGCCCAGCTGGAGGTCTTACTACTTTGCCCAGGCTGGACTCAAACTCCCGGGCTCAAAA	CAGGATGCTTCCATCTGTTCACAAAGGCAGCACAGATTCCTGAAGAGCCACGATCCCACAGCATGCATGTCGGGATGGCTGGAGACACACACAGAGGCAGACGTAAGGCTCAACTAAATCCCATCATCAGGGGATTGAGTTGAGCCATATGTCCCAATTTTTTTTTTGAGACAGTTTTTTGCTGTCACTGAGGCTGGAGTGCAGTGGCGCAATCAGTCACTGCACCCTCGACCTCCCAGGCTCAAGCAATCCTTCCACCTCAGCCTCCTGAGTAGTTGGGACAACAGGCGCATACCACCACGCCCAGCTGGAGGTCTTACTACTTTGCCCAGGCTGGACTCAAACTCCCGGGCTCAAAA	-	novel	NA	P-0007838-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	43	466	1	ENST00000389301.3:c.597-281_674del		p.X199_splice	ENST00000389301	NM_000135.2	199		7/43	0.107824386508659	5	FACETS	0.454	0.378	0.538	0.113	0.094	0.135	INDETERMINATE	1	TRUE	1	0.338898258165052	5		467	844	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0007845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	265	404	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.34806871150961	2	FACETS	0.999	0.941	1	0.999	0.941	1	CLONAL	2	FALSE	0	0.34806871150961	2		405	762	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692893	89692893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1114167656	NA	P-0007845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	96	211	0	ENST00000371953.3:c.377C>T	p.Ala126Val	p.A126V	ENST00000371953	NM_000314.4	126	gCt/gTt	5/9	0.287567151243511	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	0	0.34806871150961	1		211	403	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	106	543	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.947	0.849	1	0.947	0.849	1	CLONAL	1	TRUE	1	0.310072422106983	2		543	722	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0007855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	219	428	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.413147427282906	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.413042914161543	2		428	507	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522568	106522568	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs754441790	NA	P-0007855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	74	421	1	ENST00000359195.3:c.2545C>T	p.Arg849Ter	p.R849*	ENST00000359195	NM_002649.2	849	Cga/Tga	7/11	0.386218248411908	4	FACETS	0.983	0.863	1	0.492	0.431	0.556	CLONAL	1	TRUE	2	0.413042914161543	4		422	515	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0007861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	76	388	1	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	0.21	2		389	722	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166769	32166769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs527962523	NA	P-0007861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	35	304	0	ENST00000375023.3:c.4469G>A	p.Arg1490Gln	p.R1490Q	ENST00000375023	NM_004557.3	1490	cGg/cAg	24/30	0.184210254505261	3	FACETS	0.801	0.656	0.963	0.4	0.328	0.482	CLONAL	1	TRUE	1	0.21	3		304	460	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417614	139417634	+	inframe_deletion	In_Frame_Del	DEL	ACGGGTCAGCCTGCTGGCACG	ACGGGTCAGCCTGCTGGCACG	-	novel	NA	P-0007861-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	34	311	0	ENST00000277541.6:c.410_430del	p.Ser137_Pro143del	p.S137_P143del	ENST00000277541	NM_017617.3	137	tCGTGCCAGCAGGCTGACCCGTgc/tgc	4/34	1	2	FACETS	0.784	0.641	0.945	0.784	0.641	0.945	CLONAL	1	TRUE	1	0.21	2		311	413	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0007864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	55	213	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.976	0.837	1	0.976	0.837	1	CLONAL	1	TRUE	1	0.268959843915502	2		213	419	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0007864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	139	478	5	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.268959843915502	4	FACETS	1	0.986	1	0.739	0.672	0.808	CLONAL	1	TRUE	2	0.268959843915502	4		483	888	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0007864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	74	401	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.268959843915502	4	FACETS	0.751	0.656	0.854	0.375	0.328	0.427	SUBCLONAL	1	TRUE	2	0.268959843915502	4		401	930	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0007864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	97	461	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	0.268959843915502	1	FACETS	0.881	0.785	0.982	0.881	0.785	0.982	CLONAL	1	TRUE	0	0.268959843915502	1		461	709	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004270	150004270	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	157	737	0	ENST00000253339.5:c.1955A>G	p.Lys652Arg	p.K652R	ENST00000253339		652	aAa/aGa	3/7	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.268959843915502	2		737	1140	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713613	30713613	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	74	279	0	ENST00000295754.5:c.939del	p.Lys314ArgfsTer10	p.K314Rfs*10	ENST00000295754	NM_003242.5	313	cGg/cg	4/7	0.268959843915502	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.268959843915502	1		279	415	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	213	225	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.770166642949828	2		225	532	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690847	89690847	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587776667	NA	P-0007880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	196	307	0	ENST00000371953.3:c.253+1G>T		p.X85_splice	ENST00000371953	NM_000314.4	85			0.770166642949828	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.770166642949828	1		307	270	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916726	178916726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772110575	NA	P-0007880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1595	87	766	4	ENST00000263967.3:c.113G>A	p.Arg38His	p.R38H	ENST00000263967	NM_006218.2	38	cGt/cAt	2/21	1	2	FACETS	0.134	0.118	0.152	0.134	0.118	0.152	SUBCLONAL	1	TRUE	1	0.770166642949828	2		770	1682	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053155	180053155	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	265	428	0	ENST00000261937.6:c.1214C>T	p.Ala405Val	p.A405V	ENST00000261937	NM_182925.4	405	gCt/gTt	9/30	1	2	FACETS	0.582	0.545	0.62	0.582	0.545	0.62	SUBCLONAL	1	TRUE	1	0.770166642949828	2		428	1182	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972424	81972424	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007880-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	716	698	3	ENST00000359376.3:c.3217C>T	p.Leu1073Phe	p.L1073F	ENST00000359376	NM_002661.3	1073	Ctc/Ttc	29/33	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.770166642949828	2		701	1857	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0007885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	788	636	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	0.686594494539095	3	FACETS	1	0.997	1	0.779	0.759	0.8	CLONAL	2	TRUE	0	0.721713445707538	3		636	1271	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0007885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	387	251	1	ENST00000269305.4:c.97-1G>T		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.721713445707538	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.721713445707538	2		252	522	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646923	37646923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1572	283	654	1	ENST00000447079.4:c.2045C>T	p.Pro682Leu	p.P682L	ENST00000447079	NM_015083.1	682	cCc/cTc	3/14	0.721713445707538	4	FACETS	0.728	0.681	0.776			1	SUBCLONAL	1	TRUE	NA	0.721713445707538	4		655	1855	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528645	89528645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	295	319	2	ENST00000336596.2:c.2945C>T	p.Pro982Leu	p.P982L	ENST00000336596	NM_005233.5	982	cCc/cTc	17/17	0.664229005100137	1	FACETS	0.991	0.946	1	0.991	0.946	1	CLONAL	1	TRUE	0	0.721713445707538	1		321	527	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056568	26056568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs41266789	NA	P-0007885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	63	142	0	ENST00000343677.2:c.89G>C	p.Gly30Ala	p.G30A	ENST00000343677	NM_005319.3	30	gGt/gCt	1/1	NA	2	FACETS	0.513	0.447	0.585			1	INDETERMINATE	1	TRUE	NA	0.721713445707538	2		142	340	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971174	13971174	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	92	389	0	ENST00000405192.2:c.755C>G	p.Pro252Arg	p.P252R	ENST00000405192	NM_001163147.1	252	cCt/cGt	8/12	0.685525655289946	1	FACETS	0.248	0.22	0.277	0.248	0.22	0.277	SUBCLONAL	1	TRUE	0	0.721713445707538	1		389	658	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738669	145738669	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs34293591	NA	P-0007885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	66	232	0	ENST00000428558.2:c.2395G>C	p.Val799Leu	p.V799L	ENST00000428558	NM_004260.3	799	Gtg/Ctg	15/22	NA	2	FACETS	0.342	0.297	0.391			1	INDETERMINATE	1	TRUE	NA	0.721713445707538	2		232	535	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625159	69625159	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554980306	NA	P-0007885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1529	244	372	2	ENST00000334134.2:c.634C>T	p.Arg212Trp	p.R212W	ENST00000334134	NM_005247.2	212	Cgg/Tgg	3/3	0.721713445707538	4	FACETS	0.657	0.611	0.704			1	SUBCLONAL	1	TRUE	NA	0.721713445707538	4		374	1773	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411216	63411216	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778026	NA	P-0007885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	500	578	1	ENST00000330258.3:c.1951G>A	p.Val651Ile	p.V651I	ENST00000330258	NM_152424.3	651	Gtc/Atc	2/2	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.721713445707538	2		579	1119	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281354	15281358	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCG	CAGCG	-	novel	NA	P-0007885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	258	254	0	ENST00000263388.2:c.4898_4902del	p.Pro1633ArgfsTer44	p.P1633Rfs*44	ENST00000263388	NM_000435.2	1633	cCGCTG/c	27/33	0.721713445707538	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.721713445707538	1		254	326	SUCCESS
EED	8726	MSKCC	GRCh37	11	85967447	85967447	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	20	443	0	ENST00000263360.6:c.445A>T	p.Thr149Ser	p.T149S	ENST00000263360	NM_003797.3	149	Act/Tct	5/12	0.579630399996373	2	FACETS	0.294	0.225	0.374	0.147	0.112	0.187	SUBCLONAL	1	TRUE	0	0.579630399996373	2		443	235	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738237	145738261	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCATGTCCAAAGCCTGTACGGTA	CGGCATGTCCAAAGCCTGTACGGTA	-	novel	NA	P-0007894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	138	363	0	ENST00000428558.2:c.2724_2748del	p.Thr909ArgfsTer31	p.T909Rfs*31	ENST00000428558	NM_004260.3	908	ctTACCGTACAGGCTTTGGACATGCCG/ct	16/22	0.579630399996373	6	FACETS	1	0.984	1	0.346	0.315	0.379	CLONAL	1	TRUE	2	0.579630399996373	6		363	742	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989383	7989412	+	inframe_deletion	In_Frame_Del	DEL	GGCGGGGAAGTGGTAGATACGGCCGTTGGG	GGCGGGGAAGTGGTAGATACGGCCGTTGGG	-	novel	NA	P-0007894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	169	424	1	ENST00000319144.4:c.274_303del	p.Pro92_Ala101del	p.P92_A101del	ENST00000319144	NM_001139.2	92	CCCAACGGCCGTATCTACCACTTCCCCGCC/-	2/15	0.571352409886774	4	FACETS	1	0.987	1	0.687	0.634	0.743	CLONAL	1	TRUE	2	0.579630399996373	4		425	670	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370872	55370889	+	inframe_deletion	In_Frame_Del	DEL	CGCGGGCCGAGCCAAGGG	CGCGGGCCGAGCCAAGGG	-	novel	NA	P-0007894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	171	311	0	ENST00000297316.4:c.176_193del	p.Ala59_Gly64del	p.A59_G64del	ENST00000297316	NM_022454.3	58	gcCGCGGGCCGAGCCAAGGGc/gcc	1/2	0.571352409886774	4	FACETS	0.823	0.762	0.887	0.823	0.762	0.887	CLONAL	2	TRUE	2	0.579630399996373	4		311	566	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954341	48954344	+	frameshift_variant	Frame_Shift_Del	DEL	GCGT	GCGT	-	novel	NA	P-0007894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	86	406	0	ENST00000267163.4:c.1465_1468del	p.Cys489LeufsTer5	p.C489Lfs*5	ENST00000267163	NM_000321.2	488	GCGTgc/gc	16/27	0.579630399996373	2	FACETS	0.811	0.736	0.886	0.811	0.736	0.886	CLONAL	2	TRUE	0	0.579630399996373	2		406	183	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372135	55372135	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	68	153	0	ENST00000297316.4:c.827del	p.Pro276GlnfsTer111	p.P276Qfs*111	ENST00000297316	NM_022454.3	275	ggC/gg	2/2	0.571352409886774	4	FACETS	0.802	0.708	0.901	0.802	0.708	0.901	CLONAL	2	TRUE	2	0.579630399996373	4		153	231	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0007895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	233	239	2	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.366653231659655	2	FACETS	0.868	0.815	0.921	0.868	0.815	0.921	CLONAL	2	TRUE	0	0.4365839304442	2		241	615	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861972	57861972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	82	517	2	ENST00000228682.2:c.1273G>A	p.Glu425Lys	p.E425K	ENST00000228682	NM_005269.2	425	Gag/Aag	10/12	1	2	FACETS	0.34	0.299	0.385	0.34	0.299	0.385	SUBCLONAL	1	TRUE	1	0.4365839304442	2		519	1105	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688680	47688680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	81	433	0	ENST00000347630.2:c.620C>T	p.Ala207Val	p.A207V	ENST00000347630	NM_001007230.1	207	gCc/gTc	7/11	0.200814680762381	2	FACETS	0.394	0.346	0.446	0.197	0.173	0.223	INDETERMINATE	1	TRUE	0	0.4365839304442	2		433	942	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15365071	15365071	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	37	179	0	ENST00000263377.2:c.2050G>C	p.Glu684Gln	p.E684Q	ENST00000263377	NM_058243.2	684	Gag/Cag	11/20	0.122462367552954	3	FACETS	0.416	0.343	0.499			1	INDETERMINATE	1	TRUE	NA	0.4365839304442	3		179	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0007901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	236	735	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.325664949674494	NA		735	1075	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0007901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	174	418	1	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.325664949674494	2		419	895	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741454	145741454	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	91	651	0	ENST00000428558.2:c.1049G>C	p.Arg350Thr	p.R350T	ENST00000428558	NM_004260.3	350	aGg/aCg	5/22	0.191604172272497	3	FACETS	0.528	0.467	0.593	0.264	0.233	0.297	INDETERMINATE	1	FALSE	1	0.325664949674494	3		651	1231	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68290313	68290313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768576952	NA	P-0007901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	141	575	1	ENST00000487270.1:c.53G>A	p.Arg18His	p.R18H	ENST00000487270	NM_133509.3	18	cGt/cAt	2/11	1	2	FACETS	0.835	0.76	0.914	0.835	0.76	0.914	CLONAL	1	FALSE	1	0.325664949674494	2		576	1037	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0007916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	418	393	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.539191451904682	2	FACETS	0.954	0.916	0.993	0.954	0.916	0.993	CLONAL	2	TRUE	0	0.544091266880411	2		393	805	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265540	198265540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1181	95	518	1	ENST00000335508.6:c.2617G>A	p.Glu873Lys	p.E873K	ENST00000335508	NM_012433.2	873	Gag/Aag	18/25	0.533114478663852	3	FACETS	0.348	0.309	0.391	0.174	0.154	0.196	SUBCLONAL	1	TRUE	1	0.544091266880411	3		519	1276	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198299708	198299708	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	123	280	0	ENST00000335508.6:c.16A>G	p.Lys6Glu	p.K6E	ENST00000335508	NM_012433.2	6	Aag/Gag	1/25	0.533114478663852	3	FACETS	1	0.962	1	0.556	0.505	0.609	CLONAL	1	TRUE	1	0.544091266880411	3		280	517	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	375	709	0	ENST00000263967.3:c.331A>C	p.Lys111Gln	p.K111Q	ENST00000263967	NM_006218.2	111	Aag/Cag	2/21	0.540863644285366	2	FACETS	1	0.977	1	0.526	0.498	0.554	CLONAL	1	TRUE	0	0.544091266880411	2		709	1311	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158437	26158437	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	265	358	0	ENST00000289316.2:c.40G>T	p.Gly14Cys	p.G14C	ENST00000289316	NM_138720.2	14	Ggc/Tgc	1/2	0.544091266880411	5	FACETS	0.916	0.86	0.973	0.458	0.43	0.487	CLONAL	2	TRUE	1	0.544091266880411	5		358	966	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954919	2954919	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	65	438	0	ENST00000396946.4:c.2791G>T	p.Ala931Ser	p.A931S	ENST00000396946	NM_032415.4	931	Gcc/Tcc	21/25	0.403138171138698	5	FACETS	0.643	0.557	0.736			1	SUBCLONAL	1	TRUE	NA	0.544091266880411	5		438	675	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92244573	92244573	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	236	268	0	ENST00000265734.4:c.862A>G	p.Arg288Gly	p.R288G	ENST00000265734	NM_001259.6	288	Aga/Gga	8/8	0.544091266880411	4	FACETS	0.886	0.83	0.943	0.886	0.83	0.943	CLONAL	2	TRUE	2	0.544091266880411	4		268	756	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508034	106508034	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	58	201	0	ENST00000359195.3:c.28G>T	p.Val10Leu	p.V10L	ENST00000359195	NM_002649.2	10	Gtg/Ttg	2/11	0.544091266880411	4	FACETS	0.933	0.805	1	0.466	0.402	0.535	CLONAL	1	TRUE	2	0.544091266880411	4		201	353	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509955	106509955	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	130	393	1	ENST00000359195.3:c.1949G>T	p.Ser650Ile	p.S650I	ENST00000359195	NM_002649.2	650	aGc/aTc	2/11	0.544091266880411	4	FACETS	0.825	0.748	0.907	0.413	0.374	0.454	CLONAL	1	TRUE	2	0.544091266880411	4		394	894	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340384	8340384	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	158	428	0	ENST00000356435.5:c.5212A>T	p.Thr1738Ser	p.T1738S	ENST00000356435		1738	Acc/Tcc	31/35	1	2	FACETS	0.872	0.802	0.945	0.872	0.802	0.945	CLONAL	1	TRUE	1	0.544091266880411	2		428	666	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109998	115109998	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	66	261	0	ENST00000257566.3:c.1880C>G	p.Pro627Arg	p.P627R	ENST00000257566	NM_016569.3	627	cCc/cGc	8/8	0.181678361235635	3	FACETS	1	0.944	1	0.38	0.333	0.429	INDETERMINATE	1	TRUE	0	0.544091266880411	3		261	271	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166270	7166270	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	250	484	0	ENST00000302850.5:c.1756T>G	p.Trp586Gly	p.W586G	ENST00000302850	NM_000208.2	586	Tgg/Ggg	8/22	0.544091266880411	1	FACETS	0.796	0.758	0.834	1	0.995	1	SUBCLONAL	2	TRUE	0	0.544091266880411	1		484	420	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144003	11144003	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	45	338	0	ENST00000358026.2:c.3584A>T	p.Gln1195Leu	p.Q1195L	ENST00000358026	NM_001128849.1	1195	cAg/cTg	26/36	0.400328368987061	3	FACETS	0.46	0.387	0.541			1	SUBCLONAL	1	TRUE	NA	0.544091266880411	3		338	457	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045872	47045872	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0007916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	203	217	0	ENST00000377604.3:c.2668-1G>C		p.X890_splice	ENST00000377604	NM_001204468.1	890			0.431367852999805	2	FACETS	0.849	0.809	0.888			1	CLONAL	3	TRUE	NA	0.544091266880411	2		217	293	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972540	32972544	+	frameshift_variant	Frame_Shift_Del	DEL	CATTT	CATTT	-	novel	NA	P-0007916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	161	432	0	ENST00000380152.3:c.9892_9896del	p.Phe3298AlafsTer27	p.F3298Afs*27	ENST00000380152		3297	gCATTT/g	27/27	1	2	FACETS	0.841	0.773	0.911	0.841	0.773	0.911	CLONAL	1	TRUE	1	0.544091266880411	2		432	704	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007917-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	149	225	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.598484184911854	2		225	428	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653805	89653805	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659443	NA	P-0007917-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	415	504	1	ENST00000371953.3:c.103A>G	p.Met35Val	p.M35V	ENST00000371953	NM_000314.4	35	Atg/Gtg	2/9	0.598484184911854	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.598484184911854	1		505	826	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546958	9546958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771448843	NA	P-0007917-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	73	289	0	ENST00000353224.5:c.1064C>T	p.Ala355Val	p.A355V	ENST00000353224	NM_177990.2	355	gCc/gTc	5/10	1	2	FACETS	0.335	0.292	0.381	0.335	0.292	0.381	SUBCLONAL	1	TRUE	1	0.598484184911854	2		289	728	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794015	42794015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007917-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	117	524	0	ENST00000575354.2:c.1376G>A	p.Gly459Asp	p.G459D	ENST00000575354	NM_015125.3	459	gGc/gAc	9/20	1	2	FACETS	0.366	0.329	0.405	0.366	0.329	0.405	SUBCLONAL	1	TRUE	1	0.598484184911854	2		524	1068	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445976	49445976	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371421459	NA	P-0007917-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	85	505	0	ENST00000301067.7:c.1490C>T	p.Pro497Leu	p.P497L	ENST00000301067	NM_003482.3	497	cCg/cTg	10/54	1	2	FACETS	0.265	0.234	0.3	0.265	0.234	0.3	SUBCLONAL	1	TRUE	1	0.598484184911854	2		505	1070	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245399	46245399	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007917-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	387	552	0	ENST00000334344.6:c.3493C>T	p.Gln1165Ter	p.Q1165*	ENST00000334344	NM_152641.2	1165	Caa/Taa	15/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.598484184911854	2		552	1236	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122866	2122866	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007917-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	329	524	1	ENST00000219476.3:c.2237C>G	p.Thr746Arg	p.T746R	ENST00000219476	NM_000548.3	746	aCa/aGa	21/42	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.598484184911854	2		525	1006	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262754	16262754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007917-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	36	136	0	ENST00000375759.3:c.10019C>T	p.Ala3340Val	p.A3340V	ENST00000375759	NM_015001.2	3340	gCt/gTt	11/15	1	2	FACETS	0.356	0.293	0.426	0.356	0.293	0.426	SUBCLONAL	1	TRUE	1	0.598484184911854	2		136	338	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023175	27023175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1314991058	NA	P-0007917-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	40	111	3	ENST00000324856.7:c.281C>T	p.Pro94Leu	p.P94L	ENST00000324856	NM_006015.4	94	cCc/cTc	1/20	1	2	FACETS	0.472	0.394	0.558	0.472	0.394	0.558	SUBCLONAL	1	TRUE	1	0.598484184911854	2		114	283	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429962	78429962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007917-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	100	512	1	ENST00000370768.2:c.917G>A	p.Gly306Asp	p.G306D	ENST00000370768	NM_003902.3	306	gGt/gAt	11/20	1	2	FACETS	0.267	0.238	0.299	0.267	0.238	0.299	SUBCLONAL	1	TRUE	1	0.598484184911854	2		513	1250	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25468157	25468157	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007917-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	60	445	0	ENST00000264709.3:c.1519C>T	p.Pro507Ser	p.P507S	ENST00000264709	NM_175629.2	507	Ccc/Tcc	13/23	1	2	FACETS	0.205	0.176	0.238	0.205	0.176	0.238	SUBCLONAL	1	TRUE	1	0.598484184911854	2		445	976	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641532	47641532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553352536	NA	P-0007917-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	85	401	0	ENST00000233146.2:c.917C>T	p.Ala306Val	p.A306V	ENST00000233146	NM_000251.2	306	gCa/gTa	5/16	NA	2	FACETS	0.37	0.327	0.417			1	INDETERMINATE	1	TRUE	NA	0.598484184911854	2		401	767	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025840	48025840	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750019	NA	P-0007917-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	155	688	1	ENST00000234420.5:c.718C>T	p.Arg240Ter	p.R240*	ENST00000234420	NM_000179.2	240	Cga/Tga	4/10	NA	2	FACETS	0.407	0.372	0.445			1	INDETERMINATE	1	TRUE	NA	0.598484184911854	2		689	1272	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028225	48028225	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63749999	NA	P-0007917-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	104	559	2	ENST00000234420.5:c.3103C>T	p.Arg1035Ter	p.R1035*	ENST00000234420	NM_000179.2	1035	Cga/Tga	4/10	NA	2	FACETS	0.328	0.292	0.365			1	INDETERMINATE	1	TRUE	NA	0.598484184911854	2		561	1061	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193593	99193593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007917-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	51	228	0	ENST00000074304.5:c.2788G>A	p.Glu930Lys	p.E930K	ENST00000074304	NM_001134224.1	930	Gag/Aag	25/26	1	2	FACETS	0.393	0.334	0.457	0.393	0.334	0.457	SUBCLONAL	1	TRUE	1	0.598484184911854	2		228	434	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735395	204735395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007917-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	40	287	0	ENST00000302823.3:c.196G>A	p.Ala66Thr	p.A66T	ENST00000302823	NM_005214.4	66	Gcc/Acc	2/4	1	2	FACETS	0.197	0.163	0.235	0.197	0.163	0.235	SUBCLONAL	1	TRUE	1	0.598484184911854	2		287	680	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378297	225378297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007917-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1258	136	590	0	ENST00000264414.4:c.598G>A	p.Val200Ile	p.V200I	ENST00000264414	NM_003590.4	200	Gtc/Atc	5/16	1	2	FACETS	0.326	0.295	0.359	0.326	0.295	0.359	SUBCLONAL	1	TRUE	1	0.598484184911854	2		590	1394	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668813	52668813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007917-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	89	387	0	ENST00000394830.3:c.1106G>A	p.Gly369Glu	p.G369E	ENST00000394830	NM_018313.4	369	gGa/gAa	12/30	1	2	FACETS	0.32	0.283	0.36	0.32	0.283	0.36	SUBCLONAL	1	TRUE	1	0.598484184911854	2		387	930	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72866473	72866473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007917-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1202	99	497	0	ENST00000325599.8:c.790G>A	p.Asp264Asn	p.D264N	ENST00000325599	NM_018130.2	264	Gac/Aac	7/11	1	2	FACETS	0.254	0.226	0.285	0.254	0.226	0.285	SUBCLONAL	1	TRUE	1	0.598484184911854	2		497	1301	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504010	186504010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007917-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1606	161	834	0	ENST00000323963.5:c.575G>A	p.Gly192Asp	p.G192D	ENST00000323963		192	gGt/gAt	6/11	1	2	FACETS	0.304	0.278	0.333	0.304	0.278	0.333	SUBCLONAL	1	TRUE	1	0.598484184911854	2		834	1767	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197054	106197054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007917-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	74	380	0	ENST00000380013.4:c.5387G>A	p.Gly1796Glu	p.G1796E	ENST00000380013	NM_001127208.2	1796	gGg/gAg	11/11	1	2	FACETS	0.267	0.233	0.304	0.267	0.233	0.304	SUBCLONAL	1	TRUE	1	0.598484184911854	2		380	925	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540532	187540532	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007917-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	96	321	0	ENST00000441802.2:c.7208C>T	p.Ala2403Val	p.A2403V	ENST00000441802	NM_005245.3	2403	gCc/gTc	10/27	1	2	FACETS	0.36	0.32	0.402	0.36	0.32	0.402	SUBCLONAL	1	TRUE	1	0.598484184911854	2		321	892	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209702	98209702	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747128318	NA	P-0007917-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	65	298	0	ENST00000331920.6:c.3836C>T	p.Pro1279Leu	p.P1279L	ENST00000331920	NM_000264.3	1279	cCc/cTc	23/24	1	2	FACETS	0.319	0.276	0.366	0.319	0.276	0.366	SUBCLONAL	1	TRUE	1	0.598484184911854	2		298	680	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720847	89720847	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554825616	NA	P-0007917-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	52	245	0	ENST00000371953.3:c.998C>T	p.Ala333Val	p.A333V	ENST00000371953	NM_000314.4	333	gCc/gTc	8/9	0.598484184911854	1	FACETS	0.26	0.221	0.302	0.26	0.221	0.302	SUBCLONAL	1	TRUE	0	0.598484184911854	1		245	469	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101985091	101985091	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007917-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1213	65	551	1	ENST00000282441.5:c.538G>A	p.Ala180Thr	p.A180T	ENST00000282441	NM_001130145.2	180	Gca/Aca	2/9	1	2	FACETS	0.17	0.146	0.196	0.17	0.146	0.196	SUBCLONAL	1	TRUE	1	0.598484184911854	2		552	1278	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207682	102207682	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007917-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1604	103	946	1	ENST00000263464.3:c.1664G>A	p.Arg555Lys	p.R555K	ENST00000263464	NM_001165.4	555	aGa/aAa	9/9	1	2	FACETS	0.202	0.179	0.226	0.202	0.179	0.226	SUBCLONAL	1	TRUE	1	0.598484184911854	2		947	1707	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098403	108098403	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007917-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	62	324	0	ENST00000278616.4:c.52G>A	p.Asp18Asn	p.D18N	ENST00000278616	NM_000051.3	18	Gat/Aat	2/63	1	2	FACETS	0.229	0.197	0.264	0.229	0.197	0.264	SUBCLONAL	1	TRUE	1	0.598484184911854	2		324	904	SUCCESS
CBL	867	MSKCC	GRCh37	11	119167672	119167672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007917-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	66	632	0	ENST00000264033.4:c.2081G>A	p.Gly694Asp	p.G694D	ENST00000264033	NM_005188.3	694	gGt/gAt	13/16	1	2	FACETS	0.185	0.16	0.213	0.185	0.16	0.213	SUBCLONAL	1	TRUE	1	0.598484184911854	2		632	1192	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18478028	18478028	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs892869584	NA	P-0007917-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	97	477	0	ENST00000266497.5:c.1268C>T	p.Thr423Ile	p.T423I	ENST00000266497		423	aCc/aTc	7/31	1	2	FACETS	0.303	0.269	0.339	0.303	0.269	0.339	SUBCLONAL	1	TRUE	1	0.598484184911854	2		477	1071	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112939964	112939964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007917-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	112	560	0	ENST00000351677.2:c.1616G>A	p.Gly539Glu	p.G539E	ENST00000351677	NM_002834.3	539	gGg/gAg	14/16	1	2	FACETS	0.309	0.277	0.343	0.309	0.277	0.343	SUBCLONAL	1	TRUE	1	0.598484184911854	2		560	1211	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858292	9858292	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007917-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	87	435	0	ENST00000330684.3:c.3109G>A	p.Ala1037Thr	p.A1037T	ENST00000330684	NM_001134407.1	1037	Gca/Aca	13/13	1	2	FACETS	0.329	0.29	0.37	0.329	0.29	0.37	SUBCLONAL	1	TRUE	1	0.598484184911854	2		435	885	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348551	89348551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007917-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1484	183	1068	1	ENST00000301030.4:c.4399G>A	p.Glu1467Lys	p.E1467K	ENST00000301030	NM_001256183.1	1467	Gag/Aag	9/13	1	2	FACETS	0.367	0.337	0.398	0.367	0.337	0.398	SUBCLONAL	1	TRUE	1	0.598484184911854	2		1069	1667	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10277336	10277336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1390469147	NA	P-0007917-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	118	580	0	ENST00000340748.4:c.781G>A	p.Glu261Lys	p.E261K	ENST00000340748		261	Gag/Aag	10/40	1	2	FACETS	0.347	0.312	0.384	0.347	0.312	0.384	SUBCLONAL	1	TRUE	1	0.598484184911854	2		580	1137	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023513	31023513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007917-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	66	405	0	ENST00000375687.4:c.2998G>A	p.Asp1000Asn	p.D1000N	ENST00000375687	NM_015338.5	1000	Gat/Aat	13/13	1	2	FACETS	0.242	0.209	0.278	0.242	0.209	0.278	SUBCLONAL	1	TRUE	1	0.598484184911854	2		405	911	SUCCESS
AR	367	MSKCC	GRCh37	X	66765133	66765133	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007917-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	29	168	0	ENST00000374690.3:c.145C>T	p.Pro49Ser	p.P49S	ENST00000374690	NM_000044.3	49	Cct/Tct	1/8	1	1	FACETS	0.158	0.127	0.194	0.158	0.127	0.194	SUBCLONAL	1	TRUE	0	0.598484184911854	1		168	429	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0007919-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	29	379	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		379	1081	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007932-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	494	543	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.101336997597583	6	FACETS	0.951	0.918	0.983			1	INDETERMINATE	4	TRUE	NA	0.806160533946365	6		543	842	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721492	176721492	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007932-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	355	493	1	ENST00000439151.2:c.7123C>A	p.Leu2375Met	p.L2375M	ENST00000439151	NM_022455.4	2375	Ctg/Atg	23/23	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.806160533946365	2		494	829	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069456	30069456	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007932-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	289	465	0	ENST00000338641.4:c.1321G>T	p.Ala441Ser	p.A441S	ENST00000338641	NM_000268.3	441	Gct/Tct	12/16	1	2	FACETS	0.979	0.927	1	0.979	0.927	1	CLONAL	1	TRUE	1	0.806160533946365	2		465	732	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0007966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	189	283	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.984	0.92	1	0.984	0.92	1	CLONAL	1	TRUE	1	0.836680084029443	2		283	459	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007064	152007064	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0007966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	487	377	0	ENST00000262189.6:c.836C>G	p.Ser279Ter	p.S279*	ENST00000262189	NM_170606.2	279	tCa/tGa	6/59	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.836680084029443	2		377	1103	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651292	52651292	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	328	406	0	ENST00000394830.3:c.1804G>A	p.Glu602Lys	p.E602K	ENST00000394830	NM_018313.4	602	Gag/Aag	15/30	1	2	FACETS	0.811	0.768	0.855	0.811	0.768	0.855	CLONAL	1	TRUE	1	0.836680084029443	2		406	967	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859827	151859827	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	367	320	0	ENST00000262189.6:c.10835del	p.Arg3612LysfsTer18	p.R3612Kfs*18	ENST00000262189	NM_170606.2	3612	aGa/aa	43/59	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.836680084029443	2		320	858	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0007975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	95	428	3	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.911	0.809	1	0.911	0.809	1	CLONAL	1	TRUE	1	0.197233366936636	2		431	1057	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188317	32188317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144492578	NA	P-0007975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	57	509	1	ENST00000375023.3:c.1024G>A	p.Val342Met	p.V342M	ENST00000375023	NM_004557.3	342	Gtg/Atg	6/30	1	2	FACETS	0.605	0.518	0.702	0.605	0.518	0.702	SUBCLONAL	1	TRUE	1	0.197233366936636	2		510	955	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026841	71026842	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0007975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	58	484	0	ENST00000318789.4:c.1380_1381del	p.Asn461ArgfsTer4	p.N461Rfs*4	ENST00000318789	NM_032682.5	460	aaGAac/aaac	16/21	1	2	FACETS	0.515	0.441	0.597	0.515	0.441	0.597	SUBCLONAL	1	TRUE	1	0.197233366936636	2		484	1142	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0007979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	33	345	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.78	0.635	0.944	0.78	0.635	0.944	CLONAL	1	TRUE	1	0.18	2		345	470	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0007979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	17	473	1	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	0.398	0.296	0.52	0.398	0.296	0.52	SUBCLONAL	1	TRUE	1	0.18	2		474	475	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932410	36932410	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201699446	NA	P-0007979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	73	872	2	ENST00000361632.4:c.2059G>A	p.Gly687Ser	p.G687S	ENST00000361632		687	Ggc/Agc	16/16	1	2	FACETS	0.676	0.589	0.771	0.676	0.589	0.771	SUBCLONAL	1	TRUE	1	0.18	2		874	1199	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913517	NA	P-0007985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	223	475	0	ENST00000288135.5:c.1676T>A	p.Val559Asp	p.V559D	ENST00000288135	NM_000222.2	559	gTt/gAt	11/21	1	2	FACETS	0.997	0.935	1	0.997	0.935	1	CLONAL	1	TRUE	1	0.736654408970479	2		475	607	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054435	42054435	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	310	500	0	ENST00000219905.7:c.7619del	p.Ile2540AsnfsTer17	p.I2540Nfs*17	ENST00000219905	NM_001164273.1	2540	aTa/aa	22/24	0.736654408970479	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.736654408970479	1		500	503	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007989-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	97	225	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.893	0.808	0.981			1	INDETERMINATE	1	TRUE	NA	0.781479547713519	2		225	278	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608622	189608622	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745687224	NA	P-0007989-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	378	431	1	ENST00000264731.3:c.1697C>T	p.Thr566Met	p.T566M	ENST00000264731	NM_003722.4	566	aCg/aTg	13/14	1	2	FACETS	0.988	0.941	1	0.988	0.941	1	CLONAL	1	TRUE	1	0.781479547713519	2		432	979	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711947	89711947	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1554900615	NA	P-0007989-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	330	228	0	ENST00000371953.3:c.565A>T	p.Arg189Ter	p.R189*	ENST00000371953	NM_000314.4	189	Aga/Tga	6/9	0.781479547713519	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.781479547713519	1		228	483	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281582	15281582	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs545519407	NA	P-0007989-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	300	351	0	ENST00000263388.2:c.4791T>A	p.Asn1597Lys	p.N1597K	ENST00000263388	NM_000435.2	1597	aaT/aaA	26/33	0.781479547713519	3	FACETS	0.973	0.917	1	0.487	0.458	0.516	CLONAL	1	TRUE	1	0.781479547713519	3		351	1097	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0008000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	70	291	1	ENST00000269305.4:c.920-2A>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.198206278032805	1	FACETS	0.984	0.858	1	0.984	0.858	1	CLONAL	1	TRUE	0	0.218582984270625	1		292	580	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166772	32166772	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	66	287	0	ENST00000375023.3:c.4466G>T	p.Arg1489Leu	p.R1489L	ENST00000375023	NM_004557.3	1489	cGa/cTa	24/30	1	2	FACETS	0.992	0.861	1	0.992	0.861	1	CLONAL	1	TRUE	1	0.218582984270625	2		287	609	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599913	10599913	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1245862456	NA	P-0008000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	82	505	1	ENST00000171111.5:c.1663A>T	p.Ser555Cys	p.S555C	ENST00000171111	NM_203500.1	555	Agt/Tgt	5/6	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.218582984270625	2		506	743	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572342	41572342	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	263	390	0	ENST00000263253.7:c.4871T>A	p.Met1624Lys	p.M1624K	ENST00000263253	NM_001429.3	1624	aTg/aAg	30/31	0.216226452580042	4	FACETS	1	0.957	1			1	CLONAL	3	TRUE	NA	0.218582984270625	4		390	954	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047524	49047524	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	rs587776779	NA	P-0008000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	62	333	0	ENST00000267163.4:c.2520+1del		p.G840fs	ENST00000267163	NM_000321.2	840	Ggg/gg	24/27	0.218582984270625	3	FACETS	1	0.932	1	0.564	0.487	0.647	CLONAL	1	TRUE	1	0.218582984270625	3		333	558	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142982	47142982	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	60	593	0	ENST00000409792.3:c.4981G>C	p.Glu1661Gln	p.E1661Q	ENST00000409792	NM_014159.6	1661	Gag/Cag	8/21	0.3	1	FACETS	0.562	0.483	0.65	0.562	0.483	0.65	SUBCLONAL	1	TRUE	0	0.18	1		593	1079	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685268	89685268	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0008005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	65	227	0	ENST00000371953.3:c.165-2A>C		p.X55_splice	ENST00000371953	NM_000314.4	55			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.18	2		227	528	SUCCESS
YES1	7525	MSKCC	GRCh37	18	739803	739803	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1265223582	NA	P-0008005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	76	604	0	ENST00000314574.4:c.1069T>A	p.Leu357Ile	p.L357I	ENST00000314574	NM_005433.3	357	Tta/Ata	9/12	1	2	FACETS	0.825	0.722	0.938	0.825	0.722	0.938	CLONAL	1	TRUE	1	0.18	2		604	1023	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183765	10183770	+	inframe_deletion	In_Frame_Del	DEL	TCGCAG	TCGCAG	-	novel	NA	P-0008005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	30	371	0	ENST00000256474.2:c.236_241del	p.Arg79_Ser80del	p.R79_S80del	ENST00000256474	NM_000551.3	78	aaTCGCAGt/aat	1/3	1	2	FACETS	0.652	0.525	0.798	0.652	0.525	0.798	SUBCLONAL	1	TRUE	1	0.18	2		371	511	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008007-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	82	241	1	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	0.156048919082921	3	FACETS	0.829	0.732	0.932	0.829	0.732	0.932	CLONAL	2	TRUE	1	0.194112107845096	3		242	559	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0008007-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	138	490	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.156048919082921	3	FACETS	0.91	0.828	0.996	0.91	0.828	0.996	CLONAL	2	TRUE	1	0.194112107845096	3		490	857	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218861	133218861	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008007-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	93	336	2	ENST00000320574.5:c.5075C>A	p.Pro1692His	p.P1692H	ENST00000320574	NM_006231.2	1692	cCt/cAt	38/49	0.156048919082921	3	FACETS	1	0.975	1	0.676	0.6	0.756	CLONAL	1	TRUE	1	0.194112107845096	3		338	778	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842595	68842595	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0008007-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	64	329	0	ENST00000261769.5:c.532-1G>A		p.X178_splice	ENST00000261769	NM_004360.3	178			0.194112107845096	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.194112107845096	1		329	512	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0008016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	130	395	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	0.500504761824348	3	FACETS	1	0.945	1	0.526	0.479	0.576	CLONAL	1	TRUE	1	0.500504761824348	3		395	617	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443610	52443610	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	252	372	0	ENST00000460680.1:c.82C>T	p.Gln28Ter	p.Q28*	ENST00000460680	NM_004656.3	28	Caa/Taa	3/17	0.500504761824348	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.500504761824348	2		372	483	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95595857	95595857	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	87	494	0	ENST00000393063.1:c.686T>A	p.Ile229Asn	p.I229N	ENST00000393063	NM_030621.3	229	aTt/aAt	7/28	0.463001186098119	3	FACETS	0.657	0.581	0.737	0.328	0.29	0.369	SUBCLONAL	1	TRUE	1	0.500504761824348	3		494	662	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0008023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	241	735	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.279866749079566	2	FACETS	0.908	0.851	0.967	0.908	0.851	0.967	CLONAL	2	TRUE	0	0.338424833880178	2		735	784	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215609807	215609807	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs878854003	NA	P-0008023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	105	464	0	ENST00000260947.4:c.1887G>A	p.Trp629Ter	p.W629*	ENST00000260947	NM_000465.2	629	tgG/tgA	9/11	1	2	FACETS	0.721	0.645	0.801	0.721	0.645	0.801	SUBCLONAL	1	TRUE	1	0.338424833880178	2		464	861	SUCCESS
APC	324	MSKCC	GRCh37	5	112174352	112174352	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	50	223	0	ENST00000257430.4:c.3061C>G	p.Leu1021Val	p.L1021V	ENST00000257430	NM_000038.5	1021	Cta/Gta	16/16	0.311338504025701	1	FACETS	0.712	0.606	0.826	0.712	0.606	0.826	SUBCLONAL	1	TRUE	0	0.338424833880178	1		223	345	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729983	47730152	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCCGCCAGCGAGAGCGAGGGCTGAGGACCTTGGAGAGGCAGAGGGGCGCGGTCAGCACCCACCACCCCTCCAGGCCTCGAGGTGTCTCGGCCTGCTCCCCTCTTTCCCAGCCACTGCTCCCCGCCTCATTTCTAGTGATCCCATCGCTAGTGAGTCAATTTCTCAGCTT	CTCCGCCAGCGAGAGCGAGGGCTGAGGACCTTGGAGAGGCAGAGGGGCGCGGTCAGCACCCACCACCCCTCCAGGCCTCGAGGTGTCTCGGCCTGCTCCCCTCTTTCCCAGCCACTGCTCCCCGCCTCATTTCTAGTGATCCCATCGCTAGTGAGTCAATTTCTCAGCTT	-	novel	NA	P-0008023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	30	103	0	ENST00000449228.1:c.378-141_406del		p.X126_splice	ENST00000449228	NM_001127240.2	126		3/4	0.293392514863403	1	FACETS	0.842	0.685	1	0.842	0.685	1	CLONAL	1	TRUE	0	0.338424833880178	1		103	175	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827957	40827978	+	frameshift_variant	Frame_Shift_Del	DEL	TCGGCAGAGGCCACAGGCCCCA	TCGGCAGAGGCCACAGGCCCCA	-	novel	NA	P-0008023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	50	262	0	ENST00000373198.4:c.2450_2471del	p.Met817ThrfsTer54	p.M817Tfs*54	ENST00000373198	NM_133170.3	817	aTGGGGCCTGTGGCCTCTGCCGAc/ac	17/32	1	2	FACETS	0.64	0.543	0.745	0.64	0.543	0.745	SUBCLONAL	1	TRUE	1	0.338424833880178	2		262	462	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604673	55604673	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773828910	NA	P-0008033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	258	537	1	ENST00000288135.5:c.2881G>A	p.Gly961Ser	p.G961S	ENST00000288135	NM_000222.2	961	Ggc/Agc	21/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.788378316989352	2		538	637	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441061	149441061	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	56	726	0	ENST00000286301.3:c.1851G>T	p.Met617Ile	p.M617I	ENST00000286301	NM_005211.3	617	atG/atT	13/22	1	2	FACETS	0.156	0.133	0.182	0.156	0.133	0.182	SUBCLONAL	1	TRUE	1	0.788378316989352	2		726	910	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023178	33023178	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	77	1111	0	ENST00000300177.4:c.287C>T	p.Thr96Ile	p.T96I	ENST00000300177	NM_001191322.1	96	aCc/aTc	2/2	1	2	FACETS	0.169	0.148	0.193	0.169	0.148	0.193	SUBCLONAL	1	TRUE	1	0.788378316989352	2		1111	1153	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897430	78897430	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1280517804	NA	P-0008033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	68	749	0	ENST00000306801.3:c.2765A>G	p.Gln922Arg	p.Q922R	ENST00000306801	NM_020761.2	922	cAg/cGg	23/34	0.788378316989352	3	FACETS	0.201	0.174	0.231	0.101	0.087	0.116	SUBCLONAL	1	TRUE	1	0.788378316989352	3		749	1196	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0008042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	103	233	0	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.227333853355124	3	FACETS	0.847	0.762	0.937	0.847	0.762	0.937	CLONAL	2	FALSE	1	0.3	3		233	466	SUCCESS
APC	324	MSKCC	GRCh37	5	112174112	112174112	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	130	340	0	ENST00000257430.4:c.2821G>T	p.Glu941Ter	p.E941*	ENST00000257430	NM_000038.5	941	Gaa/Taa	16/16	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	FALSE	NA	0.3	2		340	707	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770023	56770023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759759863	NA	P-0008042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	40	315	1	ENST00000337432.4:c.19C>T	p.Arg7Cys	p.R7C	ENST00000337432	NM_058216.2	7	Cgc/Tgc	1/9	0.227333853355124	3	FACETS	0.5	0.415	0.596	0.25	0.207	0.298	SUBCLONAL	1	FALSE	1	0.3	3		316	613	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422655	47422655	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1569319031	NA	P-0008042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	111	279	1	ENST00000377045.4:c.127G>A	p.Asp43Asn	p.D43N	ENST00000377045	NM_001654.4	43	Gac/Aac	3/16	0.3	2	FACETS	1	0.954	1			1	CLONAL	1	FALSE	NA	0.3	2		280	670	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458018	120458018	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	58	248	0	ENST00000256646.2:c.7327C>A	p.Pro2443Thr	p.P2443T	ENST00000256646	NM_024408.3	2443	Cct/Act	34/34	0.224122988685193	4	FACETS	0.754	0.647	0.87	0.377	0.323	0.435	SUBCLONAL	1	FALSE	2	0.3	4		248	667	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206697	102206697	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	95	414	0	ENST00000263464.3:c.1325A>T	p.Asn442Ile	p.N442I	ENST00000263464	NM_001165.4	442	aAt/aTt	7/9	0.3	3	FACETS	0.638	0.566	0.715	0.319	0.283	0.358	SUBCLONAL	1	FALSE	1	0.3	3		414	1142	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566230	95566230	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008042-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	108	323	0	ENST00000393063.1:c.4093C>G	p.Leu1365Val	p.L1365V	ENST00000393063	NM_030621.3	1365	Cta/Gta	23/28	0.3	3	FACETS	1	0.923	1	0.518	0.464	0.574	CLONAL	1	FALSE	1	0.3	3		323	800	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0008048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	85	455	2	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.21258606529116	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.21258606529116	1		457	619	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	82	583	0	ENST00000263967.3:c.3132T>G	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaG	21/21	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.21258606529116	2		583	699	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119642269	119642269	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	43	590	0	ENST00000316626.5:c.428C>G	p.Ala143Gly	p.A143G	ENST00000316626		143	gCc/gGc	4/12	1	2	FACETS	0.554	0.462	0.656	0.554	0.462	0.656	SUBCLONAL	1	TRUE	1	0.21258606529116	2		590	730	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061102	38061200	+	inframe_deletion	In_Frame_Del	DEL	TCCTTGCGGCTCTCAGGGCCGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTC	TCCTTGCGGCTCTCAGGGCCGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTC	-	novel	NA	P-0008048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	239	93	0	ENST00000250448.2:c.789_887del	p.Gln263_Asp296delinsHis	p.Q263_D296delinsH	ENST00000250448	NM_004496.3	263	caGAAGCGCTTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGCGGCGCCAAGGGCGGCCCTGAGAGCCGCAAGGAc/cac	2/2	1	2	FACETS	1	0.985	1	1	0.996	1	CLONAL	6	TRUE	1	0.21258606529116	2		93	350	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278787	1278788	+	missense_variant	Missense_Mutation	DNP	TG	TG	AA	novel	NA	P-0008048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	44	492	0	ENST00000310581.5:c.2254_2255delinsTT	p.His752Phe	p.H752F	ENST00000310581	NM_198253.2	752	CAt/TTt	6/16	NA	2	FACETS	0.526	0.44	0.622			1	INDETERMINATE	1	TRUE	NA	0.21258606529116	2		492	787	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964321	55964332	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	CTGGGGAATTCC	CTGGGGAATTCC	-	novel	NA	P-0008069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	182	562	0	ENST00000263923.4:c.2481_2492del	p.Trp827_Arg831delinsTer	p.W827_R831delins*	ENST00000263923	NM_002253.2	827	tgGGAATTCCCCAGa/tga	17/30	1	2	FACETS	0.736	0.679	0.796	0.736	0.679	0.796	SUBCLONAL	1	TRUE	1	0.504421021508068	2		562	980	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0008078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	205	388	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.380590320628117	4	FACETS	0.977	0.909	1	0.977	0.909	1	CLONAL	2	TRUE	2	0.380590320628117	4		389	761	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0008078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	594	536	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.380590320628117	7	FACETS	0.946	0.912	0.98	0.788	0.76	0.817	CLONAL	5	TRUE	1	0.380590320628117	7		536	1288	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0008078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	199	250	0	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.380590320628117	2	FACETS	0.843	0.786	0.903	0.843	0.786	0.903	CLONAL	2	TRUE	0	0.380590320628117	2		250	620	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540459	187540459	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0008078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	83	215	0	ENST00000441802.2:c.7281T>G	p.Tyr2427Ter	p.Y2427*	ENST00000441802	NM_005245.3	2427	taT/taG	10/27	NA	2	FACETS	0.936	0.829	1			1	INDETERMINATE	1	TRUE	NA	0.380590320628117	2		215	466	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81954819	81954819	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	254	489	1	ENST00000359376.3:c.2252C>T	p.Ser751Phe	p.S751F	ENST00000359376	NM_002661.3	751	tCc/tTc	21/33	0.325777621235839	2	FACETS	1	0.968	1	0.529	0.494	0.565	CLONAL	1	TRUE	0	0.380590320628117	2		490	1261	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81954866	81954866	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1476	380	597	2	ENST00000359376.3:c.2299C>T	p.Pro767Ser	p.P767S	ENST00000359376	NM_002661.3	767	Ccg/Tcg	21/33	0.325777621235839	2	FACETS	1	0.981	1	0.538	0.509	0.568	CLONAL	1	TRUE	0	0.380590320628117	2		599	1856	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941669	48941669	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	130	350	0	ENST00000267163.4:c.983del	p.Asn328IlefsTer4	p.N328Ifs*4	ENST00000267163	NM_000321.2	327	Aaa/aa	10/27	0.374464738188304	2	FACETS	0.819	0.75	0.891	0.819	0.75	0.891	CLONAL	2	TRUE	0	0.380590320628117	2		350	417	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0008081-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	111	348	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.956	0.872	1	0.956	0.872	1	CLONAL	1	TRUE	1	0.79	2		348	294	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225603	2225603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008081-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	87	329	1	ENST00000326181.6:c.1606G>A	p.Gly536Ser	p.G536S	ENST00000326181	NM_032271.2	536	Ggc/Agc	17/21	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.79	2		330	213	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0008123-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	38	319	2	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.848031238350435	3	FACETS	1	0.957	1	0.462	0.395	0.531	CLONAL	1	FALSE	0	0.848031238350435	3		321	92	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0008154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	115	287	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.3	2	FACETS	0.939	0.844	1			1	CLONAL	1	TRUE	NA	0.22	2		287	1113	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0008154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	76	359	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	1	2	FACETS	0.832	0.729	0.944	0.832	0.729	0.944	CLONAL	1	TRUE	1	0.22	2		359	830	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168694	32168694	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	66	544	0	ENST00000375023.3:c.4229G>T	p.Arg1410Leu	p.R1410L	ENST00000375023	NM_004557.3	1410	cGc/cTc	23/30	1	2	FACETS	0.598	0.518	0.686	0.598	0.518	0.686	SUBCLONAL	1	TRUE	1	0.22	2		544	1003	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	31	225	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.796	0.651	0.957	0.796	0.651	0.957	CLONAL	1	TRUE	1	0.45	2		225	173	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354667	70354667	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1569482153	NA	P-0008166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	169	115	0	ENST00000374080.3:c.4832G>A	p.Arg1611His	p.R1611H	ENST00000374080		1611	cGt/cAt	35/45	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.45	1		115	397	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987009	69987009	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	40	186	0	ENST00000394351.3:c.70A>C	p.Ile24Leu	p.I24L	ENST00000394351	NM_000248.3	24	Ata/Cta	2/9	1	2	FACETS	0.274	0.227	0.327	0.274	0.227	0.327	SUBCLONAL	1	TRUE	1	0.45	2		186	648	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233129	69233129	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	92	220	0	ENST00000462284.1:c.994C>G	p.Arg332Gly	p.R332G	ENST00000462284	NM_002392.5	332	Cgt/Ggt	11/11	1	2	FACETS	0.761	0.678	0.849	0.761	0.678	0.849	SUBCLONAL	1	TRUE	1	0.45	2		220	537	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0008167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	46	656	1	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.471704326591332	2		657	136	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0008167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	110	386	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.471704326591332	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.471704326591332	1		386	299	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0008167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	18	446	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.675	0.515	0.859	0.675	0.515	0.859	SUBCLONAL	1	TRUE	1	0.471704326591332	2		446	113	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	198	441	1	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	0.471704326591332	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.471704326591332	1		442	474	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962529	100962529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767360879	NA	P-0008167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	100	693	2	ENST00000325455.5:c.1868G>A	p.Arg623His	p.R623H	ENST00000325455	NM_001202474.3	623	cGc/cAc	3/8	1	2	FACETS	0.928	0.833	1	0.928	0.833	1	CLONAL	1	TRUE	1	0.471704326591332	2		695	457	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41525989	41525989	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008167-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	59	452	0	ENST00000263253.7:c.1264G>A	p.Asp422Asn	p.D422N	ENST00000263253	NM_001429.3	422	Gat/Aat	5/31	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.471704326591332	2		452	214	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0008182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	199	719	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.425050421140584	2		719	837	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631839	90631839	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519906	NA	P-0008182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	170	152	0	ENST00000330062.3:c.514A>T	p.Arg172Trp	p.R172W	ENST00000330062	NM_002168.2	172	Agg/Tgg	4/11	1	2	FACETS	0.865	0.795	0.937	0.865	0.795	0.937	CLONAL	1	TRUE	1	0.425050421140584	2		152	925	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032794	30032794	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121434259	NA	P-0008182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	290	136	2	ENST00000338641.4:c.169C>T	p.Arg57Ter	p.R57*	ENST00000338641	NM_000268.3	57	Cga/Tga	2/16	0.425050421140584	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.425050421140584	1		138	919	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	240574	240574	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs748089700	NA	P-0008247-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	18	33	0	ENST00000264932.6:c.1534C>T	p.Arg512Ter	p.R512*	ENST00000264932	NM_004168.2	512	Cga/Tga	11/15	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.7	2		33	46	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	643	225	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		225	1017	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023202	27023202	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008297-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	58	86	0	ENST00000324856.7:c.308C>A	p.Ser103Ter	p.S103*	ENST00000324856	NM_006015.4	103	tCg/tAg	1/20	1	2	FACETS	0.842	0.725	0.968	0.842	0.725	0.968	CLONAL	1	TRUE	1	0.31978317478992	2		86	431	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264491	16264491	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747375812	NA	P-0008297-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	60	250	0	ENST00000375759.3:c.10694G>A	p.Arg3565Gln	p.R3565Q	ENST00000375759	NM_015001.2	3565	cGa/cAa	13/15	1	2	FACETS	0.531	0.456	0.612	0.531	0.456	0.612	SUBCLONAL	1	TRUE	1	0.31978317478992	2		250	707	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602340	10602340	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008297-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	145	276	0	ENST00000171111.5:c.1238G>T	p.Arg413Leu	p.R413L	ENST00000171111	NM_203500.1	413	cGt/cTt	3/6	0.303500877913748	1	FACETS	0.909	0.83	0.992	0.909	0.83	0.992	CLONAL	1	TRUE	0	0.31978317478992	1		276	838	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342959	225342959	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008297-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	184	485	0	ENST00000264414.4:c.2133G>A	p.Met711Ile	p.M711I	ENST00000264414	NM_003590.4	711	atG/atA	15/16	1	2	FACETS	0.994	0.916	1	0.994	0.916	1	CLONAL	1	TRUE	1	0.31978317478992	2		485	1158	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133597	55133597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553903287	NA	P-0008297-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	57	300	0	ENST00000257290.5:c.901G>A	p.Glu301Lys	p.E301K	ENST00000257290	NM_006206.4	301	Gaa/Aaa	6/23	1	2	FACETS	0.435	0.372	0.504	0.435	0.372	0.504	SUBCLONAL	1	TRUE	1	0.31978317478992	2		300	820	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111615	56111615	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1290132469	NA	P-0008297-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	59	106	0	ENST00000399503.3:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000399503	NM_005921.1	72	cAg/cTg	1/20	NA	2	FACETS	0.844	0.728	0.97			1	INDETERMINATE	1	TRUE	NA	0.31978317478992	2		106	437	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604535	43604535	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008297-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	136	287	0	ENST00000355710.3:c.1120G>A	p.Val374Met	p.V374M	ENST00000355710	NM_020975.4	374	Gtg/Atg	6/20	1	2	FACETS	0.905	0.822	0.992	0.905	0.822	0.992	CLONAL	1	TRUE	1	0.31978317478992	2		287	940	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916734	48916734	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0008297-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	74	310	0	ENST00000267163.4:c.265-1G>C		p.X89_splice	ENST00000267163	NM_000321.2	89			0.303500877913748	1	FACETS	0.676	0.592	0.766	0.676	0.592	0.766	SUBCLONAL	1	TRUE	0	0.31978317478992	1		310	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578447	7578447	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008297-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	102	250	0	ENST00000269305.4:c.483del	p.Ile162SerfsTer8	p.I162Sfs*8	ENST00000269305	NM_001126112.2	161	gcC/gc	5/11	1	2	FACETS	0.997	0.893	1	0.997	0.893	1	CLONAL	1	TRUE	1	0.31978317478992	2		250	640	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0008309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	130	287	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.672678237900271	5	FACETS	0.789	0.715	0.868	0.197	0.178	0.217	SUBCLONAL	1	TRUE	1	0.672678237900271	5		287	984	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0008309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	186	311	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	1	2	FACETS	0.844	0.783	0.907	0.844	0.783	0.907	CLONAL	1	TRUE	1	0.672678237900271	2		311	655	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763098116	NA	P-0008309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	372	516	0	ENST00000269305.4:c.830G>A	p.Cys277Tyr	p.C277Y	ENST00000269305	NM_001126112.2	277	tGt/tAt	8/11	1	2	FACETS	0.963	0.915	1	0.963	0.915	1	CLONAL	1	TRUE	1	0.672678237900271	2		516	1148	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692818	89692818	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1339631701	NA	P-0008309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	84	159	0	ENST00000371953.3:c.302T>C	p.Ile101Thr	p.I101T	ENST00000371953	NM_000314.4	101	aTc/aCc	5/9	0.61079012709408	2	FACETS	0.827	0.755	0.898	0.827	0.755	0.898	CLONAL	2	TRUE	0	0.672678237900271	2		159	151	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931463	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622007	NA	P-0008315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	551	227	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	0.824947119515307	1		227	647	SUCCESS
AR	367	MSKCC	GRCh37	X	66943543	66943543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852581	NA	P-0008315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	535	262	0	ENST00000374690.3:c.2623C>T	p.His875Tyr	p.H875Y	ENST00000374690	NM_000044.3	875	Cat/Tat	8/8	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.824947119515307	1		262	666	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572194	64572194	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	345	241	1	ENST00000312049.6:c.1445G>T	p.Gly482Val	p.G482V	ENST00000312049	NM_130799.2	482	gGc/gTc	10/10	0.815484468391831	4	FACETS	1	0.968	1	0.345	0.326	0.365	CLONAL	1	TRUE	1	0.824947119515307	4		242	1474	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098425	108098425	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0008315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	295	273	0	ENST00000278616.4:c.72+2T>C		p.X24_splice	ENST00000278616	NM_000051.3	24			1	2	FACETS	0.991	0.938	1	0.991	0.938	1	CLONAL	1	TRUE	1	0.824947119515307	2		273	722	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124552	108124552	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	301	269	0	ENST00000278616.4:c.1914del	p.Asp639IlefsTer10	p.D639Ifs*10	ENST00000278616	NM_000051.3	637	cAa/ca	13/63	1	2	FACETS	0.965	0.914	1	0.965	0.914	1	CLONAL	1	TRUE	1	0.824947119515307	2		269	756	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409156	4409156	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008325-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	251	444	0	ENST00000261254.3:c.851T>A	p.Val284Glu	p.V284E	ENST00000261254	NM_001759.3	284	gTg/gAg	5/5	1	2	FACETS	0.926	0.87	0.984	0.926	0.87	0.984	CLONAL	1	TRUE	1	0.712991764055548	2		444	760	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0008328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	365	213	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.521002466220612	4	FACETS	0.943	0.901	0.986	0.943	0.901	0.986	CLONAL	3	TRUE	1	0.520926173934942	4		213	753	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0008328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	247	819	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.926	0.866	0.988	0.926	0.866	0.988	CLONAL	1	TRUE	1	0.520926173934942	2		819	1024	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412884	49412884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	289	705	1	ENST00000418115.1:c.139G>A	p.Glu47Lys	p.E47K	ENST00000418115	NM_001664.2	47	Gag/Aag	2/5	0.520926173934942	1	FACETS	0.918	0.866	0.971	0.918	0.866	0.971	CLONAL	1	TRUE	0	0.520926173934942	1		706	894	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581157	48581157	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1555685624	NA	P-0008328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	129	305	0	ENST00000342988.3:c.461C>G	p.Ser154Ter	p.S154*	ENST00000342988	NM_005359.5	154	tCa/tGa	5/12	0.520926173934942	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.520926173934942	1		305	355	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630441	47630441	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1433060674	NA	P-0008328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	133	434	0	ENST00000233146.2:c.111C>G	p.Phe37Leu	p.F37L	ENST00000233146	NM_000251.2	37	ttC/ttG	1/16	1	2	FACETS	0.909	0.829	0.992	0.909	0.829	0.992	CLONAL	1	TRUE	1	0.520926173934942	2		434	562	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048835	180048835	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	74	565	0	ENST00000261937.6:c.1727T>A	p.Leu576Gln	p.L576Q	ENST00000261937	NM_182925.4	576	cTg/cAg	13/30	1	2	FACETS	0.412	0.361	0.468	0.412	0.361	0.468	SUBCLONAL	1	TRUE	1	0.520926173934942	2		565	689	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396305	139396305	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	88	580	0	ENST00000277541.6:c.5533C>T	p.Gln1845Ter	p.Q1845*	ENST00000277541	NM_017617.3	1845	Cag/Tag	30/34	0.327254700501913	1	FACETS	0.37	0.327	0.415	0.37	0.327	0.415	SUBCLONAL	1	TRUE	0	0.520926173934942	1		580	676	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845664	68845664	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	105	607	0	ENST00000261769.5:c.910A>G	p.Ile304Val	p.I304V	ENST00000261769	NM_004360.3	304	Atc/Gtc	7/16	1	2	FACETS	0.406	0.363	0.452	0.406	0.363	0.452	SUBCLONAL	1	TRUE	1	0.520926173934942	2		607	993	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264536	30264536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	55	148	0	ENST00000322652.5:c.271G>A	p.Glu91Lys	p.E91K	ENST00000322652	NM_015355.2	91	Gag/Aag	1/16	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.520926173934942	2		148	197	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775231	73775231	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	230	621	0	ENST00000254810.4:c.25C>A	p.Arg9Ser	p.R9S	ENST00000254810	NM_005324.3	9	Cgt/Agt	2/4	0.521002466220612	1	FACETS	0.932	0.872	0.992	0.932	0.872	0.992	CLONAL	1	TRUE	0	0.520926173934942	1		621	701	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214725	5214725	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	41	417	0	ENST00000357368.4:c.4341C>G	p.Ile1447Met	p.I1447M	ENST00000357368	NM_002850.3	1447	atC/atG	29/38	1	2	FACETS	0.253	0.21	0.301	0.253	0.21	0.301	SUBCLONAL	1	TRUE	1	0.520926173934942	2		417	623	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008329-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	53	225	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		225	144	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591892	48591892	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	119	459	0	ENST00000342988.3:c.1055G>T	p.Gly352Val	p.G352V	ENST00000342988	NM_005359.5	352	gGa/gTa	9/12	0.416664020184774	1	FACETS	0.935	0.852	1	0.935	0.852	1	CLONAL	1	TRUE	0	0.48083708071639	1		459	402	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794439	242794439	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	127	687	0	ENST00000334409.5:c.503C>A	p.Thr168Asn	p.T168N	ENST00000334409	NM_005018.2	168	aCc/aAc	3/5	0.48083708071639	3	FACETS	0.712	0.645	0.784	0.356	0.322	0.392	SUBCLONAL	1	TRUE	1	0.48083708071639	3		687	920	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821214	72821214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1044596115	NA	P-0008332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	199	703	0	ENST00000268489.5:c.10961C>T	p.Ser3654Leu	p.S3654L	ENST00000268489	NM_006885.3	3654	tCg/tTg	10/10	0.48083708071639	3	FACETS	0.976	0.904	1	0.488	0.452	0.526	CLONAL	1	TRUE	1	0.48083708071639	3		703	1052	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023864	31023864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1172005201	NA	P-0008332-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	96	332	0	ENST00000375687.4:c.3349C>T	p.Pro1117Ser	p.P1117S	ENST00000375687	NM_015338.5	1117	Ccc/Tcc	13/13	0.48083708071639	3	FACETS	0.795	0.709	0.886	0.398	0.354	0.443	SUBCLONAL	1	TRUE	1	0.48083708071639	3		332	623	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0008334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	59	446	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.341791205309959	2		446	329	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	513	384	0	ENST00000206249.3:c.1610A>G	p.Tyr537Cys	p.Y537C	ENST00000206249	NM_000125.3	537	tAt/tGt	8/8	0.341791205309959	5	FACETS	0.994	0.955	1			1	CLONAL	4	TRUE	NA	0.341791205309959	5		384	1142	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459277	120459277	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs761872871	NA	P-0008334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	47	240	0	ENST00000256646.2:c.6068A>G	p.Tyr2023Cys	p.Y2023C	ENST00000256646	NM_024408.3	2023	tAt/tGt	34/34	0.341791205309959	3	FACETS	0.714	0.603	0.836	0.357	0.301	0.418	SUBCLONAL	1	TRUE	1	0.341791205309959	3		240	451	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984739	11984739	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	59	232	0	ENST00000353533.5:c.285G>A	p.Trp95Ter	p.W95*	ENST00000353533	NM_003010.3	95	tgG/tgA	3/11	0.224426949223331	1	FACETS	0.813	0.703	0.932	0.813	0.703	0.932	CLONAL	1	TRUE	0	0.341791205309959	1		232	352	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453380	40453380	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1286	256	1049	3	ENST00000345506.4:c.1077G>T	p.Lys359Asn	p.K359N	ENST00000345506	NM_003152.3	359	aaG/aaT	10/20	1	2	FACETS	0.971	0.907	1	0.971	0.907	1	CLONAL	1	TRUE	1	0.341791205309959	2		1052	1542	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755515	39755515	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	143	531	0	ENST00000288319.7:c.1250A>T	p.Tyr417Phe	p.Y417F	ENST00000288319	NM_182918.3	417	tAc/tTc	10/10	1	2	FACETS	0.886	0.808	0.969	0.886	0.808	0.969	CLONAL	1	TRUE	1	0.341791205309959	2		531	944	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0008338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	136	179	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.300128332438941	4	FACETS	0.942	0.861	1	0.942	0.861	1	CLONAL	2	TRUE	2	0.394039201685367	4		179	511	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877996	151877996	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	141	387	0	ENST00000262189.6:c.6949C>T	p.Gln2317Ter	p.Q2317*	ENST00000262189	NM_170606.2	2317	Caa/Taa	36/59	0.394039201685367	3	FACETS	1	0.936	1			1	CLONAL	1	TRUE	NA	0.394039201685367	3		387	829	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063717	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0008338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	167	326	0	ENST00000412916.2:c.165+1G>T		p.X55_splice	ENST00000412916		55			NA	2	FACETS	0.979	0.909	1			1	INDETERMINATE	2	TRUE	NA	0.394039201685367	2		326	433	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209721	98209721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749244396	NA	P-0008344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	109	343	0	ENST00000331920.6:c.3817G>A	p.Glu1273Lys	p.E1273K	ENST00000331920	NM_000264.3	1273	Gaa/Aaa	23/24	NA	2	FACETS	0.625	0.564	0.69			1	INDETERMINATE	1	TRUE	NA	0.69154509720258	2		343	504	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380276	+	missense_variant	Missense_Mutation	DNP	TT	TT	GA	novel	NA	P-0008344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1254	507	597	1	ENST00000311936.3:c.182_183delinsTC	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAA/cTC	3/5	0.69154509720258	3	FACETS	1	0.99	1			1	CLONAL	1	TRUE	NA	0.69154509720258	3		598	1761	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020949	26020949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756006188	NA	P-0008344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	977	1153	5	ENST00000357647.3:c.232G>A	p.Asp78Asn	p.D78N	ENST00000357647	NM_003529.2	78	Gac/Aac	1/1	1	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	1	0.69154509720258	2		1158	2196	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374676	118374676	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	220	680	0	ENST00000534358.1:c.8069C>A	p.Thr2690Lys	p.T2690K	ENST00000534358	NM_005933.3	2690	aCa/aAa	27/36	0.31490429180198	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.69154509720258	0		680	904	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433532	49433532	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	475	779	0	ENST00000301067.7:c.8021A>G	p.Gln2674Arg	p.Q2674R	ENST00000301067	NM_003482.3	2674	cAa/cGa	31/54	1	2	FACETS	0.948	0.906	0.991	0.948	0.906	0.991	CLONAL	1	TRUE	1	0.69154509720258	2		779	1449	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125313	7125313	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	351	568	0	ENST00000302850.5:c.3239G>C	p.Gly1080Ala	p.G1080A	ENST00000302850	NM_000208.2	1080	gGc/gCc	17/22	0.568090190264637	3	FACETS	0.936	0.885	0.988			1	CLONAL	1	TRUE	NA	0.69154509720258	3		568	1460	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0008358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	24	330	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.958	0.752	1	0.958	0.752	1	CLONAL	1	TRUE	1	0.16	2		330	313	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781032	135781032	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1306	125	996	1	ENST00000298552.3:c.1933C>T	p.Pro645Ser	p.P645S	ENST00000298552	NM_001162426.1	645	Cca/Tca	15/23	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.16	2		997	1431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577073	7577073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	62	497	0	ENST00000269305.4:c.865C>T	p.Leu289Phe	p.L289F	ENST00000269305	NM_001126112.2	289	Ctc/Ttc	8/11	1	2	FACETS	0.858	0.739	0.988	0.858	0.739	0.988	CLONAL	1	TRUE	1	0.16	2		497	903	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974713	21974713	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	30	399	0	ENST00000304494.5:c.114del	p.Asn39ThrfsTer14	p.N39Tfs*14	ENST00000304494	NM_000077.4	38	ccC/cc	1/3	1	2	FACETS	0.734	0.59	0.897	0.734	0.59	0.897	SUBCLONAL	1	TRUE	1	0.16	2		399	511	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922871	44922871	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	54	358	0	ENST00000377967.4:c.1732C>T	p.Pro578Ser	p.P578S	ENST00000377967	NM_021140.2	578	Ccc/Tcc	16/29	1	1	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	0	0.16	1		358	612	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745541	162745541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	82	543	0	ENST00000367921.3:c.1956G>A	p.Met652Ile	p.M652I	ENST00000367921	NM_006182.2	652	atG/atA	15/18	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.16	2		543	832	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47601015	47601015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	37	494	0	ENST00000263735.4:c.253G>A	p.Glu85Lys	p.E85K	ENST00000263735	NM_002354.2	85	Gaa/Aaa	3/9	1	2	FACETS	0.694	0.571	0.833	0.694	0.571	0.833	SUBCLONAL	1	TRUE	1	0.16	2		494	666	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188932	32188932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	62	658	0	ENST00000375023.3:c.622G>A	p.Gly208Ser	p.G208S	ENST00000375023	NM_004557.3	208	Ggc/Agc	4/30	1	2	FACETS	0.956	0.824	1	0.956	0.824	1	CLONAL	1	TRUE	1	0.16	2		658	811	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846196	128846196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	52	584	0	ENST00000249373.3:c.1126C>T	p.Leu376Phe	p.L376F	ENST00000249373	NM_005631.4	376	Ctt/Ttt	5/12	1	2	FACETS	0.793	0.673	0.925	0.793	0.673	0.925	CLONAL	1	TRUE	1	0.16	2		584	820	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849948	151849948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	45	436	0	ENST00000262189.6:c.12368C>T	p.Ser4123Phe	p.S4123F	ENST00000262189	NM_170606.2	4123	tCc/tTc	49/59	1	2	FACETS	0.855	0.717	1	0.855	0.717	1	CLONAL	1	TRUE	1	0.16	2		436	658	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412376	139412376	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	41	271	0	ENST00000277541.6:c.1269C>G	p.Cys423Trp	p.C423W	ENST00000277541	NM_017617.3	423	tgC/tgG	8/34	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.16	2		271	457	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612102	43612102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	64	737	2	ENST00000355710.3:c.2207G>A	p.Gly736Glu	p.G736E	ENST00000355710	NM_020975.4	736	gGa/gAa	12/20	1	2	FACETS	0.759	0.655	0.873	0.759	0.655	0.873	SUBCLONAL	1	TRUE	1	0.16	2		739	1054	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233216	69233216	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	59	761	2	ENST00000462284.1:c.1081G>A	p.Glu361Lys	p.E361K	ENST00000462284	NM_002392.5	361	Gag/Aag	11/11	1	2	FACETS	0.698	0.598	0.807	0.698	0.598	0.807	SUBCLONAL	1	TRUE	1	0.16	2		763	1057	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274174	10274174	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	21	287	0	ENST00000330684.3:c.95C>T	p.Pro32Leu	p.P32L	ENST00000330684	NM_001134407.1	32	cCc/cTc	2/13	1	2	FACETS	0.678	0.521	0.862	0.678	0.521	0.862	SUBCLONAL	1	TRUE	1	0.16	2		287	387	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347143	89347143	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	46	614	1	ENST00000301030.4:c.5807A>T	p.Glu1936Val	p.E1936V	ENST00000301030	NM_001256183.1	1936	gAg/gTg	9/13	1	2	FACETS	0.68	0.571	0.802	0.68	0.571	0.802	SUBCLONAL	1	TRUE	1	0.16	2		615	845	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489597	40489597	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	78	835	0	ENST00000264657.5:c.653T>G	p.Val218Gly	p.V218G	ENST00000264657	NM_139276.2	218	gTg/gGg	8/24	1	2	FACETS	0.759	0.664	0.861	0.759	0.664	0.861	SUBCLONAL	1	TRUE	1	0.16	2		835	1285	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246599	41246599	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs80357211	NA	P-0008358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	47	638	0	ENST00000357654.3:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000357654	NM_007294.3	317	Caa/Taa	10/23	1	2	FACETS	0.626	0.526	0.737	0.626	0.526	0.737	SUBCLONAL	1	TRUE	1	0.16	2		638	938	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098483	11098483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	24	218	0	ENST00000358026.2:c.1001G>A	p.Gly334Glu	p.G334E	ENST00000358026	NM_001128849.1	334	gGg/gAg	6/36	1	2	FACETS	0.796	0.623	0.995	0.796	0.623	0.995	CLONAL	1	TRUE	1	0.16	2		218	377	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910345	50910345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	78	856	1	ENST00000440232.2:c.1600G>A	p.Glu534Lys	p.E534K	ENST00000440232	NM_002691.3	534	Gag/Aag	13/27	1	2	FACETS	0.92	0.806	1	0.92	0.806	1	CLONAL	1	TRUE	1	0.16	2		857	1060	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719849	52719849	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	67	667	0	ENST00000322088.6:c.1061C>T	p.Pro354Leu	p.P354L	ENST00000322088	NM_014225.5	354	cCc/cTc	9/15	1	2	FACETS	0.824	0.713	0.943	0.824	0.713	0.943	CLONAL	1	TRUE	1	0.16	2		667	1017	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021448	31021448	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	34	405	1	ENST00000375687.4:c.1447G>T	p.Val483Phe	p.V483F	ENST00000375687	NM_015338.5	483	Gtt/Ttt	12/13	1	2	FACETS	0.691	0.563	0.836	0.691	0.563	0.836	SUBCLONAL	1	TRUE	1	0.16	2		406	615	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577070	7577073	+	frameshift_variant	Frame_Shift_Del	DEL	GGAG	GGAG	AAA	novel	NA	P-0008358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	60	489	0	ENST00000269305.4:c.865_868delinsTTT	p.Leu289PhefsTer56	p.L289Ffs*56	ENST00000269305	NM_001126112.2	289	CTCCgc/TTTgc	8/11	1	2	FACETS	0.849	0.73	0.98	0.849	0.73	0.98	CLONAL	1	TRUE	1	0.16	2		489	883	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526104	63526104	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs562176077	NA	P-0008378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	498	416	2	ENST00000307078.5:c.2522G>A	p.Arg841Gln	p.R841Q	ENST00000307078	NM_004655.3	841	cGg/cAg	11/11	0.732220923368294	5	FACETS	0.932	0.891	0.973	0.621	0.594	0.649	CLONAL	2	TRUE	2	0.732220923368294	5		418	1532	SUCCESS
APC	324	MSKCC	GRCh37	5	112175852	112175852	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	370	325	0	ENST00000257430.4:c.4561G>T	p.Glu1521Ter	p.E1521*	ENST00000257430	NM_000038.5	1521	Gaa/Taa	16/16	0.732220923368294	2	FACETS	0.972	0.939	1	0.972	0.939	1	CLONAL	2	TRUE	0	0.732220923368294	2		325	520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578226	7578226	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1464727668	NA	P-0008378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	554	491	0	ENST00000269305.4:c.623A>T	p.Asp208Val	p.D208V	ENST00000269305	NM_001126112.2	208	gAc/gTc	6/11	0.732220923368294	3	FACETS	0.898	0.865	0.931	0.898	0.865	0.931	CLONAL	2	TRUE	1	0.732220923368294	3		491	1151	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871728	35871728	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528542318	NA	P-0008378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	371	607	1	ENST00000216797.5:c.778C>T	p.Arg260Cys	p.R260C	ENST00000216797	NM_020529.2	260	Cgc/Tgc	5/6	0.732220923368294	3	FACETS	0.967	0.916	1	0.483	0.458	0.51	CLONAL	1	TRUE	1	0.732220923368294	3		608	1432	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420289	49420289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768551828	NA	P-0008378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	447	380	0	ENST00000301067.7:c.15460C>T	p.Arg5154Trp	p.R5154W	ENST00000301067	NM_003482.3	5154	Cgg/Tgg	48/54	0.732220923368294	4	FACETS	0.937	0.897	0.979	0.469	0.448	0.49	CLONAL	2	TRUE	0	0.732220923368294	4		380	1128	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120548014	120548014	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	10	34	0	ENST00000256646.2:c.353G>T	p.Gly118Val	p.G118V	ENST00000256646	NM_024408.3	118	gGc/gTc	3/34	0.732220923368294	3	FACETS	0.549	0.378	0.755	0.274	0.189	0.378	SUBCLONAL	1	TRUE	1	0.732220923368294	3		34	68	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172194	99172194	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	479	388	2	ENST00000074304.5:c.1760A>G	p.Asp587Gly	p.D587G	ENST00000074304	NM_001134224.1	587	gAc/gGc	17/26	0.732220923368294	3	FACETS	0.951	0.914	0.987	0.951	0.914	0.987	CLONAL	2	TRUE	1	0.732220923368294	3		390	940	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564484	55564484	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	207	306	0	ENST00000288135.5:c.372G>C	p.Leu124Phe	p.L124F	ENST00000288135	NM_000222.2	124	ttG/ttC	3/21	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.732220923368294	2		306	546	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961104	55961104	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	241	399	0	ENST00000263923.4:c.2836C>A	p.Arg946Ser	p.R946S	ENST00000263923	NM_002253.2	946	Cgt/Agt	21/30	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.732220923368294	2		399	648	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973974	55973974	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	171	333	0	ENST00000263923.4:c.1342T>A	p.Tyr448Asn	p.Y448N	ENST00000263923	NM_002253.2	448	Tat/Aat	10/30	1	2	FACETS	0.873	0.809	0.939	0.873	0.809	0.939	CLONAL	1	TRUE	1	0.732220923368294	2		333	535	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213902	66213902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	149	483	0	ENST00000273854.3:c.2528G>A	p.Arg843Lys	p.R843K	ENST00000273854	NM_004439.5	843	aGa/aAa	15/18	1	2	FACETS	0.906	0.835	0.979	0.906	0.835	0.979	CLONAL	1	TRUE	1	0.732220923368294	2		483	449	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524462	187524462	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	223	304	1	ENST00000441802.2:c.11218G>T	p.Gly3740Ter	p.G3740*	ENST00000441802	NM_005245.3	3740	Gga/Tga	19/27	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.732220923368294	2		305	601	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225431	26225431	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	829	769	0	ENST00000360408.1:c.49C>A	p.Pro17Thr	p.P17T	ENST00000360408	NM_003532.2	17	Ccg/Acg	1/1	0.689025280949047	4	FACETS	0.998	0.967	1	0.998	0.967	1	CLONAL	2	TRUE	2	0.732220923368294	4		769	1965	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170294	32170294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	353	241	1	ENST00000375023.3:c.3314C>T	p.Ser1105Phe	p.S1105F	ENST00000375023	NM_004557.3	1105	tCc/tTc	21/30	0.689025280949047	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.732220923368294	4		242	810	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977584	2977584	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	285	397	1	ENST00000396946.4:c.1100C>A	p.Thr367Lys	p.T367K	ENST00000396946	NM_032415.4	367	aCg/aAg	8/25	0.732220923368294	3	FACETS	1	0.972	1	0.526	0.495	0.558	CLONAL	1	TRUE	1	0.732220923368294	3		398	1010	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374430	81374430	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	349	331	0	ENST00000222390.5:c.632G>C	p.Cys211Ser	p.C211S	ENST00000222390	NM_000601.4	211	tGc/tCc	6/18	0.732220923368294	3	FACETS	0.896	0.855	0.937	0.896	0.855	0.937	CLONAL	2	TRUE	1	0.732220923368294	3		331	727	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372212	55372212	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	170	91	2	ENST00000297316.4:c.902G>T	p.Gly301Val	p.G301V	ENST00000297316	NM_022454.3	301	gGc/gTc	2/2	0.689025280949047	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.732220923368294	4		93	336	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	430254	430254	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	415	439	0	ENST00000399788.2:c.2448G>T	p.Arg816Ser	p.R816S	ENST00000399788	NM_001042603.1	816	agG/agT	18/28	0.732220923368294	2	FACETS	0.946	0.915	0.977	0.946	0.915	0.977	CLONAL	2	TRUE	0	0.732220923368294	2		439	599	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249116	10249116	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	260	459	0	ENST00000340748.4:c.4066A>G	p.Arg1356Gly	p.R1356G	ENST00000340748		1356	Agg/Ggg	34/40	0.732220923368294	2	FACETS	0.881	0.828	0.935	0.441	0.414	0.468	CLONAL	1	TRUE	0	0.732220923368294	2		459	806	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573177	41573177	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	348	247	0	ENST00000263253.7:c.5462G>T	p.Arg1821Leu	p.R1821L	ENST00000263253	NM_001429.3	1821	cGa/cTa	31/31	NA	2	FACETS	0.984	0.95	1			1	INDETERMINATE	2	TRUE	NA	0.732220923368294	2		247	483	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038895	47038895	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0008378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	45	69	0	ENST00000377604.3:c.901+1G>T		p.X301_splice	ENST00000377604	NM_001204468.1	301			0.704192332935301	3	FACETS	0.857	0.729	0.994	0.428	0.364	0.497	CLONAL	1	TRUE	1	0.732220923368294	3		69	196	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649587	48649587	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	668	572	1	ENST00000376670.3:c.71T>A	p.Val24Glu	p.V24E	ENST00000376670	NM_002049.3	24	gTg/gAg	2/6	0.704192332935301	3	FACETS	0.967	0.936	0.998	0.967	0.936	0.998	CLONAL	2	TRUE	1	0.732220923368294	3		573	1289	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0008384-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	99	463	3	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.617233761612955	2		466	283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0008384-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	287	422	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.617233761612955	2	FACETS	0.852	0.823	0.879	1	0.995	1	CLONAL	3	TRUE	0	0.617233761612955	2		422	364	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520761	176520761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141530067	NA	P-0008384-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	78	350	1	ENST00000292408.4:c.1504G>A	p.Val502Ile	p.V502I	ENST00000292408	NM_213647.1	502	Gtc/Atc	11/18	1	2	FACETS	0.896	0.797	1	0.896	0.797	1	CLONAL	1	TRUE	1	0.617233761612955	2		351	282	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0008405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	27	543	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		543	664	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0008406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	303	446	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.314395751461512	2	FACETS	0.818	0.78	0.857	0.818	0.78	0.857	INDETERMINATE	2	TRUE	0	0.644036572904097	2		446	575	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031973	26031973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	253	780	0	ENST00000244661.2:c.316G>C	p.Glu106Gln	p.E106Q	ENST00000244661	NM_003537.3	106	Gag/Cag	1/1	0.32084947183998	1	FACETS	0.377	0.351	0.403	0.377	0.351	0.403	INDETERMINATE	1	TRUE	0	0.644036572904097	1		780	1414	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602823	10602823	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	367	506	0	ENST00000171111.5:c.755G>T	p.Trp252Leu	p.W252L	ENST00000171111	NM_203500.1	252	tGg/tTg	3/6	0.644036572904097	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.644036572904097	1		506	684	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851382	156851382	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	157	518	0	ENST00000524377.1:c.2339G>T	p.Arg780Leu	p.R780L	ENST00000524377	NM_002529.3	780	cGg/cTg	17/17	0.32084947183998	1	FACETS	0.399	0.365	0.434	0.399	0.365	0.434	INDETERMINATE	1	TRUE	0	0.644036572904097	1		518	829	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724521	162724521	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	187	597	2	ENST00000367921.3:c.293C>A	p.Thr98Asn	p.T98N	ENST00000367921	NM_006182.2	98	aCt/aAt	5/18	0.32084947183998	1	FACETS	0.391	0.361	0.422	0.391	0.361	0.422	INDETERMINATE	1	TRUE	0	0.644036572904097	1		599	1007	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523103	25523103	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	160	417	0	ENST00000264709.3:c.82G>T	p.Glu28Ter	p.E28*	ENST00000264709	NM_175629.2	28	Gag/Tag	3/23	0.32084947183998	1	FACETS	0.463	0.425	0.502	0.463	0.425	0.502	INDETERMINATE	1	TRUE	0	0.644036572904097	1		417	728	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125789	47125789	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	306	408	0	ENST00000409792.3:c.5481G>T	p.Trp1827Cys	p.W1827C	ENST00000409792	NM_014159.6	1827	tgG/tgT	12/21	0.644036572904097	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.644036572904097	1		408	644	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644668	134644668	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	105	457	0	ENST00000398015.3:c.69G>C	p.Met23Ile	p.M23I	ENST00000398015	NM_004441.4	23	atG/atC	2/16	0.450178427703085	1	FACETS	0.345	0.309	0.383	0.345	0.309	0.383	SUBCLONAL	1	TRUE	0	0.644036572904097	1		457	641	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680812	30680812	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1443	193	632	0	ENST00000376406.3:c.907G>T	p.Val303Leu	p.V303L	ENST00000376406	NM_014641.2	303	Gtg/Ttg	5/15	0.27077589289674	4	FACETS	0.602	0.555	0.652			1	INDETERMINATE	1	TRUE	NA	0.644036572904097	4		632	1636	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066557	94066557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	567	870	0	ENST00000369303.4:c.1202C>T	p.Thr401Ile	p.T401I	ENST00000369303	NM_004440.3	401	aCt/aTt	5/17	0.338724440260194	1	FACETS	0.828	0.796	0.861	0.828	0.796	0.861	INDETERMINATE	1	TRUE	0	0.644036572904097	1		870	1441	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739790	41739790	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	443	798	0	ENST00000242208.4:c.183C>A	p.His61Gln	p.H61Q	ENST00000242208	NM_002192.2	61	caC/caA	2/3	1	2	FACETS	0.912	0.869	0.955	0.912	0.869	0.955	CLONAL	1	TRUE	1	0.644036572904097	2		798	1509	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209511	98209511	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	225	421	1	ENST00000331920.6:c.4027G>T	p.Gly1343Trp	p.G1343W	ENST00000331920	NM_000264.3	1343	Ggg/Tgg	23/24	0.644036572904097	1	FACETS	0.949	0.894	1	0.949	0.894	1	CLONAL	1	TRUE	0	0.644036572904097	1		422	499	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900231	101900231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	480	698	0	ENST00000374994.4:c.665G>A	p.Gly222Glu	p.G222E	ENST00000374994	NM_004612.2	222	gGa/gAa	4/9	0.644036572904097	1	FACETS	0.894	0.857	0.931	0.894	0.857	0.931	CLONAL	1	TRUE	0	0.644036572904097	1		698	1131	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633641	69633641	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	52	94	0	ENST00000334134.2:c.61C>A	p.Pro21Thr	p.P21T	ENST00000334134	NM_005247.2	21	Cct/Act	1/3	0.338724440260194	1	FACETS	0.706	0.614	0.803	0.706	0.614	0.803	INDETERMINATE	1	TRUE	0	0.644036572904097	1		94	155	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344669	118344669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	429	500	1	ENST00000534358.1:c.2795G>T	p.Gly932Val	p.G932V	ENST00000534358	NM_005933.3	932	gGg/gTg	3/36	0.338724440260194	1	FACETS	0.837	0.8	0.875	0.837	0.8	0.875	INDETERMINATE	1	TRUE	0	0.644036572904097	1		501	1079	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699296	18699296	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	203	638	0	ENST00000266497.5:c.3397G>C	p.Asp1133His	p.D1133H	ENST00000266497		1133	Gac/Cac	24/31	0.338724440260194	1	FACETS	0.331	0.305	0.357	0.331	0.305	0.357	INDETERMINATE	1	TRUE	0	0.644036572904097	1		638	1293	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891714	28891714	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	542	603	0	ENST00000282397.4:c.3307G>T	p.Val1103Leu	p.V1103L	ENST00000282397	NM_002019.4	1103	Gta/Tta	25/30	0.644036572904097	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.644036572904097	1		603	990	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782264	56782264	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	483	766	0	ENST00000308159.5:c.105G>C	p.Glu35Asp	p.E35D	ENST00000308159	NM_014669.4	35	gaG/gaC	2/22	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.644036572904097	2		766	1472	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832400	72832400	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	1359	828	0	ENST00000268489.5:c.4181C>A	p.Ser1394Ter	p.S1394*	ENST00000268489	NM_006885.3	1394	tCa/tAa	9/10	0.445124094564101	4	FACETS	0.954	0.933	0.974			1	CLONAL	3	TRUE	NA	0.644036572904097	4		828	2425	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347312	89347312	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	994	805	0	ENST00000301030.4:c.5638G>C	p.Glu1880Gln	p.E1880Q	ENST00000301030	NM_001256183.1	1880	Gag/Cag	9/13	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	2	TRUE	NA	0.644036572904097	2		805	1537	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7218302	7218302	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	367	591	0	ENST00000380728.2:c.70A>G	p.Met24Val	p.M24V	ENST00000380728		24	Atg/Gtg	2/11	0.603308207392954	1	FACETS	0.942	0.899	0.986	0.942	0.899	0.986	CLONAL	1	TRUE	0	0.644036572904097	1		591	820	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546913	9546913	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	173	420	0	ENST00000353224.5:c.1109G>T	p.Ser370Ile	p.S370I	ENST00000353224	NM_177990.2	370	aGt/aTt	5/10	0.644036572904097	1	FACETS	0.711	0.66	0.764	0.711	0.66	0.764	SUBCLONAL	1	TRUE	0	0.644036572904097	1		420	512	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624824	9624824	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	138	418	0	ENST00000353224.5:c.153G>T	p.Lys51Asn	p.K51N	ENST00000353224	NM_177990.2	51	aaG/aaT	3/10	0.644036572904097	1	FACETS	0.641	0.588	0.696	0.641	0.588	0.696	SUBCLONAL	1	TRUE	0	0.644036572904097	1		418	453	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216380	7216380	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	387	508	0	ENST00000380728.2:c.868del	p.Gln290SerfsTer55	p.Q290Sfs*55	ENST00000380728		290	Cag/ag	10/11	0.603308207392954	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.644036572904097	1		508	798	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577536	+	missense_variant	Missense_Mutation	TNP	CCT	CCT	ACC	novel	NA	P-0008406-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	318	494	0	ENST00000269305.4:c.745_747delinsGGT	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	AGG/GGT	7/11	0.603308207392954	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.644036572904097	1		494	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0008422-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	155	590	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	1	2	FACETS	0.537	0.49	0.587	0.537	0.49	0.587	SUBCLONAL	1	TRUE	1	0.443923796238316	2		590	1300	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008425-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	48	225	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.19	2		225	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0008425-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	51	328	0	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	1	2	FACETS	0.644	0.546	0.753	0.644	0.546	0.753	SUBCLONAL	1	TRUE	1	0.19	2		328	833	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0008425-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	72	416	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	0.702	0.612	0.801	0.702	0.612	0.801	SUBCLONAL	1	TRUE	1	0.19	2		416	1079	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955550	48955550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913304	NA	P-0008425-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	49	345	0	ENST00000267163.4:c.1666C>T	p.Arg556Ter	p.R556*	ENST00000267163	NM_000321.2	556	Cga/Tga	17/27	1	2	FACETS	0.921	0.78	1	0.921	0.78	1	CLONAL	1	TRUE	1	0.19	2		345	560	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432741	49432741	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1315374796	NA	P-0008425-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	24	186	0	ENST00000301067.7:c.8398C>T	p.Gln2800Ter	p.Q2800*	ENST00000301067	NM_003482.3	2800	Cag/Tag	34/54	1	2	FACETS	0.556	0.435	0.697	0.556	0.435	0.697	SUBCLONAL	1	TRUE	1	0.19	2		186	454	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032069	26032069	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008425-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1789	175	762	0	ENST00000244661.2:c.220G>C	p.Glu74Gln	p.E74Q	ENST00000244661	NM_003537.3	74	Gaa/Caa	1/1	0.113415545135023	3	FACETS	1	0.938	1	0.514	0.471	0.559	INDETERMINATE	1	TRUE	1	0.19	3		762	1964	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754320	57754320	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008425-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	62	311	0	ENST00000274289.3:c.531G>C	p.Leu177Phe	p.L177F	ENST00000274289	NM_006622.3	177	ttG/ttC	4/14	1	2	FACETS	0.954	0.823	1	0.954	0.823	1	CLONAL	1	TRUE	1	0.19	2		311	684	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	279	326	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.488909117280351	2	FACETS	0.956	0.907	1	0.956	0.907	1	CLONAL	2	TRUE	0	0.491911161392685	2		326	593	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721943	176721961	+	frameshift_variant	Frame_Shift_Del	DEL	ACCCCTGGCAAGCTGTTAA	ACCCCTGGCAAGCTGTTAA	-	novel	NA	P-0008448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	22	194	0	ENST00000439151.2:c.7575_7593del	p.Pro2526HisfsTer46	p.P2526Hfs*46	ENST00000439151	NM_022455.4	2525	gACCCCTGGCAAGCTGTTAAa/ga	23/23	0.483469328732082	3	FACETS	0.281	0.217	0.355	0.14	0.108	0.178	SUBCLONAL	1	TRUE	1	0.491911161392685	3		194	397	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0008452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	159	290	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.3	0	FACETS	0.808	0.748	0.87			1	CLONAL	2	FALSE	0	0.3	0		290	459	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913399	NA	P-0008452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	164	277	0	ENST00000349496.5:c.100G>C	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Cga	3/15	1	2	FACETS	0.99	0.915	1	1	0.992	1	CLONAL	2	FALSE	1	0.3	2		277	552	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061249	38061249	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	136	223	1	ENST00000250448.2:c.740A>G	p.His247Arg	p.H247R	ENST00000250448	NM_004496.3	247	cAc/cGc	2/2	1	2	FACETS	1	0.927	1	1	0.991	1	CLONAL	2	FALSE	1	0.3	2		224	448	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0008456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	116	543	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.966	0.871	1	1	0.988	1	CLONAL	2	TRUE	1	0.15920540413238	2		543	754	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0008456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	202	399	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.159976118581082	2	FACETS	0.969	0.902	1	1	0.994	1	CLONAL	4	TRUE	0	0.15920540413238	2		399	655	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0008456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	85	641	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.159976118581082	1	FACETS	0.885	0.784	0.993	1	0.983	1	CLONAL	2	TRUE	0	0.15920540413238	1		641	555	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11999012	11999012	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0008456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	168	424	0	ENST00000353533.5:c.513+1G>A		p.X171_splice	ENST00000353533	NM_003010.3	171			0.159976118581082	2	FACETS	1	0.938	1	1	0.993	1	CLONAL	4	TRUE	0	0.15920540413238	2		424	520	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593599	55593649	+	inframe_deletion	In_Frame_Del	DEL	ACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGA	ACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGA	-	novel	NA	P-0008468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	283	566	0	ENST00000288135.5:c.1665_1715del	p.Gln556_Asp572del	p.Q556_D572del	ENST00000288135	NM_000222.2	555	gtACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGAc/gtc	11/21	1	2	FACETS	0.713	0.672	0.755	0.713	0.672	0.755	SUBCLONAL	1	TRUE	1	0.903665394379529	2		566	878	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	127	225	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.819	0.747	0.895	0.819	0.747	0.895	CLONAL	1	TRUE	1	0.640406948985819	2		225	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0008474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	249	353	2	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.616265414452376	1	FACETS	0.946	0.893	0.999	0.946	0.893	0.999	CLONAL	1	TRUE	0	0.640406948985819	1		355	559	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459531	50459531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	273	279	0	ENST00000331340.3:c.820C>T	p.Arg274Cys	p.R274C	ENST00000331340	NM_006060.4	274	Cgt/Tgt	7/8	1	2	FACETS	0.952	0.895	1	0.952	0.895	1	CLONAL	1	TRUE	1	0.640406948985819	2		279	896	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585423	29585423	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	362	345	0	ENST00000356175.3:c.4172G>T	p.Arg1391Ile	p.R1391I	ENST00000356175	NM_000267.3	1391	aGa/aTa	31/57	0.616265414452376	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.640406948985819	1		345	747	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5066678	5066704	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GATGGATTTTGCCATTAGTAAACTGAA	GATGGATTTTGCCATTAGTAAACTGAA	-	novel	NA	P-0008474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1239	236	425	0	ENST00000381652.3:c.1217_1243del	p.Met406_Lys414del	p.M406_K414del	ENST00000381652	NM_004972.3	405	tcGATGGATTTTGCCATTAGTAAACTGAAg/tcg	10/25	0.613925270608402	3	FACETS	0.66	0.614	0.707	0.33	0.307	0.354	SUBCLONAL	1	TRUE	1	0.640406948985819	3		425	1475	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845322	156845339	+	inframe_deletion	In_Frame_Del	DEL	GCTGGCTCCAGAGGATGG	GCTGGCTCCAGAGGATGG	-	novel	NA	P-0008474-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	382	596	0	ENST00000524377.1:c.1371_1388del	p.Pro458_Ala463del	p.P458_A463del	ENST00000524377	NM_002529.3	455	gtGCTGGCTCCAGAGGATGGg/gtg	12/17	1	2	FACETS	0.918	0.871	0.965	0.918	0.871	0.965	CLONAL	1	TRUE	1	0.640406948985819	2		596	1300	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593613	55593613	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913521	NA	P-0008486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	206	478	1	ENST00000288135.5:c.1679T>A	p.Val560Asp	p.V560D	ENST00000288135	NM_000222.2	560	gTt/gAt	11/21	1	2	FACETS	0.907	0.847	0.969	0.907	0.847	0.969	CLONAL	1	TRUE	1	0.753045105312062	2		479	603	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148930	119148930	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs387906664	NA	P-0008486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	11	437	0	ENST00000264033.4:c.1150T>C	p.Cys384Arg	p.C384R	ENST00000264033	NM_005188.3	384	Tgt/Cgt	8/16	1	2	FACETS	0.057	0.039	0.08	0.057	0.039	0.08	SUBCLONAL	1	TRUE	1	0.753045105312062	2		437	512	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281913	142281923	+	frameshift_variant	Frame_Shift_Del	DEL	CAATCCGCAGA	CAATCCGCAGA	-	novel	NA	P-0008486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	83	294	0	ENST00000350721.4:c.321_331del	p.Leu108SerfsTer14	p.L108Sfs*14	ENST00000350721	NM_001184.3	107	ctTCTGCGGATTGca/ctca	4/47	1	2	FACETS	0.868	0.777	0.962	0.868	0.777	0.962	CLONAL	1	TRUE	1	0.753045105312062	2		294	254	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17380454	17380454	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774266782	NA	P-0008523-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	252	473	0	ENST00000375499.3:c.61G>A	p.Ala21Thr	p.A21T	ENST00000375499	NM_003000.2	21	Gcc/Acc	1/8	1	2	FACETS	0.909	0.851	0.969	1	0.996	1	CLONAL	3	TRUE	1	0.181563398159733	2		473	1018	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0008529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	192	348	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.276918024739754	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.355544539942155	1		348	780	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0008529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	92	468	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.355544539942155	2		468	451	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0008529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	129	543	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	0.355544539942155	2		543	716	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0008529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	111	349	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	0.901	0.811	0.996	0.901	0.811	0.996	CLONAL	1	TRUE	1	0.355544539942155	2		349	693	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0008529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	112	196	2	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	0.276918024739754	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.355544539942155	1		198	479	SUCCESS
ALK	238	MSKCC	GRCh37	2	29436898	29436898	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	76	450	0	ENST00000389048.3:c.3695A>G	p.Asp1232Gly	p.D1232G	ENST00000389048	NM_004304.4	1232	gAc/gGc	24/29	0.276918024739754	1	FACETS	0.317	0.277	0.36	0.317	0.277	0.36	SUBCLONAL	1	TRUE	0	0.355544539942155	1		450	1110	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418661	49418661	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	62	378	2	ENST00000301067.7:c.15853C>A	p.Pro5285Thr	p.P5285T	ENST00000301067	NM_003482.3	5285	Cct/Act	49/54	1	2	FACETS	0.347	0.298	0.4	0.347	0.298	0.4	SUBCLONAL	1	TRUE	1	0.355544539942155	2		380	1006	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912399	32912399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	99	731	1	ENST00000380152.3:c.3907G>A	p.Gly1303Ser	p.G1303S	ENST00000380152		1303	Ggc/Agc	11/27	1	2	FACETS	0.443	0.394	0.495	0.443	0.394	0.495	SUBCLONAL	1	TRUE	1	0.355544539942155	2		732	1258	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357715	70357715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1569482448	NA	P-0008529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1253	326	597	1	ENST00000374080.3:c.5966G>A	p.Arg1989His	p.R1989H	ENST00000374080		1989	cGc/cAc	41/45	0.168952704117034	0	FACETS	0.748	0.705	0.793			1	INDETERMINATE	1	TRUE	0	0.355544539942155	0		598	1579	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0008546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	10	330	0				ENST00000310581	NM_198253.2	-/1132			0.201822651238339	0	FACETS	0.534	0.363	0.749			1	SUBCLONAL	1	FALSE	0	0.201822651238339	0		330	148	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0008546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	619	554	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	1	2	FACETS	1	0.971	1	1	0.998	1	CLONAL	5	FALSE	1	0.201822651238339	2		554	1220	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443926	18443926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	89	488	2	ENST00000266497.5:c.899C>T	p.Pro300Leu	p.P300L	ENST00000266497		300	cCt/cTt	3/31	1	2	FACETS	0.945	0.837	1	0.945	0.837	1	CLONAL	1	FALSE	1	0.201822651238339	2		490	933	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884588	111884588	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	134	810	0	ENST00000341259.2:c.764C>G	p.Ser255Cys	p.S255C	ENST00000341259	NM_005475.2	255	tCc/tGc	3/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.201822651238339	2		810	1014	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424469	49424469	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	63	563	0	ENST00000301067.7:c.13754del	p.Val4585AlafsTer7	p.V4585Afs*7	ENST00000301067	NM_003482.3	4585	gTc/gc	41/54	0.201822651238339	5	FACETS	1	0.968	1			1	CLONAL	1	FALSE	NA	0.201822651238339	5		563	564	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0008555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	195	356	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.966	0.899	1	0.966	0.899	1	CLONAL	1	TRUE	1	0.662180828004458	2		356	610	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0008576-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	43	379	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.825	0.689	0.977	0.825	0.689	0.977	CLONAL	1	TRUE	1	0.15	2		379	695	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0008576-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	55	246	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.15	2		246	694	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636286	87636286	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008576-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	59	525	0	ENST00000277120.3:c.2451G>T	p.Lys817Asn	p.K817N	ENST00000277120		817	aaG/aaT	19/19	1	2	FACETS	0.743	0.637	0.859	0.743	0.637	0.859	SUBCLONAL	1	TRUE	1	0.15	2		525	1059	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391706	139391706	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008576-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	38	301	0	ENST00000277541.6:c.6485G>T	p.Ser2162Ile	p.S2162I	ENST00000277541	NM_017617.3	2162	aGc/aTc	34/34	1	2	FACETS	0.748	0.617	0.896	0.748	0.617	0.896	SUBCLONAL	1	TRUE	1	0.15	2		301	677	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014033	14014033	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008576-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	47	248	0	ENST00000311895.7:c.11G>C	p.Gly4Ala	p.G4A	ENST00000311895	NM_005236.2	4	gGg/gCg	1/11	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.15	2		248	497	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439126	52439131	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CTGCAT	CTGCAT	-	novel	NA	P-0008648-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	141	182	0	ENST00000460680.1:c.1111_1116del	p.Met371_Gln372del	p.M371_Q372del	ENST00000460680	NM_004656.3	371	ATGCAG/-	11/17	0.447767369734396	1	FACETS	0.858	0.787	0.931	0.858	0.787	0.931	CLONAL	1	TRUE	0	0.509214592336202	1		182	481	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101206	27101207	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0008648-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	310	370	0	ENST00000324856.7:c.4488_4489del	p.Met1497ValfsTer5	p.M1497Vfs*5	ENST00000324856	NM_006015.4	1496	acCAtg/actg	18/20	0.447767369734396	1	FACETS	0.897	0.847	0.948	0.897	0.847	0.948	CLONAL	1	TRUE	0	0.509214592336202	1		370	1012	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0008656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	266	819	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.537563468664134	2		819	706	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0008656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	136	330	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.537563468664134	2		330	409	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0008656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	40	92	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.537563468664134	1	FACETS	0.955	0.815	1	0.955	0.815	1	CLONAL	1	TRUE	0	0.537563468664134	1		92	114	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271344	26271344	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	373	1000	0	ENST00000305910.3:c.269T>C	p.Val90Ala	p.V90A	ENST00000305910	NM_003534.2	90	gTg/gCg	1/1	0.174303903981429	3	FACETS	1	0.99	1	0.583	0.552	0.614	INDETERMINATE	1	TRUE	1	0.537563468664134	3		1000	1511	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885176	111885176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374931521	NA	P-0008656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	252	717	2	ENST00000341259.2:c.1064C>T	p.Thr355Met	p.T355M	ENST00000341259	NM_005475.2	355	aCg/aTg	6/8	1	2	FACETS	0.931	0.872	0.992	0.931	0.872	0.992	CLONAL	1	TRUE	1	0.537563468664134	2		719	1007	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955465	48955465	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	201	397	0	ENST00000267163.4:c.1585del	p.Tyr529ThrfsTer3	p.Y529Tfs*3	ENST00000267163	NM_000321.2	527	gaT/ga	17/27	0.537563468664134	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.537563468664134	1		397	522	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922862	39922862	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	246	238	0	ENST00000378444.4:c.3846del	p.Gly1283AlafsTer11	p.G1283Afs*11	ENST00000378444	NM_001123385.1	1282	caA/ca	8/15	0.219412318958732	2	FACETS	1	0.951	1			1	CLONAL	3	TRUE	NA	0.238190237925204	2		238	680	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111044	193111044	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	113	273	0	ENST00000367435.3:c.577A>G	p.Lys193Glu	p.K193E	ENST00000367435	NM_024529.4	193	Aaa/Gaa	7/17	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.520566374676487	2		273	418	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111061	193111061	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	101	298	1	ENST00000367435.3:c.594G>T	p.Lys198Asn	p.K198N	ENST00000367435	NM_024529.4	198	aaG/aaT	7/17	1	2	FACETS	0.913	0.821	1	0.913	0.821	1	CLONAL	1	TRUE	1	0.520566374676487	2		299	425	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494902	56494902	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs749837397	NA	P-0008661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	160	243	0	ENST00000267101.3:c.3259A>G	p.Met1087Val	p.M1087V	ENST00000267101	NM_001982.3	1087	Atg/Gtg	27/28	1	2	FACETS	0.964	0.887	1	0.964	0.887	1	CLONAL	1	TRUE	1	0.520566374676487	2		243	638	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397755	49397755	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	348	566	0	ENST00000418115.1:c.469del	p.Met157TrpfsTer11	p.M157Wfs*11	ENST00000418115	NM_001664.2	157	Atg/tg	5/5	1	2	FACETS	0.893	0.844	0.944	0.893	0.844	0.944	CLONAL	1	TRUE	1	0.520566374676487	2		566	1497	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480083	20480083	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008663-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	149	319	1	ENST00000346618.3:c.400C>T	p.Arg134Ter	p.R134*	ENST00000346618	NM_001949.4	134	Cga/Tga	2/7	0.163394977185069	5	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.507278810191669	5		320	785	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819960	170819965	+	inframe_deletion	In_Frame_Del	DEL	GATGAA	GATGAA	-	novel	NA	P-0008663-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	158	364	0	ENST00000296930.5:c.504_509del	p.Asp168_Glu169del	p.D168_E169del	ENST00000296930	NM_002520.6	168	GATGAA/-	6/11	0.507289881751028	3	FACETS	0.847	0.776	0.921	0.423	0.388	0.461	CLONAL	1	TRUE	1	0.507278810191669	3		364	922	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0008664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	97	262	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.673	0.599	0.752	0.673	0.599	0.752	SUBCLONAL	1	TRUE	1	0.314998277172364	2		262	915	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0008664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	200	553	3	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.314998277172364	2		556	1045	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743361	162743361	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs928746429	NA	P-0008664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	107	418	1	ENST00000367921.3:c.1831C>T	p.Arg611Ter	p.R611*	ENST00000367921	NM_006182.2	611	Cga/Tga	14/18	1	2	FACETS	0.75	0.672	0.833	0.75	0.672	0.833	SUBCLONAL	1	TRUE	1	0.314998277172364	2		419	906	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672191	30672191	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	155	727	0	ENST00000376406.3:c.4769C>T	p.Pro1590Leu	p.P1590L	ENST00000376406	NM_014641.2	1590	cCt/cTt	10/15	1	2	FACETS	0.826	0.755	0.902	0.826	0.755	0.902	CLONAL	1	TRUE	1	0.314998277172364	2		727	1191	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039634	47039655	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGCAGGCCCTGCACCCACCA	CCTGCAGGCCCTGCACCCACCA	-	novel	NA	P-0008664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	106	497	0	ENST00000377604.3:c.1087_1108del	p.Leu363SerfsTer115	p.L363Sfs*115	ENST00000377604	NM_001204468.1	362	atCCTGCAGGCCCTGCACCCACCA/at	11/24	1	2	FACETS	0.874	0.784	0.97	0.874	0.784	0.97	CLONAL	1	TRUE	1	0.314998277172364	2		497	770	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356170	70356170	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1658	92	903	2	ENST00000374080.3:c.5065G>A	p.Asp1689Asn	p.D1689N	ENST00000374080		1689	Gat/Aat	37/45	1	2	FACETS	0.35	0.31	0.394	0.35	0.31	0.394	SUBCLONAL	1	TRUE	1	0.3	2		905	1750	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778795	76778795	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	77	939	0	ENST00000373344.5:c.6784G>T	p.Glu2262Ter	p.E2262*	ENST00000373344	NM_000489.3	2262	Gaa/Taa	31/35	0.3	1	FACETS	0.367	0.321	0.417	0.367	0.321	0.417	SUBCLONAL	1	TRUE	0	0.3	1		939	1188	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105629	27105629	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	102	563	0	ENST00000324856.7:c.5240C>G	p.Pro1747Arg	p.P1747R	ENST00000324856	NM_006015.4	1747	cCt/cGt	20/20	1	2	FACETS	0.575	0.514	0.64	0.575	0.514	0.64	SUBCLONAL	1	TRUE	1	0.434798744546115	2		563	816	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218005	108218005	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs876660066	NA	P-0008711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	101	266	0	ENST00000278616.4:c.8585-1G>A		p.X2862_splice	ENST00000278616	NM_000051.3	2862			0.409869889129571	3	FACETS	1	0.982	1	0.723	0.651	0.798	CLONAL	1	TRUE	1	0.434798744546115	3		266	391	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007723	62007723	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	50	132	0	ENST00000392795.3:c.144G>A	p.Trp48Ter	p.W48*	ENST00000392795	NM_001039933.1	48	tgG/tgA	3/6	0.261807476342971	4	FACETS	1	0.951	1			1	CLONAL	1	TRUE	NA	0.434798744546115	4		132	258	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314608	30314608	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	50	425	0	ENST00000262643.3:c.1157C>T	p.Ala386Val	p.A386V	ENST00000262643	NM_001238.2	386	gCt/gTt	12/12	0.126490569778124	5	FACETS	0.506	0.428	0.592	0.169	0.142	0.198	INDETERMINATE	1	TRUE	2	0.434798744546115	5		425	751	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0008732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	261	334	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.575390401504138	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.575390401504138	1		334	625	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907692	111907692	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	253	726	1	ENST00000393256.3:c.466G>T	p.Gly156Ter	p.G156*	ENST00000393256	NM_006538.4	156	Gga/Tga	3/4	1	2	FACETS	0.759	0.709	0.81	0.759	0.709	0.81	SUBCLONAL	1	TRUE	1	0.575390401504138	2		727	1159	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027114	71027114	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	243	415	0	ENST00000318789.4:c.1213C>A	p.His405Asn	p.H405N	ENST00000318789	NM_032682.5	405	Cat/Aat	15/21	1	2	FACETS	0.997	0.934	1	0.997	0.934	1	CLONAL	1	TRUE	1	0.575390401504138	2		415	847	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138201337	138201337	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs140610274	NA	P-0008732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	72	366	0	ENST00000237289.4:c.2036T>C	p.Ile679Thr	p.I679T	ENST00000237289	NM_001270507.1	679	aTt/aCt	8/9	0.159772175435018	3	FACETS	0.46	0.401	0.523	0.23	0.2	0.262	INDETERMINATE	1	TRUE	1	0.575390401504138	3		366	701	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0008751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	86	388	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.849	0.751	0.954	0.849	0.751	0.954	CLONAL	1	TRUE	1	0.28646445447739	2		389	707	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333143	70333143	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767493807	NA	P-0008751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	113	662	2	ENST00000373644.4:c.1048G>A	p.Glu350Lys	p.E350K	ENST00000373644	NM_030625.2	350	Gaa/Aaa	2/12	1	2	FACETS	0.857	0.77	0.949	0.857	0.77	0.949	CLONAL	1	TRUE	1	0.28646445447739	2		664	921	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130334	11130334	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1480398200	NA	P-0008751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	112	741	1	ENST00000358026.2:c.2573C>T	p.Thr858Met	p.T858M	ENST00000358026	NM_001128849.1	858	aCg/aTg	18/36	0.28646445447739	1	FACETS	0.886	0.797	0.98	0.886	0.797	0.98	CLONAL	1	TRUE	0	0.28646445447739	1		742	756	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840069	27840069	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1225	215	1173	2	ENST00000328488.2:c.25C>T	p.Arg9Cys	p.R9C	ENST00000328488	NM_003533.2	9	Cgc/Tgc	1/1	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.28646445447739	2		1175	1440	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0008785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	152	435	0	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	0.260757918260499	2	FACETS	1	0.979	1	0.605	0.554	0.657	CLONAL	1	TRUE	0	0.352116512522352	2		435	714	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212615405	212615405	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	61	583	1	ENST00000342788.4:c.581C>G	p.Thr194Ser	p.T194S	ENST00000342788	NM_005235.2	194	aCt/aGt	5/28	0.260757918260499	2	FACETS	0.632	0.546	0.726	0.316	0.273	0.363	SUBCLONAL	1	TRUE	0	0.352116512522352	2		584	548	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934004	49934004	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	116	814	0	ENST00000296474.3:c.2408T>C	p.Phe803Ser	p.F803S	ENST00000296474	NM_002447.2	803	tTc/tCc	9/20	1	2	FACETS	0.588	0.528	0.651	0.588	0.528	0.651	SUBCLONAL	1	TRUE	1	0.352116512522352	2		814	1121	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226593	2226594	+	missense_variant	Missense_Mutation	DNP	GC	GC	TA	novel	NA	P-0008785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	132	445	0	ENST00000398665.3:c.4073_4074delinsTA	p.Gly1358Val	p.G1358V	ENST00000398665	NM_032482.2	1358	gGC/gTA	27/28	0.274158132836859	2	FACETS	1	0.96	1	0.55	0.5	0.602	CLONAL	1	TRUE	0	0.352116512522352	2		445	682	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534791	18534791	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	67	531	1	ENST00000266497.5:c.1849C>A	p.Gln617Lys	p.Q617K	ENST00000266497		617	Cag/Aag	12/31	1	2	FACETS	0.259	0.224	0.298	0.259	0.224	0.298	SUBCLONAL	1	TRUE	1	0.523815858297198	2		532	986	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100077	27100080	+	frameshift_variant	Frame_Shift_Del	DEL	GCCT	GCCT	-	novel	NA	P-0008795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	222	597	0	ENST00000324856.7:c.3874_3877del	p.Pro1292GlufsTer2	p.P1292Efs*2	ENST00000324856	NM_006015.4	1291	gaGCCT/ga	16/20	1	2	FACETS	0.753	0.7	0.808	0.753	0.7	0.808	SUBCLONAL	1	TRUE	1	0.523815858297198	2		597	1126	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579505	7579506	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0008795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	185	443	0	ENST00000269305.4:c.181_182del	p.Asp61Ter	p.D61*	ENST00000269305	NM_001126112.2	61	GAt/t	4/11	0.46537905892485	1	FACETS	0.872	0.809	0.936	0.872	0.809	0.936	CLONAL	1	TRUE	0	0.523815858297198	1		443	598	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9787030	9787030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397518423	NA	P-0008813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	81	573	0	ENST00000377346.4:c.3061G>A	p.Glu1021Lys	p.E1021K	ENST00000377346	NM_005026.3	1021	Gaa/Aaa	24/24	1	2	FACETS	0.26	0.228	0.294	0.26	0.228	0.294	SUBCLONAL	1	FALSE	1	0.606075095685458	2		573	1030	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0008851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	304	379	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.3269035220142	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.3269035220142	3		379	1010	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732981	30732981	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	252	293	0	ENST00000295754.5:c.1594C>T	p.Gln532Ter	p.Q532*	ENST00000295754	NM_003242.5	532	Cag/Tag	7/7	0.3269035220142	2	FACETS	0.905	0.849	0.962	0.905	0.849	0.962	CLONAL	2	TRUE	0	0.3269035220142	2		293	852	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372361	55372361	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	127	306	1	ENST00000297316.4:c.1051C>T	p.Pro351Ser	p.P351S	ENST00000297316	NM_022454.3	351	Ccc/Tcc	2/2	0.3269035220142	3	FACETS	1	0.908	1	0.502	0.454	0.552	CLONAL	1	TRUE	1	0.3269035220142	3		307	901	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112224	115112224	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	87	239	1	ENST00000257566.3:c.1516G>T	p.Gly506Cys	p.G506C	ENST00000257566	NM_016569.3	506	Ggc/Tgc	7/8	0.3269035220142	3	FACETS	1	0.913	1	0.518	0.459	0.581	CLONAL	1	TRUE	1	0.3269035220142	3		240	598	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557478	21557478	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	397	542	0	ENST00000382592.4:c.2367C>A	p.His789Gln	p.H789Q	ENST00000382592	NM_014572.2	789	caC/caA	5/8	0.3269035220142	3	FACETS	0.979	0.93	1	0.979	0.93	1	CLONAL	2	TRUE	1	0.3269035220142	3		542	1443	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895670	28895670	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1302	199	474	0	ENST00000282397.4:c.3104T>A	p.Val1035Glu	p.V1035E	ENST00000282397	NM_002019.4	1035	gTg/gAg	23/30	0.3269035220142	3	FACETS	0.944	0.871	1	0.472	0.435	0.51	CLONAL	1	TRUE	1	0.3269035220142	3		474	1501	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597390	10597390	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	764	424	0	ENST00000171111.5:c.1813G>C	p.Gly605Arg	p.G605R	ENST00000171111	NM_203500.1	605	Ggc/Cgc	6/6	0.2877388551712	4	FACETS	1	0.982	1			1	CLONAL	4	TRUE	NA	0.3269035220142	4		424	1522	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041583	47041584	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	T	novel	NA	P-0008851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	156	261	0	ENST00000377604.3:c.1808_1809delinsT	p.Gln603LeufsTer101	p.Q603Lfs*101	ENST00000377604	NM_001204468.1	603	cAG/cT	17/24	1	1	FACETS	0.752	0.693	0.813	1	0.989	1	SUBCLONAL	2	TRUE	0	0.3269035220142	1		261	531	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0008856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	267	388	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.376772230021229	3	FACETS	0.886	0.833	0.942	0.886	0.833	0.942	CLONAL	2	TRUE	1	0.376772230021229	3		389	950	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410930	63410930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1237	135	639	2	ENST00000330258.3:c.2237C>T	p.Pro746Leu	p.P746L	ENST00000330258	NM_152424.3	746	cCt/cTt	2/2	1	2	FACETS	0.522	0.473	0.575	0.522	0.473	0.575	SUBCLONAL	1	TRUE	1	0.376772230021229	2		641	1372	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	139	381	0	ENST00000269305.4:c.380C>A	p.Ser127Tyr	p.S127Y	ENST00000269305	NM_001126112.2	127	tCc/tAc	5/11	0.405496162181852	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.410540073983929	1		381	495	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117650522	117650522	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	30	628	1	ENST00000368508.3:c.5336G>T	p.Cys1779Phe	p.C1779F	ENST00000368508	NM_002944.2	1779	tGt/tTt	32/43	0.28361062021848	0	FACETS	0.166	0.133	0.203			1	SUBCLONAL	1	TRUE	0	0.410540073983929	0		629	520	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850688	63850688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	152	455	2	ENST00000279873.7:c.1466C>T	p.Pro489Leu	p.P489L	ENST00000279873	NM_032199.2	489	cCa/cTa	10/10	0.235683154057039	4	FACETS	1	0.942	1			1	INDETERMINATE	1	TRUE	NA	0.410540073983929	4		457	1005	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0008882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	104	345	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	0.802	0.718	0.893	0.802	0.718	0.893	CLONAL	1	FALSE	1	0.3	2		345	864	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822338	72822338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1477	384	806	0	ENST00000268489.5:c.9837G>A	p.Met3279Ile	p.M3279I	ENST00000268489	NM_006885.3	3279	atG/atA	10/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.372424537185698	2		806	1861	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688689	47688689	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	286	513	0	ENST00000347630.2:c.611T>G	p.Leu204Trp	p.L204W	ENST00000347630	NM_001007230.1	204	tTg/tGg	7/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.372424537185698	2		513	1306	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051590	30051595	+	inframe_deletion	In_Frame_Del	DEL	ATCTGT	ATCTGT	-	novel	NA	P-0008903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	206	437	0	ENST00000338641.4:c.527_532del	p.Leu176_Tyr177del	p.L176_Y177del	ENST00000338641	NM_000268.3	175	aATCTGTat/aat	6/16	0.372424537185698	1	FACETS	0.971	0.902	1	0.971	0.902	1	CLONAL	1	TRUE	0	0.372424537185698	1		437	927	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441224	52441224	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	213	356	0	ENST00000460680.1:c.546G>C	p.Glu182Asp	p.E182D	ENST00000460680	NM_004656.3	182	gaG/gaC	7/17	0.5360421056279	1	FACETS	0.994	0.931	1	0.994	0.931	1	CLONAL	1	TRUE	0	0.5360421056279	1		356	585	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537255	80537256	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0008904-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	183	215	0	ENST00000286548.4:c.142_143delinsTT	p.Gly48Leu	p.G48L	ENST00000286548	NM_002072.3	48	GGa/TTa	2/7	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.5360421056279	2		215	611	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913396	NA	P-0008907-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	212	479	1	ENST00000349496.5:c.95A>T	p.Asp32Val	p.D32V	ENST00000349496	NM_001904.3	32	gAc/gTc	3/15	1	2	FACETS	0.929	0.863	0.998	0.929	0.863	0.998	CLONAL	1	TRUE	1	0.42090211565803	2		480	1084	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057877	27057877	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008907-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	599	605	0	ENST00000324856.7:c.1585C>T	p.Gln529Ter	p.Q529*	ENST00000324856	NM_006015.4	529	Cag/Tag	3/20	0.269956103770144	2	FACETS	0.967	0.931	1	0.967	0.931	1	CLONAL	2	TRUE	0	0.42090211565803	2		605	1471	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522642	176522642	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs984035214	NA	P-0008907-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	306	564	1	ENST00000292408.4:c.1739G>A	p.Ser580Asn	p.S580N	ENST00000292408	NM_213647.1	580	aGt/aAt	13/18	0.288005204460285	1	FACETS	0.852	0.801	0.903	0.852	0.801	0.903	CLONAL	1	TRUE	0	0.42090211565803	1		565	1348	SUCCESS
CBL	867	MSKCC	GRCh37	11	119167744	119167744	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs144894769	NA	P-0008907-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	198	473	1	ENST00000264033.4:c.2153G>A	p.Arg718Gln	p.R718Q	ENST00000264033	NM_005188.3	718	cGa/cAa	13/16	0.42090211565803	1	FACETS	0.922	0.855	0.99	0.922	0.855	0.99	CLONAL	1	TRUE	0	0.42090211565803	1		474	806	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579523	7579532	+	frameshift_variant	Frame_Shift_Del	DEL	GTGAACCATT	GTGAACCATT	-	novel	NA	P-0008907-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	179	372	0	ENST00000269305.4:c.155_164del	p.Gln52LeufsTer68	p.Q52Lfs*68	ENST00000269305	NM_001126112.2	52	cAATGGTTCACt/ct	4/11	0.42090211565803	1	FACETS	0.916	0.847	0.988	0.916	0.847	0.988	CLONAL	1	TRUE	0	0.42090211565803	1		372	733	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0008913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	230	404	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.622368653472844	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.622368653472844	1		405	399	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0008913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	703	529	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.596884391029268	3	FACETS	0.93	0.905	0.954	0.93	0.905	0.954	CLONAL	3	TRUE	0	0.622368653472844	3		529	1062	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048812	180048812	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	195	436	0	ENST00000261937.6:c.1750A>G	p.Lys584Glu	p.K584E	ENST00000261937	NM_182925.4	584	Aag/Gag	13/30	NA	2	FACETS	0.969	0.901	1			1	INDETERMINATE	1	TRUE	NA	0.622368653472844	2		436	647	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200338	138200338	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753284576	NA	P-0008913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	59	210	0	ENST00000237289.4:c.1756G>A	p.Ala586Thr	p.A586T	ENST00000237289	NM_001270507.1	586	Gcc/Acc	7/9	0.596884391029268	3	FACETS	0.609	0.526	0.7	0.203	0.175	0.234	SUBCLONAL	1	TRUE	0	0.622368653472844	3		210	408	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876601	59876601	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	73	317	1	ENST00000259008.2:c.1200C>A	p.Asp400Glu	p.D400E	ENST00000259008	NM_032043.2	400	gaC/gaA	9/20	0.170652219639456	3	FACETS	0.373	0.326	0.425	0.187	0.163	0.213	INDETERMINATE	1	TRUE	1	0.622368653472844	3		318	824	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457245	89457245	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	286	438	0	ENST00000336596.2:c.1726G>T	p.Ala576Ser	p.A576S	ENST00000336596	NM_005233.5	576	Gca/Tca	9/17	1	2	FACETS	0.91	0.859	0.961	0.91	0.859	0.961	CLONAL	1	TRUE	1	0.796721123844841	2		438	789	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89851299	89851299	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1432415523	NA	P-0008923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1415	392	558	0	ENST00000389301.3:c.1433C>G	p.Ser478Ter	p.S478*	ENST00000389301	NM_000135.2	478	tCa/tGa	15/43	0.796721123844841	5	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.796721123844841	5		558	1807	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872105	76872105	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	523	760	0	ENST00000373344.5:c.5542C>T	p.Gln1848Ter	p.Q1848*	ENST00000373344	NM_000489.3	1848	Cag/Tag	22/35	0.23476951116518	1	FACETS	0.617	0.592	0.642	0.617	0.592	0.642	INDETERMINATE	1	TRUE	0	0.796721123844841	1		760	1280	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550535	29550535	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	397	577	0	ENST00000356175.3:c.1795del	p.Trp599GlyfsTer6	p.W599Gfs*6	ENST00000356175	NM_000267.3	599	Tgg/gg	16/57	1	2	FACETS	0.974	0.929	1	0.974	0.929	1	CLONAL	1	TRUE	1	0.796721123844841	2		577	1023	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008932-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	441	225	0				ENST00000310581	NM_198253.2	-/1132			0.480547490954921	6	FACETS	0.959	0.92	0.999	0.959	0.92	0.999	CLONAL	4	TRUE	2	0.480547490954921	6		225	938	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0008932-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1209	1224	877	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.480547490954921	6	FACETS	1	0.99	1	1	0.99	1	CLONAL	4	TRUE	2	0.480547490954921	6		878	2433	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412337	139412339	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0008932-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	505	426	0	ENST00000277541.6:c.1306_1308del	p.Phe436del	p.F436del	ENST00000277541	NM_017617.3	436	TTC/-	8/34	0.480547490954921	3	FACETS	0.977	0.943	1	0.977	0.943	1	CLONAL	3	TRUE	0	0.480547490954921	3		426	889	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543683	29543683	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008932-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	210	523	0	ENST00000389048.3:c.1480C>G	p.Leu494Val	p.L494V	ENST00000389048	NM_004304.4	494	Ctg/Gtg	7/29	0.480547490954921	3	FACETS	0.972	0.902	1	0.486	0.451	0.523	CLONAL	1	TRUE	1	0.480547490954921	3		523	1115	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350274	15350274	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1334182511	NA	P-0008932-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1310	91	555	1	ENST00000263377.2:c.3505G>A	p.Ala1169Thr	p.A1169T	ENST00000263377	NM_058243.2	1169	Gca/Aca	17/20	0.480547490954921	3	FACETS	0.335	0.296	0.377	0.168	0.148	0.189	SUBCLONAL	1	TRUE	1	0.480547490954921	3		556	1401	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629770	187629772	+	frameshift_variant	Frame_Shift_Del	DEL	ACT	ACT	CC	novel	NA	P-0008932-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	446	606	0	ENST00000441802.2:c.1210_1212delinsGG	p.Ser404GlyfsTer10	p.S404Gfs*10	ENST00000441802	NM_005245.3	404	AGT/GG	2/27	0.480547490954921	2	FACETS	0.891	0.853	0.929	0.891	0.853	0.929	CLONAL	2	TRUE	0	0.480547490954921	2		606	1042	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163843	47163843	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	46	458	0	ENST00000409792.3:c.2283G>T	p.Met761Ile	p.M761I	ENST00000409792	NM_014159.6	761	atG/atT	3/21	1	2	FACETS	0.253	0.213	0.297	0.253	0.213	0.297	SUBCLONAL	1	TRUE	1	0.753637770525909	2		458	483	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922970	44922970	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	193	628	1	ENST00000377967.4:c.1831C>T	p.Gln611Ter	p.Q611*	ENST00000377967	NM_021140.2	611	Cag/Tag	16/29	0.753637770525909	1	FACETS	0.721	0.674	0.767	0.721	0.674	0.767	SUBCLONAL	1	TRUE	0	0.753637770525909	1		629	443	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0008946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	454	719	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.547649633721592	3	FACETS	0.97	0.928	1	0.97	0.928	1	CLONAL	2	TRUE	1	0.547649633721592	3		719	1089	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0008946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	86	330	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.547649633721592	2		330	312	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275648	41275648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397514554	NA	P-0008946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	249	269	0	ENST00000349496.5:c.1543C>T	p.Arg515Ter	p.R515*	ENST00000349496	NM_001904.3	515	Cga/Tga	10/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.547649633721592	2		269	809	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099852	27099852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	162	298	0	ENST00000324856.7:c.3731C>T	p.Pro1244Leu	p.P1244L	ENST00000324856	NM_006015.4	1244	cCc/cTc	15/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.547649633721592	2		298	561	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570878	226570878	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1383847803	NA	P-0008946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	95	173	0	ENST00000366794.5:c.1018C>T	p.Arg340Ter	p.R340*	ENST00000366794	NM_001618.3	340	Cga/Tga	8/23	1	2	FACETS	0.975	0.876	1	0.975	0.876	1	CLONAL	1	TRUE	1	0.547649633721592	2		173	356	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519886	29519886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	135	333	1	ENST00000389048.3:c.1685G>A	p.Gly562Glu	p.G562E	ENST00000389048	NM_004304.4	562	gGa/gAa	9/29	1	2	FACETS	0.87	0.794	0.948	0.87	0.794	0.948	CLONAL	1	TRUE	1	0.547649633721592	2		334	567	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278890	1278890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	104	294	1	ENST00000310581.5:c.2152G>A	p.Asp718Asn	p.D718N	ENST00000310581	NM_198253.2	718	Gac/Aac	6/16	1	2	FACETS	0.902	0.813	0.995	0.902	0.813	0.995	CLONAL	1	TRUE	1	0.547649633721592	2		295	421	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392050	81392050	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	278	474	0	ENST00000222390.5:c.227G>A	p.Arg76Lys	p.R76K	ENST00000222390	NM_000601.4	76	aGg/aAg	2/18	1	2	FACETS	0.967	0.909	1	0.967	0.909	1	CLONAL	1	TRUE	1	0.547649633721592	2		474	1050	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912061	127912061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1481246558	NA	P-0008946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	403	614	2	ENST00000373547.4:c.809C>T	p.Ser270Leu	p.S270L	ENST00000373547	NM_002721.4	270	tCg/tTg	7/7	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.547649633721592	2		616	1362	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154404	2154404	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs868243135	NA	P-0008946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	112	415	1	ENST00000434045.2:c.524G>A	p.Trp175Ter	p.W175*	ENST00000434045	NM_001127598.1	175	tGg/tAg	5/5	0.117566577513219	0	FACETS	0.377	0.34	0.415			1	INDETERMINATE	1	TRUE	0	0.547649633721592	0		416	491	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235980	133235980	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751425952	NA	P-0008946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	163	364	2	ENST00000320574.5:c.3176G>A	p.Arg1059His	p.R1059H	ENST00000320574	NM_006231.2	1059	cGc/cAc	26/49	NA	2	FACETS	0.926	0.853	1			1	INDETERMINATE	1	TRUE	NA	0.547649633721592	2		366	643	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40477072	40477072	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	282	430	0	ENST00000264657.5:c.1373C>T	p.Ser458Phe	p.S458F	ENST00000264657	NM_139276.2	458	tCc/tTc	16/24	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.547649633721592	2		430	967	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59924472	59924472	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs565458815	NA	P-0008946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	331	441	0	ENST00000259008.2:c.617C>T	p.Ser206Leu	p.S206L	ENST00000259008	NM_032043.2	206	tCg/tTg	6/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.547649633721592	2		441	1158	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681669	78681669	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	135	309	0	ENST00000306801.3:c.377C>A	p.Thr126Asn	p.T126N	ENST00000306801	NM_020761.2	126	aCt/aAt	4/34	1	2	FACETS	0.622	0.566	0.682	0.622	0.566	0.682	SUBCLONAL	1	TRUE	1	0.547649633721592	2		309	792	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400190	41400190	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	138	263	0	ENST00000373198.4:c.569G>A	p.Arg190Lys	p.R190K	ENST00000373198	NM_133170.3	190	aGa/aAa	5/32	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.547649633721592	2		263	474	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268489	46268489	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	333	591	0	ENST00000371998.3:c.2876C>T	p.Pro959Leu	p.P959L	ENST00000371998		959	cCc/cTc	15/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.547649633721592	2		591	1171	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592333	29592335	+	missense_variant	Missense_Mutation	TNP	CTA	CTA	TTT	novel	NA	P-0008946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	288	359	0	ENST00000356175.3:c.4748_4750delinsTTT	p.Pro1583_Ile1584delinsLeuPhe	p.P1583_I1584delinsLF	ENST00000356175	NM_000267.3	1583	cCTAtt/cTTTtt	35/57	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.547649633721592	2		359	943	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0008947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	210	287	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.397138749251592	3	FACETS	0.92	0.859	0.983	0.92	0.859	0.983	CLONAL	2	TRUE	1	0.42590097318367	3		287	650	SUCCESS
FH	2271	MSKCC	GRCh37	1	241661205	241661205	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	158	382	0	ENST00000366560.3:c.1456G>T	p.Ala486Ser	p.A486S	ENST00000366560	NM_000143.3	486	Gct/Tct	10/10	0.409158836897529	5	FACETS	0.993	0.908	1	0.248	0.227	0.271	CLONAL	1	TRUE	1	0.42590097318367	5		382	1225	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391102	89391102	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	157	383	0	ENST00000336596.2:c.1168A>G	p.Thr390Ala	p.T390A	ENST00000336596	NM_005233.5	390	Acc/Gcc	5/17	1	2	FACETS	0.906	0.83	0.984	0.906	0.83	0.984	CLONAL	1	TRUE	1	0.42590097318367	2		383	814	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520549	176520549	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	144	315	0	ENST00000292408.4:c.1394A>T	p.Asp465Val	p.D465V	ENST00000292408	NM_213647.1	465	gAc/gTc	10/18	0.22718695314875	3	FACETS	1	0.967	1	0.374	0.341	0.408	INDETERMINATE	1	TRUE	0	0.42590097318367	3		315	732	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341124	8341124	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	235	403	0	ENST00000356435.5:c.5092G>C	p.Asp1698His	p.D1698H	ENST00000356435		1698	Gat/Cat	30/35	0.42590097318367	2	FACETS	0.95	0.893	1	0.95	0.893	1	CLONAL	2	TRUE	0	0.42590097318367	2		403	581	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341142	8341142	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	239	376	2	ENST00000356435.5:c.5074C>A	p.Arg1692Ser	p.R1692S	ENST00000356435		1692	Cgt/Agt	30/35	0.42590097318367	2	FACETS	0.961	0.905	1	0.961	0.905	1	CLONAL	2	TRUE	0	0.42590097318367	2		378	584	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224597	108224597	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	219	270	0	ENST00000278616.4:c.8776G>T	p.Val2926Phe	p.V2926F	ENST00000278616	NM_000051.3	2926	Gtc/Ttc	60/63	0.395082761808315	4	FACETS	0.86	0.801	0.92			1	CLONAL	2	TRUE	NA	0.42590097318367	4		270	853	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020345	123020345	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	84	309	0	ENST00000355640.3:c.833C>A	p.Ser278Ter	p.S278*	ENST00000355640		278	tCa/tAa	2/7	0.275984093415112	3	FACETS	0.654	0.577	0.736			1	SUBCLONAL	1	TRUE	NA	0.42590097318367	3		309	732	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207061	1207064	+	protein_altering_variant	In_Frame_Del	DEL	TGAT	TGAT	C	novel	NA	P-0008947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	281	349	0	ENST00000326873.7:c.149_152delinsC	p.Leu50_Met51delinsPro	p.L50_M51delinsP	ENST00000326873	NM_000455.4	50	cTGATg/cCg	1/10	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.42590097318367	NA		349	643	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445051	89445051	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	285	613	2	ENST00000336596.2:c.1371G>A	p.Trp457Ter	p.W457*	ENST00000336596	NM_005233.5	457	tgG/tgA	6/17	NA	2	FACETS	0.967	0.911	1			1	INDETERMINATE	1	TRUE	NA	0.640880433336176	2		615	920	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967860	93967860	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	107	962	0	ENST00000369303.4:c.2067T>G	p.Phe689Leu	p.F689L	ENST00000369303	NM_004440.3	689	ttT/ttG	11/17	0.580349517044292	1	FACETS	0.25	0.224	0.278	0.25	0.224	0.278	SUBCLONAL	1	TRUE	0	0.640880433336176	1		962	908	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857158	9857158	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	436	714	0	ENST00000330684.3:c.4243G>A	p.Asp1415Asn	p.D1415N	ENST00000330684	NM_001134407.1	1415	Gac/Aac	13/13	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.640880433336176	2		714	1222	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892187	9892187	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	345	687	0	ENST00000330684.3:c.2303G>T	p.Gly768Val	p.G768V	ENST00000330684	NM_001134407.1	768	gGc/gTc	11/13	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.640880433336176	2		687	1039	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223303	2223303	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	48	493	0	ENST00000326181.6:c.916del	p.Ala306ProfsTer24	p.A306Pfs*24	ENST00000326181	NM_032271.2	305	ctG/ct	10/21	1	2	FACETS	0.21	0.177	0.246	0.21	0.177	0.246	SUBCLONAL	1	TRUE	1	0.640880433336176	2		493	714	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578264	7578338	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GATAAGATGCTGAGGAGGGGCCAGACCTAAGAGCAATCAGTGAGGAATCAGAGGCCTGGGGACCCTGGGCAACCA	GATAAGATGCTGAGGAGGGGCCAGACCTAAGAGCAATCAGTGAGGAATCAGAGGCCTGGGGACCCTGGGCAACCA	TT	novel	NA	P-0008966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	280	561	0	ENST00000269305.4:c.559+33_585delinsAA		p.X187_splice	ENST00000269305	NM_001126112.2	187		6/11	0.640880433336176	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.640880433336176	1		561	556	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0009000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	231	287	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.232894957922848	2	FACETS	0.877	0.821	0.935	1	0.99	1	CLONAL	3	TRUE	0	0.231891136591034	2		287	757	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0009000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	236	656	1	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.232894957922848	3	FACETS	0.856	0.8	0.913	1	0.989	1	CLONAL	3	TRUE	1	0.231891136591034	3		657	885	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710666	114710666	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1521	325	763	2	ENST00000543371.1:c.151G>T	p.Glu51Ter	p.E51*	ENST00000543371	NM_001198531.1	51	Gaa/Taa	1/14	0.232894957922848	3	FACETS	0.847	0.797	0.899	0.847	0.797	0.899	CLONAL	2	TRUE	1	0.231891136591034	3		765	1846	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045684	26045684	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1428894577	NA	P-0009000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2032	252	907	0	ENST00000540144.1:c.46G>A	p.Ala16Thr	p.A16T	ENST00000540144	NM_003531.2	16	Gct/Act	1/1	0.232894957922848	3	FACETS	1	0.967	1	0.531	0.494	0.569	CLONAL	1	TRUE	1	0.231891136591034	3		907	2284	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151866325	151866325	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1277612900	NA	P-0009000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	127	463	0	ENST00000262189.6:c.9463A>G	p.Ile3155Val	p.I3155V	ENST00000262189	NM_170606.2	3155	Ata/Gta	41/59	0.207281684324725	5	FACETS	0.96	0.87	1	0.64	0.58	0.703	CLONAL	2	TRUE	2	0.231891136591034	5		463	769	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772438	56772438	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	104	592	0	ENST00000337432.4:c.292G>A	p.Gly98Ser	p.G98S	ENST00000337432	NM_058216.2	98	Ggc/Agc	2/9	1	2	FACETS	0.998	0.892	1	0.998	0.892	1	CLONAL	1	TRUE	1	0.231891136591034	2		592	899	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0009004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	207	719	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.303030208793776	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.2	3		719	970	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266611	198266611	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs755415626	NA	P-0009004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	41	354	0	ENST00000335508.6:c.2225G>A	p.Gly742Asp	p.G742D	ENST00000335508	NM_012433.2	742	gGt/gAt	16/25	1	2	FACETS	0.643	0.534	0.764	0.643	0.534	0.764	SUBCLONAL	1	TRUE	1	0.2	2		354	638	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468036	50468036	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	74	353	0	ENST00000331340.3:c.1271A>G	p.Asn424Ser	p.N424S	ENST00000331340	NM_006060.4	424	aAc/aGc	8/8	0.13621189021957	4	FACETS	0.894	0.781	1	0.447	0.39	0.509	CLONAL	1	TRUE	2	0.2	4		353	993	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577080	7577087	+	frameshift_variant	Frame_Shift_Del	DEL	TTCCTCTG	TTCCTCTG	-	novel	NA	P-0009004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1229	84	488	0	ENST00000269305.4:c.851_858del	p.Thr284ArgfsTer19	p.T284Rfs*19	ENST00000269305	NM_001126112.2	284	aCAGAGGAA/a	8/11	1	2	FACETS	0.64	0.563	0.723	0.64	0.563	0.723	SUBCLONAL	1	TRUE	1	0.2	2		488	1313	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0009010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	54	446	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.302416674119994	3	FACETS	1	0.95	1	0.626	0.537	0.721	CLONAL	1	TRUE	1	0.305117684970508	3		446	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0009010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	227	334	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.305117684970508	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.305117684970508	2		334	730	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74858968	74858968	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	129	189	0	ENST00000284811.8:c.236A>G	p.Tyr79Cys	p.Y79C	ENST00000284811		79	tAc/tGc	4/4	0.305117684970508	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	2	TRUE	0	0.305117684970508	2		189	420	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47061249	47061249	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0009010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	210	491	0	ENST00000409792.3:c.7431+1G>A		p.X2477_splice	ENST00000409792	NM_014159.6	2477			0.305117684970508	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.305117684970508	1		491	971	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409089	4409089	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777848359	NA	P-0009010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	112	291	2	ENST00000261254.3:c.784C>T	p.Arg262Cys	p.R262C	ENST00000261254	NM_001759.3	262	Cgt/Tgt	5/5	0.302416674119994	3	FACETS	1	0.908	1	0.505	0.454	0.56	CLONAL	1	TRUE	1	0.305117684970508	3		293	837	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416774	121416774	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	256	332	0	ENST00000257555.6:c.203G>T	p.Arg68Leu	p.R68L	ENST00000257555		68	cGg/cTg	1/10	0.302416674119994	3	FACETS	0.985	0.923	1	0.985	0.923	1	CLONAL	2	TRUE	1	0.305117684970508	3		332	982	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509060	106509060	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009014-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	127	357	0	ENST00000359195.3:c.1054G>A	p.Val352Met	p.V352M	ENST00000359195	NM_002649.2	352	Gtg/Atg	2/11	1	2	FACETS	0.986	0.893	1	0.986	0.893	1	CLONAL	1	FALSE	1	0.312271954846022	2		357	825	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0009019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	160	334	2	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	0.631958182151406	3	FACETS	0.885	0.813	0.96	0.442	0.406	0.48	CLONAL	1	TRUE	1	0.631958182151406	3		336	753	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913492	NA	P-0009019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	255	323	0	ENST00000286548.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000286548	NM_002072.3	209	cAa/cTa	5/7	0.631958182151406	3	FACETS	0.92	0.869	0.972	0.92	0.869	0.972	CLONAL	2	TRUE	1	0.631958182151406	3		323	577	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687457	37687457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	248	317	1	ENST00000447079.4:c.4361G>A	p.Gly1454Glu	p.G1454E	ENST00000447079	NM_015083.1	1454	gGa/gAa	14/14	0.631958182151406	3	FACETS	0.921	0.869	0.973	0.921	0.869	0.973	CLONAL	2	TRUE	1	0.631958182151406	3		318	561	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0009047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	142	287	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.217114931472868	2		287	975	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970969	21970969	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	100	343	0	ENST00000304494.5:c.389T>A	p.Leu130Gln	p.L130Q	ENST00000304494	NM_000077.4	130	cTg/cAg	2/3	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.217114931472868	2		343	788	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157519968	157519968	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	140	401	0	ENST00000346085.5:c.4037A>G	p.Tyr1346Cys	p.Y1346C	ENST00000346085	NM_020732.3	1346	tAt/tGt	17/20	0.217114931472868	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.217114931472868	1		401	886	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591917	48591931	+	inframe_deletion	In_Frame_Del	DEL	TCGCTTTTGTTTGGG	TCGCTTTTGTTTGGG	-	novel	NA	P-0009047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	98	480	0	ENST00000342988.3:c.1082_1096del	p.Arg361_Gly365del	p.R361_G365del	ENST00000342988	NM_005359.5	360	gaTCGCTTTTGTTTGGGt/gat	9/12	0.217114931472868	1	FACETS	0.89	0.793	0.994	0.89	0.793	0.994	CLONAL	1	TRUE	0	0.217114931472868	1		480	904	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578482	7578482	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	106	370	0	ENST00000269305.4:c.448del	p.Thr150HisfsTer20	p.T150Hfs*20	ENST00000269305	NM_001126112.2	150	Aca/ca	5/11	0.217114931472868	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.217114931472868	1		370	830	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009052-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	97	225	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.957	1			1	INDETERMINATE	1	TRUE	NA	0.544076486752085	2		225	320	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797845	45797845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782727	NA	P-0009052-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	240	358	0	ENST00000450313.1:c.926G>A	p.Arg309His	p.R309H	ENST00000450313	NM_012222.2	309	cGc/cAc	10/16	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.544076486752085	2		358	855	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047959	180047959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs933223149	NA	P-0009052-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	168	336	1	ENST00000261937.6:c.2216G>A	p.Arg739His	p.R739H	ENST00000261937	NM_182925.4	739	cGc/cAc	15/30	NA	2	FACETS	1	0.954	1			1	INDETERMINATE	1	TRUE	NA	0.544076486752085	2		337	591	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692837	89692837	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009052-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	75	116	0	ENST00000371953.3:c.321T>A	p.Asp107Glu	p.D107E	ENST00000371953	NM_000314.4	107	gaT/gaA	5/9	0.544076486752085	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.544076486752085	1		116	176	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2137942	2137942	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs137854882	NA	P-0009052-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	154	308	0	ENST00000219476.3:c.5068G>A	p.Asp1690Asn	p.D1690N	ENST00000219476	NM_000548.3	1690	Gac/Aac	39/42	1	2	FACETS	0.953	0.876	1	0.953	0.876	1	CLONAL	1	TRUE	1	0.544076486752085	2		308	594	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024684	31024684	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009052-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	211	434	0	ENST00000375687.4:c.4169A>G	p.His1390Arg	p.H1390R	ENST00000375687	NM_015338.5	1390	cAt/cGt	13/13	1	2	FACETS	0.917	0.853	0.983	0.917	0.853	0.983	CLONAL	1	TRUE	1	0.544076486752085	2		434	846	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0009063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	35	595	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.182018364649601	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		596	857	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0009063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	38	330	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.3	3	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	3		330	1071	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438296	56438296	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1334858429	NA	P-0009063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	92	283	0	ENST00000407977.2:c.697C>T	p.Gln233Ter	p.Q233*	ENST00000407977		233	Cag/Tag	7/10	0.182018364649601	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		283	539	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0009072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	489	345	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.850980705551922	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.850980705551922	3		345	814	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0009072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	204	330	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.850980705551922	2		330	467	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164805	47164805	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	297	223	0	ENST00000409792.3:c.1321C>T	p.Arg441Ter	p.R441*	ENST00000409792	NM_014159.6	441	Cga/Tga	3/21	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.850980705551922	2		223	652	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572484	95572484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	359	320	0	ENST00000393063.1:c.2881C>T	p.Pro961Ser	p.P961S	ENST00000393063	NM_030621.3	961	Cct/Tct	19/28	1	2	FACETS	0.995	0.948	1	0.995	0.948	1	CLONAL	1	TRUE	1	0.850980705551922	2		320	848	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483337	120483338	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	228	272	0	ENST00000256646.2:c.3023_3024delinsTT	p.Ser1008Phe	p.S1008F	ENST00000256646	NM_024408.3	1008	tCC/tTT	19/34	1	2	FACETS	0.836	0.784	0.889	0.836	0.784	0.889	CLONAL	1	TRUE	1	0.850980705551922	2		272	641	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0009079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	68	344	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.524	0.455	0.6	0.524	0.455	0.6	SUBCLONAL	1	TRUE	1	0.306184920075013	2		344	847	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127176	22127176	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	53	408	1	ENST00000215832.6:c.952G>A	p.Asp318Asn	p.D318N	ENST00000215832	NM_002745.4	318	Gac/Aac	7/9	1	2	FACETS	0.358	0.304	0.417	0.358	0.304	0.417	SUBCLONAL	1	TRUE	1	0.306184920075013	2		409	968	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929602	44929602	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	134	207	0	ENST00000377967.4:c.2702G>A	p.Arg901Lys	p.R901K	ENST00000377967	NM_021140.2	901	aGg/aAg	17/29	0.30700063906703	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.306184920075013	1		207	526	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847275	68847277	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0009079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	56	388	0	ENST00000261769.5:c.1199_1201del	p.Asp400del	p.D400del	ENST00000261769	NM_004360.3	399	acTGAt/act	9/16	1	2	FACETS	0.377	0.322	0.438	0.377	0.322	0.438	SUBCLONAL	1	TRUE	1	0.306184920075013	2		388	969	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913514	NA	P-0009084-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	408	388	0	ENST00000288135.5:c.2466T>A	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaA	17/21	0.210542122054247	4	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.541072912837235	4		388	998	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0009084-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	213	334	2	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	0.540262778569034	3	FACETS	1	0.98	1	0.57	0.53	0.611	CLONAL	1	TRUE	1	0.541072912837235	3		336	877	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593441	55593441	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs753212327	NA	P-0009084-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	646	575	0	ENST00000288135.5:c.1598C>A	p.Ala533Asp	p.A533D	ENST00000288135	NM_000222.2	533	gCt/gAt	10/21	0.210542122054247	4	FACETS	1	0.995	1			1	INDETERMINATE	2	TRUE	NA	0.541072912837235	4		575	1565	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	183	225	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.871	0.81	0.933	0.871	0.81	0.933	CLONAL	1	TRUE	1	0.805313673275833	2		225	522	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166218	118166218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	344	331	0	ENST00000369448.3:c.728G>A	p.Gly243Glu	p.G243E	ENST00000369448	NM_017709.3	243	gGa/gAa	2/2	1	2	FACETS	0.976	0.928	1	0.976	0.928	1	CLONAL	1	TRUE	1	0.805313673275833	2		331	875	SUCCESS
FH	2271	MSKCC	GRCh37	1	241665853	241665853	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	643	307	0	ENST00000366560.3:c.1126C>G	p.Gln376Glu	p.Q376E	ENST00000366560	NM_000143.3	376	Cag/Gag	8/10	0.805313673275833	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.805313673275833	2		307	798	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418911	116418911	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1223	312	332	0	ENST00000397752.3:c.3422C>G	p.Ser1141Trp	p.S1141W	ENST00000397752	NM_000245.2	1141	tCg/tGg	17/21	0.801584513938902	4	FACETS	0.911	0.857	0.967	0.456	0.428	0.484	CLONAL	1	TRUE	2	0.805313673275833	4		332	1535	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	63	543	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		543	947	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0009138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	85	819	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.147526848291394	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		819	1050	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0009138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	99	501	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		503	1006	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88678928	88678928	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0009138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	85	479	0	ENST00000372037.3:c.869-1G>A		p.X290_splice	ENST00000372037	NM_004329.2	290			0.147526848291394	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		479	990	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0009141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	31	386	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.183098363407487	1	FACETS	0.797	0.643	0.97	0.797	0.643	0.97	CLONAL	1	TRUE	0	0.15	1		386	480	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	89	543	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.3	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.15	1		543	754	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0009145-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	86	457	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.21	2		457	756	SUCCESS
APC	324	MSKCC	GRCh37	5	112116534	112116534	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009145-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	49	533	0	ENST00000257430.4:c.580del	p.Arg194GlyfsTer11	p.R194Gfs*11	ENST00000257430	NM_000038.5	193	gcA/gc	6/16	1	2	FACETS	0.528	0.446	0.619	0.528	0.446	0.619	SUBCLONAL	1	TRUE	1	0.21	2		533	884	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0009171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	218	379	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.490279418037125	2	FACETS	0.954	0.899	1	0.954	0.899	1	CLONAL	2	TRUE	0	0.507845545198772	2		379	450	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220640	1220640	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690940	NA	P-0009171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	271	673	1	ENST00000326873.7:c.658C>T	p.Gln220Ter	p.Q220*	ENST00000326873	NM_000455.4	220	Cag/Tag	5/10	0.495251587177099	1	FACETS	0.932	0.877	0.989	0.932	0.877	0.989	CLONAL	1	TRUE	0	0.507845545198772	1		674	854	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164591	47164591	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0009171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	134	438	0	ENST00000409792.3:c.1535C>G	p.Ser512Ter	p.S512*	ENST00000409792	NM_014159.6	512	tCa/tGa	3/21	1	2	FACETS	0.936	0.854	1	0.936	0.854	1	CLONAL	1	TRUE	1	0.507845545198772	2		438	564	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092948	29092948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201206424	NA	P-0009171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	171	459	0	ENST00000328354.6:c.1036C>T	p.Arg346Cys	p.R346C	ENST00000328354	NM_007194.3	346	Cgt/Tgt	10/15	0.507845545198772	3	FACETS	1	0.97	1	0.553	0.509	0.598	CLONAL	1	TRUE	1	0.507845545198772	3		459	764	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145620	61145620	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	147	486	0	ENST00000295025.8:c.732C>G	p.Phe244Leu	p.F244L	ENST00000295025	NM_002908.2	244	ttC/ttG	7/11	1	2	FACETS	0.926	0.849	1	0.926	0.849	1	CLONAL	1	TRUE	1	0.507845545198772	2		486	625	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794494	242794494	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	184	345	0	ENST00000334409.5:c.448G>C	p.Glu150Gln	p.E150Q	ENST00000334409	NM_005018.2	150	Gaa/Caa	3/5	1	2	FACETS	0.951	0.88	1	0.951	0.88	1	CLONAL	1	TRUE	1	0.507845545198772	2		345	762	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164900	47164900	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	127	374	0	ENST00000409792.3:c.1226C>G	p.Ser409Cys	p.S409C	ENST00000409792	NM_014159.6	409	tCt/tGt	3/21	1	2	FACETS	0.829	0.754	0.909	0.829	0.754	0.909	CLONAL	1	TRUE	1	0.507845545198772	2		374	603	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119634991	119634991	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	78	385	0	ENST00000316626.5:c.508G>T	p.Ala170Ser	p.A170S	ENST00000316626		170	Gcc/Tcc	5/12	1	2	FACETS	0.751	0.663	0.844	0.751	0.663	0.844	SUBCLONAL	1	TRUE	1	0.507845545198772	2		385	409	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130170	143130170	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	93	353	0	ENST00000262992.4:c.846G>T	p.Glu282Asp	p.E282D	ENST00000262992	NM_001101669.1	282	gaG/gaT	11/24	1	2	FACETS	0.934	0.837	1	0.934	0.837	1	CLONAL	1	TRUE	1	0.507845545198772	2		353	392	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884437	151884437	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	171	387	0	ENST00000262189.6:c.4918G>T	p.Glu1640Ter	p.E1640*	ENST00000262189	NM_170606.2	1640	Gag/Tag	33/59	0.361460496712205	3	FACETS	0.91	0.837	0.986	0.455	0.418	0.493	CLONAL	1	TRUE	1	0.507845545198772	3		387	928	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5077452	5077452	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0009171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	53	257	0	ENST00000381652.3:c.1865-1G>C		p.X622_splice	ENST00000381652	NM_004972.3	622			0.507845545198772	1	FACETS	0.731	0.631	0.837	0.731	0.631	0.837	SUBCLONAL	1	TRUE	0	0.507845545198772	1		257	213	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211483	98211483	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	260	334	0	ENST00000331920.6:c.3672G>C	p.Glu1224Asp	p.E1224D	ENST00000331920	NM_000264.3	1224	gaG/gaC	22/24	0.399049962802613	3	FACETS	1	0.964	1	0.522	0.488	0.556	CLONAL	1	TRUE	1	0.507845545198772	3		334	1231	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864883	57864883	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	463	627	0	ENST00000228682.2:c.2360C>G	p.Ser787Cys	p.S787C	ENST00000228682	NM_005269.2	787	tCt/tGt	12/12	0.490279418037125	2	FACETS	1	0.99	1	0.561	0.535	0.588	CLONAL	1	TRUE	0	0.507845545198772	2		627	1624	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434821	99434821	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	180	265	0	ENST00000268035.6:c.908G>T	p.Cys303Phe	p.C303F	ENST00000268035	NM_000875.3	303	tGc/tTc	3/21	NA	2	FACETS	0.904	0.835	0.976			1	INDETERMINATE	1	TRUE	NA	0.507845545198772	2		265	784	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220382	1220382	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	247	435	0	ENST00000326873.7:c.475C>G	p.Gln159Glu	p.Q159E	ENST00000326873	NM_000455.4	159	Cag/Gag	4/10	0.495251587177099	1	FACETS	0.964	0.905	1	0.964	0.905	1	CLONAL	1	TRUE	0	0.507845545198772	1		435	753	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7141823	7141823	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	235	371	0	ENST00000302850.5:c.2547G>C	p.Lys849Asn	p.K849N	ENST00000302850	NM_000208.2	849	aaG/aaC	13/22	0.495251587177099	1	FACETS	0.939	0.88	1	0.939	0.88	1	CLONAL	1	TRUE	0	0.507845545198772	1		371	735	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600378	10600378	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	332	531	0	ENST00000171111.5:c.1477G>A	p.Glu493Lys	p.E493K	ENST00000171111	NM_203500.1	493	Gag/Aag	4/6	0.495251587177099	1	FACETS	0.92	0.871	0.971	0.92	0.871	0.971	CLONAL	1	TRUE	0	0.507845545198772	1		531	1060	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145662	11145662	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	242	398	0	ENST00000358026.2:c.4024G>T	p.Glu1342Ter	p.E1342*	ENST00000358026	NM_001128849.1	1342	Gag/Tag	29/36	0.495251587177099	1	FACETS	0.958	0.899	1	0.958	0.899	1	CLONAL	1	TRUE	0	0.507845545198772	1		398	742	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024053	31024053	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs777253679	NA	P-0009171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	217	422	0	ENST00000375687.4:c.3538G>C	p.Asp1180His	p.D1180H	ENST00000375687	NM_015338.5	1180	Gat/Cat	13/13	0.507845545198772	3	FACETS	0.922	0.856	0.99	0.461	0.428	0.495	CLONAL	1	TRUE	1	0.507845545198772	3		422	1162	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130673	29130673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	207	288	0	ENST00000328354.6:c.37C>T	p.His13Tyr	p.H13Y	ENST00000328354	NM_007194.3	13	Cat/Tat	2/15	0.507845545198772	3	FACETS	1	0.946	1	0.512	0.475	0.55	CLONAL	1	TRUE	1	0.507845545198772	3		288	999	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003375	42003375	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	305	623	0	ENST00000219905.7:c.2913del	p.Gln972ArgfsTer22	p.Q972Rfs*22	ENST00000219905	NM_001164273.1	971	cGg/cg	8/24	0.507845545198772	1	FACETS	0.89	0.84	0.941	0.89	0.84	0.941	CLONAL	1	TRUE	0	0.507845545198772	1		623	1007	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939168	36939168	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	57	488	2	ENST00000361632.4:c.541G>A	p.Asp181Asn	p.D181N	ENST00000361632		181	Gac/Aac	5/16	1	2	FACETS	0.995	0.859	1	0.995	0.859	1	CLONAL	1	FALSE	1	0.359072792817224	2		490	319	SUCCESS
INSRR	3645	MSKCC	GRCh37	1	156812015	156812015	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	17	104	0	ENST00000368195.3:c.3286G>C	p.Ala1096Pro	p.A1096P	ENST00000368195	NM_014215.2	1096	Gct/Cct	19/22	0.335714567977913	3	FACETS	1	0.889	1	0.673	0.512	0.855	CLONAL	1	FALSE	1	0.359072792817224	3		104	83	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495384	56495384	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	53	395	0	ENST00000267101.3:c.3574G>C	p.Asp1192His	p.D1192H	ENST00000267101	NM_001982.3	1192	Gat/Cat	28/28	1	2	FACETS	0.923	0.791	1	0.923	0.791	1	CLONAL	1	FALSE	1	0.359072792817224	2		395	320	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626737	28626737	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	49	374	1	ENST00000241453.7:c.559G>A	p.Glu187Lys	p.E187K	ENST00000241453	NM_004119.2	187	Gag/Aag	5/24	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	FALSE	1	0.359072792817224	2		375	257	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32905152	32905152	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	16	243	0	ENST00000380152.3:c.778G>C	p.Glu260Gln	p.E260Q	ENST00000380152		260	Gaa/Caa	9/27	1	2	FACETS	0.407	0.301	0.533	0.407	0.301	0.533	SUBCLONAL	1	FALSE	1	0.359072792817224	2		243	219	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41021008	41021008	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	52	400	0	ENST00000267868.3:c.630G>A	p.Met210Ile	p.M210I	ENST00000267868	NM_002875.4	210	atG/atA	7/10	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	FALSE	1	0.359072792817224	2		400	271	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663428	67663428	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	520	337	0	ENST00000264010.4:c.1829C>T	p.Ser610Phe	p.S610F	ENST00000264010	NM_006565.3	610	tCt/tTt	10/12	0.359072792817224	10	FACETS	1	0.988	1			1	CLONAL	9	FALSE	NA	0.359072792817224	10		337	757	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0009194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	100	312	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.826	0.74	0.916	0.826	0.74	0.916	CLONAL	1	TRUE	1	0.44129652989485	2		312	549	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484275	8484275	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	146	299	0	ENST00000356435.5:c.3257C>G	p.Thr1086Arg	p.T1086R	ENST00000356435		1086	aCa/aGa	19/35	1	2	FACETS	0.97	0.888	1	0.97	0.888	1	CLONAL	1	TRUE	1	0.44129652989485	2		299	682	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380206	25380206	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	154	331	0	ENST00000311936.3:c.252A>G	p.Ile84Met	p.I84M	ENST00000311936	NM_004985.3	84	atA/atG	3/5	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.44129652989485	2		331	673	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944762	31944762	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	87	143	1	ENST00000340398.3:c.339C>A	p.His113Gln	p.H113Q	ENST00000340398	NM_001013699.2	113	caC/caA	1/1	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.44129652989485	2		144	380	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008251	29008251	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	142	381	1	ENST00000282397.4:c.620G>T	p.Cys207Phe	p.C207F	ENST00000282397	NM_002019.4	207	tGt/tTt	5/30	1	2	FACETS	0.956	0.874	1	0.956	0.874	1	CLONAL	1	TRUE	1	0.44129652989485	2		382	673	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599952	10599952	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	213	402	1	ENST00000171111.5:c.1624G>T	p.Glu542Ter	p.E542*	ENST00000171111	NM_203500.1	542	Gag/Tag	5/6	0.44129652989485	1	FACETS	0.996	0.929	1	0.996	0.929	1	CLONAL	1	TRUE	0	0.44129652989485	1		403	755	SUCCESS
ALK	238	MSKCC	GRCh37	2	29436860	29436860	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs281864720	NA	P-0121561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	355	281	0	ENST00000389048.3:c.3733T>A	p.Phe1245Ile	p.F1245I	ENST00000389048	NM_004304.4	1245	Ttc/Atc	24/29	1	2	FACETS	0.958	0.913	1	0.958	0.913	1	CLONAL	1	NA	1	0.899134609954546	2		281	824	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667603	29667639	+	frameshift_variant	Frame_Shift_Del	DEL	TACCGCACTTCTTGAACAAAACCTGCATACTTTAGAT	TACCGCACTTCTTGAACAAAACCTGCATACTTTAGAT	-	novel	NA	P-0009205-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	29	291	0	ENST00000356175.3:c.6939_6975del	p.Thr2314ValfsTer49	p.T2314Vfs*49	ENST00000356175	NM_000267.3	2313	ggTACCGCACTTCTTGAACAAAACCTGCATACTTTAGAT/gg	46/57	0.404808322108537	1	FACETS	0.171	0.137	0.21	0.171	0.137	0.21	INDETERMINATE	1	TRUE	0	0.694968319809382	1		291	318	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579362	7579379	+	inframe_deletion	In_Frame_Del	DEL	AACCGTAGCTGCCCTGGT	AACCGTAGCTGCCCTGGT	-	novel	NA	P-0009205-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	106	241	0	ENST00000269305.4:c.308_325del	p.Tyr103_Gly108del	p.Y103_G108del	ENST00000269305	NM_001126112.2	103	tACCAGGGCAGCTACGGTTtc/ttc	4/11	0.646305316611774	1	FACETS	0.52	0.47	0.572	0.52	0.47	0.572	SUBCLONAL	1	TRUE	0	0.694968319809382	1		241	383	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30061024	30061034	+	frameshift_variant	Frame_Shift_Del	DEL	AACTCCTCAAA	AACTCCTCAAA	-	novel	NA	P-0009205-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	202	291	0	ENST00000338641.4:c.856_866del	p.Asn286AlafsTer4	p.N286Afs*4	ENST00000338641	NM_000268.3	286	AACTCCTCAAAg/g	9/16	0.694968319809382	1	FACETS	0.872	0.819	0.925	0.872	0.819	0.925	CLONAL	1	TRUE	0	0.694968319809382	1		291	435	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0009206-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	23	260	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.865	0.673	1	0.865	0.673	1	CLONAL	1	TRUE	1	0.12	2		260	443	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555150	106555150	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009206-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	34	303	0	ENST00000369096.4:c.2267A>G	p.Glu756Gly	p.E756G	ENST00000369096	NM_001198.3	756	gAg/gGg	7/7	0.139723211547269	1	FACETS	0.822	0.67	0.994	0.822	0.67	0.994	CLONAL	1	TRUE	0	0.12	1		303	648	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334713	81334713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009206-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	30	669	3	ENST00000222390.5:c.2003C>T	p.Pro668Leu	p.P668L	ENST00000222390	NM_000601.4	668	cCa/cTa	17/18	1	2	FACETS	0.986	0.793	1	0.986	0.793	1	CLONAL	1	TRUE	1	0.12	2		672	507	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0009215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	55	262	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.336	0.286	0.391	0.336	0.286	0.391	SUBCLONAL	1	FALSE	1	0.354163596776938	2		262	924	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	12	543	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		543	398	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094826	143094842	+	frameshift_variant	Frame_Shift_Del	DEL	GAGAATGCTGGCTTGCA	GAGAATGCTGGCTTGCA	-	novel	NA	P-0009240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	364	405	0	ENST00000262992.4:c.1302_1318del	p.Ala435ArgfsTer43	p.A435Rfs*43	ENST00000262992	NM_001101669.1	434	tcTGCAAGCCAGCATTCTCca/tcca	14/24	0.722291642162321	3	FACETS	1	0.985	1	0.707	0.677	0.736	CLONAL	2	TRUE	0	0.722291642162321	3		405	647	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578535	+	protein_altering_variant	In_Frame_Del	DEL	CAGGTCTTGGCCAGTTGGCAAAACATCT	CAGGTCTTGGCCAGTTGGCAAAACATCT	G	novel	NA	P-0009240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	428	327	0	ENST00000269305.4:c.395_422delinsC	p.Lys132_Cys141delinsThr	p.K132_C141delinsT	ENST00000269305	NM_001126112.2	132	aAGATGTTTTGCCAACTGGCCAAGACCTGc/aCc	5/11	0.722291642162321	2	FACETS	0.906	0.875	0.937	0.906	0.875	0.937	CLONAL	2	TRUE	0	0.722291642162321	2		327	654	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0009249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	249	387	0	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	0.217755001047567	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	0	0.271833002073964	2		387	916	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0009249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	133	502	1	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	0.271833002073964	2	FACETS	0.901	0.817	0.99	0.451	0.408	0.495	CLONAL	1	TRUE	0	0.271833002073964	2		503	1086	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131428	202131428	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	116	352	0	ENST00000358485.4:c.396T>G	p.Asp132Glu	p.D132E	ENST00000358485	NM_001080125.1	132	gaT/gaG	2/9	0.258693458069923	3	FACETS	1	0.957	1	0.557	0.502	0.616	CLONAL	1	TRUE	1	0.271833002073964	3		352	870	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38949871	38949871	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	78	407	0	ENST00000357387.3:c.4079T>G	p.Phe1360Cys	p.F1360C	ENST00000357387	NM_152756.3	1360	tTt/tGt	31/38	0.258693458069923	3	FACETS	0.907	0.796	1	0.453	0.398	0.513	CLONAL	1	TRUE	1	0.271833002073964	3		407	719	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482295	87482295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	97	444	0	ENST00000277120.3:c.1582G>A	p.Glu528Lys	p.E528K	ENST00000277120		528	Gaa/Aaa	14/19	0.258693458069923	3	FACETS	0.79	0.703	0.884	0.395	0.351	0.442	SUBCLONAL	1	TRUE	1	0.271833002073964	3		444	1026	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865725	57865725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149870317	NA	P-0009249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	176	579	0	ENST00000228682.2:c.3202C>T	p.Arg1068Trp	p.R1068W	ENST00000228682	NM_005269.2	1068	Cgg/Tgg	12/12	0.271833002073964	2	FACETS	1	0.961	1	0.538	0.494	0.583	CLONAL	1	TRUE	0	0.271833002073964	2		579	1204	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562321	21562321	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	84	208	0	ENST00000382592.4:c.1598T>C	p.Leu533Pro	p.L533P	ENST00000382592	NM_014572.2	533	cTg/cCg	4/8	0.271833002073964	5	FACETS	1	0.913	1			1	CLONAL	1	TRUE	NA	0.271833002073964	5		208	835	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961553	54961553	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750077869	NA	P-0009249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	73	300	0	ENST00000312783.6:c.79G>A	p.Val27Met	p.V27M	ENST00000312783	NM_198436.1	27	Gtg/Atg	4/10	0.271833002073964	8	FACETS	0.78	0.68	0.889			1	SUBCLONAL	1	TRUE	NA	0.271833002073964	8		300	1250	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891508	76891508	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1557107880	NA	P-0009249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	109	492	0	ENST00000373344.5:c.4597A>G	p.Ile1533Val	p.I1533V	ENST00000373344	NM_000489.3	1533	Ata/Gta	16/35	1	2	FACETS	0.853	0.765	0.947	0.853	0.765	0.947	CLONAL	1	TRUE	1	0.271833002073964	2		492	940	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190042	123190042	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776480387	NA	P-0009249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	84	450	0	ENST00000218089.9:c.1261C>T	p.His421Tyr	p.H421Y	ENST00000218089	NM_001042749.1	421	Cac/Tac	14/35	1	2	FACETS	0.747	0.659	0.842	0.747	0.659	0.842	SUBCLONAL	1	TRUE	1	0.271833002073964	2		450	827	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396417	396421	+	missense_variant	Missense_Mutation	ONP	CTTAA	CTTAA	ATTTT	novel	NA	P-0009249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	243	435	0	ENST00000262320.3:c.605_609delinsAAAAT	p.Leu202_Lys203delinsGlnAsn	p.L202_K203delinsQN	ENST00000262320	NM_003502.3	202	cTTAAG/cAAAAT	2/11	0.271833002073964	3	FACETS	0.93	0.868	0.993	0.93	0.868	0.993	CLONAL	2	TRUE	1	0.271833002073964	3		435	1092	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0009252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	67	249	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.164652384627251	2		249	559	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405905	49405905	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	82	482	0	ENST00000418115.1:c.233A>T	p.Asp78Val	p.D78V	ENST00000418115	NM_001664.2	78	gAt/gTt	3/5	1	2	FACETS	0.796	0.699	0.9	0.796	0.699	0.9	SUBCLONAL	1	TRUE	1	0.164652384627251	2		482	1252	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200877	67200877	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs775346029	NA	P-0009252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	57	396	0	ENST00000312629.5:c.865C>A	p.Pro289Thr	p.P289T	ENST00000312629	NM_003952.2	289	Ccc/Acc	10/15	1	2	FACETS	0.716	0.612	0.83	0.716	0.612	0.83	SUBCLONAL	1	TRUE	1	0.164652384627251	2		396	967	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0009260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	259	262	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.438848537703112	2		262	1110	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249028	55249028	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1275022697	NA	P-0009260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	176	381	1	ENST00000275493.2:c.2326C>T	p.Arg776Cys	p.R776C	ENST00000275493	NM_005228.3	776	Cgc/Tgc	20/28	1	2	FACETS	0.975	0.899	1	0.975	0.899	1	CLONAL	1	TRUE	1	0.438848537703112	2		382	823	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0009269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	158	379	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.250947926156113	2	FACETS	0.944	0.865	1	0.472	0.432	0.513	CLONAL	1	TRUE	0	0.39387805846772	2		379	850	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682991	241682991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226883651	NA	P-0009269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	120	221	0	ENST00000366560.3:c.32C>T	p.Ser11Leu	p.S11L	ENST00000366560	NM_000143.3	11	tCg/tTg	1/10	0.196946863127016	3	FACETS	0.7	0.631	0.773	0.35	0.315	0.387	INDETERMINATE	1	TRUE	1	0.39387805846772	3		221	1042	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521676	89521676	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1412450341	NA	P-0009269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	113	346	0	ENST00000336596.2:c.2753A>T	p.Asp918Val	p.D918V	ENST00000336596	NM_005233.5	918	gAc/gTc	16/17	1	2	FACETS	0.642	0.577	0.711	0.642	0.577	0.711	SUBCLONAL	1	TRUE	1	0.39387805846772	2		346	894	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528639	89528639	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	68	252	0	ENST00000336596.2:c.2939C>A	p.Pro980Gln	p.P980Q	ENST00000336596	NM_005233.5	980	cCa/cAa	17/17	1	2	FACETS	0.524	0.455	0.598	0.524	0.455	0.598	SUBCLONAL	1	TRUE	1	0.39387805846772	2		252	659	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455614	189455614	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1163601484	NA	P-0009269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	102	331	0	ENST00000264731.3:c.148C>T	p.Leu50Phe	p.L50F	ENST00000264731	NM_003722.4	50	Ctc/Ttc	2/14	1	2	FACETS	0.62	0.553	0.69	0.62	0.553	0.69	SUBCLONAL	1	TRUE	1	0.39387805846772	2		331	836	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136826	55136826	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	79	409	0	ENST00000257290.5:c.1148G>T	p.Arg383Leu	p.R383L	ENST00000257290	NM_006206.4	383	cGt/cTt	8/23	1	2	FACETS	0.539	0.474	0.61	0.539	0.474	0.61	SUBCLONAL	1	TRUE	1	0.39387805846772	2		409	744	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671288	30671288	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	129	338	0	ENST00000376406.3:c.5589G>C	p.Lys1863Asn	p.K1863N	ENST00000376406	NM_014641.2	1863	aaG/aaC	11/15	0.39387805846772	4	FACETS	0.782	0.708	0.862	0.261	0.236	0.288	SUBCLONAL	1	TRUE	1	0.39387805846772	4		338	1167	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520048	106520048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	141	315	0	ENST00000359195.3:c.2476G>A	p.Glu826Lys	p.E826K	ENST00000359195	NM_002649.2	826	Gaa/Aaa	6/11	0.365714005934196	2	FACETS	0.857	0.781	0.937	0.429	0.39	0.469	CLONAL	1	TRUE	0	0.39387805846772	2		315	835	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006075	22006075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762253433	NA	P-0009269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	274	210	1	ENST00000276925.6:c.328G>A	p.Asp110Asn	p.D110N	ENST00000276925	NM_004936.3	110	Gat/Aat	2/2	1	2	FACETS	0.846	0.797	0.896	1	0.995	1	CLONAL	2	TRUE	1	0.39387805846772	2		211	822	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28897069	28897069	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	139	216	0	ENST00000282397.4:c.2811C>A	p.His937Gln	p.H937Q	ENST00000282397	NM_002019.4	937	caC/caA	21/30	1	2	FACETS	0.786	0.715	0.86	0.786	0.715	0.86	SUBCLONAL	1	TRUE	1	0.39387805846772	2		216	898	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436513	110436513	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	145	347	0	ENST00000375856.3:c.1888G>A	p.Glu630Lys	p.E630K	ENST00000375856	NM_003749.2	630	Gag/Aag	1/2	1	2	FACETS	0.54	0.491	0.592	0.54	0.491	0.592	SUBCLONAL	1	TRUE	1	0.39387805846772	2		347	1364	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609337	81609337	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	104	374	0	ENST00000298171.2:c.935G>A	p.Arg312Lys	p.R312K	ENST00000298171	NM_000369.2	312	aGa/aAa	10/10	1	2	FACETS	0.517	0.462	0.576	0.517	0.462	0.576	SUBCLONAL	1	TRUE	1	0.39387805846772	2		374	1022	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946230	81946230	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	162	515	0	ENST00000359376.3:c.1963G>C	p.Glu655Gln	p.E655Q	ENST00000359376	NM_002661.3	655	Gag/Cag	19/33	0.297541599444418	1	FACETS	0.493	0.451	0.538	0.493	0.451	0.538	SUBCLONAL	1	TRUE	0	0.39387805846772	1		515	1339	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41228526	41228526	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	138	439	0	ENST00000357654.3:c.4463A>G	p.Asn1488Ser	p.N1488S	ENST00000357654	NM_007294.3	1488	aAt/aGt	13/23	1	2	FACETS	0.79	0.719	0.865	0.79	0.719	0.865	SUBCLONAL	1	TRUE	1	0.39387805846772	2		439	887	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412791	63412791	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	85	378	0	ENST00000330258.3:c.376C>A	p.Gln126Lys	p.Q126K	ENST00000330258	NM_152424.3	126	Caa/Aaa	2/2	0.297541599444418	1	FACETS	0.414	0.365	0.467	0.414	0.365	0.467	SUBCLONAL	1	TRUE	0	0.39387805846772	1		378	837	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0009275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	131	334	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	NA	2	FACETS	0.752	0.682	0.825			1	INDETERMINATE	2	TRUE	NA	0.200297465789281	2		334	870	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0009275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	106	312	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.200297465789281	2		312	864	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220400	1220400	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1359582062	NA	P-0009275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	135	398	0	ENST00000326873.7:c.493G>T	p.Glu165Ter	p.E165*	ENST00000326873	NM_000455.4	165	Gag/Tag	4/10	0.174189258936474	2	FACETS	1	0.982	1	0.675	0.613	0.741	CLONAL	1	TRUE	0	0.200297465789281	2		398	998	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775790	9775790	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	97	207	0	ENST00000377346.4:c.333G>T	p.Lys111Asn	p.K111N	ENST00000377346	NM_005026.3	111	aaG/aaT	4/24	0.133146223537606	4	FACETS	0.941	0.84	1	0.941	0.84	1	CLONAL	2	TRUE	2	0.200297465789281	4		207	618	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254960	16254960	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	79	179	0	ENST00000375759.3:c.2225C>T	p.Ser742Phe	p.S742F	ENST00000375759	NM_015001.2	742	tCt/tTt	11/15	0.133146223537606	4	FACETS	0.783	0.689	0.883	0.783	0.689	0.883	SUBCLONAL	2	TRUE	2	0.200297465789281	4		179	605	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164040	108164040	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1034235291	NA	P-0009275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	31	159	1	ENST00000278616.4:c.4612G>T	p.Val1538Leu	p.V1538L	ENST00000278616	NM_000051.3	1538	Gta/Tta	31/63	1	2	FACETS	0.741	0.599	0.901	0.741	0.599	0.901	CLONAL	1	TRUE	1	0.200297465789281	2		160	418	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936024	44936024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009275-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	112	484	0	ENST00000377967.4:c.2785C>T	p.Pro929Ser	p.P929S	ENST00000377967	NM_021140.2	929	Cct/Tct	18/29	0.133442591330545	0	FACETS	0.694	0.622	0.77			1	SUBCLONAL	1	TRUE	0	0.200297465789281	0		484	1289	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0009303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	124	345	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.230282419455506	3	FACETS	0.904	0.82	0.991	0.904	0.82	0.991	CLONAL	2	FALSE	1	0.269394347425831	3		345	578	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166577	118166577	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773285739	NA	P-0009303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	100	189	0	ENST00000369448.3:c.1087G>A	p.Val363Ile	p.V363I	ENST00000369448	NM_017709.3	363	Gtc/Atc	2/2	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.269394347425831	2		189	608	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631128	69631128	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558206333	NA	P-0009303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1227	153	570	0	ENST00000334134.2:c.284G>A	p.Arg95Gln	p.R95Q	ENST00000334134	NM_005247.2	95	cGg/cAg	2/3	0.230282419455506	3	FACETS	0.934	0.852	1	0.467	0.426	0.51	CLONAL	1	FALSE	1	0.269394347425831	3		570	1380	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344671	118344671	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782407414	NA	P-0009303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	138	386	1	ENST00000534358.1:c.2797C>T	p.Arg933Trp	p.R933W	ENST00000534358	NM_005933.3	933	Cgg/Tgg	3/36	0.230282419455506	3	FACETS	0.812	0.74	0.887	0.812	0.74	0.887	CLONAL	2	FALSE	1	0.269394347425831	3		387	716	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419049	419049	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	336	450	0	ENST00000399788.2:c.3298G>T	p.Glu1100Ter	p.E1100*	ENST00000399788	NM_001042603.1	1100	Gaa/Taa	22/28	0.145674151991533	4	FACETS	1	0.984	1			1	INDETERMINATE	3	FALSE	NA	0.269394347425831	4		450	968	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604773	48604773	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	143	331	0	ENST00000342988.3:c.1595C>A	p.Ala532Asp	p.A532D	ENST00000342988	NM_005359.5	532	gCc/gAc	12/12	0.240991593839799	2	FACETS	1	0.985	1	0.707	0.645	0.771	CLONAL	1	FALSE	0	0.269394347425831	2		331	751	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246655	46246656	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0009303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	44	148	0	ENST00000334344.6:c.4751_4752del	p.Tyr1584CysfsTer24	p.Y1584Cfs*24	ENST00000334344	NM_152641.2	1583	acATat/acat	15/21	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	FALSE	1	0.269394347425831	2		148	283	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11292561	11292569	+	inframe_deletion	In_Frame_Del	DEL	ATTTCCTCA	ATTTCCTCA	-	novel	NA	P-0009303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	55	386	0	ENST00000361445.4:c.2438_2446del	p.Met813_Trp816delinsArg	p.M813_W816delinsR	ENST00000361445	NM_004958.3	813	aTGAGGAAATgg/agg	16/58	1	2	FACETS	0.523	0.447	0.608	0.523	0.447	0.608	SUBCLONAL	1	FALSE	1	0.269394347425831	2		386	780	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674356	86674356	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0009312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	73	145	1	ENST00000274376.6:c.2487+1G>A		p.X829_splice	ENST00000274376	NM_002890.2	829			0.413435694310587	1	FACETS	0.969	0.857	1	0.969	0.857	1	CLONAL	1	TRUE	0	0.413435694310587	1		146	289	SUCCESS
APC	324	MSKCC	GRCh37	5	112137081	112137081	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0009312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	136	225	0	ENST00000257430.4:c.834+1G>C		p.X278_splice	ENST00000257430	NM_000038.5	278			0.413435694310587	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.413435694310587	1		225	508	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287479	46287479	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	214	376	0	ENST00000334344.6:c.5338G>C	p.Gly1780Arg	p.G1780R	ENST00000334344	NM_152641.2	1780	Ggt/Cgt	20/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.413435694310587	2		376	994	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560509	65560509	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	246	411	0	ENST00000358664.4:c.88G>C	p.Ala30Pro	p.A30P	ENST00000358664	NM_002382.4	30	Gca/Cca	3/5	0.413435694310587	1	FACETS	0.98	0.917	1	0.98	0.917	1	CLONAL	1	TRUE	0	0.413435694310587	1		411	963	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21968185	21968235	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	TGATCTAAGTTTCCCGAGGTTTCTCAGAGCCTCTCTGGTTCTTTCAATCGG	TGATCTAAGTTTCCCGAGGTTTCTCAGAGCCTCTCTGGTTCTTTCAATCGG	-	novel	NA	P-0009312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	170	43	0	ENST00000304494.5:c.464_*43del		p.*155*	ENST00000304494	NM_000077.4	155		3/3	0.413435694310587	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.413435694310587	1		43	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578465	7578470	+	inframe_deletion	In_Frame_Del	DEL	GGTGCC	GGTGCC	-	novel	NA	P-0009312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	314	311	0	ENST00000269305.4:c.460_465del	p.Gly154_Thr155del	p.G154_T155del	ENST00000269305	NM_001126112.2	154	GGCACC/-	5/11	0.358598876586201	2	FACETS	0.878	0.831	0.925	0.878	0.831	0.925	CLONAL	2	TRUE	0	0.413435694310587	2		311	865	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	65	225	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.340562808486249	2		225	364	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139614	202139614	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	206	490	1	ENST00000358485.4:c.775G>T	p.Glu259Ter	p.E259*	ENST00000358485	NM_001080125.1	259	Gag/Tag	6/9	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.340562808486249	2		491	1111	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150030	202150030	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs931648756	NA	P-0009315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	127	307	0	ENST00000358485.4:c.1471C>T	p.Arg491Ter	p.R491*	ENST00000358485	NM_001080125.1	491	Cga/Tga	8/9	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.340562808486249	2		307	718	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782082	NA	P-0009315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	137	364	0	ENST00000269305.4:c.745A>T	p.Arg249Trp	p.R249W	ENST00000269305	NM_001126112.2	249	Agg/Tgg	7/11	0.33848352798782	1	FACETS	0.942	0.858	1	0.942	0.858	1	CLONAL	1	TRUE	0	0.340562808486249	1		364	709	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0009321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	21	719	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.143320541625085	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		719	911	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368213	45368213	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	60	721	0	ENST00000262160.6:c.1389C>A	p.Cys463Ter	p.C463*	ENST00000262160	NM_005901.5	463	tgC/tgA	11/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		721	829	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0009333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	406	446	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.679001980951536	4	FACETS	0.994	0.957	1	0.994	0.957	1	CLONAL	3	TRUE	1	0.679001980951536	4		446	673	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	333	283	2	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.679001980951536	3	FACETS	0.951	0.906	0.995	0.951	0.906	0.995	CLONAL	2	TRUE	1	0.679001980951536	3		285	691	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391168	89391168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772463834	NA	P-0009333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	159	317	0	ENST00000336596.2:c.1234G>A	p.Val412Ile	p.V412I	ENST00000336596	NM_005233.5	412	Gtt/Att	5/17	1	2	FACETS	0.933	0.861	1	0.933	0.861	1	CLONAL	1	TRUE	1	0.679001980951536	2		317	502	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69998291	69998291	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	250	378	0	ENST00000394351.3:c.531C>A	p.Asn177Lys	p.N177K	ENST00000394351	NM_000248.3	177	aaC/aaA	5/9	1	2	FACETS	0.998	0.937	1	0.998	0.937	1	CLONAL	1	TRUE	1	0.679001980951536	2		378	738	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222572	69222572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5584	794	465	1	ENST00000462284.1:c.545C>T	p.Ser182Phe	p.S182F	ENST00000462284	NM_002392.5	182	tCt/tTt	8/11	0.679001980951536	13	FACETS	0.868	0.834	0.903			1	CLONAL	2	TRUE	NA	0.679001980951536	13		466	6378	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222704	69222704	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5713	701	449	0	ENST00000462284.1:c.677C>G	p.Ser226Trp	p.S226W	ENST00000462284	NM_002392.5	226	tCg/tGg	8/11	0.679001980951536	13	FACETS	0.762	0.73	0.795			1	SUBCLONAL	2	TRUE	NA	0.679001980951536	13		449	6414	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	70	225	0				ENST00000310581	NM_198253.2	-/1132			0.674730954980342	4	FACETS	0.991	0.889	1	0.991	0.889	1	CLONAL	2	FALSE	2	0.89061316021778	4		225	150	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	303	591	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.592174328518408	6	FACETS	0.908	0.861	0.954	0.908	0.861	0.954	CLONAL	3	FALSE	3	0.89061316021778	6		591	695	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453145	140453145	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913366	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	342	314	0	ENST00000288602.6:c.1790T>G	p.Leu597Arg	p.L597R	ENST00000288602	NM_004333.4	597	cTa/cGa	15/18	0.592174328518408	6	FACETS	0.91	0.867	0.955	0.91	0.867	0.955	CLONAL	3	FALSE	3	0.89061316021778	6		314	782	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	466	412	0	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	0.89061316021778	4	FACETS	0.94	0.902	0.979	0.94	0.902	0.979	CLONAL	2	FALSE	2	0.89061316021778	4		412	1052	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720650	89720650	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1257124719	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	185	69	0	ENST00000371953.3:c.802-1G>A		p.X268_splice	ENST00000371953	NM_000314.4	268			0.729670773500772	4	FACETS	0.949	0.919	0.974			1	CLONAL	4	FALSE	NA	0.89061316021778	4		69	207	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979350	40979350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747923769	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	170	249	0	ENST00000373198.4:c.1783G>A	p.Asp595Asn	p.D595N	ENST00000373198	NM_133170.3	595	Gac/Aac	11/32	0.89061316021778	4	FACETS	0.911	0.849	0.974	0.911	0.849	0.974	CLONAL	2	FALSE	2	0.89061316021778	4		249	396	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523609	106523609	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1293996108	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	192	305	0	ENST00000359195.3:c.2760+1G>A		p.X920_splice	ENST00000359195	NM_002649.2	920			0.702313010099685	6	FACETS	1	0.984	1	0.788	0.736	0.842	CLONAL	2	FALSE	3	0.89061316021778	6		305	507	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420093	41420093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	135	224	0	ENST00000373198.4:c.228G>A	p.Met76Ile	p.M76I	ENST00000373198	NM_133170.3	76	atG/atA	3/32	0.496142272846314	4	FACETS	0.91	0.84	0.98			1	INDETERMINATE	2	FALSE	NA	0.89061316021778	4		224	315	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075600	8075600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145113484	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	436	592	2	ENST00000377482.5:c.80G>A	p.Gly27Glu	p.G27E	ENST00000377482	NM_018948.3	27	gGg/gAg	2/4	0.89061316021778	4	FACETS	0.951	0.911	0.992			1	CLONAL	2	FALSE	NA	0.89061316021778	4		594	973	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932259	36932259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	302	702	0	ENST00000361632.4:c.2210C>T	p.Ser737Phe	p.S737F	ENST00000361632		737	tCc/tTc	16/16	0.800130008022325	4	FACETS	0.894	0.848	0.941	0.894	0.848	0.941	CLONAL	2	FALSE	2	0.89061316021778	4		702	717	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198269834	198269834	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	542	575	0	ENST00000335508.6:c.1505T>C	p.Leu502Ser	p.L502S	ENST00000335508	NM_012433.2	502	tTa/tCa	11/25	0.592174328518408	6	FACETS	0.921	0.886	0.956	0.921	0.886	0.956	CLONAL	3	FALSE	3	0.89061316021778	6		575	1225	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131217	55131217	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	197	366	1	ENST00000257290.5:c.759+1G>A		p.X253_splice	ENST00000257290	NM_006206.4	253			0.831999109324356	4	FACETS	0.853	0.798	0.91			1	CLONAL	2	FALSE	NA	0.89061316021778	4		367	490	SUCCESS
APC	324	MSKCC	GRCh37	5	112102032	112102032	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	350	399	1	ENST00000257430.4:c.145A>G	p.Lys49Glu	p.K49E	ENST00000257430	NM_000038.5	49	Aaa/Gaa	3/16	0.592174328518408	6	FACETS	1	0.992	1	0.819	0.778	0.86	CLONAL	2	FALSE	3	0.89061316021778	6		400	890	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499043	149499043	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	195	384	0	ENST00000261799.4:c.2785G>A	p.Ala929Thr	p.A929T	ENST00000261799	NM_002609.3	929	Gcc/Acc	20/23	0.89061316021778	4	FACETS	0.974	0.913	1	0.974	0.913	1	CLONAL	2	FALSE	2	0.89061316021778	4		384	425	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048626	180048626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748514089	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	83	263	0	ENST00000261937.6:c.1936G>A	p.Glu646Lys	p.E646K	ENST00000261937	NM_182925.4	646	Gag/Aag	13/30	0.685900441783538	3	FACETS	1	0.978	1			1	CLONAL	1	FALSE	NA	0.89061316021778	3		263	201	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977620	2977620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	170	527	0	ENST00000396946.4:c.1064G>A	p.Gly355Glu	p.G355E	ENST00000396946	NM_032415.4	355	gGa/gAa	8/25	0.576527617795294	4	FACETS	0.885	0.823	0.946	0.885	0.823	0.946	CLONAL	2	FALSE	2	0.89061316021778	4		527	408	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513165	106513165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	237	237	0	ENST00000359195.3:c.2069G>A	p.Arg690Lys	p.R690K	ENST00000359195	NM_002649.2	690	aGa/aAa	4/11	0.702313010099685	6	FACETS	1	0.988	1	0.805	0.757	0.854	CLONAL	2	FALSE	3	0.89061316021778	6		237	613	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852177	128852177	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	252	538	0	ENST00000249373.3:c.2249C>T	p.Pro750Leu	p.P750L	ENST00000249373	NM_005631.4	750	cCc/cTc	12/12	0.592174328518408	6	FACETS	0.979	0.926	1	0.979	0.926	1	CLONAL	3	FALSE	3	0.89061316021778	6		538	536	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850981	63850981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	439	387	1	ENST00000279873.7:c.1759G>A	p.Glu587Lys	p.E587K	ENST00000279873	NM_032199.2	587	Gaa/Aaa	10/10	0.89061316021778	4	FACETS	0.903	0.882	0.922			1	CLONAL	4	FALSE	NA	0.89061316021778	4		388	516	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533467	533467	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894231	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	143	297	0	ENST00000451590.1:c.436G>A	p.Ala146Thr	p.A146T	ENST00000451590	NM_001130442.1	146	Gcc/Acc	4/5	0.89061316021778	4	FACETS	0.995	0.924	1	0.995	0.924	1	CLONAL	2	FALSE	2	0.89061316021778	4		297	305	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156633	2156633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	126	522	1	ENST00000434045.2:c.289C>T	p.Leu97Phe	p.L97F	ENST00000434045	NM_001127598.1	97	Ctc/Ttc	3/5	0.89061316021778	4	FACETS	0.945	0.871	1	0.945	0.871	1	CLONAL	2	FALSE	2	0.89061316021778	4		523	283	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112091	115112091	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	178	422	1	ENST00000257566.3:c.1649C>T	p.Ser550Phe	p.S550F	ENST00000257566	NM_016569.3	550	tCc/tTc	7/8	0.674730954980342	4	FACETS	0.898	0.837	0.959	0.898	0.837	0.959	CLONAL	2	FALSE	2	0.89061316021778	4		423	421	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975714	26975714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	452	466	0	ENST00000381527.3:c.1222C>T	p.Pro408Ser	p.P408S	ENST00000381527	NM_001260.1	408	Cct/Tct	12/13	0.89061316021778	4	FACETS	0.911	0.873	0.95			1	CLONAL	2	FALSE	NA	0.89061316021778	4		466	1053	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858412	9858412	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	301	411	1	ENST00000330684.3:c.2989G>A	p.Glu997Lys	p.E997K	ENST00000330684	NM_001134407.1	997	Gag/Aag	13/13	0.800130008022325	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	FALSE	2	0.89061316021778	4		412	618	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832269	72832269	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	355	628	0	ENST00000268489.5:c.4312T>A	p.Phe1438Ile	p.F1438I	ENST00000268489	NM_006885.3	1438	Ttc/Atc	9/10	0.800130008022325	4	FACETS	0.986	0.941	1	0.986	0.941	1	CLONAL	2	FALSE	2	0.89061316021778	4		628	764	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984379	72984379	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	285	515	0	ENST00000268489.5:c.3205A>T	p.Lys1069Ter	p.K1069*	ENST00000268489	NM_006885.3	1069	Aag/Tag	3/10	0.800130008022325	4	FACETS	0.931	0.882	0.98	0.931	0.882	0.98	CLONAL	2	FALSE	2	0.89061316021778	4		515	650	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243839	41243839	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	249	368	0	ENST00000357654.3:c.3709A>T	p.Ile1237Leu	p.I1237L	ENST00000357654	NM_007294.3	1237	Ata/Tta	10/23	0.576527617795294	4	FACETS	0.905	0.854	0.957	0.905	0.854	0.957	CLONAL	2	FALSE	2	0.89061316021778	4		368	584	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78831639	78831639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754090886	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	159	362	0	ENST00000306801.3:c.1448C>T	p.Ser483Leu	p.S483L	ENST00000306801	NM_020761.2	483	tCg/tTg	13/34	0.89061316021778	4	FACETS	0.87	0.808	0.933	0.87	0.808	0.933	CLONAL	2	FALSE	2	0.89061316021778	4		362	388	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546799	9546799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	147	311	0	ENST00000353224.5:c.1223C>T	p.Ser408Phe	p.S408F	ENST00000353224	NM_177990.2	408	tCc/tTc	5/10	0.89061316021778	4	FACETS	0.832	0.769	0.896	0.832	0.769	0.896	CLONAL	2	FALSE	2	0.89061316021778	4		311	375	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743956	40743956	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	144	238	0	ENST00000373198.4:c.3040-1G>A		p.X1014_splice	ENST00000373198	NM_133170.3	1014			0.89061316021778	4	FACETS	0.873	0.808	0.94	0.873	0.808	0.94	CLONAL	2	FALSE	2	0.89061316021778	4		238	350	SUCCESS
AR	367	MSKCC	GRCh37	X	66765275	66765275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	189	422	0	ENST00000374690.3:c.287C>T	p.Ser96Phe	p.S96F	ENST00000374690	NM_000044.3	96	tCt/tTt	1/8	0.800130008022325	4	FACETS	0.839	0.783	0.896	0.839	0.783	0.896	CLONAL	2	FALSE	2	0.89061316021778	4		422	478	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123199792	123199792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	355	446	0	ENST00000218089.9:c.2092C>T	p.His698Tyr	p.H698Y	ENST00000218089	NM_001042749.1	698	Cat/Tat	21/35	0.555493645659945	6	FACETS	1	0.984	1	0.721	0.684	0.758	CLONAL	2	FALSE	3	0.89061316021778	6		446	1025	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818270	43818271	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	301	557	1	ENST00000372470.3:c.1735_1736delinsTT	p.Pro579Phe	p.P579F	ENST00000372470	NM_005373.2	579	CCt/TTt	12/12	0.592174328518408	6	FACETS	0.907	0.86	0.954	0.907	0.86	0.954	CLONAL	3	FALSE	3	0.89061316021778	6		558	691	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219108	133219109	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	147	455	0	ENST00000320574.5:c.4935_4936delinsAA	p.Ala1646Thr	p.A1646T	ENST00000320574	NM_006231.2	1645	caGGcc/caAAcc	37/49	0.674730954980342	4	FACETS	0.828	0.765	0.892	0.828	0.765	0.892	CLONAL	2	FALSE	2	0.89061316021778	4		455	377	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375542	15375543	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	116	445	2	ENST00000263377.2:c.884_885delinsTT	p.Thr295Ile	p.T295I	ENST00000263377	NM_058243.2	295	aCC/aTT	6/20	0.615319256273938	4	FACETS	1	0.983	1			1	CLONAL	1	FALSE	NA	0.89061316021778	4		447	358	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426893	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0009349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	295	420	0	ENST00000356142.4:c.85_86delinsTT	p.Pro29Phe	p.P29F	ENST00000356142	NM_018890.3	29	CCt/TTt	2/7	0.576527617795294	4	FACETS	0.816	0.772	0.861	0.816	0.772	0.861	CLONAL	2	FALSE	2	0.89061316021778	4		420	767	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233143	66233143	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0009358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	421	452	0	ENST00000273854.3:c.1857-1G>T		p.X619_splice	ENST00000273854	NM_004439.5	619			0.613716420365696	4	FACETS	0.973	0.928	1	0.973	0.928	1	CLONAL	2	FALSE	2	0.613716420365696	4		452	1138	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151167738	151167738	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	264	292	0	ENST00000262187.5:c.381G>T	p.Arg127Ser	p.R127S	ENST00000262187	NM_005614.3	127	agG/agT	7/8	0.613716420365696	3	FACETS	0.983	0.93	1	0.983	0.93	1	CLONAL	2	FALSE	1	0.613716420365696	3		292	572	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80343559	80343559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	262	327	0	ENST00000286548.4:c.760C>T	p.Leu254Phe	p.L254F	ENST00000286548	NM_002072.3	254	Ctc/Ttc	6/7	0.613716420365696	3	FACETS	0.884	0.835	0.934	0.884	0.835	0.934	CLONAL	2	FALSE	1	0.613716420365696	3		327	631	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641262	23641262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555460450	NA	P-0009358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	65	378	0	ENST00000261584.4:c.2213G>A	p.Gly738Asp	p.G738D	ENST00000261584	NM_024675.3	738	gGc/gAc	5/13	0.613716420365696	3	FACETS	0.437	0.379	0.501			1	SUBCLONAL	1	FALSE	NA	0.613716420365696	3		378	633	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559090	29559090	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0009358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	45	38	0	ENST00000356175.3:c.3198-1G>T		p.X1066_splice	ENST00000356175	NM_000267.3	1066			0.324132517539437	6	FACETS	1	0.92	1	0.741	0.635	0.852	INDETERMINATE	2	FALSE	3	0.613716420365696	6		38	147	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222983	1222983	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs398123406	NA	P-0009358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	151	190	0	ENST00000326873.7:c.921-1G>C		p.X307_splice	ENST00000326873	NM_000455.4	307			0.613716420365696	2	FACETS	0.885	0.827	0.943	0.885	0.827	0.943	CLONAL	2	FALSE	0	0.613716420365696	2		190	278	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610463	10610463	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	312	355	0	ENST00000171111.5:c.247G>T	p.Val83Phe	p.V83F	ENST00000171111	NM_203500.1	83	Gtc/Ttc	2/6	0.613716420365696	2	FACETS	0.931	0.89	0.972	0.931	0.89	0.972	CLONAL	2	FALSE	0	0.613716420365696	2		355	546	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	81	225	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.621521781522127	NA		225	278	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0009365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	346	358	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.621521781522127	2		358	905	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0009365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	207	323	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	1	2	FACETS	0.96	0.894	1	0.96	0.894	1	CLONAL	1	TRUE	1	0.621521781522127	2		323	694	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966432	25966432	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	414	526	0	ENST00000435504.4:c.2774G>T	p.Ser925Ile	p.S925I	ENST00000435504		925	aGc/aTc	13/13	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.621521781522127	2		526	1197	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692847	89692847	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123321	NA	P-0009365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	233	102	0	ENST00000371953.3:c.331T>C	p.Trp111Arg	p.W111R	ENST00000371953	NM_000314.4	111	Tgg/Cgg	5/9	0.621521781522127	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	3	TRUE	0	0.621521781522127	3		102	324	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	49	225	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.938	1	1	0.979	1	CLONAL	2	FALSE	1	0.317056673329305	2		225	135	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0009371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	100	283	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.31544612169816	4	FACETS	0.936	0.847	1	0.936	0.847	1	CLONAL	3	FALSE	1	0.317056673329305	4		283	296	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0009371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	164	357	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	0.993	1	CLONAL	2	FALSE	1	0.317056673329305	2		357	490	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412884	49412884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	172	705	1	ENST00000418115.1:c.139G>A	p.Glu47Lys	p.E47K	ENST00000418115	NM_001664.2	47	Gag/Aag	2/5	0.308686850290367	1	FACETS	0.947	0.879	1	1	0.993	1	CLONAL	2	FALSE	0	0.317056673329305	1		706	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0009371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	47	341	0	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	1	2	FACETS	0.776	0.657	0.907	0.776	0.657	0.907	CLONAL	1	FALSE	1	0.317056673329305	2		341	382	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944709	206944709	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	19	265	0	ENST00000423557.1:c.217G>C	p.Asp73His	p.D73H	ENST00000423557	NM_000572.2	73	Gac/Cac	2/5	1	2	FACETS	0.332	0.251	0.427	0.332	0.251	0.427	SUBCLONAL	1	FALSE	1	0.317056673329305	2		265	361	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412878	49412878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	169	535	0	ENST00000418115.1:c.145G>A	p.Asp49Asn	p.D49N	ENST00000418115	NM_001664.2	49	Gat/Aat	2/5	0.308686850290367	1	FACETS	0.942	0.874	1	1	0.992	1	CLONAL	2	FALSE	0	0.317056673329305	1		535	476	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369110	118369110	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	133	249	0	ENST00000534358.1:c.5828G>T	p.Gly1943Val	p.G1943V	ENST00000534358	NM_005933.3	1943	gGa/gTa	22/36	1	2	FACETS	0.967	0.885	1	1	0.99	1	CLONAL	2	FALSE	1	0.317056673329305	2		249	434	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913492	32913492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	136	750	0	ENST00000380152.3:c.5000C>T	p.Ser1667Leu	p.S1667L	ENST00000380152		1667	tCa/tTa	11/27	0.317056673329305	1	FACETS	0.824	0.756	0.895	1	0.989	1	CLONAL	2	FALSE	0	0.317056673329305	1		750	438	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134540	41134540	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	34	720	0	ENST00000379561.5:c.1088C>G	p.Ser363Cys	p.S363C	ENST00000379561	NM_002015.3	363	tCt/tGt	2/3	0.317056673329305	1	FACETS	0.281	0.229	0.34	0.281	0.229	0.34	SUBCLONAL	1	FALSE	0	0.317056673329305	1		720	642	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788579	3788579	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	160	492	0	ENST00000262367.5:c.4375G>C	p.Glu1459Gln	p.E1459Q	ENST00000262367	NM_004380.2	1459	Gag/Cag	26/31	0.160106526339571	0	FACETS	0.809	0.75	0.87			1	INDETERMINATE	2	FALSE	0	0.317056673329305	0		492	426	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788600	3788600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	162	476	0	ENST00000262367.5:c.4354G>A	p.Glu1452Lys	p.E1452K	ENST00000262367	NM_004380.2	1452	Gag/Aag	26/31	0.160106526339571	0	FACETS	0.8	0.742	0.86			1	INDETERMINATE	2	FALSE	0	0.317056673329305	0		476	436	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922815	44922815	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	191	469	0	ENST00000377967.4:c.1676del	p.Arg559LeufsTer34	p.R559Lfs*34	ENST00000377967	NM_021140.2	559	cGt/ct	16/29	0.313530817741683	0	FACETS	0.81	0.755	0.865			1	CLONAL	2	FALSE	0	0.317056673329305	0		469	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0009375-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	271	553	3	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.475087341000806	1	FACETS	0.939	0.883	0.997	0.939	0.883	0.997	CLONAL	1	TRUE	0	0.475087341000806	1		556	926	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0009376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	660	379	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.214034157570214	6	FACETS	0.973	0.94	1			1	INDETERMINATE	3	TRUE	NA	0.892593216885632	6		379	1411	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704604	117704604	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	244	588	2	ENST00000368508.3:c.2372A>G	p.Asp791Gly	p.D791G	ENST00000368508	NM_002944.2	791	gAc/gGc	16/43	1	2	FACETS	0.545	0.509	0.582	0.545	0.509	0.582	SUBCLONAL	1	TRUE	1	0.892593216885632	2		590	1003	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612110	43612110	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	309	653	0	ENST00000355710.3:c.2215G>T	p.Val739Phe	p.V739F	ENST00000355710	NM_020975.4	739	Gtc/Ttc	12/20	1	2	FACETS	0.59	0.556	0.625	0.59	0.556	0.625	SUBCLONAL	1	TRUE	1	0.892593216885632	2		653	1174	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0009399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	324	476	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	0.757003158446261	4	FACETS	0.98	0.924	1	0.49	0.462	0.519	CLONAL	1	TRUE	2	0.844283173867168	4		476	1444	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150022928	150022928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	422	431	0	ENST00000253339.5:c.335C>T	p.Ala112Val	p.A112V	ENST00000253339		112	gCt/gTt	1/7	0.247317824228945	5	FACETS	1	0.992	1	0.771	0.737	0.805	INDETERMINATE	2	TRUE	2	0.844283173867168	5		431	980	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877878	151877878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	82	481	0	ENST00000262189.6:c.7067C>T	p.Pro2356Leu	p.P2356L	ENST00000262189	NM_170606.2	2356	cCt/cTt	36/59	0.768752617670773	3	FACETS	0.239	0.21	0.271	0.12	0.105	0.136	SUBCLONAL	1	TRUE	1	0.844283173867168	3		481	1155	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835662	68835662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	330	651	3	ENST00000261769.5:c.253G>T	p.Val85Phe	p.V85F	ENST00000261769	NM_004360.3	85	Gtc/Ttc	3/16	0.844283173867168	3	FACETS	0.816	0.77	0.863	0.408	0.385	0.432	CLONAL	1	TRUE	1	0.844283173867168	3		654	1363	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579378	7579378	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0009399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	546	468	0	ENST00000269305.4:c.309C>G	p.Tyr103Ter	p.Y103*	ENST00000269305	NM_001126112.2	103	taC/taG	4/11	0.833904507642668	2	FACETS	0.967	0.945	0.988	0.967	0.945	0.988	CLONAL	2	TRUE	0	0.844283173867168	2		468	669	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009414-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	13	225	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.994	0.707	1	0.994	0.707	1	CLONAL	1	TRUE	1	0.08	2		225	327	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923102	48923102	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009414-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	15	506	0	ENST00000267163.4:c.550G>T	p.Glu184Ter	p.E184*	ENST00000267163	NM_000321.2	184	Gaa/Taa	6/27	1	2	FACETS	0.477	0.347	0.636	0.477	0.347	0.636	SUBCLONAL	1	TRUE	1	0.08	2		506	786	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772235	68772236	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CC	CC	-	novel	NA	P-0009414-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	16	666	0	ENST00000261769.5:c.84_85del	p.Cys28Ter	p.C28*	ENST00000261769	NM_004360.3	28	tgCCac/tgac	2/16	1	2	FACETS	0.568	0.418	0.75	0.568	0.418	0.75	SUBCLONAL	1	TRUE	1	0.08	2		666	704	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959419	38959419	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009414-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	15	384	0	ENST00000357387.3:c.2056C>A	p.Leu686Ile	p.L686I	ENST00000357387	NM_152756.3	686	Ctt/Att	22/38	1	2	FACETS	0.653	0.476	0.869	0.653	0.476	0.869	SUBCLONAL	1	TRUE	1	0.08	2		384	574	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0009422-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	148	393	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.36	2		393	818	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0009423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	345	389	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.677530694160061	3	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.677530694160061	3		389	1248	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs786203436	NA	P-0009423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	200	322	0	ENST00000269305.4:c.487T>G	p.Tyr163Asp	p.Y163D	ENST00000269305	NM_001126112.2	163	Tac/Gac	5/11	0.122273141468628	5	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.677530694160061	5		322	986	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	96	225	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		225	214	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0009462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	131	379	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.193663783763685	1	FACETS	0.917	0.836	1	1	0.989	1	CLONAL	2	FALSE	0	0.216873894500809	1		379	587	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259389	89259389	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	172	489	0	ENST00000336596.2:c.533G>A	p.Gly178Glu	p.G178E	ENST00000336596	NM_005233.5	178	gGa/gAa	3/17	1	2	FACETS	0.808	0.743	0.876	1	0.99	1	CLONAL	2	FALSE	1	0.216873894500809	2		489	981	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11291050	11291050	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	172	397	0	ENST00000361445.4:c.2711G>T	p.Gly904Val	p.G904V	ENST00000361445	NM_004958.3	904	gGc/gTc	18/58	1	2	FACETS	0.958	0.882	1	1	0.992	1	CLONAL	2	FALSE	1	0.216873894500809	2		397	828	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111886062	111886062	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs183875955	NA	P-0009462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	93	523	0	ENST00000341259.2:c.1684C>T	p.Arg562Trp	p.R562W	ENST00000341259	NM_005475.2	562	Cgg/Tgg	8/8	0.216873894500809	1	FACETS	0.89	0.79	0.997	0.89	0.79	0.997	CLONAL	1	FALSE	0	0.216873894500809	1		523	859	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220706	1220706	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555738475	NA	P-0009462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	154	308	0	ENST00000326873.7:c.727del	p.Val243SerfsTer44	p.V243Sfs*44	ENST00000326873	NM_000455.4	242	Ggg/gg	5/10	0.216873894500809	1	FACETS	1	0.982	1	1	0.993	1	CLONAL	2	FALSE	0	0.216873894500809	1		308	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578204	7578204	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520001	NA	P-0009465-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	312	385	0	ENST00000269305.4:c.645T>G	p.Ser215Arg	p.S215R	ENST00000269305	NM_001126112.2	215	agT/agG	6/11	0.425412688662551	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.576499839214738	1		385	760	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0009465-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	321	260	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.576499839214738	2		260	1016	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101895021	101895021	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs867371544	NA	P-0009465-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	202	246	0	ENST00000374994.4:c.574G>A	p.Gly192Ser	p.G192S	ENST00000374994	NM_004612.2	192	Ggt/Agt	3/9	0.576499839214738	1	FACETS	0.97	0.908	1	0.97	0.908	1	CLONAL	1	TRUE	0	0.576499839214738	1		246	514	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440408	49440408	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009465-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	178	210	1	ENST00000301067.7:c.4402G>A	p.Gly1468Ser	p.G1468S	ENST00000301067	NM_003482.3	1468	Ggc/Agc	15/54	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.576499839214738	2		211	559	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942730	44942730	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009465-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	323	223	0	ENST00000377967.4:c.3310A>C	p.Thr1104Pro	p.T1104P	ENST00000377967	NM_021140.2	1104	Act/Cct	23/29	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.576499839214738	1		223	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0009503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	414	404	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.355328226665131	3	FACETS	1	0.991	1	1	0.997	1	CLONAL	3	TRUE	1	0.355328226665131	3		405	818	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112389	115112389	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	72	170	0	ENST00000257566.3:c.1351G>A	p.Ala451Thr	p.A451T	ENST00000257566	NM_016569.3	451	Gcg/Acg	7/8	0.355328226665131	3	FACETS	1	0.96	1	0.613	0.539	0.693	CLONAL	1	TRUE	1	0.355328226665131	3		170	389	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491645	56491645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	148	359	1	ENST00000267101.3:c.2537G>T	p.Ser846Ile	p.S846I	ENST00000267101	NM_001982.3	846	aGt/aTt	21/28	0.355328226665131	3	FACETS	0.998	0.911	1	0.499	0.455	0.545	CLONAL	1	TRUE	1	0.355328226665131	3		360	983	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984860	9984860	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	137	427	0	ENST00000330684.3:c.1105G>T	p.Asp369Tyr	p.D369Y	ENST00000330684	NM_001134407.1	369	Gac/Tac	4/13	0.328325753514758	3	FACETS	1	0.916	1	0.504	0.458	0.552	CLONAL	1	TRUE	1	0.355328226665131	3		427	901	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	96	225	0				ENST00000310581	NM_198253.2	-/1132			0.276258284250895	3	FACETS	1	0.917	1	1	0.917	1	CLONAL	2	TRUE	1	0.276258284250895	3		225	386	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863224683	NA	P-0009508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	292	264	0	ENST00000269305.4:c.388C>T	p.Leu130Phe	p.L130F	ENST00000269305	NM_001126112.2	130	Ctc/Ttc	5/11	0.276258284250895	4	FACETS	0.941	0.891	0.991	1	0.992	1	CLONAL	4	TRUE	1	0.276258284250895	4		264	717	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339224	116339224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775439897	NA	P-0009508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	288	339	0	ENST00000397752.3:c.86C>T	p.Ala29Val	p.A29V	ENST00000397752	NM_000245.2	29	gCa/gTa	2/21	0.222605449793146	4	FACETS	0.888	0.836	0.941			1	CLONAL	3	TRUE	NA	0.276258284250895	4		339	999	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46124998	46124998	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0009508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	101	313	0	ENST00000334344.6:c.187-2A>G		p.X63_splice	ENST00000334344	NM_152641.2	63			0.269714292811287	3	FACETS	0.931	0.831	1	0.465	0.415	0.519	CLONAL	1	TRUE	1	0.276258284250895	3		313	894	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144789	58144789	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	102	283	0	ENST00000257904.6:c.439C>G	p.Leu147Val	p.L147V	ENST00000257904	NM_000075.3	147	Ctg/Gtg	4/8	0.269714292811287	3	FACETS	1	0.918	1	0.516	0.461	0.574	CLONAL	1	TRUE	1	0.276258284250895	3		283	815	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734152	58734152	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs768126695	NA	P-0009508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1601	296	652	0	ENST00000305921.3:c.1210C>G	p.Gln404Glu	p.Q404E	ENST00000305921	NM_003620.3	404	Caa/Gaa	5/6	0.276258284250895	5	FACETS	0.799	0.749	0.85	0.533	0.499	0.567	SUBCLONAL	2	TRUE	2	0.276258284250895	5		652	1897	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39661100	39661100	+	stop_lost	Nonstop_Mutation	SNP	G	G	T	novel	NA	P-0009508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	180	351	0	ENST00000262039.4:c.2663G>T	p.Ter888LeuextTer4	p.*888Lext*4	ENST00000262039	NM_002647.2	888	tGa/tTa	25/25	0.237687382460626	2	FACETS	0.834	0.771	0.9	0.834	0.771	0.9	CLONAL	2	TRUE	0	0.276258284250895	2		351	781	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604806	48604806	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	171	285	0	ENST00000342988.3:c.1628T>C	p.Met543Thr	p.M543T	ENST00000342988	NM_005359.5	543	aTg/aCg	12/12	0.237687382460626	2	FACETS	0.863	0.796	0.933	0.863	0.796	0.933	CLONAL	2	TRUE	0	0.276258284250895	2		285	717	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919786	50919786	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1555793361	NA	P-0009508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	93	302	1	ENST00000440232.2:c.2953+1G>A		p.X985_splice	ENST00000440232	NM_002691.3	985			0.269714292811287	3	FACETS	1	0.91	1	0.514	0.456	0.575	CLONAL	1	TRUE	1	0.276258284250895	3		303	746	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233173	46233173	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009508-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	186	418	0	ENST00000334344.6:c.1393del	p.Val465Ter	p.V465*	ENST00000334344	NM_152641.2	464	gcG/gc	11/21	0.269714292811287	3	FACETS	0.876	0.809	0.945	0.876	0.809	0.945	CLONAL	2	TRUE	1	0.276258284250895	3		418	875	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098815	178098815	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	296	613	0	ENST00000397062.3:c.230A>G	p.Asp77Gly	p.D77G	ENST00000397062	NM_006164.4	77	gAt/gGt	2/5	0.264433201568816	4	FACETS	0.918	0.87	0.966	0.918	0.87	0.966	CLONAL	4	FALSE	0	0.293902596298984	4		613	710	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0009517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	111	429	1	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.232474536959641	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	FALSE	0	0.293902596298984	2		430	363	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952138	178952138	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	67	282	0	ENST00000263967.3:c.3193C>T	p.His1065Tyr	p.H1065Y	ENST00000263967	NM_006218.2	1065	Cat/Tat	21/21	0.114579701233315	5	FACETS	1	0.945	1	0.76	0.667	0.859	INDETERMINATE	2	FALSE	2	0.293902596298984	5		282	288	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662939	52662939	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	74	507	1	ENST00000394830.3:c.1414C>T	p.Arg472Ter	p.R472*	ENST00000394830	NM_018313.4	472	Cga/Tga	13/30	0.275288580870118	2	FACETS	0.862	0.763	0.967	0.862	0.763	0.967	CLONAL	2	FALSE	0	0.293902596298984	2		508	292	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24129420	24129420	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1417899723	NA	P-0009517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	132	409	2	ENST00000263121.7:c.64G>A	p.Asp22Asn	p.D22N	ENST00000263121	NM_003073.3	22	Gac/Aac	1/9	0.232335102116304	3	FACETS	1	0.985	1	0.718	0.653	0.787	CLONAL	1	FALSE	1	0.293902596298984	3		411	717	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911856	32911856	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs786202160	NA	P-0009546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	58	616	0	ENST00000380152.3:c.3365del	p.Gly1122GlufsTer28	p.G1122Efs*28	ENST00000380152		1122	Gga/ga	11/27	0.558594471994576	0	FACETS	0.219	0.189	0.252			1	SUBCLONAL	1	TRUE	0	0.581042468562889	0		616	382	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866242	42866281	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CCCGGGTTTATTACAGGAAATAAACACAAAGAGAATCCTA	CCCGGGTTTATTACAGGAAATAAACACAAAGAGAATCCTA	-	novel	NA	P-0009546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	16	129	0	ENST00000398585.3:c.349+2_349+41del		p.X117_splice	ENST00000398585	NM_001135099.1	117			1	2	FACETS	0.247	0.182	0.324	0.247	0.182	0.324	SUBCLONAL	1	TRUE	1	0.581042468562889	2		129	223	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913396	NA	P-0009565-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	324	479	1	ENST00000349496.5:c.95A>T	p.Asp32Val	p.D32V	ENST00000349496	NM_001904.3	32	gAc/gTc	3/15	0.363561078198147	3	FACETS	0.921	0.869	0.973	0.921	0.869	0.973	CLONAL	2	TRUE	1	0.34	3		480	1211	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456515	29456515	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009565-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1478	40	631	0	ENST00000389048.3:c.2403A>G	p.Ile801Met	p.I801M	ENST00000389048	NM_004304.4	801	atA/atG	14/29	0.363561078198147	2	FACETS	0.155	0.128	0.186			1	SUBCLONAL	1	TRUE	NA	0.34	2		631	1518	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333944	70333944	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009565-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	169	407	0	ENST00000373644.4:c.1849C>T	p.Gln617Ter	p.Q617*	ENST00000373644	NM_030625.2	617	Cag/Tag	2/12	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.34	2		407	990	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938499	76938501	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs1297294136	NA	P-0009565-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	192	235	0	ENST00000373344.5:c.2247_2249del	p.Ser750del	p.S750del	ENST00000373344	NM_000489.3	749	tcTTCa/tca	9/35	1	1	FACETS	0.772	0.718	0.828	1	0.991	1	SUBCLONAL	2	TRUE	0	0.34	1		235	607	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061227	38061241	+	inframe_deletion	In_Frame_Del	DEL	GAACATGTTGCCGGA	GAACATGTTGCCGGA	-	novel	NA	P-0009565-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	114	405	0	ENST00000250448.2:c.748_762del	p.Ser250_Phe254del	p.S250_F254del	ENST00000250448	NM_004496.3	250	TCCGGCAACATGTTC/-	2/2	1	2	FACETS	0.947	0.854	1	0.947	0.854	1	CLONAL	1	TRUE	1	0.34	2		405	708	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390986	139390986	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009565-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	41	462	0	ENST00000277541.6:c.7205T>G	p.Ile2402Ser	p.I2402S	ENST00000277541	NM_017617.3	2402	aTc/aGc	34/34	1	2	FACETS	0.346	0.287	0.411	0.346	0.287	0.411	SUBCLONAL	1	TRUE	1	0.34	2		462	698	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061212	38061232	+	inframe_deletion	In_Frame_Del	DEL	GTAGCAGCCGTTCTCGAACAT	GTAGCAGCCGTTCTCGAACAT	-	novel	NA	P-0009565-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	29	334	0	ENST00000250448.2:c.757_777del	p.Met253_Tyr259del	p.M253_Y259del	ENST00000250448	NM_004496.3	253	ATGTTCGAGAACGGCTGCTAC/-	2/2	1	2	FACETS	0.298	0.238	0.367	0.298	0.238	0.367	SUBCLONAL	1	TRUE	1	0.34	2		334	572	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0009586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	488	379	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.416709847164734	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.428326688176764	2		379	976	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0009586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	406	591	2	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.398613505316837	2	FACETS	0.869	0.828	0.91	0.869	0.828	0.91	CLONAL	2	TRUE	0	0.428326688176764	2		593	1091	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0009586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	135	591	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.409412508840096	3	FACETS	0.841	0.764	0.922	0.421	0.382	0.461	CLONAL	1	TRUE	1	0.428326688176764	3		591	910	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248732	212248732	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	276	357	0	ENST00000342788.4:c.3535G>T	p.Asp1179Tyr	p.D1179Y	ENST00000342788	NM_005235.2	1179	Gac/Tac	28/28	0.409412508840096	3	FACETS	0.964	0.908	1	0.964	0.908	1	CLONAL	2	TRUE	1	0.428326688176764	3		357	812	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955113	55955113	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	220	403	2	ENST00000263923.4:c.3432C>A	p.His1144Gln	p.H1144Q	ENST00000263923	NM_002253.2	1144	caC/caA	26/30	0.409412508840096	3	FACETS	1	0.968	1	0.535	0.497	0.574	CLONAL	1	TRUE	1	0.428326688176764	3		405	1166	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976668	55976668	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs949197675	NA	P-0009586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	499	486	0	ENST00000263923.4:c.1157T>C	p.Met386Thr	p.M386T	ENST00000263923	NM_002253.2	386	aTg/aCg	9/30	0.409412508840096	3	FACETS	0.976	0.934	1	0.976	0.934	1	CLONAL	2	TRUE	1	0.428326688176764	3		486	1449	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030485	49030485	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	69	173	0	ENST00000267163.4:c.1960G>T	p.Val654Leu	p.V654L	ENST00000267163	NM_000321.2	654	Gtg/Ttg	19/27	1	2	FACETS	0.85	0.744	0.963	0.85	0.744	0.963	CLONAL	1	TRUE	1	0.428326688176764	2		173	379	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993417	72993417	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1487	304	869	1	ENST00000268489.5:c.628G>T	p.Gly210Cys	p.G210C	ENST00000268489	NM_006885.3	210	Ggc/Tgc	2/10	0.392003814145543	3	FACETS	0.962	0.904	1	0.481	0.452	0.512	CLONAL	1	TRUE	1	0.428326688176764	3		870	1791	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40491341	40491341	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	345	427	0	ENST00000264657.5:c.459G>T	p.Lys153Asn	p.K153N	ENST00000264657	NM_139276.2	153	aaG/aaT	5/24	0.351775474720991	4	FACETS	0.876	0.828	0.924	0.876	0.828	0.924	CLONAL	2	TRUE	2	0.428326688176764	4		427	1314	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943502	17943502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	252	336	0	ENST00000458235.1:c.2506G>A	p.Val836Met	p.V836M	ENST00000458235	NM_000215.3	836	Gtg/Atg	19/24	0.398613505316837	2	FACETS	0.932	0.879	0.987	0.932	0.879	0.987	CLONAL	2	TRUE	0	0.428326688176764	2		336	631	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028820	47028821	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	T	novel	NA	P-0009586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	444	628	0	ENST00000377604.3:c.124_125delinsT	p.Arg42PhefsTer92	p.R42Ffs*92	ENST00000377604	NM_001204468.1	42	CGt/Tt	3/24	0.392003814145543	3	FACETS	0.942	0.899	0.986	0.942	0.899	0.986	CLONAL	2	TRUE	1	0.428326688176764	3		628	1336	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019560	42019560	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	620	729	1	ENST00000219905.7:c.3614del	p.Gly1205GlufsTer15	p.G1205Efs*15	ENST00000219905	NM_001164273.1	1205	Gga/ga	10/24	0.428326688176764	2	FACETS	0.943	0.908	0.978	0.943	0.908	0.978	CLONAL	2	TRUE	0	0.428326688176764	2		730	1535	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188297	10188297	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs869025653	NA	P-0009593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	179	614	0	ENST00000256474.2:c.444del	p.Phe148LeufsTer11	p.F148Lfs*11	ENST00000256474	NM_000551.3	147	aTt/at	2/3	0.352638790444223	2	FACETS	0.783	0.727	0.841	0.783	0.727	0.841	SUBCLONAL	2	TRUE	0	0.420061438183222	2		614	544	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059211	47059211	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	150	482	0	ENST00000409792.3:c.7450C>T	p.Gln2484Ter	p.Q2484*	ENST00000409792	NM_014159.6	2484	Cag/Tag	20/21	0.410430422080765	2	FACETS	0.81	0.747	0.874	0.81	0.747	0.874	CLONAL	2	TRUE	0	0.420061438183222	2		482	441	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098975	178098975	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1328994103	NA	P-0009593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	196	420	0	ENST00000397062.3:c.70T>C	p.Trp24Arg	p.W24R	ENST00000397062	NM_006164.4	24	Tgg/Cgg	2/5	0.345864094942478	4	FACETS	0.92	0.855	0.988	0.92	0.855	0.988	CLONAL	2	TRUE	2	0.420061438183222	4		420	720	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484821	57484821	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	92	578	1	ENST00000371085.3:c.801G>C	p.Gln267His	p.Q267H	ENST00000371085	NM_000516.4	267	caG/caC	10/13	NA	2	FACETS	0.682	0.607	0.763			1	INDETERMINATE	1	TRUE	NA	0.420061438183222	2		579	642	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426121	47426121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519786	NA	P-0009593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	159	417	0	ENST00000377045.4:c.641C>T	p.Ser214Phe	p.S214F	ENST00000377045	NM_001654.4	214	tCc/tTc	7/16	0.28604872011557	2	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.420061438183222	2		417	568	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643882	52643883	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	T	novel	NA	P-0009593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	222	514	0	ENST00000394830.3:c.2013_2014delinsA	p.Asn671LysfsTer15	p.N671Kfs*15	ENST00000394830	NM_018313.4	671	aaCTat/aaAat	17/30	0.410430422080765	2	FACETS	0.963	0.904	1	0.963	0.904	1	CLONAL	2	TRUE	0	0.420061438183222	2		514	549	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0009619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	44	345	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.358	0.298	0.424	0.358	0.298	0.424	SUBCLONAL	1	TRUE	1	0.251593912086446	2		345	978	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0009619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	137	409	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.251593912086446	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.251593912086446	1		409	807	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581229	48581229	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs377767331	NA	P-0009619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	178	421	0	ENST00000342988.3:c.533C>G	p.Ser178Ter	p.S178*	ENST00000342988	NM_005359.5	178	tCa/tGa	5/12	0.251593912086446	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.251593912086446	1		421	1027	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0009622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	17	344	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	1	2	FACETS	0.096	0.071	0.126	0.096	0.071	0.126	SUBCLONAL	1	TRUE	1	0.473308854859018	2		344	747	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129169	64129169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746466314	NA	P-0009622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	97	340	0	ENST00000334205.4:c.707C>T	p.Ser236Leu	p.S236L	ENST00000334205	NM_003942.2	236	tCg/tTg	7/17	1	2	FACETS	0.695	0.621	0.773	0.695	0.621	0.773	SUBCLONAL	1	TRUE	1	0.473308854859018	2		340	590	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056201	26056201	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs766517381	NA	P-0009622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	179	445	0	ENST00000343677.2:c.456G>C	p.Lys152Asn	p.K152N	ENST00000343677	NM_005319.3	152	aaG/aaC	1/1	1	2	FACETS	0.625	0.574	0.677	0.625	0.574	0.677	SUBCLONAL	1	TRUE	1	0.473308854859018	2		445	1211	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733393	85733393	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1859	206	945	0	ENST00000370580.1:c.619C>G	p.Leu207Val	p.L207V	ENST00000370580	NM_003921.4	207	Cta/Gta	3/3	1	2	FACETS	0.422	0.389	0.456	0.422	0.389	0.456	SUBCLONAL	1	TRUE	1	0.473308854859018	2		945	2065	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440328	52440328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	109	373	0	ENST00000460680.1:c.724G>A	p.Glu242Lys	p.E242K	ENST00000460680	NM_004656.3	242	Gag/Aag	9/17	0.473308854859018	1	FACETS	0.626	0.563	0.691	0.626	0.563	0.691	SUBCLONAL	1	TRUE	0	0.473308854859018	1		373	562	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675709	30675709	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1563	254	780	1	ENST00000376406.3:c.2647C>T	p.Pro883Ser	p.P883S	ENST00000376406	NM_014641.2	883	Cct/Tct	8/15	1	2	FACETS	0.591	0.55	0.632	0.591	0.55	0.632	SUBCLONAL	1	TRUE	1	0.473308854859018	2		781	1817	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858517	9858517	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs765370528	NA	P-0009622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	146	490	1	ENST00000330684.3:c.2884G>T	p.Glu962Ter	p.E962*	ENST00000330684	NM_001134407.1	962	Gaa/Taa	13/13	1	2	FACETS	0.65	0.593	0.71	0.65	0.593	0.71	SUBCLONAL	1	TRUE	1	0.473308854859018	2		491	949	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822722	72822722	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1468	125	861	0	ENST00000268489.5:c.9453G>C	p.Leu3151Phe	p.L3151F	ENST00000268489	NM_006885.3	3151	ttG/ttC	10/10	1	2	FACETS	0.332	0.299	0.367	0.332	0.299	0.367	SUBCLONAL	1	TRUE	1	0.473308854859018	2		861	1593	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969912	81969912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	337	739	0	ENST00000359376.3:c.2981C>T	p.Ser994Phe	p.S994F	ENST00000359376	NM_002661.3	994	tCt/tTt	27/33	1	2	FACETS	0.92	0.868	0.973	0.92	0.868	0.973	CLONAL	1	TRUE	1	0.473308854859018	2		739	1548	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836312	89836312	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	113	488	0	ENST00000389301.3:c.2437C>T	p.Pro813Ser	p.P813S	ENST00000389301	NM_000135.2	813	Cct/Tct	26/43	1	2	FACETS	0.534	0.479	0.591	0.534	0.479	0.591	SUBCLONAL	1	TRUE	1	0.473308854859018	2		488	895	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490289	29490289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149003051	NA	P-0009622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	168	472	0	ENST00000356175.3:c.374G>A	p.Arg125His	p.R125H	ENST00000356175	NM_000267.3	125	cGt/cAt	4/57	1	2	FACETS	0.608	0.558	0.661	0.608	0.558	0.661	SUBCLONAL	1	TRUE	1	0.473308854859018	2		472	1167	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610558	10610558	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	457	389	0	ENST00000171111.5:c.152C>G	p.Thr51Ser	p.T51S	ENST00000171111	NM_203500.1	51	aCc/aGc	2/6	0.199153999312526	5	FACETS	1	0.984	1			1	INDETERMINATE	3	TRUE	NA	0.473308854859018	5		389	1048	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943421	17943421	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	148	531	0	ENST00000458235.1:c.2587G>A	p.Asp863Asn	p.D863N	ENST00000458235	NM_000215.3	863	Gac/Aac	19/24	1	2	FACETS	0.571	0.52	0.624	0.571	0.52	0.624	SUBCLONAL	1	TRUE	1	0.473308854859018	2		531	1096	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31372563	31372563	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0009622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	80	376	0	ENST00000328111.2:c.205-1G>C		p.X69_splice	ENST00000328111	NM_006892.3	69			1	2	FACETS	0.412	0.362	0.466	0.412	0.362	0.466	SUBCLONAL	1	TRUE	1	0.473308854859018	2		376	821	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950082	44950082	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0009622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	356	357	0	ENST00000377967.4:c.3851C>G	p.Ser1284Ter	p.S1284*	ENST00000377967	NM_021140.2	1284	tCa/tGa	26/29	1	1	FACETS	0.774	0.739	0.809	1	0.996	1	SUBCLONAL	2	TRUE	0	0.473308854859018	1		357	742	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0009630-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	47	278	0	ENST00000269305.4:c.559+1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.255086931878401	1	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	0	0.18	1		278	437	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009630-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	88	326	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.168925992648213	0	FACETS	0.864	0.764	0.971			1	CLONAL	1	TRUE	0	0.18	0		326	928	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060971	38061025	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCACTGTGGTCCAGAGTCTGGGGGCTGGCGGCGGGCCCGGGGGCCGGCGCGCC	CCCCACTGTGGTCCAGAGTCTGGGGGCTGGCGGCGGGCCCGGGGGCCGGCGCGCC	-	novel	NA	P-0009630-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	37	223	0	ENST00000250448.2:c.964_1018del	p.Gly322ArgfsTer10	p.G322Rfs*10	ENST00000250448	NM_004496.3	322	GGCGCGCCGGCCCCCGGGCCCGCCGCCAGCCCCCAGACTCTGGACCACAGTGGGGcg/cg	2/2	1	2	FACETS	0.949	0.783	1	0.949	0.783	1	CLONAL	1	TRUE	1	0.18	2		223	433	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012128	16012167	+	frameshift_variant	Frame_Shift_Del	DEL	ATTGGAGGCTTCAATATCTTCATCCTCCTGAGCAGAAACA	ATTGGAGGCTTCAATATCTTCATCCTCCTGAGCAGAAACA	-	novel	NA	P-0009630-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	67	566	0	ENST00000268712.3:c.2115_2154del	p.Val706LysfsTer49	p.V706Kfs*49	ENST00000268712	NM_006311.3	705	acTGTTTCTGCTCAGGAGGATGAAGATATTGAAGCCTCCAAT/ac	19/46	0.255086931878401	1	FACETS	0.621	0.538	0.712	0.621	0.538	0.712	SUBCLONAL	1	TRUE	0	0.18	1		566	1091	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029453	16029454	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0009630-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1261	116	590	0	ENST00000268712.3:c.1576_1577del	p.Glu526LysfsTer9	p.E526Kfs*9	ENST00000268712	NM_006311.3	526	GAa/a	15/46	0.255086931878401	1	FACETS	0.852	0.765	0.944	0.852	0.765	0.944	CLONAL	1	TRUE	0	0.18	1		590	1377	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0009642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	122	393	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.16	2		393	1158	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057302	30057302	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315496	NA	P-0009642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	67	381	0	ENST00000338641.4:c.784C>T	p.Arg262Ter	p.R262*	ENST00000338641	NM_000268.3	262	Cga/Tga	8/16	1	2	FACETS	0.759	0.658	0.87	0.759	0.658	0.87	SUBCLONAL	1	TRUE	1	0.16	2		381	1103	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207092	1207092	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs778376925	NA	P-0009642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1463	122	554	0	ENST00000326873.7:c.180C>G	p.Tyr60Ter	p.Y60*	ENST00000326873	NM_000455.4	60	taC/taG	1/10	1	2	FACETS	0.962	0.866	1	0.962	0.866	1	CLONAL	1	TRUE	1	0.16	2		554	1585	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32921021	32921021	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	70	409	0	ENST00000380152.3:c.6995G>T	p.Cys2332Phe	p.C2332F	ENST00000380152		2332	tGt/tTt	13/27	1	2	FACETS	0.837	0.727	0.956	0.837	0.727	0.956	CLONAL	1	TRUE	1	0.16	2		409	1046	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602390	10602390	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0009642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1622	125	668	0	ENST00000171111.5:c.1188C>G	p.Tyr396Ter	p.Y396*	ENST00000171111	NM_203500.1	396	taC/taG	3/6	1	2	FACETS	0.894	0.806	0.988	0.894	0.806	0.988	CLONAL	1	TRUE	1	0.16	2		668	1747	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132527	11132527	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1262	104	523	0	ENST00000358026.2:c.2743C>G	p.Gln915Glu	p.Q915E	ENST00000358026	NM_001128849.1	915	Cag/Gag	19/36	1	2	FACETS	0.952	0.849	1	0.952	0.849	1	CLONAL	1	TRUE	1	0.16	2		523	1366	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253800	30253800	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009642-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1456	79	533	0	ENST00000307677.4:c.654G>T	p.Met218Ile	p.M218I	ENST00000307677	NM_138578.1	218	atG/atT	3/3	1	2	FACETS	0.643	0.563	0.73	0.643	0.563	0.73	SUBCLONAL	1	TRUE	1	0.16	2		533	1535	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0009651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	297	819	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.380795752694626	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.402523241425069	2		819	605	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	15	258	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.684	0.506	0.892	0.684	0.506	0.892	SUBCLONAL	1	TRUE	1	0.402523241425069	2		258	109	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591247	67591249	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GGT	GGT	-	rs1131692243	NA	P-0009651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	101	509	0	ENST00000274335.5:c.1748_1750del		p.X583_splice	ENST00000274335		583		13/15	0.402523241425069	6	FACETS	0.757	0.678	0.841			1	SUBCLONAL	2	TRUE	NA	0.402523241425069	6		509	598	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	168	571	1	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.402523241425069	3	FACETS	0.88	0.82	0.94	1	0.988	1	CLONAL	3	TRUE	1	0.402523241425069	3		572	380	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927616	131927616	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	69	589	0	ENST00000265335.6:c.1683T>A	p.Asp561Glu	p.D561E	ENST00000265335		561	gaT/gaA	11/25	0.346658999802249	3	FACETS	1	0.887	1	0.507	0.443	0.575	CLONAL	1	TRUE	1	0.402523241425069	3		589	406	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488223	56488223	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	130	568	0	ENST00000267101.3:c.1742A>T	p.Asp581Val	p.D581V	ENST00000267101	NM_001982.3	581	gAt/gTt	15/28	0.193350382865796	6	FACETS	1	0.974	1			1	INDETERMINATE	2	TRUE	NA	0.402523241425069	6		568	494	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302390	15302390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146578114	NA	P-0009651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	28	783	0	ENST00000263388.2:c.881C>T	p.Thr294Met	p.T294M	ENST00000263388	NM_000435.2	294	aCg/aTg	6/33	0.322316635724809	1	FACETS	0.348	0.279	0.428	0.348	0.279	0.428	SUBCLONAL	1	TRUE	0	0.402523241425069	1		783	319	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188183	11188183	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057524049	NA	P-0009657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	24	335	0	ENST00000361445.4:c.5911G>A	p.Ala1971Thr	p.A1971T	ENST00000361445	NM_004958.3	1971	Gcc/Acc	43/58	0.478210329773881	1	FACETS	0.833	0.669	1	0.833	0.669	1	CLONAL	1	TRUE	0	0.472932386443928	1		335	93	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183787	10183787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123481	NA	P-0009657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	78	359	0	ENST00000256474.2:c.256C>T	p.Pro86Ser	p.P86S	ENST00000256474	NM_000551.3	86	Ccc/Tcc	1/3	0.302513389022184	3	FACETS	1	0.954	1	0.739	0.664	0.815	CLONAL	2	TRUE	0	0.472932386443928	3		359	184	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437623	52437623	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0009657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	119	1046	0	ENST00000460680.1:c.1538C>G	p.Ser513Ter	p.S513*	ENST00000460680	NM_004656.3	513	tCa/tGa	13/17	0.205244916233191	1	FACETS	0.881	0.816	0.945	1	0.99	1	INDETERMINATE	2	TRUE	0	0.472932386443928	1		1046	218	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513025	106513025	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	61	423	0	ENST00000359195.3:c.2039T>A	p.Phe680Tyr	p.F680Y	ENST00000359195	NM_002649.2	680	tTt/tAt	3/11	0.472932386443928	5	FACETS	1	0.943	1	0.39	0.338	0.446	CLONAL	1	TRUE	2	0.472932386443928	5		423	377	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939177	76939177	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	96	432	0	ENST00000373344.5:c.1571T>G	p.Val524Gly	p.V524G	ENST00000373344	NM_000489.3	524	gTt/gGt	9/35	1	1	FACETS	0.791	0.723	0.859	1	0.986	1	SUBCLONAL	2	TRUE	0	0.472932386443928	1		432	196	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0009660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	307	379	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.612967075125318	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.612967075125318	4		379	752	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128036912	128036912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	346	654	0	ENST00000285398.2:c.1567G>A	p.Val523Met	p.V523M	ENST00000285398	NM_000122.1	523	Gtg/Atg	10/15	0.612967075125318	4	FACETS	0.966	0.917	1	0.966	0.917	1	CLONAL	2	TRUE	2	0.612967075125318	4		654	943	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098953	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	279	431	0	ENST00000397062.3:c.92G>C	p.Gly31Ala	p.G31A	ENST00000397062	NM_006164.4	31	gGa/gCa	2/5	0.612967075125318	4	FACETS	0.911	0.859	0.964	0.911	0.859	0.964	CLONAL	2	TRUE	2	0.612967075125318	4		431	806	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577112	7577112	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1131691029	NA	P-0009660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	314	687	0	ENST00000269305.4:c.826G>C	p.Ala276Pro	p.A276P	ENST00000269305	NM_001126112.2	276	Gcc/Ccc	8/11	NA	2	FACETS	0.967	0.925	1			1	INDETERMINATE	2	TRUE	NA	0.612967075125318	2		687	530	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258681	115258681	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	219	362	0	ENST00000369535.4:c.101C>G	p.Pro34Arg	p.P34R	ENST00000369535	NM_002524.4	34	cCc/cGc	2/7	0.612967075125318	3	FACETS	0.985	0.927	1	0.985	0.927	1	CLONAL	2	TRUE	1	0.612967075125318	3		362	474	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465043	120465043	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	98	423	0	ENST00000256646.2:c.5029C>T	p.Gln1677Ter	p.Q1677*	ENST00000256646	NM_024408.3	1677	Cag/Tag	28/34	0.612967075125318	3	FACETS	0.983	0.882	1	0.491	0.441	0.544	CLONAL	1	TRUE	1	0.612967075125318	3		423	425	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104698	209104698	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	219	414	1	ENST00000345146.2:c.880G>T	p.Val294Leu	p.V294L	ENST00000345146	NM_005896.2	294	Gtg/Ttg	8/10	0.612967075125318	4	FACETS	0.96	0.9	1	0.96	0.9	1	CLONAL	2	TRUE	2	0.612967075125318	4		415	600	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155400	47155400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	341	706	0	ENST00000409792.3:c.4681G>A	p.Gly1561Ser	p.G1561S	ENST00000409792	NM_014159.6	1561	Ggc/Agc	5/21	0.612967075125318	2	FACETS	0.976	0.936	1	0.976	0.936	1	CLONAL	2	TRUE	0	0.612967075125318	2		706	570	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852291	128852291	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0009660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	164	323	0	ENST00000249373.3:c.2363G>C	p.Ter788SerextTer38	p.*788Sext*38	ENST00000249373	NM_005631.4	788	tGa/tCa	12/12	0.612967075125318	2	FACETS	0.995	0.936	1	0.995	0.936	1	CLONAL	2	TRUE	0	0.612967075125318	2		323	269	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518264	8518264	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	128	479	0	ENST00000356435.5:c.1127C>G	p.Thr376Arg	p.T376R	ENST00000356435		376	aCa/aGa	10/35	0.596981043292534	3	FACETS	1	0.918	1			1	CLONAL	1	TRUE	NA	0.612967075125318	3		479	541	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776220	135776220	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs118203706	NA	P-0009660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	242	438	0	ENST00000298552.3:c.2507C>G	p.Ser836Ter	p.S836*	ENST00000298552	NM_001162426.1	836	tCa/tGa	20/23	0.612967075125318	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.612967075125318	2		438	391	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659584	88659584	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	179	510	0	ENST00000372037.3:c.367G>C	p.Glu123Gln	p.E123Q	ENST00000372037	NM_004329.2	123	Gaa/Caa	6/13	0.612967075125318	3	FACETS	1	0.971	1	0.551	0.509	0.593	CLONAL	1	TRUE	1	0.612967075125318	3		510	693	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344561	118344561	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	507	1180	0	ENST00000534358.1:c.2687G>C	p.Gly896Ala	p.G896A	ENST00000534358	NM_005933.3	896	gGa/gCa	3/36	0.612967075125318	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.612967075125318	4		1180	1315	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433004	49433004	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1057518149	NA	P-0009660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	205	428	0	ENST00000301067.7:c.8366+1G>T		p.X2789_splice	ENST00000301067	NM_003482.3	2789			0.612967075125318	4	FACETS	0.88	0.821	0.94	0.88	0.821	0.94	CLONAL	2	TRUE	2	0.612967075125318	4		428	613	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445026	49445026	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752263278	NA	P-0009660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	82	225	0	ENST00000301067.7:c.2440C>T	p.His814Tyr	p.H814Y	ENST00000301067	NM_003482.3	814	Cac/Tac	10/54	0.612967075125318	4	FACETS	0.877	0.785	0.972	0.877	0.785	0.972	CLONAL	2	TRUE	2	0.612967075125318	4		225	246	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678547	88678547	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs753629333	NA	P-0009660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	66	344	0	ENST00000360948.2:c.989C>A	p.Pro330Gln	p.P330Q	ENST00000360948	NM_001012338.2	330	cCa/cAa	9/19	0.450528809159001	3	FACETS	0.925	0.81	1	0.463	0.405	0.524	CLONAL	1	TRUE	1	0.612967075125318	3		344	304	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641726	23641726	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	361	625	0	ENST00000261584.4:c.1749G>T	p.Leu583Phe	p.L583F	ENST00000261584	NM_024675.3	583	ttG/ttT	5/13	0.612967075125318	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.612967075125318	3		625	761	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821373	72821373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775404633	NA	P-0009660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	101	649	3	ENST00000268489.5:c.10802C>T	p.Ser3601Leu	p.S3601L	ENST00000268489	NM_006885.3	3601	tCg/tTg	10/10	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.612967075125318	NA		652	526	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245006	41245006	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	336	633	1	ENST00000357654.3:c.2542G>T	p.Glu848Ter	p.E848*	ENST00000357654	NM_007294.3	848	Gaa/Taa	10/23	0.412886449550665	5	FACETS	1	0.988	1	0.75	0.711	0.79	CLONAL	2	TRUE	2	0.612967075125318	5		634	935	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876540	59876540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	324	450	0	ENST00000259008.2:c.1261G>A	p.Glu421Lys	p.E421K	ENST00000259008	NM_032043.2	421	Gaa/Aaa	9/20	0.412886449550665	5	FACETS	0.859	0.816	0.903	0.859	0.816	0.903	CLONAL	3	TRUE	2	0.612967075125318	5		450	787	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105642	11105642	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	187	461	0	ENST00000358026.2:c.1558G>T	p.Glu520Ter	p.E520*	ENST00000358026	NM_001128849.1	520	Gag/Tag	9/36	0.612967075125318	2	FACETS	0.994	0.939	1	0.994	0.939	1	CLONAL	2	TRUE	0	0.612967075125318	2		461	307	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561012	9561012	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	211	494	0	ENST00000353224.5:c.770G>T	p.Trp257Leu	p.W257L	ENST00000353224	NM_177990.2	257	tGg/tTg	4/10	0.612967075125318	4	FACETS	0.935	0.874	0.997	0.935	0.874	0.997	CLONAL	2	TRUE	2	0.612967075125318	4		494	594	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148659	20148659	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	163	256	0	ENST00000379607.5:c.404G>A	p.Gly135Glu	p.G135E	ENST00000379607	NM_001412.3	135	gGa/gAa	6/7	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.612967075125318	1		256	265	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929162	44929162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	195	331	0	ENST00000377967.4:c.2262G>A	p.Met754Ile	p.M754I	ENST00000377967	NM_021140.2	754	atG/atA	17/29	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.612967075125318	1		331	309	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183739	10183739	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs5030802	NA	P-0009683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	90	458	0	ENST00000256474.2:c.208G>T	p.Glu70Ter	p.E70*	ENST00000256474	NM_000551.3	70	Gag/Tag	1/3	0.292553851378267	1	FACETS	0.982	0.874	1	0.982	0.874	1	CLONAL	1	TRUE	0	0.292553851378267	1		458	535	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967593	90967593	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs752837508	NA	P-0009683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	167	522	2	ENST00000265433.3:c.1315A>G	p.Ile439Val	p.I439V	ENST00000265433	NM_002485.4	439	Ata/Gta	10/16	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.292553851378267	2		524	1127	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37876088	37876088	+	splice_donor_variant	In_Frame_Del	SNP	G	G	T	novel	NA	P-0009683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	132	573	0	ENST00000269571.5:c.1946+1G>T		p.C634_S649del	ENST00000269571		634			1	2	FACETS	0.975	0.884	1	0.975	0.884	1	CLONAL	1	TRUE	1	0.292553851378267	2		573	926	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141052	55141066	+	inframe_deletion	In_Frame_Del	DEL	CCCAGATGGACATGA	CCCAGATGGACATGA	-	novel	NA	P-0009695-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	391	465	0	ENST00000257290.5:c.1698_1712del	p.Ser566_Glu571delinsArg	p.S566_E571delinsR	ENST00000257290	NM_006206.4	566	agCCCAGATGGACATGAa/aga	12/23	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.7	2		465	976	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0009703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	142	404	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.220195706205946	1	FACETS	0.959	0.872	1	0.959	0.872	1	CLONAL	1	TRUE	0	0.23396290747225	1		405	1118	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs770248150	NA	P-0009703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	480	493	1	ENST00000311936.3:c.351A>T	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaT	4/5	0.23396290747225	3	FACETS	1	0.989	1	1	0.997	1	CLONAL	3	TRUE	1	0.23396290747225	3		494	1384	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109889	115109889	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	44	124	0	ENST00000257566.3:c.1989G>T	p.Met663Ile	p.M663I	ENST00000257566	NM_016569.3	663	atG/atT	8/8	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.23396290747225	2		124	285	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0009708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	276	558	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.367080389066229	5	FACETS	1	0.983	1	0.749	0.703	0.795	CLONAL	2	TRUE	2	0.367080389066229	5		558	1038	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057520005	NA	P-0009708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	344	759	0	ENST00000269305.4:c.820G>T	p.Val274Phe	p.V274F	ENST00000269305	NM_001126112.2	274	Gtt/Ttt	8/11	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	2	TRUE	NA	0.367080389066229	2		759	899	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933747	36933747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	162	813	2	ENST00000361632.4:c.1652C>T	p.Pro551Leu	p.P551L	ENST00000361632		551	cCc/cTc	12/16	0.240080410591782	3	FACETS	0.882	0.808	0.96	0.294	0.269	0.32	CLONAL	1	TRUE	0	0.367080389066229	3		815	1184	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247530	71247530	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0009708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	78	344	0	ENST00000318789.4:c.3G>A	p.Met1?	p.M1?	ENST00000318789	NM_032682.5	1	atG/atA	6/21	0.367080389066229	3	FACETS	0.795	0.698	0.898			1	SUBCLONAL	1	TRUE	NA	0.367080389066229	3		344	633	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958163	2958163	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	110	512	0	ENST00000396946.4:c.2569G>T	p.Glu857Ter	p.E857*	ENST00000396946	NM_032415.4	857	Gag/Tag	19/25	0.23962345123813	3	FACETS	0.943	0.848	1			1	CLONAL	1	TRUE	NA	0.367080389066229	3		512	752	SUCCESS
MET	4233	MSKCC	GRCh37	7	116417463	116417463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913244	NA	P-0009708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	147	631	0	ENST00000397752.3:c.3280C>T	p.His1094Tyr	p.H1094Y	ENST00000397752	NM_000245.2	1094	Cat/Tat	16/21	0.367080389066229	4	FACETS	0.888	0.809	0.972	0.296	0.269	0.324	CLONAL	1	TRUE	1	0.367080389066229	4		631	1233	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528633	8528633	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	479	644	1	ENST00000356435.5:c.499G>T	p.Asp167Tyr	p.D167Y	ENST00000356435		167	Gac/Tac	4/35	0.23962345123813	3	FACETS	0.998	0.958	1			1	CLONAL	3	TRUE	NA	0.367080389066229	3		645	1032	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974711	21974711	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	135	476	0	ENST00000304494.5:c.116A>T	p.Asn39Ile	p.N39I	ENST00000304494	NM_000077.4	39	aAc/aTc	1/3	0.248837045384752	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.367080389066229	1		476	517	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649216	23649216	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	210	698	0	ENST00000261584.4:c.166G>A	p.Asp56Asn	p.D56N	ENST00000261584	NM_024675.3	56	Gat/Aat	3/13	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.367080389066229	2		698	1007	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487490	38487490	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs150291626	NA	P-0009708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	127	488	0	ENST00000254066.5:c.20C>G	p.Ser7Cys	p.S7C	ENST00000254066	NM_000964.3	7	tCc/tGc	2/9	0.367080389066229	4	FACETS	1	0.966	1			1	CLONAL	1	TRUE	NA	0.367080389066229	4		488	830	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218494	1218494	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	130	545	0	ENST00000326873.7:c.369G>C	p.Gln123His	p.Q123H	ENST00000326873	NM_000455.4	123	caG/caC	2/10	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.367080389066229	2		545	677	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219360	1219360	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs750335052	NA	P-0009708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	172	571	0	ENST00000326873.7:c.412G>C	p.Glu138Gln	p.E138Q	ENST00000326873	NM_000455.4	138	Gaa/Caa	3/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.367080389066229	2		571	776	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220466	1220466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782032	NA	P-0009708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	155	563	3	ENST00000326873.7:c.559G>A	p.Gly187Ser	p.G187S	ENST00000326873	NM_000455.4	187	Ggt/Agt	4/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.367080389066229	2		566	735	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513240	44513240	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	78	321	0	ENST00000291552.4:c.695G>A	p.Arg232Lys	p.R232K	ENST00000291552	NM_006758.2	232	aGa/aAa	8/8	0.240080410591782	3	FACETS	0.892	0.785	1	0.297	0.261	0.336	CLONAL	1	TRUE	0	0.367080389066229	3		321	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0009709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	162	522	1	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.272983515655613	2	FACETS	1	0.983	1	0.628	0.578	0.68	CLONAL	1	TRUE	0	0.394327246963938	2		523	654	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999042	100999042	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241953281	NA	P-0009709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	254	867	1	ENST00000325455.5:c.760G>A	p.Ala254Thr	p.A254T	ENST00000325455	NM_001202474.3	254	Gcg/Acg	1/8	0.326109129208975	2	FACETS	0.922	0.867	0.977	0.922	0.867	0.977	CLONAL	2	TRUE	0	0.394327246963938	2		868	699	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928307	69928307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	39	684	0	ENST00000352241.4:c.127G>A	p.Ala43Thr	p.A43T	ENST00000352241	NM_198159.2	43	Gcc/Acc	2/10	1	2	FACETS	0.299	0.247	0.357	0.299	0.247	0.357	SUBCLONAL	1	TRUE	1	0.394327246963938	2		684	662	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120559	2120559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45517203	NA	P-0009709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	200	797	0	ENST00000219476.3:c.1819G>A	p.Ala607Thr	p.A607T	ENST00000219476	NM_000548.3	607	Gcg/Acg	17/42	0.128372325989845	3	FACETS	0.789	0.732	0.846			1	INDETERMINATE	2	TRUE	NA	0.394327246963938	3		797	770	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0009712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	144	553	3	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.224875804644103	1	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	0	0.224875804644103	1		556	1136	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0009712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1241	53	477	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.224875804644103	6	FACETS	0.528	0.448	0.617			1	SUBCLONAL	1	TRUE	NA	0.224875804644103	6		477	1294	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878749	151878749	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1211949081	NA	P-0009712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	93	422	0	ENST00000262189.6:c.6196C>T	p.Arg2066Ter	p.R2066*	ENST00000262189	NM_170606.2	2066	Cga/Tga	36/59	0.224875804644103	1	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	0	0.224875804644103	1		422	728	SUCCESS
APC	324	MSKCC	GRCh37	5	112137036	112137036	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	112	433	1	ENST00000257430.4:c.790C>T	p.Gln264Ter	p.Q264*	ENST00000257430	NM_000038.5	264	Caa/Taa	8/16	0.224875804644103	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.224875804644103	1		434	844	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227869	123227869	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	27	212	0	ENST00000218089.9:c.3580C>T	p.Arg1194Trp	p.R1194W	ENST00000218089	NM_001042749.1	1194	Cgg/Tgg	33/35	1	1	FACETS	0.431	0.342	0.533	0.431	0.342	0.533	SUBCLONAL	1	TRUE	0	0.224875804644103	1		212	495	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604794	+	frameshift_variant	Frame_Shift_Del	DEL	ACGAAGT	ACGAAGT	-	novel	NA	P-0009712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	100	477	0	ENST00000342988.3:c.1612_1618del	p.Glu538PhefsTer12	p.E538Ffs*12	ENST00000342988	NM_005359.5	537	gACGAAGTa/ga	12/12	0.224875804644103	1	FACETS	0.989	0.883	1	0.989	0.883	1	CLONAL	1	TRUE	0	0.224875804644103	1		477	798	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713834	30713834	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35766612	NA	P-0009713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	325	422	2	ENST00000295754.5:c.1159G>A	p.Val387Met	p.V387M	ENST00000295754	NM_003242.5	387	Gtg/Atg	4/7	1	2	FACETS	0.991	0.941	1	0.991	0.941	1	CLONAL	1	TRUE	1	0.846423664051871	2		424	775	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243778441	243778441	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	139	428	0	ENST00000263826.5:c.584C>G	p.Thr195Ser	p.T195S	ENST00000263826	NM_005465.4	195	aCt/aGt	6/13	NA	2	FACETS	0.941	0.868	1			1	INDETERMINATE	1	TRUE	NA	0.846423664051871	2		428	349	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636203	87636203	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	194	422	1	ENST00000277120.3:c.2368C>T	p.Arg790Ter	p.R790*	ENST00000277120		790	Cga/Tga	19/19	1	2	FACETS	0.58	0.538	0.624	0.58	0.538	0.624	SUBCLONAL	1	TRUE	1	0.846423664051871	2		423	790	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436032	56436032	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	129	310	1	ENST00000407977.2:c.1105C>A	p.Pro369Thr	p.P369T	ENST00000407977		369	Ccc/Acc	9/10	1	2	FACETS	0.625	0.57	0.682	0.625	0.57	0.682	SUBCLONAL	1	TRUE	1	0.846423664051871	2		311	488	SUCCESS
APC	324	MSKCC	GRCh37	5	112174096	112174096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs137854575	NA	P-0009716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	88	529	0	ENST00000257430.4:c.2805C>A	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	taC/taA	16/16	1	2	FACETS	0.789	0.699	0.886	0.789	0.699	0.886	SUBCLONAL	1	TRUE	1	0.29	2		529	769	SUCCESS
APC	324	MSKCC	GRCh37	5	112175513	112175513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	103	459	1	ENST00000257430.4:c.4222G>T	p.Glu1408Ter	p.E1408*	ENST00000257430	NM_000038.5	1408	Gaa/Taa	16/16	1	2	FACETS	0.94	0.841	1	0.94	0.841	1	CLONAL	1	TRUE	1	0.29	2		460	756	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0009716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	211	515	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	1	2	FACETS	0.877	0.816	0.939	1	0.993	1	CLONAL	2	TRUE	1	0.29	2		515	830	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479810	67479810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863223746	NA	P-0009716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	138	608	1	ENST00000327367.4:c.1117C>T	p.Arg373Cys	p.R373C	ENST00000327367	NM_005902.3	373	Cgc/Tgc	8/9	1	2	FACETS	0.956	0.868	1	0.956	0.868	1	CLONAL	1	TRUE	1	0.29	2		609	996	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965804	90965804	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	136	568	0	ENST00000265433.3:c.1513G>T	p.Glu505Ter	p.E505*	ENST00000265433	NM_002485.4	505	Gag/Tag	11/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.29	2		568	806	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676268	37676268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	209	750	0	ENST00000447079.4:c.3023G>A	p.Arg1008Gln	p.R1008Q	ENST00000447079	NM_015083.1	1008	cGg/cAg	11/14	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.29	2		750	1264	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368294	45368294	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	129	655	0	ENST00000262160.6:c.1308C>G	p.Cys436Trp	p.C436W	ENST00000262160	NM_005901.5	436	tgC/tgG	11/11	0.26561836591889	1	FACETS	0.926	0.84	1	0.926	0.84	1	CLONAL	1	TRUE	0	0.29	1		655	821	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207162	1207162	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs137853076	NA	P-0009732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	236	360	0	ENST00000326873.7:c.250A>T	p.Lys84Ter	p.K84*	ENST00000326873	NM_000455.4	84	Aag/Tag	1/10	0.44660839959567	1	FACETS	0.921	0.861	0.983	0.921	0.861	0.983	CLONAL	1	TRUE	0	0.44660839959567	1		360	891	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989551	212989551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	168	360	0	ENST00000342788.4:c.160G>A	p.Glu54Lys	p.E54K	ENST00000342788	NM_005235.2	54	Gaa/Aaa	2/28	1	2	FACETS	0.813	0.747	0.882	0.813	0.747	0.882	CLONAL	1	TRUE	1	0.44660839959567	2		360	925	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438535	52438535	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0009732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	193	352	0	ENST00000460680.1:c.1184C>G	p.Ser395Ter	p.S395*	ENST00000460680	NM_004656.3	395	tCa/tGa	12/17	0.39430483455964	1	FACETS	0.956	0.888	1	0.956	0.888	1	CLONAL	1	TRUE	0	0.44660839959567	1		352	702	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647657	2647657	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	226	561	0	ENST00000342085.4:c.1560C>G	p.Asn520Lys	p.N520K	ENST00000342085	NM_002613.4	520	aaC/aaG	14/14	1	2	FACETS	0.875	0.814	0.938	0.875	0.814	0.938	CLONAL	1	TRUE	1	0.44660839959567	2		561	1157	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0009755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	121	348	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.894	0.809	0.984	1	0.988	1	CLONAL	2	FALSE	1	0.197863293164867	2		348	684	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0009755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	71	591	2	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	1	2	FACETS	0.628	0.546	0.718	0.628	0.546	0.718	SUBCLONAL	1	FALSE	1	0.197863293164867	2		593	1142	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371683	55371683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753693798	NA	P-0009755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	52	390	0	ENST00000297316.4:c.373C>T	p.Arg125Cys	p.R125C	ENST00000297316	NM_022454.3	125	Cgc/Tgc	2/2	1	2	FACETS	0.857	0.729	0.998	0.857	0.729	0.998	CLONAL	1	FALSE	1	0.197863293164867	2		390	613	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009764-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	133	241	1	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	0.23390245746911	5	FACETS	1	0.975	1			1	INDETERMINATE	1	TRUE	NA	0.43776068324298	5		242	835	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724541	162724541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759709680	NA	P-0009764-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	260	631	4	ENST00000367921.3:c.313C>T	p.Arg105Cys	p.R105C	ENST00000367921	NM_006182.2	105	Cgc/Tgc	5/18	0.400821590110151	3	FACETS	0.851	0.799	0.904	0.851	0.799	0.904	CLONAL	2	TRUE	1	0.43776068324298	3		635	851	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143084	30143084	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009764-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	154	807	0	ENST00000389048.3:c.442G>T	p.Glu148Ter	p.E148*	ENST00000389048	NM_004304.4	148	Gag/Tag	1/29	0.43776068324298	3	FACETS	0.798	0.729	0.87	0.399	0.364	0.435	SUBCLONAL	1	TRUE	1	0.43776068324298	3		807	1075	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188966	142188966	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009764-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	352	742	1	ENST00000350721.4:c.6281G>T	p.Trp2094Leu	p.W2094L	ENST00000350721	NM_001184.3	2094	tGg/tTg	37/47	0.209139492776797	5	FACETS	1	0.992	1	0.811	0.769	0.854	INDETERMINATE	2	TRUE	2	0.43776068324298	5		743	1095	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520195	176520195	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009764-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	265	693	0	ENST00000292408.4:c.1114C>G	p.Leu372Val	p.L372V	ENST00000292408	NM_213647.1	372	Ctg/Gtg	9/18	0.391432535498847	2	FACETS	0.847	0.798	0.896	0.847	0.798	0.896	CLONAL	2	TRUE	0	0.43776068324298	2		693	715	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680152	30680152	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009764-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	147	742	1	ENST00000376406.3:c.1567A>T	p.Thr523Ser	p.T523S	ENST00000376406	NM_014641.2	523	Aca/Tca	5/15	0.400821590110151	3	FACETS	0.825	0.753	0.901	0.413	0.376	0.451	CLONAL	1	TRUE	1	0.43776068324298	3		743	992	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188811	32188811	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009764-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	132	622	0	ENST00000375023.3:c.743C>A	p.Thr248Asn	p.T248N	ENST00000375023	NM_004557.3	248	aCc/aAc	4/30	0.400821590110151	3	FACETS	0.842	0.764	0.924	0.421	0.382	0.462	CLONAL	1	TRUE	1	0.43776068324298	3		622	873	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120731	94120731	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009764-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	367	1075	0	ENST00000369303.4:c.320G>C	p.Arg107Thr	p.R107T	ENST00000369303	NM_004440.3	107	aGg/aCg	3/17	0.356906181685402	2	FACETS	1	0.995	1	0.741	0.704	0.78	CLONAL	1	TRUE	0	0.43776068324298	2		1075	1131	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963873	2963873	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009764-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	113	790	0	ENST00000396946.4:c.1934T>C	p.Leu645Pro	p.L645P	ENST00000396946	NM_032415.4	645	cTg/cCg	15/25	0.43776068324298	3	FACETS	0.615	0.552	0.682	0.308	0.276	0.341	SUBCLONAL	1	TRUE	1	0.43776068324298	3		790	1023	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845126	128845126	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009764-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	236	866	0	ENST00000249373.3:c.620A>T	p.Tyr207Phe	p.Y207F	ENST00000249373	NM_005631.4	207	tAc/tTc	3/12	0.206129057450705	5	FACETS	0.77	0.718	0.824	0.513	0.478	0.549	INDETERMINATE	2	TRUE	2	0.43776068324298	5		866	1160	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864349	151864349	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009764-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	299	741	0	ENST00000262189.6:c.9632C>G	p.Ala3211Gly	p.A3211G	ENST00000262189	NM_170606.2	3211	gCc/gGc	42/59	0.206129057450705	5	FACETS	1	0.977	1	0.712	0.671	0.754	INDETERMINATE	2	TRUE	2	0.43776068324298	5		741	1059	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344135	118344135	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009764-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	45	533	0	ENST00000534358.1:c.2261C>A	p.Ser754Tyr	p.S754Y	ENST00000534358	NM_005933.3	754	tCc/tAc	3/36	0.160377316125484	2	FACETS	0.387	0.325	0.456	0.194	0.162	0.228	INDETERMINATE	1	TRUE	0	0.43776068324298	2		533	531	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052623	42052623	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009764-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	458	1084	0	ENST00000219905.7:c.7294G>T	p.Glu2432Ter	p.E2432*	ENST00000219905	NM_001164273.1	2432	Gag/Tag	20/24	0.391432535498847	2	FACETS	0.889	0.85	0.928	0.889	0.85	0.928	CLONAL	2	TRUE	0	0.43776068324298	2		1084	1177	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964940	15964940	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009764-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	327	861	1	ENST00000268712.3:c.5656G>T	p.Ala1886Ser	p.A1886S	ENST00000268712	NM_006311.3	1886	Gcc/Tcc	37/46	0.356906181685402	2	FACETS	0.875	0.83	0.92	0.875	0.83	0.92	CLONAL	2	TRUE	0	0.43776068324298	2		862	854	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52705282	52705282	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009764-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	59	631	0	ENST00000322088.6:c.164T>G	p.Leu55Arg	p.L55R	ENST00000322088	NM_014225.5	55	cTt/cGt	2/15	NA	2	FACETS	0.372	0.32	0.43			1	INDETERMINATE	1	TRUE	NA	0.43776068324298	2		631	724	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727065	40727065	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009764-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	217	555	0	ENST00000373198.4:c.3899C>G	p.Ala1300Gly	p.A1300G	ENST00000373198	NM_133170.3	1300	gCc/gGc	28/32	0.139056893260629	4	FACETS	1	0.954	1	1	0.954	1	INDETERMINATE	2	TRUE	2	0.43776068324298	4		555	694	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932317	39932317	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009764-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	178	1143	1	ENST00000378444.4:c.2282G>T	p.Arg761Leu	p.R761L	ENST00000378444	NM_001123385.1	761	cGg/cTg	4/15	0.43776068324298	1	FACETS	0.711	0.655	0.768	0.711	0.655	0.768	SUBCLONAL	1	TRUE	0	0.43776068324298	1		1144	894	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410038	63410038	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009764-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	253	824	0	ENST00000330258.3:c.3129C>A	p.Ser1043Arg	p.S1043R	ENST00000330258	NM_152424.3	1043	agC/agA	2/2	0.222202420628702	3	FACETS	1	0.991	1	0.675	0.631	0.719	INDETERMINATE	1	TRUE	1	0.43776068324298	3		824	1044	SUCCESS
AR	367	MSKCC	GRCh37	X	66937366	66937366	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009764-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	228	991	0	ENST00000374690.3:c.2220C>A	p.Tyr740Ter	p.Y740*	ENST00000374690	NM_000044.3	740	taC/taA	5/8	0.222202420628702	3	FACETS	0.997	0.927	1	0.498	0.463	0.535	INDETERMINATE	1	TRUE	1	0.43776068324298	3		991	1274	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909658	76909658	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009764-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	244	1014	1	ENST00000373344.5:c.4247A>G	p.Gln1416Arg	p.Q1416R	ENST00000373344	NM_000489.3	1416	cAg/cGg	14/35	0.222202420628702	3	FACETS	1	0.974	1	0.543	0.506	0.58	INDETERMINATE	1	TRUE	1	0.43776068324298	3		1015	1252	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937372	76937372	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009764-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	166	809	0	ENST00000373344.5:c.3376G>C	p.Asp1126His	p.D1126H	ENST00000373344	NM_000489.3	1126	Gat/Cat	9/35	0.222202420628702	3	FACETS	0.957	0.879	1	0.478	0.439	0.52	INDETERMINATE	1	TRUE	1	0.43776068324298	3		809	966	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579433	7579433	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1064793279	NA	P-0009764-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	222	614	0	ENST00000269305.4:c.254del	p.Pro85LeufsTer38	p.P85Lfs*38	ENST00000269305	NM_001126112.2	85	cCt/ct	4/11	0.356906181685402	2	FACETS	0.81	0.759	0.862	0.81	0.759	0.862	CLONAL	2	TRUE	0	0.43776068324298	2		614	626	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805608	46805608	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009764-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1174	420	1219	0	ENST00000290295.7:c.348del	p.Glu118LysfsTer161	p.E118Kfs*161	ENST00000290295	NM_006361.5	116	gcC/gc	1/2	0.206129057450705	5	FACETS	0.997	0.948	1	0.665	0.632	0.698	INDETERMINATE	2	TRUE	2	0.43776068324298	5		1219	1594	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0009789-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	64	379	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.974	0.842	1	0.974	0.842	1	CLONAL	1	TRUE	1	0.19	2		379	692	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969071	93969071	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0009789-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	65	482	0	ENST00000369303.4:c.1924+1G>C		p.X642_splice	ENST00000369303	NM_004440.3	642			1	2	FACETS	0.783	0.677	0.898	0.783	0.677	0.898	SUBCLONAL	1	TRUE	1	0.19	2		482	874	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426489	49426489	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009789-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	115	559	0	ENST00000301067.7:c.11999G>T	p.Gly4000Val	p.G4000V	ENST00000301067	NM_003482.3	4000	gGc/gTc	39/54	1	2	FACETS	0.993	0.892	1	0.993	0.892	1	CLONAL	1	TRUE	1	0.19	2		559	1219	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019560	42019560	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009789-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	104	593	0	ENST00000219905.7:c.3613G>T	p.Gly1205Ter	p.G1205*	ENST00000219905	NM_001164273.1	1205	Gga/Tga	10/24	1	2	FACETS	0.981	0.876	1	0.981	0.876	1	CLONAL	1	TRUE	1	0.19	2		593	1116	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578509	7578509	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519978	NA	P-0009789-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	53	410	0	ENST00000269305.4:c.421T>C	p.Cys141Arg	p.C141R	ENST00000269305	NM_001126112.2	141	Tgc/Cgc	5/11	1	2	FACETS	0.775	0.659	0.902	0.775	0.659	0.902	CLONAL	1	TRUE	1	0.19	2		410	720	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952519	17952520	+	missense_variant	Missense_Mutation	DNP	TG	TG	AC	novel	NA	P-0009789-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	57	367	0	ENST00000458235.1:c.913_914delinsGT	p.Gln305Val	p.Q305V	ENST00000458235	NM_000215.3	305	CAg/GTg	7/24	1	2	FACETS	0.885	0.758	1	0.885	0.758	1	CLONAL	1	TRUE	1	0.19	2		367	678	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	147	225	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.964	1	1	0.992	1	CLONAL	2	TRUE	1	0.349530937827032	2		225	392	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850341	128850341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121918347	NA	P-0009792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	159	329	0	ENST00000249373.3:c.1604G>T	p.Trp535Leu	p.W535L	ENST00000249373	NM_005631.4	535	tGg/tTg	9/12	0.229910786814898	3	FACETS	1	0.986	1	0.689	0.632	0.748	CLONAL	1	TRUE	1	0.349530937827032	3		329	776	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781213	161781213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs571092914	NA	P-0009792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	139	421	0	ENST00000366898.1:c.1192G>A	p.Ala398Thr	p.A398T	ENST00000366898	NM_004562.2	398	Gcc/Acc	11/12	1	2	FACETS	0.837	0.761	0.917	0.837	0.761	0.917	CLONAL	1	TRUE	1	0.349530937827032	2		421	950	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155021	108155021	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	83	310	0	ENST00000278616.4:c.3814G>T	p.Ala1272Ser	p.A1272S	ENST00000278616	NM_000051.3	1272	Gct/Tct	26/63	1	2	FACETS	0.723	0.638	0.814	0.723	0.638	0.814	SUBCLONAL	1	TRUE	1	0.349530937827032	2		310	657	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938597	44938597	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0009792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	280	363	0	ENST00000377967.4:c.3144+1G>C		p.X1048_splice	ENST00000377967	NM_021140.2	1048			1	2	FACETS	0.994	0.937	1	1	0.995	1	CLONAL	2	TRUE	1	0.349530937827032	2		363	806	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0009794-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	321	386	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.765752443869628	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.765752443869628	2		386	377	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009794-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	413	543	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.765752443869628	3	FACETS	0.99	0.951	1	0.99	0.951	1	CLONAL	2	TRUE	1	0.765752443869628	3		543	753	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272105	15272105	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372833545	NA	P-0009794-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	61	169	0	ENST00000263388.2:c.6334G>A	p.Gly2112Ser	p.G2112S	ENST00000263388	NM_000435.2	2112	Ggt/Agt	33/33	0.765752443869628	3	FACETS	0.946	0.826	1	0.473	0.413	0.536	CLONAL	1	TRUE	1	0.765752443869628	3		169	233	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424198	47424198	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1410667957	NA	P-0009794-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	297	513	1	ENST00000377045.4:c.203G>A	p.Arg68Gln	p.R68Q	ENST00000377045	NM_001654.4	68	cGa/cAa	4/16	0.544418011337371	4	FACETS	1	0.968	1	0.522	0.491	0.554	CLONAL	1	TRUE	2	0.765752443869628	4		514	1312	SUCCESS
APC	324	MSKCC	GRCh37	5	112178088	112178088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009794-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	504	518	0	ENST00000257430.4:c.6797C>T	p.Thr2266Ile	p.T2266I	ENST00000257430	NM_000038.5	2266	aCa/aTa	16/16	0.765752443869628	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.765752443869628	2		518	606	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0009798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	498	719	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.701892577816615	2	FACETS	0.971	0.942	1	0.971	0.942	1	CLONAL	2	TRUE	0	0.702304590193815	2		719	730	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959351	26959351	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	409	238	0	ENST00000381527.3:c.518A>G	p.Asp173Gly	p.D173G	ENST00000381527	NM_001260.1	173	gAc/gGc	6/13	0.702304590193815	3	FACETS	0.985	0.944	1	0.985	0.944	1	CLONAL	2	TRUE	1	0.702304590193815	3		238	799	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11181368	11181368	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	308	436	0	ENST00000361445.4:c.6868G>A	p.Ala2290Thr	p.A2290T	ENST00000361445	NM_004958.3	2290	Gcc/Acc	49/58	0.702304590193815	1	FACETS	0.995	0.949	1	0.995	0.949	1	CLONAL	1	TRUE	0	0.702304590193815	1		436	572	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538913	23538913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	337	435	1	ENST00000380871.4:c.526C>T	p.Arg176Cys	p.R176C	ENST00000380871	NM_006167.3	176	Cgc/Tgc	2/2	0.702304590193815	1	FACETS	0.886	0.844	0.927	0.886	0.844	0.927	CLONAL	1	TRUE	0	0.702304590193815	1		436	703	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903773	114903773	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	776	524	0	ENST00000543371.1:c.777G>A	p.Trp259Ter	p.W259*	ENST00000543371	NM_001198531.1	259	tgG/tgA	7/14	0.50333935201911	3	FACETS	1	0.974	1			1	CLONAL	2	TRUE	NA	0.702304590193815	3		524	1487	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829302	72829302	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs924588701	NA	P-0009798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	477	686	1	ENST00000268489.5:c.7279G>A	p.Asp2427Asn	p.D2427N	ENST00000268489	NM_006885.3	2427	Gat/Aat	9/10	1	2	FACETS	0.915	0.874	0.956	0.915	0.874	0.956	CLONAL	1	TRUE	1	0.702304590193815	2		687	1485	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303242	15303242	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	328	462	0	ENST00000263388.2:c.286T>A	p.Ser96Thr	p.S96T	ENST00000263388	NM_000435.2	96	Tca/Aca	3/33	0.610925863317941	1	FACETS	0.917	0.874	0.96	0.917	0.874	0.96	CLONAL	1	TRUE	0	0.702304590193815	1		462	661	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342711	70342711	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	234	248	0	ENST00000374080.3:c.1472A>C	p.Lys491Thr	p.K491T	ENST00000374080		491	aAg/aCg	10/45	1	1	FACETS	0.828	0.781	0.876	0.828	0.781	0.876	CLONAL	1	TRUE	0	0.702304590193815	1		248	522	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39690040	39690051	+	inframe_deletion	In_Frame_Del	DEL	ATAAACACAAAG	ATAAACACAAAG	-	rs773155066	NA	P-0009798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	50	185	0	ENST00000361337.2:c.79_90del	p.Lys27_Asp30del	p.K27_D30del	ENST00000361337	NM_003286.2	22	cATAAACACAAAGat/cat	3/21	0.372586407137463	4	FACETS	0.35	0.296	0.409			1	INDETERMINATE	1	TRUE	NA	0.702304590193815	4		185	693	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0009813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	260	386	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.791514734534265	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.791514734534265	1		386	366	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0009813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	483	606	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.791514734534265	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.791514734534265	1		606	671	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872863	136872863	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	725	1087	0	ENST00000241393.3:c.635G>T	p.Gly212Val	p.G212V	ENST00000241393	NM_003467.2	212	gGt/gTt	2/2	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.791514734534265	2		1087	1817	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859450	57859450	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009813-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	615	1023	0	ENST00000228682.2:c.595A>G	p.Met199Val	p.M199V	ENST00000228682	NM_005269.2	199	Atg/Gtg	6/12	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.791514734534265	2		1023	1501	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0009836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	42	287	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.382	0.317	0.455	0.382	0.317	0.455	SUBCLONAL	1	TRUE	1	0.18	2		287	1222	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971029	21971029	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519852	NA	P-0009836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	35	115	0	ENST00000304494.5:c.329G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tGg/tAg	2/3	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.18	2		115	275	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448319	56448319	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	44	287	0	ENST00000407977.2:c.328G>T	p.Glu110Ter	p.E110*	ENST00000407977		110	Gag/Tag	3/10	1	2	FACETS	0.639	0.534	0.756	0.639	0.534	0.756	SUBCLONAL	1	TRUE	1	0.18	2		287	765	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0009840-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	145	328	0	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	0.302734676984338	2	FACETS	1	0.983	1	0.644	0.59	0.7	CLONAL	1	TRUE	0	0.376440590003384	2		328	598	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256056	123256056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009840-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	139	569	1	ENST00000358487.5:c.1853C>T	p.Ala618Val	p.A618V	ENST00000358487	NM_000141.4	618	gCt/gTt	13/18	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.376440590003384	2		570	675	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562433	21562433	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1215271594	NA	P-0009840-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	46	187	0	ENST00000382592.4:c.1486G>A	p.Gly496Ser	p.G496S	ENST00000382592	NM_014572.2	496	Ggc/Agc	4/8	NA	2	FACETS	1	0.858	1			1	INDETERMINATE	1	TRUE	NA	0.376440590003384	2		187	242	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0009847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	44	428	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	1	2	FACETS	0.579	0.484	0.685	0.579	0.484	0.685	SUBCLONAL	1	TRUE	1	0.18	2		428	844	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907098	101907098	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554701911	NA	P-0009847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	74	518	0	ENST00000374994.4:c.1058G>T	p.Gly353Val	p.G353V	ENST00000374994	NM_004612.2	353	gGa/gTa	6/9	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.18	2		518	737	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843704	156843704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1261	137	733	0	ENST00000524377.1:c.1130C>T	p.Ala377Val	p.A377V	ENST00000524377	NM_002529.3	377	gCc/gTc	8/17	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.18	2		733	1398	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008033	29008033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	67	516	0	ENST00000282397.4:c.736C>T	p.His246Tyr	p.H246Y	ENST00000282397	NM_002019.4	246	Cat/Tat	6/30	1	2	FACETS	0.933	0.809	1	0.933	0.809	1	CLONAL	1	TRUE	1	0.18	2		516	798	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973957	55973957	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	41	420	0	ENST00000263923.4:c.1359del	p.His454IlefsTer23	p.H454Ifs*23	ENST00000263923	NM_002253.2	453	ccG/cc	10/30	1	2	FACETS	0.625	0.519	0.743	0.625	0.519	0.743	SUBCLONAL	1	TRUE	1	0.18	2		420	729	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0009856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	412	379	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.32253633687534	5	FACETS	1	0.981	1			1	CLONAL	3	TRUE	NA	0.32253633687534	5		379	1196	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0009856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	164	473	1	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	0.302033310576852	2	FACETS	1	0.988	1	0.716	0.659	0.775	CLONAL	1	TRUE	0	0.32253633687534	2		474	710	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120284	94120284	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	441	747	1	ENST00000369303.4:c.767G>T	p.Trp256Leu	p.W256L	ENST00000369303	NM_004440.3	256	tGg/tTg	3/17	0.170279226157669	3	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.32253633687534	3		748	1440	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221776	55221776	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1412517681	NA	P-0009856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1462	151	678	0	ENST00000275493.2:c.820A>G	p.Thr274Ala	p.T274A	ENST00000275493	NM_005228.3	274	Acg/Gcg	7/28	0.32253633687534	4	FACETS	0.768	0.699	0.84	0.384	0.349	0.42	SUBCLONAL	1	TRUE	2	0.32253633687534	4		678	1613	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413065	139413066	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0009856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	140	493	0	ENST00000277541.6:c.1076_1077delinsTT	p.Cys359Phe	p.C359F	ENST00000277541	NM_017617.3	359	tGC/tTT	6/34	0.32253633687534	3	FACETS	0.916	0.833	1	0.458	0.416	0.502	CLONAL	1	TRUE	1	0.32253633687534	3		493	1100	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435425	121435425	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	123	459	1	ENST00000257555.6:c.1458G>T	p.Gln486His	p.Q486H	ENST00000257555		486	caG/caT	7/10	0.32253633687534	3	FACETS	0.991	0.895	1	0.495	0.447	0.546	CLONAL	1	TRUE	1	0.32253633687534	3		460	894	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858337	9858337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs560057284	NA	P-0009856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	90	354	0	ENST00000330684.3:c.3064C>T	p.Arg1022Cys	p.R1022C	ENST00000330684	NM_001134407.1	1022	Cgc/Tgc	13/13	0.32253633687534	3	FACETS	0.837	0.742	0.939	0.419	0.371	0.47	CLONAL	1	TRUE	1	0.32253633687534	3		354	774	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584352	39584352	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	201	420	0	ENST00000262039.4:c.1017G>T	p.Trp339Cys	p.W339C	ENST00000262039	NM_002647.2	339	tgG/tgT	10/25	0.32253633687534	3	FACETS	0.965	0.897	1	0.643	0.598	0.69	CLONAL	2	TRUE	0	0.32253633687534	3		420	750	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610427	10610427	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	534	489	0	ENST00000171111.5:c.283del	p.Ala95ProfsTer62	p.A95Pfs*62	ENST00000171111	NM_203500.1	95	Gcc/cc	2/6	0.32253633687534	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.32253633687534	3		489	1207	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0009872-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	508	595	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.342274500814532	2	FACETS	0.841	0.806	0.877	0.841	0.806	0.877	CLONAL	2	TRUE	0	0.429802704540971	2		596	1405	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508083	106508083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339698935	NA	P-0009872-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	162	192	1	ENST00000359195.3:c.77G>A	p.Arg26His	p.R26H	ENST00000359195	NM_002649.2	26	cGc/cAc	2/11	0.218299137307524	3	FACETS	1	0.985	1	0.651	0.599	0.706	INDETERMINATE	1	TRUE	1	0.429802704540971	3		193	703	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404752	70404752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376909245	NA	P-0009872-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	95	410	1	ENST00000373644.4:c.2266G>A	p.Val756Ile	p.V756I	ENST00000373644	NM_030625.2	756	Gta/Ata	4/12	0.375136652063601	2	FACETS	0.396	0.351	0.444	0.198	0.175	0.222	SUBCLONAL	1	TRUE	0	0.429802704540971	2		411	1117	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745453	162745453	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009872-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	498	371	0	ENST00000367921.3:c.1868T>C	p.Leu623Pro	p.L623P	ENST00000367921	NM_006182.2	623	cTt/cCt	15/18	0.351592645910384	3	FACETS	1	0.989	1	0.724	0.694	0.755	CLONAL	2	TRUE	0	0.429802704540971	3		371	1296	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511177	148511177	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009872-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	282	414	0	ENST00000320356.2:c.1725G>T	p.Gln575His	p.Q575H	ENST00000320356	NM_004456.4	575	caG/caT	15/20	0.429802704540971	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.429802704540971	1		414	913	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467843	50467843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009872-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	62	309	0	ENST00000331340.3:c.1078C>T	p.Arg360Cys	p.R360C	ENST00000331340	NM_006060.4	360	Cgc/Tgc	8/8	0.218299137307524	3	FACETS	0.368	0.316	0.424	0.184	0.158	0.212	INDETERMINATE	1	TRUE	1	0.429802704540971	3		309	953	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028659	42028659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009872-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2267	356	729	1	ENST00000219905.7:c.4197G>A	p.Met1399Ile	p.M1399I	ENST00000219905	NM_001164273.1	1399	atG/atA	13/24	0.429802704540971	3	FACETS	0.767	0.723	0.813	0.384	0.361	0.407	SUBCLONAL	1	TRUE	1	0.429802704540971	3		730	2623	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505351	125505351	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	88	487	0	ENST00000428830.2:c.641G>C	p.Ser214Thr	p.S214T	ENST00000428830	NM_001114121.2	214	aGc/aCc	7/14	1	2	FACETS	0.214	0.189	0.241	0.214	0.189	0.241	SUBCLONAL	1	TRUE	1	0.699065804878446	2		487	1176	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593583	55593587	+	protein_altering_variant,splice_region_variant	In_Frame_Del	DEL	AACCC	AACCC	TT	novel	NA	P-0009879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	618	539	0	ENST00000288135.5:c.1649_1653delinsTT	p.Lys550_Pro551delinsIle	p.K550_P551delinsI	ENST00000288135	NM_000222.2	550	aAACCC/aTT	11/21	0.694560641629805	2	FACETS	0.927	0.9	0.953	0.927	0.9	0.953	CLONAL	2	TRUE	0	0.699065804878446	2		539	954	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37665972	37665972	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	327	615	0	ENST00000447079.4:c.2624T>A	p.Leu875Gln	p.L875Q	ENST00000447079	NM_015083.1	875	cTa/cAa	7/14	1	2	FACETS	0.947	0.895	1	0.947	0.895	1	CLONAL	1	TRUE	1	0.607150858627634	2		615	1137	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618533	37618539	+	frameshift_variant	Frame_Shift_Del	DEL	TGGTGGA	TGGTGGA	-	novel	NA	P-0009908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	219	459	0	ENST00000447079.4:c.209_215del	p.Leu70CysfsTer20	p.L70Cfs*20	ENST00000447079	NM_015083.1	70	tTGGTGGAg/tg	1/14	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.607150858627634	2		459	695	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0009920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	38	445	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.528	0.434	0.633	0.528	0.434	0.633	SUBCLONAL	1	TRUE	1	0.16	2		445	900	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0009920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	40	312	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.622	0.515	0.742	0.622	0.515	0.742	SUBCLONAL	1	TRUE	1	0.16	2		312	804	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450906	70450906	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	39	280	0	ENST00000373644.4:c.5746C>G	p.Pro1916Ala	p.P1916A	ENST00000373644	NM_030625.2	1916	Cct/Gct	12/12	1	2	FACETS	0.911	0.754	1	0.911	0.754	1	CLONAL	1	TRUE	1	0.16	2		280	535	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715636	18715636	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0009920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	47	283	0	ENST00000266497.5:c.3468-1G>T		p.X1156_splice	ENST00000266497		1156			1	2	FACETS	0.901	0.759	1	0.901	0.759	1	CLONAL	1	TRUE	1	0.16	2		283	652	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922984	39922984	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1350912215	NA	P-0009920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	59	532	0	ENST00000378444.4:c.3724C>A	p.Gln1242Lys	p.Q1242K	ENST00000378444	NM_001123385.1	1242	Cag/Aag	8/15	1	2	FACETS	0.676	0.579	0.782	0.676	0.579	0.782	SUBCLONAL	1	TRUE	1	0.16	2		532	1091	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0009928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	104	213	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.236641790452529	6	FACETS	0.964	0.864	1			1	CLONAL	2	TRUE	NA	0.236641790452529	6		213	672	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032299	10032299	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	144	192	0	ENST00000330684.3:c.524C>T	p.Thr175Ile	p.T175I	ENST00000330684	NM_001134407.1	175	aCt/aTt	3/13	0.178658235744836	4	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	2	0.236641790452529	4		192	686	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141525	11141525	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	196	357	0	ENST00000358026.2:c.3502G>A	p.Ala1168Thr	p.A1168T	ENST00000358026	NM_001128849.1	1168	Gca/Aca	25/36	0.234603061927604	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.236641790452529	2		357	809	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223003	1223003	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	142	192	0	ENST00000326873.7:c.941del	p.Pro314LeufsTer22	p.P314Lfs*22	ENST00000326873	NM_000455.4	314	Cct/ct	8/10	0.234603061927604	2	FACETS	0.971	0.888	1	0.971	0.888	1	CLONAL	2	TRUE	0	0.236641790452529	2		192	618	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879601	37879602	+	missense_variant	Missense_Mutation	DNP	TT	TT	AA	novel	NA	P-0009928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	146	275	0	ENST00000269571.5:c.1976_1977inv	p.Val659Glu	p.V659E	ENST00000269571		659	gTT/gAA	17/27	0.219518101884157	4	FACETS	0.916	0.836	0.999	0.916	0.836	0.999	CLONAL	2	TRUE	2	0.236641790452529	4		275	833	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0009937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	130	641	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.531	0.481	0.583	0.531	0.481	0.583	SUBCLONAL	1	TRUE	1	0.54015147355294	2		641	907	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041401	47041401	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	154	578	0	ENST00000377604.3:c.1745A>G	p.Tyr582Cys	p.Y582C	ENST00000377604	NM_001204468.1	582	tAt/tGt	16/24	1	2	FACETS	0.482	0.44	0.527	0.482	0.44	0.527	SUBCLONAL	1	TRUE	1	0.54015147355294	2		578	1182	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006891	47006891	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	80	401	0	ENST00000377604.3:c.13del	p.Arg5AspfsTer129	p.R5Dfs*129	ENST00000377604	NM_001204468.1	4	gAa/ga	2/24	1	2	FACETS	0.377	0.332	0.427	0.377	0.332	0.427	SUBCLONAL	1	TRUE	1	0.54015147355294	2		401	785	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009953-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	38	543	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		543	958	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100183	27100183	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1421112233	NA	P-0009953-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	35	381	0	ENST00000324856.7:c.3979C>T	p.Gln1327Ter	p.Q1327*	ENST00000324856	NM_006015.4	1327	Cag/Tag	16/20	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		381	620	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0009960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	69	379	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.794	0.69	0.906	0.794	0.69	0.906	CLONAL	1	TRUE	1	0.22	2		379	790	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484595	57484595	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs797045203	NA	P-0009960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	53	216	0	ENST00000371085.3:c.679C>A	p.Gln227Lys	p.Q227K	ENST00000371085	NM_000516.4	227	Cag/Aag	9/13	0.3	2	FACETS	0.839	0.716	0.975			1	CLONAL	1	TRUE	NA	0.22	2		216	574	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341250	8341250	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	40	318	0	ENST00000356435.5:c.4966G>T	p.Ala1656Ser	p.A1656S	ENST00000356435		1656	Gct/Tct	30/35	1	2	FACETS	0.709	0.589	0.843	0.709	0.589	0.843	SUBCLONAL	1	TRUE	1	0.22	2		318	513	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754827	29754827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373120394	NA	P-0009960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	119	362	0	ENST00000389048.3:c.1108G>A	p.Glu370Lys	p.E370K	ENST00000389048	NM_004304.4	370	Gag/Aag	4/29	1	2	FACETS	0.801	0.724	0.882	1	0.986	1	CLONAL	2	TRUE	1	0.22	2		362	675	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745633	162745633	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	130	360	0	ENST00000367921.3:c.2048G>T	p.Ser683Ile	p.S683I	ENST00000367921	NM_006182.2	683	aGt/aTt	15/18	0.200731545865019	3	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	1	0.22	3		360	634	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012866	176012866	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	74	479	0	ENST00000367669.3:c.1510C>A	p.Gln504Lys	p.Q504K	ENST00000367669	NM_022457.5	504	Cag/Aag	13/20	0.200731545865019	3	FACETS	0.734	0.641	0.835	0.367	0.32	0.418	SUBCLONAL	1	TRUE	1	0.22	3		479	1017	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965523	25965523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	159	515	1	ENST00000435504.4:c.3683G>A	p.Ser1228Asn	p.S1228N	ENST00000435504		1228	aGc/aAc	13/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.22	2		516	1121	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156012	99156012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293996326	NA	P-0009960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	193	500	2	ENST00000074304.5:c.692G>A	p.Arg231His	p.R231H	ENST00000074304	NM_001134224.1	231	cGc/cAc	10/26	0.200731545865019	3	FACETS	0.91	0.841	0.982	0.91	0.841	0.982	CLONAL	2	TRUE	1	0.22	3		502	1070	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285262	212285262	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	60	366	0	ENST00000342788.4:c.3039G>T	p.Leu1013Phe	p.L1013F	ENST00000342788	NM_005235.2	1013	ttG/ttT	25/28	1	2	FACETS	0.708	0.609	0.817	0.708	0.609	0.817	SUBCLONAL	1	TRUE	1	0.22	2		366	770	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294214	1294214	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	52	275	0	ENST00000310581.5:c.787C>A	p.Arg263Ser	p.R263S	ENST00000310581	NM_198253.2	263	Cgt/Agt	2/16	1	2	FACETS	0.875	0.745	1	0.875	0.745	1	CLONAL	1	TRUE	1	0.22	2		275	540	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622181	117622181	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	98	412	0	ENST00000368508.3:c.6689G>T	p.Arg2230Ile	p.R2230I	ENST00000368508	NM_002944.2	2230	aGa/aTa	42/43	0.3	1	FACETS	0.959	0.855	1	0.959	0.855	1	CLONAL	1	TRUE	0	0.22	1		412	827	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718167	117718167	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	78	430	0	ENST00000368508.3:c.690A>T	p.Leu230Phe	p.L230F	ENST00000368508	NM_002944.2	230	ttA/ttT	7/43	1	2	FACETS	0.847	0.743	0.959	0.847	0.743	0.959	CLONAL	1	TRUE	1	0.22	2		430	837	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970991	21970991	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	42	244	0	ENST00000304494.5:c.367C>A	p.His123Asn	p.H123N	ENST00000304494	NM_000077.4	123	Cat/Aat	2/3	1	2	FACETS	0.839	0.701	0.992	0.839	0.701	0.992	CLONAL	1	TRUE	1	0.22	2		244	455	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759778	133759778	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	26	196	0	ENST00000318560.5:c.2101G>T	p.Gly701Cys	p.G701C	ENST00000318560	NM_005157.4	701	Ggc/Tgc	11/11	1	2	FACETS	0.799	0.634	0.987	0.799	0.634	0.987	CLONAL	1	TRUE	1	0.22	2		196	296	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211748	5211748	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs377152398	NA	P-0009960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	67	404	0	ENST00000357368.4:c.5087G>T	p.Arg1696Leu	p.R1696L	ENST00000357368	NM_002850.3	1696	cGc/cTc	33/38	0.17788755084069	1	FACETS	0.769	0.668	0.879	0.769	0.668	0.879	SUBCLONAL	1	TRUE	0	0.22	1		404	705	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944884	31944884	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	40	277	0	ENST00000340398.3:c.217del	p.Glu73ArgfsTer10	p.E73Rfs*10	ENST00000340398	NM_001013699.2	73	Gag/ag	1/1	1	2	FACETS	0.785	0.653	0.933	0.785	0.653	0.933	CLONAL	1	TRUE	1	0.22	2		277	463	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221313	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	T	novel	NA	P-0009960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	74	458	0	ENST00000326873.7:c.836_837delinsT	p.Gly279ValfsTer8	p.G279Vfs*8	ENST00000326873	NM_000455.4	279	gGC/gT	6/10	0.17788755084069	1	FACETS	0.805	0.704	0.914	0.805	0.704	0.914	CLONAL	1	TRUE	0	0.22	1		458	744	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0009962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	222	446	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.739374146677232	2	FACETS	0.921	0.865	0.979	0.461	0.432	0.49	CLONAL	1	TRUE	0	0.866653116216317	2		446	556	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16203041	16203041	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	358	352	0	ENST00000375759.3:c.749C>G	p.Ser250Cys	p.S250C	ENST00000375759	NM_015001.2	250	tCt/tGt	3/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.866653116216317	2		352	778	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059267	27059267	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	362	428	0	ENST00000324856.7:c.1904G>C	p.Arg635Thr	p.R635T	ENST00000324856	NM_006015.4	635	aGa/aCa	4/20	1	2	FACETS	0.975	0.929	1	0.975	0.929	1	CLONAL	1	TRUE	1	0.866653116216317	2		428	857	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429791	78429791	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	58	503	0	ENST00000370768.2:c.997C>G	p.Gln333Glu	p.Q333E	ENST00000370768	NM_003902.3	333	Caa/Gaa	12/20	1	2	FACETS	0.131	0.112	0.152	0.131	0.112	0.152	SUBCLONAL	1	TRUE	1	0.866653116216317	2		503	1023	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010560	48010560	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587779920	NA	P-0009962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	74	190	0	ENST00000234420.5:c.188C>G	p.Ser63Cys	p.S63C	ENST00000234420	NM_000179.2	63	tCc/tGc	1/10	1	2	FACETS	0.283	0.248	0.321	0.283	0.248	0.321	SUBCLONAL	1	TRUE	1	0.866653116216317	2		190	603	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149432	61149432	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	410	482	1	ENST00000295025.8:c.1622C>T	p.Ser541Phe	p.S541F	ENST00000295025	NM_002908.2	541	tCt/tTt	11/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.866653116216317	2		483	910	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376227	225376227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	493	562	1	ENST00000264414.4:c.727G>A	p.Glu243Lys	p.E243K	ENST00000264414	NM_003590.4	243	Gaa/Aaa	6/16	0.866653116216317	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.866653116216317	1		563	589	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155200	55155200	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	427	455	0	ENST00000257290.5:c.2799G>A	p.Trp933Ter	p.W933*	ENST00000257290	NM_006206.4	933	tgG/tgA	21/23	0.866653116216317	2	FACETS	0.959	0.916	1	0.479	0.458	0.501	CLONAL	1	TRUE	0	0.866653116216317	2		455	1028	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155213	55155213	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1328843460	NA	P-0009962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	477	478	0	ENST00000257290.5:c.2812G>C	p.Glu938Gln	p.E938Q	ENST00000257290	NM_006206.4	938	Gag/Cag	21/23	0.866653116216317	2	FACETS	0.974	0.934	1	0.487	0.467	0.508	CLONAL	1	TRUE	0	0.866653116216317	2		478	1130	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573432	55573432	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	280	344	0	ENST00000288135.5:c.1094C>T	p.Ser365Phe	p.S365F	ENST00000288135	NM_000222.2	365	tCt/tTt	6/21	0.866653116216317	2	FACETS	1	0.966	1	0.513	0.486	0.54	CLONAL	1	TRUE	0	0.866653116216317	2		344	630	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158422	26158422	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	442	414	0	ENST00000289316.2:c.25C>G	p.Pro9Ala	p.P9A	ENST00000289316	NM_138720.2	9	Cct/Gct	1/2	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.866653116216317	2		414	943	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287194	33287194	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	529	472	0	ENST00000374542.5:c.1903G>C	p.Glu635Gln	p.E635Q	ENST00000374542	NM_001141970.1	635	Gag/Cag	6/8	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.866653116216317	2		472	1056	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652129	36652129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34916193	NA	P-0009962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	450	333	0	ENST00000244741.5:c.251G>A	p.Arg84Gln	p.R84Q	ENST00000244741	NM_000389.4	84	cGa/cAa	2/3	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.866653116216317	2		333	1034	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398618	116398618	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	458	488	2	ENST00000397752.3:c.2208C>A	p.Phe736Leu	p.F736L	ENST00000397752	NM_000245.2	736	ttC/ttA	9/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.866653116216317	2		490	1021	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864904	117864904	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1216	468	603	0	ENST00000297338.2:c.1205G>C	p.Arg402Thr	p.R402T	ENST00000297338	NM_006265.2	402	aGa/aCa	10/14	0.866653116216317	3	FACETS	0.919	0.877	0.963	0.46	0.438	0.482	CLONAL	1	TRUE	1	0.866653116216317	3		603	1684	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865668	57865668	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	792	789	0	ENST00000228682.2:c.3145T>A	p.Phe1049Ile	p.F1049I	ENST00000228682	NM_005269.2	1049	Ttt/Att	12/12	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.866653116216317	2		789	1785	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623911	28623911	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	152	273	0	ENST00000241453.7:c.743A>T	p.Asp248Val	p.D248V	ENST00000241453	NM_004119.2	248	gAt/gTt	7/24	1	2	FACETS	0.7	0.645	0.757	0.7	0.645	0.757	SUBCLONAL	1	TRUE	1	0.866653116216317	2		273	501	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944674	32944674	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	479	477	0	ENST00000380152.3:c.8467C>T	p.Gln2823Ter	p.Q2823*	ENST00000380152		2823	Caa/Taa	19/27	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.866653116216317	2		477	1020	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831263	3831263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	453	486	0	ENST00000262367.5:c.1618C>T	p.Gln540Ter	p.Q540*	ENST00000262367	NM_004380.2	540	Cag/Tag	7/31	1	2	FACETS	0.996	0.954	1	0.996	0.954	1	CLONAL	1	TRUE	1	0.866653116216317	2		486	1050	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041737	14041737	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	567	521	0	ENST00000311895.7:c.2284G>C	p.Asp762His	p.D762H	ENST00000311895	NM_005236.2	762	Gac/Cac	11/11	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.866653116216317	2		521	1158	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655488	67655488	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	346	394	0	ENST00000264010.4:c.1351G>C	p.Asp451His	p.D451H	ENST00000264010	NM_006565.3	451	Gat/Cat	7/12	1	2	FACETS	0.927	0.882	0.974	0.927	0.882	0.974	CLONAL	1	TRUE	1	0.866653116216317	2		394	861	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867305	68867305	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0009962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	520	461	0	ENST00000261769.5:c.2552C>G	p.Ser851Ter	p.S851*	ENST00000261769	NM_004360.3	851	tCa/tGa	16/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.866653116216317	2		461	1169	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657384	29657384	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs774893767	NA	P-0009962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	510	598	0	ENST00000356175.3:c.5617G>C	p.Glu1873Gln	p.E1873Q	ENST00000356175	NM_000267.3	1873	Gag/Cag	38/57	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.866653116216317	2		598	1152	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56363605	56363605	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs771527830	NA	P-0009962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	199	229	0	ENST00000348428.3:c.384G>C	p.Lys128Asn	p.K128N	ENST00000348428	NM_006785.3	128	aaG/aaC	3/17	0.221234039956675	6	FACETS	0.958	0.892	1			1	INDETERMINATE	2	TRUE	NA	0.866653116216317	6		229	655	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1627414	1627414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	749	578	0	ENST00000344749.5:c.310G>A	p.Glu104Lys	p.E104K	ENST00000344749	NM_001136139.2	104	Gag/Aag	6/19	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.866653116216317	2		578	1544	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920518	50920518	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	503	445	0	ENST00000440232.2:c.3210C>G	p.Ile1070Met	p.I1070M	ENST00000440232	NM_002691.3	1070	atC/atG	26/27	NA	2	FACETS	0.966	0.927	1			1	INDETERMINATE	1	TRUE	NA	0.866653116216317	2		445	1202	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221018	5221018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009963-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	36	238	0	ENST00000357368.4:c.3448C>T	p.Pro1150Ser	p.P1150S	ENST00000357368	NM_002850.3	1150	Cct/Tct	20/38	1	2	FACETS	0.663	0.543	0.797	0.663	0.543	0.797	SUBCLONAL	1	TRUE	1	0.17	2		238	639	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295774	212295774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754127388	NA	P-0009963-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	48	354	1	ENST00000342788.4:c.2539C>T	p.Arg847Cys	p.R847C	ENST00000342788	NM_005235.2	847	Cgt/Tgt	21/28	1	2	FACETS	0.64	0.539	0.752	0.64	0.539	0.752	SUBCLONAL	1	TRUE	1	0.17	2		355	882	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988340	36988340	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009963-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	28	97	0	ENST00000354822.5:c.313del	p.Val105CysfsTer20	p.V105Cfs*20	ENST00000354822	NM_001079668.2	105	Gtg/tg	2/3	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.17	2		97	264	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576924	7576928	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GTGCT	GTGCT	CC	novel	NA	P-0009963-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	55	303	0	ENST00000269305.4:c.920-2_922delinsGG		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	1	2	FACETS	0.744	0.634	0.864	0.744	0.634	0.864	SUBCLONAL	1	TRUE	1	0.17	2		303	870	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0009969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	35	330	0				ENST00000310581	NM_198253.2	-/1132			0.131411574347567	3	FACETS	1	0.865	1	0.533	0.437	0.64	CLONAL	1	TRUE	1	0.187714794001249	3		330	383	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0009969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	200	283	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	0.187714794001249	2	FACETS	0.931	0.865	0.999	1	0.99	1	CLONAL	3	TRUE	0	0.187714794001249	2		283	763	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs878854073	NA	P-0009969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	82	362	0	ENST00000269305.4:c.673-1G>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.182662685353151	2	FACETS	0.966	0.856	1	0.966	0.856	1	CLONAL	2	TRUE	0	0.187714794001249	2		362	452	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715624	30715624	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	106	515	3	ENST00000295754.5:c.1282G>T	p.Glu428Ter	p.E428*	ENST00000295754	NM_003242.5	428	Gaa/Taa	5/7	0.182662685353151	2	FACETS	0.785	0.704	0.871	0.785	0.704	0.871	SUBCLONAL	2	TRUE	0	0.187714794001249	2		518	719	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0009997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	614	565	0	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	FALSE	NA	0.758040318151306	2		565	768	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484252	8484252	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	301	455	1	ENST00000356435.5:c.3280G>T	p.Gly1094Trp	p.G1094W	ENST00000356435		1094	Ggg/Tgg	19/35	0.21626203882857	3	FACETS	0.766	0.726	0.806	0.766	0.726	0.806	INDETERMINATE	2	FALSE	1	0.758040318151306	3		456	715	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038942	12038942	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	199	452	0	ENST00000396373.4:c.1235G>T	p.Gly412Val	p.G412V	ENST00000396373	NM_001987.4	412	gGa/gTa	7/8	0.591885338035539	4	FACETS	1	0.974	1	0.368	0.341	0.396	CLONAL	1	FALSE	1	0.758040318151306	4		452	836	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472636	88472636	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1362573987	NA	P-0009997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	128	337	0	ENST00000360948.2:c.1919T>C	p.Val640Ala	p.V640A	ENST00000360948	NM_001012338.2	640	gTg/gCg	16/19	0.714357254527268	3	FACETS	0.845	0.769	0.924	0.423	0.384	0.462	CLONAL	1	FALSE	1	0.758040318151306	3		337	551	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645174	67645174	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	436	405	0	ENST00000264010.4:c.439C>G	p.Leu147Val	p.L147V	ENST00000264010	NM_006565.3	147	Ctt/Gtt	3/12	0.714357254527268	3	FACETS	0.949	0.911	0.986	0.949	0.911	0.986	CLONAL	2	FALSE	1	0.758040318151306	3		405	836	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57569912	57569912	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	52	345	0	ENST00000316660.6:c.92G>A	p.Arg31Lys	p.R31K	ENST00000316660	NM_021127.2	31	aGa/aAa	2/2	0.451313938680413	6	FACETS	0.384	0.325	0.448	0.128	0.108	0.15	INDETERMINATE	1	FALSE	3	0.758040318151306	6		345	900	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0000302-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	101	486	4	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.184369638093712	2	FACETS	0.85	0.762	0.944	0.85	0.762	0.944	CLONAL	2	TRUE	0	0.197604627209568	2		490	601	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037972	49037972	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0000302-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	23	286	0	ENST00000267163.4:c.2211+1G>T		p.X737_splice	ENST00000267163	NM_000321.2	737			0.197604627209568	1	FACETS	0.697	0.544	0.874	0.697	0.544	0.874	SUBCLONAL	1	TRUE	0	0.197604627209568	1		286	301	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560178	29560178	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000302-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	37	261	0	ENST00000356175.3:c.3655G>A	p.Gly1219Arg	p.G1219R	ENST00000356175	NM_000267.3	1219	Gga/Aga	27/57	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.197604627209568	2		261	362	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597384	10597387	+	frameshift_variant	Frame_Shift_Del	DEL	CCAC	CCAC	AAA	novel	NA	P-0000302-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	141	741	3	ENST00000171111.5:c.1816_1819delinsTTT	p.Val606PhefsTer66	p.V606Ffs*66	ENST00000171111	NM_203500.1	606	GTGGct/TTTct	6/6	0.184369638093712	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.197604627209568	2		744	658	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52685769	52685769	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000302-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	37	401	0	ENST00000394830.3:c.703C>T	p.Gln235Ter	p.Q235*	ENST00000394830	NM_018313.4	235	Cag/Tag	7/30	0.197604627209568	1	FACETS	0.973	0.804	1	0.973	0.804	1	CLONAL	1	TRUE	0	0.197604627209568	1		401	347	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457235	5457235	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000302-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	58	288	0	ENST00000381577.3:c.209G>C	p.Gly70Ala	p.G70A	ENST00000381577	NM_014143.3	70	gGa/gCa	3/7	1	2	FACETS	0.881	0.762	1	1	0.975	1	CLONAL	2	TRUE	1	0.197604627209568	2		288	333	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971112	21971113	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0000302-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	23	318	0	ENST00000304494.5:c.245_246del	p.Val82AlafsTer37	p.V82Afs*37	ENST00000304494	NM_000077.4	82	gTG/g	2/3	1	2	FACETS	0.751	0.586	0.942	0.751	0.586	0.942	CLONAL	1	TRUE	1	0.197604627209568	2		318	310	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110251308	110251308	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000584-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	32	456	0	ENST00000374672.4:c.29T>A	p.Met10Lys	p.M10K	ENST00000374672	NM_004235.4	10	aTg/aAg	2/5	1	2	FACETS	0.373	0.302	0.454	0.373	0.302	0.454	SUBCLONAL	1	TRUE	1	0.3	2		456	572	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0000879-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	308	345	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.512257265722031	4	FACETS	0.994	0.943	1	0.994	0.943	1	CLONAL	2	TRUE	2	0.726640384554401	4		345	736	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0000879-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	188	401	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	0.726640384554401	2		401	506	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317437	1317437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000879-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1202	715	528	0	ENST00000400841.2:c.628C>T	p.Gln210Ter	p.Q210*	ENST00000400841		210	Cag/Tag	5/6	0.726640384554401	4	FACETS	0.886	0.855	0.918	0.886	0.855	0.918	CLONAL	2	TRUE	2	0.726640384554401	4		528	1917	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545564	106545564	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000879-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	133	325	0	ENST00000359195.3:c.3041T>C	p.Val1014Ala	p.V1014A	ENST00000359195	NM_002649.2	1014	gTt/gCt	11/11	0.512257265722031	4	FACETS	0.893	0.812	0.977	0.446	0.406	0.489	CLONAL	1	TRUE	2	0.726640384554401	4		325	708	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101985053	101985053	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000879-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	213	421	0	ENST00000282441.5:c.500T>C	p.Ile167Thr	p.I167T	ENST00000282441	NM_001130145.2	167	aTa/aCa	2/9	0.726640384554401	3	FACETS	1	0.945	1	0.508	0.473	0.544	CLONAL	1	TRUE	1	0.726640384554401	3		421	786	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885509	111885509	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000879-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1647	248	646	0	ENST00000341259.2:c.1286T>C	p.Leu429Pro	p.L429P	ENST00000341259	NM_005475.2	429	cTc/cCc	7/8	0.726640384554401	3	FACETS	0.491	0.457	0.526	0.246	0.228	0.263	SUBCLONAL	1	TRUE	1	0.726640384554401	3		646	1895	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761444	59761444	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000879-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	141	428	1	ENST00000259008.2:c.2963C>A	p.Ser988Tyr	p.S988Y	ENST00000259008	NM_032043.2	988	tCc/tAc	20/20	0.726640384554401	3	FACETS	0.882	0.806	0.96	0.441	0.403	0.48	CLONAL	1	TRUE	1	0.726640384554401	3		429	600	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001184-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	277	432	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.604852773929922	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.604852773929922	1		432	627	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571965	64571965	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001184-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	723	730	0	ENST00000312049.6:c.1674G>A	p.Met558Ile	p.M558I	ENST00000312049	NM_130799.2	558	atG/atA	10/10	0.604852773929922	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.604852773929922	1		730	1503	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265876	16265886	+	frameshift_variant	Frame_Shift_Del	DEL	TCTCCAACATC	TCTCCAACATC	-	novel	NA	P-0001184-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1236	473	661	0	ENST00000375759.3:c.10954_10964del	p.Asn3652ProfsTer13	p.N3652Pfs*13	ENST00000375759	NM_015001.2	3650	aTCTCCAACATC/a	15/15	1	2	FACETS	0.915	0.873	0.958	0.915	0.873	0.958	CLONAL	1	TRUE	1	0.604852773929922	2		661	1709	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431018	181431018	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001184-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	105	339	1	ENST00000325404.1:c.870C>A	p.Ser290Arg	p.S290R	ENST00000325404	NM_003106.3	290	agC/agA	1/1	1	2	FACETS	0.401	0.359	0.446	0.401	0.359	0.446	SUBCLONAL	1	TRUE	1	0.604852773929922	2		340	866	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0001640-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	210	418	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.636279691934818	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	0	0.636279691934818	3		421	271	SUCCESS
APC	324	MSKCC	GRCh37	5	112175240	112175240	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001640-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	202	370	0	ENST00000257430.4:c.3949G>T	p.Glu1317Ter	p.E1317*	ENST00000257430	NM_000038.5	1317	Gaa/Taa	16/16	0.614901313759431	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	0	0.636279691934818	3		370	269	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288553	15288553	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001640-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	19	87	0	ENST00000263388.2:c.4186C>A	p.Arg1396Ser	p.R1396S	ENST00000263388	NM_000435.2	1396	Cgc/Agc	24/33	1	2	FACETS	0.948	0.744	1	0.948	0.744	1	CLONAL	1	TRUE	1	0.636279691934818	2		87	63	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0001731-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	256	418	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.964	0.912	1	0.964	0.912	1	CLONAL	1	TRUE	1	0.965792235298945	2		421	550	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131161	55131161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001731-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	510	567	0	ENST00000257290.5:c.704G>A	p.Cys235Tyr	p.C235Y	ENST00000257290	NM_006206.4	235	tGt/tAt	5/23	1	2	FACETS	0.951	0.915	0.988	0.951	0.915	0.988	CLONAL	1	TRUE	1	0.965792235298945	2		567	1110	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0001731-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	450	497	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.985	0.945	1	0.985	0.945	1	CLONAL	1	TRUE	1	0.965792235298945	2		497	946	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457692	67457692	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs548756379	NA	P-0001731-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	458	439	0	ENST00000327367.4:c.502G>C	p.Ala168Pro	p.A168P	ENST00000327367	NM_005902.3	168	Gca/Cca	3/9	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.965792235298945	2		439	916	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938085	76938085	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001731-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	473	278	0	ENST00000373344.5:c.2663del	p.Phe888SerfsTer17	p.F888Sfs*17	ENST00000373344	NM_000489.3	888	tTc/tc	9/35	1	1	FACETS	0.999	0.984	1	0.999	0.984	1	CLONAL	1	TRUE	0	0.965792235298945	1		278	507	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252156	226252156	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001731-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	41	46	0	ENST00000366813.1:c.104G>T	p.Gly35Val	p.G35V	ENST00000366813		35	gGg/gTg	1/3	1	2	FACETS	0.849	0.731	0.971	0.849	0.731	0.971	CLONAL	1	TRUE	1	0.965792235298945	2		46	100	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0003241-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	35	138	1	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.208249863144568	4	FACETS	1	0.86	1	0.525	0.432	0.627	INDETERMINATE	1	TRUE	2	0.36	4		139	252	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712018	89712018	+	splice_donor_variant	Splice_Site	SNP	T	T	G	rs727504114	NA	P-0003241-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	47	179	0	ENST00000371953.3:c.634+2T>G		p.X212_splice	ENST00000371953	NM_000314.4	212			0.208249863144568	4	FACETS	1	0.915	1	0.56	0.475	0.653	INDETERMINATE	1	TRUE	2	0.36	4		179	317	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842680	68842692	+	frameshift_variant	Frame_Shift_Del	DEL	ATTATTGAAAGAG	ATTATTGAAAGAG	GTT	novel	NA	P-0003241-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	278	787	0	ENST00000261769.5:c.616_628delinsGTT	p.Ile206ValfsTer6	p.I206Vfs*6	ENST00000261769	NM_004360.3	206	ATTATTGAAAGAGaa/GTTaa	5/16	0.3	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.36	1		787	1035	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538949	187538949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1251415716	NA	P-0121481-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	348	513	1	ENST00000441802.2:c.8791G>A	p.Asp2931Asn	p.D2931N	ENST00000441802	NM_005245.3	2931	Gac/Aac	10/27	NA	2	FACETS	0.985	0.936	1			1	INDETERMINATE	1	NA	NA	0.734264507678042	2		514	962	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434515	110434515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0121481-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	156	253	0	ENST00000375856.3:c.3886G>A	p.Ala1296Thr	p.A1296T	ENST00000375856	NM_003749.2	1296	Gct/Act	1/2	0.161593679125924	4	FACETS	0.914	0.847	0.983	0.914	0.847	0.983	INDETERMINATE	2	NA	2	0.734264507678042	4		253	403	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42840389	42840389	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0121481-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	191	439	0	ENST00000398585.3:c.1359T>A	p.Tyr453Ter	p.Y453*	ENST00000398585	NM_001135099.1	453	taT/taA	12/14	0.734264507678042	2	FACETS	0.946	0.881	1	0.473	0.44	0.506	CLONAL	1	NA	0	0.734264507678042	2		439	550	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888760	76888760	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121481-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	395	528	1	ENST00000373344.5:c.5069C>A	p.Ala1690Asp	p.A1690D	ENST00000373344	NM_000489.3	1690	gCt/gAt	19/35	0.734264507678042	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	NA	0	0.734264507678042	1		529	674	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144118	11144129	+	inframe_deletion	In_Frame_Del	DEL	GTTCGACCAGAA	GTTCGACCAGAA	-	novel	NA	P-0121481-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	150	427	0	ENST00000358026.2:c.3701_3712del	p.Phe1234_Lys1237del	p.F1234_K1237del	ENST00000358026	NM_001128849.1	1233	atGTTCGACCAGAAg/atg	26/36	0.734264507678042	2	FACETS	0.806	0.741	0.872	0.403	0.37	0.436	CLONAL	1	NA	0	0.734264507678042	2		427	507	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092771	27092771	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121481-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	202	475	0	ENST00000324856.7:c.2792G>T	p.Gly931Val	p.G931V	ENST00000324856	NM_006015.4	931	gGa/gTa	9/20	0.734264507678042	3	FACETS	0.912	0.847	0.979	0.456	0.423	0.49	CLONAL	1	NA	1	0.734264507678042	3		475	825	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259481	55259481	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0121481-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	44	318	1	ENST00000275493.2:c.2539A>T	p.Thr847Ser	p.T847S	ENST00000275493	NM_005228.3	847	Aca/Tca	21/28	0.608540786905595	4	FACETS	0.182	0.151	0.216	0.091	0.075	0.108	SUBCLONAL	1	NA	2	0.734264507678042	4		319	1143	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710659	40710659	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0121481-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	110	204	0	ENST00000373198.4:c.4194-2A>G		p.X1398_splice	ENST00000373198	NM_133170.3	1398			0.734264507678042	3	FACETS	0.877	0.793	0.966	0.439	0.396	0.483	CLONAL	1	NA	1	0.734264507678042	3		204	467	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0003616-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	503	371	0	ENST00000374080.3:c.3670C>T	p.Leu1224Phe	p.L1224F	ENST00000374080		1224	Ctc/Ttc	26/45	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.586816149583105	1		371	860	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430562	80430562	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003616-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	149	193	0	ENST00000286548.4:c.446G>A	p.Arg149Gln	p.R149Q	ENST00000286548	NM_002072.3	149	cGa/cAa	3/7	1	2	FACETS	0.928	0.853	1	0.928	0.853	1	CLONAL	1	TRUE	1	0.586816149583105	2		193	547	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759985	63759985	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003616-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	254	325	0	ENST00000279873.7:c.638T>C	p.Ile213Thr	p.I213T	ENST00000279873	NM_032199.2	213	aTt/aCt	4/10	1	2	FACETS	0.992	0.93	1	0.992	0.93	1	CLONAL	1	TRUE	1	0.586816149583105	2		325	873	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181276	123181278	+	inframe_deletion	In_Frame_Del	DEL	AAT	AAT	-	novel	NA	P-0003616-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	180	216	0	ENST00000218089.9:c.741_743del	p.Gln247_Tyr248delinsHis	p.Q247_Y248delinsH	ENST00000218089	NM_001042749.1	247	cAATat/cat	9/35	1	1	FACETS	0.637	0.59	0.687	0.637	0.59	0.687	SUBCLONAL	1	TRUE	0	0.586816149583105	1		216	680	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	93	429	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	0.396167050282503	5	FACETS	0.624	0.555	0.699	0.208	0.185	0.233	INDETERMINATE	1	FALSE	2	0.820016690776147	5		429	810	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	1278	588	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.764866152094176	4	FACETS	1	0.997	1			1	CLONAL	4	FALSE	NA	0.820016690776147	4		589	1385	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	262	403	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.820016690776147	3	FACETS	0.979	0.932	1	0.979	0.932	1	CLONAL	2	FALSE	1	0.820016690776147	3		403	460	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937611	76937615	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTT	CTTTT	-	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	294	330	0	ENST00000373344.5:c.3133_3137del	p.Lys1045Ter	p.K1045*	ENST00000373344	NM_000489.3	1045	AAAAGt/t	9/35	0.317241477668797	6	FACETS	0.936	0.888	0.985	0.936	0.888	0.985	INDETERMINATE	3	FALSE	3	0.820016690776147	6		330	674	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778083	3778083	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	584	1036	1	ENST00000262367.5:c.6965C>T	p.Ser2322Leu	p.S2322L	ENST00000262367	NM_004380.2	2322	tCa/tTa	31/31	0.694600596121444	4	FACETS	0.925	0.89	0.96	0.925	0.89	0.96	CLONAL	2	FALSE	2	0.820016690776147	4		1037	1401	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81954830	81954830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758623675	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	108	626	0	ENST00000359376.3:c.2263G>A	p.Val755Ile	p.V755I	ENST00000359376	NM_002661.3	755	Gtc/Atc	21/33	0.704052543273126	3	FACETS	0.435	0.39	0.483	0.217	0.195	0.242	SUBCLONAL	1	FALSE	1	0.820016690776147	3		626	854	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792876	33792876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	24	294	1	ENST00000498907.2:c.445C>T	p.Arg149Cys	p.R149C	ENST00000498907	NM_004364.3	149	Cgc/Tgc	1/1	0.694600596121444	4	FACETS	0.238	0.186	0.298	0.119	0.093	0.149	SUBCLONAL	1	FALSE	2	0.820016690776147	4		295	448	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216560	108216560	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	40	370	0	ENST00000278616.4:c.8509G>A	p.Glu2837Lys	p.E2837K	ENST00000278616	NM_000051.3	2837	Gaa/Aaa	58/63	0.447079564906359	6	FACETS	0.378	0.313	0.451	0.095	0.078	0.113	INDETERMINATE	1	FALSE	2	0.820016690776147	6		370	681	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803732	1803732	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	81	930	0	ENST00000260795.2:c.910C>T	p.Pro304Ser	p.P304S	ENST00000260795		304	Ccc/Tcc	6/17	0.373843041078178	5	FACETS	0.385	0.338	0.436			1	INDETERMINATE	1	FALSE	NA	0.820016690776147	5		930	1144	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910545	32910545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	40	361	1	ENST00000380152.3:c.2053G>A	p.Asp685Asn	p.D685N	ENST00000380152		685	Gat/Aat	11/27	0.694600596121444	4	FACETS	0.241	0.199	0.287	0.12	0.099	0.144	SUBCLONAL	1	FALSE	2	0.820016690776147	4		362	738	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380346	14380346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2782	1452	523	1	ENST00000256196.4:c.71G>A	p.Gly24Asp	p.G24D	ENST00000256196		24	gGc/gAc	1/6	0.820016690776147	10	FACETS	0.895	0.872	0.918			1	CLONAL	4	FALSE	NA	0.820016690776147	10		524	4234	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262396	16262396	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	24	307	0	ENST00000375759.3:c.9661C>T	p.Pro3221Ser	p.P3221S	ENST00000375759	NM_015001.2	3221	Cca/Tca	11/15	0.820016690776147	3	FACETS	0.189	0.147	0.237	0.094	0.073	0.119	SUBCLONAL	1	FALSE	1	0.820016690776147	3		307	437	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099096	27099096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	109	604	1	ENST00000324856.7:c.3512G>A	p.Ser1171Asn	p.S1171N	ENST00000324856	NM_006015.4	1171	aGt/aAt	13/20	0.820016690776147	3	FACETS	0.475	0.426	0.527	0.238	0.213	0.264	SUBCLONAL	1	FALSE	1	0.820016690776147	3		605	789	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938146	36938146	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367774391	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	37	799	3	ENST00000361632.4:c.815C>T	p.Pro272Leu	p.P272L	ENST00000361632		272	cCg/cTg	6/16	0.820016690776147	1	FACETS	0.142	0.116	0.17	0.142	0.116	0.17	SUBCLONAL	1	FALSE	0	0.820016690776147	1		802	376	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814593	43814593	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1431767792	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	85	674	0	ENST00000372470.3:c.1388C>T	p.Ala463Val	p.A463V	ENST00000372470	NM_005373.2	463	gCc/gTc	9/12	0.429946221251633	5	FACETS	0.465	0.409	0.524			1	INDETERMINATE	1	FALSE	NA	0.820016690776147	5		674	995	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344730	65344730	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	31	397	0	ENST00000342505.4:c.307C>T	p.Leu103Phe	p.L103F	ENST00000342505	NM_002227.2	103	Ctc/Ttc	4/25	0.295976884769187	5	FACETS	0.308	0.248	0.376	0.103	0.082	0.126	INDETERMINATE	1	FALSE	2	0.820016690776147	5		397	547	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432426	78432426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	50	364	0	ENST00000370768.2:c.425G>A	p.Gly142Asp	p.G142D	ENST00000370768	NM_003902.3	142	gGc/gAc	7/20	0.295976884769187	5	FACETS	0.384	0.325	0.449	0.128	0.108	0.15	INDETERMINATE	1	FALSE	2	0.820016690776147	5		364	709	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981879	201981879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	98	1003	0	ENST00000359651.3:c.590C>T	p.Ser197Phe	p.S197F	ENST00000359651		197	tCc/tTc	4/8	0.820016690776147	3	FACETS	0.296	0.263	0.331	0.148	0.131	0.166	SUBCLONAL	1	FALSE	1	0.820016690776147	3		1003	1138	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675322	241675322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	69	615	0	ENST00000366560.3:c.500G>A	p.Gly167Asp	p.G167D	ENST00000366560	NM_000143.3	167	gGt/gAt	4/10	0.820016690776147	3	FACETS	0.282	0.245	0.323	0.141	0.122	0.162	SUBCLONAL	1	FALSE	1	0.820016690776147	3		615	840	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670476	246670476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	48	662	0	ENST00000388985.4:c.44G>A	p.Gly15Glu	p.G15E	ENST00000388985		15	gGa/gAa	1/12	0.820016690776147	3	FACETS	0.195	0.164	0.229	0.097	0.082	0.115	SUBCLONAL	1	FALSE	1	0.820016690776147	3		662	847	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852332	63852332	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	104	622	0	ENST00000279873.7:c.3110C>T	p.Ser1037Phe	p.S1037F	ENST00000279873	NM_032199.2	1037	tCc/tTc	10/10	0.810910227205268	4	FACETS	0.458	0.409	0.511	0.229	0.204	0.256	SUBCLONAL	1	FALSE	2	0.820016690776147	4		622	1007	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720846	89720846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	45	452	0	ENST00000371953.3:c.997G>A	p.Ala333Thr	p.A333T	ENST00000371953	NM_000314.4	333	Gcc/Acc	8/9	0.396167050282503	5	FACETS	0.309	0.259	0.365	0.103	0.086	0.122	INDETERMINATE	1	FALSE	2	0.820016690776147	5		452	792	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69458652	69458652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1565225289	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1233	96	733	0	ENST00000227507.2:c.467C>T	p.Thr156Ile	p.T156I	ENST00000227507	NM_053056.2	156	aCc/aTc	3/5	0.820016690776147	4	FACETS	0.321	0.284	0.36	0.16	0.142	0.18	SUBCLONAL	1	FALSE	2	0.820016690776147	4		733	1329	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465991	69465991	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1259	72	894	2	ENST00000227507.2:c.829G>A	p.Glu277Lys	p.E277K	ENST00000227507	NM_053056.2	277	Gag/Aag	5/5	0.820016690776147	4	FACETS	0.24	0.209	0.274	0.12	0.104	0.137	SUBCLONAL	1	FALSE	2	0.820016690776147	4		896	1331	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142585	119142585	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	97	378	0	ENST00000264033.4:c.584G>A	p.Gly195Glu	p.G195E	ENST00000264033	NM_005188.3	195	gGg/gAg	3/16	0.820016690776147	4	FACETS	0.481	0.428	0.538			1	SUBCLONAL	1	FALSE	NA	0.820016690776147	4		378	895	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	443503	443503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	95	643	0	ENST00000399788.2:c.1394G>A	p.Gly465Asp	p.G465D	ENST00000399788	NM_001042603.1	465	gGt/gAt	11/28	0.820016690776147	4	FACETS	0.393	0.349	0.441	0.197	0.174	0.221	SUBCLONAL	1	FALSE	2	0.820016690776147	4		643	1072	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18747504	18747504	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1299386474	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	52	379	0	ENST00000266497.5:c.3964+1G>A		p.X1322_splice	ENST00000266497		1322			0.396167050282503	5	FACETS	0.44	0.374	0.512	0.147	0.124	0.171	INDETERMINATE	1	FALSE	2	0.820016690776147	5		379	643	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912615	32912615	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	146	577	0	ENST00000380152.3:c.4123G>A	p.Glu1375Lys	p.E1375K	ENST00000380152		1375	Gag/Aag	11/27	0.694600596121444	4	FACETS	0.534	0.486	0.585	0.267	0.243	0.293	SUBCLONAL	1	FALSE	2	0.820016690776147	4		577	1213	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434983	110434983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1424684268	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1373	97	1005	2	ENST00000375856.3:c.3418C>T	p.Pro1140Ser	p.P1140S	ENST00000375856	NM_003749.2	1140	Ccg/Tcg	1/2	0.429946221251633	5	FACETS	0.359	0.318	0.402			1	INDETERMINATE	1	FALSE	NA	0.820016690776147	5		1007	1470	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590961	95590961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	28	292	0	ENST00000393063.1:c.948G>A	p.Trp316Ter	p.W316*	ENST00000393063	NM_030621.3	316	tgG/tgA	9/28	0.820016690776147	2	FACETS	0.171	0.136	0.211	0.086	0.068	0.106	SUBCLONAL	1	FALSE	0	0.820016690776147	2		292	399	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38616969	38616969	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	54	381	1	ENST00000299084.4:c.382C>T	p.Pro128Ser	p.P128S	ENST00000299084	NM_152594.2	128	Ccc/Tcc	4/7	0.295976884769187	5	FACETS	0.428	0.365	0.498	0.143	0.121	0.166	INDETERMINATE	1	FALSE	2	0.820016690776147	5		382	686	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643429	38643429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	65	613	0	ENST00000299084.4:c.899C>T	p.Thr300Ile	p.T300I	ENST00000299084	NM_152594.2	300	aCt/aTt	7/7	0.295976884769187	5	FACETS	0.36	0.311	0.413	0.12	0.103	0.138	INDETERMINATE	1	FALSE	2	0.820016690776147	5		613	983	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961148	41961148	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	37	371	0	ENST00000219905.7:c.56G>A	p.Gly19Glu	p.G19E	ENST00000219905	NM_001164273.1	19	gGa/gAa	2/24	0.295976884769187	5	FACETS	0.361	0.297	0.433	0.12	0.099	0.145	INDETERMINATE	1	FALSE	2	0.820016690776147	5		371	557	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43783918	43783918	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	126	639	0	ENST00000382044.4:c.320G>A	p.Gly107Asp	p.G107D	ENST00000382044	NM_001141980.1	107	gGt/gAt	4/28	0.295976884769187	5	FACETS	0.618	0.558	0.681	0.206	0.186	0.227	INDETERMINATE	1	FALSE	2	0.820016690776147	5		639	1109	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292785	91292785	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1275	73	664	0	ENST00000355112.3:c.287G>A	p.Gly96Glu	p.G96E	ENST00000355112	NM_000057.2	96	gGa/gAa	3/22	0.820016690776147	4	FACETS	0.24	0.209	0.274			1	SUBCLONAL	1	FALSE	NA	0.820016690776147	4		664	1348	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396616	396616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	96	682	0	ENST00000262320.3:c.410G>A	p.Arg137Lys	p.R137K	ENST00000262320	NM_003502.3	137	aGg/aAg	2/11	0.694600596121444	4	FACETS	0.448	0.398	0.501	0.224	0.199	0.251	SUBCLONAL	1	FALSE	2	0.820016690776147	4		682	952	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778264	3778264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766219870	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	76	575	0	ENST00000262367.5:c.6784G>A	p.Gly2262Ser	p.G2262S	ENST00000262367	NM_004380.2	2262	Ggc/Agc	31/31	0.694600596121444	4	FACETS	0.405	0.354	0.46	0.202	0.177	0.23	SUBCLONAL	1	FALSE	2	0.820016690776147	4		575	833	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821383	72821383	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	44	527	0	ENST00000268489.5:c.10792C>T	p.Pro3598Ser	p.P3598S	ENST00000268489	NM_006885.3	3598	Cct/Tct	10/10	0.704052543273126	3	FACETS	0.235	0.196	0.278	0.117	0.098	0.139	SUBCLONAL	1	FALSE	1	0.820016690776147	3		527	644	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821875	72821875	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745443545	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	41	480	0	ENST00000268489.5:c.10300C>T	p.Leu3434Phe	p.L3434F	ENST00000268489	NM_006885.3	3434	Ctc/Ttc	10/10	0.704052543273126	3	FACETS	0.208	0.173	0.248	0.104	0.086	0.124	SUBCLONAL	1	FALSE	1	0.820016690776147	3		480	677	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004753	16004753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	153	627	0	ENST00000268712.3:c.2501C>T	p.Ser834Phe	p.S834F	ENST00000268712	NM_006311.3	834	tCt/tTt	20/46	0.764866152094176	4	FACETS	0.609	0.556	0.664			1	SUBCLONAL	1	FALSE	NA	0.820016690776147	4		627	1116	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554542	29554542	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	29	308	2	ENST00000356175.3:c.2327C>T	p.Ala776Val	p.A776V	ENST00000356175	NM_000267.3	776	gCt/gTt	20/57	0.820016690776147	4	FACETS	0.23	0.184	0.283	0.115	0.092	0.142	SUBCLONAL	1	FALSE	2	0.820016690776147	4		310	560	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264353	30264353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	40	307	0	ENST00000322652.5:c.88G>A	p.Ala30Thr	p.A30T	ENST00000322652	NM_015355.2	30	Gcg/Acg	1/16	0.820016690776147	4	FACETS	0.34	0.282	0.405	0.17	0.141	0.203	SUBCLONAL	1	FALSE	2	0.820016690776147	4		307	522	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619211	37619211	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	51	540	0	ENST00000447079.4:c.887G>A	p.Ser296Asn	p.S296N	ENST00000447079	NM_015083.1	296	aGt/aAt	1/14	0.820016690776147	4	FACETS	0.26	0.22	0.304	0.13	0.11	0.152	SUBCLONAL	1	FALSE	2	0.820016690776147	4		540	870	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41199668	41199668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1328	121	848	0	ENST00000357654.3:c.5459G>A	p.Gly1820Asp	p.G1820D	ENST00000357654	NM_007294.3	1820	gGc/gAc	22/23	0.820016690776147	4	FACETS	0.371	0.333	0.41	0.185	0.166	0.205	SUBCLONAL	1	FALSE	2	0.820016690776147	4		848	1449	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761160	59761160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	107	602	0	ENST00000259008.2:c.3247C>T	p.Leu1083Phe	p.L1083F	ENST00000259008	NM_032043.2	1083	Ctt/Ttt	20/20	0.820016690776147	4	FACETS	0.404	0.361	0.45	0.202	0.18	0.225	SUBCLONAL	1	FALSE	2	0.820016690776147	4		602	1175	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295223	15295223	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1374631853	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1335	77	1007	1	ENST00000263388.2:c.2449C>T	p.Pro817Ser	p.P817S	ENST00000263388	NM_000435.2	817	Ccc/Tcc	16/33	0.694600596121444	4	FACETS	0.242	0.211	0.275	0.121	0.105	0.138	SUBCLONAL	1	FALSE	2	0.820016690776147	4		1008	1412	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227588	36227588	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	63	458	0	ENST00000222270.7:c.7160-3C>T		p.X2387_splice	ENST00000222270	NM_014727.1	2387			0.694600596121444	4	FACETS	0.446	0.385	0.512	0.223	0.192	0.256	SUBCLONAL	1	FALSE	2	0.820016690776147	4		458	627	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794989	42794989	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1032211455	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	166	825	1	ENST00000575354.2:c.2069C>T	p.Pro690Leu	p.P690L	ENST00000575354	NM_015125.3	690	cCc/cTc	10/20	0.820016690776147	2	FACETS	0.543	0.5	0.589	0.272	0.25	0.295	SUBCLONAL	1	FALSE	0	0.820016690776147	2		826	745	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797375	42797375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs970235621	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	61	885	3	ENST00000575354.2:c.3737G>A	p.Ser1246Asn	p.S1246N	ENST00000575354	NM_015125.3	1246	aGc/aAc	15/20	0.820016690776147	2	FACETS	0.198	0.17	0.228	0.099	0.085	0.114	SUBCLONAL	1	FALSE	0	0.820016690776147	2		888	752	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909442	50909442	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	128	814	0	ENST00000440232.2:c.1246C>T	p.Gln416Ter	p.Q416*	ENST00000440232	NM_002691.3	416	Caa/Taa	11/27	0.820016690776147	2	FACETS	0.529	0.481	0.579	0.265	0.24	0.29	SUBCLONAL	1	FALSE	0	0.820016690776147	2		814	590	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719881	52719881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373680053	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	56	797	0	ENST00000322088.6:c.1093C>T	p.Leu365Phe	p.L365F	ENST00000322088	NM_014225.5	365	Ctc/Ttc	9/15	0.820016690776147	2	FACETS	0.21	0.179	0.244	0.105	0.089	0.122	SUBCLONAL	1	FALSE	0	0.820016690776147	2		797	650	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965017	25965017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	53	491	0	ENST00000435504.4:c.4189C>T	p.Pro1397Ser	p.P1397S	ENST00000435504		1397	Cct/Tct	13/13	0.820016690776147	4	FACETS	0.242	0.205	0.282	0.121	0.102	0.141	SUBCLONAL	1	FALSE	2	0.820016690776147	4		491	974	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026542	48026542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	47	443	1	ENST00000234420.5:c.1420G>A	p.Val474Met	p.V474M	ENST00000234420	NM_000179.2	474	Gtg/Atg	4/10	0.820016690776147	4	FACETS	0.251	0.211	0.296	0.126	0.105	0.148	SUBCLONAL	1	FALSE	2	0.820016690776147	4		444	831	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388723	31388723	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	60	561	0	ENST00000328111.2:c.1988G>A	p.Gly663Asp	p.G663D	ENST00000328111	NM_006892.3	663	gGc/gAc	18/23	0.463162624713664	5	FACETS	0.391	0.336	0.452	0.13	0.112	0.151	INDETERMINATE	1	FALSE	2	0.820016690776147	5		561	834	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39746851	39746851	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	32	407	0	ENST00000361337.2:c.1865C>T	p.Ala622Val	p.A622V	ENST00000361337	NM_003286.2	622	gCc/gTc	18/21	0.463162624713664	5	FACETS	0.277	0.224	0.337	0.092	0.074	0.113	INDETERMINATE	1	FALSE	2	0.820016690776147	5		407	628	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319959	62319959	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	45	610	0	ENST00000360203.5:c.1800+1G>A		p.X600_splice	ENST00000360203	NM_001283009.1	600			0.820016690776147	2	FACETS	0.201	0.168	0.237	0.101	0.084	0.119	SUBCLONAL	1	FALSE	0	0.820016690776147	2		610	546	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845378	42845378	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	68	655	1	ENST00000398585.3:c.884G>A	p.Gly295Asp	p.G295D	ENST00000398585	NM_001135099.1	295	gGc/gAc	9/14	0.820016690776147	4	FACETS	0.251	0.217	0.288	0.126	0.108	0.144	SUBCLONAL	1	FALSE	2	0.820016690776147	4		656	1201	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41521971	41521971	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	69	742	1	ENST00000263253.7:c.833C>T	p.Thr278Ile	p.T278I	ENST00000263253	NM_001429.3	278	aCt/aTt	3/31	0.396167050282503	5	FACETS	0.302	0.262	0.346	0.101	0.087	0.116	INDETERMINATE	1	FALSE	2	0.820016690776147	5		743	1241	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181903	38181903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	43	387	1	ENST00000396334.3:c.527C>T	p.Ala176Val	p.A176V	ENST00000396334	NM_002468.4	176	gCc/gTc	3/5	0.820016690776147	4	FACETS	0.27	0.225	0.32	0.135	0.112	0.16	SUBCLONAL	1	FALSE	2	0.820016690776147	4		388	706	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456451	89456451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	51	365	0	ENST00000336596.2:c.1627G>A	p.Val543Ile	p.V543I	ENST00000336596	NM_005233.5	543	Gtc/Atc	8/17	0.373843041078178	5	FACETS	0.409	0.346	0.477			1	INDETERMINATE	1	FALSE	NA	0.820016690776147	5		365	679	SUCCESS
ATR	545	MSKCC	GRCh37	3	142180802	142180802	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568255965	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	42	364	0	ENST00000350721.4:c.7172C>T	p.Thr2391Ile	p.T2391I	ENST00000350721	NM_001184.3	2391	aCc/aTc	42/47	0.396167050282503	5	FACETS	0.315	0.262	0.374	0.105	0.087	0.125	INDETERMINATE	1	FALSE	2	0.820016690776147	5		364	725	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31521267	31521267	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1214	64	544	0	ENST00000344624.3:c.910G>A	p.Glu304Lys	p.E304K	ENST00000344624		304	Gaa/Aaa	3/33	0.820016690776147	4	FACETS	0.222	0.191	0.256	0.074	0.063	0.086	SUBCLONAL	1	FALSE	1	0.820016690776147	4		544	1278	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818762	170818762	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	85	389	0	ENST00000296930.5:c.311G>A	p.Cys104Tyr	p.C104Y	ENST00000296930	NM_002520.6	104	tGt/tAt	4/11	0.820016690776147	3	FACETS	0.475	0.42	0.533	0.237	0.21	0.267	SUBCLONAL	1	FALSE	1	0.820016690776147	3		389	616	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30682879	30682879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	100	712	0	ENST00000376406.3:c.74G>A	p.Arg25Lys	p.R25K	ENST00000376406	NM_014641.2	25	aGg/aAg	2/15	0.820016690776147	4	FACETS	0.36	0.32	0.402	0.18	0.16	0.201	SUBCLONAL	1	FALSE	2	0.820016690776147	4		712	1234	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109309810	109309810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	56	718	0	ENST00000436639.2:c.1505C>T	p.Thr502Ile	p.T502I	ENST00000436639	NM_014454.2	502	aCt/aTt	9/10	NA	2	FACETS	0.174	0.149	0.203			1	INDETERMINATE	1	FALSE	NA	0.820016690776147	2		718	783	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718196	117718196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	28	553	0	ENST00000368508.3:c.661C>T	p.Pro221Ser	p.P221S	ENST00000368508	NM_002944.2	221	Cca/Tca	7/43	NA	2	FACETS	0.132	0.105	0.163			1	INDETERMINATE	1	FALSE	NA	0.820016690776147	2		553	519	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519191	137519191	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	22	284	0	ENST00000367739.4:c.1447G>A	p.Glu483Lys	p.E483K	ENST00000367739	NM_000416.2	483	Gaa/Aaa	7/7	0.820016690776147	2	FACETS	0.167	0.129	0.211	0.083	0.064	0.106	SUBCLONAL	1	FALSE	0	0.820016690776147	2		284	322	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099397	157099397	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	58	240	0	ENST00000346085.5:c.334C>T	p.Gln112Ter	p.Q112*	ENST00000346085	NM_020732.3	112	Cag/Tag	1/20	0.820016690776147	2	FACETS	0.437	0.377	0.5	0.218	0.188	0.25	SUBCLONAL	1	FALSE	0	0.820016690776147	2		240	324	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6029587	6029587	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	46	574	0	ENST00000265849.7:c.989-1G>A		p.X330_splice	ENST00000265849	NM_000535.5	330			0.820016690776147	2	FACETS	0.191	0.161	0.225	0.096	0.08	0.113	SUBCLONAL	1	FALSE	0	0.820016690776147	2		574	586	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035256	6035256	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	25	486	0	ENST00000265849.7:c.812G>A	p.Gly271Asp	p.G271D	ENST00000265849	NM_000535.5	271	gGt/gAt	8/15	0.820016690776147	2	FACETS	0.134	0.105	0.167	0.067	0.052	0.084	SUBCLONAL	1	FALSE	0	0.820016690776147	2		486	455	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042160	6042160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	109	577	0	ENST00000265849.7:c.461G>A	p.Gly154Glu	p.G154E	ENST00000265849	NM_000535.5	154	gGg/gAg	5/15	0.820016690776147	2	FACETS	0.492	0.443	0.544	0.246	0.221	0.272	SUBCLONAL	1	FALSE	0	0.820016690776147	2		577	540	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043351	6043351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	53	308	0	ENST00000265849.7:c.323G>A	p.Gly108Glu	p.G108E	ENST00000265849	NM_000535.5	108	gGg/gAg	4/15	0.820016690776147	2	FACETS	0.497	0.428	0.572	0.249	0.214	0.286	SUBCLONAL	1	FALSE	0	0.820016690776147	2		308	260	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6045522	6045522	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1064795705	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	15	147	0	ENST00000265849.7:c.163+1G>A		p.X55_splice	ENST00000265849	NM_000535.5	55			0.820016690776147	2	FACETS	0.197	0.144	0.26	0.098	0.072	0.13	SUBCLONAL	1	FALSE	0	0.820016690776147	2		147	186	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205559	38205559	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	170	779	0	ENST00000317025.8:c.131G>A	p.Gly44Asp	p.G44D	ENST00000317025	NM_023034.1	44	gGt/gAt	2/24	0.317241477668797	6	FACETS	0.826	0.758	0.898	0.275	0.252	0.3	INDETERMINATE	1	FALSE	3	0.820016690776147	6		779	1325	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69011966	69011966	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756096317	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1371	88	842	0	ENST00000288368.4:c.2603C>T	p.Thr868Ile	p.T868I	ENST00000288368	NM_024870.2	868	aCc/aTc	23/40	0.317241477668797	6	FACETS	0.388	0.342	0.438	0.129	0.114	0.146	INDETERMINATE	1	FALSE	3	0.820016690776147	6		842	1459	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751223	128751223	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751130055	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	72	447	0	ENST00000377970.2:c.760G>A	p.Val254Met	p.V254M	ENST00000377970	NM_002467.4	254	Gtg/Atg	2/3	0.820016690776147	5	FACETS	0.405	0.353	0.462	0.135	0.117	0.154	SUBCLONAL	1	FALSE	2	0.820016690776147	5		447	966	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521418	8521418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	187	744	0	ENST00000356435.5:c.820G>A	p.Glu274Lys	p.E274K	ENST00000356435		274	Gaa/Aaa	9/35	0.820016690776147	3	FACETS	0.621	0.573	0.671	0.207	0.191	0.224	SUBCLONAL	1	FALSE	0	0.820016690776147	3		744	1035	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249455	110249455	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1330792856	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1792	170	1072	1	ENST00000374672.4:c.1118C>T	p.Ser373Phe	p.S373F	ENST00000374672	NM_004235.4	373	tCc/tTc	4/5	0.787398655766356	5	FACETS	0.471	0.431	0.513	0.157	0.143	0.171	SUBCLONAL	1	FALSE	2	0.820016690776147	5		1073	1962	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797246	135797246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264782606	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	41	314	0	ENST00000298552.3:c.623G>A	p.Ser208Asn	p.S208N	ENST00000298552	NM_001162426.1	208	aGt/aAt	7/23	0.787398655766356	5	FACETS	0.29	0.241	0.345	0.097	0.08	0.115	SUBCLONAL	1	FALSE	2	0.820016690776147	5		314	769	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402779	139402779	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1695	186	971	1	ENST00000277541.6:c.3230C>T	p.Thr1077Ile	p.T1077I	ENST00000277541	NM_017617.3	1077	aCc/aTc	20/34	0.787398655766356	5	FACETS	0.538	0.494	0.583	0.179	0.164	0.195	SUBCLONAL	1	FALSE	2	0.820016690776147	5		972	1881	SUCCESS
AR	367	MSKCC	GRCh37	X	66766346	66766346	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003822-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	79	228	0	ENST00000374690.3:c.1358G>A	p.Gly453Asp	p.G453D	ENST00000374690	NM_000044.3	453	gGt/gAt	1/8	0.317241477668797	6	FACETS	1	0.954	1	0.388	0.342	0.436	INDETERMINATE	1	FALSE	3	0.820016690776147	6		228	437	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0004066-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	87	641	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.952	0.841	1	0.952	0.841	1	CLONAL	1	TRUE	1	0.2	2		641	914	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241677	55241677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504256	NA	P-0004066-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	94	550	0	ENST00000275493.2:c.2125G>A	p.Glu709Lys	p.E709K	ENST00000275493	NM_005228.3	709	Gaa/Aaa	18/28	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.2	2		550	898	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577544	7577544	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587780074	NA	P-0004066-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	67	606	0	ENST00000269305.4:c.737T>A	p.Met246Lys	p.M246K	ENST00000269305	NM_001126112.2	246	aTg/aAg	7/11	1	2	FACETS	0.737	0.639	0.844	0.737	0.639	0.844	SUBCLONAL	1	TRUE	1	0.2	2		606	909	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0004270-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	601	588	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.705543206569951	2		589	1516	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0004270-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	401	403	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.375184539690393	1	FACETS	0.886	0.848	0.924	0.886	0.848	0.924	INDETERMINATE	1	TRUE	0	0.705543206569951	1		403	830	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890142	76890145	+	frameshift_variant	Frame_Shift_Del	DEL	TTTC	TTTC	-	novel	NA	P-0004270-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	622	289	0	ENST00000373344.5:c.4749_4752del	p.Lys1583AsnfsTer22	p.K1583Nfs*22	ENST00000373344	NM_000489.3	1583	aaGAAA/aa	17/35	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.705543206569951	1		289	879	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691003	NA	P-0004270-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	409	342	0	ENST00000269305.4:c.96+1G>T		p.X32_splice	ENST00000269305	NM_001126112.2	32			1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.705543206569951	2		342	1025	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0004270-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	10	191	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	0.375184539690393	1	FACETS	0.063	0.042	0.089	0.063	0.042	0.089	INDETERMINATE	1	TRUE	0	0.705543206569951	1		191	291	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490559	20490559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs2273914	NA	P-0004270-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	591	430	0	ENST00000346618.3:c.1296G>C	p.Glu432Asp	p.E432D	ENST00000346618	NM_001949.4	432	gaG/gaC	7/7	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.705543206569951	2		430	1525	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199678	138199678	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004270-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	175	318	0	ENST00000237289.4:c.1096G>C	p.Glu366Gln	p.E366Q	ENST00000237289	NM_001270507.1	366	Gag/Cag	7/9	1	2	FACETS	0.441	0.405	0.478	0.441	0.405	0.478	SUBCLONAL	1	TRUE	1	0.705543206569951	2		318	1126	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821822	59821822	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs750033391	NA	P-0004270-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	148	451	0	ENST00000259008.2:c.2228A>G	p.Tyr743Cys	p.Y743C	ENST00000259008	NM_032043.2	743	tAt/tGt	15/20	1	2	FACETS	0.425	0.388	0.465	0.425	0.388	0.465	SUBCLONAL	1	TRUE	1	0.705543206569951	2		451	986	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792649	33792649	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004270-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	44	54	0	ENST00000498907.2:c.672C>A	p.His224Gln	p.H224Q	ENST00000498907	NM_004364.3	224	caC/caA	1/1	1	2	FACETS	0.531	0.449	0.62	0.531	0.449	0.62	SUBCLONAL	1	TRUE	1	0.705543206569951	2		54	235	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035920	47035920	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004282-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	435	298	0	ENST00000377604.3:c.598C>T	p.Gln200Ter	p.Q200*	ENST00000377604	NM_001204468.1	200	Cag/Tag	7/24	0.116880446550047	2	FACETS	0.925	0.896	0.954			1	INDETERMINATE	4	TRUE	NA	0.382787580926751	2		298	614	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591288	67591295	+	frameshift_variant	Frame_Shift_Del	DEL	GAGTGGTT	GAGTGGTT	-	novel	NA	P-0004282-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	223	425	0	ENST00000274335.5:c.1787_1794del	p.Glu596GlyfsTer3	p.E596Gfs*3	ENST00000274335		596	GAGTGGTTg/g	13/15	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.382787580926751	2		425	815	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031973	26031973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004388-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1498	440	1660	0	ENST00000244661.2:c.316G>C	p.Glu106Gln	p.E106Q	ENST00000244661	NM_003537.3	106	Gag/Cag	1/1	0.293950531454598	3	FACETS	0.886	0.842	0.931	0.886	0.842	0.931	CLONAL	2	TRUE	1	0.293950531454598	3		1660	1938	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0004388-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	307	1077	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.237026156612804	3	FACETS	0.851	0.801	0.903	0.851	0.801	0.903	CLONAL	2	TRUE	1	0.293950531454598	3		1077	1407	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004388-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	194	1247	0	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	0.258117737202779	1	FACETS	0.814	0.751	0.88	0.814	0.751	0.88	CLONAL	1	TRUE	0	0.293950531454598	1		1247	1383	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781634	9781634	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004388-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	78	686	0	ENST00000377346.4:c.1944C>G	p.Phe648Leu	p.F648L	ENST00000377346	NM_005026.3	648	ttC/ttG	15/24	1	2	FACETS	0.682	0.599	0.772	0.682	0.599	0.772	SUBCLONAL	1	TRUE	1	0.293950531454598	2		686	778	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932338	36932338	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004388-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1473	252	1498	0	ENST00000361632.4:c.2131T>C	p.Ser711Pro	p.S711P	ENST00000361632		711	Tcc/Ccc	16/16	1	2	FACETS	0.994	0.927	1	0.994	0.927	1	CLONAL	1	TRUE	1	0.293950531454598	2		1498	1725	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682991	241682991	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1226883651	NA	P-0004388-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	92	535	0	ENST00000366560.3:c.32C>G	p.Ser11Trp	p.S11W	ENST00000366560	NM_000143.3	11	tCg/tGg	1/10	NA	2	FACETS	0.813	0.722	0.91			1	INDETERMINATE	1	TRUE	NA	0.293950531454598	2		535	770	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226907	142226907	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004388-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	135	870	0	ENST00000350721.4:c.4897C>G	p.Leu1633Val	p.L1633V	ENST00000350721	NM_001184.3	1633	Cta/Gta	28/47	1	2	FACETS	0.955	0.867	1	0.955	0.867	1	CLONAL	1	TRUE	1	0.293950531454598	2		870	962	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549689	187549689	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004388-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	97	558	0	ENST00000441802.2:c.4552G>T	p.Glu1518Ter	p.E1518*	ENST00000441802	NM_005245.3	1518	Gag/Tag	8/27	1	2	FACETS	0.905	0.807	1	0.905	0.807	1	CLONAL	1	TRUE	1	0.293950531454598	2		558	729	SUCCESS
APC	324	MSKCC	GRCh37	5	112176446	112176446	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004388-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	94	565	0	ENST00000257430.4:c.5155G>C	p.Glu1719Gln	p.E1719Q	ENST00000257430	NM_000038.5	1719	Gag/Cag	16/16	0.293950531454598	3	FACETS	0.945	0.841	1	0.473	0.42	0.529	CLONAL	1	TRUE	1	0.293950531454598	3		565	776	SUCCESS
APC	324	MSKCC	GRCh37	5	112177184	112177184	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004388-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	93	588	0	ENST00000257430.4:c.5893C>G	p.His1965Asp	p.H1965D	ENST00000257430	NM_000038.5	1965	Cat/Gat	16/16	0.293950531454598	3	FACETS	0.912	0.81	1	0.456	0.405	0.51	CLONAL	1	TRUE	1	0.293950531454598	3		588	796	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528335	157528335	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004388-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1321	134	1113	0	ENST00000346085.5:c.6060G>C	p.Leu2020Phe	p.L2020F	ENST00000346085	NM_020732.3	2020	ttG/ttC	20/20	0.237026156612804	3	FACETS	0.719	0.651	0.791	0.359	0.325	0.396	SUBCLONAL	1	TRUE	1	0.293950531454598	3		1113	1455	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381439	81381439	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004388-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	126	953	0	ENST00000222390.5:c.622G>C	p.Glu208Gln	p.E208Q	ENST00000222390	NM_000601.4	208	Gaa/Caa	5/18	1	2	FACETS	0.809	0.731	0.891	0.809	0.731	0.891	CLONAL	1	TRUE	1	0.293950531454598	2		953	1060	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874386	151874386	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004388-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	158	909	0	ENST00000262189.6:c.8152G>C	p.Glu2718Gln	p.E2718Q	ENST00000262189	NM_170606.2	2718	Gaa/Caa	38/59	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.293950531454598	2		909	1049	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403413	139403413	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004388-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	121	906	0	ENST00000277541.6:c.3080C>T	p.Ser1027Leu	p.S1027L	ENST00000277541	NM_017617.3	1027	tCa/tTa	19/34	1	2	FACETS	0.869	0.784	0.959	0.869	0.784	0.959	CLONAL	1	TRUE	1	0.293950531454598	2		906	947	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692794	89692794	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121909238	NA	P-0004388-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	87	467	0	ENST00000371953.3:c.278A>G	p.His93Arg	p.H93R	ENST00000371953	NM_000314.4	93	cAt/cGt	5/9	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.293950531454598	2		467	525	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433246	49433246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs974587965	NA	P-0004388-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	145	903	1	ENST00000301067.7:c.8201G>A	p.Arg2734Gln	p.R2734Q	ENST00000301067	NM_003482.3	2734	cGa/cAa	32/54	1	2	FACETS	0.951	0.867	1	0.951	0.867	1	CLONAL	1	TRUE	1	0.293950531454598	2		904	1037	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811655	102811655	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004388-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1307	191	1424	0	ENST00000307046.8:c.529G>C	p.Glu177Gln	p.E177Q	ENST00000307046	NM_001111285.1	177	Gag/Cag	4/4	1	2	FACETS	0.868	0.8	0.939	0.868	0.8	0.939	CLONAL	1	TRUE	1	0.293950531454598	2		1424	1498	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873811	35873811	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004388-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	126	725	0	ENST00000216797.5:c.40G>C	p.Glu14Gln	p.E14Q	ENST00000216797	NM_020529.2	14	Gag/Cag	1/6	0.293950531454598	3	FACETS	0.954	0.862	1	0.477	0.431	0.526	CLONAL	1	TRUE	1	0.293950531454598	3		725	1031	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99460028	99460028	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1427403890	NA	P-0004388-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	141	790	0	ENST00000268035.6:c.2124G>C	p.Glu708Asp	p.E708D	ENST00000268035	NM_000875.3	708	gaG/gaC	10/21	1	2	FACETS	0.997	0.908	1	0.997	0.908	1	CLONAL	1	TRUE	1	0.293950531454598	2		790	962	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56792541	56792541	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004388-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	168	1262	0	ENST00000308159.5:c.271G>C	p.Glu91Gln	p.E91Q	ENST00000308159	NM_014669.4	91	Gag/Cag	3/22	0.258117737202779	1	FACETS	0.728	0.667	0.791	0.728	0.667	0.791	SUBCLONAL	1	TRUE	0	0.293950531454598	1		1262	1340	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276185	15276185	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004388-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	114	742	0	ENST00000263388.2:c.5809G>C	p.Glu1937Gln	p.E1937Q	ENST00000263388	NM_000435.2	1937	Gag/Cag	31/33	1	2	FACETS	0.796	0.715	0.881	0.796	0.715	0.881	SUBCLONAL	1	TRUE	1	0.293950531454598	2		742	975	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651603	48651603	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004388-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1334	178	1385	1	ENST00000376670.3:c.769C>T	p.Gln257Ter	p.Q257*	ENST00000376670	NM_002049.3	257	Cag/Tag	5/6	0.258117737202779	1	FACETS	0.683	0.627	0.742	0.683	0.627	0.742	SUBCLONAL	1	TRUE	0	0.293950531454598	1		1386	1512	SUCCESS
AR	367	MSKCC	GRCh37	X	66765193	66765193	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004388-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	22	335	0	ENST00000374690.3:c.205C>T	p.Gln69Ter	p.Q69*	ENST00000374690	NM_000044.3	69	Cag/Tag	1/8	0.258117737202779	1	FACETS	0.333	0.257	0.42	0.333	0.257	0.42	SUBCLONAL	1	TRUE	0	0.293950531454598	1		335	384	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061192	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0004388-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	133	366	0	ENST00000250448.2:c.797_798del	p.Phe266Ter	p.F266*	ENST00000250448	NM_004496.3	266	tTC/t	2/2	0.293950531454598	3	FACETS	1	0.922	1	1	0.922	1	CLONAL	2	TRUE	1	0.293950531454598	3		366	514	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333069	70333069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004388-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	90	989	0	ENST00000373644.4:c.974C>T	p.Ser325Phe	p.S325F	ENST00000373644	NM_030625.2	325	tCt/tTt	2/12	1	2	FACETS	0.477	0.422	0.537	0.477	0.422	0.537	SUBCLONAL	1	TRUE	1	0.293950531454598	2		989	1283	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856313	111856313	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004388-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	28	104	1	ENST00000341259.2:c.364G>T	p.Glu122Ter	p.E122*	ENST00000341259	NM_005475.2	122	Gag/Tag	2/8	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.293950531454598	2		105	133	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988592	41988592	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004388-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1330	102	1257	0	ENST00000219905.7:c.1384G>C	p.Asp462His	p.D462H	ENST00000219905	NM_001164273.1	462	Gac/Cac	3/24	1	2	FACETS	0.485	0.432	0.541	0.485	0.432	0.541	SUBCLONAL	1	TRUE	1	0.293950531454598	2		1257	1432	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643399	52643399	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	133	738	0	ENST00000394830.3:c.2497C>A	p.Arg833Ser	p.R833S	ENST00000394830	NM_018313.4	833	Cgc/Agc	17/30	0.249223032282482	3	FACETS	0.976	0.887	1	0.488	0.443	0.535	INDETERMINATE	1	TRUE	1	0.422799758481157	3		738	781	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338683	70338683	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	89	587	0	ENST00000374080.3:c.79C>G	p.Gln27Glu	p.Q27E	ENST00000374080		27	Cag/Gag	1/45	0.246351711226887	1	FACETS	0.814	0.721	0.914	0.814	0.721	0.914	CLONAL	1	TRUE	0	0.246351711226887	1		587	778	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233143	66233143	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0004790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	78	414	0	ENST00000273854.3:c.1857-1G>A		p.X619_splice	ENST00000273854	NM_004439.5	619			0.246351711226887	1	FACETS	0.812	0.713	0.918	0.812	0.713	0.918	CLONAL	1	TRUE	0	0.246351711226887	1		414	684	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874026	151874026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	172	521	0	ENST00000262189.6:c.8512G>A	p.Glu2838Lys	p.E2838K	ENST00000262189	NM_170606.2	2838	Gaa/Aaa	38/59	0.154934035297702	2	FACETS	1	0.985	1	0.657	0.604	0.713	CLONAL	1	TRUE	0	0.246351711226887	2		521	1062	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874065	151874065	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	200	534	0	ENST00000262189.6:c.8473G>T	p.Glu2825Ter	p.E2825*	ENST00000262189	NM_170606.2	2825	Gaa/Taa	38/59	0.154934035297702	2	FACETS	1	0.989	1	0.693	0.641	0.747	CLONAL	1	TRUE	0	0.246351711226887	2		534	1172	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435438	110435438	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	43	260	0	ENST00000375856.3:c.2963C>G	p.Ser988Cys	p.S988C	ENST00000375856	NM_003749.2	988	tCt/tGt	1/2	1	2	FACETS	0.766	0.641	0.904	0.766	0.641	0.904	CLONAL	1	TRUE	1	0.246351711226887	2		260	456	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591933	48591933	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	82	383	0	ENST00000342988.3:c.1096C>G	p.Gln366Glu	p.Q366E	ENST00000342988	NM_005359.5	366	Caa/Gaa	9/12	1	2	FACETS	0.8	0.704	0.903	0.8	0.704	0.903	CLONAL	1	TRUE	1	0.246351711226887	2		383	832	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057937	27057937	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	67	439	0	ENST00000324856.7:c.1650del	p.Tyr551ThrfsTer68	p.Y551Tfs*68	ENST00000324856	NM_006015.4	549	Ccc/cc	3/20	1	2	FACETS	0.693	0.601	0.793	0.693	0.601	0.793	SUBCLONAL	1	TRUE	1	0.246351711226887	2		439	785	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177746	56177773	+	protein_altering_variant	In_Frame_Del	DEL	CATTTAGAGAAAACTGGAAAAGGATTAT	CATTTAGAGAAAACTGGAAAAGGATTAT	G	novel	NA	P-0004790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	64	475	0	ENST00000399503.3:c.2719_2746delinsG	p.His907_Cys916delinsGly	p.H907_C916delinsG	ENST00000399503	NM_005921.1	907	CATTTAGAGAAAACTGGAAAAGGATTATgt/Ggt	14/20	1	2	FACETS	0.549	0.474	0.631	0.549	0.474	0.631	SUBCLONAL	1	TRUE	1	0.246351711226887	2		475	947	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0004805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	146	559	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.343342631517402	1	FACETS	0.767	0.708	0.826	0.767	0.708	0.826	INDETERMINATE	1	TRUE	0	0.675983169444062	1		559	373	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111590	56111590	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs769021328	NA	P-0004805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	68	133	0	ENST00000399503.3:c.190A>G	p.Lys64Glu	p.K64E	ENST00000399503	NM_005921.1	64	Aaa/Gaa	1/20	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.675983169444062	2		133	193	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500965	8500965	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	74	681	0	ENST00000356435.5:c.1917T>A	p.Asn639Lys	p.N639K	ENST00000356435		639	aaT/aaA	13/35	0.343342631517402	1	FACETS	0.362	0.319	0.409	0.362	0.319	0.409	INDETERMINATE	1	TRUE	0	0.675983169444062	1		681	400	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0004851-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	541	457	1	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	1	2	FACETS	0.987	0.951	1	1	0.998	1	CLONAL	2	TRUE	1	0.505288232982063	2		458	1085	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0004851-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	193	342	0	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.505288232982063	1	FACETS	0.993	0.925	1	0.993	0.925	1	CLONAL	1	TRUE	0	0.505288232982063	1		342	575	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974721	21974721	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004851-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	213	368	2	ENST00000304494.5:c.106del	p.Ala36ArgfsTer17	p.A36Rfs*17	ENST00000304494	NM_000077.4	36	Gcg/cg	1/3	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.505288232982063	2		370	651	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056402	26056402	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004851-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	169	309	0	ENST00000343677.2:c.255G>C	p.Lys85Asn	p.K85N	ENST00000343677	NM_005319.3	85	aaG/aaC	1/1	0.505288232982063	3	FACETS	0.927	0.852	1	0.463	0.426	0.503	CLONAL	1	TRUE	1	0.505288232982063	3		309	904	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230752	53230752	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004851-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	353	343	2	ENST00000375401.3:c.2041C>T	p.Arg681Ter	p.R681*	ENST00000375401	NM_004187.3	681	Cga/Tga	14/26	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.505288232982063	1		345	713	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400827	72400827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004851-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	396	744	0	ENST00000357731.5:c.344C>A	p.Pro115Gln	p.P115Q	ENST00000357731	NM_173808.2	115	cCa/cAa	2/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.505288232982063	2		744	1496	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881518	111881518	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004851-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	203	412	1	ENST00000393256.3:c.196C>T	p.Pro66Ser	p.P66S	ENST00000393256	NM_006538.4	66	Cca/Tca	2/4	0.209065697501744	4	FACETS	1	0.986	1	0.631	0.585	0.679	INDETERMINATE	1	TRUE	2	0.505288232982063	4		413	958	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113307	209113307	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1465733605	NA	P-0004851-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	293	517	0	ENST00000345146.2:c.200A>G	p.His67Arg	p.H67R	ENST00000345146	NM_005896.2	67	cAt/cGt	4/10	1	2	FACETS	0.941	0.885	0.999	0.941	0.885	0.999	CLONAL	1	TRUE	1	0.505288232982063	2		517	1232	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056291	180056291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199942873	NA	P-0004851-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	306	583	2	ENST00000261937.6:c.953G>A	p.Arg318Gln	p.R318Q	ENST00000261937	NM_182925.4	318	cGa/cAa	7/30	0.246796500909638	1	FACETS	0.714	0.673	0.757	0.714	0.673	0.757	INDETERMINATE	1	TRUE	0	0.505288232982063	1		585	1267	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526712	106526712	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004851-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	187	320	1	ENST00000359195.3:c.3005C>A	p.Thr1002Lys	p.T1002K	ENST00000359195	NM_002649.2	1002	aCa/aAa	10/11	1	2	FACETS	0.913	0.844	0.983	0.913	0.844	0.983	CLONAL	1	TRUE	1	0.505288232982063	2		321	811	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371821	116371821	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004851-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	287	470	0	ENST00000397752.3:c.1300T>A	p.Phe434Ile	p.F434I	ENST00000397752	NM_000245.2	434	Ttc/Atc	3/21	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.505288232982063	2		470	1122	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883981	37883981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1357550606	NA	P-0004851-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	192	335	0	ENST00000269571.5:c.3452C>T	p.Ser1151Leu	p.S1151L	ENST00000269571		1151	tCg/tTg	27/27	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.505288232982063	2		335	738	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038563	47038563	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0004851-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	324	289	0	ENST00000377604.3:c.724+1G>C		p.X242_splice	ENST00000377604	NM_001204468.1	242			1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.505288232982063	1		289	655	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0004855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	105	358	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	0.346260490586253	2	FACETS	0.46	0.413	0.51	0.23	0.206	0.255	INDETERMINATE	1	TRUE	0	0.727621992079359	2		358	627	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039501	49039501	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	259	376	0	ENST00000267163.4:c.2486C>T	p.Ser829Leu	p.S829L	ENST00000267163	NM_000321.2	829	tCa/tTa	23/27	NA	2	FACETS	0.681	0.638	0.725			1	INDETERMINATE	1	TRUE	NA	0.727621992079359	2		376	1046	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90633720	90633720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	146	367	0	ENST00000330062.3:c.364C>T	p.Arg122Cys	p.R122C	ENST00000330062	NM_002168.2	122	Cgt/Tgt	3/11	0.495318222447193	1	FACETS	0.299	0.272	0.326	0.299	0.272	0.326	SUBCLONAL	1	TRUE	0	0.727621992079359	1		367	855	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035209	6035209	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0004946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	94	627	0	ENST00000265849.7:c.859A>T	p.Arg287Ter	p.R287*	ENST00000265849	NM_000535.5	287	Aga/Tga	8/15	1	2	FACETS	0.86	0.765	0.962	0.86	0.765	0.962	CLONAL	1	TRUE	1	0.290245260456111	2		627	753	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032029	10032029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747214620	NA	P-0004946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	64	719	4	ENST00000330684.3:c.794C>T	p.Thr265Met	p.T265M	ENST00000330684	NM_001134407.1	265	aCg/aTg	3/13	1	2	FACETS	0.593	0.512	0.68	0.593	0.512	0.68	SUBCLONAL	1	TRUE	1	0.290245260456111	2		723	744	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226809	2226809	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756329795	NA	P-0004946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	24	268	2	ENST00000398665.3:c.4289C>T	p.Ala1430Val	p.A1430V	ENST00000398665	NM_032482.2	1430	gCg/gTg	27/28	1	2	FACETS	0.404	0.316	0.506	0.404	0.316	0.506	SUBCLONAL	1	TRUE	1	0.290245260456111	2		270	409	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0004961-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	153	483	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.355925952503979	1	FACETS	0.925	0.847	1	0.925	0.847	1	CLONAL	1	TRUE	0	0.355925952503979	1		483	764	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0004961-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	161	559	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.333940744547368	1	FACETS	0.899	0.825	0.976	0.899	0.825	0.976	CLONAL	1	TRUE	0	0.355925952503979	1		559	827	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176338	24176338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004961-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1214	30	682	3	ENST00000263121.7:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000263121	NM_003073.3	377	Cgt/Tgt	9/9	1	2	FACETS	0.136	0.108	0.167	0.136	0.108	0.167	SUBCLONAL	1	TRUE	1	0.355925952503979	2		685	1244	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967476	38967476	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004961-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	140	472	0	ENST00000357387.3:c.1114G>T	p.Glu372Ter	p.E372*	ENST00000357387	NM_152756.3	372	Gag/Tag	13/38	0.355925952503979	3	FACETS	0.926	0.842	1	0.463	0.421	0.507	CLONAL	1	TRUE	1	0.355925952503979	3		472	1001	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560444	65560449	+	inframe_deletion	In_Frame_Del	DEL	TGGGAC	TGGGAC	-	novel	NA	P-0004961-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	167	550	0	ENST00000358664.4:c.148_153del	p.Val50_Pro51del	p.V50_P51del	ENST00000358664	NM_002382.4	50	GTCCCA/-	3/5	0.355925952503979	1	FACETS	0.84	0.772	0.912	0.84	0.772	0.912	CLONAL	1	TRUE	0	0.355925952503979	1		550	918	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0005257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	324	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.582299365769364	5	FACETS	0.858	0.815	0.9			1	CLONAL	3	TRUE	NA	0.700863218588815	5		371	737	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579463	7579463	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	187	457	0	ENST00000269305.4:c.224del	p.Pro75LeufsTer48	p.P75Lfs*48	ENST00000269305	NM_001126112.2	75	cCt/ct	4/11	0.700863218588815	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.700863218588815	1		457	346	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342596	87342596	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	111	493	0	ENST00000277120.3:c.881C>G	p.Ser294Cys	p.S294C	ENST00000277120		294	tCt/tGt	9/19	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.700863218588815	2		493	301	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762514	41762514	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	127	444	0	ENST00000301178.4:c.2194G>C	p.Val732Leu	p.V732L	ENST00000301178	NM_021913.4	732	Gtg/Ctg	18/20	0.700863218588815	1	FACETS	0.762	0.701	0.824	0.762	0.701	0.824	SUBCLONAL	1	TRUE	0	0.700863218588815	1		444	309	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54948488	54948488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	145	525	0	ENST00000312783.6:c.830G>A	p.Trp277Ter	p.W277*	ENST00000312783	NM_198436.1	277	tGg/tAg	8/10	NA	2	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.700863218588815	2		525	390	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922936	39922936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	181	716	0	ENST00000378444.4:c.3772G>A	p.Gly1258Ser	p.G1258S	ENST00000378444	NM_001123385.1	1258	Ggc/Agc	8/15	0.700863218588815	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.700863218588815	1		716	316	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411489	63411489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200798538	NA	P-0005257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	303	820	0	ENST00000330258.3:c.1678C>T	p.Arg560Trp	p.R560W	ENST00000330258	NM_152424.3	560	Cgg/Tgg	2/2	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.700863218588815	2		820	712	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573478	48573479	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0005257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	187	627	0	ENST00000342988.3:c.63_64del	p.His21GlnfsTer6	p.H21Qfs*6	ENST00000342988	NM_005359.5	21	cAT/c	2/12	0.700863218588815	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.700863218588815	1		627	326	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	58	589	1				ENST00000310581	NM_198253.2	-/1132			0.452138453771283	1	FACETS	0.73	0.651	0.808	0.73	0.651	0.808	INDETERMINATE	1	TRUE	0	0.834504239385561	1		590	111	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0005302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	241	403	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.865	0.812	0.918	0.865	0.812	0.918	CLONAL	1	TRUE	1	0.834504239385561	2		403	668	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723321	49723321	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs2985131	NA	P-0005302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	16	64	0	ENST00000449682.2:c.1222T>G	p.Trp408Gly	p.W408G	ENST00000449682	NM_020998.3	408	Tgg/Ggg	10/18	1	2	FACETS	0.599	0.455	0.76	0.599	0.455	0.76	SUBCLONAL	1	TRUE	1	0.834504239385561	2		64	64	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799051	42799051	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	185	426	0	ENST00000575354.2:c.4535G>T	p.Arg1512Leu	p.R1512L	ENST00000575354	NM_015125.3	1512	cGt/cTt	20/20	0.834504239385561	1	FACETS	0.897	0.85	0.943	0.897	0.85	0.943	CLONAL	1	TRUE	0	0.834504239385561	1		426	288	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378306	225378306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	131	413	0	ENST00000264414.4:c.589G>A	p.Gly197Arg	p.G197R	ENST00000264414	NM_003590.4	197	Gga/Aga	5/16	1	2	FACETS	0.467	0.424	0.512	0.467	0.424	0.512	SUBCLONAL	1	FALSE	1	0.743141944686833	2		413	755	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0005523-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	94	285	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		285	1086	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786502	135786502	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0005523-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	100	420	0	ENST00000298552.3:c.1030-2A>T		p.X344_splice	ENST00000298552	NM_001162426.1	344			1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		420	631	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0005584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	391	418	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.829207780581591	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.829207780581591	2		421	447	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5466794	5466794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	450	586	0	ENST00000381577.3:c.815G>A	p.Cys272Tyr	p.C272Y	ENST00000381577	NM_014143.3	272	tGt/tAt	6/7	0.703077557411278	4	FACETS	0.983	0.942	1	0.983	0.942	1	CLONAL	2	TRUE	2	0.829207780581591	4		586	1010	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862762	9862762	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	1406	611	0	ENST00000330684.3:c.2541C>G	p.Phe847Leu	p.F847L	ENST00000330684	NM_001134407.1	847	ttC/ttG	12/13	0.829207780581591	5	FACETS	0.919	0.902	0.935			1	CLONAL	4	TRUE	NA	0.829207780581591	5		611	2071	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41251790	41251790	+	splice_donor_variant	Splice_Site	SNP	A	A	T	rs80358047	NA	P-0005584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	440	495	0	ENST00000357654.3:c.547+2T>A		p.X183_splice	ENST00000357654	NM_007294.3	183			0.829207780581591	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.829207780581591	2		495	515	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021418	31021418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1358407610	NA	P-0005584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	347	299	1	ENST00000375687.4:c.1417G>A	p.Ala473Thr	p.A473T	ENST00000375687	NM_015338.5	473	Gca/Aca	12/13	0.829207780581591	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.829207780581591	2		300	400	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941658	48941682	+	frameshift_variant	Frame_Shift_Del	DEL	AAATTTATCTTAAAAATAAAGATCT	AAATTTATCTTAAAAATAAAGATCT	-	novel	NA	P-0005584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	247	374	1	ENST00000267163.4:c.969_993del	p.Ile324MetfsTer17	p.I324Mfs*17	ENST00000267163	NM_000321.2	323	gAAATTTATCTTAAAAATAAAGATCTa/ga	10/27	0.829207780581591	3	FACETS	0.946	0.915	0.974	0.946	0.915	0.974	CLONAL	3	TRUE	0	0.829207780581591	3		375	297	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664455	29664503	+	frameshift_variant	Frame_Shift_Del	DEL	GCATTAGCAAAGTCAAGTCAGCTGCTGTCATTGCCTTCCGTTCCAGTTA	GCATTAGCAAAGTCAAGTCAGCTGCTGTCATTGCCTTCCGTTCCAGTTA	CT	novel	NA	P-0005584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	307	422	0	ENST00000356175.3:c.6434_6482delinsCT	p.Gly2145AlafsTer12	p.G2145Afs*12	ENST00000356175	NM_000267.3	2145	gGCATTAGCAAAGTCAAGTCAGCTGCTGTCATTGCCTTCCGTTCCAGTTAc/gCTc	42/57	0.829207780581591	2	FACETS	0.972	0.942	1	0.972	0.942	1	CLONAL	2	TRUE	0	0.829207780581591	2		422	381	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584514	48584514	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	35	514	0	ENST00000342988.3:c.692del	p.Gly231AlafsTer10	p.G231Afs*10	ENST00000342988	NM_005359.5	229	ctG/ct	6/12	0.175095055835851	2	FACETS	0.909	0.751	1	0.909	0.751	1	CLONAL	2	FALSE	0	0.175095055835851	2		514	220	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0005755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	21	513	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	1	0.775	1	1	0.775	1	CLONAL	1	FALSE	1	0.175095055835851	2		514	239	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0005755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	54	500	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.175095055835851	3	FACETS	1	0.921	1	1	0.921	1	CLONAL	2	FALSE	1	0.175095055835851	3		500	303	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100454	8100454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766636397	NA	P-0005755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	18	686	1	ENST00000346208.3:c.428G>A	p.Gly143Glu	p.G143E	ENST00000346208		143	gGg/gAg	3/6	0.175095055835851	3	FACETS	0.656	0.493	0.849	0.328	0.246	0.425	SUBCLONAL	1	FALSE	1	0.175095055835851	3		687	341	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044497	47044497	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	36	340	0	ENST00000377604.3:c.1998del	p.Glu667LysfsTer37	p.E667Kfs*37	ENST00000377604	NM_001204468.1	665	cAa/ca	18/24	1	1	FACETS	1	0.886	1	1	0.968	1	CLONAL	2	FALSE	0	0.175095055835851	1		340	173	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118998	70118998	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	78	691	0	ENST00000245479.2:c.571del	p.Glu191ArgfsTer28	p.E191Rfs*28	ENST00000245479	NM_000346.3	190	gaG/ga	2/3	1	2	FACETS	0.897	0.795	1	1	0.987	1	CLONAL	3	FALSE	1	0.175095055835851	2		691	331	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0005772-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	539	239	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.526973782327887	5	FACETS	1	0.994	1	1	0.994	1	CLONAL	4	TRUE	1	0.526973782327887	5		239	833	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0005772-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	225	392	0	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	1	2	FACETS	0.914	0.852	0.978	0.914	0.852	0.978	CLONAL	1	TRUE	1	0.526973782327887	2		392	934	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907712	111907712	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0005772-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	268	474	0	ENST00000393256.3:c.486C>G	p.Tyr162Ter	p.Y162*	ENST00000393256	NM_006538.4	162	taC/taG	3/4	0.19872865611828	5	FACETS	0.8	0.75	0.852	0.533	0.5	0.568	INDETERMINATE	2	TRUE	2	0.526973782327887	5		474	1138	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645088	86645088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005772-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	182	324	0	ENST00000274376.6:c.1160C>T	p.Ser387Leu	p.S387L	ENST00000274376	NM_002890.2	387	tCa/tTa	8/25	1	2	FACETS	0.895	0.827	0.965	0.895	0.827	0.965	CLONAL	1	TRUE	1	0.526973782327887	2		324	772	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119998	70119998	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005772-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	41	96	0	ENST00000245479.2:c.1000G>A	p.Val334Met	p.V334M	ENST00000245479	NM_000346.3	334	Gtg/Atg	3/3	1	2	FACETS	0.864	0.73	1	0.864	0.73	1	CLONAL	1	TRUE	1	0.526973782327887	2		96	180	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191158	2191158	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005772-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	275	405	2	ENST00000398665.3:c.412G>T	p.Glu138Ter	p.E138*	ENST00000398665	NM_032482.2	138	Gag/Tag	5/28	1	2	FACETS	0.921	0.865	0.979	0.921	0.865	0.979	CLONAL	1	TRUE	1	0.526973782327887	2		407	1133	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0005817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	436	851	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	0.835989903202877	2		851	972	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867527	78867527	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	185	600	0	ENST00000306801.3:c.2263T>A	p.Ser755Thr	p.S755T	ENST00000306801	NM_020761.2	755	Tcc/Acc	20/34	1	2	FACETS	0.537	0.496	0.579	0.537	0.496	0.579	SUBCLONAL	1	TRUE	1	0.835989903202877	2		600	824	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441201	52441201	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005907-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	185	581	2	ENST00000460680.1:c.569C>A	p.Pro190His	p.P190H	ENST00000460680	NM_004656.3	190	cCc/cAc	7/17	0.500596849296451	1	FACETS	0.969	0.9	1	0.969	0.9	1	CLONAL	1	TRUE	0	0.500596849296451	1		583	572	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391577	139391577	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005907-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	451	733	1	ENST00000277541.6:c.6614C>A	p.Ser2205Ter	p.S2205*	ENST00000277541	NM_017617.3	2205	tCa/tAa	34/34	0.500596849296451	3	FACETS	0.962	0.92	1	0.962	0.92	1	CLONAL	2	TRUE	1	0.500596849296451	3		734	1171	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044735	47044735	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005907-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	242	711	0	ENST00000377604.3:c.2135A>T	p.Asp712Val	p.D712V	ENST00000377604	NM_001204468.1	712	gAt/gTt	19/24	NA	2	FACETS	0.985	0.92	1			1	INDETERMINATE	1	TRUE	NA	0.500596849296451	2		711	982	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65300283	65300283	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	378	335	0	ENST00000342505.4:c.3427C>T	p.Gln1143Ter	p.Q1143*	ENST00000342505	NM_002227.2	1143	Cag/Tag	25/25	0.869319771145226	2	FACETS	0.997	0.974	1	0.997	0.974	1	CLONAL	2	TRUE	0	0.869319771145226	2		335	436	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162147	47162147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	323	427	1	ENST00000409792.3:c.3979G>A	p.Val1327Ile	p.V1327I	ENST00000409792	NM_014159.6	1327	Gta/Ata	3/21	0.839758147087149	4	FACETS	0.971	0.915	1	0.485	0.457	0.514	CLONAL	1	TRUE	2	0.869319771145226	4		428	1431	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534462	140534462	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	728	556	0	ENST00000288602.6:c.451T>G	p.Ser151Ala	p.S151A	ENST00000288602	NM_004333.4	151	Tca/Gca	3/18	0.824155272960583	4	FACETS	1	0.97	1			1	CLONAL	2	TRUE	NA	0.869319771145226	4		556	1561	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244875	46244875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758368727	NA	P-0005976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	998	823	1	ENST00000334344.6:c.2969C>T	p.Ser990Leu	p.S990L	ENST00000334344	NM_152641.2	990	tCg/tTg	15/21	0.839758147087149	4	FACETS	0.977	0.949	1	0.977	0.949	1	CLONAL	2	TRUE	2	0.869319771145226	4		824	2197	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163754	47163754	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006031-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	36	1010	1	ENST00000409792.3:c.2372C>A	p.Ser791Ter	p.S791*	ENST00000409792	NM_014159.6	791	tCa/tAa	3/21	0.215144490586506	1	FACETS	0.725	0.596	0.869	0.725	0.596	0.869	SUBCLONAL	1	TRUE	0	0.215144490586506	1		1011	412	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271450	38271450	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006031-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	66	1383	0	ENST00000425967.3:c.2371T>G	p.Leu791Val	p.L791V	ENST00000425967	NM_001174067.1	791	Ttg/Gtg	18/19	1	2	FACETS	0.945	0.82	1	0.945	0.82	1	CLONAL	1	TRUE	1	0.215144490586506	2		1383	649	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279453	38279453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006031-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	23	751	0	ENST00000425967.3:c.1036G>A	p.Gly346Arg	p.G346R	ENST00000425967	NM_001174067.1	346	Gga/Aga	9/19	1	2	FACETS	0.596	0.464	0.748	0.596	0.464	0.748	SUBCLONAL	1	TRUE	1	0.215144490586506	2		751	359	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884819	111884819	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006031-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	50	1486	4	ENST00000341259.2:c.908C>A	p.Ser303Ter	p.S303*	ENST00000341259	NM_005475.2	303	tCg/tAg	4/8	0.148003106124382	3	FACETS	0.619	0.523	0.724	0.309	0.261	0.362	SUBCLONAL	1	TRUE	1	0.215144490586506	3		1490	832	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038204	30038204	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006031-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	33	1214	0	ENST00000338641.4:c.380del	p.Leu127Ter	p.L127*	ENST00000338641	NM_000268.3	126	aTt/at	4/16	0.215144490586506	1	FACETS	0.551	0.448	0.667	0.551	0.448	0.667	SUBCLONAL	1	TRUE	0	0.215144490586506	1		1214	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0006199-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	268	571	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.456327526413373	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.456327526413373	2		571	519	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78866583	78866583	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006199-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	79	197	0	ENST00000306801.3:c.2156C>T	p.Ser719Phe	p.S719F	ENST00000306801	NM_020761.2	719	tCt/tTt	19/34	0.456327526413373	3	FACETS	1	0.907	1	0.515	0.455	0.578	CLONAL	1	TRUE	1	0.456327526413373	3		197	413	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751902	57751902	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006268-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	68	760	0	ENST00000274289.3:c.1335T>G	p.Ile445Met	p.I445M	ENST00000274289	NM_006622.3	445	atT/atG	10/14	1	2	FACETS	0.414	0.358	0.474	0.414	0.358	0.474	SUBCLONAL	1	TRUE	1	0.27	2		760	1217	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579541	7579541	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006268-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	56	541	0	ENST00000269305.4:c.146A>T	p.Asp49Val	p.D49V	ENST00000269305	NM_001126112.2	49	gAt/gTt	4/11	0.3	1	FACETS	0.41	0.35	0.476	0.41	0.35	0.476	SUBCLONAL	1	TRUE	0	0.27	1		541	875	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035079	30035079	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006268-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	58	444	0	ENST00000338641.4:c.241G>T	p.Val81Leu	p.V81L	ENST00000338641	NM_000268.3	81	Gta/Tta	3/16	1	2	FACETS	0.452	0.387	0.523	0.452	0.387	0.523	SUBCLONAL	1	TRUE	1	0.27	2		444	951	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0006311-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	46	138	1	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.225913207429371	2	FACETS	0.808	0.688	0.938	0.808	0.688	0.938	CLONAL	2	TRUE	0	0.255230337546067	2		139	223	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747342068	NA	P-0006311-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	148	457	0	ENST00000269305.4:c.394A>G	p.Lys132Glu	p.K132E	ENST00000269305	NM_001126112.2	132	Aag/Gag	5/11	0.225913207429371	2	FACETS	0.863	0.79	0.939	0.863	0.79	0.939	CLONAL	2	TRUE	0	0.255230337546067	2		457	672	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550868	150550868	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006311-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	73	502	0	ENST00000369026.2:c.788G>A	p.Arg263Lys	p.R263K	ENST00000369026	NM_021960.4	263	aGg/aAg	2/3	0.255230337546067	4	FACETS	0.827	0.722	0.941	0.207	0.18	0.236	CLONAL	1	TRUE	0	0.255230337546067	4		502	868	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916824	178916824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201269904	NA	P-0006311-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1261	166	1143	2	ENST00000263967.3:c.211G>A	p.Val71Ile	p.V71I	ENST00000263967	NM_006218.2	71	Gta/Ata	2/21	0.225913207429371	2	FACETS	0.912	0.835	0.992	0.456	0.417	0.496	CLONAL	1	TRUE	0	0.255230337546067	2		1145	1427	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575484	64575484	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006311-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	111	764	0	ENST00000312049.6:c.533C>G	p.Ser178Cys	p.S178C	ENST00000312049	NM_130799.2	178	tCt/tGt	3/10	0.248055275287597	3	FACETS	1	0.975	1	0.634	0.569	0.701	CLONAL	1	TRUE	1	0.255230337546067	3		764	774	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216938	7216938	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006311-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	264	834	1	ENST00000380728.2:c.583C>A	p.Pro195Thr	p.P195T	ENST00000380728		195	Cct/Act	7/11	0.225913207429371	2	FACETS	0.978	0.917	1	0.978	0.917	1	CLONAL	2	TRUE	0	0.255230337546067	2		835	1058	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288352	15288352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1214687403	NA	P-0006311-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	231	914	1	ENST00000263388.2:c.4387C>T	p.Arg1463Cys	p.R1463C	ENST00000263388	NM_000435.2	1463	Cgc/Tgc	24/33	0.248055275287597	3	FACETS	0.858	0.799	0.92	0.858	0.799	0.92	CLONAL	2	TRUE	1	0.255230337546067	3		915	1189	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513339	44513339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006311-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	69	526	0	ENST00000291552.4:c.596C>T	p.Ser199Phe	p.S199F	ENST00000291552	NM_006758.2	199	tCc/tTc	8/8	0.255230337546067	7	FACETS	0.841	0.73	0.962	0.168	0.146	0.193	CLONAL	1	TRUE	2	0.255230337546067	7		526	1053	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426301	49426547	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGTTCAGTGGCCATTGACTCAGGGGTAGTTCCTATTGCTAACGGCCCTCCCTGATGTGTAGAGGGCCCCTCAGTGGCCTCTGAAGAAACGGCTGGGTCTACGGTGTTTTGTTCCTTGCCCGTCAGGAGGAGGGTTGGACCCAGGGCTCCAGGGCTAGAAAAGTGTTGAAGAGGCTTTGCTGGCATGCCAGGGCCAAGTGCCACTTGCTGCTGCTGTTGTTGCTGAGGAGACAGTAAAGTTCGACT	CTGGTTCAGTGGCCATTGACTCAGGGGTAGTTCCTATTGCTAACGGCCCTCCCTGATGTGTAGAGGGCCCCTCAGTGGCCTCTGAAGAAACGGCTGGGTCTACGGTGTTTTGTTCCTTGCCCGTCAGGAGGAGGGTTGGACCCAGGGCTCCAGGGCTAGAAAAGTGTTGAAGAGGCTTTGCTGGCATGCCAGGGCCAAGTGCCACTTGCTGCTGCTGTTGTTGCTGAGGAGACAGTAAAGTTCGACT	-	novel	NA	P-0006311-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	112	895	0	ENST00000301067.7:c.11941_12187del	p.Ser3981GlufsTer3	p.S3981Efs*3	ENST00000301067	NM_003482.3	3981	AGTCGAACTTTACTGTCTCCTCAGCAACAACAGCAGCAGCAAGTGGCACTTGGCCCTGGCATGCCAGCAAAGCCTCTTCAACACTTTTCTAGCCCTGGAGCCCTGGGTCCAACCCTCCTCCTGACGGGCAAGGAACAAAACACCGTAGACCCAGCCGTTTCTTCAGAGGCCACTGAGGGGCCCTCTACACATCAGGGAGGGCCGTTAGCAATAGGAACTACCCCTGAGTCAATGGCCACTGAACCAGga/ga	39/54	0.225913207429371	2	FACETS	0.848	0.761	0.94	0.424	0.38	0.47	CLONAL	1	TRUE	0	0.255230337546067	2		895	1035	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220674	1220709	+	inframe_deletion	In_Frame_Del	DEL	TCTCCGGCTTCAAGGTGGACATCTGGTCGGCTGGGG	TCTCCGGCTTCAAGGTGGACATCTGGTCGGCTGGGG	-	novel	NA	P-0006311-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	65	738	0	ENST00000326873.7:c.694_729del	p.Ser232_Val243del	p.S232_V243del	ENST00000326873	NM_000455.4	231	tTCTCCGGCTTCAAGGTGGACATCTGGTCGGCTGGGGtc/ttc	5/10	0.255230337546067	1	FACETS	0.6	0.52	0.688	0.6	0.52	0.688	SUBCLONAL	1	TRUE	0	0.255230337546067	1		738	740	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426660	49426662	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	rs1413843050	NA	P-0006311-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	54	331	0	ENST00000301067.7:c.11826_11828del	p.Gln3947del	p.Q3947del	ENST00000301067	NM_003482.3	3942	caACAg/cag	39/54	0.225913207429371	2	FACETS	0.986	0.844	1	0.493	0.422	0.571	CLONAL	1	TRUE	0	0.255230337546067	2		331	429	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436340	52436340	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006311-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	44	652	0	ENST00000460680.1:c.2154del	p.Lys719AsnfsTer17	p.K719Nfs*17	ENST00000460680	NM_004656.3	718	cgG/cg	17/17	0.227501376264106	2	FACETS	0.458	0.383	0.542	0.229	0.191	0.271	SUBCLONAL	1	TRUE	0	0.255230337546067	2		652	753	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426678	49426695	+	inframe_deletion	In_Frame_Del	DEL	TGCTGTTGCTGCTGTTGA	TGCTGTTGCTGCTGTTGA	-	novel	NA	P-0006311-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	37	259	0	ENST00000301067.7:c.11793_11810del	p.Gln3934_Gln3939del	p.Q3934_Q3939del	ENST00000301067	NM_003482.3	3931	ctTCAACAGCAGCAACAGCAg/ctg	39/54	0.225913207429371	2	FACETS	0.848	0.701	1	0.424	0.35	0.506	CLONAL	1	TRUE	0	0.255230337546067	2		259	342	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0006473-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	246	385	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	1	2	FACETS	0.902	0.848	0.956	0.902	0.848	0.956	CLONAL	1	TRUE	1	0.815643931239314	2		385	669	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653786	89653786	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006473-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	191	363	0	ENST00000371953.3:c.84T>G	p.Ile28Met	p.I28M	ENST00000371953	NM_000314.4	28	atT/atG	2/9	0.815643931239314	1	FACETS	0.987	0.938	1	0.987	0.938	1	CLONAL	1	TRUE	0	0.815643931239314	1		363	281	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	59	589	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.846	0.744	0.951	0.846	0.744	0.951	CLONAL	1	TRUE	1	0.861323060481221	2		590	162	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121912666	NA	P-0006538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	120	386	0	ENST00000269305.4:c.659A>C	p.Tyr220Ser	p.Y220S	ENST00000269305	NM_001126112.2	220	tAt/tCt	6/11	0.835543324408968	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.861323060481221	1		386	157	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851599	63851599	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775499447	NA	P-0006538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	51	360	0	ENST00000279873.7:c.2377C>T	p.Leu793Phe	p.L793F	ENST00000279873	NM_032199.2	793	Ctt/Ttt	10/10	0.114830427592263	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.861323060481221	0		360	118	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15821911	15821911	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	85	565	0	ENST00000307771.7:c.304G>T	p.Glu102Ter	p.E102*	ENST00000307771	NM_005089.3	102	Gaa/Taa	4/11	1	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.861323060481221	1		565	102	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266213	+	inframe_deletion	In_Frame_Del	DEL	TCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTT	TCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTT	-	novel	NA	P-0006538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	21	595	0	ENST00000349496.5:c.100_213del	p.Gly34_Ser71del	p.G34_S71del	ENST00000349496	NM_001904.3	33	TCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTT/-	3/15	0.444244520340786	1	FACETS	0.229	0.179	0.287	0.229	0.179	0.287	INDETERMINATE	1	TRUE	0	0.861323060481221	1		595	121	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006607-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	17	420	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		420	905	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0006686-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	48	452	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.88	0.746	1	0.88	0.746	1	CLONAL	1	TRUE	1	0.26537320092574	2		452	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0006686-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	56	418	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.209057592210887	1	FACETS	0.897	0.771	1	0.897	0.771	1	CLONAL	1	TRUE	0	0.26537320092574	1		421	408	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0006686-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	55	223	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.230088257779667	2	FACETS	1	0.965	1	0.717	0.618	0.824	CLONAL	1	TRUE	0	0.26537320092574	2		223	289	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665101	138665101	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006686-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	36	98	0	ENST00000330315.3:c.464C>T	p.Pro155Leu	p.P155L	ENST00000330315	NM_023067.3	155	cCg/cTg	1/1	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.26537320092574	2		98	189	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421519	32421519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006686-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	45	252	2	ENST00000332351.3:c.1073C>T	p.Thr358Met	p.T358M	ENST00000332351	NM_024426.4	358	aCg/aTg	6/10	1	2	FACETS	0.702	0.59	0.826	0.702	0.59	0.826	SUBCLONAL	1	TRUE	1	0.26537320092574	2		254	483	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880998	37880998	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs144434331	NA	P-0006686-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	73	434	0	ENST00000269571.5:c.2327G>T	p.Gly776Val	p.G776V	ENST00000269571		776	gGt/gTt	20/27	1	2	FACETS	0.764	0.668	0.868	0.764	0.668	0.868	SUBCLONAL	1	TRUE	1	0.26537320092574	2		434	720	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799177	42799177	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006686-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	22	159	0	ENST00000575354.2:c.4661C>A	p.Ala1554Glu	p.A1554E	ENST00000575354	NM_015125.3	1554	gCa/gAa	20/20	0.191306539371523	2	FACETS	0.655	0.509	0.824	0.328	0.254	0.412	SUBCLONAL	1	TRUE	0	0.26537320092574	2		159	253	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010439	48010439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881810	NA	P-0006742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	243	408	1	ENST00000234420.5:c.67G>A	p.Ala23Thr	p.A23T	ENST00000234420	NM_000179.2	23	Gcc/Acc	1/10	0.373987936796782	3	FACETS	0.82	0.767	0.874	0.82	0.767	0.874	CLONAL	2	TRUE	1	0.373987936796782	3		409	941	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183811	10183811	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs5030829	NA	P-0006742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	279	301	0	ENST00000256474.2:c.280G>T	p.Glu94Ter	p.E94*	ENST00000256474	NM_000551.3	94	Gag/Tag	1/3	0.314462004836028	4	FACETS	1	0.983	1	0.816	0.773	0.86	CLONAL	3	TRUE	0	0.373987936796782	4		301	628	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649021	86649021	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	635	418	0	ENST00000274376.6:c.1301G>A	p.Gly434Glu	p.G434E	ENST00000274376	NM_002890.2	434	gGa/gAa	9/25	0.373987936796782	12	FACETS	0.971	0.941	1			1	CLONAL	9	TRUE	NA	0.373987936796782	12		418	1115	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109935	115109935	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	132	416	0	ENST00000257566.3:c.1943C>T	p.Pro648Leu	p.P648L	ENST00000257566	NM_016569.3	648	cCg/cTg	8/8	0.332235202962217	4	FACETS	0.861	0.785	0.941	0.861	0.785	0.941	CLONAL	2	TRUE	2	0.373987936796782	4		416	563	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205156	123205156	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	59	611	0	ENST00000218089.9:c.2516A>C	p.Asp839Ala	p.D839A	ENST00000218089	NM_001042749.1	839	gAt/gCt	25/35	0.316972698564733	2	FACETS	0.553	0.475	0.637	0.276	0.237	0.319	SUBCLONAL	1	TRUE	0	0.373987936796782	2		611	571	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217347	123217347	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	40	590	2	ENST00000218089.9:c.3001G>T	p.Asp1001Tyr	p.D1001Y	ENST00000218089	NM_001042749.1	1001	Gat/Tat	29/35	0.316972698564733	2	FACETS	0.366	0.304	0.436	0.183	0.152	0.218	SUBCLONAL	1	TRUE	0	0.373987936796782	2		592	584	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442529	52442529	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	220	457	0	ENST00000460680.1:c.216del	p.Ile72MetfsTer6	p.I72Mfs*6	ENST00000460680	NM_004656.3	72	atT/at	4/17	NA	2	FACETS	0.831	0.776	0.887			1	INDETERMINATE	2	TRUE	NA	0.373987936796782	2		457	708	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253377	226253377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	60	319	0	ENST00000366813.1:c.149G>A	p.Arg50His	p.R50H	ENST00000366813		50	cGt/cAt	2/3	1	2	FACETS	0.917	0.79	1	0.917	0.79	1	CLONAL	1	TRUE	1	0.22	2		319	595	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924822	49924822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202007332	NA	P-0006750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	140	992	2	ENST00000296474.3:c.4121G>A	p.Arg1374His	p.R1374H	ENST00000296474	NM_002447.2	1374	cGt/cAt	20/20	0.3	3	FACETS	1	0.972	1	0.586	0.532	0.643	CLONAL	1	TRUE	1	0.22	3		994	1205	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029336	14029336	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	100	709	2	ENST00000311895.7:c.1547G>A	p.Arg516Gln	p.R516Q	ENST00000311895	NM_005236.2	516	cGa/cAa	8/11	1	2	FACETS	0.834	0.743	0.931	0.834	0.743	0.931	CLONAL	1	TRUE	1	0.22	2		711	1090	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577043	7577489	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTCGTGGTGAGGCTCCCCTTTCTTGCGGAGATTCTCTTCCTCTGTGCGCCGGTCTCTCCCAGGACAGGCACAAACACGCACCTCAAAGCTGTTCCGTCCCAGTAGATTACCACTACTCAGGATAGGAAAAGAGAAGCAAGAGGCAGTAAGGAAATCAGGTCCTACCTGTCCCATTTAAAAAACCAGGCTCCATCTACTCCCAACCACCCTTGTCCTTTCTGGAGCCTAAGCTCCAGCTCCAGGTAGGTGGAGGAGAAGCCACAGGTTAAGAGGTCCCAAAGCCAGAGAAAAGAAAACTGAGTGGGAGCAGTAAGGAGATTCCCCGCCGGGGATGTGATGAGAGGTGGATGGGTAGTAGTATGGAAGAAATCGGTAAGAGGTGGGCCCAGGGGTCAGAGGCAAGCAGAGGCTGGGGCACAGCAGGCCAGTGTGCAGGGTGGCAAGTG	GCTCGTGGTGAGGCTCCCCTTTCTTGCGGAGATTCTCTTCCTCTGTGCGCCGGTCTCTCCCAGGACAGGCACAAACACGCACCTCAAAGCTGTTCCGTCCCAGTAGATTACCACTACTCAGGATAGGAAAAGAGAAGCAAGAGGCAGTAAGGAAATCAGGTCCTACCTGTCCCATTTAAAAAACCAGGCTCCATCTACTCCCAACCACCCTTGTCCTTTCTGGAGCCTAAGCTCCAGCTCCAGGTAGGTGGAGGAGAAGCCACAGGTTAAGAGGTCCCAAAGCCAGAGAAAAGAAAACTGAGTGGGAGCAGTAAGGAGATTCCCCGCCGGGGATGTGATGAGAGGTGGATGGGTAGTAGTATGGAAGAAATCGGTAAGAGGTGGGCCCAGGGGTCAGAGGCAAGCAGAGGCTGGGGCACAGCAGGCCAGTGTGCAGGGTGGCAAGTG	-	novel	NA	P-0006750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	70	520	0	ENST00000269305.4:c.782+10_895del		p.X261_splice	ENST00000269305	NM_001126112.2	261		8/11	1	2	FACETS	0.982	0.856	1	0.982	0.856	1	CLONAL	1	TRUE	1	0.22	2		520	648	SUCCESS
APC	324	MSKCC	GRCh37	5	112174171	112174171	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	130	616	0	ENST00000257430.4:c.2882del	p.Asn961MetfsTer4	p.N961Mfs*4	ENST00000257430	NM_000038.5	960	tcA/tc	16/16	0.179200244635402	3	FACETS	1	0.971	1	0.591	0.535	0.65	CLONAL	1	TRUE	1	0.22	3		616	1110	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0006768-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	524	859	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.368107501142153	3	FACETS	0.874	0.842	0.906	0.874	0.842	0.906	CLONAL	3	TRUE	0	0.475881593827745	3		860	1040	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0006768-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	85	666	0	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	0.380815737994771	3	FACETS	0.606	0.535	0.682	0.202	0.178	0.228	SUBCLONAL	1	TRUE	0	0.475881593827745	3		666	730	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531749	46531749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006768-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	455	695	0	ENST00000262741.5:c.598G>A	p.Glu200Lys	p.E200K	ENST00000262741	NM_003629.3	200	Gaa/Aaa	5/10	0.475881593827745	6	FACETS	0.837	0.799	0.877	0.502	0.479	0.526	CLONAL	3	TRUE	1	0.475881593827745	6		695	1486	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420318	88420318	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006768-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	92	403	0	ENST00000360948.2:c.2368G>C	p.Glu790Gln	p.E790Q	ENST00000360948	NM_001012338.2	790	Gag/Cag	19/19	1	2	FACETS	0.974	0.871	1	0.974	0.871	1	CLONAL	1	TRUE	1	0.475881593827745	2		403	397	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819237	3819237	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006768-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	306	776	0	ENST00000262367.5:c.2998G>A	p.Glu1000Lys	p.E1000K	ENST00000262367	NM_004380.2	1000	Gag/Aag	15/31	0.475881593827745	4	FACETS	1	0.993	1	0.474	0.445	0.502	CLONAL	1	TRUE	1	0.475881593827745	4		776	1336	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923647	72923647	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006768-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	222	987	0	ENST00000268489.5:c.3431G>T	p.Cys1144Phe	p.C1144F	ENST00000268489	NM_006885.3	1144	tGc/tTc	4/10	0.475881593827745	3	FACETS	0.909	0.845	0.976			1	CLONAL	1	TRUE	NA	0.475881593827745	3		987	1270	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853923	59853923	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006768-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	151	531	0	ENST00000259008.2:c.1936G>T	p.Val646Phe	p.V646F	ENST00000259008	NM_032043.2	646	Gtt/Ttt	14/20	0.475881593827745	3	FACETS	0.976	0.893	1	0.488	0.446	0.532	CLONAL	1	TRUE	1	0.475881593827745	3		531	805	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226627	1226627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781537	NA	P-0006768-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	75	251	0	ENST00000326873.7:c.1283C>T	p.Ser428Leu	p.S428L	ENST00000326873	NM_000455.4	428	tCg/tTg	9/10	0.475881593827745	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.475881593827745	1		251	214	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561234	9561234	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006768-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	259	615	0	ENST00000353224.5:c.548C>G	p.Ser183Cys	p.S183C	ENST00000353224	NM_177990.2	183	tCt/tGt	4/10	0.349864217998927	5	FACETS	0.958	0.898	1	0.638	0.598	0.679	CLONAL	2	TRUE	2	0.475881593827745	5		615	974	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37871576	37871576	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006768-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	205	669	0	ENST00000269571.5:c.1186C>A	p.Gln396Lys	p.Q396K	ENST00000269571		396	Cag/Aag	10/27	0.475881593827745	3	FACETS	1	0.976	1	0.557	0.517	0.599	CLONAL	1	TRUE	1	0.475881593827745	3		669	957	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42861455	42861455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006768-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	176	605	1	ENST00000398585.3:c.415G>A	p.Ala139Thr	p.A139T	ENST00000398585	NM_001135099.1	139	Gct/Act	4/14	0.475881593827745	3	FACETS	0.823	0.757	0.892	0.411	0.378	0.446	CLONAL	1	TRUE	1	0.475881593827745	3		606	1113	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143352394	143352394	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006768-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	161	707	1	ENST00000262992.4:c.19G>T	p.Gly7Trp	p.G7W	ENST00000262992	NM_001101669.1	7	Ggg/Tgg	2/24	0.321229785702364	3	FACETS	1	0.974	1	0.57	0.524	0.618	CLONAL	1	TRUE	1	0.475881593827745	3		708	735	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741429	145741429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006768-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1405	336	966	0	ENST00000428558.2:c.1074G>A	p.Met358Ile	p.M358I	ENST00000428558	NM_004260.3	358	atG/atA	5/22	0.475881593827745	6	FACETS	0.792	0.746	0.838	0.317	0.298	0.336	SUBCLONAL	2	TRUE	1	0.475881593827745	6		966	1741	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006806-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	13	420	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.195078435928008	5	FACETS	0.21	0.149	0.286	0.07	0.049	0.096	INDETERMINATE	1	TRUE	2	0.381228649999636	5		420	510	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860419	151860419	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006806-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	73	911	0	ENST00000262189.6:c.10243del	p.Leu3415SerfsTer5	p.L3415Sfs*5	ENST00000262189	NM_170606.2	3415	Ctc/tc	43/59	0.230908904781667	3	FACETS	1	0.933	1	0.547	0.48	0.618	CLONAL	1	TRUE	1	0.381228649999636	3		911	417	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426423	47426423	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006806-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	27	529	0	ENST00000377045.4:c.766G>C	p.Gly256Arg	p.G256R	ENST00000377045	NM_001654.4	256	Ggg/Cgg	9/16	0.21444892424134	2	FACETS	0.694	0.556	0.85			1	INDETERMINATE	1	TRUE	NA	0.381228649999636	2		529	204	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0006819-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	514	462	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.366372326358667	2	FACETS	0.95	0.911	0.99	0.95	0.911	0.99	CLONAL	2	TRUE	0	0.405106418782866	2		463	1335	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0006819-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	274	477	1	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	0.329951253973688	2	FACETS	0.844	0.796	0.894	0.844	0.796	0.894	CLONAL	2	TRUE	0	0.405106418782866	2		478	801	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861838	57861838	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381253752	NA	P-0006819-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1704	584	1137	2	ENST00000228682.2:c.1139G>A	p.Arg380Gln	p.R380Q	ENST00000228682	NM_005269.2	380	cGa/cAa	10/12	0.195773690858541	6	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.405106418782866	6		1139	2288	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852264	128852264	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006819-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	250	550	0	ENST00000249373.3:c.2336A>T	p.Glu779Val	p.E779V	ENST00000249373	NM_005631.4	779	gAa/gTa	12/12	0.229787276157795	5	FACETS	1	0.945	1	0.674	0.63	0.718	INDETERMINATE	2	TRUE	2	0.405106418782866	5		550	982	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710706	114710706	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0006819-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	355	803	1	ENST00000543371.1:c.189+2T>C		p.X63_splice	ENST00000543371	NM_001198531.1	63			0.266786502693378	3	FACETS	0.8	0.757	0.843	0.8	0.757	0.843	SUBCLONAL	2	TRUE	1	0.405106418782866	3		804	1318	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629021	14629021	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006819-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	211	817	0	ENST00000254322.2:c.141G>C	p.Glu47Asp	p.E47D	ENST00000254322	NM_006145.1	47	gaG/gaC	1/3	1	2	FACETS	0.911	0.845	0.98	0.911	0.845	0.98	CLONAL	1	TRUE	1	0.405106418782866	2		817	1143	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48586235	48586235	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1555686070	NA	P-0006819-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	228	447	1	ENST00000342988.3:c.905-1G>A		p.X302_splice	ENST00000342988	NM_005359.5	302			0.376352538138861	2	FACETS	0.834	0.781	0.888	0.834	0.781	0.888	CLONAL	2	TRUE	0	0.405106418782866	2		448	675	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858007	9858007	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs771257899	NA	P-0006819-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1261	218	726	1	ENST00000330684.3:c.3394C>A	p.Pro1132Thr	p.P1132T	ENST00000330684	NM_001134407.1	1132	Cca/Aca	13/13	0.377426077223016	3	FACETS	0.875	0.811	0.941	0.438	0.405	0.471	CLONAL	1	TRUE	1	0.405106418782866	3		727	1479	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230734	66230734	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0006819-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	71	441	0	ENST00000273854.3:c.2236+1del		p.X746_splice	ENST00000273854	NM_004439.5	746			0.261505343374539	2	FACETS	0.549	0.479	0.624	0.274	0.239	0.312	SUBCLONAL	1	TRUE	0	0.405106418782866	2		441	639	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100117	157100119	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs797045268	NA	P-0006873-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	10	26	0	ENST00000346085.5:c.1069_1071del	p.Gly357del	p.G357del	ENST00000346085	NM_020732.3	352	GGC/-	1/20	0.249572785415423	4	FACETS	0.77	0.524	1			1	CLONAL	1	TRUE	NA	0.249572785415423	4		26	130	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872450	35872450	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006873-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1822	114	476	0	ENST00000216797.5:c.453del	p.Cys152ValfsTer12	p.C152Vfs*12	ENST00000216797	NM_020529.2	151	gcC/gc	3/6	0.234431867463564	2	FACETS	0.472	0.423	0.525	0.236	0.211	0.263	SUBCLONAL	1	TRUE	0	0.249572785415423	2		476	1936	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	84	420	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.27214848737615	3	FACETS	1	0.976	1	0.726	0.64	0.818	CLONAL	1	TRUE	1	0.15	3		420	829	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0007133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	13	191	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	0.406	0.288	0.551	0.406	0.288	0.551	SUBCLONAL	1	TRUE	1	0.15	2		191	427	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993095	72993095	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	86	789	0	ENST00000268489.5:c.950T>A	p.Leu317His	p.L317H	ENST00000268489	NM_006885.3	317	cTt/cAt	2/10	0.3	3	FACETS	1	0.902	1			1	CLONAL	1	TRUE	NA	0.15	3		789	1202	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945698	54945698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	26	189	0	ENST00000312783.6:c.872G>A	p.Gly291Asp	p.G291D	ENST00000312783	NM_198436.1	291	gGc/gAc	9/10	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.15	2		189	286	SUCCESS
APC	324	MSKCC	GRCh37	5	112175749	112175756	+	frameshift_variant	Frame_Shift_Del	DEL	TACTTTAT	TACTTTAT	-	novel	NA	P-0007133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	47	365	0	ENST00000257430.4:c.4461_4468del	p.Leu1488PhefsTer23	p.L1488Ffs*23	ENST00000257430	NM_000038.5	1486	gaTACTTTATta/gata	16/16	0.27214848737615	3	FACETS	1	0.909	1	0.559	0.471	0.656	CLONAL	1	TRUE	1	0.15	3		365	603	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167577	NA	P-0007169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	114	311	0	ENST00000257430.4:c.4463del	p.Leu1488TyrfsTer19	p.L1488Yfs*19	ENST00000257430	NM_000038.5	1487	acT/ac	16/16	1	2	FACETS	0.802	0.723	0.886	0.802	0.723	0.886	CLONAL	1	TRUE	1	0.394092384565451	2		311	721	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0007169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	185	303	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.394092384565451	2		303	775	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499462	89499462	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1323859567	NA	P-0007169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	340	451	0	ENST00000336596.2:c.2632C>A	p.Leu878Met	p.L878M	ENST00000336596	NM_005233.5	878	Ctg/Atg	15/17	0.394092384565451	3	FACETS	0.939	0.889	0.99	0.939	0.889	0.99	CLONAL	2	TRUE	1	0.394092384565451	3		451	1100	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370910	55370910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	569	448	0	ENST00000297316.4:c.212C>T	p.Pro71Leu	p.P71L	ENST00000297316	NM_022454.3	71	cCg/cTg	1/2	0.394092384565451	6	FACETS	0.922	0.887	0.958	0.922	0.887	0.958	CLONAL	4	TRUE	2	0.394092384565451	6		448	1400	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437341	121437341	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	125	408	0	ENST00000257555.6:c.1679C>G	p.Ser560Cys	p.S560C	ENST00000257555		560	tCt/tGt	9/10	0.394092384565451	3	FACETS	0.908	0.822	0.999	0.454	0.411	0.5	CLONAL	1	TRUE	1	0.394092384565451	3		408	836	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879580	37879580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	139	362	1	ENST00000269571.5:c.1955C>T	p.Thr652Met	p.T652M	ENST00000269571		652	aCg/aTg	17/27	0.394092384565451	3	FACETS	0.936	0.852	1	0.468	0.426	0.513	CLONAL	1	TRUE	1	0.394092384565451	3		363	902	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45423004	45423004	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	311	463	0	ENST00000262160.6:c.124G>C	p.Glu42Gln	p.E42Q	ENST00000262160	NM_005901.5	42	Gag/Cag	2/11	0.345066234300277	2	FACETS	0.9	0.851	0.949	0.9	0.851	0.949	CLONAL	2	TRUE	0	0.394092384565451	2		463	877	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245855	46245855	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	336	468	0	ENST00000334344.6:c.3950del	p.Asn1317IlefsTer5	p.N1317Ifs*5	ENST00000334344	NM_152641.2	1317	Aat/at	15/21	0.394092384565451	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.394092384565451	3		468	1000	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920430	114920430	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	273	590	0	ENST00000543371.1:c.1373del	p.Leu458TyrfsTer33	p.L458Yfs*33	ENST00000543371	NM_001198531.1	457	acT/ac	13/14	1	2	FACETS	0.991	0.928	1	0.991	0.928	1	CLONAL	1	TRUE	1	0.394092384565451	2		590	1398	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0007214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	239	303	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.437234063402462	2		303	1038	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0007214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	241	377	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.38682241874069	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.437234063402462	1		377	800	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0007214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	348	583	1	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.437234063402462	2		584	1382	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0007214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	106	373	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	1	2	FACETS	0.498	0.446	0.554	0.498	0.446	0.554	SUBCLONAL	1	TRUE	1	0.437234063402462	2		373	973	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81960734	81960734	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs746172717	NA	P-0007214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1556	189	740	0	ENST00000359376.3:c.2465A>C	p.Asn822Thr	p.N822T	ENST00000359376	NM_002661.3	822	aAc/aCc	23/33	0.17216588029932	1	FACETS	0.387	0.356	0.42	0.387	0.356	0.42	INDETERMINATE	1	TRUE	0	0.437234063402462	1		740	1745	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508234	38508234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367821941	NA	P-0007214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1230	148	579	0	ENST00000254066.5:c.542C>T	p.Thr181Met	p.T181M	ENST00000254066	NM_000964.3	181	aCg/aTg	5/9	1	2	FACETS	0.491	0.447	0.538	0.491	0.447	0.538	SUBCLONAL	1	TRUE	1	0.437234063402462	2		579	1378	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0007320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	481	452	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.264525258714299	8	FACETS	1	0.985	1			1	CLONAL	6	TRUE	NA	0.264525258714299	8		452	1035	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180459	94180459	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1307	260	611	0	ENST00000323929.3:c.1709G>A	p.Arg570Lys	p.R570K	ENST00000323929	NM_005591.3	570	aGa/aAa	15/20	0.264525258714299	6	FACETS	0.959	0.896	1	0.48	0.448	0.513	CLONAL	2	TRUE	2	0.264525258714299	6		611	1567	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0007320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	207	503	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.232640860133075	2	FACETS	0.894	0.831	0.96	0.894	0.831	0.96	CLONAL	2	TRUE	0	0.264525258714299	2		503	875	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858513	27858513	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1535	153	794	3	ENST00000359303.2:c.58C>T	p.Gln20Ter	p.Q20*	ENST00000359303	NM_003535.2	20	Cag/Tag	1/1	0.264525258714299	4	FACETS	0.867	0.79	0.948	0.433	0.395	0.474	CLONAL	1	TRUE	2	0.264525258714299	4		797	1688	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184818	32184818	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	154	338	0	ENST00000375023.3:c.1765G>T	p.Glu589Ter	p.E589*	ENST00000375023	NM_004557.3	589	Gag/Tag	11/30	0.264525258714299	4	FACETS	0.885	0.81	0.963	0.885	0.81	0.963	CLONAL	2	TRUE	2	0.264525258714299	4		338	832	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423617	88423617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	90	403	0	ENST00000360948.2:c.2218G>A	p.Glu740Lys	p.E740K	ENST00000360948	NM_001012338.2	740	Gaa/Aaa	18/19	0.264525258714299	2	FACETS	0.878	0.779	0.984	0.439	0.389	0.492	CLONAL	1	TRUE	0	0.264525258714299	2		403	775	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565575	41565575	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	271	531	0	ENST00000263253.7:c.4241A>G	p.Tyr1414Cys	p.Y1414C	ENST00000263253	NM_001429.3	1414	tAt/tGt	26/31	0.616829147822454	1	FACETS	0.846	0.798	0.895	0.846	0.798	0.895	CLONAL	1	TRUE	0	0.616829147822454	1		531	718	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666653	206666653	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	255	501	2	ENST00000367120.3:c.1987G>T	p.Ala663Ser	p.A663S	ENST00000367120	NM_014002.3	663	Gcc/Tcc	20/22	1	2	FACETS	0.918	0.861	0.976	0.918	0.861	0.976	CLONAL	1	TRUE	1	0.616829147822454	2		503	901	SUCCESS
FH	2271	MSKCC	GRCh37	1	241672049	241672049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	206	284	0	ENST00000366560.3:c.592G>A	p.Ala198Thr	p.A198T	ENST00000366560	NM_000143.3	198	Gct/Act	5/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.616829147822454	2		284	651	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187927	32187927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	172	422	0	ENST00000375023.3:c.1294G>A	p.Asp432Asn	p.D432N	ENST00000375023	NM_004557.3	432	Gac/Aac	7/30	1	2	FACETS	0.794	0.733	0.858	0.794	0.733	0.858	SUBCLONAL	1	TRUE	1	0.616829147822454	2		422	702	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041068	112041068	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs62620251	NA	P-0007427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1174	450	756	0	ENST00000368678.4:c.187G>A	p.Val63Ile	p.V63I	ENST00000368678		63	Gtc/Atc	3/13	1	2	FACETS	0.898	0.856	0.942	0.898	0.856	0.942	CLONAL	1	TRUE	1	0.616829147822454	2		756	1624	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36846872	36846872	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	122	479	0	ENST00000358127.4:c.1067A>T	p.Asp356Val	p.D356V	ENST00000358127	NM_001280556.1	356	gAc/gTc	9/10	0.315680136608558	1	FACETS	0.367	0.332	0.404	0.367	0.332	0.404	INDETERMINATE	1	TRUE	0	0.616829147822454	1		479	745	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100321	8100321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768583935	NA	P-0007427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	298	543	2	ENST00000346208.3:c.295G>A	p.Gly99Ser	p.G99S	ENST00000346208		99	Ggc/Agc	3/6	0.103000571161686	0	FACETS	0.425	0.401	0.449			1	INDETERMINATE	1	TRUE	0	0.616829147822454	0		545	872	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405440	70405440	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	291	470	1	ENST00000373644.4:c.2954C>T	p.Ala985Val	p.A985V	ENST00000373644	NM_030625.2	985	gCt/gTt	4/12	1	2	FACETS	0.938	0.883	0.994	0.938	0.883	0.994	CLONAL	1	TRUE	1	0.616829147822454	2		471	1006	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789606	3789606	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	158	533	0	ENST00000262367.5:c.4253G>T	p.Gly1418Val	p.G1418V	ENST00000262367	NM_004380.2	1418	gGc/gTc	25/31	0.411851065973202	1	FACETS	0.416	0.381	0.452	0.416	0.381	0.452	SUBCLONAL	1	TRUE	0	0.616829147822454	1		533	852	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832817	3832817	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	294	426	0	ENST00000262367.5:c.1441A>G	p.Met481Val	p.M481V	ENST00000262367	NM_004380.2	481	Atg/Gtg	6/31	0.411851065973202	1	FACETS	0.793	0.749	0.838	0.793	0.749	0.838	SUBCLONAL	1	TRUE	0	0.616829147822454	1		426	831	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578224	7578224	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1429743956	NA	P-0007427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	299	599	0	ENST00000269305.4:c.625A>T	p.Arg209Ter	p.R209*	ENST00000269305	NM_001126112.2	209	Aga/Tga	6/11	0.583652262506411	1	FACETS	0.893	0.845	0.941	0.893	0.845	0.941	CLONAL	1	TRUE	0	0.616829147822454	1		599	751	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676149	29676149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	195	304	0	ENST00000356175.3:c.7138C>T	p.Pro2380Ser	p.P2380S	ENST00000356175	NM_000267.3	2380	Cct/Tct	48/57	1	2	FACETS	0.999	0.929	1	0.999	0.929	1	CLONAL	1	TRUE	1	0.616829147822454	2		304	633	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954378	48954378	+	splice_donor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0007427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	137	348	0	ENST00000267163.4:c.1498+1del		p.X500_splice	ENST00000267163	NM_000321.2	500			0.583652262506411	1	FACETS	0.774	0.711	0.838	0.774	0.711	0.838	SUBCLONAL	1	TRUE	0	0.616829147822454	1		348	397	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	51	589	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.956	0.817	1	0.956	0.817	1	CLONAL	1	TRUE	1	0.314657105805487	2		590	339	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188164	11188164	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587777893	NA	P-0007606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	28	407	0	ENST00000361445.4:c.5930C>A	p.Thr1977Lys	p.T1977K	ENST00000361445	NM_004958.3	1977	aCa/aAa	43/58	1	2	FACETS	0.767	0.616	0.937	0.767	0.616	0.937	CLONAL	1	TRUE	1	0.314657105805487	2		407	232	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183797	10183797	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs5030807	NA	P-0007606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	46	365	0	ENST00000256474.2:c.266T>C	p.Leu89Pro	p.L89P	ENST00000256474	NM_000551.3	89	cTc/cCc	1/3	1	2	FACETS	0.905	0.766	1	0.905	0.766	1	CLONAL	1	TRUE	1	0.314657105805487	2		365	323	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944548	32944548	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	27	660	0	ENST00000380152.3:c.8341A>G	p.Asn2781Asp	p.N2781D	ENST00000380152		2781	Aac/Gac	19/27	1	2	FACETS	0.743	0.594	0.911	0.743	0.594	0.911	CLONAL	1	TRUE	1	0.314657105805487	2		660	231	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540654	NA	P-0007606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	9	508	2	ENST00000269305.4:c.329G>A	p.Arg110His	p.R110H	ENST00000269305	NM_001126112.2	110	cGt/cAt	4/11	1	2	FACETS	0.153	0.101	0.221	0.153	0.101	0.221	SUBCLONAL	1	TRUE	1	0.314657105805487	2		510	373	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242669	46242669	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	29	488	0	ENST00000334344.6:c.1633del	p.Met545CysfsTer12	p.M545Cfs*12	ENST00000334344	NM_152641.2	544	gAa/ga	13/21	1	2	FACETS	0.908	0.734	1	0.908	0.734	1	CLONAL	1	TRUE	1	0.314657105805487	2		488	203	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0007790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	396	418	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.33924417598629	3	FACETS	0.988	0.945	1	0.988	0.945	1	CLONAL	3	TRUE	0	0.368677685812047	3		418	858	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0007790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	409	325	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.368677685812047	3	FACETS	0.969	0.927	1	0.969	0.927	1	CLONAL	3	TRUE	0	0.368677685812047	3		325	904	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	280	291	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	0.368677685812047	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.368677685812047	2		291	711	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222555	157222555	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554265269	NA	P-0007790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	259	417	0	ENST00000346085.5:c.1822C>T	p.Gln608Ter	p.Q608*	ENST00000346085	NM_020732.3	608	Cag/Tag	4/20	0.368677685812047	3	FACETS	0.783	0.734	0.834	0.783	0.734	0.834	SUBCLONAL	2	TRUE	1	0.368677685812047	3		417	1062	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	299	465	0	ENST00000281708.4:c.1393C>A	p.Arg465Ser	p.R465S	ENST00000281708	NM_033632.3	465	Cgt/Agt	9/12	0.349630817560375	2	FACETS	0.964	0.912	1	0.964	0.912	1	CLONAL	2	TRUE	0	0.368677685812047	2		465	841	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077427	30077427	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0007790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	100	172	0	ENST00000338641.4:c.1575-1G>C		p.X525_splice	ENST00000338641	NM_000268.3	525			0.368677685812047	2	FACETS	0.762	0.687	0.84	0.762	0.687	0.84	SUBCLONAL	2	TRUE	0	0.368677685812047	2		172	356	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489796	2489796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	125	329	0	ENST00000355716.4:c.193G>A	p.Glu65Lys	p.E65K	ENST00000355716	NM_003820.2	65	Gag/Aag	3/8	1	2	FACETS	0.935	0.847	1	0.935	0.847	1	CLONAL	1	TRUE	1	0.368677685812047	2		329	725	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695932	117695932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	60	229	0	ENST00000369458.3:c.505G>A	p.Glu169Lys	p.E169K	ENST00000369458	NM_024626.3	169	Gag/Aag	4/6	1	2	FACETS	0.7	0.604	0.804	0.7	0.604	0.804	SUBCLONAL	1	TRUE	1	0.368677685812047	2		229	465	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165614	118165614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	116	370	0	ENST00000369448.3:c.124C>T	p.Pro42Ser	p.P42S	ENST00000369448	NM_017709.3	42	Cca/Tca	2/2	1	2	FACETS	0.916	0.827	1	0.916	0.827	1	CLONAL	1	TRUE	1	0.368677685812047	2		370	687	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550782	150550782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs934123900	NA	P-0007790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	257	286	0	ENST00000369026.2:c.874G>A	p.Glu292Lys	p.E292K	ENST00000369026	NM_021960.4	292	Gaa/Aaa	2/3	0.368677685812047	3	FACETS	0.996	0.935	1	0.996	0.935	1	CLONAL	2	TRUE	1	0.368677685812047	3		286	829	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175996734	175996734	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	167	542	0	ENST00000367669.3:c.1703G>C	p.Arg568Thr	p.R568T	ENST00000367669	NM_022457.5	568	aGa/aCa	15/20	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.368677685812047	2		542	894	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149568	202149568	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	292	431	1	ENST00000358485.4:c.1009C>A	p.His337Asn	p.H337N	ENST00000358485	NM_001080125.1	337	Cat/Aat	8/9	0.349630817560375	2	FACETS	0.932	0.88	0.985	0.932	0.88	0.985	CLONAL	2	TRUE	0	0.368677685812047	2		432	850	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662772	227662772	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	248	388	0	ENST00000305123.5:c.683C>G	p.Ser228Cys	p.S228C	ENST00000305123	NM_005544.2	228	tCt/tGt	1/2	0.349630817560375	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.368677685812047	2		388	664	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645693	12645693	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397516827	NA	P-0007790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	290	388	0	ENST00000251849.4:c.776C>G	p.Ser259Cys	p.S259C	ENST00000251849	NM_002880.3	259	tCc/tGc	7/17	0.305775822479283	4	FACETS	0.99	0.931	1			1	CLONAL	2	TRUE	NA	0.368677685812047	4		388	1088	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259244	89259244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	230	386	0	ENST00000336596.2:c.388G>A	p.Asp130Asn	p.D130N	ENST00000336596	NM_005233.5	130	Gat/Aat	3/17	0.305775822479283	4	FACETS	0.965	0.901	1			1	CLONAL	2	TRUE	NA	0.368677685812047	4		386	885	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217568	142217568	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748903337	NA	P-0007790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	287	397	1	ENST00000350721.4:c.5429C>T	p.Ser1810Leu	p.S1810L	ENST00000350721	NM_001184.3	1810	tCa/tTa	32/47	0.368677685812047	4	FACETS	0.999	0.94	1	0.999	0.94	1	CLONAL	2	TRUE	2	0.368677685812047	4		398	1066	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953819	55953819	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	157	494	1	ENST00000263923.4:c.3617A>T	p.Glu1206Val	p.E1206V	ENST00000263923	NM_002253.2	1206	gAa/gTa	27/30	0.368677685812047	4	FACETS	0.893	0.816	0.974			1	CLONAL	1	TRUE	NA	0.368677685812047	4		495	1305	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38949814	38949814	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	232	325	0	ENST00000357387.3:c.4136G>A	p.Arg1379Lys	p.R1379K	ENST00000357387	NM_152756.3	1379	aGg/aAg	31/38	0.368677685812047	3	FACETS	0.928	0.868	0.99	0.928	0.868	0.99	CLONAL	2	TRUE	1	0.368677685812047	3		325	803	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564633	86564633	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	129	371	0	ENST00000274376.6:c.365C>A	p.Ser122Ter	p.S122*	ENST00000274376	NM_002890.2	122	tCg/tAg	1/25	1	2	FACETS	0.843	0.764	0.926	0.843	0.764	0.926	CLONAL	1	TRUE	1	0.368677685812047	2		371	830	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499089	149499089	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	174	383	0	ENST00000261799.4:c.2739C>G	p.Phe913Leu	p.F913L	ENST00000261799	NM_002609.3	913	ttC/ttG	20/23	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.368677685812047	2		383	822	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721807	176721807	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	124	297	0	ENST00000439151.2:c.7438G>A	p.Asp2480Asn	p.D2480N	ENST00000439151	NM_022455.4	2480	Gat/Aat	23/23	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.368677685812047	2		297	669	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169207	32169207	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	111	311	0	ENST00000375023.3:c.3826G>C	p.Glu1276Gln	p.E1276Q	ENST00000375023	NM_004557.3	1276	Gag/Cag	22/30	0.368677685812047	3	FACETS	0.821	0.737	0.909	0.41	0.368	0.455	CLONAL	1	TRUE	1	0.368677685812047	3		311	869	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90970960	90970960	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	236	450	0	ENST00000265433.3:c.1117G>C	p.Asp373His	p.D373H	ENST00000265433	NM_002485.4	373	Gat/Cat	9/16	0.368677685812047	4	FACETS	0.823	0.768	0.88	0.823	0.768	0.88	CLONAL	2	TRUE	2	0.368677685812047	4		450	1064	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391559	139391559	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0007790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	303	326	0	ENST00000277541.6:c.6632C>G	p.Ser2211Ter	p.S2211*	ENST00000277541	NM_017617.3	2211	tCa/tGa	34/34	0.368677685812047	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.368677685812047	3		326	850	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865491	57865491	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	463	617	0	ENST00000228682.2:c.2968C>G	p.Arg990Gly	p.R990G	ENST00000228682	NM_005269.2	990	Cga/Gga	12/12	0.368677685812047	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.368677685812047	2		617	1173	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249789	133249789	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	286	447	0	ENST00000320574.5:c.1434C>G	p.Ile478Met	p.I478M	ENST00000320574	NM_006231.2	478	atC/atG	14/49	NA	2	FACETS	0.958	0.904	1			1	INDETERMINATE	2	TRUE	NA	0.368677685812047	2		447	810	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354025	15354025	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	47	60	1	ENST00000263377.2:c.2855C>A	p.Ser952Tyr	p.S952Y	ENST00000263377	NM_058243.2	952	tCc/tAc	14/20	0.368677685812047	3	FACETS	0.751	0.642	0.868	0.751	0.642	0.868	SUBCLONAL	2	TRUE	1	0.368677685812047	3		61	201	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867325	45867325	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	75	184	0	ENST00000391945.4:c.868G>C	p.Glu290Gln	p.E290Q	ENST00000391945	NM_000400.3	290	Gag/Cag	10/23	0.368677685812047	3	FACETS	0.862	0.756	0.975	0.431	0.378	0.488	CLONAL	1	TRUE	1	0.368677685812047	3		184	559	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741503	39741503	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	273	330	1	ENST00000361337.2:c.1390G>A	p.Asp464Asn	p.D464N	ENST00000361337	NM_003286.2	464	Gac/Aac	14/21	0.368677685812047	4	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	2	0.368677685812047	4		331	979	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39744068	39744068	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	206	341	0	ENST00000361337.2:c.1696G>C	p.Asp566His	p.D566H	ENST00000361337	NM_003286.2	566	Gat/Cat	16/21	0.368677685812047	4	FACETS	0.897	0.833	0.962	0.897	0.833	0.962	CLONAL	2	TRUE	2	0.368677685812047	4		341	853	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735487	40735487	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	254	445	0	ENST00000373198.4:c.3386T>G	p.Val1129Gly	p.V1129G	ENST00000373198	NM_133170.3	1129	gTg/gGg	25/32	0.368677685812047	4	FACETS	0.99	0.928	1	0.99	0.928	1	CLONAL	2	TRUE	2	0.368677685812047	4		445	952	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077543	30077543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	284	386	0	ENST00000338641.4:c.1690G>A	p.Glu564Lys	p.E564K	ENST00000338641	NM_000268.3	564	Gag/Aag	15/16	0.368677685812047	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.368677685812047	2		386	766	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860908	151860908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007834-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	87	138	0	ENST00000262189.6:c.9754C>T	p.Arg3252Cys	p.R3252C	ENST00000262189	NM_170606.2	3252	Cgt/Tgt	43/59	0.188472383039087	3	FACETS	1	0.981	1	0.742	0.668	0.819	INDETERMINATE	1	TRUE	1	0.63576697768034	3		138	243	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184559	11184559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007834-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	78	512	0	ENST00000361445.4:c.6658C>T	p.Leu2220Phe	p.L2220F	ENST00000361445	NM_004958.3	2220	Ctc/Ttc	47/58	1	2	FACETS	0.413	0.363	0.467	0.413	0.363	0.467	SUBCLONAL	1	TRUE	1	0.63576697768034	2		512	594	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183782	10183782	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007834-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	120	318	0	ENST00000256474.2:c.251T>A	p.Val84Glu	p.V84E	ENST00000256474	NM_000551.3	84	gTg/gAg	1/3	0.63576697768034	1	FACETS	0.954	0.877	1	0.954	0.877	1	CLONAL	1	TRUE	0	0.63576697768034	1		318	270	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52676063	52676063	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0007834-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	101	255	0	ENST00000394830.3:c.996-2A>G		p.X332_splice	ENST00000394830	NM_018313.4	332			0.63576697768034	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.63576697768034	1		255	208	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226093	2226093	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007834-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	189	642	0	ENST00000326181.6:c.1790G>T	p.Gly597Val	p.G597V	ENST00000326181	NM_032271.2	597	gGc/gTc	19/21	NA	2	FACETS	0.948	0.881	1			1	INDETERMINATE	1	TRUE	NA	0.63576697768034	2		642	627	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333664	70333664	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007834-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	35	502	0	ENST00000373644.4:c.1569del	p.Phe524SerfsTer7	p.F524Sfs*7	ENST00000373644	NM_030625.2	523	ctC/ct	2/12	1	2	FACETS	0.203	0.166	0.245	0.203	0.166	0.245	SUBCLONAL	1	TRUE	1	0.63576697768034	2		502	542	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857503	68857504	+	missense_variant	Missense_Mutation	DNP	TT	TT	AC	novel	NA	P-0007834-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	108	333	0	ENST00000261769.5:c.2138_2139delinsAC	p.Ile713Asn	p.I713N	ENST00000261769	NM_004360.3	713	aTT/aAC	13/16	1	2	FACETS	0.892	0.807	0.979	0.892	0.807	0.979	CLONAL	1	TRUE	1	0.63576697768034	2		333	381	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0007841-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	95	467	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.359887486288146	5	FACETS	0.64	0.568	0.718	0.213	0.189	0.24	SUBCLONAL	1	FALSE	2	0.359887486288146	5		467	1270	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0007841-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	174	407	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.359887486288146	5	FACETS	1	0.96	1	0.708	0.654	0.764	CLONAL	2	FALSE	2	0.359887486288146	5		407	701	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253911	NA	P-0007841-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	54	333	0	ENST00000269305.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000269305	NM_001126112.2	180	Gag/Aag	5/11	0.147642551737021	2	FACETS	0.777	0.666	0.898	0.389	0.333	0.449	INDETERMINATE	1	FALSE	0	0.359887486288146	2		333	386	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330484	65330484	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007841-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	96	234	0	ENST00000342505.4:c.1162G>A	p.Asp388Asn	p.D388N	ENST00000342505	NM_002227.2	388	Gac/Aac	8/25	0.359887486288146	4	FACETS	1	0.954	1	0.376	0.335	0.42	CLONAL	1	FALSE	1	0.359887486288146	4		234	643	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136148	11136148	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007841-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	74	775	0	ENST00000358026.2:c.3132G>C	p.Lys1044Asn	p.K1044N	ENST00000358026	NM_001128849.1	1044	aaG/aaC	22/36	NA	2	FACETS	0.479	0.419	0.545			1	INDETERMINATE	1	FALSE	NA	0.359887486288146	2		775	858	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0007871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	306	377	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.350569578990203	3	FACETS	0.927	0.896	0.956			1	INDETERMINATE	3	FALSE	NA	0.777652820090016	3		377	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579442	7579442	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs534447939	NA	P-0007871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	31	273	0	ENST00000269305.4:c.245C>T	p.Pro82Leu	p.P82L	ENST00000269305	NM_001126112.2	82	cCg/cTg	4/11	0.350569578990203	3	FACETS	0.37	0.3	0.449			1	INDETERMINATE	1	FALSE	NA	0.777652820090016	3		273	299	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344771	65344771	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	171	344	0	ENST00000342505.4:c.266A>C	p.Tyr89Ser	p.Y89S	ENST00000342505	NM_002227.2	89	tAt/tCt	4/25	0.777652820090016	3	FACETS	1	0.989	1	0.696	0.647	0.745	CLONAL	1	FALSE	1	0.777652820090016	3		344	439	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873466	136873466	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1360006297	NA	P-0007871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	192	699	0	ENST00000241393.3:c.32A>G	p.Asn11Ser	p.N11S	ENST00000241393	NM_003467.2	11	aAc/aGc	2/2	NA	2	FACETS	0.741	0.689	0.796			1	INDETERMINATE	1	FALSE	NA	0.777652820090016	2		699	666	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39751884	39751884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	173	416	2	ENST00000361337.2:c.2245C>T	p.Arg749Trp	p.R749W	ENST00000361337	NM_003286.2	749	Cgg/Tgg	21/21	0.53891337737284	4	FACETS	1	0.983	1	0.615	0.568	0.663	CLONAL	1	FALSE	2	0.777652820090016	4		418	643	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732401	74732410	+	frameshift_variant	Frame_Shift_Del	DEL	TGGACCTTCG	TGGACCTTCG	-	novel	NA	P-0007871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1347	880	585	0	ENST00000359995.5:c.499_508del	p.Arg167SerfsTer62	p.R167Sfs*62	ENST00000359995	NM_001195427.1	167	CGAAGGTCCAag/ag	2/3	0.740283577128598	4	FACETS	0.903	0.875	0.932	0.602	0.583	0.621	CLONAL	2	FALSE	1	0.777652820090016	4		585	2227	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908866	101908882	+	protein_altering_variant	In_Frame_Del	DEL	AATTGCTCGACGATGTT	AATTGCTCGACGATGTT	TA	novel	NA	P-0007871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	120	367	0	ENST00000374994.4:c.1230_1246delinsTA	p.Glu410_Ser416delinsAspThr	p.E410_S416delinsDT	ENST00000374994	NM_004612.2	410	gaAATTGCTCGACGATGTTcc/gaTAcc	7/9	0.334115479843665	6	FACETS	0.789	0.716	0.865	0.526	0.477	0.577	INDETERMINATE	2	FALSE	3	0.777652820090016	6		367	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0007961-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	219	299	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.247795811468829	3	FACETS	0.888	0.825	0.953	0.888	0.825	0.953	CLONAL	2	TRUE	1	0.247795811468829	3		299	1119	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643328	52643328	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0007961-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	198	400	0	ENST00000394830.3:c.2567+1G>C		p.X856_splice	ENST00000394830	NM_018313.4	856			0.208026361105965	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.247795811468829	2		400	698	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237596	16237596	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007961-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	62	314	0	ENST00000375759.3:c.1043A>T	p.Asp348Val	p.D348V	ENST00000375759	NM_015001.2	348	gAt/gTt	5/15	0.215293056057612	3	FACETS	0.826	0.713	0.949	0.413	0.356	0.475	CLONAL	1	TRUE	1	0.247795811468829	3		314	681	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156848942	156848942	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007961-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	130	316	0	ENST00000524377.1:c.1834G>A	p.Ala612Thr	p.A612T	ENST00000524377	NM_002529.3	612	Gct/Act	15/17	0.215293056057612	3	FACETS	1	0.962	1	0.559	0.506	0.615	CLONAL	1	TRUE	1	0.247795811468829	3		316	1054	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849036	156849036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007961-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	123	301	0	ENST00000524377.1:c.1928G>A	p.Gly643Asp	p.G643D	ENST00000524377	NM_002529.3	643	gGt/gAt	15/17	0.215293056057612	3	FACETS	1	0.928	1	0.517	0.466	0.571	CLONAL	1	TRUE	1	0.247795811468829	3		301	1079	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505508	25505508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753287419	NA	P-0007961-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1271	72	385	1	ENST00000264709.3:c.250G>A	p.Ala84Thr	p.A84T	ENST00000264709	NM_175629.2	84	Gcc/Acc	4/23	0.160143291084619	3	FACETS	0.486	0.423	0.555	0.162	0.141	0.185	SUBCLONAL	1	TRUE	0	0.247795811468829	3		386	1343	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347852	347852	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007961-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1288	107	443	0	ENST00000262320.3:c.1654G>C	p.Ala552Pro	p.A552P	ENST00000262320	NM_003502.3	552	Gcc/Ccc	6/11	0.142122655914592	4	FACETS	0.772	0.69	0.86	0.386	0.345	0.43	INDETERMINATE	1	TRUE	2	0.247795811468829	4		443	1395	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191511	10191511	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007961-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	213	345	0	ENST00000256474.2:c.505del	p.Leu169Ter	p.L169*	ENST00000256474	NM_000551.3	168	agC/ag	3/3	0.208026361105965	2	FACETS	0.934	0.869	1	0.934	0.869	1	CLONAL	2	TRUE	0	0.247795811468829	2		345	920	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007986-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	56	589	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.815	0.703	0.936	0.815	0.703	0.936	CLONAL	1	TRUE	1	0.445941118963995	2		590	308	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0007986-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	223	401	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.445941118963995	2		401	966	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112602	115112602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs865915137	NA	P-0007986-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	107	208	0	ENST00000257566.3:c.1138G>A	p.Glu380Lys	p.E380K	ENST00000257566	NM_016569.3	380	Gag/Aag	7/8	1	2	FACETS	0.926	0.834	1	0.926	0.834	1	CLONAL	1	TRUE	1	0.445941118963995	2		208	518	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403607	138403607	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs776640223	NA	P-0007986-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	223	356	0	ENST00000289153.2:c.2175A>T	p.Leu725Phe	p.L725F	ENST00000289153	NM_006219.2	725	ttA/ttT	15/22	1	2	FACETS	0.908	0.844	0.973	0.908	0.844	0.973	CLONAL	1	TRUE	1	0.445941118963995	2		356	1102	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435721	116435721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751186512	NA	P-0007986-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	260	232	0	ENST00000397752.3:c.3811G>A	p.Val1271Met	p.V1271M	ENST00000397752	NM_000245.2	1271	Gtg/Atg	20/21	0.384436820457495	3	FACETS	0.843	0.792	0.895	0.843	0.792	0.895	CLONAL	2	TRUE	1	0.445941118963995	3		232	846	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415619	49415619	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007986-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	122	284	0	ENST00000301067.7:c.16558C>T	p.Gln5520Ter	p.Q5520*	ENST00000301067	NM_003482.3	5520	Cag/Tag	54/54	1	2	FACETS	0.827	0.748	0.909	0.827	0.748	0.909	CLONAL	1	TRUE	1	0.445941118963995	2		284	662	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907620	76907620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007986-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	203	404	4	ENST00000373344.5:c.4541G>A	p.Arg1514Gln	p.R1514Q	ENST00000373344	NM_000489.3	1514	cGa/cAa	15/35	1	2	FACETS	0.726	0.672	0.783	0.726	0.672	0.783	SUBCLONAL	1	TRUE	1	0.445941118963995	2		408	1254	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207631	2207631	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	154	579	1	ENST00000398665.3:c.915G>T	p.Trp305Cys	p.W305C	ENST00000398665	NM_032482.2	305	tgG/tgT	11/28	0.262213247884811	1	FACETS	0.974	0.89	1	0.974	0.89	1	CLONAL	1	TRUE	0	0.262213247884811	1		580	1048	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs11575997	NA	P-0008058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	131	404	1	ENST00000269305.4:c.993+1G>T		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.227020047441141	1	FACETS	0.956	0.867	1	0.956	0.867	1	CLONAL	1	TRUE	0	0.262213247884811	1		405	908	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026112	71026112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs797045585	NA	P-0008058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	63	349	0	ENST00000318789.4:c.1510C>T	p.Arg504Cys	p.R504C	ENST00000318789	NM_032682.5	504	Cgc/Tgc	17/21	0.262213247884811	1	FACETS	0.507	0.437	0.583	0.507	0.437	0.583	SUBCLONAL	1	TRUE	0	0.262213247884811	1		349	824	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023261	27023261	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	87	194	0	ENST00000324856.7:c.367G>T	p.Gly123Cys	p.G123C	ENST00000324856	NM_006015.4	123	Ggc/Tgc	1/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.262213247884811	2		194	499	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215271	142215271	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747178249	NA	P-0008058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	114	469	0	ENST00000350721.4:c.5830C>G	p.Leu1944Val	p.L1944V	ENST00000350721	NM_001184.3	1944	Ctc/Gtc	34/47	1	2	FACETS	0.788	0.708	0.874	0.788	0.708	0.874	SUBCLONAL	1	TRUE	1	0.262213247884811	2		469	1103	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911214	29911214	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs199474546	NA	P-0008058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	31	260	0	ENST00000376809.5:c.513G>A	p.Trp171Ter	p.W171*	ENST00000376809	NM_002116.7	171	tgG/tgA	3/8	1	2	FACETS	0.407	0.328	0.497	0.407	0.328	0.497	SUBCLONAL	1	TRUE	1	0.262213247884811	2		260	581	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673419	30673419	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	146	429	1	ENST00000376406.3:c.3541G>T	p.Glu1181Ter	p.E1181*	ENST00000376406	NM_014641.2	1181	Gag/Tag	10/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.262213247884811	2		430	986	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117629961	117629961	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	43	390	0	ENST00000368508.3:c.6565G>C	p.Asp2189His	p.D2189H	ENST00000368508	NM_002944.2	2189	Gat/Cat	41/43	1	2	FACETS	0.48	0.401	0.569	0.48	0.401	0.569	SUBCLONAL	1	TRUE	1	0.262213247884811	2		390	683	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704661	117704661	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	69	316	0	ENST00000368508.3:c.2315A>T	p.Gln772Leu	p.Q772L	ENST00000368508	NM_002944.2	772	cAg/cTg	16/43	1	2	FACETS	0.982	0.856	1	0.982	0.856	1	CLONAL	1	TRUE	1	0.262213247884811	2		316	536	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623655	43623655	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	136	445	0	ENST00000355710.3:c.3283G>T	p.Val1095Leu	p.V1095L	ENST00000355710	NM_020975.4	1095	Gta/Tta	20/20	0.262213247884811	1	FACETS	0.847	0.769	0.93	0.847	0.769	0.93	CLONAL	1	TRUE	0	0.262213247884811	1		445	1064	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427446	49427446	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	143	479	0	ENST00000301067.7:c.11042A>T	p.Gln3681Leu	p.Q3681L	ENST00000301067	NM_003482.3	3681	cAg/cTg	39/54	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.262213247884811	2		479	1023	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574364	95574364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	95	393	0	ENST00000393063.1:c.2503G>A	p.Gly835Ser	p.G835S	ENST00000393063	NM_030621.3	835	Ggt/Agt	17/28	1	2	FACETS	0.918	0.817	1	0.918	0.817	1	CLONAL	1	TRUE	1	0.262213247884811	2		393	789	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427027	49427027	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	46	295	0	ENST00000301067.7:c.11461del	p.Gln3821ArgfsTer9	p.Q3821Rfs*9	ENST00000301067	NM_003482.3	3821	Cag/ag	39/54	1	2	FACETS	0.675	0.568	0.793	0.675	0.568	0.793	SUBCLONAL	1	TRUE	1	0.262213247884811	2		295	520	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0008156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	532	529	1	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	0.362585085688918	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	2	0.45176230851789	4		530	1571	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs864622237	NA	P-0008156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	220	361	0	ENST00000269305.4:c.700T>C	p.Tyr234His	p.Y234H	ENST00000269305	NM_001126112.2	234	Tac/Cac	7/11	0.339449023274661	2	FACETS	0.783	0.733	0.834	0.783	0.733	0.834	SUBCLONAL	2	TRUE	0	0.45176230851789	2		361	622	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450138	32450138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777166391	NA	P-0008156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	97	307	0	ENST00000332351.3:c.674C>T	p.Thr225Met	p.T225M	ENST00000332351	NM_024426.4	225	aCg/aTg	2/10	0.433083767508685	4	FACETS	0.594	0.528	0.665	0.297	0.264	0.333	SUBCLONAL	1	TRUE	2	0.45176230851789	4		307	1049	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509145	106509145	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	114	414	1	ENST00000359195.3:c.1139C>A	p.Thr380Lys	p.T380K	ENST00000359195	NM_002649.2	380	aCa/aAa	2/11	0.433083767508685	4	FACETS	0.68	0.611	0.754	0.34	0.305	0.377	SUBCLONAL	1	TRUE	2	0.45176230851789	4		415	1077	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922260	100922260	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	554	850	0	ENST00000325455.5:c.2252T>C	p.Ile751Thr	p.I751T	ENST00000325455	NM_001202474.3	751	aTt/aCt	5/8	0.351162124670564	3	FACETS	1	0.994	1	0.782	0.752	0.812	CLONAL	2	TRUE	0	0.45176230851789	3		850	1282	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832538	72832538	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1517	161	760	1	ENST00000268489.5:c.4043C>T	p.Pro1348Leu	p.P1348L	ENST00000268489	NM_006885.3	1348	cCt/cTt	9/10	0.371872234256164	3	FACETS	0.521	0.475	0.568	0.26	0.237	0.284	SUBCLONAL	1	TRUE	1	0.45176230851789	3		761	1678	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0008163-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	133	345	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	0.28	2		345	817	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008163-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	147	589	1				ENST00000310581	NM_198253.2	-/1132			0.264586387328325	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.28	3		590	517	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507362	8507362	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008163-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1223	161	573	0	ENST00000356435.5:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000356435		539	cCa/cGa	11/35	1	2	FACETS	0.831	0.76	0.906	0.831	0.76	0.906	CLONAL	1	TRUE	1	0.28	2		573	1384	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343667	118343667	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008163-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	116	317	0	ENST00000534358.1:c.1793C>T	p.Pro598Leu	p.P598L	ENST00000534358	NM_005933.3	598	cCt/cTt	3/36	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.28	2		317	785	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831042	72831042	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008163-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1330	246	916	0	ENST00000268489.5:c.5539C>T	p.Gln1847Ter	p.Q1847*	ENST00000268489	NM_006885.3	1847	Cag/Tag	9/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.28	2		916	1576	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110178	3110178	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008163-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	151	495	0	ENST00000078429.4:c.168C>G	p.Ile56Met	p.I56M	ENST00000078429	NM_002067.2	56	atC/atG	2/7	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.28	2		495	937	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0008270-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	312	403	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.787851205818814	2		403	689	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0008270-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	114	320	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.787851205818814	2		320	288	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586149	29586149	+	splice_donor_variant	Splice_Site	SNP	T	T	G	rs1555618693	NA	P-0008270-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	245	283	0	ENST00000356175.3:c.4367+2T>G		p.X1456_splice	ENST00000356175	NM_000267.3	1456			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.787851205818814	2		283	584	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791393	42791393	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0008270-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	50	766	0	ENST00000575354.2:c.452+1G>A		p.X151_splice	ENST00000575354	NM_015125.3	151			0.787851205818814	1	FACETS	0.217	0.184	0.252	0.217	0.184	0.252	SUBCLONAL	1	TRUE	0	0.787851205818814	1		766	355	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798996	42798996	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008270-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	63	380	0	ENST00000575354.2:c.4480C>T	p.Gln1494Ter	p.Q1494*	ENST00000575354	NM_015125.3	1494	Cag/Tag	20/20	0.787851205818814	1	FACETS	0.22	0.191	0.252	0.22	0.191	0.252	SUBCLONAL	1	TRUE	0	0.787851205818814	1		380	440	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439661	51439666	+	inframe_deletion	In_Frame_Del	DEL	GATGCG	GATGCG	-	novel	NA	P-0008270-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	248	334	0	ENST00000262662.1:c.227_232del	p.Asp76_Ala77del	p.D76_A77del	ENST00000262662		76	GATGCG/-	4/4	0.787851205818814	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.787851205818814	1		334	364	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794066	42794067	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0008270-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	83	315	0	ENST00000575354.2:c.1428_1429del	p.Ser476ArgfsTer37	p.S476Rfs*37	ENST00000575354	NM_015125.3	476	aGT/a	9/20	0.787851205818814	1	FACETS	0.386	0.343	0.43	0.386	0.343	0.43	SUBCLONAL	1	TRUE	0	0.787851205818814	1		315	331	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254887	16254887	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008348-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	555	518	1	ENST00000375759.3:c.2152G>T	p.Glu718Ter	p.E718*	ENST00000375759	NM_015001.2	718	Gag/Tag	11/15	1	2	FACETS	0.987	0.949	1	0.987	0.949	1	CLONAL	1	TRUE	1	0.889992776628603	2		519	1264	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332892	65332892	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0008348-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	331	314	0	ENST00000342505.4:c.648-1G>T		p.X216_splice	ENST00000342505	NM_002227.2	216			0.889992776628603	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.889992776628603	1		314	392	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467631	50467631	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008348-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	149	249	0	ENST00000331340.3:c.866C>A	p.Ser289Tyr	p.S289Y	ENST00000331340	NM_006060.4	289	tCc/tAc	8/8	0.889992776628603	3	FACETS	0.582	0.532	0.635	0.291	0.266	0.318	SUBCLONAL	1	TRUE	1	0.889992776628603	3		249	831	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0008360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	316	345	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.510172192826146	5	FACETS	0.96	0.906	1	0.64	0.604	0.676	CLONAL	2	TRUE	2	0.573743629748473	5		345	1068	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057520000	NA	P-0008360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	462	424	0	ENST00000269305.4:c.452C>A	p.Pro151His	p.P151H	ENST00000269305	NM_001126112.2	151	cCc/cAc	5/11	0.552831620256629	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.573743629748473	2		424	712	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934152	48934152	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0008360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	234	243	0	ENST00000267163.4:c.608-1G>A		p.X203_splice	ENST00000267163	NM_000321.2	203			0.287238845716028	3	FACETS	0.84	0.789	0.892	0.84	0.789	0.892	INDETERMINATE	2	TRUE	1	0.573743629748473	3		243	625	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944422	40944422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	524	650	0	ENST00000373198.4:c.2080C>T	p.Pro694Ser	p.P694S	ENST00000373198	NM_133170.3	694	Cct/Tct	12/32	0.284439611971511	4	FACETS	0.997	0.956	1			1	INDETERMINATE	2	TRUE	NA	0.573743629748473	4		650	1442	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247417	71247417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	253	391	0	ENST00000318789.4:c.116G>A	p.Gly39Glu	p.G39E	ENST00000318789	NM_032682.5	39	gGa/gAa	6/21	0.149298456827591	3	FACETS	1	0.993	1	0.721	0.677	0.766	INDETERMINATE	1	TRUE	1	0.573743629748473	3		391	787	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026436	6026436	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	78	107	0	ENST00000265849.7:c.1960C>T	p.Pro654Ser	p.P654S	ENST00000265849	NM_000535.5	654	Cct/Tct	11/15	0.380988641068585	6	FACETS	1	0.936	1	0.539	0.479	0.601	CLONAL	2	TRUE	2	0.573743629748473	6		107	271	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276938	123276938	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	338	451	0	ENST00000358487.5:c.979C>T	p.Leu327Phe	p.L327F	ENST00000358487	NM_000141.4	327	Ctc/Ttc	8/18	0.534953692423615	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.573743629748473	1		451	642	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414868	56414868	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	229	933	0	ENST00000348428.3:c.2269T>A	p.Phe757Ile	p.F757I	ENST00000348428	NM_006785.3	757	Ttc/Atc	17/17	0.346540723981253	2	FACETS	0.559	0.519	0.6	0.279	0.259	0.3	SUBCLONAL	1	TRUE	0	0.573743629748473	2		933	1429	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039506	49039506	+	splice_donor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0008360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	168	506	0	ENST00000267163.4:c.2489+2del		p.X830_splice	ENST00000267163	NM_000321.2	830			0.287238845716028	3	FACETS	0.825	0.758	0.894	0.412	0.379	0.447	INDETERMINATE	1	TRUE	1	0.573743629748473	3		506	914	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692776	89692785	+	frameshift_variant	Frame_Shift_Del	DEL	AATATCCTTT	AATATCCTTT	-	novel	NA	P-0008360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	193	326	2	ENST00000371953.3:c.260_269del	p.Gln87LeufsTer9	p.Q87Lfs*9	ENST00000371953	NM_000314.4	87	cAATATCCTTTt/ct	5/9	0.135968690688007	1	FACETS	1	0.979	1	1	0.979	1	INDETERMINATE	1	TRUE	0	0.573743629748473	1		328	433	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0008717-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	60	420	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	1	0.926	1			1	INDETERMINATE	1	TRUE	NA	0.221759082019408	2		420	486	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0008717-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	16	195	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.221759082019408	6	FACETS	0.602	0.444	0.792			1	SUBCLONAL	1	TRUE	NA	0.221759082019408	6		195	346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201059	NA	P-0008717-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	171	427	0	ENST00000269305.4:c.856G>T	p.Glu286Ter	p.E286*	ENST00000269305	NM_001126112.2	286	Gaa/Taa	8/11	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.221759082019408	2		427	1198	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349973	70349973	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1421325265	NA	P-0008717-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	79	501	1	ENST00000374080.3:c.3956G>A	p.Arg1319His	p.R1319H	ENST00000374080		1319	cGc/cAc	28/45	1	2	FACETS	0.592	0.519	0.672	0.592	0.519	0.672	SUBCLONAL	1	TRUE	1	0.221759082019408	2		502	1203	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0008719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	41	546	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.714	0.595	0.846	0.714	0.595	0.846	SUBCLONAL	1	TRUE	1	0.264475744161885	2		546	434	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067836	30067836	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315499	NA	P-0008719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	98	228	0	ENST00000338641.4:c.1021C>T	p.Arg341Ter	p.R341*	ENST00000338641	NM_000268.3	341	Cga/Tga	11/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.264475744161885	2		228	611	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0008727-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	67	500	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.296376586105202	4	FACETS	0.847	0.739	0.963	0.847	0.739	0.963	CLONAL	2	TRUE	2	0.23	4		500	423	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0008727-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	22	572	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.846	0.658	1	0.846	0.658	1	CLONAL	1	TRUE	1	0.23	2		573	226	SUCCESS
APC	324	MSKCC	GRCh37	5	112175755	112175755	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008727-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	14	358	0	ENST00000257430.4:c.4464del	p.Leu1488PhefsTer19	p.L1488Ffs*19	ENST00000257430	NM_000038.5	1488	ttA/tt	16/16	0.296376586105202	4	FACETS	1	0.824	1	0.594	0.433	0.786	CLONAL	1	TRUE	2	0.23	4		358	126	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0008727-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	16	319	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	0.296376586105202	4	FACETS	1	0.834	1	0.586	0.436	0.762	CLONAL	1	TRUE	2	0.23	4		319	146	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752845	128752845	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008727-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	76	254	1	ENST00000377970.2:c.1006G>A	p.Ala336Thr	p.A336T	ENST00000377970	NM_002467.4	336	Gct/Act	3/3	0.296376586105202	6	FACETS	1	0.962	1	0.252	0.221	0.286	CLONAL	1	TRUE	1	0.23	6		255	765	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624272	89624272	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1064796078	NA	P-0008727-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	51	183	0	ENST00000371953.3:c.46T>G	p.Tyr16Asp	p.Y16D	ENST00000371953	NM_000314.4	16	Tat/Gat	1/9	1	2	FACETS	1	0.917	1	1	0.978	1	CLONAL	2	TRUE	1	0.23	2		183	203	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40456400	40456400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008727-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	77	877	0	ENST00000345506.4:c.1210G>A	p.Glu404Lys	p.E404K	ENST00000345506	NM_003152.3	404	Gag/Aag	11/20	0.258502759685314	0	FACETS	1	0.886	1			1	CLONAL	1	TRUE	0	0.23	0		877	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579434	7579715	+	splice_donor_variant,splice_acceptor_variant,frameshift_variant,stop_lost,intron_variant	Splice_Site	DEL	GGGCCGCCGGTGTAGGAGCTGCTGGTGCAGGGGCCACGGGGGGAGCAGCCTCTGGCATTCTGGGAGCTTCATCTGGACCTGGGTCTTCAGTGAACCATTGTTCAATATCGTCCGGGGACAGCATCAAATCATCCATTGCTTGGGACGGCAAGGGGGACTGTAGATGGGTGAAAAGAGCAGTCAGAGGACCAGGTCCTCAGCCCCCCAGCCCCCCAGCCCTCCAGGTCCCCAGCCCTCCAGGTCCCCAGCCCAACCCTTGTCCTTACCAGAACGTTGTTTTCA	GGGCCGCCGGTGTAGGAGCTGCTGGTGCAGGGGCCACGGGGGGAGCAGCCTCTGGCATTCTGGGAGCTTCATCTGGACCTGGGTCTTCAGTGAACCATTGTTCAATATCGTCCGGGGACAGCATCAAATCATCCATTGCTTGGGACGGCAAGGGGGACTGTAGATGGGTGAAAAGAGCAGTCAGAGGACCAGGTCCTCAGCCCCCCAGCCCCCCAGCCCTCCAGGTCCCCAGCCCTCCAGGTCCCCAGCCCAACCCTTGTCCTTACCAGAACGTTGTTTTCA	-	novel	NA	P-0008727-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	65	412	1	ENST00000269305.4:c.81_253del		p.X27_splice	ENST00000269305	NM_001126112.2	27	ccTGAAAACAACGTTCTGGTAAGGACAAGGGTTGGGCTGGGGACCTGGAGGGCTGGGGACCTGGAGGGCTGGGGGGCTGGGGGGCTGAGGACCTGGTCCTCTGACTGCTCTTTTCACCCATCTACAGTCCCCCTTGCCGTCCCAAGCAATGGATGATTTGATGCTGTCCCCGGACGATATTGAACAATGGTTCACTGAAGACCCAGGTCCAGATGAAGCTCCCAGAATGCCAGAGGCTGCTCCCCCCGTGGCCCCTGCACCAGCAGCTCCTACACCGGCGGCCCct/ccct	3-4/11	0.296376586105202	4	FACETS	0.974	0.855	1	1	0.973	1	CLONAL	3	TRUE	2	0.23	4		413	238	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710571	114710574	+	frameshift_variant	Frame_Shift_Del	DEL	TTTC	TTTC	-	novel	NA	P-0008727-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	298	1070	0	ENST00000543371.1:c.56_59del	p.Ile19ThrfsTer22	p.I19Tfs*22	ENST00000543371	NM_001198531.1	19	aTTTCc/ac	1/14	1	2	FACETS	1	0.972	1	1	0.996	1	CLONAL	2	TRUE	1	0.23	2		1070	1229	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0008875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	84	513	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.792	0.702	0.886	0.792	0.702	0.886	SUBCLONAL	1	TRUE	1	0.48459039539306	2		514	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs878854073	NA	P-0008875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	177	405	1	ENST00000269305.4:c.673-1G>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.381470443339066	3	FACETS	0.911	0.855	0.967	0.911	0.855	0.967	CLONAL	3	TRUE	0	0.48459039539306	3		406	332	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258744	115258744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434596	NA	P-0008875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	242	400	0	ENST00000369535.4:c.38G>A	p.Gly13Asp	p.G13D	ENST00000369535	NM_002524.4	13	gGt/gAt	2/7	0.172600043557416	3	FACETS	1	0.97	1	1	0.97	1	INDETERMINATE	2	TRUE	1	0.48459039539306	3		400	592	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0008875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	39	239	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	1	2	FACETS	0.722	0.603	0.851	0.722	0.603	0.851	SUBCLONAL	1	TRUE	1	0.48459039539306	2		239	223	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076805	72076805	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	91	389	0	ENST00000357731.5:c.692A>C	p.Lys231Thr	p.K231T	ENST00000357731	NM_173808.2	231	aAa/aCa	5/7	0.172600043557416	3	FACETS	0.845	0.752	0.944	0.423	0.376	0.472	INDETERMINATE	1	TRUE	1	0.48459039539306	3		389	552	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440102	220440102	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	72	632	0	ENST00000243786.2:c.955T>G	p.Ser319Ala	p.S319A	ENST00000243786	NM_002191.3	319	Tcc/Gcc	2/2	0.48508330725988	3	FACETS	0.462	0.403	0.526	0.231	0.201	0.263	SUBCLONAL	1	TRUE	1	0.48459039539306	3		632	799	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226370	2226370	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	74	366	0	ENST00000398665.3:c.3850G>C	p.Ala1284Pro	p.A1284P	ENST00000398665	NM_032482.2	1284	Gcc/Ccc	27/28	0.48508330725988	3	FACETS	0.584	0.511	0.662	0.292	0.255	0.331	SUBCLONAL	1	TRUE	1	0.48459039539306	3		366	650	SUCCESS
AR	367	MSKCC	GRCh37	X	66931285	66931285	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	219	340	0	ENST00000374690.3:c.1927G>T	p.Glu643Ter	p.E643*	ENST00000374690	NM_000044.3	643	Gaa/Taa	4/8	0.48508330725988	2	FACETS	0.842	0.799	0.883			1	CLONAL	3	TRUE	NA	0.48459039539306	2		340	358	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0008973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	90	420	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.814	0.722	0.912	1	0.981	1	CLONAL	2	TRUE	1	0.15	2		420	737	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	86	248	0	ENST00000397752.3:c.3028G>A	p.Asp1010Asn	p.D1010N	ENST00000397752	NM_000245.2	1010	Gat/Aat	14/21	1	2	FACETS	1	0.913	1	1	0.985	1	CLONAL	2	TRUE	1	0.15	2		248	554	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186791	11186791	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	72	485	1	ENST00000361445.4:c.6414G>T	p.Leu2138Phe	p.L2138F	ENST00000361445	NM_004958.3	2138	ttG/ttT	46/58	1	2	FACETS	0.979	0.853	1	0.979	0.853	1	CLONAL	1	TRUE	1	0.15	2		486	981	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022114	5022114	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	184	518	0	ENST00000381652.3:c.127C>A	p.Leu43Ile	p.L43I	ENST00000381652	NM_004972.3	43	Ctt/Att	3/25	1	2	FACETS	1	0.971	1	1	0.993	1	CLONAL	2	TRUE	1	0.15	2		518	1108	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578467	7578498	+	frameshift_variant	Frame_Shift_Del	DEL	TGCCGGGCGGGGGTGTGGAATCAACCCACAGC	TGCCGGGCGGGGGTGTGGAATCAACCCACAGC	-	novel	NA	P-0008973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	82	378	0	ENST00000269305.4:c.432_463del	p.Gln144HisfsTer26	p.Q144Hfs*26	ENST00000269305	NM_001126112.2	144	caGCTGTGGGTTGATTCCACACCCCCGCCCGGCAcc/cacc	5/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.15	2		378	752	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939972	76939973	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0008973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1273	80	600	1	ENST00000373344.5:c.775_776delinsTT	p.Glu259Leu	p.E259L	ENST00000373344	NM_000489.3	259	GAa/TTa	9/35	1	2	FACETS	0.788	0.691	0.894	0.788	0.691	0.894	SUBCLONAL	1	TRUE	1	0.15	2		601	1353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0008995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	452	342	0	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.624488735803789	3	FACETS	1	0.994	1	0.777	0.748	0.806	CLONAL	2	FALSE	0	0.624488735803789	3		342	815	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599338	55599338	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	93	155	0	ENST00000288135.5:c.2464A>T	p.Asn822Tyr	p.N822Y	ENST00000288135	NM_000222.2	822	Aat/Tat	17/21	0.275225553923709	4	FACETS	0.979	0.886	1	0.49	0.443	0.538	INDETERMINATE	2	FALSE	0	0.624488735803789	4		155	247	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541896	187541896	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	54	480	0	ENST00000441802.2:c.5844C>A	p.Tyr1948Ter	p.Y1948*	ENST00000441802	NM_005245.3	1948	taC/taA	10/27	0.624488735803789	3	FACETS	0.222	0.189	0.259	0.111	0.094	0.13	SUBCLONAL	1	FALSE	1	0.624488735803789	3		480	1022	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564171	139564171	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008995-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	167	816	2	ENST00000308874.7:c.311C>G	p.Ala104Gly	p.A104G	ENST00000308874		104	gCa/gGa	5/10	0.366530445067424	3	FACETS	0.573	0.525	0.623	0.286	0.262	0.312	INDETERMINATE	1	FALSE	1	0.624488735803789	3		818	1225	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0009019-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	111	358	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	0.878	0.79	0.972	0.878	0.79	0.972	CLONAL	1	TRUE	1	0.359476524647517	2		358	703	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913492	NA	P-0009019-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	164	317	0	ENST00000286548.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000286548	NM_002072.3	209	cAa/cTa	5/7	0.335084538007896	3	FACETS	0.949	0.876	1	0.949	0.876	1	CLONAL	2	TRUE	1	0.359476524647517	3		317	567	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687457	37687457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009019-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	159	320	0	ENST00000447079.4:c.4361G>A	p.Gly1454Glu	p.G1454E	ENST00000447079	NM_015083.1	1454	gGa/gAa	14/14	0.335084538007896	3	FACETS	0.874	0.805	0.946	0.874	0.805	0.946	CLONAL	2	TRUE	1	0.359476524647517	3		320	597	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	74	589	1				ENST00000310581	NM_198253.2	-/1132			0.202470716111928	1	FACETS	0.834	0.73	0.946	0.834	0.73	0.946	CLONAL	1	TRUE	0	0.242790059479984	1		590	642	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0009101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	42	195	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.925	0.774	1	0.925	0.774	1	CLONAL	1	TRUE	1	0.242790059479984	2		195	374	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149589	202149589	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1045485	NA	P-0009101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	141	367	0	ENST00000358485.4:c.1030G>A	p.Asp344Asn	p.D344N	ENST00000358485	NM_001080125.1	344	Gat/Aat	8/9	1	2	FACETS	0.999	0.908	1	0.999	0.908	1	CLONAL	1	TRUE	1	0.242790059479984	2		367	1163	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0009101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	57	239	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	0.242790059479984	2		239	408	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0009101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	161	290	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.242790059479984	2		290	1034	SUCCESS
ATM	472	MSKCC	GRCh37	11	108183186	108183186	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	93	322	0	ENST00000278616.4:c.5967G>C	p.Leu1989Phe	p.L1989F	ENST00000278616	NM_000051.3	1989	ttG/ttC	40/63	1	2	FACETS	0.878	0.779	0.983	0.878	0.779	0.983	CLONAL	1	TRUE	1	0.242790059479984	2		322	873	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495692	56495702	+	frameshift_variant	Frame_Shift_Del	DEL	TTTTCAGGGGC	TTTTCAGGGGC	CCCT	novel	NA	P-0009101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	97	226	0	ENST00000267101.3:c.3882_3892delinsCCCT	p.Phe1295ProfsTer14	p.F1295Pfs*14	ENST00000267101	NM_001982.3	1294	gcTTTTCAGGGGCct/gcCCCTct	28/28	1	2	FACETS	0.983	0.876	1	0.983	0.876	1	CLONAL	1	TRUE	1	0.242790059479984	2		226	813	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40468824	40468824	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0009101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1508	186	625	0	ENST00000264657.5:c.2240C>G	p.Ser747Ter	p.S747*	ENST00000264657	NM_139276.2	747	tCa/tGa	23/24	NA	2	FACETS	0.904	0.832	0.98			1	INDETERMINATE	1	TRUE	NA	0.242790059479984	2		625	1694	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612404	1612404	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1610	164	603	0	ENST00000344749.5:c.1615G>C	p.Glu539Gln	p.E539Q	ENST00000344749	NM_001136139.2	539	Gag/Cag	18/19	1	2	FACETS	0.762	0.696	0.83	0.762	0.696	0.83	SUBCLONAL	1	TRUE	1	0.242790059479984	2		603	1774	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227124	2227124	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs368925819	NA	P-0009101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	26	123	0	ENST00000398665.3:c.4604G>T	p.Gly1535Val	p.G1535V	ENST00000398665	NM_032482.2	1535	gGa/gTa	27/28	1	2	FACETS	0.515	0.407	0.638	0.515	0.407	0.638	SUBCLONAL	1	TRUE	1	0.242790059479984	2		123	416	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2225395	2225395	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1238	129	430	1	ENST00000398665.3:c.3605del	p.Arg1202LysfsTer8	p.R1202Kfs*8	ENST00000398665	NM_032482.2	1202	aGa/aa	26/28	1	2	FACETS	0.777	0.702	0.857	0.777	0.702	0.857	SUBCLONAL	1	TRUE	1	0.242790059479984	2		431	1367	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	191	420	0	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	0.754057179257556	2		420	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0009118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	185	525	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.887	0.825	0.951	0.887	0.825	0.951	CLONAL	1	TRUE	1	0.754057179257556	2		526	553	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0009118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	205	424	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	0.754057179257556	1	FACETS	0.834	0.786	0.883	0.834	0.786	0.883	CLONAL	1	TRUE	0	0.754057179257556	1		424	406	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467814	66467814	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs780941416	NA	P-0009118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	212	384	0	ENST00000273854.3:c.455A>G	p.Asn152Ser	p.N152S	ENST00000273854	NM_004439.5	152	aAt/aGt	3/18	1	2	FACETS	0.999	0.935	1	0.999	0.935	1	CLONAL	1	TRUE	1	0.754057179257556	2		384	563	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535406	66535406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	67	79	0	ENST00000273854.3:c.55G>A	p.Gly19Ser	p.G19S	ENST00000273854	NM_004439.5	19	Ggc/Agc	1/18	1	2	FACETS	0.827	0.73	0.928	0.827	0.73	0.928	CLONAL	1	TRUE	1	0.754057179257556	2		79	215	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942194	81942194	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs147406608	NA	P-0009118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	287	492	1	ENST00000359376.3:c.1731C>A	p.Phe577Leu	p.F577L	ENST00000359376	NM_002661.3	577	ttC/ttA	17/33	0.754057179257556	1	FACETS	0.996	0.952	1	0.996	0.952	1	CLONAL	1	TRUE	0	0.754057179257556	1		493	476	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038171	128038177	+	frameshift_variant	Frame_Shift_Del	DEL	GCCTGCA	GCCTGCA	-	novel	NA	P-0009118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	220	309	0	ENST00000285398.2:c.1373_1379del	p.Val458AlafsTer7	p.V458Afs*7	ENST00000285398	NM_000122.1	458	gTGCAGGCc/gc	9/15	1	2	FACETS	0.919	0.86	0.979	0.919	0.86	0.979	CLONAL	1	TRUE	1	0.754057179257556	2		309	635	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393097	393097	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0009118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	40	38	0	ENST00000380956.4:c.-55-1G>A		p.X19_splice	ENST00000380956	NM_001195286.1	19			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.754057179257556	NA		38	85	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0009216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	331	403	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.981	0.931	1	0.981	0.931	1	CLONAL	1	TRUE	1	0.807339516889605	2		403	836	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782329	NA	P-0009216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	1044	399	0	ENST00000269305.4:c.746G>C	p.Arg249Thr	p.R249T	ENST00000269305	NM_001126112.2	249	aGg/aCg	7/11	0.807339516889605	3	FACETS	0.982	0.967	0.996	0.982	0.967	0.996	CLONAL	3	TRUE	0	0.807339516889605	3		399	1232	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939793	76939793	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0009216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	664	402	0	ENST00000373344.5:c.955A>T	p.Lys319Ter	p.K319*	ENST00000373344	NM_000489.3	319	Aag/Tag	9/35	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.807339516889605	1		402	857	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0009244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	240	403	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.50835375300834	2		403	687	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814303	76814306	+	frameshift_variant	Frame_Shift_Del	DEL	ATAA	ATAA	-	novel	NA	P-0009244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	213	343	0	ENST00000373344.5:c.6338_6341del	p.Phe2113SerfsTer9	p.F2113Sfs*9	ENST00000373344	NM_000489.3	2113	tTTATc/tc	29/35	0.330230032651368	0	FACETS		NA	1			1	NA	2	TRUE	NA	0.50835375300834	0		343	300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578537	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs879254214	NA	P-0009244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	570	375	1	ENST00000269305.4:c.393_395del	p.Asn131del	p.N131del	ENST00000269305	NM_001126112.2	131	aaCAAg/aag	5/11	0.50835375300834	2	FACETS	0.937	0.911	0.962	1	0.997	1	CLONAL	3	TRUE	0	0.50835375300834	2		376	798	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0009277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	74	483	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.965	0.843	1	0.965	0.843	1	CLONAL	1	TRUE	1	0.14	2		483	1095	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600326	10600326	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	68	439	0	ENST00000171111.5:c.1529C>T	p.Ala510Val	p.A510V	ENST00000171111	NM_203500.1	510	gCa/gTa	4/6	1	2	FACETS	0.863	0.749	0.989	0.863	0.749	0.989	CLONAL	1	TRUE	1	0.14	2		439	1125	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0009297-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	104	351	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.250507351883809	2	FACETS	1	0.97	1	0.601	0.54	0.664	CLONAL	1	TRUE	0	0.362278252812128	2		351	478	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009297-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	252	507	0	ENST00000269305.4:c.403del	p.Cys135AlafsTer35	p.C135Afs*35	ENST00000269305	NM_001126112.2	135	Tgc/gc	5/11	0.250507351883809	2	FACETS	0.764	0.716	0.813	0.764	0.716	0.813	SUBCLONAL	2	TRUE	0	0.362278252812128	2		507	911	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468382	89468382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs570346631	NA	P-0009297-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	69	295	2	ENST00000336596.2:c.1916G>A	p.Arg639His	p.R639H	ENST00000336596	NM_005233.5	639	cGc/cAc	11/17	NA	2	FACETS	1	0.963	1			1	INDETERMINATE	1	TRUE	NA	0.362278252812128	2		297	303	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243675729	243675729	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0009297-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	82	247	0	ENST00000263826.5:c.1252-1G>A		p.X418_splice	ENST00000263826	NM_005465.4	418			0.362278252812128	5	FACETS	1	0.975	1	0.353	0.312	0.397	CLONAL	1	TRUE	1	0.362278252812128	5		247	495	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391076	89391076	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009297-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	223	545	0	ENST00000336596.2:c.1142G>C	p.Arg381Pro	p.R381P	ENST00000336596	NM_005233.5	381	cGc/cCc	5/17	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	1	TRUE	NA	0.362278252812128	2		545	1121	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751576	57751576	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009297-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	178	558	0	ENST00000274289.3:c.1415C>A	p.Ala472Glu	p.A472E	ENST00000274289	NM_006622.3	472	gCa/gAa	11/14	0.362278252812128	1	FACETS	0.952	0.879	1	0.952	0.879	1	CLONAL	1	TRUE	0	0.362278252812128	1		558	845	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464372	120464387	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGTGTTCACTTGTT	CCAGTGTTCACTTGTT	-	novel	NA	P-0009297-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	65	792	2	ENST00000256646.2:c.5259_5274del	p.Thr1754SerfsTer11	p.T1754Sfs*11	ENST00000256646	NM_024408.3	1753	ggAACAAGTGAACACTGG/gg	29/34	0.362278252812128	4	FACETS	0.506	0.437	0.58			1	SUBCLONAL	1	TRUE	NA	0.362278252812128	4		794	967	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433477	138433477	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009297-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	71	537	0	ENST00000289153.2:c.1135C>T	p.His379Tyr	p.H379Y	ENST00000289153	NM_006219.2	379	Cat/Tat	7/22	0.362278252812128	7	FACETS	0.707	0.615	0.807			1	SUBCLONAL	1	TRUE	NA	0.362278252812128	7		537	1056	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433537	138433537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009297-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	47	455	0	ENST00000289153.2:c.1075C>T	p.His359Tyr	p.H359Y	ENST00000289153	NM_006219.2	359	Cat/Tat	7/22	0.362278252812128	7	FACETS	0.634	0.533	0.745			1	SUBCLONAL	1	TRUE	NA	0.362278252812128	7		455	780	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0009322-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	121	446	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	NA	2	FACETS	0.638	0.575	0.706			1	INDETERMINATE	1	FALSE	NA	0.3	2		446	1264	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009322-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	113	448	0	ENST00000269305.4:c.859G>C	p.Glu287Gln	p.E287Q	ENST00000269305	NM_001126112.2	287	Gag/Cag	8/11	NA	2	FACETS	0.624	0.56	0.693			1	INDETERMINATE	1	FALSE	NA	0.3	2		448	1207	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218282	133218282	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1476621612	NA	P-0009378-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	224	442	0	ENST00000320574.5:c.5329A>G	p.Ser1777Gly	p.S1777G	ENST00000320574	NM_006231.2	1777	Agt/Ggt	39/49	1	2	FACETS	0.85	0.791	0.911	0.85	0.791	0.911	CLONAL	1	TRUE	1	0.489186969681304	2		442	1077	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652511	48652511	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009378-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	144	325	0	ENST00000376670.3:c.1185del	p.Thr396GlnfsTer36	p.T396Qfs*36	ENST00000376670	NM_002049.3	394	ttC/tt	6/6	1	2	FACETS	0.8	0.731	0.872	0.8	0.731	0.872	SUBCLONAL	1	TRUE	1	0.489186969681304	2		325	736	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0009437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	23	491	1	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	1	2	FACETS	0.131	0.101	0.166	0.131	0.101	0.166	SUBCLONAL	1	TRUE	1	0.57	2		492	616	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0009437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	35	692	0	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	1	2	FACETS	0.135	0.11	0.163	0.135	0.11	0.163	SUBCLONAL	1	TRUE	1	0.57	2		692	911	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371962	55371962	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	10	115	0	ENST00000297316.4:c.652C>A	p.Pro218Thr	p.P218T	ENST00000297316	NM_022454.3	218	Ccg/Acg	2/2	0.152870819300521	3	FACETS	0.256	0.173	0.36	0.128	0.086	0.18	INDETERMINATE	1	TRUE	1	0.57	3		115	176	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741800	145741800	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	134	417	0	ENST00000428558.2:c.703C>G	p.Gln235Glu	p.Q235E	ENST00000428558	NM_004260.3	235	Cag/Gag	5/22	0.152870819300521	3	FACETS	0.791	0.719	0.866	0.395	0.359	0.433	INDETERMINATE	1	TRUE	1	0.57	3		417	764	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984817	72984817	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	87	566	0	ENST00000268489.5:c.2767G>T	p.Val923Leu	p.V923L	ENST00000268489	NM_006885.3	923	Gtg/Ttg	3/10	1	2	FACETS	0.309	0.272	0.348	0.309	0.272	0.348	SUBCLONAL	1	TRUE	1	0.57	2		566	989	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0009501-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	712	357	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.354438128672021	12	FACETS	1	0.975	1			1	CLONAL	10	TRUE	NA	0.354438128672021	12		357	1111	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0009501-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	166	354	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	1	2	FACETS	0.927	0.858	0.998	1	0.992	1	CLONAL	2	TRUE	1	0.354438128672021	2		354	505	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535456	66535456	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs538762829	NA	P-0009501-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	26	100	0	ENST00000273854.3:c.5G>T	p.Arg2Leu	p.R2L	ENST00000273854	NM_004439.5	2	cGg/cTg	1/18	0.158135531134248	3	FACETS	0.904	0.722	1	0.301	0.24	0.37	INDETERMINATE	1	TRUE	0	0.354438128672021	3		100	191	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427495	427495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009501-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	215	407	0	ENST00000399788.2:c.2674C>T	p.Pro892Ser	p.P892S	ENST00000399788	NM_001042603.1	892	Cca/Tca	19/28	0.354438128672021	5	FACETS	0.913	0.848	0.979			1	CLONAL	2	TRUE	NA	0.354438128672021	5		407	1018	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679538	86679538	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009501-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	99	233	0	ENST00000274376.6:c.2703del	p.Leu902PhefsTer9	p.L902Ffs*9	ENST00000274376	NM_002890.2	900	gTt/gt	21/25	0.239130771924818	4	FACETS	0.92	0.827	1	0.46	0.413	0.509	CLONAL	2	TRUE	0	0.354438128672021	4		233	411	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63810726	63810728	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	rs774134980	NA	P-0009501-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	91	280	0	ENST00000279873.7:c.819_821del	p.Asn274del	p.N274del	ENST00000279873	NM_032199.2	271	tcCAAc/tcc	5/10	0.354438128672021	6	FACETS	0.926	0.82	1			1	CLONAL	1	TRUE	NA	0.354438128672021	6		280	948	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0009526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	246	462	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.554277527281724	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.554277527281724	1		463	554	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0009526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	34	429	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	1	2	FACETS	0.158	0.128	0.192	0.158	0.128	0.192	SUBCLONAL	1	TRUE	1	0.554277527281724	2		429	776	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838432	156838432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55909005	NA	P-0009526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	269	364	0	ENST00000524377.1:c.710C>T	p.Thr237Met	p.T237M	ENST00000524377	NM_002529.3	237	aCg/aTg	6/17	0.481679194682867	3	FACETS	0.916	0.874	0.958	0.916	0.874	0.958	CLONAL	3	TRUE	0	0.554277527281724	3		364	451	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225365195	225365195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	191	319	0	ENST00000264414.4:c.1495G>A	p.Gly499Ser	p.G499S	ENST00000264414	NM_003590.4	499	Ggt/Agt	11/16	0.165606276360114	5	FACETS	0.83	0.77	0.893	0.554	0.513	0.596	INDETERMINATE	2	TRUE	2	0.554277527281724	5		319	760	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661965	227661965	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756790900	NA	P-0009526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	144	298	0	ENST00000305123.5:c.1490G>A	p.Gly497Glu	p.G497E	ENST00000305123	NM_005544.2	497	gGa/gAa	1/2	0.165606276360114	5	FACETS	0.903	0.828	0.98	0.602	0.552	0.654	INDETERMINATE	2	TRUE	2	0.554277527281724	5		298	527	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748296	41748296	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	194	374	1	ENST00000226382.2:c.473G>A	p.Arg158His	p.R158H	ENST00000226382	NM_003924.3	158	cGc/cAc	3/3	0.165606276360114	5	FACETS	1	0.974	1	0.729	0.679	0.781	INDETERMINATE	2	TRUE	2	0.554277527281724	5		375	586	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961834	55961834	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0009526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	226	393	0	ENST00000263923.4:c.2729-2A>T		p.X910_splice	ENST00000263923	NM_002253.2	910			0.165606276360114	5	FACETS	0.972	0.909	1	0.648	0.606	0.692	INDETERMINATE	2	TRUE	2	0.554277527281724	5		393	768	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249501	153249501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1316840275	NA	P-0009526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	178	361	0	ENST00000281708.4:c.1277C>T	p.Ser426Leu	p.S426L	ENST00000281708	NM_033632.3	426	tCa/tTa	9/12	0.165606276360114	5	FACETS	0.826	0.764	0.891	0.551	0.509	0.594	INDETERMINATE	2	TRUE	2	0.554277527281724	5		361	712	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829207	128829207	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1410003197	NA	P-0009526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	126	301	0	ENST00000249373.3:c.215C>T	p.Pro72Leu	p.P72L	ENST00000249373	NM_005631.4	72	cCg/cTg	1/12	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.554277527281724	NA		301	486	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804331	46804331	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	238	671	1	ENST00000290295.7:c.676G>T	p.Gly226Trp	p.G226W	ENST00000290295	NM_006361.5	226	Ggg/Tgg	2/2	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.554277527281724	2		672	740	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625615	1625615	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	188	700	3	ENST00000344749.5:c.459C>A	p.Tyr153Ter	p.Y153*	ENST00000344749	NM_001136139.2	153	taC/taA	7/19	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.554277527281724	2		703	659	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098784	178098825	+	inframe_deletion	In_Frame_Del	DEL	CTGAATTGGGAGAAATTCACCTGTCTCTTCATCTAGTTGTAA	CTGAATTGGGAGAAATTCACCTGTCTCTTCATCTAGTTGTAA	-	novel	NA	P-0009526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	428	594	0	ENST00000397062.3:c.220_261del	p.Leu74_Gln87del	p.L74_Q87del	ENST00000397062	NM_006164.4	74	TTACAACTAGATGAAGAGACAGGTGAATTTCTCCCAATTCAG/-	2/5	0.165606276360114	5	FACETS	1	0.976	1	0.691	0.658	0.725	INDETERMINATE	2	TRUE	2	0.554277527281724	5		594	1364	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0009607-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	199	572	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.253301975535814	3	FACETS	1	0.99	1	0.725	0.672	0.78	CLONAL	1	TRUE	1	0.329611128424007	3		573	970	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0009607-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	269	588	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.255497543000512	2	FACETS	0.756	0.709	0.804	0.756	0.709	0.804	SUBCLONAL	2	TRUE	0	0.329611128424007	2		589	1080	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274207	10274207	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749314552	NA	P-0009607-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	32	191	0	ENST00000330684.3:c.62C>T	p.Pro21Leu	p.P21L	ENST00000330684	NM_001134407.1	21	cCg/cTg	2/13	0.253301975535814	3	FACETS	0.683	0.556	0.827	0.342	0.278	0.414	SUBCLONAL	1	TRUE	1	0.329611128424007	3		191	331	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679326	29679326	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1555536359	NA	P-0009607-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	179	400	0	ENST00000356175.3:c.7446C>A	p.Tyr2482Ter	p.Y2482*	ENST00000356175	NM_000267.3	2482	taC/taA	50/57	0.255497543000512	2	FACETS	1	0.989	1	0.707	0.653	0.763	CLONAL	1	TRUE	0	0.329611128424007	2		400	768	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009662-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	36	589	1				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		590	233	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038923	12038923	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009746-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	104	511	0	ENST00000396373.4:c.1216A>T	p.Ile406Phe	p.I406F	ENST00000396373	NM_001987.4	406	Att/Ttt	7/8	1	2	FACETS	0.799	0.714	0.889	0.799	0.714	0.889	SUBCLONAL	1	FALSE	1	0.272073603743208	2		511	957	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498310	29498310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	55	580	0	ENST00000389048.3:c.1870G>A	p.Ala624Thr	p.A624T	ENST00000389048	NM_004304.4	624	Gct/Act	10/29	0.154633600307852	2	FACETS	0.746	0.636	0.868	0.373	0.318	0.434	SUBCLONAL	1	TRUE	0	0.154633600307852	2		580	953	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659576	88659576	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	61	501	0	ENST00000372037.3:c.359G>C	p.Arg120Pro	p.R120P	ENST00000372037	NM_004329.2	120	cGg/cCg	6/13	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.154633600307852	2		501	721	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678572	88678572	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	28	267	0	ENST00000360948.2:c.964G>T	p.Glu322Ter	p.E322*	ENST00000360948	NM_001012338.2	322	Gag/Tag	9/19	1	2	FACETS	0.81	0.647	0.997	0.81	0.647	0.997	CLONAL	1	TRUE	1	0.154633600307852	2		267	447	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740575	58740575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1385	76	804	0	ENST00000305921.3:c.1480C>T	p.Leu494Phe	p.L494F	ENST00000305921	NM_003620.3	494	Ctt/Ttt	6/6	0.154633600307852	3	FACETS	0.725	0.633	0.825	0.362	0.316	0.413	SUBCLONAL	1	TRUE	1	0.154633600307852	3		804	1461	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	154	589	1				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.853004821199298	2		590	331	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0010004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1743	19412	540	1	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.853004821199298	17	FACETS	0.995	0.992	0.998			1	CLONAL	16	TRUE	NA	0.853004821199298	17		541	21155	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509082	106509082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144565710	NA	P-0010004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	445	363	0	ENST00000359195.3:c.1076G>A	p.Arg359His	p.R359H	ENST00000359195	NM_002649.2	359	cGc/cAc	2/11	0.853004821199298	3	FACETS	0.99	0.943	1	0.495	0.471	0.519	CLONAL	1	TRUE	1	0.853004821199298	3		363	1504	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998712	100998712	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	721	559	0	ENST00000325455.5:c.1090C>G	p.Pro364Ala	p.P364A	ENST00000325455	NM_001202474.3	364	Ccg/Gcg	1/8	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.853004821199298	2		559	1578	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0010005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	127	515	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.973	0.88	1	0.973	0.88	1	CLONAL	1	TRUE	1	0.265589873648249	2		515	983	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466993	18466993	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs370262872	NA	P-0010005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	88	468	0	ENST00000266497.5:c.1132C>T	p.Arg378Ter	p.R378*	ENST00000266497		378	Cga/Tga	5/31	1	2	FACETS	0.782	0.692	0.879	0.782	0.692	0.879	SUBCLONAL	1	TRUE	1	0.265589873648249	2		468	847	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219217	94219217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	88	422	0	ENST00000323929.3:c.187C>T	p.His63Tyr	p.H63Y	ENST00000323929	NM_005591.3	63	Cat/Tat	4/20	1	2	FACETS	0.869	0.769	0.975	0.869	0.769	0.975	CLONAL	1	TRUE	1	0.265589873648249	2		422	763	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663278	227663279	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0010005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	73	379	0	ENST00000305123.5:c.176_177delinsTT	p.Ala59Val	p.A59V	ENST00000305123	NM_005544.2	59	gCC/gTT	1/2	1	2	FACETS	0.76	0.664	0.864	0.76	0.664	0.864	SUBCLONAL	1	TRUE	1	0.265589873648249	2		379	723	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509538	106509539	+	missense_variant	Missense_Mutation	DNP	AG	AG	GA	novel	NA	P-0010005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	96	516	0	ENST00000359195.3:c.1532_1533delinsGA	p.Glu511Gly	p.E511G	ENST00000359195	NM_002649.2	511	gAG/gGA	2/11	0.265210630307031	3	FACETS	0.744	0.661	0.833	0.372	0.33	0.417	SUBCLONAL	1	TRUE	1	0.265589873648249	3		516	1101	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376226	225376226	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010006-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	27	568	0	ENST00000264414.4:c.728A>G	p.Glu243Gly	p.E243G	ENST00000264414	NM_003590.4	243	gAa/gGa	6/16	1	2	FACETS	1	0.836	1	1	0.836	1	CLONAL	1	TRUE	1	0.260078857440438	2		568	198	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144708	58144708	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs780052789	NA	P-0010006-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	19	299	1	ENST00000257904.6:c.520G>A	p.Val174Met	p.V174M	ENST00000257904	NM_000075.3	174	Gtg/Atg	4/8	0.256322629717973	1	FACETS	0.928	0.711	1	0.928	0.711	1	CLONAL	1	TRUE	0	0.260078857440438	1		300	137	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247806	10247806	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147984942	NA	P-0010006-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	54	479	0	ENST00000340748.4:c.4396C>T	p.Arg1466Cys	p.R1466C	ENST00000340748		1466	Cgc/Tgc	36/40	1	2	FACETS	0.809	0.692	0.938	0.809	0.692	0.938	CLONAL	1	TRUE	1	0.260078857440438	2		479	513	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755492	39755492	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010006-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	46	477	0	ENST00000288319.7:c.1273C>A	p.Pro425Thr	p.P425T	ENST00000288319	NM_182918.3	425	Cca/Aca	10/10	0.256322629717973	1	FACETS	0.916	0.774	1	0.916	0.774	1	CLONAL	1	TRUE	0	0.260078857440438	1		477	336	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028493	42028496	+	frameshift_variant	Frame_Shift_Del	DEL	GGGA	GGGA	-	novel	NA	P-0010006-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	49	578	0	ENST00000219905.7:c.4033_4036del	p.Glu1345LysfsTer7	p.E1345Kfs*7	ENST00000219905	NM_001164273.1	1344	tGGGAg/tg	13/24	1	2	FACETS	0.849	0.727	0.979	1	0.971	1	CLONAL	2	TRUE	1	0.260078857440438	2		578	222	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0010013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	17	500	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	NA	2	FACETS	0.73	0.544	0.951			1	INDETERMINATE	1	FALSE	NA	0.148407702115138	2		500	314	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041663	47041663	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	17	299	0	ENST00000377604.3:c.1891del	p.Ala631HisfsTer73	p.A631Hfs*73	ENST00000377604	NM_001204468.1	630	Ggg/gg	17/24	1	1	FACETS	0.996	0.745	1	0.996	0.745	1	CLONAL	1	FALSE	0	0.148407702115138	1		299	213	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0010022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	92	513	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.282442147303658	3	FACETS	0.91	0.808	1	0.455	0.404	0.51	CLONAL	1	TRUE	1	0.282442147303658	3		514	817	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0010022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	199	483	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.282442147303658	3	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	1	0.282442147303658	3		483	790	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0010022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	162	537	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.282442147303658	3	FACETS	1	0.988	1	0.74	0.679	0.803	CLONAL	1	TRUE	1	0.282442147303658	3		537	885	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170088	32170088	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775047010	NA	P-0010022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	169	542	0	ENST00000375023.3:c.3520G>A	p.Gly1174Arg	p.G1174R	ENST00000375023	NM_004557.3	1174	Gga/Aga	21/30	0.282442147303658	3	FACETS	1	0.973	1	0.57	0.522	0.619	CLONAL	1	TRUE	1	0.282442147303658	3		542	1199	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0010022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	119	617	1	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	0.282442147303658	3	FACETS	1	0.93	1	0.52	0.468	0.574	CLONAL	1	TRUE	1	0.282442147303658	3		618	925	SUCCESS
APC	324	MSKCC	GRCh37	5	112175232	112175232	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	199	330	0	ENST00000257430.4:c.3942del	p.Arg1314SerfsTer7	p.R1314Sfs*7	ENST00000257430	NM_000038.5	1314	aGg/ag	16/16	0.282442147303658	3	FACETS	0.991	0.92	1	0.991	0.92	1	CLONAL	2	TRUE	1	0.282442147303658	3		330	811	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166105	118166105	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	81	696	1	ENST00000369448.3:c.615C>A	p.His205Gln	p.H205Q	ENST00000369448	NM_017709.3	205	caC/caA	2/2	1	2	FACETS	0.484	0.425	0.548	0.484	0.425	0.548	SUBCLONAL	1	TRUE	1	0.282442147303658	2		697	1184	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610030	81610030	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	56	443	0	ENST00000298171.2:c.1628T>C	p.Val543Ala	p.V543A	ENST00000298171	NM_000369.2	543	gTt/gCt	10/10	0.282442147303658	2	FACETS	0.504	0.431	0.584	0.252	0.215	0.292	SUBCLONAL	1	TRUE	0	0.282442147303658	2		443	787	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651643	48651643	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1533	515	990	0	ENST00000376670.3:c.809G>A	p.Arg270Gln	p.R270Q	ENST00000376670	NM_002049.3	270	cGg/cAg	5/6	0.151290500922761	4	FACETS	1	0.991	1	1	0.991	1	INDETERMINATE	2	TRUE	2	0.282442147303658	4		990	2048	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631132	69631132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782507721	NA	P-0010048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	160	653	4	ENST00000334134.2:c.280G>A	p.Gly94Arg	p.G94R	ENST00000334134	NM_005247.2	94	Ggg/Agg	2/3	0.276317054519697	5	FACETS	1	0.971	1	0.739	0.681	0.799	CLONAL	2	TRUE	2	0.407346058292254	5		657	571	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30311685	30311685	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	100	545	1	ENST00000262643.3:c.539A>T	p.Gln180Leu	p.Q180L	ENST00000262643	NM_001238.2	180	cAa/cTa	7/12	0.407346058292254	3	FACETS	0.814	0.727	0.906	0.271	0.242	0.302	CLONAL	1	TRUE	0	0.407346058292254	3		546	726	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0010049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	181	398	1	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.436175920891122	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.436175920891122	1		399	564	SUCCESS
APC	324	MSKCC	GRCh37	5	112102086	112102086	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	43	496	2	ENST00000257430.4:c.199G>A	p.Asp67Asn	p.D67N	ENST00000257430	NM_000038.5	67	Gat/Aat	3/16	0.379241633885746	2	FACETS	0.314	0.262	0.372	0.157	0.131	0.186	SUBCLONAL	1	TRUE	0	0.436175920891122	2		498	628	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117739	70117741	+	frameshift_variant	Frame_Shift_Del	DEL	CCC	CCC	G	novel	NA	P-0010049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	314	636	0	ENST00000245479.2:c.207_209delinsG	p.Phe69LeufsTer182	p.F69Lfs*182	ENST00000245479	NM_000346.3	69	ttCCCc/ttGc	1/3	0.199035377811727	2	FACETS	1	0.993	1	0.666	0.629	0.704	INDETERMINATE	1	TRUE	0	0.436175920891122	2		636	1081	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0010051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	379	612	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.879894358986133	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.880984006369267	2		613	410	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117739650	117739650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	227	426	0	ENST00000368508.3:c.143G>A	p.Gly48Asp	p.G48D	ENST00000368508	NM_002944.2	48	gGc/gAc	2/43	0.880984006369267	3	FACETS	1	0.971	1	0.355	0.332	0.379	CLONAL	1	TRUE	0	0.880984006369267	3		426	697	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936822	78936822	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1480686908	NA	P-0010051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	157	390	1	ENST00000306801.3:c.3904G>A	p.Gly1302Ser	p.G1302S	ENST00000306801	NM_020761.2	1302	Ggc/Agc	33/34	0.880984006369267	3	FACETS	0.882	0.812	0.955	0.294	0.27	0.319	CLONAL	1	TRUE	0	0.880984006369267	3		391	582	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010052-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	70	589	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.844307713977311	2		590	143	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0010052-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	177	379	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.844307713977311	2		379	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0010052-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	554	503	0	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	0.840730213883671	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.844307713977311	2		503	620	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685511	29685511	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010052-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	184	295	1	ENST00000356175.3:c.7921G>T	p.Asp2641Tyr	p.D2641Y	ENST00000356175	NM_000267.3	2641	Gac/Tac	54/57	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.844307713977311	2		296	402	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143269	24143269	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	286	478	0	ENST00000263121.7:c.500+1G>T		p.X167_splice	ENST00000263121	NM_003073.3	167			0.221813072604092	2	FACETS	0.913	0.858	0.97	0.913	0.858	0.97	CLONAL	2	TRUE	0	0.254198408183186	2		478	1232	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395653	31395653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866792483	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	111	386	0	ENST00000328111.2:c.2506G>A	p.Val836Met	p.V836M	ENST00000328111	NM_006892.3	836	Gtg/Atg	23/23	0.254198408183186	4	FACETS	0.823	0.737	0.914	0.274	0.245	0.305	CLONAL	1	TRUE	1	0.254198408183186	4		386	1331	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699360	47699360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	113	444	0	ENST00000347630.2:c.148G>A	p.Glu50Lys	p.E50K	ENST00000347630	NM_001007230.1	50	Gaa/Aaa	4/11	1	2	FACETS	0.768	0.689	0.852	0.768	0.689	0.852	SUBCLONAL	1	TRUE	1	0.254198408183186	2		444	1158	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	152	186	0	ENST00000269305.4:c.673-1G>C		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.221813072604092	2	FACETS	0.963	0.884	1	0.963	0.884	1	CLONAL	2	TRUE	0	0.254198408183186	2		186	621	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286171	66286171	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	99	396	0	ENST00000273854.3:c.1515G>T	p.Lys505Asn	p.K505N	ENST00000273854	NM_004439.5	505	aaG/aaT	6/18	0.249490210252355	3	FACETS	0.881	0.785	0.984	0.441	0.392	0.492	CLONAL	1	TRUE	1	0.254198408183186	3		396	996	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372209	55372209	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	69	181	0	ENST00000297316.4:c.899T>C	p.Met300Thr	p.M300T	ENST00000297316	NM_022454.3	300	aTg/aCg	2/2	0.254198408183186	3	FACETS	0.837	0.728	0.955	0.419	0.364	0.478	CLONAL	1	TRUE	1	0.254198408183186	3		181	731	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778803	9778803	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs763569477	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	84	227	1	ENST00000377346.4:c.1072G>T	p.Val358Leu	p.V358L	ENST00000377346	NM_005026.3	358	Gtg/Ttg	9/24	0.202672408110073	3	FACETS	0.947	0.835	1			1	CLONAL	1	TRUE	NA	0.254198408183186	3		228	787	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17380466	17380466	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060503756	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	139	380	0	ENST00000375499.3:c.49A>G	p.Thr17Ala	p.T17A	ENST00000375499	NM_003000.2	17	Acc/Gcc	1/8	1	2	FACETS	0.852	0.773	0.935	0.852	0.773	0.935	CLONAL	1	TRUE	1	0.254198408183186	2		380	1284	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094389	27094389	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	153	233	0	ENST00000324856.7:c.3097G>T	p.Glu1033Ter	p.E1033*	ENST00000324856	NM_006015.4	1033	Gag/Tag	11/20	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.254198408183186	NA		233	857	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690373	117690373	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	79	323	0	ENST00000369458.3:c.756G>T	p.Gln252His	p.Q252H	ENST00000369458	NM_024626.3	252	caG/caT	5/6	0.249490210252355	3	FACETS	0.751	0.659	0.85	0.375	0.329	0.425	SUBCLONAL	1	TRUE	1	0.254198408183186	3		323	933	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119447	193119447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762716583	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	75	278	0	ENST00000367435.3:c.842G>A	p.Arg281His	p.R281H	ENST00000367435	NM_024529.4	281	cGc/cAc	9/17	0.229805150547683	3	FACETS	0.702	0.613	0.797	0.351	0.306	0.399	SUBCLONAL	1	TRUE	1	0.254198408183186	3		278	948	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735342	204735342	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	150	157	0	ENST00000302823.3:c.143C>A	p.Ala48Asp	p.A48D	ENST00000302823	NM_005214.4	48	gCc/gAc	2/4	1	2	FACETS	1	0.958	1	1	0.992	1	CLONAL	2	TRUE	1	0.254198408183186	2		157	554	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920324	134920324	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	107	372	0	ENST00000398015.3:c.2139C>A	p.Asp713Glu	p.D713E	ENST00000398015	NM_004441.4	713	gaC/gaA	12/16	1	2	FACETS	0.756	0.677	0.841	0.756	0.677	0.841	SUBCLONAL	1	TRUE	1	0.254198408183186	2		372	1113	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156631	55156631	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	100	244	0	ENST00000257290.5:c.3032G>T	p.Arg1011Ile	p.R1011I	ENST00000257290	NM_006206.4	1011	aGa/aTa	22/23	0.249490210252355	3	FACETS	0.922	0.822	1	0.461	0.411	0.514	CLONAL	1	TRUE	1	0.254198408183186	3		244	962	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561681	55561681	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	64	142	0	ENST00000288135.5:c.71C>T	p.Ser24Phe	p.S24F	ENST00000288135	NM_000222.2	24	tCt/tTt	2/21	0.249490210252355	3	FACETS	0.926	0.802	1	0.463	0.401	0.531	CLONAL	1	TRUE	1	0.254198408183186	3		142	613	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99812480	99812480	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	77	263	0	ENST00000280892.6:c.189G>T	p.Trp63Cys	p.W63C	ENST00000280892	NM_001130678.1	63	tgG/tgT	3/7	0.249490210252355	3	FACETS	0.908	0.796	1	0.454	0.398	0.514	CLONAL	1	TRUE	1	0.254198408183186	3		263	752	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522518	187522518	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	95	395	0	ENST00000441802.2:c.11545A>G	p.Asn3849Asp	p.N3849D	ENST00000441802	NM_005245.3	3849	Aac/Gac	21/27	0.249490210252355	3	FACETS	0.667	0.592	0.748	0.334	0.296	0.374	SUBCLONAL	1	TRUE	1	0.254198408183186	3		395	1263	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032126	26032126	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1471034494	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1504	209	581	0	ENST00000244661.2:c.163T>C	p.Tyr55His	p.Y55H	ENST00000244661	NM_003537.3	55	Tac/Cac	1/1	0.229805150547683	3	FACETS	1	0.967	1	0.541	0.5	0.584	CLONAL	1	TRUE	1	0.254198408183186	3		581	1713	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839966	27839966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1646	207	759	1	ENST00000328488.2:c.128G>A	p.Arg43His	p.R43H	ENST00000328488	NM_003533.2	43	cGc/cAc	1/1	0.229805150547683	3	FACETS	0.991	0.915	1	0.495	0.457	0.535	CLONAL	1	TRUE	1	0.254198408183186	3		760	1853	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910680	29910680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	134	375	1	ENST00000376809.5:c.220C>T	p.Pro74Ser	p.P74S	ENST00000376809	NM_002116.7	74	Ccg/Tcg	2/8	0.254198408183186	5	FACETS	1	0.969	1	0.29	0.262	0.319	CLONAL	1	TRUE	1	0.254198408183186	5		376	1255	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120668	94120668	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	67	619	0	ENST00000369303.4:c.383A>G	p.Tyr128Cys	p.Y128C	ENST00000369303	NM_004440.3	128	tAt/tGt	3/17	0.158262072522988	0	FACETS	0.329	0.285	0.378			1	SUBCLONAL	1	TRUE	0	0.254198408183186	0		619	1194	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151164264	151164264	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	84	317	0	ENST00000262187.5:c.496G>T	p.Glu166Ter	p.E166*	ENST00000262187	NM_005614.3	166	Gag/Tag	8/8	0.254198408183186	4	FACETS	0.802	0.706	0.905	0.267	0.235	0.302	CLONAL	1	TRUE	1	0.254198408183186	4		317	1034	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341225	8341225	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	100	269	0	ENST00000356435.5:c.4991C>A	p.Ala1664Asp	p.A1664D	ENST00000356435		1664	gCc/gAc	30/35	0.221813072604092	2	FACETS	0.967	0.863	1	0.483	0.431	0.539	CLONAL	1	TRUE	0	0.254198408183186	2		269	814	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376681	8376681	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	152	255	0	ENST00000356435.5:c.4432G>C	p.Gly1478Arg	p.G1478R	ENST00000356435		1478	Gga/Cga	27/35	0.221813072604092	2	FACETS	0.846	0.775	0.919	0.846	0.775	0.919	CLONAL	2	TRUE	0	0.254198408183186	2		255	707	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465567	8465567	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	82	416	0	ENST00000356435.5:c.3613C>A	p.Leu1205Met	p.L1205M	ENST00000356435		1205	Ctg/Atg	21/35	0.221813072604092	2	FACETS	0.668	0.587	0.755	0.334	0.293	0.378	SUBCLONAL	1	TRUE	0	0.254198408183186	2		416	966	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486054	8486054	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	184	342	0	ENST00000356435.5:c.2763C>G	p.Phe921Leu	p.F921L	ENST00000356435		921	ttC/ttG	17/35	0.221813072604092	2	FACETS	1	0.987	1	0.68	0.627	0.735	CLONAL	1	TRUE	0	0.254198408183186	2		342	1065	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500982	8500982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	90	353	0	ENST00000356435.5:c.1900C>T	p.Pro634Ser	p.P634S	ENST00000356435		634	Cca/Tca	13/35	0.221813072604092	2	FACETS	0.772	0.684	0.867	0.386	0.342	0.434	SUBCLONAL	1	TRUE	0	0.254198408183186	2		353	917	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915844	127915844	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1265	134	542	0	ENST00000373547.4:c.637G>T	p.Gly213Cys	p.G213C	ENST00000373547	NM_002721.4	213	Ggt/Tgt	6/7	0.221813072604092	2	FACETS	0.754	0.682	0.829	0.377	0.341	0.415	SUBCLONAL	1	TRUE	0	0.254198408183186	2		542	1399	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850619	63850619	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	83	232	0	ENST00000279873.7:c.1399-2A>T		p.X467_splice	ENST00000279873	NM_032199.2	467			1	2	FACETS	0.88	0.776	0.992	0.88	0.776	0.992	CLONAL	1	TRUE	1	0.254198408183186	2		232	742	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450142	32450142	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs767419243	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	614	287	1	ENST00000332351.3:c.670G>C	p.Gly224Arg	p.G224R	ENST00000332351	NM_024426.4	224	Ggg/Cgg	2/10	0.254198408183186	6	FACETS	1	0.968	1			1	CLONAL	5	TRUE	NA	0.254198408183186	6		288	1450	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136052	64136052	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	81	158	0	ENST00000334205.4:c.1313C>T	p.Ala438Val	p.A438V	ENST00000334205	NM_003942.2	438	gCa/gTa	11/17	0.254198408183186	4	FACETS	1	0.97	1	0.443	0.39	0.499	CLONAL	1	TRUE	1	0.254198408183186	4		158	602	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572550	64572550	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs104894259	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	75	244	0	ENST00000312049.6:c.1306T>C	p.Trp436Arg	p.W436R	ENST00000312049	NM_130799.2	436	Tgg/Cgg	9/10	0.254198408183186	4	FACETS	0.706	0.617	0.803	0.235	0.205	0.268	SUBCLONAL	1	TRUE	1	0.254198408183186	4		244	1048	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244248	46244248	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	85	275	0	ENST00000334344.6:c.2342G>T	p.Gly781Val	p.G781V	ENST00000334344	NM_152641.2	781	gGa/gTa	15/21	1	2	FACETS	0.779	0.688	0.878	0.779	0.688	0.878	SUBCLONAL	1	TRUE	1	0.254198408183186	2		275	858	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911229	32911229	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1590	149	629	2	ENST00000380152.3:c.2737G>T	p.Asp913Tyr	p.D913Y	ENST00000380152		913	Gac/Tac	11/27	0.254198408183186	1	FACETS	0.588	0.535	0.645	0.588	0.535	0.645	SUBCLONAL	1	TRUE	0	0.254198408183186	1		631	1739	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934263	48934263	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	78	207	0	ENST00000267163.4:c.718A>T	p.Lys240Ter	p.K240*	ENST00000267163	NM_000321.2	240	Aaa/Taa	7/27	0.229805150547683	3	FACETS	0.998	0.877	1	0.499	0.438	0.565	CLONAL	1	TRUE	1	0.254198408183186	3		207	693	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610393	81610393	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	118	337	0	ENST00000298171.2:c.1991T>C	p.Val664Ala	p.V664A	ENST00000298171	NM_000369.2	664	gTa/gCa	10/10	0.221813072604092	2	FACETS	0.919	0.828	1	0.46	0.414	0.508	CLONAL	1	TRUE	0	0.254198408183186	2		337	1010	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041492	42041492	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1308	161	580	0	ENST00000219905.7:c.5687A>T	p.Gln1896Leu	p.Q1896L	ENST00000219905	NM_001164273.1	1896	cAg/cTg	17/24	0.254198408183186	1	FACETS	0.753	0.688	0.821	0.753	0.688	0.821	SUBCLONAL	1	TRUE	0	0.254198408183186	1		580	1469	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779813	3779813	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	133	353	0	ENST00000262367.5:c.5235G>T	p.Trp1745Cys	p.W1745C	ENST00000262367	NM_004380.2	1745	tgG/tgT	31/31	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.254198408183186	2		353	1009	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032370	10032370	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	56	123	0	ENST00000330684.3:c.453C>G	p.Ile151Met	p.I151M	ENST00000330684	NM_001134407.1	151	atC/atG	3/13	1	2	FACETS	0.941	0.808	1	0.941	0.808	1	CLONAL	1	TRUE	1	0.254198408183186	2		123	468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579512	7579512	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	209	293	0	ENST00000269305.4:c.175G>C	p.Gly59Arg	p.G59R	ENST00000269305	NM_001126112.2	59	Ggt/Cgt	4/11	0.221813072604092	2	FACETS	0.922	0.857	0.989	0.922	0.857	0.989	CLONAL	2	TRUE	0	0.254198408183186	2		293	892	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485970	40485970	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1601	189	652	0	ENST00000264657.5:c.895G>C	p.Val299Leu	p.V299L	ENST00000264657	NM_139276.2	299	Gta/Cta	9/24	1	2	FACETS	0.831	0.765	0.9	0.831	0.765	0.9	CLONAL	1	TRUE	1	0.254198408183186	2		652	1790	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632399	1632399	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	147	410	0	ENST00000344749.5:c.151G>T	p.Glu51Ter	p.E51*	ENST00000344749	NM_001136139.2	51	Gag/Tag	4/19	0.221813072604092	2	FACETS	0.994	0.906	1	0.497	0.453	0.544	CLONAL	1	TRUE	0	0.254198408183186	2		410	1163	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411585	63411585	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1630	135	538	0	ENST00000330258.3:c.1582C>A	p.Leu528Ile	p.L528I	ENST00000330258	NM_152424.3	528	Ctc/Atc	2/2	0.249490210252355	3	FACETS	0.678	0.614	0.747	0.339	0.307	0.374	SUBCLONAL	1	TRUE	1	0.254198408183186	3		538	1765	SUCCESS
AR	367	MSKCC	GRCh37	X	66765910	66765910	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	333	357	0	ENST00000374690.3:c.922G>T	p.Glu308Ter	p.E308*	ENST00000374690	NM_000044.3	308	Gag/Tag	1/8	0.249490210252355	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.254198408183186	3		357	1328	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778864	76778864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	127	445	0	ENST00000373344.5:c.6715G>A	p.Glu2239Lys	p.E2239K	ENST00000373344	NM_000489.3	2239	Gag/Aag	31/35	0.249490210252355	3	FACETS	0.931	0.841	1	0.465	0.42	0.513	CLONAL	1	TRUE	1	0.254198408183186	3		445	1210	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626685	100626685	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs56035945	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	102	364	0	ENST00000308731.7:c.245G>T	p.Arg82Ile	p.R82I	ENST00000308731	NM_000061.2	82	aGa/aTa	4/19	0.249490210252355	3	FACETS	0.797	0.711	0.889	0.398	0.355	0.445	SUBCLONAL	1	TRUE	1	0.254198408183186	3		364	1135	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851977	63851977	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	55	149	0	ENST00000279873.7:c.2756del	p.Gly919AlafsTer25	p.G919Afs*25	ENST00000279873	NM_032199.2	919	Ggc/gc	10/10	1	2	FACETS	0.773	0.661	0.895	0.773	0.661	0.895	SUBCLONAL	1	TRUE	1	0.254198408183186	2		149	560	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067311	37067311	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	68	333	0	ENST00000231790.2:c.1225del	p.Gln409ArgfsTer82	p.Q409Rfs*82	ENST00000231790	NM_000249.3	408	Ccc/cc	12/19	0.254198408183186	1	FACETS	0.534	0.464	0.611	0.534	0.464	0.611	SUBCLONAL	1	TRUE	0	0.254198408183186	1		333	874	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612737	228612738	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0010057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1882	184	731	0	ENST00000366696.1:c.289_290del	p.Cys97ArgfsTer9	p.C97Rfs*9	ENST00000366696	NM_003493.2	97	TGc/c	1/1	0.229805150547683	3	FACETS	0.79	0.725	0.857	0.395	0.362	0.429	SUBCLONAL	1	TRUE	1	0.254198408183186	3		731	2066	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0010060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	79	320	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.988	0.871	1			1	INDETERMINATE	1	TRUE	NA	0.32	2		320	500	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0010060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	94	291	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.29751550750069	1	FACETS	0.947	0.846	1	0.947	0.846	1	CLONAL	1	TRUE	0	0.32	1		292	521	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130427	29130427	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587781269	NA	P-0010060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	105	352	0	ENST00000328354.6:c.283C>T	p.Arg95Ter	p.R95*	ENST00000328354	NM_007194.3	95	Cga/Tga	2/15	1	2	FACETS	0.856	0.767	0.95	0.856	0.767	0.95	CLONAL	1	TRUE	1	0.32	2		352	767	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654769	29654769	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786203570	NA	P-0010060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	100	309	0	ENST00000356175.3:c.5458C>T	p.Gln1820Ter	p.Q1820*	ENST00000356175	NM_000267.3	1820	Caa/Taa	37/57	1	2	FACETS	0.803	0.717	0.895	0.803	0.717	0.895	CLONAL	1	TRUE	1	0.32	2		309	778	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29497003	29497003	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397514641	NA	P-0010060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	101	225	0	ENST00000356175.3:c.574C>T	p.Arg192Ter	p.R192*	ENST00000356175	NM_000267.3	192	Cga/Tga	5/57	1	2	FACETS	0.892	0.797	0.992	0.892	0.797	0.992	CLONAL	1	TRUE	1	0.32	2		225	708	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732413	74732413	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1456	557	873	2	ENST00000359995.5:c.496G>T	p.Ala166Ser	p.A166S	ENST00000359995	NM_001195427.1	166	Gca/Tca	2/3	0.322532722317574	5	FACETS	0.766	0.734	0.8	0.511	0.489	0.533	INDETERMINATE	2	TRUE	2	0.787739765117715	5		875	2013	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101273	27101273	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	328	549	1	ENST00000324856.7:c.4555C>T	p.Gln1519Ter	p.Q1519*	ENST00000324856	NM_006015.4	1519	Cag/Tag	18/20	0.414978505855718	1	FACETS	0.78	0.744	0.816	0.78	0.744	0.816	INDETERMINATE	1	TRUE	0	0.787739765117715	1		550	647	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78425921	78425921	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	254	431	0	ENST00000370768.2:c.1524G>T	p.Gln508His	p.Q508H	ENST00000370768	NM_003902.3	508	caG/caT	16/20	0.349056223454923	5	FACETS	1	0.992	1	0.357	0.334	0.381	INDETERMINATE	1	TRUE	1	0.787739765117715	5		431	985	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082605	16082605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	38	147	0	ENST00000281043.3:c.419C>T	p.Pro140Leu	p.P140L	ENST00000281043	NM_005378.4	140	cCg/cTg	2/3	0.380462770040447	3	FACETS	0.547	0.455	0.648	0.182	0.151	0.216	INDETERMINATE	1	TRUE	0	0.787739765117715	3		147	246	SUCCESS
ALK	238	MSKCC	GRCh37	2	29430086	29430086	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	698	589	1	ENST00000389048.3:c.3889C>A	p.Pro1297Thr	p.P1297T	ENST00000389048	NM_004304.4	1297	Ccc/Acc	26/29	0.380462770040447	3	FACETS	1	0.996	1	0.75	0.729	0.77	INDETERMINATE	2	TRUE	0	0.787739765117715	3		590	1098	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622675	158622675	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1455	270	962	0	ENST00000263640.3:c.824C>A	p.Ser275Tyr	p.S275Y	ENST00000263640	NM_001105.4	275	tCc/tAc	8/11	0.380462770040447	3	FACETS	0.554	0.518	0.592	0.185	0.172	0.198	INDETERMINATE	1	TRUE	0	0.787739765117715	3		962	1725	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138452236	138452236	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	502	622	1	ENST00000289153.2:c.1017G>T	p.Lys339Asn	p.K339N	ENST00000289153	NM_006219.2	339	aaG/aaT	6/22	0.258722542707487	3	FACETS	0.783	0.751	0.814	0.783	0.751	0.814	INDETERMINATE	2	TRUE	1	0.787739765117715	3		623	1135	SUCCESS
ATR	545	MSKCC	GRCh37	3	142241674	142241674	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	342	415	0	ENST00000350721.4:c.4162G>T	p.Glu1388Ter	p.E1388*	ENST00000350721	NM_001184.3	1388	Gaa/Taa	23/47	0.258722542707487	3	FACETS	0.8	0.762	0.839	0.8	0.762	0.839	INDETERMINATE	2	TRUE	1	0.787739765117715	3		415	756	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332473	153332473	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	409	626	0	ENST00000281708.4:c.483C>G	p.Phe161Leu	p.F161L	ENST00000281708	NM_033632.3	161	ttC/ttG	2/12	0.77443801701405	2	FACETS	0.853	0.812	0.894	0.426	0.406	0.447	CLONAL	1	TRUE	0	0.787739765117715	2		626	1218	SUCCESS
APC	324	MSKCC	GRCh37	5	112176692	112176692	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1262019297	NA	P-0010087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	405	571	0	ENST00000257430.4:c.5401G>T	p.Ala1801Ser	p.A1801S	ENST00000257430	NM_000038.5	1801	Gct/Tct	16/16	1	2	FACETS	0.973	0.928	1	0.973	0.928	1	CLONAL	1	TRUE	1	0.787739765117715	2		571	1057	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169961	32169961	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	413	652	0	ENST00000375023.3:c.3647C>A	p.Ser1216Tyr	p.S1216Y	ENST00000375023	NM_004557.3	1216	tCc/tAc	21/30	0.570828835923705	3	FACETS	1	0.993	1	0.606	0.578	0.636	CLONAL	1	TRUE	1	0.787739765117715	3		652	1205	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527658	157527658	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	242	394	0	ENST00000346085.5:c.5383A>T	p.Asn1795Tyr	p.N1795Y	ENST00000346085	NM_020732.3	1795	Aac/Tac	20/20	0.474731370224271	3	FACETS	0.967	0.905	1	0.483	0.452	0.515	CLONAL	1	TRUE	1	0.787739765117715	3		394	886	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392117	81392117	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1600	742	842	0	ENST00000222390.5:c.160G>T	p.Asp54Tyr	p.D54Y	ENST00000222390	NM_000601.4	54	Gat/Tat	2/18	0.230457369127467	5	FACETS	0.877	0.846	0.909	0.585	0.564	0.606	INDETERMINATE	2	TRUE	2	0.787739765117715	5		842	2342	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509120	106509120	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	298	501	0	ENST00000359195.3:c.1114G>T	p.Val372Phe	p.V372F	ENST00000359195	NM_002649.2	372	Gtc/Ttc	2/11	0.230457369127467	5	FACETS	1	0.992	1	0.452	0.426	0.48	INDETERMINATE	1	TRUE	2	0.787739765117715	5		501	1216	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089846	5089846	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	304	537	0	ENST00000381652.3:c.2744G>T	p.Gly915Val	p.G915V	ENST00000381652	NM_004972.3	915	gGa/gTa	20/25	0.414978505855718	1	FACETS	0.768	0.731	0.805	0.768	0.731	0.805	INDETERMINATE	1	TRUE	0	0.787739765117715	1		537	609	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331652	8331652	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	246	760	1	ENST00000356435.5:c.5464G>T	p.Asp1822Tyr	p.D1822Y	ENST00000356435		1822	Gac/Tac	33/35	0.414978505855718	1	FACETS	0.374	0.349	0.399	0.374	0.349	0.399	INDETERMINATE	1	TRUE	0	0.787739765117715	1		761	1013	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8733781	8733781	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	182	592	0	ENST00000356435.5:c.63G>T	p.Glu21Asp	p.E21D	ENST00000356435		21	gaG/gaT	1/35	0.414978505855718	1	FACETS	0.387	0.358	0.418	0.387	0.358	0.418	INDETERMINATE	1	TRUE	0	0.787739765117715	1		592	723	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169081	119169081	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	304	444	2	ENST00000264033.4:c.2265G>T	p.Leu755Phe	p.L755F	ENST00000264033	NM_005188.3	755	ttG/ttT	15/16	0.414978505855718	1	FACETS	0.757	0.72	0.794	0.757	0.72	0.794	INDETERMINATE	1	TRUE	0	0.787739765117715	1		446	618	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26911723	26911723	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	397	598	2	ENST00000381527.3:c.148G>T	p.Ala50Ser	p.A50S	ENST00000381527	NM_001260.1	50	Gct/Tct	2/13	0.414978505855718	1	FACETS	0.736	0.704	0.768	0.736	0.704	0.768	INDETERMINATE	1	TRUE	0	0.787739765117715	1		600	830	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476299	88476299	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	299	567	0	ENST00000360948.2:c.1833C>A	p.Asp611Glu	p.D611E	ENST00000360948	NM_001012338.2	611	gaC/gaA	15/19	0.744132096093369	2	FACETS	1	0.992	1	0.622	0.592	0.653	CLONAL	1	TRUE	0	0.787739765117715	2		567	610	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576183	88576183	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	358	390	1	ENST00000360948.2:c.1490G>T	p.Gly497Val	p.G497V	ENST00000360948	NM_001012338.2	497	gGg/gTg	13/19	0.744132096093369	2	FACETS	0.916	0.885	0.946	0.916	0.885	0.946	CLONAL	2	TRUE	0	0.787739765117715	2		391	496	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33433445	33433445	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs777593941	NA	P-0010087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	285	481	0	ENST00000345365.6:c.536T>C	p.Leu179Pro	p.L179P	ENST00000345365	NM_002878.3	179	cTg/cCg	6/10	0.447510628851375	4	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.787739765117715	4		481	1044	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554428	63554428	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	389	496	0	ENST00000307078.5:c.311G>T	p.Cys104Phe	p.C104F	ENST00000307078	NM_004655.3	104	tGc/tTc	2/11	0.322532722317574	5	FACETS	1	0.986	1	0.723	0.689	0.758	INDETERMINATE	2	TRUE	2	0.787739765117715	5		496	993	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375182	31375182	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	75	539	0	ENST00000328111.2:c.579G>C	p.Gln193His	p.Q193H	ENST00000328111	NM_006892.3	193	caG/caC	6/23	0.373939886637949	3	FACETS	0.268	0.234	0.305	0.134	0.117	0.153	INDETERMINATE	1	TRUE	1	0.787739765117715	3		539	989	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044926	47044926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	471	295	0	ENST00000377604.3:c.2252A>G	p.Glu751Gly	p.E751G	ENST00000377604	NM_001204468.1	751	gAg/gGg	20/24	0.670585417349555	2	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.787739765117715	2		295	562	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040955	42040955	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0010090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	399	863	0	ENST00000219905.7:c.5333C>G	p.Ser1778Ter	p.S1778*	ENST00000219905	NM_001164273.1	1778	tCa/tGa	16/24	0.594443698803437	2	FACETS	0.937	0.9	0.975	0.937	0.9	0.975	CLONAL	2	TRUE	0	0.594443698803437	2		863	716	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875958	76875961	+	frameshift_variant	Frame_Shift_Del	DEL	TTTT	TTTT	-	novel	NA	P-0010090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	363	762	0	ENST00000373344.5:c.5174_5177del	p.Lys1725MetfsTer10	p.K1725Mfs*10	ENST00000373344	NM_000489.3	1725	aAAAAt/at	20/35	0.594443698803437	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.594443698803437	1		762	574	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577375	64577375	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1057517902	NA	P-0010090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	337	649	0	ENST00000312049.6:c.207del	p.Asp70ThrfsTer49	p.D70Tfs*49	ENST00000312049	NM_130799.2	69	ccC/cc	2/10	0.594443698803437	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.594443698803437	2		649	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0010104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	327	462	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		463	806	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306677	41306677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs724159835	NA	P-0010104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	230	567	0	ENST00000373198.4:c.982C>T	p.Arg328Cys	p.R328C	ENST00000373198	NM_133170.3	328	Cgc/Tgc	7/32	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		567	907	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609759	117609759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	104	587	0	ENST00000368508.3:c.6940G>A	p.Asp2314Asn	p.D2314N	ENST00000368508	NM_002944.2	2314	Gat/Aat	43/43	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		587	1085	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528674	8528674	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	296	604	1	ENST00000356435.5:c.458C>T	p.Pro153Leu	p.P153L	ENST00000356435		153	cCg/cTg	4/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		605	742	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402755	139402755	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	354	450	2	ENST00000277541.6:c.3254G>T	p.Cys1085Phe	p.C1085F	ENST00000277541	NM_017617.3	1085	tGc/tTc	20/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		452	760	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0010124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	45	537	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.425	0.357	0.501	0.425	0.357	0.501	SUBCLONAL	1	FALSE	1	0.434384747105132	2		537	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0010124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	91	793	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			1	2	FACETS	0.652	0.579	0.729	0.652	0.579	0.729	SUBCLONAL	1	FALSE	1	0.434384747105132	2		793	643	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176975	56177003	+	frameshift_variant	Frame_Shift_Del	DEL	AACAATTGGCAAGAACTTCTTGGCCGCCT	AACAATTGGCAAGAACTTCTTGGCCGCCT	-	novel	NA	P-0010124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	43	540	0	ENST00000399503.3:c.2245_2273del	p.Asn749LeufsTer5	p.N749Lfs*5	ENST00000399503	NM_005921.1	749	AACAATTGGCAAGAACTTCTTGGCCGCCTt/t	13/20	1	2	FACETS	0.38	0.318	0.449	0.38	0.318	0.449	SUBCLONAL	1	FALSE	1	0.434384747105132	2		540	521	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0010133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	168	407	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.29303382388453	3	FACETS	0.987	0.911	1	0.658	0.607	0.711	CLONAL	2	TRUE	0	0.307883740828312	3		407	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0010133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	404	484	0	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	0.268113267074396	4	FACETS	0.896	0.855	0.936	0.896	0.855	0.936	CLONAL	4	TRUE	0	0.307883740828312	4		484	958	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042083	14042083	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	72	430	0	ENST00000311895.7:c.2630C>T	p.Ala877Val	p.A877V	ENST00000311895	NM_005236.2	877	gCa/gTa	11/11	0.278784067640108	4	FACETS	0.816	0.712	0.928	0.408	0.356	0.464	CLONAL	1	TRUE	2	0.307883740828312	4		430	750	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0010138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	38	513	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.438	0.361	0.525	0.438	0.361	0.525	SUBCLONAL	1	TRUE	1	0.257720436433775	2		514	673	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0010138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	124	457	1	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	0.257720436433775	3	FACETS	1	0.98	1	0.667	0.604	0.734	CLONAL	1	TRUE	1	0.257720436433775	3		458	814	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0010138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	140	480	0	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.257720436433775	2		480	835	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0010138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	34	334	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.64	0.523	0.772	0.64	0.523	0.772	SUBCLONAL	1	TRUE	1	0.257720436433775	2		334	412	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246177	46246177	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	19	512	0	ENST00000334344.6:c.4271G>A	p.Gly1424Asp	p.G1424D	ENST00000334344	NM_152641.2	1424	gGt/gAt	15/21	1	2	FACETS	0.52	0.401	0.656	0.52	0.401	0.656	SUBCLONAL	1	TRUE	1	0.695367856569514	2		512	105	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028660	12028660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	54	611	1	ENST00000353533.5:c.863C>T	p.Ser288Phe	p.S288F	ENST00000353533	NM_003010.3	288	tCt/tTt	8/11	0.63071225823643	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.695367856569514	1		612	98	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573987	7573987	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397516434	NA	P-0010141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	46	657	1	ENST00000269305.4:c.1040C>A	p.Ala347Asp	p.A347D	ENST00000269305	NM_001126112.2	347	gCc/gAc	10/11	0.63071225823643	1	FACETS	0.616	0.531	0.707	0.616	0.531	0.707	SUBCLONAL	1	TRUE	0	0.695367856569514	1		658	140	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143351	30143351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	71	348	0	ENST00000389048.3:c.175G>A	p.Val59Met	p.V59M	ENST00000389048	NM_004304.4	59	Gtg/Atg	1/29	0.695367856569514	3	FACETS	0.905	0.797	1	0.302	0.265	0.34	CLONAL	1	TRUE	0	0.695367856569514	3		348	304	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111509	56111509	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	43	18	0	ENST00000399503.3:c.109C>G	p.Pro37Ala	p.P37A	ENST00000399503	NM_005921.1	37	Ccc/Gcc	1/20	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.695367856569514	2		18	121	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0010159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	269	572	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.638251315339426	2		573	806	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0010159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	278	349	0	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	0.596006426408206	2	FACETS	0.902	0.86	0.944	0.902	0.86	0.944	CLONAL	2	TRUE	0	0.638251315339426	2		349	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577146	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0010159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	440	636	0	ENST00000269305.4:c.792_794del	p.Leu265del	p.L265del	ENST00000269305	NM_001126112.2	264	ctACTg/ctg	8/11	0.638251315339426	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.638251315339426	1		636	845	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39657741	39657741	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0010159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	541	237	0	ENST00000361337.2:c.33+1G>A		p.X11_splice	ENST00000361337	NM_003286.2	11			0.638251315339426	6	FACETS	1	0.995	1			1	CLONAL	5	TRUE	NA	0.638251315339426	6		237	707	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014295	70014295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756044021	NA	P-0010159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	311	744	0	ENST00000394351.3:c.1156G>A	p.Val386Ile	p.V386I	ENST00000394351	NM_000248.3	386	Gtc/Atc	9/9	1	2	FACETS	0.929	0.877	0.982	0.929	0.877	0.982	CLONAL	1	TRUE	1	0.638251315339426	2		744	1049	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253826	153253826	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	200	432	1	ENST00000281708.4:c.907C>T	p.Gln303Ter	p.Q303*	ENST00000281708	NM_033632.3	303	Caa/Taa	6/12	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.638251315339426	2		433	586	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045756	26045756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	484	886	1	ENST00000540144.1:c.118C>T	p.His40Tyr	p.H40Y	ENST00000540144	NM_003531.2	40	Cat/Tat	1/1	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.638251315339426	2		887	1454	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222582	157222582	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	297	488	0	ENST00000346085.5:c.1849C>T	p.Gln617Ter	p.Q617*	ENST00000346085	NM_020732.3	617	Cag/Tag	4/20	1	2	FACETS	0.996	0.94	1	0.996	0.94	1	CLONAL	1	TRUE	1	0.638251315339426	2		488	934	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346154	89346154	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1040188778	NA	P-0010159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	221	348	0	ENST00000301030.4:c.6796G>A	p.Ala2266Thr	p.A2266T	ENST00000301030	NM_001256183.1	2266	Gcg/Acg	9/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.638251315339426	2		348	607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587782272	NA	P-0010171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	265	367	0	ENST00000269305.4:c.994-1G>C		p.X332_splice	ENST00000269305	NM_001126112.2	332			NA	2	FACETS	0.958	0.9	1			1	INDETERMINATE	2	TRUE	NA	0.315760182792241	2		367	876	SUCCESS
AR	367	MSKCC	GRCh37	X	66766357	66766395	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	-	rs746853821	NA	P-0010171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	48	58	1	ENST00000374690.3:c.1382_1420del	p.Gly461_Gly473del	p.G461_G473del	ENST00000374690	NM_000044.3	457	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC/-	1/8	0.315760182792241	1	FACETS	0.785	0.676	0.901	1	0.968	1	CLONAL	2	TRUE	0	0.315760182792241	1		59	163	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484319	120484319	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	131	453	2	ENST00000256646.2:c.2811C>A	p.Cys937Ter	p.C937*	ENST00000256646	NM_024408.3	937	tgC/tgA	18/34	0.146771542484154	3	FACETS	0.786	0.711	0.865	0.262	0.237	0.289	INDETERMINATE	1	TRUE	0	0.315760182792241	3		455	1223	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839897	27839897	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1458	202	890	0	ENST00000328488.2:c.197T>G	p.Leu66Arg	p.L66R	ENST00000328488	NM_003533.2	66	cTa/cGa	1/1	0.152520871979965	2	FACETS	0.771	0.712	0.832	0.385	0.356	0.416	INDETERMINATE	1	TRUE	0	0.315760182792241	2		890	1660	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138145	64138145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757839757	NA	P-0010171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	108	324	0	ENST00000334205.4:c.2068G>A	p.Val690Met	p.V690M	ENST00000334205	NM_003942.2	690	Gtg/Atg	16/17	NA	2	FACETS	1	0.946	1			1	INDETERMINATE	1	TRUE	NA	0.315760182792241	2		324	633	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172462	108172462	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1060501556	NA	P-0010171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1451	166	498	0	ENST00000278616.4:c.5265G>T	p.Met1755Ile	p.M1755I	ENST00000278616	NM_000051.3	1755	atG/atT	35/63	0.315760182792241	5	FACETS	0.958	0.877	1	0.24	0.219	0.261	CLONAL	1	TRUE	1	0.315760182792241	5		498	1617	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805618	46805618	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1239	206	685	2	ENST00000290295.7:c.338C>A	p.Thr113Asn	p.T113N	ENST00000290295	NM_006361.5	113	aCt/aAt	1/2	0.146180091968918	3	FACETS	1	0.955	1			1	INDETERMINATE	1	TRUE	NA	0.315760182792241	3		687	1445	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717640	89717642	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0010171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	309	398	3	ENST00000371953.3:c.665_667del	p.Val222_Lys223delinsGlu	p.V222_K223delinsE	ENST00000371953	NM_000314.4	222	gTGAag/gag	7/9	0.315760182792241	3	FACETS	0.86	0.814	0.908			1	CLONAL	3	TRUE	NA	0.315760182792241	3		401	878	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717647	89717656	+	frameshift_variant	Frame_Shift_Del	DEL	ATATTCCTCC	ATATTCCTCC	-	novel	NA	P-0010171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	312	413	3	ENST00000371953.3:c.673_682del	p.Tyr225IlefsTer28	p.Y225Ifs*28	ENST00000371953	NM_000314.4	224	atATATTCCTCC/at	7/9	0.315760182792241	3	FACETS	0.85	0.804	0.897			1	CLONAL	3	TRUE	NA	0.315760182792241	3		416	897	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144146	55144146	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010175-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	96	417	0	ENST00000257290.5:c.1975A>T	p.Asn659Tyr	p.N659Y	ENST00000257290	NM_006206.4	659	Aac/Tac	14/23	0.429221203181612	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.429221203181612	1		417	318	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969158	93969158	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010175-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	133	806	2	ENST00000369303.4:c.1838C>A	p.Thr613Asn	p.T613N	ENST00000369303	NM_004440.3	613	aCc/aAc	10/17	0.219651454177941	3	FACETS	0.961	0.874	1	0.481	0.437	0.527	INDETERMINATE	1	TRUE	1	0.429221203181612	3		808	783	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0010177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	85	264	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.793	0.699	0.894	0.793	0.699	0.894	SUBCLONAL	1	TRUE	1	0.202311435221436	2		264	1060	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604656	48604656	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	62	376	0	ENST00000342988.3:c.1478A>G	p.Asp493Gly	p.D493G	ENST00000342988	NM_005359.5	493	gAt/gGt	12/12	0.202311435221436	1	FACETS	0.811	0.7	0.932	0.811	0.7	0.932	CLONAL	1	TRUE	0	0.202311435221436	1		376	679	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0010181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	474	533	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.434861363085249	2	FACETS	0.903	0.866	0.941	0.903	0.866	0.941	CLONAL	2	TRUE	0	0.466380320263281	2		533	1125	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0010181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1543	102	467	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.279391336746541	5	FACETS	0.452	0.402	0.505	0.151	0.134	0.169	INDETERMINATE	1	TRUE	2	0.466380320263281	5		467	1645	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0010181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	390	407	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.279391336746541	5	FACETS	0.988	0.937	1	0.658	0.625	0.693	INDETERMINATE	2	TRUE	2	0.466380320263281	5		407	1439	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0010181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	192	291	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.436236652498963	2	FACETS	1	0.989	1	0.666	0.619	0.714	CLONAL	1	TRUE	0	0.466380320263281	2		292	618	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465651	8465651	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772237001	NA	P-0010181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	228	402	1	ENST00000356435.5:c.3529C>T	p.Arg1177Cys	p.R1177C	ENST00000356435		1177	Cgc/Tgc	21/35	0.466380320263281	1	FACETS	0.896	0.837	0.957	0.896	0.837	0.957	CLONAL	1	TRUE	0	0.466380320263281	1		403	837	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678763	52678763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1490033079	NA	P-0010181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	105	426	0	ENST00000394830.3:c.856G>A	p.Glu286Lys	p.E286K	ENST00000394830	NM_018313.4	286	Gaa/Aaa	9/30	0.466380320263281	1	FACETS	0.389	0.348	0.433	0.389	0.348	0.433	SUBCLONAL	1	TRUE	0	0.466380320263281	1		426	888	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549863	187549863	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs950238146	NA	P-0010181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	110	367	0	ENST00000441802.2:c.4378A>G	p.Lys1460Glu	p.K1460E	ENST00000441802	NM_005245.3	1460	Aag/Gag	8/27	0.344442791351076	3	FACETS	0.535	0.479	0.594	0.268	0.239	0.297	SUBCLONAL	1	TRUE	1	0.466380320263281	3		367	1087	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934183	39934183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1339	278	570	1	ENST00000378444.4:c.416G>A	p.Gly139Glu	p.G139E	ENST00000378444	NM_001123385.1	139	gGa/gAa	4/15	0.270229911576479	3	FACETS	0.909	0.851	0.969			1	INDETERMINATE	1	TRUE	NA	0.466380320263281	3		571	1617	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620664	52620664	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	48	808	1	ENST00000394830.3:c.3089A>T	p.Asp1030Val	p.D1030V	ENST00000394830	NM_018313.4	1030	gAt/gTt	21/30	1	2	FACETS	0.943	0.813	1	1	0.974	1	CLONAL	2	TRUE	1	0.32	2		809	159	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144119	11144119	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	97	1227	0	ENST00000358026.2:c.3700T>A	p.Phe1234Ile	p.F1234I	ENST00000358026	NM_001128849.1	1234	Ttc/Atc	26/36	0.146227273902414	0	FACETS	0.711	0.642	0.782			1	INDETERMINATE	2	TRUE	0	0.32	0		1227	290	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940035	76940035	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	54	1156	0	ENST00000373344.5:c.713C>G	p.Ala238Gly	p.A238G	ENST00000373344	NM_000489.3	238	gCt/gGt	9/35	0.44316619318372	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.32	1		1156	204	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	35	420	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.114	0.093	0.139	0.114	0.093	0.139	SUBCLONAL	1	TRUE	1	0.795114325378346	2		420	769	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	269	403	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	0.795114325378346	2		403	674	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	163	320	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.934	0.866	1	0.934	0.866	1	CLONAL	1	TRUE	1	0.795114325378346	2		320	439	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	271	537	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.93	0.877	0.984	0.93	0.877	0.984	CLONAL	1	TRUE	1	0.795114325378346	2		537	733	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888189	112888189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507511	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	120	572	0	ENST00000351677.2:c.205G>A	p.Glu69Lys	p.E69K	ENST00000351677	NM_002834.3	69	Gag/Aag	3/16	1	2	FACETS	0.339	0.306	0.375	0.339	0.306	0.375	SUBCLONAL	1	TRUE	1	0.795114325378346	2		572	890	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508742	29508742	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057517967	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	362	615	1	ENST00000356175.3:c.669G>A	p.Trp223Ter	p.W223*	ENST00000356175	NM_000267.3	223	tgG/tgA	7/57	1	2	FACETS	0.99	0.942	1	0.99	0.942	1	CLONAL	1	TRUE	1	0.795114325378346	2		616	920	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147551	47147551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	301	393	0	ENST00000409792.3:c.4775G>A	p.Arg1592Gln	p.R1592Q	ENST00000409792	NM_014159.6	1592	cGa/cAa	6/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.795114325378346	2		393	698	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926852	112926852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507540	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	52	616	0	ENST00000351677.2:c.1472C>T	p.Pro491Leu	p.P491L	ENST00000351677	NM_002834.3	491	cCc/cTc	13/16	1	2	FACETS	0.139	0.117	0.162	0.139	0.117	0.162	SUBCLONAL	1	TRUE	1	0.795114325378346	2		616	944	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661945	29661945	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854552	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	68	479	0	ENST00000356175.3:c.5839C>T	p.Arg1947Ter	p.R1947*	ENST00000356175	NM_000267.3	1947	Cga/Tga	39/57	1	2	FACETS	0.221	0.191	0.253	0.221	0.191	0.253	SUBCLONAL	1	TRUE	1	0.795114325378346	2		479	775	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202855	133202855	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057517583	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	53	504	1	ENST00000320574.5:c.6379C>T	p.Arg2127Ter	p.R2127*	ENST00000320574	NM_006231.2	2127	Cga/Tga	46/49	1	2	FACETS	0.16	0.135	0.186	0.16	0.135	0.186	SUBCLONAL	1	TRUE	1	0.795114325378346	2		505	835	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411246	63411246	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	87	642	4	ENST00000330258.3:c.1921C>T	p.Arg641Ter	p.R641*	ENST00000330258	NM_152424.3	641	Cga/Tga	2/2	0.283443605473003	1	FACETS	0.132	0.116	0.149	0.132	0.116	0.149	INDETERMINATE	1	TRUE	0	0.795114325378346	1		646	1000	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412306	139412306	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	335	524	0	ENST00000277541.6:c.1339C>T	p.Pro447Ser	p.P447S	ENST00000277541	NM_017617.3	447	Ccc/Tcc	8/34	1	2	FACETS	0.886	0.84	0.933	0.886	0.84	0.933	CLONAL	1	TRUE	1	0.795114325378346	2		524	951	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466800	25466800	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144689354	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	85	482	0	ENST00000264709.3:c.1903C>T	p.Arg635Trp	p.R635W	ENST00000264709	NM_175629.2	635	Cgg/Tgg	16/23	1	2	FACETS	0.209	0.184	0.236	0.209	0.184	0.236	SUBCLONAL	1	TRUE	1	0.795114325378346	2		482	1025	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343042	118343042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	30	298	0	ENST00000534358.1:c.1168G>A	p.Glu390Lys	p.E390K	ENST00000534358	NM_005933.3	390	Gaa/Aaa	3/36	1	2	FACETS	0.169	0.136	0.207	0.169	0.136	0.207	SUBCLONAL	1	TRUE	1	0.795114325378346	2		298	447	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2492123	2492123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11573986	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	31	599	0	ENST00000355716.4:c.521G>A	p.Gly174Glu	p.G174E	ENST00000355716	NM_003820.2	174	gGg/gAg	5/8	0.795114325378346	1	FACETS	0.098	0.079	0.12	0.098	0.079	0.12	SUBCLONAL	1	TRUE	0	0.795114325378346	1		599	478	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255239	16255239	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393506836	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	41	583	1	ENST00000375759.3:c.2504C>T	p.Ser835Phe	p.S835F	ENST00000375759	NM_015001.2	835	tCt/tTt	11/15	0.795114325378346	1	FACETS	0.114	0.095	0.136	0.114	0.095	0.136	SUBCLONAL	1	TRUE	0	0.795114325378346	1		584	543	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261746	16261746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	320	362	0	ENST00000375759.3:c.9011G>A	p.Gly3004Glu	p.G3004E	ENST00000375759	NM_015001.2	3004	gGg/gAg	11/15	0.795114325378346	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.795114325378346	1		362	459	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089653	27089653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	60	479	0	ENST00000324856.7:c.2609C>T	p.Pro870Leu	p.P870L	ENST00000324856	NM_006015.4	870	cCt/cTt	8/20	0.795114325378346	1	FACETS	0.184	0.159	0.212	0.184	0.159	0.212	SUBCLONAL	1	TRUE	0	0.795114325378346	1		479	493	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099428	27099428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	275	503	0	ENST00000324856.7:c.3665G>A	p.Gly1222Glu	p.G1222E	ENST00000324856	NM_006015.4	1222	gGg/gAg	14/20	0.795114325378346	1	FACETS	0.976	0.934	1	0.976	0.934	1	CLONAL	1	TRUE	0	0.795114325378346	1		503	427	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468186	120468186	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749662461	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	293	398	0	ENST00000256646.2:c.4253C>T	p.Pro1418Leu	p.P1418L	ENST00000256646	NM_024408.3	1418	cCc/cTc	25/34	0.795114325378346	1	FACETS	0.969	0.929	1	0.969	0.929	1	CLONAL	1	TRUE	0	0.795114325378346	1		398	458	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176085785	176085785	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746526584	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	368	523	0	ENST00000367669.3:c.1001C>T	p.Pro334Leu	p.P334L	ENST00000367669	NM_022457.5	334	cCt/cTt	9/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.795114325378346	2		523	868	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463266	25463266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1433353413	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	331	434	0	ENST00000264709.3:c.2227C>T	p.Pro743Ser	p.P743S	ENST00000264709	NM_175629.2	743	Ccc/Tcc	19/23	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.795114325378346	2		434	817	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994353	25994353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	395	643	1	ENST00000435504.4:c.460G>A	p.Val154Ile	p.V154I	ENST00000435504		154	Gtc/Atc	6/13	1	2	FACETS	0.995	0.949	1	0.995	0.949	1	CLONAL	1	TRUE	1	0.795114325378346	2		644	999	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693919	47693919	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	325	642	0	ENST00000233146.2:c.1633C>T	p.Gln545Ter	p.Q545*	ENST00000233146	NM_000251.2	545	Cag/Tag	10/16	1	2	FACETS	0.915	0.868	0.964	0.915	0.868	0.964	CLONAL	1	TRUE	1	0.795114325378346	2		642	893	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026963	48026963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	363	533	0	ENST00000234420.5:c.1841C>T	p.Ser614Phe	p.S614F	ENST00000234420	NM_000179.2	614	tCc/tTc	4/10	1	2	FACETS	0.986	0.938	1	0.986	0.938	1	CLONAL	1	TRUE	1	0.795114325378346	2		533	926	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027254	48027254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	222	429	1	ENST00000234420.5:c.2132C>T	p.Pro711Leu	p.P711L	ENST00000234420	NM_000179.2	711	cCc/cTc	4/10	1	2	FACETS	0.99	0.929	1	0.99	0.929	1	CLONAL	1	TRUE	1	0.795114325378346	2		430	564	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027713	48027713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781306	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	285	493	0	ENST00000234420.5:c.2591G>A	p.Gly864Glu	p.G864E	ENST00000234420	NM_000179.2	864	gGa/gAa	4/10	1	2	FACETS	0.962	0.909	1	0.962	0.909	1	CLONAL	1	TRUE	1	0.795114325378346	2		493	745	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152307	99152307	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	39	491	0	ENST00000074304.5:c.386C>T	p.Thr129Ile	p.T129I	ENST00000074304	NM_001134224.1	129	aCa/aTa	6/26	1	2	FACETS	0.134	0.11	0.16	0.134	0.11	0.16	SUBCLONAL	1	TRUE	1	0.795114325378346	2		491	733	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251716	212251716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773165657	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	274	437	0	ENST00000342788.4:c.3343G>A	p.Val1115Met	p.V1115M	ENST00000342788	NM_005235.2	1115	Gtg/Atg	27/28	1	2	FACETS	0.926	0.874	0.98	0.926	0.874	0.98	CLONAL	1	TRUE	1	0.795114325378346	2		437	744	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042494	37042494	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63751421	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	63	613	1	ENST00000231790.2:c.256C>T	p.Gln86Ter	p.Q86*	ENST00000231790	NM_000249.3	86	Cag/Tag	3/19	1	2	FACETS	0.148	0.127	0.17	0.148	0.127	0.17	SUBCLONAL	1	TRUE	1	0.795114325378346	2		614	1074	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139527	47139527	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	365	690	0	ENST00000409792.3:c.5060G>A	p.Gly1687Asp	p.G1687D	ENST00000409792	NM_014159.6	1687	gGt/gAt	9/21	1	2	FACETS	0.964	0.918	1	0.964	0.918	1	CLONAL	1	TRUE	1	0.795114325378346	2		690	952	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143043	47143043	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	265	542	0	ENST00000409792.3:c.4920G>A	p.Trp1640Ter	p.W1640*	ENST00000409792	NM_014159.6	1640	tgG/tgA	8/21	1	2	FACETS	0.954	0.899	1	0.954	0.899	1	CLONAL	1	TRUE	1	0.795114325378346	2		542	699	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161832	47161832	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779275813	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	334	700	0	ENST00000409792.3:c.4294G>A	p.Glu1432Lys	p.E1432K	ENST00000409792	NM_014159.6	1432	Gag/Aag	3/21	1	2	FACETS	0.936	0.888	0.984	0.936	0.888	0.984	CLONAL	1	TRUE	1	0.795114325378346	2		700	898	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643672	52643672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	171	333	0	ENST00000394830.3:c.2224G>A	p.Glu742Lys	p.E742K	ENST00000394830	NM_018313.4	742	Gag/Aag	17/30	1	2	FACETS	0.909	0.844	0.976	0.909	0.844	0.976	CLONAL	1	TRUE	1	0.795114325378346	2		333	473	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702513	52702513	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	208	373	0	ENST00000394830.3:c.384+1G>A		p.X128_splice	ENST00000394830	NM_018313.4	128			1	2	FACETS	0.933	0.872	0.994	0.933	0.872	0.994	CLONAL	1	TRUE	1	0.795114325378346	2		373	561	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272146	142272146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	79	515	0	ENST00000350721.4:c.2728G>A	p.Glu910Lys	p.E910K	ENST00000350721	NM_001184.3	910	Gaa/Aaa	13/47	1	2	FACETS	0.241	0.212	0.274	0.241	0.212	0.274	SUBCLONAL	1	TRUE	1	0.795114325378346	2		515	823	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972047	55972047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	52	473	0	ENST00000263923.4:c.1597G>A	p.Val533Ile	p.V533I	ENST00000263923	NM_002253.2	533	Gtc/Atc	12/30	1	2	FACETS	0.161	0.136	0.188	0.161	0.136	0.188	SUBCLONAL	1	TRUE	1	0.795114325378346	2		473	813	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808297	99808297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	202	362	0	ENST00000280892.6:c.392G>A	p.Gly131Glu	p.G131E	ENST00000280892	NM_001130678.1	131	gGa/gAa	5/7	1	2	FACETS	0.966	0.903	1	0.966	0.903	1	CLONAL	1	TRUE	1	0.795114325378346	2		362	526	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251570	251570	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1302547655	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	347	490	0	ENST00000264932.6:c.1781G>A	p.Arg594Lys	p.R594K	ENST00000264932	NM_004168.2	594	aGg/aAg	13/15	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.795114325378346	2		490	870	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279503	1279503	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	332	487	0	ENST00000310581.5:c.2033C>T	p.Ala678Val	p.A678V	ENST00000310581	NM_198253.2	678	gCc/gTc	5/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.795114325378346	2		487	817	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152578	56152578	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	172	351	1	ENST00000399503.3:c.633+1G>A		p.X211_splice	ENST00000399503	NM_005921.1	211			1	2	FACETS	0.997	0.927	1	0.997	0.927	1	CLONAL	1	TRUE	1	0.795114325378346	2		352	434	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178127	56178127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1313918279	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	205	381	0	ENST00000399503.3:c.3100C>T	p.Pro1034Ser	p.P1034S	ENST00000399503	NM_005921.1	1034	Cct/Tct	14/20	1	2	FACETS	0.918	0.857	0.979	0.918	0.857	0.979	CLONAL	1	TRUE	1	0.795114325378346	2		381	562	SUCCESS
APC	324	MSKCC	GRCh37	5	112176336	112176336	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	203	378	0	ENST00000257430.4:c.5045G>A	p.Gly1682Asp	p.G1682D	ENST00000257430	NM_000038.5	1682	gGt/gAt	16/16	1	2	FACETS	0.954	0.892	1	0.954	0.892	1	CLONAL	1	TRUE	1	0.795114325378346	2		378	535	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501589	149501589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	175	325	0	ENST00000261799.4:c.2198C>T	p.Thr733Ile	p.T733I	ENST00000261799	NM_002609.3	733	aCc/aTc	16/23	1	2	FACETS	0.875	0.812	0.939	0.875	0.812	0.939	CLONAL	1	TRUE	1	0.795114325378346	2		325	503	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562454	176562454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774962938	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	294	519	0	ENST00000439151.2:c.350G>A	p.Ser117Asn	p.S117N	ENST00000439151	NM_022455.4	117	aGt/aAt	2/23	1	2	FACETS	0.979	0.927	1	0.979	0.927	1	CLONAL	1	TRUE	1	0.795114325378346	2		519	755	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20486984	20486984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	83	543	0	ENST00000346618.3:c.949G>A	p.Val317Ile	p.V317I	ENST00000346618	NM_001949.4	317	Gtt/Att	5/7	1	2	FACETS	0.232	0.204	0.262	0.232	0.204	0.262	SUBCLONAL	1	TRUE	1	0.795114325378346	2		543	899	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710974	117710974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	111	247	0	ENST00000368508.3:c.1298G>A	p.Arg433Lys	p.R433K	ENST00000368508	NM_002944.2	433	aGa/aAa	12/43	1	2	FACETS	0.966	0.882	1	0.966	0.882	1	CLONAL	1	TRUE	1	0.795114325378346	2		247	289	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771233	161771233	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	267	359	0	ENST00000366898.1:c.1296G>A	p.Met432Ile	p.M432I	ENST00000366898	NM_004562.2	432	atG/atA	12/12	1	2	FACETS	0.971	0.916	1	0.971	0.916	1	CLONAL	1	TRUE	1	0.795114325378346	2		359	692	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509712	106509712	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	264	472	0	ENST00000359195.3:c.1706C>T	p.Ala569Val	p.A569V	ENST00000359195	NM_002649.2	569	gCa/gTa	2/11	1	2	FACETS	0.925	0.872	0.979	0.925	0.872	0.979	CLONAL	1	TRUE	1	0.795114325378346	2		472	718	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371797	116371797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774779741	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	308	500	1	ENST00000397752.3:c.1276C>T	p.Arg426Cys	p.R426C	ENST00000397752	NM_000245.2	426	Cgc/Tgc	3/21	1	2	FACETS	0.933	0.884	0.984	0.933	0.884	0.984	CLONAL	1	TRUE	1	0.795114325378346	2		501	830	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878442	151878442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	290	500	0	ENST00000262189.6:c.6503C>T	p.Pro2168Leu	p.P2168L	ENST00000262189	NM_170606.2	2168	cCt/cTt	36/59	1	2	FACETS	0.971	0.919	1	0.971	0.919	1	CLONAL	1	TRUE	1	0.795114325378346	2		500	751	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884446	151884446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	80	555	0	ENST00000262189.6:c.4909C>T	p.Leu1637Phe	p.L1637F	ENST00000262189	NM_170606.2	1637	Ctt/Ttt	33/59	1	2	FACETS	0.25	0.219	0.283	0.25	0.219	0.283	SUBCLONAL	1	TRUE	1	0.795114325378346	2		555	806	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38314999	38314999	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	415	534	0	ENST00000425967.3:c.65G>A	p.Gly22Glu	p.G22E	ENST00000425967	NM_001174067.1	22	gGa/gAa	3/19	1	2	FACETS	0.954	0.911	0.998	0.954	0.911	0.998	CLONAL	1	TRUE	1	0.795114325378346	2		534	1094	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518348	8518348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	185	321	0	ENST00000356435.5:c.1043C>T	p.Pro348Leu	p.P348L	ENST00000356435		348	cCt/cTt	10/35	1	2	FACETS	0.938	0.874	1	0.938	0.874	1	CLONAL	1	TRUE	1	0.795114325378346	2		321	496	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209453	98209453	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777731495	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	244	422	0	ENST00000331920.6:c.4085C>T	p.Pro1362Leu	p.P1362L	ENST00000331920	NM_000264.3	1362	cCc/cTc	23/24	1	2	FACETS	0.838	0.787	0.891	0.838	0.787	0.891	CLONAL	1	TRUE	1	0.795114325378346	2		422	732	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402576	139402576	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777684045	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	73	450	0	ENST00000277541.6:c.3341G>A	p.Arg1114His	p.R1114H	ENST00000277541	NM_017617.3	1114	cGc/cAc	21/34	1	2	FACETS	0.247	0.215	0.281	0.247	0.215	0.281	SUBCLONAL	1	TRUE	1	0.795114325378346	2		450	744	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139411724	139411724	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	265	394	0	ENST00000277541.6:c.1555G>A	p.Gly519Ser	p.G519S	ENST00000277541	NM_017617.3	519	Ggc/Agc	9/34	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.795114325378346	2		394	645	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998631	100998631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	458	609	0	ENST00000325455.5:c.1171G>A	p.Glu391Lys	p.E391K	ENST00000325455	NM_001202474.3	391	Gag/Aag	1/8	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.795114325378346	2		609	1049	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432932	432932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	274	475	0	ENST00000399788.2:c.1984G>A	p.Glu662Lys	p.E662K	ENST00000399788	NM_001042603.1	662	Gaa/Aaa	15/28	NA	2	FACETS	1	0.948	1			1	INDETERMINATE	1	TRUE	NA	0.795114325378346	2		475	687	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246089	46246089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	35	435	0	ENST00000334344.6:c.4183C>T	p.Pro1395Ser	p.P1395S	ENST00000334344	NM_152641.2	1395	Cca/Tca	15/21	1	2	FACETS	0.137	0.112	0.166	0.137	0.112	0.166	SUBCLONAL	1	TRUE	1	0.795114325378346	2		435	642	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863451	57863451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1231	65	644	1	ENST00000228682.2:c.1546G>A	p.Gly516Ser	p.G516S	ENST00000228682	NM_005269.2	516	Ggt/Agt	11/12	1	2	FACETS	0.126	0.109	0.145	0.126	0.109	0.145	SUBCLONAL	1	TRUE	1	0.795114325378346	2		645	1296	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864628	57864628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	541	803	2	ENST00000228682.2:c.2105G>A	p.Gly702Glu	p.G702E	ENST00000228682	NM_005269.2	702	gGg/gAg	12/12	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.795114325378346	2		805	1286	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609962	81609962	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	272	341	1	ENST00000298171.2:c.1560G>A	p.Trp520Ter	p.W520*	ENST00000298171	NM_000369.2	520	tgG/tgA	10/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.795114325378346	2		342	666	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041675	42041675	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1023385479	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	417	700	0	ENST00000219905.7:c.5870G>A	p.Ser1957Asn	p.S1957N	ENST00000219905	NM_001164273.1	1957	aGc/aAc	17/24	1	2	FACETS	0.952	0.908	0.996	0.952	0.908	0.996	CLONAL	1	TRUE	1	0.795114325378346	2		700	1102	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42057206	42057206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	425	716	0	ENST00000219905.7:c.7867C>T	p.Leu2623Phe	p.L2623F	ENST00000219905	NM_001164273.1	2623	Ctc/Ttc	23/24	1	2	FACETS	0.915	0.873	0.958	0.915	0.873	0.958	CLONAL	1	TRUE	1	0.795114325378346	2		716	1168	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059122	42059122	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780110323	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	51	701	0	ENST00000219905.7:c.8842G>A	p.Gly2948Arg	p.G2948R	ENST00000219905	NM_001164273.1	2948	Ggg/Agg	24/24	1	2	FACETS	0.139	0.117	0.163	0.139	0.117	0.163	SUBCLONAL	1	TRUE	1	0.795114325378346	2		701	923	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641046	23641046	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555460335	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	38	506	1	ENST00000261584.4:c.2429C>T	p.Pro810Leu	p.P810L	ENST00000261584	NM_024675.3	810	cCt/cTt	5/13	1	2	FACETS	0.134	0.11	0.161	0.134	0.11	0.161	SUBCLONAL	1	TRUE	1	0.795114325378346	2		507	713	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641527	23641527	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	50	624	1	ENST00000261584.4:c.1948G>A	p.Glu650Lys	p.E650K	ENST00000261584	NM_024675.3	650	Gag/Aag	5/13	1	2	FACETS	0.155	0.131	0.182	0.155	0.131	0.182	SUBCLONAL	1	TRUE	1	0.795114325378346	2		625	809	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832595	72832595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	304	453	0	ENST00000268489.5:c.3986G>A	p.Gly1329Glu	p.G1329E	ENST00000268489	NM_006885.3	1329	gGa/gAa	9/10	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.795114325378346	2		453	756	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740507	58740507	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	465	781	0	ENST00000305921.3:c.1412C>T	p.Pro471Leu	p.P471L	ENST00000305921	NM_003620.3	471	cCa/cTa	6/6	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.795114325378346	2		781	1128	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554099	63554099	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	361	666	0	ENST00000307078.5:c.640G>A	p.Gly214Arg	p.G214R	ENST00000307078	NM_004655.3	214	Gga/Aga	2/11	1	2	FACETS	0.912	0.866	0.958	0.912	0.866	0.958	CLONAL	1	TRUE	1	0.795114325378346	2		666	996	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45423016	45423016	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	467	732	0	ENST00000262160.6:c.112G>A	p.Glu38Lys	p.E38K	ENST00000262160	NM_005901.5	38	Gaa/Aaa	2/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.795114325378346	2		732	1121	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3113418	3113418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	431	582	0	ENST00000078429.4:c.412G>A	p.Asp138Asn	p.D138N	ENST00000078429	NM_002067.2	138	Gac/Aac	3/7	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.795114325378346	2		582	1028	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094873	11094873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	434	573	1	ENST00000358026.2:c.46C>T	p.Pro16Ser	p.P16S	ENST00000358026	NM_001128849.1	16	Cct/Tct	2/36	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.795114325378346	2		574	1016	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793075	42793075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768695134	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	45	416	0	ENST00000575354.2:c.967C>T	p.Leu323Phe	p.L323F	ENST00000575354	NM_015125.3	323	Ctc/Ttc	7/20	0.795114325378346	1	FACETS	0.131	0.11	0.155	0.131	0.11	0.155	SUBCLONAL	1	TRUE	0	0.795114325378346	1		416	519	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902136	50902136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	57	653	0	ENST00000440232.2:c.28G>A	p.Gly10Arg	p.G10R	ENST00000440232	NM_002691.3	10	Ggg/Agg	2/27	0.795114325378346	1	FACETS	0.134	0.114	0.155	0.134	0.114	0.155	SUBCLONAL	1	TRUE	0	0.795114325378346	1		653	646	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905343	50905343	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	523	766	0	ENST00000440232.2:c.551G>A	p.Gly184Glu	p.G184E	ENST00000440232	NM_002691.3	184	gGg/gAg	5/27	0.795114325378346	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.795114325378346	1		766	773	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36022372	36022372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	54	545	0	ENST00000358208.4:c.425C>T	p.Pro142Leu	p.P142L	ENST00000358208		142	cCc/cTc	4/12	1	2	FACETS	0.132	0.112	0.154	0.132	0.112	0.154	SUBCLONAL	1	TRUE	1	0.795114325378346	2		545	1030	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733325	40733325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	17	288	0	ENST00000373198.4:c.3481G>A	p.Glu1161Lys	p.E1161K	ENST00000373198	NM_133170.3	1161	Gaa/Aaa	26/32	1	2	FACETS	0.129	0.096	0.168	0.129	0.096	0.168	SUBCLONAL	1	TRUE	1	0.795114325378346	2		288	332	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484589	57484589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	177	253	0	ENST00000371085.3:c.673G>A	p.Gly225Ser	p.G225S	ENST00000371085	NM_000516.4	225	Ggt/Agt	9/13	1	2	FACETS	0.848	0.787	0.91	0.848	0.787	0.91	CLONAL	1	TRUE	1	0.795114325378346	2		253	525	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15821827	15821827	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	64	660	0	ENST00000307771.7:c.220G>A	p.Glu74Lys	p.E74K	ENST00000307771	NM_005089.3	74	Gag/Aag	4/11	0.283443605473003	1	FACETS	0.103	0.089	0.119	0.103	0.089	0.119	INDETERMINATE	1	TRUE	0	0.795114325378346	1		660	940	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922154	39922154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	101	927	0	ENST00000378444.4:c.4018G>A	p.Asp1340Asn	p.D1340N	ENST00000378444	NM_001123385.1	1340	Gat/Aat	9/15	0.283443605473003	1	FACETS	0.119	0.106	0.134	0.119	0.106	0.134	INDETERMINATE	1	TRUE	0	0.795114325378346	1		927	1284	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426664	47426664	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	481	555	0	ENST00000377045.4:c.909G>A	p.Trp303Ter	p.W303*	ENST00000377045	NM_001654.4	303	tgG/tgA	10/16	0.283443605473003	1	FACETS	0.736	0.707	0.764	0.736	0.707	0.764	INDETERMINATE	1	TRUE	0	0.795114325378346	1		555	991	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410126	63410126	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs959631746	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	434	691	0	ENST00000330258.3:c.3041G>A	p.Gly1014Glu	p.G1014E	ENST00000330258	NM_152424.3	1014	gGg/gAg	2/2	0.283443605473003	1	FACETS	0.684	0.655	0.714	0.684	0.655	0.714	INDETERMINATE	1	TRUE	0	0.795114325378346	1		691	961	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413070	63413070	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	457	790	0	ENST00000330258.3:c.97G>A	p.Ala33Thr	p.A33T	ENST00000330258	NM_152424.3	33	Gca/Aca	2/2	0.283443605473003	1	FACETS	0.578	0.552	0.603	0.578	0.552	0.603	INDETERMINATE	1	TRUE	0	0.795114325378346	1		790	1199	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125281	47125281	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010205-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	316	489	0	ENST00000409792.3:c.5989G>T	p.Glu1997Ter	p.E1997*	ENST00000409792	NM_014159.6	1997	Gaa/Taa	12/21	0.807017831351693	1	FACETS	0.967	0.929	1	0.967	0.929	1	CLONAL	1	TRUE	0	0.807017831351693	1		489	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0010222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	120	533	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	1	2	FACETS	0.686	0.618	0.758	0.686	0.618	0.758	SUBCLONAL	1	TRUE	1	0.31	2		533	1129	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426904	6426904	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	181	482	0	ENST00000356142.4:c.97A>T	p.Ile33Phe	p.I33F	ENST00000356142	NM_018890.3	33	Atc/Ttc	2/7	0.3	3	FACETS	1	0.933	1	0.508	0.467	0.551	CLONAL	1	TRUE	1	0.31	3		482	1328	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954213	48954229	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AATTTTAGGTAAATTTT	AATTTTAGGTAAATTTT	-	novel	NA	P-0010222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1230	216	651	0	ENST00000267163.4:c.1414_1421+9del		p.X472_splice	ENST00000267163	NM_000321.2	472		15/27	0.3	3	FACETS	1	0.975	1	0.557	0.516	0.599	CLONAL	1	TRUE	1	0.31	3		651	1446	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645690	12645690	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010231-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	215	443	0	ENST00000251849.4:c.779C>A	p.Thr260Lys	p.T260K	ENST00000251849	NM_002880.3	260	aCa/aAa	7/17	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	FALSE	NA	0.314741032936327	2		443	1113	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670838	134670838	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010231-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	62	144	0	ENST00000398015.3:c.749T>C	p.Ile250Thr	p.I250T	ENST00000398015	NM_004441.4	250	aTt/aCt	3/16	0.151305056549909	1	FACETS	1	0.919	1	1	0.919	1	INDETERMINATE	1	FALSE	0	0.314741032936327	1		144	308	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099733	157099733	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1191841397	NA	P-0010231-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	39	118	0	ENST00000346085.5:c.670C>T	p.Pro224Ser	p.P224S	ENST00000346085	NM_020732.3	224	Ccg/Tcg	1/20	0.314741032936327	1	FACETS	0.842	0.703	0.995	0.842	0.703	0.995	CLONAL	1	FALSE	0	0.314741032936327	1		118	248	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349860	89349860	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010231-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2342	344	1577	0	ENST00000301030.4:c.3090G>C	p.Glu1030Asp	p.E1030D	ENST00000301030	NM_001256183.1	1030	gaG/gaC	9/13	1	2	FACETS	0.814	0.766	0.863	0.814	0.766	0.863	CLONAL	1	FALSE	1	0.314741032936327	2		1577	2686	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221962	1221962	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs398123405	NA	P-0010231-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	301	568	0	ENST00000326873.7:c.877G>T	p.Glu293Ter	p.E293*	ENST00000326873	NM_000455.4	293	Gaa/Taa	7/10	0.314741032936327	0	FACETS	0.655	0.618	0.693			1	SUBCLONAL	2	FALSE	0	0.314741032936327	0		568	1000	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602757	10602757	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010231-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	148	388	0	ENST00000171111.5:c.821A>T	p.His274Leu	p.H274L	ENST00000171111	NM_203500.1	274	cAc/cTc	3/6	0.250838543433809	1	FACETS	0.752	0.691	0.815	1	0.988	1	SUBCLONAL	2	FALSE	0	0.314741032936327	1		388	527	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010246-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	96	371	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	FALSE	1	0.212763785948201	2		371	810	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0010246-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	156	571	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.212763785948201	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	0	0.212763785948201	1		571	1045	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581229	48581229	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs377767331	NA	P-0010246-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	96	452	0	ENST00000342988.3:c.533C>G	p.Ser178Ter	p.S178*	ENST00000342988	NM_005359.5	178	tCa/tGa	5/12	0.212763785948201	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	0	0.212763785948201	1		452	699	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0010252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	334	612	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.85813059089963	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.85813059089963	1		613	422	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457216	89457216	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0010252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	231	323	0	ENST00000336596.2:c.1698-1G>C		p.X566_splice	ENST00000336596	NM_005233.5	566			1	2	FACETS	0.95	0.893	1	0.95	0.893	1	CLONAL	1	TRUE	1	0.85813059089963	2		323	567	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366981	118366981	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	434	562	0	ENST00000534358.1:c.5563G>C	p.Asp1855His	p.D1855H	ENST00000534358	NM_005933.3	1855	Gat/Cat	20/36	0.85813059089963	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.85813059089963	1		562	559	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676310	37676310	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	67	566	0	ENST00000447079.4:c.3065A>C	p.Asp1022Ala	p.D1022A	ENST00000447079	NM_015083.1	1022	gAt/gCt	11/14	0.85813059089963	2	FACETS	0.139	0.12	0.16	0.07	0.06	0.08	SUBCLONAL	1	TRUE	0	0.85813059089963	2		566	1122	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272118	18272118	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	16	22	0	ENST00000222254.8:c.628G>A	p.Glu210Lys	p.E210K	ENST00000222254	NM_005027.3	210	Gag/Aag	6/16	1	2	FACETS	1	0.79	1	1	0.79	1	CLONAL	1	TRUE	1	0.85813059089963	2		22	37	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0010257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	163	345	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	0.47328364794379	2		345	657	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912657	NA	P-0010257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	235	490	0	ENST00000269305.4:c.814G>C	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ctg	8/11	0.356033955878735	1	FACETS	0.79	0.738	0.845	0.79	0.738	0.845	SUBCLONAL	1	TRUE	0	0.47328364794379	1		490	959	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139513	47139513	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	97	822	1	ENST00000409792.3:c.5074G>T	p.Glu1692Ter	p.E1692*	ENST00000409792	NM_014159.6	1692	Gaa/Taa	9/21	0.218050357680379	1	FACETS	0.311	0.276	0.348	0.311	0.276	0.348	INDETERMINATE	1	TRUE	0	0.47328364794379	1		823	1006	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158245	47158245	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0010257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	82	240	0	ENST00000409792.3:c.4455-1G>T		p.X1485_splice	ENST00000409792	NM_014159.6	1485			0.218050357680379	1	FACETS	0.696	0.618	0.779	0.696	0.618	0.779	INDETERMINATE	1	TRUE	0	0.47328364794379	1		240	380	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502766	186502766	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	331	889	0	ENST00000323963.5:c.224C>A	p.Ala75Asp	p.A75D	ENST00000323963		75	gCt/gAt	4/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.47328364794379	2		889	1381	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878657	151878657	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	159	478	0	ENST00000262189.6:c.6288G>T	p.Gln2096His	p.Q2096H	ENST00000262189	NM_170606.2	2096	caG/caT	36/59	1	2	FACETS	0.906	0.832	0.982	0.906	0.832	0.982	CLONAL	1	TRUE	1	0.47328364794379	2		478	742	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577173	64577173	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1208267598	NA	P-0010257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1236	337	714	0	ENST00000312049.6:c.409C>G	p.Arg137Gly	p.R137G	ENST00000312049	NM_130799.2	137	Cgg/Ggg	2/10	1	2	FACETS	0.905	0.854	0.958	0.905	0.854	0.958	CLONAL	1	TRUE	1	0.47328364794379	2		714	1573	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573597	48573597	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1064794204	NA	P-0010257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	170	408	0	ENST00000342988.3:c.181A>G	p.Ile61Val	p.I61V	ENST00000342988	NM_005359.5	61	Ata/Gta	2/12	0.433682489734339	1	FACETS	0.931	0.861	1	0.931	0.861	1	CLONAL	1	TRUE	0	0.47328364794379	1		408	589	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222350	2222350	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs756038587	NA	P-0010257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	62	269	0	ENST00000398665.3:c.3182C>G	p.Ser1061Cys	p.S1061C	ENST00000398665	NM_032482.2	1061	tCc/tGc	24/28	1	2	FACETS	0.466	0.403	0.535	0.466	0.403	0.535	SUBCLONAL	1	TRUE	1	0.47328364794379	2		269	562	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517938	8517939	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0010257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	156	750	2	ENST00000356435.5:c.1452_1453delinsAA	p.Gln485Lys	p.Q485K	ENST00000356435		484	ccCCag/ccAAag	10/35	0.433682489734339	1	FACETS	0.584	0.535	0.636	0.584	0.535	0.636	SUBCLONAL	1	TRUE	0	0.47328364794379	1		752	861	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	574	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.436062929276425	9	FACETS	1	0.988	1			1	CLONAL	6	TRUE	NA	0.436062929276425	9		371	1057	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882025	NA	P-0010261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	339	533	0	ENST00000269305.4:c.646G>T	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ttg	6/11	0.436062929276425	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.436062929276425	3		533	841	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162591	47162591	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	171	490	0	ENST00000409792.3:c.3535G>C	p.Asp1179His	p.D1179H	ENST00000409792	NM_014159.6	1179	Gac/Cac	3/21	0.35343190476471	2	FACETS	0.881	0.819	0.944	0.881	0.819	0.944	CLONAL	2	TRUE	0	0.436062929276425	2		490	445	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052932	180052932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	239	526	0	ENST00000261937.6:c.1358C>T	p.Pro453Leu	p.P453L	ENST00000261937	NM_182925.4	453	cCt/cTt	10/30	0.392949113596509	3	FACETS	1	0.992	1	0.712	0.665	0.76	CLONAL	1	TRUE	1	0.436062929276425	3		526	938	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533907	533907	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1448375861	NA	P-0010261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	112	328	0	ENST00000451590.1:c.149C>T	p.Thr50Met	p.T50M	ENST00000451590	NM_001130442.1	50	aCg/aTg	3/5	0.363671105728127	3	FACETS	0.848	0.763	0.938	0.424	0.381	0.469	CLONAL	1	TRUE	1	0.436062929276425	3		328	738	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857425	9857425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1268143219	NA	P-0010261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	120	633	0	ENST00000330684.3:c.3976G>A	p.Gly1326Ser	p.G1326S	ENST00000330684	NM_001134407.1	1326	Ggc/Agc	13/13	0.363671105728127	3	FACETS	0.72	0.649	0.795	0.36	0.324	0.398	SUBCLONAL	1	TRUE	1	0.436062929276425	3		633	931	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625189	69625189	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	109	548	0	ENST00000334134.2:c.604C>A	p.Pro202Thr	p.P202T	ENST00000334134	NM_005247.2	202	Cct/Act	3/3	1	2	FACETS	0.457	0.411	0.506	0.457	0.411	0.506	SUBCLONAL	1	TRUE	1	0.705573242529629	2		548	676	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0010271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	639	705	1	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	0.866193802123481	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.866193802123481	1		706	788	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904872	101904872	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	231	505	0	ENST00000374994.4:c.860C>G	p.Ser287Cys	p.S287C	ENST00000374994	NM_004612.2	287	tCc/tGc	5/9	0.446084174837813	1	FACETS	0.361	0.337	0.385	0.361	0.337	0.385	INDETERMINATE	1	TRUE	0	0.866193802123481	1		505	838	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425890	49425890	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	238	625	0	ENST00000301067.7:c.12598C>T	p.Gln4200Ter	p.Q4200*	ENST00000301067	NM_003482.3	4200	Cag/Tag	39/54	0.494908778674835	1	FACETS	0.332	0.31	0.354	0.332	0.31	0.354	INDETERMINATE	1	TRUE	0	0.866193802123481	1		625	939	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426808	49426812	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGC	TGGGC	-	novel	NA	P-0010271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	295	381	0	ENST00000301067.7:c.11676_11680del	p.Gln3892HisfsTer118	p.Q3892Hfs*118	ENST00000301067	NM_003482.3	3892	caGCCCAtg/catg	39/54	0.494908778674835	1	FACETS	0.762	0.727	0.796	0.762	0.727	0.796	INDETERMINATE	1	TRUE	0	0.866193802123481	1		381	507	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0010296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	45	367	1	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	FALSE	1	0.135146842407677	2		368	620	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061261	38061264	+	missense_variant	Missense_Mutation	ONP	TAGG	TAGG	GAGC	novel	NA	P-0010296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1224	106	637	0	ENST00000250448.2:c.725_728delinsGCTC	p.Ser242_Tyr243delinsCysSer	p.S242_Y243delinsCS	ENST00000250448	NM_004496.3	242	tCCTAc/tGCTCc	2/2	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.135146842407677	2		637	1330	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0010303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	229	420	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.956	0.894	1	0.956	0.894	1	CLONAL	1	TRUE	1	0.601880415251331	2		420	796	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48586237	48586237	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs878854769	NA	P-0010303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	238	408	0	ENST00000342988.3:c.906G>A	p.Trp302Ter	p.W302*	ENST00000342988	NM_005359.5	302	tgG/tgA	8/12	0.601880415251331	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.601880415251331	1		408	539	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410439	139410439	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1334264743	NA	P-0010303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	163	447	0	ENST00000277541.6:c.1663A>G	p.Thr555Ala	p.T555A	ENST00000277541	NM_017617.3	555	Acg/Gcg	10/34	1	2	FACETS	0.811	0.747	0.877	0.811	0.747	0.877	CLONAL	1	TRUE	1	0.601880415251331	2		447	668	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0010304-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	361	544	2	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.686892844881169	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.686892844881169	1		546	683	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677933	58677933	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010304-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	449	302	0	ENST00000305921.3:c.158C>A	p.Pro53Gln	p.P53Q	ENST00000305921	NM_003620.3	53	cCg/cAg	1/6	0.686892844881169	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.686892844881169	1		302	739	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0010312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	18	239	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.118107022050138	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		239	415	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0010329-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	61	345	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.883	0.762	1	0.883	0.762	1	CLONAL	1	TRUE	1	0.27	2		345	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934573	NA	P-0010329-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	55	568	1	ENST00000269305.4:c.722C>A	p.Ser241Tyr	p.S241Y	ENST00000269305	NM_001126112.2	241	tCc/tAc	7/11	1	2	FACETS	0.766	0.655	0.887	0.766	0.655	0.887	SUBCLONAL	1	TRUE	1	0.27	2		569	532	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414737	56414737	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010329-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	130	927	0	ENST00000348428.3:c.2138C>T	p.Ala713Val	p.A713V	ENST00000348428	NM_006785.3	713	gCt/gTt	17/17	1	2	FACETS	0.864	0.782	0.95	0.864	0.782	0.95	CLONAL	1	TRUE	1	0.27	2		927	1115	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0010337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	451	641	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.46052217021142	3	FACETS	0.918	0.879	0.957	0.612	0.586	0.638	CLONAL	2	TRUE	0	0.592575720530649	3		641	1075	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0010337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	467	435	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.592575720530649	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.592575720530649	2		435	774	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102137	27102137	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0010337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	155	582	0	ENST00000324856.7:c.5063T>G	p.Leu1688Ter	p.L1688*	ENST00000324856	NM_006015.4	1688	tTa/tGa	19/20	0.358522012966117	1	FACETS	0.426	0.39	0.464	0.426	0.39	0.464	SUBCLONAL	1	TRUE	0	0.592575720530649	1		582	864	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820839	36820839	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	88	291	1	ENST00000373129.3:c.538G>A	p.Asp180Asn	p.D180N	ENST00000373129	NM_032017.1	180	Gac/Aac	6/12	0.358522012966117	1	FACETS	0.463	0.412	0.518	0.463	0.412	0.518	SUBCLONAL	1	TRUE	0	0.592575720530649	1		292	451	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682895	241682895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	85	334	0	ENST00000366560.3:c.128G>A	p.Arg43Gln	p.R43Q	ENST00000366560	NM_000143.3	43	cGa/cAa	1/10	0.358522012966117	1	FACETS	0.432	0.383	0.484	0.432	0.383	0.484	SUBCLONAL	1	TRUE	0	0.592575720530649	1		334	467	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589826	212589826	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	50	269	0	ENST00000342788.4:c.716C>T	p.Ser239Leu	p.S239L	ENST00000342788	NM_005235.2	239	tCa/tTa	6/28	0.299584650282902	2	FACETS	0.361	0.306	0.42	0.18	0.153	0.21	INDETERMINATE	1	TRUE	0	0.592575720530649	2		269	468	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643415	52643415	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	184	762	0	ENST00000394830.3:c.2481G>C	p.Lys827Asn	p.K827N	ENST00000394830	NM_018313.4	827	aaG/aaC	17/30	0.299584650282902	2	FACETS	0.502	0.463	0.544	0.251	0.231	0.272	INDETERMINATE	1	TRUE	0	0.592575720530649	2		762	1236	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157812	106157812	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	61	315	0	ENST00000380013.4:c.2713G>C	p.Asp905His	p.D905H	ENST00000380013	NM_001127208.2	905	Gat/Cat	3/11	0.299584650282902	2	FACETS	0.401	0.346	0.46	0.2	0.173	0.23	INDETERMINATE	1	TRUE	0	0.592575720530649	2		315	514	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839716	27839716	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs775189331	NA	P-0010337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1763	620	1569	0	ENST00000328488.2:c.378G>C	p.Gln126His	p.Q126H	ENST00000328488	NM_003533.2	126	caG/caC	1/1	1	2	FACETS	0.878	0.842	0.915	0.878	0.842	0.915	CLONAL	1	TRUE	1	0.592575720530649	2		1569	2383	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570406	87570406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	75	659	1	ENST00000277120.3:c.2146G>A	p.Asp716Asn	p.D716N	ENST00000277120		716	Gac/Aac	17/19	1	2	FACETS	0.21	0.183	0.239	0.21	0.183	0.239	SUBCLONAL	1	TRUE	1	0.592575720530649	2		660	1208	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133710877	133710877	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	183	730	0	ENST00000318560.5:c.44A>T	p.Lys15Met	p.K15M	ENST00000318560	NM_005157.4	15	aAg/aTg	1/11	1	2	FACETS	0.46	0.423	0.499	0.46	0.423	0.499	SUBCLONAL	1	TRUE	1	0.592575720530649	2		730	1342	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402574	139402574	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	103	264	0	ENST00000277541.6:c.3343C>A	p.Leu1115Met	p.L1115M	ENST00000277541	NM_017617.3	1115	Ctg/Atg	21/34	1	2	FACETS	0.629	0.564	0.697	0.629	0.564	0.697	SUBCLONAL	1	TRUE	1	0.592575720530649	2		264	553	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333087	70333087	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1564948676	NA	P-0010337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	163	610	0	ENST00000373644.4:c.992T>G	p.Leu331Trp	p.L331W	ENST00000373644	NM_030625.2	331	tTg/tGg	2/12	0.268005823897557	3	FACETS	0.606	0.555	0.66			1	INDETERMINATE	1	TRUE	NA	0.592575720530649	3		610	1176	SUCCESS
CBL	867	MSKCC	GRCh37	11	119145569	119145569	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1234	152	603	0	ENST00000264033.4:c.775A>G	p.Asn259Asp	p.N259D	ENST00000264033	NM_005188.3	259	Aac/Gac	5/16	0.506725779124009	3	FACETS	0.48	0.437	0.525			1	SUBCLONAL	1	TRUE	NA	0.592575720530649	3		603	1386	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527439	29527439	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs587781517	NA	P-0010337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	46	316	0	ENST00000356175.3:c.889-1G>A		p.X297_splice	ENST00000356175	NM_000267.3	297			0.268005823897557	3	FACETS	0.417	0.351	0.489			1	INDETERMINATE	1	TRUE	NA	0.592575720530649	3		316	483	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243830	41243830	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	77	368	0	ENST00000357654.3:c.3718C>G	p.Gln1240Glu	p.Q1240E	ENST00000357654	NM_007294.3	1240	Cag/Gag	10/23	0.592575720530649	2	FACETS	0.476	0.418	0.538	0.238	0.209	0.269	SUBCLONAL	1	TRUE	0	0.592575720530649	2		368	546	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797200	42797200	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	288	222	0	ENST00000575354.2:c.3562C>G	p.Pro1188Ala	p.P1188A	ENST00000575354	NM_015125.3	1188	Ccc/Gcc	15/20	0.183339540438266	5	FACETS	0.925	0.883	0.967			1	INDETERMINATE	4	TRUE	NA	0.592575720530649	5		222	496	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038867	47038867	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	42	68	0	ENST00000377604.3:c.874G>T	p.Glu292Ter	p.E292*	ENST00000377604	NM_001204468.1	292	Gag/Tag	9/24	0.389347247544219	2	FACETS	0.762	0.66	0.866			1	SUBCLONAL	2	TRUE	NA	0.592575720530649	2		68	93	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792642	33792642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	39	76	0	ENST00000498907.2:c.679C>T	p.Pro227Ser	p.P227S	ENST00000498907	NM_004364.3	227	Ccg/Tcg	1/1	0.367607141279063	4	FACETS	0.882	0.743	1	0.882	0.743	1	CLONAL	2	TRUE	2	0.375149428382452	4		76	162	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560851	9560851	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1320	356	661	0	ENST00000353224.5:c.931C>A	p.His311Asn	p.H311N	ENST00000353224	NM_177990.2	311	Cac/Aac	4/10	0.375149428382452	6	FACETS	0.991	0.936	1	0.661	0.624	0.698	CLONAL	2	TRUE	3	0.375149428382452	6		661	1676	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659675	NA	P-0010346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	93	389	0	ENST00000269305.4:c.764T>C	p.Ile255Thr	p.I255T	ENST00000269305	NM_001126112.2	255	aTc/aCc	7/11	0.373768814556487	1	FACETS	0.884	0.792	0.981	0.884	0.792	0.981	CLONAL	1	TRUE	0	0.425661383038107	1		389	389	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250455	110250455	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	58	326	0	ENST00000374672.4:c.220C>A	p.Leu74Met	p.L74M	ENST00000374672	NM_004235.4	74	Ctg/Atg	3/5	1	2	FACETS	0.902	0.781	1	0.902	0.781	1	CLONAL	1	TRUE	1	0.425661383038107	2		326	302	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437433	49437433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	89	623	0	ENST00000301067.7:c.5452C>T	p.Pro1818Ser	p.P1818S	ENST00000301067	NM_003482.3	1818	Ccc/Tcc	23/54	1	2	FACETS	0.683	0.606	0.765	0.683	0.606	0.765	SUBCLONAL	1	TRUE	1	0.425661383038107	2		623	612	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954379	48954379	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0010346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	151	404	0	ENST00000267163.4:c.1498+2T>C		p.X500_splice	ENST00000267163	NM_000321.2	500			0.393770532684097	3	FACETS	0.839	0.778	0.899	0.839	0.778	0.899	CLONAL	3	TRUE	0	0.425661383038107	3		404	342	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413129	63413129	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	99	640	2	ENST00000330258.3:c.38G>T	p.Gly13Val	p.G13V	ENST00000330258	NM_152424.3	13	gGa/gTa	2/2	0.145784176693986	0	FACETS	0.595	0.534	0.659			1	INDETERMINATE	1	TRUE	0	0.425661383038107	0		642	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0010350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	267	462	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.96	0.902	1	1	0.995	1	CLONAL	2	TRUE	1	0.316150453829337	2		463	880	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0010350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	81	420	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	0.316150453829337	2		420	415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0010350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	22	162	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	1	2	FACETS	0.348	0.269	0.44	0.348	0.269	0.44	SUBCLONAL	1	TRUE	1	0.316150453829337	2		162	400	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0010350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	107	348	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.316150453829337	1	FACETS	0.783	0.709	0.86	1	0.985	1	SUBCLONAL	2	TRUE	0	0.316150453829337	1		348	364	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217705	7217707	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs757139280	NA	P-0010350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	85	790	0	ENST00000380728.2:c.220_222del	p.Glu74del	p.E74del	ENST00000380728		74	GAG/-	4/11	0.189443399351706	1	FACETS	0.371	0.327	0.419	0.371	0.327	0.419	INDETERMINATE	1	TRUE	0	0.316150453829337	1		790	1220	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30061040	30061040	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755200117	NA	P-0010350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	90	547	3	ENST00000338641.4:c.872G>A	p.Arg291His	p.R291H	ENST00000338641	NM_000268.3	291	cGt/cAt	9/16	0.205493053686213	1	FACETS	0.606	0.537	0.68	0.606	0.537	0.68	SUBCLONAL	1	TRUE	0	0.316150453829337	1		550	791	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159748	20159748	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	250	598	1	ENST00000379607.5:c.11A>T	p.Asn4Ile	p.N4I	ENST00000379607	NM_001412.3	4	aAt/aTt	1/7	0.316150453829337	3	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.316150453829337	3		599	1320	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409848	63409848	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	296	623	0	ENST00000330258.3:c.3319C>T	p.Leu1107Phe	p.L1107F	ENST00000330258	NM_152424.3	1107	Ctt/Ttt	2/2	NA	2	FACETS	0.91	0.857	0.964			1	INDETERMINATE	2	TRUE	NA	0.316150453829337	2		623	1029	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0010375-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	18	483	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		483	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577095	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519984	NA	P-0010375-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1304	37	561	0	ENST00000269305.4:c.843C>G	p.Asp281Glu	p.D281E	ENST00000269305	NM_001126112.2	281	gaC/gaG	8/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		561	1341	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045116	47045116	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010375-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	79	334	0	ENST00000377604.3:c.2360del	p.Asn787ThrfsTer15	p.N787Tfs*15	ENST00000377604	NM_001204468.1	786	cAa/ca	21/24	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		334	742	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0010385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	754	452	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.326319629517951	7	FACETS	1	0.994	1			1	CLONAL	6	TRUE	NA	0.326319629517951	7		452	1303	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0010385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1247	52	448	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	0.326319629517951	2	FACETS	0.245	0.208	0.287	0.123	0.104	0.144	SUBCLONAL	1	TRUE	0	0.326319629517951	2		448	1299	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278153	142278153	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	173	348	0	ENST00000350721.4:c.1672G>T	p.Asp558Tyr	p.D558Y	ENST00000350721	NM_001184.3	558	Gac/Tac	7/47	0.141466317049894	3	FACETS	1	0.983	1	0.621	0.571	0.673	INDETERMINATE	1	TRUE	1	0.326319629517951	3		348	993	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280107	66280107	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	258	419	0	ENST00000273854.3:c.1582G>T	p.Glu528Ter	p.E528*	ENST00000273854	NM_004439.5	528	Gag/Tag	7/18	0.326319629517951	1	FACETS	0.806	0.757	0.856	1	0.994	1	CLONAL	2	TRUE	0	0.326319629517951	1		419	821	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067073	143067073	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	231	549	0	ENST00000262992.4:c.1640G>T	p.Gly547Val	p.G547V	ENST00000262992	NM_001101669.1	547	gGt/gTt	16/24	0.326319629517951	1	FACETS	0.803	0.751	0.855	1	0.993	1	CLONAL	2	TRUE	0	0.326319629517951	1		549	738	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251225	99251225	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	170	434	0	ENST00000268035.6:c.529G>T	p.Glu177Ter	p.E177*	ENST00000268035	NM_000875.3	177	Gaa/Taa	2/21	1	2	FACETS	0.886	0.813	0.962	0.886	0.813	0.962	CLONAL	1	TRUE	1	0.326319629517951	2		434	1176	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578516	7578516	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs137852794	NA	P-0010385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	324	468	1	ENST00000269305.4:c.414del	p.Lys139ArgfsTer31	p.K139Rfs*31	ENST00000269305	NM_001126112.2	138	gcC/gc	5/11	0.326319629517951	2	FACETS	0.906	0.856	0.957	0.906	0.856	0.957	CLONAL	2	TRUE	0	0.326319629517951	2		469	1096	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225549	2225550	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0010385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	154	447	0	ENST00000326181.6:c.1552_1553delinsTT	p.Gly518Phe	p.G518F	ENST00000326181	NM_032271.2	518	GGc/TTc	17/21	1	2	FACETS	0.83	0.758	0.906	0.83	0.758	0.906	CLONAL	1	TRUE	1	0.326319629517951	2		447	1137	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114276	115114276	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0010427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	227	300	0	ENST00000257566.3:c.942-1G>C		p.X314_splice	ENST00000257566	NM_016569.3	314			0.692073802501551	3	FACETS	1	0.966	1	0.527	0.492	0.563	CLONAL	1	TRUE	1	0.696768489287158	3		300	834	SUCCESS
APC	324	MSKCC	GRCh37	5	112176710	112176710	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	66	365	0	ENST00000257430.4:c.5419G>C	p.Asp1807His	p.D1807H	ENST00000257430	NM_000038.5	1807	Gac/Cac	16/16	NA	2	FACETS	0.255	0.22	0.292			1	INDETERMINATE	1	TRUE	NA	0.696768489287158	2		365	744	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158633	26158633	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	11	81	0	ENST00000289316.2:c.236C>T	p.Ser79Phe	p.S79F	ENST00000289316	NM_138720.2	79	tCc/tTc	1/2	1	2	FACETS	0.241	0.167	0.332	0.241	0.167	0.332	SUBCLONAL	1	TRUE	1	0.696768489287158	2		81	131	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246347	53246347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	446	750	1	ENST00000375401.3:c.635G>A	p.Arg212Gln	p.R212Q	ENST00000375401	NM_004187.3	212	cGg/cAg	5/26	0.671668754515583	2	FACETS	1	0.986	1	0.536	0.512	0.56	CLONAL	1	TRUE	0	0.696768489287158	2		751	1194	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019159	31019159	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	227	368	0	ENST00000375687.4:c.754T>A	p.Phe252Ile	p.F252I	ENST00000375687	NM_015338.5	252	Ttt/Att	9/13	1	2	FACETS	0.912	0.853	0.974	0.912	0.853	0.974	CLONAL	1	TRUE	1	0.642889430858091	2		368	774	SUCCESS
YES1	7525	MSKCC	GRCh37	18	732895	732895	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	583	500	0	ENST00000314574.4:c.1362del	p.Asp454GlufsTer12	p.D454Efs*12	ENST00000314574	NM_005433.3	454	gaT/ga	11/12	NA	2	FACETS	0.975	0.945	1			1	INDETERMINATE	2	TRUE	NA	0.642889430858091	2		500	930	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545914	41545914	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	197	289	0	ENST00000263253.7:c.2530del	p.His844IlefsTer6	p.H844Ifs*6	ENST00000263253	NM_001429.3	843	caC/ca	14/31	1	2	FACETS	0.891	0.828	0.955	0.891	0.828	0.955	CLONAL	1	TRUE	1	0.642889430858091	2		289	688	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418204	139418204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs187473846	NA	P-0010457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	312	325	0	ENST00000277541.6:c.368C>T	p.Thr123Met	p.T123M	ENST00000277541	NM_017617.3	123	aCg/aTg	3/34	0.60618789837595	2	FACETS	0.753	0.719	0.787	0.753	0.719	0.787	SUBCLONAL	2	TRUE	0	0.742094278438603	2		325	558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs786201057	NA	P-0010457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	236	195	0	ENST00000269305.4:c.374C>G	p.Thr125Arg	p.T125R	ENST00000269305	NM_001126112.2	125	aCg/aGg	4/11	0.535506574599266	3	FACETS	1	0.988	1	0.753	0.716	0.789	CLONAL	2	TRUE	0	0.742094278438603	3		195	386	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555706	21555706	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	340	360	0	ENST00000382592.4:c.2564A>G	p.Lys855Arg	p.K855R	ENST00000382592	NM_014572.2	855	aAg/aGg	6/8	0.597273828334767	3	FACETS	1	0.993	1	0.646	0.612	0.68	CLONAL	1	TRUE	1	0.742094278438603	3		360	973	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005422	29005422	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs141286646	NA	P-0010457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	155	244	0	ENST00000282397.4:c.839G>T	p.Arg280Leu	p.R280L	ENST00000282397	NM_002019.4	280	cGa/cTa	7/30	0.597273828334767	3	FACETS	1	0.963	1	0.538	0.496	0.582	CLONAL	1	TRUE	1	0.742094278438603	3		244	532	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215373	41215373	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0010457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	302	262	0	ENST00000357654.3:c.5170A>T	p.Lys1724Ter	p.K1724*	ENST00000357654	NM_007294.3	1724	Aaa/Taa	18/23	NA	2	FACETS	0.801	0.766	0.836			1	INDETERMINATE	2	TRUE	NA	0.742094278438603	2		262	508	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39721135	39721135	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	317	304	0	ENST00000361337.2:c.638A>G	p.Glu213Gly	p.E213G	ENST00000361337	NM_003286.2	213	gAa/gGa	9/21	0.644800267850901	3	FACETS	0.788	0.748	0.828	0.788	0.748	0.828	SUBCLONAL	2	TRUE	1	0.742094278438603	3		304	743	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	134	136	0	ENST00000397752.3:c.3028+1del		p.D1010fs	ENST00000397752	NM_000245.2	1010	Gat/at	14/21	0.440246689580352	4	FACETS	1	0.975	1	0.773	0.71	0.838	CLONAL	2	FALSE	1	0.440246689580352	4		136	378	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484349	8484349	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	26	162	0	ENST00000356435.5:c.3183A>C	p.Glu1061Asp	p.E1061D	ENST00000356435		1061	gaA/gaC	19/35	0.440246689580352	4	FACETS	0.348	0.275	0.432	0.174	0.137	0.216	SUBCLONAL	1	FALSE	2	0.440246689580352	4		162	489	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891298	101891298	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	25	283	0	ENST00000374994.4:c.259G>A	p.Ala87Thr	p.A87T	ENST00000374994	NM_004612.2	87	Gca/Aca	2/9	0.291847538126599	1	FACETS	0.253	0.198	0.315	0.253	0.198	0.315	SUBCLONAL	1	TRUE	0	0.334833140463755	1		283	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0010467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	63	223	0	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	0.298007865680418	1	FACETS	0.693	0.601	0.793	0.693	0.601	0.793	SUBCLONAL	1	TRUE	0	0.334833140463755	1		223	452	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523012	25523012	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	124	468	0	ENST00000264709.3:c.173C>T	p.Pro58Leu	p.P58L	ENST00000264709	NM_175629.2	58	cCc/cTc	3/23	1	2	FACETS	0.897	0.811	0.987	0.897	0.811	0.987	CLONAL	1	TRUE	1	0.334833140463755	2		468	826	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86676378	86676379	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0010467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	42	280	0	ENST00000274376.6:c.2656_2657del	p.Pro886TyrfsTer11	p.P886Yfs*11	ENST00000274376	NM_002890.2	886	CCt/t	20/25	0.291847538126599	1	FACETS	0.593	0.497	0.7	0.593	0.497	0.7	SUBCLONAL	1	TRUE	0	0.334833140463755	1		280	352	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676164	29676167	+	frameshift_variant	Frame_Shift_Del	DEL	GTTG	GTTG	TTT	novel	NA	P-0010467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	61	172	0	ENST00000356175.3:c.7153_7156delinsTTT	p.Val2385PhefsTer12	p.V2385Ffs*12	ENST00000356175	NM_000267.3	2385	GTTGca/TTTca	48/57	0.260081776450801	2	FACETS	1	0.96	1	0.644	0.56	0.733	CLONAL	1	TRUE	0	0.334833140463755	2		172	283	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	164	589	1				ENST00000310581	NM_198253.2	-/1132			0.882823470831479	1	FACETS	0.956	0.911	0.999	0.956	0.911	0.999	CLONAL	1	TRUE	0	0.882823470831479	1		590	217	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0010495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	306	365	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.983	0.933	1	0.983	0.933	1	CLONAL	1	TRUE	1	0.882823470831479	2		366	705	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0010495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	365	442	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	0.882823470831479	1	FACETS	0.987	0.957	1	0.987	0.957	1	CLONAL	1	TRUE	0	0.882823470831479	1		442	468	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174838	56174838	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	161	356	1	ENST00000399503.3:c.1997C>T	p.Pro666Leu	p.P666L	ENST00000399503	NM_005921.1	666	cCt/cTt	11/20	0.51719356698738	1	FACETS	0.368	0.339	0.397	0.368	0.339	0.397	INDETERMINATE	1	TRUE	0	0.882823470831479	1		357	554	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112631	115112631	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010495-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	171	158	0	ENST00000257566.3:c.1109C>T	p.Pro370Leu	p.P370L	ENST00000257566	NM_016569.3	370	cCc/cTc	7/8	0.882823470831479	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.882823470831479	1		158	207	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098944	178098944	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	69	325	0	ENST00000397062.3:c.101G>C	p.Arg34Pro	p.R34P	ENST00000397062	NM_006164.4	34	cGa/cCa	2/5	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.191168987546998	2		325	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876658468	NA	P-0010503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	84	335	0	ENST00000269305.4:c.577C>A	p.His193Asn	p.H193N	ENST00000269305	NM_001126112.2	193	Cat/Aat	6/11	NA	2	FACETS	0.949	0.842	1			1	INDETERMINATE	2	TRUE	NA	0.191168987546998	2		335	463	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655425	45655425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767656796	NA	P-0010503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	39	273	0	ENST00000407780.3:c.427G>A	p.Val143Ile	p.V143I	ENST00000407780	NM_001283052.1	143	Gtc/Atc	4/7	1	2	FACETS	1	0.834	1	1	0.834	1	CLONAL	1	TRUE	1	0.191168987546998	2		273	406	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726541	46726541	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	56	357	0	ENST00000371975.4:c.620G>C	p.Cys207Ser	p.C207S	ENST00000371975	NM_003579.3	207	tGc/tCc	7/18	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.191168987546998	2		357	493	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032039	26032039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	161	661	0	ENST00000244661.2:c.250C>T	p.Arg84Cys	p.R84C	ENST00000244661	NM_003537.3	84	Cgc/Tgc	1/1	0.177743553142583	3	FACETS	0.963	0.883	1	0.642	0.588	0.698	CLONAL	2	TRUE	0	0.191168987546998	3		661	958	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519721	137519721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	54	297	0	ENST00000367739.4:c.917C>T	p.Ser306Leu	p.S306L	ENST00000367739	NM_000416.2	306	tCa/tTa	7/7	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.191168987546998	2		297	555	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728714	39728714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	110	277	0	ENST00000361337.2:c.994G>A	p.Glu332Lys	p.E332K	ENST00000361337	NM_003286.2	332	Gaa/Aaa	12/21	0.111520012266716	4	FACETS	0.898	0.81	0.99	1	0.98	1	INDETERMINATE	3	TRUE	2	0.191168987546998	4		277	509	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566522	41566524	+	missense_variant	Missense_Mutation	TNP	TAC	TAC	AAA	novel	NA	P-0010503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	109	482	1	ENST00000263253.7:c.4399_4401delinsAAA	p.Tyr1467Lys	p.Y1467K	ENST00000263253	NM_001429.3	1467	TAC/AAA	27/31	0.189928895670725	2	FACETS	0.901	0.81	0.996	0.901	0.81	0.996	CLONAL	2	TRUE	0	0.191168987546998	2		483	633	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0010517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	15	195	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.206858586611229	2	FACETS		NA	1			1	NA	NA	FALSE	0	NA	2		195	80	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653815	89653815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	19	504	1	ENST00000371953.3:c.113C>T	p.Pro38Leu	p.P38L	ENST00000371953	NM_000314.4	38	cCt/cTt	2/9	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		505	198	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183755	10183757	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs5030648	NA	P-0010517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	33	270	0	ENST00000256474.2:c.227_229del	p.Phe76del	p.F76del	ENST00000256474	NM_000551.3	75	aTCTtc/atc	1/3	0.402859719315122	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		270	187	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155395	47155395	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	55	585	1	ENST00000409792.3:c.4686G>A	p.Trp1562Ter	p.W1562*	ENST00000409792	NM_014159.6	1562	tgG/tgA	5/21	0.402859719315122	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		586	209	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579556	7579557	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0010523-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	158	389	0	ENST00000269305.4:c.130_131del	p.Met44AlafsTer7	p.M44Afs*7	ENST00000269305	NM_001126112.2	44	ATg/g	4/11	0.410327994312706	1	FACETS	0.708	0.65	0.77	0.708	0.65	0.77	SUBCLONAL	1	TRUE	0	0.422772611729031	1		389	832	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057519990	NA	P-0010557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	362	360	0	ENST00000269305.4:c.796G>T	p.Gly266Ter	p.G266*	ENST00000269305	NM_001126112.2	266	Gga/Tga	8/11	0.664553140731591	1	FACETS	0.95	0.907	0.993	0.95	0.907	0.993	CLONAL	1	TRUE	0	0.664553140731591	1		360	766	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665422	138665422	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	198	193	0	ENST00000330315.3:c.143A>T	p.Lys48Met	p.K48M	ENST00000330315	NM_023067.3	48	aAg/aTg	1/1	1	2	FACETS	0.832	0.773	0.893	0.832	0.773	0.893	CLONAL	1	TRUE	1	0.664553140731591	2		193	716	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89871754	89871754	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	327	315	0	ENST00000389301.3:c.643T>G	p.Cys215Gly	p.C215G	ENST00000389301	NM_000135.2	215	Tgc/Ggc	7/43	NA	2	FACETS	0.924	0.874	0.975			1	INDETERMINATE	1	TRUE	NA	0.664553140731591	2		315	1065	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220506	1220506	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0010557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	191	251	0	ENST00000326873.7:c.597+2T>C		p.X199_splice	ENST00000326873	NM_000455.4	199			0.664429192552969	1	FACETS	0.845	0.79	0.901	0.845	0.79	0.901	CLONAL	1	TRUE	0	0.664553140731591	1		251	454	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610265	10610265	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	393	415	0	ENST00000171111.5:c.445G>C	p.Glu149Gln	p.E149Q	ENST00000171111	NM_203500.1	149	Gag/Cag	2/6	0.664429192552969	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.664553140731591	1		415	750	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577129	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519986	NA	P-0010585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	283	544	0	ENST00000269305.4:c.809T>G	p.Phe270Cys	p.F270C	ENST00000269305	NM_001126112.2	270	tTt/tGt	8/11	0.216664139555294	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.252642312489099	2		544	1049	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464570	25464570	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587777507	NA	P-0010585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	316	360	0	ENST00000264709.3:c.1943T>C	p.Leu648Pro	p.L648P	ENST00000264709	NM_175629.2	648	cTg/cCg	17/23	0.252642312489099	4	FACETS	0.979	0.925	1	0.979	0.925	1	CLONAL	3	TRUE	1	0.252642312489099	4		360	1067	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236675	236675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752461029	NA	P-0010585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1472	65	218	0	ENST00000264932.6:c.1393C>T	p.Arg465Trp	p.R465W	ENST00000264932	NM_004168.2	465	Cgg/Tgg	10/15	0.252642312489099	14	FACETS	0.842	0.727	0.969			1	CLONAL	1	TRUE	NA	0.252642312489099	14		218	1537	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814731	139814731	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	139	553	0	ENST00000247668.2:c.724G>C	p.Glu242Gln	p.E242Q	ENST00000247668	NM_021138.3	242	Gag/Cag	8/11	NA	2	FACETS	0.895	0.813	0.982			1	INDETERMINATE	1	TRUE	NA	0.252642312489099	2		553	1229	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923312	9923312	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	109	458	0	ENST00000330684.3:c.1975G>C	p.Val659Leu	p.V659L	ENST00000330684	NM_001134407.1	659	Gtg/Ctg	9/13	0.252642312489099	4	FACETS	0.923	0.827	1	0.308	0.275	0.342	CLONAL	1	TRUE	1	0.252642312489099	4		458	1171	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274851	38274851	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519898	NA	P-0010589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	171	418	0	ENST00000425967.3:c.1729A>G	p.Asn577Asp	p.N577D	ENST00000425967	NM_001174067.1	577	Aac/Gac	13/19	1	2	FACETS	0.86	0.794	0.928	0.86	0.794	0.928	CLONAL	1	TRUE	1	0.6	2		418	663	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0010601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	72	452	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.507	0.442	0.578	0.507	0.442	0.578	SUBCLONAL	1	TRUE	1	0.31	2		452	916	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0010601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	42	264	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.354	0.295	0.421	0.354	0.295	0.421	SUBCLONAL	1	TRUE	1	0.31	2		264	765	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0010601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	79	455	1	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			1	2	FACETS	0.708	0.622	0.8	0.708	0.622	0.8	SUBCLONAL	1	TRUE	1	0.31	2		456	720	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003799	45003799	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	48	493	0	ENST00000558401.1:c.55G>T	p.Glu19Ter	p.E19*	ENST00000558401	NM_004048.2	19	Gag/Tag	1/4	1	2	FACETS	0.347	0.292	0.408	0.347	0.292	0.408	SUBCLONAL	1	TRUE	1	0.31	2		493	892	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174917	11174917	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	86	581	0	ENST00000361445.4:c.7117G>T	p.Glu2373Ter	p.E2373*	ENST00000361445	NM_004958.3	2373	Gag/Tag	52/58	1	2	FACETS	0.47	0.414	0.53	0.47	0.414	0.53	SUBCLONAL	1	TRUE	1	0.31	2		581	1181	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053120	180053120	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	78	533	0	ENST00000261937.6:c.1249G>T	p.Val417Leu	p.V417L	ENST00000261937	NM_182925.4	417	Gtg/Ttg	9/30	NA	2	FACETS	0.513	0.449	0.582			1	INDETERMINATE	1	TRUE	NA	0.31	2		533	981	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509951	106509951	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	54	584	1	ENST00000359195.3:c.1945G>T	p.Glu649Ter	p.E649*	ENST00000359195	NM_002649.2	649	Gag/Tag	2/11	1	2	FACETS	0.348	0.296	0.405	0.348	0.296	0.405	SUBCLONAL	1	TRUE	1	0.31	2		585	1002	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434518	140434518	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	39	405	0	ENST00000288602.6:c.2180G>C	p.Ser727Thr	p.S727T	ENST00000288602	NM_004333.4	727	aGt/aCt	18/18	1	2	FACETS	0.354	0.292	0.423	0.354	0.292	0.423	SUBCLONAL	1	TRUE	1	0.31	2		405	711	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625152	69625152	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	55	573	0	ENST00000334134.2:c.641A>G	p.Lys214Arg	p.K214R	ENST00000334134	NM_005247.2	214	aAg/aGg	3/3	1	2	FACETS	0.346	0.294	0.402	0.346	0.294	0.402	SUBCLONAL	1	TRUE	1	0.31	2		573	1027	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29007958	29007959	+	stop_gained,splice_region_variant	Nonsense_Mutation	DNP	CA	CA	AT	novel	NA	P-0010601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	38	356	0	ENST00000282397.4:c.810_811delinsAT	p.Asp270_Glu271delinsGluTer	p.D270_E271delinsE*	ENST00000282397	NM_002019.4	270	gaTGaa/gaATaa	6/30	1	2	FACETS	0.38	0.313	0.455	0.38	0.313	0.455	SUBCLONAL	1	TRUE	1	0.31	2		356	645	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782177	NA	P-0010631-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1322	80	824	1	ENST00000269305.4:c.644G>A	p.Ser215Asn	p.S215N	ENST00000269305	NM_001126112.2	215	aGt/aAt	6/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		825	1402	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0010636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	797	452	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.444997432395697	4	FACETS	1	0.996	1	1	0.996	1	CLONAL	4	TRUE	0	0.444997432395697	4		452	1188	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0010636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	223	239	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.444997432395697	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.444997432395697	2		239	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782144	NA	P-0010636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	347	467	0	ENST00000269305.4:c.473G>C	p.Arg158Pro	p.R158P	ENST00000269305	NM_001126112.2	158	cGc/cCc	5/11	0.444997432395697	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.444997432395697	2		467	752	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344171	70344171	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	560	304	0	ENST00000374080.3:c.1907C>T	p.Pro636Leu	p.P636L	ENST00000374080		636	cCc/cTc	13/45	0.444997432395697	3	FACETS	0.946	0.919	0.973			1	CLONAL	4	TRUE	NA	0.444997432395697	3		304	813	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890167	76890167	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010636-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	797	355	0	ENST00000373344.5:c.4727G>T	p.Cys1576Phe	p.C1576F	ENST00000373344	NM_000489.3	1576	tGt/tTt	17/35	0.444997432395697	3	FACETS	0.988	0.965	1			1	CLONAL	4	TRUE	NA	0.444997432395697	3		355	1108	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525114	9525114	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	105	473	0	ENST00000353224.5:c.1771G>T	p.Ala591Ser	p.A591S	ENST00000353224	NM_177990.2	591	Gct/Tct	8/10	0.228523236811536	3	FACETS	0.752	0.672	0.837	0.376	0.336	0.419	SUBCLONAL	1	FALSE	1	0.291544738462527	3		473	1098	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	174	136	0	ENST00000397752.3:c.3028+1del		p.D1010fs	ENST00000397752	NM_000245.2	1010	Gat/at	14/21	0.249392022571619	3	FACETS	0.874	0.806	0.945	0.874	0.806	0.945	CLONAL	2	FALSE	1	0.291544738462527	3		136	782	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361214	66361214	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs375878596	NA	P-0010637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	97	363	0	ENST00000273854.3:c.958G>T	p.Gly320Cys	p.G320C	ENST00000273854	NM_004439.5	320	Ggc/Tgc	4/18	0.228523236811536	3	FACETS	0.92	0.819	1	0.46	0.409	0.514	CLONAL	1	FALSE	1	0.291544738462527	3		363	829	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867309	68867309	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs760315494	NA	P-0010637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	156	424	2	ENST00000261769.5:c.2556G>T	p.Glu852Asp	p.E852D	ENST00000261769	NM_004360.3	852	gaG/gaT	16/16	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.291544738462527	NA		426	885	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039904	47039904	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	159	168	2	ENST00000377604.3:c.1247A>T	p.Gln416Leu	p.Q416L	ENST00000377604	NM_001204468.1	416	cAg/cTg	12/24	0.291544738462527	2	FACETS	0.862	0.798	0.926			1	CLONAL	3	FALSE	NA	0.291544738462527	2		170	422	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380944	116380958	+	inframe_deletion	In_Frame_Del	DEL	TTTCCAGTCCTGCAG	TTTCCAGTCCTGCAG	-	novel	NA	P-0010637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	108	496	0	ENST00000397752.3:c.1567_1581del	p.Phe523_Ser527del	p.F523_S527del	ENST00000397752	NM_000245.2	522	caTTTCCAGTCCTGCAGt/cat	5/21	0.249392022571619	3	FACETS	0.715	0.64	0.795	0.358	0.32	0.398	SUBCLONAL	1	FALSE	1	0.291544738462527	3		496	1187	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577077	7577082	+	inframe_deletion	In_Frame_Del	DEL	CTCTTC	CTCTTC	-	novel	NA	P-0010645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	91	459	0	ENST00000269305.4:c.856_861del	p.Glu286_Glu287del	p.E286_E287del	ENST00000269305	NM_001126112.2	286	GAAGAG/-	8/11	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.2	2		459	829	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180816	106180816	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1460770215	NA	P-0010645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	99	339	0	ENST00000380013.4:c.3844G>T	p.Gly1282Cys	p.G1282C	ENST00000380013	NM_001127208.2	1282	Ggt/Tgt	7/11	0.144857020991277	2	FACETS	0.836	0.748	0.93	0.836	0.748	0.93	CLONAL	2	TRUE	0	0.2	2		339	592	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710641	117710641	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	64	425	0	ENST00000368508.3:c.1631A>T	p.Asn544Ile	p.N544I	ENST00000368508	NM_002944.2	544	aAc/aTc	12/43	0.19937173647673	1	FACETS	0.829	0.717	0.95	0.829	0.717	0.95	CLONAL	1	TRUE	0	0.2	1		425	695	SUCCESS
AR	367	MSKCC	GRCh37	X	66765348	66765348	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	82	286	0	ENST00000374690.3:c.360G>T	p.Gln120His	p.Q120H	ENST00000374690	NM_000044.3	120	caG/caT	1/8	1	1	FACETS	0.831	0.736	0.932	1	0.981	1	CLONAL	2	TRUE	0	0.2	1		286	444	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470011	25470011	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs749817324	NA	P-0010709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	169	409	1	ENST00000264709.3:c.1031T>C	p.Leu344Pro	p.L344P	ENST00000264709	NM_175629.2	344	cTg/cCg	9/23	0.630999096679889	3	FACETS	0.918	0.845	0.993	0.459	0.422	0.497	CLONAL	1	TRUE	1	0.630999096679889	3		410	768	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177878	56177878	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	1441	449	2	ENST00000399503.3:c.2851C>T	p.Gln951Ter	p.Q951*	ENST00000399503	NM_005921.1	951	Caa/Taa	14/20	0.630999096679889	7	FACETS	0.99	0.977	1	0.99	0.977	1	CLONAL	7	TRUE	0	0.630999096679889	7		451	1699	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677805	47677805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759358719	NA	P-0010709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1337	204	521	0	ENST00000347630.2:c.1060C>T	p.Arg354Cys	p.R354C	ENST00000347630	NM_001007230.1	354	Cgc/Tgc	11/11	0.630999096679889	5	FACETS	0.817	0.755	0.881	0.272	0.251	0.294	CLONAL	1	TRUE	2	0.630999096679889	5		521	1541	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0010712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	57	401	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.258	0.221	0.299	0.258	0.221	0.299	SUBCLONAL	1	TRUE	1	0.545545856888062	2		401	809	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0010712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	244	396	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.545545856888062	2		396	698	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	843	409	2	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	0.493688324435156	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	0	0.545545856888062	3		411	1287	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0010712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	160	405	0	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	0.545545856888062	3	FACETS	0.602	0.551	0.656	0.301	0.275	0.328	SUBCLONAL	1	TRUE	1	0.545545856888062	3		405	1240	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99204054	99204054	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs76257041	NA	P-0010712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	34	350	0	ENST00000074304.5:c.2917G>A	p.Gly973Arg	p.G973R	ENST00000074304	NM_001134224.1	973	Gga/Aga	26/26	0.545545856888062	2	FACETS	0.199	0.162	0.242	0.1	0.081	0.121	SUBCLONAL	1	TRUE	0	0.545545856888062	2		350	625	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388068	81388068	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	70	429	0	ENST00000222390.5:c.307A>T	p.Ser103Cys	p.S103C	ENST00000222390	NM_000601.4	103	Agc/Tgc	3/18	0.545545856888062	2	FACETS	0.498	0.435	0.566	0.249	0.217	0.283	SUBCLONAL	1	TRUE	0	0.545545856888062	2		429	515	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500854	8500854	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	37	372	0	ENST00000356435.5:c.2028G>T	p.Gln676His	p.Q676H	ENST00000356435		676	caG/caT	13/35	0.47989428280337	2	FACETS	0.211	0.173	0.254	0.106	0.086	0.127	SUBCLONAL	1	TRUE	0	0.545545856888062	2		372	642	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615038	43615038	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	64	365	0	ENST00000355710.3:c.2452G>C	p.Glu818Gln	p.E818Q	ENST00000355710	NM_020975.4	818	Gag/Cag	14/20	1	2	FACETS	0.272	0.235	0.313	0.272	0.235	0.313	SUBCLONAL	1	TRUE	1	0.545545856888062	2		365	863	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105238779	105238779	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	174	302	0	ENST00000349310.3:c.1183G>A	p.Gly395Ser	p.G395S	ENST00000349310	NM_001014432.1	395	Ggc/Agc	13/15	0.468336549961375	2	FACETS	0.637	0.586	0.69	0.318	0.293	0.345	SUBCLONAL	1	TRUE	0	0.545545856888062	2		302	1002	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651308	45651308	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	92	477	0	ENST00000407780.3:c.717A>T	p.Arg239Ser	p.R239S	ENST00000407780	NM_001283052.1	239	agA/agT	5/7	0.545545856888062	2	FACETS	0.355	0.314	0.398	0.177	0.157	0.199	SUBCLONAL	1	TRUE	0	0.545545856888062	2		477	951	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427339	49427339	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398123704	NA	P-0010717-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	94	285	0	ENST00000301067.7:c.11149C>T	p.Gln3717Ter	p.Q3717*	ENST00000301067	NM_003482.3	3717	Cag/Tag	39/54	1	2	FACETS	0.922	0.82	1	0.922	0.82	1	CLONAL	1	TRUE	1	0.256387278019974	2		285	795	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100414	157100414	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1438676618	NA	P-0010718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	11	64	0	ENST00000346085.5:c.1351T>C	p.Ser451Pro	p.S451P	ENST00000346085	NM_020732.3	451	Tcg/Ccg	1/20	0.86368321386432	3	FACETS	0.384	0.268	0.525	0.128	0.089	0.175	SUBCLONAL	1	TRUE	0	0.86368321386432	3		64	95	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101000	27101000	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	240	435	0	ENST00000324856.7:c.4282T>C	p.Tyr1428His	p.Y1428H	ENST00000324856	NM_006015.4	1428	Tac/Cac	18/20	0.86368321386432	4	FACETS	1	0.97	1	0.533	0.498	0.569	CLONAL	1	TRUE	2	0.86368321386432	4		435	972	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923169	39923182	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGAACTGTTTGT	GAGGAACTGTTTGT	-	novel	NA	P-0010718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	228	657	0	ENST00000378444.4:c.3526_3539del	p.Thr1176Ter	p.T1176*	ENST00000378444	NM_001123385.1	1176	ACAAACAGTTCCTCt/t	8/15	0.820713583352447	4	FACETS	0.865	0.805	0.926	0.288	0.268	0.309	CLONAL	1	TRUE	1	0.86368321386432	4		657	1138	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578481	7578481	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	434	443	0	ENST00000269305.4:c.449del	p.Thr150AsnfsTer20	p.T150Nfs*20	ENST00000269305	NM_001126112.2	150	aCa/aa	5/11	NA	2	FACETS	0.97	0.947	0.992			1	INDETERMINATE	2	TRUE	NA	0.86368321386432	2		443	518	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0010720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	140	239	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.996	0.915	1	0.996	0.915	1	CLONAL	1	TRUE	1	0.644623360147651	2		239	436	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096493	178096493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	321	391	0	ENST00000397062.3:c.838G>T	p.Asp280Tyr	p.D280Y	ENST00000397062	NM_006164.4	280	Gat/Tat	5/5	1	2	FACETS	0.923	0.872	0.975	0.923	0.872	0.975	CLONAL	1	TRUE	1	0.644623360147651	2		391	1079	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717715	89717715	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1057519368	NA	P-0010720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	244	262	1	ENST00000371953.3:c.740T>A	p.Leu247Ter	p.L247*	ENST00000371953	NM_000314.4	247	tTa/tAa	7/9	0.644623360147651	1	FACETS	0.924	0.872	0.977	0.924	0.872	0.977	CLONAL	1	TRUE	0	0.644623360147651	1		263	555	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129487	152129487	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	35	94	0	ENST00000206249.3:c.440C>A	p.Pro147Gln	p.P147Q	ENST00000206249	NM_000125.3	147	cCg/cAg	1/8	0.412192981807132	2	FACETS	1	0.834	1	0.502	0.417	0.596	CLONAL	1	TRUE	0	0.412192981807132	2		94	169	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32971075	32971075	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	118	403	0	ENST00000380152.3:c.9542T>C	p.Met3181Thr	p.M3181T	ENST00000380152		3181	aTg/aCg	26/27	NA	2	FACETS	0.873	0.789	0.961			1	INDETERMINATE	1	TRUE	NA	0.412192981807132	2		403	656	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152104	11152104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377573682	NA	P-0010728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	261	405	0	ENST00000358026.2:c.4388G>A	p.Arg1463His	p.R1463H	ENST00000358026	NM_001128849.1	1463	cGc/cAc	31/36	0.324278707916122	3	FACETS	0.955	0.898	1	0.955	0.898	1	CLONAL	2	TRUE	1	0.412192981807132	3		405	800	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156686	20156686	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	153	672	0	ENST00000379607.5:c.71G>C	p.Arg24Thr	p.R24T	ENST00000379607	NM_001412.3	24	aGa/aCa	2/7	NA	2	FACETS	0.693	0.633	0.756			1	INDETERMINATE	1	TRUE	NA	0.412192981807132	2		672	1071	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913396	NA	P-0010746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	335	511	0	ENST00000349496.5:c.95A>C	p.Asp32Ala	p.D32A	ENST00000349496	NM_001904.3	32	gAc/gCc	3/15	1	2	FACETS	0.967	0.914	1	0.967	0.914	1	CLONAL	1	TRUE	1	0.521503442770451	2		511	1328	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916933	+	missense_variant	Missense_Mutation	ONP	GCAA	GCAA	TCAG	novel	NA	P-0010746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1350	459	798	0	ENST00000263967.3:c.317_320delinsTCAG	p.Gly106_Asn107delinsValSer	p.G106_N107delinsVS	ENST00000263967	NM_006218.2	106	gGCAAc/gTCAGc	2/21	1	2	FACETS	0.973	0.927	1	0.973	0.927	1	CLONAL	1	TRUE	1	0.521503442770451	2		798	1809	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0010750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1152	412	467	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.307099737551596	7	FACETS	1	0.959	1			1	CLONAL	3	TRUE	NA	0.307099737551596	7		467	1564	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0010750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	475	558	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.307099737551596	7	FACETS	1	0.983	1			1	CLONAL	4	TRUE	NA	0.307099737551596	7		558	1297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579536	7579536	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567556930	NA	P-0010750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	203	554	1	ENST00000269305.4:c.151G>T	p.Glu51Ter	p.E51*	ENST00000269305	NM_001126112.2	51	Gaa/Taa	4/11	0.234940609134521	2	FACETS	0.835	0.776	0.896	0.835	0.776	0.896	CLONAL	2	TRUE	0	0.307099737551596	2		555	792	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591889	48591889	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1060500741	NA	P-0010750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	227	790	0	ENST00000342988.3:c.1052A>T	p.Asp351Val	p.D351V	ENST00000342988	NM_005359.5	351	gAt/gTt	9/12	0.234940609134521	2	FACETS	1	0.991	1	0.704	0.656	0.754	CLONAL	1	TRUE	0	0.307099737551596	2		790	1050	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254668	46254668	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	228	607	0	ENST00000334344.6:c.4858C>T	p.Gln1620Ter	p.Q1620*	ENST00000334344	NM_152641.2	1620	Cag/Tag	16/21	0.234940609134521	2	FACETS	1	0.991	1	0.713	0.664	0.763	CLONAL	1	TRUE	0	0.307099737551596	2		607	1042	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440360	52440360	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	171	399	0	ENST00000460680.1:c.692T>A	p.Met231Lys	p.M231K	ENST00000460680	NM_004656.3	231	aTg/aAg	9/17	0.234940609134521	2	FACETS	0.821	0.758	0.887	0.821	0.758	0.887	CLONAL	2	TRUE	0	0.307099737551596	2		399	678	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562266	95562266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs988095775	NA	P-0010750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	114	639	2	ENST00000393063.1:c.4991C>T	p.Ser1664Leu	p.S1664L	ENST00000393063	NM_030621.3	1664	tCg/tTg	24/28	0.288698189907356	4	FACETS	0.854	0.766	0.946	0.285	0.255	0.316	CLONAL	1	TRUE	1	0.307099737551596	4		641	1137	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220149	5220149	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	111	307	0	ENST00000357368.4:c.3566C>T	p.Ser1189Leu	p.S1189L	ENST00000357368	NM_002850.3	1189	tCa/tTa	22/38	0.228729197991054	2	FACETS	1	0.983	1	0.73	0.66	0.804	CLONAL	1	TRUE	0	0.307099737551596	2		307	495	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936983	48936983	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690863	NA	P-0010755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	500	406	1	ENST00000267163.4:c.751C>T	p.Arg251Ter	p.R251*	ENST00000267163	NM_000321.2	251	Cga/Tga	8/27	0.614455523710057	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.622107624735318	2		407	800	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279922	18279922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1254390009	NA	P-0010755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	865	400	3	ENST00000222254.8:c.2005G>A	p.Val669Ile	p.V669I	ENST00000222254	NM_005027.3	669	Gtc/Atc	16/16	0.622107624735318	5	FACETS	1	0.995	1	1	0.995	1	CLONAL	4	TRUE	1	0.622107624735318	5		403	1270	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs11575997	NA	P-0010793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	311	404	1	ENST00000269305.4:c.993+1G>T		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.690085929555058	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.690085929555058	1		405	590	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0010793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	874	641	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.690085929555058	6	FACETS	1	0.996	1			1	CLONAL	3	TRUE	NA	0.690085929555058	6		641	1729	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0010793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1624	287	467	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.690085929555058	6	FACETS	1	0.961	1			1	CLONAL	1	TRUE	NA	0.690085929555058	6		467	1911	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033905	49033905	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	392	462	1	ENST00000267163.4:c.2042G>A	p.Trp681Ter	p.W681*	ENST00000267163	NM_000321.2	681	tGg/tAg	20/27	0.690085929555058	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.690085929555058	1		463	686	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104681	209104681	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	118	461	0	ENST00000345146.2:c.897T>A	p.Asp299Glu	p.D299E	ENST00000345146	NM_005896.2	299	gaT/gaA	8/10	0.606026688301781	3	FACETS	0.527	0.475	0.582	0.176	0.158	0.194	SUBCLONAL	1	TRUE	0	0.690085929555058	3		461	873	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936526	49936526	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	537	812	1	ENST00000296474.3:c.1401G>T	p.Met467Ile	p.M467I	ENST00000296474	NM_002447.2	467	atG/atT	2/20	0.690085929555058	1	FACETS	0.965	0.93	1	0.965	0.93	1	CLONAL	1	TRUE	0	0.690085929555058	1		813	1056	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463286	25463286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139293773	NA	P-0010797-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	344	341	2	ENST00000264709.3:c.2207G>A	p.Arg736His	p.R736H	ENST00000264709	NM_175629.2	736	cGc/cAc	19/23	0.644141959364311	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.644141959364311	1		343	708	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17355157	17355157	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194401420	NA	P-0010797-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	502	652	0	ENST00000375499.3:c.361C>T	p.Leu121Phe	p.L121F	ENST00000375499	NM_003000.2	121	Ctc/Ttc	4/8	0.644141959364311	1	FACETS	0.992	0.954	1	0.992	0.954	1	CLONAL	1	TRUE	0	0.644141959364311	1		652	1065	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449784	8449784	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1240958736	NA	P-0010797-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	405	606	0	ENST00000356435.5:c.3929T>C	p.Ile1310Thr	p.I1310T	ENST00000356435		1310	aTc/aCc	23/35	0.644141959364311	1	FACETS	0.878	0.838	0.918	0.878	0.838	0.918	CLONAL	1	TRUE	0	0.644141959364311	1		606	971	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578528	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0010797-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	442	492	0	ENST00000269305.4:c.402_403del	p.Phe134LeufsTer14	p.F134Lfs*14	ENST00000269305	NM_001126112.2	134	ttTTgc/ttgc	5/11	0.644141959364311	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.644141959364311	1		492	877	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336166	73336166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs566599772	NA	P-0010799-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	380	481	1	ENST00000377767.4:c.2237G>A	p.Arg746His	p.R746H	ENST00000377767	NM_014953.3	746	cGc/cAc	17/21	1	2	FACETS	0.944	0.897	0.991	0.944	0.897	0.991	CLONAL	1	TRUE	1	0.730878694561216	2		482	1102	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0010801-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	81	641	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.942	0.829	1	0.942	0.829	1	CLONAL	1	TRUE	1	0.21	2		641	819	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757274881	NA	P-0010801-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	78	465	1	ENST00000269305.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	144	Cag/Tag	5/11	1	2	FACETS	0.891	0.781	1	0.891	0.781	1	CLONAL	1	TRUE	1	0.21	2		466	834	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509106	106509106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010801-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	79	522	0	ENST00000359195.3:c.1100G>A	p.Gly367Asp	p.G367D	ENST00000359195	NM_002649.2	367	gGc/gAc	2/11	1	2	FACETS	0.789	0.692	0.893	0.789	0.692	0.893	SUBCLONAL	1	TRUE	1	0.21	2		522	954	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412898	49412898	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519954	NA	P-0010810-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	121	728	0	ENST00000418115.1:c.125A>C	p.Tyr42Ser	p.Y42S	ENST00000418115	NM_001664.2	42	tAt/tCt	2/5	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.19	2		728	1234	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348526	70348526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010810-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	80	338	0	ENST00000374080.3:c.3433G>A	p.Asp1145Asn	p.D1145N	ENST00000374080		1145	Gat/Aat	24/45	0.3	2	FACETS	1	0.961	1	0.614	0.54	0.693	CLONAL	1	TRUE	0	0.19	2		338	686	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0010827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	410	561	2	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.353217429046617	2		563	1073	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728676	190728678	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs777263508	NA	P-0010827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	96	551	0	ENST00000441310.2:c.2067_2069del	p.Arg690del	p.R690del	ENST00000441310	NM_000534.4	688	aaAAGa/aaa	10/13	0.118609056047502	5	FACETS	0.866	0.77	0.969	0.217	0.192	0.243	INDETERMINATE	1	TRUE	1	0.353217429046617	5		551	960	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729601	41729601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1243	335	843	0	ENST00000242208.4:c.928C>T	p.Arg310Trp	p.R310W	ENST00000242208	NM_002192.2	310	Cgg/Tgg	3/3	0.304639065324198	3	FACETS	1	0.994	1	0.471	0.444	0.499	CLONAL	1	TRUE	0	0.353217429046617	3		843	1578	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260837	16260837	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	112	399	0	ENST00000375759.3:c.8102C>T	p.Thr2701Met	p.T2701M	ENST00000375759	NM_015001.2	2701	aCg/aTg	11/15	1	2	FACETS	0.912	0.822	1	0.912	0.822	1	CLONAL	1	TRUE	1	0.353217429046617	2		399	695	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276958	123276958	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	118	387	2	ENST00000358487.5:c.959C>T	p.Thr320Met	p.T320M	ENST00000358487	NM_000141.4	320	aCg/aTg	8/18	0.347744298898271	2	FACETS	0.991	0.896	1	0.496	0.448	0.546	CLONAL	1	TRUE	0	0.353217429046617	2		389	674	SUCCESS
AR	367	MSKCC	GRCh37	X	66943546	66943546	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	32	368	0	ENST00000374690.3:c.2626C>A	p.Gln876Lys	p.Q876K	ENST00000374690	NM_000044.3	876	Cag/Aag	8/8	1	1	FACETS	0.267	0.216	0.325	0.267	0.216	0.325	SUBCLONAL	1	TRUE	0	0.353217429046617	1		368	558	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057651	27057651	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	206	757	0	ENST00000324856.7:c.1360del	p.Tyr454MetfsTer165	p.Y454Mfs*165	ENST00000324856	NM_006015.4	453	ccT/cc	3/20	1	2	FACETS	0.978	0.906	1	0.978	0.906	1	CLONAL	1	TRUE	1	0.353217429046617	2		757	1193	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428434	47428437	+	splice_donor_variant,intron_variant	Splice_Site	DEL	TATC	TATC	-	novel	NA	P-0010827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	37	398	0	ENST00000377045.4:c.1300+7_1300+10del		p.X434_splice	ENST00000377045	NM_001654.4	434			1	1	FACETS	0.255	0.209	0.306	0.255	0.209	0.306	SUBCLONAL	1	TRUE	0	0.353217429046617	1		398	677	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111886081	111886081	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199803113	NA	P-0010830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	375	1213	0	ENST00000341259.2:c.1703T>C	p.Ile568Thr	p.I568T	ENST00000341259	NM_005475.2	568	aTa/aCa	8/8	1	2	FACETS	0.943	0.898	0.989	0.943	0.898	0.989	CLONAL	1	TRUE	1	0.799280461602704	2		1213	995	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900489	3900489	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	302	851	0	ENST00000262367.5:c.607C>T	p.Gln203Ter	p.Q203*	ENST00000262367	NM_004380.2	203	Caa/Taa	2/31	0.799280461602704	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.799280461602704	1		851	446	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845366	76845366	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	177	708	0	ENST00000373344.5:c.6155A>T	p.Asp2052Val	p.D2052V	ENST00000373344	NM_000489.3	2052	gAt/gTt	27/35	0.799280461602704	1	FACETS	0.967	0.915	1	0.967	0.915	1	CLONAL	1	TRUE	0	0.799280461602704	1		708	275	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575106	64575107	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0010830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	276	528	0	ENST00000312049.6:c.700_701del	p.Met234GlyfsTer14	p.M234Gfs*14	ENST00000312049	NM_130799.2	234	ATg/g	4/10	0.799280461602704	1	FACETS	0.997	0.955	1	0.997	0.955	1	CLONAL	1	TRUE	0	0.799280461602704	1		528	416	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0010834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	18	191	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	0.186	0.14	0.24	0.186	0.14	0.24	SUBCLONAL	1	TRUE	1	0.952781038947465	2		191	203	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0010835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	106	436	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.587357391366883	4	FACETS	0.521	0.466	0.58	0.174	0.155	0.194	SUBCLONAL	1	TRUE	1	0.587357391366883	4		436	1100	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0010835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	217	604	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.611	0.567	0.656	0.611	0.567	0.656	SUBCLONAL	1	TRUE	1	0.587357391366883	2		604	1210	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0010835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	86	656	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	1	2	FACETS	0.242	0.213	0.273	0.242	0.213	0.273	SUBCLONAL	1	TRUE	1	0.587357391366883	2		656	1210	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451077	70451077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	118	481	0	ENST00000373644.4:c.5917G>A	p.Glu1973Lys	p.E1973K	ENST00000373644	NM_030625.2	1973	Gaa/Aaa	12/12	1	2	FACETS	0.524	0.473	0.578	0.524	0.473	0.578	SUBCLONAL	1	TRUE	1	0.587357391366883	2		481	767	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166212	118166212	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	58	459	0	ENST00000369448.3:c.722G>T	p.Gly241Val	p.G241V	ENST00000369448	NM_017709.3	241	gGc/gTc	2/2	0.103921534795943	6	FACETS	0.462	0.395	0.535	0.154	0.131	0.179	INDETERMINATE	1	TRUE	3	0.587357391366883	6		459	930	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858899	89858899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	159	445	0	ENST00000389301.3:c.1063C>T	p.Leu355Phe	p.L355F	ENST00000389301	NM_000135.2	355	Ctc/Ttc	12/43	0.153155877343799	6	FACETS	1	0.936	1			1	INDETERMINATE	1	TRUE	NA	0.587357391366883	6		445	1146	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0010836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	39	641	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		641	932	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0010850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	217	320	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		320	561	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0010854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	99	567	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	1	2	FACETS	0.9	0.801	1	0.9	0.801	1	CLONAL	1	FALSE	1	0.203051707737639	2		567	1084	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0010854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	69	681	0	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	1	2	FACETS	0.777	0.675	0.887	0.777	0.675	0.887	SUBCLONAL	1	FALSE	1	0.203051707737639	2		681	875	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380264	25380264	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	115	578	0	ENST00000311936.3:c.194G>A	p.Ser65Asn	p.S65N	ENST00000311936	NM_004985.3	65	aGt/aAt	3/5	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	FALSE	1	0.203051707737639	2		578	1122	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245846	41245846	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	52	535	0	ENST00000357654.3:c.1702C>A	p.Pro568Thr	p.P568T	ENST00000357654	NM_007294.3	568	Cct/Act	10/23	0.189027722032699	0	FACETS	0.525	0.446	0.613			1	SUBCLONAL	1	FALSE	0	0.203051707737639	0		535	777	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	22	589	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.789	0.611	0.994	0.789	0.611	0.994	CLONAL	1	TRUE	1	0.18	2		590	310	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741822	162741822	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs115169993	NA	P-0010911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	44	142	0	ENST00000367921.3:c.1513G>A	p.Gly505Ser	p.G505S	ENST00000367921	NM_006182.2	505	Ggt/Agt	13/18	1	2	FACETS	0.804	0.673	0.949	0.804	0.673	0.949	CLONAL	1	TRUE	1	0.18	2		142	608	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388006	31388006	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908943	NA	P-0010911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	73	363	0	ENST00000328111.2:c.1807G>A	p.Ala603Thr	p.A603T	ENST00000328111	NM_006892.3	603	Gct/Act	17/23	1	2	FACETS	0.791	0.69	0.901	0.791	0.69	0.901	CLONAL	1	TRUE	1	0.18	2		363	1025	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711875	89711875	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587782603	NA	P-0010911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	36	198	0	ENST00000371953.3:c.493G>A	p.Gly165Arg	p.G165R	ENST00000371953	NM_000314.4	165	Gga/Aga	6/9	0.144014295986778	1	FACETS	0.897	0.738	1	0.897	0.738	1	CLONAL	1	TRUE	0	0.18	1		198	406	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813023	89813023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142833057	NA	P-0010911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	67	311	0	ENST00000389301.3:c.3482C>T	p.Thr1161Met	p.T1161M	ENST00000389301	NM_000135.2	1161	aCg/aTg	35/43	1	2	FACETS	0.833	0.722	0.953	0.833	0.722	0.953	CLONAL	1	TRUE	1	0.18	2		311	894	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491645	56491645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	408	614	3	ENST00000267101.3:c.2537G>T	p.Ser846Ile	p.S846I	ENST00000267101	NM_001982.3	846	aGt/aTt	21/28	0.211003504059727	4	FACETS	0.986	0.942	1	1	0.996	1	CLONAL	5	FALSE	1	0.211003504059727	4		617	950	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622607	158622607	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	562	993	0	ENST00000263640.3:c.892A>T	p.Thr298Ser	p.T298S	ENST00000263640	NM_001105.4	298	Act/Tct	8/11	0.211003504059727	4	FACETS	0.97	0.933	1	1	0.997	1	CLONAL	5	FALSE	1	0.211003504059727	4		993	1330	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627361	14627361	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1213	162	1063	1	ENST00000254322.2:c.709T>A	p.Phe237Ile	p.F237I	ENST00000254322	NM_006145.1	237	Ttt/Att	2/3	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.211003504059727	2		1064	1375	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76954069	76954069	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	363	976	1	ENST00000373344.5:c.182A>T	p.Lys61Met	p.K61M	ENST00000373344	NM_000489.3	61	aAg/aTg	3/35	0.1637230307199	1	FACETS	0.893	0.847	0.939	1	0.997	1	CLONAL	3	FALSE	0	0.211003504059727	1		977	1149	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0010940-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	292	377	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.486964110757625	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.486964110757625	1		377	871	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207058	1207069	+	inframe_deletion	In_Frame_Del	DEL	ACCTGATGGGGG	ACCTGATGGGGG	-	rs1131690916	NA	P-0010940-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	228	406	1	ENST00000326873.7:c.151_162del	p.Met51_Leu54del	p.M51_L54del	ENST00000326873	NM_000455.4	49	tACCTGATGGGGGac/tac	1/10	0.486964110757625	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.486964110757625	1		407	698	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383759	15383759	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs750187537	NA	P-0010940-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1900	263	532	0	ENST00000263377.2:c.152C>G	p.Ser51Cys	p.S51C	ENST00000263377	NM_058243.2	51	tCc/tGc	2/20	0.486964110757625	3	FACETS	0.621	0.579	0.665			1	SUBCLONAL	1	TRUE	NA	0.486964110757625	3		532	2163	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0010965-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	392	354	1	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.588478111076101	3	FACETS	0.943	0.901	0.986	0.943	0.901	0.986	CLONAL	2	TRUE	1	0.588478111076101	3		355	914	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554660	63554660	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010965-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	164	291	0	ENST00000307078.5:c.79C>G	p.Pro27Ala	p.P27A	ENST00000307078	NM_004655.3	27	Cca/Gca	2/11	1	2	FACETS	0.985	0.909	1	0.985	0.909	1	CLONAL	1	TRUE	1	0.588478111076101	2		291	566	SUCCESS
APC	324	MSKCC	GRCh37	5	112173835	112173838	+	frameshift_variant	Frame_Shift_Del	DEL	AGAT	AGAT	-	rs398123118	NA	P-0010965-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	194	310	0	ENST00000257430.4:c.2547_2550del	p.Asp849GlufsTer11	p.D849Efs*11	ENST00000257430	NM_000038.5	848	aaAGAT/aa	16/16	1	2	FACETS	0.951	0.884	1	0.951	0.884	1	CLONAL	1	TRUE	1	0.588478111076101	2		310	693	SUCCESS
APC	324	MSKCC	GRCh37	5	112175770	112175770	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010965-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	147	252	0	ENST00000257430.4:c.4480del	p.Glu1494LysfsTer13	p.E1494Kfs*13	ENST00000257430	NM_000038.5	1493	acG/ac	16/16	1	2	FACETS	0.79	0.724	0.86	0.79	0.724	0.86	SUBCLONAL	1	TRUE	1	0.588478111076101	2		252	632	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	260	555	0	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	0.477237102633356	3	FACETS	0.989	0.925	1	0.494	0.462	0.527	CLONAL	1	TRUE	1	0.545706353493599	3		555	1227	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0010968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	610	439	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.509105926601494	3	FACETS	0.921	0.892	0.949	0.921	0.892	0.949	CLONAL	3	TRUE	0	0.545706353493599	3		439	1030	SUCCESS
APC	324	MSKCC	GRCh37	5	112170652	112170652	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	129	339	1	ENST00000257430.4:c.1748C>A	p.Ser583Ter	p.S583*	ENST00000257430	NM_000038.5	583	tCa/tAa	15/16	NA	2	FACETS	0.914	0.834	0.999			1	INDETERMINATE	1	TRUE	NA	0.545706353493599	2		340	517	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845125	128845125	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	234	537	0	ENST00000249373.3:c.619T>G	p.Tyr207Asp	p.Y207D	ENST00000249373	NM_005631.4	207	Tac/Gac	3/12	0.526136567227562	3	FACETS	0.966	0.9	1	0.483	0.45	0.517	CLONAL	1	TRUE	1	0.545706353493599	3		537	1130	SUCCESS
APC	324	MSKCC	GRCh37	5	112175749	112175753	+	frameshift_variant	Frame_Shift_Del	DEL	TACTT	TACTT	-	novel	NA	P-0010968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	114	281	0	ENST00000257430.4:c.4460_4464del	p.Thr1487IlefsTer25	p.T1487Ifs*25	ENST00000257430	NM_000038.5	1486	gaTACTTta/gata	16/16	NA	2	FACETS	0.756	0.683	0.832			1	INDETERMINATE	1	TRUE	NA	0.545706353493599	2		281	553	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	242	589	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.8	2		590	590	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461101	120461101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs312262796	NA	P-0010999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	436	418	0	ENST00000256646.2:c.5857C>T	p.Arg1953Cys	p.R1953C	ENST00000256646	NM_024408.3	1953	Cgc/Tgc	32/34	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.8	2		418	1067	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797488	45797488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	473	419	0	ENST00000450313.1:c.1031C>T	p.Pro344Leu	p.P344L	ENST00000450313	NM_012222.2	344	cCt/cTt	12/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.8	2		419	1128	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463536	25463536	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1418039680	NA	P-0010999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	494	557	1	ENST00000264709.3:c.2146G>A	p.Val716Ile	p.V716I	ENST00000264709	NM_175629.2	716	Gtc/Atc	18/23	1	2	FACETS	0.99	0.949	1	0.99	0.949	1	CLONAL	1	TRUE	1	0.8	2		558	1248	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993597	72993597	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs759375904	NA	P-0010999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	598	661	0	ENST00000268489.5:c.448C>A	p.Leu150Met	p.L150M	ENST00000268489	NM_006885.3	150	Ctg/Atg	2/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.8	2		661	1488	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120469206	120469222	+	frameshift_variant	Frame_Shift_Del	DEL	CACATCGACGAAGGTTT	CACATCGACGAAGGTTT	-	novel	NA	P-0010999-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	352	427	0	ENST00000256646.2:c.3905_3921del	p.Glu1302ValfsTer17	p.E1302Vfs*17	ENST00000256646	NM_024408.3	1302	gAAACCTTCGTCGATGTG/g	24/34	1	2	FACETS	0.844	0.8	0.888	0.844	0.8	0.888	CLONAL	1	TRUE	1	0.8	2		427	1043	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0011028-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	455	357	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.821498999040526	1	FACETS	0.95	0.92	0.98	0.95	0.92	0.98	CLONAL	1	TRUE	0	0.839473073135037	1		357	662	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436651	52436651	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1250373530	NA	P-0011028-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	489	425	0	ENST00000460680.1:c.2023A>T	p.Ile675Phe	p.I675F	ENST00000460680	NM_004656.3	675	Atc/Ttc	16/17	1	2	FACETS	0.949	0.91	0.989	0.949	0.91	0.989	CLONAL	1	TRUE	1	0.839473073135037	2		425	1227	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937370	76937373	+	frameshift_variant	Frame_Shift_Del	DEL	ATCA	ATCA	-	novel	NA	P-0011028-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	133	421	0	ENST00000373344.5:c.3375_3378del	p.Asp1126ArgfsTer3	p.D1126Rfs*3	ENST00000373344	NM_000489.3	1125	tcTGAT/tc	9/35	0.489117239957423	1	FACETS	0.442	0.405	0.48	0.442	0.405	0.48	INDETERMINATE	1	TRUE	0	0.839473073135037	1		421	416	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0011061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	246	534	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	0.339422279136642	2		534	1333	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842408	68842408	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	227	652	0	ENST00000261769.5:c.469G>T	p.Val157Phe	p.V157F	ENST00000261769	NM_004360.3	157	Gtt/Ttt	4/16	0.339422279136642	1	FACETS	0.975	0.908	1	0.975	0.908	1	CLONAL	1	TRUE	0	0.339422279136642	1		652	1139	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954189	48954189	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	120	370	0	ENST00000267163.4:c.1390G>T	p.Glu464Ter	p.E464*	ENST00000267163	NM_000321.2	464	Gaa/Taa	15/27	0.321210674468702	1	FACETS	0.846	0.765	0.931	0.846	0.765	0.931	CLONAL	1	TRUE	0	0.339422279136642	1		370	694	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063312	67063312	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0011061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	50	192	0	ENST00000412916.2:c.2T>C	p.Met1?	p.M1?	ENST00000412916		1	aTg/aCg	1/6	0.339422279136642	1	FACETS	0.651	0.554	0.756	0.651	0.554	0.756	SUBCLONAL	1	TRUE	0	0.339422279136642	1		192	376	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880180	37880180	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	192	559	0	ENST00000269571.5:c.2224G>C	p.Asp742His	p.D742H	ENST00000269571		742	Gat/Cat	19/27	1	2	FACETS	0.967	0.893	1	0.967	0.893	1	CLONAL	1	TRUE	1	0.339422279136642	2		559	1170	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884139	37884139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753337412	NA	P-0011061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	264	680	0	ENST00000269571.5:c.3610G>A	p.Ala1204Thr	p.A1204T	ENST00000269571		1204	Gcc/Acc	27/27	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.339422279136642	2		680	1457	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352244	70352244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1335	167	673	0	ENST00000374080.3:c.4271G>A	p.Gly1424Asp	p.G1424D	ENST00000374080		1424	gGt/gAt	31/45	0.161538265812017	2	FACETS	0.655	0.6	0.713	0.328	0.3	0.357	INDETERMINATE	1	TRUE	0	0.339422279136642	2		673	1502	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0011066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	55	420	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.844	0.72	0.98	0.844	0.72	0.98	CLONAL	1	TRUE	1	0.166277047292028	2		420	784	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs863224683	NA	P-0011066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	69	406	0	ENST00000269305.4:c.388C>G	p.Leu130Val	p.L130V	ENST00000269305	NM_001126112.2	130	Ctc/Gtc	5/11	0.159920798123619	1	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	0	0.166277047292028	1		406	758	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242725	66242725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768535351	NA	P-0011066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	86	419	0	ENST00000273854.3:c.1847G>A	p.Ser616Asn	p.S616N	ENST00000273854	NM_004439.5	616	aGc/aAc	9/18	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.166277047292028	2		419	843	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340214	116340214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201274041	NA	P-0011066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	90	370	0	ENST00000397752.3:c.1076G>A	p.Arg359Gln	p.R359Q	ENST00000397752	NM_000245.2	359	cGa/cAa	2/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.166277047292028	2		370	805	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259981	16259981	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	153	510	0	ENST00000375759.3:c.7246A>T	p.Ser2416Cys	p.S2416C	ENST00000375759	NM_015001.2	2416	Agt/Tgt	11/15	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		510	920	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230774	53230774	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1296	238	959	0	ENST00000375401.3:c.2019G>A	p.Met673Ile	p.M673I	ENST00000375401	NM_004187.3	673	atG/atA	14/26	0.124639177846774	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		959	1534	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0011096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	754	293	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	0.397687647707904	1	FACETS	0.75	0.726	0.773	0.75	0.726	0.773	INDETERMINATE	1	TRUE	0	0.792118377920876	1		293	1534	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0011096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	749	303	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.739597560076337	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.792118377920876	1		303	1060	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519886	NA	P-0011096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	294	247	0	ENST00000349496.5:c.97T>G	p.Ser33Ala	p.S33A	ENST00000349496	NM_001904.3	33	Tct/Gct	3/15	NA	2	FACETS	0.528	0.496	0.561			1	INDETERMINATE	1	TRUE	NA	0.792118377920876	2		247	1406	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830136	72830136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1307	412	347	1	ENST00000268489.5:c.6445C>T	p.Arg2149Cys	p.R2149C	ENST00000268489	NM_006885.3	2149	Cgc/Tgc	9/10	0.397687647707904	1	FACETS	0.365	0.347	0.385	0.365	0.347	0.385	INDETERMINATE	1	TRUE	0	0.792118377920876	1		348	1719	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0011103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	441	500	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.389409448142494	3	FACETS	0.928	0.892	0.964			1	INDETERMINATE	2	TRUE	NA	0.822751415058939	3		500	815	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0011103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	403	377	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.814217876645164	1	FACETS	0.92	0.887	0.952	0.92	0.887	0.952	CLONAL	1	TRUE	0	0.822751415058939	1		377	627	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200629	67200629	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1034596803	NA	P-0011103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	345	480	0	ENST00000312629.5:c.740A>G	p.Asn247Ser	p.N247S	ENST00000312629	NM_003952.2	247	aAc/aGc	9/15	1	2	FACETS	0.859	0.815	0.904	0.859	0.815	0.904	CLONAL	1	TRUE	1	0.822751415058939	2		480	976	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0011104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	194	285	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	0.371707223957241	3	FACETS	0.945	0.878	1	0.945	0.878	1	CLONAL	2	TRUE	1	0.371707223957241	3		285	655	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0011104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	83	319	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.742	0.655	0.834	0.742	0.655	0.834	SUBCLONAL	1	TRUE	1	0.371707223957241	2		319	602	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088788	27088788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	161	420	0	ENST00000324856.7:c.2402del	p.Gly801ValfsTer32	p.G801Vfs*32	ENST00000324856	NM_006015.4	799	caG/ca	7/20	0.367679061985503	1	FACETS	0.917	0.843	0.995	0.917	0.843	0.995	CLONAL	1	TRUE	0	0.371707223957241	1		420	769	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163910	47163910	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs539008365	NA	P-0011104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	116	405	0	ENST00000409792.3:c.2216A>G	p.His739Arg	p.H739R	ENST00000409792	NM_014159.6	739	cAt/cGt	3/21	0.371707223957241	1	FACETS	0.991	0.897	1	0.991	0.897	1	CLONAL	1	TRUE	0	0.371707223957241	1		405	513	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584493	52584493	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	68	468	0	ENST00000394830.3:c.4520T>A	p.Ile1507Asn	p.I1507N	ENST00000394830	NM_018313.4	1507	aTt/aAt	29/30	0.371707223957241	1	FACETS	0.314	0.272	0.359	0.314	0.272	0.359	SUBCLONAL	1	TRUE	0	0.371707223957241	1		468	950	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109908	115109908	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	56	193	0	ENST00000257566.3:c.1970C>G	p.Thr657Ser	p.T657S	ENST00000257566	NM_016569.3	657	aCc/aGc	8/8	1	2	FACETS	0.817	0.702	0.94	0.817	0.702	0.94	CLONAL	1	TRUE	1	0.371707223957241	2		193	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0011112-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	562	808	2	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	0.774612065146666	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.774612065146666	1		810	757	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286851	33286858	+	frameshift_variant	Frame_Shift_Del	DEL	TGGTCACC	TGGTCACC	A	novel	NA	P-0011112-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	319	343	0	ENST00000374542.5:c.2079_2086delinsT	p.Val694AlafsTer70	p.V694Afs*70	ENST00000374542	NM_001141970.1	693	ctGGTGACCAgc/ctTgc	7/8	0.774612065146666	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.774612065146666	1		343	469	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0011127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	193	291	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.821	0.764	0.879	1	0.992	1	CLONAL	2	TRUE	1	0.398456562238416	2		292	590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574005	7574005	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	398	572	0	ENST00000269305.4:c.1022T>G	p.Phe341Cys	p.F341C	ENST00000269305	NM_001126112.2	341	tTc/tGc	10/11	0.398456562238416	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.398456562238416	1		572	1241	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0011133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	470	558	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.3	4	FACETS	0.993	0.947	1	0.744	0.71	0.779	CLONAL	3	TRUE	0	0.24	4		558	1631	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878062	48878062	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	93	276	1	ENST00000267163.4:c.19del	p.Arg7GlufsTer58	p.R7Efs*58	ENST00000267163	NM_000321.2	5	aCc/ac	1/27	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.24	2		277	715	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0011142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	74	500	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.18	2		500	809	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0011142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	116	482	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	NA	2	FACETS	0.817	0.736	0.902			1	INDETERMINATE	2	TRUE	NA	0.18	2		482	789	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466558	120466558	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1237	233	775	0	ENST00000256646.2:c.4561G>T	p.Gly1521Trp	p.G1521W	ENST00000256646	NM_024408.3	1521	Ggg/Tgg	26/34	0.128094211206419	3	FACETS	0.96	0.893	1	0.96	0.893	1	CLONAL	2	TRUE	1	0.18	3		775	1470	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47607041	47607041	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	137	781	1	ENST00000263735.4:c.791T>C	p.Leu264Pro	p.L264P	ENST00000263735	NM_002354.2	264	cTa/cCa	7/9	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.18	2		782	1274	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390201	89390201	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1167543166	NA	P-0011142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	62	742	0	ENST00000336596.2:c.950C>A	p.Pro317His	p.P317H	ENST00000336596	NM_005233.5	317	cCt/cAt	4/17	1	2	FACETS	0.729	0.628	0.84	0.729	0.628	0.84	SUBCLONAL	1	TRUE	1	0.18	2		742	945	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968212	134968212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	84	839	1	ENST00000398015.3:c.2725G>A	p.Asp909Asn	p.D909N	ENST00000398015	NM_004441.4	909	Gac/Aac	15/16	1	2	FACETS	0.849	0.748	0.959	0.849	0.748	0.959	CLONAL	1	TRUE	1	0.18	2		840	1099	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467679	66467679	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	45	554	0	ENST00000273854.3:c.590C>A	p.Thr197Lys	p.T197K	ENST00000273854	NM_004439.5	197	aCa/aAa	3/18	1	2	FACETS	0.633	0.53	0.747	0.633	0.53	0.747	SUBCLONAL	1	TRUE	1	0.18	2		554	790	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968311	2968311	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	50	690	0	ENST00000396946.4:c.1675A>T	p.Ser559Cys	p.S559C	ENST00000396946	NM_032415.4	559	Agc/Tgc	13/25	0.128094211206419	3	FACETS	0.612	0.518	0.717	0.306	0.259	0.359	SUBCLONAL	1	TRUE	1	0.18	3		690	989	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425634	49425634	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs893293173	NA	P-0011142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	53	638	1	ENST00000301067.7:c.12854G>T	p.Gly4285Val	p.G4285V	ENST00000301067	NM_003482.3	4285	gGc/gTc	39/54	1	2	FACETS	0.731	0.621	0.851	0.731	0.621	0.851	SUBCLONAL	1	TRUE	1	0.18	2		639	806	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220509	133220509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767191767	NA	P-0011142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	55	552	0	ENST00000320574.5:c.4204G>A	p.Val1402Met	p.V1402M	ENST00000320574	NM_006231.2	1402	Gtg/Atg	33/49	1	2	FACETS	0.678	0.578	0.787	0.678	0.578	0.787	SUBCLONAL	1	TRUE	1	0.18	2		552	902	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15378289	15378289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1491	150	1024	0	ENST00000263377.2:c.497C>T	p.Thr166Ile	p.T166I	ENST00000263377	NM_058243.2	166	aCa/aTa	4/20	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.18	2		1024	1641	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022481	31022481	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765459479	NA	P-0011142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	27	278	2	ENST00000375687.4:c.1966G>A	p.Asp656Asn	p.D656N	ENST00000375687	NM_015338.5	656	Gat/Aat	13/13	1	2	FACETS	0.84	0.669	1	0.84	0.669	1	CLONAL	1	TRUE	1	0.18	2		280	357	SUCCESS
AR	367	MSKCC	GRCh37	X	66765427	66765427	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	29	358	0	ENST00000374690.3:c.439C>G	p.Gln147Glu	p.Q147E	ENST00000374690	NM_000044.3	147	Cag/Gag	1/8	1	1	FACETS	0.692	0.555	0.848	0.692	0.555	0.848	SUBCLONAL	1	TRUE	0	0.18	1		358	424	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411605	63411606	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0011142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	97	551	0	ENST00000330258.3:c.1561_1562delinsTT	p.Gly521Leu	p.G521L	ENST00000330258	NM_152424.3	521	GGa/TTa	2/2	1	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.18	1		551	773	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0011143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	536	452	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.245442939586908	4	FACETS	0.891	0.854	0.928	0.891	0.854	0.928	CLONAL	4	TRUE	0	0.245442939586908	4		452	1526	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207166	1207166	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0011143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	162	554	2	ENST00000326873.7:c.254T>A	p.Leu85Ter	p.L85*	ENST00000326873	NM_000455.4	85	tTg/tAg	1/10	0.212459744292498	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.245442939586908	1		556	1046	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743277	162743277	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	144	394	2	ENST00000367921.3:c.1747G>T	p.Glu583Ter	p.E583*	ENST00000367921	NM_006182.2	583	Gag/Tag	14/18	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.245442939586908	2		396	1042	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664856	138664856	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	15	20	0	ENST00000330315.3:c.709G>T	p.Gly237Cys	p.G237C	ENST00000330315	NM_023067.3	237	Ggt/Tgt	1/1	0.204988982274041	2	FACETS	0.955	0.717	1	0.955	0.717	1	CLONAL	2	TRUE	0	0.245442939586908	2		20	64	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334785	81334785	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1253	165	528	0	ENST00000222390.5:c.1931A>T	p.Gln644Leu	p.Q644L	ENST00000222390	NM_000601.4	644	cAg/cTg	17/18	1	2	FACETS	0.948	0.868	1	0.948	0.868	1	CLONAL	1	TRUE	1	0.245442939586908	2		528	1418	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032317	10032317	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	101	312	0	ENST00000330684.3:c.506T>C	p.Val169Ala	p.V169A	ENST00000330684	NM_001134407.1	169	gTc/gCc	3/13	0.245442939586908	1	FACETS	0.953	0.851	1	0.953	0.851	1	CLONAL	1	TRUE	0	0.245442939586908	1		312	758	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951127	17951127	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1250	185	608	1	ENST00000458235.1:c.1166T>A	p.Leu389His	p.L389H	ENST00000458235	NM_000215.3	389	cTc/cAc	9/24	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.245442939586908	2		609	1435	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902181	50902181	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426253750	NA	P-0011143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1593	210	876	1	ENST00000440232.2:c.73G>A	p.Asp25Asn	p.D25N	ENST00000440232	NM_002691.3	25	Gat/Aat	2/27	1	2	FACETS	0.949	0.878	1	0.949	0.878	1	CLONAL	1	TRUE	1	0.245442939586908	2		877	1803	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100952	41100952	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	134	470	0	ENST00000373198.4:c.1404G>T	p.Glu468Asp	p.E468D	ENST00000373198	NM_133170.3	468	gaG/gaT	8/32	1	2	FACETS	0.922	0.836	1	0.922	0.836	1	CLONAL	1	TRUE	1	0.245442939586908	2		470	1184	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067929	30067929	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	157	497	0	ENST00000338641.4:c.1114G>T	p.Glu372Ter	p.E372*	ENST00000338641	NM_000268.3	372	Gaa/Taa	11/16	0.235828572413723	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.245442939586908	1		497	1045	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045677	47045677	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	134	222	0	ENST00000377604.3:c.2560del	p.Asp854ThrfsTer32	p.D854Tfs*32	ENST00000377604	NM_001204468.1	853	cGg/cg	23/24	1	1	FACETS	0.899	0.821	0.98	1	0.99	1	CLONAL	2	TRUE	0	0.245442939586908	1		222	533	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0011150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	120	452	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	0.252146485427646	2		452	758	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0011150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	153	675	1	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.252146485427646	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.252146485427646	1		676	836	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383144	42383144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764758292	NA	P-0011150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	190	674	0	ENST00000221972.3:c.164C>T	p.Pro55Leu	p.P55L	ENST00000221972	NM_021601.3	55	cCg/cTg	2/5	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.252146485427646	2		674	1091	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741877	162741877	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	94	284	0	ENST00000367921.3:c.1568A>T	p.Glu523Val	p.E523V	ENST00000367921	NM_006182.2	523	gAg/gTg	13/18	0.252146485427646	4	FACETS	1	0.936	1	0.359	0.319	0.402	CLONAL	1	TRUE	1	0.252146485427646	4		284	867	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754928	29754928	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	69	222	0	ENST00000389048.3:c.1007C>A	p.Pro336Gln	p.P336Q	ENST00000389048	NM_004304.4	336	cCg/cAg	4/29	0.252146485427646	3	FACETS	0.942	0.821	1	0.471	0.41	0.537	CLONAL	1	TRUE	1	0.252146485427646	3		222	654	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265591	198265591	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	96	347	0	ENST00000335508.6:c.2566G>A	p.Asp856Asn	p.D856N	ENST00000335508	NM_012433.2	856	Gat/Aat	18/25	0.252146485427646	3	FACETS	1	0.9	1	0.506	0.45	0.565	CLONAL	1	TRUE	1	0.252146485427646	3		347	848	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183634	10183634	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	73	365	3	ENST00000256474.2:c.103G>T	p.Ala35Ser	p.A35S	ENST00000256474	NM_000551.3	35	Gcc/Tcc	1/3	1	2	FACETS	0.981	0.859	1	0.981	0.859	1	CLONAL	1	TRUE	1	0.252146485427646	2		368	590	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183848	10183848	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	34	162	0	ENST00000256474.2:c.317G>T	p.Gly106Val	p.G106V	ENST00000256474	NM_000551.3	106	gGc/gTc	1/3	1	2	FACETS	0.933	0.765	1	0.933	0.765	1	CLONAL	1	TRUE	1	0.252146485427646	2		162	289	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397658	49397658	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	130	341	0	ENST00000418115.1:c.566G>T	p.Gly189Val	p.G189V	ENST00000418115	NM_001664.2	189	gGg/gTg	5/5	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.252146485427646	2		341	1026	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586490	189586490	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	74	231	0	ENST00000264731.3:c.1114G>C	p.Asp372His	p.D372H	ENST00000264731	NM_003722.4	372	Gat/Cat	8/14	1	2	FACETS	0.982	0.86	1	0.982	0.86	1	CLONAL	1	TRUE	1	0.252146485427646	2		231	598	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143043306	143043306	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	122	404	0	ENST00000262992.4:c.2110G>T	p.Val704Leu	p.V704L	ENST00000262992	NM_001101669.1	704	Gtg/Ttg	19/24	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.252146485427646	2		404	852	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143129590	143129590	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	65	287	2	ENST00000262992.4:c.1060C>A	p.Pro354Thr	p.P354T	ENST00000262992	NM_001101669.1	354	Cct/Act	12/24	1	2	FACETS	0.895	0.776	1	0.895	0.776	1	CLONAL	1	TRUE	1	0.252146485427646	2		289	576	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630140	187630140	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	106	326	0	ENST00000441802.2:c.842G>T	p.Cys281Phe	p.C281F	ENST00000441802	NM_005245.3	281	tGc/tTc	2/27	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.252146485427646	2		326	752	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946370	2946370	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	246	473	0	ENST00000396946.4:c.3367G>T	p.Asp1123Tyr	p.D1123Y	ENST00000396946	NM_032415.4	1123	Gac/Tac	25/25	0.252146485427646	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.252146485427646	3		473	1027	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874206	151874206	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	69	327	0	ENST00000262189.6:c.8332G>C	p.Asp2778His	p.D2778H	ENST00000262189	NM_170606.2	2778	Gac/Cac	38/59	0.252146485427646	3	FACETS	0.738	0.642	0.843	0.369	0.321	0.422	SUBCLONAL	1	TRUE	1	0.252146485427646	3		327	835	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372193	55372193	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs753081636	NA	P-0011150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	10	99	0	ENST00000297316.4:c.883G>C	p.Val295Leu	p.V295L	ENST00000297316	NM_022454.3	295	Gtg/Ctg	2/2	0.252146485427646	3	FACETS	0.513	0.348	0.721	0.257	0.174	0.361	SUBCLONAL	1	TRUE	1	0.252146485427646	3		99	174	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399309	139399309	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	96	362	0	ENST00000277541.6:c.4834G>T	p.Gly1612Cys	p.G1612C	ENST00000277541	NM_017617.3	1612	Ggc/Tgc	26/34	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.252146485427646	2		362	737	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451458	70451458	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	154	488	0	ENST00000373644.4:c.6298G>A	p.Glu2100Lys	p.E2100K	ENST00000373644	NM_030625.2	2100	Gaa/Aaa	12/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.252146485427646	2		488	1087	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420113	420113	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	186	450	0	ENST00000399788.2:c.3154G>A	p.Ala1052Thr	p.A1052T	ENST00000399788	NM_001042603.1	1052	Gca/Aca	21/28	0.211797917814375	3	FACETS	0.786	0.725	0.849			1	SUBCLONAL	2	TRUE	NA	0.252146485427646	3		450	1057	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860022	57860022	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0011150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	136	521	0	ENST00000228682.2:c.763-1G>T		p.X255_splice	ENST00000228682	NM_005269.2	255			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.252146485427646	2		521	982	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986871	36986871	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs771205427	NA	P-0011150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	19	71	0	ENST00000354822.5:c.818G>T	p.Gly273Val	p.G273V	ENST00000354822	NM_001079668.2	273	gGg/gTg	3/3	0.233695685353492	2	FACETS	1	0.811	1	0.534	0.409	0.678	CLONAL	1	TRUE	0	0.252146485427646	2		71	141	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610356	81610356	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	107	393	0	ENST00000298171.2:c.1954C>A	p.Pro652Thr	p.P652T	ENST00000298171	NM_000369.2	652	Cct/Act	10/10	0.233695685353492	2	FACETS	0.973	0.872	1	0.487	0.436	0.541	CLONAL	1	TRUE	0	0.252146485427646	2		393	872	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546102	29546102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	123	318	0	ENST00000356175.3:c.1607C>T	p.Ser536Leu	p.S536L	ENST00000356175	NM_000267.3	536	tCa/tTa	14/57	0.252146485427646	3	FACETS	1	0.978	1	0.642	0.58	0.707	CLONAL	1	TRUE	1	0.252146485427646	3		318	856	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560085	29560085	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	132	350	0	ENST00000356175.3:c.3562C>T	p.Gln1188Ter	p.Q1188*	ENST00000356175	NM_000267.3	1188	Caa/Taa	27/57	0.252146485427646	3	FACETS	1	0.968	1	0.576	0.522	0.633	CLONAL	1	TRUE	1	0.252146485427646	3		350	1023	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679298	29679298	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	85	353	1	ENST00000356175.3:c.7418G>T	p.Trp2473Leu	p.W2473L	ENST00000356175	NM_000267.3	2473	tGg/tTg	50/57	0.252146485427646	3	FACETS	0.843	0.743	0.949	0.421	0.371	0.475	CLONAL	1	TRUE	1	0.252146485427646	3		354	901	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575107	48575107	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	102	361	0	ENST00000342988.3:c.301T>A	p.Trp101Arg	p.W101R	ENST00000342988	NM_005359.5	101	Tgg/Agg	3/12	0.125669308519963	1	FACETS	0.9	0.804	1	0.9	0.804	1	INDETERMINATE	1	TRUE	0	0.252146485427646	1		361	786	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762875	40762875	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763646270	NA	P-0011150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	131	402	0	ENST00000392038.2:c.133C>T	p.Pro45Ser	p.P45S	ENST00000392038	NM_001626.4	45	Cct/Tct	3/14	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.252146485427646	2		402	909	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762951	40762951	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	91	317	0	ENST00000392038.2:c.57C>G	p.Ile19Met	p.I19M	ENST00000392038	NM_001626.4	19	atC/atG	3/14	1	2	FACETS	0.998	0.886	1	0.998	0.886	1	CLONAL	1	TRUE	1	0.252146485427646	2		317	723	SUCCESS
AR	367	MSKCC	GRCh37	X	66766213	66766213	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	52	104	0	ENST00000374690.3:c.1225G>T	p.Gly409Trp	p.G409W	ENST00000374690	NM_000044.3	409	Ggg/Tgg	1/8	0.158381057010677	0	FACETS	0.764	0.659	0.875			1	SUBCLONAL	2	TRUE	NA	0.252146485427646	0		104	202	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123505200	123505200	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0011150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	60	82	0	ENST00000371139.4:c.347-1G>T		p.X116_splice	ENST00000371139	NM_001114937.2	116			0.158381057010677	0	FACETS	0.642	0.558	0.732			1	SUBCLONAL	2	TRUE	NA	0.252146485427646	0		82	277	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0011177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	160	195	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.402141586692268	4	FACETS	0.959	0.883	1	0.959	0.883	1	CLONAL	2	TRUE	2	0.402141586692268	4		195	582	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011225	12011225	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	83	180	0	ENST00000353533.5:c.632C>A	p.Ala211Glu	p.A211E	ENST00000353533	NM_003010.3	211	gCa/gAa	5/11	1	2	FACETS	0.814	0.721	0.914	0.814	0.721	0.914	CLONAL	1	TRUE	1	0.402141586692268	2		180	507	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913396	NA	P-0011180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	68	465	0	ENST00000349496.5:c.95A>T	p.Asp32Val	p.D32V	ENST00000349496	NM_001904.3	32	gAc/gTc	3/15	0.187730980174757	2	FACETS	0.804	0.698	0.919	0.402	0.349	0.46	CLONAL	1	TRUE	0	0.19793704978756	2		465	855	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577530	7577530	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	117	436	0	ENST00000269305.4:c.751A>T	p.Ile251Phe	p.I251F	ENST00000269305	NM_001126112.2	251	Atc/Ttc	7/11	0.194260073772673	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.19793704978756	1		436	808	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0011186-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	174	348	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.56376057043968	3	FACETS	0.861	0.793	0.932	0.431	0.396	0.466	CLONAL	1	TRUE	1	0.56376057043968	3		348	919	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0011186-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	572	222	0	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	0.56376057043968	3	FACETS	0.925	0.896	0.954	0.925	0.896	0.954	CLONAL	3	TRUE	0	0.56376057043968	3		222	937	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120479949	120479949	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011186-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	224	286	0	ENST00000256646.2:c.3478C>T	p.His1160Tyr	p.H1160Y	ENST00000256646	NM_024408.3	1160	Cac/Tac	21/34	0.521602900047953	4	FACETS	0.895	0.831	0.961	0.298	0.277	0.321	CLONAL	1	TRUE	1	0.56376057043968	4		286	1389	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204737508	204737508	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011186-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	154	207	0	ENST00000302823.3:c.645T>A	p.Phe215Leu	p.F215L	ENST00000302823	NM_005214.4	215	ttT/ttA	4/4	0.423022348710104	3	FACETS	0.991	0.909	1	0.495	0.454	0.538	CLONAL	1	TRUE	1	0.56376057043968	3		207	707	SUCCESS
ATM	472	MSKCC	GRCh37	11	108213964	108213964	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs751574257	NA	P-0011186-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	249	173	0	ENST00000278616.4:c.8284C>T	p.Gln2762Ter	p.Q2762*	ENST00000278616	NM_000051.3	2762	Cag/Tag	57/63	0.48625262269725	4	FACETS	0.847	0.795	0.901	0.847	0.795	0.901	CLONAL	2	TRUE	2	0.56376057043968	4		173	815	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63531745	63531745	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011186-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1657	240	308	0	ENST00000307078.5:c.2236G>C	p.Asp746His	p.D746H	ENST00000307078	NM_004655.3	746	Gat/Cat	9/11	0.524867405939887	5	FACETS	0.828	0.77	0.889	0.276	0.256	0.297	CLONAL	1	TRUE	2	0.56376057043968	5		308	1897	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600329	10600329	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011186-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	809	307	2	ENST00000171111.5:c.1526G>C	p.Gly509Ala	p.G509A	ENST00000171111	NM_203500.1	509	gGg/gCg	4/6	0.56376057043968	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.56376057043968	3		309	1175	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231036	53231036	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011186-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	494	159	0	ENST00000375401.3:c.1866G>T	p.Trp622Cys	p.W622C	ENST00000375401	NM_004187.3	622	tgG/tgT	13/26	0.52236331721472	2	FACETS	0.839	0.815	0.863			1	CLONAL	3	TRUE	NA	0.56376057043968	2		159	696	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220613	1220615	+	frameshift_variant	Frame_Shift_Del	DEL	CGG	CGG	TT	novel	NA	P-0011186-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	726	341	1	ENST00000326873.7:c.631_633delinsTT	p.Arg211LeufsTer76	p.R211Lfs*76	ENST00000326873	NM_000455.4	211	CGG/TT	5/10	0.56376057043968	3	FACETS	0.953	0.927	0.979	0.953	0.927	0.979	CLONAL	3	TRUE	0	0.56376057043968	3		342	1155	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577579	7577579	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0011196-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	83	206	0	ENST00000269305.4:c.702C>G	p.Tyr234Ter	p.Y234*	ENST00000269305	NM_001126112.2	234	taC/taG	7/11	0.221782715004428	1	FACETS	0.769	0.685	0.856	1	0.98	1	SUBCLONAL	2	FALSE	0	0.3	1		206	306	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0011236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	214	483	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.811	0.756	0.867	1	0.993	1	CLONAL	2	TRUE	1	0.352973355555188	2		483	748	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0011236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	118	264	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.94	0.849	1	0.94	0.849	1	CLONAL	1	TRUE	1	0.352973355555188	2		264	711	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043374	6043374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	38	65	0	ENST00000265849.7:c.300G>T	p.Gln100His	p.Q100H	ENST00000265849	NM_000535.5	100	caG/caT	4/15	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.352973355555188	2		65	158	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508442	106508442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	67	99	0	ENST00000359195.3:c.436G>A	p.Glu146Lys	p.E146K	ENST00000359195	NM_002649.2	146	Gag/Aag	2/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.352973355555188	2		99	272	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738372	133738372	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	107	220	1	ENST00000318560.5:c.772G>T	p.Glu258Ter	p.E258*	ENST00000318560	NM_005157.4	258	Gag/Tag	4/11	1	2	FACETS	0.981	0.882	1	0.981	0.882	1	CLONAL	1	TRUE	1	0.352973355555188	2		221	618	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274704	123274704	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	173	348	0	ENST00000358487.5:c.1214A>G	p.Lys405Arg	p.K405R	ENST00000358487	NM_000141.4	405	aAg/aGg	9/18	0.235719069947933	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.352973355555188	1		348	806	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178712	108178712	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs869312756	NA	P-0011236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	54	128	0	ENST00000278616.4:c.5762+1G>A		p.X1921_splice	ENST00000278616	NM_000051.3	1921			0.352973355555188	1	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	0	0.352973355555188	1		128	240	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170371	119170371	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	176	364	0	ENST00000264033.4:c.2601G>T	p.Gln867His	p.Q867H	ENST00000264033	NM_005188.3	867	caG/caT	16/16	0.352973355555188	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.352973355555188	1		364	707	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16046996	16046996	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	164	284	0	ENST00000268712.3:c.1097G>C	p.Gly366Ala	p.G366A	ENST00000268712	NM_006311.3	366	gGa/gCa	11/46	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.352973355555188	2		284	718	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794623	42794623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564532974	NA	P-0011236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	38	357	0	ENST00000575354.2:c.1703C>T	p.Ala568Val	p.A568V	ENST00000575354	NM_015125.3	568	gCg/gTg	10/20	0.352973355555188	1	FACETS	0.271	0.223	0.324	0.271	0.223	0.324	SUBCLONAL	1	TRUE	0	0.352973355555188	1		357	655	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252865	36252865	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	163	263	0	ENST00000300305.3:c.497G>T	p.Arg166Leu	p.R166L	ENST00000300305		166	cGa/cTa	4/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.352973355555188	2		263	843	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225146	53225146	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	212	540	1	ENST00000375401.3:c.3072G>T	p.Glu1024Asp	p.E1024D	ENST00000375401	NM_004187.3	1024	gaG/gaT	20/26	0.18617984245368	1	FACETS	0.828	0.768	0.891	0.828	0.768	0.891	INDETERMINATE	1	TRUE	0	0.352973355555188	1		541	1194	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855939	76855939	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	103	464	0	ENST00000373344.5:c.5661G>T	p.Trp1887Cys	p.W1887C	ENST00000373344	NM_000489.3	1887	tgG/tgT	23/35	0.18617984245368	1	FACETS	0.532	0.475	0.593	0.532	0.475	0.593	INDETERMINATE	1	TRUE	0	0.352973355555188	1		464	903	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909591	76909591	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	177	493	0	ENST00000373344.5:c.4314C>G	p.Asn1438Lys	p.N1438K	ENST00000373344	NM_000489.3	1438	aaC/aaG	14/35	0.18617984245368	1	FACETS	0.975	0.899	1	0.975	0.899	1	INDETERMINATE	1	TRUE	0	0.352973355555188	1		493	847	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864478	162864479	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0011236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	145	317	1	ENST00000366898.1:c.34_35delinsTT	p.Gly12Phe	p.G12F	ENST00000366898	NM_004562.2	12	GGt/TTt	2/12	0.18617984245368	1	FACETS	0.964	0.881	1	0.964	0.881	1	INDETERMINATE	1	TRUE	0	0.352973355555188	1		318	702	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149987	202149987	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	55	550	0	ENST00000358485.4:c.1428G>T	p.Glu476Asp	p.E476D	ENST00000358485	NM_001080125.1	476	gaG/gaT	8/9	1	2	FACETS	0.731	0.624	0.848	0.731	0.624	0.848	SUBCLONAL	1	TRUE	1	0.197248552226612	2		550	763	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61197647	61197647	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	46	714	1	ENST00000301761.2:c.29C>A	p.Ser10Ter	p.S10*	ENST00000301761	NM_017841.2	10	tCg/tAg	1/4	1	2	FACETS	0.609	0.511	0.717	0.609	0.511	0.717	SUBCLONAL	1	TRUE	1	0.197248552226612	2		715	766	SUCCESS
APC	324	MSKCC	GRCh37	5	112111408	112111411	+	frameshift_variant	Frame_Shift_Del	DEL	ATAG	ATAG	-	rs387906231	NA	P-0011258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	75	607	0	ENST00000257430.4:c.509_512del	p.Asp170ValfsTer4	p.D170Vfs*4	ENST00000257430	NM_000038.5	169	ATAGat/at	5/16	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.370263012772487	2		607	385	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858738	9858738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149698593	NA	P-0011258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	61	747	2	ENST00000330684.3:c.2663C>T	p.Thr888Met	p.T888M	ENST00000330684	NM_001134407.1	888	aCg/aTg	13/13	1	2	FACETS	0.81	0.701	0.927	0.81	0.701	0.927	CLONAL	1	TRUE	1	0.370263012772487	2		749	407	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092823	27092823	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0011258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	96	970	0	ENST00000324856.7:c.2844T>A	p.Tyr948Ter	p.Y948*	ENST00000324856	NM_006015.4	948	taT/taA	9/20	1	2	FACETS	0.941	0.841	1	0.941	0.841	1	CLONAL	1	TRUE	1	0.370263012772487	2		970	551	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101195	27101195	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	98	889	1	ENST00000324856.7:c.4477C>T	p.Gln1493Ter	p.Q1493*	ENST00000324856	NM_006015.4	1493	Cag/Tag	18/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.370263012772487	2		890	480	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967254	134967254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758204492	NA	P-0011258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	56	796	2	ENST00000398015.3:c.2593C>T	p.Arg865Trp	p.R865W	ENST00000398015	NM_004441.4	865	Cgg/Tgg	14/16	1	2	FACETS	0.591	0.506	0.683	0.591	0.506	0.683	SUBCLONAL	1	TRUE	1	0.370263012772487	2		798	512	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541295	187541295	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	123	936	1	ENST00000441802.2:c.6445G>T	p.Glu2149Ter	p.E2149*	ENST00000441802	NM_005245.3	2149	Gaa/Taa	10/27	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.370263012772487	2		937	614	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117711006	117711006	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0011258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	36	284	0	ENST00000368508.3:c.1266T>A	p.Tyr422Ter	p.Y422*	ENST00000368508	NM_002944.2	422	taT/taA	12/43	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.370263012772487	2		284	162	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730874	40730874	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	109	825	0	ENST00000373198.4:c.3661A>G	p.Asn1221Asp	p.N1221D	ENST00000373198	NM_133170.3	1221	Aac/Gac	27/32	0.31625201182017	4	FACETS	0.833	0.752	0.919	0.556	0.501	0.613	CLONAL	2	TRUE	1	0.370263012772487	4		825	484	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618346	37618346	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	90	820	2	ENST00000447079.4:c.26del	p.Gly9AlafsTer48	p.G9Afs*48	ENST00000447079	NM_015083.1	8	Ggg/gg	1/14	0.204215310605438	3	FACETS	0.962	0.855	1			1	INDETERMINATE	1	TRUE	NA	0.370263012772487	3		822	599	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120236	70120239	+	frameshift_variant	Frame_Shift_Del	DEL	ACTC	ACTC	TGA	novel	NA	P-0011258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	338	937	0	ENST00000245479.2:c.1238_1241delinsTGA	p.His413LeufsTer57	p.H413Lfs*57	ENST00000245479	NM_000346.3	413	cACTCg/cTGAg	3/3	0.370263012772487	3	FACETS	0.971	0.924	1	0.971	0.924	1	CLONAL	3	TRUE	0	0.370263012772487	3		937	743	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0011261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	49	195	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.875	0.744	1	0.875	0.744	1	CLONAL	1	TRUE	1	0.320945176125124	2		195	349	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0011261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	307	483	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.320945176125124	3	FACETS	0.924	0.875	0.973	0.924	0.875	0.973	CLONAL	3	TRUE	0	0.320945176125124	3		483	801	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0011261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	131	401	0	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	1	2	FACETS	0.897	0.813	0.985	0.897	0.813	0.985	CLONAL	1	TRUE	1	0.320945176125124	2		401	910	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180646	56180646	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	74	229	0	ENST00000399503.3:c.3975G>A	p.Trp1325Ter	p.W1325*	ENST00000399503	NM_005921.1	1325	tgG/tgA	16/20	0.320945176125124	3	FACETS	0.865	0.757	0.98	0.432	0.378	0.49	CLONAL	1	TRUE	1	0.320945176125124	3		229	619	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845620	151845620	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	209	276	0	ENST00000262189.6:c.13392del	p.Cys4465ValfsTer52	p.C4465Vfs*52	ENST00000262189	NM_170606.2	4464	ttC/tt	52/59	0.269155158454082	3	FACETS	0.879	0.817	0.942	0.879	0.817	0.942	CLONAL	2	TRUE	1	0.320945176125124	3		276	860	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0011297-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	638	401	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.384913889752667	6	FACETS	0.944	0.912	0.977	0.944	0.912	0.977	CLONAL	4	TRUE	2	0.509863883207898	6		401	1338	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0011297-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	64	320	0				ENST00000310581	NM_198253.2	-/1132			0.509863883207898	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.509863883207898	1		320	143	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951813	2951813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377327574	NA	P-0011297-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	66	408	0	ENST00000396946.4:c.3137C>T	p.Ala1046Val	p.A1046V	ENST00000396946	NM_032415.4	1046	gCc/gTc	23/25	1	2	FACETS	0.692	0.604	0.787	0.692	0.604	0.787	SUBCLONAL	1	TRUE	1	0.509863883207898	2		408	374	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713479	40713479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011297-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	64	337	0	ENST00000373198.4:c.4036G>A	p.Asp1346Asn	p.D1346N	ENST00000373198	NM_133170.3	1346	Gat/Aat	30/32	1	2	FACETS	0.82	0.716	0.932	0.82	0.716	0.932	CLONAL	1	TRUE	1	0.509863883207898	2		337	306	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576114	88576115	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0011297-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	172	427	0	ENST00000360948.2:c.1558_1559delinsAA	p.Gly520Lys	p.G520K	ENST00000360948	NM_001012338.2	520	GGa/AAa	13/19	1	2	FACETS	0.756	0.703	0.811	1	0.991	1	SUBCLONAL	2	TRUE	1	0.509863883207898	2		427	446	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872366	45872366	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011304-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	207	486	0	ENST00000391945.4:c.145A>G	p.Thr49Ala	p.T49A	ENST00000391945	NM_000400.3	49	Aca/Gca	3/23	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.571012097861078	2		486	674	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721189	176721189	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011304-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	73	260	0	ENST00000439151.2:c.6820C>T	p.Gln2274Ter	p.Q2274*	ENST00000439151	NM_022455.4	2274	Cag/Tag	23/23	0.543211919730725	4	FACETS	0.72	0.63	0.816	0.36	0.315	0.408	SUBCLONAL	1	TRUE	2	0.571012097861078	4		260	558	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204511917	204511917	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011304-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	76	215	0	ENST00000367182.3:c.517G>C	p.Asp173His	p.D173H	ENST00000367182	NM_001278516.1	173	Gac/Cac	8/11	0.540384948064339	3	FACETS	0.819	0.721	0.922	0.409	0.36	0.461	CLONAL	1	TRUE	1	0.571012097861078	3		215	418	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159743	20159743	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011304-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	197	227	0	ENST00000379607.5:c.16G>C	p.Gly6Arg	p.G6R	ENST00000379607	NM_001412.3	6	Ggt/Cgt	1/7	0.487720854300429	2	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.571012097861078	2		227	612	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162898	47162919	+	frameshift_variant	Frame_Shift_Del	DEL	AGAATTCTTTGGCACAACCACA	AGAATTCTTTGGCACAACCACA	-	novel	NA	P-0011304-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	274	509	0	ENST00000409792.3:c.3207_3228del	p.Val1070LeufsTer44	p.V1070Lfs*44	ENST00000409792	NM_014159.6	1069	gtTGTGGTTGTGCCAAAGAATTCT/gt	3/21	0.571012097861078	2	FACETS	0.861	0.817	0.906	0.861	0.817	0.906	CLONAL	2	TRUE	0	0.571012097861078	2		509	557	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0011312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	103	452	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.868	0.776	0.965	1	0.985	1	CLONAL	2	TRUE	1	0.14	2		452	848	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578440	7578440	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0011312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	81	339	0	ENST00000269305.4:c.490A>T	p.Lys164Ter	p.K164*	ENST00000269305	NM_001126112.2	164	Aag/Tag	5/11	0.3	2	FACETS	1	0.972	1			1	CLONAL	1	TRUE	NA	0.14	2		339	833	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681036	37681036	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	56	347	0	ENST00000447079.4:c.3205G>C	p.Glu1069Gln	p.E1069Q	ENST00000447079	NM_015083.1	1069	Gaa/Caa	12/14	1	2	FACETS	0.909	0.777	1	0.909	0.777	1	CLONAL	1	TRUE	1	0.14	2		347	880	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069291	30069291	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	106	359	0	ENST00000338641.4:c.1156G>T	p.Glu386Ter	p.E386*	ENST00000338641	NM_000268.3	386	Gaa/Taa	12/16	0.204620138755761	3	FACETS	1	0.923	1	1	0.923	1	CLONAL	2	TRUE	1	0.14	3		359	782	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577312	64577332	+	inframe_deletion	In_Frame_Del	DEL	ATAGAGGGCGGCGATGATAGA	ATAGAGGGCGGCGATGATAGA	-	novel	NA	P-0011312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	50	441	0	ENST00000312049.6:c.250_270del	p.Ser84_Tyr90del	p.S84_Y90del	ENST00000312049	NM_130799.2	84	TCTATCATCGCCGCCCTCTAT/-	2/10	1	2	FACETS	0.799	0.676	0.935	0.799	0.676	0.935	CLONAL	1	TRUE	1	0.14	2		441	894	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161344	55161344	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	221	224	0	ENST00000257290.5:c.3175T>G	p.Phe1059Val	p.F1059V	ENST00000257290	NM_006206.4	1059	Ttc/Gtc	23/23	0.637538646750222	3	FACETS	0.955	0.891	1			1	CLONAL	1	TRUE	NA	0.774167228127398	3		224	829	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97933361	97933361	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs755283850	NA	P-0011321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	170	201	0	ENST00000289081.3:c.521G>A	p.Arg174Gln	p.R174Q	ENST00000289081	NM_000136.2	174	cGa/cAa	6/15	0.767836263618524	2	FACETS	0.902	0.836	0.969	0.451	0.418	0.485	CLONAL	1	TRUE	0	0.774167228127398	2		201	487	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123697	46123697	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	147	180	0	ENST00000334344.6:c.78C>A	p.Phe26Leu	p.F26L	ENST00000334344	NM_152641.2	26	ttC/ttA	1/21	0.273550532929799	5	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.774167228127398	5		180	613	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593587	55593643	+	inframe_deletion	In_Frame_Del	DEL	CATGTATGAAGTACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTA	CATGTATGAAGTACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTA	-	novel	NA	P-0011321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	342	248	0	ENST00000288135.5:c.1656_1712del	p.Met552_Tyr570del	p.M552_Y570del	ENST00000288135	NM_000222.2	551	ccCATGTATGAAGTACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTAc/ccc	11/21	0.714413837468191	5	FACETS	1	0.994	1			1	CLONAL	1	TRUE	NA	0.774167228127398	5		248	1366	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111496	8111512	+	frameshift_variant	Frame_Shift_Del	DEL	TGGAGGAGGAATGCCAA	TGGAGGAGGAATGCCAA	-	novel	NA	P-0011321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	252	317	1	ENST00000346208.3:c.985_1001del	p.Arg329GlyfsTer17	p.R329Gfs*17	ENST00000346208		328	TGGAGGAGGAATGCCAAt/t	5/6	NA	2	FACETS	0.902	0.848	0.957			1	INDETERMINATE	1	TRUE	NA	0.774167228127398	2		318	722	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659675	NA	P-0011338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	359	389	0	ENST00000269305.4:c.764T>C	p.Ile255Thr	p.I255T	ENST00000269305	NM_001126112.2	255	aTc/aCc	7/11	0.752419533669516	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.762851079702217	1		389	561	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790728	89790728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2231267	NA	P-0011338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	406	491	1	ENST00000336032.3:c.115C>T	p.Pro39Ser	p.P39S	ENST00000336032	NM_006813.2	39	Ccg/Tcg	1/2	0.729798387668423	3	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.762851079702217	3		492	1398	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584787	48584787	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	489	599	0	ENST00000342988.3:c.865C>T	p.Gln289Ter	p.Q289*	ENST00000342988	NM_005359.5	289	Cag/Tag	7/12	0.752419533669516	1	FACETS	0.974	0.941	1	0.974	0.941	1	CLONAL	1	TRUE	0	0.762851079702217	1		599	814	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14628978	14628978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	359	596	0	ENST00000254322.2:c.184G>A	p.Glu62Lys	p.E62K	ENST00000254322	NM_006145.1	62	Gag/Aag	1/3	1	2	FACETS	0.972	0.924	1	0.972	0.924	1	CLONAL	1	TRUE	1	0.762851079702217	2		596	968	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067386	37067386	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs63750443	NA	P-0011338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	381	392	0	ENST00000231790.2:c.1297G>C	p.Glu433Gln	p.E433Q	ENST00000231790	NM_000249.3	433	Gaa/Caa	12/19	0.762851079702217	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.762851079702217	1		392	586	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028618	12028618	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	374	393	0	ENST00000353533.5:c.821G>T	p.Arg274Ile	p.R274I	ENST00000353533	NM_003010.3	274	aGa/aTa	8/11	0.752419533669516	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.762851079702217	1		393	601	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771344	68771344	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	192	209	0	ENST00000261769.5:c.26C>A	p.Ser9Ter	p.S9*	ENST00000261769	NM_004360.3	9	tCg/tAg	1/16	0.762851079702217	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.762851079702217	1		209	265	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654516	29654516	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs876660141	NA	P-0011338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	426	417	0	ENST00000356175.3:c.5206-1G>C		p.X1736_splice	ENST00000356175	NM_000267.3	1736			0.752419533669516	1	FACETS	0.988	0.952	1	0.988	0.952	1	CLONAL	1	TRUE	0	0.762851079702217	1		417	699	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056443	26056443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1252419231	NA	P-0011338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	229	210	0	ENST00000343677.2:c.214G>A	p.Asp72Asn	p.D72N	ENST00000343677	NM_005319.3	72	Gat/Aat	1/1	0.755761179768214	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.762851079702217	1		210	367	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169787	11169787	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0011338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	309	317	0	ENST00000361445.4:c.7367-1G>C		p.X2456_splice	ENST00000361445	NM_004958.3	2456			0.762851079702217	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.762851079702217	1		317	501	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728671	190728671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	574	458	0	ENST00000441310.2:c.2059G>A	p.Glu687Lys	p.E687K	ENST00000441310	NM_000534.4	687	Gaa/Aaa	10/13	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.762851079702217	2		458	1473	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143033725	143033725	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	488	490	0	ENST00000262992.4:c.2246G>C	p.Gly749Ala	p.G749A	ENST00000262992	NM_001101669.1	749	gGa/gCa	20/24	0.762851079702217	1	FACETS	0.992	0.958	1	0.992	0.958	1	CLONAL	1	TRUE	0	0.762851079702217	1		490	798	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962679	38962679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	322	292	0	ENST00000357387.3:c.1576G>A	p.Glu526Lys	p.E526K	ENST00000357387	NM_152756.3	526	Gaa/Aaa	18/38	1	2	FACETS	0.949	0.899	0.999	0.949	0.899	0.999	CLONAL	1	TRUE	1	0.762851079702217	2		292	890	SUCCESS
APC	324	MSKCC	GRCh37	5	112177511	112177511	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	344	299	0	ENST00000257430.4:c.6220G>T	p.Glu2074Ter	p.E2074*	ENST00000257430	NM_000038.5	2074	Gaa/Taa	16/16	NA	2	FACETS	0.99	0.94	1			1	INDETERMINATE	1	TRUE	NA	0.762851079702217	2		299	911	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163305	32163305	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	430	857	0	ENST00000375023.3:c.5921C>G	p.Pro1974Arg	p.P1974R	ENST00000375023	NM_004557.3	1974	cCg/cGg	30/30	1	2	FACETS	0.959	0.915	1	0.959	0.915	1	CLONAL	1	TRUE	1	0.762851079702217	2		857	1176	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099858	157099858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	290	337	0	ENST00000346085.5:c.795G>A	p.Met265Ile	p.M265I	ENST00000346085	NM_020732.3	265	atG/atA	1/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.762851079702217	2		337	741	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738515	145738515	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs901313954	NA	P-0011338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	155	179	0	ENST00000428558.2:c.2470G>C	p.Asp824His	p.D824H	ENST00000428558	NM_004260.3	824	Gac/Cac	16/22	1	2	FACETS	0.913	0.844	0.984	0.913	0.844	0.984	CLONAL	1	TRUE	1	0.762851079702217	2		179	445	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160508	108160508	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	339	300	0	ENST00000278616.4:c.4416G>C	p.Leu1472Phe	p.L1472F	ENST00000278616	NM_000051.3	1472	ttG/ttC	29/63	1	2	FACETS	0.973	0.924	1	0.973	0.924	1	CLONAL	1	TRUE	1	0.762851079702217	2		300	913	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445893	49445893	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	388	597	0	ENST00000301067.7:c.1573G>A	p.Glu525Lys	p.E525K	ENST00000301067	NM_003482.3	525	Gag/Aag	10/54	1	2	FACETS	0.953	0.908	1	0.953	0.908	1	CLONAL	1	TRUE	1	0.762851079702217	2		597	1067	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233390	69233390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	405	371	0	ENST00000462284.1:c.1255G>A	p.Glu419Lys	p.E419K	ENST00000462284	NM_002392.5	419	Gag/Aag	11/11	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.762851079702217	2		371	989	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945141	32945141	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	391	454	0	ENST00000380152.3:c.8536G>C	p.Glu2846Gln	p.E2846Q	ENST00000380152		2846	Gag/Cag	20/27	1	2	FACETS	0.924	0.88	0.969	0.924	0.88	0.969	CLONAL	1	TRUE	1	0.762851079702217	2		454	1109	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527452	29527452	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	283	267	0	ENST00000356175.3:c.901G>C	p.Asp301His	p.D301H	ENST00000356175	NM_000267.3	301	Gac/Cac	9/57	0.752419533669516	1	FACETS	0.964	0.92	1	0.964	0.92	1	CLONAL	1	TRUE	0	0.762851079702217	1		267	476	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872145	37872145	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142456637	NA	P-0011338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5422	340	445	0	ENST00000269571.5:c.1466C>T	p.Pro489Leu	p.P489L	ENST00000269571		489	cCg/cTg	12/27	0.762851079702217	13	FACETS	0.804	0.754	0.855			1	CLONAL	1	TRUE	NA	0.762851079702217	13		445	5762	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78865559	78865559	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	310	437	0	ENST00000306801.3:c.2023G>C	p.Glu675Gln	p.E675Q	ENST00000306801	NM_020761.2	675	Gaa/Caa	18/34	0.762851079702217	1	FACETS	0.934	0.893	0.975	0.934	0.893	0.975	CLONAL	1	TRUE	0	0.762851079702217	1		437	538	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724609	724609	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	286	302	0	ENST00000314574.4:c.1447G>C	p.Glu483Gln	p.E483Q	ENST00000314574	NM_005433.3	483	Gaa/Caa	12/12	0.752419533669516	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.762851079702217	1		302	454	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0011342-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	73	517	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.741	0.646	0.843	0.741	0.646	0.843	SUBCLONAL	1	TRUE	1	0.23	2		517	857	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970972	21970972	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011342-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	53	496	0	ENST00000304494.5:c.386A>G	p.Tyr129Cys	p.Y129C	ENST00000304494	NM_000077.4	129	tAc/tGc	2/3	1	2	FACETS	0.873	0.745	1	0.873	0.745	1	CLONAL	1	TRUE	1	0.23	2		496	528	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882319	89882319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011342-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	86	787	2	ENST00000389301.3:c.155G>A	p.Arg52Gln	p.R52Q	ENST00000389301	NM_000135.2	52	cGa/cAa	2/43	0.3	2	FACETS	0.855	0.755	0.962			1	CLONAL	1	TRUE	NA	0.23	2		789	875	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636757	8636757	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011342-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	54	579	0	ENST00000356435.5:c.152C>A	p.Pro51Gln	p.P51Q	ENST00000356435		51	cCa/cAa	2/35	0.3	1	FACETS	0.633	0.539	0.735	0.633	0.539	0.735	SUBCLONAL	1	TRUE	0	0.23	1		579	657	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597417	10597417	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1415900791	NA	P-0011342-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	83	681	0	ENST00000171111.5:c.1786C>T	p.Arg596Ter	p.R596*	ENST00000171111	NM_203500.1	596	Cga/Tga	6/6	1	2	FACETS	0.872	0.768	0.983	0.872	0.768	0.983	CLONAL	1	TRUE	1	0.23	2		681	828	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524442	44524442	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0011342-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	85	524	0	ENST00000291552.4:c.115A>T	p.Lys39Ter	p.K39*	ENST00000291552	NM_006758.2	39	Aaa/Taa	2/8	0.3	3	FACETS	0.903	0.796	1			1	CLONAL	1	TRUE	NA	0.23	3		524	913	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220580	1220584	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GCACT	GCACT	-	novel	NA	P-0011342-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	49	523	0	ENST00000326873.7:c.602_606del	p.Leu201ProfsTer63	p.L201Pfs*63	ENST00000326873	NM_000455.4	200	GCACTg/g	5/10	0.1827746024029	1	FACETS	0.822	0.697	0.959	0.822	0.697	0.959	CLONAL	1	TRUE	0	0.23	1		523	459	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112567	2112567	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	147	350	0	ENST00000219476.3:c.1327C>T	p.Gln443Ter	p.Q443*	ENST00000219476	NM_000548.3	443	Cag/Tag	13/42	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.41	2		350	693	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108848	2108849	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0011346-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	118	386	0	ENST00000219476.3:c.950_951del	p.Thr317IlefsTer20	p.T317Ifs*20	ENST00000219476	NM_000548.3	317	ACa/a	10/42	1	2	FACETS	0.831	0.75	0.915	0.831	0.75	0.915	CLONAL	1	TRUE	1	0.41	2		386	693	SUCCESS
APC	324	MSKCC	GRCh37	5	112174502	112174502	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876659539	NA	P-0011347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	120	208	0	ENST00000257430.4:c.3211C>T	p.Gln1071Ter	p.Q1071*	ENST00000257430	NM_000038.5	1071	Caa/Taa	16/16	0.375248129629372	2	FACETS	0.901	0.823	0.981	0.901	0.823	0.981	CLONAL	2	TRUE	0	0.375248129629372	2		208	355	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971053	21971053	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137854598	NA	P-0011347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	58	147	0	ENST00000304494.5:c.305C>T	p.Ala102Val	p.A102V	ENST00000304494	NM_000077.4	102	gCg/gTg	2/3	0.319420561278812	3	FACETS	0.909	0.783	1	0.454	0.391	0.522	CLONAL	1	TRUE	1	0.375248129629372	3		147	404	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573123	64573123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761102084	NA	P-0011347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	42	155	0	ENST00000312049.6:c.1169C>T	p.Pro390Leu	p.P390L	ENST00000312049	NM_130799.2	390	cCg/cTg	8/10	0.32764366120951	4	FACETS	0.601	0.502	0.712	0.2	0.167	0.238	SUBCLONAL	1	TRUE	1	0.375248129629372	4		155	512	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475226	475226	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs755599417	NA	P-0011347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	105	292	0	ENST00000399788.2:c.411G>T	p.Lys137Asn	p.K137N	ENST00000399788	NM_001042603.1	137	aaG/aaT	4/28	0.319420561278812	3	FACETS	0.989	0.887	1	0.495	0.443	0.549	CLONAL	1	TRUE	1	0.375248129629372	3		292	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577521	7577521	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	225	285	0	ENST00000269305.4:c.760A>T	p.Ile254Phe	p.I254F	ENST00000269305	NM_001126112.2	254	Atc/Ttc	7/11	NA	2	FACETS	0.845	0.79	0.9			1	INDETERMINATE	2	TRUE	NA	0.375248129629372	2		285	710	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750587	128750589	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs776242757	NA	P-0011347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1333	86	288	0	ENST00000377970.2:c.130_132del	p.Glu44del	p.E44del	ENST00000377970	NM_002467.4	42	GAG/-	2/3	0.375248129629372	7	FACETS	0.626	0.551	0.707	0.089	0.078	0.101	SUBCLONAL	1	TRUE	0	0.375248129629372	7		288	1419	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	80	589	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.709147473532017	2		590	206	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591076	67591076	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	57	208	0	ENST00000274335.5:c.1669C>T	p.Arg557Ter	p.R557*	ENST00000274335		557	Cga/Tga	12/15	1	2	FACETS	0.534	0.461	0.612	0.534	0.461	0.612	SUBCLONAL	1	TRUE	1	0.709147473532017	2		208	301	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725053	89725053	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	114	231	0	ENST00000371953.3:c.1036T>G	p.Tyr346Asp	p.Y346D	ENST00000371953	NM_000314.4	346	Tac/Gac	9/9	0.709147473532017	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.709147473532017	1		231	203	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590392	67590392	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0011351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	81	221	0	ENST00000274335.5:c.1455del	p.Ala486HisfsTer6	p.A486Hfs*6	ENST00000274335		485	gAa/ga	11/15	1	2	FACETS	0.807	0.72	0.899	0.807	0.72	0.899	CLONAL	1	TRUE	1	0.709147473532017	2		221	283	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0011355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	315	537	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.468049807722766	3	FACETS	0.88	0.832	0.929	0.88	0.832	0.929	CLONAL	2	TRUE	1	0.467156308496608	3		537	945	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0011355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1192	584	1212	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	0.468049807722766	3	FACETS	0.868	0.833	0.904	0.868	0.833	0.904	CLONAL	2	TRUE	1	0.467156308496608	3		1212	1776	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120527	70120527	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0011355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	48	260	0	ENST00000245479.2:c.1529G>C	p.Ter510SerextTer49	p.*510Sext*49	ENST00000245479	NM_000346.3	510	tGa/tCa	3/3	0.412811401826171	2	FACETS	0.417	0.352	0.488	0.208	0.176	0.244	SUBCLONAL	1	TRUE	0	0.467156308496608	2		260	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	308	501	0	ENST00000269305.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	336	Gag/Tag	10/11	0.195731033367606	1	FACETS	1	0.992	1	1	0.992	1	INDETERMINATE	1	TRUE	0	0.467156308496608	1		501	812	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333266	70333266	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	89	450	0	ENST00000373644.4:c.1171G>A	p.Glu391Lys	p.E391K	ENST00000373644	NM_030625.2	391	Gag/Aag	2/12	0.436809500654076	4	FACETS	0.427	0.377	0.481	0.214	0.188	0.241	SUBCLONAL	1	TRUE	2	0.467156308496608	4		450	1308	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951053	48951053	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs587778831	NA	P-0011355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	115	230	0	ENST00000267163.4:c.1216-1G>A		p.X406_splice	ENST00000267163	NM_000321.2	406			0.467156308496608	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.467156308496608	1		230	348	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206722	36206722	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	208	305	0	ENST00000300305.3:c.790C>T	p.Gln264Ter	p.Q264*	ENST00000300305		264	Cag/Tag	6/8	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.467156308496608	2		305	741	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615698	1615698	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145878545	NA	P-0011355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	304	778	1	ENST00000344749.5:c.1573C>T	p.Arg525Trp	p.R525W	ENST00000344749	NM_001136139.2	525	Cgg/Tgg	17/19	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.467156308496608	2		779	1216	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793098	33793098	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	82	339	0	ENST00000498907.2:c.223G>A	p.Asp75Asn	p.D75N	ENST00000498907	NM_004364.3	75	Gac/Aac	1/1	0.243650826594526	3	FACETS	0.576	0.507	0.65	0.288	0.253	0.325	INDETERMINATE	1	TRUE	1	0.467156308496608	3		339	752	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027263	48027263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881796	NA	P-0011355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	68	314	0	ENST00000234420.5:c.2141C>T	p.Ser714Phe	p.S714F	ENST00000234420	NM_000179.2	714	tCt/tTt	4/10	1	2	FACETS	0.482	0.419	0.55	0.482	0.419	0.55	SUBCLONAL	1	TRUE	1	0.467156308496608	2		314	604	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103803	47103803	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	115	531	0	ENST00000409792.3:c.6143G>C	p.Arg2048Thr	p.R2048T	ENST00000409792	NM_014159.6	2048	aGa/aCa	14/21	0.460715443358427	2	FACETS	0.436	0.391	0.483	0.218	0.195	0.242	SUBCLONAL	1	TRUE	0	0.467156308496608	2		531	1130	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180845	106180845	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	83	323	0	ENST00000380013.4:c.3873G>C	p.Trp1291Cys	p.W1291C	ENST00000380013	NM_001127208.2	1291	tgG/tgC	7/11	0.243650826594526	3	FACETS	0.518	0.456	0.584	0.259	0.228	0.292	INDETERMINATE	1	TRUE	1	0.467156308496608	3		323	847	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525019	187525019	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs768202106	NA	P-0011355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	119	340	0	ENST00000441802.2:c.10661C>A	p.Ser3554Tyr	p.S3554Y	ENST00000441802	NM_005245.3	3554	tCt/tAt	19/27	0.243650826594526	3	FACETS	0.888	0.802	0.978	0.444	0.401	0.489	INDETERMINATE	1	TRUE	1	0.467156308496608	3		340	708	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264696	1264696	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532158398	NA	P-0011355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	74	471	0	ENST00000310581.5:c.2666G>A	p.Arg889Gln	p.R889Q	ENST00000310581	NM_198253.2	889	cGa/cAa	11/16	0.21983871791176	4	FACETS	0.5	0.436	0.569	0.25	0.218	0.285	INDETERMINATE	1	TRUE	2	0.467156308496608	4		471	930	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055966	180055966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	72	468	0	ENST00000261937.6:c.1019G>A	p.Gly340Glu	p.G340E	ENST00000261937	NM_182925.4	340	gGa/gAa	8/30	0.21983871791176	4	FACETS	0.434	0.378	0.496	0.217	0.189	0.248	INDETERMINATE	1	TRUE	2	0.467156308496608	4		468	1041	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983998	2983998	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	125	630	0	ENST00000396946.4:c.532G>C	p.Glu178Gln	p.E178Q	ENST00000396946	NM_032415.4	178	Gag/Cag	5/25	0.243650826594526	3	FACETS	0.57	0.514	0.628	0.285	0.257	0.314	INDETERMINATE	1	TRUE	1	0.467156308496608	3		630	1159	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522607	106522607	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	220	432	0	ENST00000359195.3:c.2584C>G	p.Leu862Val	p.L862V	ENST00000359195	NM_002649.2	862	Cta/Gta	7/11	0.262100359721145	1	FACETS	1	0.968	1	1	0.968	1	INDETERMINATE	1	TRUE	0	0.467156308496608	1		432	682	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209376	98209376	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	59	340	0	ENST00000331920.6:c.4162G>C	p.Gly1388Arg	p.G1388R	ENST00000331920	NM_000264.3	1388	Ggg/Cgg	23/24	0.21983871791176	4	FACETS	0.454	0.39	0.525	0.227	0.195	0.263	INDETERMINATE	1	TRUE	2	0.467156308496608	4		340	816	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332161	70332161	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	86	514	0	ENST00000373644.4:c.66G>C	p.Lys22Asn	p.K22N	ENST00000373644	NM_030625.2	22	aaG/aaC	2/12	0.436809500654076	4	FACETS	0.417	0.368	0.471	0.209	0.184	0.236	SUBCLONAL	1	TRUE	2	0.467156308496608	4		514	1294	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406506	70406506	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	224	409	1	ENST00000373644.4:c.4020C>G	p.Ile1340Met	p.I1340M	ENST00000373644	NM_030625.2	1340	atC/atG	4/12	0.436809500654076	4	FACETS	1	0.988	1	0.641	0.597	0.688	CLONAL	1	TRUE	2	0.467156308496608	4		410	1097	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352582	118352582	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	112	476	0	ENST00000534358.1:c.3787C>G	p.Pro1263Ala	p.P1263A	ENST00000534358	NM_005933.3	1263	Cca/Gca	7/36	NA	2	FACETS	0.45	0.403	0.499			1	INDETERMINATE	1	TRUE	NA	0.467156308496608	2		476	1066	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373884	118373884	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	80	347	0	ENST00000534358.1:c.7277G>C	p.Arg2426Thr	p.R2426T	ENST00000534358	NM_005933.3	2426	aGa/aCa	27/36	NA	2	FACETS	0.393	0.345	0.444			1	INDETERMINATE	1	TRUE	NA	0.467156308496608	2		347	872	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536692	120536692	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	255	649	1	ENST00000229340.5:c.400G>A	p.Asp134Asn	p.D134N	ENST00000229340	NM_006861.6	134	Gat/Aat	5/6	0.243650826594526	3	FACETS	1	0.981	1	0.561	0.525	0.599	INDETERMINATE	1	TRUE	1	0.467156308496608	3		650	1200	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120554439	120554439	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1297092381	NA	P-0011355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	22	156	0	ENST00000229340.5:c.16G>C	p.Asp6His	p.D6H	ENST00000229340	NM_006861.6	6	Gac/Cac	1/6	0.243650826594526	3	FACETS	0.363	0.281	0.458	0.182	0.14	0.229	INDETERMINATE	1	TRUE	1	0.467156308496608	3		156	320	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42057198	42057198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	66	601	0	ENST00000219905.7:c.7859C>T	p.Ser2620Phe	p.S2620F	ENST00000219905	NM_001164273.1	2620	tCt/tTt	23/24	0.467156308496608	1	FACETS	0.229	0.198	0.263	0.229	0.198	0.263	SUBCLONAL	1	TRUE	0	0.467156308496608	1		601	945	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942864	15942864	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	294	478	0	ENST00000268712.3:c.6838G>C	p.Glu2280Gln	p.E2280Q	ENST00000268712	NM_006311.3	2280	Gag/Cag	44/46	0.21983871791176	4	FACETS	0.819	0.77	0.868	0.819	0.77	0.868	INDETERMINATE	2	TRUE	2	0.467156308496608	4		478	1128	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527439	29527439	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs587781517	NA	P-0011355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	59	220	0	ENST00000356175.3:c.889-1G>C		p.X297_splice	ENST00000356175	NM_000267.3	297			0.412811401826171	2	FACETS	0.589	0.508	0.676	0.294	0.254	0.338	SUBCLONAL	1	TRUE	0	0.467156308496608	2		220	429	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40498688	40498688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	432	578	1	ENST00000264657.5:c.172C>T	p.His58Tyr	p.H58Y	ENST00000264657	NM_139276.2	58	Cat/Tat	3/24	0.468049807722766	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.467156308496608	1		579	1064	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961471	54961471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	31	219	0	ENST00000312783.6:c.161C>T	p.Ser54Phe	p.S54F	ENST00000312783	NM_198436.1	54	tCc/tTc	4/10	0.243650826594526	3	FACETS	0.348	0.281	0.424	0.174	0.14	0.212	INDETERMINATE	1	TRUE	1	0.467156308496608	3		219	471	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352286	70352286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	74	617	0	ENST00000374080.3:c.4313C>T	p.Ser1438Leu	p.S1438L	ENST00000374080		1438	tCa/tTa	31/45	0.468049807722766	1	FACETS	0.278	0.243	0.316	0.278	0.243	0.316	SUBCLONAL	1	TRUE	0	0.467156308496608	1		617	873	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573996	7573996	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121912662	NA	P-0011364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	86	787	0	ENST00000269305.4:c.1031T>C	p.Leu344Pro	p.L344P	ENST00000269305	NM_001126112.2	344	cTg/cCg	10/11	0.144156043174798	2	FACETS	0.771	0.686	0.861	0.771	0.686	0.861	INDETERMINATE	2	FALSE	0	0.274657990084607	2		787	406	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011399-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1304	64	594	0	ENST00000347630.2:c.399C>A	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttA	6/11	1	2	FACETS	0.668	0.576	0.769	0.668	0.576	0.769	SUBCLONAL	1	TRUE	1	0.14	2		594	1368	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247244	153247244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	117	412	0	ENST00000281708.4:c.1558G>A	p.Asp520Asn	p.D520N	ENST00000281708	NM_033632.3	520	Gat/Aat	10/12	1	2	FACETS	0.963	0.868	1	1	0.988	1	CLONAL	2	TRUE	1	0.14	2		412	868	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411279	63411279	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	41	230	0	ENST00000330258.3:c.1888G>T	p.Ala630Ser	p.A630S	ENST00000330258	NM_152424.3	630	Gcc/Tcc	2/2	1	1	FACETS	0.811	0.677	0.958	1	0.961	1	CLONAL	2	TRUE	0	0.14	1		230	336	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20153903	20153903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	31	128	0	ENST00000379607.5:c.157G>A	p.Asp53Asn	p.D53N	ENST00000379607	NM_001412.3	53	Gat/Aat	3/7	1	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.14	1		128	299	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568857	212568857	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	118	355	0	ENST00000342788.4:c.1261G>T	p.Val421Leu	p.V421L	ENST00000342788	NM_005235.2	421	Gtg/Ttg	11/28	1	2	FACETS	0.918	0.827	1	1	0.988	1	CLONAL	2	TRUE	1	0.14	2		355	918	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652816	212652816	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	108	439	0	ENST00000342788.4:c.490C>A	p.Gln164Lys	p.Q164K	ENST00000342788	NM_005235.2	164	Caa/Aaa	4/28	1	2	FACETS	0.822	0.737	0.913	1	0.985	1	CLONAL	2	TRUE	1	0.14	2		439	938	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532783	187532783	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	86	408	0	ENST00000441802.2:c.9610C>T	p.Gln3204Ter	p.Q3204*	ENST00000441802	NM_005245.3	3204	Caa/Taa	14/27	1	2	FACETS	0.835	0.738	0.938	1	0.981	1	CLONAL	2	TRUE	1	0.14	2		408	736	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564809	86564809	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0011402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	103	493	0	ENST00000274376.6:c.539+2T>G		p.X180_splice	ENST00000274376	NM_002890.2	180			1	2	FACETS	0.814	0.727	0.906	1	0.984	1	CLONAL	2	TRUE	1	0.14	2		493	904	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499666	149499666	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	82	370	0	ENST00000261799.4:c.2607G>C	p.Trp869Cys	p.W869C	ENST00000261799	NM_002609.3	869	tgG/tgC	19/23	1	2	FACETS	0.908	0.801	1	1	0.982	1	CLONAL	2	TRUE	1	0.14	2		370	645	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133731	41133731	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	110	516	0	ENST00000379561.5:c.1897G>C	p.Asp633His	p.D633H	ENST00000379561	NM_002015.3	633	Gac/Cac	2/3	1	2	FACETS	0.799	0.717	0.887	1	0.984	1	SUBCLONAL	2	TRUE	1	0.14	2		516	983	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031707	36031707	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	59	418	0	ENST00000358208.4:c.1536C>G	p.Phe512Leu	p.F512L	ENST00000358208		512	ttC/ttG	12/12	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.14	2		418	571	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692849	89692849	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554898097	NA	P-0011404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	20	66	0	ENST00000371953.3:c.333G>A	p.Trp111Ter	p.W111*	ENST00000371953	NM_000314.4	111	tgG/tgA	5/9	0.955108112506239	1	FACETS	0.199	0.154	0.25	0.199	0.154	0.25	SUBCLONAL	1	TRUE	0	0.955108112506239	1		66	110	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	563	247	0	ENST00000269305.4:c.542G>C	p.Arg181Pro	p.R181P	ENST00000269305	NM_001126112.2	181	cGc/cCc	5/11	NA	2	FACETS	0.999	0.987	1			1	INDETERMINATE	2	TRUE	NA	0.955108112506239	2		247	590	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606697	29606697	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779282861	NA	P-0011404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	387	319	0	ENST00000389048.3:c.1183C>T	p.Arg395Cys	p.R395C	ENST00000389048	NM_004304.4	395	Cgt/Tgt	5/29	1	2	FACETS	0.942	0.9	0.985	0.942	0.9	0.985	CLONAL	1	TRUE	1	0.955108112506239	2		319	860	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851892	134851892	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0011404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	320	275	0	ENST00000398015.3:c.1297+1G>A		p.X433_splice	ENST00000398015	NM_004441.4	433			0.955108112506239	3	FACETS	0.946	0.894	0.999	0.473	0.447	0.5	CLONAL	1	TRUE	1	0.955108112506239	3		275	1047	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397214	397214	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	444	372	0	ENST00000380956.4:c.599C>A	p.Pro200His	p.P200H	ENST00000380956	NM_001195286.1	200	cCc/cAc	5/9	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.955108112506239	2		372	923	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520022	106520022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	365	301	1	ENST00000359195.3:c.2450G>A	p.Cys817Tyr	p.C817Y	ENST00000359195	NM_002649.2	817	tGt/tAt	6/11	0.151217581599556	3	FACETS	1	0.992	1	0.6	0.571	0.63	INDETERMINATE	1	TRUE	1	0.955108112506239	3		302	941	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341847	8341847	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	414	420	0	ENST00000356435.5:c.4793C>G	p.Thr1598Arg	p.T1598R	ENST00000356435		1598	aCa/aGa	29/35	1	2	FACETS	0.864	0.826	0.903	0.864	0.826	0.903	CLONAL	1	TRUE	1	0.955108112506239	2		420	1003	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955394	48955394	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886043247	NA	P-0011404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	124	120	0	ENST00000267163.4:c.1510C>T	p.Gln504Ter	p.Q504*	ENST00000267163	NM_000321.2	504	Cag/Tag	17/27	0.955108112506239	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.955108112506239	1		120	134	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786770	3786770	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	417	456	0	ENST00000262367.5:c.4441G>A	p.Asp1481Asn	p.D1481N	ENST00000262367	NM_004380.2	1481	Gat/Aat	27/31	1	2	FACETS	0.952	0.911	0.993	0.952	0.911	0.993	CLONAL	1	TRUE	1	0.955108112506239	2		456	917	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0011420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	479	239	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.377306491425911	6	FACETS	0.999	0.967	1	0.832	0.806	0.858	CLONAL	5	TRUE	0	0.584179235090724	6		239	712	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952142	178952142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253171657	NA	P-0011420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	682	343	1	ENST00000263967.3:c.3197C>T	p.Ala1066Val	p.A1066V	ENST00000263967	NM_006218.2	1066	gCa/gTa	21/21	0.377306491425911	6	FACETS	0.987	0.96	1	0.822	0.8	0.844	CLONAL	5	TRUE	0	0.584179235090724	6		344	1026	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346836	91346836	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	135	584	0	ENST00000355112.3:c.3444G>T	p.Lys1148Asn	p.K1148N	ENST00000355112	NM_000057.2	1148	aaG/aaT	18/22	1	2	FACETS	0.448	0.407	0.492	0.448	0.407	0.492	SUBCLONAL	1	TRUE	1	0.584179235090724	2		584	1031	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016625	12016625	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	486	476	0	ENST00000353533.5:c.761T>G	p.Leu254Arg	p.L254R	ENST00000353533	NM_003010.3	254	cTt/cGt	7/11	0.584179235090724	2	FACETS	0.999	0.964	1	0.999	0.964	1	CLONAL	2	TRUE	0	0.584179235090724	2		476	833	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0011427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	90	420	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.992	0.878	1	0.992	0.878	1	CLONAL	1	TRUE	1	0.16	2		420	1134	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604778	48604778	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767383	NA	P-0011427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	101	553	0	ENST00000342988.3:c.1600C>T	p.Gln534Ter	p.Q534*	ENST00000342988	NM_005359.5	534	Cag/Tag	12/12	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.16	2		553	1157	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438067	49438067	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886043414	NA	P-0011427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	82	582	2	ENST00000301067.7:c.5104C>T	p.Arg1702Ter	p.R1702*	ENST00000301067	NM_003482.3	1702	Cga/Tga	21/54	1	2	FACETS	0.876	0.77	0.991	0.876	0.77	0.991	CLONAL	1	TRUE	1	0.16	2		584	1170	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0011445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	140	525	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.825	0.751	0.902	0.825	0.751	0.902	CLONAL	1	TRUE	1	0.385779205641093	2		526	880	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457303	67457303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768713596	NA	P-0011445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	173	615	1	ENST00000327367.4:c.277C>T	p.Arg93Ter	p.R93*	ENST00000327367	NM_005902.3	93	Cga/Tga	2/9	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.385779205641093	2		616	842	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406658	70406658	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	129	648	0	ENST00000373644.4:c.4172C>G	p.Ala1391Gly	p.A1391G	ENST00000373644	NM_030625.2	1391	gCa/gGa	4/12	1	2	FACETS	0.697	0.631	0.766	0.697	0.631	0.766	SUBCLONAL	1	TRUE	1	0.385779205641093	2		648	960	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592293	29592293	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	62	648	0	ENST00000356175.3:c.4708A>C	p.Ser1570Arg	p.S1570R	ENST00000356175	NM_000267.3	1570	Agt/Cgt	35/57	1	2	FACETS	0.311	0.268	0.359	0.311	0.268	0.359	SUBCLONAL	1	TRUE	1	0.385779205641093	2		648	1033	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395636	45395636	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	167	570	0	ENST00000262160.6:c.498C>G	p.His166Gln	p.H166Q	ENST00000262160	NM_005901.5	166	caC/caG	4/11	0.264021672696819	1	FACETS	0.795	0.731	0.862	0.795	0.731	0.862	SUBCLONAL	1	TRUE	0	0.385779205641093	1		570	879	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720806	89720806	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167682	NA	P-0011445-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	43	168	0	ENST00000371953.3:c.959del	p.Leu320Ter	p.L320*	ENST00000371953	NM_000314.4	319	acT/ac	8/9	0.270882331820792	1	FACETS	0.714	0.602	0.836	0.714	0.602	0.836	SUBCLONAL	1	TRUE	0	0.385779205641093	1		168	252	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	272	420	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.165723391380874	3	FACETS	0.981	0.923	1	1	0.993	1	CLONAL	3	TRUE	1	0.24	3		420	863	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	526	559	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.977	0.949	1	1	0.998	1	CLONAL	6	TRUE	1	0.24	2		559	748	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	401	911	0	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	0.915	0.87	0.959	1	0.997	1	CLONAL	3	TRUE	1	0.24	2		911	1218	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	217	342	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.3	1	FACETS	1	0.985	1	1	0.995	1	CLONAL	2	TRUE	0	0.24	1		342	674	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	211	748	0	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	1	0.97	1	1	0.994	1	CLONAL	2	TRUE	1	0.24	2		748	817	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	69	884	0	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	0.849	0.739	0.968	0.849	0.739	0.968	CLONAL	1	TRUE	1	0.24	2		884	677	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652411	206652411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781909564	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	280	711	0	ENST00000367120.3:c.1118C>T	p.Thr373Met	p.T373M	ENST00000367120	NM_014002.3	373	aCg/aTg	10/22	1	2	FACETS	1	0.972	1	1	0.996	1	CLONAL	3	TRUE	1	0.24	2		711	744	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	334	1061	11	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.3	1	FACETS	1	0.991	1	1	0.996	1	CLONAL	2	TRUE	0	0.24	1		1072	1001	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	309	622	2	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.962	0.926	0.998	1	0.997	1	CLONAL	6	TRUE	1	0.24	2		624	446	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149799	202149799	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	290	674	0	ENST00000358485.4:c.1245del	p.Phe415LeufsTer26	p.F415Lfs*26	ENST00000358485	NM_001080125.1	414	Ttt/tt	8/9	1	2	FACETS	0.952	0.899	1	1	0.996	1	CLONAL	3	TRUE	1	0.24	2		674	846	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279527	1279527	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767382450	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	151	673	0	ENST00000310581.5:c.2009C>T	p.Ala670Val	p.A670V	ENST00000310581	NM_198253.2	670	gCg/gTg	5/16	0.3	1	FACETS	1	0.983	1	1	0.993	1	CLONAL	2	TRUE	0	0.24	1		673	443	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280062	66280062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	279	704	0	ENST00000273854.3:c.1627C>T	p.Arg543Cys	p.R543C	ENST00000273854	NM_004439.5	543	Cgt/Tgt	7/18	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.24	2		704	967	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922141	39922141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1393432690	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	381	1354	1	ENST00000378444.4:c.4031C>T	p.Ala1344Val	p.A1344V	ENST00000378444	NM_001123385.1	1344	gCc/gTc	9/15	0.3	1	FACETS	1	0.993	1	1	0.997	1	CLONAL	2	TRUE	0	0.24	1		1355	1136	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366722	40366722	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	75	362	0	ENST00000397332.2:c.475C>G	p.Pro159Ala	p.P159A	ENST00000397332	NM_001033082.2	159	Ccg/Gcg	2/3	1	2	FACETS	1	0.953	1	1	0.985	1	CLONAL	2	TRUE	1	0.24	2		362	273	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65312344	65312344	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	283	686	2	ENST00000342505.4:c.1975C>A	p.Arg659Ser	p.R659S	ENST00000342505	NM_002227.2	659	Cgc/Agc	14/25	1	2	FACETS	0.977	0.921	1	1	0.996	1	CLONAL	3	TRUE	1	0.24	2		688	805	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590764	189590764	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	351	784	0	ENST00000264731.3:c.1329C>G	p.His443Gln	p.H443Q	ENST00000264731	NM_003722.4	443	caC/caG	10/14	1	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	1	0.24	2		784	1182	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133508	55133508	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	56	841	0	ENST00000257290.5:c.812T>C	p.Leu271Ser	p.L271S	ENST00000257290	NM_006206.4	271	tTg/tCg	6/23	1	2	FACETS	0.527	0.45	0.612	0.527	0.45	0.612	SUBCLONAL	1	TRUE	1	0.24	2		841	885	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502163	157502163	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554231195	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	229	453	0	ENST00000346085.5:c.3196G>T	p.Glu1066Ter	p.E1066*	ENST00000346085	NM_020732.3	1066	Gag/Tag	12/20	1	2	FACETS	1	0.969	1	1	0.996	1	CLONAL	3	TRUE	1	0.24	2		453	605	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370732	55370732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	113	352	0	ENST00000297316.4:c.34G>A	p.Asp12Asn	p.D12N	ENST00000297316	NM_022454.3	12	Gac/Aac	1/2	1	2	FACETS	0.948	0.864	1	1	0.991	1	CLONAL	3	TRUE	1	0.24	2		352	331	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753823	133753823	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	346	986	0	ENST00000318560.5:c.1292A>G	p.Glu431Gly	p.E431G	ENST00000318560	NM_005157.4	431	gAa/gGa	8/11	1	2	FACETS	1	0.981	1	1	0.997	1	CLONAL	3	TRUE	1	0.24	2		986	902	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405201	139405201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767886377	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	207	790	1	ENST00000277541.6:c.2644G>A	p.Ala882Thr	p.A882T	ENST00000277541	NM_017617.3	882	Gca/Aca	17/34	1	2	FACETS	0.941	0.879	1	1	0.995	1	CLONAL	3	TRUE	1	0.24	2		791	611	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466018	69466018	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	207	762	0	ENST00000227507.2:c.856A>G	p.Thr286Ala	p.T286A	ENST00000227507	NM_053056.2	286	Aca/Gca	5/5	1	2	FACETS	0.965	0.901	1	1	0.995	1	CLONAL	3	TRUE	1	0.24	2		762	596	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235935	108235935	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770641163	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	91	574	1	ENST00000278616.4:c.8977C>T	p.Arg2993Ter	p.R2993*	ENST00000278616	NM_000051.3	2993	Cga/Tga	62/63	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.24	2		575	622	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390432	118390432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781945281	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	346	936	0	ENST00000534358.1:c.11246G>A	p.Arg3749His	p.R3749H	ENST00000534358	NM_005933.3	3749	cGt/cAt	32/36	1	2	FACETS	0.973	0.923	1	1	0.997	1	CLONAL	3	TRUE	1	0.24	2		936	988	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26974623	26974623	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	78	786	0	ENST00000381527.3:c.967C>T	p.Arg323Ter	p.R323*	ENST00000381527	NM_001260.1	323	Cga/Tga	10/13	1	2	FACETS	0.721	0.632	0.816	0.721	0.632	0.816	SUBCLONAL	1	TRUE	1	0.24	2		786	902	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435804	110435804	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	34	117	0	ENST00000375856.3:c.2597T>C	p.Val866Ala	p.V866A	ENST00000375856	NM_003749.2	866	gTg/gCg	1/2	1	2	FACETS	1	0.852	1	1	0.966	1	CLONAL	2	TRUE	1	0.24	2		117	138	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060689	38060689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	456	1196	1	ENST00000250448.2:c.1300C>T	p.Pro434Ser	p.P434S	ENST00000250448	NM_004496.3	434	Ccc/Tcc	2/2	1	2	FACETS	1	0.99	1	1	0.998	1	CLONAL	3	TRUE	1	0.24	2		1197	1136	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456431	99456431	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	223	640	0	ENST00000268035.6:c.1748C>A	p.Ala583Asp	p.A583D	ENST00000268035	NM_000875.3	583	gCt/gAt	8/21	1	2	FACETS	0.842	0.786	0.898	1	0.995	1	CLONAL	3	TRUE	1	0.24	2		640	736	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348157	348157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1400432084	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	42	550	0	ENST00000262320.3:c.1349G>A	p.Arg450His	p.R450H	ENST00000262320	NM_003502.3	450	cGc/cAc	6/11	1	2	FACETS	0.797	0.666	0.943	0.797	0.666	0.943	CLONAL	1	TRUE	1	0.24	2		550	439	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663406	67663406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775874494	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	365	803	1	ENST00000264010.4:c.1807C>T	p.Arg603Cys	p.R603C	ENST00000264010	NM_006565.3	603	Cgc/Tgc	10/12	1	2	FACETS	0.968	0.92	1	1	0.997	1	CLONAL	3	TRUE	1	0.24	2		804	1047	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740809	58740809	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs765769406	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	531	1330	1	ENST00000305921.3:c.1714C>T	p.Arg572Ter	p.R572*	ENST00000305921	NM_003620.3	572	Cga/Tga	6/6	1	2	FACETS	0.983	0.942	1	1	0.998	1	CLONAL	3	TRUE	1	0.24	2		1331	1501	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681704	78681704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	239	789	2	ENST00000306801.3:c.412C>T	p.Arg138Cys	p.R138C	ENST00000306801	NM_020761.2	138	Cgt/Tgt	4/34	1	2	FACETS	0.978	0.918	1	1	0.996	1	CLONAL	3	TRUE	1	0.24	2		791	679	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222796	5222796	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756049037	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	72	305	0	ENST00000357368.4:c.3007G>A	p.Asp1003Asn	p.D1003N	ENST00000357368	NM_002850.3	1003	Gac/Aac	18/38	1	2	FACETS	1	0.954	1	1	0.988	1	CLONAL	3	TRUE	1	0.24	2		305	177	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909464	50909464	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199576140	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	83	1249	5	ENST00000440232.2:c.1268G>A	p.Arg423His	p.R423H	ENST00000440232	NM_002691.3	423	cGt/cAt	11/27	1	2	FACETS	0.683	0.602	0.772	0.683	0.602	0.772	SUBCLONAL	1	TRUE	1	0.24	2		1254	1012	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424679	47424679	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775921012	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	300	1347	0	ENST00000377045.4:c.487G>A	p.Gly163Arg	p.G163R	ENST00000377045	NM_001654.4	163	Gga/Aga	6/16	0.3	1	FACETS	0.911	0.857	0.965	1	0.995	1	CLONAL	2	TRUE	0	0.24	1		1347	1208	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224537	53224537	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	330	1214	5	ENST00000375401.3:c.3176G>A	p.Arg1059Gln	p.R1059Q	ENST00000375401	NM_004187.3	1059	cGg/cAg	21/26	0.3	1	FACETS	0.898	0.852	0.945	1	0.997	1	CLONAL	3	TRUE	0	0.24	1		1219	898	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875889	76875889	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	89	1209	0	ENST00000373344.5:c.5246C>T	p.Thr1749Ile	p.T1749I	ENST00000373344	NM_000489.3	1749	aCa/aTa	20/35	0.3	1	FACETS	0.564	0.498	0.634	0.564	0.498	0.634	SUBCLONAL	1	TRUE	0	0.24	1		1209	1158	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541434	187541435	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	255	781	0	ENST00000441802.2:c.6305_6306del	p.Tyr2102CysfsTer23	p.Y2102Cfs*23	ENST00000441802	NM_005245.3	2102	tAT/t	10/27	1	2	FACETS	0.926	0.87	0.983	1	0.996	1	CLONAL	3	TRUE	1	0.24	2		781	765	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798860	135798862	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	rs118203378	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	116	379	0	ENST00000298552.3:c.381_383del	p.Val128del	p.V128del	ENST00000298552	NM_001162426.1	127	gtTGTc/gtc	6/23	1	2	FACETS	1	0.966	1	1	0.99	1	CLONAL	2	TRUE	1	0.24	2		379	425	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731503	47731503	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	46	87	1	ENST00000449228.1:c.289del	p.His97ThrfsTer132	p.H97Tfs*132	ENST00000449228	NM_001127240.2	97	Cac/ac	2/4	1	2	FACETS	0.841	0.722	0.966	1	0.978	1	CLONAL	3	TRUE	1	0.24	2		88	152	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905061	50905061	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	55	979	0	ENST00000440232.2:c.347del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	115	Ccc/cc	4/27	1	2	FACETS	0.571	0.487	0.663	0.571	0.487	0.663	SUBCLONAL	1	TRUE	1	0.24	2		979	803	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0011483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	295	293	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	1	2	FACETS	0.97	0.912	1	0.97	0.912	1	CLONAL	1	TRUE	1	0.475288802034893	2		293	1280	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936107	178936107	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	124	254	1	ENST00000263967.3:c.1649T>A	p.Phe550Tyr	p.F550Y	ENST00000263967	NM_006218.2	550	tTt/tAt	10/21	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.475288802034893	2		255	482	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007633	45007633	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	143	324	0	ENST00000558401.1:c.80T>C	p.Ile27Thr	p.I27T	ENST00000558401	NM_004048.2	27	aTt/aCt	2/4	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.475288802034893	2		324	577	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265506	46265506	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	278	664	0	ENST00000371998.3:c.2376+1del		p.E792fs	ENST00000371998		792	gaG/ga	12/23	1	2	FACETS	0.929	0.872	0.988	0.929	0.872	0.988	CLONAL	1	TRUE	1	0.475288802034893	2		664	1259	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0011510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	66	195	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.31	2		195	409	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0011510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	77	303	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.834	0.732	0.942	0.834	0.732	0.942	CLONAL	1	TRUE	1	0.31	2		303	596	SUCCESS
APC	324	MSKCC	GRCh37	5	112175411	112175411	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	100	323	0	ENST00000257430.4:c.4120G>T	p.Glu1374Ter	p.E1374*	ENST00000257430	NM_000038.5	1374	Gaa/Taa	16/16	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.31	2		323	615	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371409680	NA	P-0011510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	141	584	0	ENST00000269305.4:c.848G>C	p.Arg283Pro	p.R283P	ENST00000269305	NM_001126112.2	283	cGc/cCc	8/11	0.301991294507156	1	FACETS	0.897	0.817	0.981	0.897	0.817	0.981	CLONAL	1	TRUE	0	0.31	1		584	857	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs770248150	NA	P-0011510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	318	370	0	ENST00000311936.3:c.351A>T	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaT	4/5	0.301991294507156	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.31	3		370	1109	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164680	36164684	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCT	TGGCT	-	novel	NA	P-0011510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	136	527	0	ENST00000300305.3:c.1191_1195del	p.Ala398LeufsTer200	p.A398Lfs*200	ENST00000300305		397	caAGCCAgc/cagc	8/8	1	2	FACETS	0.943	0.857	1	0.943	0.857	1	CLONAL	1	TRUE	1	0.31	2		527	930	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0011512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	375	612	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.450462423074097	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.451056277548768	2		613	808	SUCCESS
APC	324	MSKCC	GRCh37	5	112175328	112175348	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	CAGCCAGGCACAAAGCTGTTG	CAGCCAGGCACAAAGCTGTTG	-	novel	NA	P-0011512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	186	262	0	ENST00000257430.4:c.4037_4057del	p.Ser1346_Glu1353delinsTer	p.S1346_E1353delins*	ENST00000257430	NM_000038.5	1346	tCAGCCAGGCACAAAGCTGTTGaa/taa	16/16	0.450462423074097	2	FACETS	0.9	0.84	0.961	0.9	0.84	0.961	CLONAL	2	TRUE	0	0.451056277548768	2		262	458	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0011517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	70	693	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.992	0.862	1	0.992	0.862	1	CLONAL	1	TRUE	1	0.13	2		693	1086	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0011517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	65	848	1	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	1	2	FACETS	0.786	0.679	0.904	0.786	0.679	0.904	CLONAL	1	TRUE	1	0.13	2		849	1272	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604754	48604754	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	64	786	0	ENST00000342988.3:c.1576G>C	p.Glu526Gln	p.E526Q	ENST00000342988	NM_005359.5	526	Gaa/Caa	12/12	1	2	FACETS	0.889	0.767	1	0.889	0.767	1	CLONAL	1	TRUE	1	0.13	2		786	1108	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239326	105239326	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	67	797	0	ENST00000349310.3:c.1061A>T	p.His354Leu	p.H354L	ENST00000349310	NM_001014432.1	354	cAt/cTt	12/15	1	2	FACETS	0.853	0.739	0.978	0.853	0.739	0.978	CLONAL	1	TRUE	1	0.13	2		797	1208	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357089	89357089	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1442	101	932	0	ENST00000301030.4:c.545G>T	p.Arg182Leu	p.R182L	ENST00000301030	NM_001256183.1	182	cGg/cTg	6/13	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.13	2		932	1543	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541604	29541604	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1060500331	NA	P-0011517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	20	306	0	ENST00000356175.3:c.1527+1G>A		p.X509_splice	ENST00000356175	NM_000267.3	509			1	2	FACETS	0.855	0.653	1	0.855	0.653	1	CLONAL	1	TRUE	1	0.13	2		306	360	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435917	56435917	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	39	543	0	ENST00000407977.2:c.1220G>C	p.Gly407Ala	p.G407A	ENST00000407977		407	gGa/gCa	9/10	1	2	FACETS	0.823	0.68	0.983	0.823	0.68	0.983	CLONAL	1	TRUE	1	0.13	2		543	729	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436000	56436000	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	29	434	2	ENST00000407977.2:c.1137G>C	p.Gln379His	p.Q379H	ENST00000407977		379	caG/caC	9/10	1	2	FACETS	0.814	0.652	1	0.814	0.652	1	CLONAL	1	TRUE	1	0.13	2		436	548	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028790	47028790	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1289	79	942	2	ENST00000377604.3:c.94C>T	p.Arg32Ter	p.R32*	ENST00000377604	NM_001204468.1	32	Cga/Tga	3/24	1	2	FACETS	0.888	0.778	1	0.888	0.778	1	CLONAL	1	TRUE	1	0.13	2		944	1368	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256382	16256382	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	244	704	0	ENST00000375759.3:c.3647A>C	p.Gln1216Pro	p.Q1216P	ENST00000375759	NM_015001.2	1216	cAa/cCa	11/15	0.652038337347159	3	FACETS	1	0.977	1	0.545	0.51	0.581	CLONAL	1	TRUE	1	0.652038337347159	3		704	910	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78426102	78426102	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	105	629	0	ENST00000370768.2:c.1423C>G	p.Pro475Ala	p.P475A	ENST00000370768	NM_003902.3	475	Cca/Gca	15/20	0.652038337347159	5	FACETS	0.519	0.464	0.579			1	SUBCLONAL	1	TRUE	NA	0.652038337347159	5		629	1227	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190554	32190554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	174	565	1	ENST00000375023.3:c.185G>A	p.Cys62Tyr	p.C62Y	ENST00000375023	NM_004557.3	62	tGc/tAc	3/30	0.568664717235355	3	FACETS	1	0.944	1			1	CLONAL	1	TRUE	NA	0.652038337347159	3		566	689	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855932	76855932	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	601	501	0	ENST00000373344.5:c.5668C>T	p.Gln1890Ter	p.Q1890*	ENST00000373344	NM_000489.3	1890	Cag/Tag	23/35	0.635932651065152	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.652038337347159	2		501	744	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0011535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	171	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.316975639976464	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.316975639976464	1		371	776	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121912666	NA	P-0011535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	213	386	0	ENST00000269305.4:c.659A>C	p.Tyr220Ser	p.Y220S	ENST00000269305	NM_001126112.2	220	tAt/tCt	6/11	0.316975639976464	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.316975639976464	1		386	1093	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045866	47045879	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CACACAGGCCCAAA	CACACAGGCCCAAA	-	novel	NA	P-0011535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	156	312	0	ENST00000377604.3:c.2668-4_2677del		p.X890_splice	ENST00000377604	NM_001204468.1	890		24/24	0.316975639976464	1	FACETS	0.998	0.915	1	0.998	0.915	1	CLONAL	1	TRUE	0	0.316975639976464	1		312	830	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584784	48584784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	476	519	8	ENST00000342988.3:c.862C>T	p.Leu288Phe	p.L288F	ENST00000342988	NM_005359.5	288	Ctt/Ttt	7/12	0.414016447023623	1	FACETS	0.694	0.669	0.718	0.694	0.669	0.718	INDETERMINATE	1	TRUE	0	0.915982507623977	1		527	812	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0011547-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	46	420	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.471	0.395	0.555	0.471	0.395	0.555	SUBCLONAL	1	TRUE	1	0.262960442769769	2		420	743	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6036984	6036984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011547-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	92	368	0	ENST00000265849.7:c.776G>A	p.Cys259Tyr	p.C259Y	ENST00000265849	NM_000535.5	259	tGt/tAt	7/15	1	2	FACETS	0.686	0.608	0.77	0.686	0.608	0.77	SUBCLONAL	1	TRUE	1	0.262960442769769	2		368	1020	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456675	32456675	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011547-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	16	131	0	ENST00000332351.3:c.217G>T	p.Val73Leu	p.V73L	ENST00000332351	NM_024426.4	73	Gtg/Ttg	1/10	1	2	FACETS	0.398	0.293	0.523	0.398	0.293	0.523	SUBCLONAL	1	TRUE	1	0.262960442769769	2		131	306	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098600	108098600	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011547-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	32	148	0	ENST00000278616.4:c.170G>T	p.Trp57Leu	p.W57L	ENST00000278616	NM_000051.3	57	tGg/tTg	3/63	1	2	FACETS	0.644	0.523	0.78	0.644	0.523	0.78	SUBCLONAL	1	TRUE	1	0.262960442769769	2		148	378	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66523985	66523985	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011547-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	33	233	0	ENST00000358598.2:c.713G>C	p.Ser238Thr	p.S238T	ENST00000358598	NM_212471.2	238	aGc/aCc	8/11	1	2	FACETS	0.397	0.322	0.481	0.397	0.322	0.481	SUBCLONAL	1	TRUE	1	0.262960442769769	2		233	633	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033390	48033390	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	208	413	0	ENST00000234420.5:c.3694G>T	p.Val1232Phe	p.V1232F	ENST00000234420	NM_000179.2	1232	Gtt/Ttt	8/10	0.529830614932047	3	FACETS	0.933	0.866	1	0.467	0.433	0.501	CLONAL	1	TRUE	1	0.585082349246522	3		413	985	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864384	57864384	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	74	541	0	ENST00000228682.2:c.1861A>G	p.Arg621Gly	p.R621G	ENST00000228682	NM_005269.2	621	Aga/Gga	12/12	0.529830614932047	3	FACETS	0.35	0.305	0.398	0.175	0.152	0.199	SUBCLONAL	1	TRUE	1	0.585082349246522	3		541	935	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0011556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	385	401	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.961	0.915	1	0.961	0.915	1	CLONAL	1	TRUE	1	0.771284242714987	2		401	1039	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508728	148508728	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs267601395	NA	P-0011556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	437	591	0	ENST00000320356.2:c.1936T>C	p.Tyr646His	p.Y646H	ENST00000320356	NM_004456.4	646	Tac/Cac	16/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.771284242714987	2		591	1070	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441334	52441334	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0011556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	416	561	0	ENST00000460680.1:c.438-2A>T		p.X146_splice	ENST00000460680	NM_004656.3	146			0.771284242714987	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.771284242714987	1		561	636	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716042	52716042	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs372716916	NA	P-0011556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	138	618	0	ENST00000322088.6:c.607A>T	p.Ser203Cys	p.S203C	ENST00000322088	NM_014225.5	203	Agt/Tgt	5/15	1	2	FACETS	0.297	0.269	0.327	0.297	0.269	0.327	SUBCLONAL	1	TRUE	1	0.771284242714987	2		618	1204	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595901	52595901	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	93	596	0	ENST00000394830.3:c.4014del	p.Ser1338ArgfsTer4	p.S1338Rfs*4	ENST00000394830	NM_018313.4	1338	agC/ag	26/30	0.472893213788385	1	FACETS	0.678	0.606	0.754	0.678	0.606	0.754	SUBCLONAL	1	TRUE	0	0.472893213788385	1		596	443	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47205333	47205352	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGATACTTACTCAGGGGTC	CTGATACTTACTCAGGGGTC	-	novel	NA	P-0011560-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	167	421	0	ENST00000409792.3:c.63_71+11del		p.X21_splice	ENST00000409792	NM_014159.6	21		1/21	0.472893213788385	1	FACETS	0.899	0.83	0.97	0.899	0.83	0.97	CLONAL	1	TRUE	0	0.472893213788385	1		421	600	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0011594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	404	345	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.29592099608001	7	FACETS	0.93	0.89	0.97	1	0.99	1	CLONAL	6	TRUE	2	0.29592099608001	7		345	851	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0011594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	149	320	0				ENST00000310581	NM_198253.2	-/1132			0.250467536431072	3	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	1	0.29592099608001	3		320	557	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519913	29519913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	142	232	0	ENST00000389048.3:c.1658C>T	p.Ser553Phe	p.S553F	ENST00000389048	NM_004304.4	553	tCc/tTc	9/29	0.244443489395472	4	FACETS	0.96	0.877	1	0.96	0.877	1	CLONAL	2	TRUE	2	0.29592099608001	4		232	648	SUCCESS
APC	324	MSKCC	GRCh37	5	112177901	112177901	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs752654519	NA	P-0011594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	121	189	0	ENST00000257430.4:c.6610C>T	p.Arg2204Ter	p.R2204*	ENST00000257430	NM_000038.5	2204	Cga/Tga	16/16	0.250467536431072	3	FACETS	0.901	0.818	0.988	0.901	0.818	0.988	CLONAL	2	TRUE	1	0.29592099608001	3		189	521	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459852	149459852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	135	149	0	ENST00000286301.3:c.355G>A	p.Glu119Lys	p.E119K	ENST00000286301	NM_005211.3	119	Gag/Aag	4/22	0.250467536431072	3	FACETS	0.939	0.857	1	0.939	0.857	1	CLONAL	2	TRUE	1	0.29592099608001	3		149	558	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289139	33289139	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	79	243	0	ENST00000374542.5:c.413C>T	p.Ser138Leu	p.S138L	ENST00000374542	NM_001141970.1	138	tCa/tTa	3/8	0.250467536431072	3	FACETS	0.947	0.833	1	0.474	0.416	0.535	CLONAL	1	TRUE	1	0.29592099608001	3		243	647	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729961	41729961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867739441	NA	P-0011594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	458	446	0	ENST00000242208.4:c.568G>A	p.Glu190Lys	p.E190K	ENST00000242208	NM_002192.2	190	Gaa/Aaa	3/3	0.29592099608001	5	FACETS	0.911	0.868	0.954	0.911	0.868	0.954	CLONAL	3	TRUE	2	0.29592099608001	5		446	1636	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444413	50444413	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	120	154	0	ENST00000331340.3:c.343G>A	p.Gly115Arg	p.G115R	ENST00000331340	NM_006060.4	115	Gga/Aga	4/8	0.29592099608001	5	FACETS	1	0.968	1	0.768	0.697	0.843	CLONAL	2	TRUE	2	0.29592099608001	5		154	508	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160350	108160350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1800058	NA	P-0011594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	71	105	0	ENST00000278616.4:c.4258C>T	p.Leu1420Phe	p.L1420F	ENST00000278616	NM_000051.3	1420	Ctt/Ttt	29/63	0.244443489395472	4	FACETS	0.948	0.834	1	0.948	0.834	1	CLONAL	2	TRUE	2	0.29592099608001	4		105	328	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861149	57861149	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774058977	NA	P-0011594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	171	397	0	ENST00000228682.2:c.946G>A	p.Glu316Lys	p.E316K	ENST00000228682	NM_005269.2	316	Gaa/Aaa	9/12	0.250467536431072	3	FACETS	1	0.955	1	0.531	0.487	0.577	CLONAL	1	TRUE	1	0.29592099608001	3		397	1250	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520192	9520192	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	182	307	0	ENST00000353224.5:c.2077G>A	p.Glu693Lys	p.E693K	ENST00000353224	NM_177990.2	693	Gaa/Aaa	10/10	0.244443489395472	4	FACETS	0.964	0.89	1	0.964	0.89	1	CLONAL	2	TRUE	2	0.29592099608001	4		307	827	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747086	40747086	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	165	262	0	ENST00000373198.4:c.2996C>T	p.Ser999Phe	p.S999F	ENST00000373198	NM_133170.3	999	tCc/tTc	22/32	0.244443489395472	4	FACETS	0.956	0.879	1	0.956	0.879	1	CLONAL	2	TRUE	2	0.29592099608001	4		262	756	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408878	41408878	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011594-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	177	272	0	ENST00000373198.4:c.548G>C	p.Arg183Pro	p.R183P	ENST00000373198	NM_133170.3	183	cGg/cCg	4/32	0.244443489395472	4	FACETS	0.921	0.849	0.995	0.921	0.849	0.995	CLONAL	2	TRUE	2	0.29592099608001	4		272	842	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0012028-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	357	385	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	0.404367365865647	4	FACETS	0.91	0.871	0.95	1	0.993	1	CLONAL	4	TRUE	1	0.404367365865647	4		385	681	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223984	2223984	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	19	642	0	ENST00000326181.6:c.1198T>A	p.Trp400Arg	p.W400R	ENST00000326181	NM_032271.2	400	Tgg/Agg	13/21	0.215206605707455	1	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	0	0.215206605707455	1		642	132	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874626	151874626	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	26	698	0	ENST00000262189.6:c.7912del	p.Ser2638LeufsTer9	p.S2638Lfs*9	ENST00000262189	NM_170606.2	2638	Tct/ct	38/59	0.215206605707455	1	FACETS	0.625	0.495	0.774	0.625	0.495	0.774	SUBCLONAL	1	TRUE	0	0.215206605707455	1		698	345	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0012070-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	141	812	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.92	0.841	1	0.92	0.841	1	CLONAL	1	TRUE	1	0.502532249123037	2		812	610	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604790	48604790	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1568211615	NA	P-0012070-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	136	461	0	ENST00000342988.3:c.1612G>T	p.Glu538Ter	p.E538*	ENST00000342988	NM_005359.5	538	Gaa/Taa	12/12	0.502532249123037	1	FACETS	0.819	0.749	0.891	0.819	0.749	0.891	CLONAL	1	TRUE	0	0.502532249123037	1		461	495	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	100	371	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	0.2	2		371	958	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0012075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	82	342	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.898	0.79	1	0.898	0.79	1	CLONAL	1	TRUE	1	0.2	2		342	913	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249348	110249348	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1280	129	633	0	ENST00000374672.4:c.1225A>C	p.Lys409Gln	p.K409Q	ENST00000374672	NM_004235.4	409	Aag/Cag	4/5	1	2	FACETS	0.916	0.827	1	0.916	0.827	1	CLONAL	1	TRUE	1	0.2	2		633	1409	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0012093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	360	604	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.66120185900187	2		604	1053	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498526	89498526	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0012093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	231	401	2	ENST00000336596.2:c.2496+2T>A		p.X832_splice	ENST00000336596	NM_005233.5	832			1	2	FACETS	0.973	0.911	1	0.973	0.911	1	CLONAL	1	TRUE	1	0.66120185900187	2		403	718	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909232	41909232	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	477	495	0	ENST00000372991.4:c.156C>G	p.Ile52Met	p.I52M	ENST00000372991	NM_001760.3	52	atC/atG	1/5	0.625726907760922	2	FACETS	0.813	0.783	0.844	0.813	0.783	0.844	CLONAL	2	TRUE	0	0.66120185900187	2		495	887	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525467	137525467	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0012093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	360	464	0	ENST00000367739.4:c.546+2T>A		p.X182_splice	ENST00000367739	NM_000416.2	182			0.632443176583415	2	FACETS	1	0.995	1	0.721	0.688	0.754	CLONAL	1	TRUE	0	0.66120185900187	2		464	755	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372246	55372246	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	144	265	0	ENST00000297316.4:c.936G>T	p.Gln312His	p.Q312H	ENST00000297316	NM_022454.3	312	caG/caT	2/2	0.539677691101421	3	FACETS	0.814	0.744	0.887	0.407	0.372	0.444	CLONAL	1	TRUE	1	0.66120185900187	3		265	712	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376054	118376054	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	112	600	1	ENST00000534358.1:c.9447C>A	p.Phe3149Leu	p.F3149L	ENST00000534358	NM_005933.3	3149	ttC/ttA	27/36	0.408908901451924	1	FACETS	0.269	0.241	0.298	0.269	0.241	0.298	SUBCLONAL	1	TRUE	0	0.66120185900187	1		601	843	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563198	21563198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	379	413	0	ENST00000382592.4:c.721G>A	p.Ala241Thr	p.A241T	ENST00000382592	NM_014572.2	241	Gca/Aca	4/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.818463132341141	2		413	886	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266711	198266711	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012102-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	312	467	0	ENST00000335508.6:c.2221A>G	p.Lys741Glu	p.K741E	ENST00000335508	NM_012433.2	741	Aag/Gag	15/25	0.206067295802672	4	FACETS	0.827	0.782	0.873	0.827	0.782	0.873	INDETERMINATE	2	TRUE	2	0.666953034182446	4		467	943	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188204	10188204	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012102-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	244	492	1	ENST00000256474.2:c.349del	p.Trp117GlyfsTer42	p.W117Gfs*42	ENST00000256474	NM_000551.3	116	cTt/ct	2/3	0.655513295342393	1	FACETS	0.981	0.928	1	0.981	0.928	1	CLONAL	1	TRUE	0	0.666953034182446	1		493	497	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598079	52598079	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012102-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	249	702	0	ENST00000394830.3:c.3787del	p.Ile1263PhefsTer25	p.I1263Ffs*25	ENST00000394830	NM_018313.4	1263	Att/tt	24/30	0.666953034182446	1	FACETS	0.863	0.814	0.912	0.863	0.814	0.912	CLONAL	1	TRUE	0	0.666953034182446	1		702	577	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779440	3779440	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	51	571	0	ENST00000262367.5:c.5608G>C	p.Ala1870Pro	p.A1870P	ENST00000262367	NM_004380.2	1870	Gcc/Ccc	31/31	1	2	FACETS	0.253	0.215	0.295	0.253	0.215	0.295	SUBCLONAL	1	TRUE	1	0.737507107882776	2		571	547	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0012108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	96	452	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.774	0.689	0.864	1	0.981	1	SUBCLONAL	2	TRUE	1	0.161349480277198	2		452	769	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209108325	209108325	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	62	349	1	ENST00000345146.2:c.524G>T	p.Gly175Val	p.G175V	ENST00000345146	NM_005896.2	175	gGt/gTt	6/10	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.161349480277198	2		350	681	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220388	1220388	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1131690938	NA	P-0012108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	190	579	0	ENST00000326873.7:c.481A>T	p.Ile161Phe	p.I161F	ENST00000326873	NM_000455.4	161	Att/Ttt	4/10	0.161349480277198	2	FACETS	0.918	0.85	0.989	1	0.989	1	CLONAL	3	TRUE	0	0.161349480277198	2		579	855	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135066	11135066	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	69	454	2	ENST00000358026.2:c.3033G>T	p.Met1011Ile	p.M1011I	ENST00000358026	NM_001128849.1	1011	atG/atT	21/36	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.161349480277198	2		456	702	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012112-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	501	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.383105493196911	7	FACETS	0.903	0.867	0.939	0.903	0.867	0.939	CLONAL	5	TRUE	2	0.383105493196911	7		371	1134	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012112-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	178	529	0	ENST00000269305.4:c.772G>C	p.Glu258Gln	p.E258Q	ENST00000269305	NM_001126112.2	258	Gaa/Caa	7/11	0.383105493196911	2	FACETS	0.87	0.815	0.925	1	0.989	1	CLONAL	3	TRUE	0	0.383105493196911	2		529	356	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946299	81946299	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs541071022	NA	P-0012112-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	233	817	1	ENST00000359376.3:c.2032G>A	p.Asp678Asn	p.D678N	ENST00000359376	NM_002661.3	678	Gac/Aac	19/33	0.177580782642551	4	FACETS	1	0.985	1	1	0.985	1	INDETERMINATE	2	TRUE	2	0.383105493196911	4		818	724	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746131	162746131	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121964863	NA	P-0012112-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	139	583	1	ENST00000367921.3:c.2254C>T	p.Arg752Cys	p.R752C	ENST00000367921	NM_006182.2	752	Cgc/Tgc	16/18	0.218279525206838	4	FACETS	0.836	0.764	0.912			1	INDETERMINATE	2	TRUE	NA	0.383105493196911	4		584	600	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0012121-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	341	494	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.630074941089867	2		494	1064	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557642	95557642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012121-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	379	614	0	ENST00000393063.1:c.5425G>A	p.Gly1809Arg	p.G1809R	ENST00000393063	NM_030621.3	1809	Ggg/Agg	26/28	1	2	FACETS	0.989	0.939	1	0.989	0.939	1	CLONAL	1	TRUE	1	0.630074941089867	2		614	1217	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143191860	143191860	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012121-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	524	651	0	ENST00000262992.4:c.571G>A	p.Asp191Asn	p.D191N	ENST00000262992	NM_001101669.1	191	Gat/Aat	8/24	1	2	FACETS	0.998	0.955	1	0.998	0.955	1	CLONAL	1	TRUE	1	0.630074941089867	2		651	1667	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183045	32183045	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012121-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	312	582	1	ENST00000375023.3:c.1979C>A	p.Pro660Gln	p.P660Q	ENST00000375023	NM_004557.3	660	cCa/cAa	12/30	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.630074941089867	2		583	968	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199972	138199972	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012121-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	163	275	0	ENST00000237289.4:c.1390G>T	p.Ala464Ser	p.A464S	ENST00000237289	NM_001270507.1	464	Gca/Tca	7/9	1	2	FACETS	0.908	0.838	0.98	0.908	0.838	0.98	CLONAL	1	TRUE	1	0.630074941089867	2		275	570	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77054864	77054864	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012121-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	446	647	0	ENST00000356341.3:c.998G>T	p.Ser333Ile	p.S333I	ENST00000356341	NM_002576.4	333	aGt/aTt	10/15	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.630074941089867	2		647	1298	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557642	95557642	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012121-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	364	614	0	ENST00000393063.1:c.5425G>T	p.Gly1809Trp	p.G1809W	ENST00000393063	NM_030621.3	1809	Ggg/Tgg	26/28	1	2	FACETS	0.949	0.9	0.999	0.949	0.9	0.999	CLONAL	1	TRUE	1	0.630074941089867	2		614	1217	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	70	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.229201413196972	4	FACETS	1	0.902	1	0.687	0.603	0.777	CLONAL	2	TRUE	1	0.244157944966906	4		371	346	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604778	48604778	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767383	NA	P-0012133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	41	553	0	ENST00000342988.3:c.1600C>T	p.Gln534Ter	p.Q534*	ENST00000342988	NM_005359.5	534	Cag/Tag	12/12	0.231952072268457	1	FACETS	0.797	0.665	0.943	0.797	0.665	0.943	CLONAL	1	TRUE	0	0.244157944966906	1		553	370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0012133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	115	395	0	ENST00000269305.4:c.97-1G>A		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.244157944966906	4	FACETS	0.891	0.812	0.971	1	0.974	1	CLONAL	4	TRUE	1	0.244157944966906	4		395	329	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626704	28626704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144349858	NA	P-0012133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	41	461	0	ENST00000241453.7:c.592C>T	p.Leu198Phe	p.L198F	ENST00000241453	NM_004119.2	198	Ctt/Ttt	5/24	1	2	FACETS	0.861	0.719	1	0.861	0.719	1	CLONAL	1	TRUE	1	0.244157944966906	2		461	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	547	692	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.587320026375604	2	FACETS	0.966	0.934	0.998	0.966	0.934	0.998	CLONAL	2	TRUE	0	0.600509697083877	2		692	943	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797205	135797205	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0012148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	513	719	0	ENST00000298552.3:c.663+1G>T		p.X221_splice	ENST00000298552	NM_001162426.1	221			0.587320026375604	2	FACETS	0.976	0.943	1	0.976	0.943	1	CLONAL	2	TRUE	0	0.600509697083877	2		719	875	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45396897	45396897	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs984513669	NA	P-0012148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	248	621	0	ENST00000262160.6:c.275C>T	p.Thr92Met	p.T92M	ENST00000262160	NM_005901.5	92	aCg/aTg	3/11	0.189833323362376	3	FACETS	1	0.989	1	0.631	0.591	0.672	INDETERMINATE	1	TRUE	1	0.600509697083877	3		621	851	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589216	67589251	+	inframe_deletion	In_Frame_Del	DEL	GTTGAATTAATAAACCACTACCGGAATGAATCTCTA	GTTGAATTAATAAACCACTACCGGAATGAATCTCTA	-	novel	NA	P-0012148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	629	630	2	ENST00000274335.5:c.1205_1240del	p.Val402_Leu413del	p.V402_L413del	ENST00000274335		402	GTTGAATTAATAAACCACTACCGGAATGAATCTCTA/-	9/15	0.600724841101087	3	FACETS	0.883	0.857	0.909			1	CLONAL	3	TRUE	NA	0.600509697083877	3		632	1028	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0012157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	247	459	1	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.723329028680845	2		460	594	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs104886003	NA	P-0012157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	73	253	0	ENST00000263967.3:c.1633G>C	p.Glu545Gln	p.E545Q	ENST00000263967	NM_006218.2	545	Gag/Cag	10/21	0.723329028680845	3	FACETS	0.828	0.73	0.932	0.414	0.365	0.466	CLONAL	1	TRUE	1	0.723329028680845	3		253	332	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037966	49037966	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	167	479	0	ENST00000267163.4:c.2206C>T	p.Gln736Ter	p.Q736*	ENST00000267163	NM_000321.2	736	Cag/Tag	21/27	0.723329028680845	1	FACETS	0.901	0.843	0.959	0.901	0.843	0.959	CLONAL	1	TRUE	0	0.723329028680845	1		479	327	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0012157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	262	541	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.723329028680845	2		541	666	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039435	49039435	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0012157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	304	640	0	ENST00000267163.4:c.2420C>G	p.Ser807Ter	p.S807*	ENST00000267163	NM_000321.2	807	tCa/tGa	23/27	0.723329028680845	1	FACETS	0.99	0.945	1	0.99	0.945	1	CLONAL	1	TRUE	0	0.723329028680845	1		640	542	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780851	9780851	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	343	623	0	ENST00000377346.4:c.1573G>C	p.Glu525Gln	p.E525Q	ENST00000377346	NM_005026.3	525	Gag/Cag	13/24	1	2	FACETS	0.98	0.93	1	0.98	0.93	1	CLONAL	1	TRUE	1	0.723329028680845	2		623	968	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257298	16257298	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	263	531	0	ENST00000375759.3:c.4563G>C	p.Glu1521Asp	p.E1521D	ENST00000375759	NM_015001.2	1521	gaG/gaC	11/15	1	2	FACETS	0.983	0.925	1	0.983	0.925	1	CLONAL	1	TRUE	1	0.723329028680845	2		531	740	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257395	16257395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	252	454	0	ENST00000375759.3:c.4660G>A	p.Asp1554Asn	p.D1554N	ENST00000375759	NM_015001.2	1554	Gac/Aac	11/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.723329028680845	2		454	666	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257569	16257569	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	330	679	0	ENST00000375759.3:c.4834G>C	p.Asp1612His	p.D1612H	ENST00000375759	NM_015001.2	1612	Gat/Cat	11/15	1	2	FACETS	0.986	0.935	1	0.986	0.935	1	CLONAL	1	TRUE	1	0.723329028680845	2		679	925	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439706	51439706	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	242	527	0	ENST00000262662.1:c.271G>C	p.Glu91Gln	p.E91Q	ENST00000262662		91	Gag/Cag	4/4	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.723329028680845	2		527	639	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858964	243858964	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210004922	NA	P-0012157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	215	594	1	ENST00000263826.5:c.101C>T	p.Ser34Leu	p.S34L	ENST00000263826	NM_005465.4	34	tCa/tTa	2/13	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.723329028680845	2		595	580	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022340	26022340	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	372	773	0	ENST00000435504.4:c.317C>T	p.Ser106Leu	p.S106L	ENST00000435504		106	tCa/tTa	5/13	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.723329028680845	2		773	998	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650384	12650384	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs367732360	NA	P-0012157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	176	436	0	ENST00000251849.4:c.462C>G	p.Ile154Met	p.I154M	ENST00000251849	NM_002880.3	154	atC/atG	5/17	1	2	FACETS	0.911	0.845	0.979	0.911	0.845	0.979	CLONAL	1	TRUE	1	0.723329028680845	2		436	534	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163404	47163404	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	169	455	0	ENST00000409792.3:c.2722C>A	p.Leu908Met	p.L908M	ENST00000409792	NM_014159.6	908	Ctg/Atg	3/21	1	2	FACETS	0.954	0.884	1	0.954	0.884	1	CLONAL	1	TRUE	1	0.723329028680845	2		455	490	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178069	142178069	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	125	385	0	ENST00000350721.4:c.7349G>A	p.Trp2450Ter	p.W2450*	ENST00000350721	NM_001184.3	2450	tGg/tAg	43/47	0.723329028680845	3	FACETS	1	0.92	1	0.505	0.46	0.552	CLONAL	1	TRUE	1	0.723329028680845	3		385	466	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372432	55372432	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	320	892	0	ENST00000297316.4:c.1122G>C	p.Glu374Asp	p.E374D	ENST00000297316	NM_022454.3	374	gaG/gaC	2/2	1	2	FACETS	0.886	0.838	0.935	0.886	0.838	0.935	CLONAL	1	TRUE	1	0.723329028680845	2		892	999	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869521	117869521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	1237	1047	1	ENST00000297338.2:c.673G>A	p.Asp225Asn	p.D225N	ENST00000297338	NM_006265.2	225	Gat/Aat	6/14	0.723329028680845	4	FACETS	0.967	0.947	0.988	0.967	0.947	0.988	CLONAL	3	TRUE	1	0.723329028680845	4		1048	2031	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869584	117869584	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	1296	980	0	ENST00000297338.2:c.610G>A	p.Glu204Lys	p.E204K	ENST00000297338	NM_006265.2	204	Gag/Aag	6/14	0.723329028680845	4	FACETS	0.983	0.963	1	0.983	0.963	1	CLONAL	3	TRUE	1	0.723329028680845	4		980	2094	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039399	49039399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	445	876	0	ENST00000267163.4:c.2384C>T	p.Ser795Leu	p.S795L	ENST00000267163	NM_000321.2	795	tCa/tTa	23/27	0.723329028680845	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.723329028680845	1		876	734	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991316	41991316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	514	1131	0	ENST00000219905.7:c.2147C>T	p.Thr716Ile	p.T716I	ENST00000219905	NM_001164273.1	716	aCt/aTt	5/24	1	2	FACETS	0.945	0.905	0.986	0.945	0.905	0.986	CLONAL	1	TRUE	1	0.723329028680845	2		1131	1504	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844139	68844139	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	289	591	0	ENST00000261769.5:c.727G>C	p.Glu243Gln	p.E243Q	ENST00000261769	NM_004360.3	243	Gag/Cag	6/16	0.723329028680845	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.723329028680845	1		591	510	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412596	63412596	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	260	300	0	ENST00000330258.3:c.571G>C	p.Glu191Gln	p.E191Q	ENST00000330258	NM_152424.3	191	Gag/Cag	2/2	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.723329028680845	1		300	370	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	174	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.391807203580251	4	FACETS	0.994	0.939	1			1	INDETERMINATE	3	TRUE	NA	0.72316430746738	4		371	278	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031973	26031973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1280	778	1432	1	ENST00000244661.2:c.316G>A	p.Glu106Lys	p.E106K	ENST00000244661	NM_003537.3	106	Gag/Aag	1/1	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.72316430746738	2		1433	2058	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101006	27101006	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	404	667	0	ENST00000324856.7:c.4288C>T	p.Gln1430Ter	p.Q1430*	ENST00000324856	NM_006015.4	1430	Cag/Tag	18/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.72316430746738	2		667	1026	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442069	52442069	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	284	458	0	ENST00000460680.1:c.280C>G	p.His94Asp	p.H94D	ENST00000460680	NM_004656.3	94	Cat/Gat	5/17	0.72316430746738	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.72316430746738	1		458	488	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771801	135771801	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	450	942	0	ENST00000298552.3:c.3316G>A	p.Glu1106Lys	p.E1106K	ENST00000298552	NM_001162426.1	1106	Gag/Aag	23/23	1	2	FACETS	0.992	0.948	1	0.992	0.948	1	CLONAL	1	TRUE	1	0.72316430746738	2		942	1254	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923324	9923324	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	224	613	0	ENST00000330684.3:c.1963C>A	p.Gln655Lys	p.Q655K	ENST00000330684	NM_001134407.1	655	Caa/Aaa	9/13	1	2	FACETS	0.957	0.897	1	0.957	0.897	1	CLONAL	1	TRUE	1	0.72316430746738	2		613	647	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0012160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	426	558	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.454159902216653	6	FACETS	0.886	0.847	0.925	0.886	0.847	0.925	CLONAL	4	TRUE	2	0.454159902216653	6		558	1010	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593588	55593599	+	inframe_deletion	In_Frame_Del	DEL	ATGTATGAAGTA	ATGTATGAAGTA	-	novel	NA	P-0012185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	272	611	0	ENST00000288135.5:c.1654_1665del	p.Met552_Val555del	p.M552_V555del	ENST00000288135	NM_000222.2	552	ATGTATGAAGTA/-	11/21	1	2	FACETS	0.805	0.757	0.853	0.805	0.757	0.853	CLONAL	1	TRUE	1	0.767486015245675	2		611	881	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0012192-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	586	452	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.48474456162905	3	FACETS	0.991	0.969	1			1	CLONAL	3	TRUE	NA	0.754043508629977	3		452	720	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729888	30729888	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012192-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	184	192	0	ENST00000295754.5:c.1409A>G	p.Tyr470Cys	p.Y470C	ENST00000295754	NM_003242.5	470	tAt/tGt	6/7	0.754043508629977	2	FACETS	0.961	0.915	1	0.961	0.915	1	CLONAL	2	TRUE	0	0.754043508629977	2		192	254	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528486	157528486	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554237969	NA	P-0012192-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	202	442	0	ENST00000346085.5:c.6211G>T	p.Gly2071Ter	p.G2071*	ENST00000346085	NM_020732.3	2071	Gga/Tga	20/20	NA	2	FACETS	0.947	0.884	1			1	INDETERMINATE	1	TRUE	NA	0.754043508629977	2		442	566	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781193	161781193	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012192-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	316	788	0	ENST00000366898.1:c.1212A>T	p.Glu404Asp	p.E404D	ENST00000366898	NM_004562.2	404	gaA/gaT	11/12	NA	2	FACETS	0.981	0.93	1			1	INDETERMINATE	1	TRUE	NA	0.754043508629977	2		788	854	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92252400	92252400	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012192-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	45	125	1	ENST00000265734.4:c.648G>T	p.Lys216Asn	p.K216N	ENST00000265734	NM_001259.6	216	aaG/aaT	6/8	0.27140195636679	1	FACETS	0.453	0.387	0.524	0.453	0.387	0.524	INDETERMINATE	1	TRUE	0	0.754043508629977	1		126	164	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042322	42042322	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0012192-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	686	1818	0	ENST00000219905.7:c.6517A>T	p.Arg2173Ter	p.R2173*	ENST00000219905	NM_001164273.1	2173	Aga/Tga	17/24	NA	2	FACETS	0.815	0.792	0.838			1	INDETERMINATE	2	TRUE	NA	0.754043508629977	2		1818	1116	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411868	63411868	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012192-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1224	608	2170	1	ENST00000330258.3:c.1299C>A	p.His433Gln	p.H433Q	ENST00000330258	NM_152424.3	433	caC/caA	2/2	1	2	FACETS	0.88	0.846	0.915	0.88	0.846	0.915	CLONAL	1	TRUE	1	0.754043508629977	2		2171	1832	SUCCESS
AR	367	MSKCC	GRCh37	X	66765322	66765322	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012192-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	442	1509	3	ENST00000374690.3:c.334G>T	p.Glu112Ter	p.E112*	ENST00000374690	NM_000044.3	112	Gag/Tag	1/8	1	2	FACETS	0.896	0.855	0.938	0.896	0.855	0.938	CLONAL	1	TRUE	1	0.754043508629977	2		1512	1308	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608300	100608300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012192-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	334	849	0	ENST00000308731.7:c.1790C>T	p.Pro597Leu	p.P597L	ENST00000308731	NM_000061.2	597	cCa/cTa	18/19	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.754043508629977	2		849	845	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576913	7576943	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTTGTTGGGCAGTGCTAGGAAAGAGGCAAGG	GTTGTTGGGCAGTGCTAGGAAAGAGGCAAGG	-	novel	NA	P-0012192-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	209	484	0	ENST00000269305.4:c.920-17_933del		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	0.6216781138555	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.754043508629977	1		484	315	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944605	38944605	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012192-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	197	374	0	ENST00000357387.3:c.4856del	p.Leu1619Ter	p.L1619*	ENST00000357387	NM_152756.3	1619	tTa/ta	36/38	1	2	FACETS	0.847	0.789	0.907	0.847	0.789	0.907	CLONAL	1	TRUE	1	0.754043508629977	2		374	617	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251665	212251665	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012192-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	139	745	0	ENST00000342788.4:c.3394C>T	p.Pro1132Ser	p.P1132S	ENST00000342788	NM_005235.2	1132	Ccc/Tcc	27/28	1	2	FACETS	0.471	0.429	0.515	0.471	0.429	0.515	SUBCLONAL	1	TRUE	1	0.754043508629977	2		745	783	SUCCESS
APC	324	MSKCC	GRCh37	5	112173750	112173750	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012192-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	63	378	0	ENST00000257430.4:c.2459C>G	p.Thr820Ser	p.T820S	ENST00000257430	NM_000038.5	820	aCt/aGt	16/16	1	2	FACETS	0.359	0.311	0.411	0.359	0.311	0.411	SUBCLONAL	1	TRUE	1	0.754043508629977	2		378	465	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317917	8317917	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012192-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	89	518	1	ENST00000356435.5:c.5696C>A	p.Ala1899Asp	p.A1899D	ENST00000356435		1899	gCc/gAc	35/35	1	2	FACETS	0.44	0.391	0.493	0.44	0.391	0.493	SUBCLONAL	1	TRUE	1	0.754043508629977	2		519	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0012197-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	430	586	3	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.564508050595109	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.564508050595109	2		589	723	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060930	38060960	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTGGAGTCTTCAACTCCGAGGCGCCCCCT	GGCTGGAGTCTTCAACTCCGAGGCGCCCCCT	-	novel	NA	P-0012197-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	65	381	0	ENST00000250448.2:c.1029_1059del	p.Gly344ProfsTer7	p.G344Pfs*7	ENST00000250448	NM_004496.3	343	acAGGGGGCGCCTCGGAGTTGAAGACTCCAGCC/ac	2/2	0.550967686330434	3	FACETS	0.61	0.53	0.697	0.305	0.265	0.349	SUBCLONAL	1	TRUE	1	0.564508050595109	3		381	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577520	7577520	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1330865474	NA	P-0012199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	178	531	0	ENST00000269305.4:c.761T>G	p.Ile254Ser	p.I254S	ENST00000269305	NM_001126112.2	254	aTc/aGc	7/11	0.228089727793043	2	FACETS	0.857	0.791	0.927	0.857	0.791	0.927	CLONAL	2	TRUE	0	0.233812592865685	2		531	888	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483916	88483916	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	122	691	0	ENST00000360948.2:c.1654G>T	p.Val552Phe	p.V552F	ENST00000360948	NM_001012338.2	552	Gtc/Ttc	14/19	0.154313633622006	4	FACETS	1	0.902	1	0.5	0.451	0.553	CLONAL	1	TRUE	2	0.233812592865685	4		691	1287	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843410	3843410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	95	358	0	ENST00000262367.5:c.1193G>A	p.Cys398Tyr	p.C398Y	ENST00000262367	NM_004380.2	398	tGt/tAt	4/31	0.22549912580232	3	FACETS	1	0.931	1	0.532	0.473	0.595	CLONAL	1	TRUE	1	0.233812592865685	3		358	853	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0012246-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	248	639	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.463056850334389	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.483789926084964	1		639	739	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787737	135787737	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0012246-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	278	717	0	ENST00000298552.3:c.845C>G	p.Ser282Ter	p.S282*	ENST00000298552	NM_001162426.1	282	tCa/tGa	9/23	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.483789926084964	2		717	1123	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023895	27023895	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012246-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	205	210	0	ENST00000324856.7:c.1001C>A	p.Ser334Ter	p.S334*	ENST00000324856	NM_006015.4	334	tCg/tAg	1/20	0.482713565243556	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.483789926084964	3		210	467	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659794	88659794	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012246-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	209	612	0	ENST00000372037.3:c.441T>A	p.Phe147Leu	p.F147L	ENST00000372037	NM_004329.2	147	ttT/ttA	7/13	1	2	FACETS	0.928	0.862	0.996	0.928	0.862	0.996	CLONAL	1	TRUE	1	0.483789926084964	2		612	931	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876449	35876449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2229232	NA	P-0012267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	78	379	1	ENST00000303115.3:c.1241C>T	p.Thr414Met	p.T414M	ENST00000303115	NM_002185.3	414	aCg/aTg	8/8	1	2	FACETS	0.491	0.431	0.555	0.491	0.431	0.555	SUBCLONAL	1	TRUE	1	0.494127717455537	2		380	643	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188320	10188320	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	177	397	0	ENST00000256474.2:c.463G>T	p.Val155Leu	p.V155L	ENST00000256474	NM_000551.3	155	Gtg/Ttg	2/3	0.494127717455537	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.494127717455537	1		397	510	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174459	11174459	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557739557	NA	P-0012267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	38	452	0	ENST00000361445.4:c.7216G>A	p.Val2406Met	p.V2406M	ENST00000361445	NM_004958.3	2406	Gtg/Atg	53/58	0.494127717455537	1	FACETS	0.201	0.166	0.241	0.201	0.166	0.241	SUBCLONAL	1	TRUE	0	0.494127717455537	1		452	575	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978314	2978314	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	41	338	0	ENST00000396946.4:c.1016A>T	p.Lys339Met	p.K339M	ENST00000396946	NM_032415.4	339	aAg/aTg	7/25	1	2	FACETS	0.359	0.299	0.426	0.359	0.299	0.426	SUBCLONAL	1	TRUE	1	0.494127717455537	2		338	462	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163305	32163305	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012276-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	48	857	0	ENST00000375023.3:c.5921C>G	p.Pro1974Arg	p.P1974R	ENST00000375023	NM_004557.3	1974	cCg/cGg	30/30	1	2	FACETS	0.922	0.777	1	0.922	0.777	1	CLONAL	1	TRUE	1	0.12	2		857	868	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635230	87635230	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs748028871	NA	P-0012276-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	36	477	0	ENST00000277120.3:c.2282A>G	p.Glu761Gly	p.E761G	ENST00000277120		761	gAg/gGg	18/19	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.12	2		477	537	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435733	110435733	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012276-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	11	222	0	ENST00000375856.3:c.2668C>A	p.Pro890Thr	p.P890T	ENST00000375856	NM_003749.2	890	Ccc/Acc	1/2	1	2	FACETS	0.845	0.584	1	0.845	0.584	1	CLONAL	1	TRUE	1	0.12	2		222	217	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0012282-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	112	320	0				ENST00000310581	NM_198253.2	-/1132			0.394194265400191	0	FACETS	0.424	0.387	0.462			1	SUBCLONAL	1	TRUE	0	0.651890247512939	0		320	282	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0012282-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	363	367	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.651890247512939	3	FACETS	0.977	0.933	1	0.977	0.933	1	CLONAL	2	TRUE	1	0.651890247512939	3		367	756	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979281	40979281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012282-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	113	457	1	ENST00000373198.4:c.1852G>A	p.Gly618Arg	p.G618R	ENST00000373198	NM_133170.3	618	Gga/Aga	11/32	0.434465022431595	0	FACETS	0.302	0.273	0.331			1	SUBCLONAL	1	TRUE	0	0.651890247512939	0		458	400	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129869	55129869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012282-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	157	690	1	ENST00000257290.5:c.403G>A	p.Asp135Asn	p.D135N	ENST00000257290	NM_006206.4	135	Gat/Aat	4/23	0.177440547473633	0	FACETS	0.309	0.284	0.334			1	INDETERMINATE	1	TRUE	0	0.651890247512939	0		691	543	SUCCESS
AXL	558	MSKCC	GRCh37	19	41737136	41737136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761251235	NA	P-0012282-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	285	817	6	ENST00000301178.4:c.716C>T	p.Thr239Met	p.T239M	ENST00000301178	NM_021913.4	239	aCg/aTg	6/20	1	2	FACETS	0.911	0.858	0.965	0.911	0.858	0.965	CLONAL	1	TRUE	1	0.651890247512939	2		823	960	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523087	25523087	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012282-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	120	613	0	ENST00000264709.3:c.98G>T	p.Arg33Leu	p.R33L	ENST00000264709	NM_175629.2	33	cGt/cTt	3/23	1	2	FACETS	0.469	0.423	0.517	0.469	0.423	0.517	SUBCLONAL	1	TRUE	1	0.651890247512939	2		613	785	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457276	89457276	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778106353	NA	P-0012282-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	47	414	1	ENST00000336596.2:c.1757G>A	p.Gly586Glu	p.G586E	ENST00000336596	NM_005233.5	586	gGg/gAg	9/17	0.415450678751995	0	FACETS	0.164	0.139	0.192			1	SUBCLONAL	1	TRUE	0	0.651890247512939	0		415	306	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840049	27840049	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012282-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1248	314	1043	0	ENST00000328488.2:c.45A>T	p.Lys15Asn	p.K15N	ENST00000328488	NM_003533.2	15	aaA/aaT	1/1	0.166299485162139	5	FACETS	1	0.99	1	0.407	0.382	0.432	INDETERMINATE	1	TRUE	2	0.651890247512939	5		1043	1562	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656281	18656281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012282-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	71	469	0	ENST00000266497.5:c.2960G>A	p.Gly987Glu	p.G987E	ENST00000266497		987	gGa/gAa	21/31	0.434465022431595	0	FACETS	0.243	0.214	0.274			1	SUBCLONAL	1	TRUE	0	0.651890247512939	0		469	312	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858592	9858592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769602505	NA	P-0012282-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	146	863	2	ENST00000330684.3:c.2809G>A	p.Asp937Asn	p.D937N	ENST00000330684	NM_001134407.1	937	Gat/Aat	13/13	0.651890247512939	1	FACETS	0.642	0.591	0.696	0.642	0.591	0.696	SUBCLONAL	1	TRUE	0	0.651890247512939	1		865	470	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0012284-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	255	618	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	0.981	0.918	1	0.981	0.918	1	CLONAL	1	TRUE	1	0.47831531389312	2		618	1087	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541577	29541577	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012284-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	173	429	0	ENST00000356175.3:c.1501C>A	p.His501Asn	p.H501N	ENST00000356175	NM_000267.3	501	Cat/Aat	13/57	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.47831531389312	2		429	708	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830767	3830774	+	frameshift_variant	Frame_Shift_Del	DEL	TGACATGT	TGACATGT	-	novel	NA	P-0012285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	108	631	0	ENST00000262367.5:c.1782_1789del	p.Glu594AspfsTer11	p.E594Dfs*11	ENST00000262367	NM_004380.2	594	gaACATGTCAct/gact	8/31	0.427034228776368	1	FACETS	0.804	0.725	0.887	0.804	0.725	0.887	CLONAL	1	TRUE	0	0.427034228776368	1		631	495	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380276	+	missense_variant	Missense_Mutation	DNP	TT	TT	CA	novel	NA	P-0012289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	60	684	0	ENST00000311936.3:c.182_183delinsTG	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAA/cTG	3/5	1	2	FACETS	0.902	0.774	1	0.902	0.774	1	CLONAL	1	TRUE	1	0.11	2		684	1210	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728765	39728765	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012289-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	47	432	0	ENST00000361337.2:c.1045A>G	p.Arg349Gly	p.R349G	ENST00000361337	NM_003286.2	349	Agg/Ggg	12/21	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.11	2		432	790	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061193	38061193	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012304-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	35	253	0	ENST00000250448.2:c.796T>C	p.Phe266Leu	p.F266L	ENST00000250448	NM_004496.3	266	Ttc/Ctc	2/2	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		253	467	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0012325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	60	239	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.902	0.786	1	0.902	0.786	1	CLONAL	1	TRUE	1	0.536180841414372	2		239	248	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409436	80409436	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	99	203	0	ENST00000286548.4:c.678C>G	p.Ile226Met	p.I226M	ENST00000286548	NM_002072.3	226	atC/atG	5/7	0.536180841414372	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.536180841414372	1		203	261	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445995	49445995	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	340	500	0	ENST00000301067.7:c.1471G>T	p.Glu491Ter	p.E491*	ENST00000301067	NM_003482.3	491	Gaa/Taa	10/54	0.513001906662716	3	FACETS	0.96	0.912	1	0.96	0.912	1	CLONAL	2	TRUE	1	0.536180841414372	3		500	838	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448178	49448178	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	159	409	0	ENST00000301067.7:c.422G>A	p.Trp141Ter	p.W141*	ENST00000301067	NM_003482.3	141	tGg/tAg	4/54	0.513001906662716	3	FACETS	1	0.95	1	0.524	0.481	0.568	CLONAL	1	TRUE	1	0.536180841414372	3		409	718	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606167	81606167	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0012325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	159	423	0	ENST00000298171.2:c.837C>G	p.Tyr279Ter	p.Y279*	ENST00000298171	NM_000369.2	279	taC/taG	9/10	1	2	FACETS	0.871	0.801	0.944	0.871	0.801	0.944	CLONAL	1	TRUE	1	0.536180841414372	2		423	681	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245918	41245918	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs80356952	NA	P-0012325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	170	492	0	ENST00000357654.3:c.1630C>T	p.Gln544Ter	p.Q544*	ENST00000357654	NM_007294.3	544	Caa/Taa	10/23	1	2	FACETS	0.944	0.871	1	0.944	0.871	1	CLONAL	1	TRUE	1	0.536180841414372	2		492	672	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075310	16075310	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0012325-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	43	312	0	ENST00000268712.3:c.243-1G>A		p.X81_splice	ENST00000268712	NM_006311.3	81			0.536180841414372	1	FACETS	0.295	0.247	0.348	0.295	0.247	0.348	SUBCLONAL	1	TRUE	0	0.536180841414372	1		312	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0012327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	65	808	2	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.14	2		810	910	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	104	589	1				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.792236786036975	2		590	247	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0012360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	35	418	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.225	0.185	0.271	0.225	0.185	0.271	SUBCLONAL	1	TRUE	1	0.792236786036975	2		421	392	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0012360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10742	596	540	1	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.792236786036975	31	FACETS	0.829	0.79	0.869			1	CLONAL	2	TRUE	NA	0.792236786036975	31		541	11338	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639993	93639993	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	36	350	0	ENST00000375746.1:c.1322C>A	p.Ala441Asp	p.A441D	ENST00000375746	NM_001174167.1	441	gCc/gAc	10/14	0.792236786036975	3	FACETS	0.235	0.193	0.283	0.117	0.096	0.142	SUBCLONAL	1	TRUE	1	0.792236786036975	3		350	540	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288787	11288788	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0012360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	186	555	0	ENST00000361445.4:c.2967_2968delinsAT	p.Phe989Leu	p.F989L	ENST00000361445	NM_004958.3	989	ttCCtg/ttATtg	19/58	1	2	FACETS	0.756	0.702	0.812	0.756	0.702	0.812	SUBCLONAL	1	TRUE	1	0.792236786036975	2		555	621	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs967461896	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	119	428	0	ENST00000269305.4:c.526T>A	p.Cys176Ser	p.C176S	ENST00000269305	NM_001126112.2	176	Tgc/Agc	5/11	0.257794016327289	2	FACETS	0.967	0.879	1	0.967	0.879	1	CLONAL	2	TRUE	0	0.272123248289414	2		428	452	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544079	18544079	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	117	451	0	ENST00000266497.5:c.1896G>T	p.Trp632Cys	p.W632C	ENST00000266497		632	tgG/tgT	13/31	0.272123248289414	6	FACETS	1	0.957	1			1	CLONAL	2	TRUE	NA	0.272123248289414	6		451	601	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73340179	73340179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	79	527	0	ENST00000377767.4:c.1901C>T	p.Ser634Phe	p.S634F	ENST00000377767	NM_014953.3	634	tCt/tTt	15/21	0.272123248289414	3	FACETS	1	0.959	1			1	CLONAL	1	TRUE	NA	0.272123248289414	3		527	548	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428507	78428507	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	154	699	0	ENST00000370768.2:c.1292G>T	p.Gly431Val	p.G431V	ENST00000370768	NM_003902.3	431	gGc/gTc	14/20	1	2	FACETS	0.841	0.772	0.913	1	0.99	1	CLONAL	2	TRUE	1	0.272123248289414	2		699	673	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076917	41076917	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	98	758	0	ENST00000373198.4:c.1503G>T	p.Lys501Asn	p.K501N	ENST00000373198	NM_133170.3	501	aaG/aaT	9/32	0.272123248289414	5	FACETS	1	0.956	1	0.38	0.339	0.425	CLONAL	1	TRUE	2	0.272123248289414	5		758	889	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798275	45798275	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	71	534	0	ENST00000450313.1:c.661G>T	p.Gly221Trp	p.G221W	ENST00000450313	NM_012222.2	221	Ggg/Tgg	8/16	1	2	FACETS	0.878	0.767	0.998	0.878	0.767	0.998	CLONAL	1	TRUE	1	0.272123248289414	2		534	594	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462180	120462180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1410633721	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	73	513	0	ENST00000256646.2:c.5536G>A	p.Asp1846Asn	p.D1846N	ENST00000256646	NM_024408.3	1846	Gat/Aat	31/34	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.272123248289414	2		513	466	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085687	16085687	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	183	629	0	ENST00000281043.3:c.863C>G	p.Ser288Cys	p.S288C	ENST00000281043	NM_005378.4	288	tCc/tGc	3/3	0.272123248289414	4	FACETS	0.959	0.886	1	0.959	0.886	1	CLONAL	2	TRUE	2	0.272123248289414	4		629	892	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61717860	61717860	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	98	837	2	ENST00000401558.2:c.1939C>T	p.Gln647Ter	p.Q647*	ENST00000401558	NM_003400.3	647	Caa/Taa	17/25	0.272123248289414	4	FACETS	1	0.915	1	0.515	0.459	0.576	CLONAL	1	TRUE	2	0.272123248289414	4		839	889	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610499	215610499	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs369756202	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	153	696	1	ENST00000260947.4:c.1757G>T	p.Ser586Ile	p.S586I	ENST00000260947	NM_000465.2	586	aGt/aTt	8/11	0.272123248289414	4	FACETS	0.892	0.817	0.97	0.892	0.817	0.97	CLONAL	2	TRUE	2	0.272123248289414	4		697	802	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164421	47164421	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	163	586	0	ENST00000409792.3:c.1705T>C	p.Phe569Leu	p.F569L	ENST00000409792	NM_014159.6	569	Ttt/Ctt	3/21	0.272123248289414	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.272123248289414	2		586	531	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136904	55136904	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	138	605	0	ENST00000257290.5:c.1226T>C	p.Leu409Pro	p.L409P	ENST00000257290	NM_006206.4	409	cTg/cCg	8/23	0.272123248289414	3	FACETS	0.992	0.906	1	0.992	0.906	1	CLONAL	2	TRUE	1	0.272123248289414	3		605	581	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564524	55564524	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	70	519	0	ENST00000288135.5:c.412C>A	p.Leu138Ile	p.L138I	ENST00000288135	NM_000222.2	138	Ctc/Atc	3/21	0.272123248289414	3	FACETS	0.971	0.847	1	0.485	0.423	0.553	CLONAL	1	TRUE	1	0.272123248289414	3		519	602	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532858	187532858	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	139	553	2	ENST00000441802.2:c.9535G>T	p.Gly3179Ter	p.G3179*	ENST00000441802	NM_005245.3	3179	Gga/Tga	14/27	0.272123248289414	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	2	TRUE	0	0.272123248289414	2		555	511	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965709	93965709	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	97	892	0	ENST00000369303.4:c.2219G>C	p.Arg740Thr	p.R740T	ENST00000369303	NM_004440.3	740	aGa/aCa	13/17	0.272123248289414	3	FACETS	0.949	0.846	1	0.475	0.423	0.53	CLONAL	1	TRUE	1	0.272123248289414	3		892	853	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149982885	149982885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139248642	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	128	536	0	ENST00000253339.5:c.3373C>T	p.Arg1125Cys	p.R1125C	ENST00000253339		1125	Cgc/Tgc	7/7	0.272123248289414	3	FACETS	0.953	0.867	1	0.953	0.867	1	CLONAL	2	TRUE	1	0.272123248289414	3		536	561	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332814	152332814	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	196	774	0	ENST00000206249.3:c.1120G>T	p.Asp374Tyr	p.D374Y	ENST00000206249	NM_000125.3	374	Gat/Tat	5/8	0.272123248289414	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	1	0.272123248289414	3		774	788	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729844	41729844	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs908163566	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	209	844	2	ENST00000242208.4:c.685C>T	p.Arg229Trp	p.R229W	ENST00000242208	NM_002192.2	229	Cgg/Tgg	3/3	0.272123248289414	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.272123248289414	3		846	843	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739756	41739756	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	155	918	0	ENST00000242208.4:c.217G>C	p.Asp73His	p.D73H	ENST00000242208	NM_002192.2	73	Gat/Cat	2/3	0.272123248289414	3	FACETS	0.826	0.757	0.898	0.826	0.757	0.898	CLONAL	2	TRUE	1	0.272123248289414	3		918	783	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350107	81350107	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	145	749	0	ENST00000222390.5:c.1225G>T	p.Gly409Ter	p.G409*	ENST00000222390	NM_000601.4	409	Gga/Tga	10/18	0.272123248289414	3	FACETS	0.876	0.801	0.954	0.876	0.801	0.954	CLONAL	2	TRUE	1	0.272123248289414	3		749	691	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508146	106508146	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	40	258	0	ENST00000359195.3:c.140G>T	p.Ser47Ile	p.S47I	ENST00000359195	NM_002649.2	47	aGc/aTc	2/11	0.272123248289414	3	FACETS	1	0.846	1	0.508	0.423	0.601	CLONAL	1	TRUE	1	0.272123248289414	3		258	329	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482900	140482900	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	95	678	0	ENST00000288602.6:c.1235A>G	p.Asn412Ser	p.N412S	ENST00000288602	NM_004333.4	412	aAc/aGc	10/18	0.272123248289414	3	FACETS	1	0.96	1	0.583	0.519	0.651	CLONAL	1	TRUE	1	0.272123248289414	3		678	680	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878241	151878241	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	158	618	1	ENST00000262189.6:c.6704G>T	p.Arg2235Met	p.R2235M	ENST00000262189	NM_170606.2	2235	aGg/aTg	36/59	0.272123248289414	3	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	1	0.272123248289414	3		619	642	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759502	133759502	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	88	805	0	ENST00000318560.5:c.1825A>T	p.Lys609Ter	p.K609*	ENST00000318560	NM_005157.4	609	Aag/Tag	11/11	1	2	FACETS	0.964	0.854	1	0.964	0.854	1	CLONAL	1	TRUE	1	0.272123248289414	2		805	671	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609075	43609075	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs377767391	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	89	866	0	ENST00000355710.3:c.1831T>A	p.Cys611Ser	p.C611S	ENST00000355710	NM_020975.4	611	Tgc/Agc	10/20	0.272123248289414	3	FACETS	0.903	0.8	1			1	CLONAL	1	TRUE	NA	0.272123248289414	3		866	823	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574511	64574511	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	86	674	1	ENST00000312049.6:c.884G>T	p.Arg295Leu	p.R295L	ENST00000312049	NM_130799.2	295	cGg/cTg	6/10	1	2	FACETS	0.936	0.829	1	0.936	0.829	1	CLONAL	1	TRUE	1	0.272123248289414	2		675	675	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625319	69625319	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	81	758	2	ENST00000334134.2:c.474C>A	p.Asn158Lys	p.N158K	ENST00000334134	NM_005247.2	158	aaC/aaA	3/3	1	2	FACETS	0.907	0.8	1	0.907	0.8	1	CLONAL	1	TRUE	1	0.272123248289414	2		760	656	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143469	108143469	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	86	924	0	ENST00000278616.4:c.3174G>T	p.Trp1058Cys	p.W1058C	ENST00000278616	NM_000051.3	1058	tgG/tgT	22/63	1	2	FACETS	0.962	0.852	1	0.962	0.852	1	CLONAL	1	TRUE	1	0.272123248289414	2		924	657	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425501	49425501	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	96	1054	0	ENST00000301067.7:c.12987G>C	p.Gln4329His	p.Q4329H	ENST00000301067	NM_003482.3	4329	caG/caC	39/54	1	2	FACETS	0.883	0.786	0.986	0.883	0.786	0.986	CLONAL	1	TRUE	1	0.272123248289414	2		1054	799	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484043	50484043	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs747506587	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	68	646	0	ENST00000394963.4:c.893A>C	p.Asp298Ala	p.D298A	ENST00000394963	NM_003076.4	298	gAc/gCc	8/13	1	2	FACETS	0.83	0.722	0.947	0.83	0.722	0.947	CLONAL	1	TRUE	1	0.272123248289414	2		646	602	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112892369	112892369	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	71	629	0	ENST00000351677.2:c.527A>T	p.Glu176Val	p.E176V	ENST00000351677	NM_002834.3	176	gAa/gTa	5/16	0.272123248289414	3	FACETS	1	0.9	1	0.517	0.452	0.588	CLONAL	1	TRUE	1	0.272123248289414	3		629	573	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576193	88576193	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	62	569	0	ENST00000360948.2:c.1480C>A	p.Leu494Met	p.L494M	ENST00000360948	NM_001012338.2	494	Ctg/Atg	13/19	1	2	FACETS	0.86	0.743	0.986	0.86	0.743	0.986	CLONAL	1	TRUE	1	0.272123248289414	2		569	530	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877476	89877476	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	84	644	1	ENST00000389301.3:c.287C>T	p.Ser96Phe	p.S96F	ENST00000389301	NM_000135.2	96	tCt/tTt	4/43	0.272123248289414	3	FACETS	1	0.898	1	0.339	0.299	0.382	CLONAL	1	TRUE	0	0.272123248289414	3		645	689	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223061	41223061	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	98	856	1	ENST00000357654.3:c.4870G>T	p.Gly1624Trp	p.G1624W	ENST00000357654	NM_007294.3	1624	Ggg/Tgg	15/23	0.14299323077236	1	FACETS	0.876	0.782	0.977	0.876	0.782	0.977	INDETERMINATE	1	TRUE	0	0.272123248289414	1		857	710	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375004	45375004	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	62	485	0	ENST00000262160.6:c.839A>T	p.Tyr280Phe	p.Y280F	ENST00000262160	NM_005901.5	280	tAt/tTt	8/11	0.2605027222307	1	FACETS	0.776	0.672	0.89	0.776	0.672	0.89	SUBCLONAL	1	TRUE	0	0.272123248289414	1		485	507	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219413	1219413	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs730881971	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	115	488	0	ENST00000326873.7:c.464+1G>T		p.X155_splice	ENST00000326873	NM_000455.4	155			0.272123248289414	2	FACETS	0.911	0.825	1	0.911	0.825	1	CLONAL	2	TRUE	0	0.272123248289414	2		488	464	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134306	11134306	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	109	444	0	ENST00000358026.2:c.2972A>C	p.Lys991Thr	p.K991T	ENST00000358026	NM_001128849.1	991	aAg/aCg	20/36	0.272123248289414	2	FACETS	0.977	0.884	1	0.977	0.884	1	CLONAL	2	TRUE	0	0.272123248289414	2		444	410	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561204	9561204	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	332	725	2	ENST00000353224.5:c.578C>A	p.Ala193Asp	p.A193D	ENST00000353224	NM_177990.2	193	gCc/gAc	4/10	0.272123248289414	7	FACETS	1	0.986	1			1	CLONAL	4	TRUE	NA	0.272123248289414	7		727	926	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739100	40739100	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1158638222	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	187	526	3	ENST00000373198.4:c.3184C>T	p.Arg1062Cys	p.R1062C	ENST00000373198	NM_133170.3	1062	Cgc/Tgc	24/32	0.272123248289414	5	FACETS	0.967	0.897	1	0.967	0.897	1	CLONAL	3	TRUE	2	0.272123248289414	5		529	667	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938537	44938537	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	98	388	0	ENST00000377967.4:c.3085C>G	p.His1029Asp	p.H1029D	ENST00000377967	NM_021140.2	1029	Cat/Gat	20/29	0.272123248289414	2	FACETS	0.776	0.696	0.861			1	SUBCLONAL	2	TRUE	NA	0.272123248289414	2		388	464	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434839	110434839	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	35	544	0	ENST00000375856.3:c.3562G>A	p.Gly1188Ser	p.G1188S	ENST00000375856	NM_003749.2	1188	Ggc/Agc	1/2	0.885749094980396	1	FACETS	0.1	0.081	0.12	0.1	0.081	0.12	SUBCLONAL	1	TRUE	0	0.906265909223929	1		544	424	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593618	55593662	+	inframe_deletion	In_Frame_Del	DEL	GAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTT	GAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTT	-	novel	NA	P-0012411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	262	626	0	ENST00000288135.5:c.1684_1728del	p.Glu562_Leu576del	p.E562_L576del	ENST00000288135	NM_000222.2	562	GAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTT/-	11/21	1	2	FACETS	0.734	0.69	0.778	0.734	0.69	0.778	SUBCLONAL	1	TRUE	1	0.906265909223929	2		626	788	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	101	589	1				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.921	1			1	INDETERMINATE	1	TRUE	NA	0.759606103936937	2		590	262	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0012420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	799	367	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.755881988645104	3	FACETS	0.987	0.969	1	0.987	0.969	1	CLONAL	3	TRUE	0	0.759606103936937	3		367	980	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2969666	2969666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747866557	NA	P-0012420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	537	732	0	ENST00000396946.4:c.1613C>T	p.Ser538Phe	p.S538F	ENST00000396946	NM_032415.4	538	tCc/tTc	12/25	0.759606103936937	4	FACETS	1	0.996	1			1	CLONAL	1	TRUE	NA	0.759606103936937	4		732	1668	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796795	135796795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1322586198	NA	P-0012420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	336	466	1	ENST00000298552.3:c.692C>T	p.Pro231Leu	p.P231L	ENST00000298552	NM_001162426.1	231	cCg/cTg	8/23	1	2	FACETS	0.964	0.914	1	0.964	0.914	1	CLONAL	1	TRUE	1	0.759606103936937	2		467	918	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131455	202131455	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	221	364	0	ENST00000358485.4:c.423A>C	p.Arg141Ser	p.R141S	ENST00000358485	NM_001080125.1	141	agA/agC	2/9	1	2	FACETS	0.865	0.809	0.922	0.865	0.809	0.922	CLONAL	1	TRUE	1	0.759606103936937	2		364	673	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710639	117710639	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	282	549	0	ENST00000368508.3:c.1633T>A	p.Leu545Met	p.L545M	ENST00000368508	NM_002944.2	545	Ttg/Atg	12/43	1	2	FACETS	0.935	0.882	0.989	0.935	0.882	0.989	CLONAL	1	TRUE	1	0.759606103936937	2		549	794	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005036	150005036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1042139265	NA	P-0012420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	196	316	0	ENST00000253339.5:c.1189C>T	p.Pro397Ser	p.P397S	ENST00000253339		397	Cct/Tct	3/7	1	2	FACETS	0.954	0.89	1	0.954	0.89	1	CLONAL	1	TRUE	1	0.759606103936937	2		316	541	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139811032	139811032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	438	856	1	ENST00000247668.2:c.643C>T	p.Pro215Ser	p.P215S	ENST00000247668	NM_021138.3	215	Cct/Tct	7/11	1	2	FACETS	0.895	0.854	0.936	0.895	0.854	0.936	CLONAL	1	TRUE	1	0.759606103936937	2		857	1289	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692827	89692827	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	123	166	0	ENST00000371953.3:c.311T>C	p.Phe104Ser	p.F104S	ENST00000371953	NM_000314.4	104	tTt/tCt	5/9	0.749223184371155	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.759606103936937	1		166	197	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249230	133249230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754985761	NA	P-0012420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	608	502	0	ENST00000320574.5:c.1669C>T	p.Pro557Ser	p.P557S	ENST00000320574	NM_006231.2	557	Cct/Tct	15/49	0.759606103936937	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.759606103936937	2		502	792	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641289	23641289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	270	411	0	ENST00000261584.4:c.2186C>T	p.Pro729Leu	p.P729L	ENST00000261584	NM_024675.3	729	cCc/cTc	5/13	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.759606103936937	2		411	662	SUCCESS
AXL	558	MSKCC	GRCh37	19	41736919	41736919	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	323	564	0	ENST00000301178.4:c.634G>A	p.Gly212Arg	p.G212R	ENST00000301178	NM_021913.4	212	Ggg/Agg	5/20	0.740840136488088	3	FACETS	0.98	0.926	1	0.49	0.463	0.518	CLONAL	1	TRUE	1	0.759606103936937	3		564	1197	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0012437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	164	722	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.16098185490212	2	FACETS	1	0.987	1	0.718	0.658	0.78	CLONAL	1	TRUE	0	0.226870244671329	2		722	1007	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295321	1295321	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0012437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	82	471	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.949	0.836	1	0.949	0.836	1	CLONAL	1	TRUE	1	0.226870244671329	2		471	762	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254623	46254623	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	160	593	1	ENST00000334344.6:c.4813G>T	p.Gly1605Cys	p.G1605C	ENST00000334344	NM_152641.2	1605	Ggc/Tgc	16/21	0.16098185490212	2	FACETS	1	0.985	1	0.668	0.612	0.728	CLONAL	1	TRUE	0	0.226870244671329	2		594	1055	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008210	29008210	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	88	532	0	ENST00000282397.4:c.661C>T	p.Leu221Phe	p.L221F	ENST00000282397	NM_002019.4	221	Ctc/Ttc	5/30	1	2	FACETS	0.846	0.748	0.951	0.846	0.748	0.951	CLONAL	1	TRUE	1	0.226870244671329	2		532	917	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024687	14024687	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs772385411	NA	P-0012437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	62	572	0	ENST00000311895.7:c.913A>G	p.Thr305Ala	p.T305A	ENST00000311895	NM_005236.2	305	Aca/Gca	5/11	1	2	FACETS	0.556	0.479	0.641	0.556	0.479	0.641	SUBCLONAL	1	TRUE	1	0.226870244671329	2		572	983	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032535	47032535	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	100	377	0	ENST00000377604.3:c.442del	p.Gln148SerfsTer14	p.Q148Sfs*14	ENST00000377604	NM_001204468.1	147	ggC/gg	5/24	1	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.226870244671329	1		377	552	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0012460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	371	403	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.766183038622219	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	2	0.788042071240843	4		403	760	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0012460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	143	320	0				ENST00000310581	NM_198253.2	-/1132			0.788042071240843	3	FACETS	1	0.985	1	0.65	0.599	0.702	CLONAL	1	TRUE	1	0.788042071240843	3		320	389	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563252	21563252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	157	590	1	ENST00000382592.4:c.667G>A	p.Gly223Arg	p.G223R	ENST00000382592	NM_014572.2	223	Ggg/Agg	4/8	0.788042071240843	3	FACETS	0.935	0.861	1	0.468	0.43	0.506	CLONAL	1	TRUE	1	0.788042071240843	3		591	594	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169361	11169361	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519777	NA	P-0012460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	246	784	0	ENST00000361445.4:c.7514G>C	p.Arg2505Pro	p.R2505P	ENST00000361445	NM_004958.3	2505	cGa/cCa	56/58	0.788042071240843	2	FACETS	0.952	0.895	1	0.476	0.447	0.505	CLONAL	1	TRUE	0	0.788042071240843	2		784	656	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56872964	56872964	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	540	736	0	ENST00000308159.5:c.2119A>G	p.Ile707Val	p.I707V	ENST00000308159	NM_014669.4	707	Att/Gtt	19/22	0.702151025724068	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.788042071240843	4		736	1170	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668828	52669011	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCAGCTGGAAAGACAAAAAAAGTATTTATAAAGGGACGAATGAGATGAAGAAAGAACCATACTTTAAAGTTCATTTAACAACCTTCCAGATTGAACTAAATATATTTGAAAACTATTATTACTATTATTTTTGAGACAGGGTCTGGCTTTGTCACCCAGGCTGGAGTGCAAGGGTGCGATCTTG	GCAGCTGGAAAGACAAAAAAAGTATTTATAAAGGGACGAATGAGATGAAGAAAGAACCATACTTTAAAGTTCATTTAACAACCTTCCAGATTGAACTAAATATATTTGAAAACTATTATTACTATTATTTTTGAGACAGGGTCTGGCTTTGTCACCCAGGCTGGAGTGCAAGGGTGCGATCTTG	-	novel	NA	P-0012460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	86	394	0	ENST00000394830.3:c.1088-180_1091del		p.X363_splice	ENST00000394830	NM_018313.4	363		12/30	0.788042071240843	3	FACETS	0.642	0.57	0.718	0.321	0.285	0.359	SUBCLONAL	1	TRUE	1	0.788042071240843	3		394	474	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796803	42796819	+	frameshift_variant	Frame_Shift_Del	DEL	CGGAGGTCCTGTCATAA	CGGAGGTCCTGTCATAA	-	novel	NA	P-0012460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	384	774	1	ENST00000575354.2:c.3262_3278del	p.Gly1088SerfsTer57	p.G1088Sfs*57	ENST00000575354	NM_015125.3	1087	ccCGGAGGTCCTGTCATAAca/ccca	14/20	0.788042071240843	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.788042071240843	2		775	428	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0012522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	20	462	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.081	0.061	0.104	0.081	0.061	0.104	SUBCLONAL	1	TRUE	1	0.495570788526788	2		463	1000	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0012522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	118	320	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.921	0.835	1			1	INDETERMINATE	1	TRUE	NA	0.495570788526788	2		320	517	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0012522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	37	537	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.167	0.137	0.201	0.167	0.137	0.201	SUBCLONAL	1	TRUE	1	0.495570788526788	2		537	893	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562738	29562739	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555615472	NA	P-0012522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	198	350	0	ENST00000356175.3:c.3822_3823del	p.Phe1275ProfsTer8	p.F1275Pfs*8	ENST00000356175	NM_000267.3	1273	aCT/a	28/57	0.495570788526788	1	FACETS	0.864	0.803	0.926	0.864	0.803	0.926	CLONAL	1	TRUE	0	0.495570788526788	1		350	696	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740668	58740668	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs759850701	NA	P-0012522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1557	88	669	5	ENST00000305921.3:c.1573G>T	p.Glu525Ter	p.E525*	ENST00000305921	NM_003620.3	525	Gaa/Taa	6/6	1	2	FACETS	0.216	0.19	0.244	0.216	0.19	0.244	SUBCLONAL	1	TRUE	1	0.495570788526788	2		674	1645	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653840	89653840	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0012522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	159	275	0	ENST00000371953.3:c.138C>G	p.Tyr46Ter	p.Y46*	ENST00000371953	NM_000314.4	46	taC/taG	2/9	0.495570788526788	1	FACETS	0.946	0.874	1	0.946	0.874	1	CLONAL	1	TRUE	0	0.495570788526788	1		275	510	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508511	106508511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	132	154	0	ENST00000359195.3:c.505C>T	p.His169Tyr	p.H169Y	ENST00000359195	NM_002649.2	169	Cac/Tac	2/11	0.456078803940929	2	FACETS	0.83	0.787	0.87	0.83	0.787	0.87	INDETERMINATE	2	TRUE	0	0.919221570252942	2		154	173	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs121913468	NA	P-0012526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	439	651	1	ENST00000269571.5:c.2305G>A	p.Asp769Asn	p.D769N	ENST00000269571		769	Gac/Aac	19/27	0.81678569678206	3	FACETS	1	0.994	1			1	CLONAL	1	TRUE	NA	0.919221570252942	3		652	1136	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0012565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	88	354	0	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.230629211078907	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.230629211078907	1		354	527	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28929495	NA	P-0012574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	90	620	0	ENST00000275493.2:c.2155G>A	p.Gly719Ser	p.G719S	ENST00000275493	NM_005228.3	719	Ggc/Agc	18/28	1	2	FACETS	0.992	0.88	1	0.992	0.88	1	CLONAL	1	TRUE	1	0.233230062259611	2		620	778	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249029	55249029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs483352806	NA	P-0012574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	71	629	3	ENST00000275493.2:c.2327G>A	p.Arg776His	p.R776H	ENST00000275493	NM_005228.3	776	cGc/cAc	20/28	1	2	FACETS	0.886	0.773	1	0.886	0.773	1	CLONAL	1	TRUE	1	0.233230062259611	2		632	687	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873759	35873759	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	79	673	0	ENST00000216797.5:c.92A>G	p.Asp31Gly	p.D31G	ENST00000216797	NM_020529.2	31	gAc/gGc	1/6	0.10118876332178	4	FACETS	0.981	0.861	1	0.49	0.43	0.555	INDETERMINATE	1	TRUE	2	0.233230062259611	4		673	852	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0012578-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	420	639	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.742880450912141	1	FACETS	0.973	0.94	1	0.973	0.94	1	CLONAL	1	TRUE	0	0.815371555072221	1		639	627	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099518	157099518	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012578-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	266	400	3	ENST00000346085.5:c.455C>T	p.Pro152Leu	p.P152L	ENST00000346085	NM_020732.3	152	cCc/cTc	1/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.815371555072221	2		403	609	SUCCESS
RET	5979	MSKCC	GRCh37	10	43595973	43595973	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012578-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	456	667	0	ENST00000355710.3:c.140G>A	p.Gly47Asp	p.G47D	ENST00000355710	NM_020975.4	47	gGc/gAc	2/20	0.815371555072221	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.815371555072221	1		667	644	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058309	42058309	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs776096439	NA	P-0012578-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	608	1098	0	ENST00000219905.7:c.8029G>C	p.Asp2677His	p.D2677H	ENST00000219905	NM_001164273.1	2677	Gat/Cat	24/24	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.815371555072221	2		1098	1488	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012579-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	132	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.277519302739762	2		371	794	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593491	48593494	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	rs80338965	NA	P-0012579-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	73	671	1	ENST00000342988.3:c.1245_1248del	p.Asp415GlufsTer20	p.D415Efs*20	ENST00000342988	NM_005359.5	414	ttAGAC/tt	10/12	0.277519302739762	1	FACETS	0.865	0.758	0.98	0.865	0.758	0.98	CLONAL	1	TRUE	0	0.277519302739762	1		672	524	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0012591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	119	395	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	1	0.946	1	1	0.99	1	CLONAL	2	FALSE	1	0.171704817870372	2		395	649	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0012591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	396	534	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.171704817870372	5	FACETS	1	0.977	1			1	CLONAL	5	FALSE	NA	0.171704817870372	5		534	1113	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720875	89720875	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	84	195	0	ENST00000371953.3:c.1026G>T	p.Lys342Asn	p.K342N	ENST00000371953	NM_000314.4	342	aaG/aaT	8/9	1	2	FACETS	1	0.947	1	1	0.986	1	CLONAL	2	FALSE	1	0.171704817870372	2		195	438	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115701	8115704	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GATT	GATT	A	novel	NA	P-0012591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	119	391	0	ENST00000346208.3:c.1048-1_1050delinsA		p.X350_splice	ENST00000346208		350		6/6	1	2	FACETS	0.949	0.858	1	1	0.988	1	CLONAL	2	FALSE	1	0.171704817870372	2		391	730	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0012602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	241	490	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.159963488271267	1	FACETS	1	0.993	1	1	0.993	1	INDETERMINATE	1	TRUE	0	0.475176341444053	1		490	539	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0012602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	1908	558	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.475176341444053	20	FACETS	1	0.993	1			1	CLONAL	16	TRUE	NA	0.475176341444053	20		558	2616	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936096	178936096	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	138	268	0	ENST00000263967.3:c.1638G>C	p.Gln546His	p.Q546H	ENST00000263967	NM_006218.2	546	caG/caC	10/21	0.462785652316627	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	0	0.475176341444053	2		268	286	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104698	209104698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766985383	NA	P-0012602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	99	499	0	ENST00000345146.2:c.880G>A	p.Val294Met	p.V294M	ENST00000345146	NM_005896.2	294	Gtg/Atg	8/10	0.362774464889607	4	FACETS	0.867	0.774	0.966	0.433	0.387	0.483	CLONAL	1	TRUE	2	0.475176341444053	4		499	709	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839847	27839847	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	228	1455	2	ENST00000328488.2:c.247C>A	p.Leu83Met	p.L83M	ENST00000328488	NM_003533.2	83	Ctg/Atg	1/1	1	2	FACETS	0.917	0.855	0.982	0.917	0.855	0.982	CLONAL	1	TRUE	1	0.475176341444053	2		1457	1046	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0012631-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	41	418	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.17706259159008	3	FACETS	1	0.952	1	0.714	0.596	0.844	CLONAL	1	TRUE	1	0.17706259159008	3		421	353	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227019	2227019	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012631-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	20	206	0	ENST00000398665.3:c.4499C>G	p.Ser1500Cys	p.S1500C	ENST00000398665	NM_032482.2	1500	tCt/tGt	27/28	1	2	FACETS	0.93	0.713	1	0.93	0.713	1	CLONAL	1	TRUE	1	0.17706259159008	2		206	243	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012654-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	93	589	1				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.723	0.646	0.804			1	INDETERMINATE	1	TRUE	NA	0.551013096050541	2		590	467	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738801	145738801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747445357	NA	P-0012654-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	175	275	0	ENST00000428558.2:c.2264G>A	p.Arg755Gln	p.R755Q	ENST00000428558	NM_004260.3	755	cGg/cAg	14/22	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.551013096050541	2		275	605	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760932	59760932	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368610199	NA	P-0012654-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	237	364	0	ENST00000259008.2:c.3475G>A	p.Ala1159Thr	p.A1159T	ENST00000259008	NM_032043.2	1159	Gct/Act	20/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.551013096050541	2		364	849	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345264	70345264	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012654-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	265	512	1	ENST00000374080.3:c.2290C>T	p.Arg764Ter	p.R764*	ENST00000374080		764	Cga/Tga	16/45	1	2	FACETS	0.896	0.84	0.954	0.896	0.84	0.954	CLONAL	1	TRUE	1	0.551013096050541	2		513	1073	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0012655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	464	395	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.891	0.852	0.93	0.891	0.852	0.93	CLONAL	1	TRUE	1	0.826403494264824	2		395	1261	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579329	7579329	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912658	NA	P-0012655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	366	355	0	ENST00000269305.4:c.358A>G	p.Lys120Glu	p.K120E	ENST00000269305	NM_001126112.2	120	Aag/Gag	4/11	0.808949811199728	1	FACETS	0.955	0.921	0.989	0.955	0.921	0.989	CLONAL	1	TRUE	0	0.826403494264824	1		355	544	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692902	89692902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909218	NA	P-0012655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	331	246	0	ENST00000371953.3:c.386G>A	p.Gly129Glu	p.G129E	ENST00000371953	NM_000314.4	129	gGa/gAa	5/9	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.826403494264824	2		246	762	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223187	2223187	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	401	431	0	ENST00000326181.6:c.799A>T	p.Thr267Ser	p.T267S	ENST00000326181	NM_032271.2	267	Acg/Tcg	10/21	0.826403494264824	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.826403494264824	1		431	551	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338671	70338671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	514	554	0	ENST00000374080.3:c.67G>T	p.Asp23Tyr	p.D23Y	ENST00000374080		23	Gat/Tat	1/45	0.422779632108565	1	FACETS	0.643	0.618	0.668	0.643	0.618	0.668	INDETERMINATE	1	TRUE	0	0.826403494264824	1		554	1135	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492798	56492798	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	527	523	1	ENST00000407977.2:c.141del	p.Ile48SerfsTer3	p.I48Sfs*3	ENST00000407977		47	atT/at	2/10	0.808949811199728	1	FACETS	0.994	0.965	1	0.994	0.965	1	CLONAL	1	TRUE	0	0.826403494264824	1		524	753	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928081	178928105	+	protein_altering_variant	In_Frame_Del	DEL	AGATTTGCTGAACCCTATTGGTGTT	AGATTTGCTGAACCCTATTGGTGTT	C	novel	NA	P-0012655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	228	384	0	ENST00000263967.3:c.1359_1383delinsC	p.Glu453_Val461delinsAsp	p.E453_V461delinsD	ENST00000263967	NM_006218.2	453	gaAGATTTGCTGAACCCTATTGGTGTT/gaC	8/21	1	2	FACETS	0.695	0.649	0.742	0.695	0.649	0.742	SUBCLONAL	1	TRUE	1	0.826403494264824	2		384	794	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99169373	99169373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1423422253	NA	P-0012659-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	152	329	0	ENST00000074304.5:c.1303G>A	p.Ala435Thr	p.A435T	ENST00000074304	NM_001134224.1	435	Gca/Aca	15/26	1	2	FACETS	0.466	0.425	0.508	0.466	0.425	0.508	SUBCLONAL	1	TRUE	1	0.687037175239401	2		329	950	SUCCESS
EED	8726	MSKCC	GRCh37	11	85963188	85963188	+	splice_acceptor_variant	Splice_Site	DEL	A	A	-	novel	NA	P-0012659-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	252	259	0	ENST00000263360.6:c.268-2del		p.X90_splice	ENST00000263360	NM_003797.3	90			0.687037175239401	1	FACETS	0.944	0.894	0.995	0.944	0.894	0.995	CLONAL	1	TRUE	0	0.687037175239401	1		259	510	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	130	589	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.596863410512137	2		590	292	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0012663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	159	239	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	FALSE	1	0.596863410512137	2		239	510	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0012663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	53	290	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.409	0.349	0.474	0.409	0.349	0.474	SUBCLONAL	1	FALSE	1	0.596863410512137	2		290	434	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254848	16254848	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	57	434	0	ENST00000375759.3:c.2113G>C	p.Glu705Gln	p.E705Q	ENST00000375759	NM_015001.2	705	Gaa/Caa	11/15	1	2	FACETS	0.183	0.156	0.213	0.183	0.156	0.213	SUBCLONAL	1	FALSE	1	0.596863410512137	2		434	1043	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255502	16255502	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	46	309	0	ENST00000375759.3:c.2767G>C	p.Glu923Gln	p.E923Q	ENST00000375759	NM_015001.2	923	Gag/Cag	11/15	1	2	FACETS	0.239	0.2	0.281	0.239	0.2	0.281	SUBCLONAL	1	FALSE	1	0.596863410512137	2		309	646	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057788	27057788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748935625	NA	P-0012663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	183	723	0	ENST00000324856.7:c.1496C>T	p.Ser499Leu	p.S499L	ENST00000324856	NM_006015.4	499	tCg/tTg	3/20	1	2	FACETS	0.505	0.465	0.547	0.505	0.465	0.547	SUBCLONAL	1	FALSE	1	0.596863410512137	2		723	1215	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059176	27059176	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	91	443	0	ENST00000324856.7:c.1813C>T	p.Gln605Ter	p.Q605*	ENST00000324856	NM_006015.4	605	Caa/Taa	4/20	1	2	FACETS	0.292	0.258	0.328	0.292	0.258	0.328	SUBCLONAL	1	FALSE	1	0.596863410512137	2		443	1045	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087360	27087360	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	109	314	0	ENST00000324856.7:c.1934C>A	p.Ser645Ter	p.S645*	ENST00000324856	NM_006015.4	645	tCa/tAa	5/20	1	2	FACETS	0.533	0.479	0.59	0.533	0.479	0.59	SUBCLONAL	1	FALSE	1	0.596863410512137	2		314	685	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0012663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	103	459	1	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	0.826	0.744	0.911	0.826	0.744	0.911	CLONAL	1	FALSE	1	0.596863410512137	2		460	418	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852177	128852177	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	44	454	0	ENST00000249373.3:c.2249C>T	p.Pro750Leu	p.P750L	ENST00000249373	NM_005631.4	750	cCc/cTc	12/12	1	2	FACETS	0.219	0.183	0.26	0.219	0.183	0.26	SUBCLONAL	1	FALSE	1	0.596863410512137	2		454	672	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151893064	151893064	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	221	303	0	ENST00000262189.6:c.4306G>C	p.Glu1436Gln	p.E1436Q	ENST00000262189	NM_170606.2	1436	Gaa/Caa	28/59	1	2	FACETS	0.885	0.825	0.946	0.885	0.825	0.946	CLONAL	1	FALSE	1	0.596863410512137	2		303	837	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738853	145738853	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	94	140	0	ENST00000428558.2:c.2212A>G	p.Lys738Glu	p.K738E	ENST00000428558	NM_004260.3	738	Aaa/Gaa	14/22	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.596863410512137	2		140	221	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691139	18691139	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	138	327	0	ENST00000266497.5:c.3250G>C	p.Glu1084Gln	p.E1084Q	ENST00000266497		1084	Gag/Cag	23/31	1	2	FACETS	0.535	0.487	0.586	0.535	0.487	0.586	SUBCLONAL	1	FALSE	1	0.596863410512137	2		327	864	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246543	46246543	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	96	292	0	ENST00000334344.6:c.4637A>G	p.Asn1546Ser	p.N1546S	ENST00000334344	NM_152641.2	1546	aAt/aGt	15/21	1	2	FACETS	0.503	0.448	0.56	0.503	0.448	0.56	SUBCLONAL	1	FALSE	1	0.596863410512137	2		292	640	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425789	49425789	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs772782391	NA	P-0012663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	100	286	0	ENST00000301067.7:c.12699G>C	p.Gln4233His	p.Q4233H	ENST00000301067	NM_003482.3	4233	caG/caC	39/54	1	2	FACETS	0.727	0.653	0.805	0.727	0.653	0.805	SUBCLONAL	1	FALSE	1	0.596863410512137	2		286	461	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117319	115117319	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	267	437	0	ENST00000257566.3:c.855G>C	p.Gln285His	p.Q285H	ENST00000257566	NM_016569.3	285	caG/caC	4/8	1	2	FACETS	0.848	0.795	0.902	0.848	0.795	0.902	CLONAL	1	FALSE	1	0.596863410512137	2		437	1055	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41962061	41962061	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	248	564	0	ENST00000219905.7:c.969G>C	p.Lys323Asn	p.K323N	ENST00000219905	NM_001164273.1	323	aaG/aaC	2/24	1	2	FACETS	0.605	0.564	0.647	0.605	0.564	0.647	SUBCLONAL	1	FALSE	1	0.596863410512137	2		564	1374	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820624	3820624	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	84	260	0	ENST00000262367.5:c.2827C>T	p.Gln943Ter	p.Q943*	ENST00000262367	NM_004380.2	943	Cag/Tag	14/31	0.107686772365541	3	FACETS	0.632	0.559	0.71	0.211	0.186	0.237	INDETERMINATE	1	FALSE	0	0.596863410512137	3		260	578	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900873	3900873	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	262	407	2	ENST00000262367.5:c.223C>T	p.Arg75Ter	p.R75*	ENST00000262367	NM_004380.2	75	Cga/Tga	2/31	0.107686772365541	3	FACETS	1	0.988	1	0.403	0.378	0.429	INDETERMINATE	1	FALSE	0	0.596863410512137	3		409	942	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0012663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	79	398	1	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	0.352	0.309	0.398	0.352	0.309	0.398	SUBCLONAL	1	FALSE	1	0.596863410512137	2		399	752	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654700	29654700	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	165	356	0	ENST00000356175.3:c.5389G>A	p.Glu1797Lys	p.E1797K	ENST00000356175	NM_000267.3	1797	Gaa/Aaa	37/57	0.107686772365541	3	FACETS	0.856	0.786	0.928	0.285	0.262	0.31	INDETERMINATE	1	FALSE	0	0.596863410512137	3		356	839	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793378	42793378	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	33	299	0	ENST00000575354.2:c.1180C>T	p.Gln394Ter	p.Q394*	ENST00000575354	NM_015125.3	394	Cag/Tag	8/20	1	2	FACETS	0.241	0.196	0.293	0.241	0.196	0.293	SUBCLONAL	1	FALSE	1	0.596863410512137	2		299	458	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794425	42794425	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs771116358	NA	P-0012663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	245	604	0	ENST00000575354.2:c.1505C>G	p.Ser502Cys	p.S502C	ENST00000575354	NM_015125.3	502	tCc/tGc	10/20	1	2	FACETS	0.796	0.744	0.849	0.796	0.744	0.849	SUBCLONAL	1	FALSE	1	0.596863410512137	2		604	1032	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031234	36031234	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	197	430	0	ENST00000358208.4:c.1353C>G	p.Phe451Leu	p.F451L	ENST00000358208		451	ttC/ttG	11/12	1	2	FACETS	0.702	0.65	0.755	0.702	0.65	0.755	SUBCLONAL	1	FALSE	1	0.596863410512137	2		430	941	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710578	40710578	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	227	343	0	ENST00000373198.4:c.4273G>T	p.Val1425Leu	p.V1425L	ENST00000373198	NM_133170.3	1425	Gtg/Ttg	31/32	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.596863410512137	NA		343	722	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281754	46281754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	70	563	1	ENST00000371998.3:c.4201C>T	p.His1401Tyr	p.H1401Y	ENST00000371998		1401	Cac/Tac	22/23	1	2	FACETS	0.197	0.171	0.225	0.197	0.171	0.225	SUBCLONAL	1	FALSE	1	0.596863410512137	2		564	1192	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038729	47038729	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0012663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	194	155	0	ENST00000377604.3:c.736A>T	p.Lys246Ter	p.K246*	ENST00000377604	NM_001204468.1	246	Aag/Tag	9/24	1	1	FACETS	1	0.992	1	1	0.996	1	CLONAL	2	FALSE	0	0.596863410512137	1		155	212	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179050	123179050	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	450	230	0	ENST00000218089.9:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000218089	NM_001042749.1	167	Cag/Tag	8/35	1	1	FACETS	1	0.996	1	1	0.998	1	CLONAL	2	FALSE	0	0.596863410512137	1		230	498	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106300	27106300	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	110	425	0	ENST00000324856.7:c.5911C>G	p.Leu1971Val	p.L1971V	ENST00000324856	NM_006015.4	1971	Ctg/Gtg	20/20	0.262575622429295	2	FACETS	0.859	0.777	0.944	0.859	0.777	0.944	CLONAL	2	TRUE	0	0.307186892055967	2		425	417	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363602	40363602	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	126	350	0	ENST00000397332.2:c.627G>T	p.Gln209His	p.Q209H	ENST00000397332	NM_001033082.2	209	caG/caT	3/3	0.307186892055967	4	FACETS	0.995	0.905	1	0.995	0.905	1	CLONAL	2	TRUE	2	0.307186892055967	4		350	539	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546348	46546348	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1415075907	NA	P-0012684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	181	595	0	ENST00000262741.5:c.181C>T	p.Gln61Ter	p.Q61*	ENST00000262741	NM_003629.3	61	Cag/Tag	2/10	0.307186892055967	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.307186892055967	4		595	711	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015652	27015652	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	118	657	0	ENST00000335756.4:c.239G>T	p.Arg80Leu	p.R80L	ENST00000335756	NM_001809.3	80	cGt/cTt	3/5	0.307186892055967	3	FACETS	1	0.979	1	0.657	0.594	0.724	CLONAL	1	TRUE	1	0.307186892055967	3		657	674	SUCCESS
ALK	238	MSKCC	GRCh37	2	29473992	29473992	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	130	414	0	ENST00000389048.3:c.2183T>C	p.Val728Ala	p.V728A	ENST00000389048	NM_004304.4	728	gTg/gCg	12/29	0.307186892055967	3	FACETS	0.852	0.776	0.931	0.852	0.776	0.931	CLONAL	2	TRUE	1	0.307186892055967	3		414	573	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754879	29754879	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	98	329	1	ENST00000389048.3:c.1056C>A	p.His352Gln	p.H352Q	ENST00000389048	NM_004304.4	352	caC/caA	4/29	0.307186892055967	3	FACETS	0.836	0.75	0.927	0.836	0.75	0.927	CLONAL	2	TRUE	1	0.307186892055967	3		330	440	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051217	128051217	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	126	472	0	ENST00000285398.2:c.106G>T	p.Glu36Ter	p.E36*	ENST00000285398	NM_000122.1	36	Gaa/Taa	2/15	0.264541389441581	5	FACETS	1	0.951	1	0.713	0.648	0.781	CLONAL	2	TRUE	2	0.307186892055967	5		472	560	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873251	136873251	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	159	712	0	ENST00000241393.3:c.247G>T	p.Ala83Ser	p.A83S	ENST00000241393	NM_003467.2	83	Gcc/Tcc	2/2	0.264541389441581	5	FACETS	1	0.978	1	0.784	0.721	0.849	CLONAL	2	TRUE	2	0.307186892055967	5		712	643	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663185	227663185	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	130	471	0	ENST00000305123.5:c.270C>G	p.Asp90Glu	p.D90E	ENST00000305123	NM_005544.2	90	gaC/gaG	1/2	0.291370698461846	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.307186892055967	3		471	449	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266996	41266996	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	77	513	0	ENST00000349496.5:c.667C>G	p.His223Asp	p.H223D	ENST00000349496	NM_001904.3	223	Cat/Gat	5/15	0.307186892055967	3	FACETS	1	0.884	1	0.503	0.442	0.568	CLONAL	1	TRUE	1	0.307186892055967	3		513	575	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125317	47125317	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	154	587	0	ENST00000409792.3:c.5953G>T	p.Glu1985Ter	p.E1985*	ENST00000409792	NM_014159.6	1985	Gag/Tag	12/21	1	2	FACETS	0.794	0.73	0.862	1	0.989	1	SUBCLONAL	2	TRUE	1	0.307186892055967	2		587	631	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155386	106155386	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	68	420	0	ENST00000380013.4:c.287G>C	p.Arg96Pro	p.R96P	ENST00000380013	NM_001127208.2	96	cGc/cCc	3/11	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.307186892055967	2		420	428	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524465	187524465	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	69	356	0	ENST00000441802.2:c.11215G>C	p.Ala3739Pro	p.A3739P	ENST00000441802	NM_005245.3	3739	Gcg/Ccg	19/27	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.307186892055967	2		356	440	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542753	187542753	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200613891	NA	P-0012684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	64	501	0	ENST00000441802.2:c.4987G>A	p.Ala1663Thr	p.A1663T	ENST00000441802	NM_005245.3	1663	Gcc/Acc	10/27	1	2	FACETS	0.906	0.786	1	0.906	0.786	1	CLONAL	1	TRUE	1	0.307186892055967	2		501	460	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226091	226091	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	22	195	0	ENST00000264932.6:c.550G>C	p.Gly184Arg	p.G184R	ENST00000264932	NM_004168.2	184	Ggg/Cgg	5/15	0.307186892055967	3	FACETS	0.672	0.522	0.845	0.336	0.261	0.423	SUBCLONAL	1	TRUE	1	0.307186892055967	3		195	246	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983984	2983984	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	150	629	0	ENST00000396946.4:c.546G>C	p.Lys182Asn	p.K182N	ENST00000396946	NM_032415.4	182	aaG/aaC	5/25	0.291370698461846	3	FACETS	0.947	0.869	1	0.947	0.869	1	CLONAL	2	TRUE	1	0.307186892055967	3		629	595	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259488	55259488	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	122	323	0	ENST00000275493.2:c.2546A>T	p.Gln849Leu	p.Q849L	ENST00000275493	NM_005228.3	849	cAg/cTg	21/28	0.273937312973967	3	FACETS	0.945	0.859	1			1	CLONAL	2	TRUE	NA	0.307186892055967	3		323	485	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92354974	92354974	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	236	407	0	ENST00000265734.4:c.503G>C	p.Arg168Pro	p.R168P	ENST00000265734	NM_001259.6	168	cGc/cCc	4/8	0.264541389441581	5	FACETS	0.882	0.829	0.937	1	0.987	1	CLONAL	4	TRUE	2	0.307186892055967	5		407	636	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126782	5126782	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	149	293	1	ENST00000381652.3:c.3390G>T	p.Met1130Ile	p.M1130I	ENST00000381652	NM_004972.3	1130	atG/atT	25/25	0.219284234931479	3	FACETS	0.997	0.923	1	0.997	0.923	1	CLONAL	3	TRUE	0	0.307186892055967	3		294	374	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32439182	32439182	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	115	386	0	ENST00000332351.3:c.891G>T	p.Met297Ile	p.M297I	ENST00000332351	NM_024426.4	297	atG/atT	4/10	0.219284234931479	3	FACETS	1	0.955	1	0.723	0.657	0.792	CLONAL	2	TRUE	0	0.307186892055967	3		386	398	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524218	18524218	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	219	529	0	ENST00000266497.5:c.1730G>C	p.Trp577Ser	p.W577S	ENST00000266497		577	tGg/tCg	11/31	0.307186892055967	5	FACETS	1	0.955	1	1	0.955	1	CLONAL	3	TRUE	2	0.307186892055967	5		529	676	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563021	21563021	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	154	415	0	ENST00000382592.4:c.898G>T	p.Ala300Ser	p.A300S	ENST00000382592	NM_014572.2	300	Gcc/Tcc	4/8	0.262575622429295	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.307186892055967	2		415	445	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459339	99459339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199672504	NA	P-0012684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	197	379	0	ENST00000268035.6:c.1975C>T	p.Arg659Trp	p.R659W	ENST00000268035	NM_000875.3	659	Cgg/Tgg	9/21	0.264904911107611	4	FACETS	1	0.974	1	1	0.993	1	CLONAL	3	TRUE	2	0.307186892055967	4		379	515	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578254	7578255	+	stop_gained	Nonsense_Mutation	DNP	CT	CT	AA	novel	NA	P-0012684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	113	500	0	ENST00000269305.4:c.594_595delinsTT	p.Glu198_Gly199delinsAspTer	p.E198_G199delinsD*	ENST00000269305	NM_001126112.2	198	gaAGga/gaTTga	6/11	0.262575622429295	2	FACETS	0.819	0.742	0.9	0.819	0.742	0.9	CLONAL	2	TRUE	0	0.307186892055967	2		500	449	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013719	12013719	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	91	349	0	ENST00000353533.5:c.661G>T	p.Glu221Ter	p.E221*	ENST00000353533	NM_003010.3	221	Gaa/Taa	6/11	0.262575622429295	2	FACETS	0.9	0.808	0.997	0.9	0.808	0.997	CLONAL	2	TRUE	0	0.307186892055967	2		349	329	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965514	15965514	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	119	470	0	ENST00000268712.3:c.5292G>T	p.Gln1764His	p.Q1764H	ENST00000268712	NM_006311.3	1764	caG/caT	36/46	0.262575622429295	2	FACETS	0.84	0.763	0.92	0.84	0.763	0.92	CLONAL	2	TRUE	0	0.307186892055967	2		470	461	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511542	38511542	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	101	343	0	ENST00000254066.5:c.1040G>C	p.Arg347Pro	p.R347P	ENST00000254066	NM_000964.3	347	cGg/cCg	8/9	0.289187549926535	3	FACETS	0.975	0.878	1			1	CLONAL	2	TRUE	NA	0.307186892055967	3		343	389	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220504	1220504	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	97	383	0	ENST00000326873.7:c.597G>T	p.Glu199Asp	p.E199D	ENST00000326873	NM_000455.4	199	gaG/gaT	4/10	0.307186892055967	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	2	TRUE	0	0.307186892055967	2		383	311	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902143	50902143	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1389018181	NA	P-0012684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	130	505	0	ENST00000440232.2:c.35G>A	p.Gly12Glu	p.G12E	ENST00000440232	NM_002691.3	12	gGg/gAg	2/27	0.307186892055967	3	FACETS	0.829	0.754	0.907	0.829	0.754	0.907	CLONAL	2	TRUE	1	0.307186892055967	3		505	589	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710559	40710559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	65	374	0	ENST00000373198.4:c.4292C>T	p.Thr1431Ile	p.T1431I	ENST00000373198	NM_133170.3	1431	aCa/aTa	31/32	0.307186892055967	3	FACETS	1	0.894	1	0.344	0.299	0.393	CLONAL	1	TRUE	0	0.307186892055967	3		374	473	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15833966	15833966	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	68	324	0	ENST00000307771.7:c.724G>C	p.Asp242His	p.D242H	ENST00000307771	NM_005089.3	242	Gat/Cat	8/11	1	2	FACETS	0.858	0.755	0.966	1	0.979	1	CLONAL	2	TRUE	1	0.307186892055967	2		324	258	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430346	47430346	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	73	615	0	ENST00000377045.4:c.1621G>T	p.Ala541Ser	p.A541S	ENST00000377045	NM_001654.4	541	Gcc/Tcc	15/16	1	2	FACETS	0.85	0.744	0.964	0.85	0.744	0.964	CLONAL	1	TRUE	1	0.307186892055967	2		615	559	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554355	81554355	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747687365	NA	P-0012684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	70	555	0	ENST00000298171.2:c.379del	p.Leu127SerfsTer2	p.L127Sfs*2	ENST00000298171	NM_000369.2	125	ctC/ct	4/10	1	2	FACETS	0.932	0.815	1	0.932	0.815	1	CLONAL	1	TRUE	1	0.307186892055967	2		555	489	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576185	88576185	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	54	349	0	ENST00000360948.2:c.1488del	p.Asp499ThrfsTer7	p.D499Tfs*7	ENST00000360948	NM_001012338.2	496	gcC/gc	13/19	0.264904911107611	4	FACETS	0.898	0.767	1	0.449	0.383	0.52	CLONAL	1	TRUE	2	0.307186892055967	4		349	512	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098363	11098363	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	121	436	0	ENST00000358026.2:c.885del	p.Thr296ArgfsTer7	p.T296Rfs*7	ENST00000358026	NM_001128849.1	294	gCc/gc	6/36	0.307186892055967	2	FACETS	0.914	0.832	0.999	0.914	0.832	0.999	CLONAL	2	TRUE	0	0.307186892055967	2		436	431	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012689-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	168	589	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.979	0.909	1	0.979	0.909	1	CLONAL	1	TRUE	1	0.765738228740487	2		590	448	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602988	55602988	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0012689-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	157	168	0	ENST00000288135.5:c.2696+2T>G		p.X899_splice	ENST00000288135	NM_000222.2	899			1	2	FACETS	0.913	0.844	0.984	0.913	0.844	0.984	CLONAL	1	TRUE	1	0.765738228740487	2		168	449	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490601	20490601	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012689-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	368	461	0	ENST00000346618.3:c.1338T>G	p.Asp446Glu	p.D446E	ENST00000346618	NM_001949.4	446	gaT/gaG	7/7	1	2	FACETS	0.987	0.939	1	0.987	0.939	1	CLONAL	1	TRUE	1	0.765738228740487	2		461	974	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350042	89350042	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012689-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	449	661	0	ENST00000301030.4:c.2908G>T	p.Glu970Ter	p.E970*	ENST00000301030	NM_001256183.1	970	Gag/Tag	9/13	1	2	FACETS	0.893	0.853	0.934	0.893	0.853	0.934	CLONAL	1	TRUE	1	0.765738228740487	2		661	1313	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012697-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	185	589	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.961	0.896	1	0.961	0.896	1	CLONAL	1	TRUE	1	0.795264736095333	2		590	484	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0012697-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	289	403	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.965	0.913	1	0.965	0.913	1	CLONAL	1	TRUE	1	0.795264736095333	2		403	753	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131161	55131161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012697-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	107	567	0	ENST00000257290.5:c.704G>A	p.Cys235Tyr	p.C235Y	ENST00000257290	NM_006206.4	235	tGt/tAt	5/23	1	2	FACETS	0.229	0.205	0.255	0.229	0.205	0.255	SUBCLONAL	1	TRUE	1	0.795264736095333	2		567	1174	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926909	112926909	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012697-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	262	264	0	ENST00000351677.2:c.1529A>T	p.Gln510Leu	p.Q510L	ENST00000351677	NM_002834.3	510	cAg/cTg	13/16	1	2	FACETS	0.924	0.871	0.978	0.924	0.871	0.978	CLONAL	1	TRUE	1	0.795264736095333	2		264	713	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0012706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	43	604	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.528	0.44	0.626	0.528	0.44	0.626	SUBCLONAL	1	TRUE	1	0.17	2		604	959	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866686	37866686	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	66	708	0	ENST00000269571.5:c.853C>G	p.Pro285Ala	p.P285A	ENST00000269571		285	Ccc/Gcc	7/27	1	2	FACETS	0.788	0.682	0.904	0.788	0.682	0.904	CLONAL	1	TRUE	1	0.17	2		708	985	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610695	52610695	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012710-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	65	488	0	ENST00000394830.3:c.3478C>T	p.Arg1160Ter	p.R1160*	ENST00000394830	NM_018313.4	1160	Cga/Tga	23/30	0.350680182725113	1	FACETS	0.48	0.416	0.55	0.48	0.416	0.55	SUBCLONAL	1	TRUE	0	0.350680182725113	1		488	637	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0012712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	61	541	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	0.191082811278005	4	FACETS	0.402	0.345	0.463	0.201	0.172	0.232	INDETERMINATE	1	TRUE	2	0.450631728701848	4		541	978	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870205	155870205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs563231684	NA	P-0012712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	81	807	1	ENST00000368323.3:c.634C>T	p.Arg212Trp	p.R212W	ENST00000368323	NM_006912.5	212	Cgg/Tgg	6/6	1	2	FACETS	0.313	0.274	0.354	0.313	0.274	0.354	SUBCLONAL	1	TRUE	1	0.450631728701848	2		808	1150	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971022	21971022	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	121	388	0	ENST00000579755.1:c.379T>G	p.Ser127Ala	p.S127A	ENST00000579755		127	Tct/Gct	2/3	0.368358064707097	4	FACETS	0.759	0.689	0.832			1	SUBCLONAL	2	TRUE	NA	0.450631728701848	4		388	513	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012727-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	53	589	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.687	0.587	0.796	0.687	0.587	0.796	SUBCLONAL	1	TRUE	1	0.363671846503687	2		590	424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0012727-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	126	560	0	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	0.36301823138128	1	FACETS	0.839	0.761	0.92	0.839	0.761	0.92	CLONAL	1	TRUE	0	0.363671846503687	1		560	676	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608087	28608087	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs997265952	NA	P-0012727-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	171	712	2	ENST00000241453.7:c.1879G>A	p.Ala627Thr	p.A627T	ENST00000241453	NM_004119.2	627	Gca/Aca	15/24	1	2	FACETS	0.899	0.826	0.975	0.899	0.826	0.975	CLONAL	1	TRUE	1	0.363671846503687	2		714	1046	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417868	138417868	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012727-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	152	539	0	ENST00000289153.2:c.1651T>G	p.Cys551Gly	p.C551G	ENST00000289153	NM_006219.2	551	Tgt/Ggt	11/22	1	2	FACETS	0.887	0.811	0.967	0.887	0.811	0.967	CLONAL	1	TRUE	1	0.363671846503687	2		539	942	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711993	89711993	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012727-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	78	209	0	ENST00000371953.3:c.611C>G	p.Pro204Arg	p.P204R	ENST00000371953	NM_000314.4	204	cCa/cGa	6/9	0.363671846503687	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.363671846503687	1		209	335	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0012730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	262	546	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.465357164850534	5	FACETS	0.889	0.839	0.94	0.889	0.839	0.94	CLONAL	3	TRUE	2	0.528867375409254	5		546	666	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0012730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	178	406	0	ENST00000269305.4:c.920-2A>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.508378220307414	2	FACETS	0.978	0.918	1	0.978	0.918	1	CLONAL	2	TRUE	0	0.528867375409254	2		406	344	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405541	70405541	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs72799515	NA	P-0012730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	184	326	0	ENST00000373644.4:c.3055A>G	p.Lys1019Glu	p.K1019E	ENST00000373644	NM_030625.2	1019	Aaa/Gaa	4/12	0.528867375409254	3	FACETS	0.974	0.921	1	0.974	0.921	1	CLONAL	3	TRUE	0	0.528867375409254	3		326	301	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862850	9862850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751455326	NA	P-0012730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	226	540	0	ENST00000330684.3:c.2453C>T	p.Ala818Val	p.A818V	ENST00000330684	NM_001134407.1	818	gCg/gTg	12/13	0.520429202829227	2	FACETS	0.991	0.937	1	0.991	0.937	1	CLONAL	2	TRUE	0	0.528867375409254	2		540	431	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248487	59248487	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	123	515	1	ENST00000371222.2:c.256G>T	p.Gly86Trp	p.G86W	ENST00000371222	NM_002228.3	86	Ggg/Tgg	1/1	0.528867375409254	5	FACETS	1	0.965	1	0.379	0.343	0.417	CLONAL	1	TRUE	2	0.528867375409254	5		516	734	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584586	189584586	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	115	417	0	ENST00000264731.3:c.882G>C	p.Gln294His	p.Q294H	ENST00000264731	NM_003722.4	294	caG/caC	6/14	0.528867375409254	7	FACETS	1	0.913	1			1	CLONAL	1	TRUE	NA	0.528867375409254	7		417	994	SUCCESS
APC	324	MSKCC	GRCh37	5	112154972	112154972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756336949	NA	P-0012730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	273	501	0	ENST00000257430.4:c.1243G>A	p.Ala415Thr	p.A415T	ENST00000257430	NM_000038.5	415	Gct/Act	10/16	1	2	FACETS	0.752	0.711	0.795	1	0.994	1	SUBCLONAL	2	TRUE	1	0.528867375409254	2		501	686	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120658	94120658	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	258	931	0	ENST00000369303.4:c.393C>G	p.Asp131Glu	p.D131E	ENST00000369303	NM_004440.3	131	gaC/gaG	3/17	0.520429202829227	2	FACETS	0.791	0.746	0.836	0.791	0.746	0.836	SUBCLONAL	2	TRUE	0	0.528867375409254	2		931	617	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55229241	55229241	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	108	444	0	ENST00000275493.2:c.1548G>A	p.Trp516Ter	p.W516*	ENST00000275493	NM_005228.3	516	tgG/tgA	13/28	0.448827775537877	3	FACETS	1	0.975	1	0.621	0.561	0.683	CLONAL	1	TRUE	1	0.528867375409254	3		444	416	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331600	8331600	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	156	637	0	ENST00000356435.5:c.5516C>A	p.Pro1839His	p.P1839H	ENST00000356435		1839	cCc/cAc	33/35	0.528867375409254	1	FACETS	0.582	0.534	0.633	0.582	0.534	0.633	SUBCLONAL	1	TRUE	0	0.528867375409254	1		637	745	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815652	139815652	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767258846	NA	P-0012730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	359	677	4	ENST00000247668.2:c.1123G>A	p.Ala375Thr	p.A375T	ENST00000247668	NM_021138.3	375	Gcc/Acc	9/11	0.448827775537877	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.528867375409254	3		681	853	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576277	88576277	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0012730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	78	221	0	ENST00000360948.2:c.1397-1G>T		p.X466_splice	ENST00000360948	NM_001012338.2	466			0.496265240669793	2	FACETS	0.843	0.759	0.927	0.843	0.759	0.927	CLONAL	2	TRUE	0	0.528867375409254	2		221	175	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141493	11141493	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs11537675	NA	P-0012730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	256	524	0	ENST00000358026.2:c.3470G>T	p.Arg1157Leu	p.R1157L	ENST00000358026	NM_001128849.1	1157	cGg/cTg	25/36	0.520429202829227	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.528867375409254	2		524	472	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649578	48649578	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	127	867	1	ENST00000376670.3:c.62C>A	p.Pro21His	p.P21H	ENST00000376670	NM_002049.3	21	cCt/cAt	2/6	0.445934690518155	1	FACETS	0.617	0.56	0.675	0.617	0.56	0.675	SUBCLONAL	1	TRUE	0	0.528867375409254	1		868	573	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352243	70352243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	71	654	0	ENST00000374080.3:c.4270G>A	p.Gly1424Ser	p.G1424S	ENST00000374080		1424	Ggt/Agt	31/45	0.445934690518155	1	FACETS	0.334	0.291	0.379	0.334	0.291	0.379	SUBCLONAL	1	TRUE	0	0.528867375409254	1		654	592	SUCCESS
BTK	695	MSKCC	GRCh37	X	100629579	100629579	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	71	780	0	ENST00000308731.7:c.185C>A	p.Thr62Asn	p.T62N	ENST00000308731	NM_000061.2	62	aCt/aAt	3/19	0.445934690518155	1	FACETS	0.382	0.334	0.434	0.382	0.334	0.434	SUBCLONAL	1	TRUE	0	0.528867375409254	1		780	517	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537177	80537177	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	56	257	0	ENST00000286548.4:c.221del	p.Gly74AlafsTer17	p.G74Afs*17	ENST00000286548	NM_002072.3	74	gGc/gc	2/7	0.448827775537877	3	FACETS	1	0.879	1	0.509	0.44	0.583	CLONAL	1	TRUE	1	0.528867375409254	3		257	263	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295769	212295769	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	40	373	0	ENST00000342788.4:c.2544T>G	p.Asn848Lys	p.N848K	ENST00000342788	NM_005235.2	848	aaT/aaG	21/28	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		373	668	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430385	47430385	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs947894890	NA	P-0012778-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	169	433	1	ENST00000377045.4:c.1660C>T	p.Arg554Trp	p.R554W	ENST00000377045	NM_001654.4	554	Cgg/Tgg	15/16	0.3	2	FACETS	0.934	0.862	1			1	CLONAL	2	TRUE	NA	0.28	2		434	646	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0012782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1683	315	467	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.392996352867164	8	FACETS	0.874	0.821	0.929	0.291	0.273	0.31	CLONAL	2	TRUE	2	0.392996352867164	8		467	1998	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0012782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	724	407	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.392996352867164	8	FACETS	0.992	0.959	1	0.826	0.799	0.854	CLONAL	5	TRUE	2	0.392996352867164	8		407	1619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579435	7579441	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCGCC	GGCCGCC	-	novel	NA	P-0012782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	300	451	0	ENST00000269305.4:c.246_252del	p.Ala83LeufsTer38	p.A83Lfs*38	ENST00000269305	NM_001126112.2	82	ccGGCGGCC/cc	4/11	0.31036372170661	2	FACETS	0.934	0.884	0.986	0.934	0.884	0.986	CLONAL	2	TRUE	0	0.392996352867164	2		451	817	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs878854073	NA	P-0012783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	26	376	0	ENST00000269305.4:c.673-1G>A		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.221224367921605	4	FACETS	0.616	0.487	0.764	0.308	0.243	0.382	SUBCLONAL	1	TRUE	2	0.26	4		376	409	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0012783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	18	396	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.336995542301974	4	FACETS	0.239	0.179	0.311	0.12	0.089	0.156	SUBCLONAL	1	TRUE	2	0.26	4		396	729	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561564	9561564	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867333778	NA	P-0012783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	14	291	0	ENST00000353224.5:c.218G>A	p.Gly73Glu	p.G73E	ENST00000353224	NM_177990.2	73	gGa/gAa	4/10	0.120080357347993	3	FACETS	0.509	0.368	0.68	0.255	0.184	0.34	INDETERMINATE	1	TRUE	1	0.26	3		291	239	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0012783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	18	396	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.493	0.371	0.637	0.493	0.371	0.637	SUBCLONAL	1	TRUE	1	0.26	2		396	281	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0012783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	39	367	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.336995542301974	4	FACETS	0.565	0.467	0.675	0.283	0.233	0.338	SUBCLONAL	1	TRUE	2	0.26	4		367	669	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574004	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	41	902	2	ENST00000269305.4:c.1023_1024delinsTT	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	341	ttCCga/ttTTga	10/11	0.221224367921605	4	FACETS	0.499	0.414	0.593	0.249	0.207	0.297	SUBCLONAL	1	TRUE	2	0.26	4		904	797	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499706	8499706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	26	529	0	ENST00000356435.5:c.2263G>A	p.Glu755Lys	p.E755K	ENST00000356435		755	Gaa/Aaa	14/35	1	2	FACETS	0.458	0.362	0.568	0.458	0.362	0.568	SUBCLONAL	1	TRUE	1	0.26	2		529	437	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670733	134670733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	20	440	2	ENST00000398015.3:c.644G>A	p.Ser215Asn	p.S215N	ENST00000398015	NM_004441.4	215	aGc/aAc	3/16	0.120080357347993	0	FACETS	0.316	0.241	0.404			1	INDETERMINATE	1	TRUE	0	0.26	0		442	360	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573410	55573410	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	56	457	0	ENST00000288135.5:c.1072A>C	p.Lys358Gln	p.K358Q	ENST00000288135	NM_000222.2	358	Aaa/Caa	6/21	0.120080357347993	0	FACETS	0.56	0.48	0.648			1	INDETERMINATE	1	TRUE	0	0.26	0		457	569	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539624	187539624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1201286281	NA	P-0012783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	35	525	0	ENST00000441802.2:c.8116C>T	p.Pro2706Ser	p.P2706S	ENST00000441802	NM_005245.3	2706	Cct/Tct	10/27	0.120080357347993	0	FACETS	0.432	0.354	0.52			1	INDETERMINATE	1	TRUE	0	0.26	0		525	461	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955152	93955152	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	56	809	2	ENST00000369303.4:c.2746G>A	p.Asp916Asn	p.D916N	ENST00000369303	NM_004440.3	916	Gat/Aat	16/17	1	2	FACETS	0.4	0.341	0.465	0.4	0.341	0.465	SUBCLONAL	1	TRUE	1	0.26	2		811	1077	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224327	55224327	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	21	516	0	ENST00000275493.2:c.1108C>T	p.His370Tyr	p.H370Y	ENST00000275493	NM_005228.3	370	Cac/Tac	9/28	1	2	FACETS	0.386	0.297	0.491	0.386	0.297	0.491	SUBCLONAL	1	TRUE	1	0.26	2		516	418	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139562811	139562811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	35	612	0	ENST00000308874.7:c.77C>T	p.Pro26Leu	p.P26L	ENST00000308874		26	cCc/cTc	3/10	1	2	FACETS	0.65	0.533	0.782	0.65	0.533	0.782	SUBCLONAL	1	TRUE	1	0.26	2		612	414	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456324	32456324	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	17	582	0	ENST00000332351.3:c.568T>A	p.Ser190Thr	p.S190T	ENST00000332351	NM_024426.4	190	Tcc/Acc	1/10	0.120080357347993	0	FACETS	0.308	0.229	0.402			1	INDETERMINATE	1	TRUE	0	0.26	0		582	314	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922247	100922247	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	49	737	0	ENST00000325455.5:c.2265G>A	p.Trp755Ter	p.W755*	ENST00000325455	NM_001202474.3	755	tgG/tgA	5/8	0.3	1	FACETS	0.37	0.312	0.434	0.37	0.312	0.434	SUBCLONAL	1	TRUE	0	0.26	1		737	887	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041695	14041695	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	46	622	0	ENST00000311895.7:c.2242A>G	p.Met748Val	p.M748V	ENST00000311895	NM_005236.2	748	Atg/Gtg	11/11	0.120080357347993	3	FACETS	0.535	0.449	0.63	0.267	0.224	0.315	INDETERMINATE	1	TRUE	1	0.26	3		622	748	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760998	59760998	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	45	637	0	ENST00000259008.2:c.3409T>C	p.Tyr1137His	p.Y1137H	ENST00000259008	NM_032043.2	1137	Tat/Cat	20/20	0.221224367921605	4	FACETS	0.641	0.538	0.756	0.321	0.269	0.378	SUBCLONAL	1	TRUE	2	0.26	4		637	680	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793139	33793139	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	19	593	2	ENST00000498907.2:c.182C>T	p.Ser61Phe	p.S61F	ENST00000498907	NM_004364.3	61	tCc/tTc	1/1	0.221224367921605	0	FACETS	0.304	0.23	0.391			1	SUBCLONAL	1	TRUE	0	0.26	0		595	356	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412925	63412926	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	C	novel	NA	P-0012783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	47	474	0	ENST00000330258.3:c.241_242delinsG	p.Ser81ValfsTer19	p.S81Vfs*19	ENST00000330258	NM_152424.3	81	TCt/Gt	2/2	1	1	FACETS	0.765	0.647	0.895	0.765	0.647	0.895	SUBCLONAL	1	TRUE	0	0.26	1		474	411	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	1498	688	0	ENST00000397062.3:c.246A>C	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaC	2/5	0.762822075885903	4	FACETS	1	0.998	1			1	CLONAL	3	TRUE	NA	0.762822075885903	4		688	2059	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285660	46285660	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	281	528	0	ENST00000334344.6:c.5021del	p.Pro1674LeufsTer27	p.P1674Lfs*27	ENST00000334344	NM_152641.2	1674	Cct/ct	17/21	1	2	FACETS	0.894	0.843	0.946	0.894	0.843	0.946	CLONAL	1	TRUE	1	0.762822075885903	2		528	824	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0012820-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	49	195	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.836	0.712	0.972	0.836	0.712	0.972	CLONAL	1	TRUE	1	0.352986763612923	2		195	332	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178169	56178169	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012820-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	182	618	1	ENST00000399503.3:c.3142C>T	p.Gln1048Ter	p.Q1048*	ENST00000399503	NM_005921.1	1048	Cag/Tag	14/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.352986763612923	2		619	963	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991524	72991524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012820-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	255	1014	0	ENST00000268489.5:c.2521C>T	p.Gln841Ter	p.Q841*	ENST00000268489	NM_006885.3	841	Cag/Tag	2/10	0.352986763612923	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.352986763612923	1		1014	1015	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992393	72992393	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012820-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	198	923	1	ENST00000268489.5:c.1652G>T	p.Ser551Ile	p.S551I	ENST00000268489	NM_006885.3	551	aGt/aTt	2/10	0.352986763612923	1	FACETS	0.887	0.821	0.955	0.887	0.821	0.955	CLONAL	1	TRUE	0	0.352986763612923	1		924	1042	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993296	72993296	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs757253455	NA	P-0012820-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	182	917	0	ENST00000268489.5:c.749C>A	p.Ser250Tyr	p.S250Y	ENST00000268489	NM_006885.3	250	tCt/tAt	2/10	0.352986763612923	1	FACETS	0.86	0.793	0.93	0.86	0.793	0.93	CLONAL	1	TRUE	0	0.352986763612923	1		917	987	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183254	56183254	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012820-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	115	458	2	ENST00000399503.3:c.4167del	p.Phe1389LeufsTer33	p.F1389Lfs*33	ENST00000399503	NM_005921.1	1388	gaT/ga	18/20	1	2	FACETS	0.968	0.873	1	0.968	0.873	1	CLONAL	1	TRUE	1	0.352986763612923	2		460	673	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863589	68863589	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012820-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	176	689	0	ENST00000261769.5:c.2329del	p.Asp777ThrfsTer6	p.D777Tfs*6	ENST00000261769	NM_004360.3	776	ctG/ct	15/16	0.352986763612923	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.352986763612923	1		689	773	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	271	420	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.441437424592499	3	FACETS	0.857	0.806	0.908	0.857	0.806	0.908	CLONAL	2	TRUE	1	0.452606249353863	3		420	857	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0012859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	413	699	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.452606249353863	2	FACETS	0.989	0.946	1	0.989	0.946	1	CLONAL	2	TRUE	0	0.452606249353863	2		699	923	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0012859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	237	598	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.247512041540238	3	FACETS	1	0.989	1	0.635	0.593	0.679	INDETERMINATE	1	TRUE	1	0.452606249353863	3		598	1011	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097211	178097211	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	91	669	0	ENST00000397062.3:c.503C>T	p.Ser168Phe	p.S168F	ENST00000397062	NM_006164.4	168	tCt/tTt	4/5	0.452606249353863	3	FACETS	0.531	0.471	0.596	0.266	0.235	0.298	SUBCLONAL	1	TRUE	1	0.452606249353863	3		669	928	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647511	117647511	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	235	748	2	ENST00000368508.3:c.5433C>A	p.Cys1811Ter	p.C1811*	ENST00000368508	NM_002944.2	1811	tgC/tgA	33/43	0.261273139250215	1	FACETS	0.798	0.745	0.853	0.798	0.745	0.853	INDETERMINATE	1	TRUE	0	0.452606249353863	1		750	1007	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729438	41729438	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1647	339	1088	0	ENST00000242208.4:c.1091C>G	p.Ser364Cys	p.S364C	ENST00000242208	NM_002192.2	364	tCc/tGc	3/3	0.452606249353863	4	FACETS	1	0.982	1	0.274	0.258	0.291	CLONAL	1	TRUE	0	0.452606249353863	4		1088	1986	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272409	38272409	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	167	669	0	ENST00000425967.3:c.1958G>A	p.Arg653Gln	p.R653Q	ENST00000425967	NM_001174067.1	653	cGa/cAa	15/19	0.322445276050865	3	FACETS	0.869	0.798	0.944			1	CLONAL	1	TRUE	NA	0.452606249353863	3		669	1041	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097781	8097781	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763176056	NA	P-0012859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	70	776	1	ENST00000346208.3:c.163G>A	p.Gly55Ser	p.G55S	ENST00000346208		55	Ggt/Agt	2/6	0.441437424592499	3	FACETS	0.302	0.262	0.345	0.151	0.131	0.173	SUBCLONAL	1	TRUE	1	0.452606249353863	3		777	1257	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336274	73336274	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	80	250	0	ENST00000377767.4:c.2129A>C	p.Asn710Thr	p.N710T	ENST00000377767	NM_014953.3	710	aAt/aCt	17/21	0.452606249353863	4	FACETS	1	0.905	1	0.343	0.303	0.386	CLONAL	1	TRUE	1	0.452606249353863	4		250	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0012868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	58	947	0	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	0.218979130995856	4	FACETS	0.758	0.651	0.874			1	INDETERMINATE	1	TRUE	NA	0.372571753277347	4		947	564	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49413009	49413009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519953	NA	P-0012868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	72	646	0	ENST00000418115.1:c.14G>A	p.Arg5Gln	p.R5Q	ENST00000418115	NM_001664.2	5	cGg/cAg	2/5	0.163825519532599	3	FACETS	0.575	0.501	0.654	0.287	0.25	0.327	INDETERMINATE	1	TRUE	1	0.372571753277347	3		646	798	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246293	46246293	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	72	519	0	ENST00000334344.6:c.4387C>T	p.Gln1463Ter	p.Q1463*	ENST00000334344	NM_152641.2	1463	Caa/Taa	15/21	0.372571753277347	4	FACETS	0.757	0.661	0.861	0.378	0.33	0.431	SUBCLONAL	1	TRUE	2	0.372571753277347	4		519	701	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39537555	39537555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	89	539	0	ENST00000262039.4:c.89G>A	p.Arg30Lys	p.R30K	ENST00000262039	NM_002647.2	30	aGa/aAa	2/25	0.163825519532599	3	FACETS	0.723	0.64	0.811	0.361	0.32	0.406	INDETERMINATE	1	TRUE	1	0.372571753277347	3		539	784	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs878854073	NA	P-0012888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	112	405	1	ENST00000269305.4:c.673-1G>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.282113488661882	1	FACETS	0.989	0.891	1	0.989	0.891	1	CLONAL	1	TRUE	0	0.293256518021268	1		406	659	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0012888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	54	264	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.456	0.389	0.531	0.456	0.389	0.531	SUBCLONAL	1	TRUE	1	0.293256518021268	2		264	807	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937194	36937194	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1587	104	1051	0	ENST00000361632.4:c.1125G>C	p.Trp375Cys	p.W375C	ENST00000361632		375	tgG/tgC	9/16	1	2	FACETS	0.419	0.374	0.468	0.419	0.374	0.468	SUBCLONAL	1	TRUE	1	0.293256518021268	2		1051	1691	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55238870	55238870	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	77	472	1	ENST00000275493.2:c.1883G>A	p.Cys628Tyr	p.C628Y	ENST00000275493	NM_005228.3	628	tGc/tAc	16/28	1	2	FACETS	0.503	0.44	0.571	0.503	0.44	0.571	SUBCLONAL	1	TRUE	1	0.293256518021268	2		473	1044	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273014	55273014	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	61	491	1	ENST00000275493.2:c.3337C>T	p.Gln1113Ter	p.Q1113*	ENST00000275493	NM_005228.3	1113	Cag/Tag	28/28	1	2	FACETS	0.412	0.354	0.475	0.412	0.354	0.475	SUBCLONAL	1	TRUE	1	0.293256518021268	2		492	1010	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8246257	8246257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	55	467	0	ENST00000335790.3:c.377G>C	p.Gly126Ala	p.G126A	ENST00000335790	NM_002315.2	126	gGa/gCa	4/4	1	2	FACETS	0.46	0.393	0.535	0.46	0.393	0.535	SUBCLONAL	1	TRUE	1	0.293256518021268	2		467	815	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562199	21562199	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1584	101	1078	0	ENST00000382592.4:c.1720C>T	p.Gln574Ter	p.Q574*	ENST00000382592	NM_014572.2	574	Cag/Tag	4/8	1	2	FACETS	0.409	0.363	0.457	0.409	0.363	0.457	SUBCLONAL	1	TRUE	1	0.293256518021268	2		1078	1685	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914679	32914679	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1687	105	1140	1	ENST00000380152.3:c.6187G>A	p.Gly2063Arg	p.G2063R	ENST00000380152		2063	Gga/Aga	11/27	1	2	FACETS	0.4	0.356	0.446	0.4	0.356	0.446	SUBCLONAL	1	TRUE	1	0.293256518021268	2		1141	1792	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050843	49050843	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1566240914	NA	P-0012888-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	26	216	1	ENST00000267163.4:c.2527G>C	p.Glu843Gln	p.E843Q	ENST00000267163	NM_000321.2	843	Gag/Cag	25/27	1	2	FACETS	0.406	0.321	0.504	0.406	0.321	0.504	SUBCLONAL	1	TRUE	1	0.293256518021268	2		217	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0012943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	95	612	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.17	2		613	1087	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0012943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	85	597	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.999	0.881	1	0.999	0.881	1	CLONAL	1	TRUE	1	0.17	2		597	1001	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66777363	66777363	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1179	83	874	0	ENST00000307102.5:c.729G>C	p.Gln243His	p.Q243H	ENST00000307102	NM_002755.3	243	caG/caC	7/11	1	2	FACETS	0.774	0.68	0.875	0.774	0.68	0.875	SUBCLONAL	1	TRUE	1	0.17	2		874	1262	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589569	67589592	+	inframe_deletion	In_Frame_Del	DEL	TGTAGGGAAAAAATTACATGAATA	TGTAGGGAAAAAATTACATGAATA	-	novel	NA	P-0012943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	34	346	0	ENST00000274335.5:c.1333_1356del	p.Val445_Tyr452del	p.V445_Y452del	ENST00000274335		444	gcTGTAGGGAAAAAATTACATGAATAt/gct	10/15	1	2	FACETS	0.626	0.51	0.757	0.626	0.51	0.757	SUBCLONAL	1	TRUE	1	0.17	2		346	639	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107135	27107135	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0012944-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	175	289	0	ENST00000324856.7:c.6746C>G	p.Ser2249Ter	p.S2249*	ENST00000324856	NM_006015.4	2249	tCa/tGa	20/20	1	2	FACETS	0.785	0.725	0.847	1	0.99	1	SUBCLONAL	2	TRUE	1	0.32	2		289	697	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0012949-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	43	320	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.791	0.668	0.924	0.791	0.668	0.924	CLONAL	1	TRUE	1	0.492065516542865	2		320	221	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0012949-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	177	971	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	0.907	0.837	0.98	0.907	0.837	0.98	CLONAL	1	TRUE	1	0.492065516542865	2		971	793	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730916	40730916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765075213	NA	P-0012949-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	45	394	1	ENST00000373198.4:c.3619C>T	p.Arg1207Cys	p.R1207C	ENST00000373198	NM_133170.3	1207	Cgt/Tgt	27/32	0.320781207739574	1	FACETS	0.487	0.412	0.57	0.487	0.412	0.57	SUBCLONAL	1	TRUE	0	0.492065516542865	1		395	283	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888163	112888163	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397507509	NA	P-0012949-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	67	795	0	ENST00000351677.2:c.179G>T	p.Gly60Val	p.G60V	ENST00000351677	NM_002834.3	60	gGt/gTt	3/16	1	2	FACETS	0.472	0.41	0.539	0.472	0.41	0.539	SUBCLONAL	1	TRUE	1	0.492065516542865	2		795	577	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	103	589	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.506763956733883	2		590	391	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955592	55955592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560674167	NA	P-0012967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	223	730	0	ENST00000263923.4:c.3353G>A	p.Arg1118Gln	p.R1118Q	ENST00000263923	NM_002253.2	1118	cGa/cAa	25/30	1	2	FACETS	0.924	0.861	0.99	0.924	0.861	0.99	CLONAL	1	TRUE	1	0.506763956733883	2		730	952	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180802	106180802	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	138	374	0	ENST00000380013.4:c.3830A>T	p.Asp1277Val	p.D1277V	ENST00000380013	NM_001127208.2	1277	gAt/gTt	7/11	1	2	FACETS	0.88	0.803	0.96	0.88	0.803	0.96	CLONAL	1	TRUE	1	0.506763956733883	2		374	619	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624292	89624292	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	138	282	0	ENST00000371953.3:c.66C>G	p.Asp22Glu	p.D22E	ENST00000371953	NM_000314.4	22	gaC/gaG	1/9	0.506763956733883	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.506763956733883	1		282	334	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	103	589	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.827	0.745	0.914	0.827	0.745	0.914	CLONAL	1	TRUE	1	0.558207733063631	2		590	446	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0012979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	112	239	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	0.558207733063631	2		239	372	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1555525367	NA	P-0012979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	242	531	0	ENST00000269305.4:c.783-1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	0.958	0.896	1	0.958	0.896	1	CLONAL	1	TRUE	1	0.558207733063631	2		531	905	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508728	148508728	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs267601395	NA	P-0012979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	272	591	0	ENST00000320356.2:c.1936T>C	p.Tyr646His	p.Y646H	ENST00000320356	NM_004456.4	646	Tac/Cac	16/20	1	2	FACETS	0.997	0.937	1	0.997	0.937	1	CLONAL	1	TRUE	1	0.558207733063631	2		591	977	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747342068	NA	P-0012979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	189	457	0	ENST00000269305.4:c.394A>G	p.Lys132Glu	p.K132E	ENST00000269305	NM_001126112.2	132	Aag/Gag	5/11	1	2	FACETS	0.92	0.853	0.99	0.92	0.853	0.99	CLONAL	1	TRUE	1	0.558207733063631	2		457	736	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257447	16257447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	112	538	0	ENST00000375759.3:c.4712G>A	p.Ser1571Asn	p.S1571N	ENST00000375759	NM_015001.2	1571	aGc/aAc	11/15	0.376133920712912	1	FACETS	0.371	0.333	0.411	0.371	0.333	0.411	SUBCLONAL	1	TRUE	0	0.558207733063631	1		538	780	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462123	120462123	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	223	549	0	ENST00000256646.2:c.5593C>T	p.Gln1865Ter	p.Q1865*	ENST00000256646	NM_024408.3	1865	Cag/Tag	31/34	0.376133920712912	1	FACETS	0.772	0.721	0.824	0.772	0.721	0.824	SUBCLONAL	1	TRUE	0	0.558207733063631	1		549	746	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982502	25982502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	194	437	0	ENST00000435504.4:c.788G>A	p.Arg263Lys	p.R263K	ENST00000435504		263	aGa/aAa	9/13	1	2	FACETS	0.961	0.892	1	0.961	0.892	1	CLONAL	1	TRUE	1	0.558207733063631	2		437	723	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12632405	12632405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	291	692	0	ENST00000251849.4:c.1262C>T	p.Thr421Ile	p.T421I	ENST00000251849	NM_002880.3	421	aCc/aTc	12/17	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.558207733063631	2		692	1033	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167695	185167695	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	320	685	0	ENST00000265026.3:c.1018G>A	p.Gly340Arg	p.G340R	ENST00000265026	NM_004721.4	340	Gga/Aga	6/14	1	2	FACETS	0.926	0.874	0.98	0.926	0.874	0.98	CLONAL	1	TRUE	1	0.558207733063631	2		685	1238	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557992	187557992	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	164	441	0	ENST00000441802.2:c.3719A>G	p.Asp1240Gly	p.D1240G	ENST00000441802	NM_005245.3	1240	gAc/gGc	5/27	1	2	FACETS	0.835	0.768	0.904	0.835	0.768	0.904	CLONAL	1	TRUE	1	0.558207733063631	2		441	704	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584747	187584747	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1358297166	NA	P-0012979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	163	420	5	ENST00000441802.2:c.3286C>T	p.Arg1096Ter	p.R1096*	ENST00000441802	NM_005245.3	1096	Cga/Tga	3/27	1	2	FACETS	0.975	0.899	1	0.975	0.899	1	CLONAL	1	TRUE	1	0.558207733063631	2		425	599	SUCCESS
APC	324	MSKCC	GRCh37	5	112174899	112174899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141444802	NA	P-0012979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	195	448	0	ENST00000257430.4:c.3608G>A	p.Gly1203Glu	p.G1203E	ENST00000257430	NM_000038.5	1203	gGa/gAa	16/16	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.558207733063631	2		448	689	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545815	106545815	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs370598588	NA	P-0012979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	132	346	0	ENST00000359195.3:c.3292G>C	p.Glu1098Gln	p.E1098Q	ENST00000359195	NM_002649.2	1098	Gag/Cag	11/11	1	2	FACETS	0.92	0.84	1	0.92	0.84	1	CLONAL	1	TRUE	1	0.558207733063631	2		346	514	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494241	140494241	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	323	816	0	ENST00000288602.6:c.1007C>T	p.Pro336Leu	p.P336L	ENST00000288602	NM_004333.4	336	cCt/cTt	8/18	1	2	FACETS	0.991	0.936	1	0.991	0.936	1	CLONAL	1	TRUE	1	0.558207733063631	2		816	1168	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994260	21994260	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	190	441	0	ENST00000579755.1:c.71T>A	p.Val24Glu	p.V24E	ENST00000579755		24	gTg/gAg	1/3	0.558207733063631		FACETS		0.951	1				CLONAL	1	TRUE	0	0.558207733063631	1		441	480	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412303	139412304	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	469	561	1	ENST00000277541.6:c.1341_1342delinsTT	p.Arg448Ter	p.R448*	ENST00000277541	NM_017617.3	447	ccCCga/ccTTga	8/34	0.555156736572299	2	FACETS	0.945	0.909	0.981	0.945	0.909	0.981	CLONAL	2	TRUE	0	0.558207733063631	2		562	889	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417362	139417363	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AT	novel	NA	P-0012979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	188	539	0	ENST00000277541.6:c.681_682delinsAT	p.Cys227_Gln228delinsTer	p.C227_Q228delins*	ENST00000277541	NM_017617.3	227	tgCCag/tgATag	4/34	0.555156736572299	2	FACETS	0.907	0.84	0.975	0.453	0.42	0.488	CLONAL	1	TRUE	0	0.558207733063631	2		539	743	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606727	43606727	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs115423919	NA	P-0012979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	276	697	0	ENST00000355710.3:c.1336G>A	p.Gly446Ser	p.G446S	ENST00000355710	NM_020975.4	446	Ggt/Agt	7/20	1	2	FACETS	0.943	0.886	1	0.943	0.886	1	CLONAL	1	TRUE	1	0.558207733063631	2		697	1049	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195794	102195794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	380	886	1	ENST00000263464.3:c.554C>T	p.Ser185Leu	p.S185L	ENST00000263464	NM_001165.4	185	tCg/tTg	2/9	1	2	FACETS	0.97	0.92	1	0.97	0.92	1	CLONAL	1	TRUE	1	0.558207733063631	2		887	1404	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372530	118372531	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0012979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	287	732	0	ENST00000534358.1:c.6463_6464delinsTT	p.Pro2155Leu	p.P2155L	ENST00000534358	NM_005933.3	2155	CCa/TTa	26/36	1	2	FACETS	0.952	0.896	1	0.952	0.896	1	CLONAL	1	TRUE	1	0.558207733063631	2		732	1080	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231439	46231439	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	222	472	0	ENST00000334344.6:c.1279G>T	p.Glu427Ter	p.E427*	ENST00000334344	NM_152641.2	427	Gaa/Taa	10/21	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.558207733063631	2		472	757	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245000	46245000	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	322	774	0	ENST00000334344.6:c.3094C>T	p.Gln1032Ter	p.Q1032*	ENST00000334344	NM_152641.2	1032	Cag/Tag	15/21	1	2	FACETS	0.918	0.866	0.971	0.918	0.866	0.971	CLONAL	1	TRUE	1	0.558207733063631	2		774	1257	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436589	110436590	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	105	336	0	ENST00000375856.3:c.1811_1812delinsTT	p.Thr604Ile	p.T604I	ENST00000375856	NM_003749.2	604	aCC/aTT	1/2	0.558207733063631	1	FACETS	0.965	0.878	1	0.965	0.878	1	CLONAL	1	TRUE	0	0.558207733063631	1		336	281	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358521	67358521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	137	357	1	ENST00000327367.4:c.29C>T	p.Pro10Leu	p.P10L	ENST00000327367	NM_005902.3	10	cCg/cTg	1/9	0.558207733063631	1	FACETS	0.882	0.811	0.956	0.882	0.811	0.956	CLONAL	1	TRUE	0	0.558207733063631	1		358	401	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554546	63554546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	207	472	0	ENST00000307078.5:c.193C>T	p.Pro65Ser	p.P65S	ENST00000307078	NM_004655.3	65	Ccg/Tcg	2/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.558207733063631	2		472	703	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300168	15300168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	281	731	0	ENST00000263388.2:c.1108C>T	p.Pro370Ser	p.P370S	ENST00000263388	NM_000435.2	370	Ccg/Tcg	7/33	1	2	FACETS	0.967	0.909	1	0.967	0.909	1	CLONAL	1	TRUE	1	0.558207733063631	2		731	1041	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912051	50912051	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	327	969	0	ENST00000440232.2:c.1785C>A	p.Asp595Glu	p.D595E	ENST00000440232	NM_002691.3	595	gaC/gaA	15/27	1	2	FACETS	0.895	0.845	0.947	0.895	0.845	0.947	CLONAL	1	TRUE	1	0.558207733063631	2		969	1309	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164524	36164524	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012979-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	133	367	0	ENST00000300305.3:c.1351G>A	p.Asp451Asn	p.D451N	ENST00000300305		451	Gac/Aac	8/8	1	2	FACETS	0.918	0.838	1	0.918	0.838	1	CLONAL	1	TRUE	1	0.558207733063631	2		367	519	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012982-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	114	589	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.337218607234797	2		590	617	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934152	48934152	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0012982-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	48	243	0	ENST00000267163.4:c.608-1G>A		p.X203_splice	ENST00000267163	NM_000321.2	203			0.337218607234797	1	FACETS	0.89	0.758	1	0.89	0.758	1	CLONAL	1	TRUE	0	0.337218607234797	1		243	266	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692844	89692844	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1114167629	NA	P-0012982-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	50	139	0	ENST00000371953.3:c.328C>T	p.Gln110Ter	p.Q110*	ENST00000371953	NM_000314.4	110	Caa/Taa	5/9	0.337218607234797	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.337218607234797	1		139	179	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012982-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	228	388	0	ENST00000269305.4:c.380C>A	p.Ser127Tyr	p.S127Y	ENST00000269305	NM_001126112.2	127	tCc/tAc	5/11	0.321099991329234	2	FACETS	0.834	0.779	0.89	0.834	0.779	0.89	CLONAL	2	TRUE	0	0.337218607234797	2		388	811	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814728	139814728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1345839275	NA	P-0012982-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1224	223	741	6	ENST00000247668.2:c.721C>T	p.Arg241Trp	p.R241W	ENST00000247668	NM_021138.3	241	Cgg/Tgg	8/11	1	2	FACETS	0.914	0.849	0.982	0.914	0.849	0.982	CLONAL	1	TRUE	1	0.337218607234797	2		747	1447	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0012996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	179	357	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.216308429252761	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.234552738890696	2		357	717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0012996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	209	631	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.17342247859154	2	FACETS	0.766	0.71	0.824	0.766	0.71	0.824	SUBCLONAL	2	TRUE	0	0.234552738890696	2		631	1164	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276914	123276914	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	68	598	0	ENST00000358487.5:c.1003G>C	p.Glu335Gln	p.E335Q	ENST00000358487	NM_000141.4	335	Gag/Cag	8/18	0.19944427881396	3	FACETS	0.621	0.538	0.71	0.31	0.269	0.355	SUBCLONAL	1	TRUE	1	0.234552738890696	3		598	1044	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944961	31944961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1441610501	NA	P-0012996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	158	596	0	ENST00000340398.3:c.140C>T	p.Ala47Val	p.A47V	ENST00000340398	NM_001013699.2	47	gCg/gTg	1/1	0.214011470763397	3	FACETS	0.786	0.72	0.856	0.786	0.72	0.856	SUBCLONAL	2	TRUE	1	0.234552738890696	3		596	957	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262096	10262096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1557	119	850	0	ENST00000340748.4:c.2195C>T	p.Ser732Phe	p.S732F	ENST00000340748		732	tCt/tTt	23/40	0.234552738890696	2	FACETS	0.605	0.544	0.671	0.303	0.272	0.336	SUBCLONAL	1	TRUE	0	0.234552738890696	2		850	1676	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332655	65332655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	98	601	0	ENST00000342505.4:c.884C>T	p.Ser295Leu	p.S295L	ENST00000342505	NM_002227.2	295	tCa/tTa	7/25	1	2	FACETS	0.882	0.786	0.986	0.882	0.786	0.986	CLONAL	1	TRUE	1	0.234552738890696	2		601	947	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505593	186505593	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1321	112	653	0	ENST00000323963.5:c.1001C>T	p.Ala334Val	p.A334V	ENST00000323963		334	gCt/gTt	10/11	0.19944427881396	3	FACETS	0.745	0.667	0.827	0.372	0.333	0.414	SUBCLONAL	1	TRUE	1	0.234552738890696	3		653	1433	SUCCESS
APC	324	MSKCC	GRCh37	5	112179275	112179275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	85	550	0	ENST00000257430.4:c.7984G>A	p.Glu2662Lys	p.E2662K	ENST00000257430	NM_000038.5	2662	Gag/Aag	16/16	0.132640854096264	3	FACETS	0.753	0.664	0.85	0.377	0.332	0.425	INDETERMINATE	1	TRUE	1	0.234552738890696	3		550	1075	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513233	149513233	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	94	650	1	ENST00000261799.4:c.850G>C	p.Glu284Gln	p.E284Q	ENST00000261799	NM_002609.3	284	Gaa/Caa	6/23	0.132640854096264	3	FACETS	0.7	0.62	0.785	0.35	0.31	0.393	INDETERMINATE	1	TRUE	1	0.234552738890696	3		651	1280	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671765	30671765	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	79	561	0	ENST00000376406.3:c.5195C>G	p.Ser1732Cys	p.S1732C	ENST00000376406	NM_014641.2	1732	tCc/tGc	10/15	0.234552738890696	2	FACETS	0.687	0.602	0.778	0.343	0.301	0.389	SUBCLONAL	1	TRUE	0	0.234552738890696	2		561	981	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183095	32183095	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	123	679	0	ENST00000375023.3:c.1929G>C	p.Gln643His	p.Q643H	ENST00000375023	NM_004557.3	643	caG/caC	12/30	0.234552738890696	2	FACETS	0.799	0.72	0.882	0.399	0.36	0.441	SUBCLONAL	1	TRUE	0	0.234552738890696	2		679	1313	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631325	117631325	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1181	80	728	0	ENST00000368508.3:c.6353G>C	p.Arg2118Thr	p.R2118T	ENST00000368508	NM_002944.2	2118	aGa/aCa	40/43	0.234552738890696	2	FACETS	0.541	0.474	0.613	0.27	0.237	0.307	SUBCLONAL	1	TRUE	0	0.234552738890696	2		728	1261	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93607788	93607788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867869952	NA	P-0012996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	77	562	1	ENST00000375746.1:c.490G>A	p.Glu164Lys	p.E164K	ENST00000375746	NM_001174167.1	164	Gaa/Aaa	3/14	0.234552738890696	1	FACETS	0.613	0.536	0.695	0.613	0.536	0.695	SUBCLONAL	1	TRUE	0	0.234552738890696	1		563	946	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989014	85989014	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	66	468	0	ENST00000263360.6:c.1180G>C	p.Glu394Gln	p.E394Q	ENST00000263360	NM_003797.3	394	Gaa/Caa	11/12	0.19944427881396	3	FACETS	0.706	0.611	0.809	0.353	0.305	0.405	SUBCLONAL	1	TRUE	1	0.234552738890696	3		468	891	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447003	49447003	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1043654062	NA	P-0012996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1229	108	657	0	ENST00000301067.7:c.941C>G	p.Ser314Cys	p.S314C	ENST00000301067	NM_003482.3	314	tCt/tGt	7/54	0.214011470763397	3	FACETS	0.77	0.688	0.856	0.385	0.344	0.428	SUBCLONAL	1	TRUE	1	0.234552738890696	3		657	1337	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0013004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	222	452	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.233624405884172	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.233624405884172	2		452	844	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805058	43805058	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	159	819	0	ENST00000372470.3:c.508C>A	p.Arg170Ser	p.R170S	ENST00000372470	NM_005373.2	170	Cgc/Agc	4/12	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.233624405884172	2		819	1298	SUCCESS
ATR	545	MSKCC	GRCh37	3	142238593	142238593	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	111	596	1	ENST00000350721.4:c.4300G>T	p.Glu1434Ter	p.E1434*	ENST00000350721	NM_001184.3	1434	Gag/Tag	24/47	1	2	FACETS	0.949	0.852	1	0.949	0.852	1	CLONAL	1	TRUE	1	0.233624405884172	2		597	1001	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557791	187557791	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	122	630	0	ENST00000441802.2:c.3920G>T	p.Gly1307Val	p.G1307V	ENST00000441802	NM_005245.3	1307	gGa/gTa	5/27	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.233624405884172	2		630	1009	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856072	151856072	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1284	142	729	0	ENST00000262189.6:c.11546A>T	p.Gln3849Leu	p.Q3849L	ENST00000262189	NM_170606.2	3849	cAg/cTg	44/59	0.226528068979386	3	FACETS	0.952	0.865	1	0.476	0.432	0.522	CLONAL	1	TRUE	1	0.233624405884172	3		729	1426	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097644	8097644	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	65	320	0	ENST00000346208.3:c.26G>C	p.Arg9Pro	p.R9P	ENST00000346208		9	cGc/cCc	2/6	1	2	FACETS	0.983	0.853	1	0.983	0.853	1	CLONAL	1	TRUE	1	0.233624405884172	2		320	566	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608537	28608537	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	80	442	0	ENST00000241453.7:c.1605C>A	p.Phe535Leu	p.F535L	ENST00000241453	NM_004119.2	535	ttC/ttA	13/24	0.217023099940754	1	FACETS	0.911	0.802	1	0.911	0.802	1	CLONAL	1	TRUE	0	0.233624405884172	1		442	664	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281155	15281155	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	145	765	0	ENST00000263388.2:c.5101G>T	p.Ala1701Ser	p.A1701S	ENST00000263388	NM_000435.2	1701	Gcg/Tcg	27/33	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.233624405884172	2		765	1196	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790013	40790013	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	113	578	1	ENST00000373198.4:c.2718C>A	p.Tyr906Ter	p.Y906*	ENST00000373198	NM_133170.3	906	taC/taA	18/32	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.233624405884172	2		579	821	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356231	70356231	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	182	407	0	ENST00000374080.3:c.5126G>C	p.Arg1709Pro	p.R1709P	ENST00000374080		1709	cGa/cCa	37/45	1	1	FACETS	0.993	0.919	1	1	0.993	1	CLONAL	2	TRUE	0	0.233624405884172	1		407	693	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473615	67473616	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0013004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	111	635	0	ENST00000327367.4:c.695_696delinsTT	p.Trp232Phe	p.W232F	ENST00000327367	NM_005902.3	232	tGG/tTT	6/9	0.217023099940754	1	FACETS	0.891	0.8	0.988	0.891	0.8	0.988	CLONAL	1	TRUE	0	0.233624405884172	1		635	942	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162735796	162735796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	69	637	0	ENST00000367921.3:c.1105G>A	p.Ala369Thr	p.A369T	ENST00000367921	NM_006182.2	369	Gca/Aca	10/18	1	2	FACETS	0.996	0.866	1	0.996	0.866	1	CLONAL	1	TRUE	1	0.17	2		637	815	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47600634	47600634	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	41	603	0	ENST00000263735.4:c.109A>T	p.Asn37Tyr	p.N37Y	ENST00000263735	NM_002354.2	37	Aac/Tac	2/9	1	2	FACETS	0.604	0.502	0.719	0.604	0.502	0.719	SUBCLONAL	1	TRUE	1	0.17	2		603	798	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149543	61149543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759650174	NA	P-0013012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	47	514	0	ENST00000295025.8:c.1733C>T	p.Ser578Leu	p.S578L	ENST00000295025	NM_002908.2	578	tCg/tTg	11/11	1	2	FACETS	0.911	0.768	1	0.911	0.768	1	CLONAL	1	TRUE	1	0.17	2		514	607	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864938	117864938	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1259968025	NA	P-0013012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	58	618	0	ENST00000297338.2:c.1171C>T	p.Arg391Cys	p.R391C	ENST00000297338	NM_006265.2	391	Cgc/Tgc	10/14	1	2	FACETS	0.793	0.679	0.917	0.793	0.679	0.917	CLONAL	1	TRUE	1	0.17	2		618	861	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685315	89685315	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1554897280	NA	P-0013012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	39	271	0	ENST00000371953.3:c.209+1G>T		p.X70_splice	ENST00000371953	NM_000314.4	70			1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.17	2		271	319	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0013012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	43	298	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.17	2		298	398	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142008	108142008	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	32	414	0	ENST00000278616.4:c.2952A>C	p.Gln984His	p.Q984H	ENST00000278616	NM_000051.3	984	caA/caC	20/63	1	2	FACETS	0.597	0.483	0.726	0.597	0.483	0.726	SUBCLONAL	1	TRUE	1	0.17	2		414	631	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877335	28877335	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750851829	NA	P-0013012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	61	543	0	ENST00000282397.4:c.3986C>T	p.Ser1329Leu	p.S1329L	ENST00000282397	NM_002019.4	1329	tCg/tTg	30/30	1	2	FACETS	0.797	0.685	0.918	0.797	0.685	0.918	CLONAL	1	TRUE	1	0.17	2		543	901	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945970	17945970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568403015	NA	P-0013012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	53	706	1	ENST00000458235.1:c.1969C>T	p.Arg657Trp	p.R657W	ENST00000458235	NM_000215.3	657	Cgg/Tgg	15/24	1	2	FACETS	0.638	0.542	0.743	0.638	0.542	0.743	SUBCLONAL	1	TRUE	1	0.17	2		707	978	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573890	41573890	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1295897899	NA	P-0013012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	62	543	0	ENST00000263253.7:c.6175A>G	p.Arg2059Gly	p.R2059G	ENST00000263253	NM_001429.3	2059	Agg/Ggg	31/31	1	2	FACETS	0.878	0.757	1	0.878	0.757	1	CLONAL	1	TRUE	1	0.17	2		543	831	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339328	70339328	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0013012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	52	544	0	ENST00000374080.3:c.204+1G>T		p.X68_splice	ENST00000374080		68			1	2	FACETS	0.817	0.694	0.952	0.817	0.694	0.952	CLONAL	1	TRUE	1	0.17	2		544	749	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984420	72984421	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0013012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1394	88	898	0	ENST00000268489.5:c.3163_3164del	p.Leu1055AlafsTer23	p.L1055Afs*23	ENST00000268489	NM_006885.3	1055	CTg/g	3/10	1	2	FACETS	0.699	0.616	0.787	0.699	0.616	0.787	SUBCLONAL	1	TRUE	1	0.17	2		898	1482	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589663	67589673	+	splice_donor_variant,intron_variant	Splice_Site	DEL	GTGAGTTTTCT	GTGAGTTTTCT	-	novel	NA	P-0013012-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	27	172	0	ENST00000274335.5:c.1425+1_1425+11del		p.X475_splice	ENST00000274335		475			1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.17	2		172	243	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0013033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	218	537	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.196600212845442	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.202698331472113	2		537	917	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0013033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	150	856	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	0.202698331472113	2		857	1230	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293937	1293937	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	92	558	0	ENST00000310581.5:c.1064C>G	p.Thr355Ser	p.T355S	ENST00000310581	NM_198253.2	355	aCt/aGt	2/16	0.202698331472113	3	FACETS	1	0.957	1			1	CLONAL	1	TRUE	NA	0.202698331472113	3		558	862	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0013051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	325	571	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.215142724693828	3	FACETS	1	0.978	1	0.711	0.672	0.75	CLONAL	2	TRUE	0	0.329740410302318	3		571	1077	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966966	25966966	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	154	644	0	ENST00000435504.4:c.2240G>T	p.Gly747Val	p.G747V	ENST00000435504		747	gGt/gTt	13/13	0.329740410302318	4	FACETS	1	0.941	1	0.346	0.316	0.378	CLONAL	1	TRUE	1	0.329740410302318	4		644	1195	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155411	99155411	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747244472	NA	P-0013051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	151	602	3	ENST00000074304.5:c.637G>A	p.Ala213Thr	p.A213T	ENST00000074304	NM_001134224.1	213	Gct/Act	9/26	0.268593869572604	4	FACETS	1	0.96	1	0.362	0.33	0.396	CLONAL	1	TRUE	1	0.329740410302318	4		605	1120	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288529	15288529	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	77	153	0	ENST00000263388.2:c.4210G>C	p.Glu1404Gln	p.E1404Q	ENST00000263388	NM_000435.2	1404	Gag/Cag	24/33	0.329740410302318	5	FACETS	0.881	0.778	0.991	0.588	0.519	0.661	CLONAL	2	TRUE	2	0.329740410302318	5		153	396	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792285	33792285	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1188	150	655	1	ENST00000498907.2:c.1036C>T	p.Pro346Ser	p.P346S	ENST00000498907	NM_004364.3	346	Cca/Tca	1/1	0.329740410302318	3	FACETS	0.792	0.722	0.866	0.396	0.361	0.433	SUBCLONAL	1	TRUE	1	0.329740410302318	3		656	1338	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0013076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	712	484	0	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	0.808769308425095	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.808769308425095	3		484	781	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033970	49033970	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0013076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	222	328	0	ENST00000267163.4:c.2106+1G>A		p.X702_splice	ENST00000267163	NM_000321.2	702			0.796544551813008	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.808769308425095	2		328	273	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	163	371	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	0.78	2		371	395	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0013080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	103	298	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.989	0.9	1	0.989	0.9	1	CLONAL	1	TRUE	1	0.78	2		298	267	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204864	NA	P-0013080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	143	349	2	ENST00000371953.3:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000371953	NM_000314.4	171	Cag/Tag	6/9	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.78	2		351	347	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023151	27023179	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	-	novel	NA	P-0013080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	407	167	0	ENST00000324856.7:c.267_295del	p.Ser90ProfsTer11	p.S90Pfs*11	ENST00000324856	NM_006015.4	86	gGCGGAGCCGGCAGCGGCGGCGGGCCCGGC/g	1/20	1	2	FACETS	0.812	0.782	0.84	1	0.997	1	CLONAL	2	TRUE	1	0.78	2		167	643	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591135	67591136	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0013080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	97	324	0	ENST00000274335.5:c.1732_1733del	p.Asp578ProfsTer23	p.D578Pfs*23	ENST00000274335		576	acGAga/acga	12/15	1	2	FACETS	0.987	0.895	1	0.987	0.895	1	CLONAL	1	TRUE	1	0.78	2		324	252	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654721	67654721	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0013080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	131	431	0	ENST00000264010.4:c.1207+1G>A		p.X403_splice	ENST00000264010	NM_006565.3	403			1	2	FACETS	0.875	0.802	0.949	0.875	0.802	0.949	CLONAL	1	TRUE	1	0.78	2		431	384	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696597	47696597	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	209	591	0	ENST00000347630.2:c.351G>A	p.Met117Ile	p.M117I	ENST00000347630	NM_001007230.1	117	atG/atA	5/11	1	2	FACETS	0.813	0.759	0.869	0.813	0.759	0.869	CLONAL	1	TRUE	1	0.78	2		591	659	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344068	70344068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	663	1211	2	ENST00000374080.3:c.1804G>A	p.Glu602Lys	p.E602K	ENST00000374080		602	Gaa/Aaa	13/45	0.173493528329756	1	FACETS	0.705	0.681	0.729	0.705	0.681	0.729	INDETERMINATE	1	TRUE	0	0.78	1		1213	1471	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092989	27092993	+	frameshift_variant	Frame_Shift_Del	DEL	AAGTT	AAGTT	-	novel	NA	P-0013080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	214	512	0	ENST00000324856.7:c.2922_2926del	p.Lys974AsnfsTer31	p.K974Nfs*31	ENST00000324856	NM_006015.4	974	AAGTTa/a	10/20	1	2	FACETS	0.865	0.809	0.923	0.865	0.809	0.923	CLONAL	1	TRUE	1	0.78	2		512	634	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86686687	86686689	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	novel	NA	P-0013080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	133	339	0	ENST00000274376.6:c.3134_3136del	p.Asp1045del	p.D1045del	ENST00000274376	NM_002890.2	1044	aATGat/aat	25/25	1	2	FACETS	0.85	0.78	0.923	0.85	0.78	0.923	CLONAL	1	TRUE	1	0.78	2		339	401	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525121	157525122	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0013080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	110	364	0	ENST00000346085.5:c.5020_5021del	p.Ser1674ProfsTer14	p.S1674Pfs*14	ENST00000346085	NM_020732.3	1672	aaTCtc/aatc	19/20	1	2	FACETS	0.873	0.794	0.954	0.873	0.794	0.954	CLONAL	1	TRUE	1	0.78	2		364	323	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525076	157525077	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0013080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	227	533	0	ENST00000346085.5:c.4972_4973del	p.Ile1658Ter	p.I1658*	ENST00000346085	NM_020732.3	1657	acTAtt/actt	19/20	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.78	2		533	578	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591126	67591129	+	frameshift_variant	Frame_Shift_Del	DEL	GAGA	GAGA	-	novel	NA	P-0013080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	90	311	1	ENST00000274335.5:c.1719_1722del	p.Lys575ArgfsTer6	p.K575Rfs*6	ENST00000274335		573	ctGAGA/ct	12/15	1	2	FACETS	0.874	0.787	0.964	0.874	0.787	0.964	CLONAL	1	TRUE	1	0.78	2		312	264	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	31	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.689	0.558	0.838	0.689	0.558	0.838	SUBCLONAL	1	TRUE	1	0.23	2		371	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	46	507	0	ENST00000269305.4:c.403del	p.Cys135AlafsTer35	p.C135Afs*35	ENST00000269305	NM_001126112.2	135	Tgc/gc	5/11	1	2	FACETS	0.998	0.842	1	0.998	0.842	1	CLONAL	1	TRUE	1	0.23	2		507	401	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244157	41244157	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	31	468	0	ENST00000357654.3:c.3391G>C	p.Asp1131His	p.D1131H	ENST00000357654	NM_007294.3	1131	Gat/Cat	10/23	0.178105510955489	1	FACETS	0.586	0.474	0.713	0.586	0.474	0.713	SUBCLONAL	1	TRUE	0	0.23	1		468	407	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141465	11141465	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	39	596	0	ENST00000358026.2:c.3442G>T	p.Glu1148Ter	p.E1148*	ENST00000358026	NM_001128849.1	1148	Gag/Tag	25/36	0.3	6	FACETS	0.684	0.565	0.817			1	SUBCLONAL	1	TRUE	NA	0.23	6		596	724	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585519	29585519	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013164-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	30	132	0	ENST00000356175.3:c.4268A>T	p.Lys1423Met	p.K1423M	ENST00000356175	NM_000267.3	1423	aAg/aTg	31/57	0.483339471793078	1	FACETS	0.798	0.656	0.952	0.798	0.656	0.952	CLONAL	1	TRUE	0	0.483339471793078	1		132	118	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0013165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	213	851	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.3	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		851	986	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0013165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1741	488	1212	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	0.3	3	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	3		1212	2229	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0013165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	357	704	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.195197345933028	4	FACETS		NA	1			1	NA	NA	FALSE	2	NA	4		704	1142	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526314	189526314	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	354	351	0	ENST00000264731.3:c.578C>T	p.Thr193Met	p.T193M	ENST00000264731	NM_003722.4	193	aCg/aTg	4/14	0.3	3	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	3		351	638	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587179	189587179	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	281	644	0	ENST00000264731.3:c.1196A>G	p.Glu399Gly	p.E399G	ENST00000264731	NM_003722.4	399	gAa/gGa	9/14	0.3	3	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	3		644	1238	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481609	56481609	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1256589883	NA	P-0013165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	424	959	1	ENST00000267101.3:c.644A>G	p.Asn215Ser	p.N215S	ENST00000267101	NM_001982.3	215	aAt/aGt	6/28	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		960	1088	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0013165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	790	497	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.131266995578838	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		497	1184	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	349	799	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	0.131266995578838	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		799	1120	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285129	15285129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	142	595	0	ENST00000263388.2:c.4486G>A	p.Asp1496Asn	p.D1496N	ENST00000263388	NM_000435.2	1496	Gat/Aat	25/33	0.3	3	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	3		595	753	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0013165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	161	666	0	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	0.3	3	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	3		666	747	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089520	27089709	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGGCATGGCTGGAGGCATAAACCCCATGGGTGCCGGAGGTCAAATGCATGGACAGCCTGGCATCCCACCTTATGGCACACTCCCTCCAGGGAGGATGAGTCACGCCTCCATGGGCAACCGGCCTTATGGCCCTAACATGGCCAATATGCCACCTCAGGTTGGGTCAGGGATGTGTCCCCCACCAGGGG	GCAGGCATGGCTGGAGGCATAAACCCCATGGGTGCCGGAGGTCAAATGCATGGACAGCCTGGCATCCCACCTTATGGCACACTCCCTCCAGGGAGGATGAGTCACGCCTCCATGGGCAACCGGCCTTATGGCCCTAACATGGCCAATATGCCACCTCAGGTTGGGTCAGGGATGTGTCCCCCACCAGGGG	-	novel	NA	P-0013165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	326	763	0	ENST00000324856.7:c.2479_2668del	p.Gly827Ter	p.G827*	ENST00000324856	NM_006015.4	826	GCAGGCATGGCTGGAGGCATAAACCCCATGGGTGCCGGAGGTCAAATGCATGGACAGCCTGGCATCCCACCTTATGGCACACTCCCTCCAGGGAGGATGAGTCACGCCTCCATGGGCAACCGGCCTTATGGCCCTAACATGGCCAATATGCCACCTCAGGTTGGGTCAGGGATGTGTCCCCCACCAGGGGgc/gc	8/20	0.195197345933028	4	FACETS		NA	1			1	NA	NA	FALSE	2	NA	4		763	726	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0013165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	109	138	1	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.3	3	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	3		139	196	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371810	55371831	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGCCCCGAGGGCGGCCGCGT	TGGGCCCCGAGGGCGGCCGCGT	-	novel	NA	P-0013165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	85	73	0	ENST00000297316.4:c.500_521del	p.Leu167ArgfsTer213	p.L167Rfs*213	ENST00000297316	NM_022454.3	167	cTGGGCCCCGAGGGCGGCCGCGTg/cg	2/2	0.3	5	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	5		73	187	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	149	589	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.462345499419774	2		590	624	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	343	367	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.294956442638436	3	FACETS	0.955	0.907	1	0.637	0.604	0.67	CLONAL	2	TRUE	0	0.462345499419774	3		367	956	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	341	438	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.462345499419774	2		438	1107	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455644	189455644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772867228	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	164	337	0	ENST00000264731.3:c.178G>A	p.Asp60Asn	p.D60N	ENST00000264731	NM_003722.4	60	Gat/Aat	2/14	1	2	FACETS	0.94	0.864	1	0.94	0.864	1	CLONAL	1	TRUE	1	0.462345499419774	2		337	755	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	183	523	0	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	NA	2	FACETS	0.667	0.615	0.723			1	INDETERMINATE	1	TRUE	NA	0.462345499419774	2		523	1186	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1261	507	855	1	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.179339156542473	1	FACETS	0.954	0.911	0.997	0.954	0.911	0.997	INDETERMINATE	1	TRUE	0	0.462345499419774	1		856	1768	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858947	57858947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	520	986	2	ENST00000228682.2:c.443C>T	p.Ser148Phe	p.S148F	ENST00000228682	NM_005269.2	148	tCc/tTc	5/12	0.388337611907582	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.462345499419774	1		988	1720	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641174	117641174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2009	242	842	0	ENST00000368508.3:c.5797G>A	p.Glu1933Lys	p.E1933K	ENST00000368508	NM_002944.2	1933	Gag/Aag	36/43	0.294956442638436	3	FACETS	0.573	0.532	0.615	0.191	0.177	0.205	SUBCLONAL	1	TRUE	0	0.462345499419774	3		842	2251	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251817	10251817	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200950656	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	384	697	1	ENST00000340748.4:c.3310C>T	p.Arg1104Cys	p.R1104C	ENST00000340748		1104	Cgt/Tgt	30/40	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.462345499419774	2		698	1442	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561130	9561130	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	209	437	0	ENST00000353224.5:c.652G>A	p.Glu218Lys	p.E218K	ENST00000353224	NM_177990.2	218	Gag/Aag	4/10	1	2	FACETS	0.964	0.895	1	0.964	0.895	1	CLONAL	1	TRUE	1	0.462345499419774	2		437	938	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385271	41385271	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	249	427	0	ENST00000373198.4:c.690G>A	p.Trp230Ter	p.W230*	ENST00000373198	NM_133170.3	230	tgG/tgA	6/32	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.462345499419774	2		427	975	SUCCESS
INSRR	3645	MSKCC	GRCh37	1	156812033	156812033	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	106	180	0	ENST00000368195.3:c.3268G>A	p.Gly1090Arg	p.G1090R	ENST00000368195	NM_014215.2	1090	Ggg/Agg	19/22	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.462345499419774	2		180	407	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097997	178097997	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368680070	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	171	360	0	ENST00000397062.3:c.383C>T	p.Pro128Leu	p.P128L	ENST00000397062	NM_006164.4	128	cCg/cTg	3/5	1	2	FACETS	0.769	0.707	0.834	0.769	0.707	0.834	SUBCLONAL	1	TRUE	1	0.462345499419774	2		360	962	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662175	227662175	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749309744	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	281	553	0	ENST00000305123.5:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000305123	NM_005544.2	427	tCc/tTc	1/2	1	2	FACETS	0.98	0.92	1	0.98	0.92	1	CLONAL	1	TRUE	1	0.462345499419774	2		553	1240	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141020	55141020	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	130	476	0	ENST00000257290.5:c.1666G>A	p.Glu556Lys	p.E556K	ENST00000257290	NM_006206.4	556	Gaa/Aaa	12/23	0.179339156542473	1	FACETS	0.455	0.412	0.5	0.455	0.412	0.5	INDETERMINATE	1	TRUE	0	0.462345499419774	1		476	951	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106162541	106162541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1560551786	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	229	380	0	ENST00000380013.4:c.3455G>A	p.Gly1152Glu	p.G1152E	ENST00000380013	NM_001127208.2	1152	gGa/gAa	4/11	0.179339156542473	1	FACETS	0.906	0.846	0.967	0.906	0.846	0.967	INDETERMINATE	1	TRUE	0	0.462345499419774	1		380	841	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629043	187629043	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	122	364	0	ENST00000441802.2:c.1939G>A	p.Ala647Thr	p.A647T	ENST00000441802	NM_005245.3	647	Gct/Act	2/27	0.179339156542473	1	FACETS	0.526	0.475	0.579	0.526	0.475	0.579	INDETERMINATE	1	TRUE	0	0.462345499419774	1		364	772	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460582	149460582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	161	317	0	ENST00000286301.3:c.55G>A	p.Gly19Arg	p.G19R	ENST00000286301	NM_005211.3	19	Gga/Aga	3/22	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.462345499419774	2		317	630	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170312	32170312	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	331	340	0	ENST00000375023.3:c.3296G>A	p.Gly1099Glu	p.G1099E	ENST00000375023	NM_004557.3	1099	gGa/gAa	21/30	0.294956442638436	3	FACETS	1	0.982	1	0.713	0.677	0.749	CLONAL	2	TRUE	0	0.462345499419774	3		340	824	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729504	41729504	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1309	975	929	0	ENST00000242208.4:c.1025C>T	p.Pro342Leu	p.P342L	ENST00000242208	NM_002192.2	342	cCc/cTc	3/3	0.294956442638436	3	FACETS	1	0.996	1	0.758	0.736	0.78	CLONAL	2	TRUE	0	0.462345499419774	3		929	2284	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339361	116339361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	160	391	0	ENST00000397752.3:c.223G>A	p.Glu75Lys	p.E75K	ENST00000397752	NM_000245.2	75	Gag/Aag	2/21	0.294956442638436	3	FACETS	0.728	0.666	0.793	0.243	0.222	0.265	SUBCLONAL	1	TRUE	0	0.462345499419774	3		391	1171	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8501060	8501060	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	180	286	0	ENST00000356435.5:c.1823-1G>A		p.X608_splice	ENST00000356435		608			0.179339156542473	1	FACETS	0.964	0.893	1	0.964	0.893	1	INDETERMINATE	1	TRUE	0	0.462345499419774	1		286	621	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915934	127915934	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1523	226	834	1	ENST00000373547.4:c.547C>T	p.Gln183Ter	p.Q183*	ENST00000373547	NM_002721.4	183	Cag/Tag	6/7	0.179339156542473	1	FACETS	0.43	0.398	0.462	0.43	0.398	0.462	INDETERMINATE	1	TRUE	0	0.462345499419774	1		835	1749	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206711	102206711	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	212	584	0	ENST00000263464.3:c.1339A>T	p.Ile447Phe	p.I447F	ENST00000263464	NM_001165.4	447	Atc/Ttc	7/9	0.179339156542473	1	FACETS	0.552	0.512	0.594	0.552	0.512	0.594	INDETERMINATE	1	TRUE	0	0.462345499419774	1		584	1277	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344438	118344438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	129	270	0	ENST00000534358.1:c.2564C>T	p.Pro855Leu	p.P855L	ENST00000534358	NM_005933.3	855	cCc/cTc	3/36	0.179339156542473	1	FACETS	0.693	0.63	0.759	0.693	0.63	0.759	INDETERMINATE	1	TRUE	0	0.462345499419774	1		270	619	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359392	118359392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	147	469	0	ENST00000534358.1:c.4396C>T	p.Pro1466Ser	p.P1466S	ENST00000534358	NM_005933.3	1466	Cct/Tct	11/36	0.179339156542473	1	FACETS	0.438	0.399	0.479	0.438	0.399	0.479	INDETERMINATE	1	TRUE	0	0.462345499419774	1		469	1117	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244196	46244196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1355268695	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	49	480	0	ENST00000334344.6:c.2290C>T	p.His764Tyr	p.H764Y	ENST00000334344	NM_152641.2	764	Cac/Tac	15/21	0.388337611907582	1	FACETS	0.173	0.146	0.204	0.173	0.146	0.204	SUBCLONAL	1	TRUE	0	0.462345499419774	1		480	940	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865047	57865047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61734542	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	536	1029	0	ENST00000228682.2:c.2524C>T	p.Pro842Ser	p.P842S	ENST00000228682	NM_005269.2	842	Cca/Tca	12/12	0.388337611907582	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.462345499419774	1		1029	1716	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012462	29012462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	37	396	0	ENST00000282397.4:c.409G>A	p.Glu137Lys	p.E137K	ENST00000282397	NM_002019.4	137	Gag/Aag	4/30	0.388337611907582	1	FACETS	0.174	0.142	0.209	0.174	0.142	0.209	SUBCLONAL	1	TRUE	0	0.462345499419774	1		396	709	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678625	88678625	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	74	169	0	ENST00000360948.2:c.911C>T	p.Pro304Leu	p.P304L	ENST00000360948	NM_001012338.2	304	cCc/cTc	9/19	0.34823121653201	3	FACETS	0.921	0.81	1	0.46	0.405	0.52	CLONAL	1	TRUE	1	0.462345499419774	3		169	428	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625640	1625640	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773698137	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1362	374	752	0	ENST00000344749.5:c.434G>A	p.Gly145Glu	p.G145E	ENST00000344749	NM_001136139.2	145	gGg/gAg	7/19	1	2	FACETS	0.932	0.882	0.983	0.932	0.882	0.983	CLONAL	1	TRUE	1	0.462345499419774	2		752	1736	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231555	5231555	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs994725876	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	191	317	0	ENST00000357368.4:c.1921C>T	p.Pro641Ser	p.P641S	ENST00000357368	NM_002850.3	641	Ccg/Tcg	14/38	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.462345499419774	2		317	752	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385247	41385247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	274	500	0	ENST00000373198.4:c.714G>A	p.Met238Ile	p.M238I	ENST00000373198	NM_133170.3	238	atG/atA	6/32	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.462345499419774	2		500	1122	SUCCESS
AR	367	MSKCC	GRCh37	X	66765844	66765844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	361	631	3	ENST00000374690.3:c.856C>T	p.Pro286Ser	p.P286S	ENST00000374690	NM_000044.3	286	Cca/Tca	1/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.462345499419774	2		634	1439	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692801	89692821	+	inframe_deletion	In_Frame_Del	DEL	ACCACAGCTAGAACTTATCAA	ACCACAGCTAGAACTTATCAA	-	novel	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	116	273	0	ENST00000371953.3:c.288_308del	p.Gln97_Pro103del	p.Q97_P103del	ENST00000371953	NM_000314.4	95	ccACCACAGCTAGAACTTATCAAa/cca	5/9	0.462345499419774	1	FACETS	0.839	0.761	0.92	0.839	0.761	0.92	CLONAL	1	TRUE	0	0.462345499419774	1		273	460	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092990	27092997	+	frameshift_variant	Frame_Shift_Del	DEL	AGTTAACT	AGTTAACT	-	novel	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	258	577	0	ENST00000324856.7:c.2921_2928del	p.Lys974ThrfsTer30	p.K974Tfs*30	ENST00000324856	NM_006015.4	974	aAGTTAACT/a	10/20	1	2	FACETS	0.877	0.82	0.936	0.877	0.82	0.936	CLONAL	1	TRUE	1	0.462345499419774	2		577	1272	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547370	106547372	+	missense_variant	Missense_Mutation	TNP	GAC	GAC	AAG	novel	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	394	378	0	ENST00000369096.4:c.607_609delinsAAG	p.Asp203Lys	p.D203K	ENST00000369096	NM_001198.3	203	GAC/AAG	4/7	0.294956442638436	3	FACETS	1	0.975	1	0.689	0.657	0.722	CLONAL	2	TRUE	0	0.462345499419774	3		378	1015	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518033	8518034	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	novel	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	129	617	0	ENST00000356435.5:c.1357_1358delinsAA	p.Val453Asn	p.V453N	ENST00000356435		453	GTt/AAt	10/35	0.179339156542473	1	FACETS	0.375	0.339	0.413	0.375	0.339	0.413	INDETERMINATE	1	TRUE	0	0.462345499419774	1		617	1144	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947540	48947541	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	40	321	0	ENST00000267163.4:c.1128-1_1128delinsAA		p.X376_splice	ENST00000267163	NM_000321.2	376		12/27	0.388337611907582	1	FACETS	0.235	0.195	0.281	0.235	0.195	0.281	SUBCLONAL	1	TRUE	0	0.462345499419774	1		321	565	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242063	105242064	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	388	714	0	ENST00000349310.3:c.360_361delinsTT	p.Arg121Trp	p.R121W	ENST00000349310	NM_001014432.1	120	ttCCgg/ttTTgg	6/15	0.179339156542473	1	FACETS	0.859	0.815	0.904	0.859	0.815	0.904	INDETERMINATE	1	TRUE	0	0.462345499419774	1		714	1502	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15273372	15273373	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	226	520	0	ENST00000263388.2:c.5816_5817delinsAA	p.Gly1939Glu	p.G1939E	ENST00000263388	NM_000435.2	1939	gGG/gAA	32/33	1	2	FACETS	0.876	0.815	0.939	0.876	0.815	0.939	CLONAL	1	TRUE	1	0.462345499419774	2		520	1116	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39762932	39762933	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0013166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	194	405	0	ENST00000288319.7:c.903_904delinsTT	p.Arg302Cys	p.R302C	ENST00000288319	NM_182918.3	301	agCCgc/agTTgc	9/10	0.179339156542473	1	FACETS	0.737	0.682	0.793	0.737	0.682	0.793	INDETERMINATE	1	TRUE	0	0.462345499419774	1		405	876	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0013201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	352	500	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.703657613165156	3	FACETS	1	0.994	1	0.797	0.768	0.824	CLONAL	2	TRUE	0	0.819050922314048	3		500	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0013201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	280	714	1	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	0.777412278769102	1	FACETS	0.876	0.836	0.915	0.876	0.836	0.915	CLONAL	1	TRUE	0	0.819050922314048	1		715	461	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11206806	11206806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760642166	NA	P-0013201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	349	656	1	ENST00000361445.4:c.4613G>A	p.Arg1538Gln	p.R1538Q	ENST00000361445	NM_004958.3	1538	cGg/cAg	32/58	0.325746187498437	2	FACETS	1	0.994	1	0.63	0.602	0.658	INDETERMINATE	1	TRUE	0	0.819050922314048	2		657	676	SUCCESS
APC	324	MSKCC	GRCh37	5	112175682	112175682	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	72	467	0	ENST00000257430.4:c.4391A>T	p.Glu1464Val	p.E1464V	ENST00000257430	NM_000038.5	1464	gAg/gTg	16/16	0.432316257948152	1	FACETS	0.278	0.244	0.315	0.278	0.244	0.315	INDETERMINATE	1	TRUE	0	0.819050922314048	1		467	373	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020751	26020751	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	395	1162	0	ENST00000357647.3:c.34A>G	p.Thr12Ala	p.T12A	ENST00000357647	NM_003529.2	12	Act/Gct	1/1	1	2	FACETS	0.834	0.794	0.875	0.834	0.794	0.875	CLONAL	1	TRUE	1	0.819050922314048	2		1162	1156	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410611	32410611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749266841	NA	P-0013201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	388	604	2	ENST00000332351.3:c.1547C>T	p.Ala516Val	p.A516V	ENST00000332351	NM_024426.4	516	gCg/gTg	10/10	0.795468147369138	1	FACETS	0.95	0.916	0.983	0.95	0.916	0.983	CLONAL	1	TRUE	0	0.819050922314048	1		606	589	SUCCESS
APC	324	MSKCC	GRCh37	5	112175667	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCTGAAAAG	CTGCTGAAAAG	-	novel	NA	P-0013201-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	71	542	0	ENST00000257430.4:c.4376_4386del	p.Thr1459LysfsTer6	p.T1459Kfs*6	ENST00000257430	NM_000038.5	1459	aCTGCTGAAAAG/a	16/16	0.432316257948152	1	FACETS	0.245	0.215	0.278	0.245	0.215	0.278	INDETERMINATE	1	TRUE	0	0.819050922314048	1		542	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579347	7579358	+	inframe_deletion	In_Frame_Del	DEL	AGAAGCCCAGAC	AGAAGCCCAGAC	-	novel	NA	P-0013203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	122	596	0	ENST00000269305.4:c.329_340del	p.Arg110_Phe113del	p.R110_F113del	ENST00000269305	NM_001126112.2	110	cGTCTGGGCTTCTtg/ctg	4/11	1	2	FACETS	0.892	0.808	0.981	0.892	0.808	0.981	CLONAL	1	TRUE	1	0.392876213395269	2		596	696	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0013208-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	164	537	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.332161681247513	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.332161681247513	3		537	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013208-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	226	692	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.241295952372606	3	FACETS	1	0.985	1	0.774	0.725	0.825	CLONAL	2	TRUE	0	0.332161681247513	3		692	683	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257878	16257878	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013208-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	35	277	0	ENST00000375759.3:c.5143A>T	p.Met1715Leu	p.M1715L	ENST00000375759	NM_015001.2	1715	Atg/Ttg	11/15	0.295527489453668	3	FACETS	0.601	0.493	0.722	0.3	0.246	0.361	SUBCLONAL	1	TRUE	1	0.332161681247513	3		277	409	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443763	49443763	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013208-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	69	818	0	ENST00000301067.7:c.3608A>G	p.Asp1203Gly	p.D1203G	ENST00000301067	NM_003482.3	1203	gAc/gGc	11/54	0.302403478574255	4	FACETS	0.502	0.435	0.574			1	SUBCLONAL	1	TRUE	NA	0.332161681247513	4		818	1103	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041089	42041089	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	703	1337	0	ENST00000219905.7:c.5467C>T	p.Gln1823Ter	p.Q1823*	ENST00000219905	NM_001164273.1	1823	Cag/Tag	16/24	1	2	FACETS	0.924	0.891	0.957	0.924	0.891	0.957	CLONAL	1	TRUE	1	0.824777037242966	2		1337	1845	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	51	420	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.918	0.778	1	0.918	0.778	1	CLONAL	1	TRUE	1	0.15	2		420	741	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0013220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	26	418	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.662	0.523	0.822	0.662	0.523	0.822	SUBCLONAL	1	TRUE	1	0.15	2		421	524	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0013220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	20	256	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	0.995	0.762	1	0.995	0.762	1	CLONAL	1	TRUE	1	0.15	2		256	268	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212230	5212230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367918810	NA	P-0013220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	39	587	0	ENST00000357368.4:c.4801G>A	p.Val1601Ile	p.V1601I	ENST00000357368	NM_002850.3	1601	Gtc/Atc	32/38	1	2	FACETS	0.851	0.704	1	0.851	0.704	1	CLONAL	1	TRUE	1	0.15	2		587	611	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0013237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	597	320	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.994	0.971	1			1	INDETERMINATE	2	TRUE	NA	0.788848599859213	2		320	761	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962804	2962804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772900135	NA	P-0013237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	468	483	0	ENST00000396946.4:c.2104G>A	p.Glu702Lys	p.E702K	ENST00000396946	NM_032415.4	702	Gag/Aag	16/25	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.788848599859213	2		483	1150	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1555525367	NA	P-0013237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	501	531	0	ENST00000269305.4:c.783-1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	0.995	0.954	1	0.995	0.954	1	CLONAL	1	TRUE	1	0.788848599859213	2		531	1276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781371	NA	P-0013237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	495	513	2	ENST00000269305.4:c.328C>T	p.Arg110Cys	p.R110C	ENST00000269305	NM_001126112.2	110	Cgt/Tgt	4/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.788848599859213	2		515	1245	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983275	149983275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	410	468	0	ENST00000253339.5:c.2983C>T	p.Arg995Cys	p.R995C	ENST00000253339		995	Cgc/Tgc	7/7	1	2	FACETS	0.91	0.868	0.953	0.91	0.868	0.953	CLONAL	1	TRUE	1	0.788848599859213	2		468	1142	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141026	55141026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765680542	NA	P-0013237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	380	469	0	ENST00000257290.5:c.1672C>T	p.Arg558Cys	p.R558C	ENST00000257290	NM_006206.4	558	Cgc/Tgc	12/23	1	2	FACETS	0.853	0.81	0.895	0.853	0.81	0.895	CLONAL	1	TRUE	1	0.788848599859213	2		469	1130	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445067	89445067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	495	553	0	ENST00000336596.2:c.1387C>T	p.Pro463Ser	p.P463S	ENST00000336596	NM_005233.5	463	Cct/Tct	6/17	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.788848599859213	2		553	1255	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178638	32178638	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140125037	NA	P-0013237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	550	562	0	ENST00000375023.3:c.2756C>T	p.Pro919Leu	p.P919L	ENST00000375023	NM_004557.3	919	cCc/cTc	18/30	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.788848599859213	2		562	1329	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11273604	11273604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	315	355	0	ENST00000361445.4:c.3137C>T	p.Thr1046Ile	p.T1046I	ENST00000361445	NM_004958.3	1046	aCc/aTc	21/58	0.3419705139049	3	FACETS	1	0.992	1	0.633	0.599	0.667	INDETERMINATE	1	TRUE	1	0.788848599859213	3		355	880	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363460	40363460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	461	529	0	ENST00000397332.2:c.769G>A	p.Glu257Lys	p.E257K	ENST00000397332	NM_001033082.2	257	Gag/Aag	3/3	0.3419705139049	3	FACETS	1	0.992	1	0.58	0.553	0.606	INDETERMINATE	1	TRUE	1	0.788848599859213	3		529	1406	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675413	241675413	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	435	442	1	ENST00000366560.3:c.409C>T	p.Pro137Ser	p.P137S	ENST00000366560	NM_000143.3	137	Cct/Tct	4/10	0.403777671691185	1	FACETS	0.75	0.719	0.78	0.75	0.719	0.78	INDETERMINATE	1	TRUE	0	0.788848599859213	1		443	891	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966091	25966091	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	557	574	0	ENST00000435504.4:c.3115T>A	p.Phe1039Ile	p.F1039I	ENST00000435504		1039	Ttt/Att	13/13	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.788848599859213	2		574	1315	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735473	204735473	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	406	503	0	ENST00000302823.3:c.274G>A	p.Gly92Arg	p.G92R	ENST00000302823	NM_005214.4	92	Ggg/Agg	2/4	1	2	FACETS	0.901	0.859	0.944	0.901	0.859	0.944	CLONAL	1	TRUE	1	0.788848599859213	2		503	1142	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480418	89480418	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	533	528	0	ENST00000336596.2:c.2255T>A	p.Ile752Asn	p.I752N	ENST00000336596	NM_005233.5	752	aTc/aAc	13/17	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.788848599859213	2		528	1345	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467791	66467791	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774667775	NA	P-0013237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	472	530	0	ENST00000273854.3:c.478G>A	p.Asp160Asn	p.D160N	ENST00000273854	NM_004439.5	160	Gat/Aat	3/18	1	2	FACETS	0.975	0.934	1	0.975	0.934	1	CLONAL	1	TRUE	1	0.788848599859213	2		530	1227	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048754	180048754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	447	637	2	ENST00000261937.6:c.1808G>A	p.Gly603Glu	p.G603E	ENST00000261937	NM_182925.4	603	gGg/gAg	13/30	NA	2	FACETS	0.976	0.933	1			1	INDETERMINATE	1	TRUE	NA	0.788848599859213	2		639	1161	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066570	94066570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1162	737	751	0	ENST00000369303.4:c.1189G>A	p.Asp397Asn	p.D397N	ENST00000369303	NM_004440.3	397	Gat/Aat	5/17	1	2	FACETS	0.984	0.95	1	0.984	0.95	1	CLONAL	1	TRUE	1	0.788848599859213	2		751	1899	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715509	117715509	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	266	268	0	ENST00000368508.3:c.980G>A	p.Gly327Glu	p.G327E	ENST00000368508	NM_002944.2	327	gGa/gAa	10/43	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.788848599859213	2		268	631	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005147	150005147	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	531	561	1	ENST00000253339.5:c.1078C>T	p.Gln360Ter	p.Q360*	ENST00000253339		360	Caa/Taa	3/7	1	2	FACETS	0.988	0.949	1	0.988	0.949	1	CLONAL	1	TRUE	1	0.788848599859213	2		562	1362	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878652	151878652	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867645492	NA	P-0013237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	299	364	0	ENST00000262189.6:c.6293C>T	p.Pro2098Leu	p.P2098L	ENST00000262189	NM_170606.2	2098	cCc/cTc	36/59	1	2	FACETS	0.928	0.877	0.979	0.928	0.877	0.979	CLONAL	1	TRUE	1	0.788848599859213	2		364	817	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98009731	98009731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	1180	650	0	ENST00000289081.3:c.233C>T	p.Pro78Leu	p.P78L	ENST00000289081	NM_000136.2	78	cCt/cTt	3/15	0.788848599859213	2	FACETS	0.987	0.97	1	0.987	0.97	1	CLONAL	2	TRUE	0	0.788848599859213	2		650	1516	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220478	98220478	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	1114	582	1	ENST00000331920.6:c.2985G>T	p.Arg995Ser	p.R995S	ENST00000331920	NM_000264.3	995	agG/agT	18/24	0.788848599859213	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.788848599859213	2		583	1362	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245544	46245544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	340	363	1	ENST00000334344.6:c.3638C>T	p.Pro1213Leu	p.P1213L	ENST00000334344	NM_152641.2	1213	cCa/cTa	15/21	1	2	FACETS	0.997	0.947	1	0.997	0.947	1	CLONAL	1	TRUE	1	0.788848599859213	2		364	865	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248853	133248853	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753890723	NA	P-0013237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	523	565	1	ENST00000320574.5:c.1742C>T	p.Ala581Val	p.A581V	ENST00000320574	NM_006231.2	581	gCc/gTc	16/49	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.788848599859213	2		566	1287	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557509	21557509	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	616	672	0	ENST00000382592.4:c.2336T>A	p.Ile779Asn	p.I779N	ENST00000382592	NM_014572.2	779	aTt/aAt	5/8	1	2	FACETS	0.92	0.885	0.955	0.92	0.885	0.955	CLONAL	1	TRUE	1	0.788848599859213	2		672	1698	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059276	42059276	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	719	814	0	ENST00000219905.7:c.8996C>T	p.Pro2999Leu	p.P2999L	ENST00000219905	NM_001164273.1	2999	cCt/cTt	24/24	1	2	FACETS	0.97	0.936	1	0.97	0.936	1	CLONAL	1	TRUE	1	0.788848599859213	2		814	1880	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996003	73996003	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1320456567	NA	P-0013237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	311	354	0	ENST00000318443.5:c.737C>T	p.Ala246Val	p.A246V	ENST00000318443	NM_001024736.1	246	gCc/gTc	5/10	1	2	FACETS	0.981	0.929	1	0.981	0.929	1	CLONAL	1	TRUE	1	0.788848599859213	2		354	804	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801795	3801795	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	415	436	0	ENST00000262367.5:c.3711T>G	p.Cys1237Trp	p.C1237W	ENST00000262367	NM_004380.2	1237	tgT/tgG	20/31	1	2	FACETS	0.948	0.904	0.992	0.948	0.904	0.992	CLONAL	1	TRUE	1	0.788848599859213	2		436	1110	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979029	7979029	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	420	465	0	ENST00000319144.4:c.1538T>G	p.Val513Gly	p.V513G	ENST00000319144	NM_001139.2	513	gTg/gGg	12/15	1	2	FACETS	0.961	0.917	1	0.961	0.917	1	CLONAL	1	TRUE	1	0.788848599859213	2		465	1108	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686943	37686943	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	480	531	1	ENST00000447079.4:c.3847G>A	p.Glu1283Lys	p.E1283K	ENST00000447079	NM_015083.1	1283	Gaa/Aaa	14/14	1	2	FACETS	0.966	0.925	1	0.966	0.925	1	CLONAL	1	TRUE	1	0.788848599859213	2		532	1260	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512312	38512312	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	481	557	1	ENST00000254066.5:c.1223C>T	p.Pro408Leu	p.P408L	ENST00000254066	NM_000964.3	408	cCt/cTt	9/9	1	2	FACETS	0.975	0.933	1	0.975	0.933	1	CLONAL	1	TRUE	1	0.788848599859213	2		558	1251	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7120670	7120670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	676	627	0	ENST00000302850.5:c.3620C>T	p.Ser1207Phe	p.S1207F	ENST00000302850	NM_000208.2	1207	tCc/tTc	20/22	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.788848599859213	2		627	1680	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514883	44514883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	415	437	0	ENST00000291552.4:c.364G>A	p.Asp122Asn	p.D122N	ENST00000291552	NM_006758.2	122	Gat/Aat	6/8	1	2	FACETS	0.983	0.939	1	0.983	0.939	1	CLONAL	1	TRUE	1	0.788848599859213	2		437	1070	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933653	39933653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200052076	NA	P-0013237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	561	292	0	ENST00000378444.4:c.946C>T	p.Pro316Ser	p.P316S	ENST00000378444	NM_001123385.1	316	Ccc/Tcc	4/15	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.788848599859213	1		292	694	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662554	227662554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866672328	NA	P-0013241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	105	530	0	ENST00000305123.5:c.901C>T	p.Arg301Cys	p.R301C	ENST00000305123	NM_005544.2	301	Cgc/Tgc	1/2	1	2	FACETS	0.609	0.547	0.676	0.609	0.547	0.676	SUBCLONAL	1	TRUE	1	0.528590197352132	2		530	652	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932126	39932133	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGTTTG	TGGGTTTG	AGA	novel	NA	P-0013241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	134	372	0	ENST00000378444.4:c.2466_2473delinsTCT	p.Lys823LeufsTer12	p.K823Lfs*12	ENST00000378444	NM_001123385.1	822	tcCAAACCCAgc/tcTCTgc	4/15	1	1	FACETS	0.727	0.664	0.792	0.727	0.664	0.792	SUBCLONAL	1	TRUE	0	0.528590197352132	1		372	513	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	21	394	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.207	0.159	0.265	0.207	0.159	0.265	SUBCLONAL	1	TRUE	1	0.347846711058789	2		394	582	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964925	55964925	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	142	593	0	ENST00000263923.4:c.2312C>G	p.Thr771Arg	p.T771R	ENST00000263923	NM_002253.2	771	aCg/aGg	16/30	0.346761069629228	3	FACETS	0.805	0.732	0.882	0.402	0.366	0.441	CLONAL	1	TRUE	1	0.347846711058789	3		593	1191	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947161	178947161	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013264-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	162	480	0	ENST00000263967.3:c.2597T>G	p.Leu866Trp	p.L866W	ENST00000263967	NM_006218.2	866	tTg/tGg	18/21	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.347846711058789	2		480	686	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0013273-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	44	483	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	NA	2	FACETS	0.683	0.572	0.806			1	INDETERMINATE	1	TRUE	NA	0.21168679960938	2		483	609	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986638	36986639	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0013273-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	10	141	0	ENST00000354822.5:c.1050_1051del	p.Gln350HisfsTer88	p.Q350Hfs*88	ENST00000354822	NM_001079668.2	350	caGCca/caca	3/3	0.21168679960938	1	FACETS	1	0.82	1	1	0.82	1	CLONAL	1	TRUE	0	0.21168679960938	1		141	64	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465433	99465433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs987303175	NA	P-0013273-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	51	706	1	ENST00000268035.6:c.2258G>A	p.Arg753Gln	p.R753Q	ENST00000268035	NM_000875.3	753	cGa/cAa	11/21	1	2	FACETS	0.684	0.581	0.799	0.684	0.581	0.799	SUBCLONAL	1	TRUE	1	0.21168679960938	2		707	704	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0013279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	223	630	2	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.203326897559709	2	FACETS	0.962	0.895	1	0.962	0.895	1	CLONAL	2	TRUE	0	0.203326897559709	2		632	1140	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0013285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	313	462	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.519698910503085	2	FACETS	0.979	0.933	1	0.979	0.933	1	CLONAL	2	TRUE	0	0.543951834346989	2		463	588	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0013285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	183	633	1	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.97	0.898	1	0.97	0.898	1	CLONAL	1	TRUE	1	0.543951834346989	2		634	694	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92300798	92300798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs606231255	NA	P-0013285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	180	255	0	ENST00000265734.4:c.589G>A	p.Ala197Thr	p.A197T	ENST00000265734	NM_001259.6	197	Gcc/Acc	5/8	0.522330903923956	3	FACETS	0.877	0.816	0.939	0.877	0.816	0.939	CLONAL	2	TRUE	1	0.543951834346989	3		255	480	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276726	15276726	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs956073860	NA	P-0013285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	125	620	0	ENST00000263388.2:c.5539G>T	p.Ala1847Ser	p.A1847S	ENST00000263388	NM_000435.2	1847	Gcc/Tcc	30/33	0.164307659779634	3	FACETS	0.958	0.87	1	0.319	0.29	0.351	INDETERMINATE	1	TRUE	0	0.543951834346989	3		620	610	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013294-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	87	589	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.88	0.781	0.986	0.88	0.781	0.986	CLONAL	1	TRUE	1	0.36005689912789	2		590	549	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882087	36882087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013294-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	184	753	0	ENST00000358127.4:c.926G>A	p.Ser309Asn	p.S309N	ENST00000358127	NM_001280556.1	309	aGc/aAc	8/10	1	2	FACETS	0.816	0.751	0.883	0.816	0.751	0.883	CLONAL	1	TRUE	1	0.36005689912789	2		753	1253	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653814	89653814	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013294-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	155	436	0	ENST00000371953.3:c.112C>G	p.Pro38Ala	p.P38A	ENST00000371953	NM_000314.4	38	Cct/Gct	2/9	0.36005689912789	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.36005689912789	1		436	509	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504468	103504468	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013294-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	74	522	0	ENST00000355739.4:c.89A>G	p.Asp30Gly	p.D30G	ENST00000355739	NM_000123.3	30	gAt/gGt	2/15	1	2	FACETS	0.498	0.435	0.566	0.498	0.435	0.566	SUBCLONAL	1	TRUE	1	0.36005689912789	2		522	826	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121873	2121873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746315218	NA	P-0013298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	27	452	2	ENST00000219476.3:c.2035G>A	p.Val679Met	p.V679M	ENST00000219476	NM_000548.3	679	Gtg/Atg	19/42	0.263142905375119	1	FACETS	0.672	0.537	0.827	0.672	0.537	0.827	SUBCLONAL	1	TRUE	0	0.263142905375119	1		454	265	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0013298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	94	478	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	0.263142905375119	3	FACETS	0.786	0.702	0.876	0.786	0.702	0.876	SUBCLONAL	2	TRUE	1	0.263142905375119	3		478	514	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914808	32914808	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	126	1143	0	ENST00000380152.3:c.6316C>A	p.Leu2106Ile	p.L2106I	ENST00000380152		2106	Ctt/Att	11/27	1	2	FACETS	0.98	0.886	1	0.98	0.886	1	CLONAL	1	TRUE	1	0.263142905375119	2		1143	977	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222191	2222191	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs778747333	NA	P-0013298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	44	717	0	ENST00000398665.3:c.3023C>G	p.Ser1008Cys	p.S1008C	ENST00000398665	NM_032482.2	1008	tCc/tGc	24/28	0.263142905375119	1	FACETS	0.618	0.518	0.728	0.618	0.518	0.728	SUBCLONAL	1	TRUE	0	0.263142905375119	1		717	470	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223318	2223318	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	41	1035	0	ENST00000398665.3:c.3429C>G	p.Ile1143Met	p.I1143M	ENST00000398665	NM_032482.2	1143	atC/atG	25/28	0.263142905375119	1	FACETS	0.487	0.405	0.578	0.487	0.405	0.578	SUBCLONAL	1	TRUE	0	0.263142905375119	1		1035	556	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742704	39742704	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	72	644	0	ENST00000361337.2:c.1547C>G	p.Pro516Arg	p.P516R	ENST00000361337	NM_003286.2	516	cCa/cGa	15/21	1	2	FACETS	0.937	0.819	1	0.937	0.819	1	CLONAL	1	TRUE	1	0.263142905375119	2		644	584	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259949	16259949	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013301-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	315	649	0	ENST00000375759.3:c.7214T>G	p.Ile2405Ser	p.I2405S	ENST00000375759	NM_015001.2	2405	aTt/aGt	11/15	0.464728913990202	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.464728913990202	1		649	1011	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912716	100912716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1450222910	NA	P-0013301-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1343	105	821	3	ENST00000325455.5:c.2606G>A	p.Arg869His	p.R869H	ENST00000325455	NM_001202474.3	869	cGt/cAt	7/8	1	2	FACETS	0.312	0.278	0.348	0.312	0.278	0.348	SUBCLONAL	1	TRUE	1	0.464728913990202	2		824	1448	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054533	42054533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013301-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1321	81	717	0	ENST00000219905.7:c.7717C>T	p.Leu2573Phe	p.L2573F	ENST00000219905	NM_001164273.1	2573	Ctt/Ttt	22/24	1	2	FACETS	0.249	0.218	0.282	0.249	0.218	0.282	SUBCLONAL	1	TRUE	1	0.464728913990202	2		717	1402	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220439	1220439	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0013301-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	305	752	0	ENST00000326873.7:c.532A>T	p.Lys178Ter	p.K178*	ENST00000326873	NM_000455.4	178	Aag/Tag	4/10	0.421328678683425	1	FACETS	0.949	0.895	1	0.949	0.895	1	CLONAL	1	TRUE	0	0.464728913990202	1		752	1062	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610574	10610610	+	frameshift_variant	Frame_Shift_Del	DEL	GGGAGGGCGTCACCTCCGCCTTGCACTCAGTGGAGGC	GGGAGGGCGTCACCTCCGCCTTGCACTCAGTGGAGGC	-	novel	NA	P-0013301-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	121	567	0	ENST00000171111.5:c.100_136del	p.Ala34SerfsTer22	p.A34Sfs*22	ENST00000171111	NM_203500.1	34	GCCTCCACTGAGTGCAAGGCGGAGGTGACGCCCTCCCag/ag	2/6	0.410476909898939	1	FACETS	0.599	0.542	0.659	0.599	0.542	0.659	SUBCLONAL	1	TRUE	0	0.464728913990202	1		567	667	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0013360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	23	331	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.145	0.112	0.183	0.145	0.112	0.183	SUBCLONAL	1	TRUE	1	0.495893338863376	2		331	639	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439658	51439658	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	361	576	0	ENST00000262662.1:c.223C>G	p.His75Asp	p.H75D	ENST00000262662		75	Cat/Gat	4/4	0.193770241936226	2	FACETS	1	0.995	1	0.716	0.68	0.752	INDETERMINATE	1	TRUE	0	0.495893338863376	2		576	1017	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664868	29664868	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1193716348	NA	P-0013360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	150	396	0	ENST00000356175.3:c.6611G>A	p.Trp2204Ter	p.W2204*	ENST00000356175	NM_000267.3	2204	tGg/tAg	43/57	1	2	FACETS	0.942	0.864	1	0.942	0.864	1	CLONAL	1	TRUE	1	0.495893338863376	2		396	642	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845369	76845372	+	frameshift_variant	Frame_Shift_Del	DEL	TCAA	TCAA	-	novel	NA	P-0013360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	239	315	0	ENST00000373344.5:c.6149_6152del	p.Ile2050LysfsTer6	p.I2050Kfs*6	ENST00000373344	NM_000489.3	2050	aTTGAa/aa	27/35	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.495893338863376	1		315	560	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665092	29665092	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	233	387	0	ENST00000356175.3:c.6693del	p.Phe2231LeufsTer13	p.F2231Lfs*13	ENST00000356175	NM_000267.3	2231	Ttt/tt	44/57	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.495893338863376	2		387	720	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0013369-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	253	537	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.411300300270599	3	FACETS	1	0.988	1	0.624	0.583	0.666	CLONAL	1	TRUE	1	0.411300300270599	3		537	1189	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30323815	30323815	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0013369-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	183	399	0	ENST00000322652.5:c.1795-2A>T		p.X599_splice	ENST00000322652	NM_015355.2	599			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.411300300270599	2		399	727	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204798	128204798	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1760	632	1122	0	ENST00000341105.2:c.643G>C	p.Val215Leu	p.V215L	ENST00000341105	NM_032638.4	215	Gtg/Ctg	3/6	0.464925375424592	4	FACETS	0.833	0.799	0.867	0.555	0.532	0.578	CLONAL	2	TRUE	1	0.464925375424592	4		1122	2392	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840003	27840003	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1676	355	1447	4	ENST00000328488.2:c.91C>A	p.Pro31Thr	p.P31T	ENST00000328488	NM_003533.2	31	Ccg/Acg	1/1	0.448617150336147	3	FACETS	0.927	0.874	0.981			1	CLONAL	1	TRUE	NA	0.464925375424592	3		1451	2031	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016266	150016266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771498477	NA	P-0013379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	294	978	2	ENST00000253339.5:c.440G>A	p.Arg147Gln	p.R147Q	ENST00000253339		147	cGa/cAa	2/7	1	2	FACETS	0.973	0.914	1	0.973	0.914	1	CLONAL	1	TRUE	1	0.464925375424592	2		980	1300	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111956131	111956131	+	upstream_gene_variant	5'Flank	SNP	C	C	T	rs116405897	NA	P-0013379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	180	537	1				ENST00000375549	NM_003002.3	62/98			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.464925375424592	2		538	734	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919331	48919331	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1131690874	NA	P-0013379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	161	457	2	ENST00000267163.4:c.496G>T	p.Glu166Ter	p.E166*	ENST00000267163	NM_000321.2	166	Gaa/Taa	4/27	0.464925375424592	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.464925375424592	1		459	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579312	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0013379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	163	589	0	ENST00000269305.4:c.375_375+1delinsTT		p.X125_splice	ENST00000269305	NM_001126112.2	125		4/11	0.464925375424592	1	FACETS	0.933	0.861	1	0.933	0.861	1	CLONAL	1	TRUE	0	0.464925375424592	1		589	577	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210644	2210644	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	260	679	0	ENST00000398665.3:c.1141G>C	p.Ala381Pro	p.A381P	ENST00000398665	NM_032482.2	381	Gcg/Ccg	14/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.464925375424592	2		679	981	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	205	320	0				ENST00000310581	NM_198253.2	-/1132			0.296363359415057	3	FACETS	0.981	0.921	1	1	0.994	1	CLONAL	4	TRUE	1	0.25	3		320	470	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099972	27099972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	333	711	0	ENST00000324856.7:c.3851C>T	p.Pro1284Leu	p.P1284L	ENST00000324856	NM_006015.4	1284	cCt/cTt	15/20	0.2244742076208	3	FACETS	0.947	0.9	0.994	1	0.996	1	CLONAL	4	TRUE	1	0.25	3		711	791	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933685	36933685	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	490	965	1	ENST00000361632.4:c.1714C>T	p.Gln572Ter	p.Q572*	ENST00000361632		572	Cag/Tag	12/16	0.2244742076208	3	FACETS	0.903	0.865	0.941	1	0.997	1	CLONAL	4	TRUE	1	0.25	3		966	1221	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204515949	204515954	+	inframe_deletion	In_Frame_Del	DEL	GACCTG	GACCTG	-	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	722	720	0	ENST00000367182.3:c.849_854del	p.Asp283_Leu284del	p.D283_L284del	ENST00000367182	NM_001278516.1	283	GACCTG/-	10/11	0.2244742076208	3	FACETS	0.948	0.93	0.964			1	CLONAL	8	TRUE	1	0.25	3		720	857	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518560	204518560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	430	397	0	ENST00000367182.3:c.1223C>T	p.Ser408Leu	p.S408L	ENST00000367182	NM_001278516.1	408	tCa/tTa	11/11	0.2244742076208	3	FACETS	0.999	0.979	1	1	0.998	1	CLONAL	8	TRUE	1	0.25	3		397	484	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666623	206666623	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	700	712	0	ENST00000367120.3:c.1957C>G	p.Leu653Val	p.L653V	ENST00000367120	NM_014002.3	653	Ctc/Gtc	20/22	0.2244742076208	3	FACETS	0.963	0.945	0.979			1	CLONAL	8	TRUE	1	0.25	3		712	818	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462777	69462777	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4377	285	642	0	ENST00000227507.2:c.590C>T	p.Ser197Phe	p.S197F	ENST00000227507	NM_053056.2	197	tCc/tTc	4/5	0.296363359415057	3	FACETS	0.55	0.513	0.589	0.275	0.256	0.295	SUBCLONAL	1	TRUE	1	0.25	3		642	4662	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933241	100933241	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8906	524	1073	0	ENST00000325455.5:c.2149A>T	p.Ser717Cys	p.S717C	ENST00000325455	NM_001202474.3	717	Agt/Tgt	4/8	0.296363359415057	3	FACETS	0.5	0.475	0.526	0.25	0.237	0.263	SUBCLONAL	1	TRUE	1	0.25	3		1073	9430	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175528	108175528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs376603775	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	419	552	0	ENST00000278616.4:c.5623C>T	p.Arg1875Ter	p.R1875*	ENST00000278616	NM_000051.3	1875	Cga/Tga	37/63	0.296363359415057	3	FACETS	1	0.99	1	1	0.998	1	CLONAL	7	TRUE	1	0.25	3		552	520	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436024	49436024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	174	418	1	ENST00000301067.7:c.5957C>T	p.Thr1986Ile	p.T1986I	ENST00000301067	NM_003482.3	1986	aCc/aTc	28/54	1	2	FACETS	1	0.976	1	1	0.995	1	CLONAL	3	TRUE	1	0.25	2		419	420	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69230462	69230462	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	564	451	0	ENST00000462284.1:c.851T>C	p.Val284Ala	p.V284A	ENST00000462284	NM_002392.5	284	gTt/gCt	10/11	1	2	FACETS	0.953	0.922	0.983	1	0.998	1	CLONAL	5	TRUE	1	0.25	2		451	947	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001353	29001353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	333	572	0	ENST00000282397.4:c.1379C>T	p.Pro460Leu	p.P460L	ENST00000282397	NM_002019.4	460	cCt/cTt	10/30	0.296363359415057	3	FACETS	1	0.973	1	1	0.997	1	CLONAL	7	TRUE	1	0.25	3		572	426	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988433	36988433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	196	377	0	ENST00000354822.5:c.220G>A	p.Gly74Ser	p.G74S	ENST00000354822	NM_001079668.2	74	Ggc/Agc	2/3	0.3	3	FACETS	1	0.975	1	1	0.994	1	CLONAL	4	TRUE	1	0.25	3		377	410	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251120	99251120	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	307	593	1	ENST00000268035.6:c.424A>G	p.Arg142Gly	p.R142G	ENST00000268035	NM_000875.3	142	Agg/Ggg	2/21	0.3	3	FACETS	0.963	0.914	1	1	0.996	1	CLONAL	4	TRUE	1	0.25	3		594	717	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942837	15942837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	475	846	1	ENST00000268712.3:c.6865C>T	p.Pro2289Ser	p.P2289S	ENST00000268712	NM_006311.3	2289	Cct/Tct	44/46	0.2244742076208	3	FACETS	1	0.968	1	1	0.997	1	CLONAL	4	TRUE	1	0.25	3		847	1058	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541468	29541468	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1131691131	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	89	130	0	ENST00000356175.3:c.1393-1G>A		p.X465_splice	ENST00000356175	NM_000267.3	465			0.2244742076208	3	FACETS	1	0.913	1	1	0.988	1	CLONAL	4	TRUE	1	0.25	3		130	199	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562641	29562641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854562	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	543	712	1	ENST00000356175.3:c.3721C>T	p.Arg1241Ter	p.R1241*	ENST00000356175	NM_000267.3	1241	Cga/Tga	28/57	0.2244742076208	3	FACETS	1	0.983	1	1	0.998	1	CLONAL	4	TRUE	1	0.25	3		713	1178	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761106	59761106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	394	657	1	ENST00000259008.2:c.3301C>T	p.Pro1101Ser	p.P1101S	ENST00000259008	NM_032043.2	1101	Cca/Tca	20/20	1	2	FACETS	0.896	0.857	0.937	1	0.997	1	CLONAL	4	TRUE	1	0.25	2		658	879	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39595510	39595510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	413	747	0	ENST00000262039.4:c.1396C>T	p.Pro466Ser	p.P466S	ENST00000262039	NM_002647.2	466	Cca/Tca	12/25	0.3	4	FACETS	1	0.991	1	1	0.997	1	CLONAL	4	TRUE	2	0.25	4		747	919	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246446	10246446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568218498	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	316	584	0	ENST00000340748.4:c.4691G>A	p.Arg1564Gln	p.R1564Q	ENST00000340748		1564	cGg/cAg	38/40	0.28700397820811	3	FACETS	0.939	0.891	0.987	1	0.996	1	CLONAL	4	TRUE	1	0.25	3		584	757	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272140	15272140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	95	213	0	ENST00000263388.2:c.6299C>T	p.Ser2100Leu	p.S2100L	ENST00000263388	NM_000435.2	2100	tCg/tTg	33/33	0.28700397820811	3	FACETS	1	0.922	1	1	0.988	1	CLONAL	4	TRUE	1	0.25	3		213	211	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15374256	15374256	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	320	653	0	ENST00000263377.2:c.1316T>G	p.Val439Gly	p.V439G	ENST00000263377	NM_058243.2	439	gTg/gGg	7/20	0.28700397820811	3	FACETS	0.881	0.836	0.927	1	0.996	1	CLONAL	4	TRUE	1	0.25	3		653	817	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726666	41726666	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778883675	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	371	787	0	ENST00000301178.4:c.211C>T	p.Arg71Trp	p.R71W	ENST00000301178	NM_021913.4	71	Cgg/Tgg	2/20	0.28700397820811	3	FACETS	0.911	0.868	0.955	1	0.996	1	CLONAL	4	TRUE	1	0.25	3		787	916	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763421	41763421	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	461	912	0	ENST00000301178.4:c.2220G>A	p.Trp740Ter	p.W740*	ENST00000301178	NM_021913.4	740	tgG/tgA	19/20	0.28700397820811	3	FACETS	1	0.962	1	1	0.997	1	CLONAL	4	TRUE	1	0.25	3		912	1034	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498088	29498088	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144453491	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	309	562	2	ENST00000389048.3:c.1918G>A	p.Gly640Arg	p.G640R	ENST00000389048	NM_004304.4	640	Gga/Aga	11/29	0.3	3	FACETS	0.903	0.856	0.95	1	0.996	1	CLONAL	4	TRUE	1	0.25	3		564	770	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736161	204736161	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	477	876	0	ENST00000302823.3:c.518G>C	p.Gly173Ala	p.G173A	ENST00000302823	NM_005214.4	173	gGg/gCg	3/4	0.3	3	FACETS	0.9	0.862	0.938	1	0.997	1	CLONAL	4	TRUE	1	0.25	3		876	1193	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790168	40790168	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745346735	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	132	266	0	ENST00000373198.4:c.2563G>A	p.Gly855Arg	p.G855R	ENST00000373198	NM_133170.3	855	Ggg/Agg	18/32	0.296363359415057	3	FACETS	0.943	0.864	1	1	0.986	1	CLONAL	3	TRUE	1	0.25	3		266	420	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39762920	39762920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	248	447	0	ENST00000288319.7:c.916C>T	p.Pro306Ser	p.P306S	ENST00000288319	NM_182918.3	306	Cca/Tca	9/10	0.28700397820811	3	FACETS	1	0.984	1	1	0.994	1	CLONAL	3	TRUE	1	0.25	3		447	662	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30664748	30664748	+	intron_variant	Intron	SNP	C	C	T	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	228	369	0	ENST00000295754.5:c.94+16279C>T		p.*32*	ENST00000295754	NM_003242.5	51/592			0.3	3	FACETS	1	0.982	1	1	0.994	1	CLONAL	3	TRUE	1	0.25	3		369	611	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825427	134825427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	372	622	1	ENST00000398015.3:c.943C>T	p.Pro315Ser	p.P315S	ENST00000398015	NM_004441.4	315	Cca/Tca	4/16	0.296363359415057	3	FACETS	1	0.978	1	1	0.997	1	CLONAL	7	TRUE	1	0.25	3		623	474	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750581	41750581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	266	513	0	ENST00000226382.2:c.47C>T	p.Ser16Phe	p.S16F	ENST00000226382	NM_003924.3	16	tCc/tTc	1/3	1	2	FACETS	1	0.954	1	1	0.996	1	CLONAL	3	TRUE	1	0.25	2		513	700	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981479	55981479	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	429	683	0	ENST00000263923.4:c.458C>T	p.Ser153Phe	p.S153F	ENST00000263923	NM_002253.2	153	tCc/tTc	4/30	1	2	FACETS	0.894	0.856	0.932	1	0.998	1	CLONAL	4	TRUE	1	0.25	2		683	960	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84403381	84403381	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	372	645	1	ENST00000321945.7:c.104G>A	p.Gly35Glu	p.G35E	ENST00000321945	NM_139076.2	35	gGg/gAg	2/9	1	2	FACETS	0.894	0.853	0.935	1	0.997	1	CLONAL	4	TRUE	1	0.25	2		646	832	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190821	106190821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866084594	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	411	631	0	ENST00000380013.4:c.4099C>T	p.Pro1367Ser	p.P1367S	ENST00000380013	NM_001127208.2	1367	Cca/Tca	9/11	1	2	FACETS	0.917	0.878	0.957	1	0.997	1	CLONAL	4	TRUE	1	0.25	2		631	896	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045832	143045832	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	305	580	0	ENST00000262992.4:c.1802C>T	p.Ser601Phe	p.S601F	ENST00000262992	NM_001101669.1	601	tCc/tTc	17/24	1	2	FACETS	1	0.959	1	1	0.997	1	CLONAL	3	TRUE	1	0.25	2		580	801	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067008	143067008	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	355	615	0	ENST00000262992.4:c.1705C>T	p.Pro569Ser	p.P569S	ENST00000262992	NM_001101669.1	569	Ccc/Tcc	16/24	1	2	FACETS	1	0.988	1	1	0.997	1	CLONAL	3	TRUE	1	0.25	2		615	854	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540074	187540074	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs921535768	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	385	657	2	ENST00000441802.2:c.7666C>T	p.Arg2556Ter	p.R2556*	ENST00000441802	NM_005245.3	2556	Cga/Tga	10/27	1	2	FACETS	1	0.989	1	1	0.997	1	CLONAL	3	TRUE	1	0.25	2		659	923	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294102	1294102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	332	585	1	ENST00000310581.5:c.899G>A	p.Gly300Asp	p.G300D	ENST00000310581	NM_198253.2	300	gGc/gAc	2/16	0.296363359415057	3	FACETS	1	0.987	1	1	0.997	1	CLONAL	4	TRUE	1	0.25	3		586	680	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046682	180046682	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	315	604	0	ENST00000261937.6:c.2630C>T	p.Ala877Val	p.A877V	ENST00000261937	NM_182925.4	877	gCc/gTc	18/30	0.296363359415057	3	FACETS	1	0.976	1	1	0.996	1	CLONAL	4	TRUE	1	0.25	3		604	680	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398890	398890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	345	656	0	ENST00000380956.4:c.700C>T	p.Pro234Ser	p.P234S	ENST00000380956	NM_001195286.1	234	Ccc/Tcc	6/9	0.3	3	FACETS	0.937	0.887	0.987			1	CLONAL	3	TRUE	NA	0.25	3		656	1105	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117650535	117650535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	676	1175	0	ENST00000368508.3:c.5323G>A	p.Glu1775Lys	p.E1775K	ENST00000368508	NM_002944.2	1775	Gaa/Aaa	32/43	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.25	NA		1175	1422	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662562	117662562	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	281	564	1	ENST00000368508.3:c.4902+1G>A		p.X1634_splice	ENST00000368508	NM_002944.2	1634			0.296363359415057	3	FACETS	0.996	0.943	1	1	0.996	1	CLONAL	4	TRUE	1	0.25	3		565	635	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959079	2959079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542412710	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	298	579	0	ENST00000396946.4:c.2437G>A	p.Glu813Lys	p.E813K	ENST00000396946	NM_032415.4	813	Gag/Aag	18/25	0.3	3	FACETS	0.926	0.877	0.975	1	0.996	1	CLONAL	4	TRUE	1	0.25	3		579	724	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450274	50450274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	289	660	2	ENST00000331340.3:c.458C>T	p.Ser153Leu	p.S153L	ENST00000331340	NM_006060.4	153	tCa/tTa	5/8	0.3	3	FACETS	0.878	0.83	0.926	1	0.995	1	CLONAL	4	TRUE	1	0.25	3		662	741	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220337	55220337	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	220	451	0	ENST00000275493.2:c.727C>T	p.Pro243Ser	p.P243S	ENST00000275493	NM_005228.3	243	Ccc/Tcc	6/28	0.3	3	FACETS	0.956	0.898	1	1	0.994	1	CLONAL	4	TRUE	1	0.25	3		451	518	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381514	81381514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	513	913	0	ENST00000222390.5:c.547G>A	p.Glu183Lys	p.E183K	ENST00000222390	NM_000601.4	183	Gaa/Aaa	5/18	0.3	3	FACETS	0.921	0.884	0.959	1	0.997	1	CLONAL	4	TRUE	1	0.25	3		913	1253	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340210	116340210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758919662	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	358	594	0	ENST00000397752.3:c.1072G>A	p.Asp358Asn	p.D358N	ENST00000397752	NM_000245.2	358	Gat/Aat	2/21	0.3	3	FACETS	0.929	0.884	0.974	1	0.996	1	CLONAL	4	TRUE	1	0.25	3		594	867	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389285	8389285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866731155	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	456	847	0	ENST00000356435.5:c.4333G>A	p.Glu1445Lys	p.E1445K	ENST00000356435		1445	Gaa/Aaa	26/35	1	2	FACETS	0.985	0.957	1	1	0.998	1	CLONAL	6	TRUE	1	0.25	2		847	617	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642514	117642516	+	missense_variant	Missense_Mutation	TNP	CCC	CCC	TTT	novel	NA	P-0013383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	373	1158	0	ENST00000368508.3:c.5683_5685delinsAAA	p.Gly1895Lys	p.G1895K	ENST00000368508	NM_002944.2	1895	GGG/AAA	35/43	0.3	0	FACETS	0.897	0.852	0.944			1	CLONAL	2	TRUE	0	0.25	0		1158	1247	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913250	NA	P-0013392-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	70	575	0	ENST00000369535.4:c.34G>C	p.Gly12Arg	p.G12R	ENST00000369535	NM_002524.4	12	Ggt/Cgt	2/7	0.184204992253201	3	FACETS	0.983	0.856	1	0.492	0.428	0.561	CLONAL	1	TRUE	1	0.184204992253201	3		575	844	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852428	63852428	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013392-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	89	610	0	ENST00000279873.7:c.3206A>G	p.His1069Arg	p.H1069R	ENST00000279873	NM_032199.2	1069	cAc/cGc	10/10	0.184204992253201	3	FACETS	1	0.939	1	0.547	0.484	0.615	CLONAL	1	TRUE	1	0.184204992253201	3		610	964	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023112	33023112	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013392-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	93	815	0	ENST00000300177.4:c.221T>C	p.Leu74Pro	p.L74P	ENST00000300177	NM_001191322.1	74	cTg/cCg	2/2	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.184204992253201	2		815	997	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81954863	81954863	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs955126333	NA	P-0013392-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	122	864	0	ENST00000359376.3:c.2296A>C	p.Asn766His	p.N766H	ENST00000359376	NM_002661.3	766	Aat/Cat	21/33	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.184204992253201	2		864	1218	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257950	19257950	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013392-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	173	721	0	ENST00000162023.5:c.436G>C	p.Ala146Pro	p.A146P	ENST00000162023		146	Gcc/Ccc	9/13	0.119173830501777	4	FACETS	1	0.969	1			1	CLONAL	2	TRUE	NA	0.184204992253201	4		721	1007	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44948999	44948999	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013392-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	65	472	0	ENST00000377967.4:c.3560A>C	p.Asn1187Thr	p.N1187T	ENST00000377967	NM_021140.2	1187	aAt/aCt	25/29	NA	2	FACETS	0.946	0.819	1			1	INDETERMINATE	1	TRUE	NA	0.184204992253201	2		472	746	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170214	119170222	+	inframe_deletion	In_Frame_Del	DEL	AAGGTTCCC	AAGGTTCCC	-	novel	NA	P-0013392-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	105	430	0	ENST00000264033.4:c.2447_2455del	p.Gly816_Gln818del	p.G816_Q818del	ENST00000264033	NM_005188.3	815	gAAGGTTCCCaa/gaa	16/16	0.0883774606525529	3	FACETS	0.887	0.795	0.984			1	INDETERMINATE	2	TRUE	NA	0.184204992253201	3		430	702	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807893	1807894	+	missense_variant	Missense_Mutation	DNP	CG	CG	AA	novel	NA	P-0013392-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	48	633	2	ENST00000260795.2:c.1952_1953delinsAA	p.Thr651Lys	p.T651K	ENST00000260795		651	aCG/aAA	13/17	NA	2	FACETS	0.725	0.611	0.85			1	INDETERMINATE	1	TRUE	NA	0.184204992253201	2		635	719	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876085	35876085	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013412-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	100	559	0	ENST00000303115.3:c.877A>C	p.Asn293His	p.N293H	ENST00000303115	NM_002185.3	293	Aat/Cat	8/8	0.235033061151849	5	FACETS	0.939	0.836	1	0.313	0.278	0.35	CLONAL	1	TRUE	2	0.235033061151849	5		559	1226	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3795309	3795309	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs559939930	NA	P-0013412-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	175	569	1	ENST00000262367.5:c.3883G>T	p.Val1295Phe	p.V1295F	ENST00000262367	NM_004380.2	1295	Gtt/Ttt	22/31	0.235033061151849	3	FACETS	0.872	0.803	0.944	0.872	0.803	0.944	CLONAL	2	TRUE	1	0.235033061151849	3		570	954	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936766	78936766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013412-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	136	789	0	ENST00000306801.3:c.3848G>A	p.Ser1283Asn	p.S1283N	ENST00000306801	NM_020761.2	1283	aGc/aAc	33/34	0.235033061151849	3	FACETS	1	0.966	1	0.567	0.514	0.622	CLONAL	1	TRUE	1	0.235033061151849	3		789	1141	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877447	40877447	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013412-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	67	398	0	ENST00000373198.4:c.2249A>T	p.Asn750Ile	p.N750I	ENST00000373198	NM_133170.3	750	aAt/aTt	15/32	0.167161953731135	3	FACETS	0.867	0.752	0.991	0.433	0.376	0.496	CLONAL	1	TRUE	1	0.235033061151849	3		398	735	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0013417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	97	462	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.18	2		463	860	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729537	41729537	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1272	75	1417	0	ENST00000242208.4:c.992A>T	p.Lys331Met	p.K331M	ENST00000242208	NM_002192.2	331	aAg/aTg	3/3	0.165467344876258	3	FACETS	0.674	0.588	0.768	0.337	0.294	0.384	SUBCLONAL	1	TRUE	1	0.18	3		1417	1347	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971030	21971066	+	frameshift_variant	Frame_Shift_Del	DEL	AGGCATCGCGCACGTCCAGCCGCGCCCCGGCCCGGTG	AGGCATCGCGCACGTCCAGCCGCGCCCCGGCCCGGTG	-	novel	NA	P-0013417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	60	236	0	ENST00000304494.5:c.292_328del	p.His98GlyfsTer36	p.H98Gfs*36	ENST00000304494	NM_000077.4	98	CACCGGGCCGGGGCGCGGCTGGACGTGCGCGATGCCTgg/gg	2/3	1	2	FACETS	1	0.913	1	1	0.98	1	CLONAL	2	TRUE	1	0.18	2		236	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0013441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	158	644	0	ENST00000269305.4:c.96+1G>A		p.X32_splice	ENST00000269305	NM_001126112.2	32			0.116060814520439	5	FACETS	1	0.972	1	0.566	0.519	0.615	INDETERMINATE	2	FALSE	1	0.223360674720799	5		644	834	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175481	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0013441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	78	403	0	ENST00000257430.4:c.4192_4193del	p.Arg1399PhefsTer9	p.R1399Ffs*9	ENST00000257430	NM_000038.5	1397	GAg/g	16/16	0.116060814520439	5	FACETS	1	0.954	1	0.581	0.513	0.653	INDETERMINATE	2	FALSE	1	0.223360674720799	5		403	401	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453149	140453149	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913361	NA	P-0013441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	64	352	0	ENST00000288602.6:c.1786G>C	p.Gly596Arg	p.G596R	ENST00000288602	NM_004333.4	596	Ggt/Cgt	15/18	0.223360674720799	5	FACETS	0.954	0.829	1	0.636	0.553	0.725	CLONAL	2	FALSE	2	0.223360674720799	5		352	401	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696268	52696268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	59	465	0	ENST00000394830.3:c.409G>A	p.Ala137Thr	p.A137T	ENST00000394830	NM_018313.4	137	Gct/Act	5/30	0.223360674720799	6	FACETS	1	0.966	1	0.361	0.311	0.416	CLONAL	1	FALSE	2	0.223360674720799	6		465	529	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374302	138374302	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	93	609	1	ENST00000289153.2:c.3142G>A	p.Ala1048Thr	p.A1048T	ENST00000289153	NM_006219.2	1048	Gcg/Acg	22/22	0.223360674720799	0	FACETS	1	0.894	1			1	CLONAL	1	FALSE	0	0.223360674720799	0		610	644	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39593422	39593422	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013447-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	39	265	0	ENST00000262039.4:c.1187T>G	p.Leu396Arg	p.L396R	ENST00000262039	NM_002647.2	396	cTa/cGa	11/25	0.26706815682824	1	FACETS	0.224	0.186	0.267	0.224	0.186	0.267	INDETERMINATE	1	TRUE	0	0.57881191244353	1		265	427	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593582	55593597	+	protein_altering_variant,splice_region_variant	In_Frame_Del	DEL	AAACCCATGTATGAAG	AAACCCATGTATGAAG	C	novel	NA	P-0013447-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	149	518	0	ENST00000288135.5:c.1648_1663delinsC	p.Lys550_Val555delinsLeu	p.K550_V555delinsL	ENST00000288135	NM_000222.2	550	AAACCCATGTATGAAGta/Cta	11/21	1	2	FACETS	0.806	0.739	0.876	0.806	0.739	0.876	CLONAL	1	TRUE	1	0.57881191244353	2		518	639	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191570	10191570	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1559429824	NA	P-0013463-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	69	586	0	ENST00000256474.2:c.563T>A	p.Leu188Gln	p.L188Q	ENST00000256474	NM_000551.3	188	cTg/cAg	3/3	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.16	2		586	844	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188164	11188164	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013463-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	39	367	0	ENST00000361445.4:c.5930C>G	p.Thr1977Arg	p.T1977R	ENST00000361445	NM_004958.3	1977	aCa/aGa	43/58	1	2	FACETS	0.736	0.609	0.879	0.736	0.609	0.879	SUBCLONAL	1	TRUE	1	0.16	2		367	662	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699232	117699232	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs747828648	NA	P-0013463-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	76	761	1	ENST00000369458.3:c.409G>T	p.Gly137Cys	p.G137C	ENST00000369458	NM_024626.3	137	Ggc/Tgc	3/6	1	2	FACETS	0.916	0.801	1	0.916	0.801	1	CLONAL	1	TRUE	1	0.16	2		762	1037	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169242	32169242	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013463-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	67	569	0	ENST00000375023.3:c.3791A>G	p.His1264Arg	p.H1264R	ENST00000375023	NM_004557.3	1264	cAc/cGc	22/30	1	2	FACETS	0.968	0.84	1	0.968	0.84	1	CLONAL	1	TRUE	1	0.16	2		569	865	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668661	52668661	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013463-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	97	939	0	ENST00000394830.3:c.1258del	p.Tyr420IlefsTer18	p.Y420Ifs*18	ENST00000394830	NM_018313.4	420	Tat/at	12/30	1	2	FACETS	0.996	0.886	1	0.996	0.886	1	CLONAL	1	TRUE	1	0.16	2		939	1217	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0013493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	510	571	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.505961961554241	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.505961961554241	2		571	896	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0013493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	230	656	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.505961961554241	3	FACETS	1	0.981	1	0.569	0.53	0.609	CLONAL	1	TRUE	1	0.505961961554241	3		656	1001	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056053	26056067	+	inframe_deletion	In_Frame_Del	DEL	CCTTGGGCTTAGCGG	CCTTGGGCTTAGCGG	-	rs756916945	NA	P-0013493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	97	385	0	ENST00000343677.2:c.590_604del	p.Ala197_Lys201del	p.A197_K201del	ENST00000343677	NM_005319.3	197	gCCGCTAAGCCCAAGGtt/gtt	1/1	0.505961961554241	3	FACETS	0.729	0.651	0.812	0.365	0.325	0.406	SUBCLONAL	1	TRUE	1	0.505961961554241	3		385	659	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012339	176012339	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	182	718	0	ENST00000367669.3:c.1595G>C	p.Gly532Ala	p.G532A	ENST00000367669	NM_022457.5	532	gGt/gCt	14/20	0.505961961554241	3	FACETS	0.893	0.824	0.966	0.447	0.412	0.483	CLONAL	1	TRUE	1	0.505961961554241	3		718	1009	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107296	193107296	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	147	448	0	ENST00000367435.3:c.505C>G	p.Gln169Glu	p.Q169E	ENST00000367435	NM_024529.4	169	Cag/Gag	6/17	0.505961961554241	3	FACETS	0.932	0.852	1	0.466	0.426	0.508	CLONAL	1	TRUE	1	0.505961961554241	3		448	781	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136279	202136279	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	197	711	2	ENST00000358485.4:c.523G>T	p.Glu175Ter	p.E175*	ENST00000358485	NM_001080125.1	175	Gaa/Taa	3/9	1	2	FACETS	0.905	0.839	0.974	0.905	0.839	0.974	CLONAL	1	TRUE	1	0.505961961554241	2		713	860	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876379	35876379	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	59	474	0	ENST00000303115.3:c.1171A>G	p.Arg391Gly	p.R391G	ENST00000303115	NM_002185.3	391	Agg/Ggg	8/8	0.505961961554241	5	FACETS	0.488	0.419	0.564			1	SUBCLONAL	1	TRUE	NA	0.505961961554241	5		474	840	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959900	38959900	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1181	83	531	0	ENST00000357387.3:c.2032A>C	p.Lys678Gln	p.K678Q	ENST00000357387	NM_152756.3	678	Aaa/Caa	21/38	0.505961961554241	5	FACETS	0.457	0.401	0.516			1	SUBCLONAL	1	TRUE	NA	0.505961961554241	5		531	1264	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86637135	86637135	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	64	308	0	ENST00000274376.6:c.1046A>G	p.Lys349Arg	p.K349R	ENST00000274376	NM_002890.2	349	aAa/aGa	6/25	1	2	FACETS	0.695	0.605	0.792	0.695	0.605	0.792	SUBCLONAL	1	TRUE	1	0.505961961554241	2		308	364	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418893	116418893	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	150	627	0	ENST00000397752.3:c.3404G>T	p.Ser1135Ile	p.S1135I	ENST00000397752	NM_000245.2	1135	aGt/aTt	17/21	NA	2	FACETS	0.892	0.817	0.969			1	INDETERMINATE	1	TRUE	NA	0.505961961554241	2		627	665	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853068	151853068	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	134	457	0	ENST00000262189.6:c.11887G>C	p.Ala3963Pro	p.A3963P	ENST00000262189	NM_170606.2	3963	Gct/Cct	46/59	NA	2	FACETS	1	0.936	1			1	INDETERMINATE	1	TRUE	NA	0.505961961554241	2		457	515	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250154	110250154	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866192782	NA	P-0013493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	81	265	0	ENST00000374672.4:c.521G>A	p.Gly174Asp	p.G174D	ENST00000374672	NM_004235.4	174	gGc/gAc	3/5	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.505961961554241	2		265	308	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432417	49432417	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	180	690	0	ENST00000301067.7:c.8722C>T	p.Pro2908Ser	p.P2908S	ENST00000301067	NM_003482.3	2908	Cct/Tct	34/54	0.505961961554241	3	FACETS	0.925	0.853	1	0.462	0.426	0.5	CLONAL	1	TRUE	1	0.505961961554241	3		690	964	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312460	91312460	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	160	583	0	ENST00000355112.3:c.2405A>C	p.Gln802Pro	p.Q802P	ENST00000355112	NM_000057.2	802	cAg/cCg	11/22	0.505961961554241	3	FACETS	0.881	0.808	0.958	0.441	0.404	0.479	CLONAL	1	TRUE	1	0.505961961554241	3		583	899	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830003	72830003	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	223	911	0	ENST00000268489.5:c.6578T>C	p.Phe2193Ser	p.F2193S	ENST00000268489	NM_006885.3	2193	tTc/tCc	9/10	0.366374991959784	1	FACETS	0.697	0.649	0.746	0.697	0.649	0.746	SUBCLONAL	1	TRUE	0	0.505961961554241	1		911	945	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350828	89350828	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	334	1186	0	ENST00000301030.4:c.2122A>C	p.Lys708Gln	p.K708Q	ENST00000301030	NM_001256183.1	708	Aaa/Caa	9/13	0.366374991959784	1	FACETS	0.733	0.692	0.775	0.733	0.692	0.775	SUBCLONAL	1	TRUE	0	0.505961961554241	1		1186	1345	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572471	41572471	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	147	603	0	ENST00000263253.7:c.5000T>C	p.Val1667Ala	p.V1667A	ENST00000263253	NM_001429.3	1667	gTc/gCc	30/31	1	2	FACETS	0.834	0.763	0.908	0.834	0.763	0.908	CLONAL	1	TRUE	1	0.505961961554241	2		603	697	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506963	186506990	+	frameshift_variant	Frame_Shift_Del	DEL	GTTACTGAAGAAGACAAGAGGATTCTTC	GTTACTGAAGAAGACAAGAGGATTCTTC	-	novel	NA	P-0013493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	185	1016	0	ENST00000323963.5:c.1131_1158del	p.Glu379LeufsTer14	p.E379Lfs*14	ENST00000323963		377	GTTACTGAAGAAGACAAGAGGATTCTTCgt/gt	11/11	1	2	FACETS	0.666	0.614	0.72	0.666	0.614	0.72	SUBCLONAL	1	TRUE	1	0.505961961554241	2		1016	1098	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696431	47696431	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013502-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	177	737	0	ENST00000347630.2:c.392G>T	p.Trp131Leu	p.W131L	ENST00000347630	NM_001007230.1	131	tGg/tTg	6/11	1	2	FACETS	0.851	0.782	0.922	0.851	0.782	0.922	CLONAL	1	TRUE	1	0.34618863386896	2		737	1202	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12043188	12043188	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013502-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	176	762	0	ENST00000353533.5:c.1073A>G	p.Tyr358Cys	p.Y358C	ENST00000353533	NM_003010.3	358	tAt/tGt	10/11	1	2	FACETS	0.816	0.75	0.885	0.816	0.75	0.885	CLONAL	1	TRUE	1	0.34618863386896	2		762	1246	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779626	3779626	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013502-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	95	539	0	ENST00000262367.5:c.5422T>G	p.Cys1808Gly	p.C1808G	ENST00000262367	NM_004380.2	1808	Tgc/Ggc	31/31	1	2	FACETS	0.825	0.735	0.921	0.825	0.735	0.921	CLONAL	1	TRUE	1	0.34618863386896	2		539	665	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37034007	37034007	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	185	425	0	ENST00000358127.4:c.22C>A	p.Pro8Thr	p.P8T	ENST00000358127	NM_001280556.1	8	Ccg/Acg	1/10	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.541628243906407	2		425	668	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42840450	42840450	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	215	481	0	ENST00000398585.3:c.1298T>A	p.Val433Glu	p.V433E	ENST00000398585	NM_001135099.1	433	gTg/gAg	12/14	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.541628243906407	2		481	731	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852447	42852447	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	270	656	0	ENST00000398585.3:c.639G>C	p.Trp213Cys	p.W213C	ENST00000398585	NM_001135099.1	213	tgG/tgC	6/14	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.541628243906407	2		656	973	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013522-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	15	420	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.15255654931949	1	FACETS	0.581	0.425	0.768	0.581	0.425	0.768	SUBCLONAL	1	TRUE	0	0.21	1		420	220	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0013522-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	35	612	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.542	0.443	0.654	0.542	0.443	0.654	SUBCLONAL	1	TRUE	1	0.21	2		613	615	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73352368	73352368	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	290	666	0	ENST00000377767.4:c.537A>C	p.Arg179Ser	p.R179S	ENST00000377767	NM_014953.3	179	agA/agC	3/21	0.175115756150766	3	FACETS	1	0.982	1	0.553	0.52	0.586	INDETERMINATE	1	TRUE	1	0.674960879860266	3		666	1040	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029207	26029207	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0013527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	53	351	0	ENST00000435504.4:c.144-1G>T		p.X48_splice	ENST00000435504		48			0.674960879860266	1	FACETS	0.286	0.244	0.331	0.286	0.244	0.331	SUBCLONAL	1	TRUE	0	0.674960879860266	1		351	364	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070904	30070904	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	214	541	0	ENST00000338641.4:c.1420G>T	p.Glu474Ter	p.E474*	ENST00000338641	NM_000268.3	474	Gag/Tag	13/16	0.674960879860266	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.674960879860266	1		541	401	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	41	589	1				ENST00000310581	NM_198253.2	-/1132			0.250075864369631	3	FACETS	1	0.935	1	0.616	0.518	0.723	CLONAL	1	TRUE	1	0.37022120619992	3		590	213	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579410	7579426	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGCCAGGAGGGGGCT	GGGGCCAGGAGGGGGCT	-	novel	NA	P-0013553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	64	794	0	ENST00000269305.4:c.261_277del	p.Ala88ValfsTer55	p.A88Vfs*55	ENST00000269305	NM_001126112.2	87	ccAGCCCCCTCCTGGCCCCtg/cctg	4/11	0.37022120619992	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.37022120619992	1		794	260	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113711	11113711	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	56	771	0	ENST00000358026.2:c.1819G>T	p.Asp607Tyr	p.D607Y	ENST00000358026	NM_001128849.1	607	Gac/Tac	12/36	0.37022120619992	1	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	0	0.37022120619992	1		771	236	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801121	1801121	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	54	787	0	ENST00000260795.2:c.250T>G	p.Ser84Ala	p.S84A	ENST00000260795		84	Tcg/Gcg	2/17	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.37022120619992	2		787	241	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935579	13935579	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	32	526	0	ENST00000405192.2:c.1277C>G	p.Pro426Arg	p.P426R	ENST00000405192	NM_001163147.1	426	cCt/cGt	12/12	1	2	FACETS	0.762	0.622	0.917	0.762	0.622	0.917	CLONAL	1	TRUE	1	0.37022120619992	2		526	227	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058477	42058477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760533003	NA	P-0013573-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	11	1272	4	ENST00000219905.7:c.8197G>A	p.Val2733Ile	p.V2733I	ENST00000219905	NM_001164273.1	2733	Gtt/Att	24/24	0.110354833477958	5	FACETS	0.606	0.419	0.839	0.152	0.104	0.21	INDETERMINATE	1	FALSE	1	0.240931985239219	5		1276	205	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183694	10183694	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	21	666	0	ENST00000256474.2:c.163G>T	p.Glu55Ter	p.E55*	ENST00000256474	NM_000551.3	55	Gag/Tag	1/3	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.293200643695937	2		666	116	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058974	42058974	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	24	1430	0	ENST00000219905.7:c.8694T>G	p.Ser2898Arg	p.S2898R	ENST00000219905	NM_001164273.1	2898	agT/agG	24/24	0.293200643695937	0	FACETS	0.612	0.483	0.759			1	SUBCLONAL	1	TRUE	0	0.293200643695937	0		1430	189	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266636	142266636	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs758605592	NA	P-0013574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	12	888	0	ENST00000350721.4:c.3288A>G	p.Ile1096Met	p.I1096M	ENST00000350721	NM_001184.3	1096	atA/atG	16/47	1	2	FACETS	0.386	0.271	0.527	0.386	0.271	0.527	SUBCLONAL	1	TRUE	1	0.293200643695937	2		888	212	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983147	111983147	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	26	845	0	ENST00000368678.4:c.1400T>A	p.Met467Lys	p.M467K	ENST00000368678		467	aTg/aAg	13/13	0.111980466765714	4	FACETS	1	0.844	1	0.536	0.427	0.659	INDETERMINATE	1	TRUE	2	0.293200643695937	4		845	214	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938532	44938532	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	17	472	0	ENST00000377967.4:c.3080G>A	p.Arg1027Lys	p.R1027K	ENST00000377967	NM_021140.2	1027	aGa/aAa	20/29	0.293200643695937	0	FACETS	0.677	0.511	0.87			1	SUBCLONAL	1	TRUE	NA	0.293200643695937	0		472	121	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013579-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	149	589	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.945	0.871	1	0.945	0.871	1	CLONAL	1	TRUE	1	0.702282512353363	2		590	449	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0013579-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	173	442	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	NA	2	FACETS	0.839	0.777	0.904			1	INDETERMINATE	1	TRUE	NA	0.702282512353363	2		442	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013579-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	14	379	0	ENST00000269305.4:c.376T>C	p.Tyr126His	p.Y126H	ENST00000269305	NM_001126112.2	126	Tac/Cac	5/11	1	2	FACETS	0.066	0.047	0.089	0.066	0.047	0.089	SUBCLONAL	1	TRUE	1	0.702282512353363	2		379	604	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544160	18544160	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013579-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	248	472	0	ENST00000266497.5:c.1977A>T	p.Arg659Ser	p.R659S	ENST00000266497		659	agA/agT	13/31	1	2	FACETS	0.928	0.871	0.986	0.928	0.871	0.986	CLONAL	1	TRUE	1	0.702282512353363	2		472	761	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914007	32914007	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013579-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	457	1036	0	ENST00000380152.3:c.5515G>T	p.Val1839Leu	p.V1839L	ENST00000380152		1839	Gta/Tta	11/27	1	2	FACETS	0.96	0.917	1	0.96	0.917	1	CLONAL	1	TRUE	1	0.702282512353363	2		1036	1356	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48921960	48921960	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0013579-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	192	396	0	ENST00000267163.4:c.501-1G>C		p.X167_splice	ENST00000267163	NM_000321.2	167			0.702282512353363	1	FACETS	0.907	0.852	0.963	0.907	0.852	0.963	CLONAL	1	TRUE	0	0.702282512353363	1		396	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0013583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	597	571	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.656575295154804	2		571	1437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578189	7578189	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1567551150	NA	P-0013583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	465	781	0	ENST00000269305.4:c.660T>A	p.Tyr220Ter	p.Y220*	ENST00000269305	NM_001126112.2	220	taT/taA	6/11	1	2	FACETS	0.845	0.806	0.885	0.845	0.806	0.885	CLONAL	1	TRUE	1	0.656575295154804	2		781	1676	SUCCESS
APC	324	MSKCC	GRCh37	5	112175184	112175194	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCTAATACC	CTGCTAATACC	-	novel	NA	P-0013583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	167	197	0	ENST00000257430.4:c.3897_3907del	p.Thr1301SerfsTer10	p.T1301Sfs*10	ENST00000257430	NM_000038.5	1298	tCTGCTAATACC/t	16/16	0.31217456497434	2	FACETS	1	0.985	1	0.619	0.575	0.663	INDETERMINATE	1	TRUE	0	0.656575295154804	2		197	411	SUCCESS
APC	324	MSKCC	GRCh37	5	112173627	112173627	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0013583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	113	427	0	ENST00000257430.4:c.2336T>A	p.Leu779Ter	p.L779*	ENST00000257430	NM_000038.5	779	tTa/tAa	16/16	0.31217456497434	2	FACETS	0.416	0.374	0.461	0.208	0.187	0.231	INDETERMINATE	1	TRUE	0	0.656575295154804	2		427	827	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523357	176523357	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	124	690	1	ENST00000292408.4:c.2014G>T	p.Val672Leu	p.V672L	ENST00000292408	NM_213647.1	672	Gtg/Ttg	15/18	0.31217456497434	2	FACETS	0.389	0.352	0.429	0.195	0.176	0.215	INDETERMINATE	1	TRUE	0	0.656575295154804	2		691	970	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517201	NA	P-0013588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	52	284	0	ENST00000263967.3:c.1637A>C	p.Gln546Pro	p.Q546P	ENST00000263967	NM_006218.2	546	cAg/cCg	10/21	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.19	2		284	489	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0013588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	114	693	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.19	2		693	910	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099362	27099363	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0013588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	71	617	0	ENST00000324856.7:c.3600_3601del	p.Lys1201AlafsTer18	p.K1201Afs*18	ENST00000324856	NM_006015.4	1200	cAG/c	14/20	1	2	FACETS	0.884	0.77	1	0.884	0.77	1	CLONAL	1	TRUE	1	0.19	2		617	845	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692971	89692989	+	frameshift_variant	Frame_Shift_Del	DEL	TAGATTTCTATGGGGAAGT	TAGATTTCTATGGGGAAGT	CG	novel	NA	P-0013588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	50	365	2	ENST00000371953.3:c.455_473delinsCG	p.Leu152ProfsTer22	p.L152Pfs*22	ENST00000371953	NM_000314.4	152	cTAGATTTCTATGGGGAAGTa/cCGa	5/9	1	2	FACETS	0.835	0.708	0.976	0.835	0.708	0.976	CLONAL	1	TRUE	1	0.19	2		367	630	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443919	18443919	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	74	437	0	ENST00000266497.5:c.892A>G	p.Thr298Ala	p.T298A	ENST00000266497		298	Aca/Gca	3/31	1	2	FACETS	0.921	0.805	1	0.921	0.805	1	CLONAL	1	TRUE	1	0.19	2		437	846	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655344	67655344	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0013588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	68	543	0	ENST00000264010.4:c.1210del		p.X404_splice	ENST00000264010	NM_006565.3	404			1	2	FACETS	0.87	0.755	0.994	0.87	0.755	0.994	CLONAL	1	TRUE	1	0.19	2		543	823	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427428	427428	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373590748	NA	P-0013655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	427	482	1	ENST00000399788.2:c.2741C>T	p.Pro914Leu	p.P914L	ENST00000399788	NM_001042603.1	914	cCg/cTg	19/28	0.567137867796914	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	2	0.567137867796914	4		483	1143	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098674	2098689	+	frameshift_variant	Frame_Shift_Del	DEL	GGACTGGGAACACCGA	GGACTGGGAACACCGA	TTCTG	novel	NA	P-0013655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	328	578	2	ENST00000219476.3:c.58_73delinsTTCTG	p.Gly20PhefsTer11	p.G20Ffs*11	ENST00000219476	NM_000548.3	20	GGACTGGGAACACCGAgg/TTCTGgg	2/42	0.52852995219935	2	FACETS	0.796	0.757	0.834	0.796	0.757	0.834	SUBCLONAL	2	TRUE	0	0.567137867796914	2		580	727	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268150	153268150	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	238	477	1	ENST00000281708.4:c.658C>T	p.Gln220Ter	p.Q220*	ENST00000281708	NM_033632.3	220	Caa/Taa	4/12	0.517293472685962	3	FACETS	0.967	0.902	1	0.484	0.451	0.517	CLONAL	1	TRUE	1	0.567137867796914	3		478	1114	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940533	131940533	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	366	511	0	ENST00000265335.6:c.2560C>G	p.Gln854Glu	p.Q854E	ENST00000265335		854	Cag/Gag	16/25	0.388767274913484	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.567137867796914	4		511	914	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638680	176638680	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	158	438	0	ENST00000439151.2:c.3280A>G	p.Met1094Val	p.M1094V	ENST00000439151	NM_022455.4	1094	Atg/Gtg	5/23	0.529184954420111	3	FACETS	0.844	0.774	0.918			1	CLONAL	1	TRUE	NA	0.567137867796914	3		438	847	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729819	41729819	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	302	630	0	ENST00000242208.4:c.710C>A	p.Ser237Tyr	p.S237Y	ENST00000242208	NM_002192.2	237	tCc/tAc	3/3	0.532632433955966	3	FACETS	1	0.994	1	0.497	0.469	0.525	CLONAL	1	TRUE	0	0.567137867796914	3		630	917	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0013672-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	167	452	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.181113081256278	4	FACETS	1	0.987	1	0.702	0.645	0.763	INDETERMINATE	1	TRUE	2	0.316865490405584	4		452	988	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590380	67590380	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013672-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	113	345	2	ENST00000274335.5:c.1442G>T	p.Arg481Met	p.R481M	ENST00000274335		481	aGg/aTg	11/15	0.181113081256278	4	FACETS	1	0.971	1	0.608	0.547	0.673	INDETERMINATE	1	TRUE	2	0.316865490405584	4		347	772	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220579	1220579	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0013672-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	190	530	0	ENST00000326873.7:c.598-1G>T		p.X200_splice	ENST00000326873	NM_000455.4	200			0.19878765122508	2	FACETS	0.837	0.777	0.9	0.837	0.777	0.9	CLONAL	2	TRUE	0	0.316865490405584	2		530	716	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600415	10600415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013672-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	110	747	0	ENST00000171111.5:c.1440del	p.Thr481GlnfsTer19	p.T481Qfs*19	ENST00000171111	NM_203500.1	480	ggG/gg	4/6	0.19878765122508	2	FACETS	0.608	0.545	0.675	0.304	0.272	0.338	SUBCLONAL	1	TRUE	0	0.316865490405584	2		747	1142	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0013701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	66	264	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.969	0.842	1	0.969	0.842	1	CLONAL	1	TRUE	1	0.25	2		264	545	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0013701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	166	779	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.112473275019028	3	FACETS	0.789	0.724	0.856	0.789	0.724	0.856	INDETERMINATE	2	TRUE	1	0.25	3		779	947	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142016	108142016	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	104	334	1	ENST00000278616.4:c.2960G>T	p.Cys987Phe	p.C987F	ENST00000278616	NM_000051.3	987	tGt/tTt	20/63	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.25	2		335	566	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148967	119148967	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	85	365	1	ENST00000264033.4:c.1187G>T	p.Cys396Phe	p.C396F	ENST00000264033	NM_005188.3	396	tGt/tTt	8/16	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.25	2		366	629	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612319	1612319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555712474	NA	P-0013701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	91	762	1	ENST00000344749.5:c.1700G>A	p.Arg567Gln	p.R567Q	ENST00000344749	NM_001136139.2	567	cGg/cAg	18/19	0.15126823785335	0	FACETS	0.69	0.612	0.774			1	SUBCLONAL	1	TRUE	0	0.25	0		763	791	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99160363	99160363	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	59	426	0	ENST00000074304.5:c.842G>T	p.Gly281Val	p.G281V	ENST00000074304	NM_001134224.1	281	gGa/gTa	11/26	1	2	FACETS	0.852	0.733	0.981	0.852	0.733	0.981	CLONAL	1	TRUE	1	0.25	2		426	554	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212252716	212252716	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	53	217	0	ENST00000342788.4:c.3137G>T	p.Ser1046Ile	p.S1046I	ENST00000342788	NM_005235.2	1046	aGt/aTt	26/28	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.25	2		217	419	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713718	30713718	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	39	248	0	ENST00000295754.5:c.1043G>T	p.Arg348Leu	p.R348L	ENST00000295754	NM_003242.5	348	cGc/cTc	4/7	1	2	FACETS	0.806	0.669	0.958	0.806	0.669	0.958	CLONAL	1	TRUE	1	0.25	2		248	387	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346284	70346284	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	89	510	1	ENST00000374080.3:c.2635C>A	p.Leu879Ile	p.L879I	ENST00000374080		879	Ctc/Atc	19/45	1	2	FACETS	0.871	0.772	0.978	0.871	0.772	0.978	CLONAL	1	TRUE	1	0.25	2		511	817	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617622	100617622	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	149	570	0	ENST00000308731.7:c.447T>A	p.Asp149Glu	p.D149E	ENST00000308731	NM_000061.2	149	gaT/gaA	6/19	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.25	2		570	974	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0013706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	214	554	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.541268017442648	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.541268017442648	1		554	534	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	59	151	0	ENST00000304494.5:c.172del	p.Arg58GlufsTer88	p.R58Efs*88	ENST00000304494	NM_000077.4	58	Cga/ga	2/3	0.541268017442648	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.541268017442648	1		151	137	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	259	355	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.541268017442648	1		355	479	SUCCESS
AR	367	MSKCC	GRCh37	X	66765159	66765194	+	inframe_deletion	In_Frame_Del	DEL	GCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA	GCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA	-	rs3032358	NA	P-0013706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	30	172	0	ENST00000374690.3:c.204_239del	p.Gln69_Gln80del	p.Q69_Q80del	ENST00000374690	NM_000044.3	57	ctGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAg/ctg	1/8	1	1	FACETS	0.452	0.367	0.545	0.452	0.367	0.545	SUBCLONAL	1	TRUE	0	0.541268017442648	1		172	179	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098975	178098975	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1328994103	NA	P-0013706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	120	335	0	ENST00000397062.3:c.70T>C	p.Trp24Arg	p.W24R	ENST00000397062	NM_006164.4	24	Tgg/Cgg	2/5	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.541268017442648	2		335	402	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242647	16242647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777234386	NA	P-0013706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	161	519	0	ENST00000375759.3:c.1268G>A	p.Arg423His	p.R423H	ENST00000375759	NM_015001.2	423	cGc/cAc	6/15	1	2	FACETS	0.791	0.727	0.858	0.791	0.727	0.858	SUBCLONAL	1	TRUE	1	0.541268017442648	2		519	752	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780684	56780684	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	114	479	0	ENST00000337432.4:c.699C>G	p.His233Gln	p.H233Q	ENST00000337432	NM_058216.2	233	caC/caG	4/9	1	2	FACETS	0.667	0.601	0.735	0.667	0.601	0.735	SUBCLONAL	1	TRUE	1	0.541268017442648	2		479	632	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157443	106157443	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	121	398	0	ENST00000380013.4:c.2344G>T	p.Glu782Ter	p.E782*	ENST00000380013	NM_001127208.2	782	Gaa/Taa	3/11	0.541268017442648	1	FACETS	0.908	0.83	0.989	0.908	0.83	0.989	CLONAL	1	TRUE	0	0.541268017442648	1		398	359	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874620	151874620	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	274	484	0	ENST00000262189.6:c.7918C>A	p.His2640Asn	p.H2640N	ENST00000262189	NM_170606.2	2640	Cat/Aat	38/59	0.324512886882896	4	FACETS	0.839	0.789	0.89			1	INDETERMINATE	2	TRUE	NA	0.541268017442648	4		484	930	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126682	5126682	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0013706-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	99	338	0	ENST00000381652.3:c.3292-2A>G		p.X1098_splice	ENST00000381652	NM_004972.3	1098			0.541268017442648	1	FACETS	0.996	0.903	1	0.996	0.903	1	CLONAL	1	TRUE	0	0.541268017442648	1		338	268	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0013707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	55	239	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.242552413727204	4	FACETS	1	0.937	1	0.767	0.663	0.878	CLONAL	2	FALSE	1	0.242552413727204	4		239	245	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519896	NA	P-0013707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	10	459	2	ENST00000281708.4:c.1514G>A	p.Arg505His	p.R505H	ENST00000281708	NM_033632.3	505	cGc/cAc	10/12	0.165801519799809	4	FACETS	0.225	0.151	0.318	0.112	0.075	0.159	SUBCLONAL	1	FALSE	2	0.242552413727204	4		461	456	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4388008	4388008	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759672856	NA	P-0013707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	28	442	0	ENST00000261254.3:c.494G>A	p.Arg165His	p.R165H	ENST00000261254	NM_001759.3	165	cGc/cAc	3/5	0.242552413727204	4	FACETS	0.883	0.706	1	0.294	0.235	0.361	CLONAL	1	FALSE	1	0.242552413727204	4		442	325	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106058	8106058	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	34	323	0	ENST00000346208.3:c.878T>G	p.Met293Arg	p.M293R	ENST00000346208		293	aTg/aGg	4/6	0.242552413727204	3	FACETS	0.843	0.689	1	0.421	0.344	0.508	CLONAL	1	FALSE	1	0.242552413727204	3		323	373	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197819	66197819	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	57	456	0	ENST00000273854.3:c.2880C>G	p.Ser960Arg	p.S960R	ENST00000273854	NM_004439.5	960	agC/agG	17/18	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.242552413727204	2		456	352	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260328	10260328	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148987580	NA	P-0013715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	117	390	1	ENST00000340748.4:c.2339C>T	p.Thr780Met	p.T780M	ENST00000340748		780	aCg/aTg	25/40	NA	2	FACETS	1	0.932	1			1	INDETERMINATE	1	TRUE	NA	0.690555865766201	2		391	331	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696435	47696435	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	222	645	0	ENST00000347630.2:c.388G>C	p.Asp130His	p.D130H	ENST00000347630	NM_001007230.1	130	Gac/Cac	6/11	0.534632978698534	4	FACETS	1	0.985	1	0.399	0.372	0.427	CLONAL	1	TRUE	1	0.690555865766201	4		645	908	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857531	68857531	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs876661120	NA	P-0013715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	75	313	0	ENST00000261769.5:c.2164+2T>C		p.X722_splice	ENST00000261769	NM_004360.3	722			0.530106005317046	1	FACETS	0.878	0.79	0.966	0.878	0.79	0.966	CLONAL	1	TRUE	0	0.690555865766201	1		313	162	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252920	36252920	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	202	615	0	ENST00000300305.3:c.442del	p.Thr148ProfsTer4	p.T148Pfs*4	ENST00000300305		148	Acc/cc	4/8	0.32974340662914	4	FACETS	0.768	0.715	0.822			1	INDETERMINATE	2	TRUE	NA	0.690555865766201	4		615	644	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878355	151878361	+	frameshift_variant	Frame_Shift_Del	DEL	TGATTTG	TGATTTG	-	novel	NA	P-0013715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	173	678	0	ENST00000262189.6:c.6584_6590del	p.Thr2195ArgfsTer42	p.T2195Rfs*42	ENST00000262189	NM_170606.2	2195	aCAAATCAg/ag	36/59	1	2	FACETS	0.967	0.897	1	0.967	0.897	1	CLONAL	1	TRUE	1	0.690555865766201	2		678	518	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537115	41537115	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853039	NA	P-0013727-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	246	446	1	ENST00000263253.7:c.1942C>T	p.Arg648Ter	p.R648*	ENST00000263253	NM_001429.3	648	Cga/Tga	10/31	1	2	FACETS	0.929	0.873	0.987	0.929	0.873	0.987	CLONAL	1	TRUE	1	0.725302627491101	2		447	730	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044546	47044546	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs781791363	NA	P-0013727-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	263	365	0	ENST00000377604.3:c.2043T>G	p.Asp681Glu	p.D681E	ENST00000377604	NM_001204468.1	681	gaT/gaG	18/24	1	1	FACETS	0.947	0.9	0.994	0.947	0.9	0.994	CLONAL	1	TRUE	0	0.725302627491101	1		365	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0013749-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	82	418	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.255492198256611	2		421	593	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0013749-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	83	291	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.255492198256611	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.255492198256611	1		292	504	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287255	33287258	+	frameshift_variant	Frame_Shift_Del	DEL	ATTG	ATTG	-	novel	NA	P-0013749-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	87	604	0	ENST00000374542.5:c.1839_1842del	p.Phe613LeufsTer31	p.F613Lfs*31	ENST00000374542	NM_001141970.1	613	ttCAAT/tt	6/8	0.255492198256611	1	FACETS	0.813	0.719	0.913	0.813	0.719	0.913	CLONAL	1	TRUE	0	0.255492198256611	1		604	731	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0013752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	98	483	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.874	0.778	0.977	0.874	0.778	0.977	CLONAL	1	TRUE	1	0.215996483538505	2		483	1038	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677926	58677926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1438030849	NA	P-0013752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	47	443	0	ENST00000305921.3:c.151C>T	p.Pro51Ser	p.P51S	ENST00000305921	NM_003620.3	51	Ccg/Tcg	1/6	1	2	FACETS	0.518	0.436	0.61	0.518	0.436	0.61	SUBCLONAL	1	TRUE	1	0.215996483538505	2		443	840	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199896	108199896	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	90	493	0	ENST00000278616.4:c.7238A>G	p.Lys2413Arg	p.K2413R	ENST00000278616	NM_000051.3	2413	aAg/aGg	49/63	1	2	FACETS	0.834	0.738	0.937	0.834	0.738	0.937	CLONAL	1	TRUE	1	0.215996483538505	2		493	999	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162872	47162872	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	125	590	0	ENST00000409792.3:c.3254del	p.Pro1085LeufsTer36	p.P1085Lfs*36	ENST00000409792	NM_014159.6	1085	cCt/ct	3/21	1	2	FACETS	0.957	0.863	1	0.957	0.863	1	CLONAL	1	TRUE	1	0.215996483538505	2		590	1210	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112025241	112025241	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0013752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1287	164	755	0	ENST00000368678.4:c.508A>T	p.Arg170Ter	p.R170*	ENST00000368678		170	Aga/Tga	6/13	0.215996483538505	1	FACETS	0.934	0.854	1	0.934	0.854	1	CLONAL	1	TRUE	0	0.215996483538505	1		755	1451	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781375	3781375	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	67	532	1	ENST00000262367.5:c.4990C>T	p.Arg1664Cys	p.R1664C	ENST00000262367	NM_004380.2	1664	Cgc/Tgc	30/31	1	2	FACETS	0.789	0.689	0.895	1	0.975	1	SUBCLONAL	2	TRUE	1	0.240672996070034	2		533	353	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0013758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	19	345	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.475	0.361	0.609	0.475	0.361	0.609	SUBCLONAL	1	TRUE	1	0.305337884573385	2		345	262	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0013758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	47	455	1	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			1	2	FACETS	0.865	0.741	0.996	1	0.971	1	CLONAL	2	TRUE	1	0.305337884573385	2		456	178	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248599	212248599	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	45	828	0	ENST00000342788.4:c.3668A>C	p.Lys1223Thr	p.K1223T	ENST00000342788	NM_005235.2	1223	aAg/aCg	28/28	0.305337884573385	3	FACETS	0.944	0.796	1	0.472	0.398	0.553	CLONAL	1	TRUE	1	0.305337884573385	3		828	360	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756797	756797	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	21	760	0	ENST00000314574.4:c.31A>C	p.Ser11Arg	p.S11R	ENST00000314574	NM_005433.3	11	Agt/Cgt	2/12	0.305337884573385	2	FACETS	0.537	0.414	0.68	0.269	0.207	0.34	SUBCLONAL	1	TRUE	0	0.305337884573385	2		760	256	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604748	48604748	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	93	757	0	ENST00000342988.3:c.1570T>G	p.Trp524Gly	p.W524G	ENST00000342988	NM_005359.5	524	Tgg/Ggg	12/12	0.305337884573385	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	2	TRUE	0	0.305337884573385	2		757	298	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426795	212426795	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	29	480	0	ENST00000342788.4:c.2320A>C	p.Ser774Arg	p.S774R	ENST00000342788	NM_005235.2	774	Agt/Cgt	20/28	0.305337884573385	3	FACETS	0.779	0.627	0.951	0.39	0.313	0.476	CLONAL	1	TRUE	1	0.305337884573385	3		480	281	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294441	1294441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	29	383	1	ENST00000310581.5:c.560C>T	p.Pro187Leu	p.P187L	ENST00000310581	NM_198253.2	187	cCg/cTg	2/16	1	2	FACETS	1	0.83	1	1	0.83	1	CLONAL	1	TRUE	1	0.305337884573385	2		384	185	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120809	94120810	+	missense_variant	Missense_Mutation	DNP	TG	TG	GT	novel	NA	P-0013758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	41	999	2	ENST00000369303.4:c.241_242delinsAC	p.Gln81Thr	p.Q81T	ENST00000369303	NM_004440.3	81	CAa/ACa	3/17	0.305337884573385	3	FACETS	0.825	0.689	0.976	0.413	0.344	0.488	CLONAL	1	TRUE	1	0.305337884573385	3		1001	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0013762-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	209	679	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.408149035623712	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.408149035623712	1		679	770	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793030	33793030	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013762-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	64	189	1	ENST00000498907.2:c.291del	p.Thr98ArgfsTer62	p.T98Rfs*62	ENST00000498907	NM_004364.3	97	ccC/cc	1/1	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.408149035623712	2		190	252	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160759	56160759	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013762-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	126	440	0	ENST00000399503.3:c.1033C>T	p.Gln345Ter	p.Q345*	ENST00000399503	NM_005921.1	345	Cag/Tag	4/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.408149035623712	2		440	591	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176572	56176572	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013762-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	109	384	0	ENST00000399503.3:c.2122G>T	p.Glu708Ter	p.E708*	ENST00000399503	NM_005921.1	708	Gaa/Taa	12/20	1	2	FACETS	0.984	0.887	1	0.984	0.887	1	CLONAL	1	TRUE	1	0.408149035623712	2		384	543	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0013779-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	132	537	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.921	0.837	1	0.921	0.837	1	CLONAL	1	TRUE	1	0.372287611773532	2		537	770	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063717	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0013779-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	60	312	0	ENST00000412916.2:c.165+1G>T		p.X55_splice	ENST00000412916		55			0.372287611773532	1	FACETS	0.815	0.707	0.931	0.815	0.707	0.931	CLONAL	1	TRUE	0	0.372287611773532	1		312	322	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573142	64573142	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013779-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	120	627	0	ENST00000312049.6:c.1150G>T	p.Glu384Ter	p.E384*	ENST00000312049	NM_130799.2	384	Gag/Tag	8/10	1	2	FACETS	0.992	0.897	1	0.992	0.897	1	CLONAL	1	TRUE	1	0.372287611773532	2		627	650	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0013788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	18	195	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.515	0.389	0.662	0.515	0.389	0.662	SUBCLONAL	1	TRUE	1	0.346313065905539	2		195	202	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs17849781	NA	P-0013788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	358	630	2	ENST00000269305.4:c.832C>A	p.Pro278Thr	p.P278T	ENST00000269305	NM_001126112.2	278	Cct/Act	8/11	0.323796092406278	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.346313065905539	2		632	966	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998980	11998980	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	140	572	0	ENST00000353533.5:c.483del	p.Ile161MetfsTer36	p.I161Mfs*36	ENST00000353533	NM_003010.3	161	aTt/at	4/11	0.323796092406278	2	FACETS	0.871	0.799	0.945	0.871	0.799	0.945	CLONAL	2	TRUE	0	0.346313065905539	2		572	464	SUCCESS
APC	324	MSKCC	GRCh37	5	112116523	112116523	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	112	447	0	ENST00000257430.4:c.568G>T	p.Glu190Ter	p.E190*	ENST00000257430	NM_000038.5	190	Gaa/Taa	6/16	0.159397625589482	2	FACETS	1	0.984	1	0.742	0.672	0.815	INDETERMINATE	1	TRUE	0	0.346313065905539	2		447	436	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972715	76972715	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	50	297	0	ENST00000373344.5:c.26G>T	p.Ser9Ile	p.S9I	ENST00000373344	NM_000489.3	9	aGc/aTc	2/35	0.160030941850322	2	FACETS	0.966	0.825	1			1	INDETERMINATE	1	TRUE	NA	0.346313065905539	2		297	299	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0013796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	176	692	0	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.286454371565995	2		692	1152	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880219	37880220	+	missense_variant	Missense_Mutation	DNP	TT	TT	CC	rs121913469	NA	P-0013796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	169	761	0	ENST00000269571.5:c.2263_2264delinsCC	p.Leu755Pro	p.L755P	ENST00000269571		755	TTg/CCg	19/27	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	FALSE	1	0.286454371565995	2		761	1152	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013814-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	78	589	1				ENST00000310581	NM_198253.2	-/1132			0.305061282512791	4	FACETS	1	0.945	1			1	CLONAL	2	FALSE	NA	0.421382654003969	4		590	240	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032264	10032264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751692867	NA	P-0013814-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	184	519	0	ENST00000330684.3:c.559G>A	p.Val187Ile	p.V187I	ENST00000330684	NM_001134407.1	187	Gtc/Atc	3/13	NA	2	FACETS	0.856	0.797	0.917			1	INDETERMINATE	2	FALSE	NA	0.421382654003969	2		519	510	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148931	119148931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs985412813	NA	P-0013814-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	40	607	0	ENST00000264033.4:c.1151G>A	p.Cys384Tyr	p.C384Y	ENST00000264033	NM_005188.3	384	tGt/tAt	8/16	0.421382654003969	3	FACETS	0.308	0.255	0.367	0.154	0.127	0.184	SUBCLONAL	1	FALSE	1	0.421382654003969	3		607	747	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845584	63845592	+	inframe_deletion	In_Frame_Del	DEL	CAAACGCAT	CAAACGCAT	-	novel	NA	P-0013814-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	237	576	2	ENST00000279873.7:c.1328_1336del	p.Arg443_Lys445del	p.R443_K445del	ENST00000279873	NM_032199.2	441	acCAAACGCATc/acc	9/10	0.322001042548395	3	FACETS	1	0.99	1			1	CLONAL	2	FALSE	NA	0.421382654003969	3		578	545	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667606	29667607	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0013814-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	310	760	0	ENST00000356175.3:c.6943_6944del	p.Ala2315ThrfsTer3	p.A2315Tfs*3	ENST00000356175	NM_000267.3	2314	acCGca/acca	46/57	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	2	FALSE	NA	0.421382654003969	2		760	625	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952513	17952513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199815093	NA	P-0013814-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	179	564	3	ENST00000458235.1:c.920C>T	p.Pro307Leu	p.P307L	ENST00000458235	NM_000215.3	307	cCg/cTg	7/24	0.264820426512394	6	FACETS	0.857	0.794	0.922	0.643	0.595	0.691	CLONAL	3	FALSE	2	0.421382654003969	6		567	609	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	24	589	1				ENST00000310581	NM_198253.2	-/1132			0.244271767501814	4	FACETS	1	0.892	1			1	CLONAL	2	FALSE	NA	0.386999799979098	4		590	74	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	167	675	1	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.322716590101276	4	FACETS	1	0.983	1	0.804	0.745	0.865	CLONAL	2	FALSE	1	0.386999799979098	4		676	496	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746131	162746131	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121964863	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	55	583	1	ENST00000367921.3:c.2254C>T	p.Arg752Cys	p.R752C	ENST00000367921	NM_006182.2	752	Cgc/Tgc	16/18	0.322716590101276	4	FACETS	0.828	0.709	0.958	0.276	0.236	0.32	CLONAL	1	FALSE	1	0.386999799979098	4		584	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574004	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	103	902	2	ENST00000269305.4:c.1023_1024delinsTT	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	341	ttCCga/ttTTga	10/11	0.322716590101276	4	FACETS	1	0.977	1	0.441	0.396	0.489	CLONAL	1	FALSE	1	0.386999799979098	4		904	558	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16235927	16235928	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	120	853	2	ENST00000375759.3:c.993_994delinsTT	p.Arg332Cys	p.R332C	ENST00000375759	NM_015001.2	331	ccCCgt/ccTTgt	4/15	0.386999799979098	6	FACETS	0.789	0.714	0.869			1	SUBCLONAL	2	FALSE	NA	0.386999799979098	6		855	697	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255047	16255047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761816625	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	59	366	0	ENST00000375759.3:c.2312C>T	p.Pro771Leu	p.P771L	ENST00000375759	NM_015001.2	771	cCt/cTt	11/15	0.386999799979098	6	FACETS	1	0.968	1			1	CLONAL	1	FALSE	NA	0.386999799979098	6		366	368	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262724	16262724	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771397847	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	48	333	0	ENST00000375759.3:c.9989C>T	p.Ser3330Phe	p.S3330F	ENST00000375759	NM_015001.2	3330	tCt/tTt	11/15	0.386999799979098	6	FACETS	0.783	0.666	0.91			1	CLONAL	2	FALSE	NA	0.386999799979098	6		333	281	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264407	16264407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764170487	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	83	821	1	ENST00000375759.3:c.10610C>T	p.Ser3537Phe	p.S3537F	ENST00000375759	NM_015001.2	3537	tCc/tTc	13/15	0.386999799979098	6	FACETS	0.813	0.72	0.912			1	CLONAL	2	FALSE	NA	0.386999799979098	6		822	468	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805052	43805052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs6088	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	54	878	0	ENST00000372470.3:c.502G>A	p.Glu168Lys	p.E168K	ENST00000372470	NM_005373.2	168	Gaa/Aaa	4/12	0.303388346340707	4	FACETS	0.906	0.776	1	0.453	0.388	0.524	CLONAL	1	FALSE	2	0.386999799979098	4		878	427	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248552	59248552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	85	754	0	ENST00000371222.2:c.191C>T	p.Pro64Leu	p.P64L	ENST00000371222	NM_002228.3	64	cCc/cTc	1/1	0.303388346340707	4	FACETS	1	0.974	1	0.674	0.598	0.754	CLONAL	1	FALSE	2	0.386999799979098	4		754	452	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555221	226555222	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	56	857	1	ENST00000366794.5:c.2365_2366delinsTT	p.Pro789Phe	p.P789F	ENST00000366794	NM_001618.3	789	CCc/TTc	17/23	0.322716590101276	4	FACETS	1	0.923	1	0.371	0.319	0.427	CLONAL	1	FALSE	1	0.386999799979098	4		858	361	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115889	8115889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	49	740	0	ENST00000346208.3:c.1235C>T	p.Ser412Phe	p.S412F	ENST00000346208		412	tCc/tTc	6/6	0.363604232361516	3	FACETS	1	0.919	1	0.56	0.477	0.649	CLONAL	1	FALSE	1	0.386999799979098	3		740	270	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717661	89717661	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1214965807	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	125	586	0	ENST00000371953.3:c.686C>T	p.Ser229Leu	p.S229L	ENST00000371953	NM_000314.4	229	tCa/tTa	7/9	0.333635703266466	4	FACETS	0.799	0.726	0.875			1	SUBCLONAL	2	FALSE	NA	0.386999799979098	4		586	561	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276865	123276865	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	55	747	0	ENST00000358487.5:c.1052C>T	p.Ser351Phe	p.S351F	ENST00000358487	NM_000141.4	351	tCc/tTc	8/18	0.28850774053427	1	FACETS	0.661	0.568	0.761	0.661	0.568	0.761	SUBCLONAL	1	FALSE	0	0.386999799979098	1		747	347	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251893	8251893	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	42	750	0	ENST00000335790.3:c.184G>A	p.Gly62Ser	p.G62S	ENST00000335790	NM_002315.2	62	Ggc/Agc	2/4	0.386999799979098	2	FACETS	0.987	0.832	1	0.493	0.416	0.578	CLONAL	1	FALSE	0	0.386999799979098	2		750	220	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129463	64129463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	20	476	0	ENST00000334205.4:c.895C>T	p.Pro299Ser	p.P299S	ENST00000334205	NM_003942.2	299	Ccc/Tcc	8/17	0.386999799979098	5	FACETS	0.621	0.476	0.791	0.207	0.158	0.264	SUBCLONAL	1	FALSE	2	0.386999799979098	5		476	263	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376629	118376629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	91	695	0	ENST00000534358.1:c.10022C>T	p.Ser3341Phe	p.S3341F	ENST00000534358	NM_005933.3	3341	tCc/tTc	27/36	0.261823081691524	6	FACETS	0.862	0.768	0.961	0.431	0.384	0.481	CLONAL	2	FALSE	2	0.386999799979098	6		695	484	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392013	118392013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	110	615	0	ENST00000534358.1:c.11524C>T	p.His3842Tyr	p.H3842Y	ENST00000534358	NM_005933.3	3842	Cat/Tat	35/36	0.261823081691524	6	FACETS	0.979	0.884	1	0.49	0.442	0.54	CLONAL	2	FALSE	2	0.386999799979098	6		615	515	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156074	119156074	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753301731	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	102	915	1	ENST00000264033.4:c.1739C>T	p.Pro580Leu	p.P580L	ENST00000264033	NM_005188.3	580	cCt/cTt	11/16	0.261823081691524	6	FACETS	0.863	0.774	0.956	0.431	0.387	0.478	CLONAL	2	FALSE	2	0.386999799979098	6		916	542	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905397	11905397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	69	549	0	ENST00000396373.4:c.47C>T	p.Ser16Leu	p.S16L	ENST00000396373	NM_001987.4	16	tCa/tTa	2/8	0.386999799979098	6	FACETS	0.99	0.862	1	0.247	0.215	0.282	CLONAL	1	FALSE	2	0.386999799979098	6		549	639	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992098	11992098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	41	430	0	ENST00000396373.4:c.188G>A	p.Arg63Lys	p.R63K	ENST00000396373	NM_001987.4	63	aGg/aAg	3/8	0.386999799979098	6	FACETS	0.889	0.741	1	0.222	0.185	0.263	CLONAL	1	FALSE	2	0.386999799979098	6		430	423	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435508	18435508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	73	481	0	ENST00000266497.5:c.493C>T	p.His165Tyr	p.H165Y	ENST00000266497		165	Cat/Tat	1/31	0.386999799979098	9	FACETS	0.763	0.668	0.866	0.305	0.267	0.347	SUBCLONAL	2	FALSE	4	0.386999799979098	9		481	582	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641528	18641528	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	84	557	0	ENST00000266497.5:c.2527G>A	p.Glu843Lys	p.E843K	ENST00000266497		843	Gaa/Aaa	17/31	0.386999799979098	7	FACETS	1	0.977	1			1	CLONAL	1	FALSE	NA	0.386999799979098	7		557	586	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719882	18719882	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	162	570	0	ENST00000266497.5:c.3780-1G>A		p.X1260_splice	ENST00000266497		1260			0.386999799979098	7	FACETS	0.849	0.781	0.918			1	CLONAL	3	FALSE	NA	0.386999799979098	7		570	647	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425361	49425361	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1274028118	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	100	890	0	ENST00000301067.7:c.13127C>T	p.Pro4376Leu	p.P4376L	ENST00000301067	NM_003482.3	4376	cCt/cTt	39/54	0.386999799979098	6	FACETS	0.885	0.793	0.981			1	CLONAL	2	FALSE	NA	0.386999799979098	6		890	518	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438192	49438192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	104	864	2	ENST00000301067.7:c.5077C>T	p.Arg1693Trp	p.R1693W	ENST00000301067	NM_003482.3	1693	Cgg/Tgg	20/54	0.386999799979098	6	FACETS	0.774	0.694	0.858			1	SUBCLONAL	2	FALSE	NA	0.386999799979098	6		866	616	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444514	49444514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	71	461	2	ENST00000301067.7:c.2857C>T	p.Pro953Ser	p.P953S	ENST00000301067	NM_003482.3	953	Cct/Tct	11/54	0.386999799979098	6	FACETS	0.897	0.787	1			1	CLONAL	2	FALSE	NA	0.386999799979098	6		463	363	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145042	58145042	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	140	725	0	ENST00000257904.6:c.302G>A	p.Arg101Lys	p.R101K	ENST00000257904	NM_000075.3	101	aGg/aAg	3/8	0.386999799979098	4	FACETS	1	0.981	1	0.638	0.582	0.698	CLONAL	1	FALSE	2	0.386999799979098	4		725	786	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111886057	111886058	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	86	1160	1	ENST00000341259.2:c.1679_1680delinsTT	p.Ser560Phe	p.S560F	ENST00000341259	NM_005475.2	560	tCC/tTT	8/8	0.386999799979098	4	FACETS	1	0.937	1	0.543	0.481	0.609	CLONAL	1	FALSE	2	0.386999799979098	4		1161	568	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112157	115112157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	31	568	0	ENST00000257566.3:c.1583G>A	p.Gly528Glu	p.G528E	ENST00000257566	NM_016569.3	528	gGg/gAg	7/8	0.255340283410136	3	FACETS	0.947	0.772	1	0.473	0.386	0.571	CLONAL	1	FALSE	1	0.386999799979098	3		568	202	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253993	133253993	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	67	798	0	ENST00000320574.5:c.757T>G	p.Phe253Val	p.F253V	ENST00000320574	NM_006231.2	253	Ttt/Gtt	8/49	0.255340283410136	3	FACETS	0.975	0.85	1	0.487	0.425	0.554	CLONAL	1	FALSE	1	0.386999799979098	3		798	424	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21553855	21553855	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	164	810	1	ENST00000382592.4:c.2747C>T	p.Pro916Leu	p.P916L	ENST00000382592	NM_014572.2	916	cCt/cTt	7/8	0.386999799979098	1	FACETS	0.89	0.828	0.953	1	0.992	1	CLONAL	2	FALSE	0	0.386999799979098	1		811	384	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21565531	21565531	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1321418369	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	126	645	2	ENST00000382592.4:c.355C>T	p.Arg119Ter	p.R119*	ENST00000382592	NM_014572.2	119	Cga/Tga	3/8	0.386999799979098	1	FACETS	1	0.93	1	1	0.991	1	CLONAL	2	FALSE	0	0.386999799979098	1		647	261	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32899312	32899312	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs80358660	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	174	501	0	ENST00000380152.3:c.416T>G	p.Leu139Arg	p.L139R	ENST00000380152		139	cTt/cGt	4/27	0.254756777801059	4	FACETS	0.981	0.913	1	0.735	0.685	0.787	CLONAL	3	FALSE	0	0.386999799979098	4		501	424	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515280	103515280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	132	643	0	ENST00000355739.4:c.1781C>T	p.Ser594Leu	p.S594L	ENST00000355739	NM_000123.3	594	tCa/tTa	8/15	0.254756777801059	4	FACETS	0.964	0.888	1	0.723	0.666	0.782	CLONAL	3	FALSE	0	0.386999799979098	4		643	327	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518061	103518061	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	60	562	0	ENST00000355739.4:c.1999C>T	p.Gln667Ter	p.Q667*	ENST00000355739	NM_000123.3	667	Caa/Taa	9/15	0.254756777801059	4	FACETS	1	0.964	1	0.34	0.295	0.389	CLONAL	1	FALSE	0	0.386999799979098	4		562	316	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436194	110436194	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs918898281	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	116	568	0	ENST00000375856.3:c.2207C>T	p.Ser736Phe	p.S736F	ENST00000375856	NM_003749.2	736	tCc/tTc	1/2	0.254756777801059	4	FACETS	1	0.971	1	0.842	0.774	0.909	CLONAL	3	FALSE	0	0.386999799979098	4		568	247	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562629	95562629	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	133	546	0	ENST00000393063.1:c.4628C>T	p.Ser1543Phe	p.S1543F	ENST00000393063	NM_030621.3	1543	tCc/tTc	24/28	0.363604232361516	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	FALSE	1	0.386999799979098	3		546	381	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034906	42034906	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	161	1079	0	ENST00000219905.7:c.4748C>T	p.Ser1583Phe	p.S1583F	ENST00000219905	NM_001164273.1	1583	tCt/tTt	15/24	0.386999799979098	3	FACETS	1	0.986	1	0.674	0.619	0.731	CLONAL	1	FALSE	1	0.386999799979098	3		1079	737	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058882	42058882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	160	1155	0	ENST00000219905.7:c.8602C>T	p.Pro2868Ser	p.P2868S	ENST00000219905	NM_001164273.1	2868	Cct/Tct	24/24	0.386999799979098	3	FACETS	1	0.983	1	0.64	0.588	0.695	CLONAL	1	FALSE	1	0.386999799979098	3		1155	771	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483945	88483945	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1313486936	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	57	807	1	ENST00000360948.2:c.1625G>A	p.Arg542Gln	p.R542Q	ENST00000360948	NM_001012338.2	542	cGa/cAa	14/19	NA	2	FACETS	0.79	0.68	0.908			1	INDETERMINATE	1	FALSE	NA	0.386999799979098	2		808	373	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669525	88669525	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1361454724	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	61	806	0	ENST00000360948.2:c.1373G>A	p.Arg458Gln	p.R458Q	ENST00000360948	NM_001012338.2	458	cGa/cAa	12/19	NA	2	FACETS	0.792	0.686	0.907			1	INDETERMINATE	1	FALSE	NA	0.386999799979098	2		806	398	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670400	88670400	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs140016144	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	71	702	0	ENST00000360948.2:c.1286C>A	p.Thr429Asn	p.T429N	ENST00000360948	NM_001012338.2	429	aCt/aAt	11/19	NA	2	FACETS	0.976	0.857	1			1	INDETERMINATE	1	FALSE	NA	0.386999799979098	2		702	376	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88671943	88671943	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs369612960	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	31	508	0	ENST00000360948.2:c.1227G>T	p.Leu409Phe	p.L409F	ENST00000360948	NM_001012338.2	409	ttG/ttT	10/19	NA	2	FACETS	0.504	0.408	0.612			1	INDETERMINATE	1	FALSE	NA	0.386999799979098	2		508	318	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678514	88678514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	39	572	1	ENST00000360948.2:c.1022C>T	p.Pro341Leu	p.P341L	ENST00000360948	NM_001012338.2	341	cCt/cTt	9/19	NA	2	FACETS	0.833	0.695	0.984			1	INDETERMINATE	1	FALSE	NA	0.386999799979098	2		573	242	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293268	91293268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	47	253	0	ENST00000355112.3:c.770C>T	p.Ser257Phe	p.S257F	ENST00000355112	NM_000057.2	257	tCt/tTt	3/22	0.386999799979098	5	FACETS	1	0.954	1	0.452	0.384	0.526	CLONAL	1	FALSE	2	0.386999799979098	5		253	283	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500430	99500430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1412431600	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	62	715	1	ENST00000268035.6:c.3863C>T	p.Pro1288Leu	p.P1288L	ENST00000268035	NM_000875.3	1288	cCc/cTc	21/21	0.386999799979098	5	FACETS	0.767	0.667	0.875	0.512	0.445	0.583	SUBCLONAL	2	FALSE	2	0.386999799979098	5		716	330	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	338162	338162	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	70	920	0	ENST00000262320.3:c.2549T>G	p.Phe850Cys	p.F850C	ENST00000262320	NM_003502.3	850	tTt/tGt	11/11	0.386999799979098	2	FACETS	1	0.901	1	0.515	0.452	0.583	CLONAL	1	FALSE	0	0.386999799979098	2		920	351	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130269	2130269	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	68	901	0	ENST00000219476.3:c.3501G>C	p.Glu1167Asp	p.E1167D	ENST00000219476	NM_000548.3	1167	gaG/gaC	30/42	0.386999799979098	2	FACETS	1	0.93	1	0.546	0.478	0.617	CLONAL	1	FALSE	0	0.386999799979098	2		901	322	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2224003	2224003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	74	854	1	ENST00000326181.6:c.1217C>T	p.Ser406Phe	p.S406F	ENST00000326181	NM_032271.2	406	tCc/tTc	13/21	0.386999799979098	2	FACETS	1	0.921	1	0.53	0.467	0.597	CLONAL	1	FALSE	0	0.386999799979098	2		855	361	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857343	9857343	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	111	662	0	ENST00000330684.3:c.4058G>A	p.Arg1353Lys	p.R1353K	ENST00000330684	NM_001134407.1	1353	aGg/aAg	13/13	0.386999799979098	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	FALSE	0	0.386999799979098	2		662	250	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032230	10032230	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555455727	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	54	547	0	ENST00000330684.3:c.593G>A	p.Trp198Ter	p.W198*	ENST00000330684	NM_001134407.1	198	tGg/tAg	3/13	0.386999799979098	2	FACETS	1	0.93	1	0.565	0.487	0.648	CLONAL	1	FALSE	0	0.386999799979098	2		547	247	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645174	67645174	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs933470800	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	85	695	0	ENST00000264010.4:c.439C>T	p.Leu147Phe	p.L147F	ENST00000264010	NM_006565.3	147	Ctt/Ttt	3/12	0.386999799979098	2	FACETS	1	0.937	1	0.54	0.48	0.603	CLONAL	1	FALSE	0	0.386999799979098	2		695	407	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993404	72993404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	58	1244	1	ENST00000268489.5:c.641C>T	p.Ala214Val	p.A214V	ENST00000268489	NM_006885.3	214	gCt/gTt	2/10	0.386999799979098	1	FACETS	0.653	0.564	0.75	0.653	0.564	0.75	SUBCLONAL	1	FALSE	0	0.386999799979098	1		1245	370	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993791	72993791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371690491	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	51	891	0	ENST00000268489.5:c.254C>T	p.Ser85Leu	p.S85L	ENST00000268489	NM_006885.3	85	tCg/tTg	2/10	0.386999799979098	1	FACETS	0.686	0.586	0.794	0.686	0.586	0.794	SUBCLONAL	1	FALSE	0	0.386999799979098	1		891	310	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819743	81819744	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	75	966	1	ENST00000359376.3:c.149_150delinsAA	p.Arg50Gln	p.R50Q	ENST00000359376	NM_002661.3	50	cGG/cAA	2/33	0.386999799979098	1	FACETS	0.776	0.683	0.874	0.776	0.683	0.874	SUBCLONAL	1	FALSE	0	0.386999799979098	1		967	403	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217469	7217470	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	112	1021	3	ENST00000380728.2:c.326_327delinsTT	p.Thr109Ile	p.T109I	ENST00000380728		109	aCC/aTT	5/11	0.322716590101276	4	FACETS	0.965	0.867	1	0.322	0.289	0.356	CLONAL	1	FALSE	1	0.386999799979098	4		1024	832	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979559	7979559	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	80	817	0	ENST00000319144.4:c.1466G>A	p.Gly489Glu	p.G489E	ENST00000319144	NM_001139.2	489	gGg/gAg	11/15	0.322716590101276	4	FACETS	1	0.975	1	0.474	0.42	0.532	CLONAL	1	FALSE	1	0.386999799979098	4		817	403	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044470	12044470	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	56	484	0	ENST00000353533.5:c.1093C>T	p.Pro365Ser	p.P365S	ENST00000353533	NM_003010.3	365	Ccc/Tcc	11/11	0.322716590101276	4	FACETS	1	0.967	1	0.485	0.419	0.556	CLONAL	1	FALSE	1	0.386999799979098	4		484	276	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556360	29556361	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AT	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	95	628	1	ENST00000356175.3:c.2727_2728delinsAT	p.Gly910Ter	p.G910*	ENST00000356175	NM_000267.3	909	gtGGga/gtATga	21/57	0.386999799979098	5	FACETS	1	0.979	1	0.482	0.43	0.536	CLONAL	1	FALSE	2	0.386999799979098	5		629	537	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654597	29654597	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	222	690	0	ENST00000356175.3:c.5286T>A	p.Tyr1762Ter	p.Y1762*	ENST00000356175	NM_000267.3	1762	taT/taA	37/57	0.386999799979098	5	FACETS	0.988	0.925	1	0.988	0.925	1	CLONAL	3	FALSE	2	0.386999799979098	5		690	612	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325825	30325825	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	54	424	0	ENST00000322652.5:c.2023G>T	p.Asp675Tyr	p.D675Y	ENST00000322652	NM_015355.2	675	Gat/Tat	16/16	0.386999799979098	5	FACETS	1	0.944	1	0.405	0.347	0.468	CLONAL	1	FALSE	2	0.386999799979098	5		424	363	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884282	37884283	+	missense_variant	Missense_Mutation	DNP	GG	GG	CA	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	41	464	0	ENST00000269571.5:c.3753_3754delinsCA	p.Asp1252Asn	p.D1252N	ENST00000269571		1251	ctGGac/ctCAac	27/27	0.386999799979098	5	FACETS	1	0.891	1	0.362	0.303	0.428	CLONAL	1	FALSE	2	0.386999799979098	5		464	308	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41247908	41247908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881466	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	221	858	1	ENST00000357654.3:c.625C>T	p.Pro209Ser	p.P209S	ENST00000357654	NM_007294.3	209	Cct/Tct	9/23	0.386999799979098	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	FALSE	1	0.386999799979098	3		859	617	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58701074	58701074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	107	1310	1	ENST00000305921.3:c.665C>T	p.Pro222Leu	p.P222L	ENST00000305921	NM_003620.3	222	cCc/cTc	2/6	0.386999799979098	3	FACETS	0.811	0.727	0.9	0.405	0.363	0.45	CLONAL	1	FALSE	1	0.386999799979098	3		1311	814	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740564	58740564	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	291	1125	0	ENST00000305921.3:c.1469T>C	p.Leu490Ser	p.L490S	ENST00000305921	NM_003620.3	490	tTg/tCg	6/6	0.386999799979098	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	FALSE	1	0.386999799979098	3		1125	724	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554539	63554539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	103	624	0	ENST00000307078.5:c.200G>A	p.Gly67Glu	p.G67E	ENST00000307078	NM_004655.3	67	gGg/gAg	2/11	0.386999799979098	3	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	FALSE	1	0.386999799979098	3		624	301	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120295	70120295	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	75	1233	0	ENST00000245479.2:c.1297C>T	p.Pro433Ser	p.P433S	ENST00000245479	NM_000346.3	433	Ccg/Tcg	3/3	0.386999799979098	3	FACETS	1	0.929	1	0.539	0.474	0.608	CLONAL	1	FALSE	1	0.386999799979098	3		1233	429	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774680	73774680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	20	119	1	ENST00000254810.4:c.407C>T	p.Ala136Val	p.A136V	ENST00000254810	NM_005324.3	136	gCt/gTt	4/4	0.386999799979098	3	FACETS	0.786	0.606	0.993	0.393	0.303	0.497	CLONAL	1	FALSE	1	0.386999799979098	3		120	157	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796978	78796979	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	69	583	0	ENST00000306801.3:c.1091_1092delinsTT	p.Pro364Leu	p.P364L	ENST00000306801	NM_020761.2	364	cCC/cTT	9/34	0.386999799979098	3	FACETS	1	0.937	1	0.557	0.488	0.631	CLONAL	1	FALSE	1	0.386999799979098	3		583	382	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226980	2226980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	30	270	0	ENST00000398665.3:c.4460C>T	p.Ser1487Phe	p.S1487F	ENST00000398665	NM_032482.2	1487	tCc/tTc	27/28	0.386999799979098	3	FACETS	0.935	0.759	1	0.467	0.379	0.565	CLONAL	1	FALSE	1	0.386999799979098	3		270	198	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265588	10265588	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	117	727	0	ENST00000340748.4:c.1589A>C	p.Lys530Thr	p.K530T	ENST00000340748		530	aAg/aCg	19/40	0.386999799979098	5	FACETS	0.965	0.875	1	0.644	0.583	0.707	CLONAL	2	FALSE	2	0.386999799979098	5		727	495	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097209	11097209	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1291486335	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	64	330	0	ENST00000358026.2:c.700C>T	p.Pro234Ser	p.P234S	ENST00000358026	NM_001128849.1	234	Cct/Tct	4/36	0.386999799979098	5	FACETS	1	0.945	1	0.761	0.668	0.859	CLONAL	2	FALSE	2	0.386999799979098	5		330	229	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289678	15289678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1488228506	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	75	906	3	ENST00000263388.2:c.3793C>T	p.Pro1265Ser	p.P1265S	ENST00000263388	NM_000435.2	1265	Ccg/Tcg	23/33	0.255340283410136	3	FACETS	1	0.919	1	0.529	0.465	0.597	CLONAL	1	FALSE	1	0.386999799979098	3		909	437	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298692	15298692	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	111	630	0	ENST00000263388.2:c.1606G>A	p.Gly536Ser	p.G536S	ENST00000263388	NM_000435.2	536	Ggc/Agc	10/33	0.255340283410136	3	FACETS	0.978	0.889	1	0.978	0.889	1	CLONAL	2	FALSE	1	0.386999799979098	3		630	350	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349733	15349733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754054879	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	25	216	0	ENST00000263377.2:c.3841C>T	p.Arg1281Trp	p.R1281W	ENST00000263377	NM_058243.2	1281	Cgg/Tgg	19/20	0.386999799979098	4	FACETS	1	0.933	1	0.74	0.593	0.904	CLONAL	1	FALSE	2	0.386999799979098	4		216	121	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950376	17950376	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs267605358	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	40	735	0	ENST00000458235.1:c.1351C>T	p.Arg451Ter	p.R451*	ENST00000458235	NM_000215.3	451	Cga/Tga	10/24	0.386999799979098	4	FACETS	0.698	0.58	0.828	0.349	0.29	0.414	SUBCLONAL	1	FALSE	2	0.386999799979098	4		735	411	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860587	45860587	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1039239653	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	90	1090	1	ENST00000391945.4:c.1420C>T	p.His474Tyr	p.H474Y	ENST00000391945	NM_000400.3	474	Cac/Tac	15/23	0.386999799979098	5	FACETS	1	0.965	1			1	CLONAL	1	FALSE	NA	0.386999799979098	5		1091	604	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085834	16085834	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	21	555	0	ENST00000281043.3:c.1010C>T	p.Pro337Leu	p.P337L	ENST00000281043	NM_005378.4	337	cCc/cTc	3/3	0.339411806679264	4	FACETS	0.516	0.397	0.653	0.172	0.132	0.218	SUBCLONAL	1	FALSE	1	0.386999799979098	4		555	292	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085915	16085915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766312745	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	81	442	0	ENST00000281043.3:c.1091C>T	p.Pro364Leu	p.P364L	ENST00000281043	NM_005378.4	364	cCc/cTc	3/3	0.339411806679264	4	FACETS	1	0.908	1	1	0.908	1	CLONAL	3	FALSE	1	0.386999799979098	4		442	192	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086052	16086052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	134	615	0	ENST00000281043.3:c.1228G>A	p.Glu410Lys	p.E410K	ENST00000281043	NM_005378.4	410	Gag/Aag	3/3	0.339411806679264	4	FACETS	1	0.926	1	1	0.926	1	CLONAL	3	FALSE	1	0.386999799979098	4		615	319	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25458576	25458576	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	230	795	0	ENST00000264709.3:c.2597G>A	p.Arg866Lys	p.R866K	ENST00000264709	NM_175629.2	866	aGg/aAg	22/23	0.339411806679264	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	FALSE	1	0.386999799979098	4		795	504	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466842	25466842	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	115	578	0	ENST00000264709.3:c.1861A>G	p.Lys621Glu	p.K621E	ENST00000264709	NM_175629.2	621	Aag/Gag	16/23	0.339411806679264	4	FACETS	1	0.974	1	0.792	0.721	0.864	CLONAL	2	FALSE	1	0.386999799979098	4		578	347	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920609	96920609	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs377430566	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	52	638	1	ENST00000258439.3:c.371A>G	p.Lys124Arg	p.K124R	ENST00000258439	NM_001193304.2	124	aAg/aGg	3/4	0.363604232361516	3	FACETS	0.681	0.58	0.791	0.34	0.29	0.396	SUBCLONAL	1	FALSE	1	0.386999799979098	3		639	471	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920631	96920631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	56	688	0	ENST00000258439.3:c.349G>A	p.Gly117Arg	p.G117R	ENST00000258439	NM_001193304.2	117	Ggg/Agg	3/4	0.363604232361516	3	FACETS	0.706	0.606	0.816	0.353	0.303	0.408	SUBCLONAL	1	FALSE	1	0.386999799979098	3		688	489	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050239	128050239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1209294822	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	79	712	0	ENST00000285398.2:c.418C>T	p.Leu140Phe	p.L140F	ENST00000285398	NM_000122.1	140	Ctc/Ttc	3/15	0.363604232361516	3	FACETS	0.986	0.87	1	0.493	0.435	0.556	CLONAL	1	FALSE	1	0.386999799979098	3		712	494	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158594124	158594125	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	81	1019	2	ENST00000263640.3:c.1448_1449delinsTT	p.Ser483Phe	p.S483F	ENST00000263640	NM_001105.4	483	tCC/tTT	11/11	0.363604232361516	3	FACETS	0.766	0.675	0.864	0.383	0.337	0.432	SUBCLONAL	1	FALSE	1	0.386999799979098	3		1021	652	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096163	178096163	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	239	557	0	ENST00000397062.3:c.1168C>G	p.Gln390Glu	p.Q390E	ENST00000397062	NM_006164.4	390	Cag/Gag	5/5	0.386999799979098	7	FACETS	1	0.956	1			1	CLONAL	4	FALSE	NA	0.386999799979098	7		557	596	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098852	178098853	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	142	1004	1	ENST00000397062.3:c.192_193delinsAA	p.Glu65Lys	p.E65K	ENST00000397062	NM_006164.4	64	aaGGag/aaAAag	2/5	0.386999799979098	7	FACETS	1	0.985	1			1	CLONAL	1	FALSE	NA	0.386999799979098	7		1005	1012	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293194	212293194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	66	494	0	ENST00000342788.4:c.2658G>A	p.Trp886Ter	p.W886*	ENST00000342788	NM_005235.2	886	tgG/tgA	22/28	0.386999799979098	4	FACETS	1	0.951	1	0.398	0.347	0.453	CLONAL	1	FALSE	1	0.386999799979098	4		494	396	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543871	212543871	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1361402584	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	46	537	0	ENST00000342788.4:c.1528G>A	p.Asp510Asn	p.D510N	ENST00000342788	NM_005235.2	510	Gat/Aat	13/28	0.386999799979098	4	FACETS	0.669	0.563	0.785	0.223	0.187	0.262	SUBCLONAL	1	FALSE	1	0.386999799979098	4		537	493	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439749	220439750	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	101	1057	3	ENST00000243786.2:c.602_603delinsTT	p.Pro201Leu	p.P201L	ENST00000243786	NM_002191.3	201	cCC/cTT	2/2	0.386999799979098	4	FACETS	1	0.977	1	0.446	0.4	0.495	CLONAL	1	FALSE	1	0.386999799979098	4		1060	541	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661090	227661090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs78333894	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	74	686	0	ENST00000305123.5:c.2365C>T	p.Leu789Phe	p.L789F	ENST00000305123	NM_005544.2	789	Ctc/Ttc	1/2	0.386999799979098	4	FACETS	1	0.961	1	0.413	0.363	0.467	CLONAL	1	FALSE	1	0.386999799979098	4		686	428	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387101	31387101	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1226308460	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	88	583	0	ENST00000328111.2:c.1726C>T	p.Arg576Ter	p.R576*	ENST00000328111	NM_006892.3	576	Cga/Tga	16/23	0.386999799979098	5	FACETS	0.77	0.685	0.86	0.513	0.456	0.573	SUBCLONAL	2	FALSE	2	0.386999799979098	5		583	467	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713403	40713403	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	44	687	0	ENST00000373198.4:c.4112C>T	p.Ser1371Phe	p.S1371F	ENST00000373198	NM_133170.3	1371	tCt/tTt	30/32	0.170959168826022	3	FACETS	0.838	0.705	0.983			1	INDETERMINATE	1	FALSE	NA	0.386999799979098	3		687	324	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747117	40747117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	36	635	0	ENST00000373198.4:c.2965G>A	p.Asp989Asn	p.D989N	ENST00000373198	NM_133170.3	989	Gac/Aac	22/32	0.170959168826022	3	FACETS	0.755	0.623	0.902			1	INDETERMINATE	1	FALSE	NA	0.386999799979098	3		635	294	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076945	41076945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767453141	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	107	736	1	ENST00000373198.4:c.1475C>T	p.Ser492Phe	p.S492F	ENST00000373198	NM_133170.3	492	tCc/tTc	9/32	0.170959168826022	3	FACETS	0.866	0.784	0.952			1	INDETERMINATE	2	FALSE	NA	0.386999799979098	3		737	381	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306577	41306577	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	112	689	0	ENST00000373198.4:c.1082T>A	p.Leu361His	p.L361H	ENST00000373198	NM_133170.3	361	cTc/cAc	7/32	0.170959168826022	3	FACETS	0.899	0.816	0.986			1	INDETERMINATE	2	FALSE	NA	0.386999799979098	3		689	384	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420041	41420041	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	85	734	0	ENST00000373198.4:c.280A>G	p.Thr94Ala	p.T94A	ENST00000373198	NM_133170.3	94	Acc/Gcc	3/32	0.170959168826022	3	FACETS	0.755	0.673	0.842			1	INDETERMINATE	2	FALSE	NA	0.386999799979098	3		734	347	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54948503	54948503	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	105	737	0	ENST00000312783.6:c.815T>C	p.Ile272Thr	p.I272T	ENST00000312783	NM_198436.1	272	aTt/aCt	8/10	0.386999799979098	5	FACETS	1	0.982	1			1	CLONAL	1	FALSE	NA	0.386999799979098	5		737	588	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164712	36164712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	28	561	0	ENST00000300305.3:c.1163C>T	p.Ser388Leu	p.S388L	ENST00000300305		388	tCg/tTg	8/8	1	2	FACETS	0.476	0.381	0.584	0.476	0.381	0.584	SUBCLONAL	1	FALSE	1	0.386999799979098	2		561	304	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44520630	44520630	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	69	465	0	ENST00000291552.4:c.133-1G>A		p.X45_splice	ENST00000291552	NM_006758.2	45			1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	FALSE	1	0.386999799979098	2		465	336	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543879	41543879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	92	853	0	ENST00000263253.7:c.2170C>T	p.Pro724Ser	p.P724S	ENST00000263253	NM_001429.3	724	Cct/Tct	12/31	0.339411806679264	4	FACETS	1	0.968	1	0.412	0.367	0.46	CLONAL	1	FALSE	1	0.386999799979098	4		853	533	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162866	47162866	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1260151759	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	238	647	1	ENST00000409792.3:c.3260C>T	p.Ser1087Phe	p.S1087F	ENST00000409792	NM_014159.6	1087	tCt/tTt	3/21	0.386999799979098	6	FACETS	1	0.962	1	1	0.962	1	CLONAL	3	FALSE	3	0.386999799979098	6		648	703	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934002	49934002	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	99	990	0	ENST00000296474.3:c.2410C>T	p.His804Tyr	p.H804Y	ENST00000296474	NM_002447.2	804	Cat/Tat	9/20	0.244271767501814	4	FACETS	1	0.975	1			1	CLONAL	1	FALSE	NA	0.386999799979098	4		990	547	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439885	52439885	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	64	613	1	ENST00000460680.1:c.827C>T	p.Ser276Phe	p.S276F	ENST00000460680	NM_004656.3	276	tCt/tTt	10/17	0.386999799979098	8	FACETS	1	0.914	1			1	CLONAL	1	FALSE	NA	0.386999799979098	8		614	665	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623190	52623190	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	110	797	1	ENST00000394830.3:c.2861A>T	p.Lys954Ile	p.K954I	ENST00000394830	NM_018313.4	954	aAa/aTa	19/30	0.386999799979098	8	FACETS	1	0.979	1			1	CLONAL	1	FALSE	NA	0.386999799979098	8		798	891	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014292	70014292	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781298935	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	120	1155	0	ENST00000394351.3:c.1153C>T	p.Pro385Ser	p.P385S	ENST00000394351	NM_000248.3	385	Ccc/Tcc	9/9	0.386999799979098	8	FACETS	0.769	0.694	0.849			1	SUBCLONAL	2	FALSE	NA	0.386999799979098	8		1155	871	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027108	71027108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	77	487	0	ENST00000318789.4:c.1219C>T	p.Pro407Ser	p.P407S	ENST00000318789	NM_032682.5	407	Cca/Tca	15/21	0.386999799979098	8	FACETS	1	0.967	1			1	CLONAL	1	FALSE	NA	0.386999799979098	8		487	660	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799791	72799791	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	140	654	2	ENST00000325599.8:c.1378T>A	p.Ser460Thr	p.S460T	ENST00000325599	NM_018130.2	460	Tca/Aca	11/11	0.386999799979098	8	FACETS	0.85	0.777	0.927			1	CLONAL	3	FALSE	NA	0.386999799979098	8		656	613	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119562125	119562125	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	109	684	0	ENST00000316626.5:c.1211C>T	p.Pro404Leu	p.P404L	ENST00000316626		404	cCc/cTc	11/12	0.318420752994195	4	FACETS	0.904	0.818	0.995			1	CLONAL	2	FALSE	NA	0.386999799979098	4		684	432	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199993	128199993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	50	720	3	ENST00000341105.2:c.1312G>A	p.Ala438Thr	p.A438T	ENST00000341105	NM_032638.4	438	Gca/Aca	6/6	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.386999799979098	NA		723	246	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670831	134670831	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	27	255	0	ENST00000398015.3:c.742G>A	p.Val248Met	p.V248M	ENST00000398015	NM_004441.4	248	Gtg/Atg	3/16	NA	2	FACETS	0.99	0.798	1			1	INDETERMINATE	1	FALSE	NA	0.386999799979098	2		255	141	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453574	138453574	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	70	610	0	ENST00000289153.2:c.874A>G	p.Met292Val	p.M292V	ENST00000289153	NM_006219.2	292	Atg/Gtg	5/22	NA	2	FACETS	0.87	0.761	0.985			1	INDETERMINATE	1	FALSE	NA	0.386999799979098	2		610	416	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161268	185161268	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	118	887	0	ENST00000265026.3:c.695T>G	p.Ile232Ser	p.I232S	ENST00000265026	NM_004721.4	232	aTc/aGc	4/14	0.303388346340707	4	FACETS	0.831	0.753	0.912	0.831	0.753	0.912	CLONAL	2	FALSE	2	0.386999799979098	4		887	509	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504358	186504358	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	78	597	1	ENST00000323963.5:c.695C>T	p.Pro232Leu	p.P232L	ENST00000323963		232	cCa/cTa	7/11	0.303388346340707	4	FACETS	1	0.969	1	0.656	0.579	0.738	CLONAL	1	FALSE	2	0.386999799979098	4		598	426	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526145	189526145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	80	732	0	ENST00000264731.3:c.409G>A	p.Asp137Asn	p.D137N	ENST00000264731	NM_003722.4	137	Gac/Aac	4/14	0.303388346340707	4	FACETS	0.763	0.676	0.855	0.763	0.676	0.855	SUBCLONAL	2	FALSE	2	0.386999799979098	4		732	376	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582097	189582097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	97	679	0	ENST00000264731.3:c.656C>T	p.Pro219Leu	p.P219L	ENST00000264731	NM_003722.4	219	cCt/cTt	5/14	0.303388346340707	4	FACETS	1	0.979	1	0.701	0.627	0.779	CLONAL	1	FALSE	2	0.386999799979098	4		679	496	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984810	55984810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	84	793	1	ENST00000263923.4:c.319G>A	p.Glu107Lys	p.E107K	ENST00000263923	NM_002253.2	107	Gaa/Aaa	3/30	0.253254842509419	1	FACETS	0.826	0.733	0.924	0.826	0.733	0.924	CLONAL	1	FALSE	0	0.386999799979098	1		794	424	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524726	187524726	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	93	736	0	ENST00000441802.2:c.10954C>T	p.Pro3652Ser	p.P3652S	ENST00000441802	NM_005245.3	3652	Ccg/Tcg	19/27	NA	2	FACETS	1	0.978	1			1	INDETERMINATE	1	FALSE	NA	0.386999799979098	2		736	350	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628647	187628647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	168	719	0	ENST00000441802.2:c.2335C>T	p.Pro779Ser	p.P779S	ENST00000441802	NM_005245.3	779	Cct/Tct	2/27	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	2	FALSE	NA	0.386999799979098	2		719	362	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279438	1279438	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs878855300	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	26	642	0	ENST00000310581.5:c.2098C>T	p.Gln700Ter	p.Q700*	ENST00000310581	NM_198253.2	700	Cag/Tag	5/16	0.253254842509419	1	FACETS	0.486	0.387	0.598	0.486	0.387	0.598	SUBCLONAL	1	FALSE	0	0.386999799979098	1		642	223	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871292	35871292	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	197	425	0	ENST00000303115.3:c.514G>A	p.Glu172Lys	p.E172K	ENST00000303115	NM_002185.3	172	Gaa/Aaa	4/8	0.386999799979098	6	FACETS	0.941	0.88	1	0.941	0.88	1	CLONAL	4	FALSE	2	0.386999799979098	6		425	480	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38964945	38964945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	104	646	0	ENST00000357387.3:c.1349C>T	p.Pro450Leu	p.P450L	ENST00000357387	NM_152756.3	450	cCa/cTa	16/38	0.386999799979098	6	FACETS	0.789	0.708	0.875	0.395	0.354	0.438	SUBCLONAL	2	FALSE	2	0.386999799979098	6		646	604	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589017	67589017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	60	416	0	ENST00000274335.5:c.1108C>T	p.Leu370Phe	p.L370F	ENST00000274335		370	Ctt/Ttt	8/15	0.386999799979098	6	FACETS	1	0.95	1	0.306	0.264	0.351	CLONAL	1	FALSE	2	0.386999799979098	6		416	450	SUCCESS
APC	324	MSKCC	GRCh37	5	112177728	112177728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	55	395	0	ENST00000257430.4:c.6437C>T	p.Ser2146Leu	p.S2146L	ENST00000257430	NM_000038.5	2146	tCa/tTa	16/16	0.339411806679264	4	FACETS	1	0.949	1	0.412	0.354	0.474	CLONAL	1	FALSE	1	0.386999799979098	4		395	319	SUCCESS
APC	324	MSKCC	GRCh37	5	112178331	112178331	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	140	617	0	ENST00000257430.4:c.7040G>A	p.Arg2347Lys	p.R2347K	ENST00000257430	NM_000038.5	2347	aGg/aAg	16/16	0.339411806679264	4	FACETS	0.851	0.784	0.92	0.851	0.784	0.92	CLONAL	3	FALSE	1	0.386999799979098	4		617	393	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514354	149514354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs116642123	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	96	988	0	ENST00000261799.4:c.590G>A	p.Arg197Lys	p.R197K	ENST00000261799	NM_002609.3	197	aGg/aAg	4/23	0.339411806679264	4	FACETS	1	0.978	1	0.462	0.413	0.514	CLONAL	1	FALSE	1	0.386999799979098	4		988	496	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520140	176520141	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	47	653	1	ENST00000292408.4:c.1059_1060delinsAA	p.Glu354Lys	p.E354K	ENST00000292408	NM_213647.1	353	gaGGag/gaAAag	9/18	0.339411806679264	4	FACETS	1	0.955	1	0.451	0.384	0.524	CLONAL	1	FALSE	1	0.386999799979098	4		654	249	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524603	176524603	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758782236	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	75	882	2	ENST00000292408.4:c.2335G>A	p.Asp779Asn	p.D779N	ENST00000292408	NM_213647.1	779	Gat/Aat	18/18	0.339411806679264	4	FACETS	0.786	0.694	0.884	0.524	0.462	0.589	SUBCLONAL	2	FALSE	1	0.386999799979098	4		884	342	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638999	176638999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753389957	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	71	573	0	ENST00000439151.2:c.3599G>A	p.Arg1200Gln	p.R1200Q	ENST00000439151	NM_022455.4	1200	cGg/cAg	5/23	0.339411806679264	4	FACETS	1	0.949	1	0.387	0.339	0.439	CLONAL	1	FALSE	1	0.386999799979098	4		573	438	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055993	180055994	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	21	814	0	ENST00000261937.6:c.991_992delinsTT	p.Pro331Phe	p.P331F	ENST00000261937	NM_182925.4	331	CCc/TTc	8/30	0.386999799979098	1	FACETS	0.354	0.273	0.448	0.354	0.273	0.448	SUBCLONAL	1	FALSE	0	0.386999799979098	1		814	247	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056000	180056000	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	21	766	0	ENST00000261937.6:c.986-1G>A		p.X329_splice	ENST00000261937	NM_182925.4	329			0.386999799979098	1	FACETS	0.366	0.282	0.463	0.366	0.282	0.463	SUBCLONAL	1	FALSE	0	0.386999799979098	1		766	239	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057717	180057717	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200071734	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	46	857	0	ENST00000261937.6:c.238G>A	p.Val80Met	p.V80M	ENST00000261937	NM_182925.4	80	Gtg/Atg	3/30	0.386999799979098	1	FACETS	0.792	0.673	0.921	0.792	0.673	0.921	CLONAL	1	FALSE	0	0.386999799979098	1		857	242	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673119	30673119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	115	797	0	ENST00000376406.3:c.3841C>T	p.Pro1281Ser	p.P1281S	ENST00000376406	NM_014641.2	1281	Cct/Tct	10/15	0.386999799979098	7	FACETS	0.935	0.845	1	0.468	0.422	0.516	CLONAL	2	FALSE	3	0.386999799979098	7		797	625	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675823	30675823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	318	1172	1	ENST00000376406.3:c.2533G>A	p.Asp845Asn	p.D845N	ENST00000376406	NM_014641.2	845	Gat/Aat	8/15	0.386999799979098	7	FACETS	1	0.978	1	0.797	0.754	0.842	CLONAL	3	FALSE	3	0.386999799979098	7		1173	1014	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165174	32165174	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757846509	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	94	544	1	ENST00000375023.3:c.4954C>T	p.Arg1652Cys	p.R1652C	ENST00000375023	NM_004557.3	1652	Cgc/Tgc	27/30	0.386999799979098	7	FACETS	0.926	0.827	1	0.463	0.413	0.516	CLONAL	2	FALSE	3	0.386999799979098	7		545	516	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170325	32170325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	56	509	0	ENST00000375023.3:c.3283C>T	p.His1095Tyr	p.H1095Y	ENST00000375023	NM_004557.3	1095	Cac/Tac	21/30	0.386999799979098	5	FACETS	1	0.895	1	0.351	0.301	0.405	CLONAL	1	FALSE	2	0.386999799979098	5		509	435	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188925	32188925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	87	850	0	ENST00000375023.3:c.629C>T	p.Ser210Phe	p.S210F	ENST00000375023	NM_004557.3	210	tCc/tTc	4/30	0.386999799979098	5	FACETS	0.815	0.725	0.91	0.543	0.483	0.607	CLONAL	2	FALSE	2	0.386999799979098	5		850	436	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289250	33289250	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	145	548	1	ENST00000374542.5:c.302C>T	p.Ala101Val	p.A101V	ENST00000374542	NM_001141970.1	101	gCc/gTc	3/8	0.386999799979098	5	FACETS	1	0.938	1	0.685	0.628	0.745	CLONAL	2	FALSE	2	0.386999799979098	5		549	576	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969197	93969197	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	84	906	0	ENST00000369303.4:c.1799T>G	p.Phe600Cys	p.F600C	ENST00000369303	NM_004440.3	600	tTt/tGt	10/17	0.253254842509419	1	FACETS	0.842	0.747	0.941	0.842	0.747	0.941	CLONAL	1	FALSE	0	0.386999799979098	1		906	416	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662625	117662625	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	106	739	0	ENST00000368508.3:c.4840C>T	p.Pro1614Ser	p.P1614S	ENST00000368508	NM_002944.2	1614	Cca/Tca	29/43	0.253254842509419	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	0	0.386999799979098	1		739	406	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681504	117681504	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1415195324	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	181	573	0	ENST00000368508.3:c.3445+1G>A		p.X1149_splice	ENST00000368508	NM_002944.2	1149			0.253254842509419	1	FACETS	1	0.937	1	1	0.994	1	CLONAL	2	FALSE	0	0.386999799979098	1		573	377	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686283	117686283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	85	611	0	ENST00000368508.3:c.3058C>T	p.Pro1020Ser	p.P1020S	ENST00000368508	NM_002944.2	1020	Cct/Tct	20/43	0.253254842509419	1	FACETS	0.968	0.862	1	0.968	0.862	1	CLONAL	1	FALSE	0	0.386999799979098	1		611	366	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724311	117724311	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1451448120	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	160	640	0	ENST00000368508.3:c.568C>T	p.Pro190Ser	p.P190S	ENST00000368508	NM_002944.2	190	Cct/Tct	6/43	0.253254842509419	1	FACETS	1	0.977	1	1	0.993	1	CLONAL	2	FALSE	0	0.386999799979098	1		640	304	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004247	150004247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	140	817	0	ENST00000253339.5:c.1978C>T	p.Arg660Cys	p.R660C	ENST00000253339		660	Cgt/Tgt	3/7	0.386999799979098	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	0	0.386999799979098	1		817	438	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265416	152265416	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	70	613	0	ENST00000206249.3:c.869A>T	p.Asn290Ile	p.N290I	ENST00000206249	NM_000125.3	290	aAc/aTc	4/8	0.386999799979098	1	FACETS	0.999	0.88	1	0.999	0.88	1	CLONAL	1	FALSE	0	0.386999799979098	1		613	292	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951812	2951813	+	missense_variant	Missense_Mutation	DNP	GG	GG	TA	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	72	743	1	ENST00000396946.4:c.3137_3138delinsTA	p.Ala1046Val	p.A1046V	ENST00000396946	NM_032415.4	1046	gCC/gTA	23/25	0.253254842509419	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	0	0.386999799979098	1		744	256	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468158	50468158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	42	477	1	ENST00000331340.3:c.1393G>A	p.Glu465Lys	p.E465K	ENST00000331340	NM_006060.4	465	Gaa/Aaa	8/8	0.255340283410136	3	FACETS	1	0.844	1	0.502	0.422	0.59	CLONAL	1	FALSE	1	0.386999799979098	3		478	258	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55219037	55219037	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767829342	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	146	688	1	ENST00000275493.2:c.610G>A	p.Glu204Lys	p.E204K	ENST00000275493	NM_005228.3	204	Gag/Aag	5/28	0.255340283410136	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	FALSE	1	0.386999799979098	3		689	419	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508628	106508628	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	30	482	1	ENST00000359195.3:c.622C>T	p.Pro208Ser	p.P208S	ENST00000359195	NM_002649.2	208	Ccg/Tcg	2/11	0.386999799979098	5	FACETS	0.679	0.547	0.828	0.226	0.182	0.276	SUBCLONAL	1	FALSE	2	0.386999799979098	5		483	361	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398634	116398634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	120	680	0	ENST00000397752.3:c.2224C>T	p.Pro742Ser	p.P742S	ENST00000397752	NM_000245.2	742	Ccc/Tcc	9/21	0.386999799979098	5	FACETS	1	0.979	1	0.437	0.394	0.481	CLONAL	1	FALSE	2	0.386999799979098	5		680	748	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371992	55371992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	15	168	0	ENST00000297316.4:c.682G>A	p.Asp228Asn	p.D228N	ENST00000297316	NM_022454.3	228	Gac/Aac	2/2	0.303388346340707	4	FACETS	1	0.764	1	0.517	0.383	0.674	CLONAL	1	FALSE	2	0.386999799979098	4		168	104	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750750	128750750	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	44	662	0	ENST00000377970.2:c.287C>T	p.Ser96Phe	p.S96F	ENST00000377970	NM_002467.4	96	tCc/tTc	2/3	0.303388346340707	4	FACETS	0.855	0.719	1	0.427	0.359	0.502	CLONAL	1	FALSE	2	0.386999799979098	4		662	369	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341142	8341142	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	67	647	0	ENST00000356435.5:c.5074C>T	p.Arg1692Cys	p.R1692C	ENST00000356435		1692	Cgt/Tgt	30/35	0.386999799979098	2	FACETS	1	0.917	1	0.531	0.465	0.602	CLONAL	1	FALSE	0	0.386999799979098	2		647	326	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492888	8492888	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	76	803	0	ENST00000356435.5:c.2441C>T	p.Pro814Leu	p.P814L	ENST00000356435		814	cCc/cTc	16/35	0.386999799979098	2	FACETS	1	0.943	1	0.556	0.491	0.625	CLONAL	1	FALSE	0	0.386999799979098	2		803	353	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518175	8518175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1354824749	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	65	575	2	ENST00000356435.5:c.1216G>A	p.Glu406Lys	p.E406K	ENST00000356435		406	Gaa/Aaa	10/35	0.386999799979098	2	FACETS	1	0.934	1	0.554	0.484	0.629	CLONAL	1	FALSE	0	0.386999799979098	2		577	303	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528762	8528762	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	68	545	0	ENST00000356435.5:c.370G>A	p.Gly124Ser	p.G124S	ENST00000356435		124	Ggc/Agc	4/35	0.386999799979098	2	FACETS	1	0.909	1	0.523	0.458	0.592	CLONAL	1	FALSE	0	0.386999799979098	2		545	336	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971023	21971023	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	94	306	0	ENST00000304494.5:c.335G>C	p.Arg112Pro	p.R112P	ENST00000304494	NM_000077.4	112	cGt/cCt	2/3	0.386999799979098	2	FACETS	0.987	0.908	1	1	0.986	1	CLONAL	3	FALSE	0	0.386999799979098	2		306	164	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249759	110249759	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1221024853	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	72	485	0	ENST00000374672.4:c.916C>T	p.Pro306Ser	p.P306S	ENST00000374672	NM_004235.4	306	Ccc/Tcc	3/5	0.303388346340707	4	FACETS	1	0.975	1	0.744	0.654	0.839	CLONAL	1	FALSE	2	0.386999799979098	4		485	347	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781361	135781361	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1164741723	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	92	1259	1	ENST00000298552.3:c.1604C>T	p.Pro535Leu	p.P535L	ENST00000298552	NM_001162426.1	535	cCt/cTt	15/23	0.303388346340707	4	FACETS	1	0.968	1	0.619	0.551	0.69	CLONAL	1	FALSE	2	0.386999799979098	4		1260	533	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942835	44942835	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	47	535	0	ENST00000377967.4:c.3415C>T	p.Pro1139Ser	p.P1139S	ENST00000377967	NM_021140.2	1139	Cca/Tca	23/29	0.314451250701416	2	FACETS	0.527	0.445	0.617			1	SUBCLONAL	1	FALSE	NA	0.386999799979098	2		535	461	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652471	48652471	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	69	418	0	ENST00000376670.3:c.1142C>T	p.Pro381Leu	p.P381L	ENST00000376670	NM_002049.3	381	cCt/cTt	6/6	0.314451250701416	2	FACETS	0.782	0.691	0.877			1	SUBCLONAL	2	FALSE	NA	0.386999799979098	2		418	228	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652503	48652503	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	56	337	0	ENST00000376670.3:c.1174G>A	p.Gly392Ser	p.G392S	ENST00000376670	NM_002049.3	392	Ggc/Agc	6/6	0.314451250701416	2	FACETS	1	0.971	1			1	CLONAL	1	FALSE	NA	0.386999799979098	2		337	193	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556361	29556361	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	95	628	0	ENST00000356175.3:c.2728G>T	p.Gly910Ter	p.G910*	ENST00000356175	NM_000267.3	910	Gga/Tga	21/57	0.386999799979098	5	FACETS	1	0.979	1	0.482	0.43	0.536	CLONAL	1	FALSE	2	0.386999799979098	5		628	537	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158594125	158594125	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	80	1017	0	ENST00000263640.3:c.1448C>T	p.Ser483Phe	p.S483F	ENST00000263640	NM_001105.4	483	tCc/tTc	11/11	0.363604232361516	3	FACETS	0.757	0.666	0.854	0.378	0.333	0.427	SUBCLONAL	1	FALSE	1	0.386999799979098	3		1017	652	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345042	73345042	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	242	438	0	ENST00000377767.4:c.1755G>T	p.Lys585Asn	p.K585N	ENST00000377767	NM_014953.3	585	aaG/aaT	13/21	0.812561685163036	1	FACETS	0.958	0.914	1	0.958	0.914	1	CLONAL	1	TRUE	0	0.812924505583127	1		438	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0013835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	173	491	1	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.496069281739491	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.496069281739491	1		492	458	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88676911	88676911	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	60	328	0	ENST00000372037.3:c.696A>T	p.Lys232Asn	p.K232N	ENST00000372037	NM_004329.2	232	aaA/aaT	9/13	0.371999176356304	1	FACETS	0.419	0.362	0.481	0.419	0.362	0.481	SUBCLONAL	1	TRUE	0	0.496069281739491	1		328	434	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495627	56495627	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	120	461	0	ENST00000267101.3:c.3821del	p.Gly1274ValfsTer19	p.G1274Vfs*19	ENST00000267101	NM_001982.3	1273	Ggg/gg	28/28	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.496069281739491	2		461	473	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520237	9520237	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	139	486	0	ENST00000353224.5:c.2032G>C	p.Asp678His	p.D678H	ENST00000353224	NM_177990.2	678	Gac/Cac	10/10	1	2	FACETS	0.905	0.827	0.987	0.905	0.827	0.987	CLONAL	1	TRUE	1	0.496069281739491	2		486	619	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129716	47129716	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	79	499	0	ENST00000409792.3:c.5164C>G	p.Leu1722Val	p.L1722V	ENST00000409792	NM_014159.6	1722	Ctg/Gtg	10/21	0.496069281739491	1	FACETS	0.491	0.433	0.553	0.491	0.433	0.553	SUBCLONAL	1	TRUE	0	0.496069281739491	1		499	488	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663590	117663590	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs542373889	NA	P-0013835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	57	529	0	ENST00000368508.3:c.4642G>C	p.Glu1548Gln	p.E1548Q	ENST00000368508	NM_002944.2	1548	Gag/Cag	28/43	0.496069281739491	1	FACETS	0.318	0.272	0.367	0.318	0.272	0.367	SUBCLONAL	1	TRUE	0	0.496069281739491	1		529	544	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950648	38950648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776074870	NA	P-0013843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	9	1007	2	ENST00000357387.3:c.3302C>T	p.Ser1101Leu	p.S1101L	ENST00000357387	NM_152756.3	1101	tCg/tTg	31/38	1	2	FACETS	0.112	0.074	0.162	0.112	0.074	0.162	SUBCLONAL	1	TRUE	1	0.383434177945522	2		1009	418	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231379	46231379	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	47	518	0	ENST00000334344.6:c.1219C>G	p.Leu407Val	p.L407V	ENST00000334344	NM_152641.2	407	Ctc/Gtc	10/21	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.383434177945522	2		518	186	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223348	2223349	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	T	novel	NA	P-0013843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	132	1096	0	ENST00000398665.3:c.3459_3460delinsT	p.Pro1154LeufsTer19	p.P1154Lfs*19	ENST00000398665	NM_032482.2	1153	tcCCct/tcTct	25/28	1	2	FACETS	0.907	0.824	0.994	0.907	0.824	0.994	CLONAL	1	TRUE	1	0.383434177945522	2		1096	759	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0013859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	196	851	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.816	0.756	0.878	0.816	0.756	0.878	CLONAL	1	TRUE	1	0.564454237699146	2		851	851	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207162	1207162	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs137853076	NA	P-0013859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	189	659	1	ENST00000326873.7:c.250A>T	p.Lys84Ter	p.K84*	ENST00000326873	NM_000455.4	84	Aag/Tag	1/10	0.564454237699146	1	FACETS	0.971	0.906	1	0.971	0.906	1	CLONAL	1	TRUE	0	0.564454237699146	1		660	495	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874261	155874261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352822	NA	P-0013859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	38	540	0	ENST00000368323.3:c.270G>A	p.Met90Ile	p.M90I	ENST00000368323	NM_006912.5	90	atG/atA	5/6	0.459977111271463	3	FACETS	0.183	0.15	0.219	0.091	0.075	0.11	SUBCLONAL	1	TRUE	1	0.564454237699146	3		540	945	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602878	10602878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	199	619	0	ENST00000171111.5:c.700C>T	p.Arg234Trp	p.R234W	ENST00000171111	NM_203500.1	234	Cgg/Tgg	3/6	0.564454237699146	1	FACETS	0.987	0.922	1	0.987	0.922	1	CLONAL	1	TRUE	0	0.564454237699146	1		619	513	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12632388	12632388	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730881002	NA	P-0013859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	178	775	0	ENST00000251849.4:c.1279A>G	p.Ser427Gly	p.S427G	ENST00000251849	NM_002880.3	427	Agc/Ggc	12/17	1	2	FACETS	0.69	0.636	0.746	0.69	0.636	0.746	SUBCLONAL	1	TRUE	1	0.564454237699146	2		775	914	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770587	40770587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776338672	NA	P-0013864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	220	460	0	ENST00000373198.4:c.2795G>A	p.Arg932His	p.R932H	ENST00000373198	NM_133170.3	932	cGc/cAc	19/32	1	2	FACETS	0.983	0.921	1	0.983	0.921	1	CLONAL	1	TRUE	1	0.720424902811174	2		460	621	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190656579	190656589	+	frameshift_variant	Frame_Shift_Del	DEL	CTCAGATCATC	CTCAGATCATC	-	novel	NA	P-0013864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	218	490	0	ENST00000441310.2:c.44_54del	p.Ser15TyrfsTer12	p.S15Yfs*12	ENST00000441310	NM_000534.4	15	tCTCAGATCATC/t	2/13	0.720424902811174	3	FACETS	0.928	0.864	0.994	0.464	0.432	0.497	CLONAL	1	TRUE	1	0.720424902811174	3		490	887	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539071	187539071	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0013864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	278	681	0	ENST00000441802.2:c.8669C>G	p.Ser2890Ter	p.S2890*	ENST00000441802	NM_005245.3	2890	tCa/tGa	10/27	0.720424902811174	4	FACETS	0.916	0.858	0.975	0.458	0.429	0.488	CLONAL	1	TRUE	2	0.720424902811174	4		681	1450	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835593	68835593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781898	NA	P-0013869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	48	545	2	ENST00000261769.5:c.184G>A	p.Gly62Ser	p.G62S	ENST00000261769	NM_004360.3	62	Ggt/Agt	3/16	1	2	FACETS	0.532	0.448	0.625	0.532	0.448	0.625	SUBCLONAL	1	TRUE	1	0.205010530024632	2		547	880	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156731	20156731	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	177	295	0	ENST00000379607.5:c.26G>T	p.Gly9Val	p.G9V	ENST00000379607	NM_001412.3	9	gGt/gTt	2/7	0.0692705837326977	2	FACETS	1	0.986	1			1	INDETERMINATE	6	FALSE	NA	0.260084998682496	2		295	213	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0013890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	186	629	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	0.102515262786906	4	FACETS	0.995	0.929	1	1	0.994	1	INDETERMINATE	4	FALSE	2	0.260084998682496	4		629	453	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	30	589	1				ENST00000310581	NM_198253.2	-/1132			0.168508042205108	2	FACETS	1	0.915	1	0.607	0.498	0.726	INDETERMINATE	1	TRUE	0	0.392220054101483	2		590	126	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0013910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	176	365	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	0.392220054101483	2		366	720	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6414400	6414400	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	65	217	0	ENST00000356142.4:c.34G>A	p.Gly12Arg	p.G12R	ENST00000356142	NM_018890.3	12	Gga/Aga	1/7	0.392220054101483	3	FACETS	0.962	0.838	1	0.481	0.419	0.548	CLONAL	1	TRUE	1	0.392220054101483	3		217	412	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143018	7143018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753688285	NA	P-0013910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	99	503	0	ENST00000302850.5:c.2351C>T	p.Ser784Phe	p.S784F	ENST00000302850	NM_000208.2	784	tCc/tTc	12/22	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.392220054101483	2		503	493	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549725	187549725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199516712	NA	P-0013910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	129	566	0	ENST00000441802.2:c.4516C>T	p.Arg1506Cys	p.R1506C	ENST00000441802	NM_005245.3	1506	Cgt/Tgt	8/27	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.392220054101483	2		566	530	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230641	46230642	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0013910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	187	783	2	ENST00000334344.6:c.890_891delinsTT	p.Ser297Phe	p.S297F	ENST00000334344	NM_152641.2	297	tCC/tTT	8/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.392220054101483	2		785	783	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937348	32937348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80359035	NA	P-0013910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	54	452	0	ENST00000380152.3:c.8009C>T	p.Ser2670Leu	p.S2670L	ENST00000380152		2670	tCg/tTg	18/27	1	2	FACETS	0.81	0.695	0.934	0.81	0.695	0.934	CLONAL	1	TRUE	1	0.392220054101483	2		452	340	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031891	10031891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	101	705	1	ENST00000330684.3:c.932C>T	p.Ser311Phe	p.S311F	ENST00000330684	NM_001134407.1	311	tCc/tTc	3/13	1	2	FACETS	0.81	0.725	0.9	0.81	0.725	0.9	CLONAL	1	TRUE	1	0.392220054101483	2		706	636	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863556	68863557	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0013910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	101	633	2	ENST00000261769.5:c.2296-1_2296delinsAA		p.X766_splice	ENST00000261769	NM_004360.3	766		15/16	1	2	FACETS	0.69	0.617	0.768	0.69	0.617	0.768	SUBCLONAL	1	TRUE	1	0.392220054101483	2		635	746	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667840	37667840	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	221	796	1	ENST00000447079.4:c.2725G>A	p.Gly909Arg	p.G909R	ENST00000447079	NM_015083.1	909	Gga/Aga	8/14	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.392220054101483	2		797	1067	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740898	58740901	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs745470366	NA	P-0013910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	161	910	0	ENST00000305921.3:c.1806_1809del	p.Cys603PhefsTer21	p.C603Ffs*21	ENST00000305921	NM_003620.3	601	acTGTT/ac	6/6	1	2	FACETS	0.847	0.777	0.921	0.847	0.777	0.921	CLONAL	1	TRUE	1	0.392220054101483	2		910	969	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463170	25463170	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs903011938	NA	P-0013910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	188	628	0	ENST00000264709.3:c.2322+1G>A		p.X774_splice	ENST00000264709	NM_175629.2	774			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.392220054101483	2		628	828	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464507	25464507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	220	718	0	ENST00000264709.3:c.2006C>T	p.Ser669Phe	p.S669F	ENST00000264709	NM_175629.2	669	tCc/tTc	17/23	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.392220054101483	2		718	836	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483981	212483981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	108	635	0	ENST00000342788.4:c.2222G>A	p.Gly741Glu	p.G741E	ENST00000342788	NM_005235.2	741	gGa/gAa	19/28	1	2	FACETS	0.946	0.852	1	0.946	0.852	1	CLONAL	1	TRUE	1	0.392220054101483	2		635	582	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757438	40757438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	178	723	1	ENST00000373198.4:c.2860G>A	p.Asp954Asn	p.D954N	ENST00000373198	NM_133170.3	954	Gat/Aat	20/32	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.392220054101483	2		724	836	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526060	189526060	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0013910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	97	586	0	ENST00000264731.3:c.325-1G>A		p.X109_splice	ENST00000264731	NM_003722.4	109			0.27092321230548	3	FACETS	0.869	0.775	0.968	0.434	0.387	0.484	CLONAL	1	TRUE	1	0.392220054101483	3		586	681	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141096	55141096	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	100	556	1	ENST00000257290.5:c.1742C>T	p.Pro581Leu	p.P581L	ENST00000257290	NM_006206.4	581	cCt/cTt	12/23	1	2	FACETS	0.953	0.854	1	0.953	0.854	1	CLONAL	1	TRUE	1	0.392220054101483	2		557	535	SUCCESS
APC	324	MSKCC	GRCh37	5	112175795	112175796	+	missense_variant	Missense_Mutation	DNP	TG	TG	CT	novel	NA	P-0013910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	32	389	0	ENST00000257430.4:c.4504_4505delinsCT	p.Cys1502Leu	p.C1502L	ENST00000257430	NM_000038.5	1502	TGt/CTt	16/16	0.392220054101483	1	FACETS	0.41	0.333	0.496	0.41	0.333	0.496	SUBCLONAL	1	TRUE	0	0.392220054101483	1		389	320	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956637	93956637	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	73	945	2	ENST00000369303.4:c.2599C>A	p.Gln867Lys	p.Q867K	ENST00000369303	NM_004440.3	867	Cag/Aag	15/17	0.392220054101483	1	FACETS	0.324	0.282	0.369	0.324	0.282	0.369	SUBCLONAL	1	TRUE	0	0.392220054101483	1		947	925	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975481	13975481	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	203	443	1	ENST00000405192.2:c.406A>G	p.Asn136Asp	p.N136D	ENST00000405192	NM_001163147.1	136	Aac/Gac	7/12	0.392220054101483	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.392220054101483	3		444	554	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467967	50467967	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	39	547	0	ENST00000331340.3:c.1202A>G	p.Glu401Gly	p.E401G	ENST00000331340	NM_006060.4	401	gAg/gGg	8/8	0.392220054101483	3	FACETS	0.369	0.305	0.441	0.185	0.152	0.221	SUBCLONAL	1	TRUE	1	0.392220054101483	3		547	644	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355233	81355233	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	290	654	0	ENST00000222390.5:c.1141C>T	p.Pro381Ser	p.P381S	ENST00000222390	NM_000601.4	381	Cca/Tca	9/18	0.392220054101483	3	FACETS	0.962	0.907	1	0.962	0.907	1	CLONAL	2	TRUE	1	0.392220054101483	3		654	919	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271178	38271178	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	33	398	2	ENST00000425967.3:c.2530C>T	p.Gln844Ter	p.Q844*	ENST00000425967	NM_001174067.1	844	Cag/Tag	19/19	0.392220054101483	1	FACETS	0.48	0.392	0.578	0.48	0.392	0.578	SUBCLONAL	1	TRUE	0	0.392220054101483	1		400	282	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0013924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	129	546	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.791	0.717	0.87	0.791	0.717	0.87	SUBCLONAL	1	TRUE	1	0.337879535229001	2		546	965	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827892	40827892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs573377632	NA	P-0013924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	170	833	1	ENST00000373198.4:c.2536G>A	p.Val846Ile	p.V846I	ENST00000373198	NM_133170.3	846	Gtc/Atc	17/32	1	2	FACETS	0.983	0.903	1	0.983	0.903	1	CLONAL	1	TRUE	1	0.337879535229001	2		834	1024	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884881	134884881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1174327737	NA	P-0013924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	138	780	1	ENST00000398015.3:c.1657G>A	p.Val553Ile	p.V553I	ENST00000398015	NM_004441.4	553	Gtt/Att	8/16	0.290754065194493	4	FACETS	0.858	0.779	0.942	0.286	0.259	0.314	CLONAL	1	TRUE	1	0.337879535229001	4		781	1273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577075	7577075	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	247	809	0	ENST00000269305.4:c.863del	p.Asn288IlefsTer57	p.N288Ifs*57	ENST00000269305	NM_001126112.2	288	aAt/at	8/11	NA	2	FACETS	0.928	0.867	0.991			1	INDETERMINATE	2	TRUE	NA	0.235735246657789	2		809	1129	SUCCESS
APC	324	MSKCC	GRCh37	5	112175096	112175097	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs786203760	NA	P-0013929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	98	399	0	ENST00000257430.4:c.3807_3808del	p.Ile1269MetfsTer6	p.I1269Mfs*6	ENST00000257430	NM_000038.5	1269	ATa/a	16/16	0.235735246657789	2	FACETS	1	0.98	1	0.732	0.655	0.814	CLONAL	1	TRUE	0	0.235735246657789	2		399	568	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672309	30672309	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1366	132	926	0	ENST00000376406.3:c.4651C>G	p.Pro1551Ala	p.P1551A	ENST00000376406	NM_014641.2	1551	Ccc/Gcc	10/15	0.185852286708517	4	FACETS	0.924	0.836	1	0.462	0.418	0.509	CLONAL	1	TRUE	2	0.235735246657789	4		926	1498	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508424	106508424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751449393	NA	P-0013929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	30	254	0	ENST00000359195.3:c.418C>T	p.Arg140Trp	p.R140W	ENST00000359195	NM_002649.2	140	Cgg/Tgg	2/11	0.193858844122946	5	FACETS	0.846	0.682	1	0.282	0.227	0.345	CLONAL	1	TRUE	2	0.235735246657789	5		254	407	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0013952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	56	509	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.176070708200177	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.176070708200177	1		509	488	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536939	120536939	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760171048	NA	P-0013952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	72	647	0	ENST00000229340.5:c.247G>A	p.Gly83Arg	p.G83R	ENST00000229340	NM_006861.6	83	Ggg/Agg	4/6	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.176070708200177	2		647	616	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165756	108165756	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886039592	NA	P-0013953-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	74	323	0	ENST00000278616.4:c.4879C>T	p.Gln1627Ter	p.Q1627*	ENST00000278616	NM_000051.3	1627	Cag/Tag	32/63	1	2	FACETS	0.961	0.84	1	0.961	0.84	1	CLONAL	1	TRUE	1	0.21246995177362	2		323	725	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0013970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	557	588	1	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	0.998	1	CLONAL	2	TRUE	1	0.428985677416907	2		589	1272	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0013970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	458	525	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.975	0.934	1	1	0.997	1	CLONAL	2	TRUE	1	0.428985677416907	2		526	1095	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0013970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	408	403	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.99	1	1	0.997	1	CLONAL	2	TRUE	1	0.428985677416907	2		403	853	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205224	46205231	+	frameshift_variant	Frame_Shift_Del	DEL	TTCATCAT	TTCATCAT	-	novel	NA	P-0013970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	76	563	0	ENST00000334344.6:c.310_317del	p.His104TrpfsTer4	p.H104Wfs*4	ENST00000334344	NM_152641.2	103	gTTCATCAT/g	4/21	1	2	FACETS	0.285	0.249	0.324	0.285	0.249	0.324	SUBCLONAL	1	TRUE	1	0.428985677416907	2		563	1243	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582033	189582033	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	46	578	0	ENST00000264731.3:c.592C>A	p.Leu198Met	p.L198M	ENST00000264731	NM_003722.4	198	Ctg/Atg	5/14	0.428985677416907	1	FACETS	0.206	0.173	0.244	0.206	0.173	0.244	SUBCLONAL	1	TRUE	0	0.428985677416907	1		578	816	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939582	76939582	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0013970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	679	374	0	ENST00000373344.5:c.1166T>A	p.Leu389Ter	p.L389*	ENST00000373344	NM_000489.3	389	tTa/tAa	9/35	1	1	FACETS	1	0.997	1	1	0.998	1	CLONAL	3	TRUE	0	0.428985677416907	1		374	763	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107136	27107137	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0013973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	66	375	0	ENST00000324856.7:c.6749_6750del	p.Glu2250ValfsTer27	p.E2250Vfs*27	ENST00000324856	NM_006015.4	2249	tcAGag/tcag	20/20	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.24	2		375	519	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847305	68847305	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	133	651	1	ENST00000261769.5:c.1227G>A	p.Trp409Ter	p.W409*	ENST00000261769	NM_004360.3	409	tgG/tgA	9/16	0.228176734918885	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.24	1		652	953	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984487	7984487	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	77	608	0	ENST00000319144.4:c.371A>C	p.Asp124Ala	p.D124A	ENST00000319144	NM_001139.2	124	gAc/gCc	3/15	1	2	FACETS	0.806	0.707	0.913	0.806	0.707	0.913	CLONAL	1	TRUE	1	0.24	2		608	796	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791393	42791393	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0013988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	96	766	0	ENST00000575354.2:c.452+1G>A		p.X151_splice	ENST00000575354	NM_015125.3	151			0.141709395394735	3	FACETS	0.73	0.651	0.814	0.243	0.217	0.272	INDETERMINATE	1	TRUE	0	0.465991688385024	3		766	696	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374244	138374244	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	185	844	0	ENST00000289153.2:c.3200A>T	p.Asp1067Val	p.D1067V	ENST00000289153	NM_006219.2	1067	gAc/gTc	22/22	0.453100573766802	3	FACETS	1	0.925	1	0.501	0.462	0.541	CLONAL	1	TRUE	1	0.465991688385024	3		844	977	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885919	111885919	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs760685296	NA	P-0013988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	221	1212	1	ENST00000341259.2:c.1541G>T	p.Gly514Val	p.G514V	ENST00000341259	NM_005475.2	514	gGt/gTt	8/8	0.311403879819802	4	FACETS	1	0.954	1	0.518	0.48	0.556	CLONAL	1	TRUE	2	0.465991688385024	4		1213	1343	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872138	37872138	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1294	189	922	0	ENST00000269571.5:c.1459del	p.Arg487GlyfsTer69	p.R487Gfs*69	ENST00000269571		487	Cgg/gg	12/27	0.465991688385024	6	FACETS	1	0.957	1	0.264	0.243	0.286	CLONAL	1	TRUE	2	0.465991688385024	6		922	1483	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383228	42383228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782110924	NA	P-0013988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	235	1187	4	ENST00000221972.3:c.248C>T	p.Pro83Leu	p.P83L	ENST00000221972	NM_021601.3	83	cCg/cTg	2/5	0.141709395394735	3	FACETS	1	0.954	1	0.344	0.32	0.368	INDETERMINATE	1	TRUE	0	0.465991688385024	3		1191	1206	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910432	50910432	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0013988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	171	1131	0	ENST00000440232.2:c.1686+1G>T		p.X562_splice	ENST00000440232	NM_002691.3	562			0.141709395394735	3	FACETS	0.975	0.897	1	0.325	0.299	0.353	INDETERMINATE	1	TRUE	0	0.465991688385024	3		1131	928	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0013996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	74	722	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		722	1080	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0013997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	189	518	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.44	2		518	736	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143044462	143044462	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	214	749	0	ENST00000262992.4:c.2000G>T	p.Gly667Val	p.G667V	ENST00000262992	NM_001101669.1	667	gGa/gTa	18/24	1	2	FACETS	0.949	0.882	1	0.949	0.882	1	CLONAL	1	TRUE	1	0.44	2		749	1025	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249028	55249028	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1275022697	NA	P-0013997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	157	594	0	ENST00000275493.2:c.2326C>T	p.Arg776Cys	p.R776C	ENST00000275493	NM_005228.3	776	Cgc/Tgc	20/28	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.44	2		594	687	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81399277	81399277	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	133	440	0	ENST00000222390.5:c.11C>A	p.Thr4Asn	p.T4N	ENST00000222390	NM_000601.4	4	aCc/aAc	1/18	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.44	2		440	539	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117861193	117861193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2037	324	894	0	ENST00000297338.2:c.1696G>A	p.Gly566Ser	p.G566S	ENST00000297338	NM_006265.2	566	Ggt/Agt	13/14	0.3	8	FACETS	1	0.993	1			1	CLONAL	1	TRUE	NA	0.44	8		894	2361	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410978	63410978	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	235	865	0	ENST00000330258.3:c.2189C>A	p.Pro730Gln	p.P730Q	ENST00000330258	NM_152424.3	730	cCa/cAa	2/2	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.44	2		865	1014	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0014003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	355	452	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.626298967108431	4	FACETS	0.953	0.906	1	0.953	0.906	1	CLONAL	2	TRUE	2	0.680529061687554	4		452	920	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0014003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	240	162	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.680529061687554	2	FACETS	0.996	0.952	1	0.996	0.952	1	CLONAL	2	TRUE	0	0.680529061687554	2		162	354	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056314	26056314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1355795147	NA	P-0014003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	164	487	0	ENST00000343677.2:c.343G>A	p.Glu115Lys	p.E115K	ENST00000343677	NM_005319.3	115	Gaa/Aaa	1/1	0.680529061687554	4	FACETS	0.995	0.915	1			1	CLONAL	1	TRUE	NA	0.680529061687554	4		487	814	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606672	43606672	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	483	802	2	ENST00000355710.3:c.1282del	p.Glu428LysfsTer25	p.E428Kfs*25	ENST00000355710	NM_020975.4	427	gtG/gt	7/20	0.680529061687554	2	FACETS	0.94	0.909	0.971	0.94	0.909	0.971	CLONAL	2	TRUE	0	0.680529061687554	2		804	755	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63545771	63545771	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0014003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	687	533	0	ENST00000307078.5:c.823A>T	p.Lys275Ter	p.K275*	ENST00000307078	NM_004655.3	275	Aag/Tag	3/11	0.680529061687554	4	FACETS	0.967	0.946	0.988	0.967	0.946	0.988	CLONAL	4	TRUE	0	0.680529061687554	4		533	877	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467199	25467199	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1313738991	NA	P-0014003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	146	520	0	ENST00000264709.3:c.1676G>T	p.Cys559Phe	p.C559F	ENST00000264709	NM_175629.2	559	tGc/tTc	15/23	0.586638139077797	3	FACETS	0.861	0.788	0.937	0.43	0.394	0.469	CLONAL	1	TRUE	1	0.680529061687554	3		520	668	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39708706	39708725	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAATTTTTTTTCTCTTTAGT	CAATTTTTTTTCTCTTTAGT	-	novel	NA	P-0014003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	117	322	0	ENST00000361337.2:c.336-18_337del		p.X112_splice	ENST00000361337	NM_003286.2	112		6/21	NA	2	FACETS	0.712	0.645	0.781			1	INDETERMINATE	1	TRUE	NA	0.680529061687554	2		322	483	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518056	187518056	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	489	743	0	ENST00000441802.2:c.12638A>T	p.Gln4213Leu	p.Q4213L	ENST00000441802	NM_005245.3	4213	cAg/cTg	25/27	0.626298967108431	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.680529061687554	4		743	1163	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053126	180053126	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	192	642	0	ENST00000261937.6:c.1243G>T	p.Glu415Ter	p.E415*	ENST00000261937	NM_182925.4	415	Gag/Tag	9/30	0.639492239912038	3	FACETS	1	0.947	1	0.512	0.475	0.551	CLONAL	1	TRUE	1	0.680529061687554	3		642	738	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0014004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	666	612	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.761081591070194	3	FACETS	1	0.998	1	1	0.998	1	CLONAL	3	TRUE	0	0.752163005728797	3		613	722	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945543	54945543	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs774552788	NA	P-0014004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	517	796	0	ENST00000312783.6:c.1027C>T	p.Arg343Trp	p.R343W	ENST00000312783	NM_198436.1	343	Cgg/Tgg	9/10	0.752163005728797	6	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.752163005728797	6		796	1570	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274923	142274923	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	438	572	0	ENST00000350721.4:c.2137C>T	p.Gln713Ter	p.Q713*	ENST00000350721	NM_001184.3	713	Caa/Taa	10/47	0.530771228865934	5	FACETS	0.935	0.897	0.972	0.935	0.897	0.972	CLONAL	3	TRUE	2	0.752163005728797	5		572	884	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0014008-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	54	448	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.14	2		448	766	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649005	86649005	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014008-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	44	536	1	ENST00000274376.6:c.1285G>T	p.Glu429Ter	p.E429*	ENST00000274376	NM_002890.2	429	Gaa/Taa	9/25	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.14	2		537	539	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586419	189586419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1560280393	NA	P-0014008-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	49	321	0	ENST00000264731.3:c.1043C>T	p.Pro348Leu	p.P348L	ENST00000264731	NM_003722.4	348	cCa/cTa	8/14	0.150171130700004	3	FACETS	0.918	0.779	1	0.918	0.779	1	CLONAL	2	TRUE	1	0.14	3		321	408	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs730881677	NA	P-0014008-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	13	210	0	ENST00000304494.5:c.151-1G>C		p.X51_splice	ENST00000304494	NM_000077.4	51			1	2	FACETS	0.787	0.561	1	0.787	0.561	1	CLONAL	1	TRUE	1	0.14	2		210	236	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934571	NA	P-0014013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	403	630	0	ENST00000269305.4:c.747G>C	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agC	7/11	0.354705718894972	3	FACETS	1	0.994	1	0.799	0.766	0.833	CLONAL	2	TRUE	0	0.534529299950127	3		630	797	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487647	56487647	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	223	696	0	ENST00000267101.3:c.1580G>C	p.Gly527Ala	p.G527A	ENST00000267101	NM_001982.3	527	gGt/gCt	13/28	0.534529299950127	4	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.534529299950127	4		696	1159	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626714	12626714	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	137	581	0	ENST00000251849.4:c.1575C>G	p.Phe525Leu	p.F525L	ENST00000251849	NM_002880.3	525	ttC/ttG	15/17	0.443915272429669	3	FACETS	1	0.953	1	0.356	0.324	0.388	CLONAL	1	TRUE	0	0.534529299950127	3		581	609	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056227	26056227	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775258009	NA	P-0014013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	56	679	1	ENST00000343677.2:c.430G>A	p.Gly144Ser	p.G144S	ENST00000343677	NM_005319.3	144	Ggc/Agc	1/1	0.386865087773052	5	FACETS	0.372	0.318	0.433			1	SUBCLONAL	1	TRUE	NA	0.534529299950127	5		680	1014	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978330	2978330	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	74	634	0	ENST00000396946.4:c.1000G>C	p.Glu334Gln	p.E334Q	ENST00000396946	NM_032415.4	334	Gag/Cag	7/25	0.452208339271398	3	FACETS	0.588	0.515	0.666	0.294	0.257	0.333	SUBCLONAL	1	TRUE	1	0.534529299950127	3		634	597	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027750	152027750	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	270	931	0	ENST00000262189.6:c.325C>T	p.Gln109Ter	p.Q109*	ENST00000262189	NM_170606.2	109	Cag/Tag	3/59	0.488301510887332	3	FACETS	0.955	0.895	1	0.478	0.447	0.509	CLONAL	1	TRUE	1	0.534529299950127	3		931	1340	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224815	123224818	+	splice_donor_variant,intron_variant	Splice_Site	DEL	GTAA	GTAA	-	novel	NA	P-0014013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	121	921	0	ENST00000218089.9:c.3578+3_3578+6del		p.X1193_splice	ENST00000218089	NM_001042749.1	1193			0.206612599692802	3	FACETS	0.532	0.479	0.587	0.177	0.159	0.196	INDETERMINATE	1	TRUE	0	0.534529299950127	3		921	1079	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	37	589	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.596	0.491	0.713	0.596	0.491	0.713	SUBCLONAL	1	TRUE	1	0.292218481939252	2		590	425	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413072	139413072	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	115	666	0	ENST00000277541.6:c.1070T>C	p.Phe357Ser	p.F357S	ENST00000277541	NM_017617.3	357	tTc/tCc	6/34	1	2	FACETS	0.868	0.781	0.96	0.868	0.781	0.96	CLONAL	1	TRUE	1	0.292218481939252	2		666	907	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0014017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	73	387	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			1	2	FACETS	0.932	0.817	1	0.932	0.817	1	CLONAL	1	TRUE	1	0.292218481939252	2		387	536	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181530	32181530	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	54	501	0	ENST00000375023.3:c.2255A>G	p.Tyr752Cys	p.Y752C	ENST00000375023	NM_004557.3	752	tAc/tGc	14/30	1	2	FACETS	0.468	0.398	0.544	0.468	0.398	0.544	SUBCLONAL	1	TRUE	1	0.292218481939252	2		501	790	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974761	21974771	+	frameshift_variant	Frame_Shift_Del	DEL	CCGGGCCGCGG	CCGGGCCGCGG	-	novel	NA	P-0014017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	43	391	0	ENST00000304494.5:c.56_66del	p.Ala19GlyfsTer21	p.A19Gfs*21	ENST00000304494	NM_000077.4	19	gCCGCGGCCCGG/g	1/3	1	2	FACETS	0.787	0.66	0.927	0.787	0.66	0.927	CLONAL	1	TRUE	1	0.292218481939252	2		391	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0014020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	125	418	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.157907900125135	2	FACETS	0.944	0.859	1	0.944	0.859	1	CLONAL	2	TRUE	0	0.261171049388094	2		421	507	SUCCESS
APC	324	MSKCC	GRCh37	5	112175240	112175240	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	120	370	0	ENST00000257430.4:c.3949G>T	p.Glu1317Ter	p.E1317*	ENST00000257430	NM_000038.5	1317	Gaa/Taa	16/16	0.261171049388094	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.261171049388094	2		370	428	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809495	36809495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374572688	NA	P-0014020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	87	476	1	ENST00000373129.3:c.970G>A	p.Val324Ile	p.V324I	ENST00000373129	NM_032017.1	324	Gtc/Atc	10/12	1	2	FACETS	0.952	0.843	1	0.952	0.843	1	CLONAL	1	TRUE	1	0.261171049388094	2		477	700	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940554	131940554	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	207	708	1	ENST00000265335.6:c.2581C>A	p.Gln861Lys	p.Q861K	ENST00000265335		861	Caa/Aaa	16/25	0.261171049388094	2	FACETS	0.876	0.813	0.94	0.876	0.813	0.94	CLONAL	2	TRUE	0	0.261171049388094	2		709	905	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780235	9780235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1397404017	NA	P-0014060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	119	723	2	ENST00000377346.4:c.1405G>A	p.Ala469Thr	p.A469T	ENST00000377346	NM_005026.3	469	Gct/Act	11/24	0.421084263468401	1	FACETS	0.592	0.534	0.652	0.592	0.534	0.652	SUBCLONAL	1	TRUE	0	0.421084263468401	1		725	754	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412869	49412869	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	92	747	0	ENST00000418115.1:c.154C>T	p.Gln52Ter	p.Q52*	ENST00000418115	NM_001664.2	52	Cag/Tag	2/5	1	2	FACETS	0.398	0.352	0.446	0.398	0.352	0.446	SUBCLONAL	1	TRUE	1	0.421084263468401	2		747	1099	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005388	150005396	+	inframe_deletion	In_Frame_Del	DEL	TCCAGAATA	TCCAGAATA	-	novel	NA	P-0014060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	110	913	0	ENST00000253339.5:c.829_837del	p.Tyr277_Gly279del	p.Y277_G279del	ENST00000253339		277	TATTCTGGA/-	3/7	0.280289473182454	1	FACETS	0.399	0.358	0.443	0.399	0.358	0.443	SUBCLONAL	1	TRUE	0	0.421084263468401	1		913	1033	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971209	21971209	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1554654224	NA	P-0014060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	37	196	0	ENST00000304494.5:c.151-2A>G		p.X51_splice	ENST00000304494	NM_000077.4	51			0.421084263468401	1	FACETS	0.758	0.632	0.895	0.758	0.632	0.895	SUBCLONAL	1	TRUE	0	0.421084263468401	1		196	183	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388686	31388686	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	48	694	1	ENST00000328111.2:c.1951T>A	p.Cys651Ser	p.C651S	ENST00000328111	NM_006892.3	651	Tgc/Agc	18/23	1	2	FACETS	0.466	0.393	0.547	0.466	0.393	0.547	SUBCLONAL	1	TRUE	1	0.25	2		695	824	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188320	10188320	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	24	475	0	ENST00000256474.2:c.463G>C	p.Val155Leu	p.V155L	ENST00000256474	NM_000551.3	155	Gtg/Ctg	2/3	1	2	FACETS	0.271	0.211	0.34	0.271	0.211	0.34	SUBCLONAL	1	TRUE	1	0.25	2		475	709	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0014093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	112	808	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	0.200228738949472	3	FACETS	0.953	0.858	1	0.953	0.858	1	CLONAL	2	TRUE	1	0.200228738949472	3		808	646	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343132	118343132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	56	519	2	ENST00000534358.1:c.1258C>T	p.Arg420Trp	p.R420W	ENST00000534358	NM_005933.3	420	Cgg/Tgg	3/36	0.119291875844517	4	FACETS	1	0.936	1	0.585	0.501	0.677	INDETERMINATE	1	TRUE	2	0.200228738949472	4		521	574	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280624	41280624	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0014093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	107	734	0	ENST00000349496.5:c.2138-1G>T		p.X713_splice	ENST00000349496	NM_001904.3	713			0.200228738949472	2	FACETS	0.973	0.876	1	0.973	0.876	1	CLONAL	2	TRUE	0	0.200228738949472	2		734	549	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	55	589	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	FALSE	1	0.562964564535934	2		590	180	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692838	89692838	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	61	142	0	ENST00000371953.3:c.322C>T	p.Leu108Phe	p.L108F	ENST00000371953	NM_000314.4	108	Ctt/Ttt	5/9	0.562964564535934	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	0	0.562964564535934	1		142	134	SUCCESS
BLM	641	MSKCC	GRCh37	15	91341443	91341468	+	frameshift_variant	Frame_Shift_Del	DEL	TGACGATGTGAAAAGTATTGTAAGAT	TGACGATGTGAAAAGTATTGTAAGAT	-	novel	NA	P-0014099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	151	497	0	ENST00000355112.3:c.3235_3260del	p.Asp1079CysfsTer5	p.D1079Cfs*5	ENST00000355112	NM_000057.2	1078	acTGACGATGTGAAAAGTATTGTAAGATtt/actt	17/22	1	2	FACETS	0.83	0.762	0.902	0.83	0.762	0.902	CLONAL	1	FALSE	1	0.562964564535934	2		497	646	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349131	11349131	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	75	153	0	ENST00000332029.2:c.205C>T	p.Arg69Cys	p.R69C	ENST00000332029	NM_003745.1	69	Cgc/Tgc	2/2	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.562964564535934	2		153	219	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0014136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	179	195	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.474782152507677	3	FACETS	0.913	0.851	0.975			1	CLONAL	2	TRUE	NA	0.598075661079843	3		195	426	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087368	27087368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752331536	NA	P-0014136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	219	733	0	ENST00000324856.7:c.1942G>A	p.Asp648Asn	p.D648N	ENST00000324856	NM_006015.4	648	Gac/Aac	5/20	1	2	FACETS	0.933	0.87	0.997	0.933	0.87	0.997	CLONAL	1	TRUE	1	0.598075661079843	2		733	785	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711968	89711968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	152	433	0	ENST00000371953.3:c.586C>T	p.His196Tyr	p.H196Y	ENST00000371953	NM_000314.4	196	Cac/Tac	6/9	1	2	FACETS	0.955	0.879	1	0.955	0.879	1	CLONAL	1	TRUE	1	0.598075661079843	2		433	532	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244999	123244999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150015885	NA	P-0014136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	313	792	3	ENST00000358487.5:c.2105C>T	p.Ser702Leu	p.S702L	ENST00000358487	NM_000141.4	702	tCg/tTg	16/18	0.474782152507677	3	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.598075661079843	3		795	1229	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231410	46231410	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0014136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	214	542	0	ENST00000334344.6:c.1250C>G	p.Ser417Ter	p.S417*	ENST00000334344	NM_152641.2	417	tCa/tGa	10/21	1	2	FACETS	0.937	0.873	1	0.937	0.873	1	CLONAL	1	TRUE	1	0.598075661079843	2		542	764	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446723	49446723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	224	533	0	ENST00000301067.7:c.1087G>A	p.Glu363Lys	p.E363K	ENST00000301067	NM_003482.3	363	Gag/Aag	8/54	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.598075661079843	2		533	747	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858952	57858952	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs554594367	NA	P-0014136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	421	1195	1	ENST00000228682.2:c.448G>A	p.Gly150Arg	p.G150R	ENST00000228682	NM_005269.2	150	Ggg/Agg	5/12	1	2	FACETS	0.978	0.93	1	0.978	0.93	1	CLONAL	1	TRUE	1	0.598075661079843	2		1196	1440	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434146	121434146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1384502119	NA	P-0014136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	346	911	0	ENST00000257555.6:c.1037C>T	p.Thr346Ile	p.T346I	ENST00000257555		346	aCa/aTa	5/10	1	2	FACETS	0.991	0.939	1	0.991	0.939	1	CLONAL	1	TRUE	1	0.598075661079843	2		911	1167	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263850	133263850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	110	276	0	ENST00000320574.5:c.52G>A	p.Glu18Lys	p.E18K	ENST00000320574	NM_006231.2	18	Gag/Aag	1/49	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.598075661079843	2		276	312	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050866	49050866	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	29	336	0	ENST00000267163.4:c.2550G>C	p.Gln850His	p.Q850H	ENST00000267163	NM_000321.2	850	caG/caC	25/27	1	2	FACETS	0.2	0.16	0.245	0.2	0.16	0.245	SUBCLONAL	1	TRUE	1	0.598075661079843	2		336	486	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028585	42028585	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	460	1300	0	ENST00000219905.7:c.4123G>C	p.Glu1375Gln	p.E1375Q	ENST00000219905	NM_001164273.1	1375	Gag/Cag	13/24	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.598075661079843	2		1300	1467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0014136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	284	812	1	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.598075661079843	1	FACETS	0.936	0.885	0.988	0.936	0.885	0.988	CLONAL	1	TRUE	0	0.598075661079843	1		813	711	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094856	11094856	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	242	879	2	ENST00000358026.2:c.29G>A	p.Gly10Glu	p.G10E	ENST00000358026	NM_001128849.1	10	gGa/gAa	2/36	1	2	FACETS	0.74	0.691	0.791	0.74	0.691	0.791	SUBCLONAL	1	TRUE	1	0.598075661079843	2		881	1093	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209108198	209108198	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	341	722	0	ENST00000345146.2:c.651G>T	p.Lys217Asn	p.K217N	ENST00000345146	NM_005896.2	217	aaG/aaT	6/10	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.598075661079843	2		722	984	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827982	40827982	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	205	556	0	ENST00000373198.4:c.2446G>C	p.Glu816Gln	p.E816Q	ENST00000373198	NM_133170.3	816	Gag/Cag	17/32	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.598075661079843	2		556	685	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163023	47163023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	283	672	0	ENST00000409792.3:c.3103C>T	p.His1035Tyr	p.H1035Y	ENST00000409792	NM_014159.6	1035	Cat/Tat	3/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.598075661079843	2		672	886	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163187	47163187	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	279	627	0	ENST00000409792.3:c.2939C>G	p.Ser980Cys	p.S980C	ENST00000409792	NM_014159.6	980	tCt/tGt	3/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.598075661079843	2		627	827	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163512	47163512	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	171	502	0	ENST00000409792.3:c.2614C>T	p.Gln872Ter	p.Q872*	ENST00000409792	NM_014159.6	872	Caa/Taa	3/21	1	2	FACETS	0.928	0.858	1	0.928	0.858	1	CLONAL	1	TRUE	1	0.598075661079843	2		502	616	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911606	134911606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767340477	NA	P-0014136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	220	608	1	ENST00000398015.3:c.2071C>T	p.Arg691Trp	p.R691W	ENST00000398015	NM_004441.4	691	Cgg/Tgg	11/16	1	2	FACETS	0.92	0.858	0.983	0.92	0.858	0.983	CLONAL	1	TRUE	1	0.598075661079843	2		609	800	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281322	142281322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	50	510	0	ENST00000350721.4:c.922G>A	p.Glu308Lys	p.E308K	ENST00000350721	NM_001184.3	308	Gaa/Aaa	4/47	1	2	FACETS	0.234	0.198	0.274	0.234	0.198	0.274	SUBCLONAL	1	TRUE	1	0.598075661079843	2		510	714	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928093	178928093	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	455	577	0	ENST00000263967.3:c.1371C>A	p.Asn457Lys	p.N457K	ENST00000263967	NM_006218.2	457	aaC/aaA	8/21	0.474782152507677	3	FACETS	0.978	0.938	1			1	CLONAL	2	TRUE	NA	0.598075661079843	3		577	1010	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231728	66231728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	285	698	0	ENST00000273854.3:c.1972G>A	p.Asp658Asn	p.D658N	ENST00000273854	NM_004439.5	658	Gat/Aat	11/18	0.598075661079843	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.598075661079843	1		698	609	SUCCESS
APC	324	MSKCC	GRCh37	5	112176318	112176318	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs143674116	NA	P-0014136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	263	588	0	ENST00000257430.4:c.5027G>C	p.Arg1676Thr	p.R1676T	ENST00000257430	NM_000038.5	1676	aGa/aCa	16/16	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.598075661079843	2		588	755	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839850	27839850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1260	551	1544	0	ENST00000328488.2:c.244G>A	p.Asp82Asn	p.D82N	ENST00000328488	NM_003533.2	82	Gat/Aat	1/1	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.598075661079843	2		1544	1811	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652129	36652129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34916193	NA	P-0014136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	187	495	1	ENST00000244741.5:c.251G>A	p.Arg84Gln	p.R84Q	ENST00000244741	NM_000389.4	84	cGa/cAa	2/3	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.598075661079843	2		496	619	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710759	117710759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	284	760	1	ENST00000368508.3:c.1513G>A	p.Glu505Lys	p.E505K	ENST00000368508	NM_002944.2	505	Gaa/Aaa	12/43	0.598075661079843	1	FACETS	0.988	0.935	1	0.988	0.935	1	CLONAL	1	TRUE	0	0.598075661079843	1		761	674	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962337	2962337	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1185	132	811	0	ENST00000396946.4:c.2200G>C	p.Glu734Gln	p.E734Q	ENST00000396946	NM_032415.4	734	Gag/Cag	17/25	0.119089751180919	5	FACETS	0.636	0.575	0.7			1	INDETERMINATE	1	TRUE	NA	0.598075661079843	5		811	1317	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231233	98231233	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs62637629	NA	P-0014136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	247	599	0	ENST00000331920.6:c.2050G>A	p.Glu684Lys	p.E684K	ENST00000331920	NM_000264.3	684	Gag/Aag	14/24	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.598075661079843	2		599	813	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814826	139814826	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	381	1099	0	ENST00000247668.2:c.819G>C	p.Glu273Asp	p.E273D	ENST00000247668	NM_021138.3	273	gaG/gaC	8/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.598075661079843	2		1099	1229	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921430	39921430	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	65	659	0	ENST00000378444.4:c.4390G>A	p.Glu1464Lys	p.E1464K	ENST00000378444	NM_001123385.1	1464	Gag/Aag	10/15	1	2	FACETS	0.238	0.205	0.273	0.238	0.205	0.273	SUBCLONAL	1	TRUE	1	0.598075661079843	2		659	915	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937335	76937335	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	241	670	0	ENST00000373344.5:c.3413G>A	p.Arg1138Lys	p.R1138K	ENST00000373344	NM_000489.3	1138	aGa/aAa	9/35	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.598075661079843	2		670	775	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	21	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.157	0.12	0.201	0.157	0.12	0.201	SUBCLONAL	1	TRUE	1	0.35	2		371	764	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0014140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	25	418	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.213	0.167	0.266	0.213	0.167	0.266	SUBCLONAL	1	TRUE	1	0.35	2		421	672	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856469	111856469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	46	664	1	ENST00000341259.2:c.520G>A	p.Ala174Thr	p.A174T	ENST00000341259	NM_005475.2	174	Gcc/Acc	2/8	1	2	FACETS	0.306	0.256	0.361	0.306	0.256	0.361	SUBCLONAL	1	TRUE	1	0.35	2		665	860	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0014145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	168	500	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.861	0.795	0.929	0.861	0.795	0.929	CLONAL	1	TRUE	1	0.640969033279107	2		500	609	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	299	432	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	0.640969033279107	2		432	878	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0014145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	41	138	1	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.87	0.738	1	0.87	0.738	1	CLONAL	1	TRUE	1	0.640969033279107	2		139	147	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	262	474	2	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	0.640969033279107	2		476	748	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789591	3789591	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	318	555	0	ENST00000262367.5:c.4268del	p.Pro1423LeufsTer36	p.P1423Lfs*36	ENST00000262367	NM_004380.2	1423	cCt/ct	25/31	1	2	FACETS	0.9	0.85	0.952	0.9	0.85	0.952	CLONAL	1	TRUE	1	0.640969033279107	2		555	1102	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118918	70118918	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	422	730	0	ENST00000245479.2:c.490C>T	p.Gln164Ter	p.Q164*	ENST00000245479	NM_000346.3	164	Cag/Tag	2/3	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.640969033279107	2		730	1237	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987078	36987078	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	67	391	0	ENST00000354822.5:c.611A>G	p.Tyr204Cys	p.Y204C	ENST00000354822	NM_001079668.2	204	tAc/tGc	3/3	1	2	FACETS	0.362	0.314	0.413	0.362	0.314	0.413	SUBCLONAL	1	TRUE	1	0.640969033279107	2		391	578	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	179	371	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.640969033279107	2		371	525	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101751	71101751	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	236	463	0	ENST00000318789.4:c.447del	p.Lys149AsnfsTer57	p.K149Nfs*57	ENST00000318789	NM_032682.5	149	aaA/aa	9/21	1	2	FACETS	0.914	0.855	0.974	0.914	0.855	0.974	CLONAL	1	TRUE	1	0.640969033279107	2		463	806	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371755	116371755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367628460	NA	P-0014145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	230	493	1	ENST00000397752.3:c.1234C>T	p.Arg412Cys	p.R412C	ENST00000397752	NM_000245.2	412	Cgc/Tgc	3/21	1	2	FACETS	0.899	0.841	0.959	0.899	0.841	0.959	CLONAL	1	TRUE	1	0.640969033279107	2		494	798	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9770521	9770521	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	351	651	1	ENST00000377346.4:c.8C>A	p.Pro3His	p.P3H	ENST00000377346	NM_005026.3	3	cCt/cAt	3/24	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.640969033279107	2		652	1095	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099836	27099881	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GCTCCAGGGAGTGATCCCTTCATGTCCTCAGGGCAGGGCCCCAACG	GCTCCAGGGAGTGATCCCTTCATGTCCTCAGGGCAGGGCCCCAACG	-	novel	NA	P-0014145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	265	397	0	ENST00000324856.7:c.3717_3762del		p.X1239_splice	ENST00000324856	NM_006015.4	1239		15/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.640969033279107	2		397	796	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552728	226552728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1318	380	557	0	ENST00000366794.5:c.2633G>A	p.Arg878Gln	p.R878Q	ENST00000366794	NM_001618.3	878	cGg/cAg	19/23	0.640969033279107	4	FACETS	1	0.988	1	0.382	0.361	0.403	CLONAL	1	TRUE	1	0.640969033279107	4		557	1698	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100466	8100466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1166016520	NA	P-0014145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	501	807	0	ENST00000346208.3:c.440G>A	p.Ser147Asn	p.S147N	ENST00000346208		147	aGc/aAc	3/6	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.640969033279107	2		807	1486	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711904	+	frameshift_variant	Frame_Shift_Del	DEL	GCTAT	GCTAT	-	novel	NA	P-0014145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	154	428	0	ENST00000371953.3:c.519_523del	p.Tyr174ValfsTer4	p.Y174Vfs*4	ENST00000371953	NM_000314.4	173	cGCTAT/c	6/9	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.640969033279107	2		428	473	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456744	32456744	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	164	263	0	ENST00000332351.3:c.148G>A	p.Ala50Thr	p.A50T	ENST00000332351	NM_024426.4	50	Gct/Act	1/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.640969033279107	2		263	463	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466040	69466040	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	287	509	0	ENST00000227507.2:c.878T>G	p.Val293Gly	p.V293G	ENST00000227507	NM_053056.2	293	gTg/gGg	5/5	1	2	FACETS	0.993	0.936	1	0.993	0.936	1	CLONAL	1	TRUE	1	0.640969033279107	2		509	902	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528056	103528056	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765714657	NA	P-0014145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	180	316	1	ENST00000355739.4:c.3364C>T	p.Pro1122Ser	p.P1122S	ENST00000355739	NM_000123.3	1122	Cca/Tca	15/15	1	2	FACETS	0.952	0.883	1	0.952	0.883	1	CLONAL	1	TRUE	1	0.640969033279107	2		317	590	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828818	72828818	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	618	1138	0	ENST00000268489.5:c.7763del	p.Leu2588ArgfsTer24	p.L2588Rfs*24	ENST00000268489	NM_006885.3	2588	cTg/cg	9/10	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.640969033279107	2		1138	1750	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831849	72831849	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1339	657	1208	1	ENST00000268489.5:c.4732C>T	p.Gln1578Ter	p.Q1578*	ENST00000268489	NM_006885.3	1578	Caa/Taa	9/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.640969033279107	2		1209	1996	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78617542	78617542	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	243	439	0	ENST00000306801.3:c.280G>T	p.Gly94Cys	p.G94C	ENST00000306801	NM_020761.2	94	Ggt/Tgt	3/34	1	2	FACETS	0.951	0.892	1	0.951	0.892	1	CLONAL	1	TRUE	1	0.640969033279107	2		439	797	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792043	42792043	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	311	625	0	ENST00000575354.2:c.849del	p.Thr284ArgfsTer41	p.T284Rfs*41	ENST00000575354	NM_015125.3	283	Ccc/cc	6/20	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.640969033279107	2		625	969	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714571	52714571	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	378	679	0	ENST00000322088.6:c.329A>G	p.Glu110Gly	p.E110G	ENST00000322088	NM_014225.5	110	gAg/gGg	4/15	1	2	FACETS	0.968	0.92	1	0.968	0.92	1	CLONAL	1	TRUE	1	0.640969033279107	2		679	1218	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463187	25463187	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs746704362	NA	P-0014145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	420	691	0	ENST00000264709.3:c.2306T>C	p.Ile769Thr	p.I769T	ENST00000264709	NM_175629.2	769	aTc/aCc	19/23	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.640969033279107	2		691	1257	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025857	48025857	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs267608041	NA	P-0014145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	299	594	0	ENST00000234420.5:c.741del	p.Lys247AsnfsTer32	p.K247Nfs*32	ENST00000234420	NM_000179.2	245	atA/at	4/10	1	2	FACETS	0.9	0.848	0.952	0.9	0.848	0.952	CLONAL	1	TRUE	1	0.640969033279107	2		594	1037	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881594	111881594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778682749	NA	P-0014145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	328	583	2	ENST00000393256.3:c.272G>A	p.Arg91Gln	p.R91Q	ENST00000393256	NM_006538.4	91	cGa/cAa	2/4	1	2	FACETS	0.952	0.9	1	0.952	0.9	1	CLONAL	1	TRUE	1	0.640969033279107	2		585	1075	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022391	31022391	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	181	350	0	ENST00000375687.4:c.1879del	p.Ala627ArgfsTer76	p.A627Rfs*76	ENST00000375687	NM_015338.5	626	Ggg/gg	13/13	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.640969033279107	2		350	530	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523737	41523737	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	315	578	1	ENST00000263253.7:c.1153G>T	p.Gly385Cys	p.G385C	ENST00000263253	NM_001429.3	385	Ggc/Tgc	4/31	1	2	FACETS	0.956	0.903	1	0.956	0.903	1	CLONAL	1	TRUE	1	0.640969033279107	2		579	1028	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026804	71026811	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGATGC	AAAGATGC	-	novel	NA	P-0014145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	107	451	0	ENST00000318789.4:c.1411_1418del	p.Ala471AsnfsTer2	p.A471Nfs*2	ENST00000318789	NM_032682.5	471	GCATCTTTa/a	16/21	1	2	FACETS	0.614	0.552	0.678	0.614	0.552	0.678	SUBCLONAL	1	TRUE	1	0.640969033279107	2		451	544	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027182	71027182	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0014145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	172	334	0	ENST00000318789.4:c.1147-2A>T		p.X383_splice	ENST00000318789	NM_032682.5	383			1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.640969033279107	2		334	520	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225657	26225657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202067024	NA	P-0014145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1366	726	1511	1	ENST00000360408.1:c.275C>T	p.Ala92Val	p.A92V	ENST00000360408	NM_003532.2	92	gCg/gTg	1/1	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.640969033279107	2		1512	2092	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184823	32184823	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148631044	NA	P-0014145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	223	441	0	ENST00000375023.3:c.1760A>G	p.Gln587Arg	p.Q587R	ENST00000375023	NM_004557.3	587	cAa/cGa	11/30	1	2	FACETS	0.965	0.902	1	0.965	0.902	1	CLONAL	1	TRUE	1	0.640969033279107	2		441	721	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37141816	37141816	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	315	542	0	ENST00000373509.5:c.891G>T	p.Gln297His	p.Q297H	ENST00000373509	NM_002648.3	297	caG/caT	6/6	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.640969033279107	2		542	910	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820134	139820134	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0014145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	449	771	0	ENST00000247668.2:c.1288-1G>T		p.X430_splice	ENST00000247668	NM_021138.3	430			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.640969033279107	2		771	1348	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	285	589	1				ENST00000310581	NM_198253.2	-/1132			0.593291217940457	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.622165066952848	3		590	517	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097610	27097610	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	228	611	1	ENST00000324856.7:c.3199G>T	p.Val1067Phe	p.V1067F	ENST00000324856	NM_006015.4	1067	Gtc/Ttc	12/20	0.575671249750461	1	FACETS	0.871	0.818	0.924	0.871	0.818	0.924	CLONAL	1	TRUE	0	0.622165066952848	1		612	580	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244101	5244101	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	406	1030	1	ENST00000357368.4:c.1381C>T	p.Arg461Cys	p.R461C	ENST00000357368	NM_002850.3	461	Cgc/Tgc	11/38	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.622165066952848	2		1031	1101	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939182	131939182	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0014151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	327	489	0	ENST00000265335.6:c.2397+1G>T		p.X799_splice	ENST00000265335		799			0.622165066952848	3	FACETS	0.859	0.816	0.903	0.859	0.816	0.903	CLONAL	2	TRUE	1	0.622165066952848	3		489	802	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954342	48954342	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780248969	NA	P-0014175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	27	82	0	ENST00000267163.4:c.1463C>T	p.Ala488Val	p.A488V	ENST00000267163	NM_000321.2	488	gCg/gTg	16/27	0.24498159071978	3	FACETS	0.695	0.555	0.856	0.348	0.277	0.428	SUBCLONAL	1	TRUE	1	0.305481632073941	3		82	293	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0014183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	158	612	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.266276710882632	2		613	942	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0014183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	132	351	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.266276710882632	2		351	676	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578410	7578410	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	147	415	0	ENST00000269305.4:c.520A>T	p.Arg174Trp	p.R174W	ENST00000269305	NM_001126112.2	174	Agg/Tgg	5/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.266276710882632	2		415	955	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291831	15291831	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1286854173	NA	P-0014183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	224	532	2	ENST00000263388.2:c.2935G>A	p.Ala979Thr	p.A979T	ENST00000263388	NM_000435.2	979	Gcc/Acc	18/33	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.266276710882632	2		534	1342	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324564	62324564	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123017	NA	P-0014183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1202	186	615	1	ENST00000360203.5:c.2920C>T	p.Arg974Ter	p.R974*	ENST00000360203	NM_001283009.1	974	Cga/Tga	30/35	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.266276710882632	2		616	1388	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390191	89390191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1483175958	NA	P-0014183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	89	266	0	ENST00000336596.2:c.940G>A	p.Asp314Asn	p.D314N	ENST00000336596	NM_005233.5	314	Gac/Aac	4/17	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.266276710882632	2		266	553	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902409	1902409	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	129	443	0	ENST00000382891.5:c.28C>T	p.Leu10Phe	p.L10F	ENST00000382891	NM_133335.3	10	Ctt/Ttt	2/22	1	2	FACETS	0.916	0.829	1	0.916	0.829	1	CLONAL	1	TRUE	1	0.266276710882632	2		443	1058	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043378	180043378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774554521	NA	P-0014183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	172	421	0	ENST00000261937.6:c.3208C>T	p.Arg1070Cys	p.R1070C	ENST00000261937	NM_182925.4	1070	Cgc/Tgc	23/30	0.266276710882632	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.266276710882632	1		421	852	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778194	27778194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	143	421	0	ENST00000369163.2:c.343G>A	p.Ala115Thr	p.A115T	ENST00000369163	NM_003536.2	115	Gcc/Acc	1/1	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.266276710882632	2		421	924	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527665	157527668	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs1554237269	NA	P-0014189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	417	615	0	ENST00000346085.5:c.5394_5397del	p.Phe1798LeufsTer52	p.F1798Lfs*52	ENST00000346085	NM_020732.3	1797	cTGTTt/ct	20/20	1	2	FACETS	0.975	0.933	1	0.975	0.933	1	CLONAL	1	TRUE	1	0.91	2		615	940	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0014208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	424	465	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	0.486076420859878	4	FACETS	1	0.993	1	0.858	0.826	0.891	CLONAL	3	TRUE	0	0.49683565724963	4		465	744	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971000	21971000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	722	983	0	ENST00000304494.5:c.358G>T	p.Glu120Ter	p.E120*	ENST00000304494	NM_000077.4	120	Gag/Tag	2/3	0.497000233733699	2	FACETS	0.849	0.826	0.872	1	0.997	1	CLONAL	3	TRUE	0	0.49683565724963	2		983	1141	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085647	16085647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1238492356	NA	P-0014208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	265	717	0	ENST00000281043.3:c.823G>A	p.Glu275Lys	p.E275K	ENST00000281043	NM_005378.4	275	Gaa/Aaa	3/3	0.497000233733699	3	FACETS	0.859	0.809	0.911	0.859	0.809	0.911	CLONAL	2	TRUE	1	0.49683565724963	3		717	775	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589333	28589333	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	105	480	0	ENST00000241453.7:c.2714G>A	p.Gly905Glu	p.G905E	ENST00000241453	NM_004119.2	905	gGa/gAa	22/24	1	2	FACETS	0.71	0.638	0.787	0.71	0.638	0.787	SUBCLONAL	1	TRUE	1	0.49683565724963	2		480	595	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0014208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	119	244	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.909	0.824	0.998	0.909	0.824	0.998	CLONAL	1	TRUE	1	0.49683565724963	2		245	527	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026984	71026984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763413735	NA	P-0014208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	249	476	1	ENST00000318789.4:c.1343C>T	p.Ser448Leu	p.S448L	ENST00000318789	NM_032682.5	448	tCg/tTg	15/21	0.497000233733699	3	FACETS	0.967	0.91	1	0.967	0.91	1	CLONAL	2	TRUE	1	0.49683565724963	3		477	647	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076902	41076902	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	221	591	0	ENST00000373198.4:c.1518G>A	p.Trp506Ter	p.W506*	ENST00000373198	NM_133170.3	506	tgG/tgA	9/32	0.462740646490347	3	FACETS	0.845	0.791	0.901	0.845	0.791	0.901	CLONAL	2	TRUE	1	0.49683565724963	3		591	657	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858493	9858493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765257420	NA	P-0014208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	218	534	1	ENST00000330684.3:c.2908C>T	p.Arg970Trp	p.R970W	ENST00000330684	NM_001134407.1	970	Cgg/Tgg	13/13	0.49626330877545	2	FACETS	0.926	0.871	0.981	0.926	0.871	0.981	CLONAL	2	TRUE	0	0.49683565724963	2		535	474	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048115	180048115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	171	919	0	ENST00000261937.6:c.2158G>A	p.Glu720Lys	p.E720K	ENST00000261937	NM_182925.4	720	Gaa/Aaa	14/30	NA	2	FACETS	0.965	0.891	1			1	INDETERMINATE	1	TRUE	NA	0.49683565724963	2		919	713	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716359	18716359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	192	486	0	ENST00000266497.5:c.3706G>A	p.Glu1236Lys	p.E1236K	ENST00000266497		1236	Gaa/Aaa	26/31	0.497000233733699	3	FACETS	1	0.986	1	0.633	0.587	0.681	CLONAL	1	TRUE	1	0.49683565724963	3		486	762	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476264	88476264	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	137	791	1	ENST00000360948.2:c.1868G>A	p.Gly623Glu	p.G623E	ENST00000360948	NM_001012338.2	623	gGa/gAa	15/19	0.497000233733699	3	FACETS	0.831	0.756	0.909	0.415	0.378	0.455	CLONAL	1	TRUE	1	0.49683565724963	3		792	829	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579700	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0014208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	324	807	1	ENST00000269305.4:c.96_96+1delinsAA		p.X32_splice	ENST00000269305	NM_001126112.2	32		3/11	0.49626330877545	2	FACETS	0.838	0.796	0.881	0.838	0.796	0.881	CLONAL	2	TRUE	0	0.49683565724963	2		808	778	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394753	45394753	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs576952880	NA	P-0014208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	150	471	1	ENST00000262160.6:c.596C>T	p.Ser199Phe	p.S199F	ENST00000262160	NM_005901.5	199	tCc/tTc	5/11	1	2	FACETS	0.907	0.831	0.985	0.907	0.831	0.985	CLONAL	1	TRUE	1	0.49683565724963	2		472	666	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204786	128204786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	304	1383	2	ENST00000341105.2:c.655G>A	p.Glu219Lys	p.E219K	ENST00000341105	NM_032638.4	219	Gag/Aag	3/6	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.49683565724963	2		1385	1206	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156616	55156616	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	307	611	0	ENST00000257290.5:c.3017G>C	p.Gly1006Ala	p.G1006A	ENST00000257290	NM_006206.4	1006	gGt/gCt	22/23	0.497000233733699	3	FACETS	0.836	0.79	0.883	0.836	0.79	0.883	CLONAL	2	TRUE	1	0.49683565724963	3		611	923	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953871	55953871	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	128	537	0	ENST00000263923.4:c.3565G>A	p.Asp1189Asn	p.D1189N	ENST00000263923	NM_002253.2	1189	Gat/Aat	27/30	0.497000233733699	3	FACETS	0.797	0.722	0.876	0.399	0.361	0.438	SUBCLONAL	1	TRUE	1	0.49683565724963	3		537	807	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981536	55981536	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	116	463	0	ENST00000263923.4:c.401G>A	p.Gly134Glu	p.G134E	ENST00000263923	NM_002253.2	134	gGa/gAa	4/30	0.497000233733699	3	FACETS	0.729	0.657	0.805	0.364	0.328	0.403	SUBCLONAL	1	TRUE	1	0.49683565724963	3		463	800	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157454228	157454228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	133	565	0	ENST00000346085.5:c.2438C>T	p.Ser813Phe	p.S813F	ENST00000346085	NM_020732.3	813	tCc/tTc	8/20	1	2	FACETS	0.853	0.776	0.932	0.853	0.776	0.932	CLONAL	1	TRUE	1	0.49683565724963	2		565	628	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467781	50467781	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	197	520	0	ENST00000331340.3:c.1016A>T	p.Glu339Val	p.E339V	ENST00000331340	NM_006060.4	339	gAg/gTg	8/8	0.497000233733699	5	FACETS	0.94	0.873	1	0.627	0.582	0.673	CLONAL	2	TRUE	2	0.49683565724963	5		520	736	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92247496	92247496	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	288	331	1	ENST00000265734.4:c.724G>T	p.Asp242Tyr	p.D242Y	ENST00000265734	NM_001259.6	242	Gac/Tac	7/8	0.497000233733699	5	FACETS	0.905	0.856	0.955	0.905	0.856	0.955	CLONAL	3	TRUE	2	0.49683565724963	5		332	745	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207651	29207651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	115	974	0	ENST00000240100.2:c.145G>A	p.Asp49Asn	p.D49N	ENST00000240100	NM_001394.6	49	Gac/Aac	1/4	0.287701195978956	1	FACETS	0.481	0.433	0.531	0.481	0.433	0.531	INDETERMINATE	1	TRUE	0	0.49683565724963	1		974	724	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528612	8528612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	292	410	0	ENST00000356435.5:c.520C>T	p.Arg174Cys	p.R174C	ENST00000356435		174	Cgt/Tgt	4/35	0.497000233733699	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.49683565724963	2		410	588	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0014220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	148	320	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.809	0.743	0.878	0.809	0.743	0.878	CLONAL	1	TRUE	1	0.64622453121522	2		320	566	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245513	16245513	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	121	594	1	ENST00000375759.3:c.1488G>T	p.Met496Ile	p.M496I	ENST00000375759	NM_015001.2	496	atG/atT	7/15	1	2	FACETS	0.777	0.706	0.851	0.777	0.706	0.851	SUBCLONAL	1	TRUE	1	0.64622453121522	2		595	482	SUCCESS
CBL	867	MSKCC	GRCh37	11	119146841	119146841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	113	438	2	ENST00000264033.4:c.1004G>A	p.Gly335Asp	p.G335D	ENST00000264033	NM_005188.3	335	gGc/gAc	6/16	1	2	FACETS	0.892	0.81	0.977	0.892	0.81	0.977	CLONAL	1	TRUE	1	0.64622453121522	2		440	392	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488757	212488757	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	134	572	0	ENST00000342788.4:c.2092T>G	p.Leu698Val	p.L698V	ENST00000342788	NM_005235.2	698	Tta/Gta	18/28	1	2	FACETS	0.846	0.774	0.922	0.846	0.774	0.922	CLONAL	1	TRUE	1	0.64622453121522	2		572	490	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710607	40710607	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	219	790	0	ENST00000373198.4:c.4244A>G	p.Glu1415Gly	p.E1415G	ENST00000373198	NM_133170.3	1415	gAg/gGg	31/32	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.64622453121522	2		790	658	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589605	67589616	+	inframe_deletion	In_Frame_Del	DEL	TCAAGAAAAAAG	TCAAGAAAAAAG	-	novel	NA	P-0014220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	75	380	0	ENST00000274335.5:c.1370_1381del	p.Gln457_Ser460del	p.Q457_S460del	ENST00000274335		456	ttTCAAGAAAAAAGt/ttt	10/15	1	2	FACETS	0.782	0.692	0.876	0.782	0.692	0.876	SUBCLONAL	1	TRUE	1	0.64622453121522	2		380	297	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0014221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	273	452	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.263888361408576	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.263888361408576	3		452	1014	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121591	108121591	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	74	513	0	ENST00000278616.4:c.1399G>C	p.Asp467His	p.D467H	ENST00000278616	NM_000051.3	467	Gac/Cac	10/63	0.263888361408576	1	FACETS	0.549	0.479	0.624	0.549	0.479	0.624	SUBCLONAL	1	TRUE	0	0.263888361408576	1		513	887	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951140	48951140	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	153	421	0	ENST00000267163.4:c.1304del	p.Gly435AspfsTer22	p.G435Dfs*22	ENST00000267163	NM_000321.2	434	gtG/gt	13/27	0.254234715489686	2	FACETS	0.814	0.747	0.885	0.814	0.747	0.885	CLONAL	2	TRUE	0	0.263888361408576	2		421	712	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743307	743307	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1683	121	661	0	ENST00000314574.4:c.833G>T	p.Arg278Leu	p.R278L	ENST00000314574	NM_005433.3	278	cGa/cTa	7/12	0.205759092329619	4	FACETS	0.642	0.578	0.712			1	SUBCLONAL	1	TRUE	NA	0.263888361408576	4		661	1804	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593607	55593612	+	inframe_deletion	In_Frame_Del	DEL	AGGTTG	AGGTTG	-	novel	NA	P-0014241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	326	494	0	ENST00000288135.5:c.1673_1678del	p.Lys558_Val560delinsIle	p.K558_V560delinsI	ENST00000288135	NM_000222.2	558	aAGGTTGtt/att	11/21	1	2	FACETS	0.978	0.93	1	0.978	0.93	1	CLONAL	1	TRUE	1	0.902135238888413	2		494	739	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163258	32163258	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1185576654	NA	P-0014241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	637	1062	2	ENST00000375023.3:c.5968C>T	p.Leu1990Phe	p.L1990F	ENST00000375023	NM_004557.3	1990	Ctc/Ttc	30/30	1	2	FACETS	0.919	0.886	0.953	0.919	0.886	0.953	CLONAL	1	TRUE	1	0.902135238888413	2		1064	1536	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527679	157527679	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs797045282	NA	P-0014241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	413	600	0	ENST00000346085.5:c.5404C>T	p.Arg1802Ter	p.R1802*	ENST00000346085	NM_020732.3	1802	Cga/Tga	20/20	1	2	FACETS	0.909	0.868	0.95	0.909	0.868	0.95	CLONAL	1	TRUE	1	0.902135238888413	2		600	1007	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0014247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	160	511	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	1	2	FACETS	0.822	0.76	0.885	0.822	0.76	0.885	CLONAL	1	TRUE	1	0.853929492994206	2		511	456	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246445	105246445	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	146	686	1	ENST00000349310.3:c.155T>A	p.Leu52His	p.L52H	ENST00000349310	NM_001014432.1	52	cTc/cAc	4/15	0.197350591573225	1	FACETS	0.911	0.837	0.987	1	0.993	1	CLONAL	3	FALSE	0	0.197350591573225	1		687	488	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753457	42753457	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	180	971	0	ENST00000222329.4:c.807del	p.Met270Ter	p.M270*	ENST00000222329	NM_006494.2	269	ccC/cc	4/4	1	2	FACETS	1	0.985	1	1	0.994	1	CLONAL	2	FALSE	1	0.197350591573225	2		971	730	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0014266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	182	407	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	0.975	0.901	1	0.975	0.901	1	CLONAL	1	TRUE	1	0.430016414196368	2		407	868	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0014266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	239	554	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.430016414196368	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.430016414196368	1		554	801	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1952921	1952921	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0014266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	160	460	2	ENST00000382891.5:c.2004T>A	p.Tyr668Ter	p.Y668*	ENST00000382891	NM_133335.3	668	taT/taA	10/22	1	2	FACETS	0.979	0.899	1	0.979	0.899	1	CLONAL	1	TRUE	1	0.430016414196368	2		462	760	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357646	70357646	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	274	805	1	ENST00000374080.3:c.5897C>A	p.Pro1966His	p.P1966H	ENST00000374080		1966	cCc/cAc	41/45	1	2	FACETS	0.976	0.915	1	0.976	0.915	1	CLONAL	1	TRUE	1	0.430016414196368	2		806	1306	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188272	10188275	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	CTT	novel	NA	P-0014291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	220	758	2	ENST00000256474.2:c.415_418delinsCTT	p.Ser139LeufsTer20	p.S139Lfs*20	ENST00000256474	NM_000551.3	139	TCTCtc/CTTtc	2/3	0.456758227141022	1	FACETS	0.922	0.86	0.986	0.922	0.86	0.986	CLONAL	1	TRUE	0	0.456758227141022	1		760	806	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426026	138426026	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	119	473	0	ENST00000289153.2:c.1505C>T	p.Pro502Leu	p.P502L	ENST00000289153	NM_006219.2	502	cCt/cTt	9/22	1	2	FACETS	0.787	0.712	0.866	0.787	0.712	0.866	SUBCLONAL	1	TRUE	1	0.456758227141022	2		473	662	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0014298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	17	239	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.322	0.239	0.421	0.322	0.239	0.421	SUBCLONAL	1	TRUE	1	0.230682930405059	2		239	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1296	27	956	0	ENST00000269305.4:c.859G>T	p.Glu287Ter	p.E287*	ENST00000269305	NM_001126112.2	287	Gag/Tag	8/11	0.230682930405059	1	FACETS	0.157	0.123	0.195	0.157	0.123	0.195	SUBCLONAL	1	TRUE	0	0.230682930405059	1		956	1323	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011144	12011144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	22	352	0	ENST00000353533.5:c.551C>T	p.Ser184Leu	p.S184L	ENST00000353533	NM_003010.3	184	tCg/tTg	5/11	0.230682930405059	1	FACETS	0.757	0.589	0.95	0.757	0.589	0.95	CLONAL	1	TRUE	0	0.230682930405059	1		352	223	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857340	68857340	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	80	615	0	ENST00000261769.5:c.1975G>T	p.Glu659Ter	p.E659*	ENST00000261769	NM_004360.3	659	Gag/Tag	13/16	0.230682930405059	1	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	0	0.230682930405059	1		615	589	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271492	26271492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	35	459	0	ENST00000305910.3:c.121C>T	p.Arg41Cys	p.R41C	ENST00000305910	NM_003534.2	41	Cgc/Tgc	1/1	0.230682930405059	5	FACETS	0.665	0.544	0.802	0.222	0.181	0.268	SUBCLONAL	1	TRUE	2	0.230682930405059	5		459	614	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0014301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	83	500	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.973	0.859	1	0.973	0.859	1	CLONAL	1	TRUE	1	0.26	2		500	656	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469669	NA	P-0014301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	30	688	0	ENST00000374080.3:c.130G>A	p.Gly44Ser	p.G44S	ENST00000374080		44	Ggt/Agt	2/45	1	2	FACETS	0.186	0.149	0.229	0.186	0.149	0.229	SUBCLONAL	1	TRUE	1	0.26	2		688	1241	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121909229	NA	P-0014301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	109	717	0	ENST00000371953.3:c.389G>C	p.Arg130Pro	p.R130P	ENST00000371953	NM_000314.4	130	cGa/cCa	5/9	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.26	2		717	812	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107136	27107137	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0014301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	92	375	0	ENST00000324856.7:c.6749_6750del	p.Glu2250ValfsTer27	p.E2250Vfs*27	ENST00000324856	NM_006015.4	2249	tcAGag/tcag	20/20	1	2	FACETS	0.798	0.708	0.894	0.798	0.708	0.894	SUBCLONAL	1	TRUE	1	0.26	2		375	887	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624242	89624242	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	42	268	0	ENST00000371953.3:c.16A>G	p.Lys6Glu	p.K6E	ENST00000371953	NM_000314.4	6	Aaa/Gaa	1/9	1	2	FACETS	0.942	0.789	1	0.942	0.789	1	CLONAL	1	TRUE	1	0.26	2		268	343	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	96	752	0	ENST00000256196.4:c.68G>A	p.Gly23Asp	p.G23D	ENST00000256196		23	gGc/gAc	1/6	1	2	FACETS	0.735	0.653	0.822	0.735	0.653	0.822	SUBCLONAL	1	TRUE	1	0.26	2		752	1005	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281284	49281284	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	127	847	0	ENST00000282018.3:c.331T>G	p.Cys111Gly	p.C111G	ENST00000282018	NM_020377.2	111	Tgc/Ggc	1/1	1	2	FACETS	0.993	0.898	1	0.993	0.898	1	CLONAL	1	TRUE	1	0.26	2		847	984	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650711	67650711	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	112	647	0	ENST00000264010.4:c.1016G>C	p.Arg339Pro	p.R339P	ENST00000264010	NM_006565.3	339	cGg/cCg	5/12	1	2	FACETS	0.671	0.601	0.745	0.671	0.601	0.745	SUBCLONAL	1	TRUE	1	0.26	2		647	1284	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589593	67589598	+	inframe_deletion	In_Frame_Del	DEL	TAACAC	TAACAC	-	novel	NA	P-0014301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	48	355	0	ENST00000274335.5:c.1357_1362del	p.Asn453_Thr454del	p.N453_T454del	ENST00000274335		452	taTAACACt/tat	10/15	1	2	FACETS	0.747	0.632	0.874	0.747	0.632	0.874	SUBCLONAL	1	TRUE	1	0.26	2		355	494	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250833	26250833	+	start_lost	Translation_Start_Site	SNP	T	T	C	rs1160243659	NA	P-0014301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	41	225	0	ENST00000446824.2:c.1A>G	p.Met1?	p.M1?	ENST00000446824	NM_021018.2	1	Atg/Gtg	1/1	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.26	2		225	310	SUCCESS
ATM	472	MSKCC	GRCh37	11	108214053	108214053	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0014327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	298	447	0	ENST00000278616.4:c.8373C>G	p.Tyr2791Ter	p.Y2791*	ENST00000278616	NM_000051.3	2791	taC/taG	57/63	0.655723945372213	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.655723945372213	1		447	569	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126588	2126593	+	splice_donor_variant,intron_variant	Splice_Site	DEL	TACGGC	TACGGC	-	novel	NA	P-0014327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	334	672	0	ENST00000219476.3:c.2837+2_2837+7del		p.X946_splice	ENST00000219476	NM_000548.3	946			0.651388604167839	1	FACETS	0.974	0.928	1	0.974	0.928	1	CLONAL	1	TRUE	0	0.655723945372213	1		672	703	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574055	46574055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	436	724	1	ENST00000263734.3:c.70C>T	p.Arg24Trp	p.R24W	ENST00000263734	NM_001430.4	24	Cgg/Tgg	2/16	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.655723945372213	2		725	1327	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513455	41513455	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303897359	NA	P-0014327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	431	624	0	ENST00000263253.7:c.359G>A	p.Ser120Asn	p.S120N	ENST00000263253	NM_001429.3	120	aGc/aAc	2/31	0.655723945372213	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.655723945372213	1		624	830	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	131	420	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.171616779327183	5	FACETS	0.975	0.884	1	0.65	0.589	0.715	CLONAL	2	TRUE	2	0.171616779327183	5		420	984	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0014337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	101	418	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.171616779327183	2	FACETS	0.911	0.815	1	0.911	0.815	1	CLONAL	2	TRUE	0	0.171616779327183	2		421	646	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519238	137519238	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1887415	NA	P-0014337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	49	584	0	ENST00000367739.4:c.1400T>C	p.Leu467Pro	p.L467P	ENST00000367739	NM_000416.2	467	cTt/cCt	7/7	0.171616779327183	3	FACETS	0.76	0.642	0.891	0.38	0.321	0.446	SUBCLONAL	1	TRUE	1	0.171616779327183	3		584	816	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0014375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	144	195	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.934	0.854	1	0.934	0.854	1	CLONAL	1	TRUE	1	0.459632066518482	2		195	671	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372337	55372337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1281266243	NA	P-0014375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	116	801	0	ENST00000297316.4:c.1027C>T	p.Arg343Trp	p.R343W	ENST00000297316	NM_022454.3	343	Cgg/Tgg	2/2	1	2	FACETS	0.513	0.461	0.568	0.513	0.461	0.568	SUBCLONAL	1	TRUE	1	0.459632066518482	2		801	984	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155721	56155722	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0014375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	154	395	0	ENST00000399503.3:c.816_817del	p.Arg273SerfsTer27	p.R273Sfs*27	ENST00000399503	NM_005921.1	271	agAAaa/agaa	3/20	0.133027609835014	3	FACETS	1	0.986	1	0.678	0.623	0.735	INDETERMINATE	1	TRUE	1	0.459632066518482	3		395	608	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189455	56189455	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	149	547	0	ENST00000399503.3:c.4487G>C	p.Arg1496Thr	p.R1496T	ENST00000399503	NM_005921.1	1496	aGa/aCa	20/20	0.133027609835014	3	FACETS	1	0.94	1	0.517	0.473	0.563	INDETERMINATE	1	TRUE	1	0.459632066518482	3		547	771	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189047	38189047	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	175	770	0	ENST00000317025.8:c.967C>A	p.His323Asn	p.H323N	ENST00000317025	NM_023034.1	323	Cat/Aat	5/24	1	2	FACETS	0.714	0.656	0.773	0.714	0.656	0.773	SUBCLONAL	1	TRUE	1	0.459632066518482	2		770	1067	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0014379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	28	345	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.577	0.459	0.713	0.577	0.459	0.713	SUBCLONAL	1	TRUE	1	0.11	2		345	882	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0014379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	20	244	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.978	0.747	1	0.978	0.747	1	CLONAL	1	TRUE	1	0.11	2		245	372	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0014391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1544	416	904	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.323768220710048	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.323768220710048	1		904	1960	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41201199	41201199	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs80357219	NA	P-0014391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1297	293	799	0	ENST00000357654.3:c.5345G>A	p.Trp1782Ter	p.W1782*	ENST00000357654	NM_007294.3	1782	tGg/tAg	21/23	0.323768220710048	1	FACETS	0.954	0.895	1	0.954	0.895	1	CLONAL	1	TRUE	0	0.323768220710048	1		799	1590	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41209125	41209125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876659122	NA	P-0014391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	276	656	2	ENST00000357654.3:c.5221G>A	p.Val1741Ile	p.V1741I	ENST00000357654	NM_007294.3	1741	Gtc/Atc	19/23	0.323768220710048	1	FACETS	0.998	0.935	1	0.998	0.935	1	CLONAL	1	TRUE	0	0.323768220710048	1		658	1432	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517784	187517784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747368128	NA	P-0014391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	71	216	0	ENST00000441802.2:c.12910G>A	p.Val4304Met	p.V4304M	ENST00000441802	NM_005245.3	4304	Gtg/Atg	25/27	0.323768220710048	1	FACETS	0.66	0.577	0.75	0.66	0.577	0.75	SUBCLONAL	1	TRUE	0	0.323768220710048	1		216	557	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931463	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622007	NA	P-0014408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2683	995	308	0	ENST00000374690.3:c.2105T>A	p.Leu702His	p.L702H	ENST00000374690	NM_000044.3	702	cTc/cAc	4/8	0.81634440796401	6	FACETS	0.872	0.844	0.901			1	CLONAL	2	TRUE	NA	0.81634440796401	6		308	3678	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405953	49405953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	535	595	1	ENST00000418115.1:c.185G>A	p.Gly62Glu	p.G62E	ENST00000418115	NM_001664.2	62	gGg/gAg	3/5	1	2	FACETS	0.914	0.877	0.952	0.914	0.877	0.952	CLONAL	1	TRUE	1	0.81634440796401	2		596	1434	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0014408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1362	464	874	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	0.80568927867104	3	FACETS	0.877	0.835	0.919	0.438	0.417	0.46	CLONAL	1	TRUE	1	0.81634440796401	3		874	1826	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061274	38061274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	562	611	0	ENST00000250448.2:c.715G>A	p.Gly239Ser	p.G239S	ENST00000250448	NM_004496.3	239	Ggc/Agc	2/2	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.81634440796401	2		611	1357	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884849	134884849	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs540125789	NA	P-0014408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	1097	345	0	ENST00000398015.3:c.1625T>C	p.Ile542Thr	p.I542T	ENST00000398015	NM_004441.4	542	aTt/aCt	8/16	0.809990355585002	5	FACETS	0.992	0.968	1	0.992	0.968	1	CLONAL	3	TRUE	2	0.81634440796401	5		345	2009	SUCCESS
APC	324	MSKCC	GRCh37	5	112128203	112128206	+	frameshift_variant	Frame_Shift_Del	DEL	CAGT	CAGT	-	novel	NA	P-0014408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	370	460	0	ENST00000257430.4:c.707_710del	p.Gln236ProfsTer56	p.Q236Pfs*56	ENST00000257430	NM_000038.5	236	CAGTcc/cc	7/16	0.810463052705254	1	FACETS	0.887	0.852	0.921	0.887	0.852	0.921	CLONAL	1	TRUE	0	0.81634440796401	1		460	605	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0014426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	266	673	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	0.859476385351305	3	FACETS	1	0.988	1	0.588	0.553	0.623	CLONAL	1	TRUE	1	0.859476385351305	3		673	753	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577102	7577102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793881	NA	P-0014426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	733	839	0	ENST00000269305.4:c.836G>A	p.Gly279Glu	p.G279E	ENST00000269305	NM_001126112.2	279	gGg/gAg	8/11	0.845059300299267	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.859476385351305	2		839	826	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29107973	29107973	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs763892124	NA	P-0014426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	266	578	0	ENST00000328354.6:c.716A>G	p.Glu239Gly	p.E239G	ENST00000328354	NM_007194.3	239	gAg/gGg	6/15	0.771826466621228	3	FACETS	0.918	0.873	0.963	0.918	0.873	0.963	CLONAL	2	TRUE	1	0.859476385351305	3		578	482	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947166	178947166	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	340	350	0	ENST00000263967.3:c.2602G>A	p.Gly868Ser	p.G868S	ENST00000263967	NM_006218.2	868	Ggt/Agt	18/21	0.696000947395341	5	FACETS	1	0.993	1	0.859	0.826	0.892	CLONAL	3	TRUE	1	0.859476385351305	5		350	527	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182641	38182641	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs387907272	NA	P-0014430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	32	366	2	ENST00000396334.3:c.794T>C	p.Leu265Pro	p.L265P	ENST00000396334	NM_002468.4	265	cTg/cCg	5/5	0.280591467660283	1	FACETS	0.428	0.347	0.52	0.428	0.347	0.52	SUBCLONAL	1	TRUE	0	0.286346360186549	1		368	447	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849823	156849823	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	86	578	0	ENST00000524377.1:c.2079G>C	p.Trp693Cys	p.W693C	ENST00000524377	NM_002529.3	693	tgG/tgC	16/17	1	2	FACETS	0.885	0.783	0.994	0.885	0.783	0.994	CLONAL	1	TRUE	1	0.286346360186549	2		578	679	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587778720	NA	P-0014430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	169	952	0	ENST00000269305.4:c.638G>C	p.Arg213Pro	p.R213P	ENST00000269305	NM_001126112.2	213	cGa/cCa	6/11	0.286346360186549	1	FACETS	0.841	0.771	0.913	0.841	0.771	0.913	CLONAL	1	TRUE	0	0.286346360186549	1		952	1203	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37871592	37871592	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1179	88	1042	1	ENST00000269571.5:c.1202A>T	p.Glu401Val	p.E401V	ENST00000269571		401	gAg/gTg	10/27	1	2	FACETS	0.485	0.428	0.547	0.485	0.428	0.547	SUBCLONAL	1	TRUE	1	0.286346360186549	2		1043	1267	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662464	117662464	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	102	557	1	ENST00000368508.3:c.4913G>T	p.Cys1638Phe	p.C1638F	ENST00000368508	NM_002944.2	1638	tGc/tTc	30/43	0.286346360186549	5	FACETS	0.934	0.834	1	0.234	0.208	0.261	CLONAL	1	TRUE	1	0.286346360186549	5		558	1090	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0014437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	10	403	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.24	0.162	0.34	0.24	0.162	0.34	SUBCLONAL	1	TRUE	1	0.210212363968968	2		403	396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	95	590	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.210212363968968	2		590	826	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199382	16199382	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	34	457	0	ENST00000375759.3:c.155A>G	p.Asp52Gly	p.D52G	ENST00000375759	NM_015001.2	52	gAt/gGt	2/15	1	2	FACETS	0.511	0.416	0.618	0.511	0.416	0.618	SUBCLONAL	1	TRUE	1	0.210212363968968	2		457	633	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663239	227663240	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0014437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	67	589	0	ENST00000305123.5:c.215_216delinsAA	p.Ile72Lys	p.I72K	ENST00000305123	NM_005544.2	72	aTC/aAA	1/2	1	2	FACETS	0.871	0.756	0.996	0.871	0.756	0.996	CLONAL	1	TRUE	1	0.210212363968968	2		589	732	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164142	32164149	+	frameshift_variant	Frame_Shift_Del	DEL	GCGAGCGG	GCGAGCGG	-	novel	NA	P-0014437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	82	483	0	ENST00000375023.3:c.5250_5257del	p.Arg1751SerfsTer7	p.R1751Sfs*7	ENST00000375023	NM_004557.3	1750	gcCCGCTCGCtt/gctt	29/30	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.210212363968968	2		483	755	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246447	53246447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782726212	NA	P-0014437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	52	651	1	ENST00000375401.3:c.535C>T	p.Arg179Cys	p.R179C	ENST00000375401	NM_004187.3	179	Cgt/Tgt	5/26	0.210212363968968	1	FACETS	0.625	0.531	0.729	0.625	0.531	0.729	SUBCLONAL	1	TRUE	0	0.210212363968968	1		652	708	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0014453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	99	486	4	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.220186866073745	1	FACETS	0.876	0.78	0.977	0.876	0.78	0.977	CLONAL	1	TRUE	0	0.220186866073745	1		490	914	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121913370	NA	P-0014453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	59	241	0	ENST00000288602.6:c.1742A>G	p.Asn581Ser	p.N581S	ENST00000288602	NM_004333.4	581	aAt/aGt	15/18	1	2	FACETS	0.889	0.764	1	0.889	0.764	1	CLONAL	1	TRUE	1	0.220186866073745	2		241	603	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600408	10600408	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	137	650	0	ENST00000171111.5:c.1447C>A	p.Arg483Ser	p.R483S	ENST00000171111	NM_203500.1	483	Cgc/Agc	4/6	0.220186866073745	1	FACETS	0.923	0.837	1	0.923	0.837	1	CLONAL	1	TRUE	0	0.220186866073745	1		650	1200	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147241	61147241	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	98	326	0	ENST00000295025.8:c.919C>G	p.His307Asp	p.H307D	ENST00000295025	NM_002908.2	307	Cac/Gac	8/11	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.220186866073745	2		326	869	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951955	178951955	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	87	336	0	ENST00000263967.3:c.3010A>G	p.Met1004Val	p.M1004V	ENST00000263967	NM_006218.2	1004	Atg/Gtg	21/21	1	2	FACETS	0.902	0.797	1	0.902	0.797	1	CLONAL	1	TRUE	1	0.220186866073745	2		336	876	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040706	47040706	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	138	322	0	ENST00000377604.3:c.1342del	p.Gln448ArgfsTer37	p.Q448Rfs*37	ENST00000377604	NM_001204468.1	447	agC/ag	13/24	1	1	FACETS	0.869	0.793	0.948	1	0.989	1	CLONAL	2	TRUE	0	0.220186866073745	1		322	642	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956125	175956125	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	137	430	0	ENST00000367669.3:c.2087C>G	p.Thr696Arg	p.T696R	ENST00000367669	NM_022457.5	696	aCa/aGa	18/20	0.560690401934339	4	FACETS	0.699	0.635	0.767	0.35	0.317	0.384	SUBCLONAL	1	TRUE	2	0.560690401934339	4		430	1091	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574006	7574013	+	frameshift_variant	Frame_Shift_Del	DEL	ACATCTCG	ACATCTCG	-	novel	NA	P-0014455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	559	496	0	ENST00000269305.4:c.1014_1021del	p.Glu339ProfsTer5	p.E339Pfs*5	ENST00000269305	NM_001126112.2	338	ttCGAGATGTtc/tttc	10/11	0.385568850377407	3	FACETS	1	0.993	1	0.745	0.718	0.772	CLONAL	2	TRUE	0	0.560690401934339	3		496	1143	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115729	8115729	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	140	415	1	ENST00000346208.3:c.1075G>T	p.Glu359Ter	p.E359*	ENST00000346208		359	Gaa/Taa	6/6	1	2	FACETS	0.769	0.701	0.841	0.769	0.701	0.841	SUBCLONAL	1	TRUE	1	0.471962588420274	2		416	771	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060779	38060779	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1684	178	849	0	ENST00000250448.2:c.1210A>G	p.Asn404Asp	p.N404D	ENST00000250448	NM_004496.3	404	Aac/Gac	2/2	1	2	FACETS	0.405	0.371	0.44	0.405	0.371	0.44	SUBCLONAL	1	TRUE	1	0.471962588420274	2		849	1862	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982767	90982767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781333	NA	P-0014463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	145	309	2	ENST00000265433.3:c.721G>A	p.Ala241Thr	p.A241T	ENST00000265433	NM_002485.4	241	Gca/Aca	7/16	0.471962588420274	4	FACETS	0.941	0.858	1	0.314	0.286	0.343	CLONAL	1	TRUE	1	0.471962588420274	4		311	961	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913274	NA	P-0014464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	13	606	0	ENST00000263967.3:c.1634A>C	p.Glu545Ala	p.E545A	ENST00000263967	NM_006218.2	545	gAg/gCg	10/21	1	2	FACETS	0.133	0.094	0.181	0.133	0.094	0.181	SUBCLONAL	1	TRUE	1	0.343812107579656	2		606	569	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870904	12870904	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs748854742	NA	P-0014464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	105	340	0	ENST00000228872.4:c.131A>G	p.Asp44Gly	p.D44G	ENST00000228872	NM_004064.3	44	gAc/gGc	1/3	0.163591209255788	3	FACETS	1	0.964	1	0.582	0.522	0.645	INDETERMINATE	1	TRUE	1	0.343812107579656	3		340	615	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	170	589	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.965	0.89	1	0.965	0.89	1	CLONAL	1	TRUE	1	0.502619198476817	2		590	701	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55238870	55238870	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7452	4170	472	1	ENST00000275493.2:c.1883G>A	p.Cys628Tyr	p.C628Y	ENST00000275493	NM_005228.3	628	tGc/tAc	16/28	0.502619198476817	34	FACETS	0.993	0.978	1			1	CLONAL	13	TRUE	NA	0.502619198476817	34		473	11622	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944881	31944881	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	166	339	0	ENST00000340398.3:c.220A>C	p.Ile74Leu	p.I74L	ENST00000340398	NM_001013699.2	74	Atc/Ctc	1/1	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.502619198476817	2		339	614	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640428	3640428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	307	741	0	ENST00000294008.3:c.3211C>T	p.Pro1071Ser	p.P1071S	ENST00000294008	NM_032444.2	1071	Cca/Tca	12/15	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.502619198476817	2		741	1215	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221810	55221810	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16236	950	656	0	ENST00000275493.2:c.854A>G	p.Tyr285Cys	p.Y285C	ENST00000275493	NM_005228.3	285	tAc/tGc	7/28	0.502619198476817	34	FACETS	0.994	0.957	1			1	CLONAL	2	TRUE	NA	0.502619198476817	34		656	17186	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371701	55371701	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	252	547	2	ENST00000297316.4:c.391G>A	p.Asp131Asn	p.D131N	ENST00000297316	NM_022454.3	131	Gac/Aac	2/2	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.502619198476817	2		549	995	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0014481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	168	239	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.974	0.897	1	0.974	0.897	1	CLONAL	1	TRUE	1	0.460502270914943	2		239	749	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153550	108153554	+	frameshift_variant	Frame_Shift_Del	DEL	CTTAT	CTTAT	-	rs1555092477	NA	P-0014481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	86	356	0	ENST00000278616.4:c.3693_3697del	p.Leu1231PhefsTer13	p.L1231Ffs*13	ENST00000278616	NM_000051.3	1230	aaCTTATct/aact	25/63	0.421921104626115	1	FACETS	0.633	0.563	0.708	0.633	0.563	0.708	SUBCLONAL	1	TRUE	0	0.460502270914943	1		356	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0014499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	64	793	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			1	2	FACETS	0.689	0.595	0.791	0.689	0.595	0.791	SUBCLONAL	1	TRUE	1	0.238218995819319	2		793	780	SUCCESS
AR	367	MSKCC	GRCh37	X	66941796	66941796	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	30	251	0	ENST00000374690.3:c.2440T>G	p.Phe814Val	p.F814V	ENST00000374690	NM_000044.3	814	Ttc/Gtc	6/8	1	1	FACETS	0.784	0.634	0.953	0.784	0.634	0.953	CLONAL	1	TRUE	0	0.238218995819319	1		251	283	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0014502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	29	195	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.432	0.346	0.53	0.432	0.346	0.53	SUBCLONAL	1	TRUE	1	0.313734171378316	2		195	428	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0014502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	141	484	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.313734171378316	3	FACETS	1	0.978	1	0.618	0.563	0.676	CLONAL	1	TRUE	1	0.313734171378316	3		484	841	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931589	NA	P-0014502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	11	299	0	ENST00000349496.5:c.101G>A	p.Gly34Glu	p.G34E	ENST00000349496	NM_001904.3	34	gGa/gAa	3/15	1	2	FACETS	0.148	0.102	0.207	0.148	0.102	0.207	SUBCLONAL	1	TRUE	1	0.313734171378316	2		299	473	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604650	48604650	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs377767367	NA	P-0014502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	15	287	0	ENST00000342988.3:c.1472G>T	p.Gly491Val	p.G491V	ENST00000342988	NM_005359.5	491	gGt/gTt	12/12	0.24788388451008	1	FACETS	0.272	0.199	0.361	0.272	0.199	0.361	SUBCLONAL	1	TRUE	0	0.313734171378316	1		287	296	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264024	16264024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1314	410	717	0	ENST00000375759.3:c.10393C>T	p.Pro3465Ser	p.P3465S	ENST00000375759	NM_015001.2	3465	Ccc/Tcc	12/15	0.313734171378316	4	FACETS	0.996	0.945	1	0.996	0.945	1	CLONAL	2	TRUE	2	0.313734171378316	4		717	1724	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742874	17742879	+	protein_altering_variant	In_Frame_Del	DEL	CCGAGA	CCGAGA	AGG	novel	NA	P-0014502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	118	585	1	ENST00000250003.3:c.782_787delinsAGG	p.Thr261_Ser263delinsLysGly	p.T261_S263delinsKG	ENST00000250003	NM_002478.4	261	aCCGAGAgc/aAGGgc	3/3	0.313734171378316	3	FACETS	0.998	0.9	1	0.499	0.45	0.551	CLONAL	1	TRUE	1	0.313734171378316	3		586	872	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865508	57865508	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	43	506	1	ENST00000228682.2:c.2985G>T	p.Leu995Phe	p.L995F	ENST00000228682	NM_005269.2	995	ttG/ttT	12/12	0.309596035295421	3	FACETS	0.377	0.314	0.447			1	SUBCLONAL	1	TRUE	NA	0.313734171378316	3		507	842	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099221	4099221	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	76	450	0	ENST00000262948.5:c.897G>C	p.Arg299Ser	p.R299S	ENST00000262948	NM_030662.3	299	agG/agC	7/11	1	2	FACETS	0.719	0.63	0.814	0.719	0.63	0.814	SUBCLONAL	1	TRUE	1	0.313734171378316	2		450	674	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661440	227661440	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	75	396	0	ENST00000305123.5:c.2015C>G	p.Ser672Cys	p.S672C	ENST00000305123	NM_005544.2	672	tCt/tGt	1/2	0.310201336914909	3	FACETS	0.941	0.825	1	0.47	0.412	0.533	CLONAL	1	TRUE	1	0.313734171378316	3		396	588	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249315	110249315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	170	760	0	ENST00000374672.4:c.1258C>T	p.His420Tyr	p.H420Y	ENST00000374672	NM_004235.4	420	Cac/Tac	4/5	0.313734171378316	2	FACETS	1	0.969	1	0.554	0.509	0.601	CLONAL	1	TRUE	0	0.313734171378316	2		760	978	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913283	NA	P-0014511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	43	459	0	ENST00000263967.3:c.3129G>T	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atT	21/21	0.259897735122673	3	FACETS	0.387	0.322	0.459	0.193	0.161	0.23	SUBCLONAL	1	TRUE	1	0.259897735122673	3		459	967	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678626	88678626	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs751051788	NA	P-0014511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	51	328	0	ENST00000360948.2:c.910C>A	p.Pro304Thr	p.P304T	ENST00000360948	NM_001012338.2	304	Ccc/Acc	9/19	1	2	FACETS	0.654	0.555	0.763	0.654	0.555	0.763	SUBCLONAL	1	TRUE	1	0.259897735122673	2		328	600	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509915	106509915	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	165	566	0	ENST00000359195.3:c.1909G>T	p.Asp637Tyr	p.D637Y	ENST00000359195	NM_002649.2	637	Gat/Tat	2/11	0.199609669901151	3	FACETS	1	0.973	1	0.572	0.524	0.623	CLONAL	1	TRUE	1	0.259897735122673	3		566	1254	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259517	+	missense_variant	Missense_Mutation	TNP	TGG	TGG	GGT	novel	NA	P-0014511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1389	370	621	0	ENST00000275493.2:c.2573_2575delinsGGT	p.Leu858_Ala859delinsArgSer	p.L858_A859delinsRS	ENST00000275493	NM_005228.3	858	cTGGcc/cGGTcc	21/28	0.259897735122673	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	2	0.259897735122673	4		621	1759	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	64	422	0	ENST00000263967.3:c.3012G>A	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atA	21/21	1	2	FACETS	0.465	0.402	0.533	0.465	0.402	0.533	SUBCLONAL	1	TRUE	1	0.386918022734988	2		422	712	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0014515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	178	529	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.386918022734988	2		529	910	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259895	16259895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	141	512	0	ENST00000375759.3:c.7160G>A	p.Ser2387Asn	p.S2387N	ENST00000375759	NM_015001.2	2387	aGt/aAt	11/15	1	2	FACETS	0.9	0.82	0.983	0.9	0.82	0.983	CLONAL	1	TRUE	1	0.386918022734988	2		512	810	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467448	25467448	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1164367418	NA	P-0014515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	126	450	0	ENST00000264709.3:c.1628del	p.Gly543AlafsTer108	p.G543Afs*108	ENST00000264709	NM_175629.2	543	gGc/gc	14/23	1	2	FACETS	0.886	0.803	0.973	0.886	0.803	0.973	CLONAL	1	TRUE	1	0.386918022734988	2		450	735	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46714238	46714243	+	inframe_deletion	In_Frame_Del	DEL	TGTGAT	TGTGAT	-	novel	NA	P-0014524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	135	536	0	ENST00000371975.4:c.58_63del	p.Cys20_Asp21del	p.C20_D21del	ENST00000371975	NM_003579.3	20	TGTGAT/-	2/18	0.218060495764969	5	FACETS	0.759	0.688	0.833	0.506	0.459	0.555	SUBCLONAL	2	FALSE	2	0.218060495764969	5		536	1083	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202197	108202197	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0014524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	180	362	0	ENST00000278616.4:c.7542T>A	p.Tyr2514Ter	p.Y2514*	ENST00000278616	NM_000051.3	2514	taT/taA	51/63	0.218060495764969	3	FACETS	1	0.959	1	0.706	0.652	0.763	CLONAL	2	FALSE	0	0.218060495764969	3		362	864	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645681	12645681	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs397516830	NA	P-0014524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	87	235	0	ENST00000251849.4:c.788T>A	p.Val263Asp	p.V263D	ENST00000251849	NM_002880.3	263	gTc/gAc	7/17	0.218060495764969	3	FACETS	0.873	0.775	0.976	0.582	0.517	0.651	CLONAL	2	FALSE	0	0.218060495764969	3		235	507	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412046	116412046	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	G	novel	NA	P-0014524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1259	330	579	0	ENST00000397752.3:c.3028+3A>G		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.218060495764969	3	FACETS	1	0.974	1	0.704	0.664	0.746	CLONAL	2	FALSE	0	0.218060495764969	3		579	1589	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518704	204518704	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	118	263	0	ENST00000367182.3:c.1367A>G	p.His456Arg	p.H456R	ENST00000367182	NM_001278516.1	456	cAt/cGt	11/11	0.350075841642508	3	FACETS	0.945	0.852	1	0.473	0.426	0.522	CLONAL	1	FALSE	1	0.350075841642508	3		263	838	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0014559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	673	544	2	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.838411843586182	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.838411843586182	2		546	783	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0014559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	321	515	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.838411843586182	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	2	0.838411843586182	4		515	697	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937422	76937422	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	343	363	1	ENST00000373344.5:c.3326C>A	p.Ser1109Ter	p.S1109*	ENST00000373344	NM_000489.3	1109	tCa/tAa	9/35	0.487357416539711	5	FACETS	0.89	0.849	0.93	0.89	0.849	0.93	INDETERMINATE	3	TRUE	2	0.838411843586182	5		364	692	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0014562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	434	568	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.353963506441298	3	FACETS	0.841	0.803	0.879			1	CLONAL	3	TRUE	NA	0.353963506441298	3		568	1144	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295210	15295210	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1261	234	993	0	ENST00000263388.2:c.2462G>A	p.Gly821Asp	p.G821D	ENST00000263388	NM_000435.2	821	gGc/gAc	16/33	1	2	FACETS	0.884	0.823	0.949	0.884	0.823	0.949	CLONAL	1	TRUE	1	0.353963506441298	2		993	1495	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322674	39322674	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	88	543	1	ENST00000373001.3:c.318T>A	p.Asn106Lys	p.N106K	ENST00000373001	NM_022157.3	106	aaT/aaA	2/7	0.227908960403764	3	FACETS	0.504	0.445	0.567	0.252	0.222	0.284	SUBCLONAL	1	TRUE	1	0.353963506441298	3		544	1162	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111550	8111550	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1297	178	577	0	ENST00000346208.3:c.1036A>G	p.Lys346Glu	p.K346E	ENST00000346208		346	Aag/Gag	5/6	0.353963506441298	5	FACETS	1	0.949	1	0.261	0.239	0.284	CLONAL	1	TRUE	1	0.353963506441298	5		577	1475	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432154	121432154	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs555681479	NA	P-0014562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	365	617	1	ENST00000257555.6:c.901G>T	p.Ala301Ser	p.A301S	ENST00000257555		301	Gct/Tct	4/10	0.353963506441298	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.353963506441298	3		618	1201	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912885	32912885	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	257	366	0	ENST00000380152.3:c.4393G>C	p.Glu1465Gln	p.E1465Q	ENST00000380152		1465	Gaa/Caa	11/27	0.277097412202602	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.353963506441298	4		366	883	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274192	10274192	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	128	422	0	ENST00000330684.3:c.77C>A	p.Ala26Glu	p.A26E	ENST00000330684	NM_001134407.1	26	gCg/gAg	2/13	0.353963506441298	3	FACETS	0.982	0.89	1	0.491	0.445	0.54	CLONAL	1	TRUE	1	0.353963506441298	3		422	867	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556992	29556992	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1555614462	NA	P-0014562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	121	145	0	ENST00000356175.3:c.2990G>T	p.Arg997Met	p.R997M	ENST00000356175	NM_000267.3	997	aGg/aTg	22/57	0.26441818409422	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	3	TRUE	0	0.353963506441298	3		145	258	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679274	29679274	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0014562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	247	340	0	ENST00000356175.3:c.7395-1G>T		p.X2465_splice	ENST00000356175	NM_000267.3	2465			0.26441818409422	3	FACETS	0.905	0.853	0.958	0.905	0.853	0.958	CLONAL	3	TRUE	0	0.353963506441298	3		340	605	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370309	40370309	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	555	716	0	ENST00000293328.3:c.1029G>T	p.Lys343Asn	p.K343N	ENST00000293328	NM_012448.3	343	aaG/aaT	9/19	0.26441818409422	3	FACETS	0.944	0.908	0.981	0.944	0.908	0.981	CLONAL	3	TRUE	0	0.353963506441298	3		716	1303	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367939	15367939	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	197	704	0	ENST00000263377.2:c.1387G>T	p.Glu463Ter	p.E463*	ENST00000263377	NM_058243.2	463	Gag/Tag	8/20	1	2	FACETS	0.941	0.87	1	0.941	0.87	1	CLONAL	1	TRUE	1	0.353963506441298	2		704	1183	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119624685	119624685	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	283	471	0	ENST00000316626.5:c.730G>T	p.Gly244Cys	p.G244C	ENST00000316626		244	Ggc/Tgc	7/12	0.353963506441298	6	FACETS	0.894	0.838	0.952	0.447	0.419	0.476	CLONAL	2	TRUE	2	0.353963506441298	6		471	1528	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86668007	86668012	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CGTCAG	CGTCAG	-	novel	NA	P-0014562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	128	299	0	ENST00000274376.6:c.1771_1776del	p.Arg591_Gln592del	p.R591_Q592del	ENST00000274376	NM_002890.2	591	CGTCAG/-	13/25	0.353963506441298	2	FACETS	0.851	0.778	0.927	0.851	0.778	0.927	CLONAL	2	TRUE	0	0.353963506441298	2		299	425	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647499	117647499	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	225	463	0	ENST00000368508.3:c.5445C>G	p.Cys1815Trp	p.C1815W	ENST00000368508	NM_002944.2	1815	tgC/tgG	33/43	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.353963506441298	2		463	854	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263850	133263850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	118	276	0	ENST00000320574.5:c.52G>A	p.Glu18Lys	p.E18K	ENST00000320574	NM_006231.2	18	Gag/Aag	1/49	0.132095178563895	6	FACETS	1	0.954	1	0.869	0.787	0.954	CLONAL	4	TRUE	1	0.132095178563895	6		276	520	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310483	65310483	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs751933525	NA	P-0014583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	125	316	0	ENST00000342505.4:c.2205C>G	p.Ile735Met	p.I735M	ENST00000342505	NM_002227.2	735	atC/atG	16/25	0.132095178563895	11	FACETS	1	0.962	1			1	CLONAL	3	TRUE	NA	0.132095178563895	11		316	895	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0014583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	416	325	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			0.132095178563895	26	FACETS	0.996	0.947	1			1	CLONAL	11	TRUE	NA	0.132095178563895	26		325	1486	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482374	56482374	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	257	410	0	ENST00000267101.3:c.922G>C	p.Asp308His	p.D308H	ENST00000267101	NM_001982.3	308	Gac/Cac	8/28	0.127957022016598	4	FACETS	0.927	0.871	0.984	1	0.996	1	CLONAL	6	TRUE	2	0.132095178563895	4		410	792	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805413	46805413	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	70	602	0	ENST00000290295.7:c.543G>C	p.Gln181His	p.Q181H	ENST00000290295	NM_006361.5	181	caG/caC	1/2	0.132095178563895	9	FACETS	1	0.964	1	0.148	0.128	0.17	CLONAL	1	TRUE	0	0.132095178563895	9		602	1163	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725050	47725050	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	306	750	1	ENST00000449228.1:c.694del	p.Thr232ProfsTer58	p.T232Pfs*58	ENST00000449228	NM_001127240.2	232	Acc/cc	4/4	1	2	FACETS	0.96	0.907	1	1	0.997	1	CLONAL	5	TRUE	1	0.132095178563895	2		751	965	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560464	95560464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	83	705	0	ENST00000393063.1:c.5125G>A	p.Asp1709Asn	p.D1709N	ENST00000393063	NM_030621.3	1709	Gat/Aat	25/28	1	2	FACETS	0.657	0.579	0.741	0.657	0.579	0.741	SUBCLONAL	1	TRUE	1	0.3194012215404	2		705	791	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532704	46532704	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	195	467	0	ENST00000262741.5:c.374C>G	p.Ser125Cys	p.S125C	ENST00000262741	NM_003629.3	125	tCt/tGt	4/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.661618054140866	2		467	535	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846364	156846364	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	269	690	2	ENST00000524377.1:c.1805G>A	p.Arg602Gln	p.R602Q	ENST00000524377	NM_002529.3	602	cGa/cAa	14/17	0.652369764151095	3	FACETS	1	0.956	1	0.511	0.48	0.544	CLONAL	1	TRUE	1	0.661618054140866	3		692	1058	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648248	206648248	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	215	529	2	ENST00000367120.3:c.269C>G	p.Ser90Cys	p.S90C	ENST00000367120	NM_014002.3	90	tCc/tGc	5/22	0.652369764151095	3	FACETS	1	0.981	1	0.571	0.533	0.611	CLONAL	1	TRUE	1	0.661618054140866	3		531	757	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244286	5244287	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0014593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	313	899	2	ENST00000357368.4:c.1195_1196delinsTT	p.Glu399Leu	p.E399L	ENST00000357368	NM_002850.3	399	GAg/TTg	11/38	1	2	FACETS	0.973	0.92	1	0.973	0.92	1	CLONAL	1	TRUE	1	0.661618054140866	2		901	972	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015275	128015275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	265	542	0	ENST00000285398.2:c.2246C>T	p.Ser749Phe	p.S749F	ENST00000285398	NM_000122.1	749	tCt/tTt	15/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.661618054140866	2		542	777	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024342	31024342	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763784731	NA	P-0014593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	250	643	0	ENST00000375687.4:c.3827C>T	p.Ser1276Phe	p.S1276F	ENST00000375687	NM_015338.5	1276	tCt/tTt	13/13	0.652369764151095	3	FACETS	1	0.949	1	0.508	0.475	0.542	CLONAL	1	TRUE	1	0.661618054140866	3		643	990	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146649	185146649	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1447	264	668	0	ENST00000265026.3:c.280G>C	p.Glu94Gln	p.E94Q	ENST00000265026	NM_004721.4	94	Gag/Cag	2/14	0.661618054140866	5	FACETS	0.929	0.868	0.993	0.232	0.217	0.249	CLONAL	1	TRUE	1	0.661618054140866	5		668	1711	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144080	55144080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	201	649	0	ENST00000257290.5:c.1909G>A	p.Glu637Lys	p.E637K	ENST00000257290	NM_006206.4	637	Gaa/Aaa	14/23	1	2	FACETS	0.807	0.75	0.866	0.807	0.75	0.866	CLONAL	1	TRUE	1	0.661618054140866	2		649	753	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891214	151891214	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0014593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	233	587	0	ENST00000262189.6:c.4541-1G>C		p.X1514_splice	ENST00000262189	NM_170606.2	1514			1	2	FACETS	0.944	0.884	1	0.944	0.884	1	CLONAL	1	TRUE	1	0.661618054140866	2		587	746	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151948040	151948040	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	166	479	0	ENST00000262189.6:c.1633G>T	p.Glu545Ter	p.E545*	ENST00000262189	NM_170606.2	545	Gaa/Taa	12/59	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.661618054140866	2		479	496	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137325969	137325969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1318249611	NA	P-0014593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	284	765	1	ENST00000481739.1:c.1157C>T	p.Pro386Leu	p.P386L	ENST00000481739	NM_002957.4	386	cCg/cTg	9/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.661618054140866	2		766	806	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	99	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.889	0.796	0.988	0.889	0.796	0.988	CLONAL	1	TRUE	1	0.391389608717606	2		371	569	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226132	2226132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	309	1216	1	ENST00000326181.6:c.1829C>T	p.Thr610Met	p.T610M	ENST00000326181	NM_032271.2	610	aCg/aTg	19/21	0.2380317503433	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.391389608717606	2		1217	742	SUCCESS
APC	324	MSKCC	GRCh37	5	112174058	112174058	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0014596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	37	589	0	ENST00000257430.4:c.2767A>T	p.Arg923Ter	p.R923*	ENST00000257430	NM_000038.5	923	Aga/Tga	16/16	0.2380317503433	2	FACETS	0.475	0.392	0.568	0.238	0.196	0.284	SUBCLONAL	1	TRUE	0	0.391389608717606	2		589	398	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259061	16259061	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	74	909	0	ENST00000375759.3:c.6326C>A	p.Ala2109Glu	p.A2109E	ENST00000375759	NM_015001.2	2109	gCa/gAa	11/15	0.215910334773666	1	FACETS	0.646	0.567	0.73	0.646	0.567	0.73	INDETERMINATE	1	TRUE	0	0.391389608717606	1		909	471	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346357	89346357	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751378641	NA	P-0014596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	53	596	3	ENST00000301030.4:c.6593G>A	p.Arg2198Gln	p.R2198Q	ENST00000301030	NM_001256183.1	2198	cGg/cAg	9/13	0.224908656278389	2	FACETS	0.705	0.603	0.816	0.353	0.301	0.408	INDETERMINATE	1	TRUE	0	0.391389608717606	2		599	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572927	7572927	+	stop_lost	Nonstop_Mutation	SNP	T	T	C	novel	NA	P-0014596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	112	746	0	ENST00000269305.4:c.1182A>G	p.Ter394TrpextTer9	p.*394Wext*9	ENST00000269305	NM_001126112.2	394	tgA/tgG	11/11	0.391389608717606	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.391389608717606	1		746	435	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37059058	37059058	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	60	1118	0	ENST00000231790.2:c.852G>T	p.Leu284Phe	p.L284F	ENST00000231790	NM_000249.3	284	ttG/ttT	10/19	0.215910334773666	1	FACETS	0.406	0.349	0.467	0.406	0.349	0.467	INDETERMINATE	1	TRUE	0	0.391389608717606	1		1118	608	SUCCESS
APC	324	MSKCC	GRCh37	5	112175628	112175634	+	frameshift_variant	Frame_Shift_Del	DEL	CTCAAAC	CTCAAAC	-	novel	NA	P-0014596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	159	761	0	ENST00000257430.4:c.4338_4344del	p.Gln1447SerfsTer24	p.Q1447Sfs*24	ENST00000257430	NM_000038.5	1446	gCTCAAACc/gc	16/16	0.2380317503433	2	FACETS	1	0.989	1	0.735	0.677	0.794	CLONAL	1	TRUE	0	0.391389608717606	2		761	553	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843306	128843306	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752289293	NA	P-0014596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	93	1328	1	ENST00000249373.3:c.413G>A	p.Arg138Gln	p.R138Q	ENST00000249373	NM_005631.4	138	cGg/cAg	2/12	1	2	FACETS	0.605	0.538	0.678	0.605	0.538	0.678	SUBCLONAL	1	TRUE	1	0.391389608717606	2		1329	785	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0014597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	170	874	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	0.31	2		874	983	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102918	71102918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148369068	NA	P-0014597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	32	317	0	ENST00000318789.4:c.289G>A	p.Val97Met	p.V97M	ENST00000318789	NM_032682.5	97	Gtg/Atg	8/21	1	2	FACETS	0.471	0.382	0.572	0.471	0.382	0.572	SUBCLONAL	1	TRUE	1	0.31	2		317	438	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589623	67589634	+	inframe_deletion	In_Frame_Del	DEL	ATATGATAGATT	ATATGATAGATT	-	novel	NA	P-0014598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	96	403	0	ENST00000274335.5:c.1392_1403del	p.Asp464_Tyr467del	p.D464_Y467del	ENST00000274335		462	gaATATGATAGATTa/gaa	10/15	1	2	FACETS	0.809	0.727	0.895	0.809	0.727	0.895	CLONAL	1	TRUE	1	0.644554272318911	2		403	368	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426061	49426061	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	300	748	0	ENST00000301067.7:c.12427del	p.Asp4143IlefsTer6	p.D4143Ifs*6	ENST00000301067	NM_003482.3	4143	Gat/at	39/54	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.644554272318911	2		748	918	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830841	3830841	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	249	648	0	ENST00000262367.5:c.1715G>T	p.Gly572Val	p.G572V	ENST00000262367	NM_004380.2	572	gGa/gTa	8/31	1	2	FACETS	0.918	0.86	0.976	0.918	0.86	0.976	CLONAL	1	TRUE	1	0.644554272318911	2		648	842	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	168	589	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.573828158608066	2		590	578	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	221	537	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.573828158608066	3	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	1	0.573828158608066	3		537	494	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096025	11096025	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	281	878	1	ENST00000358026.2:c.299C>T	p.Ser100Leu	p.S100L	ENST00000358026	NM_001128849.1	100	tCa/tTa	3/36	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.573828158608066	2		879	941	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96930984	96930984	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs144659242	NA	P-0014600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	683	643	0	ENST00000258439.3:c.136A>G	p.Thr46Ala	p.T46A	ENST00000258439	NM_001193304.2	46	Act/Gct	2/4	0.381403377884363	5	FACETS	0.93	0.907	0.952	1	0.998	1	CLONAL	5	TRUE	2	0.573828158608066	5		643	953	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016226	31016226	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0014600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	200	320	0	ENST00000375687.4:c.471+1G>A		p.X157_splice	ENST00000375687	NM_015338.5	157			0.461800070764826	4	FACETS	0.987	0.921	1	0.987	0.921	1	CLONAL	2	TRUE	2	0.573828158608066	4		320	556	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891142	101891142	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	140	284	0	ENST00000374994.4:c.103C>T	p.Gln35Ter	p.Q35*	ENST00000374994	NM_004612.2	35	Cag/Tag	2/9	0.573828158608066	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.573828158608066	2		284	226	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579353	7579366	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CCAGACGGAAACCG	CCAGACGGAAACCG	-	novel	NA	P-0014624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	486	676	0	ENST00000269305.4:c.321_334del	p.Tyr107Ter	p.Y107*	ENST00000269305	NM_001126112.2	107	taCGGTTTCCGTCTGGgc/tagc	4/11	0.434517028160305	3	FACETS	0.894	0.859	0.929	0.894	0.859	0.929	CLONAL	3	TRUE	0	0.434517028160305	3		676	1015	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655159	45655159	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	82	312	0	ENST00000407780.3:c.693G>C	p.Gln231His	p.Q231H	ENST00000407780	NM_001283052.1	231	caG/caC	4/7	0.434517028160305	4	FACETS	0.755	0.666	0.851	0.252	0.222	0.284	SUBCLONAL	1	TRUE	1	0.434517028160305	4		312	717	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195279	102195279	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	127	396	0	ENST00000263464.3:c.39G>C	p.Leu13Phe	p.L13F	ENST00000263464	NM_001165.4	13	ttG/ttC	2/9	0.404694980906506	4	FACETS	1	0.928	1	0.343	0.31	0.377	CLONAL	1	TRUE	1	0.434517028160305	4		396	815	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0014626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	402	859	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.517027254278878	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.517027254278878	1		860	1107	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244052	46244065	+	frameshift_variant	Frame_Shift_Del	DEL	GCTACAGTTATCCA	GCTACAGTTATCCA	-	novel	NA	P-0014626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	67	571	1	ENST00000334344.6:c.2147_2160del	p.Ala716GlufsTer11	p.A716Efs*11	ENST00000334344	NM_152641.2	716	GCTACAGTTATCCAg/g	15/21	0.517027254278878	1	FACETS	0.215	0.186	0.246	0.215	0.186	0.246	SUBCLONAL	1	TRUE	0	0.517027254278878	1		572	895	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920265	50920304	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGGCCCCAGCACTTGGGCTGACCCGCCTCCCCACAGGAG	TGGGCCCCAGCACTTGGGCTGACCCGCCTCCCCACAGGAG	CAGGAA	novel	NA	P-0014626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1355	170	762	3	ENST00000440232.2:c.3068-37_3070delinsCAGGAA		p.X1023_splice	ENST00000440232	NM_002691.3	1023		25/27	1	2	FACETS	0.431	0.395	0.469	0.431	0.395	0.469	SUBCLONAL	1	TRUE	1	0.517027254278878	2		765	1525	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866322	42866322	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs754904901	NA	P-0014626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	404	714	0	ENST00000398585.3:c.310A>G	p.Thr104Ala	p.T104A	ENST00000398585	NM_001135099.1	104	Acg/Gcg	3/14	0.517027254278878	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.517027254278878	1		714	955	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143033831	143033831	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374855118	NA	P-0014626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	159	354	0	ENST00000262992.4:c.2140C>T	p.His714Tyr	p.H714Y	ENST00000262992	NM_001101669.1	714	Cat/Tat	20/24	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.517027254278878	2		354	522	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508809	106508809	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1499	97	567	0	ENST00000359195.3:c.803A>G	p.Gln268Arg	p.Q268R	ENST00000359195	NM_002649.2	268	cAg/cGg	2/11	0.517027254278878	4	FACETS	0.357	0.316	0.4	0.119	0.105	0.134	SUBCLONAL	1	TRUE	1	0.517027254278878	4		567	1596	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591125	67591267	+	splice_donor_variant,splice_acceptor_variant,stop_lost,protein_altering_variant,intron_variant	Splice_Site	DEL	TGAGAAAGACGAGAGACCAATACTTGATGTAAGTATTTGAAATGGAATCCTATACATGAATAATTGGTGATTGCTACAATTCAGGATGAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGGTTGACTCAAAAAGGTG	TGAGAAAGACGAGAGACCAATACTTGATGTAAGTATTTGAAATGGAATCCTATACATGAATAATTGGTGATTGCTACAATTCAGGATGAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGGTTGACTCAAAAAGGTG	-	novel	NA	P-0014628-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	114	280	0	ENST00000274335.5:c.1719_1766del		p.X573_splice	ENST00000274335		573	cTGAGAAAGACGAGAGACCAATACTTGATGTAAGTATTTGAAATGGAATCCTATACATGAATAATTGGTGATTGCTACAATTCAGGATGAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGGTTGACTCAAAAAGGTGtt/ctt	12-13/15	0.425494060462843	7	FACETS	1	0.928	1	1	0.928	1	CLONAL	5	FALSE	2	0.425494060462843	7		280	220	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467794	99467794	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014628-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	27	368	0	ENST00000268035.6:c.2663A>T	p.Tyr888Phe	p.Y888F	ENST00000268035	NM_000875.3	888	tAt/tTt	13/21	0.425494060462843	7	FACETS	0.779	0.626	0.951	0.39	0.313	0.476	CLONAL	2	FALSE	3	0.425494060462843	7		368	168	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019455	31019455	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	149	354	0	ENST00000375687.4:c.952C>A	p.Gln318Lys	p.Q318K	ENST00000375687	NM_015338.5	318	Cag/Aag	10/13	0.574337669943747	3	FACETS	1	0.958	1	0.536	0.491	0.582	CLONAL	1	TRUE	1	0.574337669943747	3		354	623	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	47	420	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.76	0.644	0.888	0.76	0.644	0.888	SUBCLONAL	1	TRUE	1	0.341475627205479	2		420	362	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0014635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	57	612	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.15742788678713	2	FACETS	1	0.916	1	0.542	0.468	0.621	INDETERMINATE	1	TRUE	0	0.341475627205479	2		613	308	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361160	70361160	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs79912241	NA	P-0014635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	29	415	0	ENST00000374080.3:c.6348C>A	p.His2116Gln	p.H2116Q	ENST00000374080		2116	caC/caA	43/45	1	1	FACETS	0.634	0.512	0.772	0.634	0.512	0.772	SUBCLONAL	1	TRUE	0	0.341475627205479	1		415	222	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764328	39764328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747584221	NA	P-0014635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	41	778	1	ENST00000288319.7:c.784G>A	p.Gly262Ser	p.G262S	ENST00000288319	NM_182918.3	262	Ggt/Agt	7/10	0.286975095579807	1	FACETS	0.63	0.527	0.744	0.63	0.527	0.744	SUBCLONAL	1	TRUE	0	0.341475627205479	1		779	316	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	87	589	1				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.87	0.775	0.97			1	INDETERMINATE	1	TRUE	NA	0.496403979965233	2		590	403	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562675	29562679	+	frameshift_variant	Frame_Shift_Del	DEL	TACTC	TACTC	-	novel	NA	P-0014644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	167	573	0	ENST00000356175.3:c.3758_3762del	p.Leu1253ProfsTer9	p.L1253Pfs*9	ENST00000356175	NM_000267.3	1252	tTACTC/t	28/57	0.496403979965233	1	FACETS	0.812	0.749	0.877	0.812	0.749	0.877	CLONAL	1	TRUE	0	0.496403979965233	1		573	623	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103717	47103717	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1205330893	NA	P-0014644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	106	526	1	ENST00000409792.3:c.6229C>T	p.Arg2077Ter	p.R2077*	ENST00000409792	NM_014159.6	2077	Cga/Tga	14/21	0.444669171657776	1	FACETS	0.604	0.543	0.667	0.604	0.543	0.667	SUBCLONAL	1	TRUE	0	0.496403979965233	1		527	532	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491671	120491671	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	175	432	0	ENST00000256646.2:c.2558del	p.Asn853IlefsTer31	p.N853Ifs*31	ENST00000256646	NM_024408.3	853	aAt/at	16/34	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.496403979965233	2		432	672	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692847	89692847	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	74	244	1	ENST00000371953.3:c.331T>A	p.Trp111Arg	p.W111R	ENST00000371953	NM_000314.4	111	Tgg/Agg	5/9	0.496403979965233	1	FACETS	0.979	0.87	1	0.979	0.87	1	CLONAL	1	TRUE	0	0.496403979965233	1		245	229	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845397	42845397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762854045	NA	P-0014644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	181	727	0	ENST00000398585.3:c.865C>T	p.Arg289Cys	p.R289C	ENST00000398585	NM_001135099.1	289	Cgc/Tgc	9/14	1	2	FACETS	0.975	0.901	1	0.975	0.901	1	CLONAL	1	TRUE	1	0.496403979965233	2		727	748	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936356	49936356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148258933	NA	P-0014644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	192	721	2	ENST00000296474.3:c.1492G>A	p.Val498Met	p.V498M	ENST00000296474	NM_002447.2	498	Gtg/Atg	3/20	0.444669171657776	1	FACETS	0.974	0.906	1	0.974	0.906	1	CLONAL	1	TRUE	0	0.496403979965233	1		723	597	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549418	5549418	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	115	785	1	ENST00000397747.3:c.445C>A	p.Pro149Thr	p.P149T	ENST00000397747	NM_025239.3	149	Cct/Act	4/7	1	2	FACETS	0.45	0.405	0.499	0.45	0.405	0.499	SUBCLONAL	1	TRUE	1	0.496403979965233	2		786	1029	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	69	589	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.829	0.722	0.946	0.829	0.722	0.946	CLONAL	1	TRUE	1	0.24984722224217	2		590	666	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915455	112915455	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121918463	NA	P-0014677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	60	520	0	ENST00000351677.2:c.854T>C	p.Phe285Ser	p.F285S	ENST00000351677	NM_002834.3	285	tTt/tCt	8/16	1	2	FACETS	0.951	0.82	1	0.951	0.82	1	CLONAL	1	TRUE	1	0.24984722224217	2		520	505	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254304	133254304	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	40	376	0	ENST00000320574.5:c.580G>A	p.Val194Ile	p.V194I	ENST00000320574	NM_006231.2	194	Gtt/Att	7/49	1	2	FACETS	0.729	0.606	0.866	0.729	0.606	0.866	SUBCLONAL	1	TRUE	1	0.24984722224217	2		376	439	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242111	105242111	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1038322721	NA	P-0014679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	318	717	0	ENST00000349310.3:c.313A>G	p.Thr105Ala	p.T105A	ENST00000349310	NM_001014432.1	105	Act/Gct	6/15	1	2	FACETS	0.92	0.873	0.968	0.92	0.873	0.968	CLONAL	1	TRUE	1	0.879607940970401	2		717	786	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089816	5089816	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	218	517	1	ENST00000381652.3:c.2714T>G	p.Leu905Arg	p.L905R	ENST00000381652	NM_004972.3	905	cTa/cGa	20/25	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.879607940970401	2		518	469	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524477	187524477	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	120	632	1	ENST00000441802.2:c.11203C>T	p.Gln3735Ter	p.Q3735*	ENST00000441802	NM_005245.3	3735	Cag/Tag	19/27	0.558597170093496	5	FACETS	0.906	0.817	0.999			1	CLONAL	1	TRUE	NA	0.558597170093496	5		633	872	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0014683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	231	511	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	0.369143333337543	2	FACETS	1	0.989	1	0.613	0.577	0.649	INDETERMINATE	1	TRUE	0	0.712443131006177	2		511	529	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045789	26045789	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	50	327	0	ENST00000540144.1:c.151G>A	p.Glu51Lys	p.E51K	ENST00000540144	NM_003531.2	51	Gaa/Aaa	1/1	0.121628249112774	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.712443131006177	0		327	413	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0014687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	22	452	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.506	0.39	0.641	0.506	0.39	0.641	SUBCLONAL	1	TRUE	1	0.15	2		452	580	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161293439	161293439	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	53	423	0	ENST00000367975.2:c.56G>T	p.Ser19Ile	p.S19I	ENST00000367975	NM_003001.3	19	aGc/aTc	2/6	1	2	FACETS	0.988	0.841	1	0.988	0.841	1	CLONAL	1	TRUE	1	0.15	2		423	715	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	75	420	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.921	0.807	1	0.921	0.807	1	CLONAL	1	FALSE	1	0.246746642215627	2		420	660	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0014690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	142	693	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.246746642215627	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	0	0.246746642215627	1		693	813	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436140	56436140	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	121	752	0	ENST00000407977.2:c.997del	p.Gln333LysfsTer86	p.Q333Kfs*86	ENST00000407977		333	Caa/aa	9/10	0.246746642215627	1	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	FALSE	0	0.246746642215627	1		752	860	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589552	67589552	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	28	278	0	ENST00000274335.5:c.1315G>T	p.Glu439Ter	p.E439*	ENST00000274335		439	Gaa/Taa	10/15	1	2	FACETS	0.966	0.776	1	0.966	0.776	1	CLONAL	1	FALSE	1	0.246746642215627	2		278	235	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0014706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	249	582	1	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.304185391928486	2	FACETS	0.957	0.898	1	0.957	0.898	1	CLONAL	2	TRUE	0	0.304185391928486	2		583	855	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	251	587	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	NA	2	FACETS	1	0.953	1			1	INDETERMINATE	2	TRUE	NA	0.304185391928486	2		587	811	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481787	40481787	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	71	466	0	ENST00000264657.5:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000264657	NM_139276.2	373	Ggg/Agg	12/24	0.284203856359003	3	FACETS	0.87	0.76	0.99	0.435	0.38	0.495	CLONAL	1	TRUE	1	0.304185391928486	3		466	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0014707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	295	571	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.257823269639478	3	FACETS	1	0.991	1	0.812	0.768	0.856	CLONAL	2	TRUE	0	0.376867876570857	3		571	764	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444690	49444690	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	93	879	0	ENST00000301067.7:c.2776T>A	p.Ser926Thr	p.S926T	ENST00000301067	NM_003482.3	926	Tcg/Acg	10/54	0.257823269639478	3	FACETS	0.792	0.704	0.885	0.264	0.234	0.295	SUBCLONAL	1	TRUE	0	0.376867876570857	3		879	741	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293103	91293103	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	40	505	0	ENST00000355112.3:c.605A>G	p.Asn202Ser	p.N202S	ENST00000355112	NM_000057.2	202	aAc/aGc	3/22	0.376867876570857	6	FACETS	1	0.89	1	0.273	0.227	0.324	CLONAL	1	TRUE	2	0.376867876570857	6		505	341	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271760	15271776	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	GTGCCCCAGCCGCCGGG	GTGCCCCAGCCGCCGGG	-	novel	NA	P-0014707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	247	916	0	ENST00000263388.2:c.6663_6679del	p.Tyr2221Ter	p.Y2221*	ENST00000263388	NM_000435.2	2221	taCCCGGCGGCTGGGGCACac/taac	33/33	0.376867876570857	3	FACETS	0.888	0.832	0.946	0.888	0.832	0.946	CLONAL	2	TRUE	1	0.376867876570857	3		916	877	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375362	15375362	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	46	600	0	ENST00000263377.2:c.1065G>C	p.Lys355Asn	p.K355N	ENST00000263377	NM_058243.2	355	aaG/aaC	6/20	0.376867876570857	3	FACETS	0.364	0.306	0.43	0.182	0.153	0.215	SUBCLONAL	1	TRUE	1	0.376867876570857	3		600	796	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191446	185191446	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	105	796	0	ENST00000265026.3:c.2327C>G	p.Thr776Arg	p.T776R	ENST00000265026	NM_004721.4	776	aCg/aGg	11/14	0.320376813098739	3	FACETS	0.943	0.846	1	0.314	0.282	0.349	CLONAL	1	TRUE	0	0.376867876570857	3		796	702	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050701	5050701	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	28	398	0	ENST00000381652.3:c.484G>T	p.Val162Leu	p.V162L	ENST00000381652	NM_004972.3	162	Gtg/Ttg	6/25	1	2	FACETS	0.935	0.756	1	0.935	0.756	1	CLONAL	1	TRUE	1	0.376867876570857	2		398	159	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97869366	97869376	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGATCGTGT	GGCGATCGTGT	-	novel	NA	P-0014707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	90	559	0	ENST00000289081.3:c.1505_1515del	p.His502LeufsTer12	p.H502Lfs*12	ENST00000289081	NM_000136.2	502	cACACGATCGCC/c	14/15	0.296001001956111	4	FACETS	0.905	0.802	1	0.452	0.401	0.507	CLONAL	1	TRUE	2	0.376867876570857	4		559	727	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760916	133760916	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	92	862	1	ENST00000318560.5:c.3239A>G	p.Lys1080Arg	p.K1080R	ENST00000318560	NM_005157.4	1080	aAg/aGg	11/11	0.296001001956111	4	FACETS	0.766	0.679	0.858	0.383	0.339	0.429	SUBCLONAL	1	TRUE	2	0.376867876570857	4		863	878	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0014716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	237	357	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.906	0.85	0.963	0.906	0.85	0.963	CLONAL	1	TRUE	1	0.743295584955675	2		357	704	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101710	71101712	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	rs781038123	NA	P-0014716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	126	281	0	ENST00000318789.4:c.486_488del	p.Gln162del	p.Q162del	ENST00000318789	NM_032682.5	162	caACAt/cat	9/21	1	2	FACETS	0.909	0.832	0.988	0.909	0.832	0.988	CLONAL	1	TRUE	1	0.743295584955675	2		281	373	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74868265	74868265	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	378	783	0	ENST00000284811.8:c.29G>C	p.Gly10Ala	p.G10A	ENST00000284811		10	gGc/gCc	3/4	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.743295584955675	2		783	967	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0014724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	1062	452	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.639674231553662	6	FACETS	0.965	0.944	0.985	0.965	0.944	0.985	CLONAL	5	TRUE	1	0.639674231553662	6		452	1569	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11308139	11308139	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	216	423	0	ENST00000361445.4:c.853G>C	p.Glu285Gln	p.E285Q	ENST00000361445	NM_004958.3	285	Gaa/Caa	7/58	0.639674231553662	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.639674231553662	1		423	411	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129803	108129803	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0014724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	155	292	0	ENST00000278616.4:c.2466+1G>T		p.X822_splice	ENST00000278616	NM_000051.3	822			0.639674231553662	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.639674231553662	1		292	319	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1273199332	NA	P-0014724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	303	557	0	ENST00000534358.1:c.2312C>A	p.Thr771Asn	p.T771N	ENST00000534358	NM_005933.3	771	aCc/aAc	3/36	0.639674231553662	1	FACETS	0.973	0.925	1	0.973	0.925	1	CLONAL	1	TRUE	0	0.639674231553662	1		557	662	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061433	38061433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	131	485	2	ENST00000250448.2:c.556G>A	p.Ala186Thr	p.A186T	ENST00000250448	NM_004496.3	186	Gcg/Acg	2/2	0.502234711611063	4	FACETS	0.729	0.661	0.801	0.182	0.165	0.201	SUBCLONAL	1	TRUE	0	0.639674231553662	4		487	921	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042205	42042205	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	234	554	2	ENST00000219905.7:c.6402del	p.Phe2134LeufsTer45	p.F2134Lfs*45	ENST00000219905	NM_001164273.1	2134	Ttt/tt	17/24	0.639674231553662	1	FACETS	0.95	0.895	1	0.95	0.895	1	CLONAL	1	TRUE	0	0.639674231553662	1		556	524	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943743	9943743	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766743064	NA	P-0014724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	243	523	0	ENST00000330684.3:c.1198G>A	p.Glu400Lys	p.E400K	ENST00000330684	NM_001134407.1	400	Gag/Aag	5/13	1	2	FACETS	0.935	0.876	0.995	0.935	0.876	0.995	CLONAL	1	TRUE	1	0.639674231553662	2		523	813	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0014771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	174	705	1	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	0.198318750269905	2	FACETS	1	0.969	1	0.554	0.509	0.601	CLONAL	1	TRUE	0	0.255795236712723	2		706	1228	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602289	10602290	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0014771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	74	655	3	ENST00000171111.5:c.1288_1289delinsTT	p.Gly430Phe	p.G430F	ENST00000171111	NM_203500.1	430	GGc/TTc	3/6	0.192292277878359	1	FACETS	0.528	0.461	0.601	0.528	0.461	0.601	SUBCLONAL	1	TRUE	0	0.255795236712723	1		658	955	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686239	117686239	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	44	275	0	ENST00000368508.3:c.3102del	p.Arg1035GlufsTer45	p.R1035Efs*45	ENST00000368508	NM_002944.2	1034	ctT/ct	20/43	0.192292277878359	1	FACETS	0.607	0.509	0.716	0.607	0.509	0.716	SUBCLONAL	1	TRUE	0	0.255795236712723	1		275	494	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341089	8341089	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0014771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	45	447	0	ENST00000356435.5:c.5126+1G>T		p.X1709_splice	ENST00000356435		1709			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.255795236712723	NA		447	601	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	114	420	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.186910267776437	3	FACETS	0.906	0.816	1	0.906	0.816	1	CLONAL	2	TRUE	1	0.19176411526637	3		420	719	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0014788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	63	269	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.19176411526637	2	FACETS	0.815	0.708	0.931	0.815	0.708	0.931	CLONAL	2	TRUE	0	0.19176411526637	2		269	403	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	162	552	0	ENST00000322088.6:c.767C>A	p.Ser256Tyr	p.S256Y	ENST00000322088	NM_014225.5	256	tCc/tAc	6/15	0.19176411526637	3	FACETS	0.943	0.864	1	0.943	0.864	1	CLONAL	2	TRUE	1	0.19176411526637	3		552	982	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100835	27100845	+	frameshift_variant	Frame_Shift_Del	DEL	ATGGATGGCAC	ATGGATGGCAC	-	novel	NA	P-0014788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	93	443	0	ENST00000324856.7:c.4119_4129del	p.Met1373IlefsTer68	p.M1373Ifs*68	ENST00000324856	NM_006015.4	1373	ATGGATGGCACa/a	18/20	0.186910267776437	3	FACETS	0.752	0.668	0.84	0.752	0.668	0.84	SUBCLONAL	2	TRUE	1	0.19176411526637	3		443	707	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0014788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	115	534	0	ENST00000269305.4:c.97-1G>C		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.179987486704453	2	FACETS	0.891	0.804	0.983	0.891	0.804	0.983	CLONAL	2	TRUE	0	0.19176411526637	2		534	673	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609153	46609153	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1215671249	NA	P-0014788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	72	686	0	ENST00000263734.3:c.2212A>C	p.Lys738Gln	p.K738Q	ENST00000263734	NM_001430.4	738	Aaa/Caa	14/16	0.186910267776437	3	FACETS	0.785	0.684	0.895	0.393	0.342	0.448	SUBCLONAL	1	TRUE	1	0.19176411526637	3		686	1048	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	154	395	0	ENST00000263967.3:c.3127A>C	p.Met1043Leu	p.M1043L	ENST00000263967	NM_006218.2	1043	Atg/Ctg	21/21	0.178110352018151	4	FACETS	0.897	0.823	0.975	1	0.985	1	CLONAL	3	TRUE	2	0.19176411526637	4		395	711	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	124	371	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.16	2		371	1158	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	38	537	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.559	0.461	0.671	0.559	0.461	0.671	SUBCLONAL	1	TRUE	1	0.16	2		537	849	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0014797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	71	572	1	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.16	2		573	854	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534285	534285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894226	NA	P-0014797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	31	653	1	ENST00000451590.1:c.38G>T	p.Gly13Val	p.G13V	ENST00000451590	NM_001130442.1	13	gGt/gTt	2/5	1	2	FACETS	0.443	0.356	0.542	0.443	0.356	0.542	SUBCLONAL	1	TRUE	1	0.16	2		654	875	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236087	108236087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781894	NA	P-0014797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	36	569	0	ENST00000278616.4:c.9023G>A	p.Arg3008His	p.R3008H	ENST00000278616	NM_000051.3	3008	cGt/cAt	63/63	1	2	FACETS	0.45	0.368	0.542	0.45	0.368	0.542	SUBCLONAL	1	TRUE	1	0.16	2		569	1001	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0014805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1197	68	452	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.448	0.388	0.513	0.448	0.388	0.513	SUBCLONAL	1	TRUE	1	0.24	2		452	1265	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0014805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	63	342	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.52	0.448	0.599	0.52	0.448	0.599	SUBCLONAL	1	TRUE	1	0.24	2		342	1009	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378564	25378564	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	58	480	0	ENST00000311936.3:c.434C>A	p.Ser145Ter	p.S145*	ENST00000311936	NM_004985.3	145	tCa/tAa	4/5	1	2	FACETS	0.468	0.4	0.542	0.468	0.4	0.542	SUBCLONAL	1	TRUE	1	0.24	2		480	1033	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55130004	55130004	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	75	685	0	ENST00000257290.5:c.538G>A	p.Gly180Arg	p.G180R	ENST00000257290	NM_006206.4	180	Ggg/Agg	4/23	1	2	FACETS	0.505	0.441	0.575	0.505	0.441	0.575	SUBCLONAL	1	TRUE	1	0.24	2		685	1238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0014806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	89	533	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	1	2	FACETS	0.866	0.768	0.971	0.866	0.768	0.971	CLONAL	1	FALSE	1	0.279251240078543	2		533	736	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21639513	21639513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150306543	NA	P-0014806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	43	360	1	ENST00000421138.2:c.401C>T	p.Thr134Ile	p.T134I	ENST00000421138		134	aCa/aTa	6/16	0.175873939725932	4	FACETS	0.683	0.571	0.807	0.341	0.285	0.404	SUBCLONAL	1	FALSE	2	0.279251240078543	4		361	577	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039504	49039504	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	54	483	0	ENST00000267163.4:c.2489G>A	p.Arg830Lys	p.R830K	ENST00000267163	NM_000321.2	830	aGa/aAa	23/27	0.109753729055009	4	FACETS	0.671	0.572	0.78	0.336	0.286	0.39	INDETERMINATE	1	FALSE	2	0.279251240078543	4		483	737	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267449	7267449	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868743082	NA	P-0014806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	64	493	0	ENST00000302850.5:c.559C>T	p.Pro187Ser	p.P187S	ENST00000302850	NM_000208.2	187	Ccg/Tcg	2/22	1	2	FACETS	0.691	0.598	0.793	0.691	0.598	0.793	SUBCLONAL	1	FALSE	1	0.279251240078543	2		493	663	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082471	16082471	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	61	740	0	ENST00000281043.3:c.285C>A	p.Asp95Glu	p.D95E	ENST00000281043	NM_005378.4	95	gaC/gaA	2/3	1	2	FACETS	0.782	0.674	0.898	0.782	0.674	0.898	SUBCLONAL	1	FALSE	1	0.279251240078543	2		740	559	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180996	32180996	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	52	663	0	ENST00000375023.3:c.2354G>T	p.Arg785Met	p.R785M	ENST00000375023	NM_004557.3	785	aGg/aTg	15/30	NA	2	FACETS	0.544	0.463	0.635			1	INDETERMINATE	1	FALSE	NA	0.279251240078543	2		663	684	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115853	8115854	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0014843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	100	552	0	ENST00000346208.3:c.1200_1201del	p.Met400IlefsTer106	p.M400Ifs*106	ENST00000346208		400	aTG/a	6/6	1	2	FACETS	0.561	0.501	0.626	0.561	0.501	0.626	SUBCLONAL	1	TRUE	1	0.387216859928325	2		552	920	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578480	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0014843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	213	719	1	ENST00000269305.4:c.450_451del	p.Pro152AlafsTer28	p.P152Afs*28	ENST00000269305	NM_001126112.2	150	acACcc/accc	5/11	0.36751432147467	1	FACETS	0.837	0.777	0.899	0.837	0.777	0.899	CLONAL	1	TRUE	0	0.387216859928325	1		720	1060	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954211	48954211	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	198	393	0	ENST00000267163.4:c.1415del	p.Asn472IlefsTer6	p.N472Ifs*6	ENST00000267163	NM_000321.2	471	cAa/ca	15/27	0.737319478088765	2	FACETS	0.819	0.775	0.862	0.819	0.775	0.862	CLONAL	2	TRUE	0	0.737319478088765	2		393	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577112	7577112	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1131691029	NA	P-0014844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	508	914	0	ENST00000269305.4:c.826G>C	p.Ala276Pro	p.A276P	ENST00000269305	NM_001126112.2	276	Gcc/Ccc	8/11	0.737319478088765	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.737319478088765	2		914	649	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166475	118166475	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	121	530	0	ENST00000369448.3:c.985A>G	p.Thr329Ala	p.T329A	ENST00000369448	NM_017709.3	329	Act/Gct	2/2	0.436836307176369	1	FACETS	0.846	0.781	0.911	0.846	0.781	0.911	INDETERMINATE	1	TRUE	0	0.737319478088765	1		530	245	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786651	3786651	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	455	677	0	ENST00000262367.5:c.4560G>T	p.Lys1520Asn	p.K1520N	ENST00000262367	NM_004380.2	1520	aaG/aaT	27/31	0.737319478088765	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.737319478088765	2		677	543	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948196	55948196	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs971421002	NA	P-0014844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	102	711	0	ENST00000263923.4:c.3775G>C	p.Asp1259His	p.D1259H	ENST00000263923	NM_002253.2	1259	Gac/Cac	29/30	0.26712346924197	5	FACETS	0.835	0.747	0.928			1	INDETERMINATE	1	TRUE	NA	0.737319478088765	5		711	698	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99802257	99802257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	61	367	0	ENST00000280892.6:c.636G>C	p.Lys212Asn	p.K212N	ENST00000280892	NM_001130678.1	212	aaG/aaC	7/7	0.737319478088765	2	FACETS	0.687	0.599	0.779	0.343	0.299	0.39	SUBCLONAL	1	TRUE	0	0.737319478088765	2		367	241	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922935	44922935	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	100	392	0	ENST00000377967.4:c.1796C>A	p.Thr599Lys	p.T599K	ENST00000377967	NM_021140.2	599	aCa/aAa	16/29	0.737319478088765	2	FACETS	0.595	0.534	0.659			1	SUBCLONAL	1	TRUE	NA	0.737319478088765	2		392	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0014848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	563	571	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.756325169155727	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.756325169155727	1		571	853	SUCCESS
APC	324	MSKCC	GRCh37	5	112175651	112175651	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	447	363	0	ENST00000257430.4:c.4364del	p.Asn1455IlefsTer18	p.N1455Ifs*18	ENST00000257430	NM_000038.5	1454	Aaa/aa	16/16	0.756325169155727	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.756325169155727	1		363	680	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400170	41400170	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1676	225	553	0	ENST00000373198.4:c.589C>T	p.Arg197Ter	p.R197*	ENST00000373198	NM_133170.3	197	Cga/Tga	5/32	0.330251347097599	6	FACETS	0.786	0.729	0.846	0.262	0.243	0.282	INDETERMINATE	1	TRUE	3	0.756325169155727	6		553	1901	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101257	27101257	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	663	535	0	ENST00000324856.7:c.4539del	p.Ser1513ArgfsTer14	p.S1513Rfs*14	ENST00000324856	NM_006015.4	1513	agC/ag	18/20	0.749156553315573	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.756325169155727	2		535	860	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129465	30129465	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747800465	NA	P-0014848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	341	559	0	ENST00000263025.4:c.563C>T	p.Ala188Val	p.A188V	ENST00000263025	NM_002746.2	188	gCc/gTc	4/9	0.201056195557441	4	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.756325169155727	4		559	1332	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909518	50909518	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376711125	NA	P-0014848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	114	658	5	ENST00000440232.2:c.1322C>T	p.Thr441Met	p.T441M	ENST00000440232	NM_002691.3	441	aCg/aTg	11/27	0.414421299812368	2	FACETS	0.235	0.21	0.261	0.117	0.105	0.131	INDETERMINATE	1	TRUE	0	0.756325169155727	2		663	1284	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142949984	142949984	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	227	508	0	ENST00000262992.4:c.2726C>G	p.Pro909Arg	p.P909R	ENST00000262992	NM_001101669.1	909	cCc/cGc	24/24	1	2	FACETS	0.514	0.478	0.551	0.514	0.478	0.551	SUBCLONAL	1	TRUE	1	0.756325169155727	2		508	1168	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056059	26056059	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	230	275	0	ENST00000343677.2:c.598C>A	p.Pro200Thr	p.P200T	ENST00000343677	NM_005319.3	200	Ccc/Acc	1/1	1	2	FACETS	0.92	0.863	0.979	0.92	0.863	0.979	CLONAL	1	TRUE	1	0.756325169155727	2		275	661	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0014878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	298	641	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.330334543322694	4	FACETS	0.938	0.883	0.994	0.938	0.883	0.994	CLONAL	2	TRUE	2	0.405154723623591	4		641	1102	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210075	55210075	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	322	612	0	ENST00000275493.2:c.185T>G	p.Leu62Arg	p.L62R	ENST00000275493	NM_005228.3	62	cTt/cGt	2/28	0.330334543322694	4	FACETS	0.997	0.942	1	0.997	0.942	1	CLONAL	2	TRUE	2	0.405154723623591	4		612	1120	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729606	41729606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	183	461	0	ENST00000242208.4:c.923G>A	p.Arg308His	p.R308H	ENST00000242208	NM_002192.2	308	cGt/cAt	3/3	0.330334543322694	4	FACETS	0.891	0.825	0.96	0.891	0.825	0.96	CLONAL	2	TRUE	2	0.405154723623591	4		461	712	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325807	65325807	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	175	495	0	ENST00000342505.4:c.1315G>C	p.Gly439Arg	p.G439R	ENST00000342505	NM_002227.2	439	Ggc/Cgc	9/25	0.330334543322694	4	FACETS	0.851	0.786	0.919	0.851	0.786	0.919	CLONAL	2	TRUE	2	0.405154723623591	4		495	713	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578483	7578483	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	472	1046	1	ENST00000269305.4:c.447del	p.Thr150HisfsTer20	p.T150Hfs*20	ENST00000269305	NM_001126112.2	149	tcC/tc	5/11	0.38096346413774	2	FACETS	0.99	0.948	1	0.99	0.948	1	CLONAL	2	TRUE	0	0.405154723623591	2		1047	1177	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0014879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	247	947	0	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	0.299958222103896	2	FACETS	1	0.989	1	0.639	0.597	0.682	CLONAL	1	TRUE	0	0.368254078117173	2		947	1050	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841118	15841118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763164776	NA	P-0014879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	116	877	1	ENST00000307771.7:c.1202G>A	p.Arg401His	p.R401H	ENST00000307771	NM_005089.3	401	cGt/cAt	11/11	1	2	FACETS	0.684	0.616	0.756	0.684	0.616	0.756	SUBCLONAL	1	TRUE	1	0.368254078117173	2		878	921	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670415	88670415	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	89	554	0	ENST00000360948.2:c.1271A>C	p.Lys424Thr	p.K424T	ENST00000360948	NM_001012338.2	424	aAa/aCa	11/19	1	2	FACETS	0.621	0.55	0.697	0.621	0.55	0.697	SUBCLONAL	1	TRUE	1	0.368254078117173	2		554	778	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599341	55599341	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519761	NA	P-0014933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	278	520	0	ENST00000288135.5:c.2467T>G	p.Tyr823Asp	p.Y823D	ENST00000288135	NM_000222.2	823	Tat/Gat	17/21	1	2	FACETS	0.913	0.862	0.964	0.913	0.862	0.964	CLONAL	1	TRUE	1	0.83777817632911	2		520	727	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097736	27097736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1490783133	NA	P-0014933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	489	681	1	ENST00000324856.7:c.3325C>T	p.Arg1109Trp	p.R1109W	ENST00000324856	NM_006015.4	1109	Cgg/Tgg	12/20	0.83777817632911	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.83777817632911	1		682	656	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593590	55593607	+	inframe_deletion	In_Frame_Del	DEL	GTATGAAGTACAGTGGAA	GTATGAAGTACAGTGGAA	-	novel	NA	P-0014933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	134	409	0	ENST00000288135.5:c.1657_1674del	p.Tyr553_Lys558del	p.Y553_K558del	ENST00000288135	NM_000222.2	552	atGTATGAAGTACAGTGGAAg/atg	11/21	1	2	FACETS	0.601	0.549	0.656	0.601	0.549	0.656	SUBCLONAL	1	TRUE	1	0.83777817632911	2		409	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577152	7577154	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	ACC	ACC	-	rs1567548347	NA	P-0014935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	567	622	0	ENST00000269305.4:c.784_786del	p.Gly262del	p.G262del	ENST00000269305	NM_001126112.2	262	GGT/-	8/11	NA	2	FACETS	0.988	0.959	1			1	INDETERMINATE	2	TRUE	NA	0.672996393436602	2		622	853	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967353	134967353	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0014935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	249	494	0	ENST00000398015.3:c.2690+2T>G		p.X897_splice	ENST00000398015	NM_004441.4	897			0.669884479982749	3	FACETS	1	0.987	1	0.396	0.371	0.421	CLONAL	1	TRUE	0	0.672996393436602	3		494	833	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0014953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	186	571	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.43380046388146	1	FACETS	0.963	0.893	1	0.963	0.893	1	CLONAL	1	TRUE	0	0.43380046388146	1		571	697	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032481	12032481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	75	393	0	ENST00000353533.5:c.917C>T	p.Pro306Leu	p.P306L	ENST00000353533	NM_003010.3	306	cCt/cTt	9/11	0.43380046388146	1	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	0	0.43380046388146	1		393	269	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213497	36213497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1244812690	NA	P-0014953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	117	924	2	ENST00000222270.7:c.2599C>T	p.Arg867Cys	p.R867C	ENST00000222270	NM_014727.1	867	Cgc/Tgc	5/37	1	2	FACETS	0.688	0.62	0.76	0.688	0.62	0.76	SUBCLONAL	1	TRUE	1	0.43380046388146	2		926	784	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579463	7579472	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGCCACGG	GGGGCCACGG	-	novel	NA	P-0014962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	250	730	0	ENST00000269305.4:c.215_224del	p.Pro72LeufsTer48	p.P72Lfs*48	ENST00000269305	NM_001126112.2	72	cCCGTGGCCCCt/ct	4/11	0.527047985301099	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.527047985301099	1		730	688	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692896	89692896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123322	NA	P-0014976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	198	521	0	ENST00000371953.3:c.380G>A	p.Gly127Glu	p.G127E	ENST00000371953	NM_000314.4	127	gGa/gAa	5/9	0.34196147684395	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.382783449214546	2		521	487	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0015009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	63	779	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.12	2		779	876	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879626	151879628	+	frameshift_variant	Frame_Shift_Del	DEL	AAG	AAG	T	novel	NA	P-0015009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	18	282	0	ENST00000262189.6:c.5317_5319delinsA	p.Leu1773ArgfsTer6	p.L1773Rfs*6	ENST00000262189	NM_170606.2	1773	CTT/A	36/59	1	2	FACETS	0.857	0.644	1	0.857	0.644	1	CLONAL	1	TRUE	1	0.12	2		282	350	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462393	89462393	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	328	749	0	ENST00000336596.2:c.1865C>G	p.Ser622Cys	p.S622C	ENST00000336596	NM_005233.5	622	tCc/tGc	10/17	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.859572275119687	2		749	679	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0015056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	182	367	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.248108081555369	3	FACETS	0.914	0.844	0.987	0.914	0.844	0.987	CLONAL	2	TRUE	1	0.248108081555369	3		367	902	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0015056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	72	537	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.248108081555369	3	FACETS	0.879	0.767	1	0.44	0.383	0.5	CLONAL	1	TRUE	1	0.248108081555369	3		537	742	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543379	65543397	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGACTAAAAGGCAACCAAG	GGACTAAAAGGCAACCAAG	-	novel	NA	P-0015056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	87	548	0	ENST00000358664.4:c.296-16_298del		p.X99_splice	ENST00000358664	NM_002382.4	99		5/5	0.248108081555369	2	FACETS	1	0.964	1	0.61	0.541	0.683	CLONAL	1	TRUE	0	0.248108081555369	2		548	575	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590418	67590418	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	76	355	0	ENST00000274335.5:c.1482del	p.Phe494LeufsTer16	p.F494Lfs*16	ENST00000274335		494	Ttt/tt	11/15	0.188577636402386	4	FACETS	1	0.965	1	0.639	0.561	0.723	CLONAL	1	TRUE	2	0.248108081555369	4		355	598	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166321	32166321	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	105	747	1	ENST00000375023.3:c.4633C>A	p.Pro1545Thr	p.P1545T	ENST00000375023	NM_004557.3	1545	Cca/Aca	26/30	0.248108081555369	5	FACETS	1	0.914	1	0.256	0.229	0.286	CLONAL	1	TRUE	1	0.248108081555369	5		748	1132	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956596	93956597	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0015056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	77	496	1	ENST00000369303.4:c.2639_2640delinsTT	p.Arg880Ile	p.R880I	ENST00000369303	NM_004440.3	880	aGG/aTT	15/17	0.248108081555369	1	FACETS	0.989	0.869	1	0.989	0.869	1	CLONAL	1	TRUE	0	0.248108081555369	1		497	550	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976842	2976842	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	138	691	0	ENST00000396946.4:c.1170G>T	p.Gln390His	p.Q390H	ENST00000396946	NM_032415.4	390	caG/caT	9/25	0.248108081555369	3	FACETS	1	0.984	1	0.692	0.63	0.758	CLONAL	1	TRUE	1	0.248108081555369	3		691	903	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523591	106523591	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	85	475	0	ENST00000359195.3:c.2743T>A	p.Ser915Thr	p.S915T	ENST00000359195	NM_002649.2	915	Tcc/Acc	8/11	0.248108081555369	3	FACETS	1	0.941	1	0.553	0.488	0.621	CLONAL	1	TRUE	1	0.248108081555369	3		475	697	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945020	151945020	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs751235231	NA	P-0015056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	23	82	0	ENST00000262189.6:c.2499A>T	p.Arg833Ser	p.R833S	ENST00000262189	NM_170606.2	833	agA/agT	14/59	0.248108081555369	3	FACETS	1	0.904	1	0.651	0.512	0.809	CLONAL	1	TRUE	1	0.248108081555369	3		82	160	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832438	72832438	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	119	288	1	ENST00000268489.5:c.4143del	p.Phe1381LeufsTer44	p.F1381Lfs*44	ENST00000268489	NM_006885.3	1381	ttT/tt	9/10	0.539040580390663	1	FACETS	0.891	0.813	0.971	0.891	0.813	0.971	CLONAL	1	TRUE	0	0.539040580390663	1		289	362	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0015073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	367	452	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.435505629144866	3	FACETS	0.911	0.87	0.951	0.911	0.87	0.951	CLONAL	3	TRUE	0	0.437693187568809	3		452	748	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934573	NA	P-0015073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	191	568	1	ENST00000269305.4:c.722C>A	p.Ser241Tyr	p.S241Y	ENST00000269305	NM_001126112.2	241	tCc/tAc	7/11	0.437693187568809	1	FACETS	0.977	0.906	1	0.977	0.906	1	CLONAL	1	TRUE	0	0.437693187568809	1		569	698	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0015073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	172	486	4	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.437693187568809	1	FACETS	0.927	0.856	1	0.927	0.856	1	CLONAL	1	TRUE	0	0.437693187568809	1		490	662	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149616	202149616	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	121	383	0	ENST00000358485.4:c.1057G>A	p.Glu353Lys	p.E353K	ENST00000358485	NM_001080125.1	353	Gag/Aag	8/9	1	2	FACETS	0.945	0.857	1	0.945	0.857	1	CLONAL	1	TRUE	1	0.437693187568809	2		383	585	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999492	100999492	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	277	949	0	ENST00000325455.5:c.310C>G	p.Pro104Ala	p.P104A	ENST00000325455	NM_001202474.3	104	Cca/Gca	1/8	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.437693187568809	2		949	1221	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59870990	59870990	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587780229	NA	P-0015073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	101	431	0	ENST00000259008.2:c.1441G>T	p.Gly481Cys	p.G481C	ENST00000259008	NM_032043.2	481	Ggt/Tgt	10/20	1	2	FACETS	0.807	0.723	0.895	0.807	0.723	0.895	CLONAL	1	TRUE	1	0.437693187568809	2		431	572	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187387	38187387	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	86	395	0	ENST00000317025.8:c.1090G>T	p.Glu364Ter	p.E364*	ENST00000317025	NM_023034.1	364	Gaa/Taa	6/24	1	2	FACETS	0.743	0.659	0.832	0.743	0.659	0.832	SUBCLONAL	1	TRUE	1	0.437693187568809	2		395	529	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335697	81335697	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	87	438	0	ENST00000222390.5:c.1663G>T	p.Gly555Ter	p.G555*	ENST00000222390	NM_000601.4	555	Gga/Tga	15/18	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.23	2		438	742	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609001	43609001	+	splice_region_variant,intron_variant	Splice_Region	DEL	C	C	-	novel	NA	P-0015082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	63	413	1	ENST00000355710.3:c.1760-3del		p.X587_splice	ENST00000355710	NM_020975.4	587			1	2	FACETS	0.872	0.754	1	0.872	0.754	1	CLONAL	1	TRUE	1	0.23	2		414	628	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220430	1220430	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0015082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	83	680	0	ENST00000326873.7:c.523A>T	p.Lys175Ter	p.K175*	ENST00000326873	NM_000455.4	175	Aag/Tag	4/10	0.21304597470438	1	FACETS	0.672	0.592	0.759	0.672	0.592	0.759	SUBCLONAL	1	TRUE	0	0.23	1		680	950	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212342	36212342	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	69	598	0	ENST00000222270.7:c.2093G>T	p.Arg698Leu	p.R698L	ENST00000222270	NM_014727.1	698	cGc/cTc	3/37	0.247560931183539	3	FACETS	0.733	0.637	0.837			1	SUBCLONAL	1	TRUE	NA	0.23	3		598	913	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457399	5457399	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs897885359	NA	P-0015082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	28	127	0	ENST00000381577.3:c.373C>T	p.Arg125Ter	p.R125*	ENST00000381577	NM_014143.3	125	Cga/Tga	3/7	1	2	FACETS	1	0.817	1	1	0.817	1	CLONAL	1	TRUE	1	0.23	2		127	239	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916504	39916504	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	99	691	1	ENST00000378444.4:c.4499C>T	p.Ala1500Val	p.A1500V	ENST00000378444	NM_001123385.1	1500	gCc/gTc	11/15	1	2	FACETS	0.842	0.75	0.94	0.842	0.75	0.94	CLONAL	1	TRUE	1	0.23	2		692	1023	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0000025-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	201	580	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.318873510677916	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.318873510677916	1		580	989	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225060	NA	P-0000025-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1318	269	1156	0	ENST00000263967.3:c.311C>T	p.Pro104Leu	p.P104L	ENST00000263967	NM_006218.2	104	cCa/cTa	2/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.318873510677916	2		1156	1587	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0001097-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	236	509	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.179883981967311	6	FACETS	0.956	0.893	1	0.765	0.714	0.817	CLONAL	4	TRUE	1	0.179883981967311	6		509	933	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0001097-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	40	533	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.179883981967311	6	FACETS	0.556	0.46	0.664	0.111	0.092	0.133	SUBCLONAL	1	TRUE	1	0.179883981967311	6		533	1087	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038349	180038349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373742042	NA	P-0001876-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	200	480	0	ENST00000261937.6:c.3668G>A	p.Arg1223His	p.R1223H	ENST00000261937	NM_182925.4	1223	cGc/cAc	27/30	0.343098133415337	1	FACETS	0.507	0.471	0.545	0.507	0.471	0.545	INDETERMINATE	1	TRUE	0	0.668104628609449	1		480	786	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134611	2134611	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001876-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	140	501	1	ENST00000219476.3:c.4388T>A	p.Ile1463Asn	p.I1463N	ENST00000219476	NM_000548.3	1463	aTc/aAc	34/42	1	2	FACETS	0.459	0.418	0.503	0.459	0.418	0.503	SUBCLONAL	1	TRUE	1	0.668104628609449	2		502	913	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0002620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	407	422	1	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	1	2	FACETS	0.936	0.894	0.978	0.936	0.894	0.978	CLONAL	1	TRUE	1	0.916757237774715	2		423	949	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164637	47164643	+	frameshift_variant	Frame_Shift_Del	DEL	TTTTACA	TTTTACA	-	novel	NA	P-0002620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	454	537	0	ENST00000409792.3:c.1483_1489del	p.Cys495LeufsTer6	p.C495Lfs*6	ENST00000409792	NM_014159.6	495	TGTAAAAct/ct	3/21	0.916757237774715	1	FACETS	0.995	0.972	1	0.995	0.972	1	CLONAL	1	TRUE	0	0.916757237774715	1		537	539	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955497	90955497	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	353	540	0	ENST00000265433.3:c.2168T>C	p.Leu723Pro	p.L723P	ENST00000265433	NM_002485.4	723	cTa/cCa	14/16	1	2	FACETS	0.752	0.714	0.791	0.752	0.714	0.791	SUBCLONAL	1	TRUE	1	0.916757237774715	2		540	1024	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405699	139405699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761406127	NA	P-0002620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	385	444	1	ENST00000277541.6:c.2492C>T	p.Ala831Val	p.A831V	ENST00000277541	NM_017617.3	831	gCc/gTc	16/34	1	2	FACETS	0.846	0.806	0.886	0.846	0.806	0.886	CLONAL	1	TRUE	1	0.916757237774715	2		445	993	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591857	48591857	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002898-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	453	646	0	ENST00000342988.3:c.1020G>C	p.Lys340Asn	p.K340N	ENST00000342988	NM_005359.5	340	aaG/aaC	9/12	0.590093106567673	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	FALSE	0	0.590093106567673	1		646	908	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0002898-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	554	384	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	0.499611452220053	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	FALSE	2	0.590093106567673	4		384	1364	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969468	44969471	+	frameshift_variant	Frame_Shift_Del	DEL	ATGC	ATGC	-	novel	NA	P-0002898-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	700	327	0	ENST00000377967.4:c.4151_4154del	p.Met1384LysfsTer8	p.M1384Kfs*8	ENST00000377967	NM_021140.2	1384	ATGCaa/aa	28/29	0.55450580000593	2	FACETS	1	0.997	1			1	CLONAL	2	FALSE	NA	0.590093106567673	2		327	997	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849801	156849801	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754452975	NA	P-0002898-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	506	443	1	ENST00000524377.1:c.2057G>A	p.Arg686His	p.R686H	ENST00000524377	NM_002529.3	686	cGc/cAc	16/17	0.280656572117425	5	FACETS	1	0.993	1	0.776	0.743	0.809	INDETERMINATE	2	FALSE	2	0.590093106567673	5		444	1389	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229572	5229572	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1027605608	NA	P-0002898-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	311	280	0	ENST00000357368.4:c.2279A>T	p.Tyr760Phe	p.Y760F	ENST00000357368	NM_002850.3	760	tAc/tTc	15/38	0.351212165443656	3	FACETS	0.872	0.826	0.918	0.872	0.826	0.918	INDETERMINATE	2	FALSE	1	0.590093106567673	3		280	783	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39721124	39721125	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0002898-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	530	469	0	ENST00000361337.2:c.629_630del	p.Arg210LeufsTer3	p.R210Lfs*3	ENST00000361337	NM_003286.2	209	gaGCgc/gagc	9/21	0.309648372189945	4	FACETS	1	0.974	1	1	0.974	1	INDETERMINATE	2	FALSE	2	0.590093106567673	4		469	1400	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722761	49722761	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs62262682	NA	P-0002898-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	29	33	0	ENST00000449682.2:c.1478G>T	p.Arg493Leu	p.R493L	ENST00000449682	NM_020998.3	493	cGt/cTt	13/18	0.280656572117425	5	FACETS	0.874	0.717	1	0.583	0.478	0.696	INDETERMINATE	2	FALSE	2	0.590093106567673	5		33	106	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58725412	58725412	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002898-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1912	111	669	0	ENST00000305921.3:c.986G>T	p.Cys329Phe	p.C329F	ENST00000305921	NM_003620.3	329	tGc/tTc	4/6	0.34893568713165	4	FACETS	0.296	0.264	0.329	0.148	0.132	0.165	INDETERMINATE	1	FALSE	2	0.590093106567673	4		669	2023	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099030	27099030	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0004126-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	129	641	0	ENST00000324856.7:c.3446C>G	p.Ser1149Ter	p.S1149*	ENST00000324856	NM_006015.4	1149	tCa/tGa	13/20	1	2	FACETS	0.616	0.559	0.677	0.616	0.559	0.677	SUBCLONAL	1	TRUE	1	0.54	2		641	775	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30323847	30323847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004126-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	102	462	0	ENST00000322652.5:c.1825G>A	p.Gly609Arg	p.G609R	ENST00000322652	NM_015355.2	609	Gga/Aga	15/16	1	2	FACETS	0.553	0.495	0.615	0.553	0.495	0.615	SUBCLONAL	1	TRUE	1	0.54	2		462	683	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0004605-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	162	441	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.353967838347033	6	FACETS	1	0.972	1	0.737	0.681	0.795	INDETERMINATE	2	TRUE	3	0.700884673333022	6		441	502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578414	7578414	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004605-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	805	320	0	ENST00000269305.4:c.516del	p.Val173Ter	p.V173*	ENST00000269305	NM_001126112.2	172	gtT/gt	5/11	0.700884673333022	3	FACETS	0.996	0.976	1	0.996	0.976	1	CLONAL	3	TRUE	0	0.700884673333022	3		320	1038	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998975	100998975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004605-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1825	676	524	1	ENST00000325455.5:c.827C>T	p.Ser276Leu	p.S276L	ENST00000325455	NM_001202474.3	276	tCa/tTa	1/8	0.700884673333022	6	FACETS	0.926	0.89	0.963	0.463	0.445	0.482	CLONAL	2	TRUE	2	0.700884673333022	6		525	2501	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416773	121416773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779442858	NA	P-0004605-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1670	793	576	3	ENST00000257555.6:c.202C>T	p.Arg68Trp	p.R68W	ENST00000257555		68	Cgg/Tgg	1/10	0.700884673333022	5	FACETS	0.942	0.91	0.975			1	CLONAL	2	TRUE	NA	0.700884673333022	5		579	2463	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557921	29557921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004605-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	317	187	0	ENST00000356175.3:c.3175G>A	p.Asp1059Asn	p.D1059N	ENST00000356175	NM_000267.3	1059	Gat/Aat	24/57	0.700884673333022	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	0	0.700884673333022	3		187	405	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211130	2211130	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004605-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	832	584	1	ENST00000398665.3:c.1384C>T	p.Gln462Ter	p.Q462*	ENST00000398665	NM_032482.2	462	Cag/Tag	15/28	0.700884673333022	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.700884673333022	2		585	1107	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554294	29554312	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGCAGGAAACACTGAGGTA	TGCAGGAAACACTGAGGTA	-	novel	NA	P-0004605-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	669	364	0	ENST00000356175.3:c.2313_2325+6del		p.X771_splice	ENST00000356175	NM_000267.3	771		19/57	0.700884673333022	3	FACETS	0.945	0.922	0.968	0.945	0.922	0.968	CLONAL	3	TRUE	0	0.700884673333022	3		364	909	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014035	70014035	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004605-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1253	70	641	0	ENST00000394351.3:c.896T>A	p.Leu299His	p.L299H	ENST00000394351	NM_000248.3	299	cTt/cAt	9/9	0.700884673333022	2	FACETS	0.151	0.131	0.173	0.075	0.065	0.087	SUBCLONAL	1	TRUE	0	0.700884673333022	2		641	1323	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867550	35867550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004605-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	156	389	0	ENST00000303115.3:c.364G>T	p.Asp122Tyr	p.D122Y	ENST00000303115	NM_002185.3	122	Gac/Tac	3/8	0.307577290460077	5	FACETS	0.947	0.867	1	0.316	0.289	0.344	INDETERMINATE	1	TRUE	2	0.700884673333022	5		389	964	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367776	15367776	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004605-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	80	311	1	ENST00000263377.2:c.1550A>T	p.Gln517Leu	p.Q517L	ENST00000263377	NM_058243.2	517	cAg/cTg	8/20	0.700884673333022	2	FACETS	0.29	0.255	0.329	0.145	0.127	0.165	SUBCLONAL	1	TRUE	0	0.700884673333022	2		312	786	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367781	15367781	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004605-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	81	314	0	ENST00000263377.2:c.1545G>T	p.Gln515His	p.Q515H	ENST00000263377	NM_058243.2	515	caG/caT	8/20	0.700884673333022	2	FACETS	0.283	0.249	0.32	0.142	0.124	0.16	SUBCLONAL	1	TRUE	0	0.700884673333022	2		314	816	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0005645-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	455	542	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.424967620698146	3	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.424967620698146	3		542	1078	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260036	16260036	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005645-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	152	475	0	ENST00000375759.3:c.7301C>T	p.Pro2434Leu	p.P2434L	ENST00000375759	NM_015001.2	2434	cCt/cTt	11/15	1	2	FACETS	0.835	0.764	0.909	0.835	0.764	0.909	CLONAL	1	TRUE	1	0.424967620698146	2		475	857	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433868	78433868	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005645-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	171	497	0	ENST00000370768.2:c.231A>T	p.Lys77Asn	p.K77N	ENST00000370768	NM_003902.3	77	aaA/aaT	3/20	1	2	FACETS	0.796	0.732	0.863	0.796	0.732	0.863	SUBCLONAL	1	TRUE	1	0.424967620698146	2		497	1011	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446862	187446862	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005645-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	261	527	0	ENST00000232014.4:c.1331G>T	p.Ser444Ile	p.S444I	ENST00000232014	NM_001130845.1	444	aGc/aTc	5/10	0.354244826620111	3	FACETS	1	0.992	1	0.722	0.677	0.769	CLONAL	1	TRUE	1	0.424967620698146	3		527	1031	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505133	149505133	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005645-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	206	649	0	ENST00000261799.4:c.1682G>C	p.Arg561Pro	p.R561P	ENST00000261799	NM_002609.3	561	cGt/cCt	12/23	0.325513546741408	3	FACETS	0.883	0.817	0.952	0.442	0.408	0.476	CLONAL	1	TRUE	1	0.424967620698146	3		649	1331	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114835	108114835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555066551	NA	P-0005645-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	610	419	0	ENST00000278616.4:c.652C>T	p.Gln218Ter	p.Q218*	ENST00000278616	NM_000051.3	218	Cag/Tag	6/63	0.424967620698146	4	FACETS	0.901	0.871	0.931	0.901	0.871	0.931	CLONAL	4	TRUE	0	0.424967620698146	4		419	1135	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984829	72984829	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005645-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	213	556	0	ENST00000268489.5:c.2755G>T	p.Gly919Cys	p.G919C	ENST00000268489	NM_006885.3	919	Ggc/Tgc	3/10	0.182180691121865	1	FACETS	0.743	0.69	0.798	0.743	0.69	0.798	INDETERMINATE	1	TRUE	0	0.424967620698146	1		556	1062	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426804	212426804	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005645-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	111	311	0	ENST00000342788.4:c.2311A>T	p.Ile771Phe	p.I771F	ENST00000342788	NM_005235.2	771	Atc/Ttc	20/28	1	2	FACETS	0.844	0.76	0.932	0.844	0.76	0.932	CLONAL	1	TRUE	1	0.424967620698146	2		311	619	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015106	37015106	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1313118042	NA	P-0005645-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	191	625	0	ENST00000358127.4:c.298G>A	p.Ala100Thr	p.A100T	ENST00000358127	NM_001280556.1	100	Gct/Act	3/10	1	2	FACETS	0.808	0.746	0.872	0.808	0.746	0.872	CLONAL	1	TRUE	1	0.424967620698146	2		625	1113	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061223	38061228	+	inframe_deletion	In_Frame_Del	DEL	TCTCGA	TCTCGA	-	novel	NA	P-0005760-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	185	546	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	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.569205890639653	2		546	591	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0005884-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	205	376	1	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	1	2	FACETS	0.806	0.749	0.865	0.806	0.749	0.865	CLONAL	1	TRUE	1	0.626973624189673	2		377	811	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675571	30675571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772732783	NA	P-0005884-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1895	558	884	0	ENST00000376406.3:c.2785G>A	p.Asp929Asn	p.D929N	ENST00000376406	NM_014641.2	929	Gat/Aat	8/15	0.627968933510361	3	FACETS	0.953	0.911	0.996	0.477	0.455	0.498	CLONAL	1	TRUE	1	0.626973624189673	3		884	2453	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972419	81972419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778251162	NA	P-0005884-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	471	765	1	ENST00000359376.3:c.3212G>A	p.Arg1071His	p.R1071H	ENST00000359376	NM_002661.3	1071	cGc/cAc	29/33	0.627968933510361	1	FACETS	0.962	0.923	1	0.962	0.923	1	CLONAL	1	TRUE	0	0.626973624189673	1		766	1072	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0005894-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	77	580	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.472461942782315	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	3	FALSE	0	0.468927146310183	3		580	124	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016619	12016619	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005894-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	35	419	0	ENST00000353533.5:c.755G>T	p.Gly252Val	p.G252V	ENST00000353533	NM_003010.3	252	gGa/gTa	7/11	0.472461942782315	3	FACETS	0.991	0.859	1	0.991	0.859	1	CLONAL	3	FALSE	0	0.468927146310183	3		419	62	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0006161-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	436	579	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.91	0.87	0.95	0.91	0.87	0.95	CLONAL	1	TRUE	1	0.880131139119338	2		579	1089	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0006161-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	179	441	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.942	0.878	1	0.942	0.878	1	CLONAL	1	TRUE	1	0.880131139119338	2		441	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0006161-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	477	692	2	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.874841621368127	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.880131139119338	1		694	597	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0006161-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	684	694	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.880131139119338	2		694	1516	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433399	49433399	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006161-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	28	234	0	ENST00000301067.7:c.8048G>A	p.Arg2683His	p.R2683H	ENST00000301067	NM_003482.3	2683	cGc/cAc	32/54	NA	2	FACETS	0.127	0.101	0.157			1	INDETERMINATE	1	TRUE	NA	0.880131139119338	2		234	501	SUCCESS
AR	367	MSKCC	GRCh37	X	66765025	66765025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1335991486	NA	P-0006161-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1943	966	968	0	ENST00000374690.3:c.37C>T	p.Arg13Trp	p.R13W	ENST00000374690	NM_000044.3	13	Cgg/Tgg	1/8	0.880131139119338	3	FACETS	1	0.993	1	0.543	0.526	0.561	CLONAL	1	TRUE	1	0.880131139119338	3		968	2909	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105685	27105685	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006382-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	255	861	0	ENST00000324856.7:c.5296G>T	p.Glu1766Ter	p.E1766*	ENST00000324856	NM_006015.4	1766	Gaa/Taa	20/20	0.673317184475354	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.673317184475354	1		861	466	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287893	33287893	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006382-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	302	993	1	ENST00000374542.5:c.1360G>T	p.Glu454Ter	p.E454*	ENST00000374542	NM_001141970.1	454	Gaa/Taa	5/8	0.673317184475354	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.673317184475354	1		994	586	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288804	33288804	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006382-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	190	486	0	ENST00000374542.5:c.748G>T	p.Gly250Cys	p.G250C	ENST00000374542	NM_001141970.1	250	Ggc/Tgc	3/8	0.673317184475354	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.673317184475354	1		486	359	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533503	533503	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006382-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	305	1102	0	ENST00000451590.1:c.400G>T	p.Ala134Ser	p.A134S	ENST00000451590	NM_001130442.1	134	Gcc/Tcc	4/5	0.673317184475354	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.673317184475354	1		1102	596	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575044	64575044	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006382-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	240	700	2	ENST00000312049.6:c.763G>T	p.Glu255Ter	p.E255*	ENST00000312049	NM_130799.2	255	Gag/Tag	4/10	0.673317184475354	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.673317184475354	1		702	471	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741239	40741239	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006382-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	278	903	0	ENST00000392038.2:c.1194C>A	p.Ser398Arg	p.S398R	ENST00000392038	NM_001626.4	398	agC/agA	12/14	1	2	FACETS	0.996	0.939	1	0.996	0.939	1	CLONAL	1	TRUE	1	0.673317184475354	2		903	829	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873241	136873241	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006382-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	351	1362	0	ENST00000241393.3:c.257T>A	p.Leu86His	p.L86H	ENST00000241393	NM_003467.2	86	cTc/cAc	2/2	0.673317184475354	1	FACETS	0.994	0.949	1	0.994	0.949	1	CLONAL	1	TRUE	0	0.673317184475354	1		1362	696	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520485	176520485	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006382-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	258	904	0	ENST00000292408.4:c.1330G>T	p.Ala444Ser	p.A444S	ENST00000292408	NM_213647.1	444	Gcc/Tcc	10/18	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.673317184475354	2		904	744	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481578	20481578	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006382-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	281	970	0	ENST00000346618.3:c.647G>T	p.Arg216Ile	p.R216I	ENST00000346618	NM_001949.4	216	aGa/aTa	3/7	0.673317184475354	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.673317184475354	1		970	547	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945102	151945102	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs749414492	NA	P-0006382-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	32	326	0	ENST00000262189.6:c.2417C>A	p.Ser806Tyr	p.S806Y	ENST00000262189	NM_170606.2	806	tCc/tAc	14/59	1	2	FACETS	0.332	0.27	0.402	0.332	0.27	0.402	SUBCLONAL	1	TRUE	1	0.673317184475354	2		326	286	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256071	123256071	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006382-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	279	1018	0	ENST00000358487.5:c.1838G>T	p.Gly613Val	p.G613V	ENST00000358487	NM_000141.4	613	gGc/gTc	13/18	0.673317184475354	1	FACETS	0.978	0.929	1	0.978	0.929	1	CLONAL	1	TRUE	0	0.673317184475354	1		1018	562	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131609	2131609	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006382-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	290	932	1	ENST00000219476.3:c.3624G>T	p.Trp1208Cys	p.W1208C	ENST00000219476	NM_000548.3	1208	tgG/tgT	31/42	0.673317184475354	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.673317184475354	1		933	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0007416-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	340	270	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.860322147910024	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.860322147910024	1		272	442	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0007493-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	412	888	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.406011999538663	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.406011999538663	3		888	749	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578177	7578177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs267605076	NA	P-0007493-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	405	559	0	ENST00000269305.4:c.672G>T	p.Glu224Asp	p.E224D	ENST00000269305	NM_001126112.2	224	gaG/gaT	6/11	0.406011999538663	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.406011999538663	2		559	906	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023412	27023412	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1413894127	NA	P-0007493-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	149	434	0	ENST00000324856.7:c.518A>G	p.His173Arg	p.H173R	ENST00000324856	NM_006015.4	173	cAt/cGt	1/20	0.380345481956194	3	FACETS	1	0.968	1	0.56	0.512	0.61	CLONAL	1	TRUE	1	0.406011999538663	3		434	789	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346654	225346654	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007493-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	147	422	0	ENST00000264414.4:c.1984A>T	p.Asn662Tyr	p.N662Y	ENST00000264414	NM_003590.4	662	Aat/Tat	14/16	0.380345481956194	3	FACETS	0.931	0.849	1	0.465	0.424	0.508	CLONAL	1	TRUE	1	0.406011999538663	3		422	936	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851589	134851589	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007493-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	117	378	0	ENST00000398015.3:c.995T>A	p.Ile332Asn	p.I332N	ENST00000398015	NM_004441.4	332	aTc/aAc	5/16	0.380345481956194	3	FACETS	1	0.95	1	0.54	0.488	0.595	CLONAL	1	TRUE	1	0.406011999538663	3		378	642	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131972827	131972827	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554100855	NA	P-0007493-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	101	320	0	ENST00000265335.6:c.3410G>T	p.Ser1137Ile	p.S1137I	ENST00000265335		1137	aGt/aTt	22/25	NA	2	FACETS	0.916	0.822	1			1	INDETERMINATE	1	TRUE	NA	0.406011999538663	2		320	543	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129120	152129120	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007493-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	435	605	0	ENST00000206249.3:c.73C>A	p.Pro25Thr	p.P25T	ENST00000206249	NM_000125.3	25	Ccc/Acc	1/8	0.380345481956194	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.406011999538663	3		605	1201	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509516	106509516	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007493-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1280	118	357	0	ENST00000359195.3:c.1510T>C	p.Ser504Pro	p.S504P	ENST00000359195	NM_002649.2	504	Tct/Cct	2/11	0.406011999538663	7	FACETS	0.838	0.753	0.928	0.168	0.15	0.186	CLONAL	1	TRUE	2	0.406011999538663	7		357	1398	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98011476	98011476	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007493-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	265	479	2	ENST00000289081.3:c.98A>T	p.Asp33Val	p.D33V	ENST00000289081	NM_000136.2	33	gAc/gTc	2/15	0.362163304687685	5	FACETS	0.953	0.893	1			1	CLONAL	2	TRUE	NA	0.406011999538663	5		481	1102	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100590	102100590	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007493-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	136	394	1	ENST00000282441.5:c.1434G>T	p.Leu478Phe	p.L478F	ENST00000282441	NM_001130145.2	478	ttG/ttT	9/9	0.405398176940027	4	FACETS	1	0.969	1	0.382	0.348	0.419	CLONAL	1	TRUE	1	0.406011999538663	4		395	821	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375583	118375583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781817780	NA	P-0007493-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	88	326	0	ENST00000534358.1:c.8976G>A	p.Met2992Ile	p.M2992I	ENST00000534358	NM_005933.3	2992	atG/atA	27/36	0.405398176940027	4	FACETS	0.919	0.815	1	0.306	0.271	0.344	CLONAL	1	TRUE	1	0.406011999538663	4		326	663	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864739	57864739	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007493-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	1789	806	1	ENST00000228682.2:c.2216C>A	p.Ala739Glu	p.A739E	ENST00000228682	NM_005269.2	739	gCa/gAa	12/12	0.406011999538663	9	FACETS	1	0.99	1			1	CLONAL	9	TRUE	NA	0.406011999538663	9		807	2356	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257200	133257200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007493-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	149	482	1	ENST00000320574.5:c.278G>A	p.Arg93Lys	p.R93K	ENST00000320574	NM_006231.2	93	aGa/aAa	3/49	0.406011999538663	2	FACETS	0.943	0.863	1	0.472	0.431	0.514	CLONAL	1	TRUE	0	0.406011999538663	2		483	778	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678550	88678550	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007493-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	89	303	0	ENST00000360948.2:c.986C>T	p.Pro329Leu	p.P329L	ENST00000360948	NM_001012338.2	329	cCc/cTc	9/19	0.406011999538663	2	FACETS	1	0.954	1	0.565	0.504	0.629	CLONAL	1	TRUE	0	0.406011999538663	2		303	388	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656765	45656765	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs772100262	NA	P-0007493-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	84	301	1	ENST00000407780.3:c.391A>T	p.Thr131Ser	p.T131S	ENST00000407780	NM_001283052.1	131	Aca/Tca	3/7	0.406011999538663	1	FACETS	0.904	0.804	1	0.904	0.804	1	CLONAL	1	TRUE	0	0.406011999538663	1		302	365	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343517	118343517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007493-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	116	321	0	ENST00000534358.1:c.1643C>T	p.Thr548Ile	p.T548I	ENST00000534358	NM_005933.3	548	aCt/aTt	3/36	0.405398176940027	4	FACETS	0.961	0.866	1	0.32	0.288	0.354	CLONAL	1	TRUE	1	0.406011999538663	4		321	836	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912788	100912788	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007493-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1216	215	721	1	ENST00000325455.5:c.2534G>T	p.Arg845Met	p.R845M	ENST00000325455	NM_001202474.3	845	aGg/aTg	7/8	0.405398176940027	4	FACETS	1	0.955	1	0.347	0.321	0.374	CLONAL	1	TRUE	1	0.406011999538663	4		722	1431	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552261	29552261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145891889	NA	P-0007493-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	126	387	0	ENST00000356175.3:c.1994C>T	p.Ser665Phe	p.S665F	ENST00000356175	NM_000267.3	665	tCc/tTc	17/57	0.406011999538663	2	FACETS	1	0.912	1	0.502	0.456	0.551	CLONAL	1	TRUE	0	0.406011999538663	2		387	618	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356138	66356150	+	frameshift_variant	Frame_Shift_Del	DEL	TCCTGGGCTCAAG	TCCTGGGCTCAAG	-	novel	NA	P-0007493-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	54	368	0	ENST00000273854.3:c.1347_1359del	p.Asp449GlufsTer8	p.D449Efs*8	ENST00000273854	NM_004439.5	449	gaCTTGAGCCCAGGA/ga	5/18	0.379195309871942	3	FACETS	0.36	0.306	0.419	0.12	0.102	0.14	SUBCLONAL	1	TRUE	0	0.406011999538663	3		368	890	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279564	123279564	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121918501	NA	P-0007620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	135	585	0	ENST00000358487.5:c.868T>C	p.Trp290Arg	p.W290R	ENST00000358487	NM_000141.4	290	Tgg/Cgg	7/18	1	2	FACETS	0.525	0.477	0.576	0.525	0.477	0.576	SUBCLONAL	1	TRUE	1	0.533380031701728	2		585	964	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589607	67589612	+	inframe_deletion	In_Frame_Del	DEL	AAGAAA	AAGAAA	-	novel	NA	P-0007620-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	79	286	0	ENST00000274335.5:c.1372_1377del	p.Glu458_Lys459del	p.E458_K459del	ENST00000274335		457	cAAGAAAaa/caa	10/15	1	2	FACETS	0.587	0.517	0.661	0.587	0.517	0.661	SUBCLONAL	1	TRUE	1	0.533380031701728	2		286	505	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176470	123176470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008139-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	489	563	1	ENST00000218089.9:c.437G>A	p.Arg146Gln	p.R146Q	ENST00000218089	NM_001042749.1	146	cGa/cAa	7/35	0.29632100180499	2	FACETS	0.962	0.935	0.988			1	CLONAL	5	TRUE	NA	0.31	2		564	656	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708994	117708994	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1290003301	NA	P-0008139-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	206	1086	1	ENST00000368508.3:c.1963A>G	p.Lys655Glu	p.K655E	ENST00000368508	NM_002944.2	655	Aag/Gag	13/43	0.29632100180499	2	FACETS	0.877	0.816	0.939	0.877	0.816	0.939	CLONAL	2	TRUE	0	0.31	2		1087	758	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56872947	56872947	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008139-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	281	1298	0	ENST00000308159.5:c.2102A>C	p.Glu701Ala	p.E701A	ENST00000308159	NM_014669.4	701	gAg/gCg	19/22	0.24019977025966	0	FACETS	0.62	0.583	0.658			1	SUBCLONAL	2	TRUE	0	0.31	0		1298	1008	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972654	25972654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760621031	NA	P-0008139-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	76	1045	3	ENST00000435504.4:c.1771C>T	p.Arg591Cys	p.R591C	ENST00000435504		591	Cgc/Tgc	12/13	0.29632100180499	3	FACETS	0.615	0.538	0.698	0.307	0.269	0.349	SUBCLONAL	1	TRUE	1	0.31	3		1048	921	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241677	55241677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504256	NA	P-0008145-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	583	505	0	ENST00000275493.2:c.2125G>A	p.Glu709Lys	p.E709K	ENST00000275493	NM_005228.3	709	Gaa/Aaa	18/28	0.753260241569212	3	FACETS	0.956	0.923	0.988	0.956	0.923	0.988	CLONAL	2	TRUE	1	0.753260241569212	3		505	1115	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0008145-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	517	450	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.753260241569212	3	FACETS	0.949	0.914	0.983	0.949	0.914	0.983	CLONAL	2	TRUE	1	0.753260241569212	3		450	996	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0008145-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	343	301	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.753260241569212	2	FACETS	0.924	0.89	0.956	0.924	0.89	0.956	CLONAL	2	TRUE	0	0.753260241569212	2		301	493	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077427	30077427	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0008145-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	154	232	0	ENST00000338641.4:c.1575-1G>C		p.X525_splice	ENST00000338641	NM_000268.3	525			0.753260241569212	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.753260241569212	1		232	227	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202283	133202283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764457707	NA	P-0008145-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	378	557	2	ENST00000320574.5:c.6605C>T	p.Thr2202Met	p.T2202M	ENST00000320574	NM_006231.2	2202	aCg/aTg	47/49	0.753260241569212	2	FACETS	1	0.973	1	0.516	0.491	0.541	CLONAL	1	TRUE	0	0.753260241569212	2		559	973	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106663	2106663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008145-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	244	611	0	ENST00000219476.3:c.667G>A	p.Asp223Asn	p.D223N	ENST00000219476	NM_000548.3	223	Gac/Aac	8/42	0.753260241569212	3	FACETS	0.63	0.587	0.674	0.21	0.195	0.225	SUBCLONAL	1	TRUE	0	0.753260241569212	3		611	1416	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533478	63533478	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1060502126	NA	P-0008145-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	309	437	0	ENST00000307078.5:c.1676C>G	p.Ser559Cys	p.S559C	ENST00000307078	NM_004655.3	559	tCc/tGc	6/11	0.676534643043368	3	FACETS	1	0.978	1	0.534	0.504	0.565	CLONAL	1	TRUE	1	0.753260241569212	3		437	1057	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109796	115109796	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008145-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	55	418	0	ENST00000257566.3:c.2082C>G	p.Ser694Arg	p.S694R	ENST00000257566	NM_016569.3	694	agC/agG	8/8	0.753260241569212	2	FACETS	0.173	0.147	0.201	0.086	0.073	0.101	SUBCLONAL	1	TRUE	0	0.753260241569212	2		418	846	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0008422-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	103	885	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	1	2	FACETS	0.617	0.552	0.686	0.617	0.552	0.686	SUBCLONAL	1	TRUE	1	0.419632923662675	2		885	796	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917845	29917845	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008422-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	82	691	1	ENST00000389048.3:c.823G>T	p.Glu275Ter	p.E275*	ENST00000389048	NM_004304.4	275	Gag/Tag	3/29	0.234594488332522	3	FACETS	0.649	0.571	0.731	0.324	0.285	0.366	INDETERMINATE	1	TRUE	1	0.419632923662675	3		692	729	SUCCESS
ATR	545	MSKCC	GRCh37	3	142184044	142184044	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008422-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	50	477	0	ENST00000350721.4:c.6936T>G	p.Ile2312Met	p.I2312M	ENST00000350721	NM_001184.3	2312	atT/atG	41/47	0.419632923662675	3	FACETS	0.316	0.267	0.37	0.158	0.133	0.185	SUBCLONAL	1	TRUE	1	0.419632923662675	3		477	912	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782082	NA	P-0008473-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	185	455	1	ENST00000269305.4:c.745A>T	p.Arg249Trp	p.R249W	ENST00000269305	NM_001126112.2	249	Agg/Tgg	7/11	NA	2	FACETS	0.866	0.81	0.922			1	INDETERMINATE	2	TRUE	NA	0.519701014610727	2		456	411	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972828	25972828	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008473-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	490	570	0	ENST00000435504.4:c.1597G>T	p.Val533Phe	p.V533F	ENST00000435504		533	Gtt/Ttt	12/13	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	2	TRUE	NA	0.519701014610727	2		570	796	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280147	66280147	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008473-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	96	304	0	ENST00000273854.3:c.1542C>A	p.Ser514Arg	p.S514R	ENST00000273854	NM_004439.5	514	agC/agA	7/18	1	2	FACETS	0.849	0.761	0.942	0.849	0.761	0.942	CLONAL	1	TRUE	1	0.519701014610727	2		304	435	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417943	32417943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554416372	NA	P-0008473-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	76	334	0	ENST00000332351.3:c.1109G>A	p.Arg370His	p.R370H	ENST00000332351	NM_024426.4	370	cGt/cAt	7/10	1	2	FACETS	0.95	0.841	1	0.95	0.841	1	CLONAL	1	TRUE	1	0.519701014610727	2		334	308	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160374	108160374	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008473-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	191	468	0	ENST00000278616.4:c.4282G>T	p.Glu1428Ter	p.E1428*	ENST00000278616	NM_000051.3	1428	Gaa/Taa	29/63	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.519701014610727	2		468	695	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032477	12032477	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008473-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	93	314	0	ENST00000353533.5:c.913T>A	p.Phe305Ile	p.F305I	ENST00000353533	NM_003010.3	305	Ttt/Att	9/11	0.375316862357672	0	FACETS	0.646	0.583	0.711			1	SUBCLONAL	1	TRUE	0	0.519701014610727	0		314	266	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30293198	30293198	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008473-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	159	526	0	ENST00000322652.5:c.488G>C	p.Gly163Ala	p.G163A	ENST00000322652	NM_015355.2	163	gGt/gCt	5/16	0.375316862357672	0	FACETS	0.807	0.751	0.865			1	CLONAL	1	TRUE	0	0.519701014610727	0		526	364	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155241	55155242	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	C	novel	NA	P-0008473-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	160	547	1	ENST00000257290.5:c.2840_2841delinsC	p.Ser947ThrfsTer24	p.S947Tfs*24	ENST00000257290	NM_006206.4	947	aGT/aC	21/23	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.519701014610727	2		548	593	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0008589-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	87	353	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.71329235122179	6	FACETS	1	0.965	1	0.846	0.77	0.922	CLONAL	3	TRUE	2	0.71329235122179	6		353	175	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226566888	226566888	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008589-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	162	584	0	ENST00000366794.5:c.1700A>T	p.Asn567Ile	p.N567I	ENST00000366794	NM_001618.3	567	aAc/aTc	12/23	0.71329235122179	5	FACETS	1	0.95	1	1	0.95	1	CLONAL	3	TRUE	2	0.71329235122179	5		584	308	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819960	170819965	+	inframe_deletion	In_Frame_Del	DEL	GATGAA	GATGAA	-	novel	NA	P-0008663-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	85	518	1	ENST00000296930.5:c.504_509del	p.Asp168_Glu169del	p.D168_E169del	ENST00000296930	NM_002520.6	168	GATGAA/-	6/11	0.372086964771607	5	FACETS	0.828	0.731	0.932	0.207	0.182	0.233	CLONAL	1	TRUE	1	0.372086964771607	5		519	860	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0008962-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	565	428	1	ENST00000269305.4:c.96+1G>A		p.X32_splice	ENST00000269305	NM_001126112.2	32			0.910561498690234	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.910561498690234	2		429	605	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808946	3808946	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008962-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	511	456	3	ENST00000262367.5:c.3278C>T	p.Ala1093Val	p.A1093V	ENST00000262367	NM_004380.2	1093	gCc/gTc	17/31	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.910561498690234	2		459	970	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489186	2489186	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755773744	NA	P-0008962-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	49	491	0	ENST00000355716.4:c.91G>A	p.Gly31Arg	p.G31R	ENST00000355716	NM_003820.2	31	Gga/Aga	2/8	0.220883421705275	2	FACETS	0.128	0.108	0.151	0.064	0.054	0.076	INDETERMINATE	1	TRUE	0	0.910561498690234	2		491	838	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467582	66467582	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008962-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	33	379	0	ENST00000273854.3:c.687C>A	p.Tyr229Ter	p.Y229*	ENST00000273854	NM_004439.5	229	taC/taA	3/18	0.589668973076576	1	FACETS	0.074	0.06	0.09	0.074	0.06	0.09	SUBCLONAL	1	TRUE	0	0.910561498690234	1		379	532	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045827	143045827	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008962-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	35	291	0	ENST00000262992.4:c.1807A>C	p.Thr603Pro	p.T603P	ENST00000262992	NM_001101669.1	603	Aca/Cca	17/24	0.589668973076576	1	FACETS	0.093	0.076	0.113	0.093	0.076	0.113	SUBCLONAL	1	TRUE	0	0.910561498690234	1		291	448	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149434822	149434822	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008962-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	51	669	0	ENST00000286301.3:c.2632C>G	p.Pro878Ala	p.P878A	ENST00000286301	NM_005211.3	878	Cct/Gct	20/22	0.572709116541855	1	FACETS	0.066	0.056	0.078	0.066	0.056	0.078	SUBCLONAL	1	TRUE	0	0.910561498690234	1		669	922	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0009345-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	209	484	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	0.592251459428645	2		484	609	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0009828-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	223	895	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.417537851598338	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.417537851598338	1		895	609	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115750	8115750	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs104894164	NA	P-0009828-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	718	1202	3	ENST00000346208.3:c.1096C>T	p.Arg366Ter	p.R366*	ENST00000346208		366	Cga/Tga	6/6	0.417537851598338	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.417537851598338	3		1205	1894	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72842152	72842152	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009828-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	55	518	0	ENST00000325599.8:c.1096C>G	p.His366Asp	p.H366D	ENST00000325599	NM_018130.2	366	Cac/Gac	10/11	0.348161848459609	1	FACETS	0.492	0.421	0.568	0.492	0.421	0.568	SUBCLONAL	1	TRUE	0	0.417537851598338	1		518	424	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356101	66356101	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009828-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	163	629	0	ENST00000273854.3:c.1396C>T	p.Gln466Ter	p.Q466*	ENST00000273854	NM_004439.5	466	Caa/Taa	5/18	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.417537851598338	2		629	577	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37665972	37665972	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009908-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	232	343	0	ENST00000447079.4:c.2624T>A	p.Leu875Gln	p.L875Q	ENST00000447079	NM_015083.1	875	cTa/cAa	7/14	1	2	FACETS	0.878	0.824	0.934	0.878	0.824	0.934	CLONAL	1	TRUE	1	0.820173791112963	2		343	644	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618533	37618539	+	frameshift_variant	Frame_Shift_Del	DEL	TGGTGGA	TGGTGGA	-	novel	NA	P-0009908-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	370	504	0	ENST00000447079.4:c.209_215del	p.Leu70CysfsTer20	p.L70Cfs*20	ENST00000447079	NM_015083.1	70	tTGGTGGAg/tg	1/14	1	2	FACETS	0.727	0.69	0.765	0.727	0.69	0.765	SUBCLONAL	1	TRUE	1	0.820173791112963	2		504	1241	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129364	64129364	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009908-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	419	586	0	ENST00000334205.4:c.796G>T	p.Gly266Trp	p.G266W	ENST00000334205	NM_003942.2	266	Ggg/Tgg	8/17	1	2	FACETS	0.985	0.941	1	0.985	0.941	1	CLONAL	1	TRUE	1	0.820173791112963	2		586	1037	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010008-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	77	389	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.492	0.432	0.555	0.492	0.432	0.555	SUBCLONAL	1	TRUE	1	0.58020455657862	2		389	540	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0010008-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	383	502	4	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.817	0.781	0.853	1	0.996	1	CLONAL	2	TRUE	1	0.58020455657862	2		506	808	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662248	227662248	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010008-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	198	423	1	ENST00000305123.5:c.1207A>T	p.Thr403Ser	p.T403S	ENST00000305123	NM_005544.2	403	Acc/Tcc	1/2	1	2	FACETS	0.576	0.532	0.621	0.576	0.532	0.621	SUBCLONAL	1	TRUE	1	0.58020455657862	2		424	1185	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913409	NA	P-0010008-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	175	433	1	ENST00000349496.5:c.134C>A	p.Ser45Tyr	p.S45Y	ENST00000349496	NM_001904.3	45	tCt/tAt	3/15	1	2	FACETS	0.944	0.873	1	0.944	0.873	1	CLONAL	1	TRUE	1	0.58020455657862	2		434	639	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383347	42383347	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555843587	NA	P-0010008-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	229	503	0	ENST00000221972.3:c.367C>T	p.Leu123Phe	p.L123F	ENST00000221972	NM_021601.3	123	Ctc/Ttc	2/5	1	2	FACETS	0.603	0.561	0.647	0.603	0.561	0.647	SUBCLONAL	1	TRUE	1	0.58020455657862	2		503	1309	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112546	115112547	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0010008-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	127	342	0	ENST00000257566.3:c.1193_1194delinsTT	p.Thr398Ile	p.T398I	ENST00000257566	NM_016569.3	398	aCC/aTT	7/8	1	2	FACETS	0.453	0.41	0.499	0.453	0.41	0.499	SUBCLONAL	1	TRUE	1	0.58020455657862	2		342	966	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920412	134920412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746798014	NA	P-0010015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	781	515	2	ENST00000398015.3:c.2227C>T	p.Arg743Trp	p.R743W	ENST00000398015	NM_004441.4	743	Cgg/Tgg	12/16	0.758127107838318	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	2	0.758127107838318	4		517	1679	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0010015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	703	578	1	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.758127107838318	2		579	903	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404756	404756	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3130	345	436	0	ENST00000399788.2:c.4438T>G	p.Phe1480Val	p.F1480V	ENST00000399788	NM_001042603.1	1480	Ttc/Gtc	26/28	0.758127107838318	10	FACETS	1	0.972	1			1	CLONAL	1	TRUE	NA	0.758127107838318	10		436	3475	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347172	347172	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3632	368	619	0	ENST00000262320.3:c.1839G>C	p.Lys613Asn	p.K613N	ENST00000262320	NM_003502.3	613	aaG/aaC	7/11	0.758127107838318	9	FACETS	0.887	0.835	0.94			1	CLONAL	1	TRUE	NA	0.758127107838318	9		619	4000	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0010024-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	340	683	2	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.34805222239321	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.34805222239321	1		685	1180	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201881	152201881	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010024-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	122	407	0	ENST00000206249.3:c.735C>A	p.Cys245Ter	p.C245*	ENST00000206249	NM_000125.3	245	tgC/tgA	3/8	0.172708640343897	1	FACETS	0.59	0.532	0.651	0.59	0.532	0.651	INDETERMINATE	1	TRUE	0	0.34805222239321	1		407	982	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602314	10602314	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010024-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	324	505	0	ENST00000171111.5:c.1264G>C	p.Asp422His	p.D422H	ENST00000171111	NM_203500.1	422	Gat/Cat	3/6	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.34805222239321	2		505	1527	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434936	49434936	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010024-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	190	258	0	ENST00000301067.7:c.6617del	p.Pro2206LeufsTer58	p.P2206Lfs*58	ENST00000301067	NM_003482.3	2206	cCt/ct	31/54	0.172708640343897	1	FACETS	1	0.968	1	1	0.968	1	INDETERMINATE	1	TRUE	0	0.34805222239321	1		258	835	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0010025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	249	531	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.246865736117702	2	FACETS	1	0.992	1	0.737	0.69	0.786	CLONAL	1	TRUE	0	0.343672367871903	2		531	983	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453149	140453149	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913361	NA	P-0010025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	199	312	0	ENST00000288602.6:c.1786G>C	p.Gly596Arg	p.G596R	ENST00000288602	NM_004333.4	596	Ggt/Cgt	15/18	0.343672367871903	5	FACETS	1	0.967	1	0.713	0.662	0.767	CLONAL	2	TRUE	2	0.343672367871903	5		312	820	SUCCESS
FH	2271	MSKCC	GRCh37	1	241672028	241672028	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	385	310	1	ENST00000366560.3:c.613G>A	p.Glu205Lys	p.E205K	ENST00000366560	NM_000143.3	205	Gaa/Aaa	5/10	0.343672367871903	4	FACETS	1	0.99	1	0.85	0.812	0.889	CLONAL	3	TRUE	0	0.343672367871903	4		311	885	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469567	25469567	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	231	475	0	ENST00000264709.3:c.1201G>T	p.Val401Leu	p.V401L	ENST00000264709	NM_175629.2	401	Gtg/Ttg	10/23	0.254899840781051	5	FACETS	0.827	0.77	0.886	0.551	0.513	0.591	CLONAL	2	TRUE	2	0.343672367871903	5		475	1232	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732539	190732539	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	177	483	0	ENST00000441310.2:c.2357C>G	p.Ser786Cys	p.S786C	ENST00000441310	NM_000534.4	786	tCt/tGt	11/13	0.183464305117706	5	FACETS	0.844	0.778	0.913	0.563	0.518	0.609	INDETERMINATE	2	TRUE	2	0.343672367871903	5		483	925	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89478303	89478303	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	141	365	0	ENST00000336596.2:c.2122G>C	p.Asp708His	p.D708H	ENST00000336596	NM_005233.5	708	Gat/Cat	12/17	0.239635922239155	4	FACETS	0.758	0.692	0.828	0.758	0.692	0.828	SUBCLONAL	2	TRUE	2	0.343672367871903	4		365	727	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230872	66230872	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	151	488	1	ENST00000273854.3:c.2099G>T	p.Arg700Ile	p.R700I	ENST00000273854	NM_004439.5	700	aGa/aTa	12/18	0.239635922239155	4	FACETS	1	0.985	1	0.677	0.619	0.738	CLONAL	1	TRUE	2	0.343672367871903	4		489	872	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356257	66356257	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	192	418	0	ENST00000273854.3:c.1240T>C	p.Tyr414His	p.Y414H	ENST00000273854	NM_004439.5	414	Tac/Cac	5/18	0.239635922239155	4	FACETS	0.751	0.694	0.81	0.751	0.694	0.81	SUBCLONAL	2	TRUE	2	0.343672367871903	4		418	1000	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067048	143067048	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	189	554	0	ENST00000262992.4:c.1665C>A	p.Asn555Lys	p.N555K	ENST00000262992	NM_001101669.1	555	aaC/aaA	16/24	0.239635922239155	4	FACETS	1	0.988	1	0.693	0.64	0.749	CLONAL	1	TRUE	2	0.343672367871903	4		554	1066	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929225	32929225	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	147	745	0	ENST00000380152.3:c.7235C>G	p.Thr2412Ser	p.T2412S	ENST00000380152		2412	aCt/aGt	14/27	0.255239776215537	3	FACETS	0.764	0.696	0.836	0.382	0.348	0.418	SUBCLONAL	1	TRUE	1	0.343672367871903	3		745	1312	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857311	68857311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238607560	NA	P-0010025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	176	385	1	ENST00000261769.5:c.1946C>T	p.Ser649Phe	p.S649F	ENST00000261769	NM_004360.3	649	tCt/tTt	13/16	0.343672367871903	3	FACETS	1	0.986	1	0.446	0.41	0.482	CLONAL	1	TRUE	0	0.343672367871903	3		386	898	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0010031-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	218	630	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.368965741775803	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.368965741775803	1		630	847	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491394	2491394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs565512671	NA	P-0010031-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	112	296	0	ENST00000355716.4:c.437C>T	p.Pro146Leu	p.P146L	ENST00000355716	NM_003820.2	146	cCg/cTg	4/8	1	2	FACETS	0.947	0.853	1	0.947	0.853	1	CLONAL	1	TRUE	1	0.368965741775803	2		296	641	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443592	29443592	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs769449619	NA	P-0010031-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	149	417	1	ENST00000389048.3:c.3625C>T	p.Arg1209Ter	p.R1209*	ENST00000389048	NM_004304.4	1209	Cga/Tga	23/29	1	2	FACETS	0.957	0.875	1	0.957	0.875	1	CLONAL	1	TRUE	1	0.368965741775803	2		418	844	SUCCESS
APC	324	MSKCC	GRCh37	5	112175594	112175594	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0010031-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	196	480	1	ENST00000257430.4:c.4303A>T	p.Arg1435Ter	p.R1435*	ENST00000257430	NM_000038.5	1435	Aga/Tga	16/16	0.368965741775803	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.368965741775803	1		481	863	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044505	12044505	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010031-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	156	458	1	ENST00000353533.5:c.1128G>T	p.Glu376Asp	p.E376D	ENST00000353533	NM_003010.3	376	gaG/gaT	11/11	0.368965741775803	1	FACETS	0.969	0.889	1	0.969	0.889	1	CLONAL	1	TRUE	0	0.368965741775803	1		459	712	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832880	3832880	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	181	406	0	ENST00000262367.5:c.1378G>T	p.Val460Phe	p.V460F	ENST00000262367	NM_004380.2	460	Gtt/Ttt	6/31	0.387837390121944	3	FACETS	1	0.967	1	0.545	0.502	0.589	CLONAL	1	TRUE	1	0.414554203691798	3		406	968	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564411	86564411	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010050-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	67	507	0	ENST00000274376.6:c.143C>A	p.Pro48His	p.P48H	ENST00000274376	NM_002890.2	48	cCc/cAc	1/25	1	2	FACETS	0.519	0.451	0.593	0.519	0.451	0.593	SUBCLONAL	1	TRUE	1	0.457552221352634	2		507	564	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106708	27106708	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	487	339	1	ENST00000324856.7:c.6319G>T	p.Gly2107Cys	p.G2107C	ENST00000324856	NM_006015.4	2107	Ggc/Tgc	20/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.916272603961152	2		340	1058	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474107	29474107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375105843	NA	P-0010066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	418	341	0	ENST00000389048.3:c.2068G>A	p.Ala690Thr	p.A690T	ENST00000389048	NM_004304.4	690	Gcc/Acc	12/29	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.916272603961152	2		341	869	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639653	47639653	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	452	377	0	ENST00000233146.2:c.746A>T	p.Lys249Met	p.K249M	ENST00000233146	NM_000251.2	249	aAg/aTg	4/16	1	2	FACETS	0.998	0.956	1	0.998	0.956	1	CLONAL	1	TRUE	1	0.916272603961152	2		377	989	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960072	134960072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs371334171	NA	P-0010066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1169	528	330	0	ENST00000398015.3:c.2429A>G	p.Tyr810Cys	p.Y810C	ENST00000398015	NM_004441.4	810	tAt/tGt	13/16	0.916272603961152	3	FACETS	0.99	0.948	1			1	CLONAL	1	TRUE	NA	0.916272603961152	3		330	1697	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876179	35876179	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	360	384	0	ENST00000303115.3:c.971T>C	p.Leu324Pro	p.L324P	ENST00000303115	NM_002185.3	324	cTg/cCg	8/8	0.916272603961152	3	FACETS	0.853	0.807	0.899	0.426	0.403	0.45	CLONAL	1	TRUE	1	0.916272603961152	3		384	1344	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553662	106553662	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	352	230	0	ENST00000369096.4:c.1627A>T	p.Ser543Cys	p.S543C	ENST00000369096	NM_001198.3	543	Agc/Tgc	5/7	1	2	FACETS	0.974	0.928	1	0.974	0.928	1	CLONAL	1	TRUE	1	0.916272603961152	2		230	789	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624386	140624386	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	354	250	0	ENST00000288602.6:c.118G>T	p.Asp40Tyr	p.D40Y	ENST00000288602	NM_004333.4	40	Gac/Tac	1/18	1	2	FACETS	0.945	0.9	0.99	0.945	0.9	0.99	CLONAL	1	TRUE	1	0.916272603961152	2		250	818	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589684	69589684	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	246	299	1	ENST00000168712.1:c.169C>A	p.Arg57Ser	p.R57S	ENST00000168712	NM_002007.2	57	Cgc/Agc	1/3	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.916272603961152	2		300	490	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435872	49435872	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	502	478	0	ENST00000301067.7:c.6109G>T	p.Asp2037Tyr	p.D2037Y	ENST00000301067	NM_003482.3	2037	Gac/Tac	28/54	1	2	FACETS	0.995	0.956	1	0.995	0.956	1	CLONAL	1	TRUE	1	0.916272603961152	2		478	1101	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1555525585	NA	P-0010066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	298	228	0	ENST00000269305.4:c.673-2A>G		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.916272603961152	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.916272603961152	1		228	339	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028610	12028610	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0010066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	362	336	0	ENST00000353533.5:c.814-1G>T		p.X272_splice	ENST00000353533	NM_003010.3	272			0.916272603961152	1	FACETS	0.982	0.956	1	0.982	0.956	1	CLONAL	1	TRUE	0	0.916272603961152	1		336	436	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148692	20148693	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0010066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	377	404	1	ENST00000379607.5:c.370_371delinsTT	p.Gly124Leu	p.G124L	ENST00000379607	NM_001412.3	124	GGa/TTa	6/7	NA	2	FACETS	0.774	0.736	0.813			1	INDETERMINATE	1	TRUE	NA	0.916272603961152	2		405	1063	SUCCESS
AR	367	MSKCC	GRCh37	X	66765659	66765659	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	509	559	1	ENST00000374690.3:c.671A>G	p.Asn224Ser	p.N224S	ENST00000374690	NM_000044.3	224	aAt/aGt	1/8	0.662828065576159	1	FACETS	0.577	0.555	0.599	0.577	0.555	0.599	SUBCLONAL	1	TRUE	0	0.916272603961152	1		560	1044	SUCCESS
AR	367	MSKCC	GRCh37	X	66766456	66766456	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	360	324	1	ENST00000374690.3:c.1468C>G	p.Leu490Val	p.L490V	ENST00000374690	NM_000044.3	490	Ctg/Gtg	1/8	0.662828065576159	1	FACETS	0.578	0.552	0.604	0.578	0.552	0.604	SUBCLONAL	1	TRUE	0	0.916272603961152	1		325	737	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220444	123220444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	466	544	1	ENST00000218089.9:c.3101G>A	p.Arg1034Lys	p.R1034K	ENST00000218089	NM_001042749.1	1034	aGa/aAa	30/35	0.404932316953455	1	FACETS	0.437	0.418	0.457	0.437	0.418	0.457	INDETERMINATE	1	TRUE	0	0.916272603961152	1		545	1261	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953742	48953742	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	857	304	3	ENST00000267163.4:c.1346del	p.Gly449GlufsTer8	p.G449Efs*8	ENST00000267163	NM_000321.2	449	Gga/ga	14/27	NA	2	FACETS	1	0.997	1			1	INDETERMINATE	2	TRUE	NA	0.916272603961152	2		307	906	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274822	142274822	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	443	467	0	ENST00000350721.4:c.2238del	p.Ala747ProfsTer12	p.A747Pfs*12	ENST00000350721	NM_001184.3	746	aaA/aa	10/47	0.620579026774263	3	FACETS	0.9	0.857	0.943			1	CLONAL	1	TRUE	NA	0.916272603961152	3		467	1567	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0010068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	215	453	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.363618861265194	4	FACETS	0.993	0.926	1	0.993	0.926	1	CLONAL	2	TRUE	2	0.404543796456479	4		453	752	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163606	32163606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532094081	NA	P-0010068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	89	289	1	ENST00000375023.3:c.5620G>A	p.Gly1874Arg	p.G1874R	ENST00000375023	NM_004557.3	1874	Gga/Aga	30/30	0.404543796456479	6	FACETS	0.762	0.678	0.852	0.381	0.339	0.426	SUBCLONAL	2	TRUE	2	0.404543796456479	6		290	522	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933506	36933506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	331	862	0	ENST00000361632.4:c.1781G>A	p.Ser594Asn	p.S594N	ENST00000361632		594	aGt/aAt	13/16	0.404543796456479	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.404543796456479	2		862	752	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654718	67654718	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	175	508	0	ENST00000264010.4:c.1205C>T	p.Ser402Leu	p.S402L	ENST00000264010	NM_006565.3	402	tCa/tTa	6/12	0.367193791677714	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.404543796456479	2		508	425	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028663	12028663	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	214	545	0	ENST00000353533.5:c.866A>G	p.Asp289Gly	p.D289G	ENST00000353533	NM_003010.3	289	gAt/gGt	8/11	0.369561017373716	2	FACETS	0.874	0.818	0.932	0.874	0.818	0.932	CLONAL	2	TRUE	0	0.404543796456479	2		545	605	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	351	389	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.941970580834266	2		389	742	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0010085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	421	269	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.947	0.906	0.988	0.947	0.906	0.988	CLONAL	1	TRUE	1	0.941970580834266	2		269	944	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799063	42799065	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs751580245	NA	P-0010085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	840	311	0	ENST00000575354.2:c.4550_4552del	p.Lys1517del	p.K1517del	ENST00000575354	NM_015125.3	1516	cAGAag/cag	20/20	NA	2	FACETS	0.972	0.96	0.984			1	INDETERMINATE	2	TRUE	NA	0.941970580834266	2		311	917	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400073	139400073	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	1282	551	0	ENST00000277541.6:c.4275C>G	p.Cys1425Trp	p.C1425W	ENST00000277541	NM_017617.3	1425	tgC/tgG	25/34	0.941970580834266	2	FACETS	0.992	0.983	1	0.992	0.983	1	CLONAL	2	TRUE	0	0.941970580834266	2		551	1372	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421684	49421684	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	608	493	0	ENST00000301067.7:c.14545A>G	p.Ser4849Gly	p.S4849G	ENST00000301067	NM_003482.3	4849	Agc/Ggc	47/54	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.941970580834266	2		493	1239	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0010091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	73	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.176724659294703	5	FACETS		NA	1			1	NA	NA	FALSE	2	NA	5		426	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0010091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	25	609	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.3	4	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	4		609	265	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039553	180039553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	17	494	0	ENST00000261937.6:c.3490G>A	p.Glu1164Lys	p.E1164K	ENST00000261937	NM_182925.4	1164	Gag/Aag	26/30	0.3	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		494	175	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968255	2968255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	45	453	0	ENST00000396946.4:c.1731C>A	p.Tyr577Ter	p.Y577*	ENST00000396946	NM_032415.4	577	taC/taA	13/25	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		453	246	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938836	76938836	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	31	618	0	ENST00000373344.5:c.1912C>A	p.His638Asn	p.H638N	ENST00000373344	NM_000489.3	638	Cat/Aat	9/35	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		618	529	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0010093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	328	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.478081730740154	3	FACETS	0.927	0.879	0.976	0.927	0.879	0.976	CLONAL	2	TRUE	1	0.478081730740154	3		426	917	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1555525429	NA	P-0010093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	341	438	0	ENST00000269305.4:c.782+1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.478081730740154	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.478081730740154	2		438	684	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650816	48650816	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1557020321	NA	P-0010093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	296	831	2	ENST00000376670.3:c.685G>A	p.Gly229Ser	p.G229S	ENST00000376670	NM_002049.3	229	Ggc/Agc	4/6	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.478081730740154	2		833	1211	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	201	389	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.594720950993181	2		389	460	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0010094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	34	550	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.583299282469299	4	FACETS	0.155	0.126	0.189			1	SUBCLONAL	1	TRUE	NA	0.594720950993181	4		550	1173	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104353781	104353781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369465986	NA	P-0010094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	80	630	0	ENST00000369902.3:c.715C>T	p.Arg239Trp	p.R239W	ENST00000369902	NM_016169.3	239	Cgg/Tgg	6/12	1	2	FACETS	0.349	0.307	0.395	0.349	0.307	0.395	SUBCLONAL	1	TRUE	1	0.594720950993181	2		630	771	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137522056	137522056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	65	439	0	ENST00000367739.4:c.823C>T	p.Pro275Ser	p.P275S	ENST00000367739	NM_000416.2	275	Cca/Tca	6/7	0.594720950993181	3	FACETS	0.465	0.403	0.532	0.232	0.201	0.266	SUBCLONAL	1	TRUE	1	0.594720950993181	3		439	610	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0010105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	61	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.994	0.859	1	0.994	0.859	1	CLONAL	1	TRUE	1	0.260024955472343	2		426	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0010105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	132	769	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.260024955472343	1	FACETS	0.855	0.775	0.94	0.855	0.775	0.94	CLONAL	1	TRUE	0	0.260024955472343	1		770	1033	SUCCESS
APC	324	MSKCC	GRCh37	5	112128161	112128161	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	56	468	0	ENST00000257430.4:c.664C>T	p.Gln222Ter	p.Q222*	ENST00000257430	NM_000038.5	222	Cag/Tag	7/16	0.260024955472343	1	FACETS	0.781	0.67	0.902	0.781	0.67	0.902	CLONAL	1	TRUE	0	0.260024955472343	1		468	480	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349373	89349373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111737495	NA	P-0010105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1465	227	942	1	ENST00000301030.4:c.3577G>A	p.Ala1193Thr	p.A1193T	ENST00000301030	NM_001256183.1	1193	Gcg/Acg	9/13	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.260024955472343	2		943	1692	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713195	30713195	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	62	295	0	ENST00000295754.5:c.521del	p.Pro174HisfsTer24	p.P174Hfs*24	ENST00000295754	NM_003242.5	174	Cca/ca	4/7	0.260024955472343	1	FACETS	0.908	0.786	1	0.908	0.786	1	CLONAL	1	TRUE	0	0.260024955472343	1		295	457	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	118	389	0				ENST00000310581	NM_198253.2	-/1132			0.313211013063409	3	FACETS	1	0.916	1	1	0.916	1	CLONAL	2	TRUE	1	0.313211013063409	3		389	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	138	375	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.313211013063409	2		375	828	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423632	88423632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1478926904	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	124	434	0	ENST00000360948.2:c.2203C>T	p.Arg735Cys	p.R735C	ENST00000360948	NM_001012338.2	735	Cgc/Tgc	18/19	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.313211013063409	2		434	753	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230613	46230613	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	200	616	1	ENST00000334344.6:c.862C>T	p.Gln288Ter	p.Q288*	ENST00000334344	NM_152641.2	288	Cag/Tag	8/21	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.313211013063409	2		617	1095	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	146	576	0	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	1	2	FACETS	0.978	0.892	1	0.978	0.892	1	CLONAL	1	TRUE	1	0.313211013063409	2		576	953	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230641	46230642	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	134	674	0	ENST00000334344.6:c.890_891delinsTT	p.Ser297Phe	p.S297F	ENST00000334344	NM_152641.2	297	tCC/tTT	8/21	NA	2	FACETS	0.801	0.727	0.88			1	INDETERMINATE	1	TRUE	NA	0.313211013063409	2		674	1068	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609907	117609907	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761470868	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	205	720	1	ENST00000368508.3:c.6792G>A	p.Met2264Ile	p.M2264I	ENST00000368508	NM_002944.2	2264	atG/atA	43/43	0.313211013063409	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.313211013063409	1		721	1035	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417634	139417634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749786734	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	126	505	0	ENST00000277541.6:c.410C>T	p.Ser137Leu	p.S137L	ENST00000277541	NM_017617.3	137	tCg/tTg	4/34	0.313211013063409	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.313211013063409	1		505	657	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540740	187540740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	91	464	0	ENST00000441802.2:c.7000C>T	p.His2334Tyr	p.H2334Y	ENST00000441802	NM_005245.3	2334	Cat/Tat	10/27	1	2	FACETS	0.703	0.624	0.789	0.703	0.624	0.789	SUBCLONAL	1	TRUE	1	0.313211013063409	2		464	826	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641054	117641054	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1216964547	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	157	565	0	ENST00000368508.3:c.5917G>A	p.Gly1973Arg	p.G1973R	ENST00000368508	NM_002944.2	1973	Gga/Aga	36/43	0.313211013063409	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.313211013063409	1		565	814	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944947	31944947	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868835690	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	122	412	0	ENST00000340398.3:c.154C>T	p.Arg52Cys	p.R52C	ENST00000340398	NM_001013699.2	52	Cgt/Tgt	1/1	0.313211013063409	1	FACETS	0.927	0.839	1	0.927	0.839	1	CLONAL	1	TRUE	0	0.313211013063409	1		412	709	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933480	100933480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766277966	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	93	449	0	ENST00000325455.5:c.1910G>A	p.Arg637Gln	p.R637Q	ENST00000325455	NM_001202474.3	637	cGa/cAa	4/8	1	2	FACETS	0.793	0.705	0.887	0.793	0.705	0.887	SUBCLONAL	1	TRUE	1	0.313211013063409	2		449	749	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455097	50455097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	151	443	0	ENST00000331340.3:c.644C>T	p.Ser215Phe	p.S215F	ENST00000331340	NM_006060.4	215	tCt/tTt	6/8	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.313211013063409	2		443	887	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858642	9858642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	203	680	0	ENST00000330684.3:c.2759G>A	p.Arg920Lys	p.R920K	ENST00000330684	NM_001134407.1	920	aGa/aAa	13/13	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.313211013063409	2		680	1217	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829302	72829302	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs924588701	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1222	186	914	0	ENST00000268489.5:c.7279G>A	p.Asp2427Asn	p.D2427N	ENST00000268489	NM_006885.3	2427	Gat/Aat	9/10	0.197744617070078	1	FACETS	0.711	0.655	0.77	0.711	0.655	0.77	SUBCLONAL	1	TRUE	0	0.313211013063409	1		914	1408	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597489	52597489	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	129	485	0	ENST00000394830.3:c.3821A>G	p.Lys1274Arg	p.K1274R	ENST00000394830	NM_018313.4	1274	aAg/aGg	25/30	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.313211013063409	2		485	794	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582407	119582407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199730714	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	100	317	3	ENST00000316626.5:c.994C>T	p.Arg332Cys	p.R332C	ENST00000316626		332	Cgt/Tgt	10/12	1	2	FACETS	0.949	0.848	1	0.949	0.848	1	CLONAL	1	TRUE	1	0.313211013063409	2		320	673	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106162519	106162519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	91	457	0	ENST00000380013.4:c.3433G>A	p.Gly1145Ser	p.G1145S	ENST00000380013	NM_001127208.2	1145	Ggt/Agt	4/11	1	2	FACETS	0.747	0.663	0.837	0.747	0.663	0.837	SUBCLONAL	1	TRUE	1	0.313211013063409	2		457	778	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535417	187535417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367986355	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	88	469	0	ENST00000441802.2:c.9157C>T	p.Arg3053Cys	p.R3053C	ENST00000441802	NM_005245.3	3053	Cgc/Tgc	12/27	1	2	FACETS	0.699	0.619	0.785	0.699	0.619	0.785	SUBCLONAL	1	TRUE	1	0.313211013063409	2		469	804	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876163	35876163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	276	515	0	ENST00000303115.3:c.955G>A	p.Glu319Lys	p.E319K	ENST00000303115	NM_002185.3	319	Gaa/Aaa	8/8	0.313211013063409	3	FACETS	0.991	0.932	1	0.991	0.932	1	CLONAL	2	TRUE	1	0.313211013063409	3		515	1028	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752324	57752324	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	145	497	0	ENST00000274289.3:c.1249G>C	p.Asp417His	p.D417H	ENST00000274289	NM_006622.3	417	Gat/Cat	9/14	0.313211013063409	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.313211013063409	1		497	678	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439282	149439282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766586864	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	152	548	1	ENST00000286301.3:c.2113G>A	p.Glu705Lys	p.E705K	ENST00000286301	NM_005211.3	705	Gag/Aag	15/22	0.313211013063409	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.313211013063409	1		549	778	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680245	30680245	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	190	697	0	ENST00000376406.3:c.1474T>G	p.Phe492Val	p.F492V	ENST00000376406	NM_014641.2	492	Ttt/Gtt	5/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.313211013063409	2		697	1112	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388107	81388107	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	146	434	0	ENST00000222390.5:c.268G>A	p.Asp90Asn	p.D90N	ENST00000222390	NM_000601.4	90	Gat/Aat	3/18	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.313211013063409	2		434	791	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92462418	92462418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	155	401	0	ENST00000265734.4:c.220C>T	p.Pro74Ser	p.P74S	ENST00000265734	NM_001259.6	74	Ccc/Tcc	2/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.313211013063409	2		401	798	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509582	106509582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	175	457	0	ENST00000359195.3:c.1576C>T	p.Pro526Ser	p.P526S	ENST00000359195	NM_002649.2	526	Ccg/Tcg	2/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.313211013063409	2		457	994	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851916	128851916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1418557662	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	192	594	0	ENST00000249373.3:c.1988C>T	p.Pro663Leu	p.P663L	ENST00000249373	NM_005631.4	663	cCa/cTa	12/12	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.313211013063409	2		594	1042	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140500189	140500189	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	238	742	2	ENST00000288602.6:c.953C>T	p.Pro318Leu	p.P318L	ENST00000288602	NM_004333.4	318	cCt/cTt	7/18	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.313211013063409	2		744	1262	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376627	8376627	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	174	518	1	ENST00000356435.5:c.4486C>T	p.Arg1496Ter	p.R1496*	ENST00000356435		1496	Cga/Tga	27/35	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.313211013063409	2		519	942	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760714	133760714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755821709	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	131	504	1	ENST00000318560.5:c.3037C>T	p.Arg1013Trp	p.R1013W	ENST00000318560	NM_005157.4	1013	Cgg/Tgg	11/11	0.313211013063409	1	FACETS	0.911	0.828	1	0.911	0.828	1	CLONAL	1	TRUE	0	0.313211013063409	1		505	774	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615611	43615611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs76087194	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	167	464	0	ENST00000355710.3:c.2690G>A	p.Arg897Gln	p.R897Q	ENST00000355710	NM_020975.4	897	cGa/cAa	15/20	0.313211013063409	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.313211013063409	1		464	747	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851833	63851833	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	186	522	0	ENST00000279873.7:c.2611C>T	p.Pro871Ser	p.P871S	ENST00000279873	NM_032199.2	871	Cct/Tct	10/10	0.313211013063409	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.313211013063409	1		522	835	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138122	64138122	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	97	329	2	ENST00000334205.4:c.2045C>T	p.Ser682Leu	p.S682L	ENST00000334205	NM_003942.2	682	tCg/tTg	16/17	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.313211013063409	2		331	596	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933403	100933403	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768769081	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	185	809	1	ENST00000325455.5:c.1987C>T	p.Pro663Ser	p.P663S	ENST00000325455	NM_001202474.3	663	Cca/Tca	4/8	1	2	FACETS	0.907	0.836	0.982	0.907	0.836	0.982	CLONAL	1	TRUE	1	0.313211013063409	2		810	1302	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118339509	118339509	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	110	427	0	ENST00000534358.1:c.452T>A	p.Phe151Tyr	p.F151Y	ENST00000534358	NM_005933.3	151	tTt/tAt	2/36	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.313211013063409	2		427	667	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142579	119142579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749633193	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	131	486	1	ENST00000264033.4:c.578C>T	p.Ala193Val	p.A193V	ENST00000264033	NM_005188.3	193	gCt/gTt	3/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.313211013063409	2		487	741	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4387932	4387932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	199	605	0	ENST00000261254.3:c.418G>A	p.Glu140Lys	p.E140K	ENST00000261254	NM_001759.3	140	Gaa/Aaa	3/5	0.313211013063409	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.313211013063409	1		605	851	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243878	46243878	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	149	493	0	ENST00000334344.6:c.1972C>T	p.Gln658Ter	p.Q658*	ENST00000334344	NM_152641.2	658	Caa/Taa	15/21	NA	2	FACETS	1	0.957	1			1	INDETERMINATE	1	TRUE	NA	0.313211013063409	2		493	883	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2132497	2132497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs796053497	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	119	514	0	ENST00000219476.3:c.3875C>T	p.Ser1292Phe	p.S1292F	ENST00000219476	NM_000548.3	1292	tCc/tTc	32/42	1	2	FACETS	0.891	0.804	0.983	0.891	0.804	0.983	CLONAL	1	TRUE	1	0.313211013063409	2		514	853	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857458	9857458	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759696882	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	101	445	0	ENST00000330684.3:c.3943G>A	p.Asp1315Asn	p.D1315N	ENST00000330684	NM_001134407.1	1315	Gac/Aac	13/13	1	2	FACETS	0.701	0.626	0.781	0.701	0.626	0.781	SUBCLONAL	1	TRUE	1	0.313211013063409	2		445	920	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857874	9857874	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	147	576	0	ENST00000330684.3:c.3527A>C	p.Glu1176Ala	p.E1176A	ENST00000330684	NM_001134407.1	1176	gAg/gCg	13/13	1	2	FACETS	0.946	0.863	1	0.946	0.863	1	CLONAL	1	TRUE	1	0.313211013063409	2		576	992	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9927961	9927961	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	133	507	0	ENST00000330684.3:c.1777+1G>A		p.X593_splice	ENST00000330684	NM_001134407.1	593			1	2	FACETS	0.983	0.893	1	0.983	0.893	1	CLONAL	1	TRUE	1	0.313211013063409	2		507	864	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014215	14014215	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	57	182	1	ENST00000311895.7:c.193C>A	p.Gln65Lys	p.Q65K	ENST00000311895	NM_005236.2	65	Cag/Aag	1/11	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.313211013063409	2		183	337	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993296	72993296	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757253455	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	197	797	1	ENST00000268489.5:c.749C>T	p.Ser250Phe	p.S250F	ENST00000268489	NM_006885.3	250	tCt/tTt	2/10	0.197744617070078	1	FACETS	0.778	0.718	0.84	0.778	0.718	0.84	SUBCLONAL	1	TRUE	0	0.313211013063409	1		798	1364	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346466	89346466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202219869	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	160	748	0	ENST00000301030.4:c.6484C>T	p.Pro2162Ser	p.P2162S	ENST00000301030	NM_001256183.1	2162	Cct/Tct	9/13	0.197744617070078	1	FACETS	0.747	0.684	0.814	0.747	0.684	0.814	SUBCLONAL	1	TRUE	0	0.313211013063409	1		748	1153	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554622	29554622	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1567848213	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	146	462	0	ENST00000356175.3:c.2407C>T	p.Gln803Ter	p.Q803*	ENST00000356175	NM_000267.3	803	Cag/Tag	20/57	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.313211013063409	2		462	885	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797381	42797381	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs563001303	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	98	482	1	ENST00000575354.2:c.3743C>T	p.Pro1248Leu	p.P1248L	ENST00000575354	NM_015125.3	1248	cCa/cTa	15/20	1	2	FACETS	0.795	0.709	0.887	0.795	0.709	0.887	SUBCLONAL	1	TRUE	1	0.313211013063409	2		483	787	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206818	36206818	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	98	249	1	ENST00000300305.3:c.694C>T	p.Arg232Trp	p.R232W	ENST00000300305		232	Cgg/Tgg	6/8	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.313211013063409	2		250	553	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572353	41572353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	182	519	0	ENST00000263253.7:c.4882G>A	p.Asp1628Asn	p.D1628N	ENST00000263253	NM_001429.3	1628	Gat/Aat	30/31	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.313211013063409	2		519	840	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247070	53247070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	294	400	0	ENST00000375401.3:c.430C>T	p.Pro144Ser	p.P144S	ENST00000375401	NM_004187.3	144	Cca/Tca	4/26	1	1	FACETS	1	0.975	1	1	0.996	1	CLONAL	2	TRUE	0	0.313211013063409	1		400	753	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411267	63411267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866313799	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	207	318	3	ENST00000330258.3:c.1900C>T	p.Arg634Cys	p.R634C	ENST00000330258	NM_152424.3	634	Cgt/Tgt	2/2	1	1	FACETS	0.964	0.901	1	1	0.994	1	CLONAL	2	TRUE	0	0.313211013063409	1		321	578	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220510	123220510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	555	412	0	ENST00000218089.9:c.3167C>T	p.Thr1056Ile	p.T1056I	ENST00000218089	NM_001042749.1	1056	aCc/aTc	30/35	0.313211013063409	2	FACETS	0.913	0.883	0.944			1	CLONAL	4	TRUE	NA	0.313211013063409	2		412	970	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729162	66729163	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	144	493	0	ENST00000307102.5:c.370_371delinsAT	p.Pro124Met	p.P124M	ENST00000307102	NM_002755.3	124	CCg/ATg	3/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.313211013063409	2		493	864	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577143	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0010115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	172	633	0	ENST00000269305.4:c.795_796delinsAA	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	265	ctGGga/ctAAga	8/11	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.313211013063409	2		633	1091	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0010131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	97	548	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.896	0.797	1	0.896	0.797	1	CLONAL	1	TRUE	1	0.214368267714964	2		548	1010	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034419	47034420	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0010131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	168	540	0	ENST00000377604.3:c.504_505del	p.Gln169GlufsTer10	p.Q169Efs*10	ENST00000377604	NM_001204468.1	168	ggTCag/ggag	6/24	0.209823640538254	3	FACETS	0.837	0.768	0.908	0.837	0.768	0.908	CLONAL	2	TRUE	1	0.214368267714964	3		540	1037	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143994	11143994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	143	617	3	ENST00000358026.2:c.3575G>A	p.Arg1192His	p.R1192H	ENST00000358026	NM_001128849.1	1192	cGc/cAc	26/36	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.431722892915841	2		620	606	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682896	190682896	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	91	552	0	ENST00000441310.2:c.572T>A	p.Val191Glu	p.V191E	ENST00000441310	NM_000534.4	191	gTa/gAa	5/13	0.193498010660165	3	FACETS	1	0.974	1	0.655	0.586	0.729	INDETERMINATE	1	TRUE	1	0.431722892915841	3		552	391	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52692218	52692218	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	309	689	0	ENST00000394830.3:c.642del	p.Val215CysfsTer9	p.V215Cfs*9	ENST00000394830	NM_018313.4	214	aaA/aa	6/30	0.431722892915841	3	FACETS	0.915	0.871	0.959	0.915	0.871	0.959	CLONAL	3	TRUE	0	0.431722892915841	3		689	634	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164857	47164857	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	171	621	0	ENST00000409792.3:c.1269del	p.Glu423AspfsTer61	p.E423Dfs*61	ENST00000409792	NM_014159.6	423	gaA/ga	3/21	0.431722892915841	3	FACETS	1	0.981	1	0.766	0.713	0.82	CLONAL	2	TRUE	0	0.431722892915841	3		621	419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0010165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	595	394	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.419445650068645	3	FACETS	0.964	0.931	0.996	1	0.997	1	CLONAL	3	TRUE	1	0.449154971897695	3		394	1122	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974792	21974792	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs141798398	NA	P-0010165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	218	129	0	ENST00000304494.5:c.35C>A	p.Ser12Ter	p.S12*	ENST00000304494	NM_000077.4	12	tCg/tAg	1/3	0.427096436309203	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	0	0.449154971897695	3		129	360	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557369	29557369	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	161	392	0	ENST00000356175.3:c.3082G>T	p.Asp1028Tyr	p.D1028Y	ENST00000356175	NM_000267.3	1028	Gac/Tac	23/57	0.419445650068645	3	FACETS	0.98	0.899	1	0.49	0.449	0.532	CLONAL	1	TRUE	1	0.449154971897695	3		392	896	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044408	128044408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373790042	NA	P-0010165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	427	478	0	ENST00000285398.2:c.1213G>A	p.Val405Ile	p.V405I	ENST00000285398	NM_000122.1	405	Gtt/Att	8/15	0.444292995668065	4	FACETS	0.942	0.896	0.988	0.942	0.896	0.988	CLONAL	2	TRUE	2	0.449154971897695	4		478	1463	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164886	36164891	+	inframe_deletion	In_Frame_Del	DEL	AACGCT	AACGCT	-	novel	NA	P-0010170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	127	235	0	ENST00000300305.3:c.984_989del	p.Ala329_Phe330del	p.A329_F330del	ENST00000300305		328	acAGCGTTc/acc	8/8	1	2	FACETS	0.903	0.823	0.988	0.903	0.823	0.988	CLONAL	1	TRUE	1	0.539650909142442	2		235	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0010172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	97	270	0	ENST00000269305.4:c.559+1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.170464689903971	2	FACETS	0.856	0.766	0.951	0.856	0.766	0.951	CLONAL	2	TRUE	0	0.221848255356445	2		270	511	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831953	72831953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1510	161	798	2	ENST00000268489.5:c.4628G>A	p.Arg1543His	p.R1543H	ENST00000268489	NM_006885.3	1543	cGc/cAc	9/10	0.194581476392744	3	FACETS	0.965	0.882	1			1	CLONAL	1	TRUE	NA	0.221848255356445	3		800	1671	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023895	27023895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	24	95	0	ENST00000324856.7:c.1001C>T	p.Ser334Leu	p.S334L	ENST00000324856	NM_006015.4	334	tCg/tTg	1/20	1	2	FACETS	0.813	0.639	1	0.813	0.639	1	CLONAL	1	TRUE	1	0.221848255356445	2		95	266	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147549	47147549	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	135	417	1	ENST00000409792.3:c.4777G>T	p.Val1593Leu	p.V1593L	ENST00000409792	NM_014159.6	1593	Gtg/Ttg	6/21	0.170464689903971	2	FACETS	0.753	0.685	0.825	0.753	0.685	0.825	SUBCLONAL	2	TRUE	0	0.221848255356445	2		418	808	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169554	11169554	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	343	424	0	ENST00000358026.2:c.4720G>T	p.Glu1574Ter	p.E1574*	ENST00000358026	NM_001128849.1	1574	Gag/Tag	33/36	0.204224698750195	4	FACETS	0.881	0.835	0.928	0.881	0.835	0.928	CLONAL	4	TRUE	0	0.221848255356445	4		424	1072	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1331503	1331503	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	77	454	0	ENST00000400841.2:c.25G>T	p.Gly9Ter	p.G9*	ENST00000400841		9	Gga/Tga	1/6	1	2	FACETS	0.707	0.619	0.802	0.707	0.619	0.802	SUBCLONAL	1	TRUE	1	0.221848255356445	2		454	982	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200098	123200098	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010172-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	91	644	0	ENST00000218089.9:c.2170G>C	p.Asp724His	p.D724H	ENST00000218089	NM_001042749.1	724	Gac/Cac	22/35	0.221848255356445	1	FACETS	0.673	0.596	0.756	0.673	0.596	0.756	SUBCLONAL	1	TRUE	0	0.221848255356445	1		644	1083	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462873	120462873	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	207	426	0	ENST00000256646.2:c.5458G>C	p.Asp1820His	p.D1820H	ENST00000256646	NM_024408.3	1820	Gat/Cat	30/34	0.154044859057304	5	FACETS	0.876	0.815	0.939	0.876	0.815	0.939	INDETERMINATE	3	TRUE	2	0.287925911950118	5		426	783	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935045	49935045	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	188	897	0	ENST00000296474.3:c.1954C>A	p.Pro652Thr	p.P652T	ENST00000296474	NM_002447.2	652	Cct/Act	6/20	0.272965527794845	2	FACETS	1	0.972	1	0.557	0.513	0.602	CLONAL	1	TRUE	0	0.287925911950118	2		897	1173	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687097	176687097	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	229	704	0	ENST00000439151.2:c.5074C>G	p.His1692Asp	p.H1692D	ENST00000439151	NM_022455.4	1692	Cac/Gac	14/23	0.287925911950118	2	FACETS	0.881	0.822	0.941	0.881	0.822	0.941	CLONAL	2	TRUE	0	0.287925911950118	2		704	903	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38315007	38315007	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	265	625	1	ENST00000425967.3:c.57G>T	p.Trp19Cys	p.W19C	ENST00000425967	NM_001174067.1	19	tgG/tgT	3/19	0.287925911950118	2	FACETS	0.957	0.898	1	0.957	0.898	1	CLONAL	2	TRUE	0	0.287925911950118	2		626	962	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650066	93650066	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0010174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1274	108	652	0	ENST00000375746.1:c.1617C>G	p.Tyr539Ter	p.Y539*	ENST00000375746	NM_001174167.1	539	taC/taG	12/14	0.287925911950118	6	FACETS	0.855	0.765	0.952	0.214	0.191	0.238	CLONAL	1	TRUE	2	0.287925911950118	6		652	1382	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138112	64138112	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	157	381	0	ENST00000334205.4:c.2035G>C	p.Ala679Pro	p.A679P	ENST00000334205	NM_003942.2	679	Gcg/Ccg	16/17	0.276040587219975	3	FACETS	0.96	0.882	1	0.96	0.882	1	CLONAL	2	TRUE	1	0.287925911950118	3		381	650	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549449	21549449	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	73	195	0	ENST00000382592.4:c.2827G>C	p.Glu943Gln	p.E943Q	ENST00000382592	NM_014572.2	943	Gag/Cag	8/8	NA	2	FACETS	0.821	0.724	0.922			1	INDETERMINATE	2	TRUE	NA	0.287925911950118	2		195	309	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916281	9916281	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	497	444	0	ENST00000330684.3:c.2008T>A	p.Phe670Ile	p.F670I	ENST00000330684	NM_001134407.1	670	Ttt/Att	10/13	0.287925911950118	4	FACETS	0.974	0.939	1	1	0.995	1	CLONAL	5	TRUE	0	0.287925911950118	4		444	913	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579327	7579327	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	289	451	0	ENST00000269305.4:c.360G>T	p.Lys120Asn	p.K120N	ENST00000269305	NM_001126112.2	120	aaG/aaT	4/11	0.232317556755886	3	FACETS	0.997	0.942	1			1	CLONAL	3	TRUE	NA	0.287925911950118	3		451	768	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322626	30322626	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	117	630	0	ENST00000322652.5:c.1639G>C	p.Glu547Gln	p.E547Q	ENST00000322652	NM_015355.2	547	Gaa/Caa	14/16	0.276040587219975	3	FACETS	0.88	0.792	0.974	0.44	0.396	0.487	CLONAL	1	TRUE	1	0.287925911950118	3		630	1056	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292538	15292538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1436528088	NA	P-0010174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	271	660	0	ENST00000263388.2:c.2641G>A	p.Gly881Ser	p.G881S	ENST00000263388	NM_000435.2	881	Ggc/Agc	17/33	0.287925911950118	6	FACETS	1	0.98	1			1	CLONAL	2	TRUE	NA	0.287925911950118	6		660	1335	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139438539	139438542	+	frameshift_variant	Frame_Shift_Del	DEL	TGGG	TGGG	-	novel	NA	P-0010174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	182	587	0	ENST00000277541.6:c.74_77del	p.Ser25CysfsTer7	p.S25Cfs*7	ENST00000277541	NM_017617.3	25	tCCCAg/tg	2/34	0.272965527794845	2	FACETS	0.826	0.764	0.891	0.826	0.764	0.891	CLONAL	2	TRUE	0	0.287925911950118	2		587	765	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	45	389	0				ENST00000310581	NM_198253.2	-/1132			0.218439983243712	1	FACETS	0.773	0.655	0.9	1	0.963	1	SUBCLONAL	2	TRUE	0	0.219604880001115	1		389	236	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0010199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	105	580	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.754	0.677	0.836	1	0.982	1	SUBCLONAL	2	TRUE	1	0.219604880001115	2		580	634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057519990	NA	P-0010199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	95	416	0	ENST00000269305.4:c.796G>T	p.Gly266Ter	p.G266*	ENST00000269305	NM_001126112.2	266	Gga/Tga	8/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.219604880001115	2		416	714	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748481	162748481	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	44	284	0	ENST00000367921.3:c.2395G>A	p.Glu799Lys	p.E799K	ENST00000367921	NM_006182.2	799	Gag/Aag	17/18	0.219604880001115	3	FACETS	0.659	0.551	0.778	0.329	0.275	0.389	SUBCLONAL	1	TRUE	1	0.219604880001115	3		284	675	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267752	198267752	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	51	277	0	ENST00000335508.6:c.1727T>C	p.Val576Ala	p.V576A	ENST00000335508	NM_012433.2	576	gTg/gCg	13/25	0.219604880001115	4	FACETS	0.862	0.732	1	0.431	0.366	0.503	CLONAL	1	TRUE	2	0.219604880001115	4		277	657	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650768	12650768	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2042	786	403	0	ENST00000251849.4:c.387T>G	p.Asp129Glu	p.D129E	ENST00000251849	NM_002880.3	129	gaT/gaG	4/17	0.219604880001115	21	FACETS	0.976	0.941	1			1	CLONAL	8	TRUE	NA	0.219604880001115	21		403	2828	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670521	134670521	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	109	516	0	ENST00000398015.3:c.432G>T	p.Glu144Asp	p.E144D	ENST00000398015	NM_004441.4	144	gaG/gaT	3/16	0.219604880001115	4	FACETS	0.811	0.729	0.899	0.811	0.729	0.899	CLONAL	2	TRUE	2	0.219604880001115	4		516	746	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629850	187629850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	84	585	0	ENST00000441802.2:c.1132G>A	p.Glu378Lys	p.E378K	ENST00000441802	NM_005245.3	378	Gaa/Aaa	2/27	0.219604880001115	3	FACETS	0.937	0.826	1	0.469	0.413	0.528	CLONAL	1	TRUE	1	0.219604880001115	3		585	906	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718216	117718216	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	107	380	0	ENST00000368508.3:c.641G>T	p.Ser214Ile	p.S214I	ENST00000368508	NM_002944.2	214	aGc/aTc	7/43	0.161841461930577	4	FACETS	0.751	0.674	0.834	0.751	0.674	0.834	SUBCLONAL	2	TRUE	2	0.219604880001115	4		380	791	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525831	148525831	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0010199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	73	271	0	ENST00000320356.2:c.625+1G>T		p.X209_splice	ENST00000320356	NM_004456.4	209			0.161841461930577	4	FACETS	1	0.97	1	0.695	0.609	0.789	CLONAL	1	TRUE	2	0.219604880001115	4		271	583	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156648	2156648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	118	529	1	ENST00000434045.2:c.274G>A	p.Glu92Lys	p.E92K	ENST00000434045	NM_001127598.1	92	Gag/Aag	3/5	0.218439983243712	1	FACETS	1	0.922	1	1	0.989	1	CLONAL	2	TRUE	0	0.219604880001115	1		530	470	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793363	18793363	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	66	411	0	ENST00000266497.5:c.4060C>T	p.His1354Tyr	p.H1354Y	ENST00000266497		1354	Cat/Tat	30/31	0.219604880001115	4	FACETS	0.877	0.76	1	0.438	0.38	0.503	CLONAL	1	TRUE	2	0.219604880001115	4		411	836	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122875	2122875	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766442736	NA	P-0010199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	112	452	1	ENST00000219476.3:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000219476	NM_000548.3	749	cGg/cAg	21/42	1	2	FACETS	0.773	0.696	0.854	1	0.984	1	SUBCLONAL	2	TRUE	1	0.219604880001115	2		453	660	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226170	2226170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1394758490	NA	P-0010199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	36	376	0	ENST00000326181.6:c.1867C>T	p.Arg623Trp	p.R623W	ENST00000326181	NM_032271.2	623	Cgg/Tgg	19/21	1	2	FACETS	0.931	0.767	1	0.931	0.767	1	CLONAL	1	TRUE	1	0.219604880001115	2		376	352	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351827	89351827	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1529	125	1170	0	ENST00000301030.4:c.1123A>G	p.Thr375Ala	p.T375A	ENST00000301030	NM_001256183.1	375	Acg/Gcg	9/13	1	2	FACETS	0.688	0.62	0.761	0.688	0.62	0.761	SUBCLONAL	1	TRUE	1	0.219604880001115	2		1170	1654	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17947944	17947944	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	94	253	0	ENST00000458235.1:c.1780G>T	p.Gly594Ter	p.G594*	ENST00000458235	NM_000215.3	594	Gga/Tga	13/24	1	2	FACETS	0.98	0.876	1	1	0.986	1	CLONAL	2	TRUE	1	0.219604880001115	2		253	437	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871914	45871914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760820378	NA	P-0010199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	82	508	1	ENST00000391945.4:c.334C>T	p.Arg112Cys	p.R112C	ENST00000391945	NM_000400.3	112	Cgc/Tgc	5/23	0.219604880001115	1	FACETS	0.936	0.825	1	0.936	0.825	1	CLONAL	1	TRUE	0	0.219604880001115	1		509	710	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426644	47426644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755638812	NA	P-0010199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	127	296	1	ENST00000377045.4:c.889C>T	p.Arg297Trp	p.R297W	ENST00000377045	NM_001654.4	297	Cgg/Tgg	10/16	0.186492491537349	2	FACETS	1	0.979	1			1	CLONAL	2	TRUE	NA	0.219604880001115	2		297	464	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183797	10183797	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs5030807	NA	P-0010212-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	167	286	1	ENST00000256474.2:c.266T>A	p.Leu89His	p.L89H	ENST00000256474	NM_000551.3	89	cTc/cAc	1/3	0.249796510550375	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	FALSE	0	0.253049875185568	2		287	609	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138376590	138376590	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010212-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	29	563	0	ENST00000289153.2:c.2884T>A	p.Tyr962Asn	p.Y962N	ENST00000289153	NM_006219.2	962	Tat/Aat	20/22	0.151115402698435	5	FACETS	0.62	0.497	0.761	0.207	0.165	0.254	INDETERMINATE	1	FALSE	2	0.253049875185568	5		563	510	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106182974	106182974	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010212-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	57	567	0	ENST00000380013.4:c.4013A>C	p.Lys1338Thr	p.K1338T	ENST00000380013	NM_001127208.2	1338	aAg/aCg	8/11	0.253049875185568	3	FACETS	0.788	0.68	0.904	0.788	0.68	0.904	CLONAL	2	FALSE	1	0.253049875185568	3		567	322	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348281	70348281	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010212-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	292	291	0	ENST00000374080.3:c.3345C>G	p.Cys1115Trp	p.C1115W	ENST00000374080		1115	tgC/tgG	23/45	0.218744485802626	2	FACETS	1	0.984	1			1	CLONAL	3	FALSE	NA	0.253049875185568	2		291	704	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0010221-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	158	635	1	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	0.614533110248232	1	FACETS	0.747	0.691	0.803	0.747	0.691	0.803	SUBCLONAL	1	TRUE	0	0.656607974815988	1		636	433	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456470	89456470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147450955	NA	P-0010221-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	122	555	1	ENST00000336596.2:c.1646C>T	p.Ala549Val	p.A549V	ENST00000336596	NM_005233.5	549	gCg/gTg	8/17	1	2	FACETS	0.885	0.806	0.966	0.885	0.806	0.966	CLONAL	1	TRUE	1	0.656607974815988	2		556	420	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851574	134851574	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747682274	NA	P-0010221-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	87	271	0	ENST00000398015.3:c.980G>A	p.Arg327His	p.R327H	ENST00000398015	NM_004441.4	327	cGc/cAc	5/16	1	2	FACETS	0.852	0.762	0.946	0.852	0.762	0.946	CLONAL	1	TRUE	1	0.656607974815988	2		271	311	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020817	112020817	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010221-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	286	981	0	ENST00000368678.4:c.754C>T	p.Gln252Ter	p.Q252*	ENST00000368678		252	Caa/Taa	8/13	0.238927275210572	1	FACETS	0.588	0.553	0.624	0.588	0.553	0.624	INDETERMINATE	1	TRUE	0	0.656607974815988	1		981	995	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928065	178928076	+	inframe_deletion	In_Frame_Del	DEL	TACCTCATGGAT	TACCTCATGGAT	-	novel	NA	P-0010221-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	82	438	0	ENST00000263967.3:c.1345_1356del	p.Pro449_Leu452del	p.P449_L452del	ENST00000263967	NM_006218.2	448	gTACCTCATGGATta/gta	8/21	1	2	FACETS	0.704	0.625	0.786	0.704	0.625	0.786	SUBCLONAL	1	TRUE	1	0.656607974815988	2		438	355	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0010222-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	181	585	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.628666924958706	6	FACETS	1	0.977	1	0.561	0.521	0.603	CLONAL	2	FALSE	2	0.628666924958706	6		586	579	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252869	36252869	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs993436723	NA	P-0010222-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	96	351	2	ENST00000300305.3:c.493G>A	p.Gly165Ser	p.G165S	ENST00000300305		165	Ggt/Agt	4/8	0.298175121565383	3	FACETS	0.651	0.58	0.725	0.325	0.29	0.363	INDETERMINATE	1	FALSE	1	0.628666924958706	3		353	617	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404198	139404198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010222-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	47	322	1	ENST00000277541.6:c.2956G>A	p.Asp986Asn	p.D986N	ENST00000277541	NM_017617.3	986	Gac/Aac	18/34	0.421801484229367	5	FACETS	0.975	0.827	1	0.195	0.165	0.228	CLONAL	1	FALSE	0	0.628666924958706	5		323	298	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0010222-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	117	458	0	ENST00000269305.4:c.783-1del		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.628666924958706	6	FACETS	0.982	0.892	1	0.491	0.446	0.538	CLONAL	2	FALSE	2	0.628666924958706	6		458	428	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782177	NA	P-0010238-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	818	687	1	ENST00000269305.4:c.644G>T	p.Ser215Ile	p.S215I	ENST00000269305	NM_001126112.2	215	aGt/aTt	6/11	0.840989435891676	2	FACETS	0.948	0.93	0.966	0.948	0.93	0.966	CLONAL	2	TRUE	0	0.850631580470739	2		688	1014	SUCCESS
APC	324	MSKCC	GRCh37	5	112176171	112176171	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010238-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	17	550	0	ENST00000257430.4:c.4880A>C	p.Gln1627Pro	p.Q1627P	ENST00000257430	NM_000038.5	1627	cAa/cCa	16/16	0.826397145746478	2	FACETS	0.263	0.197	0.34	0.131	0.098	0.17	SUBCLONAL	1	TRUE	0	0.850631580470739	2		550	152	SUCCESS
APC	324	MSKCC	GRCh37	5	112176309	112176309	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010238-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	40	396	0	ENST00000257430.4:c.5018A>G	p.Glu1673Gly	p.E1673G	ENST00000257430	NM_000038.5	1673	gAa/gGa	16/16	0.826397145746478	2	FACETS	0.192	0.159	0.229	0.096	0.079	0.115	SUBCLONAL	1	TRUE	0	0.850631580470739	2		396	489	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239529	123239529	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs201752803	NA	P-0010238-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	331	946	0	ENST00000358487.5:c.2308T>G	p.Leu770Val	p.L770V	ENST00000358487	NM_000141.4	770	Ttg/Gtg	18/18	0.571001022243149	1	FACETS	0.351	0.332	0.372	0.351	0.332	0.372	SUBCLONAL	1	TRUE	0	0.850631580470739	1		946	1273	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206575	108206575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138526014	NA	P-0010238-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	314	419	1	ENST00000278616.4:c.8155C>T	p.Arg2719Cys	p.R2719C	ENST00000278616	NM_000051.3	2719	Cgt/Tgt	56/63	1	2	FACETS	0.95	0.901	1	0.95	0.901	1	CLONAL	1	TRUE	1	0.850631580470739	2		420	777	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138243	2138243	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs761618860	NA	P-0010238-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	445	550	0	ENST00000219476.3:c.5176C>A	p.His1726Asn	p.H1726N	ENST00000219476	NM_000548.3	1726	Cat/Aat	41/42	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.850631580470739	2		550	1021	SUCCESS
APC	324	MSKCC	GRCh37	5	112176306	112176317	+	inframe_deletion	In_Frame_Del	DEL	GAGAAGGAGTTA	GAGAAGGAGTTA	-	novel	NA	P-0010238-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	349	404	0	ENST00000257430.4:c.5018_5029del	p.Glu1673_Arg1676del	p.E1673_R1676del	ENST00000257430	NM_000038.5	1672	gGAGAAGGAGTTAga/gga	16/16	0.826397145746478	2	FACETS	0.827	0.798	0.856	0.827	0.798	0.856	CLONAL	2	TRUE	0	0.850631580470739	2		404	496	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426628	49426645	+	inframe_deletion	In_Frame_Del	DEL	GCTGTTGCTGCTGTTGAA	GCTGTTGCTGCTGTTGAA	-	rs762810380	NA	P-0010238-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	95	411	0	ENST00000301067.7:c.11843_11860del	p.Leu3948_Gln3953del	p.L3948_Q3953del	ENST00000301067	NM_003482.3	3948	cTTCAACAGCAGCAACAGCag/cag	39/54	0.269437854782754	2	FACETS	0.375	0.334	0.418	0.187	0.167	0.209	INDETERMINATE	1	TRUE	0	0.850631580470739	2		411	596	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123833	46123833	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	172	299	0	ENST00000334344.6:c.102del	p.Phe34LeufsTer24	p.F34Lfs*24	ENST00000334344	NM_152641.2	33	ccT/cc	2/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.838081042971738	2		299	374	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069467	30069470	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	novel	NA	P-0010239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	142	306	0	ENST00000338641.4:c.1334_1337del	p.Glu445GlyfsTer9	p.E445Gfs*9	ENST00000338641	NM_000268.3	444	tcAGAG/tc	12/16	0.838081042971738	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	0	0.838081042971738	1		306	189	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0010247-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	133	548	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.267317294207449	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.12	3		548	1052	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0010247-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	97	533	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.267317294207449	3	FACETS	0.807	0.718	0.902	0.807	0.718	0.902	CLONAL	2	TRUE	1	0.12	3		533	1062	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0010256-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	31	424	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.3	1	FACETS	0.125	0.1	0.152	0.125	0.1	0.152	INDETERMINATE	1	TRUE	0	0.75	1		424	414	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220488	1220488	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913316	NA	P-0010256-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	97	422	0	ENST00000326873.7:c.581A>T	p.Asp194Val	p.D194V	ENST00000326873	NM_000455.4	194	gAc/gTc	4/10	1	2	FACETS	0.536	0.479	0.595	0.536	0.479	0.595	SUBCLONAL	1	TRUE	1	0.75	2		422	483	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799288	88799288	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010256-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	57	566	0	ENST00000360948.2:c.97C>A	p.Pro33Thr	p.P33T	ENST00000360948	NM_001012338.2	33	Cct/Act	2/19	1	2	FACETS	0.254	0.217	0.294	0.254	0.217	0.294	SUBCLONAL	1	TRUE	1	0.75	2		566	599	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306758	41306758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010256-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	22	340	0	ENST00000373198.4:c.901G>A	p.Gly301Arg	p.G301R	ENST00000373198	NM_133170.3	301	Ggg/Agg	7/32	1	2	FACETS	0.198	0.153	0.25	0.198	0.153	0.25	SUBCLONAL	1	TRUE	1	0.75	2		340	296	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670327	134670327	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373140258	NA	P-0010272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	363	232	0	ENST00000398015.3:c.238C>T	p.Arg80Trp	p.R80W	ENST00000398015	NM_004441.4	80	Cgg/Tgg	3/16	0.365771738328824	6	FACETS	1	0.989	1	0.85	0.808	0.893	CLONAL	3	TRUE	2	0.365771738328824	6		232	1011	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325851	65325851	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	227	260	0	ENST00000342505.4:c.1271G>T	p.Cys424Phe	p.C424F	ENST00000342505	NM_002227.2	424	tGc/tTc	9/25	0.365771738328824	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.365771738328824	3		260	670	SUCCESS
FH	2271	MSKCC	GRCh37	1	241671997	241671997	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs770141324	NA	P-0010272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	157	293	0	ENST00000366560.3:c.644A>G	p.His215Arg	p.H215R	ENST00000366560	NM_000143.3	215	cAt/cGt	5/10	0.365771738328824	5	FACETS	1	0.987	1	0.484	0.443	0.527	CLONAL	1	TRUE	2	0.365771738328824	5		293	916	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577504	7577507	+	protein_altering_variant	In_Frame_Del	DEL	GTCT	GTCT	C	novel	NA	P-0010272-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	199	314	0	ENST00000269305.4:c.774_777delinsG	p.Asp259del	p.D259del	ENST00000269305	NM_001126112.2	258	gaAGAC/gaG	7/11	0.365771738328824	2	FACETS	0.893	0.832	0.956	0.893	0.832	0.956	CLONAL	2	TRUE	0	0.365771738328824	2		314	609	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372163	45372163	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010301-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	185	362	0	ENST00000262160.6:c.1006G>T	p.Val336Leu	p.V336L	ENST00000262160	NM_005901.5	336	Gtg/Ttg	9/11	0.524558017505208	4	FACETS	0.756	0.704	0.81			1	INDETERMINATE	2	FALSE	NA	0.901650615773819	4		362	516	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0010302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	180	332	0				ENST00000310581	NM_198253.2	-/1132			0.413670769085814	4	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	2	0.492715738950905	4		332	544	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104264061	104264061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	387	569	0	ENST00000369902.3:c.152C>T	p.Pro51Leu	p.P51L	ENST00000369902	NM_016169.3	51	cCg/cTg	1/12	0.492715738950905	2	FACETS	0.938	0.897	0.98	0.938	0.897	0.98	CLONAL	2	TRUE	0	0.492715738950905	2		569	837	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731233	162731233	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	45	326	0	ENST00000367921.3:c.1088C>G	p.Thr363Ser	p.T363S	ENST00000367921	NM_006182.2	363	aCc/aGc	9/18	0.492715738950905	3	FACETS	0.389	0.326	0.458	0.13	0.108	0.153	SUBCLONAL	1	TRUE	0	0.492715738950905	3		326	586	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085777	16085777	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	49	361	0	ENST00000281043.3:c.953T>G	p.Leu318Arg	p.L318R	ENST00000281043	NM_005378.4	318	cTg/cGg	3/3	0.473861674244247	3	FACETS	0.418	0.353	0.489	0.209	0.176	0.245	SUBCLONAL	1	TRUE	1	0.492715738950905	3		361	593	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0010318-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	73	383	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.373589649646273	5	FACETS	1	0.964	1	0.818	0.726	0.914	CLONAL	2	TRUE	2	0.402823408718574	5		383	237	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038511	47038511	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010318-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	103	304	1	ENST00000377604.3:c.673C>T	p.Gln225Ter	p.Q225*	ENST00000377604	NM_001204468.1	225	Cag/Tag	8/24	0.242125479591057	2	FACETS	0.972	0.885	1			1	CLONAL	2	TRUE	NA	0.402823408718574	2		305	263	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879796	37879798	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0010318-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	50	203	0	ENST00000269571.5:c.2092_2094del	p.Glu698del	p.E698del	ENST00000269571		697	gtGGAg/gtg	18/27	0.373589649646273	5	FACETS	0.909	0.78	1	0.606	0.52	0.698	CLONAL	2	TRUE	2	0.402823408718574	5		203	219	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579852	7579852	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010318-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	61	477	0	ENST00000269305.4:c.61del	p.Asp21ThrfsTer23	p.D21Tfs*23	ENST00000269305	NM_001126112.2	21	Gac/ac	2/11	0.239011205346783	2	FACETS	1	0.962	1	0.642	0.56	0.728	INDETERMINATE	1	TRUE	0	0.402823408718574	2		477	236	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0010319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	103	223	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.500456360513605	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	FALSE	0	0.500456360513605	1		223	306	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612087	43612087	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	265	834	1	ENST00000355710.3:c.2192G>T	p.Gly731Val	p.G731V	ENST00000355710	NM_020975.4	731	gGa/gTa	12/20	0.178171953389342	0	FACETS	0.453	0.424	0.483			1	INDETERMINATE	1	FALSE	0	0.500456360513605	0		835	1168	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919150	178919150	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs751662352	NA	P-0010327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	112	354	0	ENST00000263967.3:c.635A>G	p.Asn212Ser	p.N212S	ENST00000263967	NM_006218.2	212	aAc/aGc	4/21	1	2	FACETS	0.921	0.829	1	1	0.987	1	CLONAL	2	TRUE	1	0.17	2		354	715	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825338	134825338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	205	292	0	ENST00000398015.3:c.854C>T	p.Ser285Phe	p.S285F	ENST00000398015	NM_004441.4	285	tCc/tTc	4/16	1	2	FACETS	0.958	0.897	1	0.958	0.897	1	CLONAL	1	TRUE	1	0.854224554434017	2		292	501	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971360	13971360	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	230	372	0	ENST00000405192.2:c.569T>A	p.Leu190His	p.L190H	ENST00000405192	NM_001163147.1	190	cTt/cAt	8/12	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.854224554434017	2		372	505	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615668	100615668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	336	788	0	ENST00000308731.7:c.664C>T	p.Leu222Phe	p.L222F	ENST00000308731	NM_000061.2	222	Ctt/Ttt	8/19	0.204584420165467	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.854224554434017	0		788	819	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010336-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	184	389	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.862543974352538	2		389	365	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699495	117699495	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010336-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	257	229	0	ENST00000369458.3:c.146G>T	p.Gly49Val	p.G49V	ENST00000369458	NM_024626.3	49	gGg/gTg	3/6	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.862543974352538	2		229	548	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185200231	185200231	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010336-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	396	338	0	ENST00000265026.3:c.2888C>A	p.Ser963Tyr	p.S963Y	ENST00000265026	NM_004721.4	963	tCt/tAt	14/14	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.862543974352538	2		338	891	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397741	116397741	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010336-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2718	357	571	0	ENST00000397752.3:c.2015G>A	p.Gly672Asp	p.G672D	ENST00000397752	NM_000245.2	672	gGc/gAc	8/21	0.862543974352538	6	FACETS	0.734	0.691	0.778			1	SUBCLONAL	1	TRUE	NA	0.862543974352538	6		571	3075	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517201	NA	P-0010345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	34	247	0	ENST00000263967.3:c.1637A>C	p.Gln546Pro	p.Q546P	ENST00000263967	NM_006218.2	546	cAg/cCg	10/21	1	2	FACETS	0.825	0.677	0.989	0.825	0.677	0.989	CLONAL	1	TRUE	1	0.311104368466772	2		247	265	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28929495	NA	P-0010345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	111	398	0	ENST00000275493.2:c.2155G>T	p.Gly719Cys	p.G719C	ENST00000275493	NM_005228.3	719	Ggc/Tgc	18/28	1	2	FACETS	0.995	0.895	1	0.995	0.895	1	CLONAL	1	TRUE	1	0.311104368466772	2		398	717	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0010345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	45	383	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	1	2	FACETS	0.778	0.655	0.912	0.778	0.655	0.912	CLONAL	1	TRUE	1	0.311104368466772	2		383	372	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127699	47127699	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0010345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	27	362	0	ENST00000409792.3:c.5383A>T	p.Lys1795Ter	p.K1795*	ENST00000409792	NM_014159.6	1795	Aag/Tag	11/21	1	2	FACETS	0.38	0.302	0.47	0.38	0.302	0.47	SUBCLONAL	1	TRUE	1	0.311104368466772	2		362	457	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251922	153251922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010345-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	94	773	0	ENST00000281708.4:c.1084G>A	p.Asp362Asn	p.D362N	ENST00000281708	NM_033632.3	362	Gat/Aat	7/12	1	2	FACETS	0.76	0.676	0.85	0.76	0.676	0.85	SUBCLONAL	1	TRUE	1	0.311104368466772	2		773	795	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0010386-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	82	301	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	0.287957436993053	2		301	449	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263979	16263979	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010386-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	42	568	0	ENST00000375759.3:c.10348C>T	p.Gln3450Ter	p.Q3450*	ENST00000375759	NM_015001.2	3450	Cag/Tag	12/15	1	2	FACETS	0.409	0.34	0.486	0.409	0.34	0.486	SUBCLONAL	1	TRUE	1	0.287957436993053	2		568	713	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246629	46246629	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010386-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	43	218	0	ENST00000334344.6:c.4723C>T	p.Gln1575Ter	p.Q1575*	ENST00000334344	NM_152641.2	1575	Cag/Tag	15/21	1	2	FACETS	0.786	0.666	0.915	1	0.963	1	CLONAL	2	TRUE	1	0.287957436993053	2		218	190	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs770248150	NA	P-0010403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	22	457	0	ENST00000311936.3:c.351A>T	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaT	4/5	1	2	FACETS	0.189	0.146	0.241	0.189	0.146	0.241	SUBCLONAL	1	TRUE	1	0.29	2		457	801	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0010407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	252	532	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.533295135314706	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.551106562571353	2		534	406	SUCCESS
APC	324	MSKCC	GRCh37	5	112175246	112175246	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1057517558	NA	P-0010407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	91	230	0	ENST00000257430.4:c.3956del	p.Pro1319LeufsTer2	p.P1319Lfs*2	ENST00000257430	NM_000038.5	1319	Cct/ct	16/16	0.412471283018817	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.551106562571353	1		230	210	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747850	41747850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	77	469	1	ENST00000226382.2:c.919G>A	p.Ala307Thr	p.A307T	ENST00000226382	NM_003924.3	307	Gcc/Acc	3/3	0.2583360963277	3	FACETS	1	0.914	1	0.346	0.306	0.389	INDETERMINATE	1	TRUE	0	0.551106562571353	3		470	343	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677876	47677876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	83	226	0	ENST00000347630.2:c.989C>T	p.Ser330Leu	p.S330L	ENST00000347630	NM_001007230.1	330	tCg/tTg	11/11	0.147208590567259	5	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.551106562571353	5		226	429	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286743	212286743	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	103	387	2	ENST00000342788.4:c.2953C>A	p.Leu985Ile	p.L985I	ENST00000342788	NM_005235.2	985	Cta/Ata	24/28	0.551106562571353	3	FACETS	0.963	0.866	1	0.482	0.433	0.533	CLONAL	1	TRUE	1	0.551106562571353	3		389	495	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495753	72495753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	85	427	0	ENST00000477973.2:c.319C>T	p.Pro107Ser	p.P107S	ENST00000477973	NM_012234.5	107	Cct/Tct	1/4	0.459785664793158	3	FACETS	0.789	0.699	0.884	0.394	0.349	0.442	SUBCLONAL	1	TRUE	1	0.551106562571353	3		427	499	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97934374	97934374	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	39	551	0	ENST00000289081.3:c.401T>G	p.Phe134Cys	p.F134C	ENST00000289081	NM_000136.2	134	tTc/tGc	5/15	1	2	FACETS	0.297	0.246	0.354	0.297	0.246	0.354	SUBCLONAL	1	TRUE	1	0.551106562571353	2		551	477	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625359	69625359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782088765	NA	P-0010407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	53	485	3	ENST00000334134.2:c.434G>A	p.Arg145Gln	p.R145Q	ENST00000334134	NM_005247.2	145	cGg/cAg	3/3	0.377902994935356	2	FACETS	0.486	0.415	0.562	0.243	0.207	0.281	SUBCLONAL	1	TRUE	0	0.551106562571353	2		488	396	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912816	32912816	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	218	1208	2	ENST00000380152.3:c.4324T>A	p.Ser1442Thr	p.S1442T	ENST00000380152		1442	Tca/Aca	11/27	0.248831870557474	5	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.551106562571353	5		1210	1363	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169468	11169468	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	91	449	1	ENST00000358026.2:c.4634G>T	p.Arg1545Leu	p.R1545L	ENST00000358026	NM_001128849.1	1545	cGc/cTc	33/36	0.225095823341182	2	FACETS	0.729	0.65	0.812	0.365	0.325	0.406	INDETERMINATE	1	TRUE	0	0.551106562571353	2		450	453	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291593	15291593	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	54	383	2	ENST00000263388.2:c.3041G>A	p.Arg1014His	p.R1014H	ENST00000263388	NM_000435.2	1014	cGc/cAc	19/33	0.225095823341182	2	FACETS	0.7	0.602	0.805	0.35	0.301	0.403	INDETERMINATE	1	TRUE	0	0.551106562571353	2		385	280	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375418	15375418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471575560	NA	P-0010407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	75	550	0	ENST00000263377.2:c.1009G>A	p.Asp337Asn	p.D337N	ENST00000263377	NM_058243.2	337	Gac/Aac	6/20	0.225095823341182	2	FACETS	0.495	0.434	0.56	0.247	0.217	0.28	INDETERMINATE	1	TRUE	0	0.551106562571353	2		550	550	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274097	18274097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751032325	NA	P-0010407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	15	294	0	ENST00000222254.8:c.1315G>A	p.Val439Met	p.V439M	ENST00000222254	NM_005027.3	439	Gtg/Atg	11/16	0.225095823341182	2	FACETS	0.202	0.147	0.267	0.101	0.073	0.134	INDETERMINATE	1	TRUE	0	0.551106562571353	2		294	270	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873688	37873716	+	frameshift_variant	Frame_Shift_Del	DEL	ATGAGGAGGGCGCATGCCAGCCTTGCCCC	ATGAGGAGGGCGCATGCCAGCCTTGCCCC	-	novel	NA	P-0010407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	30	479	0	ENST00000269571.5:c.1855_1883del	p.Glu619GlnfsTer11	p.E619Qfs*11	ENST00000269571		618	gATGAGGAGGGCGCATGCCAGCCTTGCCCC/g	15/27	0.290579153805582	3	FACETS	0.26	0.208	0.318			1	INDETERMINATE	1	TRUE	NA	0.551106562571353	3		479	535	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692884	89692884	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121909222	NA	P-0010419-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	92	509	2	ENST00000371953.3:c.368A>G	p.His123Arg	p.H123R	ENST00000371953	NM_000314.4	123	cAc/cGc	5/9	0.101959598785852	3	FACETS	0.969	0.863	1	0.485	0.431	0.541	INDETERMINATE	1	TRUE	1	0.413551247768169	3		511	554	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693005	89693010	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	AAAGGT	AAAGGT	-	novel	NA	P-0010419-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	43	541	0	ENST00000371953.3:c.491_492+4del		p.X164_splice	ENST00000371953	NM_000314.4	164		5/9	0.101959598785852	3	FACETS	0.425	0.355	0.502	0.212	0.177	0.251	INDETERMINATE	1	TRUE	1	0.413551247768169	3		541	591	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063372	67063372	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010419-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	123	670	0	ENST00000412916.2:c.62T>G	p.Leu21Arg	p.L21R	ENST00000412916		21	cTg/cGg	1/6	0.413551247768169	1	FACETS	0.822	0.746	0.902	0.822	0.746	0.902	CLONAL	1	TRUE	0	0.413551247768169	1		670	574	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862139	68862139	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010419-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	148	716	0	ENST00000261769.5:c.2231del	p.Pro744GlnfsTer26	p.P744Qfs*26	ENST00000261769	NM_004360.3	743	Ccc/cc	14/16	0.413551247768169	1	FACETS	0.937	0.859	1	0.937	0.859	1	CLONAL	1	TRUE	0	0.413551247768169	1		716	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0010425-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	85	568	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	1	2	FACETS	0.857	0.756	0.966	0.857	0.756	0.966	CLONAL	1	TRUE	1	0.215856843564111	2		568	919	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0010425-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	57	569	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.87	0.746	1	0.87	0.746	1	CLONAL	1	TRUE	1	0.215856843564111	2		569	607	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010425-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	40	347	0	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	1	2	FACETS	0.679	0.563	0.808	0.679	0.563	0.808	SUBCLONAL	1	TRUE	1	0.215856843564111	2		347	546	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394380	162394380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554256339	NA	P-0010425-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	89	790	0	ENST00000366898.1:c.688G>A	p.Ala230Thr	p.A230T	ENST00000366898	NM_004562.2	230	Gca/Aca	6/12	1	2	FACETS	0.745	0.659	0.838	0.745	0.659	0.838	SUBCLONAL	1	TRUE	1	0.215856843564111	2		790	1107	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506218	148506218	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010425-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	74	515	0	ENST00000320356.2:c.2140G>A	p.Gly714Ser	p.G714S	ENST00000320356	NM_004456.4	714	Ggt/Agt	19/20	1	2	FACETS	0.827	0.723	0.94	0.827	0.723	0.94	CLONAL	1	TRUE	1	0.215856843564111	2		515	829	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526287	189526287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	232	162	0	ENST00000264731.3:c.551C>T	p.Ser184Leu	p.S184L	ENST00000264731	NM_003722.4	184	tCg/tTg	4/14	0.32545406095617	3	FACETS	0.853	0.796	0.912			1	CLONAL	2	TRUE	NA	0.32545406095617	3		162	972	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691003	NA	P-0010426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	242	323	0	ENST00000269305.4:c.96+1G>T		p.X32_splice	ENST00000269305	NM_001126112.2	32			0.32545406095617	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.32545406095617	1		323	1230	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486070	29486070	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs746824139	NA	P-0010426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	101	312	0	ENST00000356175.3:c.247C>T	p.Gln83Ter	p.Q83*	ENST00000356175	NM_000267.3	83	Cag/Tag	3/57	0.32545406095617	1	FACETS	0.858	0.768	0.952	0.858	0.768	0.952	CLONAL	1	TRUE	0	0.32545406095617	1		312	606	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437782	52437782	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0010426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1941	531	743	0	ENST00000460680.1:c.1379C>G	p.Ser460Ter	p.S460*	ENST00000460680	NM_004656.3	460	tCa/tGa	13/17	0.32545406095617	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.32545406095617	1		743	2472	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65312410	65312410	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	144	269	0	ENST00000342505.4:c.1909G>C	p.Glu637Gln	p.E637Q	ENST00000342505	NM_002227.2	637	Gag/Cag	14/25	1	2	FACETS	0.898	0.818	0.982	0.898	0.818	0.982	CLONAL	1	TRUE	1	0.32545406095617	2		269	985	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149616	202149616	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	77	285	0	ENST00000358485.4:c.1057G>C	p.Glu353Gln	p.E353Q	ENST00000358485	NM_001080125.1	353	Gag/Cag	8/9	0.32545406095617	1	FACETS	0.727	0.639	0.821	0.727	0.639	0.821	SUBCLONAL	1	TRUE	0	0.32545406095617	1		285	545	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412905	49412905	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519951	NA	P-0010426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	229	462	0	ENST00000418115.1:c.118G>A	p.Glu40Lys	p.E40K	ENST00000418115	NM_001664.2	40	Gag/Aag	2/5	0.32545406095617	1	FACETS	0.972	0.905	1	0.972	0.905	1	CLONAL	1	TRUE	0	0.32545406095617	1		462	1212	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608305	28608305	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	65	427	0	ENST00000241453.7:c.1751C>A	p.Ser584Tyr	p.S584Y	ENST00000241453	NM_004119.2	584	tCc/tAc	14/24	0.187541629776105	1	FACETS	0.407	0.352	0.467	0.407	0.352	0.467	INDETERMINATE	1	TRUE	0	0.32545406095617	1		427	821	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532550	63532550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	201	256	0	ENST00000307078.5:c.2029C>A	p.His677Asn	p.H677N	ENST00000307078	NM_004655.3	677	Cac/Aac	8/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.32545406095617	2		256	1127	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117362	115117363	+	missense_variant	Missense_Mutation	DNP	TA	TA	AG	novel	NA	P-0010426-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	171	517	0	ENST00000257566.3:c.811_812delinsCT	p.Tyr271Leu	p.Y271L	ENST00000257566	NM_016569.3	271	TAc/CTc	4/8	1	2	FACETS	0.958	0.88	1	0.958	0.88	1	CLONAL	1	TRUE	1	0.32545406095617	2		517	1097	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	146	540	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.3	3	FACETS	1	0.963	1			1	CLONAL	3	TRUE	NA	0.13	3		540	726	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877006	151877006	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	54	448	0	ENST00000262189.6:c.7355G>T	p.Gly2452Val	p.G2452V	ENST00000262189	NM_170606.2	2452	gGa/gTa	37/59	1	2	FACETS	0.814	0.692	0.947	0.814	0.692	0.947	CLONAL	1	TRUE	1	0.13	2		448	1021	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507306	8507306	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	57	418	0	ENST00000356435.5:c.1672G>T	p.Glu558Ter	p.E558*	ENST00000356435		558	Gag/Tag	11/35	1	2	FACETS	0.968	0.828	1	0.968	0.828	1	CLONAL	1	TRUE	1	0.13	2		418	906	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205332	46205332	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	28	263	0	ENST00000334344.6:c.416C>A	p.Ser139Ter	p.S139*	ENST00000334344	NM_152641.2	139	tCg/tAg	4/21	1	2	FACETS	0.804	0.641	0.99	0.804	0.641	0.99	CLONAL	1	TRUE	1	0.13	2		263	536	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432063	49432063	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	68	558	0	ENST00000301067.7:c.9076G>A	p.Gly3026Ser	p.G3026S	ENST00000301067	NM_003482.3	3026	Ggc/Agc	34/54	1	2	FACETS	0.821	0.711	0.94	0.821	0.711	0.94	CLONAL	1	TRUE	1	0.13	2		558	1275	SUCCESS
AR	367	MSKCC	GRCh37	X	66931479	66931479	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555995856	NA	P-0010442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	52	263	0	ENST00000374690.3:c.2121A>C	p.Glu707Asp	p.E707D	ENST00000374690	NM_000044.3	707	gaA/gaC	4/8	1	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.13	1		263	556	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010451-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	25	389	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		389	336	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0010458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	51	441	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.764	0.659	0.874	0.764	0.659	0.874	SUBCLONAL	1	TRUE	1	0.721801132086662	2		441	185	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0010458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	249	532	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.643597177549299	1	FACETS	0.877	0.83	0.924	0.877	0.83	0.924	CLONAL	1	TRUE	0	0.721801132086662	1		534	503	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864400	151864427	+	frameshift_variant	Frame_Shift_Del	DEL	TGCATTTGAAGCAGCTGTTGGGTCTCCT	TGCATTTGAAGCAGCTGTTGGGTCTCCT	-	novel	NA	P-0010458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	148	307	0	ENST00000262189.6:c.9554_9581del	p.Gln3185ArgfsTer55	p.Q3185Rfs*55	ENST00000262189	NM_170606.2	3185	cAGGAGACCCAACAGCTGCTTCAAATGCAg/cg	42/59	1	2	FACETS	0.716	0.657	0.777	0.716	0.657	0.777	SUBCLONAL	1	TRUE	1	0.721801132086662	2		307	573	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141036	55141036	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121908586	NA	P-0010485-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	84	562	0	ENST00000257290.5:c.1682T>A	p.Val561Asp	p.V561D	ENST00000257290	NM_006206.4	561	gTc/gAc	12/23	0.200449467437308	1	FACETS	0.85	0.75	0.958	0.85	0.75	0.958	CLONAL	1	TRUE	0	0.200449467437308	1		562	887	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	43	540	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.354886532786256	4	FACETS	1	0.959	1	0.719	0.612	0.834	CLONAL	1	TRUE	2	0.573861149278757	4		540	164	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193597	99193597	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	64	156	0	ENST00000074304.5:c.2792G>T	p.Cys931Phe	p.C931F	ENST00000074304	NM_001134224.1	931	tGc/tTc	25/26	0.573861149278757	9	FACETS	1	0.967	1			1	CLONAL	1	TRUE	NA	0.573861149278757	9		156	479	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339002	225339002	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	24	499	0	ENST00000264414.4:c.2267G>C	p.Arg756Pro	p.R756P	ENST00000264414	NM_003590.4	756	cGa/cCa	16/16	0.316973438533012	3	FACETS	1	0.921	1	0.664	0.536	0.804	INDETERMINATE	1	TRUE	1	0.573861149278757	3		499	81	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169107	32169107	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	101	260	0	ENST00000375023.3:c.3926A>T	p.Asp1309Val	p.D1309V	ENST00000375023	NM_004557.3	1309	gAc/gTc	22/30	0.43155638312055	4	FACETS	0.829	0.749	0.912	0.829	0.749	0.912	CLONAL	2	TRUE	2	0.573861149278757	4		260	334	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023005	33023005	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	339	604	1	ENST00000300177.4:c.114G>T	p.Lys38Asn	p.K38N	ENST00000300177	NM_001191322.1	38	aaG/aaT	2/2	0.573861149278757	5	FACETS	1	0.99	1			1	CLONAL	2	TRUE	NA	0.573861149278757	5		605	934	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041737	42041737	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0010486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	36	774	0	ENST00000219905.7:c.5932A>T	p.Lys1978Ter	p.K1978*	ENST00000219905	NM_001164273.1	1978	Aaa/Taa	17/24	0.375608645853578	1	FACETS	0.852	0.72	0.991	0.852	0.72	0.991	CLONAL	1	TRUE	0	0.573861149278757	1		774	105	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302975	15302975	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	209	187	0	ENST00000263388.2:c.475G>T	p.Val159Leu	p.V159L	ENST00000263388	NM_000435.2	159	Gtg/Ttg	4/33	0.429815949557218	6	FACETS	1	0.962	1	0.698	0.65	0.747	CLONAL	2	TRUE	3	0.573861149278757	6		187	747	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0010492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	37	471	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		471	598	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842641	68842641	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	70	555	0	ENST00000261769.5:c.577A>C	p.Thr193Pro	p.T193P	ENST00000261769	NM_004360.3	193	Act/Cct	5/16	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		555	1037	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0010505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	143	424	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.155912936317549	4	FACETS	0.869	0.796	0.944	0.869	0.796	0.944	INDETERMINATE	2	TRUE	2	0.439491019360701	4		424	539	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180406	94180406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555005282	NA	P-0010505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	141	303	0	ENST00000323929.3:c.1762G>A	p.Gly588Arg	p.G588R	ENST00000323929	NM_005591.3	588	Gga/Aga	15/20	0.200912543770844	4	FACETS	0.857	0.785	0.932	0.857	0.785	0.932	INDETERMINATE	2	TRUE	2	0.439491019360701	4		303	539	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180411	94180411	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	150	317	3	ENST00000323929.3:c.1757C>A	p.Ser586Ter	p.S586*	ENST00000323929	NM_005591.3	586	tCg/tAg	15/20	0.200912543770844	4	FACETS	0.88	0.809	0.955	0.88	0.809	0.955	INDETERMINATE	2	TRUE	2	0.439491019360701	4		320	558	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075259	16075259	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775206661	NA	P-0010505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	163	392	0	ENST00000268712.3:c.293C>T	p.Pro98Leu	p.P98L	ENST00000268712	NM_006311.3	98	cCa/cTa	4/46	0.439491019360701	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.439491019360701	1		392	533	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410451	63410451	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	175	559	1	ENST00000330258.3:c.2716C>A	p.Leu906Ile	p.L906I	ENST00000330258	NM_152424.3	906	Ctc/Atc	2/2	NA	2	FACETS	0.844	0.777	0.913			1	INDETERMINATE	1	TRUE	NA	0.439491019360701	2		560	944	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0010506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	226	418	5	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.406730209684949	2	FACETS	0.921	0.865	0.977	0.921	0.865	0.977	CLONAL	2	TRUE	0	0.444698808259907	2		423	552	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610695	52610695	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	117	494	4	ENST00000394830.3:c.3478C>T	p.Arg1160Ter	p.R1160*	ENST00000394830	NM_018313.4	1160	Cga/Tga	23/30	0.411476897003059	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.444698808259907	1		498	358	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482342	56482342	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	201	618	0	ENST00000267101.3:c.890A>C	p.Asp297Ala	p.D297A	ENST00000267101	NM_001982.3	297	gAt/gCt	8/28	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.444698808259907	2		618	895	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604785	48604785	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	144	352	0	ENST00000342988.3:c.1607T>G	p.Leu536Arg	p.L536R	ENST00000342988	NM_005359.5	536	cTa/cGa	12/12	0.444698808259907	1	FACETS	0.993	0.912	1	0.993	0.912	1	CLONAL	1	TRUE	0	0.444698808259907	1		352	507	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386390	31386390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs562665925	NA	P-0010506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	186	478	0	ENST00000328111.2:c.1615C>T	p.Arg539Trp	p.R539W	ENST00000328111	NM_006892.3	539	Cgg/Tgg	15/23	0.414470316441417	3	FACETS	0.869	0.802	0.94	0.435	0.401	0.47	CLONAL	1	TRUE	1	0.444698808259907	3		478	1176	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572936	7572940	+	frameshift_variant	Frame_Shift_Del	DEL	GTCAG	GTCAG	-	novel	NA	P-0010506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	272	883	0	ENST00000269305.4:c.1169_1173del	p.Pro390LeufsTer79	p.P390Lfs*79	ENST00000269305	NM_001126112.2	390	cCTGAC/c	11/11	0.411476897003059	1	FACETS	0.862	0.809	0.917	0.862	0.809	0.917	CLONAL	1	TRUE	0	0.444698808259907	1		883	1103	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687311	37687313	+	frameshift_variant	Frame_Shift_Del	DEL	TGC	TGC	GG	novel	NA	P-0010506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2886	175	511	0	ENST00000447079.4:c.4215_4217delinsGG	p.Phe1405LeufsTer6	p.F1405Lfs*6	ENST00000447079	NM_015083.1	1405	ttTGCc/ttGGc	14/14	0.444698808259907	15	FACETS	1	0.916	1			1	CLONAL	1	TRUE	NA	0.444698808259907	15		511	3061	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274911	41274911	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	55	327	0	ENST00000349496.5:c.1161T>G	p.Asn387Lys	p.N387K	ENST00000349496	NM_001904.3	387	aaT/aaG	8/15	1	2	FACETS	0.298	0.254	0.345	0.298	0.254	0.345	SUBCLONAL	1	TRUE	1	0.6	2		327	616	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098566	11098566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776534924	NA	P-0010507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	40	251	0	ENST00000358026.2:c.1084G>A	p.Asp362Asn	p.D362N	ENST00000358026	NM_001128849.1	362	Gac/Aac	6/36	0.3	3	FACETS	0.337	0.279	0.401			1	INDETERMINATE	1	TRUE	NA	0.6	3		251	515	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578204	7578204	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520001	NA	P-0010513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	469	399	0	ENST00000269305.4:c.645T>G	p.Ser215Arg	p.S215R	ENST00000269305	NM_001126112.2	215	agT/agG	6/11	NA	2	FACETS	0.968	0.946	0.987			1	INDETERMINATE	7	TRUE	NA	0.252256146234077	2		399	549	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057744	180057744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138831198	NA	P-0010513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	115	278	0	ENST00000261937.6:c.211G>A	p.Gly71Arg	p.G71R	ENST00000261937	NM_182925.4	71	Gga/Aga	3/30	0.252256147667218	0	FACETS	0.817	0.749	0.887			1	CLONAL	3	TRUE	0	0.252256146234077	0		278	278	SUCCESS
APC	324	MSKCC	GRCh37	5	112116538	112116538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs749479682	NA	P-0010513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	151	280	0	ENST00000257430.4:c.583C>T	p.Gln195Ter	p.Q195*	ENST00000257430	NM_000038.5	195	Caa/Taa	6/16	0.252256147667218	1	FACETS	1	0.98	1	1	0.994	1	CLONAL	4	TRUE	0	0.252256146234077	1		280	238	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275343	142275343	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748238772	NA	P-0010513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	160	324	0	ENST00000350721.4:c.1960G>A	p.Ala654Thr	p.A654T	ENST00000350721	NM_001184.3	654	Gca/Aca	9/47	0.17301256993086	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.252256146234077	2		324	515	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158460	106158460	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1482652926	NA	P-0010513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	154	294	0	ENST00000380013.4:c.3361G>T	p.Asp1121Tyr	p.D1121Y	ENST00000380013	NM_001127208.2	1121	Gat/Tat	3/11	0.12046278193976	4	FACETS	0.937	0.867	1	1	0.992	1	INDETERMINATE	4	TRUE	2	0.252256146234077	4		294	408	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265629	152265629	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	86	134	0	ENST00000206249.3:c.1082C>A	p.Ala361Glu	p.A361E	ENST00000206249	NM_000125.3	361	gCg/gAg	4/8	NA	2	FACETS	0.959	0.863	1			1	INDETERMINATE	3	TRUE	NA	0.252256146234077	2		134	237	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0010514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	101	424	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.57029987501586	4	FACETS	1	0.974	1			1	CLONAL	3	TRUE	NA	0.57029987501586	4		424	165	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940466	29940466	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	20	486	0	ENST00000389048.3:c.765C>A	p.Phe255Leu	p.F255L	ENST00000389048	NM_004304.4	255	ttC/ttA	2/29	0.188335171499706	2	FACETS	1	0.85	1	0.548	0.433	0.672	INDETERMINATE	1	TRUE	0	0.57029987501586	2		486	64	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248429	212248429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	17	426	0	ENST00000342788.4:c.3838G>A	p.Glu1280Lys	p.E1280K	ENST00000342788	NM_005235.2	1280	Gag/Aag	28/28	0.553669683228502	1	FACETS	0.888	0.692	1	0.888	0.692	1	CLONAL	1	TRUE	0	0.57029987501586	1		426	48	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442024	52442024	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	44	365	0	ENST00000460680.1:c.325G>T	p.Gly109Ter	p.G109*	ENST00000460680	NM_004656.3	109	Gga/Tga	5/17	0.480645178555713	2	FACETS	0.867	0.757	0.976	0.867	0.757	0.976	CLONAL	2	TRUE	0	0.57029987501586	2		365	89	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73350062	73350062	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0010514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	21	339	1	ENST00000377767.4:c.822+1G>T		p.X274_splice	ENST00000377767	NM_014953.3	274			0.403169125251015	1	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	0	0.57029987501586	1		340	43	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0010522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	39	387	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.6	0.496	0.718	0.6	0.496	0.718	SUBCLONAL	1	TRUE	1	0.16	2		388	812	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0010522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	48	512	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.886	0.748	1	0.886	0.748	1	CLONAL	1	TRUE	1	0.16	2		512	677	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123826	46123826	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0010522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	36	251	0	ENST00000334344.6:c.93-1G>A		p.X31_splice	ENST00000334344	NM_152641.2	31			1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.16	2		251	396	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0010530-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	125	269	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.874795077584506	2		269	264	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397511	116397511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010530-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	6751	522	0	ENST00000397752.3:c.1883C>T	p.Pro628Leu	p.P628L	ENST00000397752	NM_000245.2	628	cCt/cTt	7/21	0.874795077584506	42	FACETS	0.998	0.994	1			1	CLONAL	41	TRUE	NA	0.874795077584506	42		522	6980	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs730882026	NA	P-0010530-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	269	347	0	ENST00000269305.4:c.707A>C	p.Tyr236Ser	p.Y236S	ENST00000269305	NM_001126112.2	236	tAc/tCc	7/11	0.850438537499871	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.874795077584506	2		347	288	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918950	76918951	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0010530-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	193	837	0	ENST00000373344.5:c.4040_4041del	p.Val1347GlufsTer2	p.V1347Efs*2	ENST00000373344	NM_000489.3	1347	gTG/g	12/35	0.874795077584506	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.874795077584506	1		837	233	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0010558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	532	532	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.568017755280046	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.568017755280046	2		534	828	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913351	NA	P-0010558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	262	379	1	ENST00000288602.6:c.1397G>A	p.Gly466Glu	p.G466E	ENST00000288602	NM_004333.4	466	gGa/gAa	11/18	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.568017755280046	2		380	863	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885835	23885835	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1258	76	608	0	ENST00000374561.5:c.83G>C	p.Arg28Pro	p.R28P	ENST00000374561	NM_002167.4	28	cGa/cCa	1/3	1	2	FACETS	0.201	0.175	0.228	0.201	0.175	0.228	SUBCLONAL	1	TRUE	1	0.568017755280046	2		608	1334	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803845	43803845	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	291	417	0	ENST00000372470.3:c.155G>A	p.Trp52Ter	p.W52*	ENST00000372470	NM_005373.2	52	tGg/tAg	2/12	0.396981706987424	3	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.568017755280046	3		417	1128	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812595	43812595	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	313	309	0	ENST00000372470.3:c.1298A>G	p.Gln433Arg	p.Q433R	ENST00000372470	NM_005373.2	433	cAg/cGg	8/12	0.396981706987424	3	FACETS	0.977	0.928	1			1	CLONAL	2	TRUE	NA	0.568017755280046	3		309	724	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248520	59248520	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	107	468	0	ENST00000371222.2:c.223G>T	p.Glu75Ter	p.E75*	ENST00000371222	NM_002228.3	75	Gag/Tag	1/1	0.353921643751981	1	FACETS	0.404	0.362	0.448	0.404	0.362	0.448	SUBCLONAL	1	TRUE	0	0.568017755280046	1		468	668	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849849	156849849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200022271	NA	P-0010558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	448	376	0	ENST00000524377.1:c.2105G>T	p.Arg702Leu	p.R702L	ENST00000524377	NM_002529.3	702	cGt/cTt	16/17	0.568017755280046	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.568017755280046	3		376	941	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587160	212587160	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	471	483	0	ENST00000342788.4:c.841G>T	p.Ala281Ser	p.A281S	ENST00000342788	NM_005235.2	281	Gca/Tca	7/28	0.408537815326839	3	FACETS	0.868	0.831	0.906	0.868	0.831	0.906	CLONAL	2	TRUE	1	0.568017755280046	3		483	1226	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149434875	149434875	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	186	422	0	ENST00000286301.3:c.2579T>C	p.Leu860Pro	p.L860P	ENST00000286301	NM_005211.3	860	cTg/cCg	20/22	0.247084454006923	2	FACETS	0.808	0.747	0.87	0.404	0.373	0.435	INDETERMINATE	1	TRUE	0	0.568017755280046	2		422	811	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965568	93965568	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	361	617	0	ENST00000369303.4:c.2360C>A	p.Pro787Gln	p.P787Q	ENST00000369303	NM_004440.3	787	cCa/cAa	13/17	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.568017755280046	2		617	1199	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450295	50450295	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	85	274	0	ENST00000331340.3:c.479T>G	p.Leu160Arg	p.L160R	ENST00000331340	NM_006060.4	160	cTg/cGg	5/8	NA	2	FACETS	0.596	0.528	0.668			1	INDETERMINATE	1	TRUE	NA	0.568017755280046	2		274	502	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509753	106509753	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	203	328	0	ENST00000359195.3:c.1747C>T	p.Leu583Phe	p.L583F	ENST00000359195	NM_002649.2	583	Ctt/Ttt	2/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.568017755280046	2		328	702	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436041	116436041	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	313	488	0	ENST00000397752.3:c.4036G>T	p.Gly1346Trp	p.G1346W	ENST00000397752	NM_000245.2	1346	Ggg/Tgg	21/21	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.568017755280046	2		488	955	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741594	17741594	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1224100302	NA	P-0010558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	82	74	0	ENST00000250003.3:c.265C>A	p.Gln89Lys	p.Q89K	ENST00000250003	NM_002478.4	89	Cag/Aag	1/3	1	2	FACETS	0.875	0.794	0.956	1	0.986	1	CLONAL	2	TRUE	1	0.568017755280046	2		74	165	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343710	118343710	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	237	275	0	ENST00000534358.1:c.1836G>C	p.Leu612Phe	p.L612F	ENST00000534358	NM_005933.3	612	ttG/ttC	3/36	0.163361993318072	4	FACETS	0.884	0.829	0.941	0.884	0.829	0.941	INDETERMINATE	2	TRUE	2	0.568017755280046	4		275	740	SUCCESS
CBL	867	MSKCC	GRCh37	11	119146772	119146772	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	385	466	0	ENST00000264033.4:c.935G>T	p.Gly312Val	p.G312V	ENST00000264033	NM_005188.3	312	gGg/gTg	6/16	0.163361993318072	4	FACETS	0.99	0.943	1	0.99	0.943	1	INDETERMINATE	2	TRUE	2	0.568017755280046	4		466	1073	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354561	91354561	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	403	390	0	ENST00000355112.3:c.4001G>T	p.Arg1334Met	p.R1334M	ENST00000355112	NM_000057.2	1334	aGg/aTg	21/22	0.334771868006415	2	FACETS	1	0.996	1	0.738	0.704	0.771	INDETERMINATE	1	TRUE	0	0.568017755280046	2		390	962	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641698	23641698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	152	411	0	ENST00000261584.4:c.1777C>T	p.His593Tyr	p.H593Y	ENST00000261584	NM_024675.3	593	Cat/Tat	5/13	0.330156290072767	2	FACETS	0.572	0.523	0.624	0.286	0.261	0.312	INDETERMINATE	1	TRUE	0	0.568017755280046	2		411	935	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023935	27023935	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	13	20	0	ENST00000324856.7:c.1042del	p.Ala348ProfsTer15	p.A348Pfs*15	ENST00000324856	NM_006015.4	347	gcG/gc	1/20	1	2	FACETS	0.88	0.648	1	0.88	0.648	1	CLONAL	1	TRUE	1	0.568017755280046	2		20	52	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220627	1220646	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCCCGGCTTTCCAGCCGC	CTCCCCGGCTTTCCAGCCGC	-	novel	NA	P-0010558-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	310	388	0	ENST00000326873.7:c.646_665del	p.Ser216ArgfsTer43	p.S216Rfs*43	ENST00000326873	NM_000455.4	215	ggCTCCCCGGCTTTCCAGCCGCcc/ggcc	5/10	0.568017755280046	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.568017755280046	2		388	545	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609917	81609917	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010564-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	181	477	0	ENST00000298171.2:c.1515C>A	p.Ser505Arg	p.S505R	ENST00000298171	NM_000369.2	505	agC/agA	10/10	0.875381219712691	3	FACETS	0.706	0.652	0.762	0.353	0.326	0.381	SUBCLONAL	1	TRUE	1	0.883363240631751	3		477	837	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0010566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	292	532	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.496783348500797	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.530063970724031	2		534	551	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0010566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	2570	509	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.530063970724031	28	FACETS	1	0.992	1	1	0.992	1	CLONAL	26	TRUE	2	0.530063970724031	28		509	2940	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0010566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2880	698	533	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.530063970724031	28	FACETS	0.968	0.929	1	0.223	0.214	0.233	CLONAL	6	TRUE	2	0.530063970724031	28		533	3578	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354097	15354097	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	127	207	0	ENST00000263377.2:c.2783T>C	p.Met928Thr	p.M928T	ENST00000263377	NM_058243.2	928	aTg/aCg	14/20	0.490818293613735	2	FACETS	0.986	0.914	1	0.986	0.914	1	CLONAL	2	TRUE	0	0.530063970724031	2		207	243	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120612013	120612014	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0010567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	10	53	0	ENST00000256646.2:c.7_8delinsTT	p.Ala3Phe	p.A3F	ENST00000256646	NM_024408.3	3	GCc/TTc	1/34	0.281798883868732	3	FACETS	0.446	0.304	0.621	0.223	0.152	0.311	INDETERMINATE	1	TRUE	1	0.518334888384454	3		53	109	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363621	40363623	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	rs748106151	NA	P-0010567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	80	354	0	ENST00000397332.2:c.606_608del	p.Val203del	p.V203del	ENST00000397332	NM_001033082.2	202	gtTGTg/gtg	3/3	0.281798883868732	3	FACETS	0.773	0.682	0.87	0.386	0.341	0.435	INDETERMINATE	1	TRUE	1	0.518334888384454	3		354	503	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	195	389	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.866	0.809	0.924	0.866	0.809	0.924	CLONAL	1	TRUE	1	0.920918798138587	2		389	489	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0010582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	324	648	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.920918798138587	2		648	695	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469669	NA	P-0010582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	762	550	1	ENST00000374080.3:c.130G>A	p.Gly44Ser	p.G44S	ENST00000374080		44	Ggt/Agt	2/45	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.920918798138587	1		551	837	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310517	65310517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	609	879	3	ENST00000342505.4:c.2171G>A	p.Arg724His	p.R724H	ENST00000342505	NM_002227.2	724	cGt/cAt	16/25	1	2	FACETS	0.994	0.959	1	0.994	0.959	1	CLONAL	1	TRUE	1	0.920918798138587	2		882	1330	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	387	697	1	ENST00000335508.6:c.2704G>A	p.Glu902Lys	p.E902K	ENST00000335508	NM_012433.2	902	Gaa/Aaa	18/25	1	2	FACETS	0.956	0.913	1	0.956	0.913	1	CLONAL	1	TRUE	1	0.920918798138587	2		698	879	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942761	44942761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	609	589	0	ENST00000377967.4:c.3341C>T	p.Ser1114Leu	p.S1114L	ENST00000377967	NM_021140.2	1114	tCa/tTa	23/29	1	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.920918798138587	1		589	647	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247165	153247165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	405	582	0	ENST00000281708.4:c.1637C>T	p.Ser546Leu	p.S546L	ENST00000281708	NM_033632.3	546	tCa/tTa	10/12	1	2	FACETS	0.955	0.913	0.997	0.955	0.913	0.997	CLONAL	1	TRUE	1	0.920918798138587	2		582	921	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814652	43814652	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1476959650	NA	P-0010582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	455	623	2	ENST00000372470.3:c.1447G>A	p.Val483Met	p.V483M	ENST00000372470	NM_005373.2	483	Gtg/Atg	9/12	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.920918798138587	2		625	892	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637326	47637326	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs759712763	NA	P-0010582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	553	1081	2	ENST00000233146.2:c.460G>T	p.Ala154Ser	p.A154S	ENST00000233146	NM_000251.2	154	Gca/Tca	3/16	1	2	FACETS	0.92	0.884	0.955	0.92	0.884	0.955	CLONAL	1	TRUE	1	0.920918798138587	2		1083	1306	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799658	72799658	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	597	796	0	ENST00000325599.8:c.1511T>G	p.Ile504Ser	p.I504S	ENST00000325599	NM_018130.2	504	aTt/aGt	11/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.920918798138587	2		796	1264	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100533	157100533	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	370	455	1	ENST00000346085.5:c.1470G>A	p.Trp490Ter	p.W490*	ENST00000346085	NM_020732.3	490	tgG/tgA	1/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.920918798138587	2		456	727	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827454	72827454	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	885	1347	0	ENST00000268489.5:c.9127A>G	p.Ile3043Val	p.I3043V	ENST00000268489	NM_006885.3	3043	Atc/Gtc	9/10	1	2	FACETS	0.999	0.97	1	0.999	0.97	1	CLONAL	1	TRUE	1	0.920918798138587	2		1347	1923	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089932	16089932	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	397	656	1	ENST00000268712.3:c.178C>T	p.Gln60Ter	p.Q60*	ENST00000268712	NM_006311.3	60	Cag/Tag	3/46	1	2	FACETS	0.941	0.899	0.984	0.941	0.899	0.984	CLONAL	1	TRUE	1	0.920918798138587	2		657	916	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7119490	7119490	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	667	1052	0	ENST00000302850.5:c.3764T>C	p.Leu1255Pro	p.L1255P	ENST00000302850	NM_000208.2	1255	cTg/cCg	21/22	1	2	FACETS	0.995	0.961	1	0.995	0.961	1	CLONAL	1	TRUE	1	0.920918798138587	2		1052	1456	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7150532	7150532	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1227	108	862	2	ENST00000302850.5:c.2243C>A	p.Ser748Ter	p.S748*	ENST00000302850	NM_000208.2	748	tCa/tAa	11/22	1	2	FACETS	0.176	0.157	0.196	0.176	0.157	0.196	SUBCLONAL	1	TRUE	1	0.920918798138587	2		864	1335	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856345	45856345	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	626	914	0	ENST00000391945.4:c.1827C>G	p.Asp609Glu	p.D609E	ENST00000391945	NM_000400.3	609	gaC/gaG	19/23	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.920918798138587	2		914	1257	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227924	123227924	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	608	506	0	ENST00000218089.9:c.3635T>C	p.Met1212Thr	p.M1212T	ENST00000218089	NM_001042749.1	1212	aTg/aCg	33/35	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.920918798138587	1		506	655	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772230	68772236	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTGCC	CCCTGCC	-	novel	NA	P-0010582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	557	921	0	ENST00000261769.5:c.79_85del	p.Pro27ThrfsTer27	p.P27Tfs*27	ENST00000261769	NM_004360.3	27	CCCTGCCac/ac	2/16	1	2	FACETS	0.959	0.922	0.995	0.959	0.922	0.995	CLONAL	1	TRUE	1	0.920918798138587	2		921	1262	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774175	56774190	+	protein_altering_variant	In_Frame_Del	DEL	TGCATTCAGCACCTTC	TGCATTCAGCACCTTC	A	novel	NA	P-0010582-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	499	1017	0	ENST00000337432.4:c.526_541delinsA	p.Cys176_Gln181delinsLys	p.C176_Q181delinsK	ENST00000337432	NM_058216.2	176	TGCATTCAGCACCTTCag/Aag	3/9	1	2	FACETS	0.836	0.801	0.871	0.836	0.801	0.871	CLONAL	1	TRUE	1	0.920918798138587	2		1017	1297	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218423	1218423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	482	397	0	ENST00000326873.7:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000326873	NM_000455.4	100	Caa/Taa	2/10	0.561091327299478	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.561091327299478	2		397	838	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557927	187557927	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs369805914	NA	P-0010591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	281	419	0	ENST00000441802.2:c.3784C>T	p.Arg1262Ter	p.R1262*	ENST00000441802	NM_005245.3	1262	Cga/Tga	5/27	0.561091327299478	1	FACETS	0.984	0.93	1	0.984	0.93	1	CLONAL	1	TRUE	0	0.561091327299478	1		419	732	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802689	135802689	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1309560054	NA	P-0010591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	163	240	0	ENST00000298552.3:c.109C>T	p.Arg37Cys	p.R37C	ENST00000298552	NM_001162426.1	37	Cgt/Tgt	4/23	1	2	FACETS	0.991	0.915	1	0.991	0.915	1	CLONAL	1	TRUE	1	0.561091327299478	2		240	586	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589600	69589600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760825703	NA	P-0010591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	255	331	2	ENST00000168712.1:c.253C>T	p.Arg85Trp	p.R85W	ENST00000168712	NM_002007.2	85	Cgg/Tgg	1/3	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.561091327299478	2		333	747	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416062	49416062	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0010591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	367	604	1	ENST00000301067.7:c.16412+1G>A		p.X5471_splice	ENST00000301067	NM_003482.3	5471			1	2	FACETS	0.968	0.918	1	0.968	0.918	1	CLONAL	1	TRUE	1	0.561091327299478	2		605	1351	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892293	9892293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs796052550	NA	P-0010591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	190	274	0	ENST00000330684.3:c.2197G>A	p.Ala733Thr	p.A733T	ENST00000330684	NM_001134407.1	733	Gca/Aca	11/13	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.561091327299478	2		274	640	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10267075	10267075	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	116	330	0	ENST00000340748.4:c.1343C>A	p.Ser448Tyr	p.S448Y	ENST00000340748		448	tCt/tAt	17/40	0.561091327299478	2	FACETS	0.495	0.445	0.547	0.247	0.222	0.274	SUBCLONAL	1	TRUE	0	0.561091327299478	2		330	836	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069435	30069435	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	329	275	1	ENST00000338641.4:c.1300G>T	p.Glu434Ter	p.E434*	ENST00000338641	NM_000268.3	434	Gag/Tag	12/16	1	2	FACETS	0.946	0.903	0.988	1	0.996	1	CLONAL	2	TRUE	1	0.561091327299478	2		276	620	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572831	41572831	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	494	507	0	ENST00000263253.7:c.5116G>T	p.Glu1706Ter	p.E1706*	ENST00000263253	NM_001429.3	1706	Gag/Tag	31/31	1	2	FACETS	0.951	0.916	0.986	1	0.997	1	CLONAL	2	TRUE	1	0.561091327299478	2		507	926	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400304	139400304	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	97	115	0	ENST00000277541.6:c.4044del	p.Asp1348GlufsTer97	p.D1348Efs*97	ENST00000277541	NM_017617.3	1348	gaC/ga	25/34	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.561091327299478	2		115	257	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497811	120497812	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0010591-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	187	284	0	ENST00000256646.2:c.2070_2071del	p.Cys691SerfsTer51	p.C691Sfs*51	ENST00000256646	NM_024408.3	690	ccCTgt/ccgt	13/34	1	2	FACETS	0.983	0.912	1	0.983	0.912	1	CLONAL	1	TRUE	1	0.561091327299478	2		284	678	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0010592-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	154	239	0	ENST00000311936.3:c.34_35delinsTT	p.Gly12Phe	p.G12F	ENST00000311936	NM_004985.3	12	GGt/TTt	2/5	1	2	FACETS	0.996	0.915	1	1	0.994	1	CLONAL	4	TRUE	1	0.12	2		239	644	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464899	120464899	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0010592-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	71	269	0	ENST00000256646.2:c.5173A>T	p.Lys1725Ter	p.K1725*	ENST00000256646	NM_024408.3	1725	Aag/Tag	28/34	0.200058366426414	3	FACETS	1	0.959	1			1	CLONAL	2	TRUE	NA	0.12	3		269	506	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193121540	193121540	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010592-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	116	437	0	ENST00000367435.3:c.938G>C	p.Gly313Ala	p.G313A	ENST00000367435	NM_024529.4	313	gGa/gCa	10/17	0.286479928637216	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.12	3		437	849	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555255	226555255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010592-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	152	537	0	ENST00000366794.5:c.2332C>T	p.Leu778Phe	p.L778F	ENST00000366794	NM_001618.3	778	Ctc/Ttc	17/23	0.304057347338221	4	FACETS	0.878	0.802	0.958	0.878	0.802	0.958	CLONAL	3	TRUE	1	0.12	4		537	1077	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248637	8248637	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010592-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	47	420	0	ENST00000335790.3:c.250A>G	p.Thr84Ala	p.T84A	ENST00000335790	NM_002315.2	84	Acc/Gcc	3/4	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.12	2		420	572	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436806	110436806	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1318734577	NA	P-0010592-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	216	451	0	ENST00000375856.3:c.1595A>G	p.Asp532Gly	p.D532G	ENST00000375856	NM_003749.2	532	gAc/gGc	1/2	0.209714801570688	3	FACETS	1	0.934	1	1	0.993	1	CLONAL	5	TRUE	0	0.12	3		451	762	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010603-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	197	389	0				ENST00000310581	NM_198253.2	-/1132			0.397792148786004	5	FACETS	0.932	0.872	0.993	0.932	0.872	0.993	CLONAL	3	FALSE	2	0.528480728433906	5		389	478	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0010603-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	438	394	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.294976690267107	4	FACETS	0.99	0.951	1	0.743	0.713	0.772	INDETERMINATE	3	FALSE	0	0.528480728433906	4		394	853	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729674	162729674	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010603-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	159	440	0	ENST00000367921.3:c.760T>A	p.Tyr254Asn	p.Y254N	ENST00000367921	NM_006182.2	254	Tat/Aat	8/18	0.107873967119823	4	FACETS	1	0.985	1	0.659	0.605	0.714	INDETERMINATE	1	FALSE	2	0.528480728433906	4		440	698	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191555	10191555	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs5030823	NA	P-0010603-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	353	451	0	ENST00000256474.2:c.548C>A	p.Ser183Ter	p.S183*	ENST00000256474	NM_000551.3	183	tCg/tAg	3/3	0.528480728433906	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	FALSE	0	0.528480728433906	2		451	611	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103701	47103701	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0010603-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	464	621	0	ENST00000409792.3:c.6245C>G	p.Ser2082Ter	p.S2082*	ENST00000409792	NM_014159.6	2082	tCa/tGa	14/21	0.528480728433906	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	FALSE	0	0.528480728433906	2		621	840	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191759	123191759	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0010603-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	346	302	0	ENST00000218089.9:c.1348A>T	p.Arg450Ter	p.R450*	ENST00000218089	NM_001042749.1	450	Aga/Tga	15/35	0.354703434443024	2	FACETS	0.97	0.927	1			1	CLONAL	2	FALSE	NA	0.528480728433906	2		302	675	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0010610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	211	424	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.437512713399476	4	FACETS	0.932	0.869	0.996	0.932	0.869	0.996	CLONAL	2	TRUE	2	0.477211397575047	4		424	701	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600008	10600008	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	304	399	1	ENST00000171111.5:c.1568G>T	p.Gly523Val	p.G523V	ENST00000171111	NM_203500.1	523	gGg/gTg	5/6	0.477211397575047	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.477211397575047	2		400	591	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742108	145742108	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	90	227	0	ENST00000428558.2:c.395G>C	p.Arg132Thr	p.R132T	ENST00000428558	NM_004260.3	132	aGa/aCa	5/22	0.459015911689207	4	FACETS	1	0.937	1			1	CLONAL	1	TRUE	NA	0.477211397575047	4		227	518	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147748	61147748	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	146	259	0	ENST00000295025.8:c.1058C>T	p.Ser353Leu	p.S353L	ENST00000295025	NM_002908.2	353	tCa/tTa	10/11	0.379573739907507	4	FACETS	0.845	0.775	0.917	0.845	0.775	0.917	CLONAL	2	TRUE	2	0.477211397575047	4		259	535	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467562	66467562	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	218	435	0	ENST00000273854.3:c.707T>C	p.Val236Ala	p.V236A	ENST00000273854	NM_004439.5	236	gTg/gCg	3/18	0.477211397575047	2	FACETS	0.873	0.82	0.927	0.873	0.82	0.927	CLONAL	2	TRUE	0	0.477211397575047	2		435	523	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047230	180047230	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	159	614	0	ENST00000261937.6:c.2485G>C	p.Glu829Gln	p.E829Q	ENST00000261937	NM_182925.4	829	Gaa/Caa	17/30	0.355378835240982	5	FACETS	1	0.942	1			1	CLONAL	1	TRUE	NA	0.477211397575047	5		614	1102	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481478	20481478	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	100	345	0	ENST00000346618.3:c.547C>G	p.Leu183Val	p.L183V	ENST00000346618	NM_001949.4	183	Ctt/Gtt	3/7	0.443453727715902	3	FACETS	1	0.962	1	0.383	0.344	0.424	CLONAL	1	TRUE	0	0.477211397575047	3		345	452	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739816	41739816	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	120	559	0	ENST00000242208.4:c.157G>C	p.Glu53Gln	p.E53Q	ENST00000242208	NM_002192.2	53	Gag/Cag	2/3	0.334347241449564	6	FACETS	0.828	0.746	0.915	0.276	0.248	0.305	CLONAL	1	TRUE	3	0.477211397575047	6		559	1187	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233114	55233114	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	75	289	0	ENST00000275493.2:c.1864C>G	p.Pro622Ala	p.P622A	ENST00000275493	NM_005228.3	622	Cca/Gca	15/28	0.334347241449564	6	FACETS	0.966	0.847	1	0.322	0.282	0.365	CLONAL	1	TRUE	3	0.477211397575047	6		289	636	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902241	151902241	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	71	265	0	ENST00000262189.6:c.3911G>C	p.Arg1304Thr	p.R1304T	ENST00000262189	NM_170606.2	1304	aGa/aCa	25/59	1	2	FACETS	0.936	0.823	1	0.936	0.823	1	CLONAL	1	TRUE	1	0.477211397575047	2		265	318	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175440	108175440	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	92	339	0	ENST00000278616.4:c.5535G>C	p.Leu1845Phe	p.L1845F	ENST00000278616	NM_000051.3	1845	ttG/ttC	37/63	0.477211397575047	2	FACETS	0.888	0.794	0.988	0.444	0.397	0.494	CLONAL	1	TRUE	0	0.477211397575047	2		339	434	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831421	89831421	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	148	513	0	ENST00000389301.3:c.2655G>T	p.Glu885Asp	p.E885D	ENST00000389301	NM_000135.2	885	gaG/gaT	28/43	0.477211397575047	3	FACETS	0.995	0.91	1			1	CLONAL	1	TRUE	NA	0.477211397575047	3		513	772	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578215	7578227	+	frameshift_variant	Frame_Shift_Del	DEL	AAGTGTTTCTGTC	AAGTGTTTCTGTC	-	novel	NA	P-0010610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	426	580	0	ENST00000269305.4:c.622_634del	p.Asp208PhefsTer35	p.D208Ffs*35	ENST00000269305	NM_001126112.2	208	GACAGAAACACTTtt/tt	6/11	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.477211397575047	2		580	776	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376185	225376186	+	missense_variant	Missense_Mutation	DNP	CC	CC	GT	novel	NA	P-0010610-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	117	513	0	ENST00000264414.4:c.768_769delinsAC	p.Glu257Gln	p.E257Q	ENST00000264414	NM_003590.4	256	acGGaa/acACaa	6/16	0.443453727715902	3	FACETS	0.835	0.754	0.921	0.278	0.251	0.307	CLONAL	1	TRUE	0	0.477211397575047	3		513	727	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0010611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	40	424	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.614	0.508	0.732	0.614	0.508	0.732	SUBCLONAL	1	TRUE	1	0.15	2		424	869	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146613	55146613	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	58	511	0	ENST00000257290.5:c.2287G>T	p.Asp763Tyr	p.D763Y	ENST00000257290	NM_006206.4	763	Gat/Tat	16/23	1	2	FACETS	0.754	0.646	0.874	0.754	0.646	0.874	SUBCLONAL	1	TRUE	1	0.15	2		511	1025	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514337	149514337	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	88	617	0	ENST00000261799.4:c.607G>T	p.Ala203Ser	p.A203S	ENST00000261799	NM_002609.3	203	Gcc/Tcc	4/23	1	2	FACETS	0.981	0.866	1	0.981	0.866	1	CLONAL	1	TRUE	1	0.15	2		617	1196	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514342	149514342	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	91	634	1	ENST00000261799.4:c.602C>A	p.Ser201Tyr	p.S201Y	ENST00000261799	NM_002609.3	201	tCt/tAt	4/23	1	2	FACETS	0.988	0.874	1	0.988	0.874	1	CLONAL	1	TRUE	1	0.15	2		635	1228	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225408	26225408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1656	125	833	0	ENST00000360408.1:c.26G>A	p.Arg9His	p.R9H	ENST00000360408	NM_003532.2	9	cGt/cAt	1/1	1	2	FACETS	0.936	0.843	1	0.936	0.843	1	CLONAL	1	TRUE	1	0.15	2		833	1781	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206590	108206590	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010611-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	83	470	0	ENST00000278616.4:c.8170C>A	p.Gln2724Lys	p.Q2724K	ENST00000278616	NM_000051.3	2724	Caa/Aaa	56/63	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.15	2		470	998	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	278	389	0				ENST00000310581	NM_198253.2	-/1132			0.291841132972067	5	FACETS	0.88	0.843	0.915			1	INDETERMINATE	4	TRUE	NA	0.873390262422196	5		389	418	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509436	106509436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200175951	NA	P-0010613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	280	576	1	ENST00000359195.3:c.1430G>A	p.Arg477His	p.R477H	ENST00000359195	NM_002649.2	477	cGt/cAt	2/11	0.644409513673268	4	FACETS	1	0.99	1	0.63	0.593	0.668	CLONAL	1	TRUE	2	0.873390262422196	4		577	953	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0010613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	14662	774	5	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.873390262422196	33	FACETS	1	0.999	1			1	CLONAL	32	TRUE	NA	0.873390262422196	33		779	15216	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665682	86665682	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	289	408	0	ENST00000274376.6:c.1663T>C	p.Phe555Leu	p.F555L	ENST00000274376	NM_002890.2	555	Ttt/Ctt	12/25	0.327508869769104	3	FACETS	0.814	0.773	0.855	0.814	0.773	0.855	INDETERMINATE	2	TRUE	1	0.873390262422196	3		408	584	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508733	106508733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1207051578	NA	P-0010613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	276	395	0	ENST00000359195.3:c.727G>A	p.Ala243Thr	p.A243T	ENST00000359195	NM_002649.2	243	Gcc/Acc	2/11	0.644409513673268	4	FACETS	0.843	0.797	0.891	0.843	0.797	0.891	CLONAL	2	TRUE	2	0.873390262422196	4		395	702	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650566	18650566	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	216	418	0	ENST00000266497.5:c.2777T>A	p.Leu926His	p.L926H	ENST00000266497		926	cTt/cAt	20/31	1	2	FACETS	0.991	0.931	1	0.991	0.931	1	CLONAL	1	TRUE	1	0.873390262422196	2		418	499	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906840	32906840	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	289	498	0	ENST00000380152.3:c.1225G>T	p.Glu409Ter	p.E409*	ENST00000380152		409	Gag/Tag	10/27	1	2	FACETS	0.994	0.942	1	0.994	0.942	1	CLONAL	1	TRUE	1	0.873390262422196	2		498	666	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907296	32907296	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs80358455	NA	P-0010613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	228	424	0	ENST00000380152.3:c.1681G>T	p.Gly561Ter	p.G561*	ENST00000380152		561	Gga/Tga	10/27	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.873390262422196	2		424	510	SUCCESS
AR	367	MSKCC	GRCh37	X	66863186	66863186	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	264	701	0	ENST00000374690.3:c.1705G>A	p.Gly569Arg	p.G569R	ENST00000374690	NM_000044.3	569	Ggg/Agg	2/8	1	2	FACETS	0.796	0.75	0.844	0.796	0.75	0.844	SUBCLONAL	1	TRUE	1	0.873390262422196	2		701	759	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579315	7579315	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	211	388	0	ENST00000269305.4:c.372del	p.Cys124Ter	p.C124*	ENST00000269305	NM_001126112.2	124	tgC/tg	4/11	0.873390262422196	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.873390262422196	1		388	263	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152093	55152093	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121908585	NA	P-0010629-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	186	449	0	ENST00000257290.5:c.2525A>T	p.Asp842Val	p.D842V	ENST00000257290	NM_006206.4	842	gAc/gTc	18/23	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.315017781581687	2		449	861	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346776	225346776	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010639-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	309	383	0	ENST00000264414.4:c.1862A>G	p.Asp621Gly	p.D621G	ENST00000264414	NM_003590.4	621	gAt/gGt	14/16	1	2	FACETS	0.973	0.921	1	0.973	0.921	1	CLONAL	1	TRUE	1	0.74540783564605	2		383	852	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538792	23538792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010639-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	289	304	0	ENST00000380871.4:c.647G>A	p.Ser216Asn	p.S216N	ENST00000380871	NM_006167.3	216	aGc/aAc	2/2	0.687316501437531	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.74540783564605	1		304	465	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0010648-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	112	471	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.478977888294313	1	FACETS	0.951	0.864	1	0.951	0.864	1	CLONAL	1	TRUE	0	0.478977888294313	1		471	374	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220428	1220428	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010648-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	136	699	0	ENST00000326873.7:c.521A>G	p.His174Arg	p.H174R	ENST00000326873	NM_000455.4	174	cAc/cGc	4/10	0.478977888294313	1	FACETS	0.755	0.689	0.823	0.755	0.689	0.823	SUBCLONAL	1	TRUE	0	0.478977888294313	1		699	572	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0010656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	206	736	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	0.831	0.771	0.892	0.831	0.771	0.892	CLONAL	1	TRUE	1	0.541339854812344	2		736	916	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511751	46511751	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	54	395	0	ENST00000262741.5:c.1026del	p.Phe342LeufsTer40	p.F342Lfs*40	ENST00000262741	NM_003629.3	342	ttT/tt	9/10	1	2	FACETS	0.311	0.265	0.361	0.311	0.265	0.361	SUBCLONAL	1	TRUE	1	0.541339854812344	2		395	642	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118927	70118927	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010657-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	254	585	0	ENST00000245479.2:c.499A>G	p.Lys167Glu	p.K167E	ENST00000245479	NM_000346.3	167	Aag/Gag	2/3	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.481037624132226	2		585	981	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609948	43609948	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs75076352	NA	P-0010664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	417	1033	0	ENST00000355710.3:c.1900T>C	p.Cys634Arg	p.C634R	ENST00000355710	NM_020975.4	634	Tgc/Cgc	11/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.744762993937155	2		1033	1032	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0010664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	216	543	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	1	2	FACETS	0.949	0.888	1	0.949	0.888	1	CLONAL	1	TRUE	1	0.744762993937155	2		543	611	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0010719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	213	387	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.359012530834613	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.359012530834613	1		388	829	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0010719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	120	316	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.203926738888898	3	FACETS	0.962	0.876	1	0.641	0.584	0.7	INDETERMINATE	2	TRUE	0	0.359012530834613	3		316	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0010736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	157	229	9	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.279872155022446	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	0	0.323486509545978	2		238	469	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106621	27106621	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	128	352	3	ENST00000324856.7:c.6232G>T	p.Glu2078Ter	p.E2078*	ENST00000324856	NM_006015.4	2078	Gag/Tag	20/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.323486509545978	2		355	696	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230884	53230884	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	23	210	0	ENST00000375401.3:c.1909C>T	p.Arg637Trp	p.R637W	ENST00000375401	NM_004187.3	637	Cgg/Tgg	14/26	1	1	FACETS	0.303	0.236	0.381	0.303	0.236	0.381	SUBCLONAL	1	TRUE	0	0.323486509545978	1		210	393	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162688889	162688889	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1507	92	379	1	ENST00000367921.3:c.36C>G	p.Phe12Leu	p.F12L	ENST00000367921	NM_006182.2	12	ttC/ttG	3/18	0.323486509545978	8	FACETS	0.701	0.62	0.788			1	SUBCLONAL	1	TRUE	NA	0.323486509545978	8		380	1599	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456620	138456620	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	68	457	0	ENST00000289153.2:c.730T>C	p.Tyr244His	p.Y244H	ENST00000289153	NM_006219.2	244	Tat/Cat	4/22	0.234354273160791	3	FACETS	0.474	0.411	0.543	0.158	0.137	0.181	SUBCLONAL	1	TRUE	0	0.323486509545978	3		457	1030	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509118	66509118	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	65	267	2	ENST00000273854.3:c.209T>G	p.Met70Arg	p.M70R	ENST00000273854	NM_004439.5	70	aTg/aGg	2/18	1	2	FACETS	0.619	0.536	0.709	0.619	0.536	0.709	SUBCLONAL	1	TRUE	1	0.323486509545978	2		269	649	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056544	26056544	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1178537550	NA	P-0010736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	80	131	0	ENST00000343677.2:c.113C>T	p.Pro38Leu	p.P38L	ENST00000343677	NM_005319.3	38	cCc/cTc	1/1	0.251834303600814	5	FACETS	0.809	0.715	0.909	0.539	0.476	0.606	CLONAL	2	TRUE	2	0.323486509545978	5		131	454	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508727	106508727	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	129	275	0	ENST00000359195.3:c.721C>G	p.Pro241Ala	p.P241A	ENST00000359195	NM_002649.2	241	Ccc/Gcc	2/11	0.323486509545978	3	FACETS	1	0.957	1	0.548	0.496	0.602	CLONAL	1	TRUE	1	0.323486509545978	3		275	846	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851988	128851988	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	123	453	8	ENST00000249373.3:c.2060C>A	p.Pro687Gln	p.P687Q	ENST00000249373	NM_005631.4	687	cCg/cAg	12/12	0.323486509545978	3	FACETS	1	0.953	1	0.544	0.492	0.599	CLONAL	1	TRUE	1	0.323486509545978	3		461	812	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229584	98229584	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	66	381	0	ENST00000331920.6:c.2374G>C	p.Ala792Pro	p.A792P	ENST00000331920	NM_000264.3	792	Gct/Cct	15/24	0.263358631290344	2	FACETS	0.62	0.538	0.709	0.31	0.269	0.355	SUBCLONAL	1	TRUE	0	0.323486509545978	2		381	658	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606674	43606674	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	110	484	6	ENST00000355710.3:c.1283A>G	p.Glu428Gly	p.E428G	ENST00000355710	NM_020975.4	428	gAa/gGa	7/20	1	2	FACETS	0.914	0.822	1	0.914	0.822	1	CLONAL	1	TRUE	1	0.323486509545978	2		490	744	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608351	43608351	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	87	523	12	ENST00000355710.3:c.1699G>T	p.Asp567Tyr	p.D567Y	ENST00000355710	NM_020975.4	567	Gac/Tac	9/20	1	2	FACETS	0.703	0.622	0.79	0.703	0.622	0.79	SUBCLONAL	1	TRUE	1	0.323486509545978	2		535	765	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298139	123298139	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	52	432	0	ENST00000358487.5:c.715T>C	p.Ser239Pro	p.S239P	ENST00000358487	NM_000141.4	239	Tcc/Ccc	6/18	0.117526934982884	0	FACETS	0.319	0.271	0.372			1	INDETERMINATE	1	TRUE	0	0.323486509545978	0		432	681	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201900	67201900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375294282	NA	P-0010736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	235	283	12	ENST00000312629.5:c.1100C>T	p.Pro367Leu	p.P367L	ENST00000312629	NM_003952.2	367	cCg/cTg	13/15	0.310831933899227	4	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.323486509545978	4		295	779	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860032	57860032	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	151	577	0	ENST00000228682.2:c.772A>T	p.Ser258Cys	p.S258C	ENST00000228682	NM_005269.2	258	Agc/Tgc	8/12	1	2	FACETS	0.973	0.889	1	0.973	0.889	1	CLONAL	1	TRUE	1	0.323486509545978	2		577	959	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881542	48881542	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	138	276	4	ENST00000267163.4:c.264G>C	p.Leu88Phe	p.L88F	ENST00000267163	NM_000321.2	88	ttG/ttC	2/27	0.279872155022446	2	FACETS	0.799	0.731	0.87	0.799	0.731	0.87	SUBCLONAL	2	TRUE	0	0.323486509545978	2		280	534	SUCCESS
BLM	641	MSKCC	GRCh37	15	91333951	91333951	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	106	382	8	ENST00000355112.3:c.2896C>G	p.Leu966Val	p.L966V	ENST00000355112	NM_000057.2	966	Ctc/Gtc	15/22	NA	2	FACETS	0.794	0.712	0.882			1	INDETERMINATE	1	TRUE	NA	0.323486509545978	2		390	825	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983248	7983248	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	204	399	4	ENST00000319144.4:c.766G>T	p.Glu256Ter	p.E256*	ENST00000319144	NM_001139.2	256	Gag/Tag	7/15	0.279872155022446	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.323486509545978	2		403	607	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39537699	39537699	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	83	347	0	ENST00000262039.4:c.233A>G	p.Tyr78Cys	p.Y78C	ENST00000262039	NM_002647.2	78	tAc/tGc	2/25	1	2	FACETS	0.894	0.79	1	0.894	0.79	1	CLONAL	1	TRUE	1	0.323486509545978	2		347	574	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602757	10602757	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	145	361	11	ENST00000171111.5:c.821A>G	p.His274Arg	p.H274R	ENST00000171111	NM_203500.1	274	cAc/cGc	3/6	0.263358631290344	2	FACETS	0.761	0.697	0.827	0.761	0.697	0.827	SUBCLONAL	2	TRUE	0	0.323486509545978	2		372	589	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256707	46256707	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs773592839	NA	P-0010736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	148	664	8	ENST00000371998.3:c.763A>G	p.Thr255Ala	p.T255A	ENST00000371998		255	Aca/Gca	8/23	1	2	FACETS	0.742	0.675	0.811	0.742	0.675	0.811	SUBCLONAL	1	TRUE	1	0.323486509545978	2		672	1234	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41521913	41521913	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	208	473	0	ENST00000263253.7:c.775C>T	p.Gln259Ter	p.Q259*	ENST00000263253	NM_001429.3	259	Cag/Tag	3/31	0.263358631290344	2	FACETS	0.788	0.733	0.845	0.788	0.733	0.845	SUBCLONAL	2	TRUE	0	0.323486509545978	2		473	816	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20152085	20152085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	139	206	0	ENST00000379607.5:c.245G>A	p.Arg82Gln	p.R82Q	ENST00000379607	NM_001412.3	82	cGa/cAa	4/7	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.323486509545978	1		206	493	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28908212	28908212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	157	424	3	ENST00000282397.4:c.2543del	p.Gly848AlafsTer13	p.G848Afs*13	ENST00000282397	NM_002019.4	848	gGc/gc	18/30	0.323486509545978	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.323486509545978	1		427	684	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16040683	16040683	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	54	430	1	ENST00000268712.3:c.1451del	p.Asn484MetfsTer31	p.N484Mfs*31	ENST00000268712	NM_006311.3	484	aAt/at	14/46	0.279872155022446	2	FACETS	0.375	0.319	0.436	0.187	0.159	0.218	SUBCLONAL	1	TRUE	0	0.323486509545978	2		431	891	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639574	47639613	+	frameshift_variant	Frame_Shift_Del	DEL	CTGATCACAGAAAGAAAAAAAGCTGACTTTTCCACAAAAG	CTGATCACAGAAAGAAAAAAAGCTGACTTTTCCACAAAAG	-	novel	NA	P-0010736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	131	250	0	ENST00000233146.2:c.667_706del	p.Leu223ThrfsTer10	p.L223Tfs*10	ENST00000233146	NM_000251.2	223	CTGATCACAGAAAGAAAAAAAGCTGACTTTTCCACAAAAGac/ac	4/16	0.323486509545978	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.323486509545978	1		250	504	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894228	NA	P-0010737-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	341	570	1	ENST00000451590.1:c.37G>C	p.Gly13Arg	p.G13R	ENST00000451590	NM_001130442.1	13	Ggt/Cgt	2/5	0.423422052011282	6	FACETS	1	0.99	1	0.591	0.559	0.624	CLONAL	2	TRUE	2	0.423422052011282	6		571	1258	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428507	78428507	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010737-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	388	437	0	ENST00000370768.2:c.1292G>C	p.Gly431Ala	p.G431A	ENST00000370768	NM_003902.3	431	gGc/gCc	14/20	0.266506126355362	5	FACETS	0.882	0.839	0.926	0.882	0.839	0.926	CLONAL	3	TRUE	2	0.423422052011282	5		437	1132	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627244	12627244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338799	NA	P-0010737-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	235	475	0	ENST00000251849.4:c.1472C>T	p.Thr491Ile	p.T491I	ENST00000251849	NM_002880.3	491	aCa/aTa	14/17	0.266506126355362	5	FACETS	0.779	0.726	0.834	0.519	0.484	0.556	SUBCLONAL	2	TRUE	2	0.423422052011282	5		475	1165	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941882	44941882	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	338	377	0	ENST00000377967.4:c.3206A>G	p.Asp1069Gly	p.D1069G	ENST00000377967	NM_021140.2	1069	gAt/gGt	21/29	1	1	FACETS	0.987	0.95	1	1	0.997	1	CLONAL	3	TRUE	0	0.369362877806657	1		377	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0010760-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	35	270	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.855	0.699	1	0.855	0.699	1	CLONAL	1	TRUE	1	0.13	2		272	630	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149893	202149893	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0010760-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	675	482	0	ENST00000358485.4:c.1334C>G	p.Ser445Ter	p.S445*	ENST00000358485	NM_001080125.1	445	tCa/tGa	8/9	0.3	6	FACETS	1	0.984	1			1	CLONAL	8	TRUE	NA	0.13	6		482	1583	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150039	202150039	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1368296717	NA	P-0010760-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	577	340	0	ENST00000358485.4:c.1480C>T	p.Arg494Ter	p.R494*	ENST00000358485	NM_001080125.1	494	Cga/Tga	8/9	0.3	6	FACETS	1	0.986	1			1	CLONAL	8	TRUE	NA	0.13	6		340	1336	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714396	117714396	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0010760-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	69	465	0	ENST00000368508.3:c.1253C>G	p.Ser418Ter	p.S418*	ENST00000368508	NM_002944.2	418	tCa/tGa	11/43	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.13	2		465	1006	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750863	128750863	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010760-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2910	1636	545	0	ENST00000377970.2:c.400C>G	p.Pro134Ala	p.P134A	ENST00000377970	NM_002467.4	134	Ccg/Gcg	2/3	0.3	12	FACETS	1	0.987	1			1	CLONAL	9	TRUE	NA	0.13	12		545	4546	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534567	140534567	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	93	415	0	ENST00000288602.6:c.346T>C	p.Ser116Pro	p.S116P	ENST00000288602	NM_004333.4	116	Tca/Cca	3/18	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.173003134598685	2		415	788	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158594054	158594054	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	145	526	0	ENST00000263640.3:c.1519del	p.Thr507LeufsTer14	p.T507Lfs*14	ENST00000263640	NM_001105.4	507	Act/ct	11/11	0.173003134598685	6	FACETS	0.908	0.826	0.994	0.454	0.413	0.497	CLONAL	2	TRUE	2	0.173003134598685	6		526	1243	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0010763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	67	683	2	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.202778175148587	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.202778175148587	1		685	554	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526242	189526242	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	174	601	1	ENST00000264731.3:c.506C>A	p.Thr169Asn	p.T169N	ENST00000264731	NM_003722.4	169	aCc/aAc	4/14	0.202778175148587	3	FACETS	0.763	0.701	0.829	0.763	0.701	0.829	SUBCLONAL	2	TRUE	1	0.202778175148587	3		602	1238	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188961	32188961	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1397220953	NA	P-0010763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	79	685	2	ENST00000375023.3:c.593G>T	p.Cys198Phe	p.C198F	ENST00000375023	NM_004557.3	198	tGc/tTc	4/30	0.138938911421013	1	FACETS	0.747	0.656	0.846	0.747	0.656	0.846	SUBCLONAL	1	TRUE	0	0.202778175148587	1		687	937	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468080	50468080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	57	334	0	ENST00000331340.3:c.1315C>T	p.Arg439Cys	p.R439C	ENST00000331340	NM_006060.4	439	Cgc/Tgc	8/8	0.202778175148587	6	FACETS	1	0.945	1	0.406	0.348	0.47	CLONAL	1	TRUE	3	0.202778175148587	6		334	649	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154411	2154411	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	56	620	0	ENST00000434045.2:c.517G>T	p.Asp173Tyr	p.D173Y	ENST00000434045	NM_001127598.1	173	Gac/Tac	5/5	1	2	FACETS	0.799	0.684	0.926	0.799	0.684	0.926	CLONAL	1	TRUE	1	0.202778175148587	2		620	691	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005652	42005652	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	148	700	4	ENST00000219905.7:c.3388G>T	p.Glu1130Ter	p.E1130*	ENST00000219905	NM_001164273.1	1130	Gaa/Taa	9/24	0.154463125912427	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.202778175148587	1		704	1164	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117684016	117684017	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0010763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	100	281	0	ENST00000368508.3:c.3130_3131delinsAT	p.Pro1044Ile	p.P1044I	ENST00000368508	NM_002944.2	1044	CCa/ATa	21/43	1	2	FACETS	0.815	0.729	0.906	1	0.984	1	CLONAL	2	TRUE	1	0.202778175148587	2		281	605	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012638	36012641	+	missense_variant	Missense_Mutation	ONP	GGCG	GGCG	CGCT	novel	NA	P-0010763-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	24	337	0	ENST00000358208.4:c.82_85delinsCGCT	p.Gly28_Gly29delinsArgTrp	p.G28_G29delinsRW	ENST00000358208		28	GGCGgg/CGCTgg	2/12	1	2	FACETS	0.604	0.473	0.755	0.604	0.473	0.755	SUBCLONAL	1	TRUE	1	0.202778175148587	2		337	392	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	49	389	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.893	0.757	1	0.893	0.757	1	CLONAL	1	TRUE	1	0.231620423053432	2		389	474	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665752	29665755	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1555535032	NA	P-0010787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	109	686	0	ENST00000356175.3:c.6789_6792del	p.Tyr2264ThrfsTer5	p.Y2264Tfs*5	ENST00000356175	NM_000267.3	2263	ACTTac/ac	45/57	1	2	FACETS	0.915	0.82	1	0.915	0.82	1	CLONAL	1	TRUE	1	0.231620423053432	2		686	1029	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857196	9857196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs74935155	NA	P-0010787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1259	154	808	2	ENST00000330684.3:c.4205G>A	p.Arg1402Gln	p.R1402Q	ENST00000330684	NM_001134407.1	1402	cGg/cAg	13/13	1	2	FACETS	0.941	0.859	1	0.941	0.859	1	CLONAL	1	TRUE	1	0.231620423053432	2		810	1413	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118936	70118936	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866706988	NA	P-0010787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	131	662	0	ENST00000245479.2:c.508C>A	p.Pro170Thr	p.P170T	ENST00000245479	NM_000346.3	170	Ccg/Acg	2/3	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.231620423053432	2		662	1092	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867291	45867291	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199863965	NA	P-0010787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	69	296	0	ENST00000391945.4:c.902C>T	p.Thr301Met	p.T301M	ENST00000391945	NM_000400.3	301	aCg/aTg	10/23	0.224885228040527	3	FACETS	1	0.916	1	0.534	0.465	0.609	CLONAL	1	TRUE	1	0.231620423053432	3		296	622	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496924	29496927	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs786201874	NA	P-0010787-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	52	472	0	ENST00000356175.3:c.499_502del	p.Cys167GlnfsTer10	p.C167Qfs*10	ENST00000356175	NM_000267.3	165	acTGTT/ac	5/57	1	2	FACETS	0.609	0.517	0.71	0.609	0.517	0.71	SUBCLONAL	1	TRUE	1	0.231620423053432	2		472	737	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	70	540	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.889	0.776	1	0.889	0.776	1	CLONAL	1	TRUE	1	0.280294956850265	2		540	562	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0010788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	69	301	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.280294956850265	1	FACETS	0.987	0.863	1	0.987	0.863	1	CLONAL	1	TRUE	0	0.280294956850265	1		301	429	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575194	48575194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555685186	NA	P-0010788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	72	269	0	ENST00000342988.3:c.388C>T	p.Pro130Ser	p.P130S	ENST00000342988	NM_005359.5	130	Cca/Tca	3/12	0.280294956850265	1	FACETS	0.958	0.84	1	0.958	0.84	1	CLONAL	1	TRUE	0	0.280294956850265	1		269	461	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440643	56440643	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	171	565	2	ENST00000407977.2:c.575del	p.Pro192ArgfsTer11	p.P192Rfs*11	ENST00000407977		192	cCg/cg	5/10	0.280294956850265	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.280294956850265	1		567	989	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389095	31389095	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756558325	NA	P-0010794-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	52	378	0	ENST00000328111.2:c.2008C>T	p.Arg670Trp	p.R670W	ENST00000328111	NM_006892.3	670	Cgg/Tgg	19/23	1	2	FACETS	0.697	0.592	0.812	0.697	0.592	0.812	SUBCLONAL	1	TRUE	1	0.21	2		378	711	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812340	212812340	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010796-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	137	423	0	ENST00000342788.4:c.236C>A	p.Ser79Tyr	p.S79Y	ENST00000342788	NM_005235.2	79	tCt/tAt	3/28	0.384126409070217	4	FACETS	0.885	0.809	0.963	0.59	0.539	0.642	CLONAL	2	FALSE	1	0.425131791498978	4		423	519	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0010818-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	173	332	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.897	0.829	0.968			1	INDETERMINATE	1	TRUE	NA	0.600549228010472	2		332	642	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970901	21970901	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs45476696	NA	P-0010818-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	342	407	0	ENST00000304494.5:c.457G>A	p.Asp153Asn	p.D153N	ENST00000304494	NM_000077.4	153	Gac/Aac	2/3	0.600549228010472	1	FACETS	0.994	0.946	1	0.994	0.946	1	CLONAL	1	TRUE	0	0.600549228010472	1		407	802	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729115	66729129	+	inframe_deletion	In_Frame_Del	DEL	GGAACCAGATCATAA	GGAACCAGATCATAA	-	novel	NA	P-0010818-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	693	493	0	ENST00000307102.5:c.325_339del	p.Asn109_Arg113del	p.N109_R113del	ENST00000307102	NM_002755.3	108	cGGAACCAGATCATAAgg/cgg	3/11	0.600549228010472	2	FACETS	0.906	0.878	0.934	0.906	0.878	0.934	CLONAL	2	TRUE	0	0.600549228010472	2		493	1274	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732959	74732959	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751713049	NA	P-0010818-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	321	355	0	ENST00000359995.5:c.284C>T	p.Pro95Leu	p.P95L	ENST00000359995	NM_001195427.1	95	cCc/cTc	1/3	0.600549228010472	3	FACETS	1	0.984	1	0.553	0.522	0.586	CLONAL	1	TRUE	1	0.600549228010472	3		355	1256	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754865	29754865	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010818-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	289	352	0	ENST00000389048.3:c.1070C>T	p.Pro357Leu	p.P357L	ENST00000389048	NM_004304.4	357	cCc/cTc	4/29	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.600549228010472	2		352	940	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117632205	117632205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010818-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	396	478	0	ENST00000368508.3:c.6211G>A	p.Glu2071Lys	p.E2071K	ENST00000368508	NM_002944.2	2071	Gaa/Aaa	39/43	NA	2	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.600549228010472	2		478	1292	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28897053	28897053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148112461	NA	P-0010818-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	224	326	0	ENST00000282397.4:c.2827G>A	p.Glu943Lys	p.E943K	ENST00000282397	NM_002019.4	943	Gaa/Aaa	21/30	1	2	FACETS	0.898	0.838	0.959	0.898	0.838	0.959	CLONAL	1	TRUE	1	0.600549228010472	2		326	831	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804359	43804359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749391587	NA	P-0010818-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	323	449	0	ENST00000372470.3:c.359G>A	p.Arg120Gln	p.R120Q	ENST00000372470	NM_005373.2	120	cGg/cAg	3/12	0.278804763734162	1	FACETS	0.745	0.705	0.786	0.745	0.705	0.786	INDETERMINATE	1	TRUE	0	0.600549228010472	1		449	1010	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491703	120491703	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0010818-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	468	483	0	ENST00000256646.2:c.2526T>A	p.Cys842Ter	p.C842*	ENST00000256646	NM_024408.3	842	tgT/tgA	16/34	0.278804763734162	1	FACETS	0.886	0.848	0.925	0.886	0.848	0.925	INDETERMINATE	1	TRUE	0	0.600549228010472	1		483	1231	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652797	212652797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010818-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	436	493	1	ENST00000342788.4:c.509C>T	p.Pro170Leu	p.P170L	ENST00000342788	NM_005235.2	170	cCa/cTa	4/28	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.600549228010472	2		494	1434	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191448	185191448	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1012339817	NA	P-0010818-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	306	356	0	ENST00000265026.3:c.2329G>A	p.Glu777Lys	p.E777K	ENST00000265026	NM_004721.4	777	Gaa/Aaa	11/14	0.278804763734162	1	FACETS	0.813	0.769	0.858	0.813	0.769	0.858	INDETERMINATE	1	TRUE	0	0.600549228010472	1		356	877	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457282	5457282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376993991	NA	P-0010818-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	279	278	0	ENST00000381577.3:c.256C>T	p.Arg86Trp	p.R86W	ENST00000381577	NM_014143.3	86	Cgg/Tgg	3/7	0.600549228010472	1	FACETS	0.962	0.91	1	0.962	0.91	1	CLONAL	1	TRUE	0	0.600549228010472	1		278	676	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342586	118342586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010818-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	260	542	0	ENST00000534358.1:c.712G>A	p.Gly238Arg	p.G238R	ENST00000534358	NM_005933.3	238	Gga/Aga	3/36	0.278804763734162	1	FACETS	0.438	0.409	0.468	0.438	0.409	0.468	INDETERMINATE	1	TRUE	0	0.600549228010472	1		542	1383	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350313	15350313	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010818-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	283	432	0	ENST00000263377.2:c.3466G>A	p.Asp1156Asn	p.D1156N	ENST00000263377	NM_058243.2	1156	Gat/Aat	17/20	1	2	FACETS	0.965	0.908	1	0.965	0.908	1	CLONAL	1	TRUE	1	0.600549228010472	2		432	977	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852433	42852433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010818-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	352	410	0	ENST00000398585.3:c.653G>A	p.Gly218Glu	p.G218E	ENST00000398585	NM_001135099.1	218	gGg/gAg	6/14	0.317049795055008	1	FACETS	0.864	0.821	0.908	0.864	0.821	0.908	INDETERMINATE	1	TRUE	0	0.600549228010472	1		410	949	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551282	29551284	+	stop_gained	Nonsense_Mutation	TNP	GGA	GGA	AGT	novel	NA	P-0010818-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	306	477	0	ENST00000389048.3:c.1346_1348delinsACT	p.Leu449_Gln450delinsHisTer	p.L449_Q450delinsH*	ENST00000389048	NM_004304.4	449	cTCCag/cACTag	6/29	1	2	FACETS	0.901	0.849	0.954	0.901	0.849	0.954	CLONAL	1	TRUE	1	0.600549228010472	2		477	1131	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0010843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	394	453	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.388537602635019	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	1	0.388537602635019	4		453	855	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376690	31376690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	136	346	0	ENST00000328111.2:c.685G>A	p.Val229Met	p.V229M	ENST00000328111	NM_006892.3	229	Gtg/Atg	7/23	0.388537602635019	5	FACETS	1	0.974	1	0.398	0.361	0.437	CLONAL	1	TRUE	2	0.388537602635019	5		346	928	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670673	67670673	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	595	499	0	ENST00000264010.4:c.1918C>T	p.Pro640Ser	p.P640S	ENST00000264010	NM_006565.3	640	Cct/Tct	11/12	0.348908256193186	3	FACETS	1	0.994	1			1	CLONAL	3	TRUE	NA	0.388537602635019	3		499	1082	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027517	48027517	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	136	277	0	ENST00000234420.5:c.2395A>T	p.Met799Leu	p.M799L	ENST00000234420	NM_000179.2	799	Atg/Ttg	4/10	1	2	FACETS	0.536	0.489	0.584	0.536	0.489	0.584	SUBCLONAL	1	TRUE	1	0.867995607692516	2		277	585	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508257	106508257	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766854286	NA	P-0010868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	30	170	0	ENST00000359195.3:c.251C>T	p.Ala84Val	p.A84V	ENST00000359195	NM_002649.2	84	gCg/gTg	2/11	0.867995607692516	3	FACETS	0.181	0.145	0.222	0.09	0.072	0.111	SUBCLONAL	1	TRUE	1	0.867995607692516	3		170	548	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0010869-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	15	453	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		453	664	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0010894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	130	316	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.817718996611867	3	FACETS	0.929	0.848	1	0.31	0.282	0.338	CLONAL	1	TRUE	0	0.817718996611867	3		316	482	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521565	46521565	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	151	800	0	ENST00000262741.5:c.843G>C	p.Leu281Phe	p.L281F	ENST00000262741	NM_003629.3	281	ttG/ttC	7/10	0.817718996611867	3	FACETS	0.406	0.37	0.444	0.203	0.185	0.222	SUBCLONAL	1	TRUE	1	0.817718996611867	3		800	1281	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645858	215645858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	400	739	0	ENST00000260947.4:c.740C>T	p.Ser247Phe	p.S247F	ENST00000260947	NM_000465.2	247	tCt/tTt	4/11	0.7939503924271	3	FACETS	1	0.984	1	0.359	0.341	0.377	CLONAL	1	TRUE	0	0.817718996611867	3		739	1281	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696652	176696652	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	277	558	0	ENST00000439151.2:c.5353G>A	p.Asp1785Asn	p.D1785N	ENST00000439151	NM_022455.4	1785	Gat/Aat	16/23	0.69000699794166	4	FACETS	0.954	0.895	1	0.477	0.447	0.508	CLONAL	1	TRUE	2	0.817718996611867	4		558	1291	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69458635	69458635	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	65	579	0	ENST00000227507.2:c.450G>C	p.Trp150Cys	p.W150C	ENST00000227507	NM_053056.2	150	tgG/tgC	3/5	0.785237976329352	3	FACETS	0.221	0.191	0.254	0.111	0.095	0.127	SUBCLONAL	1	TRUE	1	0.817718996611867	3		579	1012	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26956987	26956987	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	193	365	0	ENST00000381527.3:c.493G>C	p.Glu165Gln	p.E165Q	ENST00000381527	NM_001260.1	165	Gag/Cag	5/13	0.7939503924271	3	FACETS	0.977	0.907	1	0.326	0.302	0.35	CLONAL	1	TRUE	0	0.817718996611867	3		365	681	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012379	29012379	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1387615627	NA	P-0010894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	583	672	0	ENST00000282397.4:c.492C>A	p.Asn164Lys	p.N164K	ENST00000282397	NM_002019.4	164	aaC/aaA	4/30	0.7939503924271	3	FACETS	0.927	0.896	0.959	0.618	0.597	0.639	CLONAL	2	TRUE	0	0.817718996611867	3		672	1083	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663375	29663375	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1567616649	NA	P-0010894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	270	470	0	ENST00000356175.3:c.5968C>G	p.Leu1990Val	p.L1990V	ENST00000356175	NM_000267.3	1990	Cta/Gta	40/57	0.817718996611867	3	FACETS	0.982	0.923	1	0.491	0.461	0.522	CLONAL	1	TRUE	1	0.817718996611867	3		470	947	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885981	59885981	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	258	583	0	ENST00000259008.2:c.765G>C	p.Gln255His	p.Q255H	ENST00000259008	NM_032043.2	255	caG/caC	7/20	0.497610579367123	3	FACETS	0.98	0.92	1			1	CLONAL	1	TRUE	NA	0.817718996611867	3		583	907	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934261	48934261	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	545	339	0	ENST00000267163.4:c.716del	p.Tyr239LeufsTer25	p.Y239Lfs*25	ENST00000267163	NM_000321.2	239	tAt/tt	7/27	0.7939503924271	3	FACETS	0.963	0.942	0.983	0.963	0.942	0.983	CLONAL	3	TRUE	0	0.817718996611867	3		339	650	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412033	116412048	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTCCAGAAGGTATA	TTTTCCAGAAGGTATA	-	novel	NA	P-0010894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	318	406	0	ENST00000397752.3:c.3021_3028+8del		p.X1007_splice	ENST00000397752	NM_000245.2	1007		14/21	0.788757589775646	2	FACETS	0.919	0.888	0.949	0.919	0.888	0.949	CLONAL	2	TRUE	0	0.817718996611867	2		406	423	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	43	540	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.943	0.792	1	0.943	0.792	1	CLONAL	1	TRUE	1	0.254690439984145	2		540	358	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587781525	NA	P-0010923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1235	75	672	0	ENST00000269305.4:c.842A>T	p.Asp281Val	p.D281V	ENST00000269305	NM_001126112.2	281	gAc/gTc	8/11	1	2	FACETS	0.45	0.392	0.512	0.45	0.392	0.512	SUBCLONAL	1	TRUE	1	0.254690439984145	2		672	1310	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707969	47707969	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1013401625	NA	P-0010923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	26	445	0	ENST00000233146.2:c.2593A>G	p.Ile865Val	p.I865V	ENST00000233146	NM_000251.2	865	Atc/Gtc	15/16	0.208883140662942	0	FACETS	0.452	0.358	0.559			1	SUBCLONAL	1	TRUE	0	0.254690439984145	0		445	337	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430953	181430953	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	74	584	2	ENST00000325404.1:c.805G>T	p.Asp269Tyr	p.D269Y	ENST00000325404	NM_003106.3	269	Gac/Tac	1/1	1	2	FACETS	0.496	0.432	0.565	0.496	0.432	0.565	SUBCLONAL	1	TRUE	1	0.254690439984145	2		586	1172	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449612	187449612	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	62	488	1	ENST00000232014.4:c.268A>T	p.Met90Leu	p.M90L	ENST00000232014	NM_001130845.1	90	Atg/Ttg	4/10	1	2	FACETS	0.691	0.596	0.794	0.691	0.596	0.794	SUBCLONAL	1	TRUE	1	0.254690439984145	2		489	705	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478932	56478932	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	106	764	0	ENST00000267101.3:c.388G>C	p.Ala130Pro	p.A130P	ENST00000267101	NM_001982.3	130	Gct/Cct	3/28	1	2	FACETS	0.662	0.592	0.738	0.662	0.592	0.738	SUBCLONAL	1	TRUE	1	0.254690439984145	2		764	1257	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628366	86628366	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	13	432	2	ENST00000274376.6:c.739del	p.Ser247LeufsTer6	p.S247Lfs*6	ENST00000274376	NM_002890.2	245	cgT/cg	3/25	1	2	FACETS	0.564	0.403	0.759	0.564	0.403	0.759	SUBCLONAL	1	TRUE	1	0.254690439984145	2		434	181	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409146	4409147	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0010923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	83	566	0	ENST00000261254.3:c.841_842delinsAA	p.Pro281Asn	p.P281N	ENST00000261254	NM_001759.3	281	CCt/AAt	5/5	1	2	FACETS	0.658	0.579	0.743	0.658	0.579	0.743	SUBCLONAL	1	TRUE	1	0.254690439984145	2		566	991	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510627	38510628	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0010923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	82	786	1	ENST00000254066.5:c.881_882delinsAT	p.Arg294His	p.R294H	ENST00000254066	NM_000964.3	294	cGG/cAT	7/9	1	2	FACETS	0.533	0.468	0.603	0.533	0.468	0.603	SUBCLONAL	1	TRUE	1	0.254690439984145	2		787	1209	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0010924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	103	332	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.95	1			1	INDETERMINATE	1	TRUE	NA	0.471642041897648	2		332	402	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699283	117699283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144508898	NA	P-0010924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	95	1074	2	ENST00000369458.3:c.358G>A	p.Val120Met	p.V120M	ENST00000369458	NM_024626.3	120	Gtg/Atg	3/6	0.4203448643577	1	FACETS	0.511	0.455	0.569	0.511	0.455	0.569	SUBCLONAL	1	TRUE	0	0.471642041897648	1		1076	603	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439563	51439563	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0010924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	134	697	0	ENST00000262662.1:c.130-2A>G		p.X44_splice	ENST00000262662		44			1	2	FACETS	0.88	0.801	0.962	0.88	0.801	0.962	CLONAL	1	TRUE	1	0.471642041897648	2		697	646	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612247	189612247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	146	641	1	ENST00000264731.3:c.1999G>A	p.Ala667Thr	p.A667T	ENST00000264731	NM_003722.4	667	Gct/Act	14/14	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.471642041897648	2		642	576	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717730	89717730	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121909239	NA	P-0010924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	172	541	0	ENST00000371953.3:c.755A>G	p.Asp252Gly	p.D252G	ENST00000371953	NM_000314.4	252	gAt/gGt	7/9	0.471642041897648	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.471642041897648	1		541	473	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593583	55593603	+	protein_altering_variant	In_Frame_Del	DEL	AACCCATGTATGAAGTACAGT	AACCCATGTATGAAGTACAGT	TAC	novel	NA	P-0010949-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	285	406	0	ENST00000288135.5:c.1649_1669delinsTAC	p.Lys550_Trp557delinsIleArg	p.K550_W557delinsIR	ENST00000288135	NM_000222.2	550	aAACCCATGTATGAAGTACAGTgg/aTACgg	11/21	1	2	FACETS	0.849	0.802	0.896	0.849	0.802	0.896	CLONAL	1	TRUE	1	0.907522433430572	2		406	740	SUCCESS
APC	324	MSKCC	GRCh37	5	112177050	112177050	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780599	NA	P-0010958-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	289	769	0	ENST00000257430.4:c.5759G>A	p.Arg1920Gln	p.R1920Q	ENST00000257430	NM_000038.5	1920	cGa/cAa	16/16	0.337549277141858	3	FACETS	0.943	0.886	1			1	INDETERMINATE	1	FALSE	NA	0.737551937608886	3		769	1138	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61729414	61729414	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010958-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	113	460	0	ENST00000401558.2:c.333C>G	p.Ile111Met	p.I111M	ENST00000401558	NM_003400.3	111	atC/atG	5/25	0.205311815855147	5	FACETS	0.984	0.887	1	0.328	0.295	0.362	INDETERMINATE	1	FALSE	2	0.737551937608886	5		460	656	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151167680	151167680	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010958-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	87	459	0	ENST00000262187.5:c.439G>C	p.Glu147Gln	p.E147Q	ENST00000262187	NM_005614.3	147	Gaa/Caa	7/8	0.256091623820767	5	FACETS	0.721	0.638	0.81			1	INDETERMINATE	1	FALSE	NA	0.737551937608886	5		459	689	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321388	30321631	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGCAATAAATGACATAGTTAAGATTTTAACACATTTTGTTGACCCCAGGTCTTCTGACTGCCTGTTTACCATGCTGGTGTGCCTGGCCTATTTTAGTTTTCTAAATATTAAGAGCCCACAAATTCTTTAATTAAATTGGAGGGATATTTAGGATAGGATACTTAATATATTTTTTTTTTTACATTTTTGTTGCAGTATCATCCAAAAGGTGCTAGGATAGATGTTTCTATCAATGAGTGTTATG	AGCAATAAATGACATAGTTAAGATTTTAACACATTTTGTTGACCCCAGGTCTTCTGACTGCCTGTTTACCATGCTGGTGTGCCTGGCCTATTTTAGTTTTCTAAATATTAAGAGCCCACAAATTCTTTAATTAAATTGGAGGGATATTTAGGATAGGATACTTAATATATTTTTTTTTTTACATTTTTGTTGCAGTATCATCCAAAAGGTGCTAGGATAGATGTTTCTATCAATGAGTGTTATG	-	novel	NA	P-0010958-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2	92	17	0	ENST00000322652.5:c.1438-194_1487del		p.X480_splice	ENST00000322652	NM_015355.2	480		13/16	0.708774716403272	1	FACETS		NA	1	1	0.992	1	NA	2	FALSE	0	0.737551937608886	1		17	94	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205772	128205773	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AT	novel	NA	P-0010958-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	140	587	0	ENST00000341105.2:c.102_103delinsAT	p.Met34_Glu35delinsIleTer	p.M34_E35delinsI*	ENST00000341105	NM_032638.4	34	atGGaa/atATaa	2/6	1	2	FACETS	0.561	0.512	0.612	0.561	0.512	0.612	SUBCLONAL	1	FALSE	1	0.737551937608886	2		587	677	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654548	29654565	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAGCGAACAAAAGTCC	CAGAGCGAACAAAAGTCC	G	novel	NA	P-0010958-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	171	570	0	ENST00000356175.3:c.5237_5254delinsG	p.Ala1746GlyfsTer9	p.A1746Gfs*9	ENST00000356175	NM_000267.3	1746	gCAGAGCGAACAAAAGTCCta/gGta	37/57	0.708774716403272	1	FACETS	0.827	0.773	0.881	0.827	0.773	0.881	CLONAL	1	FALSE	0	0.737551937608886	1		570	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0010959-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	8	430	0	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.19505198291351	3	FACETS	0.165	0.105	0.242	0.082	0.052	0.121	INDETERMINATE	1	TRUE	1	0.331970916957878	3		430	341	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495659	72495659	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010959-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	105	345	0	ENST00000477973.2:c.413G>A	p.Gly138Asp	p.G138D	ENST00000477973	NM_012234.5	138	gGc/gAc	1/4	0.166156918308373	6	FACETS	0.841	0.755	0.932	0.56	0.503	0.621	INDETERMINATE	2	TRUE	3	0.331970916957878	6		345	626	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952135	178952135	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010959-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	78	268	0	ENST00000263967.3:c.3190del	p.Gln1064SerfsTer4	p.Q1064Sfs*4	ENST00000263967	NM_006218.2	1064	Cag/ag	21/21	0.206003088451518	4	FACETS	0.88	0.773	0.996	0.44	0.386	0.498	CLONAL	1	TRUE	2	0.331970916957878	4		268	711	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	36	540	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.1271633340247	3	FACETS	0.844	0.691	1	0.422	0.345	0.508	CLONAL	1	TRUE	1	0.12	3		540	754	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0010966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	11	316	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.586	0.403	0.814	0.586	0.403	0.814	SUBCLONAL	1	TRUE	1	0.12	2		316	313	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276723	15276723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1031506714	NA	P-0010966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	25	470	0	ENST00000263388.2:c.5542C>T	p.Arg1848Cys	p.R1848C	ENST00000263388	NM_000435.2	1848	Cgt/Tgt	30/33	1	2	FACETS	0.916	0.721	1	0.916	0.721	1	CLONAL	1	TRUE	1	0.12	2		470	455	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710672	114710672	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs184454375	NA	P-0010966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	48	596	0	ENST00000543371.1:c.157G>A	p.Glu53Lys	p.E53K	ENST00000543371	NM_001198531.1	53	Gaa/Aaa	1/14	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.12	2		596	769	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0010975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	355	449	9	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.937	0.889	0.985	0.937	0.889	0.985	CLONAL	1	TRUE	1	0.732305856199433	2		458	1035	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0010975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	374	502	4	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.902	0.856	0.947	0.902	0.856	0.947	CLONAL	1	TRUE	1	0.732305856199433	2		506	1133	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220080	133220080	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	495	581	14	ENST00000320574.5:c.4357A>G	p.Arg1453Gly	p.R1453G	ENST00000320574	NM_006231.2	1453	Agg/Ggg	34/49	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.732305856199433	2		595	1276	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253759	153253770	+	inframe_deletion	In_Frame_Del	DEL	CATTTCTCTCTC	CATTTCTCTCTC	-	novel	NA	P-0010975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	257	339	3	ENST00000281708.4:c.963_974del	p.Trp321_Lys324del	p.W321_K324del	ENST00000281708	NM_033632.3	321	tgGAGAGAGAAATGc/tgc	6/12	1	2	FACETS	0.899	0.845	0.954	0.899	0.845	0.954	CLONAL	1	TRUE	1	0.732305856199433	2		342	781	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033942	49033943	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	T	novel	NA	P-0010975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	362	363	8	ENST00000267163.4:c.2079_2080delinsT	p.Glu693AspfsTer3	p.E693Dfs*3	ENST00000267163	NM_000321.2	693	gaACtc/gaTtc	20/27	0.585520016851263	1	FACETS	0.984	0.943	1	0.984	0.943	1	CLONAL	1	TRUE	0	0.732305856199433	1		371	637	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662364	227662364	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747409858	NA	P-0010978-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	90	416	0	ENST00000305123.5:c.1091G>A	p.Arg364Gln	p.R364Q	ENST00000305123	NM_005544.2	364	cGg/cAg	1/2	NA	2	FACETS	0.979	0.873	1			1	INDETERMINATE	1	TRUE	NA	0.410388211207626	2		416	448	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	150	389	0				ENST00000310581	NM_198253.2	-/1132			0.272653887164004	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.272653887164004	4		389	618	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0010981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	67	248	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.272653887164004	4	FACETS	0.788	0.688	0.895	0.788	0.688	0.895	SUBCLONAL	2	TRUE	2	0.272653887164004	4		248	397	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894230	NA	P-0010981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	115	538	0	ENST00000451590.1:c.35G>A	p.Gly12Asp	p.G12D	ENST00000451590	NM_001130442.1	12	gGc/gAc	2/5	0.272653887164004	3	FACETS	1	0.932	1	0.523	0.47	0.578	CLONAL	1	TRUE	1	0.272653887164004	3		538	917	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524212	18524212	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs375427718	NA	P-0010981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	243	701	0	ENST00000266497.5:c.1724T>C	p.Leu575Pro	p.L575P	ENST00000266497		575	cTg/cCg	11/31	0.272653887164004	4	FACETS	0.952	0.889	1	0.952	0.889	1	CLONAL	2	TRUE	2	0.272653887164004	4		701	1191	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412045	116412045	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0010983-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	79	292	0	ENST00000397752.3:c.3028+2T>C		p.X1010_splice	ENST00000397752	NM_000245.2	1010			1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.17	2		292	777	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40458409	40458409	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010983-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	30	218	0	ENST00000345506.4:c.1624A>G	p.Ser542Gly	p.S542G	ENST00000345506	NM_003152.3	542	Agc/Ggc	14/20	1	2	FACETS	0.85	0.685	1	0.85	0.685	1	CLONAL	1	TRUE	1	0.17	2		218	415	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064370	30064370	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010990-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	261	549	0	ENST00000338641.4:c.936del	p.Ala313ProfsTer9	p.A313Pfs*9	ENST00000338641	NM_000268.3	312	Aaa/aa	10/16	0.460918108878211	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.460918108878211	1		549	812	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97879649	97879657	+	inframe_deletion	In_Frame_Del	DEL	GTAGGTCTT	GTAGGTCTT	-	novel	NA	P-0010990-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	244	463	0	ENST00000289081.3:c.1012_1020del	p.Lys338_Tyr340del	p.K338_Y340del	ENST00000289081	NM_000136.2	338	AAGACCTAC/-	11/15	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.460918108878211	2		463	1034	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576887	7576894	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTTTGG	TTCTTTGG	-	novel	NA	P-0010991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	998	614	0	ENST00000269305.4:c.952_959del	p.Pro318GlufsTer16	p.P318Efs*16	ENST00000269305	NM_001126112.2	318	CCAAAGAAg/g	9/11	0.182064923465155	6	FACETS	1	0.996	1			1	INDETERMINATE	5	TRUE	NA	0.573983099390187	6		614	1408	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882048	36882055	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGGGGG	GCGGGGGG	-	novel	NA	P-0010991-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	551	681	0	ENST00000358127.4:c.958_965del	p.Pro320TrpfsTer18	p.P320Wfs*18	ENST00000358127	NM_001280556.1	320	CCCCCCGCt/t	8/10	0.290808941560459	5	FACETS	0.838	0.805	0.872	0.838	0.805	0.872	INDETERMINATE	3	TRUE	2	0.573983099390187	5		681	1421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764146326	NA	P-0010993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	534	632	0	ENST00000269305.4:c.841G>T	p.Asp281Tyr	p.D281Y	ENST00000269305	NM_001126112.2	281	Gac/Tac	8/11	0.559434643912158	1	FACETS	0.995	0.955	1	0.995	0.955	1	CLONAL	1	TRUE	0	0.558449920504402	1		632	1385	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662977	227662977	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	361	530	0	ENST00000305123.5:c.478T>A	p.Phe160Ile	p.F160I	ENST00000305123	NM_005544.2	160	Ttc/Atc	1/2	1	2	FACETS	0.926	0.877	0.977	0.926	0.877	0.977	CLONAL	1	TRUE	1	0.558449920504402	2		530	1396	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259182	89259182	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1217	1134	395	0	ENST00000336596.2:c.326T>A	p.Ile109Asn	p.I109N	ENST00000336596	NM_005233.5	109	aTt/aAt	3/17	0.531220108260551	5	FACETS	1	0.994	1			1	CLONAL	3	TRUE	NA	0.558449920504402	5		395	2351	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100553	102100553	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	421	538	0	ENST00000282441.5:c.1397A>T	p.Glu466Val	p.E466V	ENST00000282441	NM_001130145.2	466	gAa/gTa	9/9	0.534224482405869	2	FACETS	1	0.973	1	0.517	0.491	0.542	CLONAL	1	TRUE	0	0.558449920504402	2		538	1459	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17117122	17117122	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1764	347	595	0	ENST00000285071.4:c.1587A>T	p.Lys529Asn	p.K529N	ENST00000285071	NM_144997.5	529	aaA/aaT	14/14	0.271962786754741	3	FACETS	0.753	0.71	0.798			1	INDETERMINATE	1	TRUE	NA	0.558449920504402	3		595	2111	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226147	53226147	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	356	545	0	ENST00000375401.3:c.2702T>C	p.Leu901Pro	p.L901P	ENST00000375401	NM_004187.3	901	cTg/cCg	19/26	0.240892443023765	3	FACETS	1	0.98	1	0.357	0.338	0.378	INDETERMINATE	1	TRUE	0	0.558449920504402	3		545	1521	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617210	100617210	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2416	239	699	2	ENST00000308731.7:c.539C>A	p.Ser180Tyr	p.S180Y	ENST00000308731	NM_000061.2	180	tCt/tAt	7/19	0.240892443023765	3	FACETS	0.412	0.383	0.444	0.137	0.127	0.148	INDETERMINATE	1	TRUE	0	0.558449920504402	3		701	2655	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0011003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	749	596	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	1	2	FACETS	1	0.984	1	1	0.998	1	CLONAL	3	TRUE	1	0.255022492855873	2		596	1898	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222593	69222593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194693256	NA	P-0011003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1495	91	610	0	ENST00000462284.1:c.566G>A	p.Arg189His	p.R189H	ENST00000462284	NM_002392.5	189	cGc/cAc	8/11	0.223528229450344	4	FACETS	0.565	0.499	0.635			1	SUBCLONAL	1	TRUE	NA	0.255022492855873	4		610	1586	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90970995	90970995	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1559	123	721	0	ENST00000265433.3:c.1082C>A	p.Thr361Lys	p.T361K	ENST00000265433	NM_002485.4	361	aCa/aAa	9/16	0.213954311689538	3	FACETS	0.647	0.582	0.715			1	SUBCLONAL	1	TRUE	NA	0.255022492855873	3		721	1682	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669556	88669556	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	97	632	2	ENST00000360948.2:c.1342G>T	p.Val448Phe	p.V448F	ENST00000360948	NM_001012338.2	448	Gtt/Ttt	12/19	0.183625888347647	1	FACETS	0.567	0.504	0.634	0.567	0.504	0.634	SUBCLONAL	1	TRUE	0	0.255022492855873	1		634	1171	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550505	29550505	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	125	494	1	ENST00000356175.3:c.1765C>G	p.Gln589Glu	p.Q589E	ENST00000356175	NM_000267.3	589	Caa/Gaa	16/57	0.256218028341497	3	FACETS	0.981	0.886	1			1	CLONAL	1	TRUE	NA	0.255022492855873	3		495	1127	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556391	29556391	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	176	529	0	ENST00000356175.3:c.2758C>G	p.Leu920Val	p.L920V	ENST00000356175	NM_000267.3	920	Ctg/Gtg	21/57	0.256218028341497	3	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.255022492855873	3		529	1194	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646866	37646867	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0011003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	494	802	1	ENST00000447079.4:c.1988_1989del	p.Arg663ProfsTer36	p.R663Pfs*36	ENST00000447079	NM_015083.1	663	cGT/c	3/14	0.256218028341497	3	FACETS	0.923	0.883	0.965			1	CLONAL	3	TRUE	NA	0.255022492855873	3		803	1577	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0011004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1366	39	598	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	0.086	0.071	0.104	0.086	0.071	0.104	SUBCLONAL	1	TRUE	1	0.644303231838233	2		598	1405	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933436	36933436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1402	292	674	0	ENST00000361632.4:c.1851G>A	p.Met617Ile	p.M617I	ENST00000361632		617	atG/atA	13/16	1	2	FACETS	0.535	0.502	0.57	0.535	0.502	0.57	SUBCLONAL	1	TRUE	1	0.644303231838233	2		674	1694	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344117	70344117	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	616	826	0	ENST00000374080.3:c.1853T>C	p.Leu618Pro	p.L618P	ENST00000374080		618	cTc/cCc	13/45	0.346559272630554	1	FACETS	0.829	0.798	0.86	0.829	0.798	0.86	INDETERMINATE	1	TRUE	0	0.644303231838233	1		826	1564	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215276	123215276	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	339	651	1	ENST00000218089.9:c.2822C>T	p.Ser941Leu	p.S941L	ENST00000218089	NM_001042749.1	941	tCa/tTa	28/35	0.346559272630554	1	FACETS	0.54	0.51	0.571	0.54	0.51	0.571	INDETERMINATE	1	TRUE	0	0.644303231838233	1		652	1320	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796999	78797006	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCCACG	CGCCCACG	-	novel	NA	P-0011004-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	200	326	0	ENST00000306801.3:c.1112_1119del	p.Pro371LeufsTer14	p.P371Lfs*14	ENST00000306801	NM_020761.2	371	cCGCCCACG/c	9/34	0.18233274844811	0	FACETS	0.312	0.29	0.335			1	INDETERMINATE	1	TRUE	0	0.644303231838233	0		326	707	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0011038-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	963	548	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.626667961057559	4	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	1	0.626667961057559	4		548	1480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578490	7578490	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1453167097	NA	P-0011038-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	345	451	0	ENST00000269305.4:c.440T>G	p.Val147Gly	p.V147G	ENST00000269305	NM_001126112.2	147	gTt/gGt	5/11	0.626667961057559	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.626667961057559	1		451	722	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950442	38950442	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011038-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1836	143	384	0	ENST00000357387.3:c.3508G>C	p.Glu1170Gln	p.E1170Q	ENST00000357387	NM_152756.3	1170	Gaa/Caa	31/38	0.626667961057559	6	FACETS	0.52	0.471	0.571			1	SUBCLONAL	1	TRUE	NA	0.626667961057559	6		384	1979	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0011039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	289	579	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.947	0.894	1	0.947	0.894	1	CLONAL	1	TRUE	1	0.719440656771871	2		579	848	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0011039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	282	346	1	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.929	0.876	0.983	0.929	0.876	0.983	CLONAL	1	TRUE	1	0.719440656771871	2		347	844	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236086	108236086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782292	NA	P-0011039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	367	390	0	ENST00000278616.4:c.9022C>T	p.Arg3008Cys	p.R3008C	ENST00000278616	NM_000051.3	3008	Cgt/Tgt	63/63	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.719440656771871	2		390	1004	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876098	35876098	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	195	383	0	ENST00000303115.3:c.890G>C	p.Ser297Thr	p.S297T	ENST00000303115	NM_002185.3	297	aGt/aCt	8/8	1	2	FACETS	0.566	0.524	0.61	0.566	0.524	0.61	SUBCLONAL	1	TRUE	1	0.719440656771871	2		383	958	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189377	56189377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	88	399	0	ENST00000399503.3:c.4409C>T	p.Ala1470Val	p.A1470V	ENST00000399503	NM_005921.1	1470	gCt/gTt	20/20	1	2	FACETS	0.201	0.177	0.226	0.201	0.177	0.226	SUBCLONAL	1	TRUE	1	0.719440656771871	2		399	1219	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175761	+	frameshift_variant	Frame_Shift_Del	DEL	TTTATTACAT	TTTATTACAT	-	novel	NA	P-0011039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	189	296	0	ENST00000257430.4:c.4464_4473del	p.Leu1489ProfsTer15	p.L1489Pfs*15	ENST00000257430	NM_000038.5	1487	acTTTATTACAT/ac	16/16	1	2	FACETS	0.739	0.685	0.795	0.739	0.685	0.795	SUBCLONAL	1	TRUE	1	0.719440656771871	2		296	711	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0011063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	80	329	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.789	0.695	0.89	0.789	0.695	0.89	SUBCLONAL	1	TRUE	1	0.335170254771553	2		329	605	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161270	56161270	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	87	338	0	ENST00000399503.3:c.1139T>C	p.Leu380Ser	p.L380S	ENST00000399503	NM_005921.1	380	tTa/tCa	5/20	1	2	FACETS	0.824	0.73	0.924	0.824	0.73	0.924	CLONAL	1	TRUE	1	0.335170254771553	2		338	630	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063717	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0011063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	71	243	0	ENST00000412916.2:c.165+1G>T		p.X55_splice	ENST00000412916		55			0.335170254771553	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.335170254771553	1		243	317	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106064	27106064	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	120	392	1	ENST00000324856.7:c.5675del	p.Thr1892LysfsTer31	p.T1892Kfs*31	ENST00000324856	NM_006015.4	1892	aCa/aa	20/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.368843891356305	2		393	590	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609836	81609839	+	frameshift_variant	Frame_Shift_Del	DEL	CTCT	CTCT	-	novel	NA	P-0011064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	116	331	0	ENST00000298171.2:c.1434_1437del	p.His478GlnfsTer34	p.H478Qfs*34	ENST00000298171	NM_000369.2	478	caCTCT/ca	10/10	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.368843891356305	2		331	613	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0011065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	33	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.16	2		426	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0011065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	80	532	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.149412452367435	3	FACETS	1	0.954	1			1	CLONAL	2	TRUE	NA	0.16	3		534	465	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426868	6426868	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	34	371	0	ENST00000356142.4:c.61A>G	p.Ile21Val	p.I21V	ENST00000356142	NM_018890.3	21	Atc/Gtc	2/7	1	2	FACETS	0.899	0.734	1	0.899	0.734	1	CLONAL	1	TRUE	1	0.16	2		371	473	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591894	48591894	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011065-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	21	424	0	ENST00000342988.3:c.1057T>A	p.Tyr353Asn	p.Y353N	ENST00000342988	NM_005359.5	353	Tac/Aac	9/12	1	2	FACETS	0.628	0.483	0.798	0.628	0.483	0.798	SUBCLONAL	1	TRUE	1	0.16	2		424	418	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111503	8111513	+	frameshift_variant	Frame_Shift_Del	DEL	GGAATGCCAAT	GGAATGCCAAT	-	novel	NA	P-0011072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	128	579	0	ENST00000346208.3:c.991_1001del	p.Asn331GlyfsTer17	p.N331Gfs*17	ENST00000346208		330	aGGAATGCCAAT/a	5/6	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.460368752472543	2		579	473	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0011090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	169	441	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.363852362819285	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.363852362819285	4		441	522	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582169	189582169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908836	NA	P-0011090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	329	508	0	ENST00000264731.3:c.728G>A	p.Arg243Gln	p.R243Q	ENST00000264731	NM_003722.4	243	cGg/cAg	5/14	0.363852362819285	4	FACETS	0.897	0.846	0.949	0.897	0.846	0.949	CLONAL	2	TRUE	2	0.363852362819285	4		508	1375	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111647	56111647	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	220	407	0	ENST00000399503.3:c.247T>A	p.Ser83Thr	p.S83T	ENST00000399503	NM_005921.1	83	Tca/Aca	1/20	0.190559272457813	5	FACETS	0.965	0.898	1	0.643	0.598	0.689	INDETERMINATE	2	TRUE	2	0.363852362819285	5		407	969	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633407	8633407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1564855576	NA	P-0011090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	284	621	2	ENST00000356435.5:c.262C>T	p.Arg88Trp	p.R88W	ENST00000356435		88	Cgg/Tgg	3/35	0.238558408072743	3	FACETS	1	0.992	1			1	CLONAL	1	TRUE	NA	0.363852362819285	3		623	1375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578428	7578627	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTGTGACTGCTTGTAGATGGCCATGGCGCGGACGCGGGTGCCGGGCGGGGGTGTGGAATCAACCCACAGCTGCACAGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAAGCAACTGGAAGACGGCA	GCTGTGACTGCTTGTAGATGGCCATGGCGCGGACGCGGGTGCCGGGCGGGGGTGTGGAATCAACCCACAGCTGCACAGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAAGCAACTGGAAGACGGCA	-	novel	NA	P-0011090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	111	444	0	ENST00000269305.4:c.376-73_502del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	NA	2	FACETS	0.895	0.805	0.989			1	INDETERMINATE	1	TRUE	NA	0.363852362819285	2		444	682	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0011092-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	11	608	1	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.117	0.08	0.164	0.117	0.08	0.164	SUBCLONAL	1	TRUE	1	0.437747034995911	2		609	428	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183769	10183769	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs786202787	NA	P-0011099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	103	330	0	ENST00000256474.2:c.238A>C	p.Ser80Arg	p.S80R	ENST00000256474	NM_000551.3	80	Agt/Cgt	1/3	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.282358625522657	2		330	596	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0011102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	96	456	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.390558033209162	1	FACETS	0.622	0.557	0.69	0.622	0.557	0.69	SUBCLONAL	1	TRUE	0	0.522979570378696	1		457	436	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0011102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	119	411	1	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.707	0.639	0.778	0.707	0.639	0.778	SUBCLONAL	1	TRUE	1	0.522979570378696	2		412	644	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141584	202141584	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	262	545	0	ENST00000358485.4:c.872C>G	p.Pro291Arg	p.P291R	ENST00000358485	NM_001080125.1	291	cCt/cGt	7/9	1	2	FACETS	0.972	0.911	1	0.972	0.911	1	CLONAL	1	TRUE	1	0.522979570378696	2		545	1031	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265352	152265352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142712646	NA	P-0011111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	22	378	0	ENST00000206249.3:c.805C>T	p.Arg269Cys	p.R269C	ENST00000206249	NM_000125.3	269	Cgc/Tgc	4/8	1	2	FACETS	0.845	0.655	1	0.845	0.655	1	CLONAL	1	TRUE	1	0.15	2		378	347	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0011111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	11	377	2	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.0908294185270564	0	FACETS	0.331	0.227	0.46			1	SUBCLONAL	1	TRUE	0	0.15	0		379	377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0011111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	33	538	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	1	2	FACETS	0.959	0.78	1	0.959	0.78	1	CLONAL	1	TRUE	1	0.15	2		538	459	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971088	21971088	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	10	158	0	ENST00000304494.5:c.270C>G	p.Phe90Leu	p.F90L	ENST00000304494	NM_000077.4	90	ttC/ttG	2/3	1	2	FACETS	1	0.773	1	1	0.773	1	CLONAL	1	TRUE	1	0.15	2		158	113	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0011136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	565	424	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.289234045397686	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.289234045397686	3		424	1363	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790455	3790455	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783490	NA	P-0011136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1487	179	694	1	ENST00000262367.5:c.4078C>T	p.Arg1360Ter	p.R1360*	ENST00000262367	NM_004380.2	1360	Cga/Tga	24/31	0.289234045397686	3	FACETS	0.85	0.781	0.923	0.425	0.39	0.462	CLONAL	1	TRUE	1	0.289234045397686	3		695	1666	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259192	36259192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	414	605	1	ENST00000300305.3:c.299C>T	p.Ser100Phe	p.S100F	ENST00000300305		100	tCc/tTc	3/8	0.289234045397686	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.289234045397686	3		606	1334	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725214	89725214	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	12	17	0	ENST00000371953.3:c.1197A>T	p.Gln399His	p.Q399H	ENST00000371953	NM_000314.4	399	caA/caT	9/9	0.289234045397686	3	FACETS	1	0.778	1	1	0.778	1	CLONAL	2	TRUE	1	0.289234045397686	3		17	44	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163522	108163522	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0011136-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	126	457	0	ENST00000278616.4:c.4611+2T>C		p.X1537_splice	ENST00000278616	NM_000051.3	1537			0.275705172258777	1	FACETS	0.943	0.855	1	0.943	0.855	1	CLONAL	1	TRUE	0	0.289234045397686	1		457	790	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0011144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	59	540	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.328	0.281	0.379	0.328	0.281	0.379	SUBCLONAL	1	TRUE	1	0.416773363266144	2		540	863	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs863224683	NA	P-0011144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	73	341	0	ENST00000269305.4:c.388C>G	p.Leu130Val	p.L130V	ENST00000269305	NM_001126112.2	130	Ctc/Gtc	5/11	1	2	FACETS	0.454	0.397	0.517	0.454	0.397	0.517	SUBCLONAL	1	TRUE	1	0.416773363266144	2		341	771	SUCCESS
ATR	545	MSKCC	GRCh37	3	142285010	142285010	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs373636603	NA	P-0011144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	87	441	0	ENST00000350721.4:c.245T>C	p.Met82Thr	p.M82T	ENST00000350721	NM_001184.3	82	aTg/aCg	3/47	1	2	FACETS	0.441	0.39	0.497	0.441	0.39	0.497	SUBCLONAL	1	TRUE	1	0.416773363266144	2		441	946	SUCCESS
APC	324	MSKCC	GRCh37	5	112174430	112174430	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs568149455	NA	P-0011144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	61	216	0	ENST00000257430.4:c.3139G>T	p.Glu1047Ter	p.E1047*	ENST00000257430	NM_000038.5	1047	Gaa/Taa	16/16	1	2	FACETS	0.468	0.404	0.539	0.468	0.404	0.539	SUBCLONAL	1	TRUE	1	0.416773363266144	2		216	625	SUCCESS
APC	324	MSKCC	GRCh37	5	112175535	112175542	+	frameshift_variant	Frame_Shift_Del	DEL	GTGGCATT	GTGGCATT	-	novel	NA	P-0011144-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	40	334	0	ENST00000257430.4:c.4244_4251del	p.Ser1415AsnfsTer5	p.S1415Nfs*5	ENST00000257430	NM_000038.5	1415	aGTGGCATT/a	16/16	1	2	FACETS	0.259	0.214	0.309	0.259	0.214	0.309	SUBCLONAL	1	TRUE	1	0.416773363266144	2		334	742	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0011145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	477	322	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.464544984129115	7	FACETS	1	0.988	1	1	0.988	1	CLONAL	4	FALSE	3	0.464544984129115	7		322	1032	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555526097	NA	P-0011145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	243	385	0	ENST00000269305.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000269305	NM_001126112.2	167	Cag/Tag	5/11	0.362794657096873	3	FACETS	0.932	0.883	0.981	0.932	0.883	0.981	CLONAL	3	FALSE	0	0.464544984129115	3		385	461	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	1008	632	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.464544984129115	7	FACETS	0.975	0.955	0.993			1	CLONAL	7	FALSE	NA	0.464544984129115	7		632	1375	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958505	175958505	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	357	472	0	ENST00000367669.3:c.1840G>C	p.Val614Leu	p.V614L	ENST00000367669	NM_022457.5	614	Gtc/Ctc	16/20	1	2	FACETS	0.962	0.914	1	0.962	0.914	1	CLONAL	1	TRUE	1	0.76670091428317	2		472	968	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068413	26068413	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	352	432	0	ENST00000435504.4:c.77A>G	p.Asn26Ser	p.N26S	ENST00000435504		26	aAt/aGt	2/13	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.76670091428317	2		432	863	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251610	212251610	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1187421880	NA	P-0011153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	351	441	0	ENST00000342788.4:c.3449A>G	p.Tyr1150Cys	p.Y1150C	ENST00000342788	NM_005235.2	1150	tAc/tGc	27/28	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.76670091428317	2		441	913	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332597	70332597	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	75	337	0	ENST00000373644.4:c.502G>T	p.Asp168Tyr	p.D168Y	ENST00000373644	NM_030625.2	168	Gat/Tat	2/12	0.515973585393082	1	FACETS	0.243	0.213	0.275	0.243	0.213	0.275	SUBCLONAL	1	TRUE	0	0.76670091428317	1		337	496	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633514	69633514	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	252	288	0	ENST00000334134.2:c.188G>C	p.Arg63Pro	p.R63P	ENST00000334134	NM_005247.2	63	cGc/cCc	1/3	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.76670091428317	2		288	580	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039230	49039230	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	388	427	1	ENST00000267163.4:c.2308C>T	p.Gln770Ter	p.Q770*	ENST00000267163	NM_000321.2	770	Cag/Tag	22/27	0.76670091428317	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.76670091428317	1		428	616	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577017	7577017	+	splice_donor_variant	Splice_Site	SNP	A	A	T	rs1131691016	NA	P-0011153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	283	371	1	ENST00000269305.4:c.919+2T>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.76670091428317	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.76670091428317	1		372	435	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40368082	40368082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	428	685	0	ENST00000293328.3:c.1423G>A	p.Asp475Asn	p.D475N	ENST00000293328	NM_012448.3	475	Gac/Aac	12/19	NA	2	FACETS	0.992	0.947	1			1	INDETERMINATE	1	TRUE	NA	0.76670091428317	2		685	1126	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0011161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	598	509	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.281662439689008	8	FACETS	1	0.978	1	0.853	0.821	0.886	CLONAL	5	TRUE	2	0.281662439689008	8		509	1530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs863224451	NA	P-0011161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	338	510	0	ENST00000269305.4:c.824G>C	p.Cys275Ser	p.C275S	ENST00000269305	NM_001126112.2	275	tGt/tCt	8/11	0.275105479579367	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.281662439689008	2		510	1149	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112479	115112479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs912240752	NA	P-0011162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	167	315	1	ENST00000257566.3:c.1261C>T	p.Arg421Trp	p.R421W	ENST00000257566	NM_016569.3	421	Cgg/Tgg	7/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.550183063312199	2		316	573	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591258	67591258	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	135	301	2	ENST00000274335.5:c.1756C>T	p.Gln586Ter	p.Q586*	ENST00000274335		586	Caa/Taa	13/15	0.550183063312199	3	FACETS	0.788	0.724	0.854	0.788	0.724	0.854	SUBCLONAL	2	TRUE	1	0.550183063312199	3		303	397	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52685806	52685807	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0011162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	61	429	0	ENST00000394830.3:c.665_666del	p.Ala222AspfsTer3	p.A222Dfs*3	ENST00000394830	NM_018313.4	222	gCA/g	7/30	0.550183063312199	1	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	0	0.550183063312199	1		429	160	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188256	10188257	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0011162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	128	572	0	ENST00000256474.2:c.399_400del	p.Glu134IlefsTer9	p.E134Ifs*9	ENST00000256474	NM_000551.3	133	acTGaa/acaa	2/3	0.550183063312199	1	FACETS	0.929	0.852	1	0.929	0.852	1	CLONAL	1	TRUE	0	0.550183063312199	1		572	363	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609778	81609778	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762578626	NA	P-0011203-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	75	619	1	ENST00000298171.2:c.1376C>T	p.Ala459Val	p.A459V	ENST00000298171	NM_000369.2	459	gCg/gTg	10/10	1	2	FACETS	0.606	0.53	0.689	0.606	0.53	0.689	SUBCLONAL	1	TRUE	1	0.2416508139762	2		620	1024	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0011224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	46	418	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	0.252782713029914	3	FACETS	0.296	0.248	0.349	0.148	0.124	0.175	SUBCLONAL	1	TRUE	1	0.399808326540402	3		418	934	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0011224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	164	183	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.334648397302949	2	FACETS	0.829	0.767	0.892	0.829	0.767	0.892	CLONAL	2	TRUE	0	0.399808326540402	2		183	495	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059260	27059260	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	208	400	0	ENST00000324856.7:c.1897C>T	p.Gln633Ter	p.Q633*	ENST00000324856	NM_006015.4	633	Cag/Tag	4/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.399808326540402	2		400	774	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259397	11259397	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	172	400	0	ENST00000361445.4:c.4171C>G	p.Arg1391Gly	p.R1391G	ENST00000361445	NM_004958.3	1391	Cga/Gga	28/58	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.399808326540402	2		400	853	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414887	56414887	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs768162253	NA	P-0011224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	130	528	0	ENST00000348428.3:c.2288C>G	p.Ser763Ter	p.S763*	ENST00000348428	NM_006785.3	763	tCa/tGa	17/17	1	2	FACETS	0.564	0.51	0.62	0.564	0.51	0.62	SUBCLONAL	1	TRUE	1	0.399808326540402	2		528	1154	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448504	49448505	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0011224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	115	381	0	ENST00000301067.7:c.206_207del	p.Cys69Ter	p.C69*	ENST00000301067	NM_003482.3	69	tGT/t	3/54	1	2	FACETS	0.705	0.635	0.779	0.705	0.635	0.779	SUBCLONAL	1	TRUE	1	0.399808326540402	2		381	816	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591138	67591150	+	protein_altering_variant,splice_region_variant	In_Frame_Del	DEL	AGACCAATACTTG	AGACCAATACTTG	TATT	novel	NA	P-0011224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	66	271	0	ENST00000274335.5:c.1731_1743delinsTATT	p.Arg577_Leu581delinsSerIle	p.R577_L581delinsSI	ENST00000274335		577	agAGACCAATACTTG/agTATT	12/15	1	2	FACETS	0.626	0.544	0.715	0.626	0.544	0.715	SUBCLONAL	1	TRUE	1	0.399808326540402	2		271	527	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0011234-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	119	371	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.297336152675805	4	FACETS	1	0.938	1	0.525	0.474	0.578	CLONAL	1	TRUE	2	0.476278133477774	4		371	703	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578184	7578208	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTCATAGGGCACCACCACACTAT	GGCTCATAGGGCACCACCACACTAT	-	novel	NA	P-0011234-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	236	561	0	ENST00000269305.4:c.641_665del	p.His214ArgfsTer25	p.H214Rfs*25	ENST00000269305	NM_001126112.2	214	cATAGTGTGGTGGTGCCCTATGAGCCg/cg	6/11	0.361774756995916	3	FACETS	1	0.99	1	0.653	0.61	0.698	CLONAL	1	TRUE	1	0.476278133477774	3		561	939	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0011242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	106	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.92	0.823	1	0.92	0.823	1	CLONAL	1	TRUE	1	0.21	2		426	1097	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221243	1221243	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1057520606	NA	P-0011242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1467	209	708	0	ENST00000326873.7:c.766G>T	p.Glu256Ter	p.E256*	ENST00000326873	NM_000455.4	256	Gaa/Taa	6/10	0.3	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.21	1		708	1676	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917824	29917824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	78	633	1	ENST00000389048.3:c.844G>A	p.Asp282Asn	p.D282N	ENST00000389048	NM_004304.4	282	Gac/Aac	3/29	0.3	1	FACETS	0.614	0.538	0.696	0.614	0.538	0.696	SUBCLONAL	1	TRUE	0	0.21	1		634	1083	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682459	52682459	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0011242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	109	372	0	ENST00000394830.3:c.715-1G>A		p.X239_splice	ENST00000394830	NM_018313.4	239			1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.21	2		372	866	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600519	10600519	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	114	405	0	ENST00000171111.5:c.1336G>T	p.Glu446Ter	p.E446*	ENST00000171111	NM_203500.1	446	Gag/Tag	4/6	0.246228046984306	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.21	1		405	831	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361206	70361206	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1216	152	722	0	ENST00000374080.3:c.6394C>T	p.Gln2132Ter	p.Q2132*	ENST00000374080		2132	Cag/Tag	43/45	0.201200477079249	0	FACETS	0.836	0.762	0.914			1	CLONAL	1	TRUE	0	0.21	0		722	1368	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107151	27107152	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CG	CG	-	novel	NA	P-0011242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	77	294	0	ENST00000324856.7:c.6762_6763del	p.Tyr2254Ter	p.Y2254*	ENST00000324856	NM_006015.4	2254	taCGaa/taaa	20/20	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.21	2		294	724	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99440126	99440126	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	172	542	1	ENST00000268035.6:c.1094G>T	p.Arg365Leu	p.R365L	ENST00000268035	NM_000875.3	365	cGa/cTa	4/21	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.398665226495485	2		543	833	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376152	225376160	+	inframe_deletion	In_Frame_Del	DEL	GTTCCCTTT	GTTCCCTTT	-	novel	NA	P-0011267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	183	770	0	ENST00000264414.4:c.794_802del	p.Glu265_Leu268delinsVal	p.E265_L268delinsV	ENST00000264414	NM_003590.4	265	gAAAGGGAACtc/gtc	6/16	1	2	FACETS	0.797	0.734	0.862	0.797	0.734	0.862	SUBCLONAL	1	TRUE	1	0.398665226495485	2		770	1152	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0011285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	99	540	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.224849394083374	2		540	782	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578485	7578485	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1064793929	NA	P-0011285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	106	354	0	ENST00000269305.4:c.445del	p.Ser149ProfsTer21	p.S149Pfs*21	ENST00000269305	NM_001126112.2	149	Tcc/cc	5/11	0.224849394083374	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.224849394083374	1		354	717	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267838	46267838	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1206632505	NA	P-0011285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	134	669	0	ENST00000371998.3:c.2599A>T	p.Ser867Cys	p.S867C	ENST00000371998		867	Agt/Tgt	14/23	1	2	FACETS	0.891	0.807	0.98	0.891	0.807	0.98	CLONAL	1	TRUE	1	0.224849394083374	2		669	1337	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0011305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	86	316	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.251105884110062	3	FACETS	0.827	0.735	0.925	0.827	0.735	0.925	CLONAL	2	TRUE	1	0.251105884110062	3		316	466	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106058	8106058	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	147	547	0	ENST00000346208.3:c.878T>A	p.Met293Lys	p.M293K	ENST00000346208		293	aTg/aAg	4/6	1	2	FACETS	0.765	0.699	0.834	1	0.988	1	SUBCLONAL	2	TRUE	1	0.251105884110062	2		547	765	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435317	56435317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200066146	NA	P-0011305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	84	247	0	ENST00000407977.2:c.1820C>T	p.Ser607Leu	p.S607L	ENST00000407977		607	tCg/tTg	9/10	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.251105884110062	2		247	663	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0011305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	55	535	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.251105884110062	3	FACETS	1	0.951	1	0.632	0.542	0.729	CLONAL	1	TRUE	1	0.251105884110062	3		535	390	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056314	26056314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1355795147	NA	P-0011305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	176	314	0	ENST00000343677.2:c.343G>A	p.Glu115Lys	p.E115K	ENST00000343677	NM_005319.3	115	Gaa/Aaa	1/1	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.251105884110062	2		314	1027	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437669	52437669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1516	162	726	1	ENST00000460680.1:c.1492G>A	p.Glu498Lys	p.E498K	ENST00000460680	NM_004656.3	498	Gag/Aag	13/17	0.251105884110062	3	FACETS	0.865	0.791	0.944	0.433	0.395	0.472	CLONAL	1	TRUE	1	0.251105884110062	3		727	1678	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820617	3820617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	114	268	0	ENST00000262367.5:c.2834C>T	p.Ser945Leu	p.S945L	ENST00000262367	NM_004380.2	945	tCg/tTg	14/31	0.251105884110062	3	FACETS	1	0.974	1	0.624	0.561	0.69	CLONAL	1	TRUE	1	0.251105884110062	3		268	819	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085641	16085641	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	116	324	1	ENST00000281043.3:c.817G>A	p.Glu273Lys	p.E273K	ENST00000281043	NM_005378.4	273	Gaa/Aaa	3/3	NA	2	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.251105884110062	2		325	848	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437215	52437215	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1358	142	631	1	ENST00000460680.1:c.1829G>A	p.Arg610Lys	p.R610K	ENST00000460680	NM_004656.3	610	aGa/aAa	14/17	0.251105884110062	3	FACETS	0.849	0.771	0.931	0.424	0.385	0.466	CLONAL	1	TRUE	1	0.251105884110062	3		632	1500	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72866466	72866466	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1483257759	NA	P-0011305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	120	327	0	ENST00000325599.8:c.797G>C	p.Arg266Thr	p.R266T	ENST00000325599	NM_018130.2	266	aGa/aCa	7/11	0.251105884110062	3	FACETS	1	0.928	1	0.518	0.467	0.573	CLONAL	1	TRUE	1	0.251105884110062	3		327	1038	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136826	55136826	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1368411882	NA	P-0011305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	77	390	0	ENST00000257290.5:c.1148G>A	p.Arg383His	p.R383H	ENST00000257290	NM_006206.4	383	cGt/cAt	8/23	0.203605503126607	1	FACETS	0.602	0.527	0.683	0.602	0.527	0.683	SUBCLONAL	1	TRUE	0	0.251105884110062	1		390	891	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179502	56179502	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	54	182	0	ENST00000399503.3:c.3815A>C	p.Lys1272Thr	p.K1272T	ENST00000399503	NM_005921.1	1272	aAa/aCa	15/20	1	2	FACETS	0.904	0.773	1	0.904	0.773	1	CLONAL	1	TRUE	1	0.251105884110062	2		182	476	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188794	32188794	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	80	369	0	ENST00000375023.3:c.760G>C	p.Glu254Gln	p.E254Q	ENST00000375023	NM_004557.3	254	Gag/Cag	4/30	1	2	FACETS	0.685	0.602	0.775	0.685	0.602	0.775	SUBCLONAL	1	TRUE	1	0.251105884110062	2		369	930	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139818347	139818347	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs776376824	NA	P-0011305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	68	648	0	ENST00000247668.2:c.1182C>G	p.Ile394Met	p.I394M	ENST00000247668	NM_021138.3	394	atC/atG	10/11	0.251105884110062	1	FACETS	0.421	0.365	0.483	0.421	0.365	0.483	SUBCLONAL	1	TRUE	0	0.251105884110062	1		648	1124	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871758	12871758	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0011305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	84	139	0	ENST00000228872.4:c.476-1G>T		p.X159_splice	ENST00000228872	NM_004064.3	159			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.251105884110062	2		139	493	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95573948	95573948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1211667485	NA	P-0011305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	85	344	0	ENST00000393063.1:c.2801C>T	p.Pro934Leu	p.P934L	ENST00000393063	NM_030621.3	934	cCa/cTa	18/28	1	2	FACETS	0.775	0.684	0.872	0.775	0.684	0.872	SUBCLONAL	1	TRUE	1	0.251105884110062	2		344	874	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574232	95574232	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	72	321	0	ENST00000393063.1:c.2635C>G	p.Leu879Val	p.L879V	ENST00000393063	NM_030621.3	879	Cta/Gta	17/28	1	2	FACETS	0.767	0.669	0.872	0.767	0.669	0.872	SUBCLONAL	1	TRUE	1	0.251105884110062	2		321	748	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024322	31024334	+	frameshift_variant	Frame_Shift_Del	DEL	GAGAACACCTCGT	GAGAACACCTCGT	-	novel	NA	P-0011305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	82	383	0	ENST00000375687.4:c.3807_3819del	p.Arg1270SerfsTer6	p.R1270Sfs*6	ENST00000375687	NM_015338.5	1269	tcGAGAACACCTCGT/tc	13/13	1	2	FACETS	0.772	0.68	0.871	0.772	0.68	0.871	SUBCLONAL	1	TRUE	1	0.251105884110062	2		383	846	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0011323-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	23	424	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.261	0.203	0.33	0.261	0.203	0.33	SUBCLONAL	1	TRUE	1	0.32	2		424	550	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0011333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	169	424	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.329491099154926	4	FACETS	0.757	0.696	0.82	0.757	0.696	0.82	SUBCLONAL	2	TRUE	2	0.336502570135496	4		424	887	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557230	187557230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	114	590	1	ENST00000441802.2:c.4132G>A	p.Gly1378Arg	p.G1378R	ENST00000441802	NM_005245.3	1378	Gga/Aga	6/27	0.305386249097535	3	FACETS	0.943	0.849	1	0.472	0.424	0.522	CLONAL	1	TRUE	1	0.336502570135496	3		591	839	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098593	11098593	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	134	454	0	ENST00000358026.2:c.1111G>T	p.Glu371Ter	p.E371*	ENST00000358026	NM_001128849.1	371	Gag/Tag	6/36	0.334283609424636	2	FACETS	0.86	0.787	0.936	0.86	0.787	0.936	CLONAL	2	TRUE	0	0.336502570135496	2		454	463	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204944	128204944	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	168	586	1	ENST00000341105.2:c.497C>A	p.Ser166Tyr	p.S166Y	ENST00000341105	NM_032638.4	166	tCt/tAt	3/6	0.305386249097535	3	FACETS	0.831	0.766	0.898	0.831	0.766	0.898	CLONAL	2	TRUE	1	0.336502570135496	3		587	702	SUCCESS
ATR	545	MSKCC	GRCh37	3	142232481	142232481	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs910635641	NA	P-0011333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	89	380	0	ENST00000350721.4:c.4504-1G>T		p.X1502_splice	ENST00000350721	NM_001184.3	1502			0.305386249097535	3	FACETS	0.982	0.872	1	0.491	0.436	0.55	CLONAL	1	TRUE	1	0.336502570135496	3		380	629	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564776	86564776	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	199	623	0	ENST00000274376.6:c.508G>T	p.Ala170Ser	p.A170S	ENST00000274376	NM_002890.2	170	Gcc/Tcc	1/25	0.305386249097535	3	FACETS	0.891	0.828	0.957	0.891	0.828	0.957	CLONAL	2	TRUE	1	0.336502570135496	3		623	775	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467823	50467823	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	132	403	0	ENST00000331340.3:c.1058C>A	p.Pro353Gln	p.P353Q	ENST00000331340	NM_006060.4	353	cCg/cAg	8/8	0.299713396938269	4	FACETS	1	0.918	1	1	0.918	1	CLONAL	2	TRUE	2	0.336502570135496	4		403	521	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268959	55268959	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	243	556	0	ENST00000275493.2:c.3025G>T	p.Asp1009Tyr	p.D1009Y	ENST00000275493	NM_005228.3	1009	Gac/Tac	25/28	0.299713396938269	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	2	0.336502570135496	4		556	938	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127951970	127951970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	95	564	0	ENST00000373547.4:c.28G>A	p.Val10Met	p.V10M	ENST00000373547	NM_002721.4	10	Gtg/Atg	1/7	1	2	FACETS	0.964	0.86	1	0.964	0.86	1	CLONAL	1	TRUE	1	0.336502570135496	2		564	586	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685277	89685277	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554897255	NA	P-0011333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	70	208	1	ENST00000371953.3:c.172G>T	p.Asp58Tyr	p.D58Y	ENST00000371953	NM_000314.4	58	Gat/Tat	3/9	0.305386249097535	3	FACETS	1	0.972	1	0.711	0.624	0.803	CLONAL	1	TRUE	1	0.336502570135496	3		209	342	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32439140	32439140	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	213	537	0	ENST00000332351.3:c.933A>C	p.Leu311Phe	p.L311F	ENST00000332351	NM_024426.4	311	ttA/ttC	4/10	0.305386249097535	3	FACETS	0.885	0.823	0.948	0.885	0.823	0.948	CLONAL	2	TRUE	1	0.336502570135496	3		537	836	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953574	32953574	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs786202920	NA	P-0011333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	331	816	0	ENST00000380152.3:c.8875G>T	p.Glu2959Ter	p.E2959*	ENST00000380152		2959	Gaa/Taa	22/27	0.305386249097535	3	FACETS	0.916	0.865	0.968	0.916	0.865	0.968	CLONAL	2	TRUE	1	0.336502570135496	3		816	1255	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857288	9857288	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	113	570	0	ENST00000330684.3:c.4113C>A	p.His1371Gln	p.H1371Q	ENST00000330684	NM_001134407.1	1371	caC/caA	13/13	0.305386249097535	3	FACETS	0.966	0.869	1	0.483	0.434	0.535	CLONAL	1	TRUE	1	0.336502570135496	3		570	812	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578499	7578499	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786203071	NA	P-0011333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	105	510	0	ENST00000269305.4:c.431A>T	p.Gln144Leu	p.Q144L	ENST00000269305	NM_001126112.2	144	cAg/cTg	5/11	0.30969825354601	4	FACETS	0.934	0.836	1	0.311	0.278	0.346	CLONAL	1	TRUE	1	0.336502570135496	4		510	893	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687716	29687716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	89	399	0	ENST00000356175.3:c.8309C>T	p.Ser2770Phe	p.S2770F	ENST00000356175	NM_000267.3	2770	tCc/tTc	56/57	0.305386249097535	3	FACETS	0.92	0.816	1	0.46	0.408	0.515	CLONAL	1	TRUE	1	0.336502570135496	3		399	672	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221228	1221228	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	232	657	1	ENST00000326873.7:c.751G>T	p.Gly251Cys	p.G251C	ENST00000326873	NM_000455.4	251	Ggt/Tgt	6/10	0.334283609424636	2	FACETS	0.93	0.871	0.991	0.93	0.871	0.991	CLONAL	2	TRUE	0	0.336502570135496	2		658	741	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610286	10610286	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	198	558	0	ENST00000171111.5:c.424A>G	p.Thr142Ala	p.T142A	ENST00000171111	NM_203500.1	142	Acg/Gcg	2/6	0.334283609424636	2	FACETS	0.839	0.78	0.9	0.839	0.78	0.9	CLONAL	2	TRUE	0	0.336502570135496	2		558	701	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29108001	29108001	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs748636216	NA	P-0011333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	87	484	0	ENST00000328354.6:c.688G>C	p.Ala230Pro	p.A230P	ENST00000328354	NM_007194.3	230	Gcc/Ccc	6/15	1	2	FACETS	0.819	0.726	0.919	0.819	0.726	0.919	CLONAL	1	TRUE	1	0.336502570135496	2		484	631	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039420	47039420	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	184	540	0	ENST00000377604.3:c.1043T>G	p.Ile348Ser	p.I348S	ENST00000377604	NM_001204468.1	348	aTc/aGc	10/24	0.119416156004241	5	FACETS	1	0.983	1	0.602	0.558	0.648	INDETERMINATE	2	TRUE	1	0.336502570135496	5		540	683	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793118	42793126	+	inframe_deletion	In_Frame_Del	DEL	GGGCAGAAC	GGGCAGAAC	-	novel	NA	P-0011333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	126	473	0	ENST00000575354.2:c.1012_1020del	p.Ala338_Arg340del	p.A338_R340del	ENST00000575354	NM_015125.3	337	gGGGCAGAACgg/ggg	7/20	0.206032578463532	4	FACETS	1	0.983	1	0.692	0.627	0.76	CLONAL	1	TRUE	2	0.336502570135496	4		473	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	268	484	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.224704125148695	5	FACETS	0.848	0.797	0.9	0.848	0.797	0.9	CLONAL	3	TRUE	2	0.369964011356153	5		484	886	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520017	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	356	535	0	ENST00000326873.7:c.647C>T	p.Ser216Phe	p.S216F	ENST00000326873	NM_000455.4	216	tCc/tTc	5/10	0.36876420650411	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.369964011356153	2		535	936	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	267	532	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.224704125148695	5	FACETS	0.87	0.814	0.927	0.58	0.543	0.618	CLONAL	2	TRUE	2	0.369964011356153	5		534	1290	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094477	27094477	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	185	196	0	ENST00000324856.7:c.3185G>A	p.Gly1062Asp	p.G1062D	ENST00000324856	NM_006015.4	1062	gGt/gAt	11/20	0.264789451529332	5	FACETS	1	0.983	1	0.794	0.736	0.853	CLONAL	2	TRUE	2	0.369964011356153	5		196	653	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610405	10610405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	346	391	0	ENST00000171111.5:c.305C>T	p.Ser102Leu	p.S102L	ENST00000171111	NM_203500.1	102	tCa/tTa	2/6	0.36876420650411	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.369964011356153	2		391	845	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469564	25469564	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs796065342	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	332	563	0	ENST00000264709.3:c.1204C>T	p.Gln402Ter	p.Q402*	ENST00000264709	NM_175629.2	402	Cag/Tag	10/23	0.264789451529332	5	FACETS	1	0.984	1	0.738	0.697	0.78	CLONAL	2	TRUE	2	0.369964011356153	5		563	1261	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784139	9784139	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1237870323	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	234	370	0	ENST00000377346.4:c.2707G>C	p.Glu903Gln	p.E903Q	ENST00000377346	NM_005026.3	903	Gag/Cag	21/24	0.264789451529332	5	FACETS	1	0.95	1	0.681	0.635	0.728	CLONAL	2	TRUE	2	0.369964011356153	5		370	963	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641758	12641758	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	236	305	0	ENST00000251849.4:c.883A>T	p.Ser295Cys	p.S295C	ENST00000251849	NM_002880.3	295	Agt/Tgt	9/17	0.369964011356153	7	FACETS	1	0.933	1			1	CLONAL	2	TRUE	NA	0.369964011356153	7		305	1226	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749523	41749523	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	245	275	0	ENST00000226382.2:c.272G>T	p.Gly91Val	p.G91V	ENST00000226382	NM_003924.3	91	gGc/gTc	2/3	0.23015288724977	3	FACETS	1	0.981	1	0.736	0.691	0.782	CLONAL	2	TRUE	0	0.369964011356153	3		275	711	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161398	55161398	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs752633017	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	776	440	0	ENST00000257290.5:c.3229G>T	p.Gly1077Cys	p.G1077C	ENST00000257290	NM_006206.4	1077	Ggc/Tgc	23/23	0.369964011356153	8	FACETS	0.959	0.93	0.988	0.959	0.93	0.988	CLONAL	6	TRUE	2	0.369964011356153	8		440	1538	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875614	35875614	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs912324015	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	174	245	0	ENST00000303115.3:c.801G>T	p.Arg267Ser	p.R267S	ENST00000303115	NM_002185.3	267	agG/agT	7/8	0.264789451529332	5	FACETS	1	0.975	1	0.751	0.694	0.81	CLONAL	2	TRUE	2	0.369964011356153	5		245	649	SUCCESS
APC	324	MSKCC	GRCh37	5	112174179	112174179	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	137	432	2	ENST00000257430.4:c.2888G>T	p.Ser963Ile	p.S963I	ENST00000257430	NM_000038.5	963	aGt/aTt	16/16	0.369964011356153	2	FACETS	0.867	0.796	0.941	0.867	0.796	0.941	CLONAL	2	TRUE	0	0.369964011356153	2		434	427	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908181	41908181	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1447795219	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	284	434	1	ENST00000372991.4:c.341G>T	p.Arg114Leu	p.R114L	ENST00000372991	NM_001760.3	114	cGc/cTc	2/5	0.224704125148695	5	FACETS	1	0.963	1	0.69	0.648	0.732	CLONAL	2	TRUE	2	0.369964011356153	5		435	1154	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647390	117647390	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	139	631	0	ENST00000368508.3:c.5554G>T	p.Gly1852Ter	p.G1852*	ENST00000368508	NM_002944.2	1852	Gga/Tga	33/43	0.224704125148695	5	FACETS	0.893	0.815	0.975	0.596	0.543	0.65	CLONAL	2	TRUE	2	0.369964011356153	5		631	654	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81340797	81340797	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	83	242	0	ENST00000222390.5:c.1444C>G	p.His482Asp	p.H482D	ENST00000222390	NM_000601.4	482	Cat/Gat	12/18	0.266338076751227	3	FACETS	0.889	0.793	0.989	0.593	0.529	0.66	CLONAL	2	TRUE	0	0.369964011356153	3		242	299	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273533	38273533	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	273	417	0	ENST00000425967.3:c.1802G>T	p.Arg601Leu	p.R601L	ENST00000425967	NM_001174067.1	601	cGg/cTg	14/19	0.369964011356153	3	FACETS	0.861	0.808	0.914	0.861	0.808	0.914	CLONAL	2	TRUE	1	0.369964011356153	3		417	1016	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006209	22006209	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	229	269	0	ENST00000276925.6:c.194T>C	p.Leu65Pro	p.L65P	ENST00000276925	NM_004936.3	65	cTg/cCg	2/2	0.369964011356153	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.369964011356153	2		269	572	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570268	87570268	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	130	278	0	ENST00000277120.3:c.2008C>A	p.Leu670Met	p.L670M	ENST00000277120		670	Ctg/Atg	17/19	0.369964011356153	3	FACETS	1	0.951	1	0.537	0.487	0.589	CLONAL	1	TRUE	1	0.369964011356153	3		278	776	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650135	93650135	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs762706714	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	270	386	1	ENST00000375746.1:c.1686G>T	p.Met562Ile	p.M562I	ENST00000375746	NM_001174167.1	562	atG/atT	12/14	0.369964011356153	3	FACETS	0.979	0.921	1	0.979	0.921	1	CLONAL	2	TRUE	1	0.369964011356153	3		387	883	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796793	135796793	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs118203429	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	209	365	1	ENST00000298552.3:c.694G>T	p.Glu232Ter	p.E232*	ENST00000298552	NM_001162426.1	232	Gaa/Taa	8/23	0.369964011356153	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.369964011356153	3		366	649	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407900	139407900	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs374434131	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	157	492	0	ENST00000277541.6:c.2297G>T	p.Gly766Val	p.G766V	ENST00000277541	NM_017617.3	766	gGc/gTc	14/34	0.369964011356153	3	FACETS	0.918	0.84	1	0.459	0.42	0.501	CLONAL	1	TRUE	1	0.369964011356153	3		492	1095	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456455	32456455	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	155	213	0	ENST00000332351.3:c.437G>A	p.Trp146Ter	p.W146*	ENST00000332351	NM_024426.4	146	tGg/tAg	1/10	0.369964011356153	2	FACETS	0.983	0.91	1	0.983	0.91	1	CLONAL	2	TRUE	0	0.369964011356153	2		213	426	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246679	46246679	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	50	96	0	ENST00000334344.6:c.4773G>T	p.Gln1591His	p.Q1591H	ENST00000334344	NM_152641.2	1591	caG/caT	15/21	0.369964011356153	3	FACETS	0.801	0.689	0.92	0.801	0.689	0.92	CLONAL	2	TRUE	1	0.369964011356153	3		96	200	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226091	133226091	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	221	360	0	ENST00000320574.5:c.3806T>A	p.Leu1269His	p.L1269H	ENST00000320574	NM_006231.2	1269	cTt/cAt	31/49	0.369964011356153	3	FACETS	1	0.991	1	0.709	0.659	0.759	CLONAL	1	TRUE	1	0.369964011356153	3		360	999	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001294	29001294	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	80	341	0	ENST00000282397.4:c.1436+2T>C		p.X479_splice	ENST00000282397	NM_002019.4	479			1	2	FACETS	0.888	0.784	0.999	0.888	0.784	0.999	CLONAL	1	TRUE	1	0.369964011356153	2		341	487	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293240	91293240	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs558524280	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	115	180	0	ENST00000355112.3:c.742A>G	p.Ile248Val	p.I248V	ENST00000355112	NM_000057.2	248	Ata/Gta	3/22	0.264789451529332	5	FACETS	0.846	0.769	0.925	0.846	0.769	0.925	CLONAL	3	TRUE	2	0.369964011356153	5		180	381	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223979	2223979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	431	546	1	ENST00000326181.6:c.1193C>T	p.Pro398Leu	p.P398L	ENST00000326181	NM_032271.2	398	cCt/cTt	13/21	0.36876420650411	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.369964011356153	2		547	940	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858436	9858436	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	299	463	0	ENST00000330684.3:c.2965A>T	p.Asn989Tyr	p.N989Y	ENST00000330684	NM_001134407.1	989	Aat/Tat	13/13	0.36876420650411	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.369964011356153	2		463	769	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23640988	23640988	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	123	348	0	ENST00000261584.4:c.2487G>C	p.Gln829His	p.Q829H	ENST00000261584	NM_024675.3	829	caG/caC	5/13	0.369964011356153	4	FACETS	1	0.961	1			1	CLONAL	1	TRUE	NA	0.369964011356153	4		348	814	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641142	23641142	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	222	396	0	ENST00000261584.4:c.2333G>T	p.Ser778Ile	p.S778I	ENST00000261584	NM_024675.3	778	aGt/aTt	5/13	0.369964011356153	4	FACETS	0.778	0.724	0.835			1	SUBCLONAL	2	TRUE	NA	0.369964011356153	4		396	1056	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974764	15974764	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	173	486	0	ENST00000268712.3:c.4111G>T	p.Val1371Phe	p.V1371F	ENST00000268712	NM_006311.3	1371	Gtc/Ttc	30/46	0.224704125148695	5	FACETS	1	0.988	1	0.483	0.444	0.523	CLONAL	1	TRUE	2	0.369964011356153	5		486	1004	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805763	46805763	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1195	346	759	0	ENST00000290295.7:c.193C>A	p.Pro65Thr	p.P65T	ENST00000290295	NM_006361.5	65	Cca/Aca	1/2	0.224704125148695	5	FACETS	0.944	0.891	0.997	0.629	0.594	0.665	CLONAL	2	TRUE	2	0.369964011356153	5		759	1541	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136131	11136131	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	332	490	0	ENST00000358026.2:c.3115A>T	p.Ile1039Phe	p.I1039F	ENST00000358026	NM_001128849.1	1039	Atc/Ttc	22/36	0.36876420650411	2	FACETS	0.962	0.912	1	0.962	0.912	1	CLONAL	2	TRUE	0	0.369964011356153	2		490	933	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257397	19257397	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	346	596	0	ENST00000162023.5:c.736G>C	p.Gly246Arg	p.G246R	ENST00000162023		246	Ggg/Cgg	11/13	NA	2	FACETS	1	0.972	1			1	INDETERMINATE	2	TRUE	NA	0.369964011356153	2		596	906	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547016	9547016	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	29	131	0	ENST00000353224.5:c.1006G>T	p.Ala336Ser	p.A336S	ENST00000353224	NM_177990.2	336	Gca/Tca	5/10	0.369964011356153	3	FACETS	0.523	0.42	0.64			1	SUBCLONAL	1	TRUE	NA	0.369964011356153	3		131	355	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944544	40944544	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	231	364	0	ENST00000373198.4:c.1958G>C	p.Arg653Pro	p.R653P	ENST00000373198	NM_133170.3	653	cGg/cCg	12/32	0.369964011356153	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.369964011356153	2		364	603	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101130	41101130	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	230	281	0	ENST00000373198.4:c.1226C>A	p.Pro409His	p.P409H	ENST00000373198	NM_133170.3	409	cCc/cAc	8/32	0.369964011356153	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.369964011356153	2		281	587	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306605	41306605	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	311	443	0	ENST00000373198.4:c.1054C>G	p.Pro352Ala	p.P352A	ENST00000373198	NM_133170.3	352	Ccc/Gcc	7/32	0.369964011356153	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.369964011356153	2		443	812	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091213	29091213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	22	43	0	ENST00000328354.6:c.1277C>T	p.Pro426Leu	p.P426L	ENST00000328354	NM_007194.3	426	cCt/cTt	12/15	0.369964011356153	3	FACETS	0.952	0.76	1	0.952	0.76	1	CLONAL	2	TRUE	1	0.369964011356153	3		43	74	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039411	47039411	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	284	589	0	ENST00000377604.3:c.1034T>G	p.Phe345Cys	p.F345C	ENST00000377604	NM_001204468.1	345	tTt/tGt	10/24	0.369964011356153	3	FACETS	1	0.993	1	0.746	0.7	0.792	CLONAL	1	TRUE	1	0.369964011356153	3		589	1220	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348159	70348159	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	250	594	1	ENST00000374080.3:c.3223G>A	p.Ala1075Thr	p.A1075T	ENST00000374080		1075	Gca/Aca	23/45	0.369964011356153	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.369964011356153	1		595	767	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169039	11169039	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	379	404	0	ENST00000358026.2:c.4629+1del		p.K1543fs	ENST00000358026	NM_001128849.1	1543	aaG/aa	32/36	0.36876420650411	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.369964011356153	2		404	956	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28903772	28903772	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	143	547	1	ENST00000282397.4:c.2687del	p.Gly896GlufsTer10	p.G896Efs*10	ENST00000282397	NM_002019.4	896	gGa/ga	19/30	1	2	FACETS	0.865	0.788	0.945	0.865	0.788	0.945	CLONAL	1	TRUE	1	0.369964011356153	2		548	894	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95584074	95584074	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	66	266	0	ENST00000393063.1:c.1394del	p.Gly465AlafsTer15	p.G465Afs*15	ENST00000393063	NM_030621.3	465	gGc/gc	10/28	0.369964011356153	3	FACETS	0.988	0.861	1	0.494	0.43	0.563	CLONAL	1	TRUE	1	0.369964011356153	3		266	428	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163793	47163793	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	137	396	0	ENST00000409792.3:c.2333del	p.Pro778GlnfsTer20	p.P778Qfs*20	ENST00000409792	NM_014159.6	778	cCa/ca	3/21	0.369964011356153	3	FACETS	0.819	0.749	0.892	0.819	0.749	0.892	CLONAL	2	TRUE	1	0.369964011356153	3		396	536	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254563	1254565	+	missense_variant	Missense_Mutation	TNP	CAC	CAC	AAA	novel	NA	P-0011334-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	350	447	0	ENST00000310581.5:c.3213_3215delinsTTT	p.Gln1071_Trp1072delinsHisLeu	p.Q1071_W1072delinsHL	ENST00000310581	NM_198253.2	1071	caGTGg/caTTTg	15/16	0.264789451529332	5	FACETS	1	0.99	1	0.781	0.74	0.824	CLONAL	2	TRUE	2	0.369964011356153	5		447	1255	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438491	52438491	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	81	372	0	ENST00000460680.1:c.1228C>T	p.Gln410Ter	p.Q410*	ENST00000460680	NM_004656.3	410	Cag/Tag	12/17	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.26	2		372	614	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035163	42035163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1007592948	NA	P-0011349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	154	592	0	ENST00000219905.7:c.5005C>T	p.Pro1669Ser	p.P1669S	ENST00000219905	NM_001164273.1	1669	Cct/Tct	15/24	0.3	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.26	1		592	921	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	32	185	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.249681756963949	2		185	233	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073432	8073432	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1292	136	876	0	ENST00000377482.5:c.1227A>C	p.Lys409Asn	p.K409N	ENST00000377482	NM_018948.3	409	aaA/aaC	4/4	1	2	FACETS	0.763	0.691	0.839	0.763	0.691	0.839	SUBCLONAL	1	TRUE	1	0.249681756963949	2		876	1428	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237721	16237721	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	62	417	0	ENST00000375759.3:c.1168G>T	p.Glu390Ter	p.E390*	ENST00000375759	NM_015001.2	390	Gaa/Taa	5/15	1	2	FACETS	0.648	0.559	0.746	0.648	0.559	0.746	SUBCLONAL	1	TRUE	1	0.249681756963949	2		417	766	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257860	16257860	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753992826	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	35	216	0	ENST00000375759.3:c.5125G>A	p.Asp1709Asn	p.D1709N	ENST00000375759	NM_015001.2	1709	Gat/Aat	11/15	1	2	FACETS	0.852	0.7	1	0.852	0.7	1	CLONAL	1	TRUE	1	0.249681756963949	2		216	329	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258728	16258728	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	68	438	1	ENST00000375759.3:c.5993A>T	p.Lys1998Ile	p.K1998I	ENST00000375759	NM_015001.2	1998	aAa/aTa	11/15	1	2	FACETS	0.78	0.678	0.891	0.78	0.678	0.891	SUBCLONAL	1	TRUE	1	0.249681756963949	2		439	698	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265829	16265829	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	80	602	0	ENST00000375759.3:c.10902C>A	p.Phe3634Leu	p.F3634L	ENST00000375759	NM_015001.2	3634	ttC/ttA	15/15	1	2	FACETS	0.684	0.601	0.774	0.684	0.601	0.774	SUBCLONAL	1	TRUE	1	0.249681756963949	2		602	937	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105547	27105547	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	75	545	0	ENST00000324856.7:c.5158T>G	p.Phe1720Val	p.F1720V	ENST00000324856	NM_006015.4	1720	Ttc/Gtc	20/20	1	2	FACETS	0.61	0.533	0.693	0.61	0.533	0.693	SUBCLONAL	1	TRUE	1	0.249681756963949	2		545	985	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105617	27105617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528936858	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	89	562	1	ENST00000324856.7:c.5228C>T	p.Thr1743Met	p.T1743M	ENST00000324856	NM_006015.4	1743	aCg/aTg	20/20	1	2	FACETS	0.756	0.669	0.849	0.756	0.669	0.849	SUBCLONAL	1	TRUE	1	0.249681756963949	2		563	943	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812205	43812205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866559375	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	119	661	0	ENST00000372470.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000372470	NM_005373.2	357	cGa/cAa	7/12	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.249681756963949	2		661	940	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795028	45795028	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144616312	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	84	557	0	ENST00000450313.1:c.1600C>T	p.Arg534Trp	p.R534W	ENST00000450313	NM_012222.2	534	Cgg/Tgg	16/16	1	2	FACETS	0.77	0.679	0.868	0.77	0.679	0.868	SUBCLONAL	1	TRUE	1	0.249681756963949	2		557	874	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509445	46509445	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	50	438	0	ENST00000262741.5:c.1286T>C	p.Val429Ala	p.V429A	ENST00000262741	NM_003629.3	429	gTg/gCg	10/10	1	2	FACETS	0.591	0.5	0.691	0.591	0.5	0.691	SUBCLONAL	1	TRUE	1	0.249681756963949	2		438	678	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726651	46726651	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237327590	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	47	389	0	ENST00000371975.4:c.730G>A	p.Asp244Asn	p.D244N	ENST00000371975	NM_003579.3	244	Gat/Aat	7/18	1	2	FACETS	0.541	0.455	0.636	0.541	0.455	0.636	SUBCLONAL	1	TRUE	1	0.249681756963949	2		389	696	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874286	155874286	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs868208063	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	42	366	0	ENST00000368323.3:c.245T>G	p.Phe82Cys	p.F82C	ENST00000368323	NM_006912.5	82	tTt/tGt	5/6	1	2	FACETS	0.616	0.514	0.73	0.616	0.514	0.73	SUBCLONAL	1	TRUE	1	0.249681756963949	2		366	546	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206943240	206943240	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	63	329	0	ENST00000423557.1:c.379-1G>T		p.X127_splice	ENST00000423557	NM_000572.2	127			1	2	FACETS	0.834	0.721	0.957	0.834	0.721	0.957	CLONAL	1	TRUE	1	0.249681756963949	2		329	605	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253512	226253512	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	73	633	0	ENST00000366813.1:c.282+2T>C		p.X94_splice	ENST00000366813		94			1	2	FACETS	0.579	0.505	0.659	0.579	0.505	0.659	SUBCLONAL	1	TRUE	1	0.249681756963949	2		633	1010	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243708816	243708816	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	60	420	0	ENST00000263826.5:c.1247A>C	p.Lys416Thr	p.K416T	ENST00000263826	NM_005465.4	416	aAa/aCa	11/13	1	2	FACETS	0.584	0.502	0.674	0.584	0.502	0.674	SUBCLONAL	1	TRUE	1	0.249681756963949	2		420	823	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606679	29606679	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs865931787	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	64	492	0	ENST00000389048.3:c.1201C>T	p.Arg401Ter	p.R401*	ENST00000389048	NM_004304.4	401	Cga/Tga	5/29	1	2	FACETS	0.685	0.593	0.786	0.685	0.593	0.786	SUBCLONAL	1	TRUE	1	0.249681756963949	2		492	748	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033396	48033396	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	82	465	0	ENST00000234420.5:c.3700G>T	p.Glu1234Ter	p.E1234*	ENST00000234420	NM_000179.2	1234	Gaa/Taa	8/10	1	2	FACETS	0.676	0.594	0.763	0.676	0.594	0.763	SUBCLONAL	1	TRUE	1	0.249681756963949	2		465	972	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033767	48033767	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs141464646	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	47	400	2	ENST00000234420.5:c.3978G>T	p.Met1326Ile	p.M1326I	ENST00000234420	NM_000179.2	1326	atG/atT	9/10	1	2	FACETS	0.565	0.476	0.664	0.565	0.476	0.664	SUBCLONAL	1	TRUE	1	0.249681756963949	2		402	666	SUCCESS
REL	5966	MSKCC	GRCh37	2	61121582	61121582	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	49	380	0	ENST00000295025.8:c.204G>T	p.Lys68Asn	p.K68N	ENST00000295025	NM_002908.2	68	aaG/aaT	3/11	1	2	FACETS	0.588	0.497	0.689	0.588	0.497	0.689	SUBCLONAL	1	TRUE	1	0.249681756963949	2		380	667	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149660	61149660	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	21	104	0	ENST00000295025.8:c.1850T>G	p.Phe617Cys	p.F617C	ENST00000295025	NM_002908.2	617	tTt/tGt	11/11	1	2	FACETS	0.768	0.594	0.97	0.768	0.594	0.97	CLONAL	1	TRUE	1	0.249681756963949	2		104	219	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038082	128038082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367552856	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	87	470	0	ENST00000285398.2:c.1468G>A	p.Glu490Lys	p.E490K	ENST00000285398	NM_000122.1	490	Gaa/Aaa	9/15	1	2	FACETS	0.881	0.779	0.99	0.881	0.779	0.99	CLONAL	1	TRUE	1	0.249681756963949	2		470	791	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038127	128038127	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	87	440	0	ENST00000285398.2:c.1423G>T	p.Asp475Tyr	p.D475Y	ENST00000285398	NM_000122.1	475	Gac/Tac	9/15	1	2	FACETS	0.817	0.722	0.919	0.817	0.722	0.919	CLONAL	1	TRUE	1	0.249681756963949	2		440	853	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190670480	190670480	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	35	336	0	ENST00000441310.2:c.418G>A	p.Gly140Ser	p.G140S	ENST00000441310	NM_000534.4	140	Ggt/Agt	4/13	1	2	FACETS	0.454	0.371	0.547	0.454	0.371	0.547	SUBCLONAL	1	TRUE	1	0.249681756963949	2		336	618	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267694	198267694	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	63	311	0	ENST00000335508.6:c.1785G>T	p.Glu595Asp	p.E595D	ENST00000335508	NM_012433.2	595	gaG/gaT	13/25	1	2	FACETS	0.798	0.69	0.916	0.798	0.69	0.916	CLONAL	1	TRUE	1	0.249681756963949	2		311	632	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273266	198273266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	70	418	0	ENST00000335508.6:c.944G>A	p.Arg315Gln	p.R315Q	ENST00000335508	NM_012433.2	315	cGa/cAa	8/25	1	2	FACETS	0.647	0.563	0.738	0.647	0.563	0.738	SUBCLONAL	1	TRUE	1	0.249681756963949	2		418	867	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281544	198281544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	84	555	0	ENST00000335508.6:c.587G>A	p.Arg196Gln	p.R196Q	ENST00000335508	NM_012433.2	196	cGa/cAa	6/25	1	2	FACETS	0.683	0.602	0.771	0.683	0.602	0.771	SUBCLONAL	1	TRUE	1	0.249681756963949	2		555	985	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285173	198285173	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	73	448	0	ENST00000335508.6:c.394C>T	p.Arg132Cys	p.R132C	ENST00000335508	NM_012433.2	132	Cgt/Tgt	4/25	1	2	FACETS	0.669	0.584	0.761	0.669	0.584	0.761	SUBCLONAL	1	TRUE	1	0.249681756963949	2		448	874	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131412	202131412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339962485	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	60	413	0	ENST00000358485.4:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000358485	NM_001080125.1	127	cGa/cAa	2/9	1	2	FACETS	0.667	0.573	0.768	0.667	0.573	0.768	SUBCLONAL	1	TRUE	1	0.249681756963949	2		413	721	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295800	212295800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024245860	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	64	444	3	ENST00000342788.4:c.2513G>A	p.Arg838Gln	p.R838Q	ENST00000342788	NM_005235.2	838	cGa/cAa	21/28	1	2	FACETS	0.617	0.533	0.708	0.617	0.533	0.708	SUBCLONAL	1	TRUE	1	0.249681756963949	2		447	831	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342954	225342954	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	88	564	1	ENST00000264414.4:c.2138C>A	p.Ser713Tyr	p.S713Y	ENST00000264414	NM_003590.4	713	tCt/tAt	15/16	1	2	FACETS	0.658	0.581	0.74	0.658	0.581	0.74	SUBCLONAL	1	TRUE	1	0.249681756963949	2		565	1072	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691768	30691768	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	59	437	1	ENST00000295754.5:c.270G>T	p.Lys90Asn	p.K90N	ENST00000295754	NM_003242.5	90	aaG/aaT	3/7	1	2	FACETS	0.668	0.574	0.771	0.668	0.574	0.771	SUBCLONAL	1	TRUE	1	0.249681756963949	2		438	707	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277233	41277233	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	66	384	0	ENST00000349496.5:c.1702G>A	p.Glu568Lys	p.E568K	ENST00000349496	NM_001904.3	568	Gaa/Aaa	11/15	1	2	FACETS	0.744	0.645	0.851	0.744	0.645	0.851	SUBCLONAL	1	TRUE	1	0.249681756963949	2		384	711	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008548	70008548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771113831	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	66	303	0	ENST00000394351.3:c.835C>T	p.Arg279Trp	p.R279W	ENST00000394351	NM_000248.3	279	Cgg/Tgg	8/9	1	2	FACETS	0.966	0.84	1	0.966	0.84	1	CLONAL	1	TRUE	1	0.249681756963949	2		303	547	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014371	70014371	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	92	752	0	ENST00000394351.3:c.1232G>T	p.Ser411Ile	p.S411I	ENST00000394351	NM_000248.3	411	aGc/aTc	9/9	1	2	FACETS	0.62	0.549	0.696	0.62	0.549	0.696	SUBCLONAL	1	TRUE	1	0.249681756963949	2		752	1189	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72842110	72842110	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs761610326	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	67	326	0	ENST00000325599.8:c.1138G>T	p.Asp380Tyr	p.D380Y	ENST00000325599	NM_018130.2	380	Gat/Tat	10/11	1	2	FACETS	0.733	0.636	0.838	0.733	0.636	0.838	SUBCLONAL	1	TRUE	1	0.249681756963949	2		326	732	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72866425	72866425	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	74	421	0	ENST00000325599.8:c.838C>A	p.Leu280Met	p.L280M	ENST00000325599	NM_018130.2	280	Ctg/Atg	7/11	1	2	FACETS	0.686	0.599	0.78	0.686	0.599	0.78	SUBCLONAL	1	TRUE	1	0.249681756963949	2		421	864	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670431	134670431	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	43	378	0	ENST00000398015.3:c.342C>A	p.Tyr114Ter	p.Y114*	ENST00000398015	NM_004441.4	114	taC/taA	3/16	1	2	FACETS	0.622	0.52	0.735	0.622	0.52	0.735	SUBCLONAL	1	TRUE	1	0.249681756963949	2		378	554	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968251	134968251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373797543	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	56	572	0	ENST00000398015.3:c.2764G>A	p.Ala922Thr	p.A922T	ENST00000398015	NM_004441.4	922	Gcc/Acc	15/16	1	2	FACETS	0.597	0.51	0.691	0.597	0.51	0.691	SUBCLONAL	1	TRUE	1	0.249681756963949	2		572	752	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138409963	138409963	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	41	319	0	ENST00000289153.2:c.1915C>A	p.Leu639Ile	p.L639I	ENST00000289153	NM_006219.2	639	Ctt/Att	13/22	1	2	FACETS	0.498	0.413	0.592	0.498	0.413	0.592	SUBCLONAL	1	TRUE	1	0.249681756963949	2		319	660	SUCCESS
ATR	545	MSKCC	GRCh37	3	142168390	142168390	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs749753899	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	53	394	0	ENST00000350721.4:c.7816C>T	p.Arg2606Ter	p.R2606*	ENST00000350721	NM_001184.3	2606	Cga/Tga	47/47	1	2	FACETS	0.531	0.451	0.618	0.531	0.451	0.618	SUBCLONAL	1	TRUE	1	0.249681756963949	2		394	800	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261526	142261526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	63	424	0	ENST00000350721.4:c.3431G>A	p.Gly1144Asp	p.G1144D	ENST00000350721	NM_001184.3	1144	gGc/gAc	17/47	1	2	FACETS	0.601	0.519	0.692	0.601	0.519	0.692	SUBCLONAL	1	TRUE	1	0.249681756963949	2		424	839	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	85	628	0	ENST00000263967.3:c.333G>T	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaT	2/21	1	2	FACETS	0.605	0.533	0.682	0.605	0.533	0.682	SUBCLONAL	1	TRUE	1	0.249681756963949	2		628	1126	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922300	178922300	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	52	348	1	ENST00000263967.3:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000263967	NM_006218.2	357	Cga/Tga	6/21	1	2	FACETS	0.614	0.522	0.716	0.614	0.522	0.716	SUBCLONAL	1	TRUE	1	0.249681756963949	2		349	678	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	72	394	1	ENST00000263967.3:c.3012G>T	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atT	21/21	1	2	FACETS	0.761	0.664	0.866	0.761	0.664	0.866	SUBCLONAL	1	TRUE	1	0.249681756963949	2		395	758	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665058	182665058	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	70	550	0	ENST00000292782.4:c.668T>G	p.Ile223Ser	p.I223S	ENST00000292782	NM_020640.2	223	aTt/aGt	6/7	1	2	FACETS	0.492	0.427	0.562	0.492	0.427	0.562	SUBCLONAL	1	TRUE	1	0.249681756963949	2		550	1140	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181425	185181425	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1435276633	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	87	503	1	ENST00000265026.3:c.1366C>T	p.Arg456Ter	p.R456*	ENST00000265026	NM_004721.4	456	Cga/Tga	8/14	1	2	FACETS	0.804	0.71	0.904	0.804	0.71	0.904	CLONAL	1	TRUE	1	0.249681756963949	2		504	867	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133597	55133597	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	59	423	0	ENST00000257290.5:c.901G>T	p.Glu301Ter	p.E301*	ENST00000257290	NM_006206.4	301	Gaa/Taa	6/23	1	2	FACETS	0.699	0.601	0.807	0.699	0.601	0.807	SUBCLONAL	1	TRUE	1	0.249681756963949	2		423	676	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595622	55595622	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	41	240	0	ENST00000288135.5:c.2112G>T	p.Lys704Asn	p.K704N	ENST00000288135	NM_000222.2	704	aaG/aaT	14/21	1	2	FACETS	0.674	0.562	0.8	0.674	0.562	0.8	SUBCLONAL	1	TRUE	1	0.249681756963949	2		240	487	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599248	55599248	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	61	331	0	ENST00000288135.5:c.2374G>A	p.Asp792Asn	p.D792N	ENST00000288135	NM_000222.2	792	Gac/Aac	17/21	1	2	FACETS	0.748	0.645	0.861	0.748	0.645	0.861	SUBCLONAL	1	TRUE	1	0.249681756963949	2		331	653	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55603385	55603385	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	62	566	2	ENST00000288135.5:c.2741G>T	p.Arg914Ile	p.R914I	ENST00000288135	NM_000222.2	914	aGa/aTa	20/21	1	2	FACETS	0.603	0.52	0.695	0.603	0.52	0.695	SUBCLONAL	1	TRUE	1	0.249681756963949	2		568	823	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961106	55961106	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	65	447	0	ENST00000263923.4:c.2834T>G	p.Phe945Cys	p.F945C	ENST00000263923	NM_002253.2	945	tTc/tGc	21/30	1	2	FACETS	0.612	0.529	0.702	0.612	0.529	0.702	SUBCLONAL	1	TRUE	1	0.249681756963949	2		447	851	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981579	55981579	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	37	261	1	ENST00000263923.4:c.359-1G>T		p.X120_splice	ENST00000263923	NM_002253.2	120			1	2	FACETS	0.706	0.582	0.844	0.706	0.582	0.844	SUBCLONAL	1	TRUE	1	0.249681756963949	2		262	420	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286183	66286183	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs376952898	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	71	513	0	ENST00000273854.3:c.1503G>T	p.Glu501Asp	p.E501D	ENST00000273854	NM_004439.5	501	gaG/gaT	6/18	1	2	FACETS	0.619	0.539	0.706	0.619	0.539	0.706	SUBCLONAL	1	TRUE	1	0.249681756963949	2		513	919	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467461	66467461	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	48	370	0	ENST00000273854.3:c.808G>T	p.Glu270Ter	p.E270*	ENST00000273854	NM_004439.5	270	Gaa/Taa	3/18	1	2	FACETS	0.62	0.523	0.727	0.62	0.523	0.727	SUBCLONAL	1	TRUE	1	0.249681756963949	2		370	620	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157965	106157965	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	29	242	1	ENST00000380013.4:c.2866C>A	p.Leu956Ile	p.L956I	ENST00000380013	NM_001127208.2	956	Ctc/Atc	3/11	1	2	FACETS	0.552	0.442	0.676	0.552	0.442	0.676	SUBCLONAL	1	TRUE	1	0.249681756963949	2		243	421	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196499	106196499	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs527895107	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	69	531	0	ENST00000380013.4:c.4832C>A	p.Ser1611Tyr	p.S1611Y	ENST00000380013	NM_001127208.2	1611	tCt/tAt	11/11	1	2	FACETS	0.772	0.672	0.881	0.772	0.672	0.881	SUBCLONAL	1	TRUE	1	0.249681756963949	2		531	716	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	76	470	2	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	1	2	FACETS	0.71	0.621	0.805	0.71	0.621	0.805	SUBCLONAL	1	TRUE	1	0.249681756963949	2		472	858	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539690	187539690	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs748166431	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	77	470	1	ENST00000441802.2:c.8050G>T	p.Glu2684Ter	p.E2684*	ENST00000441802	NM_005245.3	2684	Gaa/Taa	10/27	1	2	FACETS	0.704	0.617	0.798	0.704	0.617	0.798	SUBCLONAL	1	TRUE	1	0.249681756963949	2		471	876	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541523	187541523	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	110	544	2	ENST00000441802.2:c.6217G>T	p.Asp2073Tyr	p.D2073Y	ENST00000441802	NM_005245.3	2073	Gac/Tac	10/27	1	2	FACETS	0.859	0.77	0.953	0.859	0.77	0.953	CLONAL	1	TRUE	1	0.249681756963949	2		546	1026	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542753	187542753	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200613891	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	80	505	0	ENST00000441802.2:c.4987G>A	p.Ala1663Thr	p.A1663T	ENST00000441802	NM_005245.3	1663	Gcc/Acc	10/27	1	2	FACETS	0.665	0.584	0.753	0.665	0.584	0.753	SUBCLONAL	1	TRUE	1	0.249681756963949	2		505	963	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542860	187542860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767331775	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	67	382	0	ENST00000441802.2:c.4880G>A	p.Arg1627Gln	p.R1627Q	ENST00000441802	NM_005245.3	1627	cGa/cAa	10/27	1	2	FACETS	0.743	0.645	0.85	0.743	0.645	0.85	SUBCLONAL	1	TRUE	1	0.249681756963949	2		382	722	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557810	187557810	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	77	558	0	ENST00000441802.2:c.3901T>G	p.Phe1301Val	p.F1301V	ENST00000441802	NM_005245.3	1301	Ttc/Gtc	5/27	1	2	FACETS	0.671	0.588	0.761	0.671	0.588	0.761	SUBCLONAL	1	TRUE	1	0.249681756963949	2		558	919	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876216	35876216	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	74	421	2	ENST00000303115.3:c.1008G>T	p.Glu336Asp	p.E336D	ENST00000303115	NM_002185.3	336	gaG/gaT	8/8	1	2	FACETS	0.895	0.784	1	0.895	0.784	1	CLONAL	1	TRUE	1	0.249681756963949	2		423	662	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876581	35876581	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	26	185	0	ENST00000303115.3:c.1373A>G	p.Asn458Ser	p.N458S	ENST00000303115	NM_002185.3	458	aAc/aGc	8/8	1	2	FACETS	0.755	0.599	0.932	0.755	0.599	0.932	CLONAL	1	TRUE	1	0.249681756963949	2		185	276	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950561	38950561	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201384226	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	80	570	0	ENST00000357387.3:c.3389G>A	p.Arg1130Gln	p.R1130Q	ENST00000357387	NM_152756.3	1130	cGa/cAa	31/38	1	2	FACETS	0.584	0.512	0.662	0.584	0.512	0.662	SUBCLONAL	1	TRUE	1	0.249681756963949	2		570	1097	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591076	67591076	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	51	286	0	ENST00000274335.5:c.1669C>T	p.Arg557Ter	p.R557*	ENST00000274335		557	Cga/Tga	12/15	1	2	FACETS	0.709	0.602	0.827	0.709	0.602	0.827	SUBCLONAL	1	TRUE	1	0.249681756963949	2		286	576	SUCCESS
APC	324	MSKCC	GRCh37	5	112154723	112154723	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775126020	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	52	336	0	ENST00000257430.4:c.994C>T	p.Arg332Ter	p.R332*	ENST00000257430	NM_000038.5	332	Cga/Tga	10/16	1	2	FACETS	0.736	0.626	0.856	0.736	0.626	0.856	SUBCLONAL	1	TRUE	1	0.249681756963949	2		336	566	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	57	544	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.476	0.407	0.551	0.476	0.407	0.551	SUBCLONAL	1	TRUE	1	0.249681756963949	2		544	960	SUCCESS
APC	324	MSKCC	GRCh37	5	112175897	112175897	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	50	301	0	ENST00000257430.4:c.4606G>T	p.Glu1536Ter	p.E1536*	ENST00000257430	NM_000038.5	1536	Gaa/Taa	16/16	1	2	FACETS	0.675	0.572	0.789	0.675	0.572	0.789	SUBCLONAL	1	TRUE	1	0.249681756963949	2		301	593	SUCCESS
APC	324	MSKCC	GRCh37	5	112177049	112177049	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	66	637	0	ENST00000257430.4:c.5758C>T	p.Arg1920Ter	p.R1920*	ENST00000257430	NM_000038.5	1920	Cga/Tga	16/16	1	2	FACETS	0.475	0.41	0.545	0.475	0.41	0.545	SUBCLONAL	1	TRUE	1	0.249681756963949	2		637	1114	SUCCESS
APC	324	MSKCC	GRCh37	5	112177788	112177788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752091655	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	57	266	1	ENST00000257430.4:c.6497G>A	p.Arg2166Gln	p.R2166Q	ENST00000257430	NM_000038.5	2166	cGa/cAa	16/16	1	2	FACETS	0.766	0.657	0.885	0.766	0.657	0.885	SUBCLONAL	1	TRUE	1	0.249681756963949	2		267	596	SUCCESS
APC	324	MSKCC	GRCh37	5	112177901	112177901	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs752654519	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	127	540	0	ENST00000257430.4:c.6610C>T	p.Arg2204Ter	p.R2204*	ENST00000257430	NM_000038.5	2204	Cga/Tga	16/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.249681756963949	2		540	746	SUCCESS
APC	324	MSKCC	GRCh37	5	112178000	112178000	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768922431	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	66	509	0	ENST00000257430.4:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000257430	NM_000038.5	2237	Cga/Tga	16/16	1	2	FACETS	0.672	0.582	0.769	0.672	0.582	0.769	SUBCLONAL	1	TRUE	1	0.249681756963949	2		509	787	SUCCESS
APC	324	MSKCC	GRCh37	5	112178211	112178211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs901983934	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	93	523	1	ENST00000257430.4:c.6920C>T	p.Ser2307Leu	p.S2307L	ENST00000257430	NM_000038.5	2307	tCg/tTg	16/16	1	2	FACETS	0.881	0.782	0.986	0.881	0.782	0.986	CLONAL	1	TRUE	1	0.249681756963949	2		524	846	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953874	131953874	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121912628	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	66	361	0	ENST00000265335.6:c.3277C>T	p.Arg1093Ter	p.R1093*	ENST00000265335		1093	Cga/Tga	21/25	1	2	FACETS	0.741	0.643	0.849	0.741	0.643	0.849	SUBCLONAL	1	TRUE	1	0.249681756963949	2		361	713	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502666	149502666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749226501	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	45	387	0	ENST00000261799.4:c.2122C>T	p.Arg708Cys	p.R708C	ENST00000261799	NM_002609.3	708	Cgc/Tgc	15/23	1	2	FACETS	0.609	0.511	0.717	0.609	0.511	0.717	SUBCLONAL	1	TRUE	1	0.249681756963949	2		387	592	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030290	180030290	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs565053503	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	86	615	0	ENST00000261937.6:c.3994T>C	p.Phe1332Leu	p.F1332L	ENST00000261937	NM_182925.4	1332	Ttt/Ctt	30/30	1	2	FACETS	0.815	0.72	0.917	0.815	0.72	0.917	CLONAL	1	TRUE	1	0.249681756963949	2		615	845	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057642	180057642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150416750	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	88	603	3	ENST00000261937.6:c.313G>A	p.Asp105Asn	p.D105N	ENST00000261937	NM_182925.4	105	Gac/Aac	3/30	1	2	FACETS	0.772	0.683	0.868	0.772	0.683	0.868	SUBCLONAL	1	TRUE	1	0.249681756963949	2		606	913	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793647	89793647	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	73	443	0	ENST00000336032.3:c.716C>A	p.Ser239Tyr	p.S239Y	ENST00000336032	NM_006813.2	239	tCt/tAt	2/2	1	2	FACETS	0.684	0.597	0.778	0.684	0.597	0.778	SUBCLONAL	1	TRUE	1	0.249681756963949	2		443	855	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793716	89793716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754149624	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	70	431	0	ENST00000336032.3:c.785C>T	p.Ser262Leu	p.S262L	ENST00000336032	NM_006813.2	262	tCg/tTg	2/2	1	2	FACETS	0.735	0.64	0.838	0.735	0.64	0.838	SUBCLONAL	1	TRUE	1	0.249681756963949	2		431	763	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965719	93965719	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	93	684	0	ENST00000369303.4:c.2209G>T	p.Gly737Ter	p.G737*	ENST00000369303	NM_004440.3	737	Gga/Tga	13/17	1	2	FACETS	0.759	0.674	0.851	0.759	0.674	0.851	SUBCLONAL	1	TRUE	1	0.249681756963949	2		684	981	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93968000	93968000	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	90	535	0	ENST00000369303.4:c.1927G>T	p.Glu643Ter	p.E643*	ENST00000369303	NM_004440.3	643	Gaa/Taa	11/17	1	2	FACETS	0.722	0.639	0.811	0.722	0.639	0.811	SUBCLONAL	1	TRUE	1	0.249681756963949	2		535	999	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120845	94120845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465346253	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	110	707	1	ENST00000369303.4:c.206G>A	p.Arg69Gln	p.R69Q	ENST00000369303	NM_004440.3	69	cGa/cAa	3/17	1	2	FACETS	0.722	0.647	0.803	0.722	0.647	0.803	SUBCLONAL	1	TRUE	1	0.249681756963949	2		708	1220	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536164	106536164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	85	470	1	ENST00000369096.4:c.131C>T	p.Ala44Val	p.A44V	ENST00000369096	NM_001198.3	44	gCg/gTg	2/7	1	2	FACETS	0.829	0.732	0.934	0.829	0.732	0.934	CLONAL	1	TRUE	1	0.249681756963949	2		471	821	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117629975	117629975	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	59	406	0	ENST00000368508.3:c.6551G>T	p.Arg2184Ile	p.R2184I	ENST00000368508	NM_002944.2	2184	aGa/aTa	41/43	1	2	FACETS	0.703	0.604	0.811	0.703	0.604	0.811	SUBCLONAL	1	TRUE	1	0.249681756963949	2		406	672	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665261	117665261	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1158871186	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	81	412	0	ENST00000368508.3:c.4486G>T	p.Asp1496Tyr	p.D1496Y	ENST00000368508	NM_002944.2	1496	Gac/Tac	27/43	1	2	FACETS	0.845	0.744	0.954	0.845	0.744	0.954	CLONAL	1	TRUE	1	0.249681756963949	2		412	768	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715350	117715350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	90	386	0	ENST00000368508.3:c.1139G>A	p.Arg380Lys	p.R380K	ENST00000368508	NM_002944.2	380	aGa/aAa	10/43	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.249681756963949	2		386	677	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137522061	137522061	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	30	195	0	ENST00000367739.4:c.818T>G	p.Ile273Ser	p.I273S	ENST00000367739	NM_000416.2	273	aTt/aGt	6/7	1	2	FACETS	0.527	0.424	0.644	0.527	0.424	0.644	SUBCLONAL	1	TRUE	1	0.249681756963949	2		195	456	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200479	138200479	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	39	260	0	ENST00000237289.4:c.1897G>T	p.Glu633Ter	p.E633*	ENST00000237289	NM_001270507.1	633	Gaa/Taa	7/9	1	2	FACETS	0.742	0.615	0.883	0.742	0.615	0.883	SUBCLONAL	1	TRUE	1	0.249681756963949	2		260	421	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001374	150001374	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	89	541	0	ENST00000253339.5:c.2230C>T	p.Arg744Ter	p.R744*	ENST00000253339		744	Cga/Tga	4/7	1	2	FACETS	0.716	0.633	0.805	0.716	0.633	0.805	SUBCLONAL	1	TRUE	1	0.249681756963949	2		541	996	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004834	150004834	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	40	270	1	ENST00000253339.5:c.1391C>A	p.Ser464Tyr	p.S464Y	ENST00000253339		464	tCt/tAt	3/7	1	2	FACETS	0.717	0.596	0.851	0.717	0.596	0.851	SUBCLONAL	1	TRUE	1	0.249681756963949	2		271	447	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622230	162622230	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	87	443	0	ENST00000366898.1:c.467G>T	p.Arg156Ile	p.R156I	ENST00000366898	NM_004562.2	156	aGa/aTa	4/12	1	2	FACETS	0.862	0.763	0.969	0.862	0.763	0.969	CLONAL	1	TRUE	1	0.249681756963949	2		443	808	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683713	162683713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747891099	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	73	463	1	ENST00000366898.1:c.256G>A	p.Asp86Asn	p.D86N	ENST00000366898	NM_004562.2	86	Gac/Aac	3/12	1	2	FACETS	0.819	0.716	0.931	0.819	0.716	0.931	CLONAL	1	TRUE	1	0.249681756963949	2		464	714	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729390	41729390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866652548	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	123	772	2	ENST00000242208.4:c.1139G>A	p.Gly380Asp	p.G380D	ENST00000242208	NM_002192.2	380	gGc/gAc	3/3	1	2	FACETS	0.876	0.79	0.967	0.876	0.79	0.967	CLONAL	1	TRUE	1	0.249681756963949	2		774	1125	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739756	41739756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762653354	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	72	815	1	ENST00000242208.4:c.217G>A	p.Asp73Asn	p.D73N	ENST00000242208	NM_002192.2	73	Gat/Aat	2/3	1	2	FACETS	0.543	0.473	0.619	0.543	0.473	0.619	SUBCLONAL	1	TRUE	1	0.249681756963949	2		816	1062	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508490	106508490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	13	132	0	ENST00000359195.3:c.484G>A	p.Val162Ile	p.V162I	ENST00000359195	NM_002649.2	162	Gtc/Atc	2/11	1	2	FACETS	0.609	0.436	0.819	0.609	0.436	0.819	SUBCLONAL	1	TRUE	1	0.249681756963949	2		132	171	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845057	128845057	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	85	547	0	ENST00000249373.3:c.551A>G	p.Asn184Ser	p.N184S	ENST00000249373	NM_005631.4	184	aAc/aGc	3/12	1	2	FACETS	0.863	0.762	0.971	0.863	0.762	0.971	CLONAL	1	TRUE	1	0.249681756963949	2		547	789	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846196	128846196	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	78	562	1	ENST00000249373.3:c.1126C>A	p.Leu376Ile	p.L376I	ENST00000249373	NM_005631.4	376	Ctt/Att	5/12	1	2	FACETS	0.814	0.714	0.921	0.814	0.714	0.921	CLONAL	1	TRUE	1	0.249681756963949	2		563	768	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453130	140453130	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	51	292	0	ENST00000288602.6:c.1805C>A	p.Ser602Tyr	p.S602Y	ENST00000288602	NM_004333.4	602	tCt/tAt	15/18	1	2	FACETS	0.609	0.517	0.71	0.609	0.517	0.71	SUBCLONAL	1	TRUE	1	0.249681756963949	2		292	671	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543633	148543633	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	79	381	0	ENST00000320356.2:c.175G>T	p.Glu59Ter	p.E59*	ENST00000320356	NM_004456.4	59	Gaa/Taa	3/20	1	2	FACETS	0.808	0.71	0.914	0.808	0.71	0.914	CLONAL	1	TRUE	1	0.249681756963949	2		381	783	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188035	151188035	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	125	583	0	ENST00000262187.5:c.118G>T	p.Glu40Ter	p.E40*	ENST00000262187	NM_005614.3	40	Gaa/Taa	2/8	1	2	FACETS	0.836	0.755	0.923	0.836	0.755	0.923	CLONAL	1	TRUE	1	0.249681756963949	2		583	1197	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884866	151884866	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	70	437	0	ENST00000262189.6:c.4727C>A	p.Ser1576Tyr	p.S1576Y	ENST00000262189	NM_170606.2	1576	tCt/tAt	32/59	1	2	FACETS	0.801	0.698	0.913	0.801	0.698	0.913	CLONAL	1	TRUE	1	0.249681756963949	2		437	700	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151919101	151919101	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	39	341	0	ENST00000262189.6:c.3484A>C	p.Lys1162Gln	p.K1162Q	ENST00000262189	NM_170606.2	1162	Aaa/Caa	22/59	1	2	FACETS	0.48	0.397	0.573	0.48	0.397	0.573	SUBCLONAL	1	TRUE	1	0.249681756963949	2		341	651	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132768	152132768	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	48	362	1	ENST00000262189.6:c.104G>T	p.Arg35Ile	p.R35I	ENST00000262189	NM_170606.2	35	aGa/aTa	1/59	1	2	FACETS	0.705	0.596	0.826	0.705	0.596	0.826	SUBCLONAL	1	TRUE	1	0.249681756963949	2		363	545	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346284	152346284	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs778698188	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	120	746	0	ENST00000359321.1:c.286C>A	p.Leu96Ile	p.L96I	ENST00000359321	NM_005431.1	96	Ctt/Att	3/3	1	2	FACETS	0.773	0.696	0.855	0.773	0.696	0.855	SUBCLONAL	1	TRUE	1	0.249681756963949	2		746	1243	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983450	90983450	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202250	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	55	340	0	ENST00000265433.3:c.653G>T	p.Arg218Ile	p.R218I	ENST00000265433	NM_002485.4	218	aGa/aTa	6/16	1	2	FACETS	0.586	0.5	0.68	0.586	0.5	0.68	SUBCLONAL	1	TRUE	1	0.249681756963949	2		340	752	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862893	117862893	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	60	475	0	ENST00000297338.2:c.1584G>T	p.Glu528Asp	p.E528D	ENST00000297338	NM_006265.2	528	gaG/gaT	12/14	1	2	FACETS	0.581	0.499	0.671	0.581	0.499	0.671	SUBCLONAL	1	TRUE	1	0.249681756963949	2		475	827	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5055687	5055687	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1338813094	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	47	272	0	ENST00000381652.3:c.955G>A	p.Asp319Asn	p.D319N	ENST00000381652	NM_004972.3	319	Gat/Aat	8/25	1	2	FACETS	0.758	0.639	0.888	0.758	0.639	0.888	SUBCLONAL	1	TRUE	1	0.249681756963949	2		272	497	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471050	8471050	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	82	419	0	ENST00000356435.5:c.3449C>A	p.Ser1150Tyr	p.S1150Y	ENST00000356435		1150	tCt/tAt	20/35	1	2	FACETS	0.871	0.768	0.982	0.871	0.768	0.982	CLONAL	1	TRUE	1	0.249681756963949	2		419	754	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484161	8484161	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	75	515	0	ENST00000356435.5:c.3371T>G	p.Ile1124Ser	p.I1124S	ENST00000356435		1124	aTt/aGt	19/35	1	2	FACETS	0.708	0.62	0.804	0.708	0.62	0.804	SUBCLONAL	1	TRUE	1	0.249681756963949	2		515	848	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500759	8500759	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	45	249	0	ENST00000356435.5:c.2123A>C	p.Glu708Ala	p.E708A	ENST00000356435		708	gAa/gCa	13/35	1	2	FACETS	0.797	0.671	0.937	0.797	0.671	0.937	CLONAL	1	TRUE	1	0.249681756963949	2		249	452	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517878	8517878	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	73	540	0	ENST00000356435.5:c.1513A>C	p.Ser505Arg	p.S505R	ENST00000356435		505	Agt/Cgt	10/35	1	2	FACETS	0.658	0.574	0.749	0.658	0.574	0.749	SUBCLONAL	1	TRUE	1	0.249681756963949	2		540	889	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342807	87342807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	51	365	0	ENST00000277120.3:c.1092G>T	p.Lys364Asn	p.K364N	ENST00000277120		364	aaG/aaT	9/19	1	2	FACETS	0.62	0.526	0.723	0.62	0.526	0.723	SUBCLONAL	1	TRUE	1	0.249681756963949	2		365	659	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220400	98220400	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	57	457	0	ENST00000331920.6:c.3063C>A	p.Tyr1021Ter	p.Y1021*	ENST00000331920	NM_000264.3	1021	taC/taA	18/24	1	2	FACETS	0.64	0.548	0.741	0.64	0.548	0.741	SUBCLONAL	1	TRUE	1	0.249681756963949	2		457	713	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63810751	63810751	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143185576	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	69	380	1	ENST00000279873.7:c.838G>A	p.Val280Ile	p.V280I	ENST00000279873	NM_032199.2	280	Gtt/Att	5/10	1	2	FACETS	0.822	0.716	0.938	0.822	0.716	0.938	CLONAL	1	TRUE	1	0.249681756963949	2		381	672	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405725	70405725	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	46	348	0	ENST00000373644.4:c.3239A>C	p.Gln1080Pro	p.Q1080P	ENST00000373644	NM_030625.2	1080	cAg/cCg	4/12	1	2	FACETS	0.689	0.58	0.809	0.689	0.58	0.809	SUBCLONAL	1	TRUE	1	0.249681756963949	2		348	535	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405915	70405915	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1430579993	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	102	538	3	ENST00000373644.4:c.3429G>T	p.Lys1143Asn	p.K1143N	ENST00000373644	NM_030625.2	1143	aaG/aaT	4/12	1	2	FACETS	0.742	0.662	0.828	0.742	0.662	0.828	SUBCLONAL	1	TRUE	1	0.249681756963949	2		541	1101	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920404	114920404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	116	578	1	ENST00000543371.1:c.1345G>A	p.Ala449Thr	p.A449T	ENST00000543371	NM_001198531.1	449	Gca/Aca	13/14	1	2	FACETS	0.793	0.713	0.879	0.793	0.713	0.879	SUBCLONAL	1	TRUE	1	0.249681756963949	2		579	1171	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741781	17741781	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1188761200	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	56	354	0	ENST00000250003.3:c.452G>A	p.Arg151His	p.R151H	ENST00000250003	NM_002478.4	151	cGc/cAc	1/3	1	2	FACETS	0.822	0.704	0.95	0.822	0.704	0.95	CLONAL	1	TRUE	1	0.249681756963949	2		354	546	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742907	17742907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	33	251	0	ENST00000250003.3:c.815C>T	p.Ala272Val	p.A272V	ENST00000250003	NM_002478.4	272	gCg/gTg	3/3	1	2	FACETS	0.915	0.748	1	0.915	0.748	1	CLONAL	1	TRUE	1	0.249681756963949	2		251	289	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625274	69625274	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	87	591	0	ENST00000334134.2:c.519G>T	p.Gln173His	p.Q173H	ENST00000334134	NM_005247.2	173	caG/caT	3/3	1	2	FACETS	0.911	0.806	1	0.911	0.806	1	CLONAL	1	TRUE	1	0.249681756963949	2		591	765	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631101	69631101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150581924	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	73	607	1	ENST00000334134.2:c.311G>A	p.Arg104Gln	p.R104Q	ENST00000334134	NM_005247.2	104	cGa/cAa	2/3	1	2	FACETS	0.663	0.578	0.754	0.663	0.578	0.754	SUBCLONAL	1	TRUE	1	0.249681756963949	2		608	882	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999560	100999560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778465984	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	109	728	0	ENST00000325455.5:c.242C>T	p.Ser81Leu	p.S81L	ENST00000325455	NM_001202474.3	81	tCg/tTg	1/8	1	2	FACETS	0.808	0.724	0.897	0.808	0.724	0.897	CLONAL	1	TRUE	1	0.249681756963949	2		728	1081	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098519	108098519	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs876658520	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	33	236	0	ENST00000278616.4:c.89T>G	p.Phe30Cys	p.F30C	ENST00000278616	NM_000051.3	30	tTt/tGt	3/63	1	2	FACETS	0.533	0.433	0.645	0.533	0.433	0.645	SUBCLONAL	1	TRUE	1	0.249681756963949	2		236	496	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204660	108204660	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	43	219	0	ENST00000278616.4:c.7975T>G	p.Leu2659Val	p.L2659V	ENST00000278616	NM_000051.3	2659	Tta/Gta	54/63	1	2	FACETS	0.643	0.537	0.76	0.643	0.537	0.76	SUBCLONAL	1	TRUE	1	0.249681756963949	2		219	536	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992143	11992143	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	62	440	0	ENST00000396373.4:c.233C>A	p.Ser78Tyr	p.S78Y	ENST00000396373	NM_001987.4	78	tCt/tAt	3/8	1	2	FACETS	0.708	0.611	0.814	0.708	0.611	0.814	SUBCLONAL	1	TRUE	1	0.249681756963949	2		440	701	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435486	18435486	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	58	318	0	ENST00000266497.5:c.471G>T	p.Glu157Asp	p.E157D	ENST00000266497		157	gaG/gaT	1/31	1	2	FACETS	0.839	0.721	0.967	0.839	0.721	0.967	CLONAL	1	TRUE	1	0.249681756963949	2		318	554	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793432	18793432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs187869576	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	107	510	1	ENST00000266497.5:c.4129C>T	p.Arg1377Cys	p.R1377C	ENST00000266497		1377	Cgt/Tgt	30/31	1	2	FACETS	0.946	0.848	1	0.946	0.848	1	CLONAL	1	TRUE	1	0.249681756963949	2		511	906	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	49	380	1	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.544	0.46	0.638	0.544	0.46	0.638	SUBCLONAL	1	TRUE	1	0.249681756963949	2		381	721	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944867	31944867	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	68	422	0	ENST00000340398.3:c.234C>A	p.Phe78Leu	p.F78L	ENST00000340398	NM_001013699.2	78	ttC/ttA	1/1	1	2	FACETS	0.83	0.722	0.948	0.83	0.722	0.948	CLONAL	1	TRUE	1	0.249681756963949	2		422	656	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445815	49445815	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	108	738	1	ENST00000301067.7:c.1651G>T	p.Glu551Ter	p.E551*	ENST00000301067	NM_003482.3	551	Gaa/Taa	10/54	1	2	FACETS	0.815	0.73	0.906	0.815	0.73	0.906	CLONAL	1	TRUE	1	0.249681756963949	2		739	1061	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861149	57861149	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774058977	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	123	701	0	ENST00000228682.2:c.946G>A	p.Glu316Lys	p.E316K	ENST00000228682	NM_005269.2	316	Gaa/Aaa	9/12	1	2	FACETS	0.864	0.779	0.953	0.864	0.779	0.953	CLONAL	1	TRUE	1	0.249681756963949	2		701	1141	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885467	111885467	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs918140013	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	84	574	0	ENST00000341259.2:c.1244G>A	p.Arg415His	p.R415H	ENST00000341259	NM_005475.2	415	cGc/cAc	7/8	1	2	FACETS	0.83	0.732	0.935	0.83	0.732	0.935	CLONAL	1	TRUE	1	0.249681756963949	2		574	811	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218920	133218920	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	109	600	0	ENST00000320574.5:c.5016C>A	p.Phe1672Leu	p.F1672L	ENST00000320574	NM_006231.2	1672	ttC/ttA	38/49	1	2	FACETS	0.917	0.822	1	0.917	0.822	1	CLONAL	1	TRUE	1	0.249681756963949	2		600	952	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249847	133249847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	36	387	0	ENST00000320574.5:c.1376C>T	p.Ser459Phe	p.S459F	ENST00000320574	NM_006231.2	459	tCt/tTt	14/49	1	2	FACETS	0.524	0.43	0.63	0.524	0.43	0.63	SUBCLONAL	1	TRUE	1	0.249681756963949	2		387	550	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253217	133253217	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1565976801	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	72	447	0	ENST00000320574.5:c.824A>G	p.Asp275Gly	p.D275G	ENST00000320574	NM_006231.2	275	gAc/gGc	9/49	1	2	FACETS	0.791	0.69	0.9	0.791	0.69	0.9	SUBCLONAL	1	TRUE	1	0.249681756963949	2		447	729	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636175	28636175	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764656426	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	57	454	3	ENST00000241453.7:c.197C>T	p.Ala66Val	p.A66V	ENST00000241453	NM_004119.2	66	gCg/gTg	3/24	1	2	FACETS	0.642	0.55	0.743	0.642	0.55	0.743	SUBCLONAL	1	TRUE	1	0.249681756963949	2		457	711	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28644705	28644705	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	55	350	0	ENST00000241453.7:c.88C>A	p.Leu30Met	p.L30M	ENST00000241453	NM_004119.2	30	Ctg/Atg	2/24	1	2	FACETS	0.563	0.481	0.654	0.563	0.481	0.654	SUBCLONAL	1	TRUE	1	0.249681756963949	2		350	782	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893587	28893587	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	55	429	0	ENST00000282397.4:c.3259G>T	p.Val1087Leu	p.V1087L	ENST00000282397	NM_002019.4	1087	Gta/Tta	24/30	1	2	FACETS	0.543	0.463	0.63	0.543	0.463	0.63	SUBCLONAL	1	TRUE	1	0.249681756963949	2		429	812	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895689	28895689	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	52	462	0	ENST00000282397.4:c.3085C>A	p.Leu1029Ile	p.L1029I	ENST00000282397	NM_002019.4	1029	Ctt/Att	23/30	1	2	FACETS	0.465	0.395	0.543	0.465	0.395	0.543	SUBCLONAL	1	TRUE	1	0.249681756963949	2		462	895	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28963966	28963966	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	83	480	0	ENST00000282397.4:c.1936G>T	p.Glu646Ter	p.E646*	ENST00000282397	NM_002019.4	646	Gaa/Taa	13/30	1	2	FACETS	0.8	0.705	0.902	0.8	0.705	0.902	CLONAL	1	TRUE	1	0.249681756963949	2		480	831	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911141	32911141	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1287	145	785	1	ENST00000380152.3:c.2649C>A	p.Phe883Leu	p.F883L	ENST00000380152		883	ttC/ttA	11/27	1	2	FACETS	0.811	0.737	0.889	0.811	0.737	0.889	CLONAL	1	TRUE	1	0.249681756963949	2		786	1432	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911354	32911354	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	111	785	4	ENST00000380152.3:c.2862G>T	p.Glu954Asp	p.E954D	ENST00000380152		954	gaG/gaT	11/27	1	2	FACETS	0.675	0.604	0.75	0.675	0.604	0.75	SUBCLONAL	1	TRUE	1	0.249681756963949	2		789	1318	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912323	32912323	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs879255303	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	88	610	0	ENST00000380152.3:c.3831T>G	p.Asn1277Lys	p.N1277K	ENST00000380152		1277	aaT/aaG	11/27	1	2	FACETS	0.647	0.571	0.728	0.647	0.571	0.728	SUBCLONAL	1	TRUE	1	0.249681756963949	2		610	1090	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913309	32913309	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1306	133	801	0	ENST00000380152.3:c.4817C>A	p.Ser1606Tyr	p.S1606Y	ENST00000380152		1606	tCt/tAt	11/27	1	2	FACETS	0.74	0.67	0.815	0.74	0.67	0.815	SUBCLONAL	1	TRUE	1	0.249681756963949	2		801	1439	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913522	32913522	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs375304428	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	106	715	4	ENST00000380152.3:c.5030G>T	p.Arg1677Ile	p.R1677I	ENST00000380152		1677	aGa/aTa	11/27	1	2	FACETS	0.641	0.572	0.714	0.641	0.572	0.714	SUBCLONAL	1	TRUE	1	0.249681756963949	2		719	1325	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914505	32914505	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587781760	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1217	93	772	2	ENST00000380152.3:c.6013G>T	p.Asp2005Tyr	p.D2005Y	ENST00000380152		2005	Gat/Tat	11/27	1	2	FACETS	0.569	0.504	0.639	0.569	0.504	0.639	SUBCLONAL	1	TRUE	1	0.249681756963949	2		774	1310	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914877	32914877	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs886040653	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1240	133	783	2	ENST00000380152.3:c.6385G>T	p.Glu2129Ter	p.E2129*	ENST00000380152		2129	Gaa/Taa	11/27	1	2	FACETS	0.776	0.702	0.854	0.776	0.702	0.854	SUBCLONAL	1	TRUE	1	0.249681756963949	2		785	1373	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937339	32937339	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	49	316	1	ENST00000380152.3:c.8000G>T	p.Ser2667Ile	p.S2667I	ENST00000380152		2667	aGc/aTc	18/27	1	2	FACETS	0.762	0.646	0.89	0.762	0.646	0.89	SUBCLONAL	1	TRUE	1	0.249681756963949	2		317	515	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941654	48941654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776534331	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	56	302	1	ENST00000267163.4:c.964G>A	p.Glu322Lys	p.E322K	ENST00000267163	NM_000321.2	322	Gaa/Aaa	10/27	1	2	FACETS	0.624	0.533	0.723	0.624	0.533	0.723	SUBCLONAL	1	TRUE	1	0.249681756963949	2		303	719	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953748	48953748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759079385	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	46	304	0	ENST00000267163.4:c.1351C>T	p.Arg451Cys	p.R451C	ENST00000267163	NM_000321.2	451	Cgc/Tgc	14/27	1	2	FACETS	0.658	0.554	0.773	0.658	0.554	0.773	SUBCLONAL	1	TRUE	1	0.249681756963949	2		304	560	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030396	49030396	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	44	331	1	ENST00000267163.4:c.1871C>A	p.Ser624Tyr	p.S624Y	ENST00000267163	NM_000321.2	624	tCt/tAt	19/27	1	2	FACETS	0.5	0.418	0.591	0.5	0.418	0.591	SUBCLONAL	1	TRUE	1	0.249681756963949	2		332	705	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504590	103504590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1400329743	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	90	493	0	ENST00000355739.4:c.211C>T	p.Arg71Cys	p.R71C	ENST00000355739	NM_000123.3	71	Cgt/Tgt	2/15	1	2	FACETS	0.769	0.681	0.864	0.769	0.681	0.864	SUBCLONAL	1	TRUE	1	0.249681756963949	2		493	937	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873726	35873726	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	95	595	2	ENST00000216797.5:c.125A>G	p.Tyr42Cys	p.Y42C	ENST00000216797	NM_020529.2	42	tAc/tGc	1/6	1	2	FACETS	0.886	0.788	0.991	0.886	0.788	0.991	CLONAL	1	TRUE	1	0.249681756963949	2		597	859	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81558897	81558897	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	70	448	0	ENST00000298171.2:c.490A>G	p.Met164Val	p.M164V	ENST00000298171	NM_000369.2	164	Atg/Gtg	6/10	1	2	FACETS	0.697	0.606	0.794	0.697	0.606	0.794	SUBCLONAL	1	TRUE	1	0.249681756963949	2		448	805	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574344	95574344	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	51	393	0	ENST00000393063.1:c.2523A>C	p.Gln841His	p.Q841H	ENST00000393063	NM_030621.3	841	caA/caC	17/28	1	2	FACETS	0.617	0.524	0.72	0.617	0.524	0.72	SUBCLONAL	1	TRUE	1	0.249681756963949	2		393	662	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582831	95582831	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	59	398	0	ENST00000393063.1:c.1711A>C	p.Ser571Arg	p.S571R	ENST00000393063	NM_030621.3	571	Agt/Cgt	11/28	1	2	FACETS	0.666	0.572	0.768	0.666	0.572	0.768	SUBCLONAL	1	TRUE	1	0.249681756963949	2		398	710	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95596487	95596487	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs373532001	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	49	336	0	ENST00000393063.1:c.481A>C	p.Asn161His	p.N161H	ENST00000393063	NM_030621.3	161	Aat/Cat	6/28	1	2	FACETS	0.612	0.518	0.717	0.612	0.518	0.717	SUBCLONAL	1	TRUE	1	0.249681756963949	2		336	641	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42050032	42050032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	74	484	0	ENST00000219905.7:c.7186C>T	p.Arg2396Ter	p.R2396*	ENST00000219905	NM_001164273.1	2396	Cga/Tga	19/24	1	2	FACETS	0.655	0.572	0.745	0.655	0.572	0.745	SUBCLONAL	1	TRUE	1	0.249681756963949	2		484	905	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007743	45007743	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	64	379	2	ENST00000558401.1:c.190G>T	p.Glu64Ter	p.E64*	ENST00000558401	NM_004048.2	64	Gag/Tag	2/4	1	2	FACETS	0.713	0.617	0.818	0.713	0.617	0.818	SUBCLONAL	1	TRUE	1	0.249681756963949	2		381	719	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007814	45007814	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	60	377	0	ENST00000558401.1:c.261C>A	p.Tyr87Ter	p.Y87*	ENST00000558401	NM_004048.2	87	taC/taA	2/4	1	2	FACETS	0.721	0.62	0.83	0.721	0.62	0.83	SUBCLONAL	1	TRUE	1	0.249681756963949	2		377	667	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473723	67473723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223740	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	54	499	0	ENST00000327367.4:c.803G>A	p.Arg268His	p.R268H	ENST00000327367	NM_005902.3	268	cGc/cAc	6/9	1	2	FACETS	0.609	0.519	0.708	0.609	0.519	0.708	SUBCLONAL	1	TRUE	1	0.249681756963949	2		499	710	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996053	73996053	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465926642	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	31	325	0	ENST00000318443.5:c.787G>A	p.Asp263Asn	p.D263N	ENST00000318443	NM_001024736.1	263	Gat/Aat	5/10	1	2	FACETS	0.474	0.382	0.578	0.474	0.382	0.578	SUBCLONAL	1	TRUE	1	0.249681756963949	2		325	524	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423598	88423598	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	54	445	0	ENST00000360948.2:c.2237A>C	p.Lys746Thr	p.K746T	ENST00000360948	NM_001012338.2	746	aAg/aCg	18/19	1	2	FACETS	0.612	0.522	0.711	0.612	0.522	0.711	SUBCLONAL	1	TRUE	1	0.249681756963949	2		445	707	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727513	88727513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374069724	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	50	515	1	ENST00000360948.2:c.266G>A	p.Arg89His	p.R89H	ENST00000360948	NM_001012338.2	89	cGc/cAc	3/19	1	2	FACETS	0.576	0.488	0.674	0.576	0.488	0.674	SUBCLONAL	1	TRUE	1	0.249681756963949	2		516	695	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292902	91292902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	57	349	0	ENST00000355112.3:c.404C>T	p.Ala135Val	p.A135V	ENST00000355112	NM_000057.2	135	gCt/gTt	3/22	1	2	FACETS	0.681	0.584	0.788	0.681	0.584	0.788	SUBCLONAL	1	TRUE	1	0.249681756963949	2		349	670	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820846	3820846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	46	389	1	ENST00000262367.5:c.2605C>T	p.Leu869Phe	p.L869F	ENST00000262367	NM_004380.2	869	Ctc/Ttc	14/31	1	2	FACETS	0.675	0.568	0.793	0.675	0.568	0.793	SUBCLONAL	1	TRUE	1	0.249681756963949	2		390	546	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900884	3900884	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	85	497	0	ENST00000262367.5:c.212C>T	p.Ser71Leu	p.S71L	ENST00000262367	NM_004380.2	71	tCg/tTg	2/31	1	2	FACETS	0.828	0.731	0.933	0.828	0.731	0.933	CLONAL	1	TRUE	1	0.249681756963949	2		497	822	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923465	9923465	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	64	458	2	ENST00000330684.3:c.1822C>A	p.Leu608Ile	p.L608I	ENST00000330684	NM_001134407.1	608	Ctt/Att	9/13	1	2	FACETS	0.656	0.567	0.753	0.656	0.567	0.753	SUBCLONAL	1	TRUE	1	0.249681756963949	2		460	781	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829797	72829797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs953863150	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	113	808	0	ENST00000268489.5:c.6784G>A	p.Asp2262Asn	p.D2262N	ENST00000268489	NM_006885.3	2262	Gat/Aat	9/10	1	2	FACETS	0.747	0.671	0.829	0.747	0.671	0.829	SUBCLONAL	1	TRUE	1	0.249681756963949	2		808	1211	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845844	72845844	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760400785	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	134	803	0	ENST00000268489.5:c.3623C>T	p.Ser1208Leu	p.S1208L	ENST00000268489	NM_006885.3	1208	tCg/tTg	6/10	1	2	FACETS	0.919	0.833	1	0.919	0.833	1	CLONAL	1	TRUE	1	0.249681756963949	2		803	1168	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576889	7576889	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	76	446	0	ENST00000269305.4:c.957G>T	p.Lys319Asn	p.K319N	ENST00000269305	NM_001126112.2	319	aaG/aaT	9/11	1	2	FACETS	0.798	0.699	0.904	0.798	0.699	0.904	CLONAL	1	TRUE	1	0.249681756963949	2		446	763	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577575	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587782289	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	66	478	0	ENST00000269305.4:c.706T>G	p.Tyr236Asp	p.Y236D	ENST00000269305	NM_001126112.2	236	Tac/Gac	7/11	1	2	FACETS	0.686	0.594	0.785	0.686	0.594	0.785	SUBCLONAL	1	TRUE	1	0.249681756963949	2		478	771	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984773	11984773	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	41	248	1	ENST00000353533.5:c.319G>T	p.Glu107Ter	p.E107*	ENST00000353533	NM_003010.3	107	Gaa/Taa	3/11	1	2	FACETS	0.711	0.592	0.843	0.711	0.592	0.843	SUBCLONAL	1	TRUE	1	0.249681756963949	2		249	462	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942944	15942944	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	70	480	0	ENST00000268712.3:c.6758C>A	p.Ser2253Tyr	p.S2253Y	ENST00000268712	NM_006311.3	2253	tCt/tAt	44/46	1	2	FACETS	0.79	0.688	0.9	0.79	0.688	0.9	SUBCLONAL	1	TRUE	1	0.249681756963949	2		480	710	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004601	16004601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1406850631	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	48	457	1	ENST00000268712.3:c.2653G>A	p.Ala885Thr	p.A885T	ENST00000268712	NM_006311.3	885	Gct/Act	20/46	1	2	FACETS	0.586	0.495	0.687	0.586	0.495	0.687	SUBCLONAL	1	TRUE	1	0.249681756963949	2		458	656	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592269	29592269	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	70	399	0	ENST00000356175.3:c.4684G>T	p.Glu1562Ter	p.E1562*	ENST00000356175	NM_000267.3	1562	Gaa/Taa	35/57	1	2	FACETS	0.782	0.681	0.891	0.782	0.681	0.891	SUBCLONAL	1	TRUE	1	0.249681756963949	2		399	717	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684332	29684332	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	89	508	0	ENST00000356175.3:c.7852C>A	p.Leu2618Ile	p.L2618I	ENST00000356175	NM_000267.3	2618	Ctt/Att	53/57	1	2	FACETS	0.731	0.647	0.822	0.731	0.647	0.822	SUBCLONAL	1	TRUE	1	0.249681756963949	2		508	975	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763428	59763428	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	64	313	0	ENST00000259008.2:c.2674C>A	p.Leu892Ile	p.L892I	ENST00000259008	NM_032043.2	892	Ctt/Att	19/20	1	2	FACETS	0.887	0.768	1	0.887	0.768	1	CLONAL	1	TRUE	1	0.249681756963949	2		313	578	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007205	62007205	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	67	501	1	ENST00000392795.3:c.477G>T	p.Lys159Asn	p.K159N	ENST00000392795	NM_001039933.1	159	aaG/aaT	4/6	1	2	FACETS	0.717	0.622	0.819	0.717	0.622	0.819	SUBCLONAL	1	TRUE	1	0.249681756963949	2		502	749	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63537616	63537616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	91	578	0	ENST00000307078.5:c.1016G>A	p.Arg339His	p.R339H	ENST00000307078	NM_004655.3	339	cGc/cAc	4/11	1	2	FACETS	0.725	0.642	0.813	0.725	0.642	0.813	SUBCLONAL	1	TRUE	1	0.249681756963949	2		578	1006	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519919	66519919	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1383865866	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	62	354	1	ENST00000358598.2:c.402G>T	p.Lys134Asn	p.K134N	ENST00000358598	NM_212471.2	134	aaG/aaT	4/11	1	2	FACETS	0.74	0.639	0.851	0.74	0.639	0.851	SUBCLONAL	1	TRUE	1	0.249681756963949	2		355	671	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66525083	66525083	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	49	303	0	ENST00000358598.2:c.842A>C	p.Lys281Thr	p.K281T	ENST00000358598	NM_212471.2	281	aAg/aCg	9/11	1	2	FACETS	0.669	0.566	0.782	0.669	0.566	0.782	SUBCLONAL	1	TRUE	1	0.249681756963949	2		303	587	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604736	48604736	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	68	533	2	ENST00000342988.3:c.1558G>T	p.Glu520Ter	p.E520*	ENST00000342988	NM_005359.5	520	Gaa/Taa	12/12	1	2	FACETS	0.71	0.617	0.811	0.71	0.617	0.811	SUBCLONAL	1	TRUE	1	0.249681756963949	2		535	767	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3114952	3114952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	56	450	0	ENST00000078429.4:c.487G>A	p.Asp163Asn	p.D163N	ENST00000078429	NM_002067.2	163	Gac/Aac	4/7	1	2	FACETS	0.748	0.64	0.865	0.748	0.64	0.865	SUBCLONAL	1	TRUE	1	0.249681756963949	2		450	600	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215400	5215400	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	75	541	0	ENST00000357368.4:c.4218C>A	p.Phe1406Leu	p.F1406L	ENST00000357368	NM_002850.3	1406	ttC/ttA	28/38	1	2	FACETS	0.812	0.711	0.921	0.812	0.711	0.921	CLONAL	1	TRUE	1	0.249681756963949	2		541	740	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170598	7170598	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750676016	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	77	545	0	ENST00000302850.5:c.1433G>A	p.Arg478His	p.R478H	ENST00000302850	NM_000208.2	478	cGc/cAc	6/22	1	2	FACETS	0.678	0.594	0.769	0.678	0.594	0.769	SUBCLONAL	1	TRUE	1	0.249681756963949	2		545	910	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10273402	10273402	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	110	555	0	ENST00000340748.4:c.901G>T	p.Glu301Ter	p.E301*	ENST00000340748		301	Gaa/Taa	12/40	1	2	FACETS	0.862	0.773	0.957	0.862	0.773	0.957	CLONAL	1	TRUE	1	0.249681756963949	2		555	1022	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291473	10291473	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61750053	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	94	583	0	ENST00000340748.4:c.206G>A	p.Arg69His	p.R69H	ENST00000340748		69	cGt/cAt	3/40	1	2	FACETS	0.698	0.619	0.782	0.698	0.619	0.782	SUBCLONAL	1	TRUE	1	0.249681756963949	2		583	1079	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367830	15367830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867596343	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	63	427	0	ENST00000263377.2:c.1496C>T	p.Ser499Leu	p.S499L	ENST00000263377	NM_058243.2	499	tCg/tTg	8/20	1	2	FACETS	0.802	0.694	0.92	0.802	0.694	0.92	CLONAL	1	TRUE	1	0.249681756963949	2		427	629	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792496	33792496	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	48	336	0	ENST00000498907.2:c.825G>T	p.Lys275Asn	p.K275N	ENST00000498907	NM_004364.3	275	aaG/aaT	1/1	1	2	FACETS	0.697	0.588	0.816	0.697	0.588	0.816	SUBCLONAL	1	TRUE	1	0.249681756963949	2		336	552	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796237	42796237	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	49	382	1	ENST00000575354.2:c.2887-1G>T		p.X963_splice	ENST00000575354	NM_015125.3	963			1	2	FACETS	0.71	0.601	0.83	0.71	0.601	0.83	SUBCLONAL	1	TRUE	1	0.249681756963949	2		383	553	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47735857	47735857	+	start_lost	Translation_Start_Site	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	72	620	1	ENST00000449228.1:c.3G>T	p.Met1?	p.M1?	ENST00000449228	NM_001127240.2	1	atG/atT	1/4	1	2	FACETS	0.615	0.536	0.701	0.615	0.536	0.701	SUBCLONAL	1	TRUE	1	0.249681756963949	2		621	938	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022481	31022481	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765459479	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	16	193	0	ENST00000375687.4:c.1966G>A	p.Asp656Asn	p.D656N	ENST00000375687	NM_015338.5	656	Gat/Aat	13/13	1	2	FACETS	0.572	0.423	0.749	0.572	0.423	0.749	SUBCLONAL	1	TRUE	1	0.249681756963949	2		193	224	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389107	31389107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749860839	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	79	602	0	ENST00000328111.2:c.2020G>A	p.Glu674Lys	p.E674K	ENST00000328111	NM_006892.3	674	Gaa/Aaa	19/23	1	2	FACETS	0.847	0.744	0.958	0.847	0.744	0.958	CLONAL	1	TRUE	1	0.249681756963949	2		602	747	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39713125	39713125	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	38	251	0	ENST00000361337.2:c.531G>T	p.Lys177Asn	p.K177N	ENST00000361337	NM_003286.2	177	aaG/aaT	8/21	1	2	FACETS	0.504	0.416	0.603	0.504	0.416	0.603	SUBCLONAL	1	TRUE	1	0.249681756963949	2		251	604	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750375	39750375	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	63	397	2	ENST00000361337.2:c.1990G>T	p.Asp664Tyr	p.D664Y	ENST00000361337	NM_003286.2	664	Gac/Tac	19/21	1	2	FACETS	0.687	0.593	0.789	0.687	0.593	0.789	SUBCLONAL	1	TRUE	1	0.249681756963949	2		399	735	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400138	41400138	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	86	394	0	ENST00000373198.4:c.621G>T	p.Gln207His	p.Q207H	ENST00000373198	NM_133170.3	207	caG/caT	5/32	1	2	FACETS	0.878	0.776	0.987	0.878	0.776	0.987	CLONAL	1	TRUE	1	0.249681756963949	2		394	785	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256358	46256358	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1204	129	830	0	ENST00000371998.3:c.586A>C	p.Asn196His	p.N196H	ENST00000371998		196	Aat/Cat	7/23	1	2	FACETS	0.775	0.701	0.854	0.775	0.701	0.854	SUBCLONAL	1	TRUE	1	0.249681756963949	2		830	1333	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21304066	21304066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444326760	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	99	584	0	ENST00000354336.3:c.845G>A	p.Arg282His	p.R282H	ENST00000354336	NM_005207.3	282	cGc/cAc	3/3	1	2	FACETS	0.822	0.732	0.917	0.822	0.732	0.917	CLONAL	1	TRUE	1	0.249681756963949	2		584	965	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167550	24167550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749348930	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	49	340	0	ENST00000263121.7:c.934G>A	p.Ala312Thr	p.A312T	ENST00000263121	NM_003073.3	312	Gca/Aca	7/9	1	2	FACETS	0.771	0.653	0.901	0.771	0.653	0.901	CLONAL	1	TRUE	1	0.249681756963949	2		340	509	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932139	39932139	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	93	324	0	ENST00000378444.4:c.2460C>A	p.Asn820Lys	p.N820K	ENST00000378444	NM_001123385.1	820	aaC/aaA	4/15	1	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.249681756963949	1		324	543	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934037	39934037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	97	328	1	ENST00000378444.4:c.562C>T	p.Arg188Trp	p.R188W	ENST00000378444	NM_001123385.1	188	Cgg/Tgg	4/15	1	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.249681756963949	1		329	482	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937409	76937409	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	78	272	0	ENST00000373344.5:c.3339G>T	p.Glu1113Asp	p.E1113D	ENST00000373344	NM_000489.3	1113	gaG/gaT	9/35	1	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.249681756963949	1		272	407	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938841	76938841	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	79	318	0	ENST00000373344.5:c.1907A>C	p.Asn636Thr	p.N636T	ENST00000373344	NM_000489.3	636	aAt/aCt	9/35	1	1	FACETS	0.972	0.856	1	0.972	0.856	1	CLONAL	1	TRUE	0	0.249681756963949	1		318	570	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611252	100611252	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	55	158	0	ENST00000308731.7:c.1354C>A	p.Leu452Ile	p.L452I	ENST00000308731	NM_000061.2	452	Ctt/Att	15/19	1	1	FACETS	0.762	0.658	0.873	1	0.969	1	SUBCLONAL	2	TRUE	0	0.249681756963949	1		158	253	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163758	152163758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	444	239	0	ENST00000206249.3:c.479G>A	p.Gly160Asp	p.G160D	ENST00000206249	NM_000125.3	160	gGt/gAt	2/8	1	2	FACETS	0.991	0.949	1	0.991	0.949	1	CLONAL	1	TRUE	1	0.87	2		239	1030	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936073	44936073	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0011373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	562	307	0	ENST00000377967.4:c.2832+2T>C		p.X944_splice	ENST00000377967	NM_021140.2	944			1	2	FACETS	0.95	0.913	0.987	0.95	0.913	0.987	CLONAL	1	TRUE	1	0.87	2		307	1360	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0011376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	382	484	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.834240786640212	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.834240786640212	1		484	472	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40367093	40367093	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	240	465	0	ENST00000397332.2:c.104C>G	p.Ser35Trp	p.S35W	ENST00000397332	NM_001033082.2	35	tCg/tGg	2/3	1	2	FACETS	0.505	0.471	0.54	0.505	0.471	0.54	SUBCLONAL	1	TRUE	1	0.834240786640212	2		465	1140	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61722614	61722614	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	237	341	0	ENST00000401558.2:c.1023A>C	p.Leu341Phe	p.L341F	ENST00000401558	NM_003400.3	341	ttA/ttC	11/25	0.713917755105569	3	FACETS	0.614	0.571	0.657			1	SUBCLONAL	1	TRUE	NA	0.834240786640212	3		341	1312	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827783	72827783	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1419	394	490	0	ENST00000268489.5:c.8798C>G	p.Ser2933Cys	p.S2933C	ENST00000268489	NM_006885.3	2933	tCt/tGt	9/10	NA	2	FACETS	0.521	0.494	0.549			1	INDETERMINATE	1	TRUE	NA	0.834240786640212	2		490	1813	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468071	50468071	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770657999	NA	P-0011405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	282	264	0	ENST00000331340.3:c.1306G>A	p.Asp436Asn	p.D436N	ENST00000331340	NM_006060.4	436	Gac/Aac	8/8	0.30530199664724	4	FACETS	0.766	0.723	0.81	0.766	0.723	0.81	INDETERMINATE	2	TRUE	2	0.85877984342937	4		264	797	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87322773	87322773	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	359	272	0	ENST00000277120.3:c.374A>G	p.Asn125Ser	p.N125S	ENST00000277120		125	aAc/aGc	5/19	0.222548278331106	4	FACETS	0.916	0.873	0.96	0.916	0.873	0.96	INDETERMINATE	2	TRUE	2	0.85877984342937	4		272	848	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135301	2135301	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs397514988	NA	P-0011405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	516	368	0	ENST00000219476.3:c.4640T>A	p.Val1547Asp	p.V1547D	ENST00000219476	NM_000548.3	1547	gTc/gAc	36/42	0.85877984342937	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.85877984342937	1		368	656	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511686	66511708	+	frameshift_variant	Frame_Shift_Del	DEL	TCCTCAGGGAATACTTTGAGAGG	TCCTCAGGGAATACTTTGAGAGG	-	novel	NA	P-0011405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	186	269	0	ENST00000358598.2:c.147_169del	p.Leu50GlyfsTer24	p.L50Gfs*24	ENST00000358598	NM_212471.2	49	tTCCTCAGGGAATACTTTGAGAGG/t	2/11	0.85877984342937	1	FACETS	0.954	0.909	0.997	0.954	0.909	0.997	CLONAL	1	TRUE	0	0.85877984342937	1		269	259	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0011413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	98	416	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	1	2	FACETS	0.699	0.622	0.782	0.699	0.622	0.782	SUBCLONAL	1	TRUE	1	0.258770598999428	2		416	1083	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40444033	40444033	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202112433	NA	P-0011413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1484	101	1004	0	ENST00000345506.4:c.329G>A	p.Arg110Gln	p.R110Q	ENST00000345506	NM_003152.3	110	cGg/cAg	5/20	0.258770598999428	1	FACETS	0.429	0.381	0.48	0.429	0.381	0.48	SUBCLONAL	1	TRUE	0	0.258770598999428	1		1004	1585	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0011447-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	310	698	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.693454823733626	2		698	883	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752616	128752756	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTGATTTCTATTTCCTTTCTTAAAGAGGAGGAACAAGAAGATGAGGAAGAAATCGATGTTGTTTCTGTGGAAAAGAGGCAGGCTCCTGGCAAAAGGTCAGAGTCTGGATCACCTTCTGCTGGAGGCCACAGCAAACCTCC	AGTGATTTCTATTTCCTTTCTTAAAGAGGAGGAACAAGAAGATGAGGAAGAAATCGATGTTGTTTCTGTGGAAAAGAGGCAGGCTCCTGGCAAAAGGTCAGAGTCTGGATCACCTTCTGCTGGAGGCCACAGCAAACCTCC	-	novel	NA	P-0011447-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3010	1714	314	0	ENST00000377970.2:c.803-26_917del		p.X268_splice	ENST00000377970	NM_002467.4	268		3/3	0.693454823733626	24	FACETS	1	0.98	1			1	CLONAL	9	TRUE	NA	0.693454823733626	24		314	4724	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0011454-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	95	324	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.201059596226549	1	FACETS	0.787	0.7	0.88	0.787	0.7	0.88	SUBCLONAL	1	TRUE	0	0.237487681072481	1		324	896	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	1263	338	0	ENST00000269305.4:c.799C>G	p.Arg267Gly	p.R267G	ENST00000269305	NM_001126112.2	267	Cgg/Ggg	8/11	0.812341385236524	3	FACETS	1	0.998	1	1	0.998	1	CLONAL	3	TRUE	0	0.812341385236524	3		338	1363	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935327	36935327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1302283819	NA	P-0011456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1582	183	449	0	ENST00000361632.4:c.1400C>T	p.Pro467Leu	p.P467L	ENST00000361632		467	cCc/cTc	10/16	0.812341385236524	3	FACETS	0.359	0.33	0.39	0.179	0.165	0.195	SUBCLONAL	1	TRUE	1	0.812341385236524	3		449	1765	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163853	47163853	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	369	263	0	ENST00000409792.3:c.2273A>G	p.Asp758Gly	p.D758G	ENST00000409792	NM_014159.6	758	gAt/gGt	3/21	0.198250201877449	6	FACETS	0.958	0.908	1			1	INDETERMINATE	2	TRUE	NA	0.812341385236524	6		263	1245	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200751	128200751	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs797045591	NA	P-0011456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	663	297	0	ENST00000341105.2:c.1054T>C	p.Cys352Arg	p.C352R	ENST00000341105	NM_032638.4	352	Tgt/Cgt	5/6	0.812341385236524	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.812341385236524	3		297	1125	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340201	116340201	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	127	236	0	ENST00000397752.3:c.1063G>C	p.Glu355Gln	p.E355Q	ENST00000397752	NM_000245.2	355	Gaa/Caa	2/21	0.812341385236524	3	FACETS	0.447	0.404	0.493	0.224	0.202	0.247	SUBCLONAL	1	TRUE	1	0.812341385236524	3		236	983	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631192	69631192	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0011456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	346	374	0	ENST00000334134.2:c.221-1G>C		p.X74_splice	ENST00000334134	NM_005247.2	74			1	2	FACETS	0.966	0.918	1	0.966	0.918	1	CLONAL	1	TRUE	1	0.812341385236524	2		374	882	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984024	7984024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	677	202	0	ENST00000319144.4:c.602G>A	p.Arg201His	p.R201H	ENST00000319144	NM_001139.2	201	cGc/cAc	5/15	0.812341385236524	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.812341385236524	3		202	766	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044563	12044563	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	954	268	0	ENST00000353533.5:c.1186A>T	p.Met396Leu	p.M396L	ENST00000353533	NM_003010.3	396	Atg/Ttg	11/11	0.812341385236524	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.812341385236524	3		268	1054	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910270	50910270	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	1096	498	0	ENST00000440232.2:c.1525G>C	p.Ala509Pro	p.A509P	ENST00000440232	NM_002691.3	509	Gct/Cct	13/27	0.619132417197423	4	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	2	0.812341385236524	4		498	2218	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944559	40944559	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	472	222	0	ENST00000373198.4:c.1943T>G	p.Val648Gly	p.V648G	ENST00000373198	NM_133170.3	648	gTg/gGg	12/32	0.619132417197423	4	FACETS	0.992	0.952	1	0.992	0.952	1	CLONAL	2	TRUE	2	0.812341385236524	4		222	1061	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434152	121434153	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0011456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	390	340	0	ENST00000257555.6:c.1043_1044delinsAA	p.Leu348Gln	p.L348Q	ENST00000257555		348	cTC/cAA	5/10	0.812341385236524	3	FACETS	1	0.967	1	0.511	0.486	0.538	CLONAL	1	TRUE	1	0.812341385236524	3		340	1320	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0011457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	175	365	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.349272610089517	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.349272610089517	2		365	475	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519999	NA	P-0011457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	116	443	0	ENST00000269305.4:c.716A>G	p.Asn239Ser	p.N239S	ENST00000269305	NM_001126112.2	239	aAc/aGc	7/11	0.308639286563995	1	FACETS	0.818	0.739	0.902	0.818	0.739	0.902	CLONAL	1	TRUE	0	0.349272610089517	1		443	670	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106771	27106771	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	106	499	0	ENST00000324856.7:c.6382C>T	p.Gln2128Ter	p.Q2128*	ENST00000324856	NM_006015.4	2128	Cag/Tag	20/20	0.308639286563995	1	FACETS	0.774	0.695	0.858	0.774	0.695	0.858	SUBCLONAL	1	TRUE	0	0.349272610089517	1		499	647	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182615	99182615	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	70	298	0	ENST00000074304.5:c.2418G>T	p.Gln806His	p.Q806H	ENST00000074304	NM_001134224.1	806	caG/caT	22/26	1	2	FACETS	0.775	0.677	0.881	0.775	0.677	0.881	SUBCLONAL	1	TRUE	1	0.349272610089517	2		298	517	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434523	140434523	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	151	369	1	ENST00000288602.6:c.2175C>A	p.His725Gln	p.H725Q	ENST00000288602	NM_004333.4	725	caC/caA	18/18	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.349272610089517	2		370	772	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372435	55372435	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	163	580	0	ENST00000297316.4:c.1125G>T	p.Met375Ile	p.M375I	ENST00000297316	NM_022454.3	375	atG/atT	2/2	0.293711773970576	3	FACETS	1	0.923	1	0.504	0.462	0.548	CLONAL	1	TRUE	1	0.349272610089517	3		580	1088	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390302	56390302	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1304	186	611	0	ENST00000348428.3:c.1041G>C	p.Leu347Phe	p.L347F	ENST00000348428	NM_006785.3	347	ttG/ttC	10/17	1	2	FACETS	0.715	0.658	0.774	0.715	0.658	0.774	SUBCLONAL	1	TRUE	1	0.349272610089517	2		611	1490	SUCCESS
EED	8726	MSKCC	GRCh37	11	85963214	85963214	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	112	290	0	ENST00000263360.6:c.293del	p.Gly98GlufsTer14	p.G98Efs*14	ENST00000263360	NM_003797.3	98	Gga/ga	3/12	1	2	FACETS	0.92	0.828	1	0.92	0.828	1	CLONAL	1	TRUE	1	0.349272610089517	2		290	697	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294123	1294123	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	88	489	0	ENST00000310581.5:c.878del	p.Arg293ProfsTer58	p.R293Pfs*58	ENST00000310581	NM_198253.2	293	cGc/cc	2/16	0.293711773970576	3	FACETS	0.775	0.686	0.87	0.387	0.343	0.435	SUBCLONAL	1	TRUE	1	0.349272610089517	3		489	764	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435199	49435200	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	A	novel	NA	P-0011457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	72	228	0	ENST00000301067.7:c.6353_6354delinsT	p.Pro2118LeufsTer26	p.P2118Lfs*26	ENST00000301067	NM_003482.3	2118	cCC/cT	31/54	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.349272610089517	2		228	310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0011463-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	129	397	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	0.691554109901189	1	FACETS	0.866	0.799	0.932	0.866	0.799	0.932	CLONAL	1	TRUE	0	0.691554109901189	1		397	282	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584497	48584497	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011463-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	106	257	1	ENST00000342988.3:c.670C>T	p.Gln224Ter	p.Q224*	ENST00000342988	NM_005359.5	224	Cag/Tag	6/12	0.691554109901189	1	FACETS	0.92	0.844	0.996	0.92	0.844	0.996	CLONAL	1	TRUE	0	0.691554109901189	1		258	218	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430004	78430004	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011463-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	79	250	0	ENST00000370768.2:c.875G>C	p.Gly292Ala	p.G292A	ENST00000370768	NM_003902.3	292	gGa/gCa	11/20	NA	2	FACETS	0.712	0.632	0.796			1	INDETERMINATE	1	TRUE	NA	0.691554109901189	2		250	321	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201902	152201902	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1338119193	NA	P-0011463-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	159	244	0	ENST00000206249.3:c.756A>T	p.Lys252Asn	p.K252N	ENST00000206249	NM_000125.3	252	aaA/aaT	3/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.691554109901189	2		244	419	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619326	23619326	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs863224785	NA	P-0011463-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	219	417	0	ENST00000261584.4:c.3209T>C	p.Leu1070Pro	p.L1070P	ENST00000261584	NM_024675.3	1070	cTc/cCc	12/13	0.691554109901189	1	FACETS	0.97	0.916	1	0.97	0.916	1	CLONAL	1	TRUE	0	0.691554109901189	1		417	427	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409892	63409892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011463-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	614	557	1	ENST00000330258.3:c.3275C>T	p.Pro1092Leu	p.P1092L	ENST00000330258	NM_152424.3	1092	cCt/cTt	2/2	0.691554109901189	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.691554109901189	3		558	1138	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223843	53223843	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011463-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	340	656	1	ENST00000375401.3:c.3516del	p.Ser1173ValfsTer91	p.S1173Vfs*91	ENST00000375401	NM_004187.3	1172	ccC/cc	23/26	0.691554109901189	1	FACETS	0.935	0.892	0.978	0.935	0.892	0.978	CLONAL	1	TRUE	0	0.691554109901189	1		657	688	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289151	33289151	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs367710814	NA	P-0011464-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	316	340	0	ENST00000374542.5:c.401T>C	p.Leu134Pro	p.L134P	ENST00000374542	NM_001141970.1	134	cTc/cCc	3/8	0.783296178834894	2	FACETS	0.802	0.77	0.833	0.802	0.77	0.833	CLONAL	2	TRUE	0	0.81926085724723	2		340	481	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554919	106554919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368754839	NA	P-0011464-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	26	299	0	ENST00000369096.4:c.2036G>A	p.Arg679His	p.R679H	ENST00000369096	NM_001198.3	679	cGt/cAt	7/7	0.783296178834894	2	FACETS	0.126	0.099	0.157	0.063	0.049	0.079	SUBCLONAL	1	TRUE	0	0.81926085724723	2		299	504	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574482	64574482	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs398124437	NA	P-0011464-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	221	337	0	ENST00000312049.6:c.912+1G>A		p.X304_splice	ENST00000312049	NM_130799.2	304			0.81926085724723	1	FACETS	0.918	0.873	0.962	0.918	0.873	0.962	CLONAL	1	TRUE	0	0.81926085724723	1		337	347	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011473-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	181	389	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.971	0.9	1	0.971	0.9	1	CLONAL	1	TRUE	1	0.624642499214148	2		389	597	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152093	55152093	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121908585	NA	P-0011473-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	155	449	0	ENST00000257290.5:c.2525A>T	p.Asp842Val	p.D842V	ENST00000257290	NM_006206.4	842	gAc/gTc	18/23	1	2	FACETS	0.448	0.409	0.489	0.448	0.409	0.489	SUBCLONAL	1	TRUE	1	0.624642499214148	2		449	1107	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540332	187540332	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011473-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	309	420	1	ENST00000441802.2:c.7408G>A	p.Gly2470Arg	p.G2470R	ENST00000441802	NM_005245.3	2470	Gga/Aga	10/27	1	2	FACETS	0.994	0.939	1	0.994	0.939	1	CLONAL	1	TRUE	1	0.624642499214148	2		421	995	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658296	18658296	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371412006	NA	P-0011473-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	233	386	1	ENST00000266497.5:c.3101G>A	p.Arg1034His	p.R1034H	ENST00000266497		1034	cGt/cAt	22/31	0.156859572635056	1	FACETS	0.55	0.513	0.588	0.55	0.513	0.588	INDETERMINATE	1	TRUE	0	0.624642499214148	1		387	933	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589601	67589612	+	inframe_deletion	In_Frame_Del	DEL	AGTTTCAAGAAA	AGTTTCAAGAAA	-	novel	NA	P-0011473-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	181	234	0	ENST00000274335.5:c.1365_1376del	p.Phe456_Lys459del	p.F456_K459del	ENST00000274335		455	cAGTTTCAAGAAAaa/caa	10/15	1	2	FACETS	0.972	0.902	1	0.972	0.902	1	CLONAL	1	TRUE	1	0.624642499214148	2		234	596	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0011481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	23	540	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		540	967	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780071	NA	P-0011481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	22	491	0	ENST00000269305.4:c.580C>T	p.Leu194Phe	p.L194F	ENST00000269305	NM_001126112.2	194	Ctt/Ttt	6/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		491	1016	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0011499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	126	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.862	0.78	0.949	0.862	0.78	0.949	CLONAL	1	TRUE	1	0.320181892758384	2		426	913	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597401	10597401	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	210	558	2	ENST00000171111.5:c.1802G>T	p.Arg601Leu	p.R601L	ENST00000171111	NM_203500.1	601	cGg/cTg	6/6	0.320181892758384	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.320181892758384	1		560	962	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189914	66189914	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	114	469	0	ENST00000273854.3:c.3032C>A	p.Thr1011Asn	p.T1011N	ENST00000273854	NM_004439.5	1011	aCt/aAt	18/18	1	2	FACETS	0.779	0.701	0.862	0.779	0.701	0.862	SUBCLONAL	1	TRUE	1	0.320181892758384	2		469	914	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999797	100999797	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	139	648	0	ENST00000325455.5:c.5C>G	p.Thr2Ser	p.T2S	ENST00000325455	NM_001202474.3	2	aCt/aGt	1/8	0.300867106451967	1	FACETS	0.764	0.694	0.836	0.764	0.694	0.836	SUBCLONAL	1	TRUE	0	0.320181892758384	1		648	955	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563303	21563303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	146	545	0	ENST00000382592.4:c.616G>A	p.Glu206Lys	p.E206K	ENST00000382592	NM_014572.2	206	Gag/Aag	4/8	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.320181892758384	2		545	901	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440710	56440710	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	137	589	2	ENST00000407977.2:c.508G>T	p.Glu170Ter	p.E170*	ENST00000407977		170	Gag/Tag	5/10	1	2	FACETS	0.824	0.748	0.903	0.824	0.748	0.903	CLONAL	1	TRUE	1	0.320181892758384	2		591	1039	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141499	11141499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	206	488	0	ENST00000358026.2:c.3476G>A	p.Gly1159Glu	p.G1159E	ENST00000358026	NM_001128849.1	1159	gGg/gAg	25/36	0.320181892758384	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.320181892758384	1		488	780	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220498	1220498	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	160	463	0	ENST00000326873.7:c.592del	p.Ala198ProfsTer89	p.A198Pfs*89	ENST00000326873	NM_000455.4	197	gtG/gt	4/10	0.320181892758384	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.320181892758384	1		463	669	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0011502-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1267	100	532	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.692	0.615	0.773	0.692	0.615	0.773	SUBCLONAL	1	TRUE	1	0.211559010875676	2		534	1367	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720833	89720836	+	frameshift_variant	Frame_Shift_Del	DEL	AAAT	AAAT	-	rs587782304	NA	P-0011502-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	27	181	0	ENST00000371953.3:c.987_990del	p.Asn329LysfsTer14	p.N329Kfs*14	ENST00000371953	NM_000314.4	328	gcAAAT/gc	8/9	1	2	FACETS	0.562	0.447	0.695	0.562	0.447	0.695	SUBCLONAL	1	TRUE	1	0.211559010875676	2		181	454	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028640	12028647	+	frameshift_variant	Frame_Shift_Del	DEL	ACAAGGAT	ACAAGGAT	-	novel	NA	P-0011502-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	75	444	0	ENST00000353533.5:c.844_851del	p.Gln282Ter	p.Q282*	ENST00000353533	NM_003010.3	281	cgACAAGGATat/cgat	8/11	1	2	FACETS	0.566	0.494	0.645	0.566	0.494	0.645	SUBCLONAL	1	TRUE	1	0.211559010875676	2		444	1252	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0011511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	48	512	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.777	0.655	0.913	0.777	0.655	0.913	CLONAL	1	TRUE	1	0.13	2		512	950	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849663	68849663	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587780113	NA	P-0011511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	35	221	2	ENST00000261769.5:c.1565+1G>A		p.X522_splice	ENST00000261769	NM_004360.3	522			0.081277512696921	0	FACETS	0.886	0.725	1			1	CLONAL	1	TRUE	0	0.13	0		223	529	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0011511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	55	541	4	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	0.081277512696921	0	FACETS	0.873	0.745	1			1	CLONAL	1	TRUE	0	0.13	0		545	843	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0011511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	28	311	0	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	1	2	FACETS	0.78	0.622	0.962	0.78	0.622	0.962	CLONAL	1	TRUE	1	0.13	2		311	552	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712519	52712519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755035966	NA	P-0011511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	54	465	0	ENST00000394830.3:c.233G>A	p.Arg78Gln	p.R78Q	ENST00000394830	NM_018313.4	78	cGa/cAa	3/30	1	2	FACETS	0.861	0.733	1	0.861	0.733	1	CLONAL	1	TRUE	1	0.13	2		465	965	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459776	149459776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765232439	NA	P-0011511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	34	383	0	ENST00000286301.3:c.431G>A	p.Arg144His	p.R144H	ENST00000286301	NM_005211.3	144	cGt/cAt	4/22	1	2	FACETS	0.775	0.631	0.937	0.775	0.631	0.937	CLONAL	1	TRUE	1	0.13	2		383	675	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849963	151849963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	49	406	0	ENST00000262189.6:c.12353C>T	p.Ala4118Val	p.A4118V	ENST00000262189	NM_170606.2	4118	gCt/gTt	49/59	1	2	FACETS	0.958	0.809	1	0.958	0.809	1	CLONAL	1	TRUE	1	0.13	2		406	787	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435417	121435417	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	33	348	0	ENST00000257555.6:c.1450G>A	p.Val484Met	p.V484M	ENST00000257555		484	Gtg/Atg	7/10	0.081277512696921	0	FACETS	0.772	0.628	0.936			1	CLONAL	1	TRUE	0	0.13	0		348	572	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4102376	4102376	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs767381558	NA	P-0011511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	32	372	0	ENST00000262948.5:c.526G>A	p.Ala176Thr	p.A176T	ENST00000262948	NM_030662.3	176	Gcg/Acg	4/11	0.172600186693556	1	FACETS	0.926	0.751	1	0.926	0.751	1	CLONAL	1	TRUE	0	0.13	1		372	497	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245837	5245837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	44	522	0	ENST00000357368.4:c.938C>T	p.Ala313Val	p.A313V	ENST00000357368	NM_002850.3	313	gCc/gTc	10/38	0.172600186693556	1	FACETS	0.997	0.835	1	0.997	0.835	1	CLONAL	1	TRUE	0	0.13	1		522	635	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866987936	NA	P-0011520-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	219	324	0	ENST00000281708.4:c.1436G>C	p.Arg479Pro	p.R479P	ENST00000281708	NM_033632.3	479	cGa/cCa	10/12	0.550923010718176	3	FACETS	0.872	0.819	0.926	0.872	0.819	0.926	CLONAL	2	TRUE	1	0.611624423180759	3		324	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0011520-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	465	506	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.611624423180759	3	FACETS	0.982	0.951	1	0.982	0.951	1	CLONAL	3	TRUE	0	0.611624423180759	3		506	674	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0011520-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	200	312	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.611624423180759	3	FACETS	0.903	0.846	0.961	0.903	0.846	0.961	CLONAL	2	TRUE	1	0.611624423180759	3		312	473	SUCCESS
ATR	545	MSKCC	GRCh37	3	142286929	142286929	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011520-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	40	477	0	ENST00000350721.4:c.127C>T	p.Arg43Trp	p.R43W	ENST00000350721	NM_001184.3	43	Cgg/Tgg	2/47	0.611624423180759	3	FACETS	0.289	0.24	0.345	0.145	0.12	0.173	SUBCLONAL	1	TRUE	1	0.611624423180759	3		477	590	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0011520-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	292	569	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.56721448391388	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	2	0.611624423180759	4		569	748	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90995084	90995084	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0011520-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	482	241	0	ENST00000265433.3:c.38-1G>T		p.X13_splice	ENST00000265433	NM_002485.4	13			0.611624423180759	5	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	2	0.611624423180759	5		241	870	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444318	50444318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1427077431	NA	P-0011520-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	280	408	2	ENST00000331340.3:c.248G>A	p.Arg83Gln	p.R83Q	ENST00000331340	NM_006060.4	83	cGa/cAa	4/8	0.611624423180759	4	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	2	0.611624423180759	4		410	726	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411806	63411806	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0011520-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	452	768	0	ENST00000330258.3:c.1361del	p.Leu454Ter	p.L454*	ENST00000330258	NM_152424.3	454	tTg/tg	2/2	0.375608856375295	3	FACETS	1	0.987	1			1	CLONAL	2	TRUE	NA	0.611624423180759	3		768	907	SUCCESS
APC	324	MSKCC	GRCh37	5	112175788	112175788	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0011520-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	115	296	0	ENST00000257430.4:c.4497del	p.Ser1501LeufsTer6	p.S1501Lfs*6	ENST00000257430	NM_000038.5	1499	ggA/gg	16/16	0.611624423180759	3	FACETS	0.861	0.779	0.949	0.431	0.389	0.475	CLONAL	1	TRUE	1	0.611624423180759	3		296	570	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099606	157099607	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0011528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	32	130	0	ENST00000346085.5:c.543_544delinsTT	p.Lys181_Pro182delinsAsnSer	p.K181_P182delinsNS	ENST00000346085	NM_020732.3	181	aaGCcg/aaTTcg	1/20	1	2	FACETS	0.793	0.649	0.953	0.793	0.649	0.953	CLONAL	1	TRUE	1	0.401458842147961	2		130	201	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622495	158622495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316254232	NA	P-0011536-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	439	600	1	ENST00000263640.3:c.1004G>A	p.Arg335Gln	p.R335Q	ENST00000263640	NM_001105.4	335	cGa/cAa	8/11	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	FALSE	1	0.445535840551537	2		601	1421	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0011544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	112	332	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.881	0.797	0.969			1	INDETERMINATE	1	TRUE	NA	0.545503828656663	2		332	466	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0011544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	81	153	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	0.545503828656663	1	FACETS	0.847	0.757	0.941	0.847	0.757	0.941	CLONAL	1	TRUE	0	0.545503828656663	1		153	255	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577102	7577102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793881	NA	P-0011544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	340	464	1	ENST00000269305.4:c.836G>A	p.Gly279Glu	p.G279E	ENST00000269305	NM_001126112.2	279	gGg/gAg	8/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.545503828656663	2		465	1158	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61729428	61729428	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	199	345	0	ENST00000401558.2:c.319G>T	p.Val107Phe	p.V107F	ENST00000401558	NM_003400.3	107	Gtt/Ttt	5/25	1	2	FACETS	0.884	0.821	0.95	0.884	0.821	0.95	CLONAL	1	TRUE	1	0.545503828656663	2		345	825	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633831	86633831	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	320	378	0	ENST00000274376.6:c.940G>C	p.Glu314Gln	p.E314Q	ENST00000274376	NM_002890.2	314	Gaa/Caa	5/25	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.545503828656663	2		378	1139	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223584	55223584	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9955	846	320	0	ENST00000275493.2:c.951G>C	p.Glu317Asp	p.E317D	ENST00000275493	NM_005228.3	317	gaG/gaC	8/28	0.545503828656663	27	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.545503828656663	27		320	10801	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55272998	55272998	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	130	560	0	ENST00000275493.2:c.3321T>G	p.Asn1107Lys	p.N1107K	ENST00000275493	NM_005228.3	1107	aaT/aaG	28/28	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.320700570240363	2		560	802	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0011554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	94	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	0.907	0.807	1			1	INDETERMINATE	1	TRUE	NA	0.249949741306952	2		426	829	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0011554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	130	707	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.249949741306952	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.249949741306952	1		707	878	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41242984	41242984	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs876660601	NA	P-0011554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	297	518	0	ENST00000357654.3:c.4162C>T	p.Gln1388Ter	p.Q1388*	ENST00000357654	NM_007294.3	1388	Cag/Tag	11/23	0.232642293336643	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.249949741306952	2		518	1072	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492883	56492887	+	frameshift_variant	Frame_Shift_Del	DEL	GCCAT	GCCAT	-	novel	NA	P-0011554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	151	247	0	ENST00000407977.2:c.52_56del	p.Met18TyrfsTer20	p.M18Yfs*20	ENST00000407977		18	ATGGCt/t	2/10	0.232642293336643	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.249949741306952	2		247	508	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258769	115258770	+	stop_gained	Nonsense_Mutation	DNP	TG	TG	AA	novel	NA	P-0011554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	80	348	1	ENST00000369535.4:c.12_13delinsTT	p.Lys5Ter	p.K5*	ENST00000369535	NM_002524.4	4	taCAaa/taTTaa	2/7	0.249949741306952	1	FACETS	0.805	0.708	0.909	0.805	0.708	0.909	CLONAL	1	TRUE	0	0.249949741306952	1		349	696	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0011561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	242	183	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.77592732693558	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.77592732693558	1		183	367	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602314	10602314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	57	368	0	ENST00000171111.5:c.1264G>A	p.Asp422Asn	p.D422N	ENST00000171111	NM_203500.1	422	Gat/Aat	3/6	1	2	FACETS	0.157	0.134	0.183	0.157	0.134	0.183	SUBCLONAL	1	TRUE	1	0.77592732693558	2		368	935	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726917	61726917	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0011561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	423	408	0	ENST00000401558.2:c.521T>A	p.Leu174Ter	p.L174*	ENST00000401558	NM_003400.3	174	tTg/tAg	7/25	1	2	FACETS	0.998	0.953	1	0.998	0.953	1	CLONAL	1	TRUE	1	0.77592732693558	2		408	1092	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928029	49928029	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1343	71	564	0	ENST00000296474.3:c.3699C>G	p.Ile1233Met	p.I1233M	ENST00000296474	NM_002447.2	1233	atC/atG	18/20	1	2	FACETS	0.129	0.112	0.148	0.129	0.112	0.148	SUBCLONAL	1	TRUE	1	0.77592732693558	2		564	1414	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637676	176637676	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs587784084	NA	P-0011561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	327	258	0	ENST00000439151.2:c.2276C>G	p.Ser759Ter	p.S759*	ENST00000439151	NM_022455.4	759	tCa/tGa	5/23	1	2	FACETS	0.978	0.927	1	0.978	0.927	1	CLONAL	1	TRUE	1	0.77592732693558	2		258	862	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417920	32417920	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	48	290	0	ENST00000332351.3:c.1132C>G	p.Leu378Val	p.L378V	ENST00000332351	NM_024426.4	378	Ctt/Gtt	7/10	1	2	FACETS	0.139	0.117	0.164	0.139	0.117	0.164	SUBCLONAL	1	TRUE	1	0.77592732693558	2		290	889	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5246048	5246048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781664688	NA	P-0011561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	26	194	0	ENST00000357368.4:c.727G>A	p.Val243Met	p.V243M	ENST00000357368	NM_002850.3	243	Gtg/Atg	10/38	1	2	FACETS	0.132	0.104	0.164	0.132	0.104	0.164	SUBCLONAL	1	TRUE	1	0.77592732693558	2		194	508	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744494	41744494	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	507	530	0	ENST00000301178.4:c.1114C>G	p.Gln372Glu	p.Q372E	ENST00000301178	NM_021913.4	372	Caa/Gaa	8/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.77592732693558	2		530	1274	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503838	149503838	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs864309711	NA	P-0011562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	506	539	0	ENST00000261799.4:c.1998C>A	p.Asn666Lys	p.N666K	ENST00000261799	NM_002609.3	666	aaC/aaA	14/23	0.457044152549635	4	FACETS	0.933	0.896	0.97	0.933	0.896	0.97	CLONAL	3	TRUE	1	0.457044152549635	4		539	1153	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199469672	NA	P-0011562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	253	623	0	ENST00000374080.3:c.131G>T	p.Gly44Val	p.G44V	ENST00000374080		44	gGt/gTt	2/45	0.296140092768827	3	FACETS	1	0.986	1	0.59	0.552	0.63	CLONAL	1	TRUE	1	0.457044152549635	3		623	1152	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519992	NA	P-0011562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	690	575	0	ENST00000269305.4:c.641A>C	p.His214Pro	p.H214P	ENST00000269305	NM_001126112.2	214	cAt/cCt	6/11	0.137908116893388	5	FACETS	1	0.978	1			1	INDETERMINATE	4	TRUE	NA	0.457044152549635	5		575	1259	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383695	15383695	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1324	392	498	1	ENST00000263377.2:c.216G>C	p.Lys72Asn	p.K72N	ENST00000263377	NM_058243.2	72	aaG/aaC	2/20	0.457044152549635	8	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.457044152549635	8		499	1716	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383764	15383764	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1546	486	590	1	ENST00000263377.2:c.147G>C	p.Glu49Asp	p.E49D	ENST00000263377	NM_058243.2	49	gaG/gaC	2/20	0.457044152549635	8	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.457044152549635	8		591	2032	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597858	43597858	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs79014735	NA	P-0011579-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	583	1231	3	ENST00000355710.3:c.406G>A	p.Glu136Lys	p.E136K	ENST00000355710	NM_020975.4	136	Gag/Aag	3/20	0.564275268861441	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.57367933596573	2		1234	983	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0011589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	108	352	0	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	0.451094150429714	1	FACETS	0.944	0.856	1	0.944	0.856	1	CLONAL	1	TRUE	0	0.50150900513996	1		352	342	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190744	11190744	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	153	366	0	ENST00000361445.4:c.5455C>G	p.His1819Asp	p.H1819D	ENST00000361445	NM_004958.3	1819	Cat/Gat	39/58	0.50150900513996	3	FACETS	1	0.965	1	0.547	0.502	0.595	CLONAL	1	TRUE	1	0.50150900513996	3		366	697	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728761	190728761	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	62	171	0	ENST00000441310.2:c.2149G>C	p.Asp717His	p.D717H	ENST00000441310	NM_000534.4	717	Gac/Cac	10/13	0.50150900513996	5	FACETS	0.689	0.595	0.791			1	SUBCLONAL	1	TRUE	NA	0.50150900513996	5		171	629	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113254	209113254	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	161	411	0	ENST00000345146.2:c.253G>C	p.Glu85Gln	p.E85Q	ENST00000345146	NM_005896.2	85	Gag/Cag	4/10	0.50150900513996	3	FACETS	0.874	0.801	0.95	0.437	0.4	0.475	CLONAL	1	TRUE	1	0.50150900513996	3		411	919	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430987	181430987	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	27	350	0	ENST00000325404.1:c.839G>T	p.Gly280Val	p.G280V	ENST00000325404	NM_003106.3	280	gGc/gTc	1/1	0.357865587175838	3	FACETS	0.285	0.226	0.353	0.095	0.075	0.118	SUBCLONAL	1	TRUE	0	0.50150900513996	3		350	472	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210691	5210691	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	196	331	0	ENST00000357368.4:c.5360G>A	p.Arg1787Gln	p.R1787Q	ENST00000357368	NM_002850.3	1787	cGg/cAg	34/38	0.467871685415007	2	FACETS	0.888	0.832	0.945	0.888	0.832	0.945	CLONAL	2	TRUE	0	0.50150900513996	2		331	440	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426522	47426522	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	265	479	0	ENST00000377045.4:c.865A>G	p.Lys289Glu	p.K289E	ENST00000377045	NM_001654.4	289	Aag/Gag	9/16	0.454664730640324	2	FACETS	0.852	0.805	0.9	0.852	0.805	0.9	CLONAL	2	TRUE	0	0.50150900513996	2		479	620	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0012000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	42	239	0	ENST00000311936.3:c.34_35delinsTT	p.Gly12Phe	p.G12F	ENST00000311936	NM_004985.3	12	GGt/TTt	2/5	1	2	FACETS	0.109	0.09	0.13	0.109	0.09	0.13	SUBCLONAL	1	TRUE	1	1.03	2		239	750	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142099	108142099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555085210	NA	P-0012000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	146	238	2	ENST00000278616.4:c.3043C>T	p.Gln1015Ter	p.Q1015*	ENST00000278616	NM_000051.3	1015	Caa/Taa	20/63	1	2	FACETS	0.292	0.266	0.319	0.292	0.266	0.319	SUBCLONAL	1	TRUE	1	1.03	2		240	971	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218804	66218804	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	450	328	1	ENST00000273854.3:c.2254G>T	p.Val752Leu	p.V752L	ENST00000273854	NM_004439.5	752	Gtg/Ttg	13/18	0.3	4	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	1.03	4		329	1515	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420844	49420844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1363299847	NA	P-0012000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	45	330	0	ENST00000301067.7:c.14905G>A	p.Glu4969Lys	p.E4969K	ENST00000301067	NM_003482.3	4969	Gaa/Aaa	48/54	1	2	FACETS	0.098	0.081	0.116	0.098	0.081	0.116	SUBCLONAL	1	TRUE	1	1.03	2		330	895	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325335	1325335	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012000-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	68	286	0	ENST00000400841.2:c.340G>T	p.Val114Phe	p.V114F	ENST00000400841		114	Gtt/Ttt	3/6	1	1	FACETS		NA	1			1	NA	1	TRUE	0	1.03	1		286	861	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265629	152265629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	55	136	1	ENST00000206249.3:c.1082C>T	p.Ala361Val	p.A361V	ENST00000206249	NM_000125.3	361	gCg/gTg	4/8	1	2	FACETS	0.872	0.751	1	0.872	0.751	1	CLONAL	1	TRUE	1	0.385581645040413	2		137	327	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984856	72984856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	172	362	0	ENST00000268489.5:c.2728G>A	p.Glu910Lys	p.E910K	ENST00000268489	NM_006885.3	910	Gag/Aag	3/10	0.385581645040413	0	FACETS	0.826	0.762	0.891			1	CLONAL	1	TRUE	0	0.385581645040413	0		362	664	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061098	38061098	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	26	47	0	ENST00000250448.2:c.891del	p.Ser298LeufsTer23	p.S298Lfs*23	ENST00000250448	NM_004496.3	297	ccC/cc	2/2	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.385581645040413	2		47	124	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs878854073	NA	P-0012027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	193	185	0	ENST00000269305.4:c.673-1G>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.567147441334926	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.632547827409391	1		185	408	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152604	99152604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	282	309	0	ENST00000074304.5:c.400G>A	p.Gly134Ser	p.G134S	ENST00000074304	NM_001134224.1	134	Ggc/Agc	7/26	1	2	FACETS	0.916	0.862	0.972	0.916	0.862	0.972	CLONAL	1	TRUE	1	0.632547827409391	2		309	973	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480330	89480330	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs375846678	NA	P-0012027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	565	252	0	ENST00000336596.2:c.2167C>G	p.Leu723Val	p.L723V	ENST00000336596	NM_005233.5	723	Cta/Gta	13/17	0.591509687165623	2	FACETS	0.954	0.924	0.984	0.954	0.924	0.984	CLONAL	2	TRUE	0	0.632547827409391	2		252	936	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509098	66509098	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	202	224	0	ENST00000273854.3:c.229G>C	p.Ala77Pro	p.A77P	ENST00000273854	NM_004439.5	77	Gct/Cct	2/18	1	2	FACETS	0.915	0.852	0.98	0.915	0.852	0.98	CLONAL	1	TRUE	1	0.632547827409391	2		224	698	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459433	50459433	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	190	200	0	ENST00000331340.3:c.722A>G	p.Lys241Arg	p.K241R	ENST00000331340	NM_006060.4	241	aAa/aGa	7/8	1	2	FACETS	0.864	0.802	0.929	0.864	0.802	0.929	CLONAL	1	TRUE	1	0.632547827409391	2		200	695	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465578	8465578	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	359	415	0	ENST00000356435.5:c.3602C>T	p.Thr1201Ile	p.T1201I	ENST00000356435		1201	aCt/aTt	21/35	1	2	FACETS	0.896	0.849	0.944	0.896	0.849	0.944	CLONAL	1	TRUE	1	0.632547827409391	2		415	1267	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546044	29546044	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778548	NA	P-0012027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	226	226	0	ENST00000356175.3:c.1549G>A	p.Glu517Lys	p.E517K	ENST00000356175	NM_000267.3	517	Gaa/Aaa	14/57	1	2	FACETS	0.809	0.755	0.865	0.809	0.755	0.865	CLONAL	1	TRUE	1	0.632547827409391	2		226	883	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619204	37619204	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1364563564	NA	P-0012027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	205	248	0	ENST00000447079.4:c.880C>T	p.Pro294Ser	p.P294S	ENST00000447079	NM_015083.1	294	Ccc/Tcc	1/14	1	2	FACETS	0.82	0.763	0.88	0.82	0.763	0.88	CLONAL	1	TRUE	1	0.632547827409391	2		248	790	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983136	111983136	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	256	386	0	ENST00000368678.4:c.1411del	p.Glu471ArgfsTer26	p.E471Rfs*26	ENST00000368678		471	Gag/ag	13/13	0.632547827409391	1	FACETS	0.694	0.651	0.737	0.694	0.651	0.737	SUBCLONAL	1	TRUE	0	0.632547827409391	1		386	798	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245404	153245404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	172	328	0	ENST00000281708.4:c.1787C>T	p.Ser596Phe	p.S596F	ENST00000281708	NM_033632.3	596	tCt/tTt	11/12	1	2	FACETS	0.927	0.854	1	1	0.994	1	CLONAL	3	TRUE	1	0.15	2		328	825	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0012033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	60	353	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.15	2		353	761	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0012033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	26	160	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.801	0.633	0.993	0.801	0.633	0.993	CLONAL	1	TRUE	1	0.15	2		160	433	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873888	151873888	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	62	405	0	ENST00000262189.6:c.8650C>T	p.Arg2884Ter	p.R2884*	ENST00000262189	NM_170606.2	2884	Cga/Tga	38/59	1	2	FACETS	0.774	0.666	0.892	0.774	0.666	0.892	SUBCLONAL	1	TRUE	1	0.15	2		405	1068	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864937	117864937	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	141	334	0	ENST00000297338.2:c.1172G>T	p.Arg391Leu	p.R391L	ENST00000297338	NM_006265.2	391	cGc/cTc	10/14	0.18952933240185	3	FACETS	0.835	0.761	0.912	1	0.979	1	CLONAL	3	TRUE	1	0.15	3		334	807	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212167	98212167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	50	335	0	ENST00000331920.6:c.3505G>A	p.Val1169Ile	p.V1169I	ENST00000331920	NM_000264.3	1169	Gtt/Att	21/24	1	2	FACETS	0.71	0.6	0.831	0.71	0.6	0.831	SUBCLONAL	1	TRUE	1	0.15	2		335	939	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554545	63554545	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	47	340	0	ENST00000307078.5:c.194C>G	p.Pro65Arg	p.P65R	ENST00000307078	NM_004655.3	65	cCg/cGg	2/11	1	2	FACETS	0.864	0.728	1	0.864	0.728	1	CLONAL	1	TRUE	1	0.15	2		340	725	SUCCESS
APC	324	MSKCC	GRCh37	5	112174038	112174038	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	31	248	0	ENST00000257430.4:c.2747del	p.Thr916LysfsTer39	p.T916Kfs*39	ENST00000257430	NM_000038.5	916	aCa/aa	16/16	1	2	FACETS	0.668	0.538	0.815	0.668	0.538	0.815	SUBCLONAL	1	TRUE	1	0.15	2		248	619	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	180	389	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		389	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579346	7579346	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs781724995	NA	P-0012036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	524	295	0	ENST00000269305.4:c.341T>A	p.Leu114Ter	p.L114*	ENST00000269305	NM_001126112.2	114	tTg/tAg	4/11	0.708647145280397	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.708647145280397	2		295	712	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258139	16258139	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	470	250	0	ENST00000375759.3:c.5404T>C	p.Ser1802Pro	p.S1802P	ENST00000375759	NM_015001.2	1802	Tct/Cct	11/15	0.708647145280397	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.708647145280397	3		250	867	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470464	25470464	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs773208295	NA	P-0012036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	347	405	0	ENST00000264709.3:c.1010C>G	p.Ser337Ter	p.S337*	ENST00000264709	NM_175629.2	337	tCa/tGa	8/23	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.708647145280397	2		405	962	SUCCESS
APC	324	MSKCC	GRCh37	5	112162940	112162940	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	363	275	0	ENST00000257430.4:c.1544A>T	p.Asn515Ile	p.N515I	ENST00000257430	NM_000038.5	515	aAc/aTc	12/16	0.708647145280397	3	FACETS	0.953	0.911	0.995	0.953	0.911	0.995	CLONAL	2	TRUE	1	0.708647145280397	3		275	728	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271512	26271512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1484	558	665	0	ENST00000305910.3:c.101G>A	p.Gly34Asp	p.G34D	ENST00000305910	NM_003534.2	34	gGc/gAc	1/1	0.708647145280397	3	FACETS	1	0.982	1	0.522	0.5	0.545	CLONAL	1	TRUE	1	0.708647145280397	3		665	2042	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402505	139402505	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	299	400	0	ENST00000277541.6:c.3412A>G	p.Thr1138Ala	p.T1138A	ENST00000277541	NM_017617.3	1138	Aca/Gca	21/34	0.708647145280397	2	FACETS	0.999	0.944	1	0.499	0.472	0.527	CLONAL	1	TRUE	0	0.708647145280397	2		400	845	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919979	50919979	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	210	348	0	ENST00000440232.2:c.3066G>T	p.Gln1022His	p.Q1022H	ENST00000440232	NM_002691.3	1022	caG/caT	24/27	1	2	FACETS	0.989	0.925	1	0.989	0.925	1	CLONAL	1	TRUE	1	0.708647145280397	2		348	599	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841096	15841096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1549	479	634	0	ENST00000307771.7:c.1180G>A	p.Glu394Lys	p.E394K	ENST00000307771	NM_005089.3	394	Gaa/Aaa	11/11	0.119386150630196	6	FACETS	0.806	0.768	0.844			1	INDETERMINATE	2	TRUE	NA	0.708647145280397	6		634	2028	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413105	63413105	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374303948	NA	P-0012036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	233	460	1	ENST00000330258.3:c.62G>A	p.Arg21His	p.R21H	ENST00000330258	NM_152424.3	21	cGt/cAt	2/2	0.228390888494809	3	FACETS	0.829	0.773	0.887	0.276	0.257	0.296	INDETERMINATE	1	TRUE	0	0.708647145280397	3		461	1074	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0012043-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	400	580	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.666769127049512	2	FACETS	0.923	0.89	0.955	0.923	0.89	0.955	CLONAL	2	TRUE	0	0.710356503406364	2		580	610	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28929495	NA	P-0012043-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	2095	398	0	ENST00000275493.2:c.2155G>T	p.Gly719Cys	p.G719C	ENST00000275493	NM_005228.3	719	Ggc/Tgc	18/28	0.710356503406364	12	FACETS	1	0.997	1			1	CLONAL	9	TRUE	NA	0.710356503406364	12		398	2872	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0012043-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	1685	383	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.710356503406364	12	FACETS	1	0.991	1			1	CLONAL	9	TRUE	NA	0.710356503406364	12		383	2375	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739346	46739346	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012043-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	226	453	0	ENST00000371975.4:c.1537A>C	p.Ser513Arg	p.S513R	ENST00000371975	NM_003579.3	513	Agt/Cgt	14/18	1	2	FACETS	0.876	0.82	0.935	0.876	0.82	0.935	CLONAL	1	TRUE	1	0.710356503406364	2		453	726	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858916	243858916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012043-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	196	452	0	ENST00000263826.5:c.149C>T	p.Pro50Leu	p.P50L	ENST00000263826	NM_005465.4	50	cCc/cTc	2/13	0.552178773519969	4	FACETS	0.845	0.781	0.911	0.422	0.39	0.456	CLONAL	1	TRUE	2	0.710356503406364	4		452	1117	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677875	117677875	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs35269727	NA	P-0012043-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	174	438	0	ENST00000368508.3:c.4058A>C	p.Tyr1353Ser	p.Y1353S	ENST00000368508	NM_002944.2	1353	tAc/tCc	25/43	0.630146182434324	4	FACETS	0.847	0.78	0.918	0.282	0.26	0.306	CLONAL	1	TRUE	1	0.710356503406364	4		438	989	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030402	49030402	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012043-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	150	280	0	ENST00000267163.4:c.1877C>G	p.Ala626Gly	p.A626G	ENST00000267163	NM_000321.2	626	gCa/gGa	19/27	0.666769127049512	2	FACETS	0.887	0.817	0.959	0.444	0.408	0.48	CLONAL	1	TRUE	0	0.710356503406364	2		280	476	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061558	38061558	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745367241	NA	P-0012043-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	79	143	0	ENST00000250448.2:c.431C>T	p.Ala144Val	p.A144V	ENST00000250448	NM_004496.3	144	gCg/gTg	2/2	0.62600774843187	5	FACETS	1	0.963	1			1	CLONAL	1	TRUE	NA	0.710356503406364	5		143	376	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0012061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	87	424	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.998	0.882	1	0.998	0.882	1	CLONAL	1	TRUE	1	0.2	2		424	872	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0012061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	33	316	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.738	0.601	0.893	0.738	0.601	0.893	SUBCLONAL	1	TRUE	1	0.2	2		316	447	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023376	27023376	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1427038078	NA	P-0012061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	40	200	0	ENST00000324856.7:c.482T>C	p.Val161Ala	p.V161A	ENST00000324856	NM_006015.4	161	gTc/gCc	1/20	1	2	FACETS	0.707	0.586	0.841	0.707	0.586	0.841	SUBCLONAL	1	TRUE	1	0.2	2		200	566	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412023	116412023	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	70	307	0	ENST00000397752.3:c.3008A>G	p.Tyr1003Cys	p.Y1003C	ENST00000397752	NM_000245.2	1003	tAc/tGc	14/21	0.157143374116043	1	FACETS	0.931	0.811	1	0.931	0.811	1	CLONAL	1	TRUE	0	0.2	1		307	677	SUCCESS
APC	324	MSKCC	GRCh37	5	112175582	112175582	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	223	812	0	ENST00000257430.4:c.4291A>G	p.Met1431Val	p.M1431V	ENST00000257430	NM_000038.5	1431	Atg/Gtg	16/16	1	2	FACETS	0.758	0.706	0.811	1	0.992	1	SUBCLONAL	2	FALSE	1	0.313023984890058	2		812	940	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525032	187525032	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	109	566	0	ENST00000441802.2:c.10648A>G	p.Ile3550Val	p.I3550V	ENST00000441802	NM_005245.3	3550	Att/Gtt	19/27	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.313023984890058	2		566	557	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173754	108173754	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	67	398	0	ENST00000278616.4:c.5494G>T	p.Glu1832Ter	p.E1832*	ENST00000278616	NM_000051.3	1832	Gaa/Taa	36/63	0.313023984890058	3	FACETS	1	0.892	1	1	0.892	1	CLONAL	2	FALSE	1	0.313023984890058	3		398	244	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266094	41266102	+	inframe_deletion	In_Frame_Del	DEL	CTGGACTCT	CTGGACTCT	-	novel	NA	P-0012068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	114	785	0	ENST00000349496.5:c.91_99del	p.Leu31_Ser33del	p.L31_S33del	ENST00000349496	NM_001904.3	31	CTGGACTCT/-	3/15	1	2	FACETS	0.811	0.73	0.898	0.811	0.73	0.898	CLONAL	1	FALSE	1	0.313023984890058	2		785	898	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628848	187628849	+	missense_variant	Missense_Mutation	DNP	GA	GA	AC	novel	NA	P-0012068-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	138	799	1	ENST00000441802.2:c.2133_2134delinsGT	p.His712Tyr	p.H712Y	ENST00000441802	NM_005245.3	711	gcTCac/gcGTac	2/27	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.313023984890058	2		800	781	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0012086-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	371	531	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.357331716003852	2	FACETS	0.989	0.94	1	0.989	0.94	1	CLONAL	2	TRUE	0	0.359092464102411	2		531	1045	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17349116	17349116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012086-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1327	72	497	0	ENST00000375499.3:c.752G>A	p.Arg251Lys	p.R251K	ENST00000375499	NM_003000.2	251	aGg/aAg	7/8	0.34117274520087	4	FACETS	0.39	0.339	0.445	0.13	0.113	0.149	SUBCLONAL	1	TRUE	1	0.359092464102411	4		497	1399	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366767	40366767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748738471	NA	P-0012086-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4756	351	297	0	ENST00000397332.2:c.430G>A	p.Ala144Thr	p.A144T	ENST00000397332	NM_001033082.2	144	Gct/Act	2/3	0.359092464102411	35	FACETS	0.884	0.831	0.939			1	CLONAL	3	TRUE	NA	0.359092464102411	35		297	5107	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226946	142226946	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012086-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	227	304	0	ENST00000350721.4:c.4858A>T	p.Thr1620Ser	p.T1620S	ENST00000350721	NM_001184.3	1620	Act/Tct	28/47	0.359092464102411	4	FACETS	0.997	0.93	1	0.997	0.93	1	CLONAL	2	TRUE	2	0.359092464102411	4		304	862	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549052	21549052	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs746235580	NA	P-0012086-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	205	247	0	ENST00000382592.4:c.3224A>T	p.Asp1075Val	p.D1075V	ENST00000382592	NM_014572.2	1075	gAt/gTt	8/8	0.359092464102411	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.359092464102411	2		247	549	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891719	28891719	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012086-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	347	480	1	ENST00000282397.4:c.3302C>A	p.Pro1101Gln	p.P1101Q	ENST00000282397	NM_002019.4	1101	cCa/cAa	25/30	0.359092464102411	2	FACETS	0.998	0.948	1	0.998	0.948	1	CLONAL	2	TRUE	0	0.359092464102411	2		481	968	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38064141	38064141	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012086-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	165	580	0	ENST00000250448.2:c.37A>G	p.Ser13Gly	p.S13G	ENST00000250448	NM_004496.3	13	Agc/Ggc	1/2	1	2	FACETS	0.933	0.856	1	0.933	0.856	1	CLONAL	1	TRUE	1	0.359092464102411	2		580	985	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217247	7217247	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012086-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	434	689	0	ENST00000380728.2:c.458T>G	p.Met153Arg	p.M153R	ENST00000380728		153	aTg/aGg	6/11	0.357331716003852	2	FACETS	0.935	0.892	0.979	0.935	0.892	0.979	CLONAL	2	TRUE	0	0.359092464102411	2		689	1292	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375349	15375349	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012086-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	315	489	0	ENST00000263377.2:c.1078A>G	p.Ile360Val	p.I360V	ENST00000263377	NM_058243.2	360	Atc/Gtc	6/20	0.359092464102411	2	FACETS	0.885	0.837	0.935	0.885	0.837	0.935	CLONAL	2	TRUE	0	0.359092464102411	2		489	991	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427973	49427973	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012086-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	144	433	0	ENST00000301067.7:c.10617del	p.Lys3540ArgfsTer118	p.K3540Rfs*118	ENST00000301067	NM_003482.3	3539	cgG/cg	38/54	0.359092464102411	3	FACETS	0.889	0.81	0.973	0.445	0.405	0.487	CLONAL	1	TRUE	1	0.359092464102411	3		433	1064	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0012087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	1165	769	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.890519967763088	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.890519967763088	3		770	1250	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954211	48954242	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAAATTTTAGGTAAATTTTTTACTTTTAGTAA	AAAATTTTAGGTAAATTTTTTACTTTTAGTAA	-	novel	NA	P-0012087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	81	377	0	ENST00000267163.4:c.1420_1421+30del		p.X474_splice	ENST00000267163	NM_000321.2	474		15/27	0.887294415654036	2	FACETS	0.535	0.475	0.598	0.268	0.237	0.299	SUBCLONAL	1	TRUE	0	0.890519967763088	2		377	340	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396644	396644	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	591	504	1	ENST00000262320.3:c.382G>T	p.Glu128Ter	p.E128*	ENST00000262320	NM_003502.3	128	Gag/Tag	2/11	0.512239041258938	4	FACETS	0.854	0.828	0.881	0.854	0.828	0.881	INDETERMINATE	3	TRUE	1	0.890519967763088	4		505	979	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371765	45371765	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012087-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	283	530	0	ENST00000262160.6:c.1226C>G	p.Thr409Ser	p.T409S	ENST00000262160	NM_005901.5	409	aCt/aGt	10/11	0.890519967763088	3	FACETS	1	0.963	1	0.515	0.485	0.545	CLONAL	1	TRUE	1	0.890519967763088	3		530	892	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088663	27088663	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	143	683	1	ENST00000324856.7:c.2272C>T	p.Gln758Ter	p.Q758*	ENST00000324856	NM_006015.4	758	Cag/Tag	7/20	0.362217275216303	4	FACETS	0.901	0.819	0.987	0.45	0.409	0.494	CLONAL	1	TRUE	2	0.362217275216303	4		684	1194	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266828	198266828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs16865307	NA	P-0012107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	153	537	1	ENST00000335508.6:c.2104C>T	p.Arg702Trp	p.R702W	ENST00000335508	NM_012433.2	702	Cgg/Tgg	15/25	0.287747291642296	4	FACETS	1	0.986	1	0.694	0.635	0.756	CLONAL	1	TRUE	2	0.362217275216303	4		538	829	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9770586	9770586	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	218	703	0	ENST00000377346.4:c.73C>G	p.Leu25Val	p.L25V	ENST00000377346	NM_005026.3	25	Ctg/Gtg	3/24	0.346496477639339	3	FACETS	0.8	0.745	0.856			1	SUBCLONAL	2	TRUE	NA	0.362217275216303	3		703	889	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166001	118166001	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	55	412	0	ENST00000369448.3:c.511G>C	p.Asp171His	p.D171H	ENST00000369448	NM_017709.3	171	Gac/Cac	2/2	0.362217275216303	4	FACETS	0.62	0.53	0.719	0.31	0.265	0.36	SUBCLONAL	1	TRUE	2	0.362217275216303	4		412	667	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873297	136873297	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	277	1000	0	ENST00000241393.3:c.201G>C	p.Lys67Asn	p.K67N	ENST00000241393	NM_003467.2	67	aaG/aaC	2/2	0.287747291642296	4	FACETS	0.835	0.783	0.888	0.835	0.783	0.888	CLONAL	2	TRUE	2	0.362217275216303	4		1000	1248	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670597	134670597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1330628001	NA	P-0012107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	238	812	2	ENST00000398015.3:c.508C>T	p.Arg170Trp	p.R170W	ENST00000398015	NM_004441.4	170	Cgg/Tgg	3/16	0.362217275216303	5	FACETS	0.769	0.716	0.823	0.513	0.477	0.549	SUBCLONAL	2	TRUE	2	0.362217275216303	5		814	1319	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911508	134911508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201816783	NA	P-0012107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	105	482	1	ENST00000398015.3:c.1973C>T	p.Ser658Leu	p.S658L	ENST00000398015	NM_004441.4	658	tCg/tTg	11/16	0.362217275216303	5	FACETS	1	0.953	1	0.371	0.332	0.412	CLONAL	1	TRUE	2	0.362217275216303	5		483	805	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951847	2951847	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	222	657	0	ENST00000396946.4:c.3103G>T	p.Glu1035Ter	p.E1035*	ENST00000396946	NM_032415.4	1035	Gaa/Taa	23/25	0.362217275216303	5	FACETS	0.828	0.769	0.888	0.552	0.513	0.592	CLONAL	2	TRUE	2	0.362217275216303	5		657	1143	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397567	116397567	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs761727097	NA	P-0012107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	237	697	0	ENST00000397752.3:c.1939A>G	p.Thr647Ala	p.T647A	ENST00000397752	NM_000245.2	647	Aca/Gca	7/21	0.362217275216303	5	FACETS	0.799	0.744	0.855	0.533	0.496	0.57	SUBCLONAL	2	TRUE	2	0.362217275216303	5		697	1264	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415117	116415117	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	381	571	0	ENST00000397752.3:c.3211A>G	p.Ile1071Val	p.I1071V	ENST00000397752	NM_000245.2	1071	Att/Gtt	15/21	0.362217275216303	5	FACETS	0.944	0.898	0.992	0.944	0.898	0.992	CLONAL	3	TRUE	2	0.362217275216303	5		571	1146	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566251	95566251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1185001854	NA	P-0012107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	159	399	0	ENST00000393063.1:c.4072C>T	p.Arg1358Cys	p.R1358C	ENST00000393063	NM_030621.3	1358	Cgc/Tgc	23/28	0.287747291642296	4	FACETS	0.793	0.728	0.861	0.793	0.728	0.861	SUBCLONAL	2	TRUE	2	0.362217275216303	4		399	754	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772311	68772311	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0012107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	154	390	0	ENST00000261769.5:c.160A>T	p.Arg54Ter	p.R54*	ENST00000261769	NM_004360.3	54	Aga/Tga	2/16	0.27645189139575	2	FACETS	0.782	0.719	0.846	0.782	0.719	0.846	SUBCLONAL	2	TRUE	0	0.362217275216303	2		390	544	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984728	11984728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	118	261	1	ENST00000353533.5:c.274G>A	p.Glu92Lys	p.E92K	ENST00000353533	NM_003010.3	92	Gaa/Aaa	3/11	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.523459461019733	2		262	431	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575066	48575071	+	inframe_deletion	In_Frame_Del	DEL	GGAAAG	GGAAAG	-	novel	NA	P-0012117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	220	622	1	ENST00000342988.3:c.261_266del	p.Lys88_Gly89del	p.K88_G89del	ENST00000342988	NM_005359.5	87	cGGAAAGga/cga	3/12	0.523459461019733	1	FACETS	0.947	0.886	1	0.947	0.886	1	CLONAL	1	TRUE	0	0.523459461019733	1		623	655	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287485	33287485	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	204	514	0	ENST00000374542.5:c.1612del	p.Leu538TrpfsTer6	p.L538Wfs*6	ENST00000374542	NM_001141970.1	538	Ctg/tg	6/8	0.523459461019733	1	FACETS	0.982	0.917	1	0.982	0.917	1	CLONAL	1	TRUE	0	0.523459461019733	1		514	586	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841505	156841505	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145222195	NA	P-0012124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	30	497	0	ENST00000524377.1:c.808G>A	p.Asp270Asn	p.D270N	ENST00000524377	NM_002529.3	270	Gat/Aat	7/17	1	2	FACETS	0.797	0.641	0.974	0.797	0.641	0.974	CLONAL	1	TRUE	1	0.15	2		497	502	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974678	21974678	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs587778189	NA	P-0012124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	30	749	0	ENST00000304494.5:c.149A>G	p.Gln50Arg	p.Q50R	ENST00000304494	NM_000077.4	50	cAg/cGg	1/3	0.115109117719326	1	FACETS	0.705	0.567	0.862	0.705	0.567	0.862	SUBCLONAL	1	TRUE	0	0.15	1		749	525	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120479912	120479912	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	35	593	0	ENST00000256646.2:c.3515G>C	p.Arg1172Thr	p.R1172T	ENST00000256646	NM_024408.3	1172	aGa/aCa	21/34	1	2	FACETS	0.822	0.672	0.99	0.822	0.672	0.99	CLONAL	1	TRUE	1	0.15	2		593	568	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649702	206649702	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	17	331	0	ENST00000367120.3:c.537C>A	p.Tyr179Ter	p.Y179*	ENST00000367120	NM_014002.3	179	taC/taA	6/22	1	2	FACETS	0.83	0.62	1	0.83	0.62	1	CLONAL	1	TRUE	1	0.15	2		331	273	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149207	61149207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	23	360	0	ENST00000295025.8:c.1397C>T	p.Ala466Val	p.A466V	ENST00000295025	NM_002908.2	466	gCc/gTc	11/11	1	2	FACETS	0.782	0.609	0.983	0.782	0.609	0.983	CLONAL	1	TRUE	1	0.15	2		360	392	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152611	99152611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs973338386	NA	P-0012124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	33	624	0	ENST00000074304.5:c.407G>A	p.Gly136Glu	p.G136E	ENST00000074304	NM_001134224.1	136	gGa/gAa	7/26	1	2	FACETS	0.703	0.571	0.852	0.703	0.571	0.852	SUBCLONAL	1	TRUE	1	0.15	2		624	626	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430385	181430385	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	27	569	0	ENST00000325404.1:c.237G>A	p.Trp79Ter	p.W79*	ENST00000325404	NM_003106.3	79	tgG/tgA	1/1	1	2	FACETS	0.727	0.578	0.899	0.727	0.578	0.899	SUBCLONAL	1	TRUE	1	0.15	2		569	495	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677967	117677967	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	48	791	0	ENST00000368508.3:c.3966C>A	p.Asn1322Lys	p.N1322K	ENST00000368508	NM_002944.2	1322	aaC/aaA	25/43	1	2	FACETS	0.696	0.587	0.818	0.696	0.587	0.818	SUBCLONAL	1	TRUE	1	0.15	2		791	919	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779181	135779181	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202241429	NA	P-0012124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	28	508	0	ENST00000298552.3:c.2065C>T	p.Arg689Cys	p.R689C	ENST00000298552	NM_001162426.1	689	Cgc/Tgc	17/23	0.115109117719326	1	FACETS	0.73	0.583	0.899	0.73	0.583	0.899	SUBCLONAL	1	TRUE	0	0.15	1		508	473	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437596	56437596	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	30	440	0	ENST00000407977.2:c.866C>T	p.Ser289Phe	p.S289F	ENST00000407977		289	tCc/tTc	8/10	1	2	FACETS	0.83	0.668	1	0.83	0.668	1	CLONAL	1	TRUE	1	0.15	2		440	482	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743289	743289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	42	740	0	ENST00000314574.4:c.851G>A	p.Gly284Glu	p.G284E	ENST00000314574	NM_005433.3	284	gGa/gAa	7/12	1	2	FACETS	0.7	0.583	0.831	0.7	0.583	0.831	SUBCLONAL	1	TRUE	1	0.15	2		740	800	SUCCESS
AR	367	MSKCC	GRCh37	X	66905966	66905966	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1381185349	NA	P-0012124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	29	628	0	ENST00000374690.3:c.1883G>A	p.Gly628Glu	p.G628E	ENST00000374690	NM_000044.3	628	gGa/gAa	3/8	0.115109117719326	1	FACETS	0.681	0.546	0.836	0.681	0.546	0.836	SUBCLONAL	1	TRUE	0	0.15	1		628	525	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923649	72923650	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0012124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	37	868	0	ENST00000268489.5:c.3428_3429delinsAA	p.Arg1143Lys	p.R1143K	ENST00000268489	NM_006885.3	1143	aGG/aAA	4/10	0.115109117719326	1	FACETS	0.711	0.585	0.853	0.711	0.585	0.853	SUBCLONAL	1	TRUE	0	0.15	1		868	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579700	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AT	novel	NA	P-0012124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	52	588	0	ENST00000269305.4:c.96_96+1delinsAT		p.X32_splice	ENST00000269305	NM_001126112.2	32		3/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.15	2		588	529	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412045	116412045	+	splice_donor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0012149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	43	311	0	ENST00000397752.3:c.3028+2del		p.X1010_splice	ENST00000397752	NM_000245.2	1010			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		311	519	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0012160-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	263	371	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.235852743612657	7	FACETS	0.901	0.848	0.955	0.901	0.848	0.955	CLONAL	5	TRUE	2	0.235852743612657	7		371	787	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143129600	143129600	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	137	422	0	ENST00000262992.4:c.1050G>C	p.Gln350His	p.Q350H	ENST00000262992	NM_001101669.1	350	caG/caC	12/24	1	2	FACETS	0.987	0.909	1	1	0.991	1	CLONAL	2	FALSE	1	0.370062790525203	2		422	375	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434134	49434134	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	84	499	0	ENST00000301067.7:c.7419G>T	p.Gln2473His	p.Q2473H	ENST00000301067	NM_003482.3	2473	caG/caT	31/54	1	2	FACETS	0.814	0.72	0.914	0.814	0.72	0.914	CLONAL	1	FALSE	1	0.370062790525203	2		499	558	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862796	9862796	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	101	585	0	ENST00000330684.3:c.2507T>A	p.Ile836Asn	p.I836N	ENST00000330684	NM_001134407.1	836	aTc/aAc	12/13	0.261520469112859	1	FACETS	0.815	0.73	0.904	0.815	0.73	0.904	CLONAL	1	FALSE	0	0.370062790525203	1		585	546	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160199	22160199	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	93	597	0	ENST00000215832.6:c.432C>A	p.Asn144Lys	p.N144K	ENST00000215832	NM_002745.4	144	aaC/aaA	3/9	1	2	FACETS	0.855	0.761	0.954	0.855	0.761	0.954	CLONAL	1	FALSE	1	0.370062790525203	2		597	588	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0012192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	263	424	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.622819585345185	2	FACETS	0.998	0.953	1	0.998	0.953	1	CLONAL	2	TRUE	0	0.622819585345185	2		424	423	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729888	30729888	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	282	187	0	ENST00000295754.5:c.1409A>G	p.Tyr470Cys	p.Y470C	ENST00000295754	NM_003242.5	470	tAt/tGt	6/7	0.622819585345185	3	FACETS	0.997	0.958	1	0.997	0.958	1	CLONAL	3	TRUE	0	0.622819585345185	3		187	397	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528486	157528486	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554237969	NA	P-0012192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	278	386	0	ENST00000346085.5:c.6211G>T	p.Gly2071Ter	p.G2071*	ENST00000346085	NM_020732.3	2071	Gga/Tga	20/20	0.622819585345185	5	FACETS	0.898	0.845	0.953	0.599	0.563	0.635	CLONAL	2	TRUE	2	0.622819585345185	5		386	961	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781193	161781193	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	368	563	0	ENST00000366898.1:c.1212A>T	p.Glu404Asp	p.E404D	ENST00000366898	NM_004562.2	404	gaA/gaT	11/12	0.622819585345185	5	FACETS	0.838	0.795	0.883	0.559	0.53	0.589	CLONAL	2	TRUE	2	0.622819585345185	5		563	1363	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92252400	92252400	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	122	181	0	ENST00000265734.4:c.648G>T	p.Lys216Asn	p.K216N	ENST00000265734	NM_001259.6	216	aaG/aaT	6/8	0.59827820547974	4	FACETS	0.952	0.871	1	0.952	0.871	1	CLONAL	2	TRUE	2	0.622819585345185	4		181	334	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042322	42042322	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0012192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	628	944	1	ENST00000219905.7:c.6517A>T	p.Arg2173Ter	p.R2173*	ENST00000219905	NM_001164273.1	2173	Aga/Tga	17/24	0.622819585345185	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.622819585345185	2		945	917	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411868	63411868	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	568	942	2	ENST00000330258.3:c.1299C>A	p.His433Gln	p.H433Q	ENST00000330258	NM_152424.3	433	caC/caA	2/2	0.456129700546074	4	FACETS	0.864	0.829	0.9	0.864	0.829	0.9	CLONAL	2	TRUE	2	0.622819585345185	4		944	1712	SUCCESS
AR	367	MSKCC	GRCh37	X	66765322	66765322	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	521	629	0	ENST00000374690.3:c.334G>T	p.Glu112Ter	p.E112*	ENST00000374690	NM_000044.3	112	Gag/Tag	1/8	0.456129700546074	4	FACETS	0.987	0.947	1	0.987	0.947	1	CLONAL	2	TRUE	2	0.622819585345185	4		629	1375	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608300	100608300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	403	665	0	ENST00000308731.7:c.1790C>T	p.Pro597Leu	p.P597L	ENST00000308731	NM_000061.2	597	cCa/cTa	18/19	0.456129700546074	4	FACETS	0.954	0.909	0.999	0.954	0.909	0.999	CLONAL	2	TRUE	2	0.622819585345185	4		665	1101	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576913	7576943	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTTGTTGGGCAGTGCTAGGAAAGAGGCAAGG	GTTGTTGGGCAGTGCTAGGAAAGAGGCAAGG	-	novel	NA	P-0012192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	338	391	0	ENST00000269305.4:c.920-17_933del		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	0.622819585345185	3	FACETS	0.923	0.888	0.958			1	CLONAL	3	TRUE	NA	0.622819585345185	3		391	514	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944605	38944605	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	267	403	0	ENST00000357387.3:c.4856del	p.Leu1619Ter	p.L1619*	ENST00000357387	NM_152756.3	1619	tTa/ta	36/38	0.563262127569485	5	FACETS	0.978	0.92	1	0.652	0.613	0.692	CLONAL	2	TRUE	2	0.622819585345185	5		403	848	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0012204-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	89	662	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.129051135809994	4	FACETS	0.818	0.726	0.917	0.409	0.363	0.459	INDETERMINATE	1	TRUE	2	0.481672295146802	4		662	669	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240362	98240362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767273237	NA	P-0012204-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	143	526	1	ENST00000331920.6:c.1322G>A	p.Arg441His	p.R441H	ENST00000331920	NM_000264.3	441	cGc/cAc	9/24	0.31893020730414	2	FACETS	0.811	0.749	0.875	0.811	0.749	0.875	CLONAL	2	TRUE	0	0.481672295146802	2		527	366	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265795	16265795	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012204-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	106	804	2	ENST00000375759.3:c.10868C>T	p.Ala3623Val	p.A3623V	ENST00000375759	NM_015001.2	3623	gCc/gTc	15/15	0.345641444330195	1	FACETS	0.484	0.434	0.537	0.484	0.434	0.537	SUBCLONAL	1	TRUE	0	0.481672295146802	1		806	690	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44921966	44921966	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012204-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	314	665	0	ENST00000377967.4:c.1500T>G	p.Ser500Arg	p.S500R	ENST00000377967	NM_021140.2	500	agT/agG	15/29	0.179670313650914	2	FACETS	0.799	0.757	0.841	0.799	0.757	0.841	INDETERMINATE	2	TRUE	0	0.481672295146802	2		665	816	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215315	123215315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012204-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	395	899	0	ENST00000218089.9:c.2861G>A	p.Arg954His	p.R954H	ENST00000218089	NM_001042749.1	954	cGt/cAt	28/35	0.481672295146802	3	FACETS	0.897	0.853	0.94	0.897	0.853	0.94	CLONAL	2	TRUE	1	0.481672295146802	3		899	1135	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111503	8111507	+	frameshift_variant	Frame_Shift_Del	DEL	GGAAT	GGAAT	-	novel	NA	P-0012204-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	172	668	0	ENST00000346208.3:c.990_994del	p.Arg330SerfsTer20	p.R330Sfs*20	ENST00000346208		330	aGGAAT/a	5/6	0.329886276969292	2	FACETS	1	0.983	1	0.609	0.564	0.657	CLONAL	1	TRUE	0	0.481672295146802	2		668	586	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597601	28597706	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATATTCAATTTCATCTGTAAAATAGAGCCAGTCTTCACTTTTGCCAAAACTCTAAGAAGTTGCCTTATTAAATCTCTATGGGAAGGTTATTCAAGCCAGAGTTAGG	ATATTCAATTTCATCTGTAAAATAGAGCCAGTCTTCACTTTTGCCAAAACTCTAAGAAGTTGCCTTATTAAATCTCTATGGGAAGGTTATTCAAGCCAGAGTTAGG	GTAGTCA	novel	NA	P-0012204-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	71	610	0	ENST00000241453.7:c.2291-92_2304delinsTGACTAC		p.X764_splice	ENST00000241453	NM_004119.2	764		19/24	1	2	FACETS	0.752	0.66	0.851	0.752	0.66	0.851	SUBCLONAL	1	TRUE	1	0.481672295146802	2		610	392	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389107	31389107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749860839	NA	P-0012230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	157	602	0	ENST00000328111.2:c.2020G>A	p.Glu674Lys	p.E674K	ENST00000328111	NM_006892.3	674	Gaa/Aaa	19/23	0.3	1	FACETS	0.941	0.863	1	1	0.991	1	CLONAL	2	TRUE	0	0.2	1		602	751	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0012230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	54	397	0	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	0.3	3	FACETS	0.931	0.794	1			1	CLONAL	1	TRUE	NA	0.2	3		397	638	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111958593	111958593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555186772	NA	P-0012230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	100	419	0	ENST00000375549.3:c.65G>A	p.Arg22Gln	p.R22Q	ENST00000375549	NM_003002.3	22	cGa/cAa	2/4	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.2	2		419	759	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720870	89720870	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1554825652	NA	P-0012230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	114	339	0	ENST00000371953.3:c.1021T>G	p.Phe341Val	p.F341V	ENST00000371953	NM_000314.4	341	Ttt/Gtt	8/9	1	2	FACETS	1	0.953	1	1	0.989	1	CLONAL	2	TRUE	1	0.2	2		339	523	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0012230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	178	717	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	0.991	0.914	1	1	0.992	1	CLONAL	2	TRUE	1	0.2	2		717	898	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976476	25976476	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	235	934	1	ENST00000435504.4:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000435504		357	Cga/Tga	11/13	0.3	3	FACETS	0.947	0.881	1			1	CLONAL	2	TRUE	NA	0.2	3		935	1365	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347916	73347916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139907646	NA	P-0012230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	150	528	0	ENST00000377767.4:c.1145G>A	p.Arg382Gln	p.R382Q	ENST00000377767	NM_014953.3	382	cGa/cAa	8/21	0.169943196844432	3	FACETS	0.942	0.861	1	0.942	0.861	1	CLONAL	2	TRUE	1	0.2	3		528	876	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610695	52610695	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	61	494	4	ENST00000394830.3:c.3478C>T	p.Arg1160Ter	p.R1160*	ENST00000394830	NM_018313.4	1160	Cga/Tga	23/30	0.169943196844432	3	FACETS	0.848	0.73	0.977	0.424	0.365	0.489	CLONAL	1	TRUE	1	0.2	3		498	791	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333410	70333410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	187	758	0	ENST00000373644.4:c.1315C>T	p.Pro439Ser	p.P439S	ENST00000373644	NM_030625.2	439	Cca/Tca	2/12	1	2	FACETS	0.948	0.876	1	1	0.992	1	CLONAL	2	TRUE	1	0.2	2		758	986	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509395	46509395	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866927502	NA	P-0012230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	153	682	2	ENST00000262741.5:c.1336G>A	p.Val446Ile	p.V446I	ENST00000262741	NM_003629.3	446	Gtc/Atc	10/10	1	2	FACETS	0.889	0.813	0.967	1	0.99	1	CLONAL	2	TRUE	1	0.2	2		684	861	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982386	25982386	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	168	547	0	ENST00000435504.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000435504		302	Cga/Tga	9/13	0.3	3	FACETS	0.987	0.907	1			1	CLONAL	2	TRUE	NA	0.2	3		547	936	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212289020	212289020	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	109	532	0	ENST00000342788.4:c.2726C>A	p.Thr909Asn	p.T909N	ENST00000342788	NM_005235.2	909	aCt/aAt	23/28	0.3	1	FACETS	0.752	0.677	0.832	1	0.983	1	SUBCLONAL	2	TRUE	0	0.2	1		532	652	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070325	37070325	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778917	NA	P-0012230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	168	778	2	ENST00000231790.2:c.1460G>A	p.Arg487Gln	p.R487Q	ENST00000231790	NM_000249.3	487	cGa/cAa	13/19	0.169943196844432	3	FACETS	0.816	0.749	0.887	0.816	0.749	0.887	CLONAL	2	TRUE	1	0.2	3		780	1132	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181926	38181926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1559484615	NA	P-0012230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	38	518	1	ENST00000396334.3:c.550G>A	p.Asp184Asn	p.D184N	ENST00000396334	NM_002468.4	184	Gac/Aac	3/5	0.169943196844432	3	FACETS	0.569	0.469	0.681	0.284	0.234	0.341	SUBCLONAL	1	TRUE	1	0.2	3		519	735	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164385	47164385	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	141	442	0	ENST00000409792.3:c.1741G>T	p.Glu581Ter	p.E581*	ENST00000409792	NM_014159.6	581	Gaa/Taa	3/21	0.169943196844432	3	FACETS	0.965	0.879	1	0.965	0.879	1	CLONAL	2	TRUE	1	0.2	3		442	804	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521741	89521741	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	99	441	2	ENST00000336596.2:c.2818T>C	p.Cys940Arg	p.C940R	ENST00000336596	NM_005233.5	940	Tgt/Cgt	16/17	0.3	2	FACETS	0.858	0.768	0.953			1	CLONAL	2	TRUE	NA	0.2	2		443	577	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189868	66189868	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763651163	NA	P-0012230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	178	685	0	ENST00000273854.3:c.3078G>T	p.Met1026Ile	p.M1026I	ENST00000273854	NM_004439.5	1026	atG/atT	18/18	0.169943196844432	0	FACETS	0.746	0.688	0.807			1	SUBCLONAL	2	TRUE	0	0.2	0		685	954	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286249	66286249	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	151	607	0	ENST00000273854.3:c.1437A>C	p.Lys479Asn	p.K479N	ENST00000273854	NM_004439.5	479	aaA/aaC	6/18	0.169943196844432	0	FACETS	0.749	0.686	0.816			1	SUBCLONAL	2	TRUE	0	0.2	0		607	806	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38954911	38954911	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	59	517	0	ENST00000357387.3:c.2662C>A	p.His888Asn	p.H888N	ENST00000357387	NM_152756.3	888	Cac/Aac	27/38	0.169943196844432	3	FACETS	0.758	0.651	0.876	0.379	0.325	0.438	SUBCLONAL	1	TRUE	1	0.2	3		517	856	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659183	86659183	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	105	388	0	ENST00000274376.6:c.1472A>C	p.Lys491Thr	p.K491T	ENST00000274376	NM_002890.2	491	aAa/aCa	11/25	0.169943196844432	3	FACETS	1	0.902	1	1	0.902	1	CLONAL	2	TRUE	1	0.2	3		388	575	SUCCESS
APC	324	MSKCC	GRCh37	5	112177368	112177368	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	136	466	0	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	0.991	1	CLONAL	2	TRUE	1	0.2	2		466	662	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709529	176709529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777258117	NA	P-0012230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	207	808	0	ENST00000439151.2:c.5956C>T	p.Arg1986Cys	p.R1986C	ENST00000439151	NM_022455.4	1986	Cgc/Tgc	19/23	0.3	3	FACETS	0.892	0.826	0.961			1	CLONAL	2	TRUE	NA	0.2	3		808	1276	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710773	117710773	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	141	684	0	ENST00000368508.3:c.1499A>C	p.Lys500Thr	p.K500T	ENST00000368508	NM_002944.2	500	aAa/aCa	12/43	0.3	0	FACETS	0.786	0.717	0.857			1	SUBCLONAL	2	TRUE	0	0.2	0		684	718	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331930	81331930	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	63	439	0	ENST00000222390.5:c.2154A>C	p.Lys718Asn	p.K718N	ENST00000222390	NM_000601.4	718	aaA/aaC	18/18	1	2	FACETS	0.831	0.718	0.955	0.831	0.718	0.955	CLONAL	1	TRUE	1	0.2	2		439	758	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92300747	92300747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	79	304	0	ENST00000265734.4:c.640C>T	p.Arg214Cys	p.R214C	ENST00000265734	NM_001259.6	214	Cgt/Tgt	5/8	1	2	FACETS	1	0.895	1	1	0.984	1	CLONAL	2	TRUE	1	0.2	2		304	390	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089782	5089782	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	137	556	0	ENST00000381652.3:c.2680G>A	p.Asp894Asn	p.D894N	ENST00000381652	NM_004972.3	894	Gac/Aac	20/25	0.3	1	FACETS	0.834	0.76	0.912	1	0.988	1	CLONAL	2	TRUE	0	0.2	1		556	739	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690835	89690835	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs876661177	NA	P-0012230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	114	336	0	ENST00000371953.3:c.242T>G	p.Phe81Cys	p.F81C	ENST00000371953	NM_000314.4	81	tTt/tGt	4/9	1	2	FACETS	1	0.947	1	1	0.989	1	CLONAL	2	TRUE	1	0.2	2		336	532	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741687	17741687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	136	506	2	ENST00000250003.3:c.358C>T	p.Arg120Cys	p.R120C	ENST00000250003	NM_002478.4	120	Cgc/Tgc	1/3	0.264848188229878	0	FACETS	0.826	0.757	0.897			1	CLONAL	3	TRUE	0	0.2	0		508	439	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608081	28608081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746946336	NA	P-0012230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	211	900	0	ENST00000241453.7:c.1885G>A	p.Ala629Thr	p.A629T	ENST00000241453	NM_004119.2	629	Gct/Act	15/24	0.169943196844432	0	FACETS	0.861	0.8	0.925			1	CLONAL	2	TRUE	0	0.2	0		900	980	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778477	3778477	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	88	834	0	ENST00000262367.5:c.6571G>A	p.Glu2191Lys	p.E2191K	ENST00000262367	NM_004380.2	2191	Gaa/Aaa	31/31	0.3	2	FACETS	0.928	0.821	1			1	CLONAL	1	TRUE	NA	0.2	2		834	948	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858255	9858255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	96	694	2	ENST00000330684.3:c.3146C>T	p.Pro1049Leu	p.P1049L	ENST00000330684	NM_001134407.1	1049	cCt/cTt	13/13	0.3	0	FACETS	0.691	0.617	0.769			1	SUBCLONAL	2	TRUE	0	0.2	0		696	556	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830931	72830931	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	238	1259	2	ENST00000268489.5:c.5650G>T	p.Glu1884Ter	p.E1884*	ENST00000268489	NM_006885.3	1884	Gaa/Taa	9/10	0.373776097236447	0	FACETS	1	0.962	1			1	CLONAL	2	TRUE	0	0.2	0		1261	914	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654829	29654829	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	122	450	0	ENST00000356175.3:c.5518A>C	p.Asn1840His	p.N1840H	ENST00000356175	NM_000267.3	1840	Aat/Cat	37/57	0.169943196844432	3	FACETS	0.903	0.817	0.994	0.903	0.817	0.994	CLONAL	2	TRUE	1	0.2	3		450	743	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624781	9624781	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	79	322	0	ENST00000353224.5:c.196C>T	p.Pro66Ser	p.P66S	ENST00000353224	NM_177990.2	66	Cct/Tct	3/10	0.3	1	FACETS	0.985	0.872	1	1	0.984	1	CLONAL	2	TRUE	0	0.2	1		322	361	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980926	40980926	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0012230-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	86	357	0	ENST00000373198.4:c.1561-1G>A		p.X521_splice	ENST00000373198	NM_133170.3	521			0.3	0	FACETS	0.966	0.862	1			1	CLONAL	2	TRUE	0	0.2	0		357	356	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746135	162746135	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012241-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	147	467	0	ENST00000367921.3:c.2258G>T	p.Trp753Leu	p.W753L	ENST00000367921	NM_006182.2	753	tGg/tTg	16/18	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.397987692465598	2		467	656	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120830	94120830	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012241-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	241	996	4	ENST00000369303.4:c.221G>T	p.Cys74Phe	p.C74F	ENST00000369303	NM_004440.3	74	tGc/tTc	3/17	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.397987692465598	2		1000	1087	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663582	117663582	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012241-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	160	644	0	ENST00000368508.3:c.4650G>C	p.Trp1550Cys	p.W1550C	ENST00000368508	NM_002944.2	1550	tgG/tgC	28/43	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.397987692465598	2		644	698	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740751	145740751	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012241-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	167	581	1	ENST00000428558.2:c.1349T>A	p.Val450Glu	p.V450E	ENST00000428558	NM_004260.3	450	gTg/gAg	7/22	0.295668936048453	2	FACETS	1	0.989	1	0.741	0.685	0.799	CLONAL	1	TRUE	0	0.397987692465598	2		582	566	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636764	8636764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012241-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	119	479	0	ENST00000356435.5:c.145G>A	p.Gly49Arg	p.G49R	ENST00000356435		49	Gga/Aga	2/35	0.397987692465598	1	FACETS	0.899	0.815	0.987	0.899	0.815	0.987	CLONAL	1	TRUE	0	0.397987692465598	1		479	533	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465989	69465989	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1436128793	NA	P-0012241-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	130	608	0	ENST00000227507.2:c.827A>T	p.Glu276Val	p.E276V	ENST00000227507	NM_053056.2	276	gAg/gTg	5/5	0.201820321855835	1	FACETS	1	0.941	1	1	0.941	1	INDETERMINATE	1	TRUE	0	0.397987692465598	1		608	503	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383306	4383306	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012241-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	97	518	0	ENST00000261254.3:c.100G>C	p.Glu34Gln	p.E34Q	ENST00000261254	NM_001759.3	34	Gag/Cag	1/5	0.382027129981624	3	FACETS	0.789	0.703	0.88			1	SUBCLONAL	1	TRUE	NA	0.397987692465598	3		518	741	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929164	32929164	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0012241-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	194	996	2	ENST00000380152.3:c.7174A>T	p.Lys2392Ter	p.K2392*	ENST00000380152		2392	Aaa/Taa	14/27	0.397987692465598	1	FACETS	0.886	0.821	0.954	0.886	0.821	0.954	CLONAL	1	TRUE	0	0.397987692465598	1		998	881	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941675	48941675	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0012241-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	166	453	0	ENST00000267163.4:c.985A>T	p.Lys329Ter	p.K329*	ENST00000267163	NM_000321.2	329	Aaa/Taa	10/27	NA	2	FACETS	0.833	0.771	0.896			1	INDETERMINATE	2	TRUE	NA	0.397987692465598	2		453	501	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579592	7579594	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TGT	TGT	-	novel	NA	P-0012241-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	94	440	1	ENST00000269305.4:c.97-4_97-2del		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.397987692465598	1	FACETS	0.953	0.854	1	0.953	0.854	1	CLONAL	1	TRUE	0	0.397987692465598	1		441	397	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397762	139397762	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	609	442	0	ENST00000277541.6:c.5039T>A	p.Ile1680Asn	p.I1680N	ENST00000277541	NM_017617.3	1680	aTt/aAt	27/34	0.926535611707882	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.926535611707882	3		442	634	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375188	31375188	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	38	644	2	ENST00000328111.2:c.585C>A	p.Ser195Arg	p.S195R	ENST00000328111	NM_006892.3	195	agC/agA	6/23	1	2	FACETS	0.125	0.103	0.151	0.125	0.103	0.151	SUBCLONAL	1	TRUE	1	0.926535611707882	2		646	654	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776364	76776364	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	352	370	0	ENST00000373344.5:c.7102C>T	p.Gln2368Ter	p.Q2368*	ENST00000373344	NM_000489.3	2368	Caa/Taa	34/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.926535611707882	1		370	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0012273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	193	470	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.226271193680058	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.226271193680058	3		471	804	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688735	47688735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	91	398	1	ENST00000347630.2:c.565G>A	p.Glu189Lys	p.E189K	ENST00000347630	NM_001007230.1	189	Gag/Aag	7/11	0.226271193680058	4	FACETS	0.868	0.769	0.975	0.434	0.384	0.488	CLONAL	1	TRUE	2	0.226271193680058	4		399	1136	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256501	16256501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	50	409	1	ENST00000375759.3:c.3766G>A	p.Glu1256Lys	p.E1256K	ENST00000375759	NM_015001.2	1256	Gaa/Aaa	11/15	0.226271193680058	3	FACETS	0.565	0.478	0.661			1	SUBCLONAL	1	TRUE	NA	0.226271193680058	3		410	871	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849835	156849835	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	158	424	0	ENST00000524377.1:c.2091G>C	p.Glu697Asp	p.E697D	ENST00000524377	NM_002529.3	697	gaG/gaC	16/17	0.226271193680058	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	2	0.226271193680058	4		424	808	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464454	25464454	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	141	443	0	ENST00000264709.3:c.2059G>T	p.Val687Phe	p.V687F	ENST00000264709	NM_175629.2	687	Gtc/Ttc	17/23	0.226271193680058	3	FACETS	0.904	0.825	0.988	0.904	0.825	0.988	CLONAL	2	TRUE	1	0.226271193680058	3		443	767	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356385	66356385	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	34	398	0	ENST00000273854.3:c.1112C>G	p.Thr371Ser	p.T371S	ENST00000273854	NM_004439.5	371	aCt/aGt	5/18	0.226271193680058	3	FACETS	0.56	0.457	0.678	0.187	0.152	0.226	SUBCLONAL	1	TRUE	0	0.226271193680058	3		398	597	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532796	187532796	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	44	516	0	ENST00000441802.2:c.9597G>C	p.Leu3199Phe	p.L3199F	ENST00000441802	NM_005245.3	3199	ttG/ttC	14/27	0.226271193680058	3	FACETS	0.55	0.46	0.651	0.183	0.153	0.217	SUBCLONAL	1	TRUE	0	0.226271193680058	3		516	787	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120647	94120647	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	151	751	0	ENST00000369303.4:c.404G>C	p.Gly135Ala	p.G135A	ENST00000369303	NM_004440.3	135	gGc/gCc	3/17	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.226271193680058	2		751	1079	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341917	8341917	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	38	417	0	ENST00000356435.5:c.4723C>A	p.His1575Asn	p.H1575N	ENST00000356435		1575	Cat/Aat	29/35	0.162670193113683	2	FACETS	0.51	0.421	0.611	0.255	0.21	0.306	SUBCLONAL	1	TRUE	0	0.226271193680058	2		417	658	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389245	8389245	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	61	498	0	ENST00000356435.5:c.4373A>G	p.Glu1458Gly	p.E1458G	ENST00000356435		1458	gAa/gGa	26/35	0.162670193113683	2	FACETS	0.654	0.562	0.753	0.327	0.281	0.377	SUBCLONAL	1	TRUE	0	0.226271193680058	2		498	825	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755519	133755519	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs62580066	NA	P-0012273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	139	469	0	ENST00000318560.5:c.1488G>T	p.Met496Ile	p.M496I	ENST00000318560	NM_005157.4	496	atG/atT	9/11	0.162670193113683	2	FACETS	0.819	0.746	0.895	0.819	0.746	0.895	CLONAL	2	TRUE	0	0.226271193680058	2		469	750	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609007	43609007	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398378776	NA	P-0012273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	68	616	0	ENST00000355710.3:c.1763G>A	p.Gly588Asp	p.G588D	ENST00000355710	NM_020975.4	588	gGc/gAc	10/20	0.206269879183087	3	FACETS	0.786	0.682	0.899	0.393	0.341	0.45	SUBCLONAL	1	TRUE	1	0.226271193680058	3		616	851	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456485	32456485	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	55	110	1	ENST00000332351.3:c.407C>T	p.Pro136Leu	p.P136L	ENST00000332351	NM_024426.4	136	cCt/cTt	1/10	0.226271193680058	3	FACETS	0.897	0.779	1	1	0.963	1	CLONAL	3	TRUE	1	0.226271193680058	3		111	201	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102098231	102098231	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	42	428	0	ENST00000282441.5:c.1195G>C	p.Asp399His	p.D399H	ENST00000282441	NM_001130145.2	399	Gac/Cac	8/9	0.226271193680058	3	FACETS	0.536	0.446	0.636	0.268	0.223	0.318	SUBCLONAL	1	TRUE	1	0.226271193680058	3		428	771	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559764	29559764	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1567851029	NA	P-0012273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	77	422	0	ENST00000356175.3:c.3361G>T	p.Glu1121Ter	p.E1121*	ENST00000356175	NM_000267.3	1121	Gaa/Taa	26/57	0.226271193680058	3	FACETS	0.963	0.844	1	0.481	0.422	0.545	CLONAL	1	TRUE	1	0.226271193680058	3		422	787	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617679	39617679	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	101	405	1	ENST00000262039.4:c.1863G>T	p.Leu621Phe	p.L621F	ENST00000262039	NM_002647.2	621	ttG/ttT	17/25	0.226271193680058	5	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.226271193680058	5		406	899	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175811	24175811	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	37	447	0	ENST00000263121.7:c.1039G>C	p.Asp347His	p.D347H	ENST00000263121	NM_003073.3	347	Gac/Cac	8/9	0.161313362856131	3	FACETS	0.506	0.415	0.607			1	SUBCLONAL	1	TRUE	NA	0.226271193680058	3		447	720	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966723	44966723	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	98	303	0	ENST00000377967.4:c.3947A>T	p.Glu1316Val	p.E1316V	ENST00000377967	NM_021140.2	1316	gAg/gTg	27/29	1	1	FACETS	0.821	0.736	0.91	1	0.984	1	CLONAL	2	TRUE	0	0.226271193680058	1		303	468	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240997	53240997	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	142	320	0	ENST00000375401.3:c.1214A>C	p.Lys405Thr	p.K405T	ENST00000375401	NM_004187.3	405	aAa/aCa	9/26	0.226271193680058	2	FACETS	1	0.979	1			1	CLONAL	2	TRUE	NA	0.226271193680058	2		320	520	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573508	48573539	+	frameshift_variant	Frame_Shift_Del	DEL	AGAGTGAAACATTTGCAAAAAGAGCAATTGAA	AGAGTGAAACATTTGCAAAAAGAGCAATTGAA	-	novel	NA	P-0012273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	71	378	0	ENST00000342988.3:c.94_125del	p.Ser32PhefsTer11	p.S32Ffs*11	ENST00000342988	NM_005359.5	31	gAGAGTGAAACATTTGCAAAAAGAGCAATTGAA/g	2/12	0.162670193113683	2	FACETS	1	0.916	1	0.532	0.464	0.605	CLONAL	1	TRUE	0	0.226271193680058	2		378	590	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188829	32188829	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012273-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	43	433	0	ENST00000375023.3:c.725del	p.Gly242AlafsTer10	p.G242Afs*10	ENST00000375023	NM_004557.3	242	gGc/gc	4/30	0.226271193680058	3	FACETS	0.61	0.51	0.723	0.305	0.255	0.362	SUBCLONAL	1	TRUE	1	0.226271193680058	3		433	693	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0012280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	484	683	2	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.422019647477048	6	FACETS	0.941	0.901	0.981	0.941	0.901	0.981	CLONAL	3	TRUE	3	0.6278091615705	6		685	1232	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578476	7578476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767328513	NA	P-0012280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	497	553	0	ENST00000269305.4:c.454C>T	p.Pro152Ser	p.P152S	ENST00000269305	NM_001126112.2	152	Ccg/Tcg	5/11	0.422019647477048	6	FACETS	0.912	0.873	0.95	0.912	0.873	0.95	CLONAL	3	TRUE	3	0.6278091615705	6		553	1306	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125789	47125789	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	378	451	0	ENST00000409792.3:c.5481G>T	p.Trp1827Cys	p.W1827C	ENST00000409792	NM_014159.6	1827	tgG/tgT	12/21	0.526084039379596	3	FACETS	0.922	0.889	0.955	0.922	0.889	0.955	CLONAL	3	TRUE	0	0.6278091615705	3		451	572	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270177	66270177	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	205	556	2	ENST00000273854.3:c.1705C>T	p.Gln569Ter	p.Q569*	ENST00000273854	NM_004439.5	569	Caa/Taa	8/18	1	2	FACETS	0.944	0.879	1	0.944	0.879	1	CLONAL	1	TRUE	1	0.6278091615705	2		558	692	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022307	26022307	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	670	781	0	ENST00000435504.4:c.350G>C	p.Ser117Thr	p.S117T	ENST00000435504		117	aGc/aCc	5/13	0.6278091615705	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.6278091615705	3		781	1346	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551347	29551347	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	171	433	0	ENST00000389048.3:c.1283G>C	p.Gly428Ala	p.G428A	ENST00000389048	NM_004304.4	428	gGa/gCa	6/29	0.6278091615705	3	FACETS	0.827	0.762	0.896	0.414	0.381	0.448	CLONAL	1	TRUE	1	0.6278091615705	3		433	865	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851841	134851841	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	530	564	1	ENST00000398015.3:c.1247G>T	p.Ser416Ile	p.S416I	ENST00000398015	NM_004441.4	416	aGt/aTt	5/16	0.6278091615705	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.6278091615705	4		565	1296	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777904	27777904	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1231	418	1141	1	ENST00000369163.2:c.53G>T	p.Arg18Leu	p.R18L	ENST00000369163	NM_003536.2	18	cGc/cTc	1/1	0.6278091615705	3	FACETS	1	0.981	1	0.531	0.504	0.558	CLONAL	1	TRUE	1	0.6278091615705	3		1142	1649	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163560	32163560	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	197	515	0	ENST00000375023.3:c.5666G>C	p.Arg1889Pro	p.R1889P	ENST00000375023	NM_004557.3	1889	cGg/cCg	30/30	0.6278091615705	3	FACETS	0.961	0.891	1	0.481	0.445	0.517	CLONAL	1	TRUE	1	0.6278091615705	3		515	858	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317894	8317894	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	476	570	0	ENST00000356435.5:c.5719T>A	p.Phe1907Ile	p.F1907I	ENST00000356435		1907	Ttt/Att	35/35	0.553179041878202	4	FACETS	0.975	0.933	1	0.975	0.933	1	CLONAL	2	TRUE	2	0.6278091615705	4		570	1266	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500793	8500793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	351	517	1	ENST00000356435.5:c.2089C>T	p.Pro697Ser	p.P697S	ENST00000356435		697	Cct/Tct	13/35	0.553179041878202	4	FACETS	0.95	0.902	0.998	0.95	0.902	0.998	CLONAL	2	TRUE	2	0.6278091615705	4		518	958	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120954	115120954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	428	485	1	ENST00000257566.3:c.52C>T	p.His18Tyr	p.H18Y	ENST00000257566	NM_016569.3	18	Cat/Tat	1/8	0.6278091615705	3	FACETS	0.954	0.913	0.995	0.954	0.913	0.995	CLONAL	2	TRUE	1	0.6278091615705	3		486	939	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28631526	28631526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1174	509	647	0	ENST00000241453.7:c.442G>A	p.Glu148Lys	p.E148K	ENST00000241453	NM_004119.2	148	Gaa/Aaa	4/24	0.578078856864131	5	FACETS	0.935	0.894	0.977			1	CLONAL	2	TRUE	NA	0.6278091615705	5		647	1683	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954221	48954221	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0012280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	544	485	0	ENST00000267163.4:c.1421+1G>T		p.X474_splice	ENST00000267163	NM_000321.2	474			0.622615311261848	3	FACETS	0.912	0.884	0.94	0.912	0.884	0.94	CLONAL	3	TRUE	0	0.6278091615705	3		485	832	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42002991	42002991	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	810	918	1	ENST00000219905.7:c.2528G>T	p.Gly843Val	p.G843V	ENST00000219905	NM_001164273.1	843	gGt/gTt	8/24	0.6278091615705	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.6278091615705	2		919	1269	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141557	11141557	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	534	601	0	ENST00000358026.2:c.3534G>C	p.Trp1178Cys	p.W1178C	ENST00000358026	NM_001128849.1	1178	tgG/tgC	25/36	0.6278091615705	2	FACETS	0.974	0.943	1	0.974	0.943	1	CLONAL	2	TRUE	0	0.6278091615705	2		601	873	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481943	56481943	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	275	576	0	ENST00000267101.3:c.874del	p.His292IlefsTer21	p.H292Ifs*21	ENST00000267101	NM_001982.3	291	Ccc/cc	7/28	0.6278091615705	3	FACETS	1	0.976	1	0.537	0.504	0.571	CLONAL	1	TRUE	1	0.6278091615705	3		576	1071	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0012282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	219	332	0				ENST00000310581	NM_198253.2	-/1132			0.487677289681163	1	FACETS	0.885	0.831	0.94	0.885	0.831	0.94	CLONAL	1	TRUE	0	0.633470148863412	1		332	534	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0012282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	23	615	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.307151753846138	1	FACETS	0.054	0.042	0.069	0.054	0.042	0.069	INDETERMINATE	1	TRUE	0	0.633470148863412	1		615	915	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979281	40979281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	301	588	0	ENST00000373198.4:c.1852G>A	p.Gly618Arg	p.G618R	ENST00000373198	NM_133170.3	618	Gga/Aga	11/32	NA	2	FACETS	1	0.967	1			1	INDETERMINATE	1	TRUE	NA	0.633470148863412	2		588	920	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0012282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	414	620	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.633470148863412	3	FACETS	0.858	0.82	0.897	0.858	0.82	0.897	CLONAL	2	TRUE	1	0.633470148863412	3		620	1003	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129869	55129869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	416	794	0	ENST00000257290.5:c.403G>A	p.Asp135Asn	p.D135N	ENST00000257290	NM_006206.4	135	Gat/Aat	4/23	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.633470148863412	2		794	1293	SUCCESS
AXL	558	MSKCC	GRCh37	19	41737136	41737136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761251235	NA	P-0012282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	383	932	0	ENST00000301178.4:c.716C>T	p.Thr239Met	p.T239M	ENST00000301178	NM_021913.4	239	aCg/aTg	6/20	1	2	FACETS	0.89	0.844	0.936	0.89	0.844	0.936	CLONAL	1	TRUE	1	0.633470148863412	2		932	1359	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523087	25523087	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	201	672	0	ENST00000264709.3:c.98G>T	p.Arg33Leu	p.R33L	ENST00000264709	NM_175629.2	33	cGt/cTt	3/23	1	2	FACETS	0.556	0.514	0.599	0.556	0.514	0.599	SUBCLONAL	1	TRUE	1	0.633470148863412	2		672	1142	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457276	89457276	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778106353	NA	P-0012282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	122	571	0	ENST00000336596.2:c.1757G>A	p.Gly586Glu	p.G586E	ENST00000336596	NM_005233.5	586	gGg/gAg	9/17	0.312476747445706	1	FACETS	0.365	0.33	0.401	0.365	0.33	0.401	INDETERMINATE	1	TRUE	0	0.633470148863412	1		571	722	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840049	27840049	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2199	601	1234	0	ENST00000328488.2:c.45A>T	p.Lys15Asn	p.K15N	ENST00000328488	NM_003533.2	15	aaA/aaT	1/1	0.633470148863412	3	FACETS	0.892	0.854	0.931	0.446	0.427	0.466	CLONAL	1	TRUE	1	0.633470148863412	3		1234	2800	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656281	18656281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	257	601	1	ENST00000266497.5:c.2960G>A	p.Gly987Glu	p.G987E	ENST00000266497		987	gGa/gAa	21/31	1	2	FACETS	0.923	0.866	0.981	0.923	0.866	0.981	CLONAL	1	TRUE	1	0.633470148863412	2		602	879	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858592	9858592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769602505	NA	P-0012282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	386	974	1	ENST00000330684.3:c.2809G>A	p.Asp937Asn	p.D937N	ENST00000330684	NM_001134407.1	937	Gat/Aat	13/13	1	2	FACETS	0.954	0.907	1	0.954	0.907	1	CLONAL	1	TRUE	1	0.633470148863412	2		975	1277	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795407	39795407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371043321	NA	P-0012290-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	146	693	0	ENST00000288319.7:c.313G>A	p.Gly105Ser	p.G105S	ENST00000288319	NM_182918.3	105	Ggc/Agc	3/10	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.235960189635472	2		693	1165	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499382	89499382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	87	496	0	ENST00000336596.2:c.2552C>T	p.Ala851Val	p.A851V	ENST00000336596	NM_005233.5	851	gCt/gTt	15/17	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.22	2		496	742	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489457	40489457	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	60	632	0	ENST00000264657.5:c.793A>G	p.Asn265Asp	p.N265D	ENST00000264657	NM_139276.2	265	Aac/Gac	8/24	1	2	FACETS	0.524	0.45	0.605	0.524	0.45	0.605	SUBCLONAL	1	TRUE	1	0.22	2		632	1041	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0012310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	502	471	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.467002618992042	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.467002618992042	2		471	869	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0012310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	75	365	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.422102668543725	1	FACETS	0.751	0.663	0.843	0.751	0.663	0.843	SUBCLONAL	1	TRUE	0	0.467002618992042	1		365	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0012310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	210	539	1	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.426907965082569	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.467002618992042	1		540	627	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858505	9858505	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	95	529	0	ENST00000330684.3:c.2896T>G	p.Phe966Val	p.F966V	ENST00000330684	NM_001134407.1	966	Ttt/Gtt	13/13	0.215764958195887	1	FACETS	0.422	0.375	0.472	0.422	0.375	0.472	INDETERMINATE	1	TRUE	0	0.467002618992042	1		529	739	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222611	1223004	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTGGGCGCCTGGCGGGGACTGGGGCTGCCCCCCGATAGCCTCCTGGGCTGGGATGTGCTCAGGGCCCCCCAGACCCCCTTCTGGCCTTTGCTGGCTTTGCAGCCAGCATCCATCTGGTGGGTGCTGGCTTCTGAGTGCCACCTGGGACACAGGCCTCAGGGTGGAGGGGACATCTGTCAGGCTTGGAGTCAGGTCAGCCTGCCTGCTCCTAGAGGACATGGCTGAGCTTCTGTGGTCACAGCCACCCCTTGCACGGCCTGGTCCCAGCTCCTGAGTGTGTGGCAGGTACCCTGGGCCCAGAGGAGCTGGGTCGGAAAACTGGACCGCCCTGGTGCCAGCCTGACAGGCGCCACTGCTTCTGGGCGTTTGCAGCTGGTTCCGGAAGAAACATCC	TCTGGGCGCCTGGCGGGGACTGGGGCTGCCCCCCGATAGCCTCCTGGGCTGGGATGTGCTCAGGGCCCCCCAGACCCCCTTCTGGCCTTTGCTGGCTTTGCAGCCAGCATCCATCTGGTGGGTGCTGGCTTCTGAGTGCCACCTGGGACACAGGCCTCAGGGTGGAGGGGACATCTGTCAGGCTTGGAGTCAGGTCAGCCTGCCTGCTCCTAGAGGACATGGCTGAGCTTCTGTGGTCACAGCCACCCCTTGCACGGCCTGGTCCCAGCTCCTGAGTGTGTGGCAGGTACCCTGGGCCCAGAGGAGCTGGGTCGGAAAACTGGACCGCCCTGGTGCCAGCCTGACAGGCGCCACTGCTTCTGGGCGTTTGCAGCTGGTTCCGGAAGAAACATCC	-	novel	NA	P-0012310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	.	114	1	0	ENST00000326873.7:c.921-371_943del		p.X307_splice	ENST00000326873	NM_000455.4	307		8/10	0.467002618992042	1	FACETS		NA	1			1	NA	NA	TRUE	0	0.467002618992042	1		1	114	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610544	10610544	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	172	490	0	ENST00000171111.5:c.166del	p.Leu56TrpfsTer12	p.L56Wfs*12	ENST00000171111	NM_203500.1	56	Ctg/tg	2/6	0.467002618992042	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.467002618992042	1		490	520	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913250	NA	P-0012311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	393	599	0	ENST00000369535.4:c.34G>T	p.Gly12Cys	p.G12C	ENST00000369535	NM_002524.4	12	Ggt/Tgt	2/7	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.753941355708236	2		599	946	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289930	15289930	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	398	558	0	ENST00000263388.2:c.3624G>T	p.Glu1208Asp	p.E1208D	ENST00000263388	NM_000435.2	1208	gaG/gaT	22/33	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.753941355708236	2		558	1036	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653254	29653254	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	173	305	0	ENST00000356175.3:c.5190del	p.Val1732PhefsTer12	p.V1732Ffs*12	ENST00000356175	NM_000267.3	1730	aCc/ac	36/57	0.753941355708236	1	FACETS	0.882	0.828	0.937	0.882	0.828	0.937	CLONAL	1	TRUE	0	0.753941355708236	1		305	324	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0012318-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	37	316	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.803	0.669	0.951	0.803	0.669	0.951	CLONAL	1	TRUE	1	0.453773752396278	2		316	203	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115751	8115751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012318-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	135	905	2	ENST00000346208.3:c.1097G>A	p.Arg366Gln	p.R366Q	ENST00000346208		366	cGa/cAa	6/6	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.453773752396278	2		907	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	328	716	0	ENST00000269305.4:c.811G>C	p.Glu271Gln	p.E271Q	ENST00000269305	NM_001126112.2	271	Gag/Cag	8/11	0.167879980225691	3	FACETS	0.983	0.932	1			1	INDETERMINATE	3	FALSE	NA	0.282674914835646	3		716	898	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089037	37089037	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs267607862	NA	P-0012320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	88	508	0	ENST00000231790.2:c.1759A>G	p.Met587Val	p.M587V	ENST00000231790	NM_000249.3	587	Atg/Gtg	16/19	0.255900324648212	3	FACETS	1	0.888	1	0.501	0.444	0.562	CLONAL	1	FALSE	1	0.282674914835646	3		508	709	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400019	49400019	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	189	748	0	ENST00000418115.1:c.318C>G	p.Phe106Leu	p.F106L	ENST00000418115	NM_001664.2	106	ttC/ttG	4/5	0.255900324648212	3	FACETS	0.881	0.815	0.95	0.881	0.815	0.95	CLONAL	2	FALSE	1	0.282674914835646	3		748	866	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188214	142188214	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	71	509	1	ENST00000350721.4:c.6517C>T	p.Gln2173Ter	p.Q2173*	ENST00000350721	NM_001184.3	2173	Caa/Taa	38/47	0.255900324648212	3	FACETS	1	0.963	1	0.64	0.56	0.725	CLONAL	1	FALSE	1	0.282674914835646	3		510	448	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188402	142188402	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	72	355	0	ENST00000350721.4:c.6329C>G	p.Ser2110Cys	p.S2110C	ENST00000350721	NM_001184.3	2110	tCc/tGc	38/47	0.255900324648212	3	FACETS	0.759	0.667	0.857	0.759	0.667	0.857	SUBCLONAL	2	FALSE	1	0.282674914835646	3		355	383	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222975	5222975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	207	401	2	ENST00000357368.4:c.2828C>T	p.Ala943Val	p.A943V	ENST00000357368	NM_002850.3	943	gCc/gTc	18/38	0.255900324648212	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	FALSE	1	0.282674914835646	3		403	723	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012329-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	167	540	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.559404730315038	5	FACETS	0.925	0.863	0.988	0.925	0.863	0.988	CLONAL	3	TRUE	2	0.645328999942733	5		540	367	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0012329-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	222	622	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.484702343777458	2	FACETS	1	0.993	1	0.721	0.679	0.763	CLONAL	1	TRUE	0	0.645328999942733	2		622	477	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984016	2984016	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012329-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	216	753	0	ENST00000396946.4:c.514G>C	p.Glu172Gln	p.E172Q	ENST00000396946	NM_032415.4	172	Gag/Cag	5/25	0.408137017449893	4	FACETS	0.797	0.744	0.851	0.797	0.744	0.851	SUBCLONAL	2	TRUE	2	0.645328999942733	4		753	691	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436867	49436867	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012329-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	236	790	0	ENST00000301067.7:c.5636C>G	p.Ser1879Cys	p.S1879C	ENST00000301067	NM_003482.3	1879	tCc/tGc	25/54	0.559404730315038	5	FACETS	1	0.985	1	0.762	0.715	0.809	CLONAL	2	TRUE	2	0.645328999942733	5		790	630	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581219	48581222	+	stop_gained	Nonsense_Mutation	ONP	GAAG	GAAG	AAAT	novel	NA	P-0012329-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	113	685	1	ENST00000342988.3:c.523_526delinsAAAT	p.Glu175_Gly176delinsLysTer	p.E175_G176delinsK*	ENST00000342988	NM_005359.5	175	GAAGga/AAATga	5/12	0.447239917804044	2	FACETS	1	0.978	1	0.614	0.562	0.668	CLONAL	1	TRUE	0	0.645328999942733	2		686	285	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578440	7578440	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs879254249	NA	P-0012338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	156	408	0	ENST00000269305.4:c.490A>G	p.Lys164Glu	p.K164E	ENST00000269305	NM_001126112.2	164	Aag/Gag	5/11	0.76652924187632	2	FACETS	0.963	0.924	0.997	0.963	0.924	0.997	CLONAL	2	TRUE	0	0.875830468305325	2		408	185	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866710	37866710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1258412021	NA	P-0012338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	68	529	1	ENST00000269571.5:c.877G>A	p.Ala293Thr	p.A293T	ENST00000269571		293	Gcc/Acc	7/27	0.76652924187632	2	FACETS	0.769	0.681	0.86	0.384	0.34	0.43	SUBCLONAL	1	TRUE	0	0.875830468305325	2		530	202	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480494	57480496	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CGA	CGA	G	novel	NA	P-0012338-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	86	314	0	ENST00000371085.3:c.489_491delinsG	p.Tyr163Ter	p.Y163*	ENST00000371085	NM_000516.4	163	taCGAa/taGa	6/13	0.733326362164461	6	FACETS	0.801	0.708	0.899	0.267	0.236	0.3	CLONAL	1	TRUE	3	0.875830468305325	6		314	675	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812293	212812293	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569995088	NA	P-0012364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	121	427	0	ENST00000342788.4:c.283C>T	p.Arg95Cys	p.R95C	ENST00000342788	NM_005235.2	95	Cgt/Tgt	3/28	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.448222988763205	2		427	500	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183765	10183765	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012364-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	82	314	0	ENST00000256474.2:c.234T>A	p.Asn78Lys	p.N78K	ENST00000256474	NM_000551.3	78	aaT/aaA	1/3	0.448222988763205	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.448222988763205	1		314	212	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119545693	119545693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1559797928	NA	P-0012370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	98	418	0	ENST00000316626.5:c.1244C>T	p.Thr415Ile	p.T415I	ENST00000316626		415	aCt/aTt	12/12	1	2	FACETS	0.477	0.425	0.532	0.477	0.425	0.532	SUBCLONAL	1	TRUE	1	0.556373140302298	2		418	739	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	84	540	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	0.15	2		540	984	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578415	7578415	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	36	739	0	ENST00000269305.4:c.515T>A	p.Val172Asp	p.V172D	ENST00000269305	NM_001126112.2	172	gTt/gAt	5/11	1	2	FACETS	0.896	0.735	1	0.896	0.735	1	CLONAL	1	TRUE	1	0.15	2		739	536	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945336	151945336	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012371-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	12	177	0	ENST00000262189.6:c.2183A>C	p.Glu728Ala	p.E728A	ENST00000262189	NM_170606.2	728	gAa/gCa	14/59	1	2	FACETS	0.758	0.533	1	0.758	0.533	1	CLONAL	1	TRUE	1	0.15	2		177	211	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0012389-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	316	532	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.314261804518575	2	FACETS	0.826	0.78	0.873	0.826	0.78	0.873	CLONAL	2	TRUE	0	0.348558679946949	2		534	1098	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0012398-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	61	453	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.591	0.508	0.682	0.591	0.508	0.682	SUBCLONAL	1	TRUE	1	0.211179976202014	2		453	977	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015055	37015055	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1414110836	NA	P-0012398-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	52	590	1	ENST00000358127.4:c.349C>T	p.Arg117Trp	p.R117W	ENST00000358127	NM_001280556.1	117	Cgg/Tgg	3/10	1	2	FACETS	0.482	0.409	0.563	0.482	0.409	0.563	SUBCLONAL	1	TRUE	1	0.211179976202014	2		591	1021	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641686	12641686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749989518	NA	P-0012398-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	69	478	0	ENST00000251849.4:c.955G>A	p.Ala319Thr	p.A319T	ENST00000251849	NM_002880.3	319	Gca/Aca	9/17	1	2	FACETS	0.774	0.673	0.884	0.774	0.673	0.884	SUBCLONAL	1	TRUE	1	0.211179976202014	2		478	844	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374025	118374025	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012398-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	75	577	0	ENST00000534358.1:c.7418C>A	p.Thr2473Asn	p.T2473N	ENST00000534358	NM_005933.3	2473	aCt/aAt	27/36	1	2	FACETS	0.694	0.606	0.789	0.694	0.606	0.789	SUBCLONAL	1	TRUE	1	0.211179976202014	2		577	1024	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0012418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	29	888	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.23852056413699	2	FACETS	0.252	0.201	0.31	0.126	0.1	0.155	SUBCLONAL	1	TRUE	0	0.283820433811198	2		888	811	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0012418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	86	1354	2	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.221527301971951	2	FACETS	0.497	0.438	0.56	0.248	0.219	0.28	SUBCLONAL	1	TRUE	0	0.283820433811198	2		1356	1220	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578529	7578529	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs780442292	NA	P-0012418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	220	878	0	ENST00000269305.4:c.401T>G	p.Phe134Cys	p.F134C	ENST00000269305	NM_001126112.2	134	tTt/tGt	5/11	0.221527301971951	2	FACETS	0.929	0.867	0.994	0.929	0.867	0.994	CLONAL	2	TRUE	0	0.283820433811198	2		878	834	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052629	42052629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1390	329	1716	3	ENST00000219905.7:c.7300C>T	p.Arg2434Trp	p.R2434W	ENST00000219905	NM_001164273.1	2434	Cgg/Tgg	20/24	0.162102584954664	3	FACETS	0.77	0.725	0.816	0.77	0.725	0.816	INDETERMINATE	2	TRUE	1	0.283820433811198	3		1719	1719	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967269	134967269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749666684	NA	P-0012418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	90	1065	1	ENST00000398015.3:c.2608C>T	p.Arg870Trp	p.R870W	ENST00000398015	NM_004441.4	870	Cgg/Tgg	14/16	0.21582181834024	3	FACETS	0.999	0.886	1	0.499	0.443	0.56	CLONAL	1	TRUE	1	0.283820433811198	3		1066	725	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265709	41266219	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	In_Frame_Del	DEL	TCCTCCTAATGGCTTGGTGAAATAGCAAACAAGCCACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAG	TCCTCCTAATGGCTTGGTGAAATAGCAAACAAGCCACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAG	-	novel	NA	P-0012418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	113	140	0	ENST00000349496.5:c.13+141_220del		p.A5_Q72del	ENST00000349496	NM_001904.3	5		3/15	0.280992722947607	3	FACETS	0.933	0.865	0.999	1	0.989	1	CLONAL	5	TRUE	0	0.283820433811198	3		140	195	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254586	46254586	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	176	885	0	ENST00000334344.6:c.4776del	p.Asn1592LysfsTer34	p.N1592Kfs*34	ENST00000334344	NM_152641.2	1592	aaC/aa	16/21	0.0570683495769901	3	FACETS	0.836	0.771	0.904			1	INDETERMINATE	2	TRUE	NA	0.283820433811198	3		885	847	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0012419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	67	609	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		609	681	SUCCESS
APC	324	MSKCC	GRCh37	5	112155042	112155042	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs863225310	NA	P-0012419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	54	537	0	ENST00000257430.4:c.1312+1G>A		p.X438_splice	ENST00000257430	NM_000038.5	438			1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		537	585	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0012428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	482	548	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.550056739585214	3	FACETS	0.966	0.927	1	0.966	0.927	1	CLONAL	2	TRUE	1	0.550056739585214	3		548	1156	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0012428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	496	383	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.550056739585214	3	FACETS	0.981	0.941	1	0.981	0.941	1	CLONAL	2	TRUE	1	0.550056739585214	3		383	1172	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579315	7579315	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1555526478	NA	P-0012428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	295	316	0	ENST00000269305.4:c.372C>A	p.Cys124Ter	p.C124*	ENST00000269305	NM_001126112.2	124	tgC/tgA	4/11	0.494568336495043	2	FACETS	0.907	0.863	0.952	0.907	0.863	0.952	CLONAL	2	TRUE	0	0.550056739585214	2		316	591	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460359	149460359	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	62	442	0	ENST00000286301.3:c.278G>T	p.Gly93Val	p.G93V	ENST00000286301	NM_005211.3	93	gGc/gTc	3/22	0.298961418696816	2	FACETS	0.252	0.216	0.29	0.126	0.108	0.145	INDETERMINATE	1	TRUE	0	0.550056739585214	2		442	896	SUCCESS
MET	4233	MSKCC	GRCh37	7	116414961	116414961	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	526	408	0	ENST00000397752.3:c.3055G>T	p.Gly1019Cys	p.G1019C	ENST00000397752	NM_000245.2	1019	Ggt/Tgt	15/21	0.550056739585214	3	FACETS	0.978	0.939	1	0.978	0.939	1	CLONAL	2	TRUE	1	0.550056739585214	3		408	1247	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14022052	14022052	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	107	364	0	ENST00000311895.7:c.752A>T	p.Asp251Val	p.D251V	ENST00000311895	NM_005236.2	251	gAt/gTt	4/11	0.298961418696816	2	FACETS	0.479	0.429	0.531	0.239	0.214	0.266	INDETERMINATE	1	TRUE	0	0.550056739585214	2		364	813	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56798136	56798136	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	513	541	0	ENST00000337432.4:c.867G>C	p.Lys289Asn	p.K289N	ENST00000337432	NM_058216.2	289	aaG/aaC	6/9	0.36528470046086	3	FACETS	0.889	0.852	0.926	0.889	0.852	0.926	CLONAL	2	TRUE	1	0.550056739585214	3		541	1338	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622057	1622057	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763476552	NA	P-0012428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1253	96	609	1	ENST00000344749.5:c.818G>A	p.Arg273His	p.R273H	ENST00000344749	NM_001136139.2	273	cGt/cAt	10/19	0.203822735489946	2	FACETS	0.259	0.229	0.29	0.129	0.114	0.145	INDETERMINATE	1	TRUE	0	0.550056739585214	2		610	1349	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012435-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	101	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.19	2		426	897	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0012435-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	64	418	5	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.909	0.786	1	0.909	0.786	1	CLONAL	1	TRUE	1	0.19	2		423	741	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0012435-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	132	270	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.187075737921448	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.19	2		272	575	SUCCESS
APC	324	MSKCC	GRCh37	5	112175600	112175600	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012435-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	89	495	0	ENST00000257430.4:c.4312del	p.Thr1438HisfsTer35	p.T1438Hfs*35	ENST00000257430	NM_000038.5	1437	Aaa/aa	16/16	1	2	FACETS	0.863	0.763	0.97	0.863	0.763	0.97	CLONAL	1	TRUE	1	0.19	2		495	1086	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948833	17948833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746305522	NA	P-0012435-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	106	529	2	ENST00000458235.1:c.1609C>T	p.Arg537Trp	p.R537W	ENST00000458235	NM_000215.3	537	Cgg/Tgg	12/24	1	2	FACETS	0.989	0.885	1	0.989	0.885	1	CLONAL	1	TRUE	1	0.19	2		531	1128	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012451-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	98	389	0				ENST00000310581	NM_198253.2	-/1132			0.900014797703289	3	FACETS	0.86	0.774	0.95	0.43	0.387	0.475	CLONAL	1	TRUE	1	0.900014797703289	3		389	367	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0012451-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	584	406	3	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.900014797703289	3	FACETS	0.991	0.961	1	0.991	0.961	1	CLONAL	2	TRUE	1	0.900014797703289	3		409	949	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0012451-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	203	343	0	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.900014797703289	3	FACETS	0.959	0.893	1	0.48	0.446	0.514	CLONAL	1	TRUE	1	0.900014797703289	3		343	682	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0012451-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	467	385	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.900014797703289	2		385	506	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0012453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	153	472	0	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	1	2	FACETS	0.944	0.864	1	0.944	0.864	1	CLONAL	1	TRUE	1	0.39	2		472	831	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0012506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	716	453	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.511790810779172	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.511790810779172	3		453	1128	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279674	123279674	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs77543610	NA	P-0012506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	107	217	0	ENST00000358487.5:c.758C>G	p.Pro253Arg	p.P253R	ENST00000358487	NM_000141.4	253	cCt/cGt	7/18	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.511790810779172	2		217	327	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557628	95557628	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	285	593	1	ENST00000393063.1:c.5439G>T	p.Glu1813Asp	p.E1813D	ENST00000393063	NM_030621.3	1813	gaG/gaT	26/28	1	2	FACETS	0.996	0.937	1	0.996	0.937	1	CLONAL	1	TRUE	1	0.511790810779172	2		594	1118	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383281	31383281	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751976489	NA	P-0012506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	336	715	0	ENST00000328111.2:c.1193G>A	p.Arg398His	p.R398H	ENST00000328111	NM_006892.3	398	cGc/cAc	11/23	1	2	FACETS	0.998	0.943	1	0.998	0.943	1	CLONAL	1	TRUE	1	0.511790810779172	2		715	1316	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106710	27106710	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	244	494	0	ENST00000324856.7:c.6324del	p.Asn2109MetfsTer26	p.N2109Mfs*26	ENST00000324856	NM_006015.4	2107	ggC/gg	20/20	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.511790810779172	2		494	655	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910549	29910549	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45585732	NA	P-0012507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	18	72	0	ENST00000376809.5:c.89G>A	p.Arg30Lys	p.R30K	ENST00000376809	NM_002116.7	30	aGg/aAg	2/8	1	2	FACETS	0.882	0.67	1	0.882	0.67	1	CLONAL	1	FALSE	1	0.28728656699406	2		72	142	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508365	106508365	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	21	170	0	ENST00000359195.3:c.359A>G	p.Asp120Gly	p.D120G	ENST00000359195	NM_002649.2	120	gAc/gGc	2/11	1	2	FACETS	0.524	0.404	0.664	0.524	0.404	0.664	SUBCLONAL	1	FALSE	1	0.28728656699406	2		170	279	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420237	49420237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753822196	NA	P-0012507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	112	574	1	ENST00000301067.7:c.15512G>A	p.Arg5171Gln	p.R5171Q	ENST00000301067	NM_003482.3	5171	cGg/cAg	48/54	1	2	FACETS	0.743	0.666	0.824	0.743	0.666	0.824	SUBCLONAL	1	FALSE	1	0.28728656699406	2		575	1050	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141613	108142080	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGTTTCACCATATTGGCCAGGCTGTTCTCAAACTCCTGACCTTGTGATCTGCCTGCTTCAGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACTGCACCCGGCCTATGTTTATATACTTTTTAAAGTAAATGATTTGTGGATAAACCTGATTTTTTTCCCTCCTACCATCTTAGTATCTAATGCTTTTAAAGGAGCTTCCTGGAGAAGAGTACCCCTTGCCAATGGAAGATGTTCTTGAACTTCTGAAACCACTATCGTAAGAAATTAAAACCTTATGTTATGTTCACTTTAAAGTTATAAAATAACTGATGTGTTCTGTTAAGCTTATAAAGTTGAACTTTTTTTTTTTTTTTACCACAGCAATGTGTGTTCTTTGTATCGTCGTGACCAAGATGTTTGTAAAACTATTTTAAACCATGTCCTTCATGTAGTGAAAAACCTAGGTCAAAGCAATATGGACTCT	GAGTTTCACCATATTGGCCAGGCTGTTCTCAAACTCCTGACCTTGTGATCTGCCTGCTTCAGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACTGCACCCGGCCTATGTTTATATACTTTTTAAAGTAAATGATTTGTGGATAAACCTGATTTTTTTCCCTCCTACCATCTTAGTATCTAATGCTTTTAAAGGAGCTTCCTGGAGAAGAGTACCCCTTGCCAATGGAAGATGTTCTTGAACTTCTGAAACCACTATCGTAAGAAATTAAAACCTTATGTTATGTTCACTTTAAAGTTATAAAATAACTGATGTGTTCTGTTAAGCTTATAAAGTTGAACTTTTTTTTTTTTTTTACCACAGCAATGTGTGTTCTTTGTATCGTCGTGACCAAGATGTTTGTAAAACTATTTTAAACCATGTCCTTCATGTAGTGAAAAACCTAGGTCAAAGCAATATGGACTCT	-	novel	NA	P-0012507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	25	410	0	ENST00000278616.4:c.2839-175_3027del		p.X947_splice	ENST00000278616	NM_000051.3	947		19-20/63	1	2	FACETS	0.273	0.214	0.341	0.273	0.214	0.341	SUBCLONAL	1	FALSE	1	0.28728656699406	2		410	637	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196006	138196006	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012507-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	41	290	0	ENST00000237289.4:c.321del	p.Thr108LeufsTer15	p.T108Lfs*15	ENST00000237289	NM_001270507.1	107	gCc/gc	3/9	1	2	FACETS	0.463	0.385	0.551	0.463	0.385	0.551	SUBCLONAL	1	FALSE	1	0.28728656699406	2		290	616	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	148	389	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.896	0.823	0.971			1	INDETERMINATE	1	TRUE	NA	0.63172712765931	2		389	523	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0012509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	213	347	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	0.63172712765931	1	FACETS	0.977	0.919	1	0.977	0.919	1	CLONAL	1	TRUE	0	0.63172712765931	1		347	472	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0012509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4332	12851	834	3	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.63172712765931	25	FACETS	0.978	0.973	0.984			1	CLONAL	20	TRUE	NA	0.63172712765931	25		837	17183	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652411	206652411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781909564	NA	P-0012509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	279	493	2	ENST00000367120.3:c.1118C>T	p.Thr373Met	p.T373M	ENST00000367120	NM_014002.3	373	aCg/aTg	10/22	1	2	FACETS	0.898	0.844	0.952	0.898	0.844	0.952	CLONAL	1	TRUE	1	0.63172712765931	2		495	984	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656227	18656227	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1431955138	NA	P-0012509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	168	298	0	ENST00000266497.5:c.2906T>C	p.Met969Thr	p.M969T	ENST00000266497		969	aTg/aCg	21/31	1	2	FACETS	0.869	0.802	0.938	0.869	0.802	0.938	CLONAL	1	TRUE	1	0.63172712765931	2		298	612	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0012515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	257	615	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.260316414007743	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.260316414007743	3		615	1028	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0012515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	253	622	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.22506922518037	2	FACETS	0.845	0.79	0.902	0.845	0.79	0.902	CLONAL	2	TRUE	0	0.260316414007743	2		622	1150	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670452	88670452	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143617169	NA	P-0012515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	56	473	1	ENST00000360948.2:c.1234G>A	p.Glu412Lys	p.E412K	ENST00000360948	NM_001012338.2	412	Gaa/Aaa	11/19	1	2	FACETS	0.468	0.399	0.543	0.468	0.399	0.543	SUBCLONAL	1	TRUE	1	0.260316414007743	2		474	920	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874541	155874541	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	262	538	0	ENST00000368323.3:c.218T>A	p.Ile73Asn	p.I73N	ENST00000368323	NM_006912.5	73	aTt/aAt	4/6	0.218021868878969	3	FACETS	0.827	0.773	0.882	0.827	0.773	0.882	CLONAL	2	TRUE	1	0.260316414007743	3		538	1376	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518332	204518332	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1169931742	NA	P-0012515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1538	96	619	1	ENST00000367182.3:c.995C>T	p.Ser332Leu	p.S332L	ENST00000367182	NM_001278516.1	332	tCa/tTa	11/11	0.218021868878969	3	FACETS	0.51	0.452	0.572	0.255	0.226	0.286	SUBCLONAL	1	TRUE	1	0.260316414007743	3		620	1634	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161345	185161345	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1174	253	578	0	ENST00000265026.3:c.772G>C	p.Asp258His	p.D258H	ENST00000265026	NM_004721.4	258	Gac/Cac	4/14	0.260316414007743	3	FACETS	0.77	0.718	0.823	0.77	0.718	0.823	SUBCLONAL	2	TRUE	1	0.260316414007743	3		578	1427	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539435	187539435	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	66	515	0	ENST00000441802.2:c.8305G>A	p.Glu2769Lys	p.E2769K	ENST00000441802	NM_005245.3	2769	Gag/Aag	10/27	0.260316414007743	1	FACETS	0.446	0.386	0.512	0.446	0.386	0.512	SUBCLONAL	1	TRUE	0	0.260316414007743	1		515	989	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752799	57752799	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	60	319	0	ENST00000274289.3:c.1129G>C	p.Asp377His	p.D377H	ENST00000274289	NM_006622.3	377	Gac/Cac	8/14	0.218021868878969	3	FACETS	0.744	0.64	0.858	0.372	0.32	0.429	SUBCLONAL	1	TRUE	1	0.260316414007743	3		319	700	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339220	116339220	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	81	534	0	ENST00000397752.3:c.82G>C	p.Glu28Gln	p.E28Q	ENST00000397752	NM_000245.2	28	Gag/Cag	2/21	0.260316414007743	1	FACETS	0.5	0.439	0.566	0.5	0.439	0.566	SUBCLONAL	1	TRUE	0	0.260316414007743	1		534	1082	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525940	148525940	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	152	510	0	ENST00000320356.2:c.517G>C	p.Glu173Gln	p.E173Q	ENST00000320356	NM_004456.4	173	Gag/Cag	6/20	0.260316414007743	1	FACETS	0.985	0.9	1	0.985	0.9	1	CLONAL	1	TRUE	0	0.260316414007743	1		510	1031	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450124	32450124	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	160	499	1	ENST00000332351.3:c.688C>T	p.His230Tyr	p.H230Y	ENST00000332351	NM_024426.4	230	Cac/Tac	2/10	0.260316414007743	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.260316414007743	1		500	955	SUCCESS
ATM	472	MSKCC	GRCh37	11	108099946	108099946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	59	212	2	ENST00000278616.4:c.227G>T	p.Arg76Ile	p.R76I	ENST00000278616	NM_000051.3	76	aGa/aTa	4/63	0.260316414007743	1	FACETS	0.921	0.795	1	0.921	0.795	1	CLONAL	1	TRUE	0	0.260316414007743	1		214	428	SUCCESS
ATM	472	MSKCC	GRCh37	11	108127029	108127029	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	118	436	0	ENST00000278616.4:c.2212G>C	p.Glu738Gln	p.E738Q	ENST00000278616	NM_000051.3	738	Gag/Cag	14/63	0.260316414007743	1	FACETS	0.915	0.825	1	0.915	0.825	1	CLONAL	1	TRUE	0	0.260316414007743	1		436	862	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944700	31944700	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1397564819	NA	P-0012515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	11	43	0	ENST00000340398.3:c.401G>C	p.Arg134Thr	p.R134T	ENST00000340398	NM_001013699.2	134	aGa/aCa	1/1	1	2	FACETS	1	0.744	1	1	0.744	1	CLONAL	1	TRUE	1	0.260316414007743	2		43	79	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3094752	3094752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	55	352	0	ENST00000078429.4:c.103G>A	p.Asp35Asn	p.D35N	ENST00000078429	NM_002067.2	35	Gac/Aac	1/7	1	2	FACETS	0.527	0.449	0.612	0.527	0.449	0.612	SUBCLONAL	1	TRUE	1	0.260316414007743	2		352	802	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161938	47161938	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012516-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	57	374	0	ENST00000409792.3:c.4188T>A	p.Asn1396Lys	p.N1396K	ENST00000409792	NM_014159.6	1396	aaT/aaA	3/21	0.326787686344493	1	FACETS	0.682	0.586	0.785	0.682	0.586	0.785	SUBCLONAL	1	TRUE	0	0.326787686344493	1		374	428	SUCCESS
ATR	545	MSKCC	GRCh37	3	142297531	142297531	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs201753798	NA	P-0012516-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	155	471	0	ENST00000350721.4:c.16C>G	p.Leu6Val	p.L6V	ENST00000350721	NM_001184.3	6	Ctg/Gtg	1/47	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.326787686344493	2		471	861	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106194050	106194050	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012516-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	139	386	0	ENST00000380013.4:c.4512C>G	p.Asn1504Lys	p.N1504K	ENST00000380013	NM_001127208.2	1504	aaC/aaG	10/11	1	2	FACETS	0.986	0.897	1	0.986	0.897	1	CLONAL	1	TRUE	1	0.326787686344493	2		386	863	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225182	53225183	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	C	novel	NA	P-0012516-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	224	323	0	ENST00000375401.3:c.3035_3036delinsG	p.Ile1012SerfsTer43	p.I1012Sfs*43	ENST00000375401	NM_004187.3	1012	aTC/aG	20/26	1	1	FACETS	0.961	0.901	1	1	0.994	1	CLONAL	2	TRUE	0	0.326787686344493	1		323	597	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638347	117638347	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519788	NA	P-0012525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	69	578	0	ENST00000368508.3:c.6094G>A	p.Gly2032Arg	p.G2032R	ENST00000368508	NM_002944.2	2032	Gga/Aga	38/43	1	2	FACETS	0.846	0.735	0.966	0.846	0.735	0.966	CLONAL	1	TRUE	1	0.19	2		578	859	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058730	47058734	+	frameshift_variant	Frame_Shift_Del	DEL	AACAC	AACAC	T	novel	NA	P-0012525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	42	349	0	ENST00000409792.3:c.7544_7548delinsA	p.Gly2515GlufsTer2	p.G2515Efs*2	ENST00000409792	NM_014159.6	2515	gGTGTT/gA	21/21	1	2	FACETS	0.622	0.518	0.738	0.622	0.518	0.738	SUBCLONAL	1	TRUE	1	0.19	2		349	711	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178002	56178002	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs775205606	NA	P-0012531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	631	619	0	ENST00000399503.3:c.2975C>G	p.Ser992Cys	p.S992C	ENST00000399503	NM_005921.1	992	tCt/tGt	14/20	0.676221514365411	2	FACETS	0.931	0.904	0.956	0.931	0.904	0.956	CLONAL	2	TRUE	0	0.707058493768466	2		619	959	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881511	48881511	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	493	475	0	ENST00000267163.4:c.233G>A	p.Trp78Ter	p.W78*	ENST00000267163	NM_000321.2	78	tGg/tAg	2/27	0.694225780134657	2	FACETS	0.917	0.888	0.947	0.917	0.888	0.947	CLONAL	2	TRUE	0	0.707058493768466	2		475	760	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032402	10032402	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	96	169	0	ENST00000330684.3:c.421A>G	p.Thr141Ala	p.T141A	ENST00000330684	NM_001134407.1	141	Acg/Gcg	3/13	1	2	FACETS	0.908	0.819	1	0.908	0.819	1	CLONAL	1	TRUE	1	0.707058493768466	2		169	299	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627766	14627766	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1885	984	867	0	ENST00000254322.2:c.304T>C	p.Phe102Leu	p.F102L	ENST00000254322	NM_006145.1	102	Ttt/Ctt	2/3	0.698190731875398	5	FACETS	1	0.969	1	0.4	0.387	0.413	CLONAL	2	TRUE	0	0.707058493768466	5		867	2869	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577510	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0012531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	682	499	1	ENST00000269305.4:c.771_772del	p.Glu258ArgfsTer5	p.E258Rfs*5	ENST00000269305	NM_001126112.2	257	ctGGaa/ctaa	7/11	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.707058493768466	2		500	931	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0012534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	106	316	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	TRUE	1	0.388066669542197	2		316	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0012534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	122	548	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.388066669542197	1	FACETS	0.713	0.645	0.784	0.713	0.645	0.784	SUBCLONAL	1	TRUE	0	0.388066669542197	1		548	711	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855921	68855921	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	162	453	0	ENST00000261769.5:c.1730del	p.Gly577GlufsTer7	p.G577Efs*7	ENST00000261769	NM_004360.3	577	Gga/ga	12/16	0.388066669542197	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.388066669542197	1		453	621	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577543	7577543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1019340046	NA	P-0012534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	51	495	0	ENST00000269305.4:c.738G>A	p.Met246Ile	p.M246I	ENST00000269305	NM_001126112.2	246	atG/atA	7/11	0.388066669542197	1	FACETS	0.298	0.253	0.349	0.298	0.253	0.349	SUBCLONAL	1	TRUE	0	0.388066669542197	1		495	710	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426701	121426701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753998395	NA	P-0012534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	223	650	2	ENST00000257555.6:c.392G>A	p.Arg131Gln	p.R131Q	ENST00000257555		131	cGg/cAg	2/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.388066669542197	2		652	973	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968330	134968330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760621456	NA	P-0012534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	46	394	0	ENST00000398015.3:c.2843C>T	p.Ser948Leu	p.S948L	ENST00000398015	NM_004441.4	948	tCa/tTa	15/16	1	2	FACETS	0.301	0.252	0.355	0.301	0.252	0.355	SUBCLONAL	1	TRUE	1	0.388066669542197	2		394	788	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851728	63851728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1285691243	NA	P-0012534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	175	507	0	ENST00000279873.7:c.2506C>T	p.His836Tyr	p.H836Y	ENST00000279873	NM_032199.2	836	Cat/Tat	10/10	0.34201464248454	3	FACETS	1	0.945	1			1	CLONAL	1	TRUE	NA	0.388066669542197	3		507	1041	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434840	56434840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772783321	NA	P-0012534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	40	418	1	ENST00000407977.2:c.2297C>T	p.Ser766Leu	p.S766L	ENST00000407977		766	tCg/tTg	9/10	0.388066669542197	1	FACETS	0.265	0.219	0.315	0.265	0.219	0.315	SUBCLONAL	1	TRUE	0	0.388066669542197	1		419	628	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560967	9560967	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	132	461	0	ENST00000353224.5:c.815A>T	p.Tyr272Phe	p.Y272F	ENST00000353224	NM_177990.2	272	tAc/tTc	4/10	1	2	FACETS	0.705	0.639	0.774	0.705	0.639	0.774	SUBCLONAL	1	TRUE	1	0.388066669542197	2		461	965	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776294	76776294	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	243	779	0	ENST00000373344.5:c.7172A>G	p.Tyr2391Cys	p.Y2391C	ENST00000373344	NM_000489.3	2391	tAc/tGc	34/35	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.388066669542197	2		779	1193	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579346	7579346	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	456	466	0	ENST00000269305.4:c.341del	p.Leu114CysfsTer9	p.L114Cfs*9	ENST00000269305	NM_001126112.2	114	tTg/tg	4/11	0.283861143610959	5	FACETS	1	0.98	1	1	0.98	1	CLONAL	5	TRUE	0	0.283861143610959	5		466	890	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622211	117622211	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs760646608	NA	P-0012540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	52	538	0	ENST00000368508.3:c.6659A>T	p.Asn2220Ile	p.N2220I	ENST00000368508	NM_002944.2	2220	aAt/aTt	42/43	1	2	FACETS	0.624	0.531	0.726	0.624	0.531	0.726	SUBCLONAL	1	TRUE	1	0.283861143610959	2		538	587	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55963918	55963918	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	1037	488	0	ENST00000263923.4:c.2525G>T	p.Arg842Leu	p.R842L	ENST00000263923	NM_002253.2	842	cGt/cTt	18/30	0.283861143610959	12	FACETS	0.991	0.965	1			1	CLONAL	9	TRUE	NA	0.283861143610959	12		488	1982	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056623	26056623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs570629911	NA	P-0012540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	135	126	0	ENST00000343677.2:c.34G>A	p.Ala12Thr	p.A12T	ENST00000343677	NM_005319.3	12	Gcg/Acg	1/1	0.283861143610959	7	FACETS	0.943	0.868	1	0.943	0.868	1	CLONAL	5	TRUE	2	0.283861143610959	7		126	345	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163567	32163567	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs760665985	NA	P-0012540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	239	368	0	ENST00000375023.3:c.5659G>T	p.Ala1887Ser	p.A1887S	ENST00000375023	NM_004557.3	1887	Gct/Tct	30/30	0.283861143610959	7	FACETS	0.998	0.936	1	0.799	0.749	0.849	CLONAL	4	TRUE	2	0.283861143610959	7		368	721	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126332	5126332	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0012540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	23	275	0	ENST00000381652.3:c.3178-1G>T		p.X1060_splice	ENST00000381652	NM_004972.3	1060			0.195413234701164	1	FACETS	0.446	0.347	0.559	0.446	0.347	0.559	SUBCLONAL	1	TRUE	0	0.283861143610959	1		275	312	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97888850	97888850	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	157	584	0	ENST00000289081.3:c.857G>T	p.Cys286Phe	p.C286F	ENST00000289081	NM_000136.2	286	tGc/tTc	9/15	0.21711573981999	3	FACETS	0.788	0.723	0.857	0.788	0.723	0.857	SUBCLONAL	2	TRUE	1	0.283861143610959	3		584	801	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850765	63850765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	88	535	0	ENST00000279873.7:c.1543G>A	p.Glu515Lys	p.E515K	ENST00000279873	NM_032199.2	515	Gag/Aag	10/10	0.283861143610959	3	FACETS	0.883	0.781	0.991	0.441	0.39	0.496	CLONAL	1	TRUE	1	0.283861143610959	3		535	802	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32439135	32439135	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	104	523	0	ENST00000332351.3:c.938C>A	p.Ala313Asp	p.A313D	ENST00000332351	NM_024426.4	313	gCc/gAc	4/10	0.21711573981999	3	FACETS	1	0.977	1	0.661	0.593	0.733	CLONAL	1	TRUE	1	0.283861143610959	3		523	633	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456858	32456858	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1400931478	NA	P-0012540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	40	146	0	ENST00000332351.3:c.34C>A	p.Pro12Thr	p.P12T	ENST00000332351	NM_024426.4	12	Ccg/Acg	1/10	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.283861143610959	NA		146	199	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435132	49435132	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	44	270	0	ENST00000301067.7:c.6421G>T	p.Gly2141Trp	p.G2141W	ENST00000301067	NM_003482.3	2141	Ggg/Tgg	31/54	0.283861143610959	7	FACETS	0.908	0.76	1			1	CLONAL	1	TRUE	NA	0.283861143610959	7		270	584	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435962	49435962	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	173	569	3	ENST00000301067.7:c.6019G>T	p.Glu2007Ter	p.E2007*	ENST00000301067	NM_003482.3	2007	Gag/Tag	28/54	0.283861143610959	7	FACETS	0.802	0.736	0.871			1	CLONAL	2	TRUE	NA	0.283861143610959	7		572	1299	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436377	49436377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	158	560	1	ENST00000301067.7:c.5834C>T	p.Pro1945Leu	p.P1945L	ENST00000301067	NM_003482.3	1945	cCa/cTa	27/54	0.283861143610959	7	FACETS	0.771	0.704	0.84			1	SUBCLONAL	2	TRUE	NA	0.283861143610959	7		561	1235	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444060	49444060	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	63	447	0	ENST00000301067.7:c.3311C>T	p.Pro1104Leu	p.P1104L	ENST00000301067	NM_003482.3	1104	cCc/cTc	11/54	0.283861143610959	7	FACETS	0.764	0.659	0.879			1	SUBCLONAL	1	TRUE	NA	0.283861143610959	7		447	993	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436102	110436102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	64	522	0	ENST00000375856.3:c.2299C>T	p.Leu767Phe	p.L767F	ENST00000375856	NM_003749.2	767	Ctc/Ttc	1/2	0.208690518374282	3	FACETS	0.666	0.576	0.765	0.222	0.192	0.255	SUBCLONAL	1	TRUE	0	0.283861143610959	3		522	773	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961468	41961468	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	84	834	0	ENST00000219905.7:c.376G>T	p.Asp126Tyr	p.D126Y	ENST00000219905	NM_001164273.1	126	Gat/Tat	2/24	1	2	FACETS	0.682	0.601	0.769	0.682	0.601	0.769	SUBCLONAL	1	TRUE	1	0.283861143610959	2		834	868	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41999925	41999925	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs1361345025	NA	P-0012540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	119	545	1	ENST00000219905.7:c.2189-1G>T		p.X730_splice	ENST00000219905	NM_001164273.1	730			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.283861143610959	2		546	681	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669570	88669570	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	76	472	0	ENST00000360948.2:c.1328G>T	p.Cys443Phe	p.C443F	ENST00000360948	NM_001012338.2	443	tGt/tTt	12/19	1	2	FACETS	0.846	0.742	0.957	0.846	0.742	0.957	CLONAL	1	TRUE	1	0.283861143610959	2		472	633	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63531743	63531743	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0012540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	78	552	0	ENST00000307078.5:c.2237+1G>C		p.X746_splice	ENST00000307078	NM_004655.3	746			0.283861143610959	3	FACETS	0.651	0.571	0.738	0.326	0.285	0.369	SUBCLONAL	1	TRUE	1	0.283861143610959	3		552	964	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56376685	56376685	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	236	719	0	ENST00000348428.3:c.725G>T	p.Ser242Ile	p.S242I	ENST00000348428	NM_006785.3	242	aGc/aTc	5/17	0.283861143610959	3	FACETS	0.851	0.794	0.911	0.851	0.794	0.911	CLONAL	2	TRUE	1	0.283861143610959	3		719	1115	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597399	10597399	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	181	535	2	ENST00000171111.5:c.1804A>G	p.Ser602Gly	p.S602G	ENST00000171111	NM_203500.1	602	Agt/Ggt	6/6	0.241727077408176	2	FACETS	0.887	0.82	0.956	0.887	0.82	0.956	CLONAL	2	TRUE	0	0.283861143610959	2		537	719	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272140	18272140	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	11	27	0	ENST00000222254.8:c.650A>T	p.His217Leu	p.H217L	ENST00000222254	NM_005027.3	217	cAc/cTc	6/16	0.241727077408176	2	FACETS	0.994	0.715	1	0.994	0.715	1	CLONAL	2	TRUE	0	0.283861143610959	2		27	39	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944581	40944581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs900462377	NA	P-0012540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	36	324	0	ENST00000373198.4:c.1921G>A	p.Asp641Asn	p.D641N	ENST00000373198	NM_133170.3	641	Gac/Aac	12/32	0.216100244089411	5	FACETS	0.587	0.481	0.706	0.196	0.16	0.236	SUBCLONAL	1	TRUE	2	0.283861143610959	5		324	616	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348473	70348473	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	207	338	0	ENST00000374080.3:c.3380C>A	p.Ser1127Ter	p.S1127*	ENST00000374080		1127	tCg/tAg	24/45	0.283861143610959	3	FACETS	1	0.984	1			1	CLONAL	2	TRUE	NA	0.283861143610959	3		338	705	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76919036	76919036	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	156	202	0	ENST00000373344.5:c.3955C>T	p.Gln1319Ter	p.Q1319*	ENST00000373344	NM_000489.3	1319	Caa/Taa	12/35	0.283861143610959	3	FACETS	0.899	0.836	0.963			1	CLONAL	4	TRUE	NA	0.283861143610959	3		202	349	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606324	93606324	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	78	498	0	ENST00000375746.1:c.146del	p.Gly49ValfsTer22	p.G49Vfs*22	ENST00000375746	NM_001174167.1	48	ctG/ct	2/14	0.21711573981999	3	FACETS	1	0.898	1	0.512	0.45	0.578	CLONAL	1	TRUE	1	0.283861143610959	3		498	613	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314978	1314978	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	237	538	0	ENST00000400841.2:c.683del	p.Lys228SerfsTer7	p.K228Sfs*7	ENST00000400841		228	aAg/ag	6/6	0.283861143610959	3	FACETS	0.886	0.831	0.943			1	CLONAL	3	TRUE	NA	0.283861143610959	3		538	717	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491182	120491183	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0012540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	261	398	0	ENST00000256646.2:c.2606_2607delinsCT	p.Arg869Pro	p.R869P	ENST00000256646	NM_024408.3	869	cGG/cCT	17/34	0.283861143610959	7	FACETS	0.996	0.937	1	0.996	0.937	1	CLONAL	4	TRUE	3	0.283861143610959	7		398	789	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0012569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	56	424	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.13	2		424	770	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0012569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	73	185	0				ENST00000310581	NM_198253.2	-/1132			0.201696884931986	3	FACETS	0.975	0.857	1	1	0.974	1	CLONAL	3	TRUE	1	0.13	3		185	409	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913273	NA	P-0012569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	10	301	0	ENST00000263967.3:c.1624G>C	p.Glu542Gln	p.E542Q	ENST00000263967	NM_006218.2	542	Gaa/Caa	10/21	1	2	FACETS	0.386	0.26	0.545	0.386	0.26	0.545	SUBCLONAL	1	TRUE	1	0.13	2		301	399	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680489	241680489	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs200007371	NA	P-0012569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	51	481	0	ENST00000366560.3:c.260G>T	p.Arg87Leu	p.R87L	ENST00000366560	NM_000143.3	87	cGc/cTc	2/10	1	2	FACETS	0.91	0.771	1	0.91	0.771	1	CLONAL	1	TRUE	1	0.13	2		481	862	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814258	76814258	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	66	763	1	ENST00000373344.5:c.6386C>A	p.Ala2129Asp	p.A2129D	ENST00000373344	NM_000489.3	2129	gCt/gAt	29/35	1	2	FACETS	0.891	0.771	1	0.891	0.771	1	CLONAL	1	TRUE	1	0.13	2		764	1139	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164907	123164907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1194	73	820	0	ENST00000218089.9:c.220C>T	p.His74Tyr	p.H74Y	ENST00000218089	NM_001042749.1	74	Cac/Tac	5/35	0.3	2	FACETS	0.886	0.772	1			1	CLONAL	1	TRUE	NA	0.13	2		820	1267	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0012592-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	381	580	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.277610860444193	3	FACETS	1	0.991	1	0.774	0.738	0.81	CLONAL	2	TRUE	0	0.429031728599869	3		580	929	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0012592-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	431	371	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.429031728599869	6	FACETS	0.957	0.913	1	0.957	0.913	1	CLONAL	3	TRUE	3	0.429031728599869	6		371	1300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0012593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	434	501	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.322964582119704	2	FACETS	0.933	0.89	0.976	0.933	0.89	0.976	CLONAL	2	TRUE	0	0.372329754487851	2		501	1250	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928628	49928628	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0012593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	439	558	0	ENST00000296474.3:c.3644+2T>C		p.X1215_splice	ENST00000296474	NM_002447.2	1215			0.370729128308364	2	FACETS	0.942	0.9	0.986	0.942	0.9	0.986	CLONAL	2	TRUE	0	0.372329754487851	2		558	1251	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670754	134670754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752494038	NA	P-0012593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	125	336	0	ENST00000398015.3:c.665G>A	p.Arg222Gln	p.R222Q	ENST00000398015	NM_004441.4	222	cGg/cAg	3/16	0.372329754487851	4	FACETS	0.768	0.693	0.847	0.256	0.231	0.283	SUBCLONAL	1	TRUE	1	0.372329754487851	4		336	1200	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159063	143159063	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	192	461	0	ENST00000262992.4:c.790A>T	p.Ile264Phe	p.I264F	ENST00000262992	NM_001101669.1	264	Att/Ttt	10/24	1	2	FACETS	0.996	0.921	1	0.996	0.921	1	CLONAL	1	TRUE	1	0.372329754487851	2		461	1035	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92355058	92355058	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	198	385	0	ENST00000265734.4:c.419G>T	p.Arg140Leu	p.R140L	ENST00000265734	NM_001259.6	140	cGa/cTa	4/8	0.372329754487851	3	FACETS	0.99	0.915	1	0.495	0.457	0.534	CLONAL	1	TRUE	1	0.372329754487851	3		385	1274	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201350	133201350	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs748851961	NA	P-0012593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1296	161	614	0	ENST00000320574.5:c.6794A>G	p.Tyr2265Cys	p.Y2265C	ENST00000320574	NM_006231.2	2265	tAc/tGc	49/49	0.20781070764661	2	FACETS	0.594	0.542	0.647	0.297	0.271	0.324	INDETERMINATE	1	TRUE	0	0.372329754487851	2		614	1457	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383274	31383274	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138171867	NA	P-0012593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1597	864	669	0	ENST00000328111.2:c.1186C>T	p.Pro396Ser	p.P396S	ENST00000328111	NM_006892.3	396	Ccc/Tcc	11/23	0.324941894096354	5	FACETS	0.98	0.948	1			1	CLONAL	3	TRUE	NA	0.372329754487851	5		669	2461	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221987	1221987	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	452	595	0	ENST00000326873.7:c.903del	p.Gln302ArgfsTer34	p.Q302Rfs*34	ENST00000326873	NM_000455.4	301	cGg/cg	7/10	0.370729128308364	2	FACETS	0.884	0.844	0.925	0.884	0.844	0.925	CLONAL	2	TRUE	0	0.372329754487851	2		595	1373	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0012595-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	107	371	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	1	2	FACETS	0.871	0.78	0.968	0.871	0.78	0.968	CLONAL	1	FALSE	1	0.244255961018832	2		371	1006	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015132	37015132	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012595-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	121	798	2	ENST00000358127.4:c.272C>A	p.Ala91Asp	p.A91D	ENST00000358127	NM_001280556.1	91	gCc/gAc	3/10	1	2	FACETS	0.826	0.744	0.913	0.826	0.744	0.913	CLONAL	1	FALSE	1	0.244255961018832	2		800	1199	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156978	89156978	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012595-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	106	648	0	ENST00000336596.2:c.81del	p.Asn28MetfsTer55	p.N28Mfs*55	ENST00000336596	NM_005233.5	27	tCc/tc	1/17	1	2	FACETS	0.927	0.83	1	0.927	0.83	1	CLONAL	1	FALSE	1	0.244255961018832	2		648	936	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0012605-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	643	371	0	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.722581630645036	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	4	TRUE	0	0.730388090303259	4		371	758	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564329	86564329	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1389714364	NA	P-0012605-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	284	326	0	ENST00000274376.6:c.61G>T	p.Gly21Cys	p.G21C	ENST00000274376	NM_002890.2	21	Ggc/Tgc	1/25	0.373279351927863	5	FACETS	0.95	0.902	0.997	0.95	0.902	0.997	INDETERMINATE	3	TRUE	2	0.730388090303259	5		326	572	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609852	117609852	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012605-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	562	755	0	ENST00000368508.3:c.6847C>A	p.Gln2283Lys	p.Q2283K	ENST00000368508	NM_002944.2	2283	Caa/Aaa	43/43	0.728537987628662	2	FACETS	0.798	0.772	0.824	0.798	0.772	0.824	SUBCLONAL	2	TRUE	0	0.730388090303259	2		755	964	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29669996	29670042	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCATCAACCATCTCATGATTATCTTTAATAGAGTCCAGAGGAAGTAT	TCATCAACCATCTCATGATTATCTTTAATAGAGTCCAGAGGAAGTAT	-	novel	NA	P-0012605-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	283	346	0	ENST00000356175.3:c.7000-30_7016del		p.X2334_splice	ENST00000356175	NM_000267.3	2334		47/57	0.728537987628662	2	FACETS	0.931	0.894	0.968	0.931	0.894	0.968	CLONAL	2	TRUE	0	0.730388090303259	2		346	416	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033889	49033889	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012605-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	650	602	0	ENST00000267163.4:c.2027del	p.Leu676Ter	p.L676*	ENST00000267163	NM_000321.2	676	Tta/ta	20/27	0.725888509635212	2	FACETS	0.934	0.909	0.958	0.934	0.909	0.958	CLONAL	2	TRUE	0	0.730388090303259	2		602	953	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077440	30077449	+	protein_altering_variant	In_Frame_Del	DEL	GGAAAAGAGC	GGAAAAGAGC	CGAA	novel	NA	P-0012605-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	200	281	0	ENST00000338641.4:c.1587_1596delinsCGAA	p.Met529_Ser532delinsIleGlu	p.M529_S532delinsIE	ENST00000338641	NM_000268.3	529	atGGAAAAGAGC/atCGAA	15/16	0.728537987628662	2	FACETS	0.964	0.919	1	0.964	0.919	1	CLONAL	2	TRUE	0	0.730388090303259	2		281	284	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249348	110249348	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	164	684	0	ENST00000374672.4:c.1225A>C	p.Lys409Gln	p.K409Q	ENST00000374672	NM_004235.4	409	Aag/Cag	4/5	1	2	FACETS	0.804	0.738	0.873	0.804	0.738	0.873	CLONAL	1	TRUE	1	0.438026662614881	2		684	931	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225886	2225886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	216	594	1	ENST00000326181.6:c.1678G>A	p.Gly560Ser	p.G560S	ENST00000326181	NM_032271.2	560	Ggc/Agc	18/21	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.438026662614881	2		595	846	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1268692	1268692	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	72	585	0	ENST00000310581.5:c.2525G>T	p.Cys842Phe	p.C842F	ENST00000310581	NM_198253.2	842	tGc/tTc	9/16	0.0869977155918704	3	FACETS	1	0.902	1			1	INDETERMINATE	1	TRUE	NA	0.240153801189866	3		585	647	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636787	8636787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766465721	NA	P-0012622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	515	443	0	ENST00000356435.5:c.122C>T	p.Ala41Val	p.A41V	ENST00000356435		41	gCc/gTc	2/35	0.240153801189866	5	FACETS	0.964	0.926	1	0.964	0.926	1	CLONAL	5	TRUE	0	0.240153801189866	5		443	1210	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867357	45867357	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	17	266	0	ENST00000391945.4:c.836A>T	p.Gln279Leu	p.Q279L	ENST00000391945	NM_000400.3	279	cAg/cTg	10/23	0.206566818668677	3	FACETS	0.481	0.358	0.626	0.24	0.179	0.313	SUBCLONAL	1	TRUE	1	0.240153801189866	3		266	330	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855914	76855914	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0012622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	358	344	0	ENST00000373344.5:c.5686A>T	p.Lys1896Ter	p.K1896*	ENST00000373344	NM_000489.3	1896	Aaa/Taa	23/35	0.240153801189866	3	FACETS	0.884	0.841	0.929			1	CLONAL	4	TRUE	NA	0.240153801189866	3		344	944	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519988	NA	P-0012630-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	175	792	1	ENST00000269305.4:c.808T>C	p.Phe270Leu	p.F270L	ENST00000269305	NM_001126112.2	270	Ttt/Ctt	8/11	0.421708107926106	0	FACETS	0.758	0.703	0.814			1	SUBCLONAL	1	TRUE	0	0.473795298493696	0		793	513	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354369	354369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012630-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	105	604	0	ENST00000262320.3:c.1189G>A	p.Glu397Lys	p.E397K	ENST00000262320	NM_003502.3	397	Gag/Aag	5/11	0.439771011847393	1	FACETS	0.778	0.701	0.858	0.778	0.701	0.858	SUBCLONAL	1	TRUE	0	0.473795298493696	1		604	435	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0012640-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	22	453	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.054	0.041	0.069	0.054	0.041	0.069	SUBCLONAL	1	FALSE	1	0.855847557214056	2		453	957	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0012640-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	373	332	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.855847557214056	2		332	798	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0012640-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	313	269	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.965	0.916	1	0.965	0.916	1	CLONAL	1	FALSE	1	0.855847557214056	2		269	758	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796905	42796906	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0012640-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	509	736	0	ENST00000575354.2:c.3365_3366del	p.Val1122GlyfsTer28	p.V1122Gfs*28	ENST00000575354	NM_015125.3	1121	acTGtg/actg	14/20	0.855847557214056	1	FACETS	0.855	0.827	0.882	0.855	0.827	0.882	CLONAL	1	FALSE	0	0.855847557214056	1		736	796	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273138	198273138	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012640-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	421	854	0	ENST00000335508.6:c.1072A>G	p.Thr358Ala	p.T358A	ENST00000335508	NM_012433.2	358	Aca/Gca	8/25	1	2	FACETS	0.815	0.777	0.854	0.815	0.777	0.854	CLONAL	1	FALSE	1	0.855847557214056	2		854	1207	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	23	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.176938791094106	3	FACETS	0.4	0.31	0.506	0.2	0.155	0.253	SUBCLONAL	1	TRUE	1	0.12	3		426	1015	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0012645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	40	538	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	1	2	FACETS	0.629	0.52	0.751	0.629	0.52	0.751	SUBCLONAL	1	TRUE	1	0.12	2		538	1060	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960117	151960117	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1152	64	545	0	ENST00000262189.6:c.1283A>G	p.Asn428Ser	p.N428S	ENST00000262189	NM_170606.2	428	aAt/aGt	9/59	1	2	FACETS	0.877	0.757	1	0.877	0.757	1	CLONAL	1	TRUE	1	0.12	2		545	1216	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	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	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.17	2		426	917	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218492	1218492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690925	NA	P-0012647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	141	619	0	ENST00000326873.7:c.367C>T	p.Gln123Ter	p.Q123*	ENST00000326873	NM_000455.4	123	Cag/Tag	2/10	1	2	FACETS	0.943	0.858	1	1	0.99	1	CLONAL	2	TRUE	1	0.17	2		619	880	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591248	67591248	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	75	570	0	ENST00000274335.5:c.1746G>A	p.Met582Ile	p.M582I	ENST00000274335		582	atG/atA	13/15	1	2	FACETS	0.86	0.751	0.978	0.86	0.751	0.978	CLONAL	1	TRUE	1	0.17	2		570	1026	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0012649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	95	424	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.925	0.822	1	0.925	0.822	1	CLONAL	1	TRUE	1	0.23	2		424	893	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519863	29519863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	99	471	1	ENST00000389048.3:c.1708G>A	p.Glu570Lys	p.E570K	ENST00000389048	NM_004304.4	570	Gag/Aag	9/29	1	2	FACETS	0.825	0.735	0.922	0.825	0.735	0.922	CLONAL	1	TRUE	1	0.23	2		472	1043	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242757	66242757	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	96	333	0	ENST00000273854.3:c.1815G>T	p.Arg605Ser	p.R605S	ENST00000273854	NM_004439.5	605	agG/agT	9/18	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.23	2		333	833	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245494	153245494	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	84	366	1	ENST00000281708.4:c.1697G>T	p.Trp566Leu	p.W566L	ENST00000281708	NM_033632.3	566	tGg/tTg	11/12	1	2	FACETS	0.808	0.712	0.911	0.808	0.712	0.911	CLONAL	1	TRUE	1	0.23	2		367	904	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737313	145737313	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1333082439	NA	P-0012649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	77	489	1	ENST00000428558.2:c.3374C>A	p.Pro1125His	p.P1125H	ENST00000428558	NM_004260.3	1125	cCc/cAc	20/22	0.3	3	FACETS	0.627	0.549	0.713	0.314	0.274	0.357	SUBCLONAL	1	TRUE	1	0.23	3		490	1190	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112285	115112285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1286749643	NA	P-0012649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	27	103	0	ENST00000257566.3:c.1455G>C	p.Gln485His	p.Q485H	ENST00000257566	NM_016569.3	485	caG/caC	7/8	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.23	2		103	215	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483888	88483888	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	57	469	0	ENST00000360948.2:c.1682G>T	p.Ser561Ile	p.S561I	ENST00000360948	NM_001012338.2	561	aGc/aTc	14/19	1	2	FACETS	0.524	0.448	0.608	0.524	0.448	0.608	SUBCLONAL	1	TRUE	1	0.23	2		469	945	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7218284	7218284	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1327633306	NA	P-0012649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	77	390	0	ENST00000380728.2:c.88C>T	p.Arg30Trp	p.R30W	ENST00000380728		30	Cgg/Tgg	2/11	1	2	FACETS	0.811	0.71	0.919	0.811	0.71	0.919	CLONAL	1	TRUE	1	0.23	2		390	826	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39745033	39745033	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0012649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	72	364	0	ENST00000361337.2:c.1822+1G>T		p.X608_splice	ENST00000361337	NM_003286.2	608			1	2	FACETS	0.799	0.697	0.909	0.799	0.697	0.909	CLONAL	1	TRUE	1	0.23	2		364	784	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921424	39921424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	54	494	1	ENST00000378444.4:c.4396C>A	p.Leu1466Ile	p.L1466I	ENST00000378444	NM_001123385.1	1466	Ctt/Att	10/15	1	2	FACETS	0.459	0.39	0.535	0.459	0.39	0.535	SUBCLONAL	1	TRUE	1	0.23	2		495	1023	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877381	40877381	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012649-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	63	357	0	ENST00000373198.4:c.2315del	p.Gly772AlafsTer12	p.G772Afs*12	ENST00000373198	NM_133170.3	772	gGc/gc	15/32	1	2	FACETS	0.75	0.648	0.862	0.75	0.648	0.862	SUBCLONAL	1	TRUE	1	0.23	2		357	730	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970935	55970935	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1290988531	NA	P-0012665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	361	591	2	ENST00000263923.4:c.1862C>A	p.Thr621Lys	p.T621K	ENST00000263923	NM_002253.2	621	aCa/aAa	13/30	1	2	FACETS	0.992	0.942	1	0.992	0.942	1	CLONAL	1	TRUE	1	0.72729217901714	2		593	1001	SUCCESS
AR	367	MSKCC	GRCh37	X	66765866	66765866	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	319	528	0	ENST00000374690.3:c.878C>G	p.Ser293Cys	p.S293C	ENST00000374690	NM_000044.3	293	tCt/tGt	1/8	1	2	FACETS	0.892	0.844	0.942	0.892	0.844	0.942	CLONAL	1	TRUE	1	0.72729217901714	2		528	983	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897430	78897430	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1280517804	NA	P-0121434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1295	653	522	2	ENST00000306801.3:c.2765A>G	p.Gln922Arg	p.Q922R	ENST00000306801	NM_020761.2	922	cAg/cGg	23/34	0.880928156021422	6	FACETS	1	0.986	1	0.42	0.404	0.437	CLONAL	2	NA	1	0.880928156021422	6		524	1948	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028145	48028145	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	838	525	0	ENST00000234420.5:c.3023C>A	p.Thr1008Asn	p.T1008N	ENST00000234420	NM_000179.2	1008	aCc/aAc	4/10	0.512509693067377	4	FACETS	1	0.997	1	0.802	0.78	0.824	INDETERMINATE	2	NA	1	0.880928156021422	4		525	1487	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227978	55227978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0121434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1556	286	460	1	ENST00000275493.2:c.1445G>A	p.Gly482Glu	p.G482E	ENST00000275493	NM_005228.3	482	gGg/gAg	12/28	0.761681976980394	4	FACETS	0.663	0.621	0.707	0.332	0.31	0.354	SUBCLONAL	1	NA	2	0.880928156021422	4		461	1842	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830463	72830463	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1322353590	NA	P-0121434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1191	461	638	1	ENST00000268489.5:c.6118C>T	p.Pro2040Ser	p.P2040S	ENST00000268489	NM_006885.3	2040	Cca/Tca	9/10	0.226605133745237	6	FACETS	0.875	0.834	0.917			1	INDETERMINATE	2	NA	NA	0.880928156021422	6		639	1652	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511514	38511514	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0121434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	231	283	0	ENST00000254066.5:c.1013-1G>C		p.X338_splice	ENST00000254066	NM_000964.3	338			0.809809821866287	5	FACETS	0.98	0.912	1			1	CLONAL	1	NA	NA	0.880928156021422	5		283	1242	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39690100	39690100	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0121434-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	303	276	0	ENST00000361337.2:c.125A>T	p.Lys42Met	p.K42M	ENST00000361337	NM_003286.2	42	aAg/aTg	3/21	1	2	FACETS	0.85	0.805	0.897	0.85	0.805	0.897	CLONAL	1	NA	1	0.880928156021422	2		276	809	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs786203436	NA	P-0012674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	472	320	0	ENST00000269305.4:c.487T>G	p.Tyr163Asp	p.Y163D	ENST00000269305	NM_001126112.2	163	Tac/Gac	5/11	0.484724140090501	3	FACETS	0.897	0.865	0.929	0.897	0.865	0.929	CLONAL	3	TRUE	0	0.551191773329678	3		320	812	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266518	198266518	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	45	393	0	ENST00000335508.6:c.2318T>A	p.Leu773His	p.L773H	ENST00000335508	NM_012433.2	773	cTt/cAt	16/25	1	2	FACETS	0.186	0.156	0.22	0.186	0.156	0.22	SUBCLONAL	1	TRUE	1	0.551191773329678	2		393	877	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495315	212495315	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	133	290	0	ENST00000342788.4:c.1951C>G	p.Pro651Ala	p.P651A	ENST00000342788	NM_005235.2	651	Ccc/Gcc	17/28	1	2	FACETS	0.836	0.763	0.913	0.836	0.763	0.913	CLONAL	1	TRUE	1	0.551191773329678	2		290	577	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753187	128753193	+	frameshift_variant	Frame_Shift_Del	DEL	CGGAACT	CGGAACT	-	novel	NA	P-0012674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	81	165	0	ENST00000377970.2:c.1349_1355del	p.Arg450LeufsTer7	p.R450Lfs*7	ENST00000377970	NM_002467.4	450	CGGAACTct/ct	3/3	0.410371947311066	6	FACETS	0.801	0.705	0.905	0.267	0.235	0.302	CLONAL	1	TRUE	3	0.551191773329678	6		165	771	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023105	48023116	+	inframe_deletion	In_Frame_Del	DEL	AACGTGCAGATG	AACGTGCAGATG	-	novel	NA	P-0012674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	476	579	0	ENST00000234420.5:c.532_543del	p.Arg178_Glu181del	p.R178_E181del	ENST00000234420	NM_000179.2	177	cAACGTGCAGATGaa/caa	3/10	0.27239037164761	3	FACETS	0.795	0.76	0.831	0.795	0.76	0.831	INDETERMINATE	2	TRUE	1	0.551191773329678	3		579	1385	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0012675-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	95	333	2	ENST00000374080.3:c.3670C>T	p.Leu1224Phe	p.L1224F	ENST00000374080		1224	Ctc/Ttc	26/45	0.211841539737214	2	FACETS	1	0.942	1			1	CLONAL	2	FALSE	NA	0.262743907107151	2		335	338	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	88	389	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.248390040941086	2		389	544	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470570	25470570	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	159	528	0	ENST00000264709.3:c.904G>T	p.Gly302Cys	p.G302C	ENST00000264709	NM_175629.2	302	Ggc/Tgc	8/23	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.248390040941086	2		528	1105	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643682	52643682	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0012682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	110	319	0	ENST00000394830.3:c.2214C>G	p.Tyr738Ter	p.Y738*	ENST00000394830	NM_018313.4	738	taC/taG	17/30	0.248390040941086	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.248390040941086	1		319	625	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961430	54961430	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	63	126	0	ENST00000312783.6:c.202C>A	p.His68Asn	p.H68N	ENST00000312783	NM_198436.1	68	Cac/Aac	4/10	1	2	FACETS	0.813	0.708	0.925	1	0.975	1	CLONAL	2	TRUE	1	0.248390040941086	2		126	312	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127775	47127775	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	61	286	0	ENST00000409792.3:c.5307del	p.Leu1771TrpfsTer16	p.L1771Wfs*16	ENST00000409792	NM_014159.6	1769	tcC/tc	11/21	0.248390040941086	1	FACETS	0.648	0.558	0.745	0.648	0.558	0.745	SUBCLONAL	1	TRUE	0	0.248390040941086	1		286	664	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183750	10183757	+	frameshift_variant	Frame_Shift_Del	DEL	GGTCATCT	GGTCATCT	-	novel	NA	P-0012682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	110	325	0	ENST00000256474.2:c.219_226del	p.Gln73HisfsTer56	p.Q73Hfs*56	ENST00000256474	NM_000551.3	73	caGGTCATCTtc/catc	1/3	0.248390040941086	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.248390040941086	1		325	757	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339926	116339926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764052874	NA	P-0012691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	77	594	1	ENST00000397752.3:c.788C>T	p.Thr263Met	p.T263M	ENST00000397752	NM_000245.2	263	aCg/aTg	2/21	1	2	FACETS	0.642	0.561	0.729	0.642	0.561	0.729	SUBCLONAL	1	TRUE	1	0.207642796644774	2		595	1156	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878094	151878094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	113	422	0	ENST00000262189.6:c.6851C>T	p.Ser2284Leu	p.S2284L	ENST00000262189	NM_170606.2	2284	tCa/tTa	36/59	0.207642796644774	7	FACETS	1	0.981	1	0.238	0.213	0.264	CLONAL	1	TRUE	1	0.207642796644774	7		422	1158	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878206	151878206	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	87	516	0	ENST00000262189.6:c.6739C>T	p.Gln2247Ter	p.Q2247*	ENST00000262189	NM_170606.2	2247	Cag/Tag	36/59	0.207642796644774	7	FACETS	1	0.928	1	0.178	0.157	0.201	CLONAL	1	TRUE	1	0.207642796644774	7		516	1189	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712015	89712015	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	rs121909232	NA	P-0012711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	43	165	0	ENST00000371953.3:c.633C>A	p.Cys211Ter	p.C211*	ENST00000371953	NM_000314.4	211	tgC/tgA	6/9	0.349447818864151	1	FACETS	0.972	0.822	1	0.972	0.822	1	CLONAL	1	TRUE	0	0.349447818864151	1		165	209	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0012711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1588	56	969	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.195	0.166	0.227	0.195	0.166	0.227	SUBCLONAL	1	TRUE	1	0.349447818864151	2		970	1644	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28931588	NA	P-0012711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	171	499	0	ENST00000349496.5:c.94G>C	p.Asp32His	p.D32H	ENST00000349496	NM_001904.3	32	Gac/Cac	3/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.349447818864151	2		499	811	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185852	32185852	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs891577895	NA	P-0012711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	131	587	0	ENST00000375023.3:c.1544A>G	p.Asn515Ser	p.N515S	ENST00000375023	NM_004557.3	515	aAc/aGc	9/30	1	2	FACETS	0.86	0.78	0.944	0.86	0.78	0.944	CLONAL	1	TRUE	1	0.349447818864151	2		587	872	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845589	128845589	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372843274	NA	P-0012711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	131	476	1	ENST00000249373.3:c.886C>T	p.Arg296Cys	p.R296C	ENST00000249373	NM_005631.4	296	Cgt/Tgt	4/12	0.328610631132906	3	FACETS	0.99	0.898	1	0.495	0.449	0.544	CLONAL	1	TRUE	1	0.349447818864151	3		477	890	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793382	18793382	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs77070108	NA	P-0012711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	172	485	1	ENST00000266497.5:c.4079C>T	p.Ala1360Val	p.A1360V	ENST00000266497		1360	gCg/gTg	30/31	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.349447818864151	2		486	932	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2125894	2125894	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs45517252	NA	P-0012711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	83	668	0	ENST00000219476.3:c.2639+1G>A		p.X880_splice	ENST00000219476	NM_000548.3	880			1	2	FACETS	0.47	0.413	0.531	0.47	0.413	0.531	SUBCLONAL	1	TRUE	1	0.349447818864151	2		668	1011	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061151	38061222	+	inframe_deletion	In_Frame_Del	DEL	TCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTGGCGGCGCAAGTAGCAGCCGT	TCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTGGCGGCGCAAGTAGCAGCCGT	-	novel	NA	P-0012711-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	93	167	0	ENST00000250448.2:c.767_838del	p.Asn256_Gly279del	p.N256_G279del	ENST00000250448	NM_004496.3	256	aACGGCTGCTACTTGCGCCGCCAGAAGCGCTTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAgc/agc	2/2	1	2	FACETS	0.896	0.807	0.989	1	0.986	1	CLONAL	2	TRUE	1	0.349447818864151	2		167	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0012720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	167	532	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.314130273131614	3	FACETS	1	0.972	1	0.719	0.671	0.767	INDETERMINATE	2	FALSE	0	0.557988088043553	3		534	355	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225367686	225367698	+	frameshift_variant	Frame_Shift_Del	DEL	GTTGCCTGTAGAT	GTTGCCTGTAGAT	-	novel	NA	P-0012720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	30	479	0	ENST00000264414.4:c.1469_1481del	p.His490LeufsTer5	p.H490Lfs*5	ENST00000264414	NM_003590.4	490	cATCTACAGGCAACt/ct	10/16	0.503606255452286	4	FACETS	0.713	0.578	0.865	0.356	0.289	0.433	SUBCLONAL	1	FALSE	2	0.557988088043553	4		479	235	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440716	56440716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	76	599	0	ENST00000407977.2:c.502G>A	p.Asp168Asn	p.D168N	ENST00000407977		168	Gac/Aac	5/10	0.553316673724043	3	FACETS	0.981	0.867	1	0.491	0.433	0.552	CLONAL	1	FALSE	1	0.557988088043553	3		599	355	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95596457	95596457	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012737-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	189	492	0	ENST00000393063.1:c.511C>G	p.Leu171Val	p.L171V	ENST00000393063	NM_030621.3	171	Ctt/Gtt	6/28	1	2	FACETS	0.913	0.846	0.983	0.913	0.846	0.983	CLONAL	1	TRUE	1	0.527807960049529	2		492	784	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	54	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.00525357259322057	4	FACETS	0.568	0.485	0.658	0.284	0.242	0.329	INDETERMINATE	1	TRUE	2	0.541007076866796	4		426	542	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917484	178917484	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	65	388	1	ENST00000263967.3:c.359C>T	p.Ala120Val	p.A120V	ENST00000263967	NM_006218.2	120	gCt/gTt	3/21	1	2	FACETS	0.893	0.783	1	0.893	0.783	1	CLONAL	1	TRUE	1	0.541007076866796	2		389	269	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976703	2976703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	73	678	4	ENST00000396946.4:c.1309C>T	p.Arg437Cys	p.R437C	ENST00000396946	NM_032415.4	437	Cgc/Tgc	9/25	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.541007076866796	2		682	268	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866533	117866533	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	225	1190	2	ENST00000297338.2:c.1112A>C	p.Lys371Thr	p.K371T	ENST00000297338	NM_006265.2	371	aAa/aCa	9/14	0.463687481483177	4	FACETS	1	0.962	1	0.526	0.489	0.564	CLONAL	1	TRUE	2	0.541007076866796	4		1192	1219	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020486	14020486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1307031587	NA	P-0012738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	97	766	4	ENST00000311895.7:c.457C>T	p.Arg153Cys	p.R153C	ENST00000311895	NM_005236.2	153	Cgc/Tgc	3/11	0.395293477144192	1	FACETS	0.455	0.406	0.506	0.455	0.406	0.506	SUBCLONAL	1	TRUE	0	0.541007076866796	1		770	575	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437563	56437563	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	222	721	0	ENST00000407977.2:c.899A>C	p.Asp300Ala	p.D300A	ENST00000407977		300	gAc/gCc	8/10	0.528915130192157	2	FACETS	0.943	0.891	0.996	0.943	0.891	0.996	CLONAL	2	TRUE	0	0.541007076866796	2		721	435	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226443	2226443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773019943	NA	P-0012739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	42	543	0	ENST00000398665.3:c.3923C>T	p.Pro1308Leu	p.P1308L	ENST00000398665	NM_032482.2	1308	cCg/cTg	27/28	1	2	FACETS	0.606	0.504	0.72	0.606	0.504	0.72	SUBCLONAL	1	TRUE	1	0.18	2		543	770	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	39	540	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.919	0.76	1	0.919	0.76	1	CLONAL	1	TRUE	1	0.15	2		540	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0012746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	36	673	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	0.494	0.404	0.596	0.494	0.404	0.596	SUBCLONAL	1	TRUE	1	0.15	2		674	971	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0012746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	43	651	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.147364628787319	1	FACETS	0.742	0.619	0.878	0.742	0.619	0.878	SUBCLONAL	1	TRUE	0	0.15	1		651	715	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317082	11317082	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	61	685	2	ENST00000361445.4:c.412G>T	p.Asp138Tyr	p.D138Y	ENST00000361445	NM_004958.3	138	Gac/Tac	4/58	1	2	FACETS	0.909	0.782	1	0.909	0.782	1	CLONAL	1	TRUE	1	0.15	2		687	895	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178657	32178657	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	46	548	0	ENST00000375023.3:c.2737T>A	p.Ser913Thr	p.S913T	ENST00000375023	NM_004557.3	913	Tcc/Acc	18/30	1	2	FACETS	0.991	0.833	1	0.991	0.833	1	CLONAL	1	TRUE	1	0.15	2		548	619	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622151	43622151	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1302642973	NA	P-0012746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	56	646	2	ENST00000355710.3:c.3168G>T	p.Trp1056Cys	p.W1056C	ENST00000355710	NM_020975.4	1056	tgG/tgT	19/20	1	2	FACETS	0.916	0.783	1	0.916	0.783	1	CLONAL	1	TRUE	1	0.15	2		648	815	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871934	45871934	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	65	714	1	ENST00000391945.4:c.314T>C	p.Leu105Pro	p.L105P	ENST00000391945	NM_000400.3	105	cTg/cCg	5/23	1	2	FACETS	0.901	0.779	1	0.901	0.779	1	CLONAL	1	TRUE	1	0.15	2		715	962	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735541	40735541	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	37	441	0	ENST00000373198.4:c.3332G>T	p.Gly1111Val	p.G1111V	ENST00000373198	NM_133170.3	1111	gGc/gTc	25/32	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.15	2		441	460	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980862	40980862	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012746-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	42	534	0	ENST00000373198.4:c.1624G>T	p.Val542Leu	p.V542L	ENST00000373198	NM_133170.3	542	Gtg/Ttg	10/32	1	2	FACETS	0.847	0.706	1	0.847	0.706	1	CLONAL	1	TRUE	1	0.15	2		534	661	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913514	NA	P-0012753-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	295	335	0	ENST00000288135.5:c.2466T>A	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaA	17/21	0.406570633156474	2	FACETS	0.979	0.927	1	0.979	0.927	1	CLONAL	2	TRUE	0	0.406570633156474	2		335	741	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0012755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	34	332	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.743	0.607	0.895	0.743	0.607	0.895	SUBCLONAL	1	TRUE	1	0.23	2		332	398	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0012755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1601	69	682	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.359	0.311	0.412	0.359	0.311	0.412	SUBCLONAL	1	TRUE	1	0.23	2		682	1670	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0012755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	76	416	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.76	0.665	0.862	0.76	0.665	0.862	SUBCLONAL	1	TRUE	1	0.23	2		416	870	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845627	63845627	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	55	244	0	ENST00000279873.7:c.1366G>T	p.Glu456Ter	p.E456*	ENST00000279873	NM_032199.2	456	Gaa/Taa	9/10	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.23	2		244	474	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987057	69987057	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	116	463	0	ENST00000394351.3:c.118T>G	p.Leu40Val	p.L40V	ENST00000394351	NM_000248.3	40	Tta/Gta	2/9	1	2	FACETS	0.963	0.867	1	0.963	0.867	1	CLONAL	1	TRUE	1	0.23	2		463	1047	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696598	47696598	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	134	489	0	ENST00000347630.2:c.350T>C	p.Met117Thr	p.M117T	ENST00000347630	NM_001007230.1	117	aTg/aCg	5/11	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.23	2		489	1138	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0012756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	364	561	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	0.708075592667248	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.708075592667248	1		561	643	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222987	1222987	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	181	278	0	ENST00000326873.7:c.924G>T	p.Trp308Cys	p.W308C	ENST00000326873	NM_000455.4	308	tgG/tgT	8/10	0.708075592667248	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.708075592667248	1		278	322	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112499	115112499	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	81	467	0	ENST00000257566.3:c.1241C>A	p.Ala414Asp	p.A414D	ENST00000257566	NM_016569.3	414	gCt/gAt	7/8	0.708075592667248	1	FACETS	0.306	0.27	0.344	0.306	0.27	0.344	SUBCLONAL	1	TRUE	0	0.708075592667248	1		467	483	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65304264	65304385	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CATTTCCTCCTGTTTAGAAAAAACATCCATCAGTCTGAGGCTGCCAAATGAGGGAACCATGGGAGAGGCAAGGGCACAGGATATGAGACAGAGGCCCTGAGGTGACGCCAGCTTCGCCCCTT	CATTTCCTCCTGTTTAGAAAAAACATCCATCAGTCTGAGGCTGCCAAATGAGGGAACCATGGGAGAGGCAAGGGCACAGGATATGAGACAGAGGCCCTGAGGTGACGCCAGCTTCGCCCCTT	-	novel	NA	P-0012756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	141	383	0	ENST00000342505.4:c.2843-113_2851del		p.X948_splice	ENST00000342505	NM_002227.2	948		21/25	NA	2	FACETS	0.704	0.644	0.766			1	INDETERMINATE	1	TRUE	NA	0.708075592667248	2		383	566	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441270	52441273	+	frameshift_variant	Frame_Shift_Del	DEL	GCCT	GCCT	-	novel	NA	P-0012771-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	52	390	0	ENST00000460680.1:c.497_500del	p.Glu166GlyfsTer20	p.E166Gfs*20	ENST00000460680	NM_004656.3	166	gAGGCg/gg	7/17	0.131028110565947	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		390	528	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118943	+	missense_variant	Missense_Mutation	DNP	AG	AG	TT	novel	NA	P-0012771-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	56	574	0	ENST00000078429.4:c.626_627delinsTT	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAG/cTT	5/7	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		574	621	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935967	49935967	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1244120258	NA	P-0012772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	638	687	0	ENST00000296474.3:c.1703C>T	p.Pro568Leu	p.P568L	ENST00000296474	NM_002447.2	568	cCa/cTa	4/20	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		687	1387	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056587	26056587	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	136	138	0	ENST00000343677.2:c.70G>T	p.Ala24Ser	p.A24S	ENST00000343677	NM_005319.3	24	Gcg/Tcg	1/1	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		138	281	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249255	133249255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012772-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	115	546	0	ENST00000320574.5:c.1644G>T	p.Glu548Asp	p.E548D	ENST00000320574	NM_006231.2	548	gaG/gaT	15/49	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		546	1243	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0012780-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	518	301	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.817650374344209	3	FACETS	0.969	0.936	1	0.969	0.936	1	CLONAL	2	TRUE	1	0.84201973582258	3		301	902	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5462893	5462893	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012780-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	118	281	0	ENST00000381577.3:c.454G>T	p.Glu152Ter	p.E152*	ENST00000381577	NM_014143.3	152	Gaa/Taa	4/7	0.451617144086607	2	FACETS	0.458	0.414	0.504	0.229	0.207	0.252	INDETERMINATE	1	TRUE	0	0.84201973582258	2		281	612	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729154	66729154	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519731	NA	P-0012780-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	382	434	0	ENST00000307102.5:c.362G>C	p.Cys121Ser	p.C121S	ENST00000307102	NM_002755.3	121	tGc/tCc	3/11	NA	2	FACETS	0.89	0.848	0.934			1	INDETERMINATE	1	TRUE	NA	0.84201973582258	2		434	1019	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519461	176519461	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012780-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	212	575	0	ENST00000292408.4:c.867C>G	p.Ile289Met	p.I289M	ENST00000292408	NM_213647.1	289	atC/atG	7/18	0.415621863007622	2	FACETS	0.488	0.453	0.524	0.244	0.226	0.262	INDETERMINATE	1	TRUE	0	0.84201973582258	2		575	1032	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965545	93965545	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0012780-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	189	425	0	ENST00000369303.4:c.2382+1G>A		p.X794_splice	ENST00000369303	NM_004440.3	794			0.521115546079439	1	FACETS	0.327	0.302	0.352	0.327	0.302	0.352	SUBCLONAL	1	TRUE	0	0.84201973582258	1		425	796	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5462860	5462860	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012780-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	103	258	0	ENST00000381577.3:c.421A>T	p.Ile141Phe	p.I141F	ENST00000381577	NM_014143.3	141	Att/Ttt	4/7	0.451617144086607	2	FACETS	0.469	0.421	0.519	0.234	0.21	0.26	INDETERMINATE	1	TRUE	0	0.84201973582258	2		258	522	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852502	42852502	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012780-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	487	609	0	ENST00000398585.3:c.584T>C	p.Leu195Pro	p.L195P	ENST00000398585	NM_001135099.1	195	cTt/cCt	6/14	0.582359811569984	3	FACETS	1	0.994	1	0.607	0.581	0.634	CLONAL	1	TRUE	1	0.84201973582258	3		609	1354	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012781-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	160	540	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.250752405391583	2		540	939	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0012781-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	87	223	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.250752405391583	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.250752405391583	1		223	586	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244821	41244821	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012781-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	119	503	0	ENST00000357654.3:c.2727T>A	p.Asn909Lys	p.N909K	ENST00000357654	NM_007294.3	909	aaT/aaA	10/23	1	2	FACETS	0.995	0.897	1	0.995	0.897	1	CLONAL	1	TRUE	1	0.250752405391583	2		503	954	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266012	41266312	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	In_Frame_Del	DEL	TATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTG	TATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTG	-	novel	NA	P-0012781-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	32	340	0	ENST00000349496.5:c.14-1_241+72del		p.A5_D81del	ENST00000349496	NM_001904.3	5		3/15	0.138810357088124	3	FACETS	0.614	0.498	0.745			1	INDETERMINATE	1	TRUE	NA	0.250752405391583	3		340	468	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	151	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.271029034330365	2		426	822	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0012827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	140	538	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.271029034330365	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.271029034330365	1		538	668	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678504	88678504	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	162	545	0	ENST00000360948.2:c.1032G>T	p.Glu344Asp	p.E344D	ENST00000360948	NM_001012338.2	344	gaG/gaT	9/19	1	2	FACETS	0.798	0.733	0.865	1	0.99	1	SUBCLONAL	2	TRUE	1	0.271029034330365	2		545	749	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0012843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	164	526	0	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.331615523381187	1	FACETS	0.943	0.866	1	0.943	0.866	1	CLONAL	1	TRUE	0	0.331615523381187	1		526	875	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554527	63554527	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502145	NA	P-0012843-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	113	443	1	ENST00000307078.5:c.212C>T	p.Pro71Leu	p.P71L	ENST00000307078	NM_004655.3	71	cCg/cTg	2/11	0.262547768429264	3	FACETS	0.773	0.694	0.857	0.386	0.347	0.429	SUBCLONAL	1	TRUE	1	0.331615523381187	3		444	1028	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012844-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	95	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.935	0.831	1	0.935	0.831	1	CLONAL	1	FALSE	1	0.21645397476864	2		426	939	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578191	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs530941076	NA	P-0012844-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1437	157	835	0	ENST00000269305.4:c.658T>C	p.Tyr220His	p.Y220H	ENST00000269305	NM_001126112.2	220	Tat/Cat	6/11	1	2	FACETS	0.91	0.831	0.994	0.91	0.831	0.994	CLONAL	1	FALSE	1	0.21645397476864	2		835	1594	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974799	21974799	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012844-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	28	129	1	ENST00000304494.5:c.28G>T	p.Glu10Ter	p.E10*	ENST00000304494	NM_000077.4	10	Gag/Tag	1/3	0.21645397476864	1	FACETS	0.65	0.52	0.798	0.65	0.52	0.798	SUBCLONAL	1	FALSE	0	0.21645397476864	1		130	355	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751477	57751477	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012844-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1504	118	763	1	ENST00000274289.3:c.1514C>A	p.Thr505Asn	p.T505N	ENST00000274289	NM_006622.3	505	aCc/aAc	11/14	1	2	FACETS	0.672	0.604	0.745	0.672	0.604	0.745	SUBCLONAL	1	FALSE	1	0.21645397476864	2		764	1622	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423413	116423413	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913247	NA	P-0012845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	651	778	0	ENST00000397752.3:c.3688T>C	p.Tyr1230His	p.Y1230H	ENST00000397752	NM_000245.2	1230	Tat/Cat	19/21	0.404550314794885	3	FACETS	1	0.988	1	1	0.998	1	CLONAL	3	TRUE	1	0.404550314794885	3		778	1235	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843691	156843691	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	325	1035	2	ENST00000524377.1:c.1117T>A	p.Ser373Thr	p.S373T	ENST00000524377	NM_002529.3	373	Tcc/Acc	8/17	1	2	FACETS	0.848	0.803	0.894	1	0.995	1	CLONAL	2	TRUE	1	0.404550314794885	2		1037	947	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508198	38508198	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	306	895	1	ENST00000254066.5:c.506T>C	p.Val169Ala	p.V169A	ENST00000254066	NM_000964.3	169	gTg/gCg	5/9	0.404550314794885	3	FACETS	1	0.993	1	0.691	0.65	0.732	CLONAL	1	TRUE	1	0.404550314794885	3		896	1317	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098964	178098975	+	inframe_deletion	In_Frame_Del	DEL	ATCTTGCCTCCA	ATCTTGCCTCCA	-	novel	NA	P-0012845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	158	466	0	ENST00000397062.3:c.70_81del	p.Trp24_Asp27del	p.W24_D27del	ENST00000397062	NM_006164.4	24	TGGAGGCAAGAT/-	2/5	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.404550314794885	2		466	601	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183785	10183785	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs5030828	NA	P-0012853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	67	424	0	ENST00000256474.2:c.254T>C	p.Leu85Pro	p.L85P	ENST00000256474	NM_000551.3	85	cTg/cCg	1/3	0.581284176953352	3	FACETS	0.503	0.439	0.573	0.252	0.219	0.287	SUBCLONAL	1	TRUE	1	0.903063128707361	3		424	428	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66781598	66781598	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	33	760	0	ENST00000307102.5:c.1006G>T	p.Asp336Tyr	p.D336Y	ENST00000307102	NM_002755.3	336	Gat/Tat	9/11	0.146693092386412	4	FACETS	0.316	0.257	0.383	0.158	0.128	0.192	INDETERMINATE	1	TRUE	2	0.903063128707361	4		760	440	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117150	7117150	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	65	873	2	ENST00000302850.5:c.4066G>T	p.Glu1356Ter	p.E1356*	ENST00000302850	NM_000208.2	1356	Gag/Tag	22/22	1	2	FACETS	0.338	0.294	0.385	0.338	0.294	0.385	SUBCLONAL	1	TRUE	1	0.903063128707361	2		875	426	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729876	47729876	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	133	875	0	ENST00000449228.1:c.513T>A	p.Asp171Glu	p.D171E	ENST00000449228	NM_001127240.2	171	gaT/gaA	3/4	1	2	FACETS	0.245	0.222	0.27	0.245	0.222	0.27	SUBCLONAL	1	TRUE	1	0.903063128707361	2		875	1200	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900381	3900384	+	frameshift_variant	Frame_Shift_Del	DEL	GCAC	GCAC	-	novel	NA	P-0012853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	25	736	0	ENST00000262367.5:c.712_715del	p.Val238TrpfsTer5	p.V238Wfs*5	ENST00000262367	NM_004380.2	238	GTGCtg/tg	2/31	0.258369654489091	1	FACETS	0.07	0.055	0.088	0.07	0.055	0.088	INDETERMINATE	1	TRUE	0	0.903063128707361	1		736	433	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598101	52598102	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0012853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	101	793	0	ENST00000394830.3:c.3764_3765del	p.Ser1255CysfsTer2	p.S1255Cfs*2	ENST00000394830	NM_018313.4	1255	tCT/t	24/30	0.581284176953352	3	FACETS	0.777	0.699	0.858	0.388	0.349	0.429	SUBCLONAL	1	TRUE	1	0.903063128707361	3		793	418	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442486	52442494	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGACCTGGT	AGACCTGGT	-	novel	NA	P-0012853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	91	377	0	ENST00000460680.1:c.251_255+4del		p.X84_splice	ENST00000460680	NM_004656.3	84		4/17	0.581284176953352	3	FACETS	0.776	0.694	0.862	0.388	0.347	0.431	SUBCLONAL	1	TRUE	1	0.903063128707361	3		377	377	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0012862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	185	316	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.889993396150032	5	FACETS	0.815	0.751	0.882	0.204	0.187	0.221	CLONAL	1	TRUE	1	0.889993396150032	5		316	1191	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0012862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	499	623	3	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	1	2	FACETS	0.967	0.928	1	0.967	0.928	1	CLONAL	1	TRUE	1	0.889993396150032	2		626	1160	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127164	22127164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057519911	NA	P-0012862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	504	657	1	ENST00000215832.6:c.964G>A	p.Glu322Lys	p.E322K	ENST00000215832	NM_002745.4	322	Gag/Aag	7/9	1	2	FACETS	0.981	0.942	1	0.981	0.942	1	CLONAL	1	TRUE	1	0.889993396150032	2		658	1154	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195371	102195371	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	768	981	1	ENST00000263464.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000263464	NM_001165.4	44	cCt/cTt	2/9	0.889993396150032	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.889993396150032	1		982	957	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0012878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	77	375	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.198824445609635	1	FACETS	0.62	0.543	0.704	0.62	0.543	0.704	SUBCLONAL	1	TRUE	0	0.2147820611515	1		375	1032	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0012878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	135	267	1	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.163595472325303	2	FACETS	0.803	0.73	0.879	0.803	0.73	0.879	CLONAL	2	TRUE	0	0.2147820611515	2		268	783	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938239	36938239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199991273	NA	P-0012878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1899	146	530	0	ENST00000361632.4:c.722C>T	p.Ala241Val	p.A241V	ENST00000361632		241	gCg/gTg	6/16	0.2147820611515	5	FACETS	0.879	0.798	0.964			1	CLONAL	1	TRUE	NA	0.2147820611515	5		530	2045	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041211	112041211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140762956	NA	P-0012878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1790	148	641	5	ENST00000368678.4:c.44C>T	p.Thr15Met	p.T15M	ENST00000368678		15	aCg/aTg	3/13	1	2	FACETS	0.711	0.646	0.78	0.711	0.646	0.78	SUBCLONAL	1	TRUE	1	0.2147820611515	2		646	1938	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020478	14020478	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377014538	NA	P-0012878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	104	402	1	ENST00000311895.7:c.449G>A	p.Arg150His	p.R150H	ENST00000311895	NM_005236.2	150	cGc/cAc	3/11	1	2	FACETS	0.759	0.677	0.846	0.759	0.677	0.846	SUBCLONAL	1	TRUE	1	0.2147820611515	2		403	1276	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627224	37627224	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200075664	NA	P-0012878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	81	388	0	ENST00000447079.4:c.1139G>A	p.Arg380His	p.R380H	ENST00000447079	NM_015083.1	380	cGt/cAt	2/14	1	2	FACETS	0.685	0.602	0.775	0.685	0.602	0.775	SUBCLONAL	1	TRUE	1	0.2147820611515	2		388	1101	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	118	540	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.396110066249669	2		540	467	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359014	81359014	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	122	811	1	ENST00000222390.5:c.947C>A	p.Thr316Asn	p.T316N	ENST00000222390	NM_000601.4	316	aCt/aAt	8/18	1	2	FACETS	0.917	0.83	1	0.917	0.83	1	CLONAL	1	TRUE	1	0.396110066249669	2		812	672	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249411	110249411	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	212	1115	0	ENST00000374672.4:c.1162T>A	p.Trp388Arg	p.W388R	ENST00000374672	NM_004235.4	388	Tgg/Agg	4/5	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.396110066249669	2		1115	992	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518463	69518463	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	31	248	0	ENST00000294312.3:c.182G>T	p.Arg61Leu	p.R61L	ENST00000294312	NM_005117.2	61	cGc/cTc	1/3	1	2	FACETS	0.842	0.687	1	0.842	0.687	1	CLONAL	1	TRUE	1	0.396110066249669	2		248	186	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858273	9858273	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567277910	NA	P-0012879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	99	700	0	ENST00000330684.3:c.3128C>T	p.Thr1043Ile	p.T1043I	ENST00000330684	NM_001134407.1	1043	aCc/aTc	13/13	1	2	FACETS	0.978	0.877	1	0.978	0.877	1	CLONAL	1	TRUE	1	0.396110066249669	2		700	511	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435023	56435023	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	96	522	0	ENST00000407977.2:c.2114G>T	p.Gly705Val	p.G705V	ENST00000407977		705	gGc/gTc	9/10	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.396110066249669	2		522	432	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546539	9546539	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0012879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	178	504	0	ENST00000353224.5:c.1482+1G>T		p.X494_splice	ENST00000353224	NM_177990.2	494			0.253440341040682	2	FACETS	0.845	0.784	0.907	0.845	0.784	0.907	CLONAL	2	TRUE	0	0.396110066249669	2		504	532	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444401	50444401	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	279	366	2	ENST00000331340.3:c.331C>T	p.Arg111Ter	p.R111*	ENST00000331340	NM_006060.4	111	Cga/Tga	4/8	0.39638467782905	5	FACETS	0.954	0.901	1	0.954	0.901	1	CLONAL	3	TRUE	2	0.42484594618292	5		368	751	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793336	139793336	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1688	249	1119	2	ENST00000247668.2:c.144G>T	p.Gln48His	p.Q48H	ENST00000247668	NM_021138.3	48	caG/caT	2/11	0.39638467782905	5	FACETS	0.991	0.923	1	0.33	0.307	0.354	CLONAL	1	TRUE	2	0.42484594618292	5		1121	1937	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012896-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	81	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.233697680369087	3	FACETS	0.722	0.635	0.816	0.361	0.317	0.408	SUBCLONAL	1	TRUE	1	0.27	3		426	943	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0012896-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	196	695	0	ENST00000262160.6:c.1391C>G	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tGa	11/11	1	2	FACETS	0.766	0.709	0.825	1	0.991	1	SUBCLONAL	2	TRUE	1	0.27	2		695	948	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0012896-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	74	518	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.3	2	FACETS	0.69	0.603	0.784			1	SUBCLONAL	1	TRUE	NA	0.27	2		518	794	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0012908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	292	635	0	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	0.502215418914544	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.503239198091843	1		635	860	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556122	29556123	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0012908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	158	248	0	ENST00000356175.3:c.2492_2493del	p.Thr831ArgfsTer33	p.T831Rfs*33	ENST00000356175	NM_000267.3	830	gAC/g	21/57	NA	2	FACETS	0.799	0.741	0.858			1	INDETERMINATE	2	TRUE	NA	0.503239198091843	2		248	393	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157495164	157495164	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	210	654	0	ENST00000346085.5:c.3048G>A	p.Met1016Ile	p.M1016I	ENST00000346085	NM_020732.3	1016	atG/atA	11/20	1	2	FACETS	0.888	0.825	0.953	0.888	0.825	0.953	CLONAL	1	TRUE	1	0.503239198091843	2		654	940	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663355	67663355	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	265	846	1	ENST00000264010.4:c.1756G>A	p.Glu586Lys	p.E586K	ENST00000264010	NM_006565.3	586	Gaa/Aaa	10/12	0.456867609345549	2	FACETS	0.813	0.761	0.866	0.406	0.38	0.433	CLONAL	1	TRUE	0	0.503239198091843	2		847	1296	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39613837	39613837	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	293	754	0	ENST00000262039.4:c.1755G>T	p.Leu585Phe	p.L585F	ENST00000262039	NM_002647.2	585	ttG/ttT	16/25	0.502215418914544	1	FACETS	0.984	0.928	1	0.984	0.928	1	CLONAL	1	TRUE	0	0.503239198091843	1		754	886	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602341	10602341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1178941219	NA	P-0012908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	521	900	3	ENST00000171111.5:c.1237C>T	p.Arg413Cys	p.R413C	ENST00000171111	NM_203500.1	413	Cgt/Tgt	3/6	0.431788370681839	2	FACETS	0.844	0.81	0.877	0.844	0.81	0.877	CLONAL	2	TRUE	0	0.503239198091843	2		903	1227	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098450	11098451	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0012908-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	440	740	0	ENST00000358026.2:c.969_970del	p.Pro324ArgfsTer62	p.P324Rfs*62	ENST00000358026	NM_001128849.1	323	tCG/t	6/36	0.431788370681839	2	FACETS	0.856	0.82	0.893	0.856	0.82	0.893	CLONAL	2	TRUE	0	0.503239198091843	2		740	1021	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	33	426	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		426	955	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0012916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1248	67	848	0	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		848	1315	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913492	NA	P-0012924-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	254	346	0	ENST00000286548.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000286548	NM_002072.3	209	cAa/cTa	5/7	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.885084440262817	2		346	553	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0012926-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	154	365	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	1	2	FACETS	0.878	0.808	0.951	1	0.991	1	CLONAL	2	TRUE	1	0.313691336342202	2		365	559	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0012926-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	226	406	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	0.279530082816497	4	FACETS	1	0.983	1			1	CLONAL	2	TRUE	NA	0.313691336342202	4		406	818	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271734	18271734	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012926-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	84	509	0	ENST00000222254.8:c.421G>A	p.Asp141Asn	p.D141N	ENST00000222254	NM_005027.3	141	Gac/Aac	4/16	1	2	FACETS	0.632	0.557	0.713	0.632	0.557	0.713	SUBCLONAL	1	TRUE	1	0.313691336342202	2		509	847	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602907	10602907	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	70	800	0	ENST00000171111.5:c.671C>T	p.Ser224Phe	p.S224F	ENST00000171111	NM_203500.1	224	tCc/tTc	3/6	1	2	FACETS	0.883	0.767	1	0.883	0.767	1	CLONAL	1	TRUE	1	0.14	2		800	1133	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	48	583	0	ENST00000269305.4:c.524del	p.Arg175ProfsTer72	p.R175Pfs*72	ENST00000269305	NM_001126112.2	175	cGc/cc	5/11	1	2	FACETS	0.982	0.829	1	0.982	0.829	1	CLONAL	1	TRUE	1	0.14	2		583	698	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851661	134851661	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	82	702	0	ENST00000398015.3:c.1067A>G	p.Tyr356Cys	p.Y356C	ENST00000398015	NM_004441.4	356	tAc/tGc	5/16	0.288393090913968	3	FACETS	1	0.975	1	0.726	0.639	0.82	CLONAL	1	TRUE	1	0.14	3		702	863	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115828	8115828	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1306	89	1175	0	ENST00000346208.3:c.1174A>T	p.Asn392Tyr	p.N392Y	ENST00000346208		392	Aac/Tac	6/6	1	2	FACETS	0.911	0.805	1	0.911	0.805	1	CLONAL	1	TRUE	1	0.14	2		1175	1395	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434723	99434723	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	70	832	0	ENST00000268035.6:c.810G>T	p.Arg270Ser	p.R270S	ENST00000268035	NM_000875.3	270	agG/agT	3/21	1	2	FACETS	0.951	0.827	1	0.951	0.827	1	CLONAL	1	TRUE	1	0.14	2		832	1051	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602853	10602853	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	70	716	1	ENST00000171111.5:c.725A>T	p.Glu242Val	p.E242V	ENST00000171111	NM_203500.1	242	gAg/gTg	3/6	1	2	FACETS	0.858	0.745	0.98	0.858	0.745	0.98	CLONAL	1	TRUE	1	0.14	2		717	1166	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627813	14627813	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs369749322	NA	P-0012950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1578	95	1224	0	ENST00000254322.2:c.257A>G	p.Asn86Ser	p.N86S	ENST00000254322	NM_006145.1	86	aAt/aGt	2/3	1	2	FACETS	0.811	0.719	0.91	0.811	0.719	0.91	CLONAL	1	TRUE	1	0.14	2		1224	1673	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546619	9546619	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	91	999	0	ENST00000353224.5:c.1403A>T	p.Glu468Val	p.E468V	ENST00000353224	NM_177990.2	468	gAg/gTg	5/10	1	2	FACETS	0.998	0.883	1	0.998	0.883	1	CLONAL	1	TRUE	1	0.14	2		999	1302	SUCCESS
AR	367	MSKCC	GRCh37	X	66937385	66937385	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1224	66	1121	2	ENST00000374690.3:c.2239G>T	p.Val747Leu	p.V747L	ENST00000374690	NM_000044.3	747	Gtg/Ttg	5/8	1	2	FACETS	0.731	0.632	0.839	0.731	0.632	0.839	SUBCLONAL	1	TRUE	1	0.14	2		1123	1290	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0012951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	595	569	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.342006253250765	5	FACETS	0.923	0.891	0.954	1	0.997	1	CLONAL	5	TRUE	2	0.342006253250765	5		569	1141	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528633	8528633	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	260	698	0	ENST00000356435.5:c.499G>T	p.Asp167Tyr	p.D167Y	ENST00000356435		167	Gac/Tac	4/35	0.342006253250765	2	FACETS	0.96	0.903	1	0.96	0.903	1	CLONAL	2	TRUE	0	0.342006253250765	2		698	792	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023006	27023006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	37	66	0	ENST00000324856.7:c.112G>A	p.Glu38Lys	p.E38K	ENST00000324856	NM_006015.4	38	Gag/Aag	1/20	0.342006253250765	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	2	TRUE	0	0.342006253250765	2		66	106	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745988	162745988	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	202	528	0	ENST00000367921.3:c.2111T>G	p.Leu704Arg	p.L704R	ENST00000367921	NM_006182.2	704	cTt/cGt	16/18	0.342006253250765	4	FACETS	0.962	0.893	1	0.962	0.893	1	CLONAL	2	TRUE	2	0.342006253250765	4		528	824	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259510	89259510	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	222	518	0	ENST00000336596.2:c.654G>T	p.Met218Ile	p.M218I	ENST00000336596	NM_005233.5	218	atG/atT	3/17	0.342006253250765	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	2	0.342006253250765	4		518	837	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598048	55598048	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1560421189	NA	P-0012951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	99	611	0	ENST00000288135.5:c.2245G>A	p.Glu749Lys	p.E749K	ENST00000288135	NM_000222.2	749	Gaa/Aaa	16/21	0.342006253250765	3	FACETS	0.964	0.861	1	0.482	0.43	0.537	CLONAL	1	TRUE	1	0.342006253250765	3		611	703	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673010	30673010	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	271	743	0	ENST00000376406.3:c.3950C>G	p.Ser1317Cys	p.S1317C	ENST00000376406	NM_014641.2	1317	tCc/tGc	10/15	0.32990830669335	2	FACETS	0.963	0.906	1	0.963	0.906	1	CLONAL	2	TRUE	0	0.342006253250765	2		743	823	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706881	117706881	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	241	554	0	ENST00000368508.3:c.2269G>T	p.Gly757Cys	p.G757C	ENST00000368508	NM_002944.2	757	Ggt/Tgt	15/43	NA	2	FACETS	1	0.967	1			1	INDETERMINATE	2	TRUE	NA	0.342006253250765	2		554	675	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971024	21971024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	183	410	0	ENST00000304494.5:c.334C>T	p.Arg112Cys	p.R112C	ENST00000304494	NM_000077.4	112	Cgt/Tgt	2/3	0.342006253250765	2	FACETS	0.995	0.925	1	0.995	0.925	1	CLONAL	2	TRUE	0	0.342006253250765	2		410	538	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36846911	36846911	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	266	614	0	ENST00000358127.4:c.1028G>T	p.Gly343Val	p.G343V	ENST00000358127	NM_001280556.1	343	gGg/gTg	9/10	0.337230427312856	3	FACETS	1	0.99	1	0.831	0.783	0.879	CLONAL	2	TRUE	0	0.342006253250765	3		614	731	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406181	70406181	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	79	391	0	ENST00000373644.4:c.3695C>T	p.Pro1232Leu	p.P1232L	ENST00000373644	NM_030625.2	1232	cCc/cTc	4/12	0.342006253250765	3	FACETS	0.866	0.762	0.977	0.433	0.381	0.489	CLONAL	1	TRUE	1	0.342006253250765	3		391	625	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406187	70406187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	83	416	0	ENST00000373644.4:c.3701C>T	p.Thr1234Ile	p.T1234I	ENST00000373644	NM_030625.2	1234	aCa/aTa	4/12	0.342006253250765	3	FACETS	0.876	0.773	0.986	0.438	0.386	0.493	CLONAL	1	TRUE	1	0.342006253250765	3		416	649	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29002033	29002033	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	76	438	0	ENST00000282397.4:c.1132G>C	p.Glu378Gln	p.E378Q	ENST00000282397	NM_002019.4	378	Gag/Cag	9/30	NA	2	FACETS	0.979	0.862	1			1	INDETERMINATE	1	TRUE	NA	0.342006253250765	2		438	454	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042051	14042051	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	186	558	0	ENST00000311895.7:c.2598G>C	p.Leu866Phe	p.L866F	ENST00000311895	NM_005236.2	866	ttG/ttC	11/11	0.342006253250765	3	FACETS	0.914	0.847	0.983	0.914	0.847	0.983	CLONAL	2	TRUE	1	0.342006253250765	3		558	697	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362473	40362473	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1230	409	971	0	ENST00000293328.3:c.1723G>T	p.Asp575Tyr	p.D575Y	ENST00000293328	NM_012448.3	575	Gac/Tac	14/19	0.342006253250765	3	FACETS	0.854	0.811	0.898			1	CLONAL	2	TRUE	NA	0.342006253250765	3		971	1639	SUCCESS
CALR	811	MSKCC	GRCh37	19	13049530	13049530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs929780860	NA	P-0012951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	168	765	1	ENST00000316448.5:c.37G>T	p.Gly13Cys	p.G13C	ENST00000316448	NM_004343.3	13	Ggc/Tgc	1/9	0.342006253250765	4	FACETS	1	0.968	1	0.554	0.508	0.602	CLONAL	1	TRUE	2	0.342006253250765	4		766	1190	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648409	30648450	+	inframe_deletion	In_Frame_Del	DEL	CTGCACATCGTCCTGTGGACGCGTATCGCCAGCACGATCCCA	CTGCACATCGTCCTGTGGACGCGTATCGCCAGCACGATCCCA	-	novel	NA	P-0012951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	109	513	0	ENST00000295754.5:c.35_76del	p.Leu12_Pro25del	p.L12_P25del	ENST00000295754	NM_003242.5	12	CTGCACATCGTCCTGTGGACGCGTATCGCCAGCACGATCCCA/-	1/7	0.32990830669335	2	FACETS	1	0.975	1	0.626	0.565	0.691	CLONAL	1	TRUE	0	0.342006253250765	2		513	509	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385240	41385240	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	215	575	0	ENST00000373198.4:c.721del	p.Arg241ValfsTer28	p.R241Vfs*28	ENST00000373198	NM_133170.3	241	Cgt/gt	6/32	0.342006253250765	5	FACETS	0.917	0.852	0.984	0.611	0.568	0.656	CLONAL	2	TRUE	2	0.342006253250765	5		575	1037	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0012968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	129	453	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.949	0.862	1	0.949	0.862	1	CLONAL	1	TRUE	1	0.392152557334271	2		453	693	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0012968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	57	332	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.848	0.731	0.973	0.848	0.731	0.973	CLONAL	1	TRUE	1	0.392152557334271	2		332	343	SUCCESS
INSRR	3645	MSKCC	GRCh37	1	156811904	156811904	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1222103965	NA	P-0012968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	126	519	0	ENST00000368195.3:c.3397G>A	p.Asp1133Asn	p.D1133N	ENST00000368195	NM_014215.2	1133	Gac/Aac	19/22	1	2	FACETS	0.839	0.76	0.922	0.839	0.76	0.922	CLONAL	1	TRUE	1	0.392152557334271	2		519	766	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268419	142268419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs980426116	NA	P-0012968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	80	322	0	ENST00000350721.4:c.3073C>T	p.Arg1025Cys	p.R1025C	ENST00000350721	NM_001184.3	1025	Cgt/Tgt	15/47	1	2	FACETS	0.747	0.659	0.842	0.747	0.659	0.842	SUBCLONAL	1	TRUE	1	0.392152557334271	2		322	546	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37141862	37141862	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	127	284	0	ENST00000373509.5:c.937A>G	p.Lys313Glu	p.K313E	ENST00000373509	NM_002648.3	313	Aaa/Gaa	6/6	0.392152557334271	3	FACETS	0.758	0.69	0.829	0.758	0.69	0.829	SUBCLONAL	2	TRUE	1	0.392152557334271	3		284	511	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715360	117715360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1378031096	NA	P-0012968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	82	401	1	ENST00000368508.3:c.1129C>T	p.Leu377Phe	p.L377F	ENST00000368508	NM_002944.2	377	Ctt/Ttt	10/43	0.299351846250831	1	FACETS	0.65	0.575	0.731	0.65	0.575	0.731	SUBCLONAL	1	TRUE	0	0.392152557334271	1		402	517	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391190	139391190	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370135470	NA	P-0012968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	82	317	0	ENST00000277541.6:c.7001C>T	p.Pro2334Leu	p.P2334L	ENST00000277541	NM_017617.3	2334	cCc/cTc	34/34	0.392152557334271	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.392152557334271	1		317	285	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959380	26959380	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	140	413	0	ENST00000381527.3:c.547C>A	p.Pro183Thr	p.P183T	ENST00000381527	NM_001260.1	183	Cct/Act	6/13	1	2	FACETS	0.973	0.887	1	0.973	0.887	1	CLONAL	1	TRUE	1	0.392152557334271	2		413	734	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801803	3801803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	101	385	0	ENST00000262367.5:c.3703C>T	p.His1235Tyr	p.H1235Y	ENST00000262367	NM_004380.2	1235	Cat/Tat	20/31	1	2	FACETS	0.86	0.77	0.955	0.86	0.77	0.955	CLONAL	1	TRUE	1	0.392152557334271	2		385	599	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916259	9916259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	106	493	0	ENST00000330684.3:c.2030C>T	p.Ser677Phe	p.S677F	ENST00000330684	NM_001134407.1	677	tCc/tTc	10/13	1	2	FACETS	0.799	0.717	0.885	0.799	0.717	0.885	SUBCLONAL	1	TRUE	1	0.392152557334271	2		493	677	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477837	140477851	+	inframe_deletion	In_Frame_Del	DEL	TAGGTGCTGTCACAT	TAGGTGCTGTCACAT	-	novel	NA	P-0012968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	364	573	0	ENST00000288602.6:c.1457_1471del	p.Asn486_Pro490del	p.N486_P490del	ENST00000288602	NM_004333.4	486	aATGTGACAGCACCTAca/aca	12/18	0.392152557334271	4	FACETS	1	0.989	1	0.766	0.727	0.806	CLONAL	2	TRUE	1	0.392152557334271	4		573	1124	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0012976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	231	635	1	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	0.321783450824275	2	FACETS	0.894	0.837	0.953	0.894	0.837	0.953	CLONAL	2	TRUE	0	0.340245734364405	2		636	759	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0012976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	109	517	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.245198679283049	3	FACETS	0.878	0.788	0.974	0.439	0.394	0.487	CLONAL	1	TRUE	1	0.340245734364405	3		517	854	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207092	1207092	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs778376925	NA	P-0012976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	216	620	0	ENST00000326873.7:c.180C>G	p.Tyr60Ter	p.Y60*	ENST00000326873	NM_000455.4	60	taC/taG	1/10	NA	2	FACETS	0.893	0.833	0.954			1	INDETERMINATE	2	TRUE	NA	0.340245734364405	2		620	711	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431352	121431352	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	35	403	0	ENST00000257555.6:c.556A>G	p.Ile186Val	p.I186V	ENST00000257555		186	Att/Gtt	3/10	NA	2	FACETS	0.492	0.403	0.592			1	INDETERMINATE	1	TRUE	NA	0.340245734364405	2		403	418	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684314	29684314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750754640	NA	P-0012976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	271	544	0	ENST00000356175.3:c.7834G>A	p.Glu2612Lys	p.E2612K	ENST00000356175	NM_000267.3	2612	Gag/Aag	53/57	0.312298272499807	2	FACETS	0.928	0.873	0.984	0.928	0.873	0.984	CLONAL	2	TRUE	0	0.340245734364405	2		544	858	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572362	41572362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012976-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	39	494	0	ENST00000263253.7:c.4891C>T	p.Leu1631Phe	p.L1631F	ENST00000263253	NM_001429.3	1631	Ctc/Ttc	30/31	0.312298272499807	2	FACETS	0.395	0.327	0.472	0.198	0.163	0.236	SUBCLONAL	1	TRUE	0	0.340245734364405	2		494	580	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	409	418	4	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.921	0.88	0.962	0.921	0.88	0.962	CLONAL	1	TRUE	1	0.940223599930812	2		422	945	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0012977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	551	616	2	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.948	0.912	0.983	0.948	0.912	0.983	CLONAL	1	TRUE	1	0.940223599930812	2		618	1237	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0012977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	304	277	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.981	0.932	1	0.981	0.932	1	CLONAL	1	TRUE	1	0.940223599930812	2		277	659	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0012977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	338	344	1	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.977	0.93	1	0.977	0.93	1	CLONAL	1	TRUE	1	0.940223599930812	2		345	736	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0012977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	519	555	0	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	1	2	FACETS	0.996	0.958	1	0.996	0.958	1	CLONAL	1	TRUE	1	0.940223599930812	2		555	1108	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330611	65330611	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	493	504	2	ENST00000342505.4:c.1035del	p.Lys345AsnfsTer32	p.K345Nfs*32	ENST00000342505	NM_002227.2	345	aaA/aa	8/25	1	2	FACETS	0.908	0.871	0.945	0.908	0.871	0.945	CLONAL	1	TRUE	1	0.940223599930812	2		506	1155	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440912	52440912	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1205668341	NA	P-0012977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	426	442	2	ENST00000460680.1:c.592del	p.Glu198ArgfsTer33	p.E198Rfs*33	ENST00000460680	NM_004656.3	198	Gag/ag	8/17	0.940223599930812	1	FACETS	0.922	0.898	0.944	0.922	0.898	0.944	CLONAL	1	TRUE	0	0.940223599930812	1		444	521	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661664	227661664	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs761880048	NA	P-0012977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	326	404	8	ENST00000305123.5:c.1791del	p.His598ThrfsTer38	p.H598Tfs*38	ENST00000305123	NM_005544.2	597	ggG/gg	1/2	1	2	FACETS	0.87	0.826	0.914	0.87	0.826	0.914	CLONAL	1	TRUE	1	0.940223599930812	2		412	797	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223131	5223131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375155482	NA	P-0012977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	500	549	1	ENST00000357368.4:c.2672C>T	p.Thr891Met	p.T891M	ENST00000357368	NM_002850.3	891	aCg/aTg	18/38	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.940223599930812	2		550	1049	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508793	106508793	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370152741	NA	P-0012977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	400	432	0	ENST00000359195.3:c.787G>A	p.Glu263Lys	p.E263K	ENST00000359195	NM_002649.2	263	Gaa/Aaa	2/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.940223599930812	2		432	841	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624840	9624840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1184049921	NA	P-0012977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	463	473	0	ENST00000353224.5:c.137C>T	p.Thr46Met	p.T46M	ENST00000353224	NM_177990.2	46	aCg/aTg	3/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.940223599930812	2		473	977	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932171	39932171	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555918056	NA	P-0012977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	661	740	1	ENST00000378444.4:c.2428C>T	p.Arg810Ter	p.R810*	ENST00000378444	NM_001123385.1	810	Cga/Tga	4/15	0.940223599930812	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.940223599930812	1		741	711	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138915	64138915	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	315	320	0	ENST00000334205.4:c.2287del	p.Arg763AlafsTer21	p.R763Afs*21	ENST00000334205	NM_003942.2	761	gCc/gc	17/17	1	2	FACETS	0.899	0.854	0.945	0.899	0.854	0.945	CLONAL	1	TRUE	1	0.940223599930812	2		320	745	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946269	55946269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758952853	NA	P-0012977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	386	398	0	ENST00000263923.4:c.3910G>A	p.Gly1304Ser	p.G1304S	ENST00000263923	NM_002253.2	1304	Ggc/Agc	30/30	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.940223599930812	2		398	815	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132635	11132635	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	487	512	1	ENST00000358026.2:c.2854del	p.Glu952LysfsTer5	p.E952Kfs*5	ENST00000358026	NM_001128849.1	951	Ggg/gg	19/36	1	2	FACETS	0.962	0.923	1	0.962	0.923	1	CLONAL	1	TRUE	1	0.940223599930812	2		513	1077	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850322	128850322	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	483	499	0	ENST00000249373.3:c.1585G>T	p.Gly529Cys	p.G529C	ENST00000249373	NM_005631.4	529	Ggc/Tgc	9/12	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.940223599930812	2		499	1016	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139638	202139638	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	513	516	0	ENST00000358485.4:c.799A>C	p.Ile267Leu	p.I267L	ENST00000358485	NM_001080125.1	267	Atc/Ctc	6/9	1	2	FACETS	0.976	0.938	1	0.976	0.938	1	CLONAL	1	TRUE	1	0.940223599930812	2		516	1118	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522433	187522433	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	506	619	0	ENST00000441802.2:c.11630G>T	p.Ser3877Ile	p.S3877I	ENST00000441802	NM_005245.3	3877	aGc/aTc	21/27	1	2	FACETS	0.964	0.927	1	0.964	0.927	1	CLONAL	1	TRUE	1	0.940223599930812	2		619	1116	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790795	89790795	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs142250912	NA	P-0012977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	551	552	0	ENST00000336032.3:c.182T>C	p.Leu61Pro	p.L61P	ENST00000336032	NM_006813.2	61	cTa/cCa	1/2	0.940223599930812	3	FACETS	1	0.977	1	0.514	0.493	0.536	CLONAL	1	TRUE	1	0.940223599930812	3		552	1675	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553704	106553704	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	317	388	0	ENST00000369096.4:c.1669A>G	p.Thr557Ala	p.T557A	ENST00000369096	NM_001198.3	557	Acc/Gcc	5/7	0.940223599930812	2	FACETS	0.894	0.849	0.94	0.447	0.424	0.47	CLONAL	1	TRUE	0	0.940223599930812	2		388	754	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231371	98231371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1053507002	NA	P-0012977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	361	376	0	ENST00000331920.6:c.1912C>T	p.Arg638Cys	p.R638C	ENST00000331920	NM_000264.3	638	Cgc/Tgc	14/24	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.940223599930812	2		376	746	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910909	32910909	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs80358506	NA	P-0012977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1649	123	872	0	ENST00000380152.3:c.2417A>G	p.Asp806Gly	p.D806G	ENST00000380152		806	gAt/gGt	11/27	1	2	FACETS	0.148	0.133	0.164	0.148	0.133	0.164	SUBCLONAL	1	TRUE	1	0.940223599930812	2		872	1772	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647581	23647581	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	441	443	0	ENST00000261584.4:c.286A>T	p.Thr96Ser	p.T96S	ENST00000261584	NM_024675.3	96	Aca/Tca	4/13	1	2	FACETS	0.958	0.918	0.999	0.958	0.918	0.999	CLONAL	1	TRUE	1	0.940223599930812	2		443	979	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56852643	56852643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs966758586	NA	P-0012977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	649	600	3	ENST00000308159.5:c.557C>T	p.Ala186Val	p.A186V	ENST00000308159	NM_014669.4	186	gCg/gTg	6/22	1	2	FACETS	0.984	0.95	1	0.984	0.95	1	CLONAL	1	TRUE	1	0.940223599930812	2		603	1403	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118954	3118954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	567	614	0	ENST00000078429.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000078429	NM_002067.2	213	cGg/cAg	5/7	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.940223599930812	2		614	1195	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314614	30314614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	528	632	0	ENST00000262643.3:c.1163C>T	p.Pro388Leu	p.P388L	ENST00000262643	NM_001238.2	388	cCt/cTt	12/12	1	2	FACETS	0.954	0.918	0.991	0.954	0.918	0.991	CLONAL	1	TRUE	1	0.940223599930812	2		632	1177	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29115381	29115381	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs781021132	NA	P-0012977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	466	564	0	ENST00000328354.6:c.683+2T>C		p.X228_splice	ENST00000328354	NM_007194.3	228			1	2	FACETS	0.961	0.921	1	0.961	0.921	1	CLONAL	1	TRUE	1	0.940223599930812	2		564	1032	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053531	37053531	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	534	589	0	ENST00000231790.2:c.618del	p.Leu207TyrfsTer22	p.L207Yfs*22	ENST00000231790	NM_000249.3	206	acA/ac	8/19	0.940223599930812	1	FACETS	0.992	0.973	1	0.992	0.973	1	CLONAL	1	TRUE	0	0.940223599930812	1		589	607	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675274	241675276	+	inframe_deletion	In_Frame_Del	DEL	TTA	TTA	-	novel	NA	P-0012977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	410	443	0	ENST00000366560.3:c.546_548del	p.Asn182del	p.N182del	ENST00000366560	NM_000143.3	182	aaTAAa/aaa	4/10	1	2	FACETS	0.884	0.844	0.924	0.884	0.844	0.924	CLONAL	1	TRUE	1	0.940223599930812	2		443	987	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760613	133760613	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	639	686	0	ENST00000318560.5:c.2940del	p.Val981PhefsTer88	p.V981Ffs*88	ENST00000318560	NM_005157.4	979	gCc/gc	11/11	1	2	FACETS	0.949	0.916	0.983	0.949	0.916	0.983	CLONAL	1	TRUE	1	0.940223599930812	2		686	1432	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349914	89349916	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs761762028	NA	P-0012977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1244	1036	1152	0	ENST00000301030.4:c.3034_3036del	p.Lys1012del	p.K1012del	ENST00000301030	NM_001256183.1	1012	AAG/-	9/13	1	2	FACETS	0.967	0.94	0.993	0.967	0.94	0.993	CLONAL	1	TRUE	1	0.940223599930812	2		1152	2280	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163377	47163377	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	327	365	1	ENST00000409792.3:c.2749del	p.Ser917ValfsTer5	p.S917Vfs*5	ENST00000409792	NM_014159.6	917	Agt/gt	3/21	0.940223599930812	1	FACETS	0.917	0.89	0.942	0.917	0.89	0.942	CLONAL	1	TRUE	0	0.940223599930812	1		366	402	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943662	9943662	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560839364	NA	P-0012984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	67	502	0	ENST00000330684.3:c.1279G>A	p.Glu427Lys	p.E427K	ENST00000330684	NM_001134407.1	427	Gag/Aag	5/13	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.335220206439127	2		502	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578264	7578265	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0012984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	93	623	0	ENST00000269305.4:c.584_585delinsAA	p.Ile195Lys	p.I195K	ENST00000269305	NM_001126112.2	195	aTC/aAA	6/11	0.335220206439127	2	FACETS	1	0.975	1	0.657	0.588	0.731	CLONAL	1	TRUE	0	0.335220206439127	2		623	422	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275634	41275634	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	93	501	0	ENST00000349496.5:c.1529C>A	p.Thr510Asn	p.T510N	ENST00000349496	NM_001904.3	510	aCt/aAt	10/15	0.275956671782986	2	FACETS	0.806	0.724	0.893	0.806	0.724	0.893	CLONAL	2	TRUE	0	0.335220206439127	2		501	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579365	+	frameshift_variant	Frame_Shift_Del	DEL	CGGAAACC	CGGAAACC	T	novel	NA	P-0012984-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	201	547	0	ENST00000269305.4:c.322_329delinsA	p.Gly108IlefsTer13	p.G108Ifs*13	ENST00000269305	NM_001126112.2	108	GGTTTCCGt/At	4/11	0.335220206439127	2	FACETS	1	0.987	1	1	0.994	1	CLONAL	3	TRUE	0	0.335220206439127	2		547	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0012985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	415	707	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.658604735912926	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.712837259627638	1		707	724	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26021090	26021090	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs199573090	NA	P-0012985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3354	525	1375	1	ENST00000357647.3:c.373A>T	p.Ile125Phe	p.I125F	ENST00000357647	NM_003529.2	125	Atc/Ttc	1/1	0.56802434695524	4	FACETS	0.65	0.619	0.682	0.217	0.206	0.228	SUBCLONAL	1	TRUE	1	0.712837259627638	4		1376	3879	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865125	57865125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1215558059	NA	P-0012985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	357	1217	8	ENST00000228682.2:c.2602C>T	p.Pro868Ser	p.P868S	ENST00000228682	NM_005269.2	868	Cca/Tca	12/12	0.690178875389222	1	FACETS	0.439	0.415	0.464	0.439	0.415	0.464	SUBCLONAL	1	TRUE	0	0.712837259627638	1		1225	1468	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589656	67589679	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATCCCAGGTGAGTTTTCTATGAAA	ATCCCAGGTGAGTTTTCTATGAAA	-	novel	NA	P-0012985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	62	234	0	ENST00000274335.5:c.1422_1425+20del		p.X474_splice	ENST00000274335		474		10/15	0.237555019142037	2	FACETS	0.621	0.541	0.706	0.311	0.27	0.353	INDETERMINATE	1	TRUE	0	0.712837259627638	2		234	280	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0012992-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	117	453	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.825	0.743	0.912	0.825	0.743	0.912	CLONAL	1	TRUE	1	0.3	2		453	945	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0012993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	122	484	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.35	2		484	616	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481417	140481417	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913348	NA	P-0012993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	108	759	0	ENST00000288602.6:c.1391G>T	p.Gly464Val	p.G464V	ENST00000288602	NM_004333.4	464	gGa/gTa	11/18	1	2	FACETS	0.588	0.527	0.654	0.588	0.527	0.654	SUBCLONAL	1	TRUE	1	0.35	2		759	1049	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106364	27106364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	155	588	0	ENST00000324856.7:c.5975C>T	p.Ser1992Leu	p.S1992L	ENST00000324856	NM_006015.4	1992	tCa/tTa	20/20	0.133461714464828	3	FACETS	1	0.973	1	0.574	0.525	0.625	INDETERMINATE	1	TRUE	1	0.35	3		588	907	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505128	149505128	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1483057981	NA	P-0012993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1602	191	855	0	ENST00000261799.4:c.1687G>A	p.Glu563Lys	p.E563K	ENST00000261799	NM_002609.3	563	Gag/Aag	12/23	0.133461714464828	3	FACETS	0.715	0.659	0.775	0.358	0.329	0.388	INDETERMINATE	1	TRUE	1	0.35	3		855	1793	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843278	128843278	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41303402	NA	P-0012993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	179	908	3	ENST00000249373.3:c.385G>A	p.Val129Ile	p.V129I	ENST00000249373	NM_005631.4	129	Gta/Ata	2/12	1	2	FACETS	0.901	0.83	0.976	0.901	0.83	0.976	CLONAL	1	TRUE	1	0.35	2		911	1135	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787805	135787811	+	frameshift_variant	Frame_Shift_Del	DEL	ACACTCG	ACACTCG	-	novel	NA	P-0012993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	160	663	0	ENST00000298552.3:c.771_777del	p.Ile257MetfsTer59	p.I257Mfs*59	ENST00000298552	NM_001162426.1	257	atCGAGTGT/at	9/23	0.223665836611425	2	FACETS	1	0.976	1	0.584	0.536	0.634	CLONAL	1	TRUE	0	0.35	2		663	783	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661497	227661497	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	10	584	0	ENST00000305123.5:c.1958A>G	p.His653Arg	p.H653R	ENST00000305123	NM_005544.2	653	cAt/cGt	1/2	1	2	FACETS	0.347	0.235	0.487	0.347	0.235	0.487	SUBCLONAL	1	TRUE	1	0.341224700059688	2		584	169	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0013031-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	187	736	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	0.908	0.84	0.98	0.908	0.84	0.98	CLONAL	1	TRUE	1	0.46	2		736	895	SUCCESS
APC	324	MSKCC	GRCh37	5	112179000	112179000	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1561617778	NA	P-0013031-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	120	493	0	ENST00000257430.4:c.7709C>G	p.Ser2570Ter	p.S2570*	ENST00000257430	NM_000038.5	2570	tCa/tGa	16/16	0.3	1	FACETS	0.919	0.836	1	0.919	0.836	1	CLONAL	1	TRUE	0	0.46	1		493	437	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876968	151876968	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013031-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	163	695	0	ENST00000262189.6:c.7393C>T	p.Pro2465Ser	p.P2465S	ENST00000262189	NM_170606.2	2465	Ccc/Tcc	37/59	1	2	FACETS	0.92	0.846	0.998	0.92	0.846	0.998	CLONAL	1	TRUE	1	0.46	2		695	770	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877184	151877184	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013031-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	147	503	0	ENST00000262189.6:c.7177C>T	p.Gln2393Ter	p.Q2393*	ENST00000262189	NM_170606.2	2393	Cag/Tag	37/59	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.46	2		503	586	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877867	151877867	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013031-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	140	625	0	ENST00000262189.6:c.7078C>G	p.Pro2360Ala	p.P2360A	ENST00000262189	NM_170606.2	2360	Cca/Gca	36/59	1	2	FACETS	0.951	0.869	1	0.951	0.869	1	CLONAL	1	TRUE	1	0.46	2		625	640	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877885	151877885	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013031-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	128	558	0	ENST00000262189.6:c.7060C>G	p.Gln2354Glu	p.Q2354E	ENST00000262189	NM_170606.2	2354	Caa/Gaa	36/59	1	2	FACETS	0.932	0.848	1	0.932	0.848	1	CLONAL	1	TRUE	1	0.46	2		558	597	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877926	151877926	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1394961873	NA	P-0013031-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	133	457	0	ENST00000262189.6:c.7019C>G	p.Ser2340Cys	p.S2340C	ENST00000262189	NM_170606.2	2340	tCt/tGt	36/59	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.46	2		457	533	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878028	151878028	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs773368825	NA	P-0013031-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	127	507	0	ENST00000262189.6:c.6917C>G	p.Pro2306Arg	p.P2306R	ENST00000262189	NM_170606.2	2306	cCa/cGa	36/59	1	2	FACETS	0.955	0.869	1	0.955	0.869	1	CLONAL	1	TRUE	1	0.46	2		507	578	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878212	151878212	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013031-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	148	632	0	ENST00000262189.6:c.6733C>G	p.Pro2245Ala	p.P2245A	ENST00000262189	NM_170606.2	2245	Cca/Gca	36/59	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.46	2		632	636	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888065	81888065	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013031-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	239	933	2	ENST00000359376.3:c.213del	p.Glu72LysfsTer55	p.E72Kfs*55	ENST00000359376	NM_002661.3	70	atA/at	3/33	1	2	FACETS	0.968	0.903	1	0.968	0.903	1	CLONAL	1	TRUE	1	0.46	2		935	1074	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0013040-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	143	497	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.191161505548312	3	FACETS	0.996	0.908	1	0.996	0.908	1	CLONAL	2	TRUE	1	0.191161505548312	3		497	823	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578493	7578493	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1206165503	NA	P-0013040-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	208	512	0	ENST00000269305.4:c.437G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tGg/tAg	5/11	0.191161505548312	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.191161505548312	2		512	921	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503786	186503786	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs746817318	NA	P-0013040-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1695	418	1168	0	ENST00000323963.5:c.463A>G	p.Ile155Val	p.I155V	ENST00000323963		155	Att/Gtt	5/11	0.191161505548312	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.191161505548312	3		1168	2113	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967966	93967966	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013040-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1473	125	937	1	ENST00000369303.4:c.1961T>A	p.Leu654His	p.L654H	ENST00000369303	NM_004440.3	654	cTt/cAt	11/17	0.172187782336988	2	FACETS	0.818	0.738	0.904	0.409	0.369	0.452	CLONAL	1	TRUE	0	0.191161505548312	2		938	1598	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70334008	70334008	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013040-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	34	219	0	ENST00000373644.4:c.1913A>T	p.Glu638Val	p.E638V	ENST00000373644	NM_030625.2	638	gAg/gTg	2/12	0.191161505548312	3	FACETS	1	0.841	1	0.516	0.421	0.621	CLONAL	1	TRUE	1	0.191161505548312	3		219	378	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536876	120536876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013040-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1930	163	1119	1	ENST00000229340.5:c.310C>T	p.His104Tyr	p.H104Y	ENST00000229340	NM_006861.6	104	Cac/Tac	4/6	0.191161505548312	5	FACETS	1	0.946	1	0.262	0.239	0.286	CLONAL	1	TRUE	1	0.191161505548312	5		1120	2093	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985535	60985535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373065228	NA	P-0013040-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	207	625	0	ENST00000333681.4:c.365C>T	p.Thr122Met	p.T122M	ENST00000333681		122	aCg/aTg	2/3	0.191161505548312	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.191161505548312	2		625	1000	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543565	9543565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013040-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	99	580	0	ENST00000353224.5:c.1589C>T	p.Ala530Val	p.A530V	ENST00000353224	NM_177990.2	530	gCc/gTc	6/10	0.191161505548312	3	FACETS	1	0.935	1	0.535	0.476	0.598	CLONAL	1	TRUE	1	0.191161505548312	3		580	1060	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0013064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	306	332	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.909	0.861	0.958	0.909	0.861	0.958	CLONAL	1	TRUE	1	0.847750916826547	2		332	794	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922364	178922364	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	391	484	0	ENST00000263967.3:c.1133G>T	p.Cys378Phe	p.C378F	ENST00000263967	NM_006218.2	378	tGt/tTt	6/21	1	2	FACETS	0.776	0.738	0.814	0.776	0.738	0.814	SUBCLONAL	1	TRUE	1	0.847750916826547	2		484	1189	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572092	64572092	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1565637104	NA	P-0013064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	666	736	0	ENST00000312049.6:c.1547G>A	p.Arg516Gln	p.R516Q	ENST00000312049	NM_130799.2	516	cGg/cAg	10/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.847750916826547	2		736	1572	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726703	88726703	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	480	601	0	ENST00000360948.2:c.341del	p.Gly114AspfsTer19	p.G114Dfs*19	ENST00000360948	NM_001012338.2	114	gGa/ga	4/19	1	2	FACETS	0.988	0.947	1	0.988	0.947	1	CLONAL	1	TRUE	1	0.847750916826547	2		601	1146	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	82	389	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.60802938478869	2		389	254	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397142	397142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs999945656	NA	P-0013074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	182	411	1	ENST00000380956.4:c.527G>A	p.Arg176Gln	p.R176Q	ENST00000380956	NM_001195286.1	176	cGa/cAa	5/9	NA	2	FACETS	1	0.972	1			1	INDETERMINATE	1	TRUE	NA	0.60802938478869	2		412	550	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55238870	55238870	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	6752	305	0	ENST00000275493.2:c.1883G>A	p.Cys628Tyr	p.C628Y	ENST00000275493	NM_005228.3	628	tGc/tAc	16/28	0.60802938478869	37	FACETS	1	0.994	1			1	CLONAL	33	TRUE	NA	0.60802938478869	37		305	7834	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273014	55273014	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	8063	347	1	ENST00000275493.2:c.3337C>T	p.Gln1113Ter	p.Q1113*	ENST00000275493	NM_005228.3	1113	Cag/Tag	28/28	0.60802938478869	37	FACETS	1	0.998	1			1	CLONAL	33	TRUE	NA	0.60802938478869	37		348	9262	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142949	47142949	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	133	464	0	ENST00000409792.3:c.5014G>A	p.Gly1672Arg	p.G1672R	ENST00000409792	NM_014159.6	1672	Gga/Aga	8/21	0.760654381354113	1	FACETS	0.914	0.852	0.976	0.914	0.852	0.976	CLONAL	1	TRUE	0	0.760654381354113	1		464	237	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958174	2958174	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1405366406	NA	P-0013090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	291	456	2	ENST00000396946.4:c.2558G>A	p.Gly853Asp	p.G853D	ENST00000396946	NM_032415.4	853	gGc/gAc	19/25	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.760654381354113	2		458	731	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651241	45651241	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	360	646	0	ENST00000407780.3:c.784G>T	p.Val262Phe	p.V262F	ENST00000407780	NM_001283052.1	262	Gtc/Ttc	5/7	1	2	FACETS	0.975	0.927	1	0.975	0.927	1	CLONAL	1	TRUE	1	0.760654381354113	2		646	971	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188263	10188263	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs397516442	NA	P-0013090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	382	728	0	ENST00000256474.2:c.408del	p.Phe136LeufsTer23	p.F136Lfs*23	ENST00000256474	NM_000551.3	136	Ttt/tt	2/3	0.760654381354113	1	FACETS	0.94	0.903	0.977	0.94	0.903	0.977	CLONAL	1	TRUE	0	0.760654381354113	1		728	662	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430957	181430978	+	frameshift_variant	Frame_Shift_Del	DEL	TCCGGGACATGATCAGCATGTA	TCCGGGACATGATCAGCATGTA	-	novel	NA	P-0013090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	232	617	0	ENST00000325404.1:c.811_832del	p.Arg271SerfsTer93	p.R271Sfs*93	ENST00000325404	NM_003106.3	270	cTCCGGGACATGATCAGCATGTAt/ct	1/1	1	2	FACETS	0.825	0.773	0.879	0.825	0.773	0.879	CLONAL	1	TRUE	1	0.760654381354113	2		617	739	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598228	52598228	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	188	331	0	ENST00000394830.3:c.3638del	p.Phe1213SerfsTer31	p.F1213Sfs*31	ENST00000394830	NM_018313.4	1213	tTc/tc	24/30	0.760654381354113	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.760654381354113	1		331	287	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0013112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	21	579	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.781	0.604	0.987	0.781	0.604	0.987	CLONAL	1	TRUE	1	0.24	2		579	224	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	50	650	1	ENST00000206249.3:c.1607T>A	p.Leu536His	p.L536H	ENST00000206249	NM_000125.3	536	cTc/cAc	8/8	0.425774347710986	4	FACETS	0.807	0.684	0.943	0.404	0.342	0.472	CLONAL	1	TRUE	2	0.24	4		651	640	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913294	NA	P-0013112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	63	591	0	ENST00000371953.3:c.518G>C	p.Arg173Pro	p.R173P	ENST00000371953	NM_000314.4	173	cGc/cCc	6/9	0.103337783495734	3	FACETS	1	0.904	1	0.695	0.607	0.789	INDETERMINATE	2	TRUE	0	0.24	3		591	282	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0013112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	30	351	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	0.217541869388434	3	FACETS	0.753	0.607	0.918	0.376	0.303	0.459	CLONAL	1	TRUE	1	0.24	3		351	372	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023093	27023093	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	73	196	1	ENST00000324856.7:c.199C>T	p.Gln67Ter	p.Q67*	ENST00000324856	NM_006015.4	67	Cag/Tag	1/20	0.217541869388434	3	FACETS	1	0.913	1	0.527	0.461	0.599	CLONAL	1	TRUE	1	0.24	3		197	646	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831378	72831378	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	26	209	0	ENST00000268489.5:c.5203del	p.Gln1735AsnfsTer32	p.Q1735Nfs*32	ENST00000268489	NM_006885.3	1735	Caa/aa	9/10	0.366474760709731	4	FACETS	0.878	0.711	1	1	0.922	1	CLONAL	3	TRUE	2	0.24	4		209	102	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	71	389	0				ENST00000310581	NM_198253.2	-/1132			0.157019812439651	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	2	TRUE	0	0.157019812439651	2		389	448	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0013147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	312	424	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.157019812439651	6	FACETS	0.967	0.913	1			1	CLONAL	5	TRUE	NA	0.157019812439651	6		424	1080	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0013147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	127	876	0	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	0.157019812439651	2		876	1259	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974783	21974783	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658556	NA	P-0013147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	38	314	0	ENST00000304494.5:c.44G>A	p.Trp15Ter	p.W15*	ENST00000304494	NM_000077.4	15	tGg/tAg	1/3	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.157019812439651	2		314	427	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041437	47041437	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	68	440	0	ENST00000377604.3:c.1783del	p.Gln595SerfsTer109	p.Q595Sfs*109	ENST00000377604	NM_001204468.1	594	tCc/tc	16/24	1	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.157019812439651	1		440	642	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261317	16261317	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	105	424	0	ENST00000375759.3:c.8582T>G	p.Val2861Gly	p.V2861G	ENST00000375759	NM_015001.2	2861	gTc/gGc	11/15	NA	2	FACETS	0.849	0.764	0.939			1	INDETERMINATE	1	TRUE	NA	0.490728236767282	2		424	504	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158523	26158759	+	inframe_deletion	In_Frame_Del	DEL	GTACAAGGTGCTGAAGCAGGTCCATCCCGACACCGGCATCTCTTCCAAGGCAATGGGGATCATGAATTCCTTCGTCAACGACATCTTCGAGCGCATCGCAGGCGAGGCTTCCCGCCTGGCGCATTACAACAAGCGCTCGACCATCACCTCCAGGGAGATCCAGACGGCCGTGCGCCTGCTGCTTCCGGGGGAGCTGGCCAAGCACGCCGTGTCGGAGGGCACCAAGGCCGTCACCAA	GTACAAGGTGCTGAAGCAGGTCCATCCCGACACCGGCATCTCTTCCAAGGCAATGGGGATCATGAATTCCTTCGTCAACGACATCTTCGAGCGCATCGCAGGCGAGGCTTCCCGCCTGGCGCATTACAACAAGCGCTCGACCATCACCTCCAGGGAGATCCAGACGGCCGTGCGCCTGCTGCTTCCGGGGGAGCTGGCCAAGCACGCCGTGTCGGAGGGCACCAAGGCCGTCACCAA	-	novel	NA	P-0013154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	46	373	0	ENST00000289316.2:c.131_367del	p.Lys44_Tyr122del	p.K44_Y122del	ENST00000289316	NM_138720.2	42	gtGTACAAGGTGCTGAAGCAGGTCCATCCCGACACCGGCATCTCTTCCAAGGCAATGGGGATCATGAATTCCTTCGTCAACGACATCTTCGAGCGCATCGCAGGCGAGGCTTCCCGCCTGGCGCATTACAACAAGCGCTCGACCATCACCTCCAGGGAGATCCAGACGGCCGTGCGCCTGCTGCTTCCGGGGGAGCTGGCCAAGCACGCCGTGTCGGAGGGCACCAAGGCCGTCACCAAg/gtg	1/2	0.19832405963755	1	FACETS	0.315	0.265	0.37	0.315	0.265	0.37	INDETERMINATE	1	TRUE	0	0.490728236767282	1		373	449	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914311	32914682	+	inframe_deletion	In_Frame_Del	DEL	AGAAAGTTTCTAAAATATCACCTTGTGATGTTAGTTTGGAAACTTCAGATATATGTAAATGTAGTATAGGGAAGCTTCATAAGTCAGTCTCATCTGCAAATACTTGTGGGATTTTTAGCACAGCAAGTGGAAAATCTGTCCAGGTATCAGATGCTTCATTACAAAACGCAAGACAAGTGTTTTCTGAAATAGAAGATAGTACCAAGCAAGTCTTTTCCAAAGTATTGTTTAAAAGTAACGAACATTCAGACCAGCTCACAAGAGAAGAAAATACTGCTATACGTACTCCAGAACATTTAATATCCCAAAAAGGCTTTTCATATAATGTGGTAAATTCATCTGCTTTCTCTGGATTTAGTACAGCAAGTGGAA	AGAAAGTTTCTAAAATATCACCTTGTGATGTTAGTTTGGAAACTTCAGATATATGTAAATGTAGTATAGGGAAGCTTCATAAGTCAGTCTCATCTGCAAATACTTGTGGGATTTTTAGCACAGCAAGTGGAAAATCTGTCCAGGTATCAGATGCTTCATTACAAAACGCAAGACAAGTGTTTTCTGAAATAGAAGATAGTACCAAGCAAGTCTTTTCCAAAGTATTGTTTAAAAGTAACGAACATTCAGACCAGCTCACAAGAGAAGAAAATACTGCTATACGTACTCCAGAACATTTAATATCCCAAAAAGGCTTTTCATATAATGTGGTAAATTCATCTGCTTTCTCTGGATTTAGTACAGCAAGTGGAA	-	novel	NA	P-0013154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	100	924	0	ENST00000380152.3:c.5821_6192del	p.Lys1941_Lys2064del	p.K1941_K2064del	ENST00000380152		1940	gAGAAAGTTTCTAAAATATCACCTTGTGATGTTAGTTTGGAAACTTCAGATATATGTAAATGTAGTATAGGGAAGCTTCATAAGTCAGTCTCATCTGCAAATACTTGTGGGATTTTTAGCACAGCAAGTGGAAAATCTGTCCAGGTATCAGATGCTTCATTACAAAACGCAAGACAAGTGTTTTCTGAAATAGAAGATAGTACCAAGCAAGTCTTTTCCAAAGTATTGTTTAAAAGTAACGAACATTCAGACCAGCTCACAAGAGAAGAAAATACTGCTATACGTACTCCAGAACATTTAATATCCCAAAAAGGCTTTTCATATAATGTGGTAAATTCATCTGCTTTCTCTGGATTTAGTACAGCAAGTGGAAag/gag	11/27	0.35908453180474	0	FACETS	0.357	0.319	0.396			1	SUBCLONAL	1	TRUE	0	0.490728236767282	0		924	582	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883542	37884140	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCCAGAGTGGCGGTGGGGACCTGACACTAGGGCTGGAGCCCTCTGAAGAGGAGGCCCCCAGGTCTCCACTGGCACCCTCCGAAGGGGCTGGCTCCGATGTATTTGATGGTGACCTGGGAATGGGGGCAGCCAAGGGGCTGCAAAGCCTCCCCACACATGACCCCAGCCCTCTACAGCGGTACAGTGAGGACCCCACAGTACCCCTGCCCTCTGAGACTGATGGCTACGTTGCCCCCCTGACCTGCAGCCCCCAGCCTGGTATGGAGTCCAGTCTAAGCAGAGAGACTGATGGGCAGGGGAGGTGGGACCTTCAGCCCAGGGTCCACTGTGGGGGCAGAGGGAGTGGCAGAGACACCGGGGTTCCTTCCCCTAATGGGTCACCTTCTCTTGACCTTTCAGAATATGTGAACCAGCCAGATGTTCGGCCCCAGCCCCCTTCGCCCCGAGAGGGCCCTCTGCCTGCTGCCCGACCTGCTGGTGCCACTCTGGAAAGGCCCAAGACTCTCTCCCCAGGGAAGAATGGGGTCGTCAAAGACGTTTTTGCCTTTGGGGGTGCCGTGGAGAACCCCGAGTACTTGACACCCCAGGGAGGAGCTGC	CCCCAGAGTGGCGGTGGGGACCTGACACTAGGGCTGGAGCCCTCTGAAGAGGAGGCCCCCAGGTCTCCACTGGCACCCTCCGAAGGGGCTGGCTCCGATGTATTTGATGGTGACCTGGGAATGGGGGCAGCCAAGGGGCTGCAAAGCCTCCCCACACATGACCCCAGCCCTCTACAGCGGTACAGTGAGGACCCCACAGTACCCCTGCCCTCTGAGACTGATGGCTACGTTGCCCCCCTGACCTGCAGCCCCCAGCCTGGTATGGAGTCCAGTCTAAGCAGAGAGACTGATGGGCAGGGGAGGTGGGACCTTCAGCCCAGGGTCCACTGTGGGGGCAGAGGGAGTGGCAGAGACACCGGGGTTCCTTCCCCTAATGGGTCACCTTCTCTTGACCTTTCAGAATATGTGAACCAGCCAGATGTTCGGCCCCAGCCCCCTTCGCCCCGAGAGGGCCCTCTGCCTGCTGCCCGACCTGCTGGTGCCACTCTGGAAAGGCCCAAGACTCTCTCCCCAGGGAAGAATGGGGTCGTCAAAGACGTTTTTGCCTTTGGGGGTGCCGTGGAGAACCCCGAGTACTTGACACCCCAGGGAGGAGCTGC	-	novel	NA	P-0013154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	87	639	0	ENST00000269571.5:c.3160-3_3614del		p.X1054_splice	ENST00000269571		1054		26-27/27	0.341586064381941	4	FACETS	0.559	0.493	0.629			1	SUBCLONAL	1	TRUE	NA	0.490728236767282	4		639	946	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015133	37015133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223489007	NA	P-0013155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	229	803	0	ENST00000358127.4:c.271G>A	p.Ala91Thr	p.A91T	ENST00000358127	NM_001280556.1	91	Gcc/Acc	3/10	0.193566959179422	4	FACETS	1	0.987	1	0.825	0.768	0.884	CLONAL	2	TRUE	1	0.193566959179422	4		803	1141	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188302	10188302	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587780077	NA	P-0013163-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	218	786	0	ENST00000256474.2:c.445G>C	p.Ala149Pro	p.A149P	ENST00000256474	NM_000551.3	149	Gcc/Ccc	2/3	0.714987678340312	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.714987678340312	1		786	379	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622161	162622161	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0013163-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	220	477	0	ENST00000366898.1:c.534+2T>A		p.X178_splice	ENST00000366898	NM_004562.2	178			1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.714987678340312	2		477	600	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441333	52441333	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0013170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	460	665	1	ENST00000460680.1:c.438-1G>T		p.X146_splice	ENST00000460680	NM_004656.3	146			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		666	932	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0013189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	207	626	3	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.176011282136797	2	FACETS	0.799	0.74	0.86	0.799	0.74	0.86	SUBCLONAL	2	TRUE	0	0.211960621396869	2		629	1223	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0013189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2881	194	496	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	0.211960621396869	24	FACETS	0.992	0.912	1			1	CLONAL	2	TRUE	NA	0.211960621396869	24		496	3075	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0013200-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	222	604	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.397290645812298	2	FACETS	0.938	0.88	0.998	0.938	0.88	0.998	CLONAL	2	TRUE	0	0.405103743512424	2		604	584	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168516	56168516	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013200-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	96	259	0	ENST00000399503.3:c.1472G>A	p.Cys491Tyr	p.C491Y	ENST00000399503	NM_005921.1	491	tGt/tAt	8/20	0.123164921281968	5	FACETS	1	0.931	1			1	INDETERMINATE	2	TRUE	NA	0.405103743512424	5		259	364	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	126	540	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.218580448733513	2		540	1150	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0013226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	92	270	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.218580448733513	2		272	633	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743883	41743883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374699228	NA	P-0013226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	154	995	0	ENST00000301178.4:c.818C>T	p.Ala273Val	p.A273V	ENST00000301178	NM_021913.4	273	gCg/gTg	7/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.218580448733513	2		995	1301	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858958	243858958	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1248	125	689	1	ENST00000263826.5:c.107T>C	p.Ile36Thr	p.I36T	ENST00000263826	NM_005465.4	36	aTa/aCa	2/13	1	2	FACETS	0.833	0.751	0.92	0.833	0.751	0.92	CLONAL	1	TRUE	1	0.218580448733513	2		690	1373	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48586238	48586238	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	115	508	0	ENST00000342988.3:c.908del	p.Pro303LeufsTer33	p.P303Lfs*33	ENST00000342988	NM_005359.5	303	Cct/ct	8/12	0.218580448733513	1	FACETS	0.956	0.86	1	0.956	0.86	1	CLONAL	1	TRUE	0	0.218580448733513	1		508	980	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245802	46245811	+	frameshift_variant	Frame_Shift_Del	DEL	ACAGTGACTC	ACAGTGACTC	-	novel	NA	P-0013226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	124	670	0	ENST00000334344.6:c.3897_3906del	p.Tyr1299Ter	p.Y1299*	ENST00000334344	NM_152641.2	1299	tACAGTGACTCa/ta	15/21	1	2	FACETS	0.902	0.814	0.996	0.902	0.814	0.996	CLONAL	1	TRUE	1	0.218580448733513	2		670	1258	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407575	407575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748516736	NA	P-0013228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	161	663	1	ENST00000380956.4:c.1333C>T	p.Arg445Cys	p.R445C	ENST00000380956	NM_001195286.1	445	Cgc/Tgc	9/9	0.858270825766217	3	FACETS	0.956	0.882	1	0.478	0.441	0.516	CLONAL	1	TRUE	1	0.858270825766217	3		664	561	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954378	48954378	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0013228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2	135	386	0	ENST00000267163.4:c.1498+1G>C		p.X500_splice	ENST00000267163	NM_000321.2	500			0.858270825766217	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.858270825766217	2		386	137	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008431	70008431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	45	294	1	ENST00000394351.3:c.718C>T	p.Arg240Cys	p.R240C	ENST00000394351	NM_000248.3	240	Cgc/Tgc	8/9	0.858270825766217	1	FACETS	0.521	0.45	0.593	0.521	0.45	0.593	SUBCLONAL	1	TRUE	0	0.858270825766217	1		295	115	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553482	106553482	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	128	331	0	ENST00000369096.4:c.1447C>A	p.His483Asn	p.H483N	ENST00000369096	NM_001198.3	483	Cat/Aat	5/7	0.858270825766217	3	FACETS	1	0.941	1	0.519	0.474	0.565	CLONAL	1	TRUE	1	0.858270825766217	3		331	411	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65568271	65568271	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	211	373	0	ENST00000358664.4:c.56A>C	p.Gln19Pro	p.Q19P	ENST00000358664	NM_002382.4	19	cAa/cCa	2/5	0.858270825766217	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.858270825766217	3		373	346	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243963	5243963	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	370	602	0	ENST00000357368.4:c.1519G>T	p.Val507Phe	p.V507F	ENST00000357368	NM_002850.3	507	Gtc/Ttc	11/38	0.629446286114432	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.858270825766217	4		602	779	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222358	53222358	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	432	1015	1	ENST00000375401.3:c.4474G>T	p.Val1492Phe	p.V1492F	ENST00000375401	NM_004187.3	1492	Gtc/Ttc	26/26	0.600069565224838	3	FACETS	1	0.996	1	0.722	0.69	0.753	CLONAL	1	TRUE	1	0.858270825766217	3		1016	997	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641130	23641130	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	63	720	0	ENST00000261584.4:c.2345del	p.Pro782GlnfsTer69	p.P782Qfs*69	ENST00000261584	NM_024675.3	782	cCa/ca	5/13	0.321426082779155	3	FACETS	0.327	0.283	0.376	0.109	0.094	0.126	INDETERMINATE	1	TRUE	0	0.858270825766217	3		720	641	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574026	7574032	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CCACGGA	CCACGGA	-	novel	NA	P-0013228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	484	763	0	ENST00000269305.4:c.995_1001del	p.Ile332SerfsTer11	p.I332Sfs*11	ENST00000269305	NM_001126112.2	332	aTCCGTGGg/ag	10/11	0.858270825766217	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.858270825766217	2		763	502	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761381	59761381	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	409	688	0	ENST00000259008.2:c.3026del	p.Gly1009AspfsTer50	p.G1009Dfs*50	ENST00000259008	NM_032043.2	1009	gGa/ga	20/20	0.629446286114432	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.858270825766217	4		688	837	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593613	55593613	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913521	NA	P-0013235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	264	650	0	ENST00000288135.5:c.1679T>A	p.Val560Asp	p.V560D	ENST00000288135	NM_000222.2	560	gTt/gAt	11/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.914819432374537	2		650	561	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041671	42041678	+	frameshift_variant	Frame_Shift_Del	DEL	CCTAGCTC	CCTAGCTC	-	novel	NA	P-0013235-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	418	871	1	ENST00000219905.7:c.5867_5874del	p.Pro1956HisfsTer22	p.P1956Hfs*22	ENST00000219905	NM_001164273.1	1956	CCTAGCTCc/c	17/24	0.914819432374537	1	FACETS	0.963	0.938	0.987	0.963	0.938	0.987	CLONAL	1	TRUE	0	0.914819432374537	1		872	515	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0013236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	229	332	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.552557509833109	3	FACETS	0.842	0.79	0.895	0.842	0.79	0.895	CLONAL	2	TRUE	1	0.552557509833109	3		332	628	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654607	67654607	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	408	627	0	ENST00000264010.4:c.1094A>G	p.Lys365Arg	p.K365R	ENST00000264010	NM_006565.3	365	aAa/aGa	6/12	0.434266037602396	2	FACETS	1	0.995	1	0.693	0.661	0.725	CLONAL	1	TRUE	0	0.552557509833109	2		627	1066	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38506105	38506105	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs945569487	NA	P-0013236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	272	608	0	ENST00000254066.5:c.397A>G	p.Asn133Asp	p.N133D	ENST00000254066	NM_000964.3	133	Aac/Gac	4/9	1	2	FACETS	0.844	0.792	0.898	0.844	0.792	0.898	CLONAL	1	TRUE	1	0.552557509833109	2		608	1166	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788651	3788651	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013261-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	196	491	0	ENST00000262367.5:c.4303G>T	p.Asp1435Tyr	p.D1435Y	ENST00000262367	NM_004380.2	1435	Gat/Tat	26/31	0.101823239104305	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		491	576	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439292	52439292	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	165	383	0	ENST00000460680.1:c.950C>G	p.Ala317Gly	p.A317G	ENST00000460680	NM_004656.3	317	gCt/gGt	11/17	0.391449844809115	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	FALSE	0	0.399968239852057	2		383	409	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630229	187630229	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	65	385	0	ENST00000441802.2:c.753T>A	p.Asn251Lys	p.N251K	ENST00000441802	NM_005245.3	251	aaT/aaA	2/27	0.148927822733374	5	FACETS	0.935	0.812	1	0.312	0.27	0.357	INDETERMINATE	1	FALSE	2	0.399968239852057	5		385	556	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738713	145738713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536096413	NA	P-0013269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	112	401	0	ENST00000428558.2:c.2351G>A	p.Arg784Gln	p.R784Q	ENST00000428558	NM_004260.3	784	cGg/cAg	15/22	0.399968239852057	9	FACETS	1	0.975	1	0.183	0.164	0.204	CLONAL	1	FALSE	2	0.399968239852057	9		401	1048	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	532697	532697	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	43	721	0	ENST00000451590.1:c.509A>C	p.Lys170Thr	p.K170T	ENST00000451590	NM_001130442.1	170	aAg/aCg	5/5	NA	2	FACETS	0.286	0.239	0.339			1	INDETERMINATE	1	FALSE	NA	0.399968239852057	2		721	751	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0013270-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1505	1271	484	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.704769883189732	3	FACETS	0.879	0.857	0.9			1	CLONAL	2	TRUE	NA	0.704769883189732	3		484	2776	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186599	108186599	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876658415	NA	P-0013270-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	393	658	0	ENST00000278616.4:c.6056A>G	p.Tyr2019Cys	p.Y2019C	ENST00000278616	NM_000051.3	2019	tAt/tGt	41/63	0.653735742203556	1	FACETS	0.85	0.812	0.887	0.85	0.812	0.887	CLONAL	1	TRUE	0	0.704769883189732	1		658	850	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361199	66361199	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013270-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	218	641	2	ENST00000273854.3:c.973C>T	p.His325Tyr	p.H325Y	ENST00000273854	NM_004439.5	325	Cac/Tac	4/18	0.653735742203556	1	FACETS	0.512	0.478	0.548	0.512	0.478	0.548	SUBCLONAL	1	TRUE	0	0.704769883189732	1		643	782	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013273-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	29	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.16	0.128	0.197	0.16	0.128	0.197	SUBCLONAL	1	TRUE	1	0.44	2		426	823	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0013278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	307	353	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.455600729609728	3	FACETS	0.944	0.908	0.98			1	CLONAL	3	TRUE	NA	0.64	3		353	447	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151270	202151270	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	284	897	0	ENST00000358485.4:c.1570C>T	p.Gln524Ter	p.Q524*	ENST00000358485	NM_001080125.1	524	Cag/Tag	9/9	0.455600729609728	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.64	1		897	534	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245965	46245965	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	275	588	0	ENST00000334344.6:c.4059G>C	p.Leu1353Phe	p.L1353F	ENST00000334344	NM_152641.2	1353	ttG/ttC	15/21	0.284911106338863	4	FACETS	0.968	0.914	1	0.968	0.914	1	INDETERMINATE	2	TRUE	2	0.64	4		588	728	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056259	26056259	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs768431666	NA	P-0013278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	367	645	0	ENST00000343677.2:c.398G>C	p.Gly133Ala	p.G133A	ENST00000343677	NM_005319.3	133	gGg/gCg	1/1	0.455600729609728	6	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.64	6		645	1068	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518126	187518126	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	583	864	1	ENST00000441802.2:c.12568G>T	p.Ala4190Ser	p.A4190S	ENST00000441802	NM_005245.3	4190	Gca/Tca	25/27	0.455600729609728	4	FACETS	0.934	0.903	0.965	0.934	0.903	0.965	CLONAL	3	TRUE	1	0.64	4		865	1066	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309813	104309813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1347417323	NA	P-0013278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	238	607	0	ENST00000369902.3:c.404C>T	p.Thr135Ile	p.T135I	ENST00000369902	NM_016169.3	135	aCa/aTa	3/12	0.67926356077435	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.64	1		607	429	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127167	22127167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	199	742	0	ENST00000215832.6:c.961G>A	p.Asp321Asn	p.D321N	ENST00000215832	NM_002745.4	321	Gac/Aac	7/9	0.228913213718698	4	FACETS	0.774	0.72	0.829	0.774	0.72	0.829	INDETERMINATE	2	TRUE	2	0.64	4		742	659	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772089	135772092	+	missense_variant	Missense_Mutation	ONP	CTTC	CTTC	TTTT	novel	NA	P-0013278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	22	206	0	ENST00000298552.3:c.3025_3028delinsAAAA	p.Glu1009_Glu1010delinsLysLys	p.E1009_E1010delinsKK	ENST00000298552	NM_001162426.1	1009	GAAGag/AAAAag	23/23	0.228913213718698	4	FACETS	0.444	0.345	0.559	0.222	0.172	0.28	INDETERMINATE	1	TRUE	2	0.64	4		206	254	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	63	389	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.93	0.813	1	0.93	0.813	1	CLONAL	1	TRUE	1	0.52300650294936	2		389	259	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0013288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	161	542	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.52300650294936	1	FACETS	0.959	0.887	1	0.959	0.887	1	CLONAL	1	TRUE	0	0.52300650294936	1		542	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574035	7574035	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs867389695	NA	P-0013288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	187	633	0	ENST00000269305.4:c.994-2A>G		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.52300650294936	1	FACETS	0.996	0.928	1	0.996	0.928	1	CLONAL	1	TRUE	0	0.52300650294936	1		633	530	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923342	9923342	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397514557	NA	P-0013288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	210	650	0	ENST00000330684.3:c.1945C>G	p.Leu649Val	p.L649V	ENST00000330684	NM_001134407.1	649	Ctg/Gtg	9/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.52300650294936	2		650	761	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685269	89685269	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs786203847	NA	P-0013288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	78	178	0	ENST00000371953.3:c.165-1G>A		p.X55_splice	ENST00000371953	NM_000314.4	55			0.52300650294936	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.52300650294936	1		178	204	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871262	35871262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	167	420	0	ENST00000303115.3:c.484G>A	p.Val162Ile	p.V162I	ENST00000303115	NM_002185.3	162	Gtt/Att	4/8	1	2	FACETS	0.883	0.814	0.956	0.883	0.814	0.956	CLONAL	1	TRUE	1	0.52300650294936	2		420	723	SUCCESS
EED	8726	MSKCC	GRCh37	11	85979565	85979565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	168	480	0	ENST00000263360.6:c.928G>A	p.Asp310Asn	p.D310N	ENST00000263360	NM_003797.3	310	Gat/Aat	9/12	1	2	FACETS	0.861	0.793	0.932	0.861	0.793	0.932	CLONAL	1	TRUE	1	0.52300650294936	2		480	746	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941629	48941629	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs1131690860	NA	P-0013288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	224	346	1	ENST00000267163.4:c.940-1G>T		p.X314_splice	ENST00000267163	NM_000321.2	314			0.509588877210721	2	FACETS	0.835	0.785	0.885	0.835	0.785	0.885	CLONAL	2	TRUE	0	0.52300650294936	2		347	513	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877338	89877338	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs756995764	NA	P-0013288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	98	338	0	ENST00000389301.3:c.425G>C	p.Arg142Thr	p.R142T	ENST00000389301	NM_000135.2	142	aGa/aCa	4/43	1	2	FACETS	0.949	0.853	1	0.949	0.853	1	CLONAL	1	TRUE	1	0.52300650294936	2		338	395	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526133	66526133	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013288-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	160	413	1	ENST00000358598.2:c.964G>C	p.Asp322His	p.D322H	ENST00000358598	NM_212471.2	322	Gat/Cat	10/11	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.52300650294936	2		414	607	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	143	540	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.166963499554574	4	FACETS	0.824	0.754	0.898	0.824	0.754	0.898	INDETERMINATE	2	TRUE	2	0.350722288483767	4		540	668	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0013300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	97	316	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.245739985477607	5	FACETS	1	0.955	1	0.742	0.667	0.821	CLONAL	2	TRUE	2	0.350722288483767	5		316	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	G	rs11575997	NA	P-0013300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	178	657	0	ENST00000269305.4:c.993+1G>C		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.298782282562195	2	FACETS	0.78	0.721	0.84	0.78	0.721	0.84	SUBCLONAL	2	TRUE	0	0.350722288483767	2		657	651	SUCCESS
APC	324	MSKCC	GRCh37	5	112176962	112176962	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1561601614	NA	P-0013300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	93	563	0	ENST00000257430.4:c.5671G>A	p.Glu1891Lys	p.E1891K	ENST00000257430	NM_000038.5	1891	Gag/Aag	16/16	0.285234715416291	3	FACETS	0.949	0.844	1	0.474	0.422	0.53	CLONAL	1	TRUE	1	0.350722288483767	3		563	657	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266086	41266304	+	splice_donor_variant,coding_sequence_variant,intron_variant	In_Frame_Del	DEL	AGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAA	AGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAA	-	novel	NA	P-0013300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	184	713	0	ENST00000349496.5:c.86_241+63del		p.Q28_D81del	ENST00000349496	NM_001904.3	28		3/15	0.269649376211204	3	FACETS	0.803	0.743	0.865	0.535	0.495	0.577	CLONAL	2	TRUE	0	0.350722288483767	3		713	768	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458003	120458003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	197	407	1	ENST00000256646.2:c.7342G>A	p.Ala2448Thr	p.A2448T	ENST00000256646	NM_024408.3	2448	Gct/Act	34/34	0.499114678291751	1	FACETS	0.974	0.908	1	0.974	0.908	1	CLONAL	1	TRUE	0	0.500985261277108	1		408	605	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044287	128044287	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	210	498	0	ENST00000285398.2:c.1334C>T	p.Thr445Ile	p.T445I	ENST00000285398	NM_000122.1	445	aCc/aTc	8/15	0.324948955310817	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.324948955310817	3		498	629	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	210	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.210207677871537	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.330635925762946	4		426	765	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0013317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	114	645	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.330635925762946	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.330635925762946	1		645	411	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106482	27106482	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0013317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	112	669	0	ENST00000324856.7:c.6093T>G	p.Tyr2031Ter	p.Y2031*	ENST00000324856	NM_006015.4	2031	taT/taG	20/20	0.330635925762946	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.330635925762946	1		669	443	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440713	56440713	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs779337229	NA	P-0013317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	135	795	2	ENST00000407977.2:c.505G>T	p.Ala169Ser	p.A169S	ENST00000407977		169	Gct/Tct	5/10	0.330635925762946	1	FACETS	0.768	0.703	0.834	1	0.988	1	SUBCLONAL	2	TRUE	0	0.330635925762946	1		797	444	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183725	10183725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs5030826	NA	P-0013335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	182	389	0	ENST00000256474.2:c.194C>T	p.Ser65Leu	p.S65L	ENST00000256474	NM_000551.3	65	tCg/tTg	1/3	0.567651515139698	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.567651515139698	1		389	418	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620694	52620694	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	146	238	0	ENST00000394830.3:c.3059del	p.Lys1020SerfsTer114	p.K1020Sfs*114	ENST00000394830	NM_018313.4	1020	aAg/ag	21/30	0.567651515139698	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.567651515139698	1		238	359	SUCCESS
APC	324	MSKCC	GRCh37	5	112177901	112177901	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs752654519	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	95	540	0	ENST00000257430.4:c.6610C>T	p.Arg2204Ter	p.R2204*	ENST00000257430	NM_000038.5	2204	Cga/Tga	16/16	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.21	2		540	805	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106355	+	stop_gained	Nonsense_Mutation	DNP	CG	CG	TA	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	111	514	0	ENST00000324856.7:c.5965_5966delinsTA	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	CGa/TAa	20/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.21	2		514	839	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36824350	36824350	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	113	746	0	ENST00000373129.3:c.186C>A	p.Phe62Leu	p.F62L	ENST00000373129	NM_032017.1	62	ttC/ttA	4/12	1	2	FACETS	0.905	0.812	1	0.905	0.812	1	CLONAL	1	TRUE	1	0.21	2		746	1189	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363641	40363641	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	38	285	0	ENST00000397332.2:c.588G>T	p.Glu196Asp	p.E196D	ENST00000397332	NM_001033082.2	196	gaG/gaT	3/3	1	2	FACETS	0.828	0.685	0.988	0.828	0.685	0.988	CLONAL	1	TRUE	1	0.21	2		285	437	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812557	43812557	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	59	714	0	ENST00000372470.3:c.1260G>T	p.Glu420Asp	p.E420D	ENST00000372470	NM_005373.2	420	gaG/gaT	8/12	1	2	FACETS	0.577	0.495	0.667	0.577	0.495	0.667	SUBCLONAL	1	TRUE	1	0.21	2		714	974	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799124	45799124	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs748170941	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	136	821	0	ENST00000450313.1:c.309G>A	p.Trp103Ter	p.W103*	ENST00000450313	NM_012222.2	103	tgG/tgA	3/16	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.21	2		821	1225	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46736343	46736343	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	82	598	0	ENST00000371975.4:c.1055A>C	p.Glu352Ala	p.E352A	ENST00000371975	NM_003579.3	352	gAa/gCa	10/18	1	2	FACETS	0.779	0.685	0.88	0.779	0.685	0.88	SUBCLONAL	1	TRUE	1	0.21	2		598	1003	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303689	65303689	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	106	654	0	ENST00000342505.4:c.3066C>A	p.Phe1022Leu	p.F1022L	ENST00000342505	NM_002227.2	1022	ttC/ttA	22/25	1	2	FACETS	0.771	0.689	0.859	0.771	0.689	0.859	SUBCLONAL	1	TRUE	1	0.21	2		654	1309	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849818	156849818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761967383	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	57	659	0	ENST00000524377.1:c.2074C>T	p.Arg692Cys	p.R692C	ENST00000524377	NM_002529.3	692	Cgc/Tgc	16/17	1	2	FACETS	0.579	0.495	0.672	0.579	0.495	0.672	SUBCLONAL	1	TRUE	1	0.21	2		659	937	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741934	162741934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	78	658	0	ENST00000367921.3:c.1625C>T	p.Ala542Val	p.A542V	ENST00000367921	NM_006182.2	542	gCc/gTc	13/18	1	2	FACETS	0.73	0.639	0.827	0.73	0.639	0.827	SUBCLONAL	1	TRUE	1	0.21	2		658	1018	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094309	193094309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748952219	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	76	525	0	ENST00000367435.3:c.199G>A	p.Val67Met	p.V67M	ENST00000367435	NM_024529.4	67	Gtg/Atg	2/17	1	2	FACETS	0.723	0.632	0.821	0.723	0.632	0.821	SUBCLONAL	1	TRUE	1	0.21	2		525	1001	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082361	16082361	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	60	583	0	ENST00000281043.3:c.175C>T	p.Pro59Ser	p.P59S	ENST00000281043	NM_005378.4	59	Ccc/Tcc	2/3	1	2	FACETS	0.666	0.572	0.769	0.666	0.572	0.769	SUBCLONAL	1	TRUE	1	0.21	2		583	858	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47607023	47607023	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	72	646	0	ENST00000263735.4:c.773A>T	p.Glu258Val	p.E258V	ENST00000263735	NM_002354.2	258	gAa/gTa	7/9	1	2	FACETS	0.641	0.558	0.731	0.641	0.558	0.731	SUBCLONAL	1	TRUE	1	0.21	2		646	1070	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026558	48026558	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1201556163	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	94	649	0	ENST00000234420.5:c.1436A>C	p.Lys479Thr	p.K479T	ENST00000234420	NM_000179.2	479	aAa/aCa	4/10	1	2	FACETS	0.908	0.806	1	0.908	0.806	1	CLONAL	1	TRUE	1	0.21	2		649	986	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026918	48026918	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	87	656	1	ENST00000234420.5:c.1796G>T	p.Gly599Val	p.G599V	ENST00000234420	NM_000179.2	599	gGa/gTa	4/10	1	2	FACETS	0.804	0.71	0.905	0.804	0.71	0.905	CLONAL	1	TRUE	1	0.21	2		657	1031	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028004	48028004	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587781458	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	57	608	3	ENST00000234420.5:c.2882G>T	p.Arg961Ile	p.R961I	ENST00000234420	NM_000179.2	961	aGa/aTa	4/10	1	2	FACETS	0.623	0.533	0.722	0.623	0.533	0.722	SUBCLONAL	1	TRUE	1	0.21	2		611	871	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028071	48028071	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	62	630	0	ENST00000234420.5:c.2949G>T	p.Glu983Asp	p.E983D	ENST00000234420	NM_000179.2	983	gaG/gaT	4/10	1	2	FACETS	0.609	0.525	0.702	0.609	0.525	0.702	SUBCLONAL	1	TRUE	1	0.21	2		630	969	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	97	728	0	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	1	2	FACETS	0.789	0.701	0.883	0.789	0.701	0.883	SUBCLONAL	1	TRUE	1	0.21	2		728	1171	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872857	136872857	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1430	156	1054	0	ENST00000241393.3:c.641T>C	p.Val214Ala	p.V214A	ENST00000241393	NM_003467.2	214	gTc/gCc	2/2	1	2	FACETS	0.937	0.855	1	0.937	0.855	1	CLONAL	1	TRUE	1	0.21	2		1054	1586	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270171	198270171	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	97	479	0	ENST00000335508.6:c.1265T>C	p.Val422Ala	p.V422A	ENST00000335508	NM_012433.2	422	gTt/gCt	10/25	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.21	2		479	711	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593510	215593510	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876659765	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	71	454	0	ENST00000260947.4:c.2224T>A	p.Leu742Met	p.L742M	ENST00000260947	NM_000465.2	742	Ttg/Atg	11/11	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.21	2		454	650	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440237	220440237	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1308	185	998	0	ENST00000243786.2:c.1090G>C	p.Ala364Pro	p.A364P	ENST00000243786	NM_002191.3	364	Gct/Cct	2/2	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.21	2		998	1493	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147533	47147533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	78	570	0	ENST00000409792.3:c.4793G>A	p.Arg1598Gln	p.R1598Q	ENST00000409792	NM_014159.6	1598	cGa/cAa	6/21	1	2	FACETS	0.886	0.778	1	0.886	0.778	1	CLONAL	1	TRUE	1	0.21	2		570	838	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163775	47163775	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	71	623	0	ENST00000409792.3:c.2351C>A	p.Ser784Tyr	p.S784Y	ENST00000409792	NM_014159.6	784	tCt/tAt	3/21	1	2	FACETS	0.62	0.539	0.708	0.62	0.539	0.708	SUBCLONAL	1	TRUE	1	0.21	2		623	1091	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164118	47164118	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	62	480	2	ENST00000409792.3:c.2008G>T	p.Glu670Ter	p.E670*	ENST00000409792	NM_014159.6	670	Gaa/Taa	3/21	1	2	FACETS	0.808	0.697	0.929	0.808	0.697	0.929	CLONAL	1	TRUE	1	0.21	2		482	731	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725042	49725042	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs182179992	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	81	746	3	ENST00000449682.2:c.302C>T	p.Ser101Leu	p.S101L	ENST00000449682	NM_020998.3	101	tCg/tTg	3/18	1	2	FACETS	0.703	0.618	0.796	0.703	0.618	0.796	SUBCLONAL	1	TRUE	1	0.21	2		749	1097	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987135	69987135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	66	560	0	ENST00000394351.3:c.196C>T	p.Pro66Ser	p.P66S	ENST00000394351	NM_000248.3	66	Ccg/Tcg	2/9	1	2	FACETS	0.755	0.654	0.864	0.755	0.654	0.864	SUBCLONAL	1	TRUE	1	0.21	2		560	833	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178136	142178136	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	72	542	1	ENST00000350721.4:c.7282C>A	p.Leu2428Ile	p.L2428I	ENST00000350721	NM_001184.3	2428	Ctc/Atc	43/47	1	2	FACETS	0.869	0.758	0.989	0.869	0.758	0.989	CLONAL	1	TRUE	1	0.21	2		543	789	SUCCESS
ATR	545	MSKCC	GRCh37	3	142253981	142253981	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	78	580	0	ENST00000350721.4:c.3886A>C	p.Asn1296His	p.N1296H	ENST00000350721	NM_001184.3	1296	Aat/Cat	21/47	1	2	FACETS	0.813	0.713	0.921	0.813	0.713	0.921	CLONAL	1	TRUE	1	0.21	2		580	914	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269071	142269071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753553510	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	96	653	0	ENST00000350721.4:c.2879G>A	p.Arg960Gln	p.R960Q	ENST00000350721	NM_001184.3	960	cGa/cAa	14/47	1	2	FACETS	0.869	0.772	0.973	0.869	0.772	0.973	CLONAL	1	TRUE	1	0.21	2		653	1052	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280127	142280127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760248783	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	118	709	1	ENST00000350721.4:c.1307C>T	p.Ser436Leu	p.S436L	ENST00000350721	NM_001184.3	436	tCg/tTg	5/47	1	2	FACETS	0.891	0.802	0.987	0.891	0.802	0.987	CLONAL	1	TRUE	1	0.21	2		710	1261	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	115	651	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.21	2		651	999	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155325	185155325	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746379057	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	110	683	3	ENST00000265026.3:c.566C>T	p.Ala189Val	p.A189V	ENST00000265026	NM_004721.4	189	gCg/gTg	3/14	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.21	2		686	965	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443345	187443345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	63	562	0	ENST00000232014.4:c.1781G>A	p.Arg594Gln	p.R594Q	ENST00000232014	NM_001130845.1	594	cGa/cAa	8/10	1	2	FACETS	0.706	0.609	0.812	0.706	0.609	0.812	SUBCLONAL	1	TRUE	1	0.21	2		562	850	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451339	187451339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200263685	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	94	541	0	ENST00000232014.4:c.143C>T	p.Thr48Met	p.T48M	ENST00000232014	NM_001130845.1	48	aCg/aTg	3/10	1	2	FACETS	0.934	0.83	1	0.934	0.83	1	CLONAL	1	TRUE	1	0.21	2		541	958	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749438	41749438	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	72	537	0	ENST00000226382.2:c.357G>T	p.Glu119Asp	p.E119D	ENST00000226382	NM_003924.3	119	gaG/gaT	2/3	0.178066065482938	3	FACETS	0.935	0.816	1	0.468	0.408	0.533	CLONAL	1	TRUE	1	0.21	3		537	810	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133555	55133555	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	87	678	1	ENST00000257290.5:c.859G>T	p.Asp287Tyr	p.D287Y	ENST00000257290	NM_006206.4	287	Gat/Tat	6/23	0.178066065482938	3	FACETS	0.829	0.732	0.934	0.415	0.366	0.467	CLONAL	1	TRUE	1	0.21	3		679	1104	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140704	55140704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765271720	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	57	544	0	ENST00000257290.5:c.1565G>A	p.Arg522His	p.R522H	ENST00000257290	NM_006206.4	522	cGt/cAt	11/23	0.178066065482938	3	FACETS	0.686	0.586	0.794	0.343	0.293	0.397	SUBCLONAL	1	TRUE	1	0.21	3		544	875	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144623	55144623	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	59	662	1	ENST00000257290.5:c.2097G>T	p.Glu699Asp	p.E699D	ENST00000257290	NM_006206.4	699	gaG/gaT	15/23	0.178066065482938	3	FACETS	0.568	0.486	0.657	0.284	0.243	0.329	SUBCLONAL	1	TRUE	1	0.21	3		663	1094	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953804	55953804	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	86	722	0	ENST00000263923.4:c.3632A>G	p.Lys1211Arg	p.K1211R	ENST00000263923	NM_002253.2	1211	aAa/aGa	27/30	0.178066065482938	3	FACETS	0.735	0.648	0.829	0.368	0.324	0.415	SUBCLONAL	1	TRUE	1	0.21	3		722	1231	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356121	66356121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	70	640	0	ENST00000273854.3:c.1376C>T	p.Ser459Phe	p.S459F	ENST00000273854	NM_004439.5	459	tCt/tTt	5/18	0.178066065482938	3	FACETS	0.668	0.58	0.763	0.334	0.29	0.382	SUBCLONAL	1	TRUE	1	0.21	3		640	1103	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467731	66467731	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1285001325	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	174	722	2	ENST00000273854.3:c.538G>A	p.Asp180Asn	p.D180N	ENST00000273854	NM_004439.5	180	Gat/Aat	3/18	0.178066065482938	3	FACETS	0.872	0.802	0.945	0.872	0.802	0.945	CLONAL	2	TRUE	1	0.21	3		724	1050	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155851	106155851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1332525138	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	61	529	0	ENST00000380013.4:c.752C>T	p.Ala251Val	p.A251V	ENST00000380013	NM_001127208.2	251	gCc/gTc	3/11	0.178066065482938	3	FACETS	0.636	0.546	0.733	0.318	0.273	0.367	SUBCLONAL	1	TRUE	1	0.21	3		529	1010	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159099	143159099	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1332432216	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	100	642	2	ENST00000262992.4:c.754C>T	p.Arg252Ter	p.R252*	ENST00000262992	NM_001101669.1	252	Cga/Tga	10/24	0.178066065482938	3	FACETS	0.971	0.865	1	0.485	0.432	0.542	CLONAL	1	TRUE	1	0.21	3		644	1084	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332699	153332699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780061054	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	191	726	1	ENST00000281708.4:c.257C>T	p.Ser86Leu	p.S86L	ENST00000281708	NM_033632.3	86	tCg/tTg	2/12	0.178066065482938	3	FACETS	0.861	0.795	0.93	0.861	0.795	0.93	CLONAL	2	TRUE	1	0.21	3		727	1167	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525029	187525029	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	69	470	0	ENST00000441802.2:c.10651T>G	p.Phe3551Val	p.F3551V	ENST00000441802	NM_005245.3	3551	Ttc/Gtc	19/27	0.178066065482938	3	FACETS	0.954	0.83	1	0.477	0.415	0.545	CLONAL	1	TRUE	1	0.21	3		470	761	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530344	187530344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775447002	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	87	705	1	ENST00000441802.2:c.10199G>A	p.Arg3400Gln	p.R3400Q	ENST00000441802	NM_005245.3	3400	cGa/cAa	16/27	0.178066065482938	3	FACETS	0.705	0.622	0.795	0.353	0.311	0.398	SUBCLONAL	1	TRUE	1	0.21	3		706	1298	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530456	187530456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1373676802	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	178	566	0	ENST00000441802.2:c.10087G>A	p.Asp3363Asn	p.D3363N	ENST00000441802	NM_005245.3	3363	Gat/Aat	16/27	0.178066065482938	3	FACETS	0.985	0.908	1	0.985	0.908	1	CLONAL	2	TRUE	1	0.21	3		566	951	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539112	187539112	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	64	605	2	ENST00000441802.2:c.8628C>A	p.Asp2876Glu	p.D2876E	ENST00000441802	NM_005245.3	2876	gaC/gaA	10/27	0.178066065482938	3	FACETS	0.706	0.61	0.811	0.353	0.305	0.406	SUBCLONAL	1	TRUE	1	0.21	3		607	954	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1272311	1272311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141425941	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	105	628	0	ENST00000310581.5:c.2371G>A	p.Val791Ile	p.V791I	ENST00000310581	NM_198253.2	791	Gtc/Atc	7/16	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.21	2		628	941	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295274	1295274	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	70	507	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.995	0.867	1	0.995	0.867	1	CLONAL	1	TRUE	1	0.21	2		507	670	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861083	35861083	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	69	462	0	ENST00000303115.3:c.212T>G	p.Phe71Cys	p.F71C	ENST00000303115	NM_002185.3	71	tTt/tGt	2/8	1	2	FACETS	0.929	0.809	1	0.929	0.809	1	CLONAL	1	TRUE	1	0.21	2		462	707	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950622	38950622	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748585755	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1385	169	901	1	ENST00000357387.3:c.3328C>T	p.Arg1110Cys	p.R1110C	ENST00000357387	NM_152756.3	1110	Cgt/Tgt	31/38	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.21	2		902	1554	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176614	56176614	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	58	387	0	ENST00000399503.3:c.2164G>T	p.Glu722Ter	p.E722*	ENST00000399503	NM_005921.1	722	Gaa/Taa	12/20	1	2	FACETS	0.938	0.806	1	0.938	0.806	1	CLONAL	1	TRUE	1	0.21	2		387	589	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754575	57754575	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	97	650	2	ENST00000274289.3:c.472C>A	p.Leu158Ile	p.L158I	ENST00000274289	NM_006622.3	158	Ctc/Atc	3/14	1	2	FACETS	0.933	0.83	1	0.933	0.83	1	CLONAL	1	TRUE	1	0.21	2		652	990	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628323	86628323	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	81	451	0	ENST00000274376.6:c.693-1G>A		p.X231_splice	ENST00000274376	NM_002890.2	231			1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.21	2		451	743	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675576	86675576	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	57	514	1	ENST00000274376.6:c.2512A>T	p.Asn838Tyr	p.N838Y	ENST00000274376	NM_002890.2	838	Aat/Tat	19/25	1	2	FACETS	0.717	0.614	0.83	0.717	0.614	0.83	SUBCLONAL	1	TRUE	1	0.21	2		515	757	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911478	131911478	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	63	453	0	ENST00000265335.6:c.223G>T	p.Glu75Ter	p.E75*	ENST00000265335		75	Gaa/Taa	3/25	1	2	FACETS	0.781	0.674	0.898	0.781	0.674	0.898	SUBCLONAL	1	TRUE	1	0.21	2		453	768	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915104	131915104	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	67	496	0	ENST00000265335.6:c.461T>C	p.Val154Ala	p.V154A	ENST00000265335		154	gTc/gCc	4/25	1	2	FACETS	0.767	0.665	0.878	0.767	0.665	0.878	SUBCLONAL	1	TRUE	1	0.21	2		496	832	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931468	131931468	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369560280	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	55	413	2	ENST00000265335.6:c.2173C>T	p.Arg725Trp	p.R725W	ENST00000265335		725	Cgg/Tgg	13/25	1	2	FACETS	0.745	0.636	0.864	0.745	0.636	0.864	SUBCLONAL	1	TRUE	1	0.21	2		415	703	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495372	149495372	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146614144	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	48	523	0	ENST00000261799.4:c.3275C>T	p.Ser1092Leu	p.S1092L	ENST00000261799	NM_002609.3	1092	tCg/tTg	23/23	1	2	FACETS	0.632	0.533	0.742	0.632	0.533	0.742	SUBCLONAL	1	TRUE	1	0.21	2		523	723	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170815004	170815004	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	67	433	0	ENST00000296930.5:c.52C>A	p.Leu18Ile	p.L18I	ENST00000296930	NM_002520.6	18	Ctt/Att	1/11	1	2	FACETS	0.892	0.775	1	0.892	0.775	1	CLONAL	1	TRUE	1	0.21	2		433	715	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176719070	176719070	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	97	628	0	ENST00000439151.2:c.6374G>T	p.Gly2125Val	p.G2125V	ENST00000439151	NM_022455.4	2125	gGg/gTg	22/23	1	2	FACETS	0.932	0.829	1	0.932	0.829	1	CLONAL	1	TRUE	1	0.21	2		628	991	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176719098	176719098	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	79	556	0	ENST00000439151.2:c.6402G>T	p.Lys2134Asn	p.K2134N	ENST00000439151	NM_022455.4	2134	aaG/aaT	22/23	1	2	FACETS	0.851	0.747	0.963	0.851	0.747	0.963	CLONAL	1	TRUE	1	0.21	2		556	884	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057736	180057736	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	58	632	0	ENST00000261937.6:c.219G>T	p.Lys73Asn	p.K73N	ENST00000261937	NM_182925.4	73	aaG/aaT	3/30	1	2	FACETS	0.639	0.547	0.739	0.639	0.547	0.739	SUBCLONAL	1	TRUE	1	0.21	2		632	865	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166818	32166818	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1441415979	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	48	461	0	ENST00000375023.3:c.4420C>T	p.Arg1474Ter	p.R1474*	ENST00000375023	NM_004557.3	1474	Cga/Tga	24/30	1	2	FACETS	0.675	0.57	0.792	0.675	0.57	0.792	SUBCLONAL	1	TRUE	1	0.21	2		461	677	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172090	32172090	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1152	142	898	0	ENST00000375023.3:c.2942G>T	p.Gly981Val	p.G981V	ENST00000375023	NM_004557.3	981	gGa/gTa	19/30	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.21	2		898	1294	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715350	117715350	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1466068877	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	67	504	0	ENST00000368508.3:c.1139G>T	p.Arg380Ile	p.R380I	ENST00000368508	NM_002944.2	380	aGa/aTa	10/43	1	2	FACETS	0.77	0.668	0.881	0.77	0.668	0.881	SUBCLONAL	1	TRUE	1	0.21	2		504	829	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718123	117718123	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	98	641	0	ENST00000368508.3:c.734G>T	p.Arg245Ile	p.R245I	ENST00000368508	NM_002944.2	245	aGa/aTa	7/43	1	2	FACETS	0.914	0.814	1	0.914	0.814	1	CLONAL	1	TRUE	1	0.21	2		641	1021	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519317	137519317	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	87	626	0	ENST00000367739.4:c.1321G>T	p.Glu441Ter	p.E441*	ENST00000367739	NM_000416.2	441	Gaa/Taa	7/7	1	2	FACETS	0.833	0.735	0.937	0.833	0.735	0.937	CLONAL	1	TRUE	1	0.21	2		626	995	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023160	150023160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	105	814	2	ENST00000253339.5:c.103C>T	p.Arg35Trp	p.R35W	ENST00000253339		35	Cgg/Tgg	1/7	1	2	FACETS	0.804	0.718	0.896	0.804	0.718	0.896	CLONAL	1	TRUE	1	0.21	2		816	1244	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163810	152163810	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	81	655	0	ENST00000206249.3:c.531A>C	p.Glu177Asp	p.E177D	ENST00000206249	NM_000125.3	177	gaA/gaC	2/8	1	2	FACETS	0.689	0.605	0.779	0.689	0.605	0.779	SUBCLONAL	1	TRUE	1	0.21	2		655	1120	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528907	157528907	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	81	551	0	ENST00000346085.5:c.6632A>G	p.Asn2211Ser	p.N2211S	ENST00000346085	NM_020732.3	2211	aAc/aGc	20/20	1	2	FACETS	0.979	0.862	1	0.979	0.862	1	CLONAL	1	TRUE	1	0.21	2		551	788	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864502	162864502	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	54	477	0	ENST00000366898.1:c.11T>G	p.Phe4Cys	p.F4C	ENST00000366898	NM_004562.2	4	tTt/tGt	2/12	1	2	FACETS	0.752	0.641	0.873	0.752	0.641	0.873	SUBCLONAL	1	TRUE	1	0.21	2		477	684	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963988	2963988	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755527825	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	215	770	0	ENST00000396946.4:c.1819G>A	p.Glu607Lys	p.E607K	ENST00000396946	NM_032415.4	607	Gaa/Aaa	15/25	0.178066065482938	3	FACETS	0.895	0.83	0.962	0.895	0.83	0.962	CLONAL	2	TRUE	1	0.21	3		770	1264	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148504761	148504761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397515548	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	95	727	2	ENST00000320356.2:c.2233G>A	p.Glu745Lys	p.E745K	ENST00000320356	NM_004456.4	745	Gaa/Aaa	20/20	0.178066065482938	3	FACETS	0.886	0.787	0.993	0.443	0.393	0.497	CLONAL	1	TRUE	1	0.21	3		729	1128	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148526895	148526895	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	64	602	0	ENST00000320356.2:c.409G>T	p.Glu137Ter	p.E137*	ENST00000320356	NM_004456.4	137	Gaa/Taa	5/20	0.178066065482938	3	FACETS	0.587	0.506	0.675	0.294	0.253	0.338	SUBCLONAL	1	TRUE	1	0.21	3		602	1147	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878079	151878079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202108375	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	53	537	0	ENST00000262189.6:c.6866G>A	p.Arg2289His	p.R2289H	ENST00000262189	NM_170606.2	2289	cGt/cAt	36/59	0.178066065482938	3	FACETS	0.646	0.549	0.753	0.323	0.274	0.377	SUBCLONAL	1	TRUE	1	0.21	3		537	863	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896526	151896526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1011983335	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	44	347	0	ENST00000262189.6:c.4111G>T	p.Asp1371Tyr	p.D1371Y	ENST00000262189	NM_170606.2	1371	Gat/Tat	27/59	0.178066065482938	3	FACETS	0.814	0.682	0.96	0.407	0.341	0.48	CLONAL	1	TRUE	1	0.21	3		347	569	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012244	152012244	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748254163	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	282	815	0	ENST00000262189.6:c.569G>A	p.Arg190Gln	p.R190Q	ENST00000262189	NM_170606.2	190	cGa/cAa	4/59	0.178066065482938	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.21	3		815	1401	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044402	5044402	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	76	610	0	ENST00000381652.3:c.351-1G>T		p.X117_splice	ENST00000381652	NM_004972.3	117			1	2	FACETS	0.764	0.669	0.868	0.764	0.669	0.868	SUBCLONAL	1	TRUE	1	0.21	2		610	947	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5066739	5066739	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1340580425	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	59	593	0	ENST00000381652.3:c.1276C>T	p.Arg426Ter	p.R426*	ENST00000381652	NM_004972.3	426	Cga/Tga	10/25	1	2	FACETS	0.624	0.535	0.721	0.624	0.535	0.721	SUBCLONAL	1	TRUE	1	0.21	2		593	901	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5077508	5077508	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	60	300	1	ENST00000381652.3:c.1920G>T	p.Lys640Asn	p.K640N	ENST00000381652	NM_004972.3	640	aaG/aaT	15/25	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.21	2		301	437	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218598	98218598	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	73	599	2	ENST00000331920.6:c.3266C>A	p.Ser1089Tyr	p.S1089Y	ENST00000331920	NM_000264.3	1089	tCt/tAt	19/24	1	2	FACETS	0.747	0.651	0.85	0.747	0.651	0.85	SUBCLONAL	1	TRUE	1	0.21	2		601	931	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907093	101907093	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	79	530	0	ENST00000374994.4:c.1053C>A	p.Asp351Glu	p.D351E	ENST00000374994	NM_004612.2	351	gaC/gaA	6/9	1	2	FACETS	0.912	0.801	1	0.912	0.801	1	CLONAL	1	TRUE	1	0.21	2		530	825	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600556	43600556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	82	781	3	ENST00000355710.3:c.782C>T	p.Thr261Ile	p.T261I	ENST00000355710	NM_020975.4	261	aCc/aTc	4/20	0.178066065482938	3	FACETS	0.742	0.652	0.839	0.371	0.326	0.42	SUBCLONAL	1	TRUE	1	0.21	3		784	1163	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615088	43615088	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	97	758	0	ENST00000355710.3:c.2502C>A	p.Asn834Lys	p.N834K	ENST00000355710	NM_020975.4	834	aaC/aaA	14/20	0.178066065482938	3	FACETS	0.917	0.816	1	0.459	0.408	0.513	CLONAL	1	TRUE	1	0.21	3		758	1113	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845621	63845621	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	67	318	1	ENST00000279873.7:c.1360G>T	p.Glu454Ter	p.E454*	ENST00000279873	NM_032199.2	454	Gaa/Taa	9/10	0.178066065482938	3	FACETS	1	0.942	1	0.577	0.501	0.659	CLONAL	1	TRUE	1	0.21	3		319	611	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333960	70333960	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	65	465	1	ENST00000373644.4:c.1865G>T	p.Arg622Ile	p.R622I	ENST00000373644	NM_030625.2	622	aGa/aTa	2/12	0.178066065482938	3	FACETS	0.863	0.747	0.989	0.431	0.373	0.495	CLONAL	1	TRUE	1	0.21	3		466	793	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717650	89717650	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs1057520900	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	122	635	0	ENST00000371953.3:c.675T>G	p.Tyr225Ter	p.Y225*	ENST00000371953	NM_000314.4	225	taT/taG	7/9	0.178066065482938	3	FACETS	1	0.971	1	0.601	0.542	0.663	CLONAL	1	TRUE	1	0.21	3		635	1069	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588241	69588241	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs533842802	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	97	729	1	ENST00000168712.1:c.457G>A	p.Asp153Asn	p.D153N	ENST00000168712	NM_002007.2	153	Gat/Aat	3/3	1	2	FACETS	0.927	0.824	1	0.927	0.824	1	CLONAL	1	TRUE	1	0.21	2		730	997	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94224129	94224129	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	41	311	0	ENST00000323929.3:c.23A>G	p.Asp8Gly	p.D8G	ENST00000323929	NM_005591.3	8	gAt/gGt	3/20	1	2	FACETS	0.976	0.814	1	0.976	0.814	1	CLONAL	1	TRUE	1	0.21	2		311	400	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920786	100920786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752995251	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	162	747	1	ENST00000325455.5:c.2362C>T	p.Arg788Trp	p.R788W	ENST00000325455	NM_001202474.3	788	Cgg/Tgg	6/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.21	2		748	1206	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922294	100922294	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1315135533	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	123	769	4	ENST00000325455.5:c.2218C>T	p.Arg740Ter	p.R740*	ENST00000325455	NM_001202474.3	740	Cga/Tga	5/8	1	2	FACETS	0.99	0.893	1	0.99	0.893	1	CLONAL	1	TRUE	1	0.21	2		773	1183	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139230	108139230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	127	726	0	ENST00000278616.4:c.2732C>T	p.Ala911Val	p.A911V	ENST00000278616	NM_000051.3	911	gCt/gTt	18/63	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.21	2		726	975	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143506	108143506	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	94	835	0	ENST00000278616.4:c.3211A>C	p.Asn1071His	p.N1071H	ENST00000278616	NM_000051.3	1071	Aat/Cat	22/63	1	2	FACETS	0.717	0.636	0.804	0.717	0.636	0.804	SUBCLONAL	1	TRUE	1	0.21	2		835	1249	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160347	108160347	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	50	275	0	ENST00000278616.4:c.4255C>A	p.Leu1419Ile	p.L1419I	ENST00000278616	NM_000051.3	1419	Ctt/Att	29/63	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.21	2		275	463	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352742	118352742	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	69	556	0	ENST00000534358.1:c.3947G>T	p.Arg1316Ile	p.R1316I	ENST00000534358	NM_005933.3	1316	aGa/aTa	7/36	1	2	FACETS	0.792	0.688	0.904	0.792	0.688	0.904	CLONAL	1	TRUE	1	0.21	2		556	830	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435277	18435277	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	83	574	2	ENST00000266497.5:c.262G>T	p.Glu88Ter	p.E88*	ENST00000266497		88	Gaa/Taa	1/31	1	2	FACETS	0.836	0.736	0.943	0.836	0.736	0.943	CLONAL	1	TRUE	1	0.21	2		576	946	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123842	46123842	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	52	415	0	ENST00000334344.6:c.108A>C	p.Lys36Asn	p.K36N	ENST00000334344	NM_152641.2	36	aaA/aaC	2/21	1	2	FACETS	0.79	0.672	0.92	0.79	0.672	0.92	CLONAL	1	TRUE	1	0.21	2		415	627	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211668	46211668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767329695	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	51	469	3	ENST00000334344.6:c.634G>A	p.Asp212Asn	p.D212N	ENST00000334344	NM_152641.2	212	Gac/Aac	5/21	1	2	FACETS	0.552	0.468	0.645	0.552	0.468	0.645	SUBCLONAL	1	TRUE	1	0.21	2		472	880	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218237	133218237	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	79	760	0	ENST00000320574.5:c.5374T>G	p.Phe1792Val	p.F1792V	ENST00000320574	NM_006231.2	1792	Ttc/Gtc	39/49	1	2	FACETS	0.701	0.614	0.794	0.701	0.614	0.794	SUBCLONAL	1	TRUE	1	0.21	2		760	1074	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249857	133249857	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1565972665	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	87	466	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	0.21	2		466	718	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609791	28609791	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146341559	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	69	550	0	ENST00000241453.7:c.1438G>A	p.Glu480Lys	p.E480K	ENST00000241453	NM_004119.2	480	Gaa/Aaa	12/24	1	2	FACETS	0.812	0.706	0.927	0.812	0.706	0.927	CLONAL	1	TRUE	1	0.21	2		550	809	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012441	29012441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55974987	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	113	594	1	ENST00000282397.4:c.430G>A	p.Glu144Lys	p.E144K	ENST00000282397	NM_002019.4	144	Gaa/Aaa	4/30	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.21	2		595	948	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910860	32910860	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs398122746	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1624	167	1082	2	ENST00000380152.3:c.2368G>T	p.Glu790Ter	p.E790*	ENST00000380152		790	Gaa/Taa	11/27	1	2	FACETS	0.888	0.812	0.968	0.888	0.812	0.968	CLONAL	1	TRUE	1	0.21	2		1084	1791	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912750	32912750	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28897727	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1409	123	987	0	ENST00000380152.3:c.4258G>T	p.Asp1420Tyr	p.D1420Y	ENST00000380152		1420	Gat/Tat	11/27	1	2	FACETS	0.765	0.689	0.845	0.765	0.689	0.845	SUBCLONAL	1	TRUE	1	0.21	2		987	1532	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913632	32913632	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1392	179	1023	0	ENST00000380152.3:c.5140T>G	p.Tyr1714Asp	p.Y1714D	ENST00000380152		1714	Tat/Gat	11/27	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.21	2		1023	1571	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953959	32953959	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	63	470	0	ENST00000380152.3:c.9026A>C	p.Tyr3009Ser	p.Y3009S	ENST00000380152		3009	tAt/tCt	23/27	1	2	FACETS	0.797	0.688	0.915	0.797	0.688	0.915	CLONAL	1	TRUE	1	0.21	2		470	753	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028617	42028617	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1526	129	1164	2	ENST00000219905.7:c.4155G>T	p.Glu1385Asp	p.E1385D	ENST00000219905	NM_001164273.1	1385	gaG/gaT	13/24	1	2	FACETS	0.742	0.67	0.819	0.742	0.67	0.819	SUBCLONAL	1	TRUE	1	0.21	2		1166	1655	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058999	42058999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755132381	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1471	141	1015	4	ENST00000219905.7:c.8719G>A	p.Asp2907Asn	p.D2907N	ENST00000219905	NM_001164273.1	2907	Gat/Aat	24/24	1	2	FACETS	0.833	0.756	0.915	0.833	0.756	0.915	CLONAL	1	TRUE	1	0.21	2		1019	1612	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476252	88476252	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	89	579	0	ENST00000360948.2:c.1880A>C	p.Lys627Thr	p.K627T	ENST00000360948	NM_001012338.2	627	aAg/aCg	15/19	1	2	FACETS	0.974	0.863	1	0.974	0.863	1	CLONAL	1	TRUE	1	0.21	2		579	870	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99440126	99440126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1180612681	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	80	539	5	ENST00000268035.6:c.1094G>A	p.Arg365Gln	p.R365Q	ENST00000268035	NM_000875.3	365	cGa/cAa	4/21	1	2	FACETS	0.83	0.729	0.939	0.83	0.729	0.939	CLONAL	1	TRUE	1	0.21	2		544	918	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14031717	14031717	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	47	381	0	ENST00000311895.7:c.1904+2T>C		p.X635_splice	ENST00000311895	NM_005236.2	635			1	2	FACETS	0.792	0.668	0.93	0.792	0.668	0.93	CLONAL	1	TRUE	1	0.21	2		381	565	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645910	67645910	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	86	702	0	ENST00000264010.4:c.838A>C	p.Asn280His	p.N280H	ENST00000264010	NM_006565.3	280	Aat/Cat	4/12	1	2	FACETS	0.79	0.697	0.89	0.79	0.697	0.89	SUBCLONAL	1	TRUE	1	0.21	2		702	1037	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842434	68842434	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	100	660	0	ENST00000261769.5:c.495A>C	p.Glu165Asp	p.E165D	ENST00000261769	NM_004360.3	165	gaA/gaC	4/16	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.21	2		660	906	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822274	72822274	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373052102	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1471	119	1139	0	ENST00000268489.5:c.9901G>A	p.Ala3301Thr	p.A3301T	ENST00000268489	NM_006885.3	3301	Gca/Aca	10/10	1	2	FACETS	0.713	0.641	0.79	0.713	0.641	0.79	SUBCLONAL	1	TRUE	1	0.21	2		1139	1590	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827411	72827411	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1607	131	1046	1	ENST00000268489.5:c.9170G>A	p.Gly3057Glu	p.G3057E	ENST00000268489	NM_006885.3	3057	gGa/gAa	9/10	1	2	FACETS	0.718	0.648	0.792	0.718	0.648	0.792	SUBCLONAL	1	TRUE	1	0.21	2		1047	1738	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828033	72828033	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774848265	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1694	187	1147	1	ENST00000268489.5:c.8548G>A	p.Glu2850Lys	p.E2850K	ENST00000268489	NM_006885.3	2850	Gag/Aag	9/10	1	2	FACETS	0.947	0.871	1	0.947	0.871	1	CLONAL	1	TRUE	1	0.21	2		1148	1881	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953156	81953156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381167403	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1387	117	930	3	ENST00000359376.3:c.2122G>A	p.Ala708Thr	p.A708T	ENST00000359376	NM_002661.3	708	Gcc/Acc	20/33	1	2	FACETS	0.741	0.665	0.821	0.741	0.665	0.821	SUBCLONAL	1	TRUE	1	0.21	2		933	1504	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816140	89816140	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	92	684	0	ENST00000389301.3:c.3237A>T	p.Lys1079Asn	p.K1079N	ENST00000389301	NM_000135.2	1079	aaA/aaT	32/43	1	2	FACETS	0.86	0.762	0.965	0.86	0.762	0.965	CLONAL	1	TRUE	1	0.21	2		684	1019	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15952253	15952253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767227910	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	89	743	1	ENST00000268712.3:c.6442G>A	p.Glu2148Lys	p.E2148K	ENST00000268712	NM_006311.3	2148	Gag/Aag	41/46	1	2	FACETS	0.794	0.702	0.892	0.794	0.702	0.892	SUBCLONAL	1	TRUE	1	0.21	2		744	1068	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961376	15961376	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	50	534	0	ENST00000268712.3:c.6013G>T	p.Asp2005Tyr	p.D2005Y	ENST00000268712	NM_006311.3	2005	Gat/Tat	39/46	1	2	FACETS	0.617	0.522	0.722	0.617	0.522	0.722	SUBCLONAL	1	TRUE	1	0.21	2		534	772	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541513	29541513	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	34	312	0	ENST00000356175.3:c.1437A>C	p.Glu479Asp	p.E479D	ENST00000356175	NM_000267.3	479	gaA/gaC	13/57	1	2	FACETS	0.6	0.489	0.725	0.6	0.489	0.725	SUBCLONAL	1	TRUE	1	0.21	2		312	540	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553583	29553583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1479669686	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	40	261	0	ENST00000356175.3:c.2132G>A	p.Arg711His	p.R711H	ENST00000356175	NM_000267.3	711	cGc/cAc	18/57	1	2	FACETS	0.854	0.71	1	0.854	0.71	1	CLONAL	1	TRUE	1	0.21	2		261	446	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556079	29556079	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886041347	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	62	406	0	ENST00000356175.3:c.2446C>T	p.Arg816Ter	p.R816*	ENST00000356175	NM_000267.3	816	Cga/Tga	21/57	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.21	2		406	549	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	116	682	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.21	2		682	1088	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322594	30322594	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	43	499	0	ENST00000322652.5:c.1607C>A	p.Thr536Lys	p.T536K	ENST00000322652	NM_015355.2	536	aCa/aAa	14/16	1	2	FACETS	0.588	0.49	0.696	0.588	0.49	0.696	SUBCLONAL	1	TRUE	1	0.21	2		499	697	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40476865	40476865	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	146	772	0	ENST00000264657.5:c.1465-1G>T		p.X489_splice	ENST00000264657	NM_139276.2	489			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.21	2		772	1176	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244601	41244601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	90	722	0	ENST00000357654.3:c.2947C>T	p.Leu983Phe	p.L983F	ENST00000357654	NM_007294.3	983	Ctt/Ttt	10/23	1	2	FACETS	0.757	0.669	0.85	0.757	0.669	0.85	SUBCLONAL	1	TRUE	1	0.21	2		722	1133	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519009	66519009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	112	699	0	ENST00000358598.2:c.290G>A	p.Arg97Gln	p.R97Q	ENST00000358598	NM_212471.2	97	cGa/cAa	3/11	1	2	FACETS	0.916	0.822	1	0.916	0.822	1	CLONAL	1	TRUE	1	0.21	2		699	1164	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745986	745986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371352602	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	48	543	2	ENST00000314574.4:c.536G>A	p.Arg179Gln	p.R179Q	ENST00000314574	NM_005433.3	179	cGa/cAa	5/12	1	2	FACETS	0.532	0.448	0.625	0.532	0.448	0.625	SUBCLONAL	1	TRUE	1	0.21	2		545	859	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39629541	39629541	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	84	623	0	ENST00000262039.4:c.2235C>A	p.His745Gln	p.H745Q	ENST00000262039	NM_002647.2	745	caC/caA	21/25	1	2	FACETS	0.815	0.719	0.92	0.815	0.719	0.92	CLONAL	1	TRUE	1	0.21	2		623	981	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390469	56390469	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	105	770	0	ENST00000348428.3:c.1208A>C	p.Asp403Ala	p.D403A	ENST00000348428	NM_006785.3	403	gAc/gCc	10/17	1	2	FACETS	0.788	0.704	0.878	0.788	0.704	0.878	SUBCLONAL	1	TRUE	1	0.21	2		770	1269	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2194550	2194550	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1321	114	823	0	ENST00000398665.3:c.625T>G	p.Tyr209Asp	p.Y209D	ENST00000398665	NM_032482.2	209	Tat/Gat	7/28	1	2	FACETS	0.757	0.679	0.84	0.757	0.679	0.84	SUBCLONAL	1	TRUE	1	0.21	2		823	1435	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118948	3118948	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587777022	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	82	773	1	ENST00000078429.4:c.632C>T	p.Ser211Leu	p.S211L	ENST00000078429	NM_002067.2	211	tCg/tTg	5/7	1	2	FACETS	0.799	0.703	0.903	0.799	0.703	0.903	CLONAL	1	TRUE	1	0.21	2		774	977	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366207	15366207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	120	899	0	ENST00000263377.2:c.1948G>A	p.Asp650Asn	p.D650N	ENST00000263377	NM_058243.2	650	Gac/Aac	10/20	1	2	FACETS	0.879	0.791	0.972	0.879	0.791	0.972	CLONAL	1	TRUE	1	0.21	2		899	1300	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792248	33792248	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	84	632	0	ENST00000498907.2:c.1073C>T	p.Ala358Val	p.A358V	ENST00000498907	NM_004364.3	358	gCg/gTg	1/1	1	2	FACETS	0.93	0.82	1	0.93	0.82	1	CLONAL	1	TRUE	1	0.21	2		632	860	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743948	41743948	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751738506	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	97	850	0	ENST00000301178.4:c.883C>T	p.Arg295Trp	p.R295W	ENST00000301178	NM_021913.4	295	Cgg/Tgg	7/20	1	2	FACETS	0.777	0.691	0.87	0.777	0.691	0.87	SUBCLONAL	1	TRUE	1	0.21	2		850	1189	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39725963	39725963	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	38	322	0	ENST00000361337.2:c.834C>A	p.Phe278Leu	p.F278L	ENST00000361337	NM_003286.2	278	ttC/ttA	10/21	1	2	FACETS	0.685	0.566	0.819	0.685	0.566	0.819	SUBCLONAL	1	TRUE	1	0.21	2		322	528	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480443	57480443	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	43	328	0	ENST00000371085.3:c.438C>A	p.Phe146Leu	p.F146L	ENST00000371085	NM_000516.4	146	ttC/ttA	6/13	1	2	FACETS	0.721	0.603	0.853	0.721	0.603	0.853	SUBCLONAL	1	TRUE	1	0.21	2		328	568	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091838	29091838	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	29	218	0	ENST00000328354.6:c.1119G>T	p.Lys373Asn	p.K373N	ENST00000328354	NM_007194.3	373	aaG/aaT	11/15	1	2	FACETS	0.805	0.647	0.985	0.805	0.647	0.985	CLONAL	1	TRUE	1	0.21	2		218	343	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000102	30000102	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	65	698	2	ENST00000338641.4:c.114+1G>A		p.X38_splice	ENST00000338641	NM_000268.3	38			1	2	FACETS	0.599	0.518	0.688	0.599	0.518	0.688	SUBCLONAL	1	TRUE	1	0.21	2		700	1033	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20152109	20152109	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	97	830	1	ENST00000379607.5:c.221C>T	p.Ser74Leu	p.S74L	ENST00000379607	NM_001412.3	74	tCg/tTg	4/7	1	2	FACETS	0.753	0.669	0.843	0.753	0.669	0.843	SUBCLONAL	1	TRUE	1	0.21	2		831	1227	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039335	47039335	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	109	867	0	ENST00000377604.3:c.958C>A	p.Leu320Met	p.L320M	ENST00000377604	NM_001204468.1	320	Ctg/Atg	10/24	1	2	FACETS	0.876	0.784	0.974	0.876	0.784	0.974	CLONAL	1	TRUE	1	0.21	2		867	1185	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354222	70354222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	112	766	0	ENST00000374080.3:c.4633G>A	p.Asp1545Asn	p.D1545N	ENST00000374080		1545	Gac/Aac	34/45	1	2	FACETS	0.891	0.799	0.989	0.891	0.799	0.989	CLONAL	1	TRUE	1	0.21	2		766	1197	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937236	76937236	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	156	855	0	ENST00000373344.5:c.3512G>T	p.Arg1171Ile	p.R1171I	ENST00000373344	NM_000489.3	1171	aGa/aTa	9/35	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.21	2		855	1264	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937884	76937884	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs781927008	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	132	704	0	ENST00000373344.5:c.2864A>C	p.Lys955Thr	p.K955T	ENST00000373344	NM_000489.3	955	aAa/aCa	9/35	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.21	2		704	1120	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217386	123217386	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	75	679	0	ENST00000218089.9:c.3040G>T	p.Asp1014Tyr	p.D1014Y	ENST00000218089	NM_001042749.1	1014	Gac/Tac	29/35	1	2	FACETS	0.636	0.555	0.723	0.636	0.555	0.723	SUBCLONAL	1	TRUE	1	0.21	2		679	1123	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162688926	162688926	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	116	629	1	ENST00000367921.3:c.73G>T	p.Val25Phe	p.V25F	ENST00000367921	NM_006182.2	25	Gtt/Ttt	3/18	0.218608918567366	3	FACETS	1	0.956	1	0.557	0.501	0.617	CLONAL	1	TRUE	1	0.218608918567366	3		630	1056	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982481	25982481	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	110	632	0	ENST00000435504.4:c.809A>T	p.Asp270Val	p.D270V	ENST00000435504		270	gAc/gTc	9/13	1	2	FACETS	0.934	0.837	1	0.934	0.837	1	CLONAL	1	TRUE	1	0.218608918567366	2		632	1078	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390106	89390106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	110	634	1	ENST00000336596.2:c.855G>A	p.Met285Ile	p.M285I	ENST00000336596	NM_005233.5	285	atG/atA	4/17	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.218608918567366	2		635	959	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873704	35873704	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	89	650	0	ENST00000303115.3:c.660G>T	p.Trp220Cys	p.W220C	ENST00000303115	NM_002185.3	220	tgG/tgT	5/8	1	2	FACETS	0.772	0.682	0.868	0.772	0.682	0.868	SUBCLONAL	1	TRUE	1	0.218608918567366	2		650	1055	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111429	56111429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1311577375	NA	P-0013351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	79	480	0	ENST00000399503.3:c.29C>T	p.Ser10Leu	p.S10L	ENST00000399503	NM_005921.1	10	tCg/tTg	1/20	1	2	FACETS	0.968	0.85	1	0.968	0.85	1	CLONAL	1	TRUE	1	0.218608918567366	2		480	747	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504263	8504263	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0013351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	102	581	0	ENST00000356435.5:c.1820C>G	p.Ser607Ter	p.S607*	ENST00000356435		607	tCa/tGa	12/35	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.218608918567366	2		581	854	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207204	1207204	+	splice_donor_variant	Splice_Site	SNP	T	T	G	rs112235354	NA	P-0013351-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	101	483	0	ENST00000326873.7:c.290+2T>G		p.X97_splice	ENST00000326873	NM_000455.4	97			0.218608918567366	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.218608918567366	1		483	615	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183788	10183788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882034	NA	P-0013368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	91	438	0	ENST00000256474.2:c.257C>T	p.Pro86Leu	p.P86L	ENST00000256474	NM_000551.3	86	cCc/cTc	1/3	0.368412714226029	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	FALSE	0	0.368412714226029	1		438	385	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149447833	149447833	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	133	599	0	ENST00000286301.3:c.1571C>T	p.Ser524Phe	p.S524F	ENST00000286301	NM_005211.3	524	tCc/tTc	11/22	0.362271722481585	3	FACETS	1	0.928	1	0.513	0.465	0.562	CLONAL	1	FALSE	1	0.368412714226029	3		599	834	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	96	540	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.763	0.678	0.853	0.763	0.678	0.853	SUBCLONAL	1	TRUE	1	0.276620797803273	2		540	910	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828084	243828084	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	90	588	0	ENST00000263826.5:c.274C>A	p.Pro92Thr	p.P92T	ENST00000263826	NM_005465.4	92	Cca/Aca	3/13	0.152500557433914	3	FACETS	0.69	0.611	0.776	0.345	0.305	0.388	INDETERMINATE	1	TRUE	1	0.276620797803273	3		588	1073	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498343	29498343	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	49	624	1	ENST00000389048.3:c.1837G>T	p.Ala613Ser	p.A613S	ENST00000389048	NM_004304.4	613	Gca/Tca	10/29	1	2	FACETS	0.389	0.328	0.457	0.389	0.328	0.457	SUBCLONAL	1	TRUE	1	0.276620797803273	2		625	910	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881507	111881507	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	91	616	0	ENST00000393256.3:c.185G>T	p.Gly62Val	p.G62V	ENST00000393256	NM_006538.4	62	gGc/gTc	2/4	1	2	FACETS	0.762	0.676	0.855	0.762	0.676	0.855	SUBCLONAL	1	TRUE	1	0.276620797803273	2		616	863	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200762	128200762	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	89	646	0	ENST00000341105.2:c.1043G>C	p.Cys348Ser	p.C348S	ENST00000341105	NM_032638.4	348	tGt/tCt	5/6	1	2	FACETS	0.735	0.651	0.826	0.735	0.651	0.826	SUBCLONAL	1	TRUE	1	0.276620797803273	2		646	875	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946296	55946296	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	76	512	0	ENST00000263923.4:c.3883G>T	p.Ala1295Ser	p.A1295S	ENST00000263923	NM_002253.2	1295	Gca/Tca	30/30	1	2	FACETS	0.771	0.675	0.873	0.771	0.675	0.873	SUBCLONAL	1	TRUE	1	0.276620797803273	2		512	713	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520095	106520095	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	48	413	0	ENST00000359195.3:c.2523C>A	p.Asp841Glu	p.D841E	ENST00000359195	NM_002649.2	841	gaC/gaA	6/11	1	2	FACETS	0.584	0.493	0.685	0.584	0.493	0.685	SUBCLONAL	1	TRUE	1	0.276620797803273	2		413	594	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411691	116411691	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	83	556	0	ENST00000397752.3:c.2870A>C	p.Lys957Thr	p.K957T	ENST00000397752	NM_000245.2	957	aAg/aCg	13/21	1	2	FACETS	0.61	0.537	0.689	0.61	0.537	0.689	SUBCLONAL	1	TRUE	1	0.276620797803273	2		556	984	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39935765	39935765	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1250	128	941	1	ENST00000378444.4:c.107G>T	p.Gly36Val	p.G36V	ENST00000378444	NM_001123385.1	36	gGt/gTt	3/15	1	2	FACETS	0.672	0.606	0.741	0.672	0.606	0.741	SUBCLONAL	1	TRUE	1	0.276620797803273	2		942	1378	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534601	140534601	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	87	630	0	ENST00000288602.6:c.312del	p.Asn105ThrfsTer77	p.N105Tfs*77	ENST00000288602	NM_004333.4	104	ggG/gg	3/18	1	2	FACETS	0.622	0.549	0.7	0.622	0.549	0.7	SUBCLONAL	1	TRUE	1	0.276620797803273	2		630	1011	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039857	47039860	+	frameshift_variant	Frame_Shift_Del	DEL	CTCT	CTCT	-	novel	NA	P-0013376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	89	715	0	ENST00000377604.3:c.1200_1203del	p.Ser401TrpfsTer83	p.S401Wfs*83	ENST00000377604	NM_001204468.1	400	gcCTCT/gc	12/24	1	2	FACETS	0.637	0.563	0.716	0.637	0.563	0.716	SUBCLONAL	1	TRUE	1	0.276620797803273	2		715	1010	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097092	11097092	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013376-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	111	709	0	ENST00000358026.2:c.586del	p.Leu196SerfsTer107	p.L196Sfs*107	ENST00000358026	NM_001128849.1	195	Ccc/cc	4/36	1	2	FACETS	0.809	0.726	0.897	0.809	0.726	0.897	CLONAL	1	TRUE	1	0.276620797803273	2		709	992	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0013378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	494	630	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.416957985678243	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.416957985678243	2		630	1001	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089776	27089776	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1553152166	NA	P-0013378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	57	178	0	ENST00000324856.7:c.2732G>T	p.Arg911Met	p.R911M	ENST00000324856	NM_006015.4	911	aGg/aTg	8/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.416957985678243	2		178	224	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467443	66467443	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	299	583	0	ENST00000273854.3:c.826T>A	p.Cys276Ser	p.C276S	ENST00000273854	NM_004439.5	276	Tgc/Agc	3/18	0.413445597144367	3	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	1	0.416957985678243	3		583	865	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017583	112017583	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	344	1044	1	ENST00000368678.4:c.930G>T	p.Glu310Asp	p.E310D	ENST00000368678		310	gaG/gaT	9/13	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.416957985678243	2		1045	1402	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129454	30129454	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1284498604	NA	P-0013378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	499	909	1	ENST00000263025.4:c.574G>A	p.Asp192Asn	p.D192N	ENST00000263025	NM_002746.2	192	Gat/Aat	4/9	1	2	FACETS	0.907	0.869	0.946	1	0.997	1	CLONAL	2	TRUE	1	0.416957985678243	2		910	1319	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985499	60985499	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	264	827	0	ENST00000333681.4:c.401T>C	p.Val134Ala	p.V134A	ENST00000333681		134	gTg/gCg	2/3	0.413445597144367	3	FACETS	1	0.984	1	0.578	0.541	0.617	CLONAL	1	TRUE	1	0.416957985678243	3		827	1323	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871060	12871070	+	frameshift_variant	Frame_Shift_Del	DEL	AAGGTGCCTGC	AAGGTGCCTGC	-	novel	NA	P-0013378-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	482	416	0	ENST00000228872.4:c.295_305del	p.Cys99GlyfsTer22	p.C99Gfs*22	ENST00000228872	NM_004064.3	96	aAAGGTGCCTGC/a	1/3	0.416957985678243	6	FACETS	1	0.991	1	0.895	0.864	0.925	CLONAL	5	TRUE	0	0.416957985678243	6		416	790	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0013384-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	166	615	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	0.242544784456463	2		615	1033	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs760043106	NA	P-0013384-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	140	753	0	ENST00000269305.4:c.584T>A	p.Ile195Asn	p.I195N	ENST00000269305	NM_001126112.2	195	aTc/aAc	6/11	0.242544784456463	1	FACETS	0.973	0.884	1	0.973	0.884	1	CLONAL	1	TRUE	0	0.242544784456463	1		753	1043	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013384-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	149	685	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	0.242544784456463	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.242544784456463	1		685	952	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678619	88678619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148888023	NA	P-0013393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	82	251	0	ENST00000360948.2:c.917G>A	p.Arg306His	p.R306H	ENST00000360948	NM_001012338.2	306	cGt/cAt	9/19	0.603204571657808	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.603204571657808	1		251	154	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594258	55594258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913523	NA	P-0013393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	354	472	0	ENST00000288135.5:c.1961T>C	p.Val654Ala	p.V654A	ENST00000288135	NM_000222.2	654	gTg/gCg	13/21	0.479703883488577	4	FACETS	0.968	0.92	1			1	CLONAL	2	TRUE	NA	0.603204571657808	4		472	972	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916747	48916747	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690915	NA	P-0013393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	237	450	0	ENST00000267163.4:c.277C>T	p.Gln93Ter	p.Q93*	ENST00000267163	NM_000321.2	93	Caa/Taa	3/27	0.183842683601653	4	FACETS	0.773	0.723	0.824	0.773	0.723	0.824	INDETERMINATE	2	TRUE	2	0.603204571657808	4		450	815	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593635	55593662	+	protein_altering_variant	In_Frame_Del	DEL	TTATGTTTACATAGACCCAACACAACTT	TTATGTTTACATAGACCCAACACAACTT	GGAA	novel	NA	P-0013393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	334	679	0	ENST00000288135.5:c.1701_1728delinsGGAA	p.Asn567_Leu576delinsLysGlu	p.N567_L576delinsKE	ENST00000288135	NM_000222.2	567	aaTTATGTTTACATAGACCCAACACAACTT/aaGGAA	11/21	0.479703883488577	4	FACETS	1	0.994	1			1	CLONAL	1	TRUE	NA	0.603204571657808	4		679	1209	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0013394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	46	332	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		332	197	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0013407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	338	380	1	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.422706863569515	3	FACETS	0.846	0.806	0.886	0.846	0.806	0.886	CLONAL	3	TRUE	0	0.450589119129606	3		381	724	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0013407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	507	615	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.450589119129606	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.450589119129606	2		615	1074	SUCCESS
APC	324	MSKCC	GRCh37	5	112175175	112175175	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	57	182	0	ENST00000257430.4:c.3885del	p.Ala1296GlnfsTer9	p.A1296Qfs*9	ENST00000257430	NM_000038.5	1295	gAa/ga	16/16	1	2	FACETS	0.944	0.817	1	0.944	0.817	1	CLONAL	1	TRUE	1	0.450589119129606	2		182	268	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0013407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	198	518	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	1	2	FACETS	0.957	0.887	1	0.957	0.887	1	CLONAL	1	TRUE	1	0.450589119129606	2		518	918	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120160	70120160	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	149	173	2	ENST00000245479.2:c.1162G>T	p.Glu388Ter	p.E388*	ENST00000245479	NM_000346.3	388	Gag/Tag	3/3	0.450589119129606	2	FACETS	0.848	0.794	0.901	1	0.988	1	CLONAL	3	TRUE	0	0.450589119129606	2		175	260	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242757	16242757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749176332	NA	P-0013407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	227	660	2	ENST00000375759.3:c.1378C>T	p.Arg460Cys	p.R460C	ENST00000375759	NM_015001.2	460	Cgc/Tgc	6/15	1	2	FACETS	0.868	0.808	0.93	0.868	0.808	0.93	CLONAL	1	TRUE	1	0.450589119129606	2		662	1161	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022944	31022944	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	99	509	0	ENST00000375687.4:c.2429A>T	p.Asp810Val	p.D810V	ENST00000375687	NM_015338.5	810	gAc/gTc	13/13	0.425145703239418	4	FACETS	0.592	0.527	0.662	0.197	0.175	0.221	SUBCLONAL	1	TRUE	1	0.450589119129606	4		509	1076	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099963	27099963	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1332846960	NA	P-0013415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	217	750	1	ENST00000324856.7:c.3842A>G	p.Tyr1281Cys	p.Y1281C	ENST00000324856	NM_006015.4	1281	tAt/tGt	15/20	1	2	FACETS	0.977	0.91	1	0.977	0.91	1	CLONAL	1	TRUE	1	0.524370171765212	2		751	847	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0013416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	216	497	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.358804176747643	4	FACETS	0.877	0.816	0.94	0.877	0.816	0.94	CLONAL	2	TRUE	2	0.358804176747643	4		497	933	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578532	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	400	601	0	ENST00000269305.4:c.398T>G	p.Met133Arg	p.M133R	ENST00000269305	NM_001126112.2	133	aTg/aGg	5/11	0.358804176747643	3	FACETS	1	0.98	1			1	CLONAL	3	TRUE	NA	0.358804176747643	3		601	842	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	536	572	0	ENST00000263967.3:c.3132T>G	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaG	21/21	0.358804176747643	6	FACETS	0.976	0.94	1	0.976	0.94	1	CLONAL	5	TRUE	1	0.358804176747643	6		572	1052	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141686	202141686	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	85	416	0	ENST00000358485.4:c.974A>T	p.Asp325Val	p.D325V	ENST00000358485	NM_001080125.1	325	gAt/gTt	7/9	0.173526192914879	2	FACETS	0.842	0.745	0.944	0.421	0.372	0.472	INDETERMINATE	1	TRUE	0	0.358804176747643	2		416	563	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806177	1806177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761896295	NA	P-0013416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	181	811	0	ENST00000260795.2:c.1196G>A	p.Arg399His	p.R399H	ENST00000260795		399	cGc/cAc	8/17	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.358804176747643	2		811	863	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131978051	131978051	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	80	377	0	ENST00000265335.6:c.3934C>T	p.His1312Tyr	p.H1312Y	ENST00000265335		1312	Cat/Tat	25/25	0.358804176747643	3	FACETS	1	0.887	1	0.503	0.443	0.566	CLONAL	1	TRUE	1	0.358804176747643	3		377	523	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573667	48573667	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0013416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	113	243	0	ENST00000342988.3:c.249+2T>G		p.X83_splice	ENST00000342988	NM_005359.5	83			0.35732210898966	2	FACETS	0.937	0.854	1	0.937	0.854	1	CLONAL	2	TRUE	0	0.358804176747643	2		243	336	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953774	48953789	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CATGCTTAAATCAGTA	CATGCTTAAATCAGTA	-	novel	NA	P-0013416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	94	382	0	ENST00000267163.4:c.1377_1389+3del		p.X459_splice	ENST00000267163	NM_000321.2	459		14/27	0.358804176747643	2	FACETS	1	0.973	1	0.634	0.568	0.704	CLONAL	1	TRUE	0	0.358804176747643	2		382	413	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0013431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	298	453	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.289180234557807	4	FACETS	0.984	0.93	1	0.984	0.93	1	CLONAL	3	TRUE	1	0.32	4		453	833	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225365079	225365079	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0013431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	92	416	0	ENST00000264414.4:c.1610+1G>A		p.X537_splice	ENST00000264414	NM_003590.4	537			1	2	FACETS	0.936	0.833	1	0.936	0.833	1	CLONAL	1	TRUE	1	0.32	2		416	614	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729174	66729174	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	109	495	0	ENST00000307102.5:c.382G>T	p.Gly128Cys	p.G128C	ENST00000307102	NM_002755.3	128	Ggc/Tgc	3/11	1	2	FACETS	0.888	0.798	0.984	0.888	0.798	0.984	CLONAL	1	TRUE	1	0.32	2		495	767	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578444	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0013431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	175	444	0	ENST00000269305.4:c.486_487del	p.Tyr163GlnfsTer17	p.Y163Qfs*17	ENST00000269305	NM_001126112.2	162	atCTac/atac	5/11	0.3	2	FACETS	0.936	0.867	1	0.936	0.867	1	CLONAL	2	TRUE	0	0.32	2		444	584	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401196	139401196	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	307	462	0	ENST00000277541.6:c.3873C>G	p.Phe1291Leu	p.F1291L	ENST00000277541	NM_017617.3	1291	ttC/ttG	23/34	1	2	FACETS	0.951	0.903	1	0.951	0.903	1	CLONAL	1	TRUE	1	0.928536971171562	2		462	695	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117854	108117856	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	GGT	GGT	-	novel	NA	P-0013440-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	168	252	0	ENST00000278616.4:c.1065_1065+2del		p.X355_splice	ENST00000278616	NM_000051.3	355		8/63	0.920187497355588	1	FACETS	0.964	0.927	0.999	0.964	0.927	0.999	CLONAL	1	TRUE	0	0.928536971171562	1		252	201	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0013449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	40	580	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.626	0.521	0.742	0.626	0.521	0.742	SUBCLONAL	1	TRUE	1	0.333790882379502	2		580	383	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473723	67473723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223740	NA	P-0013449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	44	499	0	ENST00000327367.4:c.803G>A	p.Arg268His	p.R268H	ENST00000327367	NM_005902.3	268	cGc/cAc	6/9	1	2	FACETS	0.692	0.582	0.814	0.692	0.582	0.814	SUBCLONAL	1	TRUE	1	0.333790882379502	2		499	381	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0013449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	191	433	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.150847100293468	5	FACETS	1	0.959	1	1	0.959	1	INDETERMINATE	3	TRUE	2	0.333790882379502	5		433	550	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479810	67479810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863223746	NA	P-0013449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	66	544	0	ENST00000327367.4:c.1117C>T	p.Arg373Cys	p.R373C	ENST00000327367	NM_005902.3	373	Cgc/Tgc	8/9	1	2	FACETS	0.875	0.762	0.997	0.875	0.762	0.997	CLONAL	1	TRUE	1	0.333790882379502	2		544	452	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057835	27057835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	134	872	2	ENST00000324856.7:c.1543C>T	p.Gln515Ter	p.Q515*	ENST00000324856	NM_006015.4	515	Cag/Tag	3/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.333790882379502	2		874	619	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164949	47164949	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	60	308	0	ENST00000409792.3:c.1177C>T	p.Arg393Ter	p.R393*	ENST00000409792	NM_014159.6	393	Cga/Tga	3/21	0.335575303853703	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.333790882379502	1		308	210	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569823	67569823	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1230037871	NA	P-0013449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	36	295	0	ENST00000274335.5:c.484C>T	p.Arg162Ter	p.R162*	ENST00000274335		162	Cga/Tga	3/15	1	2	FACETS	0.656	0.54	0.784	0.656	0.54	0.784	SUBCLONAL	1	TRUE	1	0.333790882379502	2		295	329	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111958608	111958608	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200671534	NA	P-0013449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	52	286	0	ENST00000375549.3:c.80G>A	p.Arg27Lys	p.R27K	ENST00000375549	NM_003002.3	27	aGa/aAa	2/4	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.333790882379502	2		286	250	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591263	67591264	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0013449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	74	370	1	ENST00000274335.5:c.1761_1762del	p.Gly588CysfsTer13	p.G588Cfs*13	ENST00000274335		587	aaAGgt/aagt	13/15	1	2	FACETS	0.941	0.827	1	0.941	0.827	1	CLONAL	1	TRUE	1	0.333790882379502	2		371	471	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119807	70119808	+	stop_gained	Nonsense_Mutation	DNP	TC	TC	AA	novel	NA	P-0013449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	56	521	0	ENST00000245479.2:c.809_810delinsAA	p.Phe270Ter	p.F270*	ENST00000245479	NM_000346.3	270	tTC/tAA	3/3	1	2	FACETS	0.86	0.74	0.991	0.86	0.74	0.991	CLONAL	1	TRUE	1	0.333790882379502	2		521	390	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0013456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	108	497	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.77	0.692	0.853	0.77	0.692	0.853	SUBCLONAL	1	FALSE	1	0.415031358996974	2		497	676	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764146326	NA	P-0013456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	123	680	0	ENST00000269305.4:c.841G>A	p.Asp281Asn	p.D281N	ENST00000269305	NM_001126112.2	281	Gac/Aac	8/11	0.415031358996974	1	FACETS	0.905	0.822	0.991	0.905	0.822	0.991	CLONAL	1	FALSE	0	0.415031358996974	1		680	519	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48586262	48586262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658694	NA	P-0013456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	119	451	0	ENST00000342988.3:c.931C>T	p.Gln311Ter	p.Q311*	ENST00000342988	NM_005359.5	311	Cag/Tag	8/12	0.415031358996974	1	FACETS	0.955	0.867	1	0.955	0.867	1	CLONAL	1	FALSE	0	0.415031358996974	1		451	476	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157098	106157098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763242683	NA	P-0013456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	148	733	0	ENST00000380013.4:c.1999C>T	p.His667Tyr	p.H667Y	ENST00000380013	NM_001127208.2	667	Cat/Tat	3/11	1	2	FACETS	0.869	0.794	0.947	0.869	0.794	0.947	CLONAL	1	FALSE	1	0.415031358996974	2		733	821	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665281	176665281	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750684515	NA	P-0013456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	136	578	0	ENST00000439151.2:c.3965G>A	p.Arg1322Gln	p.R1322Q	ENST00000439151	NM_022455.4	1322	cGa/cAa	7/23	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	1	0.415031358996974	2		578	640	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056434	26056434	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	117	269	0	ENST00000343677.2:c.223A>G	p.Lys75Glu	p.K75E	ENST00000343677	NM_005319.3	75	Aaa/Gaa	1/1	0.415031358996974	5	FACETS	0.775	0.701	0.853			1	SUBCLONAL	2	FALSE	NA	0.415031358996974	5		269	590	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221290	1221307	+	inframe_deletion	In_Frame_Del	DEL	CTACGCCATCCCGGGCGA	CTACGCCATCCCGGGCGA	-	novel	NA	P-0013456-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	152	698	1	ENST00000326873.7:c.815_832del	p.Tyr272_Asp277del	p.Y272_D277del	ENST00000326873	NM_000455.4	271	agCTACGCCATCCCGGGCGAc/agc	6/10	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	FALSE	NA	0.415031358996974	2		699	580	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0013457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	470	630	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.676841834978874	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.676841834978874	1		630	865	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158594951	158594951	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0013457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	601	951	0	ENST00000263640.3:c.1395+1G>A		p.X465_splice	ENST00000263640	NM_001105.4	465			1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.676841834978874	2		951	1626	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852054	128852054	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	338	665	0	ENST00000249373.3:c.2126G>T	p.Arg709Leu	p.R709L	ENST00000249373	NM_005631.4	709	cGg/cTg	12/12	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.676841834978874	2		665	973	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0013459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	43	692	2	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.203322608106918	1	FACETS	0.715	0.6	0.841	0.715	0.6	0.841	SUBCLONAL	1	TRUE	0	0.3	1		694	341	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665213	138665213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	32	677	0	ENST00000330315.3:c.352G>A	p.Glu118Lys	p.E118K	ENST00000330315	NM_023067.3	118	Gag/Aag	1/1	1	2	FACETS	0.563	0.457	0.682	0.563	0.457	0.682	SUBCLONAL	1	TRUE	1	0.3	2		677	379	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796616	42796616	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0013459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	15	219	0	ENST00000575354.2:c.3173C>G	p.Ser1058Ter	p.S1058*	ENST00000575354	NM_015125.3	1058	tCa/tGa	13/20	0.3	1	FACETS	0.702	0.519	0.919	0.702	0.519	0.919	CLONAL	1	TRUE	0	0.3	1		219	121	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412639	139412639	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1037236860	NA	P-0013459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	19	531	2	ENST00000277541.6:c.1205C>T	p.Ser402Leu	p.S402L	ENST00000277541	NM_017617.3	402	tCg/tTg	7/34	0.203322608106918	1	FACETS	0.409	0.311	0.525	0.409	0.311	0.525	SUBCLONAL	1	TRUE	0	0.3	1		533	263	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551339	29551339	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	25	481	0	ENST00000389048.3:c.1291C>A	p.Pro431Thr	p.P431T	ENST00000389048	NM_004304.4	431	Cca/Aca	6/29	1	2	FACETS	0.608	0.48	0.754	0.608	0.48	0.754	SUBCLONAL	1	TRUE	1	0.3	2		481	274	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098809	178098809	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519923	NA	P-0013459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	51	715	0	ENST00000397062.3:c.236A>T	p.Glu79Val	p.E79V	ENST00000397062	NM_006164.4	79	gAg/gTg	2/5	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.3	2		715	306	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446859	187446859	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	21	499	0	ENST00000232014.4:c.1334G>T	p.Arg445Leu	p.R445L	ENST00000232014	NM_001130845.1	445	cGg/cTg	5/10	1	2	FACETS	0.452	0.348	0.573	0.452	0.348	0.573	SUBCLONAL	1	TRUE	1	0.3	2		499	310	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962977	38962977	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0013459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	24	299	0	ENST00000357387.3:c.1566+1G>T		p.X522_splice	ENST00000357387	NM_152756.3	522			1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.3	2		299	129	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056554	26056554	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	31	171	0	ENST00000343677.2:c.103G>T	p.Ala35Ser	p.A35S	ENST00000343677	NM_005319.3	35	Gcg/Tcg	1/1	1	2	FACETS	0.807	0.665	0.962	1	0.952	1	CLONAL	2	TRUE	1	0.3	2		171	128	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864386	151864386	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	19	471	0	ENST00000262189.6:c.9595G>C	p.Glu3199Gln	p.E3199Q	ENST00000262189	NM_170606.2	3199	Gaa/Caa	42/59	1	2	FACETS	0.656	0.5	0.838	0.656	0.5	0.838	SUBCLONAL	1	TRUE	1	0.3	2		471	193	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123018	5123018	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	28	383	0	ENST00000381652.3:c.3074C>T	p.Ser1025Leu	p.S1025L	ENST00000381652	NM_004972.3	1025	tCa/tTa	23/25	0.203322608106918	1	FACETS	1	0.836	1	1	0.836	1	CLONAL	1	TRUE	0	0.3	1		383	153	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518261	8518261	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	38	432	0	ENST00000356435.5:c.1130G>T	p.Arg377Leu	p.R377L	ENST00000356435		377	cGc/cTc	10/35	0.203322608106918	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.3	1		432	175	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376938	118376938	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	24	458	1	ENST00000534358.1:c.10331C>T	p.Ser3444Leu	p.S3444L	ENST00000534358	NM_005933.3	3444	tCa/tTa	27/36	1	2	FACETS	0.635	0.499	0.79	0.635	0.499	0.79	SUBCLONAL	1	TRUE	1	0.3	2		459	252	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562665	95562665	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	21	427	0	ENST00000393063.1:c.4592C>T	p.Ser1531Leu	p.S1531L	ENST00000393063	NM_030621.3	1531	tCa/tTa	24/28	0.19818445989746	1	FACETS	0.626	0.485	0.789	0.626	0.485	0.789	SUBCLONAL	1	TRUE	0	0.3	1		427	190	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124222	2124222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	17	490	0	ENST00000219476.3:c.2377G>A	p.Glu793Lys	p.E793K	ENST00000219476	NM_000548.3	793	Gag/Aag	22/42	1	2	FACETS	0.408	0.304	0.531	0.408	0.304	0.531	SUBCLONAL	1	TRUE	1	0.3	2		490	278	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220384	1220393	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGATTGAC	GCTGATTGAC	-	novel	NA	P-0013459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	63	519	0	ENST00000326873.7:c.478_487del	p.Leu160AlafsTer124	p.L160Afs*124	ENST00000326873	NM_000455.4	159	caGCTGATTGAC/ca	4/10	0.3	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.3	1		519	304	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039328	47039328	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013459-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	42	709	0	ENST00000377604.3:c.955del	p.Ala319ProfsTer16	p.A319Pfs*16	ENST00000377604	NM_001204468.1	317	ctG/ct	10/24	0.3	1	FACETS	0.645	0.54	0.761	0.645	0.54	0.761	SUBCLONAL	1	TRUE	0	0.3	1		709	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0013465-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	654	769	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.747577054900394	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.775946673906051	2		770	838	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0013481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1290	98	876	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.14	2		876	1388	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500886	8500886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	41	705	0	ENST00000356435.5:c.1996C>T	p.Pro666Ser	p.P666S	ENST00000356435		666	Cct/Tct	13/35	1	2	FACETS	0.556	0.461	0.663	0.556	0.461	0.663	SUBCLONAL	1	TRUE	1	0.14	2		705	1053	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148875	119148875	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs397517076	NA	P-0013481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	29	337	1	ENST00000264033.4:c.1096-1G>T		p.X366_splice	ENST00000264033	NM_005188.3	366			1	2	FACETS	0.792	0.634	0.972	0.792	0.634	0.972	CLONAL	1	TRUE	1	0.14	2		338	523	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0013481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	13	157	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.728	0.519	0.984	0.728	0.519	0.984	CLONAL	1	TRUE	1	0.14	2		157	255	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92300791	92300791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	38	403	0	ENST00000265734.4:c.596C>T	p.Pro199Leu	p.P199L	ENST00000265734	NM_001259.6	199	cCc/cTc	5/8	1	2	FACETS	0.782	0.645	0.936	0.782	0.645	0.936	CLONAL	1	TRUE	1	0.14	2		403	694	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593603	55593603	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913235	NA	P-0013481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	67	824	0	ENST00000288135.5:c.1669T>A	p.Trp557Arg	p.W557R	ENST00000288135	NM_000222.2	557	Tgg/Agg	11/21	1	2	FACETS	0.852	0.737	0.976	0.852	0.737	0.976	CLONAL	1	TRUE	1	0.14	2		824	1124	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257107	16257107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1476670608	NA	P-0013481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	55	596	1	ENST00000375759.3:c.4372C>T	p.Arg1458Cys	p.R1458C	ENST00000375759	NM_015001.2	1458	Cgt/Tgt	11/15	1	2	FACETS	0.835	0.712	0.97	0.835	0.712	0.97	CLONAL	1	TRUE	1	0.14	2		597	941	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539639	187539639	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	65	755	0	ENST00000441802.2:c.8101C>T	p.Pro2701Ser	p.P2701S	ENST00000441802	NM_005245.3	2701	Cca/Tca	10/27	1	2	FACETS	0.918	0.794	1	0.918	0.794	1	CLONAL	1	TRUE	1	0.14	2		755	1011	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629463	187629463	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	68	644	2	ENST00000441802.2:c.1519C>T	p.His507Tyr	p.H507Y	ENST00000441802	NM_005245.3	507	Cat/Tat	2/27	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.14	2		646	949	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562935	29562935	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1567852753	NA	P-0013481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	71	779	0	ENST00000356175.3:c.3871-1G>A		p.X1291_splice	ENST00000356175	NM_000267.3	1291			1	2	FACETS	0.918	0.799	1	0.918	0.799	1	CLONAL	1	TRUE	1	0.14	2		779	1105	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58725388	58725388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1312	86	1025	1	ENST00000305921.3:c.962C>T	p.Pro321Leu	p.P321L	ENST00000305921	NM_003620.3	321	cCa/cTa	4/6	1	2	FACETS	0.879	0.774	0.992	0.879	0.774	0.992	CLONAL	1	TRUE	1	0.14	2		1026	1398	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192659	138192659	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	34	394	0	ENST00000237289.4:c.295+1del		p.G99fs	ENST00000237289	NM_001270507.1	99	Ggt/gt	2/9	1	2	FACETS	0.724	0.59	0.876	0.724	0.59	0.876	SUBCLONAL	1	TRUE	1	0.14	2		394	671	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0013482-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	119	387	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	0.941	0.861	1	0.941	0.861	1	CLONAL	1	TRUE	1	0.785638441599894	2		387	322	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442059	52442059	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013482-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	187	552	0	ENST00000460680.1:c.290T>A	p.Leu97Gln	p.L97Q	ENST00000460680	NM_004656.3	97	cTg/cAg	5/17	0.785638441599894	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.785638441599894	1		552	264	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0013484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	312	456	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.82844622628143	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.82844622628143	2		457	371	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0013484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	1018	371	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.82844622628143	7	FACETS	0.99	0.968	1	0.99	0.968	1	CLONAL	5	TRUE	2	0.82844622628143	7		371	1525	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037877	49037877	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	187	656	0	ENST00000267163.4:c.2117G>A	p.Cys706Tyr	p.C706Y	ENST00000267163	NM_000321.2	706	tGt/tAt	21/27	0.82844622628143	2	FACETS	0.977	0.938	1	0.977	0.938	1	CLONAL	2	TRUE	0	0.82844622628143	2		656	231	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849822	156849822	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1249	478	687	1	ENST00000524377.1:c.2078G>A	p.Trp693Ter	p.W693*	ENST00000524377	NM_002529.3	693	tGg/tAg	16/17	0.82844622628143	7	FACETS	1	0.972	1	0.41	0.391	0.43	CLONAL	2	TRUE	2	0.82844622628143	7		688	1727	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519538	137519538	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs148158267	NA	P-0013484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	231	674	0	ENST00000367739.4:c.1100C>G	p.Pro367Arg	p.P367R	ENST00000367739	NM_000416.2	367	cCg/cGg	7/7	0.82844622628143	4	FACETS	1	0.957	1	0.345	0.322	0.369	CLONAL	1	TRUE	1	0.82844622628143	4		674	985	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644916	67644916	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	447	611	0	ENST00000264010.4:c.181G>T	p.Val61Leu	p.V61L	ENST00000264010	NM_006565.3	61	Gtg/Ttg	3/12	0.611909345579459	4	FACETS	0.971	0.93	1	0.971	0.93	1	CLONAL	2	TRUE	2	0.82844622628143	4		611	1016	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755745	39755745	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	251	395	0	ENST00000288319.7:c.1020G>T	p.Lys340Asn	p.K340N	ENST00000288319	NM_182918.3	340	aaG/aaT	10/10	0.82844622628143	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.82844622628143	3		395	396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577560	7577565	+	inframe_deletion	In_Frame_Del	DEL	AACTGT	AACTGT	-	novel	NA	P-0013484-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	464	657	0	ENST00000269305.4:c.716_721del	p.Asn239_Ser241delinsThr	p.N239_S241delinsT	ENST00000269305	NM_001126112.2	239	aACAGTTcc/acc	7/11	0.82844622628143	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.82844622628143	2		657	554	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0013490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	66	424	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.595	0.516	0.681	0.595	0.516	0.681	SUBCLONAL	1	TRUE	1	0.32	2		424	693	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649609	206649609	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	64	469	0	ENST00000367120.3:c.444G>T	p.Glu148Asp	p.E148D	ENST00000367120	NM_014002.3	148	gaG/gaT	6/22	0.213845142781357	3	FACETS	0.61	0.527	0.7	0.305	0.263	0.35	SUBCLONAL	1	TRUE	1	0.32	3		469	761	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183619	10183619	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	46	476	2	ENST00000256474.2:c.88G>T	p.Gly30Trp	p.G30W	ENST00000256474	NM_000551.3	30	Ggg/Tgg	1/3	1	2	FACETS	0.402	0.337	0.473	0.402	0.337	0.473	SUBCLONAL	1	TRUE	1	0.32	2		478	716	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045854	143045854	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	64	606	1	ENST00000262992.4:c.1780G>T	p.Val594Leu	p.V594L	ENST00000262992	NM_001101669.1	594	Gtg/Ttg	17/24	1	2	FACETS	0.529	0.457	0.607	0.529	0.457	0.607	SUBCLONAL	1	TRUE	1	0.32	2		607	756	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149453057	149453057	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0013490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	35	420	0	ENST00000286301.3:c.890-1G>A		p.X297_splice	ENST00000286301	NM_005211.3	297			1	2	FACETS	0.455	0.372	0.548	0.455	0.372	0.548	SUBCLONAL	1	TRUE	1	0.32	2		420	481	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409053	139409053	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	50	746	0	ENST00000277541.6:c.2116G>T	p.Glu706Ter	p.E706*	ENST00000277541	NM_017617.3	706	Gag/Tag	13/34	1	2	FACETS	0.333	0.281	0.39	0.333	0.281	0.39	SUBCLONAL	1	TRUE	1	0.32	2		746	939	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959069	28959069	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	88	729	0	ENST00000282397.4:c.2069C>G	p.Pro690Arg	p.P690R	ENST00000282397	NM_002019.4	690	cCt/cGt	14/30	1	2	FACETS	0.657	0.581	0.738	0.657	0.581	0.738	SUBCLONAL	1	TRUE	1	0.32	2		729	837	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65569036	65569036	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs752477890	NA	P-0013490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	115	618	0	ENST00000358664.4:c.22G>T	p.Glu8Ter	p.E8*	ENST00000358664	NM_002382.4	8	Gag/Tag	1/5	1	2	FACETS	0.942	0.849	1	0.942	0.849	1	CLONAL	1	TRUE	1	0.32	2		618	763	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56363597	56363597	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0013490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	25	235	1	ENST00000348428.3:c.377-1G>T		p.X126_splice	ENST00000348428	NM_006785.3	126			1	2	FACETS	0.648	0.513	0.803	0.648	0.513	0.803	SUBCLONAL	1	TRUE	1	0.32	2		236	241	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221667	22221667	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	28	201	1	ENST00000215832.6:c.64G>T	p.Gly22Trp	p.G22W	ENST00000215832	NM_002745.4	22	Ggg/Tgg	1/9	1	2	FACETS	0.648	0.52	0.794	0.648	0.52	0.794	SUBCLONAL	1	TRUE	1	0.32	2		202	270	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0013490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	18	651	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	1	FACETS	0.159	0.119	0.207	0.159	0.119	0.207	SUBCLONAL	1	TRUE	0	0.32	1		651	594	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0013491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	136	330	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.898	0.822	0.977	0.898	0.822	0.977	CLONAL	1	TRUE	1	0.631010415941472	2		330	480	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913273	NA	P-0013491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	141	301	0	ENST00000263967.3:c.1624G>C	p.Glu542Gln	p.E542Q	ENST00000263967	NM_006218.2	542	Gaa/Caa	10/21	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.631010415941472	2		301	440	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	532	514	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.631010415941472	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.631010415941472	2		514	788	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433848	78433848	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0013491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	301	681	0	ENST00000370768.2:c.250+1G>C		p.X84_splice	ENST00000370768	NM_003902.3	84			1	2	FACETS	0.974	0.92	1	0.974	0.92	1	CLONAL	1	TRUE	1	0.631010415941472	2		681	979	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0013504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	53	497	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		497	1008	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0013504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	42	270	2	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		272	619	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436576	110436576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	69	328	0	ENST00000375856.3:c.1825G>A	p.Ala609Thr	p.A609T	ENST00000375856	NM_003749.2	609	Gcg/Acg	1/2	0.168251223399691	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		328	606	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	103	540	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.955	0.858	1	0.955	0.858	1	CLONAL	1	TRUE	1	0.407024433776447	2		540	530	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0013512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	56	330	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.93	0.802	1	0.93	0.802	1	CLONAL	1	TRUE	1	0.407024433776447	2		330	296	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0013512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	64	969	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.296	0.255	0.341	0.296	0.255	0.341	SUBCLONAL	1	TRUE	1	0.407024433776447	2		970	1062	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752960	128752960	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	243	576	0	ENST00000377970.2:c.1121A>G	p.His374Arg	p.H374R	ENST00000377970	NM_002467.4	374	cAc/cGc	3/3	0.407024433776447	2	FACETS	0.906	0.852	0.961	0.906	0.852	0.961	CLONAL	2	TRUE	0	0.407024433776447	2		576	659	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	27	837	2	ENST00000263967.3:c.317G>A	p.Gly106Asp	p.G106D	ENST00000263967	NM_006218.2	106	gGc/gAc	2/21	1	2	FACETS	0.149	0.117	0.185	0.149	0.117	0.185	SUBCLONAL	1	TRUE	1	0.407024433776447	2		839	893	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451423	187451423	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	57	530	0	ENST00000232014.4:c.59T>C	p.Leu20Pro	p.L20P	ENST00000232014	NM_001130845.1	20	cTc/cCc	3/10	1	2	FACETS	0.461	0.395	0.533	0.461	0.395	0.533	SUBCLONAL	1	TRUE	1	0.407024433776447	2		530	608	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665247	176665247	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886060443	NA	P-0013512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	21	410	0	ENST00000439151.2:c.3931C>T	p.Arg1311Cys	p.R1311C	ENST00000439151	NM_022455.4	1311	Cgc/Tgc	7/23	1	2	FACETS	0.246	0.188	0.313	0.246	0.188	0.313	SUBCLONAL	1	TRUE	1	0.407024433776447	2		410	420	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319964	8319964	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	82	409	0	ENST00000356435.5:c.5537C>T	p.Ala1846Val	p.A1846V	ENST00000356435		1846	gCg/gTg	34/35	1	2	FACETS	0.87	0.77	0.977	0.87	0.77	0.977	CLONAL	1	TRUE	1	0.407024433776447	2		409	463	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840576	36840576	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	53	632	0	ENST00000358127.4:c.1157C>T	p.Thr386Ile	p.T386I	ENST00000358127	NM_001280556.1	386	aCt/aTt	10/10	1	2	FACETS	0.381	0.324	0.444	0.381	0.324	0.444	SUBCLONAL	1	TRUE	1	0.407024433776447	2		632	683	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650036	93650036	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	146	605	0	ENST00000375746.1:c.1587G>C	p.Gln529His	p.Q529H	ENST00000375746	NM_001174167.1	529	caG/caC	12/14	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.407024433776447	2		605	703	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105648	27105648	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	135	636	0	ENST00000324856.7:c.5259del	p.Ser1754LeufsTer16	p.S1754Lfs*16	ENST00000324856	NM_006015.4	1753	gtG/gt	20/20	1	2	FACETS	0.91	0.828	0.996	0.91	0.828	0.996	CLONAL	1	TRUE	1	0.407024433776447	2		636	729	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122982	2122982	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs45517226	NA	P-0013555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	58	881	0	ENST00000219476.3:c.2353C>T	p.Gln785Ter	p.Q785*	ENST00000219476	NM_000548.3	785	Cag/Tag	21/42	1	2	FACETS	0.815	0.703	0.935	0.815	0.703	0.935	CLONAL	1	TRUE	1	0.394403885060791	2		881	361	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133694	2133694	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0013555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	43	883	1	ENST00000219476.3:c.3884-2A>G		p.X1295_splice	ENST00000219476	NM_000548.3	1295			1	2	FACETS	0.713	0.599	0.837	0.713	0.599	0.837	SUBCLONAL	1	TRUE	1	0.394403885060791	2		884	306	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0013574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	33	353	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.174964633538829	2	FACETS	0.802	0.656	0.966	0.401	0.328	0.483	INDETERMINATE	1	TRUE	0	0.291679706415972	2		353	282	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183694	10183694	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	41	472	0	ENST00000256474.2:c.163G>T	p.Glu55Ter	p.E55*	ENST00000256474	NM_000551.3	55	Gag/Tag	1/3	0.152380609765084	3	FACETS	0.997	0.834	1			1	INDETERMINATE	1	TRUE	NA	0.291679706415972	3		472	323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0013597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	150	561	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	0.826430961445783	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.826430961445783	1		561	194	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776783	NA	P-0013597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	74	239	1	ENST00000267163.4:c.1215+1G>A		p.X405_splice	ENST00000267163	NM_000321.2	405			0.826430961445783	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.826430961445783	1		240	91	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361160	70361160	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs79912241	NA	P-0013597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	38	351	0	ENST00000374080.3:c.6348C>A	p.His2116Gln	p.H2116Q	ENST00000374080		2116	caC/caA	43/45	0.470116515482372	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	NA	0.826430961445783	0		351	276	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572404	41572404	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs139310551	NA	P-0013597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	55	516	2	ENST00000263253.7:c.4933C>T	p.Arg1645Ter	p.R1645*	ENST00000263253	NM_001429.3	1645	Cga/Tga	30/31	0.520737619390559	1	FACETS	0.341	0.295	0.39	0.341	0.295	0.39	SUBCLONAL	1	TRUE	0	0.826430961445783	1		518	229	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788617	3788617	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519884	NA	P-0013597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	167	561	1	ENST00000262367.5:c.4337G>T	p.Arg1446Leu	p.R1446L	ENST00000262367	NM_004380.2	1446	cGc/cTc	26/31	1	2	FACETS	0.995	0.926	1	0.995	0.926	1	CLONAL	1	TRUE	1	0.826430961445783	2		562	406	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334768	81334768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	83	604	0	ENST00000222390.5:c.1948G>A	p.Val650Met	p.V650M	ENST00000222390	NM_000601.4	650	Gtg/Atg	17/18	0.638049767095537	1	FACETS	0.402	0.359	0.448	0.402	0.359	0.448	SUBCLONAL	1	TRUE	0	0.826430961445783	1		604	293	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682944	241682944	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	150	341	0	ENST00000366560.3:c.79G>T	p.Gly27Cys	p.G27C	ENST00000366560	NM_000143.3	27	Ggc/Tgc	1/10	0.351211237183084	3	FACETS	0.891	0.831	0.95	0.891	0.831	0.95	INDETERMINATE	2	TRUE	1	0.826430961445783	3		341	288	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432650	49432650	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	153	582	0	ENST00000301067.7:c.8489del	p.Arg2830HisfsTer21	p.R2830Hfs*21	ENST00000301067	NM_003482.3	2830	cGa/ca	34/54	0.520737619390559	1	FACETS	0.739	0.69	0.788	0.739	0.69	0.788	SUBCLONAL	1	TRUE	0	0.826430961445783	1		582	294	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348082	89348082	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	91	1110	1	ENST00000301030.4:c.4868A>T	p.Lys1623Met	p.K1623M	ENST00000301030	NM_001256183.1	1623	aAg/aTg	9/13	0.826430961445783	1	FACETS	0.48	0.433	0.53	0.48	0.433	0.53	SUBCLONAL	1	TRUE	0	0.826430961445783	1		1111	269	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521520	8521520	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	71	490	0	ENST00000356435.5:c.718A>T	p.Ile240Phe	p.I240F	ENST00000356435		240	Atc/Ttc	9/35	0.394312609136373	2	FACETS	0.521	0.458	0.588	0.26	0.229	0.294	INDETERMINATE	1	TRUE	0	0.826430961445783	2		490	330	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401025	139401025	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	186	575	1	ENST00000277541.6:c.3968C>A	p.Ala1323Asp	p.A1323D	ENST00000277541	NM_017617.3	1323	gCc/gAc	24/34	0.394312609136373	2	FACETS	1	0.992	1	0.719	0.679	0.759	INDETERMINATE	1	TRUE	0	0.826430961445783	2		576	313	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0013602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	324	269	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.716687674597542	2		269	776	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934574	NA	P-0013602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	820	669	0	ENST00000269305.4:c.844C>G	p.Arg282Gly	p.R282G	ENST00000269305	NM_001126112.2	282	Cgg/Ggg	8/11	0.716687674597542	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.716687674597542	2		669	1063	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025850	48025850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370157832	NA	P-0013602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	412	617	3	ENST00000234420.5:c.728G>A	p.Arg243His	p.R243H	ENST00000234420	NM_000179.2	243	cGc/cAc	4/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.716687674597542	2		620	1113	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502864	186502864	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	197	818	0	ENST00000323963.5:c.322G>A	p.Ala108Thr	p.A108T	ENST00000323963		108	Gcc/Acc	4/11	1	2	FACETS	0.398	0.367	0.43	0.398	0.367	0.43	SUBCLONAL	1	TRUE	1	0.716687674597542	2		818	1383	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750926	128750928	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	novel	NA	P-0013602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	236	523	0	ENST00000377970.2:c.469_471del	p.Ala157del	p.A157del	ENST00000377970	NM_002467.4	155	GCC/-	2/3	1	2	FACETS	0.897	0.841	0.955	0.897	0.841	0.955	CLONAL	1	TRUE	1	0.716687674597542	2		523	734	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517993	8517993	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	146	666	0	ENST00000356435.5:c.1398G>C	p.Trp466Cys	p.W466C	ENST00000356435		466	tgG/tgC	10/35	1	2	FACETS	0.383	0.349	0.419	0.383	0.349	0.419	SUBCLONAL	1	TRUE	1	0.716687674597542	2		666	1064	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939888	76939888	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0013602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	496	354	0	ENST00000373344.5:c.860T>G	p.Leu287Ter	p.L287*	ENST00000373344	NM_000489.3	287	tTa/tGa	9/35	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.716687674597542	1		354	648	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0013618-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	205	548	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.456779230788069	7	FACETS	0.954	0.893	1	0.954	0.893	1	CLONAL	4	FALSE	3	0.456779230788069	7		548	504	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509469	46509469	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200277706	NA	P-0013618-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	27	494	0	ENST00000262741.5:c.1262T>A	p.Leu421Gln	p.L421Q	ENST00000262741	NM_003629.3	421	cTg/cAg	10/10	0.36044840817142	5	FACETS	0.639	0.509	0.786	0.213	0.169	0.262	SUBCLONAL	1	FALSE	2	0.456779230788069	5		494	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578499	7578529	+	frameshift_variant	Frame_Shift_Del	DEL	TGCACAGGGCAGGTCTTGGCCAGTTGGCAAA	TGCACAGGGCAGGTCTTGGCCAGTTGGCAAA	-	novel	NA	P-0013618-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	116	617	0	ENST00000269305.4:c.401_431del	p.Phe134CysfsTer26	p.F134Cfs*26	ENST00000269305	NM_001126112.2	134	tTTTGCCAACTGGCCAAGACCTGCCCTGTGCAg/tg	5/11	0.372907102490033	3	FACETS	0.904	0.834	0.974			1	CLONAL	3	FALSE	NA	0.456779230788069	3		617	230	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609934	43609942	+	protein_altering_variant	In_Frame_Del	DEL	TGTGCGACG	TGTGCGACG	AGTGGC	novel	NA	P-0013619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	1208	801	4	ENST00000355710.3:c.1886_1894delinsAGTGGC	p.Leu629_Glu632delinsGlnTrpGln	p.L629_E632delinsQWQ	ENST00000355710	NM_020975.4	629	cTGTGCGACGag/cAGTGGCag	11/20	0.313570051838953	6	FACETS	0.978	0.959	0.996			1	CLONAL	6	TRUE	NA	0.469766195346863	6		805	1700	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245401	41245402	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0013619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	181	600	0	ENST00000357654.3:c.2146_2147del	p.Ser716Ter	p.S716*	ENST00000357654	NM_007294.3	716	AGt/t	10/23	0.136894674825763	3	FACETS	0.848	0.781	0.918	0.283	0.26	0.306	INDETERMINATE	1	TRUE	0	0.469766195346863	3		600	1122	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048542	180048542	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013619-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	25	188	0	ENST00000261937.6:c.2020G>A	p.Ala674Thr	p.A674T	ENST00000261937	NM_182925.4	674	Gcc/Acc	13/30	0.443822377595175	3	FACETS	0.743	0.59	0.915	0.248	0.196	0.305	CLONAL	1	TRUE	0	0.469766195346863	3		188	177	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	664	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.754166061706323	3	FACETS	1	0.978	1			1	CLONAL	2	TRUE	NA	0.754166061706323	3		426	1198	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0013628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	537	769	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.754166061706323	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.754166061706323	1		770	772	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878081	48878112	+	frameshift_variant	Frame_Shift_Del	DEL	CACCGCCGCCGCTGCCGCCGCGGAACCCCCGG	CACCGCCGCCGCTGCCGCCGCGGAACCCCCGG	-	novel	NA	P-0013628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	240	154	0	ENST00000267163.4:c.45_76del	p.Ala17ProfsTer3	p.A17Pfs*3	ENST00000267163	NM_000321.2	11	gcCACCGCCGCCGCTGCCGCCGCGGAACCCCCGGca/gcca	1/27	0.754166061706323	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.754166061706323	1		154	365	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420067	41420067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	110	538	0	ENST00000373198.4:c.254G>A	p.Gly85Asp	p.G85D	ENST00000373198	NM_133170.3	85	gGc/gAc	3/32	NA	2	FACETS	0.402	0.361	0.446			1	INDETERMINATE	1	TRUE	NA	0.754166061706323	2		538	725	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533694	41533694	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013628-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	56	691	0	ENST00000263253.7:c.1660G>A	p.Gly554Ser	p.G554S	ENST00000263253	NM_001429.3	554	Ggt/Agt	8/31	0.754166061706323	1	FACETS	0.135	0.115	0.157	0.135	0.115	0.157	SUBCLONAL	1	TRUE	0	0.754166061706323	1		691	686	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	51	389	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.3060449797804	2		389	228	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231437	46231437	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	410	519	0	ENST00000334344.6:c.1277C>T	p.Thr426Met	p.T426M	ENST00000334344	NM_152641.2	426	aCg/aTg	10/21	0.3060449797804	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	TRUE	0	0.3060449797804	3		519	1000	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520017	NA	P-0013652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	234	535	0	ENST00000326873.7:c.647C>T	p.Ser216Phe	p.S216F	ENST00000326873	NM_000455.4	216	tCc/tTc	5/10	1	2	FACETS	1	0.973	1	1	0.995	1	CLONAL	2	TRUE	1	0.3060449797804	2		535	716	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136279	202136279	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	318	667	2	ENST00000358485.4:c.523G>T	p.Glu175Ter	p.E175*	ENST00000358485	NM_001080125.1	175	Gaa/Taa	3/9	0.300555681019773	2	FACETS	0.871	0.822	0.921	0.871	0.822	0.921	CLONAL	2	TRUE	0	0.3060449797804	2		669	1193	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112884135	112884135	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	140	453	0	ENST00000351677.2:c.70G>A	p.Gly24Arg	p.G24R	ENST00000351677	NM_002834.3	24	Gga/Aga	2/16	0.3060449797804	3	FACETS	1	0.966	1	0.375	0.341	0.411	CLONAL	1	TRUE	0	0.3060449797804	3		453	937	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371626	89371626	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	124	545	0	ENST00000301030.4:c.214G>C	p.Asp72His	p.D72H	ENST00000301030	NM_001256183.1	72	Gac/Cac	4/13	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.3060449797804	2		545	744	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293860	1293860	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573210043	NA	P-0013652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	83	485	0	ENST00000310581.5:c.1141C>T	p.Arg381Cys	p.R381C	ENST00000310581	NM_198253.2	381	Cgc/Tgc	2/16	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.3060449797804	2		485	506	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861079	35861079	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	95	377	0	ENST00000303115.3:c.208G>C	p.Glu70Gln	p.E70Q	ENST00000303115	NM_002185.3	70	Gaa/Caa	2/8	1	2	FACETS	0.85	0.757	0.95	0.85	0.757	0.95	CLONAL	1	TRUE	1	0.3060449797804	2		377	730	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880096	151880096	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	193	720	1	ENST00000262189.6:c.5228G>A	p.Arg1743Lys	p.R1743K	ENST00000262189	NM_170606.2	1743	aGa/aAa	35/59	1	2	FACETS	0.963	0.889	1	0.963	0.889	1	CLONAL	1	TRUE	1	0.3060449797804	2		721	1310	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399799	139399799	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554727954	NA	P-0013652-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	83	448	1	ENST00000277541.6:c.4549G>A	p.Asp1517Asn	p.D1517N	ENST00000277541	NM_017617.3	1517	Gac/Aac	25/34	1	2	FACETS	0.854	0.754	0.961	0.854	0.754	0.961	CLONAL	1	TRUE	1	0.3060449797804	2		449	635	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964358	55964358	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	46	845	4	ENST00000263923.4:c.2455C>T	p.Arg819Ter	p.R819*	ENST00000263923	NM_002253.2	819	Cga/Tga	17/30	1	2	FACETS	1	0.882	1	1	0.975	1	CLONAL	2	TRUE	1	0.308364090890286	2		849	145	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0013696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	37	313	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	0.283823815799552	3	FACETS	0.383	0.316	0.459	0.128	0.105	0.153	INDETERMINATE	1	TRUE	0	0.473687304309719	3		313	504	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222983	1222983	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs398123406	NA	P-0013696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	50	218	1	ENST00000326873.7:c.921-1G>T		p.X307_splice	ENST00000326873	NM_000455.4	307			0.473687304309719	1	FACETS	0.814	0.7	0.935	0.814	0.7	0.935	CLONAL	1	TRUE	0	0.473687304309719	1		219	198	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305390	65305390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1324660438	NA	P-0013696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	43	539	0	ENST00000342505.4:c.2738A>T	p.Glu913Val	p.E913V	ENST00000342505	NM_002227.2	913	gAg/gTg	20/25	0.252640047383434	4	FACETS	0.316	0.263	0.374			1	INDETERMINATE	1	TRUE	NA	0.473687304309719	4		539	848	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711968	89711968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	105	210	0	ENST00000371953.3:c.586C>T	p.His196Tyr	p.H196Y	ENST00000371953	NM_000314.4	196	Cac/Tac	6/9	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.473687304309719	2		210	375	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469922	25469922	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs369109129	NA	P-0013696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	67	282	0	ENST00000264709.3:c.1120C>T	p.Gln374Ter	p.Q374*	ENST00000264709	NM_175629.2	374	Cag/Tag	9/23	1	2	FACETS	0.742	0.648	0.843	0.742	0.648	0.843	SUBCLONAL	1	TRUE	1	0.473687304309719	2		282	381	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587119	189587119	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	52	353	1	ENST00000264731.3:c.1136G>T	p.Arg379Leu	p.R379L	ENST00000264731	NM_003722.4	379	cGt/cTt	9/14	1	2	FACETS	0.458	0.39	0.533	0.458	0.39	0.533	SUBCLONAL	1	TRUE	1	0.473687304309719	2		354	479	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140934	37140934	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	110	401	0	ENST00000373509.5:c.770del	p.Gln257ArgfsTer17	p.Q257Rfs*17	ENST00000373509	NM_002648.3	257	cAg/cg	5/6	0.473687304309719	4	FACETS	0.926	0.833	1	0.309	0.277	0.342	CLONAL	1	TRUE	1	0.473687304309719	4		401	739	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878215	151878215	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	28	362	0	ENST00000262189.6:c.6730A>T	p.Met2244Leu	p.M2244L	ENST00000262189	NM_170606.2	2244	Atg/Ttg	36/59	0.283823815799552	3	FACETS	0.286	0.227	0.352	0.095	0.075	0.118	INDETERMINATE	1	TRUE	0	0.473687304309719	3		362	512	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540179	23540179	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	16	51	0	ENST00000380871.4:c.224A>G	p.Gln75Arg	p.Q75R	ENST00000380871	NM_006167.3	75	cAg/cGg	1/2	0.213944741769725	2	FACETS	0.614	0.459	0.794	0.307	0.229	0.397	INDETERMINATE	1	TRUE	0	0.473687304309719	2		51	110	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0013717-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	22	549	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	1	2	FACETS	0.041	0.031	0.052	0.041	0.031	0.052	SUBCLONAL	1	TRUE	1	1.04	2		549	1043	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692980	89692980	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1060500126	NA	P-0013717-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	15	265	0	ENST00000371953.3:c.464A>G	p.Tyr155Cys	p.Y155C	ENST00000371953	NM_000314.4	155	tAt/tGt	5/9	1	2	FACETS	0.073	0.053	0.097	0.073	0.053	0.097	SUBCLONAL	1	TRUE	1	1.04	2		265	396	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510048	187510048	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	141	566	0	ENST00000441802.2:c.13465T>G	p.Tyr4489Asp	p.Y4489D	ENST00000441802	NM_005245.3	4489	Tat/Gat	27/27	0.547255576846488	4	FACETS	0.904	0.825	0.987	0.452	0.412	0.494	CLONAL	1	TRUE	2	0.730113919682198	4		566	739	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637541	176637541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	160	474	0	ENST00000439151.2:c.2141G>A	p.Gly714Asp	p.G714D	ENST00000439151	NM_022455.4	714	gGt/gAt	5/23	0.515002715608403	4	FACETS	1	0.966	1	0.546	0.502	0.592	CLONAL	1	TRUE	2	0.730113919682198	4		474	694	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344155	70344155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778208176	NA	P-0013724-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	225	855	0	ENST00000374080.3:c.1891C>T	p.Pro631Ser	p.P631S	ENST00000374080		631	Ccc/Tcc	13/45	0.315943759842871	6	FACETS	1	0.975	1	0.184	0.17	0.198	INDETERMINATE	1	TRUE	0	0.730113919682198	6		855	1374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0013726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	375	609	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.687754013066798	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.687754013066798	2		609	525	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0013726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	80	332	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.687754013066798	2		332	195	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653803	89653803	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	188	509	0	ENST00000371953.3:c.101C>G	p.Ala34Gly	p.A34G	ENST00000371953	NM_000314.4	34	gCt/gGt	2/9	0.687754013066798	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.687754013066798	1		509	340	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832124	72832124	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1399108891	NA	P-0013726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	322	1171	0	ENST00000268489.5:c.4457C>G	p.Thr1486Ser	p.T1486S	ENST00000268489	NM_006885.3	1486	aCc/aGc	9/10	1	2	FACETS	0.972	0.92	1	0.972	0.92	1	CLONAL	1	TRUE	1	0.687754013066798	2		1171	963	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980913	40980913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763915400	NA	P-0013726-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	127	417	0	ENST00000373198.4:c.1573G>A	p.Ala525Thr	p.A525T	ENST00000373198	NM_133170.3	525	Gct/Act	10/32	0.163384572644298	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.687754013066798	0		417	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577070	7577070	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	179	887	0	ENST00000269305.4:c.868del	p.Arg290AlafsTer55	p.R290Afs*55	ENST00000269305	NM_001126112.2	290	Cgc/gc	8/11	0.399011935508999	2	FACETS	0.961	0.901	1	0.961	0.901	1	CLONAL	2	FALSE	0	0.520304691449457	2		887	358	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55225430	55225430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	32	520	1	ENST00000275493.2:c.1282G>A	p.Gly428Ser	p.G428S	ENST00000275493	NM_005228.3	428	Ggc/Agc	11/28	0.185350938128619	6	FACETS	0.419	0.339	0.51	0.14	0.113	0.17	INDETERMINATE	1	FALSE	3	0.520304691449457	6		521	599	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	38	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.844	1	1	0.844	1	CLONAL	1	TRUE	1	0.12	2		426	618	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0013750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	38	651	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.611	0.503	0.733	0.611	0.503	0.733	SUBCLONAL	1	TRUE	1	0.12	2		651	1037	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0013750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	27	457	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.847	0.673	1	0.847	0.673	1	CLONAL	1	TRUE	1	0.12	2		457	531	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692790	89692790	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554898067	NA	P-0013750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	22	432	0	ENST00000371953.3:c.274G>T	p.Asp92Tyr	p.D92Y	ENST00000371953	NM_000314.4	92	Gac/Tac	5/9	1	2	FACETS	0.843	0.652	1	0.843	0.652	1	CLONAL	1	TRUE	1	0.12	2		432	435	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0013751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	128	353	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.180280855331095	2	FACETS	1	0.978	1	0.627	0.569	0.687	INDETERMINATE	1	TRUE	0	0.321631574885177	2		353	635	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063717	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0013751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	61	353	0	ENST00000412916.2:c.165+1G>C		p.X55_splice	ENST00000412916		55			0.321631574885177	1	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	0	0.321631574885177	1		353	311	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0013751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	26	1354	2	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	1	2	FACETS	0.179	0.141	0.223	0.179	0.141	0.223	SUBCLONAL	1	TRUE	1	0.321631574885177	2		1356	904	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835717	68835717	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	53	921	0	ENST00000261769.5:c.310del	p.Asp104ThrfsTer13	p.D104Tfs*13	ENST00000261769	NM_004360.3	103	tGg/tg	3/16	0.321631574885177	1	FACETS	0.285	0.241	0.332	0.285	0.241	0.332	SUBCLONAL	1	TRUE	0	0.321631574885177	1		921	972	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853280	68853281	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0013751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	121	791	0	ENST00000261769.5:c.1664_1665del	p.His555ArgfsTer32	p.H555Rfs*32	ENST00000261769	NM_004360.3	555	CAc/c	11/16	0.321631574885177	1	FACETS	0.805	0.728	0.887	0.805	0.728	0.887	CLONAL	1	TRUE	0	0.321631574885177	1		791	784	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	51	540	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.711	0.602	0.832	0.711	0.602	0.832	SUBCLONAL	1	TRUE	1	0.14	2		540	1024	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0013767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	45	424	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.63	0.527	0.744	0.63	0.527	0.744	SUBCLONAL	1	TRUE	1	0.14	2		424	1021	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044595	47044595	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	43	392	2	ENST00000377604.3:c.2092G>T	p.Glu698Ter	p.E698*	ENST00000377604	NM_001204468.1	698	Gag/Tag	18/24	1	1	FACETS	0.824	0.688	0.976	0.824	0.688	0.976	CLONAL	1	TRUE	0	0.14	1		394	693	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745576	162745576	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013767-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	68	707	0	ENST00000367921.3:c.1991A>C	p.Gln664Pro	p.Q664P	ENST00000367921	NM_006182.2	664	cAg/cCg	15/18	0.123617934676533	3	FACETS	0.842	0.729	0.964	0.421	0.364	0.482	CLONAL	1	TRUE	1	0.14	3		707	1235	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0013785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	187	270	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.338635282572505	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.39253583510186	2		272	409	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0013785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	421	695	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.351748692634685	4	FACETS	0.942	0.9	0.985	0.942	0.9	0.985	CLONAL	3	TRUE	1	0.39253583510186	4		695	1057	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411576	63411576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	493	491	3	ENST00000330258.3:c.1591C>T	p.Arg531Ter	p.R531*	ENST00000330258	NM_152424.3	531	Cga/Tga	2/2	0.271260355397805	2	FACETS	1	0.972	1			1	CLONAL	3	TRUE	NA	0.39253583510186	2		494	831	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021190	31021190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369058266	NA	P-0013785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	344	620	0	ENST00000375687.4:c.1189C>T	p.Arg397Cys	p.R397C	ENST00000375687	NM_015338.5	397	Cgt/Tgt	12/13	0.164145110330988	4	FACETS	1	0.981	1	1	0.981	1	INDETERMINATE	2	TRUE	2	0.39253583510186	4		620	1137	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0013786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	429	387	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.479209137408745	2	FACETS	0.784	0.751	0.817	0.784	0.751	0.817	SUBCLONAL	2	TRUE	0	0.588496406207808	2		388	930	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0013786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	166	565	1	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.519831035490651	1	FACETS	0.604	0.557	0.653	0.604	0.557	0.653	SUBCLONAL	1	TRUE	0	0.588496406207808	1		566	659	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922363	178922363	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	164	494	0	ENST00000263967.3:c.1132T>C	p.Cys378Arg	p.C378R	ENST00000263967	NM_006218.2	378	Tgt/Cgt	6/21	1	2	FACETS	0.824	0.759	0.892	0.824	0.759	0.892	CLONAL	1	TRUE	1	0.588496406207808	2		494	676	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089513	27089513	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	175	506	0	ENST00000324856.7:c.2472del	p.Ser825ValfsTer8	p.S825Vfs*8	ENST00000324856	NM_006015.4	823	taC/ta	8/20	1	2	FACETS	0.677	0.623	0.732	0.677	0.623	0.732	SUBCLONAL	1	TRUE	1	0.588496406207808	2		506	879	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748477	40748477	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	253	730	0	ENST00000392038.2:c.405G>C	p.Glu135Asp	p.E135D	ENST00000392038	NM_001626.4	135	gaG/gaC	5/14	1	2	FACETS	0.806	0.754	0.859	0.806	0.754	0.859	CLONAL	1	TRUE	1	0.588496406207808	2		730	1067	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855565	45855565	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555775416	NA	P-0013786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	199	692	1	ENST00000391945.4:c.2092C>T	p.Gln698Ter	p.Q698*	ENST00000391945	NM_000400.3	698	Cag/Tag	22/23	1	2	FACETS	0.761	0.705	0.818	0.761	0.705	0.818	SUBCLONAL	1	TRUE	1	0.588496406207808	2		693	889	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258207	16258207	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013808-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	106	844	1	ENST00000375759.3:c.5474del	p.Lys1825ArgfsTer9	p.K1825Rfs*9	ENST00000375759	NM_015001.2	1824	tcA/tc	11/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.171770405153229	2		845	916	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945173	44945173	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013808-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	61	536	0	ENST00000377967.4:c.3497G>A	p.Trp1166Ter	p.W1166*	ENST00000377967	NM_021140.2	1166	tGg/tAg	24/29	1	1	FACETS	0.955	0.829	1	1	0.978	1	CLONAL	2	FALSE	0	0.171770405153229	1		536	340	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057329	30057329	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs794728682	NA	P-0013815-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	21	470	1	ENST00000338641.4:c.810+1G>A		p.X270_splice	ENST00000338641	NM_000268.3	270			1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		471	124	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067822	30067822	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013815-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	22	409	0	ENST00000338641.4:c.1008del	p.Gln337SerfsTer9	p.Q337Sfs*9	ENST00000338641	NM_000268.3	336	cGg/cg	11/16	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		409	110	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444987	49444987	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	29	278	0	ENST00000301067.7:c.2479del	p.Gln827AsnfsTer103	p.Q827Nfs*103	ENST00000301067	NM_003482.3	827	Caa/aa	10/54	1	2	FACETS	0.854	0.684	1	0.854	0.684	1	CLONAL	1	TRUE	1	0.15	2		278	453	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131297	202131297	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	38	449	0	ENST00000358485.4:c.265A>G	p.Ile89Val	p.I89V	ENST00000358485	NM_001080125.1	89	Att/Gtt	2/9	1	2	FACETS	0.67	0.552	0.803	0.67	0.552	0.803	SUBCLONAL	1	TRUE	1	0.15	2		449	756	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690821	89690830	+	stop_gained	Nonsense_Mutation	DEL	TGACACCGCC	TGACACCGCC	G	novel	NA	P-0013823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	28	262	0	ENST00000371953.3:c.228_237delinsG	p.Tyr76_Ala79delinsTer	p.Y76_A79delins*	ENST00000371953	NM_000314.4	76	taTGACACCGCC/taG	4/9	0.150621432545556	3	FACETS	1	0.815	1	0.511	0.408	0.628	CLONAL	1	TRUE	1	0.15	3		262	393	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	90	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.946	0.838	1	0.946	0.838	1	CLONAL	1	TRUE	1	0.225420791365961	2		426	844	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577518	7577518	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519995	NA	P-0013830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	50	649	0	ENST00000269305.4:c.763A>T	p.Ile255Phe	p.I255F	ENST00000269305	NM_001126112.2	255	Atc/Ttc	7/11	1	2	FACETS	0.685	0.58	0.8	0.685	0.58	0.8	SUBCLONAL	1	TRUE	1	0.225420791365961	2		649	648	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013840-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	486	540	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.676094672474486	3	FACETS	0.974	0.936	1	0.974	0.936	1	CLONAL	2	TRUE	1	0.690855769291969	3		540	972	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0013849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	102	595	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	1	2	FACETS	0.762	0.685	0.842	1	0.983	1	SUBCLONAL	2	TRUE	1	0.31	2		595	432	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604656	48604656	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	79	393	0	ENST00000342988.3:c.1478A>G	p.Asp493Gly	p.D493G	ENST00000342988	NM_005359.5	493	gAt/gGt	12/12	0.301866591156009	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.31	1		393	355	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450267	50450267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	70	607	0	ENST00000331340.3:c.451G>A	p.Gly151Arg	p.G151R	ENST00000331340	NM_006060.4	151	Ggg/Agg	5/8	1	2	FACETS	0.982	0.859	1	0.982	0.859	1	CLONAL	1	TRUE	1	0.31	2		607	460	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102089	27102095	+	frameshift_variant	Frame_Shift_Del	DEL	TAATGAT	TAATGAT	-	novel	NA	P-0013849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	107	859	0	ENST00000324856.7:c.5015_5021del	p.Val1672GlyfsTer15	p.V1672Gfs*15	ENST00000324856	NM_006015.4	1672	gTAATGATg/gg	19/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.31	2		859	609	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123652	46123676	+	frameshift_variant	Frame_Shift_Del	DEL	CGAGCGGAGAAAGGGACTCGCTTTC	CGAGCGGAGAAAGGGACTCGCTTTC	-	novel	NA	P-0013849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	101	484	0	ENST00000334344.6:c.34_58del	p.Glu12TrpfsTer38	p.E12Wfs*38	ENST00000334344	NM_152641.2	11	gaCGAGCGGAGAAAGGGACTCGCTTTC/ga	1/21	0.230405574302299	3	FACETS	0.842	0.751	0.938	0.421	0.375	0.469	CLONAL	1	TRUE	1	0.31	3		484	894	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492590	56492590	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	124	585	0	ENST00000267101.3:c.2740G>C	p.Gly914Arg	p.G914R	ENST00000267101	NM_001982.3	914	Ggg/Cgg	23/28	0.230405574302299	3	FACETS	0.78	0.708	0.856	0.78	0.708	0.856	SUBCLONAL	2	TRUE	1	0.31	3		585	592	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013866-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	150	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.391366906410461	3	FACETS	0.97	0.895	1	0.97	0.895	1	CLONAL	2	TRUE	1	0.441005509478804	3		426	428	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759554	133759554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253014415	NA	P-0013866-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	145	771	0	ENST00000318560.5:c.1877G>A	p.Gly626Asp	p.G626D	ENST00000318560	NM_005157.4	626	gGc/gAc	11/11	0.441005509478804	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.441005509478804	1		771	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013866-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	75	387	0	ENST00000269305.4:c.527G>C	p.Cys176Ser	p.C176S	ENST00000269305	NM_001126112.2	176	tGc/tCc	5/11	0.441005509478804	1	FACETS	0.944	0.836	1	0.944	0.836	1	CLONAL	1	TRUE	0	0.441005509478804	1		387	281	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532765	187532765	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013866-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	98	613	0	ENST00000441802.2:c.9628C>G	p.Leu3210Val	p.L3210V	ENST00000441802	NM_005245.3	3210	Ctg/Gtg	14/27	1	2	FACETS	0.948	0.85	1	0.948	0.85	1	CLONAL	1	TRUE	1	0.441005509478804	2		613	469	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013867-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	183	540	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.238544075133482	2	FACETS	1	0.986	1	0.646	0.597	0.697	CLONAL	1	TRUE	0	0.35410285962712	2		540	800	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0013867-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	260	707	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.285855068968385	2	FACETS	0.806	0.756	0.857	0.806	0.756	0.857	CLONAL	2	TRUE	0	0.35410285962712	2		707	911	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961059	55961059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530419081	NA	P-0013867-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	121	674	0	ENST00000263923.4:c.2881C>T	p.Arg961Trp	p.R961W	ENST00000263923	NM_002253.2	961	Cgg/Tgg	21/30	0.236684055622747	2	FACETS	0.626	0.564	0.691	0.313	0.282	0.346	SUBCLONAL	1	TRUE	0	0.35410285962712	2		674	1092	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008300	29008300	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013867-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	262	665	0	ENST00000282397.4:c.571G>T	p.Gly191Cys	p.G191C	ENST00000282397	NM_002019.4	191	Ggc/Tgc	5/30	0.236684055622747	2	FACETS	1	0.989	1	0.632	0.591	0.673	CLONAL	1	TRUE	0	0.35410285962712	2		665	1171	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860440	42860440	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013867-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	202	467	0	ENST00000398585.3:c.437T>A	p.Met146Lys	p.M146K	ENST00000398585	NM_001135099.1	146	aTg/aAg	5/14	0.35410285962712	3	FACETS	0.844	0.784	0.905	0.844	0.784	0.905	CLONAL	2	TRUE	1	0.35410285962712	3		467	796	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539752	187539752	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1313728391	NA	P-0013867-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	114	550	0	ENST00000441802.2:c.7988G>T	p.Gly2663Val	p.G2663V	ENST00000441802	NM_005245.3	2663	gGc/gTc	10/27	0.236684055622747	2	FACETS	0.653	0.587	0.723	0.327	0.293	0.362	SUBCLONAL	1	TRUE	0	0.35410285962712	2		550	986	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112035593	112035593	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013867-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	375	837	2	ENST00000368678.4:c.301C>A	p.Leu101Met	p.L101M	ENST00000368678		101	Ctg/Atg	4/13	0.236684055622747	2	FACETS	1	0.995	1	0.736	0.697	0.775	CLONAL	1	TRUE	0	0.35410285962712	2		839	1439	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633329	8633329	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013867-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	143	710	0	ENST00000356435.5:c.340A>T	p.Thr114Ser	p.T114S	ENST00000356435		114	Aca/Tca	3/35	0.236684055622747	2	FACETS	0.648	0.589	0.71	0.324	0.294	0.355	SUBCLONAL	1	TRUE	0	0.35410285962712	2		710	1247	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889200	76889200	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013867-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	92	329	0	ENST00000373344.5:c.4810G>T	p.Val1604Leu	p.V1604L	ENST00000373344	NM_000489.3	1604	Gtg/Ttg	18/35	1	1	FACETS	0.85	0.758	0.948	0.85	0.758	0.948	CLONAL	1	TRUE	0	0.35410285962712	1		329	503	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0013883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	51	569	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.715	0.607	0.835	0.715	0.607	0.835	SUBCLONAL	1	TRUE	1	0.21	2		569	679	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0013883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	67	636	0	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.21	2		636	634	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600425	10600425	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	125	855	0	ENST00000171111.5:c.1430del	p.Gly477AlafsTer23	p.G477Afs*23	ENST00000171111	NM_203500.1	477	gGc/gc	4/6	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.21	2		855	966	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0013891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	86	270	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.177116499909318	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.19	1		272	669	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435300	110435302	+	inframe_deletion	In_Frame_Del	DEL	GGT	GGT	-	rs765493638	NA	P-0013891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	12	83	1	ENST00000375856.3:c.3099_3101del	p.Pro1036del	p.P1036del	ENST00000375856	NM_003749.2	1033	ccACCg/ccg	1/2	1	2	FACETS	0.964	0.682	1	0.964	0.682	1	CLONAL	1	TRUE	1	0.19	2		84	131	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762881	40762881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	100	725	0	ENST00000392038.2:c.127G>A	p.Glu43Lys	p.E43K	ENST00000392038	NM_001626.4	43	Gag/Aag	3/14	1	2	FACETS	0.843	0.75	0.942	0.843	0.75	0.942	CLONAL	1	TRUE	1	0.19	2		725	1249	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604689	55604689	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs765503364	NA	P-0013891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	93	584	0	ENST00000288135.5:c.2897C>A	p.Ser966Tyr	p.S966Y	ENST00000288135	NM_000222.2	966	tCc/tAc	21/21	1	2	FACETS	0.966	0.857	1	0.966	0.857	1	CLONAL	1	TRUE	1	0.19	2		584	1013	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777925	27777925	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1823	258	1363	2	ENST00000369163.2:c.74C>A	p.Ala25Glu	p.A25E	ENST00000369163	NM_003536.2	25	gCg/gAg	1/1	0.150782010565303	3	FACETS	1	0.991	1	0.715	0.666	0.765	CLONAL	1	TRUE	1	0.19	3		1365	2081	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942688	48942688	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0013892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	206	668	0	ENST00000267163.4:c.1075A>T	p.Lys359Ter	p.K359*	ENST00000267163	NM_000321.2	359	Aaa/Taa	11/27	0.446050268254146	1	FACETS	0.948	0.882	1	0.948	0.882	1	CLONAL	1	TRUE	0	0.451800789566358	1		668	745	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400113	41400113	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	169	565	0	ENST00000373198.4:c.646G>T	p.Gly216Cys	p.G216C	ENST00000373198	NM_133170.3	216	Ggt/Tgt	5/32	1	2	FACETS	0.992	0.914	1	0.992	0.914	1	CLONAL	1	TRUE	1	0.451800789566358	2		565	754	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856521	111856521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013893-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	38	374	0	ENST00000341259.2:c.572C>T	p.Pro191Leu	p.P191L	ENST00000341259	NM_005475.2	191	cCg/cTg	2/8	NA	2	FACETS	0.592	0.491	0.705			1	INDETERMINATE	1	TRUE	NA	0.367585574796245	2		374	349	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81916897	81916897	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013893-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	173	1006	0	ENST00000359376.3:c.716C>G	p.Ser239Cys	p.S239C	ENST00000359376	NM_002661.3	239	tCt/tGt	9/33	1	2	FACETS	0.938	0.863	1	0.938	0.863	1	CLONAL	1	TRUE	1	0.367585574796245	2		1006	1003	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523634	148523634	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013893-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	134	439	0	ENST00000320356.2:c.819G>C	p.Gln273His	p.Q273H	ENST00000320356	NM_004456.4	273	caG/caC	8/20	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.367585574796245	2		439	691	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900273	101900273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863223812	NA	P-0013893-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	163	714	0	ENST00000374994.4:c.707C>T	p.Ser236Phe	p.S236F	ENST00000374994	NM_004612.2	236	tCt/tTt	4/9	0.224260190109896	1	FACETS	0.766	0.703	0.832	0.766	0.703	0.832	SUBCLONAL	1	TRUE	0	0.367585574796245	1		714	945	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254881	16254881	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	36	588	0	ENST00000375759.3:c.2146G>T	p.Asp716Tyr	p.D716Y	ENST00000375759	NM_015001.2	716	Gac/Tac	11/15	1	2	FACETS	0.415	0.341	0.5	0.415	0.341	0.5	SUBCLONAL	1	TRUE	1	0.294807467962423	2		588	588	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78882673	78882673	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778993531	NA	P-0013911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	38	631	0	ENST00000306801.3:c.2464C>T	p.Pro822Ser	p.P822S	ENST00000306801	NM_020761.2	822	Ccc/Tcc	21/34	1	2	FACETS	0.564	0.466	0.673	0.564	0.466	0.673	SUBCLONAL	1	TRUE	1	0.294807467962423	2		631	457	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0013913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	718	453	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.761758219172968	4	FACETS	0.969	0.943	0.996	0.969	0.943	0.996	CLONAL	3	TRUE	1	0.761758219172968	4		453	1142	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0013913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	601	769	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA	2	FACETS	0.996	0.972	1			1	INDETERMINATE	2	TRUE	NA	0.761758219172968	2		770	792	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	210	632	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.761758219172968	3	FACETS	0.907	0.844	0.973	0.454	0.422	0.487	CLONAL	1	TRUE	1	0.761758219172968	3		632	839	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125523710	125523710	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	67	542	0	ENST00000428830.2:c.1303G>C	p.Asp435His	p.D435H	ENST00000428830	NM_001114121.2	435	Gat/Cat	12/14	1	2	FACETS	0.204	0.176	0.234	0.204	0.176	0.234	SUBCLONAL	1	TRUE	1	0.761758219172968	2		542	863	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828347	72828347	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760790924	NA	P-0013913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	351	921	0	ENST00000268489.5:c.8234T>C	p.Leu2745Pro	p.L2745P	ENST00000268489	NM_006885.3	2745	cTa/cCa	9/10	0.761758219172968	1	FACETS	0.913	0.874	0.951	0.913	0.874	0.951	CLONAL	1	TRUE	0	0.761758219172968	1		921	625	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475057	40475057	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555563871	NA	P-0013913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	384	857	2	ENST00000264657.5:c.1853G>A	p.Gly618Asp	p.G618D	ENST00000264657	NM_139276.2	618	gGc/gAc	20/24	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.761758219172968	2		859	918	SUCCESS
APC	324	MSKCC	GRCh37	5	112178925	112178925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064795713	NA	P-0013913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	228	562	0	ENST00000257430.4:c.7634G>A	p.Gly2545Glu	p.G2545E	ENST00000257430	NM_000038.5	2545	gGa/gAa	16/16	0.761758219172968	1	FACETS	0.948	0.899	0.996	0.948	0.899	0.996	CLONAL	1	TRUE	0	0.761758219172968	1		562	391	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862919	117862919	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1267	347	702	0	ENST00000297338.2:c.1558G>C	p.Glu520Gln	p.E520Q	ENST00000297338	NM_006265.2	520	Gaa/Caa	12/14	0.704773482241873	4	FACETS	0.994	0.939	1	0.497	0.469	0.526	CLONAL	1	TRUE	2	0.761758219172968	4		702	1614	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	131	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.3	2		426	846	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266713	198266713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776846119	NA	P-0013921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	93	593	0	ENST00000335508.6:c.2219G>A	p.Gly740Glu	p.G740E	ENST00000335508	NM_012433.2	740	gGa/gAa	15/25	1	2	FACETS	0.712	0.632	0.797	0.712	0.632	0.797	SUBCLONAL	1	TRUE	1	0.3	2		593	871	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573546	48573551	+	frameshift_variant	Frame_Shift_Del	DEL	GTAAAG	GTAAAG	TTAAA	novel	NA	P-0013921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	126	636	1	ENST00000342988.3:c.130_135delinsTTAAA	p.Val44LeufsTer4	p.V44Lfs*4	ENST00000342988	NM_005359.5	44	GTAAAG/TTAAA	2/12	0.304878329221367	1	FACETS	0.876	0.793	0.963	0.876	0.793	0.963	CLONAL	1	TRUE	0	0.3	1		637	815	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0013930-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	1148	876	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.741871674269569	3	FACETS	0.912	0.898	0.926	0.912	0.898	0.926	CLONAL	3	TRUE	0	0.8557677032583	3		876	1400	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450086	32450086	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013930-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	304	710	6	ENST00000332351.3:c.726C>G	p.His242Gln	p.H242Q	ENST00000332351	NM_024426.4	242	caC/caG	2/10	0.207170637499235	5	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.8557677032583	5		716	1143	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153445	108153445	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013930-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	114	582	0	ENST00000278616.4:c.3585G>C	p.Glu1195Asp	p.E1195D	ENST00000278616	NM_000051.3	1195	gaG/gaC	25/63	0.777332634513996	2	FACETS	0.342	0.307	0.378	0.171	0.153	0.189	SUBCLONAL	1	TRUE	0	0.8557677032583	2		582	780	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489456	56489456	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013930-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	242	525	2	ENST00000267101.3:c.1921C>A	p.His641Asn	p.H641N	ENST00000267101	NM_001982.3	641	Cat/Aat	17/28	0.769336076502985	3	FACETS	0.822	0.769	0.878	0.274	0.256	0.293	CLONAL	1	TRUE	0	0.8557677032583	3		527	982	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241529	105241529	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013930-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	395	727	2	ENST00000349310.3:c.451G>C	p.Glu151Gln	p.E151Q	ENST00000349310	NM_001014432.1	151	Gag/Cag	7/15	0.777332634513996	2	FACETS	0.957	0.913	1	0.478	0.456	0.501	CLONAL	1	TRUE	0	0.8557677032583	2		729	965	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303439	91303439	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013930-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2138	148	570	1	ENST00000355112.3:c.1150G>C	p.Asp384His	p.D384H	ENST00000355112	NM_000057.2	384	Gat/Cat	6/22	0.8557677032583	6	FACETS	0.41	0.372	0.45			1	SUBCLONAL	1	TRUE	NA	0.8557677032583	6		571	2286	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358343	91358343	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013930-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2064	234	669	5	ENST00000355112.3:c.4088C>A	p.Thr1363Lys	p.T1363K	ENST00000355112	NM_000057.2	1363	aCa/aAa	22/22	0.8557677032583	6	FACETS	0.645	0.599	0.694			1	SUBCLONAL	1	TRUE	NA	0.8557677032583	6		674	2298	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027519	48027519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013930-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	263	501	1	ENST00000234420.5:c.2397G>A	p.Met799Ile	p.M799I	ENST00000234420	NM_000179.2	799	atG/atA	4/10	0.722653556971669	4	FACETS	0.921	0.862	0.981	0.46	0.431	0.491	CLONAL	1	TRUE	2	0.8557677032583	4		502	1239	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332919	153332919	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs781123562	NA	P-0013930-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	406	603	5	ENST00000281708.4:c.37C>T	p.Arg13Ter	p.R13*	ENST00000281708	NM_033632.3	13	Cga/Tga	2/12	0.374924395367431	3	FACETS	0.784	0.75	0.818			1	INDETERMINATE	2	TRUE	NA	0.8557677032583	3		608	864	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516923	187516923	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013930-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	320	778	3	ENST00000441802.2:c.13058C>T	p.Ser4353Phe	p.S4353F	ENST00000441802	NM_005245.3	4353	tCc/tTc	26/27	1	2	FACETS	0.835	0.79	0.88	0.835	0.79	0.88	CLONAL	1	TRUE	1	0.8557677032583	2		781	896	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2966382	2966382	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013930-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2397	479	961	8	ENST00000396946.4:c.1798G>C	p.Asp600His	p.D600H	ENST00000396946	NM_032415.4	600	Gat/Cat	14/25	0.8557677032583	5	FACETS	0.889	0.845	0.934	0.178	0.169	0.187	CLONAL	1	TRUE	0	0.8557677032583	5		969	2876	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148516716	148516716	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013930-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	219	510	1	ENST00000320356.2:c.971C>T	p.Pro324Leu	p.P324L	ENST00000320356	NM_004456.4	324	cCt/cTt	9/20	0.729410273309604	4	FACETS	0.76	0.706	0.817	0.19	0.176	0.205	SUBCLONAL	1	TRUE	0	0.8557677032583	4		511	1249	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524967	8524967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013930-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	519	663	7	ENST00000356435.5:c.637G>A	p.Ala213Thr	p.A213T	ENST00000356435		213	Gcg/Acg	7/35	0.315867344216463	3	FACETS	0.848	0.817	0.879			1	INDETERMINATE	2	TRUE	NA	0.8557677032583	3		670	1021	SUCCESS
APC	324	MSKCC	GRCh37	5	112179431	112179431	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs864622205	NA	P-0013947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	196	630	1	ENST00000257430.4:c.8140C>T	p.Arg2714Cys	p.R2714C	ENST00000257430	NM_000038.5	2714	Cgt/Tgt	16/16	0.370667720172716	2	FACETS	0.908	0.839	0.979	0.454	0.419	0.49	CLONAL	1	TRUE	0	0.388320301820526	2		631	1112	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0013947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	453	424	2	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.388320301820526	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.388320301820526	3		426	863	SUCCESS
APC	324	MSKCC	GRCh37	5	112175271	112175272	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0013947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	217	323	2	ENST00000257430.4:c.3982_3983del	p.Gln1328AlafsTer3	p.Q1328Afs*3	ENST00000257430	NM_000038.5	1327	tCA/t	16/16	0.370667720172716	2	FACETS	0.888	0.831	0.947	0.888	0.831	0.947	CLONAL	2	TRUE	0	0.388320301820526	2		325	629	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101690	27101690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1442666063	NA	P-0013948-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	41	401	1	ENST00000324856.7:c.4972C>T	p.Arg1658Trp	p.R1658W	ENST00000324856	NM_006015.4	1658	Cgg/Tgg	18/20	0.471018972434058	3	FACETS	0.277	0.23	0.33	0.138	0.115	0.165	SUBCLONAL	1	TRUE	1	0.471018972434058	3		402	777	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532758	46532758	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013948-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	34	280	0	ENST00000262741.5:c.320G>C	p.Gly107Ala	p.G107A	ENST00000262741	NM_003629.3	107	gGa/gCa	4/10	0.325174226130048	5	FACETS	0.376	0.306	0.455			1	SUBCLONAL	1	TRUE	NA	0.471018972434058	5		280	655	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231774	36231774	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1569061768	NA	P-0013957-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	8	435	1	ENST00000300305.3:c.610C>T	p.Arg204Ter	p.R204*	ENST00000300305		204	Cga/Tga	5/8	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		436	233	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624246	89624263	+	inframe_deletion	In_Frame_Del	DEL	AGATCGTTAGCAGAAACA	AGATCGTTAGCAGAAACA	-	novel	NA	P-0013957-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	18	86	0	ENST00000371953.3:c.21_38del	p.Ile8_Lys13del	p.I8_K13del	ENST00000371953	NM_000314.4	7	gAGATCGTTAGCAGAAACAaa/gaa	1/9	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		86	84	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013963-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	129	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.184776821586841	3	FACETS	0.78	0.707	0.857	0.78	0.707	0.857	SUBCLONAL	2	TRUE	1	0.216671522190393	3		426	846	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0013963-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	149	449	9	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.188227552943547	2	FACETS	0.892	0.816	0.971	0.892	0.816	0.971	CLONAL	2	TRUE	0	0.216671522190393	2		458	771	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0013963-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	116	270	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.216671522190393	2	FACETS	0.988	0.894	1	0.988	0.894	1	CLONAL	2	TRUE	0	0.216671522190393	2		272	542	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777894	NA	P-0013963-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	176	741	0	ENST00000361445.4:c.6644C>T	p.Ser2215Phe	p.S2215F	ENST00000361445	NM_004958.3	2215	tCt/tTt	47/58	0.184776821586841	3	FACETS	0.983	0.906	1	0.983	0.906	1	CLONAL	2	TRUE	1	0.216671522190393	3		741	916	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0013963-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	77	505	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.954	0.837	1	0.954	0.837	1	CLONAL	1	TRUE	1	0.216671522190393	2		505	745	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742931	17742931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013963-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	39	362	1	ENST00000250003.3:c.839C>T	p.Pro280Leu	p.P280L	ENST00000250003	NM_002478.4	280	cCg/cTg	3/3	0.184776821586841	3	FACETS	1	0.862	1	0.522	0.433	0.621	CLONAL	1	TRUE	1	0.216671522190393	3		363	382	SUCCESS
APC	324	MSKCC	GRCh37	5	112175277	112175284	+	frameshift_variant	Frame_Shift_Del	DEL	ACCCTAGA	ACCCTAGA	-	novel	NA	P-0013963-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	51	447	0	ENST00000257430.4:c.3989_3996del	p.Pro1330GlnfsTer9	p.P1330Qfs*9	ENST00000257430	NM_000038.5	1329	cACCCTAGA/c	16/16	1	2	FACETS	0.708	0.601	0.826	0.708	0.601	0.826	SUBCLONAL	1	TRUE	1	0.216671522190393	2		447	665	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508682	106508682	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760803722	NA	P-0013963-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	59	467	0	ENST00000359195.3:c.676C>T	p.Arg226Cys	p.R226C	ENST00000359195	NM_002649.2	226	Cgc/Tgc	2/11	0.216671522190393	4	FACETS	0.87	0.747	1	0.29	0.249	0.335	CLONAL	1	TRUE	1	0.216671522190393	4		467	762	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578226	7578226	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1464727668	NA	P-0013964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	545	701	0	ENST00000269305.4:c.623A>T	p.Asp208Val	p.D208V	ENST00000269305	NM_001126112.2	208	gAc/gTc	6/11	0.726559598112333	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.726559598112333	1		701	913	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923601	39923601	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	449	327	0	ENST00000378444.4:c.3490C>T	p.Arg1164Ter	p.R1164*	ENST00000378444	NM_001123385.1	1164	Cga/Tga	7/15	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.726559598112333	1		327	619	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402121	402121	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	498	723	0	ENST00000399788.2:c.4670A>T	p.Lys1557Ile	p.K1557I	ENST00000399788	NM_001042603.1	1557	aAa/aTa	27/28	NA	2	FACETS	0.964	0.923	1			1	INDETERMINATE	1	TRUE	NA	0.726559598112333	2		723	1422	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226774	142226774	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	207	338	2	ENST00000350721.4:c.5030A>T	p.Gln1677Leu	p.Q1677L	ENST00000350721	NM_001184.3	1677	cAg/cTg	28/47	0.726559598112333	3	FACETS	0.867	0.805	0.931	0.433	0.402	0.466	CLONAL	1	TRUE	1	0.726559598112333	3		340	896	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0013982-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	801	804	1	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	0.852770142171395	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.852705866011487	1		805	991	SUCCESS
APC	324	MSKCC	GRCh37	5	112175746	112175746	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013982-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	147	402	1	ENST00000257430.4:c.4455del	p.Asp1486IlefsTer21	p.D1486Ifs*21	ENST00000257430	NM_000038.5	1485	gcT/gc	16/16	0.446828684563461	1	FACETS	0.34	0.312	0.37	0.34	0.312	0.37	INDETERMINATE	1	TRUE	0	0.852705866011487	1		403	581	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920422	114920422	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013982-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	868	1096	1	ENST00000543371.1:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000543371	NM_001198531.1	455	Cga/Tga	13/14	0.478255905233781	1	FACETS	0.772	0.751	0.792	0.772	0.751	0.792	INDETERMINATE	1	TRUE	0	0.852705866011487	1		1097	1513	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41962023	41962023	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013982-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	1559	1507	2	ENST00000219905.7:c.931T>G	p.Ser311Ala	p.S311A	ENST00000219905	NM_001164273.1	311	Tca/Gca	2/24	0.841693792525664	2	FACETS	0.993	0.98	1	0.993	0.98	1	CLONAL	2	TRUE	0	0.852705866011487	2		1509	1842	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221743	55221743	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519829	NA	P-0013989-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	7654	914	0	ENST00000275493.2:c.787A>C	p.Thr263Pro	p.T263P	ENST00000275493	NM_005228.3	263	Acc/Ccc	7/28	0.490767680190418	30	FACETS	0.998	0.994	1	0.965	0.961	0.97	CLONAL	29	TRUE	0	0.490767680190418	30		914	8479	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0014010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	131	441	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.521486482334167	2		441	367	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0014010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	283	569	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.473875063579167	2	FACETS	0.851	0.806	0.896	0.851	0.806	0.896	CLONAL	2	TRUE	0	0.521486482334167	2		569	638	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711339	114711339	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	230	539	0	ENST00000543371.1:c.354del	p.Asn118LysfsTer37	p.N118Kfs*37	ENST00000543371	NM_001198531.1	118	aaC/aa	3/14	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.521486482334167	2		539	704	SUCCESS
APC	324	MSKCC	GRCh37	5	112174379	112174379	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	125	319	0	ENST00000257430.4:c.3090del	p.Lys1030AsnfsTer7	p.K1030Nfs*7	ENST00000257430	NM_000038.5	1030	Aaa/aa	16/16	0.264097076413194	2	FACETS	1	0.984	1	0.681	0.624	0.74	INDETERMINATE	1	TRUE	0	0.521486482334167	2		319	352	SUCCESS
APC	324	MSKCC	GRCh37	5	112175919	112176015	+	frameshift_variant	Frame_Shift_Del	DEL	AAGAATCAAATGAAAACCAAGAGAAAGAGGCAGAAAAAACTATTGATTCTGAAAAGGACCTATTAGATGATTCAGATGATGATGATATTGAAATACT	AAGAATCAAATGAAAACCAAGAGAAAGAGGCAGAAAAAACTATTGATTCTGAAAAGGACCTATTAGATGATTCAGATGATGATGATATTGAAATACT	-	novel	NA	P-0014010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	63	370	0	ENST00000257430.4:c.4629_4725del	p.Glu1544LysfsTer74	p.E1544Kfs*74	ENST00000257430	NM_000038.5	1543	aAAGAATCAAATGAAAACCAAGAGAAAGAGGCAGAAAAAACTATTGATTCTGAAAAGGACCTATTAGATGATTCAGATGATGATGATATTGAAATACTa/aa	16/16	0.264097076413194	2	FACETS	0.499	0.432	0.571	0.25	0.216	0.286	INDETERMINATE	1	TRUE	0	0.521486482334167	2		370	484	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371915	55371915	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	27	166	1	ENST00000297316.4:c.605A>G	p.His202Arg	p.H202R	ENST00000297316	NM_022454.3	202	cAc/cGc	2/2	0.266204290038317	2	FACETS	0.433	0.346	0.532	0.217	0.173	0.266	INDETERMINATE	1	TRUE	0	0.521486482334167	2		167	239	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864942	117864942	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	70	609	0	ENST00000297338.2:c.1167T>G	p.Phe389Leu	p.F389L	ENST00000297338	NM_006265.2	389	ttT/ttG	10/14	0.266204290038317	2	FACETS	0.289	0.251	0.331	0.145	0.125	0.166	INDETERMINATE	1	TRUE	0	0.521486482334167	2		609	928	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544703	65544703	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs387906650	NA	P-0014011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	218	581	0	ENST00000358664.4:c.223C>T	p.Arg75Ter	p.R75*	ENST00000358664	NM_002382.4	75	Cga/Tga	4/5	0.402355935122215	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.402355935122215	1		581	771	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297937	15297937	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777751303	NA	P-0014011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	55	541	0	ENST00000263388.2:c.1819C>T	p.Arg607Cys	p.R607C	ENST00000263388	NM_000435.2	607	Cgc/Tgc	11/33	0.402355935122215	1	FACETS	0.424	0.363	0.491	0.424	0.363	0.491	SUBCLONAL	1	TRUE	0	0.402355935122215	1		541	515	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339603	70339603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1379	82	970	1	ENST00000374080.3:c.272G>A	p.Arg91His	p.R91H	ENST00000374080		91	cGc/cAc	3/45	1	2	FACETS	0.279	0.245	0.316	0.279	0.245	0.316	SUBCLONAL	1	TRUE	1	0.402355935122215	2		971	1461	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039164	49039164	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913297	NA	P-0014088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	135	471	1	ENST00000267163.4:c.2242G>T	p.Glu748Ter	p.E748*	ENST00000267163	NM_000321.2	748	Gag/Tag	22/27	0.847014322604652	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.847014322604652	1		472	162	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0014088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	68	250	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.847014322604652	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.847014322604652	1		250	90	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023908	27023923	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTGCGGCGGCGGCA	GGCTGCGGCGGCGGCA	-	novel	NA	P-0014088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	127	91	0	ENST00000324856.7:c.1015_1030del	p.Ala339LeufsTer19	p.A339Lfs*19	ENST00000324856	NM_006015.4	338	ggGGCTGCGGCGGCGGCA/gg	1/20	1	2	FACETS	0.761	0.712	0.808	1	0.99	1	SUBCLONAL	2	TRUE	1	0.847014322604652	2		91	197	SUCCESS
ATR	545	MSKCC	GRCh37	3	142222288	142222288	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	141	328	0	ENST00000350721.4:c.5204A>G	p.His1735Arg	p.H1735R	ENST00000350721	NM_001184.3	1735	cAt/cGt	30/47	0.847014322604652	3	FACETS	1	0.972	1	0.563	0.517	0.609	CLONAL	1	TRUE	1	0.847014322604652	3		328	421	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170291	32170291	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	239	519	0	ENST00000375023.3:c.3317C>G	p.Pro1106Arg	p.P1106R	ENST00000375023	NM_004557.3	1106	cCt/cGt	21/30	0.847014322604652	3	FACETS	0.997	0.933	1	0.498	0.466	0.531	CLONAL	1	TRUE	1	0.847014322604652	3		519	806	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97934348	97934348	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs759387035	NA	P-0014088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	124	586	0	ENST00000289081.3:c.427A>G	p.Ile143Val	p.I143V	ENST00000289081	NM_000136.2	143	Ata/Gta	5/15	1	2	FACETS	0.841	0.77	0.914	0.841	0.77	0.914	CLONAL	1	TRUE	1	0.847014322604652	2		586	348	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0014089-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	19	528	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.2116657430509	2	FACETS	0.211	0.159	0.273	0.106	0.079	0.137	SUBCLONAL	1	TRUE	0	0.31	2		528	580	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441252	52441252	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014089-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	132	506	0	ENST00000460680.1:c.518A>G	p.Tyr173Cys	p.Y173C	ENST00000460680	NM_004656.3	173	tAt/tGt	7/17	0.2116657430509	2	FACETS	1	0.984	1	0.689	0.627	0.753	CLONAL	1	TRUE	0	0.31	2		506	618	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287292	46287292	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014089-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	79	508	0	ENST00000334344.6:c.5237G>C	p.Arg1746Thr	p.R1746T	ENST00000334344	NM_152641.2	1746	aGa/aCa	19/21	1	2	FACETS	0.77	0.677	0.87	0.77	0.677	0.87	SUBCLONAL	1	TRUE	1	0.31	2		508	662	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380277	+	missense_variant	Missense_Mutation	DNP	TG	TG	GC	novel	NA	P-0014089-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	129	534	0	ENST00000311936.3:c.181_182delinsGC	p.Gln61Ala	p.Q61A	ENST00000311936	NM_004985.3	61	CAa/GCa	3/5	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.31	2		534	772	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732951	30732951	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014089-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	97	425	0	ENST00000295754.5:c.1564G>C	p.Asp522His	p.D522H	ENST00000295754	NM_003242.5	522	Gac/Cac	7/7	0.2116657430509	2	FACETS	1	0.98	1	0.723	0.648	0.801	CLONAL	1	TRUE	0	0.31	2		425	433	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852146	128852146	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014089-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	102	757	0	ENST00000249373.3:c.2218G>T	p.Glu740Ter	p.E740*	ENST00000249373	NM_005631.4	740	Gag/Tag	12/12	1	2	FACETS	0.83	0.742	0.923	0.83	0.742	0.923	CLONAL	1	TRUE	1	0.31	2		757	793	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191506	10191506	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs5030820	NA	P-0014098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	273	486	42	ENST00000256474.2:c.499C>T	p.Arg167Trp	p.R167W	ENST00000256474	NM_000551.3	167	Cgg/Tgg	3/3	0.728371799429911	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.72938201097111	1		528	435	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0014119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	137	425	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.565610895319805	2		425	468	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920413	114920413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767830105	NA	P-0014119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	586	894	2	ENST00000543371.1:c.1354G>A	p.Gly452Arg	p.G452R	ENST00000543371	NM_001198531.1	452	Ggg/Agg	13/14	0.565610895319805	2	FACETS	0.98	0.948	1	0.98	0.948	1	CLONAL	2	TRUE	0	0.565610895319805	2		896	1057	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039817	47039817	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0014119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	538	879	0	ENST00000377604.3:c.1161-1G>A		p.X387_splice	ENST00000377604	NM_001204468.1	387			0.565610895319805	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.565610895319805	2		879	916	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913250	NA	P-0014119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	192	599	0	ENST00000369535.4:c.34G>T	p.Gly12Cys	p.G12C	ENST00000369535	NM_002524.4	12	Ggt/Tgt	2/7	1	2	FACETS	0.96	0.891	1	0.96	0.891	1	CLONAL	1	TRUE	1	0.565610895319805	2		599	707	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022681	31022681	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	276	528	0	ENST00000375687.4:c.2167del	p.Ser723LeufsTer2	p.S723Lfs*2	ENST00000375687	NM_015338.5	722	ccT/cc	13/13	0.32245285999063	5	FACETS	1	0.986	1	0.759	0.716	0.804	INDETERMINATE	2	TRUE	2	0.565610895319805	5		528	792	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246550	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	TC	TC	CT	novel	NA	P-0014125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	138	429	1	ENST00000349310.3:c.49_50delinsAG	p.Glu17Arg	p.E17R	ENST00000349310	NM_001014432.1	17	GAg/AGg	4/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.442565510449208	2		430	440	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90634871	90634871	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372928432	NA	P-0014125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	65	521	0	ENST00000330062.3:c.121G>A	p.Asp41Asn	p.D41N	ENST00000330062	NM_002168.2	41	Gac/Aac	2/11	1	2	FACETS	0.634	0.551	0.724	0.634	0.551	0.724	SUBCLONAL	1	TRUE	1	0.442565510449208	2		521	463	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577916	7578268	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GATCCGCCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACTGCGCCCAGCCAAGCAGGGGAGGCCCTTAGCCTCTGTAAGCTTCAGTTTTTTCAACTGTGCAATAGTTAAACCCATTTACTTTGCACATCTCATGGGGTTATAGGGAGGTCAAATAAGCAGCAGGAGAAAGCCCCCCTACTGCTCACCTGGAGGGCCACTGACAACCACCCTTAACCCCTCCTCCCAGAGACCCCAGTTGCAAACCAGACCTCAGGCGGCTCATAGGGCACCACCACACTATGTCGAAAAGTGTTTCTGTCATCCAAATACTCCACACGCAAATTTCCTTCCACTCGGATAA	GATCCGCCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACTGCGCCCAGCCAAGCAGGGGAGGCCCTTAGCCTCTGTAAGCTTCAGTTTTTTCAACTGTGCAATAGTTAAACCCATTTACTTTGCACATCTCATGGGGTTATAGGGAGGTCAAATAAGCAGCAGGAGAAAGCCCCCCTACTGCTCACCTGGAGGGCCACTGACAACCACCCTTAACCCCTCCTCCCAGAGACCCCAGTTGCAAACCAGACCTCAGGCGGCTCATAGGGCACCACCACACTATGTCGAAAAGTGTTTCTGTCATCCAAATACTCCACACGCAAATTTCCTTCCACTCGGATAA	-	novel	NA	P-0014125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	15	15	0	ENST00000269305.4:c.581_672+261del		p.X194_splice	ENST00000269305	NM_001126112.2	194		6/11	0.442565510449208	1	FACETS	0.88	0.734	0.999	1	0.948	1	CLONAL	3	TRUE	0	0.442565510449208	1		15	20	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011144	12011144	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	82	439	0	ENST00000353533.5:c.551C>A	p.Ser184Ter	p.S184*	ENST00000353533	NM_003010.3	184	tCg/tAg	5/11	0.442565510449208	1	FACETS	0.788	0.7	0.882	0.788	0.7	0.882	SUBCLONAL	1	TRUE	0	0.442565510449208	1		439	366	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592359	29592359	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0014125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	95	442	0	ENST00000356175.3:c.4772+2T>G		p.X1591_splice	ENST00000356175	NM_000267.3	1591			0.442565510449208	1	FACETS	0.868	0.779	0.962	0.868	0.779	0.962	CLONAL	1	TRUE	0	0.442565510449208	1		442	385	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158655953	158655953	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	161	948	0	ENST00000263640.3:c.53C>T	p.Ser18Phe	p.S18F	ENST00000263640	NM_001105.4	18	tCc/tTc	3/11	1	2	FACETS	0.801	0.735	0.871	0.801	0.735	0.871	CLONAL	1	TRUE	1	0.442565510449208	2		948	908	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845430	151845430	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	136	561	1	ENST00000262189.6:c.13582C>T	p.Gln4528Ter	p.Q4528*	ENST00000262189	NM_170606.2	4528	Cag/Tag	52/59	0.436564994970152	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.442565510449208	1		562	451	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820710	3820710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756935046	NA	P-0014133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	224	517	3	ENST00000262367.5:c.2741G>A	p.Ser914Asn	p.S914N	ENST00000262367	NM_004380.2	914	aGc/aAc	14/31	0.562307421824652	3	FACETS	0.798	0.742	0.856	0.399	0.371	0.428	SUBCLONAL	1	TRUE	1	0.629979062937579	3		520	1172	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579494	7579494	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1555526721	NA	P-0014133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	422	500	0	ENST00000269305.4:c.193A>T	p.Arg65Ter	p.R65*	ENST00000269305	NM_001126112.2	65	Aga/Tga	4/11	0.629979062937579	2	FACETS	0.985	0.95	1	0.985	0.95	1	CLONAL	2	TRUE	0	0.629979062937579	2		500	680	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855889	45855889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769085031	NA	P-0014133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	227	452	5	ENST00000391945.4:c.1921C>T	p.Arg641Trp	p.R641W	ENST00000391945	NM_000400.3	641	Cgg/Tgg	21/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.629979062937579	2		457	649	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026672	48026672	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	48	294	0	ENST00000234420.5:c.1550T>C	p.Ile517Thr	p.I517T	ENST00000234420	NM_000179.2	517	aTt/aCt	4/10	0.629979062937579	3	FACETS	0.802	0.683	0.929	0.401	0.341	0.465	CLONAL	1	TRUE	1	0.629979062937579	3		294	250	SUCCESS
APC	324	MSKCC	GRCh37	5	112162933	112162934	+	stop_gained	Nonsense_Mutation	DNP	GT	GT	TG	novel	NA	P-0014133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	151	489	1	ENST00000257430.4:c.1537_1538delinsTG	p.Val513Ter	p.V513*	ENST00000257430	NM_000038.5	513	GTa/TGa	12/16	0.629979062937579	2	FACETS	0.891	0.834	0.948	0.891	0.834	0.948	CLONAL	2	TRUE	0	0.629979062937579	2		490	269	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282117	38282117	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014133-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	242	513	0	ENST00000425967.3:c.939C>A	p.Asp313Glu	p.D313E	ENST00000425967	NM_001174067.1	313	gaC/gaA	8/19	0.629979062937579	3	FACETS	0.915	0.854	0.978	0.458	0.427	0.489	CLONAL	1	TRUE	1	0.629979062937579	3		513	1104	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014135-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	53	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.996	0.85	1	0.996	0.85	1	CLONAL	1	TRUE	1	0.2	2		426	532	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176478	142176478	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014135-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	38	440	0	ENST00000350721.4:c.7623G>T	p.Arg2541Ser	p.R2541S	ENST00000350721	NM_001184.3	2541	agG/agT	45/47	1	2	FACETS	0.86	0.711	1	0.86	0.711	1	CLONAL	1	TRUE	1	0.2	2		440	442	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741555	17741555	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014135-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	16	154	0	ENST00000250003.3:c.226C>G	p.Arg76Gly	p.R76G	ENST00000250003	NM_002478.4	76	Cgt/Ggt	1/3	1	2	FACETS	0.737	0.546	0.965	0.737	0.546	0.965	CLONAL	1	TRUE	1	0.2	2		154	217	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434802	99434802	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs547142975	NA	P-0014135-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	30	421	0	ENST00000268035.6:c.889G>C	p.Val297Leu	p.V297L	ENST00000268035	NM_000875.3	297	Gtg/Ctg	3/21	1	2	FACETS	0.691	0.557	0.844	0.691	0.557	0.844	SUBCLONAL	1	TRUE	1	0.2	2		421	434	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858507	9858507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042323	NA	P-0014135-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	41	581	0	ENST00000330684.3:c.2894C>T	p.Thr965Ile	p.T965I	ENST00000330684	NM_001134407.1	965	aCa/aTa	13/13	1	2	FACETS	0.66	0.549	0.785	0.66	0.549	0.785	SUBCLONAL	1	TRUE	1	0.2	2		581	621	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59934484	59934484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014135-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	73	594	2	ENST00000259008.2:c.314C>T	p.Ser105Leu	p.S105L	ENST00000259008	NM_032043.2	105	tCa/tTa	4/20	0.269973724026066	3	FACETS	1	0.931	1	0.55	0.48	0.625	CLONAL	1	TRUE	1	0.2	3		596	730	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368419	225368433	+	inframe_deletion	In_Frame_Del	DEL	TTGTGAGAAGTCTCC	TTGTGAGAAGTCTCC	-	novel	NA	P-0014135-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	56	445	0	ENST00000264414.4:c.1313_1327del	p.Arg438_Thr442del	p.R438_T442del	ENST00000264414	NM_003590.4	438	aGGAGACTTCTCACAAat/aat	9/16	1	2	FACETS	0.862	0.737	0.997	0.862	0.737	0.997	CLONAL	1	TRUE	1	0.2	2		445	650	SUCCESS
BTK	695	MSKCC	GRCh37	X	100625041	100625041	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014135-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	79	615	0	ENST00000308731.7:c.336C>A	p.Tyr112Ter	p.Y112*	ENST00000308731	NM_000061.2	112	taC/taA	5/19	1	2	FACETS	0.965	0.847	1	0.965	0.847	1	CLONAL	1	TRUE	1	0.2	2		615	819	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184073	123184073	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014135-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	63	630	0	ENST00000218089.9:c.931G>T	p.Glu311Ter	p.E311*	ENST00000218089	NM_001042749.1	311	Gag/Tag	11/35	NA	2	FACETS	0.829	0.716	0.952			1	INDETERMINATE	1	TRUE	NA	0.2	2		630	760	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0014141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	50	497	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.545	0.461	0.638	0.545	0.461	0.638	SUBCLONAL	1	TRUE	1	0.24	2		497	764	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220080	5220080	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	287	428	0	ENST00000357368.4:c.3635G>T	p.Arg1212Leu	p.R1212L	ENST00000357368	NM_002850.3	1212	cGc/cTc	22/38	1	2	FACETS	0.949	0.898	1	0.949	0.898	1	CLONAL	1	TRUE	1	0.862994082360351	2		428	701	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505637	186505637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	542	845	0	ENST00000323963.5:c.1045G>A	p.Asp349Asn	p.D349N	ENST00000323963		349	Gat/Aat	10/11	0.82630733174084	1	FACETS	0.982	0.956	1	0.982	0.956	1	CLONAL	1	TRUE	0	0.862994082360351	1		845	727	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	33	453	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.13	2		453	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0014150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	28	270	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.879	0.701	1	0.879	0.701	1	CLONAL	1	TRUE	1	0.13	2		272	490	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0014160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	63	497	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.14	2		497	880	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593397	48593397	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs377767355	NA	P-0014160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	45	329	0	ENST00000342988.3:c.1148T>A	p.Ile383Lys	p.I383K	ENST00000342988	NM_005359.5	383	aTa/aAa	10/12	1	2	FACETS	0.952	0.799	1	0.952	0.799	1	CLONAL	1	TRUE	1	0.14	2		329	675	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285228	212285228	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	181	560	1	ENST00000342788.4:c.3073C>T	p.Pro1025Ser	p.P1025S	ENST00000342788	NM_005235.2	1025	Cct/Tct	25/28	0.723719911322822	3	FACETS	0.889	0.822	0.959	0.445	0.411	0.48	CLONAL	1	TRUE	1	0.723719911322822	3		561	766	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288499	15288499	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	103	247	0	ENST00000263388.2:c.4240G>T	p.Gly1414Cys	p.G1414C	ENST00000263388	NM_000435.2	1414	Ggc/Tgc	24/33	0.723719911322822	3	FACETS	1	0.937	1	0.525	0.474	0.578	CLONAL	1	TRUE	1	0.723719911322822	3		247	369	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932342	36932342	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs757917276	NA	P-0014169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1653	395	1251	2	ENST00000361632.4:c.2127G>A	p.Trp709Ter	p.W709*	ENST00000361632		709	tgG/tgA	16/16	0.678277175570828	4	FACETS	0.919	0.87	0.969	0.459	0.435	0.485	CLONAL	1	TRUE	2	0.723719911322822	4		1253	2048	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432396	49432396	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783729	NA	P-0014169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	233	708	3	ENST00000301067.7:c.8743C>T	p.Arg2915Ter	p.R2915*	ENST00000301067	NM_003482.3	2915	Cga/Tga	34/54	1	2	FACETS	0.909	0.852	0.968	0.909	0.852	0.968	CLONAL	1	TRUE	1	0.723719911322822	2		711	708	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23625413	23625413	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs886039619	NA	P-0014169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	146	459	0	ENST00000261584.4:c.3114-1G>A		p.X1038_splice	ENST00000261584	NM_024675.3	1038			0.723719911322822	3	FACETS	0.851	0.779	0.925	0.425	0.389	0.463	CLONAL	1	TRUE	1	0.723719911322822	3		459	646	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821358	72821358	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	259	725	0	ENST00000268489.5:c.10817C>T	p.Ser3606Phe	p.S3606F	ENST00000268489	NM_006885.3	3606	tCc/tTc	10/10	0.723719911322822	3	FACETS	0.936	0.877	0.997	0.468	0.438	0.499	CLONAL	1	TRUE	1	0.723719911322822	3		725	1041	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347177	89347177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199914958	NA	P-0014169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	297	901	0	ENST00000301030.4:c.5773C>T	p.Pro1925Ser	p.P1925S	ENST00000301030	NM_001256183.1	1925	Ccc/Tcc	9/13	0.723719911322822	3	FACETS	1	0.951	1	0.505	0.476	0.536	CLONAL	1	TRUE	1	0.723719911322822	3		901	1106	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576851	7576851	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0014169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	626	551	0	ENST00000269305.4:c.993+2T>C		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.723719911322822	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.723719911322822	3		551	762	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022565	31022565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	225	601	0	ENST00000375687.4:c.2050C>T	p.Pro684Ser	p.P684S	ENST00000375687	NM_015338.5	684	Cct/Tct	13/13	0.595104470094028	4	FACETS	0.952	0.886	1	0.476	0.443	0.51	CLONAL	1	TRUE	2	0.723719911322822	4		601	1126	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944614	40944614	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159841	NA	P-0014169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	84	253	0	ENST00000373198.4:c.1888G>A	p.Glu630Lys	p.E630K	ENST00000373198	NM_133170.3	630	Gag/Aag	12/32	0.723719911322822	3	FACETS	0.839	0.746	0.937	0.419	0.373	0.469	CLONAL	1	TRUE	1	0.723719911322822	3		253	377	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513267	44513267	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	510	556	0	ENST00000291552.4:c.668G>A	p.Gly223Glu	p.G223E	ENST00000291552	NM_006758.2	223	gGa/gAa	8/8	0.723719911322822	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.723719911322822	3		556	932	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268332	142268332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	213	225	0	ENST00000350721.4:c.3160C>T	p.His1054Tyr	p.H1054Y	ENST00000350721	NM_001184.3	1054	Cat/Tat	15/47	0.678277175570828	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.723719911322822	4		225	485	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602728	55602728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	150	538	0	ENST00000288135.5:c.2549G>A	p.Ser850Asn	p.S850N	ENST00000288135	NM_000222.2	850	aGt/aAt	18/21	0.723719911322822	3	FACETS	0.643	0.588	0.701	0.321	0.293	0.351	SUBCLONAL	1	TRUE	1	0.723719911322822	3		538	878	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081594	143081594	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773880588	NA	P-0014169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	254	657	0	ENST00000262992.4:c.1480G>A	p.Glu494Lys	p.E494K	ENST00000262992	NM_001101669.1	494	Gag/Aag	15/24	0.723719911322822	3	FACETS	0.883	0.827	0.942	0.442	0.413	0.471	CLONAL	1	TRUE	1	0.723719911322822	3		657	1082	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588991	67588991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	135	366	0	ENST00000274335.5:c.1082C>T	p.Ser361Phe	p.S361F	ENST00000274335		361	tCt/tTt	8/15	0.723719911322822	3	FACETS	0.959	0.876	1	0.479	0.438	0.523	CLONAL	1	TRUE	1	0.723719911322822	3		366	530	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510166	149510166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747109578	NA	P-0014169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	541	653	1	ENST00000261799.4:c.1303C>T	p.Arg435Cys	p.R435C	ENST00000261799	NM_002609.3	435	Cgc/Tgc	9/23	0.475646568883247	3	FACETS	1	0.975	1			1	CLONAL	2	TRUE	NA	0.723719911322822	3		654	1006	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675970	30675970	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	752	826	1	ENST00000376406.3:c.2386C>T	p.His796Tyr	p.H796Y	ENST00000376406	NM_014641.2	796	Cac/Tac	8/15	0.723719911322822	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.723719911322822	2		827	991	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30682953	30682953	+	splice_region_variant,5_prime_UTR_variant	Splice_Region	SNP	G	G	A	novel	NA	P-0014169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	500	566	0	ENST00000376406.3:c.-1C>T		p.X1_splice	ENST00000376406	NM_014641.2	1		2/15	0.723719911322822	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.723719911322822	2		566	650	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138629	37138629	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	438	599	0	ENST00000373509.5:c.163G>A	p.Gly55Ser	p.G55S	ENST00000373509	NM_002648.3	55	Ggc/Agc	2/6	0.723719911322822	2	FACETS	0.982	0.952	1	0.982	0.952	1	CLONAL	2	TRUE	0	0.723719911322822	2		599	616	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700235	117700235	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	446	617	0	ENST00000368508.3:c.2584C>T	p.Leu862Phe	p.L862F	ENST00000368508	NM_002944.2	862	Ctt/Ttt	17/43	0.723719911322822	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.723719911322822	2		617	610	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509873	106509873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375751703	NA	P-0014169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	660	747	0	ENST00000359195.3:c.1867G>A	p.Asp623Asn	p.D623N	ENST00000359195	NM_002649.2	623	Gat/Aat	2/11	0.723719911322822	2	FACETS	0.978	0.953	1	0.978	0.953	1	CLONAL	2	TRUE	0	0.723719911322822	2		747	932	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069199	5069199	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0014169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	151	385	0	ENST00000381652.3:c.1504A>T	p.Lys502Ter	p.K502*	ENST00000381652	NM_004972.3	502	Aag/Tag	11/25	0.723719911322822	3	FACETS	0.997	0.916	1	0.498	0.458	0.541	CLONAL	1	TRUE	1	0.723719911322822	3		385	570	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339283	70339283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	566	629	0	ENST00000374080.3:c.160G>A	p.Asp54Asn	p.D54N	ENST00000374080		54	Gat/Aat	2/45	0.723719911322822	4	FACETS	1	0.995	1	0.803	0.775	0.832	CLONAL	2	TRUE	1	0.723719911322822	4		629	1119	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70350003	70350003	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	493	582	0	ENST00000374080.3:c.3986G>A	p.Arg1329Gln	p.R1329Q	ENST00000374080		1329	cGa/cAa	28/45	0.723719911322822	4	FACETS	1	0.994	1	0.773	0.743	0.803	CLONAL	2	TRUE	1	0.723719911322822	4		582	1013	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0014177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1304	42	630	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		630	1346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0014179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	621	422	1	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.474807820370317	4	FACETS	0.978	0.949	1			1	CLONAL	4	TRUE	NA	0.492066725761711	4		423	963	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923394	36923394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759191217	NA	P-0014179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	178	765	1	ENST00000358127.4:c.868G>A	p.Gly290Arg	p.G290R	ENST00000358127	NM_001280556.1	290	Ggg/Agg	7/10	0.490956577492229	2	FACETS	0.969	0.895	1	0.484	0.447	0.523	CLONAL	1	TRUE	0	0.492066725761711	2		766	747	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100934	27100934	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	148	574	1	ENST00000324856.7:c.4216C>A	p.Pro1406Thr	p.P1406T	ENST00000324856	NM_006015.4	1406	Ccc/Acc	18/20	0.492066725761711	1	FACETS	0.967	0.89	1	0.967	0.89	1	CLONAL	1	TRUE	0	0.492066725761711	1		575	469	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800934	18800934	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs540870280	NA	P-0014179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	67	361	1	ENST00000266497.5:c.4310G>T	p.Trp1437Leu	p.W1437L	ENST00000266497		1437	tGg/tTg	31/31	0.48133298709517	4	FACETS	0.758	0.66	0.864	0.253	0.22	0.288	SUBCLONAL	1	TRUE	1	0.492066725761711	4		362	536	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389354	8389354	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	102	532	1	ENST00000356435.5:c.4264C>T	p.Gln1422Ter	p.Q1422*	ENST00000356435		1422	Caa/Taa	26/35	0.490956577492229	2	FACETS	0.766	0.688	0.849	0.383	0.344	0.425	SUBCLONAL	1	TRUE	0	0.492066725761711	2		533	541	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436662	8436662	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	139	482	0	ENST00000356435.5:c.4016T>C	p.Ile1339Thr	p.I1339T	ENST00000356435		1339	aTc/aCc	24/35	0.490956577492229	2	FACETS	1	0.941	1	0.518	0.474	0.564	CLONAL	1	TRUE	0	0.492066725761711	2		482	545	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0014186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	167	332	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.944	0.868	1			1	INDETERMINATE	1	TRUE	NA	0.411502240791234	2		332	860	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654535	29654535	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	60	261	0	ENST00000356175.3:c.5224C>T	p.Gln1742Ter	p.Q1742*	ENST00000356175	NM_000267.3	1742	Caa/Taa	37/57	1	2	FACETS	0.746	0.645	0.855	0.746	0.645	0.855	SUBCLONAL	1	TRUE	1	0.411502240791234	2		261	391	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711993	89711993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	108	405	0	ENST00000371953.3:c.611C>T	p.Pro204Leu	p.P204L	ENST00000371953	NM_000314.4	204	cCa/cTa	6/9	0.411502240791234	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.411502240791234	1		405	394	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664385	29664385	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs747100254	NA	P-0014186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	102	296	0	ENST00000356175.3:c.6365-1G>A		p.X2122_splice	ENST00000356175	NM_000267.3	2122			1	2	FACETS	0.97	0.871	1	0.97	0.871	1	CLONAL	1	TRUE	1	0.411502240791234	2		296	511	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573763	41573763	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	237	1063	1	ENST00000263253.7:c.6048G>T	p.Met2016Ile	p.M2016I	ENST00000263253	NM_001429.3	2016	atG/atT	31/31	1	2	FACETS	0.979	0.912	1	0.979	0.912	1	CLONAL	1	TRUE	1	0.411502240791234	2		1064	1177	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0014187-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	328	548	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.109259337701346	3	FACETS	1	0.994	1	0.745	0.704	0.786	INDETERMINATE	1	FALSE	1	0.503326155292257	3		548	1095	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	153	540	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.898	0.822	0.978	0.898	0.822	0.978	CLONAL	1	TRUE	1	0.406410556468248	2		540	838	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0014195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	297	649	2	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.406410556468248	2		651	1251	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0014195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	110	397	1	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	0.717	0.644	0.794	0.717	0.644	0.794	SUBCLONAL	1	TRUE	1	0.406410556468248	2		398	755	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0014195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	77	418	5	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.641	0.563	0.725	0.641	0.563	0.725	SUBCLONAL	1	TRUE	1	0.406410556468248	2		423	591	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133234519	133234519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	167	465	0	ENST00000320574.5:c.3313G>A	p.Val1105Met	p.V1105M	ENST00000320574	NM_006231.2	1105	Gtg/Atg	27/49	1	2	FACETS	0.942	0.866	1	0.942	0.866	1	CLONAL	1	TRUE	1	0.406410556468248	2		465	872	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482785	67482785	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	398	525	0	ENST00000327367.4:c.1189G>T	p.Glu397Ter	p.E397*	ENST00000327367	NM_005902.3	397	Gag/Tag	9/9	0.406410556468248	2	FACETS	0.97	0.925	1	0.97	0.925	1	CLONAL	2	TRUE	0	0.406410556468248	2		525	1010	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0014207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	65	887	0	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	1	2	FACETS	0.863	0.746	0.99	0.863	0.746	0.99	CLONAL	1	TRUE	1	0.16	2		887	942	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057853	27057853	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	93	1170	2	ENST00000324856.7:c.1561C>T	p.Gln521Ter	p.Q521*	ENST00000324856	NM_006015.4	521	Cag/Tag	3/20	1	2	FACETS	0.987	0.875	1	0.987	0.875	1	CLONAL	1	TRUE	1	0.16	2		1172	1178	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120431	70120431	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1396	74	1626	2	ENST00000245479.2:c.1437del	p.Ile480SerfsTer43	p.I480Sfs*43	ENST00000245479	NM_000346.3	478	aCc/ac	3/3	1	2	FACETS	0.629	0.548	0.717	0.629	0.548	0.717	SUBCLONAL	1	TRUE	1	0.16	2		1628	1470	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218454	1218454	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	56	711	0	ENST00000326873.7:c.329T>A	p.Val110Asp	p.V110D	ENST00000326873	NM_000455.4	110	gTc/gAc	2/10	1	2	FACETS	0.79	0.675	0.917	0.79	0.675	0.917	CLONAL	1	TRUE	1	0.16	2		711	886	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602584	10602584	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	67	639	0	ENST00000171111.5:c.994G>C	p.Gly332Arg	p.G332R	ENST00000171111	NM_203500.1	332	Ggc/Cgc	3/6	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.16	2		639	742	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620683	52620683	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	26	354	0	ENST00000394830.3:c.3070G>T	p.Glu1024Ter	p.E1024*	ENST00000394830	NM_018313.4	1024	Gaa/Taa	21/30	1	2	FACETS	0.886	0.701	1	0.886	0.701	1	CLONAL	1	TRUE	1	0.16	2		354	367	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52621452	52621452	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs1469145695	NA	P-0014207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	57	542	0	ENST00000394830.3:c.2966-1G>C		p.X989_splice	ENST00000394830	NM_018313.4	989			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.16	2		542	487	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968209	68968209	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	60	888	0	ENST00000288368.4:c.1238G>C	p.Ser413Thr	p.S413T	ENST00000288368	NM_024870.2	413	aGc/aCc	10/40	1	2	FACETS	0.999	0.859	1	0.999	0.859	1	CLONAL	1	TRUE	1	0.16	2		888	751	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0014222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	170	509	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.148742618514905	8	FACETS	1	0.967	1	0.729	0.671	0.788	CLONAL	4	FALSE	2	0.148742618514905	8		509	756	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0014222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	479	664	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.148742618514905	7	FACETS	0.951	0.912	0.991			1	CLONAL	8	FALSE	NA	0.148742618514905	7		664	1161	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50820764	50820764	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0014222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	56	266	0	ENST00000398568.2:c.1941-2A>T		p.X647_splice	ENST00000398568	NM_001042412.1	647			0.148742618514905	6	FACETS	0.908	0.785	1	1	0.948	1	CLONAL	4	FALSE	3	0.148742618514905	6		266	269	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	288	426	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	0.706560082471905	NA		426	599	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0014225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	542	604	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.695395855175044	1	FACETS	0.945	0.911	0.979	0.945	0.911	0.979	CLONAL	1	TRUE	0	0.706560082471905	1		604	1050	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188853	32188853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs192478549	NA	P-0014225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	102	586	0	ENST00000375023.3:c.701G>A	p.Arg234Gln	p.R234Q	ENST00000375023	NM_004557.3	234	cGg/cAg	4/30	1	2	FACETS	0.47	0.421	0.522	0.47	0.421	0.522	SUBCLONAL	1	TRUE	1	0.706560082471905	2		586	614	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0014240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	306	683	2	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.517690271695195	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.517690271695195	1		685	807	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0014240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	258	424	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.300849420527651	2	FACETS	1	0.991	1	0.641	0.603	0.681	INDETERMINATE	1	TRUE	0	0.517690271695195	2		424	777	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820624	3820624	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	201	652	0	ENST00000262367.5:c.2827C>T	p.Gln943Ter	p.Q943*	ENST00000262367	NM_004380.2	943	Cag/Tag	14/31	0.177040620646177	2	FACETS	0.722	0.668	0.777	0.361	0.334	0.389	INDETERMINATE	1	TRUE	0	0.517690271695195	2		652	1076	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162688856	162688856	+	start_lost	Translation_Start_Site	SNP	G	G	C	novel	NA	P-0014240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	129	434	0	ENST00000367921.3:c.3G>C	p.Met1?	p.M1?	ENST00000367921	NM_006182.2	1	atG/atC	3/18	0.503434130690138	4	FACETS	0.721	0.652	0.793	0.24	0.217	0.265	SUBCLONAL	1	TRUE	1	0.517690271695195	4		434	1049	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281669	49281669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	386	665	1	ENST00000282018.3:c.716G>T	p.Arg239Leu	p.R239L	ENST00000282018	NM_020377.2	239	cGg/cTg	1/1	0.21613375646321	3	FACETS	1	0.995	1	0.744	0.706	0.782	INDETERMINATE	1	TRUE	1	0.517690271695195	3		666	1262	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946264	81946264	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	156	609	0	ENST00000359376.3:c.1997A>G	p.Asp666Gly	p.D666G	ENST00000359376	NM_002661.3	666	gAc/gGc	19/33	0.199727451278374	0	FACETS	0.419	0.384	0.455			1	INDETERMINATE	1	TRUE	0	0.517690271695195	0		609	694	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288550	15288550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	13	50	0	ENST00000263388.2:c.4189G>A	p.Gly1397Arg	p.G1397R	ENST00000263388	NM_000435.2	1397	Ggg/Agg	24/33	NA	2	FACETS	0.372	0.267	0.499			1	INDETERMINATE	1	TRUE	NA	0.517690271695195	2		50	135	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573913	41573913	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	283	622	0	ENST00000263253.7:c.6198G>T	p.Gln2066His	p.Q2066H	ENST00000263253	NM_001429.3	2066	caG/caT	31/31	NA	2	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.517690271695195	2		622	1011	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535500	187535500	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0014240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	68	259	0	ENST00000441802.2:c.9076-2A>T		p.X3026_splice	ENST00000441802	NM_005245.3	3026			0.517690271695195	1	FACETS	0.773	0.68	0.87	0.773	0.68	0.87	SUBCLONAL	1	TRUE	0	0.517690271695195	1		259	252	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525469	137525469	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	47	429	0	ENST00000367739.4:c.546G>T	p.Glu182Asp	p.E182D	ENST00000367739	NM_000416.2	182	gaG/gaT	4/7	0.42034354833424	1	FACETS	0.202	0.17	0.238	0.202	0.17	0.238	SUBCLONAL	1	TRUE	0	0.517690271695195	1		429	665	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038783	47038783	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	322	681	0	ENST00000377604.3:c.790G>T	p.Glu264Ter	p.E264*	ENST00000377604	NM_001204468.1	264	Gag/Tag	9/24	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.517690271695195	2		681	978	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044577	47044577	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	274	796	3	ENST00000377604.3:c.2074G>T	p.Ala692Ser	p.A692S	ENST00000377604	NM_001204468.1	692	Gct/Tct	18/24	NA	2	FACETS	0.868	0.814	0.923			1	INDETERMINATE	1	TRUE	NA	0.517690271695195	2		799	1220	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211003	36211003	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1337392865	NA	P-0014240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	214	812	0	ENST00000222270.7:c.754C>T	p.Pro252Ser	p.P252S	ENST00000222270	NM_014727.1	252	Ccc/Tcc	3/37	0.205602633465616	2	FACETS	0.68	0.631	0.732	0.34	0.315	0.366	INDETERMINATE	1	TRUE	0	0.517690271695195	2		812	1215	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207162	1207162	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs137853076	NA	P-0014257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	656	1210	1	ENST00000326873.7:c.250A>T	p.Lys84Ter	p.K84*	ENST00000326873	NM_000455.4	84	Aag/Tag	1/10	0.480475190120677	3	FACETS	1	0.995	1	0.761	0.738	0.784	CLONAL	2	TRUE	0	0.67695236043941	3		1211	1136	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101118	41101118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751886972	NA	P-0014257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	109	526	0	ENST00000373198.4:c.1238C>T	p.Ala413Val	p.A413V	ENST00000373198	NM_133170.3	413	gCg/gTg	8/32	0.450821180592802	5	FACETS	0.975	0.876	1	0.325	0.292	0.36	CLONAL	1	TRUE	2	0.67695236043941	5		526	666	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404587	8404587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	46	304	1	ENST00000356435.5:c.4160C>T	p.Ala1387Val	p.A1387V	ENST00000356435		1387	gCg/gTg	25/35	0.493351627451769	3	FACETS	0.567	0.479	0.662	0.283	0.239	0.331	SUBCLONAL	1	TRUE	1	0.67695236043941	3		305	321	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333776	70333776	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	204	559	0	ENST00000373644.4:c.1681G>T	p.Val561Leu	p.V561L	ENST00000373644	NM_030625.2	561	Gtg/Ttg	2/12	0.456623749686547	4	FACETS	1	0.991	1	0.735	0.684	0.786	CLONAL	1	TRUE	2	0.67695236043941	4		559	688	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230728	46230728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	59	275	0	ENST00000334344.6:c.977C>T	p.Ser326Phe	p.S326F	ENST00000334344	NM_152641.2	326	tCt/tTt	8/21	0.489348673107901	3	FACETS	0.655	0.567	0.751	0.328	0.283	0.376	SUBCLONAL	1	TRUE	1	0.67695236043941	3		275	356	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112893789	112893789	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	190	444	0	ENST00000351677.2:c.678A>G	p.Ile226Met	p.I226M	ENST00000351677	NM_002834.3	226	atA/atG	6/16	0.489348673107901	3	FACETS	0.81	0.756	0.864	0.81	0.756	0.864	CLONAL	2	TRUE	1	0.67695236043941	3		444	464	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641233	3641235	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0014257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1198	200	1294	1	ENST00000294008.3:c.2404_2406del	p.Glu802del	p.E802del	ENST00000294008	NM_032444.2	802	GAG/-	12/15	0.456623749686547	4	FACETS	0.709	0.655	0.765	0.354	0.327	0.383	SUBCLONAL	1	TRUE	2	0.67695236043941	4		1295	1398	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610135	10610140	+	inframe_deletion	In_Frame_Del	DEL	TCAGCG	TCAGCG	-	novel	NA	P-0014257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	451	846	1	ENST00000171111.5:c.570_575del	p.Phe190_Glu192delinsLeu	p.F190_E192delinsL	ENST00000171111	NM_203500.1	190	ttCGCTGAg/ttg	2/6	0.480475190120677	3	FACETS	1	0.984	1	0.694	0.667	0.721	CLONAL	2	TRUE	0	0.67695236043941	3		847	856	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25468144	25468144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1472173158	NA	P-0014257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	583	1122	3	ENST00000264709.3:c.1532G>A	p.Gly511Glu	p.G511E	ENST00000264709	NM_175629.2	511	gGa/gAa	13/23	0.450821180592802	5	FACETS	1	0.995	1	0.814	0.783	0.845	CLONAL	2	TRUE	2	0.67695236043941	5		1125	1422	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457239	89457239	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	229	346	0	ENST00000336596.2:c.1720C>G	p.His574Asp	p.H574D	ENST00000336596	NM_005233.5	574	Cat/Gat	9/17	0.678821200137988	3	FACETS	0.92	0.868	0.973	0.92	0.868	0.973	CLONAL	2	TRUE	1	0.67695236043941	3		346	492	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982087	93982087	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	87	442	1	ENST00000369303.4:c.1378G>T	p.Glu460Ter	p.E460*	ENST00000369303	NM_004440.3	460	Gag/Tag	6/17	0.509066439449031	1	FACETS	0.607	0.544	0.673	0.607	0.544	0.673	SUBCLONAL	1	TRUE	0	0.67695236043941	1		443	280	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979524	2979524	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	220	518	0	ENST00000396946.4:c.723G>T	p.Glu241Asp	p.E241D	ENST00000396946	NM_032415.4	241	gaG/gaT	6/25	0.13402610145321	6	FACETS	1	0.967	1			1	INDETERMINATE	2	TRUE	NA	0.67695236043941	6		518	724	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0014259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	496	769	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.763986381150148	1	FACETS	0.986	0.953	1	0.986	0.953	1	CLONAL	1	TRUE	0	0.763986381150148	1		770	814	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717615	89717615	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909227	NA	P-0014259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	46	335	0	ENST00000371953.3:c.640C>T	p.Gln214Ter	p.Q214*	ENST00000371953	NM_000314.4	214	Cag/Tag	7/9	0.763986381150148	1	FACETS	0.251	0.213	0.294	0.251	0.213	0.294	SUBCLONAL	1	TRUE	0	0.763986381150148	1		335	296	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274500	198274500	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	70	405	0	ENST00000335508.6:c.898G>C	p.Glu300Gln	p.E300Q	ENST00000335508	NM_012433.2	300	Gag/Cag	7/25	0.763986381150148	3	FACETS	0.356	0.31	0.406	0.119	0.103	0.136	SUBCLONAL	1	TRUE	0	0.763986381150148	3		405	711	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119666144	119666144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775155403	NA	P-0014259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	216	421	1	ENST00000316626.5:c.337C>T	p.Arg113Cys	p.R113C	ENST00000316626		113	Cgt/Tgt	3/12	1	2	FACETS	0.869	0.812	0.927	0.869	0.812	0.927	CLONAL	1	TRUE	1	0.763986381150148	2		422	651	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0014267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	109	550	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.245900027724819	5	FACETS	1	0.975	1	0.43	0.386	0.478	CLONAL	1	TRUE	2	0.245900027724819	5		550	940	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0014267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	132	813	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.245900027724819	2		813	726	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544742	65544742	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	116	520	0	ENST00000358664.4:c.184del	p.Gln62LysfsTer3	p.Q62Kfs*3	ENST00000358664	NM_002382.4	62	Caa/aa	4/5	0.0723460270929941	4	FACETS	1	0.976	1	1	0.976	1	INDETERMINATE	2	TRUE	2	0.245900027724819	4		520	473	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0014276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	1022	316	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.556893354319783	6	FACETS	0.89	0.867	0.913	1	0.997	1	CLONAL	4	TRUE	3	0.715684825744533	6		316	1950	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0014276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	543	470	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.719867329193639	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.715684825744533	2		471	620	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658334	18658334	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	65	458	0	ENST00000266497.5:c.3139A>G	p.Met1047Val	p.M1047V	ENST00000266497		1047	Atg/Gtg	22/31	0.386696592334451	3	FACETS	0.454	0.394	0.519	0.227	0.197	0.26	INDETERMINATE	1	TRUE	1	0.715684825744533	3		458	543	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347392	89347392	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1169949888	NA	P-0014276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	312	985	0	ENST00000301030.4:c.5558C>T	p.Pro1853Leu	p.P1853L	ENST00000301030	NM_001256183.1	1853	cCa/cTa	9/13	0.719867329193639	3	FACETS	1	0.98	1	0.541	0.51	0.572	CLONAL	1	TRUE	1	0.715684825744533	3		985	1095	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131127	55131127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1248275606	NA	P-0014276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	69	579	0	ENST00000257290.5:c.670G>A	p.Val224Met	p.V224M	ENST00000257290	NM_006206.4	224	Gtg/Atg	5/23	0.719867329193639	4	FACETS	0.344	0.299	0.394	0.172	0.149	0.197	SUBCLONAL	1	TRUE	2	0.715684825744533	4		579	961	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106058	8106058	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	235	547	0	ENST00000346208.3:c.878T>A	p.Met293Lys	p.M293K	ENST00000346208		293	aTg/aAg	4/6	0.255287853241343	4	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	2	0.346910242868344	4		547	893	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063717	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0014283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	150	353	0	ENST00000412916.2:c.165+1G>C		p.X55_splice	ENST00000412916		55			0.346910242868344	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.346910242868344	2		353	406	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858353	27858353	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138060838	NA	P-0014283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	81	453	0	ENST00000359303.2:c.218G>A	p.Arg73Gln	p.R73Q	ENST00000359303	NM_003535.2	73	cGa/cAa	1/1	1	2	FACETS	0.815	0.719	0.918	0.815	0.719	0.918	CLONAL	1	TRUE	1	0.346910242868344	2		453	573	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0014313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	1095	316	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.502255418498446	6	FACETS	1	0.996	1			1	CLONAL	6	TRUE	NA	0.502255418498446	6		316	1393	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814667	43814667	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1302209849	NA	P-0014313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	97	379	0	ENST00000372470.3:c.1462G>C	p.Glu488Gln	p.E488Q	ENST00000372470	NM_005373.2	488	Gag/Cag	9/12	0.264340544953541	6	FACETS	0.955	0.851	1			1	INDETERMINATE	1	TRUE	NA	0.502255418498446	6		379	811	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609105	43609105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1228204486	NA	P-0014313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	471	858	0	ENST00000355710.3:c.1861G>A	p.Glu621Lys	p.E621K	ENST00000355710	NM_020975.4	621	Gag/Aag	10/20	0.127143336957778	5	FACETS	0.857	0.82	0.895			1	INDETERMINATE	3	TRUE	NA	0.502255418498446	5		858	1279	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244128	46244132	+	frameshift_variant	Frame_Shift_Del	DEL	GTTCT	GTTCT	-	novel	NA	P-0014313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	100	484	0	ENST00000334344.6:c.2225_2229del	p.Ser742CysfsTer5	p.S742Cfs*5	ENST00000334344	NM_152641.2	741	aGTTCT/a	15/21	NA	2	FACETS	0.625	0.559	0.695			1	INDETERMINATE	1	TRUE	NA	0.502255418498446	2		484	637	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577052	7577055	+	frameshift_variant	Frame_Shift_Del	DEL	GAGG	GAGG	-	novel	NA	P-0014313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	318	775	0	ENST00000269305.4:c.883_886del	p.Pro295ThrfsTer49	p.P295Tfs*49	ENST00000269305	NM_001126112.2	295	CCTCac/ac	8/11	0.392184811157438	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.502255418498446	1		775	751	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40876370	40876370	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	193	850	0	ENST00000428826.2:c.319T>G	p.Leu107Val	p.L107V	ENST00000428826		107	Ttg/Gtg	5/21	0.494470531426206	3	FACETS	0.843	0.779	0.91	0.281	0.259	0.304	CLONAL	1	TRUE	0	0.502255418498446	3		850	1140	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252994	36252994	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1562	258	595	2	ENST00000300305.3:c.368A>G	p.Asp123Gly	p.D123G	ENST00000300305		123	gAt/gGt	4/8	0.502255418498446	8	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.502255418498446	8		597	1820	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447384	12447384	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	98	506	0	ENST00000287820.6:c.623T>G	p.Ile208Ser	p.I208S	ENST00000287820	NM_015869.4	208	aTc/aGc	5/7	0.228083892304471	5	FACETS	0.836	0.746	0.933			1	INDETERMINATE	1	TRUE	NA	0.502255418498446	5		506	818	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270169	66270169	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	84	500	0	ENST00000273854.3:c.1713G>T	p.Gln571His	p.Q571H	ENST00000273854	NM_004439.5	571	caG/caT	8/18	0.23779502038677	1	FACETS	0.425	0.376	0.478	0.425	0.376	0.478	INDETERMINATE	1	TRUE	0	0.502255418498446	1		500	589	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160603	56160603	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	241	481	0	ENST00000399503.3:c.877C>G	p.Pro293Ala	p.P293A	ENST00000399503	NM_005921.1	293	Cca/Gca	4/20	0.178306425412375	3	FACETS	0.97	0.912	1			1	INDETERMINATE	2	TRUE	NA	0.502255418498446	3		481	619	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210056	55210056	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	272	597	0	ENST00000275493.2:c.166A>C	p.Asn56His	p.N56H	ENST00000275493	NM_005228.3	56	Aat/Cat	2/28	0.124929106201464	5	FACETS	0.914	0.858	0.971	0.609	0.572	0.648	INDETERMINATE	2	TRUE	2	0.502255418498446	5		597	1039	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477870	140477870	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	107	567	0	ENST00000288602.6:c.1438G>T	p.Val480Leu	p.V480L	ENST00000288602	NM_004333.4	480	Gtg/Ttg	12/18	0.41332139582306	3	FACETS	0.611	0.548	0.679	0.204	0.182	0.227	SUBCLONAL	1	TRUE	0	0.502255418498446	3		567	872	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435119	49435119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs574231443	NA	P-0014331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	28	446	0	ENST00000301067.7:c.6434C>T	p.Pro2145Leu	p.P2145L	ENST00000301067	NM_003482.3	2145	cCg/cTg	31/54	0.71317356517662	4	FACETS	0.235	0.187	0.29	0.118	0.093	0.145	SUBCLONAL	1	TRUE	2	0.793475508775946	4		446	538	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287929	33287929	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	432	381	0	ENST00000374542.5:c.1324G>T	p.Glu442Ter	p.E442*	ENST00000374542	NM_001141970.1	442	Gag/Tag	5/8	0.691472586831952	4	FACETS	1	0.995	1			1	CLONAL	3	TRUE	NA	0.793475508775946	4		381	576	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652067	36652073	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCTGG	CGCCTGG	-	novel	NA	P-0014331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	688	651	0	ENST00000244741.5:c.189_195del	p.Phe63LeufsTer83	p.F63Lfs*83	ENST00000244741	NM_000389.4	63	ttCGCCTGG/tt	2/3	0.691472586831952	4	FACETS	0.944	0.925	0.961			1	CLONAL	4	TRUE	NA	0.793475508775946	4		651	824	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0014365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	16	580	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.04	0.029	0.053	0.04	0.029	0.053	SUBCLONAL	1	TRUE	1	1.04	2		580	774	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253427	226253427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	29	29	0	ENST00000366813.1:c.199C>T	p.Pro67Ser	p.P67S	ENST00000366813		67	Ccc/Tcc	2/3	1	2	FACETS	0.969	0.801	1	1	0.971	1	CLONAL	4	TRUE	1	0.17	2		29	88	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103510680	103510680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	206	331	0	ENST00000355739.4:c.584G>A	p.Ser195Asn	p.S195N	ENST00000355739	NM_000123.3	195	aGc/aAc	6/15	1	2	FACETS	1	0.964	1	1	0.995	1	CLONAL	4	TRUE	1	0.17	2		331	578	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618629	37618629	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	637	484	1	ENST00000447079.4:c.305C>A	p.Ser102Ter	p.S102*	ENST00000447079	NM_015083.1	102	tCa/tAa	1/14	1	2	FACETS	1	0.992	1	1	0.998	1	CLONAL	5	TRUE	1	0.17	2		485	1377	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618727	37618727	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	489	442	0	ENST00000447079.4:c.403G>T	p.Glu135Ter	p.E135*	ENST00000447079	NM_015083.1	135	Gaa/Taa	1/14	1	2	FACETS	1	0.981	1	1	0.998	1	CLONAL	4	TRUE	1	0.17	2		442	1377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0014402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	254	604	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.659669467057103	3	FACETS	0.768	0.717	0.82	0.384	0.358	0.41	SUBCLONAL	1	TRUE	1	0.659669467057103	3		604	1334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0014402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	413	673	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.659669467057103	3	FACETS	0.863	0.825	0.901	0.863	0.825	0.901	CLONAL	2	TRUE	1	0.659669467057103	3		674	965	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782006	NA	P-0014402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	405	761	1	ENST00000269305.4:c.859G>A	p.Glu287Lys	p.E287K	ENST00000269305	NM_001126112.2	287	Gag/Aag	8/11	0.659669467057103	3	FACETS	0.878	0.839	0.917	0.878	0.839	0.917	CLONAL	2	TRUE	1	0.659669467057103	3		762	930	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148498	119148498	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	140	435	0	ENST00000264033.4:c.1039C>G	p.Pro347Ala	p.P347A	ENST00000264033	NM_005188.3	347	Cct/Gct	7/16	0.576915895297022	4	FACETS	0.96	0.875	1	0.24	0.218	0.262	CLONAL	1	TRUE	0	0.659669467057103	4		435	734	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435081	49435081	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	315	587	0	ENST00000301067.7:c.6472G>T	p.Glu2158Ter	p.E2158*	ENST00000301067	NM_003482.3	2158	Gag/Tag	31/54	0.659669467057103	5	FACETS	0.971	0.918	1			1	CLONAL	2	TRUE	NA	0.659669467057103	5		587	978	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436029	49436030	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0014402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	447	573	0	ENST00000301067.7:c.5951_5952del	p.Pro1984HisfsTer8	p.P1984Hfs*8	ENST00000301067	NM_003482.3	1984	cCC/c	28/54	0.659669467057103	5	FACETS	0.984	0.945	1			1	CLONAL	3	TRUE	NA	0.659669467057103	5		573	913	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884787	111884787	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	267	530	3	ENST00000341259.2:c.876G>T	p.Glu292Asp	p.E292D	ENST00000341259	NM_005475.2	292	gaG/gaT	4/8	0.213994686040028	6	FACETS	1	0.989	1	0.814	0.766	0.862	INDETERMINATE	2	TRUE	3	0.659669467057103	6		533	769	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556861	29556861	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	83	390	0	ENST00000356175.3:c.2859G>C	p.Leu953Phe	p.L953F	ENST00000356175	NM_000267.3	953	ttG/ttC	22/57	0.659669467057103	4	FACETS	0.625	0.552	0.704			1	SUBCLONAL	1	TRUE	NA	0.659669467057103	4		390	668	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174855	56174855	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	293	485	0	ENST00000399503.3:c.2014G>A	p.Glu672Lys	p.E672K	ENST00000399503	NM_005921.1	672	Gaa/Aaa	11/20	0.602941752744628	3	FACETS	0.907	0.861	0.954	0.907	0.861	0.954	CLONAL	2	TRUE	1	0.659669467057103	3		485	651	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158464	26158464	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs916752202	NA	P-0014402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1968	378	858	0	ENST00000289316.2:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000289316	NM_138720.2	23	Cag/Tag	1/2	0.659669467057103	8	FACETS	1	0.994	1	0.182	0.171	0.193	CLONAL	1	TRUE	0	0.659669467057103	8		858	2346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0014410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	533	684	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.72676430520971	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.72676430520971	2		684	727	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0014410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	118	335	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.939	0.857	1	0.939	0.857	1	CLONAL	1	TRUE	1	0.72676430520971	2		335	346	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924617	94924617	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	143	687	0	ENST00000536441.1:c.293G>C	p.Arg98Pro	p.R98P	ENST00000536441	NM_144665.3	98	cGc/cCc	3/10	0.712403287875741	4	FACETS	0.764	0.696	0.835			1	SUBCLONAL	1	TRUE	NA	0.72676430520971	4		687	890	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360847	118360847	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	154	252	0	ENST00000534358.1:c.4579T>G	p.Cys1527Gly	p.C1527G	ENST00000534358	NM_005933.3	1527	Tgt/Ggt	13/36	0.712403287875741	4	FACETS	0.938	0.869	1			1	CLONAL	2	TRUE	NA	0.72676430520971	4		252	390	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866106	37866106	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	141	525	2	ENST00000269571.5:c.615G>A	p.Trp205Ter	p.W205*	ENST00000269571		205	tgG/tgA	5/27	0.72676430520971	2	FACETS	0.884	0.812	0.958	0.442	0.406	0.479	CLONAL	1	TRUE	0	0.72676430520971	2		527	439	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095572	178095572	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs777530786	NA	P-0014410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	54	302	0	ENST00000397062.3:c.1759A>G	p.Arg587Gly	p.R587G	ENST00000397062	NM_006164.4	587	Aga/Gga	5/5	0.637743548126434	4	FACETS	0.721	0.618	0.832			1	SUBCLONAL	1	TRUE	NA	0.72676430520971	4		302	356	SUCCESS
APC	324	MSKCC	GRCh37	5	112177109	112177109	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs544669011	NA	P-0014410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	293	518	0	ENST00000257430.4:c.5818A>G	p.Ile1940Val	p.I1940V	ENST00000257430	NM_000038.5	1940	Ata/Gta	16/16	0.72676430520971	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.72676430520971	2		518	385	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613377	100613377	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	304	527	0	ENST00000308731.7:c.1023G>T	p.Gln341His	p.Q341H	ENST00000308731	NM_000061.2	341	caG/caT	12/19	0.56117570657139	4	FACETS	0.895	0.847	0.944	0.895	0.847	0.944	CLONAL	2	TRUE	2	0.72676430520971	4		527	807	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781504	NA	P-0014412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	162	630	0	ENST00000269305.4:c.314G>T	p.Gly105Val	p.G105V	ENST00000269305	NM_001126112.2	105	gGc/gTc	4/11	0.310628621547598	1	FACETS	0.809	0.741	0.88	0.809	0.741	0.88	CLONAL	1	TRUE	0	0.311661142173961	1		630	1085	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40679366	40679366	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	127	260	0	ENST00000249776.8:c.444G>A	p.Met148Ile	p.M148I	ENST00000249776	NM_033286.3	148	atG/atA	4/9	1	2	FACETS	0.981	0.888	1	0.981	0.888	1	CLONAL	1	TRUE	1	0.311661142173961	2		260	831	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	1442	540	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.3305941812668	14	FACETS	1	0.995	1			1	CLONAL	11	TRUE	NA	0.3305941812668	14		540	2276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0014462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	303	585	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.265569847011437	2	FACETS	0.866	0.817	0.917	0.866	0.817	0.917	CLONAL	2	TRUE	0	0.3305941812668	2		586	1058	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533760	63533760	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764640447	NA	P-0014462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	90	384	0	ENST00000307078.5:c.1394G>A	p.Arg465His	p.R465H	ENST00000307078	NM_004655.3	465	cGc/cAc	6/11	0.308403208926845	3	FACETS	0.726	0.643	0.815	0.363	0.321	0.408	SUBCLONAL	1	TRUE	1	0.3305941812668	3		384	874	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0014462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	91	381	0	ENST00000304494.5:c.151-1G>A		p.X51_splice	ENST00000304494	NM_000077.4	51			0.32730059388801	1	FACETS	0.872	0.777	0.973	0.872	0.777	0.973	CLONAL	1	TRUE	0	0.3305941812668	1		381	527	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533789	63533790	+	missense_variant	Missense_Mutation	DNP	TG	TG	CA	novel	NA	P-0014462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	198	407	1	ENST00000307078.5:c.1364_1365inv	p.Pro455Leu	p.P455L	ENST00000307078	NM_004655.3	455	cCA/cTG	6/11	0.308403208926845	3	FACETS	0.776	0.719	0.835	0.776	0.719	0.835	SUBCLONAL	2	TRUE	1	0.3305941812668	3		408	899	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0014471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	234	509	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.3	5	FACETS	1	0.942	1	0.675	0.629	0.722	CLONAL	2	TRUE	2	0.29	5		509	1144	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612767	228612767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	59	397	0	ENST00000366696.1:c.260G>A	p.Ser87Asn	p.S87N	ENST00000366696	NM_003493.2	87	aGc/aAc	1/1	0.248458926404134	3	FACETS	0.624	0.536	0.72	0.312	0.268	0.36	SUBCLONAL	1	TRUE	1	0.29	3		397	747	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550542	29550542	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	43	368	0	ENST00000356175.3:c.1804del	p.Glu602LysfsTer3	p.E602Kfs*3	ENST00000356175	NM_000267.3	601	cGg/cg	16/57	1	2	FACETS	0.41	0.342	0.485	0.41	0.342	0.485	SUBCLONAL	1	TRUE	1	0.29	2		368	724	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370292	40370292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1310986199	NA	P-0014471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	79	592	1	ENST00000293328.3:c.1046C>T	p.Ala349Val	p.A349V	ENST00000293328	NM_012448.3	349	gCa/gTa	9/19	1	2	FACETS	0.574	0.504	0.65	0.574	0.504	0.65	SUBCLONAL	1	TRUE	1	0.29	2		593	949	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793306	242793306	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	57	676	0	ENST00000334409.5:c.771G>T	p.Met257Ile	p.M257I	ENST00000334409	NM_005018.2	257	atG/atT	5/5	1	2	FACETS	0.45	0.385	0.521	0.45	0.385	0.521	SUBCLONAL	1	TRUE	1	0.29	2		676	874	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222764	53222764	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	32	297	0	ENST00000375401.3:c.4172T>G	p.Leu1391Arg	p.L1391R	ENST00000375401	NM_004187.3	1391	cTg/cGg	25/26	1	1	FACETS	0.413	0.335	0.501	0.413	0.335	0.501	SUBCLONAL	1	TRUE	0	0.29	1		297	457	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	436	540	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.323268380075164	4	FACETS	0.973	0.928	1	0.973	0.928	1	INDETERMINATE	2	TRUE	2	0.57129224797297	4		540	1233	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939182	131939182	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0014487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	450	436	0	ENST00000265335.6:c.2397+1G>T		p.X799_splice	ENST00000265335		799			0.57129224797297	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.57129224797297	3		436	976	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251917	8251917	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1441070721	NA	P-0014487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	212	559	0	ENST00000335790.3:c.160T>C	p.Cys54Arg	p.C54R	ENST00000335790	NM_002315.2	54	Tgt/Cgt	2/4	1	2	FACETS	0.995	0.927	1	0.995	0.927	1	CLONAL	1	TRUE	1	0.57129224797297	2		559	746	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495670	56495670	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	43	454	0	ENST00000267101.3:c.3860A>T	p.Gln1287Leu	p.Q1287L	ENST00000267101	NM_001982.3	1287	cAa/cTa	28/28	0.323268380075164	4	FACETS	0.34	0.284	0.403	0.17	0.142	0.202	INDETERMINATE	1	TRUE	2	0.57129224797297	4		454	695	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0014496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	150	424	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	0.351332848266135	2		424	849	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610498	10610498	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	165	466	0	ENST00000171111.5:c.212G>T	p.Arg71Leu	p.R71L	ENST00000171111	NM_203500.1	71	cGg/cTg	2/6	0.351332848266135	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.351332848266135	1		466	702	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193172940	193172940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1244272523	NA	P-0014496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	104	276	1	ENST00000367435.3:c.988C>T	p.Arg330Trp	p.R330W	ENST00000367435	NM_024529.4	330	Cgg/Tgg	11/17	0.226518529979615	3	FACETS	0.997	0.894	1	0.499	0.447	0.554	CLONAL	1	TRUE	1	0.351332848266135	3		277	698	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472548	88472548	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0014496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	147	387	0	ENST00000360948.2:c.2007C>G	p.Tyr669Ter	p.Y669*	ENST00000360948	NM_001012338.2	669	taC/taG	16/19	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.351332848266135	2		387	632	SUCCESS
BLM	641	MSKCC	GRCh37	15	91328175	91328175	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	39	328	0	ENST00000355112.3:c.2687T>C	p.Leu896Pro	p.L896P	ENST00000355112	NM_000057.2	896	cTc/cCc	14/22	1	2	FACETS	0.32	0.264	0.382	0.32	0.264	0.382	SUBCLONAL	1	TRUE	1	0.351332848266135	2		328	694	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497370	149497370	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	103	521	0	ENST00000261799.4:c.2948C>G	p.Pro983Arg	p.P983R	ENST00000261799	NM_002609.3	983	cCa/cGa	22/23	0.275750961244127	1	FACETS	0.674	0.603	0.749	0.674	0.603	0.749	SUBCLONAL	1	TRUE	0	0.351332848266135	1		521	717	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221923	1221960	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGCTCCTCGCCGGCTTCTCCTCAGGGATGCTTGAGTA	AGGCTCCTCGCCGGCTTCTCCTCAGGGATGCTTGAGTA	CGGCTC	novel	NA	P-0014496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	129	439	0	ENST00000326873.7:c.863-25_875delinsCGGCTC		p.X288_splice	ENST00000326873	NM_000455.4	288		7/10	0.351332848266135	1	FACETS	0.795	0.722	0.873	0.795	0.722	0.873	SUBCLONAL	1	TRUE	0	0.351332848266135	1		439	761	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0014497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	354	570	2	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	0.173799446091292	12	FACETS	1	0.973	1	0.843	0.803	0.883	CLONAL	9	TRUE	1	0.173799446091292	12		572	821	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577508	7577508	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1060501201	NA	P-0014497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	103	495	1	ENST00000269305.4:c.773A>C	p.Glu258Ala	p.E258A	ENST00000269305	NM_001126112.2	258	gAa/gCa	7/11	0.173799446091292	4	FACETS	0.837	0.751	0.928	0.837	0.751	0.928	CLONAL	3	TRUE	1	0.173799446091292	4		496	554	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811690	102811690	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1347715435	NA	P-0014497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	74	724	2	ENST00000307046.8:c.494C>A	p.Thr165Lys	p.T165K	ENST00000307046	NM_001111285.1	165	aCa/aAa	4/4	0.173799446091292	5	FACETS	1	0.973	1	0.733	0.641	0.833	CLONAL	1	TRUE	3	0.173799446091292	5		726	732	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127622	2127622	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	54	649	1	ENST00000219476.3:c.2861A>T	p.Lys954Ile	p.K954I	ENST00000219476	NM_000548.3	954	aAa/aTa	26/42	NA	2	FACETS	1	0.958	1			1	INDETERMINATE	1	TRUE	NA	0.173799446091292	2		650	459	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375389	15375389	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	45	540	0	ENST00000263377.2:c.1038G>C	p.Lys346Asn	p.K346N	ENST00000263377	NM_058243.2	346	aaG/aaC	6/20	0.103664891276685	5	FACETS	1	0.939	1	0.316	0.265	0.372	INDETERMINATE	1	TRUE	1	0.173799446091292	5		540	517	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214714	36214714	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774265693	NA	P-0014497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	34	457	1	ENST00000222270.7:c.3140G>A	p.Arg1047Gln	p.R1047Q	ENST00000222270	NM_014727.1	1047	cGg/cAg	8/37	0.173799446091292	8	FACETS	1	0.943	1			1	CLONAL	1	TRUE	NA	0.173799446091292	8		458	411	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753293	42753293	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs746938827	NA	P-0014497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	66	894	0	ENST00000222329.4:c.971A>G	p.Tyr324Cys	p.Y324C	ENST00000222329	NM_006494.2	324	tAc/tGc	4/4	0.173799446091292	6	FACETS	0.934	0.808	1			1	CLONAL	1	TRUE	NA	0.173799446091292	6		894	1096	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967284	25967284	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	44	431	0	ENST00000435504.4:c.1922G>T	p.Arg641Leu	p.R641L	ENST00000435504		641	cGt/cTt	13/13	0.173799446091292	6	FACETS	1	0.899	1			1	CLONAL	1	TRUE	NA	0.173799446091292	6		431	619	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61717785	61717785	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	48	436	0	ENST00000401558.2:c.2014G>C	p.Ala672Pro	p.A672P	ENST00000401558	NM_003400.3	672	Gca/Cca	17/25	0.173799446091292	5	FACETS	1	0.898	1	0.362	0.305	0.424	CLONAL	1	TRUE	2	0.173799446091292	5		436	642	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526205	189526205	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	148	702	2	ENST00000264731.3:c.469G>T	p.Asp157Tyr	p.D157Y	ENST00000264731	NM_003722.4	157	Gat/Tat	4/14	0.173799446091292	5	FACETS	0.842	0.769	0.918	0.842	0.769	0.918	CLONAL	3	TRUE	2	0.173799446091292	5		704	850	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057792	180057792	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	22	354	1	ENST00000261937.6:c.163C>T	p.His55Tyr	p.H55Y	ENST00000261937	NM_182925.4	55	Cac/Tac	3/30	0.173799446091292	0	FACETS	1	0.874	1			1	CLONAL	1	TRUE	0	0.173799446091292	0		355	176	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679196	30679196	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	53	487	0	ENST00000376406.3:c.2214G>C	p.Gln738His	p.Q738H	ENST00000376406	NM_014641.2	738	caG/caC	7/15	0.173799446091292	8	FACETS	1	0.941	1	0.244	0.207	0.284	CLONAL	1	TRUE	3	0.173799446091292	8		487	762	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	244	453	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.955	0.898	1	0.955	0.898	1	CLONAL	1	TRUE	1	0.787628313973323	2		453	649	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0014498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	156	269	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.978	0.906	1	0.978	0.906	1	CLONAL	1	TRUE	1	0.787628313973323	2		269	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0014498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	673	580	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.780525699312782	2	FACETS	0.998	0.976	1	0.998	0.976	1	CLONAL	2	TRUE	0	0.787628313973323	2		580	856	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014081	14014081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	46	511	0	ENST00000311895.7:c.59G>A	p.Arg20Gln	p.R20Q	ENST00000311895	NM_005236.2	20	cGa/cAa	1/11	1	2	FACETS	0.166	0.139	0.196	0.166	0.139	0.196	SUBCLONAL	1	TRUE	1	0.787628313973323	2		511	703	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180817	106180817	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs904812983	NA	P-0014498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	26	283	0	ENST00000380013.4:c.3845G>A	p.Gly1282Asp	p.G1282D	ENST00000380013	NM_001127208.2	1282	gGt/gAt	7/11	0.787628313973323	1	FACETS	0.159	0.126	0.196	0.159	0.126	0.196	SUBCLONAL	1	TRUE	0	0.787628313973323	1		283	252	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0014509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	69	441	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.30641883078417	4	FACETS	0.477	0.414	0.545	0.238	0.207	0.273	SUBCLONAL	1	TRUE	2	0.452479323147431	4		441	929	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0014509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	169	533	1	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.278828658527115	2	FACETS	1	0.979	1	0.585	0.539	0.631	CLONAL	1	TRUE	0	0.452479323147431	2		534	639	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914871	32914871	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	51	456	0	ENST00000380152.3:c.6379A>T	p.Ser2127Cys	p.S2127C	ENST00000380152		2127	Agt/Tgt	11/27	0.270722336438827	2	FACETS	0.335	0.284	0.391	0.167	0.142	0.196	INDETERMINATE	1	TRUE	0	0.452479323147431	2		456	673	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346721	89346721	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	27	397	0	ENST00000301030.4:c.6229C>A	p.Leu2077Met	p.L2077M	ENST00000301030	NM_001256183.1	2077	Ctg/Atg	9/13	1	2	FACETS	0.247	0.196	0.305	0.247	0.196	0.305	SUBCLONAL	1	TRUE	1	0.452479323147431	2		397	484	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798066	32798066	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	90	646	0	ENST00000374899.4:c.1613A>C	p.Glu538Ala	p.E538A	ENST00000374899	NM_018833.2	538	gAa/gCa	9/12	0.229731875400801	5	FACETS	0.559	0.494	0.628	0.186	0.164	0.21	INDETERMINATE	1	TRUE	2	0.452479323147431	5		646	1195	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0014517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	347	441	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.625031104864244	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.625031104864244	1		441	654	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056628	26056628	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1561927857	NA	P-0014517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	24	166	0	ENST00000343677.2:c.29C>T	p.Ala10Val	p.A10V	ENST00000343677	NM_005319.3	10	gCt/gTt	1/1	1	2	FACETS	0.244	0.191	0.305	0.244	0.191	0.305	SUBCLONAL	1	TRUE	1	0.625031104864244	2		166	315	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0014518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	203	353	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.871	0.81	0.932	1	0.993	1	CLONAL	2	TRUE	1	0.339431683839317	2		353	687	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164586	36164586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253570532	NA	P-0014518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	107	393	0	ENST00000300305.3:c.1289C>T	p.Pro430Leu	p.P430L	ENST00000300305		430	cCg/cTg	8/8	1	2	FACETS	0.902	0.81	1	0.902	0.81	1	CLONAL	1	TRUE	1	0.339431683839317	2		393	699	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6439805	6439805	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	75	307	0	ENST00000356142.4:c.331A>T	p.Asn111Tyr	p.N111Y	ENST00000356142	NM_018890.3	111	Aat/Tat	5/7	1	2	FACETS	0.705	0.618	0.798	0.705	0.618	0.798	SUBCLONAL	1	TRUE	1	0.339431683839317	2		307	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781504	NA	P-0014526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	381	630	0	ENST00000269305.4:c.314G>T	p.Gly105Val	p.G105V	ENST00000269305	NM_001126112.2	105	gGc/gTc	4/11	0.253647187155562	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.253647187155562	2		630	1409	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0014526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1235	579	548	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.253647187155562	7	FACETS	1	0.978	1	0.823	0.789	0.856	CLONAL	4	TRUE	2	0.253647187155562	7		548	1814	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221722	55221722	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1215	248	410	1	ENST00000275493.2:c.766G>T	p.Asp256Tyr	p.D256Y	ENST00000275493	NM_005228.3	256	Gac/Tac	7/28	0.253647187155562	7	FACETS	1	0.975	1	0.437	0.407	0.468	CLONAL	2	TRUE	2	0.253647187155562	7		411	1463	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145050	58145050	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	57	546	0	ENST00000257904.6:c.294G>C	p.Gln98His	p.Q98H	ENST00000257904	NM_000075.3	98	caG/caC	3/8	1	2	FACETS	0.399	0.341	0.463	0.399	0.341	0.463	SUBCLONAL	1	TRUE	1	0.253647187155562	2		546	1126	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43769886	43769886	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1371986369	NA	P-0014526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	59	586	0	ENST00000382044.4:c.860A>G	p.Gln287Arg	p.Q287R	ENST00000382044	NM_001141980.1	287	cAa/cGa	8/28	1	2	FACETS	0.423	0.362	0.489	0.423	0.362	0.489	SUBCLONAL	1	TRUE	1	0.253647187155562	2		586	1101	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976696	2976696	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	214	450	0	ENST00000396946.4:c.1316C>A	p.Ser439Tyr	p.S439Y	ENST00000396946	NM_032415.4	439	tCc/tAc	9/25	0.253647187155562	5	FACETS	0.988	0.917	1	0.659	0.611	0.708	CLONAL	2	TRUE	2	0.253647187155562	5		450	1179	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0014527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	55	616	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	0.539	0.459	0.627	0.539	0.459	0.627	SUBCLONAL	1	TRUE	1	0.2	2		616	1020	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579329	7579329	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912658	NA	P-0014527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	63	692	0	ENST00000269305.4:c.358A>G	p.Lys120Glu	p.K120E	ENST00000269305	NM_001126112.2	120	Aag/Gag	4/11	1	2	FACETS	0.659	0.568	0.758	0.659	0.568	0.758	SUBCLONAL	1	TRUE	1	0.2	2		692	956	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	255	643	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.426638843671518	1	FACETS	0.907	0.849	0.966	0.907	0.849	0.966	CLONAL	1	TRUE	0	0.426638843671518	1		643	1037	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0014550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	264	406	3	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.57211019016808	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.57211019016808	1		409	569	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244616	46244616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	262	439	0	ENST00000334344.6:c.2710C>T	p.Gln904Ter	p.Q904*	ENST00000334344	NM_152641.2	904	Cag/Tag	15/21	1	2	FACETS	0.922	0.865	0.981	0.922	0.865	0.981	CLONAL	1	TRUE	1	0.57211019016808	2		439	993	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023858	27023858	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	206	235	0	ENST00000324856.7:c.964G>C	p.Asp322His	p.D322H	ENST00000324856	NM_006015.4	322	Gac/Cac	1/20	0.57211019016808	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.57211019016808	1		235	404	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925697	114925697	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	368	420	1	ENST00000543371.1:c.1775A>T	p.Gln592Leu	p.Q592L	ENST00000543371	NM_001198531.1	592	cAg/cTg	14/14	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.57211019016808	2		421	1138	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240981	133240981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	276	372	1	ENST00000320574.5:c.2536G>A	p.Ala846Thr	p.A846T	ENST00000320574	NM_006231.2	846	Gca/Aca	22/49	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.57211019016808	2		373	781	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831281	72831281	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	175	285	2	ENST00000268489.5:c.5300T>C	p.Ile1767Thr	p.I1767T	ENST00000268489	NM_006885.3	1767	aTc/aCc	9/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.57211019016808	2		287	554	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050360	37050360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793652	NA	P-0014550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	141	316	0	ENST00000231790.2:c.509G>A	p.Ser170Asn	p.S170N	ENST00000231790	NM_000249.3	170	aGt/aAt	6/19	0.57211019016808	1	FACETS	0.714	0.655	0.775	0.714	0.655	0.775	SUBCLONAL	1	TRUE	0	0.57211019016808	1		316	493	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557879	187557879	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	288	365	0	ENST00000441802.2:c.3832G>T	p.Asp1278Tyr	p.D1278Y	ENST00000441802	NM_005245.3	1278	Gac/Tac	5/27	0.57211019016808	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.57211019016808	1		365	586	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0014552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	307	568	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	1	2	FACETS	0.751	0.708	0.796	1	0.994	1	SUBCLONAL	2	FALSE	1	0.344867720455543	2		568	1185	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0014552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	92	608	1	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.282419719175339	3	FACETS	1	0.98	1	0.729	0.651	0.811	CLONAL	1	FALSE	1	0.344867720455543	3		609	429	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941881	71941881	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1198	139	599	0	ENST00000298229.2:c.1239C>A	p.Asn413Lys	p.N413K	ENST00000298229	NM_001567.3	413	aaC/aaA	11/28	1	2	FACETS	0.603	0.547	0.662	0.603	0.547	0.662	SUBCLONAL	1	FALSE	1	0.344867720455543	2		599	1337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0014577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	50	406	3	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.422	0.357	0.494	0.422	0.357	0.494	SUBCLONAL	1	TRUE	1	0.27	2		409	878	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627730	37627730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763665826	NA	P-0014577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	76	738	0	ENST00000447079.4:c.1645C>T	p.Pro549Ser	p.P549S	ENST00000447079	NM_015083.1	549	Ccc/Tcc	2/14	1	2	FACETS	0.455	0.397	0.518	0.455	0.397	0.518	SUBCLONAL	1	TRUE	1	0.27	2		738	1237	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099957	157099957	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0014577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	61	542	1	ENST00000346085.5:c.894T>A	p.Tyr298Ter	p.Y298*	ENST00000346085	NM_020732.3	298	taT/taA	1/20	1	2	FACETS	0.47	0.404	0.542	0.47	0.404	0.542	SUBCLONAL	1	TRUE	1	0.27	2		543	962	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923382	36923382	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	57	588	0	ENST00000358127.4:c.880C>T	p.Pro294Ser	p.P294S	ENST00000358127	NM_001280556.1	294	Cca/Tca	7/10	1	2	FACETS	0.419	0.358	0.486	0.419	0.358	0.486	SUBCLONAL	1	TRUE	1	0.27	2		588	1007	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650080	93650080	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	52	410	0	ENST00000375746.1:c.1631T>C	p.Ile544Thr	p.I544T	ENST00000375746	NM_001174167.1	544	aTc/aCc	12/14	1	2	FACETS	0.51	0.433	0.594	0.51	0.433	0.594	SUBCLONAL	1	TRUE	1	0.27	2		410	756	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	187	389	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.873	0.809	0.938			1	INDETERMINATE	1	TRUE	NA	0.632917974766807	2		389	677	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0014578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	324	441	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.632917974766807	2		441	1012	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0014578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	471	604	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	1	2	FACETS	0.903	0.861	0.945	0.903	0.861	0.945	CLONAL	1	TRUE	1	0.632917974766807	2		604	1649	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795407	39795407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371043321	NA	P-0014578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	329	693	0	ENST00000288319.7:c.313G>A	p.Gly105Ser	p.G105S	ENST00000288319	NM_182918.3	105	Ggc/Agc	3/10	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.632917974766807	2		693	1037	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685308	89685308	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876660634	NA	P-0014578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	29	123	0	ENST00000371953.3:c.203A>G	p.Tyr68Cys	p.Y68C	ENST00000371953	NM_000314.4	68	tAc/tGc	3/9	0.632917974766807	1	FACETS	0.185	0.148	0.226	0.185	0.148	0.226	SUBCLONAL	1	TRUE	0	0.632917974766807	1		123	339	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506191	103506191	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs760467381	NA	P-0014578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	281	359	0	ENST00000355739.4:c.349C>G	p.Gln117Glu	p.Q117E	ENST00000355739	NM_000123.3	117	Caa/Gaa	3/15	0.614621958188033	1	FACETS	0.979	0.928	1	0.979	0.928	1	CLONAL	1	TRUE	0	0.632917974766807	1		359	620	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919734	50919734	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878854545	NA	P-0014578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	276	706	0	ENST00000440232.2:c.2902C>T	p.Arg968Cys	p.R968C	ENST00000440232	NM_002691.3	968	Cgc/Tgc	23/27	0.590318876469432	3	FACETS	0.962	0.903	1	0.481	0.451	0.512	CLONAL	1	TRUE	1	0.632917974766807	3		706	1193	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052980	180052980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	293	913	1	ENST00000261937.6:c.1310G>A	p.Arg437His	p.R437H	ENST00000261937	NM_182925.4	437	cGt/cAt	10/30	NA	2	FACETS	0.858	0.808	0.91			1	INDETERMINATE	1	TRUE	NA	0.632917974766807	2		914	1079	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	110	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.213487259250218	2		426	701	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0014614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	59	332	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.807	0.693	0.931	0.807	0.693	0.931	CLONAL	1	TRUE	1	0.213487259250218	2		332	685	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263446	123263446	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	39	491	0	ENST00000358487.5:c.1297G>C	p.Glu433Gln	p.E433Q	ENST00000358487	NM_000141.4	433	Gag/Cag	10/18	1	2	FACETS	0.711	0.589	0.847	0.711	0.589	0.847	SUBCLONAL	1	TRUE	1	0.213487259250218	2		491	514	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857056	9857056	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	31	292	0	ENST00000330684.3:c.4345A>T	p.Ser1449Cys	p.S1449C	ENST00000330684	NM_001134407.1	1449	Agc/Tgc	13/13	1	2	FACETS	0.922	0.747	1	0.922	0.747	1	CLONAL	1	TRUE	1	0.213487259250218	2		292	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576893	7576923	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTGGGGAGAGGAGCTGGTGTTGTTGGGCA	GGCTGGGGAGAGGAGCTGGTGTTGTTGGGCA	-	novel	NA	P-0014614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	50	825	0	ENST00000269305.4:c.923_953del	p.Leu308GlnfsTer27	p.L308Qfs*27	ENST00000269305	NM_001126112.2	308	cTGCCCAACAACACCAGCTCCTCTCCCCAGCCa/ca	9/11	0.0231803349232322	3	FACETS	0.616	0.521	0.722			1	INDETERMINATE	1	TRUE	NA	0.213487259250218	3		825	841	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243023	41243023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80357397	NA	P-0014614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	48	689	0	ENST00000357654.3:c.4123G>A	p.Glu1375Lys	p.E1375K	ENST00000357654	NM_007294.3	1375	Gaa/Aaa	11/23	1	2	FACETS	0.511	0.43	0.6	0.511	0.43	0.6	SUBCLONAL	1	TRUE	1	0.213487259250218	2		689	880	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549596	5549596	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs111291501	NA	P-0014614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	37	649	0	ENST00000397747.3:c.623A>G	p.Asp208Gly	p.D208G	ENST00000397747	NM_025239.3	208	gAc/gGc	4/7	1	2	FACETS	0.503	0.413	0.604	0.503	0.413	0.604	SUBCLONAL	1	TRUE	1	0.213487259250218	2		649	689	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5563193	5563193	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	33	547	0	ENST00000397747.3:c.798G>C	p.Lys266Asn	p.K266N	ENST00000397747	NM_025239.3	266	aaG/aaC	6/7	1	2	FACETS	0.516	0.419	0.626	0.516	0.419	0.626	SUBCLONAL	1	TRUE	1	0.213487259250218	2		547	599	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939033	76939034	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0014614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	40	532	0	ENST00000373344.5:c.1714_1715delinsTT	p.Gly572Leu	p.G572L	ENST00000373344	NM_000489.3	572	GGa/TTa	9/35	0.213487259250218	1	FACETS	0.668	0.555	0.794	0.668	0.555	0.794	SUBCLONAL	1	TRUE	0	0.213487259250218	1		532	501	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0014615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	136	580	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.846028004421799	2		580	308	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527590	29527590	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555610910	NA	P-0014615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	40	788	0	ENST00000356175.3:c.1039C>T	p.Gln347Ter	p.Q347*	ENST00000356175	NM_000267.3	347	Cag/Tag	9/57	1	2	FACETS	0.566	0.477	0.662	0.566	0.477	0.662	SUBCLONAL	1	TRUE	1	0.846028004421799	2		788	167	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17349166	17349174	+	inframe_deletion	In_Frame_Del	DEL	CAGCTTGGC	CAGCTTGGC	-	novel	NA	P-0014615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	123	781	0	ENST00000375499.3:c.694_702del	p.Ala232_Leu234del	p.A232_L234del	ENST00000375499	NM_003000.2	232	GCCAAGCTG/-	7/8	1	2	FACETS	0.912	0.836	0.989	0.912	0.836	0.989	CLONAL	1	TRUE	1	0.846028004421799	2		781	319	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527584	29527584	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	44	801	0	ENST00000356175.3:c.1033C>T	p.Leu345Phe	p.L345F	ENST00000356175	NM_000267.3	345	Ctt/Ttt	9/57	1	2	FACETS	0.598	0.509	0.693	0.598	0.509	0.693	SUBCLONAL	1	TRUE	1	0.846028004421799	2		801	174	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528454	29528454	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	118	779	0	ENST00000356175.3:c.1211C>T	p.Ser404Phe	p.S404F	ENST00000356175	NM_000267.3	404	tCt/tTt	11/57	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.846028004421799	2		779	274	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585360	29585360	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0014615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	114	693	1	ENST00000356175.3:c.4111-2A>T		p.X1371_splice	ENST00000356175	NM_000267.3	1371			1	2	FACETS	0.946	0.865	1	0.946	0.865	1	CLONAL	1	TRUE	1	0.846028004421799	2		694	285	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288922	212288922	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	52	460	0	ENST00000342788.4:c.2824C>G	p.Pro942Ala	p.P942A	ENST00000342788	NM_005235.2	942	Cct/Gct	23/28	0.834333184349863	2	FACETS	0.825	0.718	0.936	0.413	0.359	0.468	CLONAL	1	TRUE	0	0.846028004421799	2		460	149	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552746	226552746	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	162	479	0	ENST00000366794.5:c.2615T>C	p.Ile872Thr	p.I872T	ENST00000366794	NM_001618.3	872	aTc/aCc	19/23	1	2	FACETS	0.799	0.735	0.866	0.799	0.735	0.866	SUBCLONAL	1	TRUE	1	0.570426031260064	2		479	711	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61710167	61710167	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	105	486	0	ENST00000401558.2:c.2737A>G	p.Ser913Gly	p.S913G	ENST00000401558	NM_003400.3	913	Agt/Ggt	22/25	1	2	FACETS	0.862	0.778	0.951	0.862	0.778	0.951	CLONAL	1	TRUE	1	0.570426031260064	2		486	427	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019873	123019873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	105	317	0	ENST00000355640.3:c.361C>A	p.Leu121Met	p.L121M	ENST00000355640		121	Ctg/Atg	2/7	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.570426031260064	1		317	209	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0014623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	49	471	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.817	0.69	0.956	0.817	0.69	0.956	CLONAL	1	TRUE	1	0.17	2		471	706	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200224	67200242	+	frameshift_variant	Frame_Shift_Del	DEL	ATCACGCTGGCCCTGGGCC	ATCACGCTGGCCCTGGGCC	-	novel	NA	P-0014623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1191	67	574	0	ENST00000312629.5:c.535_553del	p.Thr179SerfsTer26	p.T179Sfs*26	ENST00000312629	NM_003952.2	178	ATCACGCTGGCCCTGGGCCat/at	7/15	1	2	FACETS	0.627	0.542	0.719	0.627	0.542	0.719	SUBCLONAL	1	TRUE	1	0.17	2		574	1258	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285038	15285038	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	93	572	0	ENST00000263388.2:c.4577G>A	p.Arg1526His	p.R1526H	ENST00000263388	NM_000435.2	1526	cGt/cAt	25/33	1	2	FACETS	0.98	0.869	1	0.98	0.869	1	CLONAL	1	TRUE	1	0.17	2		572	1116	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157635	106157635	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	31	389	0	ENST00000380013.4:c.2536G>T	p.Glu846Ter	p.E846*	ENST00000380013	NM_001127208.2	846	Gaa/Taa	3/11	1	2	FACETS	0.643	0.519	0.785	0.643	0.519	0.785	SUBCLONAL	1	TRUE	1	0.17	2		389	567	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258992	153258992	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	22	270	0	ENST00000281708.4:c.823del	p.Gln275SerfsTer67	p.Q275Sfs*67	ENST00000281708	NM_033632.3	275	Cag/ag	5/12	1	2	FACETS	0.757	0.586	0.955	0.757	0.586	0.955	CLONAL	1	TRUE	1	0.17	2		270	342	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505000	149505025	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGACTGACCCAGCACAAGCTGGTCCC	GGACTGACCCAGCACAAGCTGGTCCC	-	novel	NA	P-0014623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	50	258	0	ENST00000261799.4:c.1790_1807+8del		p.X597_splice	ENST00000261799	NM_002609.3	597		12/23	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.17	2		258	493	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859465	151859465	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	49	417	0	ENST00000262189.6:c.11197G>T	p.Glu3733Ter	p.E3733*	ENST00000262189	NM_170606.2	3733	Gag/Tag	43/59	1	2	FACETS	0.751	0.634	0.879	0.751	0.634	0.879	SUBCLONAL	1	TRUE	1	0.17	2		417	768	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579353	7579366	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CCAGACGGAAACCG	CCAGACGGAAACCG	-	novel	NA	P-0014624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	367	664	0	ENST00000269305.4:c.321_334del	p.Tyr107Ter	p.Y107*	ENST00000269305	NM_001126112.2	107	taCGGTTTCCGTCTGGgc/tagc	4/11	0.302277239299337	3	FACETS	0.874	0.833	0.914	0.874	0.833	0.914	CLONAL	3	TRUE	0	0.410642569275572	3		664	822	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655159	45655159	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	60	297	0	ENST00000407780.3:c.693G>C	p.Gln231His	p.Q231H	ENST00000407780	NM_001283052.1	231	caG/caC	4/7	0.410642569275572	5	FACETS	0.709	0.61	0.817	0.177	0.152	0.205	SUBCLONAL	1	TRUE	1	0.410642569275572	5		297	666	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056425	26056427	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	rs774779034	NA	P-0014667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	62	246	0	ENST00000343677.2:c.230_232del	p.Asn77del	p.N77del	ENST00000343677	NM_005319.3	77	aACAgc/agc	1/1	0.201920985413133	9	FACETS	1	0.953	1	0.618	0.535	0.707	CLONAL	2	TRUE	5	0.201920985413133	9		246	424	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206861	36206861	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	25	476	2	ENST00000300305.3:c.651del	p.Ser218AlafsTer19	p.S218Afs*19	ENST00000300305		217	ggG/gg	6/8	1	2	FACETS	0.504	0.396	0.629	0.504	0.396	0.629	SUBCLONAL	1	TRUE	1	0.201920985413133	2		478	491	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22417964	22417964	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1263922660	NA	P-0014667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	39	160	0	ENST00000344548.3:c.530T>A	p.Leu177Gln	p.L177Q	ENST00000344548	NM_001039802.1	177	cTg/cAg	7/7	0.190678860145479	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	2	TRUE	0	0.201920985413133	2		160	192	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	86	389	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.617	0.548	0.689	0.617	0.548	0.689	SUBCLONAL	1	TRUE	1	0.624121505412989	2		389	447	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099479	27099479	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0014668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	27	369	0	ENST00000324856.7:c.3715+1G>A		p.X1239_splice	ENST00000324856	NM_006015.4	1239			0.359406001430635	1	FACETS	0.136	0.108	0.168	0.136	0.108	0.168	INDETERMINATE	1	TRUE	0	0.624121505412989	1		369	438	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480608	123480608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	37	198	0	ENST00000371139.4:c.116G>A	p.Gly39Asp	p.G39D	ENST00000371139	NM_001114937.2	39	gGc/gAc	1/4	1	1	FACETS	0.269	0.222	0.321	0.269	0.222	0.321	SUBCLONAL	1	TRUE	0	0.624121505412989	1		198	303	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	125	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.238520359559164	2		426	831	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36814391	36814391	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	46	678	0	ENST00000373129.3:c.649T>G	p.Phe217Val	p.F217V	ENST00000373129	NM_032017.1	217	Ttc/Gtc	8/12	0.238520359559164	1	FACETS	0.467	0.392	0.55	0.467	0.392	0.55	SUBCLONAL	1	TRUE	0	0.238520359559164	1		678	728	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434015	49434015	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	60	802	0	ENST00000301067.7:c.7538G>A	p.Gly2513Glu	p.G2513E	ENST00000301067	NM_003482.3	2513	gGg/gAg	31/54	1	2	FACETS	0.668	0.575	0.77	0.668	0.575	0.77	SUBCLONAL	1	TRUE	1	0.238520359559164	2		802	753	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846140	68846140	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	46	723	0	ENST00000261769.5:c.1111A>T	p.Asn371Tyr	p.N371Y	ENST00000261769	NM_004360.3	371	Aat/Tat	8/16	0.22292444450386	1	FACETS	0.373	0.313	0.44	0.373	0.313	0.44	SUBCLONAL	1	TRUE	0	0.238520359559164	1		723	911	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577600	7577601	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0014674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	68	550	0	ENST00000269305.4:c.680_681del	p.Ser227Ter	p.S227*	ENST00000269305	NM_001126112.2	227	tCT/t	7/11	0.238520359559164	1	FACETS	0.985	0.858	1	0.985	0.858	1	CLONAL	1	TRUE	0	0.238520359559164	1		550	510	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368254	45368254	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	89	534	0	ENST00000262160.6:c.1348G>C	p.Asp450His	p.D450H	ENST00000262160	NM_005901.5	450	Gac/Cac	11/11	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.238520359559164	2		534	674	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604775	48604775	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs377767381	NA	P-0014674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	33	503	0	ENST00000342988.3:c.1597C>G	p.Leu533Val	p.L533V	ENST00000342988	NM_005359.5	533	Ctc/Gtc	12/12	1	2	FACETS	0.426	0.346	0.517	0.426	0.346	0.517	SUBCLONAL	1	TRUE	1	0.238520359559164	2		503	650	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0014675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	45	229	9	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	1	2	FACETS	0.869	0.73	1	0.869	0.73	1	CLONAL	1	TRUE	1	0.22	2		238	471	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492754	50492754	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	77	630	0	ENST00000394963.4:c.1519G>C	p.Glu507Gln	p.E507Q	ENST00000394963	NM_003076.4	507	Gag/Cag	13/13	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.22	2		630	572	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991508	72991508	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	64	932	0	ENST00000268489.5:c.2537G>T	p.Arg846Leu	p.R846L	ENST00000268489	NM_006885.3	846	cGc/cTc	2/10	1	2	FACETS	0.785	0.679	0.901	0.785	0.679	0.901	CLONAL	1	TRUE	1	0.22	2		932	741	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664918	138664918	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	22	303	0	ENST00000330315.3:c.647C>A	p.Ala216Asp	p.A216D	ENST00000330315	NM_023067.3	216	gCc/gAc	1/1	0.280604993984468	3	FACETS	0.565	0.437	0.714	0.282	0.218	0.357	SUBCLONAL	1	TRUE	1	0.22	3		303	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578193	7578193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1420675064	NA	P-0014676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	259	1010	2	ENST00000269305.4:c.656C>T	p.Pro219Leu	p.P219L	ENST00000269305	NM_001126112.2	219	cCc/cTc	6/11	0.540786641682173	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.540786641682173	1		1012	677	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685287	89685287	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	164	218	0	ENST00000371953.3:c.182del	p.His61LeufsTer38	p.H61Lfs*38	ENST00000371953	NM_000314.4	61	cAt/ct	3/9	0.540786641682173	2	FACETS	0.908	0.848	0.968	0.908	0.848	0.968	CLONAL	2	TRUE	0	0.540786641682173	2		218	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578215	7578215	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	267	951	0	ENST00000269305.4:c.634T>G	p.Phe212Val	p.F212V	ENST00000269305	NM_001126112.2	212	Ttt/Gtt	6/11	0.540786641682173	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.540786641682173	1		951	682	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0014684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	82	497	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.768	0.68	0.862	0.768	0.68	0.862	SUBCLONAL	1	TRUE	1	0.471302424690061	2		497	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs587781433	NA	P-0014684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	138	754	0	ENST00000269305.4:c.766A>C	p.Thr256Pro	p.T256P	ENST00000269305	NM_001126112.2	256	Aca/Cca	7/11	0.471302424690061	1	FACETS	0.747	0.682	0.815	0.747	0.682	0.815	SUBCLONAL	1	TRUE	0	0.471302424690061	1		754	599	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0014692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	261	332	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.342901452979611	3	FACETS	0.875	0.825	0.926	0.875	0.825	0.926	CLONAL	3	TRUE	0	0.342901452979611	3		332	679	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578518	7578518	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934875	NA	P-0014692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1215	490	1130	0	ENST00000269305.4:c.412G>C	p.Ala138Pro	p.A138P	ENST00000269305	NM_001126112.2	138	Gcc/Ccc	5/11	0.254642132792439	2	FACETS	0.838	0.8	0.877	0.838	0.8	0.877	CLONAL	2	TRUE	0	0.342901452979611	2		1130	1705	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	120	453	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.808	0.729	0.891	0.808	0.729	0.891	CLONAL	1	TRUE	1	0.34	2		453	874	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	153	540	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	0.815	0.744	0.89			1	INDETERMINATE	1	TRUE	NA	0.34	2		540	1104	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	311	540	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.566961113902893	2	FACETS	0.981	0.937	1	0.981	0.937	1	CLONAL	2	TRUE	0	0.566961113902893	2		540	559	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0014720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	9	330	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.111	0.073	0.16	0.111	0.073	0.16	SUBCLONAL	1	TRUE	1	0.566961113902893	2		330	286	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0014720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	58	449	9	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.3	0.257	0.347	0.3	0.257	0.347	SUBCLONAL	1	TRUE	1	0.566961113902893	2		458	681	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0014720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	28	417	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	0.183	0.146	0.226	0.183	0.146	0.226	SUBCLONAL	1	TRUE	1	0.566961113902893	2		417	539	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774153	66774153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	288	911	1	ENST00000307102.5:c.629G>A	p.Gly210Glu	p.G210E	ENST00000307102	NM_002755.3	210	gGg/gAg	6/11	1	2	FACETS	0.942	0.887	1	0.942	0.887	1	CLONAL	1	TRUE	1	0.566961113902893	2		912	1078	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42870110	42870110	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1334212309	NA	P-0014720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	227	561	0	ENST00000398585.3:c.62T>C	p.Ile21Thr	p.I21T	ENST00000398585	NM_001135099.1	21	aTt/aCt	2/14	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.566961113902893	2		561	695	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527491	157527491	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	127	476	1	ENST00000346085.5:c.5216A>T	p.Asp1739Val	p.D1739V	ENST00000346085	NM_020732.3	1739	gAt/gTt	20/20	1	2	FACETS	0.772	0.702	0.846	0.772	0.702	0.846	SUBCLONAL	1	TRUE	1	0.566961113902893	2		477	580	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90949304	90949304	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1057517262	NA	P-0014720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	72	242	0	ENST00000265433.3:c.2185-1G>A		p.X729_splice	ENST00000265433	NM_002485.4	729			1	2	FACETS	0.849	0.749	0.955	0.849	0.749	0.955	CLONAL	1	TRUE	1	0.566961113902893	2		242	299	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0014757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	352	705	3	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.27518750803579	2	FACETS	1	0.995	1	0.677	0.645	0.709	INDETERMINATE	1	TRUE	0	0.674351424662462	2		708	771	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0014758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	237	376	1	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	0.76383795050855	2		377	615	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0014758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	371	710	1	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	0.954	0.908	1	0.954	0.908	1	CLONAL	1	TRUE	1	0.76383795050855	2		711	1018	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226552	1226552	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	427	673	0	ENST00000326873.7:c.1208A>T	p.Lys403Ile	p.K403I	ENST00000326873	NM_000455.4	403	aAa/aTa	9/10	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.76383795050855	2		673	1118	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579533	7579533	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	260	736	0	ENST00000269305.4:c.154C>T	p.Gln52Ter	p.Q52*	ENST00000269305	NM_001126112.2	52	Caa/Taa	4/11	0.261020466299442	2	FACETS	0.959	0.899	1	0.959	0.899	1	CLONAL	2	TRUE	0	0.267848126332538	2		736	1012	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724620	162724620	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	109	516	0	ENST00000367921.3:c.392C>G	p.Ser131Cys	p.S131C	ENST00000367921	NM_006182.2	131	tCt/tGt	5/18	0.267848126332538	3	FACETS	1	0.98	1	0.687	0.617	0.76	CLONAL	1	TRUE	1	0.267848126332538	3		516	672	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872475	35872475	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	62	478	0	ENST00000216797.5:c.428G>C	p.Arg143Pro	p.R143P	ENST00000216797	NM_020529.2	143	cGa/cCa	3/6	0.20903110393447	3	FACETS	0.621	0.535	0.715	0.311	0.267	0.358	SUBCLONAL	1	TRUE	1	0.267848126332538	3		478	845	SUCCESS
APC	324	MSKCC	GRCh37	5	112174110	112174110	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs544709767	NA	P-0014764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	76	421	0	ENST00000257430.4:c.2819C>T	p.Ser940Leu	p.S940L	ENST00000257430	NM_000038.5	940	tCg/tTg	16/16	0.20903110393447	3	FACETS	1	0.945	1	0.568	0.499	0.643	CLONAL	1	TRUE	1	0.267848126332538	3		421	566	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98241347	98241347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	237	577	0	ENST00000331920.6:c.1150C>T	p.His384Tyr	p.H384Y	ENST00000331920	NM_000264.3	384	Cac/Tac	8/24	0.214754755320195	3	FACETS	1	0.988	1	0.823	0.77	0.877	CLONAL	2	TRUE	0	0.267848126332538	3		577	813	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716326	52716326	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	555	489	0	ENST00000322088.6:c.770G>T	p.Trp257Leu	p.W257L	ENST00000322088	NM_014225.5	257	tGg/tTg	6/15	0.441511094275856	4	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.525631419822527	4		489	1337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579547	7579547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567557016	NA	P-0014790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	385	557	0	ENST00000269305.4:c.140del	p.Pro47ArgfsTer76	p.P47Rfs*76	ENST00000269305	NM_001126112.2	47	cCg/cg	4/11	0.399728980182095	2	FACETS	0.759	0.723	0.795	0.759	0.723	0.795	SUBCLONAL	2	TRUE	0	0.525631419822527	2		557	965	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911590	32911590	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs141702094	NA	P-0014790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	136	351	0	ENST00000380152.3:c.3098A>T	p.Asp1033Val	p.D1033V	ENST00000380152		1033	gAt/gTt	11/27	0.357034505790381	4	FACETS	0.826	0.75	0.906	0.413	0.375	0.453	CLONAL	1	TRUE	2	0.525631419822527	4		351	956	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345977	73345977	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1194	284	425	0	ENST00000377767.4:c.1561C>G	p.Gln521Glu	p.Q521E	ENST00000377767	NM_014953.3	521	Caa/Gaa	11/21	0.525631419822527	5	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.525631419822527	5		425	1478	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322740	30322740	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1408	136	447	0	ENST00000322652.5:c.1753G>C	p.Asp585His	p.D585H	ENST00000322652	NM_015355.2	585	Gat/Cat	14/16	0.361119456011268	6	FACETS	0.687	0.623	0.756	0.229	0.207	0.252	SUBCLONAL	1	TRUE	3	0.525631419822527	6		447	1544	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158132	27158132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773256013	NA	P-0014799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	82	359	0	ENST00000380036.4:c.356G>A	p.Arg119His	p.R119H	ENST00000380036	NM_000459.3	119	cGt/cAt	2/23	0.469623773906971	1	FACETS	0.257	0.226	0.289	0.257	0.226	0.289	SUBCLONAL	1	TRUE	0	0.674283129838363	1		359	628	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0014802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	179	316	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.8	0.738	0.865	0.8	0.738	0.865	SUBCLONAL	1	TRUE	1	0.498697446970511	2		316	897	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57470704	57470704	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	38	305	0	ENST00000371085.3:c.177G>C	p.Gln59His	p.Q59H	ENST00000371085	NM_000516.4	59	caG/caC	2/13	1	2	FACETS	0.254	0.209	0.304	0.254	0.209	0.304	SUBCLONAL	1	TRUE	1	0.498697446970511	2		305	600	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37091976	37091976	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0014802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	100	363	0	ENST00000231790.2:c.2104-1G>C		p.X702_splice	ENST00000231790	NM_000249.3	702			1	2	FACETS	0.609	0.544	0.677	0.609	0.544	0.677	SUBCLONAL	1	TRUE	1	0.498697446970511	2		363	659	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057229	180057229	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754692331	NA	P-0014802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	178	578	0	ENST00000261937.6:c.509G>A	p.Arg170His	p.R170H	ENST00000261937	NM_182925.4	170	cGc/cAc	4/30	1	2	FACETS	0.915	0.845	0.988	0.915	0.845	0.988	CLONAL	1	TRUE	1	0.498697446970511	2		578	780	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395608	31395608	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	185	521	0	ENST00000328111.2:c.2461A>C	p.Met821Leu	p.M821L	ENST00000328111	NM_006892.3	821	Atg/Ctg	23/23	1	2	FACETS	0.958	0.886	1	0.958	0.886	1	CLONAL	1	TRUE	1	0.488463522861578	2		521	791	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	160	520	1	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	1	2	FACETS	0.921	0.846	1	0.921	0.846	1	CLONAL	1	TRUE	1	0.435788579832586	2		521	797	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0014855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	391	684	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.493083233315874	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.493083233315874	2		684	761	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0014855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	45	178	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.454557535037863	3	FACETS	1	0.921	1	0.377	0.321	0.438	CLONAL	1	TRUE	0	0.493083233315874	3		178	201	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594027	55594027	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	149	442	0	ENST00000288135.5:c.1813G>A	p.Glu605Lys	p.E605K	ENST00000288135	NM_000222.2	605	Gag/Aag	12/21	0.242579858937126	3	FACETS	1	0.988	1	0.72	0.662	0.78	INDETERMINATE	1	TRUE	1	0.493083233315874	3		442	523	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032603	12032603	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	302	501	0	ENST00000353533.5:c.1039T>C	p.Cys347Arg	p.C347R	ENST00000353533	NM_003010.3	347	Tgc/Cgc	9/11	0.493083233315874	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.493083233315874	2		501	563	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741614	145741614	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	303	724	0	ENST00000428558.2:c.889G>C	p.Asp297His	p.D297H	ENST00000428558	NM_004260.3	297	Gac/Cac	5/22	0.433792389653179	5	FACETS	0.997	0.94	1	0.665	0.627	0.704	CLONAL	2	TRUE	2	0.493083233315874	5		724	1072	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0014861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	491	603	2	ENST00000269305.4:c.673-1G>C		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.609588125274504	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	0	0.611806654975633	3		605	692	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575657	55575657	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	101	672	0	ENST00000288135.5:c.1183T>A	p.Ser395Thr	p.S395T	ENST00000288135	NM_000222.2	395	Tcc/Acc	7/21	0.577855653297205	2	FACETS	0.974	0.88	1	0.487	0.44	0.536	CLONAL	1	TRUE	0	0.611806654975633	2		672	339	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339610	116339610	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	74	405	0	ENST00000397752.3:c.472G>A	p.Val158Ile	p.V158I	ENST00000397752	NM_000245.2	158	Gtt/Att	2/21	0.611806654975633	4	FACETS	0.746	0.654	0.844	0.186	0.163	0.211	SUBCLONAL	1	TRUE	0	0.611806654975633	4		405	523	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0014880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3	222	316	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.939681587692577	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.939681587692577	2		316	225	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578266	7578266	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs942158624	NA	P-0014880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	408	789	0	ENST00000269305.4:c.583A>T	p.Ile195Phe	p.I195F	ENST00000269305	NM_001126112.2	195	Atc/Ttc	6/11	0.939681587692577	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.939681587692577	1		789	419	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030459	49030459	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	125	479	0	ENST00000267163.4:c.1935del	p.Ser646LeufsTer12	p.S646Lfs*12	ENST00000267163	NM_000321.2	645	aCc/ac	19/27	0.939681587692577	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.939681587692577	1		479	139	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214618	5214618	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767215087	NA	P-0014880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	253	890	1	ENST00000357368.4:c.4448G>A	p.Arg1483Gln	p.R1483Q	ENST00000357368	NM_002850.3	1483	cGg/cAg	29/38	0.939681587692577	2	FACETS	0.419	0.391	0.447	0.209	0.195	0.224	SUBCLONAL	1	TRUE	0	0.939681587692577	2		891	1286	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252792	10252792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	233	604	2	ENST00000340748.4:c.3173G>A	p.Gly1058Asp	p.G1058D	ENST00000340748		1058	gGc/gAc	29/40	0.939681587692577	2	FACETS	0.431	0.402	0.462	0.216	0.201	0.231	SUBCLONAL	1	TRUE	0	0.939681587692577	2		606	1150	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643933	52643933	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1441864184	NA	P-0014880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3	157	415	0	ENST00000394830.3:c.1963A>G	p.Met655Val	p.M655V	ENST00000394830	NM_018313.4	655	Atg/Gtg	17/30	0.939681587692577	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.939681587692577	2		415	160	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994216	21994216	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	526	573	0	ENST00000579755.1:c.115G>T	p.Ala39Ser	p.A39S	ENST00000579755		39	Gcg/Tcg	1/3	1		FACETS		0.988	1				CLONAL	1	TRUE	1	0.939681587692577	2		573	1055	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443618	29443618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200585833	NA	P-0014888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	152	647	3	ENST00000389048.3:c.3599C>T	p.Ala1200Val	p.A1200V	ENST00000389048	NM_004304.4	1200	gCg/gTg	23/29	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.353722421214531	2		650	820	SUCCESS
APC	324	MSKCC	GRCh37	5	112175246	112175246	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1057517558	NA	P-0014897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	162	230	0	ENST00000257430.4:c.3956del	p.Pro1319LeufsTer2	p.P1319Lfs*2	ENST00000257430	NM_000038.5	1319	Cct/ct	16/16	0.59601116681	2	FACETS	0.947	0.888	1	0.947	0.888	1	CLONAL	2	FALSE	0	0.59601116681	2		230	287	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0014897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	334	705	3	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.59601116681	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	0	0.59601116681	1		708	715	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912580	NA	P-0014897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	12	346	0	ENST00000342988.3:c.1157G>A	p.Gly386Asp	p.G386D	ENST00000342988	NM_005359.5	386	gGt/gAt	10/12	0.248411323586521	0	FACETS	0.041	0.028	0.057			1	INDETERMINATE	1	FALSE	0	0.59601116681	0		346	395	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998898	11998898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	86	254	0	ENST00000353533.5:c.400C>T	p.Arg134Trp	p.R134W	ENST00000353533	NM_003010.3	134	Cgg/Tgg	4/11	0.59601116681	1	FACETS	0.873	0.786	0.963	0.873	0.786	0.963	CLONAL	1	FALSE	0	0.59601116681	1		254	232	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625252	69625252	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782761826	NA	P-0014897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	339	849	1	ENST00000334134.2:c.541C>T	p.Arg181Cys	p.R181C	ENST00000334134	NM_005247.2	181	Cgc/Tgc	3/3	0.343456504090938	1	FACETS	0.803	0.762	0.846	0.803	0.762	0.846	INDETERMINATE	1	FALSE	0	0.59601116681	1		850	994	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37081785	37081785	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs63751596	NA	P-0014897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	81	378	0	ENST00000231790.2:c.1667G>A	p.Ser556Asn	p.S556N	ENST00000231790	NM_000249.3	556	aGt/aAt	14/19	0.592039567663149	2	FACETS	0.533	0.471	0.599	0.266	0.235	0.3	SUBCLONAL	1	FALSE	0	0.59601116681	2		378	510	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268766	41268766	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	343	660	0	ENST00000349496.5:c.1004A>T	p.Lys335Ile	p.K335I	ENST00000349496	NM_001904.3	335	aAa/aTa	7/15	1	2	FACETS	0.969	0.922	1	0.969	0.922	1	CLONAL	1	TRUE	1	0.903039714294497	2		660	784	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31421451	31421451	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	400	701	1	ENST00000344624.3:c.3453C>A	p.Asp1151Glu	p.D1151E	ENST00000344624		1151	gaC/gaA	27/33	1	2	FACETS	0.939	0.897	0.982	0.939	0.897	0.982	CLONAL	1	TRUE	1	0.903039714294497	2		702	943	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660071	12660071	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	100	444	0	ENST00000251849.4:c.150T>A	p.Asp50Glu	p.D50E	ENST00000251849	NM_002880.3	50	gaT/gaA	2/17	1	2	FACETS	0.417	0.371	0.465	0.417	0.371	0.465	SUBCLONAL	1	TRUE	1	0.53	2		444	906	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156711	20156711	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	309	466	0	ENST00000379607.5:c.46A>G	p.Lys16Glu	p.K16E	ENST00000379607	NM_001412.3	16	Aag/Gag	2/7	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.53	2		466	977	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0014909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	128	441	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.613	0.554	0.675	0.613	0.554	0.675	SUBCLONAL	1	TRUE	1	0.4	2		441	1044	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0014909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	132	332	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.4	2		332	527	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0014909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	28	535	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.148	0.117	0.183	0.148	0.117	0.183	SUBCLONAL	1	TRUE	1	0.4	2		535	948	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894228	NA	P-0014909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	193	570	1	ENST00000451590.1:c.37G>C	p.Gly13Arg	p.G13R	ENST00000451590	NM_001130442.1	13	Ggt/Cgt	2/5	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.4	2		571	805	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712015	89712015	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	rs121909232	NA	P-0014909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	93	165	0	ENST00000371953.3:c.633C>A	p.Cys211Ter	p.C211*	ENST00000371953	NM_000314.4	211	tgC/tgA	6/9	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.4	2		165	451	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453153	140453153	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913337	NA	P-0014909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	146	492	0	ENST00000288602.6:c.1782T>A	p.Asp594Glu	p.D594E	ENST00000288602	NM_004333.4	594	gaT/gaA	15/18	1	2	FACETS	0.976	0.892	1	0.976	0.892	1	CLONAL	1	TRUE	1	0.4	2		492	748	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786705	3786705	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	110	699	0	ENST00000262367.5:c.4506G>T	p.Trp1502Cys	p.W1502C	ENST00000262367	NM_004380.2	1502	tgG/tgT	27/31	1	2	FACETS	0.482	0.432	0.536	0.482	0.432	0.536	SUBCLONAL	1	TRUE	1	0.4	2		699	1140	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0014942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	76	316	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.256953693635512	1	FACETS	0.828	0.726	0.937	0.828	0.726	0.937	CLONAL	1	TRUE	0	0.256953693635512	1		316	623	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717661	89717661	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0014942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	112	516	0	ENST00000371953.3:c.686C>G	p.Ser229Ter	p.S229*	ENST00000371953	NM_000314.4	229	tCa/tGa	7/9	0.256953693635512	1	FACETS	0.968	0.871	1	0.968	0.871	1	CLONAL	1	TRUE	0	0.256953693635512	1		516	785	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0014951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	319	353	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.306396253945818	5	FACETS	1	0.989	1	1	0.996	1	INDETERMINATE	4	TRUE	2	0.680796256125364	5		353	443	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847332	68847333	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0014951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	322	704	0	ENST00000261769.5:c.1254_1255del	p.Asp418GlufsTer27	p.D418Efs*27	ENST00000261769	NM_004360.3	418	gaTGat/gaat	9/16	0.680796256125364	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.680796256125364	2		704	463	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	163	453	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.928	0.856	1	0.928	0.856	1	CLONAL	1	TRUE	1	0.582620533630894	2		453	603	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71008412	71008412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368167189	NA	P-0014952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	95	474	1	ENST00000318789.4:c.2020G>A	p.Glu674Lys	p.E674K	ENST00000318789	NM_032682.5	674	Gag/Aag	21/21	0.582620533630894	1	FACETS	0.486	0.434	0.54	0.486	0.434	0.54	SUBCLONAL	1	TRUE	0	0.582620533630894	1		475	476	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692775	89692775	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554898053	NA	P-0014952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	37	563	0	ENST00000371953.3:c.259C>T	p.Gln87Ter	p.Q87*	ENST00000371953	NM_000314.4	87	Caa/Taa	5/9	0.582620533630894	1	FACETS	0.332	0.275	0.395	0.332	0.275	0.395	SUBCLONAL	1	TRUE	0	0.582620533630894	1		563	271	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462759	69462759	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0014952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	56	530	0	ENST00000227507.2:c.575-3C>T		p.X192_splice	ENST00000227507	NM_053056.2	192			1	2	FACETS	0.299	0.256	0.346	0.299	0.256	0.346	SUBCLONAL	1	TRUE	1	0.582620533630894	2		530	643	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054015	42054015	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	178	597	0	ENST00000219905.7:c.7478del	p.Asn2493IlefsTer3	p.N2493Ifs*3	ENST00000219905	NM_001164273.1	2493	Aat/at	21/24	1	2	FACETS	0.992	0.919	1	0.992	0.919	1	CLONAL	1	TRUE	1	0.582620533630894	2		597	616	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063317	67063317	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	45	350	1	ENST00000412916.2:c.7C>T	p.Arg3Cys	p.R3C	ENST00000412916		3	Cgc/Tgc	1/6	0.582620533630894	1	FACETS	0.287	0.242	0.337	0.287	0.242	0.337	SUBCLONAL	1	TRUE	0	0.582620533630894	1		351	381	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790105	40790105	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	62	705	0	ENST00000373198.4:c.2626G>T	p.Glu876Ter	p.E876*	ENST00000373198	NM_133170.3	876	Gag/Tag	18/32	1	2	FACETS	0.2	0.172	0.231	0.2	0.172	0.231	SUBCLONAL	1	TRUE	1	0.582620533630894	2		705	1063	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281226	142281226	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	88	743	0	ENST00000350721.4:c.1018G>C	p.Asp340His	p.D340H	ENST00000350721	NM_001184.3	340	Gat/Cat	4/47	1	2	FACETS	0.384	0.34	0.431	0.384	0.34	0.431	SUBCLONAL	1	TRUE	1	0.582620533630894	2		743	787	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043992	180043992	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	64	660	0	ENST00000261937.6:c.3004G>A	p.Glu1002Lys	p.E1002K	ENST00000261937	NM_182925.4	1002	Gag/Aag	22/30	1	2	FACETS	0.299	0.259	0.344	0.299	0.259	0.344	SUBCLONAL	1	TRUE	1	0.582620533630894	2		660	734	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909954	100909954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	462	515	4	ENST00000325455.5:c.2695C>T	p.Arg899Trp	p.R899W	ENST00000325455	NM_001202474.3	899	Cgg/Tgg	8/8	0.620047687043853	2	FACETS	0.967	0.935	0.998	0.967	0.935	0.998	CLONAL	2	TRUE	0	0.673174032036936	2		519	710	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs863224499	NA	P-0014960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	360	708	1	ENST00000269305.4:c.672+1G>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.673174032036936	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.673174032036936	1		709	570	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	149	383	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.273146062545591	2	FACETS	0.947	0.869	1	0.947	0.869	1	CLONAL	2	TRUE	0	0.27	2		383	583	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958169	2958169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772266095	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	218	636	2	ENST00000396946.4:c.2563C>T	p.Arg855Trp	p.R855W	ENST00000396946	NM_032415.4	855	Cgg/Tgg	19/25	0.253457429288473	3	FACETS	0.848	0.788	0.91	0.848	0.788	0.91	CLONAL	2	TRUE	1	0.27	3		638	1081	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	157	569	0	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.27	2		569	1122	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641389	18641389	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1229278001	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	34	235	0	ENST00000266497.5:c.2393del	p.Asn798MetfsTer16	p.N798Mfs*16	ENST00000266497		796	ctA/ct	17/31	1	2	FACETS	0.863	0.707	1	0.863	0.707	1	CLONAL	1	TRUE	1	0.27	2		235	292	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100728	8100728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs771019738	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	116	676	2	ENST00000346208.3:c.708del	p.Ser237AlafsTer28	p.S237Afs*28	ENST00000346208		234	ttC/tt	3/6	1	2	FACETS	0.79	0.711	0.875	0.79	0.711	0.875	SUBCLONAL	1	TRUE	1	0.27	2		678	1087	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372184	55372184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs915105324	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	83	561	0	ENST00000297316.4:c.874G>A	p.Ala292Thr	p.A292T	ENST00000297316	NM_022454.3	292	Gcc/Acc	2/2	1	2	FACETS	0.807	0.711	0.909	0.807	0.711	0.909	CLONAL	1	TRUE	1	0.27	2		561	762	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204842	128204842	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs768767517	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	120	822	0	ENST00000341105.2:c.599del	p.Gly200ValfsTer18	p.G200Vfs*18	ENST00000341105	NM_032638.4	200	gGt/gt	3/6	1	2	FACETS	0.745	0.671	0.824	0.745	0.671	0.824	SUBCLONAL	1	TRUE	1	0.27	2		822	1193	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	133	645	3	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	0.27	2		648	950	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	166	751	3	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.27	2		754	1203	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084146	47084146	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	99	621	0	ENST00000409792.3:c.7143del	p.Ser2382LeufsTer29	p.S2382Lfs*29	ENST00000409792	NM_014159.6	2381	ccC/cc	17/21	0.273146062545591	2	FACETS	0.724	0.645	0.809	0.362	0.322	0.405	SUBCLONAL	1	TRUE	0	0.27	2		621	1013	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900984	114900984	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778855667	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	156	652	0	ENST00000543371.1:c.598del	p.Leu200SerfsTer25	p.L200Sfs*25	ENST00000543371	NM_001198531.1	198	caC/ca	6/14	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.27	2		652	1084	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	211	462	2	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.929	0.865	0.996	1	0.993	1	CLONAL	2	TRUE	1	0.27	2		464	841	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412946	49412946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	145	798	1	ENST00000418115.1:c.77G>A	p.Ser26Asn	p.S26N	ENST00000418115	NM_001664.2	26	aGc/aAc	2/5	0.273146062545591	2	FACETS	0.913	0.831	0.999	0.456	0.415	0.5	CLONAL	1	TRUE	0	0.27	2		799	1177	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713414	40713414	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	71	602	0	ENST00000373198.4:c.4101del	p.Ser1368ProfsTer31	p.S1368Pfs*31	ENST00000373198	NM_133170.3	1367	ccC/cc	30/32	1	2	FACETS	0.591	0.514	0.674	0.591	0.514	0.674	SUBCLONAL	1	TRUE	1	0.27	2		602	890	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812317	212812317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143662416	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	41	369	0	ENST00000342788.4:c.259G>A	p.Val87Met	p.V87M	ENST00000342788	NM_005235.2	87	Gtg/Atg	3/28	1	2	FACETS	0.5	0.415	0.594	0.5	0.415	0.594	SUBCLONAL	1	TRUE	1	0.27	2		369	608	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052626	42052626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	111	484	0	ENST00000219905.7:c.7297C>T	p.Arg2433Trp	p.R2433W	ENST00000219905	NM_001164273.1	2433	Cgg/Tgg	20/24	1	2	FACETS	0.906	0.813	1	0.906	0.813	1	CLONAL	1	TRUE	1	0.27	2		484	908	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528079	157528079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1282942992	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	84	486	0	ENST00000346085.5:c.5804C>T	p.Ala1935Val	p.A1935V	ENST00000346085	NM_020732.3	1935	gCg/gTg	20/20	1	2	FACETS	0.79	0.697	0.889	0.79	0.697	0.889	SUBCLONAL	1	TRUE	1	0.27	2		486	788	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245949	5245949	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	145	780	1	ENST00000357368.4:c.826G>A	p.Val276Met	p.V276M	ENST00000357368	NM_002850.3	276	Gtg/Atg	10/38	1	2	FACETS	0.934	0.85	1	0.934	0.85	1	CLONAL	1	TRUE	1	0.27	2		781	1150	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650799	12650799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398525119	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	84	580	1	ENST00000251849.4:c.356C>T	p.Ala119Val	p.A119V	ENST00000251849	NM_002880.3	119	gCg/gTg	4/17	0.273146062545591	2	FACETS	0.701	0.618	0.79	0.35	0.309	0.395	SUBCLONAL	1	TRUE	0	0.27	2		581	888	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	163	785	0	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.962	0.881	1	0.962	0.881	1	CLONAL	1	TRUE	1	0.27	2		785	1255	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197149	106197149	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1176763299	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	55	308	0	ENST00000380013.4:c.5482C>T	p.Gln1828Ter	p.Q1828*	ENST00000380013	NM_001127208.2	1828	Cag/Tag	11/11	1	2	FACETS	0.7	0.599	0.811	0.7	0.599	0.811	SUBCLONAL	1	TRUE	1	0.27	2		308	582	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074063	8074063	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs190510946	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	73	317	0	ENST00000377482.5:c.596G>A	p.Arg199Gln	p.R199Q	ENST00000377482	NM_018948.3	199	cGa/cAa	4/4	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.27	2		317	538	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105635	27105635	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs370901533	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	87	484	0	ENST00000324856.7:c.5246G>T	p.Arg1749Met	p.R1749M	ENST00000324856	NM_006015.4	1749	aGg/aTg	20/20	1	2	FACETS	0.852	0.754	0.958	0.852	0.754	0.958	CLONAL	1	TRUE	1	0.27	2		484	756	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458665	120458665	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	79	532	0	ENST00000256646.2:c.6680A>G	p.His2227Arg	p.H2227R	ENST00000256646	NM_024408.3	2227	cAc/cGc	34/34	1	2	FACETS	0.857	0.753	0.968	0.857	0.753	0.968	CLONAL	1	TRUE	1	0.27	2		532	683	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830826	156830826	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	115	485	2	ENST00000524377.1:c.100G>A	p.Ala34Thr	p.A34T	ENST00000524377	NM_002529.3	34	Gca/Aca	1/17	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.27	2		487	761	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426605	49426606	+	missense_variant	Missense_Mutation	DNP	TT	TT	AA	novel	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	107	478	0	ENST00000301067.7:c.11882_11883inv	p.Gln3961Leu	p.Q3961L	ENST00000301067	NM_003482.3	3961	cAA/cTT	39/54	1	2	FACETS	0.915	0.82	1	0.915	0.82	1	CLONAL	1	TRUE	1	0.27	2		478	866	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437555	49437557	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	97	553	0	ENST00000301067.7:c.5328_5330del	p.Phe1777del	p.F1777del	ENST00000301067	NM_003482.3	1776	ttCTTt/ttt	23/54	1	2	FACETS	0.902	0.803	1	0.902	0.803	1	CLONAL	1	TRUE	1	0.27	2		553	797	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913436	32913436	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	76	548	0	ENST00000380152.3:c.4948del	p.Ser1650ValfsTer20	p.S1650Vfs*20	ENST00000380152		1648	gcA/gc	11/27	0.253457429288473	3	FACETS	0.634	0.554	0.72	0.317	0.277	0.36	SUBCLONAL	1	TRUE	1	0.27	3		548	1008	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937355	32937355	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507952	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	75	416	0	ENST00000380152.3:c.8021del	p.Lys2674ArgfsTer2	p.K2674Rfs*2	ENST00000380152		2672	atA/at	18/27	0.253457429288473	3	FACETS	0.852	0.746	0.967	0.426	0.373	0.484	CLONAL	1	TRUE	1	0.27	3		416	740	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937480	32937480	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1135401923	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	132	705	0	ENST00000380152.3:c.8145del	p.Val2716TrpfsTer17	p.V2716Wfs*17	ENST00000380152		2714	cAa/ca	18/27	0.253457429288473	3	FACETS	0.955	0.865	1	0.478	0.432	0.525	CLONAL	1	TRUE	1	0.27	3		705	1162	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136246	2136246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1327099376	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	98	597	1	ENST00000219476.3:c.4715C>T	p.Thr1572Met	p.T1572M	ENST00000219476	NM_000548.3	1572	aCg/aTg	37/42	1	2	FACETS	0.759	0.676	0.848	0.759	0.676	0.848	SUBCLONAL	1	TRUE	1	0.27	2		598	956	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991674	72991674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200230716	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	71	424	0	ENST00000268489.5:c.2371G>A	p.Gly791Arg	p.G791R	ENST00000268489	NM_006885.3	791	Ggg/Agg	2/10	1	2	FACETS	0.904	0.789	1	0.904	0.789	1	CLONAL	1	TRUE	1	0.27	2		424	582	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351069	89351069	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	127	671	0	ENST00000301030.4:c.1881del	p.Val628LeufsTer25	p.V628Lfs*25	ENST00000301030	NM_001256183.1	627	aaA/aa	9/13	1	2	FACETS	0.94	0.85	1	0.94	0.85	1	CLONAL	1	TRUE	1	0.27	2		671	1001	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243989	5243989	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	125	599	0	ENST00000357368.4:c.1493C>G	p.Thr498Ser	p.T498S	ENST00000357368	NM_002850.3	498	aCc/aGc	11/38	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.27	2		599	903	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117259	7117259	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	152	732	0	ENST00000302850.5:c.3957G>T	p.Met1319Ile	p.M1319I	ENST00000302850	NM_000208.2	1319	atG/atT	22/22	1	2	FACETS	0.888	0.81	0.97	0.888	0.81	0.97	CLONAL	1	TRUE	1	0.27	2		732	1268	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118632	11118632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555771625	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	107	621	0	ENST00000358026.2:c.2056G>A	p.Glu686Lys	p.E686K	ENST00000358026	NM_001128849.1	686	Gag/Aag	14/36	1	2	FACETS	0.749	0.67	0.833	0.749	0.67	0.833	SUBCLONAL	1	TRUE	1	0.27	2		621	1058	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300134	15300134	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	164	673	0	ENST00000263388.2:c.1142C>T	p.Pro381Leu	p.P381L	ENST00000263388	NM_000435.2	381	cCc/cTc	7/33	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.27	2		673	1137	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945446	17945446	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	125	721	0	ENST00000458235.1:c.2284T>C	p.Tyr762His	p.Y762H	ENST00000458235	NM_000215.3	762	Tat/Cat	17/24	1	2	FACETS	0.885	0.8	0.976	0.885	0.8	0.976	CLONAL	1	TRUE	1	0.27	2		721	1046	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303876	30303876	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	128	693	1	ENST00000262643.3:c.116del	p.Leu39CysfsTer36	p.L39Cfs*36	ENST00000262643	NM_001238.2	38	Ttt/tt	4/12	1	2	FACETS	0.894	0.809	0.985	0.894	0.809	0.985	CLONAL	1	TRUE	1	0.27	2		694	1060	SUCCESS
AXL	558	MSKCC	GRCh37	19	41749573	41749573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144824336	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	185	785	3	ENST00000301178.4:c.1498G>A	p.Val500Met	p.V500M	ENST00000301178	NM_021913.4	500	Gtg/Atg	12/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.27	2		788	1313	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754484	42754484	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777008	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	114	551	2	ENST00000222329.4:c.256C>T	p.Arg86Cys	p.R86C	ENST00000222329	NM_006494.2	86	Cgc/Tgc	2/4	1	2	FACETS	0.909	0.817	1	0.909	0.817	1	CLONAL	1	TRUE	1	0.27	2		553	929	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015065	27015065	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	111	528	0	ENST00000335756.4:c.167A>C	p.Lys56Thr	p.K56T	ENST00000335756	NM_001809.3	56	aAg/aCg	2/5	1	2	FACETS	0.986	0.886	1	0.986	0.886	1	CLONAL	1	TRUE	1	0.27	2		528	834	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707918	47707918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746972142	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	118	555	0	ENST00000233146.2:c.2542G>A	p.Ala848Thr	p.A848T	ENST00000233146	NM_000251.2	848	Gcc/Acc	15/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.27	2		555	778	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919767	96919767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372120755	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	104	583	1	ENST00000258439.3:c.496G>A	p.Gly166Arg	p.G166R	ENST00000258439	NM_001193304.2	166	Gga/Aga	4/4	1	2	FACETS	0.835	0.746	0.929	0.835	0.746	0.929	CLONAL	1	TRUE	1	0.27	2		584	923	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919816	96919816	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	90	518	2	ENST00000258439.3:c.447G>T	p.Trp149Cys	p.W149C	ENST00000258439	NM_001193304.2	149	tgG/tgT	4/4	1	2	FACETS	0.761	0.674	0.854	0.761	0.674	0.854	SUBCLONAL	1	TRUE	1	0.27	2		520	876	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309790	30309790	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374460634	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	88	452	0	ENST00000307677.4:c.232C>T	p.Arg78Trp	p.R78W	ENST00000307677	NM_138578.1	78	Cgg/Tgg	2/3	1	2	FACETS	0.992	0.88	1	0.992	0.88	1	CLONAL	1	TRUE	1	0.27	2		452	657	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256416	46256416	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	127	587	0	ENST00000371998.3:c.644C>A	p.Pro215His	p.P215H	ENST00000371998		215	cCt/cAt	7/23	1	2	FACETS	0.859	0.777	0.946	0.859	0.777	0.946	CLONAL	1	TRUE	1	0.27	2		587	1095	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164863	36164863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	148	782	1	ENST00000300305.3:c.1012G>A	p.Ala338Thr	p.A338T	ENST00000300305		338	Gcg/Acg	8/8	1	2	FACETS	0.883	0.805	0.966	0.883	0.805	0.966	CLONAL	1	TRUE	1	0.27	2		783	1241	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089029	37089030	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	131	367	0	ENST00000231790.2:c.1751_1752del	p.Asp584AlafsTer8	p.D584Afs*8	ENST00000231790	NM_000249.3	584	gAC/g	16/19	0.273146062545591	2	FACETS	0.795	0.724	0.87	0.795	0.724	0.87	SUBCLONAL	2	TRUE	0	0.27	2		367	610	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956163	55956163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190064889	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	106	546	0	ENST00000263923.4:c.3152G>A	p.Arg1051Gln	p.R1051Q	ENST00000263923	NM_002253.2	1051	cGg/cAg	23/30	1	2	FACETS	0.918	0.823	1	0.918	0.823	1	CLONAL	1	TRUE	1	0.27	2		546	855	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193850	106193850	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	89	391	0	ENST00000380013.4:c.4317del	p.Lys1439AsnfsTer9	p.K1439Nfs*9	ENST00000380013	NM_001127208.2	1438	Aaa/aa	10/11	1	2	FACETS	0.912	0.808	1	0.912	0.808	1	CLONAL	1	TRUE	1	0.27	2		391	723	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518768	176518768	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781285001	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	114	750	0	ENST00000292408.4:c.686C>T	p.Ala229Val	p.A229V	ENST00000292408	NM_213647.1	229	gCt/gTt	6/18	1	2	FACETS	0.689	0.619	0.765	0.689	0.619	0.765	SUBCLONAL	1	TRUE	1	0.27	2		750	1225	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394890	394890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1459743512	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	93	479	1	ENST00000380956.4:c.286C>T	p.Arg96Cys	p.R96C	ENST00000380956	NM_001195286.1	96	Cgc/Tgc	3/9	1	2	FACETS	0.788	0.7	0.883	0.788	0.7	0.883	SUBCLONAL	1	TRUE	1	0.27	2		480	874	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715402	117715402	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	85	531	0	ENST00000368508.3:c.1087del	p.Tyr363ThrfsTer6	p.Y363Tfs*6	ENST00000368508	NM_002944.2	363	Tac/ac	10/43	1	2	FACETS	0.937	0.828	1	0.937	0.828	1	CLONAL	1	TRUE	1	0.27	2		531	672	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341817	8341817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	96	592	0	ENST00000356435.5:c.4823C>T	p.Ala1608Val	p.A1608V	ENST00000356435		1608	gCa/gTa	29/35	1	2	FACETS	0.737	0.655	0.824	0.737	0.655	0.824	SUBCLONAL	1	TRUE	1	0.27	2		592	965	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63661977	63661977	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	38	464	0	ENST00000279873.7:c.82del	p.His28ThrfsTer17	p.H28Tfs*17	ENST00000279873	NM_032199.2	27	ttC/tt	2/10	0.259127702882133	1	FACETS	0.602	0.498	0.718	0.602	0.498	0.718	SUBCLONAL	1	TRUE	0	0.259127702882133	1		464	424	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138773	64138773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568464055	NA	P-0015008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	104	1086	3	ENST00000334205.4:c.2140C>T	p.Arg714Trp	p.R714W	ENST00000334205	NM_003942.2	714	Cgg/Tgg	17/17	1	2	FACETS	0.762	0.684	0.843	1	0.983	1	SUBCLONAL	2	TRUE	1	0.259127702882133	2		1089	527	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578221	7578236	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTGTCATCCAAATA	TTCTGTCATCCAAATA	-	novel	NA	P-0015008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	99	986	1	ENST00000269305.4:c.613_628del	p.Tyr205ThrfsTer37	p.Y205Tfs*37	ENST00000269305	NM_001126112.2	205	TATTTGGATGACAGAAac/ac	6/11	0.259127702882133	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.259127702882133	1		987	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0015016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	161	397	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	0.26018123111026	2	FACETS	0.833	0.768	0.901	0.833	0.768	0.901	CLONAL	2	TRUE	0	0.32035627589321	2		397	603	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88679190	88679190	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	62	238	1	ENST00000372037.3:c.1130G>T	p.Cys377Phe	p.C377F	ENST00000372037	NM_004329.2	377	tGc/tTc	10/13	0.26018123111026	2	FACETS	0.824	0.72	0.932	0.824	0.72	0.932	CLONAL	2	TRUE	0	0.32035627589321	2		239	235	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247549	123247549	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918508	NA	P-0015016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	83	505	1	ENST00000358487.5:c.1942G>A	p.Ala648Thr	p.A648T	ENST00000358487	NM_000141.4	648	Gcc/Acc	14/18	0.26018123111026	2	FACETS	0.792	0.699	0.892	0.396	0.349	0.446	SUBCLONAL	1	TRUE	0	0.32035627589321	2		506	654	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251977	8251977	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	237	660	0	ENST00000335790.3:c.100C>T	p.Arg34Cys	p.R34C	ENST00000335790	NM_002315.2	34	Cgc/Tgc	2/4	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.32035627589321	2		660	1136	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0015017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	253	353	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.936	0.879	0.994	1	0.995	1	CLONAL	2	TRUE	1	0.345261800195852	2		353	783	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	163	665	2	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.345261800195852	1	FACETS	0.889	0.816	0.965	0.889	0.816	0.965	CLONAL	1	TRUE	0	0.345261800195852	1		667	879	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032451	12032458	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTAGTAT	TTTAGTAT	AAA	novel	NA	P-0015017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	54	354	2	ENST00000353533.5:c.892-5_894delinsAAA		p.X298_splice	ENST00000353533	NM_003010.3	298		9/11	0.345261800195852	1	FACETS	0.766	0.657	0.883	0.766	0.657	0.883	SUBCLONAL	1	TRUE	0	0.345261800195852	1		356	338	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0015023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	195	1029	1	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.257283304931008	2		1030	1053	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17380457	17380457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557749649	NA	P-0015023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	138	649	0	ENST00000375499.3:c.58G>A	p.Gly20Arg	p.G20R	ENST00000375499	NM_003000.2	20	Gga/Aga	1/8	1	2	FACETS	0.917	0.838	0.999	1	0.99	1	CLONAL	2	TRUE	1	0.257283304931008	2		649	585	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019279	31019279	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	40	388	0	ENST00000375687.4:c.874G>C	p.Asp292His	p.D292H	ENST00000375687	NM_015338.5	292	Gac/Cac	9/13	1	2	FACETS	0.682	0.567	0.81	0.682	0.567	0.81	SUBCLONAL	1	TRUE	1	0.257283304931008	2		388	456	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738699	145738699	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	198	837	1	ENST00000428558.2:c.2365C>G	p.Leu789Val	p.L789V	ENST00000428558	NM_004260.3	789	Ctg/Gtg	15/22	0.235739628728737	3	FACETS	0.973	0.902	1	0.648	0.601	0.698	CLONAL	2	TRUE	0	0.257283304931008	3		838	893	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	295	389	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.994	0.939	1	0.994	0.939	1	CLONAL	1	TRUE	1	0.722375653111481	2		389	822	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576138	29576138	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1555617383	NA	P-0015024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	108	331	0	ENST00000356175.3:c.4110+1G>A		p.X1370_splice	ENST00000356175	NM_000267.3	1370			0.722375653111481	1	FACETS	0.876	0.805	0.947	0.876	0.805	0.947	CLONAL	1	TRUE	0	0.722375653111481	1		331	218	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223221	36223221	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1205	696	800	0	ENST00000222270.7:c.5771C>T	p.Pro1924Leu	p.P1924L	ENST00000222270	NM_014727.1	1924	cCt/cTt	28/37	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.722375653111481	2		800	1901	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0015025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	149	453	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.888	0.815	0.963	0.888	0.815	0.963	CLONAL	1	TRUE	1	0.590730359166793	2		453	568	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993237	72993237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567606533	NA	P-0015025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	78	793	2	ENST00000268489.5:c.808G>A	p.Asp270Asn	p.D270N	ENST00000268489	NM_006885.3	270	Gat/Aat	2/10	0.590730359166793	1	FACETS	0.252	0.221	0.286	0.252	0.221	0.286	SUBCLONAL	1	TRUE	0	0.590730359166793	1		795	737	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202594	67202594	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0015025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	83	599	0	ENST00000312629.5:c.1403C>G	p.Ser468Ter	p.S468*	ENST00000312629	NM_003952.2	468	tCa/tGa	15/15	0.511270075173043	3	FACETS	0.336	0.296	0.38	0.168	0.148	0.19	SUBCLONAL	1	TRUE	1	0.590730359166793	3		599	1082	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175580	108175580	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	149	280	0	ENST00000278616.4:c.5674+1G>A		p.X1892_splice	ENST00000278616	NM_000051.3	1892			0.581456243293429	1	FACETS	0.961	0.889	1	0.961	0.889	1	CLONAL	1	TRUE	0	0.590730359166793	1		280	370	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366345	15366345	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	64	461	0	ENST00000263377.2:c.1810G>C	p.Glu604Gln	p.E604Q	ENST00000263377	NM_058243.2	604	Gag/Cag	10/20	1	2	FACETS	0.48	0.417	0.549	0.48	0.417	0.549	SUBCLONAL	1	TRUE	1	0.590730359166793	2		461	451	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637260	47637260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	93	430	0	ENST00000233146.2:c.394G>A	p.Glu132Lys	p.E132K	ENST00000233146	NM_000251.2	132	Gaa/Aaa	3/16	1	2	FACETS	0.475	0.422	0.531	0.475	0.422	0.531	SUBCLONAL	1	TRUE	1	0.590730359166793	2		430	663	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629199	187629199	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	207	471	0	ENST00000441802.2:c.1783G>A	p.Asp595Asn	p.D595N	ENST00000441802	NM_005245.3	595	Gat/Aat	2/27	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.590730359166793	2		471	633	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38942414	38942414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	56	389	0	ENST00000357387.3:c.5119G>A	p.Glu1707Lys	p.E1707K	ENST00000357387	NM_152756.3	1707	Gaa/Aaa	38/38	1	2	FACETS	0.322	0.276	0.373	0.322	0.276	0.373	SUBCLONAL	1	TRUE	1	0.590730359166793	2		389	588	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151946996	151946996	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0015025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	53	485	0	ENST00000262189.6:c.1778C>G	p.Ser593Ter	p.S593*	ENST00000262189	NM_170606.2	593	tCa/tGa	13/59	1	2	FACETS	0.263	0.224	0.306	0.263	0.224	0.306	SUBCLONAL	1	TRUE	1	0.590730359166793	2		485	682	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139562813	139562813	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs777137452	NA	P-0015025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	54	615	0	ENST00000308874.7:c.79G>A	p.Gly27Ser	p.G27S	ENST00000308874		27	Ggc/Agc	3/10	1	2	FACETS	0.257	0.219	0.299	0.257	0.219	0.299	SUBCLONAL	1	TRUE	1	0.590730359166793	2		615	711	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217918	2217918	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	133	568	0	ENST00000398665.3:c.2691+1G>A		p.X897_splice	ENST00000398665	NM_032482.2	897			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.209555529041078	2		568	1073	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143352325	143352325	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	69	362	2	ENST00000262992.4:c.88A>G	p.Thr30Ala	p.T30A	ENST00000262992	NM_001101669.1	30	Aca/Gca	2/24	0.12504272767887	3	FACETS	0.853	0.741	0.974			1	INDETERMINATE	1	FALSE	NA	0.209555529041078	3		364	853	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	104	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.988	0.886	1	0.988	0.886	1	CLONAL	1	TRUE	1	0.336950428014201	2		426	625	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577595	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0015040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	99	842	0	ENST00000269305.4:c.686_687del	p.Cys229TyrfsTer10	p.C229Yfs*10	ENST00000269305	NM_001126112.2	229	tGT/t	7/11	0.336950428014201	1	FACETS	0.759	0.678	0.844	0.759	0.678	0.844	SUBCLONAL	1	TRUE	0	0.336950428014201	1		842	644	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339864	116339864	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	118	618	0	ENST00000397752.3:c.726A>T	p.Arg242Ser	p.R242S	ENST00000397752	NM_000245.2	242	agA/agT	2/21	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.336950428014201	2		618	613	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593600	55593611	+	inframe_deletion	In_Frame_Del	DEL	CAGTGGAAGGTT	CAGTGGAAGGTT	-	novel	NA	P-0015041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	133	556	0	ENST00000288135.5:c.1666_1677del	p.Gln556_Val559del	p.Q556_V559del	ENST00000288135	NM_000222.2	556	CAGTGGAAGGTT/-	11/21	1	2	FACETS	0.692	0.634	0.751	0.692	0.634	0.751	SUBCLONAL	1	TRUE	1	0.954303988782502	2		556	403	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	54	389	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.29	2		389	370	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0015042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	75	301	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.866	0.76	0.981	0.866	0.76	0.981	CLONAL	1	TRUE	1	0.29	2		301	597	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453111	140453111	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	77	611	0	ENST00000288602.6:c.1824T>A	p.His608Gln	p.H608Q	ENST00000288602	NM_004333.4	608	caT/caA	15/18	1	2	FACETS	0.873	0.767	0.987	0.873	0.767	0.987	CLONAL	1	TRUE	1	0.29	2		611	608	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0015050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	538	558	2	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.494158793517176	4	FACETS	0.926	0.896	0.956	0.926	0.896	0.956	CLONAL	4	TRUE	0	0.494158793517176	4		560	878	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830856	156830856	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	132	517	2	ENST00000524377.1:c.130G>A	p.Gly44Ser	p.G44S	ENST00000524377	NM_002529.3	44	Ggc/Agc	1/17	0.494158793517176	6	FACETS	0.99	0.897	1	0.247	0.224	0.272	CLONAL	1	TRUE	2	0.494158793517176	6		519	1073	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38966811	38966811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	90	335	0	ENST00000357387.3:c.1231G>A	p.Val411Met	p.V411M	ENST00000357387	NM_152756.3	411	Gtg/Atg	15/38	1	2	FACETS	0.802	0.715	0.894	0.802	0.715	0.894	CLONAL	1	TRUE	1	0.494158793517176	2		335	454	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973869	131973869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	123	400	0	ENST00000265335.6:c.3572G>A	p.Gly1191Glu	p.G1191E	ENST00000265335		1191	gGa/gAa	23/25	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.494158793517176	2		400	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0015059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	149	539	1	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.332447112054766	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.332447112054766	1		540	683	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829040	128829042	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	rs570242755	NA	P-0015059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	10	80	1	ENST00000249373.3:c.67_69del	p.Leu23del	p.L23del	ENST00000249373	NM_005631.4	16	ggGCTg/ggg	1/12	0.332447112054766	3	FACETS	0.433	0.294	0.607	0.217	0.147	0.304	SUBCLONAL	1	TRUE	1	0.332447112054766	3		81	162	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319965	8319965	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs141403124	NA	P-0015059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	28	164	0	ENST00000356435.5:c.5536G>A	p.Ala1846Thr	p.A1846T	ENST00000356435		1846	Gcg/Acg	34/35	0.167640419864954	4	FACETS	0.699	0.56	0.858	0.35	0.28	0.429	INDETERMINATE	1	TRUE	2	0.332447112054766	4		164	321	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496913	29496913	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555607073	NA	P-0015059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	75	198	0	ENST00000356175.3:c.484C>T	p.Gln162Ter	p.Q162*	ENST00000356175	NM_000267.3	162	Cag/Tag	5/57	0.332447112054766	2	FACETS	0.936	0.832	1	0.936	0.832	1	CLONAL	2	TRUE	0	0.332447112054766	2		198	241	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965664	93965664	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	135	489	0	ENST00000369303.4:c.2264T>C	p.Val755Ala	p.V755A	ENST00000369303	NM_004440.3	755	gTt/gCt	13/17	0.181327594528299	3	FACETS	0.811	0.74	0.885	0.811	0.74	0.885	INDETERMINATE	2	TRUE	1	0.332447112054766	3		489	584	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553170	106553170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748814652	NA	P-0015059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	140	436	0	ENST00000369096.4:c.1135G>A	p.Ala379Thr	p.A379T	ENST00000369096	NM_001198.3	379	Gcg/Acg	5/7	0.181327594528299	3	FACETS	1	0.982	1	0.656	0.598	0.716	INDETERMINATE	1	TRUE	1	0.332447112054766	3		436	749	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0015075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	142	548	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.216327460954615	2		548	1066	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0015075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	130	618	0	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.216327460954615	2		618	1037	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120509114	120509114	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	rs782183225	NA	P-0015075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	45	345	0	ENST00000256646.2:c.1454-2A>T		p.X485_splice	ENST00000256646	NM_024408.3	485			1	2	FACETS	0.604	0.506	0.712	0.604	0.506	0.712	SUBCLONAL	1	TRUE	1	0.216327460954615	2		345	689	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862866	9862866	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	142	524	1	ENST00000330684.3:c.2437G>A	p.Asp813Asn	p.D813N	ENST00000330684	NM_001134407.1	813	Gac/Aac	12/13	0.158066876715296	2	FACETS	1	0.983	1	0.679	0.618	0.743	CLONAL	1	TRUE	0	0.216327460954615	2		525	967	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37622750	37622750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1171	71	594	0	ENST00000249071.6:c.542C>T	p.Pro181Leu	p.P181L	ENST00000249071	NM_002872.4	181	cCc/cTc	6/7	1	2	FACETS	0.529	0.459	0.604	0.529	0.459	0.604	SUBCLONAL	1	TRUE	1	0.216327460954615	2		594	1242	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245075	53245075	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0015075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	81	310	0	ENST00000375401.3:c.865A>T	p.Lys289Ter	p.K289*	ENST00000375401	NM_004187.3	289	Aag/Tag	7/26	0.156711822359172	0	FACETS	1	0.944	1			1	CLONAL	1	TRUE	NA	0.216327460954615	0		310	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578538	7578538	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1131691037	NA	P-0015083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	331	866	0	ENST00000269305.4:c.392A>T	p.Asn131Ile	p.N131I	ENST00000269305	NM_001126112.2	131	aAc/aTc	5/11	0.222356249788403	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.222356249788403	2		866	1228	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207120	1207120	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	265	785	1	ENST00000326873.7:c.208G>T	p.Glu70Ter	p.E70*	ENST00000326873	NM_000455.4	70	Gag/Tag	1/10	0.222356249788403	1	FACETS	0.951	0.891	1	1	0.995	1	CLONAL	2	TRUE	0	0.222356249788403	1		786	1114	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158510	26158510	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs767721521	NA	P-0015083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	85	472	0	ENST00000289316.2:c.113A>G	p.Tyr38Cys	p.Y38C	ENST00000289316	NM_138720.2	38	tAt/tGt	1/2	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.222356249788403	2		472	706	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600329	10600329	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	205	564	0	ENST00000171111.5:c.1526G>T	p.Gly509Val	p.G509V	ENST00000171111	NM_203500.1	509	gGg/gTg	4/6	0.222356249788403	1	FACETS	1	0.954	1	1	0.994	1	CLONAL	2	TRUE	0	0.222356249788403	1		564	792	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106593	27106593	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	176	619	0	ENST00000324856.7:c.6207del	p.Gln2070SerfsTer65	p.Q2070Sfs*65	ENST00000324856	NM_006015.4	2068	tcG/tc	20/20	0.222356249788403	2	FACETS	0.989	0.913	1	0.989	0.913	1	CLONAL	2	TRUE	0	0.222356249788403	2		619	800	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435541	110435541	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	205	563	0	ENST00000375856.3:c.2860C>A	p.Pro954Thr	p.P954T	ENST00000375856	NM_003749.2	954	Ccg/Acg	1/2	1	2	FACETS	1	0.967	1	1	0.994	1	CLONAL	2	TRUE	1	0.222356249788403	2		563	861	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169512	11169512	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	248	715	0	ENST00000358026.2:c.4678G>T	p.Asp1560Tyr	p.D1560Y	ENST00000358026	NM_001128849.1	1560	Gac/Tac	33/36	0.222356249788403	1	FACETS	0.934	0.874	0.997	1	0.994	1	CLONAL	2	TRUE	0	0.222356249788403	1		715	1061	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727835	41727835	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	220	808	0	ENST00000301178.4:c.460A>T	p.Thr154Ser	p.T154S	ENST00000301178	NM_021913.4	154	Acc/Tcc	4/20	1	2	FACETS	0.889	0.826	0.954	1	0.993	1	CLONAL	2	TRUE	1	0.222356249788403	2		808	1113	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526841	31526841	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35342496	NA	P-0015083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	303	929	0	ENST00000344624.3:c.199C>T	p.Pro67Ser	p.P67S	ENST00000344624		67	Cca/Tca	2/33	0.222356249788403	5	FACETS	0.865	0.814	0.918	0.519	0.488	0.551	CLONAL	3	TRUE	0	0.222356249788403	5		929	1400	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729706	41729706	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780414158	NA	P-0015083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	131	410	0	ENST00000242208.4:c.823G>A	p.Gly275Ser	p.G275S	ENST00000242208	NM_002192.2	275	Ggt/Agt	3/3	0.222356249788403	3	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	1	0.222356249788403	3		410	626	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046480	69046555	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCACTTTCAGTCACTTCTGTCACCAAACTTGGTAAGGAAATCACATGACTCCCACTGTCTGTGTCAACTGTAACC	TTCACTTTCAGTCACTTCTGTCACCAAACTTGGTAAGGAAATCACATGACTCCCACTGTCTGTGTCAACTGTAACC	-	novel	NA	P-0015083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	117	499	0	ENST00000288368.4:c.3954_3984+45del		p.X1318_splice	ENST00000288368	NM_024870.2	1318		32/40	0.222356249788403	6	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.222356249788403	6		499	1042	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971200	21971200	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	164	381	0	ENST00000304494.5:c.158T>C	p.Met53Thr	p.M53T	ENST00000304494	NM_000077.4	53	aTg/aCg	2/3	0.222356249788403	1	FACETS	1	0.971	1	1	0.993	1	CLONAL	2	TRUE	0	0.222356249788403	1		381	591	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344866	70344866	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	162	604	1	ENST00000374080.3:c.2096C>A	p.Pro699Gln	p.P699Q	ENST00000374080		699	cCa/cAa	15/45	1	2	FACETS	0.898	0.825	0.975	1	0.991	1	CLONAL	2	TRUE	1	0.222356249788403	2		605	811	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449925	29449926	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	T	novel	NA	P-0015083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	139	920	0	ENST00000389048.3:c.2929_2930delinsA	p.Gly977ArgfsTer3	p.G977Rfs*3	ENST00000389048	NM_004304.4	977	GGg/Ag	18/29	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.222356249788403	2		920	1190	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0015085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	161	371	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.249646208017956	3	FACETS	1	0.984	1	0.664	0.608	0.723	CLONAL	1	TRUE	1	0.249646208017956	3		371	1092	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0015085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	43	533	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.249646208017956	3	FACETS	0.351	0.292	0.416	0.175	0.146	0.208	SUBCLONAL	1	TRUE	1	0.249646208017956	3		533	1105	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563482	87563482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194954580	NA	P-0015085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	58	656	1	ENST00000277120.3:c.1870G>A	p.Val624Met	p.V624M	ENST00000277120		624	Gtg/Atg	16/19	0.249646208017956	1	FACETS	0.536	0.46	0.62	0.536	0.46	0.62	SUBCLONAL	1	TRUE	0	0.249646208017956	1		657	758	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374245	138374245	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	46	616	1	ENST00000289153.2:c.3199G>T	p.Asp1067Tyr	p.D1067Y	ENST00000289153	NM_006219.2	1067	Gac/Tac	22/22	0.161584854369823	2	FACETS	0.608	0.511	0.715	0.304	0.255	0.358	SUBCLONAL	1	TRUE	0	0.249646208017956	2		617	606	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195427	102195427	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	56	462	0	ENST00000263464.3:c.187A>G	p.Lys63Glu	p.K63E	ENST00000263464	NM_001165.4	63	Aag/Gag	2/9	1	2	FACETS	0.929	0.797	1	0.929	0.797	1	CLONAL	1	TRUE	1	0.249646208017956	2		462	483	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396413	396413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	66	822	1	ENST00000262320.3:c.613G>A	p.Asp205Asn	p.D205N	ENST00000262320	NM_003502.3	205	Gat/Aat	2/11	0.249646208017956	3	FACETS	0.519	0.448	0.595	0.259	0.224	0.298	SUBCLONAL	1	TRUE	1	0.249646208017956	3		823	1147	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600369	10600369	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs549967865	NA	P-0015085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1338	398	923	0	ENST00000171111.5:c.1486G>C	p.Glu496Gln	p.E496Q	ENST00000171111	NM_203500.1	496	Gag/Cag	4/6	0.249646208017956	1	FACETS	0.804	0.762	0.846	1	0.996	1	CLONAL	2	TRUE	0	0.249646208017956	1		923	1736	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719825	52719825	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	335	899	1	ENST00000322088.6:c.1037C>T	p.Ala346Val	p.A346V	ENST00000322088	NM_014225.5	346	gCc/gTc	9/15	0.0708969848677536	4	FACETS	0.875	0.827	0.925			1	INDETERMINATE	3	TRUE	NA	0.249646208017956	4		900	1277	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155373	106155373	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001879-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	68	661	0	ENST00000380013.4:c.274G>C	p.Gly92Arg	p.G92R	ENST00000380013	NM_001127208.2	92	Gga/Cga	3/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		661	968	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	249	528	2				ENST00000310581	NM_198253.2	-/1132			0.449441410066308	1	FACETS	0.688	0.654	0.722	0.688	0.654	0.722	INDETERMINATE	1	TRUE	0	0.903685559893922	1		530	439	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	165	472	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.449441410066308	1	FACETS	0.327	0.301	0.354	0.327	0.301	0.354	INDETERMINATE	1	TRUE	0	0.903685559893922	1		473	612	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	117	227	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.449441410066308	1	FACETS	0.281	0.254	0.308	0.281	0.254	0.308	INDETERMINATE	1	TRUE	0	0.903685559893922	1		227	506	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038231	30038231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	293	697	0	ENST00000338641.4:c.404C>T	p.Pro135Leu	p.P135L	ENST00000338641	NM_000268.3	135	cCt/cTt	4/16	1	2	FACETS	0.546	0.514	0.58	0.546	0.514	0.58	SUBCLONAL	1	TRUE	1	0.903685559893922	2		697	1187	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781509	9781509	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	188	505	0	ENST00000377346.4:c.1819G>A	p.Glu607Lys	p.E607K	ENST00000377346	NM_005026.3	607	Gag/Aag	15/24	0.889647114503413	1	FACETS	0.505	0.471	0.538	0.505	0.471	0.538	SUBCLONAL	1	TRUE	0	0.903685559893922	1		505	452	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543620	29543620	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	254	644	0	ENST00000389048.3:c.1543C>T	p.Gln515Ter	p.Q515*	ENST00000389048	NM_004304.4	515	Caa/Taa	7/29	0.48905611779894	1	FACETS	0.388	0.364	0.412	0.388	0.364	0.412	INDETERMINATE	1	TRUE	0	0.903685559893922	1		644	795	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595851	52595851	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	211	606	0	ENST00000394830.3:c.4064G>A	p.Gly1355Glu	p.G1355E	ENST00000394830	NM_018313.4	1355	gGg/gAg	26/30	0.449441410066308	1	FACETS	0.309	0.287	0.331	0.309	0.287	0.331	INDETERMINATE	1	TRUE	0	0.903685559893922	1		606	829	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447294	187447294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	164	392	1	ENST00000232014.4:c.899G>A	p.Ser300Asn	p.S300N	ENST00000232014	NM_001130845.1	300	aGc/aAc	5/10	0.449441410066308	1	FACETS	0.354	0.327	0.382	0.354	0.327	0.382	INDETERMINATE	1	TRUE	0	0.903685559893922	1		393	562	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638522	176638522	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	209	494	0	ENST00000439151.2:c.3122A>G	p.Asn1041Ser	p.N1041S	ENST00000439151	NM_022455.4	1041	aAc/aGc	5/23	0.449441410066308	1	FACETS	0.384	0.358	0.411	0.384	0.358	0.411	INDETERMINATE	1	TRUE	0	0.903685559893922	1		494	660	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405092	405092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	183	512	1	ENST00000380956.4:c.1174C>T	p.Pro392Ser	p.P392S	ENST00000380956	NM_001195286.1	392	Cca/Tca	8/9	1	2	FACETS	0.454	0.419	0.49	0.454	0.419	0.49	SUBCLONAL	1	TRUE	1	0.903685559893922	2		513	893	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166452	32166452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	218	595	0	ENST00000375023.3:c.4591C>T	p.Pro1531Ser	p.P1531S	ENST00000375023	NM_004557.3	1531	Cct/Tct	25/30	1	2	FACETS	0.497	0.463	0.533	0.497	0.463	0.533	SUBCLONAL	1	TRUE	1	0.903685559893922	2		595	970	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157519986	157519986	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	157	417	0	ENST00000346085.5:c.4055C>T	p.Pro1352Leu	p.P1352L	ENST00000346085	NM_020732.3	1352	cCc/cTc	17/20	1	2	FACETS	0.439	0.403	0.477	0.439	0.403	0.477	SUBCLONAL	1	TRUE	1	0.903685559893922	2		417	791	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683626	162683626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs529360617	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	177	477	0	ENST00000366898.1:c.343G>A	p.Asp115Asn	p.D115N	ENST00000366898	NM_004562.2	115	Gac/Aac	3/12	1	2	FACETS	0.463	0.427	0.501	0.463	0.427	0.501	SUBCLONAL	1	TRUE	1	0.903685559893922	2		477	846	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971375	13971375	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	136	343	1	ENST00000405192.2:c.555-1G>A		p.X185_splice	ENST00000405192	NM_001163147.1	185			1	2	FACETS	0.48	0.438	0.524	0.48	0.438	0.524	SUBCLONAL	1	TRUE	1	0.903685559893922	2		344	627	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415138	116415138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	190	623	0	ENST00000397752.3:c.3232G>A	p.Val1078Met	p.V1078M	ENST00000397752	NM_000245.2	1078	Gtg/Atg	15/21	1	2	FACETS	0.429	0.396	0.463	0.429	0.396	0.463	SUBCLONAL	1	TRUE	1	0.903685559893922	2		623	980	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277118	38277118	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	187	491	0	ENST00000425967.3:c.1310G>A	p.Ser437Asn	p.S437N	ENST00000425967	NM_001174067.1	437	aGt/aAt	10/19	0.449441410066308	1	FACETS	0.329	0.304	0.354	0.329	0.304	0.354	INDETERMINATE	1	TRUE	0	0.903685559893922	1		491	690	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400047	139400047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	275	633	1	ENST00000277541.6:c.4301G>A	p.Gly1434Asp	p.G1434D	ENST00000277541	NM_017617.3	1434	gGt/gAt	25/34	1	2	FACETS	0.513	0.481	0.546	0.513	0.481	0.546	SUBCLONAL	1	TRUE	1	0.903685559893922	2		634	1187	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871249	12871249	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	23	66	0	ENST00000228872.4:c.475+1G>A		p.X159_splice	ENST00000228872	NM_004064.3	159			1	2	FACETS	0.414	0.327	0.511	0.414	0.327	0.511	SUBCLONAL	1	TRUE	1	0.903685559893922	2		66	123	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231362	46231362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	175	478	0	ENST00000334344.6:c.1202G>A	p.Arg401Lys	p.R401K	ENST00000334344	NM_152641.2	401	aGa/aAa	10/21	1	2	FACETS	0.449	0.414	0.486	0.449	0.414	0.486	SUBCLONAL	1	TRUE	1	0.903685559893922	2		478	862	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442480	49442480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	259	758	0	ENST00000301067.7:c.4093G>A	p.Val1365Ile	p.V1365I	ENST00000301067	NM_003482.3	1365	Gtt/Att	13/54	1	2	FACETS	0.468	0.438	0.499	0.468	0.438	0.499	SUBCLONAL	1	TRUE	1	0.903685559893922	2		758	1225	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445163	49445163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	95	241	0	ENST00000301067.7:c.2303C>T	p.Pro768Leu	p.P768L	ENST00000301067	NM_003482.3	768	cCa/cTa	10/54	1	2	FACETS	0.509	0.456	0.565	0.509	0.456	0.565	SUBCLONAL	1	TRUE	1	0.903685559893922	2		241	413	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448200	49448200	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	114	349	0	ENST00000301067.7:c.401-1G>A		p.X134_splice	ENST00000301067	NM_003482.3	134			1	2	FACETS	0.4	0.361	0.442	0.4	0.361	0.442	SUBCLONAL	1	TRUE	1	0.903685559893922	2		349	630	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926528	59926528	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	274	821	0	ENST00000259008.2:c.469G>A	p.Glu157Lys	p.E157K	ENST00000259008	NM_032043.2	157	Gag/Aag	5/20	1	2	FACETS	0.499	0.468	0.531	0.499	0.468	0.531	SUBCLONAL	1	TRUE	1	0.903685559893922	2		821	1215	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45422953	45422953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	326	785	1	ENST00000262160.6:c.175G>A	p.Asp59Asn	p.D59N	ENST00000262160	NM_005901.5	59	Gat/Aat	2/11	0.48905611779894	1	FACETS	0.359	0.339	0.38	0.359	0.339	0.38	INDETERMINATE	1	TRUE	0	0.903685559893922	1		786	1101	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573460	48573460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	161	474	0	ENST00000342988.3:c.44C>T	p.Ala15Val	p.A15V	ENST00000342988	NM_005359.5	15	gCc/gTc	2/12	0.48905611779894	1	FACETS	0.315	0.29	0.341	0.315	0.29	0.341	INDETERMINATE	1	TRUE	0	0.903685559893922	1		474	620	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223021	1223021	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	165	336	0	ENST00000326873.7:c.958G>A	p.Val320Met	p.V320M	ENST00000326873	NM_000455.4	320	Gtg/Atg	8/10	0.44801549065893	2	FACETS	0.487	0.448	0.528	0.243	0.224	0.264	INDETERMINATE	1	TRUE	0	0.903685559893922	2		336	750	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291034	15291034	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	195	464	0	ENST00000263388.2:c.3176G>A	p.Gly1059Glu	p.G1059E	ENST00000263388	NM_000435.2	1059	gGg/gAg	20/33	1	2	FACETS	0.516	0.478	0.555	0.516	0.478	0.555	SUBCLONAL	1	TRUE	1	0.903685559893922	2		464	836	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376428	15376428	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1511	417	1124	1	ENST00000263377.2:c.586G>A	p.Val196Ile	p.V196I	ENST00000263377	NM_058243.2	196	Gta/Ata	5/20	1	2	FACETS	0.479	0.454	0.504	0.479	0.454	0.504	SUBCLONAL	1	TRUE	1	0.903685559893922	2		1125	1928	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791757	42791757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568504941	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	372	373	0	ENST00000575354.2:c.643C>T	p.Arg215Trp	p.R215W	ENST00000575354	NM_015125.3	215	Cgg/Tgg	5/20	0.903685559893922	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.903685559893922	1		373	440	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931990	39931990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	263	384	0	ENST00000378444.4:c.2609C>T	p.Thr870Ile	p.T870I	ENST00000378444	NM_001123385.1	870	aCt/aTt	4/15	1	1	FACETS	0.525	0.496	0.554	0.525	0.496	0.554	SUBCLONAL	1	TRUE	0	0.903685559893922	1		384	608	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035968	47035968	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	302	347	0	ENST00000377604.3:c.646G>A	p.Asp216Asn	p.D216N	ENST00000377604	NM_001204468.1	216	Gac/Aac	7/24	1	1	FACETS	0.548	0.521	0.577	0.548	0.521	0.577	SUBCLONAL	1	TRUE	0	0.903685559893922	1		347	668	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190057	123190057	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	257	399	0	ENST00000218089.9:c.1276G>A	p.Val426Ile	p.V426I	ENST00000218089	NM_001042749.1	426	Gta/Ata	14/35	1	1	FACETS	0.533	0.503	0.563	0.533	0.503	0.563	SUBCLONAL	1	TRUE	0	0.903685559893922	1		399	585	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433867	78433870	+	frameshift_variant	Frame_Shift_Del	DEL	CTTT	CTTT	-	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	417	582	0	ENST00000370768.2:c.229_232del	p.Lys77LeufsTer23	p.K77Lfs*23	ENST00000370768	NM_003902.3	77	AAAGtt/tt	3/20	0.903685559893922	1	FACETS	0.975	0.949	0.999	0.975	0.949	0.999	CLONAL	1	TRUE	0	0.903685559893922	1		582	519	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936109	49936109	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	281	865	2	ENST00000296474.3:c.1561C>T	p.Pro521Ser	p.P521S	ENST00000296474	NM_002447.2	521	Cct/Tct	4/20	0.639245353910202	1	FACETS	0.317	0.297	0.337	0.317	0.297	0.337	SUBCLONAL	1	TRUE	0	0.903685559893922	1		867	1076	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967961	93967961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1231037263	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	294	885	0	ENST00000369303.4:c.1966G>A	p.Gly656Arg	p.G656R	ENST00000369303	NM_004440.3	656	Ggg/Agg	11/17	1	2	FACETS	0.541	0.509	0.574	0.541	0.509	0.574	SUBCLONAL	1	TRUE	1	0.903685559893922	2		885	1203	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015851	112015851	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	301	883	0	ENST00000368678.4:c.1090C>T	p.Leu364Phe	p.L364F	ENST00000368678		364	Ctt/Ttt	10/13	1	2	FACETS	0.496	0.467	0.527	0.496	0.467	0.527	SUBCLONAL	1	TRUE	1	0.903685559893922	2		883	1342	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099641	157099641	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	46	81	0	ENST00000346085.5:c.578G>A	p.Gly193Glu	p.G193E	ENST00000346085	NM_020732.3	193	gGg/gAg	1/20	1	2	FACETS	0.553	0.473	0.64	0.553	0.473	0.64	SUBCLONAL	1	TRUE	1	0.903685559893922	2		81	184	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915819	127915819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	231	826	2	ENST00000373547.4:c.662C>T	p.Thr221Ile	p.T221I	ENST00000373547	NM_002721.4	221	aCa/aTa	6/7	1	2	FACETS	0.41	0.381	0.44	0.41	0.381	0.44	SUBCLONAL	1	TRUE	1	0.903685559893922	2		828	1247	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868039	56868039	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	219	625	0	ENST00000308159.5:c.1538-1G>A		p.X513_splice	ENST00000308159	NM_014669.4	513			1	2	FACETS	0.465	0.432	0.499	0.465	0.432	0.499	SUBCLONAL	1	TRUE	1	0.903685559893922	2		625	1043	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58725253	58725253	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	317	886	0	ENST00000305921.3:c.827G>A	p.Gly276Asp	p.G276D	ENST00000305921	NM_003620.3	276	gGt/gAt	4/6	1	2	FACETS	0.507	0.477	0.537	0.507	0.477	0.537	SUBCLONAL	1	TRUE	1	0.903685559893922	2		886	1385	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262260	46262260	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	446	721	0	ENST00000371998.3:c.844A>C	p.Thr282Pro	p.T282P	ENST00000371998		282	Aca/Cca	9/23	NA	2	FACETS	0.924	0.885	0.964			1	INDETERMINATE	1	TRUE	NA	0.903685559893922	2		721	1068	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46277842	46277842	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	222	682	0	ENST00000371998.3:c.3640G>A	p.Val1214Met	p.V1214M	ENST00000371998		1214	Gtg/Atg	19/23	NA	2	FACETS	0.477	0.444	0.512			1	INDETERMINATE	1	TRUE	NA	0.903685559893922	2		682	1029	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281155	46281155	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	307	968	0	ENST00000371998.3:c.3952G>A	p.Gly1318Arg	p.G1318R	ENST00000371998		1318	Gga/Aga	21/23	NA	2	FACETS	0.485	0.456	0.515			1	INDETERMINATE	1	TRUE	NA	0.903685559893922	2		968	1401	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	138	503	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.615131225215392	2		503	448	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	242	274	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.615131225215392	2		274	725	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702268	47702268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	297	416	0	ENST00000233146.2:c.1864C>T	p.Pro622Ser	p.P622S	ENST00000233146	NM_000251.2	622	Cca/Tca	12/16	0.615131225215392	1	FACETS	0.918	0.87	0.967	0.918	0.87	0.967	CLONAL	1	TRUE	0	0.615131225215392	1		416	728	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106544	27106544	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	383	614	0	ENST00000324856.7:c.6155G>A	p.Cys2052Tyr	p.C2052Y	ENST00000324856	NM_006015.4	2052	tGc/tAc	20/20	1	2	FACETS	0.89	0.844	0.937	0.89	0.844	0.937	CLONAL	1	TRUE	1	0.615131225215392	2		614	1399	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933798	36933798	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	107	654	0	ENST00000361632.4:c.1601A>G	p.His534Arg	p.H534R	ENST00000361632		534	cAt/cGt	12/16	1	2	FACETS	0.284	0.253	0.316	0.284	0.253	0.316	SUBCLONAL	1	TRUE	1	0.615131225215392	2		654	1227	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797127	45797127	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	82	424	0	ENST00000450313.1:c.1288C>T	p.Pro430Ser	p.P430S	ENST00000450313	NM_012222.2	430	Ccc/Tcc	13/16	1	2	FACETS	0.347	0.306	0.392	0.347	0.306	0.392	SUBCLONAL	1	TRUE	1	0.615131225215392	2		424	768	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076761	72076761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	76	649	0	ENST00000357731.5:c.736G>A	p.Glu246Lys	p.E246K	ENST00000357731	NM_173808.2	246	Gaa/Aaa	5/7	1	2	FACETS	0.201	0.175	0.229	0.201	0.175	0.229	SUBCLONAL	1	TRUE	1	0.615131225215392	2		649	1231	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550724	150550724	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	228	247	0	ENST00000369026.2:c.932G>A	p.Gly311Asp	p.G311D	ENST00000369026	NM_021960.4	311	gGc/gAc	2/3	1	2	FACETS	0.998	0.933	1	0.998	0.933	1	CLONAL	1	TRUE	1	0.615131225215392	2		247	743	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570758	226570758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	27	230	0	ENST00000366794.5:c.1138G>A	p.Val380Met	p.V380M	ENST00000366794	NM_001618.3	380	Gtg/Atg	8/23	1	2	FACETS	0.179	0.142	0.221	0.179	0.142	0.221	SUBCLONAL	1	TRUE	1	0.615131225215392	2		230	491	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61761005	61761005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	92	295	0	ENST00000401558.2:c.28G>A	p.Asp10Asn	p.D10N	ENST00000401558	NM_003400.3	10	Gac/Aac	2/25	NA	2	FACETS	0.435	0.387	0.487			1	INDETERMINATE	1	TRUE	NA	0.615131225215392	2		295	687	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584436	52584436	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1002775106	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	52	301	0	ENST00000394830.3:c.4576+1G>A		p.X1526_splice	ENST00000394830	NM_018313.4	1526			1	2	FACETS	0.223	0.189	0.26	0.223	0.189	0.26	SUBCLONAL	1	TRUE	1	0.615131225215392	2		301	758	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026178	71026178	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	277	344	0	ENST00000318789.4:c.1444C>T	p.Pro482Ser	p.P482S	ENST00000318789	NM_032682.5	482	Cca/Tca	17/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.615131225215392	2		344	806	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478070	138478070	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	67	427	0	ENST00000289153.2:c.116G>A	p.Gly39Glu	p.G39E	ENST00000289153	NM_006219.2	39	gGg/gAg	1/22	1	2	FACETS	0.216	0.187	0.248	0.216	0.187	0.248	SUBCLONAL	1	TRUE	1	0.615131225215392	2		427	1009	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176596	142176596	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	39	286	0	ENST00000350721.4:c.7505G>A	p.Gly2502Glu	p.G2502E	ENST00000350721	NM_001184.3	2502	gGa/gAa	45/47	1	2	FACETS	0.21	0.173	0.251	0.21	0.173	0.251	SUBCLONAL	1	TRUE	1	0.615131225215392	2		286	604	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541913	187541913	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs755889337	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	317	541	1	ENST00000441802.2:c.5827C>T	p.Gln1943Ter	p.Q1943*	ENST00000441802	NM_005245.3	1943	Cag/Tag	10/27	1	2	FACETS	0.92	0.869	0.973	0.92	0.869	0.973	CLONAL	1	TRUE	1	0.615131225215392	2		542	1120	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170964	56170964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	62	301	0	ENST00000399503.3:c.1792G>A	p.Ala598Thr	p.A598T	ENST00000399503	NM_005921.1	598	Gca/Aca	10/20	1	2	FACETS	0.314	0.27	0.36	0.314	0.27	0.36	SUBCLONAL	1	TRUE	1	0.615131225215392	2		301	643	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178607	56178607	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	46	229	0	ENST00000399503.3:c.3580G>A	p.Ala1194Thr	p.A1194T	ENST00000399503	NM_005921.1	1194	Gca/Aca	14/20	1	2	FACETS	0.246	0.207	0.29	0.246	0.207	0.29	SUBCLONAL	1	TRUE	1	0.615131225215392	2		229	607	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170832306	170832306	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	426	581	2	ENST00000296930.5:c.670G>A	p.Gly224Arg	p.G224R	ENST00000296930	NM_002520.6	224	Gga/Aga	9/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.615131225215392	2		583	1368	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158713	26158713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	19	82	0	ENST00000289316.2:c.316G>A	p.Glu106Lys	p.E106K	ENST00000289316	NM_138720.2	106	Gag/Aag	1/2	1	2	FACETS	0.212	0.16	0.272	0.212	0.16	0.272	SUBCLONAL	1	TRUE	1	0.615131225215392	2		82	292	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138946	37138946	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	155	343	0	ENST00000373509.5:c.286G>A	p.Val96Met	p.V96M	ENST00000373509	NM_002648.3	96	Gtg/Atg	4/6	1	2	FACETS	0.604	0.553	0.657	0.604	0.553	0.657	SUBCLONAL	1	TRUE	1	0.615131225215392	2		343	835	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138201355	138201355	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	193	240	0	ENST00000237289.4:c.2054G>A	p.Arg685Lys	p.R685K	ENST00000237289	NM_001270507.1	685	aGa/aAa	8/9	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.615131225215392	2		240	591	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510830	157510830	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs902679026	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	89	438	0	ENST00000346085.5:c.3605C>T	p.Ser1202Phe	p.S1202F	ENST00000346085	NM_020732.3	1202	tCc/tTc	14/20	1	2	FACETS	0.275	0.242	0.309	0.275	0.242	0.309	SUBCLONAL	1	TRUE	1	0.615131225215392	2		438	1054	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508169	106508169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381484125	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	23	129	0	ENST00000359195.3:c.163G>A	p.Glu55Lys	p.E55K	ENST00000359195	NM_002649.2	55	Gaa/Aaa	2/11	0.584991855122269	3	FACETS	0.311	0.243	0.391	0.156	0.121	0.196	SUBCLONAL	1	TRUE	1	0.615131225215392	3		129	314	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513252	106513252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	95	327	0	ENST00000359195.3:c.2156C>T	p.Ala719Val	p.A719V	ENST00000359195	NM_002649.2	719	gCc/gTc	4/11	0.584991855122269	3	FACETS	0.433	0.385	0.485	0.216	0.192	0.243	SUBCLONAL	1	TRUE	1	0.615131225215392	3		327	933	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874896	151874896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	294	472	0	ENST00000262189.6:c.7642G>A	p.Val2548Ile	p.V2548I	ENST00000262189	NM_170606.2	2548	Gtt/Att	38/59	0.584991855122269	3	FACETS	1	0.955	1	0.509	0.479	0.541	CLONAL	1	TRUE	1	0.615131225215392	3		472	1227	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418375	139418375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752133245	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	66	375	0	ENST00000277541.6:c.197C>T	p.Thr66Ile	p.T66I	ENST00000277541	NM_017617.3	66	aCc/aTc	3/34	1	2	FACETS	0.253	0.219	0.291	0.253	0.219	0.291	SUBCLONAL	1	TRUE	1	0.615131225215392	2		375	847	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413580	32413580	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs533043871	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	224	383	0	ENST00000332351.3:c.1370A>T	p.Gln457Leu	p.Q457L	ENST00000332351	NM_024426.4	457	cAg/cTg	9/10	1	2	FACETS	0.968	0.905	1	0.968	0.905	1	CLONAL	1	TRUE	1	0.615131225215392	2		383	752	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572543	64572543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	52	240	0	ENST00000312049.6:c.1313C>T	p.Thr438Ile	p.T438I	ENST00000312049	NM_130799.2	438	aCc/aTc	9/10	1	2	FACETS	0.301	0.256	0.351	0.301	0.256	0.351	SUBCLONAL	1	TRUE	1	0.615131225215392	2		240	561	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343018	118343018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	52	243	1	ENST00000534358.1:c.1144G>A	p.Gly382Arg	p.G382R	ENST00000534358	NM_005933.3	382	Ggg/Agg	3/36	1	2	FACETS	0.268	0.227	0.312	0.268	0.227	0.312	SUBCLONAL	1	TRUE	1	0.615131225215392	2		244	632	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497701	125497701	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	177	294	0	ENST00000428830.2:c.265G>A	p.Gly89Arg	p.G89R	ENST00000428830	NM_001114121.2	89	Gga/Aga	3/14	1	2	FACETS	0.961	0.89	1	0.961	0.89	1	CLONAL	1	TRUE	1	0.615131225215392	2		294	599	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402137	402137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528947157	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1329	100	617	0	ENST00000399788.2:c.4654G>A	p.Ala1552Thr	p.A1552T	ENST00000399788	NM_001042603.1	1552	Gcc/Acc	27/28	1	2	FACETS	0.228	0.202	0.255	0.228	0.202	0.255	SUBCLONAL	1	TRUE	1	0.615131225215392	2		617	1429	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425608	49425608	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	96	545	0	ENST00000301067.7:c.12880G>A	p.Gly4294Arg	p.G4294R	ENST00000301067	NM_003482.3	4294	Gga/Aga	39/54	0.615131225215392	1	FACETS	0.333	0.296	0.371	0.333	0.296	0.371	SUBCLONAL	1	TRUE	0	0.615131225215392	1		545	650	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425937	49425937	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	314	584	0	ENST00000301067.7:c.12551G>A	p.Gly4184Asp	p.G4184D	ENST00000301067	NM_003482.3	4184	gGt/gAt	39/54	0.615131225215392	1	FACETS	0.922	0.874	0.969	0.922	0.874	0.969	CLONAL	1	TRUE	0	0.615131225215392	1		584	767	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484348	50484348	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	279	385	0	ENST00000394963.4:c.1108C>T	p.Pro370Ser	p.P370S	ENST00000394963	NM_003076.4	370	Cct/Tct	9/13	0.615131225215392	1	FACETS	0.959	0.908	1	0.959	0.908	1	CLONAL	1	TRUE	0	0.615131225215392	1		385	655	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487947	56487947	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	80	452	1	ENST00000267101.3:c.1678G>A	p.Glu560Lys	p.E560K	ENST00000267101	NM_001982.3	560	Gag/Aag	14/28	0.615131225215392	1	FACETS	0.315	0.278	0.356	0.315	0.278	0.356	SUBCLONAL	1	TRUE	0	0.615131225215392	1		453	571	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436224	110436224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755027066	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	51	252	0	ENST00000375856.3:c.2177G>A	p.Gly726Asp	p.G726D	ENST00000375856	NM_003749.2	726	gGc/gAc	1/2	1	2	FACETS	0.319	0.271	0.372	0.319	0.271	0.372	SUBCLONAL	1	TRUE	1	0.615131225215392	2		252	519	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437472	110437472	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	55	305	0	ENST00000375856.3:c.929G>A	p.Gly310Glu	p.G310E	ENST00000375856	NM_003749.2	310	gGg/gAg	1/2	1	2	FACETS	0.293	0.25	0.34	0.293	0.25	0.34	SUBCLONAL	1	TRUE	1	0.615131225215392	2		305	611	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95583991	95583991	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	137	365	0	ENST00000393063.1:c.1477C>T	p.Gln493Ter	p.Q493*	ENST00000393063	NM_030621.3	493	Cag/Tag	10/28	1	2	FACETS	0.543	0.494	0.595	0.543	0.494	0.595	SUBCLONAL	1	TRUE	1	0.615131225215392	2		365	820	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835671	68835671	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779313390	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	68	621	0	ENST00000261769.5:c.262C>T	p.Pro88Ser	p.P88S	ENST00000261769	NM_004360.3	88	Cct/Tct	3/16	1	2	FACETS	0.182	0.157	0.209	0.182	0.157	0.209	SUBCLONAL	1	TRUE	1	0.615131225215392	2		621	1216	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346547	89346547	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs576866773	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	237	487	1	ENST00000301030.4:c.6403C>T	p.Pro2135Ser	p.P2135S	ENST00000301030	NM_001256183.1	2135	Ccc/Tcc	9/13	0.217025556002336	1	FACETS	0.656	0.614	0.7	0.656	0.614	0.7	INDETERMINATE	1	TRUE	0	0.615131225215392	1		488	813	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979992	7979992	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	54	321	0	ENST00000319144.4:c.1345G>A	p.Gly449Arg	p.G449R	ENST00000319144	NM_001139.2	449	Ggg/Agg	10/15	1	2	FACETS	0.24	0.204	0.279	0.24	0.204	0.279	SUBCLONAL	1	TRUE	1	0.615131225215392	2		321	732	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968954	15968954	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	69	392	0	ENST00000268712.3:c.4796G>A	p.Ser1599Asn	p.S1599N	ENST00000268712	NM_006311.3	1599	aGt/aAt	33/46	1	2	FACETS	0.235	0.204	0.269	0.235	0.204	0.269	SUBCLONAL	1	TRUE	1	0.615131225215392	2		392	954	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490395	29490395	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1555606137	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	49	227	1	ENST00000356175.3:c.479+1G>A		p.X160_splice	ENST00000356175	NM_000267.3	160			1	2	FACETS	0.238	0.201	0.28	0.238	0.201	0.28	SUBCLONAL	1	TRUE	1	0.615131225215392	2		228	668	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553452	29553452	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1555613743	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	94	460	0	ENST00000356175.3:c.2002-1G>A		p.X668_splice	ENST00000356175	NM_000267.3	668			1	2	FACETS	0.305	0.271	0.342	0.305	0.271	0.342	SUBCLONAL	1	TRUE	1	0.615131225215392	2		460	1001	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554250	29554250	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1567847905	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	76	386	1	ENST00000356175.3:c.2266C>T	p.Gln756Ter	p.Q756*	ENST00000356175	NM_000267.3	756	Cag/Tag	19/57	1	2	FACETS	0.306	0.268	0.347	0.306	0.268	0.347	SUBCLONAL	1	TRUE	1	0.615131225215392	2		387	808	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29563018	29563018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781900	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	295	453	0	ENST00000356175.3:c.3953G>A	p.Ser1318Asn	p.S1318N	ENST00000356175	NM_000267.3	1318	aGc/aAc	29/57	1	2	FACETS	0.909	0.856	0.963	0.909	0.856	0.963	CLONAL	1	TRUE	1	0.615131225215392	2		453	1055	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919476	78919476	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	88	521	0	ENST00000306801.3:c.3035G>A	p.Arg1012Lys	p.R1012K	ENST00000306801	NM_020761.2	1012	aGa/aAa	26/34	1	2	FACETS	0.251	0.222	0.283	0.251	0.222	0.283	SUBCLONAL	1	TRUE	1	0.615131225215392	2		521	1138	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222209	2222209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	128	326	0	ENST00000398665.3:c.3041G>A	p.Gly1014Glu	p.G1014E	ENST00000398665	NM_032482.2	1014	gGg/gAg	24/28	0.615131225215392	3	FACETS	0.62	0.562	0.682	0.31	0.281	0.341	SUBCLONAL	1	TRUE	1	0.615131225215392	3		326	877	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226824	2226824	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1322345032	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	50	195	0	ENST00000398665.3:c.4304C>T	p.Pro1435Leu	p.P1435L	ENST00000398665	NM_032482.2	1435	cCc/cTc	27/28	0.615131225215392	3	FACETS	0.419	0.356	0.489	0.21	0.178	0.245	SUBCLONAL	1	TRUE	1	0.615131225215392	3		195	507	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267813	7267813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	154	230	0	ENST00000302850.5:c.195G>A	p.Met65Ile	p.M65I	ENST00000302850	NM_000208.2	65	atG/atA	2/22	0.615131225215392	3	FACETS	0.953	0.874	1	0.476	0.437	0.518	CLONAL	1	TRUE	1	0.615131225215392	3		230	687	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138614	11138614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	52	305	0	ENST00000358026.2:c.3370C>T	p.Leu1124Phe	p.L1124F	ENST00000358026	NM_001128849.1	1124	Ctc/Ttc	24/36	0.615131225215392	3	FACETS	0.247	0.209	0.288	0.123	0.104	0.144	SUBCLONAL	1	TRUE	1	0.615131225215392	3		305	896	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791304	42791304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	52	264	0	ENST00000575354.2:c.364G>A	p.Gly122Ser	p.G122S	ENST00000575354	NM_015125.3	122	Ggt/Agt	3/20	0.615131225215392	3	FACETS	0.292	0.247	0.34	0.146	0.123	0.17	SUBCLONAL	1	TRUE	1	0.615131225215392	3		264	758	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919912	50919912	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	93	483	0	ENST00000440232.2:c.2999G>A	p.Gly1000Asp	p.G1000D	ENST00000440232	NM_002691.3	1000	gGc/gAc	24/27	NA	2	FACETS	0.248	0.219	0.278			1	INDETERMINATE	1	TRUE	NA	0.615131225215392	2		483	1221	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262355	46262355	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1267	130	684	0	ENST00000371998.3:c.939G>A	p.Trp313Ter	p.W313*	ENST00000371998		313	tgG/tgA	9/23	0.217025556002336	1	FACETS	0.21	0.189	0.231	0.21	0.189	0.231	INDETERMINATE	1	TRUE	0	0.615131225215392	1		684	1397	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259288	36259288	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs927005033	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	11	84	0	ENST00000300305.3:c.203C>T	p.Ala68Val	p.A68V	ENST00000300305		68	gCc/gTc	3/8	1	2	FACETS	0.179	0.123	0.248	0.179	0.123	0.248	SUBCLONAL	1	TRUE	1	0.615131225215392	2		84	200	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22143018	22143018	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	86	520	0	ENST00000215832.6:c.689G>A	p.Gly230Glu	p.G230E	ENST00000215832	NM_002745.4	230	gGg/gAg	5/9	1	2	FACETS	0.252	0.222	0.285	0.252	0.222	0.285	SUBCLONAL	1	TRUE	1	0.615131225215392	2		520	1108	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221664	22221664	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	79	205	0	ENST00000215832.6:c.67C>T	p.Pro23Ser	p.P23S	ENST00000215832	NM_002745.4	23	Ccg/Tcg	1/9	1	2	FACETS	0.597	0.528	0.671	0.597	0.528	0.671	SUBCLONAL	1	TRUE	1	0.615131225215392	2		205	430	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531820	41531820	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	81	500	0	ENST00000263253.7:c.1532C>T	p.Ala511Val	p.A511V	ENST00000263253	NM_001429.3	511	gCt/gTt	7/31	1	2	FACETS	0.259	0.227	0.293	0.259	0.227	0.293	SUBCLONAL	1	TRUE	1	0.615131225215392	2		500	1016	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933394	39933394	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	314	228	0	ENST00000378444.4:c.1205G>A	p.Gly402Asp	p.G402D	ENST00000378444	NM_001123385.1	402	gGt/gAt	4/15	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.615131225215392	1		228	529	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650476	48650476	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	38	356	0	ENST00000376670.3:c.446G>A	p.Gly149Glu	p.G149E	ENST00000376670	NM_002049.3	149	gGa/gAa	3/6	1	1	FACETS	0.138	0.113	0.165	0.138	0.113	0.165	SUBCLONAL	1	TRUE	0	0.615131225215392	1		356	622	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410460	63410460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	92	273	0	ENST00000330258.3:c.2707G>A	p.Glu903Lys	p.E903K	ENST00000330258	NM_152424.3	903	Gag/Aag	2/2	1	1	FACETS	0.39	0.347	0.435	0.39	0.347	0.435	SUBCLONAL	1	TRUE	0	0.615131225215392	1		273	531	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091333	193091333	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs28942098	NA	P-0002226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	533	288	0	ENST00000367435.3:c.3G>A	p.Met1?	p.M1?	ENST00000367435	NM_024529.4	1	atG/atA	1/17	0.750671960107172	3	FACETS	0.973	0.95	0.995	0.973	0.95	0.995	CLONAL	3	TRUE	0	0.750671960107172	3		288	669	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970864	55970864	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs774211387	NA	P-0002226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	388	532	0	ENST00000263923.4:c.1933C>G	p.Gln645Glu	p.Q645E	ENST00000263923	NM_002253.2	645	Caa/Gaa	13/30	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.750671960107172	2		532	1025	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609812	117609812	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	415	648	0	ENST00000368508.3:c.6887A>G	p.Glu2296Gly	p.E2296G	ENST00000368508	NM_002944.2	2296	gAa/gGa	43/43	1	2	FACETS	0.943	0.899	0.988	0.943	0.899	0.988	CLONAL	1	TRUE	1	0.750671960107172	2		648	1172	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911322	32911322	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs80358533	NA	P-0002226-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	543	740	2	ENST00000380152.3:c.2830A>T	p.Lys944Ter	p.K944*	ENST00000380152		944	Aaa/Taa	11/27	1	2	FACETS	0.93	0.892	0.969	0.93	0.892	0.969	CLONAL	1	TRUE	1	0.750671960107172	2		742	1555	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	125	528	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.854	0.781	0.929	0.854	0.781	0.929	CLONAL	1	TRUE	1	0.774426218797181	2		530	378	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2890	12158	381	0	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.774426218797181	29	FACETS	0.996	0.991	1			1	CLONAL	24	TRUE	NA	0.774426218797181	29		381	15048	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187177	11187177	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	48	440	1	ENST00000361445.4:c.6241G>A	p.Ala2081Thr	p.A2081T	ENST00000361445	NM_004958.3	2081	Gcc/Acc	45/58	1	2	FACETS	0.131	0.11	0.155	0.131	0.11	0.155	SUBCLONAL	1	TRUE	1	0.774426218797181	2		441	943	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316055	11316055	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	29	228	0	ENST00000361445.4:c.699G>A	p.Trp233Ter	p.W233*	ENST00000361445	NM_004958.3	233	tgG/tgA	5/58	1	2	FACETS	0.139	0.111	0.171	0.139	0.111	0.171	SUBCLONAL	1	TRUE	1	0.774426218797181	2		228	539	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885656	23885656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	116	646	2	ENST00000374561.5:c.262G>A	p.Ala88Thr	p.A88T	ENST00000374561	NM_002167.4	88	Gcc/Acc	1/3	1	2	FACETS	0.241	0.216	0.267	0.241	0.216	0.267	SUBCLONAL	1	TRUE	1	0.774426218797181	2		648	1243	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023054	27023054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	11	91	0	ENST00000324856.7:c.160G>A	p.Ala54Thr	p.A54T	ENST00000324856	NM_006015.4	54	Gcc/Acc	1/20	1	2	FACETS	0.142	0.098	0.197	0.142	0.098	0.197	SUBCLONAL	1	TRUE	1	0.774426218797181	2		91	200	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023921	27023921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1184595505	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	35	84	0	ENST00000324856.7:c.1027G>A	p.Ala343Thr	p.A343T	ENST00000324856	NM_006015.4	343	Gca/Aca	1/20	1	2	FACETS	0.583	0.485	0.69	0.583	0.485	0.69	SUBCLONAL	1	TRUE	1	0.774426218797181	2		84	155	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057665	27057665	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1252	71	496	0	ENST00000324856.7:c.1373G>A	p.Gly458Asp	p.G458D	ENST00000324856	NM_006015.4	458	gGc/gAc	3/20	1	2	FACETS	0.139	0.12	0.159	0.139	0.12	0.159	SUBCLONAL	1	TRUE	1	0.774426218797181	2		496	1323	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799105	45799105	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553130091	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	87	472	0	ENST00000450313.1:c.328G>A	p.Asp110Asn	p.D110N	ENST00000450313	NM_012222.2	110	Gac/Aac	3/16	1	2	FACETS	0.225	0.199	0.254	0.225	0.199	0.254	SUBCLONAL	1	TRUE	1	0.774426218797181	2		472	997	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247980	59247980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	103	355	0	ENST00000371222.2:c.763G>A	p.Ala255Thr	p.A255T	ENST00000371222	NM_002228.3	255	Gcg/Acg	1/1	1	2	FACETS	0.329	0.294	0.366	0.329	0.294	0.366	SUBCLONAL	1	TRUE	1	0.774426218797181	2		355	809	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551705	150551705	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	16	110	0	ENST00000369026.2:c.302C>T	p.Pro101Leu	p.P101L	ENST00000369026	NM_021960.4	101	cCc/cTc	1/3	1	2	FACETS	0.15	0.11	0.197	0.15	0.11	0.197	SUBCLONAL	1	TRUE	1	0.774426218797181	2		110	276	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175996812	175996812	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	106	300	2	ENST00000367669.3:c.1625C>T	p.Ser542Phe	p.S542F	ENST00000367669	NM_022457.5	542	tCt/tTt	15/20	1	2	FACETS	0.354	0.317	0.393	0.354	0.317	0.393	SUBCLONAL	1	TRUE	1	0.774426218797181	2		302	773	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176118155	176118155	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	74	214	0	ENST00000367669.3:c.818G>A	p.Arg273Lys	p.R273K	ENST00000367669	NM_022457.5	273	aGa/aAa	6/20	1	2	FACETS	0.338	0.296	0.383	0.338	0.296	0.383	SUBCLONAL	1	TRUE	1	0.774426218797181	2		214	565	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965188	25965188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	49	323	0	ENST00000435504.4:c.4018G>A	p.Asp1340Asn	p.D1340N	ENST00000435504		1340	Gac/Aac	13/13	1	2	FACETS	0.172	0.145	0.202	0.172	0.145	0.202	SUBCLONAL	1	TRUE	1	0.774426218797181	2		323	737	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143242	30143242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	30	209	1	ENST00000389048.3:c.284G>A	p.Cys95Tyr	p.C95Y	ENST00000389048	NM_004304.4	95	tGc/tAc	1/29	1	2	FACETS	0.163	0.131	0.2	0.163	0.131	0.2	SUBCLONAL	1	TRUE	1	0.774426218797181	2		210	475	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145391	61145391	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	56	288	0	ENST00000295025.8:c.601G>A	p.Gly201Arg	p.G201R	ENST00000295025	NM_002908.2	201	Gga/Aga	6/11	1	2	FACETS	0.201	0.171	0.233	0.201	0.171	0.233	SUBCLONAL	1	TRUE	1	0.774426218797181	2		288	721	SUCCESS
REL	5966	MSKCC	GRCh37	2	61148967	61148967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	48	417	2	ENST00000295025.8:c.1157C>T	p.Ser386Phe	p.S386F	ENST00000295025	NM_002908.2	386	tCc/tTc	11/11	1	2	FACETS	0.14	0.117	0.165	0.14	0.117	0.165	SUBCLONAL	1	TRUE	1	0.774426218797181	2		419	886	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182544	99182544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	69	271	0	ENST00000074304.5:c.2347C>T	p.Pro783Ser	p.P783S	ENST00000074304	NM_001134224.1	783	Ccc/Tcc	22/26	1	2	FACETS	0.249	0.216	0.285	0.249	0.216	0.285	SUBCLONAL	1	TRUE	1	0.774426218797181	2		271	715	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051153	128051153	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	164	446	0	ENST00000285398.2:c.170G>A	p.Gly57Glu	p.G57E	ENST00000285398	NM_000122.1	57	gGa/gAa	2/15	1	2	FACETS	0.479	0.44	0.52	0.479	0.44	0.52	SUBCLONAL	1	TRUE	1	0.774426218797181	2		446	884	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376245	225376245	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	48	298	0	ENST00000264414.4:c.709G>A	p.Val237Ile	p.V237I	ENST00000264414	NM_003590.4	237	Gta/Ata	6/16	1	2	FACETS	0.14	0.117	0.165	0.14	0.117	0.165	SUBCLONAL	1	TRUE	1	0.774426218797181	2		298	886	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661256	227661256	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	50	341	0	ENST00000305123.5:c.2199G>A	p.Met733Ile	p.M733I	ENST00000305123	NM_005544.2	733	atG/atA	1/2	1	2	FACETS	0.176	0.148	0.206	0.176	0.148	0.206	SUBCLONAL	1	TRUE	1	0.774426218797181	2		341	735	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661500	227661500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757021553	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	39	706	3	ENST00000305123.5:c.1955G>A	p.Arg652His	p.R652H	ENST00000305123	NM_005544.2	652	cGc/cAc	1/2	1	2	FACETS	0.131	0.108	0.158	0.131	0.108	0.158	SUBCLONAL	1	TRUE	1	0.774426218797181	2		709	766	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713456	30713456	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	26	183	0	ENST00000295754.5:c.781G>A	p.Ala261Thr	p.A261T	ENST00000295754	NM_003242.5	261	Gcc/Acc	4/7	0.753838161814229	1	FACETS	0.107	0.084	0.133	0.107	0.084	0.133	SUBCLONAL	1	TRUE	0	0.774426218797181	1		183	386	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042540	37042540	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267607727	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	95	325	0	ENST00000231790.2:c.302G>A	p.Gly101Asp	p.G101D	ENST00000231790	NM_000249.3	101	gGt/gAt	3/19	0.753838161814229	1	FACETS	0.292	0.26	0.325	0.292	0.26	0.325	SUBCLONAL	1	TRUE	0	0.774426218797181	1		325	515	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266232	41266232	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	40	242	1	ENST00000349496.5:c.229G>A	p.Glu77Lys	p.E77K	ENST00000349496	NM_001904.3	77	Gaa/Aaa	3/15	0.753838161814229	1	FACETS	0.138	0.114	0.164	0.138	0.114	0.164	SUBCLONAL	1	TRUE	0	0.774426218797181	1		243	460	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268735	41268735	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	74	316	0	ENST00000349496.5:c.973G>A	p.Val325Ile	p.V325I	ENST00000349496	NM_001904.3	325	Gta/Ata	7/15	0.753838161814229	1	FACETS	0.243	0.213	0.276	0.243	0.213	0.276	SUBCLONAL	1	TRUE	0	0.774426218797181	1		316	481	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934750	49934750	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	65	510	2	ENST00000296474.3:c.2146G>A	p.Ala716Thr	p.A716T	ENST00000296474	NM_002447.2	716	Gct/Act	7/20	0.753838161814229	1	FACETS	0.147	0.127	0.169	0.147	0.127	0.169	SUBCLONAL	1	TRUE	0	0.774426218797181	1		512	700	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441439	52441439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	36	448	0	ENST00000460680.1:c.413C>T	p.Ala138Val	p.A138V	ENST00000460680	NM_004656.3	138	gCc/gTc	6/17	0.753838161814229	1	FACETS	0.088	0.071	0.106	0.088	0.071	0.106	SUBCLONAL	1	TRUE	0	0.774426218797181	1		448	650	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468477	89468477	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	58	306	1	ENST00000336596.2:c.2011G>A	p.Ala671Thr	p.A671T	ENST00000336596	NM_005233.5	671	Gca/Aca	11/17	0.753838161814229	1	FACETS	0.196	0.168	0.226	0.196	0.168	0.226	SUBCLONAL	1	TRUE	0	0.774426218797181	1		307	468	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665101	138665101	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	47	150	0	ENST00000330315.3:c.464C>T	p.Pro155Leu	p.P155L	ENST00000330315	NM_023067.3	155	cCg/cTg	1/1	1	2	FACETS	0.455	0.386	0.529	0.455	0.386	0.529	SUBCLONAL	1	TRUE	1	0.774426218797181	2		150	267	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261583	142261583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	54	207	0	ENST00000350721.4:c.3374C>T	p.Pro1125Leu	p.P1125L	ENST00000350721	NM_001184.3	1125	cCc/cTc	17/47	1	2	FACETS	0.228	0.194	0.265	0.228	0.194	0.265	SUBCLONAL	1	TRUE	1	0.774426218797181	2		207	612	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272545	142272545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	114	387	2	ENST00000350721.4:c.2570C>T	p.Ala857Val	p.A857V	ENST00000350721	NM_001184.3	857	gCc/gTc	12/47	1	2	FACETS	0.321	0.288	0.355	0.321	0.288	0.355	SUBCLONAL	1	TRUE	1	0.774426218797181	2		389	918	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430240	181430240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	40	291	0	ENST00000325404.1:c.92G>A	p.Gly31Asp	p.G31D	ENST00000325404	NM_003106.3	31	gGc/gAc	1/1	1	2	FACETS	0.196	0.163	0.234	0.196	0.163	0.234	SUBCLONAL	1	TRUE	1	0.774426218797181	2		291	526	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146563	185146563	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	40	294	0	ENST00000265026.3:c.194C>T	p.Thr65Ile	p.T65I	ENST00000265026	NM_004721.4	65	aCc/aTc	2/14	1	2	FACETS	0.172	0.142	0.205	0.172	0.142	0.205	SUBCLONAL	1	TRUE	1	0.774426218797181	2		294	600	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589797	55589797	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1306680919	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	87	367	1	ENST00000288135.5:c.1279C>T	p.Gln427Ter	p.Q427*	ENST00000288135	NM_000222.2	427	Caa/Taa	8/21	NA	2	FACETS	0.253	0.224	0.285			1	INDETERMINATE	1	TRUE	NA	0.774426218797181	2		368	887	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233143	66233143	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	132	338	0	ENST00000273854.3:c.1857-1G>A		p.X619_splice	ENST00000273854	NM_004439.5	619			NA	2	FACETS	0.446	0.405	0.489			1	INDETERMINATE	1	TRUE	NA	0.774426218797181	2		338	765	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467932	66467932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756748785	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	199	338	0	ENST00000273854.3:c.337C>T	p.Leu113Phe	p.L113F	ENST00000273854	NM_004439.5	113	Ctt/Ttt	3/18	NA	2	FACETS	0.618	0.574	0.665			1	INDETERMINATE	1	TRUE	NA	0.774426218797181	2		338	831	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947386	38947386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776016149	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	62	280	0	ENST00000357387.3:c.4294G>A	p.Asp1432Asn	p.D1432N	ENST00000357387	NM_152756.3	1432	Gat/Aat	32/38	1	2	FACETS	0.226	0.195	0.261	0.226	0.195	0.261	SUBCLONAL	1	TRUE	1	0.774426218797181	2		280	707	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944974	131944974	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1369746254	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	23	134	0	ENST00000265335.6:c.2923-1G>A		p.X975_splice	ENST00000265335		975			1	2	FACETS	0.141	0.109	0.178	0.141	0.109	0.178	SUBCLONAL	1	TRUE	1	0.774426218797181	2		134	421	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149436881	149436881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	206	381	0	ENST00000286301.3:c.2288C>T	p.Ala763Val	p.A763V	ENST00000286301	NM_005211.3	763	gCc/gTc	17/22	1	2	FACETS	0.633	0.588	0.679	0.633	0.588	0.679	SUBCLONAL	1	TRUE	1	0.774426218797181	2		381	841	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495426	149495426	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755005245	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	96	441	0	ENST00000261799.4:c.3221C>T	p.Pro1074Leu	p.P1074L	ENST00000261799	NM_002609.3	1074	cCc/cTc	23/23	1	2	FACETS	0.247	0.219	0.277	0.247	0.219	0.277	SUBCLONAL	1	TRUE	1	0.774426218797181	2		441	1004	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176618909	176618909	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264350592	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	88	416	1	ENST00000439151.2:c.952C>T	p.Pro318Ser	p.P318S	ENST00000439151	NM_022455.4	318	Cca/Tca	3/23	1	2	FACETS	0.21	0.185	0.237	0.21	0.185	0.237	SUBCLONAL	1	TRUE	1	0.774426218797181	2		417	1082	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631183	176631183	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	57	421	0	ENST00000439151.2:c.1126G>A	p.Ala376Thr	p.A376T	ENST00000439151	NM_022455.4	376	Gcc/Acc	4/23	1	2	FACETS	0.142	0.121	0.165	0.142	0.121	0.165	SUBCLONAL	1	TRUE	1	0.774426218797181	2		421	1039	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722244	176722244	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	67	512	0	ENST00000439151.2:c.7875G>A	p.Trp2625Ter	p.W2625*	ENST00000439151	NM_022455.4	2625	tgG/tgA	23/23	1	2	FACETS	0.174	0.151	0.2	0.174	0.151	0.2	SUBCLONAL	1	TRUE	1	0.774426218797181	2		512	993	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036936	180036936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	249	530	1	ENST00000261937.6:c.3776C>T	p.Pro1259Leu	p.P1259L	ENST00000261937	NM_182925.4	1259	cCc/cTc	28/30	NA	2	FACETS	0.67	0.627	0.714			1	INDETERMINATE	1	TRUE	NA	0.774426218797181	2		531	960	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056979	180056979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1297682245	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	49	497	0	ENST00000261937.6:c.640G>A	p.Asp214Asn	p.D214N	ENST00000261937	NM_182925.4	214	Gac/Aac	5/30	NA	2	FACETS	0.13	0.109	0.153			1	INDETERMINATE	1	TRUE	NA	0.774426218797181	2		497	975	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197378	26197378	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1294	144	799	1	ENST00000356476.2:c.101G>A	p.Gly34Asp	p.G34D	ENST00000356476		34	gGc/gAc	1/1	1	2	FACETS	0.259	0.235	0.284	0.259	0.235	0.284	SUBCLONAL	1	TRUE	1	0.774426218797181	2		800	1438	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165285	32165285	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	154	395	0	ENST00000375023.3:c.4843C>T	p.Pro1615Ser	p.P1615S	ENST00000375023	NM_004557.3	1615	Ccc/Tcc	27/30	1	2	FACETS	0.446	0.408	0.486	0.446	0.408	0.486	SUBCLONAL	1	TRUE	1	0.774426218797181	2		395	891	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169140	32169140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	65	351	0	ENST00000375023.3:c.3893C>T	p.Ala1298Val	p.A1298V	ENST00000375023	NM_004557.3	1298	gCc/gTc	22/30	1	2	FACETS	0.24	0.207	0.275	0.24	0.207	0.275	SUBCLONAL	1	TRUE	1	0.774426218797181	2		351	700	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188886	32188886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	62	380	0	ENST00000375023.3:c.668C>T	p.Pro223Leu	p.P223L	ENST00000375023	NM_004557.3	223	cCt/cTt	4/30	1	2	FACETS	0.209	0.18	0.241	0.209	0.18	0.241	SUBCLONAL	1	TRUE	1	0.774426218797181	2		380	765	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190326	32190326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781213120	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	28	226	1	ENST00000375023.3:c.413C>T	p.Ser138Leu	p.S138L	ENST00000375023	NM_004557.3	138	tCg/tTg	3/30	1	2	FACETS	0.145	0.115	0.179	0.145	0.115	0.179	SUBCLONAL	1	TRUE	1	0.774426218797181	2		227	498	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41904338	41904338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	124	254	0	ENST00000372991.4:c.670G>A	p.Glu224Lys	p.E224K	ENST00000372991	NM_001760.3	224	Gag/Aag	4/5	1	2	FACETS	0.627	0.57	0.686	0.627	0.57	0.686	SUBCLONAL	1	TRUE	1	0.774426218797181	2		254	511	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553561	106553561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	92	155	0	ENST00000369096.4:c.1526C>T	p.Ala509Val	p.A509V	ENST00000369096	NM_001198.3	509	gCc/gTc	5/7	1	2	FACETS	0.671	0.601	0.744	0.671	0.601	0.744	SUBCLONAL	1	TRUE	1	0.774426218797181	2		155	354	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553623	106553623	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	27	204	0	ENST00000369096.4:c.1588C>T	p.Gln530Ter	p.Q530*	ENST00000369096	NM_001198.3	530	Cag/Tag	5/7	1	2	FACETS	0.148	0.117	0.183	0.148	0.117	0.183	SUBCLONAL	1	TRUE	1	0.774426218797181	2		204	471	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112035646	112035646	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1403522537	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	53	423	0	ENST00000368678.4:c.248G>A	p.Gly83Glu	p.G83E	ENST00000368678		83	gGa/gAa	4/13	1	2	FACETS	0.13	0.11	0.152	0.13	0.11	0.152	SUBCLONAL	1	TRUE	1	0.774426218797181	2		423	1052	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631271	117631271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	63	499	0	ENST00000368508.3:c.6407G>A	p.Gly2136Glu	p.G2136E	ENST00000368508	NM_002944.2	2136	gGa/gAa	40/43	1	2	FACETS	0.166	0.142	0.191	0.166	0.142	0.191	SUBCLONAL	1	TRUE	1	0.774426218797181	2		499	983	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001244	150001244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	63	389	0	ENST00000253339.5:c.2360G>A	p.Gly787Glu	p.G787E	ENST00000253339		787	gGg/gAg	4/7	1	2	FACETS	0.167	0.144	0.193	0.167	0.144	0.193	SUBCLONAL	1	TRUE	1	0.774426218797181	2		389	974	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222615	157222615	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554265306	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	81	344	0	ENST00000346085.5:c.1882C>T	p.Gln628Ter	p.Q628*	ENST00000346085	NM_020732.3	628	Cag/Tag	4/20	1	2	FACETS	0.276	0.242	0.311	0.276	0.242	0.311	SUBCLONAL	1	TRUE	1	0.774426218797181	2		344	759	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469812	157469812	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	67	444	0	ENST00000346085.5:c.2606G>A	p.Gly869Asp	p.G869D	ENST00000346085	NM_020732.3	869	gGc/gAc	9/20	1	2	FACETS	0.168	0.145	0.193	0.168	0.145	0.193	SUBCLONAL	1	TRUE	1	0.774426218797181	2		444	1029	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528316	157528316	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554237850	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	176	545	0	ENST00000346085.5:c.6041G>A	p.Trp2014Ter	p.W2014*	ENST00000346085	NM_020732.3	2014	tGg/tAg	20/20	1	2	FACETS	0.394	0.362	0.427	0.394	0.362	0.427	SUBCLONAL	1	TRUE	1	0.774426218797181	2		545	1155	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161807882	161807882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	207	412	0	ENST00000366898.1:c.1111G>A	p.Ala371Thr	p.A371T	ENST00000366898	NM_004562.2	371	Gcg/Acg	10/12	1	2	FACETS	0.59	0.548	0.634	0.59	0.548	0.634	SUBCLONAL	1	TRUE	1	0.774426218797181	2		412	906	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367278	50367278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	30	242	0	ENST00000331340.3:c.85G>A	p.Glu29Lys	p.E29K	ENST00000331340	NM_006060.4	29	Gag/Aag	3/8	1	2	FACETS	0.153	0.123	0.188	0.153	0.123	0.188	SUBCLONAL	1	TRUE	1	0.774426218797181	2		242	505	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340189	116340189	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782807	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	66	356	2	ENST00000397752.3:c.1051C>T	p.Pro351Ser	p.P351S	ENST00000397752	NM_000245.2	351	Cca/Tca	2/21	1	2	FACETS	0.217	0.188	0.249	0.217	0.188	0.249	SUBCLONAL	1	TRUE	1	0.774426218797181	2		358	785	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846190	128846190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	75	433	1	ENST00000249373.3:c.1120G>A	p.Ala374Thr	p.A374T	ENST00000249373	NM_005631.4	374	Gca/Aca	5/12	1	2	FACETS	0.202	0.176	0.23	0.202	0.176	0.23	SUBCLONAL	1	TRUE	1	0.774426218797181	2		434	960	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481380	140481380	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	57	241	0	ENST00000288602.6:c.1428G>A	p.Trp476Ter	p.W476*	ENST00000288602	NM_004333.4	476	tgG/tgA	11/18	1	2	FACETS	0.237	0.203	0.275	0.237	0.203	0.275	SUBCLONAL	1	TRUE	1	0.774426218797181	2		241	620	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148529725	148529725	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	39	198	0	ENST00000320356.2:c.363+1G>A		p.X121_splice	ENST00000320356	NM_004456.4	121			1	2	FACETS	0.212	0.176	0.253	0.212	0.176	0.253	SUBCLONAL	1	TRUE	1	0.774426218797181	2		198	474	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853289	151853289	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	63	188	0	ENST00000262189.6:c.11812+1G>A		p.X3938_splice	ENST00000262189	NM_170606.2	3938			1	2	FACETS	0.33	0.286	0.378	0.33	0.286	0.378	SUBCLONAL	1	TRUE	1	0.774426218797181	2		188	493	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346205	152346205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1349	71	622	1	ENST00000359321.1:c.365G>A	p.Ser122Asn	p.S122N	ENST00000359321	NM_005431.1	122	aGt/aAt	3/3	1	2	FACETS	0.129	0.112	0.148	0.129	0.112	0.148	SUBCLONAL	1	TRUE	1	0.774426218797181	2		623	1420	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882072	36882072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	74	423	0	ENST00000358127.4:c.941G>A	p.Gly314Glu	p.G314E	ENST00000358127	NM_001280556.1	314	gGg/gAg	8/10	0.774426218797181	2	FACETS	0.205	0.179	0.234	0.103	0.089	0.117	SUBCLONAL	1	TRUE	0	0.774426218797181	2		423	930	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537201	80537201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	21	157	0	ENST00000286548.4:c.197G>A	p.Gly66Glu	p.G66E	ENST00000286548	NM_002072.3	66	gGa/gAa	2/7	0.774426218797181	2	FACETS	0.134	0.102	0.17	0.067	0.051	0.085	SUBCLONAL	1	TRUE	0	0.774426218797181	2		157	406	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760300	133760300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	143	350	0	ENST00000318560.5:c.2623G>A	p.Val875Met	p.V875M	ENST00000318560	NM_005157.4	875	Gtg/Atg	11/11	0.774426218797181	2	FACETS	0.585	0.535	0.637	0.293	0.267	0.319	SUBCLONAL	1	TRUE	0	0.774426218797181	2		350	631	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760307	133760307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756003549	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	81	364	0	ENST00000318560.5:c.2630G>A	p.Arg877Lys	p.R877K	ENST00000318560	NM_005157.4	877	aGg/aAg	11/11	0.774426218797181	2	FACETS	0.323	0.285	0.365	0.162	0.142	0.183	SUBCLONAL	1	TRUE	0	0.774426218797181	2		364	647	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390837	139390837	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	33	301	0	ENST00000277541.6:c.7354G>A	p.Ala2452Thr	p.A2452T	ENST00000277541	NM_017617.3	2452	Gcg/Acg	34/34	0.774426218797181	2	FACETS	0.133	0.107	0.161	0.066	0.053	0.081	SUBCLONAL	1	TRUE	0	0.774426218797181	2		301	643	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391956	139391956	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	116	495	1	ENST00000277541.6:c.6235G>A	p.Val2079Met	p.V2079M	ENST00000277541	NM_017617.3	2079	Gtg/Atg	34/34	0.774426218797181	2	FACETS	0.267	0.24	0.296	0.134	0.12	0.148	SUBCLONAL	1	TRUE	0	0.774426218797181	2		496	1121	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401378	139401378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	38	224	0	ENST00000277541.6:c.3691C>T	p.Pro1231Ser	p.P1231S	ENST00000277541	NM_017617.3	1231	Ccc/Tcc	23/34	0.774426218797181	2	FACETS	0.132	0.108	0.158	0.066	0.054	0.079	SUBCLONAL	1	TRUE	0	0.774426218797181	2		224	746	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600429	43600429	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	36	328	0	ENST00000355710.3:c.655G>A	p.Asp219Asn	p.D219N	ENST00000355710	NM_020975.4	219	Gac/Aac	4/20	0.753838161814229	1	FACETS	0.133	0.109	0.16	0.133	0.109	0.16	SUBCLONAL	1	TRUE	0	0.774426218797181	1		328	429	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137746	64137746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	46	383	0	ENST00000334205.4:c.1847G>A	p.Gly616Asp	p.G616D	ENST00000334205	NM_003942.2	616	gGc/gAc	15/17	1	2	FACETS	0.135	0.113	0.16	0.135	0.113	0.16	SUBCLONAL	1	TRUE	1	0.774426218797181	2		383	877	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170565	108170565	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	195	281	0	ENST00000278616.4:c.5130G>A	p.Trp1710Ter	p.W1710*	ENST00000278616	NM_000051.3	1710	tgG/tgA	34/63	1	2	FACETS	0.622	0.576	0.669	0.622	0.576	0.669	SUBCLONAL	1	TRUE	1	0.774426218797181	2		281	810	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514024	125514024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1298017021	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	120	465	0	ENST00000428830.2:c.962C>T	p.Pro321Leu	p.P321L	ENST00000428830	NM_001114121.2	321	cCc/cTc	10/14	1	2	FACETS	0.309	0.278	0.341	0.309	0.278	0.341	SUBCLONAL	1	TRUE	1	0.774426218797181	2		465	1004	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	430252	430252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	50	367	0	ENST00000399788.2:c.2450C>T	p.Thr817Ile	p.T817I	ENST00000399788	NM_001042603.1	817	aCt/aTt	18/28	1	2	FACETS	0.135	0.114	0.158	0.135	0.114	0.158	SUBCLONAL	1	TRUE	1	0.774426218797181	2		367	957	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905471	11905471	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	37	222	0	ENST00000396373.4:c.121C>T	p.Leu41Phe	p.L41F	ENST00000396373	NM_001987.4	41	Ctc/Ttc	2/8	1	2	FACETS	0.177	0.145	0.212	0.177	0.145	0.212	SUBCLONAL	1	TRUE	1	0.774426218797181	2		222	540	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022546	12022546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	56	476	0	ENST00000396373.4:c.652G>A	p.Ala218Thr	p.A218T	ENST00000396373	NM_001987.4	218	Gct/Act	5/8	1	2	FACETS	0.149	0.127	0.173	0.149	0.127	0.173	SUBCLONAL	1	TRUE	1	0.774426218797181	2		476	972	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038867	12038867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1414711241	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	109	302	0	ENST00000396373.4:c.1160C>T	p.Thr387Ile	p.T387I	ENST00000396373	NM_001987.4	387	aCa/aTa	7/8	1	2	FACETS	0.348	0.312	0.387	0.348	0.312	0.387	SUBCLONAL	1	TRUE	1	0.774426218797181	2		302	808	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233280	46233280	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	147	275	0	ENST00000334344.6:c.1498+1G>A		p.X500_splice	ENST00000334344	NM_152641.2	500			1	2	FACETS	0.555	0.508	0.604	0.555	0.508	0.604	SUBCLONAL	1	TRUE	1	0.774426218797181	2		275	684	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426276	49426276	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	78	462	1	ENST00000301067.7:c.12212G>A	p.Gly4071Glu	p.G4071E	ENST00000301067	NM_003482.3	4071	gGg/gAg	39/54	1	2	FACETS	0.21	0.183	0.238	0.21	0.183	0.238	SUBCLONAL	1	TRUE	1	0.774426218797181	2		463	961	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445122	49445122	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	40	154	0	ENST00000301067.7:c.2344G>A	p.Val782Met	p.V782M	ENST00000301067	NM_003482.3	782	Gtg/Atg	10/54	1	2	FACETS	0.237	0.197	0.282	0.237	0.197	0.282	SUBCLONAL	1	TRUE	1	0.774426218797181	2		154	435	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56477556	56477556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	48	371	0	ENST00000267101.3:c.104G>A	p.Gly35Asp	p.G35D	ENST00000267101	NM_001982.3	35	gGc/gAc	2/28	1	2	FACETS	0.146	0.122	0.171	0.146	0.122	0.171	SUBCLONAL	1	TRUE	1	0.774426218797181	2		371	851	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114144	115114144	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	89	422	0	ENST00000257566.3:c.1073C>T	p.Ser358Phe	p.S358F	ENST00000257566	NM_016569.3	358	tCc/tTc	6/8	1	2	FACETS	0.248	0.22	0.28	0.248	0.22	0.28	SUBCLONAL	1	TRUE	1	0.774426218797181	2		422	925	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28897053	28897053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148112461	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	88	234	0	ENST00000282397.4:c.2827G>A	p.Glu943Lys	p.E943K	ENST00000282397	NM_002019.4	943	Gaa/Aaa	21/30	1	2	FACETS	0.408	0.362	0.457	0.408	0.362	0.457	SUBCLONAL	1	TRUE	1	0.774426218797181	2		234	557	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041754	29041754	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	46	200	1	ENST00000282397.4:c.65G>A	p.Gly22Glu	p.G22E	ENST00000282397	NM_002019.4	22	gGa/gAa	2/30	1	2	FACETS	0.236	0.198	0.277	0.236	0.198	0.277	SUBCLONAL	1	TRUE	1	0.774426218797181	2		201	504	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914187	32914187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371189402	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1236	142	632	1	ENST00000380152.3:c.5695G>A	p.Asp1899Asn	p.D1899N	ENST00000380152		1899	Gat/Aat	11/27	1	2	FACETS	0.266	0.241	0.292	0.266	0.241	0.292	SUBCLONAL	1	TRUE	1	0.774426218797181	2		633	1378	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929047	32929047	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	89	621	0	ENST00000380152.3:c.7057G>A	p.Gly2353Ser	p.G2353S	ENST00000380152		2353	Ggt/Agt	14/27	1	2	FACETS	0.184	0.162	0.208	0.184	0.162	0.208	SUBCLONAL	1	TRUE	1	0.774426218797181	2		621	1248	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134285	41134285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1429	86	629	0	ENST00000379561.5:c.1343G>A	p.Ser448Asn	p.S448N	ENST00000379561	NM_002015.3	448	aGt/aAt	2/3	1	2	FACETS	0.147	0.129	0.166	0.147	0.129	0.166	SUBCLONAL	1	TRUE	1	0.774426218797181	2		629	1515	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73334683	73334683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	58	267	0	ENST00000377767.4:c.2777C>T	p.Ser926Phe	p.S926F	ENST00000377767	NM_014953.3	926	tCc/tTc	20/21	1	2	FACETS	0.191	0.164	0.222	0.191	0.164	0.222	SUBCLONAL	1	TRUE	1	0.774426218797181	2		267	783	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347878	73347878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	96	394	1	ENST00000377767.4:c.1183G>A	p.Gly395Arg	p.G395R	ENST00000377767	NM_014953.3	395	Gga/Aga	8/21	1	2	FACETS	0.281	0.249	0.314	0.281	0.249	0.314	SUBCLONAL	1	TRUE	1	0.774426218797181	2		395	883	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435679	110435679	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	22	133	0	ENST00000375856.3:c.2722C>T	p.Pro908Ser	p.P908S	ENST00000375856	NM_003749.2	908	Cca/Tca	1/2	1	2	FACETS	0.197	0.152	0.248	0.197	0.152	0.248	SUBCLONAL	1	TRUE	1	0.774426218797181	2		133	289	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871698	35871698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1250	70	607	0	ENST00000216797.5:c.808G>A	p.Gly270Ser	p.G270S	ENST00000216797	NM_020529.2	270	Ggc/Agc	5/6	1	2	FACETS	0.137	0.119	0.157	0.137	0.119	0.157	SUBCLONAL	1	TRUE	1	0.774426218797181	2		607	1320	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543331	65543331	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1186625283	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	301	574	0	ENST00000358664.4:c.346C>T	p.Pro116Ser	p.P116S	ENST00000358664	NM_002382.4	116	Ccc/Tcc	5/5	1	2	FACETS	0.628	0.591	0.666	0.628	0.591	0.666	SUBCLONAL	1	TRUE	1	0.774426218797181	2		574	1238	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562905	95562905	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	64	210	0	ENST00000393063.1:c.4352G>A	p.Arg1451Lys	p.R1451K	ENST00000393063	NM_030621.3	1451	aGa/aAa	24/28	1	2	FACETS	0.275	0.238	0.316	0.275	0.238	0.316	SUBCLONAL	1	TRUE	1	0.774426218797181	2		210	600	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42053936	42053936	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	79	363	0	ENST00000219905.7:c.7399-1G>A		p.X2467_splice	ENST00000219905	NM_001164273.1	2467			1	2	FACETS	0.235	0.206	0.266	0.235	0.206	0.266	SUBCLONAL	1	TRUE	1	0.774426218797181	2		363	869	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058554	42058554	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1558	86	724	0	ENST00000219905.7:c.8274G>A	p.Trp2758Ter	p.W2758*	ENST00000219905	NM_001164273.1	2758	tgG/tgA	24/24	1	2	FACETS	0.135	0.119	0.153	0.135	0.119	0.153	SUBCLONAL	1	TRUE	1	0.774426218797181	2		724	1644	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059471	42059471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	60	561	1	ENST00000219905.7:c.9191G>A	p.Gly3064Glu	p.G3064E	ENST00000219905	NM_001164273.1	3064	gGg/gAg	24/24	1	2	FACETS	0.132	0.113	0.153	0.132	0.113	0.153	SUBCLONAL	1	TRUE	1	0.774426218797181	2		562	1177	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420231	88420231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	52	384	0	ENST00000360948.2:c.2455G>A	p.Glu819Lys	p.E819K	ENST00000360948	NM_001012338.2	819	Gag/Aag	19/19	1	2	FACETS	0.142	0.12	0.166	0.142	0.12	0.166	SUBCLONAL	1	TRUE	1	0.774426218797181	2		384	947	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680643	88680643	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	187	381	0	ENST00000360948.2:c.614G>A	p.Ser205Asn	p.S205N	ENST00000360948	NM_001012338.2	205	aGt/aAt	6/19	1	2	FACETS	0.623	0.577	0.671	0.623	0.577	0.671	SUBCLONAL	1	TRUE	1	0.774426218797181	2		381	775	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223244	2223244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	49	391	2	ENST00000326181.6:c.856G>A	p.Gly286Ser	p.G286S	ENST00000326181	NM_032271.2	286	Ggc/Agc	10/21	1	2	FACETS	0.145	0.122	0.171	0.145	0.122	0.171	SUBCLONAL	1	TRUE	1	0.774426218797181	2		393	871	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832859	3832859	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202225861	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	72	360	0	ENST00000262367.5:c.1399G>A	p.Ala467Thr	p.A467T	ENST00000262367	NM_004380.2	467	Gcc/Acc	6/31	1	2	FACETS	0.22	0.191	0.25	0.22	0.191	0.25	SUBCLONAL	1	TRUE	1	0.774426218797181	2		360	847	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274210	10274210	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	23	134	0	ENST00000330684.3:c.59G>A	p.Gly20Asp	p.G20D	ENST00000330684	NM_001134407.1	20	gGt/gAt	2/13	1	2	FACETS	0.184	0.143	0.231	0.184	0.143	0.231	SUBCLONAL	1	TRUE	1	0.774426218797181	2		134	323	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865765	56865765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	138	577	0	ENST00000308159.5:c.1097C>T	p.Ala366Val	p.A366V	ENST00000308159	NM_014669.4	366	gCt/gTt	11/22	1	2	FACETS	0.269	0.244	0.296	0.269	0.244	0.296	SUBCLONAL	1	TRUE	1	0.774426218797181	2		577	1324	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645067	67645067	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	158	425	2	ENST00000264010.4:c.332G>A	p.Gly111Glu	p.G111E	ENST00000264010	NM_006565.3	111	gGa/gAa	3/12	1	2	FACETS	0.457	0.418	0.497	0.457	0.418	0.497	SUBCLONAL	1	TRUE	1	0.774426218797181	2		427	893	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844200	68844200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555515456	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	56	372	0	ENST00000261769.5:c.788C>T	p.Thr263Ile	p.T263I	ENST00000261769	NM_004360.3	263	aCc/aTc	6/16	1	2	FACETS	0.159	0.135	0.185	0.159	0.135	0.185	SUBCLONAL	1	TRUE	1	0.774426218797181	2		372	909	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832302	72832302	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1154	110	571	0	ENST00000268489.5:c.4279G>A	p.Ala1427Thr	p.A1427T	ENST00000268489	NM_006885.3	1427	Gct/Act	9/10	1	2	FACETS	0.225	0.201	0.25	0.225	0.201	0.25	SUBCLONAL	1	TRUE	1	0.774426218797181	2		571	1264	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993111	72993111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1505	125	708	0	ENST00000268489.5:c.934G>A	p.Asp312Asn	p.D312N	ENST00000268489	NM_006885.3	312	Gac/Aac	2/10	1	2	FACETS	0.198	0.178	0.219	0.198	0.178	0.219	SUBCLONAL	1	TRUE	1	0.774426218797181	2		708	1630	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993584	72993584	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	281	553	0	ENST00000268489.5:c.461G>A	p.Gly154Glu	p.G154E	ENST00000268489	NM_006885.3	154	gGg/gAg	2/10	1	2	FACETS	0.653	0.614	0.694	0.653	0.614	0.694	SUBCLONAL	1	TRUE	1	0.774426218797181	2		553	1111	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81892756	81892756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	54	434	0	ENST00000359376.3:c.467C>T	p.Thr156Ile	p.T156I	ENST00000359376	NM_002661.3	156	aCc/aTc	5/33	1	2	FACETS	0.135	0.115	0.158	0.135	0.115	0.158	SUBCLONAL	1	TRUE	1	0.774426218797181	2		434	1032	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946233	81946233	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	220	635	1	ENST00000359376.3:c.1966G>A	p.Ala656Thr	p.A656T	ENST00000359376	NM_002661.3	656	Gca/Aca	19/33	1	2	FACETS	0.462	0.428	0.496	0.462	0.428	0.496	SUBCLONAL	1	TRUE	1	0.774426218797181	2		636	1231	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579497	7579497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	56	372	0	ENST00000269305.4:c.190C>T	p.Pro64Ser	p.P64S	ENST00000269305	NM_001126112.2	64	Ccc/Tcc	4/11	1	2	FACETS	0.186	0.159	0.216	0.186	0.159	0.216	SUBCLONAL	1	TRUE	1	0.774426218797181	2		372	778	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989703	15989703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	126	308	0	ENST00000268712.3:c.3070C>T	p.Leu1024Phe	p.L1024F	ENST00000268712	NM_006311.3	1024	Ctt/Ttt	23/46	1	2	FACETS	0.456	0.414	0.501	0.456	0.414	0.501	SUBCLONAL	1	TRUE	1	0.774426218797181	2		308	713	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089992	16089992	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	49	167	0	ENST00000268712.3:c.118G>A	p.Val40Ile	p.V40I	ENST00000268712	NM_006311.3	40	Gtc/Atc	3/46	1	2	FACETS	0.263	0.223	0.307	0.263	0.223	0.307	SUBCLONAL	1	TRUE	1	0.774426218797181	2		167	481	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17120382	17120382	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	119	349	0	ENST00000285071.4:c.1176+1G>A		p.X392_splice	ENST00000285071	NM_144997.5	392			1	2	FACETS	0.38	0.343	0.419	0.38	0.343	0.419	SUBCLONAL	1	TRUE	1	0.774426218797181	2		349	809	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122512	17122512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	80	432	0	ENST00000285071.4:c.883G>A	p.Glu295Lys	p.E295K	ENST00000285071	NM_144997.5	295	Gaa/Aaa	9/14	1	2	FACETS	0.216	0.189	0.245	0.216	0.189	0.245	SUBCLONAL	1	TRUE	1	0.774426218797181	2		432	957	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131240	17131240	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555611399	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	67	463	1	ENST00000285071.4:c.212C>T	p.Ser71Phe	p.S71F	ENST00000285071	NM_144997.5	71	tCc/tTc	4/14	1	2	FACETS	0.16	0.138	0.183	0.16	0.138	0.183	SUBCLONAL	1	TRUE	1	0.774426218797181	2		464	1083	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654521	29654521	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	196	305	0	ENST00000356175.3:c.5210G>A	p.Gly1737Asp	p.G1737D	ENST00000356175	NM_000267.3	1737	gGt/gAt	37/57	1	2	FACETS	0.62	0.574	0.666	0.62	0.574	0.666	SUBCLONAL	1	TRUE	1	0.774426218797181	2		305	817	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243908	41243908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80356923	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	41	327	0	ENST00000357654.3:c.3640G>A	p.Glu1214Lys	p.E1214K	ENST00000357654	NM_007294.3	1214	Gag/Aag	10/23	1	2	FACETS	0.137	0.113	0.164	0.137	0.113	0.164	SUBCLONAL	1	TRUE	1	0.774426218797181	2		327	772	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897358	78897358	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780000343	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	233	477	0	ENST00000306801.3:c.2693G>A	p.Ser898Asn	p.S898N	ENST00000306801	NM_020761.2	898	aGc/aAc	23/34	1	2	FACETS	0.619	0.578	0.662	0.619	0.578	0.662	SUBCLONAL	1	TRUE	1	0.774426218797181	2		477	972	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207599	2207599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	129	433	0	ENST00000398665.3:c.883G>A	p.Glu295Lys	p.E295K	ENST00000398665	NM_032482.2	295	Gag/Aag	11/28	1	2	FACETS	0.382	0.346	0.42	0.382	0.346	0.42	SUBCLONAL	1	TRUE	1	0.774426218797181	2		433	872	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226883	2226883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	23	108	0	ENST00000398665.3:c.4363G>A	p.Ala1455Thr	p.A1455T	ENST00000398665	NM_032482.2	1455	Gcg/Acg	27/28	1	2	FACETS	0.233	0.182	0.292	0.233	0.182	0.292	SUBCLONAL	1	TRUE	1	0.774426218797181	2		108	255	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215601	5215601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1285393473	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	31	239	1	ENST00000357368.4:c.4102C>T	p.Leu1368Phe	p.L1368F	ENST00000357368	NM_002850.3	1368	Ctt/Ttt	27/38	1	2	FACETS	0.132	0.106	0.162	0.132	0.106	0.162	SUBCLONAL	1	TRUE	1	0.774426218797181	2		240	606	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222949	5222949	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	76	239	0	ENST00000357368.4:c.2854C>T	p.Pro952Ser	p.P952S	ENST00000357368	NM_002850.3	952	Cca/Tca	18/38	1	2	FACETS	0.389	0.341	0.439	0.389	0.341	0.439	SUBCLONAL	1	TRUE	1	0.774426218797181	2		239	505	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610567	10610567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	124	329	0	ENST00000171111.5:c.143G>A	p.Gly48Asp	p.G48D	ENST00000171111	NM_203500.1	48	gGc/gAc	2/6	1	2	FACETS	0.406	0.367	0.447	0.406	0.367	0.447	SUBCLONAL	1	TRUE	1	0.774426218797181	2		329	789	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272096	15272096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1200527596	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	21	112	0	ENST00000263388.2:c.6343C>T	p.Pro2115Ser	p.P2115S	ENST00000263388	NM_000435.2	2115	Cct/Tct	33/33	1	2	FACETS	0.188	0.144	0.238	0.188	0.144	0.238	SUBCLONAL	1	TRUE	1	0.774426218797181	2		112	289	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271744	18271744	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	272	315	0	ENST00000222254.8:c.431C>G	p.Ser144Cys	p.S144C	ENST00000222254	NM_005027.3	144	tCt/tGt	4/16	1	2	FACETS	0.972	0.917	1	0.972	0.917	1	CLONAL	1	TRUE	1	0.774426218797181	2		315	723	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314583	30314583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	219	486	2	ENST00000262643.3:c.1132G>A	p.Ala378Thr	p.A378T	ENST00000262643	NM_001238.2	378	Gcc/Acc	12/12	1	2	FACETS	0.501	0.465	0.537	0.501	0.465	0.537	SUBCLONAL	1	TRUE	1	0.774426218797181	2		488	1130	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754657	41754657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	98	454	1	ENST00000301178.4:c.1643G>A	p.Gly548Glu	p.G548E	ENST00000301178	NM_021913.4	548	gGa/gAa	14/20	1	2	FACETS	0.239	0.212	0.267	0.239	0.212	0.267	SUBCLONAL	1	TRUE	1	0.774426218797181	2		455	1059	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902311	50902311	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1250	69	669	1	ENST00000440232.2:c.202+1G>A		p.X68_splice	ENST00000440232	NM_002691.3	68			1	2	FACETS	0.135	0.117	0.155	0.135	0.117	0.155	SUBCLONAL	1	TRUE	1	0.774426218797181	2		670	1319	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917023	50917023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145473716	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	266	530	1	ENST00000440232.2:c.2275G>A	p.Val759Ile	p.V759I	ENST00000440232	NM_002691.3	759	Gtc/Atc	19/27	1	2	FACETS	0.569	0.533	0.606	0.569	0.533	0.606	SUBCLONAL	1	TRUE	1	0.774426218797181	2		531	1207	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024701	31024701	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	246	406	0	ENST00000375687.4:c.4186G>A	p.Val1396Met	p.V1396M	ENST00000375687	NM_015338.5	1396	Gtg/Atg	13/13	1	2	FACETS	0.659	0.616	0.703	0.659	0.616	0.703	SUBCLONAL	1	TRUE	1	0.774426218797181	2		406	964	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375117	31375117	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	202	441	0	ENST00000328111.2:c.514G>A	p.Asp172Asn	p.D172N	ENST00000328111	NM_006892.3	172	Gac/Aac	6/23	1	2	FACETS	0.586	0.544	0.63	0.586	0.544	0.63	SUBCLONAL	1	TRUE	1	0.774426218797181	2		441	890	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376669	31376669	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	27	246	1	ENST00000328111.2:c.664G>A	p.Glu222Lys	p.E222K	ENST00000328111	NM_006892.3	222	Gag/Aag	7/23	1	2	FACETS	0.13	0.103	0.161	0.13	0.103	0.161	SUBCLONAL	1	TRUE	1	0.774426218797181	2		247	537	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57470691	57470691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	39	234	0	ENST00000371085.3:c.164C>T	p.Thr55Ile	p.T55I	ENST00000371085	NM_000516.4	55	aCc/aTc	2/13	NA	2	FACETS	0.14	0.116	0.168			1	INDETERMINATE	1	TRUE	NA	0.774426218797181	2		234	717	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485416	57485416	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1418870137	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	163	228	0	ENST00000371085.3:c.998G>A	p.Arg333His	p.R333H	ENST00000371085	NM_000516.4	333	cGc/cAc	12/13	NA	2	FACETS	0.593	0.545	0.642			1	INDETERMINATE	1	TRUE	NA	0.774426218797181	2		228	710	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839680	42839680	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	92	444	0	ENST00000398585.3:c.1559G>A	p.Trp520Ter	p.W520*	ENST00000398585	NM_001135099.1	520	tGg/tAg	13/14	1	2	FACETS	0.238	0.211	0.268	0.238	0.211	0.268	SUBCLONAL	1	TRUE	1	0.774426218797181	2		444	997	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866505	42866505	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1296	73	602	0	ENST00000398585.3:c.127G>A	p.Gly43Arg	p.G43R	ENST00000398585	NM_001135099.1	43	Ggg/Agg	3/14	1	2	FACETS	0.138	0.12	0.157	0.138	0.12	0.157	SUBCLONAL	1	TRUE	1	0.774426218797181	2		602	1369	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41489027	41489027	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	171	335	0	ENST00000263253.7:c.19G>A	p.Glu7Lys	p.E7K	ENST00000263253	NM_001429.3	7	Gaa/Aaa	1/31	0.660161128728099	1	FACETS	0.629	0.585	0.674	0.629	0.585	0.674	SUBCLONAL	1	TRUE	0	0.774426218797181	1		335	430	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39935733	39935733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	37	248	0	ENST00000378444.4:c.139G>A	p.Glu47Lys	p.E47K	ENST00000378444	NM_001123385.1	47	Gaa/Aaa	3/15	1	1	FACETS	0.102	0.084	0.123	0.102	0.084	0.123	SUBCLONAL	1	TRUE	0	0.774426218797181	1		248	572	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409817	63409817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	35	227	0	ENST00000330258.3:c.3350G>A	p.Gly1117Asp	p.G1117D	ENST00000330258	NM_152424.3	1117	gGt/gAt	2/2	1	1	FACETS	0.121	0.099	0.146	0.121	0.099	0.146	SUBCLONAL	1	TRUE	0	0.774426218797181	1		227	457	SUCCESS
AR	367	MSKCC	GRCh37	X	66931354	66931354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	123	269	0	ENST00000374690.3:c.1996G>A	p.Glu666Lys	p.E666K	ENST00000374690	NM_000044.3	666	Gaa/Aaa	4/8	1	1	FACETS	0.336	0.305	0.369	0.336	0.305	0.369	SUBCLONAL	1	TRUE	0	0.774426218797181	1		269	579	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736919	736919	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002265-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	114	327	1	ENST00000314574.4:c.1180del	p.His394ThrfsTer11	p.H394Tfs*11	ENST00000314574	NM_005433.3	394	Cac/ac	10/12	1	2	FACETS	0.307	0.275	0.34	0.307	0.275	0.34	SUBCLONAL	1	TRUE	1	0.774426218797181	2		328	960	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	244	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.262386261214736	3	FACETS	0.941	0.879	1	0.941	0.879	1	CLONAL	2	TRUE	1	0.262386261214736	3		249	1118	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	151	403	0	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	0.251477595798357	1	FACETS	0.951	0.868	1	0.951	0.868	1	CLONAL	1	TRUE	0	0.262386261214736	1		403	1052	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007635	45007635	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	69	248	0	ENST00000558401.1:c.82C>T	p.Gln28Ter	p.Q28*	ENST00000558401	NM_004048.2	28	Cag/Tag	2/4	0.251477595798357	1	FACETS	0.927	0.809	1	0.927	0.809	1	CLONAL	1	TRUE	0	0.262386261214736	1		248	493	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518099	8518099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764400127	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	69	457	2	ENST00000356435.5:c.1292C>T	p.Ser431Leu	p.S431L	ENST00000356435		431	tCg/tTg	10/35	1	2	FACETS	0.653	0.567	0.745	0.653	0.567	0.745	SUBCLONAL	1	TRUE	1	0.262386261214736	2		459	806	SUCCESS
APC	324	MSKCC	GRCh37	5	112175677	112175677	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	107	408	0	ENST00000257430.4:c.4386G>C	p.Lys1462Asn	p.K1462N	ENST00000257430	NM_000038.5	1462	aaG/aaC	16/16	1	2	FACETS	0.949	0.851	1	0.949	0.851	1	CLONAL	1	TRUE	1	0.262386261214736	2		408	859	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011144	12011144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	69	394	2	ENST00000353533.5:c.551C>T	p.Ser184Leu	p.S184L	ENST00000353533	NM_003010.3	184	tCg/tTg	5/11	0.251477595798357	1	FACETS	0.768	0.669	0.875	0.768	0.669	0.875	SUBCLONAL	1	TRUE	0	0.262386261214736	1		396	595	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223448	2223448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	96	427	0	ENST00000398665.3:c.3559G>A	p.Glu1187Lys	p.E1187K	ENST00000398665	NM_032482.2	1187	Gag/Aag	25/28	0.244600501454042	1	FACETS	0.863	0.769	0.963	0.863	0.769	0.963	CLONAL	1	TRUE	0	0.262386261214736	1		427	737	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381498	81381498	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	102	471	0	ENST00000222390.5:c.563G>A	p.Trp188Ter	p.W188*	ENST00000222390	NM_000601.4	188	tGg/tAg	5/18	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.262386261214736	2		471	770	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677993	58677993	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761219249	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	44	228	0	ENST00000305921.3:c.218G>A	p.Arg73Gln	p.R73Q	ENST00000305921	NM_003620.3	73	cGa/cAa	1/6	0.251477595798357	1	FACETS	1	0.845	1	1	0.845	1	CLONAL	1	TRUE	0	0.262386261214736	1		228	291	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548249	41548249	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	91	455	0	ENST00000263253.7:c.3037G>C	p.Glu1013Gln	p.E1013Q	ENST00000263253	NM_001429.3	1013	Gaa/Caa	16/31	1	2	FACETS	0.778	0.69	0.873	0.778	0.69	0.873	SUBCLONAL	1	TRUE	1	0.262386261214736	2		455	891	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938115	36938115	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	rs373601431	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	144	706	0	ENST00000361632.4:c.843+3G>A		p.X281_splice	ENST00000361632		281			0.262386261214736	3	FACETS	1	0.922	1			1	CLONAL	1	TRUE	NA	0.262386261214736	3		706	1223	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511637	46511637	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	165	785	0	ENST00000262741.5:c.1140C>G	p.Phe380Leu	p.F380L	ENST00000262741	NM_003629.3	380	ttC/ttG	9/10	0.236770689852558	2	FACETS	0.993	0.909	1	0.496	0.454	0.54	CLONAL	1	TRUE	0	0.262386261214736	2		785	1267	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414917	78414917	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	75	485	0	ENST00000370768.2:c.1849G>C	p.Glu617Gln	p.E617Q	ENST00000370768	NM_003902.3	617	Gag/Cag	19/20	0.236770689852558	2	FACETS	0.616	0.538	0.7	0.308	0.269	0.35	SUBCLONAL	1	TRUE	0	0.262386261214736	2		485	928	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258033	123258034	+	missense_variant	Missense_Mutation	DNP	GA	GA	AC	novel	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	127	639	2	ENST00000358487.5:c.1647_1648delinsGT	p.Asn549_Leu550delinsLysPhe	p.N549_L550delinsKF	ENST00000358487	NM_000141.4	549	aaTCtt/aaGTtt	12/18	1	2	FACETS	0.931	0.842	1	0.931	0.842	1	CLONAL	1	TRUE	1	0.262386261214736	2		641	1040	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279672	123279672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	71	364	0	ENST00000358487.5:c.760C>T	p.His254Tyr	p.H254Y	ENST00000358487	NM_000141.4	254	Cac/Tac	7/18	1	2	FACETS	0.944	0.825	1	0.944	0.825	1	CLONAL	1	TRUE	1	0.262386261214736	2		364	573	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219115	94219115	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	134	535	0	ENST00000323929.3:c.289C>T	p.Gln97Ter	p.Q97*	ENST00000323929	NM_005591.3	97	Cag/Tag	4/20	NA	2	FACETS	1	0.936	1			1	INDETERMINATE	1	TRUE	NA	0.262386261214736	2		535	982	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190746	108190746	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	164	616	0	ENST00000278616.4:c.6413G>C	p.Arg2138Thr	p.R2138T	ENST00000278616	NM_000051.3	2138	aGa/aCa	44/63	0.244600501454042	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.262386261214736	1		616	998	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65569055	65569055	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	59	549	0	ENST00000358664.4:c.3G>A	p.Met1?	p.M1?	ENST00000358664	NM_002382.4	1	atG/atA	1/5	0.251477595798357	1	FACETS	0.502	0.431	0.58	0.502	0.431	0.58	SUBCLONAL	1	TRUE	0	0.262386261214736	1		549	778	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95596468	95596468	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	121	583	0	ENST00000393063.1:c.500C>G	p.Ser167Ter	p.S167*	ENST00000393063	NM_030621.3	167	tCa/tGa	6/28	NA	2	FACETS	0.883	0.796	0.974			1	INDETERMINATE	1	TRUE	NA	0.262386261214736	2		583	1045	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639641	3639641	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1617	218	989	0	ENST00000294008.3:c.3998C>T	p.Ser1333Phe	p.S1333F	ENST00000294008	NM_032444.2	1333	tCt/tTt	12/15	0.262386261214736	3	FACETS	1	0.945	1	0.512	0.474	0.552	CLONAL	1	TRUE	1	0.262386261214736	3		989	1835	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592283	29592283	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	58	282	0	ENST00000356175.3:c.4698G>C	p.Leu1566Phe	p.L1566F	ENST00000356175	NM_000267.3	1566	ttG/ttC	35/57	0.236770689852558	2	FACETS	0.847	0.728	0.976	0.423	0.364	0.488	CLONAL	1	TRUE	0	0.262386261214736	2		282	522	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117755	70117755	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	163	786	1	ENST00000245479.2:c.223G>T	p.Glu75Ter	p.E75*	ENST00000245479	NM_000346.3	75	Gag/Tag	1/3	0.251477595798357	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.262386261214736	1		787	1067	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52722950	52722950	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	72	663	0	ENST00000322088.6:c.1135G>C	p.Glu379Gln	p.E379Q	ENST00000322088	NM_014225.5	379	Gag/Cag	10/15	1	2	FACETS	0.52	0.452	0.593	0.52	0.452	0.593	SUBCLONAL	1	TRUE	1	0.262386261214736	2		663	1056	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249879	39249879	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	148	677	0	ENST00000402219.2:c.1690G>C	p.Glu564Gln	p.E564Q	ENST00000402219	NM_005633.3	564	Gag/Cag	10/23	1	2	FACETS	0.933	0.85	1	0.933	0.85	1	CLONAL	1	TRUE	1	0.262386261214736	2		677	1209	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172230	99172230	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	124	687	0	ENST00000074304.5:c.1796C>G	p.Ser599Cys	p.S599C	ENST00000074304	NM_001134224.1	599	tCc/tGc	17/26	1	2	FACETS	0.868	0.784	0.957	0.868	0.784	0.957	CLONAL	1	TRUE	1	0.262386261214736	2		687	1089	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682855	190682855	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	86	564	0	ENST00000441310.2:c.531G>A	p.Met177Ile	p.M177I	ENST00000441310	NM_000534.4	177	atG/atA	5/13	1	2	FACETS	0.597	0.526	0.673	0.597	0.526	0.673	SUBCLONAL	1	TRUE	1	0.262386261214736	2		564	1098	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662734	227662734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	134	774	2	ENST00000305123.5:c.721G>A	p.Asp241Asn	p.D241N	ENST00000305123	NM_005544.2	241	Gat/Aat	1/2	1	2	FACETS	0.828	0.751	0.911	0.828	0.751	0.911	CLONAL	1	TRUE	1	0.262386261214736	2		776	1233	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755459	39755459	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	98	581	0	ENST00000288319.7:c.1306C>G	p.Pro436Ala	p.P436A	ENST00000288319	NM_182918.3	436	Cca/Gca	10/10	1	2	FACETS	0.773	0.689	0.864	0.773	0.689	0.864	SUBCLONAL	1	TRUE	1	0.262386261214736	2		581	966	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967496	38967496	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	119	440	0	ENST00000357387.3:c.1094C>T	p.Ser365Leu	p.S365L	ENST00000357387	NM_152756.3	365	tCa/tTa	13/38	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.262386261214736	2		440	875	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953940	131953940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	91	393	1	ENST00000265335.6:c.3343G>A	p.Glu1115Lys	p.E1115K	ENST00000265335		1115	Gaa/Aaa	21/25	1	2	FACETS	0.851	0.755	0.954	0.851	0.755	0.954	CLONAL	1	TRUE	1	0.262386261214736	2		394	815	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777876	27777876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	38	306	0	ENST00000369163.2:c.25C>T	p.Arg9Cys	p.R9C	ENST00000369163	NM_003536.2	9	Cgc/Tgc	1/1	1	2	FACETS	0.696	0.576	0.83	0.696	0.576	0.83	SUBCLONAL	1	TRUE	1	0.262386261214736	2		306	416	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436134	116436134	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	81	447	0	ENST00000397752.3:c.4129G>C	p.Asp1377His	p.D1377H	ENST00000397752	NM_000245.2	1377	Gat/Cat	21/21	1	2	FACETS	0.794	0.698	0.896	0.794	0.698	0.896	SUBCLONAL	1	TRUE	1	0.262386261214736	2		447	778	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624428	140624428	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507457	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	27	181	0	ENST00000288602.6:c.76G>A	p.Glu26Lys	p.E26K	ENST00000288602	NM_004333.4	26	Gag/Aag	1/18	1	2	FACETS	0.73	0.582	0.898	0.73	0.582	0.898	SUBCLONAL	1	TRUE	1	0.262386261214736	2		181	282	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172251	38172251	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	135	559	1	ENST00000317025.8:c.2156G>T	p.Gly719Val	p.G719V	ENST00000317025	NM_023034.1	719	gGa/gTa	12/24	0.251477595798357	1	FACETS	0.987	0.896	1	0.987	0.896	1	CLONAL	1	TRUE	0	0.262386261214736	1		560	906	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56882298	56882298	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	134	542	0	ENST00000519728.1:c.996G>C	p.Lys332Asn	p.K332N	ENST00000519728	NM_002350.3	332	aaG/aaC	10/13	1	2	FACETS	0.986	0.894	1	0.986	0.894	1	CLONAL	1	TRUE	1	0.262386261214736	2		542	1036	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129915	69129915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752310428	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	89	352	0	ENST00000288368.4:c.4669C>T	p.Arg1557Cys	p.R1557C	ENST00000288368	NM_024870.2	1557	Cgt/Tgt	38/40	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.262386261214736	2		352	675	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27203087	27203087	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002713-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	153	672	0	ENST00000380036.4:c.2179C>G	p.His727Asp	p.H727D	ENST00000380036	NM_000459.3	727	Cat/Gat	13/23	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.262386261214736	2		672	1159	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0003101-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	651	337	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.971596523695378	2	FACETS	0.996	0.986	1	0.996	0.986	1	CLONAL	2	TRUE	0	0.971596523695378	2		337	673	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857047	9857047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568622613	NA	P-0003101-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	574	612	1	ENST00000330684.3:c.4354C>T	p.Arg1452Cys	p.R1452C	ENST00000330684	NM_001134407.1	1452	Cgc/Tgc	13/13	1	2	FACETS	0.949	0.914	0.984	0.949	0.914	0.984	CLONAL	1	TRUE	1	0.971596523695378	2		613	1245	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417868	138417868	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003101-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	519	522	0	ENST00000289153.2:c.1651T>C	p.Cys551Arg	p.C551R	ENST00000289153	NM_006219.2	551	Tgt/Cgt	11/22	1	2	FACETS	0.961	0.924	0.998	0.961	0.924	0.998	CLONAL	1	TRUE	1	0.971596523695378	2		522	1112	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881505	48881505	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0003101-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	580	458	0	ENST00000267163.4:c.227T>G	p.Leu76Ter	p.L76*	ENST00000267163	NM_000321.2	76	tTa/tGa	2/27	0.971596523695378	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.971596523695378	1		458	608	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577043	7577046	+	frameshift_variant	Frame_Shift_Del	DEL	GCTC	GCTC	-	novel	NA	P-0003101-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	589	529	1	ENST00000269305.4:c.892_895del	p.Glu298CysfsTer46	p.E298Cfs*46	ENST00000269305	NM_001126112.2	298	GAGCtg/tg	8/11	0.966791301953249	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.971596523695378	1		530	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0003198-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	49	509	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.595	0.504	0.696	0.595	0.504	0.696	SUBCLONAL	1	TRUE	1	0.322796486603627	2		509	510	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039583	180039583	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs75614493	NA	P-0003198-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	47	462	1	ENST00000261937.6:c.3460G>A	p.Gly1154Arg	p.G1154R	ENST00000261937	NM_182925.4	1154	Gga/Aga	26/30	0.322796486603627	3	FACETS	0.447	0.376	0.526	0.224	0.188	0.263	SUBCLONAL	1	TRUE	1	0.322796486603627	3		463	756	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468158	50468158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003198-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	24	314	0	ENST00000331340.3:c.1393G>A	p.Glu465Lys	p.E465K	ENST00000331340	NM_006060.4	465	Gaa/Aaa	8/8	0.322796486603627	3	FACETS	0.395	0.309	0.495	0.198	0.154	0.248	SUBCLONAL	1	TRUE	1	0.322796486603627	3		314	437	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426988	70426988	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003198-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	27	324	0	ENST00000373644.4:c.4648G>T	p.Asp1550Tyr	p.D1550Y	ENST00000373644	NM_030625.2	1550	Gac/Tac	7/12	1	2	FACETS	0.33	0.262	0.408	0.33	0.262	0.408	SUBCLONAL	1	TRUE	1	0.322796486603627	2		324	507	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514889	103514889	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003198-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	59	321	0	ENST00000355739.4:c.1390G>A	p.Gly464Arg	p.G464R	ENST00000355739	NM_000123.3	464	Ggg/Agg	8/15	0.247820562400963	4	FACETS	0.794	0.683	0.915			1	CLONAL	1	TRUE	NA	0.322796486603627	4		321	609	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0004140-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	164	367	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.608523465587318	3	FACETS	1	0.974	1	0.564	0.52	0.61	CLONAL	1	TRUE	1	0.608523465587318	3		367	623	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164966	47164966	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004140-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	63	426	0	ENST00000409792.3:c.1160C>G	p.Thr387Ser	p.T387S	ENST00000409792	NM_014159.6	387	aCt/aGt	3/21	1	2	FACETS	0.513	0.445	0.585	0.513	0.445	0.585	SUBCLONAL	1	TRUE	1	0.608523465587318	2		426	404	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63829535	63829535	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004140-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	87	382	0	ENST00000279873.7:c.1178G>A	p.Cys393Tyr	p.C393Y	ENST00000279873	NM_032199.2	393	tGt/tAt	8/10	1	2	FACETS	0.799	0.713	0.889	0.799	0.713	0.889	SUBCLONAL	1	TRUE	1	0.608523465587318	2		382	358	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128482	30128482	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004140-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	315	896	0	ENST00000263025.4:c.900C>G	p.Asp300Glu	p.D300E	ENST00000263025	NM_002746.2	300	gaC/gaG	6/9	1	2	FACETS	0.953	0.9	1	0.953	0.9	1	CLONAL	1	TRUE	1	0.608523465587318	2		896	1086	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39644786	39644786	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004140-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	134	484	1	ENST00000262039.4:c.2515G>A	p.Val839Met	p.V839M	ENST00000262039	NM_002647.2	839	Gtg/Atg	23/25	0.608523465587318	1	FACETS	0.749	0.687	0.813	0.749	0.687	0.813	SUBCLONAL	1	TRUE	0	0.608523465587318	1		485	409	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560898	9560898	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767455314	NA	P-0004140-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	168	648	3	ENST00000353224.5:c.884C>T	p.Pro295Leu	p.P295L	ENST00000353224	NM_177990.2	295	cCg/cTg	4/10	1	2	FACETS	0.972	0.899	1	0.972	0.899	1	CLONAL	1	TRUE	1	0.608523465587318	2		651	568	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573651	48573677	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GATGGGAGGCTTCAGGTTAGTCTTATA	GATGGGAGGCTTCAGGTTAGTCTTATA	T	novel	NA	P-0004140-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	56	300	0	ENST00000342988.3:c.235_249+12delinsT		p.X79_splice	ENST00000342988	NM_005359.5	79		2/12	0.608523465587318	1	FACETS	0.719	0.628	0.816	0.719	0.628	0.816	SUBCLONAL	1	TRUE	0	0.608523465587318	1		300	178	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545658	106545658	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004140-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	41	606	0	ENST00000359195.3:c.3135A>T	p.Lys1045Asn	p.K1045N	ENST00000359195	NM_002649.2	1045	aaA/aaT	11/11	1	2	FACETS	0.249	0.207	0.295	0.249	0.207	0.295	SUBCLONAL	1	TRUE	1	0.608523465587318	2		606	542	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002736	37002736	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004140-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	44	495	0	ENST00000358127.4:c.513C>A	p.Ser171Arg	p.S171R	ENST00000358127	NM_001280556.1	171	agC/agA	5/10	0.608523465587318	1	FACETS	0.133	0.111	0.158	0.133	0.111	0.158	SUBCLONAL	1	TRUE	0	0.608523465587318	1		495	755	SUCCESS
APC	324	MSKCC	GRCh37	5	112176654	112176654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201472075	NA	P-0004297-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	10	489	0	ENST00000257430.4:c.5363G>A	p.Arg1788His	p.R1788H	ENST00000257430	NM_000038.5	1788	cGt/cAt	16/16	0.365031345606008	4	FACETS	0.603	0.411	0.842	0.302	0.205	0.421	SUBCLONAL	1	FALSE	2	0.365031345606008	4		489	124	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0004691-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	900	474	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.349336548406541	9	FACETS	0.948	0.924	0.972			1	CLONAL	8	TRUE	NA	0.349336548406541	9		474	1510	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955538	48955538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913303	NA	P-0004691-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	244	515	1	ENST00000267163.4:c.1654C>T	p.Arg552Ter	p.R552*	ENST00000267163	NM_000321.2	552	Cga/Tga	17/27	0.349336548406541	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.349336548406541	2		516	666	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579331	7579331	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004691-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	178	519	0	ENST00000269305.4:c.356C>G	p.Ala119Gly	p.A119G	ENST00000269305	NM_001126112.2	119	gCc/gGc	4/11	NA	2	FACETS	0.945	0.877	1			1	INDETERMINATE	2	TRUE	NA	0.349336548406541	2		519	539	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759905	133759905	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369171735	NA	P-0004691-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	104	624	1	ENST00000318560.5:c.2228C>T	p.Thr743Met	p.T743M	ENST00000318560	NM_005157.4	743	aCg/aTg	11/11	0.349336548406541	5	FACETS	0.775	0.692	0.864			1	SUBCLONAL	1	TRUE	NA	0.349336548406541	5		625	1171	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004728-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	145	391	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	0.542	0.494	0.591	0.542	0.494	0.591	SUBCLONAL	1	TRUE	1	0.676765491127397	2		391	791	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990481	69990481	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs201247895	NA	P-0004728-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	239	425	1	ENST00000394351.3:c.440C>T	p.Thr147Met	p.T147M	ENST00000394351	NM_000248.3	147	aCg/aTg	4/9	1	2	FACETS	0.985	0.924	1	0.985	0.924	1	CLONAL	1	TRUE	1	0.676765491127397	2		426	717	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557340	29557340	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0004778-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	77	553	0	ENST00000356175.3:c.3053T>A	p.Leu1018Ter	p.L1018*	ENST00000356175	NM_000267.3	1018	tTa/tAa	23/57	1	2	FACETS	0.966	0.846	1	0.966	0.846	1	CLONAL	1	TRUE	1	0.18	2		553	886	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0005150-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	128	503	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.936	0.851	1	0.936	0.851	1	CLONAL	1	TRUE	1	0.450545619503763	2		503	607	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0005150-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	1729	508	3	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	0.450545619503763	11	FACETS	0.986	0.973	0.998			1	CLONAL	11	TRUE	NA	0.450545619503763	11		511	2143	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120314	70120314	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005150-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1376	353	1222	0	ENST00000245479.2:c.1316A>T	p.Gln439Leu	p.Q439L	ENST00000245479	NM_000346.3	439	cAg/cTg	3/3	1	2	FACETS	0.906	0.856	0.958	0.906	0.856	0.958	CLONAL	1	TRUE	1	0.450545619503763	2		1222	1729	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632046	1632046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1375481873	NA	P-0005150-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	143	1038	0	ENST00000344749.5:c.289G>A	p.Gly97Arg	p.G97R	ENST00000344749	NM_001136139.2	97	Gga/Aga	5/19	1	2	FACETS	0.497	0.451	0.545	0.497	0.451	0.545	SUBCLONAL	1	TRUE	1	0.450545619503763	2		1038	1278	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953951	17953951	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005150-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	85	525	0	ENST00000458235.1:c.451C>A	p.Pro151Thr	p.P151T	ENST00000458235	NM_000215.3	151	Ccc/Acc	5/24	1	2	FACETS	0.604	0.534	0.678	0.604	0.534	0.678	SUBCLONAL	1	TRUE	1	0.450545619503763	2		525	625	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0005436-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	517	565	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.858787908193302	1	FACETS	0.999	0.972	1	0.999	0.972	1	CLONAL	1	TRUE	0	0.858787908193302	1		565	688	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434891	56434891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005436-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	415	535	0	ENST00000407977.2:c.2246C>T	p.Ser749Phe	p.S749F	ENST00000407977		749	tCt/tTt	9/10	1	2	FACETS	0.991	0.948	1	0.991	0.948	1	CLONAL	1	TRUE	1	0.858787908193302	2		535	975	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842269	151842269	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005436-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	136	595	0	ENST00000262189.6:c.14143A>G	p.Met4715Val	p.M4715V	ENST00000262189	NM_170606.2	4715	Atg/Gtg	54/59	1	2	FACETS	0.254	0.23	0.279	0.254	0.23	0.279	SUBCLONAL	1	TRUE	1	0.858787908193302	2		595	1248	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0005553-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	92	563	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.150528371422617	3	FACETS	1	0.965	1	0.615	0.545	0.69	CLONAL	1	TRUE	1	0.17	3		563	955	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075166	16075166	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005553-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	63	366	0	ENST00000268712.3:c.386T>C	p.Leu129Ser	p.L129S	ENST00000268712	NM_006311.3	129	tTa/tCa	4/46	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.17	2		366	637	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579531	7579531	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005553-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	52	586	0	ENST00000269305.4:c.156del	p.Gln52HisfsTer71	p.Q52Hfs*71	ENST00000269305	NM_001126112.2	52	caA/ca	4/11	1	2	FACETS	0.827	0.702	0.964	0.827	0.702	0.964	CLONAL	1	TRUE	1	0.17	2		586	740	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794359	242794359	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005970-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	372	480	0	ENST00000334409.5:c.583G>A	p.Ala195Thr	p.A195T	ENST00000334409	NM_005018.2	195	Gcc/Acc	3/5	0.881145145653158	3	FACETS	0.989	0.95	1			1	CLONAL	2	FALSE	NA	0.881145145653158	3		480	615	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478803	57478803	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005970-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	207	340	0	ENST00000371085.3:c.389A>G	p.Tyr130Cys	p.Y130C	ENST00000371085	NM_000516.4	130	tAc/tGc	5/13	0.678748868528301	4	FACETS	0.976	0.906	1	0.488	0.453	0.524	CLONAL	1	FALSE	2	0.881145145653158	4		340	906	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650870	48650870	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782126313	NA	P-0005970-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	263	265	0	ENST00000376670.3:c.739C>T	p.Arg247Cys	p.R247C	ENST00000376670	NM_002049.3	247	Cgc/Tgc	4/6	0.881145145653158	3	FACETS	0.966	0.908	1			1	CLONAL	1	FALSE	NA	0.881145145653158	3		265	890	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0006444-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	91	217	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.261021855167973	3	FACETS	0.958	0.857	1	0.639	0.571	0.709	CLONAL	2	TRUE	0	0.29	3		217	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0006444-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	244	571	0	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.231262430091472	2	FACETS	0.903	0.845	0.963	0.903	0.845	0.963	CLONAL	2	TRUE	0	0.29	2		571	932	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920527	134920527	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006444-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	278	477	2	ENST00000398015.3:c.2342C>A	p.Ser781Tyr	p.S781Y	ENST00000398015	NM_004441.4	781	tCc/tAc	12/16	0.261021855167973	3	FACETS	1	0.99	1	0.821	0.773	0.87	CLONAL	2	TRUE	0	0.29	3		479	891	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265975	41266211	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	In_Frame_Del	DEL	CATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGAT	CATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGAT	-	novel	NA	P-0006444-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	123	254	0	ENST00000349496.5:c.14-42_208del		p.A5_G69del	ENST00000349496	NM_001904.3	5		3/15	0.261021855167973	3	FACETS	1	0.97	1	0.767	0.699	0.837	CLONAL	2	TRUE	0	0.29	3		254	422	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006498-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	38	374	0	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	0.157163895929479	6	FACETS	0.99	0.821	1	0.495	0.41	0.589	CLONAL	2	FALSE	2	0.157163895929479	6		374	321	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183770	10183770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs5030805	NA	P-0006498-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	39	249	0	ENST00000256474.2:c.239G>A	p.Ser80Asn	p.S80N	ENST00000256474	NM_000551.3	80	aGt/aAt	1/3	0.131914938703577	3	FACETS	1	0.89	1	0.725	0.605	0.857	CLONAL	2	FALSE	0	0.157163895929479	3		249	246	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965436	25965436	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs762887744	NA	P-0006498-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	48	487	0	ENST00000435504.4:c.3770A>T	p.Asp1257Val	p.D1257V	ENST00000435504		1257	gAt/gTt	13/13	0.157163895929479	3	FACETS	1	0.896	1	1	0.896	1	CLONAL	2	FALSE	1	0.157163895929479	3		487	308	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207021	1207021	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913324	NA	P-0006814-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	119	475	1	ENST00000326873.7:c.109C>T	p.Gln37Ter	p.Q37*	ENST00000326873	NM_000455.4	37	Cag/Tag	1/10	0.286174937651789	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.286174937651789	1		476	691	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987045	36987047	+	inframe_deletion	In_Frame_Del	DEL	TAC	TAC	-	novel	NA	P-0006814-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	68	328	0	ENST00000354822.5:c.642_644del	p.Lys214_Tyr215delinsAsn	p.K214_Y215delinsN	ENST00000354822	NM_001079668.2	214	aaGTAc/aac	3/3	0.286174937651789	1	FACETS	0.823	0.717	0.936	0.823	0.717	0.936	CLONAL	1	TRUE	0	0.286174937651789	1		328	495	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477861	140477861	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs397507474	NA	P-0006814-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	190	582	0	ENST00000288602.6:c.1447A>G	p.Lys483Glu	p.K483E	ENST00000288602	NM_004333.4	483	Aaa/Gaa	12/18	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.286174937651789	2		582	1310	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041266	47041266	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0006814-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1254	224	802	3	ENST00000377604.3:c.1693+1G>A		p.X565_splice	ENST00000377604	NM_001204468.1	565			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.286174937651789	2		805	1478	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625164	69625164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115452181	NA	P-0007126-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	32	540	0	ENST00000334134.2:c.629G>A	p.Arg210Gln	p.R210Q	ENST00000334134	NM_005247.2	210	cGg/cAg	3/3	0.186338774763081	2	FACETS	0.446	0.361	0.541	0.223	0.18	0.271	SUBCLONAL	1	TRUE	0	0.290798737871108	2		540	494	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0007126-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	60	343	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	0.290798737871108	1	FACETS	0.935	0.81	1	0.935	0.81	1	CLONAL	1	TRUE	0	0.290798737871108	1		343	377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578206	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs886039484	NA	P-0007126-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	146	906	0	ENST00000269305.4:c.643A>G	p.Ser215Gly	p.S215G	ENST00000269305	NM_001126112.2	215	Agt/Ggt	6/11	0.186338774763081	2	FACETS	0.758	0.694	0.825	0.758	0.694	0.825	SUBCLONAL	2	TRUE	0	0.290798737871108	2		906	662	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926893	112926893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007126-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	72	482	0	ENST00000351677.2:c.1513G>A	p.Val505Ile	p.V505I	ENST00000351677	NM_002834.3	505	Gtc/Atc	13/16	1	2	FACETS	0.984	0.862	1	0.984	0.862	1	CLONAL	1	TRUE	1	0.290798737871108	2		482	503	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41525902	41525902	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007126-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	91	288	0	ENST00000263253.7:c.1177T>A	p.Cys393Ser	p.C393S	ENST00000263253	NM_001429.3	393	Tgt/Agt	5/31	0.186338774763081	2	FACETS	1	0.978	1	0.703	0.627	0.783	CLONAL	1	TRUE	0	0.290798737871108	2		288	445	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247103	53247103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782434611	NA	P-0007126-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	27	432	1	ENST00000375401.3:c.397C>T	p.Arg133Trp	p.R133W	ENST00000375401	NM_004187.3	133	Cgg/Tgg	4/26	0.224194935992312	2	FACETS	0.462	0.367	0.57			1	SUBCLONAL	1	TRUE	NA	0.290798737871108	2		433	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0007185-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	50	771	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.250623765303447	1	FACETS	0.406	0.343	0.476	0.406	0.343	0.476	SUBCLONAL	1	TRUE	0	0.256168686206959	1		771	838	SUCCESS
APC	324	MSKCC	GRCh37	5	112174268	112174268	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0007185-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	70	611	1	ENST00000257430.4:c.2977A>T	p.Lys993Ter	p.K993*	ENST00000257430	NM_000038.5	993	Aag/Tag	16/16	0.256168686206959	1	FACETS	0.733	0.639	0.835	0.733	0.639	0.835	SUBCLONAL	1	TRUE	0	0.256168686206959	1		612	650	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332799	152332799	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007185-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	105	804	2	ENST00000206249.3:c.1105G>T	p.Asp369Tyr	p.D369Y	ENST00000206249	NM_000125.3	369	Gat/Tat	5/8	1	2	FACETS	0.994	0.89	1	0.994	0.89	1	CLONAL	1	TRUE	1	0.256168686206959	2		806	825	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925597	114925597	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007185-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	72	1172	1	ENST00000543371.1:c.1679del	p.Pro560GlnfsTer42	p.P560Qfs*42	ENST00000543371	NM_001198531.1	559	Ccc/cc	14/14	1	2	FACETS	0.526	0.458	0.6	0.526	0.458	0.6	SUBCLONAL	1	TRUE	1	0.256168686206959	2		1173	1068	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579427	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGGCTG	GGGGGCTG	-	novel	NA	P-0007185-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	46	526	0	ENST00000269305.4:c.260_267del	p.Pro87LeufsTer59	p.P87Lfs*59	ENST00000269305	NM_001126112.2	87	cCAGCCCCC/c	4/11	0.250623765303447	1	FACETS	0.513	0.431	0.603	0.513	0.431	0.603	SUBCLONAL	1	TRUE	0	0.256168686206959	1		526	611	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036927	180036927	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007185-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	60	737	1	ENST00000261937.6:c.3785C>T	p.Pro1262Leu	p.P1262L	ENST00000261937	NM_182925.4	1262	cCa/cTa	28/30	1	2	FACETS	0.475	0.408	0.549	0.475	0.408	0.549	SUBCLONAL	1	TRUE	1	0.256168686206959	2		738	986	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117645555	117645555	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007185-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	51	799	0	ENST00000368508.3:c.5581A>C	p.Ser1861Arg	p.S1861R	ENST00000368508	NM_002944.2	1861	Agt/Cgt	34/43	0.202416030278351	0	FACETS	0.314	0.265	0.367			1	SUBCLONAL	1	TRUE	0	0.256168686206959	0		799	944	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467873	50467873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779769920	NA	P-0007185-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	30	358	1	ENST00000331340.3:c.1108G>A	p.Val370Met	p.V370M	ENST00000331340	NM_006060.4	370	Gtg/Atg	8/8	NA	2	FACETS	0.532	0.428	0.65			1	INDETERMINATE	1	TRUE	NA	0.256168686206959	2		359	440	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476376	88476376	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007185-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	29	474	0	ENST00000360948.2:c.1756C>T	p.Gln586Ter	p.Q586*	ENST00000360948	NM_001012338.2	586	Cag/Tag	15/19	0.252358087012328	1	FACETS	0.366	0.293	0.45	0.366	0.293	0.45	SUBCLONAL	1	TRUE	0	0.256168686206959	1		474	539	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593667	55593669	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	rs1060502543	NA	P-0007513-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	241	624	0	ENST00000288135.5:c.1735_1737del	p.Asp579del	p.D579del	ENST00000288135	NM_000222.2	578	tATGat/tat	11/21	1	2	FACETS	0.91	0.852	0.969	0.91	0.852	0.969	CLONAL	1	TRUE	1	0.660623776602136	2		624	802	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008179-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	105	391	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.265118066846015	3	FACETS	0.884	0.791	0.982	0.295	0.263	0.328	CLONAL	1	TRUE	0	0.334193360631154	3		391	830	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233024	55233024	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144943614	NA	P-0008179-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	248	297	0	ENST00000275493.2:c.1774G>A	p.Val592Ile	p.V592I	ENST00000275493	NM_005228.3	592	Gtc/Atc	15/28	0.192484449371045	5	FACETS	1	0.953	1	0.683	0.638	0.729	INDETERMINATE	2	TRUE	2	0.334193360631154	5		297	1088	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	463304	463304	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008179-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	352	1141	0	ENST00000399788.2:c.967C>G	p.Leu323Val	p.L323V	ENST00000399788	NM_001042603.1	323	Cta/Gta	8/28	0.213671847843562	5	FACETS	1	0.962	1	0.681	0.643	0.72	CLONAL	2	TRUE	2	0.334193360631154	5		1141	1548	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0008442-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	76	474	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.482	0.422	0.548	0.482	0.422	0.548	SUBCLONAL	1	TRUE	1	0.336384382934682	2		474	937	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0008442-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	68	257	2	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.174915161596003	3	FACETS	0.99	0.864	1	0.495	0.432	0.563	INDETERMINATE	1	TRUE	1	0.336384382934682	3		259	477	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008442-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	184	677	0	ENST00000269305.4:c.166G>T	p.Glu56Ter	p.E56*	ENST00000269305	NM_001126112.2	56	Gaa/Taa	4/11	0.165592427818718	2	FACETS	1	0.975	1	0.564	0.52	0.609	INDETERMINATE	1	TRUE	0	0.336384382934682	2		677	970	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099981	27099981	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008442-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	82	655	0	ENST00000324856.7:c.3860G>C	p.Arg1287Thr	p.R1287T	ENST00000324856	NM_006015.4	1287	aGa/aCa	15/20	1	2	FACETS	0.43	0.378	0.487	0.43	0.378	0.487	SUBCLONAL	1	TRUE	1	0.336384382934682	2		655	1133	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097687	27097687	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008442-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	116	652	0	ENST00000324856.7:c.3276G>C	p.Leu1092Phe	p.L1092F	ENST00000324856	NM_006015.4	1092	ttG/ttC	12/20	1	2	FACETS	0.536	0.482	0.594	0.536	0.482	0.594	SUBCLONAL	1	TRUE	1	0.336384382934682	2		652	1286	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094386	27094386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008442-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	78	465	0	ENST00000324856.7:c.3094G>A	p.Glu1032Lys	p.E1032K	ENST00000324856	NM_006015.4	1032	Gag/Aag	11/20	1	2	FACETS	0.538	0.472	0.61	0.538	0.472	0.61	SUBCLONAL	1	TRUE	1	0.336384382934682	2		465	862	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099054	27099054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008442-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	97	590	2	ENST00000324856.7:c.3470G>A	p.Gly1157Glu	p.G1157E	ENST00000324856	NM_006015.4	1157	gGa/gAa	13/20	1	2	FACETS	0.521	0.463	0.583	0.521	0.463	0.583	SUBCLONAL	1	TRUE	1	0.336384382934682	2		592	1107	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099121	27099121	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008442-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	73	431	0	ENST00000324856.7:c.3537G>T	p.Met1179Ile	p.M1179I	ENST00000324856	NM_006015.4	1179	atG/atT	13/20	1	2	FACETS	0.529	0.462	0.602	0.529	0.462	0.602	SUBCLONAL	1	TRUE	1	0.336384382934682	2		431	820	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099408	27099408	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008442-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	87	554	1	ENST00000324856.7:c.3645G>T	p.Met1215Ile	p.M1215I	ENST00000324856	NM_006015.4	1215	atG/atT	14/20	1	2	FACETS	0.464	0.41	0.523	0.464	0.41	0.523	SUBCLONAL	1	TRUE	1	0.336384382934682	2		555	1114	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099471	27099471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008442-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	58	401	0	ENST00000324856.7:c.3708G>A	p.Met1236Ile	p.M1236I	ENST00000324856	NM_006015.4	1236	atG/atA	14/20	1	2	FACETS	0.426	0.365	0.493	0.426	0.365	0.493	SUBCLONAL	1	TRUE	1	0.336384382934682	2		401	810	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101074	27101074	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008442-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	144	651	0	ENST00000324856.7:c.4356G>T	p.Gln1452His	p.Q1452H	ENST00000324856	NM_006015.4	1452	caG/caT	18/20	1	2	FACETS	0.651	0.591	0.713	0.651	0.591	0.713	SUBCLONAL	1	TRUE	1	0.336384382934682	2		651	1316	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101324	27101324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs999125494	NA	P-0008442-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	91	688	0	ENST00000324856.7:c.4606G>A	p.Asp1536Asn	p.D1536N	ENST00000324856	NM_006015.4	1536	Gat/Aat	18/20	1	2	FACETS	0.444	0.393	0.499	0.444	0.393	0.499	SUBCLONAL	1	TRUE	1	0.336384382934682	2		688	1218	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105565	27105565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008442-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	118	784	1	ENST00000324856.7:c.5176G>A	p.Glu1726Lys	p.E1726K	ENST00000324856	NM_006015.4	1726	Gag/Aag	20/20	1	2	FACETS	0.52	0.467	0.576	0.52	0.467	0.576	SUBCLONAL	1	TRUE	1	0.336384382934682	2		785	1350	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0008577-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	1048	474	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.240544754782811	11	FACETS	1	0.99	1			1	CLONAL	10	FALSE	NA	0.240544754782811	11		474	1769	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0008577-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	18	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.501	0.377	0.647	0.501	0.377	0.647	SUBCLONAL	1	FALSE	1	0.240544754782811	2		249	299	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0008577-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	141	771	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.957	0.87	1	0.957	0.87	1	CLONAL	1	FALSE	1	0.240544754782811	2		771	1225	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044892	47044892	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008577-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	81	693	0	ENST00000377604.3:c.2218G>T	p.Glu740Ter	p.E740*	ENST00000377604	NM_001204468.1	740	Gag/Tag	20/24	0.240544754782811	1	FACETS	0.666	0.586	0.753	0.666	0.586	0.753	SUBCLONAL	1	FALSE	0	0.240544754782811	1		693	889	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515262	103515262	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008577-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	42	662	0	ENST00000355739.4:c.1763G>T	p.Ser588Ile	p.S588I	ENST00000355739	NM_000123.3	588	aGc/aTc	8/15	1	2	FACETS	0.455	0.379	0.541	0.455	0.379	0.541	SUBCLONAL	1	FALSE	1	0.240544754782811	2		662	767	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207027	1207027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876658779	NA	P-0008577-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	46	483	0	ENST00000326873.7:c.115C>T	p.Arg39Cys	p.R39C	ENST00000326873	NM_000455.4	39	Cgc/Tgc	1/10	0.222746427264743	0	FACETS	0.463	0.389	0.545			1	SUBCLONAL	1	FALSE	0	0.240544754782811	0		483	627	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259173	36259173	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008577-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	48	706	0	ENST00000300305.3:c.318G>A	p.Trp106Ter	p.W106*	ENST00000300305		106	tgG/tgA	3/8	1	2	FACETS	0.501	0.422	0.588	0.501	0.422	0.588	SUBCLONAL	1	FALSE	1	0.240544754782811	2		706	797	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129756	108129756	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0008785-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	370	435	0	ENST00000278616.4:c.2420T>A	p.Leu807Ter	p.L807*	ENST00000278616	NM_000051.3	807	tTa/tAa	16/63	1	2	FACETS	0.966	0.921	1	0.966	0.921	1	CLONAL	1	TRUE	1	0.872459421383697	2		435	878	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445051	89445051	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008966-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	344	532	0	ENST00000336596.2:c.1371G>A	p.Trp457Ter	p.W457*	ENST00000336596	NM_005233.5	457	tgG/tgA	6/17	NA	2	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.698608931409038	2		532	959	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857158	9857158	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008966-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	811	777	1	ENST00000330684.3:c.4243G>A	p.Asp1415Asn	p.D1415N	ENST00000330684	NM_001134407.1	1415	Gac/Aac	13/13	0.693355718470924	3	FACETS	0.985	0.956	1	0.985	0.956	1	CLONAL	2	TRUE	1	0.698608931409038	3		778	1590	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892187	9892187	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008966-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	416	667	0	ENST00000330684.3:c.2303G>T	p.Gly768Val	p.G768V	ENST00000330684	NM_001134407.1	768	gGc/gTc	11/13	0.693355718470924	3	FACETS	1	0.987	1	0.55	0.523	0.578	CLONAL	1	TRUE	1	0.698608931409038	3		667	1461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578264	7578338	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GATAAGATGCTGAGGAGGGGCCAGACCTAAGAGCAATCAGTGAGGAATCAGAGGCCTGGGGACCCTGGGCAACCA	GATAAGATGCTGAGGAGGGGCCAGACCTAAGAGCAATCAGTGAGGAATCAGAGGCCTGGGGACCCTGGGCAACCA	TT	novel	NA	P-0008966-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	494	671	3	ENST00000269305.4:c.559+33_585delinsAA		p.X187_splice	ENST00000269305	NM_001126112.2	187		6/11	0.698608931409038	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.698608931409038	1		674	774	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0009181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	92	500	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.25	2		500	695	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371662	55371662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	77	333	0	ENST00000297316.4:c.352G>A	p.Val118Met	p.V118M	ENST00000297316	NM_022454.3	118	Gtg/Atg	2/2	0.229581077027541	3	FACETS	1	0.961	1	0.615	0.541	0.695	CLONAL	1	TRUE	1	0.25	3		333	563	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881426	37881426	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	72	365	0	ENST00000269571.5:c.2618A>G	p.Asp873Gly	p.D873G	ENST00000269571		873	gAc/gGc	21/27	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.25	2		365	569	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063717	+	splice_donor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0009181-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	29	177	0	ENST00000412916.2:c.165+1del		p.X55_splice	ENST00000412916		55			NA	2	FACETS	0.832	0.669	1			1	INDETERMINATE	1	TRUE	NA	0.25	2		177	279	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0009276-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	62	389	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.302	0.26	0.348	0.302	0.26	0.348	SUBCLONAL	1	TRUE	1	0.48626969984131	2		389	845	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781288	NA	P-0009276-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	116	661	2	ENST00000269305.4:c.422G>T	p.Cys141Phe	p.C141F	ENST00000269305	NM_001126112.2	141	tGc/tTc	5/11	1	2	FACETS	0.407	0.366	0.452	0.407	0.366	0.452	SUBCLONAL	1	TRUE	1	0.48626969984131	2		663	1171	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293731	1293731	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009276-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	48	392	0	ENST00000310581.5:c.1270G>T	p.Gly424Cys	p.G424C	ENST00000310581	NM_198253.2	424	Ggt/Tgt	2/16	1	2	FACETS	0.354	0.299	0.415	0.354	0.299	0.415	SUBCLONAL	1	TRUE	1	0.48626969984131	2		392	557	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719706	190719706	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009276-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	40	443	0	ENST00000441310.2:c.1708G>T	p.Val570Leu	p.V570L	ENST00000441310	NM_000534.4	570	Gta/Tta	9/13	1	2	FACETS	0.22	0.182	0.262	0.22	0.182	0.262	SUBCLONAL	1	TRUE	1	0.48626969984131	2		443	749	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868194	45868194	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1032384332	NA	P-0009786-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	47	566	3	ENST00000391945.4:c.496C>T	p.Arg166Cys	p.R166C	ENST00000391945	NM_000400.3	166	Cgt/Tgt	7/23	1	2	FACETS	0.652	0.549	0.766	0.652	0.549	0.766	SUBCLONAL	1	TRUE	1	0.194841668527574	2		569	740	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432041	49432041	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009786-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	109	952	1	ENST00000301067.7:c.9098C>T	p.Thr3033Ile	p.T3033I	ENST00000301067	NM_003482.3	3033	aCc/aTc	34/54	1	2	FACETS	0.97	0.868	1	0.97	0.868	1	CLONAL	1	TRUE	1	0.194841668527574	2		953	1154	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0009948-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	57	427	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.206462679338751	2	FACETS	0.809	0.697	0.93	0.809	0.697	0.93	CLONAL	2	TRUE	0	0.19	2		427	371	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0009948-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	127	478	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.243125473316405	4	FACETS	1	0.958	1	1	0.958	1	CLONAL	3	TRUE	1	0.19	4		478	488	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909347	41909347	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009948-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	37	305	0	ENST00000372991.4:c.41G>T	p.Arg14Leu	p.R14L	ENST00000372991	NM_001760.3	14	cGg/cTg	1/5	0.175703599952936	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	2	TRUE	0	0.19	2		305	175	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374701	118374701	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009948-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	54	602	0	ENST00000534358.1:c.8094A>T	p.Glu2698Asp	p.E2698D	ENST00000534358	NM_005933.3	2698	gaA/gaT	27/36	0.184214713153322	3	FACETS	1	0.952	1	0.646	0.552	0.748	CLONAL	1	TRUE	1	0.19	3		602	482	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81922859	81922859	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009948-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	206	1188	1	ENST00000359376.3:c.848C>A	p.Pro283His	p.P283H	ENST00000359376	NM_002661.3	283	cCt/cAt	10/33	0.3	3	FACETS	0.845	0.784	0.907	1	0.987	1	CLONAL	3	TRUE	1	0.19	3		1189	937	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965248	81965248	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009948-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	51	752	0	ENST00000359376.3:c.2728A>C	p.Ile910Leu	p.I910L	ENST00000359376	NM_002661.3	910	Att/Ctt	25/33	0.3	3	FACETS	1	0.884	1	0.524	0.445	0.611	CLONAL	1	TRUE	1	0.19	3		752	561	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381504	81381504	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009948-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	54	847	0	ENST00000222390.5:c.557del	p.Gly186AspfsTer27	p.G186Dfs*27	ENST00000222390	NM_000601.4	186	gGa/ga	5/18	0.184214713153322	3	FACETS	0.827	0.705	0.961	0.413	0.352	0.481	CLONAL	1	TRUE	1	0.19	3		847	753	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0009995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	96	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.944	0.847	1	0.944	0.847	1	CLONAL	1	TRUE	1	0.478315655796273	2		249	425	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0009995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	285	422	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.465246167901193	2	FACETS	0.816	0.772	0.861	0.816	0.772	0.861	CLONAL	2	TRUE	0	0.478315655796273	2		422	730	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939177	36939177	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs186379741	NA	P-0009995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	335	590	3	ENST00000361632.4:c.532G>A	p.Val178Met	p.V178M	ENST00000361632		178	Gtg/Atg	5/16	0.478315655796273	1	FACETS	0.953	0.902	1	0.953	0.902	1	CLONAL	1	TRUE	0	0.478315655796273	1		593	1118	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518734	204518734	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	205	382	1	ENST00000367182.3:c.1397G>T	p.Arg466Ile	p.R466I	ENST00000367182	NM_001278516.1	466	aGa/aTa	11/11	1	2	FACETS	0.922	0.855	0.99	0.922	0.855	0.99	CLONAL	1	TRUE	1	0.478315655796273	2		383	930	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480383	89480383	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	251	440	1	ENST00000336596.2:c.2220G>T	p.Met740Ile	p.M740I	ENST00000336596	NM_005233.5	740	atG/atT	13/17	0.478315655796273	1	FACETS	0.88	0.825	0.937	0.88	0.825	0.937	CLONAL	1	TRUE	0	0.478315655796273	1		441	907	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190861	32190861	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	226	425	0	ENST00000375023.3:c.76C>A	p.Leu26Met	p.L26M	ENST00000375023	NM_004557.3	26	Ctg/Atg	2/30	1	2	FACETS	0.851	0.792	0.912	0.851	0.792	0.912	CLONAL	1	TRUE	1	0.478315655796273	2		425	1110	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104352340	104352340	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	392	379	0	ENST00000369902.3:c.456G>T	p.Glu152Asp	p.E152D	ENST00000369902	NM_016169.3	152	gaG/gaT	4/12	0.467888036551328	2	FACETS	0.844	0.805	0.883	0.844	0.805	0.883	CLONAL	2	TRUE	0	0.478315655796273	2		379	971	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610281	81610281	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	238	429	0	ENST00000298171.2:c.1879G>T	p.Ala627Ser	p.A627S	ENST00000298171	NM_000369.2	627	Gct/Tct	10/10	1	2	FACETS	0.96	0.896	1	0.96	0.896	1	CLONAL	1	TRUE	1	0.478315655796273	2		429	1037	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73995414	73995414	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	109	188	0	ENST00000318443.5:c.720G>T	p.Gln240His	p.Q240H	ENST00000318443	NM_001024736.1	240	caG/caT	4/10	1	2	FACETS	0.912	0.822	1	0.912	0.822	1	CLONAL	1	TRUE	1	0.478315655796273	2		188	500	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602877	10602877	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	303	407	0	ENST00000171111.5:c.701G>C	p.Arg234Pro	p.R234P	ENST00000171111	NM_203500.1	234	cGg/cCg	3/6	0.455429750354927	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.478315655796273	1		407	941	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944405	76944405	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	180	509	0	ENST00000373344.5:c.500G>T	p.Gly167Val	p.G167V	ENST00000373344	NM_000489.3	167	gGg/gTg	7/35	0.478315655796273	1	FACETS	0.903	0.837	0.972	0.903	0.837	0.972	CLONAL	1	TRUE	0	0.478315655796273	1		509	634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064794618	NA	P-0010014-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	165	393	0	ENST00000269305.4:c.159G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgG/tgA	4/11	1	2	FACETS	0.803	0.739	0.87	1	0.99	1	CLONAL	2	TRUE	1	0.27	2		393	761	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604665	48604665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660045	NA	P-0010014-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	47	382	0	ENST00000342988.3:c.1487G>A	p.Arg496His	p.R496H	ENST00000342988	NM_005359.5	496	cGt/cAt	12/12	0.303970546019579	1	FACETS	0.641	0.541	0.751	0.641	0.541	0.751	SUBCLONAL	1	TRUE	0	0.27	1		382	470	SUCCESS
APC	324	MSKCC	GRCh37	5	112175822	112175823	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0010014-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	106	362	0	ENST00000257430.4:c.4532_4533del	p.Leu1511ArgfsTer2	p.L1511Rfs*2	ENST00000257430	NM_000038.5	1511	CTc/c	16/16	0.240434249079477	3	FACETS	1	0.961	1	0.748	0.676	0.823	CLONAL	2	TRUE	0	0.27	3		362	397	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18747427	18747427	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0010023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	89	246	0	ENST00000266497.5:c.3889-1G>C		p.X1297_splice	ENST00000266497		1297			0.690209558247997	3	FACETS	0.956	0.854	1	0.478	0.427	0.531	CLONAL	1	TRUE	1	0.690209558247997	3		246	363	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349365	73349365	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	39	525	0	ENST00000377767.4:c.971A>T	p.Glu324Val	p.E324V	ENST00000377767	NM_014953.3	324	gAa/gTa	6/21	0.690209558247997	2	FACETS	0.19	0.157	0.227	0.095	0.078	0.114	SUBCLONAL	1	TRUE	0	0.690209558247997	2		525	595	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988509	41988509	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010023-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	78	704	0	ENST00000219905.7:c.1301A>G	p.Asp434Gly	p.D434G	ENST00000219905	NM_001164273.1	434	gAc/gGc	3/24	1	2	FACETS	0.311	0.273	0.352	0.311	0.273	0.352	SUBCLONAL	1	TRUE	1	0.690209558247997	2		704	726	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89839769	89839769	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	558	511	0	ENST00000389301.3:c.1924G>A	p.Glu642Lys	p.E642K	ENST00000389301	NM_000135.2	642	Gaa/Aaa	22/43	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	2	TRUE	NA	0.437486677152321	2		511	1255	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0010027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	629	824	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.437486677152321	2		824	1344	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719113	52719113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	395	357	0	ENST00000322088.6:c.889G>A	p.Glu297Lys	p.E297K	ENST00000322088	NM_014225.5	297	Gag/Aag	7/15	0.438747330325077	3	FACETS	0.974	0.927	1	0.974	0.927	1	CLONAL	2	TRUE	1	0.437486677152321	3		357	1130	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917824	29917824	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1332	214	499	0	ENST00000389048.3:c.844G>T	p.Asp282Tyr	p.D282Y	ENST00000389048	NM_004304.4	282	Gac/Tac	3/29	0.438747330325077	4	FACETS	0.91	0.843	0.98	0.303	0.281	0.327	CLONAL	1	TRUE	1	0.437486677152321	4		499	1546	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672713	86672713	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	291	335	3	ENST00000274376.6:c.2200G>T	p.Glu734Ter	p.E734*	ENST00000274376	NM_002890.2	734	Gaa/Taa	17/25	0.437486677152321	2	FACETS	0.914	0.865	0.963	0.914	0.865	0.963	CLONAL	2	TRUE	0	0.437486677152321	2		338	728	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158602	26158602	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	317	143	0	ENST00000289316.2:c.205G>C	p.Asp69His	p.D69H	ENST00000289316	NM_138720.2	69	Gac/Cac	1/2	0.438747330325077	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	TRUE	0	0.437486677152321	3		143	579	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631243	117631243	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0010027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	133	397	0	ENST00000368508.3:c.6434+1G>A		p.X2145_splice	ENST00000368508	NM_002944.2	2145			1	2	FACETS	0.958	0.872	1	0.958	0.872	1	CLONAL	1	TRUE	1	0.437486677152321	2		397	635	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410511	139410511	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	695	366	1	ENST00000277541.6:c.1591G>T	p.Glu531Ter	p.E531*	ENST00000277541	NM_017617.3	531	Gag/Tag	10/34	0.438747330325077	3	FACETS	0.965	0.934	0.995	0.965	0.934	0.995	CLONAL	3	TRUE	0	0.437486677152321	3		367	1338	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115976	8115976	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	173	129	0	ENST00000346208.3:c.1322C>A	p.Ala441Asp	p.A441D	ENST00000346208		441	gCc/gAc	6/6	0.438747330325077	3	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	1	0.437486677152321	3		129	474	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144609	119144609	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	194	404	0	ENST00000264033.4:c.622G>C	p.Ala208Pro	p.A208P	ENST00000264033	NM_005188.3	208	Gct/Cct	4/16	0.438747330325077	3	FACETS	0.955	0.882	1	0.477	0.441	0.515	CLONAL	1	TRUE	1	0.437486677152321	3		404	1132	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415936	49415936	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0010027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	386	333	0	ENST00000301067.7:c.16413-2A>T		p.X5471_splice	ENST00000301067	NM_003482.3	5471			0.438747330325077	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.437486677152321	3		333	1057	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533039	63533039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745857521	NA	P-0010027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1231	264	513	1	ENST00000307078.5:c.1855G>A	p.Val619Ile	p.V619I	ENST00000307078	NM_004655.3	619	Gtc/Atc	7/11	0.438747330325077	3	FACETS	0.984	0.92	1	0.328	0.306	0.35	CLONAL	1	TRUE	0	0.437486677152321	3		514	1495	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719813	52719813	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	232	474	0	ENST00000322088.6:c.1025A>C	p.Lys342Thr	p.K342T	ENST00000322088	NM_014225.5	342	aAg/aCg	9/15	0.438747330325077	3	FACETS	0.89	0.828	0.955	0.445	0.414	0.478	CLONAL	1	TRUE	1	0.437486677152321	3		474	1452	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0010028-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	896	661	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.515917279225536	5	FACETS	1	0.991	1	1	0.991	1	CLONAL	4	TRUE	1	0.515917279225536	5		661	1485	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0010028-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	96	234	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.36014725035558	1	FACETS	0.778	0.699	0.86	0.778	0.699	0.86	SUBCLONAL	1	TRUE	0	0.515917279225536	1		234	355	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254962	16254962	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010028-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	52	317	0	ENST00000375759.3:c.2227C>T	p.Gln743Ter	p.Q743*	ENST00000375759	NM_015001.2	743	Cag/Tag	11/15	0.250435914425772	1	FACETS	0.33	0.281	0.384	0.33	0.281	0.384	INDETERMINATE	1	TRUE	0	0.515917279225536	1		317	453	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858901	57858901	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1476006703	NA	P-0010028-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	247	707	0	ENST00000228682.2:c.397C>G	p.Leu133Val	p.L133V	ENST00000228682	NM_005269.2	133	Ctg/Gtg	5/12	1	2	FACETS	0.775	0.723	0.828	0.775	0.723	0.828	SUBCLONAL	1	TRUE	1	0.515917279225536	2		707	1236	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828088	3828088	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010028-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	235	605	0	ENST00000262367.5:c.2037G>C	p.Leu679Phe	p.L679F	ENST00000262367	NM_004380.2	679	ttG/ttC	10/31	0.139058108748209	3	FACETS	0.94	0.876	1	0.47	0.438	0.504	INDETERMINATE	1	TRUE	1	0.515917279225536	3		605	1219	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0010028-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	396	432	0	ENST00000269305.4:c.920-2A>C		p.X307_splice	ENST00000269305	NM_001126112.2	307			NA	2	FACETS	0.934	0.894	0.974			1	INDETERMINATE	2	TRUE	NA	0.515917279225536	2		432	822	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618410	37618410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010028-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	206	474	1	ENST00000447079.4:c.86G>A	p.Ser29Asn	p.S29N	ENST00000447079	NM_015083.1	29	aGc/aAc	1/14	NA	2	FACETS	1	0.94	1			1	INDETERMINATE	1	TRUE	NA	0.515917279225536	2		475	789	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578440	7578440	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs879254249	NA	P-0010044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	200	358	0	ENST00000269305.4:c.490A>G	p.Lys164Glu	p.K164E	ENST00000269305	NM_001126112.2	164	Aag/Gag	5/11	0.287954490317345	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.305775183641495	2		358	552	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610163	28610163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770571247	NA	P-0010044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	139	502	0	ENST00000241453.7:c.1327G>A	p.Ala443Thr	p.A443T	ENST00000241453	NM_004119.2	443	Gca/Aca	11/24	0.213444123426537	5	FACETS	1	0.956	1	0.715	0.653	0.78	CLONAL	2	TRUE	2	0.305775183641495	5		502	618	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085875	16085875	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	139	302	0	ENST00000281043.3:c.1051A>C	p.Lys351Gln	p.K351Q	ENST00000281043	NM_005378.4	351	Aag/Cag	3/3	0.305775183641495	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.305775183641495	3		302	490	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482169	87482169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201028496	NA	P-0010044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	74	438	0	ENST00000277120.3:c.1456G>A	p.Val486Ile	p.V486I	ENST00000277120		486	Gtt/Att	14/19	0.305775183641495	3	FACETS	1	0.9	1	0.343	0.301	0.389	CLONAL	1	TRUE	0	0.305775183641495	3		438	542	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518577	69518577	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	12	168	1	ENST00000294312.3:c.68G>T	p.Arg23Leu	p.R23L	ENST00000294312	NM_005117.2	23	cGc/cTc	1/3	0.305775183641495	3	FACETS	0.471	0.331	0.643	0.236	0.165	0.322	SUBCLONAL	1	TRUE	1	0.305775183641495	3		169	192	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134508	41134508	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1230	80	950	3	ENST00000379561.5:c.1120C>A	p.Leu374Ile	p.L374I	ENST00000379561	NM_002015.3	374	Ctt/Att	2/3	0.213444123426537	5	FACETS	0.583	0.511	0.66	0.194	0.17	0.22	SUBCLONAL	1	TRUE	2	0.305775183641495	5		953	1310	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611132	100611132	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	48	534	0	ENST00000308731.7:c.1474C>T	p.Arg492Cys	p.R492C	ENST00000308731	NM_000061.2	492	Cgc/Tgc	15/19	0.257687038871764	2	FACETS	0.413	0.348	0.484	0.206	0.174	0.242	SUBCLONAL	1	TRUE	0	0.305775183641495	2		534	761	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0010053-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	2992	478	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.443826812221041	12	FACETS	0.98	0.97	0.989			1	CLONAL	12	TRUE	NA	0.443826812221041	12		478	3692	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0010053-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	425	403	0	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	0.361962457336777	2	FACETS	0.937	0.896	0.979	0.937	0.896	0.979	CLONAL	2	TRUE	0	0.443826812221041	2		403	1022	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	273	389	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.251786812483654	1	FACETS	0.897	0.845	0.95	0.897	0.845	0.95	INDETERMINATE	1	TRUE	0	0.546065726031579	1		389	810	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0010056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	282	645	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	0.546065726031579	2		645	911	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808239	99808239	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	309	678	0	ENST00000280892.6:c.450G>T	p.Trp150Cys	p.W150C	ENST00000280892	NM_001130678.1	150	tgG/tgT	5/7	0.286907805769097	1	FACETS	0.717	0.676	0.759	0.717	0.676	0.759	INDETERMINATE	1	TRUE	0	0.546065726031579	1		678	1148	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5029801	5029801	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	235	396	1	ENST00000381652.3:c.245A>T	p.His82Leu	p.H82L	ENST00000381652	NM_004972.3	82	cAt/cTt	4/25	1	2	FACETS	0.954	0.892	1	0.954	0.892	1	CLONAL	1	TRUE	1	0.546065726031579	2		397	902	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228325	53228325	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	175	554	0	ENST00000375401.3:c.2077G>T	p.Glu693Ter	p.E693*	ENST00000375401	NM_004187.3	693	Gag/Tag	15/26	0.363630341321692	1	FACETS	0.454	0.418	0.492	0.454	0.418	0.492	SUBCLONAL	1	TRUE	0	0.546065726031579	1		554	1026	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986786	36986920	+	inframe_deletion	In_Frame_Del	DEL	CTGGCACGGTTTGCCGTCTTTCACCAGGACCGGCACCGCCACGCGTCGCGGCGACTGCTGCTGAGCCTGTTGCTGCTGCGGGCACCCGGTGCCCCCGCCGCCCCCGCCGCCGCCGCTGTCCTGCTGCAGTTGCTG	CTGGCACGGTTTGCCGTCTTTCACCAGGACCGGCACCGCCACGCGTCGCGGCGACTGCTGCTGAGCCTGTTGCTGCTGCGGGCACCCGGTGCCCCCGCCGCCCCCGCCGCCGCCGCTGTCCTGCTGCAGTTGCTG	-	novel	NA	P-0010056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	387	107	0	ENST00000354822.5:c.769_903del	p.Gln257_Gln301del	p.Q257_Q301del	ENST00000354822	NM_001079668.2	257	CAGCAACTGCAGCAGGACAGCGGCGGCGGCGGGGGCGGCGGGGGCACCGGGTGCCCGCAGCAGCAACAGGCTCAGCAGCAGTCGCCGCGACGCGTGGCGGTGCCGGTCCTGGTGAAAGACGGCAAACCGTGCCAG/-	3/3	0.170478095915823	6	FACETS	1	0.99	1			1	INDETERMINATE	5	TRUE	NA	0.546065726031579	6		107	556	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400646	56400647	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0010056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	319	655	1	ENST00000348428.3:c.1240_1241delinsTT	p.Gly414Leu	p.G414L	ENST00000348428	NM_006785.3	414	GGa/TTa	11/17	1	2	FACETS	0.87	0.82	0.921	0.87	0.82	0.921	CLONAL	1	TRUE	1	0.546065726031579	2		656	1343	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0010067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	45	371	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.804	0.674	0.948	0.804	0.674	0.948	CLONAL	1	TRUE	1	0.16	2		371	700	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236087	108236087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781894	NA	P-0010067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	52	510	0	ENST00000278616.4:c.9023G>A	p.Arg3008His	p.R3008H	ENST00000278616	NM_000051.3	3008	cGt/cAt	63/63	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.16	2		510	465	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303220	15303220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs932099250	NA	P-0010067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	58	525	2	ENST00000263388.2:c.308G>A	p.Arg103Gln	p.R103Q	ENST00000263388	NM_000435.2	103	cGa/cAa	3/33	1	2	FACETS	0.757	0.648	0.876	0.757	0.648	0.876	SUBCLONAL	1	TRUE	1	0.16	2		527	958	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280140	66280140	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010086-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	49	326	1	ENST00000273854.3:c.1549A>T	p.Ile517Phe	p.I517F	ENST00000273854	NM_004439.5	517	Att/Ttt	7/18	1	2	FACETS	0.777	0.657	0.908	0.777	0.657	0.908	CLONAL	1	TRUE	1	0.217156549107618	2		327	581	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197255	26197255	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010086-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1976	161	984	0	ENST00000356476.2:c.224T>G	p.Ile75Ser	p.I75S	ENST00000356476		75	aTc/aGc	1/1	1	2	FACETS	0.694	0.633	0.758	0.694	0.633	0.758	SUBCLONAL	1	TRUE	1	0.217156549107618	2		984	2137	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0010098-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	241	227	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.559362994789328	6	FACETS	0.893	0.844	0.943	0.893	0.844	0.943	CLONAL	4	TRUE	2	0.559362994789328	6		227	511	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0010098-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	216	367	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.559362994789328	5	FACETS	0.798	0.743	0.855	0.532	0.495	0.57	SUBCLONAL	2	TRUE	2	0.559362994789328	5		367	890	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0010098-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	668	500	0	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	0.521856796285129	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	4	TRUE	0	0.559362994789328	4		500	931	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0010098-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	108	330	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.559362994789328	4	FACETS	0.833	0.748	0.923	0.278	0.249	0.308	CLONAL	1	TRUE	1	0.559362994789328	4		330	723	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0010098-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	415	365	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.559362994789328	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	1	0.559362994789328	4		365	751	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298032	11298032	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010098-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	413	631	0	ENST00000361445.4:c.2076C>G	p.Asn692Lys	p.N692K	ENST00000361445	NM_004958.3	692	aaC/aaG	13/58	0.559362994789328	3	FACETS	0.954	0.912	0.997	0.636	0.608	0.665	CLONAL	2	TRUE	0	0.559362994789328	3		631	990	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597829	43597829	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010098-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	1211	870	0	ENST00000355710.3:c.377T>G	p.Phe126Cys	p.F126C	ENST00000355710	NM_020975.4	126	tTc/tGc	3/20	0.537267274141558	5	FACETS	0.948	0.93	0.965	0.948	0.93	0.965	CLONAL	5	TRUE	0	0.559362994789328	5		870	1680	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224453	123224453	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010098-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	421	421	2	ENST00000218089.9:c.3306G>T	p.Met1102Ile	p.M1102I	ENST00000218089	NM_001042749.1	1102	atG/atT	31/35	0.559362994789328	4	FACETS	1	0.985	1			1	CLONAL	2	TRUE	NA	0.559362994789328	4		423	1098	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226456	133226523	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGGCCTCGGCCATCGTGACCTGGAAAGACCCAGTGAAGCCTTAAATCTCAGGATCTCGGGCTGCGCA	GAGGCCTCGGCCATCGTGACCTGGAAAGACCCAGTGAAGCCTTAAATCTCAGGATCTCGGGCTGCGCA	-	novel	NA	P-0010098-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	87	455	0	ENST00000320574.5:c.3583-48_3602del		p.X1195_splice	ENST00000320574	NM_006231.2	1195		30/49	0.536918494070948	3	FACETS	0.626	0.554	0.702	0.313	0.277	0.351	SUBCLONAL	1	TRUE	1	0.559362994789328	3		455	636	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594095	55594095	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0010098-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	206	399	0	ENST00000288135.5:c.1879+2T>C		p.X627_splice	ENST00000288135	NM_000222.2	627			0.506530416470919	2	FACETS	0.809	0.76	0.859	0.809	0.76	0.859	CLONAL	2	TRUE	0	0.559362994789328	2		399	455	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231142	98231142	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010098-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	175	343	0	ENST00000331920.6:c.2141A>T	p.Gln714Leu	p.Q714L	ENST00000331920	NM_000264.3	714	cAg/cTg	14/24	0.521856796285129	4	FACETS	0.882	0.818	0.948	0.441	0.409	0.474	CLONAL	2	TRUE	0	0.559362994789328	4		343	553	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658298	18658298	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010098-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	245	427	1	ENST00000266497.5:c.3103C>G	p.His1035Asp	p.H1035D	ENST00000266497		1035	Cac/Gac	22/31	NA	2	FACETS	0.909	0.86	0.957			1	INDETERMINATE	2	TRUE	NA	0.559362994789328	2		428	482	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528361	157528361	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010098-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	330	616	0	ENST00000346085.5:c.6087del	p.Asn2030ThrfsTer6	p.N2030Tfs*6	ENST00000346085	NM_020732.3	2029	gCc/gc	20/20	0.531849844788284	3	FACETS	0.87	0.825	0.915	0.58	0.55	0.61	CLONAL	2	TRUE	0	0.559362994789328	3		616	868	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221265	5221266	+	splice_acceptor_variant	Splice_Site	DNP	CT	CT	AA	novel	NA	P-0010098-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	161	340	1	ENST00000357368.4:c.3202-2_3202-1delinsTT		p.X1068_splice	ENST00000357368	NM_002850.3	1068			0.509366963535557	4	FACETS	0.836	0.771	0.902	0.836	0.771	0.902	CLONAL	2	TRUE	2	0.559362994789328	4		341	537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0010118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	98	237	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.2357084510141	2	FACETS	0.827	0.74	0.918	0.827	0.74	0.918	CLONAL	2	TRUE	0	0.2357084510141	2		238	503	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591825	48591825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767342	NA	P-0010118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	57	574	0	ENST00000342988.3:c.988G>A	p.Glu330Lys	p.E330K	ENST00000342988	NM_005359.5	330	Gaa/Aaa	9/12	0.2357084510141	1	FACETS	0.546	0.467	0.632	0.546	0.467	0.632	SUBCLONAL	1	TRUE	0	0.2357084510141	1		574	782	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251754	212251754	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	34	407	0	ENST00000342788.4:c.3305T>G	p.Phe1102Cys	p.F1102C	ENST00000342788	NM_005235.2	1102	tTt/tGt	27/28	1	2	FACETS	0.456	0.371	0.551	0.456	0.371	0.551	SUBCLONAL	1	TRUE	1	0.2357084510141	2		407	633	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163284	32163284	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	106	766	0	ENST00000375023.3:c.5942C>T	p.Pro1981Leu	p.P1981L	ENST00000375023	NM_004557.3	1981	cCt/cTt	30/30	1	2	FACETS	0.828	0.741	0.922	0.828	0.741	0.922	CLONAL	1	TRUE	1	0.2357084510141	2		766	1086	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0010125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	185	771	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.244087474516217	1	FACETS	0.586	0.539	0.635	0.586	0.539	0.635	SUBCLONAL	1	TRUE	0	0.379275215489631	1		771	1349	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0010125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	88	367	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.83	0.737	0.929	0.83	0.737	0.929	CLONAL	1	TRUE	1	0.379275215489631	2		367	559	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131402	17131402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398124537	NA	P-0010125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	155	401	0	ENST00000285071.4:c.50G>A	p.Arg17His	p.R17H	ENST00000285071	NM_144997.5	17	cGc/cAc	4/14	0.244087474516217	1	FACETS	0.769	0.704	0.837	0.769	0.704	0.837	SUBCLONAL	1	TRUE	0	0.379275215489631	1		401	861	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259477	89259477	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200567888	NA	P-0010125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	70	572	0	ENST00000336596.2:c.621G>T	p.Lys207Asn	p.K207N	ENST00000336596	NM_005233.5	207	aaG/aaT	3/17	1	2	FACETS	0.485	0.422	0.553	0.485	0.422	0.553	SUBCLONAL	1	TRUE	1	0.379275215489631	2		572	761	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922321	178922321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	181	351	0	ENST00000263967.3:c.1090G>A	p.Gly364Arg	p.G364R	ENST00000263967	NM_006218.2	364	Gga/Aga	6/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.379275215489631	2		351	846	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076745	72076745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	210	741	0	ENST00000357731.5:c.752C>T	p.Pro251Leu	p.P251L	ENST00000357731	NM_173808.2	251	cCg/cTg	5/7	0.345269491025622	0	FACETS	0.596	0.552	0.641			1	SUBCLONAL	1	TRUE	0	0.379275215489631	0		741	1154	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917499	178917499	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	88	355	0	ENST00000263967.3:c.374T>A	p.Val125Glu	p.V125E	ENST00000263967	NM_006218.2	125	gTg/gAg	3/21	1	2	FACETS	0.957	0.851	1	0.957	0.851	1	CLONAL	1	TRUE	1	0.379275215489631	2		355	485	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749389	41749389	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	131	332	0	ENST00000226382.2:c.406G>A	p.Asp136Asn	p.D136N	ENST00000226382	NM_003924.3	136	Gac/Aac	2/3	1	2	FACETS	0.932	0.847	1	0.932	0.847	1	CLONAL	1	TRUE	1	0.379275215489631	2		332	741	SUCCESS
APC	324	MSKCC	GRCh37	5	112157605	112157605	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	120	414	0	ENST00000257430.4:c.1325T>A	p.Val442Asp	p.V442D	ENST00000257430	NM_000038.5	442	gTt/gAt	11/16	1	2	FACETS	0.701	0.632	0.773	0.701	0.632	0.773	SUBCLONAL	1	TRUE	1	0.379275215489631	2		414	903	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007687	45007687	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	73	326	0	ENST00000558401.1:c.134G>T	p.Cys45Phe	p.C45F	ENST00000558401	NM_004048.2	45	tGc/tTc	2/4	1	2	FACETS	0.62	0.542	0.704	0.62	0.542	0.704	SUBCLONAL	1	TRUE	1	0.379275215489631	2		326	621	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943676	9943676	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	94	425	0	ENST00000330684.3:c.1265T>A	p.Ile422Lys	p.I422K	ENST00000330684	NM_001134407.1	422	aTa/aAa	5/13	NA	2	FACETS	0.514	0.456	0.576			1	INDETERMINATE	1	TRUE	NA	0.379275215489631	2		425	964	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250430	10250430	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	408	492	2	ENST00000340748.4:c.3822C>A	p.Phe1274Leu	p.F1274L	ENST00000340748		1274	ttC/ttA	33/40	0.379275215489631	3	FACETS	0.848	0.805	0.891	0.848	0.805	0.891	CLONAL	2	TRUE	1	0.379275215489631	3		494	1510	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564539	41564539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	161	498	0	ENST00000263253.7:c.3961G>A	p.Val1321Ile	p.V1321I	ENST00000263253	NM_001429.3	1321	Gtc/Atc	24/31	1	2	FACETS	0.883	0.81	0.96	0.883	0.81	0.96	CLONAL	1	TRUE	1	0.379275215489631	2		498	961	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223467	53223467	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	198	587	0	ENST00000375401.3:c.3892T>G	p.Ser1298Ala	p.S1298A	ENST00000375401	NM_004187.3	1298	Tct/Gct	23/26	1	2	FACETS	0.906	0.838	0.977	0.906	0.838	0.977	CLONAL	1	TRUE	1	0.379275215489631	2		587	1152	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007688	45007695	+	frameshift_variant	Frame_Shift_Del	DEL	CTATGTGT	CTATGTGT	-	novel	NA	P-0010125-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	60	329	0	ENST00000558401.1:c.137_144del	p.Tyr46TrpfsTer8	p.Y46Wfs*8	ENST00000558401	NM_004048.2	45	tgCTATGTGTct/tgct	2/4	1	2	FACETS	0.502	0.432	0.578	0.502	0.432	0.578	SUBCLONAL	1	TRUE	1	0.379275215489631	2		329	630	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579508	7579508	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	471	498	0	ENST00000269305.4:c.179del	p.Pro60GlnfsTer63	p.P60Qfs*63	ENST00000269305	NM_001126112.2	60	cCa/ca	4/11	0.60576047507549	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.701647059074193	1		498	846	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691184	18691191	+	frameshift_variant	Frame_Shift_Del	DEL	TGCTGTCG	TGCTGTCG	-	novel	NA	P-0010129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	85	528	1	ENST00000266497.5:c.3299_3306del	p.Cys1100LeufsTer2	p.C1100Lfs*2	ENST00000266497		1099	TGCTGTCGt/t	23/31	0.294085664922011	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.701647059074193	0		529	721	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	355	389	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.307788065379869	4	FACETS	1	0.979	1			1	CLONAL	4	FALSE	NA	0.310722491826902	4		389	718	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0010132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	62	356	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	0.759	0.656	0.87	0.759	0.656	0.87	SUBCLONAL	1	FALSE	1	0.310722491826902	2		356	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0010132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1266	386	979	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.227770927311902	2	FACETS	0.752	0.713	0.792	0.752	0.713	0.792	SUBCLONAL	2	FALSE	0	0.310722491826902	2		979	1652	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0010140-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	142	367	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.174400823019642	3	FACETS	0.882	0.806	0.962	1	0.983	1	CLONAL	3	TRUE	1	0.174400823019642	3		367	669	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509652	106509652	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs776466677	NA	P-0010140-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	51	546	0	ENST00000359195.3:c.1646A>G	p.Asn549Ser	p.N549S	ENST00000359195	NM_002649.2	549	aAc/aGc	2/11	1	2	FACETS	0.798	0.677	0.932	0.798	0.677	0.932	CLONAL	1	TRUE	1	0.174400823019642	2		546	733	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0010143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	554	378	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	0.812394287070705	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.812394287070705	3		378	612	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010163-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	174	389	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	0.805	0.748	0.864			1	INDETERMINATE	2	TRUE	NA	0.439135902332451	2		389	492	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149516607	149516607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148272095	NA	P-0010163-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	288	483	2	ENST00000261799.4:c.4C>T	p.Arg2Trp	p.R2W	ENST00000261799	NM_002609.3	2	Cgg/Tgg	2/23	0.439135902332451	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.439135902332451	3		485	749	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39576639	39576639	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	355	496	0	ENST00000262039.4:c.929A>T	p.Tyr310Phe	p.Y310F	ENST00000262039	NM_002647.2	310	tAt/tTt	9/25	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.92	2		496	745	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997447	149997449	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	novel	NA	P-0010218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	62	593	0	ENST00000253339.5:c.2830_2832del	p.Leu944del	p.L944del	ENST00000253339		944	TTG/-	6/7	0.134597440167852	1	FACETS	0.122	0.105	0.141	0.122	0.105	0.141	INDETERMINATE	1	TRUE	0	0.92	1		593	596	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0010229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	139	422	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	0.35	2		422	671	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0010229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	134	354	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.811	0.736	0.89	0.811	0.736	0.89	CLONAL	1	TRUE	1	0.35	2		354	944	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436186	56436186	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0010229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	39	397	0	ENST00000407977.2:c.953-2A>G		p.X318_splice	ENST00000407977		318			1	2	FACETS	0.297	0.245	0.355	0.297	0.245	0.355	SUBCLONAL	1	TRUE	1	0.35	2		397	750	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226733	2226733	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764863340	NA	P-0010229-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	81	260	0	ENST00000398665.3:c.4213C>G	p.Leu1405Val	p.L1405V	ENST00000398665	NM_032482.2	1405	Ctg/Gtg	27/28	1	2	FACETS	0.928	0.82	1	0.928	0.82	1	CLONAL	1	TRUE	1	0.35	2		260	499	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0010244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	22	503	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		503	1017	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182292	38182292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1353791431	NA	P-0010244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	61	569	2	ENST00000396334.3:c.728G>A	p.Ser243Asn	p.S243N	ENST00000396334	NM_002468.4	243	aGc/aAc	4/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		571	1236	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505025	186505025	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	72	660	0	ENST00000323963.5:c.881A>G	p.His294Arg	p.H294R	ENST00000323963		294	cAt/cGt	8/11	1	2	FACETS	0.638	0.557	0.725	0.638	0.557	0.725	SUBCLONAL	1	TRUE	1	0.35	2		660	645	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858926	45858926	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	54	717	0	ENST00000391945.4:c.1540A>T	p.Ile514Phe	p.I514F	ENST00000391945	NM_000400.3	514	Att/Ttt	16/23	0.0631740620918666	4	FACETS	0.532	0.452	0.619	0.266	0.226	0.31	INDETERMINATE	1	TRUE	2	0.253342470344355	4		717	1005	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111472	8111512	+	frameshift_variant	Frame_Shift_Del	DEL	TGTCAGACCACCACAACCACACTCTGGAGGAGGAATGCCAA	TGTCAGACCACCACAACCACACTCTGGAGGAGGAATGCCAA	-	novel	NA	P-0010277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	97	601	0	ENST00000346208.3:c.960_1000del	p.Cys320TrpfsTer18	p.C320Wfs*18	ENST00000346208		320	TGTCAGACCACCACAACCACACTCTGGAGGAGGAATGCCAAt/t	5/6	0.253342470344355	3	FACETS	0.758	0.674	0.848	0.379	0.337	0.424	SUBCLONAL	1	TRUE	1	0.253342470344355	3		601	1138	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0010279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	14	380	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.328	0.235	0.441	0.328	0.235	0.441	SUBCLONAL	1	TRUE	1	0.14	2		380	610	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125048	46125048	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	56	472	0	ENST00000334344.6:c.235C>G	p.Pro79Ala	p.P79A	ENST00000334344	NM_152641.2	79	Ccc/Gcc	3/21	1	2	FACETS	0.952	0.814	1	0.952	0.814	1	CLONAL	1	TRUE	1	0.14	2		472	840	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215314	123215314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	101	714	0	ENST00000218089.9:c.2860C>T	p.Arg954Cys	p.R954C	ENST00000218089	NM_001042749.1	954	Cgt/Tgt	28/35	0.277874957649082	0	FACETS	0.314	0.28	0.35			1	SUBCLONAL	1	TRUE	0	0.441983613827975	0		714	812	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271249	153271249	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	115	393	0	ENST00000281708.4:c.529del	p.Glu177ArgfsTer62	p.E177Rfs*62	ENST00000281708	NM_033632.3	177	Gag/ag	3/12	0.441983613827975	1	FACETS	0.991	0.9	1	0.991	0.9	1	CLONAL	1	TRUE	0	0.441983613827975	1		393	409	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0010309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	409	402	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.436267565777194	4	FACETS	1	0.991	1	0.775	0.739	0.812	CLONAL	2	TRUE	1	0.435212098445067	4		402	1160	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0010309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	230	478	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	0.323487390106626	4	FACETS	0.945	0.883	1	0.945	0.883	1	CLONAL	2	TRUE	2	0.435212098445067	4		478	803	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519999	NA	P-0010309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	351	466	0	ENST00000269305.4:c.716A>G	p.Asn239Ser	p.N239S	ENST00000269305	NM_001126112.2	239	aAc/aGc	7/11	0.364815561761721	2	FACETS	0.897	0.853	0.942	0.897	0.853	0.942	CLONAL	2	TRUE	0	0.435212098445067	2		466	899	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188183	11188183	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010309-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	321	347	0	ENST00000361445.4:c.5911G>C	p.Ala1971Pro	p.A1971P	ENST00000361445	NM_004958.3	1971	Gcc/Ccc	43/58	0.401507648358738	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.435212098445067	3		347	864	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0010328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	58	661	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.849	0.73	0.978	0.849	0.73	0.978	CLONAL	1	TRUE	1	0.268908163090705	2		661	508	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223311	2223311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377891776	NA	P-0010328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	136	720	0	ENST00000398665.3:c.3422C>T	p.Thr1141Ile	p.T1141I	ENST00000398665	NM_032482.2	1141	aCa/aTa	25/28	1	2	FACETS	0.797	0.723	0.876	0.797	0.723	0.876	SUBCLONAL	1	TRUE	1	0.268908163090705	2		720	1269	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850653	63850653	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	35	364	0	ENST00000279873.7:c.1433del	p.Leu478Ter	p.L478*	ENST00000279873	NM_032199.2	477	acT/ac	10/10	1	2	FACETS	0.455	0.372	0.549	0.455	0.372	0.549	SUBCLONAL	1	TRUE	1	0.268908163090705	2		364	572	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	103	389	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	FALSE	1	0.351667531050166	2		389	475	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0010330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	66	597	4	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.351667531050166	1	FACETS	0.491	0.426	0.562	0.491	0.426	0.562	SUBCLONAL	1	FALSE	0	0.351667531050166	1		601	630	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0010330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	140	365	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.351667531050166	2		365	614	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0010330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	74	229	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.351667531050166	2		229	299	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786682	3786682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780939128	NA	P-0010330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1173	332	743	1	ENST00000262367.5:c.4529C>T	p.Ala1510Val	p.A1510V	ENST00000262367	NM_004380.2	1510	gCg/gTg	27/31	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	1	0.351667531050166	2		744	1505	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523554	148523554	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	24	350	1	ENST00000320356.2:c.899G>C	p.Cys300Ser	p.C300S	ENST00000320356	NM_004456.4	300	tGc/tCc	8/20	1	2	FACETS	0.285	0.223	0.357	0.285	0.223	0.357	SUBCLONAL	1	FALSE	1	0.351667531050166	2		351	479	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564113	139564113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1304820249	NA	P-0010330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	212	443	2	ENST00000308874.7:c.253C>T	p.Arg85Cys	p.R85C	ENST00000308874		85	Cgc/Tgc	5/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.351667531050166	2		445	972	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479840	67479840	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	41	341	1	ENST00000327367.4:c.1147G>T	p.Glu383Ter	p.E383*	ENST00000327367	NM_005902.3	383	Gag/Tag	8/9	1	2	FACETS	0.311	0.258	0.371	0.311	0.258	0.371	SUBCLONAL	1	FALSE	1	0.351667531050166	2		342	749	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371840	45371840	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	18	326	0	ENST00000262160.6:c.1151T>A	p.Ile384Asn	p.I384N	ENST00000262160	NM_005901.5	384	aTc/aAc	10/11	0.351667531050166	1	FACETS	0.265	0.199	0.343	0.265	0.199	0.343	SUBCLONAL	1	FALSE	0	0.351667531050166	1		326	318	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339247	70339261	+	inframe_deletion	In_Frame_Del	DEL	AAACAAGGTTTCAAT	AAACAAGGTTTCAAT	-	rs199469690	NA	P-0010330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	71	345	0	ENST00000374080.3:c.126_140del	p.Lys42_Asn46del	p.K42_N46del	ENST00000374080		42	AAACAAGGTTTCAAT/-	2/45	1	1	FACETS	0.51	0.445	0.58	0.51	0.445	0.58	SUBCLONAL	1	FALSE	0	0.351667531050166	1		345	653	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20488390	20488390	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	273	324	0	ENST00000346618.3:c.1046A>T	p.Tyr349Phe	p.Y349F	ENST00000346618	NM_001949.4	349	tAc/tTc	6/7	0.689935513332392	3	FACETS	1	0.97	1	0.527	0.494	0.56	CLONAL	1	TRUE	1	0.689590669811506	3		324	1011	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443747	52443776	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGGTGAAGAGGCCTGGGTGGGGCGACAAG	AGGGTGAAGAGGCCTGGGTGGGGCGACAAG	-	novel	NA	P-0010339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	90	175	0	ENST00000460680.1:c.38-17_50del		p.X13_splice	ENST00000460680	NM_004656.3	13		2/17	0.678994590298798	1	FACETS	0.716	0.646	0.787	0.716	0.646	0.787	SUBCLONAL	1	TRUE	0	0.689590669811506	1		175	239	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	87	528	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.688815750020425	2		530	242	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233024	55233024	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144943614	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	241	297	0	ENST00000275493.2:c.1774G>A	p.Val592Ile	p.V592I	ENST00000275493	NM_005228.3	592	Gtc/Atc	15/28	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.688815750020425	2		297	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	404	403	0	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	0.67983527721501	2	FACETS	0.989	0.955	1	0.989	0.955	1	CLONAL	2	TRUE	0	0.688815750020425	2		403	593	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188836	32188836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1046104152	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	106	367	0	ENST00000375023.3:c.718C>T	p.Pro240Ser	p.P240S	ENST00000375023	NM_004557.3	240	Cct/Tct	4/30	0.338401376622822	1	FACETS	0.405	0.365	0.448	0.405	0.365	0.448	INDETERMINATE	1	TRUE	0	0.688815750020425	1		367	498	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523592	106523592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1383854511	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	179	268	0	ENST00000359195.3:c.2744C>T	p.Ser915Phe	p.S915F	ENST00000359195	NM_002649.2	915	tCc/tTc	8/11	1	2	FACETS	0.955	0.887	1	0.955	0.887	1	CLONAL	1	TRUE	1	0.688815750020425	2		268	544	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663611	117663611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202169003	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	181	414	1	ENST00000368508.3:c.4621G>A	p.Glu1541Lys	p.E1541K	ENST00000368508	NM_002944.2	1541	Gaa/Aaa	28/43	0.338401376622822	1	FACETS	0.424	0.391	0.458	0.424	0.391	0.458	INDETERMINATE	1	TRUE	0	0.688815750020425	1		415	813	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860308	151860308	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	382	462	0	ENST00000262189.6:c.10354C>T	p.Pro3452Ser	p.P3452S	ENST00000262189	NM_170606.2	3452	Ccc/Tcc	43/59	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.688815750020425	2		462	939	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306568	41306568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	254	380	1	ENST00000373198.4:c.1091G>A	p.Arg364Gln	p.R364Q	ENST00000373198	NM_133170.3	364	cGa/cAa	7/32	1	2	FACETS	0.929	0.872	0.987	0.929	0.872	0.987	CLONAL	1	TRUE	1	0.688815750020425	2		381	794	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937232	36937232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	501	910	2	ENST00000361632.4:c.1087G>A	p.Glu363Lys	p.E363K	ENST00000361632		363	Gaa/Aaa	9/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.688815750020425	2		912	1420	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837999	156837999	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	257	389	0	ENST00000524377.1:c.532C>T	p.His178Tyr	p.H178Y	ENST00000524377	NM_002529.3	178	Cat/Tat	5/17	0.135036116864756	3	FACETS	1	0.992	1	0.665	0.625	0.706	INDETERMINATE	1	TRUE	1	0.688815750020425	3		389	754	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162688867	162688867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	335	399	0	ENST00000367921.3:c.14C>T	p.Pro5Leu	p.P5L	ENST00000367921	NM_006182.2	5	cCc/cTc	3/18	0.135036116864756	3	FACETS	1	0.993	1	0.669	0.633	0.704	INDETERMINATE	1	TRUE	1	0.688815750020425	3		399	978	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523010	25523010	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	370	500	1	ENST00000264709.3:c.175C>T	p.Pro59Ser	p.P59S	ENST00000264709	NM_175629.2	59	Ccg/Tcg	3/23	0.370422624604711	1	FACETS	0.802	0.764	0.84	0.802	0.764	0.84	INDETERMINATE	1	TRUE	0	0.688815750020425	1		501	878	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668684	52668684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	366	562	1	ENST00000394830.3:c.1235C>T	p.Pro412Leu	p.P412L	ENST00000394830	NM_018313.4	412	cCt/cTt	12/30	0.356562501001831	1	FACETS	0.743	0.707	0.779	0.743	0.707	0.779	INDETERMINATE	1	TRUE	0	0.688815750020425	1		563	938	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008467	70008467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	3616	235	0	ENST00000394351.3:c.754G>A	p.Asp252Asn	p.D252N	ENST00000394351	NM_000248.3	252	Gac/Aac	8/9	0.688815750020425	17	FACETS	1	0.997	1			1	CLONAL	16	TRUE	NA	0.688815750020425	17		235	4021	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356362	66356362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	252	297	0	ENST00000273854.3:c.1135C>T	p.Pro379Ser	p.P379S	ENST00000273854	NM_004439.5	379	Ccg/Tcg	5/18	0.688815750020425	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.688815750020425	1		297	478	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156291	106156291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1248154619	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	194	191	0	ENST00000380013.4:c.1192C>T	p.Pro398Ser	p.P398S	ENST00000380013	NM_001127208.2	398	Cca/Tca	3/11	0.688815750020425	1	FACETS	0.937	0.88	0.994	0.937	0.88	0.994	CLONAL	1	TRUE	0	0.688815750020425	1		191	394	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197236	106197236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	152	192	0	ENST00000380013.4:c.5569C>T	p.Pro1857Ser	p.P1857S	ENST00000380013	NM_001127208.2	1857	Cct/Tct	11/11	0.688815750020425	1	FACETS	0.994	0.928	1	0.994	0.928	1	CLONAL	1	TRUE	0	0.688815750020425	1		192	291	SUCCESS
APC	324	MSKCC	GRCh37	5	112174307	112174307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253876	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	199	340	0	ENST00000257430.4:c.3016C>T	p.His1006Tyr	p.H1006Y	ENST00000257430	NM_000038.5	1006	Cat/Tat	16/16	0.135036116864756	3	FACETS	1	0.987	1	0.63	0.586	0.674	INDETERMINATE	1	TRUE	1	0.688815750020425	3		340	617	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165150	32165150	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	190	279	0	ENST00000375023.3:c.4978C>T	p.Pro1660Ser	p.P1660S	ENST00000375023	NM_004557.3	1660	Ccc/Tcc	27/30	0.338401376622822	1	FACETS	0.693	0.646	0.741	0.693	0.646	0.741	INDETERMINATE	1	TRUE	0	0.688815750020425	1		279	522	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169236	32169236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	105	226	1	ENST00000375023.3:c.3797G>A	p.Gly1266Glu	p.G1266E	ENST00000375023	NM_004557.3	1266	gGg/gAg	22/30	0.338401376622822	1	FACETS	0.478	0.431	0.527	0.478	0.431	0.527	INDETERMINATE	1	TRUE	0	0.688815750020425	1		227	418	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120510	94120510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1251	334	803	0	ENST00000369303.4:c.541G>A	p.Gly181Arg	p.G181R	ENST00000369303	NM_004440.3	181	Gga/Aga	3/17	0.338401376622822	1	FACETS	0.401	0.378	0.425	0.401	0.378	0.425	INDETERMINATE	1	TRUE	0	0.688815750020425	1		803	1585	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547420	106547420	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1412341862	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	168	154	2	ENST00000369096.4:c.657G>T	p.Met219Ile	p.M219I	ENST00000369096	NM_001198.3	219	atG/atT	4/7	0.338401376622822	1	FACETS	0.801	0.746	0.858	0.801	0.746	0.858	INDETERMINATE	1	TRUE	0	0.688815750020425	1		156	399	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631272	117631272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1459053852	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	193	559	0	ENST00000368508.3:c.6406G>A	p.Gly2136Arg	p.G2136R	ENST00000368508	NM_002944.2	2136	Gga/Aga	40/43	0.338401376622822	1	FACETS	0.4	0.37	0.431	0.4	0.37	0.431	INDETERMINATE	1	TRUE	0	0.688815750020425	1		559	919	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525838	148525838	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554498830	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	109	250	0	ENST00000320356.2:c.619C>T	p.Arg207Ter	p.R207*	ENST00000320356	NM_004456.4	207	Cga/Tga	6/20	1	2	FACETS	0.61	0.55	0.673	0.61	0.55	0.673	SUBCLONAL	1	TRUE	1	0.688815750020425	2		250	519	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998208	100998208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	267	398	0	ENST00000325455.5:c.1594G>A	p.Glu532Lys	p.E532K	ENST00000325455	NM_001202474.3	532	Gag/Aag	1/8	0.688815750020425	1	FACETS	0.995	0.945	1	0.995	0.945	1	CLONAL	1	TRUE	0	0.688815750020425	1		398	511	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245204	46245204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	375	200	0	ENST00000334344.6:c.3298C>T	p.Gln1100Ter	p.Q1100*	ENST00000334344	NM_152641.2	1100	Cag/Tag	15/21	0.688815750020425	2	FACETS	0.935	0.901	0.969	0.935	0.901	0.969	CLONAL	2	TRUE	0	0.688815750020425	2		200	582	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436375	49436375	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	606	478	0	ENST00000301067.7:c.5836G>A	p.Gly1946Ser	p.G1946S	ENST00000301067	NM_003482.3	1946	Ggc/Agc	27/54	0.688815750020425	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.688815750020425	2		478	836	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432102	121432102	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1215273865	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	477	397	0	ENST00000257555.6:c.849G>A	p.Met283Ile	p.M283I	ENST00000257555		283	atG/atA	4/10	0.688815750020425	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.688815750020425	2		397	670	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913436	28913436	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	132	306	0	ENST00000282397.4:c.2357C>T	p.Ser786Phe	p.S786F	ENST00000282397	NM_002019.4	786	tCt/tTt	17/30	0.356562501001831	1	FACETS	0.472	0.431	0.516	0.472	0.431	0.516	INDETERMINATE	1	TRUE	0	0.688815750020425	1		306	532	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557440	95557440	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	224	277	0	ENST00000393063.1:c.5534T>A	p.Phe1845Tyr	p.F1845Y	ENST00000393063	NM_030621.3	1845	tTt/tAt	27/28	0.688815750020425	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.688815750020425	1		277	395	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777993	3777993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	408	751	1	ENST00000262367.5:c.7055C>T	p.Pro2352Leu	p.P2352L	ENST00000262367	NM_004380.2	2352	cCa/cTa	31/31	1	2	FACETS	0.923	0.879	0.969	0.923	0.879	0.969	CLONAL	1	TRUE	1	0.688815750020425	2		752	1283	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858621	9858621	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	420	694	1	ENST00000330684.3:c.2780G>T	p.Arg927Ile	p.R927I	ENST00000330684	NM_001134407.1	927	aGa/aTa	13/13	1	2	FACETS	0.976	0.931	1	0.976	0.931	1	CLONAL	1	TRUE	1	0.688815750020425	2		695	1249	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031858	10031858	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	237	307	0	ENST00000330684.3:c.965G>A	p.Gly322Glu	p.G322E	ENST00000330684	NM_001134407.1	322	gGg/gAg	3/13	1	2	FACETS	0.935	0.876	0.995	0.935	0.876	0.995	CLONAL	1	TRUE	1	0.688815750020425	2		307	736	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029078	14029078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	234	315	0	ENST00000311895.7:c.1289C>T	p.Ala430Val	p.A430V	ENST00000311895	NM_005236.2	430	gCc/gTc	8/11	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.688815750020425	2		315	679	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632771	23632771	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764669864	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	260	454	0	ENST00000261584.4:c.3025C>T	p.Pro1009Ser	p.P1009S	ENST00000261584	NM_024675.3	1009	Cct/Tct	10/13	1	2	FACETS	0.954	0.897	1	0.954	0.897	1	CLONAL	1	TRUE	1	0.688815750020425	2		454	791	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925159	81925159	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773116531	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	369	587	0	ENST00000359376.3:c.950C>T	p.Pro317Leu	p.P317L	ENST00000359376	NM_002661.3	317	cCc/cTc	11/33	0.356562501001831	1	FACETS	0.618	0.586	0.65	0.618	0.586	0.65	INDETERMINATE	1	TRUE	0	0.688815750020425	1		587	1137	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81957089	81957089	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	357	670	0	ENST00000359376.3:c.2308-1G>A		p.X770_splice	ENST00000359376	NM_002661.3	770			0.356562501001831	1	FACETS	0.521	0.493	0.549	0.521	0.493	0.549	INDETERMINATE	1	TRUE	0	0.688815750020425	1		670	1305	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586049	29586049	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1418965797	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	37	265	0	ENST00000356175.3:c.4270-1G>A		p.X1424_splice	ENST00000356175	NM_000267.3	1424			0.688815750020425	1	FACETS	0.332	0.276	0.394	0.332	0.276	0.394	SUBCLONAL	1	TRUE	0	0.688815750020425	1		265	212	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475041	40475041	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	464	681	0	ENST00000264657.5:c.1869G>A	p.Trp623Ter	p.W623*	ENST00000264657	NM_139276.2	623	tgG/tgA	20/24	0.688815750020425	1	FACETS	0.988	0.95	1	0.988	0.95	1	CLONAL	1	TRUE	0	0.688815750020425	1		681	894	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247829	10247829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1361579493	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	531	438	0	ENST00000340748.4:c.4373C>T	p.Thr1458Ile	p.T1458I	ENST00000340748		1458	aCc/aTc	36/40	0.67983527721501	2	FACETS	0.993	0.964	1	0.993	0.964	1	CLONAL	2	TRUE	0	0.688815750020425	2		438	776	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271891	15271891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	82	130	0	ENST00000263388.2:c.6548C>T	p.Pro2183Leu	p.P2183L	ENST00000263388	NM_000435.2	2183	cCc/cTc	33/33	0.67983527721501	2	FACETS	1	0.947	1	0.544	0.488	0.601	CLONAL	1	TRUE	0	0.688815750020425	2		130	219	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349630	15349630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	131	221	0	ENST00000263377.2:c.3944C>T	p.Ser1315Phe	p.S1315F	ENST00000263377	NM_058243.2	1315	tCc/tTc	19/20	0.67983527721501	2	FACETS	0.998	0.916	1	0.499	0.458	0.542	CLONAL	1	TRUE	0	0.688815750020425	2		221	381	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031585	36031585	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1221989600	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	213	404	0	ENST00000358208.4:c.1414C>T	p.Arg472Cys	p.R472C	ENST00000358208		472	Cgc/Tgc	12/12	1	2	FACETS	0.96	0.897	1	0.96	0.897	1	CLONAL	1	TRUE	1	0.688815750020425	2		404	644	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39744939	39744939	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	263	367	0	ENST00000361337.2:c.1729C>T	p.Leu577Phe	p.L577F	ENST00000361337	NM_003286.2	577	Ctt/Ttt	17/21	1	2	FACETS	0.947	0.891	1	0.947	0.891	1	CLONAL	1	TRUE	1	0.688815750020425	2		367	806	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827900	40827900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767977370	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	369	496	1	ENST00000373198.4:c.2528C>T	p.Ser843Phe	p.S843F	ENST00000373198	NM_133170.3	843	tCt/tTt	17/32	1	2	FACETS	0.862	0.818	0.907	0.862	0.818	0.907	CLONAL	1	TRUE	1	0.688815750020425	2		497	1243	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755828	39755828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	38	80	0	ENST00000288319.7:c.937C>T	p.Leu313Phe	p.L313F	ENST00000288319	NM_182918.3	313	Ctt/Ttt	10/10	1	2	FACETS	0.772	0.649	0.902	0.772	0.649	0.902	CLONAL	1	TRUE	1	0.688815750020425	2		80	143	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546182	41546182	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	41	57	0	ENST00000263253.7:c.2797C>T	p.Pro933Ser	p.P933S	ENST00000263253	NM_001429.3	933	Cct/Tct	14/31	1	2	FACETS	0.984	0.84	1	0.984	0.84	1	CLONAL	1	TRUE	1	0.688815750020425	2		57	121	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613657	100613657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	354	245	0	ENST00000308731.7:c.922G>A	p.Asp308Asn	p.D308N	ENST00000308731	NM_000061.2	308	Gac/Aac	11/19	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.688815750020425	1		245	520	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15818069	15818070	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	408	267	1	ENST00000307771.7:c.202_203del	p.Arg68AlafsTer5	p.R68Afs*5	ENST00000307771	NM_005089.3	66	AGa/a	3/11	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.688815750020425	1		268	672	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319347	11319348	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	206	302	0	ENST00000361445.4:c.119_120delinsTT	p.Ala40Val	p.A40V	ENST00000361445	NM_004958.3	40	gCC/gTT	2/58	1	2	FACETS	0.845	0.787	0.904	0.845	0.787	0.904	CLONAL	1	TRUE	1	0.688815750020425	2		302	708	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209106722	209106723	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	125	293	0	ENST00000345146.2:c.845_846delinsTT	p.Ala282Val	p.A282V	ENST00000345146	NM_005896.2	282	gCC/gTT	7/10	0.370422624604711	1	FACETS	0.37	0.335	0.406	0.37	0.335	0.406	INDETERMINATE	1	TRUE	0	0.688815750020425	1		293	643	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099218	4099219	+	missense_variant	Missense_Mutation	DNP	GG	GG	AC	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	166	393	0	ENST00000262948.5:c.899_900delinsGT	p.Pro300Arg	p.P300R	ENST00000262948	NM_030662.3	300	cCC/cGT	7/11	0.67983527721501	2	FACETS	0.802	0.74	0.866	0.401	0.37	0.433	CLONAL	1	TRUE	0	0.688815750020425	2		393	601	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657056	45657057	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	135	274	0	ENST00000407780.3:c.99_100delinsAA	p.Glu34Lys	p.E34K	ENST00000407780	NM_001283052.1	33	gtGGag/gtAAag	3/7	1	2	FACETS	0.889	0.815	0.965	0.889	0.815	0.965	CLONAL	1	TRUE	1	0.688815750020425	2		274	441	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505028	149505029	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0010340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	195	309	0	ENST00000261799.4:c.1786_1787delinsTT	p.Pro596Leu	p.P596L	ENST00000261799	NM_002609.3	596	CCg/TTg	12/23	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.688815750020425	2		309	564	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0010355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	138	422	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.196668361536244	3	FACETS	0.767	0.7	0.837			1	SUBCLONAL	2	TRUE	NA	0.31127810565783	3		422	668	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098975	178098975	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1328994103	NA	P-0010355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	104	340	0	ENST00000397062.3:c.70T>C	p.Trp24Arg	p.W24R	ENST00000397062	NM_006164.4	24	Tgg/Cgg	2/5	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.31127810565783	2		340	512	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427306	49427306	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1426418887	NA	P-0010355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	111	274	0	ENST00000301067.7:c.11182A>G	p.Met3728Val	p.M3728V	ENST00000301067	NM_003482.3	3728	Atg/Gtg	39/54	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.31127810565783	2		274	510	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634293	23634293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45551636	NA	P-0010355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	166	571	1	ENST00000261584.4:c.2993G>A	p.Gly998Glu	p.G998E	ENST00000261584	NM_024675.3	998	gGa/gAa	9/13	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.31127810565783	2		572	965	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857917	89857917	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	82	255	0	ENST00000389301.3:c.1253C>T	p.Ala418Val	p.A418V	ENST00000389301	NM_000135.2	418	gCa/gTa	14/43	0.31127810565783	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.31127810565783	1		255	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0010355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	139	396	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	0.31127810565783	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.31127810565783	1		396	601	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411459	63411461	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0010355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1191	231	814	0	ENST00000330258.3:c.1706_1708del	p.Leu569del	p.L569del	ENST00000330258	NM_152424.3	569	tTGTat/tat	2/2	0.129264961539428	4	FACETS	1	0.99	1	0.342	0.318	0.367	INDETERMINATE	1	TRUE	0	0.31127810565783	4		814	1422	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	157	528	2				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.84085586918933	2		530	321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0010358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	148	166	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.84085586918933	1	FACETS	0.995	0.943	1	0.995	0.943	1	CLONAL	1	TRUE	0	0.84085586918933	1		166	205	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937001	48937005	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAA	CAGAA	-	rs1566192530	NA	P-0010358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	363	285	0	ENST00000267163.4:c.772_776del	p.Asn258GlufsTer11	p.N258Efs*11	ENST00000267163	NM_000321.2	257	CAGAAc/c	8/27	0.84085586918933	1	FACETS	0.95	0.916	0.982	0.95	0.916	0.982	CLONAL	1	TRUE	0	0.84085586918933	1		285	527	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0010358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	346	365	1	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	0.84085586918933	1	FACETS	0.827	0.793	0.86	0.827	0.793	0.86	CLONAL	1	TRUE	0	0.84085586918933	1		366	577	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281459	142281459	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1382430398	NA	P-0010358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	481	426	0	ENST00000350721.4:c.785C>G	p.Pro262Arg	p.P262R	ENST00000350721	NM_001184.3	262	cCa/cGa	4/47	1	2	FACETS	0.939	0.899	0.978	0.939	0.899	0.978	CLONAL	1	TRUE	1	0.84085586918933	2		426	1219	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195661	123195661	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	504	576	1	ENST00000218089.9:c.1575G>T	p.Met525Ile	p.M525I	ENST00000218089	NM_001042749.1	525	atG/atT	17/35	1	2	FACETS	0.892	0.855	0.93	0.892	0.855	0.93	CLONAL	1	TRUE	1	0.84085586918933	2		577	1344	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236086	108236086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782292	NA	P-0010360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	452	420	0	ENST00000278616.4:c.9022C>T	p.Arg3008Cys	p.R3008C	ENST00000278616	NM_000051.3	3008	Cgt/Tgt	63/63	0.449657862245758	2	FACETS	0.969	0.929	1	0.969	0.929	1	CLONAL	2	TRUE	0	0.479328793938573	2		420	973	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934961	49934961	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	337	923	1	ENST00000296474.3:c.2038T>A	p.Ser680Thr	p.S680T	ENST00000296474	NM_002447.2	680	Tct/Act	6/20	1	2	FACETS	0.973	0.919	1	0.973	0.919	1	CLONAL	1	TRUE	1	0.479328793938573	2		924	1445	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272235	142272235	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	162	419	0	ENST00000350721.4:c.2639C>T	p.Ala880Val	p.A880V	ENST00000350721	NM_001184.3	880	gCa/gTa	13/47	1	2	FACETS	0.935	0.86	1	0.935	0.86	1	CLONAL	1	TRUE	1	0.479328793938573	2		419	723	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346642	81346642	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	145	407	0	ENST00000222390.5:c.1311G>C	p.Glu437Asp	p.E437D	ENST00000222390	NM_000601.4	437	gaG/gaC	11/18	0.479328793938573	4	FACETS	0.939	0.856	1	0.313	0.285	0.342	CLONAL	1	TRUE	1	0.479328793938573	4		407	953	SUCCESS
APC	324	MSKCC	GRCh37	5	112175573	112175573	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	223	472	0	ENST00000257430.4:c.4283del	p.Gly1428AspfsTer45	p.G1428Dfs*45	ENST00000257430	NM_000038.5	1428	Gga/ga	16/16	0.479328793938573	3	FACETS	1	0.979	1	0.565	0.526	0.605	CLONAL	1	TRUE	1	0.479328793938573	3		472	1021	SUCCESS
APC	324	MSKCC	GRCh37	5	112137024	112137028	+	stop_gained	Nonsense_Mutation	ONP	CAGAA	CAGAA	TAGAT	novel	NA	P-0010360-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	304	394	2	ENST00000257430.4:c.778_782delinsTAGAT	p.Gln260_Asn261delinsTer	p.Q260_N261delins*	ENST00000257430	NM_000038.5	260	CAGAAt/TAGATt	8/16	0.479328793938573	3	FACETS	0.888	0.84	0.938	0.888	0.84	0.938	CLONAL	2	TRUE	1	0.479328793938573	3		396	885	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578191	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs530941076	NA	P-0010368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	581	367	0	ENST00000269305.4:c.658T>C	p.Tyr220His	p.Y220H	ENST00000269305	NM_001126112.2	220	Tat/Cat	6/11	0.910917955938839	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.910917955938839	2		367	632	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143026	30143026	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	613	488	0	ENST00000389048.3:c.500A>T	p.Gln167Leu	p.Q167L	ENST00000389048	NM_004304.4	167	cAg/cTg	1/29	0.465496668481484	2	FACETS	1	0.998	1	0.738	0.717	0.758	INDETERMINATE	1	TRUE	0	0.910917955938839	2		488	912	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499349	89499349	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	407	264	0	ENST00000336596.2:c.2519G>C	p.Gly840Ala	p.G840A	ENST00000336596	NM_005233.5	840	gGc/gCc	15/17	0.117715071663864	3	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.910917955938839	3		264	603	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503912	149503912	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1231480262	NA	P-0010368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	413	228	0	ENST00000261799.4:c.1924A>G	p.Ser642Gly	p.S642G	ENST00000261799	NM_002609.3	642	Agc/Ggc	14/23	0.910917955938839	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.910917955938839	2		228	443	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056963	180056963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	461	502	0	ENST00000261937.6:c.656C>T	p.Pro219Leu	p.P219L	ENST00000261937	NM_182925.4	219	cCc/cTc	5/30	0.910917955938839	2	FACETS	0.988	0.97	1	0.988	0.97	1	CLONAL	2	TRUE	0	0.910917955938839	2		502	512	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878902	117878902	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1828	622	624	0	ENST00000297338.2:c.67T>A	p.Trp23Arg	p.W23R	ENST00000297338	NM_006265.2	23	Tgg/Agg	2/14	0.839787788395345	4	FACETS	1	0.987	1	0.355	0.34	0.37	CLONAL	1	TRUE	1	0.910917955938839	4		624	2450	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420408	49420408	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	79	267	0	ENST00000301067.7:c.15341A>G	p.His5114Arg	p.H5114R	ENST00000301067	NM_003482.3	5114	cAt/cGt	48/54	0.545765268875878	3	FACETS	0.417	0.367	0.471	0.139	0.122	0.157	INDETERMINATE	1	TRUE	0	0.910917955938839	3		267	605	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432196	121432196	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	51	206	0	ENST00000257555.6:c.943A>C	p.Ser315Arg	p.S315R	ENST00000257555		315	Agt/Cgt	4/10	0.545765268875878	3	FACETS	0.409	0.349	0.476	0.136	0.116	0.159	INDETERMINATE	1	TRUE	0	0.910917955938839	3		206	398	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039351	49039351	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0010368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	887	503	0	ENST00000267163.4:c.2336T>A	p.Leu779Ter	p.L779*	ENST00000267163	NM_000321.2	779	tTg/tAg	23/27	0.910917955938839	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.910917955938839	2		503	967	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972617	76972617	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	301	616	0	ENST00000373344.5:c.124C>T	p.Gln42Ter	p.Q42*	ENST00000373344	NM_000489.3	42	Caa/Taa	2/35	0.547262844143425	2	FACETS	0.487	0.457	0.517	0.243	0.228	0.259	SUBCLONAL	1	TRUE	0	0.910917955938839	2		616	1358	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443641	49443641	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1064794007	NA	P-0010368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	545	351	3	ENST00000301067.7:c.3730del	p.Val1244SerfsTer86	p.V1244Sfs*86	ENST00000301067	NM_003482.3	1244	Gtc/tc	11/54	0.545765268875878	3	FACETS	1	0.997	1	0.81	0.789	0.83	INDETERMINATE	2	TRUE	0	0.910917955938839	3		354	717	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	124	389	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.814	0.737	0.895	0.814	0.737	0.895	CLONAL	1	TRUE	1	0.394738026220033	2		389	772	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0010383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	184	556	2	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.817	0.753	0.884	0.817	0.753	0.884	CLONAL	1	TRUE	1	0.394738026220033	2		558	1141	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577530	7577530	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	207	491	0	ENST00000269305.4:c.751A>T	p.Ile251Phe	p.I251F	ENST00000269305	NM_001126112.2	251	Atc/Ttc	7/11	0.355256521741317	1	FACETS	0.849	0.787	0.912	0.849	0.787	0.912	CLONAL	1	TRUE	0	0.394738026220033	1		491	992	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266450	41266450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	49	440	0	ENST00000349496.5:c.247G>A	p.Asp83Asn	p.D83N	ENST00000349496	NM_001904.3	83	Gat/Aat	4/15	1	2	FACETS	0.274	0.231	0.321	0.274	0.231	0.321	SUBCLONAL	1	TRUE	1	0.394738026220033	2		440	907	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575689	48575689	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	94	433	0	ENST00000342988.3:c.449G>T	p.Ser150Ile	p.S150I	ENST00000342988	NM_005359.5	150	aGt/aTt	4/12	0.355256521741317	1	FACETS	0.487	0.433	0.545	0.487	0.433	0.545	SUBCLONAL	1	TRUE	0	0.394738026220033	1		433	785	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445069	89445767	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAATGGGATCATATTGGACTACGAGGTCAAATACTATGAAAAGGTGGGGAAACAATGTTTAAGGGTTGGGCTGTGTAGGCAAGAAGCTGTTTCCTCATGAGCTGTGCTCTTGCAAAGAAACCAGTGACATTCCTGGTAAATGGTAGAGCACTGTTTAGAACTGTGGCCCTGTGACCCCTTTGATTTATTGGTAGAGGAAGGTTTAGAAAGAATCTTGTTGAATACCCCCTATTCTACAGCAATAAACAACATCAAAGATGCCACTGCCAACTTAATCCAGTTACTTATGGCAATAGCATGACATTTATCTCCCTTTACACCAAGACCCCTACTCTACCAACTATTTTATTGTGGTTTCTTAGTCTATTTGTGAACTGTTTTTTTAGTTCATTGCCTCAAGCATCATTTCCTGACCTTCAAATTTACATGCATTTCATTCAATACAAATAGCAACATTGTGCTAGTAAGAAAAATATTGTATTATTTAACTGATGATGAAAAGATTTTCTTGACCCTGTAGAAGGAAATTTAAAAGGTTGGGGATAGATGGATAAATTTGCGTGACATAAAGTTGTGGCTTGGTAATGCAATTATTAAAAAAAATAGGCACATGGTTATTTTTACCCCAAATTTAAAAATTATTAAAAAATAGTTATGTGGTTATTTTGCCCTGAGTGGAGTGGCGAGTATTCCATCATT	TAATGGGATCATATTGGACTACGAGGTCAAATACTATGAAAAGGTGGGGAAACAATGTTTAAGGGTTGGGCTGTGTAGGCAAGAAGCTGTTTCCTCATGAGCTGTGCTCTTGCAAAGAAACCAGTGACATTCCTGGTAAATGGTAGAGCACTGTTTAGAACTGTGGCCCTGTGACCCCTTTGATTTATTGGTAGAGGAAGGTTTAGAAAGAATCTTGTTGAATACCCCCTATTCTACAGCAATAAACAACATCAAAGATGCCACTGCCAACTTAATCCAGTTACTTATGGCAATAGCATGACATTTATCTCCCTTTACACCAAGACCCCTACTCTACCAACTATTTTATTGTGGTTTCTTAGTCTATTTGTGAACTGTTTTTTTAGTTCATTGCCTCAAGCATCATTTCCTGACCTTCAAATTTACATGCATTTCATTCAATACAAATAGCAACATTGTGCTAGTAAGAAAAATATTGTATTATTTAACTGATGATGAAAAGATTTTCTTGACCCTGTAGAAGGAAATTTAAAAGGTTGGGGATAGATGGATAAATTTGCGTGACATAAAGTTGTGGCTTGGTAATGCAATTATTAAAAAAAATAGGCACATGGTTATTTTTACCCCAAATTTAAAAATTATTAAAAAATAGTTATGTGGTTATTTTGCCCTGAGTGGAGTGGCGAGTATTCCATCATT	-	novel	NA	P-0010383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	67	500	0	ENST00000336596.2:c.1389_1431+656del		p.X463_splice	ENST00000336596	NM_005233.5	463		6/17	1	2	FACETS	0.395	0.342	0.452	0.395	0.342	0.452	SUBCLONAL	1	TRUE	1	0.394738026220033	2		500	860	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159754	20159754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010398-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	447	488	0	ENST00000379607.5:c.5C>T	p.Pro2Leu	p.P2L	ENST00000379607	NM_001412.3	2	cCc/cTc	1/7	0.515825373958857	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	2	0.686888195988402	4		488	1002	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084093	47084093	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010398-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	186	438	0	ENST00000409792.3:c.7196G>C	p.Arg2399Pro	p.R2399P	ENST00000409792	NM_014159.6	2399	cGa/cCa	17/21	0.653508625869529	4	FACETS	0.973	0.899	1	0.486	0.449	0.525	CLONAL	1	TRUE	2	0.686888195988402	4		438	939	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376455	118376455	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010398-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	369	356	0	ENST00000534358.1:c.9848del	p.Arg3283GlnfsTer7	p.R3283Qfs*7	ENST00000534358	NM_005933.3	3283	cGa/ca	27/36	0.686888195988402	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.686888195988402	3		356	676	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759752	133759752	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1332380683	NA	P-0010399-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	85	630	0	ENST00000318560.5:c.2075C>T	p.Thr692Met	p.T692M	ENST00000318560	NM_005157.4	692	aCg/aTg	11/11	1	2	FACETS	0.791	0.705	0.88	1	0.981	1	SUBCLONAL	2	TRUE	1	0.32	2		630	336	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582020	189582020	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0010450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	402	305	0	ENST00000264731.3:c.580-1G>A		p.X194_splice	ENST00000264731	NM_003722.4	194			0.70139738383223	3	FACETS	0.887	0.849	0.925	0.887	0.849	0.925	CLONAL	2	TRUE	1	0.724697101227467	3		305	852	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs967461896	NA	P-0010450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	190	190	0	ENST00000269305.4:c.526T>A	p.Cys176Ser	p.C176S	ENST00000269305	NM_001126112.2	176	Tgc/Agc	5/11	0.724697101227467	1	FACETS	0.986	0.93	1	0.986	0.93	1	CLONAL	1	TRUE	0	0.724697101227467	1		190	339	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095620	178095620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	442	666	0	ENST00000397062.3:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000397062	NM_006164.4	571	Gaa/Aaa	5/5	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.724697101227467	2		666	1124	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566842	212566842	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	178	362	0	ENST00000342788.4:c.1339T>G	p.Phe447Val	p.F447V	ENST00000342788	NM_005235.2	447	Ttc/Gtc	12/28	1	2	FACETS	0.816	0.756	0.878	0.816	0.756	0.878	CLONAL	1	TRUE	1	0.724697101227467	2		362	602	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564380	86564380	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	271	332	0	ENST00000274376.6:c.112A>G	p.Ile38Val	p.I38V	ENST00000274376	NM_002890.2	38	Ata/Gta	1/25	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.724697101227467	2		332	736	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781129	161781129	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	324	529	0	ENST00000366898.1:c.1276G>T	p.Glu426Ter	p.E426*	ENST00000366898	NM_004562.2	426	Gaa/Taa	11/12	1	2	FACETS	0.98	0.929	1	0.98	0.929	1	CLONAL	1	TRUE	1	0.724697101227467	2		529	912	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477143	67477143	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	331	398	1	ENST00000327367.4:c.950C>T	p.Ser317Phe	p.S317F	ENST00000327367	NM_005902.3	317	tCt/tTt	7/9	0.724697101227467	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.724697101227467	1		399	567	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166039	118166040	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0010450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1881	315	441	1	ENST00000369448.3:c.550_551del	p.Phe184ProfsTer12	p.F184Pfs*12	ENST00000369448	NM_017709.3	183	tcTTtc/tctc	2/2	0.724697101227467	6	FACETS	0.97	0.911	1			1	CLONAL	1	TRUE	NA	0.724697101227467	6		442	2196	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936093	178936094	+	missense_variant	Missense_Mutation	DNP	GC	GC	TA	novel	NA	P-0010450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	109	173	0	ENST00000263967.3:c.1635_1636delinsTA	p.Glu545_Gln546delinsAspLys	p.E545_Q546delinsDK	ENST00000263967	NM_006218.2	545	gaGCag/gaTAag	10/21	0.70139738383223	3	FACETS	0.971	0.878	1	0.486	0.439	0.534	CLONAL	1	TRUE	1	0.724697101227467	3		173	422	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512374	38512374	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs539116380	NA	P-0010494-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	680	238	2	ENST00000254066.5:c.1285G>T	p.Gly429Cys	p.G429C	ENST00000254066	NM_000964.3	429	Ggt/Tgt	9/9	0.809325766197742	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	1	0.809325766197742	3		240	1012	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720833	89720836	+	frameshift_variant	Frame_Shift_Del	DEL	AAAT	AAAT	-	rs587782304	NA	P-0010521-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	383	184	0	ENST00000371953.3:c.987_990del	p.Asn329LysfsTer14	p.N329Kfs*14	ENST00000371953	NM_000314.4	328	gcAAAT/gc	8/9	0.963731021412584	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.963731021412584	1		184	408	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0010521-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	675	1372	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.963731021412584	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.963731021412584	1		1372	716	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955593	55955593	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs373654225	NA	P-0010521-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	1014	864	1	ENST00000263923.4:c.3352C>T	p.Arg1118Ter	p.R1118*	ENST00000263923	NM_002253.2	1118	Cga/Tga	25/30	0.963731021412584	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.963731021412584	1		865	1070	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0010525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	57	430	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.15	2		430	727	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235837	108235837	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	54	564	2	ENST00000278616.4:c.8879G>T	p.Trp2960Leu	p.W2960L	ENST00000278616	NM_000051.3	2960	tGg/tTg	62/63	1	2	FACETS	0.829	0.706	0.964	0.829	0.706	0.964	CLONAL	1	TRUE	1	0.15	2		566	869	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431414	121431414	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	47	423	1	ENST00000257555.6:c.618G>T	p.Trp206Cys	p.W206C	ENST00000257555		206	tgG/tgT	3/10	1	2	FACETS	0.873	0.735	1	0.873	0.735	1	CLONAL	1	TRUE	1	0.15	2		424	718	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143043375	143043376	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0010525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	39	465	0	ENST00000262992.4:c.2040_2041delinsTT	p.Glu680_Asp681delinsAspTyr	p.E680_D681delinsDY	ENST00000262992	NM_001101669.1	680	gaGGac/gaTTac	19/24	1	2	FACETS	0.739	0.611	0.882	0.739	0.611	0.882	SUBCLONAL	1	TRUE	1	0.15	2		465	704	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0010535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	143	661	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.158622025200159	3	FACETS	0.914	0.835	0.996	1	0.985	1	CLONAL	3	TRUE	1	0.158622025200159	3		661	710	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0010535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	29	217	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.95	0.762	1	0.95	0.762	1	CLONAL	1	TRUE	1	0.158622025200159	2		217	385	SUCCESS
APC	324	MSKCC	GRCh37	5	112175246	112175246	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1057517558	NA	P-0010535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	69	265	0	ENST00000257430.4:c.3956del	p.Pro1319LeufsTer2	p.P1319Lfs*2	ENST00000257430	NM_000038.5	1319	Cct/ct	16/16	1	2	FACETS	0.829	0.723	0.943	1	0.977	1	CLONAL	2	TRUE	1	0.158622025200159	2		265	525	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120115	70120115	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	11	39	0	ENST00000245479.2:c.1121del	p.Pro374ArgfsTer9	p.P374Rfs*9	ENST00000245479	NM_000346.3	373	Ccc/cc	3/3	0.158622025200159	3	FACETS	0.846	0.598	1	1	0.824	1	CLONAL	3	TRUE	1	0.158622025200159	3		39	59	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429758	78429758	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	58	333	0	ENST00000370768.2:c.1030C>T	p.Arg344Ter	p.R344*	ENST00000370768	NM_003902.3	344	Cga/Tga	12/20	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.158622025200159	2		333	674	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637546	52637546	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1182	94	665	0	ENST00000394830.3:c.2770G>T	p.Glu924Ter	p.E924*	ENST00000394830	NM_018313.4	924	Gaa/Taa	18/30	1	2	FACETS	0.929	0.824	1	0.929	0.824	1	CLONAL	1	TRUE	1	0.158622025200159	2		665	1276	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976744	2976744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs577877958	NA	P-0010535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	116	566	2	ENST00000396946.4:c.1268G>A	p.Arg423Gln	p.R423Q	ENST00000396946	NM_032415.4	423	cGg/cAg	9/25	1	2	FACETS	0.822	0.74	0.908	1	0.986	1	CLONAL	2	TRUE	1	0.158622025200159	2		568	890	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285131	15285131	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	29	258	0	ENST00000263388.2:c.4484G>T	p.Trp1495Leu	p.W1495L	ENST00000263388	NM_000435.2	1495	tGg/tTg	25/33	0.148954547744706	2	FACETS	0.785	0.629	0.962	0.392	0.314	0.481	CLONAL	1	TRUE	0	0.158622025200159	2		258	466	SUCCESS
APC	324	MSKCC	GRCh37	5	112175117	112175394	+	frameshift_variant	Frame_Shift_Del	DEL	TCATTATCATCTTTGTCATCAGCTGAAGATGAAATAGGATGTAATCAGACGACACAGGAAGCAGATTCTGCTAATACCCTGCAAATAGCAGAAATAAAAGAAAAGATTGGAACTAGGTCAGCTGAAGATCCTGTGAGCGAAGTTCCAGCAGTGTCACAGCACCCTAGAACCAAATCCAGCAGACTGCAGGGTTCTAGTTTATCTTCAGAATCAGCCAGGCACAAAGCTGTTGAATTTTCTTCAGGAGCGAAATCTCCCTCCAAAAGTGGTGCTCAGAC	TCATTATCATCTTTGTCATCAGCTGAAGATGAAATAGGATGTAATCAGACGACACAGGAAGCAGATTCTGCTAATACCCTGCAAATAGCAGAAATAAAAGAAAAGATTGGAACTAGGTCAGCTGAAGATCCTGTGAGCGAAGTTCCAGCAGTGTCACAGCACCCTAGAACCAAATCCAGCAGACTGCAGGGTTCTAGTTTATCTTCAGAATCAGCCAGGCACAAAGCTGTTGAATTTTCTTCAGGAGCGAAATCTCCCTCCAAAAGTGGTGCTCAGAC	-	novel	NA	P-0010535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	75	233	0	ENST00000257430.4:c.3826_4103del	p.Ser1276ThrfsTer6	p.S1276Tfs*6	ENST00000257430	NM_000038.5	1276	TCATTATCATCTTTGTCATCAGCTGAAGATGAAATAGGATGTAATCAGACGACACAGGAAGCAGATTCTGCTAATACCCTGCAAATAGCAGAAATAAAAGAAAAGATTGGAACTAGGTCAGCTGAAGATCCTGTGAGCGAAGTTCCAGCAGTGTCACAGCACCCTAGAACCAAATCCAGCAGACTGCAGGGTTCTAGTTTATCTTCAGAATCAGCCAGGCACAAAGCTGTTGAATTTTCTTCAGGAGCGAAATCTCCCTCCAAAAGTGGTGCTCAGACa/a	16/16	1	2	FACETS	0.973	0.855	1	1	0.982	1	CLONAL	2	TRUE	1	0.158622025200159	2		233	486	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0010554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	319	474	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.212626573552227	4	FACETS	0.939	0.888	0.99	1	0.992	1	CLONAL	4	TRUE	1	0.212626573552227	4		474	969	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0010554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	70	257	2	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.892	0.782	1	1	0.98	1	CLONAL	2	TRUE	1	0.212626573552227	2		259	369	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830596	72830596	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	307	1070	0	ENST00000268489.5:c.5985C>G	p.Ile1995Met	p.I1995M	ENST00000268489	NM_006885.3	1995	atC/atG	9/10	0.212626573552227	0	FACETS	0.799	0.752	0.848			1	SUBCLONAL	2	TRUE	0	0.212626573552227	0		1070	1423	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446911	18446911	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010556-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	144	383	0	ENST00000266497.5:c.996T>A	p.His332Gln	p.H332Q	ENST00000266497		332	caT/caA	4/31	0.835028157647192	1	FACETS	0.674	0.626	0.722	0.674	0.626	0.722	SUBCLONAL	1	FALSE	0	0.835028157647192	1		383	298	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0010563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	1069	350	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	0.393988016417471	9	FACETS	0.984	0.96	1			1	CLONAL	7	TRUE	NA	0.393988016417471	9		350	1874	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579559	7579559	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	155	291	0	ENST00000269305.4:c.128del	p.Leu43Ter	p.L43*	ENST00000269305	NM_001126112.2	43	tTg/tg	4/11	0.365410435180854	1	FACETS	0.963	0.885	1	0.963	0.885	1	CLONAL	1	TRUE	0	0.393988016417471	1		291	656	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189585668	189585668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	190	347	1	ENST00000264731.3:c.929G>A	p.Ser310Asn	p.S310N	ENST00000264731	NM_003722.4	310	aGc/aAc	7/14	1	2	FACETS	0.985	0.911	1	0.985	0.911	1	CLONAL	1	TRUE	1	0.393988016417471	2		348	979	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56367749	56367749	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1354	327	612	0	ENST00000348428.3:c.575T>G	p.Val192Gly	p.V192G	ENST00000348428	NM_006785.3	192	gTt/gGt	4/17	NA	2	FACETS	0.987	0.93	1			1	INDETERMINATE	1	TRUE	NA	0.393988016417471	2		612	1681	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	197	528	2				ENST00000310581	NM_198253.2	-/1132			0.300611501962046	2	FACETS	1	0.989	1	0.613	0.578	0.648	INDETERMINATE	1	TRUE	0	0.90255221611267	2		530	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577526	7577526	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121912653	NA	P-0010570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	939	503	0	ENST00000269305.4:c.755T>C	p.Leu252Pro	p.L252P	ENST00000269305	NM_001126112.2	252	cTc/cCc	7/11	0.0900062550413014	5	FACETS	0.985	0.976	0.994			1	INDETERMINATE	5	TRUE	NA	0.90255221611267	5		503	994	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693001	89693001	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	246	210	0	ENST00000371953.3:c.485A>T	p.Asp162Val	p.D162V	ENST00000371953	NM_000314.4	162	gAc/gTc	5/9	0.90255221611267	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.90255221611267	2		210	268	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185196	123185196	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	615	471	0	ENST00000218089.9:c.1149del	p.Glu383AspfsTer9	p.E383Dfs*9	ENST00000218089	NM_001042749.1	383	gAa/ga	13/35	0.90255221611267	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.90255221611267	3		471	975	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941638	48941641	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	rs1566194323	NA	P-0010570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	322	281	0	ENST00000267163.4:c.951_954del	p.Ser318AsnfsTer13	p.S318Nfs*13	ENST00000267163	NM_000321.2	316	aaTCTT/aa	10/27	0.90255221611267	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.90255221611267	2		281	352	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0010602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	926	890	5	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.786283883685135	2	FACETS	0.979	0.961	0.997	0.979	0.961	0.997	CLONAL	2	TRUE	0	0.793332833619014	2		895	1192	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602328	10602328	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	1163	425	0	ENST00000171111.5:c.1250G>T	p.Gly417Val	p.G417V	ENST00000171111	NM_203500.1	417	gGg/gTg	3/6	0.793332833619014	3	FACETS	0.976	0.962	0.99			1	CLONAL	3	TRUE	NA	0.793332833619014	3		425	1398	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022398	26022398	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	131	312	0	ENST00000435504.4:c.259G>A	p.Val87Met	p.V87M	ENST00000435504		87	Gtg/Atg	5/13	1	2	FACETS	0.404	0.366	0.443	0.404	0.366	0.443	SUBCLONAL	1	TRUE	1	0.793332833619014	2		312	818	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139816	55139816	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	284	352	1	ENST00000257290.5:c.1477G>A	p.Val493Met	p.V493M	ENST00000257290	NM_006206.4	493	Gtg/Atg	10/23	1	2	FACETS	0.917	0.866	0.969	0.917	0.866	0.969	CLONAL	1	TRUE	1	0.793332833619014	2		353	781	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120423	94120423	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	917	615	0	ENST00000369303.4:c.628G>T	p.Glu210Ter	p.E210*	ENST00000369303	NM_004440.3	210	Gag/Tag	3/17	0.793332833619014	3	FACETS	0.989	0.963	1			1	CLONAL	2	TRUE	NA	0.793332833619014	3		615	1632	SUCCESS
ATM	472	MSKCC	GRCh37	11	108168095	108168095	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	477	354	0	ENST00000278616.4:c.4991A>G	p.Glu1664Gly	p.E1664G	ENST00000278616	NM_000051.3	1664	gAa/gGa	33/63	0.73799681012617	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.793332833619014	4		354	1017	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888162	112888162	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397507507	NA	P-0010602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1363	362	467	0	ENST00000351677.2:c.178G>C	p.Gly60Arg	p.G60R	ENST00000351677	NM_002834.3	60	Ggt/Cgt	3/16	0.793332833619014	4	FACETS	0.949	0.897	1	0.316	0.299	0.334	CLONAL	1	TRUE	1	0.793332833619014	4		467	1725	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913396	28913396	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	727	391	0	ENST00000282397.4:c.2397G>T	p.Met799Ile	p.M799I	ENST00000282397	NM_002019.4	799	atG/atT	17/30	0.789567283196058	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.793332833619014	2		391	887	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033822	49033822	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0010602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	585	343	0	ENST00000267163.4:c.1961-2A>G		p.X654_splice	ENST00000267163	NM_000321.2	654			0.789567283196058	2	FACETS	0.958	0.934	0.981	0.958	0.934	0.981	CLONAL	2	TRUE	0	0.793332833619014	2		343	770	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355129	73355129	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	367	247	0	ENST00000377767.4:c.241G>C	p.Glu81Gln	p.E81Q	ENST00000377767	NM_014953.3	81	Gag/Cag	2/21	0.789567283196058	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.793332833619014	2		247	453	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84384571	84384651	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCGAGACTCCGTCTCAAAAATAAATAAATAAATAAAAATTTTTAGCACAGAAAGTAGAGATGTGTTGTTTACTTACTTGCT	GCGAGACTCCGTCTCAAAAATAAATAAATAAATAAAAATTTTTAGCACAGAAAGTAGAGATGTGTTGTTTACTTACTTGCT	-	novel	NA	P-0010602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	184	78	0	ENST00000321945.7:c.792_796+76del		p.X264_splice	ENST00000321945	NM_139076.2	264		8/9	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.793332833619014	2		78	334	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199868	138199871	+	frameshift_variant	Frame_Shift_Del	DEL	GGCT	GGCT	-	novel	NA	P-0010602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	244	235	0	ENST00000237289.4:c.1286_1289del	p.Gly429AlafsTer47	p.G429Afs*47	ENST00000237289	NM_001270507.1	429	gGGCTc/gc	7/9	0.793332833619014	3	FACETS	0.962	0.901	1	0.481	0.45	0.513	CLONAL	1	TRUE	1	0.793332833619014	3		235	893	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220666	1220666	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010602-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	1329	470	0	ENST00000326873.7:c.685del	p.Asp229ThrfsTer58	p.D229Tfs*58	ENST00000326873	NM_000455.4	228	ctG/ct	5/10	0.793332833619014	3	FACETS	0.962	0.948	0.975	0.962	0.948	0.975	CLONAL	3	TRUE	0	0.793332833619014	3		470	1622	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0010632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	99	422	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	0.308840925513424	2		422	574	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220694	1220694	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	100	526	0	ENST00000326873.7:c.712A>T	p.Ile238Phe	p.I238F	ENST00000326873	NM_000455.4	238	Atc/Ttc	5/10	0.308840925513424	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.308840925513424	1		526	488	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979527	2979527	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	107	642	0	ENST00000396946.4:c.720G>T	p.Glu240Asp	p.E240D	ENST00000396946	NM_032415.4	240	gaG/gaT	6/25	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.308840925513424	2		642	665	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215710	133215710	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1555221894	NA	P-0010632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	81	447	1	ENST00000320574.5:c.5552+1G>T		p.X1851_splice	ENST00000320574	NM_006231.2	1851			1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.308840925513424	2		448	502	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911800	32911800	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	171	877	0	ENST00000380152.3:c.3308T>C	p.Leu1103Ser	p.L1103S	ENST00000380152		1103	tTa/tCa	11/27	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.308840925513424	2		877	1103	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47684689	47684689	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	86	546	0	ENST00000347630.2:c.760A>T	p.Met254Leu	p.M254L	ENST00000347630	NM_001007230.1	254	Atg/Ttg	9/11	1	2	FACETS	0.76	0.672	0.854	0.76	0.672	0.854	SUBCLONAL	1	TRUE	1	0.308840925513424	2		546	733	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610090	10610090	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	100	534	0	ENST00000171111.5:c.620T>G	p.Ile207Ser	p.I207S	ENST00000171111	NM_203500.1	207	aTc/aGc	2/6	0.308840925513424	1	FACETS	0.901	0.806	1	0.901	0.806	1	CLONAL	1	TRUE	0	0.308840925513424	1		534	608	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610100	10610100	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010632-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	111	568	0	ENST00000171111.5:c.610C>G	p.Arg204Gly	p.R204G	ENST00000171111	NM_203500.1	204	Cgg/Ggg	2/6	0.308840925513424	1	FACETS	0.95	0.855	1	0.95	0.855	1	CLONAL	1	TRUE	0	0.308840925513424	1		568	640	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0010635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	223	367	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.250441343346829	5	FACETS	0.856	0.798	0.917	0.571	0.532	0.611	INDETERMINATE	2	TRUE	2	0.46470222046211	5		367	951	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47600956	47600956	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs864622746	NA	P-0010635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	275	450	0	ENST00000263735.4:c.194A>C	p.Lys65Thr	p.K65T	ENST00000263735	NM_002354.2	65	aAa/aCa	3/9	0.18577850711531	3	FACETS	1	0.981	1	0.722	0.683	0.763	INDETERMINATE	2	TRUE	0	0.46470222046211	3		450	673	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182679040	182679040	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	280	443	0	ENST00000292782.4:c.494C>G	p.Ala165Gly	p.A165G	ENST00000292782	NM_020640.2	165	gCa/gGa	4/7	0.441560578803173	3	FACETS	0.909	0.857	0.962	0.909	0.857	0.962	CLONAL	2	TRUE	1	0.46470222046211	3		443	817	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0010641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	44	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.169777826121423	2	FACETS	1	0.842	1	0.501	0.421	0.589	CLONAL	1	TRUE	0	0.232471157661144	2		249	378	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497676	125497676	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	49	285	0	ENST00000428830.2:c.240A>T	p.Gln80His	p.Q80H	ENST00000428830	NM_001114121.2	80	caA/caT	3/14	0.174425538583752	1	FACETS	0.69	0.584	0.806	0.69	0.584	0.806	SUBCLONAL	1	TRUE	0	0.232471157661144	1		285	540	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210205	123210211	+	frameshift_variant	Frame_Shift_Del	DEL	AGTAAAA	AGTAAAA	-	novel	NA	P-0010641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	130	258	0	ENST00000218089.9:c.2557_2563del	p.Ser853LeufsTer17	p.S853Lfs*17	ENST00000218089	NM_001042749.1	853	AGTAAAAtt/tt	26/35	1	1	FACETS	0.95	0.867	1	1	0.99	1	CLONAL	2	TRUE	0	0.232471157661144	1		258	520	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188271	10188278	+	frameshift_variant	Frame_Shift_Del	DEL	ATCTCTCA	ATCTCTCA	-	novel	NA	P-0010641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	119	505	0	ENST00000256474.2:c.416_423del	p.Ser139CysfsTer2	p.S139Cfs*2	ENST00000256474	NM_000551.3	138	ccATCTCTCAat/ccat	2/3	NA	2	FACETS	1	0.943	1			1	INDETERMINATE	1	TRUE	NA	0.232471157661144	2		505	960	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437444	52437454	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGACTCAGC	GGGGACTCAGC	-	novel	NA	P-0010641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	87	519	0	ENST00000460680.1:c.1707_1717del	p.Leu570GlyfsTer69	p.L570Gfs*69	ENST00000460680	NM_004656.3	569	gtGCTGAGTCCCCtg/gttg	13/17	0.232471157661144	1	FACETS	0.827	0.731	0.929	0.827	0.731	0.929	CLONAL	1	TRUE	0	0.232471157661144	1		519	800	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0010651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	43	340	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		340	675	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437786	52437828	+	frameshift_variant	Frame_Shift_Del	DEL	GGTCCTTCTGGGACTCTTTGAGCTTCTCAGCCAAGACGTTGAT	GGTCCTTCTGGGACTCTTTGAGCTTCTCAGCCAAGACGTTGAT	-	novel	NA	P-0010651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	62	633	0	ENST00000460680.1:c.1333_1375del	p.Ile445SerfsTer112	p.I445Sfs*112	ENST00000460680	NM_004656.3	445	ATCAACGTCTTGGCTGAGAAGCTCAAAGAGTCCCAGAAGGACCtc/tc	13/17	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		633	1113	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777894	NA	P-0010660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	303	504	2	ENST00000361445.4:c.6644C>T	p.Ser2215Phe	p.S2215F	ENST00000361445	NM_004958.3	2215	tCt/tTt	47/58	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.516602140341372	2		506	897	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628248	187628248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200097846	NA	P-0010660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	51	313	0	ENST00000441802.2:c.2734G>A	p.Val912Ile	p.V912I	ENST00000441802	NM_005245.3	912	Gtt/Att	2/27	1	2	FACETS	0.339	0.287	0.395	0.339	0.287	0.395	SUBCLONAL	1	TRUE	1	0.516602140341372	2		313	583	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0010660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	265	482	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.516602140341372	2		482	857	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019534	123019534	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	202	495	0	ENST00000355640.3:c.22G>A	p.Gly8Arg	p.G8R	ENST00000355640		8	Gga/Aga	2/7	1	2	FACETS	0.818	0.758	0.88	0.818	0.758	0.88	CLONAL	1	TRUE	1	0.516602140341372	2		495	956	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190944	185190944	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1289	100	758	1	ENST00000265026.3:c.1825C>A	p.Gln609Lys	p.Q609K	ENST00000265026	NM_004721.4	609	Cag/Aag	11/14	1	2	FACETS	0.279	0.248	0.312	0.279	0.248	0.312	SUBCLONAL	1	TRUE	1	0.516602140341372	2		759	1389	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711965	89711965	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	456	295	0	ENST00000371953.3:c.583T>C	p.Phe195Leu	p.F195L	ENST00000371953	NM_000314.4	195	Ttt/Ctt	6/9	0.517140327516712	3	FACETS	1	0.993	1	1	0.997	1	CLONAL	3	TRUE	1	0.516602140341372	3		295	679	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052635	42052635	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	332	647	0	ENST00000219905.7:c.7306C>A	p.Arg2436Ser	p.R2436S	ENST00000219905	NM_001164273.1	2436	Cgt/Agt	20/24	0.517140327516712	1	FACETS	0.903	0.854	0.952	0.903	0.854	0.952	CLONAL	1	TRUE	0	0.516602140341372	1		647	1056	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546176	41546176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	82	140	0	ENST00000263253.7:c.2791del	p.Leu931CysfsTer15	p.L931Cfs*15	ENST00000263253	NM_001429.3	931	Ctg/tg	14/31	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.516602140341372	2		140	271	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097654	27097655	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0010660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	314	602	0	ENST00000324856.7:c.3245_3246del	p.Val1082GlyfsTer22	p.V1082Gfs*22	ENST00000324856	NM_006015.4	1081	aaTGtg/aatg	12/20	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.516602140341372	2		602	986	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589581	67589595	+	inframe_deletion	In_Frame_Del	DEL	ATTACATGAATATAA	ATTACATGAATATAA	-	novel	NA	P-0010660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	168	264	0	ENST00000274335.5:c.1344_1358del	p.Lys448_Tyr452del	p.K448_Y452del	ENST00000274335		448	aaATTACATGAATATAAc/aac	10/15	0.167743505234009				0.984	1				INDETERMINATE	1	TRUE	1	0.516602140341372	3		264	647	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711942	89711965	+	frameshift_variant	Frame_Shift_Del	DEL	ATTATAGACCAGTGGCACTGTTGT	ATTATAGACCAGTGGCACTGTTGT	C	novel	NA	P-0010660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	451	375	0	ENST00000371953.3:c.560_583delinsC	p.Asp187AlafsTer7	p.D187Afs*7	ENST00000371953	NM_000314.4	187	gATTATAGACCAGTGGCACTGTTGTtt/gCtt	6/9	0.517140327516712	3	FACETS	0.984	0.949	1	1	0.997	1	CLONAL	3	TRUE	1	0.516602140341372	3		375	744	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843506	156843506	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1434897221	NA	P-0010661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	80	413	0	ENST00000524377.1:c.932C>T	p.Pro311Leu	p.P311L	ENST00000524377	NM_002529.3	311	cCg/cTg	8/17	0.401827802213371	3	FACETS	1	0.922	1			1	CLONAL	1	TRUE	NA	0.32	3		413	547	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713865	30713865	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	121	481	0	ENST00000295754.5:c.1190A>T	p.Asp397Val	p.D397V	ENST00000295754	NM_003242.5	397	gAc/gTc	4/7	0.401827802213371	3	FACETS	0.803	0.724	0.887			1	CLONAL	1	TRUE	NA	0.32	3		481	1092	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140862	37140862	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	127	536	0	ENST00000373509.5:c.698A>G	p.Tyr233Cys	p.Y233C	ENST00000373509	NM_002648.3	233	tAt/tGt	5/6	0.401827802213371	5	FACETS	0.965	0.872	1			1	CLONAL	1	TRUE	NA	0.32	5		536	1217	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212128	98212128	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1259037941	NA	P-0010661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	76	422	0	ENST00000331920.6:c.3544C>G	p.Pro1182Ala	p.P1182A	ENST00000331920	NM_000264.3	1182	Cct/Gct	21/24	0.401827802213371	3	FACETS	0.837	0.734	0.948	0.419	0.367	0.474	CLONAL	1	TRUE	1	0.32	3		422	658	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428244	47428244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	40	549	0	ENST00000377045.4:c.1204G>A	p.Asp402Asn	p.D402N	ENST00000377045	NM_001654.4	402	Gac/Aac	11/16	0.137887674604638	0	FACETS	0.27	0.223	0.322			1	INDETERMINATE	1	TRUE	0	0.32	0		549	630	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922904	39922905	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0010661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	114	669	0	ENST00000378444.4:c.3803_3804del	p.Arg1268LysfsTer8	p.R1268Kfs*8	ENST00000378444	NM_001123385.1	1268	aGA/a	8/15	0.401827802213371	2	FACETS	0.951	0.857	1			1	CLONAL	1	TRUE	NA	0.32	2		669	749	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691039	NA	P-0010669-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	199	334	0	ENST00000269305.4:c.919+1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.416687416595383	2	FACETS	0.775	0.725	0.826	0.775	0.725	0.826	SUBCLONAL	2	TRUE	0	0.516508607659688	2		334	497	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934818	49934818	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010669-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	369	628	0	ENST00000296474.3:c.2078T>C	p.Phe693Ser	p.F693S	ENST00000296474	NM_002447.2	693	tTt/tCt	7/20	0.416687416595383	2	FACETS	0.819	0.781	0.858	0.819	0.781	0.858	CLONAL	2	TRUE	0	0.516508607659688	2		628	872	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20487032	20487032	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010669-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	235	311	0	ENST00000346618.3:c.997G>C	p.Glu333Gln	p.E333Q	ENST00000346618	NM_001949.4	333	Gag/Cag	5/7	0.394332184226022	6	FACETS	0.919	0.857	0.982	0.459	0.428	0.491	CLONAL	2	TRUE	2	0.516508607659688	6		311	1007	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020254	123020254	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010669-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	141	417	0	ENST00000355640.3:c.742A>T	p.Arg248Trp	p.R248W	ENST00000355640		248	Agg/Tgg	2/7	0.45518204090557	3	FACETS	0.798	0.727	0.872	0.399	0.363	0.436	SUBCLONAL	1	TRUE	1	0.516508607659688	3		417	861	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437747	52437771	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCCCCGCTGCTAGTCTTGATGGA	CAGCCCCGCTGCTAGTCTTGATGGA	-	novel	NA	P-0010678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1290	119	561	0	ENST00000460680.1:c.1390_1414del	p.Ser464GlyfsTer99	p.S464Gfs*99	ENST00000460680	NM_004656.3	464	TCCATCAAGACTAGCAGCGGGGCTGgg/gg	13/17	0.162099180207264	1	FACETS	0.752	0.676	0.833	0.752	0.676	0.833	SUBCLONAL	1	TRUE	0	0.201925014983838	1		561	1409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0010684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	186	166	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.492412167254927	1	FACETS	0.999	0.929	1	0.999	0.929	1	CLONAL	1	TRUE	0	0.499179476572182	1		166	560	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	242	392	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	0.499179476572182	2		392	863	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216125	7216125	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	503	924	1	ENST00000380728.2:c.934C>T	p.Arg312Trp	p.R312W	ENST00000380728		312	Cgg/Tgg	11/11	0.492412167254927	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.499179476572182	1		925	1507	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456898	149456898	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010684-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	386	602	0	ENST00000286301.3:c.830C>G	p.Ser277Cys	p.S277C	ENST00000286301	NM_005211.3	277	tCc/tGc	6/22	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.499179476572182	2		602	1346	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0010685-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	108	372	1	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	1	2	FACETS	0.895	0.804	0.991	0.895	0.804	0.991	CLONAL	1	TRUE	1	0.34	2		373	710	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0010685-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	245	316	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	TRUE	1	0.34	2		316	603	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156742	20156742	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0010685-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	235	262	0	ENST00000379607.5:c.17-2A>C		p.X6_splice	ENST00000379607	NM_001412.3	6			1	1	FACETS	0.954	0.906	1	1	0.996	1	CLONAL	3	TRUE	0	0.34	1		262	401	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0010687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	316	367	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.111454322756354	3	FACETS	1	0.979	1	1	0.979	1	INDETERMINATE	2	FALSE	1	0.340557781246153	3		367	1015	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781515	135781516	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	G	novel	NA	P-0010692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	1070	888	0	ENST00000298552.3:c.1449_1450delinsC	p.Arg484GlufsTer48	p.R484Efs*48	ENST00000298552	NM_001162426.1	483	tcTAga/tcCga	15/23	0.825596837059222	2	FACETS	0.989	0.974	1	0.989	0.974	1	CLONAL	2	TRUE	0	0.831952163209983	2		888	1300	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450145	32450145	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1193052708	NA	P-0010702-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	36	524	0	ENST00000332351.3:c.667G>A	p.Asp223Asn	p.D223N	ENST00000332351	NM_024426.4	223	Gac/Aac	2/10	1	2	FACETS	0.427	0.353	0.51	0.427	0.353	0.51	SUBCLONAL	1	TRUE	1	0.653044886695511	2		524	258	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	32	389	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.674	0.545	0.821	0.674	0.545	0.821	SUBCLONAL	1	TRUE	1	0.13	2		389	730	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0010716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	50	462	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.9	0.761	1	0.9	0.761	1	CLONAL	1	TRUE	1	0.13	2		463	855	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729962	30729962	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs104893819	NA	P-0010716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	30	315	2	ENST00000295754.5:c.1483C>T	p.Arg495Ter	p.R495*	ENST00000295754	NM_003242.5	495	Cga/Tga	6/7	1	2	FACETS	0.797	0.641	0.976	0.797	0.641	0.976	CLONAL	1	TRUE	1	0.13	2		317	579	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195761	102195761	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	66	664	0	ENST00000263464.3:c.522del	p.Thr175LeufsTer7	p.T175Lfs*7	ENST00000263464	NM_001165.4	174	cTt/ct	2/9	1	2	FACETS	0.848	0.733	0.973	0.848	0.733	0.973	CLONAL	1	TRUE	1	0.13	2		664	1198	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0010722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	171	503	0				ENST00000310581	NM_198253.2	-/1132			0.194741554598608	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.218780072888366	3		503	799	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562738	29562739	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555615472	NA	P-0010722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	81	338	0	ENST00000356175.3:c.3822_3823del	p.Phe1275ProfsTer8	p.F1275Pfs*8	ENST00000356175	NM_000267.3	1273	aCT/a	28/57	1	2	FACETS	0.648	0.569	0.734	0.648	0.569	0.734	SUBCLONAL	1	TRUE	1	0.218780072888366	2		338	1142	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295260	1295260	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0010722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	209	299	1				ENST00000310581	NM_198253.2	-/1132			0.194741554598608	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.218780072888366	3		300	864	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027244	49027244	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	127	239	0	ENST00000267163.4:c.1811A>G	p.Asp604Gly	p.D604G	ENST00000267163	NM_000321.2	604	gAt/gGt	18/27	0.218780072888366	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.218780072888366	1		239	863	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548909	29548909	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1135402820	NA	P-0010722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	64	175	0	ENST00000356175.3:c.1683G>A	p.Trp561Ter	p.W561*	ENST00000356175	NM_000267.3	561	tgG/tgA	15/57	1	2	FACETS	0.763	0.659	0.875	0.763	0.659	0.875	SUBCLONAL	1	TRUE	1	0.218780072888366	2		175	767	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918994	50918994	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	175	397	0	ENST00000440232.2:c.2731G>T	p.Asp911Tyr	p.D911Y	ENST00000440232	NM_002691.3	911	Gac/Tac	22/27	0.218780072888366	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.218780072888366	1		397	1135	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395510	116395534	+	protein_altering_variant	In_Frame_Del	DEL	TAGAGTTCTCCTTGGAAATGAGAGC	TAGAGTTCTCCTTGGAAATGAGAGC	G	novel	NA	P-0010722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	122	263	0	ENST00000397752.3:c.1803_1827delinsG	p.Arg602_Ser609del	p.R602_S609del	ENST00000397752	NM_000245.2	601	acTAGAGTTCTCCTTGGAAATGAGAGC/acG	6/21	0.194741554598608	3	FACETS	1	0.94	1	0.53	0.477	0.585	CLONAL	1	TRUE	1	0.218780072888366	3		263	1168	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411897	116411902	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TTTAAG	TTTAAG	A	novel	NA	P-0010722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	212	203	0	ENST00000397752.3:c.2888-6_2888-1delinsA		p.X963_splice	ENST00000397752	NM_000245.2	963			0.194741554598608	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.218780072888366	3		203	928	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652837	29652837	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1057518326	NA	P-0010725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	87	265	0	ENST00000356175.3:c.4773-1G>A		p.X1591_splice	ENST00000356175	NM_000267.3	1591			0.370571323160857	1	FACETS	0.907	0.807	1	0.907	0.807	1	CLONAL	1	TRUE	0	0.370571323160857	1		265	422	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992981	72992981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	231	600	1	ENST00000268489.5:c.1064C>T	p.Ala355Val	p.A355V	ENST00000268489	NM_006885.3	355	gCt/gTt	2/10	0.370571323160857	1	FACETS	0.972	0.906	1	0.972	0.906	1	CLONAL	1	TRUE	0	0.370571323160857	1		601	1045	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920466	50920466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs980793204	NA	P-0010725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	227	368	13	ENST00000440232.2:c.3158G>A	p.Arg1053His	p.R1053H	ENST00000440232	NM_002691.3	1053	cGc/cAc	26/27	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.370571323160857	2		381	889	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356450	70356450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502167	NA	P-0010725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	156	379	1	ENST00000374080.3:c.5345G>A	p.Arg1782His	p.R1782H	ENST00000374080		1782	cGc/cAc	37/45	1	2	FACETS	0.903	0.827	0.983	0.903	0.827	0.983	CLONAL	1	TRUE	1	0.370571323160857	2		380	932	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0010741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	124	371	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.222222719351282	2		371	846	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491647	56491647	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	95	427	0	ENST00000267101.3:c.2539C>G	p.Gln847Glu	p.Q847E	ENST00000267101	NM_001982.3	847	Cag/Gag	21/28	1	2	FACETS	0.892	0.793	0.999	0.892	0.793	0.999	CLONAL	1	TRUE	1	0.222222719351282	2		427	958	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554428	63554428	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567769222	NA	P-0010741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	71	385	0	ENST00000307078.5:c.311G>A	p.Cys104Tyr	p.C104Y	ENST00000307078	NM_004655.3	104	tGc/tAc	2/11	1	2	FACETS	0.84	0.732	0.956	0.84	0.732	0.956	CLONAL	1	TRUE	1	0.222222719351282	2		385	761	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032525	47032525	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0010741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	94	264	0	ENST00000377604.3:c.433-2A>G		p.X145_splice	ENST00000377604	NM_001204468.1	145			0.0998908112569559	0	FACETS	1	0.931	1			1	INDETERMINATE	1	TRUE	NA	0.222222719351282	0		264	621	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891514	76891514	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	44	278	0	ENST00000373344.5:c.4591T>C	p.Cys1531Arg	p.C1531R	ENST00000373344	NM_000489.3	1531	Tgt/Cgt	16/35	0.0998908112569559	0	FACETS	0.575	0.481	0.678			1	INDETERMINATE	1	TRUE	NA	0.222222719351282	0		278	536	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127796	47127797	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0010741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	68	230	0	ENST00000409792.3:c.5285_5286del	p.His1762LeufsTer26	p.H1762Lfs*26	ENST00000409792	NM_014159.6	1762	cAC/c	11/21	0.222222719351282	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.222222719351282	1		230	449	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0010756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	198	367	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	0.539421752902563	2		367	719	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889106	76889106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010756-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	329	772	0	ENST00000373344.5:c.4904T>C	p.Met1635Thr	p.M1635T	ENST00000373344	NM_000489.3	1635	aTg/aCg	18/35	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.539421752902563	2		772	1205	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955514	48955514	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0010784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	114	374	1	ENST00000267163.4:c.1630A>T	p.Arg544Ter	p.R544*	ENST00000267163	NM_000321.2	544	Aga/Tga	17/27	1	2	FACETS	0.763	0.686	0.845	0.763	0.686	0.845	SUBCLONAL	1	TRUE	1	0.329777362492852	2		375	906	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204842	128204842	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1536	82	470	0	ENST00000341105.2:c.599G>T	p.Gly200Val	p.G200V	ENST00000341105	NM_032638.4	200	gGt/gTt	3/6	0.193179064563014	3	FACETS	0.358	0.314	0.406	0.179	0.157	0.203	INDETERMINATE	1	TRUE	1	0.329777362492852	3		470	1618	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923346	131923346	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	97	168	0	ENST00000265335.6:c.849G>C	p.Glu283Asp	p.E283D	ENST00000265335		283	gaG/gaC	6/25	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.329777362492852	2		168	562	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967899	93967899	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs760411632	NA	P-0010784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1396	246	624	0	ENST00000369303.4:c.2028G>C	p.Arg676Ser	p.R676S	ENST00000369303	NM_004440.3	676	agG/agC	11/17	1	2	FACETS	0.909	0.846	0.973	0.909	0.846	0.973	CLONAL	1	TRUE	1	0.329777362492852	2		624	1642	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117861187	117861187	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	190	461	1	ENST00000297338.2:c.1702C>T	p.Gln568Ter	p.Q568*	ENST00000297338	NM_006265.2	568	Cag/Tag	13/14	1	2	FACETS	0.878	0.81	0.95	0.878	0.81	0.95	CLONAL	1	TRUE	1	0.329777362492852	2		462	1312	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117861208	117861208	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1204	208	503	0	ENST00000297338.2:c.1681C>T	p.Gln561Ter	p.Q561*	ENST00000297338	NM_006265.2	561	Cag/Tag	13/14	1	2	FACETS	0.893	0.827	0.963	0.893	0.827	0.963	CLONAL	1	TRUE	1	0.329777362492852	2		503	1412	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562590	95562590	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	156	312	0	ENST00000393063.1:c.4667A>C	p.Asp1556Ala	p.D1556A	ENST00000393063	NM_030621.3	1556	gAc/gCc	24/28	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.329777362492852	2		312	886	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47679245	47679245	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1274528044	NA	P-0010784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	90	375	0	ENST00000347630.2:c.962C>T	p.Ala321Val	p.A321V	ENST00000347630	NM_001007230.1	321	gCa/gTa	10/11	1	2	FACETS	0.513	0.454	0.577	0.513	0.454	0.577	SUBCLONAL	1	TRUE	1	0.329777362492852	2		375	1064	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578466	7578466	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786202752	NA	P-0010785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	61	444	0	ENST00000269305.4:c.464C>A	p.Thr155Asn	p.T155N	ENST00000269305	NM_001126112.2	155	aCc/aAc	5/11	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.14	2		444	841	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879831	37879831	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	47	414	0	ENST00000269571.5:c.2126A>T	p.Gln709Leu	p.Q709L	ENST00000269571		709	cAg/cTg	18/27	1	2	FACETS	0.885	0.745	1	0.885	0.745	1	CLONAL	1	TRUE	1	0.14	2		414	759	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204737477	204737477	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	58	488	0	ENST00000302823.3:c.614C>T	p.Pro205Leu	p.P205L	ENST00000302823	NM_005214.4	205	cCc/cTc	4/4	1	2	FACETS	0.887	0.76	1	0.887	0.76	1	CLONAL	1	TRUE	1	0.14	2		488	934	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294198	1294198	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	93	479	0	ENST00000310581.5:c.803G>C	p.Arg268Pro	p.R268P	ENST00000310581	NM_198253.2	268	cGt/cCt	2/16	0.0851653509849816	3	FACETS	0.79	0.701	0.885	0.79	0.701	0.885	SUBCLONAL	2	TRUE	1	0.14	3		479	900	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395870	395870	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	83	698	1	ENST00000380956.4:c.427G>A	p.Asp143Asn	p.D143N	ENST00000380956	NM_001195286.1	143	Gac/Aac	4/9	1	2	FACETS	0.95	0.836	1	0.95	0.836	1	CLONAL	1	TRUE	1	0.14	2		699	1248	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451038	70451038	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	36	405	3	ENST00000373644.4:c.5878G>T	p.Asp1960Tyr	p.D1960Y	ENST00000373644	NM_030625.2	1960	Gat/Tat	12/12	1	2	FACETS	0.743	0.609	0.894	0.743	0.609	0.894	SUBCLONAL	1	TRUE	1	0.14	2		408	692	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526294	189526295	+	missense_variant	Missense_Mutation	DNP	CG	CG	TT	novel	NA	P-0010785-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	33	295	2	ENST00000264731.3:c.558_559delinsTT	p.Ala187Ser	p.A187S	ENST00000264731	NM_003722.4	186	acCGcc/acTTcc	4/14	1	2	FACETS	0.721	0.585	0.874	0.721	0.585	0.874	SUBCLONAL	1	TRUE	1	0.14	2		297	654	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578202	7578202	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520004	NA	P-0010789-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	72	487	0	ENST00000269305.4:c.647T>G	p.Val216Gly	p.V216G	ENST00000269305	NM_001126112.2	216	gTg/gGg	6/11	1	2	FACETS	0.982	0.855	1	0.982	0.855	1	CLONAL	1	TRUE	1	0.12	2		487	1222	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599875	10599875	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010789-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	66	446	0	ENST00000171111.5:c.1701C>A	p.Tyr567Ter	p.Y567*	ENST00000171111	NM_203500.1	567	taC/taA	5/6	1	2	FACETS	0.949	0.821	1	0.949	0.821	1	CLONAL	1	TRUE	1	0.12	2		446	1159	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0010792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	28	388	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.214775331317485	2	FACETS	0.82	0.673	0.977	0.82	0.673	0.977	INDETERMINATE	2	TRUE	0	0.375277147623162	2		388	91	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0010792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	100	293	0	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	0.375277147623162	3	FACETS	0.945	0.886	0.999	1	0.99	1	CLONAL	5	TRUE	0	0.375277147623162	3		293	134	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829753	76829756	+	frameshift_variant	Frame_Shift_Del	DEL	CTTC	CTTC	-	novel	NA	P-0010792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	55	590	0	ENST00000373344.5:c.6285_6288del	p.Lys2096SerfsTer12	p.K2096Sfs*12	ENST00000373344	NM_000489.3	2095	agGAAG/ag	28/35	0.375277147623162	0	FACETS	0.889	0.792	0.985			1	CLONAL	2	TRUE	0	0.375277147623162	0		590	103	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0010807-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	92	503	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.509	0.453	0.569	0.509	0.453	0.569	SUBCLONAL	1	TRUE	1	0.618642198243746	2		503	584	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577316	64577316	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010807-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	122	403	0	ENST00000312049.6:c.266T>G	p.Leu89Arg	p.L89R	ENST00000312049	NM_130799.2	89	cTc/cGc	2/10	1	2	FACETS	0.548	0.495	0.603	0.548	0.495	0.603	SUBCLONAL	1	TRUE	1	0.618642198243746	2		403	720	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844245	68844245	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs878854697	NA	P-0010807-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	45	298	0	ENST00000261769.5:c.832+1G>T		p.X278_splice	ENST00000261769	NM_004360.3	278			0.478376481665203	1	FACETS	0.211	0.177	0.249	0.211	0.177	0.249	SUBCLONAL	1	TRUE	0	0.618642198243746	1		298	476	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010820-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	201	528	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.892	0.83	0.955	0.892	0.83	0.955	CLONAL	1	TRUE	1	0.67176956139368	2		530	671	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936381	49936381	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010820-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	630	640	0	ENST00000296474.3:c.1467C>G	p.Phe489Leu	p.F489L	ENST00000296474	NM_002447.2	489	ttC/ttG	3/20	0.67176956139368	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.67176956139368	1		640	1218	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527590	29527590	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555610910	NA	P-0010820-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	32	379	1	ENST00000356175.3:c.1039C>T	p.Gln347Ter	p.Q347*	ENST00000356175	NM_000267.3	347	Cag/Tag	9/57	0.67176956139368	1	FACETS	0.105	0.085	0.128	0.105	0.085	0.128	SUBCLONAL	1	TRUE	0	0.67176956139368	1		380	602	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600408	10600408	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010820-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	488	548	1	ENST00000171111.5:c.1447C>A	p.Arg483Ser	p.R483S	ENST00000171111	NM_203500.1	483	Cgc/Agc	4/6	0.67176956139368	1	FACETS	0.941	0.905	0.978	0.941	0.905	0.978	CLONAL	1	TRUE	0	0.67176956139368	1		549	1025	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509208	106509208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010822-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	333	578	1	ENST00000359195.3:c.1202C>T	p.Pro401Leu	p.P401L	ENST00000359195	NM_002649.2	401	cCc/cTc	2/11	0.441595056241252	1	FACETS	0.961	0.91	1	0.961	0.91	1	CLONAL	1	TRUE	0	0.505113821178193	1		579	1025	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457936	69457936	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010822-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4317	749	596	0	ENST00000227507.2:c.336G>C	p.Lys112Asn	p.K112N	ENST00000227507	NM_053056.2	112	aaG/aaC	2/5	0.505113821178193	11	FACETS	0.958	0.92	0.997			1	CLONAL	2	TRUE	NA	0.505113821178193	11		596	5066	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761286	59761286	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010822-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	370	660	1	ENST00000259008.2:c.3121A>T	p.Met1041Leu	p.M1041L	ENST00000259008	NM_032043.2	1041	Atg/Ttg	20/20	NA	2	FACETS	0.957	0.906	1			1	INDETERMINATE	1	TRUE	NA	0.505113821178193	2		661	1531	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925711	114925711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752060378	NA	P-0010823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1548	261	659	1	ENST00000543371.1:c.1789G>A	p.Val597Ile	p.V597I	ENST00000543371	NM_001198531.1	597	Gtc/Atc	14/14	0.460817412597475	4	FACETS	0.918	0.856	0.981	0.459	0.428	0.491	CLONAL	1	FALSE	2	0.458771704326015	4		660	1809	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170054	32170054	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	227	404	0	ENST00000375023.3:c.3554G>T	p.Gly1185Val	p.G1185V	ENST00000375023	NM_004557.3	1185	gGg/gTg	21/30	0.460817412597475	3	FACETS	1	0.975	1	0.549	0.511	0.588	CLONAL	1	FALSE	1	0.458771704326015	3		404	1108	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061192	38061192	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	94	199	0	ENST00000250448.2:c.797T>G	p.Phe266Cys	p.F266C	ENST00000250448	NM_004496.3	266	tTc/tGc	2/2	0.460817412597475	3	FACETS	1	0.926	1			1	CLONAL	1	FALSE	NA	0.458771704326015	3		199	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577115	7577115	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	436	401	0	ENST00000269305.4:c.823T>G	p.Cys275Gly	p.C275G	ENST00000269305	NM_001126112.2	275	Tgt/Ggt	8/11	0.458771704326015	2	FACETS	0.993	0.951	1	0.993	0.951	1	CLONAL	2	FALSE	0	0.458771704326015	2		401	957	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40460234	40460234	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	251	460	0	ENST00000345506.4:c.1945C>T	p.Arg649Trp	p.R649W	ENST00000345506	NM_003152.3	649	Cgg/Tgg	17/20	0.458771704326015	2	FACETS	1	0.944	1	0.505	0.472	0.539	CLONAL	1	FALSE	0	0.458771704326015	2		460	1084	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76812945	76812947	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs1557059596	NA	P-0010823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	143	164	0	ENST00000373344.5:c.6674_6676del	p.Lys2225del	p.K2225del	ENST00000373344	NM_000489.3	2225	aAGAgg/agg	30/35	1	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	0	0.458771704326015	1		164	402	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971116	21971116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552823	NA	P-0010853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	30	168	0	ENST00000304494.5:c.242C>T	p.Pro81Leu	p.P81L	ENST00000304494	NM_000077.4	81	cCc/cTc	2/3	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		168	462	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857895	9857895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761399460	NA	P-0010853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	53	398	2	ENST00000330684.3:c.3506G>A	p.Arg1169Gln	p.R1169Q	ENST00000330684	NM_001134407.1	1169	cGg/cAg	13/13	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		400	890	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505650	186505650	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	174	557	0	ENST00000323963.5:c.1058A>G	p.Asn353Ser	p.N353S	ENST00000323963		353	aAt/aGt	10/11	1	2	FACETS	0.953	0.877	1	0.953	0.877	1	CLONAL	1	TRUE	1	0.362934664753539	2		557	1006	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624404	140624425	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCGCCGGCGCCGGCGCCGGC	CGGCGCCGGCGCCGGCGCCGGC	-	novel	NA	P-0010856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	135	154	0	ENST00000288602.6:c.79_100del	p.Ala27ArgfsTer20	p.A27Rfs*20	ENST00000288602	NM_004333.4	27	GCCGGCGCCGGCGCCGGCGCCGcg/cg	1/18	1	2	FACETS	0.89	0.816	0.966	1	0.99	1	CLONAL	2	TRUE	1	0.362934664753539	2		154	418	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	233	528	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.391129253685171	2		530	997	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0010864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	25	83	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.391129253685171	1	FACETS	0.525	0.416	0.648	0.525	0.416	0.648	SUBCLONAL	1	FALSE	0	0.391129253685171	1		83	196	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287884	33287884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1632	463	467	0	ENST00000374542.5:c.1369G>A	p.Glu457Lys	p.E457K	ENST00000374542	NM_001141970.1	457	Gag/Aag	5/8	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.391129253685171	2		467	2095	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224336	55224336	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	183	393	0	ENST00000275493.2:c.1117C>T	p.Pro373Ser	p.P373S	ENST00000275493	NM_005228.3	373	Ccg/Tcg	9/28	0.391129253685171	3	FACETS	1	0.947	1	0.517	0.476	0.559	CLONAL	1	FALSE	1	0.391129253685171	3		393	1082	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138295	2138295	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs45507199	NA	P-0010890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	151	487	0	ENST00000219476.3:c.5228G>C	p.Arg1743Pro	p.R1743P	ENST00000219476	NM_000548.3	1743	cGg/cCg	41/42	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.335549884261164	2		487	606	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134318	2134318	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	162	531	1	ENST00000219476.3:c.4096del	p.Glu1366ArgfsTer17	p.E1366Rfs*17	ENST00000219476	NM_000548.3	1365	tcG/tc	34/42	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.335549884261164	2		532	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0010892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	76	395	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	1	2	FACETS	0.516	0.451	0.586	0.516	0.451	0.586	SUBCLONAL	1	TRUE	1	0.31884857148927	2		395	924	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727521	88727521	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	51	341	0	ENST00000360948.2:c.258G>T	p.Glu86Asp	p.E86D	ENST00000360948	NM_001012338.2	86	gaG/gaT	3/19	0.31884857148927	1	FACETS	0.38	0.322	0.444	0.38	0.322	0.444	SUBCLONAL	1	TRUE	0	0.31884857148927	1		341	707	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279958	18279958	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	88	369	1	ENST00000222254.8:c.2041G>A	p.Glu681Lys	p.E681K	ENST00000222254	NM_005027.3	681	Gag/Aag	16/16	1	2	FACETS	0.59	0.521	0.663	0.59	0.521	0.663	SUBCLONAL	1	TRUE	1	0.31884857148927	2		370	936	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294274	11294274	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	108	425	0	ENST00000361445.4:c.2257A>T	p.Ser753Cys	p.S753C	ENST00000361445	NM_004958.3	753	Agt/Tgt	14/58	1	2	FACETS	0.651	0.583	0.723	0.651	0.583	0.723	SUBCLONAL	1	TRUE	1	0.31884857148927	2		425	1041	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36945094	36945094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	70	629	1	ENST00000361632.4:c.4G>A	p.Ala2Thr	p.A2T	ENST00000361632		2	Gca/Aca	2/16	NA	2	FACETS	0.388	0.337	0.444			1	INDETERMINATE	1	TRUE	NA	0.31884857148927	2		630	1131	SUCCESS
ALK	238	MSKCC	GRCh37	2	29450494	29450494	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	187	463	0	ENST00000389048.3:c.2860G>A	p.Asp954Asn	p.D954N	ENST00000389048	NM_004304.4	954	Gat/Aat	17/29	0.213283198057298	2	FACETS	1	0.982	1	0.604	0.558	0.652	CLONAL	1	TRUE	0	0.31884857148927	2		463	971	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55963857	55963857	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	99	529	0	ENST00000263923.4:c.2586C>G	p.Cys862Trp	p.C862W	ENST00000263923	NM_002253.2	862	tgC/tgG	18/30	0.31884857148927	1	FACETS	0.513	0.457	0.573	0.513	0.457	0.573	SUBCLONAL	1	TRUE	0	0.31884857148927	1		529	1017	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233094	66233094	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	49	378	0	ENST00000273854.3:c.1905G>T	p.Met635Ile	p.M635I	ENST00000273854	NM_004439.5	635	atG/atT	10/18	1	2	FACETS	0.329	0.278	0.387	0.329	0.278	0.387	SUBCLONAL	1	TRUE	1	0.31884857148927	2		378	933	SUCCESS
APC	324	MSKCC	GRCh37	5	112162900	112162900	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	78	450	0	ENST00000257430.4:c.1504G>T	p.Gly502Ter	p.G502*	ENST00000257430	NM_000038.5	502	Gga/Tga	12/16	0.141069053539566	4	FACETS	0.628	0.55	0.712	0.314	0.275	0.356	INDETERMINATE	1	TRUE	2	0.31884857148927	4		450	1027	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178664	32178664	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	144	385	2	ENST00000375023.3:c.2730C>A	p.Ser910Arg	p.S910R	ENST00000375023	NM_004557.3	910	agC/agA	18/30	0.31884857148927	5	FACETS	1	0.975	1	0.597	0.543	0.654	CLONAL	1	TRUE	3	0.31884857148927	5		387	1118	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394386	162394386	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	114	412	0	ENST00000366898.1:c.682C>A	p.Leu228Met	p.L228M	ENST00000366898	NM_004562.2	228	Ctg/Atg	6/12	0.215131588124208	1	FACETS	0.61	0.548	0.675	0.61	0.548	0.675	SUBCLONAL	1	TRUE	0	0.31884857148927	1		412	986	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331710	8331710	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	170	371	1	ENST00000356435.5:c.5406G>T	p.Gln1802His	p.Q1802H	ENST00000356435		1802	caG/caT	33/35	NA	2	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.31884857148927	2		372	966	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451483	70451483	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	253	519	1	ENST00000373644.4:c.6323A>T	p.Lys2108Ile	p.K2108I	ENST00000373644	NM_030625.2	2108	aAa/aTa	12/12	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.31884857148927	2		520	1336	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114216	115114216	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	240	446	1	ENST00000257566.3:c.1001G>T	p.Gly334Val	p.G334V	ENST00000257566	NM_016569.3	334	gGg/gTg	6/8	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.31884857148927	2		447	1023	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028644	12028644	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	79	431	1	ENST00000353533.5:c.847G>C	p.Gly283Arg	p.G283R	ENST00000353533	NM_003010.3	283	Gga/Cga	8/11	1	2	FACETS	0.444	0.389	0.503	0.444	0.389	0.503	SUBCLONAL	1	TRUE	1	0.31884857148927	2		432	1117	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559161	29559161	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	51	255	0	ENST00000356175.3:c.3268G>T	p.Gly1090Ter	p.G1090*	ENST00000356175	NM_000267.3	1090	Gga/Tga	25/57	1	2	FACETS	0.403	0.341	0.471	0.403	0.341	0.471	SUBCLONAL	1	TRUE	1	0.31884857148927	2		255	794	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793242	33793242	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	21	161	0	ENST00000498907.2:c.79A>C	p.Ser27Arg	p.S27R	ENST00000498907	NM_004364.3	27	Agc/Cgc	1/1	1	2	FACETS	0.563	0.435	0.712	0.563	0.435	0.712	SUBCLONAL	1	TRUE	1	0.31884857148927	2		161	234	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790149	40790149	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	73	200	0	ENST00000373198.4:c.2582C>G	p.Thr861Ser	p.T861S	ENST00000373198	NM_133170.3	861	aCc/aGc	18/32	0.287676514939735	1	FACETS	0.797	0.699	0.902	0.797	0.699	0.902	CLONAL	1	TRUE	0	0.31884857148927	1		200	483	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944586	40944586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	81	226	0	ENST00000373198.4:c.1916C>T	p.Ala639Val	p.A639V	ENST00000373198	NM_133170.3	639	gCa/gTa	12/32	0.287676514939735	1	FACETS	0.77	0.679	0.866	0.77	0.679	0.866	SUBCLONAL	1	TRUE	0	0.31884857148927	1		226	555	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091789	29091789	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	90	279	0	ENST00000328354.6:c.1168T>G	p.Tyr390Asp	p.Y390D	ENST00000328354	NM_007194.3	390	Tac/Gac	11/15	1	2	FACETS	0.944	0.839	1	0.944	0.839	1	CLONAL	1	TRUE	1	0.31884857148927	2		279	598	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922141	39922141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1393432690	NA	P-0010892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1409	169	653	2	ENST00000378444.4:c.4031C>T	p.Ala1344Val	p.A1344V	ENST00000378444	NM_001123385.1	1344	gCc/gTc	9/15	1	2	FACETS	0.672	0.615	0.731	0.672	0.615	0.731	SUBCLONAL	1	TRUE	1	0.31884857148927	2		655	1578	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171425	123171425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010892-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1287	119	525	0	ENST00000218089.9:c.337G>A	p.Ala113Thr	p.A113T	ENST00000218089	NM_001042749.1	113	Gca/Aca	6/35	1	2	FACETS	0.531	0.477	0.588	0.531	0.477	0.588	SUBCLONAL	1	TRUE	1	0.31884857148927	2		525	1406	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156740	20156740	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010896-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	123	368	0	ENST00000379607.5:c.17G>A	p.Gly6Asp	p.G6D	ENST00000379607	NM_001412.3	6	gGt/gAt	2/7	0.128726932047027	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.697172339057591	0		368	276	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056352	27056352	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1557591264	NA	P-0010896-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	162	177	1	ENST00000324856.7:c.1348C>T	p.Gln450Ter	p.Q450*	ENST00000324856	NM_006015.4	450	Cag/Tag	2/20	0.697172339057591	3	FACETS	0.973	0.909	1	0.973	0.909	1	CLONAL	2	FALSE	1	0.697172339057591	3		178	322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0010901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	1013	617	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.828966023297387	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.828966023297387	2		617	1188	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165890	118165890	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	326	392	0	ENST00000369448.3:c.400C>G	p.Leu134Val	p.L134V	ENST00000369448	NM_017709.3	134	Ctg/Gtg	2/2	0.828966023297387	2	FACETS	1	0.987	1	0.553	0.526	0.58	CLONAL	1	TRUE	0	0.828966023297387	2		392	711	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664853	138664853	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	14	49	0	ENST00000330315.3:c.712A>G	p.Ser238Gly	p.S238G	ENST00000330315	NM_023067.3	238	Agc/Ggc	1/1	0.828966023297387	3	FACETS	0.464	0.339	0.611	0.232	0.169	0.306	SUBCLONAL	1	TRUE	1	0.828966023297387	3		49	103	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564722	55564722	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	240	361	0	ENST00000288135.5:c.610G>T	p.Val204Leu	p.V204L	ENST00000288135	NM_000222.2	204	Gtg/Ttg	3/21	1	2	FACETS	0.85	0.798	0.903	0.85	0.798	0.903	CLONAL	1	TRUE	1	0.828966023297387	2		361	681	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499808	8499808	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	422	527	0	ENST00000356435.5:c.2161G>T	p.Glu721Ter	p.E721*	ENST00000356435		721	Gag/Tag	14/35	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.828966023297387	2		527	962	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401890	139401890	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0010901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	266	407	0	ENST00000277541.6:c.3511-1G>A		p.X1171_splice	ENST00000277541	NM_017617.3	1171			1	2	FACETS	0.974	0.919	1	0.974	0.919	1	CLONAL	1	TRUE	1	0.828966023297387	2		407	659	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911646	32911646	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	594	750	3	ENST00000380152.3:c.3154G>T	p.Ala1052Ser	p.A1052S	ENST00000380152		1052	Gca/Tca	11/27	0.828966023297387	1	FACETS	0.977	0.95	1	0.977	0.95	1	CLONAL	1	TRUE	0	0.828966023297387	1		753	859	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937028	48937028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	360	444	0	ENST00000267163.4:c.796C>T	p.Gln266Ter	p.Q266*	ENST00000267163	NM_000321.2	266	Caa/Taa	8/27	0.828966023297387	1	FACETS	0.965	0.93	0.999	0.965	0.93	0.999	CLONAL	1	TRUE	0	0.828966023297387	1		444	527	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795106	42795106	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010901-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	390	605	0	ENST00000575354.2:c.2186A>T	p.Tyr729Phe	p.Y729F	ENST00000575354	NM_015125.3	729	tAt/tTt	10/20	1	2	FACETS	0.946	0.901	0.99	0.946	0.901	0.99	CLONAL	1	TRUE	1	0.828966023297387	2		605	995	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0010903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	376	771	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.268569213558743	3	FACETS	1	0.994	1	0.704	0.667	0.743	CLONAL	1	TRUE	1	0.426935705112443	3		771	1517	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	179	457	0	ENST00000304494.5:c.322G>C	p.Asp108His	p.D108H	ENST00000304494	NM_000077.4	108	Gat/Cat	2/3	0.426935705112443	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.426935705112443	1		457	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0010903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1184	219	715	1	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	0.268569213558743	3	FACETS	0.887	0.823	0.954	0.444	0.411	0.477	CLONAL	1	TRUE	1	0.426935705112443	3		716	1403	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873237	71873237	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1217	176	882	0	ENST00000357731.5:c.957G>T	p.Gln319His	p.Q319H	ENST00000357731	NM_173808.2	319	caG/caT	7/7	0.133800388292516	5	FACETS	0.971	0.892	1	0.243	0.223	0.264	INDETERMINATE	1	TRUE	1	0.426935705112443	5		882	1393	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876936	151876936	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	231	593	0	ENST00000262189.6:c.7425G>C	p.Met2475Ile	p.M2475I	ENST00000262189	NM_170606.2	2475	atG/atC	37/59	0.345211848031487	2	FACETS	1	0.992	1	0.734	0.687	0.782	CLONAL	1	TRUE	0	0.426935705112443	2		593	737	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877975	151877975	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	236	501	0	ENST00000262189.6:c.6970G>A	p.Asp2324Asn	p.D2324N	ENST00000262189	NM_170606.2	2324	Gat/Aat	36/59	0.345211848031487	2	FACETS	0.807	0.757	0.858	0.807	0.757	0.858	CLONAL	2	TRUE	0	0.426935705112443	2		501	685	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878254	151878254	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	293	655	0	ENST00000262189.6:c.6691G>T	p.Glu2231Ter	p.E2231*	ENST00000262189	NM_170606.2	2231	Gag/Tag	36/59	0.345211848031487	2	FACETS	0.806	0.761	0.851	0.806	0.761	0.851	CLONAL	2	TRUE	0	0.426935705112443	2		655	852	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426172	49426172	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	89	389	0	ENST00000301067.7:c.12316A>T	p.Ser4106Cys	p.S4106C	ENST00000301067	NM_003482.3	4106	Agc/Tgc	39/54	0.268569213558743	3	FACETS	0.823	0.73	0.921	0.411	0.365	0.461	CLONAL	1	TRUE	1	0.426935705112443	3		389	615	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199756	108199757	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0010903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	231	388	0	ENST00000278616.4:c.7098_7099del	p.Glu2366AspfsTer6	p.E2366Dfs*6	ENST00000278616	NM_000051.3	2366	gaAGtt/gatt	49/63	0.349876461417746	4	FACETS	0.874	0.821	0.927	0.874	0.821	0.927	CLONAL	3	TRUE	1	0.426935705112443	4		388	589	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	696	469	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.819843075194076	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.819843075194076	2		469	842	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	730	628	1	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.819843075194076	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.819843075194076	2		629	877	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11552822	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	89	192	0	ENST00000304494.5:c.250G>T	p.Asp84Tyr	p.D84Y	ENST00000304494	NM_000077.4	84	Gac/Tac	2/3	0.523822650540214	1	FACETS	0.468	0.42	0.517	0.468	0.42	0.517	SUBCLONAL	1	TRUE	0	0.819843075194076	1		192	274	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458225	120458225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	87	399	0	ENST00000256646.2:c.7120C>T	p.His2374Tyr	p.H2374Y	ENST00000256646	NM_024408.3	2374	Cat/Tat	34/34	0.793575740167661	3	FACETS	0.281	0.247	0.316	0.094	0.082	0.106	SUBCLONAL	1	TRUE	0	0.819843075194076	3		399	1066	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793388	18793388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	806	454	0	ENST00000266497.5:c.4085G>A	p.Ser1362Asn	p.S1362N	ENST00000266497		1362	aGt/aAt	30/31	0.819843075194076	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.819843075194076	2		454	950	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675877	30675877	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1457	1245	771	1	ENST00000376406.3:c.2479G>A	p.Glu827Lys	p.E827K	ENST00000376406	NM_014641.2	827	Gag/Aag	8/15	0.819843075194076	4	FACETS	1	0.988	1	0.682	0.665	0.699	CLONAL	2	TRUE	1	0.819843075194076	4		772	2702	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11204726	11204726	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1512	126	537	0	ENST00000361445.4:c.4851G>C	p.Gln1617His	p.Q1617H	ENST00000361445	NM_004958.3	1617	caG/caC	34/58	0.807213452303836	3	FACETS	0.265	0.238	0.293			1	SUBCLONAL	1	TRUE	NA	0.819843075194076	3		537	1638	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058578	72058578	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1866	161	739	0	ENST00000357731.5:c.862A>T	p.Thr288Ser	p.T288S	ENST00000357731	NM_173808.2	288	Aca/Tca	6/7	0.793575740167661	3	FACETS	0.273	0.249	0.299	0.091	0.083	0.1	SUBCLONAL	1	TRUE	0	0.819843075194076	3		739	2027	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61727000	61727000	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	188	353	0	ENST00000401558.2:c.438G>T	p.Trp146Cys	p.W146C	ENST00000401558	NM_003400.3	146	tgG/tgT	7/25	0.289764373596147	3	FACETS	0.822	0.761	0.885	0.274	0.253	0.295	INDETERMINATE	1	TRUE	0	0.819843075194076	3		353	787	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728706	190728706	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	261	317	0	ENST00000441310.2:c.2094G>T	p.Gln698His	p.Q698H	ENST00000441310	NM_000534.4	698	caG/caT	10/13	0.584273596615906	3	FACETS	1	0.966	1	0.52	0.488	0.553	CLONAL	1	TRUE	1	0.819843075194076	3		317	863	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652803	212652803	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	412	513	0	ENST00000342788.4:c.503G>T	p.Arg168Leu	p.R168L	ENST00000342788	NM_005235.2	168	cGg/cTg	4/28	0.584273596615906	3	FACETS	1	0.99	1	0.569	0.542	0.597	CLONAL	1	TRUE	1	0.819843075194076	3		513	1245	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989481	212989481	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	346	428	0	ENST00000342788.4:c.230T>A	p.Leu77Gln	p.L77Q	ENST00000342788	NM_005235.2	77	cTg/cAg	2/28	0.584273596615906	3	FACETS	1	0.976	1	0.526	0.498	0.555	CLONAL	1	TRUE	1	0.819843075194076	3		428	1131	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127327	55127327	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	336	459	1	ENST00000257290.5:c.115G>T	p.Val39Leu	p.V39L	ENST00000257290	NM_006206.4	39	Gtg/Ttg	3/23	1	2	FACETS	0.958	0.909	1	0.958	0.909	1	CLONAL	1	TRUE	1	0.819843075194076	2		460	856	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980311	55980311	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	364	463	0	ENST00000263923.4:c.780G>A	p.Trp260Ter	p.W260*	ENST00000263923	NM_002253.2	260	tgG/tgA	6/30	1	2	FACETS	0.988	0.94	1	0.988	0.94	1	CLONAL	1	TRUE	1	0.819843075194076	2		463	899	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249402	153249402	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs772056210	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	278	419	0	ENST00000281708.4:c.1376G>T	p.Gly459Val	p.G459V	ENST00000281708	NM_033632.3	459	gGg/gTg	9/12	0.377607809024886	1	FACETS	0.619	0.586	0.653	0.619	0.586	0.653	INDETERMINATE	1	TRUE	0	0.819843075194076	1		419	646	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630675	187630675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	406	495	0	ENST00000441802.2:c.307G>A	p.Gly103Arg	p.G103R	ENST00000441802	NM_005245.3	103	Gga/Aga	2/27	0.377607809024886	1	FACETS	0.673	0.643	0.702	0.673	0.643	0.702	INDETERMINATE	1	TRUE	0	0.819843075194076	1		495	869	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294210	1294210	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	291	369	0	ENST00000310581.5:c.791G>C	p.Gly264Ala	p.G264A	ENST00000310581	NM_198253.2	264	gGa/gCa	2/16	0.476615261461364	1	FACETS	0.745	0.709	0.782	0.745	0.709	0.782	INDETERMINATE	1	TRUE	0	0.819843075194076	1		369	562	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158486	26158486	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	114	293	0	ENST00000289316.2:c.89G>T	p.Arg30Leu	p.R30L	ENST00000289316	NM_138720.2	30	cGc/cTc	1/2	0.819843075194076	4	FACETS	0.43	0.386	0.477	0.143	0.128	0.159	SUBCLONAL	1	TRUE	1	0.819843075194076	4		293	1178	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672275	30672275	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	1118	647	0	ENST00000376406.3:c.4685G>C	p.Arg1562Thr	p.R1562T	ENST00000376406	NM_014641.2	1562	aGg/aCg	10/15	0.819843075194076	4	FACETS	1	0.994	1	0.713	0.694	0.731	CLONAL	2	TRUE	1	0.819843075194076	4		647	2321	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675744	30675744	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1562	1247	833	0	ENST00000376406.3:c.2612G>A	p.Arg871Lys	p.R871K	ENST00000376406	NM_014641.2	871	aGa/aAa	8/15	0.819843075194076	4	FACETS	0.985	0.96	1	0.657	0.64	0.674	CLONAL	2	TRUE	1	0.819843075194076	4		833	2809	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680755	30680755	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	853	505	0	ENST00000376406.3:c.964C>G	p.Gln322Glu	p.Q322E	ENST00000376406	NM_014641.2	322	Cag/Gag	5/15	0.819843075194076	4	FACETS	1	0.987	1	0.686	0.665	0.707	CLONAL	2	TRUE	1	0.819843075194076	4		505	1840	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680976	30680976	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	818	493	0	ENST00000376406.3:c.743C>G	p.Ser248Cys	p.S248C	ENST00000376406	NM_014641.2	248	tCt/tGt	5/15	0.819843075194076	4	FACETS	0.998	0.967	1	0.665	0.645	0.686	CLONAL	2	TRUE	1	0.819843075194076	4		493	1819	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681759	30681759	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1396	377	433	0	ENST00000376406.3:c.338A>C	p.His113Pro	p.H113P	ENST00000376406	NM_014641.2	113	cAc/cCc	3/15	0.819843075194076	4	FACETS	0.944	0.893	0.996	0.315	0.297	0.332	CLONAL	1	TRUE	1	0.819843075194076	4		433	1773	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962323	2962323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1266	508	630	0	ENST00000396946.4:c.2214G>T	p.Trp738Cys	p.W738C	ENST00000396946	NM_032415.4	738	tgG/tgT	17/25	0.271632607678703	6	FACETS	0.922	0.881	0.964			1	INDETERMINATE	2	TRUE	NA	0.819843075194076	6		630	1774	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494194	140494194	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	452	540	0	ENST00000288602.6:c.1054G>T	p.Asp352Tyr	p.D352Y	ENST00000288602	NM_004333.4	352	Gat/Tat	8/18	0.408281914175233	4	FACETS	1	0.995	1	0.328	0.312	0.344	INDETERMINATE	1	TRUE	0	0.819843075194076	4		540	1531	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492898	8492898	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	198	433	0	ENST00000356435.5:c.2431C>G	p.Arg811Gly	p.R811G	ENST00000356435		811	Cgc/Ggc	16/35	0.523822650540214	1	FACETS	0.43	0.4	0.461	0.43	0.4	0.461	SUBCLONAL	1	TRUE	0	0.819843075194076	1		433	663	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518054	8518054	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159855	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	304	480	0	ENST00000356435.5:c.1337G>A	p.Gly446Glu	p.G446E	ENST00000356435		446	gGa/gAa	10/35	0.523822650540214	1	FACETS	0.676	0.643	0.71	0.676	0.643	0.71	SUBCLONAL	1	TRUE	0	0.819843075194076	1		480	647	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451365	70451365	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	278	634	0	ENST00000373644.4:c.6205G>C	p.Glu2069Gln	p.E2069Q	ENST00000373644	NM_030625.2	2069	Gag/Cag	12/12	0.50733662215876	1	FACETS	0.362	0.34	0.385	0.362	0.34	0.385	SUBCLONAL	1	TRUE	0	0.819843075194076	1		634	1106	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725060	89725060	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	375	309	0	ENST00000371953.3:c.1043C>G	p.Thr348Arg	p.T348R	ENST00000371953	NM_000314.4	348	aCa/aGa	9/9	0.50733662215876	1	FACETS	0.864	0.83	0.897	0.864	0.83	0.897	CLONAL	1	TRUE	0	0.819843075194076	1		309	625	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154356	2154356	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	413	620	1	ENST00000434045.2:c.572G>C	p.Arg191Pro	p.R191P	ENST00000434045	NM_001127598.1	191	cGt/cCt	5/5	0.227013302977651	1	FACETS	0.543	0.518	0.568	0.543	0.518	0.568	INDETERMINATE	1	TRUE	0	0.819843075194076	1		621	1095	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741416	17741416	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	454	558	0	ENST00000250003.3:c.87C>A	p.Phe29Leu	p.F29L	ENST00000250003	NM_002478.4	29	ttC/ttA	1/3	0.227013302977651	1	FACETS	0.667	0.639	0.694	0.667	0.639	0.694	INDETERMINATE	1	TRUE	0	0.819843075194076	1		558	980	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922222	100922222	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	892	708	0	ENST00000325455.5:c.2290G>T	p.Gly764Ter	p.G764*	ENST00000325455	NM_001202474.3	764	Gga/Tga	5/8	0.584273596615906	3	FACETS	0.96	0.934	0.986	0.96	0.934	0.986	CLONAL	2	TRUE	1	0.819843075194076	3		708	1598	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149241	119149241	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1204	228	530	0	ENST00000264033.4:c.1249C>G	p.Pro417Ala	p.P417A	ENST00000264033	NM_005188.3	417	Cct/Gct	9/16	0.584273596615906	3	FACETS	0.548	0.509	0.588	0.274	0.254	0.294	SUBCLONAL	1	TRUE	1	0.819843075194076	3		530	1432	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434408	49434408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	85	381	0	ENST00000301067.7:c.7145C>T	p.Pro2382Leu	p.P2382L	ENST00000301067	NM_003482.3	2382	cCa/cTa	31/54	0.453705429166547	3	FACETS	0.333	0.293	0.375	0.111	0.097	0.125	INDETERMINATE	1	TRUE	0	0.819843075194076	3		381	879	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623675	28623675	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	371	350	0	ENST00000241453.7:c.883-1G>T		p.X295_splice	ENST00000241453	NM_004119.2	295			0.451453996223798	2	FACETS	0.75	0.721	0.779	0.75	0.721	0.779	INDETERMINATE	2	TRUE	0	0.819843075194076	2		350	603	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346364	73346364	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	134	322	0	ENST00000377767.4:c.1436A>T	p.Asp479Val	p.D479V	ENST00000377767	NM_014953.3	479	gAc/gTc	10/21	0.451453996223798	2	FACETS	0.478	0.435	0.523	0.239	0.217	0.262	INDETERMINATE	1	TRUE	0	0.819843075194076	2		322	684	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435247	110435247	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	164	133	0	ENST00000375856.3:c.3154A>T	p.Thr1052Ser	p.T1052S	ENST00000375856	NM_003749.2	1052	Acc/Tcc	1/2	0.451453996223798	2	FACETS	1	0.992	1	0.733	0.689	0.775	INDETERMINATE	1	TRUE	0	0.819843075194076	2		133	273	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007768	45007768	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	637	396	0	ENST00000558401.1:c.215C>G	p.Ser72Ter	p.S72*	ENST00000558401	NM_004048.2	72	tCa/tGa	2/4	0.819843075194076	2	FACETS	0.995	0.974	1	0.995	0.974	1	CLONAL	2	TRUE	0	0.819843075194076	2		396	781	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222279	2222279	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	524	581	0	ENST00000326181.6:c.563G>A	p.Cys188Tyr	p.C188Y	ENST00000326181	NM_032271.2	188	tGc/tAc	8/21	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.819843075194076	2		581	1124	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789621	3789621	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	387	524	0	ENST00000262367.5:c.4238A>C	p.His1413Pro	p.H1413P	ENST00000262367	NM_004380.2	1413	cAc/cCc	25/31	1	2	FACETS	0.828	0.788	0.869	0.828	0.788	0.869	CLONAL	1	TRUE	1	0.819843075194076	2		524	1140	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679418	29679418	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	528	393	0	ENST00000356175.3:c.7538C>G	p.Thr2513Ser	p.T2513S	ENST00000356175	NM_000267.3	2513	aCt/aGt	50/57	0.578701237037555	2	FACETS	0.862	0.837	0.886	0.862	0.837	0.886	CLONAL	2	TRUE	0	0.819843075194076	2		393	747	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349598	15349598	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	703	341	0	ENST00000263377.2:c.3976G>C	p.Glu1326Gln	p.E1326Q	ENST00000263377	NM_058243.2	1326	Gag/Cag	19/20	0.801567577479189	4	FACETS	0.963	0.937	0.989	0.963	0.937	0.989	CLONAL	3	TRUE	1	0.819843075194076	4		341	1080	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42790961	42790961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	1403	639	1	ENST00000575354.2:c.106C>T	p.Pro36Ser	p.P36S	ENST00000575354	NM_015125.3	36	Cct/Tct	2/20	0.801567577479189	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	1	0.819843075194076	4		640	2065	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546782	9546782	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	436	275	0	ENST00000353224.5:c.1240C>A	p.Pro414Thr	p.P414T	ENST00000353224	NM_177990.2	414	Ccc/Acc	5/10	0.382767740328409	6	FACETS	0.833	0.796	0.871			1	INDETERMINATE	3	TRUE	NA	0.819843075194076	6		275	1123	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106917	27106917	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	843	347	0	ENST00000324856.7:c.6532del	p.Asp2178ThrfsTer22	p.D2178Tfs*22	ENST00000324856	NM_006015.4	2176	caG/ca	20/20	0.793575740167661	3	FACETS	0.866	0.848	0.884	0.866	0.848	0.884	CLONAL	3	TRUE	0	0.819843075194076	3		347	1116	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8733839	8733840	+	missense_variant	Missense_Mutation	DNP	AC	AC	CT	novel	NA	P-0010916-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	154	267	0	ENST00000356435.5:c.4_5delinsAG	p.Val2Arg	p.V2R	ENST00000356435		2	GTg/AGg	1/35	0.523822650540214	1	FACETS	0.594	0.551	0.638	0.594	0.551	0.638	SUBCLONAL	1	TRUE	0	0.819843075194076	1		267	373	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434094	121434094	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	45	704	1	ENST00000257555.6:c.985G>T	p.Glu329Ter	p.E329*	ENST00000257555		329	Gag/Tag	5/10	1	2	FACETS	0.485	0.406	0.571	0.485	0.406	0.571	SUBCLONAL	1	TRUE	1	0.289300395246579	2		705	642	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641022	23641022	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs370908330	NA	P-0010920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	15	505	0	ENST00000261584.4:c.2453T>C	p.Phe818Ser	p.F818S	ENST00000261584	NM_024675.3	818	tTt/tCt	5/13	0.335076673752096	1	FACETS	0.303	0.221	0.401	0.303	0.221	0.401	SUBCLONAL	1	TRUE	0	0.335076673752096	1		505	246	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880219	37880220	+	missense_variant	Missense_Mutation	DNP	TT	TT	CC	rs121913469	NA	P-0010927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	505	760	0	ENST00000269571.5:c.2263_2264delinsCC	p.Leu755Pro	p.L755P	ENST00000269571		755	TTg/CCg	19/27	0.263148299375231	4	FACETS	0.851	0.815	0.888	0.851	0.815	0.888	CLONAL	3	TRUE	1	0.36497661780011	4		760	1479	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527973	157527973	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	76	214	0	ENST00000346085.5:c.5698A>G	p.Ser1900Gly	p.S1900G	ENST00000346085	NM_020732.3	1900	Agc/Ggc	20/20	0.36497661780011	3	FACETS	1	0.887	1	0.505	0.444	0.57	CLONAL	1	TRUE	1	0.36497661780011	3		214	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574032	7574032	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	197	592	0	ENST00000269305.4:c.995T>G	p.Ile332Ser	p.I332S	ENST00000269305	NM_001126112.2	332	aTc/aGc	10/11	0.36497661780011	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.36497661780011	1		592	832	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858256	59858256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356014648	NA	P-0010927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	252	570	0	ENST00000259008.2:c.1739C>T	p.Ser580Leu	p.S580L	ENST00000259008	NM_032043.2	580	tCa/tTa	12/20	0.36497661780011	3	FACETS	1	0.989	1	0.647	0.605	0.692	CLONAL	1	TRUE	1	0.36497661780011	3		570	1261	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39729894	39729895	+	missense_variant	Missense_Mutation	DNP	AG	AG	TT	novel	NA	P-0010927-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	114	597	1	ENST00000361337.2:c.1209_1210delinsTT	p.Glu403_Val404delinsAspPhe	p.E403_V404delinsDF	ENST00000361337	NM_003286.2	403	gaAGtc/gaTTtc	13/21	1	2	FACETS	0.832	0.749	0.919	0.832	0.749	0.919	CLONAL	1	TRUE	1	0.36497661780011	2		598	751	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0010943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	226	673	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.918067835140093	1	FACETS	0.986	0.954	1	0.986	0.954	1	CLONAL	1	TRUE	0	0.92570044661457	1		673	266	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372311	55372311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1359676095	NA	P-0010943-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	215	224	0	ENST00000297316.4:c.1001C>T	p.Ser334Leu	p.S334L	ENST00000297316	NM_022454.3	334	tCg/tTg	2/2	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.92570044661457	2		224	440	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0010946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	266	617	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.434789923312789	2	FACETS	0.9	0.85	0.95	0.9	0.85	0.95	CLONAL	2	TRUE	0	0.464621624288128	2		617	636	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218502	5218502	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	254	704	0	ENST00000357368.4:c.3977A>T	p.Asn1326Ile	p.N1326I	ENST00000357368	NM_002850.3	1326	aAc/aTc	25/38	0.464621624288128	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.464621624288128	1		704	709	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438024	49438032	+	inframe_deletion	In_Frame_Del	DEL	GCAGCAGGC	GCAGCAGGC	-	novel	NA	P-0010946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	219	484	0	ENST00000301067.7:c.5139_5147del	p.Pro1714_Ala1716del	p.P1714_A1716del	ENST00000301067	NM_003482.3	1713	ggGCCTGCTGCa/gga	21/54	0.187603459453805	1	FACETS	1	0.99	1	1	0.99	1	INDETERMINATE	1	TRUE	0	0.464621624288128	1		484	559	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068344	26068364	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTCACCTGATTTCTTTTAGT	ACTCACCTGATTTCTTTTAGT	-	novel	NA	P-0010946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	48	395	0	ENST00000435504.4:c.126_140+6del		p.X42_splice	ENST00000435504		42		2/13	0.360190051951826	1	FACETS	0.437	0.37	0.51	0.437	0.37	0.51	SUBCLONAL	1	TRUE	0	0.464621624288128	1		395	363	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207078	1207078	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	275	486	3	ENST00000326873.7:c.166G>T	p.Gly56Trp	p.G56W	ENST00000326873	NM_000455.4	56	Ggg/Tgg	1/10	0.342242838091502	2	FACETS	0.942	0.888	0.998	0.942	0.888	0.998	CLONAL	2	TRUE	0	0.345746681009451	2		489	844	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148875	119148875	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs397517076	NA	P-0010947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	161	233	1	ENST00000264033.4:c.1096-1G>T		p.X366_splice	ENST00000264033	NM_005188.3	366			0.342242838091502	2	FACETS	0.982	0.909	1	0.982	0.909	1	CLONAL	2	TRUE	0	0.345746681009451	2		234	474	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660660	227660660	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	113	365	0	ENST00000305123.5:c.2795G>T	p.Arg932Ile	p.R932I	ENST00000305123	NM_005544.2	932	aGa/aTa	1/2	1	2	FACETS	0.883	0.795	0.976	0.883	0.795	0.976	CLONAL	1	TRUE	1	0.345746681009451	2		365	740	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794461	242794461	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	105	359	0	ENST00000334409.5:c.481A>T	p.Arg161Trp	p.R161W	ENST00000334409	NM_005018.2	161	Agg/Tgg	3/5	1	2	FACETS	0.83	0.744	0.921	0.83	0.744	0.921	CLONAL	1	TRUE	1	0.345746681009451	2		359	732	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72861919	72861919	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	122	416	0	ENST00000325599.8:c.963G>T	p.Met321Ile	p.M321I	ENST00000325599	NM_018130.2	321	atG/atT	9/11	1	2	FACETS	0.923	0.834	1	0.923	0.834	1	CLONAL	1	TRUE	1	0.345746681009451	2		416	765	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2972201	2972201	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	127	427	2	ENST00000396946.4:c.1538C>A	p.Pro513His	p.P513H	ENST00000396946	NM_032415.4	513	cCc/cAc	11/25	1	2	FACETS	0.914	0.828	1	0.914	0.828	1	CLONAL	1	TRUE	1	0.345746681009451	2		429	804	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319853	8319853	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs747302391	NA	P-0010947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	138	555	0	ENST00000356435.5:c.5648G>T	p.Arg1883Leu	p.R1883L	ENST00000356435		1883	cGa/cTa	34/35	0.345746681009451	1	FACETS	0.887	0.809	0.97	0.887	0.809	0.97	CLONAL	1	TRUE	0	0.345746681009451	1		555	744	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69456232	69456232	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	238	420	0	ENST00000227507.2:c.151G>A	p.Glu51Lys	p.E51K	ENST00000227507	NM_053056.2	51	Gag/Aag	1/5	0.337822023789683	3	FACETS	0.966	0.904	1	0.966	0.904	1	CLONAL	2	TRUE	1	0.345746681009451	3		420	836	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2645794	2645794	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	142	463	0	ENST00000342085.4:c.1344G>T	p.Trp448Cys	p.W448C	ENST00000342085	NM_002613.4	448	tgG/tgT	12/14	1	2	FACETS	0.924	0.842	1	0.924	0.842	1	CLONAL	1	TRUE	1	0.345746681009451	2		463	889	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992190	72992190	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	159	578	0	ENST00000268489.5:c.1855C>G	p.His619Asp	p.H619D	ENST00000268489	NM_006885.3	619	Cat/Gat	2/10	1	2	FACETS	0.878	0.804	0.956	0.878	0.804	0.956	CLONAL	1	TRUE	1	0.345746681009451	2		578	1047	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602442	10602442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1014914854	NA	P-0010947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	246	372	0	ENST00000171111.5:c.1136G>A	p.Gly379Asp	p.G379D	ENST00000171111	NM_203500.1	379	gGc/gAc	3/6	0.342242838091502	2	FACETS	0.924	0.867	0.982	0.924	0.867	0.982	CLONAL	2	TRUE	0	0.345746681009451	2		372	770	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138491	11138491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	295	421	0	ENST00000358026.2:c.3247G>A	p.Glu1083Lys	p.E1083K	ENST00000358026	NM_001128849.1	1083	Gag/Aag	24/36	0.342242838091502	2	FACETS	0.971	0.916	1	0.971	0.916	1	CLONAL	2	TRUE	0	0.345746681009451	2		421	879	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984908	9984909	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0010947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	150	592	0	ENST00000330684.3:c.1056_1057delinsTT	p.Glu352_Glu353delinsAspTer	p.E352_E353delinsD*	ENST00000330684	NM_001134407.1	352	gaGGaa/gaTTaa	4/13	1	2	FACETS	0.878	0.802	0.958	0.878	0.802	0.958	CLONAL	1	TRUE	1	0.345746681009451	2		592	988	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262370	16262370	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010954-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	17	162	0	ENST00000375759.3:c.9636del	p.Ala3213ArgfsTer5	p.A3213Rfs*5	ENST00000375759	NM_015001.2	3212	gCc/gc	11/15	1	2	FACETS	0.837	0.625	1	0.837	0.625	1	CLONAL	1	TRUE	1	0.14	2		162	290	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0010971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	87	532	2	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.938	0.828	1	0.938	0.828	1	CLONAL	1	TRUE	1	0.17	2		534	1091	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582169	189582169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908836	NA	P-0010971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	94	494	2	ENST00000264731.3:c.728G>A	p.Arg243Gln	p.R243Q	ENST00000264731	NM_003722.4	243	cGg/cAg	5/14	1	2	FACETS	0.952	0.844	1	0.952	0.844	1	CLONAL	1	TRUE	1	0.17	2		496	1162	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0010973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	238	503	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.337793230060647	2		503	1214	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119789	70119789	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	435	619	0	ENST00000245479.2:c.791G>C	p.Arg264Thr	p.R264T	ENST00000245479	NM_000346.3	264	aGa/aCa	3/3	0.337793230060647	3	FACETS	0.91	0.865	0.955			1	CLONAL	2	TRUE	NA	0.337793230060647	3		619	1655	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462920	120462920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372061331	NA	P-0010973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	255	462	1	ENST00000256646.2:c.5411C>T	p.Ser1804Leu	p.S1804L	ENST00000256646	NM_024408.3	1804	tCg/tTg	30/34	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.337793230060647	2		463	1173	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489186	2489186	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755773744	NA	P-0010973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1330	173	682	0	ENST00000355716.4:c.91G>A	p.Gly31Arg	p.G31R	ENST00000355716	NM_003820.2	31	Gga/Aga	2/8	1	2	FACETS	0.682	0.625	0.741	0.682	0.625	0.741	SUBCLONAL	1	TRUE	1	0.337793230060647	2		682	1503	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941097	36941097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1906	215	917	0	ENST00000361632.4:c.242G>A	p.Gly81Glu	p.G81E	ENST00000361632		81	gGg/gAg	3/16	1	2	FACETS	0.6	0.555	0.647	0.6	0.555	0.647	SUBCLONAL	1	TRUE	1	0.337793230060647	2		917	2121	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462410	89462410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1280	99	381	0	ENST00000336596.2:c.1882G>A	p.Gly628Arg	p.G628R	ENST00000336596	NM_005233.5	628	Gga/Aga	10/17	0.337793230060647	4	FACETS	0.569	0.506	0.636			1	SUBCLONAL	1	TRUE	NA	0.337793230060647	4		381	1379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578474	+	inframe_deletion	In_Frame_Del	DEL	CCGGGC	CCGGGC	-	novel	NA	P-0010973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	215	469	0	ENST00000269305.4:c.456_461del	p.Pro153_Gly154del	p.P153_G154del	ENST00000269305	NM_001126112.2	152	ccGCCCGGc/ccc	5/11	0.337793230060647	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.337793230060647	1		469	985	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667589	29667589	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	418	693	0	ENST00000356175.3:c.6926del	p.Leu2309CysfsTer16	p.L2309Cfs*16	ENST00000356175	NM_000267.3	2309	Ttg/tg	46/57	0.317467610133208	2	FACETS	0.854	0.812	0.896	0.854	0.812	0.896	CLONAL	2	TRUE	0	0.337793230060647	2		693	1449	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971123	21971123	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010973-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	124	262	0	ENST00000304494.5:c.235del	p.Thr79ProfsTer67	p.T79Pfs*67	ENST00000304494	NM_000077.4	79	Acc/cc	2/3	0.337793230060647	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.337793230060647	1		262	586	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662364	227662364	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747409858	NA	P-0010978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	209	416	0	ENST00000305123.5:c.1091G>A	p.Arg364Gln	p.R364Q	ENST00000305123	NM_005544.2	364	cGg/cAg	1/2	NA	2	FACETS	1	0.938	1			1	INDETERMINATE	2	TRUE	NA	0.410388211207626	2		416	509	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0010982-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	86	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.242493257883378	5	FACETS	1	0.958	1	0.39	0.346	0.437	INDETERMINATE	1	TRUE	2	0.513674536477302	5		249	507	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0010982-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	1364	366	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.513674536477302	9	FACETS	0.985	0.965	1	0.985	0.965	1	CLONAL	7	TRUE	2	0.513674536477302	9		366	2156	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862749	9862749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150316865	NA	P-0010982-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	220	585	4	ENST00000330684.3:c.2554G>A	p.Val852Met	p.V852M	ENST00000330684	NM_001134407.1	852	Gtg/Atg	12/13	0.108874958999642	5	FACETS	0.77	0.716	0.825			1	INDETERMINATE	2	TRUE	NA	0.513674536477302	5		589	985	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149057	61149057	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs749726149	NA	P-0010982-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1481	280	657	0	ENST00000295025.8:c.1247C>G	p.Ala416Gly	p.A416G	ENST00000295025	NM_002908.2	416	gCc/gGc	11/11	0.337752594348315	5	FACETS	1	0.978	1	0.365	0.342	0.39	CLONAL	1	TRUE	2	0.513674536477302	5		657	1761	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459558	50459558	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010982-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	54	328	0	ENST00000331340.3:c.847C>A	p.Leu283Ile	p.L283I	ENST00000331340	NM_006060.4	283	Ctt/Att	7/8	0.439886677530594	4	FACETS	0.44	0.375	0.512	0.147	0.125	0.171	SUBCLONAL	1	TRUE	1	0.513674536477302	4		328	723	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	94	528	2				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		530	270	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0011015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1253	40	646	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.347	0.287	0.415	0.347	0.287	0.415	SUBCLONAL	1	TRUE	1	0.178112680192736	2		646	1293	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0011015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	97	422	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	0.178112680192736	2		422	908	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11264637	11264637	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	47	458	0	ENST00000361445.4:c.3925G>C	p.Ala1309Pro	p.A1309P	ENST00000361445	NM_004958.3	1309	Gcc/Ccc	26/58	1	2	FACETS	0.572	0.481	0.673	0.572	0.481	0.673	SUBCLONAL	1	TRUE	1	0.178112680192736	2		458	923	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690262	47690262	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	67	479	0	ENST00000233146.2:c.1479G>T	p.Gln493His	p.Q493H	ENST00000233146	NM_000251.2	493	caG/caT	9/16	1	2	FACETS	0.889	0.771	1	0.889	0.771	1	CLONAL	1	TRUE	1	0.178112680192736	2		479	846	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356269	66356269	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	65	499	0	ENST00000273854.3:c.1228G>T	p.Gly410Cys	p.G410C	ENST00000273854	NM_004439.5	410	Ggt/Tgt	5/18	1	2	FACETS	0.805	0.696	0.923	0.805	0.696	0.923	CLONAL	1	TRUE	1	0.178112680192736	2		499	907	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86681121	86681121	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011015-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	75	343	0	ENST00000274376.6:c.2762C>A	p.Ser921Tyr	p.S921Y	ENST00000274376	NM_002890.2	921	tCt/tAt	22/25	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.178112680192736	2		343	687	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259213	16259213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011018-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	79	278	0	ENST00000375759.3:c.6478C>T	p.Pro2160Ser	p.P2160S	ENST00000375759	NM_015001.2	2160	Cca/Tca	11/15	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.225369169489767	2		278	523	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524401	187524401	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0011018-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	62	343	0	ENST00000441802.2:c.11279C>G	p.Ser3760Ter	p.S3760*	ENST00000441802	NM_005245.3	3760	tCa/tGa	19/27	0.225369169489767	2	FACETS	0.653	0.563	0.752	0.327	0.281	0.376	SUBCLONAL	1	TRUE	0	0.225369169489767	2		343	842	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845724	68845724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011018-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	107	440	1	ENST00000261769.5:c.970G>A	p.Gly324Arg	p.G324R	ENST00000261769	NM_004360.3	324	Gga/Aga	7/16	0.225369169489767	2	FACETS	1	0.92	1	0.516	0.462	0.573	CLONAL	1	TRUE	0	0.225369169489767	2		441	921	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0011034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	104	313	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	0.274150934954263	1	FACETS	0.876	0.785	0.973	0.876	0.785	0.973	CLONAL	1	TRUE	0	0.285713738794312	1		313	712	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955514	48955514	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0011034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	119	374	1	ENST00000267163.4:c.1630A>T	p.Arg544Ter	p.R544*	ENST00000267163	NM_000321.2	544	Aga/Tga	17/27	0.274150934954263	1	FACETS	0.807	0.728	0.891	0.807	0.728	0.891	CLONAL	1	TRUE	0	0.285713738794312	1		375	885	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804985	43804985	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs757759824	NA	P-0011034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	185	417	0	ENST00000372470.3:c.435C>A	p.Ser145Arg	p.S145R	ENST00000372470	NM_005373.2	145	agC/agA	4/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.285713738794312	2		417	1159	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085626	16085626	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	86	317	0	ENST00000281043.3:c.802G>C	p.Asp268His	p.D268H	ENST00000281043	NM_005378.4	268	Gat/Cat	3/3	1	2	FACETS	0.715	0.632	0.805	0.715	0.632	0.805	SUBCLONAL	1	TRUE	1	0.285713738794312	2		317	842	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878998	151878998	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	219	424	0	ENST00000262189.6:c.5947G>A	p.Gly1983Ser	p.G1983S	ENST00000262189	NM_170606.2	1983	Ggc/Agc	36/59	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.285713738794312	2		424	1263	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137706	64137706	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	171	482	0	ENST00000334205.4:c.1807C>A	p.Leu603Met	p.L603M	ENST00000334205	NM_003942.2	603	Ctg/Atg	15/17	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.285713738794312	2		482	1171	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209348	133209348	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	193	518	0	ENST00000320574.5:c.6038A>T	p.Asp2013Val	p.D2013V	ENST00000320574	NM_006231.2	2013	gAc/gTc	44/49	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.285713738794312	2		518	1292	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820696	3820696	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	327	427	0	ENST00000262367.5:c.2755C>T	p.Gln919Ter	p.Q919*	ENST00000262367	NM_004380.2	919	Cag/Tag	14/31	0.269447036465545	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.285713738794312	2		427	1102	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290943	15290943	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1333	218	524	0	ENST00000263388.2:c.3267G>T	p.Leu1089Phe	p.L1089F	ENST00000263388	NM_000435.2	1089	ttG/ttT	20/33	1	2	FACETS	0.984	0.912	1	0.984	0.912	1	CLONAL	1	TRUE	1	0.285713738794312	2		524	1551	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655262	45655262	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	129	410	0	ENST00000407780.3:c.590A>T	p.Tyr197Phe	p.Y197F	ENST00000407780	NM_001283052.1	197	tAt/tTt	4/7	0.269447036465545	2	FACETS	0.902	0.817	0.992	0.451	0.408	0.496	CLONAL	1	TRUE	0	0.285713738794312	2		410	1001	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0011040-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	100	616	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	0.948	0.844	1	0.948	0.844	1	CLONAL	1	TRUE	1	0.17	2		616	1241	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0011040-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	69	550	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.846	0.734	0.966	0.846	0.734	0.966	CLONAL	1	TRUE	1	0.17	2		550	960	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771330	68771330	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555509636	NA	P-0011040-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	45	249	0	ENST00000261769.5:c.12G>A	p.Trp4Ter	p.W4*	ENST00000261769	NM_004360.3	4	tgG/tgA	1/16	0.119364905844937	1	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	0	0.17	1		249	451	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012205	16012205	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011040-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	75	323	0	ENST00000268712.3:c.2077G>T	p.Glu693Ter	p.E693*	ENST00000268712	NM_006311.3	693	Gag/Tag	19/46	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.17	2		323	800	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099008	27099008	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	72	404	0	ENST00000324856.7:c.3424C>T	p.Gln1142Ter	p.Q1142*	ENST00000324856	NM_006015.4	1142	Cag/Tag	13/20	1	2	FACETS	0.442	0.388	0.499	0.442	0.388	0.499	SUBCLONAL	1	TRUE	1	0.928643440693408	2		404	351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0011078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1458	45	713	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	0.461	0.385	0.545	0.461	0.385	0.545	SUBCLONAL	1	TRUE	1	0.13	2		713	1503	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158402	26158402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778040224	NA	P-0011088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	397	397	0	ENST00000289316.2:c.5C>T	p.Pro2Leu	p.P2L	ENST00000289316	NM_138720.2	2	cCt/cTt	1/2	1	2	FACETS	0.992	0.943	1	0.992	0.943	1	CLONAL	1	TRUE	1	0.639993931864518	2		397	1251	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692908	89692908	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	371	292	1	ENST00000371953.3:c.392C>A	p.Thr131Asn	p.T131N	ENST00000371953	NM_000314.4	131	aCt/aAt	5/9	0.639993931864518	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.639993931864518	1		293	760	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225367686	225367698	+	frameshift_variant	Frame_Shift_Del	DEL	GTTGCCTGTAGAT	GTTGCCTGTAGAT	-	novel	NA	P-0011088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	380	494	0	ENST00000264414.4:c.1469_1481del	p.His490LeufsTer5	p.H490Lfs*5	ENST00000264414	NM_003590.4	490	cATCTACAGGCAACt/ct	10/16	1	2	FACETS	0.815	0.773	0.858	0.815	0.773	0.858	CLONAL	1	TRUE	1	0.639993931864518	2		494	1457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0011093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	361	550	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.775497782924314	1	FACETS	0.95	0.912	0.987	0.95	0.912	0.987	CLONAL	1	TRUE	0	0.775497782924314	1		550	600	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795609	42795609	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	334	910	1	ENST00000575354.2:c.2694del	p.Ala900ProfsTer24	p.A900Pfs*24	ENST00000575354	NM_015125.3	897	Ccc/cc	10/20	0.134024443522397	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.775497782924314	0		911	1035	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0011105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	251	372	1	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	1	2	FACETS	0.924	0.868	0.981	0.924	0.868	0.981	CLONAL	1	TRUE	1	0.705550396985832	2		373	770	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0011105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	128	316	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	0.805	0.734	0.877	0.805	0.734	0.877	CLONAL	1	TRUE	1	0.705550396985832	2		316	451	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309858	104309858	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011105-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	220	284	0	ENST00000369902.3:c.449A>T	p.Gln150Leu	p.Q150L	ENST00000369902	NM_016169.3	150	cAg/cTg	3/12	1	2	FACETS	0.761	0.709	0.813	0.761	0.709	0.813	SUBCLONAL	1	TRUE	1	0.705550396985832	2		284	820	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0011124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	225	646	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.326210149939104	2	FACETS	1	0.992	1	0.732	0.684	0.781	CLONAL	1	TRUE	0	0.416617505875524	2		646	738	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0011124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	101	422	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.416617505875524	2		422	401	SUCCESS
APC	324	MSKCC	GRCh37	5	112175162	112175162	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561588104	NA	P-0011124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	41	140	1	ENST00000257430.4:c.3871C>T	p.Gln1291Ter	p.Q1291*	ENST00000257430	NM_000038.5	1291	Cag/Tag	16/16	NA	2	FACETS	1	0.957	1			1	INDETERMINATE	1	TRUE	NA	0.416617505875524	2		141	139	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97934342	97934342	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	119	396	0	ENST00000289081.3:c.433T>G	p.Tyr145Asp	p.Y145D	ENST00000289081	NM_000136.2	145	Tac/Gac	5/15	0.261813703386393	4	FACETS	0.883	0.803	0.968	0.883	0.803	0.968	CLONAL	2	TRUE	2	0.416617505875524	4		396	458	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161391	2161391	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	104	477	0	ENST00000434045.2:c.136C>T	p.Arg46Cys	p.R46C	ENST00000434045	NM_001127598.1	46	Cgc/Tgc	2/5	0.307569326629745	3	FACETS	0.738	0.661	0.821	0.369	0.33	0.411	SUBCLONAL	1	TRUE	1	0.416617505875524	3		477	817	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243551	46243551	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	69	266	0	ENST00000334344.6:c.1904C>A	p.Ser635Ter	p.S635*	ENST00000334344	NM_152641.2	635	tCa/tAa	14/21	0.318288950738723	4	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.416617505875524	4		266	314	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0011129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	780	422	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.803675950992364	5	FACETS	0.923	0.906	0.938	0.923	0.906	0.938	CLONAL	5	TRUE	0	0.803675950992364	5		422	928	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441974	6441974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	312	193	0	ENST00000356142.4:c.533C>T	p.Ala178Val	p.A178V	ENST00000356142	NM_018890.3	178	gCg/gTg	7/7	0.803675950992364	5	FACETS	0.952	0.901	1	0.635	0.601	0.67	CLONAL	2	TRUE	2	0.803675950992364	5		193	899	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935254	36935254	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	358	435	0	ENST00000361632.4:c.1473G>T	p.Lys491Asn	p.K491N	ENST00000361632		491	aaG/aaT	10/16	1	2	FACETS	0.851	0.808	0.895	0.851	0.808	0.895	CLONAL	1	TRUE	1	0.803675950992364	2		435	1047	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623217	52623217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558843390	NA	P-0011129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	203	255	0	ENST00000394830.3:c.2834G>A	p.Arg945His	p.R945H	ENST00000394830	NM_018313.4	945	cGc/cAc	19/30	0.648332721613112	4	FACETS	0.872	0.808	0.938	0.436	0.404	0.469	CLONAL	1	TRUE	2	0.803675950992364	4		255	1045	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247459	71247459	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	158	247	0	ENST00000318789.4:c.74A>G	p.His25Arg	p.H25R	ENST00000318789	NM_032682.5	25	cAc/cGc	6/21	0.648332721613112	4	FACETS	0.706	0.646	0.768	0.353	0.323	0.384	SUBCLONAL	1	TRUE	2	0.803675950992364	4		247	1005	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921554	178921554	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	188	177	0	ENST00000263967.3:c.1036G>T	p.Val346Leu	p.V346L	ENST00000263967	NM_006218.2	346	Gta/Tta	5/21	0.652337803505183	2	FACETS	0.827	0.784	0.868	0.827	0.784	0.868	CLONAL	2	TRUE	0	0.803675950992364	2		177	283	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335649	81335649	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	541	215	0	ENST00000222390.5:c.1711G>T	p.Val571Leu	p.V571L	ENST00000222390	NM_000601.4	571	Gta/Tta	15/18	0.803675950992364	5	FACETS	0.877	0.844	0.909	0.877	0.844	0.909	CLONAL	3	TRUE	2	0.803675950992364	5		215	1129	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404587	8404587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1309	370	310	0	ENST00000356435.5:c.4160C>T	p.Ala1387Val	p.A1387V	ENST00000356435		1387	gCg/gTg	25/35	0.803675950992364	7	FACETS	0.825	0.781	0.871	0.413	0.39	0.436	CLONAL	2	TRUE	3	0.803675950992364	7		310	1679	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59934463	59934463	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	384	287	0	ENST00000259008.2:c.335G>T	p.Ser112Ile	p.S112I	ENST00000259008	NM_032043.2	112	aGc/aTc	4/20	0.803675950992364	5	FACETS	0.905	0.86	0.95	0.603	0.573	0.633	CLONAL	2	TRUE	2	0.803675950992364	5		287	1165	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856340	45856340	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0011129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	206	337	0	ENST00000391945.4:c.1831+1G>T		p.X611_splice	ENST00000391945	NM_000400.3	611			0.638594872552758	3	FACETS	0.822	0.764	0.883	0.411	0.382	0.442	CLONAL	1	TRUE	1	0.803675950992364	3		337	874	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624936	9624936	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	416	327	0	ENST00000353224.5:c.41C>A	p.Pro14Gln	p.P14Q	ENST00000353224	NM_177990.2	14	cCg/cAg	3/10	0.670363543253026	3	FACETS	0.871	0.835	0.907	0.871	0.835	0.907	CLONAL	2	TRUE	1	0.803675950992364	3		327	833	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012761	36012761	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	59	116	0	ENST00000358208.4:c.205T>G	p.Ser69Ala	p.S69A	ENST00000358208		69	Tcc/Gcc	2/12	0.670363543253026	3	FACETS	0.578	0.5	0.663	0.289	0.25	0.332	SUBCLONAL	1	TRUE	1	0.803675950992364	3		116	356	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129788	108129797	+	frameshift_variant	Frame_Shift_Del	DEL	ATTTGTAAAA	ATTTGTAAAA	TTTTAT	novel	NA	P-0011129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	241	178	0	ENST00000278616.4:c.2452_2461delinsTTTTAT	p.Ile818PhefsTer4	p.I818Ffs*4	ENST00000278616	NM_000051.3	818	ATTTGTAAAAgt/TTTTATgt	16/63	0.638594872552758	3	FACETS	0.816	0.771	0.862	0.816	0.771	0.862	CLONAL	2	TRUE	1	0.803675950992364	3		178	515	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	203	528	2				ENST00000310581	NM_198253.2	-/1132			0.235764308727911	3	FACETS	0.904	0.845	0.963	0.904	0.845	0.963	INDETERMINATE	2	TRUE	1	0.556582837485867	3		530	516	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0011141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	41	234	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.512	0.428	0.603	0.512	0.428	0.603	SUBCLONAL	1	TRUE	1	0.556582837485867	2		234	288	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578223	7578223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1173	32	536	0	ENST00000269305.4:c.626G>A	p.Arg209Lys	p.R209K	ENST00000269305	NM_001126112.2	209	aGa/aAa	6/11	0.294914417492419	1	FACETS	0.069	0.055	0.084	0.069	0.055	0.084	INDETERMINATE	1	TRUE	0	0.556582837485867	1		536	1205	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0011141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	38	362	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.294914417492419	1	FACETS	0.109	0.09	0.131	0.109	0.09	0.131	INDETERMINATE	1	TRUE	0	0.556582837485867	1		362	902	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349964	15349964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1411701353	NA	P-0011141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	138	395	0	ENST00000263377.2:c.3688G>A	p.Ala1230Thr	p.A1230T	ENST00000263377	NM_058243.2	1230	Gcc/Acc	18/20	1	2	FACETS	0.528	0.479	0.578	0.528	0.479	0.578	SUBCLONAL	1	TRUE	1	0.556582837485867	2		395	940	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180360	38180360	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	166	538	0	ENST00000396334.3:c.208G>A	p.Glu70Lys	p.E70K	ENST00000396334	NM_002468.4	70	Gag/Aag	1/5	1	2	FACETS	0.447	0.41	0.487	0.447	0.41	0.487	SUBCLONAL	1	TRUE	1	0.556582837485867	2		538	1333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579506	7579506	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	47	420	0	ENST00000269305.4:c.181G>C	p.Asp61His	p.D61H	ENST00000269305	NM_001126112.2	61	Gat/Cat	4/11	0.294914417492419	1	FACETS	0.144	0.121	0.17	0.144	0.121	0.17	INDETERMINATE	1	TRUE	0	0.556582837485867	1		420	847	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501473	149501473	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	117	865	0	ENST00000261799.4:c.2314A>G	p.Met772Val	p.M772V	ENST00000261799	NM_002609.3	772	Atg/Gtg	16/23	0.241723943580107	4	FACETS	0.85	0.764	0.942	0.425	0.382	0.471	CLONAL	1	TRUE	2	0.267595115912906	4		865	1304	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30302733	30302733	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0011151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	109	122	1	ENST00000322652.5:c.823+1G>A		p.X275_splice	ENST00000322652	NM_015355.2	275			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		123	123	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541604	29541607	+	splice_donor_variant,intron_variant	Splice_Site	DEL	GTAA	GTAA	-	rs1555612294	NA	P-0011151-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	209	227	0	ENST00000356175.3:c.1527+4_1527+7del		p.X509_splice	ENST00000356175	NM_000267.3	509			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		227	252	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0011157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	142	422	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.194459998276238	3	FACETS	0.847	0.771	0.927	0.847	0.771	0.927	CLONAL	2	TRUE	1	0.194459998276238	3		422	946	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005117	150005117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56348064	NA	P-0011157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	53	369	0	ENST00000253339.5:c.1108C>T	p.Arg370Trp	p.R370W	ENST00000253339		370	Cgg/Tgg	3/7	1	2	FACETS	0.75	0.638	0.873	0.75	0.638	0.873	SUBCLONAL	1	TRUE	1	0.194459998276238	2		369	727	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495510	149495510	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0011157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	93	575	0	ENST00000261799.4:c.3138-1G>T		p.X1046_splice	ENST00000261799	NM_002609.3	1046			0.158664881154168	1	FACETS	0.89	0.79	0.998	0.89	0.79	0.998	CLONAL	1	TRUE	0	0.194459998276238	1		575	970	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90995024	90995024	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	61	354	1	ENST00000265433.3:c.97A>T	p.Ile33Phe	p.I33F	ENST00000265433	NM_002485.4	33	Att/Ttt	2/16	1	2	FACETS	0.66	0.568	0.762	0.66	0.568	0.762	SUBCLONAL	1	TRUE	1	0.194459998276238	2		355	950	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399273	139399273	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	47	414	0	ENST00000277541.6:c.4870G>T	p.Glu1624Ter	p.E1624*	ENST00000277541	NM_017617.3	1624	Gag/Tag	26/34	1	2	FACETS	0.639	0.537	0.751	0.639	0.537	0.751	SUBCLONAL	1	TRUE	1	0.194459998276238	2		414	757	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742873	17742873	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	81	304	0	ENST00000250003.3:c.781A>T	p.Thr261Ser	p.T261S	ENST00000250003	NM_002478.4	261	Acc/Tcc	3/3	1	2	FACETS	0.771	0.681	0.868	1	0.978	1	SUBCLONAL	2	TRUE	1	0.194459998276238	2		304	540	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307610	118307610	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	77	200	0	ENST00000534358.1:c.383G>T	p.Arg128Leu	p.R128L	ENST00000534358	NM_005933.3	128	cGg/cTg	1/36	1	2	FACETS	1	0.912	1	1	0.984	1	CLONAL	2	TRUE	1	0.194459998276238	2		200	381	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895610	28895610	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	147	443	0	ENST00000282397.4:c.3164G>A	p.Arg1055Lys	p.R1055K	ENST00000282397	NM_002019.4	1055	aGa/aAa	23/30	1	2	FACETS	0.768	0.701	0.839	1	0.988	1	SUBCLONAL	2	TRUE	1	0.194459998276238	2		443	984	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895675	28895675	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	148	484	1	ENST00000282397.4:c.3099C>A	p.Asn1033Lys	p.N1033K	ENST00000282397	NM_002019.4	1033	aaC/aaA	23/30	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.194459998276238	2		485	1091	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820681	3820681	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	75	429	0	ENST00000262367.5:c.2770G>T	p.Ala924Ser	p.A924S	ENST00000262367	NM_004380.2	924	Gcc/Tcc	14/31	1	2	FACETS	0.932	0.815	1	0.932	0.815	1	CLONAL	1	TRUE	1	0.194459998276238	2		429	828	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313358	30313358	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	58	476	1	ENST00000262643.3:c.958C>T	p.Gln320Ter	p.Q320*	ENST00000262643	NM_001238.2	320	Cag/Tag	11/12	0.194459998276238	3	FACETS	0.579	0.495	0.671			1	SUBCLONAL	1	TRUE	NA	0.194459998276238	3		477	1131	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858020	45858020	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs748375308	NA	P-0011157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	461	471	0	ENST00000391945.4:c.1633A>G	p.Met545Val	p.M545V	ENST00000391945	NM_000400.3	545	Atg/Gtg	17/23	0.194459998276238	6	FACETS	1	0.985	1			1	CLONAL	5	TRUE	NA	0.194459998276238	6		471	1236	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095926	29095926	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs886039721	NA	P-0011157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	92	397	0	ENST00000328354.6:c.909-1G>T		p.X303_splice	ENST00000328354	NM_007194.3	303			1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.194459998276238	2		397	906	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028847	47028847	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011157-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	84	275	0	ENST00000377604.3:c.151C>T	p.Gln51Ter	p.Q51*	ENST00000377604	NM_001204468.1	51	Cag/Tag	3/24	0.149878791651711	0	FACETS	0.76	0.674	0.851			1	SUBCLONAL	2	TRUE	NA	0.194459998276238	0		275	458	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266107	41266107	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	298	376	0	ENST00000349496.5:c.104T>G	p.Ile35Ser	p.I35S	ENST00000349496	NM_001904.3	35	aTc/aGc	3/15	1	2	FACETS	0.937	0.888	0.987	0.937	0.888	0.987	CLONAL	1	TRUE	1	0.869962720784585	2		376	731	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685316	89685316	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs878853937	NA	P-0011174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	242	179	0	ENST00000371953.3:c.209+2T>C		p.X70_splice	ENST00000371953	NM_000314.4	70			0.843487926355918	2	FACETS	0.946	0.914	0.976	0.946	0.914	0.976	CLONAL	2	TRUE	0	0.869962720784585	2		179	294	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543637	29543637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	315	444	0	ENST00000389048.3:c.1526C>T	p.Ala509Val	p.A509V	ENST00000389048	NM_004304.4	509	gCc/gTc	7/29	1	2	FACETS	0.883	0.837	0.93	0.883	0.837	0.93	CLONAL	1	TRUE	1	0.869962720784585	2		444	820	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740713	58740717	+	frameshift_variant	Frame_Shift_Del	DEL	GAGTC	GAGTC	-	novel	NA	P-0011174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	515	654	0	ENST00000305921.3:c.1618_1622del	p.Glu540GlnfsTer10	p.E540Qfs*10	ENST00000305921	NM_003620.3	540	GAGTCc/c	6/6	1	2	FACETS	0.934	0.896	0.972	0.934	0.896	0.972	CLONAL	1	TRUE	1	0.869962720784585	2		654	1268	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589622	67589624	+	inframe_deletion	In_Frame_Del	DEL	AAT	AAT	-	novel	NA	P-0011174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	150	164	0	ENST00000274335.5:c.1386_1388del	p.Glu462_Tyr463delinsAsp	p.E462_Y463delinsD	ENST00000274335		462	gAATat/gat	10/15	1	2	FACETS	0.958	0.888	1	0.958	0.888	1	CLONAL	1	TRUE	1	0.869962720784585	2		164	360	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0011184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	16	391	2	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	1	2	FACETS	0.316	0.232	0.417	0.316	0.232	0.417	SUBCLONAL	1	FALSE	1	0.146143151547481	2		393	693	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0011184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	2601	583	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.146143151547481	32	FACETS	0.991	0.978	1			1	CLONAL	31	FALSE	NA	0.146143151547481	32		583	3700	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778095	27778095	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1979	120	1188	0	ENST00000369163.2:c.244G>C	p.Asp82His	p.D82H	ENST00000369163	NM_003536.2	82	Gac/Cac	1/1	1	2	FACETS	0.782	0.703	0.867	0.782	0.703	0.867	SUBCLONAL	1	FALSE	1	0.146143151547481	2		1188	2099	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729811	41729811	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1229001644	NA	P-0011184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	75	635	0	ENST00000242208.4:c.718G>A	p.Val240Ile	p.V240I	ENST00000242208	NM_002192.2	240	Gtt/Att	3/3	0.146143151547481	2	FACETS	0.8	0.698	0.91	0.4	0.349	0.455	CLONAL	1	FALSE	0	0.146143151547481	2		635	1283	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73991994	73991994	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139808700	NA	P-0011184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	84	582	0	ENST00000318443.5:c.14G>A	p.Arg5Gln	p.R5Q	ENST00000318443	NM_001024736.1	5	cGg/cAg	2/10	1	2	FACETS	0.968	0.852	1	0.968	0.852	1	CLONAL	1	FALSE	1	0.146143151547481	2		582	1188	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99451967	99451967	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	64	516	0	ENST00000268035.6:c.1301G>A	p.Trp434Ter	p.W434*	ENST00000268035	NM_000875.3	434	tGg/tAg	6/21	1	2	FACETS	0.794	0.685	0.913	0.794	0.685	0.913	CLONAL	1	FALSE	1	0.146143151547481	2		516	1103	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16022778	16022790	+	protein_altering_variant	In_Frame_Del	DEL	GTCTCCACAGGCT	GTCTCCACAGGCT	CGGA	novel	NA	P-0011184-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	130	430	0	ENST00000268712.3:c.1862_1874delinsTCCG	p.Glu621_Thr625delinsValArg	p.E621_T625delinsVR	ENST00000268712	NM_006311.3	621	gAGCCTGTGGAGACc/gTCCGc	17/46	1	2	FACETS	0.921	0.834	1	1	0.989	1	CLONAL	2	FALSE	1	0.146143151547481	2		430	966	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0011195-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	59	239	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	0.584	0.502	0.673	0.584	0.502	0.673	SUBCLONAL	1	TRUE	1	0.34	2		239	594	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0011195-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	61	245	0	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	1	2	FACETS	0.633	0.546	0.727	0.633	0.546	0.727	SUBCLONAL	1	TRUE	1	0.34	2		245	567	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587781702	NA	P-0011195-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	139	330	0	ENST00000269305.4:c.920-1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.177274945431461	2	FACETS	1	0.98	1	0.627	0.572	0.684	INDETERMINATE	1	TRUE	0	0.34	2		330	652	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609778	81609778	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762578626	NA	P-0011203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	236	402	0	ENST00000298171.2:c.1376C>T	p.Ala459Val	p.A459V	ENST00000298171	NM_000369.2	459	gCg/gTg	10/10	0.283290794974168	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.28657584036557	2		402	771	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061105	38061174	+	frameshift_variant	Frame_Shift_Del	DEL	TTGCGGCTCTCAGGGCCGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCG	TTGCGGCTCTCAGGGCCGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCG	-	novel	NA	P-0011203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	122	68	0	ENST00000250448.2:c.815_884del	p.Pro272ArgfsTer26	p.P272Rfs*26	ENST00000250448	NM_004496.3	272	cCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGCGGCGCCAAGGGCGGCCCTGAGAGCCGCAAg/cg	2/2	0.283290794974168	2	FACETS	0.921	0.853	0.989	1	0.991	1	CLONAL	4	TRUE	0	0.28657584036557	2		68	231	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098816	178098816	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011205-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	596	4049	3	ENST00000397062.3:c.229G>T	p.Asp77Tyr	p.D77Y	ENST00000397062	NM_006164.4	77	Gat/Tat	2/5	0.187637200064415	3	FACETS	1	0.99	1	1	0.998	1	CLONAL	4	TRUE	1	0.19	3		4052	1580	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266018	41266245	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGG	TGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGG	-	novel	NA	P-0011205-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	31	2346	0	ENST00000349496.5:c.16_241+2del		p.X6_splice	ENST00000349496	NM_001904.3	6		3/15	1	2	FACETS	0.646	0.522	0.788	0.646	0.522	0.788	SUBCLONAL	1	TRUE	1	0.19	2		2346	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0011213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	771	646	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.545452101610902	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.545452101610902	2		646	1152	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252155	226252155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553260624	NA	P-0011213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	14	39	0	ENST00000366813.1:c.103G>A	p.Gly35Arg	p.G35R	ENST00000366813		35	Ggg/Agg	1/3	1	2	FACETS	0.723	0.534	0.941	0.723	0.534	0.941	CLONAL	1	TRUE	1	0.545452101610902	2		39	71	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939209	76939210	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0011213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	238	252	0	ENST00000373344.5:c.1538_1539del	p.Leu513Ter	p.L513*	ENST00000373344	NM_000489.3	513	tTA/t	9/35	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.545452101610902	1		252	453	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	135	528	2				ENST00000310581	NM_198253.2	-/1132			0.126433682471784	4	FACETS	0.848	0.781	0.916	0.848	0.781	0.916	INDETERMINATE	2	TRUE	2	0.839552796216781	4		530	349	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623587	28623587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35602083	NA	P-0011219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	249	332	2	ENST00000241453.7:c.970G>A	p.Asp324Asn	p.D324N	ENST00000241453	NM_004119.2	324	Gac/Aac	8/24	0.839552796216781	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.839552796216781	1		334	297	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439772	51439772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	177	300	0	ENST00000262662.1:c.337G>A	p.Glu113Lys	p.E113K	ENST00000262662		113	Gaa/Aaa	4/4	1	2	FACETS	0.917	0.853	0.981	0.917	0.853	0.981	CLONAL	1	TRUE	1	0.839552796216781	2		300	460	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220295	55220295	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18730	2631	380	0	ENST00000275493.2:c.685A>T	p.Ser229Cys	p.S229C	ENST00000275493	NM_005228.3	229	Agt/Tgt	6/28	0.839552796216781	30	FACETS	0.936	0.915	0.956			1	CLONAL	4	TRUE	NA	0.839552796216781	30		380	21361	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675445	30675445	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	262	397	0	ENST00000376406.3:c.2911del	p.Val971TrpfsTer27	p.V971Wfs*27	ENST00000376406	NM_014641.2	971	Gtg/tg	8/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.839552796216781	2		397	608	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0011234-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	164	576	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.110871609023394	4	FACETS	1	0.985	1	0.666	0.611	0.724	INDETERMINATE	1	TRUE	2	0.352608636437983	4		576	944	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111116	193111116	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011234-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1334	155	582	0	ENST00000367435.3:c.649G>A	p.Glu217Lys	p.E217K	ENST00000367435	NM_024529.4	217	Gag/Aag	7/17	0.352608636437983	3	FACETS	0.695	0.634	0.759	0.347	0.317	0.38	SUBCLONAL	1	TRUE	1	0.352608636437983	3		582	1489	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437714	52437714	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011238-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1517	385	1051	2	ENST00000460680.1:c.1447C>T	p.Gln483Ter	p.Q483*	ENST00000460680	NM_004656.3	483	Cag/Tag	13/17	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.34095180087094	2		1053	1902	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946126	13946126	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011238-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	141	445	0	ENST00000405192.2:c.970G>A	p.Asp324Asn	p.D324N	ENST00000405192	NM_001163147.1	324	Gac/Aac	10/12	1	2	FACETS	0.89	0.811	0.974	0.89	0.811	0.974	CLONAL	1	TRUE	1	0.34095180087094	2		445	929	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258545	19258545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368616462	NA	P-0011238-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1303	280	825	1	ENST00000162023.5:c.355G>A	p.Glu119Lys	p.E119K	ENST00000162023		119	Gaa/Aaa	8/13	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.34095180087094	2		826	1583	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436826	52436845	+	frameshift_variant	Frame_Shift_Del	DEL	TTGAGGCACGCCTCATAGTT	TTGAGGCACGCCTCATAGTT	-	novel	NA	P-0011238-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1311	221	858	0	ENST00000460680.1:c.1933_1952del	p.Asn645GlyfsTer12	p.N645Gfs*12	ENST00000460680	NM_004656.3	645	AACTATGAGGCGTGCCTCAAg/g	15/17	1	2	FACETS	0.846	0.785	0.91	0.846	0.785	0.91	CLONAL	1	TRUE	1	0.34095180087094	2		858	1532	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702581	52702581	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011246-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	76	412	0	ENST00000394830.3:c.317A>G	p.Tyr106Cys	p.Y106C	ENST00000394830	NM_018313.4	106	tAt/tGt	4/30	0.406531235688569	1	FACETS	0.758	0.668	0.853	0.758	0.668	0.853	SUBCLONAL	1	TRUE	0	0.406531235688569	1		412	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578471	7578478	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCGGGG	GGGCGGGG	-	novel	NA	P-0011246-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	131	530	2	ENST00000269305.4:c.452_459del	p.Pro151ArgfsTer27	p.P151Rfs*27	ENST00000269305	NM_001126112.2	151	cCCCCGCCC/c	5/11	0.406531235688569	1	FACETS	0.989	0.903	1	0.989	0.903	1	CLONAL	1	TRUE	0	0.406531235688569	1		532	519	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46277761	46277770	+	frameshift_variant	Frame_Shift_Del	DEL	AGCCGACAGG	AGCCGACAGG	CGC	novel	NA	P-0011246-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	139	612	0	ENST00000371998.3:c.3559_3568delinsCGC	p.Ser1187ArgfsTer5	p.S1187Rfs*5	ENST00000371998		1187	AGCCGACAGGca/CGCca	19/23	1	2	FACETS	0.935	0.853	1	0.935	0.853	1	CLONAL	1	TRUE	1	0.406531235688569	2		612	731	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0011250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	100	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.584166386274789	3	FACETS	0.974	0.889	1	0.65	0.592	0.708	CLONAL	2	FALSE	0	0.584166386274789	3		249	227	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665074	182665074	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	85	603	0	ENST00000292782.4:c.652G>C	p.Asp218His	p.D218H	ENST00000292782	NM_020640.2	218	Gac/Cac	6/7	0.584166386274789	3	FACETS	0.86	0.764	0.962	0.287	0.254	0.321	CLONAL	1	FALSE	0	0.584166386274789	3		603	437	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190509	32190509	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	57	598	2	ENST00000375023.3:c.230G>C	p.Gly77Ala	p.G77A	ENST00000375023	NM_004557.3	77	gGa/gCa	3/30	NA	2	FACETS	0.579	0.499	0.665			1	INDETERMINATE	1	FALSE	NA	0.584166386274789	2		600	337	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756592	756592	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	49	520	0	ENST00000314574.4:c.236C>T	p.Ser79Leu	p.S79L	ENST00000314574	NM_005433.3	79	tCa/tTa	2/12	0.384612521543321	4	FACETS	0.391	0.33	0.458	0.195	0.165	0.229	SUBCLONAL	1	FALSE	2	0.584166386274789	4		520	680	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023646	31023646	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1191559798	NA	P-0011250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	107	813	0	ENST00000375687.4:c.3131C>G	p.Ser1044Cys	p.S1044C	ENST00000375687	NM_015338.5	1044	tCc/tGc	13/13	0.196658274169082	5	FACETS	0.579	0.517	0.644	0.193	0.172	0.215	INDETERMINATE	1	FALSE	2	0.584166386274789	5		813	1188	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578460	+	inframe_deletion	In_Frame_Del	DEL	CGCGGA	CGCGGA	-	novel	NA	P-0011255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	261	437	0	ENST00000269305.4:c.470_475del	p.Val157_Arg158del	p.V157_R158del	ENST00000269305	NM_001126112.2	157	gTCCGCGcc/gcc	5/11	0.366673465291613	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.366673465291613	1		437	844	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0011255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	117	517	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.728	0.656	0.804	0.728	0.656	0.804	SUBCLONAL	1	TRUE	1	0.366673465291613	2		517	877	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0011255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	79	354	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	1	2	FACETS	0.671	0.59	0.758	0.671	0.59	0.758	SUBCLONAL	1	TRUE	1	0.366673465291613	2		354	642	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371941	55371941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	395	217	0	ENST00000297316.4:c.631G>A	p.Ala211Thr	p.A211T	ENST00000297316	NM_022454.3	211	Gcg/Acg	2/2	0.278392431345341	2	FACETS	0.915	0.876	0.954	1	0.995	1	CLONAL	3	TRUE	0	0.366673465291613	2		217	785	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555714	21555714	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs61745905	NA	P-0011255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1384	369	660	0	ENST00000382592.4:c.2556C>A	p.Asp852Glu	p.D852E	ENST00000382592	NM_014572.2	852	gaC/gaA	6/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.366673465291613	2		660	1753	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911779	32911779	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	178	862	0	ENST00000380152.3:c.3287A>G	p.Asp1096Gly	p.D1096G	ENST00000380152		1096	gAt/gGt	11/27	1	2	FACETS	0.729	0.67	0.791	0.729	0.67	0.791	SUBCLONAL	1	TRUE	1	0.366673465291613	2		862	1331	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0011265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	42	441	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.858	0.715	1	0.858	0.715	1	CLONAL	1	TRUE	1	0.16	2		441	612	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0011265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	28	509	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.778	0.621	0.957	0.778	0.621	0.957	CLONAL	1	TRUE	1	0.16	2		509	450	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950410	38950410	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	26	478	0	ENST00000357387.3:c.3540A>C	p.Glu1180Asp	p.E1180D	ENST00000357387	NM_152756.3	1180	gaA/gaC	31/38	1	2	FACETS	0.639	0.504	0.793	0.639	0.504	0.793	SUBCLONAL	1	TRUE	1	0.16	2		478	509	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971115	21971116	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0011265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	22	191	0	ENST00000304494.5:c.242_243del	p.Pro81ArgfsTer38	p.P81Rfs*38	ENST00000304494	NM_000077.4	81	cCC/c	2/3	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.16	2		191	217	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604763	48604763	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0011265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	36	579	0	ENST00000342988.3:c.1586del	p.Leu529TyrfsTer8	p.L529Yfs*8	ENST00000342988	NM_005359.5	529	Tta/ta	12/12	1	2	FACETS	0.787	0.646	0.946	0.787	0.646	0.946	CLONAL	1	TRUE	1	0.16	2		579	572	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0011266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	501	503	0				ENST00000310581	NM_198253.2	-/1132			0.940008782449401	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.940008782449401	1		503	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0011266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	854	624	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.940008782449401	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.940008782449401	1		624	941	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955572	48955572	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587778863	NA	P-0011266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	532	206	0	ENST00000267163.4:c.1688G>A	p.Trp563Ter	p.W563*	ENST00000267163	NM_000321.2	563	tGg/tAg	17/27	0.940008782449401	1	FACETS	0.985	0.966	1	0.985	0.966	1	CLONAL	1	TRUE	0	0.940008782449401	1		206	609	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99175959	99175959	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0011266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	1060	429	0	ENST00000074304.5:c.1870+1G>A		p.X624_splice	ENST00000074304	NM_001134224.1	624			0.904363749099653	1	FACETS	0.993	0.98	1	0.993	0.98	1	CLONAL	1	TRUE	0	0.940008782449401	1		429	1204	SUCCESS
APC	324	MSKCC	GRCh37	5	112175459	112175459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	712	255	0	ENST00000257430.4:c.4168G>A	p.Val1390Ile	p.V1390I	ENST00000257430	NM_000038.5	1390	Gtc/Atc	16/16	0.940008782449401	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.940008782449401	1		255	794	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870988	12870988	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	804	299	0	ENST00000228872.4:c.215G>C	p.Gly72Ala	p.G72A	ENST00000228872	NM_004064.3	72	gGc/gCc	1/3	0.940008782449401	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.940008782449401	1		299	898	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976471	7976471	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	49	282	0	ENST00000319144.4:c.1921G>C	p.Asp641His	p.D641H	ENST00000319144	NM_001139.2	641	Gac/Cac	14/15	0.940008782449401	1	FACETS	0.09	0.076	0.106	0.09	0.076	0.106	SUBCLONAL	1	TRUE	0	0.940008782449401	1		282	614	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0011271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	305	661	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.421943890300104	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	1	0.421943890300104	3		661	873	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917553	178917553	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1223709697	NA	P-0011271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	129	372	0	ENST00000263967.3:c.428T>C	p.Ile143Thr	p.I143T	ENST00000263967	NM_006218.2	143	aTt/aCt	3/21	0.421943890300104	3	FACETS	0.902	0.818	0.99	0.451	0.409	0.495	CLONAL	1	TRUE	1	0.421943890300104	3		372	821	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393397	139393397	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs752603308	NA	P-0011271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1201	224	514	1	ENST00000277541.6:c.6134T>C	p.Val2045Ala	p.V2045A	ENST00000277541	NM_017617.3	2045	gTt/gCt	33/34	0.357697493851429	4	FACETS	1	0.964	1	0.53	0.492	0.569	CLONAL	1	TRUE	2	0.421943890300104	4		515	1425	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70442614	70442614	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1010032837	NA	P-0011271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	180	447	2	ENST00000373644.4:c.4936C>T	p.Arg1646Ter	p.R1646*	ENST00000373644	NM_030625.2	1646	Cga/Tga	10/12	0.421943890300104	3	FACETS	0.968	0.892	1	0.484	0.446	0.524	CLONAL	1	TRUE	1	0.421943890300104	3		449	1067	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0011271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	244	284	0	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.421943890300104	2	FACETS	0.994	0.936	1	0.994	0.936	1	CLONAL	2	TRUE	0	0.421943890300104	2		284	582	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575219	48575219	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0011271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	248	343	0	ENST00000342988.3:c.413C>G	p.Ser138Ter	p.S138*	ENST00000342988	NM_005359.5	138	tCa/tGa	3/12	0.421943890300104	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.421943890300104	2		343	573	SUCCESS
AR	367	MSKCC	GRCh37	X	66931262	66931262	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	221	298	0	ENST00000374690.3:c.1904T>G	p.Leu635Arg	p.L635R	ENST00000374690	NM_000044.3	635	cTt/cGt	4/8	0.421943890300104	2	FACETS	1	0.954	1			1	CLONAL	1	TRUE	NA	0.421943890300104	2		298	1015	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878530	151878530	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1396109953	NA	P-0011296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	227	602	0	ENST00000262189.6:c.6415C>T	p.Arg2139Ter	p.R2139*	ENST00000262189	NM_170606.2	2139	Cga/Tga	36/59	1	2	FACETS	0.664	0.618	0.712	0.664	0.618	0.712	SUBCLONAL	1	TRUE	1	0.592789873176285	2		602	1153	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0011296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	418	989	6	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	0.879	0.835	0.923	0.879	0.835	0.923	CLONAL	1	TRUE	1	0.592789873176285	2		995	1605	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588162	67588162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1453144300	NA	P-0011296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	184	334	0	ENST00000274335.5:c.992C>T	p.Ala331Val	p.A331V	ENST00000274335		331	gCt/gTt	7/15	1	2	FACETS	0.866	0.802	0.932	0.866	0.802	0.932	CLONAL	1	TRUE	1	0.592789873176285	2		334	717	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131976385	131976385	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs546479838	NA	P-0011296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	366	559	1	ENST00000265335.6:c.3640C>T	p.Arg1214Cys	p.R1214C	ENST00000265335		1214	Cgc/Tgc	24/25	0.592789873176285	1	FACETS	0.972	0.926	1	0.972	0.926	1	CLONAL	1	TRUE	0	0.592789873176285	1		560	894	SUCCESS
AR	367	MSKCC	GRCh37	X	66943680	66943680	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	419	377	0	ENST00000374690.3:c.2760G>T	p.Gln920His	p.Q920H	ENST00000374690	NM_000044.3	920	caG/caT	8/8	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.592789873176285	1		377	758	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889172	76889172	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	153	384	0	ENST00000373344.5:c.4838T>G	p.Leu1613Trp	p.L1613W	ENST00000373344	NM_000489.3	1613	tTg/tGg	18/35	1	1	FACETS	0.504	0.462	0.548	0.504	0.462	0.548	SUBCLONAL	1	TRUE	0	0.592789873176285	1		384	720	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119683	70119683	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0011296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	449	641	0	ENST00000245479.2:c.687del		p.X229_splice	ENST00000245479	NM_000346.3	229			1	2	FACETS	0.967	0.921	1	0.967	0.921	1	CLONAL	1	TRUE	1	0.592789873176285	2		641	1567	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436297	110436314	+	inframe_deletion	In_Frame_Del	DEL	CGGCGGCGGCGGCGGCGG	CGGCGGCGGCGGCGGCGG	-	novel	NA	P-0011296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	46	48	0	ENST00000375856.3:c.2087_2104del	p.Ala696_Ala701del	p.A696_A701del	ENST00000375856	NM_003749.2	696	gCCGCCGCCGCCGCCGCCGtg/gtg	1/2	0.592789873176285	3	FACETS	0.981	0.837	1	0.491	0.418	0.569	CLONAL	1	TRUE	1	0.592789873176285	3		48	205	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0011301-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	130	425	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	0.185466975331876	2		425	1046	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132437	11132437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs281875227	NA	P-0011301-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	114	727	2	ENST00000358026.2:c.2653C>T	p.Arg885Cys	p.R885C	ENST00000358026	NM_001128849.1	885	Cgc/Tgc	19/36	0.185466975331876	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.185466975331876	1		729	862	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602647	10602647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011301-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	149	622	0	ENST00000171111.5:c.931C>T	p.His311Tyr	p.H311Y	ENST00000171111	NM_203500.1	311	Cac/Tac	3/6	0.185466975331876	1	FACETS	0.868	0.793	0.946	1	0.99	1	CLONAL	2	TRUE	0	0.185466975331876	1		622	840	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776087	9776087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755725121	NA	P-0011301-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	69	483	0	ENST00000377346.4:c.551G>A	p.Arg184Gln	p.R184Q	ENST00000377346	NM_005026.3	184	cGg/cAg	5/24	NA	2	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.185466975331876	2		483	593	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0011326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	162	364	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.8	0.732	0.87	0.8	0.732	0.87	SUBCLONAL	1	TRUE	1	0.358311375571889	2		364	1131	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0011326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	230	285	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.272542254398562	2	FACETS	0.873	0.817	0.931	0.873	0.817	0.931	CLONAL	2	TRUE	0	0.358311375571889	2		285	735	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0011326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1436	205	862	1	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	NA	2	FACETS	0.697	0.644	0.753			1	INDETERMINATE	1	TRUE	NA	0.358311375571889	2		863	1641	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965141	15965141	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	116	151	0	ENST00000268712.3:c.5455G>T	p.Asp1819Tyr	p.D1819Y	ENST00000268712	NM_006311.3	1819	Gat/Tat	37/46	0.272542254398562	2	FACETS	0.92	0.838	1	0.92	0.838	1	CLONAL	2	TRUE	0	0.358311375571889	2		151	352	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867295	45867295	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	78	199	0	ENST00000391945.4:c.898G>A	p.Glu300Lys	p.E300K	ENST00000391945	NM_000400.3	300	Gag/Aag	10/23	0.29184498796128	3	FACETS	0.745	0.654	0.843	0.373	0.327	0.422	SUBCLONAL	1	TRUE	1	0.358311375571889	3		199	689	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242481	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAA	AATTAAGAGAAGCAA	TTT	novel	NA	P-0011326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	431	404	0	ENST00000275493.2:c.2237_2251delinsTTT	p.Glu746_Thr751delinsValSer	p.E746_T751delinsVS	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAAca/gTTTca	19/28	0.358311375571889	5	FACETS	0.888	0.846	0.931	0.888	0.846	0.931	CLONAL	3	TRUE	2	0.358311375571889	5		404	1388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	324	979	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.374853536806455	5	FACETS	0.932	0.882	0.984	0.621	0.588	0.656	INDETERMINATE	2	FALSE	2	0.663794321559143	5		979	1045	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	286	285	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.374853536806455	5	FACETS	0.901	0.854	0.948	0.901	0.854	0.948	INDETERMINATE	3	FALSE	2	0.663794321559143	5		285	636	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520017	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	235	452	2	ENST00000326873.7:c.647C>T	p.Ser216Phe	p.S216F	ENST00000326873	NM_000455.4	216	tCc/tTc	5/10	0.639032244118549	2	FACETS	0.833	0.79	0.876	0.833	0.79	0.876	CLONAL	2	FALSE	0	0.663794321559143	2		454	425	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094477	27094477	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	244	346	0	ENST00000324856.7:c.3185G>A	p.Gly1062Asp	p.G1062D	ENST00000324856	NM_006015.4	1062	gGt/gAt	11/20	0.374853536806455	5	FACETS	0.942	0.883	1	0.628	0.589	0.668	INDETERMINATE	2	FALSE	2	0.663794321559143	5		346	779	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610405	10610405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	309	470	0	ENST00000171111.5:c.305C>T	p.Ser102Leu	p.S102L	ENST00000171111	NM_203500.1	102	tCa/tTa	2/6	0.639032244118549	2	FACETS	0.92	0.881	0.959	0.92	0.881	0.959	CLONAL	2	FALSE	0	0.663794321559143	2		470	506	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469564	25469564	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs796065342	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	428	584	1	ENST00000264709.3:c.1204C>T	p.Gln402Ter	p.Q402*	ENST00000264709	NM_175629.2	402	Cag/Tag	10/23	0.663794321559143	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	FALSE	2	0.663794321559143	4		585	1040	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784139	9784139	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1237870323	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	178	342	0	ENST00000377346.4:c.2707G>C	p.Glu903Gln	p.E903Q	ENST00000377346	NM_005026.3	903	Gag/Cag	21/24	0.374853536806455	5	FACETS	0.855	0.792	0.92	0.57	0.528	0.614	INDETERMINATE	2	FALSE	2	0.663794321559143	5		342	626	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641758	12641758	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	377	405	0	ENST00000251849.4:c.883A>T	p.Ser295Cys	p.S295C	ENST00000251849	NM_002880.3	295	Agt/Tgt	9/17	0.663794321559143	6	FACETS	0.984	0.934	1			1	CLONAL	2	FALSE	NA	0.663794321559143	6		405	1343	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749523	41749523	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	305	321	0	ENST00000226382.2:c.272G>T	p.Gly91Val	p.G91V	ENST00000226382	NM_003924.3	91	gGc/gTc	2/3	0.374536592746243	3	FACETS	1	0.992	1	0.78	0.745	0.814	INDETERMINATE	2	FALSE	0	0.663794321559143	3		321	523	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161398	55161398	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs752633017	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	579	441	0	ENST00000257290.5:c.3229G>T	p.Gly1077Cys	p.G1077C	ENST00000257290	NM_006206.4	1077	Ggc/Tgc	23/23	0.510850876845934	5	FACETS	0.959	0.925	0.994	0.959	0.925	0.994	CLONAL	3	FALSE	2	0.663794321559143	5		441	1210	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875614	35875614	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs912324015	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	273	306	1	ENST00000303115.3:c.801G>T	p.Arg267Ser	p.R267S	ENST00000303115	NM_002185.3	267	agG/agT	7/8	0.631128037657332	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	FALSE	2	0.663794321559143	4		307	665	SUCCESS
APC	324	MSKCC	GRCh37	5	112174179	112174179	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	261	465	1	ENST00000257430.4:c.2888G>T	p.Ser963Ile	p.S963I	ENST00000257430	NM_000038.5	963	aGt/aTt	16/16	0.663013310335296	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	FALSE	0	0.663794321559143	2		466	379	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908181	41908181	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1447795219	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	222	420	0	ENST00000372991.4:c.341G>T	p.Arg114Leu	p.R114L	ENST00000372991	NM_001760.3	114	cGc/cTc	2/5	0.374853536806455	5	FACETS	0.986	0.922	1	0.657	0.615	0.701	INDETERMINATE	2	FALSE	2	0.663794321559143	5		420	677	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647390	117647390	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	313	614	0	ENST00000368508.3:c.5554G>T	p.Gly1852Ter	p.G1852*	ENST00000368508	NM_002944.2	1852	Gga/Tga	33/43	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	1	FALSE	NA	0.663794321559143	2		614	659	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2952936	2952936	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	52	340	0	ENST00000396946.4:c.3004A>C	p.Thr1002Pro	p.T1002P	ENST00000396946	NM_032415.4	1002	Acc/Ccc	22/25	0.547967967554194	3	FACETS	0.441	0.376	0.513	0.221	0.188	0.257	SUBCLONAL	1	FALSE	1	0.663794321559143	3		340	473	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81340797	81340797	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	203	398	0	ENST00000222390.5:c.1444C>G	p.His482Asp	p.H482D	ENST00000222390	NM_000601.4	482	Cat/Gat	12/18	0.374536592746243	3	FACETS	1	0.986	1	0.754	0.712	0.796	INDETERMINATE	2	FALSE	0	0.663794321559143	3		398	360	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273533	38273533	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	332	372	1	ENST00000425967.3:c.1802G>T	p.Arg601Leu	p.R601L	ENST00000425967	NM_001174067.1	601	cGg/cTg	14/19	0.663794321559143	3	FACETS	0.806	0.766	0.847	0.806	0.766	0.847	CLONAL	2	FALSE	1	0.663794321559143	3		373	826	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006209	22006209	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	189	259	0	ENST00000276925.6:c.194T>C	p.Leu65Pro	p.L65P	ENST00000276925	NM_004936.3	65	cTg/cCg	2/2	0.663013310335296	2	FACETS	0.992	0.941	1	0.992	0.941	1	CLONAL	2	FALSE	0	0.663794321559143	2		259	287	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570268	87570268	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	183	320	0	ENST00000277120.3:c.2008C>A	p.Leu670Met	p.L670M	ENST00000277120		670	Ctg/Atg	17/19	0.547967967554194	3	FACETS	1	0.984	1	0.607	0.563	0.652	CLONAL	1	FALSE	1	0.663794321559143	3		320	605	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650135	93650135	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs762706714	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	432	463	0	ENST00000375746.1:c.1686G>T	p.Met562Ile	p.M562I	ENST00000375746	NM_001174167.1	562	atG/atT	12/14	0.547967967554194	3	FACETS	0.937	0.898	0.976	0.937	0.898	0.976	CLONAL	2	FALSE	1	0.663794321559143	3		463	925	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796793	135796793	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs118203429	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	310	493	0	ENST00000298552.3:c.694G>T	p.Glu232Ter	p.E232*	ENST00000298552	NM_001162426.1	232	Gaa/Taa	8/23	0.547967967554194	3	FACETS	0.96	0.913	1	0.96	0.913	1	CLONAL	2	FALSE	1	0.663794321559143	3		493	648	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407900	139407900	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs374434131	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	190	489	0	ENST00000277541.6:c.2297G>T	p.Gly766Val	p.G766V	ENST00000277541	NM_017617.3	766	gGc/gTc	14/34	0.547967967554194	3	FACETS	1	0.976	1	0.558	0.518	0.6	CLONAL	1	FALSE	1	0.663794321559143	3		489	683	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456455	32456455	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	147	165	0	ENST00000332351.3:c.437G>A	p.Trp146Ter	p.W146*	ENST00000332351	NM_024426.4	146	tGg/tAg	1/10	0.663013310335296	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	FALSE	0	0.663794321559143	2		165	211	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246679	46246679	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	97	136	0	ENST00000334344.6:c.4773G>T	p.Gln1591His	p.Q1591H	ENST00000334344	NM_152641.2	1591	caG/caT	15/21	0.534951772293511	4	FACETS	0.914	0.828	1	0.914	0.828	1	CLONAL	2	FALSE	2	0.663794321559143	4		136	266	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110056	115110056	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs755321111	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	84	290	0	ENST00000257566.3:c.1822A>T	p.Met608Leu	p.M608L	ENST00000257566	NM_016569.3	608	Atg/Ttg	8/8	0.534951772293511	4	FACETS	0.662	0.585	0.744	0.331	0.292	0.372	SUBCLONAL	1	FALSE	2	0.663794321559143	4		290	636	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226091	133226091	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	286	365	0	ENST00000320574.5:c.3806T>A	p.Leu1269His	p.L1269H	ENST00000320574	NM_006231.2	1269	cTt/cAt	31/49	0.534951772293511	4	FACETS	0.953	0.901	1	0.953	0.901	1	CLONAL	2	FALSE	2	0.663794321559143	4		365	752	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001294	29001294	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	109	425	0	ENST00000282397.4:c.1436+2T>C		p.X479_splice	ENST00000282397	NM_002019.4	479			0.273860994407903	1	FACETS	0.487	0.439	0.536	0.487	0.439	0.536	INDETERMINATE	1	FALSE	0	0.663794321559143	1		425	451	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293240	91293240	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs558524280	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	227	273	0	ENST00000355112.3:c.742A>G	p.Ile248Val	p.I248V	ENST00000355112	NM_000057.2	248	Ata/Gta	3/22	0.616751212673731	3	FACETS	0.891	0.839	0.944	0.891	0.839	0.944	CLONAL	2	FALSE	1	0.663794321559143	3		273	511	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223979	2223979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	411	537	0	ENST00000326181.6:c.1193C>T	p.Pro398Leu	p.P398L	ENST00000326181	NM_032271.2	398	cCt/cTt	13/21	0.663794321559143	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	FALSE	0	0.663794321559143	2		537	618	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858436	9858436	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	416	523	0	ENST00000330684.3:c.2965A>T	p.Asn989Tyr	p.N989Y	ENST00000330684	NM_001134407.1	989	Aat/Tat	13/13	0.663794321559143	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	FALSE	0	0.663794321559143	2		523	598	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23640988	23640988	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	175	412	0	ENST00000261584.4:c.2487G>C	p.Gln829His	p.Q829H	ENST00000261584	NM_024675.3	829	caG/caC	5/13	0.606841073636986	4	FACETS	0.945	0.871	1			1	CLONAL	1	FALSE	NA	0.663794321559143	4		412	928	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641142	23641142	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	465	462	0	ENST00000261584.4:c.2333G>T	p.Ser778Ile	p.S778I	ENST00000261584	NM_024675.3	778	aGt/aTt	5/13	0.606841073636986	4	FACETS	0.879	0.84	0.918			1	CLONAL	2	FALSE	NA	0.663794321559143	4		462	1326	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974764	15974764	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	273	587	0	ENST00000268712.3:c.4111G>T	p.Val1371Phe	p.V1371F	ENST00000268712	NM_006311.3	1371	Gtc/Ttc	30/46	0.374853536806455	5	FACETS	0.818	0.769	0.869	0.546	0.512	0.58	INDETERMINATE	2	FALSE	2	0.663794321559143	5		587	1003	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805763	46805763	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	297	594	0	ENST00000290295.7:c.193C>A	p.Pro65Thr	p.P65T	ENST00000290295	NM_006361.5	65	Cca/Aca	1/2	0.175584069830284	5	FACETS	1	0.982	1	0.724	0.684	0.765	INDETERMINATE	2	FALSE	2	0.663794321559143	5		594	822	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136131	11136131	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	396	533	0	ENST00000358026.2:c.3115A>T	p.Ile1039Phe	p.I1039F	ENST00000358026	NM_001128849.1	1039	Atc/Ttc	22/36	0.639032244118549	2	FACETS	0.953	0.918	0.987	0.953	0.918	0.987	CLONAL	2	FALSE	0	0.663794321559143	2		533	626	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257397	19257397	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	283	530	0	ENST00000162023.5:c.736G>C	p.Gly246Arg	p.G246R	ENST00000162023		246	Ggg/Cgg	11/13	NA	2	FACETS	0.927	0.886	0.967			1	INDETERMINATE	2	FALSE	NA	0.663794321559143	2		530	460	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547016	9547016	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	78	149	0	ENST00000353224.5:c.1006G>T	p.Ala336Ser	p.A336S	ENST00000353224	NM_177990.2	336	Gca/Tca	5/10	0.172427178330898	5	FACETS	1	0.97	1			1	INDETERMINATE	1	FALSE	NA	0.663794321559143	5		149	358	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944544	40944544	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	346	371	0	ENST00000373198.4:c.1958G>C	p.Arg653Pro	p.R653P	ENST00000373198	NM_133170.3	653	cGg/cCg	12/32	0.663013310335296	2	FACETS	0.999	0.961	1	0.999	0.961	1	CLONAL	2	FALSE	0	0.663794321559143	2		371	522	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101130	41101130	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	283	321	1	ENST00000373198.4:c.1226C>A	p.Pro409His	p.P409H	ENST00000373198	NM_133170.3	409	cCc/cAc	8/32	0.663013310335296	2	FACETS	0.996	0.955	1	0.996	0.955	1	CLONAL	2	FALSE	0	0.663794321559143	2		322	428	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306605	41306605	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	383	453	0	ENST00000373198.4:c.1054C>G	p.Pro352Ala	p.P352A	ENST00000373198	NM_133170.3	352	Ccc/Gcc	7/32	0.663013310335296	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	FALSE	0	0.663794321559143	2		453	569	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091213	29091213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	31	51	0	ENST00000328354.6:c.1277C>T	p.Pro426Leu	p.P426L	ENST00000328354	NM_007194.3	426	cCt/cTt	12/15	0.616751212673731	3	FACETS	0.987	0.839	1	0.987	0.839	1	CLONAL	2	FALSE	1	0.663794321559143	3		51	63	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039411	47039411	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	204	484	0	ENST00000377604.3:c.1034T>G	p.Phe345Cys	p.F345C	ENST00000377604	NM_001204468.1	345	tTt/tGt	10/24	0.547967967554194	3	FACETS	1	0.943	1	0.508	0.472	0.546	CLONAL	1	FALSE	1	0.663794321559143	3		484	805	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650871	48650871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782534643	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	114	521	1	ENST00000376670.3:c.740G>A	p.Arg247His	p.R247H	ENST00000376670	NM_002049.3	247	cGc/cAc	4/6	0.547967967554194	3	FACETS	0.46	0.413	0.509	0.23	0.206	0.255	SUBCLONAL	1	FALSE	1	0.663794321559143	3		522	995	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348159	70348159	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	381	585	0	ENST00000374080.3:c.3223G>A	p.Ala1075Thr	p.A1075T	ENST00000374080		1075	Gca/Aca	23/45	0.663794321559143	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	FALSE	0	0.663794321559143	1		585	655	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169039	11169039	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	340	446	0	ENST00000358026.2:c.4629+1del		p.K1543fs	ENST00000358026	NM_001128849.1	1543	aaG/aa	32/36	0.639032244118549	2	FACETS	0.933	0.895	0.97	0.933	0.895	0.97	CLONAL	2	FALSE	0	0.663794321559143	2		446	549	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28903772	28903772	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	102	523	0	ENST00000282397.4:c.2687del	p.Gly896GlufsTer10	p.G896Efs*10	ENST00000282397	NM_002019.4	896	gGa/ga	19/30	0.273860994407903	1	FACETS	0.441	0.396	0.488	0.441	0.396	0.488	INDETERMINATE	1	FALSE	0	0.663794321559143	1		523	466	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95584074	95584074	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	136	357	0	ENST00000393063.1:c.1394del	p.Gly465AlafsTer15	p.G465Afs*15	ENST00000393063	NM_030621.3	465	gGc/gc	10/28	0.268959437921466	3	FACETS	1	0.984	1	0.661	0.606	0.717	INDETERMINATE	1	FALSE	1	0.663794321559143	3		357	413	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163793	47163793	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	291	469	0	ENST00000409792.3:c.2333del	p.Pro778GlnfsTer20	p.P778Qfs*20	ENST00000409792	NM_014159.6	778	cCa/ca	3/21	0.616751212673731	3	FACETS	0.896	0.849	0.942	0.896	0.849	0.942	CLONAL	2	FALSE	1	0.663794321559143	3		469	652	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254563	1254565	+	missense_variant	Missense_Mutation	TNP	CAC	CAC	AAA	novel	NA	P-0011334-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	287	434	1	ENST00000310581.5:c.3213_3215delinsTTT	p.Gln1071_Trp1072delinsHisLeu	p.Q1071_W1072delinsHL	ENST00000310581	NM_198253.2	1071	caGTGg/caTTTg	15/16	0.631128037657332	4	FACETS	0.944	0.892	0.997	0.944	0.892	0.997	CLONAL	2	FALSE	2	0.663794321559143	4		435	762	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441189	52441189	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0011337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	231	328	0	ENST00000460680.1:c.580+1G>C		p.X194_splice	ENST00000460680	NM_004656.3	194			0.376924065094175	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.376924065094175	2		328	580	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630688	187630688	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs749983018	NA	P-0011337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	350	545	1	ENST00000441802.2:c.294A>G	p.Ile98Met	p.I98M	ENST00000441802	NM_005245.3	98	atA/atG	2/27	0.376924065094175	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.376924065094175	2		546	862	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056128	26056128	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761753866	NA	P-0011337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	72	342	1	ENST00000343677.2:c.529G>A	p.Ala177Thr	p.A177T	ENST00000343677	NM_005319.3	177	Gcc/Acc	1/1	0.376924065094175	2	FACETS	0.67	0.586	0.761	0.335	0.293	0.381	SUBCLONAL	1	TRUE	0	0.376924065094175	2		343	570	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2105433	2105433	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs983899092	NA	P-0011337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	56	506	0	ENST00000219476.3:c.512G>C	p.Gly171Ala	p.G171A	ENST00000219476	NM_000548.3	171	gGc/gCc	6/42	0.260312326882756	3	FACETS	0.336	0.286	0.39	0.168	0.143	0.195	SUBCLONAL	1	TRUE	1	0.376924065094175	3		506	1052	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395677	31395677	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	210	377	0	ENST00000328111.2:c.2530G>C	p.Ala844Pro	p.A844P	ENST00000328111	NM_006892.3	844	Gcc/Ccc	23/23	0.322294772593205	3	FACETS	1	0.99	1	0.712	0.661	0.764	CLONAL	1	TRUE	1	0.376924065094175	3		377	930	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067819	30067819	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1305519234	NA	P-0011337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	29	240	0	ENST00000338641.4:c.1004A>G	p.Glu335Gly	p.E335G	ENST00000338641	NM_000268.3	335	gAg/gGg	11/16	0.376924065094175	2	FACETS	0.344	0.276	0.422	0.172	0.138	0.211	SUBCLONAL	1	TRUE	0	0.376924065094175	2		240	447	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306553	41306553	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	57	437	2	ENST00000373198.4:c.1106del	p.Gly369ValfsTer28	p.G369Vfs*28	ENST00000373198	NM_133170.3	369	gGt/gt	7/32	0.322294772593205	3	FACETS	0.393	0.336	0.456	0.197	0.168	0.228	SUBCLONAL	1	TRUE	1	0.376924065094175	3		439	914	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0011339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	181	661	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	0.386855078523081	2		661	833	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0011339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	107	266	0	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	0.386855078523081	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.386855078523081	1		266	363	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0011339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	261	342	0	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.383934587443959	2	FACETS	0.954	0.899	1	0.954	0.899	1	CLONAL	2	TRUE	0	0.386855078523081	2		342	707	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099397	27099397	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	181	413	3	ENST00000324856.7:c.3634C>T	p.Gln1212Ter	p.Q1212*	ENST00000324856	NM_006015.4	1212	Cag/Tag	14/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.386855078523081	2		416	869	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023943	27023943	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	40	50	0	ENST00000324856.7:c.1049C>A	p.Ser350Ter	p.S350*	ENST00000324856	NM_006015.4	350	tCg/tAg	1/20	1	2	FACETS	0.789	0.67	0.916	1	0.963	1	CLONAL	2	TRUE	1	0.386855078523081	2		50	131	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0011350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	198	389	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.46557597961664	3	FACETS	0.973	0.908	1	0.973	0.908	1	CLONAL	2	TRUE	1	0.46557597961664	3		389	539	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0011350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	216	612	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.46557597961664	2	FACETS	0.897	0.842	0.953	0.897	0.842	0.953	CLONAL	2	TRUE	0	0.46557597961664	2		612	517	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0011350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	100	597	4	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.458813251356911	2	FACETS	1	0.951	1	0.547	0.492	0.604	CLONAL	1	TRUE	0	0.46557597961664	2		601	393	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272206	15272206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765403158	NA	P-0011350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	22	105	0	ENST00000263388.2:c.6233G>A	p.Arg2078Gln	p.R2078Q	ENST00000263388	NM_000435.2	2078	cGg/cAg	33/33	0.229211665554304	4	FACETS	0.607	0.472	0.763	0.304	0.236	0.382	INDETERMINATE	1	TRUE	2	0.46557597961664	4		105	228	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436850	52436850	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs376519545	NA	P-0011350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	103	317	0	ENST00000460680.1:c.1928T>C	p.Ile643Thr	p.I643T	ENST00000460680	NM_004656.3	643	aTt/aCt	15/17	0.273342864654978	5	FACETS	0.779	0.696	0.867	0.26	0.232	0.289	INDETERMINATE	1	TRUE	2	0.46557597961664	5		317	965	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117730805	117730805	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	71	255	2	ENST00000368508.3:c.229C>T	p.Arg77Trp	p.R77W	ENST00000368508	NM_002944.2	77	Cgg/Tgg	4/43	0.46557597961664	2	FACETS	0.553	0.483	0.628	0.276	0.241	0.314	SUBCLONAL	1	TRUE	0	0.46557597961664	2		257	552	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954916	2954916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368431453	NA	P-0011350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	310	339	0	ENST00000396946.4:c.2794C>T	p.Arg932Trp	p.R932W	ENST00000396946	NM_032415.4	932	Cgg/Tgg	21/25	0.426532912864937	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.46557597961664	4		339	901	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100469	8100469	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451961949	NA	P-0011350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	183	422	1	ENST00000346208.3:c.443C>T	p.Pro148Leu	p.P148L	ENST00000346208		148	cCg/cTg	3/6	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.46557597961664	2		423	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577508	7577508	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060501201	NA	P-0011352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	89	400	0	ENST00000269305.4:c.773A>G	p.Glu258Gly	p.E258G	ENST00000269305	NM_001126112.2	258	gAa/gGa	7/11	0.242708061338725	1	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	0	0.242708061338725	1		400	634	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	80	528	2				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		530	279	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280380	1280380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112614087	NA	P-0011365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	119	438	0	ENST00000310581.5:c.1843G>A	p.Ala615Thr	p.A615T	ENST00000310581	NM_198253.2	615	Gcc/Acc	4/16	0.443593168582212	4	FACETS	0.992	0.897	1	0.496	0.448	0.547	CLONAL	1	TRUE	2	0.510153644307361	4		438	710	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285646	46285646	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	189	433	0	ENST00000334344.6:c.5006G>C	p.Trp1669Ser	p.W1669S	ENST00000334344	NM_152641.2	1669	tGg/tCg	17/21	0.320019347111179	5	FACETS	1	0.982	1	0.401	0.37	0.433	CLONAL	1	TRUE	2	0.510153644307361	5		433	1087	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959480	26959480	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0011365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	138	370	0	ENST00000381527.3:c.646+1G>A		p.X216_splice	ENST00000381527	NM_001260.1	216			0.448725966024837	4	FACETS	1	0.921	1			1	CLONAL	1	TRUE	NA	0.510153644307361	4		370	807	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881648	37881648	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	155	443	0	ENST00000269571.5:c.2718G>C	p.Trp906Cys	p.W906C	ENST00000269571		906	tgG/tgC	22/27	NA	2	FACETS	0.972	0.894	1			1	INDETERMINATE	1	TRUE	NA	0.510153644307361	2		443	625	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78914338	78914338	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1484629953	NA	P-0011365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	182	516	2	ENST00000306801.3:c.2962C>T	p.Arg988Trp	p.R988W	ENST00000306801	NM_020761.2	988	Cgg/Tgg	25/34	0.514432251716056	5	FACETS	1	0.953	1	0.262	0.241	0.284	CLONAL	1	TRUE	1	0.510153644307361	5		518	1202	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069467	30069470	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	novel	NA	P-0011372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	79	257	0	ENST00000338641.4:c.1334_1337del	p.Glu445GlyfsTer9	p.E445Gfs*9	ENST00000338641	NM_000268.3	444	tcAGAG/tc	12/16	0.654967885926055	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.709364374175628	1		257	106	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0011377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	435	890	5	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.593437185315691	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.684700141596735	1		895	808	SUCCESS
AR	367	MSKCC	GRCh37	X	66765159	66765185	+	inframe_deletion	In_Frame_Del	DEL	GCAGCAGCAGCAGCAGCAGCAGCAGCA	GCAGCAGCAGCAGCAGCAGCAGCAGCA	-	rs3032358	NA	P-0011377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	43	116	0	ENST00000374690.3:c.213_239del	p.Gln72_Gln80del	p.Q72_Q80del	ENST00000374690	NM_000044.3	57	ctGCAGCAGCAGCAGCAGCAGCAGCAGCAg/ctg	1/8	1	1	FACETS	0.34	0.286	0.398	0.34	0.286	0.398	SUBCLONAL	1	TRUE	0	0.684700141596735	1		116	243	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798450	42798450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142012810	NA	P-0011377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	321	481	1	ENST00000575354.2:c.4321C>T	p.Arg1441Cys	p.R1441C	ENST00000575354	NM_015125.3	1441	Cgt/Tgt	18/20	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.684700141596735	2		482	869	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060953	38060965	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCCCCTGTCGC	CGCCCCCTGTCGC	-	novel	NA	P-0011377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	105	218	0	ENST00000250448.2:c.1024_1036del	p.Ala342ProfsTer4	p.A342Pfs*4	ENST00000250448	NM_004496.3	342	GCGACAGGGGGCGcc/cc	2/2	1	2	FACETS	0.664	0.598	0.733	0.664	0.598	0.733	SUBCLONAL	1	TRUE	1	0.684700141596735	2		218	462	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0011384-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	180	568	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.307559140926519	2	FACETS	0.76	0.702	0.82	0.76	0.702	0.82	SUBCLONAL	2	TRUE	0	0.307559140926519	2		568	770	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579463	7579463	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011384-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	229	551	0	ENST00000269305.4:c.224del	p.Pro75LeufsTer48	p.P75Lfs*48	ENST00000269305	NM_001126112.2	75	cCt/ct	4/11	0.275133194287286	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.307559140926519	2		551	686	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403417	139403417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772134978	NA	P-0011384-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	147	466	0	ENST00000277541.6:c.3076G>A	p.Asp1026Asn	p.D1026N	ENST00000277541	NM_017617.3	1026	Gac/Aac	19/34	0.307559140926519	3	FACETS	1	0.978	1	0.609	0.556	0.665	CLONAL	1	TRUE	1	0.307559140926519	3		466	905	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858201	9858201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011384-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	161	479	1	ENST00000330684.3:c.3200G>A	p.Arg1067Gln	p.R1067Q	ENST00000330684	NM_001134407.1	1067	cGg/cAg	13/13	0.307559140926519	5	FACETS	1	0.974	1	0.387	0.353	0.422	CLONAL	1	TRUE	2	0.307559140926519	5		480	1319	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346280	89346280	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1381957912	NA	P-0011384-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	56	409	0	ENST00000301030.4:c.6670G>A	p.Glu2224Lys	p.E2224K	ENST00000301030	NM_001256183.1	2224	Gag/Aag	9/13	1	2	FACETS	0.477	0.408	0.553	0.477	0.408	0.553	SUBCLONAL	1	TRUE	1	0.307559140926519	2		409	763	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357663	70357663	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011384-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	69	334	0	ENST00000374080.3:c.5914C>A	p.Pro1972Thr	p.P1972T	ENST00000374080		1972	Cct/Act	41/45	0.295279971026291	2	FACETS	0.544	0.473	0.621			1	SUBCLONAL	1	TRUE	NA	0.307559140926519	2		334	825	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0011386-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	167	500	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.424220498063636	1	FACETS	0.996	0.919	1	0.996	0.919	1	CLONAL	1	TRUE	0	0.424220498063636	1		500	623	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913381	NA	P-0011386-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	28	306	0	ENST00000304494.5:c.322G>A	p.Asp108Asn	p.D108N	ENST00000304494	NM_000077.4	108	Gat/Aat	2/3	0.240933085384697	1	FACETS	0.272	0.217	0.335	0.272	0.217	0.335	INDETERMINATE	1	TRUE	0	0.424220498063636	1		306	382	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395776	45395776	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011386-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	74	409	1	ENST00000262160.6:c.358C>T	p.Arg120Ter	p.R120*	ENST00000262160	NM_005901.5	120	Cga/Tga	4/11	0.31838231622106	1	FACETS	0.615	0.54	0.695	0.615	0.54	0.695	SUBCLONAL	1	TRUE	0	0.424220498063636	1		410	447	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933640	39933640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780396086	NA	P-0011386-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	97	640	1	ENST00000378444.4:c.959C>T	p.Ala320Val	p.A320V	ENST00000378444	NM_001123385.1	320	gCg/gTg	4/15	0.240933085384697	1	FACETS	0.5	0.446	0.558	0.5	0.446	0.558	INDETERMINATE	1	TRUE	0	0.424220498063636	1		641	720	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858279	27858279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011386-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1373	89	1356	1	ENST00000359303.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000359303	NM_003535.2	98	Gag/Aag	1/1	0.190054097387161	2	FACETS	0.287	0.253	0.324	0.144	0.126	0.162	INDETERMINATE	1	TRUE	0	0.424220498063636	2		1357	1462	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150318	108150318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658463	NA	P-0011386-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	45	450	0	ENST00000278616.4:c.3385G>A	p.Glu1129Lys	p.E1129K	ENST00000278616	NM_000051.3	1129	Gaa/Aaa	23/63	0.179257811571487	2	FACETS	0.338	0.284	0.399	0.169	0.142	0.2	INDETERMINATE	1	TRUE	0	0.424220498063636	2		450	627	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0011389-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	72	474	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.158874571705552	3	FACETS	0.794	0.693	0.902	0.265	0.231	0.301	INDETERMINATE	1	TRUE	0	0.294930867916866	3		474	706	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0011389-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	121	698	3	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.158874571705552	3	FACETS	0.822	0.741	0.909	0.274	0.247	0.303	INDETERMINATE	1	TRUE	0	0.294930867916866	3		701	1145	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577084	7577084	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121912667	NA	P-0011389-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	189	532	0	ENST00000269305.4:c.854A>T	p.Glu285Val	p.E285V	ENST00000269305	NM_001126112.2	285	gAg/gTg	8/11	0.189516176078048	2	FACETS	0.763	0.706	0.822	0.763	0.706	0.822	SUBCLONAL	2	TRUE	0	0.294930867916866	2		532	840	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248666	212248666	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770116535	NA	P-0011389-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	91	449	0	ENST00000342788.4:c.3601G>A	p.Glu1201Lys	p.E1201K	ENST00000342788	NM_005235.2	1201	Gag/Aag	28/28	0.257304285377788	3	FACETS	0.808	0.717	0.907	0.404	0.358	0.454	CLONAL	1	TRUE	1	0.294930867916866	3		449	876	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450876	70450876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757931991	NA	P-0011389-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	42	242	0	ENST00000373644.4:c.5716G>A	p.Glu1906Lys	p.E1906K	ENST00000373644	NM_030625.2	1906	Gaa/Aaa	12/12	1	2	FACETS	0.665	0.556	0.787	0.665	0.556	0.787	SUBCLONAL	1	TRUE	1	0.294930867916866	2		242	428	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187681	11187681	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011395-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	82	850	2	ENST00000361445.4:c.6216G>C	p.Gln2072His	p.Q2072H	ENST00000361445	NM_004958.3	2072	caG/caC	44/58	0.204882690901891	2	FACETS	0.373	0.328	0.422	0.187	0.164	0.211	INDETERMINATE	1	TRUE	0	0.398052115435036	2		852	1104	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462414	89462414	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011395-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	253	479	2	ENST00000336596.2:c.1886C>A	p.Ala629Glu	p.A629E	ENST00000336596	NM_005233.5	629	gCa/gAa	10/17	0.308186784913737	3	FACETS	1	0.985	1	0.758	0.714	0.803	CLONAL	2	TRUE	0	0.398052115435036	3		481	670	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573419	55573419	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011395-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	133	569	0	ENST00000288135.5:c.1081G>T	p.Asp361Tyr	p.D361Y	ENST00000288135	NM_000222.2	361	Gat/Tat	6/21	0.398052115435036	3	FACETS	0.989	0.899	1	0.495	0.449	0.542	CLONAL	1	TRUE	1	0.398052115435036	3		569	810	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575554	67575554	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011395-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	58	558	0	ENST00000274335.5:c.627A>T	p.Leu209Phe	p.L209F	ENST00000274335		209	ttA/ttT	4/15	0.211152603245392	1	FACETS	0.373	0.32	0.431	0.373	0.32	0.431	INDETERMINATE	1	TRUE	0	0.398052115435036	1		558	626	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472567	88472567	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1311977254	NA	P-0011395-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	301	776	0	ENST00000360948.2:c.1988T>A	p.Ile663Asn	p.I663N	ENST00000360948	NM_001012338.2	663	aTc/aAc	16/19	0.341841703913579	2	FACETS	0.818	0.773	0.865	0.818	0.773	0.865	CLONAL	2	TRUE	0	0.398052115435036	2		776	924	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979319	40979319	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011395-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	187	683	0	ENST00000373198.4:c.1814C>A	p.Thr605Lys	p.T605K	ENST00000373198	NM_133170.3	605	aCg/aAg	11/32	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.398052115435036	2		683	855	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411882	116411902	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TTTCTTTCTCTCTGTTTTAAG	TTTCTTTCTCTCTGTTTTAAG	-	novel	NA	P-0011395-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	357	322	0	ENST00000397752.3:c.2888-21_2888-1del		p.X963_splice	ENST00000397752	NM_000245.2	963			0.398052115435036	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.398052115435036	3		322	642	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720843	89720843	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0011401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	42	169	0	ENST00000371953.3:c.994A>T	p.Lys332Ter	p.K332*	ENST00000371953	NM_000314.4	332	Aaa/Taa	8/9	0.35456874775696	1	FACETS	0.534	0.447	0.63	0.534	0.447	0.63	SUBCLONAL	1	TRUE	0	0.35456874775696	1		169	365	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714588	52714588	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	147	417	1	ENST00000322088.6:c.346T>A	p.Ser116Thr	p.S116T	ENST00000322088	NM_014225.5	116	Tca/Aca	4/15	1	2	FACETS	0.884	0.807	0.965	0.884	0.807	0.965	CLONAL	1	TRUE	1	0.35456874775696	2		418	938	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938752	76938752	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	177	369	1	ENST00000373344.5:c.1996C>T	p.Arg666Ter	p.R666*	ENST00000373344	NM_000489.3	666	Cga/Tga	9/35	0.223937607908262	1	FACETS	0.761	0.701	0.825	0.761	0.701	0.825	SUBCLONAL	1	TRUE	0	0.35456874775696	1		370	1079	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0011412-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	644	537	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	0.315883564423967	4	FACETS	0.947	0.912	0.983	0.947	0.912	0.983	CLONAL	3	TRUE	1	0.338492425651421	4		537	1792	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259166	89259166	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011412-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	141	516	1	ENST00000336596.2:c.310C>T	p.Arg104Ter	p.R104*	ENST00000336596	NM_005233.5	104	Cga/Tga	3/17	0.318083052621732	2	FACETS	0.859	0.782	0.94	0.429	0.391	0.47	CLONAL	1	TRUE	0	0.338492425651421	2		517	970	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242779	66242779	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011412-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	148	493	1	ENST00000273854.3:c.1793G>T	p.Cys598Phe	p.C598F	ENST00000273854	NM_004439.5	598	tGc/tTc	9/18	1	2	FACETS	0.811	0.74	0.886	0.811	0.74	0.886	CLONAL	1	TRUE	1	0.338492425651421	2		494	1078	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38972002	38972002	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011412-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1560	659	819	0	ENST00000357387.3:c.949T>C	p.Cys317Arg	p.C317R	ENST00000357387	NM_152756.3	317	Tgc/Cgc	11/38	0.338492425651421	8	FACETS	0.884	0.85	0.919			1	CLONAL	4	TRUE	NA	0.338492425651421	8		819	2219	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219215	133219215	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011412-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	90	589	0	ENST00000320574.5:c.4829C>A	p.Pro1610His	p.P1610H	ENST00000320574	NM_006231.2	1610	cCt/cAt	37/49	0.338492425651421	3	FACETS	0.716	0.634	0.803			1	SUBCLONAL	1	TRUE	NA	0.338492425651421	3		589	869	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293066	91293066	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011412-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	98	466	0	ENST00000355112.3:c.568A>G	p.Lys190Glu	p.K190E	ENST00000355112	NM_000057.2	190	Aag/Gag	3/22	0.3030729994432	3	FACETS	0.694	0.618	0.776	0.347	0.309	0.388	SUBCLONAL	1	TRUE	1	0.338492425651421	3		466	975	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221316	1221317	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	T	novel	NA	P-0011412-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	233	610	0	ENST00000326873.7:c.839_840delinsT	p.Pro280LeufsTer7	p.P280Lfs*7	ENST00000326873	NM_000455.4	280	cCC/cT	6/10	0.338492425651421	1	FACETS	0.772	0.723	0.822	1	0.993	1	SUBCLONAL	2	TRUE	0	0.338492425651421	1		610	741	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	42	528	2				ENST00000310581	NM_198253.2	-/1132			0.30497453478186	1	FACETS	0.671	0.563	0.79	0.671	0.563	0.79	SUBCLONAL	1	TRUE	0	0.35	1		530	295	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0011431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	166	503	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	0.35	2		503	841	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0011431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	132	367	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.891	0.808	0.977	0.891	0.808	0.977	CLONAL	1	TRUE	1	0.35	2		367	847	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070841	30070841	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	137	388	0	ENST00000338641.4:c.1357C>T	p.Gln453Ter	p.Q453*	ENST00000338641	NM_000268.3	453	Cag/Tag	13/16	0.30497453478186	1	FACETS	0.98	0.894	1	0.98	0.894	1	CLONAL	1	TRUE	0	0.35	1		388	659	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0011435-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	398	661	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.351685650937994	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	TRUE	1	0.351685650937994	4		661	985	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0011435-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	327	979	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.351685650937994	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.351685650937994	2		979	927	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039347	47039347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011435-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	176	269	0	ENST00000377604.3:c.970G>A	p.Ala324Thr	p.A324T	ENST00000377604	NM_001204468.1	324	Gcg/Acg	10/24	1	1	FACETS	0.917	0.853	0.981	1	0.993	1	CLONAL	2	TRUE	0	0.351685650937994	1		269	450	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460427	8460427	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011435-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	177	279	0	ENST00000356435.5:c.3859A>G	p.Ile1287Val	p.I1287V	ENST00000356435		1287	Att/Gtt	22/35	0.351685650937994	2	FACETS	0.948	0.88	1	0.948	0.88	1	CLONAL	2	TRUE	0	0.351685650937994	2		279	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0011437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1474	55	890	5	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.3	3	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	3		895	1529	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061216	38061230	+	inframe_deletion	In_Frame_Del	DEL	CAGCCGTTCTCGAAC	CAGCCGTTCTCGAAC	-	novel	NA	P-0011437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	53	524	0	ENST00000250448.2:c.759_773del	p.Met253_Cys258delinsIle	p.M253_C258delinsI	ENST00000250448	NM_004496.3	253	atGTTCGAGAACGGCTGc/atc	2/2	0.3	4	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	4		524	959	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0011450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	24	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.422	0.33	0.527	0.422	0.33	0.527	SUBCLONAL	1	TRUE	1	0.33	2		249	345	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0011450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	77	367	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.824	0.725	0.931	0.824	0.725	0.931	CLONAL	1	TRUE	1	0.33	2		367	566	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139573	47139573	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0011450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	78	222	0	ENST00000409792.3:c.5016-2A>G		p.X1672_splice	ENST00000409792	NM_014159.6	1672			1	2	FACETS	0.897	0.79	1	0.897	0.79	1	CLONAL	1	TRUE	1	0.33	2		222	527	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147512	47147512	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	102	302	0	ENST00000409792.3:c.4814A>G	p.Tyr1605Cys	p.Y1605C	ENST00000409792	NM_014159.6	1605	tAt/tGt	6/21	1	2	FACETS	0.755	0.675	0.84	0.755	0.675	0.84	SUBCLONAL	1	TRUE	1	0.33	2		302	819	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240738	53240738	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011450-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1216	83	554	0	ENST00000375401.3:c.1342G>C	p.Glu448Gln	p.E448Q	ENST00000375401	NM_004187.3	448	Gaa/Caa	10/26	1	2	FACETS	0.387	0.34	0.438	0.387	0.34	0.438	SUBCLONAL	1	TRUE	1	0.33	2		554	1299	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs863224451	NA	P-0011451-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	851	412	2	ENST00000269305.4:c.824G>C	p.Cys275Ser	p.C275S	ENST00000269305	NM_001126112.2	275	tGt/tCt	8/11	NA	2	FACETS	0.996	0.981	1			1	INDETERMINATE	2	TRUE	NA	0.874989912389199	2		414	976	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059230	27059230	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011451-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	455	395	0	ENST00000324856.7:c.1867G>C	p.Gly623Arg	p.G623R	ENST00000324856	NM_006015.4	623	Gga/Cga	4/20	1	2	FACETS	0.904	0.865	0.944	0.904	0.865	0.944	CLONAL	1	TRUE	1	0.874989912389199	2		395	1150	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143102	30143102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011451-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	357	434	1	ENST00000389048.3:c.424G>A	p.Val142Met	p.V142M	ENST00000389048	NM_004304.4	142	Gtg/Atg	1/29	NA	2	FACETS	1	0.955	1			1	INDETERMINATE	1	TRUE	NA	0.874989912389199	2		435	814	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	123	528	2				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	NA	NA		530	366	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813023	89813023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142833057	NA	P-0011460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	296	456	0	ENST00000389301.3:c.3482C>T	p.Thr1161Met	p.T1161M	ENST00000389301	NM_000135.2	1161	aCg/aTg	35/43	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	NA	NA		456	1011	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717699	89717699	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554825210	NA	P-0011460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	254	318	0	ENST00000371953.3:c.724G>T	p.Glu242Ter	p.E242*	ENST00000371953	NM_000314.4	242	Gag/Tag	7/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	NA	NA		318	612	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888210	112888210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121918464	NA	P-0011460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	355	521	1	ENST00000351677.2:c.226G>A	p.Glu76Lys	p.E76K	ENST00000351677	NM_002834.3	76	Gag/Aag	3/16	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	NA	NA		522	1190	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258458	16258458	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1219354814	NA	P-0011460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	230	388	0	ENST00000375759.3:c.5723A>G	p.Tyr1908Cys	p.Y1908C	ENST00000375759	NM_015001.2	1908	tAt/tGt	11/15	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	NA	NA		388	567	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144865	47144865	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	345	480	0	ENST00000409792.3:c.4888A>C	p.Ser1630Arg	p.S1630R	ENST00000409792	NM_014159.6	1630	Agc/Cgc	7/21	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	NA	NA		480	788	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588851	29588851	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0011460-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	322	452	0	ENST00000356175.3:c.4637C>G	p.Ser1546Ter	p.S1546*	ENST00000356175	NM_000267.3	1546	tCa/tGa	34/57	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	NA	NA		452	1164	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587782272	NA	P-0011470-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	436	553	0	ENST00000269305.4:c.994-1G>C		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.348229344510349	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	0	0.389718229373264	3		553	876	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849870	151849870	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011470-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	112	463	0	ENST00000262189.6:c.12446C>T	p.Pro4149Leu	p.P4149L	ENST00000262189	NM_170606.2	4149	cCa/cTa	49/59	1	2	FACETS	0.736	0.662	0.814	0.736	0.662	0.814	SUBCLONAL	1	TRUE	1	0.389718229373264	2		463	781	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845727	68845727	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011470-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	190	432	1	ENST00000261769.5:c.973G>A	p.Val325Ile	p.V325I	ENST00000261769	NM_004360.3	325	Gtc/Atc	7/16	0.389718229373264	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.389718229373264	1		433	619	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40747892	40747892	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011470-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	186	589	1	ENST00000392038.2:c.526C>A	p.Arg176Ser	p.R176S	ENST00000392038	NM_001626.4	176	Cgc/Agc	6/14	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.389718229373264	2		590	879	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881492	48881502	+	frameshift_variant	Frame_Shift_Del	DEL	GAGAGAGCTTG	GAGAGAGCTTG	-	novel	NA	P-0011470-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	177	460	0	ENST00000267163.4:c.215_225del	p.Glu72ValfsTer34	p.E72Vfs*34	ENST00000267163	NM_000321.2	72	GAGAGAGCTTGg/g	2/27	0.389718229373264	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.389718229373264	1		460	713	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0011476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	498	367	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.705822138557799	4	FACETS	0.988	0.955	1	0.988	0.955	1	CLONAL	3	FALSE	1	0.705822138557799	4		367	812	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001422	29001422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752383804	NA	P-0011476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	288	248	0	ENST00000282397.4:c.1310C>T	p.Ser437Leu	p.S437L	ENST00000282397	NM_002019.4	437	tCg/tTg	10/30	0.705822138557799	4	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	FALSE	2	0.705822138557799	4		248	695	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136256	202136256	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	335	412	0	ENST00000358485.4:c.500T>C	p.Ile167Thr	p.I167T	ENST00000358485	NM_001080125.1	167	aTt/aCt	3/9	0.705822138557799	4	FACETS	0.851	0.807	0.896	0.851	0.807	0.896	CLONAL	2	FALSE	2	0.705822138557799	4		412	951	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281334	142281334	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754292203	NA	P-0011476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	123	278	0	ENST00000350721.4:c.910C>T	p.Pro304Ser	p.P304S	ENST00000350721	NM_001184.3	304	Ccc/Tcc	4/47	0.705822138557799	3	FACETS	0.785	0.712	0.861	0.392	0.356	0.431	SUBCLONAL	1	FALSE	1	0.705822138557799	3		278	601	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852764	63852764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	146	152	0	ENST00000279873.7:c.3542C>T	p.Ser1181Phe	p.S1181F	ENST00000279873	NM_032199.2	1181	tCc/tTc	10/10	0.683226343719429	2	FACETS	0.932	0.877	0.984	0.932	0.877	0.984	CLONAL	2	FALSE	0	0.705822138557799	2		152	222	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486824	56486824	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1023742896	NA	P-0011476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	606	510	0	ENST00000267101.3:c.1238C>T	p.Ser413Phe	p.S413F	ENST00000267101	NM_001982.3	413	tCc/tTc	11/28	0.705822138557799	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	FALSE	1	0.705822138557799	3		510	1059	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094961	11094961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	286	483	0	ENST00000358026.2:c.134C>T	p.Pro45Leu	p.P45L	ENST00000358026	NM_001128849.1	45	cCc/cTc	2/36	0.705822138557799	4	FACETS	0.879	0.83	0.929	0.879	0.83	0.929	CLONAL	2	FALSE	2	0.705822138557799	4		483	786	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0011504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	183	389	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.20282979783408	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.205596173606431	3		389	916	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0011504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	62	486	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.754	0.65	0.867	0.754	0.65	0.867	SUBCLONAL	1	TRUE	1	0.205596173606431	2		486	800	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0011504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	71	624	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.205596173606431	1	FACETS	0.664	0.578	0.758	0.664	0.578	0.758	SUBCLONAL	1	TRUE	0	0.205596173606431	1		624	933	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919625	28919625	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	54	678	0	ENST00000282397.4:c.2312T>C	p.Leu771Pro	p.L771P	ENST00000282397	NM_002019.4	771	cTc/cCc	16/30	0.205596173606431	1	FACETS	0.468	0.398	0.545	0.468	0.398	0.545	SUBCLONAL	1	TRUE	0	0.205596173606431	1		678	1008	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226062	2226062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1350	89	701	0	ENST00000326181.6:c.1759G>A	p.Glu587Lys	p.E587K	ENST00000326181	NM_032271.2	587	Gag/Aag	19/21	0.205596173606431	5	FACETS	0.787	0.695	0.886			1	SUBCLONAL	1	TRUE	NA	0.205596173606431	5		701	1439	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757468	40757468	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	94	708	0	ENST00000373198.4:c.2830G>T	p.Asp944Tyr	p.D944Y	ENST00000373198	NM_133170.3	944	Gac/Tac	20/32	1	2	FACETS	0.917	0.814	1	0.917	0.814	1	CLONAL	1	TRUE	1	0.205596173606431	2		708	997	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972655	76972655	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	89	955	1	ENST00000373344.5:c.86C>A	p.Ser29Tyr	p.S29Y	ENST00000373344	NM_000489.3	29	tCt/tAt	2/35	NA	2	FACETS	0.697	0.616	0.785			1	INDETERMINATE	1	TRUE	NA	0.205596173606431	2		956	1242	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419957	41419957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369230837	NA	P-0011522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	126	415	0	ENST00000373198.4:c.364G>A	p.Val122Ile	p.V122I	ENST00000373198	NM_133170.3	122	Gtc/Atc	3/32	0.147771409035067	2	FACETS	1	0.969	1	0.586	0.529	0.647	CLONAL	1	FALSE	0	0.179255994074534	2		415	1199	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174458	11174458	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1171	161	425	0	ENST00000361445.4:c.7217T>A	p.Val2406Glu	p.V2406E	ENST00000361445	NM_004958.3	2406	gTg/gAg	53/58	0.170728175270935	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	0	0.179255994074534	1		425	1332	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620008	21620008	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1254	77	451	0	ENST00000382592.4:c.158G>A	p.Gly53Glu	p.G53E	ENST00000382592	NM_014572.2	53	gGg/gAg	2/8	1	2	FACETS	0.645	0.564	0.733	0.645	0.564	0.733	SUBCLONAL	1	FALSE	1	0.179255994074534	2		451	1331	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152146	11152146	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502068	NA	P-0011522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	136	424	2	ENST00000358026.2:c.4430G>A	p.Arg1477Gln	p.R1477Q	ENST00000358026	NM_001128849.1	1477	cGg/cAg	31/36	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.179255994074534	2		426	1339	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051104	13051104	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1609	170	522	0	ENST00000316448.5:c.540C>A	p.Asn180Lys	p.N180K	ENST00000316448	NM_004343.3	180	aaC/aaA	5/9	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.179255994074534	2		522	1779	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191572	10191588	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGACCACCCAAATGT	GAAGACCACCCAAATGT	-	novel	NA	P-0011522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	108	310	0	ENST00000256474.2:c.566_582del	p.Glu189AlafsTer61	p.E189Afs*61	ENST00000256474	NM_000551.3	189	GAAGACCACCCAAATGTg/g	3/3	0.170728175270935	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	0	0.179255994074534	1		310	1025	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643432	52643434	+	frameshift_variant	Frame_Shift_Del	DEL	ATG	ATG	T	novel	NA	P-0011522-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1382	155	472	0	ENST00000394830.3:c.2462_2464delinsA	p.Thr821AsnfsTer2	p.T821Nfs*2	ENST00000394830	NM_018313.4	821	aCATtt/aAtt	17/30	0.170728175270935	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	0	0.179255994074534	1		472	1537	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0011527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	112	661	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	TRUE	1	0.182276117561183	2		661	949	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0011527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	34	356	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.182276117561183	2		356	299	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057520000	NA	P-0011527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	148	493	1	ENST00000269305.4:c.452C>A	p.Pro151His	p.P151H	ENST00000269305	NM_001126112.2	151	cCc/cAc	5/11	1	2	FACETS	0.819	0.747	0.895	1	0.989	1	CLONAL	2	TRUE	1	0.182276117561183	2		494	991	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904860	101904860	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1064796037	NA	P-0011527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	71	471	0	ENST00000374994.4:c.848A>G	p.His283Arg	p.H283R	ENST00000374994	NM_004612.2	283	cAt/cGt	5/9	0.182276117561183	1	FACETS	0.738	0.643	0.842	0.738	0.643	0.842	SUBCLONAL	1	TRUE	0	0.182276117561183	1		471	959	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0011530-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	299	590	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.913	0.863	0.964	0.913	0.863	0.964	CLONAL	1	TRUE	1	0.761344832450471	2		590	860	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	116	528	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.911	0.831	0.992	0.911	0.831	0.992	CLONAL	1	TRUE	1	0.774152394216541	2		530	329	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0011532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	110	472	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.314794742199592	1	FACETS	0.426	0.385	0.468	0.426	0.385	0.468	INDETERMINATE	1	TRUE	0	0.774152394216541	1		473	409	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791806	42791806	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	33	369	0	ENST00000575354.2:c.692G>A	p.Ser231Asn	p.S231N	ENST00000575354	NM_015125.3	231	aGc/aAc	5/20	0.774152394216541	1	FACETS	0.117	0.095	0.142	0.117	0.095	0.142	SUBCLONAL	1	TRUE	0	0.774152394216541	1		369	445	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337716	73337717	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs1428278025	NA	P-0011532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	25	308	1	ENST00000377767.4:c.1999_2000del	p.Met667ValfsTer13	p.M667Vfs*13	ENST00000377767	NM_014953.3	667	ATg/g	16/21	0.478164763180052	1	FACETS	0.142	0.112	0.177	0.142	0.112	0.177	SUBCLONAL	1	TRUE	0	0.774152394216541	1		309	278	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495732	72495732	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	137	677	6	ENST00000477973.2:c.340T>G	p.Trp114Gly	p.W114G	ENST00000477973	NM_012234.5	114	Tgg/Ggg	1/4	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.264980395532142	2		683	985	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0011539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	216	341	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	0.516118687369318	3	FACETS	0.853	0.807	0.898	0.853	0.807	0.898	CLONAL	3	TRUE	0	0.565477070516096	3		341	383	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99203955	99203955	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1835	98	337	0	ENST00000074304.5:c.2818G>C	p.Glu940Gln	p.E940Q	ENST00000074304	NM_001134224.1	940	Gaa/Caa	26/26	0.565477070516096	12	FACETS	0.686	0.609	0.769			1	SUBCLONAL	1	TRUE	NA	0.565477070516096	12		337	1933	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0011541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	122	474	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.233996314621356	5	FACETS	0.998	0.907	1	0.665	0.605	0.728	INDETERMINATE	2	TRUE	2	0.412243846597308	5		474	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578371	7578371	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	38	336	0	ENST00000269305.4:c.559G>C	p.Gly187Arg	p.G187R	ENST00000269305	NM_001126112.2	187	Ggt/Cgt	5/11	0.400802899343912	1	FACETS	0.707	0.59	0.835	0.707	0.59	0.835	SUBCLONAL	1	TRUE	0	0.412243846597308	1		336	207	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134978	2134978	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs746246149	NA	P-0011541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	22	573	0	ENST00000219476.3:c.4520C>A	p.Ser1507Tyr	p.S1507Y	ENST00000219476	NM_000548.3	1507	tCc/tAc	35/42	1	2	FACETS	0.336	0.26	0.424	0.336	0.26	0.424	SUBCLONAL	1	TRUE	1	0.412243846597308	2		573	318	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42790947	42790947	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011541-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	33	591	0	ENST00000575354.2:c.92C>G	p.Ser31Cys	p.S31C	ENST00000575354	NM_015125.3	31	tCt/tGt	2/20	0.319527474191151	2	FACETS	0.384	0.312	0.464	0.192	0.156	0.232	SUBCLONAL	1	TRUE	0	0.412243846597308	2		591	417	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220649	1220649	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	597	553	0	ENST00000326873.7:c.667G>T	p.Glu223Ter	p.E223*	ENST00000326873	NM_000455.4	223	Gag/Tag	5/10	0.800517922782494	2	FACETS	0.989	0.966	1	0.989	0.966	1	CLONAL	2	TRUE	0	0.800517922782494	2		553	754	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245350	153245350	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	254	488	0	ENST00000281708.4:c.1841T>C	p.Leu614Ser	p.L614S	ENST00000281708	NM_033632.3	614	tTa/tCa	11/12	0.800517922782494	2	FACETS	0.947	0.892	1	0.474	0.446	0.502	CLONAL	1	TRUE	0	0.800517922782494	2		488	670	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271340	26271340	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	466	1099	0	ENST00000305910.3:c.273G>T	p.Met91Ile	p.M91I	ENST00000305910	NM_003534.2	91	atG/atT	1/1	0.782544513173141	3	FACETS	1	0.965	1	0.507	0.483	0.531	CLONAL	1	TRUE	1	0.800517922782494	3		1099	1609	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232132	98232132	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	243	373	0	ENST00000331920.6:c.1810G>T	p.Glu604Ter	p.E604*	ENST00000331920	NM_000264.3	604	Gag/Tag	13/24	0.800517922782494	2	FACETS	0.917	0.862	0.973	0.459	0.431	0.487	CLONAL	1	TRUE	0	0.800517922782494	2		373	662	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102033240	102033240	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	514	479	0	ENST00000282441.5:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000282441	NM_001130145.2	209	cAg/cTg	3/9	0.800517922782494	2	FACETS	0.976	0.951	1	0.976	0.951	1	CLONAL	2	TRUE	0	0.800517922782494	2		479	658	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0011546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	231	267	0	ENST00000267163.4:c.1215+1G>C		p.X405_splice	ENST00000267163	NM_000321.2	405			0.800517922782494	2	FACETS	0.982	0.945	1	0.982	0.945	1	CLONAL	2	TRUE	0	0.800517922782494	2		267	294	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489480	40489480	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	385	708	0	ENST00000264657.5:c.770A>G	p.Asn257Ser	p.N257S	ENST00000264657	NM_139276.2	257	aAc/aGc	8/24	0.538386787664858	3	FACETS	0.996	0.946	1			1	CLONAL	1	TRUE	NA	0.800517922782494	3		708	1352	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356755	70356755	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	719	735	1	ENST00000374080.3:c.5427C>A	p.Ser1809Arg	p.S1809R	ENST00000374080		1809	agC/agA	38/45	0.422003735750041	3	FACETS	0.944	0.916	0.973			1	INDETERMINATE	2	TRUE	NA	0.800517922782494	3		736	1332	SUCCESS
BTK	695	MSKCC	GRCh37	X	100629600	100629600	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1555980796	NA	P-0011546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	555	609	0	ENST00000308731.7:c.164C>A	p.Ser55Ter	p.S55*	ENST00000308731	NM_000061.2	55	tCa/tAa	3/19	0.782544513173141	3	FACETS	0.981	0.948	1	0.981	0.948	1	CLONAL	2	TRUE	1	0.800517922782494	3		609	990	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577154	7577158	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CACTA	CACTA	-	novel	NA	P-0011546-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	249	494	0	ENST00000269305.4:c.783-3_784del		p.X261_splice	ENST00000269305	NM_001126112.2	261		8/11	0.800517922782494	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.800517922782494	1		494	370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0011551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	14	617	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.896587567117557	1	FACETS	0.026	0.018	0.036	0.026	0.018	0.036	SUBCLONAL	1	TRUE	0	0.896587567117557	1		617	655	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0011551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	22	490	1	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.896587567117557	1	FACETS	0.084	0.065	0.106	0.084	0.065	0.106	SUBCLONAL	1	TRUE	0	0.896587567117557	1		491	322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578509	7578509	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519978	NA	P-0011557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	219	429	0	ENST00000269305.4:c.421T>C	p.Cys141Arg	p.C141R	ENST00000269305	NM_001126112.2	141	Tgc/Cgc	5/11	0.336269599544195	2	FACETS	1	0.992	1	0.736	0.687	0.786	CLONAL	1	TRUE	0	0.389591427128986	2		429	764	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032739	30032739	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0011574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	138	356	0	ENST00000338641.4:c.115-1G>A		p.X39_splice	ENST00000338641	NM_000268.3	39			0.50725342136681	1	FACETS	0.902	0.828	0.979	0.902	0.828	0.979	CLONAL	1	TRUE	0	0.50725342136681	1		356	450	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322719	30322719	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	138	444	0	ENST00000322652.5:c.1732G>T	p.Glu578Ter	p.E578*	ENST00000322652	NM_015355.2	578	Gaa/Taa	14/16	1	2	FACETS	0.979	0.895	1	0.979	0.895	1	CLONAL	1	TRUE	1	0.50725342136681	2		444	556	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3114998	3114998	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	202	475	0	ENST00000078429.4:c.533A>T	p.Asp178Val	p.D178V	ENST00000078429	NM_002067.2	178	gAc/gTc	4/7	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.50725342136681	2		475	787	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419986	41419986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372989163	NA	P-0011581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	50	599	0	ENST00000373198.4:c.335G>A	p.Arg112His	p.R112H	ENST00000373198	NM_133170.3	112	cGt/cAt	3/32	1	2	FACETS	0.858	0.726	1	0.858	0.726	1	CLONAL	1	TRUE	1	0.12	2		599	971	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0011581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	60	737	6	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.12	2		743	999	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231437	46231437	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	34	349	2	ENST00000334344.6:c.1277C>T	p.Thr426Met	p.T426M	ENST00000334344	NM_152641.2	426	aCg/aTg	10/21	1	2	FACETS	0.861	0.702	1	0.861	0.702	1	CLONAL	1	TRUE	1	0.12	2		351	658	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726436	46726436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139448277	NA	P-0011581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	30	280	1	ENST00000371975.4:c.515G>A	p.Arg172His	p.R172H	ENST00000371975	NM_003579.3	172	cGc/cAc	7/18	1	2	FACETS	0.947	0.762	1	0.947	0.762	1	CLONAL	1	TRUE	1	0.12	2		281	528	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703506	47703506	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs63751640	NA	P-0011581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	37	437	0	ENST00000233146.2:c.2006G>A	p.Gly669Asp	p.G669D	ENST00000233146	NM_000251.2	669	gGc/gAc	13/16	1	2	FACETS	0.838	0.689	1	0.838	0.689	1	CLONAL	1	TRUE	1	0.12	2		437	736	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120318	94120318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41273629	NA	P-0011581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	57	688	0	ENST00000369303.4:c.733G>A	p.Ala245Thr	p.A245T	ENST00000369303	NM_004440.3	245	Gcc/Acc	3/17	1	2	FACETS	0.836	0.714	0.969	0.836	0.714	0.969	CLONAL	1	TRUE	1	0.12	2		688	1137	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435111	110435111	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1168950458	NA	P-0011581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	37	274	0	ENST00000375856.3:c.3290G>T	p.Arg1097Leu	p.R1097L	ENST00000375856	NM_003749.2	1097	cGc/cTc	1/2	1	2	FACETS	1	0.845	1	1	0.845	1	CLONAL	1	TRUE	1	0.12	2		274	599	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996096	73996096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	58	489	1	ENST00000318443.5:c.830G>A	p.Ser277Asn	p.S277N	ENST00000318443	NM_001024736.1	277	aGc/aAc	5/10	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.12	2		490	883	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934365	81934365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200919414	NA	P-0011581-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	71	602	0	ENST00000359376.3:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000359376	NM_002661.3	448	Cgg/Tgg	14/33	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.12	2		602	1116	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	204	528	2				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.741072662052911	2		530	477	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720833	89720836	+	frameshift_variant	Frame_Shift_Del	DEL	AAAT	AAAT	-	rs587782304	NA	P-0012002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	241	184	0	ENST00000371953.3:c.987_990del	p.Asn329LysfsTer14	p.N329Kfs*14	ENST00000371953	NM_000314.4	328	gcAAAT/gc	8/9	0.741072662052911	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.741072662052911	1		184	389	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100117	157100119	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs797045268	NA	P-0012002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	11	35	0	ENST00000346085.5:c.1069_1071del	p.Gly357del	p.G357del	ENST00000346085	NM_020732.3	352	GGC/-	1/20	1	2	FACETS	0.326	0.228	0.445	0.326	0.228	0.445	SUBCLONAL	1	TRUE	1	0.741072662052911	2		35	91	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891083	112891083	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397507520	NA	P-0012002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	314	362	0	ENST00000351677.2:c.417G>C	p.Glu139Asp	p.E139D	ENST00000351677	NM_002834.3	139	gaG/gaC	4/16	0.188028592600329	1	FACETS	0.517	0.489	0.547	0.517	0.489	0.547	INDETERMINATE	1	TRUE	0	0.741072662052911	1		362	1031	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107136	27107137	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0012002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	248	213	0	ENST00000324856.7:c.6749_6750del	p.Glu2250ValfsTer27	p.E2250Vfs*27	ENST00000324856	NM_006015.4	2249	tcAGag/tcag	20/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.741072662052911	2		213	651	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265278	16265278	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012031-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	288	506	1	ENST00000375759.3:c.10770C>A	p.Ser3590Arg	p.S3590R	ENST00000375759	NM_015001.2	3590	agC/agA	14/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.904026956786453	2		507	623	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0012032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	180	237	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.422484661453253	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.43353683769348	1		238	567	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	120	528	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.43353683769348	2		530	447	SUCCESS
APC	324	MSKCC	GRCh37	5	112175766	112175766	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	116	187	0	ENST00000257430.4:c.4476del	p.Thr1493ArgfsTer14	p.T1493Rfs*14	ENST00000257430	NM_000038.5	1492	gCc/gc	16/16	1	2	FACETS	0.964	0.872	1	0.964	0.872	1	CLONAL	1	TRUE	1	0.43353683769348	2		187	555	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008548	70008548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771113831	NA	P-0012032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	98	172	0	ENST00000394351.3:c.835C>T	p.Arg279Trp	p.R279W	ENST00000394351	NM_000248.3	279	Cgg/Tgg	8/9	1	2	FACETS	0.788	0.704	0.876	0.788	0.704	0.876	SUBCLONAL	1	TRUE	1	0.43353683769348	2		172	574	SUCCESS
AR	367	MSKCC	GRCh37	X	66863125	66863125	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139524801	NA	P-0012032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	332	355	0	ENST00000374690.3:c.1644G>T	p.Leu548Phe	p.L548F	ENST00000374690	NM_000044.3	548	ttG/ttT	2/8	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.43353683769348	1		355	807	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035903	47035903	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	323	258	1	ENST00000377604.3:c.583del	p.Leu195SerfsTer71	p.L195Sfs*71	ENST00000377604	NM_001204468.1	194	tCc/tc	7/24	1	1	FACETS	0.778	0.739	0.817	1	0.995	1	SUBCLONAL	2	TRUE	0	0.43353683769348	1		259	750	SUCCESS
APC	324	MSKCC	GRCh37	5	112174471	112174475	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAC	AAAAC	-	rs587779352	NA	P-0012032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	67	192	0	ENST00000257430.4:c.3183_3187del	p.Gln1062Ter	p.Q1062*	ENST00000257430	NM_000038.5	1060	atAAAACaa/ataa	16/16	1	2	FACETS	0.637	0.555	0.726	0.637	0.555	0.726	SUBCLONAL	1	TRUE	1	0.43353683769348	2		192	485	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873659	151873659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142287778	NA	P-0012046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	100	120	0	ENST00000262189.6:c.8879C>T	p.Pro2960Leu	p.P2960L	ENST00000262189	NM_170606.2	2960	cCg/cTg	38/59	1	2	FACETS	0.809	0.724	0.9	0.809	0.724	0.9	CLONAL	1	TRUE	1	0.382527152924649	2		120	646	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0012049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	51	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.516037119036483	3	FACETS	0.775	0.662	0.897	0.387	0.331	0.449	SUBCLONAL	1	TRUE	1	0.516037119036483	3		249	321	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	567	389	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.516037119036483	6	FACETS	0.987	0.956	1			1	CLONAL	5	TRUE	NA	0.516037119036483	6		389	905	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0012049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	359	385	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.17918583804317	3	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.516037119036483	3		385	707	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190894	185190894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555365583	NA	P-0012049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	303	737	0	ENST00000265026.3:c.1775G>A	p.Arg592Gln	p.R592Q	ENST00000265026	NM_004721.4	592	cGa/cAa	11/14	0.516037119036483	3	FACETS	1	0.983	1	0.559	0.526	0.593	CLONAL	1	TRUE	1	0.516037119036483	3		737	1322	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517974	8517974	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	169	547	0	ENST00000356435.5:c.1417G>T	p.Asp473Tyr	p.D473Y	ENST00000356435		473	Gac/Tac	10/35	NA	2	FACETS	0.725	0.666	0.785			1	INDETERMINATE	1	TRUE	NA	0.516037119036483	2		547	904	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97873774	97873774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs864622522	NA	P-0012049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	283	336	0	ENST00000289081.3:c.1300G>A	p.Asp434Asn	p.D434N	ENST00000289081	NM_000136.2	434	Gat/Aat	13/15	0.516037119036483	2	FACETS	0.941	0.893	0.988	0.941	0.893	0.988	CLONAL	2	TRUE	0	0.516037119036483	2		336	583	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609021	43609021	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	241	690	0	ENST00000355710.3:c.1777G>C	p.Gly593Arg	p.G593R	ENST00000355710	NM_020975.4	593	Gga/Cga	10/20	NA	2	FACETS	1	0.963	1			1	INDETERMINATE	1	TRUE	NA	0.516037119036483	2		690	896	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006363	12006363	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1290	163	401	1	ENST00000396373.4:c.331G>T	p.Asp111Tyr	p.D111Y	ENST00000396373	NM_001987.4	111	Gat/Tat	4/8	0.516037119036483	6	FACETS	0.884	0.808	0.963			1	CLONAL	1	TRUE	NA	0.516037119036483	6		402	1453	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415854	49415854	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	438	484	0	ENST00000301067.7:c.16493C>G	p.Ser5498Cys	p.S5498C	ENST00000301067	NM_003482.3	5498	tCc/tGc	53/54	0.242045084789571	5	FACETS	0.96	0.918	1			1	INDETERMINATE	3	TRUE	NA	0.516037119036483	5		484	1046	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65569030	65569030	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	774	488	0	ENST00000358664.4:c.28G>T	p.Glu10Ter	p.E10*	ENST00000358664	NM_002382.4	10	Gag/Tag	1/5	0.509801814408104	4	FACETS	0.95	0.925	0.974	0.95	0.925	0.974	CLONAL	4	TRUE	0	0.516037119036483	4		488	1197	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250929	10250929	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	246	367	0	ENST00000340748.4:c.3551C>G	p.Ser1184Cys	p.S1184C	ENST00000340748		1184	tCc/tGc	32/40	0.501140951498703	2	FACETS	0.901	0.851	0.951	0.901	0.851	0.951	CLONAL	2	TRUE	0	0.516037119036483	2		367	529	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	146	389	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.291621342265295	2		389	811	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0012054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	154	556	2	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.121969665257843	3	FACETS	0.773	0.708	0.84	0.773	0.708	0.84	INDETERMINATE	2	TRUE	1	0.291621342265295	3		558	783	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0012054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	74	190	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	1	2	FACETS	0.908	0.796	1	0.908	0.796	1	CLONAL	1	TRUE	1	0.291621342265295	2		190	559	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs80338963	NA	P-0012054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	78	449	2	ENST00000342988.3:c.1081C>A	p.Arg361Ser	p.R361S	ENST00000342988	NM_005359.5	361	Cgc/Agc	9/12	1	2	FACETS	0.648	0.569	0.734	0.648	0.569	0.734	SUBCLONAL	1	TRUE	1	0.291621342265295	2		451	825	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590590	95590590	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	121	435	0	ENST00000393063.1:c.1319A>T	p.Asn440Ile	p.N440I	ENST00000393063	NM_030621.3	440	aAc/aTc	9/28	1	2	FACETS	0.818	0.737	0.903	0.818	0.737	0.903	CLONAL	1	TRUE	1	0.291621342265295	2		435	1015	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243006	105243006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	114	360	0	ENST00000349310.3:c.277C>T	p.Pro93Ser	p.P93S	ENST00000349310	NM_001014432.1	93	Cct/Tct	5/15	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.291621342265295	2		360	731	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119041	70119041	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0012054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	98	275	0	ENST00000245479.2:c.613A>T	p.Lys205Ter	p.K205*	ENST00000245479	NM_000346.3	205	Aag/Tag	2/3	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.291621342265295	2		275	600	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775987	9775987	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	312	313	1	ENST00000377346.4:c.451G>T	p.Ala151Ser	p.A151S	ENST00000377346	NM_005026.3	151	Gcc/Tcc	5/24	0.405291045560712	3	FACETS	0.991	0.936	1			1	INDETERMINATE	1	FALSE	NA	0.860014067826273	3		314	1047	SUCCESS
FH	2271	MSKCC	GRCh37	1	241665742	241665742	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0012055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1290	332	459	0	ENST00000366560.3:c.1236+1G>T		p.X412_splice	ENST00000366560	NM_000143.3	412			0.782279433887024	4	FACETS	0.885	0.835	0.938			1	CLONAL	1	FALSE	NA	0.860014067826273	4		459	1622	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535399	66535399	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs748934698	NA	P-0012055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	446	206	0	ENST00000273854.3:c.62C>A	p.Thr21Asn	p.T21N	ENST00000273854	NM_004439.5	21	aCc/aAc	1/18	0.482468278907971	4	FACETS	0.867	0.835	0.897	0.867	0.835	0.897	INDETERMINATE	3	FALSE	1	0.860014067826273	4		206	742	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528273	157528273	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	415	424	0	ENST00000346085.5:c.5998G>C	p.Asp2000His	p.D2000H	ENST00000346085	NM_020732.3	2000	Gat/Cat	20/20	0.860014067826273	2	FACETS	1	0.99	1	0.553	0.53	0.577	CLONAL	1	FALSE	0	0.860014067826273	2		424	872	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235809	108235809	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1555151205	NA	P-0012055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	533	342	0	ENST00000278616.4:c.8851G>A	p.Val2951Ile	p.V2951I	ENST00000278616	NM_000051.3	2951	Gtc/Atc	62/63	0.696601841870268	3	FACETS	0.972	0.953	0.989			1	CLONAL	3	FALSE	NA	0.860014067826273	3		342	608	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794422	42794422	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs755996095	NA	P-0012055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	1431	665	1	ENST00000575354.2:c.1502C>A	p.Ser501Tyr	p.S501Y	ENST00000575354	NM_015125.3	501	tCc/tAc	10/20	0.67496555125813	4	FACETS	0.982	0.964	1			1	CLONAL	3	FALSE	NA	0.860014067826273	4		666	2101	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794967	42794967	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	617	310	0	ENST00000575354.2:c.2047C>G	p.Pro683Ala	p.P683A	ENST00000575354	NM_015125.3	683	Cct/Gct	10/20	0.67496555125813	4	FACETS	0.94	0.913	0.967			1	CLONAL	3	FALSE	NA	0.860014067826273	4		310	946	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972664	76972664	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	850	594	1	ENST00000373344.5:c.77C>T	p.Ser26Leu	p.S26L	ENST00000373344	NM_000489.3	26	tCa/tTa	2/35	0.696601841870268	3	FACETS	0.911	0.885	0.936			1	CLONAL	2	FALSE	NA	0.860014067826273	3		595	1552	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034475	47034476	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012055-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	502	512	2	ENST00000377604.3:c.560_561delinsAA	p.Trp187Ter	p.W187*	ENST00000377604	NM_001204468.1	187	tGG/tAA	6/24	1	2	FACETS	0.985	0.946	1	0.985	0.946	1	CLONAL	1	FALSE	1	0.860014067826273	2		514	1185	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0012057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	39	422	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.763	0.631	0.912	0.763	0.631	0.912	CLONAL	1	TRUE	1	0.13	2		422	786	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969890	161969890	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	40	347	0	ENST00000366898.1:c.1079G>T	p.Cys360Phe	p.C360F	ENST00000366898	NM_004562.2	360	tGt/tTt	9/12	1	2	FACETS	0.928	0.77	1	0.928	0.77	1	CLONAL	1	TRUE	1	0.13	2		347	663	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204809	94204809	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	32	271	0	ENST00000323929.3:c.776A>G	p.Gln259Arg	p.Q259R	ENST00000323929	NM_005591.3	259	cAg/cGg	8/20	1	2	FACETS	0.79	0.64	0.961	0.79	0.64	0.961	CLONAL	1	TRUE	1	0.13	2		271	623	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207092	1207092	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs778376925	NA	P-0012057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	108	441	0	ENST00000326873.7:c.180C>A	p.Tyr60Ter	p.Y60*	ENST00000326873	NM_000455.4	60	taC/taA	1/10	1	2	FACETS	0.927	0.831	1	1	0.987	1	CLONAL	2	TRUE	1	0.13	2		441	896	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439880	49439881	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0012058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	320	519	1	ENST00000301067.7:c.4660_4661del	p.Val1554LeufsTer48	p.V1554Lfs*48	ENST00000301067	NM_003482.3	1554	GTc/c	17/54	1	2	FACETS	0.909	0.859	0.959	0.909	0.859	0.959	CLONAL	1	TRUE	1	0.678553213713811	2		520	1038	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266112	41266112	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913228	NA	P-0012058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	337	430	0	ENST00000349496.5:c.109T>G	p.Ser37Ala	p.S37A	ENST00000349496	NM_001904.3	37	Tct/Gct	3/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.678553213713811	2		430	965	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099026	27099026	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	587	371	0	ENST00000324856.7:c.3442C>T	p.Gln1148Ter	p.Q1148*	ENST00000324856	NM_006015.4	1148	Cag/Tag	13/20	0.678553213713811	2	FACETS	0.975	0.947	1	0.975	0.947	1	CLONAL	2	TRUE	0	0.678553213713811	2		371	887	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65323354	65323354	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	241	309	1	ENST00000342505.4:c.1443C>A	p.Cys481Ter	p.C481*	ENST00000342505	NM_002227.2	481	tgC/tgA	10/25	0.678553213713811	2	FACETS	0.972	0.912	1	0.486	0.456	0.517	CLONAL	1	TRUE	0	0.678553213713811	2		310	731	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750683	128750683	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	356	465	0	ENST00000377970.2:c.220C>A	p.Pro74Thr	p.P74T	ENST00000377970	NM_002467.4	74	Ccg/Acg	2/3	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.678553213713811	2		465	963	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465985	69465985	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	284	443	0	ENST00000227507.2:c.823G>T	p.Glu275Ter	p.E275*	ENST00000227507	NM_053056.2	275	Gaa/Taa	5/5	1	2	FACETS	0.939	0.885	0.995	0.939	0.885	0.995	CLONAL	1	TRUE	1	0.678553213713811	2		443	891	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742733	39742733	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	364	474	0	ENST00000361337.2:c.1576G>T	p.Glu526Ter	p.E526*	ENST00000361337	NM_003286.2	526	Gag/Tag	15/21	1	2	FACETS	0.987	0.937	1	0.987	0.937	1	CLONAL	1	TRUE	1	0.678553213713811	2		474	1087	SUCCESS
AR	367	MSKCC	GRCh37	X	66766286	66766286	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	159	283	0	ENST00000374690.3:c.1298C>A	p.Ser433Ter	p.S433*	ENST00000374690	NM_000044.3	433	tCa/tAa	1/8	1	2	FACETS	0.831	0.766	0.898	0.831	0.766	0.898	CLONAL	1	TRUE	1	0.678553213713811	2		283	564	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717697	89717724	+	frameshift_variant	Frame_Shift_Del	DEL	TTGAGTTCCCTCAGCCGTTACCTGTGTG	TTGAGTTCCCTCAGCCGTTACCTGTGTG	-	novel	NA	P-0012058-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	413	327	0	ENST00000371953.3:c.723_750del	p.Phe241LeufsTer6	p.F241Lfs*6	ENST00000371953	NM_000314.4	241	tTTGAGTTCCCTCAGCCGTTACCTGTGTGt/tt	7/9	0.678553213713811	2	FACETS	0.887	0.854	0.92	0.887	0.854	0.92	CLONAL	2	TRUE	0	0.678553213713811	2		327	686	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0012076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1315	983	474	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.3	11	FACETS	0.946	0.919	0.974			1	CLONAL	8	TRUE	NA	0.23	11		474	2298	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047507	49047507	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0012076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	58	404	0	ENST00000267163.4:c.2501C>G	p.Ser834Ter	p.S834*	ENST00000267163	NM_000321.2	834	tCa/tGa	24/27	1	2	FACETS	0.65	0.557	0.751	0.65	0.557	0.751	SUBCLONAL	1	TRUE	1	0.23	2		404	776	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888102	81888102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	92	752	0	ENST00000359376.3:c.247G>A	p.Glu83Lys	p.E83K	ENST00000359376	NM_002661.3	83	Gag/Aag	3/33	0.154850181842619	1	FACETS	0.574	0.508	0.644	0.574	0.508	0.644	SUBCLONAL	1	TRUE	0	0.23	1		752	1234	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0012076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	125	341	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.23	2		341	908	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45649965	45649966	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0012076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	42	285	0	ENST00000407780.3:c.869_870delinsTT	p.Trp290Phe	p.W290F	ENST00000407780	NM_001283052.1	290	tGG/tTT	6/7	1	2	FACETS	0.518	0.431	0.615	0.518	0.431	0.615	SUBCLONAL	1	TRUE	1	0.23	2		285	705	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0012092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	314	237	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.867739493606888	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.872898823171145	1		238	388	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521463	8521463	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	478	520	0	ENST00000356435.5:c.775G>T	p.Ala259Ser	p.A259S	ENST00000356435		259	Gcc/Tcc	9/35	1	2	FACETS	0.948	0.909	0.988	0.948	0.909	0.988	CLONAL	1	TRUE	1	0.872898823171145	2		520	1155	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148507499	148507499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	157	328	0	ENST00000320356.2:c.1955C>T	p.Ser652Phe	p.S652F	ENST00000320356	NM_004456.4	652	tCt/tTt	17/20	0.447880585966297	1	FACETS	0.369	0.34	0.4	0.369	0.34	0.4	INDETERMINATE	1	TRUE	0	0.872898823171145	1		328	549	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245963	16245963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	339	629	0	ENST00000375759.3:c.1586C>T	p.Ser529Leu	p.S529L	ENST00000375759	NM_015001.2	529	tCa/tTa	8/15	0.447683766118258	1	FACETS	0.372	0.352	0.393	0.372	0.352	0.393	INDETERMINATE	1	TRUE	0	0.872898823171145	1		629	1177	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843499	156843499	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	189	455	0	ENST00000524377.1:c.925C>A	p.Pro309Thr	p.P309T	ENST00000524377	NM_002529.3	309	Ccg/Acg	8/17	0.447683766118258	1	FACETS	0.342	0.317	0.368	0.342	0.317	0.368	INDETERMINATE	1	TRUE	0	0.872898823171145	1		455	713	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632251	215632251	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs769529578	NA	P-0012092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	207	612	0	ENST00000260947.4:c.1523A>T	p.Asp508Val	p.D508V	ENST00000260947	NM_000465.2	508	gAt/gTt	6/11	0.556893398686624	1	FACETS	0.292	0.271	0.314	0.292	0.271	0.314	SUBCLONAL	1	TRUE	0	0.872898823171145	1		612	915	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426872	6426872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	425	583	0	ENST00000356142.4:c.65G>A	p.Ser22Asn	p.S22N	ENST00000356142	NM_018890.3	22	aGt/aAt	2/7	0.58444947202525	3	FACETS	1	0.987	1	0.547	0.521	0.573	CLONAL	1	TRUE	1	0.872898823171145	3		583	1278	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396665	396665	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	463	600	0	ENST00000262320.3:c.361T>A	p.Cys121Ser	p.C121S	ENST00000262320	NM_003502.3	121	Tgc/Agc	2/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.872898823171145	2		600	1008	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857404	9857404	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	416	551	0	ENST00000330684.3:c.3997T>C	p.Ser1333Pro	p.S1333P	ENST00000330684	NM_001134407.1	1333	Tca/Cca	13/13	1	2	FACETS	0.933	0.891	0.975	0.933	0.891	0.975	CLONAL	1	TRUE	1	0.872898823171145	2		551	1022	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143029303	143029303	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	207	294	0	ENST00000262992.4:c.2317A>T	p.Asn773Tyr	p.N773Y	ENST00000262992	NM_001101669.1	773	Aac/Tac	21/24	0.777749528258528	2	FACETS	0.85	0.794	0.908	0.425	0.397	0.454	CLONAL	1	TRUE	0	0.777749528258528	2		294	626	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0012100-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	225	366	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	FALSE	NA	0.528196944575674	2		366	680	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0012100-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	167	563	2	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.994	0.917	1	0.994	0.917	1	CLONAL	1	FALSE	1	0.528196944575674	2		565	636	SUCCESS
APC	324	MSKCC	GRCh37	5	112128163	112128164	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	TT	novel	NA	P-0012100-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	129	451	1	ENST00000257430.4:c.666_667delinsTT	p.Gln222_Gln223delinsHisTer	p.Q222_Q223delinsH*	ENST00000257430	NM_000038.5	222	caGCaa/caTTaa	7/16	1	2	FACETS	0.913	0.832	0.998	0.913	0.832	0.998	CLONAL	1	FALSE	1	0.528196944575674	2		452	535	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178663	32178663	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144069425	NA	P-0012100-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	154	447	2	ENST00000375023.3:c.2731G>A	p.Gly911Ser	p.G911S	ENST00000375023	NM_004557.3	911	Ggc/Agc	18/30	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.528196944575674	2		449	553	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410162	139410162	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376055493	NA	P-0012100-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	76	174	1	ENST00000277541.6:c.1676C>T	p.Thr559Met	p.T559M	ENST00000277541	NM_017617.3	559	aCg/aTg	11/34	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.528196944575674	2		175	213	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851531	63851531	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1373243635	NA	P-0012100-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	120	203	0	ENST00000279873.7:c.2309A>G	p.Asn770Ser	p.N770S	ENST00000279873	NM_032199.2	770	aAt/aGt	10/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.528196944575674	2		203	373	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231144	46231144	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012100-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	123	498	0	ENST00000334344.6:c.1064T>A	p.Met355Lys	p.M355K	ENST00000334344	NM_152641.2	355	aTg/aAg	9/21	NA	2	FACETS	0.83	0.754	0.91			1	INDETERMINATE	1	FALSE	NA	0.528196944575674	2		498	561	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711025	114711025	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012100-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	171	311	0	ENST00000543371.1:c.250del	p.Glu84LysfsTer24	p.E84Kfs*24	ENST00000543371	NM_001198531.1	83	ttG/tt	2/14	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.528196944575674	2		311	476	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266711	198266711	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	208	467	0	ENST00000335508.6:c.2221A>G	p.Lys741Glu	p.K741E	ENST00000335508	NM_012433.2	741	Aag/Gag	15/25	0.130130125399506	4	FACETS	0.797	0.742	0.854	0.797	0.742	0.854	INDETERMINATE	2	TRUE	2	0.519015199061992	4		467	764	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786746	3786746	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1303444757	NA	P-0012102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	79	761	0	ENST00000262367.5:c.4465C>A	p.Pro1489Thr	p.P1489T	ENST00000262367	NM_004380.2	1489	Cct/Act	27/31	0.189140338156893	0	FACETS	0.198	0.174	0.224			1	INDETERMINATE	1	TRUE	0	0.519015199061992	0		761	739	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188204	10188204	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	173	492	1	ENST00000256474.2:c.349del	p.Trp117GlyfsTer42	p.W117Gfs*42	ENST00000256474	NM_000551.3	116	cTt/ct	2/3	0.519015199061992	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.519015199061992	1		493	489	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598079	52598079	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	178	702	0	ENST00000394830.3:c.3787del	p.Ile1263PhefsTer25	p.I1263Ffs*25	ENST00000394830	NM_018313.4	1263	Att/tt	24/30	0.519015199061992	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.519015199061992	1		702	481	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0012127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	217	306	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.676166462554443	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.676166462554443	1		306	417	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189360	56189360	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	300	450	0	ENST00000399503.3:c.4392T>G	p.Ile1464Met	p.I1464M	ENST00000399503	NM_005921.1	1464	atT/atG	20/20	1	2	FACETS	0.957	0.904	1	0.957	0.904	1	CLONAL	1	TRUE	1	0.676166462554443	2		450	927	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121099	11121099	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	346	619	0	ENST00000358026.2:c.2167del	p.Ala723ProfsTer51	p.A723Pfs*51	ENST00000358026	NM_001128849.1	722	caG/ca	15/36	0.354949145555699	1	FACETS	0.835	0.795	0.876	0.835	0.795	0.876	INDETERMINATE	1	TRUE	0	0.676166462554443	1		619	811	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231707	66231707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1211795184	NA	P-0012128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	597	482	0	ENST00000273854.3:c.1993G>A	p.Glu665Lys	p.E665K	ENST00000273854	NM_004439.5	665	Gaa/Aaa	11/18	0.532993919818637	4	FACETS	0.941	0.909	0.972			1	CLONAL	3	FALSE	NA	0.592692989756328	4		482	1137	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879794	37879794	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	107	272	0	ENST00000269571.5:c.2089G>C	p.Val697Leu	p.V697L	ENST00000269571		697	Gtg/Ctg	18/27	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.592692989756328	2		272	322	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935426	36935426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	230	737	0	ENST00000361632.4:c.1301G>A	p.Arg434Lys	p.R434K	ENST00000361632		434	aGa/aAa	10/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.592692989756328	2		737	742	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440882	52440882	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	176	510	0	ENST00000460680.1:c.622C>G	p.Arg208Gly	p.R208G	ENST00000460680	NM_004656.3	208	Cgg/Ggg	8/17	1	2	FACETS	0.955	0.884	1	0.955	0.884	1	CLONAL	1	FALSE	1	0.592692989756328	2		510	622	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523654	176523654	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	237	1068	0	ENST00000292408.4:c.2065C>T	p.Pro689Ser	p.P689S	ENST00000292408	NM_213647.1	689	Ccg/Tcg	16/18	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.592692989756328	2		1068	751	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672972	30672972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	254	723	1	ENST00000376406.3:c.3988C>T	p.Pro1330Ser	p.P1330S	ENST00000376406	NM_014641.2	1330	Cct/Tct	10/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.592692989756328	2		724	815	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673742	30673742	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	172	500	0	ENST00000376406.3:c.3218C>T	p.Ser1073Phe	p.S1073F	ENST00000376406	NM_014641.2	1073	tCt/tTt	10/15	1	2	FACETS	0.893	0.825	0.963	0.893	0.825	0.963	CLONAL	1	FALSE	1	0.592692989756328	2		500	650	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984943	9984943	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	405	597	0	ENST00000330684.3:c.1022T>C	p.Val341Ala	p.V341A	ENST00000330684	NM_001134407.1	341	gTt/gCt	4/13	0.457242677229455	3	FACETS	0.982	0.939	1	0.982	0.939	1	CLONAL	2	FALSE	1	0.592692989756328	3		597	902	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775629	39775629	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	65	229	0	ENST00000288319.7:c.391C>T	p.Pro131Ser	p.P131S	ENST00000288319	NM_182918.3	131	Cct/Tct	4/10	1	2	FACETS	0.954	0.838	1	0.954	0.838	1	CLONAL	1	FALSE	1	0.592692989756328	2		229	230	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491662	120491663	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs312262800	NA	P-0012128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	208	532	0	ENST00000256646.2:c.2566_2567del	p.Ser856LeufsTer17	p.S856Lfs*17	ENST00000256646	NM_024408.3	856	AGt/t	16/34	1	2	FACETS	0.973	0.907	1	0.973	0.907	1	CLONAL	1	FALSE	1	0.592692989756328	2		532	721	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0012135-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	48	237	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.22	2		238	321	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0012135-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	21	229	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	1	2	FACETS	0.636	0.49	0.807	0.636	0.49	0.807	SUBCLONAL	1	TRUE	1	0.22	2		229	300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0012138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	169	736	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.318407035621962	1	FACETS	0.917	0.843	0.995	0.917	0.843	0.995	CLONAL	1	TRUE	0	0.318407035621962	1		737	973	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577077	7577077	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs748891343	NA	P-0012138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	167	532	0	ENST00000269305.4:c.861G>C	p.Glu287Asp	p.E287D	ENST00000269305	NM_001126112.2	287	gaG/gaC	8/11	0.318407035621962	1	FACETS	0.908	0.834	0.986	0.908	0.834	0.986	CLONAL	1	TRUE	0	0.318407035621962	1		532	971	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6045523	6045523	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012138-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	43	104	0	ENST00000265849.7:c.163G>T	p.Asp55Tyr	p.D55Y	ENST00000265849	NM_000535.5	55	Gat/Tat	2/15	0.318407035621962	3	FACETS	1	0.851	1	0.507	0.426	0.595	CLONAL	1	TRUE	1	0.318407035621962	3		104	309	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012139-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	56	389	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.97	0.831	1	0.97	0.831	1	CLONAL	1	TRUE	1	0.201863303455252	2		389	572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0012139-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	53	519	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.201863303455252	1	FACETS	0.892	0.761	1	0.892	0.761	1	CLONAL	1	TRUE	0	0.201863303455252	1		519	529	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615610	43615610	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060500759	NA	P-0012139-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	71	478	0	ENST00000355710.3:c.2689C>T	p.Arg897Ter	p.R897*	ENST00000355710	NM_020975.4	897	Cga/Tga	15/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.201863303455252	2		478	490	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610470	81610470	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012139-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	56	610	0	ENST00000298171.2:c.2068T>G	p.Phe690Val	p.F690V	ENST00000298171	NM_000369.2	690	Ttc/Gtc	10/10	1	2	FACETS	0.718	0.614	0.832	0.718	0.614	0.832	SUBCLONAL	1	TRUE	1	0.201863303455252	2		610	773	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948080	178948080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	204	420	1	ENST00000263967.3:c.2852G>A	p.Arg951His	p.R951H	ENST00000263967	NM_006218.2	951	cGt/cAt	20/21	0.468713401573426	3	FACETS	0.799	0.74	0.862	0.4	0.37	0.431	SUBCLONAL	1	TRUE	1	0.468713401573426	3		421	1344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0012155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	681	679	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.146425102678796	3	FACETS	1	0.996	1			1	INDETERMINATE	2	TRUE	NA	0.468713401573426	3		679	1463	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610265	10610265	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	617	717	1	ENST00000171111.5:c.445G>A	p.Glu149Lys	p.E149K	ENST00000171111	NM_203500.1	149	Gag/Aag	2/6	0.443453085442329	2	FACETS	0.954	0.92	0.988	0.954	0.92	0.988	CLONAL	2	TRUE	0	0.468713401573426	2		718	1380	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578445	7578445	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587780069	NA	P-0012161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	31	422	0	ENST00000269305.4:c.485T>G	p.Ile162Ser	p.I162S	ENST00000269305	NM_001126112.2	162	aTc/aGc	5/11	1	2	FACETS	0.64	0.517	0.782	0.64	0.517	0.782	SUBCLONAL	1	TRUE	1	0.16	2		422	605	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334804	81334804	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	25	420	0	ENST00000222390.5:c.1912G>A	p.Gly638Arg	p.G638R	ENST00000222390	NM_000601.4	638	Gga/Aga	17/18	1	2	FACETS	0.751	0.591	0.935	0.751	0.591	0.935	CLONAL	1	TRUE	1	0.16	2		420	416	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46240704	46240704	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0012161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	35	463	0	ENST00000334344.6:c.1564A>T	p.Lys522Ter	p.K522*	ENST00000334344	NM_152641.2	522	Aag/Tag	12/21	1	2	FACETS	1	0.837	1	1	0.837	1	CLONAL	1	TRUE	1	0.16	2		463	428	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912904	50912904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	87	922	1	ENST00000440232.2:c.2135C>T	p.Pro712Leu	p.P712L	ENST00000440232	NM_002691.3	712	cCg/cTg	17/27	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.16	2		923	1071	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987135	36987135	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	19	231	0	ENST00000354822.5:c.554del	p.Pro185ArgfsTer43	p.P185Rfs*43	ENST00000354822	NM_001079668.2	185	cCg/cg	3/3	1	2	FACETS	0.857	0.651	1	0.857	0.651	1	CLONAL	1	TRUE	1	0.16	2		231	277	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038276	30038276	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0012173-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	152	463	1	ENST00000338641.4:c.447+2T>A		p.X149_splice	ENST00000338641	NM_000268.3	149			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		464	598	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023471	27023471	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	454	1007	0	ENST00000324856.7:c.577G>T	p.Glu193Ter	p.E193*	ENST00000324856	NM_006015.4	193	Gag/Tag	1/20	0.661737869292042	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.661737869292042	1		1007	858	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594258	55594258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913523	NA	P-0012178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	155	482	0	ENST00000288135.5:c.1961T>C	p.Val654Ala	p.V654A	ENST00000288135	NM_000222.2	654	gTg/gCg	13/21	1	2	FACETS	0.918	0.845	0.993	0.918	0.845	0.993	CLONAL	1	TRUE	1	0.604116253136836	2		482	559	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-0012178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	147	657	0	ENST00000288135.5:c.1648-6_1672del		p.K550_K558del	ENST00000288135	NM_000222.2	550		11/21	1	2	FACETS	0.589	0.538	0.643	0.589	0.538	0.643	SUBCLONAL	1	TRUE	1	0.604116253136836	2		657	826	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165296	47165296	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1349108254	NA	P-0012178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	272	631	0	ENST00000409792.3:c.830T>C	p.Ile277Thr	p.I277T	ENST00000409792	NM_014159.6	277	aTt/aCt	3/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.604116253136836	2		631	859	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55987310	55987310	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012198-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	67	458	0	ENST00000263923.4:c.115G>C	p.Asp39His	p.D39H	ENST00000263923	NM_002253.2	39	Gac/Cac	2/30	1	2	FACETS	0.917	0.796	1	0.917	0.796	1	CLONAL	1	TRUE	1	0.19	2		458	769	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139003	37139003	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012198-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	81	667	0	ENST00000373509.5:c.343A>G	p.Ser115Gly	p.S115G	ENST00000373509	NM_002648.3	115	Agt/Ggt	4/6	1	2	FACETS	0.936	0.823	1	0.936	0.823	1	CLONAL	1	TRUE	1	0.19	2		667	911	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139818352	139818352	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012198-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1333	80	957	3	ENST00000247668.2:c.1187T>A	p.Leu396Gln	p.L396Q	ENST00000247668	NM_021138.3	396	cTg/cAg	10/11	1	2	FACETS	0.596	0.522	0.676	0.596	0.522	0.676	SUBCLONAL	1	TRUE	1	0.19	2		960	1413	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473747	67473747	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs753302359	NA	P-0012198-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	85	652	0	ENST00000327367.4:c.827A>G	p.Asn276Ser	p.N276S	ENST00000327367	NM_005902.3	276	aAt/aGt	6/9	1	2	FACETS	0.893	0.787	1	0.893	0.787	1	CLONAL	1	TRUE	1	0.19	2		652	1002	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343642	343642	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012198-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1258	93	1084	2	ENST00000262320.3:c.2032C>T	p.Gln678Ter	p.Q678*	ENST00000262320	NM_003502.3	678	Cag/Tag	8/11	1	2	FACETS	0.725	0.642	0.814	0.725	0.642	0.814	SUBCLONAL	1	TRUE	1	0.19	2		1086	1351	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396164	396164	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012198-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	55	460	1	ENST00000262320.3:c.862G>T	p.Glu288Ter	p.E288*	ENST00000262320	NM_003502.3	288	Gaa/Taa	2/11	1	2	FACETS	0.746	0.637	0.866	0.746	0.637	0.866	SUBCLONAL	1	TRUE	1	0.19	2		461	776	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981509	55981509	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	174	515	0	ENST00000263923.4:c.428A>G	p.Asn143Ser	p.N143S	ENST00000263923	NM_002253.2	143	aAc/aGc	4/30	0.289669346242849	3	FACETS	0.699	0.642	0.759	0.35	0.321	0.38	SUBCLONAL	1	TRUE	1	0.469382481366362	3		515	1309	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0012203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	346	567	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.304457820965609	2	FACETS	1	0.994	1	0.701	0.664	0.738	CLONAL	1	TRUE	0	0.469382481366362	2		567	1052	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113296	209113296	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs73070954	NA	P-0012203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	167	511	2	ENST00000345146.2:c.211G>A	p.Val71Ile	p.V71I	ENST00000345146	NM_005896.2	71	Gtc/Atc	4/10	0.248254693603994	3	FACETS	0.735	0.674	0.799	0.368	0.337	0.4	INDETERMINATE	1	TRUE	1	0.469382481366362	3		513	1195	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633229	12633229	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs368807126	NA	P-0012203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	291	437	0	ENST00000251849.4:c.1171A>T	p.Arg391Trp	p.R391W	ENST00000251849	NM_002880.3	391	Agg/Tgg	11/17	0.248254693603994	3	FACETS	1	0.993	1	0.699	0.658	0.741	INDETERMINATE	1	TRUE	1	0.469382481366362	3		437	1095	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038173	128038173	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	277	460	0	ENST00000285398.2:c.1377G>T	p.Gln459His	p.Q459H	ENST00000285398	NM_000122.1	459	caG/caT	9/15	0.248254693603994	3	FACETS	1	0.993	1	0.726	0.682	0.77	INDETERMINATE	1	TRUE	1	0.469382481366362	3		460	1004	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058687	47058687	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	313	444	3	ENST00000409792.3:c.7591G>T	p.Glu2531Ter	p.E2531*	ENST00000409792	NM_014159.6	2531	Gag/Tag	21/21	0.248254693603994	3	FACETS	0.777	0.733	0.821	0.777	0.733	0.821	INDETERMINATE	2	TRUE	1	0.469382481366362	3		447	1060	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200073	128200073	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1204	152	595	0	ENST00000341105.2:c.1232C>A	p.Ala411Glu	p.A411E	ENST00000341105	NM_032638.4	411	gCg/gAg	6/6	0.469382481366362	3	FACETS	0.59	0.538	0.645	0.295	0.269	0.323	SUBCLONAL	1	TRUE	1	0.469382481366362	3		595	1356	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053165	180053165	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	231	579	0	ENST00000261937.6:c.1204T>A	p.Trp402Arg	p.W402R	ENST00000261937	NM_182925.4	402	Tgg/Agg	9/30	0.32757283637287	2	FACETS	1	0.988	1	0.621	0.581	0.663	CLONAL	1	TRUE	0	0.469382481366362	2		579	792	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741937	145741937	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1564808143	NA	P-0012203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	78	357	0	ENST00000428558.2:c.566G>C	p.Gly189Ala	p.G189A	ENST00000428558	NM_004260.3	189	gGc/gCc	5/22	NA	2	FACETS	0.573	0.504	0.647			1	INDETERMINATE	1	TRUE	NA	0.469382481366362	2		357	580	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518346	8518346	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	95	206	0	ENST00000356435.5:c.1045G>C	p.Glu349Gln	p.E349Q	ENST00000356435		349	Gag/Cag	10/35	0.469382481366362	1	FACETS	0.693	0.62	0.77	0.693	0.62	0.77	SUBCLONAL	1	TRUE	0	0.469382481366362	1		206	447	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229650	98229650	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs766313615	NA	P-0012203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	71	305	2	ENST00000331920.6:c.2308C>T	p.Arg770Ter	p.R770*	ENST00000331920	NM_000264.3	770	Cga/Tga	15/24	0.160603140040434	2	FACETS	0.42	0.366	0.478	0.21	0.183	0.239	INDETERMINATE	1	TRUE	0	0.469382481366362	2		307	721	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445443	49445443	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	127	490	0	ENST00000301067.7:c.2023C>T	p.Pro675Ser	p.P675S	ENST00000301067	NM_003482.3	675	Cct/Tct	10/54	0.262710503879791	5	FACETS	0.755	0.682	0.832			1	INDETERMINATE	1	TRUE	NA	0.469382481366362	5		490	1222	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448762	49448762	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	136	404	0	ENST00000301067.7:c.97C>G	p.Leu33Val	p.L33V	ENST00000301067	NM_003482.3	33	Ctg/Gtg	2/54	0.262710503879791	5	FACETS	0.794	0.72	0.872			1	INDETERMINATE	1	TRUE	NA	0.469382481366362	5		404	1244	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626755	28626755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750445891	NA	P-0012203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	320	428	3	ENST00000241453.7:c.541G>A	p.Ala181Thr	p.A181T	ENST00000241453	NM_004119.2	181	Gcc/Acc	5/24	0.304457820965609	2	FACETS	1	0.993	1	0.681	0.644	0.719	CLONAL	1	TRUE	0	0.469382481366362	2		431	1001	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28631600	28631600	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0012203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	83	319	0	ENST00000241453.7:c.369-1G>A		p.X123_splice	ENST00000241453	NM_004119.2	123			0.304457820965609	2	FACETS	0.546	0.482	0.614	0.273	0.241	0.307	SUBCLONAL	1	TRUE	0	0.469382481366362	2		319	648	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778560	3778560	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	257	602	1	ENST00000262367.5:c.6488G>T	p.Gly2163Val	p.G2163V	ENST00000262367	NM_004380.2	2163	gGc/gTc	31/31	0.248254693603994	3	FACETS	1	0.987	1	0.606	0.567	0.646	INDETERMINATE	1	TRUE	1	0.469382481366362	3		603	1116	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829454	72829454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771717307	NA	P-0012203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	129	811	2	ENST00000268489.5:c.7127C>T	p.Thr2376Met	p.T2376M	ENST00000268489	NM_006885.3	2376	aCg/aTg	9/10	NA	2	FACETS	0.418	0.378	0.461			1	INDETERMINATE	1	TRUE	NA	0.469382481366362	2		813	1315	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836284	89836284	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	188	519	0	ENST00000389301.3:c.2465T>A	p.Leu822Gln	p.L822Q	ENST00000389301	NM_000135.2	822	cTg/cAg	26/43	NA	2	FACETS	0.717	0.661	0.774			1	INDETERMINATE	1	TRUE	NA	0.469382481366362	2		519	1118	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652932	29652932	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1131691123	NA	P-0012203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	355	469	1	ENST00000356175.3:c.4867G>T	p.Asp1623Tyr	p.D1623Y	ENST00000356175	NM_000267.3	1623	Gac/Tac	36/57	0.304457820965609	2	FACETS	1	0.995	1	0.734	0.696	0.771	CLONAL	1	TRUE	0	0.469382481366362	2		470	1031	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853131	151853829	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGTTTTGGTAACTGGAAAAGCAAAAACACAAAACCATAAATACATTCAGTCAATATTGATAAATGGGTAGAACTTTACAATTCTATTGCCATTTCACAATACACAACTGGCAGAGGCACATTTCTCCGAGGTGTGAAATTTGGAGGCTATAATCATACCTTCATGGCTCACTAACACTCCGGCTTTTCCAGCAAGTTCTTCAGTTGTTGCAAAACCATTGGCCATCTTCTGACAAGCCATAGGAGGTGGTGTAGGAGGAAGAGAGGCAGGGGGTGTTGGAGGATTACTTAAATTATTCTGCTGCAGGAGACCAAAAAATTTAAATTATATGCTACTGAGCGAATATGCAATGACCTTGCTAAAACGTAGTTCTGTGAATTTTTTGCACATAGAAGCAAGGCTACAGAAATGTAATCAAGATGTATCTTGCACACCAAGAAAACAATACCTACAAGGCCAGGAGGCTTCTTAGTGGAACAGATACTCGTGATTTTATGGACATACCAACTTGCTTACTTTACCCAGCTTGACTACTTAAGCTCTGAAATTAAGAAGCTAATTTCCTTTCTACCTGATTTTATTTATGCAATTCTTCAAGTTTCGTGGTTATAGCTAGTGAAGGATAACTTTAAAATGCAATCAAGAAATTGCAAAATATTATCAAAATATCCTTTAAGTTCTCATTAAGATATGCCCTA	GAGTTTTGGTAACTGGAAAAGCAAAAACACAAAACCATAAATACATTCAGTCAATATTGATAAATGGGTAGAACTTTACAATTCTATTGCCATTTCACAATACACAACTGGCAGAGGCACATTTCTCCGAGGTGTGAAATTTGGAGGCTATAATCATACCTTCATGGCTCACTAACACTCCGGCTTTTCCAGCAAGTTCTTCAGTTGTTGCAAAACCATTGGCCATCTTCTGACAAGCCATAGGAGGTGGTGTAGGAGGAAGAGAGGCAGGGGGTGTTGGAGGATTACTTAAATTATTCTGCTGCAGGAGACCAAAAAATTTAAATTATATGCTACTGAGCGAATATGCAATGACCTTGCTAAAACGTAGTTCTGTGAATTTTTTGCACATAGAAGCAAGGCTACAGAAATGTAATCAAGATGTATCTTGCACACCAAGAAAACAATACCTACAAGGCCAGGAGGCTTCTTAGTGGAACAGATACTCGTGATTTTATGGACATACCAACTTGCTTACTTTACCCAGCTTGACTACTTAAGCTCTGAAATTAAGAAGCTAATTTCCTTTCTACCTGATTTTATTTATGCAATTCTTCAAGTTTCGTGGTTATAGCTAGTGAAGGATAACTTTAAAATGCAATCAAGAAATTGCAAAATATTATCAAAATATCCTTTAAGTTCTCATTAAGATATGCCCTA	-	novel	NA	P-0012203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	40	208	0	ENST00000262189.6:c.11671-394_11828del		p.X3891_splice	ENST00000262189	NM_170606.2	3891		45-46/59	0.359738891891534	4	FACETS	0.403	0.334	0.48	0.202	0.167	0.24	SUBCLONAL	1	TRUE	2	0.469382481366362	4		208	621	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021158	31021159	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs886043994	NA	P-0012203-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	166	511	0	ENST00000375687.4:c.1162_1163del	p.Val388ProfsTer21	p.V388Pfs*21	ENST00000375687	NM_015338.5	386	tTG/t	12/13	NA	2	FACETS	0.608	0.557	0.661			1	INDETERMINATE	1	TRUE	NA	0.469382481366362	2		511	1163	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	56	528	2				ENST00000310581	NM_198253.2	-/1132			0.182392981557714	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.788528091217975	0		530	106	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0012209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	200	472	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.997	0.932	1	0.997	0.932	1	CLONAL	1	FALSE	1	0.788528091217975	2		473	509	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0012209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	101	341	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	0.199371017398089	4	FACETS	1	0.917	1	0.511	0.459	0.566	INDETERMINATE	1	FALSE	2	0.788528091217975	4		341	448	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791718	42791718	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1344635105	NA	P-0012209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	83	463	5	ENST00000575354.2:c.604C>T	p.Arg202Trp	p.R202W	ENST00000575354	NM_015125.3	202	Cgg/Tgg	5/20	0.663708459683897	1	FACETS	0.504	0.451	0.559	0.504	0.451	0.559	SUBCLONAL	1	FALSE	0	0.788528091217975	1		468	253	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795785	42795786	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0012209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	96	626	0	ENST00000575354.2:c.2776_2777del	p.Leu926GlyfsTer4	p.L926Gfs*4	ENST00000575354	NM_015125.3	925	cCT/c	11/20	0.663708459683897	1	FACETS	0.59	0.535	0.647	0.59	0.535	0.647	SUBCLONAL	1	FALSE	0	0.788528091217975	1		626	250	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0012222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	43	306	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.884	0.756	1	1	0.977	1	CLONAL	3	TRUE	1	0.240278493821655	2		306	135	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480627	120480627	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	51	341	0	ENST00000256646.2:c.3190G>T	p.Val1064Leu	p.V1064L	ENST00000256646	NM_024408.3	1064	Gtg/Ttg	20/34	1	2	FACETS	0.95	0.825	1	1	0.981	1	CLONAL	3	TRUE	1	0.240278493821655	2		341	149	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028662	12028662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	135	609	1	ENST00000353533.5:c.865G>A	p.Asp289Asn	p.D289N	ENST00000353533	NM_003010.3	289	Gat/Aat	8/11	0.240278493821655	2	FACETS	0.999	0.934	1	1	0.993	1	CLONAL	5	TRUE	0	0.240278493821655	2		610	225	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349704	70349704	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	91	696	1	ENST00000374080.3:c.3866A>T	p.Gln1289Leu	p.Q1289L	ENST00000374080		1289	cAg/cTg	27/45	0.240278493821655	1	FACETS	0.926	0.836	1	1	0.989	1	CLONAL	3	TRUE	0	0.240278493821655	1		697	240	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	85	661	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	TRUE	1	0.238172152572815	2		661	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0012224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	89	646	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.238172152572815	1	FACETS	0.867	0.769	0.973	0.867	0.769	0.973	CLONAL	1	TRUE	0	0.238172152572815	1		646	759	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685269	89685269	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs786203847	NA	P-0012242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	15	166	0	ENST00000371953.3:c.165-1G>A		p.X55_splice	ENST00000371953	NM_000314.4	55			1	2	FACETS	0.92	0.673	1	0.92	0.673	1	CLONAL	1	TRUE	1	0.14	2		166	233	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478902	56478902	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	64	802	0	ENST00000267101.3:c.358A>G	p.Met120Val	p.M120V	ENST00000267101	NM_001982.3	120	Atg/Gtg	3/28	1	2	FACETS	0.781	0.674	0.899	0.781	0.674	0.899	SUBCLONAL	1	TRUE	1	0.14	2		802	1170	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872466	35872466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753691609	NA	P-0012242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	62	850	0	ENST00000216797.5:c.437C>T	p.Thr146Ile	p.T146I	ENST00000216797	NM_020529.2	146	aCc/aTc	3/6	1	2	FACETS	0.722	0.621	0.832	0.722	0.621	0.832	SUBCLONAL	1	TRUE	1	0.14	2		850	1227	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	113	528	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.456935540570619	2		530	437	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0012250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	153	379	0	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	1	2	FACETS	0.794	0.727	0.865	0.794	0.727	0.865	SUBCLONAL	1	TRUE	1	0.456935540570619	2		379	843	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272319	38272319	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	160	488	0	ENST00000425967.3:c.2048A>G	p.Asp683Gly	p.D683G	ENST00000425967	NM_001174067.1	683	gAc/gGc	15/19	1	2	FACETS	0.658	0.603	0.716	0.658	0.603	0.716	SUBCLONAL	1	TRUE	1	0.456935540570619	2		488	1064	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624276	89624277	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs587781912	NA	P-0012250-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	103	195	0	ENST00000371953.3:c.50_51del	p.Gln17ArgfsTer26	p.Q17Rfs*26	ENST00000371953	NM_000314.4	17	cAA/c	1/9	0.456935540570619	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.456935540570619	1		195	337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0012254-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	460	771	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.994	1	1	0.997	1	CLONAL	2	TRUE	1	0.32	2		771	1161	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0012254-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	433	736	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	1	0.993	1	1	0.997	1	CLONAL	2	TRUE	1	0.32	2		737	1129	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0012254-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	343	234	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.298449332391481	9	FACETS	0.975	0.942	1	1	0.995	1	CLONAL	10	TRUE	1	0.32	9		234	466	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249468	153249468	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012254-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	346	460	0	ENST00000281708.4:c.1310G>T	p.Gly437Val	p.G437V	ENST00000281708	NM_033632.3	437	gGa/gTa	9/12	1	2	FACETS	0.851	0.809	0.893	1	0.997	1	CLONAL	3	TRUE	1	0.32	2		460	847	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498235	498235	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012254-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	41	345	0	ENST00000399788.2:c.23del	p.Gly8AlafsTer58	p.G8Afs*58	ENST00000399788	NM_001042603.1	8	gGc/gc	1/28	NA	2	FACETS	0.397	0.33	0.472			1	INDETERMINATE	1	TRUE	NA	0.32	2		345	645	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0012266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	63	469	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.14	2		469	765	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0012266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	49	356	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.14	2		356	574	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0012266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	68	563	2	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.991	0.86	1	0.991	0.86	1	CLONAL	1	TRUE	1	0.14	2		565	980	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772068	135772068	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554812930	NA	P-0012266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	14	156	1	ENST00000298552.3:c.3049G>A	p.Glu1017Lys	p.E1017K	ENST00000298552	NM_001162426.1	1017	Gag/Aag	23/23	1	2	FACETS	0.837	0.605	1	0.837	0.605	1	CLONAL	1	TRUE	1	0.14	2		157	239	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346258	89346258	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	36	453	0	ENST00000301030.4:c.6692C>T	p.Ala2231Val	p.A2231V	ENST00000301030	NM_001256183.1	2231	gCc/gTc	9/13	1	2	FACETS	0.861	0.707	1	0.861	0.707	1	CLONAL	1	TRUE	1	0.14	2		453	597	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271574	15271574	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	46	639	0	ENST00000263388.2:c.6865G>A	p.Ala2289Thr	p.A2289T	ENST00000263388	NM_000435.2	2289	Gcc/Acc	33/33	1	2	FACETS	0.917	0.77	1	0.917	0.77	1	CLONAL	1	TRUE	1	0.14	2		639	717	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006489	12006495	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GAAGAAG	GAAGAAG	-	novel	NA	P-0012266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	57	674	0	ENST00000396373.4:c.458_463+1del		p.EED153fs	ENST00000396373	NM_001987.4	153	GAAGAAGat/at	4/8	1	2	FACETS	0.739	0.632	0.857	0.739	0.632	0.857	SUBCLONAL	1	TRUE	1	0.14	2		674	1102	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012270-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	119	528	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.859961020155574	2		530	256	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0012270-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	175	367	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.921	0.857	0.985	0.921	0.857	0.985	CLONAL	1	TRUE	1	0.859961020155574	2		367	442	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372753	81372753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012270-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	261	430	0	ENST00000222390.5:c.781C>T	p.Arg261Cys	p.R261C	ENST00000222390	NM_000601.4	261	Cgc/Tgc	7/18	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.859961020155574	2		430	586	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267475	7267475	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012270-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	283	506	1	ENST00000302850.5:c.533A>G	p.Asp178Gly	p.D178G	ENST00000302850	NM_000208.2	178	gAc/gGc	2/22	1	2	FACETS	0.883	0.835	0.933	0.883	0.835	0.933	CLONAL	1	TRUE	1	0.859961020155574	2		507	745	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0012321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	35	340	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.161827628309968	1	FACETS	0.412	0.337	0.498	0.412	0.337	0.498	SUBCLONAL	1	TRUE	0	0.23	1		340	653	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882025	NA	P-0012321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	55	847	0	ENST00000269305.4:c.646G>T	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ttg	6/11	0.161827628309968	1	FACETS	0.427	0.364	0.496	0.427	0.364	0.496	SUBCLONAL	1	TRUE	0	0.23	1		847	992	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927977	178927988	+	inframe_deletion	In_Frame_Del	DEL	CACTGTCCATTG	CACTGTCCATTG	-	novel	NA	P-0012321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	40	288	0	ENST00000263967.3:c.1255_1266del	p.His419_Leu422del	p.H419_L422del	ENST00000263967	NM_006218.2	419	CACTGTCCATTG/-	8/21	1	2	FACETS	0.801	0.666	0.952	0.801	0.666	0.952	CLONAL	1	TRUE	1	0.23	2		288	434	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685234	89685268	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TAATGGTGGCTTTTTGTTTGTTTGTTTTGTTTTAA	TAATGGTGGCTTTTTGTTTGTTTGTTTTGTTTTAA	-	novel	NA	P-0012321-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	38	157	0	ENST00000371953.3:c.165-36_165-2del		p.X55_splice	ENST00000371953	NM_000314.4	55			0.3	1	FACETS	0.754	0.63	0.889	1	0.955	1	SUBCLONAL	2	TRUE	0	0.23	1		157	194	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0012328-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	35	441	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		441	932	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0012331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	132	623	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		623	979	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743066	743066	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1318314308	NA	P-0012331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	55	545	0	ENST00000314574.4:c.912C>G	p.Ile304Met	p.I304M	ENST00000314574	NM_005433.3	304	atC/atG	8/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		545	915	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0012331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	46	450	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		450	730	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538982	23538982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	79	698	0	ENST00000380871.4:c.457G>A	p.Glu153Lys	p.E153K	ENST00000380871	NM_006167.3	153	Gaa/Aaa	2/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		698	947	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023870	31023870	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	136	598	0	ENST00000375687.4:c.3355G>C	p.Glu1119Gln	p.E1119Q	ENST00000375687	NM_015338.5	1119	Gag/Cag	13/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		598	1030	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151216551	151216551	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	31	260	0	ENST00000262187.5:c.47C>T	p.Ser16Phe	p.S16F	ENST00000262187	NM_005614.3	16	tCt/tTt	1/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		260	337	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874261	155874261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352822	NA	P-0012331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	35	571	0	ENST00000368323.3:c.270G>A	p.Met90Ile	p.M90I	ENST00000368323	NM_006912.5	90	atG/atA	5/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		571	906	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25536793	25536793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	89	696	2	ENST00000264709.3:c.61G>A	p.Glu21Lys	p.E21K	ENST00000264709	NM_175629.2	21	Gag/Aag	2/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		698	978	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048166	180048166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1369049878	NA	P-0012331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	62	545	1	ENST00000261937.6:c.2107G>A	p.Gly703Arg	p.G703R	ENST00000261937	NM_182925.4	703	Gga/Aga	14/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		546	890	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441505	6441505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	41	386	0	ENST00000356142.4:c.352C>T	p.Pro118Ser	p.P118S	ENST00000356142	NM_018890.3	118	Cct/Tct	6/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		386	678	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468056	50468056	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	46	371	1	ENST00000331340.3:c.1291G>T	p.Glu431Ter	p.E431*	ENST00000331340	NM_006060.4	431	Gag/Tag	8/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		372	614	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151216587	151216587	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	22	204	0	ENST00000262187.5:c.11C>G	p.Ser4Cys	p.S4C	ENST00000262187	NM_005614.3	4	tCc/tGc	1/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		204	260	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362612	118362612	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	42	521	0	ENST00000534358.1:c.4973G>T	p.Arg1658Leu	p.R1658L	ENST00000534358	NM_005933.3	1658	cGg/cTg	15/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		521	835	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427995	49427995	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	53	524	0	ENST00000301067.7:c.10595T>C	p.Ile3532Thr	p.I3532T	ENST00000301067	NM_003482.3	3532	aTt/aCt	38/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		524	788	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619935	21619935	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1421639293	NA	P-0012331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	136	867	0	ENST00000382592.4:c.231G>C	p.Leu77Phe	p.L77F	ENST00000382592	NM_014572.2	77	ttG/ttC	2/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		867	1151	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817853	3817853	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	73	748	0	ENST00000262367.5:c.3118G>T	p.Glu1040Ter	p.E1040*	ENST00000262367	NM_004380.2	1040	Gag/Tag	16/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		748	1188	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867214	68867214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	51	374	0	ENST00000261769.5:c.2461G>A	p.Asp821Asn	p.D821N	ENST00000261769	NM_004360.3	821	Gac/Aac	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		374	684	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821173	72821173	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1354	121	973	0	ENST00000268489.5:c.11002C>G	p.Leu3668Val	p.L3668V	ENST00000268489	NM_006885.3	3668	Ctc/Gtc	10/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		973	1475	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029487	16029487	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	56	635	2	ENST00000268712.3:c.1543G>T	p.Glu515Ter	p.E515*	ENST00000268712	NM_006311.3	515	Gaa/Taa	15/46	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		637	924	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226450	41226450	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1194	90	791	0	ENST00000357654.3:c.4573C>G	p.Gln1525Glu	p.Q1525E	ENST00000357654	NM_007294.3	1525	Caa/Gaa	14/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		791	1284	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492807	56492807	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	61	636	0	ENST00000407977.2:c.132G>C	p.Gln44His	p.Q44H	ENST00000407977		44	caG/caC	2/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		636	1044	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281587	15281587	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	69	781	0	ENST00000263388.2:c.4786G>C	p.Glu1596Gln	p.E1596Q	ENST00000263388	NM_000435.2	1596	Gag/Cag	26/33	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		781	1197	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933958	39933958	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	87	495	1	ENST00000378444.4:c.641C>T	p.Ser214Leu	p.S214L	ENST00000378444	NM_001123385.1	214	tCa/tTa	4/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		496	721	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123199782	123199782	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	52	337	0	ENST00000218089.9:c.2082C>G	p.Ile694Met	p.I694M	ENST00000218089	NM_001042749.1	694	atC/atG	21/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		337	445	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215328	123215328	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	72	396	0	ENST00000218089.9:c.2877del	p.Phe959LeufsTer6	p.F959Lfs*6	ENST00000218089	NM_001042749.1	958	acT/ac	28/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		396	670	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080270	5080270	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	74	464	0	ENST00000381652.3:c.2173del	p.Glu725LysfsTer6	p.E725Kfs*6	ENST00000381652	NM_004972.3	725	Gaa/aa	17/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		464	742	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0012340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	42	306	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.539	0.45	0.639	0.539	0.45	0.639	SUBCLONAL	1	TRUE	1	0.291127553753496	2		306	535	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0012340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	127	646	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.832	0.752	0.916	0.832	0.752	0.916	CLONAL	1	TRUE	1	0.291127553753496	2		646	1049	SUCCESS
APC	324	MSKCC	GRCh37	5	112116601	112116601	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs863225370	NA	P-0012340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	39	305	0	ENST00000257430.4:c.645+1G>A		p.X215_splice	ENST00000257430	NM_000038.5	215			1	2	FACETS	0.524	0.434	0.625	0.524	0.434	0.625	SUBCLONAL	1	TRUE	1	0.291127553753496	2		305	511	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0012357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	21	83	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.937	0.725	1	0.937	0.725	1	CLONAL	1	TRUE	1	0.218556065008266	2		83	205	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0012357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	57	509	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.218556065008266	1	FACETS	0.606	0.519	0.701	0.606	0.519	0.701	SUBCLONAL	1	TRUE	0	0.218556065008266	1		509	767	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251991	8251991	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs760736132	NA	P-0012357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	86	552	0	ENST00000335790.3:c.86G>T	p.Arg29Leu	p.R29L	ENST00000335790	NM_002315.2	29	cGc/cTc	2/4	1	2	FACETS	0.818	0.722	0.921	0.818	0.722	0.921	CLONAL	1	TRUE	1	0.218556065008266	2		552	962	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143171	30143171	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	32	305	1	ENST00000389048.3:c.355G>T	p.Glu119Ter	p.E119*	ENST00000389048	NM_004304.4	119	Gag/Tag	1/29	1	2	FACETS	0.615	0.499	0.747	0.615	0.499	0.747	SUBCLONAL	1	TRUE	1	0.218556065008266	2		306	476	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003802	45003802	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	72	342	0	ENST00000558401.1:c.58G>C	p.Ala20Pro	p.A20P	ENST00000558401	NM_004048.2	20	Gct/Cct	1/4	1	2	FACETS	0.826	0.72	0.94	0.826	0.72	0.94	CLONAL	1	TRUE	1	0.218556065008266	2		342	798	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7174720	7174720	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012357-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	59	375	0	ENST00000302850.5:c.997G>C	p.Gly333Arg	p.G333R	ENST00000302850	NM_000208.2	333	Ggt/Cgt	4/22	1	2	FACETS	0.685	0.588	0.791	0.685	0.588	0.791	SUBCLONAL	1	TRUE	1	0.218556065008266	2		375	788	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	232	661	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.29050772260824	4	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	2	0.29050772260824	4		661	1006	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0012366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	99	515	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.832	0.742	0.928	0.832	0.742	0.928	CLONAL	1	TRUE	1	0.29050772260824	2		515	819	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374945	45374945	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	268	478	0	ENST00000262160.6:c.898G>C	p.Asp300His	p.D300H	ENST00000262160	NM_005901.5	300	Gat/Cat	8/11	0.29050772260824	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.29050772260824	2		478	801	SUCCESS
APC	324	MSKCC	GRCh37	5	112175756	112175762	+	frameshift_variant	Frame_Shift_Del	DEL	TTACATT	TTACATT	-	novel	NA	P-0012366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	75	341	0	ENST00000257430.4:c.4467_4473del	p.His1490ProfsTer15	p.H1490Pfs*15	ENST00000257430	NM_000038.5	1489	TTACATTtt/tt	16/16	1	2	FACETS	0.906	0.795	1	0.906	0.795	1	CLONAL	1	TRUE	1	0.29050772260824	2		341	570	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120123	70120132	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGCCACAG	GCAGCCACAG	-	novel	NA	P-0012366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	98	87	0	ENST00000245479.2:c.1127_1136del	p.Gln376ArgfsTer4	p.Q376Rfs*4	ENST00000245479	NM_000346.3	375	caGCAGCCACAG/ca	3/3	0.29050772260824	3	FACETS	1	0.922	1	1	0.983	1	CLONAL	4	TRUE	0	0.29050772260824	3		87	192	SUCCESS
APC	324	MSKCC	GRCh37	5	112136982	112136983	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0012366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	97	282	0	ENST00000257430.4:c.738_739del	p.Gln247GlufsTer4	p.Q247Efs*4	ENST00000257430	NM_000038.5	246	TCt/t	8/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.29050772260824	2		282	512	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0012374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	49	469	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	0.102400364548295	2		469	790	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527461	29527461	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786203950	NA	P-0012374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	66	464	0	ENST00000356175.3:c.910C>T	p.Arg304Ter	p.R304*	ENST00000356175	NM_000267.3	304	Cga/Tga	9/57	1	2	FACETS	1	0.936	1	1	0.982	1	CLONAL	2	FALSE	1	0.102400364548295	2		464	570	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094386	27094386	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	70	408	0	ENST00000324856.7:c.3094G>T	p.Glu1032Ter	p.E1032*	ENST00000324856	NM_006015.4	1032	Gag/Tag	11/20	1	2	FACETS	0.897	0.781	1	1	0.979	1	CLONAL	2	FALSE	1	0.102400364548295	2		408	762	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469919	157469928	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAACAGAC	CAGAACAGAC	-	novel	NA	P-0012374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	47	584	0	ENST00000346085.5:c.2715_2724del	p.Gln905HisfsTer6	p.Q905Hfs*6	ENST00000346085	NM_020732.3	905	CAGAACAGACca/ca	9/20	1	2	FACETS	0.979	0.823	1	0.979	0.823	1	CLONAL	1	FALSE	1	0.102400364548295	2		584	938	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294283	1294283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012390-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	62	188	0	ENST00000310581.5:c.718C>T	p.Arg240Cys	p.R240C	ENST00000310581	NM_198253.2	240	Cgt/Tgt	2/16	0.375160140396934	5	FACETS	1	0.93	1	0.372	0.322	0.426	CLONAL	1	TRUE	2	0.42994068468911	5		188	425	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288156	33288156	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0012390-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	174	292	1	ENST00000374542.5:c.1251+1G>A		p.X417_splice	ENST00000374542	NM_001141970.1	417			0.42994068468911	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.42994068468911	2		293	370	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262905	46262905	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs867083206	NA	P-0012390-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1295	528	970	0	ENST00000371998.3:c.1078C>T	p.Arg360Ter	p.R360*	ENST00000371998		360	Cga/Tga	10/23	0.378530272083937	4	FACETS	0.963	0.922	1	0.963	0.922	1	CLONAL	2	TRUE	2	0.42994068468911	4		970	1823	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500489	149500491	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0012390-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	137	537	0	ENST00000261799.4:c.2546_2548del	p.Arg849_Asp850delinsHis	p.R849_D850delinsH	ENST00000261799	NM_002609.3	849	cGAGac/cac	18/23	0.424827665618039	3	FACETS	0.747	0.679	0.82	0.374	0.339	0.41	SUBCLONAL	1	TRUE	1	0.42994068468911	3		537	1036	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0012393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	61	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.474921527310205	3	FACETS	0.734	0.636	0.841	0.367	0.318	0.421	SUBCLONAL	1	TRUE	1	0.494521700510738	3		249	419	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0012393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	1242	563	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.494521700510738	9	FACETS	0.946	0.928	0.964	0.946	0.928	0.964	CLONAL	8	TRUE	1	0.494521700510738	9		563	1812	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023408	31023408	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515401	NA	P-0012393-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	105	470	0	ENST00000375687.4:c.2893C>T	p.Arg965Ter	p.R965*	ENST00000375687	NM_015338.5	965	Cga/Tga	13/13	0.469560935385074	3	FACETS	0.73	0.654	0.81	0.365	0.327	0.405	SUBCLONAL	1	TRUE	1	0.494521700510738	3		470	726	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249007	+	missense_variant	Missense_Mutation	TNP	GCG	GCG	TCC	novel	NA	P-0012404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	265	508	0	ENST00000275493.2:c.2303_2305delinsTCC	p.Ser768_Val769delinsIleLeu	p.S768_V769delinsIL	ENST00000275493	NM_005228.3	768	aGCGtg/aTCCtg	20/28	0.200452101147749	4	FACETS	0.956	0.897	1	0.956	0.897	1	INDETERMINATE	2	TRUE	2	0.372663836616749	4		508	1021	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0012408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	77	503	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.272651377044575	2		503	445	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956220	55956220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190050670	NA	P-0012408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	142	592	1	ENST00000263923.4:c.3095G>A	p.Arg1032Gln	p.R1032Q	ENST00000263923	NM_002253.2	1032	cGa/cAa	23/30	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.272651377044575	2		593	968	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851747	134851747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	118	514	1	ENST00000398015.3:c.1153G>A	p.Gly385Ser	p.G385S	ENST00000398015	NM_004441.4	385	Ggc/Agc	5/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.272651377044575	2		515	711	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453145	140453145	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	185	420	2	ENST00000288602.6:c.1790T>C	p.Leu597Pro	p.L597P	ENST00000288602	NM_004333.4	597	cTa/cCa	15/18	0.272651377044575	3	FACETS	0.93	0.86	1			1	CLONAL	2	TRUE	NA	0.272651377044575	3		422	829	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653166	29653166	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	47	410	0	ENST00000356175.3:c.5101G>A	p.Glu1701Lys	p.E1701K	ENST00000356175	NM_000267.3	1701	Gaa/Aaa	36/57	1	2	FACETS	0.654	0.552	0.767	0.654	0.552	0.767	SUBCLONAL	1	TRUE	1	0.272651377044575	2		410	527	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366709	40366709	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	64	372	0	ENST00000397332.2:c.488C>A	p.Pro163His	p.P163H	ENST00000397332	NM_001033082.2	163	cCc/cAc	2/3	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.272651377044575	2		372	465	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567276	226567276	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	63	444	0	ENST00000366794.5:c.1610C>T	p.Ser537Phe	p.S537F	ENST00000366794	NM_001618.3	537	tCt/tTt	11/23	0.272651377044575	1	FACETS	0.749	0.648	0.858	0.749	0.648	0.858	SUBCLONAL	1	TRUE	0	0.272651377044575	1		444	533	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247240	153247240	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	148	748	0	ENST00000281708.4:c.1562T>A	p.Phe521Tyr	p.F521Y	ENST00000281708	NM_033632.3	521	tTt/tAt	10/12	1	2	FACETS	0.945	0.861	1	0.945	0.861	1	CLONAL	1	TRUE	1	0.272651377044575	2		748	1149	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031885	26031885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	135	727	1	ENST00000244661.2:c.404G>A	p.Arg135Lys	p.R135K	ENST00000244661	NM_003537.3	135	aGa/aAa	1/1	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.272651377044575	2		728	963	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392167	81392167	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1562911487	NA	P-0012408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	95	478	0	ENST00000222390.5:c.110A>G	p.Asn37Ser	p.N37S	ENST00000222390	NM_000601.4	37	aAt/aGt	2/18	1	2	FACETS	0.825	0.733	0.922	0.825	0.733	0.922	CLONAL	1	TRUE	1	0.272651377044575	2		478	845	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494164	140494164	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	364	708	0	ENST00000288602.6:c.1084C>G	p.Arg362Gly	p.R362G	ENST00000288602	NM_004333.4	362	Cga/Gga	8/18	0.272651377044575	3	FACETS	1	0.986	1			1	CLONAL	2	TRUE	NA	0.272651377044575	3		708	1363	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155093	108155093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs864622654	NA	P-0012408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	98	480	0	ENST00000278616.4:c.3886C>T	p.Pro1296Ser	p.P1296S	ENST00000278616	NM_000051.3	1296	Cct/Tct	26/63	0.272651377044575	1	FACETS	0.929	0.83	1	0.929	0.83	1	CLONAL	1	TRUE	0	0.272651377044575	1		480	668	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402008	402008	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	171	825	0	ENST00000399788.2:c.4783T>G	p.Tyr1595Asp	p.Y1595D	ENST00000399788	NM_001042603.1	1595	Tat/Gat	27/28	1	2	FACETS	0.975	0.895	1	0.975	0.895	1	CLONAL	1	TRUE	1	0.272651377044575	2		825	1286	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969779	81969779	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	145	795	1	ENST00000359376.3:c.2848C>T	p.Pro950Ser	p.P950S	ENST00000359376	NM_002661.3	950	Cct/Tct	27/33	1	2	FACETS	0.883	0.804	0.967	0.883	0.804	0.967	CLONAL	1	TRUE	1	0.272651377044575	2		796	1204	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164797	36164797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	89	555	1	ENST00000300305.3:c.1078G>A	p.Val360Ile	p.V360I	ENST00000300305		360	Gtc/Atc	8/8	1	2	FACETS	0.821	0.727	0.922	0.821	0.727	0.922	CLONAL	1	TRUE	1	0.272651377044575	2		556	795	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216555	7216556	+	missense_variant	Missense_Mutation	DNP	GT	GT	AA	novel	NA	P-0012408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1316	179	974	1	ENST00000380728.2:c.779_780delinsTT	p.Asn260Ile	p.N260I	ENST00000380728		260	aAC/aTT	9/11	1	2	FACETS	0.878	0.807	0.953	0.878	0.807	0.953	CLONAL	1	TRUE	1	0.272651377044575	2		975	1495	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012412-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	36	528	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.202985502060788	2		530	324	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653079	29653079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012412-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	79	518	0	ENST00000356175.3:c.5014C>T	p.His1672Tyr	p.H1672Y	ENST00000356175	NM_000267.3	1672	Cat/Tat	36/57	1	2	FACETS	0.999	0.878	1	0.999	0.878	1	CLONAL	1	TRUE	1	0.202985502060788	2		518	779	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711908	89711910	+	inframe_deletion	In_Frame_Del	DEL	TAT	TAT	-	rs587780711	NA	P-0012412-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	25	417	0	ENST00000371953.3:c.532_534del	p.Tyr178del	p.Y178del	ENST00000371953	NM_000314.4	176	TAT/-	6/9	0.202985502060788	1	FACETS	0.479	0.377	0.597	0.479	0.377	0.597	SUBCLONAL	1	TRUE	0	0.202985502060788	1		417	462	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730789	40730789	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012412-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	41	445	0	ENST00000373198.4:c.3746A>G	p.Asn1249Ser	p.N1249S	ENST00000373198	NM_133170.3	1249	aAt/aGt	27/32	1	2	FACETS	0.629	0.523	0.748	0.629	0.523	0.748	SUBCLONAL	1	TRUE	1	0.202985502060788	2		445	642	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663685	29663689	+	frameshift_variant	Frame_Shift_Del	DEL	GACAT	GACAT	-	novel	NA	P-0012412-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	67	533	0	ENST00000356175.3:c.6118_6122del	p.Thr2040LeufsTer15	p.T2040Lfs*15	ENST00000356175	NM_000267.3	2039	aaGACATgc/aagc	41/57	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.202985502060788	2		533	611	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0012416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	53	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.78	0.665	0.906	0.78	0.665	0.906	CLONAL	1	TRUE	1	0.246539472400755	2		249	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs864622237	NA	P-0012416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	40	443	0	ENST00000269305.4:c.700T>C	p.Tyr234His	p.Y234H	ENST00000269305	NM_001126112.2	234	Tac/Cac	7/11	1	2	FACETS	0.305	0.252	0.365	0.305	0.252	0.365	SUBCLONAL	1	TRUE	1	0.246539472400755	2		443	1063	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0012416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	110	388	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.246539472400755	2		388	815	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0012416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	59	550	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.397	0.34	0.46	0.397	0.34	0.46	SUBCLONAL	1	TRUE	1	0.246539472400755	2		550	1205	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637007	93637007	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200167353	NA	P-0012416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	120	439	4	ENST00000375746.1:c.1057G>A	p.Ala353Thr	p.A353T	ENST00000375746	NM_001174167.1	353	Gcg/Acg	9/14	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.246539472400755	2		443	922	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398279	25398279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894365	NA	P-0012416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	45	418	0	ENST00000311936.3:c.40G>A	p.Val14Ile	p.V14I	ENST00000311936	NM_004985.3	14	Gta/Ata	2/5	1	2	FACETS	0.394	0.33	0.465	0.394	0.33	0.465	SUBCLONAL	1	TRUE	1	0.246539472400755	2		418	927	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110228	3110228	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769019097	NA	P-0012416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1244	215	593	2	ENST00000078429.4:c.218G>A	p.Arg73His	p.R73H	ENST00000078429	NM_002067.2	73	cGc/cAc	2/7	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.246539472400755	2		595	1459	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992580	72992580	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201757720	NA	P-0012416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1661	98	850	0	ENST00000268489.5:c.1465G>A	p.Glu489Lys	p.E489K	ENST00000268489	NM_006885.3	489	Gag/Aag	2/10	0.237649924041549	1	FACETS	0.396	0.352	0.444	0.396	0.352	0.444	SUBCLONAL	1	TRUE	0	0.246539472400755	1		850	1759	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40500498	40500498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1558	111	810	1	ENST00000264657.5:c.37C>T	p.Arg13Trp	p.R13W	ENST00000264657	NM_139276.2	13	Cgg/Tgg	2/24	1	2	FACETS	0.54	0.483	0.6	0.54	0.483	0.6	SUBCLONAL	1	TRUE	1	0.246539472400755	2		811	1669	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495459	149495459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1382	134	912	0	ENST00000261799.4:c.3188C>T	p.Pro1063Leu	p.P1063L	ENST00000261799	NM_002609.3	1063	cCc/cTc	23/23	0.336229133961013	1	FACETS	0.406	0.367	0.447	0.406	0.367	0.447	SUBCLONAL	1	TRUE	0	0.35786602616045	1		912	1516	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45422944	45422944	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012432-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	221	842	2	ENST00000262160.6:c.184G>T	p.Glu62Ter	p.E62*	ENST00000262160	NM_005901.5	62	Gag/Tag	2/11	0.35786602616045	1	FACETS	0.915	0.851	0.982	0.915	0.851	0.982	CLONAL	1	TRUE	0	0.35786602616045	1		844	1108	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0012436-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	90	563	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	0.982	0.87	1	0.982	0.87	1	CLONAL	1	TRUE	1	0.238783293700019	2		563	768	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0012436-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	88	571	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	0.836	0.739	0.939	0.836	0.739	0.939	CLONAL	1	TRUE	1	0.238783293700019	2		571	882	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829227	72829227	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012436-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1375	163	862	2	ENST00000268489.5:c.7354C>T	p.Pro2452Ser	p.P2452S	ENST00000268489	NM_006885.3	2452	Cca/Tca	9/10	0.205171320168634	1	FACETS	0.782	0.715	0.852	0.782	0.715	0.852	SUBCLONAL	1	TRUE	0	0.238783293700019	1		864	1538	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575055	48575055	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0012436-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	47	415	0	ENST00000342988.3:c.250-1G>A		p.X84_splice	ENST00000342988	NM_005359.5	84			0.205171320168634	1	FACETS	0.818	0.691	0.957	0.818	0.691	0.957	CLONAL	1	TRUE	0	0.238783293700019	1		415	424	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242729	46242729	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012436-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	31	308	0	ENST00000334344.6:c.1691del	p.Ser564Ter	p.S564*	ENST00000334344	NM_152641.2	564	tCa/ta	13/21	1	2	FACETS	0.678	0.548	0.824	0.678	0.548	0.824	SUBCLONAL	1	TRUE	1	0.238783293700019	2		308	383	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs17849781	NA	P-0012447-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	534	568	2	ENST00000269305.4:c.832C>A	p.Pro278Thr	p.P278T	ENST00000269305	NM_001126112.2	278	Cct/Act	8/11	0.504940884971454	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.524961335088795	2		570	974	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0012447-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	156	254	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	0.504940884971454	2	FACETS	0.877	0.816	0.938	0.877	0.816	0.938	CLONAL	2	TRUE	0	0.524961335088795	2		254	339	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274526	198274526	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012447-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	88	571	0	ENST00000335508.6:c.872A>T	p.Asn291Ile	p.N291I	ENST00000335508	NM_012433.2	291	aAc/aTc	7/25	0.524961335088795	3	FACETS	0.339	0.299	0.383	0.17	0.149	0.192	SUBCLONAL	1	TRUE	1	0.524961335088795	3		571	1247	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249520	153249520	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012447-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	88	358	0	ENST00000281708.4:c.1258C>G	p.His420Asp	p.H420D	ENST00000281708	NM_033632.3	420	Cat/Gat	9/12	0.142684032324922	2	FACETS	0.645	0.573	0.721	0.322	0.286	0.361	INDETERMINATE	1	TRUE	0	0.524961335088795	2		358	520	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258953	153258953	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0012447-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	183	432	0	ENST00000281708.4:c.861+1G>A		p.X287_splice	ENST00000281708	NM_033632.3	287			0.142684032324922	2	FACETS	1	0.988	1	0.652	0.606	0.699	INDETERMINATE	1	TRUE	0	0.524961335088795	2		432	535	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737572	145737572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757703895	NA	P-0012447-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	212	419	0	ENST00000428558.2:c.3191G>A	p.Arg1064His	p.R1064H	ENST00000428558	NM_004260.3	1064	cGc/cAc	19/22	0.142684032324922	2	FACETS	1	0.989	1	0.649	0.607	0.693	INDETERMINATE	1	TRUE	0	0.524961335088795	2		419	622	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	40	503	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.758	0.631	0.899	0.758	0.631	0.899	SUBCLONAL	1	TRUE	1	0.286735306025087	2		503	368	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782363	9782363	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745896452	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	80	518	1	ENST00000377346.4:c.2296G>A	p.Glu766Lys	p.E766K	ENST00000377346	NM_005026.3	766	Gag/Aag	18/24	1	2	FACETS	0.734	0.646	0.829	0.734	0.646	0.829	SUBCLONAL	1	TRUE	1	0.286735306025087	2		519	760	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262537	16262537	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200479229	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	79	363	0	ENST00000375759.3:c.9802C>T	p.Arg3268Cys	p.R3268C	ENST00000375759	NM_015001.2	3268	Cgt/Tgt	11/15	1	2	FACETS	0.875	0.77	0.987	0.875	0.77	0.987	CLONAL	1	TRUE	1	0.286735306025087	2		363	630	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726628	46726629	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	50	512	0	ENST00000371975.4:c.707_708delinsAA	p.Gly236Glu	p.G236E	ENST00000371975	NM_003579.3	236	gGG/gAA	7/18	1	2	FACETS	0.44	0.372	0.515	0.44	0.372	0.515	SUBCLONAL	1	TRUE	1	0.286735306025087	2		512	793	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510161	120510161	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	85	460	1	ENST00000256646.2:c.1348G>A	p.Gly450Arg	p.G450R	ENST00000256646	NM_024408.3	450	Gga/Aga	8/34	1	2	FACETS	0.782	0.691	0.88	0.782	0.691	0.88	SUBCLONAL	1	TRUE	1	0.286735306025087	2		461	758	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729669	162729669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	78	442	0	ENST00000367921.3:c.755C>T	p.Pro252Leu	p.P252L	ENST00000367921	NM_006182.2	252	cCc/cTc	8/18	1	2	FACETS	0.767	0.674	0.868	0.767	0.674	0.868	SUBCLONAL	1	TRUE	1	0.286735306025087	2		442	709	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25468901	25468901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	92	504	0	ENST00000264709.3:c.1462C>T	p.Arg488Trp	p.R488W	ENST00000264709	NM_175629.2	488	Cgg/Tgg	12/23	1	2	FACETS	0.757	0.672	0.848	0.757	0.672	0.848	SUBCLONAL	1	TRUE	1	0.286735306025087	2		504	848	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720937	119720937	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	91	557	2	ENST00000316626.5:c.238G>A	p.Glu80Lys	p.E80K	ENST00000316626		80	Gaa/Aaa	2/12	1	2	FACETS	0.678	0.601	0.761	0.678	0.601	0.761	SUBCLONAL	1	TRUE	1	0.286735306025087	2		559	936	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873003	134873003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	64	444	0	ENST00000398015.3:c.1307C>T	p.Thr436Ile	p.T436I	ENST00000398015	NM_004441.4	436	aCc/aTc	6/16	1	2	FACETS	0.569	0.492	0.654	0.569	0.492	0.654	SUBCLONAL	1	TRUE	1	0.286735306025087	2		444	784	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278254	142278254	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	55	319	0	ENST00000350721.4:c.1571C>T	p.Ser524Phe	p.S524F	ENST00000350721	NM_001184.3	524	tCc/tTc	7/47	1	2	FACETS	0.772	0.661	0.893	0.772	0.661	0.893	SUBCLONAL	1	TRUE	1	0.286735306025087	2		319	497	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526232	189526232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267599729	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	127	608	0	ENST00000264731.3:c.496C>T	p.Pro166Ser	p.P166S	ENST00000264731	NM_003722.4	166	Ccc/Tcc	4/14	1	2	FACETS	0.835	0.755	0.92	0.835	0.755	0.92	CLONAL	1	TRUE	1	0.286735306025087	2		608	1061	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981492	55981492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	73	494	2	ENST00000263923.4:c.445C>T	p.Pro149Ser	p.P149S	ENST00000263923	NM_002253.2	149	Cca/Tca	4/30	1	2	FACETS	0.691	0.604	0.785	0.691	0.604	0.785	SUBCLONAL	1	TRUE	1	0.286735306025087	2		496	737	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117737447	117737447	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	55	434	1	ENST00000368508.3:c.202G>A	p.Asp68Asn	p.D68N	ENST00000368508	NM_002944.2	68	Gat/Aat	3/43	1	2	FACETS	0.619	0.529	0.717	0.619	0.529	0.717	SUBCLONAL	1	TRUE	1	0.286735306025087	2		435	620	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946081	13946081	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	29	325	0	ENST00000405192.2:c.1015G>A	p.Glu339Lys	p.E339K	ENST00000405192	NM_001163147.1	339	Gaa/Aaa	10/12	1	2	FACETS	0.42	0.336	0.515	0.42	0.336	0.515	SUBCLONAL	1	TRUE	1	0.286735306025087	2		325	482	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346608	81346608	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1450812000	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	51	511	0	ENST00000222390.5:c.1345G>A	p.Gly449Arg	p.G449R	ENST00000222390	NM_000601.4	449	Gga/Aga	11/18	1	2	FACETS	0.554	0.47	0.646	0.554	0.47	0.646	SUBCLONAL	1	TRUE	1	0.286735306025087	2		511	642	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636728	8636728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	120	281	0	ENST00000356435.5:c.181G>A	p.Gly61Arg	p.G61R	ENST00000356435		61	Gga/Aga	2/35	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.286735306025087	2		281	571	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772038	135772038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375394001	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	103	158	0	ENST00000298552.3:c.3079C>T	p.Arg1027Trp	p.R1027W	ENST00000298552	NM_001162426.1	1027	Cgg/Tgg	23/23	0.286735306025087	3	FACETS	0.835	0.756	0.917	0.835	0.756	0.917	CLONAL	3	TRUE	0	0.286735306025087	3		158	328	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412375	139412375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1341448592	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	256	367	0	ENST00000277541.6:c.1270G>A	p.Glu424Lys	p.E424K	ENST00000277541	NM_017617.3	424	Gag/Aag	8/34	0.286735306025087	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	3	TRUE	0	0.286735306025087	3		367	661	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224540	108224540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	69	436	0	ENST00000278616.4:c.8719C>T	p.Pro2907Ser	p.P2907S	ENST00000278616	NM_000051.3	2907	Cct/Tct	60/63	1	2	FACETS	0.757	0.659	0.862	0.757	0.659	0.862	SUBCLONAL	1	TRUE	1	0.286735306025087	2		436	636	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484039	50484039	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	74	473	0	ENST00000394963.4:c.889T>G	p.Leu297Val	p.L297V	ENST00000394963	NM_003076.4	297	Tta/Gta	8/13	1	2	FACETS	0.621	0.543	0.706	0.621	0.543	0.706	SUBCLONAL	1	TRUE	1	0.286735306025087	2		473	831	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891141	112891141	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	57	456	1	ENST00000351677.2:c.475G>A	p.Glu159Lys	p.E159K	ENST00000351677	NM_002834.3	159	Gag/Aag	4/16	1	2	FACETS	0.552	0.473	0.639	0.552	0.473	0.639	SUBCLONAL	1	TRUE	1	0.286735306025087	2		457	720	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626775	28626775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	73	499	0	ENST00000241453.7:c.521G>A	p.Arg174Lys	p.R174K	ENST00000241453	NM_004119.2	174	aGa/aAa	5/24	1	2	FACETS	0.651	0.569	0.74	0.651	0.569	0.74	SUBCLONAL	1	TRUE	1	0.286735306025087	2		499	782	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878154	48878154	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745822791	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	31	163	0	ENST00000267163.4:c.106G>A	p.Asp36Asn	p.D36N	ENST00000267163	NM_000321.2	36	Gac/Aac	1/27	1	2	FACETS	0.676	0.548	0.82	0.676	0.548	0.82	SUBCLONAL	1	TRUE	1	0.286735306025087	2		163	320	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003213	42003213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	77	721	3	ENST00000219905.7:c.2750C>T	p.Ser917Phe	p.S917F	ENST00000219905	NM_001164273.1	917	tCc/tTc	8/24	1	2	FACETS	0.544	0.476	0.617	0.544	0.476	0.617	SUBCLONAL	1	TRUE	1	0.286735306025087	2		724	988	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420332	88420332	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	49	308	0	ENST00000360948.2:c.2354A>G	p.Gln785Arg	p.Q785R	ENST00000360948	NM_001012338.2	785	cAa/cGa	19/19	1	2	FACETS	0.689	0.584	0.805	0.689	0.584	0.805	SUBCLONAL	1	TRUE	1	0.286735306025087	2		308	496	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2125839	2125839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45517249	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	117	657	2	ENST00000219476.3:c.2585C>T	p.Ala862Val	p.A862V	ENST00000219476	NM_000548.3	862	gCg/gTg	23/42	1	2	FACETS	0.873	0.786	0.965	0.873	0.786	0.965	CLONAL	1	TRUE	1	0.286735306025087	2		659	935	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56867301	56867301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	90	486	0	ENST00000308159.5:c.1520G>A	p.Gly507Glu	p.G507E	ENST00000308159	NM_014669.4	507	gGa/gAa	13/22	1	2	FACETS	0.733	0.649	0.822	0.733	0.649	0.822	SUBCLONAL	1	TRUE	1	0.286735306025087	2		486	857	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868166	56868166	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	98	680	2	ENST00000308159.5:c.1664G>A	p.Arg555Lys	p.R555K	ENST00000308159	NM_014669.4	555	aGg/aAg	14/22	1	2	FACETS	0.733	0.652	0.818	0.733	0.652	0.818	SUBCLONAL	1	TRUE	1	0.286735306025087	2		682	933	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81973514	81973514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	65	470	0	ENST00000359376.3:c.3331C>T	p.Pro1111Ser	p.P1111S	ENST00000359376	NM_002661.3	1111	Cct/Tct	30/33	1	2	FACETS	0.615	0.532	0.705	0.615	0.532	0.705	SUBCLONAL	1	TRUE	1	0.286735306025087	2		470	737	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577548	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	60	489	0	ENST00000269305.4:c.733_734delinsAT	p.Gly245Ile	p.G245I	ENST00000269305	NM_001126112.2	245	GGc/ATc	7/11	1	2	FACETS	0.503	0.432	0.58	0.503	0.432	0.58	SUBCLONAL	1	TRUE	1	0.286735306025087	2		489	832	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004792	16004792	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	79	534	0	ENST00000268712.3:c.2462C>T	p.Ser821Phe	p.S821F	ENST00000268712	NM_006311.3	821	tCt/tTt	20/46	1	2	FACETS	0.648	0.569	0.734	0.648	0.569	0.734	SUBCLONAL	1	TRUE	1	0.286735306025087	2		534	850	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512368	38512369	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	36	359	2	ENST00000254066.5:c.1279_1280delinsTT	p.Pro427Leu	p.P427L	ENST00000254066	NM_000964.3	427	CCg/TTg	9/9	1	2	FACETS	0.486	0.399	0.584	0.486	0.399	0.584	SUBCLONAL	1	TRUE	1	0.286735306025087	2		361	517	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119723	70119723	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	83	563	0	ENST00000245479.2:c.725A>C	p.Lys242Thr	p.K242T	ENST00000245479	NM_000346.3	242	aAa/aCa	3/3	1	2	FACETS	0.681	0.6	0.768	0.681	0.6	0.768	SUBCLONAL	1	TRUE	1	0.286735306025087	2		563	850	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400704	56400704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	66	729	1	ENST00000348428.3:c.1298C>T	p.Pro433Leu	p.P433L	ENST00000348428	NM_006785.3	433	cCa/cTa	11/17	1	2	FACETS	0.516	0.446	0.591	0.516	0.446	0.591	SUBCLONAL	1	TRUE	1	0.286735306025087	2		730	893	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222990	5222990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	60	273	0	ENST00000357368.4:c.2813C>T	p.Ala938Val	p.A938V	ENST00000357368	NM_002850.3	938	gCc/gTc	18/38	1	2	FACETS	0.896	0.774	1	0.896	0.774	1	CLONAL	1	TRUE	1	0.286735306025087	2		273	467	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270437	10270437	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	76	469	0	ENST00000340748.4:c.1129G>T	p.Glu377Ter	p.E377*	ENST00000340748		377	Gag/Tag	16/40	1	2	FACETS	0.771	0.676	0.873	0.771	0.676	0.873	SUBCLONAL	1	TRUE	1	0.286735306025087	2		469	688	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288502	15288502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	27	145	0	ENST00000263388.2:c.4237G>A	p.Asp1413Asn	p.D1413N	ENST00000263388	NM_000435.2	1413	Gac/Aac	24/33	1	2	FACETS	0.741	0.592	0.911	0.741	0.592	0.911	CLONAL	1	TRUE	1	0.286735306025087	2		145	254	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308137	30308137	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	63	550	0	ENST00000262643.3:c.274T>A	p.Cys92Ser	p.C92S	ENST00000262643	NM_001238.2	92	Tgc/Agc	5/12	1	2	FACETS	0.558	0.481	0.641	0.558	0.481	0.641	SUBCLONAL	1	TRUE	1	0.286735306025087	2		550	788	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514826	44514826	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	92	509	0	ENST00000291552.4:c.421C>T	p.His141Tyr	p.H141Y	ENST00000291552	NM_006758.2	141	Cac/Tac	6/8	1	2	FACETS	0.72	0.639	0.807	0.72	0.639	0.807	SUBCLONAL	1	TRUE	1	0.286735306025087	2		509	891	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032794	30032794	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121434259	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	136	519	0	ENST00000338641.4:c.169C>T	p.Arg57Ter	p.R57*	ENST00000338641	NM_000268.3	57	Cga/Tga	2/16	0.179454524451563	2	FACETS	1	0.977	1	0.615	0.56	0.673	CLONAL	1	TRUE	0	0.286735306025087	2		519	771	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974793	21974793	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	62	200	0	ENST00000304494.5:c.34del	p.Ser12ArgfsTer14	p.S12Rfs*14	ENST00000304494	NM_000077.4	12	Tcg/cg	1/3	1	2	FACETS	0.751	0.654	0.854	1	0.972	1	SUBCLONAL	2	TRUE	1	0.286735306025087	2		200	288	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579433	7579433	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1064793279	NA	P-0012455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	84	433	0	ENST00000269305.4:c.254del	p.Pro85LeufsTer38	p.P85Lfs*38	ENST00000269305	NM_001126112.2	85	cCt/ct	4/11	1	2	FACETS	0.809	0.714	0.911	0.809	0.714	0.911	CLONAL	1	TRUE	1	0.286735306025087	2		433	724	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0012500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	129	503	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	0.348441400232786	2		503	726	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116156	67116156	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	179	485	1	ENST00000412916.2:c.441del	p.Arg148GlufsTer31	p.R148Efs*31	ENST00000412916		147	cGg/cg	5/6	0.348441400232786	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.348441400232786	1		486	790	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0012502-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	40	320	0	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	1	2	FACETS	0.82	0.68	0.976	0.82	0.68	0.976	CLONAL	1	TRUE	1	0.16	2		320	610	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183635	10183635	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587780536	NA	P-0012502-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	52	505	0	ENST00000256474.2:c.104C>A	p.Ala35Asp	p.A35D	ENST00000256474	NM_000551.3	35	gCc/gAc	1/3	1	2	FACETS	0.652	0.553	0.761	0.652	0.553	0.761	SUBCLONAL	1	TRUE	1	0.16	2		505	997	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436429	110436430	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0012502-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	67	400	0	ENST00000375856.3:c.1971_1972delinsAA	p.Pro658Thr	p.P658T	ENST00000375856	NM_003749.2	657	acGCcc/acAAcc	1/2	1	2	FACETS	0.992	0.861	1	0.992	0.861	1	CLONAL	1	TRUE	1	0.16	2		400	844	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828513	72828513	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012502-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1271	96	804	0	ENST00000268489.5:c.8068C>A	p.Gln2690Lys	p.Q2690K	ENST00000268489	NM_006885.3	2690	Cag/Aag	9/10	1	2	FACETS	0.878	0.779	0.984	0.878	0.779	0.984	CLONAL	1	TRUE	1	0.16	2		804	1367	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829810	72829810	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012502-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1173	96	867	0	ENST00000268489.5:c.6771A>C	p.Leu2257Phe	p.L2257F	ENST00000268489	NM_006885.3	2257	ttA/ttC	9/10	1	2	FACETS	0.946	0.84	1	0.946	0.84	1	CLONAL	1	TRUE	1	0.16	2		867	1269	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339933	70339933	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012502-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	63	762	0	ENST00000374080.3:c.466G>C	p.Ala156Pro	p.A156P	ENST00000374080		156	Gct/Cct	4/45	0.124153633694455	0	FACETS	0.627	0.54	0.722			1	SUBCLONAL	1	TRUE	0	0.16	0		762	1055	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0012510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	169	425	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.205364714357898	4	FACETS	1	0.978	1	0.782	0.719	0.847	CLONAL	2	TRUE	1	0.205364714357898	4		425	846	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0012510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	70	409	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	NA	2	FACETS	0.841	0.732	0.959			1	INDETERMINATE	1	TRUE	NA	0.205364714357898	2		409	811	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0012510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	45	251	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	0.205364714357898	1	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	0	0.205364714357898	1		251	384	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398297	25398297	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	144	304	0	ENST00000311936.3:c.22G>C	p.Val8Leu	p.V8L	ENST00000311936	NM_004985.3	8	Gta/Cta	2/5	0.205364714357898	4	FACETS	1	0.971	1	0.762	0.696	0.832	CLONAL	2	TRUE	1	0.205364714357898	4		304	739	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	111	528	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.963	0.873	1	0.963	0.873	1	CLONAL	1	TRUE	1	0.571826484405041	2		530	403	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0012517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	260	524	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.569918184229878	3	FACETS	1	0.983	1	0.569	0.533	0.606	CLONAL	1	TRUE	1	0.571826484405041	3		524	1028	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127164	22127164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057519911	NA	P-0012517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	330	609	0	ENST00000215832.6:c.964G>A	p.Glu322Lys	p.E322K	ENST00000215832	NM_002745.4	322	Gag/Aag	7/9	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.571826484405041	2		609	1050	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0012517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	253	549	1	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.571826484405041	2		550	803	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131228	202131228	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	205	401	0	ENST00000358485.4:c.196C>G	p.Leu66Val	p.L66V	ENST00000358485	NM_001080125.1	66	Ctt/Gtt	2/9	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.571826484405041	2		401	702	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131480	202131480	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	190	373	1	ENST00000358485.4:c.448C>T	p.Gln150Ter	p.Q150*	ENST00000358485	NM_001080125.1	150	Cag/Tag	2/9	1	2	FACETS	0.996	0.925	1	0.996	0.925	1	CLONAL	1	TRUE	1	0.571826484405041	2		374	667	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647403	117647403	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	337	799	0	ENST00000368508.3:c.5541T>A	p.Asn1847Lys	p.N1847K	ENST00000368508	NM_002944.2	1847	aaT/aaA	33/43	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.571826484405041	2		799	1017	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578513	7578513	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012552-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	320	672	0	ENST00000269305.4:c.417G>C	p.Lys139Asn	p.K139N	ENST00000269305	NM_001126112.2	139	aaG/aaC	5/11	0.349786378047546	2	FACETS	0.984	0.931	1	0.984	0.931	1	CLONAL	2	TRUE	0	0.35558274418484	2		672	915	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0012555-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	221	612	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.24096023913604	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.369366313142515	1		612	773	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0012569-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	47	367	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		367	838	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0012569-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	81	367	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	0.2	2		367	780	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0012588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	352	503	0				ENST00000310581	NM_198253.2	-/1132			0.364004781953655	5	FACETS	0.994	0.948	1	0.994	0.948	1	CLONAL	4	TRUE	1	0.364004781953655	5		503	752	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0012588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	257	611	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.364004781953655	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.364004781953655	2		611	680	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080375	5080375	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	85	324	0	ENST00000381652.3:c.2278C>G	p.Gln760Glu	p.Q760E	ENST00000381652	NM_004972.3	760	Caa/Gaa	17/25	0.364004781953655	2	FACETS	1	0.923	1	0.525	0.466	0.587	CLONAL	1	TRUE	0	0.364004781953655	2		324	445	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92404021	92404021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	137	584	1	ENST00000265734.4:c.358G>A	p.Glu120Lys	p.E120K	ENST00000265734	NM_001259.6	120	Gaa/Aaa	3/8	0.345804293335749	4	FACETS	1	0.925	1	0.51	0.463	0.56	CLONAL	1	TRUE	2	0.364004781953655	4		585	1006	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090379	77090379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	528	828	0	ENST00000356341.3:c.346G>A	p.Glu116Lys	p.E116K	ENST00000356341	NM_002576.4	116	Gag/Aag	4/15	0.364004781953655	4	FACETS	0.925	0.887	0.963	0.925	0.887	0.963	CLONAL	3	TRUE	1	0.364004781953655	4		828	1426	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289874	15289874	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	368	320	0	ENST00000263388.2:c.3680G>A	p.Gly1227Asp	p.G1227D	ENST00000263388	NM_000435.2	1227	gGc/gAc	22/33	0.907029471783262	4	FACETS	1	0.969	1	0.679	0.648	0.709	CLONAL	2	TRUE	1	0.907029471783262	4		320	760	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0012600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	806	471	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.907029471783262	3	FACETS	1	0.998	1	1	0.998	1	CLONAL	3	TRUE	0	0.907029471783262	3		471	829	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039133	49039133	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0012600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	206	173	0	ENST00000267163.4:c.2212-1G>C		p.X738_splice	ENST00000267163	NM_000321.2	738			0.907029471783262	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.907029471783262	2		173	216	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788617	3788617	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519884	NA	P-0012600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	468	406	1	ENST00000262367.5:c.4337G>T	p.Arg1446Leu	p.R1446L	ENST00000262367	NM_004380.2	1446	cGc/cTc	26/31	0.787971721945412	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.907029471783262	4		407	972	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984940	55984940	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	289	433	0	ENST00000263923.4:c.189G>A	p.Trp63Ter	p.W63*	ENST00000263923	NM_002253.2	63	tgG/tgA	3/30	0.479564802355431	4	FACETS	0.758	0.716	0.8	0.505	0.477	0.534	INDETERMINATE	2	TRUE	1	0.907029471783262	4		433	802	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201758	66201758	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	266	420	1	ENST00000273854.3:c.2744G>A	p.Trp915Ter	p.W915*	ENST00000273854	NM_004439.5	915	tGg/tAg	16/18	0.479564802355431	4	FACETS	1	0.99	1	0.414	0.389	0.44	INDETERMINATE	1	TRUE	1	0.907029471783262	4		421	900	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584470	187584470	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6	122	310	0	ENST00000441802.2:c.3563C>A	p.Ser1188Ter	p.S1188*	ENST00000441802	NM_005245.3	1188	tCa/tAa	3/27	0.907029471783262	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.907029471783262	1		310	128	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86667940	86667940	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	650	393	0	ENST00000274376.6:c.1704G>C	p.Trp568Cys	p.W568C	ENST00000274376	NM_002890.2	568	tgG/tgC	13/25	0.907029471783262	3	FACETS	1	0.998	1	1	0.998	1	CLONAL	3	TRUE	0	0.907029471783262	3		393	666	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053212	180053212	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	255	539	1	ENST00000261937.6:c.1157T>C	p.Leu386Pro	p.L386P	ENST00000261937	NM_182925.4	386	cTc/cCc	9/30	0.907029471783262	3	FACETS	0.979	0.919	1	0.326	0.306	0.347	CLONAL	1	TRUE	0	0.907029471783262	3		540	835	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192637	138192637	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	211	303	1	ENST00000237289.4:c.273G>T	p.Lys91Asn	p.K91N	ENST00000237289	NM_001270507.1	91	aaG/aaT	2/9	0.907029471783262	3	FACETS	1	0.981	1	0.564	0.527	0.601	CLONAL	1	TRUE	1	0.907029471783262	3		304	600	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509381	106509381	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	868	478	0	ENST00000359195.3:c.1375C>T	p.Gln459Ter	p.Q459*	ENST00000359195	NM_002649.2	459	Cag/Tag	2/11	0.907029471783262	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.907029471783262	3		478	909	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347623	89347623	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	837	703	0	ENST00000301030.4:c.5327G>T	p.Ser1776Ile	p.S1776I	ENST00000301030	NM_001256183.1	1776	aGc/aTc	9/13	0.907029471783262	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.907029471783262	2		703	871	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617655	39617655	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0012600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	301	301	2	ENST00000262039.4:c.1840-1G>T		p.X614_splice	ENST00000262039	NM_002647.2	614			0.723959693462721	6	FACETS	1	0.982	1	0.727	0.687	0.768	CLONAL	2	TRUE	3	0.907029471783262	6		303	856	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56402519	56402519	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	386	396	0	ENST00000348428.3:c.1561G>C	p.Glu521Gln	p.E521Q	ENST00000348428	NM_006785.3	521	Gaa/Caa	13/17	0.723959693462721	6	FACETS	1	0.98	1	0.703	0.668	0.738	CLONAL	2	TRUE	3	0.907029471783262	6		396	1136	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252965	36252965	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	403	349	0	ENST00000300305.3:c.397A>T	p.Met133Leu	p.M133L	ENST00000300305		133	Atg/Ttg	4/8	0.907029471783262	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.907029471783262	3		349	604	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348217	70348217	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	341	612	1	ENST00000374080.3:c.3281G>C	p.Gly1094Ala	p.G1094A	ENST00000374080		1094	gGa/gCa	23/45	0.85353340925676	3	FACETS	1	0.987	1	0.56	0.531	0.589	CLONAL	1	TRUE	1	0.907029471783262	3		613	976	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357425	70357425	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	364	662	1	ENST00000374080.3:c.5766G>T	p.Leu1922Phe	p.L1922F	ENST00000374080		1922	ttG/ttT	40/45	0.85353340925676	3	FACETS	1	0.991	1	0.583	0.554	0.612	CLONAL	1	TRUE	1	0.907029471783262	3		663	1001	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0012633-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	95	83	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.815071754954163	1	FACETS	0.614	0.558	0.671	0.614	0.558	0.671	SUBCLONAL	1	TRUE	0	0.815071754954163	1		83	225	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0012633-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	906	907	3	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	1	2	FACETS	0.993	0.976	1	1	0.999	1	CLONAL	2	TRUE	1	0.815071754954163	2		910	1119	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018116	48018116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012633-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	457	515	0	ENST00000234420.5:c.311C>T	p.Pro104Leu	p.P104L	ENST00000234420	NM_000179.2	104	cCc/cTc	2/10	1	2	FACETS	0.926	0.885	0.967	0.926	0.885	0.967	CLONAL	1	TRUE	1	0.815071754954163	2		515	1211	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183554	185183554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012633-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1378	392	419	0	ENST00000265026.3:c.1408G>A	p.Glu470Lys	p.E470K	ENST00000265026	NM_004721.4	470	Gaa/Aaa	9/14	0.814761920496827	4	FACETS	0.986	0.935	1	0.329	0.311	0.347	CLONAL	1	TRUE	1	0.815071754954163	4		419	1770	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629108	86629108	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853218	NA	P-0012633-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	395	357	2	ENST00000274376.6:c.853C>T	p.Arg285Ter	p.R285*	ENST00000274376	NM_002890.2	285	Cga/Tga	4/25	0.808311665564065	1	FACETS	0.948	0.914	0.981	0.948	0.914	0.981	CLONAL	1	TRUE	0	0.815071754954163	1		359	606	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030257	180030257	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1420141608	NA	P-0012633-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	800	623	2	ENST00000261937.6:c.4027C>A	p.Pro1343Thr	p.P1343T	ENST00000261937	NM_182925.4	1343	Cca/Aca	30/30	0.457716532816782	3	FACETS	1	0.979	1			1	INDETERMINATE	2	TRUE	NA	0.815071754954163	3		625	1371	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371999	55371999	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012633-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	237	299	0	ENST00000297316.4:c.689T>C	p.Val230Ala	p.V230A	ENST00000297316	NM_022454.3	230	gTg/gCg	2/2	NA	2	FACETS	0.968	0.91	1			1	INDETERMINATE	1	TRUE	NA	0.815071754954163	2		299	601	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054682	5054682	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012633-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	405	369	0	ENST00000381652.3:c.734C>A	p.Ala245Asp	p.A245D	ENST00000381652	NM_004972.3	245	gCc/gAc	7/25	0.815071754954163	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.815071754954163	1		369	585	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856604	111856604	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1177556874	NA	P-0012633-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	313	251	1	ENST00000341259.2:c.655C>T	p.Arg219Cys	p.R219C	ENST00000341259	NM_005475.2	219	Cgc/Tgc	2/8	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.815071754954163	2		252	629	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548916	29548916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012633-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	193	273	0	ENST00000356175.3:c.1690G>A	p.Asp564Asn	p.D564N	ENST00000356175	NM_000267.3	564	Gat/Aat	15/57	0.763313332962074	1	FACETS	0.833	0.786	0.879	0.833	0.786	0.879	CLONAL	1	TRUE	0	0.815071754954163	1		273	337	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743997	41743997	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012633-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	378	571	3	ENST00000301178.4:c.932G>T	p.Cys311Phe	p.C311F	ENST00000301178	NM_021913.4	311	tGc/tTc	7/20	0.763313332962074	1	FACETS	0.916	0.881	0.95	0.916	0.881	0.95	CLONAL	1	TRUE	0	0.815071754954163	1		574	600	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933413	39933413	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012633-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	336	482	0	ENST00000378444.4:c.1186G>T	p.Ala396Ser	p.A396S	ENST00000378444	NM_001123385.1	396	Gct/Tct	4/15	0.113279509671443	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.815071754954163	0		482	970	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855928	76855929	+	missense_variant	Missense_Mutation	DNP	AG	AG	CT	novel	NA	P-0012633-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	215	607	0	ENST00000373344.5:c.5671_5672inv	p.Leu1891Arg	p.L1891R	ENST00000373344	NM_000489.3	1891	CTa/AGa	23/35	0.598485366249241	1	FACETS	0.242	0.224	0.26	0.242	0.224	0.26	SUBCLONAL	1	TRUE	0	0.815071754954163	1		607	1293	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0012637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	243	503	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.981	0.922	1	0.981	0.922	1	CLONAL	1	TRUE	1	0.744873649025429	2		503	665	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510015	187510015	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	332	518	0	ENST00000441802.2:c.13498G>A	p.Glu4500Lys	p.E4500K	ENST00000441802	NM_005245.3	4500	Gaa/Aaa	27/27	1	2	FACETS	0.994	0.943	1	0.994	0.943	1	CLONAL	1	TRUE	1	0.744873649025429	2		518	897	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692805	89692805	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204928	NA	P-0012637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	130	266	0	ENST00000371953.3:c.289C>T	p.Gln97Ter	p.Q97*	ENST00000371953	NM_000314.4	97	Cag/Tag	5/9	0.744873649025429	1	FACETS	0.894	0.83	0.958	0.894	0.83	0.958	CLONAL	1	TRUE	0	0.744873649025429	1		266	245	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426790	121426790	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201095611	NA	P-0012637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	375	579	1	ENST00000257555.6:c.481G>A	p.Ala161Thr	p.A161T	ENST00000257555		161	Gcc/Acc	2/10	1	2	FACETS	0.97	0.923	1	0.97	0.923	1	CLONAL	1	TRUE	1	0.744873649025429	2		580	1038	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977932	134977932	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	71	457	0	ENST00000398015.3:c.2925G>C	p.Gln975His	p.Q975H	ENST00000398015	NM_004441.4	975	caG/caC	16/16	0.36545519239379	1	FACETS	0.543	0.474	0.617	0.543	0.474	0.617	SUBCLONAL	1	TRUE	0	0.36545519239379	1		457	585	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0012653-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	518	469	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.688125170303144	2		469	721	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0012653-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	561	495	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.682324286069788	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.688125170303144	2		495	805	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0012653-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	293	356	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.174192972491604	3	FACETS	0.911	0.865	0.958	0.608	0.577	0.639	INDETERMINATE	2	TRUE	0	0.688125170303144	3		356	628	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076870	41076870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751972373	NA	P-0012653-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	441	571	0	ENST00000373198.4:c.1550C>T	p.Thr517Met	p.T517M	ENST00000373198	NM_133170.3	517	aCg/aTg	9/32	0.34892591162151	4	FACETS	0.957	0.914	0.999	0.957	0.914	0.999	INDETERMINATE	2	TRUE	2	0.688125170303144	4		571	1131	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012662-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	71	661	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.78	0.681	0.885	0.78	0.681	0.885	SUBCLONAL	1	TRUE	1	0.33	2		661	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0012662-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	13	448	0	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	1	2	FACETS	0.172	0.122	0.234	0.172	0.122	0.234	SUBCLONAL	1	TRUE	1	0.33	2		448	457	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0012664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	90	474	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.240657971909695	2		474	730	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0012664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	26	316	1	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	1	2	FACETS	0.371	0.293	0.462	0.371	0.293	0.462	SUBCLONAL	1	TRUE	1	0.240657971909695	2		317	582	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279464	1279464	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202123213	NA	P-0012673-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	34	469	1	ENST00000310581.5:c.2072G>A	p.Arg691His	p.R691H	ENST00000310581	NM_198253.2	691	cGc/cAc	5/16	0.136810795178261	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		470	653	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151833988	151833988	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	60	302	0	ENST00000262189.6:c.14665G>C	p.Asp4889His	p.D4889H	ENST00000262189	NM_170606.2	4889	Gac/Cac	59/59	0.229355088016324	3	FACETS	0.617	0.531	0.712	0.309	0.265	0.356	SUBCLONAL	1	TRUE	1	0.290221412479294	3		302	767	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572904	41572904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	106	410	0	ENST00000263253.7:c.5189C>T	p.Ser1730Phe	p.S1730F	ENST00000263253	NM_001429.3	1730	tCt/tTt	31/31	0.229355088016324	3	FACETS	0.887	0.794	0.986	0.444	0.397	0.493	CLONAL	1	TRUE	1	0.290221412479294	3		410	943	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573335	41573335	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	116	565	0	ENST00000263253.7:c.5620C>T	p.Gln1874Ter	p.Q1874*	ENST00000263253	NM_001429.3	1874	Cag/Tag	31/31	0.229355088016324	3	FACETS	0.82	0.737	0.908	0.41	0.368	0.454	CLONAL	1	TRUE	1	0.290221412479294	3		565	1116	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264387	30264387	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012679-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	50	288	0	ENST00000322652.5:c.123del	p.Gly42AlafsTer30	p.G42Afs*30	ENST00000322652	NM_015355.2	41	tCc/tc	1/16	0.290221412479294	4	FACETS	0.514	0.435	0.602	0.257	0.217	0.301	SUBCLONAL	1	TRUE	2	0.290221412479294	4		288	865	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	165	528	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.442049855543079	2		530	550	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661500	227661500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757021553	NA	P-0012687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	231	706	3	ENST00000305123.5:c.1955G>A	p.Arg652His	p.R652H	ENST00000305123	NM_005544.2	652	cGc/cAc	1/2	1	2	FACETS	0.958	0.893	1	0.958	0.893	1	CLONAL	1	TRUE	1	0.442049855543079	2		709	1091	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0012687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	251	516	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.442049855543079	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.442049855543079	1		516	836	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717769	89717773	+	frameshift_variant	Frame_Shift_Del	DEL	TAAAA	TAAAA	-	novel	NA	P-0012687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	131	209	0	ENST00000371953.3:c.794_798del	p.Leu265GlnfsTer31	p.L265Qfs*31	ENST00000371953	NM_000314.4	265	cTAAAA/c	7/9	0.442049855543079	1	FACETS	0.999	0.913	1	0.999	0.913	1	CLONAL	1	TRUE	0	0.442049855543079	1		209	462	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941658	48941658	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	233	338	0	ENST00000267163.4:c.970del	p.Ile324PhefsTer8	p.I324Ffs*8	ENST00000267163	NM_000321.2	323	gAa/ga	10/27	0.442049855543079	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.442049855543079	1		338	810	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	121	528	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.925	0.846	1	0.925	0.846	1	CLONAL	1	TRUE	1	0.760714126929948	2		530	344	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793663	NA	P-0012692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	492	1033	2	ENST00000263967.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000263967	NM_006218.2	93	cGg/cAg	2/21	1	2	FACETS	0.993	0.952	1	0.993	0.952	1	CLONAL	1	TRUE	1	0.760714126929948	2		1035	1302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691025	NA	P-0012692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	613	758	0	ENST00000269305.4:c.785G>T	p.Gly262Val	p.G262V	ENST00000269305	NM_001126112.2	262	gGt/gTt	8/11	1	2	FACETS	1	0.996	1	1	0.998	1	CLONAL	2	TRUE	1	0.760714126929948	2		758	752	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0012692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22081	5074	381	0	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.760714126929948	31	FACETS	0.985	0.97	1			1	CLONAL	6	TRUE	NA	0.760714126929948	31		381	27155	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029257	14029257	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1367489461	NA	P-0012692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	251	678	1	ENST00000311895.7:c.1468C>T	p.Arg490Trp	p.R490W	ENST00000311895	NM_005236.2	490	Cgg/Tgg	8/11	1	2	FACETS	0.814	0.764	0.865	0.814	0.764	0.865	CLONAL	1	TRUE	1	0.760714126929948	2		679	811	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	203	528	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.800498378635142	2		530	487	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0012718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	318	503	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.800498378635142	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.800498378635142	1		503	471	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678541	88678541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145157285	NA	P-0012718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	237	418	0	ENST00000360948.2:c.995C>T	p.Thr332Met	p.T332M	ENST00000360948	NM_001012338.2	332	aCg/aTg	9/19	0.800498378635142	1	FACETS	0.984	0.939	1	0.984	0.939	1	CLONAL	1	TRUE	0	0.800498378635142	1		418	361	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870831	12870831	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	145	264	0	ENST00000228872.4:c.58C>T	p.Gln20Ter	p.Q20*	ENST00000228872	NM_004064.3	20	Cag/Tag	1/3	1	2	FACETS	0.913	0.842	0.985	0.913	0.842	0.985	CLONAL	1	TRUE	1	0.800498378635142	2		264	397	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809496	36809496	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	293	452	0	ENST00000373129.3:c.969C>A	p.Asp323Glu	p.D323E	ENST00000373129	NM_032017.1	323	gaC/gaA	10/12	0.800498378635142	1	FACETS	0.978	0.937	1	0.978	0.937	1	CLONAL	1	TRUE	0	0.800498378635142	1		452	449	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989742	15989742	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1364228316	NA	P-0012734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	160	258	0	ENST00000268712.3:c.3031C>G	p.Pro1011Ala	p.P1011A	ENST00000268712	NM_006311.3	1011	Cca/Gca	23/46	1	2	FACETS	0.951	0.878	1	0.951	0.878	1	CLONAL	1	TRUE	1	0.647318737506837	2		258	520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0012743-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	223	464	0	ENST00000269305.4:c.97-1G>A		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.550646128120518	1	FACETS	0.895	0.838	0.953	0.895	0.838	0.953	CLONAL	1	TRUE	0	0.550646128120518	1		464	656	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319952	8319952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1460608894	NA	P-0012743-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	204	443	0	ENST00000356435.5:c.5549G>A	p.Arg1850Lys	p.R1850K	ENST00000356435		1850	aGa/aAa	34/35	0.550695736049242	1	FACETS	0.964	0.901	1	0.964	0.901	1	CLONAL	1	TRUE	0	0.550646128120518	1		443	557	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460538	8460538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs772029273	NA	P-0012743-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	278	545	2	ENST00000356435.5:c.3748G>T	p.Val1250Leu	p.V1250L	ENST00000356435		1250	Gtg/Ttg	22/35	0.550695736049242	1	FACETS	0.935	0.881	0.988	0.935	0.881	0.988	CLONAL	1	TRUE	0	0.550646128120518	1		547	783	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820133	139820133	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0012743-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	591	683	0	ENST00000247668.2:c.1288-2A>C		p.X430_splice	ENST00000247668	NM_021138.3	430			0.54468444681651	2	FACETS	0.94	0.908	0.972	0.94	0.908	0.972	CLONAL	2	TRUE	0	0.550646128120518	2		683	1142	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41203080	41203080	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs80357112	NA	P-0012743-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	242	429	0	ENST00000357654.3:c.5332G>T	p.Asp1778Tyr	p.D1778Y	ENST00000357654	NM_007294.3	1778	Gat/Tat	20/23	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.550646128120518	2		429	827	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012773-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	15	460	0	ENST00000269305.4:c.455C>A	p.Pro152Gln	p.P152Q	ENST00000269305	NM_001126112.2	152	cCg/cAg	5/11	0.476134433499262	1	FACETS	0.11	0.08	0.147	0.11	0.08	0.147	SUBCLONAL	1	TRUE	0	0.478489688049562	1		460	432	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748510	162748510	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012773-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	53	294	0	ENST00000367921.3:c.2424A>T	p.Gln808His	p.Q808H	ENST00000367921	NM_006182.2	808	caA/caT	17/18	0.165491812677693	3	FACETS	0.585	0.5	0.679	0.195	0.166	0.227	INDETERMINATE	1	TRUE	0	0.478489688049562	3		294	469	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530177	212530177	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012773-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	171	486	2	ENST00000342788.4:c.1742C>G	p.Ser581Cys	p.S581C	ENST00000342788	NM_005235.2	581	tCt/tGt	15/28	0.153481369191643	3	FACETS	1	0.979	1	0.59	0.544	0.639	INDETERMINATE	1	TRUE	1	0.478489688049562	3		488	750	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569229	67569229	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012773-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	196	549	0	ENST00000274335.5:c.346C>G	p.Pro116Ala	p.P116A	ENST00000274335		116	Ccg/Gcg	2/15	0.476134433499262	1	FACETS	0.894	0.831	0.959	0.894	0.831	0.959	CLONAL	1	TRUE	0	0.478489688049562	1		549	697	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858518	27858518	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371964190	NA	P-0012773-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	185	953	0	ENST00000359303.2:c.53G>C	p.Arg18Pro	p.R18P	ENST00000359303	NM_003535.2	18	cGg/cCg	1/1	1	2	FACETS	0.697	0.642	0.753	0.697	0.642	0.753	SUBCLONAL	1	TRUE	1	0.478489688049562	2		953	1110	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435765	110435765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781697899	NA	P-0012773-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	83	108	0	ENST00000375856.3:c.2636G>A	p.Gly879Asp	p.G879D	ENST00000375856	NM_003749.2	879	gGc/gAc	1/2	NA	2	FACETS	1	0.932	1			1	INDETERMINATE	2	TRUE	NA	0.478489688049562	2		108	168	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0012779-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	365	646	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.365365079331959	3	FACETS	1	0.991	1	0.761	0.728	0.794	CLONAL	2	TRUE	0	0.57597446290554	3		646	715	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0012779-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	216	851	3	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	0.56678367338385	3	FACETS	1	0.99	1	0.678	0.633	0.725	CLONAL	1	TRUE	1	0.57597446290554	3		854	712	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416168	416168	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012779-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1179	86	623	0	ENST00000399788.2:c.4018G>A	p.Asp1340Asn	p.D1340N	ENST00000399788	NM_001042603.1	1340	Gat/Aat	24/28	0.57597446290554	5	FACETS	0.44	0.388	0.496			1	SUBCLONAL	1	TRUE	NA	0.57597446290554	5		623	1265	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661910	29661910	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012779-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	265	374	0	ENST00000356175.3:c.5804T>G	p.Leu1935Arg	p.L1935R	ENST00000356175	NM_000267.3	1935	cTa/cGa	39/57	0.56678367338385	3	FACETS	0.935	0.883	0.987	0.935	0.883	0.987	CLONAL	2	TRUE	1	0.57597446290554	3		374	634	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556454	29556457	+	frameshift_variant	Frame_Shift_Del	DEL	ATCA	ATCA	-	novel	NA	P-0012779-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	54	264	0	ENST00000356175.3:c.2821_2824del	p.Ile941AlafsTer12	p.I941Afs*12	ENST00000356175	NM_000267.3	941	ATCAgc/gc	21/57	0.56678367338385	3	FACETS	0.813	0.699	0.936	0.407	0.349	0.468	CLONAL	1	TRUE	1	0.57597446290554	3		264	297	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46271054	46271057	+	missense_variant	Missense_Mutation	ONP	CTTC	CTTC	TTTT	novel	NA	P-0012779-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	81	757	0	ENST00000371998.3:c.3178_3181delinsTTTT	p.Leu1060_Leu1061delinsPhePhe	p.L1060_L1061delinsFF	ENST00000371998		1060	CTTCtc/TTTTtc	17/23	0.243901562865279	6	FACETS	0.509	0.447	0.577	0.127	0.111	0.145	INDETERMINATE	1	TRUE	2	0.57597446290554	6		757	1188	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0012805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	61	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.874	0.765	0.988	0.874	0.765	0.988	CLONAL	1	TRUE	1	0.664928196103067	2		249	210	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	121	391	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.659586609891063	2	FACETS	0.835	0.76	0.913	0.417	0.38	0.457	CLONAL	1	TRUE	0	0.664928196103067	2		391	436	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665032	182665032	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	165	656	1	ENST00000292782.4:c.694G>T	p.Glu232Ter	p.E232*	ENST00000292782	NM_020640.2	232	Gaa/Taa	6/7	1	2	FACETS	0.872	0.805	0.941	0.872	0.805	0.941	CLONAL	1	TRUE	1	0.664928196103067	2		657	569	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348732	11348732	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	157	671	0	ENST00000332029.2:c.604G>A	p.Asp202Asn	p.D202N	ENST00000332029	NM_003745.1	202	Gac/Aac	2/2	0.639913595226205	3	FACETS	1	0.984	1	0.633	0.584	0.683	CLONAL	1	TRUE	1	0.664928196103067	3		671	497	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649631	48649631	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs782474159	NA	P-0012805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	173	822	0	ENST00000376670.3:c.115G>C	p.Glu39Gln	p.E39Q	ENST00000376670	NM_002049.3	39	Gag/Cag	2/6	0.15968034378685	0	FACETS	0.349	0.324	0.375			1	INDETERMINATE	1	TRUE	0	0.664928196103067	0		822	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0012810-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	75	462	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.321618479309343	1	FACETS	0.338	0.296	0.384	0.338	0.296	0.384	SUBCLONAL	1	TRUE	0	0.482988811767507	1		463	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs864622237	NA	P-0012810-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	203	443	0	ENST00000269305.4:c.700T>C	p.Tyr234His	p.Y234H	ENST00000269305	NM_001126112.2	234	Tac/Cac	7/11	0.321618479309343	1	FACETS	0.984	0.917	1	0.984	0.917	1	CLONAL	1	TRUE	0	0.482988811767507	1		443	648	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0012810-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	92	313	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.482988811767507	1	FACETS	0.87	0.781	0.964	0.87	0.781	0.964	CLONAL	1	TRUE	0	0.482988811767507	1		313	332	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0012810-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	233	469	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.482988811767507	2		469	830	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610307	10610307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012810-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	120	509	0	ENST00000171111.5:c.403C>T	p.Arg135Cys	p.R135C	ENST00000171111	NM_203500.1	135	Cgc/Tgc	2/6	1	2	FACETS	0.614	0.554	0.677	0.614	0.554	0.677	SUBCLONAL	1	TRUE	1	0.482988811767507	2		509	809	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0012824-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	331	549	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.560087863438127	5	FACETS	0.876	0.834	0.919	0.876	0.834	0.919	CLONAL	3	TRUE	2	0.674421234316878	5		549	751	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0012830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	121	503	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.637671024391277	2		503	370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0012830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	622	634	1	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.618506641786873	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.637671024391277	2		635	941	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027168	49027168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913305	NA	P-0012830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	49	675	4	ENST00000267163.4:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	579	Cga/Tga	18/27	0.637671024391277	1	FACETS	0.137	0.116	0.161	0.137	0.116	0.161	SUBCLONAL	1	TRUE	0	0.637671024391277	1		679	762	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210822	133210822	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012830-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	324	870	0	ENST00000320574.5:c.5954T>C	p.Phe1985Ser	p.F1985S	ENST00000320574	NM_006231.2	1985	tTt/tCt	43/49	1	2	FACETS	0.94	0.889	0.993	0.94	0.889	0.993	CLONAL	1	TRUE	1	0.637671024391277	2		870	1081	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012840-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	52	528	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.453139353877249	2		530	196	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0012840-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	1655	508	3	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	0.453139353877249	17	FACETS	0.972	0.961	0.983			1	CLONAL	17	TRUE	NA	0.453139353877249	17		511	1944	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295801	212295801	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1423325504	NA	P-0012840-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	209	563	1	ENST00000342788.4:c.2512C>T	p.Arg838Ter	p.R838*	ENST00000342788	NM_005235.2	838	Cga/Tga	21/28	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.453139353877249	2		564	887	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215370	41215370	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012840-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	196	550	0	ENST00000357654.3:c.5173G>A	p.Glu1725Lys	p.E1725K	ENST00000357654	NM_007294.3	1725	Gaa/Aaa	18/23	0.240039712696411	3	FACETS	0.961	0.889	1			1	INDETERMINATE	1	TRUE	NA	0.453139353877249	3		550	1104	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023153	27023153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012840-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	33	54	0	ENST00000324856.7:c.259G>A	p.Gly87Arg	p.G87R	ENST00000324856	NM_006015.4	87	Gga/Aga	1/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.453139353877249	2		54	99	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802619	135802619	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012840-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	149	514	0	ENST00000298552.3:c.179del	p.Ile60ThrfsTer2	p.I60Tfs*2	ENST00000298552	NM_001162426.1	60	aTc/ac	4/23	0.453139353877249	1	FACETS	0.908	0.834	0.985	0.908	0.834	0.985	CLONAL	1	TRUE	0	0.453139353877249	1		514	560	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961745	41961766	+	frameshift_variant	Frame_Shift_Del	DEL	TAAATGGCCCTGGTGTCCACAC	TAAATGGCCCTGGTGTCCACAC	-	novel	NA	P-0012840-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1345	318	944	0	ENST00000219905.7:c.654_675del	p.Leu218PhefsTer12	p.L218Ffs*12	ENST00000219905	NM_001164273.1	218	tTAAATGGCCCTGGTGTCCACACt/tt	2/24	0.453139353877249	3	FACETS	1	0.965	1	0.518	0.487	0.549	CLONAL	1	TRUE	1	0.453139353877249	3		944	1663	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0012850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	44	576	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	1	0.11	2		576	793	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233408	69233408	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012850-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	105	529	0	ENST00000462284.1:c.1273A>C	p.Thr425Pro	p.T425P	ENST00000462284	NM_002392.5	425	Acc/Ccc	11/11	0.3	7	FACETS	0.951	0.849	1			1	CLONAL	2	TRUE	NA	0.11	7		529	1280	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644709	134644709	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1473173223	NA	P-0012855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	68	478	0	ENST00000398015.3:c.110A>G	p.Asn37Ser	p.N37S	ENST00000398015	NM_004441.4	37	aAt/aGt	2/16	1	2	FACETS	0.649	0.565	0.741	0.649	0.565	0.741	SUBCLONAL	1	TRUE	1	0.328333799005323	2		478	638	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974323	93974323	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	144	859	0	ENST00000369303.4:c.1731C>G	p.Ile577Met	p.I577M	ENST00000369303	NM_004440.3	577	atC/atG	8/17	NA	2	FACETS	0.757	0.689	0.829			1	INDETERMINATE	1	TRUE	NA	0.328333799005323	2		859	1158	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975523	13975523	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0012855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	28	215	0	ENST00000405192.2:c.366-2A>T		p.X122_splice	ENST00000405192	NM_001163147.1	122			0.328333799005323	3	FACETS	0.448	0.358	0.552	0.149	0.119	0.184	SUBCLONAL	1	TRUE	0	0.328333799005323	3		215	443	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549104	21549104	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	85	684	0	ENST00000382592.4:c.3172C>G	p.Pro1058Ala	p.P1058A	ENST00000382592	NM_014572.2	1058	Cct/Gct	8/8	1	2	FACETS	0.552	0.487	0.622	0.552	0.487	0.622	SUBCLONAL	1	TRUE	1	0.328333799005323	2		684	938	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954220	48954220	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	229	505	1	ENST00000267163.4:c.1421G>A	p.Ser474Asn	p.S474N	ENST00000267163	NM_000321.2	474	aGc/aAc	15/27	0.315709164134409	2	FACETS	0.813	0.759	0.868	0.813	0.759	0.868	CLONAL	2	TRUE	0	0.328333799005323	2		506	858	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348114	348114	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	80	563	0	ENST00000262320.3:c.1392G>T	p.Glu464Asp	p.E464D	ENST00000262320	NM_003502.3	464	gaG/gaT	6/11	0.328333799005323	1	FACETS	0.551	0.485	0.623	0.551	0.485	0.623	SUBCLONAL	1	TRUE	0	0.328333799005323	1		563	739	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383608	42383608	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782307227	NA	P-0012855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	55	792	0	ENST00000221972.3:c.383C>T	p.Pro128Leu	p.P128L	ENST00000221972	NM_021601.3	128	cCg/cTg	3/5	1	2	FACETS	0.343	0.292	0.399	0.343	0.292	0.399	SUBCLONAL	1	TRUE	1	0.328333799005323	2		792	977	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564538	41564538	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	103	768	0	ENST00000263253.7:c.3960G>C	p.Glu1320Asp	p.E1320D	ENST00000263253	NM_001429.3	1320	gaG/gaC	24/31	1	2	FACETS	0.594	0.53	0.662	0.594	0.53	0.662	SUBCLONAL	1	TRUE	1	0.328333799005323	2		768	1056	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577145	7577154	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GTAGATTACC	GTAGATTACC	-	novel	NA	P-0012855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	319	804	3	ENST00000269305.4:c.784_793del	p.Gly262TrpfsTer80	p.G262Wfs*80	ENST00000269305	NM_001126112.2	262	GGTAATCTACtg/tg	8/11	NA	2	FACETS	0.876	0.827	0.926			1	INDETERMINATE	2	TRUE	NA	0.328333799005323	2		807	1109	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41197783	41197784	+	missense_variant	Missense_Mutation	DNP	CG	CG	AA	novel	NA	P-0012855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	228	827	1	ENST00000357654.3:c.5503_5504delinsTT	p.Arg1835Leu	p.R1835L	ENST00000357654	NM_007294.3	1835	CGa/TTa	23/23	0.274375002061905	2	FACETS	1	0.988	1	0.642	0.598	0.688	CLONAL	1	TRUE	0	0.328333799005323	2		828	1081	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0012858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	210	717	1	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.365237767314291	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.365237767314291	1		718	761	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271707	15271707	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0012858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	898	1041	0	ENST00000263388.2:c.6732C>G	p.Tyr2244Ter	p.Y2244*	ENST00000263388	NM_000435.2	2244	taC/taG	33/33	0.365237767314291	5	FACETS	0.948	0.923	0.973			1	CLONAL	5	TRUE	NA	0.365237767314291	5		1041	1606	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39721200	39721200	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	44	678	0	ENST00000361337.2:c.704del	p.Pro235GlnfsTer13	p.P235Qfs*13	ENST00000361337	NM_003286.2	235	Cca/ca	9/21	1	2	FACETS	0.321	0.268	0.38	0.321	0.268	0.38	SUBCLONAL	1	TRUE	1	0.365237767314291	2		678	750	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0012863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	243	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.443012010997104	3	FACETS	0.874	0.826	0.922	0.874	0.826	0.922	CLONAL	3	TRUE	0	0.443012010997104	3		249	511	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376675	8376675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs571411218	NA	P-0012863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	178	728	0	ENST00000356435.5:c.4438G>A	p.Val1480Ile	p.V1480I	ENST00000356435		1480	Gtt/Att	27/35	1	2	FACETS	0.934	0.862	1	0.934	0.862	1	CLONAL	1	TRUE	1	0.443012010997104	2		728	860	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857935	9857935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	253	651	1	ENST00000330684.3:c.3466G>A	p.Glu1156Lys	p.E1156K	ENST00000330684	NM_001134407.1	1156	Gaa/Aaa	13/13	0.172219402829777	4	FACETS	0.819	0.767	0.873	0.819	0.767	0.873	INDETERMINATE	2	TRUE	2	0.443012010997104	4		652	1006	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612783	228612783	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1582	262	1258	0	ENST00000366696.1:c.244G>T	p.Asp82Tyr	p.D82Y	ENST00000366696	NM_003493.2	82	Gac/Tac	1/1	0.443012010997104	3	FACETS	0.784	0.731	0.838	0.392	0.365	0.419	SUBCLONAL	1	TRUE	1	0.443012010997104	3		1258	1844	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0012864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	181	628	1	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.330871285673199	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.330871285673199	1		629	803	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663653	117663653	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs369511700	NA	P-0012864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	123	546	0	ENST00000368508.3:c.4579A>G	p.Met1527Val	p.M1527V	ENST00000368508	NM_002944.2	1527	Atg/Gtg	28/43	0.194492177540994	0	FACETS	0.906	0.823	0.993			1	INDETERMINATE	1	TRUE	0	0.330871285673199	0		546	549	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593477	215593477	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	118	521	0	ENST00000260947.4:c.2257G>T	p.Gly753Cys	p.G753C	ENST00000260947	NM_000465.2	753	Ggc/Tgc	11/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.330871285673199	2		521	639	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218952	193218952	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1292596060	NA	P-0012864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	200	672	0	ENST00000367435.3:c.1510C>A	p.Arg504Ser	p.R504S	ENST00000367435	NM_024529.4	504	Cgt/Agt	16/17	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.330871285673199	2		672	965	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794130	242794130	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	141	736	1	ENST00000334409.5:c.598A>G	p.Ile200Val	p.I200V	ENST00000334409	NM_005018.2	200	Ata/Gta	4/5	1	2	FACETS	0.857	0.779	0.938	0.857	0.779	0.938	CLONAL	1	TRUE	1	0.330871285673199	2		737	995	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873074	134873074	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	70	696	0	ENST00000398015.3:c.1378C>G	p.Pro460Ala	p.P460A	ENST00000398015	NM_004441.4	460	Ccc/Gcc	6/16	0.248766199918836	3	FACETS	0.481	0.418	0.55	0.241	0.209	0.275	SUBCLONAL	1	TRUE	1	0.330871285673199	3		696	1025	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026721	6026721	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	73	442	2	ENST00000265849.7:c.1675G>T	p.Gly559Ter	p.G559*	ENST00000265849	NM_000535.5	559	Gga/Tga	11/15	0.330871285673199	1	FACETS	0.631	0.552	0.715	0.631	0.552	0.715	SUBCLONAL	1	TRUE	0	0.330871285673199	1		444	584	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729622	41729622	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	297	1046	0	ENST00000242208.4:c.907C>A	p.His303Asn	p.H303N	ENST00000242208	NM_002192.2	303	Cac/Aac	3/3	0.330871285673199	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.330871285673199	1		1046	1288	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845691	151845691	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	84	662	0	ENST00000262189.6:c.13321G>T	p.Glu4441Ter	p.E4441*	ENST00000262189	NM_170606.2	4441	Gag/Tag	52/59	0.161639271607925	0	FACETS	0.44	0.388	0.495			1	INDETERMINATE	1	TRUE	0	0.330871285673199	0		662	773	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462870	69462870	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	209	783	1	ENST00000227507.2:c.683G>T	p.Arg228Leu	p.R228L	ENST00000227507	NM_053056.2	228	cGc/cTc	4/5	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.330871285673199	2		784	1139	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491379	18491379	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs190750617	NA	P-0012864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	59	466	0	ENST00000266497.5:c.1292T>C	p.Ile431Thr	p.I431T	ENST00000266497		431	aTt/aCt	8/31	1	2	FACETS	0.601	0.517	0.693	0.601	0.517	0.693	SUBCLONAL	1	TRUE	1	0.330871285673199	2		466	593	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533068	63533068	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370618491	NA	P-0012864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	217	715	2	ENST00000307078.5:c.1826C>T	p.Pro609Leu	p.P609L	ENST00000307078	NM_004655.3	609	cCc/cTc	7/11	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.330871285673199	2		717	926	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852485	42852485	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	251	829	1	ENST00000398585.3:c.601C>T	p.Gln201Ter	p.Q201*	ENST00000398585	NM_001135099.1	201	Cag/Tag	6/14	0.267139215221693	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.330871285673199	1		830	1061	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932025	39932025	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	110	719	0	ENST00000378444.4:c.2574G>C	p.Glu858Asp	p.E858D	ENST00000378444	NM_001123385.1	858	gaG/gaC	4/15	0.161639271607925	0	FACETS	0.52	0.466	0.576			1	INDETERMINATE	1	TRUE	0	0.330871285673199	0		719	856	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354619	70354619	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	85	807	0	ENST00000374080.3:c.4784C>G	p.Ala1595Gly	p.A1595G	ENST00000374080		1595	gCt/gGt	35/45	0.161639271607925	0	FACETS	0.326	0.287	0.368			1	INDETERMINATE	1	TRUE	0	0.330871285673199	0		807	1053	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113789	11113789	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	161	638	0	ENST00000358026.2:c.1897del	p.Ala633ProfsTer13	p.A633Pfs*13	ENST00000358026	NM_001128849.1	633	Gcc/cc	12/36	0.330871285673199	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.330871285673199	1		638	730	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0012883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	207	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.633645463110737	5	FACETS	0.868	0.808	0.93	0.579	0.539	0.62	CLONAL	2	TRUE	2	0.638535496258709	5		249	731	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160227	22160227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	263	586	0	ENST00000215832.6:c.404G>A	p.Arg135Lys	p.R135K	ENST00000215832	NM_002745.4	135	aGa/aAa	3/9	1	2	FACETS	0.956	0.898	1	0.956	0.898	1	CLONAL	1	TRUE	1	0.638535496258709	2		586	862	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875031	151875031	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	224	414	0	ENST00000262189.6:c.7507C>T	p.Gln2503Ter	p.Q2503*	ENST00000262189	NM_170606.2	2503	Cag/Tag	38/59	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.638535496258709	2		414	685	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	407	944	1	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	1	2	FACETS	0.944	0.898	0.991	0.944	0.898	0.991	CLONAL	1	TRUE	1	0.638535496258709	2		945	1350	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467924	50467924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	205	408	0	ENST00000331340.3:c.1159G>A	p.Glu387Lys	p.E387K	ENST00000331340	NM_006060.4	387	Gag/Aag	8/8	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.638535496258709	2		408	612	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309866	65309866	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	270	604	0	ENST00000342505.4:c.2284G>A	p.Glu762Lys	p.E762K	ENST00000342505	NM_002227.2	762	Gag/Aag	17/25	1	2	FACETS	0.91	0.856	0.966	0.91	0.856	0.966	CLONAL	1	TRUE	1	0.638535496258709	2		604	929	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277973	41277973	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs755119590	NA	P-0012883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	268	641	0	ENST00000349496.5:c.1937C>G	p.Ser646Cys	p.S646C	ENST00000349496	NM_001904.3	646	tCt/tGt	12/15	1	2	FACETS	0.895	0.841	0.95	0.895	0.841	0.95	CLONAL	1	TRUE	1	0.638535496258709	2		641	938	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874952	151874952	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0012883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	244	577	0	ENST00000262189.6:c.7586C>G	p.Ser2529Ter	p.S2529*	ENST00000262189	NM_170606.2	2529	tCa/tGa	38/59	1	2	FACETS	0.927	0.869	0.987	0.927	0.869	0.987	CLONAL	1	TRUE	1	0.638535496258709	2		577	824	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564620	139564620	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs755108877	NA	P-0012883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	294	602	0	ENST00000308874.7:c.410-1G>C		p.X137_splice	ENST00000308874		137			1	2	FACETS	0.904	0.851	0.957	0.904	0.851	0.957	CLONAL	1	TRUE	1	0.638535496258709	2		602	1019	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137074	64137074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	318	519	0	ENST00000334205.4:c.1585C>T	p.Arg529Cys	p.R529C	ENST00000334205	NM_003942.2	529	Cgc/Tgc	13/17	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.638535496258709	2		519	925	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	441070	441070	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1348	125	713	0	ENST00000399788.2:c.1688T>C	p.Val563Ala	p.V563A	ENST00000399788	NM_001042603.1	563	gTt/gCt	13/28	0.211798262142709	5	FACETS	0.52	0.469	0.575			1	INDETERMINATE	1	TRUE	NA	0.638535496258709	5		713	1473	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245516	133245516	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	197	509	0	ENST00000320574.5:c.1804G>C	p.Glu602Gln	p.E602Q	ENST00000320574	NM_006231.2	602	Gag/Cag	17/49	1	2	FACETS	0.85	0.789	0.912	0.85	0.789	0.912	CLONAL	1	TRUE	1	0.638535496258709	2		509	726	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951163	48951163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	207	471	0	ENST00000267163.4:c.1325G>A	p.Gly442Glu	p.G442E	ENST00000267163	NM_000321.2	442	gGa/gAa	13/27	0.638535496258709	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.638535496258709	1		471	433	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822099	72822099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	422	912	0	ENST00000268489.5:c.10076C>T	p.Ser3359Phe	p.S3359F	ENST00000268489	NM_006885.3	3359	tCc/tTc	10/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.638535496258709	2		912	1299	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099256	4099256	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1461890634	NA	P-0012883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	359	705	0	ENST00000262948.5:c.862G>A	p.Glu288Lys	p.E288K	ENST00000262948	NM_030662.3	288	Gaa/Aaa	7/11	1	2	FACETS	0.933	0.885	0.983	0.933	0.885	0.983	CLONAL	1	TRUE	1	0.638535496258709	2		705	1205	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101229	4101229	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs530342723	NA	P-0012883-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	348	702	0	ENST00000262948.5:c.578G>A	p.Arg193Gln	p.R193Q	ENST00000262948	NM_030662.3	193	cGa/cAa	5/11	1	2	FACETS	0.956	0.906	1	0.956	0.906	1	CLONAL	1	TRUE	1	0.638535496258709	2		702	1140	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	113	528	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.912	0.826	1	0.912	0.826	1	CLONAL	1	TRUE	1	0.563253057978196	2		530	440	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720808	89720808	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	30	197	0	ENST00000371953.3:c.959T>C	p.Leu320Ser	p.L320S	ENST00000371953	NM_000314.4	320	tTa/tCa	8/9	0.561397232342304	1	FACETS	0.632	0.519	0.755	0.632	0.519	0.755	SUBCLONAL	1	TRUE	0	0.563253057978196	1		197	121	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426123	138426123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217537873	NA	P-0012902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	168	381	0	ENST00000289153.2:c.1408G>A	p.Glu470Lys	p.E470K	ENST00000289153	NM_006219.2	470	Gaa/Aaa	9/22	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.563253057978196	2		381	539	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857732	59857732	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	58	515	0	ENST00000259008.2:c.1825A>C	p.Thr609Pro	p.T609P	ENST00000259008	NM_032043.2	609	Acc/Ccc	13/20	1	2	FACETS	0.356	0.306	0.411	0.356	0.306	0.411	SUBCLONAL	1	TRUE	1	0.563253057978196	2		515	578	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133523	55133523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142492533	NA	P-0012905-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	239	842	2	ENST00000257290.5:c.827C>T	p.Thr276Met	p.T276M	ENST00000257290	NM_006206.4	276	aCg/aTg	6/23	0.755793260363576	3	FACETS	1	0.985	1	0.583	0.547	0.621	CLONAL	1	FALSE	1	0.755793260363576	3		844	747	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671650	67671650	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012905-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	367	577	0	ENST00000264010.4:c.2059G>A	p.Glu687Lys	p.E687K	ENST00000264010	NM_006565.3	687	Gaa/Aaa	12/12	0.755793260363576	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	FALSE	2	0.755793260363576	4		577	797	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352697	NA	P-0012910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	106	748	0	ENST00000269305.4:c.587G>A	p.Arg196Gln	p.R196Q	ENST00000269305	NM_001126112.2	196	cGa/cAa	6/11	1	2	FACETS	0.706	0.631	0.786	0.706	0.631	0.786	SUBCLONAL	1	TRUE	1	0.25775030468629	2		748	1165	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577508	7577508	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060501201	NA	P-0012910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	160	400	0	ENST00000269305.4:c.773A>G	p.Glu258Gly	p.E258G	ENST00000269305	NM_001126112.2	258	gAa/gGa	7/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.25775030468629	2		400	975	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467459	66467459	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	98	603	0	ENST00000273854.3:c.810A>T	p.Glu270Asp	p.E270D	ENST00000273854	NM_004439.5	270	gaA/gaT	3/18	1	2	FACETS	0.915	0.816	1	0.915	0.816	1	CLONAL	1	TRUE	1	0.25775030468629	2		603	831	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579327	7579327	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	66	639	0	ENST00000269305.4:c.360G>C	p.Lys120Asn	p.K120N	ENST00000269305	NM_001126112.2	120	aaG/aaC	4/11	1	2	FACETS	0.591	0.512	0.678	0.591	0.512	0.678	SUBCLONAL	1	TRUE	1	0.25775030468629	2		639	866	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970979	21970979	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	119	559	0	ENST00000304494.5:c.379del	p.Ala127HisfsTer19	p.A127Hfs*19	ENST00000304494	NM_000077.4	127	Gca/ca	2/3	0.25775030468629	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.25775030468629	1		559	681	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220556	98220559	+	frameshift_variant	Frame_Shift_Del	DEL	GATG	GATG	AT	novel	NA	P-0012910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	107	414	0	ENST00000331920.6:c.2904_2907delinsAT	p.Ile969Ter	p.I969*	ENST00000331920	NM_000264.3	968	ccCATC/ccAT	18/24	0.25775030468629	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.25775030468629	1		414	570	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609320	39609320	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	436	487	0	ENST00000262039.4:c.1622T>G	p.Leu541Trp	p.L541W	ENST00000262039	NM_002647.2	541	tTg/tGg	15/25	1	2	FACETS	0.956	0.914	0.999	0.956	0.914	0.999	CLONAL	1	TRUE	1	0.812920097613987	2		487	1122	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432497	49432497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775911186	NA	P-0012919-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	115	494	0	ENST00000301067.7:c.8642G>A	p.Arg2881Gln	p.R2881Q	ENST00000301067	NM_003482.3	2881	cGg/cAg	34/54	0.35952980403148	3	FACETS	0.694	0.624	0.769	0.347	0.312	0.385	SUBCLONAL	1	TRUE	1	0.35952980403148	3		494	1087	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348041	89348041	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012919-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	417	1158	0	ENST00000301030.4:c.4909A>T	p.Ile1637Phe	p.I1637F	ENST00000301030	NM_001256183.1	1637	Att/Ttt	9/13	0.35952980403148	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.35952980403148	1		1158	1488	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496921	29496921	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012919-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	79	356	0	ENST00000356175.3:c.492A>T	p.Leu164Phe	p.L164F	ENST00000356175	NM_000267.3	164	ttA/ttT	5/57	NA	2	FACETS	0.66	0.58	0.745			1	INDETERMINATE	1	TRUE	NA	0.35952980403148	2		356	666	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858338	59858338	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012919-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	85	332	1	ENST00000259008.2:c.1657C>T	p.Gln553Ter	p.Q553*	ENST00000259008	NM_032043.2	553	Caa/Taa	12/20	0.130553177999583	4	FACETS	0.929	0.821	1	0.464	0.41	0.522	INDETERMINATE	1	TRUE	2	0.35952980403148	4		333	692	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942752	44942752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012919-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	87	682	0	ENST00000377967.4:c.3332G>A	p.Arg1111His	p.R1111H	ENST00000377967	NM_021140.2	1111	cGt/cAt	23/29	0.359227635418638	1	FACETS	0.399	0.352	0.45	0.399	0.352	0.45	SUBCLONAL	1	TRUE	0	0.35952980403148	1		682	994	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576856	+	stop_gained,splice_region_variant	Nonsense_Mutation	DNP	GA	GA	AT	novel	NA	P-0012919-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	207	542	0	ENST00000269305.4:c.990_991delinsAT	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	330	ctTCag/ctATag	9/11	0.295365689156621	2	FACETS	1	0.99	1	0.708	0.658	0.759	CLONAL	1	TRUE	0	0.35952980403148	2		542	813	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0012925-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	118	603	1	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	NA	2	FACETS	0.792	0.732	0.853			1	INDETERMINATE	2	TRUE	NA	0.647479928105835	2		604	230	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935355	36935355	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012925-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	152	1209	0	ENST00000361632.4:c.1372G>T	p.Gly458Cys	p.G458C	ENST00000361632		458	Ggc/Tgc	10/16	0.208104900042954	3	FACETS	0.824	0.764	0.886	0.55	0.509	0.591	INDETERMINATE	2	TRUE	0	0.647479928105835	3		1209	377	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143278	58143278	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs755091270	NA	P-0012925-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	107	297	0	ENST00000257904.6:c.642C>G	p.Phe214Leu	p.F214L	ENST00000257904	NM_000075.3	214	ttC/ttG	6/8	0.647479928105835	4	FACETS	1	0.934	1			1	CLONAL	2	TRUE	NA	0.647479928105835	4		297	265	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476344	88476344	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012925-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	30	485	0	ENST00000360948.2:c.1788G>C	p.Gln596His	p.Q596H	ENST00000360948	NM_001012338.2	596	caG/caC	15/19	0.341514027939742	1	FACETS	0.448	0.366	0.537	0.448	0.366	0.537	INDETERMINATE	1	TRUE	0	0.647479928105835	1		485	140	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125353	7125353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012925-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	47	825	0	ENST00000302850.5:c.3199G>A	p.Glu1067Lys	p.E1067K	ENST00000302850	NM_000208.2	1067	Gag/Aag	17/22	0.647479928105835	1	FACETS	0.539	0.462	0.622	0.539	0.462	0.622	SUBCLONAL	1	TRUE	0	0.647479928105835	1		825	182	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117650588	117650589	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0012925-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	82	1051	0	ENST00000368508.3:c.5269_5270delinsCT	p.Gly1757Leu	p.G1757L	ENST00000368508	NM_002944.2	1757	GGc/CTc	32/43	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.647479928105835	NA		1051	192	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	165	299	0	ENST00000397062.3:c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	NM_006164.4	34	Cga/Gga	2/5	0.400710412273684	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.432352152801573	3		299	444	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033971	49033971	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0012931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	211	290	0	ENST00000267163.4:c.2106+2T>A		p.X702_splice	ENST00000267163	NM_000321.2	702			0.386895283054595	3	FACETS	0.931	0.877	0.985	0.931	0.877	0.985	CLONAL	3	TRUE	0	0.432352152801573	3		290	425	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213784	66213784	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	194	385	0	ENST00000273854.3:c.2646G>T	p.Met882Ile	p.M882I	ENST00000273854	NM_004439.5	882	atG/atT	15/18	0.309014388248041	4	FACETS	0.83	0.77	0.893	0.83	0.77	0.893	CLONAL	2	TRUE	2	0.432352152801573	4		385	774	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0012931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	285	372	0	ENST00000269305.4:c.375+1del		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.386895283054595	3	FACETS	0.956	0.909	1	0.956	0.909	1	CLONAL	3	TRUE	0	0.432352152801573	3		372	559	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096588	178096588	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	133	279	0	ENST00000397062.3:c.743A>G	p.Asn248Ser	p.N248S	ENST00000397062	NM_006164.4	248	aAt/aGt	5/5	0.400710412273684	3	FACETS	0.942	0.865	1	0.942	0.865	1	CLONAL	2	TRUE	1	0.432352152801573	3		279	397	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681928	30681928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	159	189	0	ENST00000376406.3:c.169G>A	p.Gly57Ser	p.G57S	ENST00000376406	NM_014641.2	57	Ggc/Agc	3/15	0.431027432070007	4	FACETS	0.975	0.916	1	0.975	0.916	1	CLONAL	4	TRUE	0	0.432352152801573	4		189	270	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900114	151900114	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	35	154	0	ENST00000262189.6:c.3997G>T	p.Glu1333Ter	p.E1333*	ENST00000262189	NM_170606.2	1333	Gaa/Taa	26/59	1	2	FACETS	0.767	0.634	0.914	0.767	0.634	0.914	CLONAL	1	TRUE	1	0.432352152801573	2		154	211	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961008	15961008	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	216	360	0	ENST00000268712.3:c.6212A>G	p.Gln2071Arg	p.Q2071R	ENST00000268712	NM_006311.3	2071	cAg/cGg	40/46	0.386895283054595	3	FACETS	1	0.989	1	0.825	0.775	0.875	CLONAL	2	TRUE	0	0.432352152801573	3		360	491	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39575959	39575959	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0012931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	51	201	0	ENST00000262039.4:c.891+1G>T		p.X297_splice	ENST00000262039	NM_002647.2	297			0.365195810483739	3	FACETS	1	0.862	1	0.503	0.431	0.582	CLONAL	1	TRUE	1	0.432352152801573	3		201	285	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902298	50902298	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1663	708	1892	1	ENST00000440232.2:c.190G>A	p.Gly64Arg	p.G64R	ENST00000440232	NM_002691.3	64	Ggg/Agg	2/27	0.181481166158105	5	FACETS	1	0.994	1	0.759	0.731	0.788	INDETERMINATE	2	TRUE	2	0.432352152801573	5		1893	2371	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431479	49431479	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	115	477	0	ENST00000301067.7:c.9660G>C	p.Leu3220Phe	p.L3220F	ENST00000301067	NM_003482.3	3220	ttG/ttC	34/54	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.268349829803333	2		477	769	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576837	7577056	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCCAAGACTTAGTACCTGAAGGGTGAAATATTCTCCATCCAGTGGTTTCTTCTTTGGCTGGGGAGAGGAGCTGGTGTTGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAAAGTGAATCTGAGGCATAACTGCACCCTTGGTCTCCTCCACCGCTTCTTGTCCTGCTTGCTTACCTCGCTTAGTGCTCCCTGGGGGCAGCTCGTGGTGAGGC	TCCCAAGACTTAGTACCTGAAGGGTGAAATATTCTCCATCCAGTGGTTTCTTCTTTGGCTGGGGAGAGGAGCTGGTGTTGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAAAGTGAATCTGAGGCATAACTGCACCCTTGGTCTCCTCCACCGCTTCTTGTCCTGCTTGCTTACCTCGCTTAGTGCTCCCTGGGGGCAGCTCGTGGTGAGGC	-	novel	NA	P-0012969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	79	338	0	ENST00000269305.4:c.882_993+16del		p.X294_splice	ENST00000269305	NM_001126112.2	294		8-9/11	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.268349829803333	2		338	557	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	92	661	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.3	3	FACETS	0.935	0.835	1	0.935	0.835	1	CLONAL	2	TRUE	1	0.25	3		661	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0012978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	108	385	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.246324713551427	2	FACETS	0.871	0.785	0.961	0.871	0.785	0.961	CLONAL	2	TRUE	0	0.25	2		385	496	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117389	115117405	+	frameshift_variant	Frame_Shift_Del	DEL	TTCAAGATGTCATTGGC	TTCAAGATGTCATTGGC	-	novel	NA	P-0012981-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	69	690	0	ENST00000257566.3:c.769_785del	p.Ala257ThrfsTer4	p.A257Tfs*4	ENST00000257566	NM_016569.3	257	GCCAATGACATCTTGAAa/a	4/8	1	2	FACETS	0.698	0.607	0.796	0.698	0.607	0.796	SUBCLONAL	1	FALSE	1	0.287107090958307	2		690	689	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683540	182683540	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs753281817	NA	P-0013002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	63	274	0	ENST00000292782.4:c.5A>G	p.Asn2Ser	p.N2S	ENST00000292782	NM_020640.2	2	aAc/aGc	2/7	0.751670915803132	2	FACETS	1	0.969	1	0.635	0.567	0.704	CLONAL	1	TRUE	0	0.751670915803132	2		274	132	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807521	1807521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	189	618	0	ENST00000260795.2:c.1690C>T	p.Arg564Trp	p.R564W	ENST00000260795		564	Cgg/Tgg	12/17	0.751670915803132	3	FACETS	0.622	0.574	0.672	0.311	0.287	0.336	SUBCLONAL	1	TRUE	1	0.751670915803132	3		618	1113	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0013009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	146	441	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.993	0.909	1	0.993	0.909	1	CLONAL	1	TRUE	1	0.419344650680456	2		441	701	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143283	108143283	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs780240314	NA	P-0013009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	325	460	0	ENST00000278616.4:c.3102T>G	p.Tyr1034Ter	p.Y1034*	ENST00000278616	NM_000051.3	1034	taT/taG	21/63	0.419344650680456	2	FACETS	0.919	0.872	0.967	0.919	0.872	0.967	CLONAL	2	TRUE	0	0.419344650680456	2		460	843	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971433	15971433	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	123	490	0	ENST00000268712.3:c.4516A>G	p.Thr1506Ala	p.T1506A	ENST00000268712	NM_006311.3	1506	Aca/Gca	32/46	1	2	FACETS	0.786	0.712	0.865	0.786	0.712	0.865	SUBCLONAL	1	TRUE	1	0.419344650680456	2		490	746	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575148	48575148	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0013009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	152	512	0	ENST00000342988.3:c.342T>G	p.Tyr114Ter	p.Y114*	ENST00000342988	NM_005359.5	114	taT/taG	3/12	0.419344650680456	1	FACETS	0.914	0.839	0.992	0.914	0.839	0.992	CLONAL	1	TRUE	0	0.419344650680456	1		512	627	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57470729	57470729	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	104	344	0	ENST00000371085.3:c.202T>G	p.Phe68Val	p.F68V	ENST00000371085	NM_000516.4	68	Ttt/Gtt	2/13	1	2	FACETS	0.842	0.756	0.933	0.842	0.756	0.933	CLONAL	1	TRUE	1	0.419344650680456	2		344	589	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	263	661	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.356358300548746	2	FACETS	0.881	0.83	0.933	0.881	0.83	0.933	CLONAL	2	TRUE	0	0.422234844894443	2		661	707	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691022	NA	P-0013013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	424	726	2	ENST00000269305.4:c.1024del	p.Arg342GlufsTer3	p.R342Efs*3	ENST00000269305	NM_001126112.2	342	Cga/ga	10/11	0.356358300548746	2	FACETS	0.873	0.833	0.914	0.873	0.833	0.914	CLONAL	2	TRUE	0	0.422234844894443	2		728	1150	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294208	11294208	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	221	666	0	ENST00000361445.4:c.2323A>G	p.Ile775Val	p.I775V	ENST00000361445	NM_004958.3	775	Att/Gtt	14/58	0.235130975369048	1	FACETS	0.914	0.851	0.978	0.914	0.851	0.978	INDETERMINATE	1	TRUE	0	0.422234844894443	1		666	904	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108616	8108616	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	61	652	0	ENST00000585124.1:c.779G>C	p.Gly260Ala	p.G260A	ENST00000585124	NM_004217.3	260	gGa/gCa	8/9	0.356358300548746	2	FACETS	0.275	0.236	0.317	0.137	0.118	0.159	SUBCLONAL	1	TRUE	0	0.422234844894443	2		652	1051	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349762	15349762	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	44	207	0	ENST00000263377.2:c.3812A>T	p.Gln1271Leu	p.Q1271L	ENST00000263377	NM_058243.2	1271	cAg/cTg	19/20	1	2	FACETS	0.926	0.784	1	0.926	0.784	1	CLONAL	1	TRUE	1	0.422234844894443	2		207	225	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409143	139409170	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TACACATGCTCCCTAAGGGCAGGGCGGG	TACACATGCTCCCTAAGGGCAGGGCGGG	-	novel	NA	P-0013013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	186	469	0	ENST00000277541.6:c.2015-16_2026del		p.X672_splice	ENST00000277541	NM_017617.3	672		13/34	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.422234844894443	2		469	645	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0013016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	488	474	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.427190380308277	5	FACETS	0.907	0.868	0.946	0.907	0.868	0.946	CLONAL	3	TRUE	2	0.427190380308277	5		474	1378	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997764	149997764	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	183	420	1	ENST00000253339.5:c.2703G>T	p.Gln901His	p.Q901H	ENST00000253339		901	caG/caT	5/7	0.366466511648218	3	FACETS	1	0.985	1	0.636	0.588	0.686	CLONAL	1	TRUE	1	0.427190380308277	3		421	817	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577595	7577598	+	frameshift_variant	Frame_Shift_Del	DEL	CAGT	CAGT	-	novel	NA	P-0013016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	314	397	0	ENST00000269305.4:c.683_686del	p.Asp228ValfsTer18	p.D228Vfs*18	ENST00000269305	NM_001126112.2	228	gACTGt/gt	7/11	0.309522922458237	3	FACETS	0.848	0.806	0.891	0.848	0.806	0.891	CLONAL	3	TRUE	0	0.427190380308277	3		397	701	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0013020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	47	503	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.432	0.363	0.508	0.432	0.363	0.508	SUBCLONAL	1	TRUE	1	0.243103389243608	2		503	896	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0013020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	173	367	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.899	0.828	0.971	1	0.992	1	CLONAL	2	TRUE	1	0.243103389243608	2		367	792	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0013020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	154	568	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.243103389243608	2		568	876	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0013020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	122	490	1	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.243103389243608	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.243103389243608	1		491	614	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0013020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	61	818	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.243103389243608	2		818	378	SUCCESS
APC	324	MSKCC	GRCh37	5	112174413	112174414	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs1554084712	NA	P-0013020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	133	357	0	ENST00000257430.4:c.3123_3124del	p.Pro1043PhefsTer4	p.P1043Ffs*4	ENST00000257430	NM_000038.5	1041	cAA/c	16/16	1	2	FACETS	0.904	0.824	0.988	1	0.989	1	CLONAL	2	TRUE	1	0.243103389243608	2		357	605	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143191881	143191881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs184155869	NA	P-0013020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	155	784	1	ENST00000262992.4:c.550G>A	p.Val184Met	p.V184M	ENST00000262992	NM_001101669.1	184	Gtg/Atg	8/24	0.243103389243608	1	FACETS	0.98	0.896	1	0.98	0.896	1	CLONAL	1	TRUE	0	0.243103389243608	1		785	1143	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045696	26045696	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1608	201	1137	5	ENST00000540144.1:c.58C>A	p.Gln20Lys	p.Q20K	ENST00000540144	NM_003531.2	20	Cag/Aag	1/1	1	2	FACETS	0.914	0.844	0.988	0.914	0.844	0.988	CLONAL	1	TRUE	1	0.243103389243608	2		1142	1809	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453132	140453132	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913365	NA	P-0013022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	47	439	0	ENST00000288602.6:c.1803A>T	p.Lys601Asn	p.K601N	ENST00000288602	NM_004333.4	601	aaA/aaT	15/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		439	571	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949985	44949985	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	39	301	0	ENST00000377967.4:c.3754G>C	p.Ala1252Pro	p.A1252P	ENST00000377967	NM_021140.2	1252	Gca/Cca	26/29	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		301	341	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843287	128843287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	50	761	0	ENST00000249373.3:c.394C>T	p.Pro132Ser	p.P132S	ENST00000249373	NM_005631.4	132	Ccc/Tcc	2/12	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		761	969	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228172	53228172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	59	292	0	ENST00000375401.3:c.2230C>T	p.Arg744Trp	p.R744W	ENST00000375401	NM_004187.3	744	Cgg/Tgg	15/26	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		292	413	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142971	47142971	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	137	697	0	ENST00000409792.3:c.4992del	p.Phe1664LeufsTer41	p.F1664Lfs*41	ENST00000409792	NM_014159.6	1664	ttT/tt	8/21	0.166624472005333	2	FACETS	1	0.983	1	0.674	0.613	0.739	CLONAL	1	TRUE	0	0.222812714100718	2		697	912	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760961	133760961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1003322722	NA	P-0013036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	274	752	1	ENST00000318560.5:c.3284G>A	p.Arg1095Gln	p.R1095Q	ENST00000318560	NM_005157.4	1095	cGg/cAg	11/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.463605759001679	2		753	1062	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717733	89717733	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1554825235	NA	P-0013036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	118	371	0	ENST00000371953.3:c.758T>A	p.Ile253Asn	p.I253N	ENST00000371953	NM_000314.4	253	aTc/aAc	7/9	0.463605759001679	1	FACETS	0.887	0.806	0.971	0.887	0.806	0.971	CLONAL	1	TRUE	0	0.463605759001679	1		371	441	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551426	150551426	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	209	819	0	ENST00000369026.2:c.581A>C	p.Lys194Thr	p.K194T	ENST00000369026	NM_021960.4	194	aAg/aCg	1/3	1	2	FACETS	0.851	0.789	0.914	0.851	0.789	0.914	CLONAL	1	TRUE	1	0.463605759001679	2		819	1060	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436593	8436593	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	166	499	0	ENST00000356435.5:c.4085A>T	p.Glu1362Val	p.E1362V	ENST00000356435		1362	gAg/gTg	24/35	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.463605759001679	2		499	690	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194100	94194100	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0013036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	193	632	0	ENST00000323929.3:c.1326+2T>C		p.X442_splice	ENST00000323929	NM_005591.3	442			1	2	FACETS	0.936	0.866	1	0.936	0.866	1	CLONAL	1	TRUE	1	0.463605759001679	2		632	890	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871044	12871044	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013036-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	110	293	0	ENST00000228872.4:c.275del	p.Pro92ArgfsTer27	p.P92Rfs*27	ENST00000228872	NM_004064.3	91	Ccc/cc	1/3	0.463605759001679	1	FACETS	0.902	0.817	0.991	0.902	0.817	0.991	CLONAL	1	TRUE	0	0.463605759001679	1		293	404	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0013045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	18	367	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.52	0.39	0.676	0.52	0.39	0.676	SUBCLONAL	1	TRUE	1	0.11	2		367	629	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054837	5054837	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	52	468	0	ENST00000381652.3:c.889C>A	p.Gln297Lys	p.Q297K	ENST00000381652	NM_004972.3	297	Cag/Aag	7/25	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.11	2		468	857	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904986	101904986	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs863223818	NA	P-0013045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	22	276	0	ENST00000374994.4:c.973+1G>A		p.X325_splice	ENST00000374994	NM_004612.2	325			1	2	FACETS	0.913	0.706	1	0.913	0.706	1	CLONAL	1	TRUE	1	0.11	2		276	438	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506200	120506200	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	79	138	0	ENST00000256646.2:c.1912T>G	p.Ser638Ala	p.S638A	ENST00000256646	NM_024408.3	638	Tca/Gca	11/34	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.608170788547319	2		138	245	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063313	67063313	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0013047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	203	280	0	ENST00000412916.2:c.3G>A	p.Met1?	p.M1?	ENST00000412916		1	atG/atA	1/6	0.608170788547319	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.608170788547319	1		280	455	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512327	38512327	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	247	392	0	ENST00000254066.5:c.1238T>C	p.Met413Thr	p.M413T	ENST00000254066	NM_000964.3	413	aTg/aCg	9/9	0.578815003521743	3	FACETS	0.939	0.877	1	0.47	0.438	0.502	CLONAL	1	TRUE	1	0.608170788547319	3		392	1128	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115711	8115711	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	259	490	0	ENST00000346208.3:c.1060del	p.Leu354Ter	p.L354*	ENST00000346208		353	Ccc/cc	6/6	NA	2	FACETS	0.78	0.73	0.831			1	INDETERMINATE	1	TRUE	NA	0.608170788547319	2		490	1092	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435449	49435449	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1449262096	NA	P-0013061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1233	568	997	0	ENST00000301067.7:c.6223A>C	p.Lys2075Gln	p.K2075Q	ENST00000301067	NM_003482.3	2075	Aag/Cag	30/54	1	2	FACETS	0.966	0.926	1	0.966	0.926	1	CLONAL	1	TRUE	1	0.653231514279332	2		997	1801	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790740	89790741	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0013061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1344	553	992	0	ENST00000336032.3:c.129_130del	p.Arg44AspfsTer163	p.R44Dfs*163	ENST00000336032	NM_006813.2	43	CCc/c	1/2	NA	2	FACETS	0.893	0.855	0.931			1	INDETERMINATE	1	TRUE	NA	0.653231514279332	2		992	1897	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0013063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	224	519	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.395248804637118	2		519	1030	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0013063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	253	565	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.395248804637118	2		565	1090	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098962	178098962	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	264	409	0	ENST00000397062.3:c.83T>C	p.Ile28Thr	p.I28T	ENST00000397062	NM_006164.4	28	aTa/aCa	2/5	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.395248804637118	2		409	896	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331643	8331643	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1324	79	811	0	ENST00000356435.5:c.5473G>C	p.Gly1825Arg	p.G1825R	ENST00000356435		1825	Ggc/Cgc	33/35	NA	2	FACETS	0.285	0.249	0.324			1	INDETERMINATE	1	TRUE	NA	0.395248804637118	2		811	1403	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070325	37070325	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778917	NA	P-0013063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	67	714	2	ENST00000231790.2:c.1460G>A	p.Arg487Gln	p.R487Q	ENST00000231790	NM_000249.3	487	cGa/cAa	13/19	0.395248804637118	1	FACETS	0.267	0.231	0.306	0.267	0.231	0.306	SUBCLONAL	1	TRUE	0	0.395248804637118	1		716	1019	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11205024	11205024	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0013063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	296	730	0	ENST00000361445.4:c.4764+1G>C		p.X1588_splice	ENST00000361445	NM_004958.3	1588			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.395248804637118	2		730	1446	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828083	243828083	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1216797938	NA	P-0013063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	106	514	0	ENST00000263826.5:c.275C>A	p.Pro92Gln	p.P92Q	ENST00000263826	NM_005465.4	92	cCa/cAa	3/13	0.395248804637118	3	FACETS	0.61	0.546	0.679	0.305	0.273	0.34	SUBCLONAL	1	TRUE	1	0.395248804637118	3		514	1053	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239908	41239908	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	116	210	0	ENST00000379561.5:c.442C>T	p.Gln148Ter	p.Q148*	ENST00000379561	NM_002015.3	148	Cag/Tag	1/3	0.395248804637118	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.395248804637118	1		210	333	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916256	9916256	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	200	625	2	ENST00000330684.3:c.2033C>A	p.Pro678Gln	p.P678Q	ENST00000330684	NM_001134407.1	678	cCa/cAa	10/13	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.395248804637118	2		627	1010	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556276	29556276	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376666221	NA	P-0013063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	297	714	0	ENST00000356175.3:c.2643G>A	p.Met881Ile	p.M881I	ENST00000356175	NM_000267.3	881	atG/atA	21/57	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.395248804637118	2		714	1390	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574427	41574427	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	120	542	0	ENST00000263253.7:c.6712A>C	p.Asn2238His	p.N2238H	ENST00000263253	NM_001429.3	2238	Aat/Cat	31/31	1	2	FACETS	0.535	0.482	0.592	0.535	0.482	0.592	SUBCLONAL	1	TRUE	1	0.395248804637118	2		542	1134	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852080	63852080	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	147	299	0	ENST00000279873.7:c.2858A>G	p.Lys953Arg	p.K953R	ENST00000279873	NM_032199.2	953	aAa/aGa	10/10	1	2	FACETS	0.995	0.921	1	0.995	0.921	1	CLONAL	1	TRUE	1	0.796064976738852	2		299	371	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905303	50905303	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	566	1180	0	ENST00000440232.2:c.511G>C	p.Ala171Pro	p.A171P	ENST00000440232	NM_002691.3	171	Gcc/Ccc	5/27	1	2	FACETS	0.875	0.84	0.911	0.875	0.84	0.911	CLONAL	1	TRUE	1	0.796064976738852	2		1180	1625	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256793	16256793	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	137	549	0	ENST00000375759.3:c.4058T>C	p.Val1353Ala	p.V1353A	ENST00000375759	NM_015001.2	1353	gTg/gCg	11/15	0.375174791993832	1	FACETS	0.343	0.313	0.376	0.343	0.313	0.376	INDETERMINATE	1	TRUE	0	0.718182637297587	1		549	712	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215674254	215674254	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	318	597	0	ENST00000260947.4:c.40A>G	p.Ile14Val	p.I14V	ENST00000260947	NM_000465.2	14	Atc/Gtc	1/11	0.34372042980311	2	FACETS	1	0.99	1	0.579	0.549	0.609	INDETERMINATE	1	TRUE	0	0.718182637297587	2		597	765	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0013103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	150	769	1	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	0.34372042980311	2	FACETS	0.425	0.388	0.464	0.212	0.194	0.232	INDETERMINATE	1	TRUE	0	0.718182637297587	2		770	983	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118811	115118811	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	142	782	1	ENST00000257566.3:c.530A>T	p.Asp177Val	p.D177V	ENST00000257566	NM_016569.3	177	gAc/gTc	2/8	0.375174791993832	1	FACETS	0.265	0.241	0.29	0.265	0.241	0.29	INDETERMINATE	1	TRUE	0	0.718182637297587	1		783	957	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435004	110435004	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	92	520	2	ENST00000375856.3:c.3397G>A	p.Ala1133Thr	p.A1133T	ENST00000375856	NM_003749.2	1133	Gcc/Acc	1/2	0.714217841301148	3	FACETS	0.321	0.284	0.36	0.107	0.094	0.12	SUBCLONAL	1	TRUE	0	0.718182637297587	3		522	1086	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991341	72991341	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs758423425	NA	P-0013103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	261	1111	0	ENST00000268489.5:c.2704A>G	p.Met902Val	p.M902V	ENST00000268489	NM_006885.3	902	Atg/Gtg	2/10	1	2	FACETS	0.526	0.491	0.562	0.526	0.491	0.562	SUBCLONAL	1	TRUE	1	0.718182637297587	2		1111	1382	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735447	40735447	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs745862490	NA	P-0013103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2026	134	864	0	ENST00000373198.4:c.3426G>T	p.Arg1142Ser	p.R1142S	ENST00000373198	NM_133170.3	1142	agG/agT	25/32	0.338294056664239	6	FACETS	0.421	0.38	0.464	0.105	0.095	0.116	INDETERMINATE	1	TRUE	2	0.718182637297587	6		864	2160	SUCCESS
AR	367	MSKCC	GRCh37	X	66905935	66905935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1218564193	NA	P-0013103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	483	533	1	ENST00000374690.3:c.1852C>T	p.Arg618Trp	p.R618W	ENST00000374690	NM_000044.3	618	Cgg/Tgg	3/8	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.718182637297587	1		534	666	SUCCESS
APC	324	MSKCC	GRCh37	5	112174998	112174999	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs1554085246	NA	P-0013103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	305	451	0	ENST00000257430.4:c.3709_3710del	p.Gln1237GlufsTer2	p.Q1237Efs*2	ENST00000257430	NM_000038.5	1236	gCA/g	16/16	0.34372042980311	2	FACETS	1	0.995	1	0.713	0.678	0.747	INDETERMINATE	1	TRUE	0	0.718182637297587	2		451	596	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412503	63412503	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	560	517	0	ENST00000330258.3:c.664del	p.Gln222LysfsTer60	p.Q222Kfs*60	ENST00000330258	NM_152424.3	222	Caa/aa	2/2	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.718182637297587	1		517	818	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577510	7577511	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0013103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	351	655	0	ENST00000269305.4:c.770_771del	p.Leu257ArgfsTer6	p.L257Rfs*6	ENST00000269305	NM_001126112.2	257	cTG/c	7/11	0.700644808793395	1	FACETS	0.988	0.946	1	0.988	0.946	1	CLONAL	1	TRUE	0	0.718182637297587	1		655	634	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	343	661	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.82139961488531	3	FACETS	0.871	0.832	0.911	0.871	0.832	0.911	CLONAL	2	TRUE	1	0.82139961488531	3		661	676	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0013107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	274	234	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.815336815361682	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	TRUE	0	0.82139961488531	3		234	313	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	513	667	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	0.82139961488531	3	FACETS	0.972	0.939	1	0.972	0.939	1	CLONAL	2	TRUE	1	0.82139961488531	3		667	906	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412308	139412308	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	226	640	0	ENST00000277541.6:c.1337del	p.Gly446AlafsTer185	p.G446Afs*185	ENST00000277541	NM_017617.3	446	gGc/gc	8/34	0.82139961488531	2	FACETS	1	0.962	1	0.515	0.484	0.547	CLONAL	1	TRUE	0	0.82139961488531	2		640	534	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274936	38274936	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0013107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	209	586	0	ENST00000425967.3:c.1646-2A>C		p.X549_splice	ENST00000425967	NM_001174067.1	549			0.82139961488531	3	FACETS	0.952	0.887	1	0.476	0.443	0.51	CLONAL	1	TRUE	1	0.82139961488531	3		586	754	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0013109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	843	422	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.255976865279398	7	FACETS	0.984	0.956	1	1	0.996	1	CLONAL	7	TRUE	1	0.255976865279398	7		422	1568	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565593	41565593	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	119	687	0	ENST00000263253.7:c.4259G>C	p.Gly1420Ala	p.G1420A	ENST00000263253	NM_001429.3	1420	gGa/gCa	26/31	0.255976865279398	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.255976865279398	1		687	558	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161326482	161326482	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	210	656	1	ENST00000367975.2:c.257G>T	p.Gly86Val	p.G86V	ENST00000367975	NM_003001.3	86	gGc/gTc	5/6	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.255976865279398	2		657	1410	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462328	89462328	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	128	657	0	ENST00000336596.2:c.1800T>A	p.His600Gln	p.H600Q	ENST00000336596	NM_005233.5	600	caT/caA	10/17	1	2	FACETS	0.954	0.863	1	0.954	0.863	1	CLONAL	1	TRUE	1	0.255976865279398	2		657	1048	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350109	81350109	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	87	753	0	ENST00000222390.5:c.1223C>G	p.Ser408Cys	p.S408C	ENST00000222390	NM_000601.4	408	tCt/tGt	10/18	1	2	FACETS	0.825	0.729	0.927	0.825	0.729	0.927	CLONAL	1	TRUE	1	0.255976865279398	2		753	824	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39644771	39644771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	51	552	0	ENST00000262039.4:c.2500G>A	p.Glu834Lys	p.E834K	ENST00000262039	NM_002647.2	834	Gaa/Aaa	23/25	1	2	FACETS	0.763	0.649	0.889	0.763	0.649	0.889	SUBCLONAL	1	TRUE	1	0.255976865279398	2		552	522	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388717	31388717	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	198	648	2	ENST00000328111.2:c.1982G>A	p.Arg661Lys	p.R661K	ENST00000328111	NM_006892.3	661	aGg/aAg	18/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.255976865279398	2		650	1388	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958216	54958216	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013109-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	126	589	0	ENST00000312783.6:c.391G>A	p.Glu131Lys	p.E131K	ENST00000312783	NM_198436.1	131	Gaa/Aaa	6/10	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.255976865279398	2		589	901	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0013117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	555	645	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.611414472539708	4	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	2	0.670428803816121	4		645	1378	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115745	8115745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1485	335	958	0	ENST00000346208.3:c.1091G>A	p.Arg364Lys	p.R364K	ENST00000346208		364	aGa/aAa	6/6	0.244754359972567	5	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.670428803816121	5		958	1820	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036016	180036016	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1000190222	NA	P-0013117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1349	401	1008	0	ENST00000261937.6:c.3845A>G	p.Glu1282Gly	p.E1282G	ENST00000261937	NM_182925.4	1282	gAg/gGg	29/30	0.670428803816121	3	FACETS	0.913	0.866	0.961	0.456	0.433	0.481	CLONAL	1	TRUE	1	0.670428803816121	3		1008	1750	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99472880	99472880	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	342	738	0	ENST00000268035.6:c.2876A>T	p.His959Leu	p.H959L	ENST00000268035	NM_000875.3	959	cAt/cTt	14/21	0.670428803816121	3	FACETS	0.969	0.915	1	0.484	0.457	0.512	CLONAL	1	TRUE	1	0.670428803816121	3		738	1406	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	498	575	0	ENST00000269305.4:c.503A>T	p.His168Leu	p.H168L	ENST00000269305	NM_001126112.2	168	cAc/cTc	5/11	0.670428803816121	2	FACETS	0.952	0.921	0.983	0.952	0.921	0.983	CLONAL	2	TRUE	0	0.670428803816121	2		575	780	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099388	27099498	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTGGGTATCAGCCCAGTATGAATACCTCTGACATGATGGGGCGCATGTCCTATGAGCCAAATAAGGATCCTTATGGCAGCATGAGGAAAGGTGACTGATCTGATTGCTAT	CCTGGGTATCAGCCCAGTATGAATACCTCTGACATGATGGGGCGCATGTCCTATGAGCCAAATAAGGATCCTTATGGCAGCATGAGGAAAGGTGACTGATCTGATTGCTAT	-	novel	NA	P-0013117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	121	723	0	ENST00000324856.7:c.3625_3715+20del		p.X1209_splice	ENST00000324856	NM_006015.4	1209		14/20	0.670428803816121	3	FACETS	0.403	0.363	0.446	0.202	0.181	0.223	SUBCLONAL	1	TRUE	1	0.670428803816121	3		723	1195	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs878854073	NA	P-0013140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	92	363	0	ENST00000269305.4:c.673-1G>A		p.X225_splice	ENST00000269305	NM_001126112.2	225			1	2	FACETS	0.868	0.773	0.97	0.868	0.773	0.97	CLONAL	1	TRUE	1	0.36155784339749	2		363	586	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0013140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	103	166	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.36155784339749	2		166	559	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201816	66201816	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556854839	NA	P-0013140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	73	453	0	ENST00000273854.3:c.2686C>T	p.Arg896Cys	p.R896C	ENST00000273854	NM_004439.5	896	Cgt/Tgt	16/18	1	2	FACETS	0.459	0.401	0.523	0.459	0.401	0.523	SUBCLONAL	1	TRUE	1	0.36155784339749	2		453	879	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117740	70117740	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316632405	NA	P-0013140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	129	755	1	ENST00000245479.2:c.208C>T	p.Pro70Ser	p.P70S	ENST00000245479	NM_000346.3	70	Ccc/Tcc	1/3	1	2	FACETS	0.821	0.744	0.902	0.821	0.744	0.902	CLONAL	1	TRUE	1	0.36155784339749	2		756	869	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411779	63411779	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1417	239	996	0	ENST00000330258.3:c.1388C>T	p.Ser463Phe	p.S463F	ENST00000330258	NM_152424.3	463	tCc/tTc	2/2	0.36155784339749	3	FACETS	0.943	0.877	1	0.471	0.438	0.506	CLONAL	1	TRUE	1	0.36155784339749	3		996	1656	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845878	156845878	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1223	99	805	0	ENST00000524377.1:c.1508A>C	p.His503Pro	p.H503P	ENST00000524377	NM_002529.3	503	cAc/cCc	13/17	0.266615552611107	3	FACETS	0.489	0.435	0.547	0.245	0.217	0.274	SUBCLONAL	1	TRUE	1	0.36155784339749	3		805	1322	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732614	190732614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	64	432	0	ENST00000441310.2:c.2432C>T	p.Pro811Leu	p.P811L	ENST00000441310	NM_000534.4	811	cCt/cTt	11/13	1	2	FACETS	0.511	0.442	0.586	0.511	0.442	0.586	SUBCLONAL	1	TRUE	1	0.36155784339749	2		432	693	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652777	212652777	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	55	585	0	ENST00000342788.4:c.529C>T	p.Leu177Phe	p.L177F	ENST00000342788	NM_005235.2	177	Ctt/Ttt	4/28	1	2	FACETS	0.328	0.28	0.382	0.328	0.28	0.382	SUBCLONAL	1	TRUE	1	0.36155784339749	2		585	927	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37061935	37061935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs191257018	NA	P-0013140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	84	423	0	ENST00000231790.2:c.1019C>T	p.Ser340Phe	p.S340F	ENST00000231790	NM_000249.3	340	tCc/tTc	11/19	1	2	FACETS	0.72	0.637	0.81	0.72	0.637	0.81	SUBCLONAL	1	TRUE	1	0.36155784339749	2		423	645	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392179	81392179	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	39	376	0	ENST00000222390.5:c.98G>A	p.Arg33Lys	p.R33K	ENST00000222390	NM_000601.4	33	aGg/aAg	2/18	0.310034190527011	3	FACETS	0.344	0.284	0.411	0.172	0.142	0.206	SUBCLONAL	1	TRUE	1	0.36155784339749	3		376	741	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445530	49445530	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	91	491	0	ENST00000301067.7:c.1936C>T	p.Pro646Ser	p.P646S	ENST00000301067	NM_003482.3	646	Ccc/Tcc	10/54	0.180582501738644	3	FACETS	0.808	0.717	0.904	0.404	0.358	0.452	INDETERMINATE	1	TRUE	1	0.36155784339749	3		491	736	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602408	28602408	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	56	489	0	ENST00000241453.7:c.1960G>A	p.Glu654Lys	p.E654K	ENST00000241453	NM_004119.2	654	Gaa/Aaa	16/24	1	2	FACETS	0.371	0.317	0.431	0.371	0.317	0.431	SUBCLONAL	1	TRUE	1	0.36155784339749	2		489	834	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058388	42058388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1406	212	956	0	ENST00000219905.7:c.8108C>T	p.Ser2703Phe	p.S2703F	ENST00000219905	NM_001164273.1	2703	tCc/tTc	24/24	0.250664319889851	1	FACETS	0.594	0.549	0.64	0.594	0.549	0.64	SUBCLONAL	1	TRUE	0	0.36155784339749	1		956	1618	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631880	90631880	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	98	728	0	ENST00000330062.3:c.473C>T	p.Pro158Leu	p.P158L	ENST00000330062	NM_002168.2	158	cCa/cTa	4/11	0.250664319889851	1	FACETS	0.459	0.408	0.513	0.459	0.408	0.513	SUBCLONAL	1	TRUE	0	0.36155784339749	1		728	968	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99491850	99491850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	61	557	0	ENST00000268035.6:c.3635C>T	p.Pro1212Leu	p.P1212L	ENST00000268035	NM_000875.3	1212	cCc/cTc	20/21	0.250664319889851	1	FACETS	0.318	0.274	0.367	0.318	0.274	0.367	SUBCLONAL	1	TRUE	0	0.36155784339749	1		557	868	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2115587	2115587	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	76	714	1	ENST00000219476.3:c.1667C>T	p.Ser556Phe	p.S556F	ENST00000219476	NM_000548.3	556	tCc/tTc	16/42	1	2	FACETS	0.429	0.375	0.488	0.429	0.375	0.488	SUBCLONAL	1	TRUE	1	0.36155784339749	2		715	979	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54956623	54956623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	113	441	1	ENST00000312783.6:c.571C>T	p.Pro191Ser	p.P191S	ENST00000312783	NM_198436.1	191	Cct/Tct	7/10	0.266615552611107	3	FACETS	1	0.912	1	0.507	0.456	0.56	CLONAL	1	TRUE	1	0.36155784339749	3		442	728	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937075	36937076	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0013140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	172	931	2	ENST00000361632.4:c.1243_1244delinsAA	p.Gly415Lys	p.G415K	ENST00000361632		415	GGg/AAg	9/16	0.266615552611107	3	FACETS	0.867	0.796	0.942	0.433	0.398	0.471	CLONAL	1	TRUE	1	0.36155784339749	3		933	1296	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829797	76829825	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	CAATGTTTCGAAGCCACTTCCCCTCACCT	CAATGTTTCGAAGCCACTTCCCCTCACCT	GGCTTC	novel	NA	P-0013140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1609	199	844	0	ENST00000373344.5:c.6218-2_6244delinsGAAGCC		p.X2073_splice	ENST00000373344	NM_000489.3	2073		28/35	0.36155784339749	3	FACETS	0.719	0.663	0.777	0.359	0.331	0.389	SUBCLONAL	1	TRUE	1	0.36155784339749	3		844	1808	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0013142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	158	462	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.191291889010442	2		463	1150	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143174	30143174	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1383948379	NA	P-0013142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	68	425	0	ENST00000389048.3:c.352G>T	p.Ala118Ser	p.A118S	ENST00000389048	NM_004304.4	118	Gca/Tca	1/29	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.191291889010442	2		425	514	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149447852	149447852	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	101	659	0	ENST00000286301.3:c.1552G>C	p.Val518Leu	p.V518L	ENST00000286301	NM_005211.3	518	Gtg/Ctg	11/22	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	FALSE	1	0.191291889010442	2		659	1054	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50358684	50358684	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	47	223	0	ENST00000331340.3:c.27G>C	p.Met9Ile	p.M9I	ENST00000331340	NM_006060.4	9	atG/atC	2/8	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	FALSE	1	0.191291889010442	2		223	468	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967671	90967671	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	83	500	0	ENST00000265433.3:c.1237A>C	p.Asn413His	p.N413H	ENST00000265433	NM_002485.4	413	Aat/Cat	10/16	1	2	FACETS	0.813	0.715	0.918	0.813	0.715	0.918	CLONAL	1	FALSE	1	0.191291889010442	2		500	1068	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759630	133759630	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	129	736	0	ENST00000318560.5:c.1953G>T	p.Leu651Phe	p.L651F	ENST00000318560	NM_005157.4	651	ttG/ttT	11/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.191291889010442	2		736	1123	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143545	108143545	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1213	137	619	0	ENST00000278616.4:c.3250C>T	p.Gln1084Ter	p.Q1084*	ENST00000278616	NM_000051.3	1084	Caa/Taa	22/63	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	1	0.191291889010442	2		619	1350	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89839682	89839682	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	82	615	0	ENST00000389301.3:c.2011G>C	p.Asp671His	p.D671H	ENST00000389301	NM_000135.2	671	Gat/Cat	22/43	1	2	FACETS	0.754	0.663	0.853	0.754	0.663	0.853	SUBCLONAL	1	FALSE	1	0.191291889010442	2		615	1137	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559830	29559830	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555614963	NA	P-0013142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	77	595	1	ENST00000356175.3:c.3427C>T	p.His1143Tyr	p.H1143Y	ENST00000356175	NM_000267.3	1143	Cac/Tac	26/57	1	2	FACETS	0.668	0.584	0.758	0.668	0.584	0.758	SUBCLONAL	1	FALSE	1	0.191291889010442	2		596	1206	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653151	29653151	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	76	373	0	ENST00000356175.3:c.5086G>T	p.Glu1696Ter	p.E1696*	ENST00000356175	NM_000267.3	1696	Gag/Tag	36/57	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	FALSE	1	0.191291889010442	2		373	739	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664506	29664506	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	123	536	0	ENST00000356175.3:c.6485G>T	p.Arg2162Leu	p.R2162L	ENST00000356175	NM_000267.3	2162	cGg/cTg	42/57	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.191291889010442	2		536	1186	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7163146	7163146	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1520	80	869	0	ENST00000302850.5:c.1926G>T	p.Trp642Cys	p.W642C	ENST00000302850	NM_000208.2	642	tgG/tgT	9/22	1	2	FACETS	0.523	0.458	0.593	0.523	0.458	0.593	SUBCLONAL	1	FALSE	1	0.191291889010442	2		869	1600	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757396	40757396	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1325	98	756	1	ENST00000373198.4:c.2902G>T	p.Asp968Tyr	p.D968Y	ENST00000373198	NM_133170.3	968	Gac/Tac	20/32	0.181761890935435	3	FACETS	0.789	0.701	0.883	0.394	0.35	0.442	SUBCLONAL	1	FALSE	1	0.191291889010442	3		757	1423	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193219805	193219805	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0013142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	59	347	0	ENST00000367435.3:c.1560del		p.X520_splice	ENST00000367435	NM_024529.4	520			1	2	FACETS	0.857	0.736	0.989	0.857	0.736	0.989	CLONAL	1	FALSE	1	0.191291889010442	2		347	720	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537896	212537897	+	missense_variant	Missense_Mutation	DNP	TG	TG	GT	novel	NA	P-0013142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	69	536	0	ENST00000342788.4:c.1708_1709delinsAC	p.His570Thr	p.H570T	ENST00000342788	NM_005235.2	570	CAt/ACt	14/28	1	2	FACETS	0.818	0.711	0.934	0.818	0.711	0.934	CLONAL	1	FALSE	1	0.191291889010442	2		536	882	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610118	10610121	+	frameshift_variant	Frame_Shift_Del	DEL	CCAC	CCAC	GTA	novel	NA	P-0013142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	156	666	0	ENST00000171111.5:c.589_592delinsTAC	p.Val197TyrfsTer33	p.V197Yfs*33	ENST00000171111	NM_203500.1	197	GTGGag/TACag	2/6	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.191291889010442	2		666	1200	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs879253911	NA	P-0013149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	336	365	0	ENST00000269305.4:c.538G>T	p.Glu180Ter	p.E180*	ENST00000269305	NM_001126112.2	180	Gag/Tag	5/11	0.537965066130765	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.537965066130765	2		365	567	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433375	138433375	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1348630621	NA	P-0013149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	443	578	0	ENST00000289153.2:c.1237A>G	p.Thr413Ala	p.T413A	ENST00000289153	NM_006219.2	413	Acg/Gcg	7/22	0.537965066130765	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.537965066130765	2		578	809	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001124	150001124	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	457	559	0	ENST00000253339.5:c.2480G>C	p.Arg827Thr	p.R827T	ENST00000253339		827	aGa/aCa	4/7	0.537965066130765	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.537965066130765	2		559	817	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961905	15961905	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	268	360	0	ENST00000268712.3:c.5890C>G	p.His1964Asp	p.H1964D	ENST00000268712	NM_006311.3	1964	Cac/Gac	38/46	0.537965066130765	2	FACETS	0.912	0.865	0.96	0.912	0.865	0.96	CLONAL	2	TRUE	0	0.537965066130765	2		360	546	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961910	15961912	+	missense_variant,splice_region_variant	Missense_Mutation	TNP	GAT	GAT	AAA	novel	NA	P-0013149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	236	330	2	ENST00000268712.3:c.5883_5885delinsTTT	p.Leu1961_Ser1962delinsPhePhe	p.L1961_S1962delinsFF	ENST00000268712	NM_006311.3	1961	ttATCt/ttTTTt	38/46	0.537965066130765	2	FACETS	0.876	0.826	0.925	0.876	0.826	0.925	CLONAL	2	TRUE	0	0.537965066130765	2		332	501	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984023	2984024	+	missense_variant	Missense_Mutation	DNP	CG	CG	TT	novel	NA	P-0013149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	454	583	0	ENST00000396946.4:c.506_507delinsAA	p.Thr169Lys	p.T169K	ENST00000396946	NM_032415.4	169	aCG/aAA	5/25	0.43470656480069	4	FACETS	0.972	0.928	1	0.972	0.928	1	CLONAL	2	TRUE	2	0.537965066130765	4		583	1335	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265057	46265057	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	1391	1291	0	ENST00000371998.3:c.1927G>C	p.Asp643His	p.D643H	ENST00000371998		643	Gat/Cat	12/23	0.509814063120456	7	FACETS	0.977	0.955	0.998			1	CLONAL	5	TRUE	NA	0.509814063120456	7		1291	2542	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466018	69466018	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	242	704	0	ENST00000227507.2:c.856A>G	p.Thr286Ala	p.T286A	ENST00000227507	NM_053056.2	286	Aca/Gca	5/5	0.458464812305289	1	FACETS	0.662	0.621	0.704	0.662	0.621	0.704	SUBCLONAL	1	TRUE	0	0.666926089226628	1		704	731	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023042	48023042	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs63749873	NA	P-0013209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	152	649	0	ENST00000234420.5:c.467C>G	p.Ser156Ter	p.S156*	ENST00000234420	NM_000179.2	156	tCa/tGa	3/10	0.346822304129036	3	FACETS	0.691	0.632	0.753	0.346	0.316	0.377	INDETERMINATE	1	TRUE	1	0.666926089226628	3		649	879	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651303	45651303	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	118	802	0	ENST00000407780.3:c.722A>G	p.Lys241Arg	p.K241R	ENST00000407780	NM_001283052.1	241	aAg/aGg	5/7	1	2	FACETS	0.355	0.319	0.393	0.355	0.319	0.393	SUBCLONAL	1	TRUE	1	0.666926089226628	2		802	997	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082371	16082371	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	60	618	0	ENST00000281043.3:c.185C>T	p.Ser62Leu	p.S62L	ENST00000281043	NM_005378.4	62	tCg/tTg	2/3	1	2	FACETS	0.844	0.727	0.972	0.844	0.727	0.972	CLONAL	1	TRUE	1	0.22	2		618	646	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162967	47162974	+	frameshift_variant	Frame_Shift_Del	DEL	ATCTTCTG	ATCTTCTG	-	novel	NA	P-0013240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	54	606	0	ENST00000409792.3:c.3152_3159del	p.Ser1051TyrfsTer5	p.S1051Yfs*5	ENST00000409792	NM_014159.6	1051	tCAGAAGAT/t	3/21	0.188828169575538	1	FACETS	0.597	0.509	0.694	0.597	0.509	0.694	SUBCLONAL	1	TRUE	0	0.22	1		606	732	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183769	10183770	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	T	novel	NA	P-0013240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	62	468	0	ENST00000256474.2:c.238_239delinsT	p.Ser80PhefsTer79	p.S80Ffs*79	ENST00000256474	NM_000551.3	80	AGt/Tt	1/3	0.188828169575538	1	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	0	0.22	1		468	501	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662922	52662926	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCA	CTGCA	TGC	novel	NA	P-0013240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	91	617	0	ENST00000394830.3:c.1427_1431delinsGCA	p.Leu476CysfsTer30	p.L476Cfs*30	ENST00000394830	NM_018313.4	476	tTGCAG/tGCA	13/30	0.188828169575538	1	FACETS	0.99	0.878	1	0.99	0.878	1	CLONAL	1	TRUE	0	0.22	1		617	744	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835596	68835596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587783047	NA	P-0013257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	229	560	0	ENST00000261769.5:c.187C>T	p.Arg63Ter	p.R63*	ENST00000261769	NM_004360.3	63	Cga/Tga	3/16	0.4239675383921	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.4239675383921	1		560	789	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262645	16262645	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	111	366	0	ENST00000375759.3:c.9910C>T	p.Gln3304Ter	p.Q3304*	ENST00000375759	NM_015001.2	3304	Caa/Taa	11/15	1	2	FACETS	0.746	0.671	0.825	0.746	0.671	0.825	SUBCLONAL	1	TRUE	1	0.4239675383921	2		366	702	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217127	66217127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767617774	NA	P-0013257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	81	676	4	ENST00000273854.3:c.2488G>A	p.Glu830Lys	p.E830K	ENST00000273854	NM_004439.5	830	Gag/Aag	14/18	0.223698580382331	1	FACETS	0.276	0.242	0.312	0.276	0.242	0.312	INDETERMINATE	1	TRUE	0	0.4239675383921	1		680	1092	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517857	8517857	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	151	652	0	ENST00000356435.5:c.1534C>T	p.Gln512Ter	p.Q512*	ENST00000356435		512	Cag/Tag	10/35	1	2	FACETS	0.633	0.577	0.691	0.633	0.577	0.691	SUBCLONAL	1	TRUE	1	0.4239675383921	2		652	1126	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0013265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	570	636	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.243789693906937	4	FACETS	0.884	0.853	0.914			1	INDETERMINATE	4	TRUE	NA	0.422423877215815	4		636	1086	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599252	55599252	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	276	539	0	ENST00000288135.5:c.2378T>C	p.Leu793Ser	p.L793S	ENST00000288135	NM_000222.2	793	tTg/tCg	17/21	0.42217243841792	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.422423877215815	3		539	780	SUCCESS
ATR	545	MSKCC	GRCh37	3	142297507	142297507	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1955	149	650	0	ENST00000350721.4:c.40G>T	p.Ala14Ser	p.A14S	ENST00000350721	NM_001184.3	14	Gcc/Tcc	1/47	0.422423877215815	10	FACETS	0.902	0.82	0.989			1	CLONAL	1	TRUE	NA	0.422423877215815	10		650	2104	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968641	55968641	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs139644107	NA	P-0013265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	208	742	0	ENST00000263923.4:c.2022G>C	p.Glu674Asp	p.E674D	ENST00000263923	NM_002253.2	674	gaG/gaC	14/30	0.42217243841792	3	FACETS	0.975	0.904	1	0.488	0.452	0.525	CLONAL	1	TRUE	1	0.422423877215815	3		742	1223	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848029	151848029	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	170	612	0	ENST00000262189.6:c.12730A>C	p.Ile4244Leu	p.I4244L	ENST00000262189	NM_170606.2	4244	Att/Ctt	51/59	0.42217243841792	3	FACETS	1	0.972	1	0.562	0.517	0.608	CLONAL	1	TRUE	1	0.422423877215815	3		612	868	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986592	36986592	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	90	305	0	ENST00000354822.5:c.1097G>A	p.Ser366Asn	p.S366N	ENST00000354822	NM_001079668.2	366	aGc/aAc	3/3	0.281275738852977	5	FACETS	1	0.976	1	0.461	0.41	0.515	CLONAL	1	TRUE	2	0.422423877215815	5		305	503	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16021210	16021210	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0013265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	194	761	0	ENST00000268712.3:c.2047A>T	p.Lys683Ter	p.K683*	ENST00000268712	NM_006311.3	683	Aaa/Taa	18/46	0.42217243841792	2	FACETS	0.973	0.901	1	0.486	0.45	0.524	CLONAL	1	TRUE	0	0.422423877215815	2		761	944	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851802	134851802	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1319	156	652	0	ENST00000398015.3:c.1209del	p.Phe404LeufsTer44	p.F404Lfs*44	ENST00000398015	NM_004441.4	403	aCc/ac	5/16	0.422423877215815	6	FACETS	0.924	0.843	1	0.231	0.21	0.253	CLONAL	1	TRUE	2	0.422423877215815	6		652	1475	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413744	138413749	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CTGAAG	CTGAAG	-	novel	NA	P-0013265-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1309	116	416	0	ENST00000289153.2:c.1771_1776del	p.Leu591_Gln592del	p.L591_Q592del	ENST00000289153	NM_006219.2	591	CTTCAG/-	12/22	0.422423877215815	10	FACETS	1	0.925	1			1	CLONAL	1	TRUE	NA	0.422423877215815	10		416	1425	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013276-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	77	528	2				ENST00000310581	NM_198253.2	-/1132			0.782415422297138	1	FACETS	0.624	0.566	0.681	0.624	0.566	0.681	SUBCLONAL	1	TRUE	0	0.926571332857749	1		530	143	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0013276-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	532	472	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.19778110950346	5	FACETS	1	0.994	1	0.79	0.76	0.82	INDETERMINATE	2	TRUE	2	0.926571332857749	5		473	1158	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271363	26271363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013276-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1513	96	1383	8	ENST00000305910.3:c.250C>T	p.Arg84Cys	p.R84C	ENST00000305910	NM_003534.2	84	Cgc/Tgc	1/1	1	2	FACETS	0.129	0.114	0.145	0.129	0.114	0.145	SUBCLONAL	1	TRUE	1	0.926571332857749	2		1391	1609	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926872	112926872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507541	NA	P-0013276-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	559	675	3	ENST00000351677.2:c.1492C>T	p.Arg498Trp	p.R498W	ENST00000351677	NM_002834.3	498	Cgg/Tgg	13/16	0.344842179042865	4	FACETS	0.875	0.841	0.908	0.875	0.841	0.908	INDETERMINATE	2	TRUE	2	0.926571332857749	4		678	1329	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794721	42794722	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0013276-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	372	566	0	ENST00000575354.2:c.1801_1802del	p.Lys601GlufsTer88	p.K601Efs*88	ENST00000575354	NM_015125.3	601	AAg/g	10/20	0.642646226523736	1	FACETS	0.878	0.85	0.904	0.878	0.85	0.904	CLONAL	1	TRUE	0	0.926571332857749	1		566	491	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794441	42794441	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013276-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	80	912	2	ENST00000575354.2:c.1526del	p.Pro509HisfsTer14	p.P509Hfs*14	ENST00000575354	NM_015125.3	507	cgC/cg	10/20	0.642646226523736	1	FACETS	0.11	0.096	0.125	0.11	0.096	0.125	SUBCLONAL	1	TRUE	0	0.926571332857749	1		914	843	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0013283-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	727	890	5	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.630054865636399	3	FACETS	0.952	0.928	0.975			1	CLONAL	3	TRUE	NA	0.629193372803152	3		895	1064	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289660	33289660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758327720	NA	P-0013283-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	130	514	0	ENST00000374542.5:c.43G>A	p.Glu15Lys	p.E15K	ENST00000374542	NM_001141970.1	15	Gaa/Aaa	2/8	0.630054865636399	4	FACETS	0.838	0.761	0.92	0.419	0.38	0.46	CLONAL	1	TRUE	2	0.629193372803152	4		514	803	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287286	33287286	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013283-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	188	627	0	ENST00000374542.5:c.1811G>C	p.Gly604Ala	p.G604A	ENST00000374542	NM_001141970.1	604	gGa/gCa	6/8	0.630054865636399	4	FACETS	0.98	0.906	1	0.49	0.453	0.529	CLONAL	1	TRUE	2	0.629193372803152	4		627	993	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549454	187549454	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs201060026	NA	P-0013283-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	220	545	0	ENST00000441802.2:c.4664C>G	p.Thr1555Arg	p.T1555R	ENST00000441802	NM_005245.3	1555	aCg/aGg	9/27	0.625476449495656	3	FACETS	1	0.987	1	0.609	0.568	0.651	CLONAL	1	TRUE	1	0.629193372803152	3		545	755	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022655	31022655	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013283-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1259	225	741	0	ENST00000375687.4:c.2140T>C	p.Ser714Pro	p.S714P	ENST00000375687	NM_015338.5	714	Tcc/Ccc	13/13	0.629193372803152	6	FACETS	1	0.972	1			1	CLONAL	1	TRUE	NA	0.629193372803152	6		741	1484	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368196	31368196	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367766007	NA	P-0013283-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1368	247	716	2	ENST00000328111.2:c.67G>A	p.Val23Ile	p.V23I	ENST00000328111	NM_006892.3	23	Gtc/Atc	2/23	0.629193372803152	6	FACETS	1	0.976	1			1	CLONAL	1	TRUE	NA	0.629193372803152	6		718	1615	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411567	63411567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013283-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	260	525	1	ENST00000330258.3:c.1600G>A	p.Glu534Lys	p.E534K	ENST00000330258	NM_152424.3	534	Gag/Aag	2/2	0.568473633946357	2	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.629193372803152	2		526	735	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0013284-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	235	503	0				ENST00000310581	NM_198253.2	-/1132			0.358337338717532	5	FACETS	0.958	0.903	1	1	0.991	1	CLONAL	4	TRUE	2	0.358337338717532	5		503	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0013284-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	960	646	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.358337338717532	5	FACETS	1	0.997	1	1	0.998	1	CLONAL	6	TRUE	0	0.358337338717532	5		646	1274	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374293	138374293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013284-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	552	707	0	ENST00000289153.2:c.3151G>A	p.Glu1051Lys	p.E1051K	ENST00000289153	NM_006219.2	1051	Gaa/Aaa	22/22	0.358337338717532	4	FACETS	0.884	0.851	0.917	1	0.995	1	CLONAL	4	TRUE	1	0.358337338717532	4		707	1184	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717735	89717739	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGT	AAAGT	-	rs606231169	NA	P-0013284-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	295	305	0	ENST00000371953.3:c.761_765del	p.Lys254ArgfsTer42	p.K254Rfs*42	ENST00000371953	NM_000314.4	254	AAAGTa/a	7/9	0.358337338717532	2	FACETS	1	0.969	1	1	0.995	1	CLONAL	3	TRUE	0	0.358337338717532	2		305	537	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352655	118352655	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013284-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	214	583	0	ENST00000534358.1:c.3860C>G	p.Thr1287Ser	p.T1287S	ENST00000534358	NM_005933.3	1287	aCc/aGc	7/36	1	2	FACETS	0.856	0.798	0.914	1	0.993	1	CLONAL	2	TRUE	1	0.358337338717532	2		583	698	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919215	48919215	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0013284-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	180	264	0	ENST00000267163.4:c.381-1G>C		p.X127_splice	ENST00000267163	NM_000321.2	127			0.223556494552629	1	FACETS	0.851	0.801	0.901	1	0.995	1	CLONAL	3	TRUE	0	0.358337338717532	1		264	323	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012389	29012389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161996687	NA	P-0013302-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	393	582	2	ENST00000282397.4:c.482C>T	p.Thr161Met	p.T161M	ENST00000282397	NM_002019.4	161	aCg/aTg	4/30	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.741687380450336	2		584	888	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665752	29665755	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1555535032	NA	P-0013308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	96	546	0	ENST00000356175.3:c.6789_6792del	p.Tyr2264ThrfsTer5	p.Y2264Tfs*5	ENST00000356175	NM_000267.3	2263	ACTTac/ac	45/57	1	2	FACETS	0.909	0.814	1	0.909	0.814	1	CLONAL	1	FALSE	1	0.47461139222125	2		546	445	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548887	29548887	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	49	349	0	ENST00000356175.3:c.1661A>C	p.Gln554Pro	p.Q554P	ENST00000356175	NM_000267.3	554	cAg/cCg	15/57	1	2	FACETS	0.609	0.518	0.708	0.609	0.518	0.708	SUBCLONAL	1	FALSE	1	0.47461139222125	2		349	339	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175528	108175528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs376603775	NA	P-0013340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	93	513	0	ENST00000278616.4:c.5623C>T	p.Arg1875Ter	p.R1875*	ENST00000278616	NM_000051.3	1875	Cga/Tga	37/63	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	FALSE	1	0.227623778676196	2		513	766	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201096	108201096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774281788	NA	P-0013340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	44	427	1	ENST00000278616.4:c.7463G>A	p.Cys2488Tyr	p.C2488Y	ENST00000278616	NM_000051.3	2488	tGt/tAt	50/63	1	2	FACETS	0.799	0.67	0.941	0.799	0.67	0.941	CLONAL	1	FALSE	1	0.227623778676196	2		428	484	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495684	72495684	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	38	465	0	ENST00000477973.2:c.388T>C	p.Cys130Arg	p.C130R	ENST00000477973	NM_012234.5	130	Tgc/Cgc	1/4	1	2	FACETS	0.57	0.47	0.682	0.57	0.47	0.682	SUBCLONAL	1	FALSE	1	0.227623778676196	2		465	586	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741349	17741349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013340-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	79	397	0	ENST00000250003.3:c.20C>T	p.Pro7Leu	p.P7L	ENST00000250003	NM_002478.4	7	cCg/cTg	1/3	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.227623778676196	2		397	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578537	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs879254214	NA	P-0013344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	232	501	1	ENST00000269305.4:c.393_395del	p.Asn131del	p.N131del	ENST00000269305	NM_001126112.2	131	aaCAAg/aag	5/11	0.630354611093653	1	FACETS	0.894	0.841	0.948	0.894	0.841	0.948	CLONAL	1	TRUE	0	0.630354611093653	1		502	564	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589582	67589582	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	210	350	0	ENST00000274335.5:c.1345T>A	p.Leu449Ile	p.L449I	ENST00000274335		449	Tta/Ata	10/15	0.613975689554761	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.630354611093653	1		350	439	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964332	55964332	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	350	768	0	ENST00000263923.4:c.2481G>A	p.Trp827Ter	p.W827*	ENST00000263923	NM_002253.2	827	tgG/tgA	17/30	1	2	FACETS	0.967	0.917	1	0.967	0.917	1	CLONAL	1	TRUE	1	0.630354611093653	2		768	1148	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056562	26056562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377657422	NA	P-0013344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	157	229	0	ENST00000343677.2:c.95C>T	p.Pro32Leu	p.P32L	ENST00000343677	NM_005319.3	32	cCt/cTt	1/1	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.630354611093653	2		229	460	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306653	41306653	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013344-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1615	271	652	0	ENST00000373198.4:c.1006G>C	p.Glu336Gln	p.E336Q	ENST00000373198	NM_133170.3	336	Gag/Cag	7/32	0.630354611093653	7	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.630354611093653	7		652	1886	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0013354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	601	469	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.647243105717594	3	FACETS	0.956	0.93	0.981	0.956	0.93	0.981	CLONAL	3	TRUE	0	0.647243105717594	3		469	857	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479795	67479795	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs757106110	NA	P-0013354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	781	672	1	ENST00000327367.4:c.1102C>T	p.Arg368Ter	p.R368*	ENST00000327367	NM_005902.3	368	Cga/Tga	8/9	0.630326208844277	3	FACETS	0.9	0.877	0.922	0.9	0.877	0.922	CLONAL	3	TRUE	0	0.647243105717594	3		673	1183	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198269831	198269831	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	276	708	0	ENST00000335508.6:c.1508A>G	p.Lys503Arg	p.K503R	ENST00000335508	NM_012433.2	503	aAa/aGa	11/25	0.339407790153646	4	FACETS	1	0.991	1	0.65	0.611	0.691	INDETERMINATE	1	TRUE	2	0.647243105717594	4		708	1080	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77034406	77034406	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0013354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	121	411	2	ENST00000356341.3:c.1552-1G>C		p.X518_splice	ENST00000356341	NM_002576.4	518			0.503929333583271	4	FACETS	0.943	0.854	1	0.472	0.427	0.519	CLONAL	1	TRUE	2	0.647243105717594	4		413	653	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866090	37866090	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	61	700	0	ENST00000269571.5:c.599A>G	p.Lys200Arg	p.K200R	ENST00000269571		200	aAg/aGg	5/27	0.647243105717594	3	FACETS	0.227	0.195	0.262	0.114	0.097	0.131	SUBCLONAL	1	TRUE	1	0.647243105717594	3		700	1099	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0013361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	1086	422	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.217655440492291	9	FACETS	0.994	0.971	1			1	CLONAL	10	TRUE	NA	0.217655440492291	9		422	1769	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0013361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	26	234	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.635	0.503	0.787	0.635	0.503	0.787	SUBCLONAL	1	TRUE	1	0.217655440492291	2		234	376	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245258	46245258	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	91	579	0	ENST00000334344.6:c.3352C>A	p.Gln1118Lys	p.Q1118K	ENST00000334344	NM_152641.2	1118	Cag/Aag	15/21	0.207902067896886	3	FACETS	1	0.947	1	0.558	0.495	0.626	CLONAL	1	TRUE	1	0.217655440492291	3		579	831	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472478	88472478	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	94	858	1	ENST00000360948.2:c.2077G>T	p.Val693Leu	p.V693L	ENST00000360948	NM_001012338.2	693	Gtg/Ttg	16/19	1	2	FACETS	0.859	0.762	0.962	0.859	0.762	0.962	CLONAL	1	TRUE	1	0.217655440492291	2		859	1006	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727505	88727505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	77	710	1	ENST00000360948.2:c.274C>T	p.His92Tyr	p.H92Y	ENST00000360948	NM_001012338.2	92	Cac/Tac	3/19	1	2	FACETS	0.867	0.76	0.983	0.867	0.76	0.983	CLONAL	1	TRUE	1	0.217655440492291	2		711	816	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442714	99442714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	112	665	0	ENST00000268035.6:c.1111G>A	p.Ala371Thr	p.A371T	ENST00000268035	NM_000875.3	371	Gct/Act	5/21	1	2	FACETS	0.996	0.894	1	0.996	0.894	1	CLONAL	1	TRUE	1	0.217655440492291	2		665	1033	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922929	44922930	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0013361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	40	506	0	ENST00000377967.4:c.1793_1794del	p.Ile598AsnfsTer6	p.I598Nfs*6	ENST00000377967	NM_021140.2	597	cAT/c	16/29	1	1	FACETS	0.475	0.393	0.566	0.475	0.393	0.566	SUBCLONAL	1	TRUE	0	0.217655440492291	1		506	690	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0013382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	364	503	0				ENST00000310581	NM_198253.2	-/1132			0.325856050167215	3	FACETS	0.878	0.841	0.915	0.878	0.841	0.915	INDETERMINATE	2	TRUE	1	0.909905084776302	3		503	663	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0013382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	421	367	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	TRUE	1	0.909905084776302	2		367	920	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562750	21562750	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1157842597	NA	P-0013382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	183	290	3	ENST00000382592.4:c.1169C>T	p.Pro390Leu	p.P390L	ENST00000382592	NM_014572.2	390	cCg/cTg	4/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.909905084776302	2		293	361	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865795	56865795	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	817	1062	2	ENST00000308159.5:c.1127G>T	p.Arg376Leu	p.R376L	ENST00000308159	NM_014669.4	376	cGt/cTt	11/22	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.909905084776302	2		1064	1739	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041372	47041372	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0013382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	762	546	0	ENST00000377604.3:c.1716C>G	p.Tyr572Ter	p.Y572*	ENST00000377604	NM_001204468.1	572	taC/taG	16/24	1	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.909905084776302	1		546	830	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005513	42005517	+	frameshift_variant	Frame_Shift_Del	DEL	GAAAA	GAAAA	-	novel	NA	P-0013382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	710	1107	0	ENST00000219905.7:c.3255_3259del	p.Arg1085SerfsTer5	p.R1085Sfs*5	ENST00000219905	NM_001164273.1	1083	ttGAAAAga/ttga	9/24	1	2	FACETS	0.91	0.879	0.941	0.91	0.879	0.941	CLONAL	1	TRUE	1	0.909905084776302	2		1107	1715	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0013388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	106	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.818	0.734	0.906	1	0.985	1	CLONAL	2	FALSE	1	0.19404881852113	2		249	668	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1325	31	661	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.19404881852113	5	FACETS	0.304	0.244	0.373			1	SUBCLONAL	1	FALSE	NA	0.19404881852113	5		661	1356	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003303	42003303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	212	1045	0	ENST00000219905.7:c.2840C>T	p.Ser947Leu	p.S947L	ENST00000219905	NM_001164273.1	947	tCa/tTa	8/24	1	2	FACETS	0.877	0.813	0.943	1	0.993	1	CLONAL	2	FALSE	1	0.19404881852113	2		1045	1246	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436093	110436094	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0013388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	149	582	0	ENST00000375856.3:c.2307_2308del	p.Ser770ProfsTer103	p.S770Pfs*103	ENST00000375856	NM_003749.2	769	gtGTcc/gtcc	1/2	0.186612123811241	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	FALSE	1	0.19404881852113	3		582	793	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	155	661	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.387644508035554	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.387644508035554	1		661	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578206	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs886039484	NA	P-0013391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	260	906	0	ENST00000269305.4:c.643A>G	p.Ser215Gly	p.S215G	ENST00000269305	NM_001126112.2	215	Agt/Ggt	6/11	0.387644508035554	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.387644508035554	1		906	974	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900288	101900288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111854391	NA	P-0013391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	124	814	1	ENST00000374994.4:c.722C>T	p.Ser241Leu	p.S241L	ENST00000374994	NM_004612.2	241	tCg/tTg	4/9	1	2	FACETS	0.542	0.489	0.598	0.542	0.489	0.598	SUBCLONAL	1	TRUE	1	0.387644508035554	2		815	1180	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591846	48591846	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013391-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	179	769	3	ENST00000342988.3:c.1009G>T	p.Glu337Ter	p.E337*	ENST00000342988	NM_005359.5	337	Gag/Tag	9/12	0.387644508035554	1	FACETS	0.982	0.908	1	0.982	0.908	1	CLONAL	1	TRUE	0	0.387644508035554	1		772	758	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0013397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	123	550	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.191635981465505	3	FACETS	0.903	0.817	0.994	0.903	0.817	0.994	CLONAL	2	FALSE	1	0.191635981465505	3		550	779	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021728	71021728	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1559602356	NA	P-0013397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	116	653	0	ENST00000318789.4:c.1630C>T	p.Arg544Ter	p.R544*	ENST00000318789	NM_032682.5	544	Cga/Tga	18/21	0.148448853988195	3	FACETS	1	0.948	1	0.544	0.488	0.602	CLONAL	1	FALSE	1	0.191635981465505	3		653	1220	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032466	12032466	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	105	355	0	ENST00000353533.5:c.902C>A	p.Ala301Asp	p.A301D	ENST00000353533	NM_003010.3	301	gCc/gAc	9/11	NA	2	FACETS	0.943	0.847	1			1	INDETERMINATE	2	FALSE	NA	0.191635981465505	2		355	581	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746102	162746102	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs550210469	NA	P-0013397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	77	483	0	ENST00000367921.3:c.2225G>A	p.Arg742Gln	p.R742Q	ENST00000367921	NM_006182.2	742	cGg/cAg	16/18	0.148448853988195	3	FACETS	1	0.914	1	0.527	0.462	0.598	CLONAL	1	FALSE	1	0.191635981465505	3		483	835	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622165	162622165	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	49	441	0	ENST00000366898.1:c.532C>T	p.Gln178Ter	p.Q178*	ENST00000366898	NM_004562.2	178	Cag/Tag	4/12	1	2	FACETS	0.775	0.655	0.907	0.775	0.655	0.907	CLONAL	1	FALSE	1	0.191635981465505	2		441	660	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508595	106508595	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	42	345	0	ENST00000359195.3:c.589G>T	p.Ala197Ser	p.A197S	ENST00000359195	NM_002649.2	197	Gcc/Tcc	2/11	0.191635981465505	6	FACETS	1	0.903	1	0.28	0.233	0.332	CLONAL	1	FALSE	2	0.191635981465505	6		345	541	SUCCESS
MET	4233	MSKCC	GRCh37	7	116399545	116399545	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0013397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	102	626	0	ENST00000397752.3:c.2364+1G>C		p.X788_splice	ENST00000397752	NM_000245.2	788			0.191635981465505	6	FACETS	1	0.967	1	0.305	0.272	0.341	CLONAL	1	FALSE	2	0.191635981465505	6		626	1206	SUCCESS
RET	5979	MSKCC	GRCh37	10	43598017	43598017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1210452561	NA	P-0013397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	90	515	1	ENST00000355710.3:c.565C>T	p.Arg189Cys	p.R189C	ENST00000355710	NM_020975.4	189	Cgc/Tgc	3/20	0.147408520197463	3	FACETS	0.973	0.866	1	0.649	0.577	0.725	CLONAL	2	FALSE	0	0.191635981465505	3		516	529	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170373	119170373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	49	567	0	ENST00000264033.4:c.2603G>A	p.Gly868Glu	p.G868E	ENST00000264033	NM_005188.3	868	gGg/gAg	16/16	0.148448853988195	3	FACETS	0.707	0.597	0.828	0.353	0.298	0.414	SUBCLONAL	1	FALSE	1	0.191635981465505	3		567	793	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457330	67457330	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	130	652	2	ENST00000327367.4:c.304G>T	p.Glu102Ter	p.E102*	ENST00000327367	NM_005902.3	102	Gag/Tag	2/9	0.147408520197463	3	FACETS	0.974	0.884	1	0.65	0.589	0.713	CLONAL	2	FALSE	0	0.191635981465505	3		654	763	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032174	10032174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	49	587	0	ENST00000330684.3:c.649G>A	p.Val217Ile	p.V217I	ENST00000330684	NM_001134407.1	217	Gtc/Atc	3/13	0.191635981465505	2	FACETS	0.587	0.496	0.688	0.294	0.248	0.345	SUBCLONAL	1	FALSE	0	0.191635981465505	2		587	871	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937287	76937287	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	74	266	0	ENST00000373344.5:c.3461C>T	p.Ser1154Leu	p.S1154L	ENST00000373344	NM_000489.3	1154	tCa/tTa	9/35	1	1	FACETS	0.822	0.722	0.927	1	0.979	1	CLONAL	2	FALSE	0	0.191635981465505	1		266	425	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099945	27099954	+	frameshift_variant	Frame_Shift_Del	DEL	CACGACAGCA	CACGACAGCA	-	novel	NA	P-0013397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	60	615	0	ENST00000324856.7:c.3825_3834del	p.Arg1276IlefsTer10	p.R1276Ifs*10	ENST00000324856	NM_006015.4	1275	cCACGACAGCAc/cc	15/20	0.148448853988195	3	FACETS	0.911	0.784	1	0.456	0.392	0.526	CLONAL	1	FALSE	1	0.191635981465505	3		615	753	SUCCESS
APC	324	MSKCC	GRCh37	5	112175467	112175467	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	155	469	0	ENST00000257430.4:c.4176del	p.Asp1394IlefsTer21	p.D1394Ifs*21	ENST00000257430	NM_000038.5	1392	tcA/tc	16/16	0.139787462484629	3	FACETS	1	0.949	1			1	CLONAL	2	FALSE	NA	0.191635981465505	3		469	845	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0013408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	41	437	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	0.158	0.131	0.189	0.158	0.131	0.189	SUBCLONAL	1	TRUE	1	0.7	2		437	740	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0013408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	23	531	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.088	0.068	0.111	0.088	0.068	0.111	SUBCLONAL	1	TRUE	1	0.7	2		531	750	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0013408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	237	538	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.859	0.805	0.915	0.859	0.805	0.915	CLONAL	1	TRUE	1	0.7	2		538	788	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582117	189582117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013408-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	203	559	0	ENST00000264731.3:c.676C>T	p.Arg226Cys	p.R226C	ENST00000264731	NM_003722.4	226	Cgc/Tgc	5/14	1	2	FACETS	0.693	0.643	0.744	0.693	0.643	0.744	SUBCLONAL	1	TRUE	1	0.7	2		559	837	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0013409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	1231	462	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.898372556713875	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.898372556713875	2		463	1334	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163720	32163720	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253487294	NA	P-0013409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	250	252	0	ENST00000375023.3:c.5506G>A	p.Glu1836Lys	p.E1836K	ENST00000375023	NM_004557.3	1836	Gag/Aag	30/30	0.898372556713875	3	FACETS	1	0.973	1	0.531	0.499	0.565	CLONAL	1	TRUE	1	0.898372556713875	3		252	759	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056021	26056021	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs987043105	NA	P-0013409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	275	359	0	ENST00000343677.2:c.636G>C	p.Lys212Asn	p.K212N	ENST00000343677	NM_005319.3	212	aaG/aaC	1/1	0.898372556713875	3	FACETS	0.978	0.92	1			1	CLONAL	1	TRUE	NA	0.898372556713875	3		359	907	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740467	58740467	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs773389405	NA	P-0013409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	1090	1097	2	ENST00000305921.3:c.1372C>T	p.Arg458Ter	p.R458*	ENST00000305921	NM_003620.3	458	Cga/Tga	6/6	0.456552159599941	1	FACETS	0.748	0.731	0.765	0.748	0.731	0.765	INDETERMINATE	1	TRUE	0	0.898372556713875	1		1099	1786	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81954866	81954866	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	977	1175	1	ENST00000359376.3:c.2299C>T	p.Pro767Ser	p.P767S	ENST00000359376	NM_002661.3	767	Ccg/Tcg	21/33	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.898372556713875	2		1176	1902	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044404	128044404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	1229	798	1	ENST00000285398.2:c.1217C>T	p.Ala406Val	p.A406V	ENST00000285398	NM_000122.1	406	gCc/gTc	8/15	NA	2	FACETS	0.996	0.984	1			1	INDETERMINATE	2	TRUE	NA	0.898372556713875	2		799	1374	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259322	89259322	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866821420	NA	P-0013409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	584	738	0	ENST00000336596.2:c.466G>A	p.Asp156Asn	p.D156N	ENST00000336596	NM_005233.5	156	Gat/Aat	3/17	0.898372556713875	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.898372556713875	1		738	694	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99812397	99812397	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	1153	967	0	ENST00000280892.6:c.272A>T	p.Asp91Val	p.D91V	ENST00000280892	NM_001130678.1	91	gAc/gTc	3/7	0.841486873235304	2	FACETS	0.966	0.953	0.978	0.966	0.953	0.978	CLONAL	2	TRUE	0	0.898372556713875	2		967	1329	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117717356	117717356	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	964	616	0	ENST00000368508.3:c.851C>A	p.Ser284Ter	p.S284*	ENST00000368508	NM_002944.2	284	tCa/tAa	8/43	0.898372556713875	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.898372556713875	2		616	1068	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066731	77066731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	310	694	0	ENST00000356341.3:c.754G>A	p.Glu252Lys	p.E252K	ENST00000356341	NM_002576.4	252	Gag/Aag	7/15	0.456552159599941	1	FACETS	0.339	0.32	0.359	0.339	0.32	0.359	INDETERMINATE	1	TRUE	0	0.898372556713875	1		694	1120	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378655	25378655	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	513	637	0	ENST00000311936.3:c.343G>A	p.Gly115Arg	p.G115R	ENST00000311936	NM_004985.3	115	Gga/Aga	4/5	0.444329282974412	1	FACETS	0.758	0.733	0.783	0.758	0.733	0.783	INDETERMINATE	1	TRUE	0	0.898372556713875	1		637	830	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244494	46244494	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0013409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	561	684	0	ENST00000334344.6:c.2588C>G	p.Ser863Ter	p.S863*	ENST00000334344	NM_152641.2	863	tCa/tGa	15/21	0.444329282974412	1	FACETS	0.684	0.661	0.707	0.684	0.661	0.707	INDETERMINATE	1	TRUE	0	0.898372556713875	1		684	1006	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487292	56487292	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	513	404	0	ENST00000267101.3:c.1438G>A	p.Glu480Lys	p.E480K	ENST00000267101	NM_001982.3	480	Gag/Aag	12/28	0.444329282974412	1	FACETS	0.77	0.745	0.795	0.77	0.745	0.795	INDETERMINATE	1	TRUE	0	0.898372556713875	1		404	817	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222704	69222704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	299	715	2	ENST00000462284.1:c.677C>T	p.Ser226Leu	p.S226L	ENST00000462284	NM_002392.5	226	tCg/tTg	8/11	0.444329282974412	1	FACETS	0.357	0.336	0.378	0.357	0.336	0.378	INDETERMINATE	1	TRUE	0	0.898372556713875	1		717	1027	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68934902	68934902	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	635	789	1	ENST00000487270.1:c.971A>G	p.Lys324Arg	p.K324R	ENST00000487270	NM_133509.3	324	aAg/aGg	10/11	1	2	FACETS	0.968	0.934	1	0.968	0.934	1	CLONAL	1	TRUE	1	0.898372556713875	2		790	1460	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570086	95570086	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	321	778	0	ENST00000393063.1:c.3647C>A	p.Ser1216Ter	p.S1216*	ENST00000393063	NM_030621.3	1216	tCa/tAa	22/28	1	2	FACETS	0.48	0.452	0.509	0.48	0.452	0.509	SUBCLONAL	1	TRUE	1	0.898372556713875	2		778	1489	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856066	68856066	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	814	922	0	ENST00000261769.5:c.1874C>T	p.Pro625Leu	p.P625L	ENST00000261769	NM_004360.3	625	cCc/cTc	12/16	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	1	TRUE	NA	0.898372556713875	2		922	1580	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822673	72822673	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	1185	1307	1	ENST00000268489.5:c.9502G>A	p.Gly3168Arg	p.G3168R	ENST00000268489	NM_006885.3	3168	Gga/Aga	10/10	NA	2	FACETS	1	0.998	1			1	INDETERMINATE	1	TRUE	NA	0.898372556713875	2		1308	2084	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81902830	81902830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766422892	NA	P-0013409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	661	1091	0	ENST00000359376.3:c.491G>A	p.Arg164Gln	p.R164Q	ENST00000359376	NM_002661.3	164	cGa/cAa	6/33	1	2	FACETS	0.861	0.829	0.892	0.861	0.829	0.892	CLONAL	1	TRUE	1	0.898372556713875	2		1091	1710	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347666	89347666	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1311	792	1131	2	ENST00000301030.4:c.5284G>C	p.Asp1762His	p.D1762H	ENST00000301030	NM_001256183.1	1762	Gac/Cac	9/13	1	2	FACETS	0.838	0.81	0.867	0.838	0.81	0.867	CLONAL	1	TRUE	1	0.898372556713875	2		1133	2103	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16001710	16001710	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	521	709	0	ENST00000268712.3:c.2791C>T	p.Gln931Ter	p.Q931*	ENST00000268712	NM_006311.3	931	Cag/Tag	21/46	NA	2	FACETS	0.981	0.943	1			1	INDETERMINATE	1	TRUE	NA	0.898372556713875	2		709	1182	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271831	15271831	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779902629	NA	P-0013409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	371	381	0	ENST00000263388.2:c.6608C>T	p.Ser2203Phe	p.S2203F	ENST00000263388	NM_000435.2	2203	tCc/tTc	33/33	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.898372556713875	2		381	773	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937065	48937065	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	334	495	0	ENST00000267163.4:c.833del	p.Cys278LeufsTer8	p.C278Lfs*8	ENST00000267163	NM_000321.2	278	tGt/tt	8/27	0.898372556713875	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.898372556713875	1		495	385	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920348	50920348	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1214	1019	1174	3	ENST00000440232.2:c.3114del	p.Lys1039ArgfsTer6	p.K1039Rfs*6	ENST00000440232	NM_002691.3	1038	caG/ca	25/27	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.898372556713875	2		1177	2233	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274304	5274304	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	710	757	6	ENST00000357368.4:c.143del	p.Gly48ValfsTer17	p.G48Vfs*17	ENST00000357368	NM_002850.3	48	gGt/gt	3/38	1	2	FACETS	0.99	0.957	1	0.99	0.957	1	CLONAL	1	TRUE	1	0.898372556713875	2		763	1596	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405127	139405128	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0013409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	634	826	0	ENST00000277541.6:c.2717_2718delinsTT	p.Thr906Ile	p.T906I	ENST00000277541	NM_017617.3	906	aCC/aTT	17/34	1	2	FACETS	0.869	0.837	0.901	0.869	0.837	0.901	CLONAL	1	TRUE	1	0.898372556713875	2		826	1625	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94170373	94170374	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0013409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	293	489	0	ENST00000323929.3:c.1895_1896delinsTT	p.Ser632Phe	p.S632F	ENST00000323929	NM_005591.3	632	tCC/tTT	17/20	0.456552159599941	1	FACETS	0.649	0.617	0.68	0.649	0.617	0.68	INDETERMINATE	1	TRUE	0	0.898372556713875	1		489	554	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118370592	118370593	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0013409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	387	502	0	ENST00000534358.1:c.6122_6123delinsTT	p.Ser2041Phe	p.S2041F	ENST00000534358	NM_005933.3	2041	tCC/tTT	24/36	0.456552159599941	1	FACETS	0.676	0.648	0.704	0.676	0.648	0.704	INDETERMINATE	1	TRUE	0	0.898372556713875	1		502	702	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95577771	95577773	+	frameshift_variant	Frame_Shift_Del	DEL	CAT	CAT	TA	novel	NA	P-0013409-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	674	927	1	ENST00000393063.1:c.2137_2139delinsTA	p.Met713TyrfsTer45	p.M713Yfs*45	ENST00000393063	NM_030621.3	713	ATG/TA	15/28	1	2	FACETS	0.927	0.895	0.96	0.927	0.895	0.96	CLONAL	1	TRUE	1	0.898372556713875	2		928	1618	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0013428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	108	422	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.416	0.373	0.461	0.416	0.373	0.461	SUBCLONAL	1	TRUE	1	0.66	2		422	787	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041259	47041259	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	142	717	0	ENST00000377604.3:c.1687C>T	p.Gln563Ter	p.Q563*	ENST00000377604	NM_001204468.1	563	Cag/Tag	15/24	1	2	FACETS	0.373	0.339	0.409	0.373	0.339	0.409	SUBCLONAL	1	TRUE	1	0.66	2		717	1153	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579514	7579514	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	88	464	0	ENST00000269305.4:c.173del	p.Pro58GlnfsTer65	p.P58Qfs*65	ENST00000269305	NM_001126112.2	58	cCa/ca	4/11	1	2	FACETS	0.346	0.306	0.389	0.346	0.306	0.389	SUBCLONAL	1	TRUE	1	0.66	2		464	770	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112298	115112298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772493303	NA	P-0013428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	17	59	0	ENST00000257566.3:c.1442C>T	p.Pro481Leu	p.P481L	ENST00000257566	NM_016569.3	481	cCg/cTg	7/8	1	2	FACETS	0.599	0.456	0.762	0.599	0.456	0.762	SUBCLONAL	1	TRUE	1	0.66	2		59	86	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0013435-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	149	563	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.240010068524381	3	FACETS	1	0.986	1	0.725	0.662	0.791	CLONAL	1	TRUE	1	0.240010068524381	3		563	959	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578444	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0013435-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	156	509	0	ENST00000269305.4:c.486_487del	p.Tyr163GlnfsTer17	p.Y163Qfs*17	ENST00000269305	NM_001126112.2	162	atCTac/atac	5/11	0.188371730372591	2	FACETS	0.844	0.774	0.917	0.844	0.774	0.917	CLONAL	2	TRUE	0	0.240010068524381	2		509	770	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354688	70354688	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013435-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1389	118	806	0	ENST00000374080.3:c.4853A>C	p.Lys1618Thr	p.K1618T	ENST00000374080		1618	aAg/aCg	35/45	NA	2	FACETS	0.652	0.586	0.723			1	INDETERMINATE	1	TRUE	NA	0.240010068524381	2		806	1507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0013438-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	275	509	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.206298244680382	3	FACETS	1	0.984	1	1	0.994	1	CLONAL	4	TRUE	0	0.206298244680382	3		509	666	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786926	135786926	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs185815387	NA	P-0013438-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	157	443	1	ENST00000298552.3:c.943T>A	p.Ser315Thr	p.S315T	ENST00000298552	NM_001162426.1	315	Tct/Act	10/23	0.206298244680382	3	FACETS	0.919	0.845	0.995	1	0.987	1	CLONAL	3	TRUE	1	0.206298244680382	3		444	609	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489484	56489484	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013438-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	516	435	0	ENST00000267101.3:c.1949C>T	p.Ala650Val	p.A650V	ENST00000267101	NM_001982.3	650	gCa/gTa	17/28	0.206298244680382	10	FACETS	0.963	0.931	0.995			1	CLONAL	11	TRUE	NA	0.206298244680382	10		435	862	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687065	37687065	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013438-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1182	214	680	0	ENST00000447079.4:c.3969G>C	p.Leu1323Phe	p.L1323F	ENST00000447079	NM_015083.1	1323	ttG/ttC	14/14	0.206298244680382	9	FACETS	0.853	0.791	0.918			1	CLONAL	3	TRUE	NA	0.206298244680382	9		680	1396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519975	NA	P-0013489-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	197	629	0	ENST00000269305.4:c.403T>C	p.Cys135Arg	p.C135R	ENST00000269305	NM_001126112.2	135	Tgc/Cgc	5/11	0.777908970812597	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.777908970812597	1		629	290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579463	7579463	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	296	551	0	ENST00000269305.4:c.224del	p.Pro75LeufsTer48	p.P75Lfs*48	ENST00000269305	NM_001126112.2	75	cCt/ct	4/11	0.501039305044613	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.501039305044613	1		551	769	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508539	106508539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	87	198	0	ENST00000359195.3:c.533G>A	p.Arg178His	p.R178H	ENST00000359195	NM_002649.2	178	cGt/cAt	2/11	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.501039305044613	2		198	333	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341228	8341228	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs376711468	NA	P-0013500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	50	584	0	ENST00000356435.5:c.4988G>C	p.Ser1663Thr	p.S1663T	ENST00000356435		1663	aGt/aCt	30/35	0.501039305044613	1	FACETS	0.209	0.177	0.245	0.209	0.177	0.245	SUBCLONAL	1	TRUE	0	0.501039305044613	1		584	716	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991901	72991901	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	581	786	0	ENST00000268489.5:c.2144G>C	p.Arg715Pro	p.R715P	ENST00000268489	NM_006885.3	715	cGa/cCa	2/10	0.223595767852274	3	FACETS	0.886	0.851	0.922			1	INDETERMINATE	2	TRUE	NA	0.501039305044613	3		786	1636	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453132	140453132	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913365	NA	P-0013509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	211	439	0	ENST00000288602.6:c.1803A>T	p.Lys601Asn	p.K601N	ENST00000288602	NM_004333.4	601	aaA/aaT	15/18	0.285150405674851	3	FACETS	0.902	0.84	0.967	0.902	0.84	0.967	CLONAL	2	TRUE	1	0.331267398268435	3		439	823	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199716	11199716	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0013509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	248	467	1	ENST00000361445.4:c.4873-1G>T		p.X1625_splice	ENST00000361445	NM_004958.3	1625			0.277076677537154	5	FACETS	0.964	0.905	1	0.964	0.905	1	CLONAL	3	TRUE	2	0.331267398268435	5		468	775	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285951	38285951	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	77	544	1	ENST00000425967.3:c.460G>T	p.Ala154Ser	p.A154S	ENST00000425967	NM_001174067.1	154	Gct/Tct	5/19	0.233190074401394	4	FACETS	0.811	0.711	0.919	0.406	0.355	0.46	CLONAL	1	TRUE	2	0.331267398268435	4		545	763	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341965	8341965	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	37	325	0	ENST00000356435.5:c.4675C>G	p.Arg1559Gly	p.R1559G	ENST00000356435		1559	Cgg/Ggg	29/35	0.180412771184121	2	FACETS	0.437	0.36	0.524	0.219	0.18	0.262	INDETERMINATE	1	TRUE	0	0.331267398268435	2		325	511	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891211	101891211	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	137	531	0	ENST00000374994.4:c.172G>T	p.Val58Phe	p.V58F	ENST00000374994	NM_004612.2	58	Gtc/Ttc	2/9	0.180412771184121	2	FACETS	1	0.961	1	0.55	0.501	0.602	INDETERMINATE	1	TRUE	0	0.331267398268435	2		531	752	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0013509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	261	815	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.250824618455688	3	FACETS	1	0.988	1	0.796	0.749	0.844	CLONAL	2	TRUE	0	0.331267398268435	3		815	769	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509596	29509596	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1064794273	NA	P-0013509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	201	606	1	ENST00000356175.3:c.801G>A	p.Trp267Ter	p.W267*	ENST00000356175	NM_000267.3	267	tgG/tgA	8/57	0.250824618455688	3	FACETS	0.803	0.745	0.863	0.535	0.496	0.575	CLONAL	2	TRUE	0	0.331267398268435	3		607	881	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576006	29576006	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	77	443	0	ENST00000356175.3:c.3979G>T	p.Glu1327Ter	p.E1327*	ENST00000356175	NM_000267.3	1327	Gaa/Taa	30/57	0.250824618455688	3	FACETS	0.764	0.671	0.865	0.255	0.223	0.289	SUBCLONAL	1	TRUE	0	0.331267398268435	3		443	709	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2220125	2220125	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	106	690	1	ENST00000398665.3:c.2710G>T	p.Val904Leu	p.V904L	ENST00000398665	NM_032482.2	904	Gtg/Ttg	23/28	0.27852224576143	3	FACETS	0.818	0.732	0.909	0.409	0.366	0.455	CLONAL	1	TRUE	1	0.331267398268435	3		691	912	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117180	7117180	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	139	661	1	ENST00000302850.5:c.4036G>T	p.Gly1346Trp	p.G1346W	ENST00000302850	NM_000208.2	1346	Ggg/Tgg	22/22	0.27852224576143	3	FACETS	1	0.969	1	0.571	0.52	0.625	CLONAL	1	TRUE	1	0.331267398268435	3		662	856	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281491	15281492	+	missense_variant	Missense_Mutation	DNP	CC	CC	GA	novel	NA	P-0013509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	64	501	0	ENST00000263388.2:c.4881_4882delinsTC	p.Asp1628His	p.D1628H	ENST00000263388	NM_000435.2	1627	cgGGac/cgTCac	26/33	0.27852224576143	3	FACETS	0.716	0.62	0.821	0.358	0.31	0.411	SUBCLONAL	1	TRUE	1	0.331267398268435	3		501	629	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350248	15350248	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	101	751	0	ENST00000263377.2:c.3531G>T	p.Lys1177Asn	p.K1177N	ENST00000263377	NM_058243.2	1177	aaG/aaT	17/20	0.27852224576143	3	FACETS	0.729	0.65	0.813	0.365	0.325	0.407	SUBCLONAL	1	TRUE	1	0.331267398268435	3		751	975	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412182	63412182	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	132	1009	2	ENST00000330258.3:c.985G>T	p.Gly329Cys	p.G329C	ENST00000330258	NM_152424.3	329	Ggt/Tgt	2/2	1	2	FACETS	0.732	0.664	0.805	0.732	0.664	0.805	SUBCLONAL	1	TRUE	1	0.331267398268435	2		1011	1088	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020336	123020337	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0013509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	52	512	0	ENST00000355640.3:c.824_825delinsTT	p.Trp275Phe	p.W275F	ENST00000355640		275	tGG/tTT	2/7	0.241153765214436	3	FACETS	0.42	0.356	0.49	0.21	0.178	0.245	SUBCLONAL	1	TRUE	1	0.331267398268435	3		512	872	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577138	7577138	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587780075	NA	P-0013514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	164	670	0	ENST00000269305.4:c.800G>C	p.Arg267Pro	p.R267P	ENST00000269305	NM_001126112.2	267	cGg/cCg	8/11	0.330587608173143	3	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	1	0.330587608173143	3		670	560	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142950045	142950045	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	63	582	1	ENST00000262992.4:c.2665G>T	p.Val889Leu	p.V889L	ENST00000262992	NM_001101669.1	889	Gta/Tta	24/24	1	2	FACETS	0.647	0.56	0.742	0.647	0.56	0.742	SUBCLONAL	1	TRUE	1	0.330587608173143	2		583	589	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401699	401699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	163	493	0	ENST00000380956.4:c.1021G>A	p.Ala341Thr	p.A341T	ENST00000380956	NM_001195286.1	341	Gcg/Acg	7/9	0.136902215288513	5	FACETS	1	0.976	1			1	INDETERMINATE	3	TRUE	NA	0.330587608173143	5		493	439	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407578	407578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1237888981	NA	P-0013514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	237	612	0	ENST00000380956.4:c.1336C>T	p.His446Tyr	p.H446Y	ENST00000380956	NM_001195286.1	446	Cat/Tat	9/9	0.136902215288513	5	FACETS	0.89	0.833	0.949			1	INDETERMINATE	3	TRUE	NA	0.330587608173143	5		612	803	SUCCESS
EED	8726	MSKCC	GRCh37	11	85975212	85975212	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0013514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	36	367	0	ENST00000263360.6:c.635-2A>G		p.X212_splice	ENST00000263360	NM_003797.3	212			0.181122950142495	2	FACETS	0.434	0.356	0.521	0.217	0.178	0.261	INDETERMINATE	1	TRUE	0	0.330587608173143	2		367	502	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244319	41244319	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	88	656	0	ENST00000357654.3:c.3229G>T	p.Gly1077Trp	p.G1077W	ENST00000357654	NM_007294.3	1077	Ggg/Tgg	10/23	0.330587608173143	3	FACETS	0.936	0.829	1	0.468	0.414	0.525	CLONAL	1	TRUE	1	0.330587608173143	3		656	663	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143981	11143981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	53	430	0	ENST00000358026.2:c.3562G>A	p.Asp1188Asn	p.D1188N	ENST00000358026	NM_001128849.1	1188	Gac/Aac	26/36	0.330587608173143	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.330587608173143	1		430	196	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795806	42795806	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	84	585	0	ENST00000575354.2:c.2795C>T	p.Ser932Leu	p.S932L	ENST00000575354	NM_015125.3	932	tCa/tTa	11/20	0.317687479446034	4	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.330587608173143	4		585	504	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877327	40877327	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	21	312	0	ENST00000373198.4:c.2369G>T	p.Arg790Ile	p.R790I	ENST00000373198	NM_133170.3	790	aGa/aTa	15/32	0.330587608173143	0	FACETS	0.649	0.506	0.812			1	SUBCLONAL	1	TRUE	0	0.330587608173143	0		312	131	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657449	29657449	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	155	611	0	ENST00000356175.3:c.5683del	p.Ala1895GlnfsTer9	p.A1895Qfs*9	ENST00000356175	NM_000267.3	1894	ctG/ct	38/57	0.330587608173143	3	FACETS	1	0.965	1	0.551	0.504	0.601	CLONAL	1	TRUE	1	0.330587608173143	3		611	991	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0013526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	455	507	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	0.452688201093002	3	FACETS	0.876	0.839	0.913			1	CLONAL	2	TRUE	NA	0.677104397439391	3		507	1027	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438703	49438703	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	437	499	0	ENST00000301067.7:c.4787del	p.Gly1596AlafsTer8	p.G1596Afs*8	ENST00000301067	NM_003482.3	1596	gGc/gc	19/54	0.416688984493094	2	FACETS	0.865	0.833	0.897	0.865	0.833	0.897	CLONAL	2	TRUE	0	0.677104397439391	2		499	746	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579324	7579325	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0013526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	197	392	0	ENST00000269305.4:c.362_363del	p.Ser121CysfsTer27	p.S121Cfs*27	ENST00000269305	NM_001126112.2	121	tCT/t	4/11	0.677104397439391	1	FACETS	0.921	0.864	0.978	0.921	0.864	0.978	CLONAL	1	TRUE	0	0.677104397439391	1		392	418	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662313	227662313	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013526-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	266	376	0	ENST00000305123.5:c.1142G>C	p.Arg381Pro	p.R381P	ENST00000305123	NM_005544.2	381	cGc/cCc	1/2	0.482975884094299	1	FACETS	0.998	0.947	1	0.998	0.947	1	CLONAL	1	TRUE	0	0.677104397439391	1		376	521	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138615	37138615	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778032371	NA	P-0013530-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	164	517	0	ENST00000373509.5:c.149G>A	p.Gly50Asp	p.G50D	ENST00000373509	NM_002648.3	50	gGc/gAc	2/6	1	2	FACETS	0.863	0.794	0.936	0.863	0.794	0.936	CLONAL	1	TRUE	1	0.480868916303065	2		517	790	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097689	8097689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1485724723	NA	P-0013530-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	203	573	0	ENST00000346208.3:c.71C>T	p.Pro24Leu	p.P24L	ENST00000346208		24	cCg/cTg	2/6	1	2	FACETS	0.979	0.909	1	0.979	0.909	1	CLONAL	1	TRUE	1	0.480868916303065	2		573	862	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0013534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	81	533	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	1	2	FACETS	0.947	0.835	1	0.947	0.835	1	CLONAL	1	TRUE	1	0.26	2		533	658	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044942	47044943	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	TT	novel	NA	P-0013534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	65	544	2	ENST00000377604.3:c.2268_2269delinsTT	p.Trp756_Gln757delinsCysTer	p.W756_Q757delinsC*	ENST00000377604	NM_001204468.1	756	tgGCag/tgTTag	20/24	0.178763282709008	1	FACETS	0.865	0.751	0.988	0.865	0.751	0.988	CLONAL	1	TRUE	0	0.26	1		546	503	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830135	72830135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	134	856	1	ENST00000268489.5:c.6446G>A	p.Arg2149His	p.R2149H	ENST00000268489	NM_006885.3	2149	cGc/cAc	9/10	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.234009057688193	2		857	1049	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562150	21562150	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	605	1009	0	ENST00000382592.4:c.1769G>C	p.Arg590Thr	p.R590T	ENST00000382592	NM_014572.2	590	aGa/aCa	4/8	0.234009057688193	4	FACETS	0.909	0.874	0.945			1	CLONAL	4	TRUE	NA	0.234009057688193	4		1009	1754	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562399	21562399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	175	376	1	ENST00000382592.4:c.1520G>A	p.Gly507Glu	p.G507E	ENST00000382592	NM_014572.2	507	gGa/gAa	4/8	0.234009057688193	4	FACETS	0.896	0.831	0.962			1	CLONAL	4	TRUE	NA	0.234009057688193	4		377	515	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562406	21562406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	166	373	0	ENST00000382592.4:c.1513G>A	p.Glu505Lys	p.E505K	ENST00000382592	NM_014572.2	505	Gag/Aag	4/8	0.234009057688193	4	FACETS	0.886	0.82	0.953			1	CLONAL	4	TRUE	NA	0.234009057688193	4		373	494	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266107	41266107	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	35	376	0	ENST00000349496.5:c.104T>G	p.Ile35Ser	p.I35S	ENST00000349496	NM_001904.3	35	aTc/aGc	3/15	1	2	FACETS	0.875	0.718	1	0.875	0.718	1	CLONAL	1	TRUE	1	0.2	2		376	400	SUCCESS
APC	324	MSKCC	GRCh37	5	112178714	112178714	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1246562800	NA	P-0013549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	40	371	0	ENST00000257430.4:c.7423A>G	p.Thr2475Ala	p.T2475A	ENST00000257430	NM_000038.5	2475	Act/Gct	16/16	1	2	FACETS	1	0.834	1	1	0.834	1	CLONAL	1	TRUE	1	0.2	2		371	399	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372426	118372426	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	34	409	0	ENST00000534358.1:c.6359T>C	p.Ile2120Thr	p.I2120T	ENST00000534358	NM_005933.3	2120	aTa/aCa	26/36	1	2	FACETS	0.762	0.623	0.92	0.762	0.623	0.92	CLONAL	1	TRUE	1	0.2	2		409	446	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0013554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	58	469	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.951	0.817	1	0.951	0.817	1	CLONAL	1	TRUE	1	0.224335946743954	2		469	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0013554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	64	435	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	1	2	FACETS	0.872	0.755	1	0.872	0.755	1	CLONAL	1	TRUE	1	0.224335946743954	2		435	654	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857680	9857680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303700994	NA	P-0013554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	35	417	0	ENST00000330684.3:c.3721C>T	p.Arg1241Trp	p.R1241W	ENST00000330684	NM_001134407.1	1241	Cgg/Tgg	13/13	1	2	FACETS	0.597	0.488	0.719	0.597	0.488	0.719	SUBCLONAL	1	TRUE	1	0.224335946743954	2		417	523	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221273	1221273	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013554-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	81	660	0	ENST00000326873.7:c.797del	p.Asn266ThrfsTer21	p.N266Tfs*21	ENST00000326873	NM_000455.4	266	Aac/ac	6/10	1	2	FACETS	0.885	0.779	0.999	0.885	0.779	0.999	CLONAL	1	TRUE	1	0.224335946743954	2		660	816	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0013587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	41	503	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.876	0.738	1	0.876	0.738	1	CLONAL	1	TRUE	1	0.48	2		503	195	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0013587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	11	824	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	1	2	FACETS	0.098	0.067	0.137	0.098	0.067	0.137	SUBCLONAL	1	TRUE	1	0.48	2		824	469	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412252	139412252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057523819	NA	P-0013587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	77	741	2	ENST00000277541.6:c.1393G>A	p.Ala465Thr	p.A465T	ENST00000277541	NM_017617.3	465	Gcc/Acc	8/34	1	2	FACETS	0.867	0.766	0.974	0.867	0.766	0.974	CLONAL	1	TRUE	1	0.48	2		743	370	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148815	119149378	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAACATTTATAATTGCAGTTATTTATTCAACTAATAGTCTTTTAATTTTTTTTAATCAAAGGAACAATATGAATTATACTGTGAGATGGGCTCCACATTCCAACTATGTAAAATATGTGCTGAAAATGATAAGGATGTAAAGATTGAGCCCTGTGGACACCTCATGTGCACATCCTGTCTTACATCCTGGCAGGTACGGATCTAAACAGCGACTTTTTTCAGCTATGTAATAACCTTGGAAAATTCGGTATTATATAGCCTTTACTGATACAAGGGGTGGCCTGGCTTTTGGGGTTAGGTTTAAACTTTTACTTTTTTTTGATCTCTAGGAAATGTATTTTCTAGTAGATTAATATTTTAAGTATTTTCAGATGCATCTGTTACTATCTTTTGCTTCTTCTGCAGGAATCAGAAGGTCAGGGCTGTCCTTTCTGCCGATGTGAAATTAAAGGTACTGAACCCATCGTGGTAGATCCGTTTGATCCTAGAGGGAGTGGCAGCCTGTTGAGGCAAGGAGCAGAGGGAGCTCCCTCCCCAAATTATGATGATGATGATGATGAACGA	TAACATTTATAATTGCAGTTATTTATTCAACTAATAGTCTTTTAATTTTTTTTAATCAAAGGAACAATATGAATTATACTGTGAGATGGGCTCCACATTCCAACTATGTAAAATATGTGCTGAAAATGATAAGGATGTAAAGATTGAGCCCTGTGGACACCTCATGTGCACATCCTGTCTTACATCCTGGCAGGTACGGATCTAAACAGCGACTTTTTTCAGCTATGTAATAACCTTGGAAAATTCGGTATTATATAGCCTTTACTGATACAAGGGGTGGCCTGGCTTTTGGGGTTAGGTTTAAACTTTTACTTTTTTTTGATCTCTAGGAAATGTATTTTCTAGTAGATTAATATTTTAAGTATTTTCAGATGCATCTGTTACTATCTTTTGCTTCTTCTGCAGGAATCAGAAGGTCAGGGCTGTCCTTTCTGCCGATGTGAAATTAAAGGTACTGAACCCATCGTGGTAGATCCGTTTGATCCTAGAGGGAGTGGCAGCCTGTTGAGGCAAGGAGCAGAGGGAGCTCCCTCCCCAAATTATGATGATGATGATGATGAACGA	-	novel	NA	P-0013587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	28	107	1	ENST00000264033.4:c.1096-61_1386del		p.X366_splice	ENST00000264033	NM_005188.3	366		8-9/16	1	2	FACETS	0.911	0.762	1	1	0.959	1	CLONAL	2	TRUE	1	0.48	2		108	64	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336076	73336076	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	46	416	0	ENST00000377767.4:c.2327C>A	p.Thr776Asn	p.T776N	ENST00000377767	NM_014953.3	776	aCt/aAt	17/21	1	2	FACETS	0.637	0.539	0.743	0.637	0.539	0.743	SUBCLONAL	1	TRUE	1	0.48	2		416	301	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933757	39933757	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	93	802	0	ENST00000378444.4:c.842del	p.His281LeufsTer97	p.H281Lfs*97	ENST00000378444	NM_001123385.1	281	cAt/ct	4/15	0.158681400908069	0	FACETS	0.584	0.524	0.647			1	INDETERMINATE	1	TRUE	0	0.48	0		802	345	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776340	76776340	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0013587-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	110	932	1	ENST00000373344.5:c.7126A>T	p.Arg2376Ter	p.R2376*	ENST00000373344	NM_000489.3	2376	Aga/Tga	34/35	0.158681400908069	0	FACETS	0.524	0.473	0.577			1	INDETERMINATE	1	TRUE	0	0.48	0		933	455	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971000	21971000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	64	338	0	ENST00000304494.5:c.358G>T	p.Glu120Ter	p.E120*	ENST00000304494	NM_000077.4	120	Gag/Tag	2/3	0.14118123865531	0	FACETS	0.506	0.442	0.574			1	INDETERMINATE	1	TRUE	0	0.472672316137895	0		338	282	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015395	176015395	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013601-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	204	599	0	ENST00000367669.3:c.1343A>G	p.Tyr448Cys	p.Y448C	ENST00000367669	NM_022457.5	448	tAt/tGt	12/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.472672316137895	2		599	820	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0013621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	206	590	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	0.293800605839429	2	FACETS	0.665	0.618	0.713	0.332	0.309	0.357	INDETERMINATE	1	TRUE	0	0.804805053112442	2		590	770	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0013621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	394	492	1	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	0.804805053112442	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.804805053112442	1		493	463	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557642	95557642	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	520	676	2	ENST00000393063.1:c.5425G>T	p.Gly1809Trp	p.G1809W	ENST00000393063	NM_030621.3	1809	Ggg/Tgg	26/28	0.16999225303519	5	FACETS	0.957	0.923	0.992	0.957	0.923	0.992	INDETERMINATE	3	TRUE	2	0.804805053112442	5		678	993	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254568	46254586	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTGTTCTTTTTCACAGAAC	TTGTTCTTTTTCACAGAAC	-	novel	NA	P-0013621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	58	531	3	ENST00000334344.6:c.4774-16_4776del		p.X1592_splice	ENST00000334344	NM_152641.2	1592		16/21	1	2	FACETS	0.265	0.228	0.306	0.265	0.228	0.306	SUBCLONAL	1	TRUE	1	0.804805053112442	2		534	543	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858986	57858986	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149185944	NA	P-0013621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	356	878	4	ENST00000228682.2:c.482G>A	p.Arg161Gln	p.R161Q	ENST00000228682	NM_005269.2	161	cGg/cAg	5/12	1	2	FACETS	0.943	0.897	0.99	0.943	0.897	0.99	CLONAL	1	TRUE	1	0.804805053112442	2		882	938	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566252	95566252	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0013621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	268	467	0	ENST00000393063.1:c.4071T>A	p.Tyr1357Ter	p.Y1357*	ENST00000393063	NM_030621.3	1357	taT/taA	23/28	0.16999225303519	5	FACETS	1	0.96	1	0.682	0.642	0.721	INDETERMINATE	2	TRUE	2	0.804805053112442	5		467	719	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244078	41244078	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	384	682	2	ENST00000357654.3:c.3470G>T	p.Gly1157Val	p.G1157V	ENST00000357654	NM_007294.3	1157	gGt/gTt	10/23	0.27760926047694	5	FACETS	1	0.992	1	0.782	0.746	0.818	INDETERMINATE	2	TRUE	2	0.804805053112442	5		684	898	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78933943	78933943	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	555	741	2	ENST00000306801.3:c.3543C>G	p.Ile1181Met	p.I1181M	ENST00000306801	NM_020761.2	1181	atC/atG	30/34	0.27760926047694	5	FACETS	0.908	0.876	0.941	0.908	0.876	0.941	INDETERMINATE	3	TRUE	2	0.804805053112442	5		743	1117	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965631	25965631	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1213	74	671	0	ENST00000435504.4:c.3575C>A	p.Ser1192Tyr	p.S1192Y	ENST00000435504		1192	tCt/tAt	13/13	0.314296827504265	6	FACETS	0.373	0.325	0.425	0.062	0.054	0.071	INDETERMINATE	1	TRUE	0	0.804805053112442	6		671	1287	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971004	55971004	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	242	709	0	ENST00000263923.4:c.1793T>C	p.Leu598Ser	p.L598S	ENST00000263923	NM_002253.2	598	tTg/tCg	13/30	0.350702251078815	5	FACETS	1	0.962	1			1	INDETERMINATE	1	TRUE	NA	0.804805053112442	5		709	1269	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513265	149513265	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	332	594	4	ENST00000261799.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000261799	NM_002609.3	273	cGc/cTc	6/23	0.309793408236762	1	FACETS	0.681	0.648	0.714	0.681	0.648	0.714	INDETERMINATE	1	TRUE	0	0.804805053112442	1		598	724	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043437	180043437	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	85	611	0	ENST00000261937.6:c.3149T>G	p.Val1050Gly	p.V1050G	ENST00000261937	NM_182925.4	1050	gTg/gGg	23/30	0.309793408236762	1	FACETS	0.195	0.172	0.219	0.195	0.172	0.219	INDETERMINATE	1	TRUE	0	0.804805053112442	1		611	648	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502247	157502247	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	95	533	1	ENST00000346085.5:c.3280G>T	p.Gly1094Cys	p.G1094C	ENST00000346085	NM_020732.3	1094	Ggc/Tgc	12/20	0.804805053112442	1	FACETS	0.307	0.275	0.342	0.307	0.275	0.342	SUBCLONAL	1	TRUE	0	0.804805053112442	1		534	459	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012411	152012411	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	225	426	1	ENST00000262189.6:c.402C>G	p.Cys134Trp	p.C134W	ENST00000262189	NM_170606.2	134	tgC/tgG	4/59	0.190665410363362	2	FACETS	1	0.991	1	0.646	0.61	0.681	INDETERMINATE	1	TRUE	0	0.804805053112442	2		427	433	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0013624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	289	552	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.518595211227378	2		552	1048	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037511	12037511	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	123	311	0	ENST00000396373.4:c.1142G>A	p.Gly381Glu	p.G381E	ENST00000396373	NM_001987.4	381	gGa/gAa	6/8	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.518595211227378	NA		311	561	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648274	206648274	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	282	670	0	ENST00000367120.3:c.295G>C	p.Glu99Gln	p.E99Q	ENST00000367120	NM_014002.3	99	Gag/Cag	5/22	1	2	FACETS	0.987	0.928	1	0.987	0.928	1	CLONAL	1	TRUE	1	0.518595211227378	2		670	1102	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332609	70332609	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1176805515	NA	P-0013624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	222	490	0	ENST00000373644.4:c.514C>G	p.Leu172Val	p.L172V	ENST00000373644	NM_030625.2	172	Cta/Gta	2/12	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.518595211227378	2		490	839	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88679170	88679170	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	79	170	0	ENST00000372037.3:c.1110C>G	p.Ile370Met	p.I370M	ENST00000372037	NM_004329.2	370	atC/atG	10/13	1	2	FACETS	0.989	0.879	1	0.989	0.879	1	CLONAL	1	TRUE	1	0.518595211227378	2		170	308	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422915	49422915	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0013624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	181	490	0	ENST00000301067.7:c.14180C>G	p.Ser4727Ter	p.S4727*	ENST00000301067	NM_003482.3	4727	tCa/tGa	44/54	1	2	FACETS	0.9	0.831	0.97	0.9	0.831	0.97	CLONAL	1	TRUE	1	0.518595211227378	2		490	776	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122472	17122472	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	302	731	0	ENST00000285071.4:c.923A>G	p.Glu308Gly	p.E308G	ENST00000285071	NM_144997.5	308	gAg/gGg	9/14	1	2	FACETS	0.982	0.925	1	0.982	0.925	1	CLONAL	1	TRUE	1	0.518595211227378	2		731	1186	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096874	11096874	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555752859	NA	P-0013624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	268	570	1	ENST00000358026.2:c.365C>T	p.Ser122Leu	p.S122L	ENST00000358026	NM_001128849.1	122	tCg/tTg	4/36	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.518595211227378	2		571	948	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097249	11097249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	92	253	0	ENST00000358026.2:c.740C>T	p.Pro247Leu	p.P247L	ENST00000358026	NM_001128849.1	247	cCa/cTa	4/36	1	2	FACETS	0.739	0.659	0.823	0.739	0.659	0.823	SUBCLONAL	1	TRUE	1	0.518595211227378	2		253	480	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639685	47639685	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	175	372	0	ENST00000233146.2:c.778G>C	p.Glu260Gln	p.E260Q	ENST00000233146	NM_000251.2	260	Gaa/Caa	4/16	1	2	FACETS	0.988	0.913	1	0.988	0.913	1	CLONAL	1	TRUE	1	0.518595211227378	2		372	683	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163718	47163718	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	439	538	0	ENST00000409792.3:c.2408C>G	p.Ser803Cys	p.S803C	ENST00000409792	NM_014159.6	803	tCt/tGt	3/21	0.518595211227378	2	FACETS	0.959	0.92	0.997	0.959	0.92	0.997	CLONAL	2	TRUE	0	0.518595211227378	2		538	883	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541078	187541078	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	43	447	0	ENST00000441802.2:c.6662G>C	p.Gly2221Ala	p.G2221A	ENST00000441802	NM_005245.3	2221	gGa/gCa	10/27	1	2	FACETS	0.225	0.188	0.267	0.225	0.188	0.267	SUBCLONAL	1	TRUE	1	0.518595211227378	2		447	736	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818372	170818372	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763566520	NA	P-0013624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	53	299	1	ENST00000296930.5:c.202G>A	p.Glu68Lys	p.E68K	ENST00000296930	NM_002520.6	68	Gaa/Aaa	3/11	1	2	FACETS	0.452	0.386	0.524	0.452	0.386	0.524	SUBCLONAL	1	TRUE	1	0.518595211227378	2		300	452	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241626	55241626	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	205	465	0	ENST00000275493.2:c.2074C>G	p.Leu692Val	p.L692V	ENST00000275493	NM_005228.3	692	Ctt/Gtt	18/28	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.518595211227378	2		465	763	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241688	55241688	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	223	540	0	ENST00000275493.2:c.2136C>G	p.Phe712Leu	p.F712L	ENST00000275493	NM_005228.3	712	ttC/ttG	18/28	1	2	FACETS	0.932	0.868	0.997	0.932	0.868	0.997	CLONAL	1	TRUE	1	0.518595211227378	2		540	923	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013630-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	316	637	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.605325658033398	1	FACETS	0.99	0.941	1	0.99	0.941	1	CLONAL	1	TRUE	0	0.623908629283688	1		637	704	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125525214	125525214	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0013630-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	179	405	0	ENST00000428830.2:c.1430G>C	p.Ter477SerextTer24	p.*477Sext*24	ENST00000428830	NM_001114121.2	477	tGa/tCa	13/14	1	2	FACETS	0.905	0.838	0.974	0.905	0.838	0.974	CLONAL	1	TRUE	1	0.623908629283688	2		405	634	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876153	35876153	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013630-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	108	569	0	ENST00000303115.3:c.945A>T	p.Gln315His	p.Q315H	ENST00000303115	NM_002185.3	315	caA/caT	8/8	1	2	FACETS	0.451	0.404	0.5	0.451	0.404	0.5	SUBCLONAL	1	TRUE	1	0.623908629283688	2		569	768	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504315	8504315	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013630-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1182	64	621	0	ENST00000356435.5:c.1768C>A	p.Pro590Thr	p.P590T	ENST00000356435		590	Cct/Act	12/35	0.623908629283688	3	FACETS	0.216	0.186	0.249	0.108	0.093	0.125	SUBCLONAL	1	TRUE	1	0.623908629283688	3		621	1246	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857532	68857532	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	C	novel	NA	P-0013640-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	85	274	0	ENST00000261769.5:c.2164+3A>C		p.X722_splice	ENST00000261769	NM_004360.3	722			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		274	255	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0013647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	101	249	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	0.474930153898778	2		249	357	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0013647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	224	862	1	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.474930153898778	2		863	857	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106058	8106058	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	118	357	1	ENST00000346208.3:c.878T>A	p.Met293Lys	p.M293K	ENST00000346208		293	aTg/aAg	4/6	0.474930153898778	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.474930153898778	1		358	360	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974730	21974730	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	102	412	0	ENST00000304494.5:c.97G>T	p.Glu33Ter	p.E33*	ENST00000304494	NM_000077.4	33	Gag/Tag	1/3	0.474930153898778	1	FACETS	0.944	0.853	1	0.944	0.853	1	CLONAL	1	TRUE	0	0.474930153898778	1		412	347	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933743	49933743	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772397266	NA	P-0013647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	172	727	1	ENST00000296474.3:c.2534G>A	p.Arg845Gln	p.R845Q	ENST00000296474	NM_002447.2	845	cGa/cAa	10/20	1	2	FACETS	0.92	0.848	0.995	0.92	0.848	0.995	CLONAL	1	TRUE	1	0.474930153898778	2		728	787	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255845	16255845	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	108	349	0	ENST00000375759.3:c.3110G>A	p.Arg1037Lys	p.R1037K	ENST00000375759	NM_015001.2	1037	aGa/aAa	11/15	0.474930153898778	1	FACETS	0.988	0.896	1	0.988	0.896	1	CLONAL	1	TRUE	0	0.474930153898778	1		349	351	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112073	115112091	+	frameshift_variant	Frame_Shift_Del	DEL	AGGCCCGAGACACCGGTGG	AGGCCCGAGACACCGGTGG	-	novel	NA	P-0013647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	130	481	0	ENST00000257566.3:c.1649_1667del	p.Ser550TrpfsTer76	p.S550Wfs*76	ENST00000257566	NM_016569.3	550	tCCACCGGTGTCTCGGGCCTg/tg	7/8	1	2	FACETS	0.911	0.829	0.996	0.911	0.829	0.996	CLONAL	1	TRUE	1	0.474930153898778	2		481	601	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780598	56780598	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	167	606	0	ENST00000337432.4:c.613C>T	p.Leu205Phe	p.L205F	ENST00000337432	NM_058216.2	205	Ctt/Ttt	4/9	1	2	FACETS	0.919	0.846	0.995	0.919	0.846	0.995	CLONAL	1	TRUE	1	0.474930153898778	2		606	765	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780604	56780604	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	170	591	0	ENST00000337432.4:c.619C>G	p.His207Asp	p.H207D	ENST00000337432	NM_058216.2	207	Cat/Gat	4/9	1	2	FACETS	0.943	0.869	1	0.943	0.869	1	CLONAL	1	TRUE	1	0.474930153898778	2		591	759	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414665	56414665	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	95	628	0	ENST00000348428.3:c.2066C>A	p.Ser689Ter	p.S689*	ENST00000348428	NM_006785.3	689	tCa/tAa	17/17	0.287402957473996	1	FACETS	0.416	0.37	0.465	0.416	0.37	0.465	SUBCLONAL	1	TRUE	0	0.474930153898778	1		628	733	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383704	84383704	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	105	642	0	ENST00000321945.7:c.1148C>T	p.Ser383Phe	p.S383F	ENST00000321945	NM_139076.2	383	tCc/tTc	9/9	0.218507215129247	1	FACETS	0.448	0.401	0.497	0.448	0.401	0.497	INDETERMINATE	1	TRUE	0	0.474930153898778	1		642	753	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481417	140481417	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913348	NA	P-0013647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	57	556	0	ENST00000288602.6:c.1391G>C	p.Gly464Ala	p.G464A	ENST00000288602	NM_004333.4	464	gGa/gCa	11/18	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.474930153898778	NA		556	498	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872120	76872120	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	218	718	0	ENST00000373344.5:c.5527C>G	p.Gln1843Glu	p.Q1843E	ENST00000373344	NM_000489.3	1843	Cag/Gag	22/35	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.474930153898778	2		718	878	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013673-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	86	528	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.773	0.692	0.856	1	0.982	1	SUBCLONAL	2	TRUE	1	0.398865302482425	2		530	279	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717699	89717699	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554825210	NA	P-0013673-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	169	318	0	ENST00000371953.3:c.724G>T	p.Glu242Ter	p.E242*	ENST00000371953	NM_000314.4	242	Gag/Tag	7/9	0.398865302482425	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.398865302482425	1		318	613	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528441	29528441	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013673-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	140	583	1	ENST00000356175.3:c.1198C>T	p.Gln400Ter	p.Q400*	ENST00000356175	NM_000267.3	400	Cag/Tag	11/57	0.398865302482425	1	FACETS	0.877	0.801	0.956	0.877	0.801	0.956	CLONAL	1	TRUE	0	0.398865302482425	1		584	641	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158626928	158626928	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013673-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	475	856	0	ENST00000263640.3:c.742del	p.Glu248LysfsTer8	p.E248Kfs*8	ENST00000263640	NM_001105.4	248	Gaa/aa	7/11	0.398865302482425	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.398865302482425	3		856	1420	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139818370	139818370	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013673-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	163	813	1	ENST00000247668.2:c.1205G>A	p.Gly402Glu	p.G402E	ENST00000247668	NM_021138.3	402	gGg/gAg	10/11	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.398865302482425	2		814	810	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013677-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	45	389	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		389	767	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279962	18279962	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	156	587	0	ENST00000222254.8:c.2045C>G	p.Pro682Arg	p.P682R	ENST00000222254	NM_005027.3	682	cCc/cGc	16/16	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.39278088455076	2		587	770	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0013699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	265	462	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.624464221254936	1	FACETS	0.933	0.885	0.98	0.933	0.885	0.98	CLONAL	1	TRUE	0	0.714657953247797	1		463	511	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548948	29548948	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs1131691096	NA	P-0013699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	34	65	0	ENST00000356175.3:c.1721+1G>C		p.X574_splice	ENST00000356175	NM_000267.3	574			0.624464221254936	1	FACETS	0.687	0.58	0.798	0.687	0.58	0.798	SUBCLONAL	1	TRUE	0	0.714657953247797	1		65	89	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750883	128750883	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1264	224	97	0	ENST00000377970.2:c.420C>G	p.Ile140Met	p.I140M	ENST00000377970	NM_002467.4	140	atC/atG	2/3	0.706041146427926	5	FACETS	0.873	0.81	0.938	0.218	0.202	0.235	CLONAL	1	TRUE	1	0.714657953247797	5		97	1488	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412493	80412493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514698	NA	P-0013700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	374	716	1	ENST00000286548.4:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000286548	NM_002072.3	183	cGa/cAa	4/7	1	2	FACETS	0.923	0.878	0.969	0.923	0.878	0.969	CLONAL	1	TRUE	1	0.77	2		717	1052	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233391	69233391	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs200828111	NA	P-0013700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	251	532	0	ENST00000462284.1:c.1256A>G	p.Glu419Gly	p.E419G	ENST00000462284	NM_002392.5	419	gAg/gGg	11/11	0.149683359925271	3	FACETS	1	0.991	1	0.661	0.622	0.701	INDETERMINATE	1	TRUE	1	0.77	3		532	683	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182521	99182521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373911327	NA	P-0013700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	237	526	2	ENST00000074304.5:c.2324C>T	p.Pro775Leu	p.P775L	ENST00000074304	NM_001134224.1	775	cCg/cTg	22/26	1	2	FACETS	0.953	0.895	1	0.953	0.895	1	CLONAL	1	TRUE	1	0.77	2		528	646	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098501	11098501	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756474511	NA	P-0013700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	108	289	0	ENST00000358026.2:c.1019C>T	p.Ala340Val	p.A340V	ENST00000358026	NM_001128849.1	340	gCg/gTg	6/36	1	2	FACETS	0.879	0.799	0.962	0.879	0.799	0.962	CLONAL	1	TRUE	1	0.77	2		289	319	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070324	37070324	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63749795	NA	P-0013700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	307	702	0	ENST00000231790.2:c.1459C>T	p.Arg487Ter	p.R487*	ENST00000231790	NM_000249.3	487	Cga/Tga	13/19	1	2	FACETS	0.786	0.752	0.82	1	0.996	1	SUBCLONAL	2	TRUE	1	0.77	2		702	507	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902190	50902190	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761551015	NA	P-0013700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	322	1018	1	ENST00000440232.2:c.82G>A	p.Ala28Thr	p.A28T	ENST00000440232	NM_002691.3	28	Gca/Aca	2/27	1	2	FACETS	0.948	0.899	0.999	0.948	0.899	0.999	CLONAL	1	TRUE	1	0.77	2		1019	882	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941122	36941122	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532250805	NA	P-0013700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	366	932	0	ENST00000361632.4:c.217G>A	p.Gly73Ser	p.G73S	ENST00000361632		73	Ggc/Agc	3/16	1	2	FACETS	0.927	0.881	0.973	0.927	0.881	0.973	CLONAL	1	TRUE	1	0.77	2		932	1026	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246402	46246402	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1324779117	NA	P-0013700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	292	680	0	ENST00000334344.6:c.4496T>C	p.Leu1499Pro	p.L1499P	ENST00000334344	NM_152641.2	1499	cTa/cCa	15/21	0.149683359925271	3	FACETS	1	0.991	1	0.624	0.589	0.659	INDETERMINATE	1	TRUE	1	0.77	3		680	842	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830804	3830806	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0013700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	282	621	0	ENST00000262367.5:c.1750_1752del	p.Ser585del	p.S585del	ENST00000262367	NM_004380.2	584	TCT/-	8/31	1	2	FACETS	0.933	0.881	0.986	0.933	0.881	0.986	CLONAL	1	TRUE	1	0.77	2		621	785	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979562	7979562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763468558	NA	P-0013700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	248	734	2	ENST00000319144.4:c.1463G>A	p.Arg488His	p.R488H	ENST00000319144	NM_001139.2	488	cGt/cAt	11/15	1	2	FACETS	0.885	0.831	0.94	0.885	0.831	0.94	CLONAL	1	TRUE	1	0.77	2		736	728	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559835	29559835	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0013700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	304	611	0	ENST00000356175.3:c.3432T>A	p.Cys1144Ter	p.C1144*	ENST00000356175	NM_000267.3	1144	tgT/tgA	26/57	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.77	2		611	598	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661009	227661009	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	142	496	1	ENST00000305123.5:c.2446C>A	p.Leu816Met	p.L816M	ENST00000305123	NM_005544.2	816	Ctg/Atg	1/2	1	2	FACETS	0.764	0.701	0.829	0.764	0.701	0.829	SUBCLONAL	1	TRUE	1	0.77	2		497	483	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755663	39755663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	270	718	0	ENST00000288319.7:c.1102G>A	p.Ala368Thr	p.A368T	ENST00000288319	NM_182918.3	368	Gcc/Acc	10/10	1	2	FACETS	0.811	0.763	0.86	0.811	0.763	0.86	CLONAL	1	TRUE	1	0.77	2		718	865	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437432	52437432	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	256	654	1	ENST00000460680.1:c.1729G>A	p.Glu577Lys	p.E577K	ENST00000460680	NM_004656.3	577	Gag/Aag	13/17	1	2	FACETS	0.771	0.734	0.808	1	0.995	1	SUBCLONAL	2	TRUE	1	0.77	2		655	431	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747933	41747933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	190	441	0	ENST00000226382.2:c.836C>T	p.Pro279Leu	p.P279L	ENST00000226382	NM_003924.3	279	cCc/cTc	3/3	1	2	FACETS	0.997	0.93	1	0.997	0.93	1	CLONAL	1	TRUE	1	0.77	2		441	495	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525525	137525525	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146687518	NA	P-0013700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	298	705	0	ENST00000367739.4:c.490G>A	p.Glu164Lys	p.E164K	ENST00000367739	NM_000416.2	164	Gaa/Aaa	4/7	1	2	FACETS	0.824	0.778	0.872	0.824	0.778	0.872	CLONAL	1	TRUE	1	0.77	2		705	939	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522307	157522307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013700-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	299	667	0	ENST00000346085.5:c.4579G>A	p.Ala1527Thr	p.A1527T	ENST00000346085	NM_020732.3	1527	Gcc/Acc	18/20	1	2	FACETS	0.984	0.931	1	0.984	0.931	1	CLONAL	1	TRUE	1	0.77	2		667	789	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013702-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	136	389	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.3	2		389	879	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087533	27087533	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013702-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	125	639	0	ENST00000324856.7:c.2109del	p.Ala704ProfsTer38	p.A704Pfs*38	ENST00000324856	NM_006015.4	703	Ccc/cc	5/20	1	2	FACETS	0.974	0.881	1	0.974	0.881	1	CLONAL	1	TRUE	1	0.3	2		639	856	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226564978	226564978	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs377397890	NA	P-0013702-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	100	445	0	ENST00000366794.5:c.1772G>T	p.Arg591Leu	p.R591L	ENST00000366794	NM_001618.3	591	cGt/cTt	13/23	0.3	3	FACETS	0.831	0.741	0.926	0.415	0.37	0.463	CLONAL	1	TRUE	1	0.3	3		445	923	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406221	406221	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013702-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	92	480	0	ENST00000399788.2:c.4220A>G	p.Lys1407Arg	p.K1407R	ENST00000399788	NM_001042603.1	1407	aAg/aGg	25/28	1	2	FACETS	0.81	0.72	0.907	0.81	0.72	0.907	CLONAL	1	TRUE	1	0.3	2		480	757	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857103	9857103	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013702-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	124	527	0	ENST00000330684.3:c.4298C>A	p.Ala1433Glu	p.A1433E	ENST00000330684	NM_001134407.1	1433	gCa/gAa	13/13	1	2	FACETS	0.924	0.835	1	0.924	0.835	1	CLONAL	1	TRUE	1	0.3	2		527	895	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528572	89528572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762601076	NA	P-0013702-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	60	335	0	ENST00000336596.2:c.2872G>A	p.Val958Met	p.V958M	ENST00000336596	NM_005233.5	958	Gtg/Atg	17/17	1	2	FACETS	0.608	0.523	0.7	0.608	0.523	0.7	SUBCLONAL	1	TRUE	1	0.3	2		335	658	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180872	106180872	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013702-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	74	494	0	ENST00000380013.4:c.3900T>G	p.Phe1300Leu	p.F1300L	ENST00000380013	NM_001127208.2	1300	ttT/ttG	7/11	1	2	FACETS	0.533	0.465	0.606	0.533	0.465	0.606	SUBCLONAL	1	TRUE	1	0.3	2		494	926	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168530	56168530	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013702-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	74	299	0	ENST00000399503.3:c.1486A>G	p.Arg496Gly	p.R496G	ENST00000399503	NM_005921.1	496	Aga/Gga	8/20	1	2	FACETS	0.809	0.708	0.917	0.809	0.708	0.917	CLONAL	1	TRUE	1	0.3	2		299	610	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177768	56177768	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013702-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	91	399	0	ENST00000399503.3:c.2741G>T	p.Gly914Val	p.G914V	ENST00000399503	NM_005921.1	914	gGa/gTa	14/20	1	2	FACETS	0.802	0.712	0.899	0.802	0.712	0.899	CLONAL	1	TRUE	1	0.3	2		399	756	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692935	89692935	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0013730-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	134	399	0	ENST00000371953.3:c.419T>A	p.Leu140Ter	p.L140*	ENST00000371953	NM_000314.4	140	tTa/tAa	5/9	0.429815479660514	3	FACETS	0.946	0.881	1	1	0.989	1	CLONAL	3	TRUE	1	0.490150214633262	3		399	240	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0013755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	456	907	3	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.489501334116014	2	FACETS	0.898	0.862	0.934	0.898	0.862	0.934	CLONAL	2	TRUE	0	0.533920631391222	2		910	951	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515161	106515161	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	281	578	0	ENST00000359195.3:c.2304A>T	p.Lys768Asn	p.K768N	ENST00000359195	NM_002649.2	768	aaA/aaT	5/11	0.390546543318788	3	FACETS	1	0.958	1	0.514	0.482	0.547	CLONAL	1	TRUE	1	0.533920631391222	3		578	1298	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433066	49433066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772742966	NA	P-0013755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	213	664	0	ENST00000301067.7:c.8305G>A	p.Asp2769Asn	p.D2769N	ENST00000301067	NM_003482.3	2769	Gat/Aat	33/54	1	2	FACETS	0.769	0.714	0.825	0.769	0.714	0.825	SUBCLONAL	1	TRUE	1	0.533920631391222	2		664	1038	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098815	178098815	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1405	278	746	0	ENST00000397062.3:c.230A>T	p.Asp77Val	p.D77V	ENST00000397062	NM_006164.4	77	gAt/gTt	2/5	0.533920631391222	3	FACETS	0.784	0.734	0.836	0.392	0.367	0.418	SUBCLONAL	1	TRUE	1	0.533920631391222	3		746	1683	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944813	31944813	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	322	619	0	ENST00000340398.3:c.288C>A	p.Ser96Arg	p.S96R	ENST00000340398	NM_001013699.2	96	agC/agA	1/1	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.533920631391222	2		619	1118	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231391	46231391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1317781343	NA	P-0013755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	200	480	1	ENST00000334344.6:c.1231G>A	p.Asp411Asn	p.D411N	ENST00000334344	NM_152641.2	411	Gat/Aat	10/21	1	2	FACETS	0.882	0.819	0.948	0.882	0.819	0.948	CLONAL	1	TRUE	1	0.533920631391222	2		481	849	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910545	32910545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1243	221	835	0	ENST00000380152.3:c.2053G>A	p.Asp685Asn	p.D685N	ENST00000380152		685	Gat/Aat	11/27	0.229008052151304	2	FACETS	0.565	0.525	0.608	0.283	0.262	0.304	INDETERMINATE	1	TRUE	0	0.533920631391222	2		835	1464	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604656	48604656	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	354	504	0	ENST00000342988.3:c.1478A>T	p.Asp493Val	p.D493V	ENST00000342988	NM_005359.5	493	gAt/gTt	12/12	0.484266675566188	2	FACETS	0.87	0.83	0.911	0.87	0.83	0.911	CLONAL	2	TRUE	0	0.533920631391222	2		504	762	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741972	40741972	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	554	608	0	ENST00000392038.2:c.1000T>G	p.Trp334Gly	p.W334G	ENST00000392038	NM_001626.4	334	Tgg/Ggg	11/14	0.533920631391222	2	FACETS	0.946	0.912	0.98	0.946	0.912	0.98	CLONAL	2	TRUE	0	0.533920631391222	2		608	1097	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024668	31024668	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	503	749	1	ENST00000375687.4:c.4153A>T	p.Arg1385Trp	p.R1385W	ENST00000375687	NM_015338.5	1385	Agg/Tgg	13/13	0.489501334116014	2	FACETS	0.885	0.851	0.92	0.885	0.851	0.92	CLONAL	2	TRUE	0	0.533920631391222	2		750	1064	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143269	24143269	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0013755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	421	787	0	ENST00000263121.7:c.500+1G>A		p.X167_splice	ENST00000263121	NM_003073.3	167			0.250161509420324	3	FACETS	1	0.995	1	0.706	0.671	0.74	INDETERMINATE	1	TRUE	1	0.533920631391222	3		787	1416	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131217	55131217	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0013755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	376	502	0	ENST00000257290.5:c.759+1G>T		p.X253_splice	ENST00000257290	NM_006206.4	253			0.280069265495479	2	FACETS	0.789	0.753	0.827	0.789	0.753	0.827	INDETERMINATE	2	TRUE	0	0.533920631391222	2		502	892	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467609	66467609	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	94	489	1	ENST00000273854.3:c.660C>A	p.Cys220Ter	p.C220*	ENST00000273854	NM_004439.5	220	tgC/tgA	3/18	0.484966149165916	1	FACETS	0.396	0.353	0.443	0.396	0.353	0.443	SUBCLONAL	1	TRUE	0	0.533920631391222	1		490	651	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553631	106553631	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	220	386	0	ENST00000369096.4:c.1596A>T	p.Lys532Asn	p.K532N	ENST00000369096	NM_001198.3	532	aaA/aaT	5/7	0.533920631391222	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.533920631391222	1		386	528	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545602	106545602	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	291	550	1	ENST00000359195.3:c.3079C>A	p.Leu1027Met	p.L1027M	ENST00000359195	NM_002649.2	1027	Ctg/Atg	11/11	0.390546543318788	3	FACETS	1	0.979	1	0.545	0.512	0.579	CLONAL	1	TRUE	1	0.533920631391222	3		551	1267	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439656	140439656	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	124	239	0	ENST00000288602.6:c.2083G>C	p.Glu695Gln	p.E695Q	ENST00000288602	NM_004333.4	695	Gag/Cag	17/18	0.390546543318788	3	FACETS	1	0.961	1	0.553	0.503	0.606	CLONAL	1	TRUE	1	0.533920631391222	3		239	532	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221318	1221319	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	T	novel	NA	P-0013755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	353	596	0	ENST00000326873.7:c.841_842delinsT	p.Pro281CysfsTer6	p.P281Cfs*6	ENST00000326873	NM_000455.4	281	CCg/Tg	6/10	0.533920631391222	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.533920631391222	1		596	855	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0013761-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	53	422	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.923	0.786	1	0.923	0.786	1	CLONAL	1	FALSE	1	0.159482741903733	2		422	720	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0013769-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	236	398	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.394302594618273	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.394302594618273	2		398	509	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0013769-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	140	364	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.971	0.886	1	0.971	0.886	1	CLONAL	1	TRUE	1	0.394302594618273	2		364	731	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032795	30032795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368773485	NA	P-0013769-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	142	712	0	ENST00000338641.4:c.170G>A	p.Arg57Gln	p.R57Q	ENST00000338641	NM_000268.3	57	cGa/cAa	2/16	1	2	FACETS	0.896	0.817	0.979	0.896	0.817	0.979	CLONAL	1	TRUE	1	0.394302594618273	2		712	804	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589558	67589614	+	inframe_deletion	In_Frame_Del	DEL	AATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACACTCAGTTTCAAGAAAAA	AATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACACTCAGTTTCAAGAAAAA	-	novel	NA	P-0013769-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	63	371	0	ENST00000274335.5:c.1322_1378del	p.Asn441_Lys459del	p.N441_K459del	ENST00000274335		441	AATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACACTCAGTTTCAAGAAAAA/-	10/15	1	2	FACETS	0.684	0.593	0.783	0.684	0.593	0.783	SUBCLONAL	1	TRUE	1	0.394302594618273	2		371	467	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0013790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	325	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.820250065424557	3	FACETS	1	0.972	1	0.68	0.651	0.708	CLONAL	2	TRUE	0	0.820250065424557	3		249	548	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577075	7577079	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTC	TTCTC	-	novel	NA	P-0013790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	675	566	0	ENST00000269305.4:c.859_863del	p.Glu287SerfsTer17	p.E287Sfs*17	ENST00000269305	NM_001126112.2	287	GAGAAt/t	8/11	0.731077990116484	3	FACETS	0.922	0.903	0.941	0.922	0.903	0.941	CLONAL	3	TRUE	0	0.820250065424557	3		566	839	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168975	11168975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329240441	NA	P-0013790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	137	530	1	ENST00000358026.2:c.4565C>T	p.Ser1522Leu	p.S1522L	ENST00000358026	NM_001128849.1	1522	tCg/tTg	32/36	0.813266924614622	2	FACETS	0.465	0.424	0.509	0.233	0.212	0.255	SUBCLONAL	1	TRUE	0	0.820250065424557	2		531	718	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306541	41306541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	161	437	1	ENST00000373198.4:c.1118C>T	p.Pro373Leu	p.P373L	ENST00000373198	NM_133170.3	373	cCa/cTa	7/32	0.820250065424557	5	FACETS	0.752	0.688	0.818	0.251	0.229	0.273	SUBCLONAL	1	TRUE	2	0.820250065424557	5		438	1165	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242487	+	protein_altering_variant	In_Frame_Del	DEL	GAATTAAGAGAAGCAACATCTC	GAATTAAGAGAAGCAACATCTC	ATCT	novel	NA	P-0013790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	905	515	2	ENST00000275493.2:c.2236_2257delinsATCT	p.Glu746_Pro753delinsIleSer	p.E746_P753delinsIS	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCAACATCTCcg/ATCTcg	19/28	0.748162545136759	4	FACETS	0.919	0.903	0.934	0.919	0.903	0.934	CLONAL	4	TRUE	0	0.820250065424557	4		517	1093	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848628	151848628	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1242	136	431	0	ENST00000262189.6:c.12565G>A	p.Glu4189Lys	p.E4189K	ENST00000262189	NM_170606.2	4189	Gaa/Aaa	50/59	0.748162545136759	4	FACETS	0.438	0.397	0.482	0.11	0.099	0.121	SUBCLONAL	1	TRUE	0	0.820250065424557	4		431	1378	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209504	98209504	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766315655	NA	P-0013790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	155	384	4	ENST00000331920.6:c.4034G>A	p.Arg1345His	p.R1345H	ENST00000331920	NM_000264.3	1345	cGt/cAt	23/24	0.342915770003644	5	FACETS	1	0.983	1	0.426	0.391	0.463	INDETERMINATE	1	TRUE	2	0.820250065424557	5		388	659	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696689	47696689	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519972	NA	P-0013797-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	132	944	1	ENST00000347630.2:c.259T>A	p.Tyr87Asn	p.Y87N	ENST00000347630	NM_001007230.1	87	Tac/Aac	5/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.771111197092366	2		945	295	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211548	98211548	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013797-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	20	704	1	ENST00000331920.6:c.3607A>T	p.Ser1203Cys	p.S1203C	ENST00000331920	NM_000264.3	1203	Agc/Tgc	22/24	1	2	FACETS	0.136	0.104	0.174	0.136	0.104	0.174	SUBCLONAL	1	TRUE	1	0.771111197092366	2		705	381	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247367	153247367	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	11	384	0	ENST00000281708.4:c.1435C>T	p.Arg479Ter	p.R479*	ENST00000281708	NM_033632.3	479	Cga/Tga	10/12	0.229189449505146	3	FACETS	0.134	0.092	0.187	0.067	0.046	0.094	INDETERMINATE	1	TRUE	1	0.553254241593059	3		384	379	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354255	70354255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	81	466	1	ENST00000374080.3:c.4666G>A	p.Glu1556Lys	p.E1556K	ENST00000374080		1556	Gag/Aag	34/45	1	1	FACETS	0.827	0.739	0.919	0.827	0.739	0.919	CLONAL	1	TRUE	0	0.553254241593059	1		467	256	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0013812-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	67	646	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	FALSE	1	0.469039841432872	2		646	236	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494882	56494882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376234145	NA	P-0013812-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	16	355	0	ENST00000267101.3:c.3239G>A	p.Arg1080His	p.R1080H	ENST00000267101	NM_001982.3	1080	cGt/cAt	27/28	0.313469289326844	4	FACETS	0.324	0.239	0.426	0.162	0.119	0.213	SUBCLONAL	1	FALSE	2	0.469039841432872	4		355	309	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013822-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	165	661	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.249763591494217	4	FACETS	0.955	0.879	1	0.955	0.879	1	CLONAL	2	TRUE	2	0.28444432799039	4		661	780	SUCCESS
APC	324	MSKCC	GRCh37	5	112170647	112170647	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0013822-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	86	360	0	ENST00000257430.4:c.1744-1G>A		p.X582_splice	ENST00000257430	NM_000038.5	582			0.28444432799039	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	2	TRUE	0	0.28444432799039	2		360	298	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582801	95582801	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013822-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	68	258	0	ENST00000393063.1:c.1741G>A	p.Ala581Thr	p.A581T	ENST00000393063	NM_030621.3	581	Gct/Act	11/28	0.249763591494217	4	FACETS	0.981	0.86	1	0.981	0.86	1	CLONAL	2	TRUE	2	0.28444432799039	4		258	313	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374903	45374903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013822-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	206	711	0	ENST00000262160.6:c.940G>A	p.Gly314Ser	p.G314S	ENST00000262160	NM_005901.5	314	Ggt/Agt	8/11	0.28444432799039	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.28444432799039	2		711	660	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604700	48604701	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0013822-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	133	466	1	ENST00000342988.3:c.1522_1523delinsTT	p.Gly508Phe	p.G508F	ENST00000342988	NM_005359.5	508	GGc/TTc	12/12	0.28444432799039	2	FACETS	0.82	0.748	0.896	0.82	0.748	0.896	CLONAL	2	TRUE	0	0.28444432799039	2		467	570	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145598	24145598	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013822-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	232	781	0	ENST00000263121.7:c.617G>A	p.Trp206Ter	p.W206*	ENST00000263121	NM_003073.3	206	tGg/tAg	5/9	0.249763591494217	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.28444432799039	4		781	1009	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574565	41574565	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013822-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	286	1098	0	ENST00000263253.7:c.6850A>G	p.Met2284Val	p.M2284V	ENST00000263253	NM_001429.3	2284	Atg/Gtg	31/31	0.249763591494217	4	FACETS	0.888	0.833	0.945	0.888	0.833	0.945	CLONAL	2	TRUE	2	0.28444432799039	4		1098	1454	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840053	27840053	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013825-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	131	956	3	ENST00000328488.2:c.41G>A	p.Gly14Asp	p.G14D	ENST00000328488	NM_003533.2	14	gGc/gAc	1/1	0.244371901310876	2	FACETS	0.952	0.862	1	0.476	0.431	0.524	CLONAL	1	TRUE	0	0.250506485236076	2		959	1099	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0013836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	87	503	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.492678524707485	2		503	293	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857449	9857449	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774419037	NA	P-0013836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	103	434	0	ENST00000330684.3:c.3952C>T	p.Arg1318Trp	p.R1318W	ENST00000330684	NM_001134407.1	1318	Cgg/Tgg	13/13	0.267310916402234	1	FACETS	0.446	0.399	0.496	0.446	0.399	0.496	INDETERMINATE	1	TRUE	0	0.492678524707485	1		434	706	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574005	7574005	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	279	571	0	ENST00000269305.4:c.1022T>A	p.Phe341Tyr	p.F341Y	ENST00000269305	NM_001126112.2	341	tTc/tAc	10/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.492678524707485	2		571	1037	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39567849	39567856	+	frameshift_variant	Frame_Shift_Del	DEL	AAATGATA	AAATGATA	-	novel	NA	P-0013836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	19	227	0	ENST00000262039.4:c.607_614del	p.Met203Ter	p.M203*	ENST00000262039	NM_002647.2	202	gAAATGATA/g	5/25	0.267310916402234	1	FACETS	0.166	0.126	0.214	0.166	0.126	0.214	INDETERMINATE	1	TRUE	0	0.492678524707485	1		227	350	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201746	66201746	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	209	521	0	ENST00000273854.3:c.2756G>A	p.Arg919Gln	p.R919Q	ENST00000273854	NM_004439.5	919	cGa/cAa	16/18	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.492678524707485	2		521	802	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs397518442	NA	P-0013863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	41	711	0	ENST00000326873.7:c.650del	p.Pro217ArgfsTer70	p.P217Rfs*70	ENST00000326873	NM_000455.4	216	tCc/tc	5/10	0.217076500452189	1	FACETS	0.538	0.449	0.637	0.538	0.449	0.637	SUBCLONAL	1	TRUE	0	0.318718832326776	1		711	402	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380279	25380279	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs727503108	NA	P-0013863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	92	627	0	ENST00000311936.3:c.179G>T	p.Gly60Val	p.G60V	ENST00000311936	NM_004985.3	60	gGt/gTt	3/5	1	2	FACETS	0.965	0.859	1	0.965	0.859	1	CLONAL	1	TRUE	1	0.318718832326776	2		627	598	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729154	66729154	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519731	NA	P-0013863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	59	562	0	ENST00000307102.5:c.362G>C	p.Cys121Ser	p.C121S	ENST00000307102	NM_002755.3	121	tGc/tCc	3/11	1	2	FACETS	0.716	0.617	0.824	0.716	0.617	0.824	SUBCLONAL	1	TRUE	1	0.318718832326776	2		562	517	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088723	27088723	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	63	652	1	ENST00000324856.7:c.2332G>T	p.Gly778Ter	p.G778*	ENST00000324856	NM_006015.4	778	Gga/Tga	7/20	0.290477398026854	1	FACETS	0.703	0.609	0.804	0.703	0.609	0.804	SUBCLONAL	1	TRUE	0	0.318718832326776	1		653	473	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602921	10602923	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0013863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	64	525	0	ENST00000171111.5:c.655_657del	p.Glu219del	p.E219del	ENST00000171111	NM_203500.1	219	GAG/-	3/6	0.217076500452189	1	FACETS	0.76	0.66	0.868	0.76	0.66	0.868	SUBCLONAL	1	TRUE	0	0.318718832326776	1		525	444	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691882	30691882	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	92	373	0	ENST00000295754.5:c.384G>T	p.Lys128Asn	p.K128N	ENST00000295754	NM_003242.5	128	aaG/aaT	3/7	0.276853405505253	2	FACETS	1	0.98	1	0.734	0.657	0.816	CLONAL	1	TRUE	0	0.318718832326776	2		373	393	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356275	66356275	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	59	585	0	ENST00000273854.3:c.1222T>C	p.Cys408Arg	p.C408R	ENST00000273854	NM_004439.5	408	Tgt/Cgt	5/18	0.318718832326776	1	FACETS	0.754	0.65	0.865	0.754	0.65	0.865	SUBCLONAL	1	TRUE	0	0.318718832326776	1		585	413	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0013872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	240	488	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.242844498137832	4	FACETS	1	0.981	1			1	CLONAL	2	TRUE	NA	0.261231478999476	4		488	1027	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0013872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	23	741	1	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	0.261231478999476	1	FACETS	0.14	0.108	0.177	0.14	0.108	0.177	SUBCLONAL	1	TRUE	0	0.261231478999476	1		742	1095	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044901	47044901	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	95	584	0	ENST00000377604.3:c.2227G>T	p.Glu743Ter	p.E743*	ENST00000377604	NM_001204468.1	743	Gag/Tag	20/24	1	2	FACETS	0.992	0.884	1	0.992	0.884	1	CLONAL	1	TRUE	1	0.261231478999476	2		584	733	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759697	133759697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776289598	NA	P-0013872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	44	318	0	ENST00000318560.5:c.2020C>T	p.Arg674Trp	p.R674W	ENST00000318560	NM_005157.4	674	Cgg/Tgg	11/11	1	2	FACETS	0.994	0.836	1	0.994	0.836	1	CLONAL	1	TRUE	1	0.261231478999476	2		318	339	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476383	88476383	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	50	422	0	ENST00000360948.2:c.1749G>T	p.Lys583Asn	p.K583N	ENST00000360948	NM_001012338.2	583	aaG/aaT	15/19	1	2	FACETS	0.614	0.521	0.718	0.614	0.521	0.718	SUBCLONAL	1	TRUE	1	0.261231478999476	2		422	623	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163835	152163835	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	70	612	0	ENST00000206249.3:c.556G>C	p.Ala186Pro	p.A186P	ENST00000206249	NM_000125.3	186	Gca/Cca	2/8	1	2	FACETS	0.63	0.548	0.719	0.63	0.548	0.719	SUBCLONAL	1	TRUE	1	0.261231478999476	2		612	851	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8338963	8338963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747059417	NA	P-0013872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	107	609	1	ENST00000356435.5:c.5338C>T	p.Pro1780Ser	p.P1780S	ENST00000356435		1780	Cca/Tca	32/35	1	2	FACETS	0.894	0.801	0.993	0.894	0.801	0.993	CLONAL	1	TRUE	1	0.261231478999476	2		610	916	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484202	8484203	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0013872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	101	682	0	ENST00000356435.5:c.3329_3330delinsAG	p.Thr1110Lys	p.T1110K	ENST00000356435		1110	aCC/aAG	19/35	1	2	FACETS	0.811	0.723	0.904	0.811	0.723	0.904	CLONAL	1	TRUE	1	0.261231478999476	2		682	954	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920499	134920499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013886-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	61	653	0	ENST00000398015.3:c.2314G>A	p.Asp772Asn	p.D772N	ENST00000398015	NM_004441.4	772	Gac/Aac	12/16	1	2	FACETS	0.507	0.437	0.583	0.507	0.437	0.583	SUBCLONAL	1	TRUE	1	0.42	2		653	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578501	7578506	+	frameshift_variant	Frame_Shift_Del	DEL	CACAGG	CACAGG	T	novel	NA	P-0013886-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	79	477	0	ENST00000269305.4:c.424_429delinsA	p.Pro142ThrfsTer5	p.P142Tfs*5	ENST00000269305	NM_001126112.2	142	CCTGTG/A	5/11	0.301503718132178	1	FACETS	0.734	0.649	0.824	0.734	0.649	0.824	SUBCLONAL	1	TRUE	0	0.42	1		477	405	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0013887-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	298	503	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.587169153376528	3	FACETS	1	0.991	1			1	CLONAL	2	FALSE	NA	0.584770243401766	3		503	559	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231100	98231100	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs115556836	NA	P-0013887-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	42	313	0	ENST00000331920.6:c.2183C>T	p.Thr728Met	p.T728M	ENST00000331920	NM_000264.3	728	aCg/aTg	14/24	NA	2	FACETS	0.86	0.729	1			1	INDETERMINATE	1	FALSE	NA	0.584770243401766	2		313	167	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622330	1622330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377067150	NA	P-0013887-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	40	876	0	ENST00000344749.5:c.634G>A	p.Ala212Thr	p.A212T	ENST00000344749	NM_001136139.2	212	Gcc/Acc	9/19	0.138689703630709	0	FACETS	0.113	0.094	0.135			1	INDETERMINATE	1	FALSE	0	0.584770243401766	0		876	501	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801204	1801205	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0013887-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	1134	467	3	ENST00000260795.2:c.333_334delinsTT	p.Gln111_Arg112delinsHisTrp	p.Q111_R112delinsHW	ENST00000260795		111	caGCgg/caTTgg	2/17	0.584770243401766	16	FACETS	0.996	0.976	1			1	CLONAL	12	FALSE	NA	0.584770243401766	16		470	1652	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	88	503	0				ENST00000310581	NM_198253.2	-/1132			0.233243988838096	0	FACETS	0.32	0.287	0.355			1	INDETERMINATE	1	TRUE	0	0.66	0		503	283	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523654	176523654	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	196	1068	0	ENST00000292408.4:c.2065C>T	p.Pro689Ser	p.P689S	ENST00000292408	NM_213647.1	689	Ccg/Tcg	16/18	1	2	FACETS	0.841	0.782	0.903	0.841	0.782	0.903	CLONAL	1	TRUE	1	0.66	2		1068	706	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	303	979	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.979	0.924	1	0.979	0.924	1	CLONAL	1	TRUE	1	0.66	2		979	938	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	140	490	1	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	1	2	FACETS	0.91	0.835	0.988	0.91	0.835	0.988	CLONAL	1	TRUE	1	0.66	2		491	466	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514164	69514164	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	203	869	0	ENST00000294312.3:c.517C>T	p.Pro173Ser	p.P173S	ENST00000294312	NM_005117.2	173	Cca/Tca	3/3	0.277975755514651	0	FACETS	0.335	0.312	0.358			1	INDETERMINATE	1	TRUE	0	0.66	0		869	625	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480469	89480469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	206	603	1	ENST00000336596.2:c.2306G>A	p.Arg769His	p.R769H	ENST00000336596	NM_005233.5	769	cGt/cAt	13/17	1	2	FACETS	0.929	0.866	0.994	0.929	0.866	0.994	CLONAL	1	TRUE	1	0.66	2		604	672	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259231	89259231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	146	561	0	ENST00000336596.2:c.375G>A	p.Met125Ile	p.M125I	ENST00000336596	NM_005233.5	125	atG/atA	3/17	1	2	FACETS	0.918	0.844	0.994	0.918	0.844	0.994	CLONAL	1	TRUE	1	0.66	2		561	482	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612735	228612735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	314	1509	2	ENST00000366696.1:c.292G>A	p.Glu98Lys	p.E98K	ENST00000366696	NM_003493.2	98	Gag/Aag	1/1	0.3	1	FACETS	0.668	0.631	0.705	0.668	0.631	0.705	INDETERMINATE	1	TRUE	0	0.66	1		1511	955	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292842	91292842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371100621	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	275	617	2	ENST00000355112.3:c.344C>T	p.Pro115Leu	p.P115L	ENST00000355112	NM_000057.2	115	cCg/cTg	3/22	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.66	2		619	789	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731101	162731101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761991484	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	268	988	0	ENST00000367921.3:c.956C>T	p.Ser319Phe	p.S319F	ENST00000367921	NM_006182.2	319	tCc/tTc	9/18	0.3	1	FACETS	0.609	0.572	0.646	0.609	0.572	0.646	INDETERMINATE	1	TRUE	0	0.66	1		988	894	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934864	9934864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766162952	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	205	989	0	ENST00000330684.3:c.1426G>A	p.Asp476Asn	p.D476N	ENST00000330684	NM_001134407.1	476	Gac/Aac	6/13	0.3	0	FACETS	0.312	0.291	0.335			1	INDETERMINATE	1	TRUE	0	0.66	0		989	676	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2488134	2488134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375570144	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	166	809	0	ENST00000355716.4:c.31C>T	p.Pro11Ser	p.P11S	ENST00000355716	NM_003820.2	11	Ccc/Tcc	1/8	0.3	1	FACETS	0.646	0.597	0.696	0.646	0.597	0.696	INDETERMINATE	1	TRUE	0	0.66	1		809	522	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199553	16199553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	279	728	0	ENST00000375759.3:c.326G>A	p.Gly109Glu	p.G109E	ENST00000375759	NM_015001.2	109	gGa/gAa	2/15	0.3	3	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.66	3		728	915	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937127	36937128	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	250	1335	3	ENST00000361632.4:c.1191_1192delinsTT	p.His398Tyr	p.H398Y	ENST00000361632		397	ttCCac/ttTTac	9/16	1	2	FACETS	0.844	0.79	0.898	0.844	0.79	0.898	CLONAL	1	TRUE	1	0.66	2		1338	898	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161326604	161326604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	196	605	1	ENST00000367975.2:c.379C>T	p.His127Tyr	p.H127Y	ENST00000367975	NM_003001.3	127	Cat/Tat	5/6	0.3	1	FACETS	0.667	0.621	0.714	0.667	0.621	0.714	INDETERMINATE	1	TRUE	0	0.66	1		606	597	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604647	43604647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	121	662	0	ENST00000355710.3:c.1232C>T	p.Ser411Phe	p.S411F	ENST00000355710	NM_020975.4	411	tCc/tTc	6/20	0.3	0	FACETS	0.255	0.232	0.28			1	INDETERMINATE	1	TRUE	0	0.66	0		662	488	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137731	64137731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	214	760	0	ENST00000334205.4:c.1832G>A	p.Gly611Glu	p.G611E	ENST00000334205	NM_003942.2	611	gGg/gAg	15/17	0.105698509147228	3	FACETS	1	0.991	1	0.687	0.642	0.733	INDETERMINATE	1	TRUE	1	0.66	3		760	628	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856218	111856219	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	103	343	1	ENST00000341259.2:c.269_270delinsAA	p.Arg90Gln	p.R90Q	ENST00000341259	NM_005475.2	90	cGG/cAA	2/8	1	2	FACETS	0.918	0.83	1	0.918	0.83	1	CLONAL	1	TRUE	1	0.66	2		344	340	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112892392	112892393	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	166	626	1	ENST00000351677.2:c.550_551delinsAA	p.Gly184Lys	p.G184K	ENST00000351677	NM_002834.3	184	GGa/AAa	5/16	NA	2	FACETS	0.735	0.678	0.795			1	INDETERMINATE	1	TRUE	NA	0.66	2		627	684	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219302	133219302	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	146	604	0	ENST00000320574.5:c.4742G>T	p.Gly1581Val	p.G1581V	ENST00000320574	NM_006231.2	1581	gGg/gTg	37/49	NA	2	FACETS	1	0.956	1			1	INDETERMINATE	1	TRUE	NA	0.66	2		604	420	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252723	133252723	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	238	775	0	ENST00000320574.5:c.977C>T	p.Pro326Leu	p.P326L	ENST00000320574	NM_006231.2	326	cCa/cTa	10/49	NA	2	FACETS	0.94	0.881	1			1	INDETERMINATE	1	TRUE	NA	0.66	2		775	767	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256799	133256799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500863	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	201	574	0	ENST00000320574.5:c.295C>T	p.Pro99Ser	p.P99S	ENST00000320574	NM_006231.2	99	Ccc/Tcc	4/49	NA	2	FACETS	0.924	0.861	0.99			1	INDETERMINATE	1	TRUE	NA	0.66	2		574	659	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32903612	32903612	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507873	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	217	448	0	ENST00000380152.3:c.664C>T	p.Pro222Ser	p.P222S	ENST00000380152		222	Cct/Tct	8/27	1	2	FACETS	0.905	0.844	0.966	0.905	0.844	0.966	CLONAL	1	TRUE	1	0.66	2		448	727	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110791	2110791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45517148	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	197	809	0	ENST00000219476.3:c.1096G>A	p.Glu366Lys	p.E366K	ENST00000219476	NM_000548.3	366	Gaa/Aaa	11/42	1	2	FACETS	0.918	0.854	0.984	0.918	0.854	0.984	CLONAL	1	TRUE	1	0.66	2		809	650	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916154	9916155	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TA	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	140	637	1	ENST00000330684.3:c.2134_2135delinsTA	p.Gly712Ter	p.G712*	ENST00000330684	NM_001134407.1	712	GGa/TAa	10/13	0.3	0	FACETS	0.311	0.285	0.338			1	INDETERMINATE	1	TRUE	0	0.66	0		638	464	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993275	72993275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	225	1314	0	ENST00000268489.5:c.770C>T	p.Ser257Phe	p.S257F	ENST00000268489	NM_006885.3	257	tCc/tTc	2/10	0.280874667019248	0	FACETS	0.274	0.256	0.294			1	INDETERMINATE	1	TRUE	0	0.66	0		1314	845	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682542	37682542	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	226	592	0	ENST00000447079.4:c.3733C>T	p.Pro1245Ser	p.P1245S	ENST00000447079	NM_015083.1	1245	Ccc/Tcc	13/14	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.66	2		592	654	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40364021	40364021	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	185	804	0	ENST00000293328.3:c.1661C>T	p.Ser554Phe	p.S554F	ENST00000293328	NM_012448.3	554	tCc/tTc	13/19	1	2	FACETS	0.873	0.81	0.938	0.873	0.81	0.938	CLONAL	1	TRUE	1	0.66	2		804	642	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615730	1615730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372168347	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	326	1518	4	ENST00000344749.5:c.1541C>T	p.Ser514Leu	p.S514L	ENST00000344749	NM_001136139.2	514	tCg/tTg	17/19	0.162759952425949	0	FACETS	0.365	0.345	0.384			1	INDETERMINATE	1	TRUE	0	0.66	0		1522	921	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622172	1622173	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	160	954	1	ENST00000344749.5:c.702_703delinsAA	p.Gly235Ser	p.G235S	ENST00000344749	NM_001136139.2	234	gcGGgc/gcAAgc	10/19	0.162759952425949	0	FACETS	0.309	0.285	0.334			1	INDETERMINATE	1	TRUE	0	0.66	0		955	533	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4097320	4097320	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	197	651	1	ENST00000262948.5:c.941C>T	p.Pro314Leu	p.P314L	ENST00000262948	NM_030662.3	314	cCt/cTt	8/11	0.162759952425949	0	FACETS	0.317	0.294	0.34			1	INDETERMINATE	1	TRUE	0	0.66	0		652	641	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945717	17945717	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520020	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	117	806	0	ENST00000458235.1:c.2143G>A	p.Val715Ile	p.V715I	ENST00000458235	NM_000215.3	715	Gtc/Atc	16/24	1	2	FACETS	0.708	0.641	0.777	0.708	0.641	0.777	SUBCLONAL	1	TRUE	1	0.66	2		806	501	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727125	41727125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	269	820	0	ENST00000301178.4:c.383C>T	p.Ser128Phe	p.S128F	ENST00000301178	NM_021913.4	128	tCc/tTc	3/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.66	2		820	793	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940534	29940534	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs771254732	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	212	608	2	ENST00000389048.3:c.697A>G	p.Met233Val	p.M233V	ENST00000389048	NM_004304.4	233	Atg/Gtg	2/29	1	2	FACETS	0.945	0.882	1	0.945	0.882	1	CLONAL	1	TRUE	1	0.66	2		610	680	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726927	61726927	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	298	761	0	ENST00000401558.2:c.511C>T	p.Leu171Phe	p.L171F	ENST00000401558	NM_003400.3	171	Ctt/Ttt	7/25	1	2	FACETS	0.986	0.931	1	0.986	0.931	1	CLONAL	1	TRUE	1	0.66	2		761	916	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375088	31375088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	226	815	0	ENST00000328111.2:c.485C>T	p.Pro162Leu	p.P162L	ENST00000328111	NM_006892.3	162	cCc/cTc	6/23	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.66	2		815	680	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385272	41385272	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	230	640	0	ENST00000373198.4:c.689G>A	p.Trp230Ter	p.W230*	ENST00000373198	NM_133170.3	230	tGg/tAg	6/32	0.3	1	FACETS	0.772	0.725	0.82	0.772	0.725	0.82	INDETERMINATE	1	TRUE	0	0.66	1		640	605	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164691	36164692	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	229	830	2	ENST00000300305.3:c.1183_1184delinsTT	p.Pro395Leu	p.P395L	ENST00000300305		395	CCg/TTg	8/8	1	2	FACETS	0.951	0.89	1	0.951	0.89	1	CLONAL	1	TRUE	1	0.66	2		832	730	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403500	138403500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	306	842	0	ENST00000289153.2:c.2282C>T	p.Pro761Leu	p.P761L	ENST00000289153	NM_006219.2	761	cCc/cTc	15/22	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.66	2		842	858	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226870	142226870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1216055957	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	237	663	0	ENST00000350721.4:c.4934C>T	p.Ser1645Phe	p.S1645F	ENST00000350721	NM_001184.3	1645	tCc/tTc	28/47	1	2	FACETS	0.991	0.929	1	0.991	0.929	1	CLONAL	1	TRUE	1	0.66	2		663	725	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916865	178916865	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	432	1411	0	ENST00000263967.3:c.252T>A	p.Asp84Glu	p.D84E	ENST00000263967	NM_006218.2	84	gaT/gaA	2/21	1	2	FACETS	0.958	0.913	1	0.958	0.913	1	CLONAL	1	TRUE	1	0.66	2		1411	1366	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628211	187628211	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	118	556	0	ENST00000441802.2:c.2771del	p.Pro924HisfsTer11	p.P924Hfs*11	ENST00000441802	NM_005245.3	924	cCa/ca	2/27	1	2	FACETS	0.715	0.648	0.785	0.715	0.648	0.785	SUBCLONAL	1	TRUE	1	0.66	2		556	500	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628213	187628217	+	frameshift_variant	Frame_Shift_Del	DEL	GTTGT	GTTGT	ATGG	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	118	559	0	ENST00000441802.2:c.2765_2769delinsCCAT	p.Asp922AlafsTer13	p.D922Afs*13	ENST00000441802	NM_005245.3	922	gACAAC/gCCAT	2/27	1	2	FACETS	0.751	0.682	0.824	0.751	0.682	0.824	SUBCLONAL	1	TRUE	1	0.66	2		559	476	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665643	86665643	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	208	428	0	ENST00000274376.6:c.1624C>T	p.Gln542Ter	p.Q542*	ENST00000274376	NM_002890.2	542	Cag/Tag	12/25	1	2	FACETS	0.98	0.915	1	0.98	0.915	1	CLONAL	1	TRUE	1	0.66	2		428	643	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720997	176720998	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	213	667	1	ENST00000439151.2:c.6628_6629delinsTT	p.Pro2210Phe	p.P2210F	ENST00000439151	NM_022455.4	2210	CCc/TTc	23/23	1	2	FACETS	0.952	0.889	1	0.952	0.889	1	CLONAL	1	TRUE	1	0.66	2		668	678	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858308	27858308	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	319	1575	3	ENST00000359303.2:c.263C>T	p.Ser88Leu	p.S88L	ENST00000359303	NM_003535.2	88	tCg/tTg	1/1	0.103911360007929	4	FACETS	0.756	0.714	0.799	0.756	0.714	0.799	INDETERMINATE	2	TRUE	2	0.66	4		1578	1061	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670975	30670975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	312	799	0	ENST00000376406.3:c.5771C>T	p.Ser1924Phe	p.S1924F	ENST00000376406	NM_014641.2	1924	tCc/tTc	12/15	0.103911360007929	4	FACETS	0.854	0.808	0.901	0.854	0.808	0.901	INDETERMINATE	2	TRUE	2	0.66	4		799	919	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170193	32170193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	200	667	0	ENST00000375023.3:c.3415C>T	p.Pro1139Ser	p.P1139S	ENST00000375023	NM_004557.3	1139	Cca/Tca	21/30	0.103911360007929	4	FACETS	0.814	0.758	0.871	0.814	0.758	0.871	INDETERMINATE	2	TRUE	2	0.66	4		667	618	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468145	50468146	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	81	551	0	ENST00000331340.3:c.1380_1381delinsAA	p.Val461Met	p.V461M	ENST00000331340	NM_006060.4	460	aaGGtg/aaAAtg	8/8	1	2	FACETS	0.726	0.645	0.812	0.726	0.645	0.812	SUBCLONAL	1	TRUE	1	0.66	2		551	338	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388121	81388121	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	125	424	0	ENST00000222390.5:c.255-1G>A		p.X85_splice	ENST00000222390	NM_000601.4	85			1	2	FACETS	0.825	0.752	0.901	0.825	0.752	0.901	CLONAL	1	TRUE	1	0.66	2		424	459	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538855	23538855	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	147	573	0	ENST00000380871.4:c.584C>T	p.Ser195Phe	p.S195F	ENST00000380871	NM_006167.3	195	tCc/tTc	2/2	1	2	FACETS	0.96	0.884	1	0.96	0.884	1	CLONAL	1	TRUE	1	0.66	2		573	464	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484290	8484290	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	188	674	0	ENST00000356435.5:c.3242A>C	p.Tyr1081Ser	p.Y1081S	ENST00000356435		1081	tAt/tCt	19/35	0.277975755514651	0	FACETS	0.31	0.287	0.333			1	INDETERMINATE	1	TRUE	0	0.66	0		674	625	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240336	98240336	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	226	457	0	ENST00000331920.6:c.1347+1G>A		p.X449_splice	ENST00000331920	NM_000264.3	449			0.3	1	FACETS	1	0.99	1	1	0.99	1	INDETERMINATE	1	TRUE	0	0.66	1		457	382	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418169	139418169	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	139	601	0	ENST00000277541.6:c.403G>A	p.Gly135Arg	p.G135R	ENST00000277541	NM_017617.3	135	Ggg/Agg	3/34	0.3	0	FACETS	0.463	0.429	0.498			1	INDETERMINATE	1	TRUE	0	0.66	0		601	309	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	37	661	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.116347237591284	3	FACETS	0.912	0.75	1	0.456	0.375	0.547	CLONAL	1	TRUE	1	0.13	3		661	665	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0013894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	10	211	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.557	0.377	0.786	0.557	0.377	0.786	SUBCLONAL	1	TRUE	1	0.13	2		211	276	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0013894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	24	316	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.116347237591284	3	FACETS	0.828	0.648	1	0.414	0.324	0.519	CLONAL	1	TRUE	1	0.13	3		316	475	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625251	69625251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782147248	NA	P-0013894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	39	689	1	ENST00000334134.2:c.542G>A	p.Arg181His	p.R181H	ENST00000334134	NM_005247.2	181	cGc/cAc	3/3	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.13	2		690	559	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149516594	149516594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150173975	NA	P-0013894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	38	601	3	ENST00000261799.4:c.17C>T	p.Ala6Val	p.A6V	ENST00000261799	NM_002609.3	6	gCg/gTg	2/23	0.116347237591284	3	FACETS	0.82	0.676	0.983	0.41	0.338	0.492	CLONAL	1	TRUE	1	0.13	3		604	759	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870780	12870780	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1348090532	NA	P-0013894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	23	212	0	ENST00000228872.4:c.7A>G	p.Asn3Asp	p.N3D	ENST00000228872	NM_004064.3	3	Aac/Gac	1/3	0.3	4	FACETS	1	0.913	1			1	CLONAL	1	TRUE	NA	0.13	4		212	286	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231194	98231194	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	27	402	0	ENST00000331920.6:c.2089del	p.Leu697SerfsTer49	p.L697Sfs*49	ENST00000331920	NM_000264.3	697	Ctc/tc	14/24	1	2	FACETS	0.927	0.737	1	0.927	0.737	1	CLONAL	1	TRUE	1	0.13	2		402	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0013895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	215	736	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.66905021628135	1	FACETS	0.977	0.926	1	0.977	0.926	1	CLONAL	1	TRUE	0	0.752255466821706	1		737	365	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0013895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	76	234	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.91	0.812	1	0.91	0.812	1	CLONAL	1	TRUE	1	0.752255466821706	2		234	222	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0013895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	64	211	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.877	0.773	0.985	0.877	0.773	0.985	CLONAL	1	TRUE	1	0.752255466821706	2		211	194	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0013895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	284	862	1	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	0.749506335500141	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.752255466821706	1		863	436	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650748	67650748	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	244	734	0	ENST00000264010.4:c.1053C>G	p.Phe351Leu	p.F351L	ENST00000264010	NM_006565.3	351	ttC/ttG	5/12	0.749506335500141	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.752255466821706	1		734	390	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061191	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	95	312	0	ENST00000250448.2:c.798C>G	p.Phe266Leu	p.F266L	ENST00000250448	NM_004496.3	266	ttC/ttG	2/2	1	2	FACETS	0.902	0.814	0.992	0.902	0.814	0.992	CLONAL	1	TRUE	1	0.752255466821706	2		312	280	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549134	21549134	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	209	873	1	ENST00000382592.4:c.3142G>A	p.Asp1048Asn	p.D1048N	ENST00000382592	NM_014572.2	1048	Gac/Aac	8/8	0.749506335500141	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.752255466821706	1		874	341	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772269	68772290	+	frameshift_variant	Frame_Shift_Del	DEL	ACGGTGCCCCGGCGCCACCTGG	ACGGTGCCCCGGCGCCACCTGG	-	novel	NA	P-0013895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	176	704	0	ENST00000261769.5:c.119_140del	p.Thr40ArgfsTer9	p.T40Rfs*9	ENST00000261769	NM_004360.3	40	ACGGTGCCCCGGCGCCACCTGGag/ag	2/16	0.749506335500141	1	FACETS	0.827	0.775	0.879	0.827	0.775	0.879	CLONAL	1	TRUE	0	0.752255466821706	1		704	353	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216899	7216899	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	251	987	1	ENST00000380728.2:c.622C>T	p.Gln208Ter	p.Q208*	ENST00000380728		208	Cag/Tag	7/11	0.66905021628135	1	FACETS	0.982	0.934	1	0.982	0.934	1	CLONAL	1	TRUE	0	0.752255466821706	1		988	424	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528086	29528086	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs864622107	NA	P-0013895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	88	343	0	ENST00000356175.3:c.1094C>G	p.Ser365Ter	p.S365*	ENST00000356175	NM_000267.3	365	tCa/tGa	10/57	0.752255466821706	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.752255466821706	1		343	136	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524466	44524466	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	170	452	0	ENST00000291552.4:c.91G>C	p.Asp31His	p.D31H	ENST00000291552	NM_006758.2	31	Gac/Cac	2/8	1	2	FACETS	0.989	0.918	1	0.989	0.918	1	CLONAL	1	TRUE	1	0.752255466821706	2		452	457	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259011	153259011	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	191	639	0	ENST00000281708.4:c.804G>C	p.Met268Ile	p.M268I	ENST00000281708	NM_033632.3	268	atG/atC	5/12	0.529292336265875	3	FACETS	0.968	0.898	1	0.484	0.449	0.52	CLONAL	1	TRUE	1	0.752255466821706	3		639	722	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26046026	26046026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	278	1230	0	ENST00000540144.1:c.388C>T	p.Arg130Cys	p.R130C	ENST00000540144	NM_003531.2	130	Cgc/Tgc	1/1	1	2	FACETS	0.997	0.942	1	0.997	0.942	1	CLONAL	1	TRUE	1	0.752255466821706	2		1230	741	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285903	38285903	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3639	235	864	1	ENST00000425967.3:c.508G>T	p.Glu170Ter	p.E170*	ENST00000425967	NM_001174067.1	170	Gag/Tag	5/19	0.752255466821706	14	FACETS	0.889	0.824	0.957			1	CLONAL	1	TRUE	NA	0.752255466821706	14		865	3874	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993741	90993742	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs768378152	NA	P-0013895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	84	290	0	ENST00000265433.3:c.181_182del	p.Asp61Ter	p.D61*	ENST00000265433	NM_002485.4	61	GAt/t	3/16	0.752255466821706	3	FACETS	0.896	0.798	0.999			1	CLONAL	1	TRUE	NA	0.752255466821706	3		290	343	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5081808	5081808	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013895-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	204	534	0	ENST00000381652.3:c.2518G>C	p.Asp840His	p.D840H	ENST00000381652	NM_004972.3	840	Gat/Cat	19/25	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.752255466821706	2		534	506	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101205	27101211	+	frameshift_variant	Frame_Shift_Del	DEL	CCATGTG	CCATGTG	-	novel	NA	P-0013898-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	265	702	0	ENST00000324856.7:c.4487_4493del	p.Thr1496SerfsTer7	p.T1496Sfs*7	ENST00000324856	NM_006015.4	1496	aCCATGTGg/ag	18/20	0.619798235537989	1	FACETS	0.975	0.922	1	0.975	0.922	1	CLONAL	1	TRUE	0	0.619798235537989	1		702	605	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346365	73346365	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	146	582	0	ENST00000377767.4:c.1435G>T	p.Asp479Tyr	p.D479Y	ENST00000377767	NM_014953.3	479	Gac/Tac	10/21	0.190906371807981	4	FACETS	1	0.969	1	0.568	0.517	0.621	INDETERMINATE	1	TRUE	2	0.334383076249392	4		582	1026	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312725	91312725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	239	722	0	ENST00000355112.3:c.2464C>T	p.Pro822Ser	p.P822S	ENST00000355112	NM_000057.2	822	Cct/Tct	12/22	0.237840803617123	2	FACETS	1	0.991	1	0.686	0.64	0.733	CLONAL	1	TRUE	0	0.334383076249392	2		722	1042	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346355	73346355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	138	599	0	ENST00000377767.4:c.1445G>A	p.Gly482Glu	p.G482E	ENST00000377767	NM_014953.3	482	gGa/gAa	10/21	0.190906371807981	4	FACETS	1	0.939	1	0.521	0.474	0.572	INDETERMINATE	1	TRUE	2	0.334383076249392	4		599	1056	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832864	3832864	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	79	632	2	ENST00000262367.5:c.1394A>T	p.Gln465Leu	p.Q465L	ENST00000262367	NM_004380.2	465	cAg/cTg	6/31	NA	2	FACETS	0.661	0.581	0.747			1	INDETERMINATE	1	TRUE	NA	0.334383076249392	2		634	715	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41249283	41249283	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	133	594	0	ENST00000357654.3:c.571G>T	p.Val191Phe	p.V191F	ENST00000357654	NM_007294.3	191	Gtt/Ttt	8/23	NA	2	FACETS	1	0.909	1			1	INDETERMINATE	1	TRUE	NA	0.334383076249392	2		594	795	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158079	106158079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749354184	NA	P-0013900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	153	614	0	ENST00000380013.4:c.2980C>T	p.His994Tyr	p.H994Y	ENST00000380013	NM_001127208.2	994	Cac/Tac	3/11	0.158260107538842	4	FACETS	1	0.98	1	0.62	0.567	0.677	INDETERMINATE	1	TRUE	2	0.334383076249392	4		614	984	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053149	180053150	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0013900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	59	720	1	ENST00000261937.6:c.1219_1220delinsAT	p.Gly407Ile	p.G407I	ENST00000261937	NM_182925.4	407	GGc/ATc	9/30	0.202274344071123	3	FACETS	0.655	0.563	0.755	0.327	0.281	0.378	SUBCLONAL	1	TRUE	1	0.334383076249392	3		721	629	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2969663	2969663	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	80	784	0	ENST00000396946.4:c.1616G>T	p.Cys539Phe	p.C539F	ENST00000396946	NM_032415.4	539	tGc/tTc	12/25	1	2	FACETS	0.668	0.588	0.755	0.668	0.588	0.755	SUBCLONAL	1	TRUE	1	0.334383076249392	2		784	716	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481486	140481486	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1539	298	1095	0	ENST00000288602.6:c.1322T>G	p.Leu441Arg	p.L441R	ENST00000288602	NM_004333.4	441	cTt/cGt	11/18	0.202274344071123	3	FACETS	1	0.984	1	0.566	0.531	0.603	CLONAL	1	TRUE	1	0.334383076249392	3		1095	1837	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398284	+	missense_variant	Missense_Mutation	TNP	CAC	CAC	AAT	novel	NA	P-0013900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	143	616	1	ENST00000311936.3:c.35_37delinsATT	p.Gly12_Gly13delinsAspCys	p.G12_G13delinsDC	ENST00000311936	NM_004985.3	12	gGTGgc/gATTgc	2/5	0.158260107538842	4	FACETS	1	0.952	1	0.535	0.487	0.586	INDETERMINATE	1	TRUE	2	0.334383076249392	4		617	1066	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013907-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	201	389	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.230412284151585	3	FACETS	1	0.971	1	0.727	0.674	0.782	CLONAL	2	TRUE	0	0.230412284151585	3		389	892	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935508	13935508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536563766	NA	P-0013907-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	37	317	1	ENST00000405192.2:c.1348G>A	p.Glu450Lys	p.E450K	ENST00000405192	NM_001163147.1	450	Gaa/Aaa	12/12	0.19772821776133	4	FACETS	0.664	0.546	0.796	0.332	0.273	0.398	SUBCLONAL	1	TRUE	2	0.230412284151585	4		318	595	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612028	189612028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs900140738	NA	P-0013907-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	40	464	0	ENST00000264731.3:c.1780C>T	p.Arg594Ter	p.R594*	ENST00000264731	NM_003722.4	594	Cga/Tga	14/14	0.230412284151585	3	FACETS	0.543	0.45	0.647	0.272	0.225	0.324	SUBCLONAL	1	TRUE	1	0.230412284151585	3		464	713	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578485	7578485	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1064793929	NA	P-0013907-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	181	543	0	ENST00000269305.4:c.445del	p.Ser149ProfsTer21	p.S149Pfs*21	ENST00000269305	NM_001126112.2	149	Tcc/cc	5/11	NA	2	FACETS	0.914	0.844	0.987			1	INDETERMINATE	2	TRUE	NA	0.230412284151585	2		543	859	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509060	106509060	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013907-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	53	506	0	ENST00000359195.3:c.1054G>A	p.Val352Met	p.V352M	ENST00000359195	NM_002649.2	352	Gtg/Atg	2/11	0.19772821776133	4	FACETS	0.648	0.551	0.755	0.324	0.275	0.378	SUBCLONAL	1	TRUE	2	0.230412284151585	4		506	874	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521733	89521733	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013907-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	43	497	0	ENST00000336596.2:c.2810A>T	p.Tyr937Phe	p.Y937F	ENST00000336596	NM_005233.5	937	tAc/tTc	16/17	0.230412284151585	3	FACETS	0.513	0.428	0.608	0.257	0.214	0.304	SUBCLONAL	1	TRUE	1	0.230412284151585	3		497	811	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521720	89521724	+	missense_variant	Missense_Mutation	ONP	ACGGG	ACGGG	CCGGT	novel	NA	P-0013907-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	49	550	0	ENST00000336596.2:c.2797_2801delinsCCGGT	p.Thr933_Gly934delinsProVal	p.T933_G934delinsPV	ENST00000336596	NM_005233.5	933	ACGGGt/CCGGTt	16/17	0.230412284151585	3	FACETS	0.548	0.463	0.643	0.274	0.231	0.322	SUBCLONAL	1	TRUE	1	0.230412284151585	3		550	865	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795275	42795276	+	missense_variant	Missense_Mutation	DNP	CC	CC	GT	novel	NA	P-0013933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	127	508	1	ENST00000575354.2:c.2355_2356delinsGT	p.Pro786Ser	p.P786S	ENST00000575354	NM_015125.3	785	gcCCct/gcGTct	10/20	0.437088453035512	4	FACETS	0.91	0.83	0.992			1	CLONAL	2	FALSE	NA	0.437088453035512	4		509	459	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035103	30035103	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	276	652	0	ENST00000338641.4:c.265G>T	p.Glu89Ter	p.E89*	ENST00000338641	NM_000268.3	89	Gaa/Taa	3/16	0.348988044114368	3	FACETS	1	0.991	1	0.829	0.785	0.873	CLONAL	2	FALSE	0	0.437088453035512	3		652	619	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013935-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	64	417	0	ENST00000397752.3:c.3028G>A	p.Asp1010Asn	p.D1010N	ENST00000397752	NM_000245.2	1010	Gat/Aat	14/21	1	2	FACETS	1	0.921	1	1	0.981	1	CLONAL	2	TRUE	1	0.1	2		417	586	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221989	1221989	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1085307466	NA	P-0013935-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	52	766	0	ENST00000326873.7:c.904C>T	p.Gln302Ter	p.Q302*	ENST00000326873	NM_000455.4	302	Cag/Tag	7/10	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.1	2		766	959	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149503	61149503	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013935-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	58	694	0	ENST00000295025.8:c.1693T>G	p.Ser565Ala	p.S565A	ENST00000295025	NM_002908.2	565	Tct/Gct	11/11	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.1	2		694	939	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587780070	NA	P-0013962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	26	394	0	ENST00000269305.4:c.535C>A	p.His179Asn	p.H179N	ENST00000269305	NM_001126112.2	179	Cat/Aat	5/11	1	2	FACETS	0.618	0.488	0.767	0.618	0.488	0.767	SUBCLONAL	1	TRUE	1	0.17	2		394	495	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247250	153247263	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCACTAACAACC	CTCCACTAACAACC	-	novel	NA	P-0013962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	72	614	0	ENST00000281708.4:c.1539_1552del	p.Arg513SerfsTer3	p.R513Sfs*3	ENST00000281708	NM_033632.3	513	agGGTTGTTAGTGGAGca/agca	10/12	1	2	FACETS	0.886	0.772	1	0.886	0.772	1	CLONAL	1	TRUE	1	0.17	2		614	956	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739843	41739843	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	119	440	1	ENST00000242208.4:c.130C>A	p.Pro44Thr	p.P44T	ENST00000242208	NM_002192.2	44	Cca/Aca	2/3	0.161170988410047	3	FACETS	1	0.983	1	0.735	0.662	0.812	CLONAL	1	TRUE	1	0.17	3		441	1034	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741391	145741391	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1205624933	NA	P-0013962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	56	724	1	ENST00000428558.2:c.1112G>C	p.Ser371Thr	p.S371T	ENST00000428558	NM_004260.3	371	aGc/aCc	5/22	1	2	FACETS	0.62	0.529	0.72	0.62	0.529	0.72	SUBCLONAL	1	TRUE	1	0.17	2		725	1062	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038830	47038830	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	26	272	0	ENST00000377604.3:c.837G>T	p.Gln279His	p.Q279H	ENST00000377604	NM_001204468.1	279	caG/caT	9/24	1	2	FACETS	1	0.838	1	1	0.838	1	CLONAL	1	TRUE	1	0.17	2		272	287	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441431	52441431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	63	821	1	ENST00000460680.1:c.421C>T	p.His141Tyr	p.H141Y	ENST00000460680	NM_004656.3	141	Cat/Tat	6/17	0.251039378377078	1	FACETS	0.854	0.74	0.978	0.854	0.74	0.978	CLONAL	1	FALSE	0	0.251039378377078	1		822	514	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089482	27089482	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	33	606	1	ENST00000324856.7:c.2438C>A	p.Pro813Gln	p.P813Q	ENST00000324856	NM_006015.4	813	cCa/cAa	8/20	1	2	FACETS	0.582	0.473	0.704	0.582	0.473	0.704	SUBCLONAL	1	FALSE	1	0.251039378377078	2		607	452	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47724973	47724973	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	72	829	0	ENST00000449228.1:c.771del	p.Leu258SerfsTer32	p.L258Sfs*32	ENST00000449228	NM_001127240.2	257	ttT/tt	4/4	1	2	FACETS	0.977	0.854	1	0.977	0.854	1	CLONAL	1	FALSE	1	0.251039378377078	2		829	587	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098975	178098975	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	36	419	0	ENST00000397062.3:c.70T>A	p.Trp24Arg	p.W24R	ENST00000397062	NM_006164.4	24	Tgg/Agg	2/5	1	2	FACETS	1	0.845	1	1	0.845	1	CLONAL	1	FALSE	1	0.251039378377078	2		419	280	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188215	10188215	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs869025642	NA	P-0013967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	64	702	0	ENST00000256474.2:c.358A>G	p.Arg120Gly	p.R120G	ENST00000256474	NM_000551.3	120	Aga/Gga	2/3	0.251039378377078	1	FACETS	0.943	0.818	1	0.943	0.818	1	CLONAL	1	FALSE	0	0.251039378377078	1		702	473	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47205343	47205343	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0013967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	44	641	0	ENST00000409792.3:c.71+1G>C		p.X24_splice	ENST00000409792	NM_014159.6	24			0.251039378377078	1	FACETS	0.733	0.616	0.863	0.733	0.616	0.863	SUBCLONAL	1	FALSE	0	0.251039378377078	1		641	418	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641083	117641083	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1455810428	NA	P-0013967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	31	829	0	ENST00000368508.3:c.5888C>G	p.Thr1963Arg	p.T1963R	ENST00000368508	NM_002944.2	1963	aCa/aGa	36/43	0.251039378377078	1	FACETS	0.428	0.345	0.521	0.428	0.345	0.521	SUBCLONAL	1	FALSE	0	0.251039378377078	1		829	505	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650270	48650270	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013967-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	47	338	0	ENST00000376670.3:c.240G>C	p.Leu80Phe	p.L80F	ENST00000376670	NM_002049.3	80	ttG/ttC	3/6	1	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	0	0.251039378377078	1		338	246	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0013975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	74	249	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	0.450262775954379	2		249	290	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0013975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	293	469	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.237699061660808	3	FACETS	1	0.986	1	0.743	0.704	0.783	INDETERMINATE	2	TRUE	0	0.450262775954379	3		469	715	SUCCESS
APC	324	MSKCC	GRCh37	5	112175513	112175513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	113	547	0	ENST00000257430.4:c.4222G>T	p.Glu1408Ter	p.E1408*	ENST00000257430	NM_000038.5	1408	Gaa/Taa	16/16	1	2	FACETS	0.893	0.806	0.984	0.893	0.806	0.984	CLONAL	1	TRUE	1	0.450262775954379	2		547	562	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221161	5221161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs575201235	NA	P-0013975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	98	634	1	ENST00000357368.4:c.3305G>A	p.Arg1102His	p.R1102H	ENST00000357368	NM_002850.3	1102	cGc/cAc	20/38	1	2	FACETS	0.789	0.705	0.877	0.789	0.705	0.877	SUBCLONAL	1	TRUE	1	0.450262775954379	2		635	552	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0013975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	142	506	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.450262775954379	2		506	523	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910854	114910854	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	333	1239	2	ENST00000543371.1:c.973C>T	p.Gln325Ter	p.Q325*	ENST00000543371	NM_001198531.1	325	Cag/Tag	9/14	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.450262775954379	2		1241	1441	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482377	56482377	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1272763651	NA	P-0013975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	78	816	0	ENST00000267101.3:c.925A>T	p.Lys309Ter	p.K309*	ENST00000267101	NM_001982.3	309	Aag/Tag	8/28	0.439572871559377	2	FACETS	0.414	0.363	0.47	0.207	0.181	0.235	SUBCLONAL	1	TRUE	0	0.450262775954379	2		816	836	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041708	42041708	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	130	1067	2	ENST00000219905.7:c.5903T>A	p.Met1968Lys	p.M1968K	ENST00000219905	NM_001164273.1	1968	aTg/aAg	17/24	0.439343929827923	1	FACETS	0.451	0.408	0.496	0.451	0.408	0.496	SUBCLONAL	1	TRUE	0	0.450262775954379	1		1069	992	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358654	67358656	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	novel	NA	P-0013975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	233	919	0	ENST00000327367.4:c.164_166del	p.Ile55del	p.I55del	ENST00000327367	NM_005902.3	54	gcCATc/gcc	1/9	0.439343929827923	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.450262775954379	1		919	692	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375020	45375020	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	72	465	0	ENST00000262160.6:c.823T>C	p.Cys275Arg	p.C275R	ENST00000262160	NM_005901.5	275	Tgt/Cgt	8/11	0.450262775954379	1	FACETS	0.829	0.731	0.932	0.829	0.731	0.932	CLONAL	1	TRUE	0	0.450262775954379	1		465	299	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274314	5274314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761620469	NA	P-0013975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	163	710	2	ENST00000357368.4:c.133G>A	p.Val45Met	p.V45M	ENST00000357368	NM_002850.3	45	Gtg/Atg	3/38	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.450262775954379	2		712	618	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101359	27101374	+	frameshift_variant	Frame_Shift_Del	DEL	CCATGGCACACGCCAG	CCATGGCACACGCCAG	-	novel	NA	P-0013983-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	51	682	0	ENST00000324856.7:c.4643_4658del	p.His1548ProfsTer12	p.H1548Pfs*12	ENST00000324856	NM_006015.4	1547	tcCCATGGCACACGCCAG/tc	18/20	1	2	FACETS	0.311	0.263	0.363	0.311	0.263	0.363	SUBCLONAL	1	TRUE	1	0.462022056138739	2		682	711	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151932987	151932987	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014011-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	37	55	0	ENST00000262189.6:c.2684G>C	p.Arg895Thr	p.R895T	ENST00000262189	NM_170606.2	895	aGa/aCa	16/59	1	2	FACETS	0.869	0.724	1	0.869	0.724	1	CLONAL	1	TRUE	1	0.417348972496525	2		55	204	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241678	55241681	+	protein_altering_variant	In_Frame_Del	DEL	AAAC	AAAC	G	novel	NA	P-0014011-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	176	480	0	ENST00000275493.2:c.2126_2129delinsG	p.Glu709_Thr710delinsGly	p.E709_T710delinsG	ENST00000275493	NM_005228.3	709	gAAACt/gGt	18/28	1	2	FACETS	0.874	0.805	0.946	0.874	0.805	0.946	CLONAL	1	TRUE	1	0.417348972496525	2		480	965	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0014018-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	124	472	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.32	2		473	734	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0014018-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	404	646	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.364331183474854	2	FACETS	0.895	0.855	0.936	1	0.995	1	CLONAL	3	TRUE	0	0.32	2		646	940	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144148	55144148	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519700	NA	P-0014018-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	96	420	0	ENST00000257290.5:c.1977C>G	p.Asn659Lys	p.N659K	ENST00000257290	NM_006206.4	659	aaC/aaG	14/23	1	2	FACETS	0.838	0.747	0.935	0.838	0.747	0.935	CLONAL	1	TRUE	1	0.32	2		420	716	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814303	76814306	+	frameshift_variant	Frame_Shift_Del	DEL	ATAA	ATAA	-	novel	NA	P-0014018-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	158	556	0	ENST00000373344.5:c.6338_6341del	p.Phe2113SerfsTer9	p.F2113Sfs*9	ENST00000373344	NM_000489.3	2113	tTTATc/tc	29/35	0.364331183474854	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.32	1		556	698	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696450	47696450	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014018-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	41	456	0	ENST00000347630.2:c.373T>G	p.Phe125Val	p.F125V	ENST00000347630	NM_001007230.1	125	Ttt/Gtt	6/11	0.11683833381695	0	FACETS	0.216	0.179	0.257			1	INDETERMINATE	1	TRUE	0	0.32	0		456	808	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176133018	176133018	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014018-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	108	379	0	ENST00000367669.3:c.575T>C	p.Leu192Pro	p.L192P	ENST00000367669	NM_022457.5	192	cTc/cCc	4/20	1	2	FACETS	0.835	0.749	0.927	0.835	0.749	0.927	CLONAL	1	TRUE	1	0.32	2		379	808	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831009	72831009	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014018-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	139	833	0	ENST00000268489.5:c.5572C>G	p.Leu1858Val	p.L1858V	ENST00000268489	NM_006885.3	1858	Ctc/Gtc	9/10	0.11683833381695	1	FACETS	0.617	0.56	0.677	0.617	0.56	0.677	INDETERMINATE	1	TRUE	0	0.32	1		833	1183	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46280018	46280018	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014018-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	67	705	0	ENST00000371998.3:c.3944A>G	p.Tyr1315Cys	p.Y1315C	ENST00000371998		1315	tAt/tGt	20/23	0.364331183474854	1	FACETS	0.335	0.29	0.385	0.335	0.29	0.385	SUBCLONAL	1	TRUE	0	0.32	1		705	1049	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0014033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	399	617	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.204269367232998	2	FACETS	0.917	0.874	0.961	0.917	0.874	0.961	INDETERMINATE	2	TRUE	0	0.392638770605115	2		617	1108	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	83	528	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.392638770605115	2		530	392	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528489	29528489	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764079291	NA	P-0014033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	140	692	0	ENST00000356175.3:c.1246C>T	p.Arg416Ter	p.R416*	ENST00000356175	NM_000267.3	416	Cga/Tga	11/57	0.204269367232998	2	FACETS	0.92	0.839	1	0.46	0.419	0.503	INDETERMINATE	1	TRUE	0	0.392638770605115	2		692	775	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951171	48951171	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587778846	NA	P-0014033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	93	472	1	ENST00000267163.4:c.1332+1G>A		p.X444_splice	ENST00000267163	NM_000321.2	444			0.392638770605115	1	FACETS	0.999	0.895	1	0.999	0.895	1	CLONAL	1	TRUE	0	0.392638770605115	1		473	381	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59861716	59861716	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	72	647	0	ENST00000259008.2:c.1543G>C	p.Glu515Gln	p.E515Q	ENST00000259008	NM_032043.2	515	Gaa/Caa	11/20	0.204269367232998	2	FACETS	0.452	0.394	0.515	0.226	0.197	0.258	INDETERMINATE	1	TRUE	0	0.392638770605115	2		647	811	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112633	115112633	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0014034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	165	313	0	ENST00000257566.3:c.1107T>A	p.Cys369Ter	p.C369*	ENST00000257566	NM_016569.3	369	tgT/tgA	7/8	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.573289120622695	2		313	530	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884120	37884120	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	504	1054	1	ENST00000269571.5:c.3591G>T	p.Leu1197Phe	p.L1197F	ENST00000269571		1197	ttG/ttT	27/27	0.573289120622695	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.573289120622695	1		1055	1179	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972798	25972798	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	381	702	1	ENST00000435504.4:c.1627G>T	p.Gly543Ter	p.G543*	ENST00000435504		543	Gga/Tga	12/13	0.573289120622695	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.573289120622695	1		703	878	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577590	7577592	+	missense_variant	Missense_Mutation	TNP	TGG	TGG	CGT	novel	NA	P-0014034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	233	575	0	ENST00000269305.4:c.689_691delinsACG	p.Thr230_Thr231delinsAsnAla	p.T230_T231delinsNA	ENST00000269305	NM_001126112.2	230	aCCAcc/aACGcc	7/11	0.573289120622695	1	FACETS	0.938	0.881	0.996	0.938	0.881	0.996	CLONAL	1	TRUE	0	0.573289120622695	1		575	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0014067-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	44	499	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	1	2	FACETS	0.733	0.616	0.861	0.733	0.616	0.861	SUBCLONAL	1	TRUE	1	0.324477491279265	2		499	370	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0014072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	841	425	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.670188021002954	3	FACETS	0.981	0.96	1	0.981	0.96	1	CLONAL	3	TRUE	0	0.670188021002954	3		425	1138	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540652	NA	P-0014072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	634	604	0	ENST00000269305.4:c.743G>C	p.Arg248Pro	p.R248P	ENST00000269305	NM_001126112.2	248	cGg/cCg	7/11	0.661813173334376	2	FACETS	0.967	0.94	0.994	0.967	0.94	0.994	CLONAL	2	TRUE	0	0.670188021002954	2		604	978	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877352	40877352	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	213	411	0	ENST00000373198.4:c.2344G>T	p.Gly782Cys	p.G782C	ENST00000373198	NM_133170.3	782	Ggc/Tgc	15/32	0.670188021002954	3	FACETS	1	0.962	1	0.525	0.488	0.562	CLONAL	1	TRUE	1	0.670188021002954	3		411	809	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244815	46244815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	841	850	0	ENST00000334344.6:c.2909C>T	p.Pro970Leu	p.P970L	ENST00000334344	NM_152641.2	970	cCa/cTa	15/21	NA	2	FACETS	0.974	0.95	0.998			1	INDETERMINATE	2	TRUE	NA	0.670188021002954	2		850	1288	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028377	42028377	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0014072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	550	492	0	ENST00000219905.7:c.3917-2A>T		p.X1306_splice	ENST00000219905	NM_001164273.1	1306			0.66574510641	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.670188021002954	2		492	817	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984504	72984504	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1291	449	828	1	ENST00000268489.5:c.3080G>A	p.Trp1027Ter	p.W1027*	ENST00000268489	NM_006885.3	1027	tGg/tAg	3/10	0.669972207312594	3	FACETS	1	0.972	1	0.514	0.489	0.539	CLONAL	1	TRUE	1	0.670188021002954	3		829	1740	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2199886	2199886	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	368	679	0	ENST00000398665.3:c.655G>T	p.Glu219Ter	p.E219*	ENST00000398665	NM_032482.2	219	Gag/Tag	8/28	0.66574510641	2	FACETS	1	0.965	1	0.51	0.484	0.536	CLONAL	1	TRUE	0	0.670188021002954	2		679	1077	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602767	10602767	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	683	593	0	ENST00000171111.5:c.811G>T	p.Val271Leu	p.V271L	ENST00000171111	NM_203500.1	271	Gtg/Ttg	3/6	0.66574510641	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.670188021002954	2		593	996	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265518	198265518	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	1811	585	2	ENST00000335508.6:c.2639G>T	p.Gly880Val	p.G880V	ENST00000335508	NM_012433.2	880	gGa/gTa	18/25	0.670188021002954	5	FACETS	0.996	0.984	1			1	CLONAL	5	TRUE	NA	0.670188021002954	5		587	2176	SUCCESS
ATR	545	MSKCC	GRCh37	3	142212140	142212140	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	215	415	0	ENST00000350721.4:c.5912A>T	p.Gln1971Leu	p.Q1971L	ENST00000350721	NM_001184.3	1971	cAg/cTg	35/47	1	2	FACETS	0.837	0.78	0.895	0.837	0.78	0.895	CLONAL	1	TRUE	1	0.670188021002954	2		415	767	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111579	56111579	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	166	206	2	ENST00000399503.3:c.179G>T	p.Arg60Leu	p.R60L	ENST00000399503	NM_005921.1	60	cGg/cTg	1/20	0.652936067724676	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.670188021002954	1		208	307	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225400	26225400	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2413	472	905	0	ENST00000360408.1:c.18G>C	p.Gln6His	p.Q6H	ENST00000360408	NM_003532.2	6	caG/caC	1/1	0.670188021002954	3	FACETS	0.652	0.619	0.685	0.217	0.206	0.229	SUBCLONAL	1	TRUE	0	0.670188021002954	3		905	2885	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680598	30680598	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	319	552	0	ENST00000376406.3:c.1121C>G	p.Ala374Gly	p.A374G	ENST00000376406	NM_014641.2	374	gCt/gGt	5/15	0.670188021002954	3	FACETS	1	0.95	1	0.336	0.316	0.356	CLONAL	1	TRUE	0	0.670188021002954	3		552	1262	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099802	157099802	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	621	504	0	ENST00000346085.5:c.739C>A	p.Arg247Ser	p.R247S	ENST00000346085	NM_020732.3	247	Cgc/Agc	1/20	0.670188021002954	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.670188021002954	3		504	1160	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080616	5080616	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	328	684	0	ENST00000381652.3:c.2367T>G	p.Asp789Glu	p.D789E	ENST00000381652	NM_004972.3	789	gaT/gaG	18/25	0.670188021002954	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.670188021002954	1		684	623	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87338624	87338624	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	270	584	0	ENST00000277120.3:c.720G>T	p.Met240Ile	p.M240I	ENST00000277120		240	atG/atT	7/19	0.670188021002954	3	FACETS	0.961	0.902	1	0.481	0.451	0.512	CLONAL	1	TRUE	1	0.670188021002954	3		584	1119	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089834	5089839	+	frameshift_variant	Frame_Shift_Del	DEL	TAAAGT	TAAAGT	G	novel	NA	P-0014072-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	240	517	0	ENST00000381652.3:c.2732_2737delinsG	p.Val911GlyfsTer12	p.V911Gfs*12	ENST00000381652	NM_004972.3	911	gTAAAGTac/gGac	20/25	0.670188021002954	1	FACETS	0.939	0.887	0.992	0.939	0.887	0.992	CLONAL	1	TRUE	0	0.670188021002954	1		517	507	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	46	661	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.130180922707854	0	FACETS	0.42	0.357	0.488			1	INDETERMINATE	1	FALSE	0	0.504627963896873	0		661	215	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	32	503	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	FALSE	1	0.504627963896873	2		503	97	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0014115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	138	556	2	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.504627963896873	2		558	490	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593477	48593477	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	120	444	0	ENST00000342988.3:c.1228C>T	p.Gln410Ter	p.Q410*	ENST00000342988	NM_005359.5	410	Cag/Tag	10/12	0.504627963896873	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	0	0.504627963896873	1		444	327	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46715735	46715735	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs530382665	NA	P-0014115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	144	655	0	ENST00000371975.4:c.154C>T	p.Arg52Trp	p.R52W	ENST00000371975	NM_003579.3	52	Cgg/Tgg	3/18	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.504627963896873	2		655	537	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141792	108141792	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs587779827	NA	P-0014115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	127	547	0	ENST00000278616.4:c.2840A>G	p.Tyr947Cys	p.Y947C	ENST00000278616	NM_000051.3	947	tAt/tGt	19/63	0.233313377858378	4	FACETS	1	0.984	1			1	INDETERMINATE	1	FALSE	NA	0.504627963896873	4		547	534	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492719	56492719	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	320	617	0	ENST00000407977.2:c.220G>T	p.Glu74Ter	p.E74*	ENST00000407977		74	Gaa/Taa	2/10	0.504627963896873	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	FALSE	0	0.504627963896873	2		617	594	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257856	198257856	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	149	636	0	ENST00000335508.6:c.3596T>G	p.Val1199Gly	p.V1199G	ENST00000335508	NM_012433.2	1199	gTt/gGt	24/25	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.504627963896873	2		636	452	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933888	39933892	+	frameshift_variant	Frame_Shift_Del	DEL	GACTG	GACTG	-	novel	NA	P-0014115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	318	721	0	ENST00000378444.4:c.707_711del	p.Pro236LeufsTer63	p.P236Lfs*63	ENST00000378444	NM_001123385.1	236	cCAGTC/c	4/15	1	2	FACETS	0.953	0.898	1	0.953	0.898	1	CLONAL	1	FALSE	1	0.504627963896873	2		721	1323	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041648	47041648	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	273	627	0	ENST00000377604.3:c.1873G>T	p.Gly625Ter	p.G625*	ENST00000377604	NM_001204468.1	625	Gga/Tga	17/24	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.504627963896873	2		627	990	SUCCESS
AR	367	MSKCC	GRCh37	X	66943658	66943658	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	103	767	0	ENST00000374690.3:c.2738A>G	p.Lys913Arg	p.K913R	ENST00000374690	NM_000044.3	913	aAg/aGg	8/8	0.33074941732601	0	FACETS	0.523	0.471	0.576			1	SUBCLONAL	1	FALSE	0	0.504627963896873	0		767	387	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0014120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1621	120	474	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.242029521803836	17	FACETS	0.802	0.721	0.888			1	CLONAL	2	TRUE	NA	0.242029521803836	17		474	1741	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865275	57865275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	198	982	3	ENST00000228682.2:c.2752G>A	p.Ala918Thr	p.A918T	ENST00000228682	NM_005269.2	918	Gcc/Acc	12/12	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.242029521803836	2		985	1125	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023142	33023142	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	52	905	0	ENST00000300177.4:c.251C>A	p.Thr84Lys	p.T84K	ENST00000300177	NM_001191322.1	84	aCg/aAg	2/2	1	2	FACETS	0.477	0.405	0.557	0.477	0.405	0.557	SUBCLONAL	1	TRUE	1	0.242029521803836	2		905	900	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964880	15964880	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	53	753	0	ENST00000268712.3:c.5716G>T	p.Asp1906Tyr	p.D1906Y	ENST00000268712	NM_006311.3	1906	Gat/Tat	37/46	1	2	FACETS	0.477	0.405	0.556	0.477	0.405	0.556	SUBCLONAL	1	TRUE	1	0.242029521803836	2		753	918	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089021	37089038	+	inframe_deletion	In_Frame_Del	DEL	GCTCTTTGACCTTGCCAT	GCTCTTTGACCTTGCCAT	-	novel	NA	P-0014120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	31	396	0	ENST00000231790.2:c.1746_1763del	p.Phe583_Leu588del	p.F583_L588del	ENST00000231790	NM_000249.3	581	ccGCTCTTTGACCTTGCCATg/ccg	16/19	1	2	FACETS	0.529	0.427	0.645	0.529	0.427	0.645	SUBCLONAL	1	TRUE	1	0.242029521803836	2		396	484	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0014123-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	51	371	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	NA	2	FACETS	0.763	0.649	0.887			1	INDETERMINATE	1	TRUE	NA	0.293985712137973	2		371	455	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685308	89685308	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876660634	NA	P-0014123-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	36	310	0	ENST00000371953.3:c.203A>G	p.Tyr68Cys	p.Y68C	ENST00000371953	NM_000314.4	68	tAc/tGc	3/9	0.265639436222098	1	FACETS	0.92	0.762	1	0.92	0.762	1	CLONAL	1	TRUE	0	0.293985712137973	1		310	227	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0014127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	250	519	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.44573283554991	3	FACETS	0.92	0.871	0.969	0.92	0.871	0.969	CLONAL	3	TRUE	0	0.44573283554991	3		519	497	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971187	21971197	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGCTGCCCA	GGCGCTGCCCA	-	novel	NA	P-0014127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	62	156	0	ENST00000304494.5:c.161_171del	p.Met54ThrfsTer62	p.M54Tfs*62	ENST00000304494	NM_000077.4	54	aTGGGCAGCGCC/a	2/3	0.191574160276449	5	FACETS	0.938	0.828	1			1	INDETERMINATE	3	TRUE	NA	0.44573283554991	5		156	165	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242475	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAG	TTAAGAG	C	novel	NA	P-0014127-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	188	503	0	ENST00000275493.2:c.2239_2245delinsC	p.Leu747_Glu749delinsGln	p.L747_E749delinsQ	ENST00000275493	NM_005228.3	747	TTAAGAGaa/Caa	19/28	0.422301333492437	4	FACETS	0.921	0.855	0.989	0.921	0.855	0.989	CLONAL	2	TRUE	2	0.44573283554991	4		503	662	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	30	528	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.814	1	1	0.814	1	CLONAL	1	TRUE	1	0.15	2		530	396	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469672	NA	P-0014131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	62	379	0	ENST00000374080.3:c.131G>A	p.Gly44Asp	p.G44D	ENST00000374080		44	gGt/gAt	2/45	1	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.15	1		379	622	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294313	11294313	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	42	441	0	ENST00000361445.4:c.2218G>C	p.Glu740Gln	p.E740Q	ENST00000361445	NM_004958.3	740	Gag/Cag	14/58	1	2	FACETS	0.73	0.608	0.867	0.73	0.608	0.867	SUBCLONAL	1	TRUE	1	0.15	2		441	767	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821455	72821455	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1418	106	998	1	ENST00000268489.5:c.10720C>T	p.His3574Tyr	p.H3574Y	ENST00000268489	NM_006885.3	3574	Cac/Tac	10/10	1	2	FACETS	0.927	0.828	1	0.927	0.828	1	CLONAL	1	TRUE	1	0.15	2		999	1524	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929235	44929235	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	67	476	0	ENST00000377967.4:c.2335C>T	p.Gln779Ter	p.Q779*	ENST00000377967	NM_021140.2	779	Cag/Tag	17/29	1	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.15	1		476	705	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0014135-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	132	537	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	1	2	FACETS	0.502	0.454	0.552	0.502	0.454	0.552	SUBCLONAL	1	TRUE	1	0.48	2		537	1096	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0014135-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	85	427	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	1	2	FACETS	0.444	0.392	0.5	0.444	0.392	0.5	SUBCLONAL	1	TRUE	1	0.48	2		427	798	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0014135-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	112	486	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.543	0.487	0.601	0.543	0.487	0.601	SUBCLONAL	1	TRUE	1	0.48	2		486	860	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0014135-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	102	426	1	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	1	2	FACETS	0.457	0.408	0.509	0.457	0.408	0.509	SUBCLONAL	1	TRUE	1	0.48	2		427	930	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777072	9777072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014135-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	100	703	0	ENST00000377346.4:c.836C>T	p.Ser279Phe	p.S279F	ENST00000377346	NM_005026.3	279	tCc/tTc	7/24	1	2	FACETS	0.415	0.37	0.464	0.415	0.37	0.464	SUBCLONAL	1	TRUE	1	0.48	2		703	1003	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190830	11190830	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014135-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	62	225	0	ENST00000361445.4:c.5369G>T	p.Trp1790Leu	p.W1790L	ENST00000361445	NM_004958.3	1790	tGg/tTg	39/58	1	2	FACETS	0.671	0.582	0.767	0.671	0.582	0.767	SUBCLONAL	1	TRUE	1	0.48	2		225	385	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333461	70333461	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014135-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	103	460	0	ENST00000373644.4:c.1366G>T	p.Val456Phe	p.V456F	ENST00000373644	NM_030625.2	456	Gtc/Ttc	2/12	1	2	FACETS	0.51	0.456	0.567	0.51	0.456	0.567	SUBCLONAL	1	TRUE	1	0.48	2		460	842	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125513719	125513719	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014135-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	157	650	1	ENST00000428830.2:c.847G>T	p.Val283Leu	p.V283L	ENST00000428830	NM_001114121.2	283	Gtg/Ttg	9/14	1	2	FACETS	0.511	0.467	0.558	0.511	0.467	0.558	SUBCLONAL	1	TRUE	1	0.48	2		651	1280	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022880	12022880	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014135-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	87	549	0	ENST00000396373.4:c.986C>G	p.Ala329Gly	p.A329G	ENST00000396373	NM_001987.4	329	gCc/gGc	5/8	1	2	FACETS	0.414	0.366	0.466	0.414	0.366	0.466	SUBCLONAL	1	TRUE	1	0.48	2		549	875	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63545762	63545762	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014135-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	104	481	0	ENST00000307078.5:c.832G>T	p.Asp278Tyr	p.D278Y	ENST00000307078	NM_004655.3	278	Gat/Tat	3/11	1	2	FACETS	0.52	0.465	0.578	0.52	0.465	0.578	SUBCLONAL	1	TRUE	1	0.48	2		481	834	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295720	212295720	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014135-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	94	505	0	ENST00000342788.4:c.2593G>T	p.Ala865Ser	p.A865S	ENST00000342788	NM_005235.2	865	Gcc/Tcc	21/28	1	2	FACETS	0.394	0.349	0.441	0.394	0.349	0.441	SUBCLONAL	1	TRUE	1	0.48	2		505	995	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21272358	21272358	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014135-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	115	737	0	ENST00000354336.3:c.136G>A	p.Gly46Arg	p.G46R	ENST00000354336	NM_005207.3	46	Ggg/Agg	1/3	0.18369626020033	3	FACETS	0.476	0.427	0.528	0.238	0.213	0.264	INDETERMINATE	1	TRUE	1	0.48	3		737	1249	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280139	142280139	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014135-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	137	580	0	ENST00000350721.4:c.1295G>C	p.Arg432Pro	p.R432P	ENST00000350721	NM_001184.3	432	cGt/cCt	5/47	1	2	FACETS	0.471	0.427	0.517	0.471	0.427	0.517	SUBCLONAL	1	TRUE	1	0.48	2		580	1212	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182681734	182681734	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014135-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	104	441	0	ENST00000292782.4:c.324G>T	p.Lys108Asn	p.K108N	ENST00000292782	NM_020640.2	108	aaG/aaT	3/7	1	2	FACETS	0.469	0.42	0.523	0.469	0.42	0.523	SUBCLONAL	1	TRUE	1	0.48	2		441	923	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501517	149501517	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014135-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	123	633	0	ENST00000261799.4:c.2270T>C	p.Met757Thr	p.M757T	ENST00000261799	NM_002609.3	757	aTg/aCg	16/23	1	2	FACETS	0.434	0.391	0.479	0.434	0.391	0.479	SUBCLONAL	1	TRUE	1	0.48	2		633	1182	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265377	152265377	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014135-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	90	506	0	ENST00000206249.3:c.830G>T	p.Arg277Met	p.R277M	ENST00000206249	NM_000125.3	277	aGg/aTg	4/8	1	2	FACETS	0.437	0.387	0.49	0.437	0.387	0.49	SUBCLONAL	1	TRUE	1	0.48	2		506	859	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729321	41729321	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014135-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1282	161	857	0	ENST00000242208.4:c.1208A>G	p.Tyr403Cys	p.Y403C	ENST00000242208	NM_002192.2	403	tAc/tGc	3/3	1	2	FACETS	0.465	0.425	0.507	0.465	0.425	0.507	SUBCLONAL	1	TRUE	1	0.48	2		857	1443	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763842	76763843	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0014135-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	125	657	0	ENST00000373344.5:c.7465_7466delinsTT	p.Gly2489Leu	p.G2489L	ENST00000373344	NM_000489.3	2489	GGg/TTg	35/35	1	2	FACETS	0.447	0.403	0.493	0.447	0.403	0.493	SUBCLONAL	1	TRUE	1	0.48	2		657	1166	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195644	123195644	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014135-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	105	490	0	ENST00000218089.9:c.1558G>T	p.Ala520Ser	p.A520S	ENST00000218089	NM_001042749.1	520	Gct/Tct	17/35	0.0763880301791824	3	FACETS	0.444	0.396	0.495			1	INDETERMINATE	1	TRUE	NA	0.48	3		490	1222	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	498	503	0				ENST00000310581	NM_198253.2	-/1132			0.3	7	FACETS	1	0.988	1	1	0.997	1	CLONAL	8	TRUE	1	0.19	7		503	913	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	31	437	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	0.563	0.454	0.686	0.563	0.454	0.686	SUBCLONAL	1	TRUE	1	0.19	2		437	580	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	145	367	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.3	4	FACETS	0.915	0.841	0.992			1	CLONAL	4	TRUE	NA	0.19	4		367	496	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560935	9560935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145132727	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	50	590	1	ENST00000353224.5:c.847C>T	p.Arg283Trp	p.R283W	ENST00000353224	NM_177990.2	283	Cgg/Tgg	4/10	1	2	FACETS	0.595	0.503	0.697	0.595	0.503	0.697	SUBCLONAL	1	TRUE	1	0.19	2		591	884	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610098	28610098	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	101	692	0	ENST00000241453.7:c.1392G>A	p.Trp464Ter	p.W464*	ENST00000241453	NM_004119.2	464	tgG/tgA	11/24	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.19	2		692	955	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992907	72992907	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1230	66	955	0	ENST00000268489.5:c.1138C>T	p.Pro380Ser	p.P380S	ENST00000268489	NM_006885.3	380	Cca/Tca	2/10	1	2	FACETS	0.536	0.463	0.616	0.536	0.463	0.616	SUBCLONAL	1	TRUE	1	0.19	2		955	1296	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383226	31383226	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs376213530	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	49	546	1	ENST00000328111.2:c.1138C>T	p.Arg380Ter	p.R380*	ENST00000328111	NM_006892.3	380	Cga/Tga	11/23	1	2	FACETS	0.6	0.506	0.703	0.6	0.506	0.703	SUBCLONAL	1	TRUE	1	0.19	2		547	860	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513339	44513339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	42	435	0	ENST00000291552.4:c.596C>T	p.Ser199Phe	p.S199F	ENST00000291552	NM_006758.2	199	tCc/tTc	8/8	1	2	FACETS	0.547	0.455	0.65	0.547	0.455	0.65	SUBCLONAL	1	TRUE	1	0.19	2		435	808	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101205	27101205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773031590	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	42	646	0	ENST00000324856.7:c.4487C>T	p.Thr1496Ile	p.T1496I	ENST00000324856	NM_006015.4	1496	aCc/aTc	18/20	1	2	FACETS	0.596	0.496	0.707	0.596	0.496	0.707	SUBCLONAL	1	TRUE	1	0.19	2		646	742	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259685	16259685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768625321	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	48	516	0	ENST00000375759.3:c.6950G>A	p.Gly2317Glu	p.G2317E	ENST00000375759	NM_015001.2	2317	gGg/gAg	11/15	1	2	FACETS	0.658	0.555	0.772	0.658	0.555	0.772	SUBCLONAL	1	TRUE	1	0.19	2		516	768	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468276	120468276	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	27	320	2	ENST00000256646.2:c.4163G>A	p.Ser1388Asn	p.S1388N	ENST00000256646	NM_024408.3	1388	aGc/aAc	25/34	1	2	FACETS	0.697	0.554	0.86	0.697	0.554	0.86	SUBCLONAL	1	TRUE	1	0.19	2		322	408	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132884	64132884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1173	69	873	0	ENST00000334205.4:c.1018C>T	p.Pro340Ser	p.P340S	ENST00000334205	NM_003942.2	340	Cct/Tct	9/17	1	2	FACETS	0.585	0.507	0.669	0.585	0.507	0.669	SUBCLONAL	1	TRUE	1	0.19	2		873	1242	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153564	108153564	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	21	388	0	ENST00000278616.4:c.3704C>T	p.Pro1235Leu	p.P1235L	ENST00000278616	NM_000051.3	1235	cCt/cTt	25/63	1	2	FACETS	0.632	0.486	0.802	0.632	0.486	0.802	SUBCLONAL	1	TRUE	1	0.19	2		388	350	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224608	108224608	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs17174393	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	28	380	0	ENST00000278616.4:c.8786+1G>A		p.X2929_splice	ENST00000278616	NM_000051.3	2929			1	2	FACETS	0.733	0.586	0.901	0.733	0.586	0.901	CLONAL	1	TRUE	1	0.19	2		380	402	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427510	427510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755894154	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	43	610	0	ENST00000399788.2:c.2659G>A	p.Glu887Lys	p.E887K	ENST00000399788	NM_001042603.1	887	Gaa/Aaa	19/28	1	2	FACETS	0.566	0.472	0.671	0.566	0.472	0.671	SUBCLONAL	1	TRUE	1	0.19	2		610	799	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859650	57859650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1478	87	1028	0	ENST00000228682.2:c.704C>T	p.Thr235Ile	p.T235I	ENST00000228682	NM_005269.2	235	aCt/aTt	7/12	1	2	FACETS	0.585	0.516	0.66	0.585	0.516	0.66	SUBCLONAL	1	TRUE	1	0.19	2		1028	1565	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060937	38060937	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	23	398	0	ENST00000250448.2:c.1052C>T	p.Thr351Ile	p.T351I	ENST00000250448	NM_004496.3	351	aCt/aTt	2/2	1	2	FACETS	0.63	0.491	0.792	0.63	0.491	0.792	SUBCLONAL	1	TRUE	1	0.19	2		398	384	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353757	68353757	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	15	246	0	ENST00000487270.1:c.592G>A	p.Glu198Lys	p.E198K	ENST00000487270	NM_133509.3	198	Gaa/Aaa	7/11	1	2	FACETS	0.734	0.538	0.97	0.734	0.538	0.97	CLONAL	1	TRUE	1	0.19	2		246	215	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241316	105241316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	50	720	3	ENST00000349310.3:c.592G>A	p.Glu198Lys	p.E198K	ENST00000349310	NM_001014432.1	198	Gag/Aag	8/15	1	2	FACETS	0.57	0.482	0.668	0.57	0.482	0.668	SUBCLONAL	1	TRUE	1	0.19	2		723	923	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396373	396373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	55	727	0	ENST00000262320.3:c.653C>T	p.Pro218Leu	p.P218L	ENST00000262320	NM_003502.3	218	cCc/cTc	2/11	0.0968381321705811	3	FACETS	0.636	0.542	0.739			1	INDETERMINATE	1	TRUE	NA	0.19	3		727	997	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134383	2134383	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	96	675	0	ENST00000219476.3:c.4160C>T	p.Ser1387Phe	p.S1387F	ENST00000219476	NM_000548.3	1387	tCc/tTc	34/42	0.0968381321705811	3	FACETS	0.965	0.857	1			1	INDETERMINATE	1	TRUE	NA	0.19	3		675	1147	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029575	14029575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	13	148	0	ENST00000311895.7:c.1786G>A	p.Ala596Thr	p.A596T	ENST00000311895	NM_005236.2	596	Gcg/Acg	8/11	0.0968381321705811	3	FACETS	0.735	0.524	0.99			1	INDETERMINATE	1	TRUE	NA	0.19	3		148	204	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81892759	81892759	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	52	694	0	ENST00000359376.3:c.470G>A	p.Arg157Lys	p.R157K	ENST00000359376	NM_002661.3	157	aGa/aAa	5/33	1	2	FACETS	0.695	0.59	0.81	0.695	0.59	0.81	SUBCLONAL	1	TRUE	1	0.19	2		694	788	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441540	40441540	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	65	1022	1	ENST00000345506.4:c.111G>A	p.Trp37Ter	p.W37*	ENST00000345506	NM_003152.3	37	tgG/tgA	3/20	1	2	FACETS	0.544	0.469	0.625	0.544	0.469	0.625	SUBCLONAL	1	TRUE	1	0.19	2		1023	1258	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40486033	40486033	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555566945	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	105	951	2	ENST00000264657.5:c.832C>T	p.Arg278Cys	p.R278C	ENST00000264657	NM_139276.2	278	Cgt/Tgt	9/24	1	2	FACETS	0.96	0.858	1	0.96	0.858	1	CLONAL	1	TRUE	1	0.19	2		953	1151	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867322	45867322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	25	321	0	ENST00000391945.4:c.871G>A	p.Gly291Arg	p.G291R	ENST00000391945	NM_000400.3	291	Ggg/Agg	10/23	0.176071012366724	3	FACETS	0.635	0.499	0.791	0.317	0.249	0.396	SUBCLONAL	1	TRUE	1	0.19	3		321	454	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714724	52714724	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs557584612	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	38	452	0	ENST00000322088.6:c.482C>T	p.Ala161Val	p.A161V	ENST00000322088	NM_014225.5	161	gCt/gTt	4/15	0.176071012366724	3	FACETS	0.618	0.509	0.74	0.309	0.254	0.37	SUBCLONAL	1	TRUE	1	0.19	3		452	709	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973028	25973028	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	46	565	0	ENST00000435504.4:c.1397C>T	p.Ser466Phe	p.S466F	ENST00000435504		466	tCc/tTc	12/13	1	2	FACETS	0.645	0.541	0.759	0.645	0.541	0.759	SUBCLONAL	1	TRUE	1	0.19	2		565	751	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150009	202150009	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	63	535	0	ENST00000358485.4:c.1450C>T	p.Leu484Phe	p.L484F	ENST00000358485	NM_001080125.1	484	Ctt/Ttt	8/9	1	2	FACETS	0.713	0.615	0.82	0.713	0.615	0.82	SUBCLONAL	1	TRUE	1	0.19	2		535	930	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437140	220437140	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs892484650	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1379	222	1006	0	ENST00000243786.2:c.44G>A	p.Gly15Asp	p.G15D	ENST00000243786	NM_002191.3	15	gGt/gAt	1/2	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.19	2		1006	1601	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386279	31386279	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	80	617	0	ENST00000328111.2:c.1504G>A	p.Glu502Lys	p.E502K	ENST00000328111	NM_006892.3	502	Gag/Aag	15/23	1	2	FACETS	0.965	0.848	1	0.965	0.848	1	CLONAL	1	TRUE	1	0.19	2		617	873	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180238	38180238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	52	686	0	ENST00000396334.3:c.86C>T	p.Ser29Phe	p.S29F	ENST00000396334	NM_002468.4	29	tCc/tTc	1/5	1	2	FACETS	0.666	0.565	0.777	0.666	0.565	0.777	SUBCLONAL	1	TRUE	1	0.19	2		686	822	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204692	128204692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756555004	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	60	869	0	ENST00000341105.2:c.749C>T	p.Pro250Leu	p.P250L	ENST00000341105	NM_032638.4	250	cCc/cTc	3/6	1	2	FACETS	0.646	0.555	0.747	0.646	0.555	0.747	SUBCLONAL	1	TRUE	1	0.19	2		869	977	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808322	99808322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	17	360	0	ENST00000280892.6:c.367G>A	p.Glu123Lys	p.E123K	ENST00000280892	NM_001130678.1	123	Gaa/Aaa	5/7	1	2	FACETS	0.544	0.405	0.709	0.544	0.405	0.709	SUBCLONAL	1	TRUE	1	0.19	2		360	329	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1268704	1268704	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1282	93	558	0	ENST00000310581.5:c.2513C>T	p.Ser838Phe	p.S838F	ENST00000310581	NM_198253.2	838	tCc/tTc	9/16	0.3	7	FACETS	1	0.921	1	0.175	0.155	0.197	CLONAL	1	TRUE	1	0.19	7		558	1375	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279566	1279566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	87	515	1	ENST00000310581.5:c.1970G>A	p.Arg657Lys	p.R657K	ENST00000310581	NM_198253.2	657	aGg/aAg	5/16	0.3	7	FACETS	1	0.953	1	0.193	0.17	0.218	CLONAL	1	TRUE	1	0.19	7		516	1164	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672338	30672338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	68	750	0	ENST00000376406.3:c.4622C>T	p.Thr1541Ile	p.T1541I	ENST00000376406	NM_014641.2	1541	aCc/aTc	10/15	1	2	FACETS	0.615	0.533	0.704	0.615	0.533	0.704	SUBCLONAL	1	TRUE	1	0.19	2		750	1164	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673217	30673217	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1482929280	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	56	644	0	ENST00000376406.3:c.3743C>T	p.Pro1248Leu	p.P1248L	ENST00000376406	NM_014641.2	1248	cCt/cTt	10/15	1	2	FACETS	0.741	0.634	0.86	0.741	0.634	0.86	SUBCLONAL	1	TRUE	1	0.19	2		644	795	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704559	117704559	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	41	716	0	ENST00000368508.3:c.2417T>C	p.Leu806Pro	p.L806P	ENST00000368508	NM_002944.2	806	cTc/cCc	16/43	0.163448920852187	0	FACETS	0.474	0.393	0.564			1	SUBCLONAL	1	TRUE	0	0.19	0		716	738	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441965	6441965	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	43	381	0	ENST00000356142.4:c.524A>G	p.Glu175Gly	p.E175G	ENST00000356142	NM_018890.3	175	gAg/gGg	7/7	1	2	FACETS	0.647	0.54	0.766	0.647	0.54	0.766	SUBCLONAL	1	TRUE	1	0.19	2		381	700	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851543	128851543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	52	660	0	ENST00000249373.3:c.1868C>T	p.Thr623Ile	p.T623I	ENST00000249373	NM_005631.4	623	aCc/aTc	11/12	0.3	4	FACETS	0.631	0.535	0.737			1	SUBCLONAL	1	TRUE	NA	0.19	4		660	1032	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515025	148515025	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1399	101	819	0	ENST00000320356.2:c.1184G>A	p.Gly395Glu	p.G395E	ENST00000320356	NM_004456.4	395	gGa/gAa	10/20	0.3	4	FACETS	0.843	0.751	0.943			1	CLONAL	1	TRUE	NA	0.19	4		819	1500	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132784	152132784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1461694611	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	51	593	1	ENST00000262189.6:c.88G>A	p.Ala30Thr	p.A30T	ENST00000262189	NM_170606.2	30	Gca/Aca	1/59	0.176071012366724	3	FACETS	0.577	0.489	0.675	0.289	0.244	0.338	SUBCLONAL	1	TRUE	1	0.19	3		594	1018	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38314994	38314994	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	48	555	0	ENST00000425967.3:c.70T>A	p.Leu24Met	p.L24M	ENST00000425967	NM_001174067.1	24	Ttg/Atg	3/19	1	2	FACETS	0.677	0.571	0.795	0.677	0.571	0.795	SUBCLONAL	1	TRUE	1	0.19	2		555	746	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741797	145741797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	67	579	0	ENST00000428558.2:c.706G>A	p.Gly236Ser	p.G236S	ENST00000428558	NM_004260.3	236	Ggc/Agc	5/22	1	2	FACETS	0.852	0.739	0.975	0.852	0.739	0.975	CLONAL	1	TRUE	1	0.19	2		579	828	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98009794	98009794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	22	461	0	ENST00000289081.3:c.170C>T	p.Ser57Phe	p.S57F	ENST00000289081	NM_000136.2	57	tCt/tTt	3/15	1	2	FACETS	0.728	0.564	0.918	0.728	0.564	0.918	CLONAL	1	TRUE	1	0.19	2		461	318	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250061	110250061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs894715743	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	36	363	1	ENST00000374672.4:c.614G>A	p.Arg205Gln	p.R205Q	ENST00000374672	NM_004235.4	205	cGg/cAg	3/5	1	2	FACETS	0.865	0.711	1	0.865	0.711	1	CLONAL	1	TRUE	1	0.19	2		364	438	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349969	70349969	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	83	783	0	ENST00000374080.3:c.3952C>T	p.Gln1318Ter	p.Q1318*	ENST00000374080		1318	Cag/Tag	28/45	1	2	FACETS	0.738	0.649	0.834	0.738	0.649	0.834	SUBCLONAL	1	TRUE	1	0.19	2		783	1184	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	191	389	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.301553518211253	3	FACETS	0.98	0.91	1	0.98	0.91	1	CLONAL	2	TRUE	1	0.36	3		389	639	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405575	70405575	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs762819840	NA	P-0014153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	93	392	0	ENST00000373644.4:c.3089A>G	p.Asn1030Ser	p.N1030S	ENST00000373644	NM_030625.2	1030	aAt/aGt	4/12	1	2	FACETS	0.984	0.878	1	0.984	0.878	1	CLONAL	1	TRUE	1	0.36	2		392	525	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420123	49420123	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	306	608	0	ENST00000301067.7:c.15626G>A	p.Gly5209Asp	p.G5209D	ENST00000301067	NM_003482.3	5209	gGc/gAc	48/54	0.301553518211253	3	FACETS	0.869	0.819	0.92	0.869	0.819	0.92	CLONAL	2	TRUE	1	0.36	3		608	1154	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207615	2207615	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	270	919	0	ENST00000398665.3:c.899A>T	p.Lys300Met	p.K300M	ENST00000398665	NM_032482.2	300	aAg/aTg	11/28	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.36	2		919	1438	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	865	389	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.592990593354492	4	FACETS	1	0.977	1			1	CLONAL	3	TRUE	NA	0.660313877449996	4		389	1445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578538	7578538	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1131691037	NA	P-0014158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	298	558	0	ENST00000269305.4:c.392A>T	p.Asn131Ile	p.N131I	ENST00000269305	NM_001126112.2	131	aAc/aTc	5/11	0.660313877449996	1	FACETS	0.983	0.935	1	0.983	0.935	1	CLONAL	1	TRUE	0	0.660313877449996	1		558	615	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11193154	11193154	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	309	643	0	ENST00000361445.4:c.5347G>T	p.Asp1783Tyr	p.D1783Y	ENST00000361445	NM_004958.3	1783	Gac/Tac	38/58	1	2	FACETS	0.961	0.908	1	0.961	0.908	1	CLONAL	1	TRUE	1	0.660313877449996	2		643	974	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035054	42035055	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0014158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	637	1210	0	ENST00000219905.7:c.4897_4898del	p.Thr1633HisfsTer6	p.T1633Hfs*6	ENST00000219905	NM_001164273.1	1632	gcCAcc/gccc	15/24	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.660313877449996	2		1210	1845	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202274	138202274	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	272	474	1	ENST00000237289.4:c.2191G>T	p.Glu731Ter	p.E731*	ENST00000237289	NM_001270507.1	731	Gag/Tag	9/9	0.660313877449996	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.660313877449996	1		475	538	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593605	55593610	+	inframe_deletion	In_Frame_Del	DEL	GAAGGT	GAAGGT	-	novel	NA	P-0014165-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	381	699	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	0.876	0.962	0.919	0.876	0.962	CLONAL	1	TRUE	1	0.890596981470377	2		699	931	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	580	661	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.526513039481546	5	FACETS	1	0.99	1			1	CLONAL	4	TRUE	NA	0.526513039481546	5		661	937	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522568	106522568	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs754441790	NA	P-0014188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	186	337	0	ENST00000359195.3:c.2545C>T	p.Arg849Ter	p.R849*	ENST00000359195	NM_002649.2	849	Cga/Tga	7/11	0.526513039481546	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.526513039481546	3		337	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578453	7578453	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	568	985	0	ENST00000269305.4:c.477del	p.Met160TrpfsTer10	p.M160Wfs*10	ENST00000269305	NM_001126112.2	159	gcC/gc	5/11	0.52017123461136	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.526513039481546	2		985	1068	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685330	86685330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	10	124	0	ENST00000274376.6:c.3046C>T	p.Arg1016Cys	p.R1016C	ENST00000274376	NM_002890.2	1016	Cgt/Tgt	24/25	0.381886203993056	3	FACETS	0.587	0.403	0.811	0.294	0.201	0.406	SUBCLONAL	1	TRUE	1	0.577317498472202	3		124	76	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599321	55599321	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913507	NA	P-0014198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	239	566	0	ENST00000288135.5:c.2447A>T	p.Asp816Val	p.D816V	ENST00000288135	NM_000222.2	816	gAc/gTc	17/21	0.577317498472202	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.577317498472202	2		566	358	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155766	119155766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219382952	NA	P-0014198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	29	784	0	ENST00000264033.4:c.1519G>A	p.Val507Ile	p.V507I	ENST00000264033	NM_005188.3	507	Gta/Ata	10/16	1	2	FACETS	0.343	0.276	0.419	0.343	0.276	0.419	SUBCLONAL	1	TRUE	1	0.577317498472202	2		784	293	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186808	11186808	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	16	548	0	ENST00000361445.4:c.6397T>C	p.Cys2133Arg	p.C2133R	ENST00000361445	NM_004958.3	2133	Tgc/Cgc	46/58	0.577317498472202	1	FACETS	0.236	0.175	0.308	0.236	0.175	0.308	SUBCLONAL	1	TRUE	0	0.577317498472202	1		548	167	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57569934	57569934	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	31	334	0	ENST00000316660.6:c.115del	p.Arg39GlyfsTer5	p.R39Gfs*5	ENST00000316660	NM_021127.2	38	ttC/tt	2/2	0.577317498472202	3	FACETS	0.373	0.302	0.454	0.187	0.151	0.227	SUBCLONAL	1	TRUE	1	0.577317498472202	3		334	371	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0014201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	489	907	3	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.439740756549255	2	FACETS	0.95	0.911	0.989	0.95	0.911	0.989	CLONAL	2	TRUE	0	0.448025644992784	2		910	1149	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161326496	161326496	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs144532303	NA	P-0014201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	652	1138	0	ENST00000367975.2:c.271T>G	p.Leu91Val	p.L91V	ENST00000367975	NM_003001.3	91	Tta/Gta	5/6	0.225748465903049	3	FACETS	0.987	0.95	1	0.987	0.95	1	INDETERMINATE	2	TRUE	1	0.448025644992784	3		1138	1805	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029159	26029159	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	44	522	0	ENST00000435504.4:c.191C>T	p.Ser64Phe	p.S64F	ENST00000435504		64	tCc/tTc	4/13	1	2	FACETS	0.542	0.454	0.641	0.542	0.454	0.641	SUBCLONAL	1	TRUE	1	0.24	2		522	676	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139496	47139496	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	83	605	0	ENST00000409792.3:c.5091C>G	p.Ile1697Met	p.I1697M	ENST00000409792	NM_014159.6	1697	atC/atG	9/21	1	2	FACETS	0.761	0.67	0.859	0.761	0.67	0.859	SUBCLONAL	1	TRUE	1	0.24	2		605	909	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0014230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	23	364	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.485	0.378	0.61	0.485	0.378	0.61	SUBCLONAL	1	TRUE	1	0.250725322900027	2		364	378	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0014230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	21	83	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.250725322900027	3	FACETS	0.524	0.403	0.665	0.262	0.201	0.333	SUBCLONAL	1	TRUE	1	0.250725322900027	3		83	360	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478786	56478786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324972550	NA	P-0014230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	73	512	0	ENST00000267101.3:c.242G>A	p.Arg81Gln	p.R81Q	ENST00000267101	NM_001982.3	81	cGa/cAa	3/28	1	2	FACETS	0.945	0.827	1	0.945	0.827	1	CLONAL	1	TRUE	1	0.250725322900027	2		512	616	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380350	14380350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	91	393	1	ENST00000256196.4:c.67G>A	p.Gly23Ser	p.G23S	ENST00000256196		23	Ggc/Agc	1/6	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.250725322900027	2		394	633	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120783952	120783952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754954103	NA	P-0014230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	89	585	1	ENST00000257552.2:c.1033G>A	p.Gly345Ser	p.G345S	ENST00000257552	NM_002442.3	345	Ggc/Agc	13/15	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.250725322900027	2		586	703	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797127	42797127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	134	881	0	ENST00000575354.2:c.3489C>G	p.Ser1163Arg	p.S1163R	ENST00000575354	NM_015125.3	1163	agC/agG	15/20	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.250725322900027	2		881	990	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591148	67591154	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TTGATGT	TTGATGT	-	novel	NA	P-0014230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	49	306	0	ENST00000274335.5:c.1741_1745+2del		p.X581_splice	ENST00000274335		581		12/15	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.250725322900027	2		306	372	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913237	NA	P-0014236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	185	421	0	ENST00000369535.4:c.35G>C	p.Gly12Ala	p.G12A	ENST00000369535	NM_002524.4	12	gGt/gCt	2/7	1	2	FACETS	0.817	0.757	0.879	0.817	0.757	0.879	CLONAL	1	TRUE	1	0.656320816349468	2		421	690	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	218514	218514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	70	121	0	ENST00000264932.6:c.44G>A	p.Arg15His	p.R15H	ENST00000264932	NM_004168.2	15	cGc/cAc	1/15	1	2	FACETS	0.965	0.855	1	0.965	0.855	1	CLONAL	1	TRUE	1	0.656320816349468	2		121	221	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115956	8115956	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	75	402	0	ENST00000346208.3:c.1305del	p.Ser436ProfsTer39	p.S436Pfs*39	ENST00000346208		434	caC/ca	6/6	0.3	1	FACETS	0.967	0.86	1	1	0.989	1	CLONAL	5	TRUE	0	0.12	1		402	243	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99451943	99451943	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	84	429	2	ENST00000268035.6:c.1277A>G	p.Gln426Arg	p.Q426R	ENST00000268035	NM_000875.3	426	cAg/cGg	6/21	0.421940226247736	4	FACETS	0.959	0.855	1	1	0.987	1	CLONAL	5	TRUE	2	0.12	4		431	327	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43700254	43700254	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	78	837	0	ENST00000382044.4:c.5633A>C	p.Lys1878Thr	p.K1878T	ENST00000382044	NM_001141980.1	1878	aAg/aCg	27/28	1	2	FACETS	0.94	0.828	1	0.94	0.828	1	CLONAL	1	TRUE	1	0.29	2		837	572	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0014265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	82	568	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.272600831466804	1	FACETS	0.975	0.862	1	0.975	0.862	1	CLONAL	1	TRUE	0	0.272600831466804	1		568	533	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46240692	46240695	+	frameshift_variant	Frame_Shift_Del	DEL	ATAG	ATAG	-	novel	NA	P-0014265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	72	378	0	ENST00000334344.6:c.1556_1559del	p.Asp519ValfsTer9	p.D519Vfs*9	ENST00000334344	NM_152641.2	518	ATAGat/at	12/21	1	2	FACETS	0.804	0.702	0.914	0.804	0.702	0.914	CLONAL	1	TRUE	1	0.272600831466804	2		378	657	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246074	46246075	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0014265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	62	399	0	ENST00000334344.6:c.4170_4171del	p.Pro1392AsnfsTer18	p.P1392Nfs*18	ENST00000334344	NM_152641.2	1390	ATa/a	15/21	1	2	FACETS	0.704	0.608	0.809	0.704	0.608	0.809	SUBCLONAL	1	TRUE	1	0.272600831466804	2		399	646	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105652	11105654	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0014265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	116	706	0	ENST00000358026.2:c.1570_1572del	p.Lys524del	p.K524del	ENST00000358026	NM_001128849.1	523	gAGAag/gag	9/36	1	2	FACETS	0.876	0.788	0.969	0.876	0.788	0.969	CLONAL	1	TRUE	1	0.272600831466804	2		706	972	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140165	50140165	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	133	584	0	ENST00000246792.3:c.260A>T	p.Gln87Leu	p.Q87L	ENST00000246792	NM_006270.3	87	cAg/cTg	3/6	0.272600831466804	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.272600831466804	1		584	746	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164111	47164112	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0014265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	67	282	0	ENST00000409792.3:c.2014_2015del	p.Asn672TyrfsTer10	p.N672Yfs*10	ENST00000409792	NM_014159.6	672	AAt/t	3/21	0.272600831466804	1	FACETS	0.925	0.806	1	0.925	0.806	1	CLONAL	1	TRUE	0	0.272600831466804	1		282	459	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787783	135787783	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	130	586	0	ENST00000298552.3:c.799A>G	p.Thr267Ala	p.T267A	ENST00000298552	NM_001162426.1	267	Aca/Gca	9/23	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.272600831466804	2		586	779	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229240	123229240	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs867285087	NA	P-0014269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	17	151	3	ENST00000218089.9:c.3724C>T	p.Arg1242Ter	p.R1242*	ENST00000218089	NM_001042749.1	1242	Cga/Tga	34/35	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		154	339	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0014274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	23	663	2	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	0.529	0.41	0.667	0.529	0.41	0.667	SUBCLONAL	1	TRUE	1	0.12	2		665	725	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028618	12028618	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	26	257	2	ENST00000353533.5:c.821G>T	p.Arg274Ile	p.R274I	ENST00000353533	NM_003010.3	274	aGa/aTa	8/11	1	2	FACETS	0.91	0.72	1	0.91	0.72	1	CLONAL	1	TRUE	1	0.12	2		259	476	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333560	70333560	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762889327	NA	P-0014274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	29	400	2	ENST00000373644.4:c.1465C>A	p.Pro489Thr	p.P489T	ENST00000373644	NM_030625.2	489	Cct/Act	2/12	1	2	FACETS	0.919	0.736	1	0.919	0.736	1	CLONAL	1	TRUE	1	0.12	2		402	526	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281952	142281952	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0014274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	19	204	0	ENST00000350721.4:c.293-1G>T		p.X98_splice	ENST00000350721	NM_001184.3	98			1	2	FACETS	0.918	0.696	1	0.918	0.696	1	CLONAL	1	TRUE	1	0.12	2		204	345	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242469	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	31	517	0	ENST00000275493.2:c.2239T>G	p.Leu747Val	p.L747V	ENST00000275493	NM_005228.3	747	Tta/Gta	19/28	1	2	FACETS	0.533	0.429	0.652	0.533	0.429	0.652	SUBCLONAL	1	TRUE	1	0.12	2		517	969	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045728	47045728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1184	67	884	0	ENST00000377604.3:c.2609G>A	p.Gly870Asp	p.G870D	ENST00000377604	NM_001204468.1	870	gGc/gAc	23/24	1	2	FACETS	0.893	0.773	1	0.893	0.773	1	CLONAL	1	TRUE	1	0.12	2		884	1251	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0014297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	67	422	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.906	0.787	1	0.906	0.787	1	CLONAL	1	TRUE	1	0.229016698371243	2		422	646	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298650	11298650	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs368440413	NA	P-0014297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	51	607	0	ENST00000361445.4:c.1811G>T	p.Arg604Leu	p.R604L	ENST00000361445	NM_004958.3	604	cGc/cTc	12/58	1	2	FACETS	0.741	0.629	0.864	0.741	0.629	0.864	SUBCLONAL	1	TRUE	1	0.229016698371243	2		607	601	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544682	65544682	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	66	793	0	ENST00000358664.4:c.244C>T	p.Gln82Ter	p.Q82*	ENST00000358664	NM_002382.4	82	Cag/Tag	4/5	0.229016698371243	1	FACETS	0.712	0.617	0.815	0.712	0.617	0.815	SUBCLONAL	1	TRUE	0	0.229016698371243	1		793	717	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490328	29490328	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	74	460	0	ENST00000356175.3:c.413C>A	p.Ala138Asp	p.A138D	ENST00000356175	NM_000267.3	138	gCc/gAc	4/57	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.229016698371243	2		460	546	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	26	661	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.155919550554224	4	FACETS	1	0.915	1	0.658	0.525	0.807	INDETERMINATE	1	FALSE	2	0.268140480279589	4		661	187	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0014300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	89	682	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.268140480279589	2	FACETS	0.849	0.758	0.945	0.849	0.758	0.945	CLONAL	2	FALSE	0	0.268140480279589	2		682	391	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15952272	15952272	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	26	524	0	ENST00000268712.3:c.6423C>G	p.His2141Gln	p.H2141Q	ENST00000268712	NM_006311.3	2141	caC/caG	41/46	0.268140480279589	2	FACETS	0.467	0.37	0.58	0.234	0.185	0.29	SUBCLONAL	1	FALSE	0	0.268140480279589	2		524	415	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4123815	4123815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	46	553	1	ENST00000262948.5:c.58G>A	p.Glu20Lys	p.E20K	ENST00000262948	NM_030662.3	20	Gag/Aag	1/11	0.128867348574558	3	FACETS	0.794	0.669	0.932	0.397	0.334	0.466	INDETERMINATE	1	FALSE	1	0.268140480279589	3		554	490	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0014317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	116	257	2	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.499271073918957	2		259	454	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951135	17951135	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	221	659	0	ENST00000458235.1:c.1158C>G	p.Ile386Met	p.I386M	ENST00000458235	NM_000215.3	386	atC/atG	9/24	0.499271073918957	1	FACETS	0.83	0.775	0.888	0.83	0.775	0.888	CLONAL	1	TRUE	0	0.499271073918957	1		659	800	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0014317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	266	654	0	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	0.499271073918957	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.499271073918957	1		654	698	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17355174	17355174	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200973284	NA	P-0014317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	239	671	2	ENST00000375499.3:c.344G>A	p.Arg115Gln	p.R115Q	ENST00000375499	NM_003000.2	115	cGa/cAa	4/8	1	2	FACETS	0.916	0.855	0.979	0.916	0.855	0.979	CLONAL	1	TRUE	1	0.499271073918957	2		673	1045	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097742	8097743	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0014317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	104	602	1	ENST00000346208.3:c.124_125delinsAA	p.Pro42Lys	p.P42K	ENST00000346208		42	CCg/AAg	2/6	0.259687462308082	1	FACETS	0.364	0.325	0.405	0.364	0.325	0.405	INDETERMINATE	1	TRUE	0	0.499271073918957	1		603	859	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016564	12016564	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	122	304	0	ENST00000353533.5:c.700A>T	p.Asn234Tyr	p.N234Y	ENST00000353533	NM_003010.3	234	Aat/Tat	7/11	0.499271073918957	1	FACETS	0.919	0.838	1	0.919	0.838	1	CLONAL	1	TRUE	0	0.499271073918957	1		304	399	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153603	55153603	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	163	403	0	ENST00000257290.5:c.2569C>G	p.Leu857Val	p.L857V	ENST00000257290	NM_006206.4	857	Ctg/Gtg	19/23	0.499271073918957	1	FACETS	0.933	0.862	1	0.933	0.862	1	CLONAL	1	TRUE	0	0.499271073918957	1		403	525	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84393388	84393388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	37	347	1	ENST00000321945.7:c.269C>T	p.Ser90Leu	p.S90L	ENST00000321945	NM_139076.2	90	tCa/tTa	4/9	0.499271073918957	1	FACETS	0.22	0.181	0.264	0.22	0.181	0.264	SUBCLONAL	1	TRUE	0	0.499271073918957	1		348	505	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859844	117859844	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	145	323	0	ENST00000297338.2:c.1791C>G	p.Phe597Leu	p.F597L	ENST00000297338	NM_006265.2	597	ttC/ttG	14/14	NA	2	FACETS	0.966	0.885	1			1	INDETERMINATE	1	TRUE	NA	0.499271073918957	2		323	601	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137313610	137313610	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0014317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	67	725	0	ENST00000481739.1:c.869C>G	p.Ser290Ter	p.S290*	ENST00000481739	NM_002957.4	290	tCa/tGa	6/10	0.480919139607553	2	FACETS	0.265	0.229	0.304	0.133	0.114	0.152	SUBCLONAL	1	TRUE	0	0.499271073918957	2		725	1012	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	202	389	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.287986638236107	5	FACETS	1	0.938	1	1	0.938	1	CLONAL	3	TRUE	2	0.459815773827443	5		389	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0014319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	347	568	0	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	0.459815773827443	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.459815773827443	2		568	735	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18972835	18972835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	269	437	0	ENST00000262803.5:c.2474G>A	p.Ser825Asn	p.S825N	ENST00000262803	NM_002911.3	825	aGt/aAt	18/24	0.309157774776646	5	FACETS	1	0.976	1			1	CLONAL	2	TRUE	NA	0.459815773827443	5		437	922	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0014328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	846	490	1	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	NA	2	FACETS	0.972	0.952	0.991			1	INDETERMINATE	2	TRUE	NA	0.792172477623212	2		491	1099	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951058	48951059	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0014328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	159	252	0	ENST00000267163.4:c.1220_1221del	p.Cys407TyrfsTer20	p.C407Yfs*20	ENST00000267163	NM_000321.2	407	tGC/t	13/27	0.77580282598171	2	FACETS	0.88	0.834	0.925	0.88	0.834	0.925	CLONAL	2	TRUE	0	0.792172477623212	2		252	228	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472561	88472561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	539	475	1	ENST00000360948.2:c.1994C>T	p.Ser665Leu	p.S665L	ENST00000360948	NM_001012338.2	665	tCg/tTg	16/19	0.577713284426403	4	FACETS	0.904	0.868	0.94	0.904	0.868	0.94	CLONAL	2	TRUE	2	0.792172477623212	4		476	1349	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696613	176696613	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	308	221	0	ENST00000439151.2:c.5314G>T	p.Ala1772Ser	p.A1772S	ENST00000439151	NM_022455.4	1772	Gct/Tct	16/23	0.693145427504394	3	FACETS	0.906	0.863	0.949	0.906	0.863	0.949	CLONAL	2	TRUE	1	0.792172477623212	3		221	599	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840093	27840093	+	start_lost	Translation_Start_Site	SNP	T	T	C	rs769800748	NA	P-0014328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	249	193	0	ENST00000328488.2:c.1A>G	p.Met1?	p.M1?	ENST00000328488	NM_003533.2	1	Atg/Gtg	1/1	0.537535897499195	6	FACETS	1	0.985	1	0.766	0.72	0.813	CLONAL	2	TRUE	3	0.792172477623212	6		193	707	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908874	101908874	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	718	548	0	ENST00000374994.4:c.1238G>T	p.Arg413Leu	p.R413L	ENST00000374994	NM_004612.2	413	cGa/cTa	7/9	0.737813582326116	3	FACETS	0.878	0.858	0.897	0.878	0.858	0.897	CLONAL	3	TRUE	0	0.792172477623212	3		548	961	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0014330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	361	367	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.838123971931752	3	FACETS	1	0.971	1	0.518	0.491	0.545	CLONAL	1	TRUE	1	0.838123971931752	3		367	1181	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32814943	32814943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs760014590	NA	P-0014336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	477	671	3	ENST00000354258.4:c.2122C>T	p.Arg708Ter	p.R708*	ENST00000354258	NM_000593.5	708	Cga/Tga	10/11	0.689910714576434	1	FACETS	0.935	0.898	0.971	0.935	0.898	0.971	CLONAL	1	TRUE	0	0.689910714576434	1		674	969	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418311	139418311	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	568	901	0	ENST00000277541.6:c.261C>A	p.Cys87Ter	p.C87*	ENST00000277541	NM_017617.3	87	tgC/tgA	3/34	1	2	FACETS	0.982	0.943	1	0.982	0.943	1	CLONAL	1	TRUE	1	0.689910714576434	2		901	1676	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0014398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	147	402	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.955	0.872	1	0.955	0.872	1	CLONAL	1	TRUE	1	0.352094784328679	2		402	874	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613132	52613132	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	177	476	1	ENST00000394830.3:c.3396G>A	p.Trp1132Ter	p.W1132*	ENST00000394830	NM_018313.4	1132	tgG/tgA	22/30	0.352094784328679	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.352094784328679	1		477	823	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217303	11217303	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	160	611	0	ENST00000361445.4:c.4375G>C	p.Ala1459Pro	p.A1459P	ENST00000361445	NM_004958.3	1459	Gcc/Ccc	30/58	1	2	FACETS	0.81	0.741	0.882	0.81	0.741	0.882	CLONAL	1	TRUE	1	0.352094784328679	2		611	1122	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183791	10183802	+	inframe_deletion	In_Frame_Del	DEL	TATGGCTCAACT	TATGGCTCAACT	-	novel	NA	P-0014398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	212	698	0	ENST00000256474.2:c.261_272del	p.Trp88_Phe91del	p.W88_F91del	ENST00000256474	NM_000551.3	87	gTATGGCTCAACTtc/gtc	1/3	0.352094784328679	1	FACETS	0.855	0.794	0.92	0.855	0.794	0.92	CLONAL	1	TRUE	0	0.352094784328679	1		698	1160	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391105	89391105	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	177	562	0	ENST00000336596.2:c.1172del	p.Asn391ThrfsTer4	p.N391Tfs*4	ENST00000336596	NM_005233.5	391	Aac/ac	5/17	1	2	FACETS	0.889	0.818	0.963	0.889	0.818	0.963	CLONAL	1	TRUE	1	0.352094784328679	2		562	1131	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164728	32164732	+	frameshift_variant	Frame_Shift_Del	DEL	GCTTG	GCTTG	CTTT	novel	NA	P-0014398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	156	611	3	ENST00000375023.3:c.5170_5174delinsAAAG	p.Gln1724LysfsTer21	p.Q1724Kfs*21	ENST00000375023	NM_004557.3	1724	CAAGCa/AAAGa	28/30	1	2	FACETS	0.722	0.659	0.787	0.722	0.659	0.787	SUBCLONAL	1	TRUE	1	0.352094784328679	2		614	1228	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0014406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	117	357	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	1	2	FACETS	0.792	0.714	0.875	0.792	0.714	0.875	SUBCLONAL	1	TRUE	1	0.3618783096087	2		357	816	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063667	67063667	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	129	443	0	ENST00000412916.2:c.116A>G	p.Glu39Gly	p.E39G	ENST00000412916		39	gAa/gGa	2/6	0.24557720765714	1	FACETS	0.67	0.607	0.736	0.67	0.607	0.736	SUBCLONAL	1	TRUE	0	0.3618783096087	1		443	872	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0014409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	179	1372	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.282999475492097	3	FACETS	0.848	0.788	0.909	1	0.987	1	CLONAL	3	TRUE	1	0.319392573876848	3		1372	511	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782609	9782609	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	65	1621	0	ENST00000377346.4:c.2371C>G	p.Leu791Val	p.L791V	ENST00000377346	NM_005026.3	791	Ctg/Gtg	19/24	1	2	FACETS	0.809	0.703	0.924	0.809	0.703	0.924	CLONAL	1	TRUE	1	0.319392573876848	2		1621	503	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640853	3640853	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs117707719	NA	P-0014409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	69	1471	2	ENST00000294008.3:c.2786C>T	p.Pro929Leu	p.P929L	ENST00000294008	NM_032444.2	929	cCg/cTg	12/15	0.282999475492097	3	FACETS	0.935	0.815	1	0.467	0.407	0.532	CLONAL	1	TRUE	1	0.319392573876848	3		1473	536	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62320453	62320453	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768926890	NA	P-0014409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	39	1489	3	ENST00000360203.5:c.1846G>A	p.Gly616Ser	p.G616S	ENST00000360203	NM_001283009.1	616	Ggc/Agc	22/35	0.319392573876848	4	FACETS	0.553	0.457	0.66	0.276	0.228	0.33	SUBCLONAL	1	TRUE	2	0.319392573876848	4		1492	583	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953818	131953818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	36	884	1	ENST00000265335.6:c.3221C>T	p.Ala1074Val	p.A1074V	ENST00000265335		1074	gCa/gTa	21/25	1	2	FACETS	0.802	0.662	0.957	0.802	0.662	0.957	CLONAL	1	TRUE	1	0.319392573876848	2		885	281	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566057	141566057	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1379212767	NA	P-0014409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	31	1391	0	ENST00000220592.5:c.1207G>C	p.Asp403His	p.D403H	ENST00000220592	NM_012154.3	403	Gat/Cat	10/19	0.122798693333594	4	FACETS	0.487	0.393	0.594	0.243	0.196	0.297	INDETERMINATE	1	TRUE	2	0.319392573876848	4		1391	526	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179165	123179165	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	19	246	0	ENST00000218089.9:c.614C>G	p.Thr205Arg	p.T205R	ENST00000218089	NM_001042749.1	205	aCa/aGa	8/35	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		246	305	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190645	11190645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745409542	NA	P-0014420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	137	471	1	ENST00000361445.4:c.5554G>A	p.Glu1852Lys	p.E1852K	ENST00000361445	NM_004958.3	1852	Gag/Aag	39/58	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.351056760640585	2		472	703	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607672	43607672	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	70	915	0	ENST00000355710.3:c.1648G>A	p.Gly550Arg	p.G550R	ENST00000355710	NM_020975.4	550	Ggg/Agg	8/20	1	2	FACETS	0.324	0.281	0.371	0.324	0.281	0.371	SUBCLONAL	1	TRUE	1	0.351056760640585	2		915	1230	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	115	503	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.300904296027714	3	FACETS	0.755	0.682	0.832	0.755	0.682	0.832	SUBCLONAL	2	TRUE	1	0.28	3		503	620	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0014436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	102	469	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.166530646933325	1	FACETS	1	0.94	1	1	0.94	1	INDETERMINATE	1	TRUE	0	0.28	1		469	586	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0014436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	110	609	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	NA	2	FACETS	0.95	0.853	1			1	INDETERMINATE	1	TRUE	NA	0.28	2		609	827	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519985	NA	P-0014436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	385	906	1	ENST00000269305.4:c.857A>G	p.Glu286Gly	p.E286G	ENST00000269305	NM_001126112.2	286	gAa/gGa	8/11	0.270385449539816	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.28	2		907	1264	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	169	389	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.159586684592147	4	FACETS	0.934	0.865	1			1	CLONAL	5	FALSE	NA	0.159586684592147	4		389	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	73	720	2	ENST00000269305.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	336	Gag/Tag	10/11	NA	2	FACETS	1	0.972	1			1	INDETERMINATE	1	FALSE	NA	0.159586684592147	2		722	641	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022616	31022616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	42	751	0	ENST00000375687.4:c.2101C>T	p.Pro701Ser	p.P701S	ENST00000375687	NM_015338.5	701	Cct/Tct	13/13	0.159586684592147	3	FACETS	0.829	0.69	0.983	0.276	0.23	0.328	CLONAL	1	FALSE	0	0.159586684592147	3		751	686	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981243	201981243	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	43	1027	0	ENST00000359651.3:c.322G>C	p.Glu108Gln	p.E108Q	ENST00000359651		108	Gag/Cag	2/8	0.159586684592147	2	FACETS	0.632	0.527	0.749	0.316	0.263	0.375	SUBCLONAL	1	FALSE	0	0.159586684592147	2		1027	853	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046611	30046611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556530827	NA	P-0014439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	45	658	2	ENST00000331968.5:c.2572C>T	p.Arg858Cys	p.R858C	ENST00000331968	NM_002742.2	858	Cgc/Tgc	18/18	0.159586684592147	3	FACETS	1	0.849	1	0.506	0.424	0.596	CLONAL	1	FALSE	1	0.159586684592147	3		660	602	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619361	1619361	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0014439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	32	524	0	ENST00000344749.5:c.1280C>G	p.Ser427Ter	p.S427*	ENST00000344749	NM_001136139.2	427	tCa/tGa	15/19	1	2	FACETS	0.758	0.614	0.921	0.758	0.614	0.921	CLONAL	1	FALSE	1	0.159586684592147	2		524	529	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10277291	10277291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257025095	NA	P-0014439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	47	955	0	ENST00000340748.4:c.826G>A	p.Glu276Lys	p.E276K	ENST00000340748		276	Gaa/Aaa	10/40	1	2	FACETS	0.747	0.629	0.879	0.747	0.629	0.879	SUBCLONAL	1	FALSE	1	0.159586684592147	2		955	788	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054641	13054641	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	34	518	0	ENST00000316448.5:c.1168G>C	p.Asp390His	p.D390H	ENST00000316448	NM_004343.3	390	Gac/Cac	9/9	1	2	FACETS	0.766	0.625	0.926	0.766	0.625	0.926	CLONAL	1	FALSE	1	0.159586684592147	2		518	556	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281550	198281550	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0014439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	43	593	0	ENST00000335508.6:c.581C>G	p.Ser194Ter	p.S194*	ENST00000335508	NM_012433.2	194	tCa/tGa	6/25	1	2	FACETS	0.81	0.677	0.959	0.81	0.677	0.959	CLONAL	1	FALSE	1	0.159586684592147	2		593	665	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561083	9561083	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	18	354	0	ENST00000353224.5:c.699A>C	p.Gln233His	p.Q233H	ENST00000353224	NM_177990.2	233	caA/caC	4/10	0.159586684592147	1	FACETS	0.59	0.443	0.763	0.59	0.443	0.763	SUBCLONAL	1	FALSE	0	0.159586684592147	1		354	352	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864207	117864207	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	37	500	0	ENST00000297338.2:c.1450G>C	p.Asp484His	p.D484H	ENST00000297338	NM_006265.2	484	Gac/Cac	11/14	0.159586684592147	4	FACETS	0.892	0.734	1	0.446	0.367	0.535	CLONAL	1	FALSE	2	0.159586684592147	4		500	603	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492904	8492904	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	45	509	1	ENST00000356435.5:c.2425G>T	p.Gly809Cys	p.G809C	ENST00000356435		809	Ggt/Tgt	16/35	0.159586684592147	2	FACETS	0.946	0.794	1	0.473	0.397	0.558	CLONAL	1	FALSE	0	0.159586684592147	2		510	596	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039708	47039708	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	82	968	0	ENST00000377604.3:c.1160G>T	p.Arg387Met	p.R387M	ENST00000377604	NM_001204468.1	387	aGg/aTg	11/24	0.159586684592147	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	0	0.159586684592147	1		968	694	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0014450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	220	422	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.439391665295621	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.447530948053253	2		422	400	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188164	11188164	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	48	403	0	ENST00000361445.4:c.5930C>G	p.Thr1977Arg	p.T1977R	ENST00000361445	NM_004958.3	1977	aCa/aGa	43/58	0.447530948053253	1	FACETS	0.597	0.508	0.693	0.597	0.508	0.693	SUBCLONAL	1	TRUE	0	0.447530948053253	1		403	279	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515378	103515378	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1221757639	NA	P-0014450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	46	231	0	ENST00000355739.4:c.1879G>T	p.Ala627Ser	p.A627S	ENST00000355739	NM_000123.3	627	Gca/Tca	8/15	1	2	FACETS	0.785	0.666	0.914	0.785	0.666	0.914	CLONAL	1	TRUE	1	0.447530948053253	2		231	262	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560499	65560499	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	97	332	0	ENST00000358664.4:c.98G>C	p.Arg33Pro	p.R33P	ENST00000358664	NM_002382.4	33	cGa/cCa	3/5	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.447530948053253	2		332	378	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562693	95562693	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	56	289	0	ENST00000393063.1:c.4564G>C	p.Asp1522His	p.D1522H	ENST00000393063	NM_030621.3	1522	Gac/Cac	24/28	1	2	FACETS	0.907	0.783	1	0.907	0.783	1	CLONAL	1	TRUE	1	0.447530948053253	2		289	276	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992277	72992277	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	45	588	0	ENST00000268489.5:c.1768T>G	p.Phe590Val	p.F590V	ENST00000268489	NM_006885.3	590	Ttc/Gtc	2/10	0.1891339225139	1	FACETS	0.363	0.305	0.427	0.363	0.305	0.427	INDETERMINATE	1	TRUE	0	0.447530948053253	1		588	430	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42788919	42788919	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	69	450	1	ENST00000575354.2:c.63G>T	p.Met21Ile	p.M21I	ENST00000575354	NM_015125.3	21	atG/atT	1/20	1	2	FACETS	0.646	0.564	0.735	0.646	0.564	0.735	SUBCLONAL	1	TRUE	1	0.447530948053253	2		451	477	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928417	69928417	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	30	353	0	ENST00000352241.4:c.237G>T	p.Lys79Asn	p.K79N	ENST00000352241	NM_198159.2	79	aaG/aaT	2/10	1	2	FACETS	0.466	0.376	0.566	0.466	0.376	0.566	SUBCLONAL	1	TRUE	1	0.447530948053253	2		353	288	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114233	73114233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201957466	NA	P-0014450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	36	313	0	ENST00000356692.5:c.869G>A	p.Arg290His	p.R290H	ENST00000356692		290	cGt/cAt	8/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.447530948053253	NA		313	328	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371684	55371684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	61	498	0	ENST00000297316.4:c.374G>A	p.Arg125His	p.R125H	ENST00000297316	NM_022454.3	125	cGc/cAc	2/2	0.447530948053253	1	FACETS	0.74	0.644	0.842	0.74	0.644	0.842	SUBCLONAL	1	TRUE	0	0.447530948053253	1		498	286	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041726	47041726	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0014450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	88	438	2	ENST00000377604.3:c.1950+1G>T		p.X650_splice	ENST00000377604	NM_001204468.1	650			0.416150160136126	1	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	0	0.447530948053253	1		440	301	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0014456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1212	216	469	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.170367462856572	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.16	4		469	1428	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236086	108236086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782292	NA	P-0014456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	73	420	0	ENST00000278616.4:c.9022C>T	p.Arg3008Cys	p.R3008C	ENST00000278616	NM_000051.3	3008	Cgt/Tgt	63/63	1	2	FACETS	0.982	0.857	1	0.982	0.857	1	CLONAL	1	TRUE	1	0.16	2		420	929	SUCCESS
APC	324	MSKCC	GRCh37	5	112175198	112175198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	42	196	0	ENST00000257430.4:c.3907C>T	p.Gln1303Ter	p.Q1303*	ENST00000257430	NM_000038.5	1303	Caa/Taa	16/16	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.16	2		196	504	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713272	43713272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764043263	NA	P-0014456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1324	84	661	1	ENST00000382044.4:c.4201C>T	p.Arg1401Cys	p.R1401C	ENST00000382044	NM_001141980.1	1401	Cgt/Tgt	20/28	1	2	FACETS	0.746	0.656	0.843	0.746	0.656	0.843	SUBCLONAL	1	TRUE	1	0.16	2		662	1408	SUCCESS
APC	324	MSKCC	GRCh37	5	112162834	112162834	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	43	375	0	ENST00000257430.4:c.1438C>T	p.Gln480Ter	p.Q480*	ENST00000257430	NM_000038.5	480	Caa/Taa	12/16	1	2	FACETS	0.69	0.576	0.818	0.69	0.576	0.818	SUBCLONAL	1	TRUE	1	0.16	2		375	779	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184830	32184830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150609093	NA	P-0014456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	48	394	1	ENST00000375023.3:c.1753C>T	p.Arg585Cys	p.R585C	ENST00000375023	NM_004557.3	585	Cgc/Tgc	11/30	0.134766910895736	3	FACETS	0.857	0.723	1	0.429	0.361	0.503	CLONAL	1	TRUE	1	0.16	3		395	756	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0014482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	39	306	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.103063249242127	3	FACETS	0.618	0.511	0.737	0.309	0.255	0.369	INDETERMINATE	1	TRUE	1	0.25	3		306	568	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	89	627	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.3	1	FACETS	0.964	0.856	1	0.964	0.856	1	CLONAL	1	TRUE	0	0.25	1		627	646	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063681	67063681	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	58	445	0	ENST00000412916.2:c.130T>G	p.Phe44Val	p.F44V	ENST00000412916		44	Ttc/Gtc	2/6	0.3	1	FACETS	0.785	0.675	0.905	0.785	0.675	0.905	CLONAL	1	TRUE	0	0.25	1		445	517	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0014486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	340	402	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.250914944964633	3	FACETS	0.969	0.93	1	1	0.996	1	CLONAL	5	TRUE	0	0.290526657114256	3		402	553	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189379	56189379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	332	445	0	ENST00000399503.3:c.4411C>T	p.Pro1471Ser	p.P1471S	ENST00000399503	NM_005921.1	1471	Cca/Tca	20/20	0.290526657114256	7	FACETS	0.945	0.894	0.996			1	CLONAL	4	TRUE	NA	0.290526657114256	7		445	1044	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0014489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	186	612	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.505040293006959	1	FACETS	0.961	0.893	1	0.961	0.893	1	CLONAL	1	TRUE	0	0.505040293006959	1		612	573	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181857	56181857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	120	399	0	ENST00000399503.3:c.4081C>T	p.His1361Tyr	p.H1361Y	ENST00000399503	NM_005921.1	1361	Cat/Tat	17/20	1	2	FACETS	0.855	0.775	0.938	0.855	0.775	0.938	CLONAL	1	TRUE	1	0.505040293006959	2		399	556	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220471	1220475	+	frameshift_variant	Frame_Shift_Del	DEL	CACCC	CACCC	-	novel	NA	P-0014492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	278	678	0	ENST00000326873.7:c.564_568del	p.Thr189GlnfsTer75	p.T189Qfs*75	ENST00000326873	NM_000455.4	188	ggCACCCtc/ggtc	4/10	0.766517946711467	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.766517946711467	1		678	446	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46714238	46714243	+	inframe_deletion	In_Frame_Del	DEL	TGTGAT	TGTGAT	-	novel	NA	P-0014524-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	59	536	0	ENST00000371975.4:c.58_63del	p.Cys20_Asp21del	p.C20_D21del	ENST00000371975	NM_003579.3	20	TGTGAT/-	2/18	1	2	FACETS	0.896	0.768	1	0.896	0.768	1	CLONAL	1	TRUE	1	0.14	2		536	941	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202197	108202197	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0014524-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	36	362	0	ENST00000278616.4:c.7542T>A	p.Tyr2514Ter	p.Y2514*	ENST00000278616	NM_000051.3	2514	taT/taA	51/63	1	2	FACETS	0.823	0.675	0.989	0.823	0.675	0.989	CLONAL	1	TRUE	1	0.14	2		362	625	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645681	12645681	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs397516830	NA	P-0014524-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	23	235	0	ENST00000251849.4:c.788T>A	p.Val263Asp	p.V263D	ENST00000251849	NM_002880.3	263	gTc/gAc	7/17	1	2	FACETS	0.754	0.586	0.948	0.754	0.586	0.948	CLONAL	1	TRUE	1	0.14	2		235	436	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412046	116412046	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	G	novel	NA	P-0014524-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	71	579	0	ENST00000397752.3:c.3028+3A>G		p.X1010_splice	ENST00000397752	NM_000245.2	1010			1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.14	2		579	968	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520008	NA	P-0014531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1357	56	580	0	ENST00000269305.4:c.613T>C	p.Tyr205His	p.Y205H	ENST00000269305	NM_001126112.2	205	Tat/Cat	6/11	1	2	FACETS	0.2	0.17	0.233	0.2	0.17	0.233	SUBCLONAL	1	TRUE	1	0.395868858860661	2		580	1413	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0014546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	122	422	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.286692364427012	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.286692364427012	1		422	636	SUCCESS
ATM	472	MSKCC	GRCh37	11	108128265	108128265	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1555075721	NA	P-0014546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	102	352	0	ENST00000278616.4:c.2308G>T	p.Glu770Ter	p.E770*	ENST00000278616	NM_000051.3	770	Gaa/Taa	15/63	1	2	FACETS	0.988	0.884	1	0.988	0.884	1	CLONAL	1	TRUE	1	0.286692364427012	2		352	720	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218037	108218037	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	50	289	0	ENST00000278616.4:c.8616T>A	p.His2872Gln	p.H2872Q	ENST00000278616	NM_000051.3	2872	caT/caA	59/63	1	2	FACETS	0.592	0.502	0.692	0.592	0.502	0.692	SUBCLONAL	1	TRUE	1	0.286692364427012	2		289	589	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910538	32910538	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	37	233	0	ENST00000380152.3:c.2046C>G	p.Ile682Met	p.I682M	ENST00000380152		682	atC/atG	11/27	0.133716618095639	0	FACETS	0.38	0.313	0.455			1	INDETERMINATE	1	TRUE	0	0.286692364427012	0		233	485	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514445	103514445	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	26	198	2	ENST00000355739.4:c.946G>T	p.Gly316Cys	p.G316C	ENST00000355739	NM_000123.3	316	Ggc/Tgc	8/15	0.133716618095639	0	FACETS	0.34	0.269	0.422			1	INDETERMINATE	1	TRUE	0	0.286692364427012	0		200	380	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054416	42054416	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	66	335	0	ENST00000219905.7:c.7600G>T	p.Gly2534Ter	p.G2534*	ENST00000219905	NM_001164273.1	2534	Gga/Tga	22/24	0.286692364427012	1	FACETS	0.652	0.566	0.745	0.652	0.566	0.745	SUBCLONAL	1	TRUE	0	0.286692364427012	1		335	605	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678620	88678620	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs56386352	NA	P-0014546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	33	222	0	ENST00000360948.2:c.916C>A	p.Arg306Ser	p.R306S	ENST00000360948	NM_001012338.2	306	Cgt/Agt	9/19	0.133716618095639	0	FACETS	0.405	0.33	0.49			1	INDETERMINATE	1	TRUE	0	0.286692364427012	0		222	405	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133711	2133711	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1349341137	NA	P-0014546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	84	471	0	ENST00000219476.3:c.3899T>C	p.Met1300Thr	p.M1300T	ENST00000219476	NM_000548.3	1300	aTg/aCg	33/42	1	2	FACETS	0.512	0.451	0.578	0.512	0.451	0.578	SUBCLONAL	1	TRUE	1	0.286692364427012	2		471	1144	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89874771	89874771	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs35566151	NA	P-0014546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	112	423	0	ENST00000389301.3:c.527C>G	p.Ser176Cys	p.S176C	ENST00000389301	NM_000135.2	176	tCt/tGt	6/43	1	2	FACETS	0.654	0.586	0.726	0.654	0.586	0.726	SUBCLONAL	1	TRUE	1	0.286692364427012	2		423	1195	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610446	10610449	+	frameshift_variant	Frame_Shift_Del	DEL	TGCA	TGCA	-	novel	NA	P-0014546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	190	486	0	ENST00000171111.5:c.261_264del	p.Ala88ArgfsTer68	p.A88Rfs*68	ENST00000171111	NM_203500.1	87	gaTGCA/ga	2/6	0.286692364427012	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.286692364427012	1		486	1016	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36217179	36217179	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1392	153	547	0	ENST00000222270.7:c.3928C>G	p.Pro1310Ala	p.P1310A	ENST00000222270	NM_014727.1	1310	Cca/Gca	14/37	1	2	FACETS	0.691	0.63	0.755	0.691	0.63	0.755	SUBCLONAL	1	TRUE	1	0.286692364427012	2		547	1545	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868193	45868193	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1401	138	652	0	ENST00000391945.4:c.497G>T	p.Arg166Leu	p.R166L	ENST00000391945	NM_000400.3	166	cGt/cTt	7/23	1	2	FACETS	0.626	0.567	0.688	0.626	0.567	0.688	SUBCLONAL	1	TRUE	1	0.286692364427012	2		652	1539	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422431	225422431	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	72	389	0	ENST00000264414.4:c.209G>C	p.Gly70Ala	p.G70A	ENST00000264414	NM_003590.4	70	gGa/gCa	2/16	0.133716618095639	0	FACETS	0.525	0.458	0.597			1	INDETERMINATE	1	TRUE	0	0.286692364427012	0		389	683	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468438	89468438	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	133	291	0	ENST00000336596.2:c.1972G>T	p.Gly658Cys	p.G658C	ENST00000336596	NM_005233.5	658	Ggc/Tgc	11/17	0.156056248440232	2	FACETS	0.859	0.784	0.937	0.859	0.784	0.937	INDETERMINATE	2	TRUE	0	0.286692364427012	2		291	540	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197588	106197588	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1406914931	NA	P-0014546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	132	284	0	ENST00000380013.4:c.5921G>T	p.Arg1974Met	p.R1974M	ENST00000380013	NM_001127208.2	1974	aGg/aTg	11/11	0.177633366120586	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.286692364427012	1		284	602	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159150	143159150	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	22	215	0	ENST00000262992.4:c.703G>T	p.Val235Leu	p.V235L	ENST00000262992	NM_001101669.1	235	Gta/Tta	10/24	0.177633366120586	1	FACETS	0.323	0.25	0.408	0.323	0.25	0.408	SUBCLONAL	1	TRUE	0	0.286692364427012	1		215	407	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102076	27102076	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	68	433	1	ENST00000324856.7:c.5002G>T	p.Glu1668Ter	p.E1668*	ENST00000324856	NM_006015.4	1668	Gag/Tag	19/20	1	2	FACETS	0.547	0.475	0.626	0.547	0.475	0.626	SUBCLONAL	1	TRUE	1	0.286692364427012	2		434	867	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578467	7578467	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	1030	690	0	ENST00000269305.4:c.463A>C	p.Thr155Pro	p.T155P	ENST00000269305	NM_001126112.2	155	Acc/Ccc	5/11	0.778473547146259	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.778473547146259	2		690	1279	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851772	134851772	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	311	512	0	ENST00000398015.3:c.1178T>A	p.Ile393Asn	p.I393N	ENST00000398015	NM_004441.4	393	aTc/aAc	5/16	0.512161512871944	4	FACETS	1	0.987	1	0.574	0.541	0.608	CLONAL	1	TRUE	2	0.778473547146259	4		512	1238	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913396	NA	P-0014567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	102	312	0	ENST00000349496.5:c.95A>T	p.Asp32Val	p.D32V	ENST00000349496	NM_001904.3	32	gAc/gTc	3/15	1	2	FACETS	0.565	0.508	0.624	0.565	0.508	0.624	SUBCLONAL	1	TRUE	1	0.847569651603826	2		312	426	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685269	89685269	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs786203847	NA	P-0014567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	29	166	0	ENST00000371953.3:c.165-1G>A		p.X55_splice	ENST00000371953	NM_000314.4	55			0.491944737260824	3	FACETS	0.521	0.422	0.632	0.261	0.211	0.316	INDETERMINATE	1	TRUE	1	0.847569651603826	3		166	187	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246490640	246490640	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0014567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	32	314	0	ENST00000388985.4:c.395-1G>T		p.X132_splice	ENST00000388985		132			0.847569651603826	3	FACETS	0.385	0.314	0.466	0.193	0.157	0.233	SUBCLONAL	1	TRUE	1	0.847569651603826	3		314	279	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720818	89720823	+	inframe_deletion	In_Frame_Del	DEL	TGATCT	TGATCT	-	novel	NA	P-0014567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	95	390	0	ENST00000371953.3:c.972_977del	p.Leu325_Asp326del	p.L325_D326del	ENST00000371953	NM_000314.4	323	aaTGATCTt/aat	8/9	0.491944737260824	3	FACETS	1	0.939	1	0.528	0.476	0.583	INDETERMINATE	1	TRUE	1	0.847569651603826	3		390	302	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645165	67645167	+	frameshift_variant	Frame_Shift_Del	DEL	AAA	AAA	TT	novel	NA	P-0014567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	162	649	1	ENST00000264010.4:c.430_432delinsTT	p.Lys144LeufsTer10	p.K144Lfs*10	ENST00000264010	NM_006565.3	144	AAA/TT	3/12	1	2	FACETS	0.422	0.387	0.459	0.422	0.387	0.459	SUBCLONAL	1	TRUE	1	0.847569651603826	2		650	906	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589635	67589643	+	inframe_deletion	In_Frame_Del	DEL	ATATGAAGA	ATATGAAGA	-	novel	NA	P-0014567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	34	296	0	ENST00000274335.5:c.1402_1410del	p.Glu468_Tyr470del	p.E468_Y470del	ENST00000274335		466	ttATATGAAGAa/tta	10/15	1	2	FACETS	0.371	0.306	0.444	0.371	0.306	0.444	SUBCLONAL	1	TRUE	1	0.847569651603826	2		296	216	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0014580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	241	765	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.412572703243746	1	FACETS	0.938	0.876	1	0.938	0.876	1	CLONAL	1	TRUE	0	0.412572703243746	1		765	989	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877441	89877441	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761430527	NA	P-0014580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	233	632	0	ENST00000389301.3:c.322C>T	p.Pro108Ser	p.P108S	ENST00000389301	NM_000135.2	108	Ccc/Tcc	4/43	0.383737335705161	2	FACETS	0.999	0.931	1	0.499	0.465	0.535	CLONAL	1	TRUE	0	0.412572703243746	2		632	1131	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100914	27100914	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	69	584	0	ENST00000324856.7:c.4196A>G	p.Gln1399Arg	p.Q1399R	ENST00000324856	NM_006015.4	1399	cAg/cGg	18/20	0.383737335705161	2	FACETS	0.445	0.387	0.508	0.222	0.193	0.254	SUBCLONAL	1	TRUE	0	0.412572703243746	2		584	752	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434927	49434953	+	inframe_deletion	In_Frame_Del	DEL	GGCTGCGCAGGGGCCCCCGTAGGACTA	GGCTGCGCAGGGGCCCCCGTAGGACTA	-	novel	NA	P-0014580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	137	704	0	ENST00000301067.7:c.6600_6626del	p.Ser2201_Pro2209del	p.S2201_P2209del	ENST00000301067	NM_003482.3	2200	ccTAGTCCTACGGGGGCCCCTGCGCAGCCc/ccc	31/54	0.383737335705161	2	FACETS	0.792	0.72	0.867	0.396	0.36	0.434	SUBCLONAL	1	TRUE	0	0.412572703243746	2		704	839	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483906	88483906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	211	672	1	ENST00000360948.2:c.1664C>T	p.Ala555Val	p.A555V	ENST00000360948	NM_001012338.2	555	gCc/gTc	14/19	0.383737335705161	2	FACETS	1	0.928	1	0.5	0.464	0.537	CLONAL	1	TRUE	0	0.412572703243746	2		673	1023	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61717733	61717780	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTTAAATCCCATGAAAACTTTTAAGAAAAGGTAGAAATACTTACTTTG	GTTAAATCCCATGAAAACTTTTAAGAAAAGGTAGAAATACTTACTTTG	-	novel	NA	P-0014580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	19	179	0	ENST00000401558.2:c.2019_2022+44del		p.X673_splice	ENST00000401558	NM_003400.3	673		17/25	0.383737335705161	2	FACETS	0.269	0.203	0.345	0.134	0.101	0.173	SUBCLONAL	1	TRUE	0	0.412572703243746	2		179	343	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206555	36206856	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGCTCCCAGGTGGTGCTGTTGGTTCGAGGCCTTTCTCTGAGCATCAAGGGGAAACCCCAGTTGGTCTGGGAAGGTGTGTGCACATGGGGGCCAGTTGTGGGTGGTGGCCCAGGTGCAGGAGAGGCGGGCAGTGGGCTCCATCTGGTACTTACCCTGCATCTGACTCTGAGGCTGAGGGTTAAAGGCAGTGGAGTGGTTCAGGGAGGCACGAGGGTTGGGCGTGGGGGCTGGGTGGTGTGGGCTGACCCTCATGGCTGTGCGCCGCAGCTGCTCCAGTTCACTGAGCCGCTCGGAAAAGGACA	AGCTCCCAGGTGGTGCTGTTGGTTCGAGGCCTTTCTCTGAGCATCAAGGGGAAACCCCAGTTGGTCTGGGAAGGTGTGTGCACATGGGGGCCAGTTGTGGGTGGTGGCCCAGGTGCAGGAGAGGCGGGCAGTGGGCTCCATCTGGTACTTACCCTGCATCTGACTCTGAGGCTGAGGGTTAAAGGCAGTGGAGTGGTTCAGGGAGGCACGAGGGTTGGGCGTGGGGGCTGGGTGGTGTGGGCTGACCCTCATGGCTGTGCGCCGCAGCTGCTCCAGTTCACTGAGCCGCTCGGAAAAGGACA	-	novel	NA	P-0014580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	95	578	0	ENST00000300305.3:c.656_805+152del		p.X219_splice	ENST00000300305		219		6/8	0.201946468562308	2	FACETS	0.546	0.486	0.611	0.273	0.243	0.306	INDETERMINATE	1	TRUE	0	0.412572703243746	2		578	843	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480491	89480491	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	63	218	0	ENST00000336596.2:c.2328A>T	p.Glu776Asp	p.E776D	ENST00000336596	NM_005233.5	776	gaA/gaT	13/17	1	2	FACETS	0.764	0.663	0.872	0.764	0.663	0.872	SUBCLONAL	1	TRUE	1	0.412572703243746	2		218	400	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564109	139564109	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	173	753	0	ENST00000308874.7:c.249G>C	p.Arg83Ser	p.R83S	ENST00000308874		83	agG/agC	5/10	1	2	FACETS	0.656	0.602	0.712	0.656	0.602	0.712	SUBCLONAL	1	TRUE	1	0.412572703243746	2		753	1279	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340883	70340883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	160	566	1	ENST00000374080.3:c.616C>T	p.Arg206Trp	p.R206W	ENST00000374080		206	Cgg/Tgg	5/45	1	2	FACETS	0.888	0.815	0.965	0.888	0.815	0.965	CLONAL	1	TRUE	1	0.412572703243746	2		567	873	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042209	6042209	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	316	795	1	ENST00000265849.7:c.412G>A	p.Asp138Asn	p.D138N	ENST00000265849	NM_000535.5	138	Gat/Aat	5/15	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.368056520138327	2		796	1255	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0014610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	451	441	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.517016622891751	6	FACETS	0.874	0.834	0.915	0.874	0.834	0.915	CLONAL	3	TRUE	3	0.517016622891751	6		441	1353	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427090	49427090	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	250	497	0	ENST00000301067.7:c.11398G>A	p.Gly3800Ser	p.G3800S	ENST00000301067	NM_003482.3	3800	Ggc/Agc	39/54	0.517016622891751	3	FACETS	0.969	0.913	1	0.646	0.608	0.684	CLONAL	2	TRUE	0	0.517016622891751	3		497	628	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577017	7577017	+	splice_donor_variant	Splice_Site	SNP	A	A	T	rs1131691016	NA	P-0014610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	369	691	1	ENST00000269305.4:c.919+2T>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.500873447568413	2	FACETS	0.995	0.952	1	0.995	0.952	1	CLONAL	2	TRUE	0	0.517016622891751	2		692	717	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61717854	61717855	+	missense_variant	Missense_Mutation	DNP	CT	CT	AA	novel	NA	P-0014610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	200	665	0	ENST00000401558.2:c.1944_1945delinsTT	p.Val649Leu	p.V649L	ENST00000401558	NM_003400.3	648	acAGta/acTTta	17/25	0.505127731946724	3	FACETS	0.938	0.869	1	0.469	0.434	0.505	CLONAL	1	TRUE	1	0.517016622891751	3		665	1038	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031954	26031954	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	80	291	0	ENST00000244661.2:c.335C>G	p.Ala112Gly	p.A112G	ENST00000244661	NM_003537.3	112	gCc/gGc	1/1	0.494273085504262	4	FACETS	0.8	0.705	0.901	0.4	0.352	0.451	CLONAL	1	TRUE	2	0.517016622891751	4		291	587	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	235	389	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	0.517343700488145	2		389	899	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0014621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	145	597	4	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.517343700488145	1	FACETS	0.848	0.779	0.919	0.848	0.779	0.919	CLONAL	1	TRUE	0	0.517343700488145	1		601	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0014621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	277	814	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.517343700488145	1	FACETS	0.868	0.816	0.92	0.868	0.816	0.92	CLONAL	1	TRUE	0	0.517343700488145	1		814	915	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573978	41573978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	246	768	0	ENST00000263253.7:c.6263G>A	p.Arg2088Gln	p.R2088Q	ENST00000263253	NM_001429.3	2088	cGg/cAg	31/31	1	2	FACETS	0.995	0.931	1	0.995	0.931	1	CLONAL	1	TRUE	1	0.517343700488145	2		768	956	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0014627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	70	306	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.20574013451339	2		306	668	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652129	36652129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34916193	NA	P-0014627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	63	587	0	ENST00000244741.5:c.251G>A	p.Arg84Gln	p.R84Q	ENST00000244741	NM_000389.4	84	cGa/cAa	2/3	1	2	FACETS	0.6	0.517	0.69	0.6	0.517	0.69	SUBCLONAL	1	TRUE	1	0.20574013451339	2		587	1021	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218789	66218789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	40	527	0	ENST00000273854.3:c.2269G>A	p.Glu757Lys	p.E757K	ENST00000273854	NM_004439.5	757	Gag/Aag	13/18	0.151725795878424	1	FACETS	0.486	0.402	0.579	0.486	0.402	0.579	SUBCLONAL	1	TRUE	0	0.20574013451339	1		527	718	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs786201057	NA	P-0014627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	114	449	1	ENST00000269305.4:c.374C>A	p.Thr125Lys	p.T125K	ENST00000269305	NM_001126112.2	125	aCg/aAg	4/11	0.139670825381479	3	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.20574013451339	3		450	835	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374648	118374648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1202827611	NA	P-0014627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	67	402	0	ENST00000534358.1:c.8041G>A	p.Asp2681Asn	p.D2681N	ENST00000534358	NM_005933.3	2681	Gac/Aac	27/36	0.184165706048493	1	FACETS	0.891	0.774	1	0.891	0.774	1	CLONAL	1	TRUE	0	0.20574013451339	1		402	656	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	459851	459851	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0014627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1261	91	804	0	ENST00000399788.2:c.1244C>G	p.Ser415Ter	p.S415*	ENST00000399788	NM_001042603.1	415	tCa/tGa	10/28	1	2	FACETS	0.654	0.579	0.736	0.654	0.579	0.736	SUBCLONAL	1	TRUE	1	0.20574013451339	2		804	1352	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	228	389	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.876	0.82	0.934	0.876	0.82	0.934	CLONAL	1	TRUE	1	0.713935634162593	2		389	729	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0014651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	257	313	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.678612857428379	2	FACETS	0.909	0.869	0.949	0.909	0.869	0.949	CLONAL	2	TRUE	0	0.713935634162593	2		313	396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0014651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	409	550	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.685724297209379	1	FACETS	0.978	0.939	1	0.978	0.939	1	CLONAL	1	TRUE	0	0.713935634162593	1		550	753	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479811	67479811	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500766	NA	P-0014651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	756	803	1	ENST00000327367.4:c.1118G>A	p.Arg373His	p.R373H	ENST00000327367	NM_005902.3	373	cGc/cAc	8/9	0.713935634162593	2	FACETS	0.994	0.971	1	0.994	0.971	1	CLONAL	2	TRUE	0	0.713935634162593	2		804	1065	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0014672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	96	519	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.361587822823656	2		519	528	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288966	11288966	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773908615	NA	P-0014672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	17	552	0	ENST00000361445.4:c.2789G>A	p.Ser930Asn	p.S930N	ENST00000361445	NM_004958.3	930	aGc/aAc	19/58	1	2	FACETS	0.45	0.336	0.584	0.45	0.336	0.584	SUBCLONAL	1	TRUE	1	0.361587822823656	2		552	209	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582247	52582261	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCGAGCTGAAAATTA	TCGAGCTGAAAATTA	-	novel	NA	P-0014672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	15	225	0	ENST00000394830.3:c.4577-10_4581del		p.X1526_splice	ENST00000394830	NM_018313.4	1526		30/30	0.186098115967536	3	FACETS	0.754	0.556	0.987	0.377	0.278	0.494	INDETERMINATE	1	TRUE	1	0.361587822823656	3		225	130	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739631	41739631	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	25	859	0	ENST00000242208.4:c.342T>G	p.Asn114Lys	p.N114K	ENST00000242208	NM_002192.2	114	aaT/aaG	2/3	0.299332832849182	3	FACETS	0.437	0.344	0.543	0.218	0.172	0.272	SUBCLONAL	1	TRUE	1	0.361587822823656	3		859	374	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133236	38133236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	32	714	0	ENST00000317025.8:c.4237C>T	p.Pro1413Ser	p.P1413S	ENST00000317025	NM_023034.1	1413	Cct/Tct	24/24	0.361587822823656	3	FACETS	0.483	0.391	0.586	0.241	0.195	0.293	SUBCLONAL	1	TRUE	1	0.361587822823656	3		714	433	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520273	176520273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759709290	NA	P-0014688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	32	617	0	ENST00000292408.4:c.1192C>T	p.Arg398Trp	p.R398W	ENST00000292408	NM_213647.1	398	Cgg/Tgg	9/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		617	495	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412023	116412023	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	102	722	0	ENST00000397752.3:c.3008A>T	p.Tyr1003Phe	p.Y1003F	ENST00000397752	NM_000245.2	1003	tAc/tTc	14/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		722	1012	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0014691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	178	462	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.780207219352663	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.780207219352663	2		463	223	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259650	11259650	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	177	807	0	ENST00000361445.4:c.4055A>C	p.Glu1352Ala	p.E1352A	ENST00000361445	NM_004958.3	1352	gAa/gCa	27/58	0.452793106760065	3	FACETS	1	0.973	1	0.703	0.663	0.743	INDETERMINATE	2	TRUE	0	0.780207219352663	3		807	299	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717772	89717772	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	24	498	0	ENST00000371953.3:c.797A>G	p.Lys266Arg	p.K266R	ENST00000371953	NM_000314.4	266	aAa/aGa	7/9	1	2	FACETS	0.575	0.459	0.703	0.575	0.459	0.703	SUBCLONAL	1	TRUE	1	0.780207219352663	2		498	107	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361114	70361114	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	39	675	0	ENST00000374080.3:c.6302A>G	p.Gln2101Arg	p.Q2101R	ENST00000374080		2101	cAg/cGg	43/45	0.780207219352663	1	FACETS	0.421	0.355	0.491	0.421	0.355	0.491	SUBCLONAL	1	TRUE	0	0.780207219352663	1		675	145	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0014701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	325	663	2	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	0.6370837130185	1	FACETS	0.869	0.825	0.914	0.869	0.825	0.914	CLONAL	1	TRUE	0	0.6370837130185	1		665	800	SUCCESS
AR	367	MSKCC	GRCh37	X	66937371	66937371	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	410	420	0	ENST00000374690.3:c.2225G>T	p.Trp742Leu	p.W742L	ENST00000374690	NM_000044.3	742	tGg/tTg	5/8	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.6370837130185	1		420	662	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991668	25991668	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	302	578	1	ENST00000435504.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000435504		192	Cag/Tag	7/13	0.6370837130185	1	FACETS	0.98	0.931	1	0.98	0.931	1	CLONAL	1	TRUE	0	0.6370837130185	1		579	659	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151868369	151868369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	355	691	0	ENST00000262189.6:c.9433G>A	p.Gly3145Arg	p.G3145R	ENST00000262189	NM_170606.2	3145	Gga/Aga	40/59	1	2	FACETS	0.934	0.885	0.984	0.934	0.885	0.984	CLONAL	1	TRUE	1	0.6370837130185	2		691	1193	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0014708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	21	571	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	0.150686149594214	4	FACETS	0.806	0.619	1	0.403	0.309	0.514	CLONAL	1	TRUE	2	0.1	4		571	573	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0014708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	31	552	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	0.254469057439202	4	FACETS	0.786	0.633	0.96	0.393	0.316	0.48	CLONAL	1	TRUE	2	0.1	4		552	868	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121909229	NA	P-0014708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	31	692	1	ENST00000371953.3:c.389G>T	p.Arg130Leu	p.R130L	ENST00000371953	NM_000314.4	130	cGa/cTa	5/9	0.150686149594214	4	FACETS	1	0.827	1	0.514	0.414	0.627	CLONAL	1	TRUE	2	0.1	4		693	664	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717717	89717717	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	35	682	0	ENST00000371953.3:c.743del	p.Pro248LeufsTer8	p.P248Lfs*8	ENST00000371953	NM_000314.4	248	Cct/ct	7/9	0.150686149594214	4	FACETS	1	0.904	1	0.587	0.48	0.708	CLONAL	1	TRUE	2	0.1	4		682	656	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28929495	NA	P-0014729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	211	629	0	ENST00000275493.2:c.2155G>A	p.Gly719Ser	p.G719S	ENST00000275493	NM_005228.3	719	Ggc/Agc	18/28	0.236240016282209	4	FACETS	1	0.986	1	0.816	0.759	0.875	CLONAL	2	TRUE	1	0.236240016282209	4		629	902	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0014729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	252	478	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.236240016282209	4	FACETS	0.93	0.872	0.991	0.93	0.872	0.991	CLONAL	3	TRUE	1	0.236240016282209	4		478	945	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519985	NA	P-0014729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	254	558	0	ENST00000269305.4:c.857A>C	p.Glu286Ala	p.E286A	ENST00000269305	NM_001126112.2	286	gAa/gCa	8/11	0.179326269236077	3	FACETS	0.842	0.789	0.896	0.842	0.789	0.896	CLONAL	3	TRUE	0	0.236240016282209	3		558	952	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965377	25965377	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	263	395	0	ENST00000435504.4:c.3829G>T	p.Val1277Leu	p.V1277L	ENST00000435504		1277	Gtg/Ttg	13/13	0.236240016282209	3	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.236240016282209	3		395	1034	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79960997	79960997	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	54	298	0	ENST00000265081.6:c.394A>G	p.Lys132Glu	p.K132E	ENST00000265081	NM_002439.4	132	Aag/Gag	3/24	0.236240016282209	4	FACETS	0.612	0.521	0.712	0.204	0.173	0.238	SUBCLONAL	1	TRUE	1	0.236240016282209	4		298	924	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0014733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	270	426	1	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.165738017963005	2	FACETS	0.987	0.924	1	0.987	0.924	1	CLONAL	2	TRUE	0	0.21	2		427	1303	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602329	28602329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372303125	NA	P-0014733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	74	333	0	ENST00000241453.7:c.2039C>T	p.Ala680Val	p.A680V	ENST00000241453	NM_004119.2	680	gCg/gTg	16/24	1	2	FACETS	0.731	0.638	0.832	0.731	0.638	0.832	SUBCLONAL	1	TRUE	1	0.21	2		333	964	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509639	29509639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	283	453	1	ENST00000356175.3:c.844C>T	p.Gln282Ter	p.Q282*	ENST00000356175	NM_000267.3	282	Cag/Tag	8/57	0.165738017963005	2	FACETS	0.946	0.888	1	0.946	0.888	1	CLONAL	2	TRUE	0	0.21	2		454	1424	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78422295	78422295	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	372	279	0	ENST00000370768.2:c.1667del	p.Pro556LeufsTer109	p.P556Lfs*109	ENST00000370768	NM_003902.3	556	cCt/ct	17/20	0.3	5	FACETS	0.968	0.919	1			1	CLONAL	4	TRUE	NA	0.21	5		279	1203	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274195	10274195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542256226	NA	P-0014733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	43	315	0	ENST00000330684.3:c.74C>T	p.Ala25Val	p.A25V	ENST00000330684	NM_001134407.1	25	gCg/gTg	2/13	1	2	FACETS	0.566	0.473	0.671	0.566	0.473	0.671	SUBCLONAL	1	TRUE	1	0.21	2		315	723	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597364	10597364	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1366	254	627	5	ENST00000171111.5:c.1839C>A	p.Cys613Ter	p.C613*	ENST00000171111	NM_203500.1	613	tgC/tgA	6/6	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.21	2		632	1620	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	88	661	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.792	0.7	0.891	0.792	0.7	0.891	SUBCLONAL	1	TRUE	1	0.212758033355343	2		661	1044	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602341	10602341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1178941219	NA	P-0014736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1201	184	554	1	ENST00000171111.5:c.1237C>T	p.Arg413Cys	p.R413C	ENST00000171111	NM_203500.1	413	Cgt/Tgt	3/6	0.212758033355343	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.212758033355343	1		555	1385	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851016	63851016	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	113	455	0	ENST00000279873.7:c.1797del	p.Thr600ProfsTer29	p.T600Pfs*29	ENST00000279873	NM_032199.2	598	ttC/tt	10/10	1	2	FACETS	0.878	0.788	0.974	0.878	0.788	0.974	CLONAL	1	TRUE	1	0.212758033355343	2		455	1210	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934797	9934797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749732928	NA	P-0014736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	80	405	2	ENST00000330684.3:c.1493G>A	p.Gly498Asp	p.G498D	ENST00000330684	NM_001134407.1	498	gGt/gAt	6/13	1	2	FACETS	0.703	0.617	0.797	0.703	0.617	0.797	SUBCLONAL	1	TRUE	1	0.212758033355343	2		407	1069	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210406	2210406	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	108	464	0	ENST00000398665.3:c.1013A>T	p.Gln338Leu	p.Q338L	ENST00000398665	NM_032482.2	338	cAg/cTg	13/28	0.212758033355343	1	FACETS	0.949	0.85	1	0.949	0.85	1	CLONAL	1	TRUE	0	0.212758033355343	1		464	956	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101842	11101842	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	156	483	0	ENST00000358026.2:c.1262T>A	p.Val421Glu	p.V421E	ENST00000358026	NM_001128849.1	421	gTg/gAg	8/36	0.212758033355343	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.212758033355343	1		483	1149	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0014753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	97	503	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.746	0.664	0.834	0.746	0.664	0.834	SUBCLONAL	1	TRUE	1	0.27	2		503	963	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	64	503	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	0.27	2		503	471	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0014753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	96	753	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.828	0.737	0.925	0.828	0.737	0.925	CLONAL	1	TRUE	1	0.27	2		754	859	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041662	47041663	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0014753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	140	869	0	ENST00000377604.3:c.1887_1888del	p.Ala631ThrfsTer41	p.A631Tfs*41	ENST00000377604	NM_001204468.1	629	acAGgg/acgg	17/24	1	2	FACETS	0.825	0.749	0.905	0.825	0.749	0.905	CLONAL	1	TRUE	1	0.27	2		869	1257	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156734	20156734	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	72	471	0	ENST00000379607.5:c.23G>C	p.Gly8Ala	p.G8A	ENST00000379607	NM_001412.3	8	gGa/gCa	2/7	1	2	FACETS	0.932	0.815	1	0.932	0.815	1	CLONAL	1	TRUE	1	0.27	2		471	572	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	75	528	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.785	0.693	0.883	0.785	0.693	0.883	SUBCLONAL	1	TRUE	1	0.5520334246336	2		530	346	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs139236063	NA	P-0014759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5489	501	520	0	ENST00000275493.2:c.1793G>C	p.Gly598Ala	p.G598A	ENST00000275493	NM_005228.3	598	gGa/gCa	15/28	0.5520334246336	32	FACETS	0.937	0.89	0.986			1	CLONAL	3	TRUE	NA	0.5520334246336	32		520	5990	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813023	89813023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142833057	NA	P-0014759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	189	456	0	ENST00000389301.3:c.3482C>T	p.Thr1161Met	p.T1161M	ENST00000389301	NM_000135.2	1161	aCg/aTg	35/43	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.5520334246336	2		456	630	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221783	55221783	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5010	723	541	0	ENST00000275493.2:c.827A>T	p.Gln276Leu	p.Q276L	ENST00000275493	NM_005228.3	276	cAg/cTg	7/28	0.5520334246336	32	FACETS	1	0.986	1			1	CLONAL	4	TRUE	NA	0.5520334246336	32		541	5733	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	381	528	2				ENST00000310581	NM_198253.2	-/1132			0.822335367691109	3	FACETS	0.965	0.927	1	0.965	0.927	1	CLONAL	2	TRUE	1	0.853349966675307	3		530	660	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236087	108236087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781894	NA	P-0014761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	254	510	0	ENST00000278616.4:c.9023G>A	p.Arg3008His	p.R3008H	ENST00000278616	NM_000051.3	3008	cGt/cAt	63/63	0.853349966675307	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.853349966675307	1		510	338	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0014761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	354	673	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	0.974	1	CLONAL	1	TRUE	1	0.853349966675307	2		673	803	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755612	39755612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776452839	NA	P-0014761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	195	568	2	ENST00000288319.7:c.1153C>T	p.Arg385Cys	p.R385C	ENST00000288319	NM_182918.3	385	Cgc/Tgc	10/10	1	2	FACETS	0.721	0.67	0.773	0.721	0.67	0.773	SUBCLONAL	1	TRUE	1	0.853349966675307	2		570	634	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717661	89717661	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0014761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	273	485	0	ENST00000371953.3:c.686C>G	p.Ser229Ter	p.S229*	ENST00000371953	NM_000314.4	229	tCa/tGa	7/9	0.853349966675307	1	FACETS	0.943	0.905	0.98	0.943	0.905	0.98	CLONAL	1	TRUE	0	0.853349966675307	1		485	389	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436315	110436315	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	61	371	0	ENST00000375856.3:c.2086G>C	p.Ala696Pro	p.A696P	ENST00000375856	NM_003749.2	696	Gcc/Ccc	1/2	1	2	FACETS	0.316	0.273	0.363	0.316	0.273	0.363	SUBCLONAL	1	TRUE	1	0.853349966675307	2		371	452	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728620	190728620	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	59	603	0	ENST00000441310.2:c.2008A>G	p.Thr670Ala	p.T670A	ENST00000441310	NM_000534.4	670	Acc/Gcc	10/13	1	2	FACETS	0.205	0.176	0.237	0.205	0.176	0.237	SUBCLONAL	1	TRUE	1	0.853349966675307	2		603	675	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266502	115266502	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0014768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	84	318	0	ENST00000438362.2:c.2011+2T>G		p.X671_splice	ENST00000438362	NM_001242891.1	671			0.171681215649137	2	FACETS	0.689	0.607	0.778	0.345	0.303	0.389	SUBCLONAL	1	TRUE	0	0.249481160220792	2		318	977	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1250	523	703	0	ENST00000269305.4:c.376T>C	p.Tyr126His	p.Y126H	ENST00000269305	NM_001126112.2	126	Tac/Cac	5/11	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.249481160220792	2		703	1773	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462632	29462632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371005946	NA	P-0014768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	370	532	0	ENST00000389048.3:c.2269G>A	p.Val757Met	p.V757M	ENST00000389048	NM_004304.4	757	Gtg/Atg	13/29	1	2	FACETS	1	0.948	1	1	0.996	1	CLONAL	2	TRUE	1	0.249481160220792	2		532	1481	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149946	202149946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1280661555	NA	P-0014768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	132	440	2	ENST00000358485.4:c.1387G>A	p.Ala463Thr	p.A463T	ENST00000358485	NM_001080125.1	463	Gcc/Acc	8/9	0.147675313660425	3	FACETS	0.917	0.83	1	0.306	0.276	0.337	INDETERMINATE	1	TRUE	0	0.249481160220792	3		442	1298	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0014768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	80	387	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.782	0.687	0.884	0.782	0.687	0.884	SUBCLONAL	1	TRUE	1	0.249481160220792	2		387	820	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	62	262	1	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	0.208385915688356	0	FACETS	0.703	0.607	0.806			1	SUBCLONAL	1	TRUE	0	0.249481160220792	0		263	531	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966548	36966548	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	92	380	0	ENST00000358127.4:c.778C>T	p.Gln260Ter	p.Q260*	ENST00000358127	NM_001280556.1	260	Cag/Tag	6/10	0.171681215649137	2	FACETS	0.72	0.638	0.808	0.36	0.319	0.404	SUBCLONAL	1	TRUE	0	0.249481160220792	2		380	1024	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0014772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	322	422	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.411956544895421	2	FACETS	0.975	0.927	1	0.975	0.927	1	CLONAL	2	TRUE	0	0.449379014041092	2		422	735	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0014772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	31	243	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.28	0.226	0.342	0.28	0.226	0.342	SUBCLONAL	1	TRUE	1	0.449379014041092	2		243	492	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575671	48575671	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0014772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	235	416	0	ENST00000342988.3:c.431C>G	p.Ser144Ter	p.S144*	ENST00000342988	NM_005359.5	144	tCa/tGa	4/12	0.449379014041092	2	FACETS	0.834	0.783	0.886	0.834	0.783	0.886	CLONAL	2	TRUE	0	0.449379014041092	2		416	627	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044713	47044713	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	134	727	0	ENST00000377604.3:c.2113G>T	p.Glu705Ter	p.E705*	ENST00000377604	NM_001204468.1	705	Gag/Tag	19/24	0.449576801615058	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.449379014041092	1		727	454	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204512055	204512055	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	73	245	0	ENST00000367182.3:c.655G>A	p.Asp219Asn	p.D219N	ENST00000367182	NM_001278516.1	219	Gat/Aat	8/11	0.449576801615058	4	FACETS	0.838	0.734	0.95	0.279	0.244	0.317	CLONAL	1	TRUE	1	0.449379014041092	4		245	562	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201088	108201099	+	inframe_deletion	In_Frame_Del	DEL	CCGACTTTGTTC	CCGACTTTGTTC	-	novel	NA	P-0014772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	71	354	0	ENST00000278616.4:c.7457_7468del	p.Arg2486_Ser2489del	p.R2486_S2489del	ENST00000278616	NM_000051.3	2485	ttCCGACTTTGTTCc/ttc	50/63	1	2	FACETS	0.68	0.595	0.77	0.68	0.595	0.77	SUBCLONAL	1	TRUE	1	0.449379014041092	2		354	465	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865689	57865689	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	103	706	0	ENST00000228682.2:c.3166C>G	p.Pro1056Ala	p.P1056A	ENST00000228682	NM_005269.2	1056	Ccc/Gcc	12/12	1	2	FACETS	0.797	0.715	0.884	0.797	0.715	0.884	SUBCLONAL	1	TRUE	1	0.449379014041092	2		706	575	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794384	42794384	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0014772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	106	687	1	ENST00000575354.2:c.1465-1G>T		p.X489_splice	ENST00000575354	NM_015125.3	489			0.155365313362998	0	FACETS	0.461	0.415	0.511			1	INDETERMINATE	1	TRUE	0	0.449379014041092	0		688	563	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271233	1271233	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0014772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	18	193	0	ENST00000310581.5:c.2468+1G>A		p.X823_splice	ENST00000310581	NM_198253.2	823			NA	2	FACETS	0.564	0.428	0.722			1	INDETERMINATE	1	TRUE	NA	0.449379014041092	2		193	142	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288194	33288194	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375524506	NA	P-0014772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	113	391	0	ENST00000374542.5:c.1214C>T	p.Ser405Phe	p.S405F	ENST00000374542	NM_001141970.1	405	tCt/tTt	4/8	0.161622680370072	4	FACETS	1	0.978	1	0.646	0.583	0.712	INDETERMINATE	1	TRUE	2	0.449379014041092	4		391	564	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	210	661	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.295523432099686	3	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	1	0.327565015605702	3		661	739	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0014784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	243	629	0	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	NA	2	FACETS	1	0.972	1			1	INDETERMINATE	3	TRUE	NA	0.327565015605702	2		629	475	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636754	8636754	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	135	482	0	ENST00000356435.5:c.155G>T	p.Arg52Ile	p.R52I	ENST00000356435		52	aGa/aTa	2/35	0.295523432099686	3	FACETS	0.924	0.845	1	0.924	0.845	1	CLONAL	2	TRUE	1	0.327565015605702	3		482	519	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850620	63850620	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0014784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	25	251	1	ENST00000279873.7:c.1399-1G>T		p.X467_splice	ENST00000279873	NM_032199.2	467			0.327565015605702	3	FACETS	0.43	0.338	0.536	0.215	0.169	0.268	SUBCLONAL	1	TRUE	1	0.327565015605702	3		252	413	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597459	10597459	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	256	829	0	ENST00000171111.5:c.1744G>A	p.Glu582Lys	p.E582K	ENST00000171111	NM_203500.1	582	Gag/Aag	6/6	0.327565015605702	2	FACETS	0.847	0.799	0.896	1	0.991	1	CLONAL	3	TRUE	0	0.327565015605702	2		829	615	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905343	50905343	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	128	802	0	ENST00000440232.2:c.551G>T	p.Gly184Val	p.G184V	ENST00000440232	NM_002691.3	184	gGg/gTg	5/27	1	2	FACETS	0.868	0.793	0.947	1	0.989	1	CLONAL	2	TRUE	1	0.327565015605702	2		802	450	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899067	40899067	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	114	608	1	ENST00000373198.4:c.2203C>A	p.Pro735Thr	p.P735T	ENST00000373198	NM_133170.3	735	Ccg/Acg	14/32	0.327565015605702	3	FACETS	1	0.983	1	0.732	0.662	0.807	CLONAL	1	TRUE	1	0.327565015605702	3		609	553	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306634	41306634	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	194	729	1	ENST00000373198.4:c.1025C>A	p.Ser342Tyr	p.S342Y	ENST00000373198	NM_133170.3	342	tCt/tAt	7/32	0.327565015605702	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.327565015605702	3		730	651	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945663	54945663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	14	301	0	ENST00000312783.6:c.907G>A	p.Gly303Ser	p.G303S	ENST00000312783	NM_198436.1	303	Ggt/Agt	9/10	0.327565015605702	3	FACETS	0.393	0.284	0.526	0.197	0.142	0.263	SUBCLONAL	1	TRUE	1	0.327565015605702	3		301	253	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651403	52651403	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	161	598	0	ENST00000394830.3:c.1693C>T	p.Pro565Ser	p.P565S	ENST00000394830	NM_018313.4	565	Cca/Tca	15/30	NA	2	FACETS	0.993	0.918	1			1	INDETERMINATE	2	TRUE	NA	0.327565015605702	2		598	495	SUCCESS
APC	324	MSKCC	GRCh37	5	112173789	112173789	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	103	371	0	ENST00000257430.4:c.2498G>T	p.Ser833Ile	p.S833I	ENST00000257430	NM_000038.5	833	aGc/aTc	16/16	0.214763019368447	5	FACETS	0.979	0.88	1	0.653	0.587	0.722	CLONAL	2	TRUE	2	0.327565015605702	5		371	479	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553793	106553793	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	120	389	0	ENST00000369096.4:c.1758G>C	p.Gln586His	p.Q586H	ENST00000369096	NM_001198.3	586	caG/caC	5/7	0.327565015605702	2	FACETS	0.944	0.861	1	0.944	0.861	1	CLONAL	2	TRUE	0	0.327565015605702	2		389	388	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467880	50467880	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	65	403	0	ENST00000331340.3:c.1115A>G	p.Asn372Ser	p.N372S	ENST00000331340	NM_006060.4	372	aAc/aGc	8/8	0.246156346853417	5	FACETS	0.843	0.735	0.958	0.562	0.49	0.639	CLONAL	2	TRUE	2	0.327565015605702	5		403	351	SUCCESS
AR	367	MSKCC	GRCh37	X	66937394	66937394	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	213	351	0	ENST00000374690.3:c.2248A>T	p.Met750Leu	p.M750L	ENST00000374690	NM_000044.3	750	Atg/Ttg	5/8	0.327565015605702	2	FACETS	1	0.976	1			1	CLONAL	3	TRUE	NA	0.327565015605702	2		351	408	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0014791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	104	603	1	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.287717031909366	1	FACETS	0.723	0.647	0.804	0.723	0.647	0.804	SUBCLONAL	1	TRUE	0	0.287717031909366	1		604	856	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	63	528	2				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.989	0.857	1			1	INDETERMINATE	1	TRUE	NA	0.287717031909366	2		530	443	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676270	29676270	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1135402903	NA	P-0014791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	93	418	0	ENST00000356175.3:c.7258+1G>T		p.X2420_splice	ENST00000356175	NM_000267.3	2420			1	2	FACETS	0.787	0.699	0.881	0.787	0.699	0.881	SUBCLONAL	1	TRUE	1	0.287717031909366	2		418	821	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578266	7578266	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs942158624	NA	P-0014813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	506	584	0	ENST00000269305.4:c.583A>T	p.Ile195Phe	p.I195F	ENST00000269305	NM_001126112.2	195	Atc/Ttc	6/11	0.420974163628587	6	FACETS	0.931	0.894	0.968	0.931	0.894	0.968	INDETERMINATE	3	TRUE	3	0.880405463881537	6		584	1136	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0014813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	523	627	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.420974163628587	6	FACETS	0.98	0.943	1	0.98	0.943	1	INDETERMINATE	3	TRUE	3	0.880405463881537	6		627	1116	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807439	36807439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	236	613	0	ENST00000373129.3:c.1225C>T	p.Pro409Ser	p.P409S	ENST00000373129	NM_032017.1	409	Ccg/Tcg	12/12	0.462004882604726	3	FACETS	0.925	0.865	0.986			1	INDETERMINATE	1	TRUE	NA	0.880405463881537	3		613	835	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984417	201984417	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	731	677	0	ENST00000359651.3:c.1083del	p.Trp361Ter	p.W361*	ENST00000359651		361	tGg/tg	8/8	0.880405463881537	3	FACETS	0.944	0.916	0.971			1	CLONAL	2	TRUE	NA	0.880405463881537	3		677	1267	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333449	70333449	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	213	580	0	ENST00000373644.4:c.1357del	p.Gln453LysfsTer39	p.Q453Kfs*39	ENST00000373644	NM_030625.2	452	Ccc/cc	2/12	1	2	FACETS	0.88	0.824	0.936	0.88	0.824	0.936	CLONAL	1	TRUE	1	0.880405463881537	2		580	550	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154882	2154882	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	489	660	0	ENST00000434045.2:c.339C>A	p.Ser113Arg	p.S113R	ENST00000434045	NM_001127598.1	113	agC/agA	4/5	0.420974163628587	6	FACETS	0.955	0.918	0.993	0.955	0.918	0.993	INDETERMINATE	3	TRUE	3	0.880405463881537	6		660	1070	SUCCESS
ATM	472	MSKCC	GRCh37	11	108127042	108127042	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	181	382	0	ENST00000278616.4:c.2225A>C	p.Lys742Thr	p.K742T	ENST00000278616	NM_000051.3	742	aAg/aCg	14/63	0.857999777577023	2	FACETS	0.937	0.874	1	0.468	0.437	0.5	CLONAL	1	TRUE	0	0.880405463881537	2		382	439	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870877	12870877	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375297371	NA	P-0014813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	252	191	0	ENST00000228872.4:c.104C>T	p.Pro35Leu	p.P35L	ENST00000228872	NM_004064.3	35	cCg/cTg	1/3	0.552066657841865	6	FACETS	0.983	0.929	1	0.983	0.929	1	CLONAL	3	TRUE	3	0.880405463881537	6		191	536	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28882977	28882977	+	splice_region_variant,intron_variant	Splice_Region	SNP	T	T	A	novel	NA	P-0014813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	737	577	0	ENST00000282397.4:c.3720+3A>T		p.X1240_splice	ENST00000282397	NM_002019.4	1240			0.880405463881537	3	FACETS	0.981	0.967	0.995	0.981	0.967	0.995	CLONAL	3	TRUE	0	0.880405463881537	3		577	819	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544630	65544631	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0014813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	335	427	0	ENST00000358664.4:c.295_295+1delinsTT		p.X99_splice	ENST00000358664	NM_002382.4	99		4/5	0.867910094103515	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.880405463881537	2		427	372	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678397	88678397	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	268	706	1	ENST00000360948.2:c.1139C>A	p.Ala380Asp	p.A380D	ENST00000360948	NM_001012338.2	380	gCc/gAc	9/19	1	2	FACETS	0.917	0.866	0.969	0.917	0.866	0.969	CLONAL	1	TRUE	1	0.880405463881537	2		707	664	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821683	72821683	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs773915431	NA	P-0014813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	135	208	0	ENST00000268489.5:c.10492C>G	p.Gln3498Glu	p.Q3498E	ENST00000268489	NM_006885.3	3498	Caa/Gaa	10/10	0.880405463881537	3	FACETS	0.954	0.873	1	0.477	0.436	0.519	CLONAL	1	TRUE	1	0.880405463881537	3		208	463	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350203	89350203	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	234	665	1	ENST00000301030.4:c.2747A>T	p.Asn916Ile	p.N916I	ENST00000301030	NM_001256183.1	916	aAc/aTc	9/13	NA	2	FACETS	0.631	0.589	0.673			1	INDETERMINATE	1	TRUE	NA	0.880405463881537	2		666	843	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004817	16004817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	288	514	0	ENST00000268712.3:c.2437C>T	p.Pro813Ser	p.P813S	ENST00000268712	NM_006311.3	813	Ccc/Tcc	20/46	0.420974163628587	6	FACETS	1	0.993	1	0.491	0.462	0.522	INDETERMINATE	1	TRUE	3	0.880405463881537	6		514	1225	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224440	39224440	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs727505016	NA	P-0014813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	540	537	0	ENST00000402219.2:c.2918A>T	p.Gln973Leu	p.Q973L	ENST00000402219	NM_005633.3	973	cAg/cTg	18/23	0.420974163628587	6	FACETS	0.894	0.859	0.929	0.894	0.859	0.929	INDETERMINATE	3	TRUE	3	0.880405463881537	6		537	1263	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251704	212251704	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	409	303	0	ENST00000342788.4:c.3355G>C	p.Val1119Leu	p.V1119L	ENST00000342788	NM_005235.2	1119	Gtc/Ctc	27/28	0.587301480894299	4	FACETS	0.837	0.805	0.868	0.837	0.805	0.868	CLONAL	3	TRUE	1	0.880405463881537	4		303	696	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101180	41101180	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs41279258	NA	P-0014813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	369	466	0	ENST00000373198.4:c.1176C>A	p.Asn392Lys	p.N392K	ENST00000373198	NM_133170.3	392	aaC/aaA	8/32	0.636589231843061	4	FACETS	0.907	0.864	0.95	0.907	0.864	0.95	CLONAL	2	TRUE	2	0.880405463881537	4		466	869	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385101	41385101	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0014813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	396	588	0	ENST00000373198.4:c.859+1G>T		p.X287_splice	ENST00000373198	NM_133170.3	287			0.636589231843061	4	FACETS	0.884	0.843	0.924	0.884	0.843	0.924	CLONAL	2	TRUE	2	0.880405463881537	4		588	957	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259044	89259044	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	119	210	0	ENST00000336596.2:c.188C>A	p.Thr63Lys	p.T63K	ENST00000336596	NM_005233.5	63	aCa/aAa	3/17	0.50550771223753	4	FACETS	1	0.98	1	0.426	0.387	0.465	INDETERMINATE	1	TRUE	1	0.880405463881537	4		210	398	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851685	134851685	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	198	399	0	ENST00000398015.3:c.1091G>T	p.Arg364Leu	p.R364L	ENST00000398015	NM_004441.4	364	cGg/cTg	5/16	0.50550771223753	4	FACETS	1	0.988	1	0.436	0.405	0.467	INDETERMINATE	1	TRUE	1	0.880405463881537	4		399	647	SUCCESS
ATR	545	MSKCC	GRCh37	3	142259791	142259791	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	557	549	2	ENST00000350721.4:c.3536G>T	p.Arg1179Ile	p.R1179I	ENST00000350721	NM_001184.3	1179	aGa/aTa	18/47	0.50550771223753	4	FACETS	1	0.995	1	0.788	0.762	0.815	INDETERMINATE	2	TRUE	1	0.880405463881537	4		551	1006	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518153	187518154	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AG	novel	NA	P-0014813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	170	469	2	ENST00000441802.2:c.12540_12541delinsCT	p.Glu4181Ter	p.E4181*	ENST00000441802	NM_005245.3	4180	gcGGaa/gcCTaa	25/27	1	2	FACETS	0.88	0.818	0.943	0.88	0.818	0.943	CLONAL	1	TRUE	1	0.880405463881537	2		471	439	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729475	41729475	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	1177	461	0	ENST00000242208.4:c.1054G>T	p.Gly352Cys	p.G352C	ENST00000242208	NM_002192.2	352	Ggt/Tgt	3/3	0.880405463881537	7	FACETS	1	0.98	1	1	0.98	1	CLONAL	5	TRUE	2	0.880405463881537	7		461	1712	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367286	50367286	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	381	365	1	ENST00000331340.3:c.93G>T	p.Met31Ile	p.M31I	ENST00000331340	NM_006060.4	31	atG/atT	3/8	0.880405463881537	7	FACETS	0.919	0.871	0.968	0.368	0.348	0.388	CLONAL	2	TRUE	2	0.880405463881537	7		366	1507	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38283735	38283735	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	189	524	0	ENST00000425967.3:c.743T>C	p.Met248Thr	p.M248T	ENST00000425967	NM_001174067.1	248	aTg/aCg	7/19	0.820674928169493	4	FACETS	0.779	0.719	0.841			1	SUBCLONAL	1	TRUE	NA	0.880405463881537	4		524	1037	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974693	21974710	+	frameshift_variant	Frame_Shift_Del	DEL	CCGTAACTATTCGGTGCG	CCGTAACTATTCGGTGCG	T	novel	NA	P-0014813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	330	420	0	ENST00000304494.5:c.117_134delinsA	p.Asn39LysfsTer75	p.N39Kfs*75	ENST00000304494	NM_000077.4	39	aaCGCACCGAATAGTTACGGt/aaAt	1/3	0.864389979091401	2	FACETS	0.944	0.918	0.969	0.944	0.918	0.969	CLONAL	2	TRUE	0	0.880405463881537	2		420	397	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0014817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	238	422	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.197962396489388	3	FACETS	0.985	0.918	1	0.985	0.918	1	CLONAL	2	FALSE	1	0.201840272170292	3		422	1318	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633658	69633658	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	33	49	0	ENST00000334134.2:c.44G>T	p.Gly15Val	p.G15V	ENST00000334134	NM_005247.2	15	gGc/gTc	1/3	0.197962396489388	3	FACETS	1	0.858	1	1	0.954	1	CLONAL	3	FALSE	1	0.201840272170292	3		49	116	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578209	28578209	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	104	440	2	ENST00000241453.7:c.2962G>A	p.Ala988Thr	p.A988T	ENST00000241453	NM_004119.2	988	Gct/Act	24/24	1	2	FACETS	0.929	0.83	1	0.929	0.83	1	CLONAL	1	FALSE	1	0.201840272170292	2		442	1109	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988250	36988250	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1320	991	695	0	ENST00000354822.5:c.403A>T	p.Arg135Trp	p.R135W	ENST00000354822	NM_001079668.2	135	Agg/Tgg	2/3	0.201840272170292	7	FACETS	1	0.993	1			1	CLONAL	6	FALSE	NA	0.201840272170292	7		695	2311	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391075	89391075	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1321	108	661	0	ENST00000336596.2:c.1141C>G	p.Arg381Gly	p.R381G	ENST00000336596	NM_005233.5	381	Cgc/Ggc	5/17	1	2	FACETS	0.749	0.67	0.834	0.749	0.67	0.834	SUBCLONAL	1	FALSE	1	0.201840272170292	2		661	1429	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099815	157099815	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1454	203	650	0	ENST00000346085.5:c.752G>A	p.Cys251Tyr	p.C251Y	ENST00000346085	NM_020732.3	251	tGc/tAc	1/20	0.13959368355959	4	FACETS	1	0.99	1	0.729	0.674	0.788	CLONAL	1	FALSE	2	0.201840272170292	4		650	1657	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038779	47038779	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1345	276	701	0	ENST00000377604.3:c.787del	p.Arg263GlyfsTer3	p.R263Gfs*3	ENST00000377604	NM_001204468.1	262	ggC/gg	9/24	0.155933370386115	2	FACETS	0.844	0.79	0.899	0.844	0.79	0.899	CLONAL	2	FALSE	0	0.201840272170292	2		701	1621	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0014826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	480	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.656116302227602	3	FACETS	0.921	0.884	0.958	0.921	0.884	0.958	CLONAL	2	TRUE	1	0.656116302227602	3		249	1055	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	577	627	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.656116302227602	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.656116302227602	2		627	853	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117755	70117755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	315	581	1	ENST00000245479.2:c.223G>A	p.Glu75Lys	p.E75K	ENST00000245479	NM_000346.3	75	Gag/Aag	1/3	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.656116302227602	2		582	839	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0014830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	198	234	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.416164141391989	3	FACETS	0.906	0.837	0.977	0.453	0.418	0.489	CLONAL	1	TRUE	1	0.416164141391989	3		234	1269	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857407	68857407	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0014830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	244	471	0	ENST00000261769.5:c.2042T>G	p.Leu681Ter	p.L681*	ENST00000261769	NM_004360.3	681	tTa/tGa	13/16	0.416164141391989	1	FACETS	0.973	0.911	1	0.973	0.911	1	CLONAL	1	TRUE	0	0.416164141391989	1		471	954	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577027	7577027	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	260	614	0	ENST00000269305.4:c.911del	p.Thr304IlefsTer41	p.T304Ifs*41	ENST00000269305	NM_001126112.2	304	aCt/at	8/11	0.331268252470121	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.331268252470121	1		614	1012	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112448	115112448	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	215	614	0	ENST00000257566.3:c.1292C>G	p.Ala431Gly	p.A431G	ENST00000257566	NM_016569.3	431	gCg/gGg	7/8	0.331268252470121	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.331268252470121	1		614	963	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256829	19256829	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	115	518	0	ENST00000162023.5:c.884G>C	p.Gly295Ala	p.G295A	ENST00000162023		295	gGg/gCg	13/13	1	2	FACETS	0.857	0.772	0.947	0.857	0.772	0.947	CLONAL	1	TRUE	1	0.331268252470121	2		518	810	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181943	32181943	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	105	680	0	ENST00000375023.3:c.2111G>C	p.Gly704Ala	p.G704A	ENST00000375023	NM_004557.3	704	gGg/gCg	13/30	0.20306764156464	1	FACETS	0.578	0.517	0.643	0.578	0.517	0.643	SUBCLONAL	1	TRUE	0	0.331268252470121	1		680	915	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272410	38272410	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121909628	NA	P-0014834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1326	100	371	1	ENST00000425967.3:c.1957C>T	p.Arg653Ter	p.R653*	ENST00000425967	NM_001174067.1	653	Cga/Tga	15/19	0.331268252470121	9	FACETS	0.914	0.814	1			1	CLONAL	1	TRUE	NA	0.331268252470121	9		372	1426	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006791	47006791	+	5_prime_UTR_variant	5'UTR	SNP	C	C	A	novel	NA	P-0014834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	97	598	0	ENST00000377604.3:c.-90C>A		p.*30*	ENST00000377604	NM_001204468.1	-/852		2/24	0.228840610242334	1	FACETS	0.497	0.442	0.555	0.497	0.442	0.555	SUBCLONAL	1	TRUE	0	0.331268252470121	1		598	984	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	263	661	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.313950726388196	4	FACETS	1	0.991	1	1	0.991	1	INDETERMINATE	2	TRUE	2	0.592604145514387	4		661	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0014849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	141	758	1	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	0.592604145514387	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.592604145514387	1		759	288	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0014849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	90	375	0	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	0.592604145514387	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.592604145514387	1		375	198	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476387	88476387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202056599	NA	P-0014849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	64	567	1	ENST00000360948.2:c.1745G>A	p.Arg582Gln	p.R582Q	ENST00000360948	NM_001012338.2	582	cGg/cAg	15/19	0.554111385218678	1	FACETS	0.67	0.588	0.756	0.67	0.588	0.756	SUBCLONAL	1	TRUE	0	0.592604145514387	1		568	227	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121912580	NA	P-0014849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	67	416	0	ENST00000342988.3:c.1157G>C	p.Gly386Ala	p.G386A	ENST00000342988	NM_005359.5	386	gGt/gCt	10/12	0.297247678535281	1	FACETS	0.737	0.65	0.827	0.737	0.65	0.827	INDETERMINATE	1	TRUE	0	0.592604145514387	1		416	216	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442866	187442866	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0121594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	181	397	0	ENST00000232014.4:c.1840G>C	p.Val614Leu	p.V614L	ENST00000232014	NM_001130845.1	614	Gtg/Ctg	9/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	NA	1	0.883787495502354	2		397	397	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561763	55561765	+	inframe_deletion	In_Frame_Del	DEL	CGA	CGA	-	novel	NA	P-0121594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	203	449	0	ENST00000288135.5:c.156_158del	p.Asp52del	p.D52del	ENST00000288135	NM_000222.2	51	ggCGAc/ggc	2/21	1	2	FACETS	0.84	0.785	0.896	0.84	0.785	0.896	CLONAL	1	NA	1	0.883787495502354	2		449	547	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86681129	86681129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0121594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	93	403	0	ENST00000274376.6:c.2770C>T	p.Pro924Ser	p.P924S	ENST00000274376	NM_002890.2	924	Cct/Tct	22/25	1	2	FACETS	0.683	0.615	0.755	0.683	0.615	0.755	SUBCLONAL	1	NA	1	0.883787495502354	2		403	308	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829811	76829811	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0121594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	164	383	0	ENST00000373344.5:c.6230G>A	p.Trp2077Ter	p.W2077*	ENST00000373344	NM_000489.3	2077	tGg/tAg	28/35	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	NA	0	0.883787495502354	1		383	186	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0014856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	40	257	2	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.68	0.567	0.806	0.68	0.567	0.806	SUBCLONAL	1	TRUE	1	0.346857260645742	2		259	339	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100651	67100651	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	155	510	0	ENST00000412916.2:c.349C>T	p.Gln117Ter	p.Q117*	ENST00000412916		117	Caa/Taa	4/6	0.346857260645742	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.346857260645742	1		510	732	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075230	16075230	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	99	433	0	ENST00000268712.3:c.322C>T	p.Arg108Ter	p.R108*	ENST00000268712	NM_006311.3	108	Cga/Tga	4/46	0.346857260645742	1	FACETS	0.748	0.668	0.832	0.748	0.668	0.832	SUBCLONAL	1	TRUE	0	0.346857260645742	1		433	631	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	83	389	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.758	0.673	0.849	1	0.979	1	SUBCLONAL	2	TRUE	1	0.268278522593103	2		389	408	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0014857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	107	737	6	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	0.268278522593103	3	FACETS	0.876	0.784	0.974	0.438	0.392	0.487	CLONAL	1	TRUE	1	0.268278522593103	3		743	1033	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204625	108204626	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0014857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	39	448	0	ENST00000278616.4:c.7940_7941del	p.Ile2647ThrfsTer8	p.I2647Tfs*8	ENST00000278616	NM_000051.3	2647	aTT/a	54/63	0.268278522593103	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.268278522593103	1		448	216	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0014860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	115	645	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	0.324421564520678	2		645	658	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936093	178936093	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913275	NA	P-0014860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	90	557	0	ENST00000263967.3:c.1635G>T	p.Glu545Asp	p.E545D	ENST00000263967	NM_006218.2	545	gaG/gaT	10/21	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.324421564520678	2		557	517	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28929495	NA	P-0014885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	52	629	0	ENST00000275493.2:c.2155G>A	p.Gly719Ser	p.G719S	ENST00000275493	NM_005228.3	719	Ggc/Agc	18/28	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.14	2		629	725	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241678	55241678	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517085	NA	P-0014885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	59	734	0	ENST00000275493.2:c.2126A>C	p.Glu709Ala	p.E709A	ENST00000275493	NM_005228.3	709	gAa/gCa	18/28	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.14	2		734	801	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0014904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	308	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.22696155291558	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.22696155291558	3		249	1318	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736308	243736308	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754990008	NA	P-0014904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	81	537	0	ENST00000263826.5:c.739C>T	p.Arg247Cys	p.R247C	ENST00000263826	NM_005465.4	247	Cgc/Tgc	8/13	0.198209039783235	3	FACETS	0.759	0.667	0.859	0.38	0.333	0.43	SUBCLONAL	1	TRUE	1	0.22696155291558	3		537	1047	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0014911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	71	249	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.181612335595757	3	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	1	0.1	3		249	673	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	48	528	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.915	1	1	0.975	1	CLONAL	2	TRUE	1	0.1	2		530	427	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100117	157100119	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs797045268	NA	P-0014911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	10	35	0	ENST00000346085.5:c.1069_1071del	p.Gly357del	p.G357del	ENST00000346085	NM_020732.3	352	GGC/-	1/20	1	2	FACETS	0.877	0.603	1	1	0.901	1	CLONAL	3	TRUE	1	0.1	2		35	76	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649679	48649679	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150572851	NA	P-0014911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	91	811	3	ENST00000376670.3:c.163G>A	p.Ala55Thr	p.A55T	ENST00000376670	NM_002049.3	55	Gct/Act	2/6	1	2	FACETS	0.935	0.829	1	1	0.984	1	CLONAL	2	TRUE	1	0.1	2		814	973	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945697	151945697	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	42	623	3	ENST00000262189.6:c.1822C>T	p.Gln608Ter	p.Q608*	ENST00000262189	NM_170606.2	608	Caa/Taa	14/59	1	2	FACETS	0.787	0.656	0.931	1	0.959	1	CLONAL	2	TRUE	1	0.1	2		626	534	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851837	63851837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755029955	NA	P-0014911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	83	663	0	ENST00000279873.7:c.2615C>T	p.Ser872Phe	p.S872F	ENST00000279873	NM_032199.2	872	tCc/tTc	10/10	1	2	FACETS	1	0.928	1	1	0.985	1	CLONAL	2	TRUE	1	0.1	2		663	773	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22408248	22408248	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	21	332	2	ENST00000344548.3:c.139G>A	p.Gly47Ser	p.G47S	ENST00000344548	NM_001039802.1	47	Ggt/Agt	4/7	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.1	2		334	300	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166002	118166006	+	frameshift_variant	Frame_Shift_Del	DEL	ACTCC	ACTCC	-	novel	NA	P-0014911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	66	357	0	ENST00000369448.3:c.513_517del	p.Ile173AlafsTer4	p.I173Afs*4	ENST00000369448	NM_017709.3	171	gACTCC/g	2/2	0.181612335595757	3	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	1	0.1	3		357	575	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844774	156844774	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	55	634	1	ENST00000524377.1:c.1328G>T	p.Gly443Val	p.G443V	ENST00000524377	NM_002529.3	443	gGa/gTa	11/17	0.181612335595757	3	FACETS	1	0.954	1	0.658	0.561	0.764	CLONAL	1	TRUE	1	0.1	3		635	878	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911876	94911876	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	38	584	0	ENST00000536441.1:c.1054C>G	p.Gln352Glu	p.Q352E	ENST00000536441	NM_144665.3	352	Cag/Gag	7/10	0.175076051555324	2	FACETS	0.821	0.678	0.98	0.821	0.678	0.98	CLONAL	2	TRUE	0	0.1	2		584	463	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819638	81819638	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	50	554	0	ENST00000359376.3:c.44A>T	p.Lys15Met	p.K15M	ENST00000359376	NM_002661.3	15	aAg/aTg	2/33	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.1	2		554	709	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098519	47098519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	71	410	1	ENST00000409792.3:c.6755C>T	p.Ser2252Phe	p.S2252F	ENST00000409792	NM_014159.6	2252	tCc/tTc	15/21	1	2	FACETS	1	0.929	1	1	0.983	1	CLONAL	2	TRUE	1	0.1	2		411	648	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643503	52643503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	56	454	0	ENST00000394830.3:c.2393G>A	p.Arg798Lys	p.R798K	ENST00000394830	NM_018313.4	798	aGa/aAa	17/30	1	2	FACETS	1	0.911	1	1	0.978	1	CLONAL	2	TRUE	1	0.1	2		454	515	SUCCESS
ATR	545	MSKCC	GRCh37	3	142212078	142212078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	55	589	1	ENST00000350721.4:c.5974G>A	p.Glu1992Lys	p.E1992K	ENST00000350721	NM_001184.3	1992	Gag/Aag	35/47	0.181612335595757	3	FACETS	0.951	0.813	1	0.951	0.813	1	CLONAL	2	TRUE	1	0.1	3		590	607	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524607	176524607	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	182	837	0	ENST00000292408.4:c.2339C>G	p.Ser780Cys	p.S780C	ENST00000292408	NM_213647.1	780	tCt/tGt	18/18	0.175076051555324	2	FACETS	0.952	0.878	1	1	0.992	1	CLONAL	4	TRUE	0	0.1	2		837	956	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332829	152332829	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	82	424	0	ENST00000206249.3:c.1135C>G	p.Leu379Val	p.L379V	ENST00000206249	NM_000125.3	379	Cta/Gta	5/8	1	2	FACETS	1	0.95	1	1	0.985	1	CLONAL	2	TRUE	1	0.1	2		424	714	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099173	157099173	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757718031	NA	P-0014911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	61	360	1	ENST00000346085.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000346085	NM_020732.3	37	tCc/tTc	1/20	1	2	FACETS	0.894	0.773	1	1	0.983	1	CLONAL	3	TRUE	1	0.1	2		361	455	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884933	151884933	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0014911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	22	298	0	ENST00000262189.6:c.4661-1G>C		p.X1554_splice	ENST00000262189	NM_170606.2	1554			1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.1	2		298	332	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240435	98240435	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	61	383	0	ENST00000331920.6:c.1249C>G	p.Gln417Glu	p.Q417E	ENST00000331920	NM_000264.3	417	Caa/Gaa	9/24	1	2	FACETS	0.962	0.83	1	1	0.978	1	CLONAL	2	TRUE	1	0.1	2		383	634	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93657854	93657854	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	160	489	0	ENST00000375746.1:c.1880G>A	p.Arg627His	p.R627H	ENST00000375746	NM_001174167.1	627	cGc/cAc	14/14	0.581439110929422	2	FACETS	0.92	0.848	0.995	0.46	0.424	0.498	CLONAL	1	TRUE	0	0.581439110929422	2		489	598	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119433	193119433	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0014937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	584	314	0	ENST00000367435.3:c.829-1G>C		p.X277_splice	ENST00000367435	NM_024529.4	277			0.581439110929422	6	FACETS	0.94	0.912	0.969	0.94	0.912	0.969	CLONAL	5	TRUE	1	0.581439110929422	6		314	924	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	286	503	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.433733108876207	2	FACETS	0.97	0.918	1	0.97	0.918	1	CLONAL	2	TRUE	0	0.433733108876207	2		503	680	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591825	48591825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767342	NA	P-0014943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	60	574	0	ENST00000342988.3:c.988G>A	p.Glu330Lys	p.E330K	ENST00000342988	NM_005359.5	330	Gaa/Aaa	9/12	0.411331943709777	1	FACETS	0.441	0.381	0.507	0.441	0.381	0.507	SUBCLONAL	1	TRUE	0	0.433733108876207	1		574	491	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604701	48604701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555687572	NA	P-0014943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	57	451	0	ENST00000342988.3:c.1523G>A	p.Gly508Asp	p.G508D	ENST00000342988	NM_005359.5	508	gGc/gAc	12/12	0.411331943709777	1	FACETS	0.372	0.319	0.429	0.372	0.319	0.429	SUBCLONAL	1	TRUE	0	0.433733108876207	1		451	554	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044503	12044532	+	inframe_deletion	In_Frame_Del	DEL	GAGGTCGCATGCTATGTTTGTAAAATCCTG	GAGGTCGCATGCTATGTTTGTAAAATCCTG	-	novel	NA	P-0014943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	126	497	0	ENST00000353533.5:c.1128_1157del	p.Glu376_Leu385del	p.E376_L385del	ENST00000353533	NM_003010.3	376	GAGGTCGCATGCTATGTTTGTAAAATCCTG/-	11/11	0.411331943709777	1	FACETS	0.855	0.778	0.936	0.855	0.778	0.936	CLONAL	1	TRUE	0	0.433733108876207	1		497	532	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591844	48591844	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500732	NA	P-0014943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	62	536	0	ENST00000342988.3:c.1007G>A	p.Gly336Glu	p.G336E	ENST00000342988	NM_005359.5	336	gGa/gAa	9/12	0.411331943709777	1	FACETS	0.422	0.364	0.484	0.422	0.364	0.484	SUBCLONAL	1	TRUE	0	0.433733108876207	1		536	531	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556727	41556727	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0014943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	63	449	2	ENST00000263253.7:c.3671+1G>A		p.X1224_splice	ENST00000263253	NM_001429.3	1224			1	2	FACETS	0.486	0.42	0.557	0.486	0.42	0.557	SUBCLONAL	1	TRUE	1	0.433733108876207	2		451	598	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021763	71021763	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	116	412	0	ENST00000318789.4:c.1595C>A	p.Ala532Glu	p.A532E	ENST00000318789	NM_032682.5	532	gCa/gAa	18/21	1	2	FACETS	0.864	0.781	0.952	0.864	0.781	0.952	CLONAL	1	TRUE	1	0.433733108876207	2		412	619	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936083	178936083	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519927	NA	P-0014943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	113	566	0	ENST00000263967.3:c.1625A>G	p.Glu542Gly	p.E542G	ENST00000263967	NM_006218.2	542	gAa/gGa	10/21	0.433733108876207	2	FACETS	0.93	0.84	1	0.465	0.42	0.513	CLONAL	1	TRUE	0	0.433733108876207	2		566	560	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878187	48878187	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0014949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	211	206	0	ENST00000267163.4:c.137+2T>A		p.X46_splice	ENST00000267163	NM_000321.2	46			0.232387717875482	0	FACETS		NA	1			1	NA	7	TRUE	0	0.232387717875482	0		206	235	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0014949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	578	717	1	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.232387717875482	0	FACETS		NA	1			1	NA	7	TRUE	0	0.232387717875482	0		718	614	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61713003	61713003	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	103	699	0	ENST00000401558.2:c.2408C>G	p.Thr803Ser	p.T803S	ENST00000401558	NM_003400.3	803	aCt/aGt	20/25	0.151362756241245	0	FACETS	1	0.964	1			1	CLONAL	1	TRUE	0	0.232387717875482	0		699	584	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508768	148508768	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	242	534	0	ENST00000320356.2:c.1896T>A	p.Phe632Leu	p.F632L	ENST00000320356	NM_004456.4	632	ttT/ttA	16/20	0.232387717875482	3	FACETS	0.956	0.9	1	1	0.995	1	CLONAL	4	TRUE	1	0.232387717875482	3		534	608	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38153403	38153403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	124	717	1	ENST00000317025.8:c.2826G>A	p.Met942Ile	p.M942I	ENST00000317025	NM_023034.1	942	atG/atA	16/24	0.197928190003454	4	FACETS	1	0.97	1	0.591	0.534	0.653	CLONAL	1	TRUE	2	0.232387717875482	4		718	1112	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978481	70978481	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	242	427	0	ENST00000276594.2:c.1172G>T	p.Gly391Val	p.G391V	ENST00000276594	NM_024504.3	391	gGg/gTg	5/8	0.232387717875482	8	FACETS	0.965	0.902	1	0.551	0.515	0.588	CLONAL	4	TRUE	1	0.232387717875482	8		427	916	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645210	67645210	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	344	750	1	ENST00000264010.4:c.475C>T	p.Pro159Ser	p.P159S	ENST00000264010	NM_006565.3	159	Cct/Tct	3/12	1	2	FACETS	0.947	0.896	0.999	0.947	0.896	0.999	CLONAL	1	TRUE	1	0.604569257849919	2		751	1202	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557825	21557825	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	400	819	0	ENST00000382592.4:c.2020del	p.Leu674TrpfsTer23	p.L674Wfs*23	ENST00000382592	NM_014572.2	674	Ctg/tg	5/8	0.601059553628007	1	FACETS	0.895	0.854	0.937	0.895	0.854	0.937	CLONAL	1	TRUE	0	0.604569257849919	1		819	1031	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0014972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	22	364	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.651	0.503	0.825	0.651	0.503	0.825	SUBCLONAL	1	TRUE	1	0.12	2		364	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0014972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	24	612	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	1	2	FACETS	0.422	0.329	0.531	0.422	0.329	0.531	SUBCLONAL	1	TRUE	1	0.12	2		612	947	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	22	575	0	ENST00000269305.4:c.503A>T	p.His168Leu	p.H168L	ENST00000269305	NM_001126112.2	168	cAc/cTc	5/11	1	2	FACETS	0.418	0.322	0.531	0.418	0.322	0.531	SUBCLONAL	1	TRUE	1	0.12	2		575	877	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110057	115110057	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	117	833	0	ENST00000257566.3:c.1821C>A	p.Tyr607Ter	p.Y607*	ENST00000257566	NM_016569.3	607	taC/taA	8/8	1	2	FACETS	0.785	0.706	0.869	1	0.984	1	SUBCLONAL	2	TRUE	1	0.12	2		833	1242	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891679	28891679	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	57	562	0	ENST00000282397.4:c.3342G>T	p.Arg1114Ser	p.R1114S	ENST00000282397	NM_002019.4	1114	agG/agT	25/30	1	2	FACETS	0.93	0.795	1	0.93	0.795	1	CLONAL	1	TRUE	1	0.12	2		562	1022	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895598	28895599	+	splice_donor_variant	Splice_Site	DEL	AC	AC	-	novel	NA	P-0014972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	39	419	1	ENST00000282397.4:c.3174+1_3174+2del		p.X1058_splice	ENST00000282397	NM_002019.4	1058			1	2	FACETS	0.89	0.736	1	0.89	0.736	1	CLONAL	1	TRUE	1	0.12	2		420	730	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243635	41243635	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	57	524	0	ENST00000357654.3:c.3913G>T	p.Asp1305Tyr	p.D1305Y	ENST00000357654	NM_007294.3	1305	Gac/Tac	10/23	1	2	FACETS	0.992	0.848	1	0.992	0.848	1	CLONAL	1	TRUE	1	0.12	2		524	958	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597395	10597395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	85	661	1	ENST00000171111.5:c.1808G>A	p.Gly603Glu	p.G603E	ENST00000171111	NM_203500.1	603	gGg/gAg	6/6	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.12	2		662	1079	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657156	215657156	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	38	325	0	ENST00000260947.4:c.229G>C	p.Asp77His	p.D77H	ENST00000260947	NM_000465.2	77	Gac/Cac	3/11	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.12	2		325	559	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795109	242795109	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs763228671	NA	P-0014972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	75	698	1	ENST00000334409.5:c.100C>A	p.Pro34Thr	p.P34T	ENST00000334409	NM_005018.2	34	Ccc/Acc	2/5	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.12	2		699	1075	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795386	39795386	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	59	583	0	ENST00000288319.7:c.334C>A	p.His112Asn	p.H112N	ENST00000288319	NM_182918.3	112	Cac/Aac	3/10	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.12	2		583	898	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066599	94066600	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0014972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	51	510	0	ENST00000369303.4:c.1159_1160delinsTT	p.Gly387Leu	p.G387L	ENST00000369303	NM_004440.3	387	GGa/TTa	5/17	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.12	2		510	798	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0014989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	83	771	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.871	0.767	0.982	0.871	0.767	0.982	CLONAL	1	TRUE	1	0.222112179409478	2		771	858	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0014989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	107	946	2	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.222112179409478	2		948	916	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0015005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	74	249	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	0.17	2		249	744	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0015005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	66	851	3	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	1	2	FACETS	0.842	0.729	0.965	0.842	0.729	0.965	CLONAL	1	TRUE	1	0.17	2		854	922	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0015005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	61	818	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.894	0.769	1	0.894	0.769	1	CLONAL	1	TRUE	1	0.17	2		818	803	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845682	68845682	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	74	865	1	ENST00000261769.5:c.928G>T	p.Glu310Ter	p.E310*	ENST00000261769	NM_004360.3	310	Gag/Tag	7/16	1	2	FACETS	0.989	0.864	1	0.989	0.864	1	CLONAL	1	TRUE	1	0.17	2		866	880	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200073	128200073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374457534	NA	P-0015005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	69	925	1	ENST00000341105.2:c.1232C>T	p.Ala411Val	p.A411V	ENST00000341105	NM_032638.4	411	gCg/gTg	6/6	1	2	FACETS	0.882	0.767	1	0.882	0.767	1	CLONAL	1	TRUE	1	0.17	2		926	920	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111472	8111473	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0015005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	58	709	0	ENST00000346208.3:c.959_960del	p.Cys320SerfsTer31	p.C320Sfs*31	ENST00000346208		320	TGt/t	5/6	1	2	FACETS	0.887	0.761	1	0.887	0.761	1	CLONAL	1	TRUE	1	0.17	2		709	769	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645923	67645923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	43	769	0	ENST00000264010.4:c.851A>G	p.His284Arg	p.H284R	ENST00000264010	NM_006565.3	284	cAc/cGc	4/12	1	2	FACETS	0.726	0.606	0.859	0.726	0.606	0.859	SUBCLONAL	1	TRUE	1	0.17	2		769	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0015027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	164	427	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.233095523641878	2	FACETS	1	0.984	1	0.64	0.588	0.694	CLONAL	1	TRUE	0	0.312313931418653	2		427	821	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739843	41739843	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	183	440	1	ENST00000242208.4:c.130C>A	p.Pro44Thr	p.P44T	ENST00000242208	NM_002192.2	44	Cca/Aca	2/3	0.312313931418653	5	FACETS	1	0.984	1	0.817	0.757	0.88	CLONAL	2	TRUE	2	0.312313931418653	5		441	702	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0015027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	184	625	2	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.218649691425209	4	FACETS	1	0.989	1	0.73	0.673	0.789	CLONAL	1	TRUE	2	0.312313931418653	4		627	1059	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782284	56782284	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781513723	NA	P-0015027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	83	500	2	ENST00000308159.5:c.125G>A	p.Arg42His	p.R42H	ENST00000308159	NM_014669.4	42	cGc/cAc	2/22	0.217885109773107	3	FACETS	0.87	0.768	0.98	0.435	0.384	0.49	CLONAL	1	TRUE	1	0.312313931418653	3		502	706	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248145	59248145	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	31	102	0	ENST00000371222.2:c.598C>T	p.Gln200Ter	p.Q200*	ENST00000371222	NM_002228.3	200	Caa/Taa	1/1	0.218649691425209	4	FACETS	0.972	0.799	1	0.972	0.799	1	CLONAL	2	TRUE	2	0.312313931418653	4		102	134	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32449541	32449541	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	84	843	0	ENST00000332351.3:c.833C>A	p.Thr278Asn	p.T278N	ENST00000332351	NM_024426.4	278	aCc/aAc	3/10	0.266612393680921	3	FACETS	0.672	0.592	0.757	0.336	0.296	0.379	SUBCLONAL	1	TRUE	1	0.312313931418653	3		843	926	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962530	100962530	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	44	478	0	ENST00000325455.5:c.1867C>G	p.Arg623Gly	p.R623G	ENST00000325455	NM_001202474.3	623	Cgc/Ggc	3/8	0.312313931418653	4	FACETS	0.442	0.37	0.523	0.147	0.123	0.175	SUBCLONAL	1	TRUE	1	0.312313931418653	4		478	836	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216485	108216485	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	29	207	0	ENST00000278616.4:c.8434T>A	p.Ser2812Thr	p.S2812T	ENST00000278616	NM_000051.3	2812	Tct/Act	58/63	0.312313931418653	4	FACETS	0.537	0.43	0.658	0.179	0.143	0.22	SUBCLONAL	1	TRUE	1	0.312313931418653	4		207	454	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392772	118392772	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	142	549	2	ENST00000534358.1:c.11804G>T	p.Arg3935Leu	p.R3935L	ENST00000534358	NM_005933.3	3935	cGt/cTt	36/36	0.312313931418653	4	FACETS	1	0.982	1	0.435	0.396	0.476	CLONAL	1	TRUE	1	0.312313931418653	4		551	915	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134966	41134966	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	69	256	0	ENST00000379561.5:c.662G>T	p.Ser221Ile	p.S221I	ENST00000379561	NM_002015.3	221	aGc/aTc	2/3	0.228468618538951	2	FACETS	1	0.949	1	0.583	0.51	0.661	CLONAL	1	TRUE	0	0.312313931418653	2		256	379	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972434	81972434	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	57	472	0	ENST00000359376.3:c.3227T>G	p.Leu1076Arg	p.L1076R	ENST00000359376	NM_002661.3	1076	cTt/cGt	29/33	0.233095523641878	2	FACETS	0.535	0.458	0.619	0.268	0.229	0.31	SUBCLONAL	1	TRUE	0	0.312313931418653	2		472	682	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120127	70120127	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	60	192	0	ENST00000245479.2:c.1129C>A	p.Pro377Thr	p.P377T	ENST00000245479	NM_000346.3	377	Cca/Aca	3/3	0.254392621458052	4	FACETS	0.927	0.806	1	0.927	0.806	1	CLONAL	2	TRUE	2	0.312313931418653	4		192	272	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7168103	7168103	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	55	473	0	ENST00000302850.5:c.1486G>A	p.Glu496Lys	p.E496K	ENST00000302850	NM_000208.2	496	Gaa/Aaa	7/22	1	2	FACETS	0.621	0.531	0.72	0.621	0.531	0.72	SUBCLONAL	1	TRUE	1	0.312313931418653	2		473	567	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543668	29543668	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	160	677	0	ENST00000389048.3:c.1495C>A	p.Pro499Thr	p.P499T	ENST00000389048	NM_004304.4	499	Cct/Act	7/29	0.217885109773107	3	FACETS	1	0.986	1	0.687	0.63	0.747	CLONAL	1	TRUE	1	0.312313931418653	3		677	862	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607816	46607816	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	212	795	1	ENST00000263734.3:c.2009del	p.Pro670LeufsTer26	p.P670Lfs*26	ENST00000263734	NM_001430.4	669	Ccc/cc	12/16	0.217885109773107	3	FACETS	0.793	0.736	0.851	0.793	0.736	0.851	SUBCLONAL	2	TRUE	1	0.312313931418653	3		796	990	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911166	40911166	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0015027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	92	468	1	ENST00000373198.4:c.2140-1G>A		p.X714_splice	ENST00000373198	NM_133170.3	714			0.14829702301593	4	FACETS	1	0.958	1	0.58	0.516	0.649	INDETERMINATE	1	TRUE	2	0.312313931418653	4		469	666	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164507	47164507	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	114	343	0	ENST00000409792.3:c.1619G>T	p.Arg540Leu	p.R540L	ENST00000409792	NM_014159.6	540	cGa/cTa	3/21	0.228468618538951	2	FACETS	0.809	0.733	0.889	0.809	0.733	0.889	CLONAL	2	TRUE	0	0.312313931418653	2		343	451	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89478259	89478259	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	55	391	0	ENST00000336596.2:c.2078A>C	p.Lys693Thr	p.K693T	ENST00000336596	NM_005233.5	693	aAg/aCg	12/17	NA	2	FACETS	0.626	0.535	0.725			1	INDETERMINATE	1	TRUE	NA	0.312313931418653	2		391	563	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217206	66217207	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0015027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	68	444	2	ENST00000273854.3:c.2408_2409delinsAA	p.Ala803Glu	p.A803E	ENST00000273854	NM_004439.5	803	gCC/gAA	14/18	0.217885109773107	3	FACETS	0.664	0.577	0.759	0.332	0.288	0.38	SUBCLONAL	1	TRUE	1	0.312313931418653	3		446	758	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111513	56111513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1290515612	NA	P-0015027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	43	121	0	ENST00000399503.3:c.113C>T	p.Ala38Val	p.A38V	ENST00000399503	NM_005921.1	38	gCg/gTg	1/20	0.254392621458052	4	FACETS	1	0.882	1	1	0.882	1	CLONAL	2	TRUE	2	0.312313931418653	4		121	173	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064719	80064719	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	166	492	0	ENST00000265081.6:c.2150A>T	p.Asp717Val	p.D717V	ENST00000265081	NM_002439.4	717	gAt/gTt	15/24	0.254392621458052	4	FACETS	1	0.988	1	0.727	0.667	0.789	CLONAL	1	TRUE	2	0.312313931418653	4		492	960	SUCCESS
GTF2I	2969	MSKCC	GRCh37	7	74105393	74105393	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781967568	NA	P-0015027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	148	543	0	ENST00000324896.4:c.188G>A	p.Arg63His	p.R63H	ENST00000324896	NM_032999.3	63	cGt/cAt	3/35	0.217885109773107	3	FACETS	1	0.985	1	0.692	0.632	0.754	CLONAL	1	TRUE	1	0.312313931418653	3		543	792	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829102	128829102	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	44	87	0	ENST00000249373.3:c.110C>A	p.Thr37Asn	p.T37N	ENST00000249373	NM_005631.4	37	aCc/aAc	1/12	0.217885109773107	3	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	1	0.312313931418653	3		87	136	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829138	128829138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	52	143	0	ENST00000249373.3:c.146G>A	p.Arg49Lys	p.R49K	ENST00000249373	NM_005631.4	49	aGg/aAg	1/12	0.217885109773107	3	FACETS	1	0.888	1	1	0.888	1	CLONAL	2	TRUE	1	0.312313931418653	3		143	187	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841865	151841865	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	62	343	0	ENST00000262189.6:c.14276C>A	p.Ser4759Ter	p.S4759*	ENST00000262189	NM_170606.2	4759	tCa/tAa	55/59	0.217885109773107	3	FACETS	0.918	0.794	1	0.459	0.397	0.526	CLONAL	1	TRUE	1	0.312313931418653	3		343	500	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873552	151873552	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	72	469	0	ENST00000262189.6:c.8986G>C	p.Gly2996Arg	p.G2996R	ENST00000262189	NM_170606.2	2996	Ggt/Cgt	38/59	0.217885109773107	3	FACETS	0.707	0.617	0.804	0.353	0.308	0.402	SUBCLONAL	1	TRUE	1	0.312313931418653	3		469	754	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399282	139399282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs867637156	NA	P-0015027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	176	856	0	ENST00000277541.6:c.4861G>T	p.Gly1621Cys	p.G1621C	ENST00000277541	NM_017617.3	1621	Ggc/Tgc	26/34	0.312313931418653	2	FACETS	1	0.985	1	0.646	0.595	0.698	CLONAL	1	TRUE	0	0.312313931418653	2		856	873	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732959	44732959	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	109	297	0	ENST00000377967.4:c.161+1G>A		p.X54_splice	ENST00000377967	NM_021140.2	54			0.312313931418653	4	FACETS	1	0.928	1	0.516	0.466	0.568	CLONAL	2	TRUE	0	0.312313931418653	4		297	444	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0015047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	191	422	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.325488258373985	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.325488258373985	4		422	712	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0015047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	230	815	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.31200381427069	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.325488258373985	2		815	699	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143268	24143268	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	121	816	0	ENST00000263121.7:c.500G>T	p.Cys167Phe	p.C167F	ENST00000263121	NM_003073.3	167	tGc/tTc	4/9	0.325488258373985	3	FACETS	1	0.964	1			1	CLONAL	1	TRUE	NA	0.325488258373985	3		816	758	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2493203	2493203	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	120	792	0	ENST00000355716.4:c.643G>T	p.Val215Phe	p.V215F	ENST00000355716	NM_003820.2	215	Gtt/Ttt	6/8	0.325488258373985	3	FACETS	1	0.914	1	0.507	0.457	0.559	CLONAL	1	TRUE	1	0.325488258373985	3		792	846	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163295923	163295923	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	182	776	2	ENST00000271452.3:c.82G>T	p.Gly28Cys	p.G28C	ENST00000271452	NM_145697.2	28	Ggt/Tgt	2/14	0.325488258373985	7	FACETS	0.865	0.796	0.936			1	CLONAL	2	TRUE	NA	0.325488258373985	7		778	1173	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119708	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	152	562	2	ENST00000285071.4:c.1286A>T	p.His429Leu	p.H429L	ENST00000285071	NM_144997.5	429	cAc/cTc	11/14	0.31200381427069	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.325488258373985	2		564	454	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244817	41244817	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	221	788	0	ENST00000357654.3:c.2731G>T	p.Gly911Ter	p.G911*	ENST00000357654	NM_007294.3	911	Gga/Tga	10/23	0.325488258373985	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.325488258373985	3		788	678	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804349	46804349	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	150	553	0	ENST00000290295.7:c.658C>A	p.Arg220Ser	p.R220S	ENST00000290295	NM_006361.5	220	Cgc/Agc	2/2	0.325488258373985	3	FACETS	0.989	0.909	1	0.989	0.909	1	CLONAL	2	TRUE	1	0.325488258373985	3		553	542	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25990587	25990587	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	98	643	0	ENST00000435504.4:c.640G>T	p.Glu214Ter	p.E214*	ENST00000435504		214	Gaa/Taa	8/13	0.325488258373985	4	FACETS	1	0.943	1	0.363	0.324	0.405	CLONAL	1	TRUE	1	0.325488258373985	4		643	733	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101089	26101089	+	start_lost	Translation_Start_Site	SNP	C	C	T	rs1559535727	NA	P-0015047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	207	516	0	ENST00000435504.4:c.3G>A	p.Met1?	p.M1?	ENST00000435504		1	atG/atA	1/13	0.325488258373985	4	FACETS	0.85	0.793	0.909	0.85	0.793	0.909	CLONAL	3	TRUE	1	0.325488258373985	4		516	661	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129963	55129963	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	202	725	0	ENST00000257290.5:c.497G>C	p.Gly166Ala	p.G166A	ENST00000257290	NM_006206.4	166	gGg/gCg	4/23	0.325488258373985	3	FACETS	0.905	0.841	0.972	0.905	0.841	0.972	CLONAL	2	TRUE	1	0.325488258373985	3		725	797	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729265	41729265	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	128	473	0	ENST00000242208.4:c.1264G>T	p.Glu422Ter	p.E422*	ENST00000242208	NM_002192.2	422	Gag/Tag	3/3	0.281265982745475	5	FACETS	0.984	0.894	1	0.656	0.596	0.718	CLONAL	2	TRUE	2	0.325488258373985	5		473	595	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989633	68989633	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	257	543	0	ENST00000288368.4:c.1571G>C	p.Gly524Ala	p.G524A	ENST00000288368	NM_024870.2	524	gGa/gCa	15/40	0.325488258373985	3	FACETS	0.888	0.837	0.941	1	0.992	1	CLONAL	3	TRUE	1	0.325488258373985	3		543	689	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27183552	27183552	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	96	650	0	ENST00000380036.4:c.1126C>A	p.Pro376Thr	p.P376T	ENST00000380036	NM_000459.3	376	Ccg/Acg	8/23	0.325488258373985	5	FACETS	0.856	0.761	0.958	0.214	0.19	0.24	CLONAL	1	TRUE	1	0.325488258373985	5		650	1025	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635202	87635202	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	95	612	4	ENST00000277120.3:c.2254G>T	p.Val752Phe	p.V752F	ENST00000277120		752	Gtc/Ttc	18/19	0.325488258373985	3	FACETS	0.941	0.838	1	0.471	0.419	0.526	CLONAL	1	TRUE	1	0.325488258373985	3		616	721	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894934	101894934	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	132	413	0	ENST00000374994.4:c.487G>T	p.Asp163Tyr	p.D163Y	ENST00000374994	NM_004612.2	163	Gac/Tac	3/9	0.325488258373985	3	FACETS	0.914	0.834	0.997	0.914	0.834	0.997	CLONAL	2	TRUE	1	0.325488258373985	3		413	516	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0015055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	39	367	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA	2	FACETS	0.743	0.622	0.875			1	INDETERMINATE	1	TRUE	NA	0.50724503561037	2		367	207	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0015055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	215	519	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.37901669886001	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.50724503561037	2		519	389	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491283	2491283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776730987	NA	P-0015055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	118	652	0	ENST00000355716.4:c.326G>A	p.Arg109Gln	p.R109Q	ENST00000355716	NM_003820.2	109	cGg/cAg	4/8	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.50724503561037	2		652	439	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937066	36937066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564880597	NA	P-0015055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	74	530	0	ENST00000361632.4:c.1253G>A	p.Arg418His	p.R418H	ENST00000361632		418	cGt/cAt	9/16	1	2	FACETS	0.912	0.805	1	0.912	0.805	1	CLONAL	1	TRUE	1	0.50724503561037	2		530	320	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636698	2636698	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	85	623	0	ENST00000342085.4:c.1147T>A	p.Phe383Ile	p.F383I	ENST00000342085	NM_002613.4	383	Ttt/Att	11/14	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.50724503561037	2		623	331	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395652	45395652	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	45	569	0	ENST00000262160.6:c.482G>T	p.Cys161Phe	p.C161F	ENST00000262160	NM_005901.5	161	tGt/tTt	4/11	0.314710768952558	1	FACETS	0.833	0.713	0.961	0.833	0.713	0.961	CLONAL	1	TRUE	0	0.50724503561037	1		569	159	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0015055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	53	505	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.314710768952558	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.50724503561037	1		505	134	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727926	41727926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	76	691	1	ENST00000301178.4:c.551C>T	p.Pro184Leu	p.P184L	ENST00000301178	NM_021913.4	184	cCa/cTa	4/20	1	2	FACETS	0.713	0.629	0.804	0.713	0.629	0.804	SUBCLONAL	1	TRUE	1	0.50724503561037	2		692	420	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513327	44513327	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755118626	NA	P-0015055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	123	853	0	ENST00000291552.4:c.608G>A	p.Arg203His	p.R203H	ENST00000291552	NM_006758.2	203	cGt/cAt	8/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.50724503561037	2		853	422	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646813	37646813	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	119	432	0	ENST00000447079.4:c.1938del	p.Glu647LysfsTer8	p.E647Kfs*8	ENST00000447079	NM_015083.1	645	ccA/cc	3/14	0.349891903493748	5	FACETS	0.939	0.847	1			1	CLONAL	1	TRUE	NA	0.436801871890469	5		432	960	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650842	37650842	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	883	795	0	ENST00000447079.4:c.2314del	p.Ile772PhefsTer10	p.I772Ffs*10	ENST00000447079	NM_015083.1	772	Att/tt	5/14	0.349891903493748	5	FACETS	0.997	0.969	1			1	CLONAL	4	TRUE	NA	0.436801871890469	5		795	1678	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958789	55958789	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	166	576	0	ENST00000263923.4:c.3064C>T	p.Arg1022Ter	p.R1022*	ENST00000263923	NM_002253.2	1022	Cga/Tga	22/30	NA	2	FACETS	0.992	0.913	1			1	INDETERMINATE	1	TRUE	NA	0.436801871890469	2		576	766	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910594	29910594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199474366	NA	P-0015070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	151	570	0	ENST00000376809.5:c.134G>A	p.Arg45His	p.R45H	ENST00000376809	NM_002116.7	45	cGc/cAc	2/8	1	2	FACETS	0.691	0.631	0.754	0.691	0.631	0.754	SUBCLONAL	1	TRUE	1	0.436801871890469	2		570	1001	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864220	151864229	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CTATTTATTA	CTATTTATTA	-	novel	NA	P-0015070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	24	182	0	ENST00000262189.6:c.9750+2_9750+11del		p.X3250_splice	ENST00000262189	NM_170606.2	3250			0.428362709949154	3	FACETS	0.413	0.324	0.516	0.207	0.162	0.258	SUBCLONAL	1	TRUE	1	0.436801871890469	3		182	324	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	217	389	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.386106725546277	3	FACETS	0.927	0.866	0.991	0.927	0.866	0.991	CLONAL	2	TRUE	1	0.386106725546277	3		389	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0015074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	364	806	4	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	2	TRUE	NA	0.386106725546277	2		810	890	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167577	NA	P-0015074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	44	314	0	ENST00000257430.4:c.4463del	p.Leu1488TyrfsTer19	p.L1488Yfs*19	ENST00000257430	NM_000038.5	1487	acT/ac	16/16	1	2	FACETS	0.695	0.585	0.815	0.695	0.585	0.815	SUBCLONAL	1	TRUE	1	0.386106725546277	2		314	328	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592099	67592099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	76	297	0	ENST00000274335.5:c.1915C>T	p.Arg639Ter	p.R639*	ENST00000274335		639	Cga/Tga	14/15	1	2	FACETS	0.987	0.87	1	0.987	0.87	1	CLONAL	1	TRUE	1	0.386106725546277	2		297	399	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545145	41545145	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0015074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	333	706	1	ENST00000263253.7:c.2345T>A	p.Leu782Ter	p.L782*	ENST00000263253	NM_001429.3	782	tTg/tAg	13/31	0.386106725546277	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.386106725546277	2		707	828	SUCCESS
APC	324	MSKCC	GRCh37	5	112170646	112170646	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs587783035	NA	P-0015074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	63	299	2	ENST00000257430.4:c.1744-2A>G		p.X582_splice	ENST00000257430	NM_000038.5	582			1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.386106725546277	2		301	313	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894839	101894839	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	122	256	1	ENST00000374994.4:c.392C>A	p.Ala131Asp	p.A131D	ENST00000374994	NM_004612.2	131	gCt/gAt	3/9	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	2	TRUE	NA	0.386106725546277	2		257	289	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457390	67457390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782977	NA	P-0000373-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	505	764	2	ENST00000327367.4:c.364G>A	p.Val122Met	p.V122M	ENST00000327367	NM_005902.3	122	Gtg/Atg	2/9	0.672143586994391	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.672143586994391	2		766	723	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026440	48026440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000453-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	195	342	0	ENST00000234420.5:c.1318G>A	p.Ala440Thr	p.A440T	ENST00000234420	NM_000179.2	440	Gct/Act	4/10	0.542224549318156	3	FACETS	1	0.98	1	0.572	0.532	0.613	CLONAL	1	TRUE	1	0.755843033429619	3		342	621	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433718	49433718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372935294	NA	P-0000453-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	404	677	0	ENST00000301067.7:c.7835C>T	p.Pro2612Leu	p.P2612L	ENST00000301067	NM_003482.3	2612	cCt/cTt	31/54	0.755843033429619	3	FACETS	1	0.992	1	0.59	0.561	0.619	CLONAL	1	TRUE	1	0.755843033429619	3		677	1248	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109924	115109924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754142951	NA	P-0000453-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	437	441	0	ENST00000257566.3:c.1954G>A	p.Gly652Ser	p.G652S	ENST00000257566	NM_016569.3	652	Ggc/Agc	8/8	0.755843033429619	3	FACETS	0.995	0.956	1	0.995	0.956	1	CLONAL	2	TRUE	1	0.755843033429619	3		441	801	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0000453-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	559	550	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.370817040383284	3	FACETS	1	0.996	1	0.775	0.751	0.798	INDETERMINATE	2	TRUE	0	0.755843033429619	3		550	877	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581229	48581229	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs377767331	NA	P-0000453-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	500	463	0	ENST00000342988.3:c.533C>G	p.Ser178Ter	p.S178*	ENST00000342988	NM_005359.5	178	tCa/tGa	5/12	0.755843033429619	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.755843033429619	2		463	636	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761014	59761017	+	frameshift_variant	Frame_Shift_Del	DEL	ATAG	ATAG	-	rs778664039	NA	P-0000453-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	388	684	0	ENST00000259008.2:c.3390_3393del	p.Tyr1131LeufsTer18	p.Y1131Lfs*18	ENST00000259008	NM_032043.2	1130	atCTAT/at	20/20	0.370817040383284	3	FACETS	1	0.993	1	0.759	0.731	0.787	INDETERMINATE	2	TRUE	0	0.755843033429619	3		684	621	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174927	11174927	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000453-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	218	456	0	ENST00000361445.4:c.7107G>C	p.Glu2369Asp	p.E2369D	ENST00000361445	NM_004958.3	2369	gaG/gaC	52/58	0.755843033429619	3	FACETS	0.82	0.763	0.879	0.41	0.381	0.44	CLONAL	1	TRUE	1	0.755843033429619	3		456	969	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647548	23647556	+	inframe_deletion	In_Frame_Del	DEL	AGGACTCAG	AGGACTCAG	-	novel	NA	P-0000453-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	75	509	0	ENST00000261584.4:c.311_319del	p.Pro104_Phe107delinsLeu	p.P104_F107delinsL	ENST00000261584	NM_024675.3	104	cCTGAGTCCTtt/ctt	4/13	0.755843033429619	3	FACETS	0.294	0.257	0.334	0.147	0.128	0.167	SUBCLONAL	1	TRUE	1	0.755843033429619	3		509	930	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933767	49933768	+	missense_variant	Missense_Mutation	DNP	CA	CA	AC	novel	NA	P-0000453-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	52	563	0	ENST00000296474.3:c.2509_2510delinsGT	p.Trp837Val	p.W837V	ENST00000296474	NM_002447.2	837	TGg/GTg	10/20	0.159347389579923	4	FACETS	0.26	0.221	0.304	0.13	0.11	0.152	INDETERMINATE	1	TRUE	2	0.755843033429619	4		563	928	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138431122	138431122	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000453-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	102	354	0	ENST00000289153.2:c.1327A>G	p.Thr443Ala	p.T443A	ENST00000289153	NM_006219.2	443	Acg/Gcg	8/22	0.305200661020436	4	FACETS	0.604	0.54	0.673	0.302	0.27	0.337	INDETERMINATE	1	TRUE	2	0.755843033429619	4		354	784	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057520000	NA	P-0001007-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	687	378	0	ENST00000269305.4:c.452C>A	p.Pro151His	p.P151H	ENST00000269305	NM_001126112.2	151	cCc/cAc	5/11	0.668746433772866	3	FACETS	0.964	0.941	0.986	0.964	0.941	0.986	CLONAL	3	TRUE	0	0.697342315246109	3		378	919	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557630	95557630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001007-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	973	491	0	ENST00000393063.1:c.5437G>A	p.Glu1813Lys	p.E1813K	ENST00000393063	NM_030621.3	1813	Gag/Aag	26/28	0.656274880142831	4	FACETS	0.957	0.94	0.974	0.957	0.94	0.974	CLONAL	4	TRUE	0	0.697342315246109	4		491	1237	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716321	52716321	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001007-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	237	421	0	ENST00000322088.6:c.765G>C	p.Lys255Asn	p.K255N	ENST00000322088	NM_014225.5	255	aaG/aaC	6/15	0.652990984416734	3	FACETS	0.967	0.903	1	0.484	0.451	0.516	CLONAL	1	TRUE	1	0.697342315246109	3		421	948	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001425-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	57	126	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.658	0.566	0.759			1	INDETERMINATE	1	TRUE	NA	0.363739477156176	2		126	476	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0001425-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	115	487	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.363739477156176	1	FACETS	0.855	0.772	0.942	0.855	0.772	0.942	CLONAL	1	TRUE	0	0.363739477156176	1		487	605	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579845	7579845	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001425-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	136	752	1	ENST00000269305.4:c.68G>A	p.Trp23Ter	p.W23*	ENST00000269305	NM_001126112.2	23	tGg/tAg	2/11	1	2	FACETS	0.874	0.794	0.957	0.874	0.794	0.957	CLONAL	1	TRUE	1	0.363739477156176	2		753	856	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931740	39931740	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001425-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	93	728	0	ENST00000378444.4:c.2859A>T	p.Lys953Asn	p.K953N	ENST00000378444	NM_001123385.1	953	aaA/aaT	4/15	1	2	FACETS	0.629	0.559	0.704	0.629	0.559	0.704	SUBCLONAL	1	TRUE	1	0.363739477156176	2		728	813	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667633	29667633	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001425-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	140	594	0	ENST00000356175.3:c.6971del	p.Leu2324Ter	p.L2324*	ENST00000356175	NM_000267.3	2323	acT/ac	46/57	0.363739477156176	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.363739477156176	1		594	608	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872219	45872219	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001425-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	108	759	0	ENST00000391945.4:c.215A>G	p.Tyr72Cys	p.Y72C	ENST00000391945	NM_000400.3	72	tAc/tGc	4/23	0.292022612688607	1	FACETS	0.643	0.577	0.712	0.643	0.577	0.712	SUBCLONAL	1	TRUE	0	0.363739477156176	1		759	756	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574693	64574693	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1114167472	NA	P-0001526-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	299	409	0	ENST00000312049.6:c.784-2A>G		p.X262_splice	ENST00000312049	NM_130799.2	262			0.515874829020596	1	FACETS	0.95	0.898	1	0.95	0.898	1	CLONAL	1	TRUE	0	0.515874829020596	1		409	905	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720741	89720741	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs371387815	NA	P-0001526-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	21	130	0	ENST00000371953.3:c.892C>T	p.Gln298Ter	p.Q298*	ENST00000371953	NM_000314.4	298	Caa/Taa	8/9	0.515874829020596	1	FACETS	0.491	0.383	0.613	0.491	0.383	0.613	SUBCLONAL	1	TRUE	0	0.515874829020596	1		130	123	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298726	46298726	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001526-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	69	604	0	ENST00000334344.6:c.5373del	p.Arg1792AspfsTer9	p.R1792Dfs*9	ENST00000334344	NM_152641.2	1791	aaG/aa	21/21	1	2	FACETS	0.285	0.248	0.327	0.285	0.248	0.327	SUBCLONAL	1	TRUE	1	0.515874829020596	2		604	937	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288189	33288189	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001526-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	268	621	0	ENST00000374542.5:c.1219del	p.Asp407ThrfsTer121	p.D407Tfs*121	ENST00000374542	NM_001141970.1	407	Gac/ac	4/8	0.515874829020596	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.515874829020596	1		621	734	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001558-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	19	391	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	0.526	0.397	0.678	0.526	0.397	0.678	SUBCLONAL	1	TRUE	1	0.11	2		391	657	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161856	47161856	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002253-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	376	777	0	ENST00000409792.3:c.4270del	p.Arg1424GlufsTer8	p.R1424Efs*8	ENST00000409792	NM_014159.6	1424	Aga/ga	3/21	0.908197305061831	1	FACETS	0.361	0.342	0.38	0.361	0.342	0.38	SUBCLONAL	1	TRUE	0	0.908197305061831	1		777	1252	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289242	33289245	+	frameshift_variant	Frame_Shift_Del	DEL	CCGC	CCGC	-	novel	NA	P-0002253-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	731	563	0	ENST00000374542.5:c.307_310del	p.Ala103SerfsTer40	p.A103Sfs*40	ENST00000374542	NM_001141970.1	103	GCGGag/ag	3/8	0.908197305061831	1	FACETS	0.965	0.945	0.983	0.965	0.945	0.983	CLONAL	1	TRUE	0	0.908197305061831	1		563	911	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575456	64575456	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002253-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	970	697	0	ENST00000312049.6:c.561del	p.Asn189MetfsTer35	p.N189Mfs*35	ENST00000312049	NM_130799.2	187	ggG/gg	3/10	0.908197305061831	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.908197305061831	1		697	1141	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188049	151188049	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002253-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	242	787	0	ENST00000262187.5:c.104A>C	p.Tyr35Ser	p.Y35S	ENST00000262187	NM_005614.3	35	tAc/tCc	2/8	0.566611799638621	1	FACETS	0.409	0.383	0.434	0.409	0.383	0.434	SUBCLONAL	1	TRUE	0	0.908197305061831	1		787	712	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0002464-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	354	439	1	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.868645263504023	2		440	779	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412493	80412493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514698	NA	P-0002464-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	519	390	1	ENST00000286548.4:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000286548	NM_002072.3	183	cGa/cAa	4/7	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.868645263504023	2		391	1069	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289524	33289524	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002464-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	58	427	0	ENST00000374542.5:c.179A>T	p.Lys60Met	p.K60M	ENST00000374542	NM_001141970.1	60	aAg/aTg	2/8	1	2	FACETS	0.126	0.108	0.147	0.126	0.108	0.147	SUBCLONAL	1	TRUE	1	0.868645263504023	2		427	1057	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477834	140477834	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs760614709	NA	P-0002464-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	49	423	2	ENST00000288602.6:c.1474C>A	p.Pro492Thr	p.P492T	ENST00000288602	NM_004333.4	492	Cct/Act	12/18	0.868645263504023	1	FACETS	0.092	0.077	0.108	0.092	0.077	0.108	SUBCLONAL	1	TRUE	0	0.868645263504023	1		425	697	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225137	2225137	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002464-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	57	509	0	ENST00000326181.6:c.1372G>T	p.Asp458Tyr	p.D458Y	ENST00000326181	NM_032271.2	458	Gac/Tac	15/21	1	2	FACETS	0.131	0.112	0.153	0.131	0.112	0.153	SUBCLONAL	1	TRUE	1	0.868645263504023	2		509	1000	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15809056	15809056	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002464-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	31	283	0	ENST00000307771.7:c.42-1G>A		p.X14_splice	ENST00000307771	NM_005089.3	14			1	1	FACETS	0.068	0.055	0.084	0.068	0.055	0.084	SUBCLONAL	1	TRUE	0	0.868645263504023	1		283	591	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750684	128750684	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002978-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	59	381	1	ENST00000377970.2:c.221C>A	p.Pro74Gln	p.P74Q	ENST00000377970	NM_002467.4	74	cCg/cAg	2/3	0.779634817194736	4	FACETS	1	0.935	1	1	0.935	1	CLONAL	3	TRUE	1	0.77686402989762	4		382	87	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199670	138199670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002978-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	11	323	0	ENST00000237289.4:c.1088G>A	p.Gly363Glu	p.G363E	ENST00000237289	NM_001270507.1	363	gGg/gAg	7/9	0.731947283235366	2	FACETS	0.787	0.568	1	0.393	0.284	0.516	CLONAL	1	TRUE	0	0.77686402989762	2		323	36	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0004183-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	206	382	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	0.50637319512513	2		382	691	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004183-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	178	459	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.50637319512513	2		459	625	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988348	36988348	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs546402304	NA	P-0004183-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	75	115	1	ENST00000354822.5:c.305C>T	p.Ala102Val	p.A102V	ENST00000354822	NM_001079668.2	102	gCg/gTg	2/3	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.50637319512513	2		116	235	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004628-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	21	715	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.636	0.491	0.805	0.636	0.491	0.805	SUBCLONAL	1	TRUE	1	0.247246885525814	2		715	267	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0004628-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	18	474	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	0.247246885525814	2		474	182	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845580	151845580	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1287135873	NA	P-0004628-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	35	757	1	ENST00000262189.6:c.13432C>T	p.Arg4478Ter	p.R4478*	ENST00000262189	NM_170606.2	4478	Cga/Tga	52/59	1	2	FACETS	0.99	0.815	1	0.99	0.815	1	CLONAL	1	TRUE	1	0.247246885525814	2		758	286	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448185	49448185	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004628-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	17	700	0	ENST00000301067.7:c.415C>T	p.His139Tyr	p.H139Y	ENST00000301067	NM_003482.3	139	Cac/Tac	4/54	1	2	FACETS	0.419	0.312	0.547	0.419	0.312	0.547	SUBCLONAL	1	TRUE	1	0.247246885525814	2		700	328	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264637	46264637	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004628-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	40	832	0	ENST00000371998.3:c.1507G>A	p.Val503Met	p.V503M	ENST00000371998		503	Gtg/Atg	12/23	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.247246885525814	2		832	295	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004812-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	398	126	0				ENST00000310581	NM_198253.2	-/1132			0.857339262258368	1	FACETS	0.953	0.929	0.975	0.953	0.929	0.975	CLONAL	1	TRUE	0	0.936710654039889	1		126	474	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913499	NA	P-0004812-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	295	285	0	ENST00000345146.2:c.394C>A	p.Arg132Ser	p.R132S	ENST00000345146	NM_005896.2	132	Cgt/Agt	4/10	1	2	FACETS	0.95	0.901	0.999	0.95	0.901	0.999	CLONAL	1	TRUE	1	0.936710654039889	2		285	663	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791794	42791794	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004812-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	792	704	0	ENST00000575354.2:c.680A>T	p.Asn227Ile	p.N227I	ENST00000575354	NM_015125.3	227	aAc/aTc	5/20	0.936710654039889	1	FACETS	0.967	0.95	0.982	0.967	0.95	0.982	CLONAL	1	TRUE	0	0.936710654039889	1		704	930	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802662	135802662	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004812-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	411	462	0	ENST00000298552.3:c.136del	p.Val46TrpfsTer16	p.V46Wfs*16	ENST00000298552	NM_001162426.1	46	Gtg/tg	4/23	1	2	FACETS	0.855	0.817	0.894	0.855	0.817	0.894	CLONAL	1	TRUE	1	0.936710654039889	2		462	1026	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610533	215610533	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004812-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	400	525	1	ENST00000260947.4:c.1723A>G	p.Ser575Gly	p.S575G	ENST00000260947	NM_000465.2	575	Agt/Ggt	8/11	1	2	FACETS	0.786	0.749	0.823	0.786	0.749	0.823	SUBCLONAL	1	TRUE	1	0.936710654039889	2		526	1087	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0005454-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	299	365	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.84684379836752	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.84684379836752	1		367	388	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746132	162746132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1374086542	NA	P-0005454-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	470	505	2	ENST00000367921.3:c.2255G>A	p.Arg752His	p.R752H	ENST00000367921	NM_006182.2	752	cGc/cAc	16/18	0.580050802746775	3	FACETS	0.835	0.802	0.868	0.835	0.802	0.868	CLONAL	2	TRUE	1	0.84684379836752	3		507	946	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999269	100999269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755210219	NA	P-0005454-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1592	297	943	3	ENST00000325455.5:c.533C>T	p.Thr178Met	p.T178M	ENST00000325455	NM_001202474.3	178	aCg/aTg	1/8	0.84684379836752	3	FACETS	0.529	0.495	0.563	0.264	0.247	0.282	SUBCLONAL	1	TRUE	1	0.84684379836752	3		946	1889	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999591	100999591	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005454-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2068	350	1088	0	ENST00000325455.5:c.211G>C	p.Asp71His	p.D71H	ENST00000325455	NM_001202474.3	71	Gac/Cac	1/8	0.84684379836752	3	FACETS	0.487	0.458	0.516	0.243	0.229	0.258	SUBCLONAL	1	TRUE	1	0.84684379836752	3		1088	2418	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272181	18272181	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005454-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	29	24	0	ENST00000222254.8:c.691C>G	p.Arg231Gly	p.R231G	ENST00000222254	NM_005027.3	231	Cgc/Ggc	6/16	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.84684379836752	2		24	65	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754961	29754961	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	98	964	0	ENST00000389048.3:c.974C>A	p.Thr325Asn	p.T325N	ENST00000389048	NM_004304.4	325	aCc/aAc	4/29	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		964	909	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227987	55227987	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	95	600	1	ENST00000275493.2:c.1454G>A	p.Gly485Asp	p.G485D	ENST00000275493	NM_005228.3	485	gGt/gAt	12/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		601	716	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437772	49437772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	85	597	1	ENST00000301067.7:c.5198C>T	p.Ala1733Val	p.A1733V	ENST00000301067	NM_003482.3	1733	gCt/gTt	22/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		598	699	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131609	2131609	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs796053496	NA	P-0005889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	145	838	1	ENST00000219476.3:c.3624G>A	p.Trp1208Ter	p.W1208*	ENST00000219476	NM_000548.3	1208	tgG/tgA	31/42	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		839	862	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	252	1594	0	ENST00000269305.4:c.472C>A	p.Arg158Ser	p.R158S	ENST00000269305	NM_001126112.2	158	Cgc/Agc	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1594	1424	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274348	5274348	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	133	952	1	ENST00000357368.4:c.99del	p.Arg34GlyfsTer31	p.R34Gfs*31	ENST00000357368	NM_002850.3	33	ccC/cc	3/38	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		953	1055	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792732	33792737	+	inframe_deletion	In_Frame_Del	DEL	GCGGGT	GCGGGT	-	rs762459325	NA	P-0005889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	18	287	0	ENST00000498907.2:c.584_589del	p.His195_Pro196del	p.H195_P196del	ENST00000498907	NM_004364.3	195	cACCCGCcg/ccg	1/1	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		287	281	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142910	30142910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141093002	NA	P-0005889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1345	274	1403	1	ENST00000389048.3:c.616G>A	p.Ala206Thr	p.A206T	ENST00000389048	NM_004304.4	206	Gcg/Acg	1/29	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1404	1619	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99185083	99185083	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764302181	NA	P-0005889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	73	737	1	ENST00000074304.5:c.2485C>T	p.Arg829Trp	p.R829W	ENST00000074304	NM_001134224.1	829	Cgg/Tgg	23/26	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		738	732	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803429	32803429	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs756698219	NA	P-0005889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	338	1433	0	ENST00000374899.4:c.730A>T	p.Thr244Ser	p.T244S	ENST00000374899	NM_018833.2	244	Act/Tct	4/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1433	1070	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117730744	117730744	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs746197109	NA	P-0005889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	127	1107	3	ENST00000368508.3:c.289+1G>T		p.X97_splice	ENST00000368508	NM_002944.2	97			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1110	1055	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649640	48649640	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	194	1160	2	ENST00000376670.3:c.124G>T	p.Asp42Tyr	p.D42Y	ENST00000376670	NM_002049.3	42	Gat/Tat	2/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1162	874	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480403	89480403	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006582-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	145	368	0	ENST00000336596.2:c.2240T>A	p.Leu747His	p.L747H	ENST00000336596	NM_005233.5	747	cTc/cAc	13/17	1	2	FACETS	0.912	0.831	0.997	0.912	0.831	0.997	CLONAL	1	TRUE	1	0.322395596168851	2		368	986	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671846	30671846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006582-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1391	275	480	1	ENST00000376406.3:c.5114C>T	p.Thr1705Ile	p.T1705I	ENST00000376406	NM_014641.2	1705	aCc/aTc	10/15	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.322395596168851	2		481	1666	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152041	11152041	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006582-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	872	246	0	ENST00000358026.2:c.4325C>A	p.Ser1442Ter	p.S1442*	ENST00000358026	NM_001128849.1	1442	tCa/tAa	31/36	0.322395596168851	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.322395596168851	3		246	1889	SUCCESS
AR	367	MSKCC	GRCh37	X	66941674	66941674	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0006582-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1381	185	616	0	ENST00000374690.3:c.2319-1G>A		p.X773_splice	ENST00000374690	NM_000044.3	773			1	2	FACETS	0.733	0.674	0.794	0.733	0.674	0.794	SUBCLONAL	1	TRUE	1	0.322395596168851	2		616	1566	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221983	1221999	+	frameshift_variant	Frame_Shift_Del	DEL	ATCCGGCAGATCCGGCA	ATCCGGCAGATCCGGCA	-	novel	NA	P-0006582-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1852	1391	392	0	ENST00000326873.7:c.898_914del	p.Ile300AlafsTer12	p.I300Afs*12	ENST00000326873	NM_000455.4	300	ATCCGGCAGATCCGGCAg/g	7/10	0.322395596168851	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.322395596168851	3		392	3243	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0007268-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	8	297	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.078	0.05	0.115	0.078	0.05	0.115	SUBCLONAL	1	TRUE	1	0.618314652006971	2		297	331	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978321	2978321	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs138920531	NA	P-0007268-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	81	750	0	ENST00000396946.4:c.1009C>T	p.Arg337Ter	p.R337*	ENST00000396946	NM_032415.4	337	Cga/Tga	7/25	1	2	FACETS	0.978	0.873	1	0.978	0.873	1	CLONAL	1	TRUE	1	0.618314652006971	2		750	268	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576913	7576913	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567546373	NA	P-0007307-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	365	337	0	ENST00000269305.4:c.933del	p.Asn311LysfsTer34	p.N311Kfs*34	ENST00000269305	NM_001126112.2	311	aaC/aa	9/11	0.766445191824022	2	FACETS	0.959	0.93	0.987	0.959	0.93	0.987	CLONAL	2	TRUE	0	0.809576687293853	2		337	470	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5456127	5456127	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007307-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	186	360	0	ENST00000381577.3:c.14C>A	p.Ala5Asp	p.A5D	ENST00000381577	NM_014143.3	5	gCt/gAt	2/7	0.772310969475737	3	FACETS	0.916	0.848	0.985	0.305	0.282	0.329	CLONAL	1	TRUE	0	0.809576687293853	3		360	705	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380245	25380245	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007307-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	215	410	0	ENST00000311936.3:c.213del	p.Tyr71Ter	p.Y71*	ENST00000311936	NM_004985.3	71	taC/ta	3/5	0.744808529263738	4	FACETS	0.896	0.832	0.962	0.448	0.416	0.481	CLONAL	1	TRUE	2	0.809576687293853	4		410	1073	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0007757-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	516	393	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.167045908431703	3	FACETS	1	0.965	1			1	CLONAL	4	TRUE	NA	0.197325152710951	3		393	1426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007757-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	221	533	0	ENST00000269305.4:c.313G>T	p.Gly105Cys	p.G105C	ENST00000269305	NM_001126112.2	105	Ggc/Tgc	4/11	0.209805289641436	3	FACETS	0.982	0.912	1	0.982	0.912	1	CLONAL	2	TRUE	1	0.197325152710951	3		533	1253	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8339016	8339016	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007757-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	200	490	0	ENST00000356435.5:c.5285G>C	p.Arg1762Pro	p.R1762P	ENST00000356435		1762	cGg/cCg	32/35	0.209805289641436	3	FACETS	0.861	0.796	0.929	0.861	0.796	0.929	CLONAL	2	TRUE	1	0.197325152710951	3		490	1293	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274198	10274198	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1337036703	NA	P-0007757-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	58	224	0	ENST00000330684.3:c.71G>A	p.Ser24Asn	p.S24N	ENST00000330684	NM_001134407.1	24	aGc/aAc	2/13	1	2	FACETS	0.991	0.852	1	0.991	0.852	1	CLONAL	1	TRUE	1	0.197325152710951	2		224	593	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435056	56435056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007757-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	193	371	0	ENST00000407977.2:c.2081C>T	p.Pro694Leu	p.P694L	ENST00000407977		694	cCa/cTa	9/10	1	2	FACETS	0.971	0.898	1	1	0.993	1	CLONAL	2	TRUE	1	0.197325152710951	2		371	1007	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101082	4101082	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007757-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	77	212	0	ENST00000262948.5:c.640G>T	p.Gly214Trp	p.G214W	ENST00000262948	NM_030662.3	214	Ggg/Tgg	6/11	0.15576243587496	2	FACETS	0.774	0.681	0.874	0.774	0.681	0.874	SUBCLONAL	2	TRUE	0	0.197325152710951	2		212	504	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129674	11129674	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007757-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	210	568	2	ENST00000358026.2:c.2480C>T	p.Pro827Leu	p.P827L	ENST00000358026	NM_001128849.1	827	cCc/cTc	17/36	0.15576243587496	2	FACETS	0.772	0.715	0.832	0.772	0.715	0.832	SUBCLONAL	2	TRUE	0	0.197325152710951	2		570	1378	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223685	53223685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007757-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1296	120	684	0	ENST00000375401.3:c.3674C>T	p.Pro1225Leu	p.P1225L	ENST00000375401	NM_004187.3	1225	cCc/cTc	23/26	0.117925177809356	0	FACETS	0.689	0.62	0.763			1	INDETERMINATE	1	TRUE	0	0.197325152710951	0		684	1416	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480505	123480505	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007757-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	136	379	0	ENST00000371139.4:c.13G>T	p.Ala5Ser	p.A5S	ENST00000371139	NM_001114937.2	5	Gct/Tct	1/4	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.197325152710951	2		379	1182	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0007839-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	150	474	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.792793421215414	5	FACETS	1	0.958	1	0.269	0.246	0.293	CLONAL	1	TRUE	1	0.792793421215414	5		474	770	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204864	NA	P-0007839-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	26	418	0	ENST00000371953.3:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000371953	NM_000314.4	171	Cag/Tag	6/9	0.792793421215414	1	FACETS	0.081	0.064	0.101	0.081	0.064	0.101	SUBCLONAL	1	TRUE	0	0.792793421215414	1		418	489	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0007839-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	52	103	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.792793421215414	1	FACETS	0.72	0.635	0.806	0.72	0.635	0.806	SUBCLONAL	1	TRUE	0	0.792793421215414	1		103	110	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061701	38061701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007839-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	168	186	0	ENST00000250448.2:c.288G>A	p.Met96Ile	p.M96I	ENST00000250448	NM_004496.3	96	atG/atA	2/2	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.792793421215414	2		186	418	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245335	153245335	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0007839-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	303	398	1	ENST00000281708.4:c.1855+1G>T		p.X619_splice	ENST00000281708	NM_033632.3	619			0.792793421215414	1	FACETS	0.986	0.945	1	0.986	0.945	1	CLONAL	1	TRUE	0	0.792793421215414	1		399	468	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021115	31021115	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs199846284	NA	P-0008057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	255	630	0	ENST00000375687.4:c.1114C>T	p.Gln372Ter	p.Q372*	ENST00000375687	NM_015338.5	372	Cag/Tag	12/13	0.395838982841036	5	FACETS	1	0.987	1	0.401	0.375	0.429	CLONAL	1	TRUE	2	0.615991154782347	5		630	1323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576862	7576930	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAAATATTCTCCATCCAGTGGTTTCTTCTTTGGCTGGGGAGAGGAGCTGGTGTTGTTGGGCAGTGCTAG	GAAATATTCTCCATCCAGTGGTTTCTTCTTTGGCTGGGGAGAGGAGCTGGTGTTGTTGGGCAGTGCTAG	-	novel	NA	P-0008057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	255	704	0	ENST00000269305.4:c.920-4_984del		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.615991154782347	2		704	693	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416118	49416125	+	frameshift_variant	Frame_Shift_Del	DEL	ACATGTAG	ACATGTAG	-	novel	NA	P-0008057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	210	567	0	ENST00000301067.7:c.16350_16357del	p.Tyr5451ProfsTer5	p.Y5451Pfs*5	ENST00000301067	NM_003482.3	5450	atCTACATGTtc/attc	52/54	0.610813023535167	3	FACETS	1	0.967	1	0.532	0.495	0.571	CLONAL	1	TRUE	1	0.615991154782347	3		567	838	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0008069-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	21	365	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.051	0.039	0.066	0.051	0.039	0.066	SUBCLONAL	1	FALSE	1	0.945175938071235	2		367	865	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434259	49434262	+	frameshift_variant	Frame_Shift_Del	DEL	CAGA	CAGA	-	rs1555192210	NA	P-0008069-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2313	151	1244	0	ENST00000301067.7:c.7291_7294del	p.Ser2431LeufsTer53	p.S2431Lfs*53	ENST00000301067	NM_003482.3	2431	TCTGct/ct	31/54	1	2	FACETS	0.13	0.117	0.143	0.13	0.117	0.143	SUBCLONAL	1	FALSE	1	0.945175938071235	2		1244	2464	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964321	55964332	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	CTGGGGAATTCC	CTGGGGAATTCC	-	novel	NA	P-0008069-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	388	775	0	ENST00000263923.4:c.2481_2492del	p.Trp827_Arg831delinsTer	p.W827_R831delins*	ENST00000263923	NM_002253.2	827	tgGGAATTCCCCAGa/tga	17/30	NA	2	FACETS	0.891	0.851	0.933			1	INDETERMINATE	1	FALSE	NA	0.945175938071235	2		775	921	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs587780073	NA	P-0008069-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	103	507	0	ENST00000269305.4:c.701A>C	p.Tyr234Ser	p.Y234S	ENST00000269305	NM_001126112.2	234	tAc/tCc	7/11	1	2	FACETS	0.171	0.152	0.191	0.171	0.152	0.191	SUBCLONAL	1	FALSE	1	0.945175938071235	2		507	1275	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645104	67645105	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0008069-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1266	217	720	0	ENST00000264010.4:c.370_371del	p.Val124ThrfsTer15	p.V124Tfs*15	ENST00000264010	NM_006565.3	123	acTGta/acta	3/12	1	2	FACETS	0.31	0.287	0.333	0.31	0.287	0.333	SUBCLONAL	1	FALSE	1	0.945175938071235	2		720	1483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0008160-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	728	465	1	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.89771212410238	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	4	TRUE	0	0.905899806514178	4		466	763	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241679	55241681	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	rs397517086	NA	P-0008160-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	1280	466	2	ENST00000275493.2:c.2127_2129del	p.Glu709_Thr710delinsAsp	p.E709_T710delinsD	ENST00000275493	NM_005228.3	709	gaAACt/gat	18/28	0.905899806514178	9	FACETS	1	0.992	1	1	0.992	1	CLONAL	7	TRUE	2	0.905899806514178	9		468	1662	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40462634	40462634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774831875	NA	P-0008160-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	77	660	1	ENST00000345506.4:c.2332C>T	p.Arg778Cys	p.R778C	ENST00000345506	NM_003152.3	778	Cgc/Tgc	20/20	NA	2	FACETS	0.22	0.192	0.249			1	INDETERMINATE	1	TRUE	NA	0.905899806514178	2		661	773	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0008167-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	549	393	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.642314484094524	8	FACETS	0.997	0.967	1			1	CLONAL	6	TRUE	NA	0.642314484094524	8		393	836	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578177	7578177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008167-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	383	819	0	ENST00000269305.4:c.672G>C	p.Glu224Asp	p.E224D	ENST00000269305	NM_001126112.2	224	gaG/gaC	6/11	0.626432923733767	3	FACETS	0.976	0.944	1	0.976	0.944	1	CLONAL	3	TRUE	0	0.642314484094524	3		819	538	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915049	32915049	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507867	NA	P-0008167-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	411	1245	1	ENST00000380152.3:c.6557C>T	p.Ser2186Leu	p.S2186L	ENST00000380152		2186	tCa/tTa	11/27	0.611448306507876	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.642314484094524	3		1246	818	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570078	95570078	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008167-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	288	692	0	ENST00000393063.1:c.3655A>G	p.Ile1219Val	p.I1219V	ENST00000393063	NM_030621.3	1219	Att/Gtt	22/28	0.642314484094524	3	FACETS	0.929	0.892	0.966			1	CLONAL	3	TRUE	NA	0.642314484094524	3		692	425	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292850	91292850	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008167-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	110	561	2	ENST00000355112.3:c.352G>A	p.Val118Ile	p.V118I	ENST00000355112	NM_000057.2	118	Gtt/Att	3/22	0.600613726295016	4	FACETS	1	0.959	1	0.373	0.336	0.411	CLONAL	1	TRUE	1	0.642314484094524	4		563	503	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10264971	10264971	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008167-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	134	494	0	ENST00000340748.4:c.1969G>T	p.Glu657Ter	p.E657*	ENST00000340748		657	Gag/Tag	21/40	0.492777726728767	4	FACETS	0.89	0.817	0.964	0.89	0.817	0.964	CLONAL	2	TRUE	2	0.642314484094524	4		494	385	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17380454	17380454	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774266782	NA	P-0008523-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	419	786	0	ENST00000375499.3:c.61G>A	p.Ala21Thr	p.A21T	ENST00000375499	NM_003000.2	21	Gcc/Acc	1/8	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.578249039940199	2		786	1131	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106951	27106951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008764-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	46	484	0	ENST00000324856.7:c.6562C>T	p.Gln2188Ter	p.Q2188*	ENST00000324856	NM_006015.4	2188	Cag/Tag	20/20	1	2	FACETS	0.613	0.515	0.721	0.613	0.515	0.721	SUBCLONAL	1	TRUE	1	0.23	2		484	653	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937687	76937687	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008764-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	65	313	0	ENST00000373344.5:c.3061G>T	p.Glu1021Ter	p.E1021*	ENST00000373344	NM_000489.3	1021	Gag/Tag	9/35	0.257486503426976	2	FACETS	1	0.877	1			1	CLONAL	1	TRUE	NA	0.23	2		313	559	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943284	71943284	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008764-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	103	612	0	ENST00000298229.2:c.1616G>T	p.Gly539Val	p.G539V	ENST00000298229	NM_001567.3	539	gGg/gTg	14/28	1	2	FACETS	0.974	0.87	1	0.974	0.87	1	CLONAL	1	TRUE	1	0.23	2		612	920	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943941	71943941	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008764-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	140	871	1	ENST00000298229.2:c.1874G>T	p.Arg625Met	p.R625M	ENST00000298229	NM_001567.3	625	aGg/aTg	16/28	1	2	FACETS	0.951	0.864	1	0.951	0.864	1	CLONAL	1	TRUE	1	0.23	2		872	1280	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008910-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	294	380	1	ENST00000206249.3:c.1607T>A	p.Leu536His	p.L536H	ENST00000206249	NM_000125.3	536	cTc/cAc	8/8	1	2	FACETS	0.897	0.847	0.949	0.897	0.847	0.949	CLONAL	1	TRUE	1	0.742071061358406	2		381	883	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842278	151842278	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008910-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	388	475	1	ENST00000262189.6:c.14134G>T	p.Glu4712Ter	p.E4712*	ENST00000262189	NM_170606.2	4712	Gaa/Taa	54/59	1	2	FACETS	0.934	0.888	0.98	0.934	0.888	0.98	CLONAL	1	TRUE	1	0.742071061358406	2		476	1120	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376440	118376446	+	frameshift_variant	Frame_Shift_Del	DEL	ATACTTC	ATACTTC	-	novel	NA	P-0008910-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	359	396	0	ENST00000534358.1:c.9835_9841del	p.Thr3279LeufsTer9	p.T3279Lfs*9	ENST00000534358	NM_005933.3	3278	aATACTTCa/aa	27/36	0.740586319969127	1	FACETS	0.977	0.937	1	0.977	0.937	1	CLONAL	1	TRUE	0	0.742071061358406	1		396	623	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0009013-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	173	349	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.704	0.651	0.759	0.704	0.651	0.759	SUBCLONAL	1	TRUE	1	0.781395655649605	2		350	629	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0009013-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	297	323	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.743474355327423	3	FACETS	0.877	0.833	0.92	0.877	0.833	0.92	CLONAL	2	TRUE	1	0.781395655649605	3		323	603	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856332	111856332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009013-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	32	90	0	ENST00000341259.2:c.383G>A	p.Arg128Gln	p.R128Q	ENST00000341259	NM_005475.2	128	cGg/cAg	2/8	0.743474355327423	3	FACETS	0.31	0.251	0.375	0.155	0.125	0.188	SUBCLONAL	1	TRUE	1	0.781395655649605	3		90	368	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900402	3900402	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009028-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	73	642	3	ENST00000262367.5:c.694C>T	p.Gln232Ter	p.Q232*	ENST00000262367	NM_004380.2	232	Cag/Tag	2/31	1	2	FACETS	0.206	0.179	0.236	0.206	0.179	0.236	SUBCLONAL	1	TRUE	1	0.59	2		645	1199	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441246	52441246	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009028-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	333	658	0	ENST00000460680.1:c.524C>G	p.Pro175Arg	p.P175R	ENST00000460680	NM_004656.3	175	cCt/cGt	7/17	0.560549147154089	1	FACETS	0.997	0.948	1	0.997	0.948	1	CLONAL	1	TRUE	0	0.59	1		658	798	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651519	52651519	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009028-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	513	784	0	ENST00000394830.3:c.1577T>C	p.Leu526Ser	p.L526S	ENST00000394830	NM_018313.4	526	tTa/tCa	15/30	0.560549147154089	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.59	1		784	1125	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913514	NA	P-0009084-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	500	422	0	ENST00000288135.5:c.2466T>A	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaA	17/21	0.294025289188212	5	FACETS	0.902	0.867	0.938			1	INDETERMINATE	3	TRUE	NA	0.690522263834579	5		422	1089	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0009084-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	214	439	1	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	0.67875793272241	3	FACETS	0.931	0.866	0.997	0.465	0.433	0.499	CLONAL	1	TRUE	1	0.690522263834579	3		440	896	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593441	55593441	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs753212327	NA	P-0009084-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	854	715	0	ENST00000288135.5:c.1598C>A	p.Ala533Asp	p.A533D	ENST00000288135	NM_000222.2	533	gCt/gAt	10/21	0.294025289188212	5	FACETS	0.982	0.954	1			1	INDETERMINATE	3	TRUE	NA	0.690522263834579	5		715	1709	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0009367-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	304	346	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.96	0.907	1	0.96	0.907	1	CLONAL	1	TRUE	1	0.669185279563673	2		346	946	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009367-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	296	557	0	ENST00000425967.3:c.1731C>G	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaG	13/19	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.669185279563673	2		557	870	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663730	29663730	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555534677	NA	P-0009367-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	342	610	2	ENST00000356175.3:c.6162G>A	p.Trp2054Ter	p.W2054*	ENST00000356175	NM_000267.3	2054	tgG/tgA	41/57	0.669185279563673	1	FACETS	0.961	0.916	1	0.961	0.916	1	CLONAL	1	TRUE	0	0.669185279563673	1		612	708	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099271	4099271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs185999703	NA	P-0009367-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	279	555	2	ENST00000262948.5:c.847G>A	p.Val283Met	p.V283M	ENST00000262948	NM_030662.3	283	Gtg/Atg	7/11	0.17972041740171	1	FACETS	0.591	0.556	0.627	0.591	0.556	0.627	INDETERMINATE	1	TRUE	0	0.669185279563673	1		557	939	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863688	68863688	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786203752	NA	P-0009367-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	204	304	1	ENST00000261769.5:c.2430del	p.Phe810LeufsTer6	p.F810Lfs*6	ENST00000261769	NM_004360.3	809	aaT/aa	15/16	0.669185279563673	1	FACETS	0.975	0.917	1	0.975	0.917	1	CLONAL	1	TRUE	0	0.669185279563673	1		305	416	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152506	56152506	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009367-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	258	331	0	ENST00000399503.3:c.564del	p.Lys188AsnfsTer2	p.K188Nfs*2	ENST00000399503	NM_005921.1	188	Aaa/aa	2/20	1	2	FACETS	0.96	0.902	1	0.96	0.902	1	CLONAL	1	TRUE	1	0.669185279563673	2		331	803	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120756	115120756	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009367-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	337	595	2	ENST00000257566.3:c.250del	p.Gln84ArgfsTer4	p.Q84Rfs*4	ENST00000257566	NM_016569.3	84	Cag/ag	1/8	1	2	FACETS	0.983	0.931	1	0.983	0.931	1	CLONAL	1	TRUE	1	0.669185279563673	2		597	1025	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0009874-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	128	382	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.251297314005205	4	FACETS	1	0.958	1			1	CLONAL	2	FALSE	NA	0.325818591747839	4		382	481	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846356	128846356	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1199769385	NA	P-0009874-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	133	1293	3	ENST00000249373.3:c.1192C>T	p.Arg398Ter	p.R398*	ENST00000249373	NM_005631.4	398	Cga/Tga	6/12	0.325818591747839	3	FACETS	1	0.961	1	0.553	0.502	0.607	CLONAL	1	FALSE	1	0.325818591747839	3		1296	858	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264194	46264194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009874-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	130	1370	1	ENST00000371998.3:c.1241G>A	p.Ser414Asn	p.S414N	ENST00000371998		414	aGc/aAc	11/23	0.226483757424668	4	FACETS	0.895	0.81	0.985	0.448	0.405	0.493	CLONAL	1	FALSE	2	0.325818591747839	4		1371	1182	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430799	78430799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	75	464	0	ENST00000370768.2:c.590C>T	p.Ala197Val	p.A197V	ENST00000370768	NM_003902.3	197	gCa/gTa	8/20	0.19020352998153	3	FACETS	0.838	0.736	0.948	0.279	0.245	0.316	INDETERMINATE	1	TRUE	0	0.435802419807573	3		464	500	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519029	66519029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568695288	NA	P-0010026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	110	492	0	ENST00000358598.2:c.310G>A	p.Val104Ile	p.V104I	ENST00000358598	NM_212471.2	104	Gtc/Atc	3/11	0.435802419807573	3	FACETS	0.653	0.586	0.725	0.327	0.293	0.363	SUBCLONAL	1	TRUE	1	0.435802419807573	3		492	941	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0010030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	407	454	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.647216021886001	3	FACETS	0.88	0.842	0.918	0.88	0.842	0.918	CLONAL	2	TRUE	1	0.71657517655666	3		454	877	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0010030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	497	421	1	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.625963626028997	3	FACETS	0.844	0.818	0.87	0.844	0.818	0.87	CLONAL	3	TRUE	0	0.71657517655666	3		422	744	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609803	117609803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	293	564	0	ENST00000368508.3:c.6896C>T	p.Ser2299Phe	p.S2299F	ENST00000368508	NM_002944.2	2299	tCt/tTt	43/43	1	2	FACETS	0.836	0.788	0.885	0.836	0.788	0.885	CLONAL	1	TRUE	1	0.71657517655666	2		564	978	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372209	55372209	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	90	72	0	ENST00000297316.4:c.899T>C	p.Met300Thr	p.M300T	ENST00000297316	NM_022454.3	300	aTg/aCg	2/2	0.71657517655666	3	FACETS	1	0.977	1	0.784	0.723	0.844	CLONAL	2	TRUE	0	0.71657517655666	3		72	145	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111958616	111958616	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs561759202	NA	P-0010030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	36	231	0	ENST00000375549.3:c.88C>A	p.His30Asn	p.H30N	ENST00000375549	NM_003002.3	30	Cat/Aat	2/4	0.639679929076157	3	FACETS	0.282	0.231	0.339	0.094	0.077	0.113	SUBCLONAL	1	TRUE	0	0.71657517655666	3		231	484	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233118	69233118	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	225	422	0	ENST00000462284.1:c.983G>A	p.Cys328Tyr	p.C328Y	ENST00000462284	NM_002392.5	328	tGt/tAt	11/11	0.647216021886001	3	FACETS	0.872	0.813	0.934	0.436	0.406	0.467	CLONAL	1	TRUE	1	0.71657517655666	3		422	978	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5258031	5258031	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	125	360	0	ENST00000357368.4:c.703C>T	p.Arg235Ter	p.R235*	ENST00000357368	NM_002850.3	235	Cga/Tga	8/38	0.625963626028997	3	FACETS	0.918	0.835	1	0.306	0.278	0.335	CLONAL	1	TRUE	0	0.71657517655666	3		360	516	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139269	108139269	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	739	482	1	ENST00000278616.4:c.2772del	p.Arg925GlyfsTer4	p.R925Gfs*4	ENST00000278616	NM_000051.3	924	cGg/cg	18/63	0.639679929076157	3	FACETS	0.934	0.912	0.955	0.934	0.912	0.955	CLONAL	3	TRUE	0	0.71657517655666	3		483	1000	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602788	10602790	+	inframe_deletion	In_Frame_Del	DEL	CGT	CGT	-	novel	NA	P-0010030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	492	408	0	ENST00000171111.5:c.788_790del	p.Tyr263_Val264delinsPhe	p.Y263_V264delinsF	ENST00000171111	NM_203500.1	263	tACGtc/ttc	3/6	0.625963626028997	3	FACETS	0.909	0.883	0.935	0.909	0.883	0.935	CLONAL	3	TRUE	0	0.71657517655666	3		408	684	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067144	143067145	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0010030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	273	351	0	ENST00000262992.4:c.1568_1569delinsCT	p.Arg523Thr	p.R523T	ENST00000262992	NM_001101669.1	523	aGG/aCT	16/24	0.647216021886001	3	FACETS	0.82	0.776	0.865	0.82	0.776	0.865	CLONAL	2	TRUE	1	0.71657517655666	3		351	631	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350119	81350120	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0010030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	541	484	1	ENST00000222390.5:c.1212_1213delinsAA	p.Gln405Lys	p.Q405K	ENST00000222390	NM_000601.4	404	tcCCaa/tcAAaa	10/18	0.605405548986959	4	FACETS	0.854	0.819	0.89	0.854	0.819	0.89	CLONAL	2	TRUE	2	0.71657517655666	4		485	1517	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356251	70356251	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010046-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1390	244	570	0	ENST00000374080.3:c.5146C>T	p.Arg1716Ter	p.R1716*	ENST00000374080		1716	Cga/Tga	37/45	0.437689682147582	5	FACETS	1	0.98	1	0.377	0.351	0.404	CLONAL	1	TRUE	2	0.437689682147582	5		570	1634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0010054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	105	505	2	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.210428451321638	1	FACETS	0.69	0.617	0.768	0.69	0.617	0.768	SUBCLONAL	1	FALSE	0	0.272929289766032	1		507	963	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057835	27057835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1380	155	893	1	ENST00000324856.7:c.1543C>T	p.Gln515Ter	p.Q515*	ENST00000324856	NM_006015.4	515	Cag/Tag	3/20	1	2	FACETS	0.74	0.675	0.809	0.74	0.675	0.809	SUBCLONAL	1	FALSE	1	0.272929289766032	2		894	1535	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184141	56184141	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1277	96	578	1	ENST00000399503.3:c.4346G>A	p.Trp1449Ter	p.W1449*	ENST00000399503	NM_005921.1	1449	tGg/tAg	19/20	0.190839810679007	3	FACETS	0.582	0.517	0.653	0.291	0.258	0.327	SUBCLONAL	1	FALSE	1	0.272929289766032	3		579	1373	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11273502	11273502	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	50	422	0	ENST00000361445.4:c.3239G>T	p.Arg1080Leu	p.R1080L	ENST00000361445	NM_004958.3	1080	cGt/cTt	21/58	1	2	FACETS	0.405	0.342	0.474	0.405	0.342	0.474	SUBCLONAL	1	FALSE	1	0.272929289766032	2		422	905	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439790	51439790	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	72	312	0	ENST00000262662.1:c.355G>T	p.Val119Leu	p.V119L	ENST00000262662		119	Gtg/Ttg	4/4	1	2	FACETS	0.89	0.778	1	0.89	0.778	1	CLONAL	1	FALSE	1	0.272929289766032	2		312	593	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115252217	115252217	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1338	71	609	0	ENST00000369535.4:c.423C>A	p.Phe141Leu	p.F141L	ENST00000369535	NM_002524.4	141	ttC/ttA	4/7	1	2	FACETS	0.369	0.321	0.422	0.369	0.321	0.422	SUBCLONAL	1	FALSE	1	0.272929289766032	2		609	1409	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729746	162729746	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	114	519	0	ENST00000367921.3:c.832A>T	p.Ile278Phe	p.I278F	ENST00000367921	NM_006182.2	278	Atc/Ttc	8/18	0.190839810679007	3	FACETS	0.894	0.803	0.99	0.447	0.401	0.495	CLONAL	1	FALSE	1	0.272929289766032	3		519	1062	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703547	47703547	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs267607995	NA	P-0010054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1188	184	646	3	ENST00000233146.2:c.2047G>T	p.Gly683Trp	p.G683W	ENST00000233146	NM_000251.2	683	Ggg/Tgg	13/16	1	2	FACETS	0.983	0.905	1	0.983	0.905	1	CLONAL	1	FALSE	1	0.272929289766032	2		649	1372	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499505	89499505	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	39	364	0	ENST00000336596.2:c.2675C>A	p.Thr892Asn	p.T892N	ENST00000336596	NM_005233.5	892	aCc/aAc	15/17	1	2	FACETS	0.39	0.322	0.467	0.39	0.322	0.467	SUBCLONAL	1	FALSE	1	0.272929289766032	2		364	732	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169006	32169006	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1489506589	NA	P-0010054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1327	71	827	0	ENST00000375023.3:c.4027C>T	p.Pro1343Ser	p.P1343S	ENST00000375023	NM_004557.3	1343	Cct/Tct	22/30	0.190839810679007	3	FACETS	0.423	0.367	0.484	0.211	0.183	0.242	SUBCLONAL	1	FALSE	1	0.272929289766032	3		827	1398	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444276	50444276	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144637662	NA	P-0010054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	83	369	0	ENST00000331340.3:c.206G>A	p.Arg69His	p.R69H	ENST00000331340	NM_006060.4	69	cGt/cAt	4/8	1	2	FACETS	0.755	0.665	0.851	0.755	0.665	0.851	SUBCLONAL	1	FALSE	1	0.272929289766032	2		369	806	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512623	148512623	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	70	467	0	ENST00000320356.2:c.1521C>G	p.His507Gln	p.H507Q	ENST00000320356	NM_004456.4	507	caC/caG	13/20	1	2	FACETS	0.494	0.429	0.565	0.494	0.429	0.565	SUBCLONAL	1	FALSE	1	0.272929289766032	2		467	1038	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5073740	5073740	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0010054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	61	539	0	ENST00000381652.3:c.1819A>T	p.Lys607Ter	p.K607*	ENST00000381652	NM_004972.3	607	Aag/Tag	14/25	0.272929289766032	1	FACETS	0.424	0.365	0.489	0.424	0.365	0.489	SUBCLONAL	1	FALSE	0	0.272929289766032	1		539	910	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307465	118307465	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs782191019	NA	P-0010054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	119	523	0	ENST00000534358.1:c.238G>C	p.Ala80Pro	p.A80P	ENST00000534358	NM_005933.3	80	Gcc/Ccc	1/36	0.190839810679007	3	FACETS	1	0.93	1	0.519	0.468	0.574	CLONAL	1	FALSE	1	0.272929289766032	3		523	954	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230371	46230371	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0010054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	111	434	0	ENST00000334344.6:c.706-1G>C		p.X236_splice	ENST00000334344	NM_152641.2	236			1	2	FACETS	0.72	0.645	0.799	0.72	0.645	0.799	SUBCLONAL	1	FALSE	1	0.272929289766032	2		434	1130	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243487	46243487	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	108	613	0	ENST00000334344.6:c.1840C>T	p.Gln614Ter	p.Q614*	ENST00000334344	NM_152641.2	614	Cag/Tag	14/21	1	2	FACETS	0.692	0.619	0.769	0.692	0.619	0.769	SUBCLONAL	1	FALSE	1	0.272929289766032	2		613	1144	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245765	46245765	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	115	467	1	ENST00000334344.6:c.3859G>T	p.Glu1287Ter	p.E1287*	ENST00000334344	NM_152641.2	1287	Gaa/Taa	15/21	1	2	FACETS	0.772	0.694	0.855	0.772	0.694	0.855	SUBCLONAL	1	FALSE	1	0.272929289766032	2		468	1092	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28883044	28883044	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	105	514	0	ENST00000282397.4:c.3656T>A	p.Phe1219Tyr	p.F1219Y	ENST00000282397	NM_002019.4	1219	tTc/tAc	28/30	1	2	FACETS	0.74	0.661	0.824	0.74	0.661	0.824	SUBCLONAL	1	FALSE	1	0.272929289766032	2		514	1040	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008242	29008242	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	119	606	1	ENST00000282397.4:c.629C>T	p.Thr210Ile	p.T210I	ENST00000282397	NM_002019.4	210	aCa/aTa	5/30	1	2	FACETS	0.684	0.615	0.757	0.684	0.615	0.757	SUBCLONAL	1	FALSE	1	0.272929289766032	2		607	1275	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241451	105241451	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	127	606	0	ENST00000349310.3:c.529G>T	p.Ala177Ser	p.A177S	ENST00000349310	NM_001014432.1	177	Gcc/Tcc	7/15	1	2	FACETS	0.999	0.904	1	0.999	0.904	1	CLONAL	1	FALSE	1	0.272929289766032	2		606	932	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988376	41988376	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1718	126	1047	3	ENST00000219905.7:c.1168G>T	p.Asp390Tyr	p.D390Y	ENST00000219905	NM_001164273.1	390	Gac/Tac	3/24	0.210428451321638	1	FACETS	0.432	0.389	0.478	0.432	0.389	0.478	SUBCLONAL	1	FALSE	0	0.272929289766032	1		1050	1844	SUCCESS
BLM	641	MSKCC	GRCh37	15	91333984	91333984	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	54	631	0	ENST00000355112.3:c.2929T>C	p.Ser977Pro	p.S977P	ENST00000355112	NM_000057.2	977	Tct/Cct	15/22	0.210428451321638	1	FACETS	0.318	0.27	0.37	0.318	0.27	0.37	SUBCLONAL	1	FALSE	0	0.272929289766032	1		631	1075	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134377	30134377	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1338	76	873	0	ENST00000263025.4:c.154G>C	p.Ala52Pro	p.A52P	ENST00000263025	NM_002746.2	52	Gcg/Ccg	1/9	NA	2	FACETS	0.394	0.344	0.448			1	INDETERMINATE	1	FALSE	NA	0.272929289766032	2		873	1414	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207105	1207105	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	108	609	0	ENST00000326873.7:c.193G>T	p.Glu65Ter	p.E65*	ENST00000326873	NM_000455.4	65	Gag/Tag	1/10	0.227824814708424	1	FACETS	0.669	0.599	0.744	0.669	0.599	0.744	SUBCLONAL	1	FALSE	0	0.272929289766032	1		609	1021	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0010062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1346	371	610	1	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	1	2	FACETS	0.951	0.899	1	1	0.996	1	CLONAL	2	TRUE	1	0.227264422755063	2		611	1717	SUCCESS
APC	324	MSKCC	GRCh37	5	112176027	112176027	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	40	382	0	ENST00000257430.4:c.4737del	p.Ile1580PhefsTer70	p.I1580Ffs*70	ENST00000257430	NM_000038.5	1579	aTt/at	16/16	1	2	FACETS	0.548	0.454	0.653	0.548	0.454	0.653	SUBCLONAL	1	TRUE	1	0.227264422755063	2		382	642	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0010062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	132	368	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.227264422755063	2		368	846	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240285	41240285	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1839	167	559	0	ENST00000379561.5:c.65C>G	p.Ser22Trp	p.S22W	ENST00000379561	NM_002015.3	22	tCg/tGg	1/3	0.227264422755063	3	FACETS	0.816	0.746	0.889	0.408	0.373	0.445	CLONAL	1	TRUE	1	0.227264422755063	3		559	2006	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247373	71247373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758125097	NA	P-0010062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	129	414	0	ENST00000318789.4:c.160G>A	p.Ala54Thr	p.A54T	ENST00000318789	NM_032682.5	54	Gcc/Acc	6/21	1	2	FACETS	0.974	0.881	1	0.974	0.881	1	CLONAL	1	TRUE	1	0.227264422755063	2		414	1166	SUCCESS
APC	324	MSKCC	GRCh37	5	112173377	112173377	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	43	501	0	ENST00000257430.4:c.2086G>T	p.Glu696Ter	p.E696*	ENST00000257430	NM_000038.5	696	Gaa/Taa	16/16	1	2	FACETS	0.441	0.367	0.522	0.441	0.367	0.522	SUBCLONAL	1	TRUE	1	0.227264422755063	2		501	859	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	400	247	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.263248148497191	4	FACETS	0.9	0.857	0.944			1	CLONAL	3	TRUE	NA	0.337365999312599	4		247	1174	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0010063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	117	365	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.337365999312599	1	FACETS	0.902	0.815	0.994	0.902	0.815	0.994	CLONAL	1	TRUE	0	0.337365999312599	1		367	639	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0010063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	110	301	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.337365999312599	1	FACETS	0.998	0.9	1	0.998	0.9	1	CLONAL	1	TRUE	0	0.337365999312599	1		301	543	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575090	48575090	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	209	606	0	ENST00000342988.3:c.284A>G	p.Tyr95Cys	p.Y95C	ENST00000342988	NM_005359.5	95	tAt/tGt	3/12	0.337365999312599	1	FACETS	0.901	0.836	0.969	0.901	0.836	0.969	CLONAL	1	TRUE	0	0.337365999312599	1		606	1143	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180184	38180184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	236	408	3	ENST00000396334.3:c.32C>T	p.Pro11Leu	p.P11L	ENST00000396334	NM_002468.4	11	cCg/cTg	1/5	1	2	FACETS	1	0.961	1	1	0.996	1	CLONAL	7	TRUE	1	0.118408677409776	2		411	555	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0010089-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	269	346	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.6943067389029	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	2	0.6943067389029	4		346	649	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509107	66509107	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010089-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	145	546	0	ENST00000273854.3:c.220G>T	p.Gly74Ter	p.G74*	ENST00000273854	NM_004439.5	74	Gga/Tga	2/18	0.6943067389029	3	FACETS	0.886	0.811	0.964	0.443	0.405	0.482	CLONAL	1	TRUE	1	0.6943067389029	3		546	635	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857494	9857494	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010089-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	96	424	0	ENST00000330684.3:c.3907G>T	p.Asp1303Tyr	p.D1303Y	ENST00000330684	NM_001134407.1	1303	Gac/Tac	13/13	0.6943067389029	4	FACETS	0.913	0.817	1	0.457	0.408	0.508	CLONAL	1	TRUE	2	0.6943067389029	4		424	513	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958040	54958040	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0010089-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	670	458	0	ENST00000312783.6:c.566+1G>A		p.X189_splice	ENST00000312783	NM_198436.1	189			0.6943067389029	6	FACETS	1	0.995	1	1	0.995	1	CLONAL	4	TRUE	2	0.6943067389029	6		458	1052	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24135804	24135805	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0010092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1379	274	602	0	ENST00000263121.7:c.294_295del	p.Glu98AspfsTer7	p.E98Dfs*7	ENST00000263121	NM_003073.3	97	gaAGag/gaag	3/9	1	2	FACETS	0.921	0.862	0.982	0.921	0.862	0.982	CLONAL	1	TRUE	1	0.36	2		602	1653	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145567	24145567	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	229	461	0	ENST00000263121.7:c.586del	p.Asp196MetfsTer13	p.D196Mfs*13	ENST00000263121	NM_003073.3	196	Gat/at	5/9	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.36	2		461	1215	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0010100-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	314	355	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.32698509797826	3	FACETS	0.878	0.832	0.926	0.878	0.832	0.926	CLONAL	3	TRUE	0	0.32698509797826	3		355	848	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0010100-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	113	645	1	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.32698509797826	4	FACETS	1	0.944	1	0.358	0.321	0.396	CLONAL	1	TRUE	1	0.32698509797826	4		646	855	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220644	1220644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1167609100	NA	P-0010100-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	315	553	0	ENST00000326873.7:c.662C>T	p.Pro221Leu	p.P221L	ENST00000326873	NM_000455.4	221	cCg/cTg	5/10	0.32698509797826	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.32698509797826	2		553	918	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913351	NA	P-0010100-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	350	406	0	ENST00000288602.6:c.1397G>A	p.Gly466Glu	p.G466E	ENST00000288602	NM_004333.4	466	gGa/gAa	11/18	0.32698509797826	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	0	0.32698509797826	3		406	803	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790830	89790830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010100-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	86	431	0	ENST00000336032.3:c.217C>T	p.Arg73Cys	p.R73C	ENST00000336032	NM_006813.2	73	Cgc/Tgc	1/2	0.32698509797826	2	FACETS	0.767	0.678	0.861	0.383	0.339	0.431	SUBCLONAL	1	TRUE	0	0.32698509797826	2		431	686	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335631	81335631	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010100-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	119	454	0	ENST00000222390.5:c.1729T>A	p.Ser577Thr	p.S577T	ENST00000222390	NM_000601.4	577	Tca/Aca	15/18	0.32698509797826	3	FACETS	1	0.924	1	0.343	0.309	0.378	CLONAL	1	TRUE	0	0.32698509797826	3		454	824	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002734	37002734	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010100-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	108	364	1	ENST00000358127.4:c.515C>T	p.Thr172Met	p.T172M	ENST00000358127	NM_001280556.1	172	aCg/aTg	5/10	0.32698509797826	2	FACETS	0.995	0.894	1	0.497	0.447	0.551	CLONAL	1	TRUE	0	0.32698509797826	2		365	664	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473772	67473772	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010100-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	378	417	0	ENST00000327367.4:c.852G>C	p.Glu284Asp	p.E284D	ENST00000327367	NM_005902.3	284	gaG/gaC	6/9	0.312950881508057	5	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	2	0.32698509797826	5		417	1073	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101120	41101120	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010100-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	264	319	0	ENST00000373198.4:c.1236C>A	p.Tyr412Ter	p.Y412*	ENST00000373198	NM_133170.3	412	taC/taA	8/32	0.312919038445935	3	FACETS	1	0.945	1	1	0.945	1	CLONAL	3	TRUE	0	0.32698509797826	3		319	626	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0010102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	195	462	1	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	0.296440882198822	3	FACETS	0.869	0.806	0.935	0.869	0.806	0.935	CLONAL	2	TRUE	1	0.32	3		463	813	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0010102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	318	301	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.300117246992989	5	FACETS	0.964	0.911	1	0.964	0.911	1	CLONAL	3	TRUE	2	0.32	5		301	1017	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0010102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	364	677	1	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.300117246992989	2	FACETS	0.937	0.889	0.986	0.937	0.889	0.986	CLONAL	2	TRUE	0	0.32	2		678	1214	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761014	59761017	+	frameshift_variant	Frame_Shift_Del	DEL	ATAG	ATAG	-	rs778664039	NA	P-0010102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	286	684	0	ENST00000259008.2:c.3390_3393del	p.Tyr1131LeufsTer18	p.Y1131Lfs*18	ENST00000259008	NM_032043.2	1130	atCTAT/at	20/20	0.299454579105881	4	FACETS	0.807	0.757	0.859	0.807	0.757	0.859	CLONAL	2	TRUE	2	0.32	4		684	1462	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927457	49927457	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752084153	NA	P-0010102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1724	306	875	0	ENST00000296474.3:c.3847C>T	p.Arg1283Trp	p.R1283W	ENST00000296474	NM_002447.2	1283	Cgg/Tgg	19/20	0.296440882198822	3	FACETS	1	0.979	1	0.546	0.513	0.581	CLONAL	1	TRUE	1	0.32	3		875	2030	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244392	5244392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377318412	NA	P-0010102-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	152	516	0	ENST00000357368.4:c.1090G>A	p.Val364Ile	p.V364I	ENST00000357368	NM_002850.3	364	Gtc/Atc	11/38	1	2	FACETS	0.864	0.788	0.943	0.864	0.788	0.943	CLONAL	1	TRUE	1	0.32	2		516	1100	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086133	16086133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	186	518	0	ENST00000281043.3:c.1309G>A	p.Glu437Lys	p.E437K	ENST00000281043	NM_005378.4	437	Gag/Aag	3/3	0.759589746647585	3	FACETS	0.864	0.8	0.931			1	CLONAL	1	TRUE	NA	0.759589746647585	3		518	782	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513462	149513462	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	228	602	0	ENST00000261799.4:c.741G>T	p.Trp247Cys	p.W247C	ENST00000261799	NM_002609.3	247	tgG/tgT	5/23	0.759589746647585	3	FACETS	0.998	0.932	1	0.499	0.466	0.533	CLONAL	1	TRUE	1	0.759589746647585	3		602	830	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233105	55233105	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	144	373	0	ENST00000275493.2:c.1855C>A	p.Leu619Met	p.L619M	ENST00000275493	NM_005228.3	619	Ctg/Atg	15/28	0.759589746647585	3	FACETS	0.944	0.866	1	0.472	0.433	0.513	CLONAL	1	TRUE	1	0.759589746647585	3		373	554	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206817	36206817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368711448	NA	P-0010107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	120	368	0	ENST00000300305.3:c.695G>A	p.Arg232Gln	p.R232Q	ENST00000300305		232	cGg/cAg	6/8	0.719940488979673	4	FACETS	0.924	0.836	1	0.462	0.418	0.508	CLONAL	1	TRUE	2	0.759589746647585	4		368	602	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4388004	4388009	+	frameshift_variant	Frame_Shift_Del	DEL	TTGCGC	TTGCGC	AGAG	novel	NA	P-0010107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	167	516	0	ENST00000261254.3:c.490_495delinsAGAG	p.Leu164ArgfsTer29	p.L164Rfs*29	ENST00000261254	NM_001759.3	164	TTGCGC/AGAG	3/5	0.759589746647585	3	FACETS	0.912	0.841	0.986	0.456	0.42	0.493	CLONAL	1	TRUE	1	0.759589746647585	3		516	665	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4388016	4388027	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCAGCAGCGG	CCCCAGCAGCGG	ATCA	novel	NA	P-0010107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	154	456	0	ENST00000261254.3:c.502_513delinsATCA	p.Pro168IlefsTer23	p.P168Ifs*23	ENST00000261254	NM_001759.3	168	CCCCAGCAGCGG/ATCA	3/5	0.759589746647585	3	FACETS	0.968	0.89	1	0.484	0.445	0.524	CLONAL	1	TRUE	1	0.759589746647585	3		456	578	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947852	178947852	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	356	565	0	ENST00000263967.3:c.2727C>G	p.Phe909Leu	p.F909L	ENST00000263967	NM_006218.2	909	ttC/ttG	19/21	1	2	FACETS	0.978	0.928	1	0.978	0.928	1	CLONAL	1	TRUE	1	0.666112591971451	2		565	1093	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850212	128850212	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	329	506	0	ENST00000249373.3:c.1475C>G	p.Ala492Gly	p.A492G	ENST00000249373	NM_005631.4	492	gCc/gGc	9/12	0.630939623005815	3	FACETS	1	0.963	1	0.513	0.484	0.542	CLONAL	1	TRUE	1	0.666112591971451	3		506	1284	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196062	67196062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	104	404	0	ENST00000312629.5:c.46G>A	p.Glu16Lys	p.E16K	ENST00000312629	NM_003952.2	16	Gag/Aag	1/15	1	2	FACETS	0.376	0.336	0.418	0.376	0.336	0.418	SUBCLONAL	1	TRUE	1	0.666112591971451	2		404	831	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416164	416164	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	413	621	0	ENST00000399788.2:c.4022A>T	p.Glu1341Val	p.E1341V	ENST00000399788	NM_001042603.1	1341	gAa/gTa	24/28	NA	2	FACETS	1	0.967	1			1	INDETERMINATE	1	TRUE	NA	0.666112591971451	2		621	1217	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437421	49437421	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	352	500	0	ENST00000301067.7:c.5464A>G	p.Lys1822Glu	p.K1822E	ENST00000301067	NM_003482.3	1822	Aaa/Gaa	23/54	0.666112591971451	3	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.666112591971451	3		500	1285	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845712	68845815	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AACAGGAACACAGGAGTCATCAGTGTGGTCACCACTGGGCTGGACCGAGAGGTCAGGGGTCAGGAGGATCCAGAGGGTGTGGAGGACAAATGTGTATTAGCTCA	AACAGGAACACAGGAGTCATCAGTGTGGTCACCACTGGGCTGGACCGAGAGGTCAGGGGTCAGGAGGATCCAGAGGGTGTGGAGGACAAATGTGTATTAGCTCA	-	novel	NA	P-0010110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	534	590	0	ENST00000261769.5:c.959_1008+54del		p.X320_splice	ENST00000261769	NM_004360.3	320		7/16	0.666112591971451	2	FACETS	0.877	0.848	0.906	0.877	0.848	0.906	CLONAL	2	TRUE	0	0.666112591971451	2		590	914	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206790	162206813	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CATGCTAGACTTACCCACACAAGG	CATGCTAGACTTACCCACACAAGG	-	novel	NA	P-0010110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	66	374	0	ENST00000366898.1:c.862_871+14del		p.X288_splice	ENST00000366898	NM_004562.2	288		7/12	0.665496262596377	1	FACETS	0.321	0.279	0.365	0.321	0.279	0.365	SUBCLONAL	1	TRUE	0	0.666112591971451	1		374	412	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0010119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	71	530	2	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	1	2	FACETS	0.979	0.852	1	0.979	0.852	1	CLONAL	1	TRUE	1	0.147537872290432	2		532	983	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0010119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	83	717	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.147537872290432	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.147537872290432	1		717	863	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206664980	206664980	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0010119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	71	433	0	ENST00000367120.3:c.1734-1G>A		p.X578_splice	ENST00000367120	NM_014002.3	578			0.147537872290432	4	FACETS	1	0.873	1	0.334	0.291	0.382	CLONAL	1	TRUE	1	0.147537872290432	4		433	1101	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438481	52438481	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	63	480	0	ENST00000460680.1:c.1238A>G	p.Asn413Ser	p.N413S	ENST00000460680	NM_004656.3	413	aAc/aGc	12/17	0.147537872290432	1	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	0	0.147537872290432	1		480	787	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598243	52598243	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	63	393	0	ENST00000394830.3:c.3623G>A	p.Cys1208Tyr	p.C1208Y	ENST00000394830	NM_018313.4	1208	tGt/tAt	24/30	0.147537872290432	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.147537872290432	1		393	712	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95598986	95598986	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	52	322	0	ENST00000393063.1:c.173A>G	p.His58Arg	p.H58R	ENST00000393063	NM_030621.3	58	cAt/cGt	4/28	1	2	FACETS	0.947	0.805	1	0.947	0.805	1	CLONAL	1	TRUE	1	0.147537872290432	2		322	744	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8109854	8109854	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	73	500	0	ENST00000585124.1:c.641T>C	p.Leu214Pro	p.L214P	ENST00000585124	NM_004217.3	214	cTg/cCg	7/9	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.147537872290432	2		500	910	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945218	44945218	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	105	453	2	ENST00000377967.4:c.3542G>T	p.Cys1181Phe	p.C1181F	ENST00000377967	NM_021140.2	1181	tGt/tTt	24/29	0.147537872290432	3	FACETS	1	0.979	1	0.708	0.632	0.788	CLONAL	1	TRUE	1	0.147537872290432	3		455	1080	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047700	180047700	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	80	521	0	ENST00000261937.6:c.2315del	p.Gly772AlafsTer6	p.G772Afs*6	ENST00000261937	NM_182925.4	772	gGc/gc	16/30	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.147537872290432	2		521	991	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0010135-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	53	715	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.755	0.645	0.874	1	0.966	1	SUBCLONAL	2	TRUE	1	0.16	2		715	439	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578467	7578467	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010135-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	29	768	0	ENST00000269305.4:c.463A>C	p.Thr155Pro	p.T155P	ENST00000269305	NM_001126112.2	155	Acc/Ccc	5/11	1	2	FACETS	0.489	0.391	0.602	0.489	0.391	0.602	SUBCLONAL	1	TRUE	1	0.16	2		768	741	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578463	7578463	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010135-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	26	748	0	ENST00000269305.4:c.467G>T	p.Arg156Leu	p.R156L	ENST00000269305	NM_001126112.2	156	cGc/cTc	5/11	1	2	FACETS	0.452	0.356	0.563	0.452	0.356	0.563	SUBCLONAL	1	TRUE	1	0.16	2		748	719	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	94	273	0				ENST00000310581	NM_198253.2	-/1132			0.298630613034369	4	FACETS	0.811	0.722	0.906	0.406	0.361	0.453	INDETERMINATE	1	TRUE	2	0.522930797516527	4		273	675	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754865	29754865	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	310	369	0	ENST00000389048.3:c.1070C>T	p.Pro357Leu	p.P357L	ENST00000389048	NM_004304.4	357	cCc/cTc	4/29	0.302095227398516	3	FACETS	0.895	0.847	0.943	0.895	0.847	0.943	INDETERMINATE	2	TRUE	1	0.522930797516527	3		369	836	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955382	48955382	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1485450031	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	246	208	0	ENST00000267163.4:c.1499-1G>A		p.X500_splice	ENST00000267163	NM_000321.2	500			0.522930797516527	3	FACETS	1	0.981	1			1	CLONAL	3	TRUE	NA	0.522930797516527	3		208	376	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587118	189587118	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761885185	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	164	455	0	ENST00000264731.3:c.1135C>T	p.Arg379Cys	p.R379C	ENST00000264731	NM_003722.4	379	Cgt/Tgt	9/14	0.435405438049031	3	FACETS	1	0.942	1	0.515	0.473	0.558	CLONAL	1	TRUE	1	0.522930797516527	3		455	768	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873660	35873660	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs201559094	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	231	468	1	ENST00000303115.3:c.616C>T	p.Arg206Ter	p.R206*	ENST00000303115	NM_002185.3	206	Cga/Tga	5/8	0.298630613034369	4	FACETS	0.818	0.765	0.873	0.818	0.765	0.873	INDETERMINATE	2	TRUE	2	0.522930797516527	4		469	822	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959019	2959019	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	220	304	0	ENST00000396946.4:c.2497C>T	p.Pro833Ser	p.P833S	ENST00000396946	NM_032415.4	833	Ccc/Tcc	18/25	0.373238818221543	5	FACETS	1	0.989	1	0.453	0.421	0.486	CLONAL	1	TRUE	2	0.522930797516527	5		304	1105	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057691	27057691	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	858	813	1	ENST00000324856.7:c.1399C>T	p.Gln467Ter	p.Q467*	ENST00000324856	NM_006015.4	467	Cag/Tag	3/20	0.522930797516527	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.522930797516527	3		814	2028	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073857	8073857	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1569	272	840	0	ENST00000377482.5:c.802T>A	p.Cys268Ser	p.C268S	ENST00000377482	NM_018948.3	268	Tgt/Agt	4/4	0.522930797516527	3	FACETS	0.713	0.666	0.761	0.356	0.333	0.381	SUBCLONAL	1	TRUE	1	0.522930797516527	3		840	1841	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366928	40366928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	192	336	0	ENST00000397332.2:c.269C>T	p.Pro90Leu	p.P90L	ENST00000397332	NM_001033082.2	90	cCc/cTc	2/3	0.373238818221543	5	FACETS	1	0.981	1	0.398	0.367	0.43	CLONAL	1	TRUE	2	0.522930797516527	5		336	1098	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699507	117699507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	92	307	0	ENST00000369458.3:c.134C>T	p.Ala45Val	p.A45V	ENST00000369458	NM_024626.3	45	gCt/gTt	3/6	NA	2	FACETS	0.798	0.713	0.888			1	INDETERMINATE	1	TRUE	NA	0.522930797516527	2		307	441	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176105668	176105668	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	108	498	0	ENST00000367669.3:c.847C>T	p.Gln283Ter	p.Q283*	ENST00000367669	NM_022457.5	283	Cag/Tag	7/20	1	2	FACETS	0.707	0.636	0.782	0.707	0.636	0.782	SUBCLONAL	1	TRUE	1	0.522930797516527	2		498	584	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046241	128046241	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1430093547	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	155	411	0	ENST00000285398.2:c.1022C>T	p.Pro341Leu	p.P341L	ENST00000285398	NM_000122.1	341	cCc/cTc	7/15	0.414856689656652	3	FACETS	0.908	0.831	0.987	0.454	0.415	0.494	CLONAL	1	TRUE	1	0.522930797516527	3		411	824	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934758	49934758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	889	711	1	ENST00000296474.3:c.2138C>T	p.Thr713Ile	p.T713I	ENST00000296474	NM_002447.2	713	aCc/aTc	7/20	0.44266012784814	3	FACETS	0.914	0.89	0.938	0.914	0.89	0.938	CLONAL	3	TRUE	0	0.522930797516527	3		712	1564	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455548	189455548	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	89	455	0	ENST00000264731.3:c.82C>G	p.His28Asp	p.H28D	ENST00000264731	NM_003722.4	28	Cat/Gat	2/14	0.435405438049031	3	FACETS	0.559	0.495	0.627	0.28	0.247	0.314	SUBCLONAL	1	TRUE	1	0.522930797516527	3		455	768	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607245	189607245	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	260	581	0	ENST00000264731.3:c.1624C>T	p.Pro542Ser	p.P542S	ENST00000264731	NM_003722.4	542	Ccg/Tcg	12/14	0.435405438049031	3	FACETS	0.88	0.822	0.939	0.44	0.411	0.47	CLONAL	1	TRUE	1	0.522930797516527	3		581	1426	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156495	55156495	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	142	397	2	ENST00000257290.5:c.2896C>T	p.His966Tyr	p.H966Y	ENST00000257290	NM_006206.4	966	Cac/Tac	22/23	0.302095227398516	3	FACETS	0.672	0.612	0.736	0.336	0.306	0.368	INDETERMINATE	1	TRUE	1	0.522930797516527	3		399	1019	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948145	55948145	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	146	529	0	ENST00000263923.4:c.3826A>G	p.Thr1276Ala	p.T1276A	ENST00000263923	NM_002253.2	1276	Acc/Gcc	29/30	0.302095227398516	3	FACETS	0.728	0.663	0.795	0.364	0.331	0.398	INDETERMINATE	1	TRUE	1	0.522930797516527	3		529	968	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361130	66361130	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	232	527	0	ENST00000273854.3:c.1042G>A	p.Asp348Asn	p.D348N	ENST00000273854	NM_004439.5	348	Gat/Aat	4/18	0.302095227398516	3	FACETS	1	0.991	1	0.694	0.649	0.741	INDETERMINATE	1	TRUE	1	0.522930797516527	3		527	806	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467511	66467511	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	130	470	0	ENST00000273854.3:c.758C>T	p.Ser253Phe	p.S253F	ENST00000273854	NM_004439.5	253	tCc/tTc	3/18	0.302095227398516	3	FACETS	0.56	0.507	0.617	0.28	0.253	0.309	INDETERMINATE	1	TRUE	1	0.522930797516527	3		470	1119	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527226	187527226	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs1437456803	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	269	412	0	ENST00000441802.2:c.10348C>T	p.Gln3450Ter	p.Q3450*	ENST00000441802	NM_005245.3	3450	Cag/Tag	17/27	0.449916317379194	2	FACETS	0.774	0.73	0.817	0.774	0.73	0.817	SUBCLONAL	2	TRUE	0	0.522930797516527	2		412	665	SUCCESS
APC	324	MSKCC	GRCh37	5	112154681	112154681	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	120	301	0	ENST00000257430.4:c.952T>G	p.Leu318Val	p.L318V	ENST00000257430	NM_000038.5	318	Ttg/Gtg	10/16	0.435677127466517	2	FACETS	0.874	0.793	0.959	0.437	0.396	0.48	CLONAL	1	TRUE	0	0.522930797516527	2		301	525	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501586	149501586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772861468	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	303	331	0	ENST00000261799.4:c.2201G>A	p.Gly734Glu	p.G734E	ENST00000261799	NM_002609.3	734	gGg/gAg	16/23	0.435677127466517	2	FACETS	0.837	0.795	0.88	0.837	0.795	0.88	CLONAL	2	TRUE	0	0.522930797516527	2		331	692	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956510	93956510	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	153	617	1	ENST00000369303.4:c.2726G>A	p.Arg909Lys	p.R909K	ENST00000369303	NM_004440.3	909	aGg/aAg	15/17	0.183964195991427	2	FACETS	0.617	0.564	0.672	0.308	0.282	0.336	INDETERMINATE	1	TRUE	0	0.522930797516527	2		618	949	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967203	93967203	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	145	630	0	ENST00000369303.4:c.2149G>A	p.Gly717Arg	p.G717R	ENST00000369303	NM_004440.3	717	Gga/Aga	12/17	0.183964195991427	2	FACETS	0.671	0.612	0.732	0.335	0.306	0.366	INDETERMINATE	1	TRUE	0	0.522930797516527	2		630	827	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066659	94066659	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	439	779	0	ENST00000369303.4:c.1100T>C	p.Ile367Thr	p.I367T	ENST00000369303	NM_004440.3	367	aTa/aCa	5/17	0.183964195991427	2	FACETS	1	0.995	1	0.652	0.622	0.682	INDETERMINATE	1	TRUE	0	0.522930797516527	2		779	1288	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638349	117638349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	126	301	0	ENST00000368508.3:c.6092G>A	p.Gly2031Glu	p.G2031E	ENST00000368508	NM_002944.2	2031	gGa/gAa	38/43	0.183964195991427	2	FACETS	0.622	0.563	0.684	0.311	0.281	0.342	INDETERMINATE	1	TRUE	0	0.522930797516527	2		301	775	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004511	150004511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1278837335	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	220	747	0	ENST00000253339.5:c.1714C>T	p.Pro572Ser	p.P572S	ENST00000253339		572	Cca/Tca	3/7	0.183964195991427	2	FACETS	0.706	0.656	0.759	0.353	0.328	0.38	INDETERMINATE	1	TRUE	0	0.522930797516527	2		747	1191	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161990413	161990413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766948045	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	266	467	0	ENST00000366898.1:c.907C>T	p.His303Tyr	p.H303Y	ENST00000366898	NM_004562.2	303	Cac/Tac	8/12	0.240443134394561	5	FACETS	0.912	0.856	0.97	0.608	0.571	0.647	INDETERMINATE	2	TRUE	2	0.522930797516527	5		467	995	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958199	2958199	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1254	177	461	0	ENST00000396946.4:c.2533A>C	p.Lys845Gln	p.K845Q	ENST00000396946	NM_032415.4	845	Aaa/Caa	19/25	0.373238818221543	5	FACETS	0.844	0.775	0.916	0.281	0.258	0.306	CLONAL	1	TRUE	2	0.522930797516527	5		461	1431	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148513785	148513785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	165	600	0	ENST00000320356.2:c.1496G>A	p.Arg499Lys	p.R499K	ENST00000320356	NM_004456.4	499	aGg/aAg	12/20	1	2	FACETS	0.909	0.837	0.984	0.909	0.837	0.984	CLONAL	1	TRUE	1	0.522930797516527	2		600	694	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843758	151843758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	159	467	0	ENST00000262189.6:c.13957C>T	p.Leu4653Phe	p.L4653F	ENST00000262189	NM_170606.2	4653	Ctt/Ttt	53/59	1	2	FACETS	0.839	0.77	0.91	0.839	0.77	0.91	CLONAL	1	TRUE	1	0.522930797516527	2		467	725	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012236	152012236	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	179	570	0	ENST00000262189.6:c.577A>G	p.Arg193Gly	p.R193G	ENST00000262189	NM_170606.2	193	Aga/Gga	4/59	1	2	FACETS	0.84	0.775	0.907	0.84	0.775	0.907	CLONAL	1	TRUE	1	0.522930797516527	2		570	815	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370784	55370784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	111	203	0	ENST00000297316.4:c.86C>T	p.Pro29Leu	p.P29L	ENST00000297316	NM_022454.3	29	cCc/cTc	1/2	0.522930797516527	5	FACETS	1	0.925	1	0.344	0.31	0.381	CLONAL	1	TRUE	2	0.522930797516527	5		203	733	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460540	8460540	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	114	429	0	ENST00000356435.5:c.3746C>T	p.Pro1249Leu	p.P1249L	ENST00000356435		1249	cCc/cTc	22/35	0.522930797516527	1	FACETS	0.671	0.607	0.737	0.671	0.607	0.737	SUBCLONAL	1	TRUE	0	0.522930797516527	1		429	480	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900270	101900270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554700632	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	136	620	0	ENST00000374994.4:c.704C>T	p.Ser235Phe	p.S235F	ENST00000374994	NM_004612.2	235	tCc/tTc	4/9	0.147076732822518	5	FACETS	0.862	0.782	0.946			1	INDETERMINATE	1	TRUE	NA	0.522930797516527	5		620	1077	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104268996	104268996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1187640052	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	168	643	0	ENST00000369902.3:c.253C>T	p.Pro85Ser	p.P85S	ENST00000369902	NM_016169.3	85	Ccc/Tcc	2/12	0.414856689656652	3	FACETS	0.731	0.671	0.794	0.365	0.335	0.397	SUBCLONAL	1	TRUE	1	0.522930797516527	3		643	1109	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417884	32417884	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267602850	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	202	524	1	ENST00000332351.3:c.1168C>T	p.Pro390Ser	p.P390S	ENST00000332351	NM_024426.4	390	Ccc/Tcc	7/10	NA	2	FACETS	0.754	0.698	0.811			1	INDETERMINATE	1	TRUE	NA	0.522930797516527	2		525	1025	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195526	102195526	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	192	785	0	ENST00000263464.3:c.286G>C	p.Val96Leu	p.V96L	ENST00000263464	NM_001165.4	96	Gtt/Ctt	2/9	1	2	FACETS	0.757	0.7	0.816	0.757	0.7	0.816	SUBCLONAL	1	TRUE	1	0.522930797516527	2		785	970	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186556	108186556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	108	394	1	ENST00000278616.4:c.6013C>T	p.Leu2005Phe	p.L2005F	ENST00000278616	NM_000051.3	2005	Ctc/Ttc	41/63	NA	2	FACETS	0.712	0.641	0.787			1	INDETERMINATE	1	TRUE	NA	0.522930797516527	2		395	580	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342422	118342422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	181	516	1	ENST00000534358.1:c.548C>T	p.Ser183Phe	p.S183F	ENST00000534358	NM_005933.3	183	tCt/tTt	3/36	0.522930797516527	1	FACETS	0.942	0.875	1	0.942	0.875	1	CLONAL	1	TRUE	0	0.522930797516527	1		517	543	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343042	118343042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	107	305	1	ENST00000534358.1:c.1168G>A	p.Glu390Lys	p.E390K	ENST00000534358	NM_005933.3	390	Gaa/Aaa	3/36	0.522930797516527	1	FACETS	0.866	0.785	0.95	0.866	0.785	0.95	CLONAL	1	TRUE	0	0.522930797516527	1		306	349	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243968	46243968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	316	591	1	ENST00000334344.6:c.2062C>T	p.Pro688Ser	p.P688S	ENST00000334344	NM_152641.2	688	Cct/Tct	15/21	NA	2	FACETS	0.799	0.759	0.84			1	INDETERMINATE	2	TRUE	NA	0.522930797516527	2		592	756	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864244	57864244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1314	286	744	0	ENST00000228682.2:c.1721G>A	p.Gly574Glu	p.G574E	ENST00000228682	NM_005269.2	574	gGa/gAa	12/12	0.414856689656652	3	FACETS	0.862	0.808	0.918	0.431	0.404	0.459	CLONAL	1	TRUE	1	0.522930797516527	3		744	1600	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620099	21620099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1653	170	492	2	ENST00000382592.4:c.67C>T	p.Arg23Cys	p.R23C	ENST00000382592	NM_014572.2	23	Cgt/Tgt	2/8	0.522930797516527	4	FACETS	0.543	0.497	0.592			1	SUBCLONAL	1	TRUE	NA	0.522930797516527	4		494	1823	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543258	65543258	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	583	531	0	ENST00000358664.4:c.419C>T	p.Ser140Phe	p.S140F	ENST00000358664	NM_002382.4	140	tCc/tTc	5/5	0.522930797516527	5	FACETS	0.896	0.861	0.93	0.896	0.861	0.93	CLONAL	3	TRUE	2	0.522930797516527	5		531	1481	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610033	81610033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	286	396	0	ENST00000298171.2:c.1631G>A	p.Gly544Glu	p.G544E	ENST00000298171	NM_000369.2	544	gGg/gAg	10/10	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.522930797516527	2		396	890	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778341	3778341	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774272248	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	200	278	0	ENST00000262367.5:c.6707G>A	p.Gly2236Glu	p.G2236E	ENST00000262367	NM_004380.2	2236	gGa/gAa	31/31	0.431678837596695	2	FACETS	0.871	0.817	0.925	0.871	0.817	0.925	CLONAL	2	TRUE	0	0.522930797516527	2		278	439	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934252	81934252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	251	582	0	ENST00000359376.3:c.1229G>A	p.Ser410Asn	p.S410N	ENST00000359376	NM_002661.3	410	aGc/aAc	14/33	0.474989936354439	3	FACETS	0.878	0.819	0.938	0.293	0.273	0.313	CLONAL	1	TRUE	0	0.522930797516527	3		582	1380	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357483	89357483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1681	526	728	0	ENST00000301030.4:c.335C>T	p.Ser112Phe	p.S112F	ENST00000301030	NM_001256183.1	112	tCc/tTc	5/13	0.522930797516527	4	FACETS	1	0.996	1			1	CLONAL	1	TRUE	NA	0.522930797516527	4		728	2207	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512405	38512405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	180	401	0	ENST00000254066.5:c.1316C>T	p.Pro439Leu	p.P439L	ENST00000254066	NM_000964.3	439	cCc/cTc	9/9	0.431678837596695	2	FACETS	0.939	0.868	1	0.47	0.434	0.506	CLONAL	1	TRUE	0	0.522930797516527	2		401	733	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58711312	58711312	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	185	688	0	ENST00000305921.3:c.800C>T	p.Pro267Leu	p.P267L	ENST00000305921	NM_003620.3	267	cCt/cTt	3/6	0.431678837596695	2	FACETS	0.722	0.666	0.78	0.361	0.333	0.39	SUBCLONAL	1	TRUE	0	0.522930797516527	2		688	980	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250863	10250863	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	162	448	0	ENST00000340748.4:c.3617C>T	p.Ser1206Phe	p.S1206F	ENST00000340748		1206	tCc/tTc	32/40	0.414856689656652	3	FACETS	0.804	0.737	0.874	0.402	0.368	0.437	CLONAL	1	TRUE	1	0.522930797516527	3		448	972	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10259585	10259585	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1347	230	618	2	ENST00000340748.4:c.2647C>T	p.Gln883Ter	p.Q883*	ENST00000340748		883	Cag/Tag	26/40	0.414856689656652	3	FACETS	0.704	0.654	0.756	0.352	0.327	0.378	SUBCLONAL	1	TRUE	1	0.522930797516527	3		620	1577	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296334	15296334	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866356264	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	173	494	0	ENST00000263388.2:c.2108C>T	p.Pro703Leu	p.P703L	ENST00000263388	NM_000435.2	703	cCc/cTc	13/33	0.414856689656652	3	FACETS	0.788	0.725	0.855	0.394	0.362	0.428	SUBCLONAL	1	TRUE	1	0.522930797516527	3		494	1059	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46277849	46277849	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	156	612	0	ENST00000371998.3:c.3647C>T	p.Ser1216Phe	p.S1216F	ENST00000371998		1216	tCc/tTc	19/23	0.44266012784814	3	FACETS	0.692	0.632	0.754	0.231	0.21	0.252	SUBCLONAL	1	TRUE	0	0.522930797516527	3		612	1088	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713609	52713633	+	frameshift_variant	Frame_Shift_Del	DEL	TTGGAAAGTCTCCTCCTTTTCCTGC	TTGGAAAGTCTCCTCCTTTTCCTGC	-	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	333	529	0	ENST00000394830.3:c.95_119del	p.Ser32IlefsTer5	p.S32Ifs*5	ENST00000394830	NM_018313.4	32	aGCAGGAAAAGGAGGAGACTTTCCAAt/at	2/30	0.44266012784814	3	FACETS	1	0.988	1	0.743	0.707	0.778	CLONAL	2	TRUE	0	0.522930797516527	3		529	721	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573966	7573976	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGCATCCTT	TGGGCATCCTT	-	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	412	567	0	ENST00000269305.4:c.1051_1061del	p.Lys351GlyfsTer27	p.K351Gfs*27	ENST00000269305	NM_001126112.2	351	AAGGATGCCCAg/g	10/11	0.431678837596695	2	FACETS	0.797	0.762	0.833	0.797	0.762	0.833	SUBCLONAL	2	TRUE	0	0.522930797516527	2		567	988	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67197027	67197035	+	inframe_deletion	In_Frame_Del	DEL	CAACTTGGG	CAACTTGGG	-	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	214	563	0	ENST00000312629.5:c.273_281del	p.Asn91_Gly93del	p.N91_G93del	ENST00000312629	NM_003952.2	90	acCAACTTGGGc/acc	4/15	1	2	FACETS	0.739	0.686	0.794	0.739	0.686	0.794	SUBCLONAL	1	TRUE	1	0.522930797516527	2		563	1108	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303738	65303739	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	CA	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	448	508	0	ENST00000342505.4:c.3016_3017delinsTG	p.Ala1006Ter	p.A1006*	ENST00000342505	NM_002227.2	1006	GCa/TGa	22/25	0.373238818221543	5	FACETS	1	0.994	1	0.821	0.784	0.858	CLONAL	2	TRUE	2	0.522930797516527	5		508	1242	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843533	156843534	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	204	564	0	ENST00000524377.1:c.959_960delinsTT	p.Ser320Phe	p.S320F	ENST00000524377	NM_002529.3	320	tCC/tTT	8/17	1	2	FACETS	0.751	0.696	0.808	0.751	0.696	0.808	SUBCLONAL	1	TRUE	1	0.522930797516527	2		564	1039	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434924	49434925	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	220	341	1	ENST00000301067.7:c.6628_6629delinsTT	p.Pro2210Leu	p.P2210L	ENST00000301067	NM_003482.3	2210	CCg/TTg	31/54	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.522930797516527	2		342	588	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434925	49434926	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	227	339	0	ENST00000301067.7:c.6627_6628delinsTT	p.Pro2210Ser	p.P2210S	ENST00000301067	NM_003482.3	2209	ccCCcg/ccTTcg	31/54	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.522930797516527	2		339	582	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510600	38510601	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	221	573	0	ENST00000254066.5:c.854_855delinsAT	p.Thr285Asn	p.T285N	ENST00000254066	NM_000964.3	285	aCC/aAT	7/9	0.431678837596695	2	FACETS	0.751	0.698	0.806	0.376	0.349	0.403	SUBCLONAL	1	TRUE	0	0.522930797516527	2		573	1125	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222479	2222480	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	171	199	0	ENST00000398665.3:c.3311_3312delinsTT	p.Ser1104Phe	p.S1104F	ENST00000398665	NM_032482.2	1104	tCC/tTT	24/28	0.435677127466517	2	FACETS	0.874	0.816	0.933	0.874	0.816	0.933	CLONAL	2	TRUE	0	0.522930797516527	2		199	374	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857312	9857313	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0010145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	329	451	0	ENST00000330684.3:c.4088_4089delinsTT	p.Ser1363Phe	p.S1363F	ENST00000330684	NM_001134407.1	1363	tCC/tTT	13/13	0.431678837596695	2	FACETS	1	0.995	1	0.724	0.687	0.762	CLONAL	1	TRUE	0	0.522930797516527	2		451	869	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0010160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	97	439	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.441105301001964	1	FACETS	0.832	0.749	0.918	0.832	0.749	0.918	CLONAL	1	TRUE	0	0.50308257995482	1		439	347	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175481	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0010160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	239	345	0	ENST00000257430.4:c.4192_4193del	p.Arg1399PhefsTer9	p.R1399Ffs*9	ENST00000257430	NM_000038.5	1397	GAg/g	16/16	0.50308257995482	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.50308257995482	2		345	455	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268762	41268762	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1245266458	NA	P-0010160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	50	503	0	ENST00000349496.5:c.1000G>A	p.Glu334Lys	p.E334K	ENST00000349496	NM_001904.3	334	Gaa/Aaa	7/15	0.220924530874844	2	FACETS	0.351	0.298	0.41	0.176	0.149	0.205	INDETERMINATE	1	TRUE	0	0.50308257995482	2		503	566	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683703	162683703	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238707850	NA	P-0010160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	112	385	0	ENST00000366898.1:c.266G>A	p.Arg89Lys	p.R89K	ENST00000366898	NM_004562.2	89	aGa/aAa	3/12	0.29698207417385	1	FACETS	0.793	0.719	0.871	0.793	0.719	0.871	INDETERMINATE	1	TRUE	0	0.50308257995482	1		385	420	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723118	52723118	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0010160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	45	230	0	ENST00000322088.6:c.1302+1G>A		p.X434_splice	ENST00000322088	NM_014225.5	434			1	2	FACETS	0.724	0.614	0.844	0.724	0.614	0.844	SUBCLONAL	1	TRUE	1	0.50308257995482	2		230	247	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118683	115118683	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0010178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	148	568	1	ENST00000257566.3:c.657+1G>T		p.X219_splice	ENST00000257566	NM_016569.3	219			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		569	891	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158441	108158441	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010180-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	28	350	0	ENST00000278616.4:c.4109+1del		p.G1370fs	ENST00000278616	NM_000051.3	1370	Ggg/gg	27/63	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	FALSE	1	0.219450187086525	2		350	177	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010198-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	19	247	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		247	844	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0010225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	241	255	0				ENST00000310581	NM_198253.2	-/1132			0.716130100664043	3	FACETS	0.931	0.88	0.982	0.931	0.88	0.982	CLONAL	2	TRUE	1	0.716130100664043	3		255	491	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022914	27022942	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCCGCCGCCAGCAGCCTGGGCAACCCG	CCGCCGCCGCCAGCAGCCTGGGCAACCCG	-	novel	NA	P-0010225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	18	27	0	ENST00000324856.7:c.31_59del	p.Ser11AlafsTer90	p.S11Afs*90	ENST00000324856	NM_006015.4	7	cCCGCCGCCGCCAGCAGCCTGGGCAACCCG/c	1/20	1	2	FACETS	0.653	0.503	0.82	0.653	0.503	0.82	SUBCLONAL	1	TRUE	1	0.716130100664043	2		27	77	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005200	150005200	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	212	420	1	ENST00000253339.5:c.1025C>A	p.Ser342Ter	p.S342*	ENST00000253339		342	tCa/tAa	3/7	1	2	FACETS	0.881	0.822	0.941	0.881	0.822	0.941	CLONAL	1	TRUE	1	0.716130100664043	2		421	672	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145743003	145743003	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	92	96	0	ENST00000428558.2:c.101C>T	p.Ala34Val	p.A34V	ENST00000428558	NM_004260.3	34	gCg/gTg	2/22	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.716130100664043	NA		96	391	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117624	70117624	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	208	326	0	ENST00000245479.2:c.92C>G	p.Ala31Gly	p.A31G	ENST00000245479	NM_000346.3	31	gCg/gGg	1/3	0.716130100664043	3	FACETS	0.933	0.867	1	0.466	0.433	0.5	CLONAL	1	TRUE	1	0.716130100664043	3		326	846	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579463	7579463	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	358	338	0	ENST00000269305.4:c.224del	p.Pro75LeufsTer48	p.P75Lfs*48	ENST00000269305	NM_001126112.2	75	cCt/ct	4/11	0.896463050608969	1	FACETS	0.954	0.926	0.981	0.954	0.926	0.981	CLONAL	1	TRUE	0	0.910492914058158	1		338	449	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527891	103527891	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	416	317	0	ENST00000355739.4:c.3199T>G	p.Ser1067Ala	p.S1067A	ENST00000355739	NM_000123.3	1067	Tca/Gca	15/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.910492914058158	2		317	885	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416111	29416111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	306	273	0	ENST00000389048.3:c.4842C>A	p.Ser1614Arg	p.S1614R	ENST00000389048	NM_004304.4	1614	agC/agA	29/29	1	2	FACETS	0.94	0.892	0.989	0.94	0.892	0.989	CLONAL	1	TRUE	1	0.910492914058158	2		273	715	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0010259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	543	709	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	NA	2	FACETS	1	0.967	1			1	INDETERMINATE	8	TRUE	NA	0.147774073391328	2		709	919	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631839	90631839	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519906	NA	P-0010259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	230	524	2	ENST00000330062.3:c.514A>G	p.Arg172Gly	p.R172G	ENST00000330062	NM_002168.2	172	Agg/Ggg	4/11	1	2	FACETS	0.881	0.823	0.942	1	0.996	1	CLONAL	4	TRUE	1	0.147774073391328	2		526	883	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907651	76907651	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	659	590	0	ENST00000373344.5:c.4510C>T	p.Arg1504Ter	p.R1504*	ENST00000373344	NM_000489.3	1504	Cga/Tga	15/35	1	1	FACETS	1	0.985	1			1	CLONAL	7	TRUE	0	0.147774073391328	1		590	1152	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010261-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	713	247	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.507432938506049	9	FACETS	1	0.99	1			1	CLONAL	5	TRUE	NA	0.507432938506049	9		247	1480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882025	NA	P-0010261-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	561	859	0	ENST00000269305.4:c.646G>T	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ttg	6/11	0.507432938506049	3	FACETS	0.962	0.93	0.993	1	0.997	1	CLONAL	3	TRUE	1	0.507432938506049	3		859	961	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162591	47162591	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010261-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	226	232	0	ENST00000409792.3:c.3535G>C	p.Asp1179His	p.D1179H	ENST00000409792	NM_014159.6	1179	Gac/Cac	3/21	0.503864984203656	2	FACETS	0.981	0.926	1	0.981	0.926	1	CLONAL	2	TRUE	0	0.507432938506049	2		232	454	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052932	180052932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010261-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	264	296	0	ENST00000261937.6:c.1358C>T	p.Pro453Leu	p.P453L	ENST00000261937	NM_182925.4	453	cCt/cTt	10/30	0.507432938506049	3	FACETS	0.999	0.943	1	0.999	0.943	1	CLONAL	2	TRUE	1	0.507432938506049	3		296	653	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533907	533907	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1448375861	NA	P-0010261-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	97	273	0	ENST00000451590.1:c.149C>T	p.Thr50Met	p.T50M	ENST00000451590	NM_001130442.1	50	aCg/aTg	3/5	0.507432938506049	3	FACETS	0.683	0.609	0.761	0.341	0.304	0.381	SUBCLONAL	1	TRUE	1	0.507432938506049	3		273	702	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857425	9857425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1268143219	NA	P-0010261-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	137	343	0	ENST00000330684.3:c.3976G>A	p.Gly1326Ser	p.G1326S	ENST00000330684	NM_001134407.1	1326	Ggc/Agc	13/13	0.507432938506049	3	FACETS	0.817	0.743	0.894	0.408	0.371	0.447	CLONAL	1	TRUE	1	0.507432938506049	3		343	829	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956194	175956194	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010261-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	31	295	0	ENST00000367669.3:c.2018A>T	p.Lys673Met	p.K673M	ENST00000367669	NM_022457.5	673	aAg/aTg	18/20	0.338444600326684	5	FACETS	0.4	0.323	0.488	0.133	0.107	0.163	SUBCLONAL	1	TRUE	2	0.507432938506049	5		295	538	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89809324	89809324	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010261-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	127	275	0	ENST00000389301.3:c.3649T>C	p.Ser1217Pro	p.S1217P	ENST00000389301	NM_000135.2	1217	Tcc/Ccc	37/43	0.507432938506049	3	FACETS	0.937	0.85	1			1	CLONAL	1	TRUE	NA	0.507432938506049	3		275	670	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0010267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	242	852	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.300000108083426	6	FACETS	0.971	0.905	1	0.485	0.452	0.52	CLONAL	2	TRUE	2	0.31	6		852	1303	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0010267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	253	456	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.155943560497122	3	FACETS	1	0.949	1			1	INDETERMINATE	2	TRUE	NA	0.31	3		456	929	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459037	120459037	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1484695811	NA	P-0010267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	121	493	0	ENST00000256646.2:c.6308C>G	p.Ser2103Cys	p.S2103C	ENST00000256646	NM_024408.3	2103	tCt/tGt	34/34	0.300000108083426	3	FACETS	0.966	0.872	1	0.483	0.436	0.533	CLONAL	1	TRUE	1	0.31	3		493	933	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919571	96919571	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1345	306	810	0	ENST00000258439.3:c.692A>T	p.Gln231Leu	p.Q231L	ENST00000258439	NM_001193304.2	231	cAg/cTg	4/4	0.300000108083426	3	FACETS	1	0.992	1	0.691	0.649	0.734	CLONAL	1	TRUE	1	0.31	3		810	1651	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917510	178917510	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	86	462	0	ENST00000263967.3:c.385G>C	p.Asp129His	p.D129H	ENST00000263967	NM_006218.2	129	Gat/Cat	3/21	0.300000108083426	4	FACETS	0.835	0.738	0.94	0.418	0.369	0.47	CLONAL	1	TRUE	2	0.31	4		462	870	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158696	26158696	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	12	48	1	ENST00000289316.2:c.299G>T	p.Arg100Leu	p.R100L	ENST00000289316	NM_138720.2	100	cGc/cTc	1/2	0.300000108083426	4	FACETS	1	0.814	1	0.604	0.43	0.81	CLONAL	1	TRUE	2	0.31	4		49	84	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46275898	46275898	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	645	991	2	ENST00000371998.3:c.3334G>T	p.Gly1112Ter	p.G1112*	ENST00000371998		1112	Gga/Tga	18/23	0.300000108083426	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	TRUE	0	0.31	3		993	1587	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0010269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	21	606	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	0.14	0.107	0.179	0.14	0.107	0.179	SUBCLONAL	1	TRUE	1	0.39	2		606	767	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577113	7577113	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555525279	NA	P-0010300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	55	479	0	ENST00000269305.4:c.825T>G	p.Cys275Trp	p.C275W	ENST00000269305	NM_001126112.2	275	tgT/tgG	8/11	0.45680270891801	1	FACETS	0.23	0.196	0.268	0.23	0.196	0.268	SUBCLONAL	1	TRUE	0	0.45680270891801	1		479	807	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064794618	NA	P-0010300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	139	380	0	ENST00000269305.4:c.159G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgG/tgA	4/11	0.45680270891801	1	FACETS	0.783	0.715	0.853	0.783	0.715	0.853	SUBCLONAL	1	TRUE	0	0.45680270891801	1		380	600	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880219	37880220	+	missense_variant	Missense_Mutation	DNP	TT	TT	CC	rs121913469	NA	P-0010300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	799	661	0	ENST00000269571.5:c.2263_2264delinsCC	p.Leu755Pro	p.L755P	ENST00000269571		755	TTg/CCg	19/27	0.45680270891801	6	FACETS	0.902	0.873	0.931			1	CLONAL	4	TRUE	NA	0.45680270891801	6		661	1856	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864332	151864334	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	novel	NA	P-0010300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	135	692	0	ENST00000262189.6:c.9647_9649del	p.Gln3216del	p.Q3216del	ENST00000262189	NM_170606.2	3216	cAACgt/cgt	42/59	0.434069610462972	3	FACETS	0.561	0.508	0.617	0.281	0.254	0.309	SUBCLONAL	1	TRUE	1	0.45680270891801	3		692	1294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691022	NA	P-0010306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	390	533	0	ENST00000269305.4:c.1024del	p.Arg342GlufsTer3	p.R342Efs*3	ENST00000269305	NM_001126112.2	342	Cga/ga	10/11	0.362043051300236	5	FACETS	0.937	0.904	0.969			1	CLONAL	5	TRUE	NA	0.504502465209043	5		533	580	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150549855	150549855	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	319	328	0	ENST00000369026.2:c.1049G>C	p.Arg350Thr	p.R350T	ENST00000369026	NM_021960.4	350	aGa/aCa	3/3	0.504502465209043	8	FACETS	1	0.977	1			1	CLONAL	4	TRUE	NA	0.504502465209043	8		328	758	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131348	202131348	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	78	393	0	ENST00000358485.4:c.316A>G	p.Arg106Gly	p.R106G	ENST00000358485	NM_001080125.1	106	Aga/Gga	2/9	0.504502465209043	3	FACETS	0.831	0.733	0.936	0.415	0.366	0.468	CLONAL	1	TRUE	1	0.504502465209043	3		393	466	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923216	26923216	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	90	579	0	ENST00000381527.3:c.212G>A	p.Arg71Gln	p.R71Q	ENST00000381527	NM_001260.1	71	cGa/cAa	3/13	NA	2	FACETS	0.879	0.785	0.978			1	INDETERMINATE	1	TRUE	NA	0.504502465209043	2		579	406	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223365	2223365	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	60	304	0	ENST00000326181.6:c.977T>C	p.Ile326Thr	p.I326T	ENST00000326181	NM_032271.2	326	aTc/aCc	10/21	0.480868657355761	4	FACETS	0.838	0.724	0.961			1	CLONAL	1	TRUE	NA	0.504502465209043	4		304	427	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447607	187447625	+	frameshift_variant	Frame_Shift_Del	DEL	AATAAGAGGCTGGCGGTGT	AATAAGAGGCTGGCGGTGT	-	novel	NA	P-0010306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	92	276	0	ENST00000232014.4:c.568_586del	p.Thr190ProfsTer128	p.T190Pfs*128	ENST00000232014	NM_001130845.1	190	ACACCGCCAGCCTCTTATTcc/cc	5/10	0.504502465209043	2	FACETS	0.95	0.865	1	0.95	0.865	1	CLONAL	2	TRUE	0	0.504502465209043	2		276	192	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259588	89259589	+	missense_variant	Missense_Mutation	DNP	CA	CA	GC	novel	NA	P-0010306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	76	306	0	ENST00000336596.2:c.732_733delinsGC	p.Cys244_Ser245delinsTrpArg	p.C244_S245delinsWR	ENST00000336596	NM_005233.5	244	tgCAgt/tgGCgt	3/17	0.234935378314071	4	FACETS	0.839	0.745	0.938			1	INDETERMINATE	2	TRUE	NA	0.504502465209043	4		306	270	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143293	30143293	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs748978993	NA	P-0010316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	43	340	0	ENST00000389048.3:c.233C>G	p.Ser78Trp	p.S78W	ENST00000389048	NM_004304.4	78	tCg/tGg	1/29	0.3	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		340	644	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939718	76939718	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010316-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	35	364	1	ENST00000373344.5:c.1030T>C	p.Ser344Pro	p.S344P	ENST00000373344	NM_000489.3	344	Tcc/Ccc	9/35	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		365	596	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431665	431665	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs754467075	NA	P-0010320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	180	374	0	ENST00000399788.2:c.2344C>T	p.Arg782Ter	p.R782*	ENST00000399788	NM_001042603.1	782	Cga/Tga	17/28	1	2	FACETS	0.961	0.887	1	0.961	0.887	1	CLONAL	1	FALSE	1	0.465488532955448	2		374	805	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353860	40353860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238042644	NA	P-0010320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1615	500	739	1	ENST00000293328.3:c.2260G>A	p.Asp754Asn	p.D754N	ENST00000293328	NM_012448.3	754	Gat/Aat	19/19	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.465488532955448	2		740	2115	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732963	30732963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	190	235	0	ENST00000295754.5:c.1576G>A	p.Glu526Lys	p.E526K	ENST00000295754	NM_003242.5	526	Gag/Aag	7/7	0.465488532955448	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	0	0.465488532955448	1		235	545	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210131	55210131	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0010320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	186	361	0	ENST00000275493.2:c.240+1G>T		p.X80_splice	ENST00000275493	NM_005228.3	80			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.465488532955448	2		361	717	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059011	42059011	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	403	815	0	ENST00000219905.7:c.8731G>C	p.Glu2911Gln	p.E2911Q	ENST00000219905	NM_001164273.1	2911	Gag/Cag	24/24	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.465488532955448	2		815	1522	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836332	89836332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1352100383	NA	P-0010320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	205	307	0	ENST00000389301.3:c.2417C>T	p.Pro806Leu	p.P806L	ENST00000389301	NM_000135.2	806	cCt/cTt	26/43	0.350293197528419	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	0	0.465488532955448	1		307	657	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55209986	55209993	+	frameshift_variant	Frame_Shift_Del	DEL	AGGCACGA	AGGCACGA	C	novel	NA	P-0010320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	198	409	0	ENST00000275493.2:c.96_103delinsC	p.Gln32HisfsTer46	p.Q32Hfs*46	ENST00000275493	NM_005228.3	32	caAGGCACGAgt/caCgt	2/28	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.465488532955448	2		409	794	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0010326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	321	272	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.543973498236926	2	FACETS	0.865	0.827	0.902	0.865	0.827	0.902	CLONAL	2	TRUE	0	0.66046925922966	2		272	562	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	201	254	0	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	0.528968881422958	5	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.66046925922966	5		254	916	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523505	106523505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010326-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	23	151	0	ENST00000359195.3:c.2657C>T	p.Thr886Met	p.T886M	ENST00000359195	NM_002649.2	886	aCg/aTg	8/11	0.576941279485333	3	FACETS	0.208	0.162	0.262	0.104	0.081	0.131	SUBCLONAL	1	TRUE	1	0.66046925922966	3		151	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0010349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	164	566	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.121149550758726	5	FACETS	0.975	0.903	1	0.731	0.677	0.787	INDETERMINATE	3	TRUE	1	0.349433459121487	5		568	489	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0010349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	98	322	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.259983177285522	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	1	0.349433459121487	3		322	301	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397187	397187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	47	354	1	ENST00000380956.4:c.572C>T	p.Pro191Leu	p.P191L	ENST00000380956	NM_001195286.1	191	cCg/cTg	5/9	0.272720053914827	5	FACETS	0.642	0.54	0.754	0.214	0.18	0.252	SUBCLONAL	1	TRUE	2	0.349433459121487	5		355	639	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684323	29684323	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs567988442	NA	P-0010349-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	149	618	0	ENST00000356175.3:c.7843C>T	p.Gln2615Ter	p.Q2615*	ENST00000356175	NM_000267.3	2615	Caa/Taa	53/57	0.121149550758726	5	FACETS	0.967	0.891	1	0.725	0.668	0.784	INDETERMINATE	3	TRUE	1	0.349433459121487	5		618	448	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	56	247	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.18	2		247	610	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015637	112015637	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1314	71	668	0	ENST00000368678.4:c.1205A>G	p.Lys402Arg	p.K402R	ENST00000368678		402	aAg/aGg	11/13	1	2	FACETS	0.57	0.495	0.651	0.57	0.495	0.651	SUBCLONAL	1	TRUE	1	0.18	2		668	1385	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220706	1220706	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs878853992	NA	P-0010362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	41	257	0	ENST00000326873.7:c.724G>T	p.Gly242Trp	p.G242W	ENST00000326873	NM_000455.4	242	Ggg/Tgg	5/10	1	2	FACETS	0.836	0.696	0.992	0.836	0.696	0.992	CLONAL	1	TRUE	1	0.18	2		257	545	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0010372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	128	715	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.869	0.787	0.956	0.869	0.787	0.956	CLONAL	1	TRUE	1	0.335402206167231	2		715	878	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0010372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	133	283	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.312138679316178	1	FACETS	0.99	0.901	1	0.99	0.901	1	CLONAL	1	TRUE	0	0.335402206167231	1		283	667	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0010372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	38	264	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.516	0.427	0.616	0.516	0.427	0.616	SUBCLONAL	1	TRUE	1	0.335402206167231	2		264	439	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038893	12038893	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	179	415	0	ENST00000396373.4:c.1186A>G	p.Arg396Gly	p.R396G	ENST00000396373	NM_001987.4	396	Aga/Gga	7/8	1	2	FACETS	0.943	0.868	1	0.943	0.868	1	CLONAL	1	TRUE	1	0.335402206167231	2		415	1132	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468354	89468354	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0010372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	63	262	0	ENST00000336596.2:c.1889-1G>A		p.X630_splice	ENST00000336596	NM_005233.5	630			0.324354453143603	1	FACETS	0.75	0.651	0.857	0.75	0.651	0.857	SUBCLONAL	1	TRUE	0	0.335402206167231	1		262	417	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0010373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	148	715	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.212418410231164	2	FACETS	0.885	0.81	0.963	0.885	0.81	0.963	CLONAL	2	TRUE	0	0.240031181464625	2		715	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0010373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	157	566	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.214701626634061	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.240031181464625	1		568	1098	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0010373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	91	89	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.240031181464625	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.240031181464625	2		89	313	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873712	35873712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	62	411	0	ENST00000303115.3:c.668G>A	p.Ser223Asn	p.S223N	ENST00000303115	NM_002185.3	223	aGt/aAt	5/8	1	2	FACETS	0.525	0.452	0.605	0.525	0.452	0.605	SUBCLONAL	1	TRUE	1	0.240031181464625	2		411	984	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257633	19257635	+	inframe_deletion	In_Frame_Del	DEL	GGT	GGT	-	novel	NA	P-0010373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1710	126	711	0	ENST00000162023.5:c.591_593del	p.Pro199del	p.P199del	ENST00000162023		197	ccACCc/ccc	10/13	1	2	FACETS	0.572	0.515	0.632	0.572	0.515	0.632	SUBCLONAL	1	TRUE	1	0.240031181464625	2		711	1836	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0010400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	343	593	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.315727805091121	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	1	0.315727805091121	4		593	845	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386385	31386385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs544333946	NA	P-0010400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1152	373	512	0	ENST00000328111.2:c.1610G>A	p.Arg537Gln	p.R537Q	ENST00000328111	NM_006892.3	537	cGg/cAg	15/23	0.252044191055083	5	FACETS	1	0.988	1	0.761	0.721	0.802	CLONAL	2	TRUE	2	0.315727805091121	5		512	1525	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0010404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	153	648	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	0.267081410584063	4	FACETS	1	0.986	1	0.472	0.431	0.515	CLONAL	1	TRUE	1	0.267081410584063	4		648	1025	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679789	88679789	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	52	523	0	ENST00000360948.2:c.674A>G	p.Asp225Gly	p.D225G	ENST00000360948	NM_001012338.2	225	gAc/gGc	7/19	1	2	FACETS	0.457	0.387	0.533	0.457	0.387	0.533	SUBCLONAL	1	TRUE	1	0.267081410584063	2		523	853	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	55	126	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.782	0.673	0.901	0.782	0.673	0.901	CLONAL	1	TRUE	1	0.422211685821601	2		126	333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0010421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	158	818	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.412927344836436	2	FACETS	0.882	0.808	0.958	0.441	0.404	0.479	CLONAL	1	TRUE	0	0.422211685821601	2		818	849	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356162	70356162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	173	779	1	ENST00000374080.3:c.5057C>T	p.Ser1686Leu	p.S1686L	ENST00000374080		1686	tCg/tTg	37/45	0.422211685821601	1	FACETS	0.552	0.507	0.599	0.552	0.507	0.599	SUBCLONAL	1	TRUE	0	0.422211685821601	1		780	1172	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650565	18650565	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	121	426	0	ENST00000266497.5:c.2776C>G	p.Leu926Val	p.L926V	ENST00000266497		926	Ctt/Gtt	20/31	1	2	FACETS	0.901	0.816	0.991	0.901	0.816	0.991	CLONAL	1	TRUE	1	0.422211685821601	2		426	636	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294370	1294370	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	47	140	1	ENST00000310581.5:c.631G>A	p.Gly211Arg	p.G211R	ENST00000310581	NM_198253.2	211	Ggg/Agg	2/16	1	2	FACETS	0.837	0.711	0.973	0.837	0.711	0.973	CLONAL	1	TRUE	1	0.422211685821601	2		141	266	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843649	156843649	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	159	456	0	ENST00000524377.1:c.1075T>C	p.Tyr359His	p.Y359H	ENST00000524377	NM_002529.3	359	Tac/Cac	8/17	0.108093553708626	5	FACETS	1	0.975	1	0.292	0.267	0.318	INDETERMINATE	1	TRUE	1	0.422211685821601	5		456	1054	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259646	89259646	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	37	149	0	ENST00000336596.2:c.790G>A	p.Glu264Lys	p.E264K	ENST00000336596	NM_005233.5	264	Gaa/Aaa	3/17	0.422211685821601	1	FACETS	0.724	0.603	0.856	0.724	0.603	0.856	SUBCLONAL	1	TRUE	0	0.422211685821601	1		149	191	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159088	143159088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	98	528	0	ENST00000262992.4:c.765G>A	p.Met255Ile	p.M255I	ENST00000262992	NM_001101669.1	255	atG/atA	10/24	1	2	FACETS	0.827	0.74	0.92	0.827	0.74	0.92	CLONAL	1	TRUE	1	0.422211685821601	2		528	561	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630800	90630800	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	126	228	0	ENST00000330062.3:c.686C>T	p.Ser229Leu	p.S229L	ENST00000330062	NM_002168.2	229	tCa/tTa	6/11	0.108093553708626	5	FACETS	0.84	0.768	0.914	0.63	0.576	0.685	INDETERMINATE	3	TRUE	1	0.422211685821601	5		228	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579337	7579337	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	259	360	0	ENST00000269305.4:c.350G>T	p.Gly117Val	p.G117V	ENST00000269305	NM_001126112.2	117	gGg/gTg	4/11	0.412927344836436	2	FACETS	0.884	0.833	0.936	0.884	0.833	0.936	CLONAL	2	TRUE	0	0.422211685821601	2		360	694	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974804	21974808	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCT	CTGCT	-	novel	NA	P-0010421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	17	83	0	ENST00000304494.5:c.19_23del	p.Ser7HisfsTer6	p.S7Hfs*6	ENST00000304494	NM_000077.4	7	AGCAGc/c	1/3	NA	2	FACETS	0.677	0.511	0.869			1	INDETERMINATE	1	TRUE	NA	0.422211685821601	2		83	119	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0010443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	233	284	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.340831952678675	3	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	1	0.340831952678675	3		284	786	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0010443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	293	354	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.31452592583886	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.340831952678675	4		354	1018	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0010443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	141	365	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.31452592583886	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.340831952678675	4		367	450	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470905	25470905	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs772041639	NA	P-0010443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	106	336	2	ENST00000264709.3:c.855+1G>A		p.X285_splice	ENST00000264709	NM_175629.2	285			0.340831952678675	3	FACETS	0.955	0.857	1	0.478	0.428	0.53	CLONAL	1	TRUE	1	0.340831952678675	3		338	762	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43745317	43745317	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1460	206	765	1	ENST00000523873.1:c.230G>A	p.Cys77Tyr	p.C77Y	ENST00000523873		77	tGt/tAt	3/8	0.25599731267033	5	FACETS	1	0.97	1	0.366	0.338	0.395	CLONAL	1	TRUE	2	0.340831952678675	5		766	1666	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39537591	39537591	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	126	378	0	ENST00000262039.4:c.125C>T	p.Pro42Leu	p.P42L	ENST00000262039	NM_002647.2	42	cCa/cTa	2/25	0.31452592583886	4	FACETS	0.802	0.724	0.885	0.401	0.362	0.443	CLONAL	1	TRUE	2	0.340831952678675	4		378	1236	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125016	46125017	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0010443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	383	461	0	ENST00000334344.6:c.203_204del	p.Gln68LeufsTer6	p.Q68Lfs*6	ENST00000334344	NM_152641.2	68	cAG/c	3/21	0.327991507655894	4	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.340831952678675	4		461	1245	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938379	76938397	+	frameshift_variant	Frame_Shift_Del	DEL	AAATCTGAGCCAGATGTAG	AAATCTGAGCCAGATGTAG	-	novel	NA	P-0010443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1330	498	610	0	ENST00000373344.5:c.2351_2369del	p.Ser784LeufsTer13	p.S784Lfs*13	ENST00000373344	NM_000489.3	784	tCTACATCTGGCTCAGATTTt/tt	9/35	0.25599731267033	5	FACETS	1	0.993	1	0.805	0.769	0.842	CLONAL	2	TRUE	2	0.340831952678675	5		610	1828	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0010449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	51	229	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		229	449	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159749	20159749	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	132	533	0	ENST00000379607.5:c.10A>T	p.Asn4Tyr	p.N4Y	ENST00000379607	NM_001412.3	4	Aat/Tat	1/7	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		533	900	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0010454-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	51	248	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		248	854	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0010454-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	392	393	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		393	1186	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010454-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1361	106	450	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		451	1467	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582118	189582118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs193921145	NA	P-0010454-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	75	315	0	ENST00000264731.3:c.677G>A	p.Arg226His	p.R226H	ENST00000264731	NM_003722.4	226	cGc/cAc	5/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		315	1195	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946206	55946206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010454-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1599	96	451	0	ENST00000263923.4:c.3973G>A	p.Glu1325Lys	p.E1325K	ENST00000263923	NM_002253.2	1325	Gaa/Aaa	30/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		451	1695	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197712	66197712	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010454-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	60	274	0	ENST00000273854.3:c.2987C>A	p.Ala996Asp	p.A996D	ENST00000273854	NM_004439.5	996	gCt/gAt	17/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		274	916	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250500	26250500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747335632	NA	P-0010454-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3394	330	1103	1	ENST00000446824.2:c.334G>A	p.Ala112Thr	p.A112T	ENST00000446824	NM_021018.2	112	Gct/Act	1/1	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1104	3724	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735454	40735454	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010454-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1405	135	403	0	ENST00000373198.4:c.3419C>A	p.Ala1140Asp	p.A1140D	ENST00000373198	NM_133170.3	1140	gCc/gAc	25/32	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		403	1540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	105	297	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.663	0.597	0.732	0.663	0.597	0.732	SUBCLONAL	1	TRUE	1	0.654695066576252	2		297	484	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638349	117638349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	131	301	0	ENST00000368508.3:c.6092G>A	p.Gly2031Glu	p.G2031E	ENST00000368508	NM_002944.2	2031	gGa/gAa	38/43	1	2	FACETS	0.8	0.731	0.873	0.8	0.731	0.873	SUBCLONAL	1	TRUE	1	0.654695066576252	2		301	500	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569702	95569702	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	109	194	0	ENST00000393063.1:c.4031C>T	p.Ser1344Leu	p.S1344L	ENST00000393063	NM_030621.3	1344	tCa/tTa	22/28	1	2	FACETS	0.762	0.689	0.838	0.762	0.689	0.838	SUBCLONAL	1	TRUE	1	0.654695066576252	2		194	437	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974121	2974121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760308478	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	154	354	2	ENST00000396946.4:c.1484C>T	p.Pro495Leu	p.P495L	ENST00000396946	NM_032415.4	495	cCg/cTg	10/25	1	2	FACETS	0.817	0.751	0.885	0.817	0.751	0.885	CLONAL	1	TRUE	1	0.654695066576252	2		356	576	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540188	187540188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	209	341	1	ENST00000441802.2:c.7552G>A	p.Asp2518Asn	p.D2518N	ENST00000441802	NM_005245.3	2518	Gat/Aat	10/27	1	2	FACETS	0.848	0.79	0.908	0.848	0.79	0.908	CLONAL	1	TRUE	1	0.654695066576252	2		342	753	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203756	94203756	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	105	241	0	ENST00000323929.3:c.898C>T	p.Pro300Ser	p.P300S	ENST00000323929	NM_005591.3	300	Cct/Tct	9/20	1	2	FACETS	0.786	0.71	0.866	0.786	0.71	0.866	SUBCLONAL	1	TRUE	1	0.654695066576252	2		241	408	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800900	18800900	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs372507637	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	117	285	0	ENST00000266497.5:c.4276C>T	p.Arg1426Ter	p.R1426*	ENST00000266497		1426	Cga/Tga	31/31	1	2	FACETS	0.77	0.699	0.845	0.77	0.699	0.845	SUBCLONAL	1	TRUE	1	0.654695066576252	2		285	464	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955096	17955096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201650430	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	98	191	0	ENST00000458235.1:c.131C>T	p.Ser44Phe	p.S44F	ENST00000458235	NM_000215.3	44	tCc/tTc	2/24	1	2	FACETS	0.76	0.683	0.84	0.76	0.683	0.84	SUBCLONAL	1	TRUE	1	0.654695066576252	2		191	394	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288993	212288993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867944951	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	69	235	0	ENST00000342788.4:c.2753G>A	p.Gly918Glu	p.G918E	ENST00000342788	NM_005235.2	918	gGa/gAa	23/28	1	2	FACETS	0.586	0.513	0.663	0.586	0.513	0.663	SUBCLONAL	1	TRUE	1	0.654695066576252	2		235	360	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259231	89259231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	154	237	0	ENST00000336596.2:c.375G>A	p.Met125Ile	p.M125I	ENST00000336596	NM_005233.5	125	atG/atA	3/17	1	2	FACETS	0.866	0.797	0.938	0.866	0.797	0.938	CLONAL	1	TRUE	1	0.654695066576252	2		237	543	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480480	89480480	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	168	265	0	ENST00000336596.2:c.2317G>A	p.Asp773Asn	p.D773N	ENST00000336596	NM_005233.5	773	Gat/Aat	13/17	1	2	FACETS	0.95	0.879	1	0.95	0.879	1	CLONAL	1	TRUE	1	0.654695066576252	2		265	540	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750414	41750414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	170	273	0	ENST00000226382.2:c.214G>A	p.Asp72Asn	p.D72N	ENST00000226382	NM_003924.3	72	Gac/Aac	1/3	1	2	FACETS	0.989	0.916	1	0.989	0.916	1	CLONAL	1	TRUE	1	0.654695066576252	2		273	525	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383753	84383753	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	237	393	0	ENST00000321945.7:c.1099G>A	p.Asp367Asn	p.D367N	ENST00000321945	NM_139076.2	367	Gac/Aac	9/9	1	2	FACETS	0.928	0.869	0.989	0.928	0.869	0.989	CLONAL	1	TRUE	1	0.654695066576252	2		393	780	SUCCESS
APC	324	MSKCC	GRCh37	5	112176488	112176488	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	143	181	0	ENST00000257430.4:c.5197C>G	p.Pro1733Ala	p.P1733A	ENST00000257430	NM_000038.5	1733	Ccc/Gcc	16/16	1	2	FACETS	0.906	0.832	0.983	0.906	0.832	0.983	CLONAL	1	TRUE	1	0.654695066576252	2		181	482	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515370	149515370	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	118	234	0	ENST00000261799.4:c.112C>T	p.Pro38Ser	p.P38S	ENST00000261799	NM_002609.3	38	Ccg/Tcg	3/23	1	2	FACETS	0.869	0.79	0.95	0.869	0.79	0.95	CLONAL	1	TRUE	1	0.654695066576252	2		234	415	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170157	32170157	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	135	242	0	ENST00000375023.3:c.3451G>T	p.Gly1151Cys	p.G1151C	ENST00000375023	NM_004557.3	1151	Ggc/Tgc	21/30	1	2	FACETS	0.872	0.798	0.948	0.872	0.798	0.948	CLONAL	1	TRUE	1	0.654695066576252	2		242	473	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185823	32185823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1325286020	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	126	349	0	ENST00000375023.3:c.1573C>T	p.His525Tyr	p.H525Y	ENST00000375023	NM_004557.3	525	Cac/Tac	9/30	1	2	FACETS	0.725	0.659	0.793	0.725	0.659	0.793	SUBCLONAL	1	TRUE	1	0.654695066576252	2		349	531	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522095	157522095	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	92	168	0	ENST00000346085.5:c.4367C>T	p.Ser1456Phe	p.S1456F	ENST00000346085	NM_020732.3	1456	tCc/tTc	18/20	1	2	FACETS	0.844	0.757	0.934	0.844	0.757	0.934	CLONAL	1	TRUE	1	0.654695066576252	2		168	333	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457085	5457085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs937227717	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	77	128	0	ENST00000381577.3:c.59C>T	p.Thr20Ile	p.T20I	ENST00000381577	NM_014143.3	20	aCt/aTt	3/7	1	2	FACETS	0.759	0.672	0.85	0.759	0.672	0.85	SUBCLONAL	1	TRUE	1	0.654695066576252	2		128	310	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331589	8331589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	184	450	0	ENST00000356435.5:c.5527C>T	p.His1843Tyr	p.H1843Y	ENST00000356435		1843	Cat/Tat	33/35	1	2	FACETS	0.756	0.699	0.814	0.756	0.699	0.814	SUBCLONAL	1	TRUE	1	0.654695066576252	2		450	744	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445095	49445095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	52	57	0	ENST00000301067.7:c.2371C>T	p.Gln791Ter	p.Q791*	ENST00000301067	NM_003482.3	791	Cag/Tag	10/54	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.654695066576252	2		57	158	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494012	56494012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	124	296	0	ENST00000267101.3:c.3184C>T	p.Leu1062Phe	p.L1062F	ENST00000267101	NM_001982.3	1062	Ctt/Ttt	26/28	1	2	FACETS	0.734	0.667	0.804	0.734	0.667	0.804	SUBCLONAL	1	TRUE	1	0.654695066576252	2		296	516	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608113	28608113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	240	402	3	ENST00000241453.7:c.1853C>T	p.Ser618Leu	p.S618L	ENST00000241453	NM_004119.2	618	tCa/tTa	15/24	0.599246315288244	1	FACETS	0.807	0.759	0.856	0.807	0.759	0.856	CLONAL	1	TRUE	0	0.654695066576252	1		405	611	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033862	49033862	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	142	247	0	ENST00000267163.4:c.1999G>T	p.Glu667Ter	p.E667*	ENST00000267163	NM_000321.2	667	Gaa/Taa	20/27	0.599246315288244	1	FACETS	0.853	0.789	0.919	0.853	0.789	0.919	CLONAL	1	TRUE	0	0.654695066576252	1		247	342	SUCCESS
BLM	641	MSKCC	GRCh37	15	91306291	91306291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139688226	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	134	267	0	ENST00000355112.3:c.1978C>T	p.His660Tyr	p.H660Y	ENST00000355112	NM_000057.2	660	Cat/Tat	8/22	0.55516718987399	3	FACETS	0.716	0.651	0.784	0.358	0.325	0.392	SUBCLONAL	1	TRUE	1	0.654695066576252	3		267	759	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645165	67645165	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	159	218	0	ENST00000264010.4:c.430A>T	p.Lys144Ter	p.K144*	ENST00000264010	NM_006565.3	144	Aaa/Taa	3/12	1	2	FACETS	0.908	0.837	0.98	0.908	0.837	0.98	CLONAL	1	TRUE	1	0.654695066576252	2		218	535	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221981	1221981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	135	411	0	ENST00000326873.7:c.896C>T	p.Ser299Phe	p.S299F	ENST00000326873	NM_000455.4	299	tCc/tTc	7/10	1	2	FACETS	0.777	0.71	0.846	0.777	0.71	0.846	SUBCLONAL	1	TRUE	1	0.654695066576252	2		411	531	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278082	15278082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	126	334	0	ENST00000263388.2:c.5340G>A	p.Met1780Ile	p.M1780I	ENST00000263388	NM_000435.2	1780	atG/atA	29/33	1	2	FACETS	0.787	0.717	0.86	0.787	0.717	0.86	SUBCLONAL	1	TRUE	1	0.654695066576252	2		334	489	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022637	31022637	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs755789372	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	162	309	0	ENST00000375687.4:c.2122C>T	p.Gln708Ter	p.Q708*	ENST00000375687	NM_015338.5	708	Cag/Tag	13/13	1	2	FACETS	0.868	0.801	0.938	0.868	0.801	0.938	CLONAL	1	TRUE	1	0.654695066576252	2		309	570	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130405	29130405	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	128	190	0	ENST00000328354.6:c.305G>C	p.Gly102Ala	p.G102A	ENST00000328354	NM_007194.3	102	gGa/gCa	2/15	1	2	FACETS	0.879	0.802	0.958	0.879	0.802	0.958	CLONAL	1	TRUE	1	0.654695066576252	2		190	445	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217380	123217380	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	161	226	0	ENST00000218089.9:c.3034C>T	p.Arg1012Ter	p.R1012*	ENST00000218089	NM_001042749.1	1012	Cga/Tga	29/35	1	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.654695066576252	1		226	309	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165306	32165307	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	97	228	1	ENST00000375023.3:c.4821_4822delinsAA	p.Ala1608Thr	p.A1608T	ENST00000375023	NM_004557.3	1607	ggGGca/ggAAca	27/30	1	2	FACETS	0.792	0.712	0.876	0.792	0.712	0.876	SUBCLONAL	1	TRUE	1	0.654695066576252	2		229	374	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759696	133759697	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	128	140	0	ENST00000318560.5:c.2019_2020delinsTT	p.Arg674Trp	p.R674W	ENST00000318560	NM_005157.4	673	ctCCgg/ctTTgg	11/11	0.610825160220065	3	FACETS	0.9	0.818	0.984	0.45	0.409	0.492	CLONAL	1	TRUE	1	0.654695066576252	3		140	577	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436825	110436826	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	60	223	0	ENST00000375856.3:c.1575_1576delinsAA	p.Glu526Lys	p.E526K	ENST00000375856	NM_003749.2	525	gcGGag/gcAAag	1/2	1	2	FACETS	0.679	0.59	0.773	0.679	0.59	0.773	SUBCLONAL	1	TRUE	1	0.654695066576252	2		223	270	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129636	2129637	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	158	506	1	ENST00000219476.3:c.3363_3364delinsTT	p.Arg1122Cys	p.R1122C	ENST00000219476	NM_000548.3	1121	tcCCgt/tcTTgt	29/42	1	2	FACETS	0.744	0.684	0.806	0.744	0.684	0.806	SUBCLONAL	1	TRUE	1	0.654695066576252	2		507	649	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577095	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	143	363	0	ENST00000269305.4:c.843_844delinsAT	p.Asp281_Arg282delinsGluTrp	p.D281_R282delinsEW	ENST00000269305	NM_001126112.2	281	gaCCgg/gaATgg	8/11	1	2	FACETS	0.82	0.751	0.89	0.82	0.751	0.89	CLONAL	1	TRUE	1	0.654695066576252	2		363	533	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487602	38487603	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	104	320	1	ENST00000254066.5:c.132_133delinsTT	p.Gln45Ter	p.Q45*	ENST00000254066	NM_000964.3	44	ctCCag/ctTTag	2/9	1	2	FACETS	0.663	0.597	0.733	0.663	0.597	0.733	SUBCLONAL	1	TRUE	1	0.654695066576252	2		321	479	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41209080	41209081	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	195	680	0	ENST00000357654.3:c.5265_5266delinsTT	p.Gln1756Ter	p.Q1756*	ENST00000357654	NM_007294.3	1755	tcCCag/tcTTag	19/23	1	2	FACETS	0.646	0.598	0.696	0.646	0.598	0.696	SUBCLONAL	1	TRUE	1	0.654695066576252	2		680	922	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41247939	41247940	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	AC	AC	TT	novel	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	87	209	0	ENST00000357654.3:c.594-1_594delinsAA		p.X198_splice	ENST00000357654	NM_007294.3	198		9/23	1	2	FACETS	0.714	0.637	0.796	0.714	0.637	0.796	SUBCLONAL	1	TRUE	1	0.654695066576252	2		209	372	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615617	100615618	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0010462-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	192	274	0	ENST00000308731.7:c.714_715delinsCT	p.Asp239Tyr	p.D239Y	ENST00000308731	NM_000061.2	238	ggTGat/ggCTat	8/19	1	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.654695066576252	1		274	388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010463-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	455	315	0	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.586571944310229	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	0	0.586571944310229	3		315	662	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871704	35871704	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010463-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1344	566	1120	0	ENST00000216797.5:c.802C>A	p.Gln268Lys	p.Q268K	ENST00000216797	NM_020529.2	268	Cag/Aag	5/6	0.586571944310229	2	FACETS	1	0.967	1	0.505	0.484	0.527	CLONAL	1	TRUE	0	0.586571944310229	2		1120	1910	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244138	153244138	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010463-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	133	215	0	ENST00000281708.4:c.2019del	p.Trp673CysfsTer34	p.W673Cfs*34	ENST00000281708	NM_033632.3	673	tgG/tg	12/12	0.586571944310229	3	FACETS	0.929	0.847	1	0.465	0.423	0.508	CLONAL	1	TRUE	1	0.586571944310229	3		215	631	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050840	49050841	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1566240909	NA	P-0010463-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	150	158	0	ENST00000267163.4:c.2525_2526del	p.Ser842Ter	p.S842*	ENST00000267163	NM_000321.2	842	TCt/t	25/27	0.586571944310229	2	FACETS	0.93	0.869	0.99	0.93	0.869	0.99	CLONAL	2	TRUE	0	0.586571944310229	2		158	275	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143042	47143043	+	stop_gained,splice_region_variant	Nonsense_Mutation	DNP	TC	TC	CT	novel	NA	P-0010463-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	152	288	0	ENST00000409792.3:c.4920_4921delinsAG	p.Trp1640_Thr1641delinsTer	p.W1640_T1641delins*	ENST00000409792	NM_014159.6	1640	tgGAct/tgAGct	8/21	1	2	FACETS	0.886	0.814	0.96	0.886	0.814	0.96	CLONAL	1	TRUE	1	0.586571944310229	2		288	585	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554545	29554546	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0010463-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	95	183	0	ENST00000356175.3:c.2330_2331delinsAT	p.Trp777Tyr	p.W777Y	ENST00000356175	NM_000267.3	777	tGG/tAT	20/57	0.586571944310229	3	FACETS	0.826	0.738	0.919	0.275	0.246	0.307	CLONAL	1	TRUE	0	0.586571944310229	3		183	507	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0010500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	273	368	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.480653941835386	3	FACETS	1	0.993	1			1	CLONAL	1	TRUE	NA	0.559828190471559	3		368	852	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578277	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs1555525902	NA	P-0010500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	345	464	0	ENST00000269305.4:c.572_574del	p.Pro191del	p.P191del	ENST00000269305	NM_001126112.2	191	cCTCag/cag	6/11	0.559828190471559	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.559828190471559	2		464	606	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685282	89685282	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1114167671	NA	P-0010500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	374	320	0	ENST00000371953.3:c.179del	p.Lys60SerfsTer39	p.K60Sfs*39	ENST00000371953	NM_000314.4	59	tcA/tc	3/9	0.559828190471559	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.559828190471559	2		320	630	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0010501-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	44	414	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.707	0.591	0.837	0.707	0.591	0.837	SUBCLONAL	1	TRUE	1	0.14	2		416	889	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0010501-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	49	390	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.982	0.83	1	0.982	0.83	1	CLONAL	1	TRUE	1	0.14	2		390	713	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010501-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	77	473	0	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	1	2	FACETS	0.931	0.814	1	0.931	0.814	1	CLONAL	1	TRUE	1	0.14	2		473	1182	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271193	153271193	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0010501-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	65	367	0	ENST00000281708.4:c.584+1G>A		p.X195_splice	ENST00000281708	NM_033632.3	195			1	2	FACETS	0.998	0.863	1	0.998	0.863	1	CLONAL	1	TRUE	1	0.14	2		367	930	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635555	47635555	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010501-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	65	378	0	ENST00000233146.2:c.227A>G	p.Gln76Arg	p.Q76R	ENST00000233146	NM_000251.2	76	cAg/cGg	2/16	0.3	1	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	0	0.14	1		378	838	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594055	55594055	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010501-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	77	522	1	ENST00000288135.5:c.1841C>A	p.Ser614Ter	p.S614*	ENST00000288135	NM_000222.2	614	tCa/tAa	12/21	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.14	2		523	1038	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839736	27839736	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1281167014	NA	P-0010501-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2733	197	1192	0	ENST00000328488.2:c.358A>G	p.Ile120Val	p.I120V	ENST00000328488	NM_003533.2	120	Att/Gtt	1/1	0.3	6	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.14	6		1192	2930	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778821	3778821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010501-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	32	376	0	ENST00000262367.5:c.6227C>T	p.Ser2076Leu	p.S2076L	ENST00000262367	NM_004380.2	2076	tCg/tTg	31/31	0.3	1	FACETS	0.677	0.548	0.824	0.677	0.548	0.824	SUBCLONAL	1	TRUE	0	0.14	1		376	628	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435869	56435869	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010501-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	35	263	0	ENST00000407977.2:c.1268C>G	p.Ser423Cys	p.S423C	ENST00000407977		423	tCc/tGc	9/10	1	2	FACETS	0.75	0.613	0.904	0.75	0.613	0.904	CLONAL	1	TRUE	1	0.14	2		263	667	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846029	68846047	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTCTGCAGAGTTTCCCTA	TCTCTGCAGAGTTTCCCTA	-	novel	NA	P-0010501-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	112	549	0	ENST00000261769.5:c.1009-9_1018del		p.X337_splice	ENST00000261769	NM_004360.3	337		8/16	0.3	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.14	1		549	1016	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	246	561	2	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.445454193378632	1	FACETS	0.7	0.661	0.739	0.7	0.661	0.739	INDETERMINATE	1	TRUE	0	0.79769199496588	1		563	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578507	7578507	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519977	NA	P-0010510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	512	391	0	ENST00000269305.4:c.423C>G	p.Cys141Trp	p.C141W	ENST00000269305	NM_001126112.2	141	tgC/tgG	5/11	0.789555437421387	2	FACETS	0.945	0.92	0.97	0.945	0.92	0.97	CLONAL	2	TRUE	0	0.79769199496588	2		391	679	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225060	NA	P-0010510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1209	628	801	0	ENST00000263967.3:c.311C>T	p.Pro104Leu	p.P104L	ENST00000263967	NM_006218.2	104	cCa/cTa	2/21	0.510179305570011	4	FACETS	0.77	0.741	0.8	0.77	0.741	0.8	SUBCLONAL	2	TRUE	2	0.79769199496588	4		801	1837	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028193	48028193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372705506	NA	P-0010510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	351	602	0	ENST00000234420.5:c.3071G>A	p.Arg1024Gln	p.R1024Q	ENST00000234420	NM_000179.2	1024	cGg/cAg	4/10	1	2	FACETS	0.822	0.779	0.865	0.822	0.779	0.865	CLONAL	1	TRUE	1	0.79769199496588	2		602	1071	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230571	46230571	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	192	418	1	ENST00000334344.6:c.820C>T	p.Arg274Ter	p.R274*	ENST00000334344	NM_152641.2	274	Cga/Tga	8/21	1	2	FACETS	0.82	0.76	0.883	0.82	0.76	0.883	CLONAL	1	TRUE	1	0.581441556189051	2		419	805	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111519	8111519	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1238949082	NA	P-0010515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	173	296	0	ENST00000346208.3:c.1005C>A	p.Asp335Glu	p.D335E	ENST00000346208		335	gaC/gaA	5/6	1	2	FACETS	0.876	0.809	0.946	0.876	0.809	0.946	CLONAL	1	TRUE	1	0.581441556189051	2		296	679	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274862	38274862	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010515-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	231	405	0	ENST00000425967.3:c.1718del	p.Lys573ArgfsTer90	p.K573Rfs*90	ENST00000425967	NM_001174067.1	573	aAg/ag	13/19	1	2	FACETS	0.922	0.861	0.984	0.922	0.861	0.984	CLONAL	1	TRUE	1	0.581441556189051	2		405	862	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0010527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	36	474	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.43838281111848	3	FACETS	0.736	0.608	0.878	0.368	0.304	0.439	SUBCLONAL	1	TRUE	1	0.43838281111848	3		474	272	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0010527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	10	264	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.43838281111848	3	FACETS	0.182	0.123	0.258	0.091	0.061	0.129	SUBCLONAL	1	TRUE	1	0.43838281111848	3		264	305	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437782	52437782	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0010527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	75	987	0	ENST00000460680.1:c.1379C>G	p.Ser460Ter	p.S460*	ENST00000460680	NM_004656.3	460	tCa/tGa	13/17	0.43838281111848	1	FACETS	0.225	0.196	0.256	0.225	0.196	0.256	SUBCLONAL	1	TRUE	0	0.43838281111848	1		987	1189	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436821	52436821	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	42	541	0	ENST00000460680.1:c.1957G>A	p.Glu653Lys	p.E653K	ENST00000460680	NM_004656.3	653	Gag/Aag	15/17	0.43838281111848	1	FACETS	0.204	0.169	0.242	0.204	0.169	0.242	SUBCLONAL	1	TRUE	0	0.43838281111848	1		541	734	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437465	52437465	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	71	653	0	ENST00000460680.1:c.1696G>T	p.Glu566Ter	p.E566*	ENST00000460680	NM_004656.3	566	Gag/Tag	13/17	0.43838281111848	1	FACETS	0.313	0.272	0.357	0.313	0.272	0.357	SUBCLONAL	1	TRUE	0	0.43838281111848	1		653	808	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103510646	103510646	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	86	275	0	ENST00000355739.4:c.550C>T	p.Gln184Ter	p.Q184*	ENST00000355739	NM_000123.3	184	Caa/Taa	6/15	1	2	FACETS	0.888	0.789	0.992	0.888	0.789	0.992	CLONAL	1	TRUE	1	0.43838281111848	2		275	442	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89874760	89874760	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	38	336	0	ENST00000389301.3:c.538G>C	p.Glu180Gln	p.E180Q	ENST00000389301	NM_000135.2	180	Gaa/Caa	6/43	NA	2	FACETS	0.272	0.224	0.326			1	INDETERMINATE	1	TRUE	NA	0.43838281111848	2		336	637	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208260	5208260	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	47	465	0	ENST00000357368.4:c.5630C>G	p.Ser1877Cys	p.S1877C	ENST00000357368	NM_002850.3	1877	tCt/tGt	36/38	1	2	FACETS	0.256	0.215	0.301	0.256	0.215	0.301	SUBCLONAL	1	TRUE	1	0.43838281111848	2		465	838	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260206	10260206	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	46	404	0	ENST00000340748.4:c.2461G>C	p.Glu821Gln	p.E821Q	ENST00000340748		821	Gag/Cag	25/40	1	2	FACETS	0.254	0.213	0.3	0.254	0.213	0.3	SUBCLONAL	1	TRUE	1	0.43838281111848	2		404	825	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094995	11094995	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	159	484	0	ENST00000358026.2:c.168C>G	p.Ile56Met	p.I56M	ENST00000358026	NM_001128849.1	56	atC/atG	2/36	1	2	FACETS	0.887	0.814	0.963	0.887	0.814	0.963	CLONAL	1	TRUE	1	0.43838281111848	2		484	818	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913197	39913197	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1675	103	740	0	ENST00000378444.4:c.4918G>C	p.Glu1640Gln	p.E1640Q	ENST00000378444	NM_001123385.1	1640	Gaa/Caa	14/15	0.216948709728293	4	FACETS	0.38	0.338	0.425			1	INDETERMINATE	1	TRUE	NA	0.43838281111848	4		740	1778	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201059	NA	P-0010528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	206	676	1	ENST00000269305.4:c.856G>T	p.Glu286Ter	p.E286*	ENST00000269305	NM_001126112.2	286	Gaa/Taa	8/11	0.597171912892186	2	FACETS	1	0.977	1	0.553	0.515	0.591	CLONAL	1	TRUE	0	0.597445876026548	2		677	624	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0010528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	467	827	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.597171912892186	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.597445876026548	2		828	676	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576831	212576831	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	121	585	0	ENST00000342788.4:c.1068C>G	p.Phe356Leu	p.F356L	ENST00000342788	NM_005235.2	356	ttC/ttG	9/28	0.130902445903595	4	FACETS	1	0.982	1	0.339	0.308	0.372	INDETERMINATE	1	TRUE	0	0.597445876026548	4		585	477	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673055	30673055	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1760	270	1235	0	ENST00000376406.3:c.3905C>A	p.Thr1302Asn	p.T1302N	ENST00000376406	NM_014641.2	1302	aCc/aAc	10/15	0.597445876026548	10	FACETS	0.755	0.705	0.806	0.151	0.141	0.162	SUBCLONAL	2	TRUE	0	0.597445876026548	10		1235	2030	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235883	133235883	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	79	323	0	ENST00000320574.5:c.3273G>C	p.Glu1091Asp	p.E1091D	ENST00000320574	NM_006231.2	1091	gaG/gaC	26/49	0.537918297894155	3	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.597445876026548	3		323	254	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937130	76937132	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs782162142	NA	P-0010528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	204	1294	0	ENST00000373344.5:c.3616_3618del	p.Ser1206del	p.S1206del	ENST00000373344	NM_000489.3	1206	TCT/-	9/35	0.597171912892186	1	FACETS	0.725	0.675	0.775	0.725	0.675	0.775	SUBCLONAL	1	TRUE	0	0.597445876026548	1		1294	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	153	279	0	ENST00000269305.4:c.383del	p.Pro128LeufsTer42	p.P128Lfs*42	ENST00000269305	NM_001126112.2	128	cCt/ct	5/11	0.355783762355328	1	FACETS	0.878	0.806	0.954	0.878	0.806	0.954	CLONAL	1	TRUE	0	0.40168800145147	1		279	693	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331643	8331643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770713312	NA	P-0010553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	227	593	0	ENST00000356435.5:c.5473G>A	p.Gly1825Ser	p.G1825S	ENST00000356435		1825	Ggc/Agc	33/35	0.272070023002908	2	FACETS	0.97	0.903	1	0.485	0.451	0.52	CLONAL	1	TRUE	0	0.40168800145147	2		593	1165	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001999	29001999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1004788109	NA	P-0010553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	99	329	1	ENST00000282397.4:c.1166C>T	p.Ser389Leu	p.S389L	ENST00000282397	NM_002019.4	389	tCg/tTg	9/30	0.40168800145147	1	FACETS	0.842	0.755	0.933	0.842	0.755	0.933	CLONAL	1	TRUE	0	0.40168800145147	1		330	468	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650729	67650729	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	165	438	0	ENST00000264010.4:c.1034A>C	p.His345Pro	p.H345P	ENST00000264010	NM_006565.3	345	cAc/cCc	5/12	1	2	FACETS	0.618	0.566	0.673	0.618	0.566	0.673	SUBCLONAL	1	TRUE	1	0.40168800145147	2		438	1329	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502859	186502899	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TATTGGCCCCCACCAGAGAACTGGCTCAACAGGTATTGATA	TATTGGCCCCCACCAGAGAACTGGCTCAACAGGTATTGATA	-	novel	NA	P-0010553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	162	748	0	ENST00000323963.5:c.317_348+9del		p.X106_splice	ENST00000323963		106		4/11	0.314719483059465	1	FACETS	0.492	0.45	0.536	0.492	0.45	0.536	SUBCLONAL	1	TRUE	0	0.40168800145147	1		748	1311	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0010555-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	262	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.646005683232606	2		336	809	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577115	7577115	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519983	NA	P-0010555-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	388	478	0	ENST00000269305.4:c.823T>C	p.Cys275Arg	p.C275R	ENST00000269305	NM_001126112.2	275	Tgt/Cgt	8/11	0.646005683232606	1	FACETS	0.962	0.92	1	0.962	0.92	1	CLONAL	1	TRUE	0	0.646005683232606	1		478	845	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747084	40747084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762809890	NA	P-0010555-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	345	365	2	ENST00000373198.4:c.2998G>A	p.Ala1000Thr	p.A1000T	ENST00000373198	NM_133170.3	1000	Gcc/Acc	22/32	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.646005683232606	2		367	984	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0010555-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	190	476	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.877	0.814	0.941	0.877	0.814	0.941	CLONAL	1	TRUE	1	0.646005683232606	2		476	671	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591888	48591888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519739	NA	P-0010555-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	351	462	0	ENST00000342988.3:c.1051G>A	p.Asp351Asn	p.D351N	ENST00000342988	NM_005359.5	351	Gat/Aat	9/12	0.646005683232606	1	FACETS	0.948	0.904	0.993	0.948	0.904	0.993	CLONAL	1	TRUE	0	0.646005683232606	1		462	776	SUCCESS
APC	324	MSKCC	GRCh37	5	112175754	112175754	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0010555-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	195	272	0	ENST00000257430.4:c.4463T>A	p.Leu1488Ter	p.L1488*	ENST00000257430	NM_000038.5	1488	tTa/tAa	16/16	1	2	FACETS	0.917	0.853	0.984	0.917	0.853	0.984	CLONAL	1	TRUE	1	0.646005683232606	2		272	658	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432011	49432011	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs746344900	NA	P-0010555-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	439	473	1	ENST00000301067.7:c.9128A>G	p.Asn3043Ser	p.N3043S	ENST00000301067	NM_003482.3	3043	aAt/aGt	34/54	NA	2	FACETS	1	0.972	1			1	INDETERMINATE	1	TRUE	NA	0.646005683232606	2		474	1326	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0010575-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	172	382	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	0.591519132511697	2		382	477	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665752	29665755	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1555535032	NA	P-0010575-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	238	575	0	ENST00000356175.3:c.6789_6792del	p.Tyr2264ThrfsTer5	p.Y2264Tfs*5	ENST00000356175	NM_000267.3	2263	ACTTac/ac	45/57	0.591519132511697	1	FACETS	0.956	0.899	1	0.956	0.899	1	CLONAL	1	TRUE	0	0.591519132511697	1		575	593	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016549	12016549	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0010575-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	169	386	0	ENST00000353533.5:c.686-1G>T		p.X229_splice	ENST00000353533	NM_003010.3	229			0.591519132511697	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.591519132511697	1		386	393	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0010578-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	325	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.460580635855979	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	TRUE	1	0.474832444428821	4		336	649	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267514	198267514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010578-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	200	517	0	ENST00000335508.6:c.1843C>T	p.Pro615Ser	p.P615S	ENST00000335508	NM_012433.2	615	Cct/Tct	14/25	0.417291621446373	4	FACETS	0.922	0.858	0.987	0.614	0.572	0.658	CLONAL	2	TRUE	1	0.474832444428821	4		517	674	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413244	139413244	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010578-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	190	851	0	ENST00000277541.6:c.898C>T	p.Gln300Ter	p.Q300*	ENST00000277541	NM_017617.3	300	Cag/Tag	6/34	0.461553614985967	2	FACETS	0.895	0.828	0.965	0.448	0.414	0.483	CLONAL	1	TRUE	0	0.474832444428821	2		851	894	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272775	18272775	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0010578-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	180	701	0	ENST00000222254.8:c.816-1G>A		p.X272_splice	ENST00000222254	NM_005027.3	272			0.426715662283855	5	FACETS	1	0.952	1	0.349	0.321	0.379	CLONAL	1	TRUE	2	0.474832444428821	5		701	1239	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272828	18272828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762874163	NA	P-0010578-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1315	208	902	1	ENST00000222254.8:c.868G>A	p.Glu290Lys	p.E290K	ENST00000222254	NM_005027.3	290	Gaa/Aaa	7/16	0.426715662283855	5	FACETS	0.985	0.911	1	0.328	0.303	0.354	CLONAL	1	TRUE	2	0.474832444428821	5		903	1523	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222198	53222198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010578-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	134	308	0	ENST00000375401.3:c.4634C>T	p.Pro1545Leu	p.P1545L	ENST00000375401	NM_004187.3	1545	cCc/cTc	26/26	0.428146215164599	2	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.474832444428821	2		308	472	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0010596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	107	273	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.989	0.894	1	0.989	0.894	1	CLONAL	1	TRUE	1	0.54797754066503	2		273	395	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666615	206666615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	495	475	0	ENST00000367120.3:c.1949C>T	p.Ser650Phe	p.S650F	ENST00000367120	NM_014002.3	650	tCt/tTt	20/22	0.54797754066503	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	1	0.54797754066503	3		475	964	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967173	134967173	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370164002	NA	P-0010596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	49	234	0	ENST00000398015.3:c.2512G>A	p.Glu838Lys	p.E838K	ENST00000398015	NM_004441.4	838	Gag/Aag	14/16	0.251480318357835	1	FACETS	0.38	0.323	0.442	0.38	0.323	0.442	INDETERMINATE	1	TRUE	0	0.54797754066503	1		234	342	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196241	106196241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	182	353	0	ENST00000380013.4:c.4574C>T	p.Ser1525Phe	p.S1525F	ENST00000380013	NM_001127208.2	1525	tCc/tTc	11/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.54797754066503	2		353	642	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861010	35861010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	137	304	0	ENST00000303115.3:c.139G>A	p.Glu47Lys	p.E47K	ENST00000303115	NM_002185.3	47	Gaa/Aaa	2/8	1	2	FACETS	0.898	0.82	0.978	0.898	0.82	0.978	CLONAL	1	TRUE	1	0.54797754066503	2		304	557	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056265	26056266	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0010596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	204	525	0	ENST00000343677.2:c.391_392delinsTT	p.Pro131Leu	p.P131L	ENST00000343677	NM_005319.3	131	CCa/TTa	1/1	1	2	FACETS	0.877	0.815	0.942	0.877	0.815	0.942	CLONAL	1	TRUE	1	0.54797754066503	2		525	849	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120501	94120501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760168204	NA	P-0010596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	324	1010	0	ENST00000369303.4:c.550C>T	p.Leu184Phe	p.L184F	ENST00000369303	NM_004440.3	184	Ctt/Ttt	3/17	0.525838156667249	1	FACETS	0.712	0.673	0.753	0.712	0.673	0.753	SUBCLONAL	1	TRUE	0	0.54797754066503	1		1010	1205	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0010596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	454	301	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.54797754066503	5	FACETS	0.878	0.844	0.911	0.878	0.844	0.911	CLONAL	4	TRUE	1	0.54797754066503	5		301	860	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878038	151878038	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	148	298	0	ENST00000262189.6:c.6907C>T	p.Pro2303Ser	p.P2303S	ENST00000262189	NM_170606.2	2303	Cca/Tca	36/59	0.54797754066503	5	FACETS	1	0.938	1	0.259	0.236	0.283	CLONAL	1	TRUE	1	0.54797754066503	5		298	951	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945102	151945102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	21	158	1	ENST00000262189.6:c.2417C>T	p.Ser806Phe	p.S806F	ENST00000262189	NM_170606.2	806	tCc/tTc	14/59	0.54797754066503	5	FACETS	0.394	0.303	0.501	0.099	0.075	0.126	SUBCLONAL	1	TRUE	1	0.54797754066503	5		159	354	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319853	8319853	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	227	515	0	ENST00000356435.5:c.5648G>A	p.Arg1883Gln	p.R1883Q	ENST00000356435		1883	cGa/cAa	34/35	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.54797754066503	2		515	810	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250139	110250139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs965501282	NA	P-0010596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	173	331	0	ENST00000374672.4:c.536C>T	p.Pro179Leu	p.P179L	ENST00000374672	NM_004235.4	179	cCc/cTc	3/5	0.54797754066503	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.54797754066503	1		331	446	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852319	63852319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1340574832	NA	P-0010596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	162	388	0	ENST00000279873.7:c.3097C>T	p.Pro1033Ser	p.P1033S	ENST00000279873	NM_032199.2	1033	Ccc/Tcc	10/10	1	2	FACETS	0.952	0.877	1	0.952	0.877	1	CLONAL	1	TRUE	1	0.54797754066503	2		388	621	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309776	104309776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202247756	NA	P-0010596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	219	563	0	ENST00000369902.3:c.367C>T	p.Arg123Cys	p.R123C	ENST00000369902	NM_016169.3	123	Cgt/Tgt	3/12	1	2	FACETS	0.892	0.831	0.955	0.892	0.831	0.955	CLONAL	1	TRUE	1	0.54797754066503	2		563	896	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32449554	32449554	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1170110894	NA	P-0010596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	212	495	0	ENST00000332351.3:c.820A>G	p.Thr274Ala	p.T274A	ENST00000332351	NM_024426.4	274	Acc/Gcc	3/10	0.498857583477299	3	FACETS	1	0.955	1	0.518	0.481	0.556	CLONAL	1	TRUE	1	0.54797754066503	3		495	952	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160419	108160419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555097538	NA	P-0010596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	143	251	1	ENST00000278616.4:c.4327C>T	p.His1443Tyr	p.H1443Y	ENST00000278616	NM_000051.3	1443	Cac/Tac	29/63	0.54797754066503	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.54797754066503	1		252	370	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347548	118347548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	228	414	0	ENST00000534358.1:c.3185C>T	p.Ser1062Phe	p.S1062F	ENST00000534358	NM_005933.3	1062	tCt/tTt	4/36	0.54797754066503	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.54797754066503	1		414	579	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211536	46211536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	202	434	0	ENST00000334344.6:c.502G>A	p.Gly168Arg	p.G168R	ENST00000334344	NM_152641.2	168	Gga/Aga	5/21	NA	2	FACETS	1	0.967	1			1	INDETERMINATE	1	TRUE	NA	0.54797754066503	2		434	692	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244380	46244380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	206	450	0	ENST00000334344.6:c.2474C>T	p.Ser825Leu	p.S825L	ENST00000334344	NM_152641.2	825	tCa/tTa	15/21	NA	2	FACETS	0.915	0.85	0.981			1	INDETERMINATE	1	TRUE	NA	0.54797754066503	2		450	822	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73340179	73340179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	160	344	0	ENST00000377767.4:c.1901C>T	p.Ser634Phe	p.S634F	ENST00000377767	NM_014953.3	634	tCt/tTt	15/21	0.147883864506819	3	FACETS	1	0.986	1	0.668	0.616	0.722	INDETERMINATE	1	TRUE	1	0.54797754066503	3		344	557	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028709	42028709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	335	1038	1	ENST00000219905.7:c.4247C>T	p.Thr1416Ile	p.T1416I	ENST00000219905	NM_001164273.1	1416	aCt/aTt	13/24	NA	2	FACETS	0.919	0.868	0.972			1	INDETERMINATE	1	TRUE	NA	0.54797754066503	2		1039	1330	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729175	66729175	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908596	NA	P-0010596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	98	413	1	ENST00000307102.5:c.383G>A	p.Gly128Asp	p.G128D	ENST00000307102	NM_002755.3	128	gGc/gAc	3/11	1	2	FACETS	0.449	0.4	0.501	0.449	0.4	0.501	SUBCLONAL	1	TRUE	1	0.54797754066503	2		414	797	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782214	56782214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	305	754	0	ENST00000308159.5:c.55G>A	p.Glu19Lys	p.E19K	ENST00000308159	NM_014669.4	19	Gag/Aag	2/22	0.429779596722175	1	FACETS	0.837	0.791	0.885	0.837	0.791	0.885	CLONAL	1	TRUE	0	0.54797754066503	1		754	965	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81916938	81916938	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	121	711	0	ENST00000359376.3:c.757G>A	p.Glu253Lys	p.E253K	ENST00000359376	NM_002661.3	253	Gaa/Aaa	9/33	0.40458131295337	1	FACETS	0.317	0.285	0.35	0.317	0.285	0.35	SUBCLONAL	1	TRUE	0	0.54797754066503	1		711	1013	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7218299	7218299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	212	513	1	ENST00000380728.2:c.73G>A	p.Glu25Lys	p.E25K	ENST00000380728		25	Gag/Aag	2/11	1	2	FACETS	0.847	0.788	0.909	0.847	0.788	0.909	CLONAL	1	TRUE	1	0.54797754066503	2		514	913	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243954	5243954	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	188	388	0	ENST00000357368.4:c.1528G>T	p.Gly510Trp	p.G510W	ENST00000357368	NM_002850.3	510	Ggg/Tgg	11/38	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.54797754066503	2		388	660	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793099	42793099	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	208	550	1	ENST00000575354.2:c.991C>T	p.Pro331Ser	p.P331S	ENST00000575354	NM_015125.3	331	Ccg/Tcg	7/20	1	2	FACETS	0.875	0.813	0.938	0.875	0.813	0.938	CLONAL	1	TRUE	1	0.54797754066503	2		551	868	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309968	30309969	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0010596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	134	299	0	ENST00000307677.4:c.53_54delinsTT	p.Ser18Phe	p.S18F	ENST00000307677	NM_138578.1	18	tCC/tTT	2/3	1	2	FACETS	0.946	0.864	1	0.946	0.864	1	CLONAL	1	TRUE	1	0.54797754066503	2		299	517	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36421162	36421162	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750755857	NA	P-0010596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	130	304	0	ENST00000300305.3:c.35C>T	p.Ser12Leu	p.S12L	ENST00000300305		12	tCg/tTg	1/8	1	2	FACETS	0.778	0.708	0.851	0.778	0.708	0.851	SUBCLONAL	1	TRUE	1	0.54797754066503	2		304	610	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884925	151884926	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	C	novel	NA	P-0010596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	345	218	0	ENST00000262189.6:c.4667_4668delinsG	p.Phe1556CysfsTer7	p.F1556Cfs*7	ENST00000262189	NM_170606.2	1556	tTT/tG	32/59	0.54797754066503	5	FACETS	1	0.989	1	0.832	0.795	0.87	CLONAL	3	TRUE	1	0.54797754066503	5		218	689	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023135	27023135	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	23	77	0	ENST00000324856.7:c.245del	p.Gly82ValfsTer19	p.G82Vfs*19	ENST00000324856	NM_006015.4	81	Ggg/gg	1/20	0.251480318357835	1	FACETS	0.554	0.439	0.682	0.554	0.439	0.682	INDETERMINATE	1	TRUE	0	0.54797754066503	1		77	110	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0010597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	187	453	0	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	0.655298462841104	1	FACETS	0.765	0.715	0.816	0.765	0.715	0.816	SUBCLONAL	1	TRUE	0	0.700899413335855	1		453	453	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521240	187521240	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010597-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	411	1085	0	ENST00000441802.2:c.11915G>C	p.Gly3972Ala	p.G3972A	ENST00000441802	NM_005245.3	3972	gGt/gCt	22/27	1	2	FACETS	0.81	0.771	0.851	0.81	0.771	0.851	CLONAL	1	TRUE	1	0.700899413335855	2		1085	1447	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0010605-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	29	332	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	1	2	FACETS	0.588	0.47	0.723	0.588	0.47	0.723	SUBCLONAL	1	TRUE	1	0.14	2		332	705	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0010608-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	165	606	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.185584232666875	3	FACETS	1	0.987	1	0.716	0.656	0.779	CLONAL	1	TRUE	1	0.214815687643639	3		606	1188	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555687605	NA	P-0010608-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	111	561	0	ENST00000342988.3:c.1610A>G	p.Asp537Gly	p.D537G	ENST00000342988	NM_005359.5	537	gAc/gGc	12/12	0.214815687643639	1	FACETS	0.745	0.667	0.827	0.745	0.667	0.827	SUBCLONAL	1	TRUE	0	0.214815687643639	1		561	1239	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0010609-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	270	393	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.325892676635161	1	FACETS	0.859	0.81	0.908	0.859	0.81	0.908	INDETERMINATE	1	TRUE	0	0.620471918465676	1		393	699	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207021	1207021	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913324	NA	P-0010609-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	416	304	0	ENST00000326873.7:c.109C>T	p.Gln37Ter	p.Q37*	ENST00000326873	NM_000455.4	37	Cag/Tag	1/10	0.620471918465676	2	FACETS	0.993	0.957	1	0.993	0.957	1	CLONAL	2	TRUE	0	0.620471918465676	2		304	675	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957522	175957522	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010609-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	268	310	1	ENST00000367669.3:c.1874G>A	p.Trp625Ter	p.W625*	ENST00000367669	NM_022457.5	625	tGg/tAg	17/20	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.620471918465676	2		311	836	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893629	28893629	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010609-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	242	321	0	ENST00000282397.4:c.3217G>T	p.Asp1073Tyr	p.D1073Y	ENST00000282397	NM_002019.4	1073	Gac/Tac	24/30	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.620471918465676	2		321	755	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602746	10602746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010609-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	485	423	0	ENST00000171111.5:c.832C>T	p.Pro278Ser	p.P278S	ENST00000171111	NM_203500.1	278	Ccg/Tcg	3/6	0.620471918465676	2	FACETS	0.991	0.957	1	0.991	0.957	1	CLONAL	2	TRUE	0	0.620471918465676	2		423	789	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366106	15366106	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0010609-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	440	343	0	ENST00000263377.2:c.2047+2T>A		p.X683_splice	ENST00000263377	NM_058243.2	683			0.620471918465676	2	FACETS	0.942	0.907	0.976	0.942	0.907	0.976	CLONAL	2	TRUE	0	0.620471918465676	2		343	753	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584603	187584603	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010609-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	308	486	0	ENST00000441802.2:c.3430del	p.Tyr1144IlefsTer60	p.Y1144Ifs*60	ENST00000441802	NM_005245.3	1144	Tat/at	3/27	0.620471918465676	1	FACETS	0.951	0.903	1	0.951	0.903	1	CLONAL	1	TRUE	0	0.620471918465676	1		486	720	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247954	59247955	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0010609-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	284	402	0	ENST00000371222.2:c.788_789delinsTT	p.Arg263Leu	p.R263L	ENST00000371222	NM_002228.3	263	cGC/cTT	1/1	0.620471918465676	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.620471918465676	1		402	614	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0010650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	31	414	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		416	750	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0010650-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	32	489	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		489	691	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0010659-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	34	421	0	ENST00000374080.3:c.3670C>T	p.Leu1224Phe	p.L1224F	ENST00000374080		1224	Ctc/Ttc	26/45	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		421	574	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010662-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	1078	247	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.528656131046038	8	FACETS	0.975	0.955	0.994			1	CLONAL	7	TRUE	NA	0.528656131046038	8		247	1546	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968266	2968266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773909937	NA	P-0010662-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	413	487	0	ENST00000396946.4:c.1720G>A	p.Val574Ile	p.V574I	ENST00000396946	NM_032415.4	574	Gtc/Atc	13/25	0.455397967034837	4	FACETS	0.932	0.887	0.977	0.621	0.591	0.651	CLONAL	2	TRUE	1	0.528656131046038	4		487	1282	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809275	243809275	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010662-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	263	767	0	ENST00000263826.5:c.349A>T	p.Met117Leu	p.M117L	ENST00000263826	NM_005465.4	117	Atg/Ttg	4/13	1	2	FACETS	0.928	0.87	0.988	0.928	0.87	0.988	CLONAL	1	TRUE	1	0.528656131046038	2		767	1072	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38960628	38960628	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010662-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	112	305	0	ENST00000357387.3:c.1723C>G	p.Arg575Gly	p.R575G	ENST00000357387	NM_152756.3	575	Cga/Gga	20/38	0.528656131046038	2	FACETS	0.829	0.749	0.913	0.415	0.374	0.457	CLONAL	1	TRUE	0	0.528656131046038	2		305	511	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979347	93979347	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010662-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	301	692	0	ENST00000369303.4:c.1481A>C	p.Lys494Thr	p.K494T	ENST00000369303	NM_004440.3	494	aAa/aCa	7/17	0.274514142511052	3	FACETS	1	0.991	1	0.631	0.594	0.669	INDETERMINATE	1	TRUE	1	0.528656131046038	3		692	1141	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40458269	40458269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010668-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	157	3036	0	ENST00000345506.4:c.1484C>T	p.Pro495Leu	p.P495L	ENST00000345506	NM_003152.3	495	cCa/cTa	14/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.415092806487301	2		3036	681	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53254013	53254032	+	frameshift_variant	Frame_Shift_Del	DEL	CTAGGCTCGAACACCGGGCA	CTAGGCTCGAACACCGGGCA	-	novel	NA	P-0010668-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	153	2193	0	ENST00000375401.3:c.40_59del	p.Cys14LeufsTer54	p.C14Lfs*54	ENST00000375401	NM_004187.3	14	TGCCCGGTGTTCGAGCCTAGc/c	1/26	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.415092806487301	1		2193	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0010705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	163	618	1	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.322301124484196	1	FACETS	0.698	0.639	0.76	0.698	0.639	0.76	SUBCLONAL	1	TRUE	0	0.322301124484196	1		619	1215	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780192	9780192	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	123	563	0	ENST00000377346.4:c.1362C>A	p.Asn454Lys	p.N454K	ENST00000377346	NM_005026.3	454	aaC/aaA	11/24	1	2	FACETS	0.627	0.565	0.692	0.627	0.565	0.692	SUBCLONAL	1	TRUE	1	0.322301124484196	2		563	1218	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89791112	89791112	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	11	41	0	ENST00000336032.3:c.499C>A	p.Leu167Met	p.L167M	ENST00000336032	NM_006813.2	167	Ctg/Atg	1/2	1	2	FACETS	0.578	0.402	0.794	0.578	0.402	0.794	SUBCLONAL	1	TRUE	1	0.322301124484196	2		41	118	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200315	138200315	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	122	276	0	ENST00000237289.4:c.1733C>G	p.Ser578Cys	p.S578C	ENST00000237289	NM_001270507.1	578	tCt/tGt	7/9	0.308077800233614	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.322301124484196	1		276	594	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62009593	62009593	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	271	614	0	ENST00000392795.3:c.29C>A	p.Pro10His	p.P10H	ENST00000392795	NM_001039933.1	10	cCc/cAc	1/6	0.298739565607149	2	FACETS	1	0.991	1	0.669	0.627	0.712	CLONAL	1	TRUE	0	0.322301124484196	2		614	1257	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46738565	46739208	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTCCAGAGTCATCCTCATAGAGGCCACATGTGATTCCAACCCTACCCAAGGCATGAACCCTGCATTGTGGAGTCTGTTTACCAGACCCTTTGCTTTGGAAAATTGAACTCATCTTCTGTCCAGCCCATGCTTGATGACCTGGGATGTGTCGACTGTTTGTGAGTGCTTGCATGTACACACGCTCATATACAATGTTGGGCAGGAGGAAAAATAACAAAGAAACCTTGCCTGCTCTGTTATAGCTCCCTTCTTGTTGGGAGAACACATTAGTGAGTGAGATTGTCCATCCATCGTCCCAGATGGCACCGACTATATCCTGTTGGAATTTGGTAGGATGAAGATCAAGCAAGTCTGATGTTGAGGAAGGCCTTTTGGGCTAGGCTTCTAGAGGGAGTTCTAGTGAACACTGAAGTGGAAACTTCAGAAAGCAAAGTATCTGGGTTTTGTTTTGTTTTCTCCCAGATCCAGCTCTAATCTATGATAAGTGTGTGGAAGAGGAGGATGGCTTTGTGGGTGCCTTGGACCTCTTCCCTCCTGGTTACAGCTCTAAGGCCCTGGAGCCCCAGCTGTCAGGTGACCCTTTTCCTACCAGTATTTGGGCTTCTCTAGGAGGAGGGTGGGAGATTTTTTTTTGTGCTAGGGCT	GTCCAGAGTCATCCTCATAGAGGCCACATGTGATTCCAACCCTACCCAAGGCATGAACCCTGCATTGTGGAGTCTGTTTACCAGACCCTTTGCTTTGGAAAATTGAACTCATCTTCTGTCCAGCCCATGCTTGATGACCTGGGATGTGTCGACTGTTTGTGAGTGCTTGCATGTACACACGCTCATATACAATGTTGGGCAGGAGGAAAAATAACAAAGAAACCTTGCCTGCTCTGTTATAGCTCCCTTCTTGTTGGGAGAACACATTAGTGAGTGAGATTGTCCATCCATCGTCCCAGATGGCACCGACTATATCCTGTTGGAATTTGGTAGGATGAAGATCAAGCAAGTCTGATGTTGAGGAAGGCCTTTTGGGCTAGGCTTCTAGAGGGAGTTCTAGTGAACACTGAAGTGGAAACTTCAGAAAGCAAAGTATCTGGGTTTTGTTTTGTTTTCTCCCAGATCCAGCTCTAATCTATGATAAGTGTGTGGAAGAGGAGGATGGCTTTGTGGGTGCCTTGGACCTCTTCCCTCCTGGTTACAGCTCTAAGGCCCTGGAGCCCCAGCTGTCAGGTGACCCTTTTCCTACCAGTATTTGGGCTTCTCTAGGAGGAGGGTGGGAGATTTTTTTTTGTGCTAGGGCT	-	novel	NA	P-0010705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	77	127	0	ENST00000371975.4:c.1375+95_1486+75del		p.X459_splice	ENST00000371975	NM_003579.3	459		13/18	1	2	FACETS	0.944	0.84	1	1	0.984	1	CLONAL	2	TRUE	1	0.322301124484196	2		127	253	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0010707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	56	474	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.242394673986616	1	FACETS	0.466	0.401	0.536	0.466	0.401	0.536	INDETERMINATE	1	TRUE	0	0.514836495306278	1		474	347	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755612	57755612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	103	385	1	ENST00000274289.3:c.175C>T	p.His59Tyr	p.H59Y	ENST00000274289	NM_006622.3	59	Cat/Tat	1/14	0.415932829653834	3	FACETS	0.545	0.486	0.606			1	SUBCLONAL	1	TRUE	NA	0.514836495306278	3		386	924	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319899	8319899	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	362	536	0	ENST00000356435.5:c.5602G>T	p.Gly1868Ter	p.G1868*	ENST00000356435		1868	Gga/Tga	34/35	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.514836495306278	2		536	1291	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736811	736811	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	319	628	0	ENST00000314574.4:c.1288C>T	p.Gln430Ter	p.Q430*	ENST00000314574	NM_005433.3	430	Caa/Taa	10/12	1	2	FACETS	0.822	0.774	0.871	0.822	0.774	0.871	CLONAL	1	TRUE	1	0.514836495306278	2		628	1508	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	705	373	1	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	0.660334900621807	3	FACETS	0.961	0.929	0.992	0.64	0.619	0.661	CLONAL	2	TRUE	0	0.662318788320185	3		374	1475	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776011	9776011	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	428	283	0	ENST00000377346.4:c.475T>A	p.Trp159Arg	p.W159R	ENST00000377346	NM_005026.3	159	Tgg/Agg	5/24	0.662318788320185	4	FACETS	1	0.995	1	0.356	0.338	0.374	CLONAL	1	TRUE	0	0.662318788320185	4		283	1509	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439730	51439730	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	323	283	0	ENST00000262662.1:c.295G>T	p.Glu99Ter	p.E99*	ENST00000262662		99	Gag/Tag	4/4	0.601289545141549	3	FACETS	1	0.989	1			1	CLONAL	1	TRUE	NA	0.662318788320185	3		283	1109	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838344	156838344	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2108	298	359	0	ENST00000524377.1:c.622G>T	p.Gly208Trp	p.G208W	ENST00000524377	NM_002529.3	208	Ggg/Tgg	6/17	0.662318788320185	6	FACETS	0.869	0.814	0.926			1	CLONAL	1	TRUE	NA	0.662318788320185	6		359	2406	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740252	162740252	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2094	122	314	0	ENST00000367921.3:c.1454C>G	p.Ser485Cys	p.S485C	ENST00000367921	NM_006182.2	485	tCc/tGc	12/18	0.662318788320185	6	FACETS	0.386	0.347	0.428			1	SUBCLONAL	1	TRUE	NA	0.662318788320185	6		314	2216	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518745	204518745	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	276	263	0	ENST00000367182.3:c.1408G>T	p.Ala470Ser	p.A470S	ENST00000367182	NM_001278516.1	470	Gct/Tct	11/11	0.203711131750199	3	FACETS	1	0.992	1	0.654	0.616	0.693	INDETERMINATE	1	TRUE	1	0.662318788320185	3		263	848	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172272	99172272	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs374507988	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	312	295	0	ENST00000074304.5:c.1837+1G>T		p.X613_splice	ENST00000074304	NM_001134224.1	613			0.203711131750199	3	FACETS	1	0.992	1	0.638	0.603	0.674	INDETERMINATE	1	TRUE	1	0.662318788320185	3		295	983	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430673	181430673	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1202812531	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	181	251	0	ENST00000325404.1:c.525G>T	p.Gln175His	p.Q175H	ENST00000325404	NM_003106.3	175	caG/caT	1/1	0.633468398219105	5	FACETS	0.94	0.866	1	0.235	0.216	0.255	CLONAL	1	TRUE	1	0.662318788320185	5		251	1159	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139846	55139846	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	191	255	0	ENST00000257290.5:c.1507G>C	p.Ala503Pro	p.A503P	ENST00000257290	NM_006206.4	503	Gct/Cct	10/23	0.662318788320185	3	FACETS	0.75	0.693	0.809	0.375	0.346	0.405	SUBCLONAL	1	TRUE	1	0.662318788320185	3		255	1024	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630977	187630977	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	185	195	0	ENST00000441802.2:c.5G>T	p.Gly2Val	p.G2V	ENST00000441802	NM_005245.3	2	gGg/gTg	2/27	0.662318788320185	2	FACETS	0.881	0.817	0.947	0.441	0.408	0.474	CLONAL	1	TRUE	0	0.662318788320185	2		195	634	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235396	235396	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1850	260	295	0	ENST00000264932.6:c.1202C>T	p.Pro401Leu	p.P401L	ENST00000264932	NM_004168.2	401	cCt/cTt	9/15	0.662318788320185	6	FACETS	0.865	0.807	0.926	0.216	0.201	0.232	CLONAL	1	TRUE	2	0.662318788320185	6		295	2110	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294051	1294051	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2449	642	414	0	ENST00000310581.5:c.950G>T	p.Trp317Leu	p.W317L	ENST00000310581	NM_198253.2	317	tGg/tTg	2/16	0.662318788320185	6	FACETS	1	0.997	1	0.364	0.349	0.38	CLONAL	1	TRUE	2	0.662318788320185	6		414	3091	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35860965	35860965	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1527	216	198	0	ENST00000303115.3:c.94G>A	p.Asp32Asn	p.D32N	ENST00000303115	NM_002185.3	32	Gat/Aat	2/8	0.662318788320185	6	FACETS	0.87	0.806	0.937	0.217	0.201	0.235	CLONAL	1	TRUE	2	0.662318788320185	6		198	1743	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874565	35874565	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs141111406	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2539	365	394	0	ENST00000303115.3:c.721A>G	p.Ile241Val	p.I241V	ENST00000303115	NM_002185.3	241	Atc/Gtc	6/8	0.662318788320185	6	FACETS	0.882	0.832	0.934	0.221	0.208	0.234	CLONAL	1	TRUE	2	0.662318788320185	6		394	2904	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876316	35876316	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1867	222	266	0	ENST00000303115.3:c.1108C>A	p.Leu370Met	p.L370M	ENST00000303115	NM_002185.3	370	Ctg/Atg	8/8	0.662318788320185	6	FACETS	0.746	0.691	0.803	0.186	0.172	0.201	SUBCLONAL	1	TRUE	2	0.662318788320185	6		266	2089	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876530	35876530	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1576	102	209	0	ENST00000303115.3:c.1322T>C	p.Leu441Pro	p.L441P	ENST00000303115	NM_002185.3	441	cTg/cCg	8/8	0.662318788320185	6	FACETS	0.427	0.38	0.477	0.107	0.095	0.12	SUBCLONAL	1	TRUE	2	0.662318788320185	6		209	1678	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166275	32166275	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	693	350	0	ENST00000375023.3:c.4679C>A	p.Ala1560Glu	p.A1560E	ENST00000375023	NM_004557.3	1560	gCg/gAg	26/30	0.662318788320185	2	FACETS	0.963	0.936	0.989	0.963	0.936	0.989	CLONAL	2	TRUE	0	0.662318788320185	2		350	1087	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969939	161969939	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	318	346	0	ENST00000366898.1:c.1030G>A	p.Glu344Lys	p.E344K	ENST00000366898	NM_004562.2	344	Gag/Aag	9/12	0.662318788320185	2	FACETS	1	0.947	1	0.501	0.473	0.528	CLONAL	1	TRUE	0	0.662318788320185	2		346	959	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959081	2959081	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	339	339	0	ENST00000396946.4:c.2435A>G	p.His812Arg	p.H812R	ENST00000396946	NM_032415.4	812	cAc/cGc	18/25	0.662318788320185	3	FACETS	0.991	0.936	1	0.496	0.468	0.524	CLONAL	1	TRUE	1	0.662318788320185	3		339	1375	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729984	41729984	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs766987359	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1638	592	553	2	ENST00000242208.4:c.545C>A	p.Pro182Gln	p.P182Q	ENST00000242208	NM_002192.2	182	cCg/cAg	3/3	0.662318788320185	3	FACETS	1	0.987	1	0.534	0.511	0.556	CLONAL	1	TRUE	1	0.662318788320185	3		555	2230	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341160	8341160	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	271	311	0	ENST00000356435.5:c.5056G>C	p.Val1686Leu	p.V1686L	ENST00000356435		1686	Gta/Cta	30/35	0.662318788320185	3	FACETS	0.901	0.845	0.959	0.451	0.422	0.48	CLONAL	1	TRUE	1	0.662318788320185	3		311	1209	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484345	8484345	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	205	276	0	ENST00000356435.5:c.3187G>C	p.Val1063Leu	p.V1063L	ENST00000356435		1063	Gtg/Ctg	19/35	0.662318788320185	3	FACETS	0.787	0.73	0.847	0.394	0.365	0.424	SUBCLONAL	1	TRUE	1	0.662318788320185	3		276	1047	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333051	70333051	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	976	389	0	ENST00000373644.4:c.956G>T	p.Gly319Val	p.G319V	ENST00000373644	NM_030625.2	319	gGg/gTg	2/12	0.137410534005749	3	FACETS	0.957	0.937	0.976			1	INDETERMINATE	3	TRUE	NA	0.662318788320185	3		389	1367	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574547	64574547	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	365	353	0	ENST00000312049.6:c.848T>C	p.Leu283Pro	p.L283P	ENST00000312049	NM_130799.2	283	cTg/cCg	6/10	1	2	FACETS	0.969	0.919	1	0.969	0.919	1	CLONAL	1	TRUE	1	0.662318788320185	2		353	1138	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121778	108121778	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	180	202	0	ENST00000278616.4:c.1586G>T	p.Gly529Val	p.G529V	ENST00000278616	NM_000051.3	529	gGg/gTg	10/63	1	2	FACETS	0.926	0.859	0.995	0.926	0.859	0.995	CLONAL	1	TRUE	1	0.662318788320185	2		202	587	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144576	119144576	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	59	223	0	ENST00000264033.4:c.591-2A>T		p.X197_splice	ENST00000264033	NM_005188.3	197			0.13297738865745	4	FACETS	0.362	0.311	0.418			1	INDETERMINATE	1	TRUE	NA	0.662318788320185	4		223	818	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442694	442694	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	869	366	0	ENST00000399788.2:c.1612A>T	p.Thr538Ser	p.T538S	ENST00000399788	NM_001042603.1	538	Acc/Tcc	12/28	0.662318788320185	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	2	0.662318788320185	4		366	2065	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944879	31944879	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs372444480	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	508	256	0	ENST00000340398.3:c.222C>G	p.Ile74Met	p.I74M	ENST00000340398	NM_001013699.2	74	atC/atG	1/1	0.662318788320185	4	FACETS	0.959	0.92	0.999	0.959	0.92	0.999	CLONAL	2	TRUE	2	0.662318788320185	4		256	1329	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346016	73346016	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	244	223	0	ENST00000377767.4:c.1522G>T	p.Asp508Tyr	p.D508Y	ENST00000377767	NM_014953.3	508	Gat/Tat	11/21	0.660334900621807	3	FACETS	1	0.986	1	0.393	0.368	0.419	CLONAL	1	TRUE	0	0.662318788320185	3		223	832	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515219	103515219	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	907	299	0	ENST00000355739.4:c.1720G>T	p.Ala574Ser	p.A574S	ENST00000355739	NM_000123.3	574	Gct/Tct	8/15	0.660334900621807	3	FACETS	0.952	0.932	0.973	0.952	0.932	0.973	CLONAL	3	TRUE	0	0.662318788320185	3		299	1276	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544640	65544640	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	737	353	1	ENST00000358664.4:c.286G>T	p.Glu96Ter	p.E96*	ENST00000358664	NM_002382.4	96	Gag/Tag	4/5	0.616419462297913	3	FACETS	0.925	0.902	0.948	0.925	0.902	0.948	CLONAL	3	TRUE	0	0.662318788320185	3		354	1067	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007636	45007636	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	114	197	0	ENST00000558401.1:c.83A>T	p.Gln28Leu	p.Q28L	ENST00000558401	NM_004048.2	28	cAg/cTg	2/4	1	2	FACETS	0.642	0.58	0.707	0.642	0.58	0.707	SUBCLONAL	1	TRUE	1	0.662318788320185	2		197	536	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007672	45007672	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	132	212	0	ENST00000558401.1:c.119C>G	p.Ser40Ter	p.S40*	ENST00000558401	NM_004048.2	40	tCa/tGa	2/4	1	2	FACETS	0.636	0.579	0.695	0.636	0.579	0.695	SUBCLONAL	1	TRUE	1	0.662318788320185	2		212	627	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347474	91347474	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	381	340	0	ENST00000355112.3:c.3636A>C	p.Glu1212Asp	p.E1212D	ENST00000355112	NM_000057.2	1212	gaA/gaC	19/22	1	2	FACETS	0.952	0.904	1	0.952	0.904	1	CLONAL	1	TRUE	1	0.662318788320185	2		340	1209	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992298	72992298	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	544	552	0	ENST00000268489.5:c.1747G>T	p.Glu583Ter	p.E583*	ENST00000268489	NM_006885.3	583	Gag/Tag	2/10	0.662318788320185	2	FACETS	0.947	0.908	0.988	0.474	0.454	0.494	CLONAL	1	TRUE	0	0.662318788320185	2		552	1734	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993039	72993039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	1192	549	0	ENST00000268489.5:c.1006C>T	p.Leu336Phe	p.L336F	ENST00000268489	NM_006885.3	336	Ctt/Ttt	2/10	0.662318788320185	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.662318788320185	2		549	1734	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819711	81819711	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	487	457	0	ENST00000359376.3:c.117G>T	p.Glu39Asp	p.E39D	ENST00000359376	NM_002661.3	39	gaG/gaT	2/33	0.662318788320185	2	FACETS	0.976	0.933	1	0.488	0.466	0.51	CLONAL	1	TRUE	0	0.662318788320185	2		457	1506	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942049	81942049	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1013382788	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	525	478	0	ENST00000359376.3:c.1586G>T	p.Gly529Val	p.G529V	ENST00000359376	NM_002661.3	529	gGg/gTg	17/33	0.662318788320185	2	FACETS	1	0.98	1	0.518	0.496	0.541	CLONAL	1	TRUE	0	0.662318788320185	2		478	1529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	938	455	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.662318788320185	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.662318788320185	2		455	1378	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553474	29553474	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779546178	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	199	271	0	ENST00000356175.3:c.2023G>A	p.Gly675Arg	p.G675R	ENST00000356175	NM_000267.3	675	Gga/Aga	18/57	0.662318788320185	3	FACETS	0.572	0.528	0.617	0.286	0.264	0.309	SUBCLONAL	1	TRUE	1	0.662318788320185	3		271	1399	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663413	29663413	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555534607	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	461	290	0	ENST00000356175.3:c.6006G>C	p.Leu2002Phe	p.L2002F	ENST00000356175	NM_000267.3	2002	ttG/ttC	40/57	0.662318788320185	3	FACETS	0.781	0.747	0.815	0.781	0.747	0.815	SUBCLONAL	2	TRUE	1	0.662318788320185	3		290	1186	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39537584	39537584	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	642	303	0	ENST00000262039.4:c.118G>T	p.Glu40Ter	p.E40*	ENST00000262039	NM_002647.2	40	Gaa/Taa	2/25	0.662318788320185	3	FACETS	0.94	0.907	0.972	0.94	0.907	0.972	CLONAL	2	TRUE	1	0.662318788320185	3		303	1373	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14628993	14628993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1516	204	468	0	ENST00000254322.2:c.169G>A	p.Asp57Asn	p.D57N	ENST00000254322	NM_006145.1	57	Gac/Aac	1/3	0.660334900621807	3	FACETS	0.477	0.44	0.515	0.159	0.146	0.172	SUBCLONAL	1	TRUE	0	0.662318788320185	3		468	1720	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271516	15271516	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1188	446	383	0	ENST00000263388.2:c.6923G>T	p.Gly2308Val	p.G2308V	ENST00000263388	NM_000435.2	2308	gGg/gTg	33/33	0.660334900621807	3	FACETS	1	0.987	1	0.366	0.348	0.384	CLONAL	1	TRUE	0	0.662318788320185	3		383	1634	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302372	15302372	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1274	385	409	0	ENST00000263388.2:c.899G>T	p.Cys300Phe	p.C300F	ENST00000263388	NM_000435.2	300	tGc/tTc	6/33	0.660334900621807	3	FACETS	0.933	0.884	0.983	0.311	0.294	0.328	CLONAL	1	TRUE	0	0.662318788320185	3		409	1659	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302679	15302679	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	583	370	0	ENST00000263388.2:c.680-1G>C		p.X227_splice	ENST00000263388	NM_000435.2	227			0.660334900621807	3	FACETS	1	0.997	1	0.493	0.474	0.513	CLONAL	1	TRUE	0	0.662318788320185	3		370	1584	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955129	17955129	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	1240	313	0	ENST00000458235.1:c.98G>T	p.Arg33Leu	p.R33L	ENST00000458235	NM_000215.3	33	cGg/cTg	2/24	0.601289545141549	3	FACETS	1	0.998	1			1	CLONAL	3	TRUE	NA	0.662318788320185	3		313	1518	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714660	52714660	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1248	127	325	0	ENST00000322088.6:c.418T>A	p.Trp140Arg	p.W140R	ENST00000322088	NM_014225.5	140	Tgg/Agg	4/15	0.601289545141549	3	FACETS	0.371	0.335	0.41			1	SUBCLONAL	1	TRUE	NA	0.662318788320185	3		325	1375	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932488	39932488	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs754225503	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1564	84	218	0	ENST00000378444.4:c.2111A>G	p.Tyr704Cys	p.Y704C	ENST00000378444	NM_001123385.1	704	tAt/tGt	4/15	0.662318788320185	4	FACETS	0.256	0.225	0.29			1	SUBCLONAL	1	TRUE	NA	0.662318788320185	4		218	1648	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446423	49446423	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	362	292	0	ENST00000301067.7:c.1182del	p.Gln395SerfsTer7	p.Q395Sfs*7	ENST00000301067	NM_003482.3	394	ggG/gg	9/54	0.662318788320185	3	FACETS	1	0.987	1	0.561	0.531	0.591	CLONAL	1	TRUE	1	0.662318788320185	3		292	1298	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741392	145741395	+	frameshift_variant	Frame_Shift_Del	DEL	TACG	TACG	-	novel	NA	P-0010715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1465	974	447	0	ENST00000428558.2:c.1108_1111del	p.Arg370AlafsTer35	p.R370Afs*35	ENST00000428558	NM_004260.3	370	CGTAgc/gc	5/22	0.662318788320185	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.662318788320185	4		447	2439	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246390	53246390	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	26	353	0	ENST00000375401.3:c.592C>T	p.Arg198Ter	p.R198*	ENST00000375401	NM_004187.3	198	Cga/Tga	5/26	0.192644549978502	2	FACETS	0.347	0.274	0.431			1	INDETERMINATE	1	FALSE	NA	0.338290573015447	2		353	443	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226561964	226561964	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	115	498	1	ENST00000366794.5:c.2033A>G	p.Asp678Gly	p.D678G	ENST00000366794	NM_001618.3	678	gAt/gGt	14/23	NA	2	FACETS	0.994	0.897	1			1	INDETERMINATE	1	FALSE	NA	0.338290573015447	2		499	684	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31025090	31025090	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	163	315	0	ENST00000375687.4:c.4575T>A	p.Asp1525Glu	p.D1525E	ENST00000375687	NM_015338.5	1525	gaT/gaA	13/13	0.166791840441328	4	FACETS	0.908	0.836	0.984	0.908	0.836	0.984	INDETERMINATE	2	FALSE	2	0.338290573015447	4		315	710	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720654	89720654	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	12	77	0	ENST00000371953.3:c.808del	p.Met270CysfsTer6	p.M270Cfs*6	ENST00000371953	NM_000314.4	269	Aaa/aa	8/9	1	2	FACETS	1	0.726	1	1	0.726	1	CLONAL	1	TRUE	1	0.19	2		77	123	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549134	21549134	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	54	621	1	ENST00000382592.4:c.3142G>T	p.Asp1048Tyr	p.D1048Y	ENST00000382592	NM_014572.2	1048	Gac/Tac	8/8	1	2	FACETS	0.727	0.619	0.845	0.727	0.619	0.845	SUBCLONAL	1	TRUE	1	0.19	2		622	782	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798382	42798382	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	39	487	0	ENST00000575354.2:c.4253C>G	p.Ser1418Cys	p.S1418C	ENST00000575354	NM_015125.3	1418	tCc/tGc	18/20	0.199601967319845	1	FACETS	0.922	0.765	1	0.922	0.765	1	CLONAL	1	TRUE	0	0.19	1		487	403	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428531	72428542	+	inframe_deletion	In_Frame_Del	DEL	TGTTGTGCCACT	TGTTGTGCCACT	-	novel	NA	P-0010731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	31	414	0	ENST00000477973.2:c.460_471del	p.Val155_Gln158del	p.V155_Q158del	ENST00000477973	NM_012234.5	154	caAGTGGCACAACAg/cag	2/4	0.3	1	FACETS	0.588	0.475	0.717	0.588	0.475	0.717	SUBCLONAL	1	TRUE	0	0.19	1		414	502	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631839	90631839	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519906	NA	P-0010739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	283	376	0	ENST00000330062.3:c.514A>T	p.Arg172Trp	p.R172W	ENST00000330062	NM_002168.2	172	Agg/Tgg	4/11	1	2	FACETS	0.999	0.945	1	0.999	0.945	1	CLONAL	1	TRUE	1	0.8	2		376	708	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127406	17127407	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0010739-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	286	340	0	ENST00000285071.4:c.447_448del	p.Phe150CysfsTer49	p.F150Cfs*49	ENST00000285071	NM_144997.5	149	ggCTtt/ggtt	6/14	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.8	2		340	707	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0010748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	182	484	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	0.192457375339298	1	FACETS	0.841	0.777	0.907	0.841	0.777	0.907	INDETERMINATE	1	TRUE	0	0.435741518386777	1		484	777	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0010749-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	47	450	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	1	2	FACETS	0.424	0.356	0.499	0.424	0.356	0.499	SUBCLONAL	1	TRUE	1	0.24	2		450	924	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247958	59247958	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010749-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	58	447	0	ENST00000371222.2:c.785A>G	p.Asn262Ser	p.N262S	ENST00000371222	NM_002228.3	262	aAc/aGc	1/1	1	2	FACETS	0.541	0.463	0.626	0.541	0.463	0.626	SUBCLONAL	1	TRUE	1	0.24	2		447	894	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197342	26197342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010749-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1694	103	948	0	ENST00000356476.2:c.137C>T	p.Thr46Met	p.T46M	ENST00000356476		46	aCg/aTg	1/1	1	2	FACETS	0.478	0.425	0.534	0.478	0.425	0.534	SUBCLONAL	1	TRUE	1	0.24	2		948	1797	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588847	29588847	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs757165176	NA	P-0010749-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	60	458	0	ENST00000356175.3:c.4633A>G	p.Ser1545Gly	p.S1545G	ENST00000356175	NM_000267.3	1545	Agt/Ggt	34/57	1	2	FACETS	0.542	0.465	0.625	0.542	0.465	0.625	SUBCLONAL	1	TRUE	1	0.24	2		458	923	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554540	63554540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010749-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	60	348	0	ENST00000307078.5:c.199G>A	p.Gly67Arg	p.G67R	ENST00000307078	NM_004655.3	67	Ggg/Agg	2/11	1	2	FACETS	0.529	0.454	0.61	0.529	0.454	0.61	SUBCLONAL	1	TRUE	1	0.24	2		348	946	SUCCESS
APC	324	MSKCC	GRCh37	5	112175349	112175356	+	frameshift_variant	Frame_Shift_Del	DEL	AATTTTCT	AATTTTCT	-	novel	NA	P-0010749-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	36	238	0	ENST00000257430.4:c.4058_4065del	p.Glu1353ValfsTer19	p.E1353Vfs*19	ENST00000257430	NM_000038.5	1353	gAATTTTCT/g	16/16	1	2	FACETS	0.539	0.442	0.647	0.539	0.442	0.647	SUBCLONAL	1	TRUE	1	0.24	2		238	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0010751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	231	439	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.272413897743099	2	FACETS	0.994	0.929	1	0.994	0.929	1	CLONAL	2	TRUE	0	0.272413897743099	2		439	853	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0010751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	30	282	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	1	0.823	1	1	0.823	1	CLONAL	1	TRUE	1	0.272413897743099	2		283	217	SUCCESS
APC	324	MSKCC	GRCh37	5	112175171	112175171	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085373	NA	P-0010751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	12	148	0	ENST00000257430.4:c.3880C>T	p.Gln1294Ter	p.Q1294*	ENST00000257430	NM_000038.5	1294	Cag/Tag	16/16	1	2	FACETS	0.831	0.59	1	0.831	0.59	1	CLONAL	1	TRUE	1	0.272413897743099	2		148	106	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248514	59248514	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	106	400	0	ENST00000371222.2:c.229G>T	p.Glu77Ter	p.E77*	ENST00000371222	NM_002228.3	77	Gag/Tag	1/1	1	2	FACETS	0.801	0.717	0.891	0.801	0.717	0.891	CLONAL	1	TRUE	1	0.272413897743099	2		400	971	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911379	32911379	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	54	718	0	ENST00000380152.3:c.2887A>G	p.Ile963Val	p.I963V	ENST00000380152		963	Ata/Gta	11/27	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.272413897743099	2		718	367	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120351	70120351	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0010751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1537	375	853	0	ENST00000245479.2:c.1353C>G	p.Tyr451Ter	p.Y451*	ENST00000245479	NM_000346.3	451	taC/taG	3/3	0.208480995597334	4	FACETS	0.916	0.866	0.967	0.916	0.866	0.967	CLONAL	2	TRUE	2	0.272413897743099	4		853	1912	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061226	38061237	+	inframe_deletion	In_Frame_Del	DEL	CGAACATGTTGC	CGAACATGTTGC	-	novel	NA	P-0010752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	34	416	0	ENST00000250448.2:c.752_763del	p.Gly251_Phe254del	p.G251_F254del	ENST00000250448	NM_004496.3	251	gGCAACATGTTCGag/gag	2/2	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.12	2		416	527	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512425	149512425	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	33	443	0	ENST00000261799.4:c.1015G>C	p.Val339Leu	p.V339L	ENST00000261799	NM_002609.3	339	Gtg/Ctg	7/23	1	2	FACETS	0.902	0.733	1	0.902	0.733	1	CLONAL	1	TRUE	1	0.12	2		443	610	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143315	108143315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	17	471	0	ENST00000278616.4:c.3134G>A	p.Cys1045Tyr	p.C1045Y	ENST00000278616	NM_000051.3	1045	tGc/tAc	21/63	1	2	FACETS	0.92	0.686	1	0.92	0.686	1	CLONAL	1	TRUE	1	0.12	2		471	308	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917490	178917490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	183	341	0	ENST00000263967.3:c.365G>A	p.Gly122Asp	p.G122D	ENST00000263967	NM_006218.2	122	gGc/gAc	3/21	0.811002913038361	3	FACETS	0.982	0.911	1	0.491	0.455	0.528	CLONAL	1	TRUE	1	0.812304334430664	3		341	645	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005125	150005125	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1276383398	NA	P-0010758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	49	531	0	ENST00000253339.5:c.1100C>G	p.Thr367Ser	p.T367S	ENST00000253339		367	aCt/aGt	3/7	0.811002913038361	3	FACETS	0.185	0.156	0.218	0.093	0.078	0.109	SUBCLONAL	1	TRUE	1	0.812304334430664	3		531	916	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729875	41729875	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	372	756	0	ENST00000242208.4:c.654G>C	p.Trp218Cys	p.W218C	ENST00000242208	NM_002192.2	218	tgG/tgC	3/3	0.811002913038361	3	FACETS	1	0.952	1	0.502	0.476	0.528	CLONAL	1	TRUE	1	0.812304334430664	3		756	1283	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438375	110438375	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	15	34	0	ENST00000375856.3:c.26C>G	p.Pro9Arg	p.P9R	ENST00000375856	NM_003749.2	9	cCg/cGg	1/2	0.811002913038361	4	FACETS	1	0.863	1	0.31	0.234	0.394	CLONAL	1	TRUE	0	0.812304334430664	4		34	54	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663349	67663349	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	343	611	2	ENST00000264010.4:c.1750G>C	p.Glu584Gln	p.E584Q	ENST00000264010	NM_006565.3	584	Gag/Cag	10/12	0.770020053809034	3	FACETS	0.934	0.884	0.986	0.467	0.442	0.493	CLONAL	1	TRUE	1	0.812304334430664	3		613	1271	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41222971	41222971	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	2015	750	11	ENST00000357654.3:c.4960del	p.Val1654CysfsTer4	p.V1654Cfs*4	ENST00000357654	NM_007294.3	1654	Gtg/tg	15/23	0.798904848516922	5	FACETS	1	0.996	1			1	CLONAL	5	TRUE	NA	0.812304334430664	5		761	2186	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579422	7579434	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCTGGTGCAGG	GGGCTGGTGCAGG	CAC	novel	NA	P-0010758-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	824	442	8	ENST00000269305.4:c.253_265delinsGTG	p.Pro85ValfsTer35	p.P85Vfs*35	ENST00000269305	NM_001126112.2	85	CCTGCACCAGCCCcc/GTGcc	4/11	0.811002913038361	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.812304334430664	3		450	944	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0010765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	120	663	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.297741593244754	8	FACETS	1	0.974	1	0.207	0.186	0.229	CLONAL	1	TRUE	2	0.36	8		663	1116	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0010765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	422	606	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.297741593244754	8	FACETS	1	0.99	1	0.747	0.713	0.781	CLONAL	4	TRUE	2	0.36	8		606	1088	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0010765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	84	343	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.195325765387338	2	FACETS	0.935	0.829	1	0.468	0.414	0.525	INDETERMINATE	1	TRUE	0	0.36	2		343	499	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042185	42042185	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0010765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	107	1090	0	ENST00000219905.7:c.6380C>G	p.Ser2127Ter	p.S2127*	ENST00000219905	NM_001164273.1	2127	tCa/tGa	17/24	0.19661748900819	3	FACETS	1	0.962	1	0.381	0.343	0.422	INDETERMINATE	1	TRUE	0	0.36	3		1090	613	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608351	43608351	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	79	731	2	ENST00000355710.3:c.1699G>T	p.Asp567Tyr	p.D567Y	ENST00000355710	NM_020975.4	567	Gac/Tac	9/20	0.297741593244754	3	FACETS	0.618	0.543	0.699	0.206	0.181	0.233	SUBCLONAL	1	TRUE	0	0.36	3		733	838	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363589	40363589	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1328955180	NA	P-0010765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	114	481	1	ENST00000397332.2:c.640C>T	p.Arg214Trp	p.R214W	ENST00000397332	NM_001033082.2	214	Cgg/Tgg	3/3	0.19661748900819	3	FACETS	1	0.916	1	0.339	0.305	0.375	INDETERMINATE	1	TRUE	0	0.36	3		482	734	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532645	46532645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	56	660	0	ENST00000262741.5:c.433C>T	p.Leu145Phe	p.L145F	ENST00000262741	NM_003629.3	145	Ctt/Ttt	4/10	0.19661748900819	3	FACETS	0.589	0.504	0.682	0.196	0.168	0.228	INDETERMINATE	1	TRUE	0	0.36	3		660	623	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303748	65303748	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	62	659	0	ENST00000342505.4:c.3007G>C	p.Asp1003His	p.D1003H	ENST00000342505	NM_002227.2	1003	Gac/Cac	22/25	0.19661748900819	3	FACETS	0.608	0.525	0.699	0.203	0.175	0.233	INDETERMINATE	1	TRUE	0	0.36	3		659	668	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026836	48026836	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064795256	NA	P-0010765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	44	640	2	ENST00000234420.5:c.1714C>T	p.Gln572Ter	p.Q572*	ENST00000234420	NM_000179.2	572	Cag/Tag	4/10	0.297741593244754	3	FACETS	0.542	0.454	0.64	0.181	0.151	0.214	SUBCLONAL	1	TRUE	0	0.36	3		642	532	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026983	48026983	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	38	721	0	ENST00000234420.5:c.1861C>G	p.Leu621Val	p.L621V	ENST00000234420	NM_000179.2	621	Ctg/Gtg	4/10	0.297741593244754	3	FACETS	0.472	0.389	0.564	0.157	0.129	0.188	SUBCLONAL	1	TRUE	0	0.36	3		721	528	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125251	47125251	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	82	802	0	ENST00000409792.3:c.6019G>A	p.Asp2007Asn	p.D2007N	ENST00000409792	NM_014159.6	2007	Gat/Aat	12/21	0.297741593244754	3	FACETS	0.927	0.818	1	0.309	0.272	0.348	CLONAL	1	TRUE	0	0.36	3		802	580	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125359	47125359	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	84	1001	2	ENST00000409792.3:c.5911G>A	p.Glu1971Lys	p.E1971K	ENST00000409792	NM_014159.6	1971	Gaa/Aaa	12/21	0.297741593244754	3	FACETS	0.985	0.872	1	0.328	0.29	0.369	CLONAL	1	TRUE	0	0.36	3		1003	559	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534356	187534356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770029391	NA	P-0010765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	54	608	1	ENST00000441802.2:c.9370G>A	p.Glu3124Lys	p.E3124K	ENST00000441802	NM_005245.3	3124	Gaa/Aaa	13/27	0.176026075782886	3	FACETS	0.593	0.506	0.688	0.198	0.168	0.23	INDETERMINATE	1	TRUE	0	0.36	3		609	597	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294448	1294448	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770436206	NA	P-0010765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	34	347	0	ENST00000310581.5:c.553C>T	p.Arg185Trp	p.R185W	ENST00000310581	NM_198253.2	185	Cgg/Tgg	2/16	0.297741593244754	6	FACETS	0.528	0.43	0.639	0.132	0.107	0.16	SUBCLONAL	1	TRUE	2	0.36	6		347	615	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111982974	111982974	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	138	924	0	ENST00000368678.4:c.1573G>C	p.Glu525Gln	p.E525Q	ENST00000368678		525	Gag/Cag	13/13	0.297741593244754	3	FACETS	1	0.949	1			1	CLONAL	1	TRUE	NA	0.36	3		924	851	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14027714	14027714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	71	771	0	ENST00000405192.2:c.130G>A	p.Glu44Lys	p.E44K	ENST00000405192	NM_001163147.1	44	Gaa/Aaa	3/12	0.297741593244754	8	FACETS	0.974	0.849	1	0.162	0.141	0.185	CLONAL	1	TRUE	2	0.36	8		771	842	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372490	55372490	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	64	738	0	ENST00000297316.4:c.1180G>C	p.Ala394Pro	p.A394P	ENST00000297316	NM_022454.3	394	Gcc/Ccc	2/2	0.176026075782886	3	FACETS	0.648	0.561	0.743	0.216	0.187	0.248	INDETERMINATE	1	TRUE	0	0.36	3		738	647	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312418	91312418	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	66	684	0	ENST00000355112.3:c.2363T>A	p.Leu788His	p.L788H	ENST00000355112	NM_000057.2	788	cTc/cAc	11/22	0.19661748900819	3	FACETS	0.543	0.47	0.622	0.181	0.156	0.208	INDETERMINATE	1	TRUE	0	0.36	3		684	797	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126076	2126076	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45476100	NA	P-0010765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	127	678	2	ENST00000219476.3:c.2647C>T	p.Gln883Ter	p.Q883*	ENST00000219476	NM_000548.3	883	Cag/Tag	24/42	0.297741593244754	5	FACETS	0.951	0.86	1	0.238	0.215	0.262	CLONAL	1	TRUE	1	0.36	5		680	1142	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748473	40748473	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	115	720	0	ENST00000392038.2:c.409G>T	p.Glu137Ter	p.E137*	ENST00000392038	NM_001626.4	137	Gaa/Taa	5/14	0.297741593244754	4	FACETS	0.952	0.856	1	0.476	0.428	0.527	CLONAL	1	TRUE	2	0.36	4		720	913	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239895	53239895	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	142	912	0	ENST00000375401.3:c.1546G>C	p.Glu516Gln	p.E516Q	ENST00000375401	NM_004187.3	516	Gag/Cag	11/26	0.2822850653625	2	FACETS	0.907	0.826	0.991	0.453	0.413	0.496	CLONAL	1	TRUE	0	0.36	2		912	870	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0010782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	532	715	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.67685542185377	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.67685542185377	2		715	714	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0010782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	565	801	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.67685542185377	2	FACETS	0.995	0.966	1	0.995	0.966	1	CLONAL	2	TRUE	0	0.67685542185377	2		801	839	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0010782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	471	645	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.67685542185377	2		645	1213	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429355	47429355	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	51	424	0	ENST00000377045.4:c.1483T>A	p.Tyr495Asn	p.Y495N	ENST00000377045	NM_001654.4	495	Tac/Aac	14/16	NA	2	FACETS	0.163	0.137	0.191			1	INDETERMINATE	1	TRUE	NA	0.67685542185377	2		424	926	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0010786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	170	273	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.889	0.822	0.958	0.889	0.822	0.958	CLONAL	1	TRUE	1	0.657339856129895	2		273	582	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215931	142215931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	309	447	0	ENST00000350721.4:c.5662G>A	p.Glu1888Lys	p.E1888K	ENST00000350721	NM_001184.3	1888	Gaa/Aaa	33/47	1	2	FACETS	0.908	0.857	0.96	0.908	0.857	0.96	CLONAL	1	TRUE	1	0.657339856129895	2		447	1035	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016264	150016264	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	391	507	0	ENST00000253339.5:c.442C>T	p.Arg148Ter	p.R148*	ENST00000253339		148	Cga/Tga	2/7	0.657339856129895	1	FACETS	0.888	0.848	0.929	0.888	0.848	0.929	CLONAL	1	TRUE	0	0.657339856129895	1		507	899	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259089	153259089	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0010786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	251	290	0	ENST00000281708.4:c.727-1G>C		p.X243_splice	ENST00000281708	NM_033632.3	243			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.657339856129895	2		290	733	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912141	29912141	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	25	10	0	ENST00000376809.5:c.862G>T	p.Glu288Ter	p.E288*	ENST00000376809	NM_002116.7	288	Gag/Tag	4/8	0.643855386430222	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.657339856129895	1		10	36	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508059	106508059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142380460	NA	P-0010786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	154	234	0	ENST00000359195.3:c.53G>A	p.Arg18Gln	p.R18Q	ENST00000359195	NM_002649.2	18	cGa/cAa	2/11	1	2	FACETS	0.943	0.869	1	0.943	0.869	1	CLONAL	1	TRUE	1	0.657339856129895	2		234	497	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007631	45007631	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	212	268	0	ENST00000558401.1:c.78G>C	p.Lys26Asn	p.K26N	ENST00000558401	NM_004048.2	26	aaG/aaC	2/4	1	2	FACETS	0.891	0.831	0.953	0.891	0.831	0.953	CLONAL	1	TRUE	1	0.657339856129895	2		268	724	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0010791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	35	245	0	ENST00000269305.4:c.673-2A>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.218317956854336	1	FACETS	0.52	0.426	0.627	0.52	0.426	0.627	SUBCLONAL	1	FALSE	0	0.218317956854336	1		245	549	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798734	135798734	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs118203390	NA	P-0010791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	37	174	0	ENST00000298552.3:c.508+1G>A		p.X170_splice	ENST00000298552	NM_001162426.1	170			0.218317956854336	1	FACETS	0.608	0.5	0.728	0.608	0.5	0.728	SUBCLONAL	1	FALSE	0	0.218317956854336	1		174	497	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188223	10188226	+	frameshift_variant	Frame_Shift_Del	DEL	AGGG	AGGG	-	novel	NA	P-0010791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	83	429	0	ENST00000256474.2:c.367_370del	p.Gly123HisfsTer35	p.G123Hfs*35	ENST00000256474	NM_000551.3	122	gcAGGG/gc	2/3	1	2	FACETS	0.697	0.613	0.787	0.697	0.613	0.787	SUBCLONAL	1	FALSE	1	0.218317956854336	2		429	1091	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95584079	95584081	+	missense_variant	Missense_Mutation	TNP	TTC	TTC	CTG	novel	NA	P-0010791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	34	235	0	ENST00000393063.1:c.1387_1389delinsCAG	p.Glu463Gln	p.E463Q	ENST00000393063	NM_030621.3	463	GAA/CAG	10/28	1	2	FACETS	0.477	0.388	0.577	0.477	0.388	0.577	SUBCLONAL	1	FALSE	1	0.218317956854336	2		235	653	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	172	247	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.32389091796401	11	FACETS	0.876	0.808	0.947	0.5	0.461	0.541	CLONAL	4	TRUE	4	0.32389091796401	11		247	745	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0010814-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	324	715	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.626328403480547	1	FACETS	0.988	0.94	1	0.988	0.94	1	CLONAL	1	TRUE	0	0.635763237212655	1		715	704	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578202	7578202	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520004	NA	P-0010814-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	552	687	0	ENST00000269305.4:c.647T>G	p.Val216Gly	p.V216G	ENST00000269305	NM_001126112.2	216	gTg/gGg	6/11	0.626328403480547	1	FACETS	0.985	0.949	1	0.985	0.949	1	CLONAL	1	TRUE	0	0.635763237212655	1		687	1202	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427705	72427705	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010814-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	278	384	0	ENST00000477973.2:c.785T>G	p.Phe262Cys	p.F262C	ENST00000477973	NM_012234.5	262	tTt/tGt	4/4	1	2	FACETS	0.904	0.851	0.959	0.904	0.851	0.959	CLONAL	1	TRUE	1	0.635763237212655	2		384	967	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604707	48604707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010814-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	354	592	0	ENST00000342988.3:c.1529G>A	p.Gly510Glu	p.G510E	ENST00000342988	NM_005359.5	510	gGa/gAa	12/12	0.626328403480547	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.635763237212655	1		592	760	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652297	48652297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1055251352	NA	P-0010814-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	572	451	0	ENST00000376670.3:c.968G>A	p.Gly323Asp	p.G323D	ENST00000376670	NM_002049.3	323	gGc/gAc	6/6	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.635763237212655	1		451	905	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0010818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	299	273	0				ENST00000310581	NM_198253.2	-/1132			0.252215252795611	1	FACETS	0.761	0.719	0.803	1	0.994	1	SUBCLONAL	2	TRUE	0	0.384689351464469	1		273	825	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970901	21970901	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs45476696	NA	P-0010818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	324	753	0	ENST00000304494.5:c.457G>A	p.Asp153Asn	p.D153N	ENST00000304494	NM_000077.4	153	Gac/Aac	2/3	0.384689351464469	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.384689351464469	1		753	1289	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729115	66729129	+	inframe_deletion	In_Frame_Del	DEL	GGAACCAGATCATAA	GGAACCAGATCATAA	-	novel	NA	P-0010818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	557	521	0	ENST00000307102.5:c.325_339del	p.Asn109_Arg113del	p.N109_R113del	ENST00000307102	NM_002755.3	108	cGGAACCAGATCATAAgg/cgg	3/11	0.381733450291819	3	FACETS	0.883	0.85	0.917	0.883	0.85	0.917	CLONAL	3	TRUE	0	0.384689351464469	3		521	1303	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732959	74732959	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751713049	NA	P-0010818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	138	252	0	ENST00000359995.5:c.284C>T	p.Pro95Leu	p.P95L	ENST00000359995	NM_001195427.1	95	cCc/cTc	1/3	0.384689351464469	3	FACETS	1	0.943	1	0.524	0.476	0.573	CLONAL	1	TRUE	1	0.384689351464469	3		252	817	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754865	29754865	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	131	369	0	ENST00000389048.3:c.1070C>T	p.Pro357Leu	p.P357L	ENST00000389048	NM_004304.4	357	cCc/cTc	4/29	0.163150826705959	3	FACETS	1	0.941	1	0.524	0.476	0.575	INDETERMINATE	1	TRUE	1	0.384689351464469	3		369	775	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117632205	117632205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1157	405	593	0	ENST00000368508.3:c.6211G>A	p.Glu2071Lys	p.E2071K	ENST00000368508	NM_002944.2	2071	Gaa/Aaa	39/43	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.384689351464469	2		593	1562	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28897053	28897053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148112461	NA	P-0010818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	252	400	0	ENST00000282397.4:c.2827G>A	p.Glu943Lys	p.E943K	ENST00000282397	NM_002019.4	943	Gaa/Aaa	21/30	0.210104212906074	4	FACETS	0.846	0.792	0.902	0.846	0.792	0.902	INDETERMINATE	2	TRUE	2	0.384689351464469	4		400	1072	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804359	43804359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749391587	NA	P-0010818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	243	444	0	ENST00000372470.3:c.359G>A	p.Arg120Gln	p.R120Q	ENST00000372470	NM_005373.2	120	cGg/cAg	3/12	0.200352165150966	1	FACETS	1	0.966	1	1	0.966	1	INDETERMINATE	1	TRUE	0	0.384689351464469	1		444	972	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491703	120491703	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0010818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	166	344	0	ENST00000256646.2:c.2526T>A	p.Cys842Ter	p.C842*	ENST00000256646	NM_024408.3	842	tgT/tgA	16/34	0.200352165150966	1	FACETS	0.822	0.756	0.891	0.822	0.756	0.891	INDETERMINATE	1	TRUE	0	0.384689351464469	1		344	848	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652797	212652797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	95	463	1	ENST00000342788.4:c.509C>T	p.Pro170Leu	p.P170L	ENST00000342788	NM_005235.2	170	cCa/cTa	4/28	0.20324246115292	2	FACETS	0.525	0.466	0.588	0.262	0.233	0.294	INDETERMINATE	1	TRUE	0	0.384689351464469	2		464	941	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191448	185191448	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1012339817	NA	P-0010818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	276	657	3	ENST00000265026.3:c.2329G>A	p.Glu777Lys	p.E777K	ENST00000265026	NM_004721.4	777	Gaa/Aaa	11/14	0.200352165150966	1	FACETS	0.941	0.882	1	0.941	0.882	1	INDETERMINATE	1	TRUE	0	0.384689351464469	1		660	1232	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457282	5457282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376993991	NA	P-0010818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	110	272	1	ENST00000381577.3:c.256C>T	p.Arg86Trp	p.R86W	ENST00000381577	NM_014143.3	86	Cgg/Tgg	3/7	0.384689351464469	1	FACETS	0.834	0.752	0.92	0.834	0.752	0.92	CLONAL	1	TRUE	0	0.384689351464469	1		273	554	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342586	118342586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	101	333	0	ENST00000534358.1:c.712G>A	p.Gly238Arg	p.G238R	ENST00000534358	NM_005933.3	238	Gga/Aga	3/36	1	2	FACETS	0.711	0.635	0.791	0.711	0.635	0.791	SUBCLONAL	1	TRUE	1	0.384689351464469	2		333	739	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350313	15350313	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	192	434	0	ENST00000263377.2:c.3466G>A	p.Asp1156Asn	p.D1156N	ENST00000263377	NM_058243.2	1156	Gat/Aat	17/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.384689351464469	2		434	941	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852433	42852433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	238	529	2	ENST00000398585.3:c.653G>A	p.Gly218Glu	p.G218E	ENST00000398585	NM_001135099.1	218	gGg/gAg	6/14	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.384689351464469	2		531	1232	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551282	29551284	+	stop_gained	Nonsense_Mutation	TNP	GGA	GGA	AGT	novel	NA	P-0010818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	237	560	1	ENST00000389048.3:c.1346_1348delinsACT	p.Leu449_Gln450delinsHisTer	p.L449_Q450delinsH*	ENST00000389048	NM_004304.4	449	cTCCag/cACTag	6/29	0.163150826705959	3	FACETS	1	0.972	1	0.54	0.503	0.579	INDETERMINATE	1	TRUE	1	0.384689351464469	3		561	1360	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30103715	30103715	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	234	412	0	ENST00000331968.5:c.1223G>A	p.Arg408Lys	p.R408K	ENST00000331968	NM_002742.2	408	aGg/aAg	8/18	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.384689351464469	2		412	1073	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950487	68950487	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138740482	NA	P-0010818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	157	366	1	ENST00000288368.4:c.799C>T	p.Leu267Phe	p.L267F	ENST00000288368	NM_024870.2	267	Ctt/Ttt	7/40	1	2	FACETS	0.861	0.788	0.937	0.861	0.788	0.937	CLONAL	1	TRUE	1	0.384689351464469	2		367	948	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010829-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	378	126	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		126	684	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0010839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	554	715	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.338324528994277	3	FACETS	0.921	0.89	0.953	1	0.998	1	CLONAL	4	TRUE	1	0.341753577783704	3		715	1030	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0010839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	342	733	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.341753577783704	2	FACETS	0.987	0.936	1	0.987	0.936	1	CLONAL	2	TRUE	0	0.341753577783704	2		733	1014	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871286	35871286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145210284	NA	P-0010839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	151	241	0	ENST00000303115.3:c.508C>T	p.Arg170Cys	p.R170C	ENST00000303115	NM_002185.3	170	Cgc/Tgc	4/8	0.341753577783704	5	FACETS	0.93	0.857	1	0.93	0.857	1	CLONAL	3	TRUE	2	0.341753577783704	5		241	479	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0010840-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	86	454	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.334382415746853	5	FACETS	0.95	0.852	1	0.95	0.852	1	CLONAL	3	TRUE	2	0.334382415746853	5		454	271	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041266	47041266	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0010840-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	89	628	0	ENST00000377604.3:c.1693+1G>T		p.X565_splice	ENST00000377604	NM_001204468.1	565			1	2	FACETS	0.845	0.757	0.937	1	0.984	1	CLONAL	2	TRUE	1	0.334382415746853	2		628	315	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36824424	36824424	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0010840-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	102	459	1	ENST00000373129.3:c.113-1G>T		p.X38_splice	ENST00000373129	NM_032017.1	38			NA	2	FACETS	0.944	0.854	1			1	INDETERMINATE	2	TRUE	NA	0.334382415746853	2		460	323	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843551	156843551	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010840-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	93	553	0	ENST00000524377.1:c.977G>C	p.Ser326Thr	p.S326T	ENST00000524377	NM_002529.3	326	aGc/aCc	8/17	0.334382415746853	9	FACETS	0.873	0.78	0.971	0.436	0.39	0.486	CLONAL	3	TRUE	3	0.334382415746853	9		553	461	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967312	25967312	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010840-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	110	557	0	ENST00000435504.4:c.1894C>T	p.His632Tyr	p.H632Y	ENST00000435504		632	Cat/Tat	13/13	0.334382415746853	5	FACETS	1	0.959	1	0.742	0.671	0.816	CLONAL	2	TRUE	2	0.334382415746853	5		557	444	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455570	189455570	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010840-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	95	455	0	ENST00000264731.3:c.104A>T	p.Tyr35Phe	p.Y35F	ENST00000264731	NM_003722.4	35	tAt/tTt	2/14	0.330653502484917	5	FACETS	0.914	0.824	1	0.914	0.824	1	CLONAL	3	TRUE	2	0.334382415746853	5		455	311	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748102	41748102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747713899	NA	P-0010840-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	14	83	1	ENST00000226382.2:c.667G>A	p.Ala223Thr	p.A223T	ENST00000226382	NM_003924.3	223	Gct/Act	3/3	0.334382415746853	5	FACETS	1	0.854	1	0.822	0.614	1	CLONAL	2	TRUE	2	0.334382415746853	5		84	51	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967910	93967910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010840-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	126	642	1	ENST00000369303.4:c.2017G>A	p.Glu673Lys	p.E673K	ENST00000369303	NM_004440.3	673	Gaa/Aaa	11/17	0.334382415746853	0	FACETS	0.828	0.761	0.895			1	CLONAL	2	TRUE	0	0.334382415746853	0		643	303	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778144	135778144	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010840-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	120	508	0	ENST00000298552.3:c.2239A>C	p.Ile747Leu	p.I747L	ENST00000298552	NM_001162426.1	747	Atc/Ctc	18/23	0.334382415746853	5	FACETS	0.916	0.841	0.993	1	0.979	1	CLONAL	4	TRUE	2	0.334382415746853	5		508	294	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218483	1218483	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs775595174	NA	P-0010840-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	173	393	1	ENST00000326873.7:c.358G>T	p.Glu120Ter	p.E120*	ENST00000326873	NM_000455.4	120	Gaa/Taa	2/10	0.334382415746853	4	FACETS	0.93	0.875	0.984	1	0.986	1	CLONAL	5	TRUE	0	0.334382415746853	4		394	297	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610139	10610139	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010840-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	207	561	0	ENST00000171111.5:c.571G>C	p.Ala191Pro	p.A191P	ENST00000171111	NM_203500.1	191	Gct/Cct	2/6	0.334382415746853	4	FACETS	1	0.971	1	1	0.992	1	CLONAL	5	TRUE	0	0.334382415746853	4		561	320	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0010847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	214	276	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	0.906990692322282	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.906990692322282	1		276	249	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222201	2222201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	552	510	0	ENST00000326181.6:c.485C>T	p.Pro162Leu	p.P162L	ENST00000326181	NM_032271.2	162	cCc/cTc	8/21	0.492608074603096	3	FACETS	0.964	0.932	0.994	0.964	0.932	0.994	INDETERMINATE	2	TRUE	1	0.906990692322282	3		510	918	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0010847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	493	367	0	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	0.539654492142271	3	FACETS	0.889	0.857	0.921			1	INDETERMINATE	2	TRUE	NA	0.906990692322282	3		367	889	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325105	123325105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	129	410	0	ENST00000358487.5:c.223G>A	p.Asp75Asn	p.D75N	ENST00000358487	NM_000141.4	75	Gat/Aat	3/18	0.906990692322282	1	FACETS	0.508	0.468	0.549	0.508	0.468	0.549	SUBCLONAL	1	TRUE	0	0.906990692322282	1		410	306	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729934	41729934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146325702	NA	P-0010847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	524	622	1	ENST00000242208.4:c.595G>A	p.Gly199Arg	p.G199R	ENST00000242208	NM_002192.2	199	Ggg/Agg	3/3	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	1	TRUE	NA	0.906990692322282	2		623	929	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129869	55129869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	269	434	1	ENST00000257290.5:c.403G>A	p.Asp135Asn	p.D135N	ENST00000257290	NM_006206.4	135	Gat/Aat	4/23	0.864352370785604	3	FACETS	0.973	0.915	1	0.487	0.457	0.517	CLONAL	1	TRUE	1	0.906990692322282	3		435	886	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562641	29562641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854562	NA	P-0010847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	317	472	1	ENST00000356175.3:c.3721C>T	p.Arg1241Ter	p.R1241*	ENST00000356175	NM_000267.3	1241	Cga/Tga	28/57	0.539654492142271	3	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.906990692322282	3		473	953	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176666786	176666786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	291	414	0	ENST00000439151.2:c.4222C>T	p.Pro1408Ser	p.P1408S	ENST00000439151	NM_022455.4	1408	Cca/Tca	8/23	0.333579590189286	5	FACETS	0.801	0.755	0.848			1	INDETERMINATE	2	TRUE	NA	0.906990692322282	5		414	946	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458690	120458690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1386606005	NA	P-0010847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	288	248	0	ENST00000256646.2:c.6655C>T	p.Pro2219Ser	p.P2219S	ENST00000256646	NM_024408.3	2219	Ccc/Tcc	34/34	0.5499188192091	3	FACETS	0.931	0.888	0.973	0.931	0.888	0.973	CLONAL	2	TRUE	1	0.906990692322282	3		248	496	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470977	25470977	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	302	386	0	ENST00000264709.3:c.784C>T	p.Pro262Ser	p.P262S	ENST00000264709	NM_175629.2	262	Cct/Tct	7/23	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	1	TRUE	NA	0.906990692322282	2		386	640	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439769	220439769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111982983	NA	P-0010847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	310	499	0	ENST00000243786.2:c.622C>T	p.Arg208Trp	p.R208W	ENST00000243786	NM_002191.3	208	Cgg/Tgg	2/2	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.906990692322282	2		499	617	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55974004	55974004	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754979123	NA	P-0010847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	238	300	0	ENST00000263923.4:c.1312G>A	p.Gly438Ser	p.G438S	ENST00000263923	NM_002253.2	438	Ggc/Agc	10/30	0.864352370785604	3	FACETS	0.874	0.817	0.932	0.437	0.408	0.466	CLONAL	1	TRUE	1	0.906990692322282	3		300	873	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38954953	38954953	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	226	199	0	ENST00000357387.3:c.2620C>T	p.Pro874Ser	p.P874S	ENST00000357387	NM_152756.3	874	Cct/Tct	27/38	0.906990692322282	5	FACETS	0.922	0.864	0.981	0.615	0.576	0.654	CLONAL	2	TRUE	2	0.906990692322282	5		199	638	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197396	26197396	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	649	588	1	ENST00000356476.2:c.83A>T	p.Lys28Met	p.K28M	ENST00000356476		28	aAg/aTg	1/1	0.428658835000677	4	FACETS	0.942	0.91	0.975	0.942	0.91	0.975	INDETERMINATE	2	TRUE	2	0.906990692322282	4		589	1448	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956991	2956991	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	109	307	0	ENST00000396946.4:c.2636C>T	p.Ser879Leu	p.S879L	ENST00000396946	NM_032415.4	879	tCa/tTa	20/25	0.845818330667228	1	FACETS	0.442	0.403	0.483	0.442	0.403	0.483	SUBCLONAL	1	TRUE	0	0.906990692322282	1		307	297	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367239	50367239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1045233686	NA	P-0010847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	95	216	0	ENST00000331340.3:c.46G>A	p.Glu16Lys	p.E16K	ENST00000331340	NM_006060.4	16	Gaa/Aaa	3/8	NA	2	FACETS	0.696	0.627	0.767			1	INDETERMINATE	1	TRUE	NA	0.906990692322282	2		216	301	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372059	55372059	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	43	191	0	ENST00000297316.4:c.749C>A	p.Thr250Asn	p.T250N	ENST00000297316	NM_022454.3	250	aCc/aAc	2/2	1	2	FACETS	0.42	0.354	0.491	0.42	0.354	0.491	SUBCLONAL	1	TRUE	1	0.906990692322282	2		191	226	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325128	123325128	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	112	381	1	ENST00000358487.5:c.200C>A	p.Ala67Asp	p.A67D	ENST00000358487	NM_000141.4	67	gCc/gAc	3/18	0.906990692322282	1	FACETS	0.461	0.42	0.502	0.461	0.42	0.502	SUBCLONAL	1	TRUE	0	0.906990692322282	1		382	293	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925096	81925096	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867804190	NA	P-0010847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	275	458	0	ENST00000359376.3:c.887C>T	p.Ser296Leu	p.S296L	ENST00000359376	NM_002661.3	296	tCa/tTa	11/33	0.906990692322282	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.906990692322282	1		458	324	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739007	40739007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	125	328	0	ENST00000373198.4:c.3277C>T	p.Pro1093Ser	p.P1093S	ENST00000373198	NM_133170.3	1093	Ccc/Tcc	24/32	0.742544805713695	1	FACETS	0.491	0.451	0.531	0.491	0.451	0.531	SUBCLONAL	1	TRUE	0	0.906990692322282	1		328	307	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523672	176523672	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	183	734	0	ENST00000292408.4:c.2083G>T	p.Val695Leu	p.V695L	ENST00000292408	NM_213647.1	695	Gtg/Ttg	16/18	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.345052177555017	2		734	1014	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054563	5054563	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	39	143	0	ENST00000381652.3:c.615C>G	p.Ser205Arg	p.S205R	ENST00000381652	NM_004972.3	205	agC/agG	7/25	0.345052177555017	1	FACETS	0.891	0.745	1	0.891	0.745	1	CLONAL	1	TRUE	0	0.345052177555017	1		143	210	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911534	101911534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111426349	NA	P-0010855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	214	472	2	ENST00000374994.4:c.1459C>T	p.Arg487Trp	p.R487W	ENST00000374994	NM_004612.2	487	Cgg/Tgg	9/9	0.336080576047062	2	FACETS	0.863	0.805	0.922	0.863	0.805	0.922	CLONAL	2	TRUE	0	0.345052177555017	2		474	719	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32438063	32438063	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	151	456	0	ENST00000332351.3:c.974C>A	p.Ser325Ter	p.S325*	ENST00000332351	NM_024426.4	325	tCa/tAa	5/10	0.334382381998411	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.345052177555017	1		456	672	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863434	57863434	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147931475	NA	P-0010855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	392	643	0	ENST00000228682.2:c.1529G>A	p.Arg510Gln	p.R510Q	ENST00000228682	NM_005269.2	510	cGg/cAg	11/12	0.344979325916224	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.345052177555017	2		643	1038	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562242	95562242	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	157	514	0	ENST00000393063.1:c.5015A>G	p.Lys1672Arg	p.K1672R	ENST00000393063	NM_030621.3	1672	aAa/aGa	24/28	0.336080576047062	2	FACETS	1	0.928	1	0.507	0.464	0.552	CLONAL	1	TRUE	0	0.345052177555017	2		514	897	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577563	7577563	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1567549584	NA	P-0010855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	114	450	0	ENST00000269305.4:c.718A>G	p.Ser240Gly	p.S240G	ENST00000269305	NM_001126112.2	240	Agt/Ggt	7/11	0.290499122937101	1	FACETS	0.799	0.721	0.882	0.799	0.721	0.882	SUBCLONAL	1	TRUE	0	0.345052177555017	1		450	684	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0010860-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	77	207	9	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.36	2		216	375	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0010863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	1701	262	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		262	2470	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0010867-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	687	484	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	0.710374728004315	3	FACETS	0.878	0.856	0.901	0.878	0.856	0.901	CLONAL	3	TRUE	0	0.712937095661543	3		484	992	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684025	29684025	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010867-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	273	521	0	ENST00000356175.3:c.7723G>T	p.Val2575Phe	p.V2575F	ENST00000356175	NM_000267.3	2575	Gtt/Ttt	52/57	0.712937095661543	3	FACETS	0.883	0.828	0.939	0.441	0.414	0.47	CLONAL	1	TRUE	1	0.712937095661543	3		521	1177	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880219	37880220	+	missense_variant	Missense_Mutation	DNP	TT	TT	CC	rs121913469	NA	P-0010927-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	273	661	0	ENST00000269571.5:c.2263_2264delinsCC	p.Leu755Pro	p.L755P	ENST00000269571		755	TTg/CCg	19/27	0.117099356864472	5	FACETS	1	0.971	1	0.528	0.495	0.561	INDETERMINATE	2	TRUE	1	0.396309109859888	5		661	1041	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527973	157527973	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010927-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	71	228	0	ENST00000346085.5:c.5698A>G	p.Ser1900Gly	p.S1900G	ENST00000346085	NM_020732.3	1900	Agc/Ggc	20/20	0.339131091099092	3	FACETS	0.869	0.76	0.986	0.435	0.38	0.493	CLONAL	1	TRUE	1	0.396309109859888	3		228	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574032	7574032	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010927-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	132	546	0	ENST00000269305.4:c.995T>G	p.Ile332Ser	p.I332S	ENST00000269305	NM_001126112.2	332	aTc/aGc	10/11	0.396309109859888	1	FACETS	0.745	0.677	0.816	0.745	0.677	0.816	SUBCLONAL	1	TRUE	0	0.396309109859888	1		546	717	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199495	16199495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	125	691	0	ENST00000375759.3:c.268G>A	p.Gly90Arg	p.G90R	ENST00000375759	NM_015001.2	90	Gga/Aga	2/15	0.534734134327189	3	FACETS	0.881	0.799	0.967			1	CLONAL	1	TRUE	NA	0.555247865796102	3		691	653	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106662	27106662	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	140	598	0	ENST00000324856.7:c.6273G>A	p.Trp2091Ter	p.W2091*	ENST00000324856	NM_006015.4	2091	tgG/tgA	20/20	0.534734134327189	3	FACETS	0.978	0.893	1			1	CLONAL	1	TRUE	NA	0.555247865796102	3		598	659	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619829	1619829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	201	1128	1	ENST00000344749.5:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000344749	NM_001136139.2	373	Gga/Aga	14/19	0.445815086693462	4	FACETS	0.922	0.853	0.994			1	CLONAL	1	TRUE	NA	0.555247865796102	4		1129	1221	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291902	15291902	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	186	674	0	ENST00000263388.2:c.2864C>T	p.Thr955Ile	p.T955I	ENST00000263388	NM_000435.2	955	aCa/aTa	18/33	0.555247865796102	4	FACETS	1	0.976	1	0.566	0.523	0.611	CLONAL	1	TRUE	2	0.555247865796102	4		674	920	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159752	20159752	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	245	619	0	ENST00000379607.5:c.7A>G	p.Lys3Glu	p.K3E	ENST00000379607	NM_001412.3	3	Aag/Gag	1/7	0.554315269546801	3	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	1	0.555247865796102	3		619	563	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122714	108122714	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	332	512	0	ENST00000278616.4:c.1760del	p.Gly587ValfsTer3	p.G587Vfs*3	ENST00000278616	NM_000051.3	586	gaG/ga	11/63	0.555247865796102	4	FACETS	0.915	0.88	0.95	0.915	0.88	0.95	CLONAL	4	TRUE	0	0.555247865796102	4		512	508	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	209	391	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.607662251238297	4	FACETS	1	0.973	1	0.547	0.508	0.588	CLONAL	1	TRUE	2	0.708496703677709	4		391	921	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0010933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	267	343	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.708496703677709	2	FACETS	0.984	0.944	1	0.984	0.944	1	CLONAL	2	TRUE	0	0.708496703677709	2		343	383	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0010933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	287	250	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.615608826749793	4	FACETS	0.989	0.936	1			1	CLONAL	2	TRUE	NA	0.708496703677709	4		250	700	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189908	66189908	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	145	424	0	ENST00000273854.3:c.3038T>G	p.Val1013Gly	p.V1013G	ENST00000273854	NM_004439.5	1013	gTc/gGc	18/18	0.332898829285202	5	FACETS	0.926	0.844	1	0.309	0.281	0.337	INDETERMINATE	1	TRUE	2	0.708496703677709	5		424	912	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512490	149512490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1443597666	NA	P-0010933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	341	179	0	ENST00000261799.4:c.950G>A	p.Arg317Gln	p.R317Q	ENST00000261799	NM_002609.3	317	cGg/cAg	7/23	0.708496703677709	3	FACETS	0.999	0.968	1	0.999	0.968	1	CLONAL	3	TRUE	0	0.708496703677709	3		179	435	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5462929	5462929	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	62	379	0	ENST00000381577.3:c.490G>C	p.Glu164Gln	p.E164Q	ENST00000381577	NM_014143.3	164	Gaa/Caa	4/7	0.332898829285202	5	FACETS	0.397	0.342	0.457	0.132	0.113	0.153	INDETERMINATE	1	TRUE	2	0.708496703677709	5		379	910	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921722	111921750	+	frameshift_variant	Frame_Shift_Del	DEL	AATTACCAAGCAGCCGAAGACCACCCACG	AATTACCAAGCAGCCGAAGACCACCCACG	-	novel	NA	P-0010933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	186	471	0	ENST00000393256.3:c.514_542del	p.Tyr172GlyfsTer83	p.Y172Gfs*83	ENST00000393256	NM_006538.4	171	AATTACCAAGCAGCCGAAGACCACCCACGa/a	4/4	0.700040553870653	4	FACETS	0.781	0.72	0.844	0.26	0.24	0.282	SUBCLONAL	1	TRUE	1	0.708496703677709	4		471	1149	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5463021	5463035	+	inframe_deletion	In_Frame_Del	DEL	CAGCACACTGAGAAT	CAGCACACTGAGAAT	-	novel	NA	P-0010933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	43	381	0	ENST00000381577.3:c.584_598del	p.Ser195_Ile199del	p.S195_I199del	ENST00000381577	NM_014143.3	194	acCAGCACACTGAGAATc/acc	4/7	0.332898829285202	5	FACETS	0.294	0.245	0.349	0.098	0.081	0.117	INDETERMINATE	1	TRUE	2	0.708496703677709	5		381	852	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0010936-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	20	284	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	NA	2	FACETS	1	0.867	1			1	INDETERMINATE	1	TRUE	NA	0.305873653136409	2		284	111	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190900	106190900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs977008842	NA	P-0010941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	259	230	0	ENST00000380013.4:c.4178C>T	p.Thr1393Ile	p.T1393I	ENST00000380013	NM_001127208.2	1393	aCa/aTa	9/11	0.93528442598834	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.953948675853992	1		230	278	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151921107	151921107	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	15	14	0	ENST00000262189.6:c.3316T>A	p.Cys1106Ser	p.C1106S	ENST00000262189	NM_170606.2	1106	Tgt/Agt	20/59	1	2	FACETS	0.655	0.498	0.827	0.655	0.498	0.827	SUBCLONAL	1	TRUE	1	0.953948675853992	2		14	48	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346162	89346162	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	377	347	0	ENST00000301030.4:c.6788C>G	p.Pro2263Arg	p.P2263R	ENST00000301030	NM_001256183.1	2263	cCc/cGc	9/13	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.953948675853992	2		347	740	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593630	+	inframe_deletion	In_Frame_Del	DEL	TTGTTGAGGAGATAAATGGAA	TTGTTGAGGAGATAAATGGAA	-	novel	NA	P-0010941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	371	534	2	ENST00000288135.5:c.1676_1696del	p.Val559_Asn566delinsAsp	p.V559_N566delinsD	ENST00000288135	NM_000222.2	559	gTTGTTGAGGAGATAAATGGAAac/gac	11/21	0.93528442598834	1	FACETS	0.951	0.928	0.971	0.951	0.928	0.971	CLONAL	1	TRUE	0	0.953948675853992	1		536	428	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0010948-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	376	645	1	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.423911379332773	5	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	3	0.423911379332773	5		646	1202	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143985	11143985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010948-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	307	295	1	ENST00000358026.2:c.3566G>A	p.Arg1189Gln	p.R1189Q	ENST00000358026	NM_001128849.1	1189	cGa/cAa	26/36	0.390914341451275	4	FACETS	0.982	0.927	1	0.982	0.927	1	CLONAL	2	TRUE	2	0.423911379332773	4		296	1050	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090407	37090407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750292	NA	P-0010948-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	229	512	0	ENST00000231790.2:c.2002G>A	p.Glu668Lys	p.E668K	ENST00000231790	NM_000249.3	668	Gaa/Aaa	18/19	0.215132245674166	4	FACETS	0.778	0.725	0.832	0.778	0.725	0.832	INDETERMINATE	2	TRUE	2	0.423911379332773	4		512	989	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400042	49400042	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010948-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	74	531	0	ENST00000418115.1:c.295T>C	p.Trp99Arg	p.W99R	ENST00000418115	NM_001664.2	99	Tgg/Cgg	4/5	0.215132245674166	4	FACETS	0.416	0.363	0.474	0.208	0.181	0.237	INDETERMINATE	1	TRUE	2	0.423911379332773	4		531	1194	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405025	405025	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010948-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	82	416	0	ENST00000380956.4:c.1107A>C	p.Gln369His	p.Q369H	ENST00000380956	NM_001195286.1	369	caA/caC	8/9	0.423911379332773	1	FACETS	0.518	0.457	0.583	0.518	0.457	0.583	SUBCLONAL	1	TRUE	0	0.423911379332773	1		416	589	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372325	55372325	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762216558	NA	P-0010948-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	77	248	0	ENST00000297316.4:c.1015G>A	p.Ala339Thr	p.A339T	ENST00000297316	NM_022454.3	339	Gca/Aca	2/2	0.215132245674166	4	FACETS	0.708	0.621	0.801	0.354	0.31	0.401	INDETERMINATE	1	TRUE	2	0.423911379332773	4		248	731	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737838	145737838	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010948-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	42	301	0	ENST00000428558.2:c.2992T>C	p.Trp998Arg	p.W998R	ENST00000428558	NM_004260.3	998	Tgg/Cgg	18/22	0.215132245674166	4	FACETS	0.356	0.296	0.423	0.178	0.148	0.212	INDETERMINATE	1	TRUE	2	0.423911379332773	4		301	793	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485767	8485767	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010948-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	91	403	1	ENST00000356435.5:c.3050A>T	p.Asp1017Val	p.D1017V	ENST00000356435		1017	gAt/gTt	17/35	0.423911379332773	2	FACETS	0.624	0.554	0.699	0.312	0.277	0.35	SUBCLONAL	1	TRUE	0	0.423911379332773	2		404	688	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904894	101904894	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010948-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	97	442	0	ENST00000374994.4:c.882A>T	p.Arg294Ser	p.R294S	ENST00000374994	NM_004612.2	294	agA/agT	5/9	0.423911379332773	2	FACETS	0.546	0.486	0.61	0.273	0.243	0.305	SUBCLONAL	1	TRUE	0	0.423911379332773	2		442	838	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986895	36986895	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010948-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	51	160	0	ENST00000354822.5:c.794G>C	p.Gly265Ala	p.G265A	ENST00000354822	NM_001079668.2	265	gGc/gCc	3/3	0.423911379332773	2	FACETS	0.542	0.461	0.63	0.271	0.23	0.315	SUBCLONAL	1	TRUE	0	0.423911379332773	2		160	444	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591905	48591931	+	inframe_deletion	In_Frame_Del	DEL	TTCTGGAGGAGATCGCTTTTGTTTGGG	TTCTGGAGGAGATCGCTTTTGTTTGGG	-	novel	NA	P-0010948-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	151	569	0	ENST00000342988.3:c.1069_1095del	p.Ser357_Gly365del	p.S357_G365del	ENST00000342988	NM_005359.5	356	ccTTCTGGAGGAGATCGCTTTTGTTTGGGt/cct	9/12	0.423911379332773	1	FACETS	0.835	0.766	0.908	0.835	0.766	0.908	CLONAL	1	TRUE	0	0.423911379332773	1		569	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577133	+	frameshift_variant	Frame_Shift_Del	DEL	CGCACCTCAAAGCT	CGCACCTCAAAGCT	-	novel	NA	P-0010948-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	816	547	0	ENST00000269305.4:c.805_818del	p.Ser269CysfsTer32	p.S269Cfs*32	ENST00000269305	NM_001126112.2	269	AGCTTTGAGGTGCGt/t	8/11	0.218260486634484	5	FACETS	0.911	0.886	0.935			1	INDETERMINATE	5	TRUE	NA	0.423911379332773	5		547	1383	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528495	29528518	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATCACCAATGTAAGTCCAAAAGGT	ATCACCAATGTAAGTCCAAAAGGT	-	novel	NA	P-0010948-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	148	557	0	ENST00000356175.3:c.1254_1260+17del		p.X418_splice	ENST00000356175	NM_000267.3	418		11/57	0.423911379332773	2	FACETS	0.746	0.681	0.814	0.373	0.34	0.407	SUBCLONAL	1	TRUE	0	0.423911379332773	2		557	936	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0010951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	107	439	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.312436480482633	1	FACETS	0.727	0.652	0.807	0.727	0.652	0.807	SUBCLONAL	1	TRUE	0	0.313388085378852	1		439	792	SUCCESS
APC	324	MSKCC	GRCh37	5	112154723	112154723	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775126020	NA	P-0010951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	161	274	0	ENST00000257430.4:c.994C>T	p.Arg332Ter	p.R332*	ENST00000257430	NM_000038.5	332	Cga/Tga	10/16	0.266967529001246	2	FACETS	0.893	0.824	0.965	0.893	0.824	0.965	CLONAL	2	TRUE	0	0.313388085378852	2		274	575	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142982	30142982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1229550831	NA	P-0010951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	128	458	1	ENST00000389048.3:c.544G>A	p.Glu182Lys	p.E182K	ENST00000389048	NM_004304.4	182	Gaa/Aaa	1/29	1	2	FACETS	0.895	0.81	0.984	0.895	0.81	0.984	CLONAL	1	TRUE	1	0.313388085378852	2		459	913	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0010953-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	97	340	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	1	2	FACETS	0.999	0.889	1	0.999	0.889	1	CLONAL	1	TRUE	1	0.22	2		340	883	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555083	106555083	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010953-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	38	245	0	ENST00000369096.4:c.2200G>A	p.Asp734Asn	p.D734N	ENST00000369096	NM_001198.3	734	Gac/Aac	7/7	1	2	FACETS	0.456	0.375	0.546	0.456	0.375	0.546	SUBCLONAL	1	TRUE	1	0.22	2		245	758	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0010960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	163	393	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.182706395016066	3	FACETS	0.772	0.709	0.838	0.772	0.709	0.838	SUBCLONAL	2	TRUE	1	0.286738272945997	3		393	842	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0010960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	289	566	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.210135364786404	2	FACETS	0.919	0.864	0.975	0.919	0.864	0.975	CLONAL	2	TRUE	0	0.286738272945997	2		568	1097	SUCCESS
APC	324	MSKCC	GRCh37	5	112173926	112173926	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060503287	NA	P-0010960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	114	320	0	ENST00000257430.4:c.2635C>T	p.Gln879Ter	p.Q879*	ENST00000257430	NM_000038.5	879	Cag/Tag	16/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.286738272945997	2		320	693	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45423040	45423040	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	258	606	0	ENST00000262160.6:c.88G>A	p.Gly30Arg	p.G30R	ENST00000262160	NM_005901.5	30	Gga/Aga	2/11	0.210135364786404	2	FACETS	0.802	0.751	0.855	0.802	0.751	0.855	CLONAL	2	TRUE	0	0.286738272945997	2		606	1122	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0010960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1290	336	802	2	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	0.235782150913157	3	FACETS	0.824	0.777	0.872	0.824	0.777	0.872	CLONAL	2	TRUE	1	0.286738272945997	3		804	1626	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426806	212426806	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	62	293	0	ENST00000342788.4:c.2309T>A	p.Leu770Gln	p.L770Q	ENST00000342788	NM_005235.2	770	cTg/cAg	20/28	0.286738272945997	3	FACETS	0.912	0.789	1	0.304	0.263	0.349	CLONAL	1	TRUE	0	0.286738272945997	3		293	542	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332805	153332805	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	133	644	1	ENST00000281708.4:c.151G>T	p.Glu51Ter	p.E51*	ENST00000281708	NM_033632.3	51	Gag/Tag	2/12	0.235782150913157	3	FACETS	0.821	0.743	0.903	0.41	0.371	0.452	CLONAL	1	TRUE	1	0.286738272945997	3		645	1292	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512406	149512406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201250234	NA	P-0010960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	98	461	0	ENST00000261799.4:c.1034C>T	p.Pro345Leu	p.P345L	ENST00000261799	NM_002609.3	345	cCg/cTg	7/23	1	2	FACETS	0.78	0.695	0.871	0.78	0.695	0.871	SUBCLONAL	1	TRUE	1	0.286738272945997	2		461	876	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514406	148514406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1255	186	696	1	ENST00000320356.2:c.1318G>A	p.Ala440Thr	p.A440T	ENST00000320356	NM_004456.4	440	Gct/Act	11/20	0.191155493125735	4	FACETS	1	0.977	1	0.579	0.533	0.627	CLONAL	1	TRUE	2	0.286738272945997	4		697	1441	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250914	153250916	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	novel	NA	P-0010960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	141	407	0	ENST00000281708.4:c.1144_1146del	p.His382del	p.H382del	ENST00000281708	NM_033632.3	382	CAT/-	8/12	0.235782150913157	3	FACETS	0.799	0.729	0.871	0.799	0.729	0.871	SUBCLONAL	2	TRUE	1	0.286738272945997	3		407	704	SUCCESS
APC	324	MSKCC	GRCh37	5	112175754	112175755	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0010960-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	71	341	0	ENST00000257430.4:c.4464_4465del	p.Leu1488PhefsTer25	p.L1488Ffs*25	ENST00000257430	NM_000038.5	1488	tTA/t	16/16	1	2	FACETS	0.809	0.706	0.92	0.809	0.706	0.92	CLONAL	1	TRUE	1	0.286738272945997	2		341	612	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434225	49434225	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780776865	NA	P-0010961-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	644	795	1	ENST00000301067.7:c.7328G>A	p.Arg2443His	p.R2443H	ENST00000301067	NM_003482.3	2443	cGc/cAc	31/54	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.873073551036488	2		796	1308	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	118	126	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.925	0.844	1			1	INDETERMINATE	1	TRUE	NA	0.71039618682864	2		126	359	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862749	9862749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150316865	NA	P-0010970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	340	367	0	ENST00000330684.3:c.2554G>A	p.Val852Met	p.V852M	ENST00000330684	NM_001134407.1	852	Gtg/Atg	12/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.71039618682864	2		367	920	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957432	175957432	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	206	485	0	ENST00000367669.3:c.1964T>G	p.Ile655Arg	p.I655R	ENST00000367669	NM_022457.5	655	aTa/aGa	17/20	1	2	FACETS	0.518	0.48	0.557	0.518	0.48	0.557	SUBCLONAL	1	TRUE	1	0.71039618682864	2		485	1120	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687604	29687604	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	430	556	0	ENST00000356175.3:c.8197T>G	p.Ser2733Ala	p.S2733A	ENST00000356175	NM_000267.3	2733	Tcc/Gcc	56/57	1	2	FACETS	0.868	0.827	0.91	0.868	0.827	0.91	CLONAL	1	TRUE	1	0.71039618682864	2		556	1395	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179188	123179189	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0010970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	397	208	0	ENST00000218089.9:c.639_640del	p.Arg213SerfsTer25	p.R213Sfs*25	ENST00000218089	NM_001042749.1	213	AGa/a	8/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.71039618682864	1		208	545	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010986-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	241	247	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.972	0.908	1	0.972	0.908	1	CLONAL	1	TRUE	1	0.50311492645186	2		247	986	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266107	41266107	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010986-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	57	396	0	ENST00000349496.5:c.104T>G	p.Ile35Ser	p.I35S	ENST00000349496	NM_001904.3	35	aTc/aGc	3/15	1	2	FACETS	0.196	0.167	0.227	0.196	0.167	0.227	SUBCLONAL	1	TRUE	1	0.50311492645186	2		396	1159	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159754	20159754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010986-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	70	337	0	ENST00000379607.5:c.5C>T	p.Pro2Leu	p.P2L	ENST00000379607	NM_001412.3	2	cCc/cTc	1/7	1	2	FACETS	0.318	0.276	0.363	0.318	0.276	0.363	SUBCLONAL	1	TRUE	1	0.50311492645186	2		337	876	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058075	27058075	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010986-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	41	117	0	ENST00000324856.7:c.1783C>T	p.Gln595Ter	p.Q595*	ENST00000324856	NM_006015.4	595	Cag/Tag	3/20	1	2	FACETS	0.351	0.292	0.417	0.351	0.292	0.417	SUBCLONAL	1	TRUE	1	0.50311492645186	2		117	464	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602890	55602890	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010986-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	264	294	2	ENST00000288135.5:c.2600G>T	p.Ser867Ile	p.S867I	ENST00000288135	NM_000222.2	867	aGc/aTc	19/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.50311492645186	2		296	1017	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7977052	7977052	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010986-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	80	364	0	ENST00000319144.4:c.1678G>T	p.Val560Leu	p.V560L	ENST00000319144	NM_001139.2	560	Gtg/Ttg	13/15	0.195452536836736	0	FACETS	0.195	0.171	0.221			1	INDETERMINATE	1	TRUE	0	0.50311492645186	0		364	810	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667647	29667647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs864622065	NA	P-0010986-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1238	98	419	1	ENST00000356175.3:c.6983G>A	p.Arg2328His	p.R2328H	ENST00000356175	NM_000267.3	2328	cGt/cAt	46/57	NA	2	FACETS	0.292	0.259	0.327			1	INDETERMINATE	1	TRUE	NA	0.50311492645186	2		420	1336	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267388	198267399	+	inframe_deletion	In_Frame_Del	DEL	ACTTCTTGCTTT	ACTTCTTGCTTT	-	novel	NA	P-0010986-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1252	87	458	0	ENST00000335508.6:c.1958_1969del	p.Lys653_Ser657delinsThr	p.K653_S657delinsT	ENST00000335508	NM_012433.2	653	aAAAGCAAGAAGTcc/acc	14/25	1	2	FACETS	0.258	0.227	0.292	0.258	0.227	0.292	SUBCLONAL	1	TRUE	1	0.50311492645186	2		458	1339	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0010988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	95	645	1	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.220696443270228	2		646	811	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0010988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	78	502	1	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.135762384732834	1	FACETS	0.716	0.628	0.811	0.716	0.628	0.811	SUBCLONAL	1	TRUE	0	0.220696443270228	1		503	878	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577518	7577518	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519995	NA	P-0010988-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	148	624	0	ENST00000269305.4:c.763A>T	p.Ile255Phe	p.I255F	ENST00000269305	NM_001126112.2	255	Atc/Ttc	7/11	1	2	FACETS	0.754	0.689	0.823	1	0.987	1	SUBCLONAL	2	TRUE	1	0.220696443270228	2		624	889	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0010994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	556	593	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.672380499453884	2	FACETS	0.981	0.952	1	0.981	0.952	1	CLONAL	2	TRUE	0	0.68610036204768	2		593	826	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521675	89521675	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	239	538	0	ENST00000336596.2:c.2752G>A	p.Asp918Asn	p.D918N	ENST00000336596	NM_005233.5	918	Gac/Aac	16/17	NA	2	FACETS	0.646	0.603	0.691			1	INDETERMINATE	1	TRUE	NA	0.68610036204768	2		538	1078	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396503	139396503	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	197	683	1	ENST00000277541.6:c.5422G>T	p.Asp1808Tyr	p.D1808Y	ENST00000277541	NM_017617.3	1808	Gac/Tac	29/34	0.644247419781038	4	FACETS	0.747	0.69	0.807	0.249	0.23	0.269	SUBCLONAL	1	TRUE	1	0.68610036204768	4		684	1296	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179144	123179144	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	587	653	1	ENST00000218089.9:c.593A>T	p.Asp198Val	p.D198V	ENST00000218089	NM_001042749.1	198	gAt/gTt	8/35	0.68610036204768	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.68610036204768	2		654	851	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0010996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	245	414	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.197741295399171	2	FACETS	0.909	0.851	0.968	1	0.991	1	CLONAL	3	TRUE	0	0.197741295399171	2		416	909	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917689	151917689	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010996-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	54	166	0	ENST00000262189.6:c.3631C>T	p.Gln1211Ter	p.Q1211*	ENST00000262189	NM_170606.2	1211	Cag/Tag	23/59	0.197741295399171	5	FACETS	1	0.894	1			1	CLONAL	2	TRUE	NA	0.197741295399171	5		166	337	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149170	119149220	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTAAGTATTTTCAGATGCATCTGTTACTATCTTTTGCTTCTTCTGCAGG	TTTTAAGTATTTTCAGATGCATCTGTTACTATCTTTTGCTTCTTCTGCAGG	-	novel	NA	P-0011008-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	158	205	1	ENST00000264033.4:c.1228-50_1228del		p.X410_splice	ENST00000264033	NM_005188.3	410		9/16	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		206	549	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0011017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	364	761	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.315175121734677	2	FACETS	0.868	0.823	0.915	0.868	0.823	0.915	CLONAL	2	TRUE	0	0.315175121734677	2		761	1330	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217872	7217875	+	frameshift_variant	Frame_Shift_Del	DEL	CTTC	CTTC	-	novel	NA	P-0011017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	332	592	2	ENST00000380728.2:c.136_139del	p.Glu46AsnfsTer16	p.E46Nfs*16	ENST00000380728		46	GAAGaa/aa	3/11	0.315175121734677	2	FACETS	1	0.994	1	0.723	0.682	0.766	CLONAL	1	TRUE	0	0.315175121734677	2		594	1456	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592150	55592150	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	155	398	0	ENST00000288135.5:c.1474A>G	p.Lys492Glu	p.K492E	ENST00000288135	NM_000222.2	492	Aag/Gag	9/21	0.290234152431301	1	FACETS	0.865	0.791	0.942	0.865	0.791	0.942	CLONAL	1	TRUE	0	0.315175121734677	1		398	958	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610330	10610330	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	277	391	0	ENST00000171111.5:c.380G>C	p.Gly127Ala	p.G127A	ENST00000171111	NM_203500.1	127	gGt/gCt	2/6	0.315175121734677	3	FACETS	0.994	0.934	1	0.994	0.934	1	CLONAL	2	TRUE	1	0.315175121734677	3		391	1024	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781504	NA	P-0011030-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	216	435	0	ENST00000269305.4:c.314G>T	p.Gly105Val	p.G105V	ENST00000269305	NM_001126112.2	105	gGc/gTc	4/11	0.887971097772432	1	FACETS	0.987	0.949	1	0.987	0.949	1	CLONAL	1	TRUE	0	0.887971097772432	1		435	274	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977858	134977858	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	60	370	0	ENST00000398015.3:c.2851C>A	p.Leu951Ile	p.L951I	ENST00000398015	NM_004441.4	951	Ctc/Atc	16/16	1	2	FACETS	0.885	0.762	1	0.885	0.762	1	CLONAL	1	TRUE	1	0.2	2		370	678	SUCCESS
ATM	472	MSKCC	GRCh37	11	108168092	108168092	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	59	384	0	ENST00000278616.4:c.4988G>T	p.Gly1663Val	p.G1663V	ENST00000278616	NM_000051.3	1663	gGt/gTt	33/63	1	2	FACETS	0.673	0.577	0.777	0.673	0.577	0.777	SUBCLONAL	1	TRUE	1	0.2	2		384	877	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435391	121435391	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193922580	NA	P-0011041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	52	391	0	ENST00000257555.6:c.1424C>T	p.Pro475Leu	p.P475L	ENST00000257555		475	cCg/cTg	7/10	1	2	FACETS	0.729	0.62	0.85	0.729	0.62	0.85	SUBCLONAL	1	TRUE	1	0.2	2		391	713	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842459	68842459	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	47	304	0	ENST00000261769.5:c.520A>T	p.Asn174Tyr	p.N174Y	ENST00000261769	NM_004360.3	174	Aac/Tac	4/16	0.165789747360694	1	FACETS	0.734	0.619	0.862	0.734	0.619	0.862	SUBCLONAL	1	TRUE	0	0.2	1		304	576	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827928	40827928	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	63	471	0	ENST00000373198.4:c.2500C>A	p.Arg834Ser	p.R834S	ENST00000373198	NM_133170.3	834	Cgc/Agc	17/32	1	2	FACETS	0.727	0.627	0.836	0.727	0.627	0.836	SUBCLONAL	1	TRUE	1	0.2	2		471	867	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317461	1317461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs781459586	NA	P-0011041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	77	546	0	ENST00000400841.2:c.604G>T	p.Asp202Tyr	p.D202Y	ENST00000400841		202	Gac/Tac	5/6	1	2	FACETS	0.706	0.618	0.801	0.706	0.618	0.801	SUBCLONAL	1	TRUE	1	0.2	2		546	1091	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933515	39933515	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	57	486	0	ENST00000378444.4:c.1084G>T	p.Ala362Ser	p.A362S	ENST00000378444	NM_001123385.1	362	Gcc/Tcc	4/15	1	2	FACETS	0.586	0.501	0.679	0.586	0.501	0.679	SUBCLONAL	1	TRUE	1	0.2	2		486	973	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972671	76972671	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1191670776	NA	P-0011041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	79	563	0	ENST00000373344.5:c.70C>A	p.His24Asn	p.H24N	ENST00000373344	NM_000489.3	24	Cac/Aac	2/35	1	2	FACETS	0.654	0.573	0.742	0.654	0.573	0.742	SUBCLONAL	1	TRUE	1	0.2	2		563	1208	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155145	108155145	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0011041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	65	421	0	ENST00000278616.4:c.3938del	p.Glu1313GlyfsTer36	p.E1313Gfs*36	ENST00000278616	NM_000051.3	1313	gAg/gg	26/63	1	2	FACETS	0.807	0.699	0.926	0.807	0.699	0.926	CLONAL	1	TRUE	1	0.2	2		421	805	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220597	1220597	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	52	373	0	ENST00000326873.7:c.616del	p.Ala206ArgfsTer81	p.A206Rfs*81	ENST00000326873	NM_000455.4	205	gcG/gc	5/10	1	2	FACETS	0.731	0.621	0.852	0.731	0.621	0.852	SUBCLONAL	1	TRUE	1	0.2	2		373	711	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539096	23539096	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0011041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	58	400	0	ENST00000380871.4:c.343del	p.Arg115GlyfsTer22	p.R115Gfs*22	ENST00000380871	NM_006167.3	115	Agg/gg	2/2	1	2	FACETS	0.695	0.596	0.804	0.695	0.596	0.804	SUBCLONAL	1	TRUE	1	0.2	2		400	834	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426127	47426127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011050-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	414	699	0	ENST00000377045.4:c.647C>G	p.Pro216Arg	p.P216R	ENST00000377045	NM_001654.4	216	cCc/cGc	7/16	0.541870796111913	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.555456195948881	1		699	1049	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0011073-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	52	715	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.22367734020196	3	FACETS	0.776	0.664	0.898	0.776	0.664	0.898	SUBCLONAL	2	TRUE	1	0.22	3		715	338	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0011073-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	214	657	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.22367734020196	3	FACETS	0.912	0.846	0.98	0.912	0.846	0.98	CLONAL	2	TRUE	1	0.22	3		657	1184	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575077	48575077	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011073-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	26	211	0	ENST00000342988.3:c.272del	p.Pro91LeufsTer3	p.P91Lfs*3	ENST00000342988	NM_005359.5	91	Cct/ct	3/12	0.3	2	FACETS	0.838	0.665	1			1	CLONAL	1	TRUE	NA	0.22	2		211	282	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	224	126	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.713442834885566	2		126	598	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343720	343720	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0011085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	205	973	0	ENST00000262320.3:c.1956-2A>G		p.X652_splice	ENST00000262320	NM_003502.3	652			0.713442834885566	1	FACETS	0.563	0.524	0.602	0.563	0.524	0.602	SUBCLONAL	1	TRUE	0	0.713442834885566	1		973	657	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354408	354408	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	158	931	0	ENST00000262320.3:c.1150G>T	p.Glu384Ter	p.E384*	ENST00000262320	NM_003502.3	384	Gag/Tag	5/11	0.713442834885566	1	FACETS	0.394	0.361	0.427	0.394	0.361	0.427	SUBCLONAL	1	TRUE	0	0.713442834885566	1		931	724	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553561	29553561	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	208	305	1	ENST00000356175.3:c.2110C>A	p.Leu704Met	p.L704M	ENST00000356175	NM_000267.3	704	Ctg/Atg	18/57	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.713442834885566	2		306	531	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152524	56152524	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs758995748	NA	P-0011086-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	87	254	0	ENST00000399503.3:c.580A>G	p.Met194Val	p.M194V	ENST00000399503	NM_005921.1	194	Atg/Gtg	2/20	0.246511168745481	4	FACETS	0.765	0.676	0.86	0.383	0.338	0.43	SUBCLONAL	1	TRUE	2	0.386451493150127	4		254	816	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579514	7579514	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011086-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	428	380	0	ENST00000269305.4:c.173del	p.Pro58GlnfsTer65	p.P58Qfs*65	ENST00000269305	NM_001126112.2	58	cCa/ca	4/11	0.359499920798447	4	FACETS	0.981	0.942	1			1	CLONAL	4	TRUE	NA	0.386451493150127	4		380	783	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690802	89690802	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs1114167621	NA	P-0011091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	150	158	0	ENST00000371953.3:c.210-1G>C		p.X70_splice	ENST00000371953	NM_000314.4	70			0.680423234839864	1	FACETS	0.979	0.913	1	0.979	0.913	1	CLONAL	1	TRUE	0	0.680423234839864	1		158	297	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93607720	93607720	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	288	277	0	ENST00000375746.1:c.422A>G	p.Gln141Arg	p.Q141R	ENST00000375746	NM_001174167.1	141	cAg/cGg	3/14	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.680423234839864	2		277	844	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207176	1207176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	422	368	0	ENST00000326873.7:c.267del	p.Asn90ThrfsTer6	p.N90Tfs*6	ENST00000326873	NM_000455.4	88	atC/at	1/10	0.680423234839864	1	FACETS	0.958	0.919	0.998	0.958	0.919	0.998	CLONAL	1	TRUE	0	0.680423234839864	1		368	854	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028845	47028845	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	606	240	0	ENST00000377604.3:c.149del	p.Ser50ThrfsTer84	p.S50Tfs*84	ENST00000377604	NM_001204468.1	50	aGc/ac	3/24	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.680423234839864	1		240	864	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662939	52662939	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	63	603	0	ENST00000394830.3:c.1414C>T	p.Arg472Ter	p.R472*	ENST00000394830	NM_018313.4	472	Cga/Tga	13/30	0.600048522423725	1	FACETS	0.783	0.69	0.88	0.783	0.69	0.88	SUBCLONAL	1	TRUE	0	0.601436893506611	1		603	187	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506988	186506988	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	199	1148	0	ENST00000323963.5:c.1154T>C	p.Leu385Pro	p.L385P	ENST00000323963		385	cTt/cCt	11/11	0.600048522423725	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.601436893506611	1		1148	383	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400256	139400256	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	77	282	0	ENST00000277541.6:c.4092C>G	p.Ile1364Met	p.I1364M	ENST00000277541	NM_017617.3	1364	atC/atG	25/34	1	2	FACETS	0.848	0.752	0.949	0.848	0.752	0.949	CLONAL	1	TRUE	1	0.601436893506611	2		282	302	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227814	53227814	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	208	352	0	ENST00000375401.3:c.2374G>T	p.Glu792Ter	p.E792*	ENST00000375401	NM_004187.3	792	Gaa/Taa	17/26	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.601436893506611	1		352	437	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53253929	53253929	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	40	370	0	ENST00000375401.3:c.143C>A	p.Pro48Gln	p.P48Q	ENST00000375401	NM_004187.3	48	cCa/cAa	1/26	1	1	FACETS	0.25	0.208	0.297	0.25	0.208	0.297	SUBCLONAL	1	TRUE	0	0.601436893506611	1		370	372	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191511	10191516	+	inframe_deletion	In_Frame_Del	DEL	CCTAGT	CCTAGT	-	novel	NA	P-0011097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	156	446	0	ENST00000256474.2:c.505_510del	p.Leu169_Val170del	p.L169_V170del	ENST00000256474	NM_000551.3	168	agCCTAGTc/agc	3/3	0.600048522423725	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.601436893506611	1		446	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0011098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	472	365	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.585053824126203	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.585053824126203	2		367	802	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0011098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	457	432	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.585053824126203	3	FACETS	0.956	0.916	0.996	0.956	0.916	0.996	CLONAL	2	TRUE	1	0.585053824126203	3		432	1056	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0011101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	66	248	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.227371924268931	2	FACETS	1	0.95	1	0.589	0.515	0.668	CLONAL	1	TRUE	0	0.337483734487618	2		248	332	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	61	561	2	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	1	2	FACETS	0.489	0.421	0.563	0.489	0.421	0.563	SUBCLONAL	1	TRUE	1	0.337483734487618	2		563	740	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727451	66727451	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519729	NA	P-0011101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	29	616	0	ENST00000307102.5:c.167A>C	p.Gln56Pro	p.Q56P	ENST00000307102	NM_002755.3	56	cAg/cCg	2/11	0.337483734487618	1	FACETS	0.18	0.143	0.222	0.18	0.143	0.222	SUBCLONAL	1	TRUE	0	0.337483734487618	1		616	794	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0011101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	53	389	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.603	0.514	0.7	0.603	0.514	0.7	SUBCLONAL	1	TRUE	1	0.337483734487618	2		389	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0011101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	208	685	3	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	0.227371924268931	2	FACETS	1	0.988	1	0.661	0.613	0.709	CLONAL	1	TRUE	0	0.337483734487618	2		688	933	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557569	21557569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750816560	NA	P-0011101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	77	711	2	ENST00000382592.4:c.2276G>A	p.Arg759Gln	p.R759Q	ENST00000382592	NM_014572.2	759	cGg/cAg	5/8	1	2	FACETS	0.492	0.43	0.558	0.492	0.43	0.558	SUBCLONAL	1	TRUE	1	0.337483734487618	2		713	928	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828504	72828504	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	165	1086	3	ENST00000268489.5:c.8077C>T	p.Arg2693Ter	p.R2693*	ENST00000268489	NM_006885.3	2693	Cga/Tga	9/10	1	2	FACETS	0.754	0.691	0.821	0.754	0.691	0.821	SUBCLONAL	1	TRUE	1	0.337483734487618	2		1089	1296	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578541	7578541	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	26	531	0	ENST00000269305.4:c.389T>G	p.Leu130Arg	p.L130R	ENST00000269305	NM_001126112.2	130	cTc/cGc	5/11	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		531	889	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380276	+	missense_variant	Missense_Mutation	DNP	TT	TT	CA	novel	NA	P-0011115-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	21	619	1	ENST00000311936.3:c.182_183delinsTG	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAA/cTG	3/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		620	1038	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0011131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	532	354	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	FALSE	1	0.652325905529045	2		354	1241	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0011131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	174	264	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.570086476196075	2	FACETS	0.876	0.81	0.944	0.438	0.405	0.472	CLONAL	1	FALSE	0	0.652325905529045	2		264	609	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167577	NA	P-0011131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	256	241	0	ENST00000257430.4:c.4463del	p.Leu1488TyrfsTer19	p.L1488Yfs*19	ENST00000257430	NM_000038.5	1487	acT/ac	16/16	0.570086476196075	2	FACETS	0.934	0.877	0.993	0.467	0.438	0.497	CLONAL	1	FALSE	0	0.652325905529045	2		241	840	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670476	134670476	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	310	324	0	ENST00000398015.3:c.387G>C	p.Trp129Cys	p.W129C	ENST00000398015	NM_004441.4	129	tgG/tgC	3/16	0.570086476196075	2	FACETS	0.91	0.859	0.962	0.455	0.429	0.481	CLONAL	1	FALSE	0	0.652325905529045	2		324	1044	SUCCESS
APC	324	MSKCC	GRCh37	5	112174757	112174757	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	296	294	0	ENST00000257430.4:c.3466G>T	p.Glu1156Ter	p.E1156*	ENST00000257430	NM_000038.5	1156	Gaa/Taa	16/16	0.570086476196075	2	FACETS	0.976	0.921	1	0.488	0.46	0.516	CLONAL	1	FALSE	0	0.652325905529045	2		294	930	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435277	18435277	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	389	370	0	ENST00000266497.5:c.262G>T	p.Glu88Ter	p.E88*	ENST00000266497		88	Gaa/Taa	1/31	0.570086476196075	2	FACETS	1	0.979	1	0.525	0.5	0.552	CLONAL	1	FALSE	0	0.652325905529045	2		370	1135	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	214	321	0	ENST00000269305.4:c.388del	p.Leu130SerfsTer40	p.L130Sfs*40	ENST00000269305	NM_001126112.2	130	Ctc/tc	5/11	1	2	FACETS	0.665	0.618	0.714	0.665	0.618	0.714	SUBCLONAL	1	FALSE	1	0.652325905529045	2		321	986	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0011135-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	76	89	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.330034615626487	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.330034615626487	1		89	278	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0011135-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	413	247	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.330034615626487	4	FACETS	0.932	0.888	0.976			1	CLONAL	3	TRUE	NA	0.330034615626487	4		247	1191	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578219	+	inframe_deletion	In_Frame_Del	DEL	TGTCGAAAAGTG	TGTCGAAAAGTG	-	novel	NA	P-0011135-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	196	452	0	ENST00000269305.4:c.630_641del	p.Thr211_His214del	p.T211_H214del	ENST00000269305	NM_001126112.2	210	aaCACTTTTCGACAt/aat	6/11	0.330034615626487	1	FACETS	0.939	0.869	1	0.939	0.869	1	CLONAL	1	TRUE	0	0.330034615626487	1		452	1056	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0011154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	196	393	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.228276066171657	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	1	0.228276066171657	4		393	641	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0011154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	47	274	1	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.829	0.699	0.971	0.829	0.699	0.971	CLONAL	1	TRUE	1	0.228276066171657	2		275	497	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182858	123182858	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	54	182	0	ENST00000218089.9:c.823C>T	p.Gln275Ter	p.Q275*	ENST00000218089	NM_001042749.1	275	Cag/Tag	10/35	0.132238021382134	2	FACETS	1	0.96	1			1	INDETERMINATE	1	TRUE	NA	0.228276066171657	2		182	345	SUCCESS
ALK	238	MSKCC	GRCh37	2	29448419	29448419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140733978	NA	P-0011154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	65	551	2	ENST00000389048.3:c.3080C>T	p.Pro1027Leu	p.P1027L	ENST00000389048	NM_004304.4	1027	cCg/cTg	19/29	0.189913587780401	3	FACETS	0.693	0.599	0.795	0.346	0.299	0.398	SUBCLONAL	1	TRUE	1	0.228276066171657	3		553	916	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884839	134884839	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	47	440	0	ENST00000398015.3:c.1615C>A	p.Leu539Met	p.L539M	ENST00000398015	NM_004441.4	539	Ctg/Atg	8/16	1	2	FACETS	0.651	0.548	0.764	0.651	0.548	0.764	SUBCLONAL	1	TRUE	1	0.228276066171657	2		440	633	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55603348	55603348	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1435319685	NA	P-0011154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	93	386	0	ENST00000288135.5:c.2704A>G	p.Ile902Val	p.I902V	ENST00000288135	NM_000222.2	902	Ata/Gta	20/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.228276066171657	2		386	545	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467778	66467778	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	36	364	0	ENST00000273854.3:c.491G>A	p.Arg164Lys	p.R164K	ENST00000273854	NM_004439.5	164	aGa/aAa	3/18	1	2	FACETS	0.527	0.432	0.633	0.527	0.432	0.633	SUBCLONAL	1	TRUE	1	0.228276066171657	2		364	599	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588870	69588870	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	182	424	0	ENST00000168712.1:c.366G>T	p.Glu122Asp	p.E122D	ENST00000168712	NM_002007.2	122	gaG/gaT	2/3	0.228276066171657	3	FACETS	0.98	0.909	1	0.98	0.909	1	CLONAL	3	TRUE	0	0.228276066171657	3		424	604	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205781	108205781	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	153	311	0	ENST00000278616.4:c.8096C>T	p.Pro2699Leu	p.P2699L	ENST00000278616	NM_000051.3	2699	cCa/cTa	55/63	0.228276066171657	3	FACETS	0.969	0.892	1	0.969	0.892	1	CLONAL	3	TRUE	0	0.228276066171657	3		311	514	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26978105	26978105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	58	556	0	ENST00000381527.3:c.1282C>T	p.His428Tyr	p.H428Y	ENST00000381527	NM_001260.1	428	Cat/Tat	13/13	0.187700254923863	1	FACETS	0.604	0.518	0.699	0.604	0.518	0.699	SUBCLONAL	1	TRUE	0	0.228276066171657	1		556	745	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862854	9862854	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs796052551	NA	P-0011154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	54	407	0	ENST00000330684.3:c.2449A>G	p.Met817Val	p.M817V	ENST00000330684	NM_001134407.1	817	Atg/Gtg	12/13	1	2	FACETS	0.69	0.588	0.801	0.69	0.588	0.801	SUBCLONAL	1	TRUE	1	0.228276066171657	2		407	686	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054549	13054549	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	98	741	1	ENST00000316448.5:c.1076A>T	p.Asp359Val	p.D359V	ENST00000316448	NM_004343.3	359	gAc/gTc	9/9	1	2	FACETS	0.886	0.789	0.99	0.886	0.789	0.99	CLONAL	1	TRUE	1	0.228276066171657	2		742	969	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513417	41513417	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	60	478	2	ENST00000263253.7:c.321G>T	p.Gln107His	p.Q107H	ENST00000263253	NM_001429.3	107	caG/caT	2/31	1	2	FACETS	0.838	0.722	0.965	0.838	0.722	0.965	CLONAL	1	TRUE	1	0.228276066171657	2		480	627	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867528	78867534	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCCGG	CCCCCGG	-	novel	NA	P-0011154-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	149	361	1	ENST00000306801.3:c.2264_2270del	p.Ser755Ter	p.S755*	ENST00000306801	NM_020761.2	755	tCCCCCGGa/ta	20/34	0.228276066171657	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	1	0.228276066171657	3		362	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0011158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	269	365	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.682717061606247	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.696800550314114	1		367	472	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0011158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	160	446	1	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.696800550314114	3	FACETS	0.881	0.81	0.955	0.44	0.405	0.478	CLONAL	1	TRUE	1	0.696800550314114	3		447	703	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645687	12645687	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397516828	NA	P-0011158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	263	314	0	ENST00000251849.4:c.782C>G	p.Pro261Arg	p.P261R	ENST00000251849	NM_002880.3	261	cCt/cGt	7/17	0.682717061606247	1	FACETS	0.964	0.915	1	0.964	0.915	1	CLONAL	1	TRUE	0	0.696800550314114	1		314	510	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0011158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	181	175	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.696800550314114	2		175	459	SUCCESS
APC	324	MSKCC	GRCh37	5	112175720	112175720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	142	248	0	ENST00000257430.4:c.4429C>T	p.Gln1477Ter	p.Q1477*	ENST00000257430	NM_000038.5	1477	Cag/Tag	16/16	1	2	FACETS	0.894	0.821	0.969	0.894	0.821	0.969	CLONAL	1	TRUE	1	0.696800550314114	2		248	456	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921567	178921567	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	119	204	0	ENST00000263967.3:c.1049A>T	p.Asp350Val	p.D350V	ENST00000263967	NM_006218.2	350	gAc/gTc	5/21	0.664435498153581	2	FACETS	0.941	0.859	1	0.47	0.429	0.513	CLONAL	1	TRUE	0	0.696800550314114	2		204	363	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068352	16068352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778810900	NA	P-0011158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	15	14	0	ENST00000268712.3:c.559C>T	p.Arg187Cys	p.R187C	ENST00000268712	NM_006311.3	187	Cgt/Tgt	5/46	0.682717061606247	1	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	0	0.696800550314114	1		14	24	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977901	134977901	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	109	560	0	ENST00000398015.3:c.2894T>A	p.Ile965Asn	p.I965N	ENST00000398015	NM_004441.4	965	aTc/aAc	16/16	0.188480179208952	3	FACETS	1	0.906	1	0.506	0.453	0.563	CLONAL	1	TRUE	1	0.188480179208952	3		560	1250	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068118	94068118	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1435	114	698	1	ENST00000369303.4:c.844G>T	p.Gly282Trp	p.G282W	ENST00000369303	NM_004440.3	282	Ggg/Tgg	4/17	0.180921522707465	2	FACETS	0.781	0.7	0.867	0.39	0.35	0.434	SUBCLONAL	1	TRUE	0	0.188480179208952	2		699	1549	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578515	7578515	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1212996409	NA	P-0011175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	255	465	0	ENST00000269305.4:c.415A>T	p.Lys139Ter	p.K139*	ENST00000269305	NM_001126112.2	139	Aag/Tag	5/11	0.180921522707465	2	FACETS	0.843	0.789	0.898	1	0.989	1	CLONAL	3	TRUE	0	0.188480179208952	2		465	1070	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028682	12028682	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	69	480	0	ENST00000353533.5:c.885C>G	p.Ile295Met	p.I295M	ENST00000353533	NM_003010.3	295	atC/atG	8/11	0.180921522707465	2	FACETS	0.606	0.525	0.693	0.303	0.262	0.347	SUBCLONAL	1	TRUE	0	0.188480179208952	2		480	1209	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919924	50919924	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1284	93	616	0	ENST00000440232.2:c.3011C>G	p.Ala1004Gly	p.A1004G	ENST00000440232	NM_002691.3	1004	gCc/gGc	24/27	NA	2	FACETS	0.717	0.635	0.805			1	INDETERMINATE	1	TRUE	NA	0.188480179208952	2		616	1377	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742620	39742620	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011175-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	51	254	0	ENST00000361337.2:c.1463G>C	p.Arg488Thr	p.R488T	ENST00000361337	NM_003286.2	488	aGa/aCa	15/21	0.188480179208952	3	FACETS	0.979	0.831	1	0.326	0.277	0.381	CLONAL	1	TRUE	0	0.188480179208952	3		254	605	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152093	55152093	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121908585	NA	P-0011178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	242	378	0	ENST00000257290.5:c.2525A>T	p.Asp842Val	p.D842V	ENST00000257290	NM_006206.4	842	gAc/gTc	18/23	1	2	FACETS	0.994	0.929	1	0.994	0.929	1	CLONAL	1	TRUE	1	0.48	2		378	1014	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484336	120484337	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0011178-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	234	368	6	ENST00000256646.2:c.2793_2794del	p.Thr932PhefsTer13	p.T932Ffs*13	ENST00000256646	NM_024408.3	931	aaTAct/aact	18/34	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.48	2		374	889	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0011182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	414	677	1	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.620796012365305	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.620796012365305	1		678	885	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782097	9782097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	177	631	0	ENST00000377346.4:c.2120C>T	p.Pro707Leu	p.P707L	ENST00000377346	NM_005026.3	707	cCc/cTc	17/24	1	2	FACETS	0.443	0.407	0.481	0.443	0.407	0.481	SUBCLONAL	1	TRUE	1	0.620796012365305	2		631	1287	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634716	158634716	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	571	881	0	ENST00000263640.3:c.470T>A	p.Leu157His	p.L157H	ENST00000263640	NM_001105.4	157	cTc/cAc	5/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.620796012365305	2		881	1715	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356247	66356247	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199614818	NA	P-0011182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	71	472	1	ENST00000273854.3:c.1250G>A	p.Arg417Gln	p.R417Q	ENST00000273854	NM_004439.5	417	cGg/cAg	5/18	0.190543099605518	1	FACETS	0.177	0.154	0.202	0.177	0.154	0.202	INDETERMINATE	1	TRUE	0	0.620796012365305	1		473	891	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436057	110436057	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1204032443	NA	P-0011182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	260	386	0	ENST00000375856.3:c.2344G>A	p.Asp782Asn	p.D782N	ENST00000375856	NM_003749.2	782	Gac/Aac	1/2	0.617622792950229	3	FACETS	0.978	0.916	1	0.489	0.458	0.521	CLONAL	1	TRUE	1	0.620796012365305	3		386	1122	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573628	48574039	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTGTTACCATACAGAGAACATTGGATGGGAGGCTTCAGGTTAGTCTTATAAGAGTTTTTCTATACCCTCTATGGTGGCAGATTTAAAAACTTGCTACGTTTCCTTTCAAGCTACTACAGGGTAATTTAATTTGTGCTCCATCTCTTCAGATACTGTGCATCCTGTACAAATATGCATTATGGGAATTTCTGGAAGAATATGCAAAAGATAAAATCTTAAAGTTTTTTAATGTTCTACTCAGAAAAATGTTCAATGGAGAAAATTTGGAAAATAAAAATAAAAAGCAGAAAACCCACACTTCGCAAGAACTACCTTTAGCACTTTGGTATTCATTTTTGTAGCCTGTTGTTTTCTTTTTTTTTTTTTTCCTAGACGGAGTCTTGCTCTGTCACCCAGGCTGGAGTACAGTGGC	GTGTTACCATACAGAGAACATTGGATGGGAGGCTTCAGGTTAGTCTTATAAGAGTTTTTCTATACCCTCTATGGTGGCAGATTTAAAAACTTGCTACGTTTCCTTTCAAGCTACTACAGGGTAATTTAATTTGTGCTCCATCTCTTCAGATACTGTGCATCCTGTACAAATATGCATTATGGGAATTTCTGGAAGAATATGCAAAAGATAAAATCTTAAAGTTTTTTAATGTTCTACTCAGAAAAATGTTCAATGGAGAAAATTTGGAAAATAAAAATAAAAAGCAGAAAACCCACACTTCGCAAGAACTACCTTTAGCACTTTGGTATTCATTTTTGTAGCCTGTTGTTTTCTTTTTTTTTTTTTTCCTAGACGGAGTCTTGCTCTGTCACCCAGGCTGGAGTACAGTGGC	-	novel	NA	P-0011182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	84	275	0	ENST00000342988.3:c.215_249+377del		p.X72_splice	ENST00000342988	NM_005359.5	72		2/12	0.620796012365305	1	FACETS	0.644	0.575	0.715	0.644	0.575	0.715	SUBCLONAL	1	TRUE	0	0.620796012365305	1		275	290	SUCCESS
APC	324	MSKCC	GRCh37	5	112174929	112174929	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	220	351	0	ENST00000257430.4:c.3638del	p.Ser1213Ter	p.S1213*	ENST00000257430	NM_000038.5	1213	tCa/ta	16/16	1	2	FACETS	0.848	0.79	0.907	0.848	0.79	0.907	CLONAL	1	TRUE	1	0.620796012365305	2		351	836	SUCCESS
APC	324	MSKCC	GRCh37	5	112175596	112175596	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0011182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	351	523	0	ENST00000257430.4:c.4306del	p.Ser1436ValfsTer37	p.S1436Vfs*37	ENST00000257430	NM_000038.5	1435	agA/ag	16/16	1	2	FACETS	0.932	0.883	0.983	0.932	0.883	0.983	CLONAL	1	TRUE	1	0.620796012365305	2		523	1213	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0011191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	715	715	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.501832898768886	7	FACETS	0.984	0.958	1	0.984	0.958	1	CLONAL	6	TRUE	1	0.501832898768886	7		715	1088	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0011191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	402	272	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.501832898768886	2	FACETS	0.973	0.942	1	1	0.997	1	CLONAL	3	TRUE	0	0.501832898768886	2		272	549	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422611	49422611	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	470	434	0	ENST00000301067.7:c.14382G>C	p.Lys4794Asn	p.K4794N	ENST00000301067	NM_003482.3	4794	aaG/aaC	45/54	0.151706858689986	6	FACETS	1	0.992	1			1	INDETERMINATE	4	TRUE	NA	0.501832898768886	6		434	854	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971094	21971101	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCCGGG	CTCCCGGG	-	novel	NA	P-0011191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	281	250	0	ENST00000304494.5:c.257_264del	p.Ala86GlyfsTer31	p.A86Gfs*31	ENST00000304494	NM_000077.4	86	gCCCGGGAG/g	2/3	0.501832898768886	3	FACETS	0.887	0.852	0.92	1	0.993	1	CLONAL	4	TRUE	0	0.501832898768886	3		250	395	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971094	21971102	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCCGGGC	CTCCCGGGC	A	novel	NA	P-0011191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	281	250	0	ENST00000304494.5:c.256_264delinsT	p.Ala86TrpfsTer31	p.A86Wfs*31	ENST00000304494	NM_000077.4	86	GCCCGGGAG/T	2/3	0.501832898768886				0.852	0.92				CLONAL	4	TRUE	0	0.501832898768886	3		250	395	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0011192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	83	395	2	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.3	3	FACETS	0.768	0.676	0.866	0.384	0.338	0.433	SUBCLONAL	1	TRUE	1	0.3	3		397	829	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098944	178098944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	71	280	0	ENST00000397062.3:c.101G>A	p.Arg34Gln	p.R34Q	ENST00000397062	NM_006164.4	34	cGa/cAa	2/5	1	2	FACETS	0.947	0.828	1	0.947	0.828	1	CLONAL	1	TRUE	1	0.3	2		280	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs483352695	NA	P-0011192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	142	434	0	ENST00000269305.4:c.736A>C	p.Met246Leu	p.M246L	ENST00000269305	NM_001126112.2	246	Atg/Ctg	7/11	1	2	FACETS	0.744	0.676	0.816	0.744	0.676	0.816	SUBCLONAL	1	TRUE	1	0.3	2		434	1272	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121913370	NA	P-0011192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	18	263	0	ENST00000288602.6:c.1742A>G	p.Asn581Ser	p.N581S	ENST00000288602	NM_004333.4	581	aAt/aGt	15/18	0.3	3	FACETS	0.879	0.666	1			1	CLONAL	1	TRUE	NA	0.3	3		263	157	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288672	198288672	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1222778757	NA	P-0011192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	88	459	0	ENST00000335508.6:c.55C>G	p.Gln19Glu	p.Q19E	ENST00000335508	NM_012433.2	19	Caa/Gaa	2/25	1	2	FACETS	0.756	0.669	0.849	0.756	0.669	0.849	SUBCLONAL	1	TRUE	1	0.3	2		459	776	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073704	8073704	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	46	639	0	ENST00000377482.5:c.955G>C	p.Val319Leu	p.V319L	ENST00000377482	NM_018948.3	319	Gta/Cta	4/4	NA	2	FACETS	0.43	0.361	0.507			1	INDETERMINATE	1	TRUE	NA	0.3	2		639	713	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165789	118165789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	63	222	0	ENST00000369448.3:c.299C>T	p.Pro100Leu	p.P100L	ENST00000369448	NM_017709.3	100	cCa/cTa	2/2	0.3	3	FACETS	0.697	0.602	0.8	0.348	0.301	0.4	SUBCLONAL	1	TRUE	1	0.3	3		222	693	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664880	138664880	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757038357	NA	P-0011192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	10	36	0	ENST00000330315.3:c.685G>A	p.Ala229Thr	p.A229T	ENST00000330315	NM_023067.3	229	Gct/Act	1/1	0.14171380467385	4	FACETS	0.456	0.309	0.641	0.228	0.154	0.321	INDETERMINATE	1	TRUE	2	0.3	4		36	190	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839802	27839802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2161	285	883	0	ENST00000328488.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000328488	NM_003533.2	98	Gag/Aag	1/1	0.260036779844506	4	FACETS	1	0.944	1			1	CLONAL	1	TRUE	NA	0.3	4		883	2446	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017737	31017737	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	167	323	0	ENST00000375687.4:c.599G>T	p.Gly200Val	p.G200V	ENST00000375687	NM_015338.5	200	gGc/gTc	8/13	0.14171380467385	4	FACETS	1	0.967	1	0.552	0.506	0.601	INDETERMINATE	1	TRUE	2	0.3	4		323	1310	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325456	1325456	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	45	383	0	ENST00000400841.2:c.219C>G	p.Asn73Lys	p.N73K	ENST00000400841		73	aaC/aaG	3/6	NA	2	FACETS	0.448	0.376	0.529			1	INDETERMINATE	1	TRUE	NA	0.3	2		383	669	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522598	157522598	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554236040	NA	P-0011197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	293	365	2	ENST00000346085.5:c.4870C>T	p.Arg1624Ter	p.R1624*	ENST00000346085	NM_020732.3	1624	Cga/Tga	18/20	1	2	FACETS	0.922	0.87	0.975	0.922	0.87	0.975	CLONAL	1	TRUE	1	0.703180957096486	2		367	904	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0011212-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	27	715	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		715	1006	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0011212-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	34	349	1	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		350	1051	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0011215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	74	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.39	0.34	0.444	0.39	0.34	0.444	SUBCLONAL	1	TRUE	1	0.39	2		336	973	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0011215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	117	440	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	0.518	0.466	0.574	0.518	0.466	0.574	SUBCLONAL	1	TRUE	1	0.39	2		440	1158	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271190	38271190	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs775166971	NA	P-0011215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	93	258	0	ENST00000425967.3:c.2518C>T	p.Arg840Ter	p.R840*	ENST00000425967	NM_001174067.1	840	Cga/Tga	19/19	0.187375912818874	1	FACETS	0.661	0.589	0.737	0.661	0.589	0.737	INDETERMINATE	1	TRUE	0	0.39	1		258	581	SUCCESS
AR	367	MSKCC	GRCh37	X	66905936	66905936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759988495	NA	P-0011215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	138	247	0	ENST00000374690.3:c.1853G>A	p.Arg618Gln	p.R618Q	ENST00000374690	NM_000044.3	618	cGg/cAg	3/8	1	1	FACETS	0.73	0.665	0.799	0.73	0.665	0.799	SUBCLONAL	1	TRUE	0	0.39	1		247	780	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437851	56438214	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAAATGAATCTAACCCCACCCTTCATTGCCATGGGTCTAAAATGAGATAATGCATCCAAAGCACCACTGCAGCCTGGCACGTGGTACACTCTCAACAAACAATAGTGCTCTTTCACTGGAAGGTCAGAAAAGTGACCAAACTTCAGGCTGGTCCCTGATCTCTGCCTCATGCAGGACACATGGGAAACAGATGTAGCCAGGGTACCCATACCAGCCCCTAGGCCTGCCCACCCCTCCCCCAGCTTCAATCTCCCCAGTCTGGTCATGGAGGTGAACCACAAGACCTGCCTTACCTGCCCCTCAGAGAACTCCTCCAGACAGATGGCACACACAGGGGCTGAGCTGCAGCTGCTCCCTGAGTCTG	AAAATGAATCTAACCCCACCCTTCATTGCCATGGGTCTAAAATGAGATAATGCATCCAAAGCACCACTGCAGCCTGGCACGTGGTACACTCTCAACAAACAATAGTGCTCTTTCACTGGAAGGTCAGAAAAGTGACCAAACTTCAGGCTGGTCCCTGATCTCTGCCTCATGCAGGACACATGGGAAACAGATGTAGCCAGGGTACCCATACCAGCCCCTAGGCCTGCCCACCCCTCCCCCAGCTTCAATCTCCCCAGTCTGGTCATGGAGGTGAACCACAAGACCTGCCTTACCTGCCCCTCAGAGAACTCCTCCAGACAGATGGCACACACAGGGGCTGAGCTGCAGCTGCTCCCTGAGTCTG	-	novel	NA	P-0011215-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	84	12	0	ENST00000407977.2:c.779_850-239del		p.X260_splice	ENST00000407977		260		7/10	0.175583392545758	2	FACETS	0.945	0.88	1	1	0.989	1	INDETERMINATE	4	TRUE	0	0.39	2		12	114	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498432	89498432	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	57	445	0	ENST00000336596.2:c.2404A>G	p.Thr802Ala	p.T802A	ENST00000336596	NM_005233.5	802	Acg/Gcg	14/17	1	2	FACETS	0.968	0.828	1	0.968	0.828	1	CLONAL	1	TRUE	1	0.13	2		445	906	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624296	89624298	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	novel	NA	P-0011225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	33	276	0	ENST00000371953.3:c.70_72del	p.Asp24del	p.D24del	ENST00000371953	NM_000314.4	24	GAC/-	1/9	1	2	FACETS	0.905	0.736	1	0.905	0.736	1	CLONAL	1	TRUE	1	0.13	2		276	561	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0011239-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	28	645	1	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		646	942	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0011259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	119	566	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.293777212981383	1	FACETS	0.983	0.888	1	0.983	0.888	1	CLONAL	1	TRUE	0	0.293777212981383	1		568	703	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791719	42791719	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	61	500	0	ENST00000575354.2:c.605G>A	p.Arg202Gln	p.R202Q	ENST00000575354	NM_015125.3	202	cGg/cAg	5/20	1	2	FACETS	0.638	0.55	0.734	0.638	0.55	0.734	SUBCLONAL	1	TRUE	1	0.293777212981383	2		500	651	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420315	88420315	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773244598	NA	P-0011259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	49	389	1	ENST00000360948.2:c.2371C>T	p.Arg791Trp	p.R791W	ENST00000360948	NM_001012338.2	791	Cgg/Tgg	19/19	1	2	FACETS	0.851	0.723	0.991	0.851	0.723	0.991	CLONAL	1	TRUE	1	0.293777212981383	2		390	392	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900984	114900984	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778855667	NA	P-0011259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	188	1024	0	ENST00000543371.1:c.598del	p.Leu200SerfsTer25	p.L200Sfs*25	ENST00000543371	NM_001198531.1	198	caC/ca	6/14	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.293777212981383	2		1024	1078	SUCCESS
APC	324	MSKCC	GRCh37	5	112174835	112174835	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0011259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	93	434	3	ENST00000257430.4:c.3544A>T	p.Lys1182Ter	p.K1182*	ENST00000257430	NM_000038.5	1182	Aaa/Taa	16/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.293777212981383	2		437	548	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554446	63554446	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	124	533	0	ENST00000307078.5:c.293T>G	p.Phe98Cys	p.F98C	ENST00000307078	NM_004655.3	98	tTc/tGc	2/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.293777212981383	2		533	660	SUCCESS
APC	324	MSKCC	GRCh37	5	112175039	112175040	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs1114167583	NA	P-0011259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	31	380	0	ENST00000257430.4:c.3749_3750del	p.Lys1250SerfsTer5	p.K1250Sfs*5	ENST00000257430	NM_000038.5	1250	AAa/a	16/16	1	2	FACETS	0.473	0.382	0.576	0.473	0.382	0.576	SUBCLONAL	1	TRUE	1	0.293777212981383	2		380	446	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969327	44969327	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	126	272	1	ENST00000377967.4:c.4009G>T	p.Glu1337Ter	p.E1337*	ENST00000377967	NM_021140.2	1337	Gag/Tag	28/29	1	1	FACETS	0.818	0.749	0.889	1	0.988	1	CLONAL	2	TRUE	0	0.35	1		273	363	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0011269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	46	559	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.241	0.202	0.284	0.241	0.202	0.284	SUBCLONAL	1	TRUE	1	0.485239130122478	2		559	786	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0011269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	71	301	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	1	2	FACETS	0.334	0.291	0.382	0.334	0.291	0.382	SUBCLONAL	1	TRUE	1	0.485239130122478	2		301	875	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101024	27101024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	73	441	0	ENST00000324856.7:c.4306C>T	p.Pro1436Ser	p.P1436S	ENST00000324856	NM_006015.4	1436	Cct/Tct	18/20	1	2	FACETS	0.392	0.342	0.446	0.392	0.342	0.446	SUBCLONAL	1	TRUE	1	0.485239130122478	2		441	767	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798497	45798497	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	116	531	1	ENST00000450313.1:c.514C>T	p.Gln172Ter	p.Q172*	ENST00000450313	NM_012222.2	172	Caa/Taa	7/16	1	2	FACETS	0.437	0.393	0.484	0.437	0.393	0.484	SUBCLONAL	1	TRUE	1	0.485239130122478	2		532	1094	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991668	25991668	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	104	385	0	ENST00000435504.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000435504		192	Cag/Tag	7/13	1	2	FACETS	0.447	0.399	0.497	0.447	0.399	0.497	SUBCLONAL	1	TRUE	1	0.485239130122478	2		385	960	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526221	189526221	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	76	553	1	ENST00000264731.3:c.485C>T	p.Ser162Leu	p.S162L	ENST00000264731	NM_003722.4	162	tCa/tTa	4/14	1	2	FACETS	0.298	0.261	0.339	0.298	0.261	0.339	SUBCLONAL	1	TRUE	1	0.485239130122478	2		554	1050	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193857	106193857	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1157107314	NA	P-0011269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	74	458	0	ENST00000380013.4:c.4319G>A	p.Arg1440Gln	p.R1440Q	ENST00000380013	NM_001127208.2	1440	cGg/cAg	10/11	1	2	FACETS	0.306	0.266	0.348	0.306	0.266	0.348	SUBCLONAL	1	TRUE	1	0.485239130122478	2		458	998	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0011269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	29	161	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.387	0.311	0.473			1	INDETERMINATE	1	TRUE	NA	0.485239130122478	2		161	309	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441147	149441147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	56	487	0	ENST00000286301.3:c.1765G>A	p.Gly589Arg	p.G589R	ENST00000286301	NM_005211.3	589	Gga/Aga	13/22	0.353089907171054	1	FACETS	0.242	0.207	0.281	0.242	0.207	0.281	SUBCLONAL	1	TRUE	0	0.485239130122478	1		487	722	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183126	32183126	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	83	462	0	ENST00000375023.3:c.1898T>G	p.Leu633Arg	p.L633R	ENST00000375023	NM_004557.3	633	cTg/cGg	12/30	0.485239130122478	3	FACETS	0.421	0.371	0.476	0.211	0.185	0.238	SUBCLONAL	1	TRUE	1	0.485239130122478	3		462	1009	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0011269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	79	436	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	1	2	FACETS	0.328	0.288	0.372	0.328	0.288	0.372	SUBCLONAL	1	TRUE	1	0.485239130122478	2		436	992	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241677	55241677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504256	NA	P-0011269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	21	402	1	ENST00000275493.2:c.2125G>A	p.Glu709Lys	p.E709K	ENST00000275493	NM_005228.3	709	Gaa/Aaa	18/28	1	2	FACETS	0.106	0.081	0.135	0.106	0.081	0.135	SUBCLONAL	1	TRUE	1	0.485239130122478	2		403	818	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341196	8341196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	47	335	0	ENST00000356435.5:c.5020C>T	p.Arg1674Cys	p.R1674C	ENST00000356435		1674	Cgc/Tgc	30/35	1	2	FACETS	0.26	0.218	0.306	0.26	0.218	0.306	SUBCLONAL	1	TRUE	1	0.485239130122478	2		335	746	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528755	8528755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	59	352	0	ENST00000356435.5:c.377C>T	p.Pro126Leu	p.P126L	ENST00000356435		126	cCt/cTt	4/35	1	2	FACETS	0.351	0.302	0.406	0.351	0.302	0.406	SUBCLONAL	1	TRUE	1	0.485239130122478	2		352	692	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650807	93650807	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	50	360	0	ENST00000375746.1:c.1733G>A	p.Gly578Glu	p.G578E	ENST00000375746	NM_001174167.1	578	gGa/gAa	13/14	1	2	FACETS	0.315	0.267	0.369	0.315	0.267	0.369	SUBCLONAL	1	TRUE	1	0.485239130122478	2		360	654	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239851	98239851	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	67	426	0	ENST00000331920.6:c.1481C>T	p.Ser494Phe	p.S494F	ENST00000331920	NM_000264.3	494	tCc/tTc	10/24	1	2	FACETS	0.317	0.275	0.364	0.317	0.275	0.364	SUBCLONAL	1	TRUE	1	0.485239130122478	2		426	870	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563098	21563098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	58	319	0	ENST00000382592.4:c.821C>T	p.Ser274Phe	p.S274F	ENST00000382592	NM_014572.2	274	tCc/tTc	4/8	1	2	FACETS	0.417	0.358	0.481	0.417	0.358	0.481	SUBCLONAL	1	TRUE	1	0.485239130122478	2		319	573	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022962	33022962	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	100	618	0	ENST00000300177.4:c.71G>A	p.Gly24Glu	p.G24E	ENST00000300177	NM_001191322.1	24	gGg/gAg	2/2	1	2	FACETS	0.376	0.334	0.42	0.376	0.334	0.42	SUBCLONAL	1	TRUE	1	0.485239130122478	2		618	1097	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729162	66729162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519732	NA	P-0011269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	49	474	0	ENST00000307102.5:c.370C>T	p.Pro124Ser	p.P124S	ENST00000307102	NM_002755.3	124	Ccg/Tcg	3/11	1	2	FACETS	0.226	0.191	0.266	0.226	0.191	0.266	SUBCLONAL	1	TRUE	1	0.485239130122478	2		474	892	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678406	88678406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	104	596	0	ENST00000360948.2:c.1130C>T	p.Thr377Ile	p.T377I	ENST00000360948	NM_001012338.2	377	aCc/aTc	9/19	1	2	FACETS	0.413	0.369	0.46	0.413	0.369	0.46	SUBCLONAL	1	TRUE	1	0.485239130122478	2		596	1038	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858016	9858016	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	78	544	0	ENST00000330684.3:c.3385C>T	p.His1129Tyr	p.H1129Y	ENST00000330684	NM_001134407.1	1129	Cac/Tac	13/13	NA	2	FACETS	0.354	0.311	0.402			1	INDETERMINATE	1	TRUE	NA	0.485239130122478	2		544	907	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862775	9862775	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555483669	NA	P-0011269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	62	459	1	ENST00000330684.3:c.2528G>A	p.Trp843Ter	p.W843*	ENST00000330684	NM_001134407.1	843	tGg/tAg	12/13	NA	2	FACETS	0.341	0.294	0.393			1	INDETERMINATE	1	TRUE	NA	0.485239130122478	2		460	749	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892263	9892263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	68	404	0	ENST00000330684.3:c.2227G>A	p.Glu743Lys	p.E743K	ENST00000330684	NM_001134407.1	743	Gaa/Aaa	11/13	NA	2	FACETS	0.399	0.347	0.456			1	INDETERMINATE	1	TRUE	NA	0.485239130122478	2		404	702	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865793	56865794	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0011269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	124	657	1	ENST00000308159.5:c.1125_1126delinsTT	p.Arg376Cys	p.R376C	ENST00000308159	NM_014669.4	375	taCCgt/taTTgt	11/22	1	2	FACETS	0.401	0.362	0.443	0.401	0.362	0.443	SUBCLONAL	1	TRUE	1	0.485239130122478	2		658	1274	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121131	11121131	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	59	487	1	ENST00000358026.2:c.2198C>T	p.Ala733Val	p.A733V	ENST00000358026	NM_001128849.1	733	gCc/gTc	15/36	1	2	FACETS	0.268	0.23	0.31	0.268	0.23	0.31	SUBCLONAL	1	TRUE	1	0.485239130122478	2		488	907	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763407	41763407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1371273703	NA	P-0011269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	77	524	1	ENST00000301178.4:c.2206G>A	p.Gly736Arg	p.G736R	ENST00000301178	NM_021913.4	736	Ggg/Agg	19/20	1	2	FACETS	0.303	0.265	0.344	0.303	0.265	0.344	SUBCLONAL	1	TRUE	1	0.485239130122478	2		525	1049	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905315	50905315	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	95	686	1	ENST00000440232.2:c.523G>T	p.Asp175Tyr	p.D175Y	ENST00000440232	NM_002691.3	175	Gac/Tac	5/27	NA	2	FACETS	0.402	0.357	0.451			1	INDETERMINATE	1	TRUE	NA	0.485239130122478	2		687	973	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735448	40735448	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	70	482	0	ENST00000373198.4:c.3425G>A	p.Arg1142Lys	p.R1142K	ENST00000373198	NM_133170.3	1142	aGg/aAg	25/32	1	2	FACETS	0.398	0.346	0.454	0.398	0.346	0.454	SUBCLONAL	1	TRUE	1	0.485239130122478	2		482	725	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735554	40735554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	25	273	0	ENST00000373198.4:c.3319G>A	p.Ala1107Thr	p.A1107T	ENST00000373198	NM_133170.3	1107	Gct/Act	25/32	1	2	FACETS	0.229	0.18	0.286	0.229	0.18	0.286	SUBCLONAL	1	TRUE	1	0.485239130122478	2		273	449	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945660	54945660	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756649666	NA	P-0011269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	16	111	0	ENST00000312783.6:c.910C>T	p.Arg304Trp	p.R304W	ENST00000312783	NM_198436.1	304	Cgg/Tgg	9/10	1	2	FACETS	0.338	0.25	0.442	0.338	0.25	0.442	SUBCLONAL	1	TRUE	1	0.485239130122478	2		111	195	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349333	73349360	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGCTTAGATTCATACCATTCGTTCTGT	CTGCTTAGATTCATACCATTCGTTCTGT	-	novel	NA	P-0011278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	75	303	0	ENST00000377767.4:c.976_987+16del		p.X326_splice	ENST00000377767	NM_014953.3	326		6/21	0.424702789639264	1	FACETS	0.67	0.59	0.756	0.67	0.59	0.756	SUBCLONAL	1	TRUE	0	0.424702789639264	1		303	415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577564	+	frameshift_variant	Frame_Shift_Del	DEL	TCCGGTTCATGCCGCCCATGCAGGAACTG	TCCGGTTCATGCCGCCCATGCAGGAACTG	-	novel	NA	P-0011278-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	111	438	0	ENST00000269305.4:c.717_745del	p.Asn239LysfsTer15	p.N239Kfs*15	ENST00000269305	NM_001126112.2	239	aaCAGTTCCTGCATGGGCGGCATGAACCGGAgg/aagg	7/11	0.424702789639264	1	FACETS	0.798	0.72	0.879	0.798	0.72	0.879	SUBCLONAL	1	TRUE	0	0.424702789639264	1		438	516	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0011279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	303	284	0	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	0.880804204137317	2		284	663	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578286	7578286	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0011279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	611	483	0	ENST00000269305.4:c.563del	p.Leu188ArgfsTer59	p.L188Rfs*59	ENST00000269305	NM_001126112.2	188	cTg/cg	6/11	1	2	FACETS	1	0.985	1	1	0.998	1	CLONAL	2	TRUE	1	0.880804204137317	2		483	692	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890157	76890158	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0011279-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	489	673	0	ENST00000373344.5:c.4736_4737del	p.Val1579GlufsTer21	p.V1579Efs*21	ENST00000373344	NM_000489.3	1579	gTG/g	17/35	0.880804204137317	1	FACETS	0.952	0.925	0.977	0.952	0.925	0.977	CLONAL	1	TRUE	0	0.880804204137317	1		673	653	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0011281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	158	250	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.256205990383072	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.256205990383072	4		250	644	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201059	NA	P-0011281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	190	676	1	ENST00000269305.4:c.856G>T	p.Glu286Ter	p.E286*	ENST00000269305	NM_001126112.2	286	Gaa/Taa	8/11	0.256205990383072	2	FACETS	0.993	0.92	1	0.993	0.92	1	CLONAL	2	TRUE	0	0.256205990383072	2		677	747	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413206	139413206	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	128	498	1	ENST00000277541.6:c.936C>A	p.Cys312Ter	p.C312*	ENST00000277541	NM_017617.3	312	tgC/tgA	6/34	0.256205990383072	3	FACETS	1	0.969	1	0.582	0.527	0.641	CLONAL	1	TRUE	1	0.256205990383072	3		499	968	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216958	2216958	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	87	402	0	ENST00000398665.3:c.2413G>A	p.Glu805Lys	p.E805K	ENST00000398665	NM_032482.2	805	Gag/Aag	21/28	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.256205990383072	2		402	626	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0011282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	273	801	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.353986018532624	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.353986018532624	1		801	1158	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779452	3779452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011282-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	190	404	1	ENST00000262367.5:c.5596C>T	p.Arg1866Cys	p.R1866C	ENST00000262367	NM_004380.2	1866	Cgc/Tgc	31/31	0.253708264382031	1	FACETS	0.933	0.863	1	0.933	0.863	1	CLONAL	1	TRUE	0	0.353986018532624	1		405	947	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0011300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	447	414	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.399323979778433	3	FACETS	1	0.994	1	0.809	0.777	0.841	CLONAL	2	TRUE	0	0.534358747878976	3		416	874	SUCCESS
APC	324	MSKCC	GRCh37	5	112174406	112174406	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	155	230	1	ENST00000257430.4:c.3115G>T	p.Gly1039Ter	p.G1039*	ENST00000257430	NM_000038.5	1039	Gga/Tga	16/16	0.412887882020487	2	FACETS	0.806	0.748	0.864	0.806	0.748	0.864	CLONAL	2	TRUE	0	0.534358747878976	2		231	360	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393422	139393422	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1060502237	NA	P-0011300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	345	424	1	ENST00000277541.6:c.6109G>T	p.Ala2037Ser	p.A2037S	ENST00000277541	NM_017617.3	2037	Gcc/Tcc	33/34	0.299953409394704	4	FACETS	1	0.972	1	1	0.972	1	INDETERMINATE	2	TRUE	2	0.534358747878976	4		425	958	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433784	49433784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760007799	NA	P-0011300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	594	520	0	ENST00000301067.7:c.7769C>T	p.Ser2590Leu	p.S2590L	ENST00000301067	NM_003482.3	2590	tCg/tTg	31/54	0.499917321387162	4	FACETS	0.855	0.824	0.886	0.855	0.824	0.886	CLONAL	3	TRUE	1	0.534358747878976	4		520	1330	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144713	58144713	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	103	272	0	ENST00000257904.6:c.515C>G	p.Thr172Arg	p.T172R	ENST00000257904	NM_000075.3	172	aCa/aGa	4/8	0.499917321387162	4	FACETS	0.685	0.612	0.762	0.228	0.204	0.254	SUBCLONAL	1	TRUE	1	0.534358747878976	4		272	864	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420245	88420245	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1191745945	NA	P-0011300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	257	406	0	ENST00000360948.2:c.2441G>A	p.Arg814Gln	p.R814Q	ENST00000360948	NM_001012338.2	814	cGg/cAg	19/19	0.299953409394704	4	FACETS	0.812	0.761	0.863	0.812	0.761	0.863	INDETERMINATE	2	TRUE	2	0.534358747878976	4		406	909	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612205	1612205	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0011300-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	228	333	0	ENST00000344749.5:c.1813+1G>A		p.X605_splice	ENST00000344749	NM_001136139.2	605			0.344059470638464	4	FACETS	0.838	0.783	0.894	0.838	0.783	0.894	CLONAL	2	TRUE	2	0.534358747878976	4		333	781	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0011310-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	133	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	0.902	1	0.988	0.902	1	CLONAL	1	TRUE	1	0.494794326044195	2		284	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577500	7577514	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TGGAGTCTTCCAGTG	TGGAGTCTTCCAGTG	-	novel	NA	P-0011319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	59	417	0	ENST00000269305.4:c.767_781del	p.Thr256_Ser260del	p.T256_S260del	ENST00000269305	NM_001126112.2	256	aCACTGGAAGACTCCAgt/agt	7/11	0.184569557711471	1	FACETS	0.721	0.619	0.833	0.721	0.619	0.833	SUBCLONAL	1	FALSE	0	0.184569557711471	1		417	805	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547030	9547030	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	25	120	0	ENST00000353224.5:c.992T>A	p.Val331Glu	p.V331E	ENST00000353224	NM_177990.2	331	gTg/gAg	5/10	1	2	FACETS	1	0.842	1	1	0.842	1	CLONAL	1	FALSE	1	0.184569557711471	2		120	251	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244692	46244720	+	frameshift_variant	Frame_Shift_Del	DEL	TAAGCCAGCCAGCTCAACAAGGTCAAACT	TAAGCCAGCCAGCTCAACAAGGTCAAACT	-	novel	NA	P-0011319-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	86	531	0	ENST00000334344.6:c.2788_2816del	p.Ser930CysfsTer11	p.S930Cfs*11	ENST00000334344	NM_152641.2	929	gTAAGCCAGCCAGCTCAACAAGGTCAAACT/g	15/21	1	2	FACETS	0.749	0.66	0.844	0.749	0.66	0.844	SUBCLONAL	1	FALSE	1	0.184569557711471	2		531	1245	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0011370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	434	422	1	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.601773311692646	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.670074551207297	1		423	855	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0011379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	69	715	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	0.17	2		715	735	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0011379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	46	355	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.3	2	FACETS	0.997	0.839	1			1	CLONAL	1	TRUE	NA	0.17	2		355	543	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046703	180046703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	42	332	0	ENST00000261937.6:c.2609G>A	p.Gly870Asp	p.G870D	ENST00000261937	NM_182925.4	870	gGc/gAc	18/30	1	2	FACETS	0.84	0.701	0.996	0.84	0.701	0.996	CLONAL	1	TRUE	1	0.17	2		332	588	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778847	9778847	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	50	251	0	ENST00000377346.4:c.1116G>C	p.Lys372Asn	p.K372N	ENST00000377346	NM_005026.3	372	aaG/aaC	9/24	1	2	FACETS	0.929	0.788	1	0.929	0.788	1	CLONAL	1	TRUE	1	0.17	2		251	633	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022402	26022402	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	38	289	0	ENST00000435504.4:c.255A>C	p.Lys85Asn	p.K85N	ENST00000435504		85	aaA/aaC	5/13	1	2	FACETS	0.675	0.557	0.808	0.675	0.557	0.808	SUBCLONAL	1	TRUE	1	0.17	2		289	662	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604680	48604680	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	56	318	0	ENST00000342988.3:c.1502T>G	p.Leu501Arg	p.L501R	ENST00000342988	NM_005359.5	501	cTc/cGc	12/12	1	2	FACETS	0.951	0.813	1	0.951	0.813	1	CLONAL	1	TRUE	1	0.17	2		318	693	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0011390-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	187	273	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		273	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0011396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	199	354	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.297443103372658	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.29	1		354	1074	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0011396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	106	260	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.275522972584838	1	FACETS	0.95	0.853	1	0.95	0.853	1	CLONAL	1	TRUE	0	0.29	1		260	658	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604673	48604673	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060500738	NA	P-0011396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	45	345	0	ENST00000342988.3:c.1495T>C	p.Cys499Arg	p.C499R	ENST00000342988	NM_005359.5	499	Tgc/Cgc	12/12	0.223845693501018	1	FACETS	0.301	0.252	0.356	0.301	0.252	0.356	SUBCLONAL	1	TRUE	0	0.29	1		345	881	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911598	39911598	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	259	259	0	ENST00000378444.4:c.5032C>G	p.Arg1678Gly	p.R1678G	ENST00000378444	NM_001123385.1	1678	Cgc/Ggc	15/15	1	1	FACETS	0.988	0.929	1	1	0.995	1	CLONAL	2	TRUE	0	0.29	1		259	773	SUCCESS
APC	324	MSKCC	GRCh37	5	112163671	112163671	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554081901	NA	P-0011396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	93	490	0	ENST00000257430.4:c.1594C>T	p.Gln532Ter	p.Q532*	ENST00000257430	NM_000038.5	532	Caa/Taa	13/16	0.297443103372658	1	FACETS	0.49	0.434	0.55	0.49	0.434	0.55	SUBCLONAL	1	TRUE	0	0.29	1		490	1119	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051595	30051595	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	87	387	0	ENST00000338641.4:c.529T>C	p.Tyr177His	p.Y177H	ENST00000338641	NM_000268.3	177	Tat/Cat	6/16	1	2	FACETS	0.595	0.525	0.67	0.595	0.525	0.67	SUBCLONAL	1	TRUE	1	0.29	2		387	1009	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442557	52442557	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747311942	NA	P-0011397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	216	377	0	ENST00000460680.1:c.188C>G	p.Ser63Cys	p.S63C	ENST00000460680	NM_004656.3	63	tCt/tGt	4/17	0.3	1	FACETS	0.836	0.779	0.894	1	0.993	1	CLONAL	2	TRUE	0	0.29	1		377	762	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271503	26271503	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1725	155	914	0	ENST00000305910.3:c.110A>T	p.Lys37Met	p.K37M	ENST00000305910	NM_003534.2	37	aAg/aTg	1/1	1	2	FACETS	0.569	0.518	0.622	0.569	0.518	0.622	SUBCLONAL	1	TRUE	1	0.29	2		914	1880	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994296	21994296	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201877069	NA	P-0011397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	108	391	1	ENST00000579755.1:c.35G>A	p.Arg12Gln	p.R12Q	ENST00000579755		12	cGg/cAg	1/3	1		FACETS		0.792	0.98				CLONAL	1	TRUE	1	0.29	2		392	843	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214706	5214706	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457749790	NA	P-0011397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	71	501	0	ENST00000357368.4:c.4360G>A	p.Gly1454Ser	p.G1454S	ENST00000357368	NM_002850.3	1454	Ggc/Agc	29/38	1	2	FACETS	0.443	0.385	0.506	0.443	0.385	0.506	SUBCLONAL	1	TRUE	1	0.29	2		501	1105	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	841	461	0	ENST00000206249.3:c.1610A>G	p.Tyr537Cys	p.Y537C	ENST00000206249	NM_000125.3	537	tAt/tGt	8/8	0.824176288515084	2	FACETS	0.979	0.961	0.995	0.979	0.961	0.995	CLONAL	2	TRUE	0	0.845710739068842	2		461	1016	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115700	8115714	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGATTAACAGACCCC	AGATTAACAGACCCC	-	novel	NA	P-0011415-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	440	492	0	ENST00000346208.3:c.1048-2_1060del		p.X350_splice	ENST00000346208		350		6/6	0.798423358617308	3	FACETS	1	0.995	1	0.657	0.628	0.687	CLONAL	1	TRUE	1	0.845710739068842	3		492	1126	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0011433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	892	346	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.449958807733262	9	FACETS	1	0.984	1			1	CLONAL	6	TRUE	NA	0.449958807733262	9		346	1674	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579547	7579547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567557016	NA	P-0011433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	414	342	1	ENST00000269305.4:c.140del	p.Pro47ArgfsTer76	p.P47Rfs*76	ENST00000269305	NM_001126112.2	47	cCg/cg	4/11	0.37147828375565	3	FACETS	0.883	0.846	0.92			1	CLONAL	3	TRUE	NA	0.449958807733262	3		343	851	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719107	52719107	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	269	288	0	ENST00000322088.6:c.883G>A	p.Glu295Lys	p.E295K	ENST00000322088	NM_014225.5	295	Gag/Aag	7/15	0.342111957006329	4	FACETS	0.809	0.759	0.86	0.809	0.759	0.86	CLONAL	2	TRUE	2	0.449958807733262	4		288	1072	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191485	10191485	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	75	281	0	ENST00000256474.2:c.478G>T	p.Glu160Ter	p.E160*	ENST00000256474	NM_000551.3	160	Gag/Tag	3/3	0.122117594627253	1	FACETS	0.841	0.736	0.953	1	0.979	1	CLONAL	2	TRUE	0	0.122117594627253	1		281	686	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727877	41727877	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	135	501	0	ENST00000301178.4:c.502C>A	p.Pro168Thr	p.P168T	ENST00000301178	NM_021913.4	168	Ccc/Acc	4/20	1	2	FACETS	0.912	0.827	1	1	0.989	1	CLONAL	2	TRUE	1	0.122117594627253	2		501	1212	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247557	53247557	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	155	270	0	ENST00000375401.3:c.252C>G	p.Asn84Lys	p.N84K	ENST00000375401	NM_004187.3	84	aaC/aaG	3/26	1	1	FACETS	1	0.975	1	1	0.994	1	CLONAL	3	TRUE	0	0.122117594627253	1		270	688	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29106002	29106002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	18	241	0	ENST00000328354.6:c.838del	p.Leu280Ter	p.L280*	ENST00000328354	NM_007194.3	280	Cta/ta	7/15	0.122117594627253	1	FACETS	0.961	0.724	1	0.961	0.724	1	CLONAL	1	TRUE	0	0.122117594627253	1		241	288	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104353446	104353446	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	367	442	0	ENST00000369902.3:c.653del	p.Gly218AlafsTer17	p.G218Afs*17	ENST00000369902	NM_016169.3	217	caG/ca	5/12	0.889652146707774	1	FACETS	0.966	0.937	0.994	0.966	0.937	0.994	CLONAL	1	TRUE	0	0.892794185093198	1		442	471	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0011468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	259	247	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.37243195018119	4	FACETS	0.9	0.843	0.959			1	CLONAL	2	TRUE	NA	0.37243195018119	4		247	1060	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0011468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	300	365	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.36325547999388	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.37243195018119	2		367	704	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460390	149460390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753954924	NA	P-0011468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	293	700	1	ENST00000286301.3:c.247C>T	p.Arg83Cys	p.R83C	ENST00000286301	NM_005211.3	83	Cgc/Tgc	3/22	0.280629358848126	4	FACETS	0.786	0.739	0.836	0.786	0.739	0.836	SUBCLONAL	2	TRUE	2	0.37243195018119	4		701	1373	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650566	18650566	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	53	474	1	ENST00000266497.5:c.2777T>A	p.Leu926His	p.L926H	ENST00000266497		926	cTt/cAt	20/31	0.37243195018119	4	FACETS	0.407	0.346	0.475			1	SUBCLONAL	1	TRUE	NA	0.37243195018119	4		475	960	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976509	7976509	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	324	543	0	ENST00000319144.4:c.1883C>T	p.Thr628Met	p.T628M	ENST00000319144	NM_001139.2	628	aCg/aTg	14/15	0.36325547999388	2	FACETS	0.99	0.938	1	0.99	0.938	1	CLONAL	2	TRUE	0	0.37243195018119	2		543	879	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268399	46268399	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2249	132	1203	0	ENST00000371998.3:c.2786G>C	p.Arg929Thr	p.R929T	ENST00000371998		929	aGa/aCa	15/23	0.37243195018119	5	FACETS	0.464	0.419	0.512	0.093	0.083	0.103	SUBCLONAL	1	TRUE	0	0.37243195018119	5		1203	2381	SUCCESS
APC	324	MSKCC	GRCh37	5	112173657	112173658	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0011468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	222	486	0	ENST00000257430.4:c.2369_2370del	p.Arg790ThrfsTer8	p.R790Tfs*8	ENST00000257430	NM_000038.5	789	cAG/c	16/16	0.37243195018119	2	FACETS	0.891	0.834	0.95	0.891	0.834	0.95	CLONAL	2	TRUE	0	0.37243195018119	2		486	669	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660504	227660521	+	inframe_deletion	In_Frame_Del	DEL	CTGGGCACTGCCCGGGTA	CTGGGCACTGCCCGGGTA	-	novel	NA	P-0011468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	145	325	0	ENST00000305123.5:c.2934_2951del	p.Thr979_Ser984del	p.T979_S984del	ENST00000305123	NM_005544.2	978	ccTACCCGGGCAGTGCCCAGc/ccc	1/2	0.37243195018119	4	FACETS	0.849	0.778	0.924	0.849	0.778	0.924	CLONAL	2	TRUE	2	0.37243195018119	4		325	629	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129738	47129738	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1553691550	NA	P-0011505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	225	260	0	ENST00000409792.3:c.5143-1G>A		p.X1715_splice	ENST00000409792	NM_014159.6	1715			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		260	408	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139703	55139703	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0011505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4951	325	243	0	ENST00000257290.5:c.1365-1G>C		p.X455_splice	ENST00000257290	NM_006206.4	455			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		243	5276	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690258	117690328	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	GCTTTTTTGTGGCCGAGGCACATTATTTTAGCATCAGGTAAGGGCTGAGAGGCAGAAGTGCCCAGCTGATG	GCTTTTTTGTGGCCGAGGCACATTATTTTAGCATCAGGTAAGGGCTGAGAGGCAGAAGTGCCCAGCTGATG	-	novel	NA	P-0011505-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	212	252	0	ENST00000369458.3:c.801_*22del		p.*267*	ENST00000369458	NM_024626.3	267		5/6	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		252	581	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0011506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	158	382	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.35418113994075	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.35418113994075	1		382	708	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47108592	47108592	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011514-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	213	458	0	ENST00000409792.3:c.6077C>T	p.Pro2026Leu	p.P2026L	ENST00000409792	NM_014159.6	2026	cCa/cTa	13/21	0.446297701377363	1	FACETS	0.969	0.903	1	0.969	0.903	1	CLONAL	1	TRUE	0	0.446297701377363	1		458	765	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	97	126	0				ENST00000310581	NM_198253.2	-/1132			0.274411231230067	3	FACETS	0.825	0.739	0.917	0.825	0.739	0.917	CLONAL	2	TRUE	1	0.274411231230067	3		126	487	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936983	48936983	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690863	NA	P-0011524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	122	557	0	ENST00000267163.4:c.751C>T	p.Arg251Ter	p.R251*	ENST00000267163	NM_000321.2	251	Cga/Tga	8/27	1	2	FACETS	0.797	0.718	0.88	0.797	0.718	0.88	SUBCLONAL	1	TRUE	1	0.274411231230067	2		557	1116	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390822	139390822	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs61755043	NA	P-0011524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	44	543	0	ENST00000277541.6:c.7369C>G	p.Leu2457Val	p.L2457V	ENST00000277541	NM_017617.3	2457	Ctg/Gtg	34/34	1	2	FACETS	0.61	0.511	0.719	0.61	0.511	0.719	SUBCLONAL	1	TRUE	1	0.274411231230067	2		543	526	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771344	68771344	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	42	354	0	ENST00000261769.5:c.26C>A	p.Ser9Ter	p.S9*	ENST00000261769	NM_004360.3	9	tCg/tAg	1/16	0.274411231230067	1	FACETS	0.734	0.614	0.866	0.734	0.614	0.866	SUBCLONAL	1	TRUE	0	0.274411231230067	1		354	360	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917639	178917639	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	82	403	0	ENST00000263967.3:c.514G>C	p.Glu172Gln	p.E172Q	ENST00000263967	NM_006218.2	172	Gaa/Caa	3/21	1	2	FACETS	0.908	0.801	1	0.908	0.801	1	CLONAL	1	TRUE	1	0.274411231230067	2		403	658	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38991131	38991131	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	87	548	0	ENST00000357387.3:c.503C>A	p.Ser168Ter	p.S168*	ENST00000357387	NM_152756.3	168	tCa/tAa	7/38	0.274411231230067	3	FACETS	0.698	0.616	0.786	0.349	0.308	0.393	SUBCLONAL	1	TRUE	1	0.274411231230067	3		548	1033	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20488398	20488398	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	86	741	0	ENST00000346618.3:c.1054C>T	p.Pro352Ser	p.P352S	ENST00000346618	NM_001949.4	352	Cca/Tca	6/7	0.247389728106527	1	FACETS	0.462	0.407	0.521	0.462	0.407	0.521	SUBCLONAL	1	TRUE	0	0.274411231230067	1		741	1171	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30682901	30682901	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	77	797	0	ENST00000376406.3:c.52G>C	p.Glu18Gln	p.E18Q	ENST00000376406	NM_014641.2	18	Gag/Cag	2/15	0.247389728106527	1	FACETS	0.414	0.362	0.471	0.414	0.362	0.471	SUBCLONAL	1	TRUE	0	0.274411231230067	1		797	1169	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169033	32169033	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	47	711	0	ENST00000375023.3:c.4000G>C	p.Asp1334His	p.D1334H	ENST00000375023	NM_004557.3	1334	Gat/Cat	22/30	0.247389728106527	1	FACETS	0.348	0.292	0.409	0.348	0.292	0.409	SUBCLONAL	1	TRUE	0	0.274411231230067	1		711	850	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860512	151860512	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	109	703	0	ENST00000262189.6:c.10150G>C	p.Glu3384Gln	p.E3384Q	ENST00000262189	NM_170606.2	3384	Gaa/Caa	43/59	1	2	FACETS	0.662	0.593	0.736	0.662	0.593	0.736	SUBCLONAL	1	TRUE	1	0.274411231230067	2		703	1200	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125525174	125525174	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	41	528	0	ENST00000428830.2:c.1390G>A	p.Asp464Asn	p.D464N	ENST00000428830	NM_001114121.2	464	Gat/Aat	13/14	0.274411231230067	1	FACETS	0.355	0.294	0.422	0.355	0.294	0.422	SUBCLONAL	1	TRUE	0	0.274411231230067	1		528	727	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609800	28609800	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	44	459	0	ENST00000241453.7:c.1429G>C	p.Glu477Gln	p.E477Q	ENST00000241453	NM_004119.2	477	Gag/Cag	12/24	1	2	FACETS	0.386	0.322	0.457	0.386	0.322	0.457	SUBCLONAL	1	TRUE	1	0.274411231230067	2		459	831	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477109	67477109	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	116	627	0	ENST00000327367.4:c.916G>C	p.Glu306Gln	p.E306Q	ENST00000327367	NM_005902.3	306	Gag/Cag	7/9	0.247389728106527	1	FACETS	0.778	0.701	0.861	0.778	0.701	0.861	SUBCLONAL	1	TRUE	0	0.274411231230067	1		627	937	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343497	343497	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	75	673	0	ENST00000262320.3:c.2177C>G	p.Ser726Cys	p.S726C	ENST00000262320	NM_003502.3	726	tCc/tGc	8/11	0.274411231230067	1	FACETS	0.672	0.588	0.762	0.672	0.588	0.762	SUBCLONAL	1	TRUE	0	0.274411231230067	1		673	702	SUCCESS
YES1	7525	MSKCC	GRCh37	18	732915	732915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542568142	NA	P-0011524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1244	128	721	1	ENST00000314574.4:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000314574	NM_005433.3	448	Cgg/Tgg	11/12	1	2	FACETS	0.68	0.614	0.75	0.68	0.614	0.75	SUBCLONAL	1	TRUE	1	0.274411231230067	2		722	1372	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229510	5229510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1303613614	NA	P-0011524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	29	161	0	ENST00000357368.4:c.2341G>A	p.Asp781Asn	p.D781N	ENST00000357368	NM_002850.3	781	Gat/Aat	15/38	1	2	FACETS	0.892	0.719	1	0.892	0.719	1	CLONAL	1	TRUE	1	0.274411231230067	2		161	237	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937422	76937422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	79	694	0	ENST00000373344.5:c.3326C>T	p.Ser1109Leu	p.S1109L	ENST00000373344	NM_000489.3	1109	tCa/tTa	9/35	1	2	FACETS	0.605	0.531	0.685	0.605	0.531	0.685	SUBCLONAL	1	TRUE	1	0.274411231230067	2		694	952	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576868	7576868	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0011549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	427	550	0	ENST00000269305.4:c.978del	p.Glu326AspfsTer19	p.E326Dfs*19	ENST00000269305	NM_001126112.2	326	gaA/ga	9/11	0.313552412509999	3	FACETS	0.99	0.95	1			1	CLONAL	3	TRUE	NA	0.411983279459841	3		550	842	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939700	76939721	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGCACAATTAGTGCGGAATA	TGGGCACAATTAGTGCGGAATA	CC	novel	NA	P-0011549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	276	360	0	ENST00000373344.5:c.1027_1048delinsGG	p.Tyr343GlyfsTer5	p.Y343Gfs*5	ENST00000373344	NM_000489.3	343	TATTCCGCACTAATTGTGCCCAaa/GGaa	9/35	0.344481372866768	2	FACETS	0.977	0.933	1			1	CLONAL	3	TRUE	NA	0.411983279459841	2		360	457	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011552-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	98	459	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.984	0.877	1	0.984	0.877	1	CLONAL	1	TRUE	1	0.24	2		459	830	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0011552-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	140	628	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.24	2		628	1142	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846065	68846065	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011552-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	131	649	0	ENST00000261769.5:c.1036C>T	p.Gln346Ter	p.Q346*	ENST00000261769	NM_004360.3	346	Caa/Taa	8/16	0.277177853020857	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	0	0.24	1		649	960	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427494	49427494	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011552-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	88	564	0	ENST00000301067.7:c.10994del	p.Pro3665LeufsTer84	p.P3665Lfs*84	ENST00000301067	NM_003482.3	3665	cCt/ct	39/54	1	2	FACETS	0.727	0.642	0.818	0.727	0.642	0.818	SUBCLONAL	1	TRUE	1	0.24	2		564	1009	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876939	151876939	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011552-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	93	415	0	ENST00000262189.6:c.7422del	p.Met2475Ter	p.M2475*	ENST00000262189	NM_170606.2	2474	ggG/gg	37/59	1	2	FACETS	0.959	0.852	1	0.959	0.852	1	CLONAL	1	TRUE	1	0.24	2		415	808	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063715	67063721	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCGTAAG	TCGTAAG	-	novel	NA	P-0011552-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	31	220	0	ENST00000412916.2:c.165+2_165+8del		p.X55_splice	ENST00000412916		55		2/6	0.277177853020857	1	FACETS	0.677	0.548	0.822	0.677	0.548	0.822	SUBCLONAL	1	TRUE	0	0.24	1		220	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0011559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	24	457	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	1	2	FACETS	0.491	0.383	0.617	0.491	0.383	0.617	SUBCLONAL	1	TRUE	1	0.11	2		457	889	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390964	89390964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	53	491	0	ENST00000336596.2:c.1030G>A	p.Asp344Asn	p.D344N	ENST00000336596	NM_005233.5	344	Gac/Aac	5/17	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.11	2		491	941	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557834	21557834	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	75	541	0	ENST00000382592.4:c.2011A>C	p.Ile671Leu	p.I671L	ENST00000382592	NM_014572.2	671	Atc/Ctc	5/8	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.11	2		541	1061	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959112	28959112	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	59	564	0	ENST00000282397.4:c.2026A>G	p.Ser676Gly	p.S676G	ENST00000282397	NM_002019.4	676	Agt/Ggt	14/30	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.11	2		564	1031	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0011571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	107	414	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.358360845402355	1	FACETS	0.832	0.748	0.921	0.832	0.748	0.921	CLONAL	1	TRUE	0	0.358360845402355	1		416	589	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687059	176687059	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1064796184	NA	P-0011571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	52	613	0	ENST00000439151.2:c.5036C>G	p.Ser1679Ter	p.S1679*	ENST00000439151	NM_022455.4	1679	tCa/tGa	14/23	1	2	FACETS	0.338	0.287	0.395	0.338	0.287	0.395	SUBCLONAL	1	TRUE	1	0.358360845402355	2		613	858	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425412	49425412	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	33	698	0	ENST00000301067.7:c.13076C>T	p.Ser4359Leu	p.S4359L	ENST00000301067	NM_003482.3	4359	tCa/tTa	39/54	1	2	FACETS	0.324	0.263	0.393	0.324	0.263	0.393	SUBCLONAL	1	TRUE	1	0.358360845402355	2		698	569	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117910	70117910	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	41	350	0	ENST00000245479.2:c.378G>C	p.Gln126His	p.Q126H	ENST00000245479	NM_000346.3	126	caG/caC	1/3	0.358360845402355	1	FACETS	0.854	0.718	1	0.854	0.718	1	CLONAL	1	TRUE	0	0.358360845402355	1		350	220	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664999	29665081	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAACACAAAGGTTTTTATAAGTTCTGTGGATCTTTTAATTGCAGATTTGCATTCCAATATAATCCATCCCTGCAACCAAGAGC	AAACACAAAGGTTTTTATAAGTTCTGTGGATCTTTTAATTGCAGATTTGCATTCCAATATAATCCATCCCTGCAACCAAGAGC	-	novel	NA	P-0011571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	19	127	0	ENST00000356175.3:c.6642-44_6680del		p.X2214_splice	ENST00000356175	NM_000267.3	2214		44/57	0.358360845402355	1	FACETS	0.879	0.679	1	0.879	0.679	1	CLONAL	1	TRUE	0	0.358360845402355	1		127	99	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246679	41246679	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1555592956	NA	P-0011571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	86	498	0	ENST00000357654.3:c.869del	p.Leu290TyrfsTer8	p.L290Yfs*8	ENST00000357654	NM_007294.3	290	tTa/ta	10/23	0.358360845402355	1	FACETS	0.816	0.724	0.913	0.816	0.724	0.913	CLONAL	1	TRUE	0	0.358360845402355	1		498	483	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374305	138374305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	60	606	1	ENST00000289153.2:c.3139G>A	p.Glu1047Lys	p.E1047K	ENST00000289153	NM_006219.2	1047	Gag/Aag	22/22	0.12918208413192	3	FACETS	0.293	0.251	0.339	0.147	0.125	0.17	INDETERMINATE	1	TRUE	1	0.41944389142008	3		607	1181	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680556	30680556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	179	434	0	ENST00000376406.3:c.1163C>T	p.Ala388Val	p.A388V	ENST00000376406	NM_014641.2	388	gCt/gTt	5/15	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.41944389142008	2		434	695	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843722	151843722	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	209	407	0	ENST00000262189.6:c.13993G>C	p.Gly4665Arg	p.G4665R	ENST00000262189	NM_170606.2	4665	Ggc/Cgc	53/59	0.12918208413192	3	FACETS	1	0.988	1	0.66	0.613	0.709	INDETERMINATE	1	TRUE	1	0.41944389142008	3		407	913	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572156	64572156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs898745144	NA	P-0011577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	246	702	1	ENST00000312049.6:c.1483C>T	p.Pro495Ser	p.P495S	ENST00000312049	NM_130799.2	495	Ccc/Tcc	10/10	1	2	FACETS	0.911	0.85	0.974	0.911	0.85	0.974	CLONAL	1	TRUE	1	0.41944389142008	2		703	1288	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579434	7579441	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCCGCC	GGGCCGCC	-	rs1567556270	NA	P-0011577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	164	381	0	ENST00000269305.4:c.246_253del	p.Ala83CysfsTer63	p.A83Cfs*63	ENST00000269305	NM_001126112.2	82	ccGGCGGCCCct/ccct	4/11	0.41944389142008	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.41944389142008	1		381	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576915	7576916	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0011577-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	48	414	0	ENST00000269305.4:c.930_931del	p.Asn310LysfsTer26	p.N310Kfs*26	ENST00000269305	NM_001126112.2	310	aaCAac/aaac	9/11	0.41944389142008	1	FACETS	0.324	0.273	0.379	0.324	0.273	0.379	SUBCLONAL	1	TRUE	0	0.41944389142008	1		414	559	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660529	67660529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	27	500	0	ENST00000264010.4:c.1429C>T	p.His477Tyr	p.H477Y	ENST00000264010	NM_006565.3	477	Cat/Tat	8/12	1	2	FACETS	0.272	0.217	0.335	0.272	0.217	0.335	SUBCLONAL	1	FALSE	1	0.750890284000138	2		500	264	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853186	68853193	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	TCGGATTT	TCGGATTT	-	novel	NA	P-0011590-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	66	460	0	ENST00000261769.5:c.1569_1576del	p.Tyr523Ter	p.Y523*	ENST00000261769	NM_004360.3	523	taTCGGATTTgg/tagg	11/16	1	2	FACETS	0.689	0.605	0.778	0.689	0.605	0.778	SUBCLONAL	1	FALSE	1	0.750890284000138	2		460	255	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781504	NA	P-0012001-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	137	435	0	ENST00000269305.4:c.314G>T	p.Gly105Val	p.G105V	ENST00000269305	NM_001126112.2	105	gGc/gTc	4/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.166750171673504	2		435	1235	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0012001-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	260	448	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.166750171673504	3	FACETS	0.953	0.892	1			1	CLONAL	3	TRUE	NA	0.166750171673504	3		448	1182	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602923	10602923	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370923924	NA	P-0012001-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	138	435	0	ENST00000171111.5:c.655G>A	p.Glu219Lys	p.E219K	ENST00000171111	NM_203500.1	219	Gag/Aag	3/6	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.166750171673504	2		435	1205	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651331	52651331	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012001-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	155	535	0	ENST00000394830.3:c.1765G>A	p.Asp589Asn	p.D589N	ENST00000394830	NM_018313.4	589	Gac/Aac	15/30	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.166750171673504	2		535	1363	SUCCESS
ATR	545	MSKCC	GRCh37	3	142232402	142232402	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012001-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	111	412	0	ENST00000350721.4:c.4582C>G	p.Leu1528Val	p.L1528V	ENST00000350721	NM_001184.3	1528	Ctt/Gtt	26/47	1	2	FACETS	0.755	0.678	0.836	1	0.983	1	SUBCLONAL	2	TRUE	1	0.166750171673504	2		412	882	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724308	117724308	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012001-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	54	356	0	ENST00000368508.3:c.571C>T	p.His191Tyr	p.H191Y	ENST00000368508	NM_002944.2	191	Cat/Tat	6/43	1	2	FACETS	0.699	0.595	0.813	0.699	0.595	0.813	SUBCLONAL	1	TRUE	1	0.166750171673504	2		356	927	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032739	30032739	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0012001-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	121	324	0	ENST00000338641.4:c.115-1G>C		p.X39_splice	ENST00000338641	NM_000268.3	39			1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.166750171673504	2		324	995	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551043	41551043	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012001-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1479	189	561	0	ENST00000263253.7:c.3187G>T	p.Glu1063Ter	p.E1063*	ENST00000263253	NM_001429.3	1063	Gag/Tag	17/31	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.166750171673504	2		561	1668	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781328	135781329	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0012001-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2081	251	865	0	ENST00000298552.3:c.1636_1637del	p.Asp546HisfsTer17	p.D546Hfs*17	ENST00000298552	NM_001162426.1	546	GAc/c	15/23	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.166750171673504	2		865	2332	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572117	64572117	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	179	536	1	ENST00000312049.6:c.1522C>T	p.Gln508Ter	p.Q508*	ENST00000312049	NM_130799.2	508	Cag/Tag	10/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.271297681084715	2		537	1011	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111514	8111515	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0012005-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	149	431	0	ENST00000346208.3:c.1002_1003del	p.Asp335ProfsTer16	p.D335Pfs*16	ENST00000346208		334	GGg/g	5/6	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.271297681084715	2		431	1069	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952088	+	missense_variant	Missense_Mutation	ONP	ATCA	ATCA	GTCG	novel	NA	P-0012006-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	121	274	0	ENST00000263967.3:c.3140_3143delinsGTCG	p.His1047_His1048delinsArgArg	p.H1047_H1048delinsRR	ENST00000263967	NM_006218.2	1047	cATCAt/cGTCGt	21/21	1	2	FACETS	0.89	0.804	0.981	0.89	0.804	0.981	CLONAL	1	TRUE	1	0.340193672133562	2		274	799	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052725	42052725	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	52	511	0	ENST00000219905.7:c.7396C>T	p.Arg2466Ter	p.R2466*	ENST00000219905	NM_001164273.1	2466	Cga/Tga	20/24	0.430913501769364	0	FACETS	0.174	0.148	0.203			1	SUBCLONAL	1	TRUE	0	0.495159350891641	0		511	609	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857968	9857968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779746293	NA	P-0012048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	242	437	0	ENST00000330684.3:c.3433G>A	p.Val1145Met	p.V1145M	ENST00000330684	NM_001134407.1	1145	Gtg/Atg	13/13	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.495159350891641	2		437	836	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303012	15303012	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	29	232	0	ENST00000263388.2:c.438C>G	p.Cys146Trp	p.C146W	ENST00000263388	NM_000435.2	146	tgC/tgG	4/33	1	2	FACETS	0.356	0.286	0.436	0.356	0.286	0.436	SUBCLONAL	1	TRUE	1	0.495159350891641	2		232	329	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934574	NA	P-0012056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	180	550	0	ENST00000269305.4:c.844C>G	p.Arg282Gly	p.R282G	ENST00000269305	NM_001126112.2	282	Cgg/Ggg	8/11	0.568649248693348	1	FACETS	0.66	0.61	0.711	0.66	0.61	0.711	SUBCLONAL	1	TRUE	0	0.568649248693348	1		550	687	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108259	8108259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	203	526	0	ENST00000585124.1:c.965C>T	p.Ser322Leu	p.S322L	ENST00000585124	NM_004217.3	322	tCa/tTa	9/9	0.568649248693348	1	FACETS	0.742	0.69	0.794	0.742	0.69	0.794	SUBCLONAL	1	TRUE	0	0.568649248693348	1		526	689	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059223	47059223	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	227	359	0	ENST00000409792.3:c.7438C>G	p.Gln2480Glu	p.Q2480E	ENST00000409792	NM_014159.6	2480	Cag/Gag	20/21	0.568649248693348	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.568649248693348	1		359	560	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273230	55273230	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	317	471	0	ENST00000275493.2:c.3553G>A	p.Gly1185Ser	p.G1185S	ENST00000275493	NM_005228.3	1185	Ggc/Agc	28/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.568649248693348	2		471	1012	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673793	37673793	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2901	299	337	0	ENST00000447079.4:c.2947C>G	p.Arg983Gly	p.R983G	ENST00000447079	NM_015083.1	983	Cga/Gga	10/14	0.568649248693348	9	FACETS	0.983	0.92	1			1	CLONAL	1	TRUE	NA	0.568649248693348	9		337	3200	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141512	11141513	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0012056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	277	515	0	ENST00000358026.2:c.3489_3490delinsTT	p.Asn1164Tyr	p.N1164Y	ENST00000358026	NM_001128849.1	1163	ctGAac/ctTTac	25/36	0.568649248693348	1	FACETS	0.995	0.94	1	0.995	0.94	1	CLONAL	1	TRUE	0	0.568649248693348	1		515	701	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0012059-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	219	393	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.186007094263057	4	FACETS	0.784	0.729	0.84	0.784	0.729	0.84	INDETERMINATE	2	TRUE	2	0.400604670057537	4		393	977	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0012059-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	187	242	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.389249265018719	2	FACETS	0.966	0.901	1	0.966	0.901	1	CLONAL	2	TRUE	0	0.400604670057537	2		242	483	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890348	72890348	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012059-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	115	277	0	ENST00000325599.8:c.334G>T	p.Ala112Ser	p.A112S	ENST00000325599	NM_018130.2	112	Gct/Tct	4/11	0.304121758177496	3	FACETS	0.93	0.838	1	0.465	0.419	0.514	CLONAL	1	TRUE	1	0.400604670057537	3		277	741	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445001	89445001	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012059-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	146	409	0	ENST00000336596.2:c.1321C>A	p.Leu441Met	p.L441M	ENST00000336596	NM_005233.5	441	Ctg/Atg	6/17	0.304121758177496	3	FACETS	0.966	0.881	1	0.483	0.44	0.527	CLONAL	1	TRUE	1	0.400604670057537	3		409	906	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587134	189587134	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012059-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	159	341	0	ENST00000264731.3:c.1151G>A	p.Gly384Asp	p.G384D	ENST00000264731	NM_003722.4	384	gGt/gAt	9/14	0.304121758177496	3	FACETS	0.935	0.856	1	0.468	0.428	0.509	CLONAL	1	TRUE	1	0.400604670057537	3		341	1019	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038480	180038480	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0012059-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	67	273	0	ENST00000261937.6:c.3538-1G>T		p.X1180_splice	ENST00000261937	NM_182925.4	1180			1	2	FACETS	0.685	0.597	0.781	0.685	0.597	0.781	SUBCLONAL	1	TRUE	1	0.400604670057537	2		273	488	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683669	162683669	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1256316516	NA	P-0012059-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	275	331	0	ENST00000366898.1:c.300G>C	p.Gln100His	p.Q100H	ENST00000366898	NM_004562.2	100	caG/caC	3/12	0.389249265018719	2	FACETS	0.968	0.914	1	0.968	0.914	1	CLONAL	2	TRUE	0	0.400604670057537	2		331	709	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81399248	81399248	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012059-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	317	338	0	ENST00000222390.5:c.40C>G	p.His14Asp	p.H14D	ENST00000222390	NM_000601.4	14	Cat/Gat	1/18	0.40441059417329	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.400604670057537	3		338	899	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250167	110250167	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1564294835	NA	P-0012059-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	93	207	0	ENST00000374672.4:c.508G>T	p.Gly170Cys	p.G170C	ENST00000374672	NM_004235.4	170	Ggc/Tgc	3/5	0.184019602005849	3	FACETS	1	0.979	1	0.704	0.63	0.781	INDETERMINATE	1	TRUE	1	0.400604670057537	3		207	396	SUCCESS
AXL	558	MSKCC	GRCh37	19	41737201	41737201	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012059-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	328	382	1	ENST00000301178.4:c.781C>T	p.Gln261Ter	p.Q261*	ENST00000301178	NM_021913.4	261	Cag/Tag	6/20	0.333463423121289	5	FACETS	1	0.988	1	0.771	0.729	0.814	CLONAL	2	TRUE	2	0.400604670057537	5		383	1133	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409815	63409815	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012059-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	154	431	0	ENST00000330258.3:c.3352G>C	p.Ala1118Pro	p.A1118P	ENST00000330258	NM_152424.3	1118	Gcc/Ccc	2/2	0.141742405252737	3	FACETS	0.884	0.808	0.964	0.295	0.269	0.322	INDETERMINATE	1	TRUE	0	0.400604670057537	3		431	1044	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217651	7217651	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012059-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	74	523	0	ENST00000380728.2:c.276del	p.Val93PhefsTer16	p.V93Ffs*16	ENST00000380728		92	aaA/aa	4/11	0.389249265018719	2	FACETS	0.336	0.292	0.382	0.168	0.146	0.191	SUBCLONAL	1	TRUE	0	0.400604670057537	2		523	1101	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340439	8340439	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012059-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	209	343	0	ENST00000356435.5:c.5157del	p.Leu1721TrpfsTer19	p.L1721Wfs*19	ENST00000356435		1719	ggG/gg	31/35	0.184019602005849	3	FACETS	1	0.989	1	0.68	0.632	0.73	INDETERMINATE	1	TRUE	1	0.400604670057537	3		343	921	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0012079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	94	852	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.992	0.882	1	0.992	0.882	1	CLONAL	1	TRUE	1	0.255842590349903	2		852	741	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245972	46245972	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	88	452	0	ENST00000334344.6:c.4066C>A	p.Pro1356Thr	p.P1356T	ENST00000334344	NM_152641.2	1356	Ccg/Acg	15/21	0.255842590349903	1	FACETS	0.882	0.782	0.989	0.882	0.782	0.989	CLONAL	1	TRUE	0	0.255842590349903	1		452	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519996	NA	P-0012079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	82	480	0	ENST00000269305.4:c.395A>T	p.Lys132Met	p.K132M	ENST00000269305	NM_001126112.2	132	aAg/aTg	5/11	0.255842590349903	1	FACETS	0.848	0.748	0.956	0.848	0.748	0.956	CLONAL	1	TRUE	0	0.255842590349903	1		480	659	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672932	30672932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	262	906	0	ENST00000376406.3:c.4028C>T	p.Thr1343Ile	p.T1343I	ENST00000376406	NM_014641.2	1343	aCc/aTc	10/15	1	2	FACETS	0.905	0.847	0.964	1	0.994	1	CLONAL	2	TRUE	1	0.255842590349903	2		906	1132	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816231	89816231	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	53	715	0	ENST00000389301.3:c.3146T>C	p.Phe1049Ser	p.F1049S	ENST00000389301	NM_000135.2	1049	tTt/tCt	32/43	NA	2	FACETS	0.517	0.44	0.603			1	INDETERMINATE	1	TRUE	NA	0.255842590349903	2		715	801	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973634	15973634	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	90	549	0	ENST00000268712.3:c.4358G>C	p.Ser1453Thr	p.S1453T	ENST00000268712	NM_006311.3	1453	aGc/aCc	31/46	0.255842590349903	1	FACETS	0.867	0.769	0.971	0.867	0.769	0.971	CLONAL	1	TRUE	0	0.255842590349903	1		549	708	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038822	47038822	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	56	157	0	ENST00000377604.3:c.829C>T	p.Gln277Ter	p.Q277*	ENST00000377604	NM_001204468.1	277	Cag/Tag	9/24	0.0975308507057062	2	FACETS	1	0.928	1			1	INDETERMINATE	3	FALSE	NA	0.164066286660116	2		157	206	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	37	450	1	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	1	2	FACETS	0.635	0.522	0.763	0.635	0.522	0.763	SUBCLONAL	1	FALSE	1	0.164066286660116	2		451	710	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0012088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	43	274	1	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.759	0.633	0.898	0.759	0.633	0.898	SUBCLONAL	1	FALSE	1	0.164066286660116	2		275	691	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0012088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	84	590	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.164066286660116	2		590	894	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258625	16258630	+	stop_gained	Nonsense_Mutation	ONP	GAGGAG	GAGGAG	TAGGAA	novel	NA	P-0012088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	29	300	0	ENST00000375759.3:c.5890_5895delinsTAGGAA	p.Glu1964Ter	p.E1964*	ENST00000375759	NM_015001.2	1964	GAGGAG/TAGGAA	11/15	1	2	FACETS	0.77	0.617	0.944	0.77	0.617	0.944	CLONAL	1	FALSE	1	0.164066286660116	2		300	459	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61720134	61720134	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	55	638	0	ENST00000401558.2:c.1300G>C	p.Glu434Gln	p.E434Q	ENST00000401558	NM_003400.3	434	Gag/Cag	13/25	1	2	FACETS	0.663	0.565	0.77	0.663	0.565	0.77	SUBCLONAL	1	FALSE	1	0.164066286660116	2		638	1012	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139454	47139454	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1152	63	736	0	ENST00000409792.3:c.5133G>C	p.Lys1711Asn	p.K1711N	ENST00000409792	NM_014159.6	1711	aaG/aaC	9/21	1	2	FACETS	0.632	0.544	0.728	0.632	0.544	0.728	SUBCLONAL	1	FALSE	1	0.164066286660116	2		736	1215	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665358	138665358	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	49	552	0	ENST00000330315.3:c.207G>C	p.Glu69Asp	p.E69D	ENST00000330315	NM_023067.3	69	gaG/gaC	1/1	0.164066286660116	3	FACETS	0.799	0.675	0.936	0.399	0.337	0.468	CLONAL	1	FALSE	1	0.164066286660116	3		552	809	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120855	94120855	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1347	113	750	0	ENST00000369303.4:c.196A>C	p.Thr66Pro	p.T66P	ENST00000369303	NM_004440.3	66	Acc/Ccc	3/17	1	2	FACETS	0.943	0.846	1	0.943	0.846	1	CLONAL	1	FALSE	1	0.164066286660116	2		750	1460	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112035575	112035575	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1159797492	NA	P-0012088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	73	652	0	ENST00000368678.4:c.319G>C	p.Glu107Gln	p.E107Q	ENST00000368678		107	Gaa/Caa	4/13	1	2	FACETS	0.809	0.705	0.922	0.809	0.705	0.922	CLONAL	1	FALSE	1	0.164066286660116	2		652	1100	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956955	2956955	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	74	392	1	ENST00000396946.4:c.2672G>T	p.Arg891Leu	p.R891L	ENST00000396946	NM_032415.4	891	cGa/cTa	20/25	0.142831992076289	3	FACETS	1	0.974	1	0.749	0.655	0.849	CLONAL	1	FALSE	1	0.164066286660116	3		393	652	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460538	8460538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772029273	NA	P-0012088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	38	441	0	ENST00000356435.5:c.3748G>A	p.Val1250Met	p.V1250M	ENST00000356435		1250	Gtg/Atg	22/35	0.145774886757187	0	FACETS	0.592	0.488	0.709			1	SUBCLONAL	1	FALSE	0	0.164066286660116	0		441	654	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441780	49441780	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555195442	NA	P-0012088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	95	733	1	ENST00000301067.7:c.4204C>T	p.Gln1402Ter	p.Q1402*	ENST00000301067	NM_003482.3	1402	Cag/Tag	14/54	0.0975308507057062	3	FACETS	1	0.966	1			1	INDETERMINATE	1	FALSE	NA	0.164066286660116	3		734	1019	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052520	42052520	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0012088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	153	671	0	ENST00000219905.7:c.7192-1G>T		p.X2398_splice	ENST00000219905	NM_001164273.1	2398			0.164066286660116	2	FACETS	0.911	0.832	0.993	0.911	0.832	0.993	CLONAL	2	FALSE	0	0.164066286660116	2		671	1024	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304065	91304065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1477193473	NA	P-0012088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	58	631	0	ENST00000355112.3:c.1462G>A	p.Glu488Lys	p.E488K	ENST00000355112	NM_000057.2	488	Gaa/Aaa	7/22	0.164066286660116	2	FACETS	0.736	0.63	0.852	0.368	0.315	0.426	SUBCLONAL	1	FALSE	0	0.164066286660116	2		631	961	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857551	9857551	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	50	409	0	ENST00000330684.3:c.3850C>G	p.Leu1284Val	p.L1284V	ENST00000330684	NM_001134407.1	1284	Cta/Gta	13/13	0.164066286660116	5	FACETS	0.981	0.831	1	0.327	0.277	0.383	CLONAL	1	FALSE	2	0.164066286660116	5		409	774	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37856552	37856552	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	291	454	0	ENST00000269571.5:c.61G>T	p.Ala21Ser	p.A21S	ENST00000269571		21	Gcg/Tcg	1/27	0.164066286660116	6	FACETS	1	0.979	1			1	CLONAL	5	FALSE	NA	0.164066286660116	6		454	877	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141449	11141449	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	51	599	0	ENST00000358026.2:c.3426C>G	p.Phe1142Leu	p.F1142L	ENST00000358026	NM_001128849.1	1142	ttC/ttG	25/36	1	2	FACETS	0.725	0.614	0.847	0.725	0.614	0.847	SUBCLONAL	1	FALSE	1	0.164066286660116	2		599	858	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375572	15375572	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	90	416	0	ENST00000263377.2:c.855G>C	p.Lys285Asn	p.K285N	ENST00000263377	NM_058243.2	285	aaG/aaC	6/20	0.133094548857703	3	FACETS	0.994	0.884	1			1	CLONAL	2	FALSE	NA	0.164066286660116	3		416	597	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17940919	17940919	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	30	446	1	ENST00000458235.1:c.3205G>A	p.Glu1069Lys	p.E1069K	ENST00000458235	NM_000215.3	1069	Gag/Aag	23/24	1	2	FACETS	0.666	0.535	0.815	0.666	0.535	0.815	SUBCLONAL	1	FALSE	1	0.164066286660116	2		447	549	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224449	123224449	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747270306	NA	P-0012088-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	70	365	0	ENST00000218089.9:c.3302G>A	p.Ser1101Asn	p.S1101N	ENST00000218089	NM_001042749.1	1101	aGt/aAt	31/35	0.0975308507057062	2	FACETS	1	0.971	1			1	INDETERMINATE	1	FALSE	NA	0.164066286660116	2		365	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0012091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	741	566	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.945103905481296	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.945103905481296	1		568	808	SUCCESS
APC	324	MSKCC	GRCh37	5	112174840	112174840	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0012091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	494	332	0	ENST00000257430.4:c.3549T>A	p.Tyr1183Ter	p.Y1183*	ENST00000257430	NM_000038.5	1183	taT/taA	16/16	0.945103905481296	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.945103905481296	1		332	535	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120478151	120478151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	649	360	0	ENST00000256646.2:c.3599G>A	p.Gly1200Asp	p.G1200D	ENST00000256646	NM_024408.3	1200	gGc/gAc	22/34	1	2	FACETS	0.981	0.947	1	0.981	0.947	1	CLONAL	1	TRUE	1	0.945103905481296	2		360	1400	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117756	115117756	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	595	383	0	ENST00000257566.3:c.679C>A	p.His227Asn	p.H227N	ENST00000257566	NM_016569.3	227	Cac/Aac	3/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.945103905481296	2		383	1234	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031971	10031971	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555455618	NA	P-0012091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	806	538	0	ENST00000330684.3:c.852G>A	p.Trp284Ter	p.W284*	ENST00000330684	NM_001134407.1	284	tgG/tgA	3/13	1	2	FACETS	0.991	0.961	1	0.991	0.961	1	CLONAL	1	TRUE	1	0.945103905481296	2		538	1721	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3094675	3094675	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	328	292	0	ENST00000078429.4:c.26G>T	p.Cys9Phe	p.C9F	ENST00000078429	NM_002067.2	9	tGt/tTt	1/7	1	2	FACETS	0.886	0.842	0.931	0.886	0.842	0.931	CLONAL	1	TRUE	1	0.945103905481296	2		292	783	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242482	+	protein_altering_variant	In_Frame_Del	DEL	GGAATTAAGAGAAGCAAC	GGAATTAAGAGAAGCAAC	AAT	novel	NA	P-0012098-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	205	430	0	ENST00000275493.2:c.2235_2252delinsAAT	p.Glu746_Thr751delinsIle	p.E746_T751delinsI	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCAACa/aaAATa	19/28	0.194890575811643	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		430	1197	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0012106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	139	645	1	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.958	0.871	1	0.958	0.871	1	CLONAL	1	TRUE	1	0.276164021866113	2		646	1051	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782082	NA	P-0012106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	140	431	0	ENST00000269305.4:c.745A>T	p.Arg249Trp	p.R249W	ENST00000269305	NM_001126112.2	249	Agg/Tgg	7/11	0.276164021866113	1	FACETS	0.856	0.778	0.938	0.856	0.778	0.938	CLONAL	1	TRUE	0	0.276164021866113	1		431	1021	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858985	57858985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142957882	NA	P-0012106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1567	216	669	2	ENST00000228682.2:c.481C>T	p.Arg161Trp	p.R161W	ENST00000228682	NM_005269.2	161	Cgg/Tgg	5/12	1	2	FACETS	0.877	0.812	0.945	0.877	0.812	0.945	CLONAL	1	TRUE	1	0.276164021866113	2		671	1783	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841201	15841201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1473782265	NA	P-0012106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	171	214	0	ENST00000307771.7:c.1285C>T	p.Arg429Cys	p.R429C	ENST00000307771	NM_005089.3	429	Cgc/Tgc	11/11	1	1	FACETS	0.848	0.784	0.915	1	0.991	1	CLONAL	2	TRUE	0	0.276164021866113	1		214	629	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0012110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	219	641	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.334921656108996	1	FACETS	0.952	0.884	1	0.952	0.884	1	CLONAL	1	TRUE	0	0.334921656108996	1		641	1144	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512383	38512383	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1188389540	NA	P-0012110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	110	296	0	ENST00000254066.5:c.1294C>T	p.Arg432Trp	p.R432W	ENST00000254066	NM_000964.3	432	Cgg/Tgg	9/9	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.334921656108996	2		296	610	SUCCESS
APC	324	MSKCC	GRCh37	5	112174884	112174884	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs879254089	NA	P-0012110-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	176	329	1	ENST00000257430.4:c.3593C>G	p.Ser1198Ter	p.S1198*	ENST00000257430	NM_000038.5	1198	tCa/tGa	16/16	0.334921656108996	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.334921656108996	1		330	773	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0012116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	165	346	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.381094721220117	3	FACETS	1	0.981	1	0.603	0.556	0.652	CLONAL	1	TRUE	1	0.550394316466914	3		346	634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1555525429	NA	P-0012116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	285	500	0	ENST00000269305.4:c.782+1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.550394316466914	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.550394316466914	2		500	477	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612923	228612923	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	249	845	1	ENST00000366696.1:c.104G>T	p.Gly35Val	p.G35V	ENST00000366696	NM_003493.2	35	gGc/gTc	1/1	0.550394316466914	3	FACETS	1	0.977	1	0.546	0.51	0.582	CLONAL	1	TRUE	1	0.550394316466914	3		846	1057	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	484	463	1	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	0.328411485972731	4	FACETS	1	0.991	1			1	CLONAL	3	FALSE	NA	0.328411485972731	4		464	1179	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579349	7579349	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1567555667	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	60	628	0	ENST00000269305.4:c.338T>G	p.Phe113Cys	p.F113C	ENST00000269305	NM_001126112.2	113	tTc/tGc	4/11	0.328411485972731	4	FACETS	0.429	0.368	0.496			1	SUBCLONAL	1	FALSE	NA	0.328411485972731	4		628	1131	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251745	212251745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	51	547	1	ENST00000342788.4:c.3314C>T	p.Ser1105Phe	p.S1105F	ENST00000342788	NM_005235.2	1105	tCc/tTc	27/28	1	2	FACETS	0.417	0.353	0.487	0.417	0.353	0.487	SUBCLONAL	1	FALSE	1	0.328411485972731	2		548	745	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912865	50912865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	81	977	0	ENST00000440232.2:c.2096C>T	p.Ser699Phe	p.S699F	ENST00000440232	NM_002691.3	699	tCc/tTc	17/27	0.157824135252829	1	FACETS	0.377	0.331	0.427	0.377	0.331	0.427	INDETERMINATE	1	FALSE	0	0.328411485972731	1		977	1093	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285666	46285666	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	117	538	0	ENST00000334344.6:c.5026C>T	p.Gln1676Ter	p.Q1676*	ENST00000334344	NM_152641.2	1676	Cag/Tag	17/21	1	2	FACETS	0.908	0.819	1	0.908	0.819	1	CLONAL	1	FALSE	1	0.328411485972731	2		538	785	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750945	128750945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	122	500	0	ENST00000377970.2:c.482C>T	p.Ser161Leu	p.S161L	ENST00000377970	NM_002467.4	161	tCa/tTa	2/3	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.328411485972731	2		500	673	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663425	67663425	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	109	674	1	ENST00000264010.4:c.1826C>T	p.Ser609Phe	p.S609F	ENST00000264010	NM_006565.3	609	tCc/tTc	10/12	0.157824135252829	1	FACETS	0.629	0.564	0.698	0.629	0.564	0.698	INDETERMINATE	1	FALSE	0	0.328411485972731	1		675	882	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245204	46245204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	124	567	0	ENST00000334344.6:c.3298C>T	p.Gln1100Ter	p.Q1100*	ENST00000334344	NM_152641.2	1100	Cag/Tag	15/21	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	FALSE	1	0.328411485972731	2		567	724	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693874	47693874	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	303	766	1	ENST00000233146.2:c.1588G>A	p.Glu530Lys	p.E530K	ENST00000233146	NM_000251.2	530	Gaa/Aaa	10/16	1	2	FACETS	0.835	0.787	0.884	1	0.995	1	CLONAL	2	FALSE	1	0.328411485972731	2		767	1105	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248617	212248617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765120252	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	67	711	0	ENST00000342788.4:c.3650G>A	p.Gly1217Glu	p.G1217E	ENST00000342788	NM_005235.2	1217	gGa/gAa	28/28	1	2	FACETS	0.426	0.369	0.488	0.426	0.369	0.488	SUBCLONAL	1	FALSE	1	0.328411485972731	2		711	958	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522521	187522521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	73	790	0	ENST00000441802.2:c.11542G>T	p.Glu3848Ter	p.E3848*	ENST00000441802	NM_005245.3	3848	Gaa/Taa	21/27	0.25857832032591	0	FACETS	0.361	0.315	0.411			1	SUBCLONAL	1	FALSE	0	0.328411485972731	0		790	826	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517758	176517758	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1305938137	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	188	997	1	ENST00000292408.4:c.368C>T	p.Ser123Phe	p.S123F	ENST00000292408	NM_213647.1	123	tCc/tTc	4/18	0.328411485972731	1	FACETS	0.919	0.849	0.993	0.919	0.849	0.993	CLONAL	1	FALSE	0	0.328411485972731	1		998	1041	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520268	176520268	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	104	546	0	ENST00000292408.4:c.1187A>G	p.His396Arg	p.H396R	ENST00000292408	NM_213647.1	396	cAc/cGc	9/18	0.328411485972731	1	FACETS	0.968	0.869	1	0.968	0.869	1	CLONAL	1	FALSE	0	0.328411485972731	1		546	547	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909348	41909348	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762507772	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	80	359	0	ENST00000372991.4:c.40C>T	p.Arg14Trp	p.R14W	ENST00000372991	NM_001760.3	14	Cgg/Tgg	1/5	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	FALSE	1	0.328411485972731	2		359	449	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997434	149997434	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	175	719	0	ENST00000253339.5:c.2845C>T	p.Pro949Ser	p.P949S	ENST00000253339		949	Cct/Tct	6/7	0.166156583618565	3	FACETS	1	0.975	1	0.572	0.526	0.62	INDETERMINATE	1	FALSE	1	0.328411485972731	3		719	1084	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150512	157150512	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754042537	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	127	502	0	ENST00000346085.5:c.1694G>A	p.Arg565Gln	p.R565Q	ENST00000346085	NM_020732.3	565	cGg/cAg	2/20	0.166156583618565	3	FACETS	1	0.98	1	0.652	0.592	0.716	INDETERMINATE	1	FALSE	1	0.328411485972731	3		502	690	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508967	106508967	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1361906308	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	62	355	1	ENST00000359195.3:c.961G>A	p.Glu321Lys	p.E321K	ENST00000359195	NM_002649.2	321	Gaa/Aaa	2/11	1	2	FACETS	0.872	0.755	0.998	0.872	0.755	0.998	CLONAL	1	FALSE	1	0.328411485972731	2		356	433	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412223	139412223	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	84	693	1	ENST00000277541.6:c.1422C>A	p.Phe474Leu	p.F474L	ENST00000277541	NM_017617.3	474	ttC/ttA	8/34	0.153723900779615	0	FACETS	0.41	0.362	0.463			1	INDETERMINATE	1	FALSE	0	0.328411485972731	0		694	837	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417602	139417602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	83	724	0	ENST00000277541.6:c.442C>T	p.Pro148Ser	p.P148S	ENST00000277541	NM_017617.3	148	Ccc/Tcc	4/34	0.153723900779615	0	FACETS	0.409	0.36	0.461			1	INDETERMINATE	1	FALSE	0	0.328411485972731	0		724	831	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405202	70405202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	173	451	0	ENST00000373644.4:c.2716G>A	p.Glu906Lys	p.E906K	ENST00000373644	NM_030625.2	906	Gag/Aag	4/12	0.237796076564178	2	FACETS	0.846	0.782	0.911	0.846	0.782	0.911	CLONAL	2	FALSE	0	0.328411485972731	2		451	623	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376157	118376157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	151	624	0	ENST00000534358.1:c.9550C>T	p.Pro3184Ser	p.P3184S	ENST00000534358	NM_005933.3	3184	Cct/Tct	27/36	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.328411485972731	2		624	833	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431120	49431120	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	171	689	0	ENST00000301067.7:c.10019A>G	p.Gln3340Arg	p.Q3340R	ENST00000301067	NM_003482.3	3340	cAg/cGg	34/54	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.328411485972731	2		689	930	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492558	56492558	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	60	776	0	ENST00000267101.3:c.2708A>G	p.Glu903Gly	p.E903G	ENST00000267101	NM_001982.3	903	gAg/gGg	23/28	1	2	FACETS	0.348	0.298	0.402	0.348	0.298	0.402	SUBCLONAL	1	FALSE	1	0.328411485972731	2		776	1051	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110092	115110092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1437311804	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	62	351	1	ENST00000257566.3:c.1786C>T	p.Pro596Ser	p.P596S	ENST00000257566	NM_016569.3	596	Cct/Tct	8/8	1	2	FACETS	0.83	0.719	0.95	0.83	0.719	0.95	CLONAL	1	FALSE	1	0.328411485972731	2		352	455	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420258	88420258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550257984	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	165	543	0	ENST00000360948.2:c.2428G>A	p.Glu810Lys	p.E810K	ENST00000360948	NM_001012338.2	810	Gaa/Aaa	19/19	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.328411485972731	2		543	784	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274162	10274162	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	65	438	0	ENST00000330684.3:c.107T>A	p.Ile36Asn	p.I36N	ENST00000330684	NM_001134407.1	36	aTt/aAt	2/13	0.157824135252829	1	FACETS	0.558	0.484	0.638	0.558	0.484	0.638	INDETERMINATE	1	FALSE	0	0.328411485972731	1		438	593	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663933	29663933	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	180	583	0	ENST00000356175.3:c.6364+1G>T		p.X2122_splice	ENST00000356175	NM_000267.3	2122			0.328411485972731	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	0	0.328411485972731	1		583	729	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681030	37681030	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	202	663	0	ENST00000447079.4:c.3199C>T	p.Arg1067Ter	p.R1067*	ENST00000447079	NM_015083.1	1067	Cga/Tga	12/14	0.328411485972731	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	0	0.328411485972731	1		663	735	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40490782	40490782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	288	838	0	ENST00000264657.5:c.517G>A	p.Asp173Asn	p.D173N	ENST00000264657	NM_139276.2	173	Gat/Aat	6/24	0.328411485972731	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	FALSE	0	0.328411485972731	1		838	1034	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226569	1226569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368466538	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	142	625	1	ENST00000326873.7:c.1225C>T	p.Arg409Trp	p.R409W	ENST00000326873	NM_000455.4	409	Cgg/Tgg	9/10	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	FALSE	1	0.328411485972731	2		626	862	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7119497	7119497	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	156	781	0	ENST00000302850.5:c.3757G>A	p.Gly1253Arg	p.G1253R	ENST00000302850	NM_000208.2	1253	Ggg/Agg	21/22	1	2	FACETS	0.837	0.765	0.913	0.837	0.765	0.913	CLONAL	1	FALSE	1	0.328411485972731	2		781	1135	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247764	10247764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	163	917	0	ENST00000340748.4:c.4438G>A	p.Glu1480Lys	p.E1480K	ENST00000340748		1480	Gaa/Aaa	36/40	1	2	FACETS	0.925	0.848	1	0.925	0.848	1	CLONAL	1	FALSE	1	0.328411485972731	2		917	1073	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793293	33793293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555742327	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	46	481	0	ENST00000498907.2:c.28G>A	p.Glu10Lys	p.E10K	ENST00000498907	NM_004364.3	10	Gag/Aag	1/1	0.157824135252829	1	FACETS	0.46	0.387	0.54	0.46	0.387	0.54	INDETERMINATE	1	FALSE	0	0.328411485972731	1		481	509	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745616	41745616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	299	884	2	ENST00000301178.4:c.1303C>T	p.His435Tyr	p.H435Y	ENST00000301178	NM_021913.4	435	Cac/Tac	10/20	0.157824135252829	1	FACETS	1	0.988	1	1	0.988	1	INDETERMINATE	1	FALSE	0	0.328411485972731	1		886	1277	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902268	50902268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1368414810	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	236	1288	0	ENST00000440232.2:c.160G>A	p.Glu54Lys	p.E54K	ENST00000440232	NM_002691.3	54	Gag/Aag	2/27	0.157824135252829	1	FACETS	0.861	0.802	0.923	0.861	0.802	0.923	INDETERMINATE	1	FALSE	0	0.328411485972731	1		1288	1395	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560833	9560833	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	160	676	0	ENST00000353224.5:c.949A>T	p.Thr317Ser	p.T317S	ENST00000353224	NM_177990.2	317	Acc/Tcc	4/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.328411485972731	2		676	872	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426435	47426435	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	187	481	0	ENST00000377045.4:c.778C>T	p.Pro260Ser	p.P260S	ENST00000377045	NM_001654.4	260	Cca/Tca	9/16	1	1	FACETS	0.763	0.708	0.819	1	0.991	1	SUBCLONAL	2	FALSE	0	0.328411485972731	1		481	624	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443387	187443388	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	47	585	1	ENST00000232014.4:c.1738_1739delinsAA	p.Gly580Lys	p.G580K	ENST00000232014	NM_001130845.1	580	GGg/AAg	8/10	1	2	FACETS	0.408	0.343	0.479	0.408	0.343	0.479	SUBCLONAL	1	FALSE	1	0.328411485972731	2		586	702	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030630	48030631	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	88	947	2	ENST00000234420.5:c.3244_3245delinsTT	p.Pro1082Leu	p.P1082L	ENST00000234420	NM_000179.2	1082	CCg/TTg	5/10	1	2	FACETS	0.458	0.405	0.516	0.458	0.405	0.516	SUBCLONAL	1	FALSE	1	0.328411485972731	2		949	1169	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162535	47162536	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	50	499	0	ENST00000409792.3:c.3590_3591delinsAA	p.Arg1197Lys	p.R1197K	ENST00000409792	NM_014159.6	1197	aGG/aAA	3/21	1	2	FACETS	0.477	0.404	0.557	0.477	0.404	0.557	SUBCLONAL	1	FALSE	1	0.328411485972731	2		499	639	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412205	139412206	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	65	634	0	ENST00000277541.6:c.1439_1440delinsTT	p.Pro480Leu	p.P480L	ENST00000277541	NM_017617.3	480	cCC/cTT	8/34	0.153723900779615	0	FACETS	0.367	0.318	0.421			1	INDETERMINATE	1	FALSE	0	0.328411485972731	0		634	724	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56792470	56792471	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	107	1000	1	ENST00000308159.5:c.200_201delinsAA	p.Arg67Gln	p.R67Q	ENST00000308159	NM_014669.4	67	cGG/cAA	3/22	0.157824135252829	1	FACETS	0.471	0.421	0.524	0.471	0.421	0.524	INDETERMINATE	1	FALSE	0	0.328411485972731	1		1001	1156	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376940	118376941	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	137	541	0	ENST00000534358.1:c.10333_10334delinsAT	p.Pro3445Ile	p.P3445I	ENST00000534358	NM_005933.3	3445	CCt/ATt	27/36	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.328411485972731	2		541	761	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248650	59248651	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	222	855	0	ENST00000371222.2:c.92_93delinsTT	p.Pro31Leu	p.P31L	ENST00000371222	NM_002228.3	31	cCC/cTT	1/1	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.328411485972731	2		855	1014	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541689	120541690	+	missense_variant	Missense_Mutation	DNP	CT	CT	TC	novel	NA	P-0012129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1257	205	1084	2	ENST00000229340.5:c.167_168delinsGA	p.Lys56Arg	p.K56R	ENST00000229340	NM_006861.6	56	aAG/aGA	3/6	1	2	FACETS	0.854	0.79	0.921	0.854	0.79	0.921	CLONAL	1	FALSE	1	0.328411485972731	2		1086	1462	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	91	126	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		126	227	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435653	56435653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	41	325	0	ENST00000407977.2:c.1484C>T	p.Ser495Phe	p.S495F	ENST00000407977		495	tCt/tTt	9/10	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	FALSE	1	0.251948374352339	2		325	287	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	59	600	0	ENST00000262189.6:c.13488T>A	p.Phe4496Leu	p.F4496L	ENST00000262189	NM_170606.2	4496	ttT/ttA	52/59	1	2	FACETS	0.935	0.805	1	0.935	0.805	1	CLONAL	1	FALSE	1	0.251948374352339	2		600	501	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999303	100999303	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372324844	NA	P-0012145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	88	975	0	ENST00000325455.5:c.499C>T	p.Arg167Trp	p.R167W	ENST00000325455	NM_001202474.3	167	Cgg/Tgg	1/8	1	2	FACETS	0.758	0.67	0.852	0.758	0.67	0.852	SUBCLONAL	1	FALSE	1	0.251948374352339	2		975	922	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911788	32911788	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs397507663	NA	P-0012145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	79	1074	0	ENST00000380152.3:c.3296C>A	p.Ser1099Ter	p.S1099*	ENST00000380152		1099	tCa/tAa	11/27	0.251948374352339	1	FACETS	0.891	0.784	1	0.891	0.784	1	CLONAL	1	FALSE	0	0.251948374352339	1		1074	615	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435366	56435366	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	75	532	0	ENST00000407977.2:c.1771C>T	p.Pro591Ser	p.P591S	ENST00000407977		591	Cca/Tca	9/10	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	FALSE	1	0.251948374352339	2		532	584	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945586	151945613	+	frameshift_variant	Frame_Shift_Del	DEL	CTTCAATTTGATCTTCGCCACAAATATG	CTTCAATTTGATCTTCGCCACAAATATG	-	novel	NA	P-0012145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	14	109	0	ENST00000262189.6:c.1906_1933del	p.His636IlefsTer5	p.H636Ifs*5	ENST00000262189	NM_170606.2	636	CATATTTGTGGCGAAGATCAAATTGAAGat/at	14/59	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	FALSE	1	0.251948374352339	2		109	82	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435090	56435090	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	70	563	1	ENST00000407977.2:c.2047del	p.His683IlefsTer17	p.H683Ifs*17	ENST00000407977		683	Cat/at	9/10	1	2	FACETS	0.978	0.854	1	0.978	0.854	1	CLONAL	1	FALSE	1	0.251948374352339	2		564	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0012153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	305	463	1	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	0.43096546658095	2	FACETS	0.986	0.935	1	0.986	0.935	1	CLONAL	2	TRUE	0	0.43096546658095	2		464	718	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0012153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	173	264	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.43096546658095	5	FACETS	0.984	0.922	1	0.984	0.922	1	CLONAL	4	TRUE	1	0.43096546658095	5		264	336	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013737	12013737	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	148	316	0	ENST00000353533.5:c.679C>G	p.His227Asp	p.H227D	ENST00000353533	NM_003010.3	227	Cac/Gac	6/11	0.43096546658095	2	FACETS	0.916	0.847	0.986	0.916	0.847	0.986	CLONAL	2	TRUE	0	0.43096546658095	2		316	375	SUCCESS
AR	367	MSKCC	GRCh37	X	66765229	66765229	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs760454396	NA	P-0012153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	232	415	0	ENST00000374690.3:c.241G>C	p.Glu81Gln	p.E81Q	ENST00000374690	NM_000044.3	81	Gag/Cag	1/8	0.43096546658095	2	FACETS	0.977	0.919	1	0.977	0.919	1	CLONAL	2	TRUE	0	0.43096546658095	2		415	551	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012180-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	183	126	0				ENST00000310581	NM_198253.2	-/1132			0.131437111501224	5	FACETS	0.904	0.844	0.964			1	INDETERMINATE	3	FALSE	NA	0.593634711587268	5		126	430	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0012180-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	192	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.951	0.883	1	0.951	0.883	1	CLONAL	1	FALSE	1	0.593634711587268	2		336	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0012180-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	647	590	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.509463796726651	3	FACETS	0.877	0.851	0.903	0.877	0.851	0.903	CLONAL	3	FALSE	0	0.593634711587268	3		590	1074	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762959	40762959	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs387906659	NA	P-0012180-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	138	347	0	ENST00000392038.2:c.49G>A	p.Glu17Lys	p.E17K	ENST00000392038	NM_001626.4	17	Gaa/Aaa	3/14	0.434253087814935	1	FACETS	0.681	0.624	0.74	0.681	0.624	0.74	SUBCLONAL	1	FALSE	0	0.593634711587268	1		347	480	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649065	37649065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777164311	NA	P-0012180-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	383	399	0	ENST00000447079.4:c.2170G>A	p.Val724Met	p.V724M	ENST00000447079	NM_015083.1	724	Gtg/Atg	4/14	0.536348099009709	2	FACETS	0.843	0.807	0.88	0.843	0.807	0.88	CLONAL	2	FALSE	0	0.593634711587268	2		399	765	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45854924	45854924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373363992	NA	P-0012180-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	100	530	1	ENST00000391945.4:c.2246C>T	p.Thr749Met	p.T749M	ENST00000391945	NM_000400.3	749	aCg/aTg	23/23	0.434253087814935	1	FACETS	0.324	0.289	0.361	0.324	0.289	0.361	SUBCLONAL	1	FALSE	0	0.593634711587268	1		531	731	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934571	NA	P-0012188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	271	615	0	ENST00000269305.4:c.747G>C	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agC	7/11	NA	2	FACETS	1	0.972	1			1	INDETERMINATE	2	TRUE	NA	0.482666536657196	2		615	542	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850272	128850272	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs777204354	NA	P-0012188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	280	768	0	ENST00000249373.3:c.1535G>T	p.Arg512Leu	p.R512L	ENST00000249373	NM_005631.4	512	cGc/cTc	9/12	0.47405678851515	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	1	0.482666536657196	3		768	719	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076787	72076787	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	419	869	0	ENST00000357731.5:c.710C>A	p.Pro237His	p.P237H	ENST00000357731	NM_173808.2	237	cCc/cAc	5/7	0.47405678851515	3	FACETS	0.951	0.907	0.995	0.951	0.907	0.995	CLONAL	2	TRUE	1	0.482666536657196	3		869	1133	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430916	78430916	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0012188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	181	276	0	ENST00000370768.2:c.474-1G>T		p.X158_splice	ENST00000370768	NM_003902.3	158			0.47405678851515	3	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	1	0.482666536657196	3		276	464	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054972	176054972	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1015214834	NA	P-0012188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	180	771	0	ENST00000367669.3:c.1081A>T	p.Thr361Ser	p.T361S	ENST00000367669	NM_022457.5	361	Act/Tct	10/20	0.47405678851515	3	FACETS	0.883	0.813	0.955	0.441	0.406	0.478	CLONAL	1	TRUE	1	0.482666536657196	3		771	1049	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967012	25967012	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	383	699	0	ENST00000435504.4:c.2194G>T	p.Ala732Ser	p.A732S	ENST00000435504		732	Gca/Tca	13/13	0.47405678851515	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.482666536657196	3		699	912	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248619	212248619	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	208	624	0	ENST00000342788.4:c.3648G>T	p.Leu1216Phe	p.L1216F	ENST00000342788	NM_005235.2	1216	ttG/ttT	28/28	0.47405678851515	3	FACETS	1	0.944	1	0.51	0.473	0.549	CLONAL	1	TRUE	1	0.482666536657196	3		624	1048	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530102	212530102	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	379	601	0	ENST00000342788.4:c.1817A>T	p.Lys606Met	p.K606M	ENST00000342788	NM_005235.2	606	aAg/aTg	15/28	0.47405678851515	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.482666536657196	3		601	972	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163194	47163194	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	306	585	0	ENST00000409792.3:c.2932G>T	p.Glu978Ter	p.E978*	ENST00000409792	NM_014159.6	978	Gaa/Taa	3/21	0.47405678851515	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	1	0.482666536657196	3		585	786	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143181716	143181716	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	279	480	0	ENST00000262992.4:c.617G>A	p.Cys206Tyr	p.C206Y	ENST00000262992	NM_001101669.1	206	tGt/tAt	9/24	0.482666536657196	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.482666536657196	2		480	564	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541727	187541727	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	168	696	0	ENST00000441802.2:c.6013G>T	p.Gly2005Trp	p.G2005W	ENST00000441802	NM_005245.3	2005	Ggg/Tgg	10/27	0.454574807837576	1	FACETS	0.962	0.89	1	0.962	0.89	1	CLONAL	1	TRUE	0	0.482666536657196	1		696	549	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32182000	32182000	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	384	943	0	ENST00000375023.3:c.2054G>T	p.Gly685Val	p.G685V	ENST00000375023	NM_004557.3	685	gGg/gTg	13/30	0.435843146423631	4	FACETS	0.968	0.919	1	0.968	0.919	1	CLONAL	2	TRUE	2	0.482666536657196	4		943	1219	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508164	106508164	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	37	198	0	ENST00000359195.3:c.158G>T	p.Ser53Ile	p.S53I	ENST00000359195	NM_002649.2	53	aGc/aTc	2/11	0.47405678851515	3	FACETS	0.842	0.7	0.999	0.421	0.35	0.5	CLONAL	1	TRUE	1	0.482666536657196	3		198	226	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111442	8111442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	122	532	0	ENST00000346208.3:c.928G>A	p.Ala310Thr	p.A310T	ENST00000346208		310	Gcc/Acc	5/6	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.482666536657196	2		532	493	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615130	43615130	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772684105	NA	P-0012188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	218	768	2	ENST00000355710.3:c.2544G>A	p.Met848Ile	p.M848I	ENST00000355710	NM_020975.4	848	atG/atA	14/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.482666536657196	2		770	690	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343658	118343658	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	276	318	0	ENST00000534358.1:c.1784C>T	p.Pro595Leu	p.P595L	ENST00000534358	NM_005933.3	595	cCa/cTa	3/36	0.43865031253153	5	FACETS	1	0.969	1			1	CLONAL	3	TRUE	NA	0.482666536657196	5		318	635	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95598862	95598862	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	305	526	0	ENST00000393063.1:c.297G>T	p.Leu99Phe	p.L99F	ENST00000393063	NM_030621.3	99	ttG/ttT	4/28	0.482666536657196	3	FACETS	0.913	0.864	0.963	0.913	0.864	0.963	CLONAL	2	TRUE	1	0.482666536657196	3		526	859	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007723	62007723	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	132	238	1	ENST00000392795.3:c.144G>T	p.Trp48Cys	p.W48C	ENST00000392795	NM_001039933.1	48	tgG/tgT	3/6	0.482666536657196	3	FACETS	0.951	0.885	1	0.951	0.885	1	CLONAL	3	TRUE	0	0.482666536657196	3		239	238	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395770	45395770	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	243	379	0	ENST00000262160.6:c.364G>A	p.Gly122Arg	p.G122R	ENST00000262160	NM_005901.5	122	Gga/Aga	4/11	0.47405678851515	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.482666536657196	3		379	609	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278090	15278090	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	375	926	0	ENST00000263388.2:c.5332G>T	p.Asp1778Tyr	p.D1778Y	ENST00000263388	NM_000435.2	1778	Gat/Tat	29/33	0.482666536657196	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.482666536657196	2		926	740	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321382	1321382	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367657347	NA	P-0012188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	623	545	0	ENST00000400841.2:c.373G>A	p.Val125Met	p.V125M	ENST00000400841		125	Gtg/Atg	4/6	0.408267063546496	2	FACETS	0.862	0.837	0.887			1	CLONAL	3	TRUE	NA	0.482666536657196	2		545	998	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012206-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	223	450	1	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.264583811795689	2	FACETS	0.9	0.84	0.961	0.9	0.84	0.961	CLONAL	2	TRUE	0	0.31062612679724	2		451	798	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412950	49412950	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012206-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1201	191	1038	0	ENST00000418115.1:c.73T>G	p.Phe25Val	p.F25V	ENST00000418115	NM_001664.2	25	Ttc/Gtc	2/5	1	2	FACETS	0.883	0.815	0.955	0.883	0.815	0.955	CLONAL	1	TRUE	1	0.31062612679724	2		1038	1392	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836278	151836278	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012206-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	248	366	0	ENST00000262189.6:c.14527C>A	p.Pro4843Thr	p.P4843T	ENST00000262189	NM_170606.2	4843	Ccc/Acc	57/59	0.31062612679724	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	1	0.31062612679724	4		366	658	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611809	1611809	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779908158	NA	P-0012206-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1409	166	1093	1	ENST00000344749.5:c.1853G>A	p.Arg618Gln	p.R618Q	ENST00000344749	NM_001136139.2	618	cGa/cAa	19/19	0.194905822482224	2	FACETS	0.679	0.621	0.739	0.339	0.31	0.37	SUBCLONAL	1	TRUE	0	0.31062612679724	2		1094	1575	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212023	5212023	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012206-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	119	623	0	ENST00000357368.4:c.5008C>G	p.Gln1670Glu	p.Q1670E	ENST00000357368	NM_002850.3	1670	Cag/Gag	32/38	0.194905822482224	2	FACETS	0.879	0.793	0.97	0.439	0.396	0.485	CLONAL	1	TRUE	0	0.31062612679724	2		623	872	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44515577	44515577	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012206-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	67	868	0	ENST00000291552.4:c.319G>C	p.Asp107His	p.D107H	ENST00000291552	NM_006758.2	107	Gac/Cac	5/8	0.194905822482224	2	FACETS	0.357	0.309	0.41	0.179	0.154	0.205	SUBCLONAL	1	TRUE	0	0.31062612679724	2		868	1208	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650400	48650400	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012206-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1279	267	978	0	ENST00000376670.3:c.370C>A	p.Leu124Met	p.L124M	ENST00000376670	NM_002049.3	124	Ctg/Atg	3/6	0.31062612679724	3	FACETS	1	0.99	1	0.642	0.6	0.686	CLONAL	1	TRUE	1	0.31062612679724	3		978	1546	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224411	53224411	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0012206-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1249	140	821	0	ENST00000375401.3:c.3300+2T>C		p.X1100_splice	ENST00000375401	NM_004187.3	1100			0.31062612679724	3	FACETS	0.75	0.68	0.823	0.375	0.34	0.412	SUBCLONAL	1	TRUE	1	0.31062612679724	3		821	1389	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0012213-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	16	513	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.427	0.314	0.562	0.427	0.314	0.562	SUBCLONAL	1	TRUE	1	0.15	2		513	500	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030585	47030585	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs377667483	NA	P-0012213-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	28	646	1	ENST00000377604.3:c.360T>G	p.Asp120Glu	p.D120E	ENST00000377604	NM_001204468.1	120	gaT/gaG	4/24	0.144068081780686	0	FACETS	0.774	0.618	0.952			1	CLONAL	1	TRUE	0	0.15	0		647	410	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39690040	39690051	+	inframe_deletion	In_Frame_Del	DEL	ATAAACACAAAG	ATAAACACAAAG	-	rs773155066	NA	P-0012213-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	10	307	0	ENST00000361337.2:c.79_90del	p.Lys27_Asp30del	p.K27_D30del	ENST00000361337	NM_003286.2	22	cATAAACACAAAGat/cat	3/21	1	2	FACETS	0.771	0.523	1	0.771	0.523	1	CLONAL	1	TRUE	1	0.15	2		307	173	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579317	7579317	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012213-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	15	505	0	ENST00000269305.4:c.370T>C	p.Cys124Arg	p.C124R	ENST00000269305	NM_001126112.2	124	Tgc/Cgc	4/11	1	2	FACETS	0.909	0.666	1	0.909	0.666	1	CLONAL	1	TRUE	1	0.15	2		505	220	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805318	89805318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201494304	NA	P-0012244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	53	491	0	ENST00000389301.3:c.4232C>T	p.Pro1411Leu	p.P1411L	ENST00000389301	NM_000135.2	1411	cCg/cTg	42/43	1	2	FACETS	0.182	0.154	0.212	0.182	0.154	0.212	SUBCLONAL	1	TRUE	1	0.714297915730383	2		491	816	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530162	63530162	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777885192	NA	P-0012244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	141	614	0	ENST00000307078.5:c.2273C>T	p.Ala758Val	p.A758V	ENST00000307078	NM_004655.3	758	gCg/gTg	10/11	1	2	FACETS	0.39	0.355	0.427	0.39	0.355	0.427	SUBCLONAL	1	TRUE	1	0.714297915730383	2		614	1012	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206865	102206865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138752976	NA	P-0012244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	436	891	2	ENST00000263464.3:c.1493C>T	p.Thr498Met	p.T498M	ENST00000263464	NM_001165.4	498	aCg/aTg	7/9	0.233327530903545	1	FACETS	0.571	0.544	0.598	0.571	0.544	0.598	INDETERMINATE	1	TRUE	0	0.714297915730383	1		893	1375	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946334	2946334	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	318	733	0	ENST00000396946.4:c.3403G>A	p.Val1135Ile	p.V1135I	ENST00000396946	NM_032415.4	1135	Gtc/Atc	25/25	0.714297915730383	4	FACETS	1	0.972	1	0.525	0.495	0.557	CLONAL	1	TRUE	2	0.714297915730383	4		733	1453	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877873	151877873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1410837774	NA	P-0012244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	259	476	0	ENST00000262189.6:c.7072C>T	p.Pro2358Ser	p.P2358S	ENST00000262189	NM_170606.2	2358	Cct/Tct	36/59	0.714297915730383	3	FACETS	0.972	0.911	1	0.486	0.455	0.517	CLONAL	1	TRUE	1	0.714297915730383	3		476	1013	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274155	18274155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148515229	NA	P-0012244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	66	622	0	ENST00000222254.8:c.1373G>A	p.Arg458His	p.R458H	ENST00000222254	NM_005027.3	458	cGc/cAc	11/16	1	2	FACETS	0.194	0.168	0.223	0.194	0.168	0.223	SUBCLONAL	1	TRUE	1	0.714297915730383	2		622	951	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1327742	1327742	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	81	723	0	ENST00000400841.2:c.139A>T	p.Asn47Tyr	p.N47Y	ENST00000400841		47	Aat/Tat	2/6	1	1	FACETS	0.139	0.122	0.158	0.139	0.122	0.158	SUBCLONAL	1	TRUE	0	0.714297915730383	1		723	1049	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1327790	1327790	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	75	588	1	ENST00000400841.2:c.91C>T	p.Gln31Ter	p.Q31*	ENST00000400841		31	Cag/Tag	2/6	1	1	FACETS	0.152	0.132	0.173	0.152	0.132	0.173	SUBCLONAL	1	TRUE	0	0.714297915730383	1		589	889	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717676	89717676	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	273	538	0	ENST00000371953.3:c.703del	p.Glu235LysfsTer21	p.E235Kfs*21	ENST00000371953	NM_000314.4	234	cGg/cg	7/9	0.714297915730383	1	FACETS	0.965	0.918	1	0.965	0.918	1	CLONAL	1	TRUE	0	0.714297915730383	1		538	509	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	428	715	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.366197807110204	4	FACETS	0.987	0.944	1	0.987	0.944	1	CLONAL	3	TRUE	1	0.366197807110204	4		715	1078	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0012252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	221	365	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.366197807110204	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.366197807110204	2		367	580	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0012252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	168	337	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.366197807110204	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	0	0.366197807110204	2		337	453	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158539	26158539	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	41	319	0	ENST00000289316.2:c.142C>G	p.Gln48Glu	p.Q48E	ENST00000289316	NM_138720.2	48	Cag/Gag	1/2	0.3	3	FACETS	1	0.943	1			1	CLONAL	1	TRUE	NA	0.12	3		319	540	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813307	102813307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764732420	NA	P-0012253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	61	613	2	ENST00000307046.8:c.382G>A	p.Asp128Asn	p.D128N	ENST00000307046	NM_001111285.1	128	Gac/Aac	3/4	0.196864162001823	3	FACETS	1	0.95	1	0.619	0.533	0.714	CLONAL	1	TRUE	1	0.12	3		615	870	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170805	11170805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1029465394	NA	P-0012253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	23	369	0	ENST00000358026.2:c.4949G>A	p.Arg1650Gln	p.R1650Q	ENST00000358026	NM_001128849.1	1650	cGa/cAa	35/36	1	2	FACETS	0.837	0.651	1	0.837	0.651	1	CLONAL	1	TRUE	1	0.12	2		369	458	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183755	10183757	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs5030648	NA	P-0012253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	30	401	0	ENST00000256474.2:c.227_229del	p.Phe76del	p.F76del	ENST00000256474	NM_000551.3	75	aTCTtc/atc	1/3	1	2	FACETS	1	0.844	1	1	0.844	1	CLONAL	1	TRUE	1	0.12	2		401	473	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651347	52651347	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	55	670	1	ENST00000394830.3:c.1749A>T	p.Glu583Asp	p.E583D	ENST00000394830	NM_018313.4	583	gaA/gaT	15/30	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.12	2		671	805	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850837	128850837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138072219	NA	P-0012253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	49	527	7	ENST00000249373.3:c.1684C>T	p.Arg562Trp	p.R562W	ENST00000249373	NM_005631.4	562	Cgg/Tgg	10/12	1	2	FACETS	0.921	0.777	1	0.921	0.777	1	CLONAL	1	TRUE	1	0.12	2		534	887	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63816898	63816898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	26	266	0	ENST00000279873.7:c.869C>T	p.Ala290Val	p.A290V	ENST00000279873	NM_032199.2	290	gCc/gTc	6/10	1	2	FACETS	0.897	0.709	1	0.897	0.709	1	CLONAL	1	TRUE	1	0.12	2		266	483	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922716	44922717	+	missense_variant	Missense_Mutation	DNP	GG	GG	TA	novel	NA	P-0012253-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	89	326	0	ENST00000377967.4:c.1577_1578delinsTA	p.Gly526Val	p.G526V	ENST00000377967	NM_021140.2	526	gGG/gTA	16/29	0.215994363189362	2	FACETS	0.874	0.776	0.977			1	CLONAL	3	TRUE	NA	0.12	2		326	566	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0012259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	173	284	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.923	0.858	0.989	0.923	0.858	0.989	CLONAL	1	FALSE	1	0.826077590654427	2		284	454	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	159	126	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.826077590654427	2		126	335	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0012259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	36	645	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.099	0.081	0.12	0.099	0.081	0.12	SUBCLONAL	1	FALSE	1	0.826077590654427	2		645	876	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123693	11123693	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	331	608	0	ENST00000358026.2:c.2343G>A	p.Met781Ile	p.M781I	ENST00000358026	NM_001128849.1	781	atG/atA	16/36	1	2	FACETS	0.968	0.919	1	0.968	0.919	1	CLONAL	1	FALSE	1	0.826077590654427	2		608	828	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188078	11188078	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	34	373	0	ENST00000361445.4:c.6016G>T	p.Val2006Phe	p.V2006F	ENST00000361445	NM_004958.3	2006	Gtc/Ttc	43/58	0.826077590654427	1	FACETS	0.158	0.129	0.19	0.158	0.129	0.19	SUBCLONAL	1	FALSE	0	0.826077590654427	1		373	306	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413129	139413131	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	novel	NA	P-0012259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	70	793	0	ENST00000277541.6:c.1011_1013del	p.Asp338del	p.D338del	ENST00000277541	NM_017617.3	337	gaTGAc/gac	6/34	1	2	FACETS	0.166	0.144	0.191	0.166	0.144	0.191	SUBCLONAL	1	FALSE	1	0.826077590654427	2		793	1018	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303029	15303029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1174625611	NA	P-0012259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	25	426	0	ENST00000263388.2:c.421C>T	p.Arg141Cys	p.R141C	ENST00000263388	NM_000435.2	141	Cgc/Tgc	4/33	1	2	FACETS	0.132	0.103	0.165	0.132	0.103	0.165	SUBCLONAL	1	FALSE	1	0.826077590654427	2		426	459	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78426045	78426046	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0012259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	370	699	0	ENST00000370768.2:c.1479_1480del	p.Pro494ArgfsTer30	p.P494Rfs*30	ENST00000370768	NM_003902.3	493	ccACca/ccca	15/20	0.826077590654427	1	FACETS	0.916	0.882	0.95	0.916	0.882	0.95	CLONAL	1	FALSE	0	0.826077590654427	1		699	574	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796292	42796293	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0012259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	97	781	0	ENST00000575354.2:c.2941_2942del	p.Leu981GlufsTer169	p.L981Efs*169	ENST00000575354	NM_015125.3	981	CTg/g	12/20	0.826077590654427	1	FACETS	0.245	0.218	0.273	0.245	0.218	0.273	SUBCLONAL	1	FALSE	0	0.826077590654427	1		781	563	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391913	139391914	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0012259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	49	779	0	ENST00000277541.6:c.6277_6278del	p.Met2093GlyfsTer174	p.M2093Gfs*174	ENST00000277541	NM_017617.3	2093	ATg/g	34/34	1	2	FACETS	0.138	0.116	0.162	0.138	0.116	0.162	SUBCLONAL	1	FALSE	1	0.826077590654427	2		779	859	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413065	139413067	+	inframe_deletion	In_Frame_Del	DEL	GCA	GCA	-	novel	NA	P-0012259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	119	617	0	ENST00000277541.6:c.1075_1077del	p.Cys359del	p.C359del	ENST00000277541	NM_017617.3	359	TGC/-	6/34	1	2	FACETS	0.403	0.364	0.444	0.403	0.364	0.444	SUBCLONAL	1	FALSE	1	0.826077590654427	2		617	715	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794606	42794607	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0012259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	125	520	0	ENST00000575354.2:c.1686_1687del	p.Gly563SerfsTer126	p.G563Sfs*126	ENST00000575354	NM_015125.3	562	tcTGgt/tcgt	10/20	0.826077590654427	1	FACETS	0.463	0.423	0.504	0.463	0.423	0.504	SUBCLONAL	1	FALSE	0	0.826077590654427	1		520	384	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0012260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	198	346	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.958	0.889	1	0.958	0.889	1	CLONAL	1	TRUE	1	0.526807922657291	2		346	785	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519874	NA	P-0012260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	21	401	0	ENST00000356142.4:c.85C>A	p.Pro29Thr	p.P29T	ENST00000356142	NM_018890.3	29	Cct/Act	2/7	1	2	FACETS	0.078	0.059	0.1	0.078	0.059	0.1	SUBCLONAL	1	TRUE	1	0.526807922657291	2		401	1021	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426196	49426196	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1388458596	NA	P-0012260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	65	344	0	ENST00000301067.7:c.12292C>T	p.Pro4098Ser	p.P4098S	ENST00000301067	NM_003482.3	4098	Cca/Tca	39/54	0.279187199671333	3	FACETS	0.47	0.407	0.539	0.235	0.203	0.27	INDETERMINATE	1	TRUE	1	0.526807922657291	3		344	663	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	44	247	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.858	0.718	1	0.858	0.718	1	CLONAL	1	TRUE	1	0.16	2		247	641	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0012269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	53	416	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.916	0.78	1	0.916	0.78	1	CLONAL	1	TRUE	1	0.16	2		416	723	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944157	81944157	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761094228	NA	P-0012269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	80	674	2	ENST00000359376.3:c.1766G>A	p.Arg589His	p.R589H	ENST00000359376	NM_002661.3	589	cGc/cAc	18/33	1	2	FACETS	0.935	0.82	1	0.935	0.82	1	CLONAL	1	TRUE	1	0.16	2		676	1070	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911104	29911104	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41543413	NA	P-0012269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	61	457	1	ENST00000376809.5:c.403C>T	p.Arg135Cys	p.R135C	ENST00000376809	NM_002116.7	135	Cgc/Tgc	3/8	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.16	2		458	706	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127933461	127933461	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0012269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	62	534	0	ENST00000373547.4:c.76-2A>G		p.X26_splice	ENST00000373547	NM_002721.4	26			1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.16	2		534	721	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696653	47696653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866898949	NA	P-0012269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	54	647	1	ENST00000347630.2:c.295C>T	p.Arg99Trp	p.R99W	ENST00000347630	NM_001007230.1	99	Cgg/Tgg	5/11	1	2	FACETS	0.73	0.621	0.849	0.73	0.621	0.849	SUBCLONAL	1	TRUE	1	0.16	2		648	925	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0012287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	99	635	1	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.274659559122651	2	FACETS	1	0.956	1	0.563	0.504	0.625	CLONAL	1	TRUE	0	0.319185073523602	2		636	551	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256846	16256846	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	44	650	1	ENST00000375759.3:c.4111C>T	p.Arg1371Ter	p.R1371*	ENST00000375759	NM_015001.2	1371	Cga/Tga	11/15	0.113102326000113	0	FACETS	0.313	0.262	0.37			1	INDETERMINATE	1	TRUE	0	0.319185073523602	0		651	599	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158626907	158626907	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1177191263	NA	P-0012287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	91	1055	0	ENST00000263640.3:c.763G>T	p.Val255Leu	p.V255L	ENST00000263640	NM_001105.4	255	Gtg/Ttg	7/11	1	2	FACETS	0.618	0.547	0.693	0.618	0.547	0.693	SUBCLONAL	1	TRUE	1	0.319185073523602	2		1055	923	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430756	181430756	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	122	614	3	ENST00000325404.1:c.608G>T	p.Ser203Ile	p.S203I	ENST00000325404	NM_003106.3	203	aGc/aTc	1/1	1	2	FACETS	0.923	0.834	1	0.923	0.834	1	CLONAL	1	TRUE	1	0.319185073523602	2		617	828	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230830	66230830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	35	850	0	ENST00000273854.3:c.2141C>T	p.Thr714Ile	p.T714I	ENST00000273854	NM_004439.5	714	aCt/aTt	12/18	1	2	FACETS	0.403	0.33	0.486	0.403	0.33	0.486	SUBCLONAL	1	TRUE	1	0.319185073523602	2		850	544	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508556	106508556	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	64	259	0	ENST00000359195.3:c.550C>A	p.Arg184Ser	p.R184S	ENST00000359195	NM_002649.2	184	Cgc/Agc	2/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.319185073523602	2		259	317	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912288	97912288	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1060502516	NA	P-0012287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	163	684	1	ENST00000289081.3:c.603G>T	p.Glu201Asp	p.E201D	ENST00000289081	NM_000136.2	201	gaG/gaT	7/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.319185073523602	2		685	912	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435600	18435600	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	94	649	0	ENST00000266497.5:c.585T>A	p.Ser195Arg	p.S195R	ENST00000266497		195	agT/agA	1/31	0.274659559122651	2	FACETS	1	0.955	1	0.565	0.504	0.63	CLONAL	1	TRUE	0	0.319185073523602	2		649	521	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49054172	49054172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	46	561	0	ENST00000267163.4:c.2752G>A	p.Asp918Asn	p.D918N	ENST00000267163	NM_000321.2	918	Gat/Aat	27/27	1	2	FACETS	0.512	0.431	0.602	0.512	0.431	0.602	SUBCLONAL	1	TRUE	1	0.319185073523602	2		561	563	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829448	72829448	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	179	1077	0	ENST00000268489.5:c.7133C>G	p.Thr2378Ser	p.T2378S	ENST00000268489	NM_006885.3	2378	aCc/aGc	9/10	1	2	FACETS	0.998	0.919	1	0.998	0.919	1	CLONAL	1	TRUE	1	0.319185073523602	2		1077	1124	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509596	29509596	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1064794273	NA	P-0012287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	82	736	0	ENST00000356175.3:c.801G>A	p.Trp267Ter	p.W267*	ENST00000356175	NM_000267.3	267	tgG/tgA	8/57	1	2	FACETS	0.861	0.76	0.969	0.861	0.76	0.969	CLONAL	1	TRUE	1	0.319185073523602	2		736	597	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429011	47429011	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	80	922	0	ENST00000377045.4:c.1374C>A	p.Ser458Arg	p.S458R	ENST00000377045	NM_001654.4	458	agC/agA	13/16	1	2	FACETS	0.543	0.477	0.615	0.543	0.477	0.615	SUBCLONAL	1	TRUE	1	0.319185073523602	2		922	923	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410884	63410884	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	180	1002	0	ENST00000330258.3:c.2283G>T	p.Lys761Asn	p.K761N	ENST00000330258	NM_152424.3	761	aaG/aaT	2/2	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.319185073523602	2		1002	947	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412221	63412221	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	197	1067	0	ENST00000330258.3:c.946G>C	p.Val316Leu	p.V316L	ENST00000330258	NM_152424.3	316	Gtg/Ctg	2/2	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.319185073523602	2		1067	985	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012287-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	94	478	0	ENST00000269305.4:c.524del	p.Arg175ProfsTer72	p.R175Pfs*72	ENST00000269305	NM_001126112.2	175	cGc/cc	5/11	0.229813223673296	1	FACETS	0.908	0.81	1	0.908	0.81	1	CLONAL	1	TRUE	0	0.319185073523602	1		478	545	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121913370	NA	P-0012308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	28	263	0	ENST00000288602.6:c.1742A>G	p.Asn581Ser	p.N581S	ENST00000288602	NM_004333.4	581	aAt/aGt	15/18	1	2	FACETS	0.858	0.685	1	0.858	0.685	1	CLONAL	1	TRUE	1	0.15	2		263	435	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222982	1222982	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs727504172	NA	P-0012308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	27	281	0	ENST00000326873.7:c.921-2A>T		p.X307_splice	ENST00000326873	NM_000455.4	307			1	2	FACETS	0.978	0.779	1	0.978	0.779	1	CLONAL	1	TRUE	1	0.15	2		281	368	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645984	215645984	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	68	559	0	ENST00000260947.4:c.614A>C	p.Lys205Thr	p.K205T	ENST00000260947	NM_000465.2	205	aAg/aCg	4/11	1	2	FACETS	0.908	0.788	1	0.908	0.788	1	CLONAL	1	TRUE	1	0.15	2		559	998	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999111	100999111	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	57	753	1	ENST00000325455.5:c.691G>T	p.Glu231Ter	p.E231*	ENST00000325455	NM_001202474.3	231	Gag/Tag	1/8	1	2	FACETS	0.809	0.692	0.938	0.809	0.692	0.938	CLONAL	1	TRUE	1	0.15	2		754	939	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610099	10610099	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	65	599	0	ENST00000171111.5:c.611G>C	p.Arg204Pro	p.R204P	ENST00000171111	NM_203500.1	204	cGg/cCg	2/6	1	2	FACETS	0.978	0.846	1	0.978	0.846	1	CLONAL	1	TRUE	1	0.15	2		599	886	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387084	31387084	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	66	581	0	ENST00000328111.2:c.1709C>G	p.Ala570Gly	p.A570G	ENST00000328111	NM_006892.3	570	gCc/gGc	16/23	1	2	FACETS	0.976	0.845	1	0.976	0.845	1	CLONAL	1	TRUE	1	0.15	2		581	902	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331589	8331589	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	77	752	0	ENST00000356435.5:c.5527del	p.His1843IlefsTer13	p.H1843Ifs*13	ENST00000356435		1843	Cat/at	33/35	0.152032768430532	1	FACETS	0.882	0.772	1	0.882	0.772	1	CLONAL	1	TRUE	0	0.15	1		752	1077	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696689	47696689	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519972	NA	P-0012324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	147	812	0	ENST00000347630.2:c.259T>A	p.Tyr87Asn	p.Y87N	ENST00000347630	NM_001007230.1	87	Tac/Aac	5/11	1	2	FACETS	0.895	0.815	0.979	0.895	0.815	0.979	CLONAL	1	TRUE	1	0.28	2		812	1173	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020719	26020719	+	start_lost	Translation_Start_Site	SNP	T	T	G	novel	NA	P-0012324-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	62	1016	0	ENST00000357647.3:c.2T>G	p.Met1?	p.M1?	ENST00000357647	NM_003529.2	1	aTg/aGg	1/1	1	2	FACETS	0.38	0.327	0.439	0.38	0.327	0.439	SUBCLONAL	1	TRUE	1	0.28	2		1016	1164	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0012325-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	46	264	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	0.34	2		264	255	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409436	80409436	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012325-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	57	260	0	ENST00000286548.4:c.678C>G	p.Ile226Met	p.I226M	ENST00000286548	NM_002072.3	226	atC/atG	5/7	NA	2	FACETS	1	0.943	1			1	INDETERMINATE	1	TRUE	NA	0.34	2		260	285	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445995	49445995	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012325-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	326	650	2	ENST00000301067.7:c.1471G>T	p.Glu491Ter	p.E491*	ENST00000301067	NM_003482.3	491	Gaa/Taa	10/54	0.263465977439631	3	FACETS	0.877	0.828	0.928	0.877	0.828	0.928	CLONAL	2	TRUE	1	0.34	3		652	1279	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448178	49448178	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012325-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	111	750	1	ENST00000301067.7:c.422G>A	p.Trp141Ter	p.W141*	ENST00000301067	NM_003482.3	141	tGg/tAg	4/54	0.263465977439631	3	FACETS	0.734	0.658	0.814	0.367	0.329	0.407	SUBCLONAL	1	TRUE	1	0.34	3		751	1041	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606167	81606167	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0012325-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	110	562	0	ENST00000298171.2:c.837C>G	p.Tyr279Ter	p.Y279*	ENST00000298171	NM_000369.2	279	taC/taG	9/10	1	2	FACETS	0.658	0.59	0.73	0.658	0.59	0.73	SUBCLONAL	1	TRUE	1	0.34	2		562	984	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245918	41245918	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs80356952	NA	P-0012325-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	144	697	0	ENST00000357654.3:c.1630C>T	p.Gln544Ter	p.Q544*	ENST00000357654	NM_007294.3	544	Caa/Taa	10/23	1	2	FACETS	0.959	0.875	1	0.959	0.875	1	CLONAL	1	TRUE	1	0.34	2		697	883	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0012341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	76	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.92	0.807	1	0.92	0.807	1	CLONAL	1	TRUE	1	0.236646106497372	2		336	698	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs17849781	NA	P-0012341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	150	634	3	ENST00000269305.4:c.832C>A	p.Pro278Thr	p.P278T	ENST00000269305	NM_001126112.2	278	Cct/Act	8/11	0.219251120936002	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.236646106497372	1		637	1017	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023954	27023954	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	27	59	0	ENST00000324856.7:c.1060C>T	p.Gln354Ter	p.Q354*	ENST00000324856	NM_006015.4	354	Caa/Taa	1/20	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.236646106497372	2		59	184	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026649	6026649	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63751459	NA	P-0012341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	52	541	0	ENST00000265849.7:c.1747G>A	p.Glu583Lys	p.E583K	ENST00000265849	NM_000535.5	583	Gaa/Aaa	11/15	1	2	FACETS	0.443	0.375	0.517	0.443	0.375	0.517	SUBCLONAL	1	TRUE	1	0.236646106497372	2		541	993	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486568	56486568	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	99	586	0	ENST00000267101.3:c.1147A>C	p.Lys383Gln	p.K383Q	ENST00000267101	NM_001982.3	383	Aag/Cag	10/28	1	2	FACETS	0.801	0.713	0.894	0.801	0.713	0.894	CLONAL	1	TRUE	1	0.236646106497372	2		586	1045	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246414	10246414	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs1331424954	NA	P-0012341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	54	457	0	ENST00000340748.4:c.4723C>T	p.Gln1575Ter	p.Q1575*	ENST00000340748		1575	Cag/Tag	38/40	1	2	FACETS	0.594	0.506	0.691	0.594	0.506	0.691	SUBCLONAL	1	TRUE	1	0.236646106497372	2		457	768	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0012367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	471	801	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.669675864987897	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.683795664358351	2		801	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0012377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	412	354	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.701809223831887	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.701809223831887	1		354	733	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809217	243809217	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1217463895	NA	P-0012377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	342	883	0	ENST00000263826.5:c.407C>T	p.Ser136Phe	p.S136F	ENST00000263826	NM_005465.4	136	tCt/tTt	4/13	1	2	FACETS	0.923	0.875	0.972	0.923	0.875	0.972	CLONAL	1	TRUE	1	0.701809223831887	2		883	1056	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257118	198257118	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	300	649	0	ENST00000335508.6:c.3824G>C	p.Gly1275Ala	p.G1275A	ENST00000335508	NM_012433.2	1275	gGt/gCt	25/25	1	2	FACETS	0.972	0.918	1	0.972	0.918	1	CLONAL	1	TRUE	1	0.701809223831887	2		649	880	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223776	2223787	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CTTGGCCCTGCA	CTTGGCCCTGCA	-	novel	NA	P-0012377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	320	760	0	ENST00000326181.6:c.1087-13_1087-2del		p.X363_splice	ENST00000326181	NM_032271.2	363			1	2	FACETS	0.978	0.926	1	0.978	0.926	1	CLONAL	1	TRUE	1	0.701809223831887	2		760	932	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0012384-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	203	354	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.162961242338907	2	FACETS	1	0.99	1	0.719	0.666	0.774	CLONAL	1	TRUE	0	0.27	2		354	1046	SUCCESS
APC	324	MSKCC	GRCh37	5	112175770	112175773	+	frameshift_variant	Frame_Shift_Del	DEL	GGAA	GGAA	-	novel	NA	P-0012384-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	80	336	1	ENST00000257430.4:c.4479_4482del	p.Glu1494ValfsTer12	p.E1494Vfs*12	ENST00000257430	NM_000038.5	1493	acGGAA/ac	16/16	0.134009306921231	3	FACETS	1	0.935	1	0.546	0.481	0.616	INDETERMINATE	1	TRUE	1	0.27	3		337	616	SUCCESS
APC	324	MSKCC	GRCh37	5	112173531	112173531	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs773020689	NA	P-0012384-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	92	517	3	ENST00000257430.4:c.2240C>G	p.Ser747Ter	p.S747*	ENST00000257430	NM_000038.5	747	tCa/tGa	16/16	0.134009306921231	3	FACETS	1	0.899	1	0.506	0.449	0.567	INDETERMINATE	1	TRUE	1	0.27	3		520	764	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40497609	40497609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs964892419	NA	P-0012384-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1603	138	955	3	ENST00000264657.5:c.340C>T	p.Arg114Cys	p.R114C	ENST00000264657	NM_139276.2	114	Cgc/Tgc	4/24	0.104217028697443	4	FACETS	0.746	0.676	0.82	0.373	0.338	0.41	INDETERMINATE	1	TRUE	2	0.27	4		958	1741	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141601	202141603	+	inframe_deletion	In_Frame_Del	DEL	ATC	ATC	-	novel	NA	P-0012384-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	174	557	0	ENST00000358485.4:c.893_895del	p.Ile298del	p.I298del	ENST00000358485	NM_001080125.1	297	ATC/-	7/9	0.104217028697443	4	FACETS	0.768	0.707	0.833	0.768	0.707	0.833	INDETERMINATE	2	TRUE	2	0.27	4		557	1065	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	37	247	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.639	0.524	0.768	0.639	0.524	0.768	SUBCLONAL	1	TRUE	1	0.11	2		247	1053	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857517	57857517	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1910	126	995	0	ENST00000228682.2:c.43G>T	p.Glu15Ter	p.E15*	ENST00000228682	NM_005269.2	15	Gag/Tag	2/12	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.11	2		995	2036	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397516435	NA	P-0012387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	50	715	0	ENST00000269305.4:c.586C>G	p.Arg196Gly	p.R196G	ENST00000269305	NM_001126112.2	196	Cga/Gga	6/11	1	2	FACETS	0.721	0.609	0.845	0.721	0.609	0.845	SUBCLONAL	1	TRUE	1	0.11	2		715	1261	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591115	67591123	+	inframe_deletion	In_Frame_Del	DEL	CTTATCCAG	CTTATCCAG	-	novel	NA	P-0012387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	55	373	0	ENST00000274335.5:c.1710_1718del	p.Ile571_Leu573del	p.I571_L573del	ENST00000274335		570	CTTATCCAG/-	12/15	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.11	2		373	836	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204864	NA	P-0012396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	73	418	0	ENST00000371953.3:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000371953	NM_000314.4	171	Cag/Tag	6/9	1	2	FACETS	0.981	0.858	1	0.981	0.858	1	CLONAL	1	TRUE	1	0.254099384141401	2		418	586	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0012396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	122	894	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	0.878	0.792	0.969	0.878	0.792	0.969	CLONAL	1	TRUE	1	0.254099384141401	2		894	1094	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274042	10274042	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184494228	NA	P-0012396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	94	657	0	ENST00000330684.3:c.227G>A	p.Arg76His	p.R76H	ENST00000330684	NM_001134407.1	76	cGc/cAc	2/13	1	2	FACETS	0.78	0.692	0.873	0.78	0.692	0.873	SUBCLONAL	1	TRUE	1	0.254099384141401	2		657	949	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692883	89692883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204931	NA	P-0012396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	39	258	0	ENST00000371953.3:c.367C>T	p.His123Tyr	p.H123Y	ENST00000371953	NM_000314.4	123	Cac/Tac	5/9	1	2	FACETS	0.942	0.783	1	0.942	0.783	1	CLONAL	1	TRUE	1	0.254099384141401	2		258	326	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216572	108216572	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	74	579	0	ENST00000278616.4:c.8521G>A	p.Asp2841Asn	p.D2841N	ENST00000278616	NM_000051.3	2841	Gat/Aat	58/63	1	2	FACETS	0.744	0.65	0.845	0.744	0.65	0.845	SUBCLONAL	1	TRUE	1	0.254099384141401	2		579	783	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557673	21557673	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs762544451	NA	P-0012396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	53	730	1	ENST00000382592.4:c.2172C>A	p.Asp724Glu	p.D724E	ENST00000382592	NM_014572.2	724	gaC/gaA	5/8	1	2	FACETS	0.478	0.406	0.557	0.478	0.406	0.557	SUBCLONAL	1	TRUE	1	0.254099384141401	2		731	873	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032510	12032510	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	63	333	1	ENST00000353533.5:c.946C>T	p.Gln316Ter	p.Q316*	ENST00000353533	NM_003010.3	316	Caa/Taa	9/11	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.254099384141401	2		334	481	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229561	5229561	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012396-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	28	203	0	ENST00000357368.4:c.2290G>C	p.Glu764Gln	p.E764Q	ENST00000357368	NM_002850.3	764	Gag/Cag	15/38	1	2	FACETS	0.745	0.596	0.913	0.745	0.596	0.913	CLONAL	1	TRUE	1	0.254099384141401	2		203	296	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	42	715	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.875	0.728	1	0.875	0.728	1	CLONAL	1	TRUE	1	0.12	2		715	800	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0012431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	621	297	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.417311586521847	4	FACETS	1	0.995	1			1	CLONAL	3	TRUE	NA	0.417311586521847	4		297	1217	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101099	27101099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	471	769	0	ENST00000324856.7:c.4381C>T	p.Arg1461Ter	p.R1461*	ENST00000324856	NM_006015.4	1461	Cga/Tga	18/20	0.275048860508804	3	FACETS	1	0.989	1	0.731	0.699	0.763	CLONAL	2	TRUE	0	0.417311586521847	3		769	1244	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922294	100922294	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1315135533	NA	P-0012431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	335	776	1	ENST00000325455.5:c.2218C>T	p.Arg740Ter	p.R740*	ENST00000325455	NM_001202474.3	740	Cga/Tga	5/8	0.317534377209549	2	FACETS	1	0.993	1	0.67	0.633	0.707	CLONAL	1	TRUE	0	0.417311586521847	2		777	1199	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265479	152265479	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766779326	NA	P-0012431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	306	373	0	ENST00000206249.3:c.932C>T	p.Thr311Met	p.T311M	ENST00000206249	NM_000125.3	311	aCg/aTg	4/8	0.275048860508804	3	FACETS	1	0.99	1	0.784	0.743	0.825	CLONAL	2	TRUE	0	0.417311586521847	3		373	754	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435066	56435066	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1485983033	NA	P-0012431-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	286	406	0	ENST00000407977.2:c.2071C>G	p.Pro691Ala	p.P691A	ENST00000407977		691	Cct/Gct	9/10	0.317706751175421	3	FACETS	1	0.991	1	0.825	0.782	0.87	CLONAL	2	TRUE	0	0.417311586521847	3		406	669	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0012439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	126	852	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.98	0.886	1	0.98	0.886	1	CLONAL	1	TRUE	1	0.264048634665529	2		852	974	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041397	42041397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1435	205	887	1	ENST00000219905.7:c.5592G>A	p.Met1864Ile	p.M1864I	ENST00000219905	NM_001164273.1	1864	atG/atA	17/24	0.182458736158188	1	FACETS	0.822	0.759	0.887	0.822	0.759	0.887	CLONAL	1	TRUE	0	0.264048634665529	1		888	1640	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945373	151945373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370267189	NA	P-0012439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	28	163	0	ENST00000262189.6:c.2146G>A	p.Val716Ile	p.V716I	ENST00000262189	NM_170606.2	716	Gtt/Att	14/59	1	2	FACETS	0.848	0.681	1	0.848	0.681	1	CLONAL	1	TRUE	1	0.264048634665529	2		163	250	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563401	87563401	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	46	391	0	ENST00000277120.3:c.1789G>T	p.Ala597Ser	p.A597S	ENST00000277120		597	Gca/Tca	16/19	1	2	FACETS	0.515	0.433	0.607	0.515	0.433	0.607	SUBCLONAL	1	TRUE	1	0.264048634665529	2		391	676	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042733	42042733	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	135	875	0	ENST00000219905.7:c.6928G>C	p.Glu2310Gln	p.E2310Q	ENST00000219905	NM_001164273.1	2310	Gag/Cag	17/24	0.182458736158188	1	FACETS	0.704	0.638	0.774	0.704	0.638	0.774	SUBCLONAL	1	TRUE	0	0.264048634665529	1		875	1261	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0012442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	126	641	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.213695967482157	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.225671966938515	1		641	918	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	168	247	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.225671966938515	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	0	0.225671966938515	2		247	724	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0012448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	206	283	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.412706545090036	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.412706545090036	2		283	480	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	232	247	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.214746968158071	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.288241289964141	3		247	826	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189892	66189892	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	92	610	0	ENST00000273854.3:c.3054G>T	p.Lys1018Asn	p.K1018N	ENST00000273854	NM_004439.5	1018	aaG/aaT	18/18	0.214746968158071	3	FACETS	0.764	0.677	0.857	0.382	0.338	0.429	SUBCLONAL	1	TRUE	1	0.288241289964141	3		610	956	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456842	32456842	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	42	176	1	ENST00000332351.3:c.50C>T	p.Thr17Met	p.T17M	ENST00000332351	NM_024426.4	17	aCg/aTg	1/10	0.214746968158071	3	FACETS	1	0.908	1	0.561	0.471	0.661	CLONAL	1	TRUE	1	0.288241289964141	3		177	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576857	7576857	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	182	563	0	ENST00000269305.4:c.989T>G	p.Leu330Arg	p.L330R	ENST00000269305	NM_001126112.2	330	cTt/cGt	9/11	0.21727044353314	2	FACETS	1	0.988	1	0.702	0.648	0.759	CLONAL	1	TRUE	0	0.288241289964141	2		563	899	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041657	47041657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012449-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	191	350	1	ENST00000377604.3:c.1882G>T	p.Glu628Ter	p.E628*	ENST00000377604	NM_001204468.1	628	Gag/Tag	17/24	1	1	FACETS	1	0.946	1	1	0.994	1	CLONAL	2	TRUE	0	0.288241289964141	1		351	557	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0012452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	170	454	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	0.993	1	CLONAL	2	TRUE	1	0.14	2		454	992	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0012452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	38	422	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.664	0.547	0.796	0.664	0.547	0.796	SUBCLONAL	1	TRUE	1	0.14	2		422	817	SUCCESS
ATR	545	MSKCC	GRCh37	3	142255042	142255042	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs756859157	NA	P-0012452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	32	194	0	ENST00000350721.4:c.3727G>T	p.Asp1243Tyr	p.D1243Y	ENST00000350721	NM_001184.3	1243	Gat/Tat	20/47	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.14	2		194	403	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831972	72831972	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1212	66	836	0	ENST00000268489.5:c.4609A>G	p.Lys1537Glu	p.K1537E	ENST00000268489	NM_006885.3	1537	Aag/Gag	9/10	1	2	FACETS	0.738	0.638	0.847	0.738	0.638	0.847	SUBCLONAL	1	TRUE	1	0.14	2		836	1278	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41522040	41522040	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012452-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	41	426	0	ENST00000263253.7:c.902A>T	p.Asn301Ile	p.N301I	ENST00000263253	NM_001429.3	301	aAc/aTc	3/31	1	2	FACETS	0.801	0.666	0.953	0.801	0.666	0.953	CLONAL	1	TRUE	1	0.14	2		426	731	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0012457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	357	818	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.642333891548901	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	0	0.674970383525894	1		818	685	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0012458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	84	393	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.97	0.859	1	0.97	0.859	1	CLONAL	1	TRUE	1	0.328087918004156	2		393	528	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100117	157100119	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs797045268	NA	P-0012458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	11	35	0	ENST00000346085.5:c.1069_1071del	p.Gly357del	p.G357del	ENST00000346085	NM_020732.3	352	GGC/-	1/20	1	2	FACETS	0.944	0.664	1	0.944	0.664	1	CLONAL	1	TRUE	1	0.328087918004156	2		35	71	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602619	10602619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	143	482	0	ENST00000171111.5:c.959G>A	p.Arg320Gln	p.R320Q	ENST00000171111	NM_203500.1	320	cGg/cAg	3/6	0.328087918004156	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.328087918004156	1		482	636	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220482	1220482	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	116	568	0	ENST00000326873.7:c.575T>A	p.Ile192Asn	p.I192N	ENST00000326873	NM_000455.4	192	aTc/aAc	4/10	0.328087918004156	1	FACETS	0.915	0.826	1	0.915	0.826	1	CLONAL	1	TRUE	0	0.328087918004156	1		568	646	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	213	391	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.584587426975361	3	FACETS	1	0.99	1	0.676	0.63	0.722	CLONAL	1	TRUE	1	0.584587426975361	3		391	697	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398867	398867	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1191	208	633	0	ENST00000380956.4:c.677C>A	p.Pro226His	p.P226H	ENST00000380956	NM_001195286.1	226	cCt/cAt	6/9	0.569030249353682	5	FACETS	0.955	0.884	1	0.239	0.221	0.258	CLONAL	1	TRUE	1	0.584587426975361	5		633	1399	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913074	44913074	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	508	565	0	ENST00000377967.4:c.749G>C	p.Gly250Ala	p.G250A	ENST00000377967	NM_021140.2	250	gGt/gCt	10/29	0.541506107847184	4	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.584587426975361	4		565	1246	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0012520-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	348	273	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.773529474774291	2		273	850	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0012520-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	508	621	1	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.773529474774291	2		622	1220	SUCCESS
ATM	472	MSKCC	GRCh37	11	108225590	108225590	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012520-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	336	476	0	ENST00000278616.4:c.8839A>G	p.Thr2947Ala	p.T2947A	ENST00000278616	NM_000051.3	2947	Acc/Gcc	61/63	1	2	FACETS	0.875	0.829	0.921	0.875	0.829	0.921	CLONAL	1	TRUE	1	0.773529474774291	2		476	993	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044941	47044941	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012520-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	466	582	0	ENST00000377604.3:c.2267G>A	p.Trp756Ter	p.W756*	ENST00000377604	NM_001204468.1	756	tGg/tAg	20/24	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.773529474774291	2		582	1185	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012523-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	95	715	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.969	0.862	1	0.969	0.862	1	CLONAL	1	TRUE	1	0.232095916530024	2		715	845	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713832	30713832	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012523-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	107	481	0	ENST00000295754.5:c.1157T>C	p.Leu386Pro	p.L386P	ENST00000295754	NM_003242.5	386	cTc/cCc	4/7	0.232095916530024	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.232095916530024	1		481	698	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0012529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	405	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.517357535060563	6	FACETS	1	0.978	1	1	0.978	1	CLONAL	4	FALSE	2	0.517357535060563	6		336	773	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0012529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	192	273	0				ENST00000310581	NM_198253.2	-/1132			0.288138921192774	4	FACETS	0.983	0.915	1	0.983	0.915	1	INDETERMINATE	2	FALSE	2	0.517357535060563	4		273	573	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851285	63851285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	299	417	1	ENST00000279873.7:c.2063C>T	p.Ser688Phe	p.S688F	ENST00000279873	NM_032199.2	688	tCc/tTc	10/10	0.517357535060563	2	FACETS	0.923	0.877	0.969	0.923	0.877	0.969	CLONAL	2	FALSE	0	0.517357535060563	2		418	626	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	384	574	1	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.49739753924957	2	FACETS	0.845	0.807	0.884	0.845	0.807	0.884	CLONAL	2	FALSE	0	0.517357535060563	2		575	878	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959144	28959144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767259336	NA	P-0012529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	499	547	0	ENST00000282397.4:c.1994G>A	p.Arg665Gln	p.R665Q	ENST00000282397	NM_002019.4	665	cGa/cAa	14/30	0.504584881051194	3	FACETS	0.962	0.929	0.995	0.962	0.929	0.995	CLONAL	3	FALSE	0	0.517357535060563	3		547	841	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307700	11307700	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	275	619	2	ENST00000361445.4:c.1207C>T	p.Arg403Ter	p.R403*	ENST00000361445	NM_004958.3	403	Cga/Tga	8/58	0.448978537319906	4	FACETS	1	0.993	1	0.714	0.67	0.759	CLONAL	1	FALSE	2	0.517357535060563	4		621	1130	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258503	16258503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	233	424	0	ENST00000375759.3:c.5768C>T	p.Pro1923Leu	p.P1923L	ENST00000375759	NM_015001.2	1923	cCc/cTc	11/15	0.448978537319906	4	FACETS	0.77	0.719	0.822	0.77	0.719	0.822	SUBCLONAL	2	FALSE	2	0.517357535060563	4		424	888	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541888	187541888	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	404	736	2	ENST00000441802.2:c.5852C>T	p.Thr1951Ile	p.T1951I	ENST00000441802	NM_005245.3	1951	aCc/aTc	10/27	0.517357535060563	2	FACETS	0.769	0.733	0.804	0.769	0.733	0.804	SUBCLONAL	2	FALSE	0	0.517357535060563	2		738	1016	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891325	151891325	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	512	523	1	ENST00000262189.6:c.4529A>T	p.Tyr1510Phe	p.Y1510F	ENST00000262189	NM_170606.2	1510	tAt/tTt	30/59	0.517357535060563	6	FACETS	0.999	0.962	1	0.999	0.962	1	CLONAL	4	FALSE	2	0.517357535060563	6		524	1008	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131397	17131397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	342	513	0	ENST00000285071.4:c.55C>T	p.Leu19Phe	p.L19F	ENST00000285071	NM_144997.5	19	Ctc/Ttc	4/14	0.49739753924957	2	FACETS	0.881	0.84	0.923	0.881	0.84	0.923	CLONAL	2	FALSE	0	0.517357535060563	2		513	750	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546949	9546949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs921511471	NA	P-0012529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	313	446	0	ENST00000353224.5:c.1073C>T	p.Pro358Leu	p.P358L	ENST00000353224	NM_177990.2	358	cCt/cTt	5/10	0.517357535060563	6	FACETS	1	0.953	1	0.506	0.477	0.536	CLONAL	2	FALSE	2	0.517357535060563	6		446	1216	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511715	66511720	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGGTA	AAGGTA	-	novel	NA	P-0012529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	236	390	0	ENST00000358598.2:c.177_177+5del		p.X59_splice	ENST00000358598	NM_212471.2	59		2/11	0.49739753924957	2	FACETS	0.939	0.887	0.991	0.939	0.887	0.991	CLONAL	2	FALSE	0	0.517357535060563	2		390	486	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0012538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	256	559	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.934	0.878	0.991	0.934	0.878	0.991	CLONAL	1	TRUE	1	0.719598021903032	2		559	762	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023482	27023483	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0012538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	326	445	0	ENST00000324856.7:c.590_591del	p.Gly197AlafsTer202	p.G197Afs*202	ENST00000324856	NM_006015.4	196	gcGGgg/gcgg	1/20	0.611851226947862	1	FACETS	0.992	0.948	1	0.992	0.948	1	CLONAL	1	TRUE	0	0.719598021903032	1		445	585	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0012551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	249	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.418249203557672	3	FACETS	1	0.966	1	0.521	0.489	0.554	INDETERMINATE	1	TRUE	1	0.887223667245109	3		336	777	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0012551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	272	273	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.929	0.878	0.981	0.929	0.878	0.981	CLONAL	1	TRUE	1	0.887223667245109	2		273	660	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538374	9538374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868564987	NA	P-0012551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	299	249	0	ENST00000353224.5:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000353224	NM_177990.2	542	Gaa/Aaa	7/10	0.418249203557672	3	FACETS	0.754	0.716	0.792	0.754	0.716	0.792	INDETERMINATE	2	TRUE	1	0.887223667245109	3		249	645	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727443	66727443	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	334	369	0	ENST00000307102.5:c.159T>A	p.Phe53Leu	p.F53L	ENST00000307102	NM_002755.3	53	ttT/ttA	2/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.887223667245109	2		369	752	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474031	29474031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763862465	NA	P-0012551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	180	428	0	ENST00000389048.3:c.2144G>A	p.Gly715Glu	p.G715E	ENST00000389048	NM_004304.4	715	gGg/gAg	12/29	0.453620624081166	2	FACETS	0.451	0.416	0.487	0.225	0.208	0.244	INDETERMINATE	1	TRUE	0	0.887223667245109	2		428	900	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041725	29041725	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	637	283	0	ENST00000282397.4:c.94C>T	p.Pro32Ser	p.P32S	ENST00000282397	NM_002019.4	32	Cct/Tct	2/30	0.887223667245109	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.887223667245109	3		283	1030	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465049	120465049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	26	265	0	ENST00000256646.2:c.5023C>T	p.Arg1675Cys	p.R1675C	ENST00000256646	NM_024408.3	1675	Cgc/Tgc	28/34	0.887223667245109	1	FACETS	0.082	0.064	0.102	0.082	0.064	0.102	SUBCLONAL	1	TRUE	0	0.887223667245109	1		265	398	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039607	180039607	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	346	445	0	ENST00000261937.6:c.3436C>G	p.Arg1146Gly	p.R1146G	ENST00000261937	NM_182925.4	1146	Cgc/Ggc	26/30	0.887223667245109	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.887223667245109	1		445	424	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518190	8518190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	178	321	1	ENST00000356435.5:c.1201C>T	p.Arg401Trp	p.R401W	ENST00000356435		401	Cgg/Tgg	10/35	0.887223667245109	1	FACETS	0.53	0.494	0.567	0.53	0.494	0.567	SUBCLONAL	1	TRUE	0	0.887223667245109	1		322	421	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587390	29587390	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	259	294	0	ENST00000356175.3:c.4371T>A	p.Phe1457Leu	p.F1457L	ENST00000356175	NM_000267.3	1457	ttT/ttA	33/57	1	2	FACETS	0.933	0.88	0.986	0.933	0.88	0.986	CLONAL	1	TRUE	1	0.887223667245109	2		294	626	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78599548	78599548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	268	392	0	ENST00000306801.3:c.220G>A	p.Asp74Asn	p.D74N	ENST00000306801	NM_020761.2	74	Gat/Aat	2/34	0.384052973680256	1	FACETS	0.449	0.423	0.475	0.449	0.423	0.475	INDETERMINATE	1	TRUE	0	0.887223667245109	1		392	749	SUCCESS
BTK	695	MSKCC	GRCh37	X	100609658	100609658	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782740486	NA	P-0012551-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	278	616	0	ENST00000308731.7:c.1591G>A	p.Asp531Asn	p.D531N	ENST00000308731	NM_000061.2	531	Gat/Aat	16/19	0.760225987249208	1	FACETS	0.394	0.37	0.417	0.394	0.37	0.417	SUBCLONAL	1	TRUE	0	0.887223667245109	1		616	886	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0012562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	270	527	0	ENST00000269305.4:c.920-2A>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.341330137746495	2	FACETS	0.963	0.907	1	0.963	0.907	1	CLONAL	2	TRUE	0	0.341330137746495	2		527	821	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740300	162740300	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	rs1259672230	NA	P-0012562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	171	400	1	ENST00000367921.3:c.1502C>A	p.Ser501Ter	p.S501*	ENST00000367921	NM_006182.2	501	tCa/tAa	12/18	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.341330137746495	2		401	741	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442729	187442729	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	158	374	1	ENST00000232014.4:c.1977T>A	p.His659Gln	p.H659Q	ENST00000232014	NM_001130845.1	659	caT/caA	9/10	0.270359875199988	3	FACETS	1	0.988	1	0.733	0.673	0.796	CLONAL	1	TRUE	1	0.341330137746495	3		375	739	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100405	8100405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	158	953	1	ENST00000346208.3:c.379C>T	p.Pro127Ser	p.P127S	ENST00000346208		127	Ccg/Tcg	3/6	0.341330137746495	1	FACETS	0.575	0.525	0.627	0.575	0.525	0.627	SUBCLONAL	1	TRUE	0	0.341330137746495	1		954	1336	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942673	48942673	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764547244	NA	P-0012562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	148	628	0	ENST00000267163.4:c.1060C>T	p.Gln354Ter	p.Q354*	ENST00000267163	NM_000321.2	354	Cag/Tag	11/27	0.341330137746495	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.341330137746495	1		628	694	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196967	123196967	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012562-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	66	303	0	ENST00000218089.9:c.1733A>G	p.Tyr578Cys	p.Y578C	ENST00000218089	NM_001042749.1	578	tAc/tGc	19/35	0.0702823100305658	2	FACETS	1	0.912	1			1	INDETERMINATE	1	TRUE	NA	0.341330137746495	2		303	366	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26928012	26928012	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	49	490	0	ENST00000381527.3:c.451G>C	p.Asp151His	p.D151H	ENST00000381527	NM_001260.1	151	Gat/Cat	4/13	0.587610826960077	2	FACETS	0.295	0.249	0.345	0.147	0.124	0.173	SUBCLONAL	1	TRUE	0	0.587610826960077	2		490	566	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056738	180056738	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1195	184	614	1	ENST00000261937.6:c.774T>A	p.Phe258Leu	p.F258L	ENST00000261937	NM_182925.4	258	ttT/ttA	6/30	0.587610826960077	3	FACETS	0.588	0.541	0.637	0.196	0.18	0.213	SUBCLONAL	1	TRUE	0	0.587610826960077	3		615	1379	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160489	108160489	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012582-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	63	516	0	ENST00000278616.4:c.4397G>C	p.Arg1466Pro	p.R1466P	ENST00000278616	NM_000051.3	1466	cGa/cCa	29/63	0.260056982909331	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	2	TRUE	0	0.260056982909331	2		516	231	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36934759	36934759	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012582-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	49	1002	0	ENST00000361632.4:c.1574T>A	p.Met525Lys	p.M525K	ENST00000361632		525	aTg/aAg	11/16	NA	2	FACETS	0.979	0.831	1			1	INDETERMINATE	1	TRUE	NA	0.260056982909331	2		1002	385	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61717863	61717863	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012582-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	36	830	0	ENST00000401558.2:c.1936G>C	p.Asp646His	p.D646H	ENST00000401558	NM_003400.3	646	Gat/Cat	17/25	0.254154646945669	4	FACETS	0.798	0.656	0.957			1	CLONAL	1	TRUE	NA	0.260056982909331	4		830	437	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437325	220437325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012582-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	52	1154	1	ENST00000243786.2:c.229G>A	p.Glu77Lys	p.E77K	ENST00000243786	NM_002191.3	77	Gag/Aag	1/2	0.260056982909331	3	FACETS	1	0.938	1	0.596	0.509	0.691	CLONAL	1	TRUE	1	0.260056982909331	3		1155	379	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961354	54961354	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1420463153	NA	P-0012582-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	37	499	0	ENST00000312783.6:c.278A>G	p.Asn93Ser	p.N93S	ENST00000312783	NM_198436.1	93	aAt/aGt	4/10	0.243650249228688	4	FACETS	1	0.935	1	0.647	0.536	0.77	CLONAL	1	TRUE	2	0.260056982909331	4		499	277	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250922	153250922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012582-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	33	489	0	ENST00000281708.4:c.1138G>A	p.Asp380Asn	p.D380N	ENST00000281708	NM_033632.3	380	Gat/Aat	8/12	0.231595298503812	2	FACETS	1	0.907	1	0.587	0.482	0.704	CLONAL	1	TRUE	0	0.260056982909331	2		489	216	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742025	145742025	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs758124770	NA	P-0012582-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	44	654	0	ENST00000428558.2:c.478C>G	p.Pro160Ala	p.P160A	ENST00000428558	NM_004260.3	160	Cca/Gca	5/22	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.260056982909331	2		654	267	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411540	63411540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012582-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	45	1231	2	ENST00000330258.3:c.1627G>A	p.Glu543Lys	p.E543K	ENST00000330258	NM_152424.3	543	Gag/Aag	2/2	0.231595298503812	2	FACETS	0.797	0.671	0.937	0.399	0.335	0.469	CLONAL	1	TRUE	0	0.260056982909331	2		1233	434	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342445	70342445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012582-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	23	848	0	ENST00000374080.3:c.1336G>A	p.Glu446Lys	p.E446K	ENST00000374080		446	Gaa/Aaa	9/45	0.231595298503812	2	FACETS	0.467	0.363	0.587	0.233	0.181	0.294	SUBCLONAL	1	TRUE	0	0.260056982909331	2		848	379	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	421	247	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.462533922184108	6	FACETS	0.883	0.844	0.922	0.883	0.844	0.922	CLONAL	4	TRUE	2	0.462533922184108	6		247	992	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0012586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	132	273	0	ENST00000269305.4:c.375+1G>T		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.283223635604985	3	FACETS	0.802	0.734	0.873	0.535	0.489	0.582	CLONAL	2	TRUE	0	0.462533922184108	3		273	438	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244020	5244020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752283871	NA	P-0012586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	211	576	1	ENST00000357368.4:c.1462G>A	p.Val488Met	p.V488M	ENST00000357368	NM_002850.3	488	Gtg/Atg	11/38	0.283223635604985	3	FACETS	0.922	0.862	0.984	0.615	0.575	0.656	CLONAL	2	TRUE	0	0.462533922184108	3		577	609	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899087	40899087	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	176	623	0	ENST00000373198.4:c.2183T>A	p.Met728Lys	p.M728K	ENST00000373198	NM_133170.3	728	aTg/aAg	14/32	NA	2	FACETS	1	0.949	1			1	INDETERMINATE	1	TRUE	NA	0.462533922184108	2		623	735	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0012596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	55	801	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.101978517504283	2		801	1075	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865432	57865432	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012596-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1499	114	923	1	ENST00000228682.2:c.2909G>T	p.Cys970Phe	p.C970F	ENST00000228682	NM_005269.2	970	tGc/tTc	12/12	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.101978517504283	2		924	1613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0012623-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	408	593	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.36793810668395	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.36793810668395	2		593	1047	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0012623-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	709	419	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.290446191649567	4	FACETS	0.995	0.964	1			1	CLONAL	4	TRUE	NA	0.36793810668395	4		419	1325	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0012623-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	192	218	1	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	0.36793810668395	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.36793810668395	2		219	499	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0012624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	197	382	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.204032662682328	3	FACETS	0.909	0.845	0.976	0.909	0.845	0.976	INDETERMINATE	2	TRUE	1	0.34677603000166	3		382	733	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0012624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	192	450	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.34677603000166	2		450	1025	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11227497	11227497	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0012624-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	222	483	0	ENST00000361445.4:c.4329+2T>A		p.X1443_splice	ENST00000361445	NM_004958.3	1443			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.34677603000166	2		483	1234	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0012627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	314	414	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.279672769582565	2	FACETS	0.818	0.772	0.865	0.818	0.772	0.865	CLONAL	2	TRUE	0	0.340666878023694	2		416	1127	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508835	106508835	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	276	320	1	ENST00000359195.3:c.829C>T	p.Arg277Trp	p.R277W	ENST00000359195	NM_002649.2	277	Cgg/Tgg	2/11	0.340666878023694	3	FACETS	0.868	0.815	0.923	0.868	0.815	0.923	CLONAL	2	TRUE	1	0.340666878023694	3		321	1092	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515143	148515143	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	212	454	0	ENST00000320356.2:c.1066G>A	p.Gly356Arg	p.G356R	ENST00000320356	NM_004456.4	356	Gga/Aga	10/20	1	2	FACETS	0.937	0.869	1	0.937	0.869	1	CLONAL	1	TRUE	1	0.340666878023694	2		454	1328	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460494	8460494	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	225	403	0	ENST00000356435.5:c.3792A>C	p.Glu1264Asp	p.E1264D	ENST00000356435		1264	gaA/gaC	22/35	0.340666878023694	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.340666878023694	1		403	1031	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851456	63851456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201542647	NA	P-0012627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	97	244	0	ENST00000279873.7:c.2234C>T	p.Ala745Val	p.A745V	ENST00000279873	NM_032199.2	745	gCg/gTg	10/10	0.307264789102232	3	FACETS	0.834	0.743	0.931	0.417	0.371	0.466	CLONAL	1	TRUE	1	0.340666878023694	3		244	799	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474339	40474339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1661	213	571	1	ENST00000264657.5:c.2062C>T	p.Arg688Trp	p.R688W	ENST00000264657	NM_139276.2	688	Cgg/Tgg	21/24	0.217156731784756	4	FACETS	0.895	0.828	0.965	0.447	0.414	0.483	CLONAL	1	TRUE	2	0.340666878023694	4		572	1874	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574159	41574159	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	141	360	0	ENST00000263253.7:c.6444G>T	p.Gln2148His	p.Q2148H	ENST00000263253	NM_001429.3	2148	caG/caT	31/31	0.217156731784756	4	FACETS	0.966	0.878	1	0.483	0.439	0.529	CLONAL	1	TRUE	2	0.340666878023694	4		360	1149	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604777	48604833	+	inframe_deletion	In_Frame_Del	DEL	CCAGCTCCTAGACGAAGTACTTCATACCATGCCGATTGCAGACCCACAACCTTTAGA	CCAGCTCCTAGACGAAGTACTTCATACCATGCCGATTGCAGACCCACAACCTTTAGA	-	novel	NA	P-0012627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	45	400	0	ENST00000342988.3:c.1600_1656del	p.Gln534_Asp552del	p.Q534_D552del	ENST00000342988	NM_005359.5	533	ctCCAGCTCCTAGACGAAGTACTTCATACCATGCCGATTGCAGACCCACAACCTTTAGAc/ctc	12/12	0.289116188026929	1	FACETS	0.244	0.204	0.288	0.244	0.204	0.288	SUBCLONAL	1	TRUE	0	0.340666878023694	1		400	900	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971024	21971039	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCCCAGGCATCGCG	GGCCCCAGGCATCGCG	-	novel	NA	P-0012627-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	233	255	0	ENST00000304494.5:c.319_334del	p.Arg107ValfsTer34	p.R107Vfs*34	ENST00000304494	NM_000077.4	107	CGCGATGCCTGGGGCCgt/gt	2/3	0.149146279519724	3	FACETS	1	0.981	1			1	INDETERMINATE	2	TRUE	NA	0.340666878023694	3		255	718	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0012660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	19	462	1	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		463	787	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190072	123190072	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	29	232	0	ENST00000218089.9:c.1291T>G	p.Phe431Val	p.F431V	ENST00000218089	NM_001042749.1	431	Ttt/Gtt	14/35	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		232	515	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519998	NA	P-0012667-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	508	585	0	ENST00000269305.4:c.581T>A	p.Leu194His	p.L194H	ENST00000269305	NM_001126112.2	194	cTt/cAt	6/11	0.394904852752113	4	FACETS	0.939	0.906	0.971	0.939	0.906	0.971	CLONAL	4	TRUE	0	0.435475341866579	4		585	892	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231858	36231858	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012667-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	83	433	0	ENST00000300305.3:c.526A>G	p.Thr176Ala	p.T176A	ENST00000300305		176	Acc/Gcc	5/8	0.391510118368966	3	FACETS	0.746	0.659	0.84	0.373	0.329	0.42	SUBCLONAL	1	TRUE	1	0.435475341866579	3		433	622	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927390	178927390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012667-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	348	452	0	ENST00000263967.3:c.1153G>A	p.Glu385Lys	p.E385K	ENST00000263967	NM_006218.2	385	Gaa/Aaa	7/21	0.394904852752113	4	FACETS	1	0.988	1	0.823	0.786	0.86	CLONAL	3	TRUE	0	0.435475341866579	4		452	697	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927405	178927405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012667-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	432	525	0	ENST00000263967.3:c.1168G>A	p.Asp390Asn	p.D390N	ENST00000263967	NM_006218.2	390	Gat/Aat	7/21	0.394904852752113	4	FACETS	1	0.993	1	0.863	0.829	0.897	CLONAL	3	TRUE	0	0.435475341866579	4		525	825	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624394	140624394	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1390903353	NA	P-0012667-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	102	207	1	ENST00000288602.6:c.110C>T	p.Ser37Leu	p.S37L	ENST00000288602	NM_004333.4	37	tCg/tTg	1/18	0.384865937719511	5	FACETS	1	0.948	1	0.717	0.647	0.79	CLONAL	2	TRUE	2	0.435475341866579	5		208	360	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389326	8389326	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012667-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	269	682	0	ENST00000356435.5:c.4292C>G	p.Ser1431Cys	p.S1431C	ENST00000356435		1431	tCt/tGt	26/35	0.435475341866579	4	FACETS	1	0.992	1	0.461	0.432	0.492	CLONAL	1	TRUE	1	0.435475341866579	4		682	1281	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36421171	36421171	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0012667-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	85	510	0	ENST00000300305.3:c.26C>G	p.Ser9Ter	p.S9*	ENST00000300305		9	tCa/tGa	1/8	0.391510118368966	3	FACETS	0.672	0.594	0.756	0.336	0.297	0.378	SUBCLONAL	1	TRUE	1	0.435475341866579	3		510	707	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	191	645	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.846	0.781	0.914	0.846	0.781	0.914	CLONAL	1	TRUE	1	0.39	2		645	1158	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47684731	47684731	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	46	251	0	ENST00000347630.2:c.718C>T	p.Arg240Ter	p.R240*	ENST00000347630	NM_001007230.1	240	Cga/Tga	9/11	1	2	FACETS	0.68	0.574	0.795	0.68	0.574	0.795	SUBCLONAL	1	TRUE	1	0.39	2		251	347	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	123	484	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.39	2		484	440	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20483060	20483060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750169257	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	110	407	1	ENST00000346618.3:c.793G>A	p.Glu265Lys	p.E265K	ENST00000346618	NM_001949.4	265	Gag/Aag	4/7	0.166639481091972	3	FACETS	0.906	0.814	1	0.453	0.407	0.502	INDETERMINATE	1	TRUE	1	0.39	3		408	744	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050770	5050770	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	72	339	0	ENST00000381652.3:c.553G>T	p.Asp185Tyr	p.D185Y	ENST00000381652	NM_004972.3	185	Gat/Tat	6/25	1	2	FACETS	0.779	0.682	0.882	0.779	0.682	0.882	SUBCLONAL	1	TRUE	1	0.39	2		339	474	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337650	73337650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	79	336	0	ENST00000377767.4:c.2066G>A	p.Arg689Gln	p.R689Q	ENST00000377767	NM_014953.3	689	cGa/cAa	16/21	1	2	FACETS	0.976	0.863	1	0.976	0.863	1	CLONAL	1	TRUE	1	0.39	2		336	415	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	125	358	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.973	0.882	1	0.973	0.882	1	CLONAL	1	TRUE	1	0.39	2		358	659	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	338239	338239	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	104	423	0	ENST00000262320.3:c.2472C>A	p.Phe824Leu	p.F824L	ENST00000262320	NM_003502.3	824	ttC/ttA	11/11	1	2	FACETS	0.869	0.779	0.963	0.869	0.779	0.963	CLONAL	1	TRUE	1	0.39	2		423	614	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	65	264	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	1	2	FACETS	0.868	0.756	0.988	0.868	0.756	0.988	CLONAL	1	TRUE	1	0.39	2		264	384	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374881	45374881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	75	354	0	ENST00000262160.6:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000262160	NM_005901.5	321	cGa/cAa	8/11	0.113486771141372	0	FACETS	0.523	0.459	0.59			1	INDETERMINATE	1	TRUE	0	0.39	0		354	449	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670615	134670615	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781004053	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	143	522	3	ENST00000398015.3:c.526G>A	p.Ala176Thr	p.A176T	ENST00000398015	NM_004441.4	176	Gct/Act	3/16	1	2	FACETS	0.899	0.82	0.981	0.899	0.82	0.981	CLONAL	1	TRUE	1	0.39	2		525	816	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111048	193111048	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	59	268	0	ENST00000367435.3:c.581G>T	p.Arg194Ile	p.R194I	ENST00000367435	NM_024529.4	194	aGa/aTa	7/17	1	2	FACETS	0.937	0.811	1	0.937	0.811	1	CLONAL	1	TRUE	1	0.39	2		268	323	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344036	118344036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	68	309	1	ENST00000534358.1:c.2162G>A	p.Arg721Gln	p.R721Q	ENST00000534358	NM_005933.3	721	cGa/cAa	3/36	1	2	FACETS	0.859	0.75	0.975	0.859	0.75	0.975	CLONAL	1	TRUE	1	0.39	2		310	406	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134988	41134988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	112	602	0	ENST00000379561.5:c.640C>T	p.Arg214Cys	p.R214C	ENST00000379561	NM_002015.3	214	Cgt/Tgt	2/3	1	2	FACETS	0.719	0.646	0.796	0.719	0.646	0.796	SUBCLONAL	1	TRUE	1	0.39	2		602	799	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117639416	117639416	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	53	365	0	ENST00000368508.3:c.5941-1G>A		p.X1981_splice	ENST00000368508	NM_002944.2	1981			0.166639481091972	3	FACETS	0.727	0.621	0.842	0.363	0.31	0.421	INDETERMINATE	1	TRUE	1	0.39	3		365	447	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915952	127915952	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs865855853	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	150	568	2	ENST00000373547.4:c.529C>T	p.Arg177Ter	p.R177*	ENST00000373547	NM_002721.4	177	Cga/Tga	6/7	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.39	2		570	732	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940000	76940000	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1311466929	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	86	451	1	ENST00000373344.5:c.748C>T	p.Arg250Ter	p.R250*	ENST00000373344	NM_000489.3	250	Cga/Tga	9/35	0.166639481091972	0	FACETS	0.487	0.432	0.546			1	INDETERMINATE	1	TRUE	0	0.39	0		452	552	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026643	6026643	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs63750947	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	92	468	0	ENST00000265849.7:c.1753C>A	p.Leu585Ile	p.L585I	ENST00000265849	NM_000535.5	585	Ctt/Att	11/15	1	2	FACETS	0.864	0.77	0.964	0.864	0.77	0.964	CLONAL	1	TRUE	1	0.39	2		468	546	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131895051	131895051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370769989	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	46	233	0	ENST00000265335.6:c.205G>A	p.Asp69Asn	p.D69N	ENST00000265335		69	Gat/Aat	2/25	1	2	FACETS	0.842	0.714	0.982	0.842	0.714	0.982	CLONAL	1	TRUE	1	0.39	2		233	280	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950860	32950860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373203204	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	163	399	1	ENST00000380152.3:c.8686C>T	p.Arg2896Cys	p.R2896C	ENST00000380152		2896	Cgt/Tgt	21/27	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.39	2		400	799	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416133	49416133	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1422752351	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	73	310	0	ENST00000301067.7:c.16342C>T	p.Arg5448Ter	p.R5448*	ENST00000301067	NM_003482.3	5448	Cga/Tga	52/54	0.166639481091972	3	FACETS	1	0.942	1	0.562	0.494	0.635	INDETERMINATE	1	TRUE	1	0.39	3		310	398	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578349	212578349	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	79	263	1	ENST00000342788.4:c.908C>A	p.Ser303Tyr	p.S303Y	ENST00000342788	NM_005235.2	303	tCt/tAt	8/28	1	2	FACETS	0.991	0.876	1	0.991	0.876	1	CLONAL	1	TRUE	1	0.39	2		264	409	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938406	76938406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	110	585	0	ENST00000373344.5:c.2342G>A	p.Arg781Gln	p.R781Q	ENST00000373344	NM_000489.3	781	cGa/cAa	9/35	0.166639481091972	0	FACETS	0.572	0.515	0.632			1	INDETERMINATE	1	TRUE	0	0.39	0		585	602	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696704	47696704	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	79	417	1	ENST00000347630.2:c.244G>T	p.Asp82Tyr	p.D82Y	ENST00000347630	NM_001007230.1	82	Gat/Tat	5/11	1	2	FACETS	0.55	0.484	0.622	0.55	0.484	0.622	SUBCLONAL	1	TRUE	1	0.39	2		418	736	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	172	496	0	ENST00000267101.3:c.273G>T	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atT	3/28	0.166639481091972	3	FACETS	1	0.98	1	0.596	0.548	0.645	INDETERMINATE	1	TRUE	1	0.39	3		496	885	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692940	89692940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746152219	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	56	294	0	ENST00000371953.3:c.424C>T	p.Arg142Trp	p.R142W	ENST00000371953	NM_000314.4	142	Cgg/Tgg	5/9	1	2	FACETS	0.811	0.698	0.933	0.811	0.698	0.933	CLONAL	1	TRUE	1	0.39	2		294	354	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105736	27105736	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	61	361	0	ENST00000324856.7:c.5347G>T	p.Glu1783Ter	p.E1783*	ENST00000324856	NM_006015.4	1783	Gaa/Taa	20/20	1	2	FACETS	0.688	0.594	0.788	0.688	0.594	0.788	SUBCLONAL	1	TRUE	1	0.39	2		361	455	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193889	106193889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1395976555	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	148	333	0	ENST00000380013.4:c.4351C>T	p.Arg1451Trp	p.R1451W	ENST00000380013	NM_001127208.2	1451	Cgg/Tgg	10/11	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.39	2		333	733	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609707	28609707	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1216208857	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	179	432	0	ENST00000241453.7:c.1522A>C	p.Lys508Gln	p.K508Q	ENST00000241453	NM_004119.2	508	Aaa/Caa	12/24	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.39	2		432	676	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137487	202137487	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	230	400	1	ENST00000358485.4:c.715G>T	p.Glu239Ter	p.E239*	ENST00000358485	NM_001080125.1	239	Gaa/Taa	4/9	1	2	FACETS	0.983	0.923	1	1	0.995	1	CLONAL	2	TRUE	1	0.39	2		401	600	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027661	48027661	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	18	185	0	ENST00000234420.5:c.2539G>T	p.Glu847Ter	p.E847*	ENST00000234420	NM_000179.2	847	Gaa/Taa	4/10	1	2	FACETS	0.81	0.618	1	0.81	0.618	1	CLONAL	1	TRUE	1	0.39	2		185	114	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242628	16242628	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	63	324	0	ENST00000375759.3:c.1249G>T	p.Glu417Ter	p.E417*	ENST00000375759	NM_015001.2	417	Gaa/Taa	6/15	0.3	5	FACETS	1	0.916	1			1	CLONAL	1	TRUE	NA	0.39	5		324	475	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023197	27023197	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	105	170	0	ENST00000324856.7:c.303G>T	p.Lys101Asn	p.K101N	ENST00000324856	NM_006015.4	101	aaG/aaT	1/20	1	2	FACETS	0.893	0.802	0.989	0.893	0.802	0.989	CLONAL	1	TRUE	1	0.39	2		170	603	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521644	46521644	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	13	215	0	ENST00000262741.5:c.765-1G>T		p.X255_splice	ENST00000262741	NM_003629.3	255			1	2	FACETS	0.49	0.352	0.657	0.49	0.352	0.657	SUBCLONAL	1	TRUE	1	0.39	2		215	136	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736480	85736480	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	137	559	0	ENST00000370580.1:c.167C>A	p.Ser56Tyr	p.S56Y	ENST00000370580	NM_003921.4	56	tCt/tAt	2/3	1	2	FACETS	0.863	0.785	0.945	0.863	0.785	0.945	CLONAL	1	TRUE	1	0.39	2		559	814	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464967	120464967	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	82	271	0	ENST00000256646.2:c.5105G>T	p.Arg1702Leu	p.R1702L	ENST00000256646	NM_024408.3	1702	cGa/cTa	28/34	1	2	FACETS	0.906	0.802	1	0.906	0.802	1	CLONAL	1	TRUE	1	0.39	2		271	464	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667422	241667422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756990249	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	169	534	0	ENST00000366560.3:c.1028G>A	p.Arg343Gln	p.R343Q	ENST00000366560	NM_000143.3	343	cGa/cAa	7/10	1	2	FACETS	0.977	0.899	1	0.977	0.899	1	CLONAL	1	TRUE	1	0.39	2		534	887	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800930	243800930	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	51	408	0	ENST00000263826.5:c.544G>T	p.Glu182Ter	p.E182*	ENST00000263826	NM_005465.4	182	Gaa/Taa	5/13	1	2	FACETS	0.694	0.592	0.805	0.694	0.592	0.805	SUBCLONAL	1	TRUE	1	0.39	2		408	377	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202123005	202123005	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	177	432	0	ENST00000358485.4:c.51C>A	p.Phe17Leu	p.F17L	ENST00000358485	NM_001080125.1	17	ttC/ttA	1/9	1	2	FACETS	0.844	0.777	0.915	0.844	0.777	0.915	CLONAL	1	TRUE	1	0.39	2		432	1075	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116217	209116217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201258988	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	38	448	1	ENST00000345146.2:c.59G>A	p.Arg20Gln	p.R20Q	ENST00000345146	NM_005896.2	20	cGa/cAa	3/10	1	2	FACETS	0.355	0.293	0.425	0.355	0.293	0.425	SUBCLONAL	1	TRUE	1	0.39	2		449	549	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275649	41275649	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	127	338	0	ENST00000349496.5:c.1544G>A	p.Arg515Gln	p.R515Q	ENST00000349496	NM_001904.3	515	cGa/cAa	10/15	1	2	FACETS	0.996	0.904	1	0.996	0.904	1	CLONAL	1	TRUE	1	0.39	2		338	654	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098463	47098463	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	138	409	0	ENST00000409792.3:c.6811A>C	p.Ser2271Arg	p.S2271R	ENST00000409792	NM_014159.6	2271	Agt/Cgt	15/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.39	2		409	573	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164855	47164855	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424607930	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	62	315	0	ENST00000409792.3:c.1271G>A	p.Arg424Gln	p.R424Q	ENST00000409792	NM_014159.6	424	cGa/cAa	3/21	1	2	FACETS	0.708	0.613	0.811	0.708	0.613	0.811	SUBCLONAL	1	TRUE	1	0.39	2		315	449	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468462	89468462	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	78	333	0	ENST00000336596.2:c.1996G>T	p.Asp666Tyr	p.D666Y	ENST00000336596	NM_005233.5	666	Gac/Tac	11/17	1	2	FACETS	0.662	0.582	0.748	0.662	0.582	0.748	SUBCLONAL	1	TRUE	1	0.39	2		333	604	SUCCESS
ATR	545	MSKCC	GRCh37	3	142212044	142212044	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	116	414	0	ENST00000350721.4:c.6008T>G	p.Met2003Arg	p.M2003R	ENST00000350721	NM_001184.3	2003	aTg/aGg	35/47	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.39	2		414	520	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161258	185161258	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	127	391	0	ENST00000265026.3:c.685T>G	p.Tyr229Asp	p.Y229D	ENST00000265026	NM_004721.4	229	Tat/Gat	4/14	1	2	FACETS	0.798	0.73	0.869	1	0.988	1	SUBCLONAL	2	TRUE	1	0.39	2		391	408	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133894	55133894	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	48	295	1	ENST00000257290.5:c.1107G>T	p.Lys369Asn	p.K369N	ENST00000257290	NM_006206.4	369	aaG/aaT	7/23	1	2	FACETS	0.575	0.487	0.672	0.575	0.487	0.672	SUBCLONAL	1	TRUE	1	0.39	2		296	428	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230813	66230813	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	104	476	2	ENST00000273854.3:c.2158G>T	p.Asp720Tyr	p.D720Y	ENST00000273854	NM_004439.5	720	Gat/Tat	12/18	1	2	FACETS	0.794	0.711	0.881	0.794	0.711	0.881	SUBCLONAL	1	TRUE	1	0.39	2		478	672	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270102	66270102	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	140	362	0	ENST00000273854.3:c.1780C>A	p.Leu594Ile	p.L594I	ENST00000273854	NM_004439.5	594	Ctc/Atc	8/18	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.39	2		362	696	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280155	66280155	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	41	229	0	ENST00000273854.3:c.1534G>T	p.Glu512Ter	p.E512*	ENST00000273854	NM_004439.5	512	Gag/Tag	7/18	1	2	FACETS	0.803	0.673	0.945	0.803	0.673	0.945	CLONAL	1	TRUE	1	0.39	2		229	262	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332670	153332670	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	97	564	0	ENST00000281708.4:c.286G>T	p.Glu96Ter	p.E96*	ENST00000281708	NM_033632.3	96	Gaa/Taa	2/12	1	2	FACETS	0.695	0.619	0.775	0.695	0.619	0.775	SUBCLONAL	1	TRUE	1	0.39	2		564	716	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630459	187630459	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	171	514	2	ENST00000441802.2:c.523G>A	p.Asp175Asn	p.D175N	ENST00000441802	NM_005245.3	175	Gat/Aat	2/27	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.39	2		516	846	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871265	35871265	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	74	301	0	ENST00000303115.3:c.487T>G	p.Leu163Val	p.L163V	ENST00000303115	NM_002185.3	163	Tta/Gta	4/8	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.39	2		301	349	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38978718	38978718	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	48	365	0	ENST00000357387.3:c.788G>T	p.Arg263Ile	p.R263I	ENST00000357387	NM_152756.3	263	aGa/aTa	9/38	1	2	FACETS	0.542	0.459	0.634	0.542	0.459	0.634	SUBCLONAL	1	TRUE	1	0.39	2		365	454	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751173	57751173	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	50	306	0	ENST00000274289.3:c.1694T>G	p.Phe565Cys	p.F565C	ENST00000274289	NM_006622.3	565	tTt/tGt	12/14	1	2	FACETS	0.487	0.413	0.568	0.487	0.413	0.568	SUBCLONAL	1	TRUE	1	0.39	2		306	527	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131972841	131972841	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	36	333	1	ENST00000265335.6:c.3424G>T	p.Glu1142Ter	p.E1142*	ENST00000265335		1142	Gaa/Taa	22/25	1	2	FACETS	0.632	0.522	0.755	0.632	0.522	0.755	SUBCLONAL	1	TRUE	1	0.39	2		334	292	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778229	27778229	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1366	229	765	0	ENST00000369163.2:c.378G>T	p.Gln126His	p.Q126H	ENST00000369163	NM_003536.2	126	caG/caT	1/1	0.166639481091972	3	FACETS	0.88	0.817	0.945	0.44	0.408	0.473	INDETERMINATE	1	TRUE	1	0.39	3		765	1595	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910556	29910556	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	50	58	0	ENST00000376809.5:c.96C>A	p.Phe32Leu	p.F32L	ENST00000376809	NM_002116.7	32	ttC/ttA	2/8	0.166639481091972	3	FACETS	1	0.965	1	0.733	0.63	0.843	INDETERMINATE	1	TRUE	1	0.39	3		58	209	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673344	30673344	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1357	89	699	1	ENST00000376406.3:c.3616G>T	p.Ala1206Ser	p.A1206S	ENST00000376406	NM_014641.2	1206	Gcc/Tcc	10/15	0.166639481091972	3	FACETS	0.377	0.333	0.425	0.189	0.166	0.213	INDETERMINATE	1	TRUE	1	0.39	3		700	1446	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43749777	43749777	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	224	507	2	ENST00000523873.1:c.630C>A	p.Asp210Glu	p.D210E	ENST00000523873		210	gaC/gaA	7/8	0.166639481091972	3	FACETS	1	0.939	1	0.506	0.47	0.544	INDETERMINATE	1	TRUE	1	0.39	3		509	1356	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793662	89793662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	91	383	0	ENST00000336032.3:c.731G>T	p.Arg244Ile	p.R244I	ENST00000336032	NM_006813.2	244	aGa/aTa	2/2	0.166639481091972	3	FACETS	0.771	0.685	0.864	0.386	0.342	0.432	INDETERMINATE	1	TRUE	1	0.39	3		383	723	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527367	157527367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	66	375	0	ENST00000346085.5:c.5092C>T	p.Leu1698Phe	p.L1698F	ENST00000346085	NM_020732.3	1698	Ctt/Ttt	20/20	0.166639481091972	3	FACETS	0.963	0.839	1	0.482	0.419	0.548	INDETERMINATE	1	TRUE	1	0.39	3		375	420	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206908	162206908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1233588284	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	111	257	0	ENST00000366898.1:c.767G>A	p.Arg256His	p.R256H	ENST00000366898	NM_004562.2	256	cGc/cAc	7/12	0.166639481091972	3	FACETS	1	0.968	1	0.589	0.531	0.651	INDETERMINATE	1	TRUE	1	0.39	3		257	577	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080620	5080620	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	76	450	0	ENST00000381652.3:c.2371G>T	p.Glu791Ter	p.E791*	ENST00000381652	NM_004972.3	791	Gaa/Taa	18/25	1	2	FACETS	0.866	0.762	0.977	0.866	0.762	0.977	CLONAL	1	TRUE	1	0.39	2		450	450	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966588	36966588	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	186	456	0	ENST00000358127.4:c.738C>A	p.Tyr246Ter	p.Y246*	ENST00000358127	NM_001280556.1	246	taC/taA	6/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.39	2		456	829	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93607788	93607788	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	108	429	0	ENST00000375746.1:c.490G>T	p.Glu164Ter	p.E164*	ENST00000375746	NM_001174167.1	164	Gaa/Taa	3/14	1	2	FACETS	0.878	0.789	0.971	0.878	0.789	0.971	CLONAL	1	TRUE	1	0.39	2		429	631	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106042	8106042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	132	265	1	ENST00000346208.3:c.862G>A	p.Gly288Arg	p.G288R	ENST00000346208		288	Ggg/Agg	4/6	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.39	2		266	611	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850625	63850625	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	56	243	0	ENST00000279873.7:c.1403C>A	p.Ser468Ter	p.S468*	ENST00000279873	NM_032199.2	468	tCa/tAa	10/10	1	2	FACETS	0.663	0.569	0.765	0.663	0.569	0.765	SUBCLONAL	1	TRUE	1	0.39	2		243	433	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851837	63851837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755029955	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	104	373	0	ENST00000279873.7:c.2615C>T	p.Ser872Phe	p.S872F	ENST00000279873	NM_032199.2	872	tCc/tTc	10/10	1	2	FACETS	0.779	0.698	0.864	0.779	0.698	0.864	SUBCLONAL	1	TRUE	1	0.39	2		373	685	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70412307	70412307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771994540	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	36	452	2	ENST00000373644.4:c.4417G>A	p.Gly1473Ser	p.G1473S	ENST00000373644	NM_030625.2	1473	Ggt/Agt	6/12	1	2	FACETS	0.321	0.263	0.386	0.321	0.263	0.386	SUBCLONAL	1	TRUE	1	0.39	2		454	575	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624244	89624244	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	12	106	0	ENST00000371953.3:c.18A>T	p.Lys6Asn	p.K6N	ENST00000371953	NM_000314.4	6	aaA/aaT	1/9	1	2	FACETS	0.456	0.322	0.619	0.456	0.322	0.619	SUBCLONAL	1	TRUE	1	0.39	2		106	135	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692978	89692978	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	45	262	0	ENST00000371953.3:c.462C>A	p.Phe154Leu	p.F154L	ENST00000371953	NM_000314.4	154	ttC/ttA	5/9	1	2	FACETS	0.912	0.773	1	0.912	0.773	1	CLONAL	1	TRUE	1	0.39	2		262	253	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720826	89720826	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	36	166	0	ENST00000371953.3:c.977A>G	p.Asp326Gly	p.D326G	ENST00000371953	NM_000314.4	326	gAc/gGc	8/9	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.39	2		166	164	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123324046	123324046	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	51	482	1	ENST00000358487.5:c.424G>T	p.Asp142Tyr	p.D142Y	ENST00000358487	NM_000141.4	142	Gat/Tat	4/18	1	2	FACETS	0.318	0.269	0.372	0.318	0.269	0.372	SUBCLONAL	1	TRUE	1	0.39	2		483	823	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192748	94192748	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	32	257	0	ENST00000323929.3:c.1327-1G>T		p.X443_splice	ENST00000323929	NM_005591.3	443			1	2	FACETS	0.599	0.488	0.723	0.599	0.488	0.723	SUBCLONAL	1	TRUE	1	0.39	2		257	274	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94224026	94224026	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	94	461	0	ENST00000323929.3:c.126A>C	p.Glu42Asp	p.E42D	ENST00000323929	NM_005591.3	42	gaA/gaC	3/20	1	2	FACETS	0.923	0.824	1	0.923	0.824	1	CLONAL	1	TRUE	1	0.39	2		461	522	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100439	102100439	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	101	397	0	ENST00000282441.5:c.1283C>A	p.Thr428Asn	p.T428N	ENST00000282441	NM_001130145.2	428	aCt/aAt	9/9	1	2	FACETS	0.681	0.608	0.758	0.681	0.608	0.758	SUBCLONAL	1	TRUE	1	0.39	2		397	761	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196812	108196812	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	50	302	0	ENST00000278616.4:c.6835A>C	p.Lys2279Gln	p.K2279Q	ENST00000278616	NM_000051.3	2279	Aaa/Caa	47/63	1	2	FACETS	0.866	0.74	1	0.866	0.74	1	CLONAL	1	TRUE	1	0.39	2		302	296	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203597	108203597	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs587779868	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	33	202	0	ENST00000278616.4:c.7897T>G	p.Leu2633Val	p.L2633V	ENST00000278616	NM_000051.3	2633	Tta/Gta	53/63	1	2	FACETS	0.78	0.64	0.935	0.78	0.64	0.935	CLONAL	1	TRUE	1	0.39	2		202	217	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373954	118373954	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1232295347	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	70	368	0	ENST00000534358.1:c.7347T>G	p.Phe2449Leu	p.F2449L	ENST00000534358	NM_005933.3	2449	ttT/ttG	27/36	1	2	FACETS	0.853	0.746	0.966	0.853	0.746	0.966	CLONAL	1	TRUE	1	0.39	2		368	421	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374174	118374174	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	106	445	0	ENST00000534358.1:c.7567G>A	p.Val2523Ile	p.V2523I	ENST00000534358	NM_005933.3	2523	Gtc/Atc	27/36	1	2	FACETS	0.882	0.793	0.977	0.882	0.793	0.977	CLONAL	1	TRUE	1	0.39	2		445	616	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375309	118375309	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	27	301	1	ENST00000534358.1:c.8702C>A	p.Ser2901Tyr	p.S2901Y	ENST00000534358	NM_005933.3	2901	tCt/tAt	27/36	1	2	FACETS	0.324	0.257	0.401	0.324	0.257	0.401	SUBCLONAL	1	TRUE	1	0.39	2		302	427	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499758	18499758	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	70	202	0	ENST00000266497.5:c.1613C>A	p.Thr538Asn	p.T538N	ENST00000266497		538	aCc/aAc	10/31	0.166639481091972	3	FACETS	1	0.937	1	0.556	0.487	0.629	INDETERMINATE	1	TRUE	1	0.39	3		202	386	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425403	49425403	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	128	453	0	ENST00000301067.7:c.13085C>T	p.Ala4362Val	p.A4362V	ENST00000301067	NM_003482.3	4362	gCt/gTt	39/54	0.166639481091972	3	FACETS	1	0.973	1	0.592	0.537	0.649	INDETERMINATE	1	TRUE	1	0.39	3		453	663	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425643	49425643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1020472849	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	78	414	0	ENST00000301067.7:c.12845G>A	p.Arg4282Gln	p.R4282Q	ENST00000301067	NM_003482.3	4282	cGa/cAa	39/54	0.166639481091972	3	FACETS	1	0.959	1	0.596	0.526	0.67	INDETERMINATE	1	TRUE	1	0.39	3		414	401	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864466	57864466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367789336	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	136	503	1	ENST00000228682.2:c.1943G>A	p.Arg648His	p.R648H	ENST00000228682	NM_005269.2	648	cGt/cAt	12/12	0.166639481091972	3	FACETS	1	0.949	1	0.532	0.483	0.582	INDETERMINATE	1	TRUE	1	0.39	3		504	784	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117391	115117391	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	91	466	0	ENST00000257566.3:c.783G>T	p.Leu261Phe	p.L261F	ENST00000257566	NM_016569.3	261	ttG/ttT	4/8	0.166639481091972	3	FACETS	0.818	0.726	0.915	0.409	0.363	0.458	INDETERMINATE	1	TRUE	1	0.39	3		466	682	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117749	115117749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs554364556	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	106	374	0	ENST00000257566.3:c.686C>T	p.Thr229Met	p.T229M	ENST00000257566	NM_016569.3	229	aCg/aTg	3/8	0.166639481091972	3	FACETS	0.781	0.699	0.867	0.39	0.349	0.434	INDETERMINATE	1	TRUE	1	0.39	3		374	832	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249857	133249857	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1565972665	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	69	305	0	ENST00000320574.5:c.1366G>C	p.Ala456Pro	p.A456P	ENST00000320574	NM_006231.2	456	Gcc/Ccc	14/49	0.166639481091972	3	FACETS	1	0.933	1	0.551	0.482	0.624	INDETERMINATE	1	TRUE	1	0.39	3		305	384	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28631550	28631550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772468040	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	51	392	1	ENST00000241453.7:c.418G>A	p.Glu140Lys	p.E140K	ENST00000241453	NM_004119.2	140	Gaa/Aaa	4/24	1	2	FACETS	0.646	0.55	0.75	0.646	0.55	0.75	SUBCLONAL	1	TRUE	1	0.39	2		393	405	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28886141	28886141	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	83	336	0	ENST00000282397.4:c.3481A>C	p.Asn1161His	p.N1161H	ENST00000282397	NM_002019.4	1161	Aat/Cat	26/30	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.39	2		336	365	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28979966	28979966	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs61763181	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	82	479	1	ENST00000282397.4:c.1502G>T	p.Arg501Ile	p.R501I	ENST00000282397	NM_002019.4	501	aGa/aTa	11/30	1	2	FACETS	0.618	0.545	0.697	0.618	0.545	0.697	SUBCLONAL	1	TRUE	1	0.39	2		480	680	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913407	32913407	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	86	604	0	ENST00000380152.3:c.4915G>T	p.Val1639Leu	p.V1639L	ENST00000380152		1639	Gta/Tta	11/27	1	2	FACETS	0.925	0.821	1	0.925	0.821	1	CLONAL	1	TRUE	1	0.39	2		604	477	SUCCESS
BLM	641	MSKCC	GRCh37	15	91337454	91337454	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	63	338	0	ENST00000355112.3:c.3077T>C	p.Met1026Thr	p.M1026T	ENST00000355112	NM_000057.2	1026	aTg/aCg	16/22	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.39	2		338	289	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134400	2134400	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	194	495	0	ENST00000219476.3:c.4177A>G	p.Thr1393Ala	p.T1393A	ENST00000219476	NM_000548.3	1393	Act/Gct	34/42	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.39	2		495	760	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858310	9858310	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs569342611	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	82	299	0	ENST00000330684.3:c.3091G>C	p.Val1031Leu	p.V1031L	ENST00000330684	NM_001134407.1	1031	Gtc/Ctc	13/13	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.39	2		299	386	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858384	9858384	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200526162	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	103	352	1	ENST00000330684.3:c.3017C>T	p.Ala1006Val	p.A1006V	ENST00000330684	NM_001134407.1	1006	gCg/gTg	13/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.39	2		353	474	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348706	11348706	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	156	468	0	ENST00000332029.2:c.630G>T	p.Gln210His	p.Q210H	ENST00000332029	NM_003745.1	210	caG/caT	2/2	1	2	FACETS	0.705	0.644	0.769	0.705	0.644	0.769	SUBCLONAL	1	TRUE	1	0.39	2		468	1135	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14022037	14022037	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	47	341	0	ENST00000311895.7:c.737C>A	p.Ser246Ter	p.S246*	ENST00000311895	NM_005236.2	246	tCg/tAg	4/11	1	2	FACETS	0.695	0.588	0.811	0.695	0.588	0.811	SUBCLONAL	1	TRUE	1	0.39	2		341	347	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888096	81888096	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	156	558	2	ENST00000359376.3:c.241G>T	p.Asp81Tyr	p.D81Y	ENST00000359376	NM_002661.3	81	Gat/Tat	3/33	1	2	FACETS	0.822	0.752	0.895	0.822	0.752	0.895	CLONAL	1	TRUE	1	0.39	2		560	973	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877178	89877178	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	72	328	0	ENST00000389301.3:c.459G>T	p.Gln153His	p.Q153H	ENST00000389301	NM_000135.2	153	caG/caT	5/43	1	2	FACETS	0.705	0.617	0.799	0.705	0.617	0.799	SUBCLONAL	1	TRUE	1	0.39	2		328	524	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982843	7982843	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	138	411	0	ENST00000319144.4:c.942C>A	p.Tyr314Ter	p.Y314*	ENST00000319144	NM_001139.2	314	taC/taA	8/15	1		FACETS		0.957	1				CLONAL	1	TRUE	1	0.39	2		411	656	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964793	15964793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	142	550	1	ENST00000268712.3:c.5803G>A	p.Val1935Met	p.V1935M	ENST00000268712	NM_006311.3	1935	Gtg/Atg	37/46	1	2	FACETS	0.796	0.725	0.87	0.796	0.725	0.87	SUBCLONAL	1	TRUE	1	0.39	2		551	915	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650879	37650879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs191899574	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	106	431	1	ENST00000447079.4:c.2351G>A	p.Arg784Gln	p.R784Q	ENST00000447079	NM_015083.1	784	cGa/cAa	5/14	1	2	FACETS	0.853	0.766	0.945	0.853	0.766	0.945	CLONAL	1	TRUE	1	0.39	2		432	637	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475318	40475318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	65	612	0	ENST00000264657.5:c.1708G>A	p.Asp570Asn	p.D570N	ENST00000264657	NM_139276.2	570	Gac/Aac	19/24	1	2	FACETS	0.299	0.258	0.344	0.299	0.258	0.344	SUBCLONAL	1	TRUE	1	0.39	2		612	1115	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526499	66526499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	115	372	1	ENST00000358598.2:c.1055G>A	p.Arg352Gln	p.R352Q	ENST00000358598	NM_212471.2	352	cGa/cAa	11/11	1	2	FACETS	0.781	0.704	0.863	0.781	0.704	0.863	SUBCLONAL	1	TRUE	1	0.39	2		373	755	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374862	45374862	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	50	306	0	ENST00000262160.6:c.981G>T	p.Met327Ile	p.M327I	ENST00000262160	NM_005901.5	327	atG/atT	8/11	0.113486771141372	0	FACETS	0.409	0.348	0.476			1	INDETERMINATE	1	TRUE	0	0.39	0		306	382	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763488	41763488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746364612	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	159	446	0	ENST00000301178.4:c.2287C>T	p.Arg763Cys	p.R763C	ENST00000301178	NM_021913.4	763	Cgc/Tgc	19/20	1	2	FACETS	0.95	0.871	1	0.95	0.871	1	CLONAL	1	TRUE	1	0.39	2		446	858	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383489	31383489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1203334353	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	180	432	0	ENST00000328111.2:c.1286G>A	p.Ser429Asn	p.S429N	ENST00000328111	NM_006892.3	429	aGc/aAc	12/23	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.39	2		432	864	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386388	31386388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	126	388	0	ENST00000328111.2:c.1613G>A	p.Arg538His	p.R538H	ENST00000328111	NM_006892.3	538	cGc/cAc	15/23	1	2	FACETS	0.932	0.846	1	0.932	0.846	1	CLONAL	1	TRUE	1	0.39	2		388	693	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714491	40714491	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	59	250	0	ENST00000373198.4:c.3906C>A	p.Phe1302Leu	p.F1302L	ENST00000373198	NM_133170.3	1302	ttC/ttA	29/32	1	2	FACETS	0.877	0.759	1	0.877	0.759	1	CLONAL	1	TRUE	1	0.39	2		250	345	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385195	41385195	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	126	408	1	ENST00000373198.4:c.766G>T	p.Asp256Tyr	p.D256Y	ENST00000373198	NM_133170.3	256	Gac/Tac	6/32	1	2	FACETS	0.947	0.859	1	0.947	0.859	1	CLONAL	1	TRUE	1	0.39	2		409	682	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29106038	29106038	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	13	221	0	ENST00000328354.6:c.802C>A	p.Leu268Ile	p.L268I	ENST00000328354	NM_007194.3	268	Ctc/Atc	7/15	1	2	FACETS	0.271	0.193	0.366	0.271	0.193	0.366	SUBCLONAL	1	TRUE	1	0.39	2		221	246	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044542	47044542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782739450	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	97	430	0	ENST00000377604.3:c.2039G>A	p.Arg680Gln	p.R680Q	ENST00000377604	NM_001204468.1	680	cGa/cAa	18/24	0.166639481091972	0	FACETS	0.493	0.44	0.549			1	INDETERMINATE	1	TRUE	0	0.39	0		430	616	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343521	70343521	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	183	493	0	ENST00000374080.3:c.1695T>G	p.Ile565Met	p.I565M	ENST00000374080		565	atT/atG	12/45	0.166639481091972	0	FACETS	0.642	0.593	0.694			1	INDETERMINATE	1	TRUE	0	0.39	0		493	891	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845361	76845361	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	42	424	0	ENST00000373344.5:c.6160C>A	p.Leu2054Ile	p.L2054I	ENST00000373344	NM_000489.3	2054	Ctt/Att	27/35	0.166639481091972	0	FACETS	0.301	0.251	0.357			1	INDETERMINATE	1	TRUE	0	0.39	0		424	436	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920255	76920255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	38	442	1	ENST00000373344.5:c.3822G>T	p.Lys1274Asn	p.K1274N	ENST00000373344	NM_000489.3	1274	aaG/aaT	11/35	0.166639481091972	0	FACETS	0.32	0.265	0.382			1	INDETERMINATE	1	TRUE	0	0.39	0		443	371	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937173	76937173	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	88	624	0	ENST00000373344.5:c.3575G>T	p.Ser1192Ile	p.S1192I	ENST00000373344	NM_000489.3	1192	aGc/aTc	9/35	0.166639481091972	0	FACETS	0.38	0.336	0.426			1	INDETERMINATE	1	TRUE	0	0.39	0		624	725	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937950	76937950	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	49	338	1	ENST00000373344.5:c.2798C>A	p.Ser933Tyr	p.S933Y	ENST00000373344	NM_000489.3	933	tCt/tAt	9/35	0.166639481091972	0	FACETS	0.404	0.343	0.471			1	INDETERMINATE	1	TRUE	0	0.39	0		339	379	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200277	123200277	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	83	459	0	ENST00000218089.9:c.2256C>A	p.Ser752Arg	p.S752R	ENST00000218089	NM_001042749.1	752	agC/agA	23/35	0.166639481091972	0	FACETS	0.378	0.333	0.426			1	INDETERMINATE	1	TRUE	0	0.39	0		459	687	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0012677-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	14	414	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.382201936772807	1	FACETS	0.095	0.068	0.128	0.095	0.068	0.128	SUBCLONAL	1	FALSE	0	0.382201936772807	1		416	624	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143994	11143994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012677-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	128	359	2	ENST00000358026.2:c.3575G>A	p.Arg1192His	p.R1192H	ENST00000358026	NM_001128849.1	1192	cGc/cAc	26/36	0.136534321456098	0	FACETS	0.713	0.649	0.781			1	INDETERMINATE	1	FALSE	0	0.382201936772807	0		361	580	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665426	117665426	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1177764371	NA	P-0012677-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	84	206	0	ENST00000368508.3:c.4322-1G>A		p.X1441_splice	ENST00000368508	NM_002944.2	1441			1	2	FACETS	0.807	0.714	0.905	0.807	0.714	0.905	CLONAL	1	FALSE	1	0.382201936772807	2		206	545	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857609	78857609	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012677-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	132	340	0	ENST00000306801.3:c.1679C>A	p.Ala560Asp	p.A560D	ENST00000306801	NM_020761.2	560	gCc/gAc	16/34	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.382201936772807	2		340	552	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575174	48575174	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012677-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	175	318	0	ENST00000342988.3:c.368G>C	p.Cys123Ser	p.C123S	ENST00000342988	NM_005359.5	123	tGt/tCt	3/12	1	2	FACETS	0.934	0.86	1	0.934	0.86	1	CLONAL	1	FALSE	1	0.382201936772807	2		318	980	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225235	53225235	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012677-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	119	213	0	ENST00000375401.3:c.2983C>T	p.Gln995Ter	p.Q995*	ENST00000375401	NM_004187.3	995	Cag/Tag	20/26	1	1	FACETS	0.775	0.709	0.843	1	0.987	1	SUBCLONAL	2	FALSE	0	0.382201936772807	1		213	325	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183703	10183734	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCCGCGGCCCGTGCTGCGCTCGGTGAACTC	CGGCCGCGGCCCGTGCTGCGCTCGGTGAACTC	-	novel	NA	P-0012677-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	193	336	0	ENST00000256474.2:c.172_203del	p.Arg58AlafsTer63	p.R58Afs*63	ENST00000256474	NM_000551.3	58	CGGCCGCGGCCCGTGCTGCGCTCGGTGAACTCg/g	1/3	0.349281483464187	2	FACETS	0.977	0.911	1	0.977	0.911	1	CLONAL	2	FALSE	0	0.382201936772807	2		336	517	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692897	89692897	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012677-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	222	188	0	ENST00000371953.3:c.383del	p.Lys128ArgfsTer6	p.K128Rfs*6	ENST00000371953	NM_000314.4	127	ggA/gg	5/9	0.382201936772807	2	FACETS	0.883	0.826	0.941	0.883	0.826	0.941	CLONAL	2	FALSE	0	0.382201936772807	2		188	658	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0012708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	71	454	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.699	0.61	0.796	0.699	0.61	0.796	SUBCLONAL	1	TRUE	1	0.277392287676311	2		454	732	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268156	153268156	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	59	497	2	ENST00000281708.4:c.652C>T	p.Gln218Ter	p.Q218*	ENST00000281708	NM_033632.3	218	Caa/Taa	4/12	1	2	FACETS	0.491	0.421	0.568	0.491	0.421	0.568	SUBCLONAL	1	TRUE	1	0.277392287676311	2		499	866	SUCCESS
APC	324	MSKCC	GRCh37	5	112155043	112155043	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1114167579	NA	P-0012708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	137	416	0	ENST00000257430.4:c.1312+2T>C		p.X438_splice	ENST00000257430	NM_000038.5	438			0.18591874277911	2	FACETS	0.765	0.697	0.835	0.765	0.697	0.835	SUBCLONAL	2	TRUE	0	0.277392287676311	2		416	646	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134608	2134608	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	49	489	0	ENST00000219476.3:c.4385C>T	p.Thr1462Ile	p.T1462I	ENST00000219476	NM_000548.3	1462	aCc/aTc	34/42	1	2	FACETS	0.467	0.395	0.548	0.467	0.395	0.548	SUBCLONAL	1	TRUE	1	0.277392287676311	2		489	756	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574002	7574002	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012708-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	127	648	0	ENST00000269305.4:c.1025del	p.Arg342GlnfsTer3	p.R342Qfs*3	ENST00000269305	NM_001126112.2	342	cGa/ca	10/11	1	2	FACETS	0.895	0.81	0.986	0.895	0.81	0.986	CLONAL	1	TRUE	1	0.277392287676311	2		648	1023	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0012723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	116	393	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.922	0.83	1	0.922	0.83	1	CLONAL	1	TRUE	1	0.281418182632341	2		393	894	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	73	126	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.966	0.846	1	0.966	0.846	1	CLONAL	1	TRUE	1	0.281418182632341	2		126	537	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913315	NA	P-0012723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	78	632	0	ENST00000326873.7:c.580G>A	p.Asp194Asn	p.D194N	ENST00000326873	NM_000455.4	194	Gac/Aac	4/10	1	2	FACETS	0.6	0.526	0.68	0.6	0.526	0.68	SUBCLONAL	1	TRUE	1	0.281418182632341	2		632	924	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520208	9520208	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012723-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	72	529	0	ENST00000353224.5:c.2061G>C	p.Gln687His	p.Q687H	ENST00000353224	NM_177990.2	687	caG/caC	10/10	1	2	FACETS	0.525	0.457	0.598	0.525	0.457	0.598	SUBCLONAL	1	TRUE	1	0.281418182632341	2		529	975	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0012728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	385	365	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.715002362275206	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.715002362275206	2		367	527	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0012728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	30	379	0	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	0.715002362275206	3	FACETS	0.183	0.146	0.224	0.061	0.048	0.075	SUBCLONAL	1	TRUE	0	0.715002362275206	3		379	624	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938264	36938264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150616658	NA	P-0012728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	377	891	2	ENST00000361632.4:c.697C>T	p.Arg233Trp	p.R233W	ENST00000361632		233	Cgg/Tgg	6/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.715002362275206	2		893	1009	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497944	25497944	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1203651882	NA	P-0012728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	151	358	1	ENST00000264709.3:c.505C>T	p.Arg169Trp	p.R169W	ENST00000264709	NM_175629.2	169	Cgg/Tgg	6/23	0.715002362275206	3	FACETS	0.989	0.908	1	0.33	0.302	0.358	CLONAL	1	TRUE	0	0.715002362275206	3		359	580	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880241	151880241	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	36	276	0	ENST00000262189.6:c.5083C>A	p.Gln1695Lys	p.Q1695K	ENST00000262189	NM_170606.2	1695	Caa/Aaa	35/59	0.703386166254659	4	FACETS	0.254	0.208	0.306	0.127	0.104	0.153	SUBCLONAL	1	TRUE	2	0.715002362275206	4		276	679	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437704	49437704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770835064	NA	P-0012728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	916	972	1	ENST00000301067.7:c.5266C>T	p.Arg1756Trp	p.R1756W	ENST00000301067	NM_003482.3	1756	Cgg/Tgg	22/54	0.715002362275206	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.715002362275206	2		973	1238	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029258	14029258	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs912480692	NA	P-0012728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	257	550	2	ENST00000311895.7:c.1469G>A	p.Arg490Gln	p.R490Q	ENST00000311895	NM_005236.2	490	cGg/cAg	8/11	0.707451152051453	3	FACETS	1	0.941	1	0.502	0.47	0.535	CLONAL	1	TRUE	1	0.715002362275206	3		552	972	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352238	70352238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1255849432	NA	P-0012728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1270	326	789	0	ENST00000374080.3:c.4265G>A	p.Arg1422His	p.R1422H	ENST00000374080		1422	cGc/cAc	31/45	0.386972495327746	5	FACETS	1	0.989	1	0.395	0.372	0.419	INDETERMINATE	1	TRUE	2	0.715002362275206	5		789	1596	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266065	41266100	+	inframe_deletion	In_Frame_Del	DEL	CTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACT	CTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACT	-	novel	NA	P-0012728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	325	599	0	ENST00000349496.5:c.65_100del	p.Val22_Ser33del	p.V22_S33del	ENST00000349496	NM_001904.3	21	gCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTct/gct	3/15	0.715002362275206	2	FACETS	0.819	0.784	0.854	0.819	0.784	0.854	CLONAL	2	TRUE	0	0.715002362275206	2		599	555	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56171121	56171127	+	frameshift_variant	Frame_Shift_Del	DEL	TGTACGT	TGTACGT	-	novel	NA	P-0012728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	111	360	0	ENST00000399503.3:c.1951_1957del	p.Tyr651LeufsTer3	p.Y651Lfs*3	ENST00000399503	NM_005921.1	650	gTGTACGTt/gt	10/20	0.715002362275206	2	FACETS	0.743	0.673	0.816	0.371	0.336	0.408	SUBCLONAL	1	TRUE	0	0.715002362275206	2		360	418	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	23	715	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.278	0.216	0.352	0.278	0.216	0.352	SUBCLONAL	1	TRUE	1	0.2	2		715	826	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577126	7577126	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	36	675	0	ENST00000269305.4:c.812A>T	p.Glu271Val	p.E271V	ENST00000269305	NM_001126112.2	271	gAg/gTg	8/11	1	2	FACETS	0.371	0.303	0.447	0.371	0.303	0.447	SUBCLONAL	1	TRUE	1	0.2	2		675	971	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829040	128829042	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	rs570242755	NA	P-0012733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	12	97	1	ENST00000249373.3:c.67_69del	p.Leu23del	p.L23del	ENST00000249373	NM_005631.4	16	ggGCTg/ggg	1/12	1	2	FACETS	0.945	0.668	1	0.945	0.668	1	CLONAL	1	TRUE	1	0.2	2		98	127	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916726	178916726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772110575	NA	P-0012741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1341	166	942	3	ENST00000263967.3:c.113G>A	p.Arg38His	p.R38H	ENST00000263967	NM_006218.2	38	cGt/cAt	2/21	1	2	FACETS	0.906	0.83	0.987	0.906	0.83	0.987	CLONAL	1	TRUE	1	0.243056473915527	2		945	1507	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0012750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	297	382	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.39750626642367	4	FACETS	0.97	0.919	1	1	0.994	1	CLONAL	3	TRUE	2	0.39750626642367	4		382	718	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100584	67100584	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0012750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	301	455	0	ENST00000412916.2:c.283-1G>A		p.X95_splice	ENST00000412916		95			0.39750626642367	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.39750626642367	2		455	671	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115743	8115760	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAAACCGAAAAATGTC	CAGAAACCGAAAAATGTC	G	novel	NA	P-0012750-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	96	723	0	ENST00000346208.3:c.1089_1106delinsG	p.Arg364Ter	p.R364*	ENST00000346208		363	acCAGAAACCGAAAAATGTCt/acGt	6/6	0.39750626642367	3	FACETS	0.537	0.477	0.601	0.269	0.238	0.301	SUBCLONAL	1	TRUE	1	0.39750626642367	3		723	1078	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782144	NA	P-0012784-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	154	511	0	ENST00000269305.4:c.473G>C	p.Arg158Pro	p.R158P	ENST00000269305	NM_001126112.2	158	cGc/cCc	5/11	0.175158678063886	3	FACETS	1	0.982	1	0.833	0.763	0.905	CLONAL	2	TRUE	0	0.184245542721328	3		511	731	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834199	156834199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1257963281	NA	P-0012786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	342	409	0	ENST00000524377.1:c.266G>A	p.Gly89Asp	p.G89D	ENST00000524377	NM_002529.3	89	gGc/gAc	2/17	0.378542614312297	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.378542614312297	3		409	895	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206942015	206942015	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1310781150	NA	P-0012786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	169	456	0	ENST00000423557.1:c.503T>C	p.Ile168Thr	p.I168T	ENST00000423557	NM_000572.2	168	aTa/aCa	5/5	0.378542614312297	3	FACETS	1	0.955	1	0.529	0.486	0.574	CLONAL	1	TRUE	1	0.378542614312297	3		456	1004	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562949	21562949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1461231287	NA	P-0012786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	121	295	2	ENST00000382592.4:c.970G>A	p.Ala324Thr	p.A324T	ENST00000382592	NM_014572.2	324	Gcg/Acg	4/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.378542614312297	2		297	577	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156723	20156723	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	199	528	0	ENST00000379607.5:c.34A>G	p.Arg12Gly	p.R12G	ENST00000379607	NM_001412.3	12	Aga/Gga	2/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.378542614312297	2		528	930	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012794-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	115	126	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.735453890801183	2		126	257	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057976	27057976	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012794-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	236	418	0	ENST00000324856.7:c.1684C>T	p.Gln562Ter	p.Q562*	ENST00000324856	NM_006015.4	562	Cag/Tag	3/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.735453890801183	2		418	602	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509619	106509619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142822484	NA	P-0012794-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	309	610	0	ENST00000359195.3:c.1613C>T	p.Pro538Leu	p.P538L	ENST00000359195	NM_002649.2	538	cCg/cTg	2/11	0.675430985658151	3	FACETS	0.966	0.91	1	0.483	0.455	0.512	CLONAL	1	TRUE	1	0.735453890801183	3		610	1190	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221722	55221722	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012794-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7988	14101	537	1	ENST00000275493.2:c.766G>T	p.Asp256Tyr	p.D256Y	ENST00000275493	NM_005228.3	256	Gac/Tac	7/28	0.735453890801183	32	FACETS	0.995	0.988	1			1	CLONAL	21	TRUE	NA	0.735453890801183	32		538	22089	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845410	89845410	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs775255736	NA	P-0012794-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	180	376	0	ENST00000389301.3:c.1717A>G	p.Ile573Val	p.I573V	ENST00000389301	NM_000135.2	573	Ata/Gta	19/43	NA	2	FACETS	0.941	0.875	1			1	INDETERMINATE	1	TRUE	NA	0.735453890801183	2		376	520	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794454	42794454	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012794-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	428	848	0	ENST00000575354.2:c.1534C>T	p.Pro512Ser	p.P512S	ENST00000575354	NM_015125.3	512	Cct/Tct	10/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.735453890801183	2		848	1105	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101271	27101271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	389	740	2	ENST00000324856.7:c.4553C>T	p.Pro1518Leu	p.P1518L	ENST00000324856	NM_006015.4	1518	cCc/cTc	18/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.835449947297297	2		742	917	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937932	36937932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	499	1171	2	ENST00000361632.4:c.904G>A	p.Ala302Thr	p.A302T	ENST00000361632		302	Gcc/Acc	7/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.835449947297297	2		1173	1189	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471812	120471812	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	371	725	1	ENST00000256646.2:c.3679G>T	p.Asp1227Tyr	p.D1227Y	ENST00000256646	NM_024408.3	1227	Gat/Tat	23/34	1	2	FACETS	0.958	0.912	1	0.958	0.912	1	CLONAL	1	TRUE	1	0.835449947297297	2		726	927	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474020	29474020	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759652463	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	390	829	0	ENST00000389048.3:c.2155C>T	p.Pro719Ser	p.P719S	ENST00000389048	NM_004304.4	719	Ccc/Tcc	12/29	1	2	FACETS	0.906	0.864	0.95	0.906	0.864	0.95	CLONAL	1	TRUE	1	0.835449947297297	2		829	1030	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61725813	61725813	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	243	403	0	ENST00000401558.2:c.754T>A	p.Tyr252Asn	p.Y252N	ENST00000401558	NM_003400.3	252	Tat/Aat	9/25	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.835449947297297	2		403	565	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872696	136872696	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	710	1404	2	ENST00000241393.3:c.802G>A	p.Glu268Lys	p.E268K	ENST00000241393	NM_003467.2	268	Gaa/Aaa	2/2	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.835449947297297	2		1406	1610	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251583	212251583	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	315	508	0	ENST00000342788.4:c.3476A>G	p.Lys1159Arg	p.K1159R	ENST00000342788	NM_005235.2	1159	aAa/aGa	27/28	1	2	FACETS	0.997	0.947	1	0.997	0.947	1	CLONAL	1	TRUE	1	0.835449947297297	2		508	756	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566849	212566850	+	missense_variant	Missense_Mutation	DNP	AG	AG	GA	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	241	488	0	ENST00000342788.4:c.1331_1332delinsTC	p.Ser444Phe	p.S444F	ENST00000342788	NM_005235.2	444	tCT/tTC	12/28	1	2	FACETS	0.937	0.881	0.993	0.937	0.881	0.993	CLONAL	1	TRUE	1	0.835449947297297	2		488	616	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890344	72890344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	207	499	0	ENST00000325599.8:c.338C>T	p.Ser113Phe	p.S113F	ENST00000325599	NM_018130.2	113	tCt/tTt	4/11	1	2	FACETS	0.774	0.722	0.827	0.774	0.722	0.827	SUBCLONAL	1	TRUE	1	0.835449947297297	2		499	640	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880882	134880882	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs936404830	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	354	794	0	ENST00000398015.3:c.1445C>T	p.Ser482Phe	p.S482F	ENST00000398015	NM_004441.4	482	tCc/tTc	7/16	1	2	FACETS	0.959	0.912	1	0.959	0.912	1	CLONAL	1	TRUE	1	0.835449947297297	2		794	884	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129986	55129986	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	401	792	0	ENST00000257290.5:c.520A>T	p.Ser174Cys	p.S174C	ENST00000257290	NM_006206.4	174	Agc/Tgc	4/23	1	2	FACETS	0.936	0.892	0.979	0.936	0.892	0.979	CLONAL	1	TRUE	1	0.835449947297297	2		792	1026	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467434	66467434	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369606981	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	221	513	0	ENST00000273854.3:c.835G>A	p.Glu279Lys	p.E279K	ENST00000273854	NM_004439.5	279	Gaa/Aaa	3/18	1	2	FACETS	0.836	0.782	0.89	0.836	0.782	0.89	CLONAL	1	TRUE	1	0.835449947297297	2		513	633	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959885	38959885	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs267600621	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	235	591	0	ENST00000357387.3:c.2047C>T	p.Gln683Ter	p.Q683*	ENST00000357387	NM_152756.3	683	Cag/Tag	21/38	1	2	FACETS	0.801	0.751	0.853	0.801	0.751	0.853	CLONAL	1	TRUE	1	0.835449947297297	2		591	702	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047710	180047710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144822344	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	368	667	1	ENST00000261937.6:c.2305G>A	p.Glu769Lys	p.E769K	ENST00000261937	NM_182925.4	769	Gag/Aag	16/30	0.15402836373251	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.835449947297297	0		668	836	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163522	32163522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	264	593	0	ENST00000375023.3:c.5704G>A	p.Gly1902Arg	p.G1902R	ENST00000375023	NM_004557.3	1902	Gga/Aga	30/30	1	2	FACETS	0.995	0.94	1	0.995	0.94	1	CLONAL	1	TRUE	1	0.835449947297297	2		593	635	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287917	33287917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	379	649	0	ENST00000374542.5:c.1336G>A	p.Glu446Lys	p.E446K	ENST00000374542	NM_001141970.1	446	Gaa/Aaa	5/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.835449947297297	2		649	893	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631272	117631272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1459053852	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	438	858	1	ENST00000368508.3:c.6406G>A	p.Gly2136Arg	p.G2136R	ENST00000368508	NM_002944.2	2136	Gga/Aga	40/43	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.835449947297297	2		859	1048	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117650491	117650491	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	668	1261	0	ENST00000368508.3:c.5366+1G>A		p.X1789_splice	ENST00000368508	NM_002944.2	1789			1	2	FACETS	0.912	0.879	0.946	0.912	0.879	0.946	CLONAL	1	TRUE	1	0.835449947297297	2		1261	1753	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714396	117714396	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	373	769	0	ENST00000368508.3:c.1253C>T	p.Ser418Leu	p.S418L	ENST00000368508	NM_002944.2	418	tCa/tTa	11/43	1	2	FACETS	0.972	0.926	1	0.972	0.926	1	CLONAL	1	TRUE	1	0.835449947297297	2		769	919	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954871	2954871	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	348	737	0	ENST00000396946.4:c.2839G>A	p.Glu947Lys	p.E947K	ENST00000396946	NM_032415.4	947	Gag/Aag	21/25	1	2	FACETS	0.977	0.929	1	0.977	0.929	1	CLONAL	1	TRUE	1	0.835449947297297	2		737	853	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441974	6441974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	268	421	0	ENST00000356142.4:c.533C>T	p.Ala178Val	p.A178V	ENST00000356142	NM_018890.3	178	gCg/gTg	7/7	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.835449947297297	2		421	598	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494238	140494238	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	583	1010	1	ENST00000288602.6:c.1010C>T	p.Ser337Leu	p.S337L	ENST00000288602	NM_004333.4	337	tCa/tTa	8/18	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.835449947297297	2		1011	1376	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523681	148523681	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	263	506	0	ENST00000320356.2:c.772C>A	p.Pro258Thr	p.P258T	ENST00000320356	NM_004456.4	258	Cct/Act	8/20	1	2	FACETS	0.948	0.895	1	0.948	0.895	1	CLONAL	1	TRUE	1	0.835449947297297	2		506	664	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853095	151853095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	200	342	0	ENST00000262189.6:c.11860C>T	p.Gln3954Ter	p.Q3954*	ENST00000262189	NM_170606.2	3954	Cag/Tag	46/59	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.835449947297297	2		342	439	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876977	151876977	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	359	695	0	ENST00000262189.6:c.7384C>T	p.Gln2462Ter	p.Q2462*	ENST00000262189	NM_170606.2	2462	Cag/Tag	37/59	1	2	FACETS	0.919	0.874	0.965	0.919	0.874	0.965	CLONAL	1	TRUE	1	0.835449947297297	2		695	935	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876986	151876986	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	409	712	0	ENST00000262189.6:c.7375C>T	p.Pro2459Ser	p.P2459S	ENST00000262189	NM_170606.2	2459	Cca/Tca	37/59	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.835449947297297	2		712	917	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372274	55372274	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	240	498	0	ENST00000297316.4:c.964C>T	p.Gln322Ter	p.Q322*	ENST00000297316	NM_022454.3	322	Cag/Tag	2/2	0.835449947297297	3	FACETS	1	0.977	1	0.544	0.51	0.579	CLONAL	1	TRUE	1	0.835449947297297	3		498	748	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751014	128751014	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	224	457	0	ENST00000377970.2:c.551G>A	p.Ser184Asn	p.S184N	ENST00000377970	NM_002467.4	184	aGc/aAc	2/3	0.835449947297297	4	FACETS	1	0.967	1	0.353	0.329	0.378	CLONAL	1	TRUE	1	0.835449947297297	4		457	929	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	308	528	0	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.835449947297297	2		528	636	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781470	135781470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1416	322	1298	2	ENST00000298552.3:c.1495C>T	p.Pro499Ser	p.P499S	ENST00000298552	NM_001162426.1	499	Cct/Tct	15/23	0.21754732556702	3	FACETS	0.629	0.592	0.667	0.314	0.296	0.334	INDETERMINATE	1	TRUE	1	0.835449947297297	3		1300	1738	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399857	139399857	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	474	802	1	ENST00000277541.6:c.4491G>A	p.Trp1497Ter	p.W1497*	ENST00000277541	NM_017617.3	1497	tgG/tgA	25/34	0.21754732556702	3	FACETS	0.768	0.737	0.8	0.768	0.737	0.8	INDETERMINATE	2	TRUE	1	0.835449947297297	3		803	1047	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413973	139413973	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	464	946	1	ENST00000277541.6:c.787G>T	p.Gly263Ter	p.G263*	ENST00000277541	NM_017617.3	263	Gga/Tga	5/34	NA	2	FACETS	0.916	0.877	0.957			1	INDETERMINATE	1	TRUE	NA	0.835449947297297	2		947	1212	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450712	70450712	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	366	696	0	ENST00000373644.4:c.5552C>T	p.Ser1851Phe	p.S1851F	ENST00000373644	NM_030625.2	1851	tCc/tTc	12/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.835449947297297	2		696	853	SUCCESS
CBL	867	MSKCC	GRCh37	11	119158561	119158561	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	373	630	0	ENST00000264033.4:c.1942-1G>A		p.X648_splice	ENST00000264033	NM_005188.3	648			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.835449947297297	2		630	870	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861185	57861185	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	156	1206	1	ENST00000228682.2:c.982G>A	p.Glu328Lys	p.E328K	ENST00000228682	NM_005269.2	328	Gag/Aag	9/12	1	2	FACETS	0.295	0.27	0.323	0.295	0.27	0.323	SUBCLONAL	1	TRUE	1	0.835449947297297	2		1207	1264	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865500	57865500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	546	1310	1	ENST00000228682.2:c.2977C>T	p.Pro993Ser	p.P993S	ENST00000228682	NM_005269.2	993	Ccc/Tcc	12/12	1	2	FACETS	0.944	0.906	0.981	0.944	0.906	0.981	CLONAL	1	TRUE	1	0.835449947297297	2		1311	1385	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133208953	133208953	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs890951073	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	418	780	0	ENST00000320574.5:c.6278C>T	p.Ser2093Phe	p.S2093F	ENST00000320574	NM_006231.2	2093	tCc/tTc	45/49	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.835449947297297	2		780	950	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947540	48947540	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	325	451	0	ENST00000267163.4:c.1128-1G>A		p.X376_splice	ENST00000267163	NM_000321.2	376			0.835449947297297	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.835449947297297	1		451	451	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422104	81422104	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532920088	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	293	618	1	ENST00000298171.2:c.80C>T	p.Pro27Leu	p.P27L	ENST00000298171	NM_000369.2	27	cCa/cTa	1/10	1	2	FACETS	0.922	0.872	0.972	0.922	0.872	0.972	CLONAL	1	TRUE	1	0.835449947297297	2		619	761	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042035	42042036	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	625	1336	1	ENST00000219905.7:c.6230_6231delinsTT	p.Ser2077Phe	p.S2077F	ENST00000219905	NM_001164273.1	2077	tCC/tTT	17/24	1	2	FACETS	0.898	0.864	0.932	0.898	0.864	0.932	CLONAL	1	TRUE	1	0.835449947297297	2		1337	1666	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860705	3860705	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	451	874	1	ENST00000262367.5:c.874G>T	p.Gly292Ter	p.G292*	ENST00000262367	NM_004380.2	292	Gga/Tga	3/31	0.749872409808061	3	FACETS	0.962	0.917	1	0.481	0.458	0.504	CLONAL	1	TRUE	1	0.835449947297297	3		875	1591	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989366	7989366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	640	798	0	ENST00000319144.4:c.320G>A	p.Gly107Asp	p.G107D	ENST00000319144	NM_001139.2	107	gGc/gAc	2/15	0.835449947297297	2	FACETS	0.977	0.957	0.997	0.977	0.957	0.997	CLONAL	2	TRUE	0	0.835449947297297	2		798	784	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16097829	16097829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1325843352	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	327	635	1	ENST00000268712.3:c.55C>T	p.Arg19Cys	p.R19C	ENST00000268712	NM_006311.3	19	Cgt/Tgt	2/46	1	2	FACETS	0.982	0.933	1	0.982	0.933	1	CLONAL	1	TRUE	1	0.835449947297297	2		636	797	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244077	5244078	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	402	948	1	ENST00000357368.4:c.1404_1405delinsAA	p.Glu469Lys	p.E469K	ENST00000357368	NM_002850.3	468	ccGGag/ccAAag	11/38	1	2	FACETS	0.904	0.862	0.947	0.904	0.862	0.947	CLONAL	1	TRUE	1	0.835449947297297	2		949	1064	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299842	15299842	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	386	792	0	ENST00000263388.2:c.1336T>A	p.Cys446Ser	p.C446S	ENST00000263388	NM_000435.2	446	Tgc/Agc	8/33	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.835449947297297	2		792	901	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024084	31024084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779117478	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	359	625	0	ENST00000375687.4:c.3569G>A	p.Arg1190Lys	p.R1190K	ENST00000375687	NM_015338.5	1190	aGg/aAg	13/13	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.835449947297297	2		625	837	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39729871	39729871	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	442	788	2	ENST00000361337.2:c.1186C>T	p.Pro396Ser	p.P396S	ENST00000361337	NM_003286.2	396	Cct/Tct	13/21	1	2	FACETS	0.995	0.952	1	0.995	0.952	1	CLONAL	1	TRUE	1	0.835449947297297	2		790	1063	SUCCESS
BTK	695	MSKCC	GRCh37	X	100625006	100625006	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555980049	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	63	383	0	ENST00000308731.7:c.371G>A	p.Trp124Ter	p.W124*	ENST00000308731	NM_000061.2	124	tGg/tAg	5/19	1	1	FACETS	0.176	0.152	0.202	0.176	0.152	0.202	SUBCLONAL	1	TRUE	0	0.835449947297297	1		383	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578207	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0012804-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	941	959	0	ENST00000269305.4:c.642_643del	p.His214GlnfsTer7	p.H214Qfs*7	ENST00000269305	NM_001126112.2	214	caTAgt/cagt	6/11	0.835449947297297	2	FACETS	0.973	0.957	0.99	0.973	0.957	0.99	CLONAL	2	TRUE	0	0.835449947297297	2		959	1157	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0012806-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	121	597	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	NA	2	FACETS	1	0.962	1			1	INDETERMINATE	2	TRUE	NA	0.312726015682163	2		597	354	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223970	2223970	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012806-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	80	654	0	ENST00000326181.6:c.1184A>T	p.His395Leu	p.H395L	ENST00000326181	NM_032271.2	395	cAc/cTc	13/21	0.21580173967347	5	FACETS	1	0.976	1	0.487	0.43	0.549	CLONAL	1	TRUE	2	0.312726015682163	5		654	514	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858475	9858475	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012806-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	31	595	0	ENST00000330684.3:c.2926A>T	p.Asn976Tyr	p.N976Y	ENST00000330684	NM_001134407.1	976	Aat/Tat	13/13	0.21580173967347	5	FACETS	0.859	0.696	1	0.286	0.232	0.348	CLONAL	1	TRUE	2	0.312726015682163	5		595	339	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123204991	123205017	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTAAATAGGCCTTCACTATTCTGTGTG	TTAAATAGGCCTTCACTATTCTGTGTG	-	novel	NA	P-0012806-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	11	338	0	ENST00000218089.9:c.2359-8_2377del		p.X787_splice	ENST00000218089	NM_001042749.1	787		25/35	0.29760429780529	2	FACETS	0.434	0.301	0.599	0.217	0.15	0.3	SUBCLONAL	1	TRUE	0	0.312726015682163	2		338	162	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012814-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	37	247	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.949	0.78	1	0.949	0.78	1	CLONAL	1	TRUE	1	0.11	2		247	709	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0012814-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	20	301	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	1	2	FACETS	1	0.769	1	1	0.769	1	CLONAL	1	TRUE	1	0.11	2		301	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577029	7577042	+	frameshift_variant	Frame_Shift_Del	DEL	GCTCCCTGGGGGCA	GCTCCCTGGGGGCA	-	rs1555525054	NA	P-0012814-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	42	548	0	ENST00000269305.4:c.896_909del	p.Leu299HisfsTer2	p.L299Hfs*2	ENST00000269305	NM_001126112.2	299	cTGCCCCCAGGGAGC/c	8/11	1	2	FACETS	0.918	0.764	1	0.918	0.764	1	CLONAL	1	TRUE	1	0.11	2		548	832	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098562	11098562	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	792	489	0	ENST00000358026.2:c.1081del	p.Leu361SerfsTer50	p.L361Sfs*50	ENST00000358026	NM_001128849.1	360	ggC/gg	6/36	0.908692040107735	2	FACETS	0.998	0.985	1	0.998	0.985	1	CLONAL	2	TRUE	0	0.908692040107735	2		489	873	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0012837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	90	454	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.263276604311916	1	FACETS	0.723	0.641	0.81	0.723	0.641	0.81	SUBCLONAL	1	TRUE	0	0.29	1		454	734	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913996	32913996	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1282916502	NA	P-0012841-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	675	968	0	ENST00000380152.3:c.5504A>G	p.Asn1835Ser	p.N1835S	ENST00000380152		1835	aAt/aGt	11/27	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		968	1417	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346364	73346364	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012841-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	352	547	0	ENST00000377767.4:c.1436A>C	p.Asp479Ala	p.D479A	ENST00000377767	NM_014953.3	479	gAc/gCc	10/21	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		547	786	SUCCESS
APC	324	MSKCC	GRCh37	5	112175246	112175246	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1057517558	NA	P-0012847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	210	403	0	ENST00000257430.4:c.3956del	p.Pro1319LeufsTer2	p.P1319Lfs*2	ENST00000257430	NM_000038.5	1319	Cct/ct	16/16	0.228196119754784	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.347755846831785	3		403	648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578260	7578260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204041	NA	P-0012847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	340	788	0	ENST00000269305.4:c.589G>A	p.Val197Met	p.V197M	ENST00000269305	NM_001126112.2	197	Gtg/Atg	6/11	0.237790611101478	3	FACETS	0.938	0.888	0.99			1	CLONAL	2	TRUE	NA	0.347755846831785	3		788	1223	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729465	41729465	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747474916	NA	P-0012847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1351	137	1243	1	ENST00000242208.4:c.1064C>T	p.Pro355Leu	p.P355L	ENST00000242208	NM_002192.2	355	cCg/cTg	3/3	0.347755846831785	3	FACETS	0.622	0.563	0.683	0.311	0.281	0.342	SUBCLONAL	1	TRUE	1	0.347755846831785	3		1244	1488	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0012849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	567	393	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.375336836896868	6	FACETS	1	0.993	1			1	CLONAL	4	TRUE	NA	0.375336836896868	6		393	1188	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0012849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	337	631	1	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	NA	2	FACETS	1	0.961	1			1	INDETERMINATE	2	TRUE	NA	0.375336836896868	2		632	885	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042709	42042709	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	532	1090	1	ENST00000219905.7:c.6904G>T	p.Glu2302Ter	p.E2302*	ENST00000219905	NM_001164273.1	2302	Gaa/Taa	17/24	0.362188848776055	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.375336836896868	3		1091	1613	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111447	8111447	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	156	546	0	ENST00000346208.3:c.933G>T	p.Arg311Ser	p.R311S	ENST00000346208		311	agG/agT	5/6	0.375336836896868	4	FACETS	1	0.973	1	0.383	0.35	0.418	CLONAL	1	TRUE	1	0.375336836896868	4		546	994	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938272	36938272	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	226	972	2	ENST00000361632.4:c.689C>A	p.Pro230His	p.P230H	ENST00000361632		230	cCc/cAc	6/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.375336836896868	2		974	1118	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663263	227663263	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	113	522	0	ENST00000305123.5:c.192C>G	p.Ile64Met	p.I64M	ENST00000305123	NM_005544.2	64	atC/atG	1/2	0.23255649869832	4	FACETS	1	0.924	1			1	CLONAL	1	TRUE	NA	0.375336836896868	4		522	802	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1253931	1253931	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1218	343	821	0	ENST00000310581.5:c.3311G>T	p.Ser1104Ile	p.S1104I	ENST00000310581	NM_198253.2	1104	aGt/aTt	16/16	0.375336836896868	5	FACETS	0.915	0.864	0.968	0.61	0.576	0.645	CLONAL	2	TRUE	2	0.375336836896868	5		821	1561	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	459806	459806	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1989	356	919	2	ENST00000399788.2:c.1289A>T	p.Lys430Met	p.K430M	ENST00000399788	NM_001042603.1	430	aAg/aTg	10/28	0.375336836896868	7	FACETS	0.784	0.739	0.83	0.314	0.295	0.332	SUBCLONAL	2	TRUE	2	0.375336836896868	7		921	2345	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961502	41961502	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1522	305	1178	0	ENST00000219905.7:c.410G>A	p.Trp137Ter	p.W137*	ENST00000219905	NM_001164273.1	137	tGg/tAg	2/24	0.362188848776055	3	FACETS	1	0.971	1	0.528	0.496	0.562	CLONAL	1	TRUE	1	0.375336836896868	3		1178	1827	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297743	15297743	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	210	778	0	ENST00000263388.2:c.1897G>T	p.Val633Phe	p.V633F	ENST00000263388	NM_000435.2	633	Gtc/Ttc	12/33	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.375336836896868	2		778	1109	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	748	247	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.613047011886904	6	FACETS	1	0.995	1			1	CLONAL	5	FALSE	NA	0.721968949870945	6		247	963	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644709	134644709	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1473173223	NA	P-0012855-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	43	358	1	ENST00000398015.3:c.110A>G	p.Asn37Ser	p.N37S	ENST00000398015	NM_004441.4	37	aAt/aGt	2/16	0.291115317493724	1	FACETS	0.401	0.337	0.473	0.401	0.337	0.473	SUBCLONAL	1	TRUE	0	0.460643766558308	1		359	358	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549104	21549104	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012855-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	114	490	0	ENST00000382592.4:c.3172C>G	p.Pro1058Ala	p.P1058A	ENST00000382592	NM_014572.2	1058	Cct/Gct	8/8	0.460643766558308	1	FACETS	0.795	0.72	0.874	0.795	0.72	0.874	SUBCLONAL	1	TRUE	0	0.460643766558308	1		490	479	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954220	48954220	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012855-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	164	372	0	ENST00000267163.4:c.1421G>A	p.Ser474Asn	p.S474N	ENST00000267163	NM_000321.2	474	aGc/aAc	15/27	0.358973382447061	2	FACETS	1	0.988	1	0.702	0.649	0.756	CLONAL	1	TRUE	0	0.460643766558308	2		372	507	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564538	41564538	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012855-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	71	560	0	ENST00000263253.7:c.3960G>C	p.Glu1320Asp	p.E1320D	ENST00000263253	NM_001429.3	1320	gaG/gaC	24/31	0.216702174780245	2	FACETS	0.443	0.386	0.504	0.221	0.193	0.252	INDETERMINATE	1	TRUE	0	0.460643766558308	2		560	696	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577145	7577154	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GTAGATTACC	GTAGATTACC	-	novel	NA	P-0012855-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	132	562	2	ENST00000269305.4:c.784_793del	p.Gly262TrpfsTer80	p.G262Wfs*80	ENST00000269305	NM_001126112.2	262	GGTAATCTACtg/tg	8/11	0.460643766558308	1	FACETS	0.974	0.891	1	0.974	0.891	1	CLONAL	1	TRUE	0	0.460643766558308	1		564	453	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645406	67645406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012855-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	38	363	0	ENST00000264010.4:c.671C>T	p.Ser224Phe	p.S224F	ENST00000264010	NM_006565.3	224	tCt/tTt	3/12	0.310513501410895	0	FACETS	0.213	0.176	0.254			1	SUBCLONAL	1	TRUE	0	0.460643766558308	0		363	418	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11114016	11114571	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTATGAAGTAGCTCCGAGGTCTGATAGTGAAGAAAGTGGCTCAGAAGAAGAGGAAGAGGTAAGAGTGCATTTCCTGGCTTTCAAGGCTCTCAGTGCCCACTGGCAGTGACTTCCACCCTGTGTGTTGTGACCGTCTCCTGCCCTGGCTGGGCATCTTGTGGGGCAGGGAACAGCAGGGCCCAGGCCTGCCCGAAGTCGGTGCTTTAGAGCTGTCCTATCCAATAGGGCAGCTTCTGGCGACATGTGACCATTTCCATTTTAAATTAAATCAGTCACATTACATAAAATTTAAGACTCATTTTCTCTTTCACACTGGCTGCATTTCAGGTGCTTGGCATCCCTTATCTGGGAATGGTCTGCCTCATTTGCCCATTTTTTTTTTTTTTTTTTGAAACGGAGTCTCACTCTGTCACCCAGGCTGGAGTGCACTGGTGCAATCTCAGCTCATTGCAACCTCCACCTCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGCGCCTGCCACCACGTCCAGCTAGTTTTTTTATGTTTAGTA	GTATGAAGTAGCTCCGAGGTCTGATAGTGAAGAAAGTGGCTCAGAAGAAGAGGAAGAGGTAAGAGTGCATTTCCTGGCTTTCAAGGCTCTCAGTGCCCACTGGCAGTGACTTCCACCCTGTGTGTTGTGACCGTCTCCTGCCCTGGCTGGGCATCTTGTGGGGCAGGGAACAGCAGGGCCCAGGCCTGCCCGAAGTCGGTGCTTTAGAGCTGTCCTATCCAATAGGGCAGCTTCTGGCGACATGTGACCATTTCCATTTTAAATTAAATCAGTCACATTACATAAAATTTAAGACTCATTTTCTCTTTCACACTGGCTGCATTTCAGGTGCTTGGCATCCCTTATCTGGGAATGGTCTGCCTCATTTGCCCATTTTTTTTTTTTTTTTTTGAAACGGAGTCTCACTCTGTCACCCAGGCTGGAGTGCACTGGTGCAATCTCAGCTCATTGCAACCTCCACCTCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGCGCCTGCCACCACGTCCAGCTAGTTTTTTTATGTTTAGTA	-	novel	NA	P-0012855-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	31	548	0	ENST00000358026.2:c.1945_2001+499del		p.X649_splice	ENST00000358026	NM_001128849.1	649		13/36	0.386000402889661	1	FACETS	0.259	0.209	0.315	0.259	0.209	0.315	SUBCLONAL	1	TRUE	0	0.460643766558308	1		548	400	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55130008	55130008	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs746299618	NA	P-0012855-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	54	614	0	ENST00000257290.5:c.542C>A	p.Thr181Asn	p.T181N	ENST00000257290	NM_006206.4	181	aCc/aAc	4/23	NA	2	FACETS	0.288	0.245	0.336			1	INDETERMINATE	1	TRUE	NA	0.460643766558308	2		614	813	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975523	13975523	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0012855-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	28	185	0	ENST00000405192.2:c.366-2A>T		p.X122_splice	ENST00000405192	NM_001163147.1	122			0.42762664082837	3	FACETS	0.507	0.406	0.622	0.169	0.135	0.208	SUBCLONAL	1	TRUE	0	0.460643766558308	3		185	295	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117186	7117186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	43	877	0	ENST00000302850.5:c.4030G>A	p.Asp1344Asn	p.D1344N	ENST00000302850	NM_000208.2	1344	Gat/Aat	22/22	0.300563874630581	1	FACETS	0.451	0.377	0.533	0.451	0.377	0.533	SUBCLONAL	1	FALSE	0	0.300563874630581	1		877	539	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28903761	28903761	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	52	886	0	ENST00000282397.4:c.2698A>G	p.Lys900Glu	p.K900E	ENST00000282397	NM_002019.4	900	Aag/Gag	19/30	0.300563874630581	0	FACETS	0.567	0.483	0.658			1	SUBCLONAL	1	FALSE	0	0.300563874630581	0		886	427	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618930	37618930	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	144	694	3	ENST00000447079.4:c.610del	p.Arg204GlyfsTer134	p.R204Gfs*134	ENST00000447079	NM_015083.1	202	cgA/cg	1/14	0.300563874630581	5	FACETS	0.79	0.72	0.863			1	SUBCLONAL	2	FALSE	NA	0.300563874630581	5		697	880	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676228	37676230	+	frameshift_variant	Frame_Shift_Del	DEL	GAT	GAT	AA	novel	NA	P-0012857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	113	895	0	ENST00000447079.4:c.2983_2985delinsAA	p.Asp995AsnfsTer7	p.D995Nfs*7	ENST00000447079	NM_015083.1	995	GAT/AA	11/14	0.300563874630581	5	FACETS	1	0.982	1			1	CLONAL	1	FALSE	NA	0.300563874630581	5		895	750	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295242	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	78	415	0				ENST00000310581	NM_198253.2	-/1132			0.192263615633777	2	FACETS	1	0.96	1	0.609	0.536	0.688	CLONAL	1	TRUE	0	0.217689155563291	2		415	588	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652129	36652129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34916193	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	103	473	1	ENST00000244741.5:c.251G>A	p.Arg84Gln	p.R84Q	ENST00000244741	NM_000389.4	84	cGa/cAa	2/3	0.217689155563291	1	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	0	0.217689155563291	1		474	830	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606646	29606646	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147102592	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	64	626	0	ENST00000389048.3:c.1234C>T	p.Arg412Cys	p.R412C	ENST00000389048	NM_004304.4	412	Cgc/Tgc	5/29	0.217689155563291	1	FACETS	0.466	0.402	0.536	0.466	0.402	0.536	SUBCLONAL	1	TRUE	0	0.217689155563291	1		626	1124	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973911	55973911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs941528100	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	43	389	0	ENST00000263923.4:c.1405G>A	p.Glu469Lys	p.E469K	ENST00000263923	NM_002253.2	469	Gag/Aag	10/30	1	2	FACETS	0.563	0.47	0.666	0.563	0.47	0.666	SUBCLONAL	1	TRUE	1	0.217689155563291	2		389	702	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203436	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	200	517	0	ENST00000269305.4:c.487T>C	p.Tyr163His	p.Y163H	ENST00000269305	NM_001126112.2	163	Tac/Cac	5/11	0.0490908791866906	3	FACETS	1	0.938	1			1	INDETERMINATE	2	TRUE	NA	0.217689155563291	3		517	1005	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804242	43804242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1246	75	750	0	ENST00000372470.3:c.242C>T	p.Ser81Phe	p.S81F	ENST00000372470	NM_005373.2	81	tCc/tTc	3/12	0.207747009156612	3	FACETS	0.578	0.505	0.658	0.289	0.252	0.329	SUBCLONAL	1	TRUE	1	0.217689155563291	3		750	1321	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679811	88679811	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	72	564	0	ENST00000360948.2:c.652A>C	p.Asn218His	p.N218H	ENST00000360948	NM_001012338.2	218	Aac/Cac	7/19	1	2	FACETS	0.612	0.533	0.699	0.612	0.533	0.699	SUBCLONAL	1	TRUE	1	0.217689155563291	2		564	1080	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041375	42041375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764277967	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2086	115	1387	1	ENST00000219905.7:c.5570C>T	p.Ser1857Leu	p.S1857L	ENST00000219905	NM_001164273.1	1857	tCg/tTg	17/24	1	2	FACETS	0.48	0.43	0.534	0.48	0.43	0.534	SUBCLONAL	1	TRUE	1	0.217689155563291	2		1388	2201	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968280	2968280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1293	86	675	0	ENST00000396946.4:c.1706G>A	p.Gly569Glu	p.G569E	ENST00000396946	NM_032415.4	569	gGa/gAa	13/25	1	2	FACETS	0.573	0.505	0.647	0.573	0.505	0.647	SUBCLONAL	1	TRUE	1	0.217689155563291	2		675	1379	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215312	123215312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1214610561	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1282	85	928	0	ENST00000218089.9:c.2858G>A	p.Arg953Gln	p.R953Q	ENST00000218089	NM_001042749.1	953	cGa/cAa	28/35	1	2	FACETS	0.571	0.503	0.645	0.571	0.503	0.645	SUBCLONAL	1	TRUE	1	0.217689155563291	2		928	1367	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258049	16258049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	132	425	0	ENST00000375759.3:c.5314C>T	p.Pro1772Ser	p.P1772S	ENST00000375759	NM_015001.2	1772	Cca/Tca	11/15	0.207747009156612	3	FACETS	0.829	0.753	0.909	0.829	0.753	0.909	CLONAL	2	TRUE	1	0.217689155563291	3		425	811	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25536837	25536837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	54	510	0	ENST00000264709.3:c.17C>T	p.Ser6Phe	p.S6F	ENST00000264709	NM_175629.2	6	tCc/tTc	2/23	0.217689155563291	1	FACETS	0.481	0.409	0.559	0.481	0.409	0.559	SUBCLONAL	1	TRUE	0	0.217689155563291	1		510	920	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661383	227661383	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	51	648	1	ENST00000305123.5:c.2072C>T	p.Ser691Phe	p.S691F	ENST00000305123	NM_005544.2	691	tCc/tTc	1/2	0.192263615633777	2	FACETS	0.497	0.421	0.581	0.248	0.21	0.291	SUBCLONAL	1	TRUE	0	0.217689155563291	2		649	943	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042476	37042476	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	48	743	0	ENST00000231790.2:c.238T>C	p.Phe80Leu	p.F80L	ENST00000231790	NM_000249.3	80	Ttc/Ctc	3/19	1	2	FACETS	0.495	0.417	0.582	0.495	0.417	0.582	SUBCLONAL	1	TRUE	1	0.217689155563291	2		743	891	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266182	41266182	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	66	586	0	ENST00000349496.5:c.179C>T	p.Ser60Phe	p.S60F	ENST00000349496	NM_001904.3	60	tCc/tTc	3/15	1	2	FACETS	0.691	0.598	0.791	0.691	0.598	0.791	SUBCLONAL	1	TRUE	1	0.217689155563291	2		586	878	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090535	71090535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1440938806	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1304	103	772	1	ENST00000318789.4:c.813G>A	p.Met271Ile	p.M271I	ENST00000318789	NM_032682.5	271	atG/atA	11/21	1	2	FACETS	0.673	0.6	0.751	0.673	0.6	0.751	SUBCLONAL	1	TRUE	1	0.217689155563291	2		773	1407	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519339	176519339	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	128	417	1	ENST00000292408.4:c.745C>T	p.Pro249Ser	p.P249S	ENST00000292408	NM_213647.1	249	Ccc/Tcc	7/18	0.217689155563291	2	FACETS	1	0.985	1	0.741	0.672	0.814	CLONAL	1	TRUE	0	0.217689155563291	2		418	793	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287604	33287604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	45	457	0	ENST00000374542.5:c.1493C>T	p.Ser498Phe	p.S498F	ENST00000374542	NM_001141970.1	498	tCc/tTc	6/8	0.217689155563291	1	FACETS	0.486	0.407	0.574	0.486	0.407	0.574	SUBCLONAL	1	TRUE	0	0.217689155563291	1		457	758	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748578	43748578	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1602	138	905	2	ENST00000523873.1:c.532C>T	p.Leu178Phe	p.L178F	ENST00000523873		178	Ctc/Ttc	6/8	0.217689155563291	1	FACETS	0.649	0.588	0.714	0.649	0.588	0.714	SUBCLONAL	1	TRUE	0	0.217689155563291	1		907	1740	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240687	55240687	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770443325	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	82	702	1	ENST00000275493.2:c.1931C>T	p.Pro644Leu	p.P644L	ENST00000275493	NM_005228.3	644	cCg/cTg	17/28	1	2	FACETS	0.622	0.547	0.704	0.622	0.547	0.704	SUBCLONAL	1	TRUE	1	0.217689155563291	2		703	1211	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415040	116415040	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	82	699	0	ENST00000397752.3:c.3134C>T	p.Pro1045Leu	p.P1045L	ENST00000397752	NM_000245.2	1045	cCa/cTa	15/21	1	2	FACETS	0.682	0.599	0.771	0.682	0.599	0.771	SUBCLONAL	1	TRUE	1	0.217689155563291	2		699	1105	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738349	145738349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137975310	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	243	626	0	ENST00000428558.2:c.2636C>T	p.Pro879Leu	p.P879L	ENST00000428558	NM_004260.3	879	cCt/cTt	16/22	1	2	FACETS	0.984	0.919	1	1	0.994	1	CLONAL	2	TRUE	1	0.217689155563291	2		626	1134	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650837	93650837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	60	594	0	ENST00000375746.1:c.1763G>A	p.Gly588Glu	p.G588E	ENST00000375746	NM_001174167.1	588	gGa/gAa	13/14	0.217689155563291	1	FACETS	0.421	0.361	0.487	0.421	0.361	0.487	SUBCLONAL	1	TRUE	0	0.217689155563291	1		594	1167	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250169	110250169	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	104	462	0	ENST00000374672.4:c.506G>A	p.Gly169Glu	p.G169E	ENST00000374672	NM_004235.4	169	gGa/gAa	3/5	0.217689155563291	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.217689155563291	1		462	584	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912094	127912094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1536	103	1039	1	ENST00000373547.4:c.776C>T	p.Pro259Leu	p.P259L	ENST00000373547	NM_002721.4	259	cCt/cTt	7/7	0.217689155563291	1	FACETS	0.515	0.458	0.575	0.515	0.458	0.575	SUBCLONAL	1	TRUE	0	0.217689155563291	1		1040	1639	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609010	43609010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1321	85	983	3	ENST00000355710.3:c.1766G>A	p.Ser589Asn	p.S589N	ENST00000355710	NM_020975.4	589	aGc/aAc	10/20	1	2	FACETS	0.555	0.489	0.627	0.555	0.489	0.627	SUBCLONAL	1	TRUE	1	0.217689155563291	2		986	1406	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136004	64136004	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	122	478	0	ENST00000334205.4:c.1265T>G	p.Phe422Cys	p.F422C	ENST00000334205	NM_003942.2	422	tTt/tGt	11/17	0.217689155563291	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.217689155563291	1		478	877	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137830	64137830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	77	777	0	ENST00000334205.4:c.1931C>T	p.Ser644Phe	p.S644F	ENST00000334205	NM_003942.2	644	tCc/tTc	15/17	0.217689155563291	1	FACETS	0.477	0.417	0.542	0.477	0.417	0.542	SUBCLONAL	1	TRUE	0	0.217689155563291	1		777	1322	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691226	18691226	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	71	432	0	ENST00000266497.5:c.3337C>G	p.Leu1113Val	p.L1113V	ENST00000266497		1113	Ctc/Gtc	23/31	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.217689155563291	2		432	601	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435003	49435003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1230537280	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	43	383	0	ENST00000301067.7:c.6550C>T	p.Pro2184Ser	p.P2184S	ENST00000301067	NM_003482.3	2184	Ccc/Tcc	31/54	1	2	FACETS	0.642	0.537	0.76	0.642	0.537	0.76	SUBCLONAL	1	TRUE	1	0.217689155563291	2		383	615	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437403	121437403	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	53	447	0	ENST00000257555.6:c.1741G>A	p.Ala581Thr	p.A581T	ENST00000257555		581	Gcc/Acc	9/10	1	2	FACETS	0.63	0.536	0.733	0.63	0.536	0.733	SUBCLONAL	1	TRUE	1	0.217689155563291	2		447	773	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345115	73345115	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	33	461	0	ENST00000377767.4:c.1682C>T	p.Ser561Leu	p.S561L	ENST00000377767	NM_014953.3	561	tCa/tTa	13/21	1	2	FACETS	0.567	0.461	0.687	0.567	0.461	0.687	SUBCLONAL	1	TRUE	1	0.217689155563291	2		461	535	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435223	110435223	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	34	362	1	ENST00000375856.3:c.3178T>C	p.Ser1060Pro	p.S1060P	ENST00000375856	NM_003749.2	1060	Tca/Cca	1/2	1	2	FACETS	0.464	0.378	0.562	0.464	0.378	0.562	SUBCLONAL	1	TRUE	1	0.217689155563291	2		363	673	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061393	38061393	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	56	647	0	ENST00000250448.2:c.596G>A	p.Trp199Ter	p.W199*	ENST00000250448	NM_004496.3	199	tGg/tAg	2/2	1	2	FACETS	0.522	0.445	0.606	0.522	0.445	0.606	SUBCLONAL	1	TRUE	1	0.217689155563291	2		647	986	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562807	95562807	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	66	617	0	ENST00000393063.1:c.4450C>G	p.Pro1484Ala	p.P1484A	ENST00000393063	NM_030621.3	1484	Ccc/Gcc	24/28	1	2	FACETS	0.698	0.604	0.8	0.698	0.604	0.8	SUBCLONAL	1	TRUE	1	0.217689155563291	2		617	869	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849479	68849479	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876659268	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1212	65	699	0	ENST00000261769.5:c.1382C>T	p.Pro461Leu	p.P461L	ENST00000261769	NM_004360.3	461	cCt/cTt	10/16	1	2	FACETS	0.468	0.404	0.538	0.468	0.404	0.538	SUBCLONAL	1	TRUE	1	0.217689155563291	2		699	1277	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882322	89882322	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1284	107	871	0	ENST00000389301.3:c.152T>C	p.Leu51Pro	p.L51P	ENST00000389301	NM_000135.2	51	cTg/cCg	2/43	1	2	FACETS	0.707	0.632	0.787	0.707	0.632	0.787	SUBCLONAL	1	TRUE	1	0.217689155563291	2		871	1391	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006620	62006620	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1235	105	685	0	ENST00000392795.3:c.659A>C	p.Lys220Thr	p.K220T	ENST00000392795	NM_001039933.1	220	aAg/aCg	6/6	1	2	FACETS	0.72	0.643	0.802	0.72	0.643	0.802	SUBCLONAL	1	TRUE	1	0.217689155563291	2		685	1340	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120055	70120055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	17	17	0	ENST00000245479.2:c.1057C>T	p.Pro353Ser	p.P353S	ENST00000245479	NM_000346.3	353	Ccg/Tcg	3/3	0.210437963849422	3	FACETS	0.936	0.743	1	1	0.926	1	CLONAL	5	TRUE	0	0.217689155563291	3		17	37	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271633	15271633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1727	92	983	0	ENST00000263388.2:c.6806C>T	p.Ser2269Phe	p.S2269F	ENST00000263388	NM_000435.2	2269	tCc/tTc	33/33	0.143529917131033	3	FACETS	0.515	0.455	0.58	0.258	0.227	0.29	SUBCLONAL	1	TRUE	1	0.217689155563291	3		983	1819	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291806	15291806	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	73	485	0	ENST00000263388.2:c.2960C>T	p.Thr987Ile	p.T987I	ENST00000263388	NM_000435.2	987	aCc/aTc	18/33	0.143529917131033	3	FACETS	0.723	0.63	0.823	0.361	0.315	0.412	SUBCLONAL	1	TRUE	1	0.217689155563291	3		485	1029	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560998	9560998	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	54	645	0	ENST00000353224.5:c.784G>A	p.Asp262Asn	p.D262N	ENST00000353224	NM_177990.2	262	Gat/Aat	4/10	1	2	FACETS	0.484	0.412	0.564	0.484	0.412	0.564	SUBCLONAL	1	TRUE	1	0.217689155563291	2		645	1025	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376727	31376727	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	51	499	0	ENST00000328111.2:c.722C>T	p.Ala241Val	p.A241V	ENST00000328111	NM_006892.3	241	gCc/gTc	7/23	1	2	FACETS	0.545	0.462	0.637	0.545	0.462	0.637	SUBCLONAL	1	TRUE	1	0.217689155563291	2		499	860	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757461	40757461	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866132388	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	62	608	2	ENST00000373198.4:c.2837C>T	p.Ser946Phe	p.S946F	ENST00000373198	NM_133170.3	946	tCc/tTc	20/32	1	2	FACETS	0.495	0.426	0.571	0.495	0.426	0.571	SUBCLONAL	1	TRUE	1	0.217689155563291	2		610	1150	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922103	39922103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2318	155	1173	2	ENST00000378444.4:c.4069C>T	p.Pro1357Ser	p.P1357S	ENST00000378444	NM_001123385.1	1357	Cca/Tca	9/15	1	2	FACETS	0.576	0.524	0.631	0.576	0.524	0.631	SUBCLONAL	1	TRUE	1	0.217689155563291	2		1175	2473	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345942	70345942	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1530	97	976	0	ENST00000374080.3:c.2479G>A	p.Glu827Lys	p.E827K	ENST00000374080		827	Gaa/Aaa	18/45	1	2	FACETS	0.548	0.486	0.614	0.548	0.486	0.614	SUBCLONAL	1	TRUE	1	0.217689155563291	2		976	1627	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227889	123227889	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	85	686	0	ENST00000218089.9:c.3600G>A	p.Met1200Ile	p.M1200I	ENST00000218089	NM_001042749.1	1200	atG/atA	33/35	1	2	FACETS	0.742	0.654	0.837	0.742	0.654	0.837	SUBCLONAL	1	TRUE	1	0.217689155563291	2		686	1052	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912144	97912209	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACCACAGCCTTCTAAGAAAAGGAAAAACGACGCAGGATGACAGGAAACATTTGCCACTTACAGCAA	ACCACAGCCTTCTAAGAAAAGGAAAAACGACGCAGGATGACAGGAAACATTTGCCACTTACAGCAA	-	novel	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	94	306	0	ENST00000289081.3:c.682_686+61del		p.X228_splice	ENST00000289081	NM_000136.2	228		7/15	0.217689155563291	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.217689155563291	1		306	624	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683984	29683985	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1135402907	NA	P-0012865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	167	649	2	ENST00000356175.3:c.7684_7685del	p.Arg2562AspfsTer12	p.R2562Dfs*12	ENST00000356175	NM_000267.3	2561	cAG/c	52/57	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.217689155563291	2		651	1046	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0012875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	94	524	0	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	1	2	FACETS	0.907	0.806	1	0.907	0.806	1	CLONAL	1	TRUE	1	0.25	2		524	829	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449781	149449781	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	106	509	0	ENST00000286301.3:c.1283A>T	p.Asn428Ile	p.N428I	ENST00000286301	NM_005211.3	428	aAc/aTc	9/22	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.25	2		509	847	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180076538	180076538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1254608660	NA	P-0012875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	59	178	0	ENST00000261937.6:c.8G>T	p.Arg3Leu	p.R3L	ENST00000261937	NM_182925.4	3	cGg/cTg	1/30	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.25	2		178	359	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554879	106554879	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	41	349	1	ENST00000369096.4:c.1996G>C	p.Ala666Pro	p.A666P	ENST00000369096	NM_001198.3	666	Gcc/Ccc	7/7	1	2	FACETS	0.434	0.361	0.517	0.434	0.361	0.517	SUBCLONAL	1	TRUE	1	0.25	2		350	755	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513335	106513335	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	101	560	0	ENST00000359195.3:c.2239C>A	p.Leu747Ile	p.L747I	ENST00000359195	NM_002649.2	747	Ctt/Att	4/11	1	2	FACETS	0.646	0.575	0.721	0.646	0.575	0.721	SUBCLONAL	1	TRUE	1	0.25	2		560	1251	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375991	8375991	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	149	694	0	ENST00000356435.5:c.4606C>G	p.Arg1536Gly	p.R1536G	ENST00000356435		1536	Cgt/Ggt	28/35	1	2	FACETS	0.922	0.84	1	0.922	0.84	1	CLONAL	1	TRUE	1	0.25	2		694	1293	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251946	8251946	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	71	701	0	ENST00000335790.3:c.131G>C	p.Trp44Ser	p.W44S	ENST00000335790	NM_002315.2	44	tGg/tCg	2/4	1	2	FACETS	0.462	0.401	0.528	0.462	0.401	0.528	SUBCLONAL	1	TRUE	1	0.25	2		701	1230	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944943	31944943	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	73	439	0	ENST00000340398.3:c.158G>T	p.Arg53Leu	p.R53L	ENST00000340398	NM_001013699.2	53	cGt/cTt	1/1	1	2	FACETS	0.629	0.548	0.716	0.629	0.548	0.716	SUBCLONAL	1	TRUE	1	0.25	2		439	929	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349904	89349904	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2282	136	1271	1	ENST00000301030.4:c.3046G>T	p.Asp1016Tyr	p.D1016Y	ENST00000301030	NM_001256183.1	1016	Gat/Tat	9/13	1	2	FACETS	0.45	0.407	0.496	0.45	0.407	0.496	SUBCLONAL	1	TRUE	1	0.25	2		1272	2418	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756566	756566	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	82	425	0	ENST00000314574.4:c.262G>T	p.Gly88Cys	p.G88C	ENST00000314574	NM_005433.3	88	Ggt/Tgt	2/12	1	2	FACETS	0.805	0.709	0.908	0.805	0.709	0.908	CLONAL	1	TRUE	1	0.25	2		425	815	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143003	7143003	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	78	510	0	ENST00000302850.5:c.2366C>T	p.Pro789Leu	p.P789L	ENST00000302850	NM_000208.2	789	cCc/cTc	12/22	1	2	FACETS	0.672	0.589	0.761	0.672	0.589	0.761	SUBCLONAL	1	TRUE	1	0.25	2		510	929	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076911	41076911	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	80	685	0	ENST00000373198.4:c.1509C>A	p.Tyr503Ter	p.Y503*	ENST00000373198	NM_133170.3	503	taC/taA	9/32	1	2	FACETS	0.561	0.492	0.636	0.561	0.492	0.636	SUBCLONAL	1	TRUE	1	0.25	2		685	1140	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15840919	15840919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	79	508	0	ENST00000307771.7:c.1003C>T	p.Pro335Ser	p.P335S	ENST00000307771	NM_005089.3	335	Ccc/Tcc	11/11	1	2	FACETS	0.737	0.647	0.835	0.737	0.647	0.835	SUBCLONAL	1	TRUE	1	0.25	2		508	857	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971132	21971132	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	59	168	0	ENST00000304494.5:c.226del	p.Ala76ProfsTer70	p.A76Pfs*70	ENST00000304494	NM_000077.4	76	Gcc/cc	2/3	1	2	FACETS	0.942	0.812	1	0.942	0.812	1	CLONAL	1	TRUE	1	0.25	2		168	501	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971132	21971133	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	A	novel	NA	P-0012875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	59	362	0	ENST00000304494.5:c.225_226delinsT	p.Ala76ProfsTer70	p.A76Pfs*70	ENST00000304494	NM_000077.4	75	ccCGcc/ccTcc	2/3	1				0.812	1				CLONAL	1	TRUE	1	0.25	2		362	501	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0012885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	55	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	821	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	129	247	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.758	0.687	0.833	1	0.985	1	SUBCLONAL	2	TRUE	1	0.19	2		247	896	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0012890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	16	591	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	0.144226501257487	1	FACETS	0.201	0.147	0.266	0.201	0.147	0.266	SUBCLONAL	1	TRUE	0	0.19	1		591	758	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739866	145739866	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755425093	NA	P-0012890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	71	810	0	ENST00000428558.2:c.1664C>T	p.Ser555Leu	p.S555L	ENST00000428558	NM_004260.3	555	tCg/tTg	10/22	1	2	FACETS	0.66	0.574	0.754	0.66	0.574	0.754	SUBCLONAL	1	TRUE	1	0.19	2		810	1132	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944410	131944410	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	28	214	0	ENST00000265335.6:c.2822A>T	p.Gln941Leu	p.Q941L	ENST00000265335		941	cAg/cTg	17/25	1	2	FACETS	0.766	0.612	0.941	0.766	0.612	0.941	CLONAL	1	TRUE	1	0.19	2		214	385	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572097	95572097	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	65	506	0	ENST00000393063.1:c.3011A>T	p.His1004Leu	p.H1004L	ENST00000393063	NM_030621.3	1004	cAt/cTt	20/28	1	2	FACETS	0.838	0.726	0.961	0.838	0.726	0.961	CLONAL	1	TRUE	1	0.19	2		506	816	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577504	7577504	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	45	540	0	ENST00000269305.4:c.777C>A	p.Asp259Glu	p.D259E	ENST00000269305	NM_001126112.2	259	gaC/gaA	7/11	0.144226501257487	1	FACETS	0.636	0.533	0.75	0.636	0.533	0.75	SUBCLONAL	1	TRUE	0	0.19	1		540	674	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561324	9561324	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012890-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	56	486	0	ENST00000353224.5:c.458del	p.Gly153GlufsTer20	p.G153Efs*20	ENST00000353224	NM_177990.2	153	gGa/ga	4/10	1	2	FACETS	0.901	0.771	1	0.901	0.771	1	CLONAL	1	TRUE	1	0.19	2		486	654	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	40	206	0	ENST00000288602.6:c.1742A>T	p.Asn581Ile	p.N581I	ENST00000288602	NM_004333.4	581	aAt/aTt	15/18	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.18	2		206	384	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108872	2108872	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs397515097	NA	P-0012894-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	133	515	0	ENST00000219476.3:c.973C>T	p.Gln325Ter	p.Q325*	ENST00000219476	NM_000548.3	325	Cag/Tag	10/42	0.183164332063413	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	2	TRUE	0	0.18	2		515	728	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0012903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	35	264	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.698	0.574	0.837	0.698	0.574	0.837	SUBCLONAL	1	TRUE	1	0.30933358689186	2		264	324	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100663	67100663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	108	774	1	ENST00000412916.2:c.361G>A	p.Gly121Ser	p.G121S	ENST00000412916		121	Ggt/Agt	4/6	0.30933358689186	1	FACETS	0.716	0.642	0.795	0.716	0.642	0.795	SUBCLONAL	1	TRUE	0	0.30933358689186	1		775	824	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111452	8111452	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	86	606	0	ENST00000346208.3:c.938del	p.Ala313GlufsTer42	p.A313Efs*42	ENST00000346208		313	gCa/ga	5/6	1	2	FACETS	0.764	0.675	0.858	0.764	0.675	0.858	SUBCLONAL	1	TRUE	1	0.30933358689186	2		606	728	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904843	101904843	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	269	503	0	ENST00000374994.4:c.831G>A	p.Trp277Ter	p.W277*	ENST00000374994	NM_004612.2	277	tgG/tgA	5/9	0.203075777658208	4	FACETS	0.877	0.825	0.93	0.877	0.825	0.93	CLONAL	4	TRUE	0	0.219930268481383	4		503	851	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377171	118377171	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	219	744	0	ENST00000534358.1:c.10564C>G	p.Pro3522Ala	p.P3522A	ENST00000534358	NM_005933.3	3522	Cca/Gca	27/36	0.202204788703765	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.219930268481383	2		744	952	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915679	112915679	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	205	527	0	ENST00000351677.2:c.952T>G	p.Cys318Gly	p.C318G	ENST00000351677	NM_002834.3	318	Tgc/Ggc	9/16	0.219930268481383	5	FACETS	0.935	0.868	1	0.935	0.868	1	CLONAL	3	TRUE	2	0.219930268481383	5		527	884	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15838337	15838337	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	263	991	0	ENST00000307771.7:c.835G>C	p.Glu279Gln	p.E279Q	ENST00000307771	NM_005089.3	279	Gaa/Caa	10/11	NA	2	FACETS	0.904	0.846	0.964			1	INDETERMINATE	2	TRUE	NA	0.219930268481383	2		991	1323	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933688	39933688	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1351182053	NA	P-0012909-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	179	734	0	ENST00000378444.4:c.911A>G	p.Tyr304Cys	p.Y304C	ENST00000378444	NM_001123385.1	304	tAt/tGt	4/15	NA	2	FACETS	0.8	0.736	0.865			1	INDETERMINATE	2	TRUE	NA	0.219930268481383	2		734	1018	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0012913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	283	393	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.316722413898387	3	FACETS	1	0.948	1	0.668	0.632	0.704	CLONAL	2	TRUE	0	0.527064617793081	3		393	677	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220579	123220579	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1169	249	764	0	ENST00000218089.9:c.3236C>G	p.Thr1079Arg	p.T1079R	ENST00000218089	NM_001042749.1	1079	aCa/aGa	30/35	0.527064617793081	3	FACETS	0.842	0.785	0.9	0.421	0.392	0.45	CLONAL	1	TRUE	1	0.527064617793081	3		764	1418	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368176	31368176	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	373	684	0	ENST00000328111.2:c.47G>T	p.Gly16Val	p.G16V	ENST00000328111	NM_006892.3	16	gGg/gTg	2/23	0.181761319827263	6	FACETS	1	0.978	1	0.703	0.667	0.741	INDETERMINATE	2	TRUE	3	0.527064617793081	6		684	1378	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058610	72058610	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	119	749	1	ENST00000357731.5:c.830G>T	p.Ser277Ile	p.S277I	ENST00000357731	NM_173808.2	277	aGc/aTc	6/7	0.124924246530195	4	FACETS	0.581	0.523	0.643	0.291	0.261	0.322	INDETERMINATE	1	TRUE	2	0.527064617793081	4		750	1186	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716193	243716193	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	247	557	0	ENST00000263826.5:c.1001T>A	p.Val334Asp	p.V334D	ENST00000263826	NM_005465.4	334	gTt/gAt	10/13	0.446225802327675	3	FACETS	1	0.954	1			1	CLONAL	1	TRUE	NA	0.527064617793081	3		557	1153	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915022	131915022	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	246	358	1	ENST00000265335.6:c.379G>T	p.Val127Phe	p.V127F	ENST00000265335		127	Gtc/Ttc	4/25	0.4329749858131	2	FACETS	0.891	0.842	0.94	0.891	0.842	0.94	CLONAL	2	TRUE	0	0.527064617793081	2		359	524	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359046	81359046	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	323	596	0	ENST00000222390.5:c.915C>A	p.Cys305Ter	p.C305*	ENST00000222390	NM_000601.4	305	tgC/tgA	8/18	0.371949848409059	3	FACETS	0.819	0.776	0.864	0.819	0.776	0.864	CLONAL	2	TRUE	1	0.527064617793081	3		596	945	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508370	106508370	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	103	173	0	ENST00000359195.3:c.364C>A	p.Leu122Met	p.L122M	ENST00000359195	NM_002649.2	122	Ctg/Atg	2/11	0.371949848409059	3	FACETS	0.898	0.816	0.982	0.898	0.816	0.982	CLONAL	2	TRUE	1	0.527064617793081	3		173	275	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431383	121431383	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	86	484	0	ENST00000257555.6:c.587C>T	p.Thr196Ile	p.T196I	ENST00000257555		196	aCc/aTc	3/10	0.330458571804889	2	FACETS	0.546	0.483	0.612	0.273	0.241	0.306	SUBCLONAL	1	TRUE	0	0.527064617793081	2		484	598	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916734	48916734	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0012913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	394	363	0	ENST00000267163.4:c.265-1G>A		p.X89_splice	ENST00000267163	NM_000321.2	89			0.476619565017374	4	FACETS	0.896	0.862	0.929	0.896	0.862	0.929	CLONAL	4	TRUE	0	0.527064617793081	4		363	637	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476309	88476309	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	40	535	0	ENST00000360948.2:c.1823G>T	p.Gly608Val	p.G608V	ENST00000360948	NM_001012338.2	608	gGc/gTc	15/19	0.4329749858131	2	FACETS	0.254	0.211	0.303	0.127	0.105	0.152	SUBCLONAL	1	TRUE	0	0.527064617793081	2		535	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577555	7577556	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	A	novel	NA	P-0012913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	609	477	1	ENST00000269305.4:c.725_726delinsT	p.Cys242LeufsTer5	p.C242Lfs*5	ENST00000269305	NM_001126112.2	242	tGC/tT	7/11	0.527064617793081	3	FACETS	0.979	0.949	1	0.979	0.949	1	CLONAL	3	TRUE	0	0.527064617793081	3		478	994	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0012922-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	662	606	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.335289942252606	5	FACETS	1	0.968	1	0.801	0.774	0.827	CLONAL	4	TRUE	0	0.399574183870802	5		606	1324	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0012922-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	33	594	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.309169899774341	2	FACETS	0.171	0.138	0.208	0.085	0.069	0.104	SUBCLONAL	1	TRUE	0	0.399574183870802	2		594	966	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012922-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	98	692	0	ENST00000269305.4:c.811G>C	p.Glu271Gln	p.E271Q	ENST00000269305	NM_001126112.2	271	Gag/Cag	8/11	0.309169899774341	2	FACETS	0.407	0.361	0.455	0.203	0.18	0.228	SUBCLONAL	1	TRUE	0	0.399574183870802	2		692	1206	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012922-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	449	772	2	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	0.309169899774341	2	FACETS	0.755	0.719	0.791	0.755	0.719	0.791	SUBCLONAL	2	TRUE	0	0.399574183870802	2		774	1489	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164123	47164123	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012922-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	101	409	0	ENST00000409792.3:c.2003C>T	p.Pro668Leu	p.P668L	ENST00000409792	NM_014159.6	668	cCc/cTc	3/21	1	2	FACETS	0.697	0.623	0.776	0.697	0.623	0.776	SUBCLONAL	1	TRUE	1	0.399574183870802	2		409	725	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530423	187530423	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs138364727	NA	P-0012922-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	166	644	0	ENST00000441802.2:c.10120A>G	p.Ile3374Val	p.I3374V	ENST00000441802	NM_005245.3	3374	Att/Gtt	16/27	1	2	FACETS	0.805	0.739	0.875	0.805	0.739	0.875	CLONAL	1	TRUE	1	0.399574183870802	2		644	1032	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858112	9858112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012922-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1396	85	806	2	ENST00000330684.3:c.3289G>A	p.Asp1097Asn	p.D1097N	ENST00000330684	NM_001134407.1	1097	Gac/Aac	13/13	0.304729686164889	3	FACETS	0.345	0.303	0.39	0.172	0.151	0.195	SUBCLONAL	1	TRUE	1	0.399574183870802	3		808	1481	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098358	108098358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs7112053	NA	P-0012923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	361	494	0	ENST00000278616.4:c.7C>G	p.Leu3Val	p.L3V	ENST00000278616	NM_000051.3	3	Cta/Gta	2/63	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		494	855	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	119	487	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.438446881866019	4	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.438446881866019	4		487	587	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511578	66511578	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	43	227	1	ENST00000358598.2:c.38G>A	p.Arg13His	p.R13H	ENST00000358598	NM_212471.2	13	cGc/cAc	2/11	0.205383735971074	4	FACETS	0.913	0.768	1	0.457	0.384	0.537	INDETERMINATE	1	TRUE	2	0.438446881866019	4		228	309	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339111	65339111	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	87	484	1	ENST00000342505.4:c.425del	p.Lys142ArgfsTer26	p.K142Rfs*26	ENST00000342505	NM_002227.2	142	aAg/ag	5/25	0.26775162016726	4	FACETS	0.918	0.821	1	0.918	0.821	1	CLONAL	2	TRUE	2	0.438446881866019	4		485	311	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867541	35867541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	35	218	0	ENST00000303115.3:c.361del	p.Ile121Ter	p.I121*	ENST00000303115	NM_002185.3	119	Aaa/aa	3/8	0.343763686478995	4	FACETS	0.908	0.748	1	0.454	0.374	0.542	CLONAL	1	TRUE	2	0.438446881866019	4		218	253	SUCCESS
AR	367	MSKCC	GRCh37	X	66931247	66931247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868669253	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	99	478	2	ENST00000374690.3:c.1889G>A	p.Arg630Gln	p.R630Q	ENST00000374690	NM_000044.3	630	cGg/cAg	4/8	1	1	FACETS	0.757	0.689	0.825	1	0.985	1	SUBCLONAL	2	TRUE	0	0.438446881866019	1		480	233	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692791	89692791	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1114167623	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	38	246	0	ENST00000371953.3:c.275A>G	p.Asp92Gly	p.D92G	ENST00000371953	NM_000314.4	92	gAc/gGc	5/9	0.438446881866019	4	FACETS	0.907	0.753	1			1	CLONAL	1	TRUE	NA	0.438446881866019	4		246	275	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6036958	6036958	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	45	461	0	ENST00000265849.7:c.802del	p.Tyr268ThrfsTer39	p.Y268Tfs*39	ENST00000265849	NM_000535.5	268	Tac/ac	7/15	0.130228826517583	4	FACETS	1	0.923	1	0.577	0.488	0.673	INDETERMINATE	1	TRUE	2	0.438446881866019	4		461	256	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	65	1202	0	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	0.205383735971074	4	FACETS	0.645	0.559	0.739	0.323	0.279	0.37	INDETERMINATE	1	TRUE	2	0.438446881866019	4		1202	661	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874013	151874013	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1248944002	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	61	494	1	ENST00000262189.6:c.8525del	p.Asn2842MetfsTer21	p.N2842Mfs*21	ENST00000262189	NM_170606.2	2842	aAt/at	38/59	0.205383735971074	4	FACETS	1	0.962	1	0.658	0.572	0.75	INDETERMINATE	1	TRUE	2	0.438446881866019	4		495	304	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	145	1466	5	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	0.404135017151929	1	FACETS	0.75	0.685	0.817	0.75	0.685	0.817	SUBCLONAL	1	TRUE	0	0.438446881866019	1		1471	689	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255338	16255338	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200134542	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	76	525	0	ENST00000375759.3:c.2603C>T	p.Ala868Val	p.A868V	ENST00000375759	NM_015001.2	868	gCg/gTg	11/15	0.436705848655485	4	FACETS	1	0.972	1			1	CLONAL	1	TRUE	NA	0.438446881866019	4		525	367	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795378	42795378	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	37	525	0	ENST00000575354.2:c.2462del	p.Gly821GlufsTer103	p.G821Efs*103	ENST00000575354	NM_015125.3	820	Ggg/gg	10/20	1	2	FACETS	0.943	0.787	1	0.943	0.787	1	CLONAL	1	TRUE	1	0.438446881866019	2		525	179	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067836	30067836	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315499	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	40	309	0	ENST00000338641.4:c.1021C>T	p.Arg341Ter	p.R341*	ENST00000338641	NM_000268.3	341	Cga/Tga	11/16	0.26775162016726	4	FACETS	0.795	0.671	0.929	0.795	0.671	0.929	CLONAL	2	TRUE	2	0.438446881866019	4		309	165	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755427	39755427	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	32	704	1	ENST00000288319.7:c.1338del	p.Phe446LeufsTer59	p.F446Lfs*59	ENST00000288319	NM_182918.3	446	ttT/tt	10/10	1	2	FACETS	0.547	0.445	0.66	0.547	0.445	0.66	SUBCLONAL	1	TRUE	1	0.438446881866019	2		705	267	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262669	16262669	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138432235	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	27	354	0	ENST00000375759.3:c.9934C>T	p.Arg3312Cys	p.R3312C	ENST00000375759	NM_015001.2	3312	Cgc/Tgc	11/15	0.436705848655485	4	FACETS	0.868	0.696	1			1	CLONAL	1	TRUE	NA	0.438446881866019	4		354	204	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622516	158622516	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs387906589	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	127	1252	2	ENST00000263640.3:c.983G>T	p.Gly328Val	p.G328V	ENST00000263640	NM_001105.4	328	gGg/gTg	8/11	0.26775162016726	4	FACETS	1	0.983	1	0.686	0.624	0.752	CLONAL	1	TRUE	2	0.438446881866019	4		1254	607	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095828	178095828	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	63	359	0	ENST00000397062.3:c.1503A>G	p.Ile501Met	p.I501M	ENST00000397062	NM_006164.4	501	atA/atG	5/5	0.26775162016726	4	FACETS	1	0.947	1	0.589	0.512	0.671	CLONAL	1	TRUE	2	0.438446881866019	4		359	351	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190717481	190717481	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	30	241	0	ENST00000441310.2:c.800T>C	p.Val267Ala	p.V267A	ENST00000441310	NM_000534.4	267	gTa/gCa	7/13	0.26775162016726	4	FACETS	0.879	0.712	1	0.439	0.356	0.533	CLONAL	1	TRUE	2	0.438446881866019	4		241	224	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37081683	37081683	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63751630	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	54	431	0	ENST00000231790.2:c.1565G>A	p.Arg522Gln	p.R522Q	ENST00000231790	NM_000249.3	522	cGg/cAg	14/19	0.343763686478995	4	FACETS	1	0.934	1	0.577	0.496	0.665	CLONAL	1	TRUE	2	0.438446881866019	4		431	307	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668729	52668729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759670972	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	64	543	0	ENST00000394830.3:c.1190G>A	p.Arg397Gln	p.R397Q	ENST00000394830	NM_018313.4	397	cGg/cAg	12/30	0.26775162016726	4	FACETS	1	0.956	1	0.616	0.536	0.701	CLONAL	1	TRUE	2	0.438446881866019	4		543	341	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696184	52696184	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	90	762	0	ENST00000394830.3:c.493G>T	p.Asp165Tyr	p.D165Y	ENST00000394830	NM_018313.4	165	Gat/Tat	5/30	0.26775162016726	4	FACETS	1	0.966	1	0.606	0.54	0.677	CLONAL	1	TRUE	2	0.438446881866019	4		762	487	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247496	71247496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1202112901	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	77	526	0	ENST00000318789.4:c.37G>A	p.Gly13Ser	p.G13S	ENST00000318789	NM_032682.5	13	Ggt/Agt	6/21	0.26775162016726	4	FACETS	1	0.975	1	0.714	0.631	0.801	CLONAL	1	TRUE	2	0.438446881866019	4		526	354	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940624	131940624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs558302979	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	45	378	2	ENST00000265335.6:c.2651G>A	p.Arg884His	p.R884H	ENST00000265335		884	cGt/cAt	16/25	0.343763686478995	4	FACETS	0.884	0.746	1	0.442	0.373	0.518	CLONAL	1	TRUE	2	0.438446881866019	4		380	334	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510904	157510904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554232979	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	73	460	1	ENST00000346085.5:c.3679C>T	p.Gln1227Ter	p.Q1227*	ENST00000346085	NM_020732.3	1227	Caa/Taa	14/20	0.205383735971074	4	FACETS	1	0.971	1	0.688	0.606	0.775	INDETERMINATE	1	TRUE	2	0.438446881866019	4		461	348	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508470	106508470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1463222028	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	10	145	0	ENST00000359195.3:c.464C>T	p.Thr155Met	p.T155M	ENST00000359195	NM_002649.2	155	aCg/aTg	2/11	0.205383735971074	4	FACETS	0.625	0.426	0.87	0.312	0.213	0.435	INDETERMINATE	1	TRUE	2	0.438446881866019	4		145	105	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435769	116435769	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780102059	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	63	632	0	ENST00000397752.3:c.3859G>A	p.Val1287Ile	p.V1287I	ENST00000397752	NM_000245.2	1287	Gta/Ata	20/21	0.205383735971074	4	FACETS	1	0.967	1	0.682	0.595	0.776	INDETERMINATE	1	TRUE	2	0.438446881866019	4		632	303	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606436	93606436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201455170	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	50	615	0	ENST00000375746.1:c.256G>A	p.Ala86Thr	p.A86T	ENST00000375746	NM_001174167.1	86	Gcc/Acc	2/14	0.12687325957759	4	FACETS	1	0.933	1	0.584	0.499	0.676	INDETERMINATE	1	TRUE	2	0.438446881866019	4		615	281	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915951	127915951	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	101	1183	1	ENST00000373547.4:c.530G>A	p.Arg177Gln	p.R177Q	ENST00000373547	NM_002721.4	177	cGa/cAa	6/7	0.12687325957759	4	FACETS	1	0.969	1	0.606	0.543	0.672	INDETERMINATE	1	TRUE	2	0.438446881866019	4		1184	547	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750290	133750290	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	44	617	2	ENST00000318560.5:c.1121A>G	p.Asn374Ser	p.N374S	ENST00000318560	NM_005157.4	374	aAc/aGc	7/11	0.12687325957759	4	FACETS	1	0.903	1	0.549	0.463	0.642	INDETERMINATE	1	TRUE	2	0.438446881866019	4		619	263	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104359294	104359294	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773037813	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	38	562	1	ENST00000369902.3:c.1015C>T	p.Arg339Trp	p.R339W	ENST00000369902	NM_016169.3	339	Cgg/Tgg	8/12	0.438446881866019	4	FACETS	1	0.875	1			1	CLONAL	1	TRUE	NA	0.438446881866019	4		563	235	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138137	64138137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	49	623	3	ENST00000334205.4:c.2060C>T	p.Thr687Met	p.T687M	ENST00000334205	NM_003942.2	687	aCg/aTg	16/17	0.392732779896714	4	FACETS	1	0.961	1	0.705	0.603	0.814	CLONAL	1	TRUE	2	0.438446881866019	4		626	228	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50482302	50482302	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	22	307	0	ENST00000394963.4:c.655-2A>G		p.X219_splice	ENST00000394963	NM_003076.4	219			0.26775162016726	4	FACETS	0.744	0.58	0.932	0.372	0.29	0.466	CLONAL	1	TRUE	2	0.438446881866019	4		307	194	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129462	30129462	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768111899	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	74	1281	2	ENST00000263025.4:c.566G>A	p.Arg189Gln	p.R189Q	ENST00000263025	NM_002746.2	189	cGg/cAg	4/9	1	2	FACETS	0.829	0.73	0.936	0.829	0.73	0.936	CLONAL	1	TRUE	1	0.438446881866019	2		1283	407	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662277	67662277	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	38	482	0	ENST00000264010.4:c.1523G>T	p.Arg508Met	p.R508M	ENST00000264010	NM_006565.3	508	aGg/aTg	9/12	1	2	FACETS	0.744	0.62	0.88	0.744	0.62	0.88	SUBCLONAL	1	TRUE	1	0.438446881866019	2		482	233	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348136	89348136	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	61	1957	0	ENST00000301030.4:c.4814T>C	p.Met1605Thr	p.M1605T	ENST00000301030	NM_001256183.1	1605	aTg/aCg	9/13	1	2	FACETS	0.802	0.696	0.916	0.802	0.696	0.916	CLONAL	1	TRUE	1	0.438446881866019	2		1957	347	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982785	7982785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	54	1056	0	ENST00000319144.4:c.1000C>T	p.Gln334Ter	p.Q334*	ENST00000319144	NM_001139.2	334	Cag/Tag	8/15	0.205383735971074	4	FACETS	1	0.948	1	0.615	0.529	0.708	INDETERMINATE	1	TRUE	2	0.438446881866019	4		1056	288	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40462667	40462667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	58	1491	0	ENST00000345506.4:c.2365G>A	p.Ala789Thr	p.A789T	ENST00000345506	NM_003152.3	789	Gcc/Acc	20/20	0.337587035181061	0	FACETS	0.361	0.311	0.415			1	SUBCLONAL	1	TRUE	0	0.438446881866019	0		1491	412	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45422904	45422904	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	76	545	0	ENST00000262160.6:c.224T>C	p.Val75Ala	p.V75A	ENST00000262160	NM_005901.5	75	gTt/gCt	2/11	0.205383735971074	4	FACETS	1	0.951	1	0.579	0.509	0.652	INDETERMINATE	1	TRUE	2	0.438446881866019	4		545	431	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271853	15271853	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	34	375	0	ENST00000263388.2:c.6586C>A	p.Leu2196Ile	p.L2196I	ENST00000263388	NM_000435.2	2196	Ctc/Atc	33/33	0.12687325957759	4	FACETS	1	0.935	1	0.656	0.543	0.78	INDETERMINATE	1	TRUE	2	0.438446881866019	4		375	170	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130576	29130576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs558321010	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	44	670	0	ENST00000328354.6:c.134C>T	p.Thr45Met	p.T45M	ENST00000328354	NM_007194.3	45	aCg/aTg	2/15	0.438446881866019	1	FACETS	0.637	0.538	0.744	0.637	0.538	0.744	SUBCLONAL	1	TRUE	0	0.438446881866019	1		670	246	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759781	133759783	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs1008368368	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	14	301	0	ENST00000318560.5:c.2111_2113del	p.Glu704del	p.E704del	ENST00000318560	NM_005157.4	702	GAG/-	11/11	0.12687325957759	4	FACETS	0.928	0.679	1	0.464	0.339	0.61	INDETERMINATE	1	TRUE	2	0.438446881866019	4		301	99	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088770	27088770	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	87	589	0	ENST00000324856.7:c.2382del	p.Ser795AlafsTer38	p.S795Afs*38	ENST00000324856	NM_006015.4	793	atG/at	7/20	0.356155404944716	4	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.438446881866019	4		589	406	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682810	190682810	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	31	184	0	ENST00000441310.2:c.492del	p.Lys164AsnfsTer6	p.K164Nfs*6	ENST00000441310	NM_000534.4	162	gcA/gc	5/13	0.26775162016726	4	FACETS	1	0.928	1	0.648	0.531	0.777	CLONAL	1	TRUE	2	0.438446881866019	4		184	157	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105715	27105717	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs765246223	NA	P-0012928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	29	445	0	ENST00000324856.7:c.5334_5336del	p.Glu1780del	p.E1780del	ENST00000324856	NM_006015.4	1776	GAA/-	20/20	0.356155404944716	4	FACETS	0.924	0.747	1			1	CLONAL	1	TRUE	NA	0.438446881866019	4		445	206	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0012929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	195	519	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.586593518693128	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.586593518693128	1		519	454	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061334	38061334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012929-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	368	930	3	ENST00000250448.2:c.655C>A	p.Arg219Ser	p.R219S	ENST00000250448	NM_004496.3	219	Cgc/Agc	2/2	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.586593518693128	2		933	1176	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105238736	105238736	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012946-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	262	733	0	ENST00000349310.3:c.1226C>T	p.Ala409Val	p.A409V	ENST00000349310	NM_001014432.1	409	gCc/gTc	13/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.67	2		733	760	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0012971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	12	264	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.161318479893999	5	FACETS	0.382	0.268	0.522	0.127	0.089	0.174	INDETERMINATE	1	TRUE	2	0.495226081704005	5		264	221	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099338	193099338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	18	220	0	ENST00000367435.3:c.272G>A	p.Arg91Gln	p.R91Q	ENST00000367435	NM_024529.4	91	cGa/cAa	3/17	0.313372531801273	3	FACETS	0.304	0.229	0.394	0.152	0.114	0.197	SUBCLONAL	1	TRUE	1	0.495226081704005	3		220	298	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435895	149435895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397515556	NA	P-0012971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	85	320	2	ENST00000286301.3:c.2329C>T	p.Arg777Trp	p.R777W	ENST00000286301	NM_005211.3	777	Cgg/Tgg	18/22	1	2	FACETS	0.964	0.859	1	0.964	0.859	1	CLONAL	1	TRUE	1	0.495226081704005	2		322	356	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523589	106523589	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	35	304	0	ENST00000359195.3:c.2741A>T	p.Lys914Ile	p.K914I	ENST00000359195	NM_002649.2	914	aAa/aTa	8/11	1	2	FACETS	0.462	0.38	0.554	0.462	0.38	0.554	SUBCLONAL	1	TRUE	1	0.495226081704005	2		304	306	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422661	47422661	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	130	670	0	ENST00000377045.4:c.133C>G	p.Leu45Val	p.L45V	ENST00000377045	NM_001654.4	45	Cta/Gta	3/16	0.257163872560375	1	FACETS	0.808	0.737	0.881	0.808	0.737	0.881	INDETERMINATE	1	TRUE	0	0.495226081704005	1		670	489	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349294	89349320	+	inframe_deletion	In_Frame_Del	DEL	TCCTTGTACTTTTCTGTGGACTCTTTA	TCCTTGTACTTTTCTGTGGACTCTTTA	-	novel	NA	P-0012971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	29	1028	0	ENST00000301030.4:c.3630_3656del	p.Lys1211_Asp1219del	p.K1211_D1219del	ENST00000301030	NM_001256183.1	1210	gaTAAAGAGTCCACAGAAAAGTACAAGGAc/gac	9/13	0.495226081704005	1	FACETS	0.158	0.126	0.194	0.158	0.126	0.194	SUBCLONAL	1	TRUE	0	0.495226081704005	1		1028	559	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947588	48947595	+	frameshift_variant	Frame_Shift_Del	DEL	CAAGTGAT	CAAGTGAT	-	novel	NA	P-0012971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	27	272	0	ENST00000267163.4:c.1178_1185del	p.Ser393ThrfsTer10	p.S393Tfs*10	ENST00000267163	NM_000321.2	392	gCAAGTGAT/g	12/27	0.429851621348617	1	FACETS	0.427	0.342	0.523	0.427	0.342	0.523	SUBCLONAL	1	TRUE	0	0.495226081704005	1		272	192	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743339	162743363	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGGTGGCTGTGAAAATGCTCCGA	CCTGGTGGCTGTGAAAATGCTCCGA	TG	novel	NA	P-0012971-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	72	342	0	ENST00000367921.3:c.1809_1833delinsTG	p.Leu604GlyfsTer10	p.L604Gfs*10	ENST00000367921	NM_006182.2	603	gtCCTGGTGGCTGTGAAAATGCTCCGA/gtTG	14/18	0.313372531801273	3	FACETS	0.947	0.832	1	0.474	0.416	0.535	CLONAL	1	TRUE	1	0.495226081704005	3		342	383	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0012975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	191	346	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	0.478840333700194	2		346	723	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs775623976	NA	P-0012975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	128	358	0	ENST00000335508.6:c.1873C>G	p.Arg625Gly	p.R625G	ENST00000335508	NM_012433.2	625	Cgt/Ggt	14/25	1	2	FACETS	0.93	0.846	1	0.93	0.846	1	CLONAL	1	TRUE	1	0.478840333700194	2		358	575	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100403	8100403	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	267	597	1	ENST00000346208.3:c.377C>A	p.Ser126Tyr	p.S126Y	ENST00000346208		126	tCc/tAc	3/6	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.478840333700194	2		598	1051	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344603	118344604	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0012975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	301	702	0	ENST00000534358.1:c.2730_2731del	p.Arg910SerfsTer9	p.R910Sfs*9	ENST00000534358	NM_005933.3	910	aGG/a	3/36	0.443410749243898	1	FACETS	0.92	0.868	0.974	0.92	0.868	0.974	CLONAL	1	TRUE	0	0.478840333700194	1		702	1039	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0012977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	352	509	1	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.989	0.941	1	0.989	0.941	1	CLONAL	1	TRUE	1	0.790648825105581	2		510	900	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330611	65330611	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	249	521	0	ENST00000342505.4:c.1035del	p.Lys345AsnfsTer32	p.K345Nfs*32	ENST00000342505	NM_002227.2	345	aaA/aa	8/25	1	2	FACETS	0.88	0.827	0.934	0.88	0.827	0.934	CLONAL	1	TRUE	1	0.790648825105581	2		521	716	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675274	241675276	+	inframe_deletion	In_Frame_Del	DEL	TTA	TTA	-	novel	NA	P-0012977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	201	498	0	ENST00000366560.3:c.546_548del	p.Asn182del	p.N182del	ENST00000366560	NM_000143.3	182	aaTAAa/aaa	4/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.790648825105581	2		498	471	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138915	64138915	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	300	454	0	ENST00000334205.4:c.2287del	p.Arg763AlafsTer21	p.R763Afs*21	ENST00000334205	NM_003942.2	761	gCc/gc	17/17	1	2	FACETS	0.944	0.893	0.996	0.944	0.893	0.996	CLONAL	1	TRUE	1	0.790648825105581	2		454	804	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0012977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	286	443	1	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.957	0.904	1	0.957	0.904	1	CLONAL	1	TRUE	1	0.790648825105581	2		444	756	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647581	23647581	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	280	614	0	ENST00000261584.4:c.286A>T	p.Thr96Ser	p.T96S	ENST00000261584	NM_024675.3	96	Aca/Tca	4/13	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.790648825105581	2		614	706	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56852643	56852643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs966758586	NA	P-0012977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	343	478	0	ENST00000308159.5:c.557C>T	p.Ala186Val	p.A186V	ENST00000308159	NM_014669.4	186	gCg/gTg	6/22	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.790648825105581	2		478	864	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349914	89349916	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs761762028	NA	P-0012977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	461	853	0	ENST00000301030.4:c.3034_3036del	p.Lys1012del	p.K1012del	ENST00000301030	NM_001256183.1	1012	AAG/-	9/13	1	2	FACETS	0.847	0.809	0.886	0.847	0.809	0.886	CLONAL	1	TRUE	1	0.790648825105581	2		853	1376	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0012977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	384	559	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.998	0.951	1	0.998	0.951	1	CLONAL	1	TRUE	1	0.790648825105581	2		564	973	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118954	3118954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	497	830	2	ENST00000078429.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000078429	NM_002067.2	213	cGg/cAg	5/7	1	2	FACETS	0.951	0.911	0.991	0.951	0.911	0.991	CLONAL	1	TRUE	1	0.790648825105581	2		832	1322	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223131	5223131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375155482	NA	P-0012977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	541	777	0	ENST00000357368.4:c.2672C>T	p.Thr891Met	p.T891M	ENST00000357368	NM_002850.3	891	aCg/aTg	18/38	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.790648825105581	2		777	1313	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0012977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	485	373	1	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.790648825105581	2		374	1165	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132635	11132635	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	490	633	0	ENST00000358026.2:c.2854del	p.Glu952LysfsTer5	p.E952Kfs*5	ENST00000358026	NM_001128849.1	951	Ggg/gg	19/36	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.790648825105581	2		633	1165	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314614	30314614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	434	626	0	ENST00000262643.3:c.1163C>T	p.Pro388Leu	p.P388L	ENST00000262643	NM_001238.2	388	cCt/cTt	12/12	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.790648825105581	2		626	1084	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218411	36218411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368960815	NA	P-0012977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	494	620	1	ENST00000222270.7:c.4190C>T	p.Ala1397Val	p.A1397V	ENST00000222270	NM_014727.1	1397	gCg/gTg	16/37	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.790648825105581	2		621	1086	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139638	202139638	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	232	480	0	ENST00000358485.4:c.799A>C	p.Ile267Leu	p.I267L	ENST00000358485	NM_001080125.1	267	Atc/Ctc	6/9	1	2	FACETS	0.836	0.783	0.89	0.836	0.783	0.89	CLONAL	1	TRUE	1	0.790648825105581	2		480	702	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661664	227661664	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs761880048	NA	P-0012977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	240	432	10	ENST00000305123.5:c.1791del	p.His598ThrfsTer38	p.H598Tfs*38	ENST00000305123	NM_005544.2	597	ggG/gg	1/2	1	2	FACETS	0.927	0.871	0.984	0.927	0.871	0.984	CLONAL	1	TRUE	1	0.790648825105581	2		442	655	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624840	9624840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1184049921	NA	P-0012977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	360	460	0	ENST00000353224.5:c.137C>T	p.Thr46Met	p.T46M	ENST00000353224	NM_177990.2	46	aCg/aTg	3/10	1	2	FACETS	0.995	0.947	1	0.995	0.947	1	CLONAL	1	TRUE	1	0.790648825105581	2		460	915	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29115381	29115381	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs781021132	NA	P-0012977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	168	565	0	ENST00000328354.6:c.683+2T>C		p.X228_splice	ENST00000328354	NM_007194.3	228			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.790648825105581	2		565	393	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053531	37053531	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	303	615	0	ENST00000231790.2:c.618del	p.Leu207TyrfsTer22	p.L207Yfs*22	ENST00000231790	NM_000249.3	206	acA/ac	8/19	0.790648825105581	1	FACETS	0.98	0.939	1	0.98	0.939	1	CLONAL	1	TRUE	0	0.790648825105581	1		615	473	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163377	47163377	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	191	396	3	ENST00000409792.3:c.2749del	p.Ser917ValfsTer5	p.S917Vfs*5	ENST00000409792	NM_014159.6	917	Agt/gt	3/21	0.790648825105581	1	FACETS	0.893	0.844	0.943	0.893	0.844	0.943	CLONAL	1	TRUE	0	0.790648825105581	1		399	327	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440912	52440912	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1205668341	NA	P-0012977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	380	556	3	ENST00000460680.1:c.592del	p.Glu198ArgfsTer33	p.E198Rfs*33	ENST00000460680	NM_004656.3	198	Gag/ag	8/17	0.790648825105581	1	FACETS	0.992	0.956	1	0.992	0.956	1	CLONAL	1	TRUE	0	0.790648825105581	1		559	586	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170002338	170002338	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	44	217	0	ENST00000295797.4:c.1157T>C	p.Leu386Pro	p.L386P	ENST00000295797	NM_002740.5	386	cTg/cCg	12/18	1	2	FACETS	0.742	0.634	0.856	0.742	0.634	0.856	SUBCLONAL	1	TRUE	1	0.790648825105581	2		217	150	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946269	55946269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758952853	NA	P-0012977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	284	349	1	ENST00000263923.4:c.3910G>A	p.Gly1304Ser	p.G1304S	ENST00000263923	NM_002253.2	1304	Ggc/Agc	30/30	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.790648825105581	2		350	682	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522433	187522433	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	309	539	0	ENST00000441802.2:c.11630G>T	p.Ser3877Ile	p.S3877I	ENST00000441802	NM_005245.3	3877	aGc/aTc	21/27	1	2	FACETS	0.969	0.917	1	0.969	0.917	1	CLONAL	1	TRUE	1	0.790648825105581	2		539	807	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790795	89790795	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs142250912	NA	P-0012977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	439	647	0	ENST00000336032.3:c.182T>C	p.Leu61Pro	p.L61P	ENST00000336032	NM_006813.2	61	cTa/cCa	1/2	0.790648825105581	3	FACETS	0.959	0.913	1	0.479	0.456	0.503	CLONAL	1	TRUE	1	0.790648825105581	3		647	1616	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553704	106553704	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	339	564	0	ENST00000369096.4:c.1669A>G	p.Thr557Ala	p.T557A	ENST00000369096	NM_001198.3	557	Acc/Gcc	5/7	0.789824118805129	2	FACETS	0.879	0.833	0.925	0.439	0.416	0.463	CLONAL	1	TRUE	0	0.790648825105581	2		564	976	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508793	106508793	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370152741	NA	P-0012977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	373	434	2	ENST00000359195.3:c.787G>A	p.Glu263Lys	p.E263K	ENST00000359195	NM_002649.2	263	Gaa/Aaa	2/11	1	2	FACETS	0.984	0.937	1	0.984	0.937	1	CLONAL	1	TRUE	1	0.790648825105581	2		436	959	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850322	128850322	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	442	736	0	ENST00000249373.3:c.1585G>T	p.Gly529Cys	p.G529C	ENST00000249373	NM_005631.4	529	Ggc/Tgc	9/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.790648825105581	2		736	1070	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566369	141566369	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	242	363	0	ENST00000220592.5:c.1043C>T	p.Ala348Val	p.A348V	ENST00000220592	NM_012154.3	348	gCa/gTa	9/19	1	2	FACETS	0.987	0.929	1	0.987	0.929	1	CLONAL	1	TRUE	1	0.790648825105581	2		363	620	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	344	521	2	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.953	0.905	1	0.953	0.905	1	CLONAL	1	TRUE	1	0.790648825105581	2		523	913	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231371	98231371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1053507002	NA	P-0012977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	508	668	0	ENST00000331920.6:c.1912C>T	p.Arg638Cys	p.R638C	ENST00000331920	NM_000264.3	638	Cgc/Tgc	14/24	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.790648825105581	2		668	1244	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760613	133760613	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	574	869	0	ENST00000318560.5:c.2940del	p.Val981PhefsTer88	p.V981Ffs*88	ENST00000318560	NM_005157.4	979	gCc/gc	11/11	1	2	FACETS	0.934	0.897	0.971	0.934	0.897	0.971	CLONAL	1	TRUE	1	0.790648825105581	2		869	1555	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932171	39932171	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555918056	NA	P-0012977-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	391	726	0	ENST00000378444.4:c.2428C>T	p.Arg810Ter	p.R810*	ENST00000378444	NM_001123385.1	810	Cga/Tga	4/15	0.790648825105581	1	FACETS	0.715	0.683	0.746	0.715	0.683	0.746	SUBCLONAL	1	TRUE	0	0.790648825105581	1		726	837	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118704	115118706	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0012998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	288	654	0	ENST00000257566.3:c.635_637del	p.Asn212del	p.N212del	ENST00000257566	NM_016569.3	212	aACAtt/att	2/8	0.542761731322354	1	FACETS	0.746	0.702	0.791	0.746	0.702	0.791	SUBCLONAL	1	TRUE	0	0.542761731322354	1		654	1037	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061220	38061225	+	inframe_deletion	In_Frame_Del	DEL	CGTTCT	CGTTCT	-	novel	NA	P-0012998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	207	535	0	ENST00000250448.2:c.764_769del	p.Glu255_Asn256del	p.E255_N256del	ENST00000250448	NM_004496.3	255	gAGAACGgc/ggc	2/2	1	2	FACETS	0.941	0.875	1	0.941	0.875	1	CLONAL	1	TRUE	1	0.542761731322354	2		535	811	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740479	58740479	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012998-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1391	569	985	0	ENST00000305921.3:c.1384C>T	p.Gln462Ter	p.Q462*	ENST00000305921	NM_003620.3	462	Caa/Taa	6/6	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.542761731322354	2		985	1960	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	18	715	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		715	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0013019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1371	56	709	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		709	1427	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0013035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	107	439	1	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	0.32948912008105	3	FACETS	1	0.96	1	0.57	0.511	0.631	CLONAL	1	TRUE	1	0.32948912008105	3		440	664	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0013035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	299	621	1	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.32948912008105	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.32948912008105	3		622	962	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391062	139391062	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	91	361	0	ENST00000277541.6:c.7129C>G	p.Pro2377Ala	p.P2377A	ENST00000277541	NM_017617.3	2377	Cct/Gct	34/34	1	2	FACETS	0.939	0.836	1	0.939	0.836	1	CLONAL	1	TRUE	1	0.32948912008105	2		361	588	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222160	5222160	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013035-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	365	611	1	ENST00000357368.4:c.3175A>G	p.Asn1059Asp	p.N1059D	ENST00000357368	NM_002850.3	1059	Aac/Gac	19/38	0.32948912008105	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.32948912008105	4		612	1335	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013053-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	423	715	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.296373146782068	5	FACETS	0.925	0.885	0.966	0.925	0.885	0.966	INDETERMINATE	3	TRUE	2	0.592025541436107	5		715	972	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578509	7578509	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519978	NA	P-0013053-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	438	581	2	ENST00000269305.4:c.421T>G	p.Cys141Gly	p.C141G	ENST00000269305	NM_001126112.2	141	Tgc/Ggc	5/11	0.592025541436107	2	FACETS	0.958	0.922	0.994	0.958	0.922	0.994	CLONAL	2	TRUE	0	0.592025541436107	2		583	772	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506428	148506428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013053-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	224	630	0	ENST00000320356.2:c.2084C>T	p.Ser695Leu	p.S695L	ENST00000320356	NM_004456.4	695	tCg/tTg	18/20	0.59172486189877	3	FACETS	0.889	0.827	0.953	0.445	0.413	0.477	CLONAL	1	TRUE	1	0.592025541436107	3		630	1103	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0013062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	88	440	2	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	1	2	FACETS	0.951	0.841	1	0.951	0.841	1	CLONAL	1	TRUE	1	0.221163963864138	2		442	837	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0013079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	68	332	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	0.46456463041571	2	FACETS	0.564	0.491	0.642	0.282	0.245	0.321	SUBCLONAL	1	TRUE	0	0.46456463041571	2		332	519	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578466	7578466	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786202752	NA	P-0013079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	165	446	0	ENST00000269305.4:c.464C>A	p.Thr155Asn	p.T155N	ENST00000269305	NM_001126112.2	155	aCc/aAc	5/11	0.46456463041571	1	FACETS	0.866	0.798	0.935	0.866	0.798	0.935	CLONAL	1	TRUE	0	0.46456463041571	1		446	630	SUCCESS
YES1	7525	MSKCC	GRCh37	18	751726	751726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	97	307	0	ENST00000314574.4:c.350G>A	p.Arg117Lys	p.R117K	ENST00000314574	NM_005433.3	117	aGa/aAa	3/12	0.46456463041571	1	FACETS	0.799	0.718	0.885	0.799	0.718	0.885	SUBCLONAL	1	TRUE	0	0.46456463041571	1		307	401	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266225	198266225	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	68	288	0	ENST00000335508.6:c.2395G>C	p.Asp799His	p.D799H	ENST00000335508	NM_012433.2	799	Gat/Cat	17/25	1	2	FACETS	0.723	0.631	0.821	0.723	0.631	0.821	SUBCLONAL	1	TRUE	1	0.46456463041571	2		288	405	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960100	151960100	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0013079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	362	516	0	ENST00000262189.6:c.1299+1G>A		p.X433_splice	ENST00000262189	NM_170606.2	433			NA	2	FACETS	0.953	0.908	0.997			1	INDETERMINATE	2	TRUE	NA	0.46456463041571	2		516	818	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562710	29562710	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs863224660	NA	P-0013079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	196	602	1	ENST00000356175.3:c.3790G>T	p.Glu1264Ter	p.E1264*	ENST00000356175	NM_000267.3	1264	Gaa/Taa	28/57	0.46456463041571	1	FACETS	0.936	0.87	1	0.936	0.87	1	CLONAL	1	TRUE	0	0.46456463041571	1		603	692	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427700	49427700	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	167	488	1	ENST00000301067.7:c.10788del	p.Asn3597ThrfsTer61	p.N3597Tfs*61	ENST00000301067	NM_003482.3	3596	cgG/cg	39/54	1	2	FACETS	0.925	0.852	1	0.925	0.852	1	CLONAL	1	TRUE	1	0.46456463041571	2		489	777	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10273394	10273397	+	frameshift_variant	Frame_Shift_Del	DEL	TTCT	TTCT	-	novel	NA	P-0013079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	235	745	0	ENST00000340748.4:c.906_909del	p.Lys302AsnfsTer5	p.K302Nfs*5	ENST00000340748		302	aaAGAA/aa	12/40	1	2	FACETS	0.813	0.757	0.87	0.813	0.757	0.87	CLONAL	1	TRUE	1	0.46456463041571	2		745	1245	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0013091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	647	346	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.334805558498145	8	FACETS	1	0.992	1	1	0.997	1	CLONAL	7	FALSE	2	0.334805558498145	8		346	1047	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0013091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	377	698	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.334805558498145	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	3	FALSE	0	0.334805558498145	2		698	679	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052632	42052632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779811318	NA	P-0013091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	438	941	2	ENST00000219905.7:c.7303C>T	p.Arg2435Trp	p.R2435W	ENST00000219905	NM_001164273.1	2435	Cgg/Tgg	20/24	0.28032874598073	1	FACETS	0.925	0.883	0.967	1	0.997	1	CLONAL	2	FALSE	0	0.334805558498145	1		943	1178	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309731	30309731	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	202	525	0	ENST00000307677.4:c.291T>G	p.Phe97Leu	p.F97L	ENST00000307677	NM_138578.1	97	ttT/ttG	2/3	0.334805558498145	3	FACETS	0.906	0.842	0.973	0.906	0.842	0.973	CLONAL	2	FALSE	1	0.334805558498145	3		525	777	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907719	76907719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013091-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	167	1118	2	ENST00000373344.5:c.4442G>A	p.Arg1481Gln	p.R1481Q	ENST00000373344	NM_000489.3	1481	cGg/cAg	15/35	0.313538475758351	0	FACETS	0.588	0.539	0.639			1	SUBCLONAL	1	FALSE	0	0.334805558498145	0		1120	1128	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574693	64574693	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1114167472	NA	P-0013095-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	263	409	0	ENST00000312049.6:c.784-2A>G		p.X262_splice	ENST00000312049	NM_130799.2	262			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		409	546	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0013096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	52	393	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.748	0.635	0.872	0.748	0.635	0.872	SUBCLONAL	1	TRUE	1	0.17	2		393	818	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0013096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	90	354	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.17	2		354	1051	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0013096-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1445	116	882	4	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.874	0.785	0.97	0.874	0.785	0.97	CLONAL	1	TRUE	1	0.17	2		886	1561	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061334	38061334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013100-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	969	930	3	ENST00000250448.2:c.655C>A	p.Arg219Ser	p.R219S	ENST00000250448	NM_004496.3	219	Cgc/Agc	2/2	0.909486809233265	3	FACETS	1	0.998	1	0.742	0.721	0.763	CLONAL	1	TRUE	1	0.909486809233265	3		933	2088	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692844	89692844	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1114167629	NA	P-0013100-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	188	134	0	ENST00000371953.3:c.328C>T	p.Gln110Ter	p.Q110*	ENST00000371953	NM_000314.4	110	Caa/Taa	5/9	0.909486809233265	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.909486809233265	2		134	204	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459522	50459522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1410124404	NA	P-0013100-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	495	519	1	ENST00000331340.3:c.811G>A	p.Val271Ile	p.V271I	ENST00000331340	NM_006060.4	271	Gtc/Atc	7/8	0.902824546537928	4	FACETS	0.936	0.899	0.974	0.936	0.899	0.974	CLONAL	2	TRUE	2	0.909486809233265	4		520	1110	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0013108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	119	382	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.294168177304774	3	FACETS	0.794	0.729	0.861	0.794	0.729	0.861	INDETERMINATE	2	TRUE	1	0.699600073119161	3		382	289	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0013116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	428	414	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.735519376477266	1	FACETS	0.984	0.946	1	0.984	0.946	1	CLONAL	1	TRUE	0	0.735519376477266	1		416	748	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868903	117868903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1318	141	454	0	ENST00000297338.2:c.796G>A	p.Glu266Lys	p.E266K	ENST00000297338	NM_006265.2	266	Gag/Aag	7/14	0.71691655074633	3	FACETS	0.359	0.326	0.395	0.18	0.163	0.198	SUBCLONAL	1	TRUE	1	0.735519376477266	3		454	1459	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090496	5090496	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs750978665	NA	P-0013116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	326	390	0	ENST00000381652.3:c.2812C>T	p.Arg938Ter	p.R938*	ENST00000381652	NM_004972.3	938	Cga/Tga	21/25	0.735519376477266	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.735519376477266	1		390	551	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63816969	63816969	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	275	329	1	ENST00000279873.7:c.940G>A	p.Gly314Ser	p.G314S	ENST00000279873	NM_032199.2	314	Ggt/Agt	6/10	0.735519376477266	1	FACETS	0.959	0.913	1	0.959	0.913	1	CLONAL	1	TRUE	0	0.735519376477266	1		330	493	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039506	49039506	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1555294636	NA	P-0013116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	497	355	1	ENST00000267163.4:c.2489+2T>C		p.X830_splice	ENST00000267163	NM_000321.2	830			0.735519376477266	2	FACETS	0.907	0.879	0.935	0.907	0.879	0.935	CLONAL	2	TRUE	0	0.735519376477266	2		356	745	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410035	63410035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013116-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	43	344	0	ENST00000330258.3:c.3132G>A	p.Met1044Ile	p.M1044I	ENST00000330258	NM_152424.3	1044	atG/atA	2/2	1	1	FACETS	0.107	0.089	0.127	0.107	0.089	0.127	SUBCLONAL	1	TRUE	0	0.735519376477266	1		344	693	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	111	126	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.41	1		126	389	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0013150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	295	661	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	0.41	2		661	962	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140454029	140454029	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	231	418	0	ENST00000288602.6:c.1699T>G	p.Leu567Val	p.L567V	ENST00000288602	NM_004333.4	567	Tta/Gta	14/18	1	2	FACETS	0.776	0.726	0.827	1	0.993	1	SUBCLONAL	2	TRUE	1	0.41	2		418	726	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179198	123179198	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	104	309	0	ENST00000218089.9:c.647G>C	p.Arg216Pro	p.R216P	ENST00000218089	NM_001042749.1	216	cGa/cCa	8/35	1	1	FACETS	0.75	0.674	0.83	0.75	0.674	0.83	SUBCLONAL	1	TRUE	0	0.41	1		309	538	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820697	3820703	+	frameshift_variant	Frame_Shift_Del	DEL	GACTGTA	GACTGTA	-	novel	NA	P-0013150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	195	582	1	ENST00000262367.5:c.2748_2754del	p.Thr917ArgfsTer8	p.T917Rfs*8	ENST00000262367	NM_004380.2	916	ccTACAGTC/cc	14/31	0.0844002913517962	0	FACETS	0.786	0.73	0.844			1	INDETERMINATE	1	TRUE	0	0.41	0		583	714	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41554479	41554491	+	protein_altering_variant	In_Frame_Del	DEL	GCCACTTATTACA	GCCACTTATTACA	T	novel	NA	P-0013150-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	159	645	0	ENST00000263253.7:c.3565_3577delinsT	p.Ala1189_Ser1193delinsCys	p.A1189_S1193delinsC	ENST00000263253	NM_001429.3	1189	GCCACTTATTACAgt/Tgt	19/31	0.0844002913517962	0	FACETS	0.584	0.536	0.634			1	INDETERMINATE	1	TRUE	0	0.41	0		645	784	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	38	247	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.245539249958292	2		247	230	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0013153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	52	849	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.245539249958292	2		849	369	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508823	106508823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	39	443	0	ENST00000359195.3:c.817C>T	p.Arg273Cys	p.R273C	ENST00000359195	NM_002649.2	273	Cgc/Tgc	2/11	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.245539249958292	2		443	265	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729115	66729115	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs727504819	NA	P-0013153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	38	627	0	ENST00000307102.5:c.323G>T	p.Arg108Leu	p.R108L	ENST00000307102	NM_002755.3	108	cGg/cTg	3/11	1	2	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	TRUE	1	0.245539249958292	2		627	299	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573492	48573496	+	frameshift_variant	Frame_Shift_Del	DEL	CATAG	CATAG	-	novel	NA	P-0013153-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	44	609	0	ENST00000342988.3:c.76_80del	p.His26ThrfsTer6	p.H26Tfs*6	ENST00000342988	NM_005359.5	26	CATAGa/a	2/12	0.245539249958292	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.245539249958292	1		609	257	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0013162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	32	577	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	1	2	FACETS	0.422	0.34	0.514	0.422	0.34	0.514	SUBCLONAL	1	TRUE	1	0.15	2		577	1012	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519999	NA	P-0013162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	33	638	0	ENST00000269305.4:c.716A>G	p.Asn239Ser	p.N239S	ENST00000269305	NM_001126112.2	239	aAc/aGc	7/11	1	2	FACETS	0.491	0.398	0.597	0.491	0.398	0.597	SUBCLONAL	1	TRUE	1	0.15	2		638	896	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100117	157100119	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs797045268	NA	P-0013162-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	14	35	0	ENST00000346085.5:c.1069_1071del	p.Gly357del	p.G357del	ENST00000346085	NM_020732.3	352	GGC/-	1/20	1	2	FACETS	0.982	0.72	1	1	0.914	1	CLONAL	2	TRUE	1	0.15	2		35	95	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441333	52441333	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0013170-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	181	665	1	ENST00000460680.1:c.438-1G>T		p.X146_splice	ENST00000460680	NM_004656.3	146			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		666	409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0013182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	306	761	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.273959888641272	2	FACETS	1	0.993	1	0.693	0.652	0.735	CLONAL	1	TRUE	0	0.332730365056101	2		761	1327	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381485	81381485	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1213509732	NA	P-0013182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	118	918	0	ENST00000222390.5:c.576C>A	p.Ser192Arg	p.S192R	ENST00000222390	NM_000601.4	192	agC/agA	5/18	0.315997644380228	1	FACETS	0.47	0.423	0.521	0.47	0.423	0.521	SUBCLONAL	1	TRUE	0	0.332730365056101	1		918	1257	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120035	70120035	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	16	53	0	ENST00000245479.2:c.1037C>G	p.Pro346Arg	p.P346R	ENST00000245479	NM_000346.3	346	cCg/cGg	3/3	0.332730365056101	3	FACETS	1	0.825	1	0.378	0.283	0.487	CLONAL	1	TRUE	0	0.332730365056101	3		53	99	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289710	15289710	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	517	741	0	ENST00000263388.2:c.3761C>A	p.Pro1254Gln	p.P1254Q	ENST00000263388	NM_000435.2	1254	cCa/cAa	23/33	0.332730365056101	6	FACETS	1	0.991	1	0.845	0.809	0.881	CLONAL	3	TRUE	2	0.332730365056101	6		741	1531	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314932	1314932	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	366	783	0	ENST00000400841.2:c.729G>T	p.Met243Ile	p.M243I	ENST00000400841		243	atG/atT	6/6	1	2	FACETS	0.796	0.754	0.839	1	0.995	1	SUBCLONAL	2	TRUE	1	0.332730365056101	2		783	1382	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183725	10183725	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs5030826	NA	P-0013234-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	121	410	1	ENST00000256474.2:c.194C>A	p.Ser65Ter	p.S65*	ENST00000256474	NM_000551.3	65	tCg/tAg	1/3	0.339542758016541	0	FACETS	0.653	0.597	0.709			1	SUBCLONAL	2	TRUE	0	0.359703125729408	0		411	330	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144909	47144909	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1373021859	NA	P-0013234-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	153	459	0	ENST00000409792.3:c.4844T>C	p.Ile1615Thr	p.I1615T	ENST00000409792	NM_014159.6	1615	aTa/aCa	7/21	0.283138081306776	0	FACETS	0.671	0.62	0.722			1	SUBCLONAL	2	TRUE	0	0.359703125729408	0		459	406	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945452	151945452	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs76704065	NA	P-0013234-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	50	363	0	ENST00000262189.6:c.2067G>T	p.Met689Ile	p.M689I	ENST00000262189	NM_170606.2	689	atG/atT	14/59	0.140231990459024	4	FACETS	0.95	0.808	1	0.475	0.404	0.553	INDETERMINATE	1	TRUE	2	0.359703125729408	4		363	398	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18473949	18473949	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1195643107	NA	P-0013234-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	159	460	0	ENST00000266497.5:c.1191T>A	p.His397Gln	p.H397Q	ENST00000266497		397	caT/caA	6/31	0.359703125729408	3	FACETS	1	0.985	1	0.673	0.618	0.731	CLONAL	1	TRUE	1	0.359703125729408	3		460	775	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668670	52668670	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013234-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	223	638	0	ENST00000394830.3:c.1249del	p.Tyr417ThrfsTer21	p.Y417Tfs*21	ENST00000394830	NM_018313.4	417	Tac/ac	12/30	0.358716278590487	0	FACETS	0.62	0.581	0.661			1	SUBCLONAL	2	TRUE	0	0.359703125729408	0		638	640	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0013243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	234	284	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.208191782415125	4	FACETS	0.848	0.796	0.9	0.848	0.796	0.9	INDETERMINATE	2	TRUE	2	0.768959232816523	4		284	635	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0013243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	66	273	0				ENST00000310581	NM_198253.2	-/1132			0.603163561417412	1	FACETS	0.729	0.651	0.807	0.729	0.651	0.807	SUBCLONAL	1	TRUE	0	0.768959232816523	1		273	145	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412203	139412203	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0013243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	24	513	0	ENST00000277541.6:c.1441+1G>A		p.X481_splice	ENST00000277541	NM_017617.3	481			0.208191782415125	4	FACETS	0.259	0.202	0.324	0.129	0.101	0.162	INDETERMINATE	1	TRUE	2	0.768959232816523	4		513	427	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399862	139399862	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	74	656	0	ENST00000277541.6:c.4486T>C	p.Cys1496Arg	p.C1496R	ENST00000277541	NM_017617.3	1496	Tgc/Cgc	25/34	0.208191782415125	4	FACETS	0.795	0.699	0.898	0.398	0.349	0.449	INDETERMINATE	1	TRUE	2	0.768959232816523	4		656	428	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791750	42791750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	33	517	1	ENST00000575354.2:c.636G>T	p.Lys212Asn	p.K212N	ENST00000575354	NM_015125.3	212	aaG/aaT	5/20	0.768959232816523	1	FACETS	0.189	0.154	0.228	0.189	0.154	0.228	SUBCLONAL	1	TRUE	0	0.768959232816523	1		518	279	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123899	46123903	+	frameshift_variant	Frame_Shift_Del	DEL	TACTT	TACTT	-	novel	NA	P-0013243-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	52	462	0	ENST00000334344.6:c.167_171del	p.Thr56ArgfsTer8	p.T56Rfs*8	ENST00000334344	NM_152641.2	55	acTACTTta/acta	2/21	0.26875523987977	4	FACETS	0.376	0.319	0.438	0.188	0.159	0.219	INDETERMINATE	1	TRUE	2	0.768959232816523	4		462	637	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0013266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	17	368	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.368104402327158	2	FACETS	0.921	0.725	1	0.921	0.725	1	CLONAL	2	FALSE	0	0.45010444843903	2		368	41	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0013266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	227	827	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.420154947099097	4	FACETS	0.98	0.932	1			1	CLONAL	4	FALSE	NA	0.45010444843903	4		828	373	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0013266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	27	274	1	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.238888913096568	5	FACETS	1	0.828	1	1	0.828	1	INDETERMINATE	3	FALSE	2	0.45010444843903	5		275	67	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0013266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	25	292	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	0.207734483936453	3	FACETS	1	0.883	1	1	0.883	1	INDETERMINATE	3	FALSE	0	0.45010444843903	3		292	43	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258779	115258779	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0013266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	15	438	0	ENST00000369535.4:c.3G>A	p.Met1?	p.M1?	ENST00000369535	NM_002524.4	1	atG/atA	2/7	0.378667262294592	3	FACETS	1	0.794	1	0.537	0.401	0.693	CLONAL	1	FALSE	1	0.45010444843903	3		438	76	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141997	108141997	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	17	427	0	ENST00000278616.4:c.2941C>A	p.Arg981Ser	p.R981S	ENST00000278616	NM_000051.3	981	Cgt/Agt	20/63	0.378667262294592	3	FACETS	0.798	0.616	0.998	0.798	0.616	0.998	CLONAL	2	FALSE	1	0.45010444843903	3		427	58	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476408	88476408	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	16	395	0	ENST00000360948.2:c.1724A>C	p.Lys575Thr	p.K575T	ENST00000360948	NM_001012338.2	575	aAg/aCg	15/19	0.291606613791872	4	FACETS	0.973	0.745	1	0.973	0.745	1	CLONAL	2	FALSE	2	0.45010444843903	4		395	53	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	81	126	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.58	2		126	265	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0013268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	45	255	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	1	2	FACETS	0.379	0.319	0.446	0.379	0.319	0.446	SUBCLONAL	1	TRUE	1	0.58	2		255	409	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631837	90631837	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519736	NA	P-0013268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	192	513	0	ENST00000330062.3:c.516G>C	p.Arg172Ser	p.R172S	ENST00000330062	NM_002168.2	172	agG/agC	4/11	1	2	FACETS	0.85	0.788	0.914	0.85	0.788	0.914	CLONAL	1	TRUE	1	0.58	2		513	779	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233073	69233073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013268-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	168	427	1	ENST00000462284.1:c.938C>T	p.Ser313Leu	p.S313L	ENST00000462284	NM_002392.5	313	tCa/tTa	11/11	1	2	FACETS	0.808	0.744	0.874	0.808	0.744	0.874	CLONAL	1	TRUE	1	0.58	2		428	717	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0013271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	93	439	1	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	0.646985635542098	3	FACETS	0.988	0.885	1	0.494	0.442	0.548	CLONAL	1	TRUE	1	0.646985635542098	3		440	385	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143000	7143000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369025474	NA	P-0013271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	134	464	0	ENST00000302850.5:c.2369C>T	p.Thr790Met	p.T790M	ENST00000302850	NM_000208.2	790	aCg/aTg	12/22	0.646985635542098	7	FACETS	1	0.976	1			1	CLONAL	1	TRUE	NA	0.646985635542098	7		464	888	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900986	114900986	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	50	1112	0	ENST00000543371.1:c.596C>G	p.Pro199Arg	p.P199R	ENST00000543371	NM_001198531.1	199	cCc/cGc	6/14	0.271093765309762	3	FACETS	0.246	0.208	0.288			1	INDETERMINATE	1	TRUE	NA	0.646985635542098	3		1112	832	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148885	119148887	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0013271-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	139	332	0	ENST00000264033.4:c.1105_1107del	p.Glu369del	p.E369del	ENST00000264033	NM_005188.3	369	GAA/-	8/16	0.646985635542098	2	FACETS	0.99	0.929	1	0.99	0.929	1	CLONAL	2	TRUE	0	0.646985635542098	2		332	217	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490261	29490290	+	inframe_deletion	In_Frame_Del	DEL	GAAATCTGCCATTTTCTTCACACCTGTCGT	GAAATCTGCCATTTTCTTCACACCTGTCGT	-	novel	NA	P-0013280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	71	907	0	ENST00000356175.3:c.349_378del	p.Ile117_Glu126del	p.I117_E126del	ENST00000356175	NM_000267.3	116	GAAATCTGCCATTTTCTTCACACCTGTCGT/-	4/57	0.157097208167205	1	FACETS	0.834	0.726	0.951	0.834	0.726	0.951	CLONAL	1	FALSE	0	0.157097208167205	1		907	999	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578499	7578510	+	inframe_deletion	In_Frame_Del	DEL	TGCACAGGGCAG	TGCACAGGGCAG	-	novel	NA	P-0013280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	42	760	0	ENST00000269305.4:c.420_431del	p.Cys141_Gln144del	p.C141_Q144del	ENST00000269305	NM_001126112.2	140	acCTGCCCTGTGCAg/acg	5/11	0.157097208167205	1	FACETS	0.624	0.519	0.741	0.624	0.519	0.741	SUBCLONAL	1	FALSE	0	0.157097208167205	1		760	790	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0013281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	188	284	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.309157469043025	3	FACETS	0.858	0.799	0.919	0.858	0.799	0.919	CLONAL	2	FALSE	1	0.511395606722473	3		284	538	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882025	NA	P-0013281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	845	859	0	ENST00000269305.4:c.646G>T	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ttg	6/11	0.511395606722473	6	FACETS	1	0.998	1			1	CLONAL	7	FALSE	NA	0.511395606722473	6		859	903	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909629	76909629	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs919106518	NA	P-0013281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	357	1149	4	ENST00000373344.5:c.4276C>T	p.Arg1426Ter	p.R1426*	ENST00000373344	NM_000489.3	1426	Cga/Tga	14/35	0.520813534325505	1	FACETS	0.769	0.735	0.802	1	0.996	1	SUBCLONAL	2	FALSE	0	0.511395606722473	1		1153	676	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455640	189455640	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013281-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	45	471	0	ENST00000264731.3:c.174C>G	p.Ile58Met	p.I58M	ENST00000264731	NM_003722.4	58	atC/atG	2/14	0.287809120455998	3	FACETS	0.558	0.47	0.655	0.279	0.235	0.328	INDETERMINATE	1	FALSE	1	0.511395606722473	3		471	396	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0013291-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	154	264	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.808859665386598	4	FACETS	0.979	0.898	1	0.326	0.299	0.355	CLONAL	1	TRUE	1	0.812139447265747	4		264	702	SUCCESS
ATR	545	MSKCC	GRCh37	3	142184028	142184028	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013291-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	214	541	0	ENST00000350721.4:c.6952G>A	p.Asp2318Asn	p.D2318N	ENST00000350721	NM_001184.3	2318	Gat/Aat	41/47	0.808859665386598	4	FACETS	0.903	0.838	0.969	0.301	0.279	0.323	CLONAL	1	TRUE	1	0.812139447265747	4		541	1058	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247217	153247217	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013291-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	767	707	0	ENST00000281708.4:c.1585G>T	p.Glu529Ter	p.E529*	ENST00000281708	NM_033632.3	529	Gag/Tag	10/12	0.8092188222184	2	FACETS	0.977	0.957	0.996	0.977	0.957	0.996	CLONAL	2	TRUE	0	0.812139447265747	2		707	967	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151847995	151847995	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0013291-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	204	387	0	ENST00000262189.6:c.12764C>G	p.Ser4255Ter	p.S4255*	ENST00000262189	NM_170606.2	4255	tCa/tGa	51/59	0.794115632864499	1	FACETS	0.893	0.846	0.939	0.893	0.846	0.939	CLONAL	1	TRUE	0	0.812139447265747	1		387	334	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907037	101907037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013291-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	316	323	0	ENST00000374994.4:c.997G>A	p.Asp333Asn	p.D333N	ENST00000374994	NM_004612.2	333	Gat/Aat	6/9	0.8092188222184	2	FACETS	0.983	0.952	1	0.983	0.952	1	CLONAL	2	TRUE	0	0.812139447265747	2		323	396	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426270	49426270	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0013291-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	420	803	0	ENST00000301067.7:c.12218C>G	p.Ser4073Ter	p.S4073*	ENST00000301067	NM_003482.3	4073	tCa/tGa	39/54	0.812139447265747	2	FACETS	1	0.985	1	0.531	0.508	0.555	CLONAL	1	TRUE	0	0.812139447265747	2		803	974	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864858	57864858	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013291-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	589	1024	0	ENST00000228682.2:c.2335A>G	p.Thr779Ala	p.T779A	ENST00000228682	NM_005269.2	779	Aca/Gca	12/12	0.812139447265747	2	FACETS	0.992	0.955	1	0.496	0.477	0.515	CLONAL	1	TRUE	0	0.812139447265747	2		1024	1462	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054727	13054727	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0013291-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	407	699	0	ENST00000316448.5:c.1254G>C	p.Ter418TyrextTer9	p.*418Yext*9	ENST00000316448	NM_004343.3	418	taG/taC	9/9	0.426670693850006	3	FACETS	1	0.989	1	0.561	0.534	0.589	INDETERMINATE	1	TRUE	1	0.812139447265747	3		699	1256	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513776	41513776	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013291-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	354	522	0	ENST00000263253.7:c.680C>A	p.Ser227Tyr	p.S227Y	ENST00000263253	NM_001429.3	227	tCt/tAt	2/31	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.812139447265747	2		522	828	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	213	461	0	ENST00000206249.3:c.1610A>G	p.Tyr537Cys	p.Y537C	ENST00000206249	NM_000125.3	537	tAt/tGt	8/8	0.308345969451894	3	FACETS	0.921	0.857	0.987	0.921	0.857	0.987	CLONAL	2	TRUE	1	0.313208299305572	3		461	854	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692902	89692902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909218	NA	P-0013296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	173	381	0	ENST00000371953.3:c.386G>A	p.Gly129Glu	p.G129E	ENST00000371953	NM_000314.4	129	gGa/gAa	5/9	0.308345969451894	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.313208299305572	3		381	587	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092993	27092993	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0013296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	165	601	0	ENST00000324856.7:c.2924T>G	p.Leu975Ter	p.L975*	ENST00000324856	NM_006015.4	975	tTa/tGa	10/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.313208299305572	2		601	985	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711892	89711892	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	108	390	0	ENST00000371953.3:c.510T>G	p.Ser170Arg	p.S170R	ENST00000371953	NM_000314.4	170	agT/agG	6/9	0.308345969451894	3	FACETS	1	0.955	1	0.557	0.5	0.617	CLONAL	1	TRUE	1	0.313208299305572	3		390	716	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252857	10252857	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	202	425	0	ENST00000340748.4:c.3108C>G	p.His1036Gln	p.H1036Q	ENST00000340748		1036	caC/caG	29/40	0.308345969451894	3	FACETS	0.991	0.921	1	0.991	0.921	1	CLONAL	2	TRUE	1	0.313208299305572	3		425	753	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589586	67589612	+	inframe_deletion	In_Frame_Del	DEL	ATGAATATAACACTCAGTTTCAAGAAA	ATGAATATAACACTCAGTTTCAAGAAA	-	novel	NA	P-0013296-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	41	269	0	ENST00000274335.5:c.1350_1376del	p.His450_Lys459delinsGln	p.H450_K459delinsQ	ENST00000274335		450	cATGAATATAACACTCAGTTTCAAGAAAaa/caa	10/15	1	2	FACETS	0.75	0.627	0.887	0.75	0.627	0.887	SUBCLONAL	1	TRUE	1	0.313208299305572	2		269	349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0013304-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	658	354	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.955368661116137	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.973309289741578	1		354	687	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	29	126	0				ENST00000310581	NM_198253.2	-/1132			0.259532191132679	1	FACETS	0.913	0.738	1	0.913	0.738	1	CLONAL	1	FALSE	0	0.259532191132679	1		126	213	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241722	55241722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1051753269	NA	P-0013305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	165	486	1	ENST00000275493.2:c.2170G>A	p.Gly724Ser	p.G724S	ENST00000275493	NM_005228.3	724	Ggc/Agc	18/28	0.259532191132679	3	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	FALSE	1	0.259532191132679	3		487	703	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510627	38510627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	231	877	0	ENST00000254066.5:c.881G>A	p.Arg294Gln	p.R294Q	ENST00000254066	NM_000964.3	294	cGg/cAg	7/9	0.176486751855433	2	FACETS	0.991	0.925	1	0.991	0.925	1	CLONAL	2	FALSE	0	0.259532191132679	2		877	898	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578537	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs879254214	NA	P-0013305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	106	528	1	ENST00000269305.4:c.393_395del	p.Asn131del	p.N131del	ENST00000269305	NM_001126112.2	131	aaCAAg/aag	5/11	0.176486751855433	2	FACETS	1	0.962	1	0.576	0.517	0.639	CLONAL	1	FALSE	0	0.259532191132679	2		529	709	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437539	52437540	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0013305-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	142	1093	1	ENST00000460680.1:c.1621_1622del	p.Val541Ter	p.V541*	ENST00000460680	NM_004656.3	541	GTt/t	13/17	0.168568228359482	0	FACETS	0.829	0.755	0.908			1	CLONAL	1	FALSE	0	0.259532191132679	0		1094	977	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148504782	148504782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	34	513	0	ENST00000320356.2:c.2212G>A	p.Ala738Thr	p.A738T	ENST00000320356	NM_004456.4	738	Gcc/Acc	20/20	1	2	FACETS	0.244	0.199	0.295	0.244	0.199	0.295	SUBCLONAL	1	TRUE	1	0.525744820093514	2		513	530	SUCCESS
FH	2271	MSKCC	GRCh37	1	241669417	241669417	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	29	446	0	ENST00000366560.3:c.790G>C	p.Ala264Pro	p.A264P	ENST00000366560	NM_000143.3	264	Gct/Cct	6/10	1	2	FACETS	0.194	0.155	0.239	0.194	0.155	0.239	SUBCLONAL	1	TRUE	1	0.525744820093514	2		446	568	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183694	10183694	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	113	526	0	ENST00000256474.2:c.163G>T	p.Glu55Ter	p.E55*	ENST00000256474	NM_000551.3	55	Gag/Tag	1/3	0.525744820093514	1	FACETS	0.99	0.903	1	0.99	0.903	1	CLONAL	1	TRUE	0	0.525744820093514	1		526	320	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426856	6426856	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	79	609	0	ENST00000356142.4:c.49A>T	p.Thr17Ser	p.T17S	ENST00000356142	NM_018890.3	17	Act/Tct	2/7	1	2	FACETS	0.669	0.591	0.753	0.669	0.591	0.753	SUBCLONAL	1	TRUE	1	0.525744820093514	2		609	449	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827568	72827568	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	73	1169	0	ENST00000268489.5:c.9013A>C	p.Lys3005Gln	p.K3005Q	ENST00000268489	NM_006885.3	3005	Aag/Cag	9/10	1	2	FACETS	0.279	0.243	0.318	0.279	0.243	0.318	SUBCLONAL	1	TRUE	1	0.525744820093514	2		1169	995	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52677306	52677309	+	frameshift_variant	Frame_Shift_Del	DEL	CCTT	CCTT	-	novel	NA	P-0013311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	89	748	0	ENST00000394830.3:c.950_953del	p.Lys317ThrfsTer44	p.K317Tfs*44	ENST00000394830	NM_018313.4	317	aAAGGc/ac	10/30	0.525744820093514	1	FACETS	0.453	0.402	0.507	0.453	0.402	0.507	SUBCLONAL	1	TRUE	0	0.525744820093514	1		748	551	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138383932	138383933	+	missense_variant	Missense_Mutation	DNP	GC	GC	AG	novel	NA	P-0013311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	113	625	0	ENST00000289153.2:c.2617_2618delinsCT	p.Ala873Leu	p.A873L	ENST00000289153	NM_006219.2	873	GCa/CTa	18/22	1	2	FACETS	0.603	0.543	0.666	0.603	0.543	0.666	SUBCLONAL	1	TRUE	1	0.525744820093514	2		625	713	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0013312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	120	439	1	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	0.628931440032549	4	FACETS	0.715	0.645	0.788	0.357	0.322	0.394	SUBCLONAL	1	TRUE	2	0.701016923542321	4		440	815	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	228	126	0				ENST00000310581	NM_198253.2	-/1132			0.628931440032549	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.701016923542321	4		126	523	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931589	NA	P-0013312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	214	599	0	ENST00000349496.5:c.101G>A	p.Gly34Glu	p.G34E	ENST00000349496	NM_001904.3	34	gGa/gAa	3/15	0.701016923542321	3	FACETS	0.898	0.835	0.963	0.449	0.417	0.482	CLONAL	1	TRUE	1	0.701016923542321	3		599	918	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410496	139410496	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	309	787	2	ENST00000277541.6:c.1606C>T	p.Pro536Ser	p.P536S	ENST00000277541	NM_017617.3	536	Ccc/Tcc	10/34	0.701016923542321	3	FACETS	1	0.965	1	0.515	0.486	0.546	CLONAL	1	TRUE	1	0.701016923542321	3		789	1155	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465538	99465538	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	236	632	0	ENST00000268035.6:c.2363C>A	p.Thr788Asn	p.T788N	ENST00000268035	NM_000875.3	788	aCt/aAt	11/21	0.628931440032549	4	FACETS	0.861	0.802	0.923	0.431	0.401	0.462	CLONAL	1	TRUE	2	0.701016923542321	4		632	1330	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716257	52716257	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs748878328	NA	P-0013312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	214	550	0	ENST00000322088.6:c.701T>G	p.Leu234Arg	p.L234R	ENST00000322088	NM_014225.5	234	cTt/cGt	6/15	0.701016923542321	3	FACETS	1	0.957	1	0.518	0.482	0.555	CLONAL	1	TRUE	1	0.701016923542321	3		550	796	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098942	178098950	+	inframe_deletion	In_Frame_Del	DEL	CTCGACTTA	CTCGACTTA	-	novel	NA	P-0013312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	285	468	0	ENST00000397062.3:c.95_103del	p.Val32_Arg34del	p.V32_R34del	ENST00000397062	NM_006164.4	32	gTAAGTCGAGaa/gaa	2/5	0.628931440032549	4	FACETS	0.76	0.716	0.805	0.76	0.716	0.805	SUBCLONAL	2	TRUE	2	0.701016923542321	4		468	910	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0013315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	2029	852	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.523237436178335	15	FACETS	0.973	0.96	0.986			1	CLONAL	13	TRUE	NA	0.523237436178335	15		852	2698	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0013315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3301	215	663	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.523237436178335	15	FACETS	1	0.945	1			1	CLONAL	1	TRUE	NA	0.523237436178335	15		663	3516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0013315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	395	494	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.523237436178335	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.523237436178335	2		494	663	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98244270	98244270	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	192	557	0	ENST00000331920.6:c.707G>C	p.Trp236Ser	p.W236S	ENST00000331920	NM_000264.3	236	tGg/tCg	5/24	1	2	FACETS	0.877	0.812	0.944	0.877	0.812	0.944	CLONAL	1	TRUE	1	0.523237436178335	2		557	837	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665047	29665047	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	94	242	0	ENST00000356175.3:c.6646G>T	p.Ala2216Ser	p.A2216S	ENST00000356175	NM_000267.3	2216	Gca/Tca	44/57	0.523237436178335	3	FACETS	0.979	0.875	1	0.49	0.437	0.544	CLONAL	1	TRUE	1	0.523237436178335	3		242	463	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041174	47041193	+	frameshift_variant	Frame_Shift_Del	DEL	GCTCAAATCTGAGCTCCAGA	GCTCAAATCTGAGCTCCAGA	-	novel	NA	P-0013315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	254	766	0	ENST00000377604.3:c.1604_1623del	p.Leu535ProfsTer5	p.L535Pfs*5	ENST00000377604	NM_001204468.1	534	gtGCTCAAATCTGAGCTCCAGAgc/gtgc	15/24	0.206492970666363	3	FACETS	1	0.987	1	0.603	0.565	0.643	INDETERMINATE	1	TRUE	1	0.523237436178335	3		766	1015	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231766	66231767	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	A	novel	NA	P-0013315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	157	432	0	ENST00000273854.3:c.1933_1934delinsT	p.Pro645Ter	p.P645*	ENST00000273854	NM_004439.5	645	CCa/Ta	11/18	0.206492970666363	3	FACETS	1	0.976	1	0.578	0.531	0.627	INDETERMINATE	1	TRUE	1	0.523237436178335	3		432	655	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0013347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	183	273	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.782683144078709	2		273	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0013347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	394	801	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.782683144078709	2		801	991	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131142	55131142	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15309	3312	695	0	ENST00000257290.5:c.685G>A	p.Glu229Lys	p.E229K	ENST00000257290	NM_006206.4	229	Gaa/Aaa	5/23	0.782683144078709	26	FACETS	0.945	0.927	0.963			1	CLONAL	5	TRUE	NA	0.782683144078709	26		695	18621	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006218	22006218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1204549439	NA	P-0013347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	164	295	0	ENST00000276925.6:c.185C>T	p.Ala62Val	p.A62V	ENST00000276925	NM_004936.3	62	gCg/gTg	2/2	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.782683144078709	2		295	409	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606334	93606334	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs796052158	NA	P-0013347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	290	525	0	ENST00000375746.1:c.154G>A	p.Ala52Thr	p.A52T	ENST00000375746	NM_001174167.1	52	Gcc/Acc	2/14	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.782683144078709	2		525	706	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578439	7578439	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	246	469	0	ENST00000269305.4:c.491A>G	p.Lys164Arg	p.K164R	ENST00000269305	NM_001126112.2	164	aAg/aGg	5/11	1	2	FACETS	0.901	0.846	0.956	0.901	0.846	0.956	CLONAL	1	TRUE	1	0.782683144078709	2		469	698	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138301	55138590	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATCACAACCATGGACTTTTCACTTTCTTCACTCCAGGTTAAAAACATCACAGGGATAAATCTCAAAACACCAAAACTGTGAAAATGCTGCTAACCATGTGGGTCTGTCTAAACTGGAGTGTTACTTGTACAACTGGTTTCAGCCCCTCCGGAGTGTTTTGAATGCCATGTAGATGAGTTGTGAACTCATATTCCACTTTGTAGTCTCATATGTTCTGGGACACGAGCTATTCCATTCTGACTTCTTTCTGCCTCTTGCAGTTCCTTCATCCATTCTGGACTTGGTCGATG	ATCACAACCATGGACTTTTCACTTTCTTCACTCCAGGTTAAAAACATCACAGGGATAAATCTCAAAACACCAAAACTGTGAAAATGCTGCTAACCATGTGGGTCTGTCTAAACTGGAGTGTTACTTGTACAACTGGTTTCAGCCCCTCCGGAGTGTTTTGAATGCCATGTAGATGAGTTGTGAACTCATATTCCACTTTGTAGTCTCATATGTTCTGGGACACGAGCTATTCCATTCTGACTTCTTTCTGCCTCTTGCAGTTCCTTCATCCATTCTGGACTTGGTCGATG	-	novel	NA	P-0013347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	181	7	0	ENST00000257290.5:c.1238-255_1272del		p.X413_splice	ENST00000257290	NM_006206.4	413		9/23	0.782683144078709	26	FACETS	1	0.97	1			1	CLONAL	19	TRUE	NA	0.782683144078709	26		7	247	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631129	69631129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs281860303	NA	P-0013348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	112	695	1	ENST00000334134.2:c.283C>T	p.Arg95Trp	p.R95W	ENST00000334134	NM_005247.2	95	Cgg/Tgg	2/3	0.19632848169591	3	FACETS	1	0.971	1	0.397	0.359	0.437	INDETERMINATE	1	TRUE	0	0.505242474460711	3		696	466	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	687	247	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.627041906647044	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	1	0.627041906647044	4		247	1175	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692902	89692902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909218	NA	P-0013352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	168	381	0	ENST00000371953.3:c.386G>A	p.Gly129Glu	p.G129E	ENST00000371953	NM_000314.4	129	gGa/gAa	5/9	1	2	FACETS	0.924	0.854	0.996	0.924	0.854	0.996	CLONAL	1	TRUE	1	0.627041906647044	2		381	580	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690819	89690820	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0013352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	141	326	0	ENST00000371953.3:c.227_228del	p.Tyr76Ter	p.Y76*	ENST00000371953	NM_000314.4	76	TAt/t	4/9	1	2	FACETS	0.967	0.888	1	0.967	0.888	1	CLONAL	1	TRUE	1	0.627041906647044	2		326	465	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305391	65305391	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	39	836	0	ENST00000342505.4:c.2737G>C	p.Glu913Gln	p.E913Q	ENST00000342505	NM_002227.2	913	Gag/Cag	20/25	0.627041906647044	1	FACETS	0.123	0.101	0.147	0.123	0.101	0.147	SUBCLONAL	1	TRUE	0	0.627041906647044	1		836	694	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952149	178952149	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	150	385	1	ENST00000263967.3:c.3204C>A	p.Asn1068Lys	p.N1068K	ENST00000263967	NM_006218.2	1068	aaC/aaA	21/21	1	2	FACETS	0.968	0.892	1	0.968	0.892	1	CLONAL	1	TRUE	1	0.627041906647044	2		386	494	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31372612	31372612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	288	712	1	ENST00000328111.2:c.253C>T	p.Pro85Ser	p.P85S	ENST00000328111	NM_006892.3	85	Cca/Tca	4/23	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.627041906647044	2		713	899	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657007	47657008	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0013352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	290	731	0	ENST00000233146.2:c.1204_1205del	p.Gln402ArgfsTer14	p.Q402Rfs*14	ENST00000233146	NM_000251.2	401	ttACaa/ttaa	7/16	1	2	FACETS	0.856	0.805	0.907	0.856	0.805	0.907	CLONAL	1	TRUE	1	0.627041906647044	2		731	1081	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0013355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	40	393	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.7	0.58	0.835	0.7	0.58	0.835	SUBCLONAL	1	TRUE	1	0.15	2		393	762	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175493	108175493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013355-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	70	577	0	ENST00000278616.4:c.5588C>T	p.Ser1863Phe	p.S1863F	ENST00000278616	NM_000051.3	1863	tCt/tTt	37/63	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.15	2		577	770	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266111	+	inframe_deletion	In_Frame_Del	DEL	TCTGGAATCCAT	TCTGGAATCCAT	-	novel	NA	P-0013367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	242	636	0	ENST00000349496.5:c.102_113del	p.Ile35_Gly38del	p.I35_G38del	ENST00000349496	NM_001904.3	33	TCTGGAATCCAT/-	3/15	0.439414212897979	7	FACETS	1	0.986	1	0.869	0.816	0.922	CLONAL	3	FALSE	3	0.439414212897979	7		636	665	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0013372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	921	594	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.499175935396223	3	FACETS	0.879	0.859	0.898	1	0.997	1	CLONAL	4	TRUE	0	0.485709592561119	3		594	1341	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0013381-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	155	393	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	0.233345061149472	2		393	1054	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560500	65560500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs387906651	NA	P-0013381-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1192	189	713	1	ENST00000358664.4:c.97C>T	p.Arg33Ter	p.R33*	ENST00000358664	NM_002382.4	33	Cga/Tga	3/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.233345061149472	2		714	1381	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052889	180052889	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1346106548	NA	P-0013381-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	150	586	0	ENST00000261937.6:c.1401G>C	p.Lys467Asn	p.K467N	ENST00000261937	NM_182925.4	467	aaG/aaC	10/30	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.233345061149472	2		586	1073	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219938	1220553	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGGGCCTGCTGCCTGAGGCCAGTGGCCTGCTTCCAGCCCATCGCTGGCAGCCGCCTGCCCTGACCAGATCTCCTGGATGCAGGTCTGTGGCCTCAGAGTCAGGGCCCCTTGCTGCTGCAGGACCACAGGGGCAGGGAGGGGCCTGCTGTTCCAGCAAGACTTTGGGGTGCAGCCGGCCTGTGGCCCACAGGAAAATGAGACCTGTGGACATCCGGGGCCCTGCCAGACGTGGCTCGGCCGGACGAGGGTGGCCACTGCAGGCGCAGGTGTGGCTCCCTGCTGGACCTAGCCTTTCCTCTGTCCTGTGTGCCTGGACTTCTGTGACTTCCCAGCTGGGCCTGTGGTGTTTGGGAGGCTCCCAGGCAGCTGCAAAGGGGACCCCTGTGAGGGGCAGGGAGGCCTCGGCCCCAGGACGGGTGTGTGCTGCCCGCAGGTACTTCTGTCAGCTGATTGACGGCCTGGAGTACCTGCATAGCCAGGGCATTGTGCACAAGGACATCAAGCCGGGGAACCTGCTGCTCACCACCGGTGGCACCCTCAAAATCTCCGACCTGGGCGTGGCCGAGGTAGGCACGTGCTAGGGGGGGCCCTGGGGCGCCCCCTCCCGGGCACTCC	CTGGGCCTGCTGCCTGAGGCCAGTGGCCTGCTTCCAGCCCATCGCTGGCAGCCGCCTGCCCTGACCAGATCTCCTGGATGCAGGTCTGTGGCCTCAGAGTCAGGGCCCCTTGCTGCTGCAGGACCACAGGGGCAGGGAGGGGCCTGCTGTTCCAGCAAGACTTTGGGGTGCAGCCGGCCTGTGGCCCACAGGAAAATGAGACCTGTGGACATCCGGGGCCCTGCCAGACGTGGCTCGGCCGGACGAGGGTGGCCACTGCAGGCGCAGGTGTGGCTCCCTGCTGGACCTAGCCTTTCCTCTGTCCTGTGTGCCTGGACTTCTGTGACTTCCCAGCTGGGCCTGTGGTGTTTGGGAGGCTCCCAGGCAGCTGCAAAGGGGACCCCTGTGAGGGGCAGGGAGGCCTCGGCCCCAGGACGGGTGTGTGCTGCCCGCAGGTACTTCTGTCAGCTGATTGACGGCCTGGAGTACCTGCATAGCCAGGGCATTGTGCACAAGGACATCAAGCCGGGGAACCTGCTGCTCACCACCGGTGGCACCCTCAAAATCTCCGACCTGGGCGTGGCCGAGGTAGGCACGTGCTAGGGGGGGCCCTGGGGCGCCCCCTCCCGGGCACTCC	-	novel	NA	P-0013381-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1	95	2	0	ENST00000326873.7:c.465-431_598-24del		p.X155_splice	ENST00000326873	NM_000455.4	155		4/10	1	2	FACETS	1	0.991	1	1	0.992	1	CLONAL	8	TRUE	1	0.233345061149472	2		2	96	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578266	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0013381-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	142	678	0	ENST00000269305.4:c.583_584del	p.Ile195ProfsTer13	p.I195Pfs*13	ENST00000269305	NM_001126112.2	195	ATc/c	6/11	1	2	FACETS	0.943	0.857	1	0.943	0.857	1	CLONAL	1	TRUE	1	0.233345061149472	2		678	1291	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574000	7574000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013390-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	732	715	0	ENST00000269305.4:c.1027G>T	p.Glu343Ter	p.E343*	ENST00000269305	NM_001126112.2	343	Gag/Tag	10/11	0.639577214638048	2	FACETS	0.884	0.86	0.907	0.884	0.86	0.907	CLONAL	2	TRUE	0	0.728671891232886	2		715	1137	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258577	19258577	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013390-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	286	740	0	ENST00000162023.5:c.323A>C	p.Glu108Ala	p.E108A	ENST00000162023		108	gAg/gCg	8/13	0.158755660589288	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.728671891232886	0		740	898	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817469	39817469	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013429-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	92	555	0	ENST00000288319.7:c.94G>C	p.Glu32Gln	p.E32Q	ENST00000288319	NM_182918.3	32	Gag/Cag	2/10	1	2	FACETS	0.673	0.597	0.755	0.673	0.597	0.755	SUBCLONAL	1	TRUE	1	0.281901067232968	2		555	970	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0013429-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	245	895	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.237062030226143	2	FACETS	1	0.988	1	0.627	0.584	0.671	CLONAL	1	TRUE	0	0.281901067232968	2		895	1387	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204499942	204499942	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013429-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	74	490	0	ENST00000367182.3:c.284C>A	p.Pro95Gln	p.P95Q	ENST00000367182	NM_001278516.1	95	cCa/cAa	4/11	1	2	FACETS	0.545	0.476	0.62	0.545	0.476	0.62	SUBCLONAL	1	TRUE	1	0.281901067232968	2		490	963	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519831	29519831	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013429-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	203	660	1	ENST00000389048.3:c.1740G>T	p.Met580Ile	p.M580I	ENST00000389048	NM_004304.4	580	atG/atT	9/29	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.281901067232968	2		661	1140	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627235	12627235	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013429-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	88	594	0	ENST00000251849.4:c.1481C>T	p.Ser494Leu	p.S494L	ENST00000251849	NM_002880.3	494	tCa/tTa	14/17	0.281901067232968	1	FACETS	0.49	0.433	0.551	0.49	0.433	0.551	SUBCLONAL	1	TRUE	0	0.281901067232968	1		594	1095	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2969655	2969655	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs753678528	NA	P-0013429-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	116	704	0	ENST00000396946.4:c.1624C>G	p.Leu542Val	p.L542V	ENST00000396946	NM_032415.4	542	Ctg/Gtg	12/25	1	2	FACETS	0.672	0.604	0.744	0.672	0.604	0.744	SUBCLONAL	1	TRUE	1	0.281901067232968	2		704	1225	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336145	73336145	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013429-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	80	592	0	ENST00000377767.4:c.2258A>G	p.Tyr753Cys	p.Y753C	ENST00000377767	NM_014953.3	753	tAc/tGc	17/21	0.281901067232968	1	FACETS	0.585	0.514	0.662	0.585	0.514	0.662	SUBCLONAL	1	TRUE	0	0.281901067232968	1		592	833	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331857	68331857	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0013429-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	76	519	1	ENST00000487270.1:c.452+1G>A		p.X151_splice	ENST00000487270	NM_133509.3	151			1	2	FACETS	0.637	0.558	0.723	0.637	0.558	0.723	SUBCLONAL	1	TRUE	1	0.281901067232968	2		520	846	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026792	48026793	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0013429-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	151	497	0	ENST00000234420.5:c.1675_1676del	p.Cys559LeufsTer3	p.C559Lfs*3	ENST00000234420	NM_000179.2	557	gGT/g	4/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.281901067232968	2		497	788	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653046	29653047	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0013429-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	316	659	2	ENST00000356175.3:c.4982_4983del	p.Cys1661Ter	p.C1661*	ENST00000356175	NM_000267.3	1661	TGt/t	36/57	0.237062030226143	2	FACETS	0.963	0.909	1	0.963	0.909	1	CLONAL	2	TRUE	0	0.281901067232968	2		661	1164	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152093	55152093	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121908585	NA	P-0013433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	372	378	0	ENST00000257290.5:c.2525A>T	p.Asp842Val	p.D842V	ENST00000257290	NM_006206.4	842	gAc/gTc	18/23	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.748018312595302	2		378	915	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	459943	459943	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	99	606	0	ENST00000399788.2:c.1152G>A	p.Met384Ile	p.M384I	ENST00000399788	NM_001042603.1	384	atG/atA	10/28	NA	2	FACETS	0.304	0.27	0.339			1	INDETERMINATE	1	TRUE	NA	0.748018312595302	2		606	872	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0013443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	777	775	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.914377569888534	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.914377569888534	1		775	852	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471597	120471597	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0013443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	260	393	0	ENST00000256646.2:c.3892+2T>G		p.X1298_splice	ENST00000256646	NM_024408.3	1298			1	2	FACETS	0.956	0.903	1	0.956	0.903	1	CLONAL	1	TRUE	1	0.914377569888534	2		393	595	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280004	66280004	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	258	379	1	ENST00000273854.3:c.1685T>A	p.Val562Glu	p.V562E	ENST00000273854	NM_004439.5	562	gTg/gAg	7/18	1	2	FACETS	0.98	0.926	1	0.98	0.926	1	CLONAL	1	TRUE	1	0.914377569888534	2		380	576	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589646	67589646	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	138	224	0	ENST00000274335.5:c.1409A>G	p.Tyr470Cys	p.Y470C	ENST00000274335		470	tAt/tGt	10/15	1	2	FACETS	0.946	0.875	1	0.946	0.875	1	CLONAL	1	TRUE	1	0.914377569888534	2		224	319	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523699	148523699	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	229	396	0	ENST00000320356.2:c.754C>G	p.Leu252Val	p.L252V	ENST00000320356	NM_004456.4	252	Ctc/Gtc	8/20	1	2	FACETS	0.89	0.836	0.944	0.89	0.836	0.944	CLONAL	1	TRUE	1	0.914377569888534	2		396	563	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130484	29130484	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	867	680	0	ENST00000328354.6:c.226G>T	p.Glu76Ter	p.E76*	ENST00000328354	NM_007194.3	76	Gag/Tag	2/15	0.914377569888534	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.914377569888534	2		680	935	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400221	139400221	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	361	335	0	ENST00000277541.6:c.4127del	p.Gly1376AlafsTer69	p.G1376Afs*69	ENST00000277541	NM_017617.3	1376	gGc/gc	25/34	0.914377569888534	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.914377569888534	1		335	427	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561847	55561848	+	missense_variant	Missense_Mutation	DNP	GA	GA	CT	novel	NA	P-0013443-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	124	571	0	ENST00000288135.5:c.237_238delinsCT	p.Gln79_Asn80delinsHisTyr	p.Q79_N80delinsHY	ENST00000288135	NM_000222.2	79	caGAat/caCTat	2/21	1	2	FACETS	0.329	0.297	0.363	0.329	0.297	0.363	SUBCLONAL	1	TRUE	1	0.914377569888534	2		571	824	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013451-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	147	126	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.930679755527836	NA		126	248	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540161	187540161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373112377	NA	P-0013451-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	470	546	0	ENST00000441802.2:c.7579G>A	p.Val2527Ile	p.V2527I	ENST00000441802	NM_005245.3	2527	Gtt/Att	10/27	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.930679755527836	2		546	991	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935532	49935532	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013451-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	748	852	0	ENST00000296474.3:c.1832T>G	p.Val611Gly	p.V611G	ENST00000296474	NM_002447.2	611	gTg/gGg	5/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.930679755527836	2		852	1566	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340971	70340971	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013451-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	477	600	0	ENST00000374080.3:c.704A>G	p.Tyr235Cys	p.Y235C	ENST00000374080		235	tAc/tGc	5/45	0.930679755527836	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.930679755527836	1		600	524	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534285	534285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894226	NA	P-0013458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	51	649	1	ENST00000451590.1:c.38G>T	p.Gly13Val	p.G13V	ENST00000451590	NM_001130442.1	13	gGt/gTt	2/5	1	2	FACETS	0.656	0.555	0.766	0.656	0.555	0.766	SUBCLONAL	1	TRUE	1	0.179252987525636	2		650	868	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144724	119144724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253824253	NA	P-0013458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	73	452	1	ENST00000264033.4:c.737G>A	p.Arg246Gln	p.R246Q	ENST00000264033	NM_005188.3	246	cGa/cAa	4/16	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.179252987525636	2		453	704	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339937	70339937	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1388	106	890	1	ENST00000374080.3:c.470C>A	p.Ala157Asp	p.A157D	ENST00000374080		157	gCc/gAc	4/45	0.0751471718077299	4	FACETS	0.934	0.834	1	0.467	0.417	0.52	INDETERMINATE	1	TRUE	2	0.179252987525636	4		891	1494	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716291	52716305	+	inframe_deletion	In_Frame_Del	DEL	GCCCACTCTGCGCCA	GCCCACTCTGCGCCA	-	novel	NA	P-0013458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	130	558	0	ENST00000322088.6:c.736_750del	p.Pro246_Gln250del	p.P246_Q250del	ENST00000322088	NM_014225.5	245	atGCCCACTCTGCGCCAg/atg	6/15	0.166963211762752	3	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	1	0.179252987525636	3		558	762	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207198	1207203	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	AAGAAG	AAGAAG	T	novel	NA	P-0013458-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	78	422	0	ENST00000326873.7:c.286_290+1delinsT		p.X96_splice	ENST00000326873	NM_000455.4	96		1/10	0.155363322293069	2	FACETS	1	0.975	1	0.735	0.646	0.83	CLONAL	1	TRUE	0	0.179252987525636	2		422	592	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0013460-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	34	393	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.774	0.63	0.937	0.774	0.63	0.937	CLONAL	1	TRUE	1	0.12	2		393	732	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588243	69588243	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013460-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	52	689	0	ENST00000168712.1:c.455C>A	p.Thr152Asn	p.T152N	ENST00000168712	NM_002007.2	152	aCc/aAc	3/3	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.12	2		689	854	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013461-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	217	715	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.126003388628912	4	FACETS	1	0.962	1			1	INDETERMINATE	4	TRUE	NA	0.270892202827452	4		715	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0013461-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	132	657	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.270892202827452	1	FACETS	0.902	0.825	0.982	1	0.99	1	CLONAL	2	TRUE	0	0.270892202827452	1		657	467	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141026	55141026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765680542	NA	P-0013461-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	85	642	0	ENST00000257290.5:c.1672C>T	p.Arg558Cys	p.R558C	ENST00000257290	NM_006206.4	558	Cgc/Tgc	12/23	0.215117200943858	3	FACETS	0.783	0.695	0.876	0.783	0.695	0.876	SUBCLONAL	2	TRUE	1	0.270892202827452	3		642	455	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003202	143003202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766146483	NA	P-0013461-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	119	622	1	ENST00000262992.4:c.2624C>T	p.Ala875Val	p.A875V	ENST00000262992	NM_001101669.1	875	gCg/gTg	23/24	0.215117200943858	3	FACETS	0.822	0.744	0.904	0.822	0.744	0.904	CLONAL	2	TRUE	1	0.270892202827452	3		623	607	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10284548	10284548	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013461-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	120	712	2	ENST00000340748.4:c.634C>T	p.Arg212Ter	p.R212*	ENST00000340748		212	Cga/Tga	7/40	0.270892202827452	3	FACETS	0.857	0.776	0.941	0.857	0.776	0.941	CLONAL	2	TRUE	1	0.270892202827452	3		714	587	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720741	89720741	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs371387815	NA	P-0013486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	41	130	0	ENST00000371953.3:c.892C>T	p.Gln298Ter	p.Q298*	ENST00000371953	NM_000314.4	298	Caa/Taa	8/9	0.516458229231335	7	FACETS	1	0.899	1			1	CLONAL	4	TRUE	NA	0.516458229231335	7		130	87	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0013486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	281	297	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.516458229231335	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.516458229231335	2		297	532	SUCCESS
AR	367	MSKCC	GRCh37	X	66766450	66766450	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	90	265	0	ENST00000374690.3:c.1462C>T	p.Gln488Ter	p.Q488*	ENST00000374690	NM_000044.3	488	Cag/Tag	1/8	0.516458229231335	3	FACETS	1	0.936	1	0.535	0.477	0.595	CLONAL	1	TRUE	1	0.516458229231335	3		265	410	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683892	117683892	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	130	601	0	ENST00000368508.3:c.3255C>G	p.Phe1085Leu	p.F1085L	ENST00000368508	NM_002944.2	1085	ttC/ttG	21/43	0.516458229231335	3	FACETS	0.913	0.829	1	0.456	0.414	0.5	CLONAL	1	TRUE	1	0.516458229231335	3		601	694	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102098222	102098222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	134	511	0	ENST00000282441.5:c.1186G>A	p.Glu396Lys	p.E396K	ENST00000282441	NM_001130145.2	396	Gag/Aag	8/9	0.126096104569953	5	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.516458229231335	5		511	689	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659982	227659982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1166934768	NA	P-0013486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	149	567	0	ENST00000305123.5:c.3473G>A	p.Gly1158Glu	p.G1158E	ENST00000305123	NM_005544.2	1158	gGa/gAa	1/2	0.516458229231335	4	FACETS	1	0.925	1	0.507	0.463	0.553	CLONAL	1	TRUE	2	0.516458229231335	4		567	863	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591127	67591129	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0013486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	185	405	0	ENST00000274335.5:c.1721_1723del	p.Arg574del	p.R574del	ENST00000274335		574	AGA/-	12/15	0.459207653865858	4	FACETS	0.907	0.842	0.973	0.907	0.842	0.973	CLONAL	2	TRUE	2	0.516458229231335	4		405	599	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781912	9781912	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	154	366	0	ENST00000377346.4:c.2049G>T	p.Met683Ile	p.M683I	ENST00000377346	NM_005026.3	683	atG/atT	16/24	0.516458229231335	6	FACETS	0.927	0.851	1	0.463	0.425	0.503	CLONAL	2	TRUE	2	0.516458229231335	6		366	654	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262204	16262204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757464458	NA	P-0013486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	42	105	0	ENST00000375759.3:c.9469G>A	p.Glu3157Lys	p.E3157K	ENST00000375759	NM_015001.2	3157	Gag/Aag	11/15	0.374560466960164	5	FACETS	1	0.903	1	0.369	0.31	0.433	CLONAL	1	TRUE	2	0.516458229231335	5		105	261	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458068	120458068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	522	676	0	ENST00000256646.2:c.7277C>T	p.Ser2426Leu	p.S2426L	ENST00000256646	NM_024408.3	2426	tCa/tTa	34/34	0.516458229231335	5	FACETS	1	0.969	1			1	CLONAL	3	TRUE	NA	0.516458229231335	5		676	1184	SUCCESS
ALK	238	MSKCC	GRCh37	2	29436872	29436872	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	153	576	0	ENST00000389048.3:c.3721G>C	p.Glu1241Gln	p.E1241Q	ENST00000389048	NM_004304.4	1241	Gag/Cag	24/29	0.516458229231335	4	FACETS	0.904	0.826	0.985	0.452	0.413	0.493	CLONAL	1	TRUE	2	0.516458229231335	4		576	994	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47612334	47612334	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	366	697	0	ENST00000263735.4:c.888G>C	p.Lys296Asn	p.K296N	ENST00000263735	NM_002354.2	296	aaG/aaC	8/9	0.516458229231335	4	FACETS	0.995	0.945	1	0.995	0.945	1	CLONAL	2	TRUE	2	0.516458229231335	4		697	1080	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147730	61147730	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	111	378	0	ENST00000295025.8:c.1040G>C	p.Arg347Thr	p.R347T	ENST00000295025	NM_002908.2	347	aGa/aCa	10/11	0.516458229231335	4	FACETS	1	0.939	1	0.529	0.476	0.585	CLONAL	1	TRUE	2	0.516458229231335	4		378	616	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660458	227660458	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs747866903	NA	P-0013486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	84	300	0	ENST00000305123.5:c.2997G>C	p.Gln999His	p.Q999H	ENST00000305123	NM_005544.2	999	caG/caC	1/2	0.516458229231335	4	FACETS	0.908	0.804	1	0.454	0.402	0.51	CLONAL	1	TRUE	2	0.516458229231335	4		300	543	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356281	66356281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	152	504	0	ENST00000273854.3:c.1216G>A	p.Glu406Lys	p.E406K	ENST00000273854	NM_004439.5	406	Gag/Aag	5/18	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.516458229231335	2		504	560	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539282	187539282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	158	499	0	ENST00000441802.2:c.8458G>A	p.Glu2820Lys	p.E2820K	ENST00000441802	NM_005245.3	2820	Gaa/Aaa	10/27	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.516458229231335	2		499	594	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628788	187628788	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	156	498	0	ENST00000441802.2:c.2194G>A	p.Val732Met	p.V732M	ENST00000441802	NM_005245.3	732	Gtg/Atg	2/27	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.516458229231335	2		498	583	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527839	157527839	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs771295398	NA	P-0013486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	125	448	0	ENST00000346085.5:c.5564G>C	p.Arg1855Thr	p.R1855T	ENST00000346085	NM_020732.3	1855	aGa/aCa	20/20	0.516458229231335	3	FACETS	0.978	0.887	1			1	CLONAL	1	TRUE	NA	0.516458229231335	3		448	623	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404456	70404456	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	148	543	0	ENST00000373644.4:c.1970C>A	p.Ala657Glu	p.A657E	ENST00000373644	NM_030625.2	657	gCa/gAa	4/12	0.483084122318243	3	FACETS	1	0.949	1			1	CLONAL	1	TRUE	NA	0.516458229231335	3		543	687	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242668	46242668	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	113	430	0	ENST00000334344.6:c.1630G>T	p.Glu544Ter	p.E544*	ENST00000334344	NM_152641.2	544	Gaa/Taa	13/21	0.32697982452082	6	FACETS	1	0.956	1			1	CLONAL	1	TRUE	NA	0.516458229231335	6		430	801	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572101	95572101	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1060503605	NA	P-0013486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	167	503	0	ENST00000393063.1:c.3007C>T	p.Arg1003Ter	p.R1003*	ENST00000393063	NM_030621.3	1003	Cga/Tga	20/28	0.516458229231335	3	FACETS	1	0.966	1	0.544	0.501	0.589	CLONAL	1	TRUE	1	0.516458229231335	3		503	748	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763940	76763940	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	161	786	0	ENST00000373344.5:c.7368G>A	p.Met2456Ile	p.M2456I	ENST00000373344	NM_000489.3	2456	atG/atA	35/35	0.516458229231335	3	FACETS	0.925	0.849	1	0.463	0.424	0.502	CLONAL	1	TRUE	1	0.516458229231335	3		786	848	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854897	76854897	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	194	695	0	ENST00000373344.5:c.5939C>G	p.Ser1980Cys	p.S1980C	ENST00000373344	NM_000489.3	1980	tCt/tGt	25/35	0.516458229231335	3	FACETS	1	0.963	1	0.532	0.492	0.573	CLONAL	1	TRUE	1	0.516458229231335	3		695	889	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178236	56178236	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	325	603	0	ENST00000399503.3:c.3209del	p.Thr1070LysfsTer12	p.T1070Kfs*12	ENST00000399503	NM_005921.1	1070	aCa/aa	14/20	0.459207653865858	4	FACETS	0.989	0.936	1	0.989	0.936	1	CLONAL	2	TRUE	2	0.516458229231335	4		603	965	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	302	715	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.374038116197102	3	FACETS	0.998	0.942	1	0.998	0.942	1	CLONAL	2	TRUE	1	0.374038116197102	3		715	960	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0013488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	139	382	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.364548412670135	2	FACETS	1	0.975	1	0.591	0.539	0.644	CLONAL	1	TRUE	0	0.374038116197102	2		382	629	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0013488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	315	297	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.364548412670135	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.374038116197102	2		297	829	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514495	NA	P-0013488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	205	440	1	ENST00000269305.4:c.542G>A	p.Arg181His	p.R181H	ENST00000269305	NM_001126112.2	181	cGc/cAc	5/11	0.364548412670135	2	FACETS	0.923	0.861	0.985	0.923	0.861	0.985	CLONAL	2	TRUE	0	0.374038116197102	2		441	594	SUCCESS
APC	324	MSKCC	GRCh37	5	112173926	112173926	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060503287	NA	P-0013488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	259	320	0	ENST00000257430.4:c.2635C>T	p.Gln879Ter	p.Q879*	ENST00000257430	NM_000038.5	879	Cag/Tag	16/16	0.364548412670135	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.374038116197102	2		320	648	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187847	11187847	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	161	322	0	ENST00000361445.4:c.6050T>C	p.Ile2017Thr	p.I2017T	ENST00000361445	NM_004958.3	2017	aTc/aCc	44/58	0.368315519423986	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.374038116197102	3		322	467	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972029	55972029	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013488-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	148	710	0	ENST00000263923.4:c.1615G>C	p.Gly539Arg	p.G539R	ENST00000263923	NM_002253.2	539	Gga/Cga	12/30	1	2	FACETS	0.882	0.806	0.963	0.882	0.806	0.963	CLONAL	1	TRUE	1	0.374038116197102	2		710	897	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013496-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	124	715	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	0.219688503144471	2		715	973	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0013496-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	138	354	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.219688503144471	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.219688503144471	1		354	859	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001091	150001091	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753995655	NA	P-0013496-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	94	717	2	ENST00000253339.5:c.2513G>A	p.Arg838His	p.R838H	ENST00000253339		838	cGt/cAt	4/7	1	2	FACETS	0.864	0.767	0.967	0.864	0.767	0.967	CLONAL	1	TRUE	1	0.219688503144471	2		719	991	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833925	44833925	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013496-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	148	429	0	ENST00000377967.4:c.349C>T	p.Gln117Ter	p.Q117*	ENST00000377967	NM_021140.2	117	Cag/Tag	4/29	1	1	FACETS	0.923	0.845	1	1	0.991	1	CLONAL	2	TRUE	0	0.219688503144471	1		429	650	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0013532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	58	645	1	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.3	3	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	3		646	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578390	7578410	+	inframe_deletion	In_Frame_Del	DEL	CTCATGGTGGGGGCAGCGCCT	CTCATGGTGGGGGCAGCGCCT	-	novel	NA	P-0013532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	10	434	0	ENST00000269305.4:c.520_540del	p.Arg175_Arg181del	p.R175_R181del	ENST00000269305	NM_001126112.2	174	AGGCGCTGCCCCCACCATGAG/-	5/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		434	176	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138375111	138375111	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771812474	NA	P-0013536-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	41	330	0	ENST00000289153.2:c.2948G>A	p.Arg983His	p.R983H	ENST00000289153	NM_006219.2	983	cGc/cAc	21/22	0.276292279587541	3	FACETS	0.307	0.255	0.365	0.153	0.127	0.183	INDETERMINATE	1	TRUE	1	0.575334426519876	3		330	598	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391850	139391850	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013536-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	17	416	0	ENST00000277541.6:c.6341A>C	p.Asp2114Ala	p.D2114A	ENST00000277541	NM_017617.3	2114	gAc/gCc	34/34	0.557537957058089	2	FACETS	0.215	0.16	0.28	0.107	0.08	0.14	SUBCLONAL	1	TRUE	0	0.575334426519876	2		416	275	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0013550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	169	264	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.694564599950344	3	FACETS	0.915	0.857	0.973	0.915	0.857	0.973	CLONAL	2	TRUE	1	0.784088890559757	3		264	328	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250890	99250890	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013550-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	83	663	0	ENST00000268035.6:c.194C>A	p.Ser65Tyr	p.S65Y	ENST00000268035	NM_000875.3	65	tCc/tAc	2/21	0.0641519064551082	5	FACETS	0.785	0.694	0.882	0.262	0.231	0.294	INDETERMINATE	1	TRUE	2	0.784088890559757	5		663	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0013569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	192	494	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.163972796968245	2	FACETS	0.844	0.78	0.911	0.844	0.78	0.911	CLONAL	2	TRUE	0	0.208714229747576	2		494	1090	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1329443726	NA	P-0013569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	222	337	0	ENST00000304494.5:c.262del	p.Glu88ArgfsTer58	p.E88Rfs*58	ENST00000304494	NM_000077.4	88	Gag/ag	2/3	0.208714229747576	3	FACETS	0.922	0.863	0.982	1	0.988	1	CLONAL	4	TRUE	0	0.208714229747576	3		337	637	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348846	118348846	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1317	88	631	0	ENST00000534358.1:c.3499T>A	p.Cys1167Ser	p.C1167S	ENST00000534358	NM_005933.3	1167	Tgt/Agt	5/36	0.18711145099599	3	FACETS	0.663	0.585	0.747	0.331	0.292	0.374	SUBCLONAL	1	TRUE	1	0.208714229747576	3		631	1405	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348850	118348850	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1292	76	618	0	ENST00000534358.1:c.3503G>T	p.Gly1168Val	p.G1168V	ENST00000534358	NM_005933.3	1168	gGt/gTt	5/36	0.18711145099599	3	FACETS	0.588	0.513	0.669	0.294	0.256	0.335	SUBCLONAL	1	TRUE	1	0.208714229747576	3		618	1368	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352513	89352513	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1481	233	978	0	ENST00000301030.4:c.826T>G	p.Ser276Ala	p.S276A	ENST00000301030	NM_001256183.1	276	Tcc/Gcc	8/13	0.125470083179738	3	FACETS	1	0.991	1	0.48	0.445	0.515	CLONAL	1	TRUE	0	0.208714229747576	3		978	1714	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677957	58677957	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1042657194	NA	P-0013569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	129	543	0	ENST00000305921.3:c.182G>T	p.Gly61Val	p.G61V	ENST00000305921	NM_003620.3	61	gGc/gTc	1/6	0.120100296831764	4	FACETS	0.8	0.724	0.879	0.533	0.483	0.586	INDETERMINATE	2	TRUE	1	0.208714229747576	4		543	934	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794766	42794766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368976470	NA	P-0013569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	112	589	0	ENST00000575354.2:c.1846G>A	p.Val616Ile	p.V616I	ENST00000575354	NM_015125.3	616	Gtc/Atc	10/20	0.120100296831764	4	FACETS	1	0.965	1	0.39	0.349	0.432	INDETERMINATE	1	TRUE	1	0.208714229747576	4		589	1110	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251824	212251824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	72	533	0	ENST00000342788.4:c.3235G>A	p.Val1079Met	p.V1079M	ENST00000342788	NM_005235.2	1079	Gtg/Atg	27/28	0.127740710692928	3	FACETS	0.748	0.652	0.853	0.374	0.326	0.427	SUBCLONAL	1	TRUE	1	0.208714229747576	3		533	1018	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098450	47098450	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0013569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	95	690	0	ENST00000409792.3:c.6824C>G	p.Ser2275Ter	p.S2275*	ENST00000409792	NM_014159.6	2275	tCa/tGa	15/21	0.163972796968245	2	FACETS	0.738	0.655	0.828	0.369	0.327	0.414	SUBCLONAL	1	TRUE	0	0.208714229747576	2		690	1233	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851561	134851561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	160	498	1	ENST00000398015.3:c.967C>T	p.Pro323Ser	p.P323S	ENST00000398015	NM_004441.4	323	Cca/Tca	5/16	0.163972796968245	2	FACETS	0.861	0.79	0.936	0.861	0.79	0.936	CLONAL	2	TRUE	0	0.208714229747576	2		499	890	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956543	93956590	+	inframe_deletion	In_Frame_Del	DEL	TTTGGGTTTCGAATCATTTTGTCTAGAATTCCAACTATCTGTTCAAAT	TTTGGGTTTCGAATCATTTTGTCTAGAATTCCAACTATCTGTTCAAAT	-	novel	NA	P-0013569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1804	229	945	0	ENST00000369303.4:c.2646_2693del	p.Lys882_Pro897del	p.K882_P897del	ENST00000369303	NM_004440.3	882	aaATTTGAACAGATAGTTGGAATTCTAGACAAAATGATTCGAAACCCAAAt/aat	15/17	0.170179064109905	3	FACETS	1	0.983	1	0.596	0.553	0.641	CLONAL	1	TRUE	1	0.208714229747576	3		945	2033	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70362032	70362032	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013569-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1586	112	905	0	ENST00000374080.3:c.6498G>C	p.Gln2166His	p.Q2166H	ENST00000374080		2166	caG/caC	45/45	0.18711145099599	3	FACETS	0.698	0.625	0.776	0.349	0.312	0.388	SUBCLONAL	1	TRUE	1	0.208714229747576	3		905	1698	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0013576-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	223	273	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.770194308257952	2		273	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0013576-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	824	709	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.770194308257952	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.770194308257952	2		709	1048	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692779	89692779	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013576-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	259	326	1	ENST00000371953.3:c.263A>G	p.Tyr88Cys	p.Y88C	ENST00000371953	NM_000314.4	88	tAt/tGt	5/9	0.718708617108259	2	FACETS	0.945	0.907	0.98	0.945	0.907	0.98	CLONAL	2	TRUE	0	0.770194308257952	2		327	356	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729807	41729807	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756546726	NA	P-0013576-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	300	819	1	ENST00000242208.4:c.722G>A	p.Arg241Gln	p.R241Q	ENST00000242208	NM_002192.2	241	cGg/cAg	3/3	0.64323385986081	3	FACETS	0.797	0.749	0.846	0.398	0.374	0.423	SUBCLONAL	1	TRUE	1	0.770194308257952	3		820	1354	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0013585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	124	474	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.474738323291632	4	FACETS	0.815	0.746	0.886	0.815	0.746	0.886	CLONAL	2	TRUE	2	0.761181125842929	4		474	352	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48922000	48922000	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1566187856	NA	P-0013585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	98	428	1	ENST00000267163.4:c.539+1G>A		p.X180_splice	ENST00000267163	NM_000321.2	180			0.460102560989417	4	FACETS	0.949	0.85	1			1	CLONAL	1	TRUE	NA	0.761181125842929	4		429	478	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247516	123247516	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519795	NA	P-0013585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	59	563	0	ENST00000358487.5:c.1975A>G	p.Lys659Glu	p.K659E	ENST00000358487	NM_000141.4	659	Aag/Gag	14/18	0.421847880838053	4	FACETS	0.417	0.358	0.481	0.208	0.179	0.241	INDETERMINATE	1	TRUE	2	0.761181125842929	4		563	655	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480546	123480546	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013585-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	67	545	1	ENST00000371139.4:c.54G>T	p.Lys18Asn	p.K18N	ENST00000371139	NM_001114937.2	18	aaG/aaT	1/4	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.761181125842929	NA		546	336	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0013586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	54	264	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.73304701083512	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	3	TRUE	0	0.73304701083512	3		264	64	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0013586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	40	654	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.73304701083512	3	FACETS	1	0.928	1	0.583	0.495	0.675	CLONAL	1	TRUE	1	0.73304701083512	3		654	128	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198474	108198474	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	43	398	0	ENST00000278616.4:c.7078T>A	p.Tyr2360Asn	p.Y2360N	ENST00000278616	NM_000051.3	2360	Tat/Aat	48/63	0.71313450527326	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.73304701083512	2		398	50	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611845	100611845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782813365	NA	P-0013586-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	33	1048	1	ENST00000308731.7:c.1276G>A	p.Asp426Asn	p.D426N	ENST00000308731	NM_000061.2	426	Gac/Aac	14/19	0.35684288795076	2	FACETS	0.75	0.624	0.886	0.375	0.312	0.443	INDETERMINATE	1	TRUE	0	0.73304701083512	2		1049	120	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	76	126	0				ENST00000310581	NM_198253.2	-/1132			0.243932885643066	4	FACETS	0.793	0.708	0.88	0.793	0.708	0.88	INDETERMINATE	2	TRUE	2	0.840260211439965	4		126	210	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0013595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	601	297	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.832446834585765	3	FACETS	0.977	0.959	0.994	0.977	0.959	0.994	CLONAL	3	TRUE	0	0.840260211439965	3		297	693	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0013595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	186	328	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.404801526685474	1	FACETS	1	0.975	1	1	0.975	1	INDETERMINATE	1	TRUE	0	0.840260211439965	1		329	249	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0013595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28041	1473	684	2	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.840260211439965	40	FACETS	1	0.976	1			1	CLONAL	2	TRUE	NA	0.840260211439965	40		686	29514	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0013595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24610	527	447	0	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.840260211439965	40	FACETS	0.847	0.804	0.891			1	CLONAL	1	TRUE	NA	0.840260211439965	40		447	25137	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013623-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	74	391	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.417815826267177	6	FACETS	1	0.95	1			1	CLONAL	1	TRUE	NA	0.417815826267177	6		391	558	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451403	70451404	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0013623-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	106	709	0	ENST00000373644.4:c.6245_6246del	p.Glu2082AlafsTer7	p.E2082Afs*7	ENST00000373644	NM_030625.2	2081	tcAGag/tcag	12/12	0.114009077583512	4	FACETS	0.858	0.775	0.946	0.858	0.775	0.946	INDETERMINATE	2	TRUE	2	0.417815826267177	4		709	419	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790072	40790072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61753667	NA	P-0013623-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	53	483	2	ENST00000373198.4:c.2659G>A	p.Ala887Thr	p.A887T	ENST00000373198	NM_133170.3	887	Gcc/Acc	18/32	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.417815826267177	2		485	221	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678076	117678076	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs373090808	NA	P-0013648-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	274	380	0	ENST00000368508.3:c.3857G>A	p.Arg1286His	p.R1286H	ENST00000368508	NM_002944.2	1286	cGc/cAc	25/43	0.549747838487083	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.549747838487083	2		380	498	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220640	1220640	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690940	NA	P-0013648-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	281	546	1	ENST00000326873.7:c.658C>T	p.Gln220Ter	p.Q220*	ENST00000326873	NM_000455.4	220	Cag/Tag	5/10	0.549823023921306	2	FACETS	0.991	0.943	1	0.991	0.943	1	CLONAL	2	TRUE	0	0.549747838487083	2		547	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578435	7578444	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCTTGTAG	CTGCTTGTAG	-	novel	NA	P-0013648-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	211	358	0	ENST00000269305.4:c.486_495del	p.Tyr163HisfsTer4	p.Y163Hfs*4	ENST00000269305	NM_001126112.2	162	atCTACAAGCAG/at	5/11	0.549747838487083	2	FACETS	0.997	0.942	1	0.997	0.942	1	CLONAL	2	TRUE	0	0.549747838487083	2		358	385	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15840974	15840974	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013648-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	247	369	0	ENST00000307771.7:c.1058C>A	p.Thr353Asn	p.T353N	ENST00000307771	NM_005089.3	353	aCt/aAt	11/11	0.472923609002556	2	FACETS	1	0.993	1			1	CLONAL	1	TRUE	NA	0.549747838487083	2		369	635	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921998	39921998	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0013648-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	34	353	0	ENST00000378444.4:c.4173+1G>A		p.X1391_splice	ENST00000378444	NM_001123385.1	1391			0.472923609002556	2	FACETS	0.244	0.199	0.296			1	SUBCLONAL	1	TRUE	NA	0.549747838487083	2		353	506	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061223	38061228	+	inframe_deletion	In_Frame_Del	DEL	TCTCGA	TCTCGA	-	novel	NA	P-0013660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	156	437	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	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.444120489198768	2		437	624	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202295	133202295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	150	547	0	ENST00000320574.5:c.6593C>T	p.Ala2198Val	p.A2198V	ENST00000320574	NM_006231.2	2198	gCc/gTc	47/49	1	2	FACETS	0.875	0.801	0.953	0.875	0.801	0.953	CLONAL	1	TRUE	1	0.444120489198768	2		547	772	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772316	68772316	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0013660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	84	414	0	ENST00000261769.5:c.163+2T>G		p.X55_splice	ENST00000261769	NM_004360.3	55			0.444120489198768	1	FACETS	0.772	0.687	0.863	0.772	0.687	0.863	SUBCLONAL	1	TRUE	0	0.444120489198768	1		414	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0013674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	255	272	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.444260755433737	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.444260755433737	1		272	878	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0013680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	24	689	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	1	2	FACETS	0.242	0.189	0.305	0.242	0.189	0.305	SUBCLONAL	1	TRUE	1	0.17	2		689	1165	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0013680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	34	715	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.316	0.257	0.384	0.316	0.257	0.384	SUBCLONAL	1	TRUE	1	0.17	2		715	1266	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	210	247	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.158925360654582	2	FACETS	1	0.991	1	0.717	0.668	0.766	INDETERMINATE	1	TRUE	0	0.43223420373103	2		247	678	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0013704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	119	322	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.43223420373103	2		322	549	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0013704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	132	364	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.9	0.818	0.985	0.9	0.818	0.985	CLONAL	1	TRUE	1	0.43223420373103	2		365	679	SUCCESS
APC	324	MSKCC	GRCh37	5	112175600	112175600	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	217	471	0	ENST00000257430.4:c.4312del	p.Thr1438HisfsTer35	p.T1438Hfs*35	ENST00000257430	NM_000038.5	1437	Aaa/aa	16/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.43223420373103	2		471	862	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211097	55211097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219568637	NA	P-0013704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	158	446	1	ENST00000275493.2:c.340G>A	p.Glu114Lys	p.E114K	ENST00000275493	NM_005228.3	114	Gaa/Aaa	3/28	0.204972314736001	3	FACETS	1	0.973	1	0.571	0.523	0.62	INDETERMINATE	1	TRUE	1	0.43223420373103	3		447	779	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0013704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	151	430	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	1	2	FACETS	0.987	0.904	1	0.987	0.904	1	CLONAL	1	TRUE	1	0.43223420373103	2		430	708	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350069	89350069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758856347	NA	P-0013704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	388	833	2	ENST00000301030.4:c.2881C>T	p.Arg961Cys	p.R961C	ENST00000301030	NM_001256183.1	961	Cgc/Tgc	9/13	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.43223420373103	2		835	1331	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544155	18544155	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs774380325	NA	P-0013704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	196	424	0	ENST00000266497.5:c.1972G>T	p.Ala658Ser	p.A658S	ENST00000266497		658	Gcc/Tcc	13/31	0.158925360654582	2	FACETS	1	0.989	1	0.671	0.623	0.719	INDETERMINATE	1	TRUE	0	0.43223420373103	2		424	676	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578210	7578211	+	missense_variant	Missense_Mutation	DNP	TC	TC	CT	novel	NA	P-0013704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	540	306	295	ENST00000269305.4:c.638_639delinsAG	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGA/cAG	6/11	0.414538059115838	2	FACETS	1	0.984	1	1	0.997	1	CLONAL	3	TRUE	0	0.43223420373103	2		601	815	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054719	13054719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769424711	NA	P-0013704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	195	603	2	ENST00000316448.5:c.1246G>A	p.Glu416Lys	p.E416K	ENST00000316448	NM_004343.3	416	Gag/Aag	9/9	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.43223420373103	2		605	874	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281288	46281288	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	521	629	1	ENST00000371998.3:c.4085T>A	p.Met1362Lys	p.M1362K	ENST00000371998		1362	aTg/aAg	21/23	0.186279719119751	3	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.43223420373103	3		630	1249	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956675	93956675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776802108	NA	P-0013704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	285	703	0	ENST00000369303.4:c.2561G>A	p.Arg854His	p.R854H	ENST00000369303	NM_004440.3	854	cGt/cAt	15/17	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.43223420373103	2		703	1050	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0013719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	274	852	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.23263252920337	5	FACETS	0.836	0.784	0.889	0.836	0.784	0.889	CLONAL	3	TRUE	2	0.269869454612375	5		852	1138	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0013719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	203	528	1	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	0.253060019969273	2	FACETS	0.859	0.797	0.922	0.859	0.797	0.922	CLONAL	2	TRUE	0	0.269869454612375	2		529	876	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350198	89350198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1982	129	1213	1	ENST00000301030.4:c.2752G>A	p.Glu918Lys	p.E918K	ENST00000301030	NM_001256183.1	918	Gag/Aag	9/13	0.132478520717858	5	FACETS	0.636	0.574	0.703	0.212	0.191	0.235	INDETERMINATE	1	TRUE	2	0.269869454612375	5		1214	2111	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984844	9984844	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	61	562	0	ENST00000330684.3:c.1121A>T	p.Lys374Met	p.K374M	ENST00000330684	NM_001134407.1	374	aAg/aTg	4/13	0.269869454612375	3	FACETS	0.47	0.404	0.543	0.235	0.202	0.272	SUBCLONAL	1	TRUE	1	0.269869454612375	3		562	1091	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641544	23641544	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1376	74	679	0	ENST00000261584.4:c.1931G>C	p.Gly644Ala	p.G644A	ENST00000261584	NM_024675.3	644	gGa/gCa	5/13	0.132478520717858	5	FACETS	0.531	0.463	0.606	0.177	0.154	0.202	INDETERMINATE	1	TRUE	2	0.269869454612375	5		679	1450	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440688	56440688	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1242	85	760	0	ENST00000407977.2:c.530A>G	p.Tyr177Cys	p.Y177C	ENST00000407977		177	tAc/tGc	5/10	0.253060019969273	2	FACETS	0.475	0.418	0.536	0.237	0.209	0.268	SUBCLONAL	1	TRUE	0	0.269869454612375	2		760	1327	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0013720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	203	346	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.366472417528211	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	1	0.366472417528211	4		346	479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	226	694	1	ENST00000269305.4:c.833del	p.Pro278LeufsTer67	p.P278Lfs*67	ENST00000269305	NM_001126112.2	278	cCt/ct	8/11	0.366472417528211	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.366472417528211	2		695	545	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951001	48951105	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AATTCTGATTACACAGTATCCTCGACATTGATTTCTGTTTTTACCTCCTAAAGAACTGCACAGTGAATCCAAAAGAAAGTATACTGAAAAGAGTGAAGGATATAG	AATTCTGATTACACAGTATCCTCGACATTGATTTCTGTTTTTACCTCCTAAAGAACTGCACAGTGAATCCAAAAGAAAGTATACTGAAAAGAGTGAAGGATATAG	TCTCTTTAAAGATGTATCCTATATCCTTCAC	novel	NA	P-0013720-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	49	295	2	ENST00000267163.4:c.1216-53_1267delinsTCTCTTTAAAGATGTATCCTATATCCTTCAC		p.X406_splice	ENST00000267163	NM_000321.2	406		13/27	0.366472417528211	3	FACETS	0.816	0.7	0.938	0.544	0.467	0.626	CLONAL	2	TRUE	0	0.366472417528211	3		297	194	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0013722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	223	433	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.24483227717652	2	FACETS	0.913	0.852	0.976	0.913	0.852	0.976	CLONAL	2	TRUE	0	0.294964499374651	2		433	828	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0013722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	101	459	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	1	2	FACETS	0.851	0.76	0.947	0.851	0.76	0.947	CLONAL	1	TRUE	1	0.294964499374651	2		459	805	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714661	52714661	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	211	475	0	ENST00000322088.6:c.419G>T	p.Trp140Leu	p.W140L	ENST00000322088	NM_014225.5	140	tGg/tTg	4/15	0.294964499374651	1	FACETS	0.86	0.802	0.92	1	0.993	1	CLONAL	2	TRUE	0	0.294964499374651	1		475	709	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467631	50467631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	39	270	0	ENST00000331340.3:c.866C>T	p.Ser289Phe	p.S289F	ENST00000331340	NM_006060.4	289	tCc/tTc	8/8	1	2	FACETS	0.594	0.493	0.708	0.594	0.493	0.708	SUBCLONAL	1	TRUE	1	0.294964499374651	2		270	445	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933722	39933722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs899486642	NA	P-0013722-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	121	590	0	ENST00000378444.4:c.877G>A	p.Val293Ile	p.V293I	ENST00000378444	NM_001123385.1	293	Gtc/Atc	4/15	1	2	FACETS	0.93	0.84	1	0.93	0.84	1	CLONAL	1	TRUE	1	0.294964499374651	2		590	882	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0013732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	169	717	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.519287799367261	5	FACETS	0.975	0.895	1	0.325	0.298	0.354	CLONAL	1	TRUE	2	0.519287799367261	5		717	1187	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479963	50479963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	204	849	0	ENST00000394963.4:c.197G>A	p.Gly66Asp	p.G66D	ENST00000394963	NM_003076.4	66	gGc/gAc	2/13	0.474264890477824	4	FACETS	0.991	0.917	1	0.495	0.458	0.534	CLONAL	1	TRUE	2	0.519287799367261	4		849	1205	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828873	26828873	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	118	588	0	ENST00000381527.3:c.95A>T	p.Tyr32Phe	p.Y32F	ENST00000381527	NM_001260.1	32	tAt/tTt	1/13	0.519287799367261	4	FACETS	0.85	0.767	0.938	0.283	0.255	0.313	CLONAL	1	TRUE	1	0.519287799367261	4		588	812	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730140	41730140	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1461	273	1173	0	ENST00000242208.4:c.389G>A	p.Gly130Glu	p.G130E	ENST00000242208	NM_002192.2	130	gGa/gAa	3/3	0.519287799367261	5	FACETS	1	0.974	1	0.36	0.336	0.384	CLONAL	1	TRUE	2	0.519287799367261	5		1173	1734	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965912	90965912	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013732-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	87	315	0	ENST00000265433.3:c.1405del	p.Asp469MetfsTer15	p.D469Mfs*15	ENST00000265433	NM_002485.4	469	Gat/at	11/16	0.519287799367261	9	FACETS	1	0.929	1	0.153	0.135	0.173	CLONAL	1	TRUE	2	0.519287799367261	9		315	881	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923029	39923041	+	frameshift_variant	Frame_Shift_Del	DEL	CATCTGCTGCCGA	CATCTGCTGCCGA	-	novel	NA	P-0013746-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	57	393	0	ENST00000378444.4:c.3667_3679del	p.Ser1223AlafsTer11	p.S1223Afs*11	ENST00000378444	NM_001123385.1	1223	TCGGCAGCAGATGgc/gc	8/15	1	1	FACETS	0.104	0.088	0.12	0.104	0.088	0.12	SUBCLONAL	1	TRUE	0	0.9	1		393	672	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0013748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	135	756	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	1	2	FACETS	0.981	0.889	1	0.981	0.889	1	CLONAL	1	TRUE	1	0.229019446505886	2		756	1202	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs985033810	NA	P-0013748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	150	668	0	ENST00000269305.4:c.731G>C	p.Gly244Ala	p.G244A	ENST00000269305	NM_001126112.2	244	gGc/gCc	7/11	0.229019446505886	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.229019446505886	1		668	967	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673703	176673703	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	144	710	0	ENST00000439151.2:c.4403C>G	p.Pro1468Arg	p.P1468R	ENST00000439151	NM_022455.4	1468	cCa/cGa	10/23	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.229019446505886	2		710	1137	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	87	414	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.575	0.507	0.647	0.575	0.507	0.647	SUBCLONAL	1	TRUE	1	0.279047383579025	2		416	1085	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	144	365	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.279047383579025	2		367	1000	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802659	135802659	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	37	489	0	ENST00000298552.3:c.139G>A	p.Asp47Asn	p.D47N	ENST00000298552	NM_001162426.1	47	Gat/Aat	4/23	0.163567605679316	1	FACETS	0.308	0.253	0.371	0.308	0.253	0.371	INDETERMINATE	1	TRUE	0	0.279047383579025	1		489	740	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	123	328	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.252486392077422	1	FACETS	0.857	0.775	0.944	0.857	0.775	0.944	CLONAL	1	TRUE	0	0.279047383579025	1		329	885	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524113	187524113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	60	785	2	ENST00000441802.2:c.11426C>T	p.Pro3809Leu	p.P3809L	ENST00000441802	NM_005245.3	3809	cCc/cTc	20/27	0.174964171627586	0	FACETS	0.293	0.251	0.338			1	SUBCLONAL	1	TRUE	0	0.279047383579025	0		787	1059	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741849	17741849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750173588	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	30	224	2	ENST00000250003.3:c.520G>A	p.Ala174Thr	p.A174T	ENST00000250003	NM_002478.4	174	Gcc/Acc	1/3	0.252486392077422	1	FACETS	0.496	0.4	0.605	0.496	0.4	0.605	SUBCLONAL	1	TRUE	0	0.279047383579025	1		226	373	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431338	121431338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	38	362	0	ENST00000257555.6:c.542G>A	p.Gly181Glu	p.G181E	ENST00000257555		181	gGg/gAg	3/10	1	2	FACETS	0.42	0.346	0.502	0.42	0.346	0.502	SUBCLONAL	1	TRUE	1	0.279047383579025	2		362	649	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457244	67457244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	46	587	0	ENST00000327367.4:c.218G>A	p.Gly73Asp	p.G73D	ENST00000327367	NM_005902.3	73	gGc/gAc	2/9	0.252486392077422	1	FACETS	0.348	0.292	0.41	0.348	0.292	0.41	SUBCLONAL	1	TRUE	0	0.279047383579025	1		587	816	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272104	15272104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	61	792	0	ENST00000263388.2:c.6335G>A	p.Gly2112Asp	p.G2112D	ENST00000263388	NM_000435.2	2112	gGt/gAt	33/33	1	2	FACETS	0.36	0.309	0.415	0.36	0.309	0.415	SUBCLONAL	1	TRUE	1	0.279047383579025	2		792	1216	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39763629	39763629	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542821839	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	37	374	0	ENST00000288319.7:c.823C>T	p.Pro275Ser	p.P275S	ENST00000288319	NM_182918.3	275	Cca/Tca	8/10	0.279047383579025	1	FACETS	0.383	0.315	0.459	0.383	0.315	0.459	SUBCLONAL	1	TRUE	0	0.279047383579025	1		374	596	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375496	15375496	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373874073	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1394	77	878	0	ENST00000263377.2:c.931C>T	p.Pro311Ser	p.P311S	ENST00000263377	NM_058243.2	311	Ccg/Tcg	6/20	1	2	FACETS	0.375	0.328	0.427	0.375	0.328	0.427	SUBCLONAL	1	TRUE	1	0.279047383579025	2		878	1471	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349369	89349369	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1281251007	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	66	840	0	ENST00000301030.4:c.3581G>A	p.Gly1194Glu	p.G1194E	ENST00000301030	NM_001256183.1	1194	gGg/gAg	9/13	0.279047383579025	1	FACETS	0.359	0.31	0.413	0.359	0.31	0.413	SUBCLONAL	1	TRUE	0	0.279047383579025	1		840	1133	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488222	56488222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	49	561	1	ENST00000267101.3:c.1741G>A	p.Asp581Asn	p.D581N	ENST00000267101	NM_001982.3	581	Gat/Aat	15/28	1	2	FACETS	0.358	0.302	0.421	0.358	0.302	0.421	SUBCLONAL	1	TRUE	1	0.279047383579025	2		562	980	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146518	185146518	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1358772216	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	46	584	0	ENST00000265026.3:c.149G>A	p.Gly50Glu	p.G50E	ENST00000265026	NM_004721.4	50	gGg/gAg	2/14	0.279047383579025	1	FACETS	0.363	0.304	0.428	0.363	0.304	0.428	SUBCLONAL	1	TRUE	0	0.279047383579025	1		584	782	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287255	33287258	+	frameshift_variant	Frame_Shift_Del	DEL	ATTG	ATTG	-	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	124	586	0	ENST00000374542.5:c.1839_1842del	p.Phe613LeufsTer31	p.F613Lfs*31	ENST00000374542	NM_001141970.1	613	ttCAAT/tt	6/8	0.252486392077422	1	FACETS	0.913	0.825	1	0.913	0.825	1	CLONAL	1	TRUE	0	0.279047383579025	1		586	838	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952081	76952081	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	48	488	1	ENST00000373344.5:c.354G>A	p.Met118Ile	p.M118I	ENST00000373344	NM_000489.3	118	atG/atA	5/35	1	2	FACETS	0.443	0.373	0.52	0.443	0.373	0.52	SUBCLONAL	1	TRUE	1	0.279047383579025	2		489	777	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073446	8073446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	41	493	0	ENST00000377482.5:c.1213G>A	p.Asp405Asn	p.D405N	ENST00000377482	NM_018948.3	405	Gac/Aac	4/4	0.279047383579025	1	FACETS	0.345	0.287	0.411	0.345	0.287	0.411	SUBCLONAL	1	TRUE	0	0.279047383579025	1		493	732	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101568	27101568	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760575192	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	65	896	1	ENST00000324856.7:c.4850G>A	p.Gly1617Asp	p.G1617D	ENST00000324856	NM_006015.4	1617	gGt/gAt	18/20	0.279047383579025	1	FACETS	0.342	0.295	0.394	0.342	0.295	0.394	SUBCLONAL	1	TRUE	0	0.279047383579025	1		897	1171	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106183	27106183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781038652	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	57	615	0	ENST00000324856.7:c.5794G>A	p.Ala1932Thr	p.A1932T	ENST00000324856	NM_006015.4	1932	Gcc/Acc	20/20	0.279047383579025	1	FACETS	0.398	0.34	0.461	0.398	0.34	0.461	SUBCLONAL	1	TRUE	0	0.279047383579025	1		615	884	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106678	27106678	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	69	696	1	ENST00000324856.7:c.6289G>A	p.Ala2097Thr	p.A2097T	ENST00000324856	NM_006015.4	2097	Gct/Act	20/20	0.279047383579025	1	FACETS	0.472	0.41	0.54	0.472	0.41	0.54	SUBCLONAL	1	TRUE	0	0.279047383579025	1		697	901	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28607227	28607227	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	49	513	0	ENST00000253063.3:c.1357G>A	p.Val453Ile	p.V453I	ENST00000253063	NM_031459.4	453	Gtc/Atc	10/10	0.279047383579025	1	FACETS	0.423	0.357	0.496	0.423	0.357	0.496	SUBCLONAL	1	TRUE	0	0.279047383579025	1		513	714	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363414	40363414	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	57	661	2	ENST00000397332.2:c.815C>T	p.Ala272Val	p.A272V	ENST00000397332	NM_001033082.2	272	gCt/gTt	3/3	0.279047383579025	1	FACETS	0.369	0.315	0.428	0.369	0.315	0.428	SUBCLONAL	1	TRUE	0	0.279047383579025	1		663	953	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532698	46532698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	52	471	1	ENST00000262741.5:c.380C>T	p.Pro127Leu	p.P127L	ENST00000262741	NM_003629.3	127	cCt/cTt	4/10	0.279047383579025	1	FACETS	0.461	0.392	0.538	0.461	0.392	0.538	SUBCLONAL	1	TRUE	0	0.279047383579025	1		472	695	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439857	51439857	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	38	413	1	ENST00000262662.1:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000262662		141	tGt/tAt	4/4	0.279047383579025	1	FACETS	0.368	0.303	0.441	0.368	0.303	0.441	SUBCLONAL	1	TRUE	0	0.279047383579025	1		414	637	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058509	72058509	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs546160294	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	41	402	0	ENST00000357731.5:c.931C>T	p.Pro311Ser	p.P311S	ENST00000357731	NM_173808.2	311	Cct/Tct	6/7	0.252486392077422	1	FACETS	0.424	0.352	0.503	0.424	0.352	0.503	SUBCLONAL	1	TRUE	0	0.279047383579025	1		402	597	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430028	78430028	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	38	369	0	ENST00000370768.2:c.851G>A	p.Arg284Lys	p.R284K	ENST00000370768	NM_003902.3	284	aGa/aAa	11/20	0.252486392077422	1	FACETS	0.446	0.368	0.534	0.446	0.368	0.534	SUBCLONAL	1	TRUE	0	0.279047383579025	1		369	525	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165896	118165896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	44	360	0	ENST00000369448.3:c.406G>A	p.Glu136Lys	p.E136K	ENST00000369448	NM_017709.3	136	Gag/Aag	2/2	0.252486392077422	1	FACETS	0.482	0.404	0.569	0.482	0.404	0.569	SUBCLONAL	1	TRUE	0	0.279047383579025	1		360	563	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724988	162724988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	47	435	0	ENST00000367921.3:c.460G>A	p.Asp154Asn	p.D154N	ENST00000367921	NM_006182.2	154	Gac/Aac	6/18	0.252486392077422	1	FACETS	0.387	0.325	0.455	0.387	0.325	0.455	SUBCLONAL	1	TRUE	0	0.279047383579025	1		435	749	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094256	193094256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	40	507	0	ENST00000367435.3:c.146G>A	p.Gly49Asp	p.G49D	ENST00000367435	NM_024529.4	49	gGc/gAc	2/17	0.252486392077422	1	FACETS	0.328	0.271	0.391	0.328	0.271	0.391	SUBCLONAL	1	TRUE	0	0.279047383579025	1		507	752	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651124	206651124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1157	63	879	1	ENST00000367120.3:c.734C>T	p.Ala245Val	p.A245V	ENST00000367120	NM_014002.3	245	gCc/gTc	8/22	0.279047383579025	1	FACETS	0.318	0.274	0.367	0.318	0.274	0.367	SUBCLONAL	1	TRUE	0	0.279047383579025	1		880	1220	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246493836	246493836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	42	548	0	ENST00000388985.4:c.340G>A	p.Asp114Asn	p.D114N	ENST00000388985		114	Gat/Aat	4/12	0.279047383579025	1	FACETS	0.342	0.284	0.406	0.342	0.284	0.406	SUBCLONAL	1	TRUE	0	0.279047383579025	1		548	758	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653866	89653866	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	39	456	0	ENST00000371953.3:c.164G>A	p.Arg55Lys	p.R55K	ENST00000371953	NM_000314.4	55	aGg/aAg	2/9	0.252486392077422	1	FACETS	0.344	0.284	0.411	0.344	0.284	0.411	SUBCLONAL	1	TRUE	0	0.279047383579025	1		456	699	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104264007	104264007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	52	644	0	ENST00000369902.3:c.98G>A	p.Gly33Glu	p.G33E	ENST00000369902	NM_016169.3	33	gGa/gAa	1/12	0.252486392077422	1	FACETS	0.308	0.261	0.36	0.308	0.261	0.36	SUBCLONAL	1	TRUE	0	0.279047383579025	1		644	1040	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925549	114925549	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1462838841	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	58	661	0	ENST00000543371.1:c.1627G>A	p.Ala543Thr	p.A543T	ENST00000543371	NM_001198531.1	543	Gcc/Acc	14/14	0.252486392077422	1	FACETS	0.383	0.327	0.443	0.383	0.327	0.443	SUBCLONAL	1	TRUE	0	0.279047383579025	1		661	935	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742892	17742892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1343275574	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	60	679	0	ENST00000250003.3:c.800C>T	p.Pro267Leu	p.P267L	ENST00000250003	NM_002478.4	267	cCc/cTc	3/3	0.252486392077422	1	FACETS	0.412	0.354	0.476	0.412	0.354	0.476	SUBCLONAL	1	TRUE	0	0.279047383579025	1		679	898	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456564	32456564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs916583720	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	23	214	0	ENST00000332351.3:c.328C>T	p.Pro110Ser	p.P110S	ENST00000332351	NM_024426.4	110	Ccc/Tcc	1/10	0.252486392077422	1	FACETS	0.476	0.371	0.597	0.476	0.371	0.597	SUBCLONAL	1	TRUE	0	0.279047383579025	1		214	298	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102056776	102056776	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	46	534	0	ENST00000282441.5:c.716C>T	p.Ala239Val	p.A239V	ENST00000282441	NM_001130145.2	239	gCc/gTc	4/9	0.252486392077422	1	FACETS	0.365	0.306	0.43	0.365	0.306	0.43	SUBCLONAL	1	TRUE	0	0.279047383579025	1		534	777	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153491	108153491	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745467552	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	44	496	1	ENST00000278616.4:c.3631G>A	p.Ala1211Thr	p.A1211T	ENST00000278616	NM_000051.3	1211	Gca/Aca	25/63	0.252486392077422	1	FACETS	0.342	0.286	0.405	0.342	0.286	0.405	SUBCLONAL	1	TRUE	0	0.279047383579025	1		497	793	SUCCESS
ATM	472	MSKCC	GRCh37	11	108159725	108159725	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	63	799	0	ENST00000278616.4:c.4131T>A	p.Asn1377Lys	p.N1377K	ENST00000278616	NM_000051.3	1377	aaT/aaA	28/63	0.252486392077422	1	FACETS	0.337	0.29	0.388	0.337	0.29	0.388	SUBCLONAL	1	TRUE	0	0.279047383579025	1		799	1153	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169242	119169242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	39	428	1	ENST00000264033.4:c.2426C>T	p.Pro809Leu	p.P809L	ENST00000264033	NM_005188.3	809	cCt/cTt	15/16	0.252486392077422	1	FACETS	0.357	0.295	0.426	0.357	0.295	0.426	SUBCLONAL	1	TRUE	0	0.279047383579025	1		429	674	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416885	416885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	37	405	0	ENST00000399788.2:c.3665G>A	p.Arg1222Lys	p.R1222K	ENST00000399788	NM_001042603.1	1222	aGg/aAg	23/28	1	2	FACETS	0.382	0.314	0.459	0.382	0.314	0.459	SUBCLONAL	1	TRUE	1	0.279047383579025	2		405	694	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435052	18435052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	96	389	0	ENST00000266497.5:c.37G>A	p.Glu13Lys	p.E13K	ENST00000266497		13	Gaa/Aaa	1/31	1	2	FACETS	0.948	0.845	1	0.948	0.845	1	CLONAL	1	TRUE	1	0.279047383579025	2		389	726	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434484	49434484	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1317	75	845	0	ENST00000301067.7:c.7069G>A	p.Ala2357Thr	p.A2357T	ENST00000301067	NM_003482.3	2357	Gct/Act	31/54	1	2	FACETS	0.386	0.337	0.44	0.386	0.337	0.44	SUBCLONAL	1	TRUE	1	0.279047383579025	2		845	1392	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557561	21557561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	57	693	0	ENST00000382592.4:c.2284G>A	p.Val762Ile	p.V762I	ENST00000382592	NM_014572.2	762	Gtc/Atc	5/8	0.163567605679316	1	FACETS	0.325	0.277	0.377	0.325	0.277	0.377	INDETERMINATE	1	TRUE	0	0.279047383579025	1		693	1083	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29068956	29068956	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs942859011	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	34	491	0	ENST00000282397.4:c.25G>A	p.Val9Ile	p.V9I	ENST00000282397	NM_002019.4	9	Gtc/Atc	1/30	0.163567605679316	1	FACETS	0.312	0.254	0.378	0.312	0.254	0.378	INDETERMINATE	1	TRUE	0	0.279047383579025	1		491	671	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944653	32944653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555287651	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	46	539	2	ENST00000380152.3:c.8446G>A	p.Gly2816Ser	p.G2816S	ENST00000380152		2816	Ggt/Agt	19/27	0.163567605679316	1	FACETS	0.333	0.279	0.393	0.333	0.279	0.393	INDETERMINATE	1	TRUE	0	0.279047383579025	1		541	852	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945195	32945195	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	56	566	2	ENST00000380152.3:c.8590G>A	p.Ala2864Thr	p.A2864T	ENST00000380152		2864	Gcc/Acc	20/27	0.163567605679316	1	FACETS	0.351	0.3	0.408	0.351	0.3	0.408	INDETERMINATE	1	TRUE	0	0.279047383579025	1		568	983	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986760	36986760	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	24	191	0	ENST00000354822.5:c.929C>T	p.Ala310Val	p.A310V	ENST00000354822	NM_001079668.2	310	gCc/gTc	3/3	1	2	FACETS	0.483	0.379	0.604	0.483	0.379	0.604	SUBCLONAL	1	TRUE	1	0.279047383579025	2		191	356	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420312	88420312	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	47	539	1	ENST00000360948.2:c.2374C>T	p.Pro792Ser	p.P792S	ENST00000360948	NM_001012338.2	792	Ccc/Tcc	19/19	0.252486392077422	1	FACETS	0.345	0.29	0.406	0.345	0.29	0.406	SUBCLONAL	1	TRUE	0	0.279047383579025	1		540	841	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647172	23647172	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	65	719	0	ENST00000261584.4:c.695G>A	p.Gly232Asp	p.G232D	ENST00000261584	NM_024675.3	232	gGt/gAt	4/13	0.163567605679316	1	FACETS	0.315	0.272	0.363	0.315	0.272	0.363	INDETERMINATE	1	TRUE	0	0.279047383579025	1		719	1272	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129072	30129072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	61	690	0	ENST00000263025.4:c.694G>A	p.Gly232Ser	p.G232S	ENST00000263025	NM_002746.2	232	Ggc/Agc	5/9	0.163567605679316	1	FACETS	0.333	0.286	0.385	0.333	0.286	0.385	INDETERMINATE	1	TRUE	0	0.279047383579025	1		690	1129	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819758	81819758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	39	463	1	ENST00000359376.3:c.164G>A	p.Ser55Asn	p.S55N	ENST00000359376	NM_002661.3	55	aGc/aAc	2/33	0.163567605679316	1	FACETS	0.337	0.278	0.403	0.337	0.278	0.403	INDETERMINATE	1	TRUE	0	0.279047383579025	1		464	714	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805545	89805545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769115368	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	40	530	0	ENST00000389301.3:c.4163G>A	p.Gly1388Asp	p.G1388D	ENST00000389301	NM_000135.2	1388	gGt/gAt	41/43	0.279047383579025	1	FACETS	0.329	0.273	0.393	0.329	0.273	0.393	SUBCLONAL	1	TRUE	0	0.279047383579025	1		530	749	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15960865	15960865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	26	264	0	ENST00000268712.3:c.6355G>A	p.Val2119Ile	p.V2119I	ENST00000268712	NM_006311.3	2119	Gtc/Atc	40/46	1	2	FACETS	0.391	0.309	0.485	0.391	0.309	0.485	SUBCLONAL	1	TRUE	1	0.279047383579025	2		264	477	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075254	16075254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	46	477	0	ENST00000268712.3:c.298G>A	p.Asp100Asn	p.D100N	ENST00000268712	NM_006311.3	100	Gat/Aat	4/46	1	2	FACETS	0.363	0.304	0.428	0.363	0.304	0.428	SUBCLONAL	1	TRUE	1	0.279047383579025	2		477	909	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685503	29685503	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	84	327	0	ENST00000356175.3:c.7913A>T	p.Asn2638Ile	p.N2638I	ENST00000356175	NM_000267.3	2638	aAt/aTt	54/57	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.279047383579025	2		327	562	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441509	40441509	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1321	75	796	0	ENST00000345506.4:c.80C>T	p.Pro27Leu	p.P27L	ENST00000345506	NM_003152.3	27	cCc/cTc	3/20	1	2	FACETS	0.385	0.336	0.439	0.385	0.336	0.439	SUBCLONAL	1	TRUE	1	0.279047383579025	2		796	1396	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740658	58740658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774404279	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	62	756	0	ENST00000305921.3:c.1563G>A	p.Met521Ile	p.M521I	ENST00000305921	NM_003620.3	521	atG/atA	6/6	1	2	FACETS	0.388	0.334	0.448	0.388	0.334	0.448	SUBCLONAL	1	TRUE	1	0.279047383579025	2		756	1144	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775192	73775192	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	55	574	0	ENST00000254810.4:c.64G>A	p.Ala22Thr	p.A22T	ENST00000254810	NM_005324.3	22	Gcc/Acc	2/4	1	2	FACETS	0.415	0.353	0.482	0.415	0.353	0.482	SUBCLONAL	1	TRUE	1	0.279047383579025	2		574	951	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78933900	78933900	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	56	700	0	ENST00000306801.3:c.3500G>A	p.Ser1167Asn	p.S1167N	ENST00000306801	NM_020761.2	1167	aGc/aAc	30/34	1	2	FACETS	0.384	0.328	0.447	0.384	0.328	0.447	SUBCLONAL	1	TRUE	1	0.279047383579025	2		700	1044	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743097	743097	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	47	496	0	ENST00000314574.4:c.881G>A	p.Gly294Glu	p.G294E	ENST00000314574	NM_005433.3	294	gGa/gAa	8/12	1	2	FACETS	0.391	0.329	0.461	0.391	0.329	0.461	SUBCLONAL	1	TRUE	1	0.279047383579025	2		496	861	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39537704	39537704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201632301	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	32	347	0	ENST00000262039.4:c.238G>A	p.Ala80Thr	p.A80T	ENST00000262039	NM_002647.2	80	Gca/Aca	2/25	1	2	FACETS	0.369	0.299	0.45	0.369	0.299	0.45	SUBCLONAL	1	TRUE	1	0.279047383579025	2		347	621	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226553	2226553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1243	76	827	5	ENST00000398665.3:c.4033G>A	p.Ala1345Thr	p.A1345T	ENST00000398665	NM_032482.2	1345	Gcc/Acc	27/28	0.178807658844693	1	FACETS	0.355	0.31	0.404	0.355	0.31	0.404	SUBCLONAL	1	TRUE	0	0.279047383579025	1		832	1319	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226988	2226988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs925877630	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	64	782	1	ENST00000398665.3:c.4468G>A	p.Gly1490Ser	p.G1490S	ENST00000398665	NM_032482.2	1490	Ggc/Agc	27/28	0.178807658844693	1	FACETS	0.374	0.323	0.43	0.374	0.323	0.43	SUBCLONAL	1	TRUE	0	0.279047383579025	1		783	1055	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629073	14629073	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	38	471	0	ENST00000254322.2:c.89G>T	p.Arg30Leu	p.R30L	ENST00000254322	NM_006145.1	30	cGc/cTc	1/3	1	2	FACETS	0.392	0.323	0.47	0.392	0.323	0.47	SUBCLONAL	1	TRUE	1	0.279047383579025	2		471	694	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271594	15271594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs893908856	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1564	84	1146	1	ENST00000263388.2:c.6845C>T	p.Thr2282Ile	p.T2282I	ENST00000263388	NM_000435.2	2282	aCc/aTc	33/33	1	2	FACETS	0.365	0.321	0.413	0.365	0.321	0.413	SUBCLONAL	1	TRUE	1	0.279047383579025	2		1147	1648	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299941	15299941	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755361843	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	73	644	0	ENST00000263388.2:c.1237G>A	p.Gly413Ser	p.G413S	ENST00000263388	NM_000435.2	413	Ggc/Agc	8/33	1	2	FACETS	0.439	0.383	0.501	0.439	0.383	0.501	SUBCLONAL	1	TRUE	1	0.279047383579025	2		644	1191	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302861	15302861	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746681101	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1369	73	868	0	ENST00000263388.2:c.589C>T	p.Pro197Ser	p.P197S	ENST00000263388	NM_000435.2	197	Ccc/Tcc	4/33	1	2	FACETS	0.363	0.316	0.414	0.363	0.316	0.414	SUBCLONAL	1	TRUE	1	0.279047383579025	2		868	1442	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222821	36222821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1355	83	951	0	ENST00000222270.7:c.5450G>A	p.Gly1817Asp	p.G1817D	ENST00000222270	NM_014727.1	1817	gGt/gAt	27/37	1	2	FACETS	0.414	0.363	0.468	0.414	0.363	0.468	SUBCLONAL	1	TRUE	1	0.279047383579025	2		951	1438	SUCCESS
ALK	238	MSKCC	GRCh37	2	29436886	29436886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	51	668	0	ENST00000389048.3:c.3707G>A	p.Gly1236Asp	p.G1236D	ENST00000389048	NM_004304.4	1236	gGc/gAc	24/29	0.279047383579025	1	FACETS	0.345	0.292	0.404	0.345	0.292	0.404	SUBCLONAL	1	TRUE	0	0.279047383579025	1		668	911	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519909	29519909	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	47	586	0	ENST00000389048.3:c.1662G>A	p.Trp554Ter	p.W554*	ENST00000389048	NM_004304.4	554	tgG/tgA	9/29	0.279047383579025	1	FACETS	0.395	0.333	0.465	0.395	0.333	0.465	SUBCLONAL	1	TRUE	0	0.279047383579025	1		586	733	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248498	212248498	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	39	510	2	ENST00000342788.4:c.3769G>A	p.Asp1257Asn	p.D1257N	ENST00000342788	NM_005235.2	1257	Gac/Aac	28/28	0.279047383579025	1	FACETS	0.335	0.276	0.4	0.335	0.276	0.4	SUBCLONAL	1	TRUE	0	0.279047383579025	1		512	719	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248732	212248732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775424927	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	26	357	0	ENST00000342788.4:c.3535G>A	p.Asp1179Asn	p.D1179N	ENST00000342788	NM_005235.2	1179	Gac/Aac	28/28	0.279047383579025	1	FACETS	0.343	0.271	0.426	0.343	0.271	0.426	SUBCLONAL	1	TRUE	0	0.279047383579025	1		357	467	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662397	227662397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879145611	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	62	590	0	ENST00000305123.5:c.1058G>A	p.Arg353Lys	p.R353K	ENST00000305123	NM_005544.2	353	aGa/aAa	1/2	0.279047383579025	1	FACETS	0.468	0.403	0.539	0.468	0.403	0.539	SUBCLONAL	1	TRUE	0	0.279047383579025	1		590	817	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662754	227662754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	66	780	1	ENST00000305123.5:c.701G>A	p.Gly234Glu	p.G234E	ENST00000305123	NM_005544.2	234	gGg/gAg	1/2	0.279047383579025	1	FACETS	0.362	0.313	0.416	0.362	0.313	0.416	SUBCLONAL	1	TRUE	0	0.279047383579025	1		781	1124	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40709529	40709529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	54	524	1	ENST00000373198.4:c.4373G>A	p.Ser1458Asn	p.S1458N	ENST00000373198	NM_133170.3	1458	aGc/aAc	32/32	1	2	FACETS	0.413	0.351	0.481	0.413	0.351	0.481	SUBCLONAL	1	TRUE	1	0.279047383579025	2		525	937	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790018	40790018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752454448	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	45	466	0	ENST00000373198.4:c.2713G>A	p.Gly905Ser	p.G905S	ENST00000373198	NM_133170.3	905	Ggc/Agc	18/32	1	2	FACETS	0.397	0.332	0.469	0.397	0.332	0.469	SUBCLONAL	1	TRUE	1	0.279047383579025	2		466	813	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62293297	62293297	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	54	576	0	ENST00000360203.5:c.395+1G>A		p.X132_splice	ENST00000360203	NM_001283009.1	132			1	2	FACETS	0.413	0.352	0.481	0.413	0.352	0.481	SUBCLONAL	1	TRUE	1	0.279047383579025	2		576	936	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62316903	62316903	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	50	686	0	ENST00000360203.5:c.1219G>A	p.Gly407Ser	p.G407S	ENST00000360203	NM_001283009.1	407	Ggc/Agc	15/35	1	2	FACETS	0.364	0.308	0.427	0.364	0.308	0.427	SUBCLONAL	1	TRUE	1	0.279047383579025	2		686	984	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324165	62324165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568717000	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	57	601	1	ENST00000360203.5:c.2660C>T	p.Pro887Leu	p.P887L	ENST00000360203	NM_001283009.1	887	cCc/cTc	29/35	1	2	FACETS	0.433	0.37	0.502	0.433	0.37	0.502	SUBCLONAL	1	TRUE	1	0.279047383579025	2		602	944	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130606	29130606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786203185	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	42	487	0	ENST00000328354.6:c.104C>T	p.Ser35Phe	p.S35F	ENST00000328354	NM_007194.3	35	tCc/tTc	2/15	0.252486392077422	1	FACETS	0.336	0.28	0.4	0.336	0.28	0.4	SUBCLONAL	1	TRUE	0	0.279047383579025	1		487	770	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564604	41564604	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	55	661	1	ENST00000263253.7:c.4025+1G>A		p.X1342_splice	ENST00000263253	NM_001429.3	1342			0.252486392077422	1	FACETS	0.369	0.315	0.43	0.369	0.315	0.43	SUBCLONAL	1	TRUE	0	0.279047383579025	1		662	918	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067368	37067368	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1559553501	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	94	474	0	ENST00000231790.2:c.1279C>T	p.Gln427Ter	p.Q427*	ENST00000231790	NM_000249.3	427	Caa/Taa	12/19	0.252486392077422	1	FACETS	0.794	0.707	0.888	0.794	0.707	0.888	SUBCLONAL	1	TRUE	0	0.279047383579025	1		474	730	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147554	47147554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	47	542	0	ENST00000409792.3:c.4772C>T	p.Ala1591Val	p.A1591V	ENST00000409792	NM_014159.6	1591	gCt/gTt	6/21	0.252486392077422	1	FACETS	0.343	0.288	0.403	0.343	0.288	0.403	SUBCLONAL	1	TRUE	0	0.279047383579025	1		542	846	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162299	47162299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1224797626	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	31	377	0	ENST00000409792.3:c.3827G>A	p.Ser1276Asn	p.S1276N	ENST00000409792	NM_014159.6	1276	aGt/aAt	3/21	0.252486392077422	1	FACETS	0.337	0.272	0.412	0.337	0.272	0.412	SUBCLONAL	1	TRUE	0	0.279047383579025	1		377	567	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928902	49928902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1269	76	993	3	ENST00000296474.3:c.3464G>A	p.Gly1155Asp	p.G1155D	ENST00000296474	NM_002447.2	1155	gGc/gAc	16/20	0.252486392077422	1	FACETS	0.348	0.304	0.397	0.348	0.304	0.397	SUBCLONAL	1	TRUE	0	0.279047383579025	1		996	1345	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933519	49933519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1387	79	1056	3	ENST00000296474.3:c.2671G>A	p.Ala891Thr	p.A891T	ENST00000296474	NM_002447.2	891	Gct/Act	11/20	0.252486392077422	1	FACETS	0.332	0.291	0.377	0.332	0.291	0.377	SUBCLONAL	1	TRUE	0	0.279047383579025	1		1059	1466	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52661386	52661386	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	26	346	0	ENST00000394830.3:c.1444G>A	p.Ala482Thr	p.A482T	ENST00000394830	NM_018313.4	482	Gca/Aca	14/30	0.252486392077422	1	FACETS	0.32	0.253	0.398	0.32	0.253	0.398	SUBCLONAL	1	TRUE	0	0.279047383579025	1		346	501	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205754	128205754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143590990	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	60	881	0	ENST00000341105.2:c.121C>T	p.Pro41Ser	p.P41S	ENST00000341105	NM_032638.4	41	Cct/Tct	2/6	0.279047383579025	1	FACETS	0.326	0.28	0.377	0.326	0.28	0.377	SUBCLONAL	1	TRUE	0	0.279047383579025	1		881	1135	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281925	142281925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	32	408	0	ENST00000350721.4:c.319C>T	p.Leu107Phe	p.L107F	ENST00000350721	NM_001184.3	107	Ctt/Ttt	4/47	0.279047383579025	1	FACETS	0.31	0.25	0.377	0.31	0.25	0.377	SUBCLONAL	1	TRUE	0	0.279047383579025	1		408	637	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806180	1806180	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1330	70	974	1	ENST00000260795.2:c.1199G>A	p.Ser400Asn	p.S400N	ENST00000260795		400	aGc/aAc	8/17	NA	2	FACETS	0.358	0.311	0.41			1	INDETERMINATE	1	TRUE	NA	0.279047383579025	2		975	1400	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902470	1902470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	54	652	1	ENST00000382891.5:c.89G>A	p.Ser30Asn	p.S30N	ENST00000382891	NM_133335.3	30	aGt/aAt	2/22	NA	2	FACETS	0.365	0.31	0.425			1	INDETERMINATE	1	TRUE	NA	0.279047383579025	2		653	1061	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518048	187518048	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1289723175	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	45	715	0	ENST00000441802.2:c.12646C>T	p.Pro4216Ser	p.P4216S	ENST00000441802	NM_005245.3	4216	Cct/Tct	25/27	0.174964171627586	0	FACETS	0.265	0.222	0.314			1	SUBCLONAL	1	TRUE	0	0.279047383579025	0		715	876	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278793	1278793	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867111529	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	50	560	2	ENST00000310581.5:c.2249C>T	p.Ala750Val	p.A750V	ENST00000310581	NM_198253.2	750	gCc/gTc	6/16	NA	2	FACETS	0.376	0.317	0.44			1	INDETERMINATE	1	TRUE	NA	0.279047383579025	2		562	954	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294018	1294018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1635	87	1228	1	ENST00000310581.5:c.983C>T	p.Thr328Ile	p.T328I	ENST00000310581	NM_198253.2	328	aCc/aTc	2/16	NA	2	FACETS	0.362	0.319	0.409			1	INDETERMINATE	1	TRUE	NA	0.279047383579025	2		1229	1722	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86658440	86658440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	46	268	0	ENST00000274376.6:c.1405G>A	p.Asp469Asn	p.D469N	ENST00000274376	NM_002890.2	469	Gat/Aat	10/25	1	2	FACETS	0.63	0.531	0.741	0.63	0.531	0.741	SUBCLONAL	1	TRUE	1	0.279047383579025	2		268	523	SUCCESS
APC	324	MSKCC	GRCh37	5	112173965	112173965	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	37	357	0	ENST00000257430.4:c.2674G>A	p.Glu892Lys	p.E892K	ENST00000257430	NM_000038.5	892	Gaa/Aaa	16/16	1	2	FACETS	0.371	0.305	0.445	0.371	0.305	0.445	SUBCLONAL	1	TRUE	1	0.279047383579025	2		357	715	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176700690	176700690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	47	522	0	ENST00000439151.2:c.5527G>A	p.Ala1843Thr	p.A1843T	ENST00000439151	NM_022455.4	1843	Gca/Aca	17/23	1	2	FACETS	0.361	0.304	0.426	0.361	0.304	0.426	SUBCLONAL	1	TRUE	1	0.279047383579025	2		522	932	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675538	30675538	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	83	731	0	ENST00000376406.3:c.2818G>A	p.Val940Met	p.V940M	ENST00000376406	NM_014641.2	940	Gtg/Atg	8/15	0.252486392077422	1	FACETS	0.456	0.401	0.516	0.456	0.401	0.516	SUBCLONAL	1	TRUE	0	0.279047383579025	1		731	1122	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948279	31948279	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	55	719	0	ENST00000375333.2:c.867G>A	p.Trp289Ter	p.W289*	ENST00000375333	NM_032454.1	289	tgG/tgA	6/8	0.252486392077422	1	FACETS	0.327	0.279	0.381	0.327	0.279	0.381	SUBCLONAL	1	TRUE	0	0.279047383579025	1		719	1037	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805365	32805365	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	54	697	1	ENST00000374899.4:c.557C>T	p.Pro186Leu	p.P186L	ENST00000374899	NM_018833.2	186	cCc/cTc	3/12	0.252486392077422	1	FACETS	0.311	0.264	0.362	0.311	0.264	0.362	SUBCLONAL	1	TRUE	0	0.279047383579025	1		698	1072	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287794	33287794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1209	65	836	0	ENST00000374542.5:c.1459G>A	p.Ala487Thr	p.A487T	ENST00000374542	NM_001141970.1	487	Gca/Aca	5/8	0.252486392077422	1	FACETS	0.315	0.271	0.362	0.315	0.271	0.362	SUBCLONAL	1	TRUE	0	0.279047383579025	1		836	1274	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099590	157099590	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	30	200	0	ENST00000346085.5:c.527C>T	p.Pro176Leu	p.P176L	ENST00000346085	NM_020732.3	176	cCg/cTg	1/20	0.279047383579025	1	FACETS	0.607	0.49	0.738	0.607	0.49	0.738	SUBCLONAL	1	TRUE	0	0.279047383579025	1		200	305	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6048628	6048628	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1352544158	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	62	674	1	ENST00000265849.7:c.23G>A	p.Ser8Asn	p.S8N	ENST00000265849	NM_000535.5	8	aGt/aAt	1/15	1	2	FACETS	0.385	0.331	0.445	0.385	0.331	0.445	SUBCLONAL	1	TRUE	1	0.279047383579025	2		675	1153	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340049	116340049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1254719560	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	23	270	0	ENST00000397752.3:c.911G>A	p.Arg304Lys	p.R304K	ENST00000397752	NM_000245.2	304	aGa/aAa	2/21	1	2	FACETS	0.359	0.279	0.452	0.359	0.279	0.452	SUBCLONAL	1	TRUE	1	0.279047383579025	2		270	459	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418952	116418952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	40	369	0	ENST00000397752.3:c.3463G>A	p.Val1155Met	p.V1155M	ENST00000397752	NM_000245.2	1155	Gtg/Atg	17/21	1	2	FACETS	0.441	0.365	0.526	0.441	0.365	0.526	SUBCLONAL	1	TRUE	1	0.279047383579025	2		369	650	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453148	140453148	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507483	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	24	546	0	ENST00000288602.6:c.1787G>A	p.Gly596Asp	p.G596D	ENST00000288602	NM_004333.4	596	gGt/gAt	15/18	1	2	FACETS	0.187	0.145	0.235	0.187	0.145	0.235	SUBCLONAL	1	TRUE	1	0.279047383579025	2		546	921	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481457	140481457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	67	785	1	ENST00000288602.6:c.1351G>A	p.Glu451Lys	p.E451K	ENST00000288602	NM_004333.4	451	Gag/Aag	11/18	1	2	FACETS	0.418	0.362	0.479	0.418	0.362	0.479	SUBCLONAL	1	TRUE	1	0.279047383579025	2		786	1149	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849944	151849944	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241408105	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	40	537	0	ENST00000262189.6:c.12372G>A	p.Met4124Ile	p.M4124I	ENST00000262189	NM_170606.2	4124	atG/atA	49/59	1	2	FACETS	0.358	0.297	0.428	0.358	0.297	0.428	SUBCLONAL	1	TRUE	1	0.279047383579025	2		537	800	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372412	55372412	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1396	80	1043	1	ENST00000297316.4:c.1102C>T	p.His368Tyr	p.H368Y	ENST00000297316	NM_022454.3	368	Cac/Tac	2/2	0.252486392077422	1	FACETS	0.334	0.293	0.379	0.334	0.293	0.379	SUBCLONAL	1	TRUE	0	0.279047383579025	1		1044	1476	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866473	56866473	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	63	812	0	ENST00000519728.1:c.720G>A	p.Trp240Ter	p.W240*	ENST00000519728	NM_002350.3	240	tgG/tgA	8/13	0.252486392077422	1	FACETS	0.342	0.294	0.394	0.342	0.294	0.394	SUBCLONAL	1	TRUE	0	0.279047383579025	1		812	1137	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126332	5126332	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	30	261	0	ENST00000381652.3:c.3178-1G>A		p.X1060_splice	ENST00000381652	NM_004972.3	1060			1	2	FACETS	0.457	0.367	0.558	0.457	0.367	0.558	SUBCLONAL	1	TRUE	1	0.279047383579025	2		261	471	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484147	8484147	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	49	476	0	ENST00000356435.5:c.3385C>T	p.Pro1129Ser	p.P1129S	ENST00000356435		1129	Cct/Tct	19/35	1	2	FACETS	0.403	0.34	0.472	0.403	0.34	0.472	SUBCLONAL	1	TRUE	1	0.279047383579025	2		476	872	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840600	36840600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1389803999	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1216	76	782	0	ENST00000358127.4:c.1133G>A	p.Gly378Glu	p.G378E	ENST00000358127	NM_001280556.1	378	gGa/gAa	10/10	1	2	FACETS	0.422	0.368	0.48	0.422	0.368	0.48	SUBCLONAL	1	TRUE	1	0.279047383579025	2		782	1292	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93607728	93607728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	28	279	0	ENST00000375746.1:c.430G>A	p.Glu144Lys	p.E144K	ENST00000375746	NM_001174167.1	144	Gag/Aag	3/14	1	2	FACETS	0.372	0.296	0.458	0.372	0.296	0.458	SUBCLONAL	1	TRUE	1	0.279047383579025	2		279	540	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641047	93641047	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	38	318	1	ENST00000375746.1:c.1393C>T	p.His465Tyr	p.H465Y	ENST00000375746	NM_001174167.1	465	Cat/Tat	11/14	1	2	FACETS	0.454	0.374	0.543	0.454	0.374	0.543	SUBCLONAL	1	TRUE	1	0.279047383579025	2		319	600	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209351	98209351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747923595	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	45	512	0	ENST00000331920.6:c.4187G>A	p.Gly1396Glu	p.G1396E	ENST00000331920	NM_000264.3	1396	gGa/gAa	23/24	1	2	FACETS	0.376	0.315	0.445	0.376	0.315	0.445	SUBCLONAL	1	TRUE	1	0.279047383579025	2		512	857	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760609	133760609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1541	83	1173	2	ENST00000318560.5:c.2932C>T	p.Pro978Ser	p.P978S	ENST00000318560	NM_005157.4	978	Cca/Tca	11/11	0.163567605679316	1	FACETS	0.315	0.277	0.357	0.315	0.277	0.357	INDETERMINATE	1	TRUE	0	0.279047383579025	1		1175	1624	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401362	139401362	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1241855040	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	74	889	0	ENST00000277541.6:c.3707C>T	p.Pro1236Leu	p.P1236L	ENST00000277541	NM_017617.3	1236	cCc/cTc	23/34	0.163567605679316	1	FACETS	0.37	0.323	0.422	0.37	0.323	0.422	INDETERMINATE	1	TRUE	0	0.279047383579025	1		889	1233	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345273	70345273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	68	779	2	ENST00000374080.3:c.2299G>A	p.Ala767Thr	p.A767T	ENST00000374080		767	Gcc/Acc	16/45	1	2	FACETS	0.378	0.328	0.434	0.378	0.328	0.434	SUBCLONAL	1	TRUE	1	0.279047383579025	2		781	1288	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0013760-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	43	264	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.911	0.762	1	0.911	0.762	1	CLONAL	1	FALSE	1	0.175188036812721	2		264	539	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0013760-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	119	476	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.164880484307808	3	FACETS	0.851	0.768	0.939	0.851	0.768	0.939	CLONAL	2	FALSE	1	0.175188036812721	3		476	868	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0013760-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	197	657	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.175188036812721	2	FACETS	0.921	0.851	0.994	0.921	0.851	0.994	CLONAL	2	FALSE	0	0.175188036812721	2		657	1221	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0013760-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	238	207	9	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	0.157275892718561	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	3	FALSE	1	0.175188036812721	4		216	1034	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013760-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	92	607	1	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	0.989	0.877	1	0.989	0.877	1	CLONAL	1	FALSE	1	0.175188036812721	2		608	1062	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976872	55976872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs551579207	NA	P-0013760-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	102	572	1	ENST00000263923.4:c.1040G>A	p.Arg347His	p.R347H	ENST00000263923	NM_002253.2	347	cGt/cAt	8/30	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	1	0.175188036812721	2		573	1080	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817489	39817489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763409220	NA	P-0013760-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	125	617	0	ENST00000288319.7:c.74C>T	p.Thr25Met	p.T25M	ENST00000288319	NM_182918.3	25	aCg/aTg	2/10	0.164880484307808	3	FACETS	1	0.977	1	0.633	0.572	0.699	CLONAL	1	FALSE	1	0.175188036812721	3		617	1225	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178669	32178669	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766521222	NA	P-0013760-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	178	601	0	ENST00000375023.3:c.2725G>A	p.Asp909Asn	p.D909N	ENST00000375023	NM_004557.3	909	Gac/Aac	18/30	0.141872461907448	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	FALSE	2	0.175188036812721	4		601	1080	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652336	206652336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149219314	NA	P-0013760-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	98	546	1	ENST00000367120.3:c.1043G>A	p.Arg348Gln	p.R348Q	ENST00000367120	NM_014002.3	348	cGa/cAa	10/22	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	FALSE	1	0.175188036812721	2		547	1088	SUCCESS
APC	324	MSKCC	GRCh37	5	112175748	112175754	+	frameshift_variant	Frame_Shift_Del	DEL	ATACTTT	ATACTTT	-	novel	NA	P-0013760-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	67	418	0	ENST00000257430.4:c.4459_4465del	p.Thr1487TyrfsTer18	p.T1487Yfs*18	ENST00000257430	NM_000038.5	1486	gATACTTTa/ga	16/16	0.164880484307808	3	FACETS	0.993	0.861	1	0.496	0.43	0.568	CLONAL	1	FALSE	1	0.175188036812721	3		418	838	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983307	149983307	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013760-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	88	442	0	ENST00000253339.5:c.2951T>G	p.Leu984Arg	p.L984R	ENST00000253339		984	cTt/cGt	7/7	0.164880484307808	3	FACETS	1	0.939	1	0.549	0.485	0.618	CLONAL	1	FALSE	1	0.175188036812721	3		442	995	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600369	10600369	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013773-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	461	691	0	ENST00000171111.5:c.1486G>T	p.Glu496Ter	p.E496*	ENST00000171111	NM_203500.1	496	Gag/Tag	4/6	0.114577495670113	6	FACETS	1	0.992	1			1	INDETERMINATE	3	FALSE	NA	0.442765714449022	6		691	1142	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577569	7577569	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519981	NA	P-0013773-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	379	553	0	ENST00000269305.4:c.712T>C	p.Cys238Arg	p.C238R	ENST00000269305	NM_001126112.2	238	Tgt/Cgt	7/11	0.332111173720858	3	FACETS	1	0.988	1	0.74	0.705	0.775	CLONAL	2	FALSE	0	0.442765714449022	3		553	942	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717699	89717699	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554825210	NA	P-0013773-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	339	458	0	ENST00000371953.3:c.724G>T	p.Glu242Ter	p.E242*	ENST00000371953	NM_000314.4	242	Gag/Tag	7/9	0.442765714449022	3	FACETS	1	0.984	1	0.722	0.686	0.759	CLONAL	2	FALSE	0	0.442765714449022	3		458	863	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098521	11098521	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013773-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	306	428	0	ENST00000358026.2:c.1039C>T	p.Gln347Ter	p.Q347*	ENST00000358026	NM_001128849.1	347	Cag/Tag	6/36	0.114577495670113	6	FACETS	0.968	0.92	1			1	INDETERMINATE	4	FALSE	NA	0.442765714449022	6		428	673	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148645	20148645	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013773-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	162	426	0	ENST00000379607.5:c.418G>C	p.Asp140His	p.D140H	ENST00000379607	NM_001412.3	140	Gat/Cat	6/7	0.234590002847136	5	FACETS	0.937	0.857	1	0.312	0.285	0.34	INDETERMINATE	1	FALSE	2	0.442765714449022	5		426	1300	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0013794-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	71	393	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.877	0.765	0.999	1	0.979	1	CLONAL	2	TRUE	1	0.11	2		393	736	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730870	40730870	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs780215457	NA	P-0013794-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	35	572	0	ENST00000373198.4:c.3665A>G	p.His1222Arg	p.H1222R	ENST00000373198	NM_133170.3	1222	cAt/cGt	27/32	1	2	FACETS	1	0.845	1	1	0.845	1	CLONAL	1	TRUE	1	0.11	2		572	614	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579359	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587780066	NA	P-0013798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	307	632	0	ENST00000269305.4:c.328del	p.Arg110ValfsTer13	p.R110Vfs*13	ENST00000269305	NM_001126112.2	110	Cgt/gt	4/11	0.246088447752152	2	FACETS	0.841	0.793	0.89	0.841	0.793	0.89	CLONAL	2	TRUE	0	0.331895408547651	2		632	1100	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143032	58143032	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs143670820	NA	P-0013798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	152	550	0	ENST00000257904.6:c.752C>G	p.Pro251Arg	p.P251R	ENST00000257904	NM_000075.3	251	cCc/cGc	7/8	1	2	FACETS	0.756	0.689	0.825	0.756	0.689	0.825	SUBCLONAL	1	TRUE	1	0.331895408547651	2		550	1212	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163618	32163618	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013798-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	86	467	0	ENST00000375023.3:c.5608C>A	p.Pro1870Thr	p.P1870T	ENST00000375023	NM_004557.3	1870	Cct/Act	30/30	0.264316461139171	4	FACETS	0.733	0.647	0.825	0.366	0.323	0.413	SUBCLONAL	1	TRUE	2	0.331895408547651	4		467	942	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	274	715	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.246983587792397	1	FACETS	0.724	0.685	0.764	0.724	0.685	0.764	INDETERMINATE	1	TRUE	0	0.745927567441651	1		715	636	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0013828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	332	414	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.745927567441651	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.745927567441651	1		416	519	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0013828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	22	264	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	NA	2	FACETS	0.188	0.146	0.238			1	INDETERMINATE	1	TRUE	NA	0.745927567441651	2		264	313	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0013828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	348	572	2	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.925	0.877	0.973	0.925	0.877	0.973	CLONAL	1	TRUE	1	0.745927567441651	2		574	1009	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0013828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	351	559	2	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.745927567441651	2		561	940	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968251	134968251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373797543	NA	P-0013828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	622	669	1	ENST00000398015.3:c.2764G>A	p.Ala922Thr	p.A922T	ENST00000398015	NM_004441.4	922	Gcc/Acc	15/16	0.745927567441651	2	FACETS	0.967	0.942	0.992	0.967	0.942	0.992	CLONAL	2	TRUE	0	0.745927567441651	2		670	862	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120546223	120546223	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0013828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	78	629	2	ENST00000229340.5:c.101C>G	p.Ser34Ter	p.S34*	ENST00000229340	NM_006861.6	34	tCa/tGa	2/6	0.246983587792397	1	FACETS	0.137	0.12	0.156	0.137	0.12	0.156	INDETERMINATE	1	TRUE	0	0.745927567441651	1		631	955	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726687	88726687	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	284	554	1	ENST00000360948.2:c.357G>T	p.Gln119His	p.Q119H	ENST00000360948	NM_001012338.2	119	caG/caT	4/19	0.463525870982826	1	FACETS	0.707	0.669	0.746	0.707	0.669	0.746	SUBCLONAL	1	TRUE	0	0.745927567441651	1		555	675	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382145	152382145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	110	346	0	ENST00000206249.3:c.1255G>A	p.Glu419Lys	p.E419K	ENST00000206249	NM_000125.3	419	Gag/Aag	6/8	0.453943443164964	1	FACETS	0.372	0.336	0.41	0.372	0.336	0.41	SUBCLONAL	1	TRUE	0	0.745927567441651	1		346	497	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080626	5080626	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	41	587	1	ENST00000381652.3:c.2377G>A	p.Asp793Asn	p.D793N	ENST00000381652	NM_004972.3	793	Gat/Aat	18/25	0.369751739065292	1	FACETS	0.093	0.077	0.111	0.093	0.077	0.111	INDETERMINATE	1	TRUE	0	0.745927567441651	1		588	740	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759984	133759984	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013828-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	50	628	0	ENST00000318560.5:c.2307G>C	p.Glu769Asp	p.E769D	ENST00000318560	NM_005157.4	769	gaG/gaC	11/11	0.369751739065292	1	FACETS	0.097	0.082	0.114	0.097	0.082	0.114	INDETERMINATE	1	TRUE	0	0.745927567441651	1		628	866	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013830-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	108	715	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.824	0.742	0.91	0.824	0.742	0.91	CLONAL	1	TRUE	1	0.46571357430806	2		715	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577518	7577518	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519995	NA	P-0013830-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	139	624	0	ENST00000269305.4:c.763A>T	p.Ile255Phe	p.I255F	ENST00000269305	NM_001126112.2	255	Atc/Ttc	7/11	0.46571357430806	1	FACETS	0.981	0.899	1	0.981	0.899	1	CLONAL	1	TRUE	0	0.46571357430806	1		624	467	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786652	3786652	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013853-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	47	745	1	ENST00000262367.5:c.4559A>G	p.Lys1520Arg	p.K1520R	ENST00000262367	NM_004380.2	1520	aAg/aGg	27/31	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		746	543	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398255	25398255	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913236	NA	P-0013854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	839	541	0	ENST00000311936.3:c.64C>A	p.Gln22Lys	p.Q22K	ENST00000311936	NM_004985.3	22	Cag/Aag	2/5	0.421458478266139	4	FACETS	0.943	0.919	0.968	0.943	0.919	0.968	CLONAL	4	TRUE	0	0.470972353592772	4		541	1389	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556993	29556993	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1135402836	NA	P-0013854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	68	298	0	ENST00000356175.3:c.2990+1G>A		p.X997_splice	ENST00000356175	NM_000267.3	997			0.426724975774316	1	FACETS	0.638	0.559	0.723	0.638	0.559	0.723	SUBCLONAL	1	TRUE	0	0.470972353592772	1		298	346	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65316492	65316492	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1422122219	NA	P-0013854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	144	454	1	ENST00000342505.4:c.1750G>A	p.Val584Met	p.V584M	ENST00000342505	NM_002227.2	584	Gtg/Atg	12/25	0.470972353592772	1	FACETS	0.819	0.75	0.89	0.819	0.75	0.89	CLONAL	1	TRUE	0	0.470972353592772	1		455	571	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289851	15289851	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	71	479	0	ENST00000263388.2:c.3703C>G	p.His1235Asp	p.H1235D	ENST00000263388	NM_000435.2	1235	Cat/Gat	22/33	0.226234317551177	3	FACETS	0.515	0.449	0.587	0.258	0.224	0.294	INDETERMINATE	1	TRUE	1	0.470972353592772	3		479	723	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944623	40944623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	73	253	0	ENST00000373198.4:c.1879G>A	p.Val627Ile	p.V627I	ENST00000373198	NM_133170.3	627	Gtt/Att	12/32	1	2	FACETS	0.861	0.758	0.971	0.861	0.758	0.971	CLONAL	1	TRUE	1	0.470972353592772	2		253	360	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964944	55964944	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013854-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	86	534	0	ENST00000263923.4:c.2293A>G	p.Ile765Val	p.I765V	ENST00000263923	NM_002253.2	765	Atc/Gtc	16/30	0.470972353592772	1	FACETS	0.428	0.378	0.48	0.428	0.378	0.48	SUBCLONAL	1	TRUE	0	0.470972353592772	1		534	653	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0013856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	106	410	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	0.594930664208818	3	FACETS	0.923	0.858	0.986	0.923	0.858	0.986	CLONAL	3	FALSE	0	0.594930664208818	3		410	167	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0013856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	113	437	3	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.580753808850007	2	FACETS	0.945	0.875	1	0.945	0.875	1	CLONAL	2	FALSE	0	0.594930664208818	2		440	201	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912149	114912149	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	157	1025	3	ENST00000543371.1:c.1219C>T	p.Arg407Ter	p.R407*	ENST00000543371	NM_001198531.1	407	Cga/Tga	11/14	NA	2	FACETS	1	0.972	1			1	INDETERMINATE	1	FALSE	NA	0.594930664208818	2		1028	476	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268514	142268514	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013856-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	94	291	0	ENST00000350721.4:c.2978G>A	p.Arg993Lys	p.R993K	ENST00000350721	NM_001184.3	993	aGg/aAg	15/47	0.580682221606656	3	FACETS	0.882	0.813	0.948	0.882	0.813	0.948	CLONAL	3	FALSE	0	0.594930664208818	3		291	155	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0013862-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	10	223	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.122	0.082	0.173	0.122	0.082	0.173	SUBCLONAL	1	TRUE	1	0.365932155131615	2		223	449	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831465	72831465	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	637	934	1	ENST00000268489.5:c.5116del	p.Glu1706SerfsTer13	p.E1706Sfs*13	ENST00000268489	NM_006885.3	1706	Gag/ag	9/10	0.767192523652937	1	FACETS	0.987	0.958	1	0.987	0.958	1	CLONAL	1	TRUE	0	0.767192523652937	1		935	1037	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557628	95557628	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	156	630	0	ENST00000393063.1:c.5439G>T	p.Glu1813Asp	p.E1813D	ENST00000393063	NM_030621.3	1813	gaG/gaT	26/28	0.373968131560527	1	FACETS	0.871	0.798	0.946	0.871	0.798	0.946	CLONAL	1	TRUE	0	0.373968131560527	1		630	779	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200267	138200267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	83	462	0	ENST00000237289.4:c.1685G>A	p.Arg562His	p.R562H	ENST00000237289	NM_001270507.1	562	cGt/cAt	7/9	1	2	FACETS	0.664	0.585	0.748	0.664	0.585	0.748	SUBCLONAL	1	TRUE	1	0.327217909293874	2		462	764	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186507012	186507012	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1401	313	822	0	ENST00000323963.5:c.1178A>G	p.Asn393Ser	p.N393S	ENST00000323963		393	aAt/aGt	11/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.327217909293874	2		822	1714	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247186	153247186	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1419	107	585	0	ENST00000281708.4:c.1616G>C	p.Gly539Ala	p.G539A	ENST00000281708	NM_033632.3	539	gGg/gCg	10/12	0.327217909293874	4	FACETS	0.569	0.508	0.634			1	SUBCLONAL	1	TRUE	NA	0.327217909293874	4		585	1526	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0013899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	131	645	1	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.20375836042572	2	FACETS	0.863	0.786	0.944	0.863	0.786	0.944	CLONAL	2	TRUE	0	0.251621503098781	2		646	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691039	NA	P-0013899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	163	672	0	ENST00000269305.4:c.919+1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.20375836042572	2	FACETS	0.943	0.868	1	0.943	0.868	1	CLONAL	2	TRUE	0	0.251621503098781	2		672	687	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608369	43608369	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1270	82	1236	1	ENST00000355710.3:c.1717G>T	p.Val573Leu	p.V573L	ENST00000355710	NM_020975.4	573	Gtg/Ttg	9/20	0.196734053313345	4	FACETS	0.603	0.53	0.683	0.302	0.265	0.342	SUBCLONAL	1	TRUE	2	0.251621503098781	4		1237	1352	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492817	56492817	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	120	676	0	ENST00000407977.2:c.122del	p.Ser41Ter	p.S41*	ENST00000407977		41	tCa/ta	2/10	0.20375836042572	2	FACETS	0.885	0.802	0.971	0.885	0.802	0.971	CLONAL	2	TRUE	0	0.251621503098781	2		676	539	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584467	39584467	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554581051	NA	P-0013899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	59	683	0	ENST00000262039.4:c.1132C>T	p.Arg378Cys	p.R378C	ENST00000262039	NM_002647.2	378	Cgt/Tgt	10/25	0.251621503098781	1	FACETS	0.884	0.762	1	0.884	0.762	1	CLONAL	1	TRUE	0	0.251621503098781	1		683	464	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339566	116339566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35469582	NA	P-0013899-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	35	433	0	ENST00000397752.3:c.428G>A	p.Arg143Gln	p.R143Q	ENST00000397752	NM_000245.2	143	cGa/cAa	2/21	0.20375836042572	2	FACETS	0.742	0.609	0.891	0.371	0.304	0.446	SUBCLONAL	1	TRUE	0	0.251621503098781	2		433	375	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0013912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	239	346	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.923	0.872	0.974	1	0.995	1	CLONAL	2	TRUE	1	0.521147135481319	2		346	497	SUCCESS
H3C13	653604	MSKCC	GRCh37	1	149785221	149785221	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1553755012	NA	P-0013925-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	31	59	0	ENST00000331491.1:c.16C>T	p.Gln6Ter	p.Q6*	ENST00000331491	NM_001123375.2	6	Cag/Tag	1/1	0.473218669723417	7	FACETS	1	0.858	1			1	CLONAL	2	TRUE	NA	0.473218669723417	7		59	136	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884769	111884769	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013925-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1205	113	963	0	ENST00000341259.2:c.858C>G	p.Ile286Met	p.I286M	ENST00000341259	NM_005475.2	286	atC/atG	4/8	0.478570503248502	3	FACETS	0.448	0.402	0.498	0.149	0.134	0.166	SUBCLONAL	1	TRUE	0	0.473218669723417	3		963	1318	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437102	110437107	+	inframe_deletion	In_Frame_Del	DEL	CATGGA	CATGGA	-	novel	NA	P-0013925-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	18	51	0	ENST00000375856.3:c.1294_1299del	p.Ser432_Met433del	p.S432_M433del	ENST00000375856	NM_003749.2	432	TCCATG/-	1/2	0.478570503248502	3	FACETS	0.84	0.656	1	0.84	0.656	1	CLONAL	2	TRUE	1	0.473218669723417	3		51	56	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0013925-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	311	453	0	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	0.263904063177434	6	FACETS	1	0.953	1			1	INDETERMINATE	4	TRUE	NA	0.473218669723417	6		453	639	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696644	47696644	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519964	NA	P-0013950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	17	502	0	ENST00000347630.2:c.304T>G	p.Phe102Val	p.F102V	ENST00000347630	NM_001007230.1	102	Ttc/Gtc	5/11	1	2	FACETS	0.125	0.092	0.164	0.125	0.092	0.164	SUBCLONAL	1	TRUE	1	0.4	2		502	682	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0013956-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	88	273	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.82	0.736	0.907	0.82	0.736	0.907	CLONAL	1	TRUE	1	0.774650062412785	2		273	277	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0013956-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	179	446	1	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.732536270491665	3	FACETS	0.967	0.895	1	0.484	0.447	0.521	CLONAL	1	TRUE	1	0.774650062412785	3		447	663	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947540	48947540	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0013956-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	143	392	0	ENST00000267163.4:c.1128-1G>C		p.X376_splice	ENST00000267163	NM_000321.2	376			0.741329178177941	1	FACETS	0.931	0.871	0.99	0.931	0.871	0.99	CLONAL	1	TRUE	0	0.774650062412785	1		392	243	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729180	66729180	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013956-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	247	608	0	ENST00000307102.5:c.388T>A	p.Tyr130Asn	p.Y130N	ENST00000307102	NM_002755.3	130	Tat/Aat	3/11	1	2	FACETS	0.934	0.878	0.991	0.934	0.878	0.991	CLONAL	1	TRUE	1	0.774650062412785	2		608	683	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362164	40362195	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GACATAAGAAGGGAGGGGCACTCACGAGAATC	GACATAAGAAGGGAGGGGCACTCACGAGAATC	-	novel	NA	P-0013956-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	211	599	0	ENST00000293328.3:c.1900_1906+25del		p.X634_splice	ENST00000293328	NM_012448.3	634		15/19	0.436092831144013	1	FACETS	0.57	0.532	0.607	0.57	0.532	0.607	INDETERMINATE	1	TRUE	0	0.774650062412785	1		599	586	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905494	50905494	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013956-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	546	683	1	ENST00000440232.2:c.622C>T	p.Pro208Ser	p.P208S	ENST00000440232	NM_002691.3	208	Ccg/Tcg	6/27	0.753732423664479	2	FACETS	0.913	0.887	0.938	0.913	0.887	0.938	CLONAL	2	TRUE	0	0.774650062412785	2		684	772	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014325	70014325	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013956-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	343	907	0	ENST00000394351.3:c.1186G>C	p.Val396Leu	p.V396L	ENST00000394351	NM_000248.3	396	Gtg/Ctg	9/9	1	2	FACETS	0.88	0.835	0.927	0.88	0.835	0.927	CLONAL	1	TRUE	1	0.774650062412785	2		907	1006	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0013965-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	149	801	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.249516737430815	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.249516737430815	1		801	998	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087388	27087397	+	frameshift_variant	Frame_Shift_Del	DEL	AGGAGCTCTG	AGGAGCTCTG	-	novel	NA	P-0013965-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	114	813	0	ENST00000324856.7:c.1964_1973del	p.Gly655ValfsTer4	p.G655Vfs*4	ENST00000324856	NM_006015.4	654	gaAGGAGCTCTG/ga	5/20	1	2	FACETS	0.871	0.783	0.965	0.871	0.783	0.965	CLONAL	1	TRUE	1	0.249516737430815	2		813	1049	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77054967	77054967	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013965-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	44	643	0	ENST00000356341.3:c.895A>C	p.Lys299Gln	p.K299Q	ENST00000356341	NM_002576.4	299	Aag/Cag	10/15	0.249516737430815	1	FACETS	0.428	0.357	0.506	0.428	0.357	0.506	SUBCLONAL	1	TRUE	0	0.249516737430815	1		643	722	SUCCESS
APC	324	MSKCC	GRCh37	5	112175213	112175213	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013965-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	43	412	0	ENST00000257430.4:c.3922A>G	p.Lys1308Glu	p.K1308E	ENST00000257430	NM_000038.5	1308	Aaa/Gaa	16/16	0.225023948341885	1	FACETS	0.606	0.507	0.716	0.606	0.507	0.716	SUBCLONAL	1	TRUE	0	0.249516737430815	1		412	498	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340072	116340072	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751572663	NA	P-0013965-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	29	465	0	ENST00000397752.3:c.934G>A	p.Glu312Lys	p.E312K	ENST00000397752	NM_000245.2	312	Gaa/Aaa	2/21	0.249516737430815	3	FACETS	0.504	0.403	0.618	0.252	0.201	0.309	SUBCLONAL	1	TRUE	1	0.249516737430815	3		465	519	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0013966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	54	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.738	0.629	0.857	0.738	0.629	0.857	SUBCLONAL	1	TRUE	1	0.2	2		336	732	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11210198	11210198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	97	675	1	ENST00000361445.4:c.4555G>A	p.Ala1519Thr	p.A1519T	ENST00000361445	NM_004958.3	1519	Gct/Act	31/58	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.2	2		676	949	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162383	47162388	+	frameshift_variant	Frame_Shift_Del	DEL	CCATCC	CCATCC	AT	novel	NA	P-0013966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	51	412	2	ENST00000409792.3:c.3738_3743delinsAT	p.Asp1247SerfsTer11	p.D1247Sfs*11	ENST00000409792	NM_014159.6	1246	gtGGATGGc/gtATc	3/21	1	2	FACETS	0.801	0.68	0.934	0.801	0.68	0.934	CLONAL	1	TRUE	1	0.2	2		414	637	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165164	47165164	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0013966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	68	472	0	ENST00000409792.3:c.962C>G	p.Ser321Ter	p.S321*	ENST00000409792	NM_014159.6	321	tCa/tGa	3/21	1	2	FACETS	0.943	0.82	1	0.943	0.82	1	CLONAL	1	TRUE	1	0.2	2		472	721	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	263	574	1	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.336737863313451	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.336737863313451	2		575	752	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502874	186502874	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013985-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	473	967	1	ENST00000323963.5:c.332G>A	p.Arg111Lys	p.R111K	ENST00000323963		111	aGa/aAa	4/11	0.336737863313451	1	FACETS	0.839	0.801	0.876	1	0.997	1	CLONAL	2	TRUE	0	0.336737863313451	1		968	1393	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104441	2104441	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014007-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	148	442	0	ENST00000219476.3:c.481G>C	p.Ala161Pro	p.A161P	ENST00000219476	NM_000548.3	161	Gct/Cct	5/42	NA	2	FACETS	0.775	0.71	0.843			1	INDETERMINATE	1	TRUE	NA	0.59363668595358	2		442	643	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0014062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	127	454	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.903	0.819	0.992	0.903	0.819	0.992	CLONAL	1	TRUE	1	0.36995475013269	2		454	760	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0014062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	10	231	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	1	FACETS	0.093	0.062	0.132	0.093	0.062	0.132	SUBCLONAL	1	TRUE	0	0.36995475013269	1		231	473	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602646	10602646	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	99	410	0	ENST00000171111.5:c.932A>G	p.His311Arg	p.H311R	ENST00000171111	NM_203500.1	311	cAc/cGc	3/6	0.36995475013269	1	FACETS	0.732	0.655	0.814	0.732	0.655	0.814	SUBCLONAL	1	TRUE	0	0.36995475013269	1		410	596	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221302	1221302	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	173	449	0	ENST00000326873.7:c.827del	p.Gly276AlafsTer11	p.G276Afs*11	ENST00000326873	NM_000455.4	275	ccG/cc	6/10	0.36995475013269	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.36995475013269	1		449	752	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039389	47039389	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	162	276	0	ENST00000377604.3:c.1012del	p.Gln338ArgfsTer4	p.Q338Rfs*4	ENST00000377604	NM_001204468.1	338	Cag/ag	10/24	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.36995475013269	1		276	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0014066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	363	297	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.703690529023524	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.707694777221923	2		297	500	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348142	348142	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	55	448	0	ENST00000262320.3:c.1364G>T	p.Gly455Val	p.G455V	ENST00000262320	NM_003502.3	455	gGc/gTc	6/11	0.707694777221923	3	FACETS	0.409	0.35	0.473	0.204	0.175	0.237	SUBCLONAL	1	TRUE	1	0.707694777221923	3		448	515	SUCCESS
APC	324	MSKCC	GRCh37	5	112137030	112137030	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	233	405	0	ENST00000257430.4:c.784G>T	p.Glu262Ter	p.E262*	ENST00000257430	NM_000038.5	262	Gaa/Taa	8/16	0.707694777221923	2	FACETS	0.933	0.89	0.975	0.933	0.89	0.975	CLONAL	2	TRUE	0	0.707694777221923	2		405	353	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225788	26225788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs911990384	NA	P-0014066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1318	487	1344	4	ENST00000360408.1:c.406G>A	p.Ala136Thr	p.A136T	ENST00000360408	NM_003532.2	136	Gcg/Acg	1/1	0.707694777221923	3	FACETS	1	0.975	1	0.516	0.492	0.54	CLONAL	1	TRUE	1	0.707694777221923	3		1348	1805	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188198	10188198	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	101	657	3	ENST00000256474.2:c.341G>T	p.Gly114Val	p.G114V	ENST00000256474	NM_000551.3	114	gGt/gTt	2/3	0.385360304217005	1	FACETS	0.874	0.785	0.968	0.874	0.785	0.968	CLONAL	1	TRUE	0	0.385360304217005	1		660	484	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188208	10188208	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014069-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	113	715	0	ENST00000256474.2:c.351G>C	p.Trp117Cys	p.W117C	ENST00000256474	NM_000551.3	117	tgG/tgC	2/3	0.385360304217005	1	FACETS	0.904	0.817	0.995	0.904	0.817	0.995	CLONAL	1	TRUE	0	0.385360304217005	1		715	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578456	7578467	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGACGCGGGT	GCGGACGCGGGT	CC	novel	NA	P-0014075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	209	499	2	ENST00000269305.4:c.463_474delinsGG	p.Thr155GlyfsTer12	p.T155Gfs*12	ENST00000269305	NM_001126112.2	155	ACCCGCGTCCGC/GG	5/11	0.296329207635961	2	FACETS	0.945	0.879	1	0.945	0.879	1	CLONAL	2	TRUE	0	0.29	2		501	763	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340015	116340015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	54	347	0	ENST00000397752.3:c.877G>A	p.Glu293Lys	p.E293K	ENST00000397752	NM_000245.2	293	Gaa/Aaa	2/21	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.29	2		347	359	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411879	116411918	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCTTTCTTTCTCTCTGTTTTAAGATCTGGGCAGTGAATT	CTCTTTCTTTCTCTCTGTTTTAAGATCTGGGCAGTGAATT	-	novel	NA	P-0014075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	75	289	0	ENST00000397752.3:c.2888-24_2903del		p.X963_splice	ENST00000397752	NM_000245.2	963		14/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.29	2		289	363	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349892	70349892	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	124	337	0	ENST00000374080.3:c.3875T>A	p.Val1292Glu	p.V1292E	ENST00000374080		1292	gTa/gAa	28/45	1	1	FACETS	0.952	0.87	1	1	0.99	1	CLONAL	2	TRUE	0	0.29	1		337	384	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0014077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	66	337	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.437239955142698	1	FACETS	0.365	0.318	0.415	0.365	0.318	0.415	SUBCLONAL	1	TRUE	0	0.653121291913426	1		337	373	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961630	41961630	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0014077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	198	932	1	ENST00000219905.7:c.538A>T	p.Lys180Ter	p.K180*	ENST00000219905	NM_001164273.1	180	Aaa/Taa	2/24	0.653121291913426	1	FACETS	0.488	0.453	0.525	0.488	0.453	0.525	SUBCLONAL	1	TRUE	0	0.653121291913426	1		933	836	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223478	2223478	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	55	287	0	ENST00000398665.3:c.3589A>T	p.Ser1197Cys	p.S1197C	ENST00000398665	NM_032482.2	1197	Agt/Tgt	25/28	1	2	FACETS	0.517	0.444	0.595	0.517	0.444	0.595	SUBCLONAL	1	TRUE	1	0.653121291913426	2		287	326	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527428	41527428	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	315	739	0	ENST00000263253.7:c.1319C>G	p.Pro440Arg	p.P440R	ENST00000263253	NM_001429.3	440	cCt/cGt	6/31	0.274721634026232	0	FACETS	0.333	0.314	0.352			1	INDETERMINATE	1	TRUE	0	0.653121291913426	0		739	1005	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861090	35861090	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	194	408	0	ENST00000303115.3:c.219A>G	p.Ile73Met	p.I73M	ENST00000303115	NM_002185.3	73	atA/atG	2/8	0.652931025297699	3	FACETS	1	0.971	1	0.543	0.504	0.583	CLONAL	1	TRUE	1	0.653121291913426	3		408	726	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0014090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	768	414	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.740114857893607	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.740114857893607	2		416	956	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971132	21971132	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	128	168	0	ENST00000304494.5:c.226del	p.Ala76ProfsTer70	p.A76Pfs*70	ENST00000304494	NM_000077.4	76	Gcc/cc	2/3	0.740078649658399	2	FACETS	0.86	0.805	0.914	0.86	0.805	0.914	CLONAL	2	TRUE	0	0.740114857893607	2		168	201	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475078	40475078	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	363	830	0	ENST00000264657.5:c.1832G>T	p.Ser611Ile	p.S611I	ENST00000264657	NM_139276.2	611	aGt/aTt	20/24	0.740114857893607	2	FACETS	0.859	0.815	0.904	0.429	0.407	0.452	CLONAL	1	TRUE	0	0.740114857893607	2		830	1142	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827678	72827678	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1475232597	NA	P-0014090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	865	833	1	ENST00000268489.5:c.8903A>G	p.Tyr2968Cys	p.Y2968C	ENST00000268489	NM_006885.3	2968	tAc/tGc	9/10	0.740114857893607	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.740114857893607	2		834	1165	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320326	30320326	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	507	402	5	ENST00000322652.5:c.1267C>T	p.Arg423Ter	p.R423*	ENST00000322652	NM_015355.2	423	Cga/Tga	11/16	0.740114857893607	2	FACETS	0.926	0.898	0.953	0.926	0.898	0.953	CLONAL	2	TRUE	0	0.740114857893607	2		407	740	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747949	41747949	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	28	267	0	ENST00000226382.2:c.820G>C	p.Ala274Pro	p.A274P	ENST00000226382	NM_003924.3	274	Gct/Cct	3/3	0.562342333623266	3	FACETS	0.213	0.17	0.263			1	SUBCLONAL	1	TRUE	NA	0.740114857893607	3		267	486	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939183	131939183	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0014090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	538	392	2	ENST00000265335.6:c.2397+2T>G		p.X799_splice	ENST00000265335		799			0.740114857893607	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.740114857893607	2		394	686	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163300	32163300	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	335	823	1	ENST00000375023.3:c.5926C>G	p.Pro1976Ala	p.P1976A	ENST00000375023	NM_004557.3	1976	Ccg/Gcg	30/30	0.638747149809473	3	FACETS	0.858	0.81	0.907	0.286	0.27	0.303	CLONAL	1	TRUE	0	0.740114857893607	3		824	1446	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400140	139400140	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014090-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	1047	688	0	ENST00000277541.6:c.4208G>T	p.Cys1403Phe	p.C1403F	ENST00000277541	NM_017617.3	1403	tGt/tTt	25/34	0.624168798254718	3	FACETS	1	0.996	1			1	CLONAL	3	TRUE	NA	0.740114857893607	3		688	1246	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs864622237	NA	P-0014097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	381	569	0	ENST00000269305.4:c.700T>A	p.Tyr234Asn	p.Y234N	ENST00000269305	NM_001126112.2	234	Tac/Aac	7/11	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.815701722552237	2		569	449	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030451	49030451	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	226	296	1	ENST00000267163.4:c.1926del	p.Lys643AsnfsTer15	p.K643Nfs*15	ENST00000267163	NM_000321.2	642	ttG/tt	19/27	0.815701722552237	2	FACETS	0.969	0.932	1	0.969	0.932	1	CLONAL	2	TRUE	0	0.815701722552237	2		297	286	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111547	8111565	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TACAAGCTTCACAATGTAA	TACAAGCTTCACAATGTAA	-	novel	NA	P-0014121-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1233	356	553	0	ENST00000346208.3:c.1033_1047+4del		p.X345_splice	ENST00000346208		345		5/6	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		553	1589	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	340	459	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.77927477492637	1	FACETS	0.957	0.918	0.995	0.957	0.918	0.995	CLONAL	1	TRUE	0	0.779636697760801	1		459	556	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0014130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	156	259	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	1	2	FACETS	0.971	0.899	1	0.971	0.899	1	CLONAL	1	TRUE	1	0.779636697760801	2		259	412	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841466	156841466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	1299	537	2	ENST00000524377.1:c.769G>A	p.Asp257Asn	p.D257N	ENST00000524377	NM_002529.3	257	Gac/Aac	7/17	0.779636697760801	5	FACETS	0.994	0.976	1	0.994	0.976	1	CLONAL	4	TRUE	1	0.779636697760801	5		539	1819	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	67	715	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	0.154496753893398	NA		715	326	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0014156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	47	349	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.154496753893398	2		350	411	SUCCESS
APC	324	MSKCC	GRCh37	5	112175921	112175921	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014156-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	19	329	0	ENST00000257430.4:c.4630G>T	p.Glu1544Ter	p.E1544*	ENST00000257430	NM_000038.5	1544	Gaa/Taa	16/16	0.154496753893398	2	FACETS	1	0.897	1	0.691	0.527	0.881	CLONAL	1	TRUE	0	0.154496753893398	2		329	178	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0014164-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	77	273	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.792	0.702	0.887	0.792	0.702	0.887	SUBCLONAL	1	TRUE	1	0.617115231688767	2		273	315	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546125	29546125	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014164-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	164	374	3	ENST00000356175.3:c.1630G>T	p.Glu544Ter	p.E544*	ENST00000356175	NM_000267.3	544	Gaa/Taa	14/57	1	2	FACETS	0.966	0.893	1	0.966	0.893	1	CLONAL	1	TRUE	1	0.617115231688767	2		377	550	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486050	29486050	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1438566555	NA	P-0014164-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	112	314	0	ENST00000356175.3:c.233del	p.Asn78IlefsTer7	p.N78Ifs*7	ENST00000356175	NM_000267.3	76	gAa/ga	3/57	1	2	FACETS	0.96	0.872	1	0.96	0.872	1	CLONAL	1	TRUE	1	0.617115231688767	2		314	378	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692811	89692811	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014164-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	11	233	0	ENST00000371953.3:c.295G>T	p.Glu99Ter	p.E99*	ENST00000371953	NM_000314.4	99	Gaa/Taa	5/9	0.617115231688767	1	FACETS	0.129	0.089	0.179	0.129	0.089	0.179	SUBCLONAL	1	TRUE	0	0.617115231688767	1		233	191	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0014187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	184	852	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.169829793860681	4	FACETS	0.862	0.795	0.931	0.862	0.795	0.931	CLONAL	2	TRUE	2	0.270444310289635	4		852	1003	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051652	30051652	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555993336	NA	P-0014196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	132	330	0	ENST00000338641.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000338641	NM_000268.3	196	Cga/Tga	6/16	0.598187019332896	1	FACETS	0.795	0.729	0.863	0.795	0.729	0.863	SUBCLONAL	1	TRUE	0	0.598187019332896	1		330	389	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441219	52441219	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	216	437	0	ENST00000460680.1:c.551A>T	p.Asp184Val	p.D184V	ENST00000460680	NM_004656.3	184	gAt/gTt	7/17	0.591490712347108	1	FACETS	0.838	0.784	0.893	0.838	0.784	0.893	CLONAL	1	TRUE	0	0.598187019332896	1		437	604	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584475	52584475	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	252	487	0	ENST00000394830.3:c.4538del	p.Glu1513GlyfsTer34	p.E1513Gfs*34	ENST00000394830	NM_018313.4	1513	gAg/gg	29/30	0.591490712347108	1	FACETS	0.937	0.883	0.992	0.937	0.883	0.992	CLONAL	1	TRUE	0	0.598187019332896	1		487	630	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156731	20156731	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	83	275	1	ENST00000379607.5:c.26G>T	p.Gly9Val	p.G9V	ENST00000379607	NM_001412.3	9	gGt/gTt	2/7	1	1	FACETS	0.785	0.709	0.863	1	0.983	1	SUBCLONAL	2	TRUE	0	0.426472194444871	1		276	195	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191513	10191515	+	inframe_deletion	In_Frame_Del	DEL	TAG	TAG	-	novel	NA	P-0014205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	123	496	0	ENST00000256474.2:c.507_509del	p.Val170del	p.V170del	ENST00000256474	NM_000551.3	169	cTAGtc/ctc	3/3	0.426472194444871	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.426472194444871	1		496	425	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125797	47125797	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	76	283	0	ENST00000409792.3:c.5473C>T	p.Gln1825Ter	p.Q1825*	ENST00000409792	NM_014159.6	1825	Caa/Taa	12/21	0.426472194444871	1	FACETS	0.932	0.825	1	0.932	0.825	1	CLONAL	1	TRUE	0	0.426472194444871	1		283	301	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0014237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	200	410	1	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.860076126839842	2		411	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057520005	NA	P-0014237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	545	730	0	ENST00000269305.4:c.820G>T	p.Val274Phe	p.V274F	ENST00000269305	NM_001126112.2	274	Gtt/Ttt	8/11	0.788302473278153	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.860076126839842	1		730	669	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0014271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	740	382	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.55120679838382	6	FACETS	0.958	0.932	0.984			1	CLONAL	5	TRUE	NA	0.55120679838382	6		382	1178	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578281	7578281	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660254	NA	P-0014271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	333	691	0	ENST00000269305.4:c.568C>A	p.Pro190Thr	p.P190T	ENST00000269305	NM_001126112.2	190	Cct/Act	6/11	0.485059183878125	2	FACETS	0.941	0.898	0.984	0.941	0.898	0.984	CLONAL	2	TRUE	0	0.55120679838382	2		691	642	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828360	72828361	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0014271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	180	513	0	ENST00000268489.5:c.8220_8221del	p.Arg2740SerfsTer15	p.R2740Sfs*15	ENST00000268489	NM_006885.3	2740	agAGct/agct	9/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.55120679838382	2		513	610	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101985002	101985002	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	181	430	2	ENST00000282441.5:c.449G>A	p.Gly150Asp	p.G150D	ENST00000282441	NM_001130145.2	150	gGc/gAc	2/9	0.38807803457495	3	FACETS	1	0.979	1	0.58	0.536	0.625	CLONAL	1	TRUE	1	0.55120679838382	3		432	722	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2114359	2114359	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1360209954	NA	P-0014271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1351	261	947	0	ENST00000219476.3:c.1530G>C	p.Gln510His	p.Q510H	ENST00000219476	NM_000548.3	510	caG/caC	15/42	0.497716471154212	4	FACETS	0.911	0.851	0.974	0.456	0.425	0.487	CLONAL	1	TRUE	2	0.55120679838382	4		947	1612	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435381	56435381	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1403551128	NA	P-0014271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	190	700	0	ENST00000407977.2:c.1756C>T	p.Gln586Ter	p.Q586*	ENST00000407977		586	Cag/Tag	9/10	0.55120679838382	3	FACETS	0.879	0.812	0.948	0.439	0.406	0.474	CLONAL	1	TRUE	1	0.55120679838382	3		700	1001	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300226	15300226	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	45	871	0	ENST00000263388.2:c.1050C>A	p.His350Gln	p.H350Q	ENST00000263388	NM_000435.2	350	caC/caA	7/33	1	2	FACETS	0.233	0.196	0.275	0.233	0.196	0.275	SUBCLONAL	1	TRUE	1	0.781506119108026	2		871	494	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014285-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	94	715	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.295898578227601	1	FACETS	0.8	0.712	0.893	0.8	0.712	0.893	SUBCLONAL	1	TRUE	0	0.295898578227601	1		715	677	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255086	16255086	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014285-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	112	595	1	ENST00000375759.3:c.2351G>T	p.Arg784Leu	p.R784L	ENST00000375759	NM_015001.2	784	cGc/cTc	11/15	1	2	FACETS	0.856	0.769	0.949	0.856	0.769	0.949	CLONAL	1	TRUE	1	0.295898578227601	2		596	884	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56862971	56862971	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014285-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	141	611	0	ENST00000308159.5:c.877G>T	p.Val293Phe	p.V293F	ENST00000308159	NM_014669.4	293	Gtt/Ttt	9/22	0.28379063402513	2	FACETS	1	0.964	1	0.557	0.507	0.609	CLONAL	1	TRUE	0	0.295898578227601	2		611	856	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654676	67654676	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014285-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	167	669	0	ENST00000264010.4:c.1163G>T	p.Ser388Ile	p.S388I	ENST00000264010	NM_006565.3	388	aGc/aTc	6/12	0.28379063402513	2	FACETS	1	0.982	1	0.62	0.569	0.672	CLONAL	1	TRUE	0	0.295898578227601	2		669	911	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593620	55593664	+	inframe_deletion	In_Frame_Del	DEL	GATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTTCC	GATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTTCC	-	novel	NA	P-0014295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	144	496	0	ENST00000288135.5:c.1686_1730del	p.Glu562_Pro577delinsAsp	p.E562_P577delinsD	ENST00000288135	NM_000222.2	562	gaGATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTTCCt/gat	11/21	1	2	FACETS	0.758	0.695	0.823	0.758	0.695	0.823	SUBCLONAL	1	TRUE	1	0.718629923632782	2		496	529	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0014309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1389	6764	795	1	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.606315841876924	30	FACETS	0.999	0.992	1			1	CLONAL	26	TRUE	NA	0.606315841876924	30		796	8153	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612675	228612675	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	57	860	0	ENST00000366696.1:c.352G>T	p.Val118Phe	p.V118F	ENST00000366696	NM_003493.2	118	Gtc/Ttc	1/1	0.523326730967	3	FACETS	0.304	0.26	0.353	0.152	0.13	0.177	SUBCLONAL	1	TRUE	1	0.606315841876924	3		860	805	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727110	243727110	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	432	774	1	ENST00000263826.5:c.860T>A	p.Ile287Asn	p.I287N	ENST00000263826	NM_005465.4	287	aTt/aAt	9/13	0.523326730967	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.606315841876924	3		775	924	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89828375	89828375	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	364	811	0	ENST00000389301.3:c.2834C>A	p.Ala945Asp	p.A945D	ENST00000389301	NM_000135.2	945	gCt/gAt	29/43	0.214101762614639	5	FACETS	1	0.988	1	0.749	0.712	0.787	INDETERMINATE	2	TRUE	2	0.606315841876924	5		811	1020	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577138	7577162	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGTCCCAGTAGATTACCACTACTCA	CGTCCCAGTAGATTACCACTACTCA	-	novel	NA	P-0014309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	328	869	0	ENST00000269305.4:c.783-7_800del		p.X261_splice	ENST00000269305	NM_001126112.2	261		8/11	0.606315841876924	2	FACETS	0.891	0.851	0.931	0.891	0.851	0.931	CLONAL	2	TRUE	0	0.606315841876924	2		869	607	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144506	11144506	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	512	736	1	ENST00000358026.2:c.3838G>T	p.Gly1280Cys	p.G1280C	ENST00000358026	NM_001128849.1	1280	Ggc/Tgc	27/36	0.214101762614639	5	FACETS	0.958	0.921	0.995	0.958	0.921	0.995	INDETERMINATE	3	TRUE	2	0.606315841876924	5		737	1122	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99162531	99162531	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1461504431	NA	P-0014309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	125	406	2	ENST00000074304.5:c.1049G>A	p.Gly350Glu	p.G350E	ENST00000074304	NM_001134224.1	350	gGa/gAa	12/26	0.606315841876924	3	FACETS	1	0.95	1	0.533	0.485	0.583	CLONAL	1	TRUE	1	0.606315841876924	3		408	504	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509033	106509033	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752037338	NA	P-0014312-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	39	762	1	ENST00000359195.3:c.1027G>A	p.Gly343Ser	p.G343S	ENST00000359195	NM_002649.2	343	Ggc/Agc	2/11	1	2	FACETS	0.261	0.215	0.312	0.261	0.215	0.312	SUBCLONAL	1	TRUE	1	0.452775003161216	2		763	661	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530097	212530097	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	401	436	0	ENST00000342788.4:c.1822G>T	p.Ala608Ser	p.A608S	ENST00000342788	NM_005235.2	608	Gct/Tct	15/28	0.486959712081866	5	FACETS	1	0.993	1	0.891	0.86	0.921	CLONAL	4	TRUE	0	0.554416025159196	5		436	595	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553065	106553065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs550094148	NA	P-0014326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	157	806	1	ENST00000369096.4:c.1030G>A	p.Asp344Asn	p.D344N	ENST00000369096	NM_001198.3	344	Gac/Aac	5/7	0.538128762783824	4	FACETS	0.728	0.665	0.794	0.243	0.221	0.265	SUBCLONAL	1	TRUE	1	0.554416025159196	4		807	1209	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	17	715	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.688772233359142	1	FACETS	0.063	0.046	0.083	0.063	0.046	0.083	SUBCLONAL	1	FALSE	0	0.688772233359142	1		715	515	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577586	7577586	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587781589	NA	P-0014339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	39	862	0	ENST00000269305.4:c.695T>G	p.Ile232Ser	p.I232S	ENST00000269305	NM_001126112.2	232	aTc/aGc	7/11	NA	2	FACETS	0.151	0.125	0.181			1	INDETERMINATE	1	FALSE	NA	0.688772233359142	2		862	749	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0014368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	204	807	0	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.268846627918879	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.37	1		807	826	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589147	67589147	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0014368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	50	210	0	ENST00000274335.5:c.1135A>T	p.Lys379Ter	p.K379*	ENST00000274335		379	Aaa/Taa	9/15	1	2	FACETS	0.938	0.802	1	0.938	0.802	1	CLONAL	1	TRUE	1	0.37	2		210	288	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591092	67591100	+	inframe_deletion	In_Frame_Del	DEL	GTATGAACA	GTATGAACA	-	novel	NA	P-0014368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	75	300	0	ENST00000274335.5:c.1686_1694del	p.Met563_Ser565del	p.M563_S565del	ENST00000274335		562	cGTATGAACAgc/cgc	12/15	1	2	FACETS	0.705	0.618	0.798	0.705	0.618	0.798	SUBCLONAL	1	TRUE	1	0.37	2		300	575	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0014369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	75	250	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.275938522263044	2		250	468	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0014369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	91	483	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.275938522263044	2		483	628	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2493212	2493212	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	97	562	0	ENST00000355716.4:c.652A>G	p.Thr218Ala	p.T218A	ENST00000355716	NM_003820.2	218	Aca/Gca	6/8	1	2	FACETS	0.872	0.777	0.974	0.872	0.777	0.974	CLONAL	1	TRUE	1	0.275938522263044	2		562	806	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871875	12871875	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	85	179	0	ENST00000228872.4:c.592A>G	p.Thr198Ala	p.T198A	ENST00000228872	NM_004064.3	198	Acg/Gcg	2/3	0.248987293276949	2	FACETS	0.809	0.719	0.902	0.809	0.719	0.902	CLONAL	2	TRUE	0	0.275938522263044	2		179	381	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212420	36212420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	210	637	0	ENST00000222270.7:c.2171C>T	p.Ala724Val	p.A724V	ENST00000222270	NM_014727.1	724	gCt/gTt	3/37	1	2	FACETS	0.807	0.75	0.866	1	0.992	1	CLONAL	2	TRUE	1	0.275938522263044	2		637	943	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485049	57485049	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	77	307	0	ENST00000371085.3:c.883G>C	p.Asp295His	p.D295H	ENST00000371085	NM_000516.4	295	Gat/Cat	11/13	1	2	FACETS	0.91	0.8	1	0.91	0.8	1	CLONAL	1	TRUE	1	0.275938522263044	2		307	613	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415471	152415673	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTCATCCTCTTTGAGCTTCTCTCTCTCACTCTCTCTCTGCGCATTCAGGAGTGTACACATTTCTGTCCAGCACCCTGAAGTCTCTGGAAGAGAAGGACCATATCCACCGAGTCCTGGACAAGATCACAGACACTTTGATCCACCTGATGGCCAAGGCAGGCCTGACCCTGCAGCAGCAGCACCAGCGGCTGGCCCAGCTCCT	CCTCATCCTCTTTGAGCTTCTCTCTCTCACTCTCTCTCTGCGCATTCAGGAGTGTACACATTTCTGTCCAGCACCCTGAAGTCTCTGGAAGAGAAGGACCATATCCACCGAGTCCTGGACAAGATCACAGACACTTTGATCCACCTGATGGCCAAGGCAGGCCTGACCCTGCAGCAGCAGCACCAGCGGCTGGCCCAGCTCCT	-	novel	NA	P-0014369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	52	158	0	ENST00000206249.3:c.1370-38_1534del		p.X457_splice	ENST00000206249	NM_000125.3	457		7/8	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.275938522263044	2		158	268	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578234	7578234	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs786202222	NA	P-0014376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	264	695	0	ENST00000269305.4:c.615T>A	p.Tyr205Ter	p.Y205*	ENST00000269305	NM_001126112.2	205	taT/taA	6/11	0.288465339753648	1	FACETS	0.935	0.875	0.997	0.935	0.875	0.997	CLONAL	1	TRUE	0	0.35517653560843	1		695	1307	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29913035	29913035	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	139	583	0	ENST00000376809.5:c.1070A>G	p.Asp357Gly	p.D357G	ENST00000376809	NM_002116.7	357	gAt/gGt	7/8	1	2	FACETS	0.608	0.552	0.668	0.608	0.552	0.668	SUBCLONAL	1	TRUE	1	0.35517653560843	2		583	1287	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574572	64574572	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0014394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	343	506	0	ENST00000312049.6:c.825-2A>C		p.X275_splice	ENST00000312049	NM_130799.2	275			0.756569947815336	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.756569947815336	1		506	547	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861952	57861952	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777289743	NA	P-0014394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	308	381	1	ENST00000228682.2:c.1253G>A	p.Arg418Gln	p.R418Q	ENST00000228682	NM_005269.2	418	cGg/cAg	10/12	1	2	FACETS	0.95	0.899	1	0.95	0.899	1	CLONAL	1	TRUE	1	0.756569947815336	2		382	857	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361191	70361191	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	691	828	1	ENST00000374080.3:c.6379C>T	p.Pro2127Ser	p.P2127S	ENST00000374080		2127	Ccc/Tcc	43/45	1	2	FACETS	0.997	0.962	1	0.997	0.962	1	CLONAL	1	TRUE	1	0.756569947815336	2		829	1832	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624259	89624260	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0014395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	85	371	0	ENST00000371953.3:c.34_35del	p.Asn12GlnfsTer31	p.N12Qfs*31	ENST00000371953	NM_000314.4	11	agAAac/agac	1/9	0.294276497450554	0	FACETS	0.347	0.308	0.389			1	INDETERMINATE	1	TRUE	0	0.519977899546905	0		371	452	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259629	89259629	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	67	353	1	ENST00000336596.2:c.773C>A	p.Ser258Tyr	p.S258Y	ENST00000336596	NM_005233.5	258	tCc/tAc	3/17	1	2	FACETS	0.666	0.581	0.756	0.666	0.581	0.756	SUBCLONAL	1	TRUE	1	0.519977899546905	2		354	387	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	60	346	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.18	2		346	657	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	43	459	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.588	0.49	0.697	0.588	0.49	0.697	SUBCLONAL	1	TRUE	1	0.18	2		459	813	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	205	715	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.386672586206626	3	FACETS	0.838	0.782	0.894	0.838	0.782	0.894	CLONAL	2	TRUE	1	0.524413786128435	3		715	589	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246164	46246164	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	106	577	3	ENST00000334344.6:c.4258G>T	p.Val1420Leu	p.V1420L	ENST00000334344	NM_152641.2	1420	Gta/Tta	15/21	1	2	FACETS	0.703	0.632	0.778	0.703	0.632	0.778	SUBCLONAL	1	TRUE	1	0.524413786128435	2		580	575	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015636	112015636	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	91	534	0	ENST00000368678.4:c.1206G>T	p.Lys402Asn	p.K402N	ENST00000368678		402	aaG/aaT	11/13	1	2	FACETS	0.555	0.493	0.621	0.555	0.493	0.621	SUBCLONAL	1	TRUE	1	0.524413786128435	2		534	625	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68982086	68982086	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	87	925	0	ENST00000288368.4:c.1460G>T	p.Cys487Phe	p.C487F	ENST00000288368	NM_024870.2	487	tGt/tTt	13/40	0.386672586206626	3	FACETS	0.516	0.456	0.58	0.258	0.228	0.29	SUBCLONAL	1	TRUE	1	0.524413786128435	3		925	812	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356308	70356308	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	139	741	1	ENST00000374080.3:c.5203C>A	p.Arg1735Ser	p.R1735S	ENST00000374080		1735	Cgc/Agc	37/45	1	2	FACETS	0.688	0.627	0.753	0.688	0.627	0.753	SUBCLONAL	1	TRUE	1	0.524413786128435	2		742	770	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024504	16024504	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	52	503	0	ENST00000268712.3:c.1714C>T	p.Arg572Ter	p.R572*	ENST00000268712	NM_006311.3	572	Cga/Tga	16/46	0.642274178205983	1	FACETS	0.194	0.165	0.226	0.194	0.165	0.226	SUBCLONAL	1	TRUE	0	0.642274178205983	1		503	567	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0014423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	169	645	1	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.158079810985331	2	FACETS	0.797	0.734	0.863	0.797	0.734	0.863	SUBCLONAL	2	TRUE	0	0.260819575998199	2		646	813	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0014423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	124	628	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.158079810985331	2	FACETS	0.937	0.846	1	0.468	0.423	0.517	CLONAL	1	TRUE	0	0.260819575998199	2		628	1015	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921786	111921786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1466732626	NA	P-0014423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	50	384	1	ENST00000393256.3:c.575G>A	p.Arg192His	p.R192H	ENST00000393256	NM_006538.4	192	cGc/cAc	4/4	1	2	FACETS	0.523	0.443	0.612	0.523	0.443	0.612	SUBCLONAL	1	TRUE	1	0.260819575998199	2		385	733	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591901	48591901	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	35	397	0	ENST00000342988.3:c.1064A>T	p.Asp355Val	p.D355V	ENST00000342988	NM_005359.5	355	gAc/gTc	9/12	0.196816940083601	1	FACETS	0.383	0.313	0.462	0.383	0.313	0.462	SUBCLONAL	1	TRUE	0	0.260819575998199	1		397	610	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249149	55249149	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	137	707	0	ENST00000275493.2:c.2447A>G	p.Asn816Ser	p.N816S	ENST00000275493	NM_005228.3	816	aAc/aGc	20/28	0.196816940083601	1	FACETS	0.91	0.827	0.998	0.91	0.827	0.998	CLONAL	1	TRUE	0	0.260819575998199	1		707	1004	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272308	38272308	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs869320694	NA	P-0014433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	568	637	0	ENST00000425967.3:c.2059A>G	p.Lys687Glu	p.K687E	ENST00000425967	NM_001174067.1	687	Aag/Gag	15/19	0.955411434167395	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.955411434167395	1		637	615	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543174	65543196	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	GCTGGCCTGCCCCGAGTGGCTTA	GCTGGCCTGCCCCGAGTGGCTTA	-	novel	NA	P-0014433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	229	156	0	ENST00000358664.4:c.481_*20del		p.*161*	ENST00000358664	NM_002382.4	161		5/5	0.955411434167395	1	FACETS	0.974	0.947	0.998	0.974	0.947	0.998	CLONAL	1	TRUE	0	0.955411434167395	1		156	257	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	187	715	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.219472084304921	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.248940430809459	2		715	728	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0014457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	172	196	0	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	0.194811055167246	2	FACETS	0.968	0.893	1	0.968	0.893	1	CLONAL	2	TRUE	0	0.248940430809459	2		196	714	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578470	7578482	+	frameshift_variant	Frame_Shift_Del	DEL	CGGGCGGGGGTGT	CGGGCGGGGGTGT	-	rs1064792930	NA	P-0014457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	92	398	0	ENST00000269305.4:c.448_460del	p.Thr150AlafsTer16	p.T150Afs*16	ENST00000269305	NM_001126112.2	150	ACACCCCCGCCCGgc/gc	5/11	1	2	FACETS	0.582	0.516	0.654	0.582	0.516	0.654	SUBCLONAL	1	TRUE	1	0.248940430809459	2		398	1269	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651902	36651902	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	203	313	0	ENST00000244741.5:c.25del	p.Arg9ValfsTer22	p.R9Vfs*22	ENST00000244741	NM_000389.4	8	gtC/gt	2/3	0.194811055167246	2	FACETS	0.838	0.777	0.901	0.838	0.777	0.901	CLONAL	2	TRUE	0	0.248940430809459	2		313	973	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0014466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	74	248	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.826	0.724	0.936	0.826	0.724	0.936	CLONAL	1	TRUE	1	0.31	2		248	578	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0014466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	161	621	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	NA	2	FACETS	1	0.932	1			1	INDETERMINATE	1	TRUE	NA	0.31	2		621	1019	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	126	792	3	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.29582737541769	1	FACETS	0.915	0.829	1	0.915	0.829	1	CLONAL	1	TRUE	0	0.31	1		795	751	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107125	27107125	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	96	426	0	ENST00000324856.7:c.6736G>T	p.Glu2246Ter	p.E2246*	ENST00000324856	NM_006015.4	2246	Gag/Tag	20/20	0.29582737541769	1	FACETS	0.779	0.694	0.869	0.779	0.694	0.869	SUBCLONAL	1	TRUE	0	0.31	1		426	672	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220382	1220382	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	112	503	1	ENST00000326873.7:c.475C>T	p.Gln159Ter	p.Q159*	ENST00000326873	NM_000455.4	159	Cag/Tag	4/10	0.265881565294713	0	FACETS	0.783	0.705	0.864			1	SUBCLONAL	1	TRUE	0	0.31	0		504	637	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021492	42021492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	167	662	0	ENST00000219905.7:c.3788C>T	p.Ser1263Leu	p.S1263L	ENST00000219905	NM_001164273.1	1263	tCa/tTa	11/24	1	2	FACETS	0.846	0.775	0.92	0.846	0.775	0.92	CLONAL	1	TRUE	1	0.31	2		662	1274	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222886	5222886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372440262	NA	P-0014466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	83	474	1	ENST00000357368.4:c.2917G>A	p.Gly973Ser	p.G973S	ENST00000357368	NM_002850.3	973	Ggt/Agt	18/38	0.265881565294713	0	FACETS	0.674	0.596	0.758			1	SUBCLONAL	1	TRUE	0	0.31	0		475	548	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098929	47098929	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	64	558	0	ENST00000409792.3:c.6345del	p.Lys2115AsnfsTer32	p.K2115Nfs*32	ENST00000409792	NM_014159.6	2115	aaA/aa	15/21	0.29582737541769	1	FACETS	0.33	0.284	0.379	0.33	0.284	0.379	SUBCLONAL	1	TRUE	0	0.31	1		558	1058	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510101	149510101	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0014466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	111	504	0	ENST00000261799.4:c.1367+1del		p.X456_splice	ENST00000261799	NM_002609.3	456			1	2	FACETS	0.843	0.757	0.933	0.843	0.757	0.933	CLONAL	1	TRUE	1	0.31	2		504	850	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	87	126	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.804	0.712	0.903	0.804	0.712	0.903	CLONAL	1	TRUE	1	0.305985750612322	2		126	707	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0014470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	140	550	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	1	2	FACETS	0.834	0.758	0.914	0.834	0.758	0.914	CLONAL	1	TRUE	1	0.305985750612322	2		550	1097	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183554	185183554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	78	295	1	ENST00000265026.3:c.1408G>A	p.Glu470Lys	p.E470K	ENST00000265026	NM_004721.4	470	Gaa/Aaa	9/14	0.225074841263602	3	FACETS	0.841	0.739	0.951	0.42	0.369	0.476	CLONAL	1	TRUE	1	0.305985750612322	3		296	699	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143293	30143293	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748978993	NA	P-0014470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	321	552	0	ENST00000389048.3:c.233C>T	p.Ser78Leu	p.S78L	ENST00000389048	NM_004304.4	78	tCg/tTg	1/29	0.305985750612322	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.305985750612322	2		552	993	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458911	120458911	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	110	622	0	ENST00000256646.2:c.6434C>A	p.Ser2145Ter	p.S2145*	ENST00000256646	NM_024408.3	2145	tCa/tAa	34/34	1	2	FACETS	0.82	0.736	0.909	0.82	0.736	0.909	CLONAL	1	TRUE	1	0.305985750612322	2		622	877	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459305	120459305	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	101	319	0	ENST00000256646.2:c.6040C>G	p.Leu2014Val	p.L2014V	ENST00000256646	NM_024408.3	2014	Ctg/Gtg	34/34	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.305985750612322	2		319	621	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246490562	246490562	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	79	461	0	ENST00000388985.4:c.472G>C	p.Glu158Gln	p.E158Q	ENST00000388985		158	Gaa/Caa	5/12	1	2	FACETS	0.924	0.814	1	0.924	0.814	1	CLONAL	1	TRUE	1	0.305985750612322	2		461	559	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949356	71949356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	132	528	0	ENST00000298229.2:c.3736C>T	p.His1246Tyr	p.H1246Y	ENST00000298229	NM_001567.3	1246	Cac/Tac	28/28	1	2	FACETS	0.937	0.85	1	0.937	0.85	1	CLONAL	1	TRUE	1	0.305985750612322	2		528	921	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192065	108192065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1317619286	NA	P-0014470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	89	405	1	ENST00000278616.4:c.6490G>A	p.Glu2164Lys	p.E2164K	ENST00000278616	NM_000051.3	2164	Gag/Aag	45/63	0.305985750612322	1	FACETS	0.835	0.742	0.935	0.835	0.742	0.935	CLONAL	1	TRUE	0	0.305985750612322	1		406	590	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374309	118374309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	117	423	0	ENST00000534358.1:c.7702C>T	p.Pro2568Ser	p.P2568S	ENST00000534358	NM_005933.3	2568	Cca/Tca	27/36	0.305985750612322	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.305985750612322	1		423	577	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442985	49442985	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	143	480	0	ENST00000301067.7:c.3923del	p.Phe1308SerfsTer22	p.F1308Sfs*22	ENST00000301067	NM_003482.3	1308	tTc/tc	12/54	1	2	FACETS	0.998	0.909	1	0.998	0.909	1	CLONAL	1	TRUE	1	0.305985750612322	2		480	937	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033739	49033826	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTAGAGCGATTTCATGATTTGAAAAAAATCTACTTGTAATTCAAAATGAACAGTAAAAATGACTAATTTTTCTTATTCCCACAGTGT	ATTAGAGCGATTTCATGATTTGAAAAAAATCTACTTGTAATTCAAAATGAACAGTAAAAATGACTAATTTTTCTTATTCCCACAGTGT	-	novel	NA	P-0014470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	102	52	0	ENST00000267163.4:c.1961-83_1965del		p.X654_splice	ENST00000267163	NM_000321.2	654		20/27	0.305985750612322	2	FACETS	0.907	0.847	0.964	1	0.991	1	CLONAL	5	TRUE	0	0.305985750612322	2		52	147	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832721	3832721	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	122	351	1	ENST00000262367.5:c.1537C>T	p.Gln513Ter	p.Q513*	ENST00000262367	NM_004380.2	513	Caa/Taa	6/31	0.305985750612322	1	FACETS	0.957	0.866	1	0.957	0.866	1	CLONAL	1	TRUE	0	0.305985750612322	1		352	706	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81892752	81892752	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	63	391	0	ENST00000359376.3:c.463C>G	p.Gln155Glu	p.Q155E	ENST00000359376	NM_002661.3	155	Caa/Gaa	5/33	0.305985750612322	1	FACETS	0.703	0.609	0.805	0.703	0.609	0.805	SUBCLONAL	1	TRUE	0	0.305985750612322	1		391	496	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357508	89357508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	160	609	1	ENST00000301030.4:c.310G>A	p.Gly104Arg	p.G104R	ENST00000301030	NM_001256183.1	104	Gga/Aga	5/13	0.305985750612322	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.305985750612322	1		610	881	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023771	31023771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	138	528	0	ENST00000375687.4:c.3256G>A	p.Glu1086Lys	p.E1086K	ENST00000375687	NM_015338.5	1086	Gag/Aag	13/13	1	2	FACETS	0.89	0.808	0.975	0.89	0.808	0.975	CLONAL	1	TRUE	1	0.305985750612322	2		528	1014	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024759	31024759	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143328954	NA	P-0014470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	87	487	0	ENST00000375687.4:c.4244G>A	p.Arg1415Gln	p.R1415Q	ENST00000375687	NM_015338.5	1415	cGa/cAa	13/13	1	2	FACETS	0.778	0.688	0.874	0.778	0.688	0.874	SUBCLONAL	1	TRUE	1	0.305985750612322	2		487	731	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735556	40735556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	99	397	0	ENST00000373198.4:c.3317G>A	p.Gly1106Glu	p.G1106E	ENST00000373198	NM_133170.3	1106	gGg/gAg	25/32	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.305985750612322	2		397	634	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513223	44513223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	83	266	1	ENST00000291552.4:c.712G>A	p.Gly238Arg	p.G238R	ENST00000291552	NM_006758.2	238	Ggg/Agg	8/8	0.305985750612322	1	FACETS	0.984	0.872	1	0.984	0.872	1	CLONAL	1	TRUE	0	0.305985750612322	1		267	467	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839941	27839941	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	83	434	0	ENST00000328488.2:c.153G>C	p.Glu51Asp	p.E51D	ENST00000328488	NM_003533.2	51	gaG/gaC	1/1	1	2	FACETS	0.676	0.595	0.762	0.676	0.595	0.762	SUBCLONAL	1	TRUE	1	0.305985750612322	2		434	803	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971119	21971119	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519883	NA	P-0014470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	458	451	0	ENST00000304494.5:c.239G>C	p.Arg80Pro	p.R80P	ENST00000304494	NM_000077.4	80	cGa/cCa	2/3	0.147724779362947	3	FACETS	1	0.989	1			1	INDETERMINATE	3	TRUE	NA	0.305985750612322	3		451	1057	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923421	36923421	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1379	167	591	0	ENST00000358127.4:c.841C>G	p.Leu281Val	p.L281V	ENST00000358127	NM_001280556.1	281	Ctg/Gtg	7/10	0.305985750612322	4	FACETS	0.922	0.844	1	0.307	0.281	0.335	CLONAL	1	TRUE	1	0.305985750612322	4		591	1546	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220365	98220365	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	113	326	0	ENST00000331920.6:c.3098G>A	p.Ser1033Asn	p.S1033N	ENST00000331920	NM_000264.3	1033	aGc/aAc	18/24	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.305985750612322	2		326	714	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0014470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	189	627	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.305985750612322	2		627	1204	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs11575997	NA	P-0014476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	244	524	0	ENST00000269305.4:c.993+1G>T		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.519240086473939	1	FACETS	0.942	0.884	1	0.942	0.884	1	CLONAL	1	TRUE	0	0.530810310845339	1		524	717	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549498	21549498	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	56	389	0	ENST00000382592.4:c.2778C>G	p.Ile926Met	p.I926M	ENST00000382592	NM_014572.2	926	atC/atG	8/8	0.530814757270517	1	FACETS	0.276	0.236	0.32	0.276	0.236	0.32	SUBCLONAL	1	TRUE	0	0.530810310845339	1		389	561	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103365	2103403	+	inframe_deletion	In_Frame_Del	DEL	AGGCGGTCGCGGATCTGTTGCAGCCGGAGCGGCCGCTGG	AGGCGGTCGCGGATCTGTTGCAGCCGGAGCGGCCGCTGG	-	novel	NA	P-0014476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	72	539	0	ENST00000219476.3:c.252_290del	p.Val85_Ala97del	p.V85_A97del	ENST00000219476	NM_000548.3	83	aAGGCGGTCGCGGATCTGTTGCAGCCGGAGCGGCCGCTGGag/aag	4/42	0.530814757270517	1	FACETS	0.251	0.219	0.286	0.251	0.219	0.286	SUBCLONAL	1	TRUE	0	0.530810310845339	1		539	793	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982769	7982769	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	297	590	3	ENST00000319144.4:c.1016C>A	p.Pro339His	p.P339H	ENST00000319144	NM_001139.2	339	cCc/cAc	8/15	0.519240086473939	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.530810310845339	1		593	757	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726032	61726034	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0014476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1298	177	462	0	ENST00000401558.2:c.605_607del	p.Phe202del	p.F202del	ENST00000401558	NM_003400.3	202	tTCTca/tca	8/25	0.530814757270517	4	FACETS	0.692	0.636	0.751			1	SUBCLONAL	1	TRUE	NA	0.530810310845339	4		462	1475	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201834	66201834	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	53	350	1	ENST00000273854.3:c.2668G>T	p.Ala890Ser	p.A890S	ENST00000273854	NM_004439.5	890	Gcg/Tcg	16/18	1	2	FACETS	0.269	0.229	0.314	0.269	0.229	0.314	SUBCLONAL	1	TRUE	1	0.530810310845339	2		351	741	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181831	56181831	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	189	380	0	ENST00000399503.3:c.4055A>T	p.Gln1352Leu	p.Q1352L	ENST00000399503	NM_005921.1	1352	cAg/cTg	17/20	0.519240086473939	1	FACETS	0.921	0.857	0.987	0.921	0.857	0.987	CLONAL	1	TRUE	0	0.530810310845339	1		380	568	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139398874	139399572	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGTCCAGGGGAAGGCAGTGGCCCAGGAAAAGGGTGTGGCTGTGGGGTCAGGGCCCTGAGCTGGAATGCTGCCTCTACTCCTTGCCTGCGCAGGCCCTGAAGTCCCAGGTCCTCTCGGAACCTCCGTCTCTTTTACCATAAAGTGGGGAGAGTACTGCTTGCCATGGCGCCGGCCGTGAGGGGCAGGGAGGCCGTCGGGGAGGGCCCAGGAGAGTTGCGGGGATTGACCGTGGGCGCCGGGTCTCACTCACCCGCGGACGTCCATGGGGTCCAGCTCCCTCCGCCGCCGCCCACCCTCGCTGCCACCAGGGAGCAGCGAGGCCTTCACCTGGCCCAGCAGGGCGTCAGGTGCGGCCCAGCCCTCGGCGGCACGCTTGATGGGGTGCTTGCGCAGCTCCTCCTCGCGGCCGTAGTAGGGGAAGATCATCTGCTGGCCGTGTGCGTCACGCTTGAAGACCACGTTGGTGTGCAGCACGCGGCTGAGCTCCCGCAGGAAGTGGAAGGAGCTGTTGCGCAGCTGCTCCGGCGGCATCAGCACCACCACCACCAGCGTGCCGGCCGCCAGCCTCTCGGGTACATGCTCCGCACAGTCCAGCCCGTCCCACTCGCACTCCGCGCTGTTGCAGCCCTGGTCGCAGTGCCCGTCGCTGAAGTGGTCCTTGCAGTACTGGTCGTACAGGGGGCTGTGGGGGGCGGGAC	CTGTCCAGGGGAAGGCAGTGGCCCAGGAAAAGGGTGTGGCTGTGGGGTCAGGGCCCTGAGCTGGAATGCTGCCTCTACTCCTTGCCTGCGCAGGCCCTGAAGTCCCAGGTCCTCTCGGAACCTCCGTCTCTTTTACCATAAAGTGGGGAGAGTACTGCTTGCCATGGCGCCGGCCGTGAGGGGCAGGGAGGCCGTCGGGGAGGGCCCAGGAGAGTTGCGGGGATTGACCGTGGGCGCCGGGTCTCACTCACCCGCGGACGTCCATGGGGTCCAGCTCCCTCCGCCGCCGCCCACCCTCGCTGCCACCAGGGAGCAGCGAGGCCTTCACCTGGCCCAGCAGGGCGTCAGGTGCGGCCCAGCCCTCGGCGGCACGCTTGATGGGGTGCTTGCGCAGCTCCTCCTCGCGGCCGTAGTAGGGGAAGATCATCTGCTGGCCGTGTGCGTCACGCTTGAAGACCACGTTGGTGTGCAGCACGCGGCTGAGCTCCCGCAGGAAGTGGAAGGAGCTGTTGCGCAGCTGCTCCGGCGGCATCAGCACCACCACCACCAGCGTGCCGGCCGCCAGCCTCTCGGGTACATGCTCCGCACAGTCCAGCCCGTCCCACTCGCACTCCGCGCTGTTGCAGCCCTGGTCGCAGTGCCCGTCGCTGAAGTGGTCCTTGCAGTACTGGTCGTACAGGGGGCTGTGGGGGGCGGGAC	-	novel	NA	P-0014476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	490	13	0	ENST00000277541.6:c.4587-15_5018+252del		p.X1529_splice	ENST00000277541	NM_017617.3	1529		26/34	0.530810310845339	2	FACETS		NA	1	1	0.998	1	NA	4	TRUE	0	0.530810310845339	2		13	512	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0014480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	201	474	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.189261544510163	5	FACETS	0.973	0.906	1	0.973	0.906	1	CLONAL	3	TRUE	2	0.314882240054936	5		474	644	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0014480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	129	439	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.189261544510163	5	FACETS	1	0.953	1	0.716	0.651	0.782	CLONAL	2	TRUE	2	0.314882240054936	5		439	562	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193884	106193884	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	122	388	0	ENST00000380013.4:c.4346C>A	p.Ser1449Tyr	p.S1449Y	ENST00000380013	NM_001127208.2	1449	tCt/tAt	10/11	0.276538440560944	3	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	1	0.314882240054936	3		388	440	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551295	141551295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	259	739	0	ENST00000220592.5:c.2002C>T	p.Arg668Cys	p.R668C	ENST00000220592	NM_012154.3	668	Cgc/Tgc	15/19	0.314882240054936	5	FACETS	1	0.989	1	0.827	0.776	0.88	CLONAL	2	TRUE	2	0.314882240054936	5		739	976	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0014485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	75	223	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.935	0.821	1	0.935	0.821	1	CLONAL	1	FALSE	1	0.315903073881921	2		223	508	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466413	120466413	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	203	512	0	ENST00000256646.2:c.4706T>C	p.Leu1569Pro	p.L1569P	ENST00000256646	NM_024408.3	1569	cTg/cCg	26/34	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.315903073881921	2		512	928	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882019	NA	P-0014504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	457	641	2	ENST00000269305.4:c.455del	p.Pro152ArgfsTer18	p.P152Rfs*18	ENST00000269305	NM_001126112.2	152	cCg/cg	5/11	0.339573286722026	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	TRUE	0	0.339573286722026	3		643	1023	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919595	28919595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs553261958	NA	P-0014504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	214	504	0	ENST00000282397.4:c.2342G>A	p.Arg781Gln	p.R781Q	ENST00000282397	NM_002019.4	781	cGa/cAa	16/30	0.315543944023742	4	FACETS	0.955	0.889	1	0.955	0.889	1	CLONAL	2	TRUE	2	0.339573286722026	4		504	884	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999029	100999029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771950812	NA	P-0014504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	83	440	1	ENST00000325455.5:c.773C>T	p.Pro258Leu	p.P258L	ENST00000325455	NM_001202474.3	258	cCg/cTg	1/8	0.339573286722026	3	FACETS	0.955	0.844	1	0.477	0.422	0.537	CLONAL	1	TRUE	1	0.339573286722026	3		441	599	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624370	21624370	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1565561502	NA	P-0014504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	67	317	0	ENST00000421138.2:c.1659G>C	p.Gln553His	p.Q553H	ENST00000421138		553	caG/caC	14/16	0.315543944023742	4	FACETS	0.877	0.762	1	0.438	0.381	0.501	CLONAL	1	TRUE	2	0.339573286722026	4		317	603	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46215251	46215263	+	frameshift_variant	Frame_Shift_Del	DEL	CTGATAGAGACTT	CTGATAGAGACTT	-	novel	NA	P-0014504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	57	273	0	ENST00000334344.6:c.687_699del	p.Asp230LeufsTer58	p.D230Lfs*58	ENST00000334344	NM_152641.2	229	aCTGATAGAGACTTc/ac	6/21	0.289580193165658	3	FACETS	1	0.938	1	0.581	0.501	0.667	CLONAL	1	TRUE	1	0.339573286722026	3		273	338	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62009575	62009575	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs114330958	NA	P-0014504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	194	572	1	ENST00000392795.3:c.47C>T	p.Ala16Val	p.A16V	ENST00000392795	NM_001039933.1	16	gCg/gTg	1/6	0.339573286722026	4	FACETS	0.764	0.706	0.823	0.509	0.471	0.549	SUBCLONAL	2	TRUE	1	0.339573286722026	4		573	1002	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100999	41100999	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	113	398	0	ENST00000373198.4:c.1357C>A	p.Arg453Ser	p.R453S	ENST00000373198	NM_133170.3	453	Cgc/Agc	8/32	0.252454635393846	3	FACETS	1	0.971	1			1	CLONAL	1	TRUE	NA	0.339573286722026	3		398	645	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370762	55370762	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	120	491	0	ENST00000297316.4:c.64G>A	p.Ala22Thr	p.A22T	ENST00000297316	NM_022454.3	22	Gcg/Acg	1/2	0.199111393760008	3	FACETS	1	0.979	1	0.646	0.584	0.711	INDETERMINATE	1	TRUE	1	0.339573286722026	3		491	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0014505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	339	711	2	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.709258071834873	1	FACETS	0.975	0.932	1	0.975	0.932	1	CLONAL	1	TRUE	0	0.709258071834873	1		713	633	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	258	715	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.924	0.865	0.986	0.924	0.865	0.986	CLONAL	1	TRUE	1	0.481232921938291	2		715	1160	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138521	11138521	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	386	497	0	ENST00000358026.2:c.3277C>T	p.Arg1093Ter	p.R1093*	ENST00000358026	NM_001128849.1	1093	Cga/Tga	24/36	0.481232921938291	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.481232921938291	1		497	1197	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218489	1218489	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0014513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	263	424	0	ENST00000326873.7:c.364A>T	p.Lys122Ter	p.K122*	ENST00000326873	NM_000455.4	122	Aag/Tag	2/10	0.481232921938291	1	FACETS	0.933	0.876	0.991	0.933	0.876	0.991	CLONAL	1	TRUE	0	0.481232921938291	1		424	890	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913517	NA	P-0014521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	336	347	0	ENST00000288135.5:c.1676T>G	p.Val559Gly	p.V559G	ENST00000288135	NM_000222.2	559	gTt/gGt	11/21	1	2	FACETS	0.905	0.86	0.951	0.905	0.86	0.951	CLONAL	1	TRUE	1	0.895554050741678	2		347	829	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0014523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	78	284	0	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	0.468410243574267	2		284	321	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418643	49418643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs936142615	NA	P-0014523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	281	570	0	ENST00000301067.7:c.15871G>A	p.Glu5291Lys	p.E5291K	ENST00000301067	NM_003482.3	5291	Gag/Aag	49/54	0.460319262321891	4	FACETS	0.98	0.923	1	0.98	0.923	1	CLONAL	2	TRUE	2	0.468410243574267	4		570	899	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445901	49445901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	203	941	0	ENST00000301067.7:c.1565C>T	p.Pro522Leu	p.P522L	ENST00000301067	NM_003482.3	522	cCa/cTa	10/54	0.460319262321891	4	FACETS	1	0.954	1	0.521	0.482	0.562	CLONAL	1	TRUE	2	0.468410243574267	4		941	1221	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435289	121435289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371544082	NA	P-0014523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	150	529	1	ENST00000257555.6:c.1322C>T	p.Thr441Met	p.T441M	ENST00000257555		441	aCg/aTg	7/10	0.460319262321891	4	FACETS	1	0.972	1	0.573	0.524	0.625	CLONAL	1	TRUE	2	0.468410243574267	4		530	820	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166390	7166390	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	310	551	0	ENST00000302850.5:c.1636G>C	p.Asp546His	p.D546H	ENST00000302850	NM_000208.2	546	Gac/Cac	8/22	0.468410243574267	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.468410243574267	2		551	605	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471057	25471057	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	167	545	0	ENST00000264709.3:c.704del	p.Glu235GlyfsTer81	p.E235Gfs*81	ENST00000264709	NM_175629.2	235	gAg/gg	7/23	0.468410243574267	3	FACETS	0.968	0.89	1	0.484	0.445	0.525	CLONAL	1	TRUE	1	0.468410243574267	3		545	909	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0014528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1423	46	827	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.522	0.437	0.617	0.522	0.437	0.617	SUBCLONAL	1	TRUE	1	0.12	2		828	1469	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0014528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	27	645	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.505	0.4	0.626	0.505	0.4	0.626	SUBCLONAL	1	TRUE	1	0.12	2		645	891	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0014528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	24	484	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.571	0.446	0.717	0.571	0.446	0.717	SUBCLONAL	1	TRUE	1	0.12	2		484	700	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443345	187443345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	36	461	1	ENST00000232014.4:c.1781G>A	p.Arg594Gln	p.R594Q	ENST00000232014	NM_001130845.1	594	cGa/cAa	8/10	1	2	FACETS	0.664	0.543	0.8	0.664	0.543	0.8	SUBCLONAL	1	TRUE	1	0.12	2		462	904	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0014528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	45	593	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	0.688	0.576	0.813	0.688	0.576	0.813	SUBCLONAL	1	TRUE	1	0.12	2		593	1090	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428511	78428511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408536007	NA	P-0014528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	36	557	0	ENST00000370768.2:c.1288C>T	p.Arg430Cys	p.R430C	ENST00000370768	NM_003902.3	430	Cgt/Tgt	14/20	1	2	FACETS	0.865	0.709	1	0.865	0.709	1	CLONAL	1	TRUE	1	0.12	2		557	694	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0014528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	30	355	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	1	0.12	2		355	469	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209101857	209101857	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	39	610	0	ENST00000345146.2:c.1191C>A	p.Phe397Leu	p.F397L	ENST00000345146	NM_005896.2	397	ttC/ttA	10/10	1	2	FACETS	0.884	0.731	1	0.884	0.731	1	CLONAL	1	TRUE	1	0.12	2		610	735	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587777894	NA	P-0014528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	27	564	2	ENST00000361445.4:c.6644C>A	p.Ser2215Tyr	p.S2215Y	ENST00000361445	NM_004958.3	2215	tCt/tAt	47/58	1	2	FACETS	0.424	0.336	0.526	0.424	0.336	0.526	SUBCLONAL	1	TRUE	1	0.12	2		566	1061	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	24	555	1	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	1	2	FACETS	0.669	0.523	0.839	0.669	0.523	0.839	SUBCLONAL	1	TRUE	1	0.12	2		556	598	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950648	38950648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776074870	NA	P-0014528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	15	334	0	ENST00000357387.3:c.3302C>T	p.Ser1101Leu	p.S1101L	ENST00000357387	NM_152756.3	1101	tCg/tTg	31/38	1	2	FACETS	0.477	0.347	0.635	0.477	0.347	0.635	SUBCLONAL	1	TRUE	1	0.12	2		334	524	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012441	29012441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55974987	NA	P-0014528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	44	622	0	ENST00000282397.4:c.430G>A	p.Glu144Lys	p.E144K	ENST00000282397	NM_002019.4	144	Gaa/Aaa	4/30	1	2	FACETS	0.836	0.699	0.989	0.836	0.699	0.989	CLONAL	1	TRUE	1	0.12	2		622	877	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203625	108203625	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	18	232	0	ENST00000278616.4:c.7925G>T	p.Arg2642Ile	p.R2642I	ENST00000278616	NM_000051.3	2642	aGa/aTa	53/63	1	2	FACETS	1	0.845	1	1	0.845	1	CLONAL	1	TRUE	1	0.12	2		232	255	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55569904	55569904	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs753318751	NA	P-0014528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	17	248	0	ENST00000288135.5:c.771G>T	p.Glu257Asp	p.E257D	ENST00000288135	NM_000222.2	257	gaG/gaT	5/21	1	2	FACETS	1	0.747	1	1	0.747	1	CLONAL	1	TRUE	1	0.12	2		248	283	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064749	80064749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148896355	NA	P-0014528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	31	580	0	ENST00000265081.6:c.2180G>A	p.Arg727Gln	p.R727Q	ENST00000265081	NM_002439.4	727	cGa/cAa	15/24	1	2	FACETS	0.905	0.73	1	0.905	0.73	1	CLONAL	1	TRUE	1	0.12	2		580	571	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86648999	86648999	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs975191415	NA	P-0014528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	28	445	0	ENST00000274376.6:c.1279C>T	p.Arg427Ter	p.R427*	ENST00000274376	NM_002890.2	427	Cga/Tga	9/25	1	2	FACETS	0.941	0.751	1	0.941	0.751	1	CLONAL	1	TRUE	1	0.12	2		445	496	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205043	123205043	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	36	479	0	ENST00000218089.9:c.2403G>T	p.Gln801His	p.Q801H	ENST00000218089	NM_001042749.1	801	caG/caT	25/35	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.12	2		479	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0014530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	88	567	1	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.16	2		568	909	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061113	38061120	+	frameshift_variant	Frame_Shift_Del	DEL	CTCAGGGC	CTCAGGGC	-	novel	NA	P-0014530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	26	256	0	ENST00000250448.2:c.869_876del	p.Gly290GlufsTer10	p.G290Efs*10	ENST00000250448	NM_004496.3	290	gGCCCTGAG/g	2/2	1	2	FACETS	0.662	0.523	0.822	0.662	0.523	0.822	SUBCLONAL	1	TRUE	1	0.16	2		256	491	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217891	7217891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	59	445	1	ENST00000380728.2:c.120G>A	p.Met40Ile	p.M40I	ENST00000380728		40	atG/atA	3/11	1	2	FACETS	0.95	0.816	1	0.95	0.816	1	CLONAL	1	TRUE	1	0.16	2		446	776	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001340	150001340	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	68	610	0	ENST00000253339.5:c.2264A>G	p.Asp755Gly	p.D755G	ENST00000253339		755	gAt/gGt	4/7	1	2	FACETS	0.892	0.774	1	0.892	0.774	1	CLONAL	1	TRUE	1	0.16	2		610	953	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0014561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	477	547	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.591096607656485	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.591096607656485	2		547	761	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0014561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	172	264	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.48139117394189	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.591096607656485	4		264	418	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623558	43623558	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0014561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	78	308	0	ENST00000355710.3:c.3188-2A>T		p.X1063_splice	ENST00000355710	NM_020975.4	1063			0.48139117394189	4	FACETS	0.997	0.881	1	0.499	0.44	0.561	CLONAL	1	TRUE	2	0.591096607656485	4		308	421	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993405	72993405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	594	733	0	ENST00000268489.5:c.640G>A	p.Ala214Thr	p.A214T	ENST00000268489	NM_006885.3	214	Gct/Act	2/10	0.591096607656485	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.591096607656485	2		733	960	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650447	48650447	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	248	842	0	ENST00000376670.3:c.417G>T	p.Glu139Asp	p.E139D	ENST00000376670	NM_002049.3	139	gaG/gaT	3/6	0.591096607656485	3	FACETS	0.834	0.778	0.891	0.417	0.389	0.446	CLONAL	1	TRUE	1	0.591096607656485	3		842	1304	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352271	70352271	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	74	624	0	ENST00000374080.3:c.4298C>A	p.Ala1433Asp	p.A1433D	ENST00000374080		1433	gCt/gAt	31/45	0.591096607656485	3	FACETS	0.285	0.248	0.325	0.143	0.124	0.163	SUBCLONAL	1	TRUE	1	0.591096607656485	3		624	1138	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442569	52442569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1298276806	NA	P-0014576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	172	389	1	ENST00000460680.1:c.176G>A	p.Arg59Gln	p.R59Q	ENST00000460680	NM_004656.3	59	cGg/cAg	4/17	0.764576688319877	3	FACETS	0.706	0.65	0.764	0.353	0.325	0.382	SUBCLONAL	1	TRUE	1	0.764576688319877	3		390	881	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40367558	40367561	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	CATG	CATG	-	novel	NA	P-0014576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	4	17	0	ENST00000397332.2:c.-1_3del		p.*1*	ENST00000397332	NM_001033082.2	?-1/394		1/3	0.764576688319877	3	FACETS	0.904	0.502	1	0.452	0.251	0.704	CLONAL	1	TRUE	1	0.764576688319877	3		17	16	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577137	7577138	+	missense_variant	Missense_Mutation	DNP	CC	CC	GG	novel	NA	P-0014576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	484	575	1	ENST00000269305.4:c.800_801inv	p.Arg267Pro	p.R267P	ENST00000269305	NM_001126112.2	267	cGG/cCC	8/11	NA	2	FACETS	0.936	0.909	0.963			1	INDETERMINATE	2	TRUE	NA	0.764576688319877	2		576	676	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638900	176638900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763399938	NA	P-0014576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	267	552	0	ENST00000439151.2:c.3500G>A	p.Arg1167His	p.R1167H	ENST00000439151	NM_022455.4	1167	cGc/cAc	5/23	0.764576688319877	4	FACETS	0.909	0.851	0.969			1	CLONAL	1	TRUE	NA	0.764576688319877	4		552	1356	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944629	40944639	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GATAAACACTG	GATAAACACTG	-	novel	NA	P-0014581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	135	227	0	ENST00000373198.4:c.1866-3_1873del		p.X622_splice	ENST00000373198	NM_133170.3	622		12/32	1	2	FACETS	0.952	0.87	1	0.952	0.87	1	CLONAL	1	TRUE	1	0.543238470509994	2		227	522	SUCCESS
APC	324	MSKCC	GRCh37	5	112179312	112179326	+	inframe_deletion	In_Frame_Del	DEL	CTCCCACAGGTAATA	CTCCCACAGGTAATA	-	novel	NA	P-0014581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	99	278	0	ENST00000257430.4:c.8026_8040del	p.Thr2676_Pro2680del	p.T2676_P2680del	ENST00000257430	NM_000038.5	2674	tCTCCCACAGGTAATAct/tct	16/16	1	2	FACETS	0.659	0.59	0.732	0.659	0.59	0.732	SUBCLONAL	1	TRUE	1	0.543238470509994	2		278	553	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0014612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	107	852	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	0.17	2		852	947	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363211	40363211	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	69	755	0	ENST00000397332.2:c.1018A>T	p.Thr340Ser	p.T340S	ENST00000397332	NM_001033082.2	340	Acc/Tcc	3/3	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.17	2		755	696	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716140	243716140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	86	940	0	ENST00000263826.5:c.1054G>A	p.Glu352Lys	p.E352K	ENST00000263826	NM_005465.4	352	Gag/Aag	10/13	0.148547626296599	3	FACETS	1	0.902	1	0.512	0.452	0.578	CLONAL	1	TRUE	1	0.17	3		940	1071	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900833	3900833	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	79	760	0	ENST00000262367.5:c.263A>C	p.Asn88Thr	p.N88T	ENST00000262367	NM_004380.2	88	aAt/aCt	2/31	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.17	2		760	720	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032566	47032566	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	92	510	0	ENST00000377604.3:c.472G>T	p.Glu158Ter	p.E158*	ENST00000377604	NM_001204468.1	158	Gag/Tag	5/24	1	1	FACETS	1	0.935	1	1	0.987	1	CLONAL	2	TRUE	0	0.17	1		510	464	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715786	18715786	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	12	477	0	ENST00000266497.5:c.3617A>G	p.Glu1206Gly	p.E1206G	ENST00000266497		1206	gAa/gGa	25/31	1	2	FACETS	0.606	0.429	0.82	0.606	0.429	0.82	SUBCLONAL	1	TRUE	1	0.347308832210299	2		477	114	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441260	52441260	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	165	782	0	ENST00000460680.1:c.510del	p.Phe170LeufsTer17	p.F170Lfs*17	ENST00000460680	NM_004656.3	170	ttT/tt	7/17	0.347308832210299	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.347308832210299	1		782	568	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183733	10183735	+	missense_variant	Missense_Mutation	TNP	TCG	TCG	CCT	novel	NA	P-0014619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	220	1007	1	ENST00000256474.2:c.202_204delinsCCT	p.Ser68Pro	p.S68P	ENST00000256474	NM_000551.3	68	TCG/CCT	1/3	0.347308832210299	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.347308832210299	1		1008	860	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80168985	80168986	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0014620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	36	713	0	ENST00000265081.6:c.3183_3184del	p.Gly1062AsnfsTer12	p.G1062Nfs*12	ENST00000265081	NM_002439.4	1061	AGa/a	23/24	0.305540217085694	1	FACETS	0.285	0.233	0.344	0.285	0.233	0.344	SUBCLONAL	1	TRUE	0	0.305540217085694	1		713	700	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8523519	8523519	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	64	396	0	ENST00000356435.5:c.685C>T	p.Arg229Ter	p.R229*	ENST00000356435		229	Cga/Tga	8/35	1	2	FACETS	0.858	0.745	0.981	0.858	0.745	0.981	CLONAL	1	TRUE	1	0.305540217085694	2		396	488	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0014631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	48	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.614	0.523	0.711	0.614	0.523	0.711	SUBCLONAL	1	TRUE	1	0.638388822893361	2		336	245	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205781	108205781	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	123	490	0	ENST00000278616.4:c.8096C>A	p.Pro2699Gln	p.P2699Q	ENST00000278616	NM_000051.3	2699	cCa/cAa	55/63	0.638388822893361	2	FACETS	0.931	0.867	0.993	0.931	0.867	0.993	CLONAL	2	TRUE	0	0.638388822893361	2		490	207	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996745	73996745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1320648606	NA	P-0014631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	93	200	0	ENST00000318443.5:c.1301G>A	p.Gly434Asp	p.G434D	ENST00000318443	NM_001024736.1	434	gGc/gAc	6/10	0.118750568537182	0	FACETS	0.322	0.289	0.357			1	INDETERMINATE	1	TRUE	0	0.638388822893361	0		200	327	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020916	26020916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369516106	NA	P-0014631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	108	349	0	ENST00000357647.3:c.199C>T	p.Pro67Ser	p.P67S	ENST00000357647	NM_003529.2	67	Cct/Tct	1/1	0.622405173765411	3	FACETS	0.88	0.794	0.971	0.44	0.397	0.486	CLONAL	1	TRUE	1	0.638388822893361	3		349	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579401	7579402	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0014637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	481	727	1	ENST00000269305.4:c.285_286del	p.Ser96CysfsTer52	p.S96Cfs*52	ENST00000269305	NM_001126112.2	95	tcTTct/tcct	4/11	0.654198976877537	2	FACETS	0.937	0.907	0.966	0.937	0.907	0.966	CLONAL	2	TRUE	0	0.710364927990391	2		728	723	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29120986	29120986	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555926762	NA	P-0014637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	172	499	0	ENST00000328354.6:c.571C>G	p.Leu191Val	p.L191V	ENST00000328354	NM_007194.3	191	Ctg/Gtg	4/15	0.706155588134338	2	FACETS	0.817	0.755	0.88	0.408	0.377	0.44	CLONAL	1	TRUE	0	0.710364927990391	2		499	593	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890188	76890188	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	100	567	0	ENST00000373344.5:c.4706A>G	p.Gln1569Arg	p.Q1569R	ENST00000373344	NM_000489.3	1569	cAg/cGg	17/35	NA	2	FACETS	0.417	0.373	0.464			1	INDETERMINATE	1	TRUE	NA	0.710364927990391	2		567	675	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	326	126	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.71	2		126	854	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631839	90631839	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519906	NA	P-0014647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	376	376	0	ENST00000330062.3:c.514A>T	p.Arg172Trp	p.R172W	ENST00000330062	NM_002168.2	172	Agg/Tgg	4/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.71	2		376	1041	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430794	78430798	+	frameshift_variant	Frame_Shift_Del	DEL	ATCCT	ATCCT	-	novel	NA	P-0014647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	64	600	0	ENST00000370768.2:c.591_595del	p.Gly198SerfsTer10	p.G198Sfs*10	ENST00000370768	NM_003902.3	197	gcAGGATta/gcta	8/20	0.727016443360994	1	FACETS	0.169	0.146	0.194	0.169	0.146	0.194	SUBCLONAL	1	TRUE	0	0.71	1		600	688	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791727	42791727	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	96	678	0	ENST00000575354.2:c.614del	p.Asn205MetfsTer4	p.N205Mfs*4	ENST00000575354	NM_015125.3	205	Aat/at	5/20	0.727016443360994	1	FACETS	0.296	0.264	0.33	0.296	0.264	0.33	SUBCLONAL	1	TRUE	0	0.71	1		678	589	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	210	126	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.845	0.786	0.906	1	0.993	1	CLONAL	2	TRUE	1	0.286552407453204	2		126	867	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0014657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	202	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.856	0.794	0.919	1	0.992	1	CLONAL	2	TRUE	1	0.286552407453204	2		336	824	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260476	16260476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	202	356	0	ENST00000375759.3:c.7741C>T	p.Pro2581Ser	p.P2581S	ENST00000375759	NM_015001.2	2581	Cct/Tct	11/15	1	2	FACETS	0.883	0.821	0.948	1	0.993	1	CLONAL	2	TRUE	1	0.286552407453204	2		356	798	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158326	108158326	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0014657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	148	390	0	ENST00000278616.4:c.3994-1G>C		p.X1332_splice	ENST00000278616	NM_000051.3	1332			1	2	FACETS	0.793	0.727	0.863	1	0.989	1	SUBCLONAL	2	TRUE	1	0.286552407453204	2		390	651	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	37	715	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.122	0.1	0.147	0.122	0.1	0.147	SUBCLONAL	1	TRUE	1	0.71	2		715	853	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0014670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1174	56	641	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	0.128	0.109	0.149	0.128	0.109	0.149	SUBCLONAL	1	TRUE	1	0.71	2		641	1230	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121912580	NA	P-0014670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	27	350	0	ENST00000342988.3:c.1157G>T	p.Gly386Val	p.G386V	ENST00000342988	NM_005359.5	386	gGt/gTt	10/12	1	2	FACETS	0.125	0.099	0.155	0.125	0.099	0.155	SUBCLONAL	1	TRUE	1	0.71	2		350	608	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309745	65309745	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0014670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	42	409	0	ENST00000342505.4:c.2403+2T>G		p.X801_splice	ENST00000342505	NM_002227.2	801			1	2	FACETS	0.158	0.131	0.188	0.158	0.131	0.188	SUBCLONAL	1	TRUE	1	0.71	2		409	748	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880531	155880531	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	485	766	2	ENST00000368323.3:c.22G>C	p.Val8Leu	p.V8L	ENST00000368323	NM_006912.5	8	Gtt/Ctt	2/6	0.505974332136349	4	FACETS	0.931	0.893	0.97	0.931	0.893	0.97	CLONAL	2	TRUE	2	0.774767367409202	4		768	1193	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717709	89717713	+	frameshift_variant	Frame_Shift_Del	DEL	AGCCG	AGCCG	-	novel	NA	P-0014685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	255	581	0	ENST00000371953.3:c.734_738del	p.Gln245LeufsTer6	p.Q245Lfs*6	ENST00000371953	NM_000314.4	245	cAGCCG/c	7/9	0.740343619583308	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.774767367409202	1		581	390	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251067	99251067	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs748252733	NA	P-0014685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	258	669	0	ENST00000268035.6:c.371A>G	p.Asn124Ser	p.N124S	ENST00000268035	NM_000875.3	124	aAt/aGt	2/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.774767367409202	2		669	618	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943375	71943393	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCTCGGTGAGGGGGCGCC	GGCTCGGTGAGGGGGCGCC	A	novel	NA	P-0014685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	175	636	1	ENST00000298229.2:c.1707_1712+13delinsA		p.X569_splice	ENST00000298229	NM_001567.3	569		14/28	0.774767367409202	1	FACETS	0.87	0.818	0.922	0.87	0.818	0.922	CLONAL	1	TRUE	0	0.774767367409202	1		637	318	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0014697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	624	711	2	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.637867197885985	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.642801427553875	2		713	921	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381472	81381472	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777593933	NA	P-0014697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	120	460	1	ENST00000222390.5:c.589C>T	p.Arg197Cys	p.R197C	ENST00000222390	NM_000601.4	197	Cgc/Tgc	5/18	1	2	FACETS	0.744	0.675	0.815	0.744	0.675	0.815	SUBCLONAL	1	TRUE	1	0.642801427553875	2		461	502	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188309	10188309	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs869025655	NA	P-0014698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	265	633	0	ENST00000256474.2:c.452T>G	p.Ile151Ser	p.I151S	ENST00000256474	NM_000551.3	151	aTc/aGc	2/3	0.421126698475189	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.421126698475189	1		633	935	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0014728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	200	284	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.933	0.874	0.992	0.933	0.874	0.992	CLONAL	1	TRUE	1	0.918231642519818	2		284	467	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955381	48955381	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs1258442224	NA	P-0014728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	145	95	0	ENST00000267163.4:c.1499-2A>T		p.X500_splice	ENST00000267163	NM_000321.2	500			0.918231642519818	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.918231642519818	1		95	166	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs864622237	NA	P-0014728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	536	395	0	ENST00000269305.4:c.700T>C	p.Tyr234His	p.Y234H	ENST00000269305	NM_001126112.2	234	Tac/Cac	7/11	0.907302832518812	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.918231642519818	1		395	579	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106861	27106861	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	771	331	0	ENST00000324856.7:c.6472C>T	p.Arg2158Ter	p.R2158*	ENST00000324856	NM_006015.4	2158	Cga/Tga	20/20	0.647986178262058	3	FACETS	0.962	0.936	0.988	0.962	0.936	0.988	CLONAL	2	TRUE	1	0.918231642519818	3		331	1273	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713601	30713601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202168735	NA	P-0014728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	396	296	0	ENST00000295754.5:c.926C>T	p.Thr309Met	p.T309M	ENST00000295754	NM_003242.5	309	aCg/aTg	4/7	1	2	FACETS	0.998	0.954	1	0.998	0.954	1	CLONAL	1	TRUE	1	0.918231642519818	2		296	864	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845889	156845889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757590743	NA	P-0014728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1910	162	550	1	ENST00000524377.1:c.1519C>T	p.Arg507Cys	p.R507C	ENST00000524377	NM_002529.3	507	Cgc/Tgc	13/17	0.647986178262058	3	FACETS	0.248	0.227	0.272	0.124	0.113	0.136	SUBCLONAL	1	TRUE	1	0.918231642519818	3		551	2072	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939510	76939510	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0014728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	537	221	0	ENST00000373344.5:c.1238T>A	p.Leu413Ter	p.L413*	ENST00000373344	NM_000489.3	413	tTa/tAa	9/35	1	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.918231642519818	1		221	559	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574693	64574693	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1114167472	NA	P-0014731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	290	409	0	ENST00000312049.6:c.784-2A>G		p.X262_splice	ENST00000312049	NM_130799.2	262			0.892889826774537	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.893536517909017	1		409	353	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594221	55594221	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913512	NA	P-0014731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	222	328	0	ENST00000288135.5:c.1924A>G	p.Lys642Glu	p.K642E	ENST00000288135	NM_000222.2	642	Aaa/Gaa	13/21	1	2	FACETS	0.917	0.861	0.973	0.917	0.861	0.973	CLONAL	1	TRUE	1	0.893536517909017	2		328	542	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236074	108236074	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555151737	NA	P-0014731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	257	334	0	ENST00000278616.4:c.9010A>G	p.Lys3004Glu	p.K3004E	ENST00000278616	NM_000051.3	3004	Aaa/Gaa	63/63	0.892889826774537	1	FACETS	0.964	0.93	0.997	0.964	0.93	0.997	CLONAL	1	TRUE	0	0.893536517909017	1		334	330	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654610	67654610	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0014731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	299	320	0	ENST00000264010.4:c.1097T>A	p.Leu366Ter	p.L366*	ENST00000264010	NM_006565.3	366	tTa/tAa	6/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.893536517909017	2		320	633	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337248	89337248	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	321	386	0	ENST00000301030.4:c.7783G>C	p.Asp2595His	p.D2595H	ENST00000301030	NM_001256183.1	2595	Gat/Cat	12/13	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.893536517909017	2		386	685	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579717	7579717	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	273	546	0	ENST00000269305.4:c.79C>G	p.Pro27Ala	p.P27A	ENST00000269305	NM_001126112.2	27	Cct/Gct	3/11	1	2	FACETS	0.756	0.712	0.801	0.756	0.712	0.801	SUBCLONAL	1	TRUE	1	0.893536517909017	2		546	808	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512270	38512270	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	302	480	0	ENST00000254066.5:c.1181G>C	p.Arg394Pro	p.R394P	ENST00000254066	NM_000964.3	394	cGg/cCg	9/9	1	2	FACETS	0.906	0.859	0.954	0.906	0.859	0.954	CLONAL	1	TRUE	1	0.893536517909017	2		480	746	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55478818	55478818	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	258	433	0	ENST00000284073.2:c.391G>C	p.Glu131Gln	p.E131Q	ENST00000284073	NM_138962.2	131	Gag/Cag	6/14	1	2	FACETS	0.829	0.78	0.878	0.829	0.78	0.878	CLONAL	1	TRUE	1	0.893536517909017	2		433	697	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589798	212589798	+	splice_region_variant,intron_variant	Splice_Region	SNP	T	T	A	novel	NA	P-0014731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	192	279	0	ENST00000342788.4:c.741+3A>T		p.X247_splice	ENST00000342788	NM_005235.2	247			1	2	FACETS	0.953	0.891	1	0.953	0.891	1	CLONAL	1	TRUE	1	0.893536517909017	2		279	451	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591099	67591099	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs773686816	NA	P-0014731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	146	237	0	ENST00000274335.5:c.1692C>A	p.Asn564Lys	p.N564K	ENST00000274335		564	aaC/aaA	12/15	0.876810483807489	3	FACETS	0.821	0.753	0.892	0.41	0.376	0.446	CLONAL	1	TRUE	1	0.893536517909017	3		237	576	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973882	131973882	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	201	262	0	ENST00000265335.6:c.3585G>C	p.Leu1195Phe	p.L1195F	ENST00000265335		1195	ttG/ttC	23/25	0.876810483807489	3	FACETS	0.952	0.886	1	0.476	0.443	0.51	CLONAL	1	TRUE	1	0.893536517909017	3		262	684	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638705	176638705	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	360	522	1	ENST00000439151.2:c.3305G>C	p.Gly1102Ala	p.G1102A	ENST00000439151	NM_022455.4	1102	gGt/gCt	5/23	0.876810483807489	3	FACETS	0.988	0.937	1	0.494	0.468	0.52	CLONAL	1	TRUE	1	0.893536517909017	3		523	1180	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052974	180052974	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	455	751	0	ENST00000261937.6:c.1316G>T	p.Ser439Ile	p.S439I	ENST00000261937	NM_182925.4	439	aGc/aTc	10/30	0.876810483807489	3	FACETS	1	0.961	1	0.504	0.481	0.528	CLONAL	1	TRUE	1	0.893536517909017	3		751	1461	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909204	41909204	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1215975688	NA	P-0014731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	405	662	2	ENST00000372991.4:c.184T>A	p.Tyr62Asn	p.Y62N	ENST00000372991	NM_001760.3	62	Tac/Aac	1/5	1	2	FACETS	0.976	0.933	1	0.976	0.933	1	CLONAL	1	TRUE	1	0.893536517909017	2		664	929	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69012035	69012035	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	324	528	0	ENST00000288368.4:c.2672A>G	p.Glu891Gly	p.E891G	ENST00000288368	NM_024870.2	891	gAa/gGa	23/40	1	2	FACETS	0.964	0.916	1	0.964	0.916	1	CLONAL	1	TRUE	1	0.893536517909017	2		528	752	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428161	47428161	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	432	573	1	ENST00000377045.4:c.1121C>A	p.Thr374Asn	p.T374N	ENST00000377045	NM_001654.4	374	aCc/aAc	11/16	0.192798799968018	1	FACETS	0.567	0.543	0.591	0.567	0.543	0.591	INDETERMINATE	1	TRUE	0	0.893536517909017	1		574	944	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345222	70345222	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	277	449	0	ENST00000374080.3:c.2248T>G	p.Cys750Gly	p.C750G	ENST00000374080		750	Tgc/Ggc	16/45	0.192798799968018	1	FACETS	0.586	0.556	0.617	0.586	0.556	0.617	INDETERMINATE	1	TRUE	0	0.893536517909017	1		449	585	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573957	18573957	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	53	240	0	ENST00000266497.5:c.2275C>T	p.Gln759Ter	p.Q759*	ENST00000266497		759	Cag/Tag	15/31	1	2	FACETS	0.91	0.777	1	0.91	0.777	1	CLONAL	1	TRUE	1	0.26	2		240	448	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971029	21971029	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519852	NA	P-0014752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	167	416	0	ENST00000304494.5:c.329G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tGg/tAg	2/3	0.328258053566321	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.328258053566321	1		416	773	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581157	48581157	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1555685624	NA	P-0014752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	39	237	0	ENST00000342988.3:c.461C>G	p.Ser154Ter	p.S154*	ENST00000342988	NM_005359.5	154	tCa/tGa	5/12	0.328258053566321	1	FACETS	0.521	0.433	0.62	0.521	0.433	0.62	SUBCLONAL	1	TRUE	0	0.328258053566321	1		237	381	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0014752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	207	577	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	0.156375318252354	3	FACETS	1	0.982	1	0.592	0.549	0.638	INDETERMINATE	1	TRUE	1	0.328258053566321	3		577	1239	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218396	133218396	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1064794641	NA	P-0014752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	184	631	0	ENST00000320574.5:c.5215A>G	p.Ile1739Val	p.I1739V	ENST00000320574	NM_006231.2	1739	Att/Gtt	39/49	1	2	FACETS	0.938	0.864	1	0.938	0.864	1	CLONAL	1	TRUE	1	0.328258053566321	2		631	1195	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514494	41514494	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs879079672	NA	P-0014752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	74	500	0	ENST00000373198.4:c.167A>G	p.Gln56Arg	p.Q56R	ENST00000373198	NM_133170.3	56	cAg/cGg	2/32	1	2	FACETS	0.413	0.36	0.47	0.413	0.36	0.47	SUBCLONAL	1	TRUE	1	0.328258053566321	2		500	1092	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413049	139413049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064795070	NA	P-0014766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	63	412	0	ENST00000277541.6:c.1093C>T	p.Arg365Cys	p.R365C	ENST00000277541	NM_017617.3	365	Cgc/Tgc	6/34	1	2	FACETS	0.784	0.68	0.897	0.784	0.68	0.897	SUBCLONAL	1	TRUE	1	0.35	2		412	459	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61722661	61722661	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	86	340	0	ENST00000401558.2:c.976C>G	p.Leu326Val	p.L326V	ENST00000401558	NM_003400.3	326	Ctc/Gtc	11/25	1	2	FACETS	0.641	0.566	0.721	0.641	0.566	0.721	SUBCLONAL	1	TRUE	1	0.35	2		340	767	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664825	138664825	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	122	237	0	ENST00000330315.3:c.740G>A	p.Gly247Glu	p.G247E	ENST00000330315	NM_023067.3	247	gGg/gAg	1/1	0.3	3	FACETS	0.985	0.897	1	0.985	0.897	1	CLONAL	2	TRUE	1	0.35	3		237	416	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630110	187630110	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	172	500	0	ENST00000441802.2:c.872C>G	p.Ser291Cys	p.S291C	ENST00000441802	NM_005245.3	291	tCt/tGt	2/27	0.166998826589333	3	FACETS	1	0.985	1	0.642	0.591	0.696	INDETERMINATE	1	TRUE	1	0.35	3		500	899	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139818360	139818360	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	179	663	3	ENST00000247668.2:c.1195G>A	p.Asp399Asn	p.D399N	ENST00000247668	NM_021138.3	399	Gac/Aac	10/11	1	2	FACETS	0.998	0.919	1	0.998	0.919	1	CLONAL	1	TRUE	1	0.35	2		666	1025	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0014775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	145	250	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.915	0.838	0.995	0.915	0.838	0.995	CLONAL	1	TRUE	1	0.52484714909141	2		250	604	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878803	151878803	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	106	521	0	ENST00000262189.6:c.6142C>T	p.Gln2048Ter	p.Q2048*	ENST00000262189	NM_170606.2	2048	Caa/Taa	36/59	1	2	FACETS	0.536	0.48	0.595	0.536	0.48	0.595	SUBCLONAL	1	TRUE	1	0.52484714909141	2		521	754	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610247	10610247	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	229	713	1	ENST00000171111.5:c.463G>T	p.Val155Phe	p.V155F	ENST00000171111	NM_203500.1	155	Gtc/Ttc	2/6	0.495714589606623	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.495714589606623	2		714	439	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913471	NA	P-0014786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	21	592	1	ENST00000269571.5:c.2329G>A	p.Val777Met	p.V777M	ENST00000269571		777	Gtg/Atg	20/27	0.396363248360103	3	FACETS	0.226	0.174	0.288	0.075	0.058	0.096	SUBCLONAL	1	TRUE	0	0.495714589606623	3		593	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579355	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519997	NA	P-0014786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	217	608	0	ENST00000269305.4:c.332T>G	p.Leu111Arg	p.L111R	ENST00000269305	NM_001126112.2	111	cTg/cGg	4/11	0.396363248360103	3	FACETS	0.979	0.928	1	0.979	0.928	1	CLONAL	3	TRUE	0	0.495714589606623	3		608	372	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954379	48954379	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0014786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	243	291	0	ENST00000267163.4:c.1498+2T>C		p.X500_splice	ENST00000267163	NM_000321.2	500			0.451245306549811	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	3	TRUE	0	0.495714589606623	3		291	402	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106016	27106016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761267675	NA	P-0014786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	60	418	0	ENST00000324856.7:c.5627C>T	p.Pro1876Leu	p.P1876L	ENST00000324856	NM_006015.4	1876	cCa/cTa	20/20	0.495714589606623	3	FACETS	0.781	0.675	0.894	0.39	0.337	0.447	SUBCLONAL	1	TRUE	1	0.495714589606623	3		418	387	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954301	48954301	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	76	287	0	ENST00000267163.4:c.1422C>G	p.Ser474Arg	p.S474R	ENST00000267163	NM_000321.2	474	agC/agG	16/27	0.451245306549811	3	FACETS	0.952	0.839	1	0.317	0.279	0.358	CLONAL	1	TRUE	0	0.495714589606623	3		287	402	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56863014	56863014	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	110	369	0	ENST00000308159.5:c.920G>T	p.Gly307Val	p.G307V	ENST00000308159	NM_014669.4	307	gGa/gTa	9/22	0.213287484073704	4	FACETS	1	0.984	1	0.741	0.67	0.815	INDETERMINATE	1	TRUE	2	0.495714589606623	4		369	448	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678735	52678735	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0014786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	217	478	0	ENST00000394830.3:c.884C>G	p.Ser295Ter	p.S295*	ENST00000394830	NM_018313.4	295	tCa/tGa	9/30	0.396363248360103	3	FACETS	1	0.989	1	0.815	0.768	0.862	CLONAL	2	TRUE	0	0.495714589606623	3		478	447	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818182	32818182	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	223	557	1	ENST00000354258.4:c.1343A>T	p.Gln448Leu	p.Q448L	ENST00000354258	NM_000593.5	448	cAg/cTg	5/11	0.427655488049329	3	FACETS	1	0.989	1	0.815	0.769	0.862	CLONAL	2	TRUE	0	0.495714589606623	3		558	459	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545728	106545728	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	444	494	0	ENST00000359195.3:c.3205C>G	p.Leu1069Val	p.L1069V	ENST00000359195	NM_002649.2	1069	Ctt/Gtt	11/11	0.495714589606623	7	FACETS	1	0.987	1			1	CLONAL	4	TRUE	NA	0.495714589606623	7		494	938	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396758	139396758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	172	541	1	ENST00000277541.6:c.5350C>T	p.Arg1784Trp	p.R1784W	ENST00000277541	NM_017617.3	1784	Cgg/Tgg	28/34	0.495714589606623	3	FACETS	0.902	0.846	0.957	0.902	0.846	0.957	CLONAL	3	TRUE	0	0.495714589606623	3		542	320	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15809066	15809066	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	113	437	0	ENST00000307771.7:c.51G>T	p.Lys17Asn	p.K17N	ENST00000307771	NM_005089.3	17	aaG/aaT	2/11	0.248972812892542	1	FACETS	1	0.968	1	1	0.968	1	INDETERMINATE	1	TRUE	0	0.495714589606623	1		437	304	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937863	76937863	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	161	487	0	ENST00000373344.5:c.2885C>G	p.Ser962Cys	p.S962C	ENST00000373344	NM_000489.3	962	tCt/tGt	9/35	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.495714589606623	2		487	511	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0014803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	400	382	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.226440667554793	4	FACETS	0.985	0.94	1	1	0.996	1	INDETERMINATE	3	TRUE	2	0.398224728105102	4		382	951	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578533	7578536	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0014803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	439	811	0	ENST00000269305.4:c.394_397del	p.Lys132CysfsTer37	p.K132Cfs*37	ENST00000269305	NM_001126112.2	132	AAGAtg/tg	5/11	0.340140588366898	2	FACETS	0.885	0.845	0.926	0.885	0.845	0.926	CLONAL	2	TRUE	0	0.398224728105102	2		811	1246	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0014807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	143	597	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.21835269697248	2	FACETS	0.957	0.875	1	0.957	0.875	1	CLONAL	2	TRUE	0	0.21835269697248	2		597	684	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851545	63851545	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	79	565	0	ENST00000279873.7:c.2323C>A	p.His775Asn	p.H775N	ENST00000279873	NM_032199.2	775	Cat/Aat	10/10	0.21835269697248	3	FACETS	1	0.908	1	0.52	0.457	0.588	CLONAL	1	TRUE	1	0.21835269697248	3		565	772	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811648	102811648	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	85	673	0	ENST00000307046.8:c.536G>T	p.Arg179Met	p.R179M	ENST00000307046	NM_001111285.1	179	aGg/aTg	4/4	0.21835269697248	3	FACETS	0.969	0.855	1	0.485	0.427	0.546	CLONAL	1	TRUE	1	0.21835269697248	3		673	891	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271447	26271447	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	129	318	0	ENST00000305910.3:c.166C>G	p.Gln56Glu	p.Q56E	ENST00000305910	NM_003534.2	56	Cag/Gag	1/1	0.21835269697248	10	FACETS	0.985	0.894	1			1	CLONAL	3	TRUE	NA	0.21835269697248	10		318	749	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579355	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519997	NA	P-0014809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	328	693	0	ENST00000269305.4:c.332T>A	p.Leu111Gln	p.L111Q	ENST00000269305	NM_001126112.2	111	cTg/cAg	4/11	0.242305252138623	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.243044362476083	2		693	1318	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023895	27023895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	42	120	0	ENST00000324856.7:c.1001C>T	p.Ser334Leu	p.S334L	ENST00000324856	NM_006015.4	334	tCg/tTg	1/20	0.243044362476083	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.243044362476083	1		120	228	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023756	27023756	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	115	494	0	ENST00000324856.7:c.862C>T	p.Gln288Ter	p.Q288*	ENST00000324856	NM_006015.4	288	Cag/Tag	1/20	0.243044362476083	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.243044362476083	1		494	744	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512286	120512286	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs144936899	NA	P-0014809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	125	407	0	ENST00000256646.2:c.956A>G	p.Asn319Ser	p.N319S	ENST00000256646	NM_024408.3	319	aAt/aGt	6/34	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.243044362476083	2		407	847	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600402	43600402	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	47	304	0	ENST00000355710.3:c.628G>C	p.Glu210Gln	p.E210Q	ENST00000355710	NM_020975.4	210	Gag/Cag	4/20	1	2	FACETS	0.807	0.682	0.946	0.807	0.682	0.946	CLONAL	1	TRUE	1	0.243044362476083	2		304	479	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119736	108119736	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	53	274	0	ENST00000278616.4:c.1142G>C	p.Ser381Thr	p.S381T	ENST00000278616	NM_000051.3	381	aGt/aCt	9/63	1	2	FACETS	0.777	0.663	0.903	0.777	0.663	0.903	CLONAL	1	TRUE	1	0.243044362476083	2		274	561	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244395	46244395	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	59	435	1	ENST00000334344.6:c.2489A>T	p.Gln830Leu	p.Q830L	ENST00000334344	NM_152641.2	830	cAa/cTa	15/21	1	2	FACETS	0.654	0.562	0.755	0.654	0.562	0.755	SUBCLONAL	1	TRUE	1	0.243044362476083	2		436	742	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724498	724498	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	49	358	0	ENST00000314574.4:c.1558G>A	p.Glu520Lys	p.E520K	ENST00000314574	NM_005433.3	520	Gaa/Aaa	12/12	0.243044362476083	1	FACETS	0.589	0.499	0.69	0.589	0.499	0.69	SUBCLONAL	1	TRUE	0	0.243044362476083	1		358	601	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231576	5231576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	96	323	1	ENST00000357368.4:c.1900G>A	p.Ala634Thr	p.A634T	ENST00000357368	NM_002850.3	634	Gcc/Acc	14/38	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.243044362476083	2		324	731	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212401	36212401	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	149	690	0	ENST00000222270.7:c.2152G>T	p.Glu718Ter	p.E718*	ENST00000222270	NM_014727.1	718	Gag/Tag	3/37	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.243044362476083	2		690	1184	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754921	29754921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	109	410	1	ENST00000389048.3:c.1014G>A	p.Met338Ile	p.M338I	ENST00000389048	NM_004304.4	338	atG/atA	4/29	0.239355607680986	3	FACETS	1	0.92	1	0.515	0.462	0.572	CLONAL	1	TRUE	1	0.243044362476083	3		411	976	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691889	30691889	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	64	361	0	ENST00000295754.5:c.391G>C	p.Glu131Gln	p.E131Q	ENST00000295754	NM_003242.5	131	Gag/Cag	3/7	0.243044362476083	1	FACETS	0.927	0.804	1	0.927	0.804	1	CLONAL	1	TRUE	0	0.243044362476083	1		361	499	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845176	128845176	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	129	567	0	ENST00000249373.3:c.670G>C	p.Glu224Gln	p.E224Q	ENST00000249373	NM_005631.4	224	Gag/Cag	3/12	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.243044362476083	2		567	1054	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974805	21974808	+	frameshift_variant	Frame_Shift_Del	DEL	TGCT	TGCT	-	novel	NA	P-0014809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	19	110	0	ENST00000304494.5:c.19_22del	p.Ser7AlafsTer18	p.S7Afs*18	ENST00000304494	NM_000077.4	7	AGCAgc/gc	1/3	0.243044362476083	1	FACETS	0.954	0.731	1	0.954	0.731	1	CLONAL	1	TRUE	0	0.243044362476083	1		110	144	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195728	102195731	+	missense_variant	Missense_Mutation	ONP	ACTG	ACTG	TCTT	novel	NA	P-0014809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	59	272	0	ENST00000263464.3:c.488_491delinsTCTT	p.His163_Cys164delinsLeuPhe	p.H163_C164delinsLF	ENST00000263464	NM_001165.4	163	cACTGt/cTCTTt	2/9	1	2	FACETS	0.852	0.733	0.981	0.852	0.733	0.981	CLONAL	1	TRUE	1	0.243044362476083	2		272	570	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692893	89692893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1114167656	NA	P-0014816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	195	347	1	ENST00000371953.3:c.377C>T	p.Ala126Val	p.A126V	ENST00000371953	NM_000314.4	126	gCt/gTt	5/9	0.372639289564039	2	FACETS	1	0.99	1	0.692	0.645	0.739	CLONAL	1	TRUE	0	0.532016654783696	2		348	530	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943668	71943668	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0014816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	26	480	0	ENST00000298229.2:c.1713-2A>T		p.X571_splice	ENST00000298229	NM_001567.3	571			0.430914871239956	1	FACETS	0.138	0.109	0.172	0.138	0.109	0.172	SUBCLONAL	1	TRUE	0	0.532016654783696	1		480	518	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948298	71948298	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	174	739	0	ENST00000298229.2:c.3011del	p.Pro1004LeufsTer127	p.P1004Lfs*127	ENST00000298229	NM_001567.3	1004	Cct/ct	26/28	0.430914871239956	1	FACETS	0.561	0.517	0.607	0.561	0.517	0.607	SUBCLONAL	1	TRUE	0	0.532016654783696	1		739	856	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034522	123034522	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	104	357	0	ENST00000355640.3:c.1279A>G	p.Ser427Gly	p.S427G	ENST00000355640		427	Agt/Ggt	6/7	1	2	FACETS	0.667	0.599	0.739	0.667	0.599	0.739	SUBCLONAL	1	TRUE	1	0.532016654783696	2		357	586	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0014824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	227	382	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	0.985	1	CLONAL	1	TRUE	1	0.429185716618451	2		382	893	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139411768	139411768	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201768800	NA	P-0014824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	295	892	2	ENST00000277541.6:c.1511G>A	p.Arg504His	p.R504H	ENST00000277541	NM_017617.3	504	cGc/cAc	9/34	1	2	FACETS	0.926	0.87	0.985	0.926	0.87	0.985	CLONAL	1	TRUE	1	0.429185716618451	2		894	1484	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835596	68835596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587783047	NA	P-0014824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	124	378	0	ENST00000261769.5:c.187C>T	p.Arg63Ter	p.R63*	ENST00000261769	NM_004360.3	63	Cga/Tga	3/16	0.429185716618451	1	FACETS	0.66	0.598	0.725	0.66	0.598	0.725	SUBCLONAL	1	TRUE	0	0.429185716618451	1		378	688	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111526	8111526	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	65	572	0	ENST00000346208.3:c.1012del	p.Cys338AlafsTer17	p.C338Afs*17	ENST00000346208		338	Tgc/gc	5/6	1	2	FACETS	0.27	0.233	0.311	0.27	0.233	0.311	SUBCLONAL	1	TRUE	1	0.429185716618451	2		572	1121	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100603	67100603	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	209	394	2	ENST00000412916.2:c.301A>G	p.Met101Val	p.M101V	ENST00000412916		101	Atg/Gtg	4/6	0.429185716618451	1	FACETS	0.992	0.924	1	0.992	0.924	1	CLONAL	1	TRUE	0	0.429185716618451	1		396	771	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390684	139390684	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	40	722	0	ENST00000277541.6:c.7507C>T	p.Gln2503Ter	p.Q2503*	ENST00000277541	NM_017617.3	2503	Cag/Tag	34/34	1	2	FACETS	0.439	0.364	0.524	0.439	0.364	0.524	SUBCLONAL	1	TRUE	1	0.241531259107561	2		722	754	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885836	23885836	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	59	342	0	ENST00000374561.5:c.82C>G	p.Arg28Gly	p.R28G	ENST00000374561	NM_002167.4	28	Cga/Gga	1/3	0.241531259107561	1	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	0	0.241531259107561	1		342	420	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458436	120458436	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs771237928	NA	P-0014847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	56	448	1	ENST00000256646.2:c.6909del	p.Ile2304LeufsTer2	p.I2304Lfs*2	ENST00000256646	NM_024408.3	2303	ccC/cc	34/34	0.241531259107561	1	FACETS	0.79	0.677	0.913	0.79	0.677	0.913	CLONAL	1	TRUE	0	0.241531259107561	1		449	516	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524612	106524612	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	33	260	0	ENST00000359195.3:c.2773G>T	p.Val925Leu	p.V925L	ENST00000359195	NM_002649.2	925	Gtg/Ttg	9/11	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.241531259107561	2		260	201	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591917	48591925	+	inframe_deletion	In_Frame_Del	DEL	TCGCTTTTG	TCGCTTTTG	-	novel	NA	P-0014859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	342	538	0	ENST00000342988.3:c.1081_1089del	p.Arg361_Cys363del	p.R361_C363del	ENST00000342988	NM_005359.5	360	gaTCGCTTTTGt/gat	9/12	0.579584489892351	2	FACETS	0.918	0.877	0.958	0.918	0.877	0.958	CLONAL	2	TRUE	0	0.579584489892351	2		538	643	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0014865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	79	284	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	0.943	1	CLONAL	1	TRUE	1	0.524252322870938	2		284	275	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0014865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	106	273	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.524252322870938	2		273	346	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344987	118344987	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	21	375	0	ENST00000534358.1:c.3113A>G	p.Glu1038Gly	p.E1038G	ENST00000534358	NM_005933.3	1038	gAg/gGg	3/36	1	2	FACETS	0.281	0.216	0.356	0.281	0.216	0.356	SUBCLONAL	1	TRUE	1	0.524252322870938	2		375	285	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141484	11141484	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	79	703	0	ENST00000358026.2:c.3461T>G	p.Leu1154Arg	p.L1154R	ENST00000358026	NM_001128849.1	1154	cTc/cGc	25/36	1	2	FACETS	0.53	0.466	0.597	0.53	0.466	0.597	SUBCLONAL	1	TRUE	1	0.524252322870938	2		703	569	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015293	128015293	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	104	497	0	ENST00000285398.2:c.2228G>C	p.Arg743Pro	p.R743P	ENST00000285398	NM_000122.1	743	cGc/cCc	15/15	1	2	FACETS	0.916	0.826	1	0.916	0.826	1	CLONAL	1	TRUE	1	0.524252322870938	2		497	433	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670598	134670598	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs563780078	NA	P-0014865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	12	807	1	ENST00000398015.3:c.509G>A	p.Arg170Gln	p.R170Q	ENST00000398015	NM_004441.4	170	cGg/cAg	3/16	1	2	FACETS	0.079	0.055	0.109	0.079	0.055	0.109	SUBCLONAL	1	TRUE	1	0.524252322870938	2		808	581	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0014875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	540	852	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.572999641934506	3	FACETS	0.941	0.905	0.978	0.941	0.905	0.978	CLONAL	2	TRUE	1	0.578150471998764	3		852	1279	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591891	48591892	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0014875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	23	459	1	ENST00000342988.3:c.1054_1055delinsTT	p.Gly352Leu	p.G352L	ENST00000342988	NM_005359.5	352	GGa/TTa	9/12	0.578150471998764	1	FACETS	0.134	0.104	0.169	0.134	0.104	0.169	SUBCLONAL	1	TRUE	0	0.578150471998764	1		460	423	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56871634	56871634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764196494	NA	P-0014875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	109	459	0	ENST00000308159.5:c.2014G>A	p.Glu672Lys	p.E672K	ENST00000308159	NM_014669.4	672	Gaa/Aaa	18/22	1	2	FACETS	0.594	0.534	0.657	0.594	0.534	0.657	SUBCLONAL	1	TRUE	1	0.578150471998764	2		459	635	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33430499	33430499	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1275	367	813	1	ENST00000345365.6:c.641del	p.Pro214HisfsTer13	p.P214Hfs*13	ENST00000345365	NM_002878.3	214	cCa/ca	7/10	0.511770387267859	3	FACETS	0.997	0.943	1			1	CLONAL	1	TRUE	NA	0.578150471998764	3		814	1642	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575194	48575194	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	20	296	0	ENST00000342988.3:c.388C>A	p.Pro130Thr	p.P130T	ENST00000342988	NM_005359.5	130	Cca/Aca	3/12	0.578150471998764	1	FACETS	0.135	0.103	0.173	0.135	0.103	0.173	SUBCLONAL	1	TRUE	0	0.578150471998764	1		296	364	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575206	48575206	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	29	281	1	ENST00000342988.3:c.400del	p.Glu134AsnfsTer13	p.E134Nfs*13	ENST00000342988	NM_005359.5	134	Gaa/aa	3/12	0.578150471998764	1	FACETS	0.197	0.158	0.241	0.197	0.158	0.241	SUBCLONAL	1	TRUE	0	0.578150471998764	1		282	362	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873005	134873005	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs183234182	NA	P-0014875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	202	591	1	ENST00000398015.3:c.1309G>A	p.Val437Ile	p.V437I	ENST00000398015	NM_004441.4	437	Gtt/Att	6/16	1	2	FACETS	0.803	0.745	0.863	0.803	0.745	0.863	CLONAL	1	TRUE	1	0.578150471998764	2		592	870	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224599	123224599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	441	565	0	ENST00000218089.9:c.3452C>T	p.Thr1151Ile	p.T1151I	ENST00000218089	NM_001042749.1	1151	aCa/aTa	31/35	0.371904297686088	3	FACETS	0.961	0.92	1			1	CLONAL	2	TRUE	NA	0.578150471998764	3		565	1023	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37665992	37665992	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	123	316	0	ENST00000447079.4:c.2644C>T	p.Arg882Trp	p.R882W	ENST00000447079	NM_015083.1	882	Cgg/Tgg	7/14	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.328343800782979	2		316	643	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061218	38061235	+	inframe_deletion	In_Frame_Del	DEL	GCCGTTCTCGAACATGTT	GCCGTTCTCGAACATGTT	-	novel	NA	P-0014892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	114	482	0	ENST00000250448.2:c.754_771del	p.Asn252_Gly257del	p.N252_G257del	ENST00000250448	NM_004496.3	252	AACATGTTCGAGAACGGC/-	2/2	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.328343800782979	2		482	693	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375868	118375868	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	128	404	0	ENST00000534358.1:c.9261C>A	p.Asn3087Lys	p.N3087K	ENST00000534358	NM_005933.3	3087	aaC/aaA	27/36	1	2	FACETS	0.994	0.902	1	0.994	0.902	1	CLONAL	1	TRUE	1	0.328343800782979	2		404	784	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627916	37627944	+	frameshift_variant	Frame_Shift_Del	DEL	ACTCAAGTATCTGTAACAGCTGCTATTCC	ACTCAAGTATCTGTAACAGCTGCTATTCC	-	novel	NA	P-0014892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	143	466	0	ENST00000447079.4:c.1833_1861del	p.Gln612ProfsTer19	p.Q612Pfs*19	ENST00000447079	NM_015083.1	611	ACTCAAGTATCTGTAACAGCTGCTATTCCa/a	2/14	1	2	FACETS	0.91	0.829	0.995	0.91	0.829	0.995	CLONAL	1	TRUE	1	0.328343800782979	2		466	957	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0014905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	28	466	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	0.24	0.191	0.296	0.24	0.191	0.296	SUBCLONAL	1	TRUE	1	0.493032486292049	2		466	473	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056201	26056201	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs766517381	NA	P-0014905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	145	407	0	ENST00000343677.2:c.456G>C	p.Lys152Asn	p.K152N	ENST00000343677	NM_005319.3	152	aaG/aaC	1/1	0.0317869425133628	4	FACETS	1	0.984	1	0.668	0.611	0.728	INDETERMINATE	1	TRUE	2	0.493032486292049	4		407	657	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482439	56482449	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTGGGTAGG	AGGTGGGTAGG	-	novel	NA	P-0014905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	46	594	0	ENST00000267101.3:c.988+1_988+11del		p.X330_splice	ENST00000267101	NM_001982.3	330		8/28	1	2	FACETS	0.33	0.278	0.388	0.33	0.278	0.388	SUBCLONAL	1	TRUE	1	0.493032486292049	2		594	565	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494849	56494849	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	50	424	0	ENST00000267101.3:c.3206C>A	p.Ser1069Tyr	p.S1069Y	ENST00000267101	NM_001982.3	1069	tCt/tAt	27/28	1	2	FACETS	0.297	0.252	0.348	0.297	0.252	0.348	SUBCLONAL	1	TRUE	1	0.493032486292049	2		424	682	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39294789	39294789	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	93	429	0	ENST00000402219.2:c.193C>G	p.Arg65Gly	p.R65G	ENST00000402219	NM_005633.3	65	Cga/Gga	2/23	1	2	FACETS	0.852	0.761	0.947	0.852	0.761	0.947	CLONAL	1	TRUE	1	0.493032486292049	2		429	443	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041202	47041202	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	122	976	0	ENST00000377604.3:c.1630C>G	p.His544Asp	p.H544D	ENST00000377604	NM_001204468.1	544	Cat/Gat	15/24	1	2	FACETS	0.424	0.382	0.469	0.424	0.382	0.469	SUBCLONAL	1	TRUE	1	0.493032486292049	2		976	1166	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1485978447	NA	P-0014927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	105	425	1	ENST00000324856.7:c.5164C>T	p.Arg1722Ter	p.R1722*	ENST00000324856	NM_006015.4	1722	Cga/Tga	20/20	0.310725428165465	5	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.23	5		426	850	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853327	68853327	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	153	505	0	ENST00000261769.5:c.1710del	p.Asn570LysfsTer14	p.N570Kfs*14	ENST00000261769	NM_004360.3	570	aaT/aa	11/16	0.310725428165465	2	FACETS	1	0.969	1			1	CLONAL	2	TRUE	NA	0.23	2		505	598	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928066	178928086	+	protein_altering_variant	In_Frame_Del	DEL	ACCTCATGGATTAGAAGATTT	ACCTCATGGATTAGAAGATTT	CCC	novel	NA	P-0014927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	73	533	1	ENST00000263967.3:c.1344_1364delinsCCC	p.His450_Leu455del	p.H450_L455del	ENST00000263967	NM_006218.2	448	gtACCTCATGGATTAGAAGATTTg/gtCCCg	8/21	0.177020665278765	5	FACETS	0.727	0.634	0.829	0.242	0.211	0.277	SUBCLONAL	1	TRUE	2	0.23	5		534	1174	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851498	128851498	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs755362549	NA	P-0014927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	124	532	0	ENST00000249373.3:c.1823A>G	p.Asn608Ser	p.N608S	ENST00000249373	NM_005631.4	608	aAt/aGt	11/12	0.177020665278765	4	FACETS	0.879	0.796	0.967	0.879	0.796	0.967	CLONAL	2	TRUE	2	0.23	4		532	754	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	40	715	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.458	0.381	0.544	0.458	0.381	0.544	SUBCLONAL	1	TRUE	1	0.43	2		715	406	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504136	123504136	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	80	507	0	ENST00000371139.4:c.312G>T	p.Lys104Asn	p.K104N	ENST00000371139	NM_001114937.2	104	aaG/aaT	3/4	1	2	FACETS	0.639	0.563	0.721	0.639	0.563	0.721	SUBCLONAL	1	TRUE	1	0.43	2		507	582	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371708	225371708	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	191	760	0	ENST00000264414.4:c.896T>G	p.Met299Arg	p.M299R	ENST00000264414	NM_003590.4	299	aTg/aGg	7/16	0.125814080397931	5	FACETS	1	0.981	1	0.78	0.723	0.84	INDETERMINATE	2	TRUE	2	0.282671165659033	5		760	822	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132617	11132617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1445478818	NA	P-0014931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	244	769	6	ENST00000358026.2:c.2833G>A	p.Ala945Thr	p.A945T	ENST00000358026	NM_001128849.1	945	Gca/Aca	19/36	1	2	FACETS	1	0.95	1	1	0.995	1	CLONAL	2	TRUE	1	0.282671165659033	2		775	849	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100913	27100913	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	160	562	2	ENST00000324856.7:c.4195C>T	p.Gln1399Ter	p.Q1399*	ENST00000324856	NM_006015.4	1399	Cag/Tag	18/20	1	2	FACETS	0.897	0.826	0.971	1	0.991	1	CLONAL	2	TRUE	1	0.282671165659033	2		564	631	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415901	49415902	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0014931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	154	443	0	ENST00000301067.7:c.16445_16446del	p.Val5482GlyfsTer7	p.V5482Gfs*7	ENST00000301067	NM_003482.3	5482	gTG/g	53/54	0.215068792919171	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.282671165659033	4		443	614	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109322498	109322498	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	212	573	0	ENST00000436639.2:c.539G>T	p.Gly180Val	p.G180V	ENST00000436639	NM_014454.2	180	gGa/gTa	3/10	0.282671165659033	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	0	0.282671165659033	2		573	746	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0014936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	28	284	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.079891315939445	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		284	379	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0014936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	30	264	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.079891315939445	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		264	814	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061204	38061204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	72	409	1	ENST00000250448.2:c.785G>A	p.Arg262His	p.R262H	ENST00000250448	NM_004496.3	262	cGc/cAc	2/2	0.079891315939445	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		410	471	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115722	8115724	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0014936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	42	426	0	ENST00000346208.3:c.1072_1074del	p.Lys358del	p.K358del	ENST00000346208		356	atGAAg/atg	6/6	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		426	597	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168468	56168468	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	38	172	0	ENST00000399503.3:c.1424G>A	p.Trp475Ter	p.W475*	ENST00000399503	NM_005921.1	475	tGg/tAg	8/20	0.147674184795044	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		172	362	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0014973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	263	606	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	FALSE	NA	0.307990507540506	2		606	692	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0014990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	220	297	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.24036663572312	2	FACETS	0.876	0.817	0.938	0.876	0.817	0.938	CLONAL	2	TRUE	0	0.292302486918305	2		297	859	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913351	NA	P-0014990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	114	382	1	ENST00000288602.6:c.1397G>T	p.Gly466Val	p.G466V	ENST00000288602	NM_004333.4	466	gGa/gTa	11/18	0.25223714165871	4	FACETS	1	0.983	1	0.727	0.655	0.803	CLONAL	1	TRUE	2	0.292302486918305	4		383	693	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220691	1220691	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs878853247	NA	P-0014990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	253	569	0	ENST00000326873.7:c.709G>T	p.Asp237Tyr	p.D237Y	ENST00000326873	NM_000455.4	237	Gac/Tac	5/10	0.2591893429026	2	FACETS	0.882	0.826	0.94	0.882	0.826	0.94	CLONAL	2	TRUE	0	0.292302486918305	2		569	981	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203543	108203543	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	89	363	0	ENST00000278616.4:c.7843C>T	p.Gln2615Ter	p.Q2615*	ENST00000278616	NM_000051.3	2615	Cag/Tag	53/63	0.2591893429026	2	FACETS	0.777	0.693	0.865	0.777	0.693	0.865	SUBCLONAL	2	TRUE	0	0.292302486918305	2		363	392	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570059	95570059	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs146584765	NA	P-0014990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	90	473	0	ENST00000393063.1:c.3674A>G	p.Tyr1225Cys	p.Y1225C	ENST00000393063	NM_030621.3	1225	tAc/tGc	22/28	NA	2	FACETS	0.86	0.763	0.964			1	INDETERMINATE	1	TRUE	NA	0.292302486918305	2		473	716	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226386	2226386	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	240	644	0	ENST00000398665.3:c.3866C>A	p.Ala1289Asp	p.A1289D	ENST00000398665	NM_032482.2	1289	gCc/gAc	27/28	0.2591893429026	2	FACETS	0.795	0.742	0.849	0.795	0.742	0.849	SUBCLONAL	2	TRUE	0	0.292302486918305	2		644	1033	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222662	157222662	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	novel	NA	P-0014990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	74	406	0	ENST00000346085.5:c.1926+3G>A		p.X642_splice	ENST00000346085	NM_020732.3	642			0.255322098210459	3	FACETS	0.89	0.779	1	0.445	0.389	0.505	CLONAL	1	TRUE	1	0.292302486918305	3		406	652	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	338190	338190	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs370661416	NA	P-0014992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	13	851	1	ENST00000262320.3:c.2521C>T	p.Arg841Ter	p.R841*	ENST00000262320	NM_003502.3	841	Cga/Tga	11/11	0.19522183764021	0	FACETS	0.415	0.296	0.562			1	SUBCLONAL	1	FALSE	0	0.195219232731002	0		852	258	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945970	17945970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568403015	NA	P-0014992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	11	824	1	ENST00000458235.1:c.1969C>T	p.Arg657Trp	p.R657W	ENST00000458235	NM_000215.3	657	Cgg/Tgg	15/24	1	2	FACETS	0.257	0.176	0.358	0.257	0.176	0.358	SUBCLONAL	1	FALSE	1	0.195219232731002	2		825	439	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037394	12037394	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	58	678	0	ENST00000396373.4:c.1025G>A	p.Trp342Ter	p.W342*	ENST00000396373	NM_001987.4	342	tGg/tAg	6/8	0.195219232731002	10	FACETS	1	0.915	1	0.363	0.312	0.418	CLONAL	2	FALSE	4	0.195219232731002	10		678	486	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230571	46230571	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	40	418	1	ENST00000334344.6:c.820C>T	p.Arg274Ter	p.R274*	ENST00000334344	NM_152641.2	274	Cga/Tga	8/21	1	2	FACETS	0.686	0.57	0.816	0.686	0.57	0.816	SUBCLONAL	1	TRUE	1	0.22	2		419	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	100	698	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	1	2	FACETS	0.749	0.667	0.837	0.749	0.667	0.837	SUBCLONAL	1	TRUE	1	0.22	2		698	1214	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	87	501	0	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	0.3	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.22	1		501	676	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574004	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	120	713	3	ENST00000269305.4:c.1023_1024delinsTT	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	341	ttCCga/ttTTga	10/11	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.22	2		716	1066	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086133	16086133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	106	518	0	ENST00000281043.3:c.1309G>A	p.Glu437Lys	p.E437K	ENST00000281043	NM_005378.4	437	Gag/Aag	3/3	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.22	2		518	896	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124437	94124437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	57	466	0	ENST00000369303.4:c.146C>T	p.Ser49Phe	p.S49F	ENST00000369303	NM_004440.3	49	tCc/tTc	2/17	1	2	FACETS	0.88	0.755	1	0.88	0.755	1	CLONAL	1	TRUE	1	0.22	2		466	589	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737160	145737160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	225	629	0	ENST00000428558.2:c.3406G>A	p.Glu1136Lys	p.E1136K	ENST00000428558	NM_004260.3	1136	Gag/Aag	21/22	0.244132660682994	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.22	3		629	958	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566478	41566478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	77	899	0	ENST00000263253.7:c.4355C>T	p.Pro1452Leu	p.P1452L	ENST00000263253	NM_001429.3	1452	cCt/cTt	27/31	1	2	FACETS	0.826	0.724	0.937	0.826	0.724	0.937	CLONAL	1	TRUE	1	0.22	2		899	847	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099042	27099043	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	82	610	0	ENST00000324856.7:c.3458_3459delinsTT	p.Ser1153Phe	p.S1153F	ENST00000324856	NM_006015.4	1153	tCC/tTT	13/20	1	2	FACETS	0.735	0.646	0.831	0.735	0.646	0.831	SUBCLONAL	1	TRUE	1	0.22	2		610	1014	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303739	65303739	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1158877935	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	102	551	0	ENST00000342505.4:c.3016G>A	p.Ala1006Thr	p.A1006T	ENST00000342505	NM_002227.2	1006	Gca/Aca	22/25	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.22	2		551	842	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114917796	114917796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	75	385	0	ENST00000543371.1:c.1286G>A	p.Arg429Lys	p.R429K	ENST00000543371	NM_001198531.1	429	aGg/aAg	12/14	1	2	FACETS	0.988	0.866	1	0.988	0.866	1	CLONAL	1	TRUE	1	0.22	2		385	690	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572520	64572521	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	71	518	2	ENST00000312049.6:c.1335_1336delinsTT	p.Arg446Cys	p.R446C	ENST00000312049	NM_130799.2	445	ggCCgt/ggTTgt	9/10	1	2	FACETS	0.718	0.625	0.819	0.718	0.625	0.819	SUBCLONAL	1	TRUE	1	0.22	2		520	899	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25368395	25368395	+	intron_variant	Intron	SNP	T	T	A	rs749267065	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	64	337	0	ENST00000311936.3:c.451-5550A>T		p.*151*	ENST00000311936	NM_004985.3	184/189			1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.22	2		337	526	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211623	46211623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	53	391	0	ENST00000334344.6:c.589C>T	p.Pro197Ser	p.P197S	ENST00000334344	NM_152641.2	197	Cct/Tct	5/21	1	2	FACETS	0.964	0.822	1	0.964	0.822	1	CLONAL	1	TRUE	1	0.22	2		391	500	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254583	46254583	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	79	411	0	ENST00000334344.6:c.4774-1G>A		p.X1592_splice	ENST00000334344	NM_152641.2	1592			1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.22	2		411	679	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448705	49448705	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	68	442	0	ENST00000301067.7:c.154C>T	p.Gln52Ter	p.Q52*	ENST00000301067	NM_003482.3	52	Cag/Tag	2/54	1	2	FACETS	0.834	0.725	0.953	0.834	0.725	0.953	CLONAL	1	TRUE	1	0.22	2		442	741	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112940024	112940024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	143	691	0	ENST00000351677.2:c.1676C>T	p.Pro559Leu	p.P559L	ENST00000351677	NM_002834.3	559	cCt/cTt	14/16	1	2	FACETS	0.973	0.884	1	0.973	0.884	1	CLONAL	1	TRUE	1	0.22	2		691	1336	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563317	21563318	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	102	850	1	ENST00000382592.4:c.601_602delinsTT	p.Pro201Phe	p.P201F	ENST00000382592	NM_014572.2	201	CCc/TTc	4/8	1	2	FACETS	0.832	0.742	0.928	0.832	0.742	0.928	CLONAL	1	TRUE	1	0.22	2		851	1115	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004277	29004277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370686484	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	37	430	0	ENST00000282397.4:c.1016G>A	p.Arg339Gln	p.R339Q	ENST00000282397	NM_002019.4	339	cGa/cAa	8/30	1	2	FACETS	0.521	0.428	0.625	0.521	0.428	0.625	SUBCLONAL	1	TRUE	1	0.22	2		430	646	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675108	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	51	758	3	ENST00000249776.8:c.71_72delinsTT	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCC/tTT	1/9	1	2	FACETS	0.461	0.39	0.54	0.461	0.39	0.54	SUBCLONAL	1	TRUE	1	0.22	2		761	1005	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923397	9923397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	79	586	0	ENST00000330684.3:c.1890G>A	p.Met630Ile	p.M630I	ENST00000330684	NM_001134407.1	630	atG/atA	9/13	1	2	FACETS	0.905	0.795	1	0.905	0.795	1	CLONAL	1	TRUE	1	0.22	2		586	794	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828585	72828585	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	94	704	0	ENST00000268489.5:c.7996C>T	p.Pro2666Ser	p.P2666S	ENST00000268489	NM_006885.3	2666	Ccg/Tcg	9/10	1	2	FACETS	0.799	0.709	0.896	0.799	0.709	0.896	SUBCLONAL	1	TRUE	1	0.22	2		704	1069	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347656	89347656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567564452	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	105	567	0	ENST00000301030.4:c.5294C>T	p.Ser1765Phe	p.S1765F	ENST00000301030	NM_001256183.1	1765	tCc/tTc	9/13	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.22	2		567	891	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15975487	15975488	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	70	585	1	ENST00000268712.3:c.3866_3867delinsAA	p.Arg1289Lys	p.R1289K	ENST00000268712	NM_006311.3	1289	aGG/aAA	29/46	1	2	FACETS	0.8	0.697	0.913	0.8	0.697	0.913	CLONAL	1	TRUE	1	0.22	2		586	795	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40483533	40483533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1456534236	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	72	480	0	ENST00000264657.5:c.1066C>T	p.Pro356Ser	p.P356S	ENST00000264657	NM_139276.2	356	Cct/Tct	11/24	1	2	FACETS	0.791	0.689	0.9	0.791	0.689	0.9	SUBCLONAL	1	TRUE	1	0.22	2		480	828	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245937	41245937	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1316419984	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	103	578	0	ENST00000357654.3:c.1611C>G	p.Asn537Lys	p.N537K	ENST00000357654	NM_007294.3	537	aaC/aaG	10/23	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.22	2		578	908	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350513	15350514	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	101	630	2	ENST00000263377.2:c.3401_3402delinsTT	p.Pro1134Leu	p.P1134L	ENST00000263377	NM_058243.2	1134	cCC/cTT	16/20	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.22	2		632	842	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905476	50905476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	124	798	1	ENST00000440232.2:c.604C>T	p.His202Tyr	p.H202Y	ENST00000440232	NM_002691.3	202	Cac/Tac	6/27	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.22	2		799	1045	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610505	215610505	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1392588415	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	55	507	0	ENST00000260947.4:c.1751T>C	p.Met584Thr	p.M584T	ENST00000260947	NM_000465.2	584	aTg/aCg	8/11	1	2	FACETS	0.727	0.621	0.843	0.727	0.621	0.843	SUBCLONAL	1	TRUE	1	0.22	2		507	688	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39729875	39729875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1473712126	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	66	468	0	ENST00000361337.2:c.1190C>T	p.Pro397Leu	p.P397L	ENST00000361337	NM_003286.2	397	cCa/cTa	13/21	1	2	FACETS	0.832	0.721	0.952	0.832	0.721	0.952	CLONAL	1	TRUE	1	0.22	2		468	721	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267922	46267922	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	71	584	0	ENST00000371998.3:c.2683C>T	p.Gln895Ter	p.Q895*	ENST00000371998		895	Cag/Tag	14/23	1	2	FACETS	0.776	0.676	0.884	0.776	0.676	0.884	SUBCLONAL	1	TRUE	1	0.22	2		584	832	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514810	44514811	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	70	479	1	ENST00000291552.4:c.436_437delinsTT	p.Pro146Phe	p.P146F	ENST00000291552	NM_006758.2	146	CCc/TTc	6/8	1	2	FACETS	0.722	0.628	0.824	0.722	0.628	0.824	SUBCLONAL	1	TRUE	1	0.22	2		480	881	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032760	30032761	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	63	375	1	ENST00000338641.4:c.135_136delinsTT	p.Leu46Phe	p.L46F	ENST00000338641	NM_000268.3	45	gaCCtc/gaTTtc	2/16	1	2	FACETS	0.846	0.731	0.971	0.846	0.731	0.971	CLONAL	1	TRUE	1	0.22	2		376	677	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090032	37090032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	83	608	1	ENST00000231790.2:c.1921C>T	p.Leu641Phe	p.L641F	ENST00000231790	NM_000249.3	641	Ctt/Ttt	17/19	1	2	FACETS	0.916	0.807	1	0.916	0.807	1	CLONAL	1	TRUE	1	0.22	2		609	824	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165275	47165275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	55	347	0	ENST00000409792.3:c.851C>T	p.Ser284Phe	p.S284F	ENST00000409792	NM_014159.6	284	tCc/tTc	3/21	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.22	2		347	459	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021803	71021803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	44	313	0	ENST00000318789.4:c.1555C>T	p.Leu519Phe	p.L519F	ENST00000318789	NM_032682.5	519	Ctt/Ttt	18/21	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.22	2		313	382	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280044	66280044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	41	336	1	ENST00000273854.3:c.1645G>A	p.Gly549Ser	p.G549S	ENST00000273854	NM_004439.5	549	Ggt/Agt	7/18	1	2	FACETS	0.772	0.643	0.915	0.772	0.643	0.915	CLONAL	1	TRUE	1	0.22	2		337	483	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196927	106196927	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs557302168	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	30	317	0	ENST00000380013.4:c.5260G>A	p.Gly1754Ser	p.G1754S	ENST00000380013	NM_001127208.2	1754	Ggt/Agt	11/11	1	2	FACETS	0.735	0.593	0.897	0.735	0.593	0.897	SUBCLONAL	1	TRUE	1	0.22	2		317	371	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628329	187628329	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	92	619	1	ENST00000441802.2:c.2653C>T	p.Arg885Ter	p.R885*	ENST00000441802	NM_005245.3	885	Cga/Tga	2/27	1	2	FACETS	0.901	0.799	1	0.901	0.799	1	CLONAL	1	TRUE	1	0.22	2		620	928	SUCCESS
APC	324	MSKCC	GRCh37	5	112177610	112177611	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	34	376	1	ENST00000257430.4:c.6319_6320delinsAA	p.Gly2107Asn	p.G2107N	ENST00000257430	NM_000038.5	2107	GGt/AAt	16/16	1	2	FACETS	0.693	0.566	0.836	0.693	0.566	0.836	SUBCLONAL	1	TRUE	1	0.22	2		377	446	SUCCESS
APC	324	MSKCC	GRCh37	5	112178484	112178485	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	40	418	2	ENST00000257430.4:c.7193_7194delinsTT	p.Ser2398Phe	p.S2398F	ENST00000257430	NM_000038.5	2398	tCC/tTT	16/16	1	2	FACETS	0.713	0.592	0.848	0.713	0.592	0.848	SUBCLONAL	1	TRUE	1	0.22	2		420	510	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055997	180055997	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	78	662	0	ENST00000261937.6:c.988A>T	p.Asn330Tyr	p.N330Y	ENST00000261937	NM_182925.4	330	Aat/Tat	8/30	1	2	FACETS	0.735	0.644	0.833	0.735	0.644	0.833	SUBCLONAL	1	TRUE	1	0.22	2		662	965	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111995806	111995806	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	75	461	0	ENST00000368678.4:c.1292C>T	p.Ala431Val	p.A431V	ENST00000368678		431	gCc/gTc	12/13	1	2	FACETS	0.91	0.797	1	0.91	0.797	1	CLONAL	1	TRUE	1	0.22	2		461	749	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725482	117725482	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs867025812	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	83	535	1	ENST00000368508.3:c.399G>A	p.Trp133Ter	p.W133*	ENST00000368508	NM_002944.2	133	tgG/tgA	5/43	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.22	2		536	734	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511227	157511228	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	61	602	2	ENST00000346085.5:c.3745_3746delinsAT	p.Pro1249Met	p.P1249M	ENST00000346085	NM_020732.3	1249	CCg/ATg	15/20	1	2	FACETS	0.651	0.56	0.75	0.651	0.56	0.75	SUBCLONAL	1	TRUE	1	0.22	2		604	852	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622210	162622210	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	64	426	1	ENST00000366898.1:c.487A>T	p.Arg163Trp	p.R163W	ENST00000366898	NM_004562.2	163	Agg/Tgg	4/12	1	2	FACETS	0.832	0.72	0.955	0.832	0.72	0.955	CLONAL	1	TRUE	1	0.22	2		427	699	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959074	2959074	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	115	579	1	ENST00000396946.4:c.2442G>A	p.Trp814Ter	p.W814*	ENST00000396946	NM_032415.4	814	tgG/tgA	18/25	1	2	FACETS	0.977	0.878	1	0.977	0.878	1	CLONAL	1	TRUE	1	0.22	2		580	1070	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848086	151848086	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	73	408	0	ENST00000262189.6:c.12673C>G	p.Arg4225Gly	p.R4225G	ENST00000262189	NM_170606.2	4225	Cga/Gga	51/59	1	2	FACETS	0.983	0.86	1	0.983	0.86	1	CLONAL	1	TRUE	1	0.22	2		408	675	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934283	68934283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773476490	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	66	591	0	ENST00000288368.4:c.349C>T	p.Arg117Cys	p.R117C	ENST00000288368	NM_024870.2	117	Cgt/Tgt	4/40	0.244132660682994	3	FACETS	0.86	0.746	0.985	0.43	0.373	0.493	CLONAL	1	TRUE	1	0.22	3		591	774	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993658	90993659	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AT	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	72	458	0	ENST00000265433.3:c.264_265delinsAT	p.Arg89Ter	p.R89*	ENST00000265433	NM_002485.4	88	tcCCga/tcATga	3/16	0.244132660682994	3	FACETS	0.955	0.833	1	0.477	0.416	0.543	CLONAL	1	TRUE	1	0.22	3		458	761	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869539	117869539	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	107	471	0	ENST00000297338.2:c.655A>T	p.Asn219Tyr	p.N219Y	ENST00000297338	NM_006265.2	219	Aat/Tat	6/14	0.244132660682994	3	FACETS	0.753	0.676	0.835	0.753	0.676	0.835	SUBCLONAL	2	TRUE	1	0.22	3		471	717	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389296	8389296	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	107	672	0	ENST00000356435.5:c.4322G>A	p.Arg1441Lys	p.R1441K	ENST00000356435		1441	aGa/aAa	26/35	0.3	1	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	0	0.22	1		672	860	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039404	47039404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556778215	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	171	304	0	ENST00000377604.3:c.1027C>T	p.Arg343Cys	p.R343C	ENST00000377604	NM_001204468.1	343	Cgc/Tgc	10/24	0.170038931363605	2	FACETS	0.935	0.866	1			1	CLONAL	3	TRUE	NA	0.22	2		304	554	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406292	406293	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0014993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	83	698	0	ENST00000399788.2:c.4148_4149delinsTT	p.Ser1383Phe	p.S1383F	ENST00000399788	NM_001042603.1	1383	tCC/tTT	25/28	0.013881449006774	3	FACETS	0.86	0.757	0.971			1	INDETERMINATE	1	TRUE	NA	0.22	3		698	974	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0015002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	138	393	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.240964430037981	3	FACETS	0.986	0.901	1	0.986	0.901	1	CLONAL	2	FALSE	1	0.269737990244474	3		393	589	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099026	27099026	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	75	721	0	ENST00000324856.7:c.3442C>T	p.Gln1148Ter	p.Q1148*	ENST00000324856	NM_006015.4	1148	Cag/Tag	13/20	0.251494912416563	3	FACETS	0.794	0.695	0.901	0.265	0.231	0.301	CLONAL	1	FALSE	0	0.269737990244474	3		721	795	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0015003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	135	250	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.13561517387763	6	FACETS	1	0.94	1	0.693	0.632	0.756	INDETERMINATE	2	TRUE	3	0.395918079283487	6		250	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578196	7578196	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	336	827	1	ENST00000269305.4:c.653T>A	p.Val218Glu	p.V218E	ENST00000269305	NM_001126112.2	218	gTg/gAg	6/11	0.344995055772767	2	FACETS	0.973	0.924	1	0.973	0.924	1	CLONAL	2	TRUE	0	0.395918079283487	2		828	872	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841541	156841541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774654606	NA	P-0015003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	158	787	1	ENST00000524377.1:c.844G>A	p.Val282Ile	p.V282I	ENST00000524377	NM_002529.3	282	Gtc/Atc	7/17	0.395918079283487	4	FACETS	0.875	0.8	0.954	0.292	0.266	0.318	CLONAL	1	TRUE	1	0.395918079283487	4		788	1273	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569792	95569792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	54	278	0	ENST00000393063.1:c.3941G>A	p.Arg1314Gln	p.R1314Q	ENST00000393063	NM_030621.3	1314	cGg/cAg	22/28	0.34501358075704	2	FACETS	0.869	0.747	1	0.434	0.373	0.501	CLONAL	1	TRUE	0	0.395918079283487	2		278	314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0015015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	8	909	0	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	1	2	FACETS	0.247	0.158	0.363	0.247	0.158	0.363	SUBCLONAL	1	TRUE	1	0.22	2		909	294	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16097825	16097825	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs73281920	NA	P-0015015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	12	771	2	ENST00000268712.3:c.59A>C	p.Tyr20Ser	p.Y20S	ENST00000268712	NM_006311.3	20	tAt/tCt	2/46	1	2	FACETS	0.46	0.323	0.629	0.46	0.323	0.629	SUBCLONAL	1	TRUE	1	0.22	2		773	237	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121522	2121522	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	403	865	0	ENST00000219476.3:c.1852del	p.Leu618CysfsTer80	p.L618Cfs*80	ENST00000219476	NM_000548.3	617	ttC/tt	18/42	0.559944720931927	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.559944720931927	1		865	997	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288967	33288969	+	inframe_deletion	In_Frame_Del	DEL	CAG	CAG	-	novel	NA	P-0015043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	205	488	0	ENST00000374542.5:c.583_585del	p.Leu195del	p.L195del	ENST00000374542	NM_001141970.1	195	CTG/-	3/8	0.559944720931927	1	FACETS	0.898	0.839	0.959	0.898	0.839	0.959	CLONAL	1	TRUE	0	0.559944720931927	1		488	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0015054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	111	670	2	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	0.279513893615256	1	FACETS	0.942	0.848	1	0.942	0.848	1	CLONAL	1	TRUE	0	0.279513893615256	1		672	725	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	195	715	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.227819690451487	3	FACETS	0.974	0.908	1	0.649	0.605	0.695	INDETERMINATE	2	TRUE	0	0.41708747487299	3		715	580	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0015068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	107	365	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.918	0.826	1	0.918	0.826	1	CLONAL	1	TRUE	1	0.41708747487299	2		367	559	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0015068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	145	381	1	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.340896343369783	4	FACETS	0.784	0.718	0.854	0.784	0.718	0.854	SUBCLONAL	2	TRUE	2	0.41708747487299	4		382	628	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577543	7577543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1019340046	NA	P-0015068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	122	504	1	ENST00000269305.4:c.738G>A	p.Met246Ile	p.M246I	ENST00000269305	NM_001126112.2	246	atG/atA	7/11	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.41708747487299	2		505	581	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250865	153250865	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	83	368	0	ENST00000281708.4:c.1195G>T	p.Asp399Tyr	p.D399Y	ENST00000281708	NM_033632.3	399	Gat/Tat	8/12	1	2	FACETS	0.884	0.784	0.991	0.884	0.784	0.991	CLONAL	1	TRUE	1	0.41708747487299	2		368	450	SUCCESS
APC	324	MSKCC	GRCh37	5	112175302	112175303	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	CT	novel	NA	P-0015068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	103	232	0	ENST00000257430.4:c.4011_4012delinsCT	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1337	ctGCag/ctCTag	16/16	0.340896343369783	4	FACETS	0.969	0.876	1	0.969	0.876	1	CLONAL	2	TRUE	2	0.41708747487299	4		232	361	SUCCESS
APC	324	MSKCC	GRCh37	5	112175319	112175319	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	104	220	0	ENST00000257430.4:c.4028C>G	p.Ser1343Cys	p.S1343C	ENST00000257430	NM_000038.5	1343	tCt/tGt	16/16	0.340896343369783	4	FACETS	0.973	0.88	1	0.973	0.88	1	CLONAL	2	TRUE	2	0.41708747487299	4		220	363	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931794	68931794	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0015068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	98	399	0	ENST00000288368.4:c.224C>G	p.Ser75Ter	p.S75*	ENST00000288368	NM_024870.2	75	tCa/tGa	3/40	0.416308696836413	3	FACETS	0.951	0.85	1	0.476	0.425	0.529	CLONAL	1	TRUE	1	0.41708747487299	3		399	597	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	203	126	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.692998737119984	2		126	429	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159750	20159750	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	52	324	0	ENST00000379607.5:c.9G>C	p.Lys3Asn	p.K3N	ENST00000379607	NM_001412.3	3	aaG/aaC	1/7	0.621152607845175	2	FACETS	0.209	0.177	0.244			1	SUBCLONAL	1	TRUE	NA	0.692998737119984	2		324	717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0015077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	58	354	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.28782835039835	3	FACETS	0.354	0.303	0.41			1	SUBCLONAL	1	TRUE	NA	0.37458249153907	3		354	1038	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0015080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	108	393	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.120950421919426	4	FACETS	1	0.935	1	0.529	0.474	0.588	INDETERMINATE	1	TRUE	2	0.3	4		393	884	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431793	49431793	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765227366	NA	P-0015080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	51	512	0	ENST00000301067.7:c.9346C>T	p.Pro3116Ser	p.P3116S	ENST00000301067	NM_003482.3	3116	Cct/Tct	34/54	0.120950421919426	4	FACETS	0.486	0.411	0.568	0.243	0.205	0.284	INDETERMINATE	1	TRUE	2	0.3	4		512	910	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165283	47165283	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	27	242	2	ENST00000409792.3:c.843del	p.Glu282LysfsTer19	p.E282Kfs*19	ENST00000409792	NM_014159.6	281	aaA/aa	3/21	1	2	FACETS	0.397	0.315	0.491	0.397	0.315	0.491	SUBCLONAL	1	TRUE	1	0.3	2		244	453	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038822	47038822	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	185	157	0	ENST00000377604.3:c.829C>T	p.Gln277Ter	p.Q277*	ENST00000377604	NM_001204468.1	277	Cag/Tag	9/24	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.3	2		157	1074	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179165	123179165	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	54	412	0	ENST00000218089.9:c.614C>G	p.Thr205Arg	p.T205R	ENST00000218089	NM_001042749.1	205	aCa/aGa	8/35	NA	2	FACETS	0.517	0.441	0.601			1	INDETERMINATE	1	TRUE	NA	0.3	2		412	696	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325803	65325803	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	103	408	0	ENST00000342505.4:c.1319G>T	p.Cys440Phe	p.C440F	ENST00000342505	NM_002227.2	440	tGt/tTt	9/25	0.23107392198363	3	FACETS	1	0.94	1	0.536	0.48	0.596	CLONAL	1	TRUE	1	0.3	3		408	736	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933424	100933424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	41	321	0	ENST00000325455.5:c.1966C>A	p.Leu656Ile	p.L656I	ENST00000325455	NM_001202474.3	656	Ctc/Atc	4/8	0.23107392198363	3	FACETS	0.566	0.471	0.673	0.283	0.235	0.337	SUBCLONAL	1	TRUE	1	0.3	3		321	555	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622411	28622411	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0015080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	72	323	0	ENST00000241453.7:c.1205+1G>T		p.X402_splice	ENST00000241453	NM_004119.2	402			1	2	FACETS	0.868	0.759	0.985	0.868	0.759	0.985	CLONAL	1	TRUE	1	0.3	2		323	553	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878185	48878185	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	24	233	0	ENST00000267163.4:c.137G>T	p.Arg46Met	p.R46M	ENST00000267163	NM_000321.2	46	aGg/aTg	1/27	1	2	FACETS	0.448	0.351	0.56	0.448	0.351	0.56	SUBCLONAL	1	TRUE	1	0.3	2		233	357	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348365	89348365	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	55	717	0	ENST00000301030.4:c.4585A>C	p.Lys1529Gln	p.K1529Q	ENST00000301030	NM_001256183.1	1529	Aaa/Caa	9/13	0.179613537084031	1	FACETS	0.338	0.288	0.394	0.338	0.288	0.394	INDETERMINATE	1	TRUE	0	0.3	1		717	921	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578518	7578518	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	203	886	3	ENST00000269305.4:c.412G>A	p.Ala138Thr	p.A138T	ENST00000269305	NM_001126112.2	138	Gcc/Acc	5/11	1	2	FACETS	0.993	0.918	1	0.993	0.918	1	CLONAL	1	TRUE	1	0.3	2		889	1363	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1623974	1623974	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	123	491	1	ENST00000344749.5:c.525G>T	p.Lys175Asn	p.K175N	ENST00000344749	NM_001136139.2	175	aaG/aaT	8/19	0.173118234696299	3	FACETS	1	0.91	1	0.504	0.455	0.555	INDETERMINATE	1	TRUE	1	0.3	3		492	936	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098434	11098434	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	62	614	0	ENST00000358026.2:c.952del	p.Val318SerfsTer8	p.V318Sfs*8	ENST00000358026	NM_001128849.1	318	Gtc/tc	6/36	0.173118234696299	3	FACETS	0.477	0.41	0.549	0.238	0.205	0.275	INDETERMINATE	1	TRUE	1	0.3	3		614	997	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169991085	169991085	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	83	360	0	ENST00000295797.4:c.603G>T	p.Met201Ile	p.M201I	ENST00000295797	NM_002740.5	201	atG/atT	7/18	1	2	FACETS	0.962	0.851	1	0.962	0.851	1	CLONAL	1	TRUE	1	0.3	2		360	575	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141582974	141582974	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	204	649	0	ENST00000220592.5:c.273G>C	p.Lys91Asn	p.K91N	ENST00000220592	NM_012154.3	91	aaG/aaC	3/19	0.3	3	FACETS	1	0.984	1	0.612	0.567	0.66	CLONAL	1	TRUE	1	0.3	3		649	1277	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486175	8486175	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	33	297	0	ENST00000356435.5:c.2642C>A	p.Thr881Lys	p.T881K	ENST00000356435		881	aCa/aAa	17/35	0.176889970306107	2	FACETS	0.41	0.333	0.498	0.205	0.166	0.249	INDETERMINATE	1	TRUE	0	0.3	2		297	536	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651667	48651667	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	70	723	0	ENST00000376670.3:c.833T>C	p.Val278Ala	p.V278A	ENST00000376670	NM_002049.3	278	gTg/gCg	5/6	1	2	FACETS	0.415	0.36	0.475	0.415	0.36	0.475	SUBCLONAL	1	TRUE	1	0.3	2		723	1124	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228223	53228223	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	81	638	2	ENST00000375401.3:c.2179G>T	p.Gly727Cys	p.G727C	ENST00000375401	NM_004187.3	727	Ggc/Tgc	15/26	1	2	FACETS	0.539	0.474	0.61	0.539	0.474	0.61	SUBCLONAL	1	TRUE	1	0.3	2		640	1001	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0000234-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	74	666	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.288886923971134	4	FACETS	1	0.946	1			1	CLONAL	2	TRUE	NA	0.34392488301275	4		667	259	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0000234-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	148	313	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	0.288886923971134	4	FACETS	0.951	0.872	1			1	CLONAL	2	TRUE	NA	0.34392488301275	4		313	608	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000234-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	130	402	0	ENST00000269305.4:c.715A>C	p.Asn239His	p.N239H	ENST00000269305	NM_001126112.2	239	Aac/Cac	7/11	NA	2	FACETS	0.853	0.78	0.929			1	INDETERMINATE	2	TRUE	NA	0.34392488301275	2		402	443	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805187	43805187	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000234-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	71	356	0	ENST00000372470.3:c.637C>T	p.Gln213Ter	p.Q213*	ENST00000372470	NM_005373.2	213	Cag/Tag	4/12	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.34392488301275	2		356	393	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58725275	58725275	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000234-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	425	867	0	ENST00000305921.3:c.849C>A	p.Phe283Leu	p.F283L	ENST00000305921	NM_003620.3	283	ttC/ttA	4/6	0.34392488301275	3	FACETS	0.883	0.843	0.923			1	CLONAL	3	TRUE	NA	0.34392488301275	3		867	1094	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841000	15841000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754101239	NA	P-0000234-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	227	887	1	ENST00000307771.7:c.1084G>A	p.Glu362Lys	p.E362K	ENST00000307771	NM_005089.3	362	Gaa/Aaa	11/11	0.34392488301275	1	FACETS	0.788	0.737	0.839	1	0.993	1	SUBCLONAL	2	TRUE	0	0.34392488301275	1		888	694	SUCCESS
APC	324	MSKCC	GRCh37	5	112179438	112179443	+	inframe_deletion	In_Frame_Del	DEL	TGGGTT	TGGGTT	-	novel	NA	P-0000234-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	73	661	0	ENST00000257430.4:c.8150_8155del	p.Gly2717_Leu2718del	p.G2717_L2718del	ENST00000257430	NM_000038.5	2716	gTGGGTTtg/gtg	16/16	0.340945507495797	3	FACETS	0.669	0.584	0.76			1	SUBCLONAL	1	TRUE	NA	0.34392488301275	3		661	744	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577550	+	frameshift_variant	Frame_Shift_Del	DEL	TGCCGC	TGCCGC	GGCGG	novel	NA	P-0000234-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	143	460	0	ENST00000269305.4:c.731_736delinsCCGCC	p.Gly244AlafsTer3	p.G244Afs*3	ENST00000269305	NM_001126112.2	244	gGCGGCAtg/gCCGCCtg	7/11	NA	2	FACETS	0.879	0.807	0.953			1	INDETERMINATE	2	TRUE	NA	0.34392488301275	2		460	473	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0000984-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	407	495	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.631358811280487	3	FACETS	0.974	0.932	1	0.974	0.932	1	CLONAL	2	TRUE	1	0.631358811280487	3		495	871	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099406	157099426	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAGCAA	CAGCAGCAGCAGCAGCAGCAA	-	rs762617219	NA	P-0000984-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	108	369	0	ENST00000346085.5:c.363_383del	p.Gln125_Gln131del	p.Q125_Q131del	ENST00000346085	NM_020732.3	115	CAGCAGCAGCAGCAGCAGCAA/-	1/20	NA	2	FACETS	0.733	0.661	0.808			1	INDETERMINATE	1	TRUE	NA	0.631358811280487	2		369	467	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138642	55138642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143344944	NA	P-0000984-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	179	465	1	ENST00000257290.5:c.1319C>T	p.Thr440Met	p.T440M	ENST00000257290	NM_006206.4	440	aCg/aTg	9/23	0.396110500268201	1	FACETS	0.655	0.607	0.705	0.655	0.607	0.705	SUBCLONAL	1	TRUE	0	0.631358811280487	1		466	592	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645934	67645934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000984-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	294	569	2	ENST00000264010.4:c.862C>T	p.His288Tyr	p.H288Y	ENST00000264010	NM_006565.3	288	Cac/Tac	4/12	0.631358811280487	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.631358811280487	1		571	567	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612645	228612645	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000984-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	303	968	0	ENST00000366696.1:c.382G>T	p.Ala128Ser	p.A128S	ENST00000366696	NM_003493.2	128	Gca/Tca	1/1	1	2	FACETS	0.952	0.898	1	0.952	0.898	1	CLONAL	1	TRUE	1	0.631358811280487	2		968	1008	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001204-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	269	510	0	ENST00000347630.2:c.399C>A	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttA	6/11	0.739525323661046	3	FACETS	1	0.987	1	0.582	0.547	0.617	CLONAL	1	FALSE	1	0.73647652407121	3		510	859	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158551	26158551	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001204-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	310	313	0	ENST00000289316.2:c.154G>C	p.Asp52His	p.D52H	ENST00000289316	NM_138720.2	52	Gac/Cac	1/2	0.739525323661046	4	FACETS	0.938	0.889	0.988	0.938	0.889	0.988	CLONAL	2	FALSE	2	0.73647652407121	4		313	779	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527594	29527594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001204-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	287	487	0	ENST00000356175.3:c.1043C>T	p.Ser348Phe	p.S348F	ENST00000356175	NM_000267.3	348	tCc/tTc	9/57	0.636074843573772	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	FALSE	2	0.73647652407121	4		487	586	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0005937-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	97	310	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.934	0.832	1	0.934	0.832	1	CLONAL	1	TRUE	1	0.229217825143507	2		310	906	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266709	198266709	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005937-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	85	403	0	ENST00000335508.6:c.2223G>T	p.Lys741Asn	p.K741N	ENST00000335508	NM_012433.2	741	aaG/aaT	15/25	1	2	FACETS	0.934	0.825	1	0.934	0.825	1	CLONAL	1	TRUE	1	0.229217825143507	2		403	794	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271256	1271256	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005937-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	65	333	0	ENST00000310581.5:c.2446C>A	p.His816Asn	p.H816N	ENST00000310581	NM_198253.2	816	Cac/Aac	8/16	1	2	FACETS	0.861	0.746	0.985	0.861	0.746	0.985	CLONAL	1	TRUE	1	0.229217825143507	2		333	659	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497292	149497292	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005937-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	85	490	0	ENST00000261799.4:c.3026A>C	p.Tyr1009Ser	p.Y1009S	ENST00000261799	NM_002609.3	1009	tAt/tCt	22/23	1	2	FACETS	0.774	0.683	0.873	0.774	0.683	0.873	SUBCLONAL	1	TRUE	1	0.229217825143507	2		490	958	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1042167	1042167	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005937-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	82	491	0	ENST00000358495.3:c.58G>T	p.Gly20Cys	p.G20C	ENST00000358495	NM_134424.2	20	Ggc/Tgc	2/12	1	2	FACETS	0.573	0.503	0.648	0.573	0.503	0.648	SUBCLONAL	1	TRUE	1	0.229217825143507	2		491	1249	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562246	21562246	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005937-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	88	651	0	ENST00000382592.4:c.1673G>C	p.Arg558Pro	p.R558P	ENST00000382592	NM_014572.2	558	cGc/cCc	4/8	1	2	FACETS	0.628	0.554	0.707	0.628	0.554	0.707	SUBCLONAL	1	TRUE	1	0.229217825143507	2		651	1223	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934230	39934230	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005937-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1406	118	740	1	ENST00000378444.4:c.369G>T	p.Gln123His	p.Q123H	ENST00000378444	NM_001123385.1	123	caG/caT	4/15	1	2	FACETS	0.676	0.607	0.749	0.676	0.607	0.749	SUBCLONAL	1	TRUE	1	0.229217825143507	2		741	1524	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928854	44928854	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005937-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	100	483	0	ENST00000377967.4:c.1954G>T	p.Ala652Ser	p.A652S	ENST00000377967	NM_021140.2	652	Gca/Tca	17/29	1	2	FACETS	0.952	0.849	1	0.952	0.849	1	CLONAL	1	TRUE	1	0.229217825143507	2		483	917	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161442	2161442	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005937-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1227	119	677	0	ENST00000434045.2:c.85del	p.Val29Ter	p.V29*	ENST00000434045	NM_001127598.1	29	Gta/ta	2/5	1	2	FACETS	0.771	0.694	0.854	0.771	0.694	0.854	SUBCLONAL	1	TRUE	1	0.229217825143507	2		677	1346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578226	7578226	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1464727668	NA	P-0006286-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	792	486	0	ENST00000269305.4:c.623A>T	p.Asp208Val	p.D208V	ENST00000269305	NM_001126112.2	208	gAc/gTc	6/11	NA	2	FACETS	0.996	0.967	1			1	INDETERMINATE	2	TRUE	NA	0.548819095471568	2		486	1449	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512029	148512029	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006286-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	302	346	0	ENST00000320356.2:c.1649A>C	p.Lys550Thr	p.K550T	ENST00000320356	NM_004456.4	550	aAg/aCg	14/20	0.548819095471568	3	FACETS	0.888	0.84	0.936	0.888	0.84	0.936	CLONAL	2	TRUE	1	0.548819095471568	3		346	790	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219401	1219401	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006286-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	471	472	0	ENST00000326873.7:c.454del	p.Gln152ArgfsTer9	p.Q152Rfs*9	ENST00000326873	NM_000455.4	151	tgC/tg	3/10	0.548819095471568	2	FACETS	0.887	0.853	0.922	0.887	0.853	0.922	CLONAL	2	TRUE	0	0.548819095471568	2		472	967	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841428	156841428	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006286-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	201	389	0	ENST00000524377.1:c.731T>C	p.Leu244Pro	p.L244P	ENST00000524377	NM_002529.3	244	cTg/cCg	7/17	0.548819095471568	4	FACETS	0.97	0.898	1	0.485	0.449	0.523	CLONAL	1	TRUE	2	0.548819095471568	4		389	1169	SUCCESS
BLM	641	MSKCC	GRCh37	15	91328297	91328297	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006286-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	173	361	2	ENST00000355112.3:c.2809C>T	p.Gln937Ter	p.Q937*	ENST00000355112	NM_000057.2	937	Cag/Tag	14/22	0.548819095471568	3	FACETS	0.934	0.861	1	0.467	0.43	0.506	CLONAL	1	TRUE	1	0.548819095471568	3		363	860	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59820438	59820438	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0006286-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4587	301	580	0	ENST00000259008.2:c.2315C>G	p.Ser772Ter	p.S772*	ENST00000259008	NM_032043.2	772	tCa/tGa	16/20	0.548819095471568	15	FACETS	1	0.954	1			1	CLONAL	1	TRUE	NA	0.548819095471568	15		580	4888	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591116	67591148	+	inframe_deletion	In_Frame_Del	DEL	TTATCCAGCTGAGAAAGACGAGAGACCAATACT	TTATCCAGCTGAGAAAGACGAGAGACCAATACT	-	novel	NA	P-0006286-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	186	302	0	ENST00000274335.5:c.1710_1742del	p.Ile571_Leu581del	p.I571_L581del	ENST00000274335		570	cTTATCCAGCTGAGAAAGACGAGAGACCAATACTtg/ctg	12/15	0.548819095471568	3	FACETS	1	0.988	1	0.66	0.612	0.71	CLONAL	1	TRUE	1	0.548819095471568	3		302	654	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007620-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	186	292	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.762	0.708	0.816	0.762	0.708	0.816	SUBCLONAL	1	FALSE	1	0.88157113626446	2		292	554	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0007620-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	488	666	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.855062335743099	4	FACETS	1	0.994	1	0.775	0.747	0.803	CLONAL	2	FALSE	1	0.88157113626446	4		667	896	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037923	49037923	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007620-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	224	419	0	ENST00000267163.4:c.2163C>A	p.Phe721Leu	p.F721L	ENST00000267163	NM_000321.2	721	ttC/ttA	21/27	1	2	FACETS	0.783	0.733	0.834	0.783	0.733	0.834	SUBCLONAL	1	FALSE	1	0.88157113626446	2		419	649	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039161	49039161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007620-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	200	313	1	ENST00000267163.4:c.2239G>A	p.Glu747Lys	p.E747K	ENST00000267163	NM_000321.2	747	Gag/Aag	22/27	1	2	FACETS	0.845	0.789	0.902	0.845	0.789	0.902	CLONAL	1	FALSE	1	0.88157113626446	2		314	537	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128216	30128216	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007620-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	246	470	0	ENST00000263025.4:c.1016A>T	p.Glu339Val	p.E339V	ENST00000263025	NM_002746.2	339	gAg/gTg	7/9	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.88157113626446	2		470	538	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465527	8465527	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007620-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	98	605	0	ENST00000356435.5:c.3653A>G	p.Gln1218Arg	p.Q1218R	ENST00000356435		1218	cAa/cGa	21/35	0.72401188625601	1	FACETS	0.252	0.225	0.28	0.252	0.225	0.28	SUBCLONAL	1	FALSE	0	0.88157113626446	1		605	494	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0008744-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	2368	360	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.584215353559653	11	FACETS	1	0.994	1	1	0.994	1	CLONAL	9	TRUE	2	0.584215353559653	11		360	3230	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102094475	102094475	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008744-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	257	343	0	ENST00000282441.5:c.1155C>A	p.Phe385Leu	p.F385L	ENST00000282441	NM_001130145.2	385	ttC/ttA	7/9	0.584215353559653	3	FACETS	1	0.963	1	0.52	0.487	0.554	CLONAL	1	TRUE	1	0.584215353559653	3		343	1093	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2199926	2199926	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008744-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	339	556	0	ENST00000398665.3:c.695T>A	p.Ile232Asn	p.I232N	ENST00000398665	NM_032482.2	232	aTc/aAc	8/28	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.584215353559653	2		556	1142	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0010018-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	585	448	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.509638062224434	2	FACETS	0.996	0.962	1	0.996	0.962	1	CLONAL	2	TRUE	0	0.509638062224434	2		450	1152	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0010018-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	120	276	0	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	1	2	FACETS	0.909	0.825	0.997	0.909	0.825	0.997	CLONAL	1	TRUE	1	0.509638062224434	2		276	518	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222660	157222660	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0010018-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	117	211	0	ENST00000346085.5:c.1926+1G>A		p.X642_splice	ENST00000346085	NM_020732.3	642			0.482326479941502	3	FACETS	0.993	0.899	1	0.331	0.299	0.365	CLONAL	1	TRUE	0	0.509638062224434	3		211	580	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793466	18793466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193113798	NA	P-0010018-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	255	468	1	ENST00000266497.5:c.4163C>T	p.Thr1388Met	p.T1388M	ENST00000266497		1388	aCg/aTg	30/31	0.503148008433475	2	FACETS	0.957	0.906	1	0.957	0.906	1	CLONAL	2	TRUE	0	0.509638062224434	2		469	523	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813345	102813345	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010018-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	503	409	0	ENST00000307046.8:c.344C>A	p.Ala115Asp	p.A115D	ENST00000307046	NM_001111285.1	115	gCc/gAc	3/4	0.503148008433475	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.509638062224434	2		409	964	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223061	1223061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782267	NA	P-0010018-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	189	372	0	ENST00000326873.7:c.998G>A	p.Arg333His	p.R333H	ENST00000326873	NM_000455.4	333	cGc/cAc	8/10	0.48180805602722	3	FACETS	0.813	0.75	0.878	0.406	0.375	0.439	CLONAL	1	TRUE	1	0.509638062224434	3		372	1145	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711866	89711890	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTCCACCAGGGAGTAACTATTCCCA	GTCCACCAGGGAGTAACTATTCCCA	-	novel	NA	P-0010073-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	58	348	1	ENST00000371953.3:c.493-6_511del		p.X165_splice	ENST00000371953	NM_000314.4	165		6/9	0.172053403250413	1	FACETS	0.679	0.583	0.784	0.679	0.583	0.784	SUBCLONAL	1	TRUE	0	0.227670238354977	1		349	665	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528098	103528113	+	frameshift_variant	Frame_Shift_Del	DEL	GCTCCCGTGAAGAATG	GCTCCCGTGAAGAATG	-	novel	NA	P-0010073-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	48	226	0	ENST00000355739.4:c.3407_3422del	p.Ala1136GlufsTer23	p.A1136Efs*23	ENST00000355739	NM_000123.3	1136	GCTCCCGTGAAGAATGga/ga	15/15	0.227670238354977	1	FACETS	0.84	0.711	0.981	0.84	0.711	0.981	CLONAL	1	TRUE	0	0.227670238354977	1		226	445	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0010079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	319	419	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.358927313394478	4	FACETS	0.934	0.881	0.989			1	CLONAL	2	TRUE	NA	0.364955395391765	4		420	1277	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004630	16004630	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0010079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1214	74	576	0	ENST00000268712.3:c.2624C>G	p.Ser875Ter	p.S875*	ENST00000268712	NM_006311.3	875	tCa/tGa	20/46	0.364955395391765	3	FACETS	0.372	0.324	0.424			1	SUBCLONAL	1	TRUE	NA	0.364955395391765	3		576	1288	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004707	16004708	+	missense_variant	Missense_Mutation	DNP	GG	GG	TA	novel	NA	P-0010079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1389	164	691	0	ENST00000268712.3:c.2546_2547delinsTA	p.Ala849Val	p.A849V	ENST00000268712	NM_006311.3	849	gCC/gTA	20/46	0.364955395391765	3	FACETS	0.684	0.626	0.746			1	SUBCLONAL	1	TRUE	NA	0.364955395391765	3		691	1553	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600006	10600006	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010182-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	426	681	0	ENST00000171111.5:c.1570G>A	p.Gly524Ser	p.G524S	ENST00000171111	NM_203500.1	524	Ggc/Agc	5/6	0.507811886070277	1	FACETS	0.958	0.913	1	0.958	0.913	1	CLONAL	1	TRUE	0	0.507811886070277	1		681	1306	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278343	39278343	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010182-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	379	642	0	ENST00000402219.2:c.806T>A	p.Met269Lys	p.M269K	ENST00000402219	NM_005633.3	269	aTg/aAg	6/23	1	2	FACETS	0.989	0.938	1	0.989	0.938	1	CLONAL	1	TRUE	1	0.507811886070277	2		642	1509	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035154	30035154	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010182-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	366	490	4	ENST00000338641.4:c.316G>T	p.Glu106Ter	p.E106*	ENST00000338641	NM_000268.3	106	Gaa/Taa	3/16	0.507811886070277	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.507811886070277	1		494	1034	SUCCESS
APC	324	MSKCC	GRCh37	5	112151198	112151198	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs769727966	NA	P-0010182-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	228	328	0	ENST00000257430.4:c.841A>G	p.Thr281Ala	p.T281A	ENST00000257430	NM_000038.5	281	Act/Gct	9/16	1	2	FACETS	0.925	0.862	0.989	0.925	0.862	0.989	CLONAL	1	TRUE	1	0.507811886070277	2		328	971	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141545628	141545628	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010182-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1416	492	702	0	ENST00000220592.5:c.2210A>G	p.Asp737Gly	p.D737G	ENST00000220592	NM_012154.3	737	gAc/gGc	17/19	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.507811886070277	2		702	1908	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271453	26271453	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs767623078	NA	P-0010206-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	359	1414	0	ENST00000305910.3:c.160C>G	p.Arg54Gly	p.R54G	ENST00000305910	NM_003534.2	54	Cgc/Ggc	1/1	0.241200043707431	5	FACETS	0.883	0.836	0.932	0.589	0.557	0.622	INDETERMINATE	2	TRUE	2	0.467464483187859	5		1414	1479	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	165	321	0				ENST00000310581	NM_198253.2	-/1132			0.193640959629128	4	FACETS	0.909	0.836	0.985	0.909	0.836	0.985	CLONAL	2	TRUE	2	0.309516368275124	4		321	768	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469669	NA	P-0010236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	421	346	0	ENST00000374080.3:c.130G>A	p.Gly44Ser	p.G44S	ENST00000374080		44	Ggt/Agt	2/45	0.309516368275124	2	FACETS	0.886	0.846	0.925			1	CLONAL	3	TRUE	NA	0.309516368275124	2		346	1024	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788617	3788617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519884	NA	P-0010236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1235	154	0	0	ENST00000262367.5:c.4337G>A	p.Arg1446His	p.R1446H	ENST00000262367	NM_004380.2	1446	cGc/cAc	26/31	1	2	FACETS	0.716	0.653	0.783	0.716	0.653	0.783	SUBCLONAL	1	TRUE	1	0.309516368275124	2		0	1389	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971029	21971029	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519852	NA	P-0010236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	628	263	0	ENST00000304494.5:c.329G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tGg/tAg	2/3	0.309516368275124	5	FACETS	1	0.988	1	1	0.988	1	CLONAL	5	TRUE	0	0.309516368275124	5		263	1142	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534473	187534473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	220	323	3	ENST00000441802.2:c.9253del	p.Asp3086IlefsTer30	p.D3086Ifs*30	ENST00000441802	NM_005245.3	3085	Ctt/tt	13/27	0.219057188318119	3	FACETS	1	0.961	1	0.695	0.649	0.743	CLONAL	2	TRUE	0	0.309516368275124	3		326	787	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182858	123182858	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	287	271	0	ENST00000218089.9:c.823C>T	p.Gln275Ter	p.Q275*	ENST00000218089	NM_001042749.1	275	Cag/Tag	10/35	0.309516368275124	2	FACETS	0.846	0.8	0.892			1	CLONAL	3	TRUE	NA	0.309516368275124	2		271	731	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610563	215610563	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	102	442	1	ENST00000260947.4:c.1693C>A	p.Arg565Ser	p.R565S	ENST00000260947	NM_000465.2	565	Cgt/Agt	8/11	0.2731851691901	3	FACETS	0.726	0.648	0.81	0.363	0.324	0.405	SUBCLONAL	1	TRUE	1	0.309516368275124	3		443	1048	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467968	66467968	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	187	449	0	ENST00000273854.3:c.301G>T	p.Val101Leu	p.V101L	ENST00000273854	NM_004439.5	101	Gta/Tta	3/18	0.21771945525733	2	FACETS	1	0.987	1	0.658	0.608	0.71	CLONAL	1	TRUE	0	0.309516368275124	2		449	918	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224531	108224531	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	250	472	0	ENST00000278616.4:c.8710G>C	p.Glu2904Gln	p.E2904Q	ENST00000278616	NM_000051.3	2904	Gag/Cag	60/63	0.232730340831721	2	FACETS	1	0.992	1	0.743	0.695	0.793	CLONAL	1	TRUE	0	0.309516368275124	2		472	1087	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435294	49435294	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1411803906	NA	P-0010236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	205	349	0	ENST00000301067.7:c.6259C>T	p.Gln2087Ter	p.Q2087*	ENST00000301067	NM_003482.3	2087	Cag/Tag	31/54	0.248956672485513	3	FACETS	0.852	0.791	0.915	0.852	0.791	0.915	CLONAL	2	TRUE	1	0.309516368275124	3		349	898	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222339	2222339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771191963	NA	P-0010236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	141	502	0	ENST00000326181.6:c.623G>A	p.Arg208Gln	p.R208Q	ENST00000326181	NM_032271.2	208	cGa/cAa	8/21	1	2	FACETS	0.829	0.754	0.908	0.829	0.754	0.908	CLONAL	1	TRUE	1	0.309516368275124	2		502	1099	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533772	41533772	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853038	NA	P-0010236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	286	510	0	ENST00000263253.7:c.1738C>T	p.Arg580Ter	p.R580*	ENST00000263253	NM_001429.3	580	Cga/Tga	8/31	0.2731851691901	3	FACETS	0.808	0.759	0.859	0.808	0.759	0.859	CLONAL	2	TRUE	1	0.309516368275124	3		510	1320	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435702	49435708	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GGTAGGG	GGTAGGG	-	novel	NA	P-0010236-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1317	146	509	0	ENST00000301067.7:c.6175_6181del	p.Pro2059CysfsTer33	p.P2059Cfs*33	ENST00000301067	NM_003482.3	2059	CCCTACCtg/tg	29/54	0.248956672485513	3	FACETS	0.745	0.677	0.816	0.372	0.338	0.408	SUBCLONAL	1	TRUE	1	0.309516368275124	3		509	1463	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0010317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	392	436	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.610908883869865	2	FACETS	0.953	0.916	0.99	0.953	0.916	0.99	CLONAL	2	TRUE	0	0.610908883869865	2		436	673	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508133	106508133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1346474355	NA	P-0010317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	71	152	0	ENST00000359195.3:c.127G>A	p.Val43Met	p.V43M	ENST00000359195	NM_002649.2	43	Gtg/Atg	2/11	0.610908883869865	2	FACETS	0.919	0.812	1	0.459	0.406	0.516	CLONAL	1	TRUE	0	0.610908883869865	2		152	253	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591894	48591894	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010317-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	374	699	0	ENST00000342988.3:c.1057T>G	p.Tyr353Asp	p.Y353D	ENST00000342988	NM_005359.5	353	Tac/Gac	9/12	0.610908883869865	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.610908883869865	1		699	789	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0010359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	60	495	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.923	0.796	1	0.923	0.796	1	CLONAL	1	TRUE	1	0.243470199430938	2		495	534	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0010359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	43	313	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.243470199430938	4	FACETS	0.607	0.506	0.719	0.303	0.253	0.36	SUBCLONAL	1	TRUE	2	0.243470199430938	4		313	724	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979530	7979530	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368323729	NA	P-0010359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	45	284	1	ENST00000319144.4:c.1495C>T	p.Arg499Cys	p.R499C	ENST00000319144	NM_001139.2	499	Cgc/Tgc	11/15	0.243470199430938	3	FACETS	0.592	0.496	0.698	0.296	0.248	0.349	SUBCLONAL	1	TRUE	1	0.243470199430938	3		285	701	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574558	64574558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	602	513	0	ENST00000312049.6:c.837del	p.Leu280Ter	p.L280*	ENST00000312049	NM_130799.2	279	gcC/gc	6/10	0.550249789558817	4	FACETS	0.905	0.88	0.93	0.905	0.88	0.93	CLONAL	4	TRUE	0	0.605357300807767	4		513	882	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101417	27101417	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010533-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	208	435	0	ENST00000324856.7:c.4703del	p.Pro1568LeufsTer44	p.P1568Lfs*44	ENST00000324856	NM_006015.4	1567	Ccc/cc	18/20	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.334252419726032	2		435	945	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0010614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	456	439	1	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.793898734227126	2		440	1054	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441255	52441258	+	frameshift_variant	Frame_Shift_Del	DEL	CTGA	CTGA	-	novel	NA	P-0010614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	370	385	0	ENST00000460680.1:c.512_515del	p.Val171AlafsTer15	p.V171Afs*15	ENST00000460680	NM_004656.3	171	gTCAGc/gc	7/17	0.793898734227126	1	FACETS	0.979	0.943	1	0.979	0.943	1	CLONAL	1	TRUE	0	0.793898734227126	1		385	574	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412493	80412493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514698	NA	P-0010644-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	498	509	0	ENST00000286548.4:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000286548	NM_002072.3	183	cGa/cAa	4/7	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.813050372901315	2		509	1168	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61709561	61709561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	426	403	0	ENST00000401558.2:c.2926G>A	p.Glu976Lys	p.E976K	ENST00000401558	NM_003400.3	976	Gaa/Aaa	23/25	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.845463181406876	2		403	973	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272240	142272241	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0010670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	155	248	0	ENST00000350721.4:c.2634-1_2634delinsAA		p.X878_splice	ENST00000350721	NM_001184.3	878		13/47	1	2	FACETS	0.789	0.728	0.851	0.789	0.728	0.851	SUBCLONAL	1	TRUE	1	0.845463181406876	2		248	465	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959091	2959091	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	192	222	0	ENST00000396946.4:c.2425C>T	p.Gln809Ter	p.Q809*	ENST00000396946	NM_032415.4	809	Cag/Tag	18/25	0.160160277325787	6	FACETS	0.851	0.79	0.914			1	INDETERMINATE	2	TRUE	NA	0.845463181406876	6		222	718	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739866	41739866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	406	478	3	ENST00000242208.4:c.107C>T	p.Pro36Leu	p.P36L	ENST00000242208	NM_002192.2	36	cCg/cTg	2/3	1	2	FACETS	0.987	0.943	1	0.987	0.943	1	CLONAL	1	TRUE	1	0.845463181406876	2		481	973	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0010670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	342	333	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.845463181406876	3	FACETS	0.996	0.954	1	0.996	0.954	1	CLONAL	2	TRUE	1	0.845463181406876	3		333	578	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331688	8331688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	306	350	0	ENST00000356435.5:c.5428G>A	p.Glu1810Lys	p.E1810K	ENST00000356435		1810	Gag/Aag	33/35	1	2	FACETS	0.959	0.909	1	0.959	0.909	1	CLONAL	1	TRUE	1	0.845463181406876	2		350	755	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0010670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	55	68	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.740875036709943	1	FACETS	0.905	0.819	0.986	0.905	0.819	0.986	CLONAL	1	TRUE	0	0.845463181406876	1		68	83	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650881	93650881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200438123	NA	P-0010670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	475	224	2	ENST00000375746.1:c.1807G>A	p.Asp603Asn	p.D603N	ENST00000375746	NM_001174167.1	603	Gat/Aat	13/14	0.751118046204417	3	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.845463181406876	3		226	737	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252030	133252030	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1565975090	NA	P-0010670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	286	353	0	ENST00000320574.5:c.1180C>T	p.Gln394Ter	p.Q394*	ENST00000320574	NM_006231.2	394	Cag/Tag	12/49	1	2	FACETS	0.902	0.853	0.952	0.902	0.853	0.952	CLONAL	1	TRUE	1	0.845463181406876	2		353	750	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527474	29527474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	506	247	0	ENST00000356175.3:c.923C>T	p.Ala308Val	p.A308V	ENST00000356175	NM_000267.3	308	gCt/gTt	9/57	0.845463181406876	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.845463181406876	3		247	843	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619168	1619169	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0010670-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	412	528	1	ENST00000344749.5:c.1391_1392delinsTT	p.Ala464Val	p.A464V	ENST00000344749	NM_001136139.2	464	gCC/gTT	16/19	1	2	FACETS	0.954	0.911	0.997	0.954	0.911	0.997	CLONAL	1	TRUE	1	0.845463181406876	2		529	1022	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	71	305	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.633	0.55	0.722	0.633	0.55	0.722	SUBCLONAL	1	TRUE	1	0.199554521172736	2		305	1125	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0010691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	86	308	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.809	0.713	0.911	0.809	0.713	0.911	CLONAL	1	TRUE	1	0.199554521172736	2		308	1066	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980903	40980903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs906977293	NA	P-0010691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	41	394	0	ENST00000373198.4:c.1583C>T	p.Ser528Leu	p.S528L	ENST00000373198	NM_133170.3	528	tCg/tTg	10/32	0.186432352002104	0	FACETS	0.483	0.401	0.574			1	SUBCLONAL	1	TRUE	0	0.199554521172736	0		394	681	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253772	30253772	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010691-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1347	105	574	0	ENST00000307677.4:c.682T>G	p.Ser228Ala	p.S228A	ENST00000307677	NM_138578.1	228	Tca/Gca	3/3	1	2	FACETS	0.725	0.647	0.808	0.725	0.647	0.808	SUBCLONAL	1	TRUE	1	0.199554521172736	2		574	1452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0010738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	348	442	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.558069824639046	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.558069824639046	2		443	609	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510560	38510560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	139	336	0	ENST00000254066.5:c.814C>T	p.Arg272Trp	p.R272W	ENST00000254066	NM_000964.3	272	Cgg/Tgg	7/9	0.558069824639046	3	FACETS	0.983	0.898	1	0.328	0.299	0.358	CLONAL	1	TRUE	0	0.558069824639046	3		336	648	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5286145	5286145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010738-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	125	342	0	ENST00000357368.4:c.7C>T	p.Pro3Ser	p.P3S	ENST00000357368	NM_002850.3	3	Ccc/Tcc	2/38	0.558069824639046	2	FACETS	1	0.912	1	0.5	0.456	0.546	CLONAL	1	TRUE	0	0.558069824639046	2		342	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0010742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	569	620	1	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.47614832356593	3	FACETS	0.871	0.842	0.901	0.871	0.842	0.901	CLONAL	3	TRUE	0	0.529536405720632	3		621	1040	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0010742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	75	191	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.774	0.683	0.871	0.774	0.683	0.871	SUBCLONAL	1	TRUE	1	0.529536405720632	2		191	366	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0010742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	783	0	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.529536405720632	5	FACETS	0.999	0.971	1			1	CLONAL	4	TRUE	NA	0.529536405720632	5		0	1328	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518080	8518080	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	120	367	0	ENST00000356435.5:c.1311G>C	p.Gln437His	p.Q437H	ENST00000356435		437	caG/caC	10/35	0.529536405720632	5	FACETS	0.741	0.668	0.819	0.247	0.222	0.273	SUBCLONAL	1	TRUE	2	0.529536405720632	5		367	1097	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487588	38487588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs576185106	NA	P-0010742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	687	617	1	ENST00000254066.5:c.118G>A	p.Ala40Thr	p.A40T	ENST00000254066	NM_000964.3	40	Gct/Act	2/9	0.130384322882045	3	FACETS	0.925	0.898	0.953			1	INDETERMINATE	3	TRUE	NA	0.529536405720632	3		618	1182	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0010781-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	90	502	1	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	0.986	0.872	1	0.986	0.872	1	CLONAL	1	FALSE	1	0.167395200537258	2		503	1091	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0010781-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	51	195	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	FALSE	1	0.167395200537258	2		195	513	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0010781-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1173	157	629	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.167395200537258	2		629	1330	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743865	40743865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758531464	NA	P-0010781-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	87	461	1	ENST00000373198.4:c.3130G>A	p.Val1044Ile	p.V1044I	ENST00000373198	NM_133170.3	1044	Gtc/Atc	23/32	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	1	0.167395200537258	2		462	917	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574432	41574448	+	frameshift_variant	Frame_Shift_Del	DEL	GGGACAGATAGGCCAGC	GGGACAGATAGGCCAGC	T	novel	NA	P-0010781-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	84	446	0	ENST00000263253.7:c.6717_6733delinsT	p.Met2239IlefsTer35	p.M2239Ifs*35	ENST00000263253	NM_001429.3	2239	atGGGACAGATAGGCCAGCtt/atTtt	31/31	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	FALSE	1	0.167395200537258	2		446	937	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947827	178947827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	968	833	3	ENST00000263967.3:c.2702G>T	p.Cys901Phe	p.C901F	ENST00000263967	NM_006218.2	901	tGt/tTt	19/21	0.571086789574733	3	FACETS	0.931	0.91	0.952	0.931	0.91	0.952	CLONAL	3	TRUE	0	0.626546581024355	3		836	1453	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191474	10191474	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397516441	NA	P-0010819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	183	542	0	ENST00000256474.2:c.467A>G	p.Tyr156Cys	p.Y156C	ENST00000256474	NM_000551.3	156	tAt/tGt	3/3	0.626546581024355	1	FACETS	0.995	0.931	1	0.995	0.931	1	CLONAL	1	TRUE	0	0.626546581024355	1		542	403	SUCCESS
APC	324	MSKCC	GRCh37	5	112177104	112177104	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	393	948	0	ENST00000257430.4:c.5813A>T	p.Lys1938Ile	p.K1938I	ENST00000257430	NM_000038.5	1938	aAa/aTa	16/16	0.171299740358109	4	FACETS	0.761	0.723	0.8	0.761	0.723	0.8	INDETERMINATE	2	TRUE	2	0.626546581024355	4		948	1341	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358966	81358966	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	390	836	0	ENST00000222390.5:c.995A>T	p.Gln332Leu	p.Q332L	ENST00000222390	NM_000601.4	332	cAg/cTg	8/18	0.171299740358109	4	FACETS	0.798	0.758	0.838	0.798	0.758	0.838	INDETERMINATE	2	TRUE	2	0.626546581024355	4		836	1269	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955596	90955596	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0010819-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	291	501	0	ENST00000265433.3:c.2071-2A>G		p.X691_splice	ENST00000265433	NM_002485.4	691			0.171299740358109	4	FACETS	0.857	0.808	0.906	0.857	0.808	0.906	INDETERMINATE	2	TRUE	2	0.626546581024355	4		501	882	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0010832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	74	502	1	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.387361343665459	1	FACETS	0.922	0.814	1	0.922	0.814	1	CLONAL	1	TRUE	0	0.387361343665459	1		503	334	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0010832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	64	310	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.939	0.818	1	0.939	0.818	1	CLONAL	1	TRUE	1	0.387361343665459	2		310	352	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578213	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs864309495	NA	P-0010832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	117	685	0	ENST00000269305.4:c.636del	p.Arg213AspfsTer34	p.R213Dfs*34	ENST00000269305	NM_001126112.2	212	ttT/tt	6/11	0.387361343665459	1	FACETS	0.976	0.885	1	0.976	0.885	1	CLONAL	1	TRUE	0	0.387361343665459	1		685	499	SUCCESS
APC	324	MSKCC	GRCh37	5	112154824	112154824	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	80	501	0	ENST00000257430.4:c.1095A>T	p.Lys365Asn	p.K365N	ENST00000257430	NM_000038.5	365	aaA/aaT	10/16	1	2	FACETS	0.871	0.77	0.98	0.871	0.77	0.98	CLONAL	1	TRUE	1	0.387361343665459	2		501	474	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212130	5212130	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529643294	NA	P-0010832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	114	658	1	ENST00000357368.4:c.4901C>T	p.Thr1634Met	p.T1634M	ENST00000357368	NM_002850.3	1634	aCg/aTg	32/38	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.387361343665459	2		659	562	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17949188	17949188	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010832-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	91	618	0	ENST00000458235.1:c.1453C>A	p.Leu485Met	p.L485M	ENST00000458235	NM_000215.3	485	Ctg/Atg	11/24	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.387361343665459	2		618	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	268	360	1	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.27944234829166	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.27944234829166	2		361	783	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941741	48941741	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0010849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	61	230	0	ENST00000267163.4:c.1049+2T>C		p.X350_splice	ENST00000267163	NM_000321.2	350			0.27944234829166	2	FACETS	0.846	0.738	0.961	0.846	0.738	0.961	CLONAL	2	TRUE	0	0.27944234829166	2		230	258	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523605	41523605	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	203	385	0	ENST00000263253.7:c.1021C>T	p.Gln341Ter	p.Q341*	ENST00000263253	NM_001429.3	341	Cag/Tag	4/31	0.27944234829166	2	FACETS	0.978	0.909	1	0.978	0.909	1	CLONAL	2	TRUE	0	0.27944234829166	2		385	743	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	57	510	0	ENST00000347630.2:c.399C>A	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttA	6/11	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.15	2		510	693	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911743	32911743	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs543748012	NA	P-0010950-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	55	1016	0	ENST00000380152.3:c.3251G>A	p.Ser1084Asn	p.S1084N	ENST00000380152		1084	aGt/aAt	11/27	1	2	FACETS	0.967	0.826	1	0.967	0.826	1	CLONAL	1	TRUE	1	0.15	2		1016	758	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476376	88476376	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	45	392	0	ENST00000360948.2:c.1756C>A	p.Gln586Lys	p.Q586K	ENST00000360948	NM_001012338.2	586	Cag/Aag	15/19	1	2	FACETS	0.154	0.129	0.182	0.154	0.129	0.182	SUBCLONAL	1	TRUE	1	0.8	2		392	730	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426127	47426127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010977-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1228	95	741	0	ENST00000377045.4:c.647C>T	p.Pro216Leu	p.P216L	ENST00000377045	NM_001654.4	216	cCc/cTc	7/16	1	2	FACETS	0.18	0.159	0.202	0.18	0.159	0.202	SUBCLONAL	1	TRUE	1	0.8	2		741	1323	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0011002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	102	292	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	0.856	0.764	0.955			1	INDETERMINATE	1	TRUE	NA	0.226414027700903	2		292	1052	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047190	180047190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770500099	NA	P-0011002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	134	545	1	ENST00000261937.6:c.2525G>A	p.Arg842Gln	p.R842Q	ENST00000261937	NM_182925.4	842	cGa/cAa	17/30	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.226414027700903	2		546	1134	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456317	99456317	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	59	451	4	ENST00000268035.6:c.1634G>A	p.Gly545Asp	p.G545D	ENST00000268035	NM_000875.3	545	gGc/gAc	8/21	1	2	FACETS	0.542	0.465	0.626	0.542	0.465	0.626	SUBCLONAL	1	TRUE	1	0.226414027700903	2		455	962	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230662	46230684	+	protein_altering_variant	In_Frame_Del	DEL	AGCTCTTGGCAGCTAATCGTACC	AGCTCTTGGCAGCTAATCGTACC	GGTACGAT	novel	NA	P-0011002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	112	683	0	ENST00000334344.6:c.911_933delinsGGTACGAT	p.Lys304_Thr311delinsArgTyrAsp	p.K304_T311delinsRYD	ENST00000334344	NM_152641.2	304	aAGCTCTTGGCAGCTAATCGTACC/aGGTACGAT	8/21	0.220574076937031	1	FACETS	0.722	0.647	0.802	0.722	0.647	0.802	SUBCLONAL	1	TRUE	0	0.226414027700903	1		683	1215	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0011074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	314	554	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.759992070737206	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.759992070737206	1		554	510	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258744	115258744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434596	NA	P-0011074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	278	479	0	ENST00000369535.4:c.38G>A	p.Gly13Asp	p.G13D	ENST00000369535	NM_002524.4	13	gGt/gAt	2/7	1	2	FACETS	0.812	0.764	0.861	0.812	0.764	0.861	CLONAL	1	TRUE	1	0.759992070737206	2		479	901	SUCCESS
APC	324	MSKCC	GRCh37	5	112173975	112173975	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0011074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	107	178	0	ENST00000257430.4:c.2684C>G	p.Ser895Ter	p.S895*	ENST00000257430	NM_000038.5	895	tCa/tGa	16/16	0.759992070737206	1	FACETS	0.794	0.729	0.859	0.794	0.729	0.859	SUBCLONAL	1	TRUE	0	0.759992070737206	1		178	220	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411276	63411276	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	782	382	0	ENST00000330258.3:c.1891C>T	p.Arg631Ter	p.R631*	ENST00000330258	NM_152424.3	631	Cga/Tga	2/2	0.759992070737206	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.759992070737206	2		382	954	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426645	47426645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	816	401	1	ENST00000377045.4:c.890G>A	p.Arg297Gln	p.R297Q	ENST00000377045	NM_001654.4	297	cGg/cAg	10/16	0.759992070737206	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.759992070737206	2		402	995	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636739	176636739	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	158	264	0	ENST00000439151.2:c.1339A>C	p.Ile447Leu	p.I447L	ENST00000439151	NM_022455.4	447	Atc/Ctc	5/23	1	2	FACETS	0.83	0.766	0.896	0.83	0.766	0.896	CLONAL	1	TRUE	1	0.759992070737206	2		264	501	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486845	56486845	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	276	475	0	ENST00000267101.3:c.1259G>C	p.Gly420Ala	p.G420A	ENST00000267101	NM_001982.3	420	gGc/gCc	11/28	1	2	FACETS	0.85	0.8	0.9	0.85	0.8	0.9	CLONAL	1	TRUE	1	0.759992070737206	2		475	855	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428258	33428258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782129	NA	P-0011074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	427	684	0	ENST00000345365.6:c.865G>A	p.Gly289Ser	p.G289S	ENST00000345365	NM_002878.3	289	Ggc/Agc	9/10	0.759992070737206	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.759992070737206	1		684	675	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0011126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	59	375	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.286525853487605	2		375	289	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	82	327	0	ENST00000269305.4:c.461del	p.Gly154AlafsTer16	p.G154Afs*16	ENST00000269305	NM_001126112.2	154	gGc/gc	5/11	1	2	FACETS	0.733	0.645	0.827	0.733	0.645	0.827	SUBCLONAL	1	FALSE	1	0.286525853487605	2		327	781	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947529	38947529	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	12	248	0	ENST00000357387.3:c.4151T>C	p.Leu1384Ser	p.L1384S	ENST00000357387	NM_152756.3	1384	tTa/tCa	32/38	0.286525853487605	1	FACETS	0.755	0.537	1	0.755	0.537	1	CLONAL	1	FALSE	0	0.286525853487605	1		248	95	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939715	76939715	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149249195	NA	P-0011126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	17	232	0	ENST00000373344.5:c.1033G>A	p.Ala345Thr	p.A345T	ENST00000373344	NM_000489.3	345	Gca/Aca	9/35	0.246793172830142	0	FACETS	1	0.817	1			1	CLONAL	1	FALSE	NA	0.286525853487605	0		232	78	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851793	134851793	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	95	345	0	ENST00000398015.3:c.1203del	p.Tyr402ThrfsTer46	p.Y402Tfs*46	ENST00000398015	NM_004441.4	400	aCc/ac	5/16	0.182509931175899	2	FACETS	1	0.949	1	0.555	0.495	0.619	CLONAL	1	FALSE	0	0.286525853487605	2		345	597	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112479	115112479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs912240752	NA	P-0011162-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	346	426	3	ENST00000257566.3:c.1261C>T	p.Arg421Trp	p.R421W	ENST00000257566	NM_016569.3	421	Cgg/Tgg	7/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.668025752170675	2		429	995	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591258	67591258	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011162-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	488	460	0	ENST00000274335.5:c.1756C>T	p.Gln586Ter	p.Q586*	ENST00000274335		586	Caa/Taa	13/15	0.668025752170675	2	FACETS	0.941	0.91	0.972	0.941	0.91	0.972	CLONAL	2	TRUE	0	0.668025752170675	2		460	776	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52685806	52685807	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0011162-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	183	539	0	ENST00000394830.3:c.665_666del	p.Ala222AspfsTer3	p.A222Dfs*3	ENST00000394830	NM_018313.4	222	gCA/g	7/30	0.668025752170675	1	FACETS	0.865	0.808	0.922	0.865	0.808	0.922	CLONAL	1	TRUE	0	0.668025752170675	1		539	422	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188256	10188257	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0011162-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	519	645	0	ENST00000256474.2:c.399_400del	p.Glu134IlefsTer9	p.E134Ifs*9	ENST00000256474	NM_000551.3	133	acTGaa/acaa	2/3	0.668025752170675	1	FACETS	0.991	0.954	1	0.991	0.954	1	CLONAL	1	TRUE	0	0.668025752170675	1		645	1044	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372149	55372149	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011162-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	102	153	0	ENST00000297316.4:c.839G>A	p.Gly280Asp	p.G280D	ENST00000297316	NM_022454.3	280	gGt/gAt	2/2	0.668025752170675	3	FACETS	1	0.936	1	0.525	0.473	0.579	CLONAL	1	TRUE	1	0.668025752170675	3		153	388	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602637	10602637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777523734	NA	P-0011198-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	53	468	0	ENST00000171111.5:c.941C>T	p.Thr314Met	p.T314M	ENST00000171111	NM_203500.1	314	aCg/aTg	3/6	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		468	735	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0011206-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	61	310	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.15	2		310	766	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420234	88420234	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011206-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	44	442	0	ENST00000360948.2:c.2452A>G	p.Lys818Glu	p.K818E	ENST00000360948	NM_001012338.2	818	Aag/Gag	19/19	1	2	FACETS	0.715	0.598	0.846	0.715	0.598	0.846	SUBCLONAL	1	TRUE	1	0.15	2		442	820	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123022468	123022469	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	CT	novel	NA	P-0011206-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	66	618	0	ENST00000355640.3:c.878-1_878delinsCT		p.X293_splice	ENST00000355640		293		3/7	1	2	FACETS	0.732	0.633	0.84	0.732	0.633	0.84	SUBCLONAL	1	TRUE	1	0.15	2		618	1202	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0011249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	65	292	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.0843660547144717	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		292	1013	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559852	29559852	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1555614972	NA	P-0011343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	179	293	0	ENST00000356175.3:c.3449C>G	p.Ser1150Ter	p.S1150*	ENST00000356175	NM_000267.3	1150	tCa/tGa	26/57	0.271339125198797	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.271339125198797	3		293	662	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0011343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	159	229	0	ENST00000269305.4:c.673-2A>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.271339125198797	3	FACETS	0.863	0.797	0.932	1	0.985	1	CLONAL	3	TRUE	1	0.271339125198797	3		229	514	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437245	220437245	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1174996687	NA	P-0011343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	184	477	0	ENST00000243786.2:c.149G>T	p.Gly50Val	p.G50V	ENST00000243786	NM_002191.3	50	gGt/gTt	1/2	0.184359604724587	5	FACETS	0.854	0.787	0.924	0.569	0.525	0.616	CLONAL	2	TRUE	2	0.271339125198797	5		477	1117	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628760	187628760	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	63	346	0	ENST00000441802.2:c.2222C>G	p.Ser741Cys	p.S741C	ENST00000441802	NM_005245.3	741	tCc/tGc	2/27	0.271339125198797	3	FACETS	0.815	0.705	0.935	0.408	0.352	0.468	CLONAL	1	TRUE	1	0.271339125198797	3		346	647	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740820	145740820	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	253	377	0	ENST00000428558.2:c.1280C>T	p.Ala427Val	p.A427V	ENST00000428558	NM_004260.3	427	gCt/gTt	7/22	0.271339125198797	7	FACETS	0.859	0.803	0.917			1	CLONAL	3	TRUE	NA	0.271339125198797	7		377	1214	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992626	72992626	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	110	442	1	ENST00000268489.5:c.1419G>T	p.Glu473Asp	p.E473D	ENST00000268489	NM_006885.3	473	gaG/gaT	2/10	0.225535865754966	4	FACETS	1	0.971	1	0.614	0.551	0.681	CLONAL	1	TRUE	2	0.271339125198797	4		443	839	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369245	40369245	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1349	136	498	0	ENST00000293328.3:c.1313A>T	p.Glu438Val	p.E438V	ENST00000293328	NM_012448.3	438	gAa/gTa	11/19	0.2705467107237	4	FACETS	0.858	0.778	0.944	0.215	0.194	0.236	CLONAL	1	TRUE	0	0.271339125198797	4		498	1485	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0011453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	51	310	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.807	0.685	0.941	0.807	0.685	0.941	CLONAL	1	TRUE	1	0.2	2		310	632	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682778	190682778	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	35	150	0	ENST00000441310.2:c.454C>A	p.Leu152Ile	p.L152I	ENST00000441310	NM_000534.4	152	Cta/Ata	5/13	1	2	FACETS	0.758	0.621	0.912	0.758	0.621	0.912	CLONAL	1	TRUE	1	0.2	2		150	462	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437792	52437792	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0011453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	107	567	0	ENST00000460680.1:c.1369A>T	p.Lys457Ter	p.K457*	ENST00000460680	NM_004656.3	457	Aag/Tag	13/17	1	2	FACETS	0.827	0.739	0.921	0.827	0.739	0.921	CLONAL	1	TRUE	1	0.2	2		567	1294	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610163	10610163	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	87	311	0	ENST00000171111.5:c.547A>C	p.Asn183His	p.N183H	ENST00000171111	NM_203500.1	183	Aat/Cat	2/6	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.2	2		311	857	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412038	63412038	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	55	366	0	ENST00000330258.3:c.1129G>A	p.Asp377Asn	p.D377N	ENST00000330258	NM_152424.3	377	Gat/Aat	2/2	1	1	FACETS	0.624	0.533	0.725	0.624	0.533	0.725	SUBCLONAL	1	TRUE	0	0.2	1		366	793	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437803	52437809	+	protein_altering_variant	In_Frame_Del	DEL	TTGAGCT	TTGAGCT	A	novel	NA	P-0011453-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	90	568	0	ENST00000460680.1:c.1352_1358delinsT	p.Lys451_Lys453delinsIle	p.K451_K453delinsI	ENST00000460680	NM_004656.3	451	aAGCTCAAa/aTa	13/17	1	2	FACETS	0.698	0.617	0.785	0.698	0.617	0.785	SUBCLONAL	1	TRUE	1	0.2	2		568	1289	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0011461-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	63	297	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.143811738282182	1	FACETS	0.727	0.628	0.835	0.727	0.628	0.835	SUBCLONAL	1	FALSE	0	0.203219336896893	1		297	766	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971000	21971000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011461-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	55	376	0	ENST00000304494.5:c.358G>T	p.Glu120Ter	p.E120*	ENST00000304494	NM_000077.4	120	Gag/Tag	2/3	1	2	FACETS	0.789	0.674	0.915	0.789	0.674	0.915	CLONAL	1	FALSE	1	0.203219336896893	2		376	686	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913381	NA	P-0011461-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	32	301	1	ENST00000304494.5:c.322G>T	p.Asp108Tyr	p.D108Y	ENST00000304494	NM_000077.4	108	Gat/Tat	2/3	1	2	FACETS	0.592	0.479	0.719	0.592	0.479	0.719	SUBCLONAL	1	FALSE	1	0.203219336896893	2		302	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578217	7578217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011461-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	67	488	0	ENST00000269305.4:c.632C>T	p.Thr211Ile	p.T211I	ENST00000269305	NM_001126112.2	211	aCt/aTt	6/11	0.143811738282182	1	FACETS	0.566	0.49	0.649	0.566	0.49	0.649	SUBCLONAL	1	FALSE	0	0.203219336896893	1		488	1046	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509082	66509082	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011461-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	52	235	0	ENST00000273854.3:c.245G>T	p.Gly82Val	p.G82V	ENST00000273854	NM_004439.5	82	gGg/gTg	2/18	1	2	FACETS	0.768	0.653	0.895	0.768	0.653	0.895	SUBCLONAL	1	FALSE	1	0.203219336896893	2		235	666	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342653	87342653	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011461-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	73	322	0	ENST00000277120.3:c.938C>A	p.Pro313Gln	p.P313Q	ENST00000277120		313	cCa/cAa	9/19	1	2	FACETS	0.837	0.731	0.953	0.837	0.731	0.953	CLONAL	1	FALSE	1	0.203219336896893	2		322	858	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138122	2138122	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011461-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	60	346	0	ENST00000219476.3:c.5142G>C	p.Gln1714His	p.Q1714H	ENST00000219476	NM_000548.3	1714	caG/caC	40/42	1	2	FACETS	0.789	0.679	0.91	0.789	0.679	0.91	CLONAL	1	FALSE	1	0.203219336896893	2		346	748	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41209121	41209121	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011461-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	190	490	0	ENST00000357654.3:c.5225A>T	p.Asn1742Ile	p.N1742I	ENST00000357654	NM_007294.3	1742	aAt/aTt	19/23	0.196439716990364	3	FACETS	0.851	0.785	0.92	0.851	0.785	0.92	CLONAL	2	FALSE	1	0.203219336896893	3		490	1210	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410441	63410441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011461-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	77	477	1	ENST00000330258.3:c.2726C>T	p.Ser909Phe	p.S909F	ENST00000330258	NM_152424.3	909	tCc/tTc	2/2	0.143811738282182	1	FACETS	0.726	0.636	0.823	0.726	0.636	0.823	SUBCLONAL	1	FALSE	0	0.203219336896893	1		478	938	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136298	2136303	+	inframe_deletion	In_Frame_Del	DEL	GGACAA	GGACAA	-	novel	NA	P-0011461-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	61	407	0	ENST00000219476.3:c.4769_4774del	p.Asp1590_Lys1591del	p.D1590_K1591del	ENST00000219476	NM_000548.3	1589	ccGGACAAg/ccg	37/42	1	2	FACETS	0.646	0.555	0.744	0.646	0.555	0.744	SUBCLONAL	1	FALSE	1	0.203219336896893	2		407	930	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0011542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	790	426	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	0.487490938881349	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	4	TRUE	0	0.487490938881349	4		426	1167	SUCCESS
APC	324	MSKCC	GRCh37	5	112175582	112175582	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	134	367	0	ENST00000257430.4:c.4291A>G	p.Met1431Val	p.M1431V	ENST00000257430	NM_000038.5	1431	Atg/Gtg	16/16	0.47409712574907	4	FACETS	0.847	0.769	0.93	0.424	0.384	0.465	CLONAL	1	TRUE	2	0.487490938881349	4		367	965	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs760043106	NA	P-0011542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	314	347	0	ENST00000269305.4:c.584T>G	p.Ile195Ser	p.I195S	ENST00000269305	NM_001126112.2	195	aTc/aGc	6/11	0.487490938881349	2	FACETS	0.957	0.91	1	0.957	0.91	1	CLONAL	2	TRUE	0	0.487490938881349	2		347	673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579536	7579536	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012089-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	120	395	2	ENST00000269305.4:c.151del	p.Glu51AsnfsTer72	p.E51Nfs*72	ENST00000269305	NM_001126112.2	51	Gaa/aa	4/11	0.368960153154994	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.378879631927851	1		397	481	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0012089-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	439	304	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.378879631927851	5	FACETS	0.959	0.92	0.999	0.959	0.92	0.999	CLONAL	4	TRUE	1	0.378879631927851	5		304	947	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0012126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	139	308	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.192495031440177	3	FACETS	1	0.934	1	0.684	0.625	0.745	CLONAL	2	TRUE	0	0.251331540466813	3		308	607	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027161	49027161	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012126-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	118	616	0	ENST00000267163.4:c.1730del	p.Lys577ArgfsTer34	p.K577Rfs*34	ENST00000267163	NM_000321.2	576	tcA/tc	18/27	0.22527977802972	2	FACETS	0.837	0.758	0.92	0.837	0.758	0.92	CLONAL	2	TRUE	0	0.251331540466813	2		616	561	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748155	72748155	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	244	993	0	ENST00000357731.5:c.23A>T	p.Gln8Leu	p.Q8L	ENST00000357731	NM_173808.2	8	cAg/cTg	1/7	1	2	FACETS	0.686	0.64	0.734	0.686	0.64	0.734	SUBCLONAL	1	TRUE	1	0.576626249948544	2		993	1233	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059226	47059226	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	110	430	0	ENST00000409792.3:c.7435T>G	p.Ser2479Ala	p.S2479A	ENST00000409792	NM_014159.6	2479	Tcc/Gcc	20/21	1	2	FACETS	0.772	0.697	0.851	0.772	0.697	0.851	SUBCLONAL	1	TRUE	1	0.576626249948544	2		430	494	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249269	133249269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1279012935	NA	P-0012182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	179	604	0	ENST00000320574.5:c.1630G>A	p.Val544Met	p.V544M	ENST00000320574	NM_006231.2	544	Gtg/Atg	15/49	1	2	FACETS	0.796	0.735	0.859	0.796	0.735	0.859	SUBCLONAL	1	TRUE	1	0.576626249948544	2		604	780	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396155	396155	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	295	417	0	ENST00000262320.3:c.871G>T	p.Glu291Ter	p.E291*	ENST00000262320	NM_003502.3	291	Gag/Tag	2/11	0.576626249948544	2	FACETS	0.967	0.922	1	0.967	0.922	1	CLONAL	2	TRUE	0	0.576626249948544	2		417	529	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266106	+	inframe_deletion	In_Frame_Del	DEL	ACTCTGGAA	ACTCTGGAA	-	novel	NA	P-0012182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	128	528	0	ENST00000349496.5:c.95_103del	p.Asp32_Ile35delinsVal	p.D32_I35delinsV	ENST00000349496	NM_001904.3	32	gACTCTGGAAtc/gtc	3/15	1	2	FACETS	0.607	0.551	0.667	0.607	0.551	0.667	SUBCLONAL	1	TRUE	1	0.576626249948544	2		528	731	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574006	7574012	+	frameshift_variant	Frame_Shift_Del	DEL	ACATCTC	ACATCTC	-	novel	NA	P-0012314-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	122	654	0	ENST00000269305.4:c.1015_1021del	p.Glu339SerfsTer4	p.E339Sfs*4	ENST00000269305	NM_001126112.2	339	GAGATGTtc/tc	10/11	1	2	FACETS	0.993	0.896	1	0.993	0.896	1	CLONAL	1	TRUE	1	0.231590617875272	2		654	1061	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578529	7578529	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs780442292	NA	P-0012418-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	271	543	0	ENST00000269305.4:c.401T>G	p.Phe134Cys	p.F134C	ENST00000269305	NM_001126112.2	134	tTt/tGt	5/11	0.311828983109165	3	FACETS	1	0.946	1	0.668	0.63	0.707	CLONAL	2	TRUE	0	0.46377021405487	3		543	718	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052629	42052629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012418-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	493	906	1	ENST00000219905.7:c.7300C>T	p.Arg2434Trp	p.R2434W	ENST00000219905	NM_001164273.1	2434	Cgg/Tgg	20/24	0.46377021405487	3	FACETS	0.903	0.864	0.943	0.903	0.864	0.943	CLONAL	2	TRUE	1	0.46377021405487	3		907	1450	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967269	134967269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749666684	NA	P-0012418-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	159	580	2	ENST00000398015.3:c.2608C>T	p.Arg870Trp	p.R870W	ENST00000398015	NM_004441.4	870	Cgg/Tgg	14/16	0.46377021405487	3	FACETS	0.998	0.916	1	0.499	0.458	0.543	CLONAL	1	TRUE	1	0.46377021405487	3		582	846	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265709	41266219	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	In_Frame_Del	DEL	TCCTCCTAATGGCTTGGTGAAATAGCAAACAAGCCACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAG	TCCTCCTAATGGCTTGGTGAAATAGCAAACAAGCCACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAG	-	novel	NA	P-0012418-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	179	100	0	ENST00000349496.5:c.13+141_220del		p.A5_Q72del	ENST00000349496	NM_001904.3	5		3/15	0.46377021405487	3	FACETS	0.951	0.905	0.995	1	0.992	1	CLONAL	4	TRUE	0	0.46377021405487	3		100	250	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254586	46254586	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012418-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	297	536	0	ENST00000334344.6:c.4776del	p.Asn1592LysfsTer34	p.N1592Kfs*34	ENST00000334344	NM_152641.2	1592	aaC/aa	16/21	0.310768192832543	3	FACETS	1	0.967	1	0.687	0.65	0.724	CLONAL	2	TRUE	0	0.46377021405487	3		536	766	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015390	176015390	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	139	696	0	ENST00000367669.3:c.1348T>C	p.Tyr450His	p.Y450H	ENST00000367669	NM_022457.5	450	Tat/Cat	12/20	1	2	FACETS	0.667	0.607	0.731	0.667	0.607	0.731	SUBCLONAL	1	TRUE	1	0.419064612761114	2		696	994	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563461	87563461	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1211018594	NA	P-0012513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	55	547	0	ENST00000277120.3:c.1849G>A	p.Val617Ile	p.V617I	ENST00000277120		617	Gtc/Atc	16/19	1	2	FACETS	0.446	0.381	0.517	0.446	0.381	0.517	SUBCLONAL	1	TRUE	1	0.419064612761114	2		547	589	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117843	108117843	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	42	339	0	ENST00000278616.4:c.1054A>C	p.Ile352Leu	p.I352L	ENST00000278616	NM_000051.3	352	Atc/Ctc	8/63	0.41367146395631	1	FACETS	0.461	0.386	0.543	0.461	0.386	0.543	SUBCLONAL	1	TRUE	0	0.419064612761114	1		339	344	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435219	49435219	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	106	392	0	ENST00000301067.7:c.6334G>T	p.Ala2112Ser	p.A2112S	ENST00000301067	NM_003482.3	2112	Gca/Tca	31/54	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.419064612761114	2		392	422	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487947	56487947	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	69	675	0	ENST00000267101.3:c.1678G>C	p.Glu560Gln	p.E560Q	ENST00000267101	NM_001982.3	560	Gag/Cag	14/28	1	2	FACETS	0.363	0.315	0.415	0.363	0.315	0.415	SUBCLONAL	1	TRUE	1	0.419064612761114	2		675	908	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624231	89624252	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCCATCATCAAAGAGATCGT	CAGCCATCATCAAAGAGATCGT	-	novel	NA	P-0012513-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	68	96	0	ENST00000371953.3:c.5_26del	p.Thr2IlefsTer15	p.T2Ifs*15	ENST00000371953	NM_000314.4	2	aCAGCCATCATCAAAGAGATCGTt/at	1/9	1	2	FACETS	1	0.947	1	1	0.985	1	CLONAL	2	TRUE	1	0.419064612761114	2		96	148	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012549-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	236	321	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		321	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0012685-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	86	790	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	1	2	FACETS	0.835	0.737	0.94	0.835	0.737	0.94	CLONAL	1	TRUE	1	0.21	2		790	981	SUCCESS
APC	324	MSKCC	GRCh37	5	112175174	112175174	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012685-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	40	155	0	ENST00000257430.4:c.3883G>T	p.Glu1295Ter	p.E1295*	ENST00000257430	NM_000038.5	1295	Gaa/Taa	16/16	1	2	FACETS	0.972	0.809	1	0.972	0.809	1	CLONAL	1	TRUE	1	0.21	2		155	392	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526071	189526071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012685-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	81	353	1	ENST00000264731.3:c.335C>T	p.Thr112Met	p.T112M	ENST00000264731	NM_003722.4	112	aCg/aTg	4/14	1	2	FACETS	0.782	0.688	0.885	0.782	0.688	0.885	SUBCLONAL	1	TRUE	1	0.21	2		354	986	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562477	21562477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757658067	NA	P-0012731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	14	105	0	ENST00000382592.4:c.1442C>T	p.Ala481Val	p.A481V	ENST00000382592	NM_014572.2	481	gCg/gTg	4/8	1	2	FACETS	0.88	0.644	1	0.88	0.644	1	CLONAL	1	TRUE	1	0.315190497575826	2		105	101	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012812-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	23	292	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.944	0.739	1	0.944	0.739	1	CLONAL	1	FALSE	1	0.224521149185098	2		292	217	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0012812-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	93	308	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.224521149185098	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	0	0.224521149185098	1		308	497	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022277	31022277	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1486082302	NA	P-0012812-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	89	503	0	ENST00000375687.4:c.1762C>T	p.Gln588Ter	p.Q588*	ENST00000375687	NM_015338.5	588	Cag/Tag	13/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.224521149185098	2		503	646	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098358	108098358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs7112053	NA	P-0012923-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	186	290	0	ENST00000278616.4:c.7C>G	p.Leu3Val	p.L3V	ENST00000278616	NM_000051.3	3	Cta/Gta	2/63	1	2	FACETS	0.909	0.85	0.969	1	0.993	1	CLONAL	2	TRUE	1	0.471354526556067	2		290	434	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012965-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	197	292	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.427049556273317	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.454030951909768	3		292	505	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0012965-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	33	222	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.782	0.643	0.934	0.782	0.643	0.934	CLONAL	1	TRUE	1	0.454030951909768	2		222	186	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0012965-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	64	480	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.450874925971669	3	FACETS	0.898	0.782	1	0.449	0.391	0.512	CLONAL	1	TRUE	1	0.454030951909768	3		480	385	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509769	106509769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1178692056	NA	P-0012965-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	97	468	0	ENST00000359195.3:c.1763C>T	p.Ala588Val	p.A588V	ENST00000359195	NM_002649.2	588	gCa/gTa	2/11	0.450874925971669	3	FACETS	0.94	0.84	1	0.47	0.42	0.523	CLONAL	1	TRUE	1	0.454030951909768	3		468	558	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857252	78857252	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760863690	NA	P-0012965-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	79	386	1	ENST00000306801.3:c.1618G>A	p.Ala540Thr	p.A540T	ENST00000306801	NM_020761.2	540	Gcc/Acc	15/34	0.450874925971669	3	FACETS	0.753	0.663	0.849	0.377	0.331	0.425	SUBCLONAL	1	TRUE	1	0.454030951909768	3		387	567	SUCCESS
APC	324	MSKCC	GRCh37	5	112175750	112175750	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012965-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	107	275	0	ENST00000257430.4:c.4459del	p.Thr1487LeufsTer20	p.T1487Lfs*20	ENST00000257430	NM_000038.5	1487	Act/ct	16/16	0.450874925971669	3	FACETS	0.856	0.776	0.938	0.856	0.776	0.938	CLONAL	2	TRUE	1	0.454030951909768	3		275	338	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577112	7577112	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1131691029	NA	P-0012966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	463	634	0	ENST00000269305.4:c.826G>C	p.Ala276Pro	p.A276P	ENST00000269305	NM_001126112.2	276	Gcc/Ccc	8/11	0.514349268251491	2	FACETS	0.997	0.958	1	0.997	0.958	1	CLONAL	2	TRUE	0	0.514349268251491	2		634	903	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155137	106155137	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	415	522	0	ENST00000380013.4:c.38G>C	p.Arg13Thr	p.R13T	ENST00000380013	NM_001127208.2	13	aGa/aCa	3/11	0.514349268251491	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.514349268251491	2		522	783	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426057	47426057	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012966-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	257	775	1	ENST00000377045.4:c.577G>A	p.Asp193Asn	p.D193N	ENST00000377045	NM_001654.4	193	Gac/Aac	7/16	0.359966741300907	3	FACETS	1	0.967	1	0.527	0.492	0.562	CLONAL	1	TRUE	1	0.514349268251491	3		776	1193	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0013101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	186	844	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.904	0.836	0.974	0.904	0.836	0.974	CLONAL	1	TRUE	1	0.508800922394168	2		844	809	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0013101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	369	568	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	0.446919955555926	3	FACETS	0.888	0.851	0.925	0.888	0.851	0.925	CLONAL	3	TRUE	0	0.508800922394168	3		568	683	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448565	89448565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	360	782	1	ENST00000336596.2:c.1529G>A	p.Arg510Gln	p.R510Q	ENST00000336596	NM_005233.5	510	cGa/cAa	7/17	0.491675236207729	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.508800922394168	4		783	972	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952117	178952117	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	214	560	0	ENST00000263967.3:c.3172A>T	p.Ile1058Phe	p.I1058F	ENST00000263967	NM_006218.2	1058	Atc/Ttc	21/21	0.284822405882618	6	FACETS	1	0.98	1	0.752	0.701	0.805	INDETERMINATE	2	TRUE	3	0.508800922394168	6		560	752	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741782	145742480	+	splice_donor_variant,splice_acceptor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	CTGAAGCCTCTGGGCCCTGGGAGCCAGCACCAGGACCAAGGACAGCCGACTCACCAGGGATCAGAAGTTGTGATTCCTCTGAGCCTAGATCAGGCCTGCAGGCTTTGGGGGCCCCCAGAAAATCTGGGACCTCACTGTGACATCGCTGTAACCAGCCAGGATCTAGGGAGCCCAGCCGCTGGCTCAGGGATGCCTGCAGATGCTGGAGCCGGCCTGGCCTTGGCTGGGGCTCAGGGAGCTGTGGAGGCTCATCACTGACTTTTTCTGCAAAGGAGGGGACAGGCCCTGTACCTGGGGGCTTTGGGGTGGATGCCTTAGATGAGGCTCTTCCTAGAGGCCACGGTCTGCGGCCCAGGGCTGGTCCGGCCTGGGAGGGGAACAACAGAACAGCAGGAGGAACTCAGGCCCCTGAGCTACTGTAGACTCTAAAACCTACCTGAGTCCCCACGCTCAATTGTAGAGCAGGCTAATTAGCACAAGGCTGGACTAGAAAGGGAGTCAAGGGCGAAGGCCCCGAGAAGCTCCCTGAAGACTCGTGCCCTGGTTGGCACAGGGGCCCGTGCCTGTCTGTGTGGAAAAAATGACAAGAGGGCGACCCGGACCGGAAGCAGCTGTGGACCTAGCGTGGACTCACTGCCTGCCCACTCCTCACCTGCAGGGTGCCTTTCAGATTGGCCTTGAGCCGCTGCCCGTAGTCCG	CTGAAGCCTCTGGGCCCTGGGAGCCAGCACCAGGACCAAGGACAGCCGACTCACCAGGGATCAGAAGTTGTGATTCCTCTGAGCCTAGATCAGGCCTGCAGGCTTTGGGGGCCCCCAGAAAATCTGGGACCTCACTGTGACATCGCTGTAACCAGCCAGGATCTAGGGAGCCCAGCCGCTGGCTCAGGGATGCCTGCAGATGCTGGAGCCGGCCTGGCCTTGGCTGGGGCTCAGGGAGCTGTGGAGGCTCATCACTGACTTTTTCTGCAAAGGAGGGGACAGGCCCTGTACCTGGGGGCTTTGGGGTGGATGCCTTAGATGAGGCTCTTCCTAGAGGCCACGGTCTGCGGCCCAGGGCTGGTCCGGCCTGGGAGGGGAACAACAGAACAGCAGGAGGAACTCAGGCCCCTGAGCTACTGTAGACTCTAAAACCTACCTGAGTCCCCACGCTCAATTGTAGAGCAGGCTAATTAGCACAAGGCTGGACTAGAAAGGGAGTCAAGGGCGAAGGCCCCGAGAAGCTCCCTGAAGACTCGTGCCCTGGTTGGCACAGGGGCCCGTGCCTGTCTGTGTGGAAAAAATGACAAGAGGGCGACCCGGACCGGAAGCAGCTGTGGACCTAGCGTGGACTCACTGCCTGCCCACTCCTCACCTGCAGGGTGCCTTTCAGATTGGCCTTGAGCCGCTGCCCGTAGTCCG	-	novel	NA	P-0013101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1925	105	767	0	ENST00000428558.2:c.309_722del		p.X103_splice	ENST00000428558	NM_004260.3	103	cCGGACTACGGGCAGCGGCTCAAGGCCAATCTGAAAGGCACCCTGCAGGTGAGGAGTGGGCAGGCAGTGAGTCCACGCTAGGTCCACAGCTGCTTCCGGTCCGGGTCGCCCTCTTGTCATTTTTTCCACACAGACAGGCACGGGCCCCTGTGCCAACCAGGGCACGAGTCTTCAGGGAGCTTCTCGGGGCCTTCGCCCTTGACTCCCTTTCTAGTCCAGCCTTGTGCTAATTAGCCTGCTCTACAATTGAGCGTGGGGACTCAGGTAGGTTTTAGAGTCTACAGTAGCTCAGGGGCCTGAGTTCCTCCTGCTGTTCTGTTGTTCCCCTCCCAGGCCGGACCAGCCCTGGGCCGCAGACCGTGGCCTCTAGGAAGAGCCTCATCTAAGGCATCCACCCCAAAGCCCCCAGGTACAGGGCCTGTCCCCTCCTTTGCAGAAAAAGTCAGTGATGAGCCTCCACAGCTCCCTGAGCCCCAGCCAAGGCCAGGCCGGCTCCAGCATCTGCAGGCATCCCTGAGCCAGCGGCTGGGCTCCCTAGATCCTGGCTGGTTACAGCGATGTCACAGTGAGGTCCCAGATTTTCTGGGGGCCCCCAAAGCCTGCAGGCCTGATCTAGGCTCAGAGGAATCACAACTTCTGATCCCTGGTGAGTCGGCTGTCCTTGGTCCTGGTGCTGGCTCCCAGGGCCCAGAGGCTTCAGcc/ccc	4-5/22	0.508800922394168	8	FACETS	0.514	0.458	0.574			1	SUBCLONAL	1	TRUE	NA	0.508800922394168	8		767	2030	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	77	305	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.986	0.865	1	1	0.982	1	CLONAL	2	TRUE	1	0.1	2		305	781	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9770524	9770524	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	63	611	1	ENST00000377346.4:c.11G>T	p.Gly4Val	p.G4V	ENST00000377346	NM_005026.3	4	gGg/gTg	3/24	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.1	2		612	998	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143171	30143171	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	26	359	0	ENST00000389048.3:c.355G>A	p.Glu119Lys	p.E119K	ENST00000389048	NM_004304.4	119	Gag/Aag	1/29	1	2	FACETS	1	0.823	1	1	0.823	1	CLONAL	1	TRUE	1	0.1	2		359	497	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149447873	149447873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	68	728	1	ENST00000286301.3:c.1531G>T	p.Asp511Tyr	p.D511Y	ENST00000286301	NM_005211.3	511	Gat/Tat	11/22	0.148527312937664	3	FACETS	1	0.967	1	0.693	0.601	0.793	CLONAL	1	TRUE	1	0.1	3		729	1031	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597539	28597539	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	91	699	0	ENST00000241453.7:c.2366T>C	p.Leu789Pro	p.L789P	ENST00000241453	NM_004119.2	789	cTt/cCt	19/24	1	2	FACETS	0.791	0.7	0.889	1	0.98	1	SUBCLONAL	2	TRUE	1	0.1	2		699	1150	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434777	110434777	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	68	489	0	ENST00000375856.3:c.3624G>T	p.Gln1208His	p.Q1208H	ENST00000375856	NM_003749.2	1208	caG/caT	1/2	1	2	FACETS	0.999	0.868	1	1	0.98	1	CLONAL	2	TRUE	1	0.1	2		489	681	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934260	81934260	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	91	699	0	ENST00000359376.3:c.1237C>A	p.Gln413Lys	p.Q413K	ENST00000359376	NM_002661.3	413	Caa/Aaa	14/33	1	2	FACETS	0.885	0.784	0.994	1	0.983	1	CLONAL	2	TRUE	1	0.1	2		699	1028	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112162	115112163	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0013233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	58	502	0	ENST00000257566.3:c.1577_1578delinsAT	p.Ala526Asp	p.A526D	ENST00000257566	NM_016569.3	526	gCC/gAT	7/8	1	2	FACETS	0.784	0.672	0.906	1	0.969	1	CLONAL	2	TRUE	1	0.1	2		502	740	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	340	292	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	0.996	1	CLONAL	2	TRUE	1	0.26568526912245	2		292	1129	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0013263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	137	503	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.946	0.859	1	0.946	0.859	1	CLONAL	1	TRUE	1	0.26568526912245	2		503	1090	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0013263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	143	369	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.915	0.832	1	0.915	0.832	1	CLONAL	1	TRUE	1	0.26568526912245	2		369	1177	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0013263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	100	660	1	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.767	0.683	0.855	0.767	0.683	0.855	SUBCLONAL	1	TRUE	1	0.26568526912245	2		661	982	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152491	56152491	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561183082	NA	P-0013263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	74	412	1	ENST00000399503.3:c.547C>T	p.Arg183Ter	p.R183*	ENST00000399503	NM_005921.1	183	Cga/Tga	2/20	1	2	FACETS	0.894	0.783	1	0.894	0.783	1	CLONAL	1	TRUE	1	0.26568526912245	2		413	623	SUCCESS
APC	324	MSKCC	GRCh37	5	112175245	112175245	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	85	415	0	ENST00000257430.4:c.3954del	p.Pro1319LeufsTer2	p.P1319Lfs*2	ENST00000257430	NM_000038.5	1318	gaT/ga	16/16	1	2	FACETS	0.962	0.851	1	0.962	0.851	1	CLONAL	1	TRUE	1	0.26568526912245	2		415	665	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271228	153271228	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs866145254	NA	P-0013263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	168	505	0	ENST00000281708.4:c.550G>T	p.Gly184Ter	p.G184*	ENST00000281708	NM_033632.3	184	Gga/Tga	3/12	0.242191087154371	2	FACETS	1	0.989	1	0.747	0.687	0.81	CLONAL	1	TRUE	0	0.26568526912245	2		505	846	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478928	56478928	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	138	858	0	ENST00000267101.3:c.384C>G	p.Ser128Arg	p.S128R	ENST00000267101	NM_001982.3	128	agC/agG	3/28	1	2	FACETS	0.924	0.839	1	0.924	0.839	1	CLONAL	1	TRUE	1	0.26568526912245	2		858	1124	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523522	41523626	+	inframe_deletion	In_Frame_Del	DEL	CAGGCCTGGTGACTCCAGTTGCCCAAGGGATGGGTTCTGGAGCACATACAGCTGATCCAGAGAAGCGCAAGCTCATCCAGCAGCAGCTTGTTCTCCTTTTGCATG	CAGGCCTGGTGACTCCAGTTGCCCAAGGGATGGGTTCTGGAGCACATACAGCTGATCCAGAGAAGCGCAAGCTCATCCAGCAGCAGCTTGTTCTCCTTTTGCATG	-	novel	NA	P-0013263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	248	497	0	ENST00000263253.7:c.939_1043del	p.Gly314_Ala348del	p.G314_A348del	ENST00000263253	NM_001429.3	313	cCAGGCCTGGTGACTCCAGTTGCCCAAGGGATGGGTTCTGGAGCACATACAGCTGATCCAGAGAAGCGCAAGCTCATCCAGCAGCAGCTTGTTCTCCTTTTGCATGct/cct	4/31	0.242191087154371	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.26568526912245	2		497	773	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	483	292	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.717938094395349	3	FACETS	0.918	0.884	0.951	0.918	0.884	0.951	CLONAL	2	TRUE	1	0.838318994325558	3		292	891	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0013277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	105	480	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.457762404526986	3	FACETS	0.509	0.456	0.565	0.17	0.152	0.189	INDETERMINATE	1	TRUE	0	0.838318994325558	3		480	698	SUCCESS
APC	324	MSKCC	GRCh37	5	112175513	112175513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	513	550	0	ENST00000257430.4:c.4222G>T	p.Glu1408Ter	p.E1408*	ENST00000257430	NM_000038.5	1408	Gaa/Taa	16/16	0.457762404526986	3	FACETS	1	0.996	1	0.801	0.778	0.823	INDETERMINATE	2	TRUE	0	0.838318994325558	3		550	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587780070	NA	P-0013277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	434	386	0	ENST00000269305.4:c.535C>G	p.His179Asp	p.H179D	ENST00000269305	NM_001126112.2	179	Cat/Gat	5/11	0.838318994325558	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.838318994325558	2		386	496	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481823	56481823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1296453299	NA	P-0013277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	216	732	0	ENST00000267101.3:c.751G>A	p.Asp251Asn	p.D251N	ENST00000267101	NM_001982.3	251	Gac/Aac	7/28	0.821223933540229	3	FACETS	0.675	0.627	0.725	0.338	0.313	0.363	SUBCLONAL	1	TRUE	1	0.838318994325558	3		732	1083	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440081	220440081	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1464	161	1079	0	ENST00000243786.2:c.934C>T	p.Pro312Ser	p.P312S	ENST00000243786	NM_002191.3	312	Cct/Tct	2/2	0.730817696899847	4	FACETS	0.435	0.397	0.474	0.145	0.132	0.158	SUBCLONAL	1	TRUE	1	0.838318994325558	4		1079	1625	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504360	186504360	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs755032307	NA	P-0013277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	171	504	0	ENST00000323963.5:c.697A>G	p.Ile233Val	p.I233V	ENST00000323963		233	Att/Gtt	7/11	0.838318994325558	3	FACETS	0.731	0.673	0.791	0.366	0.336	0.396	SUBCLONAL	1	TRUE	1	0.838318994325558	3		504	792	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911478	32911478	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2173	481	1206	0	ENST00000380152.3:c.2986C>G	p.Leu996Val	p.L996V	ENST00000380152		996	Ctc/Gtc	11/27	0.756205943178667	5	FACETS	0.976	0.929	1	0.325	0.309	0.342	CLONAL	1	TRUE	2	0.838318994325558	5		1206	2654	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772278	68772278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	210	689	0	ENST00000261769.5:c.127C>T	p.Arg43Trp	p.R43W	ENST00000261769	NM_004360.3	43	Cgg/Tgg	2/16	0.838318994325558	3	FACETS	0.819	0.762	0.878	0.41	0.381	0.439	CLONAL	1	TRUE	1	0.838318994325558	3		689	868	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0013370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	312	366	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	0.468377085190722	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.684920744304481	1		366	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578509	7578509	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519978	NA	P-0013370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	765	690	1	ENST00000269305.4:c.421T>C	p.Cys141Arg	p.C141R	ENST00000269305	NM_001126112.2	141	Tgc/Cgc	5/11	0.684920744304481	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.684920744304481	2		691	936	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512356	38512356	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	101	598	0	ENST00000254066.5:c.1267C>G	p.Leu423Val	p.L423V	ENST00000254066	NM_000964.3	423	Ctg/Gtg	9/9	1	2	FACETS	0.455	0.407	0.506	0.455	0.407	0.506	SUBCLONAL	1	TRUE	1	0.684920744304481	2		598	648	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369209	40369209	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1433	195	1104	1	ENST00000293328.3:c.1349T>C	p.Val450Ala	p.V450A	ENST00000293328	NM_012448.3	450	gTt/gCt	11/19	1	2	FACETS	0.35	0.322	0.379	0.35	0.322	0.379	SUBCLONAL	1	TRUE	1	0.684920744304481	2		1105	1628	SUCCESS
APC	324	MSKCC	GRCh37	5	112175322	112175322	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	213	488	0	ENST00000257430.4:c.4031del	p.Ser1344Ter	p.S1344*	ENST00000257430	NM_000038.5	1344	tCa/ta	16/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.684920744304481	2		488	560	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813053	76813053	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	576	490	0	ENST00000373344.5:c.6568del	p.Val2190LeufsTer12	p.V2190Lfs*12	ENST00000373344	NM_000489.3	2190	Gtt/tt	30/35	1	1	FACETS		NA	1	1	0.998	1	NA	2	TRUE	0	0.684920744304481	1		490	724	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131972881	131972881	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1554100868	NA	P-0013442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	133	434	0	ENST00000265335.6:c.3464A>G	p.Tyr1155Cys	p.Y1155C	ENST00000265335		1155	tAt/tGt	22/25	1	2	FACETS	0.649	0.592	0.708	0.649	0.592	0.708	SUBCLONAL	1	TRUE	1	0.75336277955888	2		434	544	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888199	112888199	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121918454	NA	P-0013603-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	33	514	0	ENST00000351677.2:c.215C>G	p.Ala72Gly	p.A72G	ENST00000351677	NM_002834.3	72	gCc/gGc	3/16	1	2	FACETS	0.538	0.436	0.652	0.538	0.436	0.652	SUBCLONAL	1	TRUE	1	0.18	2		514	682	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557277	29557277	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs1060500273	NA	P-0013603-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	41	333	0	ENST00000356175.3:c.2991-1G>C		p.X997_splice	ENST00000356175	NM_000267.3	997			1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.18	2		333	371	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191480	10191480	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913346	NA	P-0013728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	119	383	1	ENST00000256474.2:c.473T>A	p.Leu158Gln	p.L158Q	ENST00000256474	NM_000551.3	158	cTg/cAg	3/3	0.396180993668984	1	FACETS	0.997	0.905	1	0.997	0.905	1	CLONAL	1	FALSE	0	0.396180993668984	1		384	483	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239741	53239741	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	309	403	0	ENST00000375401.3:c.1601G>C	p.Trp534Ser	p.W534S	ENST00000375401	NM_004187.3	534	tGg/tCg	12/26	0.277452108649701	2	FACETS	1	0.963	1			1	CLONAL	3	FALSE	NA	0.396180993668984	2		403	516	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761014	59761017	+	frameshift_variant	Frame_Shift_Del	DEL	ATAG	ATAG	-	rs778664039	NA	P-0013731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	392	727	0	ENST00000259008.2:c.3390_3393del	p.Tyr1131LeufsTer18	p.Y1131Lfs*18	ENST00000259008	NM_032043.2	1130	atCTAT/at	20/20	0.304790052891503	3	FACETS	1	0.971	1	0.516	0.49	0.543	INDETERMINATE	1	FALSE	1	0.694241785110109	3		727	1474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0013731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	219	750	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.694241785110109	1	FACETS	0.603	0.564	0.644	0.603	0.564	0.644	SUBCLONAL	1	FALSE	0	0.694241785110109	1		750	683	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375002	45375002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	283	514	0	ENST00000262160.6:c.841G>A	p.Glu281Lys	p.E281K	ENST00000262160	NM_005901.5	281	Gaa/Aaa	8/11	0.694241785110109	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	0	0.694241785110109	1		514	518	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043904	180043904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56082504	NA	P-0013731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	495	888	3	ENST00000261937.6:c.3092G>A	p.Arg1031Gln	p.R1031Q	ENST00000261937	NM_182925.4	1031	cGa/cAa	22/30	1	2	FACETS	0.979	0.936	1	0.979	0.936	1	CLONAL	1	FALSE	1	0.694241785110109	2		891	1457	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120666	94120666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	628	1149	0	ENST00000369303.4:c.385G>A	p.Glu129Lys	p.E129K	ENST00000369303	NM_004440.3	129	Gaa/Aaa	3/17	1	2	FACETS	0.984	0.946	1	0.984	0.946	1	CLONAL	1	FALSE	1	0.694241785110109	2		1149	1839	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572904	41572904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	455	674	0	ENST00000263253.7:c.5189C>T	p.Ser1730Phe	p.S1730F	ENST00000263253	NM_001429.3	1730	tCt/tTt	31/31	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	FALSE	1	0.694241785110109	2		674	1075	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495393	56495393	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	472	815	3	ENST00000267101.3:c.3583G>A	p.Glu1195Lys	p.E1195K	ENST00000267101	NM_001982.3	1195	Gag/Aag	28/28	1	2	FACETS	0.964	0.921	1	0.964	0.921	1	CLONAL	1	FALSE	1	0.694241785110109	2		818	1411	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495402	56495402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	463	815	2	ENST00000267101.3:c.3592G>A	p.Glu1198Lys	p.E1198K	ENST00000267101	NM_001982.3	1198	Gaa/Aaa	28/28	1	2	FACETS	0.941	0.898	0.984	0.941	0.898	0.984	CLONAL	1	FALSE	1	0.694241785110109	2		817	1418	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562856	95562856	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	125	410	0	ENST00000393063.1:c.4401C>G	p.Ile1467Met	p.I1467M	ENST00000393063	NM_030621.3	1467	atC/atG	24/28	0.331645975766744	1	FACETS	0.372	0.337	0.408	0.372	0.337	0.408	INDETERMINATE	1	FALSE	0	0.694241785110109	1		410	632	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646702	23646702	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555461427	NA	P-0013731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	168	641	0	ENST00000261584.4:c.1165C>G	p.Leu389Val	p.L389V	ENST00000261584	NM_024675.3	389	Ctt/Gtt	4/13	1	2	FACETS	0.432	0.396	0.47	0.432	0.396	0.47	SUBCLONAL	1	FALSE	1	0.694241785110109	2		641	1120	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796511	42796511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	177	533	0	ENST00000575354.2:c.3068C>T	p.Ser1023Phe	p.S1023F	ENST00000575354	NM_015125.3	1023	tCc/tTc	13/20	1	2	FACETS	0.572	0.527	0.619	0.572	0.527	0.619	SUBCLONAL	1	FALSE	1	0.694241785110109	2		533	891	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182057	38182057	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	277	482	0	ENST00000396334.3:c.681G>C	p.Lys227Asn	p.K227N	ENST00000396334	NM_002468.4	227	aaG/aaC	3/5	1	2	FACETS	0.965	0.909	1	0.965	0.909	1	CLONAL	1	FALSE	1	0.694241785110109	2		482	827	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890276	72890276	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	172	711	2	ENST00000325599.8:c.406G>T	p.Glu136Ter	p.E136*	ENST00000325599	NM_018130.2	136	Gag/Tag	4/11	1	2	FACETS	0.389	0.357	0.423	0.389	0.357	0.423	SUBCLONAL	1	FALSE	1	0.694241785110109	2		713	1274	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951979	178951979	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	344	571	0	ENST00000263967.3:c.3034G>C	p.Glu1012Gln	p.E1012Q	ENST00000263967	NM_006218.2	1012	Gaa/Caa	21/21	1	2	FACETS	0.963	0.913	1	0.963	0.913	1	CLONAL	1	FALSE	1	0.694241785110109	2		571	1029	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680869	30680869	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1620	172	1135	0	ENST00000376406.3:c.850C>G	p.Pro284Ala	p.P284A	ENST00000376406	NM_014641.2	284	Cca/Gca	5/15	1	2	FACETS	0.277	0.253	0.301	0.277	0.253	0.301	SUBCLONAL	1	FALSE	1	0.694241785110109	2		1135	1792	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6031610	6031610	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013731-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	80	259	0	ENST00000265849.7:c.982G>A	p.Asp328Asn	p.D328N	ENST00000265849	NM_000535.5	328	Gat/Aat	9/15	1	2	FACETS	0.488	0.431	0.549	0.488	0.431	0.549	SUBCLONAL	1	FALSE	1	0.694241785110109	2		259	472	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	34	321	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.902	0.74	1	0.902	0.74	1	CLONAL	1	TRUE	1	0.273102112373022	2		321	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912656	NA	P-0013885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	100	616	0	ENST00000269305.4:c.734G>C	p.Gly245Ala	p.G245A	ENST00000269305	NM_001126112.2	245	gGc/gCc	7/11	NA	2	FACETS	1	0.942	1			1	INDETERMINATE	1	TRUE	NA	0.273102112373022	2		616	677	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554900	187554900	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1216423829	NA	P-0013885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	144	798	1	ENST00000441802.2:c.4261C>T	p.Gln1421Ter	p.Q1421*	ENST00000441802	NM_005245.3	1421	Cag/Tag	7/27	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.273102112373022	2		799	955	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294280	1294280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	31	284	0	ENST00000310581.5:c.721G>A	p.Gly241Ser	p.G241S	ENST00000310581	NM_198253.2	241	Ggc/Agc	2/16	1	2	FACETS	1	0.838	1	1	0.838	1	CLONAL	1	TRUE	1	0.273102112373022	2		284	220	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645152	86645162	+	frameshift_variant	Frame_Shift_Del	DEL	GTTTATGATGG	GTTTATGATGG	-	novel	NA	P-0013885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	49	394	0	ENST00000274376.6:c.1225_1235del	p.Phe409ArgfsTer5	p.F409Rfs*5	ENST00000274376	NM_002890.2	408	caGTTTATGATGGga/caga	8/25	1	2	FACETS	0.66	0.558	0.771	0.66	0.558	0.771	SUBCLONAL	1	TRUE	1	0.273102112373022	2		394	544	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63829486	63829486	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013936-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	140	422	0	ENST00000279873.7:c.1129A>G	p.Ile377Val	p.I377V	ENST00000279873	NM_032199.2	377	Att/Gtt	8/10	1	2	FACETS	0.8	0.731	0.873	0.8	0.731	0.873	SUBCLONAL	1	TRUE	1	0.5228836416872	2		422	669	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	58	292	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.88	0.756	1	0.88	0.756	1	CLONAL	1	TRUE	1	0.205630000636663	2		292	641	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554453	63554453	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014039-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	73	669	0	ENST00000307078.5:c.286C>T	p.Arg96Ter	p.R96*	ENST00000307078	NM_004655.3	96	Cga/Tga	2/11	1	2	FACETS	0.979	0.856	1	0.979	0.856	1	CLONAL	1	TRUE	1	0.205630000636663	2		669	725	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164928	47164928	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014043-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	76	366	0	ENST00000409792.3:c.1198C>T	p.Arg400Ter	p.R400*	ENST00000409792	NM_014159.6	400	Cga/Tga	3/21	0.340277095685636	1	FACETS	0.958	0.845	1	0.958	0.845	1	CLONAL	1	TRUE	0	0.340277095685636	1		366	387	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209574	98209574	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs896779358	NA	P-0014043-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	49	218	0	ENST00000331920.6:c.3964G>A	p.Ala1322Thr	p.A1322T	ENST00000331920	NM_000264.3	1322	Gct/Act	23/24	0.340277095685636	1	FACETS	0.875	0.747	1	0.875	0.747	1	CLONAL	1	TRUE	0	0.340277095685636	1		218	273	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161332191	161332191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553266502	NA	P-0014080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	33	178	1	ENST00000367975.2:c.478G>A	p.Val160Met	p.V160M	ENST00000367975	NM_003001.3	160	Gtg/Atg	6/6	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.381810749146114	2		179	146	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519989	NA	P-0014080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	124	466	0	ENST00000269305.4:c.730G>C	p.Gly244Arg	p.G244R	ENST00000269305	NM_001126112.2	244	Ggc/Cgc	7/11	0.381810749146114	1	FACETS	0.916	0.831	1	0.916	0.831	1	CLONAL	1	TRUE	0	0.381810749146114	1		466	574	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0014161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	144	503	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.224590754466141	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.224590754466141	1		503	951	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031854	10031854	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	34	540	1	ENST00000330684.3:c.969G>T	p.Gln323His	p.Q323H	ENST00000330684	NM_001134407.1	323	caG/caT	3/13	1	2	FACETS	0.507	0.413	0.613	0.507	0.413	0.613	SUBCLONAL	1	TRUE	1	0.224590754466141	2		541	597	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711984	89711988	+	frameshift_variant	Frame_Shift_Del	DEL	AAACT	AAACT	-	novel	NA	P-0014161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	56	308	0	ENST00000371953.3:c.603_607del	p.Glu201AspfsTer40	p.E201Dfs*40	ENST00000371953	NM_000314.4	201	gAAACT/g	6/9	0.224590754466141	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.224590754466141	1		308	357	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6038860	6038860	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	65	761	2	ENST00000265849.7:c.584C>T	p.Ser195Leu	p.S195L	ENST00000265849	NM_000535.5	195	tCa/tTa	6/15	1	2	FACETS	0.643	0.556	0.738	0.643	0.556	0.738	SUBCLONAL	1	TRUE	1	0.224590754466141	2		763	900	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124552	108124552	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	98	321	0	ENST00000278616.4:c.1910A>C	p.Gln637Pro	p.Q637P	ENST00000278616	NM_000051.3	637	cAa/cCa	13/63	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.451573188619093	2		321	386	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	84	305	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.783	0.691	0.882	0.783	0.691	0.882	SUBCLONAL	1	TRUE	1	0.285580588788756	2		305	751	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0014197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	78	586	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.248672702929861	3	FACETS	1	0.969	1	0.657	0.579	0.74	CLONAL	1	TRUE	1	0.285580588788756	3		586	475	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176176012	176176018	+	frameshift_variant	Frame_Shift_Del	DEL	GGGAAGA	GGGAAGA	-	novel	NA	P-0014204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	461	659	0	ENST00000367669.3:c.97_103del	p.Ser33ArgfsTer65	p.S33Rfs*65	ENST00000367669	NM_022457.5	33	TCTTCCCcg/cg	1/20	0.367500151115685	3	FACETS	0.997	0.957	1	1	0.996	1	CLONAL	3	FALSE	1	0.376802461246948	3		659	972	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038900	12038900	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	449	513	0	ENST00000396373.4:c.1193T>G	p.Leu398Arg	p.L398R	ENST00000396373	NM_001987.4	398	cTg/cGg	7/8	0.325846627762293	4	FACETS	1	0.985	1	1	0.996	1	CLONAL	3	FALSE	2	0.376802461246948	4		513	1032	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624803	9624803	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	105	396	0	ENST00000353224.5:c.174C>A	p.Cys58Ter	p.C58*	ENST00000353224	NM_177990.2	58	tgC/tgA	3/10	0.376083325753063	4	FACETS	1	0.938	1	0.355	0.318	0.395	CLONAL	1	FALSE	1	0.376802461246948	4		396	720	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0014248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	42	871	2	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	1	2	FACETS	0.606	0.504	0.721	0.606	0.504	0.721	SUBCLONAL	1	TRUE	1	0.13	2		873	1066	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0014272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	112	333	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.765	0.689	0.845	0.765	0.689	0.845	SUBCLONAL	1	TRUE	1	0.44790222954609	2		333	654	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667381	241667381	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	122	449	0	ENST00000366560.3:c.1069A>G	p.Ile357Val	p.I357V	ENST00000366560	NM_000143.3	357	Atc/Gtc	7/10	0.44790222954609	3	FACETS	0.722	0.651	0.796	0.361	0.325	0.398	SUBCLONAL	1	TRUE	1	0.44790222954609	3		449	924	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779719	3779719	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	149	411	0	ENST00000262367.5:c.5329C>T	p.Gln1777Ter	p.Q1777*	ENST00000262367	NM_004380.2	1777	Cag/Tag	31/31	1	2	FACETS	0.996	0.913	1	0.996	0.913	1	CLONAL	1	TRUE	1	0.44790222954609	2		411	668	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163698	47163698	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	81	273	1	ENST00000409792.3:c.2428G>T	p.Glu810Ter	p.E810*	ENST00000409792	NM_014159.6	810	Gaa/Taa	3/21	0.274236647415422	1	FACETS	0.716	0.635	0.802	0.716	0.635	0.802	SUBCLONAL	1	TRUE	0	0.44790222954609	1		274	392	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139438537	139438538	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0014272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	174	644	0	ENST00000277541.6:c.78_79delinsTT	p.Gln26_Pro27delinsHisSer	p.Q26_P27delinsHS	ENST00000277541	NM_017617.3	26	caGCcc/caTTcc	2/34	1	2	FACETS	0.799	0.735	0.865	0.799	0.735	0.865	SUBCLONAL	1	TRUE	1	0.44790222954609	2		644	973	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0014278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	164	666	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.888	0.814	0.964	0.888	0.814	0.964	CLONAL	1	TRUE	1	0.382950574090615	2		667	965	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0014278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	141	592	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.829	0.755	0.907	0.829	0.755	0.907	CLONAL	1	TRUE	1	0.382950574090615	2		592	888	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754431	41754431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	296	583	0	ENST00000301178.4:c.1550G>A	p.Gly517Asp	p.G517D	ENST00000301178	NM_021913.4	517	gGc/gAc	13/20	0.382950574090615	3	FACETS	0.906	0.854	0.96	0.906	0.854	0.96	CLONAL	2	TRUE	1	0.382950574090615	3		583	1016	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624405	140624426	+	protein_altering_variant	In_Frame_Del	DEL	GGCGCCGGCGCCGGCGCCGGCC	GGCGCCGGCGCCGGCGCCGGCC	A	novel	NA	P-0014278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	123	212	0	ENST00000288602.6:c.78_99delinsT	p.Glu26_Ala33delinsAsp	p.E26_A33delinsD	ENST00000288602	NM_004333.4	26	gaGGCCGGCGCCGGCGCCGGCGCC/gaT	1/18	1	2	FACETS	0.805	0.735	0.878	1	0.988	1	CLONAL	2	TRUE	1	0.382950574090615	2		212	399	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	146	321	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.649238155741129	2		321	360	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0014396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	59	333	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA	2	FACETS	0.808	0.704	0.918			1	INDETERMINATE	1	TRUE	NA	0.649238155741129	2		333	225	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0014396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	163	464	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.649238155741129	2		464	500	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152093	55152093	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121908585	NA	P-0014452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	348	500	0	ENST00000257290.5:c.2525A>T	p.Asp842Val	p.D842V	ENST00000257290	NM_006206.4	842	gAc/gTc	18/23	1	2	FACETS	0.999	0.947	1	0.999	0.947	1	CLONAL	1	TRUE	1	0.628890612408186	2		500	1108	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219933	36219933	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	365	457	2	ENST00000222270.7:c.4735C>T	p.Arg1579Cys	p.R1579C	ENST00000222270	NM_014727.1	1579	Cgt/Tgt	21/37	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.628890612408186	2		459	1128	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	129	495	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.222236492079275	4	FACETS	0.99	0.899	1	0.99	0.899	1	CLONAL	2	TRUE	2	0.23799071534514	4		495	678	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0014460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	181	625	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.200109454798582	2	FACETS	0.957	0.884	1	0.957	0.884	1	CLONAL	2	TRUE	0	0.23799071534514	2		625	795	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057642	27057642	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0014460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	162	497	0	ENST00000324856.7:c.1351-1G>C		p.X451_splice	ENST00000324856	NM_006015.4	451			0.23799071534514	3	FACETS	0.994	0.914	1	0.994	0.914	1	CLONAL	2	TRUE	1	0.23799071534514	3		497	766	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22412937	22412937	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	27	141	0	ENST00000344548.3:c.184G>C	p.Glu62Gln	p.E62Q	ENST00000344548	NM_001039802.1	62	Gag/Cag	5/7	0.23799071534514	3	FACETS	1	0.854	1	0.543	0.434	0.666	CLONAL	1	TRUE	1	0.23799071534514	3		141	234	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46725767	46725767	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	38	296	1	ENST00000371975.4:c.403G>A	p.Asp135Asn	p.D135N	ENST00000371975	NM_003579.3	135	Gac/Aac	5/18	0.23799071534514	3	FACETS	0.792	0.655	0.946	0.396	0.327	0.473	CLONAL	1	TRUE	1	0.23799071534514	3		297	451	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487153	56487153	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	64	498	0	ENST00000267101.3:c.1299G>C	p.Met433Ile	p.M433I	ENST00000267101	NM_001982.3	433	atG/atC	12/28	0.171372415141341	4	FACETS	0.969	0.839	1	0.323	0.279	0.371	CLONAL	1	TRUE	1	0.23799071534514	4		498	687	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435390	56435390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	96	660	0	ENST00000407977.2:c.1747C>T	p.Pro583Ser	p.P583S	ENST00000407977		583	Cct/Tct	9/10	0.23799071534514	6	FACETS	0.985	0.875	1	0.246	0.218	0.276	CLONAL	1	TRUE	2	0.23799071534514	6		660	1209	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275142	41275142	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	86	300	2	ENST00000349496.5:c.1308G>T	p.Met436Ile	p.M436I	ENST00000349496	NM_001904.3	436	atG/atT	9/15	0.23799071534514	7	FACETS	0.773	0.683	0.869	0.309	0.273	0.348	SUBCLONAL	2	TRUE	2	0.23799071534514	7		302	746	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49724993	49724993	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	111	373	1	ENST00000449682.2:c.351G>T	p.Lys117Asn	p.K117N	ENST00000449682	NM_020998.3	117	aaG/aaT	3/18	0.23799071534514	7	FACETS	1	0.906	1	0.403	0.362	0.446	CLONAL	2	TRUE	2	0.23799071534514	7		374	738	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873098	134873098	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	76	577	0	ENST00000398015.3:c.1402G>C	p.Glu468Gln	p.E468Q	ENST00000398015	NM_004441.4	468	Gag/Cag	6/16	0.222236492079275	4	FACETS	0.915	0.801	1	0.458	0.4	0.519	CLONAL	1	TRUE	2	0.23799071534514	4		577	864	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717732	89717749	+	inframe_deletion	In_Frame_Del	DEL	ATCAAAGTAGAGTTCTTC	ATCAAAGTAGAGTTCTTC	-	novel	NA	P-0014477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	91	311	0	ENST00000371953.3:c.757_774del	p.Ile253_Phe258del	p.I253_F258del	ENST00000371953	NM_000314.4	253	ATCAAAGTAGAGTTCTTC/-	7/9	0.307143408846811	1	FACETS	0.881	0.784	0.985	0.881	0.784	0.985	CLONAL	1	TRUE	0	0.307143408846811	1		311	569	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115898	8115899	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0014477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	124	448	0	ENST00000346208.3:c.1244_1245del	p.Met415ThrfsTer91	p.M415Tfs*91	ENST00000346208		415	aTG/a	6/6	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.307143408846811	2		448	734	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578551	7578551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	230	907	0	ENST00000269305.4:c.379T>C	p.Ser127Pro	p.S127P	ENST00000269305	NM_001126112.2	127	Tcc/Ccc	5/11	0.163869924885733	2	FACETS	0.815	0.758	0.873	0.815	0.758	0.873	CLONAL	2	TRUE	0	0.220051409707406	2		907	1283	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030478	49030478	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0014695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	94	429	0	ENST00000267163.4:c.1953T>A	p.Tyr651Ter	p.Y651*	ENST00000267163	NM_000321.2	651	taT/taA	19/27	0.220051409707406	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.220051409707406	1		429	640	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949127	44949127	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	23	294	0	ENST00000377967.4:c.3688G>A	p.Ala1230Thr	p.A1230T	ENST00000377967	NM_021140.2	1230	Gct/Act	25/29	1	1	FACETS	0.407	0.316	0.512	0.407	0.316	0.512	SUBCLONAL	1	TRUE	0	0.220051409707406	1		294	457	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430322	181430322	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	147	305	2	ENST00000325404.1:c.174G>T	p.Lys58Asn	p.K58N	ENST00000325404	NM_003106.3	58	aaG/aaT	1/1	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.52702184986307	2		307	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0015014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	228	790	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.459840696625128	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.459840696625128	1		790	580	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0015014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	141	415	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.112253019031967	0	FACETS	0.472	0.43	0.515			1	INDETERMINATE	1	TRUE	0	0.459840696625128	0		415	702	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602328	10602328	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	148	1124	0	ENST00000171111.5:c.1250G>T	p.Gly417Val	p.G417V	ENST00000171111	NM_203500.1	417	gGg/gTg	3/6	0.293664652380425	2	FACETS	0.648	0.591	0.708	0.324	0.295	0.354	SUBCLONAL	1	TRUE	0	0.459840696625128	2		1124	993	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022914	27022942	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCCGCCGCCAGCAGCCTGGGCAACCCG	CCGCCGCCGCCAGCAGCCTGGGCAACCCG	-	novel	NA	P-0015014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	17	107	0	ENST00000324856.7:c.31_59del	p.Ser11AlafsTer90	p.S11Afs*90	ENST00000324856	NM_006015.4	7	cCCGCCGCCGCCAGCAGCCTGGGCAACCCG/c	1/20	0.267684418763861	1	FACETS	0.564	0.427	0.721	0.564	0.427	0.721	INDETERMINATE	1	TRUE	0	0.459840696625128	1		107	101	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023441	27023441	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	109	1005	3	ENST00000324856.7:c.547G>T	p.Ala183Ser	p.A183S	ENST00000324856	NM_006015.4	183	Gcg/Tcg	1/20	0.267684418763861	1	FACETS	0.452	0.406	0.502	0.452	0.406	0.502	INDETERMINATE	1	TRUE	0	0.459840696625128	1		1008	807	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429983	78429983	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	215	593	0	ENST00000370768.2:c.896A>G	p.Lys299Arg	p.K299R	ENST00000370768	NM_003902.3	299	aAa/aGa	11/20	0.267684418763861	1	FACETS	0.988	0.922	1	0.988	0.922	1	INDETERMINATE	1	TRUE	0	0.459840696625128	1		593	729	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652413	206652413	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	109	876	1	ENST00000367120.3:c.1120A>T	p.Thr374Ser	p.T374S	ENST00000367120	NM_014002.3	374	Acg/Tcg	10/22	0.165239355292001	2	FACETS	0.553	0.496	0.614	0.277	0.248	0.307	INDETERMINATE	1	TRUE	0	0.459840696625128	2		877	857	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727020	243727020	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0015014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	77	517	0	ENST00000263826.5:c.948+2T>A		p.X316_splice	ENST00000263826	NM_005465.4	316			0.165239355292001	2	FACETS	0.537	0.471	0.607	0.268	0.235	0.304	INDETERMINATE	1	TRUE	0	0.459840696625128	2		517	624	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783747	50783747	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs745498288	NA	P-0015014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	142	887	0	ENST00000398568.2:c.138A>G	p.Ile46Met	p.I46M	ENST00000398568	NM_001042412.1	46	atA/atG	3/18	0.402484935223482	1	FACETS	0.614	0.56	0.671	0.614	0.56	0.671	SUBCLONAL	1	TRUE	0	0.459840696625128	1		887	774	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983630	7983631	+	missense_variant	Missense_Mutation	DNP	AG	AG	TT	novel	NA	P-0015014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	69	700	1	ENST00000319144.4:c.676_677delinsAA	p.Leu226Lys	p.L226K	ENST00000319144	NM_001139.2	226	CTg/AAg	6/15	0.459840696625128	1	FACETS	0.502	0.439	0.571	0.502	0.439	0.571	SUBCLONAL	1	TRUE	0	0.459840696625128	1		701	460	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276687	15276702	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGCAGCCGCTTGGC	CCAGCAGCCGCTTGGC	-	novel	NA	P-0015014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	409	968	0	ENST00000263388.2:c.5563_5578del	p.Ala1855MetfsTer51	p.A1855Mfs*51	ENST00000263388	NM_000435.2	1855	GCCAAGCGGCTGCTGGat/at	30/33	0.293664652380425	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.459840696625128	2		968	861	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18972856	18972856	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	79	808	0	ENST00000262803.5:c.2495G>A	p.Arg832His	p.R832H	ENST00000262803	NM_002911.3	832	cGc/cAc	18/24	0.293664652380425	2	FACETS	0.454	0.399	0.514	0.227	0.199	0.257	SUBCLONAL	1	TRUE	0	0.459840696625128	2		808	756	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248681	212248681	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	183	571	0	ENST00000342788.4:c.3586C>T	p.Pro1196Ser	p.P1196S	ENST00000342788	NM_005235.2	1196	Ccc/Tcc	28/28	0.459840696625128	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.459840696625128	1		571	536	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566521	41566521	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	237	654	1	ENST00000263253.7:c.4398G>T	p.Trp1466Cys	p.W1466C	ENST00000263253	NM_001429.3	1466	tgG/tgT	27/31	0.165239355292001	2	FACETS	1	0.992	1	0.705	0.661	0.75	INDETERMINATE	1	TRUE	0	0.459840696625128	2		655	731	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131096	55131096	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	236	566	1	ENST00000257290.5:c.639G>T	p.Glu213Asp	p.E213D	ENST00000257290	NM_006206.4	213	gaG/gaT	5/23	0.276747721512686	2	FACETS	1	0.992	1	0.722	0.677	0.768	CLONAL	1	TRUE	0	0.459840696625128	2		567	711	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80160631	80160631	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0015014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	91	753	1	ENST00000265081.6:c.3001-1G>T		p.X1001_splice	ENST00000265081	NM_002439.4	1001			1	2	FACETS	0.504	0.447	0.564	0.504	0.447	0.564	SUBCLONAL	1	TRUE	1	0.459840696625128	2		754	786	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519236	137519236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	71	631	0	ENST00000367739.4:c.1402G>A	p.Val468Met	p.V468M	ENST00000367739	NM_000416.2	468	Gtg/Atg	7/7	1	2	FACETS	0.423	0.369	0.482	0.423	0.369	0.482	SUBCLONAL	1	TRUE	1	0.459840696625128	2		631	730	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0015044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	177	0	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	0.816115099284446	2		0	400	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576863	7576864	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0015044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	796	623	0	ENST00000269305.4:c.982_983del	p.Phe328HisfsTer8	p.F328Hfs*8	ENST00000269305	NM_001126112.2	328	TTc/c	9/11	0.816115099284446	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.816115099284446	2		623	919	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281847	39281847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	15649	602	2	ENST00000402219.2:c.628G>A	p.Ala210Thr	p.A210T	ENST00000402219	NM_005633.3	210	Gca/Aca	5/23	0.816115099284446	49	FACETS	0.995	0.993	0.996			1	CLONAL	49	TRUE	NA	0.816115099284446	49		604	15879	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47596657	47596657	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs747738988	NA	P-0015044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	19053	405	0	ENST00000263735.4:c.13C>T	p.Gln5Ter	p.Q5*	ENST00000263735	NM_002354.2	5	Cag/Tag	1/9	0.816115099284446	63	FACETS	0.995	0.994	0.996			1	CLONAL	63	TRUE	NA	0.816115099284446	63		405	19284	SUCCESS
